{"2":{"model_id":"2","model_name":"CblA-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"575"}},"model_sequences":{"sequence":{"1188":{"protein_sequence":{"accession":"ACT97415.1","sequence":"MKAYFIAILTLFTCIATVVRAQQMSELENRIDSLLNGKKATVGIAVWTDKGDMLRYNDHVHFPLLSVFKFHVALAVLDKMDKQSISLDSIVSIKASQMPPNTYSPLRKKFPDQDFTITLRELMQYSISQSDNNACDILIEYAGGIKHINDYIHRLSIDSFNLSETEDGMHSSFEAVYRNWSTPSAMVRLLRTADEKELFSNKELKDFLWQTMIDTETGANKLKGMLPAKTVVGHKTGSSDRNADGMKTADNDAGLVILPDGRKYYIAAFVMDSYETDEDNANIIARISRMVYDAMR"},"dna_sequence":{"accession":"GQ343019.1","fmin":"132","fmax":"1023","strand":"+","sequence":"ATGAAAGCATATTTCATCGCCATACTTACCTTATTCACTTGTATAGCTACCGTCGTCCGGGCGCAGCAAATGTCTGAACTTGAAAACCGGATTGACAGTCTGCTCAATGGCAAGAAAGCCACCGTTGGTATAGCCGTATGGACAGACAAAGGAGACATGCTCCGGTATAACGACCATGTACACTTCCCCTTGCTCAGTGTATTCAAATTCCATGTGGCACTGGCCGTACTGGACAAGATGGATAAGCAAAGCATCAGTCTGGACAGCATTGTTTCCATAAAGGCATCCCAAATGCCGCCCAATACCTACAGCCCCCTGCGGAAGAAGTTTCCCGACCAGGATTTCACGATTACGCTTAGGGAACTGATGCAATACAGCATTTCCCAAAGCGACAACAATGCCTGCGACATCTTGATAGAATATGCAGGAGGCATCAAACATATCAACGACTATATCCACCGGTTGAGTATCGACTCCTTCAACCTCTCGGAAACAGAAGACGGCATGCACTCCAGCTTCGAGGCTGTATACCGCAACTGGAGTACTCCTTCCGCTATGGTCCGACTACTGAGAACGGCTGATGAAAAAGAGTTGTTCTCCAACAAGGAGCTGAAAGACTTCTTGTGGCAGACCATGATAGATACTGAAACCGGTGCCAACAAACTGAAAGGTATGTTGCCAGCCAAAACCGTGGTAGGACACAAGACCGGCTCTTCCGACCGCAATGCCGACGGTATGAAAACTGCAGATAATGATGCCGGCCTCGTTATCCTTCCCGACGGCCGGAAATACTACATTGCCGCCTTCGTCATGGACTCATACGAGACGGATGAGGACAATGCGAACATCATCGCCCGCATATCACGCATGGTATATGATGCGATGAGATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39659","NCBI_taxonomy_name":"mixed culture bacterium AX_gF3SD01_15","NCBI_taxonomy_id":"663108"}}}},"ARO_accession":"3002999","ARO_id":"39433","ARO_name":"CblA-1","CARD_short_name":"CblA-1","ARO_description":"CblA-1 beta-lactamase is a class A beta-lactamase found in Bacteroides uniformis that is species-specific.","ARO_category":{"39432":{"category_aro_accession":"3002998","category_aro_cvterm_id":"39432","category_aro_name":"CblA beta-lactamase","category_aro_description":"CblA beta-lactamases are class A beta-lactamases that confer resistance to cephalosporins.","category_aro_class_name":"AMR Gene Family"},"41256":{"category_aro_accession":"3004129","category_aro_cvterm_id":"41256","category_aro_name":"cephaloridine","category_aro_description":"Cephaloridine is a semisynthetic, broad-spectrum, first-generation cephalosporin with antibacterial activity. Cephaloridine binds to and inactivates penicillin-binding proteins (PBPs) located on the inner membrane of the bacterial cell wall. PBPs are enzymes involved in the terminal stages of assembling the bacterial cell wall and in reshaping the cell wall during growth and division. Inactivation of PBPs interferes with the cross-linkage of peptidoglycan chains necessary for bacterial cell wall strength and rigidity. This results in the weakening of the bacterial cell wall and causes cell lysis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4":{"model_id":"4","model_name":"SHV-52","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1393":{"protein_sequence":{"accession":"AEJ08681.1","sequence":"MRYIRLCIISLLAALPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMISTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLAIVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"HQ845196.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCGCCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATAAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATTTGCTGCTGGCCATCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTAGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001109","ARO_id":"37489","ARO_name":"SHV-52","CARD_short_name":"SHV-52","ARO_description":"SHV-52 is a beta-lactamase that has been found in clinical isolates.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5":{"model_id":"5","model_name":"dfrF","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"677":{"protein_sequence":{"accession":"AAD01868.1","sequence":"MIGLIVARSKNNVIGKNGNIPWKIKGEQKQFRELTTGNVVIMGRKSYEEIGHPLPNRMNIVVSTTTEYQGDNLVSVKSLEDALLLAKGRDVYISGGYGLFKEALQIVDKMYITEVDLNIEDGDTFFPEFDINDFEVLIGETLGEEVKYTRTFYVRKNELSRFWI"},"dna_sequence":{"accession":"AF028812.1","fmin":"392","fmax":"887","strand":"+","sequence":"ATGATAGGTTTGATTGTTGCGAGGTCAAAGAATAATGTTATAGGCAAGAATGGTAATATACCATGGAAAATAAAGGGAGAACAAAAGCAATTTAGAGAGTTAACAACGGGTAATGTGGTTATTATGGGGCGAAAGTCTTATGAAGAAATCGGTCATCCGTTGCCTAATAGAATGAATATTGTTGTTTCCACCACAACAGAGTATCAAGGAGATAATTTAGTTTCAGTTAAATCATTAGAAGATGCATTATTATTGGCTAAAGGACGAGATGTATACATATCTGGTGGATATGGACTATTTAAGGAAGCTTTGCAAATAGTAGATAAAATGTATATCACAGAAGTAGATTTAAATATTGAAGATGGAGATACATTCTTTCCAGAATTTGATATCAATGATTTTGAAGTTTTGATAGGGGAAACACTTGGTGAGGAAGTGAAATATACGAGAACATTTTATGTAAGGAAAAATGAATTGAGTAGATTTTGGATTTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35918","NCBI_taxonomy_name":"Enterococcus faecalis","NCBI_taxonomy_id":"1351"}}}},"ARO_accession":"3002867","ARO_id":"39301","ARO_name":"dfrF","CARD_short_name":"dfrF","ARO_description":"dfrF is a chromosome-encoded dihydrofolate reductase found in Streptococcus pyogenes.","ARO_category":{"37617":{"category_aro_accession":"3001218","category_aro_cvterm_id":"37617","category_aro_name":"trimethoprim resistant dihydrofolate reductase dfr","category_aro_description":"Alternative dihydropteroate synthase dfr present on plasmids produces alternate proteins that are less sensitive to trimethoprim from inhibiting its role in folate synthesis, thus conferring trimethoprim resistance.","category_aro_class_name":"AMR Gene Family"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7":{"model_id":"7","model_name":"CTX-M-130","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1703":{"protein_sequence":{"accession":"AFJ59957.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAERRHDVLASAARIIAEGL"},"dna_sequence":{"accession":"JX017365.1","fmin":"244","fmax":"1120","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGACTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGCGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAGACGCCACGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001989","ARO_id":"38389","ARO_name":"CTX-M-130","CARD_short_name":"CTX-M-130","ARO_description":"CTX-M-130 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8":{"model_id":"8","model_name":"NDM-6","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1103":{"protein_sequence":{"accession":"AEX08599.1","sequence":"MELPNIMHPVAKLSTALAAALMLSGCMPGEIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASVRAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR"},"dna_sequence":{"accession":"JN967644.1","fmin":"0","fmax":"813","strand":"+","sequence":"ATGGAATTGCCCAATATTATGCACCCGGTCGCGAAGCTGAGCACCGCATTAGCCGCTGCATTGATGCTGAGCGGGTGCATGCCCGGTGAAATCCGCCCGACGATTGGCCAGCAAATGGAAACTGGCGACCAACGGTTTGGCGATCTGGTTTTCCGCCAGCTCGCACCGAATGTCTGGCAGCACACTTCCTATCTCGACATGCCGGGTTTCGGGGCAGTCGCTTCCAACGGTTTGATCGTCAGGGATGGCGGCCGCGTGCTGGTGGTCGATACCGCCTGGACCGATGACCAGACCGCCCAGATCCTCAACTGGATCAAGCAGGAGATCAACCTGCCGGTCGCGCTGGCGGTGGTGACTCACGCGCATCAGGACAAGATGGGCGGTATGGACGCGCTGCATGCGGCGGGGATTGCGACTTATGCCAATGCGTTGTCGAACCAGCTTGCCCCGCAAGAGGGGATGGTTGCGGCGCAACACAGCCTGACTTTCGCCGCCAATGGCTGGGTCGAACCAGCAACCGCGCCCAACTTTGGCCCGCTCAAGGTATTTTACCCCGGCCCCGGCCACACCAGTGACAATATCACCGTTGGGATCGACGGCACCGACATCGCTTTTGGTGGCTGCCTGATCAAGGACAGCAAGGCCAAGTCGCTCGGCAATCTCGGTGATGCCGACACTGAGCACTACGCCGCGTCAGTGCGCGCGTTTGGTGCGGCGTTCCCCAAGGCCAGCATGATCGTGATGAGCCATTCCGCCCCCGATAGCCGCGCCGCAATCACTCATACGGCCCGCATGGCCGACAAGCTGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002356","ARO_id":"38756","ARO_name":"NDM-6","CARD_short_name":"NDM-6","ARO_description":"NDM-6 is a beta-lactamase found in the Enterobacteriaceae family.","ARO_category":{"36196":{"category_aro_accession":"3000057","category_aro_cvterm_id":"36196","category_aro_name":"NDM beta-lactamase","category_aro_description":"NDM beta-lactamases or New Delhi metallo-beta-lactamases are class B beta-lactamases that confer resistance to a broad range of antibiotics including carbapenems, cephalosporins and penicillins.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"9":{"model_id":"9","model_name":"ACT-35","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1584":{"protein_sequence":{"accession":"BAP68758.1","sequence":"MMKKSLCCALLLGISCSALATPVSEKQLAEVVANTVTPLMKAQSVPGMAVAVIYQGKPHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMPYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPENVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVVEGSDSKVALAPLPVVEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANTSYPNPARVEAAYYILEALQ"},"dna_sequence":{"accession":"LC004922.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCCCTTTGCTGCGCCCTGCTGCTCGGCATCTCTTGCTCTGCTCTCGCCACGCCAGTGTCAGAAAAACAGCTGGCGGAGGTGGTAGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCTGTTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGAAAACCGCACTATTACACGTTTGGCAAGGCCGATATCGCGGCGAATAAACCCGTTACGCCTCAGACCCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGCGTGTTAGGTGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTGACGGGCAAGCAGTGGCAGGGTATTCGTATGCTGGATCTCGCCACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTCAAACCTTCTGGCATGCCCTATGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTGCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGTATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCGGAGAACGTTGCTGATGCCTCACTTAAGCAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGGTCGAGGGCAGCGACAGTAAGGTAGCGCTGGCGCCGTTGCCCGTGGTAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGCTCTACTGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATACAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACTATATCCTCGAGGCGCTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3001855","ARO_id":"38255","ARO_name":"ACT-35","CARD_short_name":"ACT-35","ARO_description":"ACT-35 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"10":{"model_id":"10","model_name":"CARB-5","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1661":{"protein_sequence":{"accession":"AAF61417.1","sequence":"MNVRKHKASFFSVVITFLCLTLSLNANATDSVLEAVTNAETELGARIGLAVHDLETGKRWEHKSNERFPLSSTFKTLACANVLQRVDLGKERIDRVVRFSESNLVTYSPVTEKHVGKKGMSLAELCQATLSTSDNSAANFILQAIGGPKALTKFLRSIGDDTTRLDRWETELNEAVPGDKRDTTTPIAMVTTLEKLLIDETLSIKSRQQLESWLKGNEVGDALFRKGVPSDWIVADRTGAGGYGSRAITAVMWPPNRKPIVAALYITETDASFEERNAVIAKIGEQIAKTVLMENSRN"},"dna_sequence":{"accession":"AF135373.1","fmin":"11","fmax":"908","strand":"+","sequence":"ATGAACGTACGTAAACACAAGGCTAGTTTTTTTAGCGTAGTAATTACTTTTTTATGTCTCACGCTATCATTAAATGCTAATGCAACAGACTCAGTACTTGAAGCGGTTACCAATGCTGAAACTGAATTAGGCGCTAGAATTGGTCTAGCTGTGCATGATTTGGAAACGGGAAAACGTTGGGAACATAAATCTAATGAACGTTTTCCTCTAAGTAGTACCTTTAAAACACTTGCCTGTGCAAACGTTCTTCAAAGAGTTGATCTAGGTAAAGAAAGAATTGATAGAGTTGTGAGATTCTCTGAAAGCAATCTCGTTACATACTCACCTGTAACAGAAAAACATGTGGGTAAAAAAGGGATGTCGCTCGCAGAGCTGTGTCAGGCCACATTATCAACCAGTGATAATTCAGCTGCCAATTTTATTCTACAAGCGATTGGTGGACCTAAGGCTCTAACGAAATTTTTGCGTTCCATTGGCGACGATACTACGCGCCTTGATCGCTGGGAAACAGAACTTAACGAAGCGGTGCCTGGAGATAAGCGAGACACGACAACACCAATTGCAATGGTAACGACACTTGAAAAGTTACTAATTGACGAAACACTATCTATCAAATCTCGTCAACAACTAGAATCTTGGCTTAAAGGTAATGAGGTTGGCGATGCATTGTTTCGTAAAGGCGTTCCAAGTGACTGGATAGTAGCAGATAGAACAGGCGCTGGTGGTTATGGGTCGCGTGCTATTACTGCGGTGATGTGGCCTCCAAATCGCAAGCCTATCGTAGCCGCTCTATACATTACAGAGACAGACGCCTCGTTTGAAGAAAGAAATGCTGTCATTGCAAAAATTGGTGAGCAAATAGCGAAGACAGTATTAATGGAGAATAGCCGTAACTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36918","NCBI_taxonomy_name":"Acinetobacter calcoaceticus subsp. anitratus","NCBI_taxonomy_id":"107673"}}}},"ARO_accession":"3002244","ARO_id":"38644","ARO_name":"CARB-5","CARD_short_name":"CARB-5","ARO_description":"CARB-5 is a beta-lactamase found in Acinetobacter calcoaceticus.","ARO_category":{"36230":{"category_aro_accession":"3000091","category_aro_cvterm_id":"36230","category_aro_name":"CARB beta-lactamase","category_aro_description":"CARB beta-lactamases are class A lactamases that can hydrolyze carbenicillin. Many of the PSE beta-lactamases have been renamed as CARB-lactamases with the notable exception of PSE-2 which is now OXA-10.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"11":{"model_id":"11","model_name":"Erm(34)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"162":{"protein_sequence":{"accession":"AAP74657.1","sequence":"MTKKMNKYNGKKLSRGEPPNFSGQHFMHNKRLLKEIVDKADVSVRDTVLELGAGKGALTTILSERADRVLAVEYDQKCIEALQWKLVGSKNVSILHQDIMKVALPTEPFVVVSNIPYSITTAIMKMLLNNPKNKLQRGAIVMEKGAAKRFTSVSPKDAYVMAWHMWFDIHYERGISRSSFSPPPKVDSALVRIVRKQHPLFPYKEAKAMHDFLSYALNNPRAPLDQVLRGIFTAPQAKKVRQAIGVKPETPVAMLHARQWAMVCDAMVRHVPKVYWPRRKR"},"dna_sequence":{"accession":"AY234334.1","fmin":"0","fmax":"846","strand":"+","sequence":"ATGACGAAAAAAATGAACAAGTATAATGGGAAAAAACTTAGCCGTGGAGAACCTCCCAATTTTAGCGGTCAGCATTTTATGCACAATAAACGGCTACTGAAGGAAATTGTTGATAAAGCTGACGTCTCTGTTCGTGATACGGTTTTAGAGCTGGGAGCAGGAAAAGGCGCGTTGACGACGATTTTAAGCGAACGCGCGGACCGGGTTCTAGCCGTCGAGTATGACCAAAAATGTATTGAAGCGCTGCAATGGAAACTAGTTGGGTCAAAAAACGTGTCCATTCTCCATCAAGATATTATGAAGGTGGCATTGCCAACGGAACCGTTTGTTGTTGTTTCCAACATCCCTTATTCGATCACAACGGCAATCATGAAAATGCTGTTAAACAATCCAAAAAACAAACTACAACGAGGGGCAATTGTAATGGAGAAAGGAGCAGCAAAGCGGTTTACAAGCGTTTCGCCGAAAGACGCTTATGTGATGGCTTGGCATATGTGGTTTGACATCCACTATGAAAGGGGAATTTCCAGAAGTTCATTTTCGCCGCCGCCGAAAGTCGATTCTGCCCTTGTCCGCATTGTCCGCAAACAGCATCCCCTTTTTCCATATAAAGAGGCGAAAGCGATGCATGACTTTTTATCGTACGCACTAAACAACCCTAGAGCACCCCTTGATCAGGTATTACGAGGAATTTTTACCGCCCCTCAAGCAAAAAAAGTGCGGCAGGCAATCGGCGTCAAACCTGAGACACCAGTGGCCATGCTTCATGCCAGGCAGTGGGCGATGGTTTGTGACGCGATGGTTCGGCATGTTCCAAAAGTGTATTGGCCAAGGCGAAAGAGATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36882","NCBI_taxonomy_name":"Alkalihalobacillus clausii","NCBI_taxonomy_id":"79880"}}}},"ARO_accession":"3000600","ARO_id":"36739","ARO_name":"Erm(34)","CARD_short_name":"Erm(34)","ARO_description":"ErmD confers MLSb phenotype.","ARO_category":{"36699":{"category_aro_accession":"3000560","category_aro_cvterm_id":"36699","category_aro_name":"Erm 23S ribosomal RNA methyltransferase","category_aro_description":"Erm proteins are part of the RNA methyltransferase family and methylate A2058 (E. coli nomenclature) of the 23S ribosomal RNA conferring degrees of resistance to Macrolides, Lincosamides and Streptogramin b. This is called the MLSb phenotype.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35946":{"category_aro_accession":"0000027","category_aro_cvterm_id":"35946","category_aro_name":"roxithromycin","category_aro_description":"Roxithromycin is a semi-synthetic, 14-carbon ring macrolide antibiotic derived from erythromycin. It is used to treat respiratory tract, urinary and soft tissue infections. Roxithromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35974":{"category_aro_accession":"0000057","category_aro_cvterm_id":"35974","category_aro_name":"telithromycin","category_aro_description":"Telithromycin is a semi-synthetic derivative of erythromycin. It is a 14-membered macrolide and is the first ketolide antibiotic to be used in clinics. Telithromycin binds the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"35982":{"category_aro_accession":"0000065","category_aro_cvterm_id":"35982","category_aro_name":"clarithromycin","category_aro_description":"Clarithromycin is a methyl derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome and is used to treat pharyngitis, tonsillitis, acute maxillary sinusitis, acute bacterial exacerbation of chronic bronchitis, pneumonia (especially atypical pneumonias associated with Chlamydia pneumoniae or TWAR), and skin structure infections.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"36284":{"category_aro_accession":"3000145","category_aro_cvterm_id":"36284","category_aro_name":"tylosin","category_aro_description":"Tylosin is a 16-membered macrolide, naturally produced by Streptomyces fradiae. It interacts with the bacterial ribosome 50S subunit to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"36295":{"category_aro_accession":"3000156","category_aro_cvterm_id":"36295","category_aro_name":"spiramycin","category_aro_description":"Spiramycin is a 16-membered macrolide and is natural product produced by Streptomyces ambofaciens. It binds to the 50S subunit of bacterial ribosomes and inhibits peptidyl transfer activity to disrupt protein synthesis.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"36315":{"category_aro_accession":"3000176","category_aro_cvterm_id":"36315","category_aro_name":"dirithromycin","category_aro_description":"Dirithromycin is an oxazine derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome to inhibit bacterial protein synthesis.","category_aro_class_name":"Antibiotic"},"36722":{"category_aro_accession":"3000583","category_aro_cvterm_id":"36722","category_aro_name":"pristinamycin IA","category_aro_description":"Pristinamycin IA is a type B streptogramin antibiotic produced by Streptomyces pristinaespiralis. It binds to the P site of the 50S subunit of the bacterial ribosome, preventing the extension of protein chains.","category_aro_class_name":"Antibiotic"},"36723":{"category_aro_accession":"3000584","category_aro_cvterm_id":"36723","category_aro_name":"quinupristin","category_aro_description":"Quinupristin is a type B streptogramin and a semisynthetic derivative of pristinamycin 1A. It is a component of the drug Synercid and interacts with the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"virginiamycin M1","category_aro_description":"Virginiamycin M1 is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37016":{"category_aro_accession":"3000672","category_aro_cvterm_id":"37016","category_aro_name":"madumycin II","category_aro_description":"Madumycin II is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37017":{"category_aro_accession":"3000673","category_aro_cvterm_id":"37017","category_aro_name":"griseoviridin","category_aro_description":"Griseoviridin is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"37019":{"category_aro_accession":"3000675","category_aro_cvterm_id":"37019","category_aro_name":"pristinamycin IB","category_aro_description":"Pristinamycin IB is a class B streptogramin similar to pristinamycin IA, the former containing a N-methyl-4-(methylamino)phenylalanine instead of a N-methyl-4-(dimethylamino)phenylalanine in its class A streptogramin counterpart (one less methyl group).","category_aro_class_name":"Antibiotic"},"37021":{"category_aro_accession":"3000677","category_aro_cvterm_id":"37021","category_aro_name":"virginiamycin S2","category_aro_description":"Virginiamycin S2 is a streptogramin B antibiotic.","category_aro_class_name":"Antibiotic"},"37022":{"category_aro_accession":"3000678","category_aro_cvterm_id":"37022","category_aro_name":"pristinamycin IC","category_aro_description":"Pristinamycin IC is a class B streptogramin derived from virginiamycin S1.","category_aro_class_name":"Antibiotic"},"37023":{"category_aro_accession":"3000679","category_aro_cvterm_id":"37023","category_aro_name":"vernamycin C","category_aro_description":"Vernamycin C is a streptogramin B antibiotic.","category_aro_class_name":"Antibiotic"},"37024":{"category_aro_accession":"3000680","category_aro_cvterm_id":"37024","category_aro_name":"patricin A","category_aro_description":"Patricin A is a streptogramin B antibiotic.","category_aro_class_name":"Antibiotic"},"37025":{"category_aro_accession":"3000681","category_aro_cvterm_id":"37025","category_aro_name":"patricin B","category_aro_description":"Patricin B is a streptogramin B antibiotic.","category_aro_class_name":"Antibiotic"},"37026":{"category_aro_accession":"3000682","category_aro_cvterm_id":"37026","category_aro_name":"ostreogrycin B3","category_aro_description":"Ostreogrycin B3 is a derivative of pristinamycin IA, with an additional 3-hydroxy group on its 4-oxopipecolic acid.","category_aro_class_name":"Antibiotic"},"37247":{"category_aro_accession":"3000867","category_aro_cvterm_id":"37247","category_aro_name":"oleandomycin","category_aro_description":"Oleandomycin is a 14-membered macrolide produced by Streptomyces antibioticus. It is ssimilar to erythromycin, and contains a desosamine amino sugar and an oleandrose sugar. It targets the 50S ribosomal subunit to prevent protein synthesis.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35952":{"category_aro_accession":"0000034","category_aro_cvterm_id":"35952","category_aro_name":"streptogramin A antibiotic","category_aro_description":"Streptogramin A antibiotics are cyclic polyketide peptide hybrids that bind to the ribosomal peptidyl transfer centre. Structural variation arises from substituting a proline for its desaturated derivative and by its substitution for Ala or Cys. Used alone, streptogramin A antibiotics are bacteriostatic, but is bactericidal when used with streptogramin B antibiotics.","category_aro_class_name":"Drug Class"},"35967":{"category_aro_accession":"0000050","category_aro_cvterm_id":"35967","category_aro_name":"streptogramin B antibiotic","category_aro_description":"Streptogramin B antibiotics are are cyclic hepta- or hexa-depsipeptides.  Type B streptogramins block the peptide exit tunnel of the 50S bacterial ribosome. The general composition of group B streptogramins is 3-hydroxypicolinic acid-L-Thr-D-aminobutyric acid (or D-Ala)-L-Pro-L-Phe (or 4-N-,N-(dimethylamino)-L-Phe)-X-L-phenylglycine. Used alone, streptogramin B antibiotics are bacteriostatic, but is bactericidal when used with streptogramin A antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"12":{"model_id":"12","model_name":"TEM-126","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1567":{"protein_sequence":{"accession":"AAT45742.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERETTTPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AY628199.1","fmin":"203","fmax":"1064","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGAAACCACGACGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000988","ARO_id":"37368","ARO_name":"TEM-126","CARD_short_name":"TEM-126","ARO_description":"TEM-126 is an extended-spectrum beta-lactamase found in E. coli.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"13":{"model_id":"13","model_name":"LRA-12","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1445":{"protein_sequence":{"accession":"ACH58990.1","sequence":"MNVQNCMVKAVSVSIILFASLSLAAQKVKEPTVSNADWSKPYRPFRIAGNLYYIGTYDLACYLITTKQGNIIVNTGLAASALQIKNNIKALGFKLTDTKILLTTQAHYDHLGAMAEIKKITGAKLMADEGDATVMADGGSSDYAFGGHGSMFEPIIADRLLHDKDTIQLGDTKLVMLHHPGHTKGSCSFLFDTKDEQRSYRILIANMPTIVIEKKFSEVSSYPGIAKDYAYTLQAMKNLSFDIWVASHASQFSMHSKHKPGDGYNPKSFMDRKGYDESLDKLQKEYEKHLNEN"},"dna_sequence":{"accession":"EU408351.1","fmin":"16572","fmax":"17454","strand":"+","sequence":"ATGAATGTTCAAAATTGTATGGTAAAAGCCGTTTCCGTTAGCATCATTTTATTTGCATCCCTTTCCCTTGCTGCGCAAAAGGTAAAGGAACCAACCGTTAGTAACGCAGACTGGTCAAAGCCGTACCGGCCCTTTAGAATTGCCGGCAATTTATATTACATCGGTACATATGATCTCGCTTGTTATCTTATTACTACTAAACAGGGTAATATCATTGTCAATACCGGGCTGGCGGCTTCTGCATTACAAATAAAAAATAATATCAAAGCGTTAGGCTTTAAGTTAACTGACACCAAAATACTCTTAACAACACAGGCCCATTATGACCATTTGGGTGCAATGGCTGAAATTAAGAAAATAACAGGCGCAAAGCTCATGGCAGATGAGGGCGATGCGACGGTAATGGCTGATGGAGGCAGTTCTGATTACGCCTTCGGCGGGCATGGCAGTATGTTTGAACCTATAATAGCAGACCGCCTGCTGCATGATAAGGATACCATTCAGTTAGGGGATACAAAATTGGTGATGTTGCATCATCCCGGTCACACGAAGGGTTCCTGCAGTTTTTTATTTGATACAAAAGATGAGCAACGATCTTACAGGATATTAATCGCCAACATGCCTACCATCGTTATTGAAAAAAAATTTAGTGAAGTAAGTAGTTATCCCGGCATTGCTAAAGACTATGCCTATACTTTACAGGCAATGAAAAATCTTTCTTTTGATATATGGGTTGCATCTCATGCCAGCCAGTTTAGTATGCATAGCAAACACAAGCCGGGCGATGGGTATAATCCCAAGTCTTTTATGGACAGGAAGGGTTATGATGAATCTTTGGATAAGCTGCAAAAAGAGTATGAAAAGCACTTGAATGAAAATTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39084","NCBI_taxonomy_name":"uncultured bacterium BLR12","NCBI_taxonomy_id":"506514"}}}},"ARO_accession":"3002511","ARO_id":"38911","ARO_name":"LRA-12","CARD_short_name":"LRA-12","ARO_description":"LRA-12 is a beta-lactamase isolated from soil samples in Alaska.","ARO_category":{"41390":{"category_aro_accession":"3004226","category_aro_cvterm_id":"41390","category_aro_name":"subclass B3 LRA beta-lactamase","category_aro_description":"Beta-lactamases that are part of the LRA gene family and are classified as B3 (metallo-) beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"14":{"model_id":"14","model_name":"TEM-72","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1651":{"protein_sequence":{"accession":"AAF19151.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDKLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTTPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGASKRGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AF157553.1","fmin":"147","fmax":"1008","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATAAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGACGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCAGTAAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36917","NCBI_taxonomy_name":"Morganella morganii","NCBI_taxonomy_id":"582"}}}},"ARO_accession":"3000938","ARO_id":"37318","ARO_name":"TEM-72","CARD_short_name":"TEM-72","ARO_description":"TEM-72 is an extended-spectrum beta-lactamase found in Proteus mirabilis and Morganella morganii.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"15":{"model_id":"15","model_name":"TEM-59","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"931":{"protein_sequence":{"accession":"AAD45935.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDKLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMGDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAE"},"dna_sequence":{"accession":"AF062386.1","fmin":"31","fmax":"862","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATAAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGGGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAG","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3000928","ARO_id":"37308","ARO_name":"TEM-59","CARD_short_name":"TEM-59","ARO_description":"TEM-59 is an inhibitor-resistant beta-lactamase that has been found in clinical isolates.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"16":{"model_id":"16","model_name":"KPC-10","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1633":{"protein_sequence":{"accession":"ACS35345.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVRWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKYSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"GQ140348.1","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCGGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGTACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3002320","ARO_id":"38720","ARO_name":"KPC-10","CARD_short_name":"KPC-10","ARO_description":"KPC-10 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"18":{"model_id":"18","model_name":"OXA-212","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1048":{"protein_sequence":{"accession":"AEV91551.1","sequence":"MKTLQSGLIALITTFGSACTTISPSVETAKNQQQQSAQQQIQQAFDQLQTTGVIVVKDKHSLHSYGNDLSRAQTPYIPASTFKMLNALIGLEHGKATSTEVFKWDGQKRSFPTWEKDMTLGQAMQASAVPVYQELARRIGLDLMKKEVQRIGYGNQQIGTVVDNFWLVGPLQITPVQEVLFVEKLANTQLAFKPDVQHAVQDMLLIEQKPNYKLYAKSGWGMDLEPQVGWWAGWVETSTGEKVYFALNMHMKTGISASVREQLVKQSLTALGII"},"dna_sequence":{"accession":"JN861780.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAAAACTTTACAGTCGGGCCTCATCGCCCTCATTACAACCTTCGGTTCCGCATGTACCACAATAAGCCCCTCGGTAGAAACAGCTAAAAACCAACAGCAACAAAGTGCGCAGCAGCAGATCCAACAGGCCTTCGATCAACTCCAAACCACTGGGGTGATTGTCGTTAAAGATAAGCATAGCTTACACAGCTACGGCAATGACTTGAGCCGTGCTCAGACACCCTATATACCCGCCTCTACCTTTAAAATGCTGAATGCCTTAATCGGACTAGAACATGGTAAAGCAACCAGCACCGAGGTATTTAAATGGGATGGTCAAAAGCGCAGCTTCCCTACTTGGGAAAAAGACATGACTTTAGGGCAAGCCATGCAAGCATCTGCCGTTCCCGTTTATCAGGAGCTAGCACGGCGCATTGGCCTAGACCTGATGAAAAAAGAAGTGCAGCGCATTGGATATGGCAATCAACAGATTGGCACCGTTGTCGATAATTTTTGGTTAGTCGGTCCACTGCAAATTACGCCTGTTCAAGAAGTCCTTTTTGTAGAGAAGCTGGCCAATACACAACTCGCTTTTAAACCCGATGTACAACATGCAGTACAAGACATGCTGCTGATTGAACAAAAACCGAATTATAAACTCTATGCCAAATCTGGTTGGGGCATGGACCTAGAACCGCAAGTGGGCTGGTGGGCAGGCTGGGTCGAAACTTCAACAGGTGAAAAAGTGTATTTTGCTTTGAATATGCATATGAAAACAGGGATTTCAGCCAGCGTGCGTGAGCAACTGGTCAAACAAAGTCTGACAGCACTGGGGATAATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39092","NCBI_taxonomy_name":"Acinetobacter johnsonii","NCBI_taxonomy_id":"40214"}}}},"ARO_accession":"3001711","ARO_id":"38111","ARO_name":"OXA-212","CARD_short_name":"OXA-212","ARO_description":"OXA-212 is a beta-lactamase found in Acinetobacter spp.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46494":{"category_aro_accession":"3007705","category_aro_cvterm_id":"46494","category_aro_name":"OXA-211-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-211.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"19":{"model_id":"19","model_name":"IMP-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1091":{"protein_sequence":{"accession":"CAB94707.1","sequence":"MKKLFVLCVCFLCSITAAGARLPDLKIEKLEEGVYVHTSFEEVNGWGVVSKHGLVVLVNTDAYLIDTPFTATDTEKLVNWFVERGYKIKGTISSHFHSDSTGGIEWLNSQSIPTYASELTNELLKKDGKVQAKNSFSGVSYWLVKNKIEVFYPGPGHTQDNVVVWLPEKKILFGGCFVKPDGLGNLGDANLEAWPKSAKILMSKYVKAKLVVSSHSEIGDASLLKRTWEQAVKGLNESKKPSQPSN"},"dna_sequence":{"accession":"AJ243491.1","fmin":"0","fmax":"741","strand":"+","sequence":"ATGAAGAAATTATTTGTTTTATGTGTATGCTTCCTTTGTAGCATTACTGCCGCGGGAGCGCGTTTGCCTGATTTAAAAATCGAGAAGCTTGAAGAAGGTGTTTATGTTCATACATCGTTCGAAGAAGTTAACGGTTGGGGTGTTGTTTCTAAACACGGTTTGGTGGTTCTTGTAAACACTGACGCCTATCTGATTGACACTCCATTTACTGCTACAGATACTGAAAAGTTAGTCAATTGGTTTGTGGAGCGCGGCTATAAAATCAAAGGCACTATTTCCTCACATTTCCATAGCGACAGCACAGGGGGAATAGAGTGGCTTAATTCTCAATCTATTCCCACGTATGCATCTGAATTAACAAATGAACTTCTTAAAAAAGACGGTAAGGTGCAAGCTAAAAACTCATTTAGCGGAGTTAGTTATTGGCTAGTTAAAAATAAAATTGAAGTTTTTTATCCCGGCCCGGGGCACACTCAAGATAACGTAGTGGTTTGGTTACCTGAAAAGAAAATTTTATTCGGTGGTTGTTTTGTTAAACCGGACGGTCTTGGTAATTTGGGTGACGCAAATTTAGAAGCTTGGCCAAAGTCCGCCAAAATATTAATGTCTAAATATGTTAAAGCAAAACTGGTTGTTTCAAGTCATAGTGAAATTGGGGACGCATCACTCTTGAAACGTACATGGGAACAGGCTGTTAAAGGGCTAAATGAAAGTAAAAAACCATCACAGCCAAGTAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3002193","ARO_id":"38593","ARO_name":"IMP-2","CARD_short_name":"IMP-2","ARO_description":"IMP-2 is a beta-lactamase found in Acinetobacter baumannii.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"20":{"model_id":"20","model_name":"CMY-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1034":{"protein_sequence":{"accession":"CAA63264.1","sequence":"MQQRQSILWGAVATLMWAGLAHAGEASPVDPLRPVVDASIQPLLKEHRIPGMAVAVLKDGKAHYFNYGVANRESGAGVSEQTLFEIGSVSKTLTATLGAYAVVKGAMQLDDKASRHAPWLKGSAFDSITMGELATYSAGGLPLQFPEEVDSSEKMRAYYRQWAPVYSPGSHRQYSNPSIGLFGHLAASSLKQPFAPLMEQTLLPGLGMHHTYVNVPKQAMASYAYGYSKEDKPIRVNPGMLADEAYGIKTSSADLLRFVKANIGGVDDKALQQAISLTHQGHYSVGGMTQGLGWESYAYPVTEQTLLAGNSAKVILEANPTAAPRESGSQVLFNKTGSTNGFGAYVAFVPARGIGIVMLANRNYPNEARIKAAHAILAQLAG"},"dna_sequence":{"accession":"X92508.1","fmin":"332","fmax":"1481","strand":"+","sequence":"ATGCAACAACGACAATCCATCCTGTGGGGGGCCGTGGCCACCCTGATGTGGGCCGGTCTGGCCCATGCAGGTGAGGCTTCACCGGTCGATCCCCTGCGCCCCGTGGTGGATGCCAGCATCCAGCCGCTGCTCAAGGAGCACAGGATCCCGGGCATGGCGGTGGCCGTGCTCAAGGATGGCAAGGCCCACTACTTCAATTACGGGGTGGCCAACCGGGAGAGCGGGGCCGGCGTCAGCGAGCAGACCCTGTTCGAGATAGGATCCGTGAGCAAGACCCTGACTGCGACCCTGGGGGCCTATGCGGTGGTCAAGGGAGCGATGCAGCTGGATGACAAGGCGAGCCGGCACGCGCCCTGGCTCAAGGGATCCGCCTTTGACAGCATCACCATGGGGGAGCTTGCCACCTACAGCGCCGGAGGCCTGCCACTGCAATTCCCCGAGGAGGTGGATTCATCCGAGAAGATGCGCGCCTACTACCGCCAGTGGGCCCCTGTCTATTCGCCGGGCTCCCATCGCCAGTACTCCAACCCCAGCATAGGGCTGTTCGGCCACCTGGCGGCGAGCAGCCTGAAGCAGCCGTTTGCCCCCTTGATGGAGCAGACCCTGCTGCCCGGGCTCGGCATGCACCACACCTATGTCAATGTGCCGAAGCAGGCCATGGCGAGTTATGCCTATGGCTATTCGAAAGAGGACAAGCCCATCCGTGTCAACCCTGGCATGCTGGCGGACGAGGCCTATGGCATCAAGACCAGCTCGGCGGATCTGCTGCGTTTTGTGAAGGCCAACATCGGCGGGGTTGATGACAAGGCGTTGCAGCAGGCCATCTCCCTGACCCACCAAGGGCATTACTCGGTAGGCGGGATGACCCAGGGGCTGGGTTGGGAGAGTTACGCCTATCCCGTCACCGAGCAGACATTGCTGGCGGGCAATTCGGCCAAGGTGATCCTCGAAGCCAATCCGACGGCGGCGCCCCGGGAGTCGGGGAGCCAGGTGCTCTTCAACAAGACCGGCTCGACCAATGGCTTTGGCGCCTATGTGGCCTTCGTGCCGGCCAGGGGGATCGGCATCGTCATGCTGGCCAATCGCAACTACCCCAACGAGGCGCGCATCAAGGCGGCCCACGCCATCCTGGCGCAGTTGGCCGGTTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002012","ARO_id":"38412","ARO_name":"CMY-1","CARD_short_name":"CMY-1","ARO_description":"CMY-1 is a beta-lactamase found in the Enterobacteriaceae family.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"21":{"model_id":"21","model_name":"OXA-329","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1212":{"protein_sequence":{"accession":"AGW16411.1","sequence":"MYKKALIVATSILFLSACSSNTVKQHQIHSISANKNSEAIKSLFDQAQTTGVLVIKRGQTEEIYGNDLKRASTAYVPASTFKMLNALIGLEHHKAITTEVFKWDGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMSKEVKRIGFGNANIGSKVDDFWLVGPLKITPQQETQFAYQLAHKMLPFSKDVQEQVQSMVFIEEKNGRKIYAKSGWGWDIEPQVGWLTGWVVQPQGEIVAFSLNLEMKKGTPSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"KF203103.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGTATAAAAAAGCCCTTATCGTTGCAACAAGTATCCTATTTTTATCCGCCTGTTCTTCCAATACGGTAAAACAACATCAAATACACTCTATTTCTGCCAATAAAAATTCAGAAGCAATTAAATCACTTTTTGATCAAGCACAGACCACGGGAGTTTTGGTGATTAAGCGAGGGCAAACAGAAGAAATTTATGGCAATGATCTTAAAAGAGCATCAACCGCCTATGTTCCCGCCTCTACCTTTAAAATGTTAAATGCTTTAATTGGACTTGAACATCATAAGGCAATTACAACTGAAGTATTTAAATGGGATGGGCAAAAACGTTTATTTCCTGATTGGGAAAAGGACATGACACTGGGTGATGCCATGAAAGCTTCTGCAATCCCAGTTTACCAAGAATTAGCCCGACGAATTGGTCTGGATCTTATGTCTAAAGAGGTAAAGCGAATTGGTTTCGGTAATGCTAACATTGGCTCAAAAGTAGATGATTTCTGGCTTGTTGGTCCTCTAAAAATTACACCTCAACAAGAAACCCAATTTGCTTATCAATTAGCCCATAAAATGCTTCCATTTAGTAAAGATGTACAAGAACAAGTTCAATCAATGGTGTTCATAGAAGAAAAAAATGGACGTAAAATTTATGCAAAAAGCGGTTGGGGATGGGATATTGAGCCACAAGTTGGTTGGTTAACAGGCTGGGTCGTTCAACCACAAGGAGAAATTGTGGCATTCTCACTTAATTTAGAAATGAAAAAAGGAACTCCTAGCTCTATTCGCAAAGAAATTGCTTATAAAGGCTTAGAACAACTGGGTATCTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39094","NCBI_taxonomy_name":"Acinetobacter calcoaceticus","NCBI_taxonomy_id":"471"}}}},"ARO_accession":"3001517","ARO_id":"37917","ARO_name":"OXA-329","CARD_short_name":"OXA-329","ARO_description":"OXA-329 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46495":{"category_aro_accession":"3007706","category_aro_cvterm_id":"46495","category_aro_name":"OXA-213-like beta-lactamase","category_aro_description":"OXA-213-like enzymes have been identified to be intrinsic to A. calcoaceticus and have been subsequently detected in A. pittii. Phylogenetic analysis of OXA-213-like proteins identified two distinct subgroups within the OXA family. The first group was linked to A. pittii and the second group to A. calcoaceticus. The carbapenemase activity of these OXAs may be related to the species-dependent effect.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"22":{"model_id":"22","model_name":"ACT-10","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"940":{"protein_sequence":{"accession":"AEV91214.1","sequence":"MMKKSVCCALLLSTSCSVLAAPMSEKQLAEVVERTVTPLMKAQAIPGIAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPELTGKQWKGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMSYEQAITTRVFKPLKLDHTWINVPKTEEAHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVKDMASWVMVNMKPDSLEDSSLRKGFTLAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVEGSDNKVALAPLPAREVNPPAPPVNASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILDALQ"},"dna_sequence":{"accession":"JN848330.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCCGTTTGCTGCGCCCTGCTGCTCAGCACCTCCTGCTCGGTATTGGCTGCCCCGATGTCAGAAAAACAGCTGGCTGAGGTGGTGGAACGTACCGTTACGCCGCTGATGAAAGCTCAGGCCATTCCGGGTATAGCGGTGGCGGTGATTTATCAGGGTCAGCCGCACTACTTTACCTTCGGTAAAGCCGATGTTGCGGCGAATAAACCTGTCACCCCACAAACCTTATTCGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTACTCGGCGGCGATGCCATTGCTCGGGGTGAAATATCGCTGGGCGATCCGGTGACAAAATACTGGCCTGAGCTGACAGGCAAGCAGTGGAAGGGGATCCGCATGCTGGATCTGGCAACCTATACCGCAGGAGGTTTGCCGTTACAGGTACCGGATGAGGTCACGGATAACGCCTCTCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCGGGCACCACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGCGCGCTGGCGGTCAAACCTTCCGGCATGAGCTATGAGCAGGCCATAACGACGCGGGTCTTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTTCCGAAAACGGAAGAGGCGCATTACGCCTGGGGATACCGCGACGGTAAGGCGGTACACGTTTCGCCAGGAATGCTGGACGCTGAAGCCTATGGCGTAAAAACCAACGTGAAGGATATGGCAAGCTGGGTGATGGTCAACATGAAGCCGGACTCGCTTGAGGATAGTTCACTCAGGAAAGGCTTTACCCTGGCGCAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAGGGGTTAGGCTGGGAAATGCTTAACTGGCCGGTCGATGCCAAAACCGTGGTTGAAGGTAGCGACAATAAGGTGGCGCTGGCACCGTTGCCTGCGAGAGAAGTGAATCCACCGGCGCCCCCGGTCAACGCATCCTGGGTCCATAAAACCGGCTCTACCGGCGGGTTTGGCAGCTACGTGGCGTTTATTCCCGAAAAGCAGCTCGGCATTGTGATGCTGGCGAATAAAAGCTATCCCAACCCGGCACGCGTTGAGGCGGCATACCGTATCCTCGACGCGCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36783","NCBI_taxonomy_name":"Serratia marcescens","NCBI_taxonomy_id":"615"}}}},"ARO_accession":"3001832","ARO_id":"38232","ARO_name":"ACT-10","CARD_short_name":"ACT-10","ARO_description":"ACT-10 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"23":{"model_id":"23","model_name":"OXA-371","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1301":{"protein_sequence":{"accession":"BAO09635.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDDKAEKIKNLFNEAHTTGVLVIHQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGEKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVKPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"AB871653.1","fmin":"11870","fmax":"12695","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGACAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCATCAAGGTCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAATGGGATGGGGAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTCTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTAAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001557","ARO_id":"37957","ARO_name":"OXA-371","CARD_short_name":"OXA-371","ARO_description":"OXA-371 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"24":{"model_id":"24","model_name":"fusB","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"375"}},"model_sequences":{"sequence":{"3451":{"protein_sequence":{"accession":"AAL12234.1","sequence":"MKTMIYPHQYNYIRSVILRLKNVYKTVNDKETVKVIQSETYNDINEIFGHIDDDIEESLKVLMNIRLSNKEIEAILNKFLEYVVPFELPSPQKLQKVFKKVKKIKIPQFEEYDLKVSSFVGWNELASNRKYIIYYDEKKQLKGLYGEISNQVVKGFCTICNKESNVSLFMKKSKTNSDGQYVKKGDYICRDSIHCNKQLTDINQFYNFIDKLD"},"dna_sequence":{"accession":"AY047358.1","fmin":"1710","fmax":"2352","strand":"+","sequence":"ATGAAAACAATGATTTATCCTCACCAATATAATTATATCAGATCGGTTATTTTAAGATTGAAAAATGTATATAAAACGGTAAATGATAAAGAAACCGTCAAAGTTATTCAATCGGAAACCTATAATGATATTAATGAGATTTTTGGTCATATAGATGACGATATTGAAGAATCTTTAAAAGTATTAATGAACATCAGATTATCAAACAAAGAAATTGAAGCAATACTTAATAAATTTTTAGAATATGTAGTACCTTTTGAACTACCTAGTCCGCAAAAACTTCAGAAAGTATTTAAGAAAGTTAAAAAAATAAAAATACCTCAATTTGAAGAATATGATTTGAAGGTAAGTTCATTTGTAGGATGGAATGAACTTGCATCAAATCGGAAATATATAATATATTACGATGAAAAAAAACAATTAAAAGGACTTTATGGAGAAATTTCTAATCAGGTTGTAAAGGGGTTCTGCACAATTTGTAATAAAGAATCTAATGTTTCATTATTCATGAAAAAGTCAAAAACCAATTCGGATGGTCAATATGTAAAAAAAGGTGACTATATATGTCGAGATAGCATTCATTGTAATAAACAATTAACAGATATTAATCAGTTTTATAATTTTATTGATAAACTAGATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35508","NCBI_taxonomy_name":"Staphylococcus aureus","NCBI_taxonomy_id":"1280"}}}},"ARO_accession":"3003552","ARO_id":"40155","ARO_name":"fusB","CARD_short_name":"fusB","ARO_description":"FusB encodes a 2-domain zinc-binding protein that binds the ribosomal translocase EF-G, causing it to dissociate from the ribosome. This action increases the ribosomal turnover rate and confers resistance to fusidic acid. This protein is considered a FusB-type protein.","ARO_category":{"43297":{"category_aro_accession":"3005086","category_aro_cvterm_id":"43297","category_aro_name":"Target protecting FusB-type protein conferring resistance to Fusidic acid","category_aro_description":"Fusidic acid resistance determinants through the mediation of target protection. These protein drive the dissociation of EF-G from the ribosome thus counteracting the action of Fusidic acid.","category_aro_class_name":"AMR Gene Family"},"37139":{"category_aro_accession":"3000759","category_aro_cvterm_id":"37139","category_aro_name":"fusidic acid","category_aro_description":"Fusidic acid is the only commercially available fusidane, a group of steroid-like antibiotics. It is most active against Gram-positive bacteria, and acts by inhibiting elongation factor G to  block protein synthesis.","category_aro_class_name":"Antibiotic"},"45735":{"category_aro_accession":"3007153","category_aro_cvterm_id":"45735","category_aro_name":"fusidane antibiotic","category_aro_description":"A group of antibiotics possessing steroid rings or steroid-like structures.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"25":{"model_id":"25","model_name":"CTX-M-121","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1085":{"protein_sequence":{"accession":"AFA51699.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPITEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGGYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"JN790862.1","fmin":"244","fmax":"1120","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTACCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGGCTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001980","ARO_id":"38380","ARO_name":"CTX-M-121","CARD_short_name":"CTX-M-121","ARO_description":"CTX-M-121 is a beta-lactamase found in Escherichia coli.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"26":{"model_id":"26","model_name":"VEB-3","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1406":{"protein_sequence":{"accession":"AAS48620.1","sequence":"MKIVKRILLVLLSLFFTVVYSNAQTDNLTLKIENVLKAKNARIGVAIFNSNEKDTFKINNDFHFPMQSVMKFPIALAVLSEIDKGNLSFEQKIEITPQDLLPKTWSPIKEEFPNGTTLTIEQILNYTVSESDNIGCDILLKLIGGTDSVQKFLNANHFTDISIKANEEQMHKDWNTQYQNWATPTAMNKLLIDTYNNKNQLLSKKSYDFIWKIMRETTTGSNRLKGQLPKNTIVAHKTGTSGINNGIAAATNDVGVITLPNGQLIFISVFVAESKETSEINEKIISDIAKITWNYYLNK"},"dna_sequence":{"accession":"AY536519.1","fmin":"37","fmax":"937","strand":"+","sequence":"ATGAAAATCGTAAAAAGGATATTATTAGTATTGTTAAGTTTATTTTTTACAGTTGTGTATTCAAATGCTCAAACTGACAACTTAACTTTGAAAATTGAGAATGTTTTAAAGGCAAAAAATGCCAGAATAGGAGTAGCAATATTCAACAGCAATGAGAAGGATACTTTTAAGATTAATAACGACTTCCATTTCCCGATGCAAAGCGTTATGAAATTTCCGATTGCTTTAGCCGTTTTGTCTGAGATAGATAAAGGGAATCTTTCTTTTGAACAAAAAATAGAGATTACCCCTCAAGACCTTTTGCCTAAAACGTGGAGTCCGATTAAAGAGGAATTCCCTAATGGAACAACTTTGACGATTGAACAAATACTAAATTATACAGTATCAGAGAGCGACAATATTGGTTGTGATATTTTGCTAAAATTAATCGGAGGAACTGATTCTGTTCAAAAATTCTTGAATGCTAATCATTTCACTGATATTTCAATCAAAGCAAACGAAGAACAAATGCACAAGGATTGGAATACCCAATATCAAAATTGGGCAACCCCAACAGCGATGAACAAACTGTTAATAGATACTTATAATAATAAGAACCAATTACTTTCTAAAAAAAGTTATGATTTTATTTGGAAAATTATGAGAGAAACAACAACAGGAAGTAACCGATTAAAAGGACAATTACCAAAGAATACAATTGTTGCTCATAAAACAGGGACTTCCGGAATAAATAATGGAATTGCAGCAGCCACTAATGATGTTGGGGTAATTACTTTACCGAATGGACAATTAATTTTTATAAGCGTATTTGTTGCAGAGTCCAAAGAAACTTCGGAAATTAATGAAAAGATTATTTCAGACATTGCAAAAATAACGTGGAATTACTATTTGAATAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3002372","ARO_id":"38772","ARO_name":"VEB-3","CARD_short_name":"VEB-3","ARO_description":"VEB-3 is a beta-lactamase found in Enterobacter cloacae.","ARO_category":{"36182":{"category_aro_accession":"3000043","category_aro_cvterm_id":"36182","category_aro_name":"VEB beta-lactamase","category_aro_description":"VEB beta-lactamases or Vietnamese extended-spectrum beta-lactamases are class A beta-lactamases that confer high-level resistance to oxyimino cephalosporins and to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"27":{"model_id":"27","model_name":"lnuA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"5230":{"protein_sequence":{"accession":"AAA26652.1","sequence":"MKNNNVTEKELFYILDLFEHMKVTYWLDGGWGVDVLTGKQQREHRDIDIDFDAQHTQKVIQKLEDIGYKIEVHWMPSRMELKHEEYGYLDIHPINLNDDGSITQANPEGGNYVFQNDWFSETNYKDRKIPCISKEAQLLFHSGYDLTETDHFDIKNLKSIT"},"dna_sequence":{"accession":"M14039.1","fmin":"412","fmax":"898","strand":"+","sequence":"ATGAAAAATAATAATGTAACAGAAAAAGAATTATTTTATATTTTAGATTTATTTGAACACATGAAAGTAACTTATTGGTTAGATGGTGGCTGGGGGGTAGATGTATTAACTGGAAAACAACAAAGAGAACACAGAGATATAGATATAGATTTTGACGCTCAACACACTCAAAAAGTTATACAAAAATTAGAAGATATAGGATACAAAATAGAAGTTCATTGGATGCCTTCACGTATGGAACTTAAGCATGAAGAATATGGGTATTTAGATATTCATCCTATAAATCTAAATGATGATGGATCAATTACCCAAGCAAACCCAGAAGGTGGTAATTATGTTTTCCAAAATGACTGGTTTTCAGAAACTAATTACAAAGATCGAAAAATACCATGTATTTCAAAAGAAGCTCAACTTCTTTTTCATTCTGGTTATGATTTAACAGAAACAGACCATTTTGATATAAAAAATTTAAAATCAATAACATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36827","NCBI_taxonomy_name":"Staphylococcus haemolyticus","NCBI_taxonomy_id":"1283"}}}},"ARO_accession":"3002835","ARO_id":"39269","ARO_name":"lnuA","CARD_short_name":"lnuA","ARO_description":"lnuA is a plasmid-mediated nucleotidyltransferase found in Staphylococcus chromogenes.","ARO_category":{"36360":{"category_aro_accession":"3000221","category_aro_cvterm_id":"36360","category_aro_name":"lincosamide nucleotidyltransferase (LNU)","category_aro_description":"Resistance to the lincosamide antibiotic by ATP-dependent modification of the 3' and\/or 4'-hydroxyl groups of the methylthiolincosamide sugar.","category_aro_class_name":"AMR Gene Family"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"45751":{"category_aro_accession":"3007169","category_aro_cvterm_id":"45751","category_aro_name":"pirlimycin","category_aro_description":"Pirlimycin is an experimental\/veterinary lincosamide antibiotic. Although not approved for use in humans, pirlimycin is commonly used to treat mammary gland infections in cattle.","category_aro_class_name":"Antibiotic"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"28":{"model_id":"28","model_name":"OXA-45","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1463":{"protein_sequence":{"accession":"CAD58780.1","sequence":"MRGKHTVILGAALSALFAGAAGAQMLECTLVADAASGQELYRKGACDKAFAPMSTFKVPLAVMGYDAGILVDAHNPRWDYKPEFNGYKFQQKTTDPTIWEKDSIVWYSQQLTRKMGQKRFAAYVAGFGYGNGDISGEPGKSNGLTHSWLGSSLKISPEGQVRFVRDLLSAKLPASKDAQQMTVSILPHFAAGDWAVQGKTGTGSFIDARGAKAPLGWFIGWATHEERRVVFARMTAGGKKGEQPAGPAARDAFLKALPDLAKRF"},"dna_sequence":{"accession":"AJ519683.1","fmin":"281","fmax":"1076","strand":"+","sequence":"ATGCGCGGTAAACACACTGTCATTCTGGGCGCGGCACTGTCGGCGCTTTTTGCCGGCGCGGCTGGCGCGCAGATGCTCGAATGCACGCTGGTCGCCGATGCCGCGAGCGGTCAGGAGCTTTACCGCAAGGGTGCCTGTGACAAGGCCTTCGCGCCAATGTCGACGTTCAAGGTGCCGTTGGCCGTCATGGGCTACGATGCTGGCATTCTTGTGGACGCGCATAATCCGCGCTGGGACTACAAGCCGGAATTCAATGGCTACAAATTCCAGCAGAAAACCACCGACCCTACGATCTGGGAAAAGGACTCGATCGTCTGGTATTCGCAGCAATTGACCCGCAAGATGGGGCAAAAACGCTTTGCCGCATACGTGGCCGGGTTCGGCTATGGCAATGGCGATATCTCCGGTGAGCCCGGTAAGAGCAACGGCCTGACGCATTCATGGCTGGGCTCCTCGCTGAAGATTTCTCCGGAAGGACAGGTGCGGTTCGTACGCGATCTGCTGTCGGCGAAACTGCCGGCTTCGAAAGACGCCCAGCAAATGACGGTTTCCATCCTGCCGCATTTCGCGGCCGGTGATTGGGCTGTGCAGGGCAAGACCGGCACCGGCTCGTTCATCGACGCCAGGGGTGCGAAGGCGCCGCTCGGATGGTTCATCGGCTGGGCGACGCACGAGGAACGCCGCGTCGTCTTCGCCCGCATGACTGCGGGCGGGAAGAAGGGCGAGCAACCCGCCGGACCGGCTGCCCGCGACGCCTTCCTCAAGGCATTGCCGGATCTCGCGAAAAGGTTCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3001794","ARO_id":"38194","ARO_name":"OXA-45","CARD_short_name":"OXA-45","ARO_description":"OXA-45 is a beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"30":{"model_id":"30","model_name":"OXA-226","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1927":{"protein_sequence":{"accession":"ACM67635.1","sequence":"MAIRIFAILFSIFSLATFAHAQEGTLERSDWRKFFSEFQAKGTIVVADERQADRAMLVFDPVRSKKRYSPASTFKIPHTLFALDAGAVRDEFQIFRWDGVNRGFAGHNQDQDLRSAMRNSTVWVYELFAKEIGDDKARRYLKKIDYGNADPSTSNGDYRIEGSLAISAQEQIAFLRKLYRNELPFRVEHQRLVKDLMIVEAGRNWILRAKTGWEGRMGWWVGWVEWPTGSVFFALNIDTPNRMDDLFKREAIVRAILRSIEALPPNPAVNSDAAR"},"dna_sequence":{"accession":"FJ617207.1","fmin":"0","fmax":"828","strand":"+","sequence":"ATGGCAATCCGAATCTTCGCGATACTTTTCTCCATTTTTTCTCTTGCCACTTTCGCGCATGCGCAAGAAGGCACGCTAGAACGTTCTGACTGGAGGAAGTTTTTCAGCGAATTTCAAGCCAAAGGCACGATAGTTGTGGCAGACGAACGCCAAGCGGATCGTGCCATGTTGGTTTTTGATCCTGTGCGATCGAAGAAACGCTACTCGCCTGCATCGACATTCAAGATACCTCATACACTTTTTGCACTTGATGCAGGCGCTGTTCGTGATGAGTTCCAGATTTTTCGATGGGACGGCGTTAACAGGGGCTTTGCAGGCCACAATCAAGACCAAGATTTGCGATCAGCAATGCGGAATTCTACTGTTTGGGTGTATGAGCTATTTGCAAAGGAAATTGGTGATGACAAAGCTCGGCGCTATTTGAAGAAAATCGACTATGGCAACGCCGATCCTTCGACAAGTAATGGCGATTACAGGATAGAAGGCAGCCTTGCAATCTCGGCGCAGGAGCAAATTGCATTTCTCAGGAAGCTCTATCGTAACGAGCTGCCCTTTCGGGTAGAACATCAGCGCTTGGTCAAGGATCTCATGATTGTGGAAGCCGGTCGCAACTGGATACTGCGTGCAAAGACGGGCTGGGAAGGCCGTATGGGTTGGTGGGTAGGATGGGTTGAGTGGCCGACTGGCTCCGTATTCTTCGCACTGAATATTGATACGCCAAACAGAATGGATGATCTTTTCAAGAGGGAGGCAATCGTGCGGGCAATCCTTCGCTCTATTGAAGCGTTACCGCCCAACCCGGCAGTCAACTCGGACGCTGCGCGATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3001800","ARO_id":"38200","ARO_name":"OXA-226","CARD_short_name":"OXA-226","ARO_description":"OXA-226 is a beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46493":{"category_aro_accession":"3007704","category_aro_cvterm_id":"46493","category_aro_name":"OXA-2-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-2.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"31":{"model_id":"31","model_name":"CTX-M-155","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1666":{"protein_sequence":{"accession":"AIS67611.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTAPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASGAKIVTDGL"},"dna_sequence":{"accession":"KM211508.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGCACCGCGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGGCGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3003163","ARO_id":"39740","ARO_name":"CTX-M-155","CARD_short_name":"CTX-M-155","ARO_description":"CTX-M-155 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"32":{"model_id":"32","model_name":"DHA-15","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"910":{"protein_sequence":{"accession":"AIT76106.1","sequence":"MKKSLSATLISALLAFSAPGFSAADNVAAVVDSTIKPLMAQQDIPGMAVAVSVKGKPYYFNYGFADIQAKQPVTENTLFELGSVSKTFTGVLGAVSVAKKEMALNDPAAKYQPELALPQWKGITLLDLATYTAGGLPLQVPDAVKSRADLLNFYQQWQPSRKPGYMRLYANSSIGLFGALTANAAGMPYEQLLTARILAPLGLSHTFITVPESAQSQYAYGYKNKKPVRVSPGQLDAESYGVKSASKDMLRWAEMNMEPSRAGNADLEMAMYLAQTRYYKTAAINQGLGWEMYDWPQQKDMIINGVTNEVALQPHPVTDNQVQPYNRASWVHKTGATTGFGAYVAFIPEKQVAIVILANKNYPNTERVKAAQAILSALE"},"dna_sequence":{"accession":"KM087853.1","fmin":"0","fmax":"1140","strand":"+","sequence":"ATGAAAAAATCGTTATCTGCAACACTGATTTCCGCTCTGCTGGCGTTTTCCGCCCCGGGGTTTTCTGCCGCTGATAATGTCGCGGCGGTGGTGGACAGCACCATTAAACCGCTGATGGCACAGCAGGATATTCCCGGGATGGCGGTTGCCGTCTCCGTAAAGGGTAAGCCCTATTATTTCAATTATGGTTTTGCCGATATTCAGGCAAAACAGCCGGTCACTGAAAATACACTATTTGAGCTCGGATCTGTAAGTAAAACTTTCACAGGTGTGCTGGGTGCGGTTTCTGTGGCGAAAAAAGAGATGGCGCTGAATGATCCGGCGGCAAAATACCAGCCGGAGCTGGCTCTGCCGCAGTGGAAGGGGATCACATTGCTGGATCTGGCTACCTATACCGCAGGCGGACTGCCGTTACAGGTGCCGGATGCGGTAAAAAGCCGTGCGGATCTGCTGAATTTCTATCAGCAGTGGCAGCCGTCCCGGAAACCGGGCTATATGCGTCTGTATGCAAACAGCAGTATCGGCCTGTTTGGTGCTCTGACCGCAAACGCGGCGGGGATGCCGTATGAGCAGTTGCTGACTGCACGGATCCTGGCACCGCTGGGGTTATCTCACACCTTTATTACTGTGCCGGAAAGTGCGCAAAGCCAGTATGCGTACGGTTATAAAAACAAAAAACCGGTCCGCGTGTCGCCGGGACAGCTTGATGCGGAATCTTACGGCGTGAAATCCGCCTCAAAAGATATGCTGCGCTGGGCGGAAATGAATATGGAGCCGTCACGGGCCGGTAATGCGGATCTGGAAATGGCAATGTATCTCGCCCAGACCCGCTACTATAAAACCGCCGCGATTAACCAGGGGCTGGGCTGGGAAATGTATGACTGGCCGCAGCAGAAAGATATGATCATTAACGGTGTGACCAACGAGGTCGCATTGCAGCCGCATCCGGTAACAGACAACCAGGTTCAGCCGTATAACCGTGCTTCCTGGGTGCATAAAACGGGCGCAACAACTGGTTTCGGCGCCTATGTCGCCTTTATTCCGGAAAAACAGGTGGCGATTGTGATTCTGGCGAATAAAAACTACCCGAATACCGAAAGAGTCAAAGCTGCACAGGCTATTTTGAGTGCACTGGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002146","ARO_id":"38546","ARO_name":"DHA-15","CARD_short_name":"DHA-15","ARO_description":"DHA-15 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36207":{"category_aro_accession":"3000068","category_aro_cvterm_id":"36207","category_aro_name":"DHA beta-lactamase","category_aro_description":"DHA beta-lactamases are plasmid-mediated AmpC \u03b2-lactamases that confer resistance to cephamycins and oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"33":{"model_id":"33","model_name":"msrE","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"950"}},"model_sequences":{"sequence":{"5181":{"protein_sequence":{"accession":"ACB05808.1","sequence":"MSLIIKARNIRLDYAGRDVLDIDELEIHSYDRIGLVGDNGAGKSSLLKVLNGEIVLAEATLQRFGDFAHISQLGGIEIETVEDRAMLSRLGVSNVQNDTMSGGEETRAKIAAAFSQQVHGILADEPTSHLDLNGIDLLIGQLKAFDGALLVISHDRYFLDMVVDKIWELKDGKITEYWGGYSDYLRQKEEERQHQAVEYELMMKERERLESAVQEKRQQANRLDNKKKGEKSKNSTESAGRLGHAKMTGTKQRKLYQAAKSMEKRLAALEDIQAPEHLRSIRFRQSSALELHNKFPITADGLSLKFGSRTIFDDANFIIPLGAKVAITGSNGTGKTSLLKMISERADGLTISPKAEIGYFTQTGYKFNTHKSVLSFMQEECEYTVAEIRAVLASMGIGANDIQKNLSDLSGGEIIKLLLSKMLLGKYNILLMDEPGNYLDLKSIAALETMMKSYAGTIIFVSHDKQLVDNIADIIYEIKDHKIIKTFERDC"},"dna_sequence":{"accession":"EU294228.1","fmin":"21241","fmax":"22717","strand":"+","sequence":"ATGAGTTTAATTATTAAAGCGAGAAACATACGCTTGGATTATGCTGGGCGTGATGTTTTGGATATTGATGAATTGGAAATTCACTCTTATGACCGTATTGGTCTTGTGGGTGATAACGGAGCAGGAAAGAGTAGTTTACTCAAAGTACTTAATGGCGAAATTGTTTTAGCCGAAGCGACATTACAGCGTTTTGGTGATTTTGCACATATCAGCCAACTGGGCGGAATCGAAATAGAAACGGTCGAAGACCGGGCAATGTTATCTCGCCTTGGTGTTTCCAATGTACAAAACGACACAATGAGTGGCGGAGAGGAAACTCGTGCAAAAATTGCTGCCGCATTTTCCCAACAAGTACATGGCATTCTAGCGGATGAACCAACCAGCCACCTTGATCTCAATGGAATAGATCTACTTATTGGTCAACTTAAAGCATTTGATGGAGCATTACTTGTTATCAGTCATGACCGATATTTTCTTGATATGGTTGTAGACAAGATATGGGAGTTAAAAGACGGTAAAATTACGGAATATTGGGGTGGTTACTCGGATTACTTGCGTCAAAAAGAAGAAGAGCGACAACACCAAGCCGTAGAATATGAGCTGATGATGAAGGAACGGGAGCGATTAGAATCTGCTGTGCAAGAAAAACGCCAGCAAGCTAATCGATTAGACAATAAGAAAAAAGGAGAAAAATCCAAAAACTCTACCGAAAGTGCTGGACGACTTGGGCATGCAAAAATGACTGGCACCAAGCAAAGAAAACTGTATCAGGCAGCTAAGAGTATGGAAAAGCGTTTGGCTGCATTAGAAGATATTCAAGCACCAGAGCATTTGCGTTCTATTCGTTTTCGTCAAAGTTCAGCCCTAGAACTGCACAATAAGTTCCCGATTACGGCAGATGGTCTGAGCTTAAAATTTGGTAGCCGTACTATCTTTGATGACGCTAACTTTATAATACCGCTTGGCGCTAAAGTCGCTATAACTGGATCGAATGGAACAGGGAAAACGTCCTTGTTAAAAATGATATCAGAACGTGCTGATGGATTAACCATATCTCCAAAAGCTGAAATTGGCTACTTTACACAAACAGGATATAAATTTAACACGCATAAATCTGTGCTCTCCTTTATGCAGGAAGAGTGCGAGTACACAGTTGCGGAAATTCGTGCAGTATTGGCTTCAATGGGGATCGGAGCGAATGATATTCAAAAAAACTTATCCGACTTATCGGGAGGTGAAATCATCAAACTGCTTTTATCCAAAATGCTTTTAGGAAAATATAATATTTTGCTTATGGATGAACCAGGAAACTATCTTGACCTAAAAAGTATTGCCGCATTAGAAACAATGATGAAGTCCTATGCAGGAACTATTATCTTCGTATCTCATGACAAGCAATTGGTCGATAATATTGCTGACATTATCTACGAGATCAAAGACCACAAAATCATCAAGACTTTTGAGAGAGATTGTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3003109","ARO_id":"39685","ARO_name":"msrE","CARD_short_name":"msrE","ARO_description":"MsrE is an ABC-F subfamily protein expressed to Klebsiella pneumoniae that confers resistance to erythromycin and streptogramin B antibiotics. It is associated with plasmid DNA. It is also 100% identical to ABC-F type ribosomal protection protein Msr(E) which is in multiple species.","ARO_category":{"41695":{"category_aro_accession":"3004471","category_aro_cvterm_id":"41695","category_aro_name":"msr-type ABC-F protein","category_aro_description":"msr-type ABC-F subfamily ribosomal protection proteins expression in Staphylococci species and confer resistance to erythromycin and streptogramin B antibiotics through antibiotic target protection mechanisms.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"34":{"model_id":"34","model_name":"OXY-6-3","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1060":{"protein_sequence":{"accession":"CAI43424.1","sequence":"MLKSSWRKSALMAAAAVPLLLASGSLWASADAIQQKLADLEKRSGGRLGVALINTTDDSQTLYRGDERFAMCSTGKVMAAAAVLKQSESHPDVVNKRLEIKKSDLVVWSPITEKHLQSGMTLAELSAAALQYSDNTAMNKMISYLGGPEKVTAFAQSIGDVTFRLDRTEPALNSAIPGDKRDTTTPLAMAESLRKLTLGNALGEQQRAQLVTWLKGNTTGGQSIRAGLPASWAVGDKTGAGDYGTTNDIAVIWPENHAPLVLVTYFTQPQQDAKSRKEVLAAAAKIVTEGL"},"dna_sequence":{"accession":"AJ871876.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGTTGAAAAGTTCGTGGCGTAAAAGCGCCCTGATGGCCGCCGCCGCCGTTCCGCTGCTGCTGGCGAGCGGTTCATTATGGGCCAGTGCCGATGCTATCCAGCAAAAGCTGGCTGATTTAGAAAAACGGTCCGGTGGCCGGCTGGGCGTGGCGCTGATTAACACGACGGATGATTCGCAAACCCTTTATCGCGGCGATGAACGTTTTGCCATGTGCAGCACCGGTAAAGTGATGGCCGCCGCCGCGGTGTTAAAGCAGAGCGAAAGCCATCCCGATGTGGTGAATAAAAGGCTGGAGATTAAAAAATCGGATTTAGTGGTCTGGAGCCCGATTACCGAAAAACATCTGCAAAGCGGAATGACCCTGGCGGAACTCAGCGCGGCGGCGCTGCAGTACAGCGACAATACCGCGATGAATAAGATGATTAGCTACCTTGGCGGACCGGAAAAGGTGACCGCATTCGCCCAGAGCATCGGGGACGTTACTTTTCGTCTCGATCGTACGGAGCCGGCGCTGAACAGCGCGATTCCCGGCGATAAGCGCGATACCACCACTCCGTTGGCGATGGCCGAAAGCCTGCGCAAGCTGACGCTGGGCAATGCGCTGGGCGAACAGCAGCGCGCCCAGTTAGTGACGTGGCTAAAAGGCAATACCACCGGCGGGCAAAGCATTCGCGCAGGCCTGCCCGCAAGCTGGGCGGTCGGGGATAAAACCGGCGCCGGAGATTACGGCACCACCAACGATATCGCGGTGATCTGGCCGGAAAATCATGCCCCGCTGGTGTTAGTGACCTATTTTACCCAGCCGCAGCAGGATGCGAAAAGCCGCAAAGAGGTGTTAGCCGCGGCGGCGAAAATCGTGACCGAAGGGCTGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3002415","ARO_id":"38815","ARO_name":"OXY-6-3","CARD_short_name":"OXY-6-3","ARO_description":"OXY-6-3 is a beta-lactamase found in Klebsiella oxytoca.","ARO_category":{"38788":{"category_aro_accession":"3002388","category_aro_cvterm_id":"38788","category_aro_name":"OXY beta-lactamase","category_aro_description":"OXY beta-lactamases are chromosomal class A beta-lactamases that are found in Klebsiella oxytoca. At constitutive low levels, OXY beta-lactamases confer resistance to aminopenicillins and carboxypenicillins. At high induced levels,  OXY beta-lactamases confer resistance to penicillins, cephalosporins and aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"35":{"model_id":"35","model_name":"FosA2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"200"}},"model_sequences":{"sequence":{"341":{"protein_sequence":{"accession":"ACC85616.1","sequence":"MLQSLNHLTLAVSDLQKSVTFWHELLGLTLHARWNTGAYLTCGDLWVCLSYDEARGYVPPQESDYTHYAFTVAAEDFEPFSHKLEQAGVTVWKQNKSEGASFYFLDPDGHKLELHVGSLAARLAACREKPYAGMVFTSDEA"},"dna_sequence":{"accession":"EU487198.1","fmin":"216","fmax":"642","strand":"+","sequence":"ATGCTGCAATCACTCAACCATCTGACCCTCGCGGTCAGCGACCTGCAAAAAAGCGTTACCTTCTGGCACGAGCTGCTGGGGCTGACGCTGCACGCCCGCTGGAATACCGGGGCCTATCTTACCTGCGGCGATCTGTGGGTCTGCCTGTCCTATGACGAGGCGCGCGGTTACGTGCCGCCGCAGGAGAGCGACTATACCCATTACGCGTTTACCGTTGCGGCGGAAGATTTTGAGCCGTTCTCGCACAAGCTGGAGCAGGCGGGCGTTACCGTCTGGAAGCAAAACAAAAGTGAGGGGGCATCGTTCTATTTTCTCGACCCGGACGGGCACAAGCTGGAGCTGCACGTGGGCAGCCTCGCCGCGCGGCTGGCGGCGTGCCGGGAGAAACCCTATGCCGGAATGGTCTTCACCTCAGACGAGGCTTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3002804","ARO_id":"39238","ARO_name":"FosA2","CARD_short_name":"FosA2","ARO_description":"An enzyme that confers resistance to fosfomycin in Enterobacter cloacae by breaking the epoxide ring of the molecule. It depends on the cofactors Manganese (II) and Potassium and uses Glutathione (GSH) as the nucleophilic molecule.","ARO_category":{"36272":{"category_aro_accession":"3000133","category_aro_cvterm_id":"36272","category_aro_name":"fosfomycin thiol transferase","category_aro_description":"Catalyzes the addition of a thiol group from a nucleophilic molecule to fosfomycin.","category_aro_class_name":"AMR Gene Family"},"35944":{"category_aro_accession":"0000025","category_aro_cvterm_id":"35944","category_aro_name":"fosfomycin","category_aro_description":"Fosfomycin (also known as phosphomycin and phosphonomycin) is a broad-spectrum antibiotic produced by certain Streptomyces species. It is effective on gram positive and negative bacteria as it targets the cell wall, an essential feature shared by both bacteria. Its specific target is MurA (MurZ in E.coli), which attaches phosphoenolpyruvate (PEP) to UDP-N-acetylglucosamine, a step of commitment to cell wall synthesis. In the active site of MurA, the active cysteine molecule is alkylated which stops the catalytic reaction.","category_aro_class_name":"Antibiotic"},"45731":{"category_aro_accession":"3007149","category_aro_cvterm_id":"45731","category_aro_name":"phosphonic acid antibiotic","category_aro_description":"A group of antibiotics derived from phosphonic acids.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"38":{"model_id":"38","model_name":"APH(3')-Va","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"371":{"protein_sequence":{"accession":"AAA26699.1","sequence":"MDDSTLRRKYPHHEWHAVNEGDSGAFVYQLTGGPEPQPELYAKIAPRAPENSAFDLSGEADRLEWLHRHGIPVPRVVERGADDTAAWLVTEAVPGVAAAEEWPEHQRFAVVEAMAELARALHELPVEDCPSDRRLDAAVAEARRNVAEGLVDLDDLQEERAGWTGDQLLAELDRTRPEKEDLVVCHGDLCPNNVLLDPGTCRVTGVIDVGRLGVADRHADIALAARELEIDEDPWFGPAYAERFLERYGAHRVDKEKLAFYQLLDEFF"},"dna_sequence":{"accession":"K00432.1","fmin":"306","fmax":"1113","strand":"+","sequence":"ATGGACGACAGCACGTTGCGCCGGAAGTACCCGCACCACGAGTGGCACGCAGTGAACGAAGGAGACTCGGGCGCCTTCGTCTACCAGCTCACCGGCGGCCCCGAGCCCCAGCCCGAGCTCTACGCGAAGATCGCCCCCCGCGCCCCCGAGAACTCCGCCTTCGACCTGTCCGGCGAGGCCGACCGGCTGGAGTGGCTCCACCGCCACGGGATCCCCGTCCCCCGCGTCGTCGAGCGCGGTGCCGACGACACCGCCGCGTGGCTCGTCACGGAGGCCGTCCCCGGCGTCGCGGCGGCCGAGGAGTGGCCCGAGCACCAGCGGTTCGCCGTGGTCGAGGCGATGGCGGAGCTGGCCCGCGCCCTCCACGAGCTGCCCGTGGAGGACTGCCCCTCCGACCGGCGCCTCGACGCGGCGGTCGCCGAGGCCCGGCGGAACGTCGCCGAGGGCTTGGTGGACCTCGACGACCTGCAGGAGGAGCGGGCCGGGTGGACCGGCGACCAGCTCCTGGCGGAGCTCGACCGCACCCGTCCCGAGAAGGAGGACCTGGTCGTCTGCCATGGCGACCTGTGCCCCAACAACGTCCTGCTCGACCCCGGGACCTGCCGGGTCACCGGCGTGATCGACGTCGGCCGCCTCGGGGTCGCCGACCGCCACGCCGACATCGCCTTGGCCGCCCGCGAGCTGGAGATCGACGAGGACCCCTGGTTCGGCCCCGCCTACGCCGAGCGGTTCCTGGAGCGGTACGGCGCCCACCGCGTCGACAAGGAGAAGCTGGCCTTCTACCAGCTTCTCGACGAGTTCTTCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36838","NCBI_taxonomy_name":"Streptomyces fradiae","NCBI_taxonomy_id":"1906"}}}},"ARO_accession":"3002649","ARO_id":"39049","ARO_name":"APH(3')-Va","CARD_short_name":"APH(3')-Va","ARO_description":"APH(3')-Va is a chromosomal-encoded aminoglycoside phosphotransferase in Streptomyces fradiae.","ARO_category":{"36265":{"category_aro_accession":"3000126","category_aro_cvterm_id":"36265","category_aro_name":"APH(3')","category_aro_description":"A category of aminoglycoside O-phosphotransferase enzymes with modification regiospecificity based at the 3'-hydroxyl group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics, specifically kanamycin and neomycin, by the ATP-dependent phosphorylation of the 3'-hydroxyl group of the compound.","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35940":{"category_aro_accession":"0000021","category_aro_cvterm_id":"35940","category_aro_name":"ribostamycin","category_aro_description":"Ribostamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Ribostamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"37001":{"category_aro_accession":"3000657","category_aro_cvterm_id":"37001","category_aro_name":"paromomycin","category_aro_description":"An aminoglycoside antibiotic used for the treatment of parasitic infections. It is similar to neomycin sharing a similar spectrum of activity, but its hydroxyl group at the 6'-position instead of an amino group makes it resistant to AAC(6') modifying enzymes.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"39":{"model_id":"39","model_name":"AAC(3)-Ia","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"8360":{"protein_sequence":{"accession":"AAG15269.1","sequence":"MGIIRTCRLGPDQVKSMRAALDLFGREFGDVATYSQHQPDSDYLGNLLRSKTFIALAAFDQEAVVGALAAYVLPRFEQPRSEIYIYDLAVSGEHRRQGIATALINLLKHEANALGAYVIYVQADYGDDPAVALYTKLGIREEVMHFDIDPSTAT"},"dna_sequence":{"accession":"U12338.3","fmin":"5055","fmax":"5520","strand":"+","sequence":"ATGGGCATCATTCGCACATGTAGGCTCGGCCCTGACCAAGTCAAATCCATGCGGGCTGCTCTTGATCTTTTCGGTCGTGAGTTCGGAGACGTAGCCACCTACTCCCAACATCAGCCGGACTCCGATTACCTCGGGAACTTGCTCCGTAGTAAGACATTCATCGCGCTTGCTGCCTTCGACCAAGAAGCGGTTGTTGGCGCTCTCGCGGCTTACGTTCTGCCCAGGTTTGAGCAGCCGCGTAGTGAGATCTATATCTATGATCTCGCAGTCTCCGGCGAGCACCGGAGGCAGGGCATTGCCACCGCGCTCATCAATCTCCTCAAGCATGAGGCCAACGCGCTTGGTGCTTATGTGATCTACGTGCAAGCAGATTACGGTGACGATCCCGCAGTGGCTCTCTATACAAAGTTGGGCATACGGGAAGAAGTGATGCACTTTGATATCGACCCAAGTACCGCCACCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002528","ARO_id":"38928","ARO_name":"AAC(3)-Ia","CARD_short_name":"AAC(3)-Ia","ARO_description":"AAC(3)-Ia is an aminoglycoside acetyltransferase encoded by plasmids, transposons, integrons in S. marcescens, E. coli, Acinetobacter baumannii, Klebsiella pneumoniae, Klebsiella oxytoca, P. aeruginosa, Salmonella typhimurium and Proteus mirabilis.","ARO_category":{"36461":{"category_aro_accession":"3000322","category_aro_cvterm_id":"36461","category_aro_name":"AAC(3)","category_aro_description":"A category of aminoglycoside N-acetyltransferase enzymes with modification regiospecificity based at the 3-amino group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics through acetylation of the 3-amino group of the compound.","category_aro_class_name":"AMR Gene Family"},"35922":{"category_aro_accession":"0000003","category_aro_cvterm_id":"35922","category_aro_name":"astromicin","category_aro_description":"Astromicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Astromicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"46133":{"category_aro_accession":"3007382","category_aro_cvterm_id":"46133","category_aro_name":"gentamicin","category_aro_description":"Gentamicin is a commonly used aminoglycoside antibiotic derived from members of the Micromonospora genus of bacteria. It acts by binding the 30S ribosomal subunit, thus inhibiting protein synthesis. Gentamicin is typically used to treat Gram-negative infections of the repiratory and urinary tract, as well as infections of the bone and soft tissue. It also exhibits considerable nephrotoxicity and ototoxicity. Gentamicin is administered as a mixture of gentamicin type C (which makes about around 80% of the complex) and types A, B, and X (distributed in the remaining 20% of the complex).","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"40":{"model_id":"40","model_name":"QnrB58","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"532":{"protein_sequence":{"accession":"AFR46589.1","sequence":"MTPLLYKKTGTNMALALVGEKIDRNRFTGEKIDNSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNASALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGAQVLGATFSGSDLSGGEFSTFDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDNYQASLLMERLGIAIIG"},"dna_sequence":{"accession":"JX259319.1","fmin":"0","fmax":"681","strand":"+","sequence":"ATGACGCCATTACTGTATAAAAAAACAGGTACAAATATGGCTCTGGCACTCGTTGGCGAAAAAATTGACAGAAACCGTTTCACCGGTGAGAAAATTGATAATAGTACATTTTTTAACTGTGATTTTTCAGGTGCCGACCTGAGCGGCACTGAATTTATCGGCTGTCAGTTCTATGATCGTGAAAGCCAGAAAGGGTGCAATTTTAGTCGTGCGATGCTGAAAGATGCCATTTTTAAAAGCTGTGATTTATCCATGGCGGATTTTCGCAATGCCAGTGCGCTGGGCATTGAAATTCGCCACTGCCGCGCACAAGGCGCAGATTTCCGCGGCGCAAGTTTTATGAATATGATCACTACTCGCACCTGGTTTTGTAGTGCATATATCACTAACACAAATCTAAGCTACGCCAATTTTTCGAAAGTCGTGCTGGAAAAGTGTGAGCTGTGGGAAAACCGTTGGATGGGTGCCCAGGTACTGGGCGCGACGTTCAGTGGTTCAGATCTCTCCGGCGGCGAGTTTTCGACTTTCGACTGGCGAGCAGCAAACTTCACACATTGCGATCTGACCAATTCGGAGTTGGGGGACTTAGATATTCGGGGCGTTGATTTACAAGGCGTTAAGTTGGACAACTACCAGGCATCGTTGCTCATGGAACGTCTTGGCATCGCGATTATTGGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002771","ARO_id":"39205","ARO_name":"QnrB58","CARD_short_name":"QnrB58","ARO_description":"QnrB58 is a plasmid-mediated quinolone resistance protein found in Citrobacter freundii.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"41":{"model_id":"41","model_name":"rmtH","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"3309":{"protein_sequence":{"accession":"AGH19769.1","sequence":"MTIEQAAADILSSKKYQLLCPDTVVRILTQEWGRHKKPKQAVERTRERLHGICGAYLAPQVEKQASTALAAGDVQKALALHASTRERLDTYPQLYQFVFENNLPARVLDIACGLNPLMLHRQGVASVWGCDIHQGLGNVLTPYAQKHGWDFTFALHDVLCAPVAASGDMALVFKLLPLLEREQPGAALALLRTLDAPVICVSFPTRSLGGRGKGMHQHYATWFEGLVAPHFTVQHHTLIGDELLYRIQPNPA"},"dna_sequence":{"accession":"KC544262.1","fmin":"665","fmax":"1424","strand":"+","sequence":"ATGACCATTGAACAGGCAGCGGCCGACATCCTCTCCTCAAAAAAATATCAACTGCTGTGCCCGGATACCGTGGTGCGCATCCTCACGCAGGAGTGGGGACGCCACAAAAAGCCCAAGCAGGCGGTGGAGCGCACCCGCGAGCGGCTGCACGGCATCTGCGGTGCCTACCTGGCCCCCCAGGTGGAAAAGCAGGCAAGCACCGCACTGGCTGCGGGCGATGTGCAAAAAGCGCTGGCACTGCATGCCTCCACCCGTGAGCGGCTGGATACCTATCCCCAGCTGTATCAGTTTGTGTTTGAAAACAATCTGCCCGCCCGTGTGCTGGATATCGCCTGCGGCTTAAACCCGCTGATGCTGCACCGCCAGGGGGTGGCATCGGTTTGGGGGTGTGATATCCATCAGGGGCTGGGCAATGTGCTAACCCCCTATGCCCAAAAACACGGGTGGGATTTTACCTTTGCCCTGCACGATGTGCTGTGCGCACCGGTGGCGGCCAGCGGCGATATGGCACTGGTGTTTAAACTGCTGCCCCTTTTGGAAAGAGAGCAGCCCGGCGCAGCCCTTGCGCTGCTGCGCACATTGGATGCCCCGGTGATCTGCGTCAGCTTCCCCACCCGCAGCTTGGGCGGCAGGGGTAAGGGGATGCACCAGCACTACGCCACCTGGTTTGAGGGCCTGGTCGCCCCGCATTTTACCGTGCAGCACCACACCCTTATCGGGGACGAGCTGCTTTACCGCATCCAGCCAAACCCAGCTTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3003198","ARO_id":"39781","ARO_name":"rmtH","CARD_short_name":"rmtH","ARO_description":"rmtH is a 16s ribosomal RNA methyltransferase found in Klebsiella pneumoniae strain MRSN2404 that was isolated from the chronic wound of a soldier wounded in Iraq in 2006. It confers high resistance to aminoglycosides.","ARO_category":{"41435":{"category_aro_accession":"3004271","category_aro_cvterm_id":"41435","category_aro_name":"16S rRNA methyltransferase (G1405)","category_aro_description":"Methyltransferases that methylate the G1405 position of 16S rRNA, which is part of an aminoglycoside binding site.","category_aro_class_name":"AMR Gene Family"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"40942":{"category_aro_accession":"3004015","category_aro_cvterm_id":"40942","category_aro_name":"gentamicin A","category_aro_description":"Gentamicin A is part of a complex of broad spectrum aminoglycoside antibiotics. Gentamicin inhibits protein synthesis, resulting in bacterial cell death.","category_aro_class_name":"Antibiotic"},"46133":{"category_aro_accession":"3007382","category_aro_cvterm_id":"46133","category_aro_name":"gentamicin","category_aro_description":"Gentamicin is a commonly used aminoglycoside antibiotic derived from members of the Micromonospora genus of bacteria. It acts by binding the 30S ribosomal subunit, thus inhibiting protein synthesis. Gentamicin is typically used to treat Gram-negative infections of the repiratory and urinary tract, as well as infections of the bone and soft tissue. It also exhibits considerable nephrotoxicity and ototoxicity. Gentamicin is administered as a mixture of gentamicin type C (which makes about around 80% of the complex) and types A, B, and X (distributed in the remaining 20% of the complex).","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"42":{"model_id":"42","model_name":"OXY-6-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"897":{"protein_sequence":{"accession":"CAI43422.1","sequence":"MLKSSWRKSALMAAAAVPLLLASGSLWASADAIQQKLADLEKRSGGRLGVALINTADDSQTLYRGDERFAMCSTGKVMAAAAVLKQSESHPDVVNKRLEIKKSDLVVWSPITEKHLQSGMTLAELSAAALQYSDNTAMNKMISYLGGPEKVTAFAQSIGDVTFRLDRTEPALNSAIPGDKRDTTTPLAMAESLRKLTLGNALGEQQRAQLVTWLKGNTTGGQSIRAGLPASWAVGDKTGAGDYGTTNDIAVIWPENHAPLVLVTYFTQPQQDAKSRKEVLAAAAKIVTEGL"},"dna_sequence":{"accession":"AJ871874.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGTTGAAAAGTTCGTGGCGTAAAAGCGCCCTGATGGCCGCCGCCGCCGTTCCGCTGCTGCTGGCGAGCGGTTCATTATGGGCCAGTGCCGATGCTATCCAGCAAAAGCTGGCTGATTTAGAAAAACGGTCCGGTGGCCGGCTGGGCGTGGCGCTGATTAACACGGCGGATGATTCGCAAACCCTTTATCGCGGCGACGAACGTTTTGCCATGTGCAGCACCGGTAAAGTGATGGCCGCCGCCGCGGTGTTAAAGCAGAGCGAAAGCCATCCCGATGTGGTGAATAAAAGGCTGGAGATTAAAAAATCGGATTTAGTGGTCTGGAGCCCGATTACCGAAAAACATCTGCAAAGCGGAATGACCCTGGCGGAACTCAGCGCGGCGGCGCTGCAGTACAGCGACAATACCGCGATGAATAAGATGATTAGCTACCTTGGCGGACCGGAAAAGGTGACCGCATTCGCCCAGAGCATCGGGGACGTTACTTTTCGTCTCGATCGTACGGAGCCGGCGCTGAACAGCGCGATACCCGGCGATAAGCGCGATACCACCACCCCGTTGGCGATGGCCGAAAGCCTGCGCAAGCTGACGCTGGGCAATGCGCTGGGCGAACAGCAGCGCGCCCAGTTAGTGACGTGGCTAAAAGGCAATACCACCGGCGGGCAAAGCATTCGCGCAGGCCTGCCCGCAAGCTGGGCGGTCGGGGATAAAACCGGCGCCGGAGATTACGGCACCACCAACGATATCGCGGTGATCTGGCCGGAAAATCATGCCCCGCTGGTGTTAGTGACCTATTTTACCCAGCCGCAGCAGGATGCGAAAAGCCGCAAAGAGGTGTTAGCCGCGGCGGCGAAAATCGTGACCGAAGGGCTGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3002413","ARO_id":"38813","ARO_name":"OXY-6-1","CARD_short_name":"OXY-6-1","ARO_description":"OXY-6-1 is a beta-lactamase found in Klebsiella oxytoca.","ARO_category":{"38788":{"category_aro_accession":"3002388","category_aro_cvterm_id":"38788","category_aro_name":"OXY beta-lactamase","category_aro_description":"OXY beta-lactamases are chromosomal class A beta-lactamases that are found in Klebsiella oxytoca. At constitutive low levels, OXY beta-lactamases confer resistance to aminopenicillins and carboxypenicillins. At high induced levels,  OXY beta-lactamases confer resistance to penicillins, cephalosporins and aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"44":{"model_id":"44","model_name":"golS","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"290"}},"model_sequences":{"sequence":{"5224":{"protein_sequence":{"accession":"AAL19308.1","sequence":"MNIGKAAKASKVSAKMIRYYEQIGLIPAASRTDSGYRAYTQADVNQLHFIRRARDLGFSVAEISDLLNLWNNQSRQSADVKRLAQTHIDELDRRIQNMQHMAQTLKALIHCCAGDALPDCPILHTLGQPDDSEPEARTGAVLRRPRRHGLAKRL"},"dna_sequence":{"accession":"AE006468.2","fmin":"400860","fmax":"401325","strand":"+","sequence":"ATGAACATCGGTAAAGCAGCTAAAGCATCGAAAGTCTCGGCCAAAATGATTCGCTACTATGAACAGATTGGTCTGATTCCCGCGGCAAGTCGGACGGATTCCGGCTATCGGGCCTATACCCAGGCTGATGTTAATCAATTGCATTTTATACGCCGCGCGCGCGACCTCGGTTTTTCAGTTGCTGAAATCAGCGACTTACTGAATCTTTGGAATAACCAGTCGCGGCAAAGCGCTGACGTCAAACGCCTGGCGCAGACGCACATTGATGAACTGGACAGACGTATCCAGAACATGCAGCACATGGCGCAAACCCTCAAAGCGCTGATTCACTGCTGCGCCGGCGACGCGCTGCCAGATTGCCCCATTCTGCATACGCTTGGACAACCTGACGATAGCGAGCCGGAGGCGCGTACCGGAGCGGTATTGCGACGTCCTCGTCGCCACGGACTGGCAAAGCGTCTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35734","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Typhimurium str. LT2","NCBI_taxonomy_id":"99287"}}}},"ARO_accession":"3000504","ARO_id":"36643","ARO_name":"golS","CARD_short_name":"golS","ARO_description":"GolS is a regulator activated by the presence of golD, and promotes the expression of the MdsABC efflux pump.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"45":{"model_id":"45","model_name":"mdtP","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"875"}},"model_sequences":{"sequence":{"4454":{"protein_sequence":{"accession":"BAE78082.1","sequence":"MINRQLSRLLLCSILGSTTLISGCALVRKDSAPHQQLKPEQIKLADDIHLASSGWPQAQWWKQLNDPQLDALIQRTLSGSHTLAEAKLREEKAQSQADLLDAGSQLQVAALGMLNRQRVSANGFLSPYSMDAPALGMDGPYYTEATVGLFAGLDLDLWGVHRSAVAAAIGAHNAALAETAAVELSLATGVAQLYYSMQASYQMLDLLEQTHDVIDYAVKAHQSKVAHGLEAQVPFHGARAQILAVDKQIVAVKGQITETRESLRALIGAGASDMPEIRPVALPQVQTGIPATLSYELLARRPDLQAMRWYVQASLDQVDSARALFYPSFDIKAFFGLDSIHLHTLFKKTSRQFNFIPGLKLPLFDGGRLNANLEGTRAASNMMIERYNQSVLNAVRDVAVNGTRLQTLNDEREMQAERVEATRFTQRAAEAAYQRGLTSRLQATEARLPVLAEEMSLLMLDSRRVIQSIQLMKSLGGGYQAGPVVEKK"},"dna_sequence":{"accession":"AP009048.1","fmin":"4303042","fmax":"4304509","strand":"-","sequence":"ATGATCAATCGTCAACTTTCACGTCTGCTGTTGTGCAGCATTCTCGGCAGCACGACGCTGATTTCCGGCTGTGCCCTGGTACGTAAGGATTCTGCACCTCATCAACAGCTCAAACCGGAACAAATCAAACTGGCCGACGATATTCATCTTGCCAGCTCCGGCTGGCCGCAGGCGCAGTGGTGGAAACAACTCAATGACCCGCAGCTGGATGCGCTGATCCAACGGACGCTAAGTGGTTCACACACCCTCGCCGAAGCGAAACTGCGGGAAGAAAAAGCGCAGTCCCAGGCCGATTTGTTAGATGCCGGTTCACAATTACAGGTCGCAGCGTTAGGGATGCTCAACCGCCAACGTGTCTCGGCGAACGGCTTTTTAAGCCCTTATTCAATGGATGCGCCAGCACTGGGTATGGACGGGCCGTACTATACGGAAGCCACAGTAGGTTTGTTTGCCGGACTGGATCTTGATTTGTGGGGTGTGCATCGCTCAGCGGTTGCCGCCGCCATTGGCGCGCATAATGCCGCGCTGGCAGAAACCGCAGCAGTAGAGCTATCGCTGGCCACGGGCGTAGCGCAGCTTTATTACAGTATGCAGGCCAGCTATCAGATGCTCGATCTGTTAGAACAAACTCACGATGTGATTGATTACGCGGTGAAAGCGCACCAGAGTAAAGTGGCGCACGGTCTGGAAGCGCAAGTGCCTTTCCACGGCGCGCGGGCACAGATTCTGGCGGTCGATAAACAAATTGTTGCCGTCAAAGGGCAAATCACCGAAACGCGAGAATCTCTGCGTGCATTGATTGGCGCGGGAGCCAGCGATATGCCGGAGATCAGACCGGTGGCATTACCGCAAGTCCAGACCGGCATTCCGGCGACACTCTCTTATGAGTTGCTCGCCAGACGCCCGGATCTGCAAGCCATGCGCTGGTATGTTCAGGCGTCATTAGATCAGGTGGATTCCGCGCGGGCGTTGTTCTATCCGAGCTTTGATATCAAAGCGTTTTTCGGTCTGGACTCCATCCATCTGCATACCTTATTCAAAAAAACCAGTCGCCAGTTCAACTTCATCCCGGGTCTGAAATTGCCGCTGTTTGACGGTGGACGGTTGAATGCCAATCTCGAAGGCACGCGCGCCGCCAGCAACATGATGATTGAACGTTACAACCAGTCAGTACTGAACGCGGTGCGTGACGTTGCCGTCAACGGCACGCGTCTGCAAACGCTCAACGACGAGCGAGAAATGCAGGCTGAACGCGTGGAAGCCACGCGCTTTACCCAGCGCGCTGCCGAGGCCGCCTATCAGCGCGGCTTAACCAGCCGCTTACAGGCCACCGAAGCCCGGTTGCCAGTGCTTGCCGAAGAGATGTCATTACTGATGCTGGACAGCCGCCGGGTGATCCAAAGCATTCAGTTGATGAAATCGCTGGGCGGCGGGTATCAGGCAGGTCCCGTCGTCGAGAAAAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36839","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. W3110","NCBI_taxonomy_id":"316407"}}}},"ARO_accession":"3003550","ARO_id":"40152","ARO_name":"mdtP","CARD_short_name":"mdtP","ARO_description":"Multidrug resistance efflux pump. Could be involved in resistance to puromycin, acriflavine and tetraphenylarsonium chloride.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35963":{"category_aro_accession":"0000045","category_aro_cvterm_id":"35963","category_aro_name":"acriflavine","category_aro_description":"Acriflavine is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish.","category_aro_class_name":"Antibiotic"},"35965":{"category_aro_accession":"0000047","category_aro_cvterm_id":"35965","category_aro_name":"puromycin","category_aro_description":"Puromycin is an aminonucleoside antibiotic, derived from Streptomyces alboniger, that causes premature chain termination during ribosomal protein translation.","category_aro_class_name":"Antibiotic"},"36174":{"category_aro_accession":"3000034","category_aro_cvterm_id":"36174","category_aro_name":"nucleoside antibiotic","category_aro_description":"Nucleoside antibiotics are made of modified nucleosides and nucleotides with wide-ranging activities and means of antibacterial effects. This drug class includes aminonucleoside antibiotics, which contain an amino group.","category_aro_class_name":"Drug Class"},"43746":{"category_aro_accession":"3005386","category_aro_cvterm_id":"43746","category_aro_name":"disinfecting agents and antiseptics","category_aro_description":"Disinfectants that can also interact with antimicrobial resistance mechanisms, e.g. molecule efflux, and thus are the targets of disinfectant resistance.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"46":{"model_id":"46","model_name":"CMY-114","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"943":{"protein_sequence":{"accession":"AIT76099.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAIIYEGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWRGISLLHLATYTAGGLPLQIPDYVTDKAELLRFYQNWQPQWTPGAKRLYANSSIGLFGALVVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQSEQKNYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIELAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPARVEAAWRILEKLQ"},"dna_sequence":{"accession":"KM087846.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCGCTGCTGCTGACAGCCTCTTTCTCCACGTTTGCTGCCGCAAAAACAGAACAACAAATTGCCGATATCGTTAACCGCACCATCACACCACTGATGCAGGAGCAGGCTATTCCGGGCATGGCCGTGGCAATTATCTACGAGGGGAAACCTTATTACTTTACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGTTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGACGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCGGGGTATCAGCCTGCTGCACTTAGCCACCTATACAGCGGGTGGCCTGCCGCTGCAGATCCCCGATTACGTTACGGATAAAGCCGAATTACTGCGCTTTTATCAAAACTGGCAACCACAATGGACTCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGTGCGCTGGTGGTAAAACCTTCAGGTATGAGCTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAAAGCGAACAAAAAAATTATGCCTGGGGCTATCGCGAAGGGAAGCCTGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATCGATATGGCCCGCTGGGTTCAGGCCAACATGGACGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGAGCTTGCGCAGTCTCGCTACTGGCGTATTGGTGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCAGCACCTGCCGTGAAAGCCTCATGGGTGCATAAAACAGGATCCACAGGCGGATTTGGCAGCTACGTTGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTAATGTTGGCAAACAAAAGCTACCCCAACCCGGCTCGCGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002125","ARO_id":"38525","ARO_name":"CMY-114","CARD_short_name":"CMY-114","ARO_description":"CMY-114 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"47":{"model_id":"47","model_name":"OXA-60","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8146":{"protein_sequence":{"accession":"AAQ08905.1","sequence":"MLSRYSKTLAFAVVACTLAISTATAHAELVVRNDLKRVFDDAGVSGTFVLMDITADRTYVVDPARAARSIHPASTFKIPNSLIAFDTGAVRDDQEVLPYGGKPQPYEQWEHDMALPEAIRLSAVPIYQEVARRVGFERMQAYVDAFDYGNRQLGSAIDQFWLRGPLEISAFEEARFTSRMALKQLPVKPRTWDMVQRMLLIEQQGDAALYAKTGVATEYQPEIGWWAGWVERAGHVYAFALNIDMPREGDMAKRIPLGKQLMRALEVWPAP"},"dna_sequence":{"accession":"AF525303.2","fmin":"2770","fmax":"3586","strand":"+","sequence":"ATGCTGTCTCGCTACTCGAAGACCCTCGCGTTTGCCGTGGTGGCCTGCACGCTCGCAATAAGCACCGCCACCGCTCATGCCGAGCTGGTCGTGCGCAATGACCTCAAGCGCGTGTTCGACGACGCCGGCGTCTCCGGCACCTTCGTGCTGATGGACATCACCGCCGACCGTACCTATGTCGTCGATCCGGCGCGTGCCGCGCGGAGCATCCATCCGGCTTCGACGTTCAAGATTCCGAACAGCCTGATCGCCTTCGACACCGGGGCCGTGCGCGACGATCAGGAAGTGCTGCCCTACGGCGGCAAGCCGCAGCCTTACGAGCAGTGGGAGCACGACATGGCGTTACCCGAGGCGATTCGCCTGTCGGCCGTGCCGATCTATCAGGAAGTCGCGCGCCGCGTTGGCTTCGAGCGCATGCAGGCTTATGTCGATGCGTTCGACTACGGCAATCGCCAGCTCGGCAGCGCGATCGACCAGTTCTGGCTGCGTGGCCCGCTGGAGATTTCCGCTTTCGAAGAAGCACGCTTCACCAGCCGCATGGCGCTCAAGCAGTTGCCGGTGAAGCCGCGCACGTGGGACATGGTCCAGCGCATGCTGTTGATCGAGCAGCAGGGCGATGCCGCGCTATATGCCAAGACCGGCGTCGCCACCGAATACCAGCCGGAGATCGGTTGGTGGGCCGGCTGGGTGGAGCGTGCGGGGCATGTCTATGCATTCGCGCTGAACATCGACATGCCGCGCGAGGGCGATATGGCCAAGCGCATTCCGCTGGGCAAGCAGTTGATGCGGGCGCTCGAGGTGTGGCCGGCACCGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36921","NCBI_taxonomy_name":"Ralstonia pickettii","NCBI_taxonomy_id":"329"}}}},"ARO_accession":"3001808","ARO_id":"38208","ARO_name":"OXA-60","CARD_short_name":"OXA-60","ARO_description":"OXA-60 is a beta-lactamase found in Ralstonia pickettii.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46518":{"category_aro_accession":"3007729","category_aro_cvterm_id":"46518","category_aro_name":"OXA-60-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-60.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"48":{"model_id":"48","model_name":"OXA-90","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1306":{"protein_sequence":{"accession":"CAJ77809.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"AM231719.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCCCTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTAGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAACAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001650","ARO_id":"38050","ARO_name":"OXA-90","CARD_short_name":"OXA-90","ARO_description":"OXA-90 is a beta-lactamase found in A. baumannii.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"50":{"model_id":"50","model_name":"SME-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"1396":{"protein_sequence":{"accession":"AAG29813.1","sequence":"MSNKVNFKTASFLFSVCLALSAFNAHANKSDAAAKQIKKLEEDFDGRIGVFAIDTGSGNTFGYRSDERFPLCSSFKGFLAAAVLERVQQKKLDINQKVKYESRDLEYHSPITTKYKGSGMTLGDMASAALQYSDNGATNIIMERFLGGPEGMTKFMRSIGDNEFRLDRWELELNTAIPGDKRDTSTPKAVANSLNKLALGNVLNAKEKAIYQNWLKGNTTGDARIRASVPADWVVGDKTGSCGAYGTANDYAVIWPKNRAPLIVSIYTTRKSKDDKHSDKTIAEASRIAIQAID"},"dna_sequence":{"accession":"AF275256.1","fmin":"0","fmax":"885","strand":"+","sequence":"ATGTCAAACAAAGTAAATTTTAAAACGGCTTCATTTTTGTTTAGTGTTTGTTTAGCTTTGTCGGCATTTAATGCTCATGCTAACAAAAGTGATGCTGCGGCAAAACAAATAAAAAAATTAGAGGAAGACTTTGATGGGAGGATTGGCGTCTTTGCAATAGATACAGGATCGGGTAATACATTTGGGTATAGATCAGATGAGCGGTTCCCTTTATGCAGTTCATTTAAAGGTTTTTTGGCGGCTGCTGTTTTAGAGAGAGTGCAACAAAAAAAACTAGATATCAACCAAAAGGTTAAATATGAGAGTAGGGATCTAGAATATCATTCACCTATTACAACAAAATATAAAGGCTCAGGTATGACATTAGGTGATATGGCTTCTGCTGCATTGCAATATAGCGACAATGGGGCAACAAATATAATTATGGAACGATTTCTTGGCGGTCCTGAGGGGATGACTAAATTTATGCGTTCTATTGGAGATAATGAGTTTAGGTTAGATCGCTGGGAACTGGAACTTAACACTGCAATCCCAGGAGATAAACGTGACACTTCAACGCCAAAAGCTGTTGCAAATAGTTTGAATAAACTAGCTTTGGGGAATGTTCTCAATGCTAAAGAGAAAGCGATTTATCAAAATTGGTTAAAAGGTAATACAACTGGTGATGCTCGAATTCGTGCTAGTGTTCCTGCTGATTGGGTTGTAGGTGACAAAACTGGGAGCTGTGGGGCATATGGTACTGCGAATGATTATGCCGTCATTTGGCCTAAAAATAGAGCACCATTAATTGTCTCTATATATACAACACGAAAATCGAAAGATGATAAGCACAGTGATAAAACTATTGCGGAAGCATCACGTATTGCAATTCAGGCAATTGATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36783","NCBI_taxonomy_name":"Serratia marcescens","NCBI_taxonomy_id":"615"}}}},"ARO_accession":"3002380","ARO_id":"38780","ARO_name":"SME-2","CARD_short_name":"SME-2","ARO_description":"SME-2 is a beta-lactamase found in Serratia marcescens.","ARO_category":{"36194":{"category_aro_accession":"3000055","category_aro_cvterm_id":"36194","category_aro_name":"SME beta-lactamase","category_aro_description":"SME beta-lactamases are chromosome-mediated class A beta-lactamases that hydrolyze carbapenems in Serratia marcescens.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"51":{"model_id":"51","model_name":"AAC(3)-IIIc","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"9":{"protein_sequence":{"accession":"AAA25683.1","sequence":"MFSRWSKPLVLAAVTRASLAADLAALGLAAGDAVMVHAAVSKVGRLLDGPDTIIAALSDAGRPAGTILAYADWEARYEDLVDEDGRVPQEWREHIPPFDPRRSRAIRDNGVLPEFLRTTPGALRSGNPGASMVGLGARAEWFTADHPLDYGYGEGSPLARLVEAGGKVLMLGAPLDTLTLLHHAEHLADIPGKRIRRIEVPLATPTGTQWRMIEEFDTGDPIVEGLAEDYFAEIVTAFLAGGRGRQGLIGTAPSVLVDAAAITAFGVAWLESRFGSPSS"},"dna_sequence":{"accession":"L06161.1","fmin":"105","fmax":"945","strand":"+","sequence":"ATGTTCTCTCGTTGGTCGAAACCTCTCGTGCTTGCCGCCGTGACCCGCGCCTCGCTCGCCGCTGATCTCGCCGCGCTTGGCCTTGCCGCGGGCGATGCGGTCATGGTCCATGCCGCCGTCAGCAAGGTCGGCCGCCTGCTCGACGGTCCCGACACGATCATCGCCGCTCTGTCCGACGCCGGTCGGCCTGCCGGCACCATCCTCGCCTATGCCGATTGGGAAGCGCGCTACGAGGACCTCGTGGACGAGGACGGCCGCGTGCCGCAGGAATGGCGCGAGCACATCCCACCCTTCGATCCGCGGCGCTCACGCGCGATCCGCGACAATGGCGTGCTTCCGGAATTCCTGCGGACGACACCGGGTGCGTTGCGCAGCGGCAATCCCGGCGCCTCGATGGTCGGGCTCGGCGCCAGAGCGGAATGGTTCACCGCAGACCATCCCCTCGACTACGGCTATGGCGAGGGTTCGCCGCTGGCCAGGCTGGTCGAAGCCGGCGGCAAGGTGCTGATGCTCGGGGCGCCGCTCGACACGCTGACCCTGCTGCACCATGCCGAGCATCTGGCCGACATCCCCGGCAAGCGCATCCGGCGGATCGAGGTGCCGCTGGCGACGCCGACCGGCACGCAATGGCGCATGATCGAGGAATTCGATACCGGCGATCCGATCGTCGAAGGTTTGGCCGAGGACTACTTCGCCGAGATCGTGACGGCGTTCCTTGCCGGCGGCCGAGGACGGCAGGGCTTGATCGGCACCGCGCCATCCGTGCTGGTCGATGCTGCCGCAATCACGGCTTTCGGCGTCGCCTGGCTGGAATCGCGCTTCGGCTCGCCCTCATCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002538","ARO_id":"38938","ARO_name":"AAC(3)-IIIc","CARD_short_name":"AAC(3)-IIIc","ARO_description":"AAC(3)-IIIc is an aminoglycoside acetyltransferase in P. aeruginosa.","ARO_category":{"36461":{"category_aro_accession":"3000322","category_aro_cvterm_id":"36461","category_aro_name":"AAC(3)","category_aro_description":"A category of aminoglycoside N-acetyltransferase enzymes with modification regiospecificity based at the 3-amino group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics through acetylation of the 3-amino group of the compound.","category_aro_class_name":"AMR Gene Family"},"40942":{"category_aro_accession":"3004015","category_aro_cvterm_id":"40942","category_aro_name":"gentamicin A","category_aro_description":"Gentamicin A is part of a complex of broad spectrum aminoglycoside antibiotics. Gentamicin inhibits protein synthesis, resulting in bacterial cell death.","category_aro_class_name":"Antibiotic"},"46133":{"category_aro_accession":"3007382","category_aro_cvterm_id":"46133","category_aro_name":"gentamicin","category_aro_description":"Gentamicin is a commonly used aminoglycoside antibiotic derived from members of the Micromonospora genus of bacteria. It acts by binding the 30S ribosomal subunit, thus inhibiting protein synthesis. Gentamicin is typically used to treat Gram-negative infections of the repiratory and urinary tract, as well as infections of the bone and soft tissue. It also exhibits considerable nephrotoxicity and ototoxicity. Gentamicin is administered as a mixture of gentamicin type C (which makes about around 80% of the complex) and types A, B, and X (distributed in the remaining 20% of the complex).","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"52":{"model_id":"52","model_name":"OXY-2-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1220":{"protein_sequence":{"accession":"AAL79541.1","sequence":"MIKSSWRKIAMLAAAVPLLLASGALWASTDAIHQKLTDLEKRSGGRLGVALINTADNSQILYRGDERFAMCSTSKVMAAAAVLKQSESNKEVVNKRLEINAADLVVWSPITEKHLQSGMTLAELSAATLQYSDNTAMNLIIGYLGGPEKVTAFARSIGDATFRLDRTEPTLNTAIPGDERDTSTPLAMAESLRKLTLGDALGEQQRAQLVTWLKGNTTGGQSIRAGLPESWVVGDKTGAGDYGTTNDIAVIWPEDHAPLILVTYFTQPQQDAKNRKEVLAAAAKIVTEGL"},"dna_sequence":{"accession":"AF473577.1","fmin":"0","fmax":"873","strand":"+","sequence":"ATGATAAAAAGTTCGTGGCGTAAAATTGCAATGCTAGCCGCCGCCGTTCCGCTGCTGCTGGCGAGCGGCGCACTGTGGGCCAGTACCGATGCTATCCATCAGAAGCTGACAGATCTCGAGAAGCGTTCAGGCGGCAGGTTGGGCGTGGCGCTAATCAACACGGCAGATAATTCTCAAATCTTATATCGCGGCGACGAGCGTTTTGCCATGTGCAGCACCAGTAAAGTGATGGCCGCCGCCGCGGTATTAAAACAGAGCGAAAGCAATAAAGAGGTGGTAAATAAAAGGCTGGAGATTAACGCAGCCGATTTGGTGGTCTGGAGTCCGATTACCGAAAAACATCTCCAGAGCGGAATGACGCTGGCTGAGCTAAGCGCGGCGACGCTGCAATATAGCGACAATACGGCGATGAATCTGATCATCGGCTACCTTGGCGGGCCGGAAAAAGTCACCGCCTTCGCCCGCAGTATCGGCGATGCCACCTTTCGTCTCGATCGTACGGAGCCCACGCTGAATACCGCCATCCCGGGCGATGAGCGTGATACCAGCACGCCGCTGGCGATGGCTGAAAGCCTGCGCAAGCTGACGCTTGGCGATGCGCTGGGCGAACAGCAACGCGCCCAGTTAGTCACCTGGCTGAAAGGCAATACCACCGGCGGGCAAAGCATTCGCGCGGGCCTGCCTGAAAGCTGGGTGGTCGGCGATAAAACCGGCGCCGGAGATTACGGCACCACCAATGATATTGCGGTTATCTGGCCGGAAGATCACGCTCCGCTGATATTAGTCACCTACTTTACCCAGCCGCAGCAGGATGCGAAAAACCGCAAAGAGGTGTTAGCCGCAGCGGCAAAAATCGTGACCGAAGGGCTTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3002397","ARO_id":"38797","ARO_name":"OXY-2-2","CARD_short_name":"OXY-2-2","ARO_description":"OXY-2-2 is a beta-lactamase found in Klebsiella oxytoca.","ARO_category":{"38788":{"category_aro_accession":"3002388","category_aro_cvterm_id":"38788","category_aro_name":"OXY beta-lactamase","category_aro_description":"OXY beta-lactamases are chromosomal class A beta-lactamases that are found in Klebsiella oxytoca. At constitutive low levels, OXY beta-lactamases confer resistance to aminopenicillins and carboxypenicillins. At high induced levels,  OXY beta-lactamases confer resistance to penicillins, cephalosporins and aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"53":{"model_id":"53","model_name":"MOX-5","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1286":{"protein_sequence":{"accession":"ACS44783.1","sequence":"MQQRQSILWGALATLMWAGLAHAGDKAATDPLRPVVDASIRPLLKEHRIPGMAVAVLKDGKAHYFNYGVADRERAVGVSEQTLFEIGSVSKTLTATLGAYAVVQGGFELDDKASLFAPWLKGSAFDNITMGELATYSAGGLPLQFPEEVDSLEKMQAYYRQWTPAYSRGSHRQYANPSIGLFGYLAASSMKQPFDRLMEQTMLPGLGLYHTYLNVPEQPMGHYAYGYWKEDKPFRVTPAMLAEEPYGIKTSSADLLRFVKANISGVDNAAMQQAIDLTHQGQYAVGEMTQGLGWERYPYPVSEQTLLAGNSPAMIYNANPAAPAPAAAGHPVLFKKTGSTNGFGAYVAFVPAKGIGVVMLANRNYPNEGTLKAGHAILTQLAR"},"dna_sequence":{"accession":"GQ152600.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCAACAACGACAATCCATCCTGTGGGGCGCTCTGGCCACCCTGATGTGGGCCGGTTTGGCCCATGCCGGTGACAAGGCGGCGACCGATCCCCTGCGCCCCGTGGTGGATGCCAGCATCCGGCCGCTGCTCAAGGAGCACAGGATCCCGGGCATGGCGGTGGCCGTGCTCAAGGATGGCAAGGCCCACTATTTCAACTACGGTGTGGCCGATCGGGAGCGCGCGGTCGGTGTCAGCGAGCAGACCCTGTTCGAGATAGGCTCCGTGAGCAAGACCCTGACCGCGACGCTGGGGGCCTACGCCGTGGTGCAGGGGGGCTTCGAGCTCGATGACAAGGCGAGTCTGTTCGCCCCCTGGCTCAAGGGATCCGCCTTTGACAACATCACCATGGGGGAGCTGGCTACCTACAGCGCGGGCGGCTTGCCGCTGCAATTCCCCGAGGAGGTGGATTCGCTCGAGAAGATGCAGGCCTACTACCGCCAGTGGACCCCAGCCTACTCGCGGGGTTCCCATCGCCAGTACGCCAACCCCAGCATCGGGCTTTTTGGCTATCTGGCGGCGAGCAGCATGAAGCAGCCGTTCGATCGCTTGATGGAGCAGACGATGCTGCCGGGGCTTGGCCTGTACCATACCTACCTCAATGTGCCCGAGCAGCCCATGGGGCACTACGCCTACGGTTACTGGAAGGAGGACAAGCCATTCCGCGTCACTCCCGCCATGCTGGCGGAGGAGCCTTACGGCATCAAGACCAGCTCGGCGGATCTGCTGCGCTTCGTGAAGGCGAACATCAGCGGGGTGGATAATGCGGCCATGCAGCAGGCCATCGATCTGACTCACCAGGGCCAGTATGCGGTGGGGGAGATGACCCAGGGACTGGGCTGGGAGCGTTACCCCTATCCCGTCAGCGAGCAGACGCTGCTGGCGGGCAACTCCCCGGCGATGATTTACAATGCCAACCCGGCGGCGCCCGCGCCCGCTGCGGCAGGGCACCCTGTGCTCTTCAAAAAGACCGGCTCGACCAATGGCTTCGGGGCCTATGTGGCCTTCGTGCCGGCCAAAGGGATCGGCGTCGTCATGCTGGCCAATCGCAACTACCCCAACGAGGGCACGCTCAAGGCGGGCCACGCCATCCTGACGCAACTGGCCAGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36936","NCBI_taxonomy_name":"Aeromonas caviae","NCBI_taxonomy_id":"648"}}}},"ARO_accession":"3002188","ARO_id":"38588","ARO_name":"MOX-5","CARD_short_name":"MOX-5","ARO_description":"MOX-5 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36222":{"category_aro_accession":"3000083","category_aro_cvterm_id":"36222","category_aro_name":"MOX beta-lactamase","category_aro_description":"MOX beta-lactamases are plasmid-mediated AmpC-type beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"54":{"model_id":"54","model_name":"TEM-34","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1160":{"protein_sequence":{"accession":"AGE11905.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMVSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"KC292503.1","fmin":"4334","fmax":"5195","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGGTGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36927","NCBI_taxonomy_name":"Haemophilus parainfluenzae","NCBI_taxonomy_id":"729"}}}},"ARO_accession":"3000904","ARO_id":"37284","ARO_name":"TEM-34","CARD_short_name":"TEM-34","ARO_description":"TEM-34 is an inhibitor-resistant beta-lactamase that has been found in clinical isolates.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"55":{"model_id":"55","model_name":"OXA-69","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"5522":{"protein_sequence":{"accession":"CAM86994.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDDKAEKIKNLFNEAHTTGVLVIHQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGEKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"CU459141.1","fmin":"2175316","fmax":"2176141","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGACAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCATCAAGGTCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAATGGGATGGGGAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTCTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35535","NCBI_taxonomy_name":"Acinetobacter baumannii AYE","NCBI_taxonomy_id":"509173"}}}},"ARO_accession":"3001617","ARO_id":"38017","ARO_name":"OXA-69","CARD_short_name":"OXA-69","ARO_description":"OXA-69 is a beta-lactamase found in A. baumannii.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"56":{"model_id":"56","model_name":"TEM-7","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8424":{"protein_sequence":{"accession":"AAO33760.1","sequence":"FFAAFCLPVFAHPETLVKVKDAEDKLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDSWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNR"},"dna_sequence":{"accession":"AF527798.1","fmin":"0","fmax":"783","strand":"+","sequence":"TTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATAAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATAGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGA","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000879","ARO_id":"37259","ARO_name":"TEM-7","CARD_short_name":"TEM-7","ARO_description":"TEM-7 is an extended-spectrum beta-lactamase that has been found in clinical isolates.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"57":{"model_id":"57","model_name":"SHV-24","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1637":{"protein_sequence":{"accession":"BAA84973.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARGTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AB023477.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTACTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGGCACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001082","ARO_id":"37462","ARO_name":"SHV-24","CARD_short_name":"SHV-24","ARO_description":"SHV-24 is an extended-spectrum beta-lactamase found in E. coli.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"58":{"model_id":"58","model_name":"QnrB47","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"147":{"protein_sequence":{"accession":"AFU25658.1","sequence":"MTLALVGEKIDRNRFTGEKVENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLRDAIFKSCDLSMADFRNVSALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGTQVLGATFSGSDLSGGEFSTFDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDNYQASLLMERLGIAVIG"},"dna_sequence":{"accession":"JX440358.1","fmin":"130","fmax":"775","strand":"+","sequence":"ATGACTCTGGCATTAGTTGGCGAAAAAATTGACAGAAATCGCTTCACCGGTGAGAAAGTTGAAAATAGTACATTTTTTAACTGCGATTTTTCAGGTGCCGACCTGAGCGGCACTGAATTTATCGGCTGCCAGTTCTATGATCGCGAAAGTCAGAAAGGATGCAATTTTAGTCGCGCAATGCTGAGAGATGCCATTTTCAAAAGCTGTGATTTATCAATGGCAGATTTCCGCAACGTCAGCGCATTGGGCATTGAAATTCGCCACTGCCGTGCACAAGGCGCAGATTTCCGCGGTGCAAGCTTTATGAATATGATCACCACGCGCACCTGGTTTTGCAGCGCATATATCACTAATACCAATCTAAGCTACGCCAATTTTTCGAAAGTCGTGTTGGAAAAGTGTGAGCTATGGGAAAACCGCTGGATGGGGACTCAGGTACTGGGTGCGACGTTCAGTGGTTCAGATCTCTCCGGCGGCGAGTTTTCGACTTTCGACTGGCGAGCAGCAAACTTCACACATTGCGATCTGACCAATTCGGAGTTAGGTGACTTAGATATTCGGGGTGTTGATTTACAAGGCGTTAAGTTAGACAACTACCAGGCATCGTTGCTCATGGAGCGGCTTGGCATCGCTGTGATTGGTTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002762","ARO_id":"39196","ARO_name":"QnrB47","CARD_short_name":"QnrB47","ARO_description":"QnrB47 is a plasmid-mediated quinolone resistance protein found in Escherichia coli.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"59":{"model_id":"59","model_name":"OXA-256","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1685":{"protein_sequence":{"accession":"CCE94500.1","sequence":"MKTFAAYVIIACLSSTALAGSITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFKIPDAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGIIGG"},"dna_sequence":{"accession":"HE616889.1","fmin":"1826","fmax":"2627","strand":"+","sequence":"ATGAAAACATTTGCCGCATATGTAATTATCGCGTGTCTTTCGAGTACGGCATTAGCTGGTTCAATTACAGAAAATACGTCTTGGAACAAAGAGTTCTCTGCCGAAGCCGTCAATGGTGTCTTCGTGCTTTGTAAAAGTAGCAGTAAATCCTGCGCTACCAATGACTTAGCTCGTGCATCAAAGGAATATCTTCCAGCATCAACATTTAAGATCCCCGACGCAATTATCGGCCTAGAAACTGGTGTCATAAAGAATGAGCATCAGGTTTTCAAATGGGACGGAAAGCCAAGAGCCATGAAGCAATGGGAAAGAGACTTGACCTTAAGAGGGGCAATACAAGTTTCAGCTGTTCCCGTATTTCAACAAATCGCCAGAGAAGTTGGCGAAGTAAGAATGCAGAAATACCTTAAAAAATTTTCCTATGGCAACCAGAATATCAGTGGTGGCATTGACAAATTCTGGTTGGAAGGCCAGCTTAGAATTTCCGCAGTTAATCAAGTGGAGTTTCTAGAGTCTCTATATTTAAATAAATTGTCAGCATCTAAAGAAAACCAGCTAATAGTAAAAGAGGCTTTGGTAACGGAGGCGGCACCTGAATATCTAGTGCATTCAAAAACTGGTTTTTCTGGTGTGGGAACTGAGTCAAATCCTGGTGTCGCATGGTGGGTTGGGTGGGTTGAGAAGGAGACAGAGGTTTACTTTTTCGCCTTTAACATGGATATAGACAACGAAAGTAAGTTGCCGCTAAGAAAATCCATTCCCACCAAAATCATGGAAAGTGAGGGCATCATTGGTGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3001502","ARO_id":"37902","ARO_name":"OXA-256","CARD_short_name":"OXA-256","ARO_description":"OXA-256 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46486":{"category_aro_accession":"3007697","category_aro_cvterm_id":"46486","category_aro_name":"OXA-10-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-10.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"60":{"model_id":"60","model_name":"QnrS6","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"296":{"protein_sequence":{"accession":"AEG74318.1","sequence":"METYRHTYRHHSFSHQDLSDITFTACTFIRCDFRRANLRDATFINCKFIEQGDIEGCHFDVADLRDASFQQCQLAMANFSNANCYGIELRECDLKGANFSRANFANQVSNRMYFCSAFITGCNLSYANMERVCLEKCELYENRWIGTHLAGASLKESDLSRGVFSEDVWGQFSLQGANLCHAELDGLDPRKVDTSGIKIASWQQEQLLEALGIVVFPD"},"dna_sequence":{"accession":"HQ631376.1","fmin":"0","fmax":"657","strand":"+","sequence":"ATGGAAACCTACCGTCACACATATCGACACCACAGTTTTTCACATCAAGATCTAAGTGATATTACTTTCACTGCTTGCACCTTTATCCGATGCGATTTTCGACGTGCTAACTTGCGTGATGCGACATTTATTAACTGCAAGTTCATTGAACAGGGTGATATCGAAGGTTGCCATTTTGATGTCGCAGACCTTCGCGATGCAAGTTTCCAACAATGCCAGCTTGCGATGGCAAACTTTAGTAACGCCAATTGCTACGGTATTGAGTTACGTGAGTGTGATTTAAAAGGGGCCAACTTTTCCCGAGCAAACTTTGCCAATCAAGTGAGTAATCGTATGTACTTTTGCTCAGCCTTTATTACTGGATGTAACCTGTCTTATGCCAATATGGAGCGGGTCTGTTTAGAAAAATGTGAGCTGTATGAAAATCGCTGGATAGGGACTCACCTCGCGGGCGCATCACTGAAAGAGTCAGACTTAAGTCGAGGTGTTTTTTCTGAAGATGTCTGGGGACAGTTTAGCCTACAGGGTGCTAATTTATGTCACGCCGAACTCGACGGTTTAGATCCTCGAAAAGTCGATACATCAGGTATCAAAATTGCCAGCTGGCAACAAGAACAGCTTCTCGAAGCGTTGGGTATTGTTGTTTTTCCTGACTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36810","NCBI_taxonomy_name":"Aeromonas hydrophila","NCBI_taxonomy_id":"644"}}}},"ARO_accession":"3002795","ARO_id":"39229","ARO_name":"QnrS6","CARD_short_name":"QnrS6","ARO_description":"QnrS6 is a plasmid-mediated quinolone resistance protein found in Aeromonas hydrophila.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"61":{"model_id":"61","model_name":"OXA-330","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1377":{"protein_sequence":{"accession":"AGW16412.1","sequence":"MYKKALIVATSILFLSACSSNLVKQHQIHSISANKSSEEIKSLFDQAQTTGVLVIKRGQTEEIYGNDLKRASTAYVPASTFKMLNALIGLEHHKATTTEVFKWNGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMSKEVKRIGFGNANIGSKVDNFWLVGPLKITPQQETQFAYQLAHKTLPFSKNVQEQVQSMVFIEKKNGSKIYAKSGWGWDVEPQVGWLTGWVVQPQGEIVAFSLNLEMKKGTSSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"KF203104.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGTATAAAAAAGCCCTTATCGTTGCAACAAGTATCCTATTTTTATCCGCCTGTTCTTCTAATTTAGTAAAACAACATCAAATACACTCTATTTCTGCCAATAAAAGTTCAGAAGAAATTAAATCACTGTTTGATCAAGCACAGACGACGGGTGTTTTGGTGATTAAGCGAGGGCAAACAGAAGAAATTTATGGCAATGATCTTAAAAGAGCATCAACCGCCTATGTTCCCGCCTCTACCTTTAAAATGTTAAATGCTTTAATTGGACTTGAACATCATAAGGCAACTACAACTGAAGTATTTAAATGGAATGGGCAAAAACGTTTATTTCCTGATTGGGAAAAGGACATGACACTGGGTGATGCCATGAAAGCTTCTGCAATTCCAGTTTACCAAGAATTAGCCCGACGAATTGGACTTGACCTTATGTCCAAAGAGGTGAAAAGAATTGGTTTCGGTAATGCTAACATTGGTTCAAAAGTAGATAATTTTTGGCTCGTTGGCCCTCTAAAAATTACACCTCAACAAGAAACCCAATTTGCTTATCAATTAGCCCATAAAACGCTTCCATTTAGCAAAAATGTACAAGAGCAAGTTCAATCAATGGTGTTCATAGAGAAAAAAAATGGAAGTAAAATTTATGCCAAAAGTGGTTGGGGATGGGATGTTGAACCACAAGTTGGTTGGCTAACAGGCTGGGTCGTTCAACCACAAGGAGAAATTGTGGCATTCTCACTTAATTTAGAAATGAAAAAAGGAACTTCTAGCTCTATTCGCAAAGAAATTGCTTATAAAGGCTTAGAACAACTGGGTATCTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39094","NCBI_taxonomy_name":"Acinetobacter calcoaceticus","NCBI_taxonomy_id":"471"}}}},"ARO_accession":"3001518","ARO_id":"37918","ARO_name":"OXA-330","CARD_short_name":"OXA-330","ARO_description":"OXA-330 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46495":{"category_aro_accession":"3007706","category_aro_cvterm_id":"46495","category_aro_name":"OXA-213-like beta-lactamase","category_aro_description":"OXA-213-like enzymes have been identified to be intrinsic to A. calcoaceticus and have been subsequently detected in A. pittii. Phylogenetic analysis of OXA-213-like proteins identified two distinct subgroups within the OXA family. The first group was linked to A. pittii and the second group to A. calcoaceticus. The carbapenemase activity of these OXAs may be related to the species-dependent effect.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"62":{"model_id":"62","model_name":"CMY-42","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1422":{"protein_sequence":{"accession":"ADM21467.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHSSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"HM146927.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACAGTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002053","ARO_id":"38453","ARO_name":"CMY-42","CARD_short_name":"CMY-42","ARO_description":"CMY-42 is a plasmid-borne AmpC cephalosporinase gene found in Escherichia coli.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35927":{"category_aro_accession":"0000008","category_aro_cvterm_id":"35927","category_aro_name":"cefoxitin","category_aro_description":"Cefoxitin is a cephamycin antibiotic often grouped with the second generation cephalosporins. Cefoxitin is bactericidal and acts by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. Cefoxitin's 7-alpha-methoxy group and 3' leaving group make it a poor substrate for most beta-lactamases.","category_aro_class_name":"Antibiotic"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"63":{"model_id":"63","model_name":"AAC(6')-Ib","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"350"}},"model_sequences":{"sequence":{"231":{"protein_sequence":{"accession":"AFJ11384.1","sequence":"MTNSNDSVTLRLMTEHDLAMLYEWLNRSHIVEWWGGEEARPTLADVQEQYLPSVLAQESVTPYIAMLNGEPIGYAQSYVALGSGDGWWEEETDPGVRGIDQSLANASQLGKGLGTKLVRALVELLFNDPEVTKIQTDPSPSNLRAIRCYEKAGFEKQGTVTTPDGPAVYMVQTRQAFERTRSDA"},"dna_sequence":{"accession":"JQ808129.1","fmin":"633","fmax":"1188","strand":"+","sequence":"GTGACCAACAGCAACGATTCCGTAACACTGCGCCTCATGACTGAGCATGACCTTGCGATGCTCTATGAGTGGCTAAATCGATCTCATATCGTCGAGTGGTGGGGCGGAGAAGAAGCACGCCCGACACTTGCTGACGTACAGGAACAGTACTTGCCAAGCGTTTTAGCGCAAGAGTCCGTCACTCCATACATTGCAATGCTGAATGGAGAGCCGATTGGGTATGCCCAGTCGTACGTTGCTCTTGGAAGCGGGGACGGATGGTGGGAAGAAGAAACCGATCCAGGAGTACGCGGAATAGACCAGTCACTGGCGAATGCATCACAACTGGGCAAAGGCTTGGGAACCAAGCTGGTTCGAGCTCTGGTTGAGTTGCTGTTCAATGATCCCGAGGTCACCAAGATCCAAACGGACCCGTCGCCGAGCAACTTGCGAGCGATCCGATGCTACGAGAAAGCGGGGTTTGAGAAGCAAGGTACCGTAACCACCCCAGATGGTCCAGCCGTGTACATGGTTCAAACACGCCAGGCATTCGAGCGAACACGCAGTGATGCCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002546","ARO_id":"38946","ARO_name":"AAC(6')-Ib","CARD_short_name":"AAC(6')-Ib","ARO_description":"AAC(6')-Ib is an aminoglycoside acetyltransferase encoded by plasmids, transposons, integrons in K. pneumoniae, P. mirabilis, P. aeruginosa, S. enterica, K. oxytoca, S. maltophilia, E. cloacae and V. cholerae.","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"A category of aminoglycoside N-acetyltransferase enzymes with modification regiospecificity based at the 6'-amino group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics through acetylation of the 6-amino group of the compound.","category_aro_class_name":"AMR Gene Family"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"64":{"model_id":"64","model_name":"CMY-70","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1180":{"protein_sequence":{"accession":"AFU25635.1","sequence":"MMKKSICCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAIIYQGKPYYFTWGKADIANNRPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTQYWPELTGKQWQGISLLHLATYTAGGLPLQVPDDVTDKAALLRFYQNWQPQWAPGAKRLYANSSIGLFGALAVKPSGMSYEEAMSKRVLHPLKLAHTWITVPQSEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMTRWVQANMDASQVQEKTLQQGIELAQSRYWRIGDMYQGLGWEMLNWPVKADSIISGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"JX440350.1","fmin":"1026","fmax":"2172","strand":"+","sequence":"ATGATGAAAAAATCGATATGCTGCGCGCTGCTGCTGACAGCTTCTTTCTCCACGTTTGCCGCCGCAAAAACAGAACAACAAATTGCCGATATCGTTAACCGCACCATCACACCGCTGATGCAGGAGCAGGCAATTCCGGGTATGGCCGTTGCGATTATCTATCAGGGGAAACCTTATTACTTTACCTGGGGTAAAGCCGATATCGCCAATAACCGTCCAGTCACGCAACAAACGCTGTTTGAACTCGGATCGGTCAGTAAAACGTTCAACGGTGTGCTGGGCGGCGATGCTATAGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGCAGTACTGGCCTGAACTGACTGGTAAGCAGTGGCAGGGTATCAGCCTGCTGCACTTAGCCACCTACACGGCAGGCGGCCTGCCGCTTCAGGTTCCGGACGACGTTACGGATAAAGCCGCGTTACTACGCTTTTATCAAAACTGGCAGCCGCAATGGGCCCCAGGCGCTAAACGTCTTTATGCTAACTCCAGCATTGGTCTGTTTGGCGCCCTGGCAGTGAAACCCTCAGGCATGAGCTACGAAGAGGCGATGTCCAAACGCGTCCTGCACCCCTTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAGCGAACAAAAAGATTATGCCTGGGGTTATCGCGAAGGAAAGCCAGTGCATGTATCCCCTGGCCAACTTGATGCCGAAGCATACGGGGTGAAATCGAGCGTTATCGATATGACCCGTTGGGTTCAGGCCAACATGGACGCCAGCCAGGTTCAGGAGAAAACGCTCCAGCAGGGCATCGAGCTTGCGCAGTCACGTTACTGGCGTATTGGCGATATGTACCAGGGCCTGGGCTGGGAGATGCTGAACTGGCCGGTGAAGGCCGACTCGATAATTAGCGGTAGCGACAGCAAAGTGGCACTGGCAGCGCTTCCTGCCGTTGAGGTAAACCCGCCCGCGCCTGCCGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGCGGATTCGGCAGCTACGTTGCTTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAGAGCTACCCAAACCCTGTTCGCGTCGAGGCCGCCTGGCGCATTCTTGAAAAACTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39584","NCBI_taxonomy_name":"Citrobacter braakii","NCBI_taxonomy_id":"57706"}}}},"ARO_accession":"3002083","ARO_id":"38483","ARO_name":"CMY-70","CARD_short_name":"CMY-70","ARO_description":"CMY-70 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"65":{"model_id":"65","model_name":"GES-21","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1338":{"protein_sequence":{"accession":"AFK80745.1","sequence":"MRFIHALLLAGIAHSAYASEKLTFKTDLEKLEREKAAQIGVAIVDPQGEIVAGHRMAQRFAMCSTFKFPLAALVLERIDSGTERGDRKLSYGPDMIVEWSPATERFLASGHMTVLEAAQAAVQLSDNGATNLLLREIGGPAAMTQYFRKIGDSVSRLDRKEPEMSDNTPGDLRDTTTPIAMARTVAKVLYGGALTSTSTHTIERWLIGNQTGDATLRAGFPKDWVVGEKTGTCANGGRNDIGFFKAQERDYAVAVYTTAPKLSAVERDELVASVGQVITQLILSTDK"},"dna_sequence":{"accession":"JQ772478.1","fmin":"140","fmax":"1004","strand":"+","sequence":"ATGCGCTTCATTCACGCTCTATTACTGGCAGGGATCGCTCACTCTGCATATGCGTCGGAAAAATTAACCTTCAAGACCGATCTTGAGAAGCTAGAGCGCGAAAAAGCAGCTCAGATCGGTGTTGCGATCGTCGATCCCCAAGGAGAGATCGTCGCGGGCCACCGAATGGCGCAGCGTTTTGCAATGTGCTCAACGTTCAAGTTTCCGCTAGCCGCGCTGGTCCTTGAAAGAATTGACTCAGGCACCGAGCGGGGGGATCGAAAACTTTCATATGGGCCGGACATGATCGTCGAATGGTCTCCTGCCACGGAGCGGTTTCTAGCATCGGGACACATGACGGTTCTCGAGGCAGCGCAAGCTGCGGTGCAGCTTAGCGACAATGGGGCTACTAACCTCTTACTGAGAGAAATTGGCGGACCTGCTGCAATGACGCAGTATTTTCGTAAAATTGGCGACTCTGTGAGTCGGCTAGACCGGAAAGAGCCGGAGATGAGCGACAACACACCTGGCGACCTCAGAGATACAACTACGCCTATTGCTATGGCACGTACTGTGGCTAAAGTCCTCTATGGCGGCGCACTGACGTCCACCTCGACCCACACCATTGAAAGGTGGCTGATCGGAAACCAAACGGGAGACGCGACACTACGAGCGGGTTTTCCTAAAGATTGGGTTGTTGGAGAGAAAACTGGTACCTGCGCCAACGGGGGCCGGAACGACATTGGTTTTTTTAAAGCCCAGGAGAGAGATTACGCTGTAGCGGTGTATACAACGGCCCCGAAACTATCGGCCGTAGAACGTGACGAATTAGTTGCCTCTGTCGGTCAAGTTATTACACAACTCATCCTGAGCACGGACAAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36791","NCBI_taxonomy_name":"uncultured bacterium","NCBI_taxonomy_id":"77133"}}}},"ARO_accession":"3002350","ARO_id":"38750","ARO_name":"GES-21","CARD_short_name":"GES-21","ARO_description":"GES-21 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36205":{"category_aro_accession":"3000066","category_aro_cvterm_id":"36205","category_aro_name":"GES beta-lactamase","category_aro_description":"GES beta-lactamases or Guiana extended-spectrum beta-lactamases are related to the other plasmid-located class A beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"66":{"model_id":"66","model_name":"SHV-41","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1790":{"protein_sequence":{"accession":"AAN04883.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATFGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AF535129.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGTATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCTTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGCATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAACACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001099","ARO_id":"37479","ARO_name":"SHV-41","CARD_short_name":"SHV-41","ARO_description":"SHV-41 is an extended-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"67":{"model_id":"67","model_name":"OXA-391","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1462":{"protein_sequence":{"accession":"AHN53381.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDKKAEKIKNLFNEVHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWNGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"KJ427797.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATAAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGTACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGAACGGGCAAAAAAGGCTGTTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTACGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001577","ARO_id":"37977","ARO_name":"OXA-391","CARD_short_name":"OXA-391","ARO_description":"OXA-391 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"68":{"model_id":"68","model_name":"TEM-132","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"2031":{"protein_sequence":{"accession":"AAR84298.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDHWEPELNEAVPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGKRGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AY491682.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCATTGGGAACCGGAGCTGAATGAAGCCGTACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTAAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3000996","ARO_id":"37376","ARO_name":"TEM-132","CARD_short_name":"TEM-132","ARO_description":"TEM-132 is an extended-spectrum beta-lactamase found in E. coli and Klebsiella pneumoniae.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"69":{"model_id":"69","model_name":"aadA23","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"280":{"protein_sequence":{"accession":"CAH10847.1","sequence":"MTIEISNQLSEVLSVIERHLESTLLAVHLYGSAVDGGLKPYSDIDLLVTVTVRLDETTRRALINDLLETSASPGESEILRAVEVTIVVHDDIIPWRYPAKRELQFGEWQRNDILAGIFEPATIDIDLAILLTKAREHSVALVGPAAEELFDPVPEQDLFEALNETLTLWNSPPDWAGDERNVVLTLSRIWYSAVTGKIAPKDVAADWAMERLPAQYQPVILEARQAYLGQEEDRLASRADQLEEFVHYVKGEITKVVGK"},"dna_sequence":{"accession":"AJ809407.1","fmin":"118","fmax":"898","strand":"+","sequence":"GTGACCATCGAAATTTCGAACCAACTATCAGAGGTGCTAAGCGTCATTGAGCGCCATCTGGAATCAACGTTGCTGGCCGTGCATTTGTACGGCTCCGCAGTGGATGGCGGCCTGAAGCCATACAGCGATATTGATTTGCTGGTTACGGTGACCGTAAGGCTTGATGAAACAACGCGGCGAGCTTTGATCAACGACCTTTTGGAAACTTCGGCTTCCCCTGGAGAGAGCGAGATTCTCCGCGCTGTAGAAGTCACCATTGTTGTGCACGACGACATCATTCCGTGGCGTTATCCAGCTAAGCGCGAACTGCAATTTGGAGAATGGCAGCGCAATGACATTCTTGCAGGTATCTTCGAGCCAGCCACGATCGACATTGATCTGGCTATCTTGCTGACAAAAGCAAGAGAACATAGCGTTGCCTTAGTAGGTCCAGCGGCGGAGGAACTCTTTGATCCGGTTCCTGAACAGGATCTATTTGAGGCGCTAAATGAAACCTTAACGCTATGGAACTCGCCGCCCGACTGGGCTGGCGATGAGCGAAATGTAGTGCTTACGTTGTCCCGCATTTGGTACAGCGCAGTAACCGGCAAAATCGCGCCGAAGGATGTCGCTGCCGACTGGGCAATGGAGCGCCTGCCGGCCCAGTATCAGCCCGTCATACTTGAAGCTAGACAGGCTTATCTTGGACAAGAAGAAGATCGCTTGGCCTCGCGCGCAGATCAGTTGGAAGAATTTGTCCACTACGTGAAAGGCGAGATCACCAAGGTAGTCGGCAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35709","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Agona","NCBI_taxonomy_id":"58095"}}}},"ARO_accession":"3002620","ARO_id":"39020","ARO_name":"aadA23","CARD_short_name":"aadA23","ARO_description":"aadA23 is an integron-encoded aminoglycoside nucleotidyltransferase gene in S. enterica.","ARO_category":{"41439":{"category_aro_accession":"3004275","category_aro_cvterm_id":"41439","category_aro_name":"ANT(3'')","category_aro_description":"A category of aminoglycoside O-nucleotidyltransferase enzymes with modification regiospecificity based at the 3''-hydroxyl group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics by transfer of an AMP group from an ATP substrate to the 3''-hydroxyl group of the compound.","category_aro_class_name":"AMR Gene Family"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"70":{"model_id":"70","model_name":"NDM-10","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1749":{"protein_sequence":{"accession":"AGT37351.1","sequence":"MELPNIMHPVAKLSTALAAALMLSGCMPGEISPTIDQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPSFGAVTSNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDRTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR"},"dna_sequence":{"accession":"KF361506.1","fmin":"0","fmax":"813","strand":"+","sequence":"ATGGAATTGCCCAATATTATGCACCCGGTCGCGAAGCTGAGCACCGCATTAGCCGCTGCATTGATGCTGAGCGGGTGCATGCCCGGTGAAATCAGCCCGACGATTGACCAGCAAATGGAAACTGGCGACCAACGGTTTGGCGATCTGGTTTTCCGCCAGCTCGCACCGAATGTCTGGCAGCACACTTCCTATCTCGACATGCCGAGTTTCGGGGCAGTCACTTCCAACGGTTTGATCGTCAGGGATGGCGGCCGCGTGCTGGTGGTCGATACCGCCTGGACCGATGACCAGACCGCCCAGATCCTCAACTGGATCAAGCAGGAGATCAACCTGCCGGTCGCGCTGGCGGTGGTGACTCACGCGCATCAGGACAAGATGGGCGGTATGGACGCGCTGCATGCGGCGGGGATTGCGACTTATGCCAATGCGTTGTCGAACCAGCTTGCCCCGCAAGAGGGGATGGTTGCGGCGCAACACAGCCTGACTTTCGCCGCCAATGGCTGGGTCGAACCAGCAACCGCGCCCAACTTTGGCCCGCTCAAGGTATTTTACCCCGGCCCCGGCCACACCAGTGACAATATCACCGTTGGGATCGACCGCACCGACATCGCTTTTGGTGGCTGCCTGATCAAGGACAGCAAGGCCAAGTCGCTCGGCAATCTCGGTGATGCCGACACTGAGCACTACGCCGCGTCAGCGCGCGCGTTTGGTGCGGCGTTCCCCAAGGCCAGCATGATCGTGATGAGCCATTCCGCCCCCGATAGCCGCGCCGCAATCACTCATACGGCCCGCATGGCCGACAAGCTGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39097","NCBI_taxonomy_name":"Klebsiella pneumoniae subsp. pneumoniae","NCBI_taxonomy_id":"72407"}}}},"ARO_accession":"3002360","ARO_id":"38760","ARO_name":"NDM-10","CARD_short_name":"NDM-10","ARO_description":"NDM-10 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36196":{"category_aro_accession":"3000057","category_aro_cvterm_id":"36196","category_aro_name":"NDM beta-lactamase","category_aro_description":"NDM beta-lactamases or New Delhi metallo-beta-lactamases are class B beta-lactamases that confer resistance to a broad range of antibiotics including carbapenems, cephalosporins and penicillins.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"71":{"model_id":"71","model_name":"QnrB66","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"157":{"protein_sequence":{"accession":"AGL43627.1","sequence":"MALALVGEKINRNRFTGEKIENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNSSALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGAQVLGATFSGSDLSGGEFSTFDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDNYQASLLMERLGIAVIG"},"dna_sequence":{"accession":"KC580655.1","fmin":"0","fmax":"645","strand":"+","sequence":"ATGGCTCTGGCACTCGTTGGCGAAAAAATTAACAGAAACCGTTTCACCGGTGAGAAAATTGAAAATAGTACATTTTTTAACTGTGATTTTTCAGGTGCCGACCTGAGCGGCACTGAATTTATCGGCTGTCAGTTCTATGATCGTGAAAGCCAGAAAGGGTGCAATTTTAGTCGTGCGATGCTGAAAGATGCCATTTTTAAAAGCTGTGATTTATCCATGGCGGATTTTCGCAATTCCAGTGCGCTGGGCATTGAAATTCGCCACTGCCGCGCACAAGGCGCAGATTTCCGCGGCGCAAGCTTTATGAATATGATCACCACGCGCACCTGGTTTTGTAGCGCATATATCACGAATACCAATCTAAGCTACGCCAATTTTTCGAAAGTCGTGTTGGAAAAGTGTGAGCTGTGGGAAAACCGTTGGATGGGTGCCCAGGTACTGGGCGCGACGTTCAGTGGTTCAGATCTCTCCGGCGGCGAGTTTTCGACTTTCGACTGGCGAGCAGCGAACTTCACACATTGCGATCTGACCAATTCGGAGTTGGGTGACTTAGATATTCGGGGCGTTGATTTACAAGGCGTTAAGCTGGACAACTACCAGGCGTCGTTGCTCATGGAGCGGCTTGGCATCGCGGTGATTGGTTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002778","ARO_id":"39212","ARO_name":"QnrB66","CARD_short_name":"QnrB66","ARO_description":"QnrB66 is a plasmid-mediated quinolone resistance protein found in Citrobacter freundii.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"72":{"model_id":"72","model_name":"SHV-42","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1874":{"protein_sequence":{"accession":"AAN04884.1","sequence":"MRYIRLCIISLLATLPLAVHSSPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITVSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AF535130.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACTCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACCCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCGTGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001100","ARO_id":"37480","ARO_name":"SHV-42","CARD_short_name":"SHV-42","ARO_description":"SHV-42 is an extended-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"73":{"model_id":"73","model_name":"OXA-35","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"975":{"protein_sequence":{"accession":"AAK49460.1","sequence":"MKTFAAYVITACLSSTALASSITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNNLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLSLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLFLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKGTEVYFFAFNMDIDNENKLPLRKSIPTKIMASEGIIGG"},"dna_sequence":{"accession":"AF315786.1","fmin":"1313","fmax":"2114","strand":"+","sequence":"ATGAAAACATTTGCCGCATATGTAATTACTGCGTGTCTTTCAAGTACGGCATTAGCTAGTTCAATTACAGAAAATACGTCTTGGAACAAAGAGTTCTCTGCCGAAGCCGTCAATGGTGTTTTCGTGCTTTGTAAAAGTAGCAGTAAATCCTGCGCTACCAATAACTTAGCTCGTGCATCAAAGGAATATCTTCCAGCATCAACATTTAAGATCCCCAACGCAATTATCGGCCTAGAAACTGGTGTCATAAAGAATGAGCATCAGGTTTTCAAATGGGACGGAAAGCCAAGAGCCATGAAACAATGGGAAAGAGACTTGAGCTTAAGAGGGGCAATACAAGTTTCAGCGGTTCCCGTATTTCAACAAATCGCCAGAGAAGTTGGCGAAGTAAGAATGCAGAAATACCTTAAAAAATTTTCATATGGCAACCAGAATATCAGTGGTGGCATTGACAAATTCTGGTTGGAGGGTCAGCTAAGAATTTCCGCAGTTAATCAAGTGGAGTTTCTAGAGTCTCTATTTTTAAATAAATTGTCAGCATCAAAAGAAAATCAGCTAATAGTAAAAGAGGCTTTGGTAACGGAGGCTGCGCCTGAATATCTTGTGCATTCAAAAACTGGTTTTTCTGGTGTGGGAACTGAGTCAAATCCTGGTGTCGCATGGTGGGTTGGTTGGGTTGAGAAGGGAACAGAGGTTTACTTTTTCGCCTTTAACATGGATATAGACAACGAAAATAAGTTGCCGCTAAGAAAATCCATTCCCACCAAAATCATGGCAAGTGAGGGCATCATTGGTGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3001429","ARO_id":"37829","ARO_name":"OXA-35","CARD_short_name":"OXA-35","ARO_description":"OXA-35 is a beta-lactamase found in P. aeruginosa.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46486":{"category_aro_accession":"3007697","category_aro_cvterm_id":"46486","category_aro_name":"OXA-10-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-10.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"74":{"model_id":"74","model_name":"SHV-18","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1636":{"protein_sequence":{"accession":"AAF64386.1","sequence":"MRYFRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGSVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAAKRGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AF132290.1","fmin":"87","fmax":"948","strand":"+","sequence":"ATGCGTTATTTTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCAGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGCCAAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGGATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001076","ARO_id":"37456","ARO_name":"SHV-18","CARD_short_name":"SHV-18","ARO_description":"SHV-18 is an extended-spectrum beta-lactamase found in Acinetobacter baumannii and Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"75":{"model_id":"75","model_name":"fusH","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"950"}},"model_sequences":{"sequence":{"201":{"protein_sequence":{"accession":"CAA90432.1","sequence":"MLNKGIRTRRARGALAGGTVLTAAAALLTAVPAAQAISGEPPAATDHAFTARLHIGEGDTLRGCSAALVHQQWLLTATSCFAATPGGEVKSGKPALKSTATLGGKTLGIVEVVPRDDRDVAMVRLAEPVTTVEPVRLAADAPVAAETLLGAGFGRTRTEWAPDQLHTGEFRVDSVTGTTVELTGQDGVSVCKGDTGGPALRGTGGEVELAAVHSRSWQGGCFGETETRTGAVDARADGLADWVTDVRNRDRTQSADVDGDGRADLVVLRSNGDVVVHRNLGDSFAAGRVMSGGWGLFVTWKDLGRLYFADVDGDRKADMIVHTSDGNIEVRFNHGTYWDQGTHWSGGWGRFIDGSDLGRLYFADVDGDGRADMIVHTGDGNVEVRFNHGTYWDQGTHWSGGWGRFVTWKDLGRLYFADVDGDGRADMIVHTGDGNVEVRFNHGTYWDQGTHWSGGWGRFVDGSDLGSLEFGDATGDGKADLLVRTKDGKVALRTNHGTYWDQGKFMITL"},"dna_sequence":{"accession":"Z50108.1","fmin":"238","fmax":"1768","strand":"+","sequence":"TTGCTCAACAAAGGAATCCGCACGCGGCGGGCTCGCGGGGCACTGGCCGGCGGCACGGTCCTGACGGCCGCCGCCGCCCTGCTCACCGCGGTGCCGGCCGCGCAGGCGATTTCCGGCGAGCCCCCGGCCGCGACCGACCACGCCTTCACCGCCCGGCTGCACATCGGCGAGGGCGACACCCTCCGCGGCTGTTCCGCCGCTCTGGTGCACCAGCAGTGGCTGCTGACCGCCACGAGCTGTTTCGCCGCCACCCCGGGTGGCGAGGTCAAGTCGGGCAAGCCCGCGCTGAAGTCGACGGCGACCCTGGGCGGCAAGACCCTCGGCATAGTCGAGGTCGTTCCGCGCGACGACCGGGACGTGGCCATGGTCCGGCTCGCCGAACCCGTCACCACGGTCGAGCCCGTGCGGCTGGCCGCGGACGCCCCCGTGGCGGCCGAGACCCTGCTCGGTGCAGGGTTCGGGCGGACCCGGACGGAGTGGGCCCCGGACCAGTTGCACACCGGCGAGTTCCGAGTGGACTCCGTCACCGGCACCACCGTGGAGCTGACCGGTCAGGACGGGGTGTCCGTGTGCAAGGGCGACACCGGCGGCCCGGCCCTGCGCGGCACGGGTGGTGAGGTCGAGCTGGCCGCCGTGCACAGCCGGTCCTGGCAGGGCGGGTGCTTCGGCGAGACGGAGACCCGGACCGGCGCGGTGGACGCCAGGGCCGACGGCCTGGCGGACTGGGTGACGGACGTCCGCAACCGCGACCGGACGCAGTCGGCCGACGTCGACGGCGACGGCAGGGCCGACCTCGTCGTCCTGCGCTCGAACGGCGACGTCGTCGTCCACCGCAACCTGGGCGACAGCTTCGCCGCCGGCCGGGTCATGTCCGGCGGCTGGGGCCTCTTCGTGACCTGGAAGGACCTGGGCCGGCTCTATTTCGCCGACGTCGACGGCGACCGCAAGGCCGACATGATCGTCCACACCAGCGACGGCAACATCGAGGTCCGCTTCAACCACGGCACCTACTGGGACCAGGGCACGCACTGGTCCGGCGGCTGGGGCCGCTTCATCGACGGCAGCGACCTGGGCCGGCTCTACTTCGCCGATGTGGACGGCGACGGCAGGGCGGACATGATCGTCCACACCGGCGACGGCAACGTCGAGGTGCGCTTCAACCACGGCACGTACTGGGACCAGGGGACGCACTGGTCGGGCGGCTGGGGCCGCTTCGTGACCTGGAAGGACCTGGGCCGGCTCTACTTCGCCGATGTCGACGGCGACGGCAGGGCGGACATGATCGTCCACACCGGCGACGGCAACGTAGAGGTCCGCTTCAACCACGGCACGTACTGGGACCAGGGCACGCACTGGTCCGGCGGCTGGGGCCGCTTCGTCGACGGCAGCGACCTGGGGTCCCTCGAGTTCGGCGACGCCACCGGTGACGGCAAGGCCGACCTGCTCGTCCGCACCAAGGACGGGAAGGTCGCCCTCCGTACCAACCACGGCACCTACTGGGACCAGGGCAAGTTCATGATCACGCTCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39569","NCBI_taxonomy_name":"Streptomyces lividans","NCBI_taxonomy_id":"1916"}}}},"ARO_accession":"3003026","ARO_id":"39460","ARO_name":"fusH","CARD_short_name":"fusH","ARO_description":"fusH is a highly specific fusidic acid esterase found in Streptomyces lividans.","ARO_category":{"39459":{"category_aro_accession":"3003025","category_aro_cvterm_id":"39459","category_aro_name":"fusidic acid inactivation enzyme","category_aro_description":"Enzymes that confer resistance to fusidic acid by inactivation.","category_aro_class_name":"AMR Gene Family"},"37139":{"category_aro_accession":"3000759","category_aro_cvterm_id":"37139","category_aro_name":"fusidic acid","category_aro_description":"Fusidic acid is the only commercially available fusidane, a group of steroid-like antibiotics. It is most active against Gram-positive bacteria, and acts by inhibiting elongation factor G to  block protein synthesis.","category_aro_class_name":"Antibiotic"},"45735":{"category_aro_accession":"3007153","category_aro_cvterm_id":"45735","category_aro_name":"fusidane antibiotic","category_aro_description":"A group of antibiotics possessing steroid rings or steroid-like structures.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"76":{"model_id":"76","model_name":"SHV-79","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"8240":{"protein_sequence":{"accession":"CAJ47134.2","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEVLPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AM176554.2","fmin":"30","fmax":"891","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGTGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATCGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001133","ARO_id":"37513","ARO_name":"SHV-79","CARD_short_name":"SHV-79","ARO_description":"SHV-79 is a broad-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"77":{"model_id":"77","model_name":"TEM-47","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1573":{"protein_sequence":{"accession":"CAA71322.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGASKRGSRGIIAALGPDGKPSRIVVIYMTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"Y10279.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCAGTAAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACATGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3000916","ARO_id":"37296","ARO_name":"TEM-47","CARD_short_name":"TEM-47","ARO_description":"TEM-47 is an extended-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"78":{"model_id":"78","model_name":"TEM-16","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1722":{"protein_sequence":{"accession":"CAA46346.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDKLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVKYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDHWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"X65254.1","fmin":"175","fmax":"1036","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATAAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTAAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATCATTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3000887","ARO_id":"37267","ARO_name":"TEM-16","CARD_short_name":"TEM-16","ARO_description":"TEM-16 is an extended-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"79":{"model_id":"79","model_name":"VIM-37","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1655":{"protein_sequence":{"accession":"AGC50807.1","sequence":"MLKVISSLLVYMTASVMAVASPLAHSGEPSGEYPTVNEIPVGEVRLYQIADGVWSHISTQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEAEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSANVLYGGCAVHELSRTSAGNVADADLAEWPTSVERIQKHYPEAEVVIPGHGLPGGLDLLQHTANVVKAHKNRSVAE"},"dna_sequence":{"accession":"JX982636.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGTTAAAAGTTATTAGTAGTTTATTGGTCTACATGACCGCGTCTGTCATGGCTGTCGCAAGTCCGTTAGCCCATTCCGGGGAGCCGAGTGGTGAGTATCCGACAGTCAACGAAATTCCGGTCGGAGAGGTCCGACTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCTCAACGCAGTCGTTTGATGGCGCGGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAAAAGCAAATTGGACTTCCCGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGCAGAGGGGAACGAGATTCCCACGCATTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAGCTCTTCTATCCTGGTGCTGCGCATTCGACCGACAATCTGGTTGTATACGTCCCGTCAGCGAACGTGCTATACGGTGGTTGTGCCGTTCATGAGTTGTCACGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCGTTGAGCGGATTCAAAAACACTACCCGGAAGCAGAGGTCGTCATTCCCGGGCACGGTCTACCGGGCGGTCTAGACTTGCTCCAGCACACAGCGAACGTTGTCAAAGCACACAAAAATCGCTCAGTCGCCGAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002307","ARO_id":"38707","ARO_name":"VIM-37","CARD_short_name":"VIM-37","ARO_description":"VIM-37 is a beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"80":{"model_id":"80","model_name":"ACT-29","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1095":{"protein_sequence":{"accession":"AIT76085.1","sequence":"MMKKSLCCALLLSTSCSVLAAPMSEKQLAEMVERTVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMSYEQAITTRVFKPLKLDHTWINVPKAEEAHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVKDMASWVMVNMKPDSLQDSSLRKGITLAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVEGSDNKVALAPLPAREVNPPAPPVNASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILDALQ"},"dna_sequence":{"accession":"KM087832.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCTCTTTGCTGCGCCCTGCTGCTCAGCACATCCTGCTCGGTATTGGCTGCACCGATGTCAGAAAAACAGCTGGCTGAGATGGTGGAACGTACCGTTACGCCGCTGATGAAAGCGCAGGCCATTCCGGGTATGGCGGTGGCGGTGATTTATCAGGGTCAGCCGCACTACTTTACCTTCGGTAAAGCCGATGTCGCGGCGAATAAACCTGTCACTCCACAAACCTTATTCGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTACTGGGCGGCGATGCCATTGCTCGCGGTGAAATATCGCTGGGCGATCCGGTGACAAAATACTGGCCTGAGCTGACAGGCAAGCAGTGGCAGGGGATCCGCATGCTGGATCTGGCAACCTATACCGCAGGAGGTTTGCCGTTACAGGTACCGGATGAGGTCACGGATAACGCCTCTCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCGGGCACCACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGCGCGCTGGCGGTCAAACCTTCCGGTATGAGCTATGAGCAGGCCATAACGACGCGGGTCTTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTTCCCAAAGCGGAAGAGGCGCATTACGCCTGGGGATACCGCGACGGTAAGGCGGTACACGTTTCGCCAGGAATGCTGGACGCTGAAGCCTATGGCGTAAAAACCAACGTGAAGGATATGGCAAGCTGGGTGATGGTCAATATGAAGCCGGACTCGCTTCAGGATAGTTCACTCAGGAAAGGCATTACCCTGGCGCAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAGGGGTTAGGCTGGGAAATGCTTAACTGGCCGGTCGATGCCAAAACCGTGGTTGAAGGTAGCGACAATAAGGTGGCACTGGCACCGTTGCCTGCGAGAGAAGTGAATCCACCGGCTCCCCCGGTCAATGCGTCCTGGGTCCATAAAACCGGCTCTACCGGCGGGTTTGGCAGCTACGTGGCATTTATTCCCGAAAAGCAGCTCGGCATTGTGATGCTGGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCGTATCCTCGACGCGCTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36926","NCBI_taxonomy_name":"Enterobacter asburiae","NCBI_taxonomy_id":"61645"}}}},"ARO_accession":"3001849","ARO_id":"38249","ARO_name":"ACT-29","CARD_short_name":"ACT-29","ARO_description":"ACT-29 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"81":{"model_id":"81","model_name":"FOX-3","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1109":{"protein_sequence":{"accession":"CAA71947.1","sequence":"MQQRRAFALLTLGSLLLAPCTYASGEAPLTATVDGIIQPMLKEYRIPGIAVAVLKDGKAHYFNYGVANRESGQRVSEQTLFEIGSVSKTLTATLGAYAAVKGGFVLDDKVSQHAPWLKGSALDGVTMAELATYSAGGLPLQFPDKVDSNDKMQTYYRSWSPVYPAGTHRQYSNPSIGLFGHLAANSLGQPFEQLMSQTLLPKLGLHHTYIQVPESAMANYAYGYSKEDKPIRVTPGVLAAEAYGIKTGSADLLKFAEANMGYQGDALVKSAIALTHTGFYSVGEMTQGLGWESYDYPVTEQVLLAGNSPAVSFQANPVTRFAVPKAMGEQRLYNKTGSTGGFGAYVAFVPARGIAIVMLANRNYPIEARVKAAHAILSQLAE"},"dna_sequence":{"accession":"Y11068.1","fmin":"16","fmax":"1165","strand":"+","sequence":"ATGCAACAACGACGTGCGTTCGCGCTACTGACGCTGGGTAGCCTGCTGCTAGCCCCTTGTACTTATGCCAGCGGGGAGGCCCCGCTGACCGCCACTGTGGACGGCATTATCCAGCCGATGCTCAAGGAGTATCGGATCCCGGGGATAGCGGTCGCCGTACTGAAAGATGGCAAGGCCCACTATTTCAACTATGGGGTTGCCAACCGCGAGAGTGGCCAGCGCGTCAGCGAGCAGACCCTGTTCGAGATTGGCTCGGTCAGCAAGACCCTGACCGCGACCCTCGGTGCCTATGCTGCGGTCAAGGGGGGCTTTGTGCTGGATGACAAGGTGAGCCAGCACGCCCCCTGGCTCAAAGGTTCCGCCTTGGATGGTGTGACCATGGCCGAGCTTGCCACCTACAGTGCGGGTGGTTTGCCGCTGCAGTTCCCCGATAAGGTGGATTCGAATGACAAGATGCAAACTTACTATCGGAGCTGGTCACCGGTTTATCCGGCAGGGACTCATCGCCAGTATTCCAACCCCAGCATAGGCCTGTTTGGTCACCTGGCCGCAAATAGTCTGGGCCAGCCATTTGAGCAACTGATGAGCCAGACCCTGCTGCCCAAGCTGGGTTTGCACCACACCTATATCCAGGTGCCGGAGTCGGCCATGGCGAACTATGCCTACGGCTATTCGAAGGAAGATAAGCCCATCCGGGTCACTCCGGGCGTGCTGGCGGCCGAGGCTTACGGGATCAAGACCGGCTCGGCGGATCTGCTGAAGTTTGCCGAGGCAAACATGGGGTATCAGGGAGATGCCCTGGTAAAAAGCGCAATCGCGCTGACCCACACCGGTTTCTACTCGGTGGGGGAAATGACCCAGGGGCTGGGCTGGGAGAGTTACGACTATCCCGTCACCGAGCAGGTGCTGCTGGCGGGCAACTCCCCGGCGGTGAGCTTCCAGGCCAATCCGGTTACGCGCTTTGCGGTGCCCAAAGCGATGGGCGAGCAGCGGCTCTATAACAAGACGGGCTCGACTGGCGGCTTTGGCGCCTATGTGGCGTTCGTGCCCGCCAGAGGGATCGCCATCGTCATGCTGGCCAATCGCAACTATCCCATCGAGGCCAGGGTGAAGGCGGCTCACGCCATCCTGAGTCAGTTGGCCGAGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3002157","ARO_id":"38557","ARO_name":"FOX-3","CARD_short_name":"FOX-3","ARO_description":"FOX-3 is a beta-lactamase found in Klebsiella oxytoca.","ARO_category":{"36206":{"category_aro_accession":"3000067","category_aro_cvterm_id":"36206","category_aro_name":"FOX beta-lactamase","category_aro_description":"FOX beta-lactamases are plasmid-encoded AmpC-type beta-lactamase which conferred resistance to broad-spectrum cephalosporins and cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"82":{"model_id":"82","model_name":"PER-4","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1061":{"protein_sequence":{"accession":"ACE77058.1","sequence":"MNVIIKAVVTASTLLMVSFSSFETSAQSPLLKEQIESIVIGKKATVGVAVWGPDDLEPLLINPFEKFPMQSVFKLHLAMLVLHQVDQGKLDLNQTVIVNRAKVLQNTWAPIMKAYQGDEFSVPVQQLLQYSVSHTDNVACDLLFELVGGPAALHDYIQSMGIKETAVVANEAQMHADDQVQYQNWTSMKGAAEILKKFEQKTQLSETSQALLWKWMVETTTGPERLKGLLPAGTVVAHKTGTSGIKAGKTAATNDLGIILLPDGRPLLVAVFVKDSAESSRTNEAIIAQVAQTAYQFELKKLSALSPN"},"dna_sequence":{"accession":"EU748544.1","fmin":"0","fmax":"927","strand":"+","sequence":"ATGAATGTCATTATAAAAGCTGTAGTTACTGCCTCGACGCTACTGATGGTATCTTTTAGTTCATTCGAAACCTCAGCGCAATCCCCACTGTTAAAAGAGCAAATTGAATCCATAGTCATTGGAAAAAAAGCCACTGTAGGCGTTGCAGTGTGGGGGCCTGACGATCTGGAACCTTTACTGATTAATCCTTTTGAAAAATTCCCAATGCAAAGTGTATTTAAATTGCATTTAGCTATGTTGGTACTGCATCAGGTTGATCAGGGAAAGTTGGATTTAAATCAGACCGTTATCGTAAACAGGGCTAAGGTTTTACAGAATACCTGGGCTCCGATAATGAAAGCGTATCAGGGAGACGAGTTTAGTGTTCCAGTGCAGCAACTGCTGCAATACTCGGTCTCGCACACCGATAACGTGGCCTGTGATTTGTTATTTGAACTGGTTGGTGGACCAGCTGCTTTGCATGACTATATCCAGTCTATGGGTATAAAGGAGACCGCTGTGGTCGCAAATGAAGCGCAGATGCACGCCGATGATCAGGTGCAGTATCAAAACTGGACCTCGATGAAAGGTGCTGCAGAGATCCTGAAAAAGTTTGAGCAAAAAACACAGCTGTCTGAAACCTCGCAGGCTTTGTTATGGAAGTGGATGGTCGAAACCACCACAGGACCAGAGCGGTTAAAAGGTTTGTTACCAGCTGGTACTGTGGTCGCACATAAAACTGGTACTTCGGGTATCAAAGCCGGAAAAACTGCGGCCACTAATGATTTAGGTATCATTCTGTTGCCTGATGGACGGCCCTTGCTGGTTGCTGTTTTTGTGAAAGACTCAGCCGAGTCAAGCCGAACCAATGAAGCTATCATTGCGCAGGTTGCTCAGACTGCGTATCAATTTGAATTGAAAAAGCTTTCTGCCCTAAGCCCAAATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36943","NCBI_taxonomy_name":"Proteus vulgaris","NCBI_taxonomy_id":"585"}}}},"ARO_accession":"3002366","ARO_id":"38766","ARO_name":"PER-4","CARD_short_name":"PER-4","ARO_description":"PER-4 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36195":{"category_aro_accession":"3000056","category_aro_cvterm_id":"36195","category_aro_name":"PER beta-lactamase","category_aro_description":"PER beta-lactamases are plasmid-mediated extended spectrum beta-lactamases found in the Enterobacteriaceae family.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"84":{"model_id":"84","model_name":"GIM-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"952":{"protein_sequence":{"accession":"CAF05908.1","sequence":"MKNVLVFLILLVALPALAQGHKPLEVIKIEDGVYLHTSFKNIEGYGLVDSNGLVVLDNNQAYIIDTPWSEEDTKLLLSWATDRGYQVMASISTHSHEDRTAGIKLLNSKSIPTYTSELTKKLLAREGKPVPTHYFKDDEFTLGNGLIELYYPGAGHTEDNIVAWLPKSKILFGGCLVRSHEWEGLGYVGDASISSWADSIKNIVSKKYPIQMVVPGHGKVGSSDILDHTIDLAESASNKLMQPTAEASAD"},"dna_sequence":{"accession":"AJ620678.1","fmin":"0","fmax":"753","strand":"+","sequence":"ATGAAAAATGTATTAGTGTTTTTAATATTACTTGTAGCGTTGCCAGCTTTAGCTCAGGGTCATAAACCGCTAGAAGTTATAAAAATTGAAGATGGAGTATATCTTCATACCTCCTTTAAGAATATTGAAGGCTATGGGTTAGTTGATTCGAATGGGTTGGTAGTTCTGGATAATAATCAAGCCTATATTATCGACACACCTTGGTCTGAAGAAGACACGAAGTTGTTATTATCCTGGGCGACTGACAGGGGATACCAGGTTATGGCTAGCATCTCAACTCATTCTCATGAAGATCGCACTGCTGGTATCAAGTTGCTAAATTCAAAGTCAATTCCTACATACACATCAGAGTTAACTAAAAAGCTTCTTGCCCGTGAAGGAAAGCCGGTTCCTACCCACTACTTTAAAGACGACGAATTCACACTGGGAAATGGGCTTATAGAGCTCTACTATCCAGGTGCTGGGCATACAGAGGATAATATTGTTGCTTGGTTACCCAAAAGCAAAATACTATTTGGTGGCTGCCTCGTGAGGAGTCATGAGTGGGAAGGCTTAGGTTACGTAGGCGACGCCTCAATTAGCTCTTGGGCTGACTCAATTAAAAATATTGTATCGAAAAAATATCCCATTCAAATGGTCGTTCCGGGGCATGGCAAAGTTGGAAGTTCAGATATATTAGATCACACCATTGATCTTGCTGAATCAGCTTCTAACAAATTAATGCAACCGACCGCTGAAGCGTCGGCTGATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3000845","ARO_id":"37225","ARO_name":"GIM-1","CARD_short_name":"GIM-1","ARO_description":"GIM-1 is an integron-encoded B1 beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"39772":{"category_aro_accession":"3003195","category_aro_cvterm_id":"39772","category_aro_name":"GIM beta-lactamase","category_aro_description":"GIM beta-lactamase enzymes isolated from Pseudomonas aeruginosa, and found to confer broad-spectrum resistance to beta-lactam antibiotics.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"85":{"model_id":"85","model_name":"IMP-42","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"2048":{"protein_sequence":{"accession":"BAM62793.1","sequence":"MSKLSVFFIFLFCSIATAAESLPDLKIEKLDEGVYVHTSFEEVNRWGVVPKHGLVVLVNAEAYLIDTPFTAKDTEKLVTWFVERGYKIKGSISSHFHSDSTGGIEWLNSRSIPTYASELTNELLKKDGKVQATNSFSGVNYWLVKNKIEVFYPGPGHTPDNVVVWLPERKILFGGCFIKPYGLGNLGDANIEAWPKSAKLLKSKYGKAKLVVPSHSEVGDASLLKLTLEQAVKGLNESKKPSKPSN"},"dna_sequence":{"accession":"AB753456.1","fmin":"0","fmax":"741","strand":"+","sequence":"ATGAGCAAGTTATCTGTATTCTTTATATTTTTGTTTTGCAGCATTGCTACCGCAGCAGAGTCTTTGCCAGATTTAAAAATTGAAAAGCTTGATGAAGGCGTTTATGTTCATACTTCGTTTGAAGAAGTTAACAGGTGGGGCGTTGTTCCTAAACATGGTTTGGTGGTTCTTGTAAATGCTGAGGCTTACCTAATTGACACTCCATTTACGGCTAAAGATACTGAAAAGTTAGTCACTTGGTTTGTGGAGCGTGGCTATAAAATAAAAGGCAGCATTTCCTCTCATTTTCATAGCGACAGCACGGGCGGAATAGAGTGGCTTAATTCTCGATCTATCCCCACGTATGCATCTGAATTAACAAATGAACTGCTTAAAAAAGACGGTAAGGTTCAAGCCACAAATTCATTTAGCGGAGTTAACTATTGGCTAGTTAAAAATAAAATTGAAGTTTTTTATCCAGGCCCGGGACACACTCCAGATAACGTAGTGGTTTGGTTGCCTGAAAGGAAAATATTATTCGGTGGTTGTTTTATTAAACCGTACGGTTTAGGCAATTTGGGTGACGCAAATATAGAAGCTTGGCCAAAGTCCGCCAAATTATTAAAGTCCAAATATGGTAAGGCAAAACTGGTTGTTCCAAGTCACAGTGAAGTTGGAGACGCATCACTCTTGAAACTTACATTAGAGCAGGCGGTTAAAGGGTTAAACGAAAGTAAAAAACCATCAAAACCAAGCAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39070","NCBI_taxonomy_name":"Acinetobacter soli","NCBI_taxonomy_id":"487316"}}}},"ARO_accession":"3002233","ARO_id":"38633","ARO_name":"IMP-42","CARD_short_name":"IMP-42","ARO_description":"IMP-42 is a beta-lactamase found in Pseudomonas and Acinetobacter spp.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"86":{"model_id":"86","model_name":"TEM-102","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"923":{"protein_sequence":{"accession":"AAK82652.1","sequence":"MSIQHFRVALIPFFAAFCLPVFVRPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPVAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAAVGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AY040093.1","fmin":"68","fmax":"929","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGTACGCCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGACGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGTAGCAATGGCAACGACTTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGGGGGTCTCGCGGTATCATTGCAGCAGTCGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39077","NCBI_taxonomy_name":"Plasmid pWW100","NCBI_taxonomy_id":"167474"}}}},"ARO_accession":"3000965","ARO_id":"37345","ARO_name":"TEM-102","CARD_short_name":"TEM-102","ARO_description":"TEM-102 is an extended-spectrum beta-lactamase that has been found in clinical isolates.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"87":{"model_id":"87","model_name":"TEM-116","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"5504":{"protein_sequence":{"accession":"AAB39956.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRIDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPVAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"U36911.1","fmin":"1429","fmax":"2290","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTATTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGTAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35508","NCBI_taxonomy_name":"Staphylococcus aureus","NCBI_taxonomy_id":"1280"}}}},"ARO_accession":"3000979","ARO_id":"37359","ARO_name":"TEM-116","CARD_short_name":"TEM-116","ARO_description":"TEM-116 is a broad-spectrum beta-lactamase found in many species of bacteria.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"88":{"model_id":"88","model_name":"CMY-55","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1116":{"protein_sequence":{"accession":"ADK55605.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGEAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"HM544040.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACATGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGAAGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002066","ARO_id":"38466","ARO_name":"CMY-55","CARD_short_name":"CMY-55","ARO_description":"CMY-55 is a beta-lactamase found in the Enterobacteriaceae family.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"91":{"model_id":"91","model_name":"gadX","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"5417":{"protein_sequence":{"accession":"BAE77778.1","sequence":"MQSLHGNCLIAYARHKYILTMVNGEYRYFNGGDLVFADASQIRVDKCVENFVFVSRDTLSLFLPMLKEEALNLHAHKKVSSLLVHHCSRDIPVFQEVAQLSQNKNLRYAEMLRKRALIFALLSVFLEDEHFIPLLLNVLQPNMRTRVCTVINNNIAHEWTLARIASELLMSPSLLKKKLREEETSYSQLLTECRMQRALQLIVIHGFSIKRVAVSCGYHSVSYFIYVFRNYYGMTPTEYQERSAQRLSNRDSAASIVAQGNFYGTDRSAEGIRL"},"dna_sequence":{"accession":"AP009048.1","fmin":"3974604","fmax":"3975429","strand":"+","sequence":"ATGCAATCACTACATGGGAATTGTCTAATTGCGTATGCAAGACATAAATATATTCTCACCATGGTTAATGGTGAATATCGCTATTTTAATGGCGGTGACCTGGTTTTTGCGGATGCAAGCCAAATTCGAGTAGATAAGTGTGTTGAAAATTTTGTATTCGTGTCAAGGGACACGCTTTCATTATTTCTCCCGATGCTCAAGGAGGAGGCATTAAATCTTCATGCACATAAAAAAGTTTCTTCATTACTCGTTCATCACTGTAGTAGAGATATTCCTGTTTTTCAGGAAGTTGCGCAACTATCGCAGAATAAGAATCTTCGCTATGCAGAAATGCTACGTAAAAGAGCATTAATCTTTGCGTTGTTATCTGTTTTTCTTGAGGATGAGCACTTTATACCGCTGCTTCTGAACGTTTTACAACCGAACATGCGAACACGAGTTTGTACGGTTATCAATAATAATATCGCCCATGAGTGGACACTAGCCCGAATCGCCAGCGAGCTGTTGATGAGTCCAAGTCTGTTAAAGAAAAAATTGCGCGAAGAAGAGACATCATATTCACAGTTGCTTACTGAGTGTAGAATGCAACGTGCTTTGCAACTTATTGTTATACATGGTTTTTCAATTAAGCGAGTTGCAGTATCCTGTGGATATCACAGCGTGTCGTATTTCATTTACGTCTTTCGAAATTATTATGGGATGACGCCCACAGAGTATCAGGAGCGATCGGCGCAGAGATTGTCGAACCGTGACTCGGCGGCAAGTATTGTTGCGCAAGGGAATTTTTACGGCACTGACCGTTCTGCGGAAGGAATAAGATTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36839","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. W3110","NCBI_taxonomy_id":"316407"}}}},"ARO_accession":"3000508","ARO_id":"36647","ARO_name":"gadX","CARD_short_name":"gadX","ARO_description":"GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35930":{"category_aro_accession":"0000011","category_aro_cvterm_id":"35930","category_aro_name":"cloxacillin","category_aro_description":"Cloxacillin is a semisynthetic, isoxazolyl penicillin derivative in the beta-lactam class of antibiotics. It interferes with peptidogylcan synthesis and is commonly used for treating penicillin-resistant Staphylococcus aureus infections.","category_aro_class_name":"Antibiotic"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"92":{"model_id":"92","model_name":"CTX-M-42","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1742":{"protein_sequence":{"accession":"AAY84742.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTETTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGDYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"DQ061159.1","fmin":"346","fmax":"1222","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGACGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGACTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001904","ARO_id":"38304","ARO_name":"CTX-M-42","CARD_short_name":"CTX-M-42","ARO_description":"CTX-M-42 is a beta-lactamase found in Escherichia coli.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"93":{"model_id":"93","model_name":"SHV-105","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1941":{"protein_sequence":{"accession":"ACI22621.1","sequence":"MRYFRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGSVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIDDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGASKRGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"FJ194944.1","fmin":"46","fmax":"907","strand":"+","sequence":"ATGCGTTATTTTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCAGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGACGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTAGCAAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGGATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001154","ARO_id":"37534","ARO_name":"SHV-105","CARD_short_name":"SHV-105","ARO_description":"SHV-105 is an extended-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"94":{"model_id":"94","model_name":"CMY-79","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1897":{"protein_sequence":{"accession":"AFK73446.1","sequence":"MMKKSICCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAIIYEGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWRGISLLHLATYTAGGLPLQIPDDITDKAALLRFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQSEQKNYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQDKTLQQGIELAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPVPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"JQ733576.1","fmin":"1027","fmax":"2173","strand":"+","sequence":"ATGATGAAAAAATCGATATGCTGCGCACTGCTGCTGACAGCCTCTTTCTCCACGTTTGCTGCCGCAAAAACAGAACAACAAATTGCCGATATCGTTAACCGCACCATCACACCACTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTGGCGATTATCTACGAGGGGAAACCTTATTACTTTACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGACGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCGGGGTATCAGCCTGCTGCACTTAGCCACCTATACAGCGGGTGGCCTGCCGCTGCAGATCCCCGATGACATTACGGATAAAGCCGCATTACTGCGCTTTTATCAAAACTGGCAACCACAATGGACTCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGTGCGCTGGCGGTGAAACCTTCAGGTATGAGCTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAAAGCGAACAAAAAAACTATGCCTGGGGCTATCGCGAAGGGAAGCCTGTGCACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATCGATATGGCCCGCTGGGTTCAGGCCAACATGGACGCCAGCCACGTTCAGGATAAAACGCTCCAGCAGGGCATTGAGCTTGCGCAGTCTCGCTACTGGCGTATTGGTGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCAGTACCTGCCGTGAAAGCCTCATGGGTGCATAAAACGGGATCCACAGGTGGATTTGGCAGCTACGTTGCCTTCGTTCCAGAAAAAAACCTTGGCATAGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGCGTCGAGGCGGCCTGGCGCATTCTTGAAAAACTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002092","ARO_id":"38492","ARO_name":"CMY-79","CARD_short_name":"CMY-79","ARO_description":"CMY-79 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"95":{"model_id":"95","model_name":"CMY-56","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1196":{"protein_sequence":{"accession":"ADT91162.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKTDSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"HQ322613.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAACTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002067","ARO_id":"38467","ARO_name":"CMY-56","CARD_short_name":"CMY-56","ARO_description":"CMY-56 is a beta-lactamase found in the Enterobacteriaceae family.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"96":{"model_id":"96","model_name":"OXA-426","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1216":{"protein_sequence":{"accession":"AJA32744.1","sequence":"MNIKALLLITSAIFISACSPYIVSANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDFARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQEVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"KM588354.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGTCTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATTTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACTACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTAGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAGAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3003149","ARO_id":"39726","ARO_name":"OXA-426","CARD_short_name":"OXA-426","ARO_description":"OXA-426 is a beta-lactamase found in clinical isolates of Acinetobacter baumannii. It is carbapenem resistant.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"98":{"model_id":"98","model_name":"CMY-48","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"8245":{"protein_sequence":{"accession":"ADP02979.1","sequence":"MMKKSICCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAIIYEGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWRGISLLHLATYTAGGLPLQIPDDVTDKAALLRFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQSEQKNYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIELAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPARVEAAWRILEKLQ"},"dna_sequence":{"accession":"HM569226.2","fmin":"1039","fmax":"2185","strand":"+","sequence":"ATGATGAAAAAATCGATATGCTGCGCGCTGCTGCTGACAGCCTCTTTCTCCACGTTTGCTGCCGCAAAAACAGAACAACAAATTGCCGATATCGTTAACCGCACCATCACACCACTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTGGCGATTATCTACGAGGGGAAACCTTATTACTTTACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGACGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCGGGGTATCAGCCTGCTGCACTTAGCCACCTATACAGCGGGTGGCCTGCCGCTGCAGATCCCCGATGACGTTACGGATAAAGCCGCATTACTGCGCTTTTATCAAAACTGGCAACCACAATGGACTCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGTGCGCTGGCGGTGAAACCTTCAGGTATGAGCTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAAAGCGAACAAAAAAATTATGCCTGGGGCTATCGCGAAGGGAAGCCTGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATCGATATGGCCCGCTGGGTTCAGGCCAACATGGACGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGAGCTTGCGCAGTCTCGTTACTGGCGTATTGGTGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCAGCACCTGCCGTGAAAGCCTCATGGGTGCATAAAACGGGATCCACAGGTGGATTTGGCAGCTACGTTGCCTTCGTTCCAGAAAAAAACCTTGGCATAGTGATGCTGGCAAACAAAAGCTATCCTAACCCGGCTCGCGTAGAGGCGGCCTGGCGCATTCTTGAAAAACTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002059","ARO_id":"38459","ARO_name":"CMY-48","CARD_short_name":"CMY-48","ARO_description":"CMY-48 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"99":{"model_id":"99","model_name":"QnrB38","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"8281":{"protein_sequence":{"accession":"AEL00461.1","sequence":"MALALIGEKIDRNRFTGEKVENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAILKDAIFKSCDLSMADFRNVSALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKAVLEKCELWENRWMGTQVLGATLSGSDLSGGEFSSFDWRTANFTHCDLTNSELGDLDIRGVDLQGVKLDSYQAALLMERLGIAVIG"},"dna_sequence":{"accession":"JN173060.2","fmin":"2306","fmax":"2951","strand":"+","sequence":"ATGGCTCTGGCATTAATTGGCGAAAAAATTGACAGAAACCGCTTCACCGGTGAAAAAGTTGAAAATAGCACTTTTTTTAACTGTGATTTTTCGGGTGCCGACCTTAGCGGTACTGAATTTATCGGCTGTCAGTTCTATGATCGAGAAAGCCAGAAAGGGTGCAATTTCAGTCGCGCAATACTGAAAGATGCCATTTTTAAAAGCTGTGATTTATCCATGGCGGATTTTCGCAACGTCAGTGCGTTGGGCATAGAAATTCGCCACTGCCGCGCACAGGGTGCAGATTTTCGCGGCGCAAGTTTCATGAATATGATCACCACGCGCACCTGGTTTTGCAGCGCATATATCACTAATACCAATCTAAGCTACGCCAACTTTTCGAAGGCCGTGCTTGAAAAGTGCGAATTGTGGGAAAATCGCTGGATGGGAACTCAGGTACTGGGTGCGACGTTGAGTGGTTCCGATCTCTCCGGTGGCGAGTTTTCGTCGTTCGACTGGCGGACGGCAAATTTCACGCACTGTGATTTGACCAATTCAGAACTGGGTGATTTAGATATTCGGGGCGTCGATTTACAAGGTGTCAAATTGGACAGCTATCAGGCCGCATTGCTCATGGAACGTCTTGGCATCGCTGTCATTGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002753","ARO_id":"39187","ARO_name":"QnrB38","CARD_short_name":"QnrB38","ARO_description":"QnrB38 is a plasmid-mediated quinolone resistance protein found in Citrobacter freundii.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"101":{"model_id":"101","model_name":"TEM-109","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1397":{"protein_sequence":{"accession":"AAT46413.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMLSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVKYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDHWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AY628175.1","fmin":"210","fmax":"1071","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGCTGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTAAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCATTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000972","ARO_id":"37352","ARO_name":"TEM-109","CARD_short_name":"TEM-109","ARO_description":"TEM-109 is an inhibitor-resistant, extended-spectrum beta-lactamase found in E. coli.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"102":{"model_id":"102","model_name":"TLA-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"4456":{"protein_sequence":{"accession":"CAG27800.1","sequence":"MNIKYFKFAEKFILLVLIMSFSSLAFCKSDDSLEQRINSIISGKKASVGVAVAGIEDNFSLSINGKKNFPMMSVYKLHIVLAVLNKVDGGSLKLDEKIPLNKKDLHPGTWSPLRDKYPNGGVSIPLSEIIEYTITQSDNNGCDILIALAGGTEAVKRYIISKGISDFDIRATEKECHESWNVQYSNWSTPVSAVALLKKFNDRKILSSVSTEYLMNVMIHTSTGNKRIKGLIPPSADVAHKTGTSGIRNGITPGTNDIGIVTLPNGKHFAIAVFVSDSRENNAANERIIAEISKAAWDYFVKMN"},"dna_sequence":{"accession":"AJ698325.1","fmin":"14502","fmax":"15417","strand":"-","sequence":"ATGAATATAAAATATTTTAAATTTGCAGAAAAATTCATTTTATTAGTTCTTATAATGTCTTTTTCTTCTTTAGCTTTCTGCAAGTCTGATGATTCTCTCGAACAGCGCATCAATTCAATCATATCAGGAAAAAAAGCATCAGTCGGTGTTGCTGTTGCGGGCATAGAAGATAATTTTTCGCTGAGCATAAACGGAAAGAAAAATTTTCCGATGATGAGCGTTTATAAATTGCATATCGTGCTTGCTGTTTTGAACAAAGTTGACGGCGGCAGTTTGAAGCTTGATGAAAAAATTCCGCTTAATAAAAAAGATCTTCATCCCGGAACTTGGAGTCCTCTGCGCGACAAATATCCGAATGGCGGAGTGAGCATTCCGCTTTCAGAAATTATAGAATATACAATCACTCAAAGCGACAACAACGGCTGTGATATTTTGATTGCTCTTGCGGGCGGAACTGAAGCTGTTAAGAGATATATTATATCAAAAGGAATTTCTGATTTTGATATCAGAGCAACAGAGAAAGAATGCCACGAGTCATGGAATGTTCAGTATTCGAACTGGTCAACGCCGGTTTCTGCGGTGGCTCTTCTAAAGAAGTTTAATGACAGAAAAATCCTTTCTTCTGTATCAACTGAATATCTGATGAATGTAATGATTCATACTTCAACCGGCAATAAAAGAATAAAGGGTCTGATTCCGCCAAGTGCTGATGTTGCGCATAAAACCGGAACATCTGGAATTCGAAACGGAATTACTCCAGGAACTAATGATATCGGAATAGTCACGCTGCCGAACGGGAAGCATTTTGCGATTGCAGTTTTTGTGTCGGATTCCCGCGAGAACAATGCGGCAAATGAAAGAATAATTGCTGAAATATCAAAGGCTGCTTGGGATTATTTTGTTAAAATGAATTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36791","NCBI_taxonomy_name":"uncultured bacterium","NCBI_taxonomy_id":"77133"}}}},"ARO_accession":"3003203","ARO_id":"39787","ARO_name":"TLA-2","CARD_short_name":"TLA-2","ARO_description":"TLA-2 is a beta-lactamase is present on a plasmid isolated from an unidentified bacterial strain from a waste water treatment plant. The enzyme mostly hydrolyzes cephalosporins.","ARO_category":{"39785":{"category_aro_accession":"3003201","category_aro_cvterm_id":"39785","category_aro_name":"TLA beta-lactamase","category_aro_description":"The TLA beta-lactamases are resistant to expanded-spectrum cephalosporins, and aztreonam but was susceptible to amikacin, cefotetan, and imipenem.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"103":{"model_id":"103","model_name":"SHV-12","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"8444":{"protein_sequence":{"accession":"AHN60527.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGASKRGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"KF976405.1","fmin":"7837","fmax":"8698","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTAGCAAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3001071","ARO_id":"37451","ARO_name":"SHV-12","CARD_short_name":"SHV-12","ARO_description":"SHV-12 is an extended-spectrum beta-lactamase found in Acinetobacter baumannii.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"35979":{"category_aro_accession":"0000062","category_aro_cvterm_id":"35979","category_aro_name":"ceftriaxone","category_aro_description":"Ceftriaxone is a third-generation cephalosporin antibiotic. The presence of an aminothiazolyl sidechain increases ceftriazone's resistance to beta-lactamases. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"37084":{"category_aro_accession":"3000704","category_aro_cvterm_id":"37084","category_aro_name":"cefalotin","category_aro_description":"Cefalotin is a semisynthetic cephalosporin antibiotic activate against staphylococci. It is resistant to staphylococci beta-lactamases but hydrolyzed by enterobacterial beta-lactamases.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"104":{"model_id":"104","model_name":"OXA-61","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1464":{"protein_sequence":{"accession":"AAT01092.1","sequence":"MKKITLFLLFLNLVFGQDKILNNWFKEYNTSGTFVFYDGKTWASNDFSRAMETFSPASTFKIFNALIALDSGVIKTKKEIFYHYRGEKVFLSSWAQDMNLSSAIKYSNVLAFKEVARRIGIKTMQEYLNKLHYGNAKISKIDTFWLDNSLKISAKEQAILLFRLSQNSLPFSQEAMNSVKEMIYLKNMENLELFGKTGFNDGQKIAWIVGFVYLKDENKYKAFALNLDIDKFEDLYKREKILEKYLDELVKKVKNDG"},"dna_sequence":{"accession":"AY587956.1","fmin":"0","fmax":"774","strand":"+","sequence":"ATGAAAAAAATAACTTTATTTTTACTTTTCTTAAATTTAGTGTTTGGGCAAGATAAGATATTAAATAATTGGTTTAAAGAGTATAATACAAGCGGCACTTTTGTTTTTTATGATGGAAAAACTTGGGCGAGTAACGACTTTTCAAGGGCTATGGAGACTTTCTCTCCCGCTTCCACTTTTAAAATTTTTAATGCTCTAATTGCACTTGATAGTGGTGTGATAAAAACTAAAAAAGAAATTTTTTATCACTATAGAGGTGAAAAAGTATTTTTATCTTCTTGGGCGCAAGATATGAATTTAAGTTCAGCTATAAAATATTCTAATGTTCTTGCTTTTAAAGAAGTGGCAAGAAGAATTGGTATCAAAACTATGCAAGAATATTTAAACAAGCTTCATTATGGTAATGCTAAAATTTCCAAGATCGATACTTTTTGGCTTGACAACTCACTAAAAATAAGCGCTAAAGAACAAGCAATTTTGCTTTTTAGACTTTCACAAAATAGCTTACCTTTTTCTCAAGAAGCAATGAATAGTGTTAAGGAAATGATTTATTTAAAAAATATGGAAAATTTAGAGCTTTTTGGAAAAACAGGTTTTAATGATGGGCAAAAAATTGCTTGGATTGTAGGTTTTGTGTATTTAAAAGATGAAAATAAATATAAGGCTTTCGCGCTAAATTTAGATATTGATAAATTTGAAGATTTATATAAAAGAGAAAAAATTTTAGAAAAATATTTAGATGAACTTGTAAAAAAAGTTAAAAATGATGGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36772","NCBI_taxonomy_name":"Campylobacter jejuni","NCBI_taxonomy_id":"197"}}}},"ARO_accession":"3001773","ARO_id":"38173","ARO_name":"OXA-61","CARD_short_name":"OXA-61","ARO_description":"OXA-61 is a beta-lactamase found in Campylobacter jejuni.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46519":{"category_aro_accession":"3007730","category_aro_cvterm_id":"46519","category_aro_name":"OXA-61-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-61.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"105":{"model_id":"105","model_name":"CARB-4","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1585":{"protein_sequence":{"accession":"AAC09012.1","sequence":"MKLLLVFSLLIPSMVFANSSKFQQVEQDAKVIEASLSAHIGISVLDTQTGEYWDYNGNQRFPLTSTFKTIACAKLLYDAEQGEINPKSTIEIKKADLVTYSPVIEKQVGQAITLDDACFATMTTSDNAAANIILNALGGPESVTDFLRQIGDKETRLDRIEPELNEGKLGDLRDTTTPNAIVNTLNELLFGSTLSQDGQKKLEYWMVNNQVTGNLLRSVLPEGWNIADRSGAGGFGARSITAVVWSEAQSPIIVSIYLAQTEASIADRNDAIVKIGRSIFEVYSSQSR"},"dna_sequence":{"accession":"U14749.1","fmin":"690","fmax":"1557","strand":"+","sequence":"ATGAAGCTTTTACTGGTATTTTCGCTTTTAATACCGTCTATGGTGTTTGCAAATAGTTCAAAGTTTCAACAGGTTGAACAAGATGCTAAGGTAATTGAAGCATCTCTTTCTGCGCATATAGGGATTTCTGTTCTTGATACTCAAACTGGAGAGTATTGGGATTACAATGGCAATCAGCGTTTTCCTTTGACAAGTACTTTTAAAACAATAGCTTGTGCTAAATTATTATATGATGCTGAGCAAGGGGAAATAAACCCTAAGAGTACAATTGAGATCAAAAAAGCAGATCTTGTGACCTATTCTCCCGTAATAGAAAAGCAAGTAGGACAAGCAATAACGCTCGATGATGCGTGTTTTGCAACTATGACGACAAGTGATAATGCAGCAGCAAATATCATCCTAAATGCCCTAGGAGGTCCTGAAAGCGTGACGGATTTTCTAAGACAAATCGGAGATAAAGAAACCCGTCTAGACCGTATTGAACCTGAATTAAATGAAGGCAAGCTTGGTGATTTGAGGGATACGACAACTCCTAATGCAATAGTGAATACTTTAAATGAATTATTATTTGGTTCCACATTGTCTCAAGATGGCCAGAAAAAATTAGAGTATTGGATGGTGAATAATCAAGTCACTGGTAATTTATTGCGGTCAGTATTGCCAGAGGGATGGAATATTGCGGATCGTTCAGGTGCTGGCGGATTTGGTGCTCGGAGTATTACAGCCGTTGTTTGGAGTGAAGCTCAATCCCCAATCATAGTTAGTATCTATCTAGCGCAAACAGAGGCTTCAATAGCAGATCGAAATGATGCAATTGTTAAAATTGGTCGTTCAATTTTTGAAGTTTATTCATCACAATCGCGTTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002243","ARO_id":"38643","ARO_name":"CARB-4","CARD_short_name":"CARB-4","ARO_description":"CARB-4 is a beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36230":{"category_aro_accession":"3000091","category_aro_cvterm_id":"36230","category_aro_name":"CARB beta-lactamase","category_aro_description":"CARB beta-lactamases are class A lactamases that can hydrolyze carbenicillin. Many of the PSE beta-lactamases have been renamed as CARB-lactamases with the notable exception of PSE-2 which is now OXA-10.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"106":{"model_id":"106","model_name":"catB9","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"386":{"protein_sequence":{"accession":"AAL68645.1","sequence":"MNFFTSPFSGIPLDQQVTNPNIIVGKHSYYSGYYHGHSFDDCVRYLHPERDDVDKLVIGSFCSIGSGAVFMMAGNQGHRSDWISTFPFFYQDNDNFADARDGFTRSGDTIIGHDVWIGTEAMIMPGVKIGHGAIIASRSVVTKDVAPYEVVGSNPAKHIKFRFSDVEIAMLLEMAWWNWPESWLKESMQSLCSSDIEGLYLNWQSKART"},"dna_sequence":{"accession":"AF462019.1","fmin":"26","fmax":"656","strand":"+","sequence":"ATGAACTTCTTTACGTCTCCATTTTCTGGGATTCCCTTAGATCAGCAAGTAACAAATCCGAACATTATTGTGGGAAAACACAGTTATTATTCTGGTTATTATCACGGGCACAGTTTCGATGATTGTGTGCGATATTTACATCCAGAAAGAGATGACGTTGATAAGTTAGTCATAGGGAGTTTTTGTTCTATAGGCTCTGGTGCTGTATTTATGATGGCCGGTAATCAAGGGCATCGCAGTGATTGGATAAGTACATTCCCATTTTTCTATCAGGATAATGATAATTTTGCAGATGCACGCGATGGTTTTACGCGTTCAGGAGACACAATTATTGGTCATGATGTGTGGATTGGCACTGAGGCTATGATAATGCCTGGGGTTAAAATTGGACATGGAGCGATAATCGCCAGTCGTTCAGTAGTGACTAAGGATGTTGCACCTTATGAAGTGGTCGGTTCAAATCCTGCTAAACATATCAAGTTTAGATTTTCTGATGTGGAAATAGCGATGTTACTTGAAATGGCATGGTGGAATTGGCCAGAATCGTGGTTGAAAGAGAGTATGCAGTCTCTGTGTTCATCAGACATTGAAGGGCTTTATCTCAATTGGCAGTCAAAAGCACGCACATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36789","NCBI_taxonomy_name":"Vibrio cholerae","NCBI_taxonomy_id":"666"}}}},"ARO_accession":"3002681","ARO_id":"39115","ARO_name":"catB9","CARD_short_name":"catB9","ARO_description":"catB9 is a chromosome-encoded variant of the cat gene found in Vibrio cholerae.","ARO_category":{"36261":{"category_aro_accession":"3000122","category_aro_cvterm_id":"36261","category_aro_name":"chloramphenicol acetyltransferase (CAT)","category_aro_description":"Inactivates chloramphenicol by addition of an acyl group. CAT is used to describe many variants of the chloramphenicol acetyltransferase gene in a range of organisms including Acinetobacter calcoaceticus, Agrobacterium tumefaciens, Alkalihalobacillus clausii, Bacillus subtilis, Campylobacter coli, Enterococcus faecalis, Enterococcus faecium, Lactococcus lactis, Listeria monocytogenes, Listonella anguillarum, Morganella morganii, Photobacterium damselae subsp. piscicida, Proteus mirabilis, Salmonella typhi, Serratia marcescens, Shigella flexneri, Staphylococcus aureus, Staphylococcus haemolyticus, Staphylococcus intermedius, Streptococcus agalactiae, Streptococcus suis and Streptomyces acrimycini.","category_aro_class_name":"AMR Gene Family"},"36521":{"category_aro_accession":"3000382","category_aro_cvterm_id":"36521","category_aro_name":"azidamfenicol","category_aro_description":"Azidamfenicol is a water soluble derivative of chloramphenicol, sharing the same mode of action of inhibiting peptide synthesis by interacting with the 23S RNA of the 50S ribosomal subunit.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36595":{"category_aro_accession":"3000456","category_aro_cvterm_id":"36595","category_aro_name":"thiamphenicol","category_aro_description":"Derivative of Chloramphenicol. The nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3).","category_aro_class_name":"Antibiotic"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"107":{"model_id":"107","model_name":"TEM-43","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8238":{"protein_sequence":{"accession":"AAC32889.2","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVKYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDHWEPELNEAIPNDERDTTTPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"U95363.2","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTAAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCATTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGACGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3000912","ARO_id":"37292","ARO_name":"TEM-43","CARD_short_name":"TEM-43","ARO_description":"TEM-43 is an extended-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"108":{"model_id":"108","model_name":"PDC-8","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"1940":{"protein_sequence":{"accession":"ACQ82813.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRRYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"FJ666071.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCGCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTATGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002507","ARO_id":"38907","ARO_name":"PDC-8","CARD_short_name":"PDC-8","ARO_description":"PDC-8 is a extended-spectrum beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"109":{"model_id":"109","model_name":"ErmE","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"384":{"protein_sequence":{"accession":"CAB60001.1","sequence":"MSSSDEQPRPRRRNQDRQHPNQNRPVLGRTERDRNRRQFGQNFLRDRKTIARIAETAELRPDLPVLEAGPGEGLLTRELADRARQVTSYEIDPRLAKSLREKLSGHPNIEVVNADFLTAEPPPEPFAFVGAIPYGITSAIVDWCLEAPTIETATMVTQLEFARKRTGDYGRWSRLTVMTWPLFEWEFVEKVDRRLFKPVPKVDSAIMRLRRRAEPLLEGAALERYESMVELCFTGVGGNIQASLLRKYPRRRVEAALDHAGVGGGAVVAYVRPEQWLRLFERLDQKNEPRGGQPQRGRRTGGRDHGDRRTGGQDRGDRRTGGRDHRDRQASGHGDRRSSGRNRDDGRTGEREQGDQGGRRGPSGGGRTGGRPGRRGGPGQR"},"dna_sequence":{"accession":"X51891.1","fmin":"189","fmax":"1335","strand":"+","sequence":"GTGAGCAGTTCGGACGAGCAGCCGCGCCCGCGTCGCCGCAACCAGGATCGGCAGCACCCCAACCAGAACCGGCCGGTGCTGGGCCGTACCGAGCGGGACCGCAACCGGCGCCAGTTCGGGCAGAACTTCCTCCGCGACCGCAAGACCATCGCGCGCATCGCCGAGACAGCCGAGCTGCGGCCCGATCTGCCGGTGCTGGAAGCCGGCCCCGGCGAAGGGCTGCTCACCAGGGAACTCGCCGACCGCGCGCGTCAGGTGACGTCGTACGAGATCGACCCCCGGCTGGCGAAGTCGTTGCGGGAGAAGCTTTCCGGCCACCCGAACATCGAAGTCGTCAACGCCGACTTCCTCACCGCCGAACCGCCGCCCGAGCCGTTCGCCTTCGTCGGCGCGATCCCCTACGGCATCACCTCGGCGATCGTGGACTGGTGCCTGGAGGCGCCGACGATCGAGACGGCGACGATGGTCACGCAGCTGGAGTTCGCCCGGAAGCGGACCGGCGATTACGGCCGCTGGAGCCGCCTCACGGTGATGACCTGGCCGCTGTTCGAGTGGGAGTTCGTCGAGAAGGTCGACCGCCGGCTGTTCAAGCCGGTGCCCAAGGTCGACTCGGCGATCATGCGGCTGCGCAGGCGCGCCGAACCGCTGCTGGAAGGCGCGGCGCTCGAACGCTACGAGTCGATGGTCGAGCTGTGCTTCACCGGCGTCGGCGGCAACATCCAGGCGTCGCTTCTGCGCAAGTACCCGAGGCGCCGCGTCGAGGCGGCGCTCGACCACGCGGGGGTCGGGGGCGGCGCCGTGGTCGCCTACGTCCGGCCGGAGCAGTGGCTCCGGCTGTTCGAGCGGCTGGATCAGAAGAACGAACCGAGGGGTGGGCAGCCCCAGCGGGGCAGGCGAACCGGCGGACGGGACCACGGGGACCGGCGAACCGGCGGGCAGGATCGCGGCGATCGGCGAACCGGCGGCCGCGACCACAGGGACCGGCAAGCCAGCGGCCACGGCGATCGTCGCAGCAGCGGACGCAATCGCGACGACGGACGAACCGGCGAGCGCGAGCAGGGGGACCAAGGCGGGCGGCGGGGGCCGTCCGGGGGTGGACGGACCGGCGGACGTCCAGGGCGACGCGGCGGACCCGGGCAGCGGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36902","NCBI_taxonomy_name":"Saccharopolyspora erythraea NRRL 2338","NCBI_taxonomy_id":"405948"}}}},"ARO_accession":"3000326","ARO_id":"36465","ARO_name":"ErmE","CARD_short_name":"ErmE","ARO_description":"ErmE is a methyltransferase found in the erythromycin producer Saccharopolyspora erythraea. Like other Erm enzymes, it catalyzes the methylation of A2058 of the 23S ribosomal RNA. The gene is found within the erythromycin biosynthetic cluster and is responsible for self-resistance.","ARO_category":{"36699":{"category_aro_accession":"3000560","category_aro_cvterm_id":"36699","category_aro_name":"Erm 23S ribosomal RNA methyltransferase","category_aro_description":"Erm proteins are part of the RNA methyltransferase family and methylate A2058 (E. coli nomenclature) of the 23S ribosomal RNA conferring degrees of resistance to Macrolides, Lincosamides and Streptogramin b. This is called the MLSb phenotype.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35946":{"category_aro_accession":"0000027","category_aro_cvterm_id":"35946","category_aro_name":"roxithromycin","category_aro_description":"Roxithromycin is a semi-synthetic, 14-carbon ring macrolide antibiotic derived from erythromycin. It is used to treat respiratory tract, urinary and soft tissue infections. Roxithromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35974":{"category_aro_accession":"0000057","category_aro_cvterm_id":"35974","category_aro_name":"telithromycin","category_aro_description":"Telithromycin is a semi-synthetic derivative of erythromycin. It is a 14-membered macrolide and is the first ketolide antibiotic to be used in clinics. Telithromycin binds the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"35982":{"category_aro_accession":"0000065","category_aro_cvterm_id":"35982","category_aro_name":"clarithromycin","category_aro_description":"Clarithromycin is a methyl derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome and is used to treat pharyngitis, tonsillitis, acute maxillary sinusitis, acute bacterial exacerbation of chronic bronchitis, pneumonia (especially atypical pneumonias associated with Chlamydia pneumoniae or TWAR), and skin structure infections.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"36284":{"category_aro_accession":"3000145","category_aro_cvterm_id":"36284","category_aro_name":"tylosin","category_aro_description":"Tylosin is a 16-membered macrolide, naturally produced by Streptomyces fradiae. It interacts with the bacterial ribosome 50S subunit to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"36295":{"category_aro_accession":"3000156","category_aro_cvterm_id":"36295","category_aro_name":"spiramycin","category_aro_description":"Spiramycin is a 16-membered macrolide and is natural product produced by Streptomyces ambofaciens. It binds to the 50S subunit of bacterial ribosomes and inhibits peptidyl transfer activity to disrupt protein synthesis.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"36315":{"category_aro_accession":"3000176","category_aro_cvterm_id":"36315","category_aro_name":"dirithromycin","category_aro_description":"Dirithromycin is an oxazine derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome to inhibit bacterial protein synthesis.","category_aro_class_name":"Antibiotic"},"36722":{"category_aro_accession":"3000583","category_aro_cvterm_id":"36722","category_aro_name":"pristinamycin IA","category_aro_description":"Pristinamycin IA is a type B streptogramin antibiotic produced by Streptomyces pristinaespiralis. It binds to the P site of the 50S subunit of the bacterial ribosome, preventing the extension of protein chains.","category_aro_class_name":"Antibiotic"},"36723":{"category_aro_accession":"3000584","category_aro_cvterm_id":"36723","category_aro_name":"quinupristin","category_aro_description":"Quinupristin is a type B streptogramin and a semisynthetic derivative of pristinamycin 1A. It is a component of the drug Synercid and interacts with the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"virginiamycin M1","category_aro_description":"Virginiamycin M1 is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37016":{"category_aro_accession":"3000672","category_aro_cvterm_id":"37016","category_aro_name":"madumycin II","category_aro_description":"Madumycin II is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37017":{"category_aro_accession":"3000673","category_aro_cvterm_id":"37017","category_aro_name":"griseoviridin","category_aro_description":"Griseoviridin is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"37019":{"category_aro_accession":"3000675","category_aro_cvterm_id":"37019","category_aro_name":"pristinamycin IB","category_aro_description":"Pristinamycin IB is a class B streptogramin similar to pristinamycin IA, the former containing a N-methyl-4-(methylamino)phenylalanine instead of a N-methyl-4-(dimethylamino)phenylalanine in its class A streptogramin counterpart (one less methyl group).","category_aro_class_name":"Antibiotic"},"37021":{"category_aro_accession":"3000677","category_aro_cvterm_id":"37021","category_aro_name":"virginiamycin S2","category_aro_description":"Virginiamycin S2 is a streptogramin B antibiotic.","category_aro_class_name":"Antibiotic"},"37022":{"category_aro_accession":"3000678","category_aro_cvterm_id":"37022","category_aro_name":"pristinamycin IC","category_aro_description":"Pristinamycin IC is a class B streptogramin derived from virginiamycin S1.","category_aro_class_name":"Antibiotic"},"37023":{"category_aro_accession":"3000679","category_aro_cvterm_id":"37023","category_aro_name":"vernamycin C","category_aro_description":"Vernamycin C is a streptogramin B antibiotic.","category_aro_class_name":"Antibiotic"},"37024":{"category_aro_accession":"3000680","category_aro_cvterm_id":"37024","category_aro_name":"patricin A","category_aro_description":"Patricin A is a streptogramin B antibiotic.","category_aro_class_name":"Antibiotic"},"37025":{"category_aro_accession":"3000681","category_aro_cvterm_id":"37025","category_aro_name":"patricin B","category_aro_description":"Patricin B is a streptogramin B antibiotic.","category_aro_class_name":"Antibiotic"},"37026":{"category_aro_accession":"3000682","category_aro_cvterm_id":"37026","category_aro_name":"ostreogrycin B3","category_aro_description":"Ostreogrycin B3 is a derivative of pristinamycin IA, with an additional 3-hydroxy group on its 4-oxopipecolic acid.","category_aro_class_name":"Antibiotic"},"37247":{"category_aro_accession":"3000867","category_aro_cvterm_id":"37247","category_aro_name":"oleandomycin","category_aro_description":"Oleandomycin is a 14-membered macrolide produced by Streptomyces antibioticus. It is ssimilar to erythromycin, and contains a desosamine amino sugar and an oleandrose sugar. It targets the 50S ribosomal subunit to prevent protein synthesis.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35952":{"category_aro_accession":"0000034","category_aro_cvterm_id":"35952","category_aro_name":"streptogramin A antibiotic","category_aro_description":"Streptogramin A antibiotics are cyclic polyketide peptide hybrids that bind to the ribosomal peptidyl transfer centre. Structural variation arises from substituting a proline for its desaturated derivative and by its substitution for Ala or Cys. Used alone, streptogramin A antibiotics are bacteriostatic, but is bactericidal when used with streptogramin B antibiotics.","category_aro_class_name":"Drug Class"},"35967":{"category_aro_accession":"0000050","category_aro_cvterm_id":"35967","category_aro_name":"streptogramin B antibiotic","category_aro_description":"Streptogramin B antibiotics are are cyclic hepta- or hexa-depsipeptides.  Type B streptogramins block the peptide exit tunnel of the 50S bacterial ribosome. The general composition of group B streptogramins is 3-hydroxypicolinic acid-L-Thr-D-aminobutyric acid (or D-Ala)-L-Pro-L-Phe (or 4-N-,N-(dimethylamino)-L-Phe)-X-L-phenylglycine. Used alone, streptogramin B antibiotics are bacteriostatic, but is bactericidal when used with streptogramin A antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"110":{"model_id":"110","model_name":"AAC(6')-Iu","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"27":{"protein_sequence":{"accession":"AAD03493.1","sequence":"MNILPISESQLSDWLALRSLLWPDHEEAHLQEMRQLLKQTDTLQLLAYSETQHAIAMLEASIRHEYVNGTQTSPVAFLEGIYVLPEYRRSGIATQLVQCVEEWAKQFACTEFASDAALDNTISHAMHRALGFHETERVVYFKKNIS"},"dna_sequence":{"accession":"AF031329.1","fmin":"0","fmax":"441","strand":"+","sequence":"ATGAATATTTTGCCGATATCTGAATCACAATTATCAGATTGGCTAGCATTAAGAAGCTTACTCTGGCCTGATCATGAAGAAGCACATTTACAGGAAATGCGCCAACTACTTAAACAAACCGATACTTTACAGTTATTGGCGTATTCGGAAACGCAACATGCGATAGCAATGTTGGAAGCATCGATTCGGCATGAATATGTGAATGGTACGCAAACCTCACCCGTGGCTTTTCTTGAAGGGATTTATGTATTGCCTGAATATCGACGTTCAGGCATCGCGACCCAGTTGGTTCAGTGCGTAGAGGAATGGGCGAAACAATTTGCATGTACTGAGTTTGCTTCAGATGCAGCGCTTGACAATACGATTAGCCATGCAATGCATCGAGCACTGGGTTTTCATGAAACTGAACGCGTGGTTTATTTTAAGAAAAATATCAGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39516","NCBI_taxonomy_name":"Acinetobacter dispersus","NCBI_taxonomy_id":"70348"}}}},"ARO_accession":"3002565","ARO_id":"38965","ARO_name":"AAC(6')-Iu","CARD_short_name":"AAC(6')-Iu","ARO_description":"AAC(6')-Iu is a chromosomal-encoded aminoglycoside acetyltransferase in Acinetobacter genomosp. 17.","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"A category of aminoglycoside N-acetyltransferase enzymes with modification regiospecificity based at the 6'-amino group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics through acetylation of the 6-amino group of the compound.","category_aro_class_name":"AMR Gene Family"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"46128":{"category_aro_accession":"3007378","category_aro_cvterm_id":"46128","category_aro_name":"2'-N-ethylnetilmicin","category_aro_description":"2'-N-ethylnetilmicin is an aminoglycoside antibiotic and a derivative of netilmicin.","category_aro_class_name":"Antibiotic"},"46129":{"category_aro_accession":"3007379","category_aro_cvterm_id":"46129","category_aro_name":"5-episisomicin","category_aro_description":"5-episosomicin is a semisynthetic aminoglycoside antibiotic similar to sisomicin.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"113":{"model_id":"113","model_name":"VEB-5","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1576":{"protein_sequence":{"accession":"ABN80430.1","sequence":"MKIVKRILLVLLSLFFTVEYSNAQTDNLTLKIENVLKAKNARIGVAIFNSNEKDTLKINNDFHFPMQSVMKFPIALAVLSEIDKGNLSFEQKIEITPQDLLPKMWSPIKEEFPNGTTLTIEQILNYTVSESDNIGCDILLKLIGGTDSVQKFLNANHFTDISIKANEEQMHKDWNTQYQNWATPTAMNKLLIDTYNNKNQLLSKKSYDFIWKIMRETTTGSNRLKGQLPKNTIVAHKTGTSGINNGIAAATNDVGVITLPNGQLIFISVFVAESKETSEINEKIISDIAKITWNYYLNK"},"dna_sequence":{"accession":"EF420108.1","fmin":"37","fmax":"937","strand":"+","sequence":"ATGAAAATCGTAAAAAGGATATTATTAGTATTGTTAAGTTTATTTTTTACAGTTGAGTATTCAAATGCTCAAACTGACAACTTAACTTTGAAAATTGAGAATGTTTTAAAGGCAAAAAATGCCAGAATAGGAGTAGCAATATTCAACAGCAATGAGAAGGATACTTTGAAGATTAATAACGACTTCCATTTCCCGATGCAAAGCGTTATGAAATTTCCGATTGCTTTAGCCGTTTTGTCTGAGATAGATAAAGGGAATCTTTCTTTTGAACAAAAAATAGAGATTACCCCTCAAGACCTTTTGCCTAAAATGTGGAGTCCGATTAAAGAGGAATTCCCTAATGGAACAACTTTGACGATTGAACAAATACTAAATTATACAGTATCAGAGAGCGACAATATTGGTTGTGATATTTTGCTAAAATTAATCGGAGGAACTGATTCTGTTCAAAAATTCTTGAATGCTAATCATTTCACTGATATTTCAATCAAAGCAAACGAAGAACAAATGCACAAGGATTGGAATACCCAATATCAAAATTGGGCAACCCCAACAGCGATGAACAAACTGTTAATAGATACTTATAATAATAAGAACCAATTACTTTCTAAAAAAAGTTATGATTTTATTTGGAAAATTATGAGAGAAACAACAACAGGAAGTAACCGATTAAAAGGACAATTACCAAAGAATACAATTGTTGCTCATAAAACAGGGACTTCCGGAATAAATAATGGAATTGCAGCAGCCACTAATGATGTTGGGGTAATTACTTTACCGAATGGACAATTAATTTTTATAAGCGTATTTGTTGCAGAGTCCAAAGAAACTTCGGAAATTAATGAAAAGATTATTTCAGACATTGCAAAAATAACGTGGAATTACTATTTGAATAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002375","ARO_id":"38775","ARO_name":"VEB-5","CARD_short_name":"VEB-5","ARO_description":"VEB-5 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36182":{"category_aro_accession":"3000043","category_aro_cvterm_id":"36182","category_aro_name":"VEB beta-lactamase","category_aro_description":"VEB beta-lactamases or Vietnamese extended-spectrum beta-lactamases are class A beta-lactamases that confer high-level resistance to oxyimino cephalosporins and to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"114":{"model_id":"114","model_name":"dfrA13","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"8268":{"protein_sequence":{"accession":"CAA90683.1","sequence":"MNPESVRIYLVAAMGANRVIGNGPDIPWKIPGEQKIFRRLTESKVVVMGRKTFESIGKPLPNRHTVVLSRQAGYSAPGCAVVSTLSHVSPSTAEHGKELYVARGAEVYALALPHANGVFLSEVHQTFEGDAFFPVLNAAEFEVVSSETIQGTITYTHSVYARRNG"},"dna_sequence":{"accession":"Z50802.3","fmin":"717","fmax":"1215","strand":"+","sequence":"ATGAACCCGGAATCGGTCCGCATTTATCTGGTCGCTGCCATGGGTGCCAATCGGGTTATTGGCAATGGTCCCGATATCCCCTGGAAAATCCCAGGTGAGCAGAAGATTTTTCGCAGGCTCACCGAGAGCAAAGTGGTCGTTATGGGCCGCAAGACATTTGAGTCCATAGGCAAGCCCTTACCAAACCGCCACACAGTGGTGCTCTCGCGCCAAGCTGGTTATAGCGCTCCTGGTTGTGCAGTTGTTTCAACGCTGTCACACGTATCGCCATCGACAGCCGAACACGGCAAAGAACTCTACGTAGCGCGCGGAGCCGAGGTATATGCGCTGGCGCTACCGCATGCCAACGGCGTCTTTCTATCTGAGGTACATCAAACCTTTGAGGGTGACGCCTTCTTCCCAGTGCTTAACGCAGCAGAATTCGAGGTTGTCTCATCCGAAACCATTCAAGGCACAATCACGTACACGCACTCCGTCTATGCGCGTCGTAACGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3003012","ARO_id":"39446","ARO_name":"dfrA13","CARD_short_name":"dfrA13","ARO_description":"dfrA13 is an integron-encoded dihydrofolate reductase found in Escherichia coli.","ARO_category":{"37617":{"category_aro_accession":"3001218","category_aro_cvterm_id":"37617","category_aro_name":"trimethoprim resistant dihydrofolate reductase dfr","category_aro_description":"Alternative dihydropteroate synthase dfr present on plasmids produces alternate proteins that are less sensitive to trimethoprim from inhibiting its role in folate synthesis, thus conferring trimethoprim resistance.","category_aro_class_name":"AMR Gene Family"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"115":{"model_id":"115","model_name":"TEM-87","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1575":{"protein_sequence":{"accession":"AAG44570.1","sequence":"MSIKHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVKYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLHCWEPELNEAIPNDERDTTTPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AF250872.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTAAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTAAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTCATTGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGACGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3000954","ARO_id":"37334","ARO_name":"TEM-87","CARD_short_name":"TEM-87","ARO_description":"TEM-87 is an extended-spectrum beta-lactamase found in Proteus mirabilis.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"116":{"model_id":"116","model_name":"QnrB18","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"424":{"protein_sequence":{"accession":"CAP45903.1","sequence":"MTPLLYKKTGTNMALALVGEKIDRNRFTGEKIDNSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNASALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGAQVLGATFSGSDLSGGEFSTFDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDNYQASLLMERLGIAVIG"},"dna_sequence":{"accession":"AM919399.1","fmin":"0","fmax":"681","strand":"+","sequence":"ATGACGCCATTACTGTATAAAAAAACAGGTACAAATATGGCTCTGGCACTCGTTGGCGAAAAAATTGACAGAAACCGTTTCACCGGTGAGAAAATTGATAATAGTACATTTTTTAACTGTGATTTTTCAGGTGCCGACCTGAGCGGCACTGAATTTATCGGCTGTCAGTTCTATGATCGTGAAAGCCAGAAAGGGTGCAATTTTAGTCGTGCGATGCTGAAAGATGCCATTTTTAAAAGCTGTGATTTATCCATGGCGGATTTTCGCAATGCCAGTGCGCTGGGCATTGAAATTCGCCACTGCCGCGCACAAGGCGCAGATTTCCGCGGCGCAAGTTTTATGAATATGATCACTACTCGCACCTGGTTTTGTAGTGCATATATCACTAACACAAATCTAAGCTACGCCAATTTTTCGAAAGTCGTGCTGGAAAAGTGTGAGCTGTGGGAAAACCGTTGGATGGGTGCCCAGGTACTGGGCGCGACGTTCAGTGGTTCAGATCTCTCCGGCGGCGAGTTTTCGACTTTCGACTGGCGAGCAGCAAACTTCACACATTGCGATCTGACCAATTCGGAGTTGGGGGACTTAGATATTCGGGGCGTTGATTTACAAGGCGTTAAGTTGGACAACTACCAGGCATCGTTGCTCATGGAGCGACTTGGCATCGCGGTGATTGGTTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002733","ARO_id":"39167","ARO_name":"QnrB18","CARD_short_name":"QnrB18","ARO_description":"QnrB18 is a plasmid-mediated quinolone resistance protein found in Citrobacter freundii.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"118":{"model_id":"118","model_name":"LRA-9","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"4459":{"protein_sequence":{"accession":"ACH58989.1","sequence":"MKLRYLLAAALLMTTASAFGADAPKRLPVNITNKEWLMPFPGFKIVGNMYYVGTYDLGCYLIDTGAGLILVNTGIMGSYPLMKASIESLGFKTSDIKIITATHGHSDHVGDIALFKKDAPGATVYMSERDVESLESGGNFDYRRPAPEGRGGLVYDPIHVDVKTKPGDHIKLGNVDMTVLQAYGHTPGATSFSFQQTDAGKTYNVLIVNMNGINAGVKLLGSPHYPTIVEDFKNTIDMQATYKPDIWVSSHSGQFNLHQVYKPGDAYNPARFGDLAAYQKKIATAKANYEKQLAEERAAAK"},"dna_sequence":{"accession":"EU408350.1","fmin":"11679","fmax":"12585","strand":"-","sequence":"ATGAAATTGCGATATCTGCTCGCCGCCGCGCTTCTGATGACCACGGCCAGCGCGTTCGGCGCGGACGCGCCCAAGCGCCTGCCGGTCAACATCACCAACAAAGAATGGCTGATGCCGTTCCCCGGCTTCAAGATCGTCGGCAACATGTATTACGTCGGCACCTATGATCTGGGCTGCTATCTGATCGATACGGGCGCCGGCCTGATCCTCGTCAACACCGGGATCATGGGTTCCTATCCGCTGATGAAGGCGAGCATCGAATCCCTCGGCTTCAAGACCAGCGACATCAAGATCATCACCGCAACCCACGGCCATTCGGACCATGTCGGCGATATCGCGCTGTTCAAGAAGGATGCGCCGGGCGCCACCGTGTATATGAGCGAGCGCGATGTGGAGAGCCTCGAATCCGGCGGCAATTTCGATTACCGCCGGCCCGCGCCCGAAGGCCGCGGCGGCCTCGTCTACGATCCCATCCATGTCGACGTGAAGACGAAGCCTGGCGATCACATCAAGCTCGGCAATGTCGACATGACCGTGCTGCAGGCTTATGGCCACACGCCGGGCGCGACGAGCTTCTCGTTCCAGCAGACGGATGCGGGCAAGACCTACAACGTCCTCATCGTCAACATGAACGGCATCAACGCGGGCGTGAAGCTGTTGGGCTCGCCGCATTATCCGACCATCGTCGAGGACTTCAAGAACACGATCGACATGCAGGCGACCTACAAGCCCGATATCTGGGTGTCGTCGCATTCCGGGCAGTTCAACCTGCACCAGGTCTATAAGCCGGGCGATGCGTACAATCCGGCGCGCTTCGGCGACCTCGCGGCCTATCAGAAGAAGATCGCGACCGCGAAGGCGAATTACGAAAAGCAGCTCGCGGAAGAACGCGCCGCGGCGAAGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39083","NCBI_taxonomy_name":"uncultured bacterium BLR9","NCBI_taxonomy_id":"506525"}}}},"ARO_accession":"3002488","ARO_id":"38888","ARO_name":"LRA-9","CARD_short_name":"LRA-9","ARO_description":"LRA-9 is a beta-lactamase isolated from soil samples in Alaska.","ARO_category":{"41390":{"category_aro_accession":"3004226","category_aro_cvterm_id":"41390","category_aro_name":"subclass B3 LRA beta-lactamase","category_aro_description":"Beta-lactamases that are part of the LRA gene family and are classified as B3 (metallo-) beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"119":{"model_id":"119","model_name":"VIM-12","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"934":{"protein_sequence":{"accession":"AAZ73123.1","sequence":"MLKVISSLLVYMTASVMAVASPLAHSGEPSGEYPTVNEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEAEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSANVLYGGCAVHELSSTSAGNVADADLAEWPTSIERIQQHYPEAQFVIPGHGLPGGLDLLKHTTNVVKAHTNRSVVE"},"dna_sequence":{"accession":"DQ143913.1","fmin":"1774","fmax":"2575","strand":"+","sequence":"ATGTTAAAAGTTATTAGTAGTTTATTGGTCTACATGACCGCGTCTGTCATGGCTGTCGCAAGTCCGTTAGCCCATTCCGGGGAGCCGAGTGGTGAGTATCCGACAGTCAACGAAATTCCGGTCGGAGAGGTCCGACTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCGGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAAAAGCAAATTGGACTTCCCGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGCAGAGGGGAACGAGATTCCCACGCATTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAGCTCTTCTATCCTGGTGCTGCGCATTCGACCGACAATCTGGTTGTATACGTCCCGTCAGCGAACGTGCTATACGGTGGTTGTGCCGTTCATGAGTTGTCAAGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCATTGAGCGGATTCAACAACACTACCCGGAAGCACAGTTCGTCATTCCGGGGCACGGCCTGCCGGGCGGTCTAGACTTGCTCAAGCACACAACGAATGTTGTAAAAGCGCACACAAATCGCTCAGTCGTTGAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002282","ARO_id":"38682","ARO_name":"VIM-12","CARD_short_name":"VIM-12","ARO_description":"VIM-12 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"120":{"model_id":"120","model_name":"aadA4","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"408":{"protein_sequence":{"accession":"AAN34365.1","sequence":"MGEFFPAQISEQLSHARGVIERHLAATLDTIHLFGSALDGGLKPDSNIDLLVTVSAAPNDSLRQALMLDLLKVSSPPGNGGPWRPLEVTVVARSEVVPWRYPARRGLQFGEWLRHDILSGTFEPAVLDHDLAILLTKARQHSLALLGPSAVTFFEPVPNEHFSKALFDTIAQWNSESDWKGDERNVVLALARIWYSASTGLIAPKDVAAAWVSERLPAEHRPIICKARAAYLGSEDDDLAMRVEETAAFVRYAKATIERILR"},"dna_sequence":{"accession":"AY138986.1","fmin":"0","fmax":"789","strand":"+","sequence":"ATGGGTGAATTCTTTCCTGCACAAATTTCCGAGCAGCTATCCCACGCTCGCGGGGTGATCGAGCGCCATCTAGCTGCAACGCTGGACACAATCCACCTGTTCGGATCTGCGCTCGATGGAGGGTTGAAGCCGGACAGCAACATCGACTTGCTCGTGACCGTCAGCGCCGCACCTAACGATTCGCTCCGGCAGGCACTAATGCTCGACCTGCTAAAAGTCTCATCACCGCCAGGCAATGGCGGACCATGGCGACCGCTGGAGGTGACTGTTGTCGCTCGAAGCGAAGTAGTGCCCTGGCGCTATCCGGCGCGACGTGGGCTTCAGTTCGGTGAGTGGCTCCGCCACGACATCCTCTCCGGAACGTTCGAGCCTGCCGTTCTGGATCACGATCTTGCGATTTTGCTGACCAAGGCGAGGCAACACAGCCTTGCACTGCTAGGTCCATCCGCAGTCACGTTCTTCGAGCCGGTGCCGAACGAGCATTTTTCCAAGGCGCTTTTCGACACGATTGCCCAGTGGAATTCAGAGTCGGATTGGAAGGGTGACGAGCGGAACGTCGTTCTTGCTCTTGCTCGCATTTGGTACAGTGCTTCAACGGGTCTCATTGCTCCTAAGGACGTTGCTGCCGCATGGGTATCGGAGCGTTTGCCTGCCGAGCATCGGCCCATCATTTGCAAGGCACGCGCGGCGTACCTGGGTAGCGAGGACGACGACCTAGCAATGCGCGTCGAAGAGACGGCTGCGTTCGTTCGATATGCCAAAGCAACGATTGAGAGAATCTTGCGTTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3002604","ARO_id":"39004","ARO_name":"aadA4","CARD_short_name":"aadA4","ARO_description":"aadA4 is an aminoglycoside nucleotidyltransferase gene encoded by plasmids and chromosomes in Bordetella parapertussis and E. coli.","ARO_category":{"41439":{"category_aro_accession":"3004275","category_aro_cvterm_id":"41439","category_aro_name":"ANT(3'')","category_aro_description":"A category of aminoglycoside O-nucleotidyltransferase enzymes with modification regiospecificity based at the 3''-hydroxyl group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics by transfer of an AMP group from an ATP substrate to the 3''-hydroxyl group of the compound.","category_aro_class_name":"AMR Gene Family"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"121":{"model_id":"121","model_name":"mdtF","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1850"}},"model_sequences":{"sequence":{"286":{"protein_sequence":{"accession":"AAC76539.1","sequence":"MANYFIDRPVFAWVLAIIMMLAGGLAIMNLPVAQYPQIAPPTITVSATYPGADAQTVEDSVTQVIEQNMNGLDGLMYMSSTSDAAGNASITLTFETGTSPDIAQVQVQNKLQLAMPSLPEAVQQQGISVDKSSSNILMVAAFISDNGSLNQYDIADYVASNIKDPLSRTAGVGSVQLFGSEYAMRIWLDPQKLNKYNLVPSDVISQIKVQNNQISGGQLGGMPQAADQQLNASIIVQTRLQTPEEFGKILLKVQQDGSQVLLRDVARVELGAEDYSTVARYNGKPAAGIAIKLAAGANALDTSRAVKEELNRLSAYFPASLKTVYPYDTTPFIEISIQEVFKTLVEAIILVFLVMYLFLQNFRATIIPTIAVPVVILGTFAILSAVGFTINTLTMFGMVLAIGLLVDDAIVVVENVERVIAEDKLPPKEATHKSMGQIQRALVGIAVVLSAVFMPMAFMSGATGEIYRQFSITLISSMLLSVFVAMSLTPALCATILKAAPEGGHKPNALFARFNTLFEKSTQHYTDSTRSLLRCTGRYMVVYLLICAGMAVLFLRTPTSFLPEEDQGVFMTTAQLPSGATMVNTTKVLQQVTDYYLTKEKDNVQSVFTVGGFGFSGQGQNNGLAFISLKPWSERVGEENSVTAIIQRAMIALSSINKAVVFPFNLPAVAELGTASGFDMELLDNGNLGHEKLTQARNELLSLAAQSPNQVTGVRPNGLEDTPMFKVNVNAAKAEAMGVALSDINQTISTAFGSSYVNDFLNQGRVKKVYVQAGTPFRMLPDNINQWYVRNASGTMAPLSAYSSTEWTYGSPRLERYNGIPSMEILGEAAAGKSTGDAMKFMADLVAKLPAGVGYSWTGLSYQEALSSNQAPALYAISLVVVFLALAALYESWSIPFSVMLVVPLGVVGALLATDLRGLSNDVYFQVGLLTTIGLSAKNAILIVEFAVEMMQKEGKTPIEAIIEAARMRLRPILMTSLAFILGVLPLVISHGAGSGAQNAVGTGVMGGMFAATVLAIYFVPVFFVVVEHLFARFKKA"},"dna_sequence":{"accession":"U00096.1","fmin":"3660413","fmax":"3663527","strand":"+","sequence":"ATGGCTAACTATTTTATTGATCGCCCGGTTTTTGCCTGGGTACTTGCCATTATTATGATGCTTGCAGGTGGTCTGGCGATCATGAACTTACCGGTTGCGCAGTATCCGCAGATTGCGCCACCGACCATTACCGTCAGCGCTACCTATCCAGGTGCCGATGCGCAAACGGTAGAAGACTCGGTCACTCAGGTGATTGAGCAAAATATGAATGGGCTTGATGGCCTGATGTACATGTCTTCAACCAGTGATGCGGCGGGCAATGCCTCTATCACTCTGACCTTCGAGACTGGGACATCTCCTGATATCGCACAGGTTCAAGTGCAAAATAAACTGCAACTCGCTATGCCTTCATTACCTGAAGCAGTGCAGCAGCAGGGGATTAGCGTCGATAAGTCGAGCAGTAATATCCTGATGGTAGCGGCGTTTATTTCTGATAACGGCAGCCTCAACCAGTACGATATCGCGGACTATGTAGCGTCTAATATCAAAGACCCGCTAAGCCGTACCGCGGGCGTTGGTAGCGTACAACTCTTTGGTTCCGAGTATGCCATGCGTATCTGGCTGGACCCGCAAAAACTCAATAAATATAACCTGGTACCTTCCGATGTTATTTCCCAGATTAAGGTGCAAAACAACCAGATTTCCGGTGGTCAACTGGGTGGCATGCCACAGGCGGCAGACCAGCAGCTAAACGCCTCGATCATTGTGCAGACGCGTCTGCAAACGCCGGAAGAATTTGGCAAAATCCTGTTGAAAGTTCAGCAAGATGGTTCGCAAGTGCTGCTGCGTGATGTCGCTCGCGTCGAACTTGGGGCGGAAGATTATTCCACCGTGGCACGCTATAACGGCAAACCTGCTGCCGGGATCGCCATCAAACTGGCTGCCGGAGCAAACGCCCTGGATACCTCGCGGGCAGTCAAAGAGGAACTGAACCGCTTATCAGCCTATTTCCCGGCAAGTCTGAAGACGGTTTATCCTTACGACACCACGCCGTTTATCGAAATTTCTATTCAGGAAGTTTTCAAAACACTGGTTGAGGCTATCATCCTAGTCTTCCTGGTCATGTATCTGTTTTTGCAGAATTTCCGTGCCACAATCATCCCGACGATTGCCGTACCGGTGGTTATTCTCGGGACGTTTGCGATCTTGTCGGCGGTCGGTTTCACCATCAACACGTTGACTATGTTCGGGATGGTGCTGGCGATAGGGTTACTGGTGGATGACGCCATCGTGGTGGTGGAGAACGTCGAGCGTGTCATTGCGGAAGATAAGCTACCGCCGAAGGAAGCGACGCATAAATCGATGGGGCAGATCCAACGTGCGCTGGTCGGTATTGCCGTTGTTCTTTCCGCAGTGTTTATGCCGATGGCCTTTATGAGCGGTGCAACCGGGGAGATCTACCGCCAGTTCTCCATCACGCTGATCTCCTCCATGCTGCTTTCAGTATTTGTGGCAATGAGCCTGACCCCTGCCCTGTGCGCCACCATTCTGAAAGCCGCGCCGGAAGGCGGTCACAAACCTAACGCCCTGTTCGCACGCTTCAACACGCTGTTTGAAAAATCAACTCAACACTATACCGATAGCACCCGCTCGCTGTTGCGTTGTACCGGTCGCTACATGGTGGTCTACCTGCTGATTTGCGCCGGGATGGCGGTGCTGTTCCTGCGCACGCCGACCTCTTTCTTACCAGAAGAGGATCAGGGGGTATTTATGACCACCGCGCAGTTACCTTCCGGTGCCACCATGGTTAACACCACGAAAGTGCTGCAACAGGTGACGGATTATTATCTGACTAAAGAGAAAGATAATGTCCAGTCGGTGTTTACCGTTGGCGGCTTTGGCTTCAGCGGTCAGGGGCAAAACAACGGCCTGGCGTTTATCAGTCTCAAGCCGTGGTCTGAACGTGTCGGTGAGGAAAACTCGGTTACCGCGATCATTCAGCGGGCAATGATTGCGTTAAGCAGTATCAATAAAGCCGTCGTCTTCCCGTTCAACTTACCCGCGGTGGCTGAACTGGGTACCGCGTCAGGTTTTGATATGGAACTGCTGGACAACGGTAACCTGGGGCACGAAAAACTAACCCAGGCGCGAAACGAGCTGTTATCACTGGCAGCGCAATCACCGAATCAGGTCACCGGGGTACGCCCGAACGGCCTGGAAGATACGCCGATGTTCAAAGTGAACGTCAACGCTGCGAAAGCTGAAGCGATGGGCGTGGCGCTGTCTGATATCAACCAGACAATTTCCACCGCCTTCGGCAGCAGCTACGTGAACGACTTCCTCAACCAGGGGCGGGTGAAAAAAGTGTATGTCCAGGCAGGCACGCCGTTCCGTATGTTGCCGGATAACATCAACCAATGGTATGTACGCAACGCCTCTGGCACGATGGCACCGCTTTCTGCCTACTCGTCTACCGAATGGACCTATGGTTCACCGCGACTGGAACGCTACAACGGCATCCCGTCAATGGAGATTTTAGGTGAAGCGGCGGCCGGGAAAAGTACCGGTGACGCCATGAAATTTATGGCAGACCTGGTCGCTAAACTTCCGGCAGGCGTCGGCTACTCATGGACCGGACTATCGTATCAGGAAGCGTTATCCTCAAATCAGGCTCCTGCGCTGTATGCGATTTCACTGGTCGTGGTGTTCCTCGCCCTCGCCGCACTCTATGAGAGCTGGTCAATTCCGTTCTCGGTGATGTTGGTTGTTCCGTTAGGCGTCGTTGGCGCATTACTGGCCACCGATCTGCGCGGCTTAAGTAATGACGTCTACTTCCAGGTTGGTTTGCTGACCACCATCGGGCTTTCCGCCAAAAACGCCATCCTGATTGTCGAATTTGCCGTTGAGATGATGCAGAAAGAAGGGAAAACGCCGATAGAGGCAATCATCGAAGCGGCGCGGATGCGTTTACGCCCAATCCTGATGACCTCTCTGGCCTTTATTCTCGGCGTGCTGCCGCTGGTTATCAGTCATGGTGCCGGTTCTGGCGCGCAAAACGCGGTAGGTACCGGCGTGATGGGCGGGATGTTTGCCGCAACAGTGCTGGCAATTTACTTCGTTCCGGTCTTTTTCGTTGTAGTGGAACATCTCTTTGCCCGCTTTAAAAAAGCGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36849","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. MG1655","NCBI_taxonomy_id":"511145"}}}},"ARO_accession":"3000796","ARO_id":"37176","ARO_name":"mdtF","CARD_short_name":"mdtF","ARO_description":"MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35930":{"category_aro_accession":"0000011","category_aro_cvterm_id":"35930","category_aro_name":"cloxacillin","category_aro_description":"Cloxacillin is a semisynthetic, isoxazolyl penicillin derivative in the beta-lactam class of antibiotics. It interferes with peptidogylcan synthesis and is commonly used for treating penicillin-resistant Staphylococcus aureus infections.","category_aro_class_name":"Antibiotic"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"122":{"model_id":"122","model_name":"VIM-34","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1408":{"protein_sequence":{"accession":"AFN88953.1","sequence":"MLKVISSLLVYMTASVMAVASPLAHSGEPSGEYPTVNEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAISTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEAEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSANVLYGGCAVHELSSTSAGNVADADLAEWPTSVERIQKHYPEAEVVIPGHGLPGGLDLLQHTANVVKAHKNRSVAE"},"dna_sequence":{"accession":"JX013656.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGTTAAAAGTTATTAGTAGTTTATTGGTCTACATGACCGCGTCTGTCATGGCTGTCGCAAGTCCGTTAGCCCATTCCGGGGAGCCGAGTGGTGAGTATCCGACAGTCAACGAAATTCCGGTCGGAGAGGTCCGACTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCGGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAAAAGCAAATTGGACTTCCCGTAACGCGTGCAATCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGCAGAGGGGAACGAGATTCCCACGCATTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAGCTCTTCTATCCTGGTGCTGCGCATTCGACCGACAATCTGGTTGTATACGTCCCGTCAGCGAACGTGCTATACGGTGGTTGTGCCGTTCATGAGTTGTCAAGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCGTTGAGCGGATTCAAAAACACTACCCGGAAGCAGAGGTCGTCATTCCCGGGCACGGTCTACCGGGCGGTCTAGACTTGCTCCAGCACACAGCGAACGTTGTCAAAGCACACAAAAATCGCTCAGTCGCCGAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002304","ARO_id":"38704","ARO_name":"VIM-34","CARD_short_name":"VIM-34","ARO_description":"VIM-34 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"123":{"model_id":"123","model_name":"SHV-64","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"992":{"protein_sequence":{"accession":"ABA06586.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVLLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGASKRGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"DQ174304.1","fmin":"4","fmax":"865","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTACTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGTCCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTAGCAAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001119","ARO_id":"37499","ARO_name":"SHV-64","CARD_short_name":"SHV-64","ARO_description":"SHV-64 is an extended-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"124":{"model_id":"124","model_name":"IND-7","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1261":{"protein_sequence":{"accession":"BAJ05825.1","sequence":"MKKSIRFFIVSILLSPFASAQVKDFVIEPPIKNNLHIYKTFGVFGGKEYSANSMYLVTKKGVVLFDVPWEKVQYQSLMDTIKKRHNLPVVAVFATHSHDDRAGDLSFFNNKGIKTYATAKTNEFLKKDGKATSTEIIKTGKPYRIGGEEFVVDFLGEGHTADNVVVWFPKYNVLDGGCLVKSNSATDLGYIKEANVEQWPKTINKLKAKYSKATLIIPGHDEWKGGGHVEHTLELLNKK"},"dna_sequence":{"accession":"AB529520.1","fmin":"0","fmax":"720","strand":"+","sequence":"ATGAAAAAAAGCATCCGTTTTTTTATTGTTTCGATATTGTTGAGCCCTTTTGCAAGTGCGCAGGTAAAAGATTTTGTAATAGAACCACCCATCAAAAATAACCTGCATATTTATAAAACTTTTGGAGTATTTGGTGGTAAAGAATATTCTGCAAATTCAATGTATCTGGTTACTAAAAAAGGAGTTGTTCTCTTTGACGTTCCATGGGAAAAAGTACAGTACCAAAGCCTCATGGATACCATTAAAAAACGTCATAATTTACCGGTTGTAGCGGTATTTGCCACACACTCCCATGATGACCGCGCCGGTGACCTTAGCTTTTTCAATAATAAAGGGATTAAAACATATGCAACTGCCAAAACCAACGAGTTCTTGAAAAAAGACGGAAAAGCAACATCCACAGAAATCATCAAAACCGGAAAACCGTACCGCATTGGCGGAGAAGAATTTGTGGTAGATTTTCTTGGTGAAGGGCATACTGCTGATAATGTAGTGGTATGGTTCCCTAAATACAATGTATTGGATGGTGGCTGTCTTGTAAAAAGTAATTCAGCTACTGATTTAGGATATATTAAGGAAGCCAATGTAGAACAGTGGCCCAAAACTATAAATAAATTAAAAGCCAAATATTCTAAAGCAACATTAATTATTCCGGGACATGATGAATGGAAAGGCGGTGGACATGTTGAACACACTTTAGAACTTCTGAATAAAAAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36916","NCBI_taxonomy_name":"Chryseobacterium indologenes","NCBI_taxonomy_id":"253"}}}},"ARO_accession":"3002263","ARO_id":"38663","ARO_name":"IND-7","CARD_short_name":"IND-7","ARO_description":"IND-7 is a beta-lactamase found in Chryseobacterium indologenes.","ARO_category":{"36199":{"category_aro_accession":"3000060","category_aro_cvterm_id":"36199","category_aro_name":"IND beta-lactamase","category_aro_description":"IND beta-lactamases are class B carbapenem-hydrolyzing beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"125":{"model_id":"125","model_name":"SHV-182","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"2124":{"protein_sequence":{"accession":"AJO16042.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYTPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"KP050489.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACACGCCGGTCAGCGAAAAACATCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGTATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001364","ARO_id":"37764","ARO_name":"SHV-182","CARD_short_name":"SHV-182","ARO_description":"SHV-182 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"126":{"model_id":"126","model_name":"TEM-183","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1647":{"protein_sequence":{"accession":"ADR71220.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWLIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"HQ529916.1","fmin":"110","fmax":"971","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGCTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001045","ARO_id":"37425","ARO_name":"TEM-183","CARD_short_name":"TEM-183","ARO_description":"TEM-183 is a broad-spectrum beta-lactamase.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"127":{"model_id":"127","model_name":"clbB","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"5410":{"protein_sequence":{"accession":"BAH45481.1","sequence":"MKLTSKYETIRRILSECKQPEYRYAQIMDAIFKQNIGEYERMTILPKFLRDELNRILGPNVCSIAPVKELTSKQVSKVLFAIPGDEQVEAVRLTYERGWKSYCISTQCGCGFRCKFCATGTIGLKRNLTADEITDQLLYFRLNGHSLDSISFMGMGEALANPHIFEAMTILTDPYLFGLGHRRITISTIGLLPGIDKLTREFPQVNLTFSLHSPFDDQRSELMPINDRFPVRDVLIALDRHIRETGRKVYIAYILLRGVNDSTAHAEAVAELLRGRGAWEHLYHVNLIPFNSTEVTPDSYRQSDPSRIKAFVRILKSRGISVTVRTQFGSDINAACGQLYRSE"},"dna_sequence":{"accession":"AP008955.1","fmin":"4758175","fmax":"4759207","strand":"-","sequence":"ATGAAACTAACCTCGAAATATGAAACGATTCGGCGAATCTTGTCCGAATGCAAGCAGCCTGAGTATCGGTATGCTCAGATTATGGACGCCATTTTCAAGCAAAACATCGGCGAATACGAACGGATGACCATCCTACCCAAATTTTTGCGCGACGAGTTGAATCGGATACTTGGACCGAACGTTTGCAGTATCGCTCCGGTAAAGGAGCTCACGTCGAAACAGGTTAGCAAGGTGCTGTTTGCGATTCCGGGCGACGAACAGGTCGAGGCCGTACGACTTACTTATGAACGGGGGTGGAAATCGTATTGTATTTCCACACAGTGCGGCTGCGGATTCAGGTGCAAGTTTTGTGCTACCGGTACCATTGGTCTGAAACGAAATCTGACCGCCGACGAAATTACCGACCAATTGCTGTACTTTCGTTTGAACGGCCACTCTTTGGACAGCATCTCATTCATGGGCATGGGAGAGGCGCTCGCCAACCCGCATATTTTTGAGGCCATGACGATATTGACCGACCCGTATCTCTTCGGTTTAGGACATCGACGAATTACGATTTCCACGATCGGCCTGTTGCCGGGGATTGACAAGCTGACTCGGGAGTTCCCCCAGGTCAATCTAACCTTCTCGCTGCATTCACCGTTCGACGATCAGCGAAGCGAGCTGATGCCGATCAACGACCGATTTCCAGTCCGTGACGTACTGATAGCATTGGATCGTCACATCAGGGAAACAGGGAGAAAGGTATATATTGCGTATATTCTTCTTCGTGGAGTAAACGACTCGACAGCGCATGCGGAAGCAGTTGCCGAGTTGCTAAGGGGAAGGGGAGCTTGGGAACATCTCTACCACGTTAACCTGATTCCATTCAATTCGACCGAAGTTACGCCAGACAGCTATCGGCAATCCGATCCTTCGCGGATTAAAGCGTTTGTTCGGATCTTGAAGTCAAGGGGGATAAGCGTCACGGTCCGAACTCAATTCGGATCGGACATAAACGCGGCATGCGGCCAGTTATACCGCTCTGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39604","NCBI_taxonomy_name":"Brevibacillus brevis NBRC 100599","NCBI_taxonomy_id":"358681"}}}},"ARO_accession":"3002815","ARO_id":"39249","ARO_name":"clbB","CARD_short_name":"clbB","ARO_description":"clbB is a plasmid-encoded cfr gene found in Bacillus brevis.","ARO_category":{"36341":{"category_aro_accession":"3000202","category_aro_cvterm_id":"36341","category_aro_name":"Cfr 23S ribosomal RNA methyltransferase","category_aro_description":"Cfr genes produce enzymes which catalyze the methylation of the 23S rRNA subunit at position 8 of adenine-2503. Methylation of 23S rRNA at this site confers resistance to some classes of antibiotics, including streptogramins, chloramphenicols, florfenicols, linezolids and clindamycin.","category_aro_class_name":"AMR Gene Family"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"36521":{"category_aro_accession":"3000382","category_aro_cvterm_id":"36521","category_aro_name":"azidamfenicol","category_aro_description":"Azidamfenicol is a water soluble derivative of chloramphenicol, sharing the same mode of action of inhibiting peptide synthesis by interacting with the 23S RNA of the 50S ribosomal subunit.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36595":{"category_aro_accession":"3000456","category_aro_cvterm_id":"36595","category_aro_name":"thiamphenicol","category_aro_description":"Derivative of Chloramphenicol. The nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3).","category_aro_class_name":"Antibiotic"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"virginiamycin M1","category_aro_description":"Virginiamycin M1 is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37015":{"category_aro_accession":"3000671","category_aro_cvterm_id":"37015","category_aro_name":"tiamulin","category_aro_description":"Tiamulin is a pleuromutilin derivative currently used in veterinary medicine. It binds to the 23 rRNA of the 50S ribosomal subunit to inhibit protein translation.","category_aro_class_name":"Antibiotic"},"37016":{"category_aro_accession":"3000672","category_aro_cvterm_id":"37016","category_aro_name":"madumycin II","category_aro_description":"Madumycin II is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37017":{"category_aro_accession":"3000673","category_aro_cvterm_id":"37017","category_aro_name":"griseoviridin","category_aro_description":"Griseoviridin is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35952":{"category_aro_accession":"0000034","category_aro_cvterm_id":"35952","category_aro_name":"streptogramin A antibiotic","category_aro_description":"Streptogramin A antibiotics are cyclic polyketide peptide hybrids that bind to the ribosomal peptidyl transfer centre. Structural variation arises from substituting a proline for its desaturated derivative and by its substitution for Ala or Cys. Used alone, streptogramin A antibiotics are bacteriostatic, but is bactericidal when used with streptogramin B antibiotics.","category_aro_class_name":"Drug Class"},"36218":{"category_aro_accession":"3000079","category_aro_cvterm_id":"36218","category_aro_name":"oxazolidinone antibiotic","category_aro_description":"Oxazolidinones are a class of synthetic antibiotics discovered the the 1980's.  They inhibit protein synthesis by binding to domain V of the 23S rRNA of the 50S subunit of bacterial ribosomes.  Linezolid is the only member of this class currently in clinical use.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"37014":{"category_aro_accession":"3000670","category_aro_cvterm_id":"37014","category_aro_name":"pleuromutilin antibiotic","category_aro_description":"Pleuromutilins are natural fungal products that target bacterial protein translation by binding the the 23S rRNA, blocking the ribosome P site at the 50S subunit. They are mostly used for agriculture and veterinary purposes.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"128":{"model_id":"128","model_name":"srmB","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1050"}},"model_sequences":{"sequence":{"189":{"protein_sequence":{"accession":"CAA45050.1","sequence":"MSIAQYALHDITKRYHDCVVLDRVGFSIKPGEKVGVIGDNGSGKSTLLKILAGRVEPDNGALTVVAPGGVGYLAQTLELPLDATVQDAVDLALSDLRELEAAMREAEAELGESDENGSERELSAGLQRYAALVEQYQARGGYEADVRVEVALHGLGLPSLDRDRKLGTLSGGERSRLALAATLASSPELLLLDEPTNDLDDRAMEWLEDHLAGHRGTVIAVTHDRVFLDRLTTTILEVDSGSVTRYGNGYEGYLTAKAVERERRLREYEEWRAELDRNRGLITSNVARMDGIPRKMSLSVFGHGAYRRRGRDHGAMVRIRNAKQRVAQLTENPVHAPADPLSFAARIDTAGPEAEEAVAELTDVRVAGRLAVDSLTIRPGERLLVTGPNGAGKSTLLRVLSGELEPDGGSVRVGCRVGHLRQDETPWAPGLTVLRAFAQGREGYLEDHAEKLLSLGLFSPSDLRRRVKDLSYGQRRRIEIARLVSDPMDLLLLDEPTNHLTPVLVEELEQALADYRGAVVVVTHDRRMRSRFTGARLTMGDGRIAEFSAG"},"dna_sequence":{"accession":"X63451.1","fmin":"0","fmax":"1653","strand":"+","sequence":"GTGTCGATTGCGCAATACGCCCTACACGACATCACGAAGCGCTACCACGACTGTGTCGTGCTCGACCGGGTCGGTTTCAGCATCAAGCCGGGCGAGAAGGTCGGCGTGATCGGCGACAACGGTTCCGGCAAGTCCACGCTGCTCAAGATCCTCGCCGGCCGCGTGGAGCCCGACAACGGCGCGCTCACCGTGGTCGCTCCCGGCGGCGTCGGCTACCTGGCGCAGACACTGGAACTGCCCCTCGACGCCACCGTCCAGGACGCCGTCGACCTGGCCCTGTCCGACCTGCGCGAGCTCGAAGCGGCGATGCGCGAGGCCGAGGCGGAGCTGGGCGAGAGCGACGAGAACGGCTCCGAGCGCGAGCTGTCCGCCGGCCTCCAGCGCTACGCCGCTCTGGTCGAGCAGTACCAGGCGCGTGGCGGCTACGAGGCCGACGTGCGCGTGGAGGTCGCGCTGCACGGCCTCGGACTGCCGAGCCTGGACCGCGACCGCAAGCTCGGAACCCTCTCCGGTGGCGAACGCTCCCGCCTCGCGCTCGCCGCGACCCTCGCCTCGTCGCCGGAGCTGCTGCTCCTGGACGAACCGACCAACGACCTCGACGACCGGGCGATGGAATGGCTGGAGGACCACCTGGCCGGCCACCGCGGCACGGTGATCGCGGTCACCCACGACCGGGTCTTCCTCGACCGGCTCACCACCACGATCCTGGAGGTCGACTCCGGCAGCGTCACCCGCTACGGCAACGGCTACGAGGGCTACCTGACGGCCAAGGCCGTGGAACGCGAGCGGCGGCTGCGGGAGTACGAGGAGTGGCGTGCCGAACTCGACCGCAACCGCGGGCTGATCACCTCCAACGTGGCGCGGATGGACGGCATCCCGCGCAAGATGTCCCTCTCCGTGTTCGGCCACGGCGCCTACCGCAGGCGAGGGCGCGACCACGGCGCGATGGTGCGGATCCGCAACGCGAAGCAACGCGTGGCGCAGCTGACCGAGAACCCGGTCCACGCTCCCGCCGACCCGTTGTCCTTCGCCGCCCGCATCGACACCGCGGGCCCGGAGGCGGAGGAGGCGGTGGCCGAACTCACCGACGTGCGCGTCGCGGGTCGGCTCGCCGTGGACTCCCTGACGATCCGGCCCGGCGAACGGCTGCTCGTCACAGGTCCCAACGGTGCGGGCAAGTCCACCTTGTTGCGGGTGCTGTCCGGGGAACTGGAGCCGGACGGCGGCTCGGTGCGCGTCGGCTGCCGGGTCGGTCATCTGCGGCAGGACGAGACGCCCTGGGCGCCCGGACTGACCGTGCTGCGGGCCTTCGCCCAGGGCCGGGAGGGCTACCTGGAGGACCACGCGGAGAAACTGCTGTCGCTCGGCCTGTTCAGCCCGTCCGACCTGCGGCGACGCGTGAAGGATCTGTCCTACGGGCAGCGCCGCCGGATCGAGATCGCCCGGCTGGTGAGCGACCCGATGGACCTGCTGCTGCTGGACGAGCCCACCAACCACCTCACCCCGGTGCTGGTGGAGGAGTTGGAGCAGGCACTCGCGGACTACCGCGGCGCCGTCGTGGTCGTCACCCACGACCGTCGGATGCGGTCCCGGTTCACCGGCGCCCGGCTGACCATGGGAGACGGGCGCATCGCCGAGTTCAGCGCCGGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36864","NCBI_taxonomy_name":"Streptomyces ambofaciens","NCBI_taxonomy_id":"1889"}}}},"ARO_accession":"3002828","ARO_id":"39262","ARO_name":"srmB","CARD_short_name":"srmB","ARO_description":"srmB is an ABC-F subfamily protein found in Streptomyces ambofaciens that confers resistance to spiramycin.","ARO_category":{"45630":{"category_aro_accession":"3007068","category_aro_cvterm_id":"45630","category_aro_name":"Miscellaneous ABC-F subfamily ATP-binding cassette ribosomal protection proteins","category_aro_description":"ABC-F subfamily ATP-binding cassette ribosomal protection proteins of unknown, unclear or miscellaneous classification which nevertheless confer resistance to antibiotics through ribosomal protection and not through antibiotic efflux. These proteins should be further reviewed to elucidate associated genes, their function, origin and classification.","category_aro_class_name":"AMR Gene Family"},"36295":{"category_aro_accession":"3000156","category_aro_cvterm_id":"36295","category_aro_name":"spiramycin","category_aro_description":"Spiramycin is a 16-membered macrolide and is natural product produced by Streptomyces ambofaciens. It binds to the 50S subunit of bacterial ribosomes and inhibits peptidyl transfer activity to disrupt protein synthesis.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"129":{"model_id":"129","model_name":"FosX","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"200"}},"model_sequences":{"sequence":{"3611":{"protein_sequence":{"accession":"CWV56762.1","sequence":"MISGLSHITLIVKDLNKTTAFLQNIFNAEEIYSSGDKTFSLSKEKFFLIAGLWICIMEGDSLQERTYNHIAFQIQSEEVDEYTERIKALGVEMKPERPRVQGEGRSIYFYDFDNHLFELHAGTLEERLKRYHE"},"dna_sequence":{"accession":"FFFO01000009.1","fmin":"81760","fmax":"82162","strand":"+","sequence":"ATGATTTCAGGATTAAGCCATATCACTTTAATTGTGAAAGATTTGAATAAAACAACTGCTTTCTTACAGAATATTTTTAATGCAGAAGAAATCTATTCTAGTGGCGACAAAACATTTTCGCTTTCCAAAGAAAAATTTTTTCTAATAGCTGGTTTGTGGATTTGCATTATGGAAGGAGATTCTTTACAAGAGCGAACTTACAATCATATTGCTTTCCAAATTCAATCCGAGGAAGTGGATGAATATACTGAGCGGATTAAAGCTCTCGGTGTGGAAATGAAACCAGAACGTCCCAGAGTCCAAGGTGAAGGACGTTCCATTTATTTTTATGATTTTGATAATCATCTGTTTGAATTACACGCTGGTACATTAGAAGAACGCTTAAAAAGGTATCACGAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36757","NCBI_taxonomy_name":"Listeria monocytogenes","NCBI_taxonomy_id":"1639"}}}},"ARO_accession":"3000198","ARO_id":"36337","ARO_name":"FosX","CARD_short_name":"FosX","ARO_description":"FosX is an enzyme used to confer resistance to fosfomycin. It's dependent on the cofactor, manganese (II), and uses water to generate a vicinal diol.","ARO_category":{"36272":{"category_aro_accession":"3000133","category_aro_cvterm_id":"36272","category_aro_name":"fosfomycin thiol transferase","category_aro_description":"Catalyzes the addition of a thiol group from a nucleophilic molecule to fosfomycin.","category_aro_class_name":"AMR Gene Family"},"35944":{"category_aro_accession":"0000025","category_aro_cvterm_id":"35944","category_aro_name":"fosfomycin","category_aro_description":"Fosfomycin (also known as phosphomycin and phosphonomycin) is a broad-spectrum antibiotic produced by certain Streptomyces species. It is effective on gram positive and negative bacteria as it targets the cell wall, an essential feature shared by both bacteria. Its specific target is MurA (MurZ in E.coli), which attaches phosphoenolpyruvate (PEP) to UDP-N-acetylglucosamine, a step of commitment to cell wall synthesis. In the active site of MurA, the active cysteine molecule is alkylated which stops the catalytic reaction.","category_aro_class_name":"Antibiotic"},"45731":{"category_aro_accession":"3007149","category_aro_cvterm_id":"45731","category_aro_name":"phosphonic acid antibiotic","category_aro_description":"A group of antibiotics derived from phosphonic acids.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"130":{"model_id":"130","model_name":"CTX-M-112","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1818":{"protein_sequence":{"accession":"AEM44652.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELGAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"JF274246.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGGGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGACTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36954","NCBI_taxonomy_name":"Shigella sp. SH257","NCBI_taxonomy_id":"1074435"}}}},"ARO_accession":"3001972","ARO_id":"38372","ARO_name":"CTX-M-112","CARD_short_name":"CTX-M-112","ARO_description":"CTX-M-112 is a beta-lactamase found in Shigella spp.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"131":{"model_id":"131","model_name":"CTX-M-50","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1169":{"protein_sequence":{"accession":"AAV97955.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVPLIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"AY847146.1","fmin":"82","fmax":"958","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCCCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGACTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001912","ARO_id":"38312","ARO_name":"CTX-M-50","CARD_short_name":"CTX-M-50","ARO_description":"CTX-M-50 is a beta-lactamase found in the Enterobacteriaceae family.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"132":{"model_id":"132","model_name":"TEM-198","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1571":{"protein_sequence":{"accession":"BAL68178.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQAIMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AB700703.1","fmin":"161","fmax":"1022","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAATTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001057","ARO_id":"37437","ARO_name":"TEM-198","CARD_short_name":"TEM-198","ARO_description":"TEM-198 is a beta-lactamase.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"133":{"model_id":"133","model_name":"arr-8","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"250"}},"model_sequences":{"sequence":{"682":{"protein_sequence":{"accession":"AGC29882.1","sequence":"MIKDWIPTTHENCKKMQGPFYHGTKAKLSVGELLTTGFNTHFEEGRTLKHVYFSAMLEPAIWGAELAVSLSGLDGRGYIYLVEPTGPFEDDPNLTNKKFPGNPTMSYRTSEPLQIVGVVEEWEGHSAEALKAMLDSLENLERNGLHVIYD"},"dna_sequence":{"accession":"KC199968.1","fmin":"0","fmax":"453","strand":"+","sequence":"ATGATTAAAGATTGGATTCCAACCACACATGAAAATTGTAAAAAAATGCAGGGACCGTTTTATCATGGCACCAAAGCTAAATTATCGGTAGGTGAACTCCTAACAACTGGGTTCAACACTCATTTTGAAGAGGGTCGCACACTCAAGCACGTTTATTTTTCAGCTATGCTTGAGCCAGCAATTTGGGGGGCTGAACTCGCTGTTTCACTGTCTGGTCTAGATGGCCGGGGATACATATACTTAGTTGAACCAACTGGACCTTTCGAGGATGACCCGAATCTTACCAATAAAAAATTTCCAGGAAATCCAACAATGTCCTATCGAACTTCTGAGCCTCTCCAGATTGTGGGGGTCGTTGAAGAGTGGGAGGGACACTCCGCTGAAGCCCTGAAAGCGATGCTGGATTCCTTGGAGAATCTAGAGCGCAATGGACTTCATGTCATATATGATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3002853","ARO_id":"39287","ARO_name":"arr-8","CARD_short_name":"arr-8","ARO_description":"arr-8 is an integron-encoded ribosyltransferase found in Klebsiella oxytoca.","ARO_category":{"36529":{"category_aro_accession":"3000390","category_aro_cvterm_id":"36529","category_aro_name":"rifampin ADP-ribosyltransferase (Arr)","category_aro_description":"Enzyme responsible for the ADP-ribosylative inactivation of rifampin at the 23-OH position using NAD+.","category_aro_class_name":"AMR Gene Family"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36656":{"category_aro_accession":"3000517","category_aro_cvterm_id":"36656","category_aro_name":"rifaximin","category_aro_description":"Rifaximin is a semi-synthetic rifamycin used to treat traveller's diarrhea. Rifaximin inhibits RNA synthesis by binding to the beta subunit of bacterial RNA polymerase.","category_aro_class_name":"Antibiotic"},"36669":{"category_aro_accession":"3000530","category_aro_cvterm_id":"36669","category_aro_name":"rifabutin","category_aro_description":"Rifabutin is a semisynthetic rifamycin used in tuberculosis therapy. It inhibits DNA-dependent RNA synthesis.","category_aro_class_name":"Antibiotic"},"36673":{"category_aro_accession":"3000534","category_aro_cvterm_id":"36673","category_aro_name":"rifapentine","category_aro_description":"Rifapentine is a semisynthetic rifamycin that inhibits DNA-dependent RNA synthesis. It is often used in the treatment of tuberculosis and leprosy.","category_aro_class_name":"Antibiotic"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"134":{"model_id":"134","model_name":"rgt1438","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"4461":{"protein_sequence":{"accession":"AFO53532.1","sequence":"MRMLLTTYGSRGDVEPLAGLAAGLRKLGVEARVCAPPDEEFAALPARAGVPLIPLGPPVRPVVAGERPPTPQDAFRLAAELVTARFDTLTEAAEGCQAVLATGLMPAGVRDVAEKLGIPYVFACFHIYGLPSRHFPPGARPGTPPAPDGTDHRELWEQDARSVNALYGDALNRHRTGIGLPPVRNVRDHVLTDRPWLAADPVLCPAEGMTEFDLVQTGPWFLPDERPLPAGLEEFLGAGAPPVYVGFGSMGAYAPEGIARVAVEACRAQGRRVVLARGWAGLTPDDGGADCFAVGEVNQQALFRRVAAVVHHGGAGTTTTAARAGAPQVVVPRIADQPYWAERVRDLGIGSAHPDPVVTFDSLSAALTTALAPEVRARARTVAGTIRTDGASVAARLLVETADRAGRPVSP"},"dna_sequence":{"accession":"JX028276.1","fmin":"35585","fmax":"36821","strand":"-","sequence":"ATGCGCATGCTGCTGACCACGTACGGATCGCGCGGAGATGTCGAGCCGCTGGCCGGACTCGCGGCGGGATTGCGAAAGTTGGGCGTGGAGGCGCGGGTGTGCGCGCCGCCGGACGAGGAGTTCGCGGCGTTGCCGGCGCGTGCGGGCGTTCCGCTGATTCCGCTCGGCCCGCCGGTGCGTCCGGTGGTGGCCGGTGAGCGGCCACCGACACCTCAGGACGCCTTCCGGCTCGCCGCCGAACTGGTCACCGCCCGCTTCGACACGCTCACCGAGGCGGCCGAGGGTTGTCAGGCGGTGCTGGCCACGGGGTTGATGCCGGCCGGTGTCCGCGACGTGGCCGAGAAGCTGGGGATTCCCTACGTCTTCGCCTGCTTCCACATCTACGGGCTGCCGTCGCGGCACTTTCCTCCGGGCGCGCGTCCGGGCACCCCGCCCGCACCGGACGGGACCGACCACCGGGAGTTGTGGGAACAGGACGCCCGGAGCGTGAACGCGCTGTACGGCGACGCCCTCAACCGTCACCGCACCGGGATCGGCCTGCCGCCCGTGCGGAACGTCCGGGACCACGTCCTCACCGACCGGCCGTGGCTCGCAGCGGACCCGGTGCTGTGTCCCGCGGAGGGGATGACGGAGTTCGACCTCGTACAGACCGGACCGTGGTTCCTGCCGGACGAACGTCCGCTGCCCGCCGGGCTGGAGGAGTTCCTCGGCGCCGGGGCACCACCGGTGTACGTGGGCTTCGGCAGCATGGGCGCCTACGCTCCGGAGGGCATCGCCCGGGTGGCCGTCGAAGCCTGCCGTGCGCAGGGGCGCCGTGTGGTCCTCGCTCGCGGGTGGGCCGGGCTGACTCCGGACGACGGCGGTGCCGACTGCTTCGCGGTCGGCGAGGTCAACCAGCAGGCGCTGTTCCGCCGGGTGGCCGCCGTGGTGCACCACGGCGGGGCGGGGACCACGACGACGGCCGCCCGCGCGGGGGCGCCCCAGGTGGTGGTTCCGAGGATCGCGGACCAGCCGTACTGGGCCGAGAGGGTGAGGGACCTCGGCATCGGCTCGGCTCATCCCGACCCGGTGGTGACCTTCGACTCCCTGTCCGCCGCGCTGACGACGGCTCTGGCACCCGAAGTCCGGGCACGGGCACGGACGGTGGCGGGCACCATCCGCACGGACGGTGCCTCGGTGGCCGCGCGGCTCCTCGTCGAGACCGCCGACCGGGCGGGGCGGCCGGTGTCCCCGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39592","NCBI_taxonomy_name":"Streptomyces sp. WAC 01438","NCBI_taxonomy_id":"1214076"}}}},"ARO_accession":"3002883","ARO_id":"39317","ARO_name":"rgt1438","CARD_short_name":"rgt1438","ARO_description":"rgt1438 is a glycosyltransferase that confers rifampin resistance in Streptomyces.","ARO_category":{"36582":{"category_aro_accession":"3000443","category_aro_cvterm_id":"36582","category_aro_name":"rifampin glycosyltransferase","category_aro_description":"The enzymatic inactivation of rifampin by glycosylation at the 23-OH position.","category_aro_class_name":"AMR Gene Family"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36656":{"category_aro_accession":"3000517","category_aro_cvterm_id":"36656","category_aro_name":"rifaximin","category_aro_description":"Rifaximin is a semi-synthetic rifamycin used to treat traveller's diarrhea. Rifaximin inhibits RNA synthesis by binding to the beta subunit of bacterial RNA polymerase.","category_aro_class_name":"Antibiotic"},"36669":{"category_aro_accession":"3000530","category_aro_cvterm_id":"36669","category_aro_name":"rifabutin","category_aro_description":"Rifabutin is a semisynthetic rifamycin used in tuberculosis therapy. It inhibits DNA-dependent RNA synthesis.","category_aro_class_name":"Antibiotic"},"36673":{"category_aro_accession":"3000534","category_aro_cvterm_id":"36673","category_aro_name":"rifapentine","category_aro_description":"Rifapentine is a semisynthetic rifamycin that inhibits DNA-dependent RNA synthesis. It is often used in the treatment of tuberculosis and leprosy.","category_aro_class_name":"Antibiotic"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"135":{"model_id":"135","model_name":"SME-5","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"1642":{"protein_sequence":{"accession":"AHV85514.1","sequence":"MSNKVNFKTASFLFSVCLALSAFNAHANKSDAAAKQIKKLEEDFDGRIGVFAIDTGSGNTFGYRSDERFPLCSSFKGFLAAAVLERVQQKKLDINQKVKYESRDLEYHSPITPKYKGSGMTLGDMASAALQYSDNGATNIIMERFLGGPEGMTKFMRSIGDNEFRLDRWELELNTAIPGDKRDTSTPKAVANSLNKLALGNVLNAKVKAIYQNWLKGNTTGDARIRASVPADWVVGDKTGSCGAYGTANDYAVIWPKNRAPLIVSIYTTRKSKDDKHSDKTIAEASRIAIQAID"},"dna_sequence":{"accession":"KJ188748.1","fmin":"0","fmax":"885","strand":"+","sequence":"ATGTCAAACAAAGTAAATTTTAAAACGGCTTCATTTTTGTTTAGTGTTTGTTTAGCTTTGTCGGCATTTAATGCTCATGCTAACAAAAGTGATGCTGCGGCAAAACAAATAAAAAAATTAGAGGAAGACTTTGATGGGAGGATTGGCGTCTTTGCAATAGATACAGGATCGGGTAATACATTTGGGTATAGATCAGATGAGCGGTTCCCTTTATGCAGTTCATTTAAAGGTTTTTTGGCGGCTGCTGTTTTAGAGAGGGTGCAACAAAAAAAACTAGATATCAACCAAAAGGTTAAATATGAGAGTAGGGATCTAGAATATCATTCACCTATTACACCAAAATATAAAGGCTCAGGTATGACATTAGGTGATATGGCTTCTGCTGCATTGCAATATAGCGACAATGGGGCAACAAATATAATTATGGAACGATTTCTTGGCGGTCCTGAGGGGATGACTAAATTTATGCGTTCTATTGGAGATAATGAGTTTAGGTTAGATCGCTGGGAACTGGAACTTAACACTGCAATCCCAGGAGATAAACGTGACACTTCAACGCCAAAAGCTGTTGCAAATAGTTTGAATAAACTAGCTTTGGGGAATGTTCTCAATGCTAAAGTGAAAGCGATTTATCAAAATTGGTTAAAAGGTAATACAACTGGTGATGCTCGAATTCGTGCTAGTGTTCCTGCTGATTGGGTTGTAGGTGACAAAACTGGGAGCTGTGGGGCATATGGTACTGCGAATGATTATGCCGTCATTTGGCCTAAAAATAGAGCACCATTAATTGTCTCTATATATACAACACGAAAATCGAAAGATGATAAGCACAGTGATAAAACTATTGCGGAAGCATCACGTATTGCAATTCAGGCAATTGATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36783","NCBI_taxonomy_name":"Serratia marcescens","NCBI_taxonomy_id":"615"}}}},"ARO_accession":"3002383","ARO_id":"38783","ARO_name":"SME-5","CARD_short_name":"SME-5","ARO_description":"SME-5 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36194":{"category_aro_accession":"3000055","category_aro_cvterm_id":"36194","category_aro_name":"SME beta-lactamase","category_aro_description":"SME beta-lactamases are chromosome-mediated class A beta-lactamases that hydrolyze carbapenems in Serratia marcescens.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"136":{"model_id":"136","model_name":"CMY-9","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1363":{"protein_sequence":{"accession":"BAB72158.1","sequence":"MQQRQSILWGAVATLMWAGLAHAGEASPVDPLRPVVDASIQPLLKEHRIPGMAVAVLKDGKAHYFNYGVANRESGASVSEQTLFDIGSVSKTLTATLGAYAVVKGAMQLDDKASRHAPWLKGSVFDSITMGELATYSAGGLPLQFPEEVDSSEKMRAYYRQWAPVYSPGSHRQYSNPSIGLFGHLAASSLKQPFAQLMEQTLLPGLGMHHTYVNVPKQAMASYAYGYSKEDKPIRVNPGMLADEAYGIKTSSADLLAFVKANIGGVDDKALQQAISLTHKGHYSVGGMTQGLGWESYAYPVTEQTLLAGNSAKVILEANPTAAPRESGSQVLFNKTGSTNGFGAYVAFVPARGIGIVMLANRNYPIPARVKAAHAILAQLAG"},"dna_sequence":{"accession":"AB061794.1","fmin":"6017","fmax":"7166","strand":"+","sequence":"ATGCAACAACGACAATCCATCCTGTGGGGGGCCGTGGCCACCCTGATGTGGGCCGGTCTGGCCCATGCAGGTGAGGCTTCACCGGTCGATCCCCTGCGCCCCGTGGTGGATGCCAGCATCCAGCCGCTGCTCAAGGAGCACAGGATCCCGGGCATGGCGGTGGCCGTGCTCAAGGATGGCAAGGCCCACTATTTCAATTACGGGGTGGCCAACCGGGAGAGCGGGGCCAGCGTCAGCGAGCAGACCCTGTTCGATATAGGATCCGTGAGCAAGACCCTGACTGCGACCCTGGGGGCCTATGCGGTGGTCAAGGGAGCGATGCAGCTGGATGACAAGGCGAGCCGGCACGCGCCCTGGCTCAAGGGATCCGTCTTTGACAGCATCACCATGGGGGAGCTTGCCACCTACAGCGCCGGAGGCCTGCCACTGCAATTCCCCGAGGAGGTGGATTCATCCGAGAAGATGCGCGCCTACTACCGCCAGTGGGCCCCTGTCTATTCGCCGGGCTCCCATCGCCAGTACTCCAACCCCAGCATAGGGCTGTTCGGCCACCTGGCGGCGAGCAGCCTGAAGCAGCCATTTGCCCAGTTGATGGAGCAGACCCTGCTGCCCGGGCTCGGCATGCACCACACCTATGTCAATGTGCCGAAGCAGGCCATGGCGAGTTATGCCTATGGCTATTCGAAAGAGGACAAGCCCATCCGGGTCAACCCTGGCATGCTGGCGGACGAGGCCTACGGCATCAAGACCAGCTCGGCGGATCTGCTCGCCTTCGTGAAGGCCAACATCGGCGGGGTTGATGACAAGGCGTTGCAGCAGGCCATCTCCCTGACCCACAAAGGGCATTACTCGGTAGGCGGGATGACCCAGGGGCTGGGTTGGGAGAGTTACGCCTATCCCGTCACCGAGCAGACATTGCTGGCGGGCAATTCGGCCAAGGTGATCCTCGAAGCCAATCCGACGGCGGCTCCCCGGGAGTCGGGGAGCCAGGTGCTCTTCAACAAGACCGGCTCGACCAATGGCTTTGGCGCCTATGTGGCCTTCGTGCCGGCCAGGGGGATCGGCATCGTCATGCTGGCCAATCGCAACTATCCCATCCCGGCCAGGGTGAAGGCGGCCCACGCCATCCTGGCGCAGTTGGCCGGTTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002020","ARO_id":"38420","ARO_name":"CMY-9","CARD_short_name":"CMY-9","ARO_description":"CMY-9 is a beta-lactamase found in Escherichia coli.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"137":{"model_id":"137","model_name":"APH(2'')-Ie","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"18":{"protein_sequence":{"accession":"AAX38178.1","sequence":"MTTYTFDQVEEAIEQLYPDFTINTIEISGEGNDCIAYEINGNFIFKFPKHSRASINLLNEVTVLKTIHNELSLPIPEVVFTGMPSEMCQMSFAGFTKIKGVPLTPLLLKNLPKQSQDQAAKDLARFLSELHSINISGFKSNLVLDFREKINEDNKKIKKLLSRELKGHQMKKVDDFYRDILDNEIYFKYYPCLIHNDFSSDHILFDTEKNTICGIIDFGDAAISDPDNDFISLMEDDEEYGMEFVSKILNHYKHKDIPTVLEKYMMKEKYWSFEKIIYGKEYGYMDWYEEGLNEIRSIKIK"},"dna_sequence":{"accession":"AY939911.1","fmin":"3535","fmax":"4441","strand":"+","sequence":"ATGACAACTTATACTTTCGACCAGGTAGAAGAGGCAATAGAGCAGTTATATCCTGATTTTACTATCAATACAATAGAGATTTCAGGAGAAGGCAATGACTGTATTGCATATGAAATAAACGGGAATTTTATTTTTAAATTTCCAAAGCATTCAAGAGCTTCGATTAATCTCTTGAATGAAGTAACCGTACTCAAAACAATCCACAATGAATTATCACTACCCATTCCCGAGGTGGTTTTTACAGGAATGCCATCAGAAATGTGCCAAATGTCTTTCGCAGGTTTTACAAAAATTAAAGGAGTACCTTTGACACCTCTTCTACTCAAAAATCTGCCGAAGCAATCTCAAGATCAGGCAGCTAAGGACCTGGCCCGATTTTTAAGTGAACTTCACAGCATAAATATCTCTGGATTCAAAAGTAATCTGGTATTAGATTTTCGAGAGAAGATAAATGAAGATAATAAAAAAATCAAAAAGTTACTATCCAGGGAATTAAAGGGTCACCAGATGAAGAAAGTGGATGATTTTTACAGGGATATTCTAGACAACGAAATCTACTTCAAATACTATCCTTGTCTTATTCATAACGATTTCAGCAGCGATCATATTTTATTTGATACCGAAAAAAATACCATTTGTGGAATAATCGATTTTGGAGATGCAGCTATTTCTGATCCCGACAATGATTTTATAAGTTTGATGGAAGATGATGAAGAGTACGGCATGGAATTCGTATCAAAAATATTGAACCATTACAAACATAAGGATATACCGACAGTTTTGGAAAAATATATGATGAAAGAAAAATACTGGTCGTTCGAAAAGATTATCTATGGAAAGGAATATGGTTATATGGATTGGTATGAAGAGGGATTAAATGAAATCAGAAGCATTAAAATTAAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36767","NCBI_taxonomy_name":"Enterococcus casseliflavus","NCBI_taxonomy_id":"37734"}}}},"ARO_accession":"3002634","ARO_id":"39034","ARO_name":"APH(2'')-Ie","CARD_short_name":"APH(2'')-Ie","ARO_description":"APH(2'')-Ie is a plasmid or transposon-encoded aminoglycoside phosphotransferase in E. faecium and E. casseliflavus.","ARO_category":{"36267":{"category_aro_accession":"3000128","category_aro_cvterm_id":"36267","category_aro_name":"APH(2'')","category_aro_description":"A category of aminoglycoside O-phosphotransferase enzymes with modification regiospecificity based at the 2''-hydroxyl group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics, specifically kanamycin, tobramycin and amikacin, by the ATP-dependent phosphorylation of the 3'-hydroxyl group of the compound.","category_aro_class_name":"AMR Gene Family"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"40942":{"category_aro_accession":"3004015","category_aro_cvterm_id":"40942","category_aro_name":"gentamicin A","category_aro_description":"Gentamicin A is part of a complex of broad spectrum aminoglycoside antibiotics. Gentamicin inhibits protein synthesis, resulting in bacterial cell death.","category_aro_class_name":"Antibiotic"},"46133":{"category_aro_accession":"3007382","category_aro_cvterm_id":"46133","category_aro_name":"gentamicin","category_aro_description":"Gentamicin is a commonly used aminoglycoside antibiotic derived from members of the Micromonospora genus of bacteria. It acts by binding the 30S ribosomal subunit, thus inhibiting protein synthesis. Gentamicin is typically used to treat Gram-negative infections of the repiratory and urinary tract, as well as infections of the bone and soft tissue. It also exhibits considerable nephrotoxicity and ototoxicity. Gentamicin is administered as a mixture of gentamicin type C (which makes about around 80% of the complex) and types A, B, and X (distributed in the remaining 20% of the complex).","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"139":{"model_id":"139","model_name":"QnrB10","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"88":{"protein_sequence":{"accession":"ABG56269.1","sequence":"MLSLLYKNTGIDMTLALVGEKIDRNRFTGEKVENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNVSALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGTQVLGATFSGSDLSGGEFSTFDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDNYQASLLMERLGIAVIG"},"dna_sequence":{"accession":"DQ631414.1","fmin":"0","fmax":"681","strand":"+","sequence":"ATGTTGTCATTACTGTATAAAAACACAGGCATAGATATGACTCTGGCATTAGTTGGCGAAAAAATTGACAGAAACCGCTTCACCGGTGAGAAAGTTGAAAATAGTACATTTTTTAACTGCGATTTTTCAGGTGCCGACCTGAGCGGCACTGAATTTATCGGCTGCCAGTTCTATGATCGCGAAAGTCAGAAAGGGTGCAATTTTAGTCGCGCAATGCTGAAAGATGCCATTTTCAAAAGCTGTGATTTATCAATGGCAGATTTCCGCAACGTCAGCGCATTGGGCATTGAAATTCGCCACTGTCGCGCACAAGGCGCAGATTTTCGCGGTGCAAGCTTTATGAATATGATCACCACGCGCACCTGGTTTTGCAGCGCATATATCACTAATACCAATCTAAGCTACGCCAATTTTTCGAAAGTCGTGTTGGAAAAGTGTGAGCTATGGGAAAACCGCTGGATGGGGACTCAGGTACTGGGTGCGACGTTCAGTGGTTCAGATCTCTCCGGCGGCGAGTTTTCGACTTTCGACTGGCGAGCCGCAAACTTCACACATTGCGATCTGACCAATTCGGAGTTAGGTGACTTAGATATTCGGGGTGTTGATTTACAAGGCGTTAAGTTAGACAACTACCAGGCATCGTTGCTCATGGAGCGACTTGGCATCGCTGTGATTGGTTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002724","ARO_id":"39158","ARO_name":"QnrB10","CARD_short_name":"QnrB10","ARO_description":"QnrB10 is a plasmid-mediated quinolone resistance protein found in Citrobacter freundii.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"140":{"model_id":"140","model_name":"AAC(6')-IIb","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"497":{"protein_sequence":{"accession":"AAA25680.1","sequence":"MHPGVVTLRPMTEDDIGMLHEWLNRPHIVEWWGGERPSLEEVKEDYRPSALAEEGVTPYIGLLDGTPFAFAQSYVALGSGGGWWEEETDPGVRGIDQSIADSGLLGRGYGTRLVQALVDLLFADPQVSKVQTDPSPNNMRAIRCYEKAGFRKVKVVSTPDGPAMYMLHERPLVNGLRSAA"},"dna_sequence":{"accession":"L06163.1","fmin":"531","fmax":"1074","strand":"+","sequence":"ATGCATCCCGGCGTTGTTACTCTGCGTCCGATGACCGAAGACGACATCGGTATGCTTCACGAATGGTTGAATCGGCCGCACATTGTCGAATGGTGGGGTGGTGAGCGGCCCTCGCTCGAAGAGGTGAAAGAGGACTATCGGCCCAGCGCGTTGGCCGAAGAAGGAGTGACGCCGTACATCGGTTTGCTTGACGGAACTCCATTCGCGTTCGCACAGTCGTACGTTGCGCTCGGGTCGGGTGGTGGATGGTGGGAGGAAGAGACCGATCCTGGTGTCCGCGGAATCGATCAATCAATCGCCGATTCCGGGCTTCTCGGAAGAGGTTACGGCACTCGGCTGGTGCAGGCGCTTGTTGATTTGCTGTTCGCCGACCCGCAGGTATCCAAGGTTCAGACGGACCCCTCCCCGAACAACATGCGCGCGATACGCTGCTATGAGAAGGCAGGCTTCCGGAAGGTCAAGGTCGTTTCAACACCGGATGGGCCGGCCATGTACATGTTGCACGAGCGTCCGTTGGTGAACGGTTTGCGCAGTGCGGCCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36937","NCBI_taxonomy_name":"Pseudomonas fluorescens","NCBI_taxonomy_id":"294"}}}},"ARO_accession":"3002595","ARO_id":"38995","ARO_name":"AAC(6')-IIb","CARD_short_name":"AAC(6')-IIb","ARO_description":"AAC(6')-IIb is an integron-encoded aminoglycoside acetyltransferase in P. fluorescens.","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"A category of aminoglycoside N-acetyltransferase enzymes with modification regiospecificity based at the 6'-amino group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics through acetylation of the 6-amino group of the compound.","category_aro_class_name":"AMR Gene Family"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"46128":{"category_aro_accession":"3007378","category_aro_cvterm_id":"46128","category_aro_name":"2'-N-ethylnetilmicin","category_aro_description":"2'-N-ethylnetilmicin is an aminoglycoside antibiotic and a derivative of netilmicin.","category_aro_class_name":"Antibiotic"},"46129":{"category_aro_accession":"3007379","category_aro_cvterm_id":"46129","category_aro_name":"5-episisomicin","category_aro_description":"5-episosomicin is a semisynthetic aminoglycoside antibiotic similar to sisomicin.","category_aro_class_name":"Antibiotic"},"46133":{"category_aro_accession":"3007382","category_aro_cvterm_id":"46133","category_aro_name":"gentamicin","category_aro_description":"Gentamicin is a commonly used aminoglycoside antibiotic derived from members of the Micromonospora genus of bacteria. It acts by binding the 30S ribosomal subunit, thus inhibiting protein synthesis. Gentamicin is typically used to treat Gram-negative infections of the repiratory and urinary tract, as well as infections of the bone and soft tissue. It also exhibits considerable nephrotoxicity and ototoxicity. Gentamicin is administered as a mixture of gentamicin type C (which makes about around 80% of the complex) and types A, B, and X (distributed in the remaining 20% of the complex).","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"143":{"model_id":"143","model_name":"cphA7","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6071":{"protein_sequence":{"accession":"AAP69915.1","sequence":"MMKGWMKCGLAGAVVLMASFWGGSVRAAGISLKQVSGPVYVVEDNYYVKENSMVYFGAKGVTAVGATWTPDTARELHKLIKRVSSKPVLEVINTNYHTDRAGGNAYWKSIGAKVVATRQTRDLMKSDWAEIVAFTRKGLPEYPDLPLVLPNVVHDGDFKLQDGKVRAFYAGPAHTPDGIFVYFPDEQVLYGNCILKEKLGNLSFANVKEYPQTIERLKAMKLPIKTVIGGHDSPLHGPELIDHYEALIKAAAHS"},"dna_sequence":{"accession":"AY227053.1","fmin":"0","fmax":"765","strand":"+","sequence":"ATGATGAAAGGTTGGATGAAATGCGGATTGGCCGGAGCCGTGGTGCTGATGGCGAGTTTTTGGGGCGGCAGCGTGCGGGCGGCGGGGATCTCCCTCAAGCAGGTGAGCGGCCCTGTCTATGTGGTGGAGGATAACTACTACGTCAAAGAGAACTCCATGGTCTATTTCGGGGCCAAGGGGGTGACTGCGGTGGGGGCGACCTGGACGCCGGATACCGCCCGCGAGTTGCACAAGCTGATCAAACGGGTCAGCAGCAAGCCGGTGCTGGAGGTGATCAACACCAACTACCACACCGATCGGGCGGGCGGTAACGCCTACTGGAAGTCCATCGGGGCCAAGGTGGTGGCGACGCGCCAGACCCGGGATCTGATGAAGAGCGACTGGGCCGAGATTGTTGCCTTTACCCGCAAGGGGCTGCCGGAGTACCCGGATCTGCCGCTGGTGCTGCCGAACGTGGTGCACGATGGCGACTTCAAGCTGCAAGATGGCAAGGTGCGTGCCTTCTATGCGGGCCCGGCCCACACGCCGGACGGCATCTTTGTCTACTTCCCCGACGAGCAGGTGCTCTATGGCAACTGCATCCTCAAGGAGAAGCTGGGCAACCTGAGCTTTGCCAATGTGAAGGAGTATCCGCAGACCATCGAGCGGCTCAAGGCGATGAAGTTGCCGATCAAGACGGTGATCGGCGGTCACGACTCACCGCTGCACGGCCCCGAGCTGATTGATCACTACGAAGCGCTGATCAAGGCCGCTGCTCATTCATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42604","NCBI_taxonomy_name":"Aeromonas jandaei","NCBI_taxonomy_id":"650"}}}},"ARO_accession":"3003103","ARO_id":"39669","ARO_name":"cphA7","CARD_short_name":"cphA7","ARO_description":"cphA7 is an Ambler Class B MBL; subclass B2 originally isolated from Aeromonas jandaei. This enzyme has specific activity against carbapenems and is active as a mono-zinc protein.","ARO_category":{"36720":{"category_aro_accession":"3000581","category_aro_cvterm_id":"36720","category_aro_name":"CphA beta-lactamase","category_aro_description":"CphA is an Ambler Class B MBL; subclass B2 originally isolated from Aeromonas hydrophilia.  This enzyme has specific activity against carbapenems and is active as a mono-zinc protein.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"144":{"model_id":"144","model_name":"IMP-12","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1824":{"protein_sequence":{"accession":"CAD12765.1","sequence":"MKKLFVLCIFLFLSITASGEVLPDLKIEKLEEGVYLHTSFEEVSGWGVVTKHGLVVLVNNDAYLIDTPFTNKDTEKLVAWFVGRGFTIKGSVSSHFHSDSTGGIEWLNSQSIPTYASELTNELLKKNGKVQATNSFSGVSYWLVKNKIEIFYPGPGHTQDNVVVWLPENKILFGGCFVKPDGLGNLDDANLKAWPKSAKILMSKYGKAKLVVSGHSEIGNASLLKLTWEQAVKGLKESKKPLLPSN"},"dna_sequence":{"accession":"AJ420864.1","fmin":"155","fmax":"896","strand":"+","sequence":"ATGAAGAAATTATTTGTTTTATGCATTTTTTTGTTTTTAAGTATTACTGCCTCAGGTGAGGTTTTGCCTGATTTGAAAATTGAGAAGCTTGAAGAGGGTGTTTATCTTCATACATCTTTTGAAGAGGTTAGCGGTTGGGGTGTTGTTACTAAACATGGTTTGGTAGTTCTTGTAAATAATGACGCCTATCTAATTGACACTCCATTTACAAATAAAGATACTGAAAAATTAGTTGCTTGGTTTGTAGGGCGCGGCTTTACAATAAAGGGAAGTGTTTCCTCACATTTTCATAGCGACAGTACGGGTGGAATAGAGTGGCTTAATTCTCAATCTATTCCCACGTATGCATCTGAGTTAACAAATGAACTTCTGAAAAAGAACGGTAAGGTGCAAGCTACAAATTCATTTAGCGGGGTTAGTTATTGGCTAGTTAAAAATAAAATTGAAATTTTTTATCCCGGCCCAGGACATACTCAAGATAACGTAGTGGTTTGGCTACCTGAAAACAAAATTTTATTCGGTGGTTGTTTTGTTAAACCGGACGGTCTTGGTAATTTGGATGACGCAAATTTAAAAGCTTGGCCAAAGTCCGCAAAAATATTAATGTCTAAATATGGTAAAGCAAAGTTAGTTGTTTCAGGTCATAGTGAAATTGGGAACGCATCACTCTTGAAACTTACTTGGGAGCAGGCTGTTAAAGGGCTAAAAGAAAGTAAAAAACCATTACTGCCAAGTAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36803","NCBI_taxonomy_name":"Pseudomonas putida","NCBI_taxonomy_id":"303"}}}},"ARO_accession":"3002203","ARO_id":"38603","ARO_name":"IMP-12","CARD_short_name":"IMP-12","ARO_description":"IMP-12 is a beta-lactamase found in Pseudomonas putida.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"145":{"model_id":"145","model_name":"OXA-229","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"804":{"protein_sequence":{"accession":"AFM55000.1","sequence":"MKFKMKGLFCVILSSLAFSGCVYDSKLQRPVISERETEIPLLFDQAQTQAVFVTYDGIHLKSYGNDLSRAKTEYIPASTFKMLNALIGLQNAKATNTEVFHWNGEKRAFSAWEKDMTLAEAMQASAVPVYQELARRIGLELMREEVKRVGFGNAEIGQQVDNFWLVGPLKISPEQEVQFAYQLAMKQLPFDSNVQQQVKDMLYIERRGDSKLYAKSGWGMDVEPQVGWYTGWVEQPNGKVTAFALNMNMQAGDDPTERKQLTLSILDKLGLFFYLR"},"dna_sequence":{"accession":"JQ422052.1","fmin":"1099","fmax":"1930","strand":"+","sequence":"ATGAAGTTTAAAATGAAAGGTTTATTTTGTGTCATCCTCAGTAGTTTGGCATTTTCAGGTTGTGTTTATGATTCAAAACTACAACGCCCAGTCATATCAGAGCGAGAAACTGAGATTCCTTTATTATTTGATCAAGCACAGACTCAAGCTGTGTTTGTTACTTATGATGGGATTCATCTAAAAAGTTATGGTAATGATCTAAGCCGAGCAAAGACTGAATATATTCCTGCATCTACATTTAAGATGTTGAATGCTTTAATTGGCTTGCAAAATGCAAAAGCAACCAATACTGAAGTATTTCATTGGAATGGTGAAAAGCGCGCTTTTTCAGCATGGGAAAAAGATATGACTTTGGCAGAAGCGATGCAGGCTTCAGCTGTTCCCGTATATCAGGAGCTTGCTCGACGTATTGGCTTGGAATTGATGCGTGAAGAAGTGAAGCGTGTAGGTTTTGGCAATGCGGAGATTGGTCAGCAAGTCGATAATTTTTGGTTGGTGGGGCCTTTAAAAATCTCTCCTGAACAAGAAGTTCAATTTGCCTATCAACTGGCAATGAAGCAATTGCCTTTTGATTCAAATGTACAGCAACAAGTCAAAGATATGCTTTATATCGAGAGACGTGGTGACAGTAAACTGTATGCTAAAAGTGGTTGGGGAATGGATGTTGAACCTCAAGTGGGTTGGTATACGGGATGGGTTGAACAACCCAATGGCAAGGTGACTGCATTTGCGTTAAATATGAACATGCAAGCAGGTGATGATCCAACTGAACGTAAACAATTAACCTTAAGTATTTTGGACAAATTGGGTCTATTTTTTTATTTAAGATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39090","NCBI_taxonomy_name":"Acinetobacter bereziniae","NCBI_taxonomy_id":"106648"}}}},"ARO_accession":"3001692","ARO_id":"38092","ARO_name":"OXA-229","CARD_short_name":"OXA-229","ARO_description":"OXA-229 is a beta-lactamase found in A. bereziniae.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46498":{"category_aro_accession":"3007709","category_aro_cvterm_id":"46498","category_aro_name":"OXA-229-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-229.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"146":{"model_id":"146","model_name":"OXA-98","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1769":{"protein_sequence":{"accession":"CAK50801.1","sequence":"MNIKALLLITSAIFISACSPYIVSANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"AM279652.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGTCTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACTACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACGCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001646","ARO_id":"38046","ARO_name":"OXA-98","CARD_short_name":"OXA-98","ARO_description":"OXA-98 is a beta-lactamase found in A. baumannii.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"147":{"model_id":"147","model_name":"OXA-27","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4236":{"protein_sequence":{"accession":"AAG35609.2","sequence":"MNKYFTCYVVASLFLSGCTVQHNLINETPSQIVQGHNQVIHQYFDEKNTSGVLVIQTDKKINLYGNALSRANTEYVPASTFKMLNALIGLENQKADINEIFKWKGEKRSFTAWEKDMTLGEAMKLSAVPVYQELARRIGLDLMQKEVKRIGFGNAEIGQQVDNFWLVGPLKVTPIQEVEFVSQLAHTQLPFSEKVQANVKNMLLLEESNGYKIFGKTGWAMDIKPQVGWLTGWVEQPDGKIVAFALKMEMRSEMPASIRNELLMKSLKQLNII"},"dna_sequence":{"accession":"AF201828.2","fmin":"115","fmax":"937","strand":"+","sequence":"ATGAATAAATATTTTACTTGCTATGTGGTTGCTTCTCTTTTTCTTTCTGGTTGTACGGTTCAGCATAATTTAATAAATGAAACCCCGAGTCAGATTGTTCAAGGACATAATCAGGTGATTCATCAATACTTTGATGAAAAAAACACCTCAGGTGTGCTGGTCATTCAAACAGATAAAAAAATTAATCTATATGGTAATGCTCTAAGCCGCGCAAATACAGAATATGTGCCAGCCTCTACATTTAAAATGTTGAATGCCCTGATCGGATTGGAGAACCAGAAAGCGGATATTAATGAAATATTTAAATGGAAGGGCGAGAAAAGGTCATTTACCGCTTGGGAAAAAGACATGACACTAGGAGAAGCCATGAAGCTTTCTGCAGTCCCAGTCTATCAGGAACTTGCGCGACGTATCGGTCTTGATCTCATGCAAAAAGAAGTAAAACGTATTGGTTTCGGTAATGCTGAAATTGGACAGCAGGTTGATAATTTCTGGTTGGTAGGACCATTAAAGGTTACGCCTATTCAAGAGGTAGAGTTTGTTTCCCAATTAGCACATACACAGCTTCCATTTAGTGAAAAAGTGCAGGCTAATGTAAAAAATATGCTTCTTTTAGAAGAGAGTAATGGCTACAAAATTTTTGGAAAGACTGGTTGGGCAATGGATATAAAACCACAAGTGGGCTGGTTGACCGGCTGGGTTGAGCAGCCAGATGGAAAAATTGTCGCTTTTGCATTAAAAATGGAAATGCGGTCAGAAATGCCGGCATCTATACGTAATGAATTATTGATGAAATCATTAAAACAGCTGAATATTATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001422","ARO_id":"37822","ARO_name":"OXA-27","CARD_short_name":"OXA-27","ARO_description":"OXA-27 is a beta-lactamase found in A. baumannii.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46499":{"category_aro_accession":"3007710","category_aro_cvterm_id":"46499","category_aro_name":"OXA-23-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases, specifically imipenem, derived from OXA-23, first identified in Acinetobacter baumannii.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"148":{"model_id":"148","model_name":"SHV-92","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1793":{"protein_sequence":{"accession":"ABH04327.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMISTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLAIVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"DQ836922.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATAAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATTTGCTGCTGGCCATCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTAGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001144","ARO_id":"37524","ARO_name":"SHV-92","CARD_short_name":"SHV-92","ARO_description":"SHV-92 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"149":{"model_id":"149","model_name":"aadA12","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"57":{"protein_sequence":{"accession":"ACJ47200.1","sequence":"MRVAVTIEISNQLSEVLSVIERHLESTLLAVHLYGSAVDGGLKPYSDIDLLVTVTVRLDETTRRALINDLLETSASPGESEILRAVEVTIVVHDDIIPWRYPAKRELQFGEWQRNDILAGIFEPATIDIDLAILLTKAREHSVALVGPAAEELFDPVPEQDLFEALNETLTLWNSPPDWAGDERNVVLTLSRIWYSAITGKIAPKDVAADWAIKRLPAQYQPVLLEAKQAYLGQKEDHLASRADHLEEFIRFVKGEIIKSVGK"},"dna_sequence":{"accession":"FJ381668.1","fmin":"56","fmax":"848","strand":"+","sequence":"ATGAGGGTAGCGGTGACCATCGAAATTTCGAACCAACTATCAGAGGTGCTAAGCGTCATTGAGCGCCATCTGGAATCAACGTTGCTGGCCGTGCATTTGTACGGCTCCGCAGTGGATGGCGGCCTGAAGCCATACAGCGATATTGATTTGCTGGTTACGGTGACCGTAAGGCTTGATGAAACAACGCGGCGAGCTTTGATCAACGACCTTTTGGAAACTTCGGCTTCCCCTGGAGAGAGCGAGATTCTCCGCGCTGTAGAAGTCACCATTGTTGTGCACGACGACATCATTCCGTGGCGTTATCCAGCTAAGCGCGAACTGCAATTTGGAGAATGGCAGCGCAATGACATTCTTGCAGGTATCTTCGAGCCAGCCACGATCGACATTGATCTGGCTATCTTGCTGACAAAAGCAAGAGAACATAGCGTTGCCTTGGTAGGTCCAGCGGCGGAGGAACTCTTTGATCCGGTTCCTGAACAGGATCTATTTGAGGCGCTAAATGAAACCTTAACGCTATGGAACTCGCCGCCCGACTGGGCTGGCGATGAGCGAAATGTAGTGCTTACGTTGTCCCGCATTTGGTACAGCGCAATAACCGGCAAAATCGCGCCGAAGGATGTCGCTGCCGACTGGGCAATAAAACGCCTACCTGCCCAGTATCAGCCCGTCTTACTTGAAGCTAAGCAAGCTTATCTGGGACAAAAAGAAGATCACTTGGCCTCACGCGCAGATCACTTGGAAGAATTTATTCGCTTTGTGAAAGGCGAGATCATCAAGTCAGTTGGTAAATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002612","ARO_id":"39012","ARO_name":"aadA12","CARD_short_name":"aadA12","ARO_description":"aadA12 is an integron-encoded aminoglycoside nucleotidyltransferase gene in E. coli, Yersinia enterocolitica and S. enterica.","ARO_category":{"41439":{"category_aro_accession":"3004275","category_aro_cvterm_id":"41439","category_aro_name":"ANT(3'')","category_aro_description":"A category of aminoglycoside O-nucleotidyltransferase enzymes with modification regiospecificity based at the 3''-hydroxyl group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics by transfer of an AMP group from an ATP substrate to the 3''-hydroxyl group of the compound.","category_aro_class_name":"AMR Gene Family"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"150":{"model_id":"150","model_name":"catB3","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"350"}},"model_sequences":{"sequence":{"5450":{"protein_sequence":{"accession":"AFQ93498.1","sequence":"MTNYFDSPFKGKLLSEQVKNPNIKVGRYSYYSGYYHGHSFDDCARYLFPDRDDVDKLIIGSFCSIGSGASFIMAGNQGHRYDWASSFPFFYMQEEPAFSSALDAFQKAGNTVIGNDVWIGSEAMVMPGIKIGHGAVIGSRSLVTKDVEPYAIVGGNPAKKIKKRFTDEEISLLLEMEWWNWSLEKIKAAMPMLCSSNIVGLHKYWLEFAV"},"dna_sequence":{"accession":"JX101693.1","fmin":"58200","fmax":"58833","strand":"+","sequence":"ATGACCAACTACTTTGATAGCCCCTTCAAAGGCAAGCTGCTTTCTGAGCAAGTGAAGAACCCCAATATCAAAGTTGGGCGGTACAGCTATTACTCTGGCTACTATCATGGGCACTCATTCGATGACTGCGCACGGTATCTGTTTCCGGACCGTGATGACGTTGATAAGTTGATCATCGGTAGTTTCTGCTCTATCGGGAGTGGGGCTTCCTTTATCATGGCTGGCAATCAGGGGCATCGGTACGACTGGGCATCATCTTTCCCGTTCTTTTATATGCAGGAAGAACCTGCATTCTCAAGCGCACTCGATGCCTTCCAAAAAGCAGGTAATACTGTCATTGGCAATGACGTTTGGATCGGCTCTGAGGCAATGGTCATGCCCGGAATCAAGATCGGGCACGGTGCGGTGATAGGCAGCCGCTCGTTGGTGACAAAAGATGTGGAGCCTTACGCTATCGTTGGCGGCAATCCCGCTAAGAAGATTAAGAAACGCTTCACCGATGAGGAAATTTCATTGCTTCTGGAGATGGAGTGGTGGAATTGGTCACTGGAGAAGATCAAAGCGGCAATGCCCATGCTGTGCTCGTCTAATATTGTTGGCCTGCACAAGTATTGGCTCGAGTTTGCCGTCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3002676","ARO_id":"39110","ARO_name":"catB3","CARD_short_name":"catB3","ARO_description":"catB3 is a plasmid or chromosome-encoded variant of the cat gene found in Salmonella typhimurium, Acinetobacter baumannii and Escherichia coli.","ARO_category":{"36261":{"category_aro_accession":"3000122","category_aro_cvterm_id":"36261","category_aro_name":"chloramphenicol acetyltransferase (CAT)","category_aro_description":"Inactivates chloramphenicol by addition of an acyl group. CAT is used to describe many variants of the chloramphenicol acetyltransferase gene in a range of organisms including Acinetobacter calcoaceticus, Agrobacterium tumefaciens, Alkalihalobacillus clausii, Bacillus subtilis, Campylobacter coli, Enterococcus faecalis, Enterococcus faecium, Lactococcus lactis, Listeria monocytogenes, Listonella anguillarum, Morganella morganii, Photobacterium damselae subsp. piscicida, Proteus mirabilis, Salmonella typhi, Serratia marcescens, Shigella flexneri, Staphylococcus aureus, Staphylococcus haemolyticus, Staphylococcus intermedius, Streptococcus agalactiae, Streptococcus suis and Streptomyces acrimycini.","category_aro_class_name":"AMR Gene Family"},"36521":{"category_aro_accession":"3000382","category_aro_cvterm_id":"36521","category_aro_name":"azidamfenicol","category_aro_description":"Azidamfenicol is a water soluble derivative of chloramphenicol, sharing the same mode of action of inhibiting peptide synthesis by interacting with the 23S RNA of the 50S ribosomal subunit.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36595":{"category_aro_accession":"3000456","category_aro_cvterm_id":"36595","category_aro_name":"thiamphenicol","category_aro_description":"Derivative of Chloramphenicol. The nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3).","category_aro_class_name":"Antibiotic"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"151":{"model_id":"151","model_name":"OKP-A-15","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"1200":{"protein_sequence":{"accession":"ACN65419.1","sequence":"MRYVRLCLFSLIAALPLAVFASPPPLEQITRSESQLAGRVGYVEMDLLAAWRASERFPLMSTFKVLLCGAVLARVDAGDEQLDRRIRYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAGNLLLKSVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDVRDTTTPASMAATLRKLLTSHTLSARSQQQLLQWMVDDQVAGPLIRAVLPAGWFIADKTGAGERGSRGIVALLGPNGKAERIVVIYLRDTPATMAERNQQIARIGAALIEHWQR"},"dna_sequence":{"accession":"FJ755841.1","fmin":"0","fmax":"846","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGCCTTTTCTCCCTGATTGCCGCCCTGCCACTGGCGGTATTCGCCAGCCCTCCGCCGCTTGAGCAAATTACACGCAGCGAAAGTCAGCTGGCGGGCCGCGTGGGCTATGTTGAAATGGATCTGCTGGCCGCCTGGCGCGCCAGTGAGCGCTTTCCGCTGATGAGCACCTTTAAAGTGCTGCTCTGCGGCGCGGTGCTGGCCCGGGTGGATGCCGGAGACGAACAGCTGGATCGGCGGATCCGCTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGCCGACGGGATGACCGTTGGCGAACTCTGCGCCGCCGCCATCACCATGAGCGACAACAGCGCCGGCAATCTGCTGTTGAAGAGCGTTGGCGGCCCCGCGGGATTGACCGCTTTTTTGCGCCAGATCGGTGACAACGTCACCCGCCTCGACCGCTGGGAAACGGAGCTCAATGAAGCGCTTCCCGGCGACGTGCGCGACACCACCACCCCAGCCAGCATGGCCGCCACCCTGCGCAAGCTGCTAACCAGCCACACTCTGAGCGCCCGTTCGCAGCAGCAGCTGCTGCAGTGGATGGTGGACGACCAGGTAGCCGGTCCGCTGATCCGCGCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAAACCGGGGCCGGCGAGCGGGGCTCACGTGGCATTGTCGCCCTGCTCGGCCCGAACGGCAAAGCGGAGCGCATCGTGGTGATCTATCTGCGGGATACGCCGGCGACCATGGCCGAGCGTAACCAGCAGATCGCCAGAATAGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002432","ARO_id":"38832","ARO_name":"OKP-A-15","CARD_short_name":"OKP-A-15","ARO_description":"OKP-A-15 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"38817":{"category_aro_accession":"3002417","category_aro_cvterm_id":"38817","category_aro_name":"OKP beta-lactamase","category_aro_description":"OKP beta-lactamases are chromosomal class A beta-lactamase that confer resistance to penicillins and early cephalosporins in Klebsiella pneumoniae. OKP beta-lactamases can be subdivided into two groups: OKP-A and OKP-B which diverge by about 4.2%.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"152":{"model_id":"152","model_name":"cpxA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"890"}},"model_sequences":{"sequence":{"5407":{"protein_sequence":{"accession":"BAB38260.1","sequence":"MIGSLTARIFAIFWLTLALVLMLVLMLPKLDSRQMTELLDSEQRQGLMIEQHVEAELANDPPNDLMWWRRLFRAIDKWAPPGQRLLLVTTEGRVIGAERSEMQIIRNFIGQADNADHPQKKKYGRVELVGPFSVRDGEDNYQLYLIRPASSSQSDFINLLFDRPLLLLIVTMLVSTPLLLWLAWSLAKPARKLKNAADEVAQGNLRQHPELEAGPQEFLAAGASFNQMVTALERMMTSQQRLLSDISHELRTPLTRLQLGTALLRRRSGESKELERIETEAQRLDSMINDLLVMSRNQQKNALVSETIKANQLWSEVLDNAAFEAEQMGKSLTVNFPPGPWPLYGNPNALESALENIVRNALRYSHTKIEVGFAVDKDGITITVDDDGPGVSPEDREQIFRPFYRTDEARDRESGGTGLGLAIVETAIQQHRGWVKAEDSPLGGLRLVIWLPLYKRS"},"dna_sequence":{"accession":"BA000007.3","fmin":"4903688","fmax":"4905062","strand":"-","sequence":"ATGATAGGCAGCTTAACCGCGCGCATCTTCGCCATCTTCTGGCTGACGCTGGCGCTGGTGTTGATGTTGGTTTTGATGTTACCCAAGCTCGATTCACGCCAGATGACCGAGCTTCTGGATAGCGAACAGCGTCAGGGTCTGATGATTGAGCAGCATGTTGAAGCGGAGCTGGCGAACGATCCGCCCAACGATTTAATGTGGTGGCGGCGTCTGTTCCGGGCGATTGATAAGTGGGCACCGCCAGGACAGCGTTTGTTATTGGTGACCACCGAAGGCCGCGTGATCGGCGCTGAACGCAGCGAAATGCAGATCATTCGTAACTTTATTGGTCAGGCCGATAACGCCGATCATCCGCAGAAGAAAAAGTATGGCCGCGTGGAACTGGTCGGTCCGTTCTCCGTGCGTGATGGCGAAGATAATTACCAACTTTATCTGATTCGTCCGGCCAGCAGTTCTCAATCCGATTTCATTAACTTACTGTTTGACCGCCCGCTATTACTGCTGATTGTCACCATGTTGGTCAGTACGCCGCTGCTGTTGTGGTTGGCCTGGAGTCTGGCAAAACCGGCGCGTAAGCTGAAAAACGCTGCCGATGAAGTTGCCCAGGGAAACTTACGCCAGCACCCGGAACTGGAAGCGGGGCCACAGGAATTCCTTGCCGCAGGTGCCAGTTTTAACCAGATGGTCACCGCGCTGGAGCGCATGATGACCTCTCAGCAGCGTCTGCTTTCTGATATCTCTCACGAGCTGCGCACCCCGCTGACGCGTCTGCAACTGGGTACGGCGTTACTGCGCCGTCGTAGTGGTGAAAGCAAGGAACTGGAGCGTATTGAAACCGAAGCGCAACGTCTGGACAGCATGATTAACGACCTGTTGGTGATGTCACGTAATCAGCAAAAAAACGCGCTGGTTAGCGAGACCATCAAAGCCAATCAGTTGTGGAGTGAAGTGCTGGATAACGCGGCGTTCGAAGCCGAGCAAATGGGCAAGTCGTTGACAGTTAACTTCCCGCCTGGGCCGTGGCCGCTGTACGGCAACCCGAACGCCCTGGAGAGTGCGCTGGAAAACATTGTTCGTAATGCCCTGCGTTATTCCCATACGAAGATTGAAGTGGGCTTTGCGGTAGATAAAGACGGTATCACCATTACGGTGGACGACGATGGTCCTGGCGTTAGCCCGGAAGATCGCGAACAGATTTTCCGTCCGTTCTATCGGACCGATGAAGCGCGCGATCGTGAATCTGGCGGTACAGGTTTGGGACTGGCGATTGTTGAAACCGCCATTCAGCAGCATCGTGGCTGGGTGAAAGCAGAAGACAGCCCGCTGGGCGGTTTACGGCTGGTGATTTGGTTGCCGCTGTATAAGCGGAGTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36747","NCBI_taxonomy_name":"Escherichia coli O157:H7 str. Sakai","NCBI_taxonomy_id":"386585"}}}},"ARO_accession":"3000830","ARO_id":"37210","ARO_name":"cpxA","CARD_short_name":"cpxA","ARO_description":"CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR, which promotes efflux complex expression.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36250":{"category_aro_accession":"3000111","category_aro_cvterm_id":"36250","category_aro_name":"novobiocin","category_aro_description":"Novobiocin is an aminocoumarin antibiotic produced by Streptomyces spheroides and Streptomyces niveus, and binds DNA gyrase subunit B inhibiting ATP-dependent DNA supercoiling.","category_aro_class_name":"Antibiotic"},"46133":{"category_aro_accession":"3007382","category_aro_cvterm_id":"46133","category_aro_name":"gentamicin","category_aro_description":"Gentamicin is a commonly used aminoglycoside antibiotic derived from members of the Micromonospora genus of bacteria. It acts by binding the 30S ribosomal subunit, thus inhibiting protein synthesis. Gentamicin is typically used to treat Gram-negative infections of the repiratory and urinary tract, as well as infections of the bone and soft tissue. It also exhibits considerable nephrotoxicity and ototoxicity. Gentamicin is administered as a mixture of gentamicin type C (which makes about around 80% of the complex) and types A, B, and X (distributed in the remaining 20% of the complex).","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36242":{"category_aro_accession":"3000103","category_aro_cvterm_id":"36242","category_aro_name":"aminocoumarin antibiotic","category_aro_description":"Aminocoumarin antibiotics bind DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"153":{"model_id":"153","model_name":"adeF","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"6250":{"protein_sequence":{"accession":"CAJ77856.1","sequence":"MNISKFFIDRPIFAGVLSVLILLAGLLSVFQLPISEYPEVVPPSVVVRAQYPGANPKVIAETVASPLEESINGVEDMLYMQSQANSDGNLTITVNFKLGIDPDKAQQLVQNRVSQAMPRLPEDVQRLGVTTLKSSPTLTMVVHLTSPDNRYDMTYLRNYAVLNVKDRLARLQGVGEVGLFGSGDYAMRVWLDPQKVAQRNLTATEIVNAIREQNIQVAAGTIGASPSNSPLQLSVNAQGRLTTEQEFADIILKTAPDGAVTRLGDVARVELAASQYGLRSLLDNKQAVAIPIFQAPGANALQVSDQVRSTMKELSKDFPSSIKYDIVYDPTQFVRASIKAVVHTLLEAITLVVVVVILFLQTWRASIIPLLAVPVSIIGTFALMLAFGYSINALSLFGMVLAIGIVVDDAIVVVENVERNIEAGLNPREATYRAMREVSGPIIAIALTLVAVFVPLAFMTGLTGQFYKQFAMTIAISTVISAFNSLTLSPALAALLLKGHDAKPDALTRIMNRVFGRFFALFNRVFSRASDRYSQGVSRVISHKASAMGVYAALLGLTVGISYIVPGGFVPAQDKQYLISFAQLPNGASLDRTEAVIRKMSDTALKQPGVESAVAFPGLSINGFTNSSSAGIVFVTLKPFDERKAKDLSANAIAGALNQKYSAIQDAYIAVFPPPPVMGLGTMGGFKLQLEDRGALGYSALNDAAQNFMKAAQSAPELGPMFSSYQINVPQLNVDLDRVKAKQQGVAVTDVFNTMQIYLGSQYVNDFNRFGRVYQVRAQADAPFRANPEDILQLKTRNSAGQMVPLSSLVNVTQTYGPEMVVRYNGYTSADINGGPAPGYSSSQAEAAVERIAAQTLPRGIKFEWTDLTYQKILAGNAGLWVFPISVLLVFLVLAAQYESLTLPLAVILIVPMGILAALTGVWLTAGDNNIFTQIGLMVLVGLACKNAILIVEFARELEMQGATAFKAAVEASRLRLRPILMTSIAFIMGVVPLVTSTGAGSEMRHAMGVAVFFGMIGVTFFGLFLTPAFYVLIRTLNSKHKLHSAAVHEAPLASPHDH"},"dna_sequence":{"accession":"CT025801.2","fmin":"0","fmax":"3180","strand":"+","sequence":"ATGAATATTTCTAAATTTTTTATTGATCGGCCGATCTTTGCTGGTGTGCTATCAGTCTTGATTTTACTCGCCGGTCTCCTTTCGGTATTTCAGTTACCGATTTCTGAATATCCCGAGGTTGTTCCACCATCTGTGGTGGTACGCGCCCAATATCCGGGTGCAAACCCAAAAGTGATTGCTGAAACGGTTGCATCTCCGCTCGAAGAGTCAATCAACGGCGTCGAAGACATGCTGTATATGCAATCTCAAGCAAACAGCGACGGTAACCTAACCATTACGGTGAACTTTAAGCTCGGTATCGACCCAGACAAAGCCCAACAATTGGTTCAAAACCGTGTGTCTCAGGCCATGCCCCGTTTACCTGAAGATGTACAGCGCTTAGGTGTAACCACACTAAAAAGCTCACCTACTTTAACTATGGTAGTGCATCTGACCTCACCAGATAATCGCTATGACATGACCTACTTACGTAACTATGCGGTGCTCAACGTGAAAGACCGTTTAGCGCGTTTACAAGGGGTTGGTGAAGTCGGATTATTTGGTTCTGGTGACTACGCGATGCGTGTATGGCTTGACCCGCAAAAAGTAGCGCAGCGTAACCTCACCGCGACCGAAATTGTGAATGCAATCCGTGAACAAAATATTCAGGTTGCAGCGGGTACAATCGGTGCATCACCAAGTAATTCACCTTTACAGCTTTCAGTCAATGCTCAAGGTCGTTTAACTACTGAACAAGAATTCGCAGATATCATTTTAAAAACTGCACCAGATGGCGCGGTTACCCGATTGGGTGATGTTGCTCGTGTCGAACTTGCAGCCTCTCAATATGGCTTACGTTCATTGCTTGATAATAAACAAGCGGTCGCGATTCCAATTTTCCAAGCACCGGGTGCGAATGCTTTACAAGTTTCCGATCAAGTGCGTAGCACAATGAAGGAGCTTTCAAAAGATTTCCCATCTTCAATTAAATACGACATTGTTTATGACCCGACTCAATTCGTACGTGCAAGTATTAAAGCGGTCGTTCATACCTTACTTGAAGCAATTACACTGGTTGTTGTGGTCGTTATTTTATTCTTGCAAACATGGCGTGCCTCAATCATTCCATTGCTTGCCGTACCGGTTTCAATTATTGGTACATTCGCGCTCATGCTCGCTTTTGGTTACTCAATCAATGCGCTATCACTGTTCGGAATGGTACTTGCCATCGGGATTGTCGTCGATGACGCGATTGTGGTCGTCGAAAATGTCGAGAGGAATATTGAAGCAGGCTTAAACCCAAGGGAGGCGACTTACCGTGCCATGCGAGAAGTCAGTGGACCGATTATTGCCATTGCTTTAACACTTGTTGCAGTATTCGTACCTCTTGCCTTTATGACAGGCTTAACAGGGCAATTCTATAAACAATTTGCCATGACCATTGCCATTTCAACGGTTATTTCGGCATTTAACTCGCTTACCCTATCTCCTGCTTTGGCAGCGCTGTTACTGAAAGGACATGATGCTAAACCGGATGCCTTAACACGTATTATGAATCGTGTATTCGGTCGTTTCTTTGCACTGTTTAACCGTGTGTTTTCACGTGCTTCAGACCGTTATAGTCAAGGCGTCAGCCGTGTCATTTCCCATAAAGCTTCGGCAATGGGTGTCTATGCAGCACTCTTAGGTTTAACCGTTGGTATTTCCTATATTGTTCCAGGTGGTTTCGTTCCTGCGCAGGACAAACAATATTTAATTAGCTTTGCGCAGCTACCAAACGGCGCATCATTAGATCGTACCGAAGCGGTCATTCGTAAAATGAGTGACACTGCACTTAAACAACCTGGTGTAGAAAGTGCAGTTGCCTTTCCTGGCCTATCAATTAACGGTTTCACCAATAGCTCAAGTGCCGGTATTGTCTTTGTGACTTTAAAGCCATTTGATGAACGTAAGGCAAAAGACTTATCTGCAAATGCAATTGCAGGTGCGCTCAACCAGAAATATTCAGCTATTCAAGATGCCTATATCGCGGTTTTCCCACCGCCACCAGTGATGGGCTTAGGTACTATGGGCGGCTTTAAACTACAACTTGAAGACCGAGGTGCCTTAGGCTATTCAGCCTTGAACGATGCTGCACAAAACTTTATGAAGGCAGCACAATCAGCCCCTGAACTGGGTCCAATGTTCTCAAGTTATCAAATTAACGTACCTCAACTCAACGTAGATCTGGACCGTGTAAAAGCTAAACAGCAAGGCGTTGCTGTGACAGATGTTTTCAATACTATGCAGATTTATTTAGGTTCTCAGTACGTTAACGACTTTAACCGCTTTGGACGTGTTTATCAGGTTCGTGCACAAGCCGATGCGCCTTTCCGTGCTAACCCTGAAGATATTTTGCAGCTTAAAACCCGTAATAGTGCCGGACAAATGGTGCCATTATCTTCATTGGTGAATGTAACTCAAACCTATGGTCCTGAAATGGTCGTTCGTTATAACGGTTACACATCAGCAGATATTAACGGTGGCCCTGCCCCAGGTTATTCATCTAGCCAAGCAGAAGCTGCGGTTGAACGTATTGCTGCACAAACTCTACCGCGTGGTATCAAGTTTGAATGGACAGATTTAACTTATCAAAAAATCTTGGCTGGTAATGCTGGACTTTGGGTATTCCCTATTAGCGTATTACTCGTGTTCTTAGTGTTAGCTGCTCAGTATGAAAGCTTAACCCTACCATTAGCAGTTATCTTAATTGTACCAATGGGAATCTTAGCGGCTCTGACAGGTGTCTGGTTGACAGCTGGAGATAACAACATCTTTACTCAAATCGGTCTAATGGTACTGGTCGGGCTAGCCTGTAAAAATGCCATCTTAATTGTCGAATTTGCGAGGGAACTTGAAATGCAAGGTGCGACTGCCTTTAAAGCAGCCGTTGAAGCAAGTCGTCTACGTTTACGCCCAATTTTAATGACCTCTATTGCATTTATTATGGGTGTAGTGCCACTGGTTACTTCAACTGGCGCAGGTTCTGAAATGCGACATGCGATGGGTGTTGCCGTATTCTTCGGTATGATCGGTGTAACATTCTTTGGTTTATTCCTCACCCCGGCCTTTTACGTTCTGATTCGTACCCTCAACAGCAAACATAAACTGCATTCTGCGGCAGTTCATGAAGCGCCGTTAGCTAGCCCACATGATCATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35535","NCBI_taxonomy_name":"Acinetobacter baumannii AYE","NCBI_taxonomy_id":"509173"}}}},"ARO_accession":"3000777","ARO_id":"37157","ARO_name":"adeF","CARD_short_name":"adeF","ARO_description":"AdeF is the membrane fusion protein of the multidrug efflux complex AdeFGH.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"154":{"model_id":"154","model_name":"mgrA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"270"}},"model_sequences":{"sequence":{"5404":{"protein_sequence":{"accession":"BAB41874.1","sequence":"MSDQHNLKEQLCFSLYNAQRQVNRYYSNKVFKKYNLTYPQFLVLTILWDESPVNVKKVVTELALDTGTVSPLLKRMEQVDLIKRERSEVDQREVFIHLTDKSETIRPELSNASDKVASASSLSQDEVKELNRLLGKVIHAFDETKEK"},"dna_sequence":{"accession":"BA000018.3","fmin":"735416","fmax":"735860","strand":"-","sequence":"ATGTCTGATCAACATAATTTAAAAGAACAGCTATGCTTTAGTTTGTACAATGCTCAAAGACAAGTTAATCGCTACTACTCTAACAAAGTTTTTAAGAAGTACAATCTAACATACCCACAATTTCTTGTCTTAACAATTTTATGGGATGAATCTCCTGTAAACGTCAAGAAAGTCGTAACTGAATTAGCACTCGATACTGGTACAGTATCACCATTATTAAAACGAATGGAACAAGTAGACTTAATTAAGCGTGAACGTTCCGAAGTCGATCAACGTGAAGTATTTATTCACTTGACTGACAAAAGTGAAACTATTAGACCAGAATTAAGTAATGCATCTGACAAAGTCGCTTCAGCTTCTTCTTTATCTCAAGATGAAGTTAAAGAACTTAATCGCTTATTAGGTAAAGTCATTCATGCATTTGATGAAACAAAGGAAAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35514","NCBI_taxonomy_name":"Staphylococcus aureus subsp. aureus N315","NCBI_taxonomy_id":"158879"}}}},"ARO_accession":"3000815","ARO_id":"37195","ARO_name":"mgrA","CARD_short_name":"mgrA","ARO_description":"MgrA, also known as NorR, is a regulator for norA, norB, and tet38. It is a positive regulator for norA expression, but is a direct repressor for norB and an indirect repressor of tet38.","ARO_category":{"36002":{"category_aro_accession":"0010001","category_aro_cvterm_id":"36002","category_aro_name":"ATP-binding cassette (ABC) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding\/hydrolysis to transport substrates across cell membranes.","category_aro_class_name":"AMR Gene Family"},"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35934":{"category_aro_accession":"0000015","category_aro_cvterm_id":"35934","category_aro_name":"methicillin","category_aro_description":"Derived from penicillin to combat penicillin-resistance, methicillin is insensitive to beta-lactamases (also known as penicillinases) secreted by many penicillin-resistant bacteria. Methicillin is bactericidal, and acts by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35963":{"category_aro_accession":"0000045","category_aro_cvterm_id":"35963","category_aro_name":"acriflavine","category_aro_description":"Acriflavine is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35985":{"category_aro_accession":"0000068","category_aro_cvterm_id":"35985","category_aro_name":"daptomycin","category_aro_description":"Daptomycin is a novel lipopeptide antibiotic used in the treatment of certain infections caused by Gram-positive organisms. Daptomycin interferes with the bacterial cell membrane, reducing membrane potential and inhibiting cell wall synthesis.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"36989":{"category_aro_accession":"3000645","category_aro_cvterm_id":"36989","category_aro_name":"cefotaxime","category_aro_description":"Cefotaxime is a semisynthetic cephalosporin taken parenterally. It is resistant to most beta-lactamases and active against Gram-negative rods and cocci due to its aminothiazoyl and methoximino functional groups.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"37041":{"category_aro_accession":"3000697","category_aro_cvterm_id":"37041","category_aro_name":"moenomycin A1","category_aro_description":"Moenomycin A1 is a major component of moenomycin mixtures. It is produced by Streptomyces ghanaensis, S. bambergiensis, S. ederensis, and S. geysiriensis.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"37031":{"category_aro_accession":"3000687","category_aro_cvterm_id":"37031","category_aro_name":"moenomycin antibiotic","category_aro_description":"Moemomycin antibiotics are phosphoglycolipids that contain a 3-phosphoglyceric acid, often used as a mixture. They inhibit petidoglycan glycosyltransferases to prevent bacterial cell wall biosynthesis.","category_aro_class_name":"Drug Class"},"43746":{"category_aro_accession":"3005386","category_aro_cvterm_id":"43746","category_aro_name":"disinfecting agents and antiseptics","category_aro_description":"Disinfectants that can also interact with antimicrobial resistance mechanisms, e.g. molecule efflux, and thus are the targets of disinfectant resistance.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"155":{"model_id":"155","model_name":"TEM-195","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1402":{"protein_sequence":{"accession":"AFC75525.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSRNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDCWEPELNEAIPHDERDTTMPAAVATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"JN935137.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCGGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTCACCGCTTTTTTGCACAACATGGGGGATCATGTCACCCGCCTTGATTGTTGGGAACCGGAGCTGAATGAAGCCATACCACACGACGAGCGTGACACCACGATGCCTGCTGCAGTGGCCACCACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001055","ARO_id":"37435","ARO_name":"TEM-195","CARD_short_name":"TEM-195","ARO_description":"TEM-195 is a beta-lactamase.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"156":{"model_id":"156","model_name":"AAC(6')-Iaf","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"672":{"protein_sequence":{"accession":"BAH66386.1","sequence":"MDYSICDIAESNELILEAAKILKKSFLDVGNESWGDIKKAIEEVEECIEHPNICLGICLDDKLIGWTGLRPMYDKTWELHPMVIKTEYQGKDFGKVLLRELETRAKGRGIIGIALGTDDEYQKTSLSMIDINERNIFDEIENIKNINNHPYEFYKKCGYMIVGIIPNANGKRKPDIWMWKDIS"},"dna_sequence":{"accession":"AB462903.1","fmin":"1199","fmax":"1751","strand":"+","sequence":"TTGGACTATTCAATATGCGATATAGCTGAATCAAATGAATTAATCCTTGAAGCAGCAAAGATTCTTAAGAAAAGCTTTCTTGATGTTGGAAATGAATCATGGGGAGATATTAAAAAAGCTATTGAAGAAGTTGAAGAATGTATAGAACATCCAAATATATGCTTGGGAATATGTCTGGATGATAAACTGATTGGCTGGACCGGATTAAGGCCGATGTACGATAAGACCTGGGAACTTCATCCCATGGTTATAAAAACTGAATATCAAGGCAAGGATTTTGGGAAAGTACTACTAAGAGAACTAGAGACGAGAGCGAAGGGTAGGGGAATTATCGGAATAGCTCTTGGAACTGATGATGAATATCAGAAAACTAGTTTGTCTATGATTGATATAAACGAACGAAATATCTTCGATGAAATCGAGAATATAAAGAACATTAATAATCATCCATATGAGTTTTATAAGAAATGTGGTTATATGATCGTTGGAATAATCCCTAATGCTAATGGAAAAAGGAAACCAGATATATGGATGTGGAAAGATATTAGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002574","ARO_id":"38974","ARO_name":"AAC(6')-Iaf","CARD_short_name":"AAC(6')-Iaf","ARO_description":"AAC(6')-Iaf is an aminoglycoside acetyltransferase encoded by plasmids and integrons in P. aeruginosa.","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"A category of aminoglycoside N-acetyltransferase enzymes with modification regiospecificity based at the 6'-amino group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics through acetylation of the 6-amino group of the compound.","category_aro_class_name":"AMR Gene Family"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"46128":{"category_aro_accession":"3007378","category_aro_cvterm_id":"46128","category_aro_name":"2'-N-ethylnetilmicin","category_aro_description":"2'-N-ethylnetilmicin is an aminoglycoside antibiotic and a derivative of netilmicin.","category_aro_class_name":"Antibiotic"},"46129":{"category_aro_accession":"3007379","category_aro_cvterm_id":"46129","category_aro_name":"5-episisomicin","category_aro_description":"5-episosomicin is a semisynthetic aminoglycoside antibiotic similar to sisomicin.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"157":{"model_id":"157","model_name":"dfrA21","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"383":{"protein_sequence":{"accession":"CAP69659.1","sequence":"MNPESVRIYLVAAMGANRVIGNGPDIPWKIPGEQKIFRRLTESKVVVMGRKTFESIGKPLPNRHTVVLSRQARYSAPGCAVVSTLSQAIAIAAEHGKELYVAGGAEVYALALPHANGVFLSEVHQTFEGDAFFPVLNAAEFEVVSSETIQGTITYTHSVYARRNG"},"dna_sequence":{"accession":"AM932669.1","fmin":"105","fmax":"603","strand":"+","sequence":"ATGAACCCGGAATCGGTCCGCATTTATCTGGTCGCTGCCATGGGTGCCAATCGGGTTATTGGCAATGGTCCCGATATCCCCTGGAAAATCCCAGGTGAGCAGAAGATTTTTCGCAGGCTCACCGAGAGCAAAGTGGTCGTTATGGGCCGCAAGACATTTGAGTCCATAGGCAAGCCCTTACCAAACCGCCACACAGTGGTGCTCTCGCGCCAAGCTCGTTATAGCGCTCCTGGTTGTGCAGTTGTTTCAACGCTGTCACAGGCTATCGCCATCGCAGCCGAACACGGCAAAGAACTCTACGTAGCCGGCGGAGCCGAGGTATATGCGCTGGCGCTACCGCATGCCAACGGCGTCTTTCTATCTGAGGTACATCAAACCTTTGAGGGTGACGCCTTCTTCCCAGTGCTTAACGCAGCAGAATTCGAGGTTGTCTCATCCGAAACCATTCAAGGCACAATCACGTACACGCACTCCGTCTATGCGCGTCGTAACGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35739","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Bredeney","NCBI_taxonomy_id":"134047"}}}},"ARO_accession":"3003017","ARO_id":"39451","ARO_name":"dfrA21","CARD_short_name":"dfrA21","ARO_description":"dfrA21 is an integron-encoded dihydrofolate reductase found in Salmonella enterica.","ARO_category":{"37617":{"category_aro_accession":"3001218","category_aro_cvterm_id":"37617","category_aro_name":"trimethoprim resistant dihydrofolate reductase dfr","category_aro_description":"Alternative dihydropteroate synthase dfr present on plasmids produces alternate proteins that are less sensitive to trimethoprim from inhibiting its role in folate synthesis, thus conferring trimethoprim resistance.","category_aro_class_name":"AMR Gene Family"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"158":{"model_id":"158","model_name":"myrA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"204":{"protein_sequence":{"accession":"BAA03674.1","sequence":"MHPDLLPHLRCPVCGQPLHQADAAPPRALRCPAGHSFDIARQGYVNLLTGRAPHVGDTAEMIAAREEFLAAGHYDPFSAALATAAARAVPRRVRPGDGVGEPVAYPDLVVDAGAGTGRHLAAVLDAVPTAVGLALDVSKPALRRAARAHPRAGAAVCDTWGRLPLADATVAVLVNVFAPRNGPEFRRVLRPDGALLVVTPTAEHLVELVDRLGLLRVDPAKDARVADSLTRHFEPAGQSTHRHRLQLTRKEVLTLVGMGPSAWHTDPARLTARVAALSEPVTVTAAVRLARYRPI"},"dna_sequence":{"accession":"D16099.1","fmin":"409","fmax":"1297","strand":"+","sequence":"GTGCACCCCGACCTGCTCCCCCACCTCCGCTGCCCGGTCTGCGGCCAGCCGCTGCACCAGGCCGACGCGGCACCACCACGCGCCCTGCGCTGCCCGGCCGGGCACAGCTTCGACATCGCCCGACAGGGTTACGTCAACCTGCTCACGGGCCGGGCACCGCACGTCGGCGACACCGCCGAGATGATCGCCGCCAGGGAGGAGTTTCTGGCCGCCGGGCACTACGACCCGTTCTCGGCGGCACTCGCCACCGCGGCCGCGCGGGCGGTGCCACGTCGTGTCCGGCCCGGCGACGGCGTGGGCGAACCGGTGGCGTACCCGGATCTGGTGGTGGACGCCGGAGCCGGTACCGGCCGGCACCTCGCCGCAGTGCTCGACGCGGTGCCGACCGCCGTCGGCCTGGCGCTGGACGTCTCGAAGCCCGCACTACGCCGGGCGGCCCGGGCGCATCCCCGGGCCGGCGCGGCCGTCTGCGACACCTGGGGCCGGTTGCCGCTGGCCGATGCCACGGTCGCAGTACTGGTCAACGTCTTCGCCCCGCGCAACGGGCCGGAATTCCGTCGGGTGCTCCGGCCGGACGGCGCCCTGCTCGTGGTGACACCGACCGCCGAACACCTGGTCGAGCTGGTGGACCGGCTGGGGCTGCTGCGGGTCGACCCGGCCAAGGACGCCCGGGTGGCCGACAGCCTCACGAGACACTTCGAACCGGCCGGGCAGAGCACCCACCGGCACCGGCTTCAGCTGACCCGGAAGGAGGTGCTGACCCTGGTTGGTATGGGGCCGAGCGCCTGGCACACCGACCCGGCCCGGCTCACCGCGCGGGTCGCAGCCCTGTCCGAGCCGGTCACGGTCACCGCCGCTGTCCGGCTCGCCCGTTACCGCCCGATCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39571","NCBI_taxonomy_name":"Micromonospora griseorubida","NCBI_taxonomy_id":"28040"}}}},"ARO_accession":"3001300","ARO_id":"37699","ARO_name":"myrA","CARD_short_name":"myrA","ARO_description":"myrA is a methyltransferase found in Micromonospora griseorubida and confers resistance to mycinamicin and tylosin. Specifically, this enzyme adds a methyl group to guanosine 748 (E. coli numbering) of 23S ribosomal RNA. MyrA is found in the mycinamicin biosynthetic cluster and is one mechanism by which M. griseorubida protects itself from self-destruction when producing this macrolide.","ARO_category":{"37697":{"category_aro_accession":"3001298","category_aro_cvterm_id":"37697","category_aro_name":"non-erm 23S ribosomal RNA methyltransferase (G748)","category_aro_description":"Non-erm 23S ribosomal RNA methyltransferases modify guanosine 748 (E. coli numbering) to confer resistance to some macrolides and lincosamides.","category_aro_class_name":"AMR Gene Family"},"36284":{"category_aro_accession":"3000145","category_aro_cvterm_id":"36284","category_aro_name":"tylosin","category_aro_description":"Tylosin is a 16-membered macrolide, naturally produced by Streptomyces fradiae. It interacts with the bacterial ribosome 50S subunit to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"37623":{"category_aro_accession":"3001224","category_aro_cvterm_id":"37623","category_aro_name":"mycinamicin","category_aro_description":"Produced by Micromonospora\u00a0griseorubida.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"159":{"model_id":"159","model_name":"vgaALC","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1050"}},"model_sequences":{"sequence":{"412":{"protein_sequence":{"accession":"ABH10964.1","sequence":"MKILLEGLHIKHYVQDRLLLNINRLKIYQNDRIGLIGKNGSGKTTLLHILYKKIVPEEGIVKQFSHCELIPQLKLIESTKSGGEVTRNYIRQALDKNPELLLADEPTTNLDNNYIEKLEQDLKNWHGAFIIVSHDRAFLDNLCTTIWEIDEGRITEYKGNYSNYVEQKELERHREELEYEKYEKEKKRLEKAINIKEQKAQRATKKPKNLSSSEGKIKVTKPYFASKQKKLRKTVKSLETRLEKLERVEKRNELPPLKMDLVNLESVKNRTIIRGEDVSGTIEGRVLWKAKSFSIRGGDKMAIIGSNGTGKTTFIKKIVHGNPGISLSPSVKIGYFSQKIDTLELDKSILENVQSSSQQNETLIRTILARMHFFRDDVYKPISVLSGGERVKVALTKVFLSEVNTLVLDEPTNFLDMEAIEAFESLLKEYNGSIIFVSHDRKFIEKVATRIMTIDNKEIKIFDGTYEQFKQAEKPTRNIKEDKKLLLETKITEVLSRLSIEPSEELEQEFQNLINEKRNLDK"},"dna_sequence":{"accession":"DQ823382.1","fmin":"0","fmax":"1569","strand":"+","sequence":"ATGAAAATACTGTTAGAGGGACTTCATATAAAACATTATGTTCAAGATCGTTTATTGTTGAACATAAATCGCCTAAAGATTTATCAGAATGATCGTATTGGTTTAATTGGTAAAAATGGAAGTGGAAAAACAACGTTACTTCACATATTATATAAAAAAATTGTGCCTGAAGAAGGTATTGTAAAACAATTTTCACATTGTGAACTTATTCCTCAATTGAAGCTCATAGAATCAACTAAAAGTGGTGGTGAAGTAACACGAAACTATATTCGGCAAGCGCTTGATAAAAATCCAGAACTGCTATTAGCAGATGAACCAACAACTAACTTAGATAATAACTATATAGAAAAATTAGAACAGGATTTAAAAAATTGGCATGGAGCATTTATTATAGTTTCACATGATCGCGCTTTTTTAGATAACTTATGTACTACTATATGGGAAATTGACGAGGGGAGAATAACTGAATATAAGGGGAATTATAGTAACTATGTTGAACAAAAAGAATTAGAAAGACATCGAGAAGAATTAGAATATGAAAAATATGAAAAAGAAAAGAAACGATTGGAAAAAGCTATAAATATAAAAGAACAGAAAGCTCAACGAGCAACTAAAAAACCGAAAAACTTAAGTTCATCTGAAGGCAAAATAAAAGTAACAAAGCCATACTTTGCAAGTAAGCAAAAGAAGTTACGAAAAACTGTAAAATCTCTAGAAACCAGACTAGAAAAACTTGAAAGGGTCGAAAAGAGAAACGAACTTCCTCCACTTAAAATGGATTTAGTGAACTTAGAAAGTGTAAAAAATAGAACTATAATACGTGGTGAAGATGTCTCGGGTACAATTGAAGGACGGGTATTGTGGAAAGCAAAAAGTTTTAGTATTCGCGGAGGAGACAAGATGGCAATTATCGGATCTAATGGTACAGGAAAGACAACGTTTATTAAAAAAATTGTGCATGGGAATCCTGGTATTTCATTATCGCCATCTGTCAAAATCGGTTATTTTAGCCAAAAAATAGATACATTAGAATTAGATAAGAGTATTTTAGAAAATGTTCAATCTTCTTCACAACAAAATGAAACTCTTATTCGAACTATTCTAGCTAGAATGCATTTTTTTAGAGATGATGTTTATAAACCAATAAGTGTCTTAAGTGGTGGAGAGCGAGTTAAAGTAGCACTAACTAAAGTATTCTTAAGTGAAGTTAATACGTTGGTACTAGATGAACCAACAAACTTTCTTGATATGGAAGCTATAGAGGCGTTTGAATCTTTGTTAAAGGAATATAATGGCAGTATAATCTTTGTATCTCACGATCGTAAATTTATCGAAAAAGTAGCCACTCGAATAATGACAATTGATAATAAAGAAATAAAAATATTTGATGGCACATATGAACAATTTAAACAAGCTGAAAAGCCAACAAGGAATATTAAAGAAGATAAAAAACTTTTACTTGAGACAAAAATTACAGAAGTACTCAGTCGATTGAGTATTGAACCTTCGGAAGAATTAGAACAAGAGTTTCAAAACTTAATAAATGAAAAAAGAAATTTAGATAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36827","NCBI_taxonomy_name":"Staphylococcus haemolyticus","NCBI_taxonomy_id":"1283"}}}},"ARO_accession":"3002830","ARO_id":"39264","ARO_name":"vgaALC","CARD_short_name":"vgaALC","ARO_description":"vgaALC is an ABC-F subfamily protein expressed in staphylococci that confers resistance to streptogramin A antibiotics and related compounds. It is associated with plasmid DNA.","ARO_category":{"36252":{"category_aro_accession":"3000113","category_aro_cvterm_id":"36252","category_aro_name":"vga-type ABC-F protein","category_aro_description":"Vga-type plasmid-borne ABC-F proteins, expressed in staphylococci that confer resistance to streptogramin A antibiotics through ribosomal protection.","category_aro_class_name":"AMR Gene Family"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"virginiamycin M1","category_aro_description":"Virginiamycin M1 is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35952":{"category_aro_accession":"0000034","category_aro_cvterm_id":"35952","category_aro_name":"streptogramin A antibiotic","category_aro_description":"Streptogramin A antibiotics are cyclic polyketide peptide hybrids that bind to the ribosomal peptidyl transfer centre. Structural variation arises from substituting a proline for its desaturated derivative and by its substitution for Ala or Cys. Used alone, streptogramin A antibiotics are bacteriostatic, but is bactericidal when used with streptogramin B antibiotics.","category_aro_class_name":"Drug Class"},"37014":{"category_aro_accession":"3000670","category_aro_cvterm_id":"37014","category_aro_name":"pleuromutilin antibiotic","category_aro_description":"Pleuromutilins are natural fungal products that target bacterial protein translation by binding the the 23S rRNA, blocking the ribosome P site at the 50S subunit. They are mostly used for agriculture and veterinary purposes.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"160":{"model_id":"160","model_name":"OXA-236","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1374":{"protein_sequence":{"accession":"AFH36332.1","sequence":"MKTLILLPLLSCLSLTACSLPVSNSSSQITSTQSIQTIAKLFDQAQSSGVLVIQRGPHLQVYGNDLSRAHTEYIPASTFKILNALIGLQHGKATTNEIFKWDGKKRSFAAWEKDMTLGQAMQASAVPVYQELARRIGLELMQQEVQRIRFGNQQIGQHIDNFWLVGPLKITPVQEVEFASALAQEQLAFDPQVQQQVKAMLLLQERQDYRLYAKSGWGMDVEPQVGWLTGWIETPQDEIVAFSLNMQMQSNMDPAIRLKILQQALAELALYPKAEG"},"dna_sequence":{"accession":"JQ820242.1","fmin":"0","fmax":"831","strand":"+","sequence":"ATGAAAACTCTTATTTTGTTGCCTTTACTTAGTTGCTTGAGCCTGACAGCCTGTAGCTTGCCTGTTTCAAATTCGTCCTCTCAAATCACTTCAACTCAATCTATTCAAACCATTGCCAAATTATTTGATCAGGCACAAAGCTCTGGCGTTTTAGTAATTCAACGGGGCCCACATCTACAGGTCTATGGCAATGATTTGAGTCGTGCACATACCGAATATATTCCTGCTTCAACCTTTAAAATACTCAATGCCCTGATTGGCCTGCAACATGGTAAAGCCACGACCAATGAAATCTTTAAATGGGATGGCAAGAAGCGCAGTTTTGCAGCCTGGGAAAAAGACATGACTCTCGGCCAAGCCATGCAAGCTTCTGCTGTACCCGTCTATCAGGAACTGGCACGTCGCATTGGTCTGGAACTAATGCAACAGGAAGTGCAACGCATTCGATTTGGTAATCAGCAGATTGGTCAGCATATCGACAACTTCTGGTTAGTCGGACCTTTGAAAATCACCCCGGTACAAGAAGTCGAATTTGCCTCTGCGCTTGCTCAAGAGCAACTTGCCTTTGATCCTCAAGTCCAGCAACAAGTCAAAGCCATGTTACTGTTACAGGAGCGACAAGATTATCGACTATATGCCAAATCTGGTTGGGGTATGGATGTGGAGCCGCAAGTCGGCTGGCTCACCGGCTGGATCGAAACACCTCAGGACGAAATCGTGGCATTTTCACTGAATATGCAGATGCAAAGTAATATGGATCCGGCGATCCGTCTTAAAATTTTGCAGCAGGCCTTGGCCGAATTAGCGCTTTATCCGAAAGCTGAAGGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001677","ARO_id":"38077","ARO_name":"OXA-236","CARD_short_name":"OXA-236","ARO_description":"OXA-236 is a beta-lactamase found in A. baumannii.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46489":{"category_aro_accession":"3007700","category_aro_cvterm_id":"46489","category_aro_name":"OXA-134-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-134.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"161":{"model_id":"161","model_name":"SHV-56","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1639":{"protein_sequence":{"accession":"ACB73258.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADRTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"EU586041.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAGGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATCGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001112","ARO_id":"37492","ARO_name":"SHV-56","CARD_short_name":"SHV-56","ARO_description":"SHV-56 is an inhibitor-resistant beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"162":{"model_id":"162","model_name":"KPC-8","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1870":{"protein_sequence":{"accession":"ACI95258.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGGYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKYSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"FJ234412.1","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGGGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGTACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002318","ARO_id":"38718","ARO_name":"KPC-8","CARD_short_name":"KPC-8","ARO_description":"KPC-8 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"163":{"model_id":"163","model_name":"OXA-376","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1534":{"protein_sequence":{"accession":"AHL30276.1","sequence":"MNIKTLLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEVHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEYHKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"KF986257.1","fmin":"20","fmax":"845","strand":"+","sequence":"ATGAACATTAAAACACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGTACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGTACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAACGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001562","ARO_id":"37962","ARO_name":"OXA-376","CARD_short_name":"OXA-376","ARO_description":"OXA-376 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"164":{"model_id":"164","model_name":"vanN","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"684":{"protein_sequence":{"accession":"AEP40500.1","sequence":"MKKIALIFGGTSAEYEVSLKSAASVLSVLENLNVEIYRIGIASNGKWYLTFSDNETIANDLWLQDKKLNEITPSFDGRGFYDQAEKVYFKPDVLFPMLHGGTGENGTLQGVFECMQIPYVGCGVASSAICMNKYLLHQFAKSVGVMSTPTQLISSTDEQQVIKNFTELYGFPIFIKPNEAGSSKGISKVHTEAELTKALTEAFQFSQTVILQKAVSGVEIGCAILGNDQLLVGECDEVSLATDFFDYTEKYQMTTAKLTVPAKIPVATSREIKRQAQLLYQLLGCQGLARIDFFLTEAGEILLNEINTMPGFTNHSRFPAMMAATGITYQELISTLITLAEDK"},"dna_sequence":{"accession":"JF802084.1","fmin":"559","fmax":"1591","strand":"+","sequence":"ATGAAAAAAATCGCCTTAATTTTTGGTGGTACTTCAGCAGAATATGAAGTATCCCTCAAATCAGCAGCTAGTGTTTTGTCTGTATTAGAAAATCTAAATGTTGAAATTTACAGAATTGGCATAGCTTCGAACGGAAAATGGTATTTAACCTTTAGTGATAATGAAACTATTGCAAATGACTTATGGTTACAAGATAAAAAATTAAATGAGATCACTCCCTCCTTCGATGGGAGAGGGTTTTATGACCAAGCAGAAAAAGTATATTTTAAACCAGATGTCTTATTTCCGATGCTACACGGTGGCACTGGAGAAAATGGTACATTACAAGGAGTTTTTGAATGTATGCAAATTCCTTATGTTGGTTGCGGCGTTGCCTCCTCTGCCATTTGTATGAATAAATATCTATTACATCAGTTTGCAAAAAGTGTCGGAGTGATGAGTACGCCTACACAGCTGATCTCATCGACGGACGAACAACAAGTAATCAAAAATTTTACTGAGTTGTACGGTTTTCCTATATTTATCAAACCAAATGAAGCTGGTTCTTCAAAGGGAATCAGCAAAGTTCATACCGAAGCAGAGTTAACTAAAGCGCTGACCGAAGCGTTCCAATTCAGTCAGACAGTCATTTTACAAAAAGCTGTTTCTGGAGTAGAGATCGGTTGCGCCATCCTAGGAAATGATCAATTGCTTGTTGGGGAATGTGATGAAGTATCCTTAGCGACCGACTTTTTTGATTATACGGAAAAATATCAAATGACTACAGCAAAGTTGACCGTTCCAGCAAAAATTCCAGTGGCAACTAGTAGAGAAATCAAGCGTCAAGCACAATTACTGTATCAATTACTTGGATGTCAGGGCTTAGCTCGCATTGATTTTTTTCTAACAGAAGCAGGTGAAATTCTCTTAAATGAAATCAATACAATGCCAGGCTTTACCAATCATTCTAGATTTCCAGCCATGATGGCAGCTACGGGTATCACTTATCAGGAGCTTATTTCAACATTAATTACTTTAGCGGAGGATAAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36779","NCBI_taxonomy_name":"Enterococcus faecium","NCBI_taxonomy_id":"1352"}}}},"ARO_accession":"3002912","ARO_id":"39346","ARO_name":"vanN","CARD_short_name":"vanN","ARO_description":"VanN is a D-Ala-D-Ala ligase homolog that can synthesize D-Ala-D-Ser, an alternative substrate for peptidoglycan synthesis that reduces vancomycin binding affinity in Enterococcus faecium.","ARO_category":{"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"39340":{"category_aro_accession":"3002906","category_aro_cvterm_id":"39340","category_aro_name":"Van ligase","category_aro_description":"Van ligases synthesize alternative substrates for peptidoglycan synthesis that reduce vancomycin binding affinity.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"165":{"model_id":"165","model_name":"VIM-29","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"935":{"protein_sequence":{"accession":"AFP99885.1","sequence":"MLKVISSLLVYMTASVMAVASPLAHSGEPSGEYPTVNEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEAEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSAKVLYGGCAVHELSSTSAGNVADADLAEWPTSVERIQKRYPEAEVVIPGHGLPGGLDLLQHTANVVKAHKNRSVAE"},"dna_sequence":{"accession":"JX311308.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGTTAAAAGTTATTAGTAGTTTATTGGTCTACATGACCGCGTCTGTCATGGCTGTCGCAAGTCCGTTAGCCCATTCCGGGGAGCCGAGTGGTGAGTATCCGACAGTCAACGAAATTCCGGTCGGAGAGGTCCGACTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCGGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAAAAGCAAATTGGACTTCCCGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGCAGAGGGGAACGAGATTCCCACGCATTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAGCTCTTCTATCCTGGTGCTGCGCATTCGACCGACAATCTGGTTGTATACGTCCCGTCAGCGAAAGTGCTATACGGTGGTTGTGCCGTTCATGAGTTGTCAAGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCGTTGAGCGGATTCAAAAACGCTACCCGGAAGCAGAGGTCGTCATTCCCGGGCACGGTCTACCGGGCGGTCTAGACTTGCTCCAGCACACAGCGAACGTTGTCAAAGCACACAAAAATCGCTCAGTCGCCGAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002299","ARO_id":"38699","ARO_name":"VIM-29","CARD_short_name":"VIM-29","ARO_description":"VIM-29 is a beta-lactamase found in the Enterobacteriaceae family.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"43":{"model_id":"43","model_name":"tet(42)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"734":{"protein_sequence":{"accession":"ACD35503.1","sequence":"MTSPTSLTRRDQNRAWIMLIVLTMLTVIGMTVVLPVLPFVVLQYVSHESDLAIWVGVLEAINGLCAFLVAPFLGRLSDRFGRRPVIIVAAFGAAFSMALFGFGGALWVLVLARVIQGLTAGDLPALFAYLADITPPEQRAKRFGLLGALSGIGTMIGPAIGGLLAAISIQLPVFLTAAVALTIAILSIFLLPESLKPGNRITAIKLRDVQPFAVFKEAFGRKELRGLMIGFGLLALPFGFFVNNFSVLALDSIQWGPTQIGLLTAAVGIIDILIQGVLLGILLPRIGERGVIVSGIVAQMIGLAALAVVASVFAQPWVFIVGALMLAAGQGASQAAMDGAMSNAVGDDEQGWLGGATQSLNAAMGTAAPLIAGALYALVSHAAPYWLGVALMIVAVTVVSRAHIANTAKRPAGETTGDAPAALVETAG"},"dna_sequence":{"accession":"EU523697.1","fmin":"686","fmax":"1973","strand":"+","sequence":"ATGACTTCACCCACCTCTCTCACGCGACGGGACCAGAACCGCGCGTGGATCATGCTCATCGTGCTCACGATGCTCACCGTCATCGGAATGACGGTCGTCCTCCCGGTCCTGCCCTTCGTCGTGCTCCAGTACGTCTCGCACGAGAGCGACCTGGCCATCTGGGTCGGCGTGCTCGAAGCGATCAACGGCCTCTGCGCCTTCCTGGTCGCGCCCTTCCTCGGACGTCTCTCAGACCGCTTCGGACGTCGACCCGTGATCATCGTCGCGGCATTCGGTGCGGCCTTCTCGATGGCGCTGTTCGGATTCGGCGGCGCCCTCTGGGTGCTCGTGCTCGCTCGCGTCATCCAGGGCCTCACCGCGGGCGATCTACCCGCCCTCTTCGCCTACCTGGCCGACATCACCCCGCCGGAGCAGCGCGCCAAGCGCTTCGGCCTCCTCGGTGCGCTCTCGGGGATCGGCACCATGATCGGTCCAGCCATCGGAGGACTGCTCGCCGCGATCAGCATCCAGCTCCCGGTGTTCCTGACCGCCGCCGTCGCCCTCACGATCGCGATCCTCAGCATCTTCCTCCTCCCGGAGAGCCTGAAGCCGGGCAACAGGATCACCGCGATCAAGCTGCGCGACGTGCAGCCCTTCGCCGTCTTCAAGGAGGCCTTCGGACGCAAGGAGCTGCGCGGGCTGATGATCGGCTTCGGCCTGCTCGCGCTGCCGTTCGGCTTCTTCGTGAACAACTTCAGCGTGCTCGCCCTGGACTCCATCCAGTGGGGACCGACCCAGATCGGACTCCTGACCGCGGCCGTCGGCATCATCGACATCCTCATCCAGGGCGTGCTGCTGGGCATCCTGCTTCCGCGCATCGGCGAGCGCGGAGTGATCGTGAGCGGCATCGTCGCGCAGATGATCGGTCTCGCGGCCCTCGCCGTCGTGGCTTCCGTCTTCGCGCAGCCGTGGGTGTTCATCGTCGGCGCCCTGATGCTGGCCGCCGGCCAGGGGGCGTCCCAGGCCGCGATGGACGGGGCGATGTCCAACGCCGTCGGCGACGACGAGCAGGGCTGGCTCGGCGGAGCCACCCAGTCGTTGAATGCGGCGATGGGCACGGCAGCCCCGCTCATCGCCGGTGCGCTCTACGCACTGGTCAGCCACGCGGCCCCGTACTGGCTCGGGGTCGCGCTCATGATCGTGGCGGTGACCGTCGTCAGCCGCGCGCACATCGCGAACACCGCGAAGCGCCCGGCCGGCGAGACGACGGGCGACGCTCCCGCGGCACTCGTGGAGACGGCTGGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37079","NCBI_taxonomy_name":"Micrococcus sp. SMCC G887","NCBI_taxonomy_id":"526920"}}}},"ARO_accession":"3000572","ARO_id":"36711","ARO_name":"tet(42)","CARD_short_name":"tet(42)","ARO_description":"Tet42 is a tetracycline efflux pump found in both Gram-negative (Pseudomonas) and Gram-positive (Microbacterium, Bacillus, Staphylococcus, Paenibacillus) bacteria.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"17":{"model_id":"17","model_name":"tet(45)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"5590":{"protein_sequence":{"accession":"AEM62948.1","sequence":"MNTPHSHSNLRHNQILLWLCVLSFFSVLNEMVLNVSLPDIASDFNKEPASINWVNSSFILTFSIGTAVYGKLSDQLGIKKLLLFGIIVNCFGSVIGFVGHFFFPVLILARFIQGVGAAAFPALVMVVIARYIPKENRGKAFGIIGSIVTMGEGVGPSVGGVIAEYAHWSYILLLPVVTIITVPFLAKLLKQEEVIKGSFDTKGIIFMSVGIVFFIMFTTCYRVSFLVVSIICFLIFVKNIRKVSNPFINPSLGKNVSFMIGIICGGLIFGTVAGFISMVPYMMKDVYQLSTAAIGSGIIFPGAMSVIVFGYIGGLLVDKKGSLFVLTTGVAFLSISFLVAALFIETTPWLITIILIFVFGGLSFTKTVISTIVSSSLEQKEAGAGMSLLNFTSFLSEGTGIAIVGGLLSIHLLNRKLLPINAEPSTHLYSNLLLLFAGITIISWLVTIKMHKRSRGNI"},"dna_sequence":{"accession":"JF837330.1","fmin":"1966","fmax":"3343","strand":"-","sequence":"GTGAATACACCTCATTCACATTCAAATTTGCGCCATAATCAAATTTTATTATGGCTCTGTGTTCTTTCTTTTTTCAGCGTTTTAAATGAAATGGTTTTGAATGTTTCATTACCTGATATTGCTAGTGATTTTAATAAGGAACCAGCAAGTATAAACTGGGTAAACTCATCGTTCATATTAACTTTTTCTATAGGAACAGCTGTATATGGAAAGCTATCGGACCAGCTAGGAATAAAAAAGCTACTCCTATTTGGGATTATAGTAAATTGCTTCGGATCAGTTATCGGGTTTGTTGGACATTTTTTCTTTCCCGTACTTATTTTGGCTCGGTTTATTCAGGGAGTTGGCGCAGCTGCATTTCCAGCACTTGTGATGGTGGTTATTGCGCGCTATATTCCAAAAGAAAATAGGGGTAAAGCATTTGGTATTATTGGGTCCATTGTAACTATGGGAGAAGGTGTCGGACCATCTGTTGGTGGAGTGATTGCCGAATATGCCCATTGGTCTTATATACTGCTTTTGCCTGTTGTAACGATTATCACTGTTCCATTCCTTGCAAAATTATTGAAACAGGAAGAGGTAATAAAAGGATCTTTTGATACTAAAGGAATAATATTTATGTCCGTAGGCATTGTATTTTTTATAATGTTTACGACATGTTATAGAGTTTCCTTTCTAGTCGTTAGCATAATATGTTTCTTAATATTTGTTAAGAATATTAGGAAAGTGTCTAATCCTTTTATTAATCCTTCGCTAGGAAAAAATGTCTCATTTATGATTGGAATCATTTGTGGAGGACTTATATTTGGAACCGTAGCAGGATTTATTTCTATGGTCCCTTATATGATGAAAGATGTCTATCAATTAAGTACTGCTGCAATTGGAAGTGGGATTATTTTTCCTGGGGCAATGAGTGTTATTGTTTTCGGTTATATTGGGGGATTGCTTGTTGATAAGAAAGGTTCACTATTTGTATTAACAACTGGAGTTGCATTTCTTTCTATAAGCTTTTTAGTAGCTGCCCTTTTTATAGAAACAACGCCTTGGCTTATAACAATTATATTAATTTTTGTTTTTGGGGGGCTTTCTTTTACGAAAACAGTTATATCCACCATTGTTTCAAGTAGTTTGGAACAAAAGGAAGCTGGTGCTGGAATGAGTTTGCTTAATTTCACAAGCTTTTTATCAGAAGGAACAGGTATTGCAATTGTAGGTGGATTATTATCGATACATTTGCTAAATCGAAAATTACTACCTATAAATGCTGAGCCATCCACTCATTTGTATAGTAATTTGCTATTACTTTTTGCAGGAATCACAATTATTAGCTGGTTGGTTACTATAAAAATGCATAAACGCTCAAGAGGAAATATATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42759","NCBI_taxonomy_name":"Bhargavaea cecembensis","NCBI_taxonomy_id":"394098"}}}},"ARO_accession":"3003196","ARO_id":"39779","ARO_name":"tet(45)","CARD_short_name":"tet(45)","ARO_description":"Tet45 is a tetracycline efflux pump found in Bhargavaea cecembensis strain previously isolated from a poultry-litter-impacted soil.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"142":{"model_id":"142","model_name":"tet(E)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"587":{"protein_sequence":{"accession":"AAA71915.1","sequence":"MNRTVMMALVIIFLDAMGIGIIMPVLPALLREFVGKANVAENYGVLLALYAMMQVIFAPLLGRWSDRIGRRPVLLLSLLGATLDYALMATASVVWVLYLGRLIAGITGATGAVAASTIADVTPEESRTHWFGMMGACFGGGMIAGPVIGGFAGQLSVQAPFMFAAAINGLAFLVSLFILHETHNANQVSDELKNETINETTSSIREMISPLSGLLVVFFIIQLIGQIPATLWVLFGEERFAWDGVMVGVSLAVFGLTHALFQGLAAGFIAKHLGERKAIAVGILADGCGLFLLAVITQSWMVWPVLLLLACGGITLPALQGIISVRVGQVAQGQLQGVLTSLTHLTAVIGPLVFAFLYSATRETWNGWVWIIGCGLYVVALIILRFFHPGRVIHPINKSDVQQRI"},"dna_sequence":{"accession":"L06940.1","fmin":"0","fmax":"1218","strand":"+","sequence":"ATGAACCGCACTGTGATGATGGCACTGGTCATCATTTTTTTAGATGCTATGGGGATTGGCATAATTATGCCTGTCTTGCCGGCGTTATTACGGGAGTTTGTTGGAAAGGCTAATGTTGCAGAGAACTACGGTGTTTTATTGGCGCTGTATGCAATGATGCAAGTGATTTTTGCCCCTCTTCTCGGCCGCTGGTCAGATCGCATAGGTCGTCGCCCTGTATTGTTACTTTCACTTTTAGGTGCAACACTGGACTACGCATTAATGGCAACAGCCAGCGTAGTGTGGGTGTTGTATTTGGGACGCTTAATTGCTGGTATTACCGGTGCGACTGGAGCTGTTGCAGCCTCAACAATTGCCGATGTCACACCTGAGGAATCCAGGACACATTGGTTTGGTATGATGGGTGCCTGTTTTGGTGGCGGTATGATTGCTGGACCAGTCATTGGTGGTTTTGCCGGTCAACTTTCGGTACAGGCACCGTTTATGTTCGCTGCTGCTATTAACGGGCTGGCATTTCTGGTCTCCCTATTCATTTTACATGAGACCCATAATGCTAATCAGGTTAGTGACGAGTTAAAGAATGAAACAATCAATGAAACCACATCCTCCATACGCGAGATGATCTCCCCATTATCGGGATTGTTAGTTGTCTTTTTCATCATTCAATTGATTGGCCAAATCCCCGCAACATTATGGGTTTTATTCGGAGAAGAGCGCTTCGCATGGGATGGCGTAATGGTCGGTGTTTCATTGGCTGTGTTCGGGCTGACACACGCACTGTTTCAAGGACTTGCTGCTGGTTTTATCGCTAAACATTTGGGAGAACGGAAAGCTATAGCGGTTGGCATTTTGGCTGACGGTTGTGGCCTATTTTTATTGGCGGTCATTACACAAAGCTGGATGGTTTGGCCGGTTTTGCTGTTACTAGCTTGTGGTGGCATCACACTTCCCGCCTTGCAGGGAATTATATCTGTTCGTGTCGGTCAGGTAGCACAGGGACAATTACAAGGGGTGCTGACCAGTTTGACCCACCTGACAGCTGTAATCGGTCCACTTGTTTTTGCATTTTTGTATAGTGCAACCCGCGAAACGTGGAATGGATGGGTATGGATAATTGGCTGCGGATTATATGTAGTTGCATTGATTATACTGAGGTTTTTCCATCCAGGTAGGGTAATCCACCCGATAAATAAGAGCGATGTACAGCAGAGAATTTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000173","ARO_id":"36312","ARO_name":"tet(E)","CARD_short_name":"tet(E)","ARO_description":"TetE is a tetracycline efflux pump found in many Gram-negative bacteria, especially those in water environments. The gene is found on large plasmids.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"49":{"model_id":"49","model_name":"tsnR","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"4186":{"protein_sequence":{"accession":"AAA99931.1","sequence":"MANLDVIVDRSDPAVQRIVDVTKHSRSVVRTVLIEDIEPLTQSIRAGVEFTEVYGLDTVPFPGDLLAACEKRGIRVRLLSAAVANQVFKTEKKPKVFGIAKVPPAGRFADLESLSGDVVLLDGVKIVGNIGAIVRTRSALGAAGIVLVDSGLGTIADRRLIRASRGYVFSLPIVLATRDEALAFFRDGGMRPVVFEADGKLSIGELDGIDERLVLVFGSEKTGPSGEFAGVATESVSIPMNPAAESLNVSVSAGIALHRRARRNLSRPRG"},"dna_sequence":{"accession":"L39157.1","fmin":"345","fmax":"1158","strand":"+","sequence":"GTGGCCAATCTTGACGTTATTGTCGACCGTTCCGACCCCGCGGTGCAGCGCATCGTCGATGTGACCAAGCATTCCCGGTCCGTCGTGCGAACGGTGCTGATCGAGGACATCGAGCCCCTGACGCAGAGCATCCGCGCCGGGGTCGAGTTCACCGAGGTCTACGGTCTCGACACCGTGCCGTTCCCGGGTGATCTGCTCGCCGCCTGCGAAAAGCGCGGAATTCGGGTGCGGCTGCTCTCCGCCGCGGTCGCGAATCAGGTTTTCAAGACCGAGAAGAAGCCCAAGGTCTTCGGTATCGCGAAGGTTCCGCCGGCCGGCCGTTTCGCCGACCTGGAGAGCCTTTCCGGCGATGTCGTCCTGCTCGACGGCGTGAAGATCGTCGGCAACATCGGCGCCATCGTGCGGACGCGTTCGGCGCTCGGCGCCGCCGGCATCGTCCTGGTCGACAGCGGCCTCGGCACCATCGCGGACCGCCGGCTCATCCGCGCCAGCCGCGGCTACGTGTTCTCCCTGCCGATCGTGCTCGCGACGCGCGACGAGGCGCTGGCCTTCTTCCGTGACGGCGGGATGCGGCCCGTGGTCTTCGAGGCGGACGGCAAGCTGTCCATCGGAGAGCTCGACGGCATCGACGAGCGGCTCGTGCTCGTGTTCGGCAGCGAGAAGACCGGCCCGTCGGGCGAGTTCGCCGGGGTCGCCACCGAGTCGGTGTCCATCCCGATGAACCCCGCCGCCGAGTCGCTCAACGTCTCGGTGTCGGCCGGCATCGCCCTGCACCGGCGGGCCCGCCGCAACCTCTCGCGCCCGCGCGGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41352","NCBI_taxonomy_name":"Streptomyces laurentii","NCBI_taxonomy_id":"39478"}}}},"ARO_accession":"3003060","ARO_id":"39494","ARO_name":"tsnR","CARD_short_name":"tsnR","ARO_description":"tsnR is a 23S ribosomal RNA methyltransferase that methylates adenosine-1067 to confer resistance to thiostrepton.","ARO_category":{"39499":{"category_aro_accession":"3003065","category_aro_cvterm_id":"39499","category_aro_name":"non-erm 23S ribosomal RNA methyltransferase (A1067)","category_aro_description":"Non-erm 23S ribosomal RNA methyltransferases modify adenosine 1067 to confer resistance to peptide antibiotics.","category_aro_class_name":"AMR Gene Family"},"37030":{"category_aro_accession":"3000686","category_aro_cvterm_id":"37030","category_aro_name":"thiostrepton","category_aro_description":"Thiostrepton is a cyclic peptide active against Gram-positive bacteria. It is produced by streptomyces bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"167":{"model_id":"167","model_name":"CMY-39","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1099":{"protein_sequence":{"accession":"BAF95726.1","sequence":"MMKKSLCCALLLTAPLSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADITNNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGISLLHLATYTAGGLPLQIPDDVTDKAALLRFYQNWQPQWAPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWIKVPQSEQKDYAWGYREGKAVHVSPGQLDAEAYGVKSSVIDMARWVQVNMDASRVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"AB372224.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCCCTTTATCCACGTTTGCCGCCGCCAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCTGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCACCAATAACCACCCAGTCACGCAGCAAACTCTGTTTGAGCTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCAGCCTGCTGCACTTAGCCACCTACACGGCAGGCGGCCTGCCGCTGCAGATCCCCGATGACGTTACGGATAAAGCCGCATTACTGCGTTTTTATCAAAACTGGCAGCCGCAATGGGCCCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTAAAGTTCCGCAAAGCGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGGCTGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGTCAACATGGACGCCAGCCGCGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCAATCATCAACGGTAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGATCCACTGGAGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002050","ARO_id":"38450","ARO_name":"CMY-39","CARD_short_name":"CMY-39","ARO_description":"CMY-39 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"168":{"model_id":"168","model_name":"VIM-17","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"8239":{"protein_sequence":{"accession":"ABW90721.1","sequence":"MFKLLSKLLVYLTASMMAIASPLAFSVDSSGEYPTVSEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEVEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSASVLYGGCAIYELSRTSAGNVADADLAEWPTSIERIQQHYPEAQFVIPGHGLPGGLDLLKHTTNVVKAHTNRSVVE"},"dna_sequence":{"accession":"EU118148.2","fmin":"1010","fmax":"1811","strand":"+","sequence":"ATGTTCAAACTTTTGAGTAAGTTATTGGTCTATTTGACCGCGTCTATGATGGCTATTGCGAGTCCGCTCGCTTTTTCCGTAGATTCTAGCGGTGAGTATCCGACAGTCAGCGAAATTCCGGTCGGGGAGGTCCGGCTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCAGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAGAAGCAAATTGGACTTCCTGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGTAGAGGGGAACGAGATTCCCACGCACTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAACTCTTCTATCCTGGTGCTGCGCATTCGACCGACAACTTAGTTGTGTACGTCCCGTCTGCGAGTGTGCTCTATGGTGGTTGTGCGATTTATGAGTTGTCACGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCATTGAGCGGATTCAACAACACTACCCGGAAGCACAGTTCGTCATTCCGGGGCACGGCCTGCCGGGCGGTCTAGACTTGCTCAAGCACACAACGAATGTTGTAAAAGCGCACACAAATCGCTCAGTCGTTGAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002287","ARO_id":"38687","ARO_name":"VIM-17","CARD_short_name":"VIM-17","ARO_description":"VIM-17 is a beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"112":{"model_id":"112","model_name":"fosA5","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"200"}},"model_sequences":{"sequence":{"4457":{"protein_sequence":{"accession":"AJE60855.1","sequence":"MLSGLNHLTLAVSQLAPSVAFYQQLLGMMLHARWDSGAYLSCGDLWLCLSLDPQRRVTPPEESDYTHYAFSISEADFASFAARLEAAGVAVWKLNRSEGASHYFLDPDGHKLELHVGSLAQRLAACREQPYKGMVFFAE"},"dna_sequence":{"accession":"KP143090.1","fmin":"1199","fmax":"1619","strand":"-","sequence":"ATGCTGAGTGGACTGAATCACCTGACCCTGGCAGTCAGCCAGCTGGCGCCGAGCGTGGCGTTTTATCAGCAGCTGCTGGGCATGATGCTGCATGCCCGCTGGGACAGCGGGGCTTATCTCTCCTGCGGCGATCTGTGGCTGTGCCTGTCGCTGGATCCGCAGCGGCGCGTTACTCCGCCGGAAGAGAGCGACTACACCCATTATGCGTTTAGTATTAGCGAAGCCGATTTTGCTAGCTTCGCCGCCCGCCTTGAGGCTGCCGGCGTAGCGGTCTGGAAGCTGAACCGTAGCGAAGGCGCTTCGCACTATTTCCTCGATCCCGATGGCCATAAGCTGGAGCTGCACGTCGGCAGTCTCGCCCAGCGTCTGGCCGCCTGCCGCGAGCAGCCGTATAAGGGGATGGTGTTTTTTGCTGAGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3003209","ARO_id":"39793","ARO_name":"fosA5","CARD_short_name":"fosA5","ARO_description":"fosA5 is a fosfomycin resistance gene isolated from clinical strain of Escherichia coli E265. It is susceptible to amikacin, tetracycline and imipenem, and resistant to sulphonamide, cephalosporins, gentamicin, ciprofloxacin, chloramphenicol and streptomycin.","ARO_category":{"36272":{"category_aro_accession":"3000133","category_aro_cvterm_id":"36272","category_aro_name":"fosfomycin thiol transferase","category_aro_description":"Catalyzes the addition of a thiol group from a nucleophilic molecule to fosfomycin.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"46133":{"category_aro_accession":"3007382","category_aro_cvterm_id":"46133","category_aro_name":"gentamicin","category_aro_description":"Gentamicin is a commonly used aminoglycoside antibiotic derived from members of the Micromonospora genus of bacteria. It acts by binding the 30S ribosomal subunit, thus inhibiting protein synthesis. Gentamicin is typically used to treat Gram-negative infections of the repiratory and urinary tract, as well as infections of the bone and soft tissue. It also exhibits considerable nephrotoxicity and ototoxicity. Gentamicin is administered as a mixture of gentamicin type C (which makes about around 80% of the complex) and types A, B, and X (distributed in the remaining 20% of the complex).","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"45731":{"category_aro_accession":"3007149","category_aro_cvterm_id":"45731","category_aro_name":"phosphonic acid antibiotic","category_aro_description":"A group of antibiotics derived from phosphonic acids.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"138":{"model_id":"138","model_name":"Streptomyces lividans cmlR","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"755":{"protein_sequence":{"accession":"CAA42594.1","sequence":"MPLPLYLLAVAVCAMGTSEFMLAGLVPDIASDLGVTVGTAGTLTSAFATGMIVGAPLVAALARTWPRRSSLLGFILAFAAAHAVGAGTTSFPVLVACRVVAALANAGFLAVALTTAAALVPADKQGRALAVLLSGTTVATVAGVPGGSLLGTWLGWRATFWAVAVCCLPAAFGVLKAIPAGRATAAATGGPPLRVELAALKTPRLLLAMLLGALVNAATFASFTFLAPVVTDTAGLGDLWISVALVLFGAGSFAGVTVAGRLSDRRPAQVLAVAGPLLLVGWPALAMLADRPVALLTLVFVQGALSFALGSTLITRVLYEAAGAPTMAGSYATAALNVGAAAGPLVAATTLGHTTGNLGPLWASGLLVAVALLVAFPFRTVITTAAPADATR"},"dna_sequence":{"accession":"X59968.1","fmin":"507","fmax":"1686","strand":"+","sequence":"ATGCCTCTTCCGCTGTACCTGCTCGCCGTGGCCGTCTGCGCCATGGGCACCTCGGAGTTCATGCTCGCCGGTCTCGTGCCGGACATCGCCTCGGATCTCGGCGTCACCGTCGGGACCGCAGGCACGCTCACCTCCGCCTTCGCGACCGGCATGATCGTCGGCGCTCCCCTCGTGGCGGCGCTGGCCCGCACCTGGCCCAGGCGTTCCAGCCTCCTCGGATTCATCCTCGCCTTCGCGGCGGCACACGCCGTGGGAGCCGGCACCACGAGCTTCCCCGTCCTGGTGGCCTGCCGGGTCGTGGCCGCGCTCGCGAACGCGGGATTCCTCGCGGTCGCACTGACGACTGCCGCCGCACTGGTCCCTGCCGACAAGCAGGGACGCGCGCTGGCCGTGCTGCTGTCCGGCACGACGGTGGCCACGGTCGCCGGCGTCCCCGGCGGGTCACTCCTCGGCACGTGGCTCGGCTGGCGGGCCACGTTCTGGGCCGTCGCCGTCTGCTGCCTGCCCGCGGCGTTCGGCGTGCTGAAGGCAATCCCCGCCGGACGTGCGACGGCAGCGGCGACCGGTGGGCCGCCGCTGCGAGTCGAGCTCGCCGCGCTCAAGACCCCCCGGTTGCTGCTGGCGATGCTGCTGGGCGCGCTGGTGAACGCGGCAACCTTCGCGAGCTTCACCTTCCTGGCCCCCGTCGTGACCGACACCGCAGGGCTGGGCGACCTGTGGATCTCTGTCGCCCTGGTGCTCTTCGGCGCCGGTTCCTTCGCCGGCGTCACCGTCGCCGGACGACTGTCCGACCGACGCCCCGCCCAGGTGCTCGCCGTCGCCGGTCCGCTGCTGCTCGTCGGCTGGCCCGCGCTGGCGATGCTGGCCGACCGGCCGGTCGCCCTGCTGACCCTCGTGTTCGTCCAAGGCGCACTGTCGTTCGCGCTGGGCAGCACGCTGATCACGCGGGTCCTCTACGAGGCGGCGGGAGCACCCACCATGGCCGGTTCGTACGCGACCGCCGCCCTCAACGTGGGCGCCGCGGCCGGACCGCTCGTCGCCGCGACCACTCTCGGCCACACGACCGGCAACCTCGGGCCGCTGTGGGCGAGCGGGCTCCTGGTCGCCGTCGCGCTGCTCGTCGCGTTCCCCTTCCGCACGGTGATCACGACGGCCGCACCCGCCGACGCGACCCGGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39551","NCBI_taxonomy_name":"Streptomyces lividans 1326","NCBI_taxonomy_id":"1200984"}}}},"ARO_accession":"3002690","ARO_id":"39124","ARO_name":"Streptomyces lividans cmlR","CARD_short_name":"Sliv_cmlR","ARO_description":"cmlR is a plasmid or chromosome-encoded chloramphenicol resistance determinant (putative transmembrane protein) that is found in Escherichia coli and Streptomyces lividans.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"141":{"model_id":"141","model_name":"vanR gene in vanB cluster","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"3453":{"protein_sequence":{"accession":"AAB05622.1","sequence":"MSIRILLVEDDDHICNTVRAFLAEARYEVDACTDGNEAHTKFYENTYQLVILDIMLPGMNGHELLREFRAQNDTPILMMTALSDDENQIRAFDAEADDYVTKPFKMRILLKRVEALLRRSGALAKEFRVGRLTLLPEDFRVLCDGTELPLTRKEFEILLLLVQNKGRTLTHEIILSRIWGYDFDGDGSTVHTHIKNLRAKLPENIIKTIRGVGYRLEESL"},"dna_sequence":{"accession":"U35369.1","fmin":"177","fmax":"840","strand":"+","sequence":"ATGTCGATACGAATTCTACTTGTCGAGGATGATGATCATATCTGCAATACAGTAAGGGCGTTTTTGGCTGAAGCAAGATATGAGGTGGATGCCTGCACAGATGGAAACGAAGCACACACCAAGTTCTATGAAAACACCTATCAACTGGTTATTCTTGATATTATGCTGCCCGGTATGAATGGGCATGAACTTCTACGTGAATTTCGGGCGCAAAATGATACCCCCATTCTGATGATGACAGCCCTGTCGGATGACGAAAACCAAATCCGGGCGTTTGATGCAGAGGCAGACGACTATGTAACAAAGCCATTCAAGATGCGGATTTTACTAAAGCGGGTGGAAGCCCTGTTACGGCGCAGCGGTGCGCTGGCAAAGGAATTTCGTGTGGGCAGGCTGACACTTCTGCCGGAGGATTTTAGGGTACTTTGTGACGGTACGGAGCTGCCCCTGACACGAAAAGAATTTGAAATCCTTTTGCTGCTGGTGCAGAACAAAGGCAGAACCTTAACCCATGAAATCATTTTGTCCCGCATATGGGGATATGACTTTGACGGTGATGGCAGCACAGTCCACACTCATATCAAAAATCTGCGGGCGAAGCTGCCGGAAAATATCATCAAAACCATCCGCGGTGTAGGTTACCGATTGGAGGAATCATTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35918","NCBI_taxonomy_name":"Enterococcus faecalis","NCBI_taxonomy_id":"1351"}}}},"ARO_accession":"3002921","ARO_id":"39355","ARO_name":"vanR gene in vanB cluster","CARD_short_name":"vanR_in_vanB_cl","ARO_description":"Also known as vanRB, is a vanR variant found in the vanB gene cluster.","ARO_category":{"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"36713":{"category_aro_accession":"3000574","category_aro_cvterm_id":"36713","category_aro_name":"vanR","category_aro_description":"VanR is a OmpR-family transcriptional activator in the VanSR regulatory system. When activated by VanS, it promotes cotranscription of VanA, VanH, and VanX.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"169":{"model_id":"169","model_name":"IMP-33","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"8214":{"protein_sequence":{"accession":"AEU17778.1","sequence":"MKKLFVLCVCFFCSITAAGSSLPDLKIEKLEEGVFVHTSFEEVNGWGVVTKHGLVVLVNTDAYLIDTPFTATDTEKLVNWFVERGYKIKGTISSHFHSDSTGGIEWLNSQSIPTYASELTNELLKKSGKVQAKYSFSEVSYWLVKNKIEVFYPGPGHTQDNLVVWLPESKILFGGCFVKPHGLGNLGDANLEAWPKSAKILMSKYGKAKLVVSSHSEKGDASLLKRTWEQALKGLKESKKTSSPSN"},"dna_sequence":{"accession":"JN848782.2","fmin":"1827","fmax":"2568","strand":"+","sequence":"ATGAAGAAATTATTTGTTTTATGTGTATGCTTCTTTTGTAGCATTACTGCCGCAGGATCGTCTTTACCTGATTTAAAAATTGAGAAGCTTGAAGAAGGTGTTTTTGTTCATACATCGTTCGAAGAAGTTAACGGTTGGGGGGTTGTTACTAAACACGGTTTGGTGGTGCTTGTAAACACAGACGCCTATCTAATTGACACTCCATTTACTGCTACAGACACTGAAAAATTAGTCAATTGGTTTGTGGAGCGCGGCTATAAAATCAAAGGCACTATTTCATCACATTTCCATAGCGACAGCACAGGAGGAATAGAGTGGCTTAATTCTCAATCTATTCCCACGTATGCATCTGAATTAACAAATGAACTTTTGAAAAAATCCGGTAAGGTACAAGCTAAATATTCATTTAGCGAAGTTAGCTATTGGCTAGTTAAAAATAAAATTGAAGTTTTTTATCCTGGCCCAGGTCACACTCAAGATAACCTAGTGGTTTGGTTGCCTGAAAGTAAAATTTTATTCGGTGGTTGCTTTGTTAAACCTCACGGTCTTGGCAATTTAGGTGACGCAAATTTAGAAGCTTGGCCAAAGTCCGCCAAAATATTAATGTCTAAATATGGCAAAGCAAAGCTTGTTGTTTCAAGTCATAGTGAGAAAGGGGACGCATCACTATTGAAACGTACATGGGAACAAGCTCTTAAAGGGCTTAAAGAAAGTAAAAAAACATCATCACCAAGTAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002224","ARO_id":"38624","ARO_name":"IMP-33","CARD_short_name":"IMP-33","ARO_description":"IMP-33 is a beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"170":{"model_id":"170","model_name":"IMP-19","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1014":{"protein_sequence":{"accession":"ABM67078.1","sequence":"MKKLFVLCVCFLCSITAAGAALPDLKIEKLEEGVYVHTSFEEVNGWGVVSKHGLVVLVNTDAYLIDTPFTATDTEKLVNWFVERGYKIKGTISSHFHSDSTGGIEWLNSQSIPTYASELTNELLKKDGKVQAKNSFSGVSYWLVKNKIEVFYPGPGHTQDNVVVWLPEKKILFGGCFVKPDGLGNLGDANLEAWPKSAKILMSKYVKAKLVVSSHSEIGDASLLKRTWEQAVKGLNESKKPSQPSN"},"dna_sequence":{"accession":"EF118171.1","fmin":"3181","fmax":"3922","strand":"+","sequence":"ATGAAGAAATTATTTGTTTTATGTGTATGCTTCCTTTGTAGCATTACTGCCGCAGGAGCGGCTTTGCCTGATTTAAAAATCGAGAAGCTTGAAGAAGGTGTTTATGTTCATACATCGTTCGAAGAAGTTAACGGTTGGGGTGTTGTTTCTAAACACGGTTTGGTGGTTCTTGTAAACACTGACGCCTATCTGATTGACACTCCATTTACTGCTACAGATACTGAAAAGTTAGTCAATTGGTTTGTGGAGCGCGGCTATAAAATCAAAGGCACTATTTCCTCACATTTCCATAGCGACAGCACAGGGGGAATAGAGTGGCTTAATTCTCAATCTATTCCCACGTATGCATCTGAATTAACAAATGAACTTCTTAAAAAAGACGGTAAGGTGCAAGCTAAAAACTCATTTAGCGGAGTTAGTTATTGGCTAGTTAAAAATAAAATTGAAGTTTTTTATCCCGGCCCGGGGCACACTCAAGATAACGTAGTGGTTTGGTTACCTGAAAAGAAAATTTTATTCGGTGGTTGTTTTGTTAAACCGGACGGTCTTGGTAATTTGGGTGACGCAAATTTAGAAGCTTGGCCAAAGTCCGCCAAAATATTAATGTCTAAATATGTTAAAGCAAAACTGGTTGTTTCAAGTCATAGTGAAATTGGGGACGCATCACTCTTGAAACGTACATGGGAACAGGCTGTTAAAGGGCTAAATGAAAGTAAAAAACCATCACAGCCAAGTAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36936","NCBI_taxonomy_name":"Aeromonas caviae","NCBI_taxonomy_id":"648"}}}},"ARO_accession":"3002210","ARO_id":"38610","ARO_name":"IMP-19","CARD_short_name":"IMP-19","ARO_description":"IMP-19 is a beta-lactamase found in Aeromonas caviae.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"171":{"model_id":"171","model_name":"TEM-78","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"2038":{"protein_sequence":{"accession":"AAF05612.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMVSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRREPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERDRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AF190693.1","fmin":"208","fmax":"1069","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGGTGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATCGTCGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAGATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000944","ARO_id":"37324","ARO_name":"TEM-78","CARD_short_name":"TEM-78","ARO_description":"TEM-78 is an inhibitor-resistant beta-lactamase found in E. coli.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"173":{"model_id":"173","model_name":"arr-4","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"250"}},"model_sequences":{"sequence":{"524":{"protein_sequence":{"accession":"ABV26705.1","sequence":"MTNDWIPTSHDNCSQVAGPFYHGTKAKLTVGDLLSPGHPSHFEQGRKLKHIYFAALMEPAIWGAELAMSLSSLEGRGHIYIVEPLGPFEDDPNLTNKKFPGNPTKSYRTTEPLRIVGIVEDWQGHSPEVLQGMLASLEDLQRRGLAIIED"},"dna_sequence":{"accession":"EF660562.1","fmin":"1671","fmax":"2124","strand":"+","sequence":"ATGACGAATGACTGGATTCCCACTTCGCATGACAACTGCTCGCAAGTAGCGGGGCCGTTCTATCACGGCACCAAAGCCAAACTCACGGTTGGTGACTTGCTTTCCCCAGGACACCCGTCTCACTTTGAGCAAGGTCGCAAGCTCAAACACATCTACTTTGCCGCCCTGATGGAACCAGCCATCTGGGGAGCGGAGCTTGCGATGTCGCTGTCAAGCCTAGAGGGGCGCGGCCACATCTACATCGTTGAACCGCTCGGCCCATTTGAGGACGACCCGAACCTTACAAACAAGAAATTCCCGGGAAATCCAACCAAGTCCTATCGCACCACTGAGCCGCTGCGGATTGTTGGGATCGTAGAAGACTGGCAAGGCCACTCACCGGAGGTGTTACAGGGCATGTTGGCGTCTCTGGAGGATCTTCAGCGTCGTGGCCTCGCCATCATTGAGGACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002849","ARO_id":"39283","ARO_name":"arr-4","CARD_short_name":"arr-4","ARO_description":"arr-4 is an integron-encoded ribosyltransferase found in Pseudomonas aeruginosa.","ARO_category":{"36529":{"category_aro_accession":"3000390","category_aro_cvterm_id":"36529","category_aro_name":"rifampin ADP-ribosyltransferase (Arr)","category_aro_description":"Enzyme responsible for the ADP-ribosylative inactivation of rifampin at the 23-OH position using NAD+.","category_aro_class_name":"AMR Gene Family"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36656":{"category_aro_accession":"3000517","category_aro_cvterm_id":"36656","category_aro_name":"rifaximin","category_aro_description":"Rifaximin is a semi-synthetic rifamycin used to treat traveller's diarrhea. Rifaximin inhibits RNA synthesis by binding to the beta subunit of bacterial RNA polymerase.","category_aro_class_name":"Antibiotic"},"36669":{"category_aro_accession":"3000530","category_aro_cvterm_id":"36669","category_aro_name":"rifabutin","category_aro_description":"Rifabutin is a semisynthetic rifamycin used in tuberculosis therapy. It inhibits DNA-dependent RNA synthesis.","category_aro_class_name":"Antibiotic"},"36673":{"category_aro_accession":"3000534","category_aro_cvterm_id":"36673","category_aro_name":"rifapentine","category_aro_description":"Rifapentine is a semisynthetic rifamycin that inhibits DNA-dependent RNA synthesis. It is often used in the treatment of tuberculosis and leprosy.","category_aro_class_name":"Antibiotic"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"174":{"model_id":"174","model_name":"CfxA2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"4470":{"protein_sequence":{"accession":"AAD23513.1","sequence":"MEKNRKKQIVVLSIALVCIFILVFSLFHKSATKDSANPPLTNVLTDSISQIVSACPGEIGVAVIVNNRDTVKVNNKSVYPMMSVFKVHQALALCNDFDNKGISLDTLVNINRDKLDPKTWSPMLKDYSGPVISLTVRDLLRYTLTQSDNNASNLMFKDMVNVAQTDSFIATLIPRSSFQIAYTEEEMSADHNKAYSNYTSPLGAAMLMNRLFTEGLIDDEKQSFIKNTLKECKTGVDRIAAPLLDKEGVVIAHKTGSGYVNENGVLAAHNDVAYICLPNNISYTLAVFVKDFKGNESQASQYVAHISAVVYSLLMQTSVKS"},"dna_sequence":{"accession":"AF118110.1","fmin":"71","fmax":"1037","strand":"-","sequence":"ATGGAAAAAAACAGAAAAAAACAAATCGTAGTTTTGAGTATAGCTTTAGTTTGCATTTTCATCTTGGTATTTTCATTGTTCCATAAATCAGCGACAAAAGATAGCGCAAATCCTCCTTTAACAAATGTTTTGACTGATAGCATTTCTCAAATTGTCTCAGCTTGTCCTGGCGAAATTGGTGTGGCGGTTATTGTTAATAACAGAGATACGGTTAAGGTCAATAATAAGAGTGTTTATCCTATGATGAGTGTGTTTAAGGTTCATCAGGCATTAGCTCTTTGTAATGACTTTGACAATAAAGGAATTTCACTTGATACCTTAGTAAATATAAATAGGGATAAACTTGACCCAAAGACTTGGAGTCCTATGCTGAAAGATTATTCAGGGCCAGTCATATCATTGACAGTGAGAGATTTGCTGCGTTATACTCTTACTCAGAGTGACAACAATGCAAGCAACCTTATGTTTAAGGATATGGTTAATGTCGCTCAAACAGATAGTTTTATAGCCACACTCATTCCTCGTTCAAGTTTTCAGATAGCTTATACGGAAGAGGAAATGTCGGCTGACCATAACAAGGCTTACTCTAACTATACATCTCCTCTTGGTGCTGCAATGTTGATGAATCGTTTGTTTACTGAAGGTCTTATCGATGATGAGAAACAAAGTTTCATTAAGAATACGTTAAAAGAATGCAAAACAGGTGTAGATAGGATAGCAGCTCCACTTCTTGATAAAGAAGGGGTTGTTATAGCGCATAAGACAGGTTCAGGTTATGTTAATGAAAATGGTGTTCTTGCAGCTCACAATGATGTTGCCTATATATGTCTGCCTAATAATATCAGTTATACCTTAGCGGTATTTGTTAAGGATTTCAAGGGAAATGAATCACAAGCGTCACAATATGTTGCGCATATATCAGCTGTAGTATATTCTTTATTAATGCAAACTTCAGTAAAATCTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39547","NCBI_taxonomy_name":"Prevotella intermedia","NCBI_taxonomy_id":"28131"}}}},"ARO_accession":"3003002","ARO_id":"39436","ARO_name":"CfxA2","CARD_short_name":"CfxA2","ARO_description":"CfxA2 beta-lactamase is a class A beta-lactamase found in Prevotella intermedia.","ARO_category":{"39434":{"category_aro_accession":"3003000","category_aro_cvterm_id":"39434","category_aro_name":"CfxA beta-lactamase","category_aro_description":"CfxA beta-lactamases are class A beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"175":{"model_id":"175","model_name":"CTX-M-24","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1477":{"protein_sequence":{"accession":"AAN38836.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAERRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"AY143430.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGACTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGCGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001886","ARO_id":"38286","ARO_name":"CTX-M-24","CARD_short_name":"CTX-M-24","ARO_description":"CTX-M-24 is a beta-lactamase found in the Enterobacteriaceae family.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"176":{"model_id":"176","model_name":"CMY-25","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1282":{"protein_sequence":{"accession":"ACA30420.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVTDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"EU515249.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACTGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTACGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACAGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAACCCGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002036","ARO_id":"38436","ARO_name":"CMY-25","CARD_short_name":"CMY-25","ARO_description":"CMY-25 is a beta-lactamase found in the Enterobacteriaceae family.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"177":{"model_id":"177","model_name":"IMP-51","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"2108":{"protein_sequence":{"accession":"BAQ56016.1","sequence":"MKKLSVFFMFLFCSIAASGEALPDLKIEKLDEGVYVHTSFEEVNGWGVVPKHGLVVLVNTDAYLIDTPFTAKDTEKLVTWFVERGYKIKGSISSHFHSDSTGGIEWLNSQSIPTYASELTNELLKKDGKVQAKNSFSGASYWLVKKKIEIFYPGPGHTPDNVVVWLPEHRVLFGGCFVKPYGLGNLGDANLEAWPKSAKLLVSKYGKAKLVVPGHSEVGDASLLKRTLEQAVKGLNESKKLSKPSN"},"dna_sequence":{"accession":"LC031883.1","fmin":"5071","fmax":"5812","strand":"+","sequence":"ATGAAAAAGTTATCAGTATTCTTTATGTTTTTGTTTTGTAGCATTGCTGCCTCAGGAGAGGCTTTGCCAGATTTAAAAATTGAGAAGCTTGACGAAGGCGTTTATGTTCATACTTCGTTTGAGGAAGTTAACGGCTGGGGCGTGGTTCCTAAACACGGCTTGGTGGTTCTTGTAAATACTGACGCTTATTTGATTGACACTCCATTTACAGCTAAAGATACTGAAAAGTTAGTTACTTGGTTTGTAGAGCGCGGCTATAAAATAAAAGGCAGTATCTCCTCTCATTTTCATAGCGACAGCACGGGCGGAATAGAGTGGCTTAATTCTCAATCTATTCCAACATATGCATCTGAATTAACAAATGAACTTCTTAAAAAAGACGGTAAGGTACAAGCTAAAAATTCATTTAGCGGAGCCAGCTATTGGTTAGTTAAGAAAAAGATTGAAATTTTTTATCCTGGCCCAGGGCACACTCCAGATAACGTAGTGGTTTGGCTACCTGAACATAGAGTTTTGTTTGGTGGTTGTTTTGTTAAACCGTATGGTCTAGGTAATTTGGGTGACGCAAATTTAGAAGCTTGGCCAAAGTCTGCCAAATTATTAGTGTCCAAATATGGTAAGGCAAAACTGGTTGTTCCAGGTCACAGTGAAGTTGGAGATGCATCACTCTTGAAACGTACATTAGAACAGGCTGTTAAAGGATTAAACGAAAGTAAAAAGCTATCAAAACCAAGTAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3003659","ARO_id":"40269","ARO_name":"IMP-51","CARD_short_name":"IMP-51","ARO_description":"IMP-51 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"179":{"model_id":"179","model_name":"QnrA5","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"588":{"protein_sequence":{"accession":"AAZ04784.1","sequence":"MDIIDKVFQQEDFSRQDLSDSRFRRCRFYQCDFSHCQLRDASFEDCSFIESGAVEGCHFSYADLRDASFKACRLSLANFSGANCFGIEFRECDLKGANFSRARFYNQISHKMYFCSAYISGCNLAYANLSGQCLEKCELFENNWSNANLSGASLMGSDLSCGTFSRDCWQQVNLRGCDLTFADLDGLDPRRVNLEGVKICAWQQEQLLEPLGVIVLPD"},"dna_sequence":{"accession":"DQ058663.1","fmin":"0","fmax":"657","strand":"+","sequence":"ATGGATATTATTGATAAAGTTTTTCAGCAAGAGGATTTCTCACGCCAGGATTTGAGTGACAGCCGTTTTCGCCGCTGCCGCTTTTATCAGTGTGACTTCAGCCATTGCCAGCTAAGGGATGCCAGTTTCGAGGATTGCAGTTTCATTGAAAGCGGCGCCGTCGAAGGGTGCCACTTCAGCTATGCCGATCTGCGCGATGCCAGTTTCAAGGCCTGCCGCCTGTCTTTGGCCAATTTCAGCGGTGCCAACTGCTTTGGCATAGAGTTCAGGGAGTGCGATCTCAAGGGCGCCAATTTTTCCCGGGCCCGTTTTTACAATCAAATCAGCCATAAGATGTACTTCTGCTCGGCTTATATCTCAGGCTGCAACCTGGCCTATGCCAATTTGAGCGGCCAATGCCTGGAAAAGTGCGAGCTGTTTGAAAACAACTGGAGCAATGCCAACCTCAGCGGCGCTTCCTTGATGGGCTCCGACCTCAGCTGCGGCACCTTCTCCCGCGACTGCTGGCAGCAGGTAAACCTGCGGGGCTGTGACCTGACTTTTGCCGATCTGGATGGGCTCGATCCCAGACGGGTCAACCTCGAAGGGGTCAAGATCTGTGCCTGGCAGCAGGAGCAACTGCTGGAACCCTTGGGAGTCATAGTGCTGCCGGATTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36891","NCBI_taxonomy_name":"Shewanella algae","NCBI_taxonomy_id":"38313"}}}},"ARO_accession":"3002711","ARO_id":"39145","ARO_name":"QnrA5","CARD_short_name":"QnrA5","ARO_description":"QnrA5 is a plasmid-mediated quinolone resistance protein found in Shewanella algae.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"180":{"model_id":"180","model_name":"DHA-19","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1258":{"protein_sequence":{"accession":"AIT76102.1","sequence":"MKKSLSATLISALLAFSAPGFSAADNVAAVVDSTIKPLMAQQDIPGMAVAVSVKGKPYYFNYGFADVQAKQPVTENTLFELGSVSKTFTGVLGAVSVAKKEMALNDPAAKYQPELALPQWKGITLLDLATYTAGGLPLQVPDAVKSRADLLNFYQQWQPSWKPGDMRLYANSSIGLFGALTANAAGMPYEQLLTARILAPLGLSHTFITVPESAQSQYAYGYKNKKPVRVSPEQLDAESYGVKSASKDMLRWAEMNMEPSRAGNADLEMAMYLAQTRYYKTAAINQGLGWEMYDWPQQKDMIINGVTNEVALQPHPVTDNQVQPYNRASWVHKTGATTGFGAYVAFIPEKQVAIVILANKNYPNTERVKAAQAILSALE"},"dna_sequence":{"accession":"KM087849.1","fmin":"0","fmax":"1140","strand":"+","sequence":"ATGAAAAAATCGTTATCTGCAACACTGATTTCCGCTCTGCTGGCGTTTTCCGCCCCGGGGTTTTCTGCCGCTGATAATGTCGCGGCGGTGGTGGACAGCACCATTAAACCGCTGATGGCACAGCAGGATATTCCCGGGATGGCGGTTGCCGTCTCCGTAAAGGGTAAGCCCTATTATTTCAATTACGGTTTTGCCGATGTTCAGGCAAAACAGCCTGTCACTGAAAATACACTATTTGAGCTCGGATCTGTAAGTAAAACTTTCACAGGTGTGCTGGGTGCGGTTTCCGTGGCGAAAAAAGAGATGGCGCTGAATGATCCGGCGGCAAAATATCAGCCGGAGCTGGCTCTGCCGCAGTGGAAGGGGATCACGCTGCTGGATCTGGCCACCTATACCGCAGGCGGGCTGCCGTTACAGGTACCGGATGCGGTGAAAAGCCGTGCGGATCTGCTGAATTTCTATCAGCAGTGGCAGCCATCATGGAAACCGGGCGATATGCGTCTGTATGCAAACAGCAGTATCGGCCTGTTTGGTGCTCTGACCGCCAACGCGGCGGGGATGCCGTATGAGCAGTTGCTGACTGCACGGATCCTGGCACCGCTGGGGTTATCTCACACCTTTATTACTGTGCCGGAAAGTGCGCAAAGCCAGTATGCGTACGGTTATAAAAACAAAAAACCGGTCCGCGTGTCGCCGGAACAGCTTGATGCGGAATCTTACGGCGTGAAATCCGCCTCAAAAGATATGCTGCGCTGGGCGGAAATGAATATGGAGCCGTCACGGGCCGGTAATGCGGATCTGGAAATGGCAATGTATCTTGCACAGACCCGCTACTATAAAACCGCCGCGATTAACCAGGGGCTGGGCTGGGAAATGTATGACTGGCCGCAGCAGAAAGATATGATCATTAACGGCGTGACCAACGAGGTCGCATTGCAGCCGCACCCGGTAACAGACAACCAGGTTCAGCCGTATAACCGTGCTTCCTGGGTGCATAAAACGGGGGCAACAACTGGTTTCGGCGCCTATGTGGCCTTTATTCCGGAAAAACAGGTGGCGATTGTGATTCTGGCGAATAAAAACTACCCGAATACCGAAAGAGTCAAAGCCGCACAGGCTATTTTGAGTGCACTGGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36917","NCBI_taxonomy_name":"Morganella morganii","NCBI_taxonomy_id":"582"}}}},"ARO_accession":"3002150","ARO_id":"38550","ARO_name":"DHA-19","CARD_short_name":"DHA-19","ARO_description":"DHA-19 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36207":{"category_aro_accession":"3000068","category_aro_cvterm_id":"36207","category_aro_name":"DHA beta-lactamase","category_aro_description":"DHA beta-lactamases are plasmid-mediated AmpC \u03b2-lactamases that confer resistance to cephamycins and oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"181":{"model_id":"181","model_name":"GES-14","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1984":{"protein_sequence":{"accession":"ADC91899.1","sequence":"MRFIHALLLAGIAHSAYASEKLTFKTDLEKLEREKAAQIGVAIVDPQGEIVAGHRMAQRFAMCSTFKFPLAALVFERIDSGTERGDRKLSYGPDMIVEWSPATERFLASGHMTVLEAAQAAVQLSDNGATNLLLREIGGPAAMTQYFRKIGDSVSRLDRKEPEMSDNTPGDLRDTTTPIAMARTVAKVLYGGALTSTSTHTIERWLIGNQTGDATLRAGFPKDWVVGEKTGTCANGARNDIGFFKAQERDYAVAVYTTAPKLSAVERDELVASVGQVITQLILSTDK"},"dna_sequence":{"accession":"GU207844.1","fmin":"0","fmax":"864","strand":"+","sequence":"ATGCGCTTCATTCACGCACTATTACTGGCAGGGATCGCTCACTCTGCATATGCGTCGGAAAAATTAACCTTCAAGACCGATCTTGAGAAGCTAGAGCGCGAAAAAGCAGCTCAGATCGGTGTTGCGATCGTCGATCCCCAAGGAGAGATCGTCGCGGGCCACCGAATGGCGCAGCGTTTTGCAATGTGCTCAACGTTCAAGTTTCCGCTAGCCGCGCTGGTCTTTGAAAGAATTGACTCAGGCACCGAGCGGGGGGATCGAAAACTTTCATATGGGCCGGACATGATCGTCGAATGGTCTCCTGCCACGGAGCGGTTTCTAGCATCGGGACACATGACGGTTCTCGAGGCAGCGCAAGCTGCGGTGCAGCTTAGCGACAATGGGGCTACTAACCTCTTACTGAGAGAAATTGGCGGACCTGCTGCAATGACGCAGTATTTTCGTAAAATTGGCGACTCTGTGAGTCGGCTAGACCGGAAAGAGCCGGAGATGAGCGACAACACACCTGGCGACCTCAGAGATACAACTACGCCTATTGCTATGGCACGTACTGTGGCTAAAGTCCTCTATGGCGGCGCACTGACGTCCACCTCGACCCACACCATTGAGAGGTGGCTGATCGGAAACCAAACGGGAGACGCGACACTACGAGCGGGTTTTCCTAAAGATTGGGTTGTTGGAGAGAAAACTGGTACCTGCGCCAACGGGGCCCGGAACGACATTGGTTTTTTTAAAGCCCAGGAGAGAGATTACGCTGTAGCGGTGTATACAACGGCCCCGAAACTATCGGCCGTAGAACGTGACGAATTAGTTGCCTCTGTCGGTCAAGTTATTACACAACTCATCCTGAGCACGGACAAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3002343","ARO_id":"38743","ARO_name":"GES-14","CARD_short_name":"GES-14","ARO_description":"GES-14 is a beta-lactamase found in Acinetobacter baumannii.","ARO_category":{"36205":{"category_aro_accession":"3000066","category_aro_cvterm_id":"36205","category_aro_name":"GES beta-lactamase","category_aro_description":"GES beta-lactamases or Guiana extended-spectrum beta-lactamases are related to the other plasmid-located class A beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"182":{"model_id":"182","model_name":"arlS","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"880"}},"model_sequences":{"sequence":{"5398":{"protein_sequence":{"accession":"ABD30512.1","sequence":"MTKRKLRNNWIIVTTMITFVTIFLFCLIIIFFLKDTLHNSELDDAERSSSDINNLFHSKPVKDISALDLNASLGNFQEIIIYDEHNNKLFETSNDNTVRVEPGYEHRYFDRVIKKRYKGIEYLIIKEPITTQDFKGYSLLIHSLENYDNIVKSLYIIALAFGVIATIITATISYVFSTQITKPLVSLSNKMIEIRRDGFQNKLQLNTNYEEIDNLANTFNEMMSQIEESFNQQRQFVEDASHELRTPLQIIQGHLNLIQRWGKKDPAVLEESLNISIEEMNRIIKLVEELLELTKGDVNDISSEAQTVHINDEIRSRIHSLKQLHPDYQFDTDLTSKNLEIKMKPHQFEQLFLIFIDNAIKYDVKNKKIKVKTRLKNKQKIIEITDHGIGIPEEDQDFIFDRFYRVDKSRSRSQGGNGLGLSIAQKIIQLNGGSIKIKSEINKGTTFKIIF"},"dna_sequence":{"accession":"CP000253.1","fmin":"1360280","fmax":"1361636","strand":"-","sequence":"ATGACAAAACGTAAATTGCGCAATAACTGGATTATTGTTACCACGATGATTACGTTTGTCACGATATTTTTGTTTTGTTTAATTATTATTTTTTTCTTGAAAGATACACTGCATAATAGTGAGCTTGATGATGCAGAACGAAGCTCAAGCGATATTAATAATTTATTTCATTCTAAGCCTGTTAAAGATATATCTGCATTAGACTTGAATGCATCTTTAGGTAATTTTCAAGAGATAATTATTTATGATGAGCATAATAATAAATTATTTGAGACATCGAATGATAACACAGTGAGAGTTGAACCAGGTTATGAACACCGTTATTTTGACCGCGTAATAAAAAAACGCTATAAAGGCATTGAATATTTAATTATTAAAGAACCAATTACAACGCAAGATTTCAAAGGGTATAGCTTGTTAATTCATTCACTAGAAAATTATGATAACATCGTAAAATCATTGTATATCATTGCGCTGGCATTTGGAGTGATTGCAACAATTATAACTGCCACAATCAGTTATGTATTTTCAACACAAATTACTAAACCGCTTGTCAGTTTATCAAATAAAATGATTGAGATTCGACGAGATGGTTTTCAAAATAAATTGCAATTAAATACAAATTATGAAGAAATAGATAATTTAGCAAATACGTTTAATGAGATGATGAGCCAAATTGAAGAATCATTTAATCAACAAAGACAATTTGTTGAAGATGCGTCACATGAATTACGAACACCATTACAAATTATTCAAGGTCATTTAAATTTGATTCAGCGATGGGGAAAAAAAGACCCAGCAGTATTAGAAGAATCGTTAAATATTTCTATTGAAGAAATGAATCGTATCATAAAATTAGTCGAAGAATTACTTGAATTGACTAAAGGAGATGTAAATGACATTTCTTCTGAAGCACAGACCGTGCATATTAATGATGAAATTCGCTCGCGAATACACTCATTAAAACAATTGCATCCTGATTATCAATTTGATACGGATCTGACATCTAAAAATCTAGAAATTAAAATGAAACCTCATCAATTCGAACAATTATTTTTAATCTTTATTGATAATGCAATCAAATATGATGTGAAGAATAAGAAAATTAAAGTTAAGACAAGGTTAAAAAATAAGCAAAAAATAATTGAAATTACAGATCATGGAATTGGTATTCCAGAGGAAGATCAAGATTTCATTTTTGATCGCTTTTATCGAGTGGATAAATCTCGTTCAAGAAGTCAAGGCGGTAATGGACTCGGATTATCTATTGCTCAAAAAATCATTCAATTAAACGGAGGATCGATTAAAATTAAAAGTGAAATTAACAAAGGAACAACGTTTAAAATCATATTTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35511","NCBI_taxonomy_name":"Staphylococcus aureus subsp. aureus NCTC 8325","NCBI_taxonomy_id":"93061"}}}},"ARO_accession":"3000839","ARO_id":"37219","ARO_name":"arlS","CARD_short_name":"arlS","ARO_description":"ArlS is a protein histidine kinase that phosphorylates ArlR, a promoter for norA expression.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35963":{"category_aro_accession":"0000045","category_aro_cvterm_id":"35963","category_aro_name":"acriflavine","category_aro_description":"Acriflavine is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"43746":{"category_aro_accession":"3005386","category_aro_cvterm_id":"43746","category_aro_name":"disinfecting agents and antiseptics","category_aro_description":"Disinfectants that can also interact with antimicrobial resistance mechanisms, e.g. molecule efflux, and thus are the targets of disinfectant resistance.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"183":{"model_id":"183","model_name":"adeS","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"596":{"protein_sequence":{"accession":"ADM92606.1","sequence":"MKSKLGISKQLFIALTIVNLSVTLFSIVLGYIIYNYAIEKGWISLSSFQQEDWTSFHFVDWIWLATVIFCGCIISLVIGMRLAKRFIVPINFLVEAAKKISHGDLSARAYDNRIHSAEMSELLYNFNDMAQKLEVSVKNAQVWNAAIAHELRTPITILQGRLQGIIDGVFKPDEVLFKSLLNQVEGLSHLVEDLRTLSLVENQQLRLNYELFDLKAVVEKVLKAFEDRLDQAKLVPELDLTSTPVYCDRRRIEQVLIALIDNAIRYSNAGKLKISSEVVADNWILKIEDEGPGIATEFRDDLFKPFFRLEESRNKEFGGTGLGLAVVHAIIVALKGTIKYSNQGSKSVFTIKISMGHEEMG"},"dna_sequence":{"accession":"HM440348.1","fmin":"775","fmax":"1861","strand":"+","sequence":"ATGAAAAGTAAGTTAGGAATTAGTAAGCAACTTTTTATTGCCTTAACTATTGTGAATTTAAGCGTTACGCTATTTTCTATAGTATTGGGTTATATCATTTATAACTATGCGATTGAAAAAGGCTGGATTAGCTTAAGCTCATTTCAACAAGAAGATTGGACCAGTTTTCATTTTGTAGACTGGATCTGGTTAGCCACTGTTATCTTCTGTGGCTGTATTATTTCATTAGTGATTGGCATGCGCCTCGCAAAGCGTTTTATTGTGCCAATTAACTTCTTAGTCGAAGCAGCAAAAAAAATTAGTCACGGCGACCTCTCTGCTAGAGCTTACGATAATAGAATTCACTCCGCCGAAATGTCGGAGCTTTTATATAATTTTAATGATATGGCTCAAAAGCTAGAGGTTTCCGTCAAAAATGCGCAGGTTTGGAATGCAGCTATCGCACATGAGTTAAGAACGCCTATAACGATATTACAAGGTCGTTTACAGGGAATTATTGATGGCGTTTTTAAACCTGATGAAGTCCTATTTAAAAGCCTTTTAAATCAAGTTGAAGGTTTATCTCACTTAGTCGAAGACTTACGGACTTTAAGCTTAGTAGAGAACCAGCAACTCCGGTTAAATTATGAATTGTTTGACTTGAAGGCGGTAGTTGAAAAAGTTCTTAAAGCATTTGAAGATCGTTTGGATCAAGCTAAGCTAGTACCAGAACTTGACCTAACGTCCACTCCTGTATATTGCGACCGCCGTCGTATTGAGCAAGTTTTAATTGCTTTAATTGATAATGCGATTCGCTATTCAAATGCAGGCAAACTTAAAATCTCTTCAGAAGTGGTTGCAGACAACTGGATATTAAAAATTGAGGATGAAGGCCCCGGCATTGCAACCGAGTTTCGGGACGATTTATTTAAGCCTTTCTTTAGATTAGAAGAATCAAGGAATAAAGAATTTGGCGGCACAGGTTTAGGTCTTGCTGTTGTACATGCAATTATTGTGGCACTGAAAGGCACTATTAAATATAGCAATCAAGGCTCGAAAAGTGTTTTCACCATAAAAATTTCTATGGGTCATGAAGAGATGGGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3000549","ARO_id":"36688","ARO_name":"adeS","CARD_short_name":"adeS","ARO_description":"AdeS is a sensor kinase in the AdeRS regulatory system of AdeABC. It is essential for AdeABC expression.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"184":{"model_id":"184","model_name":"OCH-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1426":{"protein_sequence":{"accession":"CAC04522.1","sequence":"MRKSTTLLIGFLTTAAIIPNSGALAASKVNDGDLRRIVDETVRPLMAEQKIPGMAVAITIDGKSHFFGYGVASKESGQKVTEDTIFEIGSVSKTFTAMLGGYGLATGAFSLSDPATKWAPELAGSSFDKITMRDLGTYTPGGLPLQFPDAVTDDSSMLAYFKKWKPDYPAGTQRRYSNPSIGLFGYLAARSMDKPFDVLMEQKLLPAFGLKNTFINVPASQMKNYAYGYSKANKPIRVSGGALDAQAYGIKTTALDLARFVELNIDSSSLEPDFQKAVAATHTGYYHVGANNQGLGWEFYNYPTALKTLLEGNSSDMALKSHKIEKFDTPRQPSADVLINKTGSTNGFGAYAAFIPAKKTGIVLLANRNYPIDERVKAAYRILQALDNKQ"},"dna_sequence":{"accession":"AJ401618.1","fmin":"1971","fmax":"3144","strand":"+","sequence":"ATGAGAAAATCTACGACACTTTTGATCGGTTTCCTCACCACTGCCGCTATTATCCCGAATAGCGGCGCGCTGGCTGCGAGCAAGGTGAATGATGGCGACTTGCGCCGTATTGTCGATGAAACGGTGCGCCCGCTCATGGCCGAGCAGAAAATCCCCGGCATGGCGGTTGCCATAACCATCGACGGCAAGAGCCACTTCTTCGGTTATGGTGTGGCATCGAAAGAAAGCGGGCAAAAAGTCACTGAAGACACGATTTTCGAGATCGGTTCGGTCAGCAAGACCTTCACTGCAATGCTTGGCGGTTACGGGCTGGCGACAGGCGCGTTCTCCCTGTCCGATCCCGCGACCAAATGGGCTCCTGAACTGGCAGGCAGCAGCTTCGACAAGATCACCATGCGTGATCTTGGGACCTACACGCCGGGCGGATTGCCCCTCCAGTTTCCCGATGCTGTCACCGATGACAGTTCGATGCTGGCATATTTCAAGAAATGGAAGCCGGACTATCCGGCAGGGACGCAGCGTCGCTATTCGAATCCCAGCATCGGCCTGTTCGGCTATCTGGCGGCACGAAGCATGGACAAGCCGTTCGACGTTTTGATGGAGCAAAAGCTTCTGCCTGCATTCGGCCTGAAGAACACCTTCATCAATGTGCCGGCAAGCCAGATGAAGAACTACGCCTACGGCTATTCCAAAGCCAACAAGCCGATCCGGGTATCGGGCGGGGCGCTGGATGCACAAGCCTATGGCATCAAGACCACCGCGCTTGATCTTGCCCGCTTCGTCGAACTGAACATCGACAGCTCATCTCTGGAGCCTGATTTCCAGAAAGCCGTCGCCGCAACGCATACCGGTTACTACCATGTCGGAGCGAACAATCAGGGACTTGGCTGGGAGTTCTACAACTATCCGACTGCGCTCAAGACGCTTCTTGAGGGCAACTCGTCGGACATGGCGCTGAAGTCGCACAAAATCGAGAAATTCGATACACCTCGCCAACCGTCAGCTGATGTGCTGATCAATAAGACAGGCTCAACCAACGGCTTTGGCGCTTATGCGGCCTTTATTCCTGCGAAGAAGACCGGAATTGTTCTGCTTGCCAACCGGAATTATCCGATCGATGAGCGCGTAAAGGCTGCCTATCGGATATTGCAGGCGCTCGACAACAAGCAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37077","NCBI_taxonomy_name":"Brucella anthropi","NCBI_taxonomy_id":"529"}}}},"ARO_accession":"3002514","ARO_id":"38914","ARO_name":"OCH-1","CARD_short_name":"OCH-1","ARO_description":"OCH-1 beta-lactamase is an Ambler class C chromosomal-encoded beta-lactamases in Brucella anthropi.","ARO_category":{"36233":{"category_aro_accession":"3000094","category_aro_cvterm_id":"36233","category_aro_name":"OCH beta-lactamase","category_aro_description":"OCH beta-lactamases are Ambler class C chromosomal-encoded beta-lactamases in Brucella anthropi.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"185":{"model_id":"185","model_name":"OXA-232","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1129":{"protein_sequence":{"accession":"AGD91915.1","sequence":"MRVLALSAVFLVASIIGMPAVAKEWQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGQTRDIAAWNRDHDLITAMKYSVVPVYQEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISATQQIAFLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYSTSIEPKIGWWVGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP"},"dna_sequence":{"accession":"JX423831.1","fmin":"2676","fmax":"3474","strand":"+","sequence":"ATGCGTGTATTAGCCTTATCGGCTGTGTTTTTGGTGGCATCGATTATCGGAATGCCAGCGGTAGCAAAGGAATGGCAAGAAAACAAAAGTTGGAATGCTCACTTTACTGAACATAAATCACAGGGCGTAGTTGTGCTCTGGAATGAGAATAAGCAGCAAGGATTTACCAATAATCTTAAACGGGCGAACCAAGCATTTTTACCCGCATCTACCTTTAAAATTCCCAATAGCTTGATCGCCCTCGATTTGGGCGTGGTTAAGGATGAACACCAAGTCTTTAAGTGGGATGGACAGACGCGTGATATCGCCGCTTGGAATCGTGACCATGACTTAATTACCGCGATGAAGTACTCAGTTGTGCCTGTTTATCAAGAATTTGCCCGCCAAATTGGTGAGGCACGTATGAGTAAAATGCTGCACGCCTTCGATTATGGCAATGAGGATATCTCGGGCAATGTAGACAGTTTTTGGCTCGATGGTGGTATTCGCATTTCGGCTACCCAGCAAATCGCTTTTTTACGCAAGCTGTATCACAACAAGCTGCACGTTTCTGAGCGTAGTCAGCGCATCGTGAAACAAGCCATGCTGACCGAAGCCAATGGCGACTATATTATTCGGGCTAAAACGGGATACTCGACTAGTATCGAACCTAAGATTGGCTGGTGGGTTGGTTGGGTTGAACTTGATGATAATGTGTGGTTTTTTGCGATGAATATGGATATGCCCACATCGGATGGTTTAGGGCTGCGCCAAGCCATCACAAAAGAAGTGCTCAAACAGGAGAAAATTATTCCCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001778","ARO_id":"38178","ARO_name":"OXA-232","CARD_short_name":"OXA-232","ARO_description":"OXA-232 is a beta-lactamase found in Enterobacteriaceae.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46510":{"category_aro_accession":"3007721","category_aro_cvterm_id":"46510","category_aro_name":"OXA-48-like beta-lactamase","category_aro_description":"OXA-48-type beta-lactamases are now routinely encountered in bacterial infections caused by carbapenam-resistant Enterobacterales. OXA-48-like proteins confer resistance to penicillin (which is efficiently hydrolyzed) and carbapenam antibiotics (which is more slowly broken down). The spectrum of activity of these variants varies, with some hydrolyzing expanded-spectrum oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"186":{"model_id":"186","model_name":"OXA-12","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1123":{"protein_sequence":{"accession":"AAA83417.1","sequence":"MSRLLLSGLLATGLLCAVPASAASGCFLYADGNGQTLSSEGDCSSQLPPASTFKIPLALMGYDSGFLVNEEHPALPYKPSYDGWLPAWRETTTPRRWETYSVVWFSQQITEWLGMERFQQYVDRFDYGNRDLSGNPGKHDGLTQAWLSSSLAISPEEQARFLGKMVSGKLPVSAQTLQYTANILKVSEVEGWQIHGKTGMGYPKKLDGSLNRDQQIGWFVGWASKPGKQLIFVHTVVQKPGKQFASIKAKEEVLAALPAQLKKL"},"dna_sequence":{"accession":"U10251.1","fmin":"180","fmax":"975","strand":"+","sequence":"ATGTCTCGCCTGCTTCTTTCCGGCCTGCTGGCTACCGGTCTGCTCTGTGCAGTACCGGCCTCCGCCGCCAGCGGCTGTTTTCTCTATGCCGATGGCAACGGTCAGACCCTCTCCAGCGAAGGGGACTGCTCCAGCCAGCTGCCGCCCGCATCCACCTTCAAGATCCCGCTGGCGCTGATGGGTTATGACAGTGGCTTTCTGGTGAATGAAGAGCATCCGGCGCTGCCCTACAAGCCGAGCTATGACGGCTGGCTGCCCGCCTGGCGCGAAACCACTACCCCGCGCCGCTGGGAAACCTATTCGGTGGTCTGGTTCTCCCAGCAGATCACCGAGTGGCTGGGGATGGAGCGCTTCCAGCAATACGTCGACCGCTTCGACTACGGCAACCGGGATCTCTCCGGCAATCCGGGCAAGCATGACGGTCTGACCCAAGCCTGGCTCAGCTCGAGCCTCGCCATCAGTCCGGAGGAGCAGGCTCGCTTCCTCGGCAAGATGGTGAGCGGCAAGCTGCCGGTCTCGGCGCAGACCCTGCAGTACACCGCCAATATCCTCAAGGTGAGCGAGGTCGAGGGCTGGCAGATCCACGGCAAGACCGGCATGGGCTACCCGAAGAAACTGGATGGCAGCCTCAACCGCGATCAGCAGATCGGCTGGTTCGTCGGCTGGGCCAGCAAACCGGGCAAGCAGCTCATTTTCGTTCATACCGTGGTGCAGAAACCGGGCAAGCAATTCGCCTCTATCAAGGCGAAAGAAGAGGTGCTGGCCGCCCTGCCCGCGCAACTCAAGAAACTCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36957","NCBI_taxonomy_name":"Aeromonas sobria","NCBI_taxonomy_id":"646"}}}},"ARO_accession":"3001407","ARO_id":"37807","ARO_name":"OXA-12","CARD_short_name":"OXA-12","ARO_description":"OXA-12 is a beta-lactamase found in Aeromonas jandaei.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46488":{"category_aro_accession":"3007699","category_aro_cvterm_id":"46488","category_aro_name":"OXA-12-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-12.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"187":{"model_id":"187","model_name":"OXA-348","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"808":{"protein_sequence":{"accession":"AGW83446.1","sequence":"MYKKALIVATSILFLSACSSNMVKQHQIHSISANKNSEEIKSLFDQAQTTGVLVIKRGQTEEIYGNDLKRASTDYVPASTFKMLNALIGLEHHKATTTEVFKWNGQKRLFPDWEKDMTLSDAMKASAIPVYQELARRIGLDLMSKEVKRIGFGNANIGSKVDDFWLVGPLKITPQQETQFAYQLAHKTLPFSKNVQEQVQSMVFIEEKNGSKIYAKSGWGWDVEPQVGWLTGWVVQPQGEIVAFSLNLEMKKGTPSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"KF297577.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGTATAAAAAAGCCCTTATCGTTGCAACAAGTATCCTATTTTTATCCGCCTGTTCTTCCAATATGGTCAAACAACATCAAATACACTCTATTTCTGCCAATAAAAATTCAGAAGAAATTAAATCACTGTTTGATCAAGCACAGACCACTGGAGTTTTGGTGATTAAGCGAGGGCAAACAGAAGAAATTTATGGCAATGATCTTAAAAGAGCATCAACCGACTATGTTCCCGCCTCTACCTTTAAAATGTTAAATGCTTTAATTGGACTTGAACATCATAAGGCAACTACAACTGAAGTATTTAAATGGAATGGGCAAAAACGTTTATTTCCTGATTGGGAAAAGGACATGACACTGAGCGATGCCATGAAAGCTTCTGCAATTCCAGTTTACCAAGAATTAGCCCGACGGATTGGTCTGGATCTTATGTCCAAAGAGGTGAAACGAATTGGTTTCGGTAATGCTAACATTGGCTCAAAAGTAGATGATTTTTGGCTTGTTGGCCCTCTAAAAATTACACCTCAACAAGAAACCCAATTTGCTTATCAATTAGCCCATAAAACTCTTCCATTTAGCAAAAATGTACAAGAACAAGTTCAATCGATGGTGTTCATAGAGGAAAAAAATGGAAGTAAAATTTATGCCAAAAGTGGTTGGGGATGGGATGTTGAACCGCAAGTTGGTTGGTTAACAGGCTGGGTCGTTCAACCACAAGGAGAAATTGTGGCATTTTCACTTAATTTAGAAATGAAAAAAGGAACTCCTAGCTCTATTCGCAAAGAAATTGCTTATAAAGGCTTAGAACAACTGGGTATTTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39094","NCBI_taxonomy_name":"Acinetobacter calcoaceticus","NCBI_taxonomy_id":"471"}}}},"ARO_accession":"3001535","ARO_id":"37935","ARO_name":"OXA-348","CARD_short_name":"OXA-348","ARO_description":"OXA-348 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46495":{"category_aro_accession":"3007706","category_aro_cvterm_id":"46495","category_aro_name":"OXA-213-like beta-lactamase","category_aro_description":"OXA-213-like enzymes have been identified to be intrinsic to A. calcoaceticus and have been subsequently detected in A. pittii. Phylogenetic analysis of OXA-213-like proteins identified two distinct subgroups within the OXA family. The first group was linked to A. pittii and the second group to A. calcoaceticus. The carbapenemase activity of these OXAs may be related to the species-dependent effect.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"188":{"model_id":"188","model_name":"SHV-89","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1641":{"protein_sequence":{"accession":"ABA60809.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITVSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"DQ193536.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCGTGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATCGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001141","ARO_id":"37521","ARO_name":"SHV-89","CARD_short_name":"SHV-89","ARO_description":"SHV-89 is a broad-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"189":{"model_id":"189","model_name":"CTX-M-19","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1009":{"protein_sequence":{"accession":"AAK55534.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTESTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"AF325134.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAATCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGACTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001881","ARO_id":"38281","ARO_name":"CTX-M-19","CARD_short_name":"CTX-M-19","ARO_description":"CTX-M-19 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"190":{"model_id":"190","model_name":"OXA-195","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"2003":{"protein_sequence":{"accession":"AEB98921.1","sequence":"MNIKALFLITSAIFISACSPYIVTANPNHSASKSDVKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWVVGPLKITPQQEAQFAYKLANKTLPSSQKVQDEVQSMLFIEEKNGNKMYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"HQ425493.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGAACATTAAAGCACTCTTCCTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGTAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGGTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATCTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAGAAGAATGGAAACAAAATGTACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTA","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36949","NCBI_taxonomy_name":"Acinetobacter nosocomialis","NCBI_taxonomy_id":"106654"}}}},"ARO_accession":"3001480","ARO_id":"37880","ARO_name":"OXA-195","CARD_short_name":"OXA-195","ARO_description":"OXA-195 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"191":{"model_id":"191","model_name":"OXA-199","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1047":{"protein_sequence":{"accession":"AFC95894.1","sequence":"MRVLALSAVFLVASIIGMPAVAKEWQENKSWNAHFTEYKSQGVVALWNENKQQGFTNNLKRANQAFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGQTRDIATWNRDHNLITAMKYSVVPVYQEFARQIGEARMSKMLHAFDYGNEDISGNVGSFWLDGGIRISATEQISFLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYSTRIEPKIGWWVGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP"},"dna_sequence":{"accession":"JN704570.1","fmin":"4038","fmax":"4836","strand":"+","sequence":"ATGCGTGTATTAGCCTTATCGGCTGTGTTTTTGGTGGCATCGATTATCGGAATGCCTGCGGTAGCAAAGGAATGGCAAGAAAACAAAAGTTGGAATGCTCACTTTACTGAATATAAATCACAGGGCGTAGTTGCGCTCTGGAATGAGAATAAGCAGCAAGGATTTACCAATAATCTTAAACGGGCGAACCAAGCATTTTTACCCGCATCTACCTTTAAAATTCCCAATAGCTTGATCGCCCTCGATTTGGGCGTGGTTAAGGATGAACACCAAGTCTTTAAGTGGGATGGACAGACGCGCGATATCGCCACTTGGAATCGCGATCATAATCTAATCACCGCGATGAAATATTCAGTTGTGCCTGTTTATCAAGAATTTGCCCGCCAAATTGGCGAGGCACGTATGAGCAAGATGCTACATGCTTTCGATTATGGTAATGAGGACATTTCGGGCAATGTAGGCAGTTTCTGGCTCGACGGTGGTATTCGAATTTCGGCCACTGAGCAAATCAGCTTTTTAAGAAAGCTGTATCACAATAAGTTACACGTATCGGAGCGCAGCCAGCGTATTGTCAAACAAGCCATGCTGACCGAAGCCAATGGCGACTATATTATTCGGGCTAAAACTGGATACTCGACTAGAATCGAACCTAAGATTGGCTGGTGGGTCGGTTGGGTTGAACTTGATGATAATGTGTGGTTTTTTGCGATGAATATGGATATGCCCACATCGGATGGTTTAGGGCTGCGCCAAGCCATCACAAAAGAAGTGCTCAAACAGGAAAAAATTATTCCCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39674","NCBI_taxonomy_name":"Shewanella xiamenensis","NCBI_taxonomy_id":"332186"}}}},"ARO_accession":"3001814","ARO_id":"38214","ARO_name":"OXA-199","CARD_short_name":"OXA-199","ARO_description":"OXA-199 is a beta-lactamase found in Shewanella spp.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46510":{"category_aro_accession":"3007721","category_aro_cvterm_id":"46510","category_aro_name":"OXA-48-like beta-lactamase","category_aro_description":"OXA-48-type beta-lactamases are now routinely encountered in bacterial infections caused by carbapenam-resistant Enterobacterales. OXA-48-like proteins confer resistance to penicillin (which is efficiently hydrolyzed) and carbapenam antibiotics (which is more slowly broken down). The spectrum of activity of these variants varies, with some hydrolyzing expanded-spectrum oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"192":{"model_id":"192","model_name":"CTX-M-38","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1352":{"protein_sequence":{"accession":"AAV70602.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAARIRAGLPTSWTVGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"AY822595.1","fmin":"22","fmax":"898","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGAATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGACTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001900","ARO_id":"38300","ARO_name":"CTX-M-38","CARD_short_name":"CTX-M-38","ARO_description":"CTX-M-38 is a beta-lactamase found in Escherichia coli.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"193":{"model_id":"193","model_name":"TEM-121","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1154":{"protein_sequence":{"accession":"AAQ01671.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDKLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVKYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDSWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGTGKRGSSGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AY271267.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATAAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTAAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATAGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAACCGGTAAGCGTGGGTCTAGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000983","ARO_id":"37363","ARO_name":"TEM-121","CARD_short_name":"TEM-121","ARO_description":"TEM-121 is an inhibitor-resistant, extended-spectrum beta-lactamase found in E. coli and Klebsiella aerogenes.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"194":{"model_id":"194","model_name":"SHV-61","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"8137":{"protein_sequence":{"accession":"CAI30650.2","sequence":"MRYIRRCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AJ866284.2","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCGGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGCATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001116","ARO_id":"37496","ARO_name":"SHV-61","CARD_short_name":"SHV-61","ARO_description":"SHV-61 is a broad-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"195":{"model_id":"195","model_name":"CTX-M-58","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1705":{"protein_sequence":{"accession":"ABM97538.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAVAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVDGTMSLAELSAAALQYSDNVAMNKLISHVGGPASVTAFARQLGDETFRLDRTETTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGDYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTNGL"},"dna_sequence":{"accession":"EF210159.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGTCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGAAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGTGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACTTGGTTAACTATAATCCGATTGCGGAAAAGCACGTCGATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTTCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGACGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGTAATCTGACGCTGGGTAAAGCATTGGGTGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGACTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCAACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001919","ARO_id":"38319","ARO_name":"CTX-M-58","CARD_short_name":"CTX-M-58","ARO_description":"CTX-M-58 is a beta-lactamase found in Escherichia coli.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"197":{"model_id":"197","model_name":"CTX-M-56","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1629":{"protein_sequence":{"accession":"ABN48311.1","sequence":"MMTQSIRRSMLTVMATLPLLFSSATLHAQANSVQQQLEALEKSSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKQSESDKHLLNQRVEIKKSDLVNYNPIAEKHVNGTMTLAELGAAALQYSDNTAMNKLIAHLGGPDKVTAFARSLGDETFRLDRTEPTLNTAIPGDPRDTTTPLAMAQTLKNLTLGKALAETQRAQLVTWLKGNTTGSASIRAGLPKSWVVGDKTGSGDYGTTNDIAVIWPENHAPLVLVTYFTQPEQKAENRRDILAAAAKIVTHGF"},"dna_sequence":{"accession":"EF374097.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGATGACTCAGAGCATTCGCCGCTCAATGTTAACGGTGATGGCGACGCTACCCCTGCTATTTAGCAGCGCAACGCTGCATGCGCAGGCGAACAGCGTGCAACAGCAGCTGGAAGCCCTGGAGAAAAGTTCGGGAGGTCGGCTTGGCGTTGCGCTGATTAACACCGCCGATAATTCGCAGATTCTCTACCGTGCCGATGAACGTTTTGCGATGTGCAGTACCAGTAAGGTGATGGCGGCCGCGGCGGTGCTTAAACAGAGCGAGAGCGATAAGCACCTGCTAAATCAGCGCGTTGAAATCAAGAAGAGCGACCTGGTTAACTACAATCCCATTGCGGAGAAACACGTTAACGGCACGATGACGCTGGCTGAGCTTGGCGCAGCGGCGCTGCAGTATAGCGACAATACTGCCATGAATAAGCTGATTGCCCATCTGGGTGGTCCCGATAAAGTGACGGCGTTTGCTCGCTCGTTGGGTGATGAGACCTTCCGTCTGGACAGAACCGAGCCCACGCTCAATACCGCCATTCCAGGCGACCCGCGTGATACCACCACGCCGCTCGCGATGGCGCAGACCCTGAAAAATCTGACGCTGGGTAAAGCGCTGGCGGAAACTCAGCGGGCACAGTTGGTGACGTGGCTTAAGGGCAATACTACCGGTAGCGCGAGCATTCGGGCGGGTCTGCCGAAATCATGGGTAGTGGGCGATAAAACCGGCAGCGGAGATTATGGCACCACCAACGATATCGCGGTTATCTGGCCGGAAAACCACGCACCGCTGGTTCTGGTGACCTACTTTACCCAACCGGAGCAGAAGGCGGAAAACCGTCGGGATATTCTGGCTGCGGCGGCGAAAATCGTAACCCACGGTTTCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001918","ARO_id":"38318","ARO_name":"CTX-M-56","CARD_short_name":"CTX-M-56","ARO_description":"CTX-M-56 is a beta-lactamase found in Escherichia coli.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"198":{"model_id":"198","model_name":"TEM-138","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1242":{"protein_sequence":{"accession":"AAW47922.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVKYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPIDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGASERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AY853593.1","fmin":"214","fmax":"1075","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTAAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAATCGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCAGTGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35672","NCBI_taxonomy_name":"Salmonella enterica","NCBI_taxonomy_id":"28901"}}}},"ARO_accession":"3001002","ARO_id":"37382","ARO_name":"TEM-138","CARD_short_name":"TEM-138","ARO_description":"TEM-138 is an extended-spectrum beta-lactamase found in Salmonella enterica.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"199":{"model_id":"199","model_name":"SRT-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"725"}},"model_sequences":{"sequence":{"1718":{"protein_sequence":{"accession":"BAA23130.1","sequence":"MTKMNRLAAALIAALILPTAQAAQQQDIDAVIQPLMKKYGVPGMAIAVSVDGKQQIYPYGVASKQTGKPITEQTLFEVGSLSKTFTATLAVYAQQQGKLSFNDPASRYLPELRGSAFDGVSLLNLATHTSGLPLFVPDDVTNDAQLMAYYRAWQPKHPAGSYRVYSNLGIVMLGMIAAKSLDQPFIQAMEQGMLPALGMSHTYVQVPAAQMANYAQGYSKDDKPVRVNPGPLDAKSYGIKSNARDLIRYLDANLQQVKVAHAWRDALAATHVGYYKAGAFTQDLMWENYPYPVKLSRLIEGNNAGMIMNGTPATAITPPQPELRAGWYNKTGSTGGFSTYAVFIPAKNIAVVMLANKWFPNDDRVEAAYHIVQALEKR"},"dna_sequence":{"accession":"AB008454.1","fmin":"153","fmax":"1290","strand":"+","sequence":"ATGACGAAAATGAACCGCCTGGCGGCCGCGCTGATCGCCGCACTGATCTTGCCGACCGCGCAGGCCGCGCAGCAGCAGGATATCGACGCCGTTATTCAGCCGCTGATGAAAAAATATGGCGTACCGGGCATGGCGATCGCCGTGTCGGTCGACGGCAAACAGCAGATTTACCCGTATGGCGTCGCCTCGAAGCAGACCGGCAAACCGATCACCGAGCAGACGCTGTTCGAAGTGGGCTCGCTGAGCAAAACCTTTACCGCGACGCTGGCGGTCTATGCGCAGCAGCAGGGCAAGCTGTCGTTCAACGATCCGGCCAGCCGCTATCTGCCCGAGCTGCGCGGCAGCGCCTTCGACGGCGTCAGCCTGCTGAATCTGGCGACGCATACCTCCGGCCTGCCGCTGTTCGTGCCGGACGACGTCACCAACGACGCCCAGCTGATGGCCTACTACCGGGCCTGGCAGCCGAAACACCCGGCGGGCAGCTACCGCGTCTATTCCAACCTCGGCATCGTCATGCTGGGCATGATCGCCGCCAAGAGCCTCGACCAGCCGTTTATCCAGGCGATGGAACAGGGGATGCTGCCGGCGCTGGGCATGAGCCACACCTACGTTCAGGTGCCGGCGGCGCAGATGGCTAACTATGCGCAGGGTTACAGCAAGGACGATAAGCCGGTGCGGGTCAATCCCGGCCCGCTGGACGCCAAATCTTACGGCATCAAGTCCAACGCTCGCGATCTGATTCGCTATCTGGACGCCAACCTGCAGCAGGTGAAGGTGGCGCACGCGTGGCGCGACGCGCTGGCCGCGACGCACGTCGGGTATTACAAGGCGGGCGCGTTCACGCAGGATCTGATGTGGGAGAACTACCCGTATCCGGTGAAACTGTCGCGTTTGATTGAAGGCAACAACGCCGGGATGATCATGAACGGCACGCCGGCCACCGCCATCACGCCACCGCAGCCGGAATTGCGCGCCGGCTGGTATAACAAAACCGGCTCCACCGGCGGCTTCTCCACCTACGCGGTATTTATCCCGGCGAAAAATATCGCCGTGGTGATGCTGGCCAACAAGTGGTTCCCGAACGACGATCGCGTCGAGGCGGCTTACCACATCGTCCAGGCGCTGGAGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36783","NCBI_taxonomy_name":"Serratia marcescens","NCBI_taxonomy_id":"615"}}}},"ARO_accession":"3002493","ARO_id":"38893","ARO_name":"SRT-1","CARD_short_name":"SRT-1","ARO_description":"SRT-1, isolated from Serratia marcescens, confers resistance to cephalosporins but not carbapenems, penems and monobactams.","ARO_category":{"36234":{"category_aro_accession":"3000095","category_aro_cvterm_id":"36234","category_aro_name":"SRT beta-lactamase","category_aro_description":"SRT beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"200":{"model_id":"200","model_name":"LEN-14","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"8427":{"protein_sequence":{"accession":"AAP93847.1","sequence":"SLLATLPLAVYAGPQPLEQIKQSESQLSGRVGMVEMDLASGRTLAAWRADERFPMVSTFKVLLCGAVLARVDAGLEQLDRRIHYRQQDLVDYSPVSEKHLTDGMTIGELCAAAITLSDNCAGNLLLATVGGPAGLTAFLRQIGDNVTRLDRW"},"dna_sequence":{"accession":"AY265889.1","fmin":"2","fmax":"458","strand":"+","sequence":"TCCCTGTTAGCCACCCTGCCACTGGCGGTATACGCCGGTCCACAGCCGCTTGAGCAGATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTGGGGATGGTGGAAATGGATCTGGCCAGCGGCCGCACGCTGGCGGCCTGGCGCGCCGATGAACGCTTTCCCATGGTGAGCACCTTTAAAGTGCTGCTGTGCGGCGCGGTGCTGGCGCGGGTGGATGCCGGGCTCGAACAACTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTACCGACGGGATGACGATCGGCGAACTCTGCGCCGCCGCCATCACCCTGAGCGATAACTGCGCTGGCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCGGGATTAACTGCCTTTCTGCGCCAGATCGGTGACAACGTCACCCGTCTTGACCGCTGG","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3002477","ARO_id":"38877","ARO_name":"LEN-14","CARD_short_name":"LEN-14","ARO_description":"LEN-14 is a beta-lactamase. From the Pasteur Institute list of LEN beta-lactamases.","ARO_category":{"36236":{"category_aro_accession":"3000097","category_aro_cvterm_id":"36236","category_aro_name":"LEN beta-lactamase","category_aro_description":"LEN beta-lactamases are chromosomal class A beta-lactamases that confer resistance to ampicillin, amoxicillin, carbenicillin, and ticarcillin but not to extended-spectrum beta-lactams.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"201":{"model_id":"201","model_name":"OCH-3","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1582":{"protein_sequence":{"accession":"CAC17623.1","sequence":"MRKSTTLLIGFLTTAAIIPNNGALAASKANDGDLRRIVDETVRPLMAEQKIPGMAVAITIDGKSHFFGYGVASKESGQKVTEDTIFEIGSVSKTFTAMLGGYGLATGAFTLSDPATKWAPELADSSFDKITMLDLGTYTPGGLPLQFPDAVSDDSSMLAYFKKWKPDYPAGTQRRYSNPSIGLFGYLAARSMDKPFDVLMEQKLLPAFGLKNTFINVPESQMKNYAYGYSKANKPIRVSGGALDAQAYGIKTTALDLARFVELNIDSSSLEPDFQKAVAATHTGYYRVDANNQGLGWEFYNYPTALKTLLEGNSSDMALKSHKIEKFDTPSQPSADVWLNKTGSTNGFGAYAAFIPAKKIGIVLLANRNYPIDERVKAAYRILQALDNKQ"},"dna_sequence":{"accession":"AJ295341.1","fmin":"0","fmax":"1173","strand":"+","sequence":"ATGAGAAAATCTACGACACTTTTGATCGGTTTCCTCACCACTGCCGCTATTATCCCGAATAATGGCGCGCTGGCTGCGAGCAAGGCGAATGATGGCGACTTGCGCCGTATTGTCGATGAAACGGTGCGCCCGCTCATGGCCGAGCAGAAAATCCCCGGCATGGCCGTCGCTATAACCATCGACGGCAAGAGCCACTTCTTCGGTTATGGTGTGGCATCGAAGGAAAGCGGGCAAAAAGTCACCGAAGACACGATTTTCGAGATCGGCTCGGTCAGCAAGACCTTCACTGCAATGCTCGGCGGCTACGGGCTGGCGACAGGCGCGTTCACTCTGTCCGATCCCGCGACCAAATGGGCCCCCGAACTGGCAGACAGCAGCTTCGACAAGATCACCATGCTTGATCTTGGGACCTACACGCCGGGCGGATTGCCCCTCCAGTTTCCCGATGCTGTCTCCGATGACAGTTCGATGCTGGCATATTTCAAGAAATGGAAGCCGGACTATCCGGCAGGCACGCAGCGTCGCTATTCGAATCCCAGCATCGGCCTGTTCGGCTATCTGGCGGCACGAAGCATGGACAAGCCGTTCGACGTTTTGATGGAGCAAAAGCTTCTGCCTGCATTCGGCCTGAAGAACACCTTCATCAATGTGCCGGAAAGCCAGATGAAGAACTACGCCTACGGCTATTCCAAAGCCAACAAGCCGATCCGGGTATCGGGCGGGGCGCTGGATGCACAAGCCTATGGCATCAAGACCACCGCGCTTGATCTTGCCCGCTTCGTCGAACTGAACATCGACAGCTCATCTCTGGAGCCTGATTTCCAGAAAGCCGTCGCCGCAACGCATACCGGTTACTACCGTGTCGATGCGAACAATCAGGGGCTTGGCTGGGAGTTCTACAACTATCCGACCGCGCTCAAGACGCTTCTTGAGGGCAACTCGTCGGACATGGCGCTGAAGTCGCACAAAATCGAGAAATTCGATACACCTAGCCAACCGTCAGCTGATGTGTGGCTCAACAAGACAGGCTCAACCAACGGCTTTGGCGCTTATGCGGCCTTTATTCCTGCGAAGAAGATCGGAATTGTTCTGCTTGCCAACCGGAACTATCCGATTGATGAGCGCGTAAAGGCTGCCTATCGGATATTGCAGGCGCTCGACAACAAGCAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37077","NCBI_taxonomy_name":"Brucella anthropi","NCBI_taxonomy_id":"529"}}}},"ARO_accession":"3002516","ARO_id":"38916","ARO_name":"OCH-3","CARD_short_name":"OCH-3","ARO_description":"OCH-3 beta-lactamase is an Ambler class C chromosomal-encoded beta-lactamases in Brucella anthropi.","ARO_category":{"36233":{"category_aro_accession":"3000094","category_aro_cvterm_id":"36233","category_aro_name":"OCH beta-lactamase","category_aro_description":"OCH beta-lactamases are Ambler class C chromosomal-encoded beta-lactamases in Brucella anthropi.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"202":{"model_id":"202","model_name":"SHV-101","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1620":{"protein_sequence":{"accession":"ABV72593.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDGRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"EU155018.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGGTCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGCATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATATATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001150","ARO_id":"37530","ARO_name":"SHV-101","CARD_short_name":"SHV-101","ARO_description":"SHV-101 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"203":{"model_id":"203","model_name":"OXY-2-8","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1695":{"protein_sequence":{"accession":"AAL17873.1","sequence":"MIKSSWRKIAMLAAAVPLLLASSALWASTDAIHQKLTDLEKRSGGRLGVALINTADNSQILYRGDERFAMCSTSKVMAAAAVLKQSESNKEVVNKRLEINAADLVVWSPITEKHLQSGMTLAELSAATLQYSDNTAMNLIIGYLGGPEKVTAFARSIGDATFRLDRTEPTLNTAIPGDERDTSTPLAMAESLRKLTLGNALGEQQRAQLVTWLKGNTTGGQSIRAGLPESWVVGDKTGAGDYGTTNDIAVIWPENHAPLVLVTYFTQPQQDAKNRKEVLAAAAKIVTEGL"},"dna_sequence":{"accession":"AY055205.1","fmin":"181","fmax":"1054","strand":"+","sequence":"ATGATAAAAAGTTCGTGGCGTAAAATTGCAATGCTAGCCGCCGCCGTTCCGCTGCTGCTGGCGAGCAGCGCACTGTGGGCCAGTACCGATGCTATCCATCAGAAGCTGACAGATCTCGAGAAGCGTTCAGGCGGCAGGTTGGGCGTGGCGCTAATCAACACGGCAGATAATTCTCAAATCTTATATCGCGGCGACGAGCGTTTTGCCATGTGCAGCACCAGTAAAGTGATGGCCGCCGCCGCGGTATTAAAACAGAGCGAAAGCAATAAAGAGGTGGTAAATAAAAGGCTGGAGATTAACGCAGCCGATTTGGTGGTCTGGAGTCCGATTACCGAAAAACATCTCCAGAGCGGAATGACGCTGGCTGAGCTAAGCGCGGCGACGCTGCAATATAGCGACAATACGGCGATGAATCTGATCATCGGCTACCTTGGCGGGCCGGAAAAAGTCACCGCCTTCGCCCGCAGTATCGGCGATGCCACCTTTCGTCTCGATCGTACGGAGCCCACGCTGAATACCGCCATCCCGGGCGATGAGCGTGATACCAGCACGCCGCTGGCGATGGCTGAAAGCCTGCGCAAGCTGACGCTTGGCAATGCGCTGGGCGAACAGCAACGCGCCCAGTTAGTCACCTGGCTGAAAGGCAATACCACCGGCGGGCAAAGCATTCGCGCGGGCCTGCCTGAAAGCTGGGTGGTCGGCGATAAAACCGGCGCCGGAGATTACGGCACCACCAATGATATTGCGGTTATCTGGCCGGAAAATCACGCTCCGCTGGTATTAGTCACCTACTTTACCCAGCCGCAGCAGGATGCGAAAAACCGCAAGGAGGTGTTAGCCGCAGCGGCAAAAATCGTGACCGAAGGGCTTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3002403","ARO_id":"38803","ARO_name":"OXY-2-8","CARD_short_name":"OXY-2-8","ARO_description":"OXY-2-8 is a beta-lactamase found in Klebsiella oxytoca.","ARO_category":{"38788":{"category_aro_accession":"3002388","category_aro_cvterm_id":"38788","category_aro_name":"OXY beta-lactamase","category_aro_description":"OXY beta-lactamases are chromosomal class A beta-lactamases that are found in Klebsiella oxytoca. At constitutive low levels, OXY beta-lactamases confer resistance to aminopenicillins and carboxypenicillins. At high induced levels,  OXY beta-lactamases confer resistance to penicillins, cephalosporins and aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"204":{"model_id":"204","model_name":"VIM-43","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"2129":{"protein_sequence":{"accession":"AJP67511.1","sequence":"MLKVISSLLVYMTASVMAVASPLVHSGEPSGEYPTVNEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEAEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSANVLYGGCAVHELSRTSAGNVADADLAEWPTSVERIQKHYPEAEVVIPGHGLPGGLDLLQHTANVVKAHKNRSVAE"},"dna_sequence":{"accession":"KP096412.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGTTAAAAGTTATTAGTAGTTTATTGGTCTACATGACCGCGTCTGTCATGGCTGTCGCAAGTCCGTTAGTCCATTCCGGGGAGCCGAGTGGTGAGTATCCGACAGTCAACGAAATTCCGGTCGGAGAGGTCCGACTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCGGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAAAAGCAAATTGGACTTCCCGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGCAGAGGGGAACGAGATTCCCACGCATTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAGCTCTTCTATCCTGGTGCTGCGCATTCGACCGACAATCTGGTTGTATACGTCCCGTCAGCGAACGTGCTATACGGTGGTTGTGCCGTTCATGAGTTGTCACGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCGTTGAGCGGATTCAAAAACACTACCCGGAAGCAGAGGTCGTCATTCCCGGGCACGGTCTACCGGGCGGTCTAGACTTGCTCCAGCACACAGCGAACGTTGTCAAAGCACACAAAAATCGCTCAGTCGCCGAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3003179","ARO_id":"39756","ARO_name":"VIM-43","CARD_short_name":"VIM-43","ARO_description":"VIM-43 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"205":{"model_id":"205","model_name":"APH(4)-Ia","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"221":{"protein_sequence":{"accession":"CAA24743.1","sequence":"MKKPELTATSVEKFLIEKFDSVSDLMQLSEGEESRAFSFDVGGRGYVLRVNSCADGFYKDRYVYRHFASAALPIPEVLDIGEFSESLTYCISRRAQGVTLQDLPETELPAVLQPVAEAMDAIAAADLSQTSGFGPFGPQGIGQYTTWRDFICAIADPHVYHWQTVMDDTVSASVAQALDELMLWAEDCPEVRHLVHADFGSNNVLTDNGRITAVIDWSEAMFGDSQYEVANIFFWRPWLACMEQQTRYFERRHPELAGSPRLRAYMLRIGLDQLYQSLVDGNFDDAAWAQGRCDAIVRSGAGTVGRTQIARRSAAVWTDGCVEVLADSGNRRPSTRPRAKE"},"dna_sequence":{"accession":"V01499.1","fmin":"230","fmax":"1256","strand":"+","sequence":"ATGAAAAAGCCTGAACTCACCGCGACGTCTGTCGAGAAGTTTCTGATCGAAAAGTTCGACAGCGTCTCCGACCTGATGCAGCTCTCGGAGGGCGAAGAATCTCGTGCTTTCAGCTTCGATGTAGGAGGGCGTGGATATGTCCTGCGGGTAAATAGCTGCGCCGATGGTTTCTACAAAGATCGTTATGTTTATCGGCACTTTGCATCGGCCGCGCTCCCGATTCCGGAAGTGCTTGACATTGGGGAATTCAGCGAGAGCCTGACCTATTGCATCTCCCGCCGTGCACAGGGTGTCACGTTGCAAGACCTGCCTGAAACCGAACTGCCCGCTGTTCTGCAGCCGGTCGCGGAGGCCATGGATGCGATCGCTGCGGCCGATCTTAGCCAGACGAGCGGGTTCGGCCCATTCGGACCGCAAGGAATCGGTCAATACACTACATGGCGTGATTTCATATGCGCGATTGCTGATCCCCATGTGTATCACTGGCAAACTGTGATGGACGACACCGTCAGTGCGTCCGTCGCGCAGGCTCTCGATGAGCTGATGCTTTGGGCCGAGGACTGCCCCGAAGTCCGGCACCTCGTGCACGCGGATTTCGGCTCCAACAATGTCCTGACGGACAATGGCCGCATAACAGCGGTCATTGACTGGAGCGAGGCGATGTTCGGGGATTCCCAATACGAGGTCGCCAACATCTTCTTCTGGAGGCCGTGGTTGGCTTGTATGGAGCAGCAGACGCGCTACTTCGAGCGGAGGCATCCGGAGCTTGCAGGATCGCCGCGGCTCCGGGCGTATATGCTCCGCATTGGTCTTGACCAACTCTATCAGAGCTTGGTTGACGGCAATTTCGATGATGCAGCTTGGGCGCAGGGTCGATGCGACGCAATCGTCCGATCCGGAGCCGGGACTGTCGGGCGTACACAAATCGCCCGCAGAAGCGCGGCCGTCTGGACCGATGGCTGTGTAGAAGTACTCGCCGATAGTGGAAACCGACGCCCCAGCACTCGTCCGAGGGCAAAGGAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002655","ARO_id":"39055","ARO_name":"APH(4)-Ia","CARD_short_name":"APH(4)-Ia","ARO_description":"APH(4)-Ia is a plasmid-encoded aminoglycoside phosphotransferase in E. coli.","ARO_category":{"36294":{"category_aro_accession":"3000155","category_aro_cvterm_id":"36294","category_aro_name":"APH(4)","category_aro_description":"A category of aminoglycoside O-phosphotransferase enzymes with modification regiospecificity based at the 4-hydroxyl group of the respective antibiotic. These enzymes are characterized by enzymatic antibiotic inactivation, specifically of hygromycin, by the ATP-dependent phosphorylation of the 4-hydroxyl group of the compound.","category_aro_class_name":"AMR Gene Family"},"36353":{"category_aro_accession":"3000214","category_aro_cvterm_id":"36353","category_aro_name":"hygromycin B","category_aro_description":"Hygromycin B is an aminoglycoside antibiotic used to treat different types of bacterial infections. Hygromycin B works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Hygromycin B has also been shown to interact with eukaryotic cells.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"206":{"model_id":"206","model_name":"FomA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"614":{"protein_sequence":{"accession":"BAA32493.1","sequence":"MTPDFLAIKVGGSLFSRKDEPGSLDDDAVTPFARNFARLAETYRGRMVLISGGGAFGHGAIRDHDSTHAFSLAGLTEATFEVKKRWAEKLRGIGVDAFPLQLAAMCTLRNGIPQLRSEVLRDVLDHGALPVLAGDALFDEHGKLWAFSSDRVPEVLLPMVEGRLRVVTLTDVDGIVTDGAGGDTILPEVDARSPEQAYAALWGSSEWDATGAMHTKLDALVTCARRGAECFIMRGDPGSDLEFLTAPFSSWPAHVRSTRITTTASA"},"dna_sequence":{"accession":"AB016934.1","fmin":"6575","fmax":"7376","strand":"+","sequence":"ATGACGCCCGATTTCTTGGCCATCAAGGTTGGCGGCAGCCTGTTCTCCCGCAAGGACGAACCCGGCAGCCTGGACGACGACGCGGTGACGCCGTTCGCCAGGAACTTCGCCCGGCTCGCCGAGACCTACCGGGGCCGGATGGTTCTCATCAGCGGCGGCGGCGCCTTCGGCCACGGGGCCATCCGTGACCACGACAGCACGCACGCGTTCTCCCTCGCCGGCCTGACCGAGGCCACCTTCGAGGTGAAGAAGCGGTGGGCCGAGAAGCTCCGCGGGATCGGCGTGGACGCCTTCCCGCTCCAGCTGGCGGCCATGTGCACGCTCCGCAACGGCATACCGCAGCTCCGGTCCGAGGTCCTCCGGGACGTCCTCGACCACGGCGCGCTGCCCGTCCTCGCCGGCGACGCCCTGTTCGACGAGCACGGAAAGCTGTGGGCGTTCTCCAGCGACCGCGTCCCCGAGGTCCTCCTGCCCATGGTCGAGGGGCGCCTCCGGGTCGTCACCCTGACCGACGTCGACGGCATCGTGACCGACGGCGCCGGCGGCGACACGATCCTGCCCGAGGTCGACGCCCGGTCCCCCGAGCAGGCGTACGCCGCGCTCTGGGGCAGCAGCGAATGGGACGCCACCGGCGCCATGCACACCAAGCTCGACGCACTGGTCACCTGCGCCCGCCGCGGTGCCGAGTGCTTCATCATGCGGGGCGACCCCGGCAGCGACCTGGAGTTCCTGACCGCCCCCTTCTCCTCCTGGCCGGCGCACGTGCGGTCCACCAGGATCACCACGACTGCTTCTGCGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39587","NCBI_taxonomy_name":"Streptomyces wedmorensis","NCBI_taxonomy_id":"43759"}}}},"ARO_accession":"3000423","ARO_id":"36562","ARO_name":"FomA","CARD_short_name":"FomA","ARO_description":"In the presence of ATP and magnesium (II), fosfomycin gets phosphorylated at the phosphate group resulting in a diphosphate group which inactivates the antibiotic.","ARO_category":{"41410":{"category_aro_accession":"3004246","category_aro_cvterm_id":"41410","category_aro_name":"Fom phosphotransferase family","category_aro_description":"Two members of the Fom family have been identified, FomA and FomB. FomB must interact with FomA confer resistance to fosfomycin, however FomA is capable of conferring resistance alone.","category_aro_class_name":"AMR Gene Family"},"35944":{"category_aro_accession":"0000025","category_aro_cvterm_id":"35944","category_aro_name":"fosfomycin","category_aro_description":"Fosfomycin (also known as phosphomycin and phosphonomycin) is a broad-spectrum antibiotic produced by certain Streptomyces species. It is effective on gram positive and negative bacteria as it targets the cell wall, an essential feature shared by both bacteria. Its specific target is MurA (MurZ in E.coli), which attaches phosphoenolpyruvate (PEP) to UDP-N-acetylglucosamine, a step of commitment to cell wall synthesis. In the active site of MurA, the active cysteine molecule is alkylated which stops the catalytic reaction.","category_aro_class_name":"Antibiotic"},"45731":{"category_aro_accession":"3007149","category_aro_cvterm_id":"45731","category_aro_name":"phosphonic acid antibiotic","category_aro_description":"A group of antibiotics derived from phosphonic acids.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"207":{"model_id":"207","model_name":"GES-12","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1823":{"protein_sequence":{"accession":"CBG22732.1","sequence":"MRFIHALLLAGIAHSAYASEKLTFKTDLEKLEREKAAQIGVAIVDPQGEIVAGHRMAQRFAMCSTFKFPLAALVFERIDSGTERGDRKLSYGPDMIVEWSPATERFLASGHMTVLEAAQAAVQLSDNGATNLLLREIGGPAAMTQYFRKIGDSVSRLDRKEPEMGDNTPGDLRDTTTPIAMARTVAKVLYGGALTSTSTHTIERWLIGNQTGDATLRAGFPKDWVVGEKTGACANGARNDIGFFKAQERDYAVAVYTTAPKLSAVERDELVASVGQVITQLILSTDK"},"dna_sequence":{"accession":"FN554543.1","fmin":"0","fmax":"864","strand":"+","sequence":"ATGCGCTTCATTCACGCACTATTACTGGCAGGGATCGCTCACTCTGCATATGCGTCGGAAAAATTAACCTTCAAGACCGATCTTGAGAAGCTAGAGCGCGAAAAAGCAGCTCAGATCGGTGTTGCGATCGTCGATCCCCAAGGAGAGATCGTCGCGGGCCACCGAATGGCGCAGCGTTTTGCAATGTGCTCAACGTTCAAGTTTCCGCTAGCCGCGCTGGTCTTTGAAAGAATTGACTCAGGCACCGAGCGGGGGGATCGAAAACTTTCATATGGGCCGGACATGATCGTCGAATGGTCTCCTGCCACGGAGCGGTTTCTAGCATCGGGACACATGACGGTTCTCGAGGCAGCGCAAGCTGCGGTGCAGCTTAGCGACAATGGGGCTACTAACCTCTTACTGAGAGAAATTGGCGGACCTGCTGCAATGACGCAGTATTTTCGTAAAATTGGCGACTCTGTGAGTCGGCTAGACCGGAAAGAGCCGGAGATGGGCGACAACACACCTGGCGACCTCAGAGATACAACTACGCCTATTGCTATGGCACGTACTGTGGCTAAAGTCCTCTATGGCGGCGCACTGACGTCCACCTCGACCCACACCATTGAGAGGTGGCTGATCGGAAACCAAACGGGAGACGCGACACTACGAGCGGGTTTTCCTAAAGATTGGGTTGTTGGAGAGAAAACTGGTGCCTGCGCCAACGGGGCCCGGAACGACATTGGTTTTTTTAAAGCCCAGGAGAGAGATTACGCTGTAGCGGTGTATACAACGGCCCCGAAACTATCGGCCGTAGAACGTGACGAATTAGTTGCCTCTGTCGGTCAAGTTATTACACAACTCATCCTGAGCACGGACAAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3002341","ARO_id":"38741","ARO_name":"GES-12","CARD_short_name":"GES-12","ARO_description":"GES-12 is a beta-lactamase found in Acinetobacter baumannii.","ARO_category":{"36205":{"category_aro_accession":"3000066","category_aro_cvterm_id":"36205","category_aro_name":"GES beta-lactamase","category_aro_description":"GES beta-lactamases or Guiana extended-spectrum beta-lactamases are related to the other plasmid-located class A beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"208":{"model_id":"208","model_name":"CMY-105","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1623":{"protein_sequence":{"accession":"AHL39330.1","sequence":"MMKKSICCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAIIYEGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWRGISLLHLATYTAGGLPLQIPDEVTDKAELLRFYQNWQPQWTPGAKRLYANSSIGLFGALVVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQSEQKNYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIELAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"KJ207205.1","fmin":"1039","fmax":"2185","strand":"+","sequence":"ATGATGAAAAAATCGATATGCTGCGCACTGCTGCTGACAGCCTCTTTCTCCACGTTTGCTGCCGCAAAAACAGAACAACAAATTGCCGATATCGTTAACCGCACCATCACACCACTGATGCAGGAGCAGGCTATTCCGGGCATGGCCGTGGCAATTATCTACGAGGGGAAACCTTATTACTTTACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAATTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGACGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCGGGGTATCAGCCTGCTGCACTTAGCCACCTATACAGCGGGTGGCCTGCCGCTGCAGATCCCCGATGAAGTTACGGATAAAGCCGAATTACTGCGCTTTTATCAAAACTGGCAACCACAATGGACTCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGTGCGCTGGTGGTAAAACCTTCAGGTATGAGCTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAAAGCGAACAAAAAAATTATGCCTGGGGCTATCGCGAAGGGAAGCCTGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATCGATATGGCCCGCTGGGTTCAGGCCAACATGGACGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGAGCTTGCGCAGTCTCGCTACTGGCGTATTGGTGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCAGCACCTGCCGTGAAAGCCTCATGGGTGCATAAAACGGGATCCACAGGTGGATTTGGCAGCTACGTTGCCTTCGTTCCAGAAAAAAACCTTGGCATAGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGCGTCGAGGCGGCCTGGCGCATTCTTGAAAAACTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002117","ARO_id":"38517","ARO_name":"CMY-105","CARD_short_name":"CMY-105","ARO_description":"CMY-105 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"210":{"model_id":"210","model_name":"SHV-35","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1315":{"protein_sequence":{"accession":"AAL68926.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDKQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGGRGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AY070258.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACAAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGGGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001093","ARO_id":"37473","ARO_name":"SHV-35","CARD_short_name":"SHV-35","ARO_description":"SHV-35 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"211":{"model_id":"211","model_name":"TEM-206","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"2035":{"protein_sequence":{"accession":"AGK82336.1","sequence":"MSIQHFRVTLIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"KC783461.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCACCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001383","ARO_id":"37783","ARO_name":"TEM-206","CARD_short_name":"TEM-206","ARO_description":"TEM-206 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"213":{"model_id":"213","model_name":"OXA-21","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8191":{"protein_sequence":{"accession":"CAA71699.2","sequence":"MAIRIFAILFSTFVFGTFAHAQEGMRERSDWRKFFSEFQAKGTIVVADERQTDRVILVFDQVRSEKRYSPASTFKIPHTLFALDAGAARDEFQVFRWDGIKRSFAAHNQDQDLRSAMRNSTVWIYELFAKEIGEDKARRYLKQIDYGNADPSTSNGDYWIDGNLAIAAQEQIAFLRKLYHNELPFRVEHQRLVKDLMIVEAGRNWILRAKTGWEGRMGWWVGWVEWPTGPVFFALNIDTPNRMDDLFKREAIVRAILRSIEALPPNPAVNSDAAR"},"dna_sequence":{"accession":"Y10693.2","fmin":"0","fmax":"828","strand":"+","sequence":"ATGGCAATCCGAATCTTCGCAATACTTTTCTCCACTTTTGTTTTTGGCACGTTCGCGCATGCACAAGAAGGCATGCGCGAACGTTCTGACTGGCGGAAGTTTTTCAGCGAATTTCAAGCCAAAGGCACGATAGTTGTGGCAGACGAACGCCAAACAGATCGTGTCATATTGGTTTTTGATCAGGTGCGGTCAGAGAAACGCTACTCGCCGGCCTCGACATTCAAGATTCCACATACACTTTTTGCACTTGACGCAGGCGCTGCACGTGATGAGTTTCAAGTTTTCCGATGGGACGGCATCAAAAGAAGCTTTGCAGCTCACAACCAAGACCAAGACTTGCGATCAGCAATGCGGAATTCTACTGTCTGGATTTATGAGCTATTTGCAAAAGAGATCGGTGAAGACAAGGCTCGACGCTATTTGAAGCAAATCGACTATGGCAACGCCGATCCTTCGACAAGTAATGGCGATTACTGGATAGATGGCAATCTTGCTATCGCGGCACAAGAACAGATTGCATTTCTCAGGAAGCTCTATCATAACGAGTTGCCCTTTCGGGTAGAACATCAGCGCTTGGTCAAGGACCTCATGATTGTGGAAGCCGGTCGCAACTGGATACTGCGCGCAAAGACGGGCTGGGAAGGCCGCATGGGTTGGTGGGTAGGATGGGTTGAGTGGCCGACTGGCCCCGTATTTTTCGCACTGAATATTGATACGCCAAACAGGATGGATGACCTTTTCAAAAGGGAGGCAATAGTGCGGGCAATCCTTCGCTCTATCGAAGCGTTGCCGCCCAACCCGGCAGTCAACTCGGACGCAGCGCGATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001416","ARO_id":"37816","ARO_name":"OXA-21","CARD_short_name":"OXA-21","ARO_description":"OXA-21 is a beta-lactamase found in A. baumannii.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46493":{"category_aro_accession":"3007704","category_aro_cvterm_id":"46493","category_aro_name":"OXA-2-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-2.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"214":{"model_id":"214","model_name":"SHV-121","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1621":{"protein_sequence":{"accession":"AEI83429.1","sequence":"MRYIRLCIISLLAALPLVVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITVSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"HQ661362.1","fmin":"71","fmax":"932","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCGCCCTGCCGCTGGTGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCGTGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001168","ARO_id":"37548","ARO_name":"SHV-121","CARD_short_name":"SHV-121","ARO_description":"SHV-121 is a beta-lactamase that has been found in clinical isolates. Identical to SHV-136.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"215":{"model_id":"215","model_name":"bcrC","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"350"}},"model_sequences":{"sequence":{"2050":{"protein_sequence":{"accession":"AAA99503.1","sequence":"MSFSELNIDAFRFINDLGKEYSMLNPVVYFLAEYMMYFLALGLVVYWLTRTTKNRLMVIYAVIAFVVAEILGKIMGSLHSNYQPFATLPNVNKLIEHEIDNSFPSDHTILFFSIGFLIFLFHKKTGWLWLVLAFAVGISRIWSGVHYPLDVAAGALLGVLSALFVFWTAPKLSFIHQMLSLYEKVEQRIVPSKNKSNDKSKNF"},"dna_sequence":{"accession":"L20573.1","fmin":"2064","fmax":"2676","strand":"+","sequence":"ATGTCTTTTTCAGAATTAAATATTGATGCTTTTCGTTTCATTAATGATTTGGGAAAAGAGTATTCGATGCTGAATCCGGTCGTTTACTTTCTAGCCGAATATATGATGTACTTTCTCGCATTAGGTCTTGTCGTTTATTGGCTGACCCGGACGACAAAAAACAGATTGATGGTCATTTATGCAGTCATCGCATTTGTGGTTGCCGAAATTCTCGGGAAAATCATGGGCTCTCTGCATTCCAACTATCAACCGTTTGCAACGCTTCCGAATGTCAACAAGCTGATAGAGCATGAAATTGACAATTCGTTTCCGAGCGACCATACGATTTTGTTTTTTTCAATTGGTTTTTTAATCTTTCTGTTTCACAAAAAGACGGGCTGGCTGTGGCTTGTACTTGCGTTTGCCGTGGGAATTTCCCGCATTTGGTCGGGCGTTCACTATCCGCTCGACGTTGCGGCGGGAGCCCTTCTTGGCGTGTTGTCAGCTCTGTTTGTATTCTGGACAGCACCGAAGCTGTCATTTATTCATCAAATGCTGTCCCTTTATGAAAAGGTGGAACAGCGGATTGTTCCTTCCAAAAACAAATCGAACGATAAATCGAAGAACTTTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36834","NCBI_taxonomy_name":"Bacillus licheniformis","NCBI_taxonomy_id":"1402"}}}},"ARO_accession":"3003250","ARO_id":"39834","ARO_name":"bcrC","CARD_short_name":"bcrC","ARO_description":"The bcrC gene product (BcrC) is an undecaprenyl pyrophosphate phosphatase originally isolated from Bacillus subtilis. When overexpressed it can confer resistance to bacitracin.","ARO_category":{"39982":{"category_aro_accession":"3003398","category_aro_cvterm_id":"39982","category_aro_name":"undecaprenyl pyrophosphate related proteins","category_aro_description":"Undecaprenyl phosphate is a universal lipid carrier of glycan biosynthetic intermediates for carbohydrate polymers that are exported to the bacterial cell envelope. Antibiotics that targets this compound or proteins associated with the production of this compound leads to cell death.","category_aro_class_name":"AMR Gene Family"},"35959":{"category_aro_accession":"0000041","category_aro_cvterm_id":"35959","category_aro_name":"bacitracin","category_aro_description":"Bacitracin is a mixture of related cyclic polypeptides produced by organisms of the licheniformis group of Bacillus subtilis var Tracy. Bacitracin interferes with the dephosphorylation of the C55-isoprenyl pyrophosphate, a molecule which carries the building blocks of the peptidoglycan bacterial cell wall outside of the inner membrane.","category_aro_class_name":"Antibiotic"},"36973":{"category_aro_accession":"3000629","category_aro_cvterm_id":"36973","category_aro_name":"bacitracin A","category_aro_description":"Bacitracin A is the primary component of bacitracin. It contains many uncommon amino acids and interferes with bacterial cell wall synthesis.","category_aro_class_name":"Antibiotic"},"36974":{"category_aro_accession":"3000630","category_aro_cvterm_id":"36974","category_aro_name":"bacitracin B","category_aro_description":"Bacitracin B is a component of bacitracin, an antibiotic mixture that interferes with bacterial cell wall synthesis. It differs from Bacitracin A with a valine instead of an isoleucine in its peptide.","category_aro_class_name":"Antibiotic"},"36975":{"category_aro_accession":"3000631","category_aro_cvterm_id":"36975","category_aro_name":"bacitracin F","category_aro_description":"Bacitracin F is a component of bacitracin, an antibiotic mixture that interferes with bacterial cell wall synthesis. It is formed when the thiazoline ring of bacitracin A is oxidatively deaminated.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"216":{"model_id":"216","model_name":"LEN-9","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"5358":{"protein_sequence":{"accession":"AXA30439.1","sequence":"MRYVRLCVISLLATLPLVVYAGPQPLEQIKQSESQLSGRVGMVEMDLASGRTLAAWRADERFPMVSTFKVLLCGAVLARVDAGLEQLDRRIHYRQQDLVDYSPVSEKHLVDGMTIGELCAAAITLSDNSAGNLLLATVGGPAGLTAFLRQIGDNVTRLDRWETALNEALPGDARDTTTPASMAATLRKLLTAQHLSARSQQQLLQWMVDDRVAGPLIRAVLPPGWFIADKTGAGERGARGIVALLGPDGKPERIVVIYLRDTPASMAERNQHIAGIGAALIEHWQR"},"dna_sequence":{"accession":"CP016344.1","fmin":"2782791","fmax":"2783652","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGTGTTATCTCCCTGTTAGCCACCCTGCCACTGGTGGTATACGCCGGTCCACAGCCGCTTGAGCAGATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTGGGGATGGTGGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCGATGAACGCTTTCCCATGGTGAGCACCTTTAAAGTGCTGCTGTGCGGCGCGGTGCTGGCGCGGGTGGATGCCGGGCTCGAACAACTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGTCGACGGGATGACGATCGGCGAACTCTGCGCCGCCGCCATCACCCTGAGCGATAACAGCGCTGGCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCGGGATTAACTGCCTTTCTGCGCCAGATCGGTGACAACGTCACCCGTCTTGACCGCTGGGAAACGGCACTGAATGAGGCGCTTCCCGGCGACGCGCGCGACACCACCACCCCGGCCAGCATGGCCGCCACGCTGCGCAAACTACTGACCGCGCAGCATCTGAGCGCCCGTTCGCAACAGCAACTCCTGCAGTGGATGGTGGACGATCGGGTTGCCGGCCCGCTGATCCGCGCCGTGCTGCCGCCGGGCTGGTTTATCGCCGACAAAACCGGGGCTGGCGAACGGGGTGCGCGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAACCGGAGCGCATTGTGGTGATCTATCTGCGGGATACCCCGGCGAGTATGGCCGAGCGTAATCAACATATCGCCGGGATCGGCGCAGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42612","NCBI_taxonomy_name":"Klebsiella variicola","NCBI_taxonomy_id":"244366"}}}},"ARO_accession":"3002459","ARO_id":"38859","ARO_name":"LEN-9","CARD_short_name":"LEN-9","ARO_description":"LEN-9 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36236":{"category_aro_accession":"3000097","category_aro_cvterm_id":"36236","category_aro_name":"LEN beta-lactamase","category_aro_description":"LEN beta-lactamases are chromosomal class A beta-lactamases that confer resistance to ampicillin, amoxicillin, carbenicillin, and ticarcillin but not to extended-spectrum beta-lactams.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"218":{"model_id":"218","model_name":"npmA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"8165":{"protein_sequence":{"accession":"BAF80809.1","sequence":"MLILKGTKTVDLSKDELTEIIGQFDRVHIDLGTGDGRNIYKLAINDQNTFYIGIDPVKENLFDISKKIIKKPSKGGLSNVVFVIAAAESLPFELKNIADSISILFPWGTLLEYVIKPNRDILSNVADLAKKEAHFEFVTTYSDSYEEAEIKKRGLPLLSKAYFLSEQYKAELSNSGFRIDDVKELDNEYVKQFNSLWAKRLAFGRKRSFFRVSGHVSKH"},"dna_sequence":{"accession":"AB261016.2","fmin":"91163","fmax":"91823","strand":"-","sequence":"TTGTTAATACTCAAAGGAACAAAGACGGTTGATTTATCAAAAGATGAATTGACAGAAATAATAGGTCAGTTTGATCGTGTGCATATAGATTTGGGTACTGGAGACGGTAGAAATATATATAAACTTGCAATTAATGATCAAAACACTTTCTATATCGGAATAGATCCGGTAAAAGAAAACTTGTTTGATATATCCAAAAAAATTATAAAGAAGCCCTCAAAAGGAGGGCTATCTAATGTGGTGTTTGTTATTGCAGCTGCAGAGTCTCTCCCTTTTGAATTGAAAAACATTGCTGATTCAATTTCCATTTTGTTTCCTTGGGGGACATTGCTTGAATATGTAATTAAACCGAATAGAGATATTCTTTCGAATGTTGCAGATTTGGCTAAAAAAGAAGCTCACTTTGAATTTGTGACCACATACTCAGATTCATACGAAGAAGCGGAAATAAAAAAAAGAGGACTTCCTCTTTTAAGTAAGGCCTATTTTTTGAGCGAACAATACAAAGCTGAATTATCAAACTCAGGTTTTCGCATTGATGATGTTAAGGAATTGGACAATGAGTATGTAAAACAGTTTAATTCTCTTTGGGCAAAGCGATTAGCTTTTGGGCGAAAACGTTCTTTCTTTCGAGTTTCTGGCCATGTTTCAAAACATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002665","ARO_id":"39065","ARO_name":"npmA","CARD_short_name":"npmA","ARO_description":"NpmA is a plasmid-mediated aminoglycoside-resistance 16S rRNA methyltransferase by interfering with aminoglycoside binding with the A site of 16S rRNA through N-1 methylation at position A1408.","ARO_category":{"41436":{"category_aro_accession":"3004272","category_aro_cvterm_id":"41436","category_aro_name":"16S rRNA methyltransferase (A1408)","category_aro_description":"Methyltransferases that methylate the A1408 position of 16S rRNA, which is part of an aminoglycoside binding site.","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35940":{"category_aro_accession":"0000021","category_aro_cvterm_id":"35940","category_aro_name":"ribostamycin","category_aro_description":"Ribostamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Ribostamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"40942":{"category_aro_accession":"3004015","category_aro_cvterm_id":"40942","category_aro_name":"gentamicin A","category_aro_description":"Gentamicin A is part of a complex of broad spectrum aminoglycoside antibiotics. Gentamicin inhibits protein synthesis, resulting in bacterial cell death.","category_aro_class_name":"Antibiotic"},"46133":{"category_aro_accession":"3007382","category_aro_cvterm_id":"46133","category_aro_name":"gentamicin","category_aro_description":"Gentamicin is a commonly used aminoglycoside antibiotic derived from members of the Micromonospora genus of bacteria. It acts by binding the 30S ribosomal subunit, thus inhibiting protein synthesis. Gentamicin is typically used to treat Gram-negative infections of the repiratory and urinary tract, as well as infections of the bone and soft tissue. It also exhibits considerable nephrotoxicity and ototoxicity. Gentamicin is administered as a mixture of gentamicin type C (which makes about around 80% of the complex) and types A, B, and X (distributed in the remaining 20% of the complex).","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"219":{"model_id":"219","model_name":"OKP-A-12","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"8273":{"protein_sequence":{"accession":"CAP12354.2","sequence":"MRYVRLCLISLIAALPLAAFASPQPLEQVTRSESQLAGRVGYVEMDLASGRTLAAWRASERFPLMSTFKVLLCGAVLARVDAGDEQLDRRIRYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAGNLLLKSVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDVRDTTTPASMAATLRKLLTSHALSARSQQQLLQWMVDDQVAGPLIRAVLPAGWFIADKTGAGERGSRGIVALLGPNGKAERIVVIYLRDTPATMAERNQQIARIGAALIEHWQR"},"dna_sequence":{"accession":"AM850916.2","fmin":"18","fmax":"879","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGCCTTATCTCCCTGATTGCCGCCCTGCCACTGGCGGCATTCGCCAGCCCTCAGCCGCTCGAGCAAGTTACACGCAGCGAAAGTCAGCTGGCGGGCCGCGTGGGCTATGTTGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCAGTGAGCGCTTTCCACTGATGAGCACCTTTAAAGTGCTGCTCTGCGGCGCGGTGCTGGCCCGGGTGGATGCCGGAGACGAACAGCTGGATCGGCGGATCCGCTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGCCGACGGGATGACCGTTGGTGAACTCTGCGCCGCCGCCATCACCATGAGCGACAACAGCGCCGGCAATCTGCTGTTGAAGAGCGTTGGCGGCCCCGCGGGATTGACCGCTTTTCTGCGCCAGATCGGTGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAGCTCAATGAAGCGCTTCCCGGCGACGTGCGCGACACCACCACCCCAGCCAGCATGGCCGCCACCCTGCGCAAGCTGCTAACCAGCCACGCGCTGAGCGCCCGTTCGCAGCAGCAGCTGCTGCAGTGGATGGTGGACGACCAGGTGGCCGGCCCGCTGATCCGCGCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAAACCGGGGCCGGCGAGCGGGGCTCACGCGGCATTGTCGCCCTGCTCGGCCCGAACGGCAAAGCGGAGCGCATCGTGGTGATCTATCTGCGGGATACGCCGGCGACCATGGCCGAACGTAACCAGCAGATCGCCAGAATAGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002429","ARO_id":"38829","ARO_name":"OKP-A-12","CARD_short_name":"OKP-A-12","ARO_description":"OKP-A-12 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"38817":{"category_aro_accession":"3002417","category_aro_cvterm_id":"38817","category_aro_name":"OKP beta-lactamase","category_aro_description":"OKP beta-lactamases are chromosomal class A beta-lactamase that confer resistance to penicillins and early cephalosporins in Klebsiella pneumoniae. OKP beta-lactamases can be subdivided into two groups: OKP-A and OKP-B which diverge by about 4.2%.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"220":{"model_id":"220","model_name":"TEM-92","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1961":{"protein_sequence":{"accession":"AAF66653.1","sequence":"MSIKHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVKYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTTPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGASERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AF143804.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTAAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTAAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGACGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCAGTGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3000959","ARO_id":"37339","ARO_name":"TEM-92","CARD_short_name":"TEM-92","ARO_description":"TEM-92 is an extended-spectrum beta-lactamase found in Proteus mirabilis.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"221":{"model_id":"221","model_name":"CMY-100","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1194":{"protein_sequence":{"accession":"AHA80101.1","sequence":"MMKKSICCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAIIYQGKPYYFTWGKADIANNRPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTQYWPELTGKQWQGISLLHLATYTAGGLPLQVPDDVTDKAALLHFYQNWQPQWASGAKRLYANSSIGLFGALAVKPSGMSYEEAMTKRVLHPLKLAHTWITVPQSEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMTRWVQANMDASQVQEKTLQQGIELAQSRYWRIGDMYQGLGWEMLNWPVKADSIISGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"KF526113.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGATATGCTGCGCGCTGCTGCTGACAGCTTCTTTCTCCACGTTTGCCGCCGCAAAAACAGAACAACAAATTGCCGATATCGTTAACCGCACCATCACACCGCTGATGCAGGAGCAGGCAATTCCGGGCATGGCCGTTGCGATTATCTATCAGGGGAAACCTTATTACTTTACCTGGGGTAAAGCCGATATCGCCAATAACCGTCCAGTCACTCAACAAACGCTGTTTGAACTCGGTTCGGTCAGTAAAACGTTCAACGGTGTGCTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGCAGTACTGGCCTGAACTGACGGGTAAGCAGTGGCAGGGTATCAGCCTGCTGCACTTAGCCACCTACACGGCAGGCGGCCTGCCGCTTCAGGTTCCGGACGACGTTACGGATAAAGCCGCATTACTACACTTTTATCAAAACTGGCAGCCGCAATGGGCCTCAGGCGCTAAACGTCTTTATGCTAACTCCAGCATTGGTCTGTTTGGCGCCCTGGCGGTGAAACCTTCAGGCATGAGCTACGAAGAGGCGATGACCAAACGCGTCCTGCACCCCTTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAGCGAACAAAAAGATTATGCCTGGGGTTATCGCGAAGGAAAGCCAGTGCATGTATCCCCTGGCCAACTTGATGCCGAAGCCTACGGGGTGAAATCGAGCGTTATCGATATGACCCGTTGGGTTCAGGCCAACATGGACGCCAGCCAGGTTCAGGAGAAAACGCTCCAGCAGGGAATCGAGCTTGCGCAGTCACGTTACTGGCGTATTGGCGATATGTACCAGGGCCTGGGTTGGGAGATGCTGAACTGGCCGGTGAAGGCCGACTCGATAATTAGCGGTAGCGACAGCAAAGTAGCACTGGCAGCGCTTCCTGCCGTTGAGGTAAACCCGCCCGCGCCTGCCGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGCGGATTTGGCAGCTACGTTGCTTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAGAGCTACCCAAACCCTGTTCGCGTCGAGGCCGCCTGGCGCATTCTTGAAAAACTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002112","ARO_id":"38512","ARO_name":"CMY-100","CARD_short_name":"CMY-100","ARO_description":"CMY-100 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"223":{"model_id":"223","model_name":"GES-3","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1708":{"protein_sequence":{"accession":"BAD06399.1","sequence":"MRFIHALLLAGIAHSAYASEKLTFKTDLEKLEREKAAQIGVAIVDPQGEIVAGHRTAQRFAMCSTFKFPLAALVFERIDSGTERGDRKLSYGPDMIVKWSPATERFLASGHMTVLEAAQAAVQLSDNGATNLLLREIGGPAAMTQYFRKIGDSVSRLDRKEPEMGDNTPGDLRDTTTPIAMARTVAKVLYGGALTSTSTHTIERWLIGNQTGDATLRAGFPKDWVVGEKTGTCANGGRNDIGFFKAQERDYAVAVYTTAPKLSAVERDELVASVGQVITQLILSTDK"},"dna_sequence":{"accession":"AB113580.1","fmin":"1329","fmax":"2193","strand":"+","sequence":"ATGCGCTTCATTCACGCACTATTACTGGCAGGGATCGCTCACTCTGCATATGCGTCGGAAAAATTAACCTTCAAGACCGATCTTGAGAAGCTAGAGCGCGAAAAAGCAGCTCAGATCGGTGTTGCGATCGTCGATCCCCAAGGAGAGATCGTCGCGGGCCACCGAACGGCGCAGCGCTTTGCAATGTGCTCAACGTTCAAGTTTCCGCTAGCCGCGCTGGTCTTTGAAAGAATTGACTCAGGCACCGAGCGGGGGGATCGAAAACTTTCATATGGGCCGGACATGATCGTCAAATGGTCTCCTGCCACGGAGCGGTTTCTAGCATCGGGACACATGACGGTTCTCGAGGCAGCGCAAGCTGCGGTGCAGCTTAGCGACAATGGGGCTACTAACCTCTTACTGAGAGAAATTGGCGGACCTGCTGCAATGACGCAGTATTTTCGTAAAATTGGCGACTCTGTGAGTCGGCTAGACCGGAAAGAGCCGGAGATGGGCGACAACACACCTGGCGACCTCAGAGATACAACTACGCCTATTGCTATGGCACGTACTGTGGCTAAAGTCCTCTATGGCGGCGCACTGACGTCCACCTCGACCCACACCATTGAGAGGTGGCTGATCGGAAACCAAACGGGAGACGCGACACTACGAGCGGGTTTTCCTAAAGATTGGGTTGTTGGAGAGAAAACTGGTACCTGCGCCAACGGGGGCCGGAACGACATTGGTTTTTTTAAAGCCCAGGAGAGAGATTACGCTGTAGCGGTGTATACAACGGCCCCGAAACTATCGGCCGTAGAACGTGACGAATTAGTTGCCTCTGTCGGTCAAGTTATTACACAACTCATCCTGAGCACGGACAAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002332","ARO_id":"38732","ARO_name":"GES-3","CARD_short_name":"GES-3","ARO_description":"GES-3 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36205":{"category_aro_accession":"3000066","category_aro_cvterm_id":"36205","category_aro_name":"GES beta-lactamase","category_aro_description":"GES beta-lactamases or Guiana extended-spectrum beta-lactamases are related to the other plasmid-located class A beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"224":{"model_id":"224","model_name":"MIR-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"1733":{"protein_sequence":{"accession":"AAO42602.1","sequence":"MMTKSLSCALLLSVASAAFAAPMSETQLAEVVERTVTPLMNAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEIALGDPVAKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDTASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMSYEQAMTTRVFKPLKLDHTWINVPKAEEAHYAWGYREGKAVHVSPGMLDAEAYGVKTNVKDMASWVIANMKPDSLQAPSLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVGGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYHILDALQ"},"dna_sequence":{"accession":"AY227752.1","fmin":"88","fmax":"1234","strand":"+","sequence":"ATGATGACAAAATCCCTAAGCTGTGCCCTGCTGCTCAGCGTCGCCAGCGCTGCATTCGCCGCACCGATGTCCGAAACACAGCTGGCTGAGGTGGTGGAACGTACCGTTACGCCGCTGATGAACGCGCAGGCCATTCCGGGTATGGCGGTGGCGGTAATTTATCAGGGTCAGCCACACTACTTTACCTTCGGTAAAGCCGATGTTGCGGCGAACAAACCCGTCACCCCGCAAACCCTGTTTGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTACTGGGCGGCGATGCCATTGCCCGGGGTGAAATAGCGCTGGGCGATCCGGTAGCAAAATACTGGCCTGAGCTCACGGGCAAGCAGTGGCAGGGCATTCGCATGCTGGATCTGGCAACCTATACCGCAGGCGGTCTGCCGTTACAGGTGCCGGATGAGGTCACGGATACCGCCTCTCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCGGGCACCACGCGTCTTTACGCTAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTTAAACCTTCCGGCATGAGCTATGAGCAGGCCATGACGACGCGGGTCTTTAAACCCCTCAAGCTGGACCATACCTGGATTAACGTCCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGATACCGTGAGGGTAAAGCGGTCCACGTTTCGCCAGGGATGCTGGACGCGGAAGCCTATGGCGTAAAAACTAACGTGAAGGATATGGCGAGCTGGGTGATAGCCAACATGAAGCCGGATTCTCTTCAGGCTCCCTCACTCAAGCAAGGCATTGCTCTGGCGCAGTCTCGCTACTGGCGCGTGGGGGCTATGTATCAGGGGTTAGGCTGGGAGATGCTCAACTGGCCGGTCGATGCCAAAACCGTCGTCGGAGGCAGTGATAACAAGGTGGCGCTGGCACCATTGCCCGTGGCAGAAGTGAATCCACCCGCGCCGCCGGTCAAGGCCTCCTGGGTCCATAAAACAGGCTCGACGGGCGGGTTTGGCAGCTACGTGGCATTTATTCCTGAAAAGCAGCTCGGCATTGTGATGCTGGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCGACGCGCTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3002168","ARO_id":"38568","ARO_name":"MIR-2","CARD_short_name":"MIR-2","ARO_description":"MIR-2 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36197":{"category_aro_accession":"3000058","category_aro_cvterm_id":"36197","category_aro_name":"MIR beta-lactamase","category_aro_description":"MIR beta-lactamases are plasmid-mediated beta-lactamases that confer resistance to oxyimino- and alpha-methoxy beta-lactams.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"225":{"model_id":"225","model_name":"CTX-M-88","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"5891":{"protein_sequence":{"accession":"WP_063860086.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRHDVLASAAKIVTDGL"},"dna_sequence":{"accession":"NZ_SQNR01000043.1","fmin":"1505","fmax":"2381","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCACGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001948","ARO_id":"38348","ARO_name":"CTX-M-88","CARD_short_name":"CTX-M-88","ARO_description":"CTX-M-88 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"226":{"model_id":"226","model_name":"OXA-113","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1832":{"protein_sequence":{"accession":"ABW70410.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKTTTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWVVGPLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"EF653400.1","fmin":"434","fmax":"1259","strand":"+","sequence":"ATGAACATTAAAGCCCTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTCTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGACAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGACGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGGTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001644","ARO_id":"38044","ARO_name":"OXA-113","CARD_short_name":"OXA-113","ARO_description":"OXA-113 is a beta-lactamase found in A. baumannii.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"227":{"model_id":"227","model_name":"OKP-B-3","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"1521":{"protein_sequence":{"accession":"CAJ19611.1","sequence":"MRYVRLCLISLIAALPLAVFASPQPLEQIKISESQLAGRVGYVEMDLASGRTLAAWRASERFPLMSTFKVLLCGAVLARVDAGDEQLDRRIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAGNLLLKIVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDVRDTTTPASMATTLRKLLTTPSLSARSQQQLLQWMVDDRVAGPLIRAVLPAGWFIADKTGAGERGSRGIVALLGPDGKAERIVVIYLRDTAATMVERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AM051152.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGCCTTATCTCCCTGATTGCCGCCCTGCCACTGGCGGTATTCGCCAGCCCTCAGCCGCTTGAGCAGATTAAAATCAGCGAAAGTCAGCTGGCGGGCCGGGTGGGCTATGTTGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCAGTGAGCGCTTTCCGCTGATGAGCACCTTTAAAGTGCTGCTCTGCGGCGCGGTGCTGGCCCGGGTGGATGCCGGCGACGAACAGCTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGCCGACGGGATGACCGTTGGCGAACTCTGCGCCGCCGCCATCACCATGAGCGACAACAGCGCCGGCAATCTGCTGTTGAAGATCGTCGGCGGCCCCGCGGGATTGACCGCTTTTCTGCGCCAGATCGGTGACAACGTCACCCGTCTTGACCGCTGGGAAACGGAACTCAATGAGGCGCTTCCCGGCGACGTGCGCGACACCACCACCCCGGCCAGCATGGCCACCACCCTGCGCAAGCTGCTAACCACCCCCTCTCTGAGCGCCCGTTCGCAGCAGCAGCTGCTGCAGTGGATGGTTGACGACCGGGTGGCCGGCCCGTTGATCCGCGCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAAACCGGGGCCGGTGAGCGGGGCTCACGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAAGCGGAGCGTATCGTGGTGATCTATCTGCGGGATACCGCGGCGACCATGGTCGAGCGTAACCAGCAGATCGCCGGGATAGGCGCGGCGCTGATCGAGCACTGGCAGCGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002436","ARO_id":"38836","ARO_name":"OKP-B-3","CARD_short_name":"OKP-B-3","ARO_description":"OKP-B-3 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"38817":{"category_aro_accession":"3002417","category_aro_cvterm_id":"38817","category_aro_name":"OKP beta-lactamase","category_aro_description":"OKP beta-lactamases are chromosomal class A beta-lactamase that confer resistance to penicillins and early cephalosporins in Klebsiella pneumoniae. OKP beta-lactamases can be subdivided into two groups: OKP-A and OKP-B which diverge by about 4.2%.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"228":{"model_id":"228","model_name":"sdiA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"470"}},"model_sequences":{"sequence":{"5397":{"protein_sequence":{"accession":"AAL20862.1","sequence":"MQENDFFTWRRAMLLRFQEMAAAEDVYTELQYQTQRLEFDYYALCVRHPVPFTRPKISLRTTYPPAWVTHYQSENYFAIDPVLKPENFRQGHLHWDDVLFHEAKAMWDAAQRFGLRRGVTQCVMLPNRALGFLSFSRSSLRCSSFTYDEVELRLQLLARESLSALTRFEDDMVMAPEMRFSKREKEILKWTAEGKTSSEIAIILSISENTVNFHQKNMQKKFNAPNKTQIACYAAATGLI"},"dna_sequence":{"accession":"AE006468.2","fmin":"2039654","fmax":"2040377","strand":"-","sequence":"ATGCAGGAAAATGATTTCTTCACCTGGCGACGCGCAATGTTGTTACGCTTTCAGGAGATGGCGGCAGCAGAGGATGTTTATACTGAATTGCAATATCAGACACAGCGGCTGGAATTTGATTATTATGCCCTGTGTGTTCGTCATCCCGTCCCCTTTACCCGGCCTAAAATATCGCTTCGTACCACTTATCCTCCGGCGTGGGTAACGCATTACCAGTCCGAAAACTATTTCGCGATCGATCCGGTATTAAAGCCGGAAAATTTCAGGCAGGGTCATTTACATTGGGATGACGTGCTATTTCATGAAGCGAAGGCGATGTGGGATGCCGCCCAGCGTTTCGGATTACGCAGAGGCGTAACCCAGTGTGTGATGTTGCCGAACCGGGCGCTGGGCTTTTTATCTTTCTCCCGTAGCAGTTTACGCTGCTCCTCGTTTACCTACGACGAAGTGGAGCTGAGGTTGCAACTGCTGGCGCGGGAGAGTCTTTCGGCGCTGACAAGATTTGAAGACGACATGGTGATGGCGCCTGAAATGCGTTTCAGTAAACGTGAGAAAGAGATTCTGAAGTGGACGGCGGAAGGGAAGACCTCATCGGAGATCGCCATTATTCTGTCGATTTCTGAAAATACCGTTAACTTCCATCAGAAAAATATGCAGAAGAAATTCAATGCGCCAAATAAAACACAGATTGCCTGCTACGCTGCGGCGACAGGTCTGATATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35734","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Typhimurium str. LT2","NCBI_taxonomy_id":"99287"}}}},"ARO_accession":"3000826","ARO_id":"37206","ARO_name":"sdiA","CARD_short_name":"sdiA","ARO_description":"SdiA is a cell division regulator that is also a positive regulator of AcrAB only when it's expressed from a plasmid. When the sdiA gene is on the chromosome, it has no effect on expression of acrAB.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"37084":{"category_aro_accession":"3000704","category_aro_cvterm_id":"37084","category_aro_name":"cefalotin","category_aro_description":"Cefalotin is a semisynthetic cephalosporin antibiotic activate against staphylococci. It is resistant to staphylococci beta-lactamases but hydrolyzed by enterobacterial beta-lactamases.","category_aro_class_name":"Antibiotic"},"37250":{"category_aro_accession":"3000870","category_aro_cvterm_id":"37250","category_aro_name":"triclosan","category_aro_description":"Triclosan is a common antibacterial agent added to many consumer products as a biocide.  It is an inhibitor of fatty acid biosynthesis by blocking enoyl-carrier protein reductase (FabI).","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"43746":{"category_aro_accession":"3005386","category_aro_cvterm_id":"43746","category_aro_name":"disinfecting agents and antiseptics","category_aro_description":"Disinfectants that can also interact with antimicrobial resistance mechanisms, e.g. molecule efflux, and thus are the targets of disinfectant resistance.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"230":{"model_id":"230","model_name":"OXA-422","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"892":{"protein_sequence":{"accession":"AIY30331.1","sequence":"MNKYFTCYVVASPFLSGCTVQHNLINETPSQIVQGHNQVIHQYFDEKNTSGVLVIQTDKKINLYGNALSRANTEYVPASTFKMLNALIGLENQKTDINEIFKWKGEKRSFTAWEKDMTLGEAMKLSAVPVYQELARRIGLDLMQKEVKRIGFGNAEIGQQVDNFWLVGPLKVTPIQEVEFVSQLAHTQLPFSEKVQANVKNMLLLEESNGYKIFGKTGWAMDIKPQVGWLTGWVEQPDGKIVAFALNMEMRSEMPASIRNELLMKSLKQLNII"},"dna_sequence":{"accession":"KM433671.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGAATAAATATTTTACTTGCTATGTGGTTGCTTCTCCTTTTCTTTCTGGTTGTACGGTTCAGCATAATTTAATAAATGAAACCCCGAGTCAGATTGTTCAAGGACATAATCAGGTGATTCATCAATACTTTGATGAAAAAAACACCTCAGGTGTGCTGGTTATTCAAACAGATAAAAAAATTAATCTATATGGTAATGCTCTAAGCCGCGCAAATACAGAATATGTGCCAGCCTCTACATTTAAAATGTTGAATGCCCTGATCGGATTGGAGAACCAGAAAACGGATATTAATGAAATATTTAAATGGAAGGGCGAGAAAAGGTCATTTACCGCTTGGGAAAAAGACATGACACTAGGAGAAGCCATGAAGCTTTCTGCAGTCCCAGTCTATCAGGAACTTGCGCGACGTATCGGTCTTGATCTCATGCAAAAAGAAGTAAAACGTATTGGTTTCGGTAATGCTGAAATTGGACAGCAGGTTGATAATTTCTGGTTGGTAGGACCATTAAAGGTTACGCCTATTCAAGAGGTAGAGTTTGTTTCCCAATTAGCACATACACAGCTTCCATTTAGTGAAAAAGTGCAGGCTAATGTAAAAAATATGCTTCTTTTAGAAGAGAGTAATGGCTACAAAATTTTTGGAAAGACTGGTTGGGCAATGGATATAAAACCACAAGTGGGCTGGTTGACCGGCTGGGTTGAGCAGCCAGATGGAAAAATTGTCGCTTTTGCATTAAATATGGAAATGCGGTCAGAAATGCCGGCATCTATACGTAATGAATTATTGATGAAATCATTAAAACAGCTGAATATTATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3003160","ARO_id":"39737","ARO_name":"OXA-422","CARD_short_name":"OXA-422","ARO_description":"OXA-422 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46499":{"category_aro_accession":"3007710","category_aro_cvterm_id":"46499","category_aro_name":"OXA-23-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases, specifically imipenem, derived from OXA-23, first identified in Acinetobacter baumannii.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"231":{"model_id":"231","model_name":"OXA-178","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1046":{"protein_sequence":{"accession":"ADI58622.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDVKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDSKKRLFPEWEKDMTLGDAMKASAILVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"HM113564.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGTAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATAGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCTAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAACAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001472","ARO_id":"37872","ARO_name":"OXA-178","CARD_short_name":"OXA-178","ARO_description":"OXA-178 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"232":{"model_id":"232","model_name":"imiH","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"1808":{"protein_sequence":{"accession":"CAD69003.1","sequence":"MMKGWMKCGLAGAVVLMASFWGGSVRAAGMSLTQVSGPVYVVEDNYYVQENSMVYFGAKGVTVVGATWTPDTARELHKLIKRVSRQPVLEVINTNYHTDRAGGNAYWKSIGAKVVSTRQTRDLMKSDWAEIVAFTRKGLPEYPDLPLVLPNVVHDGDFTLQEGKLRAFYAGPAHTPDGIFVYFPDQLVLYGNCILKEKLGNLSFADVKAYPQTLERLKAMKLPIKTVVGGHDSPLHGPELIDHYEALIKAAPQS"},"dna_sequence":{"accession":"AJ548797.1","fmin":"923","fmax":"1688","strand":"+","sequence":"ATGATGAAAGGTTGGATGAAGTGTGGATTGGCCGGCGCCGTGGTGCTGATGGCGAGTTTCTGGGGTGGCAGCGTGCGGGCGGCGGGGATGTCGCTGACGCAGGTGAGCGGCCCTGTGTATGTGGTAGAGGACAACTACTACGTGCAGGAAAATTCCATGGTCTATTTCGGGGCCAAGGGCGTGACTGTGGTGGGGGCGACCTGGACGCCGGACACCGCCCGCGAGCTGCACAAGCTGATCAAACGGGTCAGCCGCCAGCCGGTGCTGGAGGTGATCAACACCAACTACCACACCGACCGGGCTGGCGGTAACGCCTACTGGAAGTCCATCGGTGCCAAGGTGGTATCGACCCGCCAGACCCGGGATCTGATGAAGAGCGACTGGGCCGAGATCGTTGCCTTTACCCGCAAGGGGTTGCCGGAGTACCCGGATCTGCCCCTGGTGCTGCCCAACGTGGTGCACGATGGCGACTTCACCCTGCAAGAGGGCAAGCTGCGCGCCTTCTACGCGGGCCCGGCCCACACGCCGGACGGCATCTTTGTCTACTTCCCCGACCAGCTGGTGCTCTATGGCAACTGCATCCTCAAGGAGAAGCTGGGCAACCTGAGCTTTGCCGATGTGAAGGCCTATCCGCAGACACTTGAGCGGCTGAAAGCGATGAAGCTGCCGATCAAGACGGTGGTGGGCGGTCACGACTCGCCACTGCACGGCCCCGAGCTTATCGATCACTACGAAGCGCTGATCAAGGCCGCACCCCAGTCATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36810","NCBI_taxonomy_name":"Aeromonas hydrophila","NCBI_taxonomy_id":"644"}}}},"ARO_accession":"3003094","ARO_id":"39647","ARO_name":"imiH","CARD_short_name":"imiH","ARO_description":"imiH is an Ambler Class B MBL; subclass B2 originally isolated from Aeromonas hydrophila. This enzyme has specific activity against carbapenems.","ARO_category":{"36720":{"category_aro_accession":"3000581","category_aro_cvterm_id":"36720","category_aro_name":"CphA beta-lactamase","category_aro_description":"CphA is an Ambler Class B MBL; subclass B2 originally isolated from Aeromonas hydrophilia.  This enzyme has specific activity against carbapenems and is active as a mono-zinc protein.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"233":{"model_id":"233","model_name":"LEN-21","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"8266":{"protein_sequence":{"accession":"CAP12349.2","sequence":"MRYVRLCVISLLATLPLAVDAGPQPLEQIKQSESQLSGRVGMVEMDLASGRTLAAWRADERFPMVSTFKVLLCGAVLARVDAGVEQLVRRIHYRQQDLVDYSPVSEKHLVDGMTIGELCAAAITLSDNSAGNLLLATVGGPAGLTAFLRQIGDNVTRLDRWETALNEALPGDARDTTTPASMAATLRKLLTAQHLSARSQQQLLQWMVDDRVAGPLIRAVLPAGWFIADKTGAGERGARGIVALLGPDGKPERIVVIYLRDTPASMAERNQHIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AM850911.2","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGTGTTATCTCCCTGTTAGCCACCCTGCCACTGGCGGTAGACGCCGGTCCACAGCCGCTTGAGCAGATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTGGGGATGGTGGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCGATGAACGCTTTCCCATGGTGAGCACCTTTAAAGTGCTGCTGTGCGGCGCGGTGCTGGCGCGGGTGGATGCAGGGGTCGAACAACTGGTTCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGTCGACGGGATGACGATCGGCGAACTCTGCGCCGCCGCCATCACCCTGAGCGATAACAGCGCTGGCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCGGGATTAACTGCCTTTCTGCGCCAGATCGGTGACAACGTCACCCGTCTTGACCGCTGGGAAACGGCACTGAATGAGGCGCTTCCCGGCGACGCGCGCGACACCACCACCCCGGCCAGCATGGCCGCCACGCTGCGCAAACTACTGACCGCGCAGCATCTGAGCGCCCGTTCGCAACAGCAACTCCTGCAGTGGATGGTGGACGATCGGGTTGCCGGCCCGCTGATCCGCGCCGTGCTGCCGGCGGGCTGGTTTATCGCCGACAAAACCGGGGCTGGCGAACGGGGTGCGCGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAACCGGAGCGCATTGTGGTGATCTATCTGCGGGATACCCCGGCGAGTATGGCCGAGCGTAATCAACATATCGCCGGGATCGGCGCAGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002468","ARO_id":"38868","ARO_name":"LEN-21","CARD_short_name":"LEN-21","ARO_description":"LEN-21 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36236":{"category_aro_accession":"3000097","category_aro_cvterm_id":"36236","category_aro_name":"LEN beta-lactamase","category_aro_description":"LEN beta-lactamases are chromosomal class A beta-lactamases that confer resistance to ampicillin, amoxicillin, carbenicillin, and ticarcillin but not to extended-spectrum beta-lactams.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"234":{"model_id":"234","model_name":"QnrS8","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"387":{"protein_sequence":{"accession":"AHE41345.1","sequence":"METYNHTYRHHNFSHKDLSDLTFTACTLIRSDFRRANLRDTTFVNCKFIEQGDIEGCHFDVADLRDASFQQCQLAMANFSNANCYGIEFRACDLKGANFSRTNFAHQVSNRMYFCSAFISGCNLSYANMERVCLEKCELFENRWIGTNLAGASLKESDLSRGVFSEDVWGQFSLQGANLCHAELDGLDPRKVDTSGIKIAAWQQELILEALGIVVYPD"},"dna_sequence":{"accession":"KF730652.1","fmin":"0","fmax":"657","strand":"+","sequence":"ATGGAAACCTACAATCATACATATCGGCACCACAACTTTTCACATAAAGACTTAAGTGATCTCACCTTCACCGCTTGCACACTCATTCGCAGCGACTTTCGACGTGCTAACTTGCGTGATACGACATTCGTCAACTGCAAGTTCATTGAACAGGGTGATATCGAAGGCTGCCACTTTGATGTCGCAGATCTTCGTGATGCAAGTTTCCAACAATGCCAACTTGCGATGGCAAACTTCAGTAATGCCAATTGCTACGGTATAGAGTTCCGTGCGTGTGATTTAAAAGGTGCCAACTTTTCCCGAACAAACTTTGCCCATCAAGTGAGTAATCGTATGTACTTTTGCTCAGCATTTATTTCTGGATGTAATCTTTCCTATGCCAATATGGAGAGGGTTTGTTTAGAAAAATGTGAGTTGTTTGAAAATCGCTGGATAGGAACGAACCTAGCGGGTGCATCACTGAAAGAGTCAGACTTAAGTCGAGGTGTTTTTTCCGAAGATGTCTGGGGGCAATTTAGCCTACAGGGTGCCAATTTATGCCACGCCGAACTCGACGGTTTAGATCCCCGCAAAGTCGATACATCAGGTATCAAAATTGCAGCCTGGCAGCAAGAACTGATTCTCGAAGCACTGGGTATTGTTGTTTATCCTGACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002797","ARO_id":"39231","ARO_name":"QnrS8","CARD_short_name":"QnrS8","ARO_description":"QnrS8 is a plasmid-mediated quinolone resistance protein found in Klebsiella pneumoniae.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"235":{"model_id":"235","model_name":"OXA-181","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1371":{"protein_sequence":{"accession":"AEP16366.1","sequence":"MRVLALSAVFLVASIIGMPAVAKEWQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGQTRDIAAWNRDHDLITAMKYSVVPVYQEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISATQQIAFLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYSTRIEPKIGWWVGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP"},"dna_sequence":{"accession":"JN205800.1","fmin":"4140","fmax":"4938","strand":"+","sequence":"ATGCGTGTATTAGCCTTATCGGCTGTGTTTTTGGTGGCATCGATTATCGGAATGCCAGCGGTAGCAAAGGAATGGCAAGAAAACAAAAGTTGGAATGCTCACTTTACTGAACATAAATCACAGGGCGTAGTTGTGCTCTGGAATGAGAATAAGCAGCAAGGATTTACCAATAATCTTAAACGGGCGAACCAAGCATTTTTACCCGCATCTACCTTTAAAATTCCCAATAGCTTGATCGCCCTCGATTTGGGCGTGGTTAAGGATGAACACCAAGTCTTTAAGTGGGATGGACAGACGCGTGATATCGCCGCTTGGAATCGTGACCATGACTTAATTACCGCGATGAAGTACTCAGTTGTGCCTGTTTATCAAGAATTTGCCCGCCAAATTGGTGAGGCACGTATGAGTAAAATGCTGCACGCCTTCGATTATGGCAATGAGGATATCTCGGGCAATGTAGACAGTTTTTGGCTCGATGGTGGTATTCGCATTTCGGCTACCCAGCAAATCGCTTTTTTACGCAAGCTGTATCACAACAAGCTGCACGTTTCTGAGCGTAGTCAGCGCATCGTGAAACAAGCCATGCTGACCGAAGCCAATGGCGACTATATTATTCGGGCTAAAACGGGATACTCGACTAGAATCGAACCTAAGATTGGCTGGTGGGTTGGTTGGGTTGAACTTGATGATAATGTGTGGTTTTTTGCGATGAATATGGATATGCCCACATCGGATGGTTTAGGGCTGCGCCAAGCCATCACAAAAGAAGTGCTCAAACAGGAGAAAATTATTCCCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001784","ARO_id":"38184","ARO_name":"OXA-181","CARD_short_name":"OXA-181","ARO_description":"OXA-181 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46510":{"category_aro_accession":"3007721","category_aro_cvterm_id":"46510","category_aro_name":"OXA-48-like beta-lactamase","category_aro_description":"OXA-48-type beta-lactamases are now routinely encountered in bacterial infections caused by carbapenam-resistant Enterobacterales. OXA-48-like proteins confer resistance to penicillin (which is efficiently hydrolyzed) and carbapenam antibiotics (which is more slowly broken down). The spectrum of activity of these variants varies, with some hydrolyzing expanded-spectrum oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"236":{"model_id":"236","model_name":"ACT-19","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1583":{"protein_sequence":{"accession":"AHM76779.1","sequence":"MMKKSFCCALLLAISGSALAAPVSEKQLAEVVANTVTPLMKTQAIPGMAVAVIYQGKPHYYTFGEADIAAKKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTKFWPELTGKQWQGIRMLDLATYTAGGLPLQVPEEVTDNASLLRFYQHWQPQWKPGTTRLYANASIGLFGALAVKPSGMRYEQAMTKRVFKPLRLNHTWINVPKAEAAHYAWGYRDGKAVHISPGMLDAEAYGVKTNVQDMANWVMANMAPENIADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEAKMVIEGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANKSYPNPARVEAAYHILDALQ"},"dna_sequence":{"accession":"KF992029.1","fmin":"748","fmax":"1894","strand":"+","sequence":"ATGATGAAAAAATCCTTTTGCTGCGCCCTGCTGCTCGCCATCTCTGGCTCTGCTCTCGCCGCGCCAGTGTCAGAAAAACAGCTGGCGGAGGTGGTCGCGAATACGGTTACCCCGCTGATGAAAACCCAGGCTATTCCAGGCATGGCGGTGGCCGTTATCTATCAGGGAAAACCGCACTATTACACGTTTGGCGAAGCCGATATTGCGGCCAAAAAACCTGTTACGCCACAGACCCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGCGTTTTAGGTGGGGATGCCATTGCTCGCGGTGAAATTTCCCTGGACGATCCGGTGACCAAATTCTGGCCTGAACTGACGGGCAAGCAGTGGCAGGGTATTCGTATGCTGGATCTCGCAACCTACACCGCGGGCGGCCTGCCGCTACAGGTACCGGAAGAGGTCACGGATAACGCCTCCCTGCTGCGCTTTTATCAACACTGGCAACCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAATGCCAGCATCGGACTTTTTGGCGCGCTGGCGGTCAAACCTTCCGGCATGCGCTATGAGCAGGCCATGACGAAGCGGGTCTTCAAGCCGCTCAGGCTGAACCATACCTGGATTAACGTTCCGAAAGCGGAAGCGGCGCATTACGCCTGGGGTTATCGTGACGGTAAAGCGGTCCACATTTCACCGGGTATGCTGGACGCAGAGGCCTATGGCGTGAAAACTAACGTGCAGGATATGGCGAACTGGGTGATGGCGAACATGGCGCCGGAGAACATTGCTGATGCCTCACTCAAGCAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGCATCGGGTCAATGTATCAGGGCCTGGGCTGGGAAATGCTCAACTGGCCCGTGGAGGCCAAAATGGTGATCGAGGGCAGCGACAATAAGGTGGCACTGGCGCCGTTGCCCGTGGCAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACAGGCTCTACTGGCGGGTTTGGCAGCTACGTGGCATTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATAAAAGCTATCCGAATCCGGCACGCGTTGAGGCGGCATACCATATCCTCGACGCACTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3001840","ARO_id":"38240","ARO_name":"ACT-19","CARD_short_name":"ACT-19","ARO_description":"ACT-19 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"238":{"model_id":"238","model_name":"SHV-137","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1388":{"protein_sequence":{"accession":"AEI83430.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAALTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPHNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"HQ661363.1","fmin":"71","fmax":"932","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACATCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGCATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGCATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001181","ARO_id":"37561","ARO_name":"SHV-137","CARD_short_name":"SHV-137","ARO_description":"SHV-137 is a beta-lactamase.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"239":{"model_id":"239","model_name":"OXA-83","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1937":{"protein_sequence":{"accession":"ABC26007.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDVKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASALPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"DQ309277.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGTAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTCTTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAACAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001623","ARO_id":"38023","ARO_name":"OXA-83","CARD_short_name":"OXA-83","ARO_description":"OXA-83 is a beta-lactamase found in A. baumannii.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"241":{"model_id":"241","model_name":"ACT-30","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1263":{"protein_sequence":{"accession":"AIT76086.1","sequence":"MMKKSLCCALLLGLSCSALAAPVSEKQLAEVVANTVTPLMIAQSVPGMAVAVIYQGKSHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMPYEQAMTTRVLKPLKLDHTWINVPKAEEAHYARGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPEKVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVVEGSDSKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQVGIVMLANKSYPNPARVEAAYHILDALQ"},"dna_sequence":{"accession":"KM087833.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCTCTTTGCTGCGCCCTGCTGCTCGGCCTCTCTTGCTCTGCTCTCGCCGCGCCAGTATCAGAAAAACAGCTGGCGGAGGTGGTCGCGAATACGGTTACCCCGCTGATGATAGCCCAGTCTGTTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGAAAATCGCACTATTACACGTTTGGCAAGGCCGATATCGCGGCGAATAAACCCGTTACGCCTCAGACCCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGCGTTTTAGGTGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTGACGGGCAAGCAGTGGCAGGGTATTCGTATGCTGGATCTCGCCACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTCAAACCTTCTGGCATGCCCTATGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTTCCGAAAGCGGAAGAGGCGCATTACGCCAGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGAATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCGGAGAAGGTTGCCGATGCCTCACTTAAGCAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGGTCGAAGGCAGCGACAGTAAGGTAGCGCTGGCGCCGTTACCCGTGGCAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCATGGGTCCATAAAACGGGTTCTACTGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGGTCGGTATTGTAATGCTCGCGAATAAAAGCTATCCGAATCCGGCACGCGTTGAGGCGGCATACCATATCCTCGACGCGCTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3001850","ARO_id":"38250","ARO_name":"ACT-30","CARD_short_name":"ACT-30","ARO_description":"ACT-30 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"242":{"model_id":"242","model_name":"SHV-152","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1232":{"protein_sequence":{"accession":"AFQ23958.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTARRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGASERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"JX121119.1","fmin":"0","fmax":"858","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCCGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACATCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTAGCGAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGC","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001191","ARO_id":"37571","ARO_name":"SHV-152","CARD_short_name":"SHV-152","ARO_description":"SHV-152 is a beta-lactamase.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"243":{"model_id":"243","model_name":"OXA-9","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1219":{"protein_sequence":{"accession":"AAA98406.1","sequence":"MKKILLLHMLVFVSATLPISSVASDEVETLKCTIIADAITGNTLYETGECARRVSPCSSFKLPLAIMGFDSGILQSPKSPTWELKPEYNPSPRDRTYKQVYPALWQSDSVVWFSQQLTSRLGVDRFTEYVKKFEYGNQDVSGDSGKHNGLTQSWLMSSLTISPKEQIQFLLRFVAHKLPVSEAAYDMAYATIPQYQAAEGWAVHGKSGSGWLRDNNGKINESRPQGWFVGWAEKNGRQVVFARLEIGKEKSDIPGGSKAREDILVELPVLMGNK"},"dna_sequence":{"accession":"M55547.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAAAAAAATTTTGCTGCTGCATATGTTGGTGTTCGTTTCCGCCACTCTCCCAATCAGTTCCGTGGCTTCTGATGAGGTTGAAACGCTTAAATGCACCATCATCGCAGACGCCATTACCGGAAATACCTTATATGAGACCGGAGAATGTGCCCGTCGTGTGTCTCCGTGCTCGTCTTTTAAACTTCCATTGGCAATCATGGGGTTTGATAGTGGAATCTTGCAGTCGCCAAAATCACCTACGTGGGAATTGAAGCCGGAATACAACCCGTCTCCGAGAGATCGCACATACAAACAAGTCTATCCGGCGCTATGGCAAAGCGACTCTGTTGTCTGGTTCTCGCAGCAATTAACAAGCCGTCTGGGAGTTGATCGGTTCACGGAATACGTAAAGAAATTTGAGTACGGTAATCAAGATGTTTCCGGTGACTCGGGGAAGCATAACGGCTTGACCCAGTCATGGCTGATGTCGTCGCTCACCATATCTCCCAAGGAGCAAATTCAGTTTCTTCTACGCTTTGTCGCGCATAAGCTGCCTGTATCCGAAGCGGCTTATGACATGGCGTATGCCACAATCCCGCAGTACCAGGCAGCCGAAGGATGGGCTGTACATGGAAAAAGCGGCAGCGGCTGGCTTCGGGACAATAACGGCAAGATAAATGAAAGTCGTCCGCAGGGCTGGTTCGTGGGCTGGGCTGAAAAAAACGGACGGCAAGTTGTTTTCGCCCGATTGGAAATAGGAAAGGAAAAGTCCGATATTCCCGGCGGGTCTAAAGCACGAGAGGATATTCTCGTGGAATTACCCGTGTTGATGGGTAACAAATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001404","ARO_id":"37804","ARO_name":"OXA-9","CARD_short_name":"OXA-9","ARO_description":"OXA-9 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46524":{"category_aro_accession":"3007735","category_aro_cvterm_id":"46524","category_aro_name":"OXA-9-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-9.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"244":{"model_id":"244","model_name":"SHV-164","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"988":{"protein_sequence":{"accession":"CCK86744.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGEQGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"HE981194.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACCCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGAGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACAGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATCGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001347","ARO_id":"37747","ARO_name":"SHV-164","CARD_short_name":"SHV-164","ARO_description":"SHV-164 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"245":{"model_id":"245","model_name":"cmlA5","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"695":{"protein_sequence":{"accession":"AAM77075.1","sequence":"MRSKNFSWRYSLAATVLLLSPFDLLASLGMDMYLPAVPFMPNALGTTASTIQLTLTTYLVMIGAGQLLFGPLSDRLGRRPVLLGGGLAYVVASMGLALTSSAEVFLGLRILQACGASACLVSTFATVRDIYAGREESNVIYGILGSMLAMVPAVGPLLGALVDMWLGWRAIFAFLGLGMIAASAAAWRFWPETRVQRVAGLQWSQLLLPVKCLNFWLYTLCYAAGMGSFFVFFSIAPGLMMGRQGVSQLGFSLLFATVAIAMVFTARFMGRVIPKWGSPSVLRMGMGCLIAGAVLLAITEIWASQSVLGFIAPMWLVGIGVATAVSVSPNGALRGFDHVAGTVTAVYFCLGGVLLGSIGTLIISLLPRNTAWPVVVYCLTLATVVLGLSCVSRVKGSRGQGEHDVVALQSAESTSNPNR"},"dna_sequence":{"accession":"AY115475.1","fmin":"3337","fmax":"4597","strand":"+","sequence":"GTGCGCTCAAAAAACTTTAGTTGGCGGTACTCCCTTGCCGCCACGGTGTTGTTGTTATCACCGTTCGATTTATTGGCATCACTCGGCATGGACATGTACTTGCCAGCAGTGCCGTTTATGCCAAACGCGCTTGGTACGACAGCGAGCACAATTCAGCTTACGCTGACAACGTACTTGGTCATGATTGGTGCCGGTCAGCTCTTGTTTGGACCGCTATCGGACCGACTGGGGCGCCGCCCCGTTCTACTGGGAGGTGGCCTCGCCTACGTTGTGGCGTCAATGGGCCTCGCTCTTACGTCATCGGCTGAAGTCTTTCTGGGGCTTCGGATTCTTCAGGCTTGTGGTGCCTCGGCGTGCCTTGTTTCCACATTTGCAACAGTACGTGACATTTACGCAGGTCGCGAGGAAAGTAATGTCATTTACGGCATACTCGGATCCATGCTGGCCATGGTCCCGGCGGTAGGCCCATTGCTCGGAGCGCTCGTCGACATGTGGCTTGGGTGGCGGGCTATCTTTGCGTTTCTAGGTTTGGGCATGATCGCTGCATCTGCAGCAGCGTGGCGATTCTGGCCTGAAACCCGGGTGCAACGAGTTGCGGGCTTGCAATGGTCGCAGCTGCTACTCCCCGTTAAGTGCCTGAACTTCTGGTTGTACACGTTGTGTTACGCCGCTGGAATGGGTAGCTTCTTCGTCTTTTTCTCCATTGCGCCCGGACTAATGATGGGCAGGCAAGGTGTGTCTCAGCTTGGCTTCAGCCTGCTGTTCGCCACAGTGGCAATTGCCATGGTGTTTACGGCTCGTTTTATGGGGCGTGTGATACCCAAGTGGGGCAGCCCAAGTGTCTTGCGAATGGGAATGGGATGCCTGATAGCTGGAGCAGTATTGCTTGCCATCACCGAAATATGGGCTTCGCAGTCCGTGTTAGGCTTTATTGCTCCAATGTGGCTAGTGGGTATTGGTGTCGCCACAGCGGTATCTGTGTCGCCCAATGGCGCTCTTCGAGGATTCGACCATGTTGCTGGAACGGTCACGGCAGTCTACTTCTGCTTGGGCGGTGTACTGCTAGGAAGCATCGGAACGTTGATCATTTCGCTGTTGCCGCGCAACACGGCTTGGCCGGTTGTCGTGTACTGTTTGACCCTTGCAACAGTCGTGCTCGGTCTGTCTTGTGTTTCCCGAGTGAAGGGCTCTCGCGGCCAGGGGGAGCATGATGTGGTCGCGCTACAAAGTGCGGAAAGTACATCAAATCCCAATCGTTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36791","NCBI_taxonomy_name":"uncultured bacterium","NCBI_taxonomy_id":"77133"}}}},"ARO_accession":"3002695","ARO_id":"39129","ARO_name":"cmlA5","CARD_short_name":"cmlA5","ARO_description":"cmlA5 is a plasmid or transposon-encoded chloramphenicol exporter that is found in Escherichia coli.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"246":{"model_id":"246","model_name":"CTX-M-126","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1476":{"protein_sequence":{"accession":"BAL72196.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEATLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"AB703103.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAAGCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGACTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAGCAGAACGCAGAGAGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001985","ARO_id":"38385","ARO_name":"CTX-M-126","CARD_short_name":"CTX-M-126","ARO_description":"CTX-M-126 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"247":{"model_id":"247","model_name":"TEM-158","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1569":{"protein_sequence":{"accession":"ABQ00181.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMLSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDSWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERDRQIAEIGASLIKHW"},"dna_sequence":{"accession":"EF534736.1","fmin":"213","fmax":"1074","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGCTGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATAGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAGATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001024","ARO_id":"37404","ARO_name":"TEM-158","CARD_short_name":"TEM-158","ARO_description":"TEM-158 is an inhibitor-resistant, extended-spectrum beta-lactamase found in E. coli.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"248":{"model_id":"248","model_name":"OKP-B-9","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"1998":{"protein_sequence":{"accession":"CAJ19618.1","sequence":"MRYVRLCLISLIAALPLAVFASPQPLEQIKISESQLAGRVGYIEMDLASGRTLAAWRASERFPLMSTFKVLLCGAVLARVDAGDEQLDRRIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAGNLLLKSVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDVRDTTTPASMATTLRRLLTTPSLSARSQQQLLQWMVDDRVAGPLIRAVLPAGWFIADKTGAGERGSRGIVALLGPDGKAERIVVIYLRDTAATMVERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AM051159.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGCCTTATCTCCCTGATTGCCGCCCTGCCACTGGCGGTATTCGCCAGCCCTCAGCCGCTTGAGCAGATTAAAATCAGCGAAAGTCAGCTGGCGGGCCGGGTGGGCTATATTGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCAGTGAGCGCTTTCCGCTGATGAGCACCTTTAAAGTGCTGCTCTGCGGCGCGGTGCTGGCCCGGGTGGATGCCGGCGACGAACAGCTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGCCGACGGGATGACCGTTGGCGAACTCTGCGCCGCCGCCATCACCATGAGCGACAACAGCGCCGGCAATCTGCTGTTGAAGAGCGTCGGCGGCCCTGCGGGATTGACCGCTTTTCTGCGCCAGATCGGTGACAACGTCACCCGTCTTGACCGCTGGGAAACGGAACTCAATGAGGCGCTTCCCGGCGACGTGCGCGACACCACCACCCCGGCCAGCATGGCCACCACCCTGCGCAGGCTGCTAACCACCCCCTCTCTGAGCGCCCGTTCGCAGCAGCAGCTGCTGCAGTGGATGGTGGACGACCGGGTGGCCGGCCCGTTGATCCGCGCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAAACCGGGGCCGGTGAGCGGGGCTCACGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAAGCGGAGCGTATCGTGGTGATCTATCTGCGGGATACCGCGGCGACCATGGTCGAGCGTAACCAGCAGATCGCCGGGATAGGCGCGGCGCTGATCGAGCACTGGCAGCGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002442","ARO_id":"38842","ARO_name":"OKP-B-9","CARD_short_name":"OKP-B-9","ARO_description":"OKP-B-9 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"38817":{"category_aro_accession":"3002417","category_aro_cvterm_id":"38817","category_aro_name":"OKP beta-lactamase","category_aro_description":"OKP beta-lactamases are chromosomal class A beta-lactamase that confer resistance to penicillins and early cephalosporins in Klebsiella pneumoniae. OKP beta-lactamases can be subdivided into two groups: OKP-A and OKP-B which diverge by about 4.2%.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3303":{"model_id":"3303","model_name":"ermZ","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"5231":{"protein_sequence":{"accession":"CAM96571.1","sequence":"MTLKSPLPPQSVSAPADSRSTARREWGQNFFRTAAAACRFSAQLDGSDTIPPDSPNDLMTVEIGAGSGRVTKVLASPGTPLLAVEIDPRWARRLAAESLPDVTVVNEDFLTLQLPGQPVRLIGNLPFVTGTRMLRRCLDMGPARMRQGVFLLQREYVGKRTGAWGGNLFNAQWEPWYSFDRGLAFSRQDFTPVPRADTQTLMVAPHRRPSVPWREKAAYQRFVQRVFDTGQMTVGDAARKVLRRGHAQFVRGAGVRPADRVKDLTVPEWTALFRAYGRTADR"},"dna_sequence":{"accession":"AM709783.1","fmin":"2816","fmax":"3665","strand":"-","sequence":"GTGACATTGAAATCCCCACTGCCACCGCAATCCGTCTCCGCACCCGCTGATTCACGCAGCACCGCGCGGAGAGAATGGGGTCAGAACTTCTTTCGTACAGCCGCCGCGGCCTGTCGTTTCTCCGCTCAGCTGGACGGTTCGGACACCATTCCGCCCGATTCTCCGAATGACCTGATGACCGTCGAAATAGGCGCGGGATCAGGGCGGGTGACCAAAGTGCTCGCCTCACCCGGGACGCCTTTACTCGCGGTGGAAATAGATCCCCGCTGGGCTCGGCGGCTGGCCGCCGAATCGCTGCCGGACGTCACGGTGGTGAACGAGGATTTCCTGACCCTGCAACTGCCCGGGCAGCCGGTCAGACTCATCGGGAATCTTCCCTTCGTCACCGGCACCAGAATGCTGAGGCGCTGCCTCGACATGGGTCCGGCGCGCATGCGGCAGGGCGTGTTCCTGTTGCAGCGGGAGTACGTGGGAAAGCGGACCGGAGCCTGGGGCGGAAACCTCTTCAACGCCCAGTGGGAGCCGTGGTACTCGTTCGACCGGGGCCTGGCCTTCTCACGCCAGGACTTCACCCCCGTACCGCGCGCGGACACCCAGACCCTGATGGTCGCCCCGCACCGCAGGCCGTCCGTGCCCTGGCGTGAGAAGGCCGCCTACCAGCGGTTCGTCCAACGGGTCTTCGACACCGGCCAGATGACGGTGGGCGACGCCGCGCGGAAGGTGCTGCGCCGCGGACACGCCCAGTTCGTGCGCGGGGCGGGCGTGAGGCCGGCCGACCGGGTCAAGGACCTCACGGTCCCGGAGTGGACCGCACTCTTCCGCGCCTACGGGCGGACGGCCGACCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36864","NCBI_taxonomy_name":"Streptomyces ambofaciens","NCBI_taxonomy_id":"1889"}}}},"ARO_accession":"3004605","ARO_id":"42565","ARO_name":"ermZ","CARD_short_name":"ermZ","ARO_description":"ermZ is an methyltransferase modifying 23S rRNA conferring resistance to Spiramycin.","ARO_category":{"36699":{"category_aro_accession":"3000560","category_aro_cvterm_id":"36699","category_aro_name":"Erm 23S ribosomal RNA methyltransferase","category_aro_description":"Erm proteins are part of the RNA methyltransferase family and methylate A2058 (E. coli nomenclature) of the 23S ribosomal RNA conferring degrees of resistance to Macrolides, Lincosamides and Streptogramin b. This is called the MLSb phenotype.","category_aro_class_name":"AMR Gene Family"},"36295":{"category_aro_accession":"3000156","category_aro_cvterm_id":"36295","category_aro_name":"spiramycin","category_aro_description":"Spiramycin is a 16-membered macrolide and is natural product produced by Streptomyces ambofaciens. It binds to the 50S subunit of bacterial ribosomes and inhibits peptidyl transfer activity to disrupt protein synthesis.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"251":{"model_id":"251","model_name":"APH(3')-VIIa","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"326":{"protein_sequence":{"accession":"AAA76822.1","sequence":"MKYIDEIQILGKCSEGMSPAEVYKCQLKNTVCYLKKIDDIFSKTTYSVKREAEMMMWLSDKLKVPDVIEYGVREHSEYLIMSELRGKHIDCFIDHPIKYIECLVNALHQLQAIDIRNCPFSSKIDVRLKELKYLLDNRIADIDVSNWEDTTEFDDPMTLYQWLCENQPQEELCLSHGDMSANFFVSHDGIYFYDLARCGVADKWLDIAFCVREIREYYPDSDYEKFFFNMLGLEPDYKKINYYILLDEMF"},"dna_sequence":{"accession":"M29953.1","fmin":"295","fmax":"1048","strand":"+","sequence":"ATGAAATATATCGATGAAATTCAAATTCTGGGAAAATGTTCAGAGGGTATGTCTCCAGCAGAAGTATATAAATGCCAGCTTAAAAATACTGTATGCTATCTGAAAAAAATTGACGATATATTTTCAAAAACCACATACAGCGTGAAAAGAGAAGCTGAGATGATGATGTGGTTATCCGATAAACTGAAAGTACCAGATGTAATCGAATACGGAGTACGAGAACATTCAGAATATTTGATCATGAGTGAGTTAAGGGGGAAACACATAGATTGCTTTATTGATCATCCAATAAAATATATTGAGTGCTTGGTAAACGCACTTCATCAGCTACAAGCAATAGATATAAGAAACTGCCCATTTTCATCCAAAATAGATGTTCGATTAAAAGAACTAAAATATCTTTTGGATAACAGAATTGCCGATATTGATGTATCGAATTGGGAAGATACAACAGAATTTGATGATCCAATGACGTTATATCAGTGGCTTTGCGAAAATCAACCTCAAGAAGAACTGTGTCTCTCTCATGGAGATATGAGCGCTAATTTTTTTGTATCTCATGATGGAATATATTTTTATGATTTGGCAAGATGTGGAGTTGCAGACAAATGGTTGGATATAGCATTTTGTGTCAGAGAGATTCGAGAATATTATCCTGATTCTGATTATGAAAAATTCTTTTTTAACATGTTGGGACTTGAACCGGATTATAAAAAAATTAACTATTACATTTTATTAGATGAGATGTTTTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36772","NCBI_taxonomy_name":"Campylobacter jejuni","NCBI_taxonomy_id":"197"}}}},"ARO_accession":"3002654","ARO_id":"39054","ARO_name":"APH(3')-VIIa","CARD_short_name":"APH(3')-VIIa","ARO_description":"APH(3')-VIIa is a plasmid-encoded aminoglycoside phosphotransferase in C. jejuni.","ARO_category":{"36265":{"category_aro_accession":"3000126","category_aro_cvterm_id":"36265","category_aro_name":"APH(3')","category_aro_description":"A category of aminoglycoside O-phosphotransferase enzymes with modification regiospecificity based at the 3'-hydroxyl group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics, specifically kanamycin and neomycin, by the ATP-dependent phosphorylation of the 3'-hydroxyl group of the compound.","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"252":{"model_id":"252","model_name":"APH(9)-Ia","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"514":{"protein_sequence":{"accession":"AAB58447.1","sequence":"MLKQPIQAQQLIELLKVHYGIDIHTAQFIQGGADTNAFAYQADSESKSYFIKLKYGYHDEINLSIIRLLHDSGIKEIIFPIHTLEAKLFQQLKHFKIIAYPFIHAPNGFTQNLTGKQWKQLGKVLRQIHETSVPISIQQQLRKEIYSPKWREIVRSFYNQIEFDNSDDKLTAAFKSFFNQNSAAIHRLVDTSEKLSKKIQPDLDKYVLCHSDIHAGNVLVGNEESIYIIDWDEPMLAPKERDLMFIGGGVGNVWNKPHEIQYFYEGYGEINVDKTILSYYRHERIVEDIAVYGQDLLSRNQNNQSRLESFKYFKEMFDPNNVVEIAFATEQ"},"dna_sequence":{"accession":"U94857.1","fmin":"0","fmax":"996","strand":"+","sequence":"ATGCTAAAACAACCAATTCAAGCTCAACAACTTATCGAACTTTTGAAAGTGCATTATGGAATTGATATTCATACAGCACAATTCATCCAGGGTGGTGCTGATACGAATGCATTTGCATATCAAGCAGATTCAGAATCCAAGTCTTATTTCATAAAGCTAAAATACGGCTATCATGATGAAATTAATTTATCGATAATCCGTCTTTTACATGATTCTGGAATAAAAGAAATTATTTTTCCTATCCATACACTTGAAGCAAAATTATTCCAGCAACTAAAGCATTTTAAAATAATTGCGTATCCATTTATTCATGCGCCCAATGGTTTCACCCAAAATTTAACAGGAAAACAGTGGAAACAGCTTGGAAAAGTATTAAGACAAATTCATGAAACATCAGTTCCCATCTCGATTCAACAACAATTAAGAAAAGAAATATACTCCCCTAAATGGCGTGAAATAGTCAGATCCTTTTATAATCAAATTGAATTTGATAATTCAGATGATAAGCTCACGGCTGCCTTTAAATCTTTTTTTAACCAAAATAGTGCTGCAATTCATCGATTAGTTGATACTTCAGAAAAACTATCTAAAAAAATTCAACCTGATTTAGATAAATACGTACTATGTCATTCTGATATACATGCGGGCAATGTGTTAGTCGGTAATGAAGAGTCGATTTACATTATTGATTGGGATGAGCCTATGTTAGCTCCAAAAGAACGTGATTTGATGTTCATAGGTGGTGGCGTTGGTAATGTATGGAATAAACCCCATGAAATCCAATATTTTTATGAAGGTTATGGTGAAATAAATGTCGATAAAACAATTTTGTCTTATTACAGGCATGAACGAATTGTCGAAGATATCGCAGTATACGGGCAAGACTTGCTTTCACGTAATCAAAACAATCAGTCCAGACTTGAAAGTTTTAAATATTTTAAAGAAATGTTTGATCCAAACAACGTTGTTGAAATAGCTTTTGCTACAGAGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36899","NCBI_taxonomy_name":"Legionella pneumophila 130b","NCBI_taxonomy_id":"866628"}}}},"ARO_accession":"3002662","ARO_id":"39062","ARO_name":"APH(9)-Ia","CARD_short_name":"APH(9)-Ia","ARO_description":"APH(9)-Ia is a chromosomal-encoded aminoglycoside phosphotransferase in L. pneumophila.","ARO_category":{"36292":{"category_aro_accession":"3000153","category_aro_cvterm_id":"36292","category_aro_name":"APH(9)","category_aro_description":"A category of aminoglycoside O-phosphotransferase enzymes with modification regiospecificity based at the 9-hydroxyl group of the respective antibiotic. These enzymes are characterized by enzymatic antibiotic inactivation, specifically of spectinomycin, by the ATP-dependent phosphorylation of the 9-hydroxyl group of the compound.","category_aro_class_name":"AMR Gene Family"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"254":{"model_id":"254","model_name":"OXA-150","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1923":{"protein_sequence":{"accession":"ACX31142.1","sequence":"MNIKALLLITSAIFISACSPYIVSANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSNEVKHVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"GQ853681.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGTCTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATTCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACTACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCATGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTGTTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001455","ARO_id":"37855","ARO_name":"OXA-150","CARD_short_name":"OXA-150","ARO_description":"OXA-150 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"256":{"model_id":"256","model_name":"CMY-21","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"957":{"protein_sequence":{"accession":"AAZ66866.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGELAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHVSPGKLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"DQ139328.1","fmin":"160","fmax":"1306","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGAGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGAAAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002032","ARO_id":"38432","ARO_name":"CMY-21","CARD_short_name":"CMY-21","ARO_description":"CMY-21 is a beta-lactamase found in Escherichia coli.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"257":{"model_id":"257","model_name":"ACT-37","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1735":{"protein_sequence":{"accession":"AJG06172.1","sequence":"MMKKSFCCALLLAISGAALAAPVSEKQLAEVVANTVTPLMKAQAIPGMAVAVIYQGKPHYYTFGEADIAAKKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVIKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPEEVTDNASLLRFYQHWQPQWKPGTTRLYANASIGLFGALAVKPSGMRYEQAMTKRVFKPLRLNHTWINVPKAEAAHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVQDMANWVMANMAPENVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEAKTVIEGSDNKVALAPLPVAEVNPPVPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANKSYPNPARVEAAYHILDALQ"},"dna_sequence":{"accession":"KM926622.1","fmin":"238","fmax":"1384","strand":"+","sequence":"ATGATGAAAAAATCCTTTTGCTGCGCCCTGCTGCTCGCCATCTCTGGCGCTGCTCTCGCCGCGCCAGTATCAGAAAAACAGCTGGCGGAGGTGGTCGCGAATACGGTTACCCCGCTGATGAAAGCCCAGGCTATTCCAGGCATGGCGGTGGCCGTTATCTATCAGGGAAAACCGCACTATTACACGTTTGGCGAAGCCGATATTGCGGCCAAAAAACCCGTTACGCCACAAACCCTGTTCGAGCTAGGTTCTATAAGTAAAACCTTCACCGGCGTTTTAGGTGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGATGATCCGGTGATCAAATACTGGCCTGAACTGACGGGCAAGCAGTGGCAGGGTATTCGTATGCTGGATCTCGCAACCTACACCGCGGGCGGCCTGCCGCTACAGGTACCGGAAGAGGTCACGGATAACGCCTCCCTGCTGCGCTTTTATCAACACTGGCAACCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAATGCCAGCATCGGACTTTTTGGCGCGCTGGCGGTCAAACCTTCCGGCATGCGCTATGAGCAGGCCATGACGAAGCGGGTCTTCAAGCCGCTCAGGCTGAACCATACCTGGATTAACGTTCCGAAAGCGGAAGCGGCGCATTACGCCTGGGGTTATCGTGACGGTAAAGCGGTCCACGTTTCACCGGGTATGCTGGACGCAGAGGCCTATGGCGTGAAAACTAACGTGCAGGATATGGCGAACTGGGTGATGGCGAACATGGCGCCGGAGAACGTTGCTGATGCCTCACTCAAGCAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGCCTGGGCTGGGAAATGCTCAACTGGCCCGTGGAGGCCAAAACAGTGATCGAGGGCAGCGACAATAAGGTGGCACTGGCGCCGTTGCCCGTGGCAGAAGTGAATCCACCGGTTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGCTCTACTGGCGGGTTTGGCAGCTACGTGGCATTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATAAAAGCTATCCGAATCCGGCACGCGTTGAGGCGGCATACCATATCCTCGACGCACTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3003172","ARO_id":"39749","ARO_name":"ACT-37","CARD_short_name":"ACT-37","ARO_description":"ACT-37 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"258":{"model_id":"258","model_name":"OXA-208","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1926":{"protein_sequence":{"accession":"CCA94644.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDDKAEKIKNLFNEAHTTGVLVIHQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWNGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"FR853176.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGACAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCATCAAGGTCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGAACGGGCAAAAAAGGCTGTTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001486","ARO_id":"37886","ARO_name":"OXA-208","CARD_short_name":"OXA-208","ARO_description":"OXA-208 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"260":{"model_id":"260","model_name":"ErmN","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"4244":{"protein_sequence":{"accession":"CAA66307.2","sequence":"MPSRPRTDSPHRHEGPAGPARLDRDEARRVWGQNFFRSAGSARRFARQLTGAESAGNDSVTVEVGPGAGRITKELVRDGHPIVAVEVDPHWADRLAELELPNLTVVNDDFTTWPLPDGPLRFIGNLPFGTGTRMLRRCLALGPDRCREGVFLLQKQYTRKRTGAYGGNLFNAQWEPWYTFRRGLGFPRQEFAPVPGSDTETLLVRSRPRPLAPWSRHAAYQRFVEDVFNTSRLTIGEAARALDRRAGPGWLRGARVPPGLRVKDITAEQWADLFHACTPPPARRISPQRRR"},"dna_sequence":{"accession":"X97721.2","fmin":"159","fmax":"1035","strand":"+","sequence":"ATGCCGTCCCGGCCACGTACCGATTCGCCCCACCGGCACGAGGGGCCGGCCGGCCCGGCCCGTCTCGACCGGGACGAGGCCCGCCGTGTATGGGGCCAGAATTTCTTCCGCTCGGCGGGTTCGGCCCGCCGTTTCGCCCGGCAGTTGACCGGCGCGGAATCGGCCGGAAACGACTCGGTCACCGTCGAGGTGGGTCCCGGGGCCGGCCGTATCACCAAGGAGTTAGTGAGGGACGGTCATCCGATCGTCGCGGTGGAGGTGGACCCCCATTGGGCCGACCGCCTCGCCGAACTGGAACTGCCGAACCTCACCGTCGTCAACGACGACTTCACGACCTGGCCGCTGCCCGACGGGCCGCTGCGGTTCATCGGCAATCTGCCCTTCGGCACCGGCACCAGGATGCTCCGCCGCTGCCTCGCCCTCGGCCCGGACCGCTGCCGCGAAGGCGTGTTCCTTCTCCAGAAGCAGTACACGCGCAAGCGCACCGGTGCCTACGGCGGCAATCTCTTCAACGCCCAGTGGGAGCCCTGGTACACGTTCCGCCGCGGACTGGGCTTCCCCCGGCAGGAGTTCGCCCCGGTCCCGGGCTCCGACACCGAGACCCTGCTGGTGAGATCGCGCCCGCGCCCGCTGGCGCCCTGGTCCCGCCATGCCGCCTACCAGCGGTTCGTGGAGGACGTGTTCAACACCTCCCGGCTCACCATCGGTGAGGCCGCCCGCGCGCTGGACCGCCGGGCCGGCCCGGGCTGGCTCCGGGGCGCGCGGGTGCCTCCCGGGTTGCGGGTCAAGGACATCACGGCCGAGCAGTGGGCCGATCTCTTCCACGCGTGCACCCCGCCGCCCGCCCGGCGCATCTCGCCGCAGCGGAGGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36838","NCBI_taxonomy_name":"Streptomyces fradiae","NCBI_taxonomy_id":"1906"}}}},"ARO_accession":"3000592","ARO_id":"36731","ARO_name":"ErmN","CARD_short_name":"ErmN","ARO_description":"ErmN is a methyltransferase found in the tylosin producer Streptomyces fradiae. Like other Erm enzymes, it catalyzes the methylation of A2058 of the 23S ribosomal RNA. Specifically, this enzyme transfers only one methyl group. The gene is found in the tylosin biosynthetic cluster and is responsible for self-resistance to tylosin.","ARO_category":{"36699":{"category_aro_accession":"3000560","category_aro_cvterm_id":"36699","category_aro_name":"Erm 23S ribosomal RNA methyltransferase","category_aro_description":"Erm proteins are part of the RNA methyltransferase family and methylate A2058 (E. coli nomenclature) of the 23S ribosomal RNA conferring degrees of resistance to Macrolides, Lincosamides and Streptogramin b. This is called the MLSb phenotype.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35946":{"category_aro_accession":"0000027","category_aro_cvterm_id":"35946","category_aro_name":"roxithromycin","category_aro_description":"Roxithromycin is a semi-synthetic, 14-carbon ring macrolide antibiotic derived from erythromycin. It is used to treat respiratory tract, urinary and soft tissue infections. Roxithromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35974":{"category_aro_accession":"0000057","category_aro_cvterm_id":"35974","category_aro_name":"telithromycin","category_aro_description":"Telithromycin is a semi-synthetic derivative of erythromycin. It is a 14-membered macrolide and is the first ketolide antibiotic to be used in clinics. Telithromycin binds the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"35982":{"category_aro_accession":"0000065","category_aro_cvterm_id":"35982","category_aro_name":"clarithromycin","category_aro_description":"Clarithromycin is a methyl derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome and is used to treat pharyngitis, tonsillitis, acute maxillary sinusitis, acute bacterial exacerbation of chronic bronchitis, pneumonia (especially atypical pneumonias associated with Chlamydia pneumoniae or TWAR), and skin structure infections.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"36284":{"category_aro_accession":"3000145","category_aro_cvterm_id":"36284","category_aro_name":"tylosin","category_aro_description":"Tylosin is a 16-membered macrolide, naturally produced by Streptomyces fradiae. It interacts with the bacterial ribosome 50S subunit to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"36295":{"category_aro_accession":"3000156","category_aro_cvterm_id":"36295","category_aro_name":"spiramycin","category_aro_description":"Spiramycin is a 16-membered macrolide and is natural product produced by Streptomyces ambofaciens. It binds to the 50S subunit of bacterial ribosomes and inhibits peptidyl transfer activity to disrupt protein synthesis.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"36315":{"category_aro_accession":"3000176","category_aro_cvterm_id":"36315","category_aro_name":"dirithromycin","category_aro_description":"Dirithromycin is an oxazine derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome to inhibit bacterial protein synthesis.","category_aro_class_name":"Antibiotic"},"36722":{"category_aro_accession":"3000583","category_aro_cvterm_id":"36722","category_aro_name":"pristinamycin IA","category_aro_description":"Pristinamycin IA is a type B streptogramin antibiotic produced by Streptomyces pristinaespiralis. It binds to the P site of the 50S subunit of the bacterial ribosome, preventing the extension of protein chains.","category_aro_class_name":"Antibiotic"},"36723":{"category_aro_accession":"3000584","category_aro_cvterm_id":"36723","category_aro_name":"quinupristin","category_aro_description":"Quinupristin is a type B streptogramin and a semisynthetic derivative of pristinamycin 1A. It is a component of the drug Synercid and interacts with the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"virginiamycin M1","category_aro_description":"Virginiamycin M1 is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37016":{"category_aro_accession":"3000672","category_aro_cvterm_id":"37016","category_aro_name":"madumycin II","category_aro_description":"Madumycin II is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37017":{"category_aro_accession":"3000673","category_aro_cvterm_id":"37017","category_aro_name":"griseoviridin","category_aro_description":"Griseoviridin is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"37019":{"category_aro_accession":"3000675","category_aro_cvterm_id":"37019","category_aro_name":"pristinamycin IB","category_aro_description":"Pristinamycin IB is a class B streptogramin similar to pristinamycin IA, the former containing a N-methyl-4-(methylamino)phenylalanine instead of a N-methyl-4-(dimethylamino)phenylalanine in its class A streptogramin counterpart (one less methyl group).","category_aro_class_name":"Antibiotic"},"37021":{"category_aro_accession":"3000677","category_aro_cvterm_id":"37021","category_aro_name":"virginiamycin S2","category_aro_description":"Virginiamycin S2 is a streptogramin B antibiotic.","category_aro_class_name":"Antibiotic"},"37022":{"category_aro_accession":"3000678","category_aro_cvterm_id":"37022","category_aro_name":"pristinamycin IC","category_aro_description":"Pristinamycin IC is a class B streptogramin derived from virginiamycin S1.","category_aro_class_name":"Antibiotic"},"37023":{"category_aro_accession":"3000679","category_aro_cvterm_id":"37023","category_aro_name":"vernamycin C","category_aro_description":"Vernamycin C is a streptogramin B antibiotic.","category_aro_class_name":"Antibiotic"},"37024":{"category_aro_accession":"3000680","category_aro_cvterm_id":"37024","category_aro_name":"patricin A","category_aro_description":"Patricin A is a streptogramin B antibiotic.","category_aro_class_name":"Antibiotic"},"37025":{"category_aro_accession":"3000681","category_aro_cvterm_id":"37025","category_aro_name":"patricin B","category_aro_description":"Patricin B is a streptogramin B antibiotic.","category_aro_class_name":"Antibiotic"},"37026":{"category_aro_accession":"3000682","category_aro_cvterm_id":"37026","category_aro_name":"ostreogrycin B3","category_aro_description":"Ostreogrycin B3 is a derivative of pristinamycin IA, with an additional 3-hydroxy group on its 4-oxopipecolic acid.","category_aro_class_name":"Antibiotic"},"37247":{"category_aro_accession":"3000867","category_aro_cvterm_id":"37247","category_aro_name":"oleandomycin","category_aro_description":"Oleandomycin is a 14-membered macrolide produced by Streptomyces antibioticus. It is ssimilar to erythromycin, and contains a desosamine amino sugar and an oleandrose sugar. It targets the 50S ribosomal subunit to prevent protein synthesis.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35952":{"category_aro_accession":"0000034","category_aro_cvterm_id":"35952","category_aro_name":"streptogramin A antibiotic","category_aro_description":"Streptogramin A antibiotics are cyclic polyketide peptide hybrids that bind to the ribosomal peptidyl transfer centre. Structural variation arises from substituting a proline for its desaturated derivative and by its substitution for Ala or Cys. Used alone, streptogramin A antibiotics are bacteriostatic, but is bactericidal when used with streptogramin B antibiotics.","category_aro_class_name":"Drug Class"},"35967":{"category_aro_accession":"0000050","category_aro_cvterm_id":"35967","category_aro_name":"streptogramin B antibiotic","category_aro_description":"Streptogramin B antibiotics are are cyclic hepta- or hexa-depsipeptides.  Type B streptogramins block the peptide exit tunnel of the 50S bacterial ribosome. The general composition of group B streptogramins is 3-hydroxypicolinic acid-L-Thr-D-aminobutyric acid (or D-Ala)-L-Pro-L-Phe (or 4-N-,N-(dimethylamino)-L-Phe)-X-L-phenylglycine. Used alone, streptogramin B antibiotics are bacteriostatic, but is bactericidal when used with streptogramin A antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"261":{"model_id":"261","model_name":"CMY-65","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1994":{"protein_sequence":{"accession":"AEI52842.1","sequence":"MMKKSICCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAIIYEGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWRGISLLHLATYTAGGLPLQIPDDVTDKAELLRFYQNWQPQWTPGAKRLYANSSIGLFGALVVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQSEQKNYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIELAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPARVEAAWRILEKLQ"},"dna_sequence":{"accession":"JF780936.1","fmin":"63","fmax":"1209","strand":"+","sequence":"ATGATGAAAAAATCGATATGCTGCGCACTGCTGCTGACAGCCTCTTTCTCCACGTTTGCTGCCGCAAAAACAGAACAACAAATTGCCGATATCGTTAACCGCACCATCACACCACTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTGGCGATTATCTACGAGGGGAAACCTTATTACTTTACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGACGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCGGGGTATCAGCCTGCTGCACTTAGCCACCTATACAGCGGGTGGCCTGCCGCTGCAGATCCCCGATGACGTTACGGATAAAGCCGAATTACTGCGCTTTTATCAAAACTGGCAACCACAATGGACTCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGTGCGCTGGTGGTAAAACCTTCAGGTATGAGCTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAAAGCGAACAAAAAAATTATGCCTGGGGCTATCGCGAAGGGAAGCCTGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATCGATATGGCCCGCTGGGTTCAGGCCAACATGGACGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGAGCTTGCGCAGTCTCGCTACTGGCGTATTGGTGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCAGCACCTGCCGTGAAAGCCTCATGGGTGCATAAAACAGGATCCACAGGCGGATTTGGCAGCTACGTTGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTAATGTTGGCAAACAAAAGCTACCCCAACCCGGCTCGCGTCGAGGCGGCCTGGCGCATTCTTGAAAAACTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39093","NCBI_taxonomy_name":"Citrobacter sp. 913","NCBI_taxonomy_id":"1037358"}}}},"ARO_accession":"3002078","ARO_id":"38478","ARO_name":"CMY-65","CARD_short_name":"CMY-65","ARO_description":"CMY-65 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"262":{"model_id":"262","model_name":"VIM-8","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1084":{"protein_sequence":{"accession":"AAS13759.1","sequence":"MFKLLSKLLVYLTASIMAIASPLAFSVDSSGEYPTVSEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSARRLAEVEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSASVLYGGCAIYELSRTSAGNVADADLAEWPTSIERIQQHYPEAQFVIPGHGLPGGLDLLKHTTNVVKAHTNRSVVE"},"dna_sequence":{"accession":"AY524987.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGTTCAAACTTTTGAGTAAGTTATTGGTCTATTTGACCGCGTCTATCATGGCTATTGCGAGTCCGCTCGCTTTTTCCGTAGATTCTAGCGGTGAGTATCCGACAGTCAGCGAAATTCCGGTCGGGGAGGTCCGGCTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCAGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAGAAGCAAATTGGACTTCCTGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGGCACGCCGGCTAGCCGAGGTAGAGGGGAACGAGATTCCCACGCACTCTCTAGAAGGACTCTCATCGAGCGGGGACGCGGTGCGCTTCGGTCCAGTAGAACTCTTCTATCCTGGTGCTGCGCATTCGACCGACAACTTAGTTGTGTACGTCCCGTCTGCGAGTGTGCTCTATGGTGGTTGTGCGATTTATGAGTTGTCACGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCATTGAGCGGATTCAACAACACTACCCAGAAGCACAGTTCGTCATTCCGGGGCACGGCCTGCCGGGCGGTCTAGACTTGCTCAAGCACACAACGAATGTTGTAAAAGCGCACACAAATCGCTCAGTCGTTGAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002278","ARO_id":"38678","ARO_name":"VIM-8","CARD_short_name":"VIM-8","ARO_description":"VIM-8 is a beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"263":{"model_id":"263","model_name":"dfrA24","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"66":{"protein_sequence":{"accession":"CAI99385.1","sequence":"MTYQLDVSKILSFDLEAIVAATENGGIGYKGDLPWRLQGDLKRFREITQGGIVIMGAGTYKSLPSPLKDRINIVITKKSEISWTACYDVRVVNSPEDALRMVGRIIDEKEEQGRDRPRVFVIGGASIYQALMPFVSTLHWTEVHVEQLPEEIGLDTYIEDFLSLRGTSTPKRKSNLVLPPTPTTP"},"dna_sequence":{"accession":"AJ972619.1","fmin":"82","fmax":"640","strand":"+","sequence":"ATGACCTATCAGTTGGACGTGAGCAAAATTCTGTCGTTTGACCTGGAGGCCATCGTTGCTGCTACTGAGAACGGCGGCATCGGTTACAAAGGTGACCTCCCATGGCGTCTACAAGGCGATCTGAAGCGTTTTCGCGAAATCACCCAAGGCGGTATAGTCATCATGGGTGCAGGCACGTATAAGAGCCTCCCAAGTCCTCTGAAAGACCGCATCAATATCGTCATCACCAAGAAGTCAGAGATTTCTTGGACGGCTTGCTATGACGTGCGTGTGGTCAACAGTCCAGAAGACGCTTTGCGCATGGTTGGTCGCATTATCGACGAGAAAGAAGAGCAAGGTCGTGATCGACCTCGTGTATTCGTTATCGGCGGGGCTTCGATCTATCAGGCACTGATGCCTTTCGTTTCTACGCTCCACTGGACTGAGGTGCATGTTGAACAACTGCCAGAGGAAATCGGTCTCGATACGTATATCGAAGACTTCCTTTCTCTGCGTGGGACTTCTACACCGAAGAGAAAGTCGAATCTGGTTTTACCACCCACACCTACCACACCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002856","ARO_id":"39290","ARO_name":"dfrA24","CARD_short_name":"dfrA24","ARO_description":"dfrA24 is an integron-encoded dihydrofolate reductase found in Escherichia coli.","ARO_category":{"37617":{"category_aro_accession":"3001218","category_aro_cvterm_id":"37617","category_aro_name":"trimethoprim resistant dihydrofolate reductase dfr","category_aro_description":"Alternative dihydropteroate synthase dfr present on plasmids produces alternate proteins that are less sensitive to trimethoprim from inhibiting its role in folate synthesis, thus conferring trimethoprim resistance.","category_aro_class_name":"AMR Gene Family"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"264":{"model_id":"264","model_name":"lsaE","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"8600":{"protein_sequence":{"accession":"AAL05553.1","sequence":"MSLINVSNLTFSYEGSYDNIFENVSFQIDTDWKLGFIGRNGRGKTTFLNLLLGKYAYSGNISSTVKFEYFPYDVEDKSLYTIEVMKSICTECMDWEIFREISLLDVQEDALYRPFNTLSNGEQTKVLLAALFLTASCFLLIDEPTNHLDIDARNVVQNYLKRKKGFILVSHDRSLLDQCVDHILSINKTNIEIQKGNFTSWWENKTLQDNFELAENKKLLKEIGRLSYAAKRSSNWSNKVEKSKYGTTNSGSKLDKGYVGHKAAKAMKRAKNIESRHQEAVLQKSELLHNIEQYDDLKISPLEFHKECLIEANDLSLSYGDKEVCSNLNFRVNIGDRVAIIGKNGSGKSSILKLINGDDIKFTGNFMLASGLKISYISQDTSYLKGNLSEFAYNNKIDETLFKTILRKLDFNREQFDKNMVDFSAGQKKKVLIAKSLCESAHLYIWDEPLNYIDIFSRIQIEKMILEYCPTLLFVEHDDAFCNNICTKNINLGL"},"dna_sequence":{"accession":"AF408195.1","fmin":"7908","fmax":"9393","strand":"+","sequence":"ATGTCCTTAATAAATGTTTCAAATCTAACTTTTTCATATGAAGGAAGTTATGACAATATTTTTGAAAATGTAAGTTTTCAGATAGATACAGATTGGAAACTCGGTTTTATTGGAAGAAACGGACGCGGTAAAACTACTTTCTTAAATTTACTGCTTGGCAAATATGCGTATTCCGGCAATATAAGTTCTACAGTTAAGTTTGAGTATTTTCCTTATGATGTGGAAGATAAGAGTCTATATACAATTGAAGTAATGAAGAGTATTTGTACGGAATGTATGGATTGGGAGATTTTTCGTGAAATATCATTGCTTGATGTTCAAGAAGATGCTTTATATCGTCCGTTTAATACATTGTCAAATGGTGAGCAAACGAAGGTCCTTCTTGCAGCTTTATTCCTTACAGCGAGTTGTTTCCTGCTTATTGATGAACCTACAAACCATCTTGACATCGATGCACGTAATGTAGTGCAAAACTATTTGAAACGCAAGAAGGGGTTTATTTTGGTATCTCATGATAGAAGCTTACTTGATCAATGTGTTGACCATATACTATCTATCAATAAAACGAATATCGAAATCCAAAAGGGAAATTTTACTTCTTGGTGGGAGAACAAAACGTTACAAGATAATTTTGAACTGGCAGAAAACAAGAAACTCCTTAAAGAAATAGGAAGGTTGTCTTATGCAGCAAAACGTAGTTCAAACTGGTCAAATAAAGTAGAAAAAAGTAAATATGGAACAACAAATTCTGGTTCAAAACTGGATAAGGGTTATGTTGGACATAAGGCTGCAAAAGCGATGAAACGTGCCAAAAATATTGAGTCAAGACATCAGGAAGCCGTTTTACAAAAATCAGAACTGCTCCACAACATTGAACAATATGATGACTTAAAAATTTCACCACTTGAATTTCACAAAGAGTGCTTAATAGAAGCGAATGATTTATCATTGTCTTATGGAGATAAAGAAGTATGCAGTAATCTTAATTTCAGAGTCAATATTGGTGATAGAGTTGCCATTATCGGAAAAAATGGGAGTGGTAAGTCTAGTATCCTAAAATTGATTAATGGAGATGATATTAAATTTACCGGAAATTTTATGCTAGCAAGTGGACTAAAAATTTCTTATATTTCGCAAGATACTTCATATTTAAAAGGTAATCTATCTGAATTTGCCTATAATAATAAGATCGATGAAACTCTATTTAAAACGATTCTTCGTAAACTGGATTTTAATAGAGAGCAGTTTGATAAGAACATGGTGGATTTTAGTGCTGGTCAGAAAAAGAAAGTACTAATTGCTAAAAGCCTTTGTGAAAGTGCACATTTGTATATATGGGATGAGCCATTGAACTATATTGATATTTTTTCACGTATCCAAATTGAAAAAATGATTTTGGAATATTGTCCTACACTATTGTTTGTGGAGCATGATGATGCTTTTTGCAATAACATTTGTACGAAAAATATTAATTTAGGTTTGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35918","NCBI_taxonomy_name":"Enterococcus faecalis","NCBI_taxonomy_id":"1351"}}}},"ARO_accession":"3003206","ARO_id":"39790","ARO_name":"lsaE","CARD_short_name":"lsaE","ARO_description":"lsaE is an ABC-F subfamily protein found in porcine MRSA isolates. It confers resistance to pleuromutilin, lincosamide, and streptogramin A.","ARO_category":{"41696":{"category_aro_accession":"3004472","category_aro_cvterm_id":"41696","category_aro_name":"lsa-type ABC-F protein","category_aro_description":"A subgroup of the ABC-F protein subfamily of ATP-binding cassette proteins. lsa-type ABC-F proteins confer resistance to streptogramin, lincosamide and pleuromutilin antibiotics through antibiotic target protection of the ribosome.","category_aro_class_name":"AMR Gene Family"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"37716":{"category_aro_accession":"3001317","category_aro_cvterm_id":"37716","category_aro_name":"pleuromutilin","category_aro_description":"Pleuromutilin is a natural product antibiotic produced by Clitopilus passeckerianus. Related antibiotics of clinical significance, such as tiamulin and retapamulin, are semi-synthetic derivatives of this compound.","category_aro_class_name":"Antibiotic"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"37014":{"category_aro_accession":"3000670","category_aro_cvterm_id":"37014","category_aro_name":"pleuromutilin antibiotic","category_aro_description":"Pleuromutilins are natural fungal products that target bacterial protein translation by binding the the 23S rRNA, blocking the ribosome P site at the 50S subunit. They are mostly used for agriculture and veterinary purposes.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"265":{"model_id":"265","model_name":"SHV-128","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"900":{"protein_sequence":{"accession":"ADE58494.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELRAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGASKRGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGTGAAPIEHWQR"},"dna_sequence":{"accession":"GU932590.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAGCTCCGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTAGCAAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGACTGGCGCGGCGCCGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3001175","ARO_id":"37555","ARO_name":"SHV-128","CARD_short_name":"SHV-128","ARO_description":"SHV-128 is an extended-spectrum beta-lactamase that has been found in clinical isolates.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"266":{"model_id":"266","model_name":"QnrB13","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"213":{"protein_sequence":{"accession":"ABX72042.1","sequence":"MTPLLYKKTGTNMALALVGEKIDRNRFTGEKIENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNASALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGAQVLGATFSGSDLSGGEFSTFDWRAANFTHCDLTNSELGDLDIRRVDLQGVKLDNYQASLLMERLGIAIIG"},"dna_sequence":{"accession":"EU273755.1","fmin":"0","fmax":"681","strand":"+","sequence":"ATGACGCCATTACTGTATAAAAAAACAGGTACAAATATGGCTCTGGCACTCGTTGGCGAAAAAATTGACAGAAACCGCTTCACCGGTGAGAAAATTGAAAATAGTACATTTTTTAACTGTGATTTTTCAGGTGCCGACCTGAGCGGCACTGAATTTATCGGCTGTCAGTTCTATGATCGTGAAAGCCAGAAAGGGTGCAATTTTAGTCGTGCGATGCTGAAAGATGCCATTTTTAAAAGCTGTGATTTATCCATGGCGGATTTTCGCAATGCCAGTGCGCTTGGCATTGAAATTCGCCACTGTCGTGCGCAAGGCGCAGATTTCCGCGGCGCAAGCTTTATGAATATGATCACTACTCGCACCTGGTTTTGCAGCGCATATATCACTAACACAAATCTAAGCTACGCCAATTTTTCGAAAGTCGTGTTGGAAAAATGTGAGCTGTGGGAAAACCGTTGGATGGGTGCCCAGGTACTGGGCGCGACGTTCAGTGGTTCAGATCTTTCCGGCGGCGAGTTTTCGACTTTCGACTGGCGAGCAGCAAACTTCACACATTGCGATCTGACCAATTCGGAGTTGGGTGACTTAGATATTCGGCGCGTTGATTTACAAGGCGTTAAGTTGGACAACTACCAGGCATCGTTGCTCATGGAACGTCTTGGCATCGCGATTATTGGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002727","ARO_id":"39161","ARO_name":"QnrB13","CARD_short_name":"QnrB13","ARO_description":"QnrB13 is a plasmid-mediated quinolone resistance protein found in Citrobacter freundii.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"267":{"model_id":"267","model_name":"OXA-43","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1303":{"protein_sequence":{"accession":"CAD32565.1","sequence":"MKFRHALSSAFVLLGCIAASAHAKTICTAIADAGTGKLLVQDGDCGRRASPASTFKIAISLMGYDAGFLRNEHDPVLPYRDSYIAWGGEAWKQPTDPTRWLKYPVVWYSQQVAHHLGAQRFAQYAKAFGYGNADVSGDPGQNNGLDRAWIGSSLQISPLEQLEFLGKMLNRKLPVSPTAVDMTERIVESTTLADGTVVHGKTGVSYPLLADGTRDWARGSGWFVGWIVRGKQTLVFARLTQDERKQPVSAGIRTREAFLRDLPRLLAAR"},"dna_sequence":{"accession":"AJ488303.1","fmin":"0","fmax":"810","strand":"+","sequence":"ATGAAATTCCGACACGCGCTGTCGAGCGCATTCGTTTTGCTGGGTTGCATCGCCGCGTCGGCGCATGCGAAGACGATCTGCACGGCGATCGCCGATGCGGGCACGGGCAAGCTGCTGGTGCAGGACGGCGATTGCGGCCGCCGCGCATCGCCCGCGTCGACGTTCAAGATCGCGATCAGCCTGATGGGCTACGACGCAGGCTTCCTGCGCAACGAGCATGACCCGGTGCTGCCGTATCGCGACAGTTACATCGCGTGGGGTGGCGAAGCATGGAAGCAGCCGACCGATCCGACGCGCTGGCTCAAGTATCCGGTCGTGTGGTATTCGCAGCAGGTGGCGCACCATCTCGGCGCGCAGCGCTTCGCGCAGTATGCGAAGGCGTTCGGCTACGGCAATGCGGACGTGTCCGGCGATCCCGGCCAGAACAACGGCCTCGATCGCGCGTGGATCGGCTCGTCGCTGCAGATCTCGCCGCTCGAACAATTGGAATTCCTCGGCAAGATGCTCAATCGCAAGCTGCCCGTGTCGCCCACAGCCGTCGACATGACGGAGCGGATCGTCGAATCGACGACGCTTGCCGACGGAACGGTGGTGCACGGCAAGACCGGCGTGTCCTATCCGCTGCTGGCCGACGGCACACGCGACTGGGCGCGTGGATCCGGCTGGTTTGTCGGCTGGATCGTGCGTGGCAAGCAGACGCTGGTGTTCGCGCGCCTCACGCAGGACGAGCGCAAGCAGCCCGTTTCAGCCGGCATACGGACGCGCGAGGCCTTCCTGCGCGACTTGCCCCGGCTTCTCGCCGCGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36923","NCBI_taxonomy_name":"Burkholderia pseudomallei","NCBI_taxonomy_id":"28450"}}}},"ARO_accession":"3001770","ARO_id":"38170","ARO_name":"OXA-43","CARD_short_name":"OXA-43","ARO_description":"OXA-43 is a beta-lactamase found in Burkholderia pseudomallei.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46507":{"category_aro_accession":"3007718","category_aro_cvterm_id":"46507","category_aro_name":"OXA-42-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-42.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"268":{"model_id":"268","model_name":"CfxA6","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"1744":{"protein_sequence":{"accession":"ACT97371.1","sequence":"MSNYSVAELRNMKKNRKKQIVVLCIALVCIFILVFSLSHKSATKGSANPPLTDVLTDSISQIVSACPGEIGVAVIINNTDTVSVNNKSIYPMMSVFKVHQALALCNDFDKKGLSLDTLVKINREKLDPKTWSPMMKDYSAPVISLTVRDLLRYTLSQSDNNASNIMFKNMLNTAQTDSFIAKLIPRSSFQIAYTEEEMSADHDKAYSNYTSPLGAAMLMNRLFTESLISNEKQDFIKNALKECKTGIDRIVAPLLDKEGVVIAHKTGSGNVNENGILAAQNDVAYICLPNKVCYTLAVFVKDFKGNESQASQFVAHISAVVYSLLINTALN"},"dna_sequence":{"accession":"GQ342996.1","fmin":"797","fmax":"1793","strand":"+","sequence":"ATGTCAAACTATAGTGTTGCGGAATTAAGAAACATGAAAAAAAACAGAAAAAAGCAAATCGTAGTTTTGTGTATAGCTTTAGTTTGCATCTTCATCTTGGTGTTCTCATTGTCCCATAAATCAGCTACAAAAGGTAGCGCGAATCCTCCATTAACAGATGTTTTGACTGATAGCATTTCTCAGATTGTCTCGGCTTGTCCTGGTGAAATTGGTGTGGCGGTTATTATTAATAACACAGATACGGTTAGTGTTAATAATAAAAGCATTTATCCTATGATGAGTGTATTTAAGGTTCATCAGGCATTAGCTCTTTGCAATGATTTTGACAAAAAAGGCCTTTCCCTTGATACCTTGGTAAAGATAAATAGGGAAAAACTTGATCCAAAGACATGGAGCCCTATGATGAAAGATTATTCAGCACCAGTTATATCGTTGACAGTAAGAGATCTGTTGCGCTATACTCTTTCCCAGAGCGACAATAATGCAAGCAATATCATGTTTAAGAATATGCTCAATACTGCACAAACAGACAGTTTTATAGCGAAACTCATACCACGTTCGAGTTTTCAGATAGCTTATACAGAAGAGGAAATGTCCGCTGACCATGACAAAGCTTACTCTAATTACACATCTCCTCTTGGTGCTGCAATGTTGATGAATCGTTTGTTTACAGAAAGTCTTATCAGTAATGAGAAACAAGATTTCATTAAGAATGCATTGAAAGAATGTAAAACAGGTATAGATAGGATAGTAGCTCCACTTCTTGATAAAGAAGGGGTTGTAATAGCACATAAGACAGGTTCTGGTAATGTCAATGAAAATGGTATTCTTGCAGCTCAGAATGATGTAGCCTATATATGTCTGCCTAATAAGGTCTGCTATACCTTAGCTGTATTTGTTAAGGATTTCAAGGGAAATGAATCACAAGCGTCACAATTTGTTGCGCATATATCAGCGGTAGTATATTCTTTATTAATCAATACTGCGTTAAATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39661","NCBI_taxonomy_name":"uncultured organism","NCBI_taxonomy_id":"155900"}}}},"ARO_accession":"3003097","ARO_id":"39650","ARO_name":"CfxA6","CARD_short_name":"CfxA6","ARO_description":"CfxA6 beta-lactamase is a class A beta-lactamase found in an uncultured bacterium.","ARO_category":{"39434":{"category_aro_accession":"3003000","category_aro_cvterm_id":"39434","category_aro_name":"CfxA beta-lactamase","category_aro_description":"CfxA beta-lactamases are class A beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"269":{"model_id":"269","model_name":"CMY-8","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"8198":{"protein_sequence":{"accession":"AAD50818.2","sequence":"MQQRQSILWGAVATLMWAGLAHAGEASPVDPLRPVVDASIQPLLKEHRIPGMAVAVLKDGKAHYFNYGVANRESGASVSEQTLFEIGSVSKTLTATLGAYAVVKGAMQLDDKASRHAPWLKGSVFDSITMGELATYSAGGLPLQFPEEVDSSEKMRAYYRQWAPVYSPGSHRQYSNPSIGLFGHLAASSLKQPFAQLMEQTLLPGLGMHHTYVNVPKQAMASYAYGYSKEDKPIRVNPGMLADEAYGIKTSSADLLAFVKANIGGVDDKALQQAISLTHKGHYSVGGMTQGLGWESYAYPVTEQTLLAGNSAKVILEANPTAAPRESGSQVLFNKTGSTNGFGAYVAFVPARGIGIVMLANRNYPIPARVKAAHAILAQLAG"},"dna_sequence":{"accession":"AF167990.3","fmin":"612","fmax":"1761","strand":"+","sequence":"ATGCAACAACGACAATCCATCCTGTGGGGGGCCGTGGCCACCCTGATGTGGGCCGGTCTGGCCCATGCAGGTGAGGCTTCACCGGTCGATCCCCTGCGCCCCGTGGTGGATGCCAGCATCCAGCCGCTGCTCAAGGAGCACAGGATCCCGGGCATGGCGGTGGCCGTGCTCAAGGATGGCAAGGCCCACTATTTCAATTACGGGGTGGCCAACCGGGAGAGCGGGGCCAGCGTCAGCGAGCAGACCCTGTTCGAGATAGGATCCGTGAGCAAGACCCTGACTGCGACCCTGGGGGCCTATGCGGTGGTCAAGGGAGCGATGCAGCTGGATGACAAGGCGAGCCGGCACGCGCCCTGGCTCAAGGGATCCGTCTTTGACAGCATCACCATGGGGGAGCTTGCCACCTACAGCGCCGGAGGCCTGCCACTGCAATTCCCCGAGGAGGTGGATTCATCCGAGAAGATGCGCGCCTACTACCGCCAGTGGGCCCCTGTCTATTCGCCGGGCTCCCATCGCCAGTACTCCAACCCCAGCATAGGGCTGTTCGGCCACCTGGCGGCGAGCAGCCTGAAGCAGCCATTTGCCCAGTTGATGGAGCAGACCCTGCTGCCCGGGCTCGGCATGCACCACACCTATGTCAATGTGCCGAAGCAGGCCATGGCGAGTTATGCCTATGGCTATTCGAAAGAGGACAAGCCCATCCGGGTCAACCCTGGCATGCTGGCGGACGAGGCCTACGGCATCAAGACCAGCTCGGCGGATCTGCTCGCCTTCGTGAAGGCCAACATCGGCGGGGTTGATGACAAGGCGTTGCAGCAGGCCATCTCCCTGACCCACAAAGGGCATTACTCGGTAGGCGGGATGACCCAGGGGCTGGGTTGGGAGAGTTACGCCTATCCCGTCACCGAGCAGACATTGCTGGCGGGCAATTCGGCCAAGGTGATCCTCGAAGCCAATCCGACGGCGGCTCCCCGGGAGTCGGGGAGCCAGGTGCTCTTCAACAAGACCGGCTCGACCAATGGCTTTGGCGCCTATGTGGCCTTCGTGCCGGCCAGGGGGATCGGCATCGTCATGCTGGCCAATCGCAACTATCCCATCCCGGCCAGGGTGAAGGCGGCCCACGCCATCCTGGCGCAGTTGGCCGGTTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002019","ARO_id":"38419","ARO_name":"CMY-8","CARD_short_name":"CMY-8","ARO_description":"CMY-8 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"270":{"model_id":"270","model_name":"LEN-20","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"8276":{"protein_sequence":{"accession":"CAP12348.2","sequence":"MRYVRLCVISLLATLPLAVDAGPQPLEQIKQSESQLSGRVGMVEMDLASGRTLAAWRADERFPMVSTFKVLLCGAVLARVDAGLEQLDRRIHYRQQDLVDYSPVSEKHLTDGMTVGELCAAAITLSDNSAGNLLLATVGGPAGLTAFLRQIGDNVTRLDRWETALNEALPGDARDTTTPASMAATLRKLLTAQHLSARSQQQLLQWMVDDRVAGPLIRAVLPPGWFIADKTGAGERGARGIVALLGPDGKPERIVVIYLRDTPVSMAERNQHIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AM850910.2","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGTGTTATCTCCCTGTTAGCCACCCTGCCACTGGCGGTAGACGCCGGTCCACAGCCGCTTGAGCAGATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTGGGGATGGTGGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCGATGAACGCTTTCCCATGGTGAGCACCTTTAAAGTGCTGCTGTGCGGCGCGGTGCTGGCGCGGGTGGATGCCGGGCTCGAACAACTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTACCGACGGGATGACGGTCGGCGAACTCTGCGCCGCCGCCATCACCCTGAGCGATAACAGCGCTGGCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCGGGATTAACTGCCTTTCTGCGCCAGATCGGTGACAACGTCACCCGTCTTGACCGCTGGGAAACGGCACTGAATGAGGCGCTTCCCGGCGACGCGCGCGACACCACCACCCCGGCCAGCATGGCCGCCACGCTGCGCAAACTACTGACCGCGCAGCATCTGAGCGCCCGTTCGCAACAGCAACTCCTGCAGTGGATGGTGGACGATCGGGTTGCCGGCCCGCTGATCCGCGCCGTGCTGCCGCCGGGCTGGTTTATCGCCGACAAAACCGGGGCTGGCGAACGGGGTGCGCGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAACCGGAGCGCATTGTGGTGATCTATCTGCGGGATACCCCGGTGAGTATGGCCGAGCGTAATCAACATATCGCCGGGATCGGCGCAGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002467","ARO_id":"38867","ARO_name":"LEN-20","CARD_short_name":"LEN-20","ARO_description":"LEN-20 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36236":{"category_aro_accession":"3000097","category_aro_cvterm_id":"36236","category_aro_name":"LEN beta-lactamase","category_aro_description":"LEN beta-lactamases are chromosomal class A beta-lactamases that confer resistance to ampicillin, amoxicillin, carbenicillin, and ticarcillin but not to extended-spectrum beta-lactams.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"271":{"model_id":"271","model_name":"CMY-4","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1179":{"protein_sequence":{"accession":"CAA75402.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYARGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"Y15130.1","fmin":"0","fmax":"1143","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCAGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTACAA","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3002015","ARO_id":"38415","ARO_name":"CMY-4","CARD_short_name":"CMY-4","ARO_description":"CMY-4 is a beta-lactamase found in Proteus mirabilis.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"272":{"model_id":"272","model_name":"QnrB36","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"591":{"protein_sequence":{"accession":"AEL00458.1","sequence":"MTLALVGEKIDRNRFTGEKVENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDTIFKSCDLSMADFRNVSALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGTQVLGATFSGSDLSGGEFSTFDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDNYQASLLMERLGIAVIG"},"dna_sequence":{"accession":"JN173058.1","fmin":"36","fmax":"681","strand":"+","sequence":"ATGACTCTGGCATTAGTTGGCGAAAAAATTGACAGAAATCGCTTCACCGGTGAGAAAGTTGAAAATAGTACATTTTTTAACTGCGATTTTTCAGGTGCCGACCTGAGCGGCACTGAATTTATCGGCTGCCAGTTCTATGATCGCGAAAGTCAGAAAGGATGCAATTTTAGTCGCGCAATGCTGAAAGATACCATTTTCAAAAGCTGTGATTTATCAATGGCAGATTTCCGCAACGTCAGCGCATTGGGCATTGAAATTCGCCACTGCCGCGCACAAGGCGCAGATTTCCGCGGTGCAAGCTTTATGAATATGATCACCACGCGCACCTGGTTTTGCAGCGCATATATCACTAATACCAATCTAAGCTACGCCAATTTTTCGAAAGTCGTGTTGGAAAAGTGTGAGCTATGGGAAAACCGCTGGATGGGGACTCAGGTACTGGGTGCGACGTTCAGTGGTTCAGATCTCTCCGGCGGCGAGTTTTCGACTTTCGACTGGCGAGCAGCAAACTTCACACATTGCGATCTGACCAATTCGGAGTTAGGTGACTTAGATATTCGGGGTGTTGATTTACAAGGCGTTAAGTTAGACAACTACCAGGCATCGTTGCTCATGGAGCGGCTTGGCATCGCTGTGATTGGTTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002751","ARO_id":"39185","ARO_name":"QnrB36","CARD_short_name":"QnrB36","ARO_description":"QnrB36 is a plasmid-mediated quinolone resistance protein found in Citrobacter freundii.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"273":{"model_id":"273","model_name":"VEB-7","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1728":{"protein_sequence":{"accession":"ACO56763.1","sequence":"MKIVKRILLVLLSLFFTVEYSNAQTDNLTLKIENVLKAKNARIGVAIFNSNEKDTLKINNDFHFPMQSVMKFPIALAVLSEIDKGNLSFEQKIEITPQDLLPKTWSPIKEEFPNGTTLTIEQILNYTVSESDNIGCDILLKLIGGTDSVQKFLNANHFTDISIKANEEQMHKDWNTQYQNWATPTAMNKLLIDTYNNKNQLLSKKSYDFIWKIMRETTTGSNRLKGQLPKNTIVAHKTGTSGINNGITAATNDVGVITLPNGQLIFISVFVAESKETSEINEKIISDIAKITWNYYLNK"},"dna_sequence":{"accession":"FJ825622.1","fmin":"0","fmax":"900","strand":"+","sequence":"ATGAAAATCGTAAAAAGGATATTATTAGTATTGTTAAGTTTATTTTTTACAGTTGAGTATTCAAATGCTCAAACTGACAACTTAACTTTGAAAATTGAGAATGTTTTAAAGGCAAAAAATGCCAGAATAGGAGTAGCAATATTCAACAGCAATGAGAAGGATACTTTGAAGATTAATAACGACTTCCATTTCCCGATGCAAAGCGTTATGAAATTTCCGATTGCTTTAGCCGTTTTGTCTGAGATAGATAAAGGGAATCTTTCTTTTGAACAAAAAATAGAGATTACCCCTCAAGACCTTTTGCCTAAAACGTGGAGTCCGATTAAAGAGGAATTCCCTAATGGAACAACTTTGACGATTGAACAAATACTAAATTATACAGTATCAGAGAGCGACAATATTGGTTGTGATATTTTGCTAAAATTAATCGGAGGAACTGATTCTGTTCAAAAATTCTTGAATGCTAATCATTTCACTGATATTTCAATCAAAGCAAACGAAGAACAAATGCACAAGGATTGGAATACCCAATATCAAAATTGGGCAACCCCAACAGCGATGAACAAACTGTTAATAGATACTTATAATAATAAGAACCAATTACTTTCTAAAAAAAGTTATGATTTTATTTGGAAAATTATGAGAGAAACAACAACAGGAAGTAACCGATTAAAAGGACAATTACCAAAGAATACAATTGTTGCTCATAAAACAGGGACTTCCGGAATAAATAATGGAATTACAGCAGCCACTAATGATGTTGGGGTAATTACTTTACCGAATGGACAATTAATTTTTATAAGCGTATTTGTTGCAGAGTCCAAAGAAACTTCGGAAATTAATGAAAAGATTATTTCAGACATTGCAAAAATAACGTGGAATTACTATTTGAATAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3002376","ARO_id":"38776","ARO_name":"VEB-7","CARD_short_name":"VEB-7","ARO_description":"VEB-7 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36182":{"category_aro_accession":"3000043","category_aro_cvterm_id":"36182","category_aro_name":"VEB beta-lactamase","category_aro_description":"VEB beta-lactamases or Vietnamese extended-spectrum beta-lactamases are class A beta-lactamases that confer high-level resistance to oxyimino cephalosporins and to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"274":{"model_id":"274","model_name":"OXA-174","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"2002":{"protein_sequence":{"accession":"ADI58618.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDVKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWVVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEKLGIL"},"dna_sequence":{"accession":"HM113560.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGTAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGGTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAACAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAAAAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001658","ARO_id":"38058","ARO_name":"OXA-174","CARD_short_name":"OXA-174","ARO_description":"OXA-174 is a beta-lactamase found in A. baumannii.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"275":{"model_id":"275","model_name":"OKP-B-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"1366":{"protein_sequence":{"accession":"CAJ19610.1","sequence":"MRYVRLCLISLIAALPLAVFASPQPLEQIKISEGQLAGRVGYVEMDLASGRTLAAWRASERFPLMSTFKVLLCGAVLARVDAGDEQLDRRIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAGNLLLKSVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDVRDTTTPASMATTLRKLLTTPSLSARSQQQLLQWMVDDRVAGPLIRAVLPAGWFIADKTGAGERGSRGIVALLGPDGKAERIVVIYLRDTAATMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AM051151.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGCCTTATCTCCCTGATTGCCGCCCTGCCACTGGCGGTATTCGCCAGCCCTCAGCCGCTTGAGCAGATTAAAATCAGCGAAGGTCAGCTGGCGGGCCGGGTGGGCTATGTTGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCAGTGAGCGCTTTCCGCTGATGAGCACCTTTAAAGTGCTGCTCTGCGGCGCGGTGCTGGCCCGGGTGGATGCCGGCGACGAACAGCTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGCCGACGGGATGACCGTTGGCGAACTCTGCGCCGCCGCCATCACCATGAGCGACAACAGCGCCGGCAATCTGCTGTTGAAGAGCGTCGGCGGCCCCGCGGGATTGACCGCTTTTCTGCGCCAGATCGGTGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTCAATGAGGCGCTTCCCGGCGACGTGCGCGACACCACCACCCCGGCCAGCATGGCCACCACCCTGCGCAAGTTGCTAACCACCCCCTCTCTGAGCGCCCGTTCGCAGCAGCAGCTGCTGCAGTGGATGGTGGACGACCGGGTGGCCGGCCCGTTGATCCGCGCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAAACCGGGGCCGGTGAGCGGGGCTCACGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAAGCGGAGCGTATCGTGGTGATCTATCTGCGGGATACCGCAGCGACCATGGCCGAACGTAACCAGCAGATCGCCGGGATAGGCGCGGCGCTGATCGAGCACTGGCAGCGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002435","ARO_id":"38835","ARO_name":"OKP-B-2","CARD_short_name":"OKP-B-2","ARO_description":"OKP-B-2 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"38817":{"category_aro_accession":"3002417","category_aro_cvterm_id":"38817","category_aro_name":"OKP beta-lactamase","category_aro_description":"OKP beta-lactamases are chromosomal class A beta-lactamase that confer resistance to penicillins and early cephalosporins in Klebsiella pneumoniae. OKP beta-lactamases can be subdivided into two groups: OKP-A and OKP-B which diverge by about 4.2%.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"277":{"model_id":"277","model_name":"TEM-91","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1888":{"protein_sequence":{"accession":"BAB16308.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDCWEPELNEAIPNDERDTTTPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGKRGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AB049569.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATTGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGACGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTAAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000958","ARO_id":"37338","ARO_name":"TEM-91","CARD_short_name":"TEM-91","ARO_description":"TEM-91 is an extended-spectrum beta-lactamase found in E. coli.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"278":{"model_id":"278","model_name":"imiS","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"1892":{"protein_sequence":{"accession":"CAA71441.1","sequence":"MMKGWIKCGLAGAVVLMASFWGGSVRAAGMSLTQQVSGPVYVVEDNYYVQENSMVYFGAKGVTVVGATWTPDTARELHKLIKRVSRKPVLEVINTNYHTDRAGGNAYWKSIGAKVISTRQTRDLMKSDWAEIVAFTRKGLPEYPDLPLVLPNVVHEGDFTLQEGKLRAFYLGPAHSPDGIFVYFPDQQVLYGNCILKEKLGNLSFADVKAYPQTLERLKAMKLPIKTVVGGHDSPLHGPELIDHYEALIKAASQS"},"dna_sequence":{"accession":"Y10415.1","fmin":"125","fmax":"893","strand":"+","sequence":"ATGATGAAGGGTTGGATAAAGTGCGGGCTGGCCGGGGCCGTGGTGCTGATGGCGAGTTTTTGGGGGGGCAGCGTGCGGGCGGCGGGGATGTCGCTGACGCAGCAGGTGAGCGGCCCTGTTTACGTCGTAGAGGACAACTACTACGTGCAGGAAAATTCCATGGTCTATTTCGGGGCCAAGGGAGTGACTGTGGTGGGGGCGACCTGGACGCCGGATACCGCCCGCGAGCTGCACAAGCTGATCAAACGGGTCAGCCGCAAGCCGGTGCTGGAGGTGATCAACACCAACTACCACACCGACCGGGCAGGCGGTAACGCCTACTGGAAGTCCATCGGTGCCAAGGTGATATCGACCCGCCAGACCCGGGATCTGATGAAGAGCGACTGGGCCGAGATTGTCGCCTTTACCCGCAAGGGGCTGCCGGAGTACCCGGACTTGCCGCTGGTGCTGCCCAACGTGGTGCACGAAGGCGACTTCACGCTGCAAGAAGGCAAGCTGCGCGCCTTCTACCTGGGCCCGGCTCACAGCCCGGACGGCATCTTTGTTTACTTCCCCGACCAGCAGGTGCTTTATGGCAACTGCATCCTCAAGGAGAAGCTGGGCAACCTGAGCTTTGCCGATGTGAAGGCTTATCCGCAGACACTTGAGCGGCTGAAAGCGATGAAGCTGCCGATCAAGACGGTGGTGGGCGGTCACGACTCACCGCTGCACGGCCCGGAGCTTATCGATCACTACGAAGCGCTGATCAAGGCGGCTTCACAATCATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39677","NCBI_taxonomy_name":"Aeromonas veronii","NCBI_taxonomy_id":"654"}}}},"ARO_accession":"3003095","ARO_id":"39648","ARO_name":"imiS","CARD_short_name":"imiS","ARO_description":"imiS is an Ambler Class B MBL; subclass B2 originally isolated from Aeromonas veronii. This enzyme has specific activity against carbapenems.","ARO_category":{"36720":{"category_aro_accession":"3000581","category_aro_cvterm_id":"36720","category_aro_name":"CphA beta-lactamase","category_aro_description":"CphA is an Ambler Class B MBL; subclass B2 originally isolated from Aeromonas hydrophilia.  This enzyme has specific activity against carbapenems and is active as a mono-zinc protein.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"279":{"model_id":"279","model_name":"CTX-M-107","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8431":{"protein_sequence":{"accession":"AEM44650.1","sequence":"VKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDRTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVT"},"dna_sequence":{"accession":"JF274244.1","fmin":"2","fmax":"863","strand":"-","sequence":"GTTAAAAAATCACTGCGTCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAGAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACC","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39656","NCBI_taxonomy_name":"Shigella sp. SH219","NCBI_taxonomy_id":"1074433"}}}},"ARO_accession":"3001967","ARO_id":"38367","ARO_name":"CTX-M-107","CARD_short_name":"CTX-M-107","ARO_description":"CTX-M-107 is a beta-lactamase found in Shigella spp.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"280":{"model_id":"280","model_name":"CTX-M-11","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1588":{"protein_sequence":{"accession":"AAF93177.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAGLERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSPAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGDYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRHVLAS"},"dna_sequence":{"accession":"AY005110.1","fmin":"0","fmax":"846","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGGATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACCGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCCGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGACTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCCATGTATTAGCGTCG","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001874","ARO_id":"38274","ARO_name":"CTX-M-11","CARD_short_name":"CTX-M-11","ARO_description":"CTX-M-11 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"281":{"model_id":"281","model_name":"CMY-110","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"5299":{"protein_sequence":{"accession":"BAO05497.1","sequence":"MMKKSICCALLLTASFSKFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAIIYEGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWRGISLLHLATYTAGGLPLQIPDDVTDKAALLRFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQSEQKNYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIELAQSRYWGIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPARVEAAWRILEKLQ"},"dna_sequence":{"accession":"AB872957.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGATATGCTGCGCGCTGCTGCTGACAGCCTCTTTCTCCAAGTTTGCTGCCGCAAAAACAGAACAACAAATTGCCGATATCGTTAACCGCACCATCACACCACTGATGCAGGAGCAGGCTATTCCGGGCATGGCCGTGGCAATTATCTACGAGGGGAAACCTTATTACTTTACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAATTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGACGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCGGGGTATCAGCCTGCTGCACTTAGCCACCTATACAGCGGGTGGCCTGCCGCTGCAGATCCCCGATGACGTTACGGATAAAGCCGCATTACTGCGCTTTTATCAAAACTGGCAACCACAATGGACTCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGTGCGCTGGCGGTGAAACCTTCAGGTATGAGCTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAAAGCGAACAAAAAAATTATGCCTGGGGCTATCGCGAAGGGAAGCCTGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATCGATATGGCCCGCTGGGTTCAGGCCAACATGGACGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGAGCTTGCGCAGTCTCGTTACTGGGGTATTGGTGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCAGCACCTGCCGTGAAAGCCTCATGGGTGCATAAAACGGGATCCACAGGTGGATTTGGCAGCTACGTTGCCTTCGTTCCAGAAAAAAACCTTGGCATAGTGATGCTGGCAAACAAAAGCTATCCTAACCCGGCTCGCGTAGAGGCGGCCTGGCGCATTCTTGAAAAACTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002071","ARO_id":"38471","ARO_name":"CMY-110","CARD_short_name":"CMY-110","ARO_description":"CMY-110 is a beta-lactamase found in Escherichia coli.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"282":{"model_id":"282","model_name":"CTX-M-125","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1410":{"protein_sequence":{"accession":"AFO69261.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAEHRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"JQ724542.1","fmin":"174","fmax":"1050","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGACTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGCACCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3001984","ARO_id":"38384","ARO_name":"CTX-M-125","CARD_short_name":"CTX-M-125","ARO_description":"CTX-M-125 is a beta-lactamase found in Escherichia coli.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"283":{"model_id":"283","model_name":"CMY-85","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1117":{"protein_sequence":{"accession":"AHL39322.1","sequence":"MMKKSICCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAIIYEGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWRGISLLHLATYTAGGLPLQIPDDVTDKAALLRFYQNWQPQWTPGAKRLYANSSIGLFGALAVKSSGMSYEEAMTRRVLQPLKLAHTWITVPQSEQKNYAWGYLEGKPLHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQLGIELAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"KJ207202.1","fmin":"548","fmax":"1694","strand":"+","sequence":"ATGATGAAAAAATCGATATGCTGCGCGCTGCTGCTGACAGCCTCTTTCTCCACGTTTGCTGCCGCAAAAACAGAACAACAAATTGCCGATATCGTTAACCGCACCATCACACCACTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTGGCGATTATCTACGAGGGGAAACCTTATTACTTTACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGACGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCGGGGTATCAGCCTGCTGCACTTAGCCACCTATACAGCGGGTGGCCTGCCGCTGCAGATCCCCGATGACGTTACGGATAAAGCCGCATTACTGCGCTTTTATCAAAACTGGCAACCACAATGGACTCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGTGCGCTGGCGGTGAAATCTTCAGGTATGAGCTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAAAGCGAACAAAAAAACTATGCCTGGGGCTATCTCGAAGGGAAGCCTTTGCACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATCGATATGGCCCGCTGGGTTCAGGCCAACATGGACGCCAGCCACGTTCAGGAGAAAACGCTCCAGCTGGGCATTGAGCTTGCGCAGTCTCGCTACTGGCGTATTGGTGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCAGCACCTGCCGTGAAAGCCTCATGGGTGCATAAAACGGGATCCACAGGTGGATTTGGCAGCTACGTTGCCTTCGTTCCAGAAAAAAACCTTGGCATAGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGCGTCGAGGCGGCCTGGCGCATTCTTGAAAAACTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002098","ARO_id":"38498","ARO_name":"CMY-85","CARD_short_name":"CMY-85","ARO_description":"CMY-85 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"284":{"model_id":"284","model_name":"smeD","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"570":{"protein_sequence":{"accession":"CAC14594.1","sequence":"MLLSRIRPFALSLAIAATVAACGGQPQAPEQGPGDVTVVTLKSETVGLTRELPGRTNAFLVAEVRPQVNGIVAKRLFTEGGMVKAGEPLYQLDDASYRAQANNARAQLARAEATANAARLSAKRITELAKVDAVSQQDLENAVAAQKQAEADVGAAKASLDAANVTLGYARITAPISGRIGKSSVTQGALVSAGQANALATVQQLDPIYVDLTQSSAELLQLRRELAAGRLQDNQTLPVSILMEDGSTFEHKGTLEFSEVSVDPTTGSFGLRVKVDNPDGLLMPGMYVRAVIGGGVRSDAVLVPMQGIARDPKGDTTAMVVGKDNKVEVRPVKVSRTVGDKWLVEDGLKAGDKVIVEGLQKIGPGMPVKATEKGDAPAKPAAAAQPAAPAGDAK"},"dna_sequence":{"accession":"AJ252200.1","fmin":"81","fmax":"1266","strand":"+","sequence":"ATGTTGCTGAGCCGAATCCGACCCTTTGCACTGTCGCTGGCAATCGCCGCGACCGTGGCTGCCTGCGGCGGCCAACCCCAGGCCCCCGAGCAGGGCCCGGGTGACGTCACCGTGGTCACGCTGAAGTCCGAGACCGTGGGCCTGACCCGCGAACTGCCGGGCCGTACCAATGCCTTCCTGGTCGCCGAAGTGCGCCCGCAGGTCAATGGCATCGTGGCCAAGCGCCTGTTTACCGAGGGCGGCATGGTCAAGGCCGGCGAGCCGCTGTACCAGCTCGACGATGCCAGCTACCGGGCCCAGGCCAACAACGCCCGCGCCCAGCTGGCCCGCGCCGAAGCCACCGCCAATGCCGCGCGCCTGAGTGCCAAGCGCATCACCGAGCTGGCCAAGGTCGATGCGGTCAGCCAGCAGGACCTGGAGAACGCCGTCGCCGCGCAGAAGCAGGCCGAGGCCGACGTCGGTGCCGCCAAGGCCTCGCTGGATGCGGCCAACGTCACCCTGGGCTACGCCCGCATCACCGCGCCGATCAGCGGCCGCATCGGCAAGTCCAGCGTCACCCAGGGTGCGCTGGTCAGCGCCGGCCAGGCCAACGCACTGGCCACCGTGCAGCAGCTGGACCCGATCTATGTCGACCTGACCCAGTCCTCGGCCGAGCTGCTGCAGCTGCGCCGCGAACTGGCCGCCGGCCGCCTGCAGGACAACCAGACCCTGCCGGTCAGCATCCTGATGGAAGACGGCAGCACCTTCGAGCACAAGGGCACTCTGGAGTTCTCCGAAGTCAGCGTTGATCCGACCACCGGCAGCTTCGGCCTGCGCGTGAAGGTGGACAACCCGGACGGCCTGCTGATGCCGGGCATGTACGTGCGTGCGGTGATCGGCGGCGGCGTGCGCAGCGACGCGGTGCTGGTGCCGATGCAGGGCATCGCGCGCGATCCGAAGGGCGACACCACCGCGATGGTGGTCGGCAAGGACAACAAGGTCGAAGTGCGCCCGGTCAAGGTCAGCCGCACGGTCGGCGACAAGTGGCTGGTCGAGGACGGCCTGAAGGCCGGTGACAAGGTCATCGTCGAAGGCCTGCAGAAGATCGGCCCCGGCATGCCGGTCAAGGCCACCGAGAAGGGCGACGCACCGGCCAAGCCGGCGGCAGCCGCCCAGCCTGCCGCCCCGGCCGGCGACGCGAAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37076","NCBI_taxonomy_name":"Stenotrophomonas maltophilia","NCBI_taxonomy_id":"40324"}}}},"ARO_accession":"3003055","ARO_id":"39489","ARO_name":"smeD","CARD_short_name":"smeD","ARO_description":"smeD is the membrane fusion protein of the smeDEF multidrug efflux complex in Stenotrophomonas maltophilia.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"285":{"model_id":"285","model_name":"TEM-11","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1488":{"protein_sequence":{"accession":"AAW66604.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDKLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDHWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AY874537.1","fmin":"177","fmax":"1038","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATAAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATCATTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3000883","ARO_id":"37263","ARO_name":"TEM-11","CARD_short_name":"TEM-11","ARO_description":"TEM-11 is an extended-spectrum beta-lactamase found in Proteus mirabilis.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"286":{"model_id":"286","model_name":"SHV-162","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"830":{"protein_sequence":{"accession":"AFQ23968.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGSVGMVEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGASERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"JX121129.1","fmin":"0","fmax":"858","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCAGCGTAGGCATGGTAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCAGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTAGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGGATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGC","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001201","ARO_id":"37581","ARO_name":"SHV-162","CARD_short_name":"SHV-162","ARO_description":"SHV-162 is a beta-lactamase.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"287":{"model_id":"287","model_name":"TEM-67","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8159":{"protein_sequence":{"accession":"AAD33116.2","sequence":"MSIQHFRVALIPFFAAFCIPVFAHPETLVKVKDAEDKLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSCGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AF091113.2","fmin":"450","fmax":"1311","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCATTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATAAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGATCTTGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3000934","ARO_id":"37314","ARO_name":"TEM-67","CARD_short_name":"TEM-67","ARO_description":"TEM-67 is an inhibitor-resistant beta-lactamase found in Proteus mirabilis.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"288":{"model_id":"288","model_name":"CMY-60","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1625":{"protein_sequence":{"accession":"AEM97672.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFIGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"JF460794.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTATCGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002073","ARO_id":"38473","ARO_name":"CMY-60","CARD_short_name":"CMY-60","ARO_description":"CMY-60 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"289":{"model_id":"289","model_name":"OXA-85","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"814":{"protein_sequence":{"accession":"AAP69916.1","sequence":"MLLFMFSIISFGNENQFMKEIFERKGLNGTFVVYDLKNDKIDYYNLDRANERFYPASSFKIFNTLIGLENGIVKNVDEMFYYYDGSKVFLDSWAKDSNLRYAIKVSQVPAYKKLARELGKERMQEGLNKLNYGNKEIGSEIDKFWLEGPLKISAMEQVKLLNLLSQSKLPFKLENQEQVKDITILEKKDDFILHGKTGWATDNIVVPIGWFVGWIETSDNIYSFAINLDISDSKFLPKREEIVREYFKNINVIK"},"dna_sequence":{"accession":"AY227054.1","fmin":"0","fmax":"765","strand":"+","sequence":"ATGTTATTATTTATGTTCTCGATTATTTCTTTTGGTAATGAAAATCAATTTATGAAAGAGATTTTTGAAAGAAAAGGTTTAAACGGAACTTTTGTTGTTTATGATTTAAAAAATGATAAAATTGATTATTATAATTTGGATAGAGCTAATGAGAGATTTTATCCTGCTTCATCATTTAAAATTTTTAATACTTTGATAGGATTAGAAAATGGGATAGTAAAAAATGTTGATGAAATGTTTTATTATTATGATGGTTCTAAAGTTTTTCTTGATTCATGGGCAAAAGATTCGAATTTAAGATATGCAATAAAGGTATCTCAAGTTCCAGCTTATAAAAAGCTTGCAAGAGAATTGGGAAAAGAAAGAATGCAAGAAGGATTAAATAAATTAAATTATGGAAATAAGGAAATAGGTAGTGAGATTGATAAGTTTTGGTTAGAAGGTCCATTAAAAATAAGTGCAATGGAACAAGTTAAATTATTAAATCTATTATCACAATCAAAACTTCCTTTTAAATTAGAAAATCAAGAACAAGTAAAAGATATTACGATTTTAGAGAAAAAAGATGATTTTATTTTACATGGAAAAACTGGGTGGGCTACTGATAATATAGTTGTTCCTATTGGTTGGTTTGTAGGTTGGATAGAAACTTCTGATAATATATATTCATTTGCTATTAATTTAGATATTTCTGATAGTAAATTTTTACCTAAACGTGAAGAAATTGTAAGAGAATATTTCAAAAATATAAATGTTATAAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36931","NCBI_taxonomy_name":"Fusobacterium nucleatum","NCBI_taxonomy_id":"851"}}}},"ARO_accession":"3001780","ARO_id":"38180","ARO_name":"OXA-85","CARD_short_name":"OXA-85","ARO_description":"OXA-85 is a beta-lactamase found in Fusobacterium nucleatum.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"290":{"model_id":"290","model_name":"vatD","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"462":{"protein_sequence":{"accession":"AAK84316.1","sequence":"MKMYPIEGNKSVQFIKPILEKLENVEVGEYSYYDSKNGETFDKQILYHYPILNDKLKIGKFCSIGPGVTIIMNGANHRMDGSTYPFNLFGNGWEKHMPKLDQLPIKGDTIIGNDVWIGKDVVIMPGVKIGDGAIVAANSVVVKDIAPYMLAGGNPANEIKQRFDQDTINQLLDIKWWNWPIDIINENIDKILDNSIIREVIWKK"},"dna_sequence":{"accession":"AF368302.1","fmin":"2716","fmax":"3331","strand":"+","sequence":"ATGAAAATGTATCCTATAGAAGGAAACAAATCAGTACAATTTATCAAACCTATTTTAGAAAAATTAGAAAATGTTGAGGTTGGAGAATACTCATATTATGATTCTAAGAATGGAGAAACTTTTGATAAGCAAATTTTATATCATTATCCAATCTTAAACGATAAGTTAAAAATAGGTAAATTTTGCTCAATAGGACCAGGTGTAACTATTATTATGAATGGAGCAAATCATAGAATGGATGGCTCAACATATCCATTTAATTTATTTGGTAATGGATGGGAGAAACATATGCCAAAATTAGATCAACTACCTATTAAGGGGGATACAATAATAGGTAATGATGTATGGATAGGAAAAGATGTTGTAATTATGCCAGGAGTAAAAATCGGGGATGGTGCAATAGTAGCTGCTAATTCTGTTGTTGTAAAAGATATAGCGCCATACATGTTAGCTGGAGGAAATCCTGCTAACGAAATAAAACAAAGATTTGATCAAGATACAATAAATCAGCTGCTTGATATAAAATGGTGGAATTGGCCAATAGACATTATTAATGAGAATATAGATAAAATTCTTGATAATAGCATCATTAGAGAAGTCATATGGAAAAAATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36779","NCBI_taxonomy_name":"Enterococcus faecium","NCBI_taxonomy_id":"1352"}}}},"ARO_accession":"3002843","ARO_id":"39277","ARO_name":"vatD","CARD_short_name":"vatD","ARO_description":"vatD is a transposon-mediated acetyltransferase found in Enterococcus faecium.","ARO_category":{"36592":{"category_aro_accession":"3000453","category_aro_cvterm_id":"36592","category_aro_name":"streptogramin vat acetyltransferase","category_aro_description":"vat (Virginiamycin acetyltransferases) enzymes catalyze the transfer of an acetyl group from acetyl-CoA to the secondary alcohol of streptogramin A compounds, thus inactivating virginiamycin-like antibiotics and conferring resistance to these compounds.","category_aro_class_name":"AMR Gene Family"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"virginiamycin M1","category_aro_description":"Virginiamycin M1 is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37016":{"category_aro_accession":"3000672","category_aro_cvterm_id":"37016","category_aro_name":"madumycin II","category_aro_description":"Madumycin II is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37017":{"category_aro_accession":"3000673","category_aro_cvterm_id":"37017","category_aro_name":"griseoviridin","category_aro_description":"Griseoviridin is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35952":{"category_aro_accession":"0000034","category_aro_cvterm_id":"35952","category_aro_name":"streptogramin A antibiotic","category_aro_description":"Streptogramin A antibiotics are cyclic polyketide peptide hybrids that bind to the ribosomal peptidyl transfer centre. Structural variation arises from substituting a proline for its desaturated derivative and by its substitution for Ala or Cys. Used alone, streptogramin A antibiotics are bacteriostatic, but is bactericidal when used with streptogramin B antibiotics.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"291":{"model_id":"291","model_name":"APH(3')-Ia","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4475":{"protein_sequence":{"accession":"CAE51638.1","sequence":"MSHIQRETSCSRPRLNSNLDADLYGYRWARDNVGQSGATIYRLYGKPNAPELFLKHGKGSVANDVTDEMVRLNWLTAFMPLPTIKHFIRTPDDAWLLTTAIPGKTAFQVLEEYPDSGENIVDALAVFLRRLHSIPVCNCPFNSDRVFRLAQAQSRMNNGLVDASDFDDERNGWPVEQVWKEMHKLLPFSPDSVVTHGDFSLDNLIFDEGKLIGCIDVGRVGIADRYQDLAILWNCLGEFSPSLQKRLFQKYGIDNPDMNKLQFHLMLDEFF"},"dna_sequence":{"accession":"BX664015.1","fmin":"103017","fmax":"103833","strand":"-","sequence":"ATGAGCCATATTCAACGGGAAACGTCTTGCTCGAGGCCGCGATTAAATTCCAACCTGGATGCTGATTTATATGGGTATAGATGGGCTCGCGATAATGTCGGGCAATCAGGTGCGACAATCTATCGATTGTATGGGAAGCCCAATGCGCCAGAGTTGTTTCTGAAACATGGCAAAGGTAGCGTTGCCAATGATGTTACAGATGAGATGGTCAGACTAAACTGGCTGACGGCATTTATGCCTCTTCCGACCATCAAGCATTTTATCCGTACTCCTGATGATGCATGGTTACTCACCACTGCGATCCCCGGGAAAACAGCATTCCAGGTATTAGAAGAATATCCTGATTCAGGTGAAAATATTGTTGATGCGCTGGCAGTGTTCCTGCGCCGGTTGCATTCGATTCCTGTTTGTAATTGTCCTTTTAACAGCGATCGCGTATTTCGTCTCGCTCAGGCGCAATCACGAATGAATAACGGTTTGGTTGATGCTAGTGATTTTGATGACGAGCGTAATGGCTGGCCTGTTGAACAAGTCTGGAAAGAAATGCATAAGCTTTTGCCATTCTCACCGGATTCAGTCGTCACTCATGGTGATTTCTCACTTGATAACCTTATTTTTGACGAGGGGAAATTAATAGGTTGTATTGATGTTGGACGAGTCGGAATCGCAGACCGATACCAGGATCTTGCCATCCTATGGAACTGCCTCGGTGAGTTTTCTCCTTCATTACAGAAACGGCTTTTTCAAAAATATGGTATTGATAATCCTGATATGAATAAATTGCAGTTTCATTTGATGCTCGATGAGTTTTTCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36783","NCBI_taxonomy_name":"Serratia marcescens","NCBI_taxonomy_id":"615"}}}},"ARO_accession":"3002641","ARO_id":"39041","ARO_name":"APH(3')-Ia","CARD_short_name":"APH(3')-Ia","ARO_description":"APH(3')-Ia is a transposon-encoded aminoglycoside phosphotransferase in E. coli and S. enterica. It is identical at the protein sequence to APH(3')-Ic, an aminoglycoside phosphotransferase encoded by plasmids, transposons and genomic islands in K. pneumoniae, A. baumannii, S. marcescens, Corynebacterium spp., Photobacterium spp. and Citrobacter spp.","ARO_category":{"36265":{"category_aro_accession":"3000126","category_aro_cvterm_id":"36265","category_aro_name":"APH(3')","category_aro_description":"A category of aminoglycoside O-phosphotransferase enzymes with modification regiospecificity based at the 3'-hydroxyl group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics, specifically kanamycin and neomycin, by the ATP-dependent phosphorylation of the 3'-hydroxyl group of the compound.","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35940":{"category_aro_accession":"0000021","category_aro_cvterm_id":"35940","category_aro_name":"ribostamycin","category_aro_description":"Ribostamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Ribostamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"37001":{"category_aro_accession":"3000657","category_aro_cvterm_id":"37001","category_aro_name":"paromomycin","category_aro_description":"An aminoglycoside antibiotic used for the treatment of parasitic infections. It is similar to neomycin sharing a similar spectrum of activity, but its hydroxyl group at the 6'-position instead of an amino group makes it resistant to AAC(6') modifying enzymes.","category_aro_class_name":"Antibiotic"},"37002":{"category_aro_accession":"3000658","category_aro_cvterm_id":"37002","category_aro_name":"lividomycin","category_aro_description":"Lividomycins are aminoglycosidic antibiotics produced by Streptomyces lividus. They contain 2-amino-2,3-dideoxy-D-glucose.","category_aro_class_name":"Antibiotic"},"46133":{"category_aro_accession":"3007382","category_aro_cvterm_id":"46133","category_aro_name":"gentamicin","category_aro_description":"Gentamicin is a commonly used aminoglycoside antibiotic derived from members of the Micromonospora genus of bacteria. It acts by binding the 30S ribosomal subunit, thus inhibiting protein synthesis. Gentamicin is typically used to treat Gram-negative infections of the repiratory and urinary tract, as well as infections of the bone and soft tissue. It also exhibits considerable nephrotoxicity and ototoxicity. Gentamicin is administered as a mixture of gentamicin type C (which makes about around 80% of the complex) and types A, B, and X (distributed in the remaining 20% of the complex).","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"292":{"model_id":"292","model_name":"TEM-17","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8244":{"protein_sequence":{"accession":"CAA74912.2","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVKYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"Y14574.2","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTGTTGACGCCGGGCAAGAACAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTAAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTTTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATTTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36958","NCBI_taxonomy_name":"Capnocytophaga ochracea","NCBI_taxonomy_id":"1018"}}}},"ARO_accession":"3000888","ARO_id":"37268","ARO_name":"TEM-17","CARD_short_name":"TEM-17","ARO_description":"TEM-17 is an extended-spectrum beta-lactamase found in Capnocytophaga ochracea.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"293":{"model_id":"293","model_name":"SHV-180","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"3768":{"protein_sequence":{"accession":"AJO16040.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGHVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMTATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"KP050487.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCACGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGACCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGCATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001350","ARO_id":"37750","ARO_name":"SHV-180","CARD_short_name":"SHV-180","ARO_description":"SHV-180 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"294":{"model_id":"294","model_name":"CfxA4","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"1592":{"protein_sequence":{"accession":"AAV37205.1","sequence":"MEKNRKKQIVVLSIALVCIFILVFSLFHKSATKDSANPPLTNVLTDSISQIVSACPGEIGVAVIVNNRDTVKVNNKSVYPMMSVFKVHQALALCNDFDNKGISLDTLVNINRDKLDPKTWSPMLKDYSGPVISLTVRDLLRYTLTQSDNNASNLMFKDMVNVAQTDSFIATLIPRSSFQIAYTEEEMSADHNKAYSNYTSPLGAAMLMNRLFTEGLIDDEKQSFIKNTLKECKTGVDRIAAPLLDKEGVVIAHKTGSGNVNENGVLAAHNDVAYICLPNNISYTLAVFVKDFKGNESQASQYVAHISAVVYSLLMQTSVKS"},"dna_sequence":{"accession":"AY769933.1","fmin":"0","fmax":"966","strand":"+","sequence":"ATGGAAAAAAACAGAAAAAAACAAATCGTAGTTTTGAGTATAGCTTTAGTTTGCATTTTCATCTTGGTATTTTCATTGTTCCATAAATCAGCGACAAAAGATAGCGCAAATCCTCCTTTAACAAATGTTTTGACTGATAGCATTTCTCAAATTGTCTCAGCTTGTCCTGGCGAAATTGGTGTGGCGGTTATTGTTAATAACAGAGATACGGTTAAGGTCAATAATAAGAGTGTTTATCCTATGATGAGTGTGTTTAAGGTTCATCAGGCATTAGCTCTTTGTAATGACTTTGACAATAAAGGAATTTCACTTGATACCTTAGTAAATATAAATAGGGATAAACTTGACCCAAAGACTTGGAGTCCTATGCTGAAAGATTATTCAGGGCCAGTCATATCATTGACAGTGAGAGATTTGCTGCGTTATACTCTTACTCAGAGTGACAACAATGCAAGCAACCTTATGTTTAAGGATATGGTTAATGTCGCTCAAACAGATAGTTTTATAGCCACACTCATTCCTCGTTCAAGTTTTCAGATAGCTTATACGGAAGAGGAAATGTCGGCTGACCATAACAAGGCTTACTCTAACTATACATCTCCTCTTGGTGCTGCAATGTTGATGAATCGTTTGTTTACTGAAGGTCTTATCGATGATGAGAAACAAAGTTTCATTAAGAATACGTTAAAAGAATGCAAAACAGGTGTAGATAGGATAGCAGCTCCACTTCTTGATAAAGAAGGGGTTGTTATAGCGCATAAGACAGGTTCAGGTAATGTTAATGAAAATGGTGTTCTTGCAGCTCACAATGATGTTGCCTATATATGTCTGCCTAATAATATCAGTTATACCTTAGCGGTATTTGTTAAGGATTTCAAGGGAAATGAATCACAAGCGTCACAATATGTTGCGCATATATCAGCTGTAGTATATTCTTTATTAATGCAAACTTCAGTAAAATCTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35916","NCBI_taxonomy_name":"Bacteroides fragilis","NCBI_taxonomy_id":"817"}}}},"ARO_accession":"3003005","ARO_id":"39439","ARO_name":"CfxA4","CARD_short_name":"CfxA4","ARO_description":"cfxA4 beta-lactamase is a class A beta-lactamase found in Bacteroides fragilis.","ARO_category":{"39434":{"category_aro_accession":"3003000","category_aro_cvterm_id":"39434","category_aro_name":"CfxA beta-lactamase","category_aro_description":"CfxA beta-lactamases are class A beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"295":{"model_id":"295","model_name":"OXA-145","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1451":{"protein_sequence":{"accession":"ACN85419.1","sequence":"MKTFAAYVITACLSSTALASSITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNNLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLSLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWEGQLRISAVNQVEFLESLFLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKGTEVYFFAFNMDIDNENKLPLRKSIPTKIMASEGIIGG"},"dna_sequence":{"accession":"FJ790516.1","fmin":"1287","fmax":"2085","strand":"+","sequence":"ATGAAAACATTTGCCGCATATGTAATTACTGCGTGTCTTTCAAGTACGGCATTAGCTAGTTCAATTACAGAAAATACGTCTTGGAACAAAGAGTTCTCTGCCGAAGCCGTCAATGGTGTTTTCGTGCTTTGTAAAAGTAGCAGTAAATCCTGCGCTACCAATAACTTAGCTCGTGCATCAAAGGAATATCTTCCAGCATCAACATTTAAGATCCCCAACGCAATTATCGGCCTAGAAACTGGTGTCATAAAGAATGAGCATCAGGTTTTCAAATGGGACGGAAAGCCAAGAGCCATGAAACAATGGGAAAGAGACTTGAGCTTAAGAGGGGCAATACAAGTTTCAGCGGTTCCCGTATTTCAACAAATCGCCAGAGAAGTTGGCGAAGTAAGAATGCAGAAATACCTTAAAAAATTTTCATATGGCAACCAGAATATCAGTGGTGGCATTGACAAATTCTGGGAGGGTCAGCTAAGAATTTCCGCAGTTAATCAAGTGGAGTTTCTAGAGTCTCTATTTTTAAATAAATTGTCAGCATCAAAAGAAAATCAGCTAATAGTAAAAGAGGCTTTGGTAACGGAGGCTGCGCCTGAATATCTTGTGCATTCAAAAACTGGTTTTTCTGGTGTGGGAACTGAGTCAAATCCTGGTGTCGCATGGTGGGTTGGTTGGGTTGAGAAGGGAACAGAGGTTTACTTTTTCGCCTTTAACATGGATATAGACAACGAAAATAAGTTGCCGCTAAGAAAATCCATTCCCACCAAAATCATGGCAAGTGAGGGCATCATTGGTGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3001804","ARO_id":"38204","ARO_name":"OXA-145","CARD_short_name":"OXA-145","ARO_description":"OXA-145 is a beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46486":{"category_aro_accession":"3007697","category_aro_cvterm_id":"46486","category_aro_name":"OXA-10-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-10.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"296":{"model_id":"296","model_name":"VIM-23","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1729":{"protein_sequence":{"accession":"ACT33323.1","sequence":"MFKLLSKLLVYLTASIMAIASPLAFSVDSSGEYPTVSEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEVEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSASVLYGGCAIYELSSTSAGNVADADLAEWPTSIERIQQHYPEAQFVIPGHGLPGGLDLLKHTTNVVKAHTNRSVVE"},"dna_sequence":{"accession":"GQ242167.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGTTCAAACTTTTGAGTAAGTTATTGGTCTATTTGACCGCGTCTATCATGGCTATTGCGAGTCCGCTCGCTTTTTCCGTAGATTCTAGCGGTGAGTATCCGACAGTCAGCGAAATTCCGGTCGGGGAGGTCCGGCTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCAGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAGAAGCAAATTGGACTTCCTGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGTAGAGGGGAACGAGATTCCCACGCACTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAACTCTTCTATCCTGGTGCTGCGCATTCGACCGACAACTTAGTTGTGTACGTCCCGTCTGCGAGTGTGCTCTATGGTGGTTGTGCGATTTATGAGTTGTCAAGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCATTGAGCGGATTCAACAACACTACCCGGAAGCACAGTTCGTCATTCCGGGGCACGGCCTGCCGGGCGGTCTAGACTTGCTCAAGCACACAACGAATGTTGTAAAAGCGCACACAAATCGCTCAGTCGTTGAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3002293","ARO_id":"38693","ARO_name":"VIM-23","CARD_short_name":"VIM-23","ARO_description":"VIM-23 is a beta-lactamase found in Enterobacter cloacae.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"297":{"model_id":"297","model_name":"CMY-98","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1778":{"protein_sequence":{"accession":"AGH70380.1","sequence":"MAAQSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAIIYQGKPYYFTWGKADIANDRPVTRQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTQYWPELTGKQWQGISLLHLATYTAGGLPLQVPDDVTDKAALLRFYQNWQPQWAPGAKRLYANSSIGLFGALAVKPSGMGYEEAMTKRVLQPLKLAHTWITVPQSEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSSLVDMTRWIQANMDASQVQEKTLRQGIEIAQARYWHIGDMYQGLGWEMLNWPVNADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPARVEAAWRI"},"dna_sequence":{"accession":"KC603538.1","fmin":"0","fmax":"1131","strand":"+","sequence":"ATGGCTGCACAATCGTTATGCTGCGCGTTGCTGCTGACAGCCTCTTTCTCTACGTTTGCCGCCGCAAAAACAGAACAACAGATTGCCGATATCGTAAACCGTACCATCACACCGCTGATGCAAGAACAGGCTATTCCGGGTATGGCCGTAGCAATTATCTACCAGGGAAAACCCTATTACTTTACCTGGGGGAAAGCCGATATCGCCAATGACCGCCCCGTCACCCGGCAAACGCTGTTTGAGCTTGGATCGGTAAGTAAGACGTTTAACGGTGTGCTGGGCGGCGATGCTATCGCCCGTGGTGAAATTAAGCTCAGCGATCCGGTCACCCAATACTGGCCCGAATTAACTGGCAAACAATGGCAGGGTATCAGCCTGCTGCACCTGGCCACCTATACGGCGGGTGGTCTGCCGCTTCAGGTACCTGACGACGTTACAGATAAAGCGGCATTACTGCGCTTTTATCAAAACTGGCAGCCGCAATGGGCCCCGGGTGCTAAACGCCTGTATGCTAACTCCAGTATTGGTCTGTTTGGCGCACTGGCGGTGAAACCTTCAGGAATGGGCTATGAAGAGGCGATGACCAAACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCACAGAGCGAACAAAAGGATTATGCCTGGGGTTATCGCGAAGGGAAGCCCGTACACGTATCTCCGGGCCAGCTTGATGCCGAAGCCTACGGGGTGAAATCCAGCCTTGTCGATATGACTCGTTGGATTCAGGCCAACATGGACGCCAGCCAGGTGCAGGAGAAAACGCTCCGACAGGGAATTGAAATTGCGCAGGCTCGTTACTGGCATATTGGCGATATGTACCAGGGATTAGGTTGGGAGATGCTGAACTGGCCGGTGAATGCCGACTCGATAATCAACGGTAGCGACAGTAAAGTCGCACTAGCGGCGCTTCCCGCCGTTGAGGTCAATCCGCCCGCCCCTGCAGTGAAAGCCTCATGGGTGCACAAAACCGGCTCCACTGGCGGATTTGGCAGCTACGTTGCGTTCGTTCCGGAAAAAAATCTCGGCATCGTGATGCTGGCAAACAAAAGCTACCCAAACCCTGCTCGCGTCGAGGCCGCCTGGCGCATCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002111","ARO_id":"38511","ARO_name":"CMY-98","CARD_short_name":"CMY-98","ARO_description":"CMY-98 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"300":{"model_id":"300","model_name":"AAC(6')-29a","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"250"}},"model_sequences":{"sequence":{"5868":{"protein_sequence":{"accession":"WP_064190968.1","sequence":"MSVSILPVKEQDAADWLALRNLLWLADDHASEIEQYFSGGLEGLVEVLIARDATGAAVGHVELSIRHDLEELQGIKTGYIEGLYVAPSHRSTDLVRRFLRESEKWALEQGCSAFASDRSDRVITHRKFAGSAV"},"dna_sequence":{"accession":"NG_048575.1","fmin":"100","fmax":"502","strand":"+","sequence":"TTGAGCGTTTCGATCTTACCTGTGAAAGAACAAGACGCTGCCGACTGGCTAGCGCTGCGGAATCTTCTTTGGCTCGCGGATGATCACGCCTCGGAGATTGAGCAGTACTTCTCTGGTGGACTTGAGGGGCTTGTAGAAGTGCTCATCGCCCGTGATGCTACCGGCGCGGCTGTTGGGCATGTCGAACTCTCGATAAGACATGACTTGGAAGAACTCCAAGGAATCAAGACCGGCTACATCGAAGGCCTTTATGTGGCCCCAAGCCATCGATCAACAGACCTTGTGAGGCGTTTCTTGCGTGAGTCCGAGAAGTGGGCCCTAGAACAAGGGTGCAGCGCATTTGCCTCAGACAGAAGTGATCGGGTCATCACGCACCGCAAGTTCGCAGGCAGCGCCGTCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002583","ARO_id":"38983","ARO_name":"AAC(6')-29a","CARD_short_name":"AAC(6')-29a","ARO_description":"AAC(6')-29a is an integron-encoded aminoglycoside acetyltransferase in P. aeruginosa.","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"A category of aminoglycoside N-acetyltransferase enzymes with modification regiospecificity based at the 6'-amino group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics through acetylation of the 6-amino group of the compound.","category_aro_class_name":"AMR Gene Family"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"301":{"model_id":"301","model_name":"CMY-95","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1702":{"protein_sequence":{"accession":"AGC54799.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHASPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVASAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"JX514369.1","fmin":"296","fmax":"1442","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGCTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATCGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002108","ARO_id":"38508","ARO_name":"CMY-95","CARD_short_name":"CMY-95","ARO_description":"CMY-95 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"302":{"model_id":"302","model_name":"TEM-207","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"848":{"protein_sequence":{"accession":"AGK40892.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGGRGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"KC818234.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGGGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001384","ARO_id":"37784","ARO_name":"TEM-207","CARD_short_name":"TEM-207","ARO_description":"TEM-207 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"303":{"model_id":"303","model_name":"ErmQ","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"678":{"protein_sequence":{"accession":"AAC36915.1","sequence":"MKAKSNNYRGKVDISVSQNFITSKNTIYKLIKKTNISKNDFVIEIGPGKGHITEALCEKSYWVTAIELDRSLYGNLINKFKSKNNVTLINKDFLNWKLPKKREYKVFSNIPFYITTKIIKKLLLEELNSPTDMWLVMEKGSAKRFMGIPRESKLSLLLKTKFDIKIVHYFNREDFHPMPSVDCVLVYFKRKYKYDISKDEWNEYTSFISKSINNLRDVFTKNQIHAVIKYLGINLNNISEVSYNDWIQLFRYKQKID"},"dna_sequence":{"accession":"L22689.1","fmin":"261","fmax":"1035","strand":"+","sequence":"ATGAAAGCTAAAAGTAATAATTATAGAGGAAAAGTTGATATTAGTGTATCGCAAAATTTTATTACTAGTAAAAATACTATATATAAATTAATAAAAAAAACAAATATATCCAAAAATGATTTTGTTATTGAAATTGGACCAGGAAAAGGTCATATAACAGAAGCTTTATGTGAAAAAAGTTATTGGGTTACAGCTATAGAACTAGATAGAAGTTTATATGGAAATTTAATAAATAAATTTAAAAGTAAAAATAATGTTACTCTTATTAATAAAGATTTTTTAAATTGGAAATTACCTAAAAAAAGAGAATATAAGGTATTTTCTAATATTCCTTTTTATATAACAACAAAGATTATTAAGAAATTATTATTAGAAGAGTTAAATTCACCAACTGATATGTGGCTAGTTATGGAGAAAGGTTCCGCAAAAAGATTTATGGGAATACCTAGAGAGAGTAAATTATCATTACTTTTAAAAACTAAATTTGATATTAAGATAGTGCACTATTTTAATAGAGAAGACTTCCATCCCATGCCTAGTGTAGATTGCGTCTTAGTATATTTTAAAAGAAAATATAAATATGATATATCTAAAGATGAATGGAATGAATATACAAGTTTTATATCTAAGTCTATTAATAACTTAAGAGATGTATTTACAAAAAATCAAATTCATGCAGTAATTAAATACCTAGGTATAAATCTTAATAATATTAGTGAAGTTTCTTATAATGATTGGATACAGTTATTTAGATATAAACAAAAGATAGATTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36812","NCBI_taxonomy_name":"Clostridium perfringens","NCBI_taxonomy_id":"1502"}}}},"ARO_accession":"3000593","ARO_id":"36732","ARO_name":"ErmQ","CARD_short_name":"ErmQ","ARO_description":"ErmQ confers MLSb phenotype.","ARO_category":{"36699":{"category_aro_accession":"3000560","category_aro_cvterm_id":"36699","category_aro_name":"Erm 23S ribosomal RNA methyltransferase","category_aro_description":"Erm proteins are part of the RNA methyltransferase family and methylate A2058 (E. coli nomenclature) of the 23S ribosomal RNA conferring degrees of resistance to Macrolides, Lincosamides and Streptogramin b. This is called the MLSb phenotype.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35946":{"category_aro_accession":"0000027","category_aro_cvterm_id":"35946","category_aro_name":"roxithromycin","category_aro_description":"Roxithromycin is a semi-synthetic, 14-carbon ring macrolide antibiotic derived from erythromycin. It is used to treat respiratory tract, urinary and soft tissue infections. Roxithromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35974":{"category_aro_accession":"0000057","category_aro_cvterm_id":"35974","category_aro_name":"telithromycin","category_aro_description":"Telithromycin is a semi-synthetic derivative of erythromycin. It is a 14-membered macrolide and is the first ketolide antibiotic to be used in clinics. Telithromycin binds the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"35982":{"category_aro_accession":"0000065","category_aro_cvterm_id":"35982","category_aro_name":"clarithromycin","category_aro_description":"Clarithromycin is a methyl derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome and is used to treat pharyngitis, tonsillitis, acute maxillary sinusitis, acute bacterial exacerbation of chronic bronchitis, pneumonia (especially atypical pneumonias associated with Chlamydia pneumoniae or TWAR), and skin structure infections.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"36284":{"category_aro_accession":"3000145","category_aro_cvterm_id":"36284","category_aro_name":"tylosin","category_aro_description":"Tylosin is a 16-membered macrolide, naturally produced by Streptomyces fradiae. It interacts with the bacterial ribosome 50S subunit to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"36295":{"category_aro_accession":"3000156","category_aro_cvterm_id":"36295","category_aro_name":"spiramycin","category_aro_description":"Spiramycin is a 16-membered macrolide and is natural product produced by Streptomyces ambofaciens. It binds to the 50S subunit of bacterial ribosomes and inhibits peptidyl transfer activity to disrupt protein synthesis.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"36315":{"category_aro_accession":"3000176","category_aro_cvterm_id":"36315","category_aro_name":"dirithromycin","category_aro_description":"Dirithromycin is an oxazine derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome to inhibit bacterial protein synthesis.","category_aro_class_name":"Antibiotic"},"36722":{"category_aro_accession":"3000583","category_aro_cvterm_id":"36722","category_aro_name":"pristinamycin IA","category_aro_description":"Pristinamycin IA is a type B streptogramin antibiotic produced by Streptomyces pristinaespiralis. It binds to the P site of the 50S subunit of the bacterial ribosome, preventing the extension of protein chains.","category_aro_class_name":"Antibiotic"},"36723":{"category_aro_accession":"3000584","category_aro_cvterm_id":"36723","category_aro_name":"quinupristin","category_aro_description":"Quinupristin is a type B streptogramin and a semisynthetic derivative of pristinamycin 1A. It is a component of the drug Synercid and interacts with the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"virginiamycin M1","category_aro_description":"Virginiamycin M1 is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37016":{"category_aro_accession":"3000672","category_aro_cvterm_id":"37016","category_aro_name":"madumycin II","category_aro_description":"Madumycin II is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37017":{"category_aro_accession":"3000673","category_aro_cvterm_id":"37017","category_aro_name":"griseoviridin","category_aro_description":"Griseoviridin is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"37019":{"category_aro_accession":"3000675","category_aro_cvterm_id":"37019","category_aro_name":"pristinamycin IB","category_aro_description":"Pristinamycin IB is a class B streptogramin similar to pristinamycin IA, the former containing a N-methyl-4-(methylamino)phenylalanine instead of a N-methyl-4-(dimethylamino)phenylalanine in its class A streptogramin counterpart (one less methyl group).","category_aro_class_name":"Antibiotic"},"37021":{"category_aro_accession":"3000677","category_aro_cvterm_id":"37021","category_aro_name":"virginiamycin S2","category_aro_description":"Virginiamycin S2 is a streptogramin B antibiotic.","category_aro_class_name":"Antibiotic"},"37022":{"category_aro_accession":"3000678","category_aro_cvterm_id":"37022","category_aro_name":"pristinamycin IC","category_aro_description":"Pristinamycin IC is a class B streptogramin derived from virginiamycin S1.","category_aro_class_name":"Antibiotic"},"37023":{"category_aro_accession":"3000679","category_aro_cvterm_id":"37023","category_aro_name":"vernamycin C","category_aro_description":"Vernamycin C is a streptogramin B antibiotic.","category_aro_class_name":"Antibiotic"},"37024":{"category_aro_accession":"3000680","category_aro_cvterm_id":"37024","category_aro_name":"patricin A","category_aro_description":"Patricin A is a streptogramin B antibiotic.","category_aro_class_name":"Antibiotic"},"37025":{"category_aro_accession":"3000681","category_aro_cvterm_id":"37025","category_aro_name":"patricin B","category_aro_description":"Patricin B is a streptogramin B antibiotic.","category_aro_class_name":"Antibiotic"},"37026":{"category_aro_accession":"3000682","category_aro_cvterm_id":"37026","category_aro_name":"ostreogrycin B3","category_aro_description":"Ostreogrycin B3 is a derivative of pristinamycin IA, with an additional 3-hydroxy group on its 4-oxopipecolic acid.","category_aro_class_name":"Antibiotic"},"37247":{"category_aro_accession":"3000867","category_aro_cvterm_id":"37247","category_aro_name":"oleandomycin","category_aro_description":"Oleandomycin is a 14-membered macrolide produced by Streptomyces antibioticus. It is ssimilar to erythromycin, and contains a desosamine amino sugar and an oleandrose sugar. It targets the 50S ribosomal subunit to prevent protein synthesis.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35952":{"category_aro_accession":"0000034","category_aro_cvterm_id":"35952","category_aro_name":"streptogramin A antibiotic","category_aro_description":"Streptogramin A antibiotics are cyclic polyketide peptide hybrids that bind to the ribosomal peptidyl transfer centre. Structural variation arises from substituting a proline for its desaturated derivative and by its substitution for Ala or Cys. Used alone, streptogramin A antibiotics are bacteriostatic, but is bactericidal when used with streptogramin B antibiotics.","category_aro_class_name":"Drug Class"},"35967":{"category_aro_accession":"0000050","category_aro_cvterm_id":"35967","category_aro_name":"streptogramin B antibiotic","category_aro_description":"Streptogramin B antibiotics are are cyclic hepta- or hexa-depsipeptides.  Type B streptogramins block the peptide exit tunnel of the 50S bacterial ribosome. The general composition of group B streptogramins is 3-hydroxypicolinic acid-L-Thr-D-aminobutyric acid (or D-Ala)-L-Pro-L-Phe (or 4-N-,N-(dimethylamino)-L-Phe)-X-L-phenylglycine. Used alone, streptogramin B antibiotics are bacteriostatic, but is bactericidal when used with streptogramin A antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"304":{"model_id":"304","model_name":"IND-11","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1747":{"protein_sequence":{"accession":"ADK25050.1","sequence":"MKKSIQLLMMSMFLSPLINAQVKDFVIEPPVKPNLYLYKSFGVFGGKEYSANAVYLTTKKGVVLFDVPWQKEQYQTLMDTIQKRHHLPVIAVFATHSHDDRAGDLSFYNQKGIKTYATAKTNELLKKDGKATSTEIIKTGKPYKIGGEEFMVDFLGEGHTVDNVVVWFPKYKVLDGGCLVKSRTATDLGYTGEANVKQWPETMRKLKTKYAHATLVIPGHDEWKGGGHVQHTLDLLDKNKKPE"},"dna_sequence":{"accession":"HM245379.1","fmin":"56","fmax":"788","strand":"+","sequence":"ATGAAAAAAAGTATTCAGCTTTTGATGATGTCAATGTTTTTAAGCCCATTGATCAATGCCCAGGTTAAAGATTTTGTAATTGAGCCGCCTGTTAAACCCAACCTGTATCTTTATAAAAGTTTCGGAGTTTTCGGGGGTAAAGAATATTCTGCCAATGCTGTATATCTTACCACTAAGAAAGGAGTTGTCTTATTTGATGTCCCATGGCAAAAGGAACAATATCAAACCCTTATGGACACCATACAAAAGCGTCATCACCTTCCTGTAATTGCTGTATTTGCCACCCACTCTCATGATGACAGAGCGGGTGATCTAAGCTTTTACAATCAAAAAGGAATTAAAACATATGCGACCGCCAAGACCAATGAACTGTTGAAAAAAGACGGAAAAGCAACCTCAACCGAAATTATAAAAACAGGAAAACCTTACAAAATTGGTGGTGAAGAATTTATGGTAGACTTTCTTGGAGAAGGACATACAGTTGATAATGTTGTTGTATGGTTCCCCAAATATAAAGTACTGGACGGAGGATGTCTTGTAAAAAGCAGGACAGCCACTGACCTGGGATATACCGGTGAAGCAAATGTAAAACAATGGCCGGAAACCATGCGAAAACTAAAAACGAAATATGCTCATGCCACTCTGGTAATCCCGGGACACGACGAATGGAAAGGCGGTGGCCATGTACAGCATACTCTGGATCTTCTGGATAAGAATAAAAAGCCGGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36916","NCBI_taxonomy_name":"Chryseobacterium indologenes","NCBI_taxonomy_id":"253"}}}},"ARO_accession":"3002267","ARO_id":"38667","ARO_name":"IND-11","CARD_short_name":"IND-11","ARO_description":"IND-11 is a beta-lactamase found in Escherichia coli.","ARO_category":{"36199":{"category_aro_accession":"3000060","category_aro_cvterm_id":"36199","category_aro_name":"IND beta-lactamase","category_aro_description":"IND beta-lactamases are class B carbapenem-hydrolyzing beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"305":{"model_id":"305","model_name":"chrB","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4490":{"protein_sequence":{"accession":"AAS79458.1","sequence":"MLNRIVRYLACPHCGASLAQGDRALFCPAGHSFDIAKQGYVNLLPRATKLRADTKEMVEARDAFLSAGHYDPVMDALVDLARRTADPAVPGCVVDIGGGTGHYHAGVMEAFPDAQGLLLDISKYAVRRAAKAHPRIAAAVTDAWQTLPLRDAAAGMVINTFAPRNGPELHRVLHPRGVLLVVTPLPDHLREVIGALGLLQVDEGKESRLAEQLAPHFSAVATEELTRTMALDHQALAHLVGMGPNAWHRDAQRDLETIQRLPAPTRVTLSVRLSAYRLSA"},"dna_sequence":{"accession":"AY509120.1","fmin":"22652","fmax":"23495","strand":"-","sequence":"ATGCTCAACAGGATCGTGCGCTACCTCGCCTGCCCGCACTGCGGTGCTTCGCTGGCTCAGGGCGACCGCGCACTTTTCTGCCCCGCCGGACACTCCTTCGACATCGCGAAGCAGGGTTATGTGAATCTGCTTCCCAGGGCGACGAAGCTGCGGGCCGACACCAAGGAAATGGTGGAGGCCCGGGACGCATTCCTGTCGGCGGGTCACTACGACCCCGTGATGGATGCGCTGGTCGATCTGGCGCGGCGGACGGCCGATCCGGCCGTGCCCGGCTGTGTGGTCGACATCGGTGGGGGGACGGGCCACTATCACGCCGGGGTCATGGAAGCGTTCCCCGATGCCCAGGGCCTGCTGCTGGACATCTCCAAGTACGCCGTGCGGCGTGCCGCGAAGGCGCATCCGCGGATCGCGGCCGCGGTGACCGACGCCTGGCAGACGCTTCCGCTGCGGGATGCCGCAGCCGGCATGGTGATCAACACGTTCGCTCCCCGCAACGGTCCTGAACTGCATCGCGTTCTCCATCCCCGTGGCGTTCTCCTGGTTGTCACTCCTCTGCCCGATCACCTGCGGGAGGTGATCGGCGCCCTCGGCCTGCTGCAGGTGGACGAAGGCAAGGAGTCGCGTCTCGCGGAGCAGCTCGCTCCGCACTTCTCGGCCGTCGCCACGGAGGAGTTGACCCGGACCATGGCTCTCGACCACCAGGCTCTGGCGCACCTGGTCGGCATGGGGCCCAATGCCTGGCACCGTGACGCGCAGCGGGATCTGGAGACGATCCAGCGGCTGCCGGCGCCGACTCGGGTCACGCTCTCCGTGCGGCTCTCCGCCTACCGGTTGTCGGCGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39573","NCBI_taxonomy_name":"Streptomyces bikiniensis","NCBI_taxonomy_id":"1896"}}}},"ARO_accession":"3001302","ARO_id":"37701","ARO_name":"chrB","CARD_short_name":"chrB","ARO_description":"ChrB is a methyltransferase found in Streptomyces bikiniensis and confers resistance to chalcomycin, mycinamicin, and tylosin. Specifically, this enzyme adds a methyl group to guanosine 748 (E. coli numbering). chrB is found in the chalcomycin biosynthetic cluster and is responsible for self-resistance in S. bikiniensis.","ARO_category":{"37697":{"category_aro_accession":"3001298","category_aro_cvterm_id":"37697","category_aro_name":"non-erm 23S ribosomal RNA methyltransferase (G748)","category_aro_description":"Non-erm 23S ribosomal RNA methyltransferases modify guanosine 748 (E. coli numbering) to confer resistance to some macrolides and lincosamides.","category_aro_class_name":"AMR Gene Family"},"36284":{"category_aro_accession":"3000145","category_aro_cvterm_id":"36284","category_aro_name":"tylosin","category_aro_description":"Tylosin is a 16-membered macrolide, naturally produced by Streptomyces fradiae. It interacts with the bacterial ribosome 50S subunit to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"37621":{"category_aro_accession":"3001222","category_aro_cvterm_id":"37621","category_aro_name":"chalcomycin","category_aro_description":"Produced by Streptomyces bikiniensis.","category_aro_class_name":"Antibiotic"},"37623":{"category_aro_accession":"3001224","category_aro_cvterm_id":"37623","category_aro_name":"mycinamicin","category_aro_description":"Produced by Micromonospora\u00a0griseorubida.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"306":{"model_id":"306","model_name":"SHV-32","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1066":{"protein_sequence":{"accession":"AAK69828.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAVITMSDNSAANLLLATVGGPAGLTAFLRQIDDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AY037778.1","fmin":"91","fmax":"952","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACATCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGTCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGACGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001090","ARO_id":"37470","ARO_name":"SHV-32","CARD_short_name":"SHV-32","ARO_description":"SHV-32 is a broad-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"307":{"model_id":"307","model_name":"CTX-M-101","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"865":{"protein_sequence":{"accession":"ADY02545.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELIAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"HQ398214.1","fmin":"249","fmax":"1125","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTATCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001960","ARO_id":"38360","ARO_name":"CTX-M-101","CARD_short_name":"CTX-M-101","ARO_description":"CTX-M-101 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"308":{"model_id":"308","model_name":"CMY-118","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1265":{"protein_sequence":{"accession":"AIT76091.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAIIYEGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWRGISLLHLATYTAGGLPLQIPDDVTDKAALLRFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQSEQKNYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIELAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPARVEAAWRILEKLQ"},"dna_sequence":{"accession":"KM087838.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCGCTGCTGCTGACAGCCTCTTTCTCCACGTTTGCTGCCGCAAAAACAGAACAACAAATTGCCGATATCGTTAACCGCACCATCACACCACTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTGGCGATTATCTACGAGGGGAAACCTTATTACTTTACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGACGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCGGGGTATCAGCCTGCTGCACTTAGCCACCTATACAGCGGGTGGCCTGCCGCTGCAGATCCCCGATGACGTTACGGATAAAGCCGCATTACTGCGCTTTTATCAAAACTGGCAACCACAATGGACTCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGTGCGCTGGCGGTGAAACCTTCAGGTATGAGCTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAAAGCGAACAAAAAAATTATGCCTGGGGCTATCGCGAAGGGAAGCCTGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATCGATATGGCCCGCTGGGTTCAGGCCAACATGGACGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGAGCTTGCGCAGTCTCGTTACTGGCGTATTGGTGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCAGCACCTGCCGTGAAAGCCTCATGGGTGCATAAAACGGGATCCACAGGTGGATTTGGCAGCTACGTTGCCTTCGTTCCAGAAAAAAACCTTGGCATAGTGATGCTGGCAAACAAAAGCTATCCTAACCCGGCTCGCGTAGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002129","ARO_id":"38529","ARO_name":"CMY-118","CARD_short_name":"CMY-118","ARO_description":"CMY-118 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"309":{"model_id":"309","model_name":"CMY-35","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"782":{"protein_sequence":{"accession":"ABN51007.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKAVHVSPGQLDAEAYGVKSSVIDMARWVQVNMDASRVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"EF394371.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACATGGATTACAGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGGCTGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGTGTTATTGATATGGCCCGCTGGGTTCAGGTCAACATGGACGCCAGCCGCGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCAATCATCAACGGTAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCTGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGATCCACTGGAGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002046","ARO_id":"38446","ARO_name":"CMY-35","CARD_short_name":"CMY-35","ARO_description":"CMY-35 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"310":{"model_id":"310","model_name":"SHV-78","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"8187":{"protein_sequence":{"accession":"CAJ47133.2","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASSRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AM176553.2","fmin":"30","fmax":"891","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCAGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGCATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001132","ARO_id":"37512","ARO_name":"SHV-78","CARD_short_name":"SHV-78","ARO_description":"SHV-78 is a broad-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"311":{"model_id":"311","model_name":"IND-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"774":{"protein_sequence":{"accession":"AAG29757.1","sequence":"MKKSIQLLMMSMFLSPLINAQVKDFVIEPPVKPNLYLYKSFGVFGGKEYSANAVYLTTKKGVVLFDVPWQKEQYQTLMDTIQKRHHLPVIAVFATHSHDDRAGDLSFYNQKGIKTYATAKTNELLKKDGKATSTEIIKTGKPYKIGGEEFMVDFLGEGHTVDNVVVWFPKYKVLDGGCLVKSRTATDLGYTGEANVKQWPETMRKLKTKYAQATLVIPGHDEWKGGGHVQHTLDLLDKNKKPE"},"dna_sequence":{"accession":"AF219127.1","fmin":"0","fmax":"732","strand":"+","sequence":"ATGAAAAAAAGTATTCAGCTTTTGATGATGTCAATGTTTTTAAGCCCATTGATCAATGCCCAGGTTAAAGATTTTGTAATTGAGCCGCCTGTTAAACCCAACCTGTATCTTTATAAAAGTTTCGGAGTTTTCGGGGGTAAAGAATATTCTGCCAATGCTGTATATCTTACCACTAAGAAAGGAGTTGTCTTATTTGATGTCCCATGGCAAAAGGAACAATATCAAACCCTTATGGACACCATACAAAAGCGTCATCACCTTCCTGTAATTGCTGTATTTGCCACCCACTCTCATGATGACAGAGCGGGCGATCTAAGCTTTTACAATCAAAAAGGAATTAAAACATATGCGACCGCCAAGACCAATGAACTGTTGAAAAAAGACGGAAAAGCAACCTCAACCGAAATTATAAAAACAGGAAAACCTTACAAAATTGGTGGTGAAGAATTTATGGTAGACTTTCTTGGAGAAGGACATACAGTTGATAATGTTGTTGTATGGTTCCCCAAATATAAAGTACTGGACGGAGGATGTCTTGTAAAAAGCAGGACAGCCACTGACCTGGGATATACAGGTGAAGCAAACGTAAAACAATGGCCGGAAACCATGCGAAAACTAAAAACGAAATATGCTCAGGCCACTCTGGTAATCCCGGGACACGACGAATGGAAAGGCGGTGGCCATGTACAGCATACTCTGGATCTTCTGGATAAGAATAAAAAGCCGGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36916","NCBI_taxonomy_name":"Chryseobacterium indologenes","NCBI_taxonomy_id":"253"}}}},"ARO_accession":"3002257","ARO_id":"38657","ARO_name":"IND-2","CARD_short_name":"IND-2","ARO_description":"IND-2 is a beta-lactamase found in Chryseobacterium indologenes.","ARO_category":{"36199":{"category_aro_accession":"3000060","category_aro_cvterm_id":"36199","category_aro_name":"IND beta-lactamase","category_aro_description":"IND beta-lactamases are class B carbapenem-hydrolyzing beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"312":{"model_id":"312","model_name":"OXA-167","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1370":{"protein_sequence":{"accession":"ADK35871.1","sequence":"MNKYFTCYVVASLFLSGCTVQHNLINETPSQIVQGHNQVIHQYFDEKNTSGVLVIQTDKKINLYGNALSRANTEYVPASTFKMLNALIGLENQKTDINEIFKWKGEKRSFTAWEKDMTLGEAMKLSAVPVYQELARRIGLDLMQKEVKRIGFGNAEIGQQVDNFWLVGPLKVTPIQEVEFVSQLAHTQLPFSEKVQANVKNMLLLEESNGYKIFGKTGWAMDIKPQVGWLTGWVEQPDGKIVAFALNMEMRSEMPASIRNELMMKSLKQLNII"},"dna_sequence":{"accession":"HM488988.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGAATAAATATTTTACTTGCTATGTGGTTGCTTCTCTTTTTCTTTCTGGTTGTACGGTTCAGCATAATTTAATAAATGAAACCCCGAGTCAGATTGTTCAAGGACATAATCAGGTGATTCATCAATACTTTGATGAAAAAAACACCTCAGGTGTGCTGGTTATTCAAACAGATAAAAAAATTAATCTATATGGTAATGCTCTAAGCCGCGCAAATACAGAATATGTGCCAGCCTCTACATTTAAAATGTTGAATGCCCTGATCGGATTGGAGAACCAGAAAACGGATATTAATGAAATATTTAAATGGAAGGGCGAGAAAAGGTCATTTACCGCTTGGGAAAAAGACATGACACTAGGAGAAGCCATGAAGCTTTCTGCAGTCCCAGTCTATCAGGAACTTGCGCGACGTATCGGTCTTGATCTCATGCAAAAAGAAGTAAAACGTATTGGTTTCGGTAATGCTGAAATTGGACAGCAGGTTGATAATTTCTGGTTGGTAGGACCATTAAAGGTTACGCCTATTCAAGAGGTAGAGTTTGTTTCCCAATTAGCACATACACAGCTTCCATTTAGTGAAAAAGTGCAGGCTAATGTAAAAAATATGCTTCTTTTAGAAGAGAGTAATGGCTACAAAATTTTTGGAAAGACTGGTTGGGCAATGGATATAAAACCACAAGTGGGCTGGTTGACCGGCTGGGTTGAGCAGCCAGATGGAAAAATTGTCGCTTTTGCATTAAATATGGAAATGCGGTCAGAAATGCCGGCATCTATACGTAATGAATTAATGATGAAATCATTAAAACAGCTGAATATTATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001467","ARO_id":"37867","ARO_name":"OXA-167","CARD_short_name":"OXA-167","ARO_description":"OXA-167 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46499":{"category_aro_accession":"3007710","category_aro_cvterm_id":"46499","category_aro_name":"OXA-23-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases, specifically imipenem, derived from OXA-23, first identified in Acinetobacter baumannii.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"313":{"model_id":"313","model_name":"OXA-143","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1291":{"protein_sequence":{"accession":"ACX70402.1","sequence":"MKKFILPILSISTLLSVSACSSIQTKFEDTFHTSNQQHEKAIKSYFDEAQTQGVIIIKKGKNISTYGNNLTRAHTEYVPASTFKMLNALIGLENHKATTTEIFKWDGKKRSYPMWEKDMTLGDAMALSAVPVYQELARRTGLDLMQKEVKRVGFGNMNIGTQVDNFWLVGPLKITPIQEVNFADDFANNRLPFKLETQEEVKKMLLIKEFNGSKIYAKSGWGMDVTPQVGWLTGWVEKSNGEKVAFSLNIEMKQGMPGSIRNEITYKSLENLGII"},"dna_sequence":{"accession":"GQ861437.1","fmin":"2913","fmax":"3741","strand":"+","sequence":"ATGAAAAAATTTATACTTCCTATTCTCAGCATTTCTACTCTACTTTCTGTCAGTGCATGCTCATCTATTCAAACTAAATTTGAAGACACTTTTCATACTTCTAATCAGCAACATGAAAAAGCCATTAAAAGCTATTTTGATGAAGCTCAAACACAGGGTGTAATCATTATTAAAAAGGGAAAAAATATTAGTACCTATGGTAATAACCTGACACGAGCACATACAGAATATGTCCCTGCATCAACATTTAAGATGCTAAATGCCTTAATTGGACTAGAAAATCATAAAGCTACAACAACTGAGATTTTCAAATGGGACGGTAAAAAGAGATCTTATCCCATGTGGGAAAAAGATATGACTTTAGGTGATGCCATGGCACTTTCAGCAGTTCCTGTATATCAAGAACTTGCAAGACGGACTGGCTTAGACCTAATGCAAAAAGAAGTTAAACGGGTTGGTTTTGGTAATATGAACATTGGAACACAAGTTGATAACTTCTGGTTGGTTGGCCCCCTCAAGATTACACCAATACAAGAGGTTAATTTTGCCGATGATTTTGCAAATAATCGATTACCCTTTAAATTAGAGACTCAAGAAGAAGTTAAAAAAATGCTTCTGATTAAAGAATTCAATGGTAGTAAAATTTATGCAAAAAGCGGCTGGGGAATGGATGTAACCCCTCAAGTAGGTTGGTTAACAGGTTGGGTAGAAAAATCTAATGGAGAAAAAGTTGCCTTTTCTCTAAACATAGAAATGAAGCAAGGAATGCCTGGTTCTATTCGTAATGAAATTACTTATAAATCATTAGAGAATTTAGGGATTATATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001654","ARO_id":"38054","ARO_name":"OXA-143","CARD_short_name":"OXA-143","ARO_description":"OXA-143 is a beta-lactamase found in A. baumannii.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46490":{"category_aro_accession":"3007701","category_aro_cvterm_id":"46490","category_aro_name":"OXA-143-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-143.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"314":{"model_id":"314","model_name":"TEM-176","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1324":{"protein_sequence":{"accession":"ADB90239.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSVLPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"GU550123.1","fmin":"144","fmax":"1005","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGTCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001041","ARO_id":"37421","ARO_name":"TEM-176","CARD_short_name":"TEM-176","ARO_description":"TEM-176 is a beta-lactamase.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"315":{"model_id":"315","model_name":"DHA-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1337":{"protein_sequence":{"accession":"AAG36927.1","sequence":"MKKSLSATLISALLAFSAPGFSAADNVAAVVDSTIKPLMAQQDIPGMAVAVSVKGKPYYFNYGFADVQAKQPVTENTLFELGSVSKTFTGVLGAVSVAKKEMMLNDPAEKYQPELALPQWKGITLLDLATYTTGGLPLQVPDAVKNRAELLHFYQQWQPSRKPGDMRLYANSSIGLFGALTANAAGMPYEQLLTARILAPLGLSHTFITVPESAQSQYAYGYKNKKPVRVSPGQLDAESYGVKSASKDMLRWAEMNMEPSRAGNADLEMAMYLAQTRYYKTAAINQGLGWEMYDWPQQKDMIINGVTNEVALQPHPVTDNQVQPYNRASWVHKTGATTGFGAYVAFIPEKQVAIVILANKNYPNTERVKAAQAILSALE"},"dna_sequence":{"accession":"AF259520.1","fmin":"1512","fmax":"2652","strand":"+","sequence":"ATGAAAAAATCGTTATCTGCAACACTGATTTCCGCTCTGCTGGCGTTTTCCGCCCCGGGGTTTTCTGCCGCTGATAATGTCGCGGCGGTGGTGGACAGCACCATTAAACCGCTGATGGCACAGCAGGATATTCCCGGGATGGCGGTTGCCGTCTCTGTAAAGGGCAAGCCCTATTATTTCAATTATGGTTTTGCCGATGTTCAGGCAAAACAGCCGGTCACTGAAAATACACTATTTGAGCTGGGATCTGTAAGTAAAACTTTCACAGGTGTGCTGGGTGCGGTTTCTGTGGCGAAAAAAGAGATGATGTTGAATGACCCGGCAGAAAAATACCAGCCGGAGCTGGCTCTGCCGCAGTGGAAGGGGATCACACTGCTGGATCTGGCCACCTACACCACAGGCGGGCTGCCGTTACAGGTGCCGGATGCGGTGAAAAACCGTGCGGAACTGCTGCACTTCTATCAGCAGTGGCAGCCGTCCCGGAAACCGGGCGATATGCGTCTGTATGCAAACAGCAGTATCGGCCTGTTTGGTGCTCTGACCGCCAACGCAGCGGGGATGCCGTATGAGCAGTTGCTGACCGCGCGGATCCTGGCACCGCTGGGATTATCTCACACCTTTATTACCGTGCCGGAAAGCGCGCAAAGCCAGTATGCGTACGGCTATAAAAACAAAAAACCGGTCCGCGTGTCGCCGGGACAGCTTGATGCGGAGTCTTACGGCGTGAAATCCGCCTCAAAAGATATGCTGCGCTGGGCGGAAATGAATATGGAGCCGTCACGGGCCGGTAATGCGGATCTGGAAATGGCAATGTATCTTGCACAGACCCGCTACTATAAAACCGCCGCGATTAACCAGGGGCTGGGCTGGGAGATGTATGACTGGCCGCAGCAGAAAGATATGATCATTAACGGCGTGACCAACGAGGTCGCACTGCAGCCGCACCCGGTAACAGACAACCAGGTTCAGCCGTATAACCGTGCTTCCTGGGTGCATAAAACGGGGGCAACAACTGGTTTCGGCGCCTATGTGGCCTTTATTCCGGAAAAACAGGTGGCGATTGTGATTCTGGCGAATAAAAACTACCCGAATACCGAAAGAGTCAAAGCCGCACAGGCTATTTTGAGTGCGCTGGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002133","ARO_id":"38533","ARO_name":"DHA-2","CARD_short_name":"DHA-2","ARO_description":"DHA-2 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36207":{"category_aro_accession":"3000068","category_aro_cvterm_id":"36207","category_aro_name":"DHA beta-lactamase","category_aro_description":"DHA beta-lactamases are plasmid-mediated AmpC \u03b2-lactamases that confer resistance to cephamycins and oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"316":{"model_id":"316","model_name":"CTX-M-36","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1186":{"protein_sequence":{"accession":"BAD16611.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVDGTMSLAELSAAALQYSDNVAMNKLISHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGDYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTNGL"},"dna_sequence":{"accession":"AB177384.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGTCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGAAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACTTGGTTAACTATAATCCGATTGCGGAAAAGCACGTCGATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTTCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGTAATCTGACGCTGGGTAAAGCATTGGGTGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGACTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCAACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001898","ARO_id":"38298","ARO_name":"CTX-M-36","CARD_short_name":"CTX-M-36","ARO_description":"CTX-M-36 is a beta-lactamase found in Escherichia coli.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"317":{"model_id":"317","model_name":"TEM-148","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1954":{"protein_sequence":{"accession":"CAJ32372.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMAKTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AM087454.1","fmin":"208","fmax":"1069","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAAAAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001015","ARO_id":"37395","ARO_name":"TEM-148","CARD_short_name":"TEM-148","ARO_description":"TEM-148 is a TEM beta-lactamase.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"318":{"model_id":"318","model_name":"OXA-358","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1688":{"protein_sequence":{"accession":"AGZ83154.1","sequence":"MYKKALIVATSILFLSACSSNTVKQHQIHSISANKNSEEIKSLFDQAQTTGVLVIKRGQTEEIYGNDLKRASTAYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMSQEVKRVGFGNANIGSKVDNFWLVGPLKITPQQETQFAYQLAHKTLPFSQDVQEQVQSMVFIEEKNGSKIYAKSGWGWDVEPQVGWLTGWVVQPQGEIVAFSLNLEMKKGIPSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"KF421161.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGTATAAAAAAGCCCTTATCGTTGCAACAAGTATCCTATTTTTATCCGCCTGTTCTTCCAATACGGTAAAACAACATCAAATACACTCTATTTCTGCCAATAAAAATTCAGAAGAAATTAAATCACTGTTTGATCAGGCACAGACCACGGGTGTTTTGGTGATTAAGCGAGGGCAAACAGAAGAAATTTATGGCAATGATCTTAAAAGAGCATCAACCGCCTATGTTCCCGCCTCTACCTTTAAAATGTTAAATGCTTTAATTGGACTTGAACATCATAAGGCAACTACAACTGAAGTATTTAAATGGGATGGGCAAAAACGTTTATTTCCTGATTGGGAAAAGGACATGACACTGGGTGATGCCATGAAAGCTTCTGCGATTCCAGTTTACCAAGAATTAGCCCGACGAATTGGTCTAGATCTTATGTCCCAAGAGGTGAAACGAGTTGGTTTTGGTAATGCTAACATTGGTTCAAAAGTAGATAATTTTTGGCTCGTTGGCCCTCTAAAAATTACACCTCAACAAGAAACCCAATTTGCTTATCAATTAGCCCATAAAACGCTTCCATTTAGCCAAGATGTACAAGAACAAGTTCAATCAATGGTGTTCATAGAGGAAAAAAATGGAAGTAAAATTTATGCCAAAAGTGGTTGGGGATGGGATGTTGAACCACAAGTTGGTTGGCTAACAGGCTGGGTCGTTCAACCACAAGGAGAAATTGTGGCATTCTCACTAAATTTAGAAATGAAAAAAGGAATCCCTAGTTCTATCCGAAAAGAAATTGCTTATAAAGGATTAGAACAACTCGGTATTTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39094","NCBI_taxonomy_name":"Acinetobacter calcoaceticus","NCBI_taxonomy_id":"471"}}}},"ARO_accession":"3001545","ARO_id":"37945","ARO_name":"OXA-358","CARD_short_name":"OXA-358","ARO_description":"OXA-358 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46495":{"category_aro_accession":"3007706","category_aro_cvterm_id":"46495","category_aro_name":"OXA-213-like beta-lactamase","category_aro_description":"OXA-213-like enzymes have been identified to be intrinsic to A. calcoaceticus and have been subsequently detected in A. pittii. Phylogenetic analysis of OXA-213-like proteins identified two distinct subgroups within the OXA family. The first group was linked to A. pittii and the second group to A. calcoaceticus. The carbapenemase activity of these OXAs may be related to the species-dependent effect.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"319":{"model_id":"319","model_name":"OXA-366","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"2111":{"protein_sequence":{"accession":"AJO16038.1","sequence":"MNKYFTCYVVASLFLSGCTAQHNLINETPSQIVQGHNQVIHQYFDEKNTSGVLVIQTDKKINLYGNALSRANTEYVPASTFKMLNALIGLENQKTDINEIFKWKGEKRSFTAWEKDMTLGEAMKLSAVPVYQELARRIGLDLMQKEVKRIGFGNAEIGQQVDNFWLVGPLKVTPIQEVEFVSQLAHTQLPFSEKVQANVKNMLLLEESNGYKIFGKTGWAMDIKPQVGWLTGWVEQPDGKIVAFALNMEMRSEMPASIRNELLMKSLKQLNII"},"dna_sequence":{"accession":"KP050485.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGAATAAATATTTTACTTGCTATGTGGTTGCTTCTCTTTTTCTTTCTGGTTGTACGGCTCAGCATAATTTAATAAATGAAACCCCGAGTCAGATTGTTCAAGGACATAATCAGGTGATTCATCAATACTTTGATGAAAAAAACACCTCAGGTGTGCTGGTTATTCAAACAGATAAAAAAATTAATCTATATGGTAATGCTCTAAGCCGCGCAAATACAGAATATGTGCCAGCCTCTACATTTAAAATGTTGAATGCCCTGATCGGATTGGAGAACCAGAAAACGGATATTAATGAAATATTTAAATGGAAGGGCGAGAAAAGGTCATTTACCGCTTGGGAAAAAGACATGACACTAGGAGAAGCCATGAAGCTTTCTGCAGTCCCAGTCTATCAGGAACTTGCGCGACGTATCGGTCTTGATCTCATGCAAAAAGAAGTAAAACGTATTGGTTTCGGTAATGCTGAAATTGGACAGCAGGTTGATAATTTCTGGTTGGTAGGACCATTAAAGGTTACGCCTATTCAAGAGGTAGAGTTTGTTTCCCAATTAGCACATACACAGCTTCCATTTAGTGAAAAAGTGCAGGCTAATGTAAAAAATATGCTTCTTTTAGAAGAGAGTAATGGCTACAAAATTTTTGGAAAGACTGGTTGGGCAATGGATATAAAACCACAAGTGGGCTGGTTGACCGGCTGGGTTGAGCAGCCAGATGGAAAAATTGTCGCTTTTGCATTAAATATGGAAATGCGGTCAGAAATGCCGGCATCTATACGTAATGAATTATTGATGAAATCATTAAAACAGCTGAATATTATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001553","ARO_id":"37953","ARO_name":"OXA-366","CARD_short_name":"OXA-366","ARO_description":"OXA-366 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46499":{"category_aro_accession":"3007710","category_aro_cvterm_id":"46499","category_aro_name":"OXA-23-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases, specifically imipenem, derived from OXA-23, first identified in Acinetobacter baumannii.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"321":{"model_id":"321","model_name":"CTX-M-35","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1106":{"protein_sequence":{"accession":"BAD83775.1","sequence":"MMTQSIRRSMLTVMATLPLLFSSATLHAQANSVQQQLEALEKSSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKQSESDKHLLNQRVEIKKSDLVNYNPIAEKHVNGTMTLAELGAAALQYSDNTAMNKLIAHLGGPDKVTAFARSLGDETFRLDRTESTLNTAIPGDPRDTTTPLAMAQTLKNLTLGKALAETQRAQLVTWLKGNTTGSASIRAGLPKSWVVGDKTGSGDYGTTNDIAVIWPENHAPLVLVTYFTQPEQKAESRRDILAAAAKIVTHGF"},"dna_sequence":{"accession":"AB176534.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGATGACTCAGAGCATTCGCCGCTCAATGTTAACGGTGATGGCGACGCTACCCCTGCTATTTAGCAGCGCAACGCTGCATGCGCAGGCGAACAGCGTGCAACAGCAGCTGGAAGCCCTGGAGAAAAGTTCGGGAGGTCGGCTTGGCGTTGCGCTGATTAACACCGCCGATAATTCGCAGATTCTCTACCGTGCCGATGAACGTTTTGCGATGTGCAGTACCAGTAAGGTGATGGCGGCCGCGGCGGTGCTTAAACAGAGCGAGAGCGATAAGCACCTGCTAAATCAGCGCGTTGAAATCAAGAAGAGCGACCTGGTTAACTACAATCCCATTGCGGAGAAACACGTTAACGGCACGATGACGCTGGCTGAGCTTGGCGCAGCGGCGCTGCAGTATAGCGACAATACTGCCATGAATAAGCTGATTGCCCATCTGGGTGGTCCCGATAAAGTGACGGCGTTTGCTCGCTCGTTGGGTGATGAGACCTTCCGTCTGGACAGAACCGAGTCCACGCTCAATACCGCCATTCCAGGCGACCCGCGTGATACCACCACGCCGCTCGCGATGGCGCAGACCCTGAAAAATCTGACGCTGGGTAAAGCGCTGGCGGAAACTCAGCGGGCACAGTTGGTGACGTGGCTTAAGGGCAATACTACCGGTAGCGCGAGCATTCGGGCGGGTCTGCCGAAATCATGGGTAGTGGGCGATAAAACCGGCAGCGGAGATTATGGCACCACCAACGATATCGCGGTTATCTGGCCGGAAAACCACGCACCGCTGGTTCTGGTGACCTACTTTACCCAACCGGAGCAGAAGGCGGAAAGCCGTCGGGATATTCTGGCTGCGGCGGCGAAAATCGTAACCCACGGTTTCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3001897","ARO_id":"38297","ARO_name":"CTX-M-35","CARD_short_name":"CTX-M-35","ARO_description":"CTX-M-35 is a beta-lactamase found in Citrobacter koseri.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"323":{"model_id":"323","model_name":"aadA9","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"4491":{"protein_sequence":{"accession":"ABG49324.1","sequence":"MLWSSNDVTQQGSRPKTKLDMMSNSIHTGISRQLSQARDVIKRHLASTLKAIHLYGSAIDGGLKPYSDIDLLVTVDARLDEATRRSLMLDFLNISAPPCESSILRPLEVTVVACNEVVPWRYPARRELQFGEWLREDILEGVFEPAALDADLAILITKARQHSIALVGPVAQKVFMPVPEHDFLQVLSDTLKLWNTHEDWENEERNIVLTLARIWYSTETGGIVPKDVAAEWVLERLPAEHKPILVEARQAYLGLCKDSLALRADETSAFIGYAKSAVADLLEKRKSQTSHICDGAKNV"},"dna_sequence":{"accession":"DQ390458.1","fmin":"3095","fmax":"3995","strand":"-","sequence":"ATGTTATGGAGCAGCAACGATGTTACGCAGCAGGGCAGTCGCCCTAAAACAAAGTTAGACATGATGAGCAACTCTATACACACCGGAATCTCAAGACAGCTTTCACAGGCACGCGATGTAATTAAACGCCATTTGGCATCAACGCTGAAAGCCATACACTTGTATGGTTCTGCAATTGATGGTGGCCTCAAACCATATAGCGACATTGATCTGCTGGTTACCGTGGATGCACGCTTGGATGAAGCTACCAGACGCTCCCTGATGCTCGATTTCTTGAATATCTCGGCACCACCATGCGAAAGCTCAATACTCCGGCCGCTAGAGGTAACTGTTGTTGCATGCAACGAAGTAGTGCCTTGGCGTTATCCGGCACGACGAGAACTGCAGTTCGGGGAGTGGCTGCGGGAGGATATTCTTGAAGGTGTCTTCGAGCCAGCCGCCTTGGACGCCGACCTTGCAATTCTAATAACGAAAGCTAGGCAACACAGCATCGCTTTAGTAGGTCCAGTGGCTCAAAAAGTCTTCATGCCGGTGCCAGAGCATGACTTTCTCCAGGTGCTTTCCGATACCCTTAAGCTGTGGAATACTCATGAGGATTGGGAAAATGAGGAGCGGAACATCGTACTCACGTTAGCTCGGATCTGGTATAGCACTGAAACTGGAGGAATCGTCCCCAAGGATGTGGCCGCCGAATGGGTTTTAGAGCGCTTGCCAGCTGAGCATAAGCCAATACTGGTTGAGGCGCGGCAAGCCTATCTTGGGCTTTGCAAGGATAGTCTTGCTTTGCGTGCAGATGAGACTTCGGCGTTCATTGGCTATGCAAAGTCTGCGGTCGCTGATTTGCTCGAAAAGCGAAAATCTCAAACTTCGCATATTTGCGATGGCGCCAAGAACGTCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39645","NCBI_taxonomy_name":"Corynebacterium sp. L2-79-05","NCBI_taxonomy_id":"373068"}}}},"ARO_accession":"3002609","ARO_id":"39009","ARO_name":"aadA9","CARD_short_name":"aadA9","ARO_description":"aadA9 is a plasmid-encoded aminoglycoside nucleotidyltransferase gene in C. glutamicum.","ARO_category":{"41439":{"category_aro_accession":"3004275","category_aro_cvterm_id":"41439","category_aro_name":"ANT(3'')","category_aro_description":"A category of aminoglycoside O-nucleotidyltransferase enzymes with modification regiospecificity based at the 3''-hydroxyl group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics by transfer of an AMP group from an ATP substrate to the 3''-hydroxyl group of the compound.","category_aro_class_name":"AMR Gene Family"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"324":{"model_id":"324","model_name":"QnrB54","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"8200":{"protein_sequence":{"accession":"CCI51002.2","sequence":"MALALVSEKIDRNRFTGEKIENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNASALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGTQVLGATFSGSDLSGGEFSTFDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDNYQASLLMERLGIAIIG"},"dna_sequence":{"accession":"HE820727.2","fmin":"586","fmax":"1231","strand":"+","sequence":"ATGGCACTGGCACTCGTTAGCGAAAAAATTGACAGAAACCGCTTCACCGGTGAGAAAATTGAAAATAGTACATTTTTTAACTGTGATTTTTCAGGTGCCGACCTGAGCGGCACTGAATTTATCGGCTGTCAGTTCTATGATCGTGAAAGCCAGAAAGGGTGCAATTTTAGTCGTGCGATGCTGAAAGATGCCATTTTTAAAAGCTGTGATTTATCCATGGCGGATTTTCGCAATGCCAGTGCGCTTGGCATTGAAATTCGCCACTGTCGTGCGCAAGGCGCAGATTTCCGCGGCGCAAGCTTTATGAATATGATCACTACTCGCACCTGGTTTTGTAGTGCATATATCACTAACACAAATCTAAGCTACGCCAATTTTTCGAAAGTCGTGCTGGAAAAGTGTGAGCTGTGGGAAAACCGTTGGATGGGTACCCAGGTACTGGGCGCGACGTTCAGTGGTTCAGATCTCTCCGGCGGCGAGTTTTCGACTTTCGACTGGCGAGCAGCAAACTTCACACATTGCGATCTGACCAATTCGGAGTTGGGTGACTTAGATATTCGGGGCGTTGATTTACAAGGCGTTAAGTTGGACAACTACCAGGCATCGTTGCTCATGGAACGTCTTGGCATCGCGATTATTGGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002767","ARO_id":"39201","ARO_name":"QnrB54","CARD_short_name":"QnrB54","ARO_description":"QnrB54 is a plasmid-mediated quinolone resistance protein found in Citrobacter freundii.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"325":{"model_id":"325","model_name":"LEN-23","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"8270":{"protein_sequence":{"accession":"CAP12351.2","sequence":"MRYVRLCVISLLATLPLAVYAGPQPLEQIKQSESQLSGRVGMVEMDLASGRTLAAWRADERFPMVSTFKVLLCGAVLARVDAGLEQLDRRIHYRQQDLVDYSPVSEKHLTDGMTIGELCAAAITLSDNSAGNLLLATVGGPAGLTAFLRQIGDNVTRLDRWETALNEALPGDARDTTTPASMAATLRKLLTAQHLSARSQQQLLQWMVDDRVAGPLIRAVLPPGWFIADKTGAGERGARGIVALLGPDGKPERIVVLYLRDTPASMAERNQHIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AM850913.2","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGTGTTATCTCCCTGTTAGCCACCCTGCCACTGGCGGTATACGCCGGTCCACAGCCGCTTGAGCAGATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTGGGGATGGTGGAAATGGATCTGGCCAGCGGCCGCACGCTGGCGGCCTGGCGCGCCGATGAACGCTTTCCCATGGTGAGCACCTTTAAAGTGCTGCTGTGCGGCGCGGTGCTGGCGCGGGTAGATGCCGGGCTCGAACAACTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTACCGACGGGATGACGATCGGCGAACTCTGCGCCGCCGCCATCACCCTGAGCGATAACAGCGCTGGCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCGGGATTAACTGCCTTTCTGCGCCAGATCGGTGACAACGTCACCCGTCTTGACCGCTGGGAAACGGCACTGAATGAGGCGCTTCCCGGCGACGCGCGCGACACCACCACCCCGGCCAGCATGGCCGCCACGCTGCGCAAACTACTGACCGCGCAGCATCTGAGCGCCCGTTCGCAACAGCAACTCCTGCAGTGGATGGTGGACGATCGGGTTGCCGGCCCGCTGATCCGCGCCGTGCTGCCGCCGGGCTGGTTTATCGCCGACAAAACCGGGGCTGGCGAACGGGGTGCGCGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAACCGGAGCGCATTGTGGTGCTCTATCTGCGGGATACCCCGGCGAGTATGGCCGAGCGTAATCAACATATCGCCGGGATCGGCGCAGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002470","ARO_id":"38870","ARO_name":"LEN-23","CARD_short_name":"LEN-23","ARO_description":"LEN-23 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36236":{"category_aro_accession":"3000097","category_aro_cvterm_id":"36236","category_aro_name":"LEN beta-lactamase","category_aro_description":"LEN beta-lactamases are chromosomal class A beta-lactamases that confer resistance to ampicillin, amoxicillin, carbenicillin, and ticarcillin but not to extended-spectrum beta-lactams.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"172":{"model_id":"172","model_name":"OprN","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"5524":{"protein_sequence":{"accession":"AAG05883.1","sequence":"MIHAQSIRSGLASALGLFSLLALSACTVGPDYRTPDTAAAKIDATASKPYDRSRFESLWWKQFDDPTLNQLVEQSLSGNRDLRVAFARLRAARALRDDVANDRFPVVTSRASADIGKGQQPGVTEDRVNSERYDLGLDSAWELDLFGRIRRQLESSDALSEAAEADLQQLQVSLIAELVDAYGQLRGAQLREKIALSNLENQKESRQLTEQLRDAGVGAELDVLRADARLAATAASVPQLQAEAERARHRIATLLGQRPEELTVDLSPRDLPAITKALPIGDPGELLRRRPDIRAAERRLAASTADVGVATADLFPRVSLSGFLGFTAGRGSQIGSSAARAWSVGPSISWAAFDLGSVRARLRGAKADADAALASYEQQVLLALEESANAFSDYGKRQERLVSLVRQSEASRAAAQQAAIRYREGTTDFLVLLDAEREQLSAEDAQAQAEVELYRGIVAIYRSLGGGWQPSA"},"dna_sequence":{"accession":"AE004091.2","fmin":"2813193","fmax":"2814612","strand":"+","sequence":"ATGATTCACGCGCAGTCGATCCGGAGCGGGCTCGCGTCCGCCCTGGGTCTGTTCAGTCTGCTGGCGCTCAGCGCCTGCACGGTGGGTCCGGACTACCGGACCCCCGACACCGCGGCGGCGAAGATCGACGCCACGGCGAGCAAGCCCTACGACCGCAGCCGCTTCGAAAGCCTGTGGTGGAAACAGTTCGACGATCCGACCCTGAACCAGTTGGTCGAACAGTCGCTGAGCGGCAACCGCGACCTGCGCGTGGCCTTCGCCCGCCTGCGCGCCGCCCGCGCCCTGCGCGACGACGTGGCCAACGATCGCTTCCCGGTGGTCACCAGCCGCGCCAGCGCCGACATCGGCAAGGGCCAGCAACCGGGAGTGACCGAGGACCGGGTCAACAGCGAGCGCTACGACCTTGGCCTGGATAGCGCCTGGGAGCTTGACCTGTTCGGGCGCATCCGCCGTCAGCTGGAGTCCAGCGACGCCCTCAGCGAAGCGGCCGAGGCCGACCTGCAGCAACTGCAGGTCAGCCTGATCGCCGAGCTGGTGGACGCCTACGGCCAACTGCGCGGCGCGCAACTGCGCGAGAAGATTGCCCTGAGCAACCTGGAGAACCAGAAGGAGTCGCGCCAGCTCACCGAGCAACTGCGCGACGCCGGGGTCGGTGCCGAACTCGACGTACTGCGCGCCGATGCGCGCCTGGCGGCCACCGCCGCCAGCGTGCCGCAACTGCAGGCGGAAGCCGAGCGCGCCAGGCACCGTATCGCCACCCTCCTCGGCCAACGGCCGGAAGAGTTGACAGTGGACCTTTCGCCGCGCGACCTGCCGGCGATCACCAAGGCCCTGCCGATCGGCGATCCCGGCGAACTGCTGCGCCGCCGGCCGGACATCCGCGCCGCCGAACGGCGCCTGGCCGCCAGCACCGCCGACGTCGGCGTGGCCACCGCCGACCTGTTCCCGCGGGTCAGCCTCAGCGGCTTCCTCGGCTTCACCGCCGGGCGGGGCTCGCAGATCGGCTCAAGCGCCGCCCGCGCCTGGAGCGTCGGCCCGAGCATCAGTTGGGCCGCCTTCGACCTCGGCAGCGTGCGTGCCCGCCTGCGCGGCGCCAAGGCCGACGCCGACGCCGCGCTGGCCAGCTACGAACAGCAGGTGCTGCTGGCCCTGGAAGAATCGGCGAATGCCTTCAGCGACTATGGCAAGCGCCAGGAGCGCCTGGTCTCGCTGGTCCGCCAGTCGGAAGCCAGCCGCGCCGCCGCGCAACAGGCGGCGATCCGCTACCGCGAAGGCACCACCGATTTCCTGGTGCTGCTGGACGCCGAACGCGAGCAACTCTCCGCCGAAGATGCCCAGGCCCAGGCCGAGGTCGAGCTGTACCGCGGCATCGTGGCGATCTACCGCTCCCTCGGCGGTGGCTGGCAACCCAGCGCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36804","NCBI_taxonomy_name":"Pseudomonas aeruginosa PAO1","NCBI_taxonomy_id":"208964"}}}},"ARO_accession":"3000805","ARO_id":"37185","ARO_name":"OprN","CARD_short_name":"OprN","ARO_description":"OprN is the outer membrane channel component of the MexEF-OprN multidrug efflux complex.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"250":{"model_id":"250","model_name":"Rhodococcus fascians cmr","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"663":{"protein_sequence":{"accession":"CAA78046.1","sequence":"MPFAIYVLGIAVFAQGTSEFMLSGLIPDMAQDLQVSVPTAGLLTSAFAIGMIIGAPLMAIVSMRWQRRRALLTFLITFMVVHVIGALTDSFGVLLVTRIVGALANAGFLAVALGAAMSMVPADMKGRATSVLLGGVTIACVVGVPGGALLGELWGWRASFWEVVLISAPAVAAIMASTPADSPTDSVPNATRELSSLRQRKLQLILVLGALINGATFCSFTYLAPTLTDVAGFDSRWIPLLLGLFGLGSFIGVSVGGRLADTRPFQLLVAGSAALLVGWIVFAITASHPVVTLVMLFVQGTLSFAVGSTLISRVLYVADGAPTLGGSFATAAFNVGAALGPALGGVAIGIGMGYRAPLWTSAALVALAIVIGAATWTRWREPRPALDTVPP"},"dna_sequence":{"accession":"Z12001.1","fmin":"992","fmax":"2168","strand":"+","sequence":"GTGCCATTCGCCATCTATGTCCTGGGTATTGCTGTATTCGCCCAGGGCACATCGGAATTCATGCTGTCCGGACTCATACCGGATATGGCTCAGGATCTACAGGTTTCGGTCCCCACTGCAGGACTTCTCACTTCGGCATTCGCAATCGGCATGATCATCGGTGCCCCGTTGATGGCAATTGTCAGTATGCGGTGGCAACGTCGACGAGCGCTCTTGACCTTCCTCATCACTTTTATGGTTGTGCATGTCATCGGCGCACTCACCGACAGTTTCGGCGTCTTGCTGGTCACCCGGATCGTAGGAGCACTGGCCAACGCCGGTTTCCTGGCTGTAGCGCTGGGCGCAGCCATGTCGATGGTTCCTGCCGACATGAAGGGACGAGCGACCTCAGTTCTACTGGGCGGAGTGACCATCGCCTGCGTAGTTGGAGTCCCGGGCGGAGCGCTATTGGGCGAACTGTGGGGATGGCGCGCCTCGTTCTGGGAGGTAGTGCTGATTTCCGCACCGGCAGTGGCAGCGATCATGGCATCGACCCCTGCTGATTCCCCTACAGATTCTGTTCCGAACGCGACCCGCGAACTGTCCTCGCTGCGTCAACGCAAACTTCAACTGATCTTGGTGCTGGGCGCGCTGATCAACGGTGCCACCTTCTGTTCCTTCACCTACCTGGCTCCGACGCTCACCGACGTCGCCGGGTTCGACTCTCGCTGGATCCCTTTGCTTCTCGGACTGTTCGGACTGGGGTCGTTCATCGGCGTCAGTGTCGGTGGCCGGCTCGCTGACACCCGTCCGTTTCAATTGCTGGTGGCGGGCTCGGCAGCTCTTCTGGTCGGGTGGATCGTGTTCGCTATCACTGCCTCTCACCCGGTAGTGACCCTGGTGATGCTGTTCGTGCAAGGAACGCTGTCGTTCGCTGTGGGGTCGACGTTGATCTCGCGAGTGCTCTACGTCGCCGACGGTGCTCCGACTTTGGGGGGATCCTTCGCTACGGCTGCCTTCAATGTCGGAGCCGCATTGGGGCCGGCCCTCGGCGGTGTGGCCATCGGTATCGGAATGGGCTATCGCGCTCCACTGTGGACCAGCGCGGCTCTGGTGGCACTTGCGATCGTGATCGGTGCCGCGACGTGGACGCGTTGGCGGGAACCACGTCCAGCGCTGGACACCGTTCCTCCGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39552","NCBI_taxonomy_name":"Rhodococcus fascians","NCBI_taxonomy_id":"1828"}}}},"ARO_accession":"3002701","ARO_id":"39135","ARO_name":"Rhodococcus fascians cmr","CARD_short_name":"Rfas_cmr","ARO_description":"cmr is a plasmid-encoded chloramphenicol exporter that is found in Rhodococcus fascians and Corynebacterium glutamicum.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"326":{"model_id":"326","model_name":"OXA-225","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1837":{"protein_sequence":{"accession":"AEP43731.1","sequence":"MNKYFTCYVVASLFLSGCTVQHNLINETPSQIVQGHNQVIHQYFDEKNTSGVLVIQTDKKINLYGNALSRANTEYVPASTFKMLNALIGLENQKTDINEIFKWKGEKRSFTAWEKDMTLGEAMKLSAVPVYQELARRIGLDLMQKEVKRIGFGNAEIGQQVDNFWLVGPLKVTPIQEVEFVSQLAHTQLPFSEKVQANVKNMLLLEESNGYKIFGKTGWAMDIKSQVGWLTGWVEQPDGKIVAFALNMEMRSEMPASIRNELLMKSLKQLNII"},"dna_sequence":{"accession":"JN638887.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGAATAAATATTTTACTTGCTATGTGGTTGCTTCTCTTTTTCTTTCTGGTTGTACGGTTCAGCATAATTTAATAAATGAAACCCCGAGTCAGATTGTTCAAGGACATAATCAGGTGATTCATCAATACTTTGATGAAAAAAACACCTCAGGTGTGCTGGTTATTCAAACAGATAAAAAAATTAATCTATATGGTAATGCTCTAAGCCGCGCAAATACAGAATATGTGCCAGCCTCTACATTTAAAATGTTGAATGCCCTGATCGGATTGGAGAACCAGAAAACGGATATTAATGAAATATTTAAATGGAAGGGCGAGAAAAGGTCATTTACCGCTTGGGAAAAAGACATGACACTAGGAGAAGCCATGAAGCTTTCTGCAGTCCCAGTCTATCAGGAACTTGCGCGACGTATCGGTCTTGATCTCATGCAAAAAGAAGTAAAACGTATTGGTTTCGGTAATGCTGAAATTGGACAGCAGGTTGATAATTTCTGGTTGGTAGGACCATTAAAGGTTACGCCTATTCAAGAGGTAGAGTTTGTTTCCCAATTAGCACATACACAGCTTCCATTTAGTGAAAAAGTGCAGGCTAATGTAAAAAATATGCTTCTTTTAGAAGAGAGTAATGGCTACAAAATTTTTGGAAAGACTGGTTGGGCAATGGATATAAAATCACAAGTGGGCTGGTTGACCGGCTGGGTTGAGCAGCCAGATGGAAAAATTGTCGCTTTTGCATTAAATATGGAAATGCGGTCAGAAATGCCGGCATCTATACGTAATGAATTATTGATGAAATCATTAAAACAGCTGAATATTATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001493","ARO_id":"37893","ARO_name":"OXA-225","CARD_short_name":"OXA-225","ARO_description":"OXA-225 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46499":{"category_aro_accession":"3007710","category_aro_cvterm_id":"46499","category_aro_name":"OXA-23-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases, specifically imipenem, derived from OXA-23, first identified in Acinetobacter baumannii.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"327":{"model_id":"327","model_name":"GES-17","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"911":{"protein_sequence":{"accession":"ADZ48685.1","sequence":"MRFIHALLLAGIAHSAYASEKLTFKTDLEKLEREKAAQIGVAIVDPQGEIVAGHRMAQRFAMCSTFKFPLAALVFERIDSGTERGDRKLSYGPDMIVKWSPATERFLASGHMTVLEAAQAAVQLSDNGATNLLLREIGGPAAMTQYFRKIGDSVSRLDRKEPEMGDNTPGDLRDTTTPIAMARTVAKVLYGGALTSTSTHTIERWLIGNQTGDATLRAGFPKDWVVGEKTGTCANGARNDIGFFKAQERDYAVAVYTTAPKLSAVERDELVASVGQVITQLILSTDK"},"dna_sequence":{"accession":"HQ874631.1","fmin":"0","fmax":"864","strand":"+","sequence":"ATGCGCTTCATTCACGCACTATTACTGGCAGGGATCGCTCACTCTGCATATGCGTCGGAAAAATTAACCTTCAAGACCGATCTTGAGAAGCTAGAGCGCGAAAAAGCAGCTCAGATCGGTGTTGCGATCGTCGATCCCCAAGGAGAGATCGTCGCGGGCCACCGAATGGCGCAGCGTTTTGCAATGTGCTCAACGTTCAAGTTTCCGCTAGCCGCGCTGGTCTTTGAAAGAATTGACTCAGGCACCGAGCGGGGGGATCGAAAACTTTCATATGGGCCGGACATGATCGTCAAATGGTCTCCTGCCACGGAGCGGTTTCTAGCATCGGGACACATGACGGTTCTCGAGGCAGCGCAAGCTGCGGTGCAGCTTAGCGACAATGGGGCTACTAACCTCTTACTGAGAGAAATTGGCGGACCTGCTGCAATGACGCAGTATTTTCGTAAAATTGGCGACTCTGTGAGTCGGCTAGACCGGAAAGAGCCGGAGATGGGCGACAACACACCTGGCGACCTCAGAGATACAACTACGCCTATTGCTATGGCACGTACTGTGGCTAAAGTCCTCTATGGCGGCGCACTGACGTCCACCTCGACCCACACCATTGAGAGGTGGCTGATCGGAAACCAAACGGGAGACGCGACACTACGAGCGGGTTTTCCTAAAGATTGGGTTGTTGGAGAGAAAACTGGTACCTGCGCCAACGGGGCCCGGAACGACATTGGTTTTTTTAAAGCCCAGGAGAGAGATTACGCTGTAGCGGTGTATACAACGGCCCCGAAACTATCGGCCGTAGAACGTGACGAATTAGTTGCCTCTGTCGGTCAAGTTATTACACAACTCATCCTGAGCACGGACAAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002346","ARO_id":"38746","ARO_name":"GES-17","CARD_short_name":"GES-17","ARO_description":"GES-17 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36205":{"category_aro_accession":"3000066","category_aro_cvterm_id":"36205","category_aro_name":"GES beta-lactamase","category_aro_description":"GES beta-lactamases or Guiana extended-spectrum beta-lactamases are related to the other plasmid-located class A beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"222":{"model_id":"222","model_name":"JOHN-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1483":{"protein_sequence":{"accession":"AAK38324.1","sequence":"MRKLASIILFLAAVSNSLGQSKNSPLQISHLTGDFYVYRTFNDYKGTKISANAMYVVTDKGVVLFDAPWDKTQFQPLLDSIKAKHNKEVVMLFGTHSHEDRAGGFDFYKKKGIKTYSIKLTDDILKKNKEPRAEFIISNDTTFTVGNHTFEVYYPGKGHAPDNIVAWFKKEKILYGGCFVKSAEALDLGYLGDADVKEWQKSIKKVQAKFKKPDYIISGHDDWTSKESLNHTLKLVDEYLAQKSAGKK"},"dna_sequence":{"accession":"AY028464.1","fmin":"442","fmax":"1189","strand":"+","sequence":"ATGCGAAAATTAGCTTCGATAATTTTATTCTTAGCCGCGGTTTCAAATAGTTTGGGACAATCTAAGAATTCGCCATTACAAATAAGTCATCTTACAGGTGACTTTTATGTTTATAGAACTTTTAATGATTACAAAGGAACTAAGATTTCTGCCAATGCTATGTATGTTGTTACAGATAAAGGCGTTGTGCTTTTTGATGCGCCTTGGGATAAAACACAGTTTCAGCCGTTATTAGACAGCATAAAAGCAAAACACAATAAAGAGGTTGTGATGCTTTTTGGCACGCATTCTCATGAAGATCGTGCAGGAGGATTTGATTTTTACAAGAAAAAAGGAATCAAAACGTACTCAATTAAACTGACTGATGATATTCTTAAAAAGAATAAGGAACCAAGAGCAGAATTTATAATTTCAAATGATACAACATTTACTGTTGGAAATCATACTTTTGAAGTTTATTACCCAGGAAAAGGACATGCTCCTGATAATATTGTAGCATGGTTTAAAAAAGAGAAAATTCTTTACGGAGGCTGTTTTGTAAAAAGTGCAGAAGCATTAGATTTAGGTTATCTGGGTGATGCTGATGTTAAAGAATGGCAGAAATCTATAAAAAAAGTGCAGGCAAAATTCAAAAAACCGGATTATATAATTTCGGGACATGATGACTGGACTAGTAAAGAATCTTTAAATCATACTTTGAAATTGGTTGACGAGTATTTGGCTCAAAAATCTGCCGGAAAAAAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39076","NCBI_taxonomy_name":"Flavobacterium johnsoniae UW101","NCBI_taxonomy_id":"376686"}}}},"ARO_accession":"3000840","ARO_id":"37220","ARO_name":"JOHN-1","CARD_short_name":"JOHN-1","ARO_description":"JOHN-1 is an Ambler class B carbapenem-hydrolysing beta-lactamase from Flavobacterium johnsoniae.","ARO_category":{"41366":{"category_aro_accession":"3004202","category_aro_cvterm_id":"41366","category_aro_name":"JOHN beta-lactamase","category_aro_description":"JOHN beta-lactamases hydrolyse penicillins, narrow- and expanded-spectrum cephalosporins, and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"240":{"model_id":"240","model_name":"vanR gene in vanF cluster","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"202":{"protein_sequence":{"accession":"AAR84672.1","sequence":"MKNITILIADDDAEIADLVAIHLEKEGYRVIKVSDGQETIDVIQNQPIDLLILDIMMPKMDGFEVTRRIREKHNMPIIFLSAKTSDFDKVQGLVIGADDYMTKPFIPIELVARVNAQLRRFMKLNQPKTKQNSNLEFGGLTISPEQRTVTLYGKNIELTPKEFEILFLLASNPNKVYRAEDIFQKVWGDAYYEGGNTVMVHIRTLRKKLEEDKRKNKLIQTVWGVGYKFNG"},"dna_sequence":{"accession":"AF155139.1","fmin":"1511","fmax":"2207","strand":"+","sequence":"ATGAAAAATATAACAATATTAATAGCTGATGATGATGCTGAAATTGCTGATTTGGTTGCTATACATTTAGAGAAAGAAGGGTATCGTGTCATTAAGGTATCGGATGGGCAAGAAACCATTGATGTTATCCAGAACCAACCCATTGATTTACTGATTTTGGATATTATGATGCCGAAAATGGATGGATTTGAAGTGACACGTCGCATTCGCGAAAAACATAATATGCCCATTATTTTTTTGAGCGCTAAAACGTCTGATTTTGATAAAGTGCAGGGACTCGTGATTGGAGCAGACGATTATATGACGAAACCATTTATACCCATTGAATTGGTAGCTCGGGTAAATGCACAGCTGCGACGCTTTATGAAGTTGAATCAACCTAAAACCAAACAGAACTCAAACTTGGAATTTGGAGGATTAACGATTTCTCCTGAACAACGTACAGTTACTCTATATGGTAAGAATATTGAGTTAACACCGAAAGAGTTTGAAATTTTATTTTTATTAGCCAGTAATCCAAATAAAGTTTATCGTGCAGAAGATATTTTTCAGAAGGTATGGGGGGATGCATACTATGAAGGTGGGAATACCGTTATGGTTCATATTCGTACTTTGCGGAAAAAACTTGAAGAGGATAAACGAAAAAACAAATTGATACAAACTGTATGGGGGGTAGGTTATAAATTCAATGGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39542","NCBI_taxonomy_name":"Paenibacillus popilliae ATCC 14706","NCBI_taxonomy_id":"1212764"}}}},"ARO_accession":"3002925","ARO_id":"39359","ARO_name":"vanR gene in vanF cluster","CARD_short_name":"vanR_in_vanF_cl","ARO_description":"Also known as vanRF, is a vanR variant found in the vanF gene cluster.","ARO_category":{"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"36713":{"category_aro_accession":"3000574","category_aro_cvterm_id":"36713","category_aro_name":"vanR","category_aro_description":"VanR is a OmpR-family transcriptional activator in the VanSR regulatory system. When activated by VanS, it promotes cotranscription of VanA, VanH, and VanX.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"299":{"model_id":"299","model_name":"CepS","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"725"}},"model_sequences":{"sequence":{"3286":{"protein_sequence":{"accession":"CAA56561.1","sequence":"MKQTRALPLLALGTLLLAPLSLAAPVDPLKAVVDDAIRPVLKQHRIPGMAVAVLKGGQAHYFNYGLADVATGAKVNEQTLFEIGSVSKTYTATLGAYAVVKGGFKLDDQVSGHAPWLKGSAFDGITMAELATYSAGGLPLQFPDEVDSSDTMRAYYRHWTPPYQAGTQRQYSNPSIGLFGHLAASSLQQPFSTLMEQTLLPALGLEHTYLQVPEAAMARYAFGYSKEDKPIRVNPGMLADEAYGIKTGSADLLAFVKANISGVDDKALQQAIALTHTGFYRIGEMSQGLGWESYAYPVSEQTLLAGNSPAVSLKANPVTKFETPAAPGAMRLYNKTGSTGGFGAYVAFVPAKGIGIVMLANRNYPIEARVSAAHAILSQLAP"},"dna_sequence":{"accession":"X80277.1","fmin":"0","fmax":"1149","strand":"+","sequence":"ATGAAACAGACCAGAGCCCTGCCACTGCTGGCCCTCGGCACCCTGCTGCTTGCCCCGCTCTCCCTGGCGGCCCCCGTCGATCCGCTGAAGGCGGTGGTGGATGACGCCATCCGCCCCGTGCTCAAGCAGCACAGGATCCCGGGCATGGCGGTCGCCGTGCTGAAGGGGGGGCAGGCCCACTACTTCAACTACGGGCTGGCCGATGTGGCGACCGGGGCCAAGGTCAATGAGCAGACCCTGTTCGAGATTGGCTCGGTCAGCAAGACCTATACCGCCACCCTTGGCGCCTACGCCGTGGTCAAGGGGGGCTTCAAGCTCGATGACCAGGTGAGCGGGCACGCACCCTGGCTCAAGGGCTCCGCCTTCGATGGCATCACCATGGCGGAACTTGCCACCTACAGTGCCGGGGGGCTGCCGCTGCAATTCCCCGACGAGGTTGATTCGAGCGATACCATGCGGGCCTATTACCGGCACTGGACGCCGCCATATCAGGCGGGAACCCAGCGCCAATACTCCAATCCCAGCATCGGCCTGTTCGGCCATCTGGCGGCGAGCAGCCTGCAGCAGCCGTTTTCCACGTTGATGGAGCAGACCCTGCTGCCAGCACTCGGGTTGGAGCACACCTATCTGCAGGTGCCCGAGGCCGCCATGGCTCGCTACGCCTTCGGCTACTCGAAGGAGGACAAACCCATCAGGGTCAACCCTGGCATGCTGGCCGACGAGGCCTACGGCATCAAGACCGGCTCGGCGGATCTGCTCGCCTTCGTGAAGGCCAATATCAGCGGGGTTGATGACAAGGCGTTGCAACAGGCGATCGCCCTGACCCACACCGGTTTTTATCGGATAGGGGAGATGAGCCAGGGGCTGGGCTGGGAGAGCTACGCCTACCCGGTCAGCGAGCAGACGCTGCTGGCGGGCAACTCCCCGGCGGTGAGCCTCAAGGCCAATCCGGTCACTAAGTTCGAGACGCCAGCCGCGCCCGGGGCTATGCGCCTCTACAACAAGACCGGGTCGACCGGTGGCTTCGGCGCCTACGTGGCCTTCGTGCCCGCCAAAGGGATCGGCATCGTCATGCTGGCCAATCGCAATTATCCCATCGAGGCCAGAGTCAGCGCGGCCCATGCCATTTTGAGCCAGCTGGCACCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36957","NCBI_taxonomy_name":"Aeromonas sobria","NCBI_taxonomy_id":"646"}}}},"ARO_accession":"3003553","ARO_id":"40156","ARO_name":"CepS","CARD_short_name":"CepS","ARO_description":"CEPS is a typical class C cephalosporinase found in Aeromonas sobria, first isolated from strain 163a.","ARO_category":{"41363":{"category_aro_accession":"3004199","category_aro_cvterm_id":"41363","category_aro_name":"CepS beta-lactamase","category_aro_description":"CepS beta-lactamases are Class C beta-lactamases capable of hydrolyzing cephalosporin.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"322":{"model_id":"322","model_name":"FEZ-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"789":{"protein_sequence":{"accession":"CAB96921.1","sequence":"MKKVLSLTALMMVLNHSSFAYPMPNPFPPFRIAGNLYYVGTDDLASYLIVTPRGNILINSDLEANVPMIKASIKKLGFKFSDTKILLISHAHFDHAAGSELIKQQTKAKYMVMDEDVSVILSGGKSDFHYANDSSTYFTQSTVDKVLHDGERVELGGTVLTAHLTPGHTRGCTTWTMKLKDHGKQYQAVIIGSIGVNPGYKLVDNITYPKIAEDYKHSIKVLESMRCDIFLGSHAGMFDLKNKYVLLQKGQNNPFVDPTGCKNYIEQKANDFYTELKKQETA"},"dna_sequence":{"accession":"Y17896.1","fmin":"0","fmax":"849","strand":"+","sequence":"ATGAAAAAAGTATTAAGTTTAACCGCATTGATGATGGTATTGAACCATTCAAGCTTCGCATATCCAATGCCAAATCCTTTTCCCCCATTCCGTATTGCTGGAAACTTGTACTATGTAGGCACTGATGATCTCGCAAGCTACCTGATTGTCACACCGAGAGGGAACATTTTGATCAATAGTGATCTTGAGGCTAATGTTCCCATGATTAAAGCAAGTATAAAAAAACTAGGTTTTAAATTCAGTGATACTAAAATTTTGCTGATTAGCCATGCTCATTTTGATCATGCGGCCGGTAGCGAATTAATTAAGCAACAAACAAAAGCAAAATATATGGTTATGGACGAGGATGTTTCGGTGATCCTGTCTGGCGGTAAATCTGATTTTCATTATGCTAATGATTCCAGTACTTATTTTACTCAGAGTACTGTGGATAAGGTTCTTCACGACGGAGAACGGGTGGAATTAGGAGGGACCGTATTAACTGCTCATTTGACTCCTGGACACACTAGAGGCTGTACCACCTGGACAATGAAACTAAAAGATCACGGCAAGCAATATCAGGCCGTAATTATAGGAAGTATTGGCGTAAATCCTGGGTATAAATTGGTTGATAATATAACTTATCCAAAAATTGCCGAAGATTATAAGCACTCCATAAAGGTACTTGAGTCAATGCGTTGCGATATTTTTCTAGGATCGCATGCCGGAATGTTTGATCTGAAGAATAAATATGTACTATTACAAAAAGGTCAAAACAATCCCTTTGTTGATCCCACAGGCTGTAAAAATTATATTGAACAAAAGGCAAACGATTTTTACACAGAACTTAAGAAGCAAGAAACTGCCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36922","NCBI_taxonomy_name":"Fluoribacter gormanii","NCBI_taxonomy_id":"464"}}}},"ARO_accession":"3000606","ARO_id":"36745","ARO_name":"FEZ-1","CARD_short_name":"FEZ-1","ARO_description":"FEZ-1 is an Ambler class B MBL; subclass B3 first isolated from Legionella gormanii.  It has activity against a broad range of beta-lactams and is only active with two Zn(II) ions in the active site.","ARO_category":{"41375":{"category_aro_accession":"3004211","category_aro_cvterm_id":"41375","category_aro_name":"FEZ beta-lactamase","category_aro_description":"The FEZ family of beta-lactamases are subclass B3 beta-lactamases that hydrolyze penicillins, cephalosporins, and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"329":{"model_id":"329","model_name":"CTX-M-159","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6063":{"protein_sequence":{"accession":"BAP18874.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAKLSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGGYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"AB976602.1","fmin":"135","fmax":"1011","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAAAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGGCTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3003167","ARO_id":"39744","ARO_name":"CTX-M-159","CARD_short_name":"CTX-M-159","ARO_description":"CTX-M-159 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"330":{"model_id":"330","model_name":"IMP-26","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"773":{"protein_sequence":{"accession":"ACY01749.1","sequence":"MSKLSVFFIFLFCSIATAAEPLPDLKIEKLDEGVYVHTSFEEVNGWGVFPKHGLVVLVDAEAYLIDTPFTAKDTEKLVTWFVERGYKIKGSISSHFHSDSTGGIEWLNSQSIPTYASELTNELLKKDGKVQAKNSFGGVNYWLVKNKIEVFYPGPGHTPDNLVVWLPERKILFGGCFIKPYGLGNLGDANLEAWPKSAKLLISKYGKAKLVVPSHSEAGDASLLKLTLEQAVKGLNESKKPSKLSN"},"dna_sequence":{"accession":"GU045307.1","fmin":"100","fmax":"841","strand":"+","sequence":"ATGAGCAAGTTATCTGTATTCTTTATATTTTTGTTTTGTAGCATTGCTACCGCAGCAGAGCCTTTGCCAGATTTAAAAATTGAAAAACTTGATGAAGGCGTTTATGTTCATACTTCGTTTGAAGAAGTTAACGGGTGGGGCGTTTTTCCTAAACATGGTTTGGTTGTTCTTGTAGATGCTGAAGCTTATCTAATTGACACTCCATTTACGGCTAAAGATACTGAAAAGTTAGTCACTTGGTTTGTGGAACGTGGCTATAAAATAAAAGGCAGTATTTCCTCTCATTTTCATAGTGACAGCACGGGCGGAATAGAGTGGCTTAATTCTCAATCCATCCCCACGTATGCGTCTGAATTAACTAATGAGCTGCTTAAAAAAGACGGTAAGGTTCAAGCTAAAAATTCATTTGGCGGGGTTAACTATTGGCTAGTTAAAAATAAAATTGAAGTTTTTTATCCAGGCCCAGGACACACTCCAGATAACCTAGTAGTTTGGCTGCCTGAAAGGAAAATATTATTCGGTGGTTGTTTTATTAAACCGTACGGTCTAGGTAATTTGGGTGACGCAAATTTAGAAGCTTGGCCAAAGTCCGCTAAATTATTAATATCCAAATATGGTAAGGCAAAACTGGTTGTTCCAAGTCACAGTGAAGCTGGAGACGCATCACTCTTGAAACTTACATTAGAGCAGGCGGTTAAAGGGTTAAACGAAAGTAAAAAACCATCAAAACTAAGCAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002217","ARO_id":"38617","ARO_name":"IMP-26","CARD_short_name":"IMP-26","ARO_description":"IMP-26 is a beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"331":{"model_id":"331","model_name":"TEM-166","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"846":{"protein_sequence":{"accession":"ACI25375.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVGELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"FJ197316.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAGGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001032","ARO_id":"37412","ARO_name":"TEM-166","CARD_short_name":"TEM-166","ARO_description":"TEM-166 is a beta-lactamase found in E. coli.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"253":{"model_id":"253","model_name":"vanXY gene in vanG cluster","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"125"}},"model_sequences":{"sequence":{"123":{"protein_sequence":{"accession":"ABA71732.1","sequence":"MMKTIELEKEEIYCGNLLLVNKNYPLRDNNVKGLVPADIRFPNILMKRDVANVLQLIFEKISAGNSIVPVSGYRSLEEQTAIYDGSLKDNGEDFTRKYVALPNHSEHQTGLAIDLGLNKKDIDFIRPDFPYDGICDEFRRAAPDYGFTQRYARDKEEITGISHEPWHFRYVGYPHSKIMQENGFSLEEYTQFIKAYLEDNKYLFEQAHRAEIEIYYVPAKDDKTLIKIPENCVYQISGNNIDGFVVTIWRKTDD"},"dna_sequence":{"accession":"DQ212986.1","fmin":"7030","fmax":"7795","strand":"+","sequence":"ATGATGAAAACGATTGAGCTTGAAAAGGAAGAAATTTATTGTGGAAATTTGCTGCTCGTCAACAAAAATTATCCGCTACGAGATAACAATGTAAAGGGTTTAGTTCCTGCTGATATACGCTTTCCAAATATTCTTATGAAGCGTGATGTGGCAAATGTTTTGCAGCTTATTTTTGAAAAAATCTCGGCAGGTAACTCTATCGTTCCTGTAAGCGGTTATCGCTCATTAGAAGAACAGACAGCCATATATGACGGCTCTCTCAAAGATAATGGAGAGGATTTTACAAGAAAATATGTTGCTCTGCCCAATCATAGTGAACATCAAACAGGTCTTGCCATTGATTTAGGACTGAATAAAAAGGATATAGACTTTATCCGTCCCGATTTTCCCTATGACGGTATTTGCGATGAATTTAGGAGAGCTGCCCCAGACTATGGCTTTACCCAGCGTTATGCAAGGGATAAAGAAGAAATAACAGGGATTTCACACGAGCCGTGGCATTTTCGATATGTAGGATACCCACACTCAAAAATTATGCAGGAAAATGGTTTTTCACTTGAAGAATACACACAATTTATAAAAGCCTATCTGGAAGATAACAAATATCTTTTTGAGCAGGCTCACAGAGCTGAGATTGAAATATATTATGTTCCTGCAAAAGACGACAAAACGCTGATAAAAATACCAGAAAATTGTGTTTATCAGATTTCTGGTAATAACATAGACGGTTTTGTTGTGACCATATGGAGGAAAACAGATGACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35918","NCBI_taxonomy_name":"Enterococcus faecalis","NCBI_taxonomy_id":"1351"}}}},"ARO_accession":"3003069","ARO_id":"39549","ARO_name":"vanXY gene in vanG cluster","CARD_short_name":"vanXY_in_vanG","ARO_description":"Also known as vanXYG, is a vanXY variant found in the vanG gene cluster.","ARO_category":{"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"36635":{"category_aro_accession":"3000496","category_aro_cvterm_id":"36635","category_aro_name":"vanXY","category_aro_description":"VanXY is a protein with both D,D-carboxypeptidase and D,D-dipeptidase activity, found in Enterococcus gallinarum. It cleaves and removes the terminal D-Ala of peptidoglycan subunits for the incorporation of D-Ser by VanC. D-Ala-D-Ser has low binding affinity with vancomycin.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"333":{"model_id":"333","model_name":"CARB-23","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1420":{"protein_sequence":{"accession":"AHJ02283.1","sequence":"MVRVFTRYSLLNIAKVRIKTKERRTPRMKKLFLLVGLMVCSTVSYASKLNLNEDISLIEKQTSGRIGVSVWDTQTDERWDYRGDERFPLMSTFKTLACATMLSDMDSGKLNKNATAKIDERNIVVWSPVMDKLAGQSTRIEHACEAAMLMSDNTAANLVLNEIGGPKAVTLFLRSIGDKATRLDRLEPRLNEAKPGDKRDTTTPNAMVNTLHTLMEDNALSYESRTQLKIWMQDNKVSDSLMRSVLPKGWSIADRSGAGNYGSRGISAMIWKDNYKPVYISIYVTDTDLSLQARDQLIAQISQLILEHYKES"},"dna_sequence":{"accession":"CP007005.1","fmin":"1250264","fmax":"1251203","strand":"+","sequence":"GTGGTTAGAGTATTCACTCGTTATAGTTTGCTTAACATCGCCAAAGTGCGAATCAAAACCAAAGAACGAAGAACACCACGCATGAAAAAGTTATTCCTGTTGGTTGGGCTGATGGTTTGCTCAACTGTTAGTTACGCCTCCAAATTAAATTTAAATGAAGACATCTCCCTCATCGAGAAACAAACATCTGGGCGAATTGGAGTGTCAGTCTGGGATACACAAACGGACGAGCGTTGGGATTATCGCGGAGACGAACGTTTCCCATTAATGAGCACATTTAAAACGTTAGCGTGTGCCACCATGCTAAGCGACATGGACAGCGGCAAACTCAACAAAAATGCCACAGCGAAAATCGATGAACGCAATATTGTGGTTTGGTCTCCGGTGATGGATAAACTGGCTGGACAAAGTACACGTATCGAACACGCTTGTGAGGCCGCCATGTTGATGAGCGACAACACCGCCGCGAACTTAGTGCTAAATGAAATTGGTGGTCCTAAAGCGGTCACACTGTTTTTGCGCTCTATTGGCGACAAAGCAACGCGACTTGACCGATTGGAGCCCCGTTTGAATGAAGCAAAACCGGGCGACAAGCGAGACACCACAACGCCTAACGCCATGGTAAACACCCTACACACCTTGATGGAAGATAACGCCCTATCTTACGAGTCACGCACACAGCTGAAAATCTGGATGCAAGACAACAAAGTATCGGATTCTCTCATGCGCTCTGTTCTGCCAAAAGGCTGGTCGATTGCAGACCGCTCTGGCGCAGGTAACTACGGTTCACGCGGCATTAGCGCGATGATTTGGAAAGACAACTACAAGCCGGTTTACATCAGTATTTACGTCACAGACACTGACCTTTCGCTTCAAGCTCGCGATCAACTGATCGCGCAAATCAGCCAACTGATTTTAGAGCACTACAAAGAAAGTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39777","NCBI_taxonomy_name":"Vibrio parahaemolyticus UCM-V493","NCBI_taxonomy_id":"1429044"}}}},"ARO_accession":"3003186","ARO_id":"39763","ARO_name":"CARB-23","CARD_short_name":"CARB-23","ARO_description":"CARB-23 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36230":{"category_aro_accession":"3000091","category_aro_cvterm_id":"36230","category_aro_name":"CARB beta-lactamase","category_aro_description":"CARB beta-lactamases are class A lactamases that can hydrolyze carbenicillin. Many of the PSE beta-lactamases have been renamed as CARB-lactamases with the notable exception of PSE-2 which is now OXA-10.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"334":{"model_id":"334","model_name":"mexX","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"730"}},"model_sequences":{"sequence":{"244":{"protein_sequence":{"accession":"BAA34299.1","sequence":"MDRLAARLLAALVALFLLGCEEAADAGKTAEAPAEVGVIVARPAPIGITSELPGRLEAYRQAEVRARVAGIVTRRLYEEGQDVRAGTVLFQIDPAPLKAALDISRGALPGRGQPRAAADKLKAYADLIKDRAISEREYTEAQTDARQALAQIASAKAELEQARLRLGYATVTAPIDGRARRALVTEGALVGEDSPTPLTRVEQIDPIYVNFSQPAAKSRHAAGDPRRPGEGCRRQGHRRAPGPGRRQRVPLAGELLFIDLAVDPGTDTIAMRALFRNPHRELLPGGYVQVRLQRAVNPQAITVPDALIRTAQSAVVKVVNPKGLVEDVEVRADTLQGRDWIISRGLKGGEWVIVENAAQHAAGSSVQAVVRQPASADAPSPLAASPAGQ"},"dna_sequence":{"accession":"AB015853.1","fmin":"145","fmax":"1315","strand":"+","sequence":"ATGGACCGGCTCGCTGCGCGGCTGCTGGCGGCCCTGGTCGCCCTATTCCTGCTGGGCTGCGAAGAAGCAGCGGACGCCGGGAAGACTGCGGAGGCCCCCGCCGAGGTCGGCGTGATCGTCGCCAGGCCGGCGCCTATCGGCATCACCAGCGAGCTGCCCGGACGCCTGGAAGCGTACCGCCAGGCTGAAGTGCGGGCGCGCGTCGCCGGCATCGTCACCCGTCGCCTGTACGAGGAAGGCCAGGACGTCCGCGCCGGCACCGTGCTGTTCCAGATCGACCCTGCGCCCTTGAAGGCGGCCCTGGACATCAGCCGCGGCGCCCTGCCCGGCCGAGGCCAGCCACGCGCGGCGGCCGACAAGCTCAAGGCGTACGCCGACCTGATCAAGGACCGCGCCATCAGCGAACGCGAGTACACCGAAGCGCAGACCGACGCGCGCCAGGCCCTGGCGCAGATCGCCTCGGCCAAGGCCGAACTGGAGCAGGCCCGCCTGCGCCTGGGCTACGCCACGGTCACCGCGCCGATCGACGGCCGCGCGCGGCGTGCGCTGGTCACCGAAGGCGCGCTGGTCGGCGAGGACTCGCCGACACCGCTGACCCGCGTCGAGCAGATCGATCCGATCTACGTGAACTTCTCCCAGCCGGCCGCGAAGTCGCGCCATGCAGCGGGCGATCCGCGAAGGCCAGGTGAAGGGTGTCGCCGACAAGGACATCGCCGTGCGCCTGGTCCTGGCCGACGGCAGCGAGTACCGCTGGCCGGCGAGCTGCTGTTCATCGACCTGGCGGTCGACCCCGGCACCGACACCATCGCCATGCGTGCCCTGTTCCGCAATCCGCATCGCGAATTGCTGCCCGGCGGCTACGTGCAGGTGCGCCTGCAGCGCGCGGTGAACCCGCAGGCGATCACCGTCCCGGACGCGCTGATCCGTACCGCCCAGTCCGCCGTGGTCAAGGTGGTCAACCCAAAGGGCTTGGTGGAAGACGTGGAGGTCCGCGCCGACACCCTGCAGGGCCGCGACTGGATCATCAGCCGCGGGCTCAAGGGCGGCGAGTGGGTGATCGTCGAGAACGCCGCCCAGCATGCCGCCGGCTCCAGCGTCCAGGCGGTGGTCCGCCAGCCGGCCAGCGCCGACGCCCCCTCACCGCTGGCCGCCTCGCCGGCGGGCCAGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36804","NCBI_taxonomy_name":"Pseudomonas aeruginosa PAO1","NCBI_taxonomy_id":"208964"}}}},"ARO_accession":"3003034","ARO_id":"39468","ARO_name":"mexX","CARD_short_name":"mexX","ARO_description":"MexX is the membrane fusion protein of the MexXY-OprM multidrug efflux complex.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35963":{"category_aro_accession":"0000045","category_aro_cvterm_id":"35963","category_aro_name":"acriflavine","category_aro_description":"Acriflavine is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35990":{"category_aro_accession":"0000073","category_aro_cvterm_id":"35990","category_aro_name":"meropenem","category_aro_description":"Meropenem is an ultra-broad spectrum injectable antibiotic used to treat a wide variety of infections, including meningitis and pneumonia. It is a beta-lactam and belongs to the subgroup of carbapenem, similar to imipenem and ertapenem.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37007":{"category_aro_accession":"3000663","category_aro_cvterm_id":"37007","category_aro_name":"ofloxacin","category_aro_description":"Ofloxacin is a 6-fluoro, 7-piperazinyl quinolone with a methyl-substituted oxazine ring. It has a broad spectrum of activity including many enterobacteria and mycoplasma but most anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"46133":{"category_aro_accession":"3007382","category_aro_cvterm_id":"46133","category_aro_name":"gentamicin","category_aro_description":"Gentamicin is a commonly used aminoglycoside antibiotic derived from members of the Micromonospora genus of bacteria. It acts by binding the 30S ribosomal subunit, thus inhibiting protein synthesis. Gentamicin is typically used to treat Gram-negative infections of the repiratory and urinary tract, as well as infections of the bone and soft tissue. It also exhibits considerable nephrotoxicity and ototoxicity. Gentamicin is administered as a mixture of gentamicin type C (which makes about around 80% of the complex) and types A, B, and X (distributed in the remaining 20% of the complex).","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"43746":{"category_aro_accession":"3005386","category_aro_cvterm_id":"43746","category_aro_name":"disinfecting agents and antiseptics","category_aro_description":"Disinfectants that can also interact with antimicrobial resistance mechanisms, e.g. molecule efflux, and thus are the targets of disinfectant resistance.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"337":{"model_id":"337","model_name":"adeC","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"850"}},"model_sequences":{"sequence":{"3839":{"protein_sequence":{"accession":"ALX99516.1","sequence":"MSKSTIVSRGLILSTLSIALVACVNMQAPQPAITSHIPQNFSQNHSGKMIAEKSYKEFISDPKLLQVIEISLNNNRDLRTATLNIERVQQEYQITKNSQLPTIGVTGNAVRQVSPSINPNNPVSTFQVGLGMTAYELDFWGRVQNLKDAALNNYLATQSAKEAVQIGLISNITQVWLNYAFAQANLNLAEQTLKAQVDAYNLNKKRFDVGIDSEVPLKQAQISVETARNDVATYKTQIQQAKNLLDLLAGHPVPQNLLPDHAIQNITFEKNFAAGLPSDLLNHRPDLKAAEYELRVAGANIGAAKARMFPTISLTGSTGYASSELKDLFKTGNFAWSIGPNIDLPIFDWGTRKTNIKIAETDQKIALAKYEKAIQSAFREVNDALATHAHIGERLDAQRRLVSATAATYKLSMARYKAGVDSYFTVLDAQRSAYAAQQGLLALEQIKLNNQIEIYKVLGGGISKV"},"dna_sequence":{"accession":"CP013924.1","fmin":"2063742","fmax":"2065140","strand":"+","sequence":"ATGTCTAAATCGACAATCGTATCTCGTGGACTCATTCTTTCTACACTCTCAATTGCACTCGTTGCATGTGTCAATATGCAAGCGCCACAGCCTGCAATTACATCTCATATTCCTCAAAATTTTAGTCAAAATCATTCTGGAAAAATGATTGCAGAAAAAAGTTATAAAGAATTTATTTCTGATCCGAAATTATTACAGGTCATTGAAATCAGTTTAAATAACAACCGTGATTTACGGACTGCTACGCTTAATATTGAACGTGTACAGCAAGAATACCAAATCACAAAAAATAGCCAGCTCCCAACCATTGGTGTAACGGGAAATGCAGTGCGGCAGGTTAGCCCATCGATTAACCCCAATAACCCAGTTTCTACATTTCAAGTTGGCTTGGGAATGACTGCCTATGAGCTAGATTTTTGGGGCCGTGTTCAAAATTTAAAAGATGCTGCATTAAATAACTATCTTGCAACTCAAAGTGCAAAAGAAGCTGTACAAATTGGTTTAATCAGTAATATTACACAGGTCTGGTTAAATTATGCTTTTGCACAAGCAAATTTAAACCTTGCCGAGCAAACCTTAAAAGCACAAGTCGATGCTTATAACCTTAACAAGAAGCGCTTTGATGTTGGTATTGATAGTGAAGTGCCATTAAAACAAGCACAAATTTCGGTAGAGACTGCTCGAAATGATGTTGCAACTTATAAAACTCAAATTCAACAGGCAAAAAATTTACTGGATTTGTTAGCAGGTCATCCTGTTCCGCAAAATTTACTTCCGGATCATGCTATTCAAAATATTACCTTTGAGAAAAACTTTGCAGCCGGTTTACCAAGTGATTTATTAAATCATCGTCCAGACCTTAAAGCTGCCGAATATGAGTTACGTGTTGCAGGAGCAAATATTGGTGCTGCTAAAGCACGGATGTTCCCAACCATAAGCTTGACAGGCTCGACGGGTTATGCATCATCTGAACTGAAAGATTTATTTAAAACAGGCAATTTTGCATGGTCGATTGGACCTAATATCGATCTACCAATTTTTGATTGGGGAACAAGAAAAACTAATATTAAAATTGCGGAAACTGACCAGAAAATTGCTTTAGCTAAATATGAAAAAGCCATTCAATCAGCTTTTCGTGAAGTTAATGATGCACTTGCTACACATGCACATATTGGTGAACGATTAGACGCTCAGCGTCGCTTAGTCTCTGCGACTGCTGCAACCTATAAACTCTCAATGGCACGTTACAAAGCTGGAGTGGATAGTTATTTTACGGTTTTAGATGCTCAGCGTTCTGCTTATGCTGCACAACAAGGCTTACTTGCACTTGAACAAATAAAATTAAATAACCAAATTGAAATTTATAAAGTTTTAGGAGGAGGAATATCAAAAGTCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3003811","ARO_id":"40499","ARO_name":"adeC","CARD_short_name":"adeC","ARO_description":"AdeC is the outer membrane factor of the AdeABC multidrug efflux complex. It can be replaced by other outer membrane channels, and is not essential for antibiotic resistance.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"338":{"model_id":"338","model_name":"OXY-1-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"2016":{"protein_sequence":{"accession":"CAI43413.1","sequence":"MLKSSWRKTALMAAAAVPLLLASGSLWASADAIQQKLADLEKRSGGRLGVALINTADDSQTLYRGDERFAMCSTGKVMAAAAVLKQSESNPEVVNKRLEIKKSDLVVWSPITEKHLQSGMTLAELSAAALQYSDNTAMNKMISYLGGPEKVTAFAQSIGDVTFRLDRTEPALNSAIPGDKRDTTTPLAMAESLRKLTLGNALGEQQRAQLVTWLKGNTTGGQSIRAGLPASWVVGDKTGGGDYGTTNDIAVIWPENHAPLVLVTYFTQPQQDAKSRKEVLAAAAKIVTEGL"},"dna_sequence":{"accession":"AJ871865.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGTTGAAAAGTTCGTGGCGTAAAACCGCCCTGATGGCCGCCGCCGCCGTTCCGCTGCTGCTGGCGAGCGGTTCATTATGGGCCAGTGCCGATGCTATCCAGCAAAAGCTGGCTGATTTAGAAAAACGTTCCGGCGGTCGGCTGGGCGTAGCGCTGATTAACACGGCAGATGATTCGCAAACCCTCTATCGCGGCGATGAACGTTTTGCCATGTGCAGCACCGGTAAAGTGATGGCCGCCGCCGCGGTGTTAAAACAGAGCGAAAGCAATCCAGAGGTGGTGAATAAAAGGCTGGAGATTAAAAAATCGGATTTAGTGGTCTGGAGCCCGATCACCGAAAAACATCTGCAAAGCGGAATGACCCTGGCGGAACTCAGCGCGGCGGCGCTGCAGTACAGCGACAATACCGCGATGAATAAGATGATTAGCTACCTTGGCGGACCGGAAAAGGTGACCGCATTCGCCCAGAGTATCGGGGATGTCACTTTTCGTCTCGATCGTACGGAGCCGGCGCTGAACAGCGCGATTCCCGGCGATAAGCGCGATACCACCACCCCGTTGGCGATGGCCGAAAGCCTGCGCAAGCTGACGCTGGGCAATGCGCTGGGCGAACAGCAGCGCGCCCAGTTAGTAACGTGGCTAAAAGGCAATACCACCGGCGGGCAAAGCATTCGCGCAGGCCTGCCCGCAAGCTGGGTGGTCGGGGATAAAACCGGCGGCGGAGATTACGGCACCACCAACGATATCGCGGTGATCTGGCCCGAAAATCATGCCCCGCTGGTGCTGGTGACCTATTTTACCCAGCCGCAGCAGGATGCGAAAAGCCGCAAAGAGGTGTTAGCCGCGGCGGCAAAAATCGTCACCGAAGGGCTTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3002390","ARO_id":"38790","ARO_name":"OXY-1-2","CARD_short_name":"OXY-1-2","ARO_description":"OXY-1-2 is a beta-lactamase found in Klebsiella oxytoca.","ARO_category":{"38788":{"category_aro_accession":"3002388","category_aro_cvterm_id":"38788","category_aro_name":"OXY beta-lactamase","category_aro_description":"OXY beta-lactamases are chromosomal class A beta-lactamases that are found in Klebsiella oxytoca. At constitutive low levels, OXY beta-lactamases confer resistance to aminopenicillins and carboxypenicillins. At high induced levels,  OXY beta-lactamases confer resistance to penicillins, cephalosporins and aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3664":{"model_id":"3664","model_name":"NDM-23","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"5937":{"protein_sequence":{"accession":"AWU66462.1","sequence":"MELPNIMHPVAKLSTALAAALMLSGCMPGEIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQLLNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR"},"dna_sequence":{"accession":"MH450214.1","fmin":"0","fmax":"813","strand":"+","sequence":"ATGGAATTGCCCAATATTATGCACCCGGTCGCGAAGCTGAGCACCGCATTAGCCGCTGCATTGATGCTGAGCGGGTGCATGCCCGGTGAAATCCGCCCGACGATTGGCCAGCAAATGGAAACTGGCGACCAACGGTTTGGCGATCTGGTTTTCCGCCAGCTCGCACCGAATGTCTGGCAGCACACTTCCTATCTCGACATGCCGGGTTTCGGGGCAGTCGCTTCCAACGGTTTGATCGTCAGGGATGGCGGCCGCGTGCTGGTGGTCGATACCGCCTGGACCGATGACCAGACCGCCCAGCTCCTCAACTGGATCAAGCAGGAGATCAACCTGCCGGTCGCGCTGGCGGTGGTGACTCACGCGCATCAGGACAAGATGGGCGGTATGGACGCGCTGCATGCGGCGGGGATTGCGACTTATGCCAATGCGTTGTCGAACCAGCTTGCCCCGCAAGAGGGGATGGTTGCGGCGCAACACAGCCTGACTTTCGCCGCCAATGGCTGGGTCGAACCAGCAACCGCGCCCAACTTTGGCCCGCTCAAGGTATTTTACCCCGGCCCCGGCCACACCAGTGACAATATCACCGTTGGGATCGACGGCACCGACATCGCTTTTGGTGGCTGCCTGATCAAGGACAGCAAGGCCAAGTCGCTCGGCAATCTCGGTGATGCCGACACTGAGCACTACGCCGCGTCAGCGCGCGCGTTTGGTGCGGCGTTCCCCAAGGCCAGCATGATCGTGATGAGCCATTCCGCCCCCGATAGCCGCGCCGCAATCACTCATACGGCCCGCATGGCCGACAAGCTGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3004866","ARO_id":"43004","ARO_name":"NDM-23","CARD_short_name":"NDM-23","ARO_description":"A class B New Delhi metallo-beta-lactamase.","ARO_category":{"36196":{"category_aro_accession":"3000057","category_aro_cvterm_id":"36196","category_aro_name":"NDM beta-lactamase","category_aro_description":"NDM beta-lactamases or New Delhi metallo-beta-lactamases are class B beta-lactamases that confer resistance to a broad range of antibiotics including carbapenems, cephalosporins and penicillins.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"340":{"model_id":"340","model_name":"CMY-51","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"904":{"protein_sequence":{"accession":"AFK73431.1","sequence":"MMKKSICCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAIIYEGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLNDPVTKYWPELTGKQWRGISLLHLATYTAGGLPLQIPDDVTDKAALLRFYQNWQPQWTPGAKRLYANSSIGLFGALAVQPSGMSYEEAMTRRVLQPLKLAHTWITVPQSEQKNYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIELAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPARVEAAWRILEKLQ"},"dna_sequence":{"accession":"JQ733571.1","fmin":"1027","fmax":"2173","strand":"+","sequence":"ATGATGAAAAAATCGATATGCTGCGCGCTGCTGCTGACAGCCTCTTTCTCCACGTTTGCTGCCGCAAAAACAGAACAACAAATTGCCGATATCGTTAACCGCACCATCACACCACTGATGCAGGAGCAGGCTATTCCGGGCATGGCCGTGGCAATTATCTACGAGGGGAAACCTTATTACTTTACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGTTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGACGCTATCGCCCGCGGCGAAATTAAGCTCAACGACCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCGGGGTATCAGCCTGCTACACTTAGCCACCTATACAGCGGGTGGCCTGCCGCTGCAGATCCCCGATGACGTTACGGATAAAGCCGCATTACTGCGCTTTTATCAAAACTGGCAACCACAATGGACTCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGTGCGCTGGCGGTGCAACCTTCAGGTATGAGCTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAAAGCGAACAAAAAAATTATGCCTGGGGCTATCGCGAAGGGAAGCCTGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATCGATATGGCCCGCTGGGTTCAGGCCAACATGGACGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGAGCTTGCGCAGTCTCGCTACTGGCGTATTGGTGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCAGCACCTGCCGTGAAAGCCTCATGGGTGCATAAAACGGGATCCACAGGTGGATTTGGCAGCTACGTTGCCTTCGTTCCAGAAAAAAACCTTGGCATAGTGATGCTGGCAAACAAAAGCTATCCTAACCCGGCTCGCGTAGAGGCGGCCTGGCGCATTCTTGAAAAACTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002062","ARO_id":"38462","ARO_name":"CMY-51","CARD_short_name":"CMY-51","ARO_description":"CMY-51 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"341":{"model_id":"341","model_name":"IMP-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1594":{"protein_sequence":{"accession":"CAA11471.1","sequence":"MSKLSVFFIFLFCSIATAAESLPDLKIEKLDEGVYVHTSFEEVNGWGVVPKHGLVVLVNAEAYLIDTPFTAKDTEKLVTWFVERGYKIKGSISSHFHSDSTGGIEWLNSRSIPTYASELTNELLKKDGKVQATNSFSGVNYWLVKNKIEVFYPGPGHTPDNVVVWLPERKILFGGCFIKPYGLGNLGDANIEAWPKSAKLLKSKYGKAKLVVPSHSEVGDASLLKLTLEQAVKGLNESKKPSKPSN"},"dna_sequence":{"accession":"AJ223604.1","fmin":"1484","fmax":"2225","strand":"+","sequence":"ATGAGCAAGTTATCTGTATTCTTTATATTTTTGTTTTGCAGCATTGCTACCGCAGCAGAGTCTTTGCCAGATTTAAAAATTGAAAAGCTTGATGAAGGCGTTTATGTTCATACTTCGTTTGAAGAAGTTAACGGGTGGGGCGTTGTTCCTAAACATGGTTTGGTGGTTCTTGTAAATGCTGAGGCTTACCTAATTGACACTCCATTTACGGCTAAAGATACTGAAAAGTTAGTCACTTGGTTTGTGGAGCGTGGCTATAAAATAAAAGGCAGCATTTCCTCTCATTTTCATAGCGACAGCACGGGCGGAATAGAGTGGCTTAATTCTCGATCTATCCCCACGTATGCATCTGAATTAACAAATGAACTGCTTAAAAAAGACGGTAAGGTTCAAGCCACAAATTCATTTAGCGGAGTTAACTATTGGCTAGTTAAAAATAAAATTGAAGTTTTTTATCCAGGCCCGGGACACACTCCAGATAACGTAGTGGTTTGGTTGCCTGAAAGGAAAATATTATTCGGTGGTTGTTTTATTAAACCGTACGGTTTAGGCAATTTGGGTGACGCAAATATAGAAGCTTGGCCAAAGTCCGCCAAATTATTAAAGTCCAAATATGGTAAGGCAAAACTGGTTGTTCCAAGTCACAGTGAAGTTGGAGACGCATCACTCTTGAAACTTACATTAGAGCAGGCGGTTAAAGGGTTAAACGAAAGTAAAAAACCATCAAAACCAAGCAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002192","ARO_id":"38592","ARO_name":"IMP-1","CARD_short_name":"IMP-1","ARO_description":"IMP-1 is a beta-lactamase found in Serratia marcescens.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"342":{"model_id":"342","model_name":"smeS","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"910"}},"model_sequences":{"sequence":{"4492":{"protein_sequence":{"accession":"AAD51347.1","sequence":"MAFAMAKFQLKFGLTAKTFLAIFTACLLVLAVNGIASRVAFQTGFLDYLNDQGDLRMQRLMPHLQREYREHGGWEHLHGDGDRWARLLRPDLAHGHEGPVPSLSDQTGVPSRLGLFDAQHRFVAGNPDATSDDEPHAVQVDGQTVGWLGMVPFQTVIATNDLNFYNTQVRAWWVIGIALLLVTVLLAWLVSRALRQRLAKLAAATHRLAAGDYATRIERTSDDELDALVNDFNRMAQALDDTERNRRAFIADISHELRTPLAVVRAELEAIEDGIRPLDRANLVGLQGEIRQLGKLIDDLHDLSMTQSGGLAYRFAPLDLVALLRSELNGMRVRFANAGLALEEDLPATPLQVSGDERRLQQVLANLLENALRYTHAGGRVRVQAARVPAGVQLVVEDTAPGVPPDKCALVFERFYRVESSRNRASGGSGLGLAISHNIILAHHGVIHAAPSPLGGLRVVITLPEPA"},"dna_sequence":{"accession":"AF173226.1","fmin":"1037","fmax":"2441","strand":"-","sequence":"ATGGCCTTCGCGATGGCGAAGTTCCAACTCAAATTCGGCCTGACCGCGAAGACCTTCCTCGCGATCTTCACCGCCTGCCTGCTGGTGCTGGCAGTGAACGGTATTGCCAGCCGCGTGGCCTTCCAGACCGGCTTCCTGGACTACCTCAACGACCAGGGCGACCTGCGCATGCAGCGGCTGATGCCACACCTGCAGCGCGAGTACCGCGAGCACGGTGGCTGGGAGCATCTGCACGGTGATGGCGACCGCTGGGCGCGGCTGCTGCGCCCGGACCTGGCCCATGGGCACGAAGGACCGGTGCCGTCGCTGTCCGACCAGACCGGCGTGCCGTCGCGCCTGGGCCTGTTCGACGCGCAGCACCGTTTCGTGGCCGGCAACCCCGACGCCACCAGCGATGACGAGCCGCATGCGGTGCAGGTGGACGGGCAGACCGTCGGTTGGCTGGGCATGGTGCCGTTCCAGACCGTCATCGCCACCAACGACCTGAATTTCTACAACACCCAGGTGCGCGCCTGGTGGGTGATCGGCATCGCGCTACTGCTGGTGACGGTACTGCTGGCCTGGCTGGTATCGCGTGCGCTGCGCCAGCGCCTTGCCAAGCTGGCCGCTGCCACCCACCGGTTGGCCGCCGGTGACTACGCCACCCGCATCGAGCGCACCAGTGACGATGAGCTGGACGCGCTGGTCAACGACTTCAACCGGATGGCGCAGGCGCTGGACGATACCGAACGCAACCGCCGCGCCTTCATTGCCGACATCTCGCATGAGCTGCGCACGCCATTGGCCGTGGTGCGGGCCGAGCTGGAGGCGATCGAAGATGGCATCCGTCCGCTGGACCGGGCCAACCTGGTGGGCCTGCAGGGCGAGATCCGCCAGCTGGGCAAGCTGATCGACGACCTGCACGACCTGTCGATGACCCAGTCCGGCGGCCTGGCGTACCGCTTCGCGCCACTGGACCTGGTGGCGCTGCTGCGCAGCGAACTCAATGGCATGCGCGTGCGCTTCGCCAATGCAGGCCTGGCGTTGGAAGAAGACCTGCCCGCCACGCCGTTGCAGGTGTCCGGTGACGAGCGGCGCCTGCAGCAGGTGCTGGCCAACCTGCTGGAAAACGCACTGCGCTACACCCATGCCGGTGGCCGCGTACGCGTGCAGGCGGCGCGCGTGCCTGCCGGCGTGCAGCTGGTCGTGGAAGACACCGCGCCGGGCGTTCCGCCCGACAAGTGTGCACTGGTGTTCGAACGCTTCTACCGCGTGGAAAGTTCGCGCAACCGCGCCAGTGGCGGCAGCGGGCTGGGCCTGGCCATCAGCCACAACATCATCCTCGCCCACCACGGCGTCATCCACGCCGCGCCCTCGCCGCTGGGCGGGCTGCGCGTGGTCATCACCCTGCCGGAGCCTGCATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37076","NCBI_taxonomy_name":"Stenotrophomonas maltophilia","NCBI_taxonomy_id":"40324"}}}},"ARO_accession":"3003067","ARO_id":"39501","ARO_name":"smeS","CARD_short_name":"smeS","ARO_description":"smeS is the protein kinase sensor component of a two component signal transduction system that includes smeR.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"343":{"model_id":"343","model_name":"OXA-31","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1211":{"protein_sequence":{"accession":"AAK52604.1","sequence":"MKNTIHINFAIFLIIANIIYSSASASTDISTVASPLFEGTEGCFLLYDVSTNAEIAQFNKAKCATQMPPDSTFKIALSLMAFDAEIIDQKTIFKWDKTPKGMEIWNSNHTPKTWMQFSVVWVSQEITQKIGLNKIKNYLKDFDYGNQDFSGDKERNNGLTEAWLESSLKISPEEQIQFLRKIINHNLPVKNSAIENTIENMYLQDLENSTKLYGKTGAGFTANRTLQNGWFEGFIISKSGHKYVFVSALTGNLGSNLTSSIKAKKNAITILNTLNL"},"dna_sequence":{"accession":"AF294653.1","fmin":"753","fmax":"1584","strand":"+","sequence":"ATGAAAAACACAATACATATCAACTTCGCTATTTTTTTAATAATTGCAAATATTATCTACAGCAGCGCCAGTGCATCAACAGATATCTCTACTGTTGCATCTCCATTATTTGAAGGAACTGAAGGTTGTTTTTTACTTTACGATGTATCCACAAACGCTGAAATTGCTCAATTCAATAAAGCAAAGTGTGCAACGCAAATGCCACCAGATTCAACTTTCAAGATCGCATTATCACTTATGGCATTTGATGCGGAAATAATAGATCAGAAAACCATATTCAAATGGGATAAAACCCCCAAAGGAATGGAGATCTGGAACAGCAATCATACACCAAAGACGTGGATGCAATTTTCTGTTGTTTGGGTTTCGCAAGAAATAACCCAAAAAATTGGATTAAATAAAATCAAGAATTATCTCAAAGATTTTGATTATGGAAATCAAGACTTCTCTGGAGATAAAGAAAGAAACAACGGATTAACAGAAGCATGGCTCGAAAGTAGCTTAAAAATTTCACCAGAAGAACAAATTCAATTCCTGCGTAAAATTATTAATCACAATCTCCCAGTTAAAAACTCAGCCATAGAAAACACCATAGAGAACATGTATCTACAAGATCTGGAGAATAGTACAAAACTGTATGGGAAAACTGGTGCAGGATTCACAGCAAATAGAACCTTACAAAACGGATGGTTTGAAGGGTTTATTATAAGCAAATCAGGACATAAATATGTTTTTGTGTCCGCACTTACAGGAAACTTGGGGTCGAATTTAACATCAAGCATAAAAGCCAAGAAAAATGCGATCACCATTCTAAACACACTAAATTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3001425","ARO_id":"37825","ARO_name":"OXA-31","CARD_short_name":"OXA-31","ARO_description":"OXA-31 is a beta-lactamase found in P. aeruginosa.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46485":{"category_aro_accession":"3007696","category_aro_cvterm_id":"46485","category_aro_name":"OXA-1-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-1.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"344":{"model_id":"344","model_name":"SHV-188","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"989":{"protein_sequence":{"accession":"CEA29751.1","sequence":"MVKRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELKLNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"LN515534.1","fmin":"0","fmax":"873","strand":"+","sequence":"GTGGTTAAGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGGATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3003155","ARO_id":"39732","ARO_name":"SHV-188","CARD_short_name":"SHV-188","ARO_description":"SHV-188 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"345":{"model_id":"345","model_name":"bcrA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"570"}},"model_sequences":{"sequence":{"745":{"protein_sequence":{"accession":"AAA99504.1","sequence":"MSTIIKTTDLTKMYGSQKSVDHLNINVKQGDIYGFLGRNGAGKTTTIRMLLGLIKPTSGQIEIFGENFFKNKKEILRRIGSIVEVPGFYANLTARENLLINAKIIGIHKKNAIDEVLEIVGLQHETKKLVGKFSLGMKQRLGIARALLHYPELLILDEPTNGLDPIGIKEMRRLIHSLAKERNITIFISSHILSEIEQLVDHVGIIHEGKLLEEIPFDHLKKRNRKYLEFQLSDQNKAVVLMEQHFDIHDYEVHQDGIIRVYSHLGQQGKLNKLFVENGIDVLKITMSEDSLEDYFVKLIGGGTIG"},"dna_sequence":{"accession":"L20573.1","fmin":"297","fmax":"1218","strand":"+","sequence":"TTGAGCACAATTATTAAAACGACGGATCTCACGAAAATGTACGGGTCGCAAAAGTCTGTAGACCATCTCAATATCAATGTAAAACAAGGAGATATATACGGCTTTTTGGGACGGAACGGCGCCGGCAAAACGACGACGATCAGAATGCTGCTGGGTCTGATCAAACCGACCAGTGGGCAGATAGAAATTTTCGGAGAAAATTTTTTCAAGAATAAAAAAGAAATTTTAAGAAGAATCGGATCTATCGTGGAAGTGCCCGGCTTTTACGCGAACTTGACGGCGAGGGAAAACCTGCTGATCAATGCGAAAATCATAGGTATCCATAAAAAAAATGCGATCGATGAAGTATTGGAGATCGTGGGCCTGCAGCATGAAACGAAAAAGCTCGTCGGCAAGTTTTCCTTGGGCATGAAACAAAGGCTGGGAATTGCAAGAGCCTTGCTTCACTATCCGGAGCTGTTGATACTGGACGAGCCGACAAACGGCTTGGACCCGATCGGGATCAAAGAAATGAGAAGACTCATTCATTCTCTCGCCAAAGAAAGAAACATCACCATCTTTATATCAAGCCACATTTTGTCTGAAATCGAACAGCTCGTCGATCATGTCGGGATCATTCATGAAGGAAAACTGCTTGAAGAAATTCCGTTTGACCATCTTAAAAAAAGAAACCGCAAATATCTGGAATTTCAATTATCCGATCAAAATAAAGCGGTCGTTCTGATGGAACAGCATTTTGATATTCATGACTACGAAGTTCACCAGGACGGGATCATCCGGGTATACTCCCATTTGGGCCAGCAGGGAAAGCTCAATAAATTGTTTGTCGAAAACGGAATAGACGTATTGAAGATTACGATGAGCGAAGACAGTCTTGAAGACTACTTCGTGAAGTTGATAGGGGGCGGGACGATTGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36834","NCBI_taxonomy_name":"Bacillus licheniformis","NCBI_taxonomy_id":"1402"}}}},"ARO_accession":"3002987","ARO_id":"39421","ARO_name":"bcrA","CARD_short_name":"bcrA","ARO_description":"bcrA is an ABC transporter found in Bacillus licheniformis that confers bacitracin resistance.","ARO_category":{"36002":{"category_aro_accession":"0010001","category_aro_cvterm_id":"36002","category_aro_name":"ATP-binding cassette (ABC) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding\/hydrolysis to transport substrates across cell membranes.","category_aro_class_name":"AMR Gene Family"},"35959":{"category_aro_accession":"0000041","category_aro_cvterm_id":"35959","category_aro_name":"bacitracin","category_aro_description":"Bacitracin is a mixture of related cyclic polypeptides produced by organisms of the licheniformis group of Bacillus subtilis var Tracy. Bacitracin interferes with the dephosphorylation of the C55-isoprenyl pyrophosphate, a molecule which carries the building blocks of the peptidoglycan bacterial cell wall outside of the inner membrane.","category_aro_class_name":"Antibiotic"},"36973":{"category_aro_accession":"3000629","category_aro_cvterm_id":"36973","category_aro_name":"bacitracin A","category_aro_description":"Bacitracin A is the primary component of bacitracin. It contains many uncommon amino acids and interferes with bacterial cell wall synthesis.","category_aro_class_name":"Antibiotic"},"36974":{"category_aro_accession":"3000630","category_aro_cvterm_id":"36974","category_aro_name":"bacitracin B","category_aro_description":"Bacitracin B is a component of bacitracin, an antibiotic mixture that interferes with bacterial cell wall synthesis. It differs from Bacitracin A with a valine instead of an isoleucine in its peptide.","category_aro_class_name":"Antibiotic"},"36975":{"category_aro_accession":"3000631","category_aro_cvterm_id":"36975","category_aro_name":"bacitracin F","category_aro_description":"Bacitracin F is a component of bacitracin, an antibiotic mixture that interferes with bacterial cell wall synthesis. It is formed when the thiazoline ring of bacitracin A is oxidatively deaminated.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"346":{"model_id":"346","model_name":"QnrB23","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"720":{"protein_sequence":{"accession":"ACS71747.1","sequence":"MTPLLYKKTGTNMALALVGEKIDRNRFTGEKIENSTFFYCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNASALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGAQVLGATFSGSDLSGGEFSTFDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDNYQASLLMERLGIAIIG"},"dna_sequence":{"accession":"FJ981622.1","fmin":"0","fmax":"681","strand":"+","sequence":"ATGACGCCATTACTGTATAAAAAAACAGGTACAAATATGGCTCTGGCACTCGTTGGCGAAAAAATTGACAGAAACCGCTTCACCGGTGAGAAAATTGAAAATAGTACATTTTTTTACTGTGATTTTTCAGGTGCCGACCTGAGCGGCACTGAATTTATCGGCTGTCAGTTCTATGATCGTGAAAGCCAGAAAGGGTGCAATTTTAGTCGTGCGATGCTGAAAGATGCCATTTTTAAAAGCTGTGATTTATCCATGGCGGATTTTCGCAATGCCAGTGCGCTTGGCATTGAAATTCGCCACTGTCGTGCGCAAGGCGCAGATTTCCGCGGCGCAAGCTTTATGAATATGATCACTACTCGCACCTGGTTTTGCAGCGCATATATCACTAACACAAATCTAAGCTACGCCAATTTTTCGAAAGTCGTGCTGGAAAAGTGTGAGCTGTGGGAAAACCGTTGGATGGGTGCCCAGGTACTGGGCGCGACGTTCAGTGGTTCAGATCTCTCCGGCGGCGAGTTTTCGACTTTCGACTGGCGAGCAGCAAACTTCACACATTGCGATCTGACCAATTCGGAGTTGGGGGACTTAGATATTCGGGGCGTTGATTTACAAGGCGTTAAGTTGGACAACTACCAGGCATCGTTGCTCATGGAACGTCTTGGCATCGCGATTATTGGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002738","ARO_id":"39172","ARO_name":"QnrB23","CARD_short_name":"QnrB23","ARO_description":"QnrB23 is a plasmid-mediated quinolone resistance protein found in Citrobacter freundii.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"348":{"model_id":"348","model_name":"OXY-3-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1848":{"protein_sequence":{"accession":"AAN28732.1","sequence":"MIKTSWRKSALIAAALPLLLCSSSLWANAIQQKLADLEKSTGGRLGVALIDTTDNSQILYRGDERFAMCSTGKVMAAAAVLKQSESNKDVVNKRLEIKASDLVVWSPVTEKHLQSGMTLAELSAAALQYSDNTAMNKMIGYLGGPEKVTAFARSIGDVTFRLDRTEPALNTAIPGDERDTTTPLAMAESLHKLTLGNALGEQQRAQLVTWLKGNTTGGQSIRAGLPASWVVGDKTGAGDYGTTNDIAVIWPENHAPLVLVTYFTQPLQDAKSRKDVLAAAAKIVTEGL"},"dna_sequence":{"accession":"AF491278.1","fmin":"183","fmax":"1050","strand":"+","sequence":"ATGATTAAAACTTCGTGGCGTAAAAGCGCCCTGATTGCCGCCGCCCTGCCTTTATTGCTCTGTAGCAGTTCATTATGGGCCAATGCTATTCAGCAGAAGCTGGCCGATTTGGAAAAAAGTACCGGCGGGCGACTGGGCGTCGCGCTGATTGACACCACAGATAACTCTCAAATTCTATATCGCGGTGACGAGCGTTTTGCTATGTGCAGTACCGGTAAAGTGATGGCTGCCGCCGCGGTGTTAAAACAGAGCGAAAGCAATAAAGATGTGGTGAATAAAAGGCTGGAGATTAAAGCATCGGATCTGGTGGTCTGGAGCCCGGTGACTGAAAAACATCTGCAGAGCGGAATGACGTTGGCGGAATTAAGCGCCGCCGCGCTGCAATATAGCGACAATACCGCGATGAATAAGATGATTGGTTATCTTGGCGGACCGGAAAAAGTGACCGCCTTCGCCCGCAGTATCGGCGATGTCACTTTTCGTCTCGATCGTACGGAGCCTGCACTAAACACCGCGATCCCGGGTGACGAACGCGATACCACCACGCCGCTGGCGATGGCCGAAAGCCTGCACAAGCTGACGCTGGGTAATGCGCTGGGTGAACAACAGCGCGCACAGTTAGTGACATGGTTGAAAGGCAACACCACCGGCGGGCAGAGTATTCGTGCGGGGCTGCCTGCAAGCTGGGTCGTGGGAGATAAAACCGGAGCTGGTGATTACGGCACCACCAATGATATCGCCGTTATCTGGCCGGAAAATCATGCTCCGCTGGTATTAGTCACTTATTTCACCCAACCGCTGCAGGATGCGAAAAGCCGCAAAGATGTGCTAGCCGCAGCGGCAAAAATCGTGACCGAAGGGCTTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3002409","ARO_id":"38809","ARO_name":"OXY-3-1","CARD_short_name":"OXY-3-1","ARO_description":"OXY-3-1 is a beta-lactamase found in Klebsiella oxytoca.","ARO_category":{"38788":{"category_aro_accession":"3002388","category_aro_cvterm_id":"38788","category_aro_name":"OXY beta-lactamase","category_aro_description":"OXY beta-lactamases are chromosomal class A beta-lactamases that are found in Klebsiella oxytoca. At constitutive low levels, OXY beta-lactamases confer resistance to aminopenicillins and carboxypenicillins. At high induced levels,  OXY beta-lactamases confer resistance to penicillins, cephalosporins and aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"349":{"model_id":"349","model_name":"vanL","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"612":{"protein_sequence":{"accession":"ABX54687.1","sequence":"MMKLKKIAIIFGGQSSEYEVSLKSTVSVLETLSTCNFEIIKIGIDLGGKWYLTTSNNKDIEYDVWQTDPSLQEIIPCFNNRGFYNKTTNKYFRPDVLFPILHGGTGEDGTLQGVFELMNIPYVGCGVTPSAICMDKYLLHEFAQSVGVKSAPTLIIRTRNCKDEIDKFIEKNDFPIFVKPNEAGSSKGINKVNEPDKLEDALTEAFKYSKSVIIQKAIIGREIGCAVLGNEKLLVGECDEVSLNSDFFDYTEKYQMISAKVNIPASISVEFSNEMKKQAQLLYRLLGCSGLARIDFFLSDNNEILLNEINTLPGFTEHSRYPKMMEAVGVTYKEIITKLINLAEEKYYG"},"dna_sequence":{"accession":"EU250284.1","fmin":"954","fmax":"2004","strand":"+","sequence":"ATGATGAAATTGAAAAAGATAGCCATAATATTCGGAGGTCAATCTTCGGAATATGAAGTCTCACTTAAATCAACAGTAAGTGTACTAGAAACTCTATCAACTTGTAATTTTGAAATTATAAAAATAGGAATTGATTTAGGCGGAAAGTGGTATCTCACCACAAGCAACAACAAAGATATTGAATATGATGTTTGGCAAACTGATCCTTCATTACAAGAAATAATCCCATGTTTCAATAATCGAGGCTTTTATAACAAAACTACAAATAAATATTTCAGACCAGATGTACTCTTTCCAATTCTTCATGGGGGGACTGGAGAAGATGGAACCCTCCAAGGTGTATTTGAATTAATGAATATTCCTTACGTTGGATGTGGGGTGACGCCTTCGGCTATTTGTATGGACAAATACTTATTGCATGAGTTTGCTCAGAGTGTGGGTGTAAAAAGTGCCCCTACGCTCATAATTCGCACTAGAAACTGCAAAGATGAAATTGACAAGTTCATAGAAAAAAATGACTTCCCTATTTTTGTAAAGCCTAACGAAGCGGGCTCATCAAAAGGAATAAACAAAGTAAATGAGCCAGATAAGCTAGAGGATGCTTTAACAGAAGCGTTTAAGTATAGTAAAAGTGTTATCATTCAGAAAGCTATAATTGGAAGAGAAATTGGCTGTGCTGTCTTAGGTAATGAAAAACTCCTAGTAGGAGAATGTGATGAAGTTTCCCTTAATAGCGATTTTTTTGATTATACCGAGAAATACCAAATGATCTCAGCAAAGGTAAATATACCTGCTTCTATATCTGTAGAATTTTCTAATGAAATGAAGAAACAAGCTCAGCTGTTATATAGGTTACTAGGCTGTTCAGGACTAGCACGAATTGATTTCTTCTTATCAGATAATAACGAAATACTATTAAACGAAATTAATACTTTGCCTGGTTTTACTGAGCATTCCAGATATCCCAAAATGATGGAAGCTGTAGGTGTTACCTATAAAGAGATTATCACGAAGTTAATCAATTTAGCGGAGGAAAAATATTATGGATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35918","NCBI_taxonomy_name":"Enterococcus faecalis","NCBI_taxonomy_id":"1351"}}}},"ARO_accession":"3002910","ARO_id":"39344","ARO_name":"vanL","CARD_short_name":"vanL","ARO_description":"VanL is a D-Ala-D-Ala ligase homolog that can synthesize D-Ala-D-Ser, an alternative substrate for peptidoglycan synthesis that reduces vancomycin binding affinity in Enterococcus faecalis.","ARO_category":{"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"39340":{"category_aro_accession":"3002906","category_aro_cvterm_id":"39340","category_aro_name":"Van ligase","category_aro_description":"Van ligases synthesize alternative substrates for peptidoglycan synthesis that reduce vancomycin binding affinity.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"350":{"model_id":"350","model_name":"ykkD","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"180"}},"model_sequences":{"sequence":{"536":{"protein_sequence":{"accession":"CAB13167.1","sequence":"MLHWISLLCAGCLEMAGVALMNQYAKEKSVKWVLLIIVGFAASFSLLSYAMETTPMGTAYAVWTGIGTAGGALIGILFYKEQKDAKRIFFIALILCSAVGLKILS"},"dna_sequence":{"accession":"AL009126.1","fmin":"1376854","fmax":"1377172","strand":"+","sequence":"ATGCTGCACTGGATCAGTTTATTGTGCGCGGGCTGTTTAGAAATGGCCGGCGTGGCCCTTATGAATCAATATGCGAAAGAAAAAAGCGTGAAATGGGTGCTGTTGATCATTGTTGGTTTTGCCGCTTCATTTTCCTTGCTGTCGTACGCAATGGAAACCACTCCGATGGGAACGGCTTACGCGGTCTGGACAGGAATTGGCACCGCCGGCGGGGCGCTTATCGGCATCCTCTTTTACAAGGAGCAGAAAGACGCCAAACGGATCTTCTTTATCGCGTTGATTTTATGCTCAGCAGTTGGTTTAAAAATTCTGTCATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39579","NCBI_taxonomy_name":"Bacillus subtilis subsp. subtilis str. 168","NCBI_taxonomy_id":"224308"}}}},"ARO_accession":"3003064","ARO_id":"39498","ARO_name":"ykkD","CARD_short_name":"ykkD","ARO_description":"ykkD is an SMR-type protein that is a subunit of the ykkCD efflux pump.","ARO_category":{"36004":{"category_aro_accession":"0010003","category_aro_cvterm_id":"36004","category_aro_name":"small multidrug resistance (SMR) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Small multidrug resistance (SMR) proteins are a relatively small family of transporters, restricted to prokaryotic cells. They are also the smallest multidrug transporters, with only four transmembrane alpha-helices and no significant extramembrane domain.","category_aro_class_name":"AMR Gene Family"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"351":{"model_id":"351","model_name":"SHV-6","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8842":{"protein_sequence":{"accession":"HBX2855210.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARATTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"DAGOBI010000132.1","fmin":"1383","fmax":"2244","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACATCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGCCACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGAGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATCGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001065","ARO_id":"37445","ARO_name":"SHV-6","CARD_short_name":"SHV-6","ARO_description":"SHV-6 is an extended-spectrum beta-lactamase that has been found in clinical isolates.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"352":{"model_id":"352","model_name":"PDC-5","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"1696":{"protein_sequence":{"accession":"ACQ82810.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"FJ666068.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTATGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002502","ARO_id":"38902","ARO_name":"PDC-5","CARD_short_name":"PDC-5","ARO_description":"PDC-5 is a extended-spectrum beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35927":{"category_aro_accession":"0000008","category_aro_cvterm_id":"35927","category_aro_name":"cefoxitin","category_aro_description":"Cefoxitin is a cephamycin antibiotic often grouped with the second generation cephalosporins. Cefoxitin is bactericidal and acts by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. Cefoxitin's 7-alpha-methoxy group and 3' leaving group make it a poor substrate for most beta-lactamases.","category_aro_class_name":"Antibiotic"},"35975":{"category_aro_accession":"0000058","category_aro_cvterm_id":"35975","category_aro_name":"cefazolin","category_aro_description":"Cefazolin, also known as cefazoline or cephazolin, is a first generation cephalosporin antibiotic. It is administered parenterally, and is active against a broad spectrum of bacteria.","category_aro_class_name":"Antibiotic"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"35979":{"category_aro_accession":"0000062","category_aro_cvterm_id":"35979","category_aro_name":"ceftriaxone","category_aro_description":"Ceftriaxone is a third-generation cephalosporin antibiotic. The presence of an aminothiazolyl sidechain increases ceftriazone's resistance to beta-lactamases. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"36990":{"category_aro_accession":"3000646","category_aro_cvterm_id":"36990","category_aro_name":"cefixime","category_aro_description":"Cefixime is a cephalosporin resistant to most beta-lactamases. It is active against many enterobacteria, but activity against staphylococci is poor.","category_aro_class_name":"Antibiotic"},"37084":{"category_aro_accession":"3000704","category_aro_cvterm_id":"37084","category_aro_name":"cefalotin","category_aro_description":"Cefalotin is a semisynthetic cephalosporin antibiotic activate against staphylococci. It is resistant to staphylococci beta-lactamases but hydrolyzed by enterobacterial beta-lactamases.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"353":{"model_id":"353","model_name":"QnrB2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"531":{"protein_sequence":{"accession":"ABO93588.1","sequence":"MALALVGEKINRNRFTGEKIENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNASALGIEISHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGAQVLGATFSGSDLSGGEFSTFDWRAANFTHCDLTNSELGDLDIRRVDLQGVKLDNYQASLLMERLGIAIIG"},"dna_sequence":{"accession":"EF488762.1","fmin":"0","fmax":"645","strand":"+","sequence":"ATGGCTCTGGCACTCGTTGGCGAAAAAATTAACAGAAACCGCTTCACCGGTGAGAAAATTGAAAATAGTACATTTTTTAACTGTGATTTTTCAGGTGCCGACCTGAGCGGCACTGAATTTATCGGCTGTCAGTTCTATGATCGTGAAAGCCAGAAAGGGTGCAATTTTAGTCGTGCGATGCTGAAAGATGCCATTTTTAAAAGCTGTGATTTATCCATGGCGGATTTTCGCAATGCCAGTGCGCTTGGCATTGAAATTAGCCACTGTCGTGCGCAAGGCGCAGATTTTCGCGGCGCAAGTTTTATGAATATGATCACTACTCGCACCTGGTTTTGCAGTGCATATATCACTAACACAAATCTAAGCTACGCCAATTTTTCGAAAGTCGTGTTGGAAAAGTGTGAGCTGTGGGAAAACCGTTGGATGGGGGCCCAGGTACTGGGCGCGACGTTCAGTGGTTCAGATCTCTCCGGCGGCGAGTTTTCGACTTTCGACTGGCGAGCAGCAAACTTCACACATTGCGATCTGACCAATTCGGAGTTGGGTGACTTAGATATTCGGCGCGTTGATTTACAAGGCGTTAAGTTGGACAACTACCAGGCATCGTTGCTCATGGAACGTCTTGGCATCGCGATTATTGGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3002715","ARO_id":"39149","ARO_name":"QnrB2","CARD_short_name":"QnrB2","ARO_description":"QnrB2 is a plasmid-mediated quinolone resistance protein found in Citrobacter koseri.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"354":{"model_id":"354","model_name":"QnrB24","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"756":{"protein_sequence":{"accession":"ADI46626.1","sequence":"MTPLLYKKTGTNMALALVGEKIDRNRFTGEKIENSTFFNCDFSGADMSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMVDFRNASALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGAQVLGATFSGSDLSGGEFSTFDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDNYQASLLMERLGIAVIG"},"dna_sequence":{"accession":"HM192542.1","fmin":"0","fmax":"681","strand":"+","sequence":"ATGACGCCATTACTGTATAAAAAAACAGGTACAAATATGGCACTGGCACTCGTTGGCGAAAAAATTGACAGAAACCGCTTCACCGGTGAGAAAATTGAAAATAGTACATTTTTTAACTGTGATTTTTCAGGTGCCGACATGAGCGGCACTGAATTTATCGGCTGTCAGTTCTATGATCGTGAAAGCCAGAAAGGGTGCAATTTTAGTCGTGCGATGCTGAAAGATGCCATTTTTAAAAGCTGTGATTTATCCATGGTGGATTTTCGCAATGCCAGTGCGCTTGGCATTGAAATTCGCCACTGTCGTGCGCAAGGCGCAGATTTCCGCGGCGCAAGCTTTATGAATATGATCACTACTCGCACCTGGTTTTGCAGCGCATATATCACTAACACAAATCTAAGCTACGCCAATTTTTCGAAAGTCGTGCTGGAAAAATGTGAGCTGTGGGAAAACCGTTGGATGGGTGCCCAGGTACTGGGCGCGACGTTCAGTGGTTCAGATCTTTCCGGCGGCGAGTTTTCGACTTTCGACTGGCGAGCAGCAAACTTCACACATTGCGATCTGACCAATTCGGAGTTGGGTGACTTAGATATTCGGGGCGTTGATTTACAAGGCGTTAAGTTGGACAACTACCAGGCATCGTTGCTCATGGAACGTCTTGGCATCGCGGTGATTGGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002739","ARO_id":"39173","ARO_name":"QnrB24","CARD_short_name":"QnrB24","ARO_description":"QnrB24 is a plasmid-mediated quinolone resistance protein found in Citrobacter freundii.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"356":{"model_id":"356","model_name":"ErmU","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"5176":{"protein_sequence":{"accession":"CAA44667.1","sequence":"MPSRYGSRQDLGQNFLVDPDIIKLIRRAPNERKVPSLIWRRRGHVTLPLSRLGRPVTAVELDPRRVKRLSARAPENVKVVGEDILRFRLPTVPHTVVGNIPFHVTTATMRRILVAPAWVSAVLVVQWEVARRRAGIGGCSLVTAESWPWFDFSVLKRVPRFAFRPAPSVDGGILVIERRPEPLVRERREYQAFVRQVFTGRGHGLREILQRIGRVQDSDLSAWFRAHGVSPQALPKDLTAEQWASLWGMARGGRSVPRTRRPRGLPPRTSRGPRRNSG"},"dna_sequence":{"accession":"X62867.1","fmin":"360","fmax":"1197","strand":"+","sequence":"GTGCCCAGCCGGTACGGCAGCCGGCAGGACCTCGGTCAGAACTTCCTCGTCGACCCCGACATCATCAAGCTGATCCGCCGAGCGCCGAACGAGCGGAAGGTCCCATCGTTGATCTGGCGCCGGAGAGGGCACGTGACGCTGCCCTTGAGTCGCTTGGGCCGCCCGGTCACCGCGGTTGAGCTCGACCCCCGCCGGGTCAAACGGCTCTCGGCGCGTGCCCCGGAAAACGTCAAGGTCGTCGGCGAGGACATCCTGCGCTTCCGGCTCCCGACCGTTCCGCACACCGTCGTGGGGAACATCCCCTTCCATGTCACGACGGCCACGATGCGCCGGATCCTCGTGGCTCCCGCATGGGTGTCGGCCGTCCTCGTGGTGCAGTGGGAAGTGGCGCGCCGCCGGGCCGGCATCGGCGGCTGCTCGCTGGTCACGGCGGAGTCCTGGCCGTGGTTCGACTTCTCGGTGCTCAAGCGGGTGCCGAGGTTCGCCTTCCGGCCCGCGCCCTCCGTGGACGGCGGGATCCTCGTCATCGAGCGGCGGCCCGAGCCACTGGTGCGGGAGCGCAGGGAGTACCAGGCATTCGTCAGACAGGTCTTCACCGGGCGCGGTCACGGGCTGCGGGAGATCCTCCAACGCATCGGGCGGGTCCAGGACAGCGACCTGTCCGCGTGGTTCAGGGCACATGGAGTCTCGCCGCAGGCGCTGCCGAAGGACCTCACCGCCGAGCAGTGGGCGTCGCTCTGGGGCATGGCGCGTGGCGGCCGGTCCGTGCCGCGGACGCGGCGACCCCGGGGCCTGCCGCCCCGCACGTCCCGCGGGCCGCGGCGCAACAGCGGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36862","NCBI_taxonomy_name":"Streptomyces lincolnensis","NCBI_taxonomy_id":"1915"}}}},"ARO_accession":"3001305","ARO_id":"37704","ARO_name":"ErmU","CARD_short_name":"ErmU","ARO_description":"ErmU is a methyltransferase found in the lincomycin producer Streptomyces lincolnensis. Like other Erm enzymes, it catalyzes the methylation of A2058 of the 23S ribosomal RNA. Specifically, this enzyme transfers only one methyl group. The gene is found in the lincomycin biosynthetic cluster and is responsible for self-resistance.","ARO_category":{"36699":{"category_aro_accession":"3000560","category_aro_cvterm_id":"36699","category_aro_name":"Erm 23S ribosomal RNA methyltransferase","category_aro_description":"Erm proteins are part of the RNA methyltransferase family and methylate A2058 (E. coli nomenclature) of the 23S ribosomal RNA conferring degrees of resistance to Macrolides, Lincosamides and Streptogramin b. This is called the MLSb phenotype.","category_aro_class_name":"AMR Gene Family"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"357":{"model_id":"357","model_name":"VIM-38","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"8265":{"protein_sequence":{"accession":"AGE83081.2","sequence":"MLKVISSLLVYLTASVMAVASPLAHSGEPSGEYPTVNEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRKAGVATYASPSTRRLAEAEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSANVLYGGCAVLALSRTSAGNVADADLAEWPTSVERIQKHYPEAEVVIPGHGLPGGLDLLQHTANVVTAHKNRSVVE"},"dna_sequence":{"accession":"KC469971.2","fmin":"0","fmax":"801","strand":"+","sequence":"ATGTTAAAAGTTATTAGTAGTTTATTGGTCTATTTGACCGCGTCTGTCATGGCTGTAGCTAGTCCGTTAGCCCATTCCGGGGAGCCGAGTGGTGAGTATCCGACAGTCAACGAAATTCCGGTCGGAGAGGTCCGGCTTTACCAGATTGCTGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCGGTCTACCCATCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCCCTTCTCGCGGAGATTGAGAAGCAAATTGGACTTCCCGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGAAGGCTGGAGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGCAGAGGGGAACGAGATTCCCACGCACTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAGCTCTTCTATCCCGGTGCTGCGCATTCGACCGACAATCTGGTTGTATACGTCCCGTCAGCGAACGTGCTATACGGTGGTTGTGCCGTTCTTGCGTTGTCACGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCGTTGAGCGGATTCAAAAACACTACCCGGAAGCAGAGGTCGTCATTCCCGGGCACGGTCTACCGGGCGGTCTAGACTTGCTCCAGCACACAGCGAACGTTGTCACAGCACACAAAAATCGCTCAGTCGTTGAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002308","ARO_id":"38708","ARO_name":"VIM-38","CARD_short_name":"VIM-38","ARO_description":"VIM-38 is a beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"358":{"model_id":"358","model_name":"QnrB42","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"35":{"protein_sequence":{"accession":"AEQ94272.1","sequence":"MALVLVGEKIDRNCFTGEKIENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNSSALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWIGAQVLGATFSGSDLSGGEFSTFDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDNYQASLLMERLGIAIIG"},"dna_sequence":{"accession":"JN680743.1","fmin":"0","fmax":"645","strand":"+","sequence":"ATGGCTCTGGTATTAGTTGGCGAAAAAATTGACAGAAACTGTTTCACCGGTGAGAAAATTGAAAATAGTACATTTTTTAACTGTGATTTTTCAGGTGCCGACCTGAGCGGCACTGAATTTATCGGCTGTCAGTTCTATGATCGTGAAAGCCAGAAAGGGTGCAATTTTAGTCGTGCGATGCTGAAAGATGCCATTTTTAAAAGCTGTGATTTATCCATGGCGGATTTTCGCAATTCCAGTGCGCTGGGCATTGAAATTCGCCACTGCCGCGCACAAGGCGCAGATTTCCGCGGCGCAAGCTTTATGAATATGATCACCACGCGCACCTGGTTTTGTAGCGCATATATCACGAATACCAATCTAAGCTACGCCAATTTTTCGAAAGTCGTGTTGGAAAAGTGTGAGCTGTGGGAAAACCGTTGGATAGGTGCCCAGGTACTGGGCGCGACGTTCAGTGGTTCAGATCTCTCCGGCGGCGAGTTTTCGACTTTCGACTGGCGAGCAGCAAACTTCACACATTGCGATCTGACCAATTCGGAGTTGGGTGACTTAGATATTCGGGGCGTTGATTTACAAGGCGTTAAGTTGGACAACTACCAGGCATCGTTGCTCATGGAGCGACTTGGCATCGCTATTATTGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002757","ARO_id":"39191","ARO_name":"QnrB42","CARD_short_name":"QnrB42","ARO_description":"QnrB42 is a plasmid-mediated quinolone resistance protein found in Klebsiella pneumoniae.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"359":{"model_id":"359","model_name":"TEM-112","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1719":{"protein_sequence":{"accession":"AAS89982.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLRNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGASERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AY589493.1","fmin":"166","fmax":"1027","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCGCAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCAGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000975","ARO_id":"37355","ARO_name":"TEM-112","CARD_short_name":"TEM-112","ARO_description":"TEM-112 is an extended-spectrum beta-lactamase found in E. coli.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"360":{"model_id":"360","model_name":"AAC(6')-Iy","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"397":{"protein_sequence":{"accession":"AAF03531.1","sequence":"MDIRQMNKTHLEHWRGLRKQLWPGHPDDAHLADGEEILQADHLASFIAMADGVAIGFADASIRHDYVNGCDSSPVVFLEGIFVLPSFRQRGVAKQLIAAVQRWGTNKGCREMASDTSPENTISQKVHQALGFEETERVIFYRKRC"},"dna_sequence":{"accession":"AF144880.1","fmin":"3541","fmax":"3979","strand":"+","sequence":"ATGGACATCAGGCAAATGAACAAAACCCATCTGGAGCACTGGCGCGGATTGCGAAAACAGCTCTGGCCTGGTCACCCGGATGACGCCCATCTGGCGGACGGCGAAGAAATTCTGCAAGCCGATCATCTGGCATCATTTATTGCGATGGCAGACGGGGTGGCGATTGGCTTTGCGGATGCCTCAATCCGCCACGATTATGTCAATGGCTGTGACAGTTCGCCCGTGGTTTTCCTTGAAGGTATTTTTGTTCTCCCCTCATTCCGTCAACGCGGCGTAGCGAAACAATTGATTGCAGCGGTGCAACGATGGGGAACGAATAAAGGGTGTCGGGAAATGGCCTCCGATACCTCGCCGGAAAATACAATTTCCCAGAAAGTTCATCAGGCGTTAGGATTTGAGGAAACAGAGCGCGTCATTTTCTACCGAAAGCGTTGTTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35750","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Enteritidis","NCBI_taxonomy_id":"149539"}}}},"ARO_accession":"3002569","ARO_id":"38969","ARO_name":"AAC(6')-Iy","CARD_short_name":"AAC(6')-Iy","ARO_description":"AAC(6')-Iy is a chromosomal-encoded aminoglycoside acetyltransferase in S. enteritidis and S. enterica. Regulatory mutation required to increase expression of this chromosomally-encoded gene for resistance. In the specific system, aminoglycoside resistance was due to a transcriptional fusion secondary to a chromosomal deletion in which the downstream aac(6')-Iy gene was placed under the control of the upstream nmpC promoter.","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"A category of aminoglycoside N-acetyltransferase enzymes with modification regiospecificity based at the 6'-amino group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics through acetylation of the 6-amino group of the compound.","category_aro_class_name":"AMR Gene Family"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"46128":{"category_aro_accession":"3007378","category_aro_cvterm_id":"46128","category_aro_name":"2'-N-ethylnetilmicin","category_aro_description":"2'-N-ethylnetilmicin is an aminoglycoside antibiotic and a derivative of netilmicin.","category_aro_class_name":"Antibiotic"},"46129":{"category_aro_accession":"3007379","category_aro_cvterm_id":"46129","category_aro_name":"5-episisomicin","category_aro_description":"5-episosomicin is a semisynthetic aminoglycoside antibiotic similar to sisomicin.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"361":{"model_id":"361","model_name":"OXA-278","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"806":{"protein_sequence":{"accession":"AGI65307.1","sequence":"MKILILWPLLSYLSLTACSFPVSNSPSQITSTQSIQAIAKLFDQAQSSGVLVIQRGPHLQVYGNDLSRAHTEYVPASTFKIFNALIGLQHGKATTNEIFKWDGKKRSFAAWEKDMTLGQAMQASAVPVYQELARRIGLELMEQEVRRIQFGNQHIGQQVDNFWLVGPLKITPKQEVEFVSALAQEQLAFDPQVQQQVKAMLLLQEQQAYRLYAKSGWGMDVEPQVGWLTGWVETPQAEIVAFSLNMQMQSNMDPAIRLKILQQALAELGLYPKAEG"},"dna_sequence":{"accession":"KC771279.1","fmin":"0","fmax":"831","strand":"+","sequence":"ATGAAAATTCTTATTTTGTGGCCTTTACTCAGTTACTTGAGCCTGACAGCCTGTAGCTTCCCTGTTTCAAATTCGCCCTCTCAAATCACTTCAACTCAATCTATTCAAGCTATTGCAAAGTTATTTGATCAGGCACAAAGCTCTGGCGTTTTAGTAATTCAACGGGGTCCACATCTACAGGTCTATGGCAATGATTTGAGTCGTGCACATACCGAATATGTTCCTGCTTCAACCTTTAAAATATTTAATGCTCTGATTGGCCTGCAACATGGTAAAGCCACGACCAATGAAATCTTTAAATGGGATGGCAAGAAGCGCAGTTTTGCAGCCTGGGAAAAAGACATGACTCTCGGCCAAGCCATGCAAGCTTCTGCTGTACCCGTCTATCAGGAACTAGCACGTCGCATTGGCCTTGAATTGATGGAACAGGAAGTGAGACGTATTCAATTCGGCAATCAACATATTGGGCAGCAGGTCGATAACTTCTGGTTGGTAGGCCCTTTGAAAATCACTCCAAAACAGGAAGTCGAATTTGTCTCTGCGCTTGCTCAAGAGCAGCTTGCCTTTGATCCTCAAGTCCAGCAACAAGTCAAAGCCATGTTACTTTTACAGGAACAGCAAGCTTATCGCCTATATGCCAAATCCGGTTGGGGCATGGATGTGGAACCGCAAGTCGGCTGGCTCACCGGCTGGGTTGAAACACCGCAGGCTGAAATCGTGGCATTTTCACTGAATATGCAGATGCAAAGTAATATGGATCCGGCGATCCGTCTTAAAATTTTGCAGCAGGCCTTGGCCGAATTAGGGCTTTATCCGAAAGCTGAAGGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39096","NCBI_taxonomy_name":"Acinetobacter schindleri","NCBI_taxonomy_id":"108981"}}}},"ARO_accession":"3001681","ARO_id":"38081","ARO_name":"OXA-278","CARD_short_name":"OXA-278","ARO_description":"OXA-278 is a beta-lactamase found in A. baumannii.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46489":{"category_aro_accession":"3007700","category_aro_cvterm_id":"46489","category_aro_name":"OXA-134-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-134.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"362":{"model_id":"362","model_name":"CTX-M-151","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1511":{"protein_sequence":{"accession":"BAP34782.1","sequence":"MINKRLSIALALAAMIGTPVAMALESQKPGSDSANHIQHQMVQQLSALEKSANGRLGVAVIDTGSGAIAGWRMDEPFPMCSTSKVMAVAALLKQSEQTPELMSQPQPVASGDLVNYNPITERFVGKSMTFDELSAATLQYSDNAAMNLILAKLGGPQKVTAFARSIGDDKFRLDRNEPSLNTAIPGDLRDTSTPRAMALSLQKLALGDALGQVQREKLSHWLRGNTTGAASIRAGLPSGWSVGDKTGSGDYGTTNDIAVVWPTGRPPLVIVTYFTQPQQQAESQRPVLAKAAAIVASHYVLPKG"},"dna_sequence":{"accession":"AB916359.1","fmin":"793","fmax":"1708","strand":"+","sequence":"ATGATCAATAAACGGCTGAGTATTGCTCTGGCGCTGGCGGCCATGATAGGTACGCCTGTGGCGATGGCCCTCGAGAGCCAGAAGCCGGGGAGCGATTCTGCTAATCATATTCAGCACCAGATGGTGCAACAGCTGTCGGCGCTGGAGAAAAGCGCTAACGGGCGGCTTGGCGTAGCGGTTATCGATACCGGCAGCGGCGCAATTGCGGGCTGGCGGATGGATGAACCTTTCCCCATGTGCAGTACCAGTAAAGTGATGGCGGTAGCGGCGCTGCTGAAACAGAGCGAACAGACTCCTGAACTTATGAGTCAGCCTCAGCCGGTAGCGAGCGGAGATCTGGTGAACTACAACCCGATAACTGAACGTTTTGTGGGTAAGAGCATGACGTTTGATGAGCTAAGCGCCGCAACGCTGCAATATAGCGATAACGCCGCAATGAACCTGATTCTGGCCAAACTGGGTGGGCCGCAAAAAGTAACGGCGTTTGCCCGCAGTATTGGCGATGATAAATTCCGGCTCGACCGCAATGAACCTTCGCTAAATACCGCCATTCCCGGCGATCTTCGGGATACCAGCACTCCACGAGCTATGGCCTTAAGCCTGCAAAAGCTGGCGCTGGGGGATGCTTTAGGCCAGGTTCAGCGCGAGAAACTTAGCCACTGGTTGCGCGGCAATACCACCGGTGCGGCCAGCATTCGGGCCGGGCTGCCATCGGGATGGAGCGTTGGGGATAAGACCGGCAGCGGTGATTACGGCACAACCAACGATATTGCCGTGGTATGGCCGACCGGCAGACCGCCGCTGGTTATTGTGACTTACTTTACTCAGCCGCAGCAGCAGGCAGAAAGCCAGCGGCCGGTGCTGGCGAAAGCGGCTGCTATCGTTGCCAGCCATTATGTATTGCCTAAAGGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35672","NCBI_taxonomy_name":"Salmonella enterica","NCBI_taxonomy_id":"28901"}}}},"ARO_accession":"3002008","ARO_id":"38408","ARO_name":"CTX-M-151","CARD_short_name":"CTX-M-151","ARO_description":"CTX-M-151 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"363":{"model_id":"363","model_name":"TEM-155","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1323":{"protein_sequence":{"accession":"ABG77582.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDKLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDSWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGKRGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"DQ679961.1","fmin":"114","fmax":"975","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATAAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATAGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTAAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3001021","ARO_id":"37401","ARO_name":"TEM-155","CARD_short_name":"TEM-155","ARO_description":"TEM-155 is an extended-spectrum beta-lactamase.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"364":{"model_id":"364","model_name":"CMY-83","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"959":{"protein_sequence":{"accession":"AFU25638.1","sequence":"MMKKSICCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAIIYQGKPYYFTWGKADIANNRPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTHYWPELTGKQWQGISLLHLATYTAGGLPLQVPDDVTDKAALLRFYQNWQPQWAPGAKRLYANSSIGLFGALAVNPSGMSYEEAMTKRVLRPLKLAHTWITVPQSEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMTRWVQANMDASQVQEKTLQQGIELAQSRYWRIGDMYQGLGWEMLNWPVKADSIISGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"JX440351.1","fmin":"1026","fmax":"2172","strand":"+","sequence":"ATGATGAAAAAATCGATATGCTGCGCGCTGCTGCTGACAGCTTCGTTCTCCACGTTTGCCGCCGCAAAAACAGAACAACAAATTGCCGATATCGTTAACCGCACCATCACACCGCTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCGATTATCTATCAGGGGAAACCTTATTACTTTACCTGGGGTAAAGCCGATATCGCCAATAACCGTCCAGTCACTCAACAAACGCTGTTTGAACTCGGATCGGTCAGTAAAACGTTCAACGGCGTGCTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGCATTACTGGCCTGAACTGACTGGTAAGCAGTGGCAGGGTATCAGCCTGCTGCACTTAGCCACCTACACGGCAGGCGGCCTGCCGCTTCAGGTTCCGGACGACGTTACGGATAAAGCCGCGTTACTACGCTTTTATCAAAACTGGCAGCCGCAATGGGCCCCAGGCGCTAAACGTCTTTATGCTAACTCCAGCATTGGTCTGTTTGGCGCCCTGGCGGTGAACCCCTCAGGCATGAGCTACGAAGAGGCGATGACCAAACGCGTCCTGCGCCCCTTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAGCGAACAAAAAGATTATGCCTGGGGTTATCGCGAAGGAAAGCCAGTGCATGTATCCCCTGGGCAACTTGATGCCGAAGCCTACGGGGTGAAATCGAGCGTTATCGATATGACCCGTTGGGTTCAGGCCAACATGGACGCCAGCCAGGTTCAGGAGAAAACGCTCCAGCAGGGCATCGAGCTTGCGCAGTCACGTTACTGGCGTATTGGCGATATGTACCAGGGCCTGGGCTGGGAGATGCTGAACTGGCCGGTGAAGGCCGACTCGATAATTAGCGGTAGCGACAGCAAAGTGGCCCTGGCAGCGCTTCCTGCCGTTGAGGTAAACCCGCCCGCGCCTGCCGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGCGGATTCGGCAGCTACGTTGCTTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAGAGCTACCCAAACCCTGTTCGCGTCGAAGCCGCCTGGCGCATTCTTGAAAAACTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39584","NCBI_taxonomy_name":"Citrobacter braakii","NCBI_taxonomy_id":"57706"}}}},"ARO_accession":"3002096","ARO_id":"38496","ARO_name":"CMY-83","CARD_short_name":"CMY-83","ARO_description":"CMY-83 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"365":{"model_id":"365","model_name":"TEM-122","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1241":{"protein_sequence":{"accession":"AAQ98890.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDEQNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AY307100.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACAAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000984","ARO_id":"37364","ARO_name":"TEM-122","CARD_short_name":"TEM-122","ARO_description":"TEM-122 is an inhibitor-resistant beta-lactamase found in E. coli.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"367":{"model_id":"367","model_name":"CTX-M-25","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8221":{"protein_sequence":{"accession":"AAM70498.1","sequence":"MMRKSVRRAMLMTTACVSLLLASVPLCAQANDVQQKLAALEKSSGGRLGVALINTADNTQTLYRADERFAMCSTSKVMAVAAVLKQSETQKGLLSQRVEIKPSDLINYNPIAEKHVNGTMTFGELSAAALQYSDNTAMNKLIAHLGGPDKVTAFARTIGDDTFRLDRTEPTLNTAIPGDPRDTTTPLAMAQALRNLTLGNALGDTQRAQLVMWLKGNTTGAASIQAGLPTSWVVGDKTGSGGYGTTNDIAVIWPEGRAPLVLVTYFTQSEPKAESRRDVLAAAARIVTDGY"},"dna_sequence":{"accession":"AF518567.2","fmin":"2320","fmax":"3196","strand":"+","sequence":"ATGATGAGAAAAAGCGTAAGGCGGGCGATGTTAATGACGACAGCCTGTGTTTCGCTGCTGTTGGCCAGTGTGCCGCTGTGTGCCCAGGCGAACGATGTTCAACAAAAGCTCGCGGCGCTGGAGAAAAGCAGCGGGGGACGACTGGGTGTGGCGTTGATTAACACCGCCGATAACACGCAGACGCTCTACCGCGCCGACGAGCGTTTTGCCATGTGCAGCACCAGTAAAGTGATGGCGGTAGCGGCGGTGCTTAAGCAAAGTGAAACGCAAAAGGGCTTGTTGAGTCAGCGGGTTGAAATTAAGCCCTCAGACTTGATTAACTACAACCCCATTGCGGAAAAACACGTCAATGGCACGATGACATTCGGGGAGTTGAGCGCGGCGGCGCTACAGTACAGCGATAATACTGCCATGAATAAGCTGATTGCCCATCTCGGGGGGCCGGATAAAGTGACGGCATTTGCCCGTACGATTGGCGATGACACGTTCCGGCTCGATCGTACCGAGCCGACGCTCAACACCGCGATCCCCGGCGACCCGCGCGATACCACCACGCCGTTAGCGATGGCGCAGGCTCTGCGCAATCTGACGTTGGGCAATGCCCTGGGTGACACTCAGCGTGCGCAGCTGGTGATGTGGCTGAAAGGCAACACCACCGGCGCTGCCAGCATTCAGGCAGGGCTACCCACATCGTGGGTTGTCGGGGATAAAACCGGCAGCGGCGGTTATGGTACGACGAATGATATCGCGGTTATTTGGCCGGAAGGTCGCGCGCCGCTCGTTCTGGTGACTTACTTCACCCAGTCGGAGCCGAAGGCAGAGAGCCGTCGTGACGTGCTCGCTGCTGCCGCCAGAATTGTCACCGACGGTTATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001887","ARO_id":"38287","ARO_name":"CTX-M-25","CARD_short_name":"CTX-M-25","ARO_description":"CTX-M-25 is a beta-lactamase found in Escherichia coli.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"368":{"model_id":"368","model_name":"CARB-14","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1991":{"protein_sequence":{"accession":"AFI72872.1","sequence":"MDVRKHKASFFSVVITFLCLTLSLNANATDSVLEAVTNAETELGARIGLAVHDLETGKRWEHKSNERFPLSSTFKTLACANVLQRVDLGKERIDRVVRFSESNLVTYSPVTEKHVGKKGMSLAELCQATLSTSDNSAANFILQAIGGPKALTKFLRSIGDDTTRLDRWETELNEAVPGDKRDTTTPIAMVTTLEKLLIDETLSIKSRQQLESWLKGNEVGDALFRKGVPSDWIVADRTGAGGYGSRAITAVMWPPNRKPIVAALYITETDASFEERNAVIAKIGEQIAKIVLMENSRN"},"dna_sequence":{"accession":"JQ364968.1","fmin":"3332","fmax":"4229","strand":"+","sequence":"ATGGACGTACGTAAACACAAGGCTAGTTTTTTTAGCGTAGTAATTACTTTTTTATGTCTCACGCTATCATTAAATGCTAATGCAACAGACTCAGTACTTGAAGCGGTTACCAATGCTGAAACTGAATTAGGCGCTAGAATTGGTCTAGCTGTGCATGATTTGGAAACGGGAAAACGTTGGGAACATAAATCTAATGAACGTTTTCCTCTAAGTAGTACCTTTAAAACACTTGCCTGTGCAAACGTTCTTCAAAGAGTTGATCTAGGTAAAGAAAGAATTGATAGAGTTGTGAGATTCTCTGAAAGCAATCTCGTTACATACTCACCTGTAACAGAAAAACATGTGGGTAAAAAAGGGATGTCGCTCGCAGAGCTGTGTCAGGCCACATTATCAACCAGTGATAATTCAGCTGCCAATTTTATTCTACAAGCGATTGGTGGACCTAAGGCTCTAACGAAATTTTTGCGTTCCATTGGCGACGATACTACGCGCCTTGATCGCTGGGAAACAGAACTTAACGAAGCGGTACCTGGAGATAAGCGAGACACGACAACACCAATTGCAATGGTAACGACACTTGAAAAGTTACTAATTGACGAAACACTATCTATCAAATCTCGTCAACAACTAGAATCTTGGCTTAAAGGTAATGAGGTTGGCGATGCATTGTTTCGTAAAGGCGTTCCAAGTGACTGGATAGTAGCAGATAGAACAGGCGCTGGTGGTTATGGGTCGCGTGCTATTACTGCGGTGATGTGGCCTCCAAATCGCAAGCCTATCGTAGCCGCTCTATACATTACAGAGACAGACGCCTCGTTTGAAGAAAGAAATGCTGTCATTGCAAAAATTGGTGAGCAAATAGCGAAGATAGTATTAATGGAGAATAGCCGTAACTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3002252","ARO_id":"38652","ARO_name":"CARB-14","CARD_short_name":"CARB-14","ARO_description":"CARB-14 is a beta-lactamase found in Acinetobacter baumannii.","ARO_category":{"36230":{"category_aro_accession":"3000091","category_aro_cvterm_id":"36230","category_aro_name":"CARB beta-lactamase","category_aro_description":"CARB beta-lactamases are class A lactamases that can hydrolyze carbenicillin. Many of the PSE beta-lactamases have been renamed as CARB-lactamases with the notable exception of PSE-2 which is now OXA-10.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"369":{"model_id":"369","model_name":"SHV-15","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"8259":{"protein_sequence":{"accession":"CAB37325.2","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAMLARVDAGDKQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGASKRGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AJ011428.2","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAATGCTGGCGCGGGTGGATGCCGGTGACAAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTAGCAAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001074","ARO_id":"37454","ARO_name":"SHV-15","CARD_short_name":"SHV-15","ARO_description":"SHV-15 is an extended-spectrum beta-lactamase found in E. coli.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"371":{"model_id":"371","model_name":"SHV-8","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"993":{"protein_sequence":{"accession":"AAB51384.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARNTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"U92041.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTACTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCAACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001067","ARO_id":"37447","ARO_name":"SHV-8","CARD_short_name":"SHV-8","ARO_description":"SHV-8 is an extended-spectrum beta-lactamase found in E. coli.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"372":{"model_id":"372","model_name":"qacA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"990"}},"model_sequences":{"sequence":{"265":{"protein_sequence":{"accession":"BAJ09383.1","sequence":"MISFFTKTTDMMTSKKRWTALVVLAVSLFVVTMDMTILIMALPELVRELDPSGTQQLWIVDIYSLVLAGFIIPLSAFADKWGRKKALLTGFALFGLVSLAIFFAESAEFVIAIRFLLGIAGALIMPTTLSMIRVIFENPKERATALAVWSIASSIGAVFGPIIGGALLEQFSWHSAFLINVPFAIIAVVAGLFLLPESKLSKEKSHSWDIPSTILSIAGMIGLVWSIKEFSKEGLADIIPWVVIVLAITMIVIFVKRNLSSSDPMLDVRLFKKRSFSAGTIAAFMTMFAMASVLLLASQWLQVVEELSPFKAGLYLLPMAIGDMVFAPIAPGLAARFGPKIVLPSGIGIAAIGMFIMYFFGHPLSYSTMALALILVGAGMASLAVASALIMLETPTSKAGNAAAVEESMYDLGNVFGVAVLGSLSSMLYRVFLDISSFSSKGIVGDLAHVAEESVVGAVEVAKATGIKQLANEAVTSFNDAFVATALVGGIIMIIISIVVYLLIPKSLDITKQK"},"dna_sequence":{"accession":"AB566411.1","fmin":"0","fmax":"1545","strand":"+","sequence":"ATGATTTCATTTTTTACAAAAACTACTGATATGATGACATCAAAAAAAAGATGGACTGCACTAGTAGTATTAGCTGTTAGTTTGTTTGTTGTTACAATGGATATGACAATATTAATTATGGCTTTACCGGAATTAGTAAGAGAGTTAGACCCTTCTGGTACCCAACAGTTATGGATAGTTGATATATACTCTCTTGTTTTAGCTGGCTTTATAATTCCATTGAGTGCCTTTGCTGATAAATGGGGAAGAAAAAAAGCATTATTAACTGGATTTGCTTTATTTGGCCTCGTTTCATTAGCTATATTTTTCGCAGAAAGTGCAGAGTTCGTAATAGCTATTCGATTTTTACTTGGTATTGCAGGTGCTTTAATAATGCCAACTACTCTTTCAATGATAAGAGTAATTTTTGAAAACCCTAAAGAAAGGGCCACTGCATTAGCTGTATGGTCAATCGCTTCATCGATAGGTGCTGTTTTTGGACCAATTATCGGAGGAGCTTTACTTGAGCAATTTTCATGGCACTCGGCATTTTTAATTAATGTACCGTTTGCGATAATAGCAGTTGTAGCAGGTTTATTTTTATTACCAGAGTCTAAGTTATCAAAAGAAAAGTCTCACTCGTGGGATATTCCTTCTACAATTTTATCAATTGCAGGCATGATTGGACTGGTATGGAGTATCAAAGAATTTTCAAAAGAAGGACTAGCAGATATTATTCCATGGGTTGTAATAGTATTAGCAATTACCATGATAGTGATATTTGTTAAACGTAATTTATCAAGTTCTGATCCAATGTTAGACGTAAGACTTTTTAAAAAGAGATCATTTTCAGCTGGTACAATTGCTGCATTTATGACAATGTTTGCAATGGCATCTGTTTTGTTATTAGCTTCACAATGGTTACAGGTTGTGGAAGAACTTTCTCCTTTTAAAGCTGGCTTATACCTATTACCTATGGCAATAGGAGATATGGTGTTTGCACCAATTGCACCCGGATTAGCGGCGCGATTTGGACCGAAAATAGTGTTACCTTCCGGAATTGGAATTGCAGCCATTGGCATGTTTATTATGTATTTCTTTGGTCATCCATTATCATATTCTACAATGGCTTTAGCATTAATTTTAGTTGGAGCTGGTATGGCTTCACTAGCAGTTGCATCTGCTCTAATAATGTTAGAAACACCTACATCAAAAGCAGGTAATGCAGCTGCTGTTGAAGAGTCTATGTATGACCTTGGAAATGTTTTTGGTGTAGCAGTACTTGGTAGCCTATCTTCTATGCTTTATCGTGTATTTTTAGATATTTCATCTTTTTCATCAAAAGGTATAGTTGGAGATTTAGCTCATGTAGCTGAAGAATCTGTAGTGGGCGCTGTCGAAGTAGCTAAAGCTACGGGGATAAAACAGCTTGCAAACGAGGCTGTAACATCATTTAATGATGCTTTTGTAGCAACTGCTTTAGTAGGTGGGATTATCATGATTATCATTTCAATAGTTGTCTATTTGTTAATTCCCAAATCACTTGATATAACTAAACAAAAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35508","NCBI_taxonomy_name":"Staphylococcus aureus","NCBI_taxonomy_id":"1280"}}}},"ARO_accession":"3003046","ARO_id":"39480","ARO_name":"qacA","CARD_short_name":"qacA","ARO_description":"qacA is a subunit of the qac multidrug efflux pump.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"373":{"model_id":"373","model_name":"MIR-3","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"1810":{"protein_sequence":{"accession":"AAU95779.1","sequence":"MMTKSLSCALLLSVASAAFAAPMSEKQLAEVVERTVTPLMNAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEIALGDPVAKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDTASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMSYEQAMTTRVFKPLKLDHTWINVPKAEEAHYAWGYREGKAVHVSPGMLDAEAYGVKTNVKDMASWLIANMKPDSLHAPSLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVGGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILDALQ"},"dna_sequence":{"accession":"AY743435.1","fmin":"13","fmax":"1159","strand":"+","sequence":"ATGATGACAAAATCCCTAAGCTGTGCCCTGCTGCTCAGCGTCGCCAGCGCTGCATTCGCCGCACCGATGTCCGAAAAACAGCTGGCTGAGGTGGTGGAACGTACCGTTACGCCGCTGATGAACGCGCAGGCCATTCCGGGTATGGCGGTGGCGGTAATTTATCAGGGTCAGCCACACTACTTTACCTTCGGTAAAGCCGATGTTGCGGCGAACAAACCCGTCACCCCGCAAACCCTGTTTGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTACTGGGCGGCGATGCCATTGCCCGGGGTGAAATAGCGCTGGGCGATCCGGTAGCAAAATACTGGCCTGAGCTCACGGGCAAGCAGTGGCAGGGCATTCGCATGCTGGATCTGGCAACCTATACCGCAGGCGGTCTGCCGTTACAGGTGCCGGATGAGGTCACGGATACCGCCTCTCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCGGGCACCACGCGTCTTTACGCTAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTCAAACCTTCCGGCATGAGCTATGAGCAGGCCATGACGACGCGGGTCTTTAAACCCCTCAAGCTGGACCATACCTGGATTAACGTCCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGATACCGTGAGGGTAAAGCGGTCCACGTTTCGCCAGGGATGCTGGACGCGGAAGCCTATGGCGTAAAAACTAACGTGAAGGATATGGCGAGCTGGCTGATAGCCAACATGAAGCCGGATTCTCTTCACGCTCCCTCACTCAAGCAAGGCATTGCTCTGGCGCAGTCTCGCTACTGGCGCGTGGGTGCTATGTATCAGGGGTTAGGCTGGGAGATGCTCAACTGGCCGGTCGATGCCAAAACCGTCGTCGGAGGCAGTGATAACAAGGTGGCGCTGGCACCATTGCCCGTGGCAGAAGTGAATCCACCCGCGCCGCCGGTCAAAGCCTCCTGGGTCCATAAAACAGGCTCGACGGGCGGGTTTGGCAGCTACGTGGCATTTATTCCTGAAAAGCAGCTCGGCATTGTGATGCTGGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCGTATCCTCGACGCGCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3002169","ARO_id":"38569","ARO_name":"MIR-3","CARD_short_name":"MIR-3","ARO_description":"MIR-3 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36197":{"category_aro_accession":"3000058","category_aro_cvterm_id":"36197","category_aro_name":"MIR beta-lactamase","category_aro_description":"MIR beta-lactamases are plasmid-mediated beta-lactamases that confer resistance to oxyimino- and alpha-methoxy beta-lactams.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"374":{"model_id":"374","model_name":"SHV-21","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1391":{"protein_sequence":{"accession":"AAF34335.1","sequence":"MLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGEFCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEAFPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGASERGARGIVALLGPNNKAERIVVIYLRDTPASMAERN"},"dna_sequence":{"accession":"AF117745.1","fmin":"0","fmax":"780","strand":"+","sequence":"CTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAATTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTACTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGTTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTAGCGAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAAT","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001079","ARO_id":"37459","ARO_name":"SHV-21","CARD_short_name":"SHV-21","ARO_description":"SHV-21 is a broad-spectrum beta-lactamase that has been found in clinical isolates.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"375":{"model_id":"375","model_name":"mdtH","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"4493":{"protein_sequence":{"accession":"AAC74149.2","sequence":"MSRVSQARNLGKYFLLIDNMLVVLGFFVVFPLISIRFVDQMGWAAVMVGIALGLRQFIQQGLGIFGGAIADRFGAKPMIVTGMLMRAAGFATMGIAHEPWLLWFSCLLSGLGGTLFDPPRSALVVKLIRPQQRGRFFSLLMMQDSAGAVIGALLGSWLLQYDFRLVCATGAVLFVLCAAFNAWLLPAWKLSTVRTPVREGMTRVMRDKRFVTYVLTLAGYYMLAVQVMLMLPIMVNDVAGAPSAVKWMYAIEACLSLTLLYPIARWSEKHFRLEHRLMAGLLIMSLSMMPVGMVSGLQQLFTLICLFYIGSIIAEPARETLSASLADARARGSYMGFSRLGLAIGGAIGYIGGGWLFDLGKSAHQPELPWMMLGIIGIFTFLALGWQFSQKRAARRLLERDA"},"dna_sequence":{"accession":"U00096.1","fmin":"1124117","fmax":"1125326","strand":"-","sequence":"ATGTCCCGCGTGTCGCAGGCGAGGAACCTGGGTAAATATTTCCTGCTCATCGATAATATGCTGGTCGTGCTGGGGTTCTTTGTTGTCTTCCCGCTGATCTCTATCCGCTTCGTTGATCAAATGGGCTGGGCCGCCGTCATGGTCGGTATTGCTCTCGGTCTACGCCAATTTATTCAGCAAGGTCTGGGTATTTTCGGCGGTGCAATTGCCGACCGCTTTGGTGCCAAACCGATGATTGTTACCGGTATGCTGATGCGCGCCGCCGGATTCGCCACAATGGGTATCGCCCACGAACCGTGGCTATTGTGGTTTTCATGCCTGCTCTCGGGACTCGGTGGCACGTTGTTTGATCCGCCGCGTTCGGCGCTGGTGGTGAAATTAATCCGTCCACAGCAGCGTGGTCGTTTTTTCTCGCTGTTGATGATGCAGGACAGTGCCGGTGCGGTCATTGGCGCATTGTTGGGGAGCTGGCTGTTGCAATACGACTTTCGCCTGGTCTGCGCCACAGGGGCAGTTCTATTTGTGCTATGTGCGGCGTTCAATGCGTGGTTGTTACCAGCATGGAAACTCTCCACCGTACGCACGCCCGTTCGCGAAGGCATGACCCGCGTGATGCGTGACAAGCGTTTTGTCACCTATGTTCTGACGCTGGCGGGTTACTACATGCTGGCTGTACAAGTGATGCTGATGCTGCCAATTATGGTCAACGACGTGGCTGGCGCGCCCTCTGCCGTTAAATGGATGTATGCCATTGAAGCGTGTCTGTCGTTAACGTTGCTCTACCCTATCGCCCGCTGGAGTGAAAAGCATTTTCGTCTGGAACACCGGTTGATGGCTGGGCTGTTGATAATGTCATTAAGCATGATGCCGGTGGGCATGGTCAGCGGCCTGCAACAACTTTTCACCCTGATTTGTCTGTTTTATATCGGGTCGATCATTGCCGAGCCTGCGCGTGAAACCTTAAGTGCTTCGCTGGCGGACGCAAGAGCTCGCGGCAGCTATATGGGGTTTAGCCGTCTGGGTCTGGCGATTGGCGGCGCTATTGGTTATATCGGTGGCGGCTGGCTGTTTGACCTGGGCAAATCGGCGCACCAGCCAGAGCTTCCGTGGATGATGCTGGGCATTATTGGCATCTTCACTTTCCTTGCGCTGGGTTGGCAGTTTAGCCAGAAACGCGCCGCGCGTCGTTTGCTTGAACGCGACGCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36849","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. MG1655","NCBI_taxonomy_id":"511145"}}}},"ARO_accession":"3001216","ARO_id":"37615","ARO_name":"mdtH","CARD_short_name":"mdtH","ARO_description":"Multidrug resistance protein MdtH.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35942":{"category_aro_accession":"0000023","category_aro_cvterm_id":"35942","category_aro_name":"enoxacin","category_aro_description":"Enoxacin belongs to a group called fluoroquinolones. Its mode of action depends upon blocking bacterial DNA replication by binding itself to DNA gyrase and causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"376":{"model_id":"376","model_name":"lnuC","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"110":{"protein_sequence":{"accession":"AAY32951.1","sequence":"MVNITDVNQIFQFAIDAEIKVFLDGGWGVDALLGYQSRAHNDIDIFVEKNDYQNFIEIMKANGFYEIKMEYTTLNHTVWEDLKNRIIDLHCFEYTDEGEILYDGDCFPVETLSGKGRIEEIEVSCIEPYSQVMFHLGYEFDENDAHDVKLLCETLHIEIPNEYR"},"dna_sequence":{"accession":"AY928180.1","fmin":"0","fmax":"495","strand":"+","sequence":"ATGGTCAATATAACAGATGTAAACCAGATTTTCCAATTTGCAATAGATGCGGAGATTAAAGTCTTTCTTGATGGTGGCTGGGGTGTAGATGCTCTTCTTGGATATCAGTCAAGAGCCCATAATGATATTGACATTTTTGTAGAAAAGAACGATTATCAGAACTTTATAGAAATAATGAAAGCTAATGGCTTTTATGAGATTAAGATGGAATATACAACATTGAACCATACTGTATGGGAAGATTTGAAAAACAGAATTATTGATTTGCATTGTTTTGAATATACGGACGAAGGTGAAATTCTTTATGATGGGGATTGTTTTCCGGTAGAAACTCTTTCGGGTAAAGGAAGAATTGAGGAAATAGAGGTTTCCTGTATTGAACCATATAGTCAAGTAATGTTCCATCTGGGATACGAGTTTGATGAAAATGATGCACATGATGTGAAGTTATTGTGTGAGACACTTCATATCGAAATTCCAAATGAGTATAGATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36847","NCBI_taxonomy_name":"Streptococcus agalactiae","NCBI_taxonomy_id":"1311"}}}},"ARO_accession":"3002837","ARO_id":"39271","ARO_name":"lnuC","CARD_short_name":"lnuC","ARO_description":"lnuC is a transposon-mediated nucleotidyltransferase found in Streptococcus agalactiae.","ARO_category":{"36360":{"category_aro_accession":"3000221","category_aro_cvterm_id":"36360","category_aro_name":"lincosamide nucleotidyltransferase (LNU)","category_aro_description":"Resistance to the lincosamide antibiotic by ATP-dependent modification of the 3' and\/or 4'-hydroxyl groups of the methylthiolincosamide sugar.","category_aro_class_name":"AMR Gene Family"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"377":{"model_id":"377","model_name":"mepA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"850"}},"model_sequences":{"sequence":{"3623":{"protein_sequence":{"accession":"AAU95768.1","sequence":"MKDEQLYYFEKSPVFKAMMHFSLPMMIGTLLSVIYGILNIYFIGFLEDSHMISAISLTLPVFAILMGLGNLFGVGAGTYISRLLGAKDYSKSKFVSSFSIYGGIALGLIVILVTLPFSDQIAAILGARGETLALTSNYLKVMFLSAPFVILFFILEQFARAIGAPMVSMIGMLASVGLNIILDPILIFGFDLNVVGAALGTAISNVAAALFFIIYFMKNSDVVSVNIKLAKPNKEMLSEIFKIGIPAFLMSILMGFTGLVLNLFLAHYGNFAIASYGISFRLVQFPELIIMGLCEGVVPLIAYNFMANKGRMKDVIKAVIMSIGVIFVVCMSAVFTIGHHMVGLFTTDQAIVEMATFILKVTMASLLLNGIGFLFTGMLQATGQGRGATIMAILQGAIIIPVLFIMNALFGLTGVIWSLLIAESLCALAAMLIVYLLRDRLTVDTSELIEG"},"dna_sequence":{"accession":"AY661734.1","fmin":"839","fmax":"2195","strand":"+","sequence":"ATGAAAGACGAACAATTATATTATTTTGAGAAATCGCCAGTATTTAAAGCGATGATGCATTTCTCATTGCCAATGATGATAGGGACTTTATTAAGCGTTATTTATGGCATATTAAATATTTACTTTATAGGATTTTTAGAAGATAGCCACATGATTTCTGCTATCTCTCTAACACTGCCAGTATTTGCTATCTTAATGGGGTTAGGTAATTTATTTGGCGTTGGTGCAGGAACTTATATTTCACGTTTATTAGGTGCGAAAGACTATAGTAAGAGTAAATTTGTAAGTAGTTTCTCTATTTATGGTGGTATTGCACTAGGACTTATCGTGATTTTAGTTACTTTACCATTCAGTGATCAAATCGCAGCAATTTTAGGGGCGAGAGGTGAAACGTTAGCTTTAACAAGTAATTATTTGAAAGTAATGTTTTTAAGTGCACCTTTTGTAATTTTGTTCTTCATATTAGAACAATTTGCACGTGCAATTGGGGCACCAATGGTTTCTATGATTGGTATGTTAGCTAGTGTAGGCTTAAATATTATTTTAGATCCAATTTTAATTTTTGGTTTTGATTTAAACGTTGTTGGTGCAGCTTTGGGTACTGCAATCAGTAATGTTGCTGCTGCTCTGTTCTTTATCATTTATTTTATGAAAAATAGTGACGTTGTGTCAGTTAATATTAAACTTGCGAAACCTAATAAAGAAATGCTTTCTGAAATCTTTAAAATCGGTATTCCTGCATTTTTAATGAGTATCTTAATGGGATTCACAGGATTAGTTTTAAATTTATTTTTAGCACATTATGGAAACTTCGCGATTGCAAGTTATGGTATCTCATTTAGACTTGTGCAATTTCCAGAACTTATTATCATGGGATTATGTGAAGGTGTTGTACCACTAATTGCATATAACTTTATGGCAAATAAAGGCCGTATGAAAGACGTTATCAAAGCAGTTATCATGTCTATCGGCGTTATCTTTGTTGTATGTATGAGTGCTGTATTTACAATTGGACATCATATGGTCGGACTATTTACTACTGATCAAGCCATTGTTGAGATGGCGACATTTATTTTGAAAGTAACAATGGCATCATTATTATTAAATGGTATAGGTTTCTTGTTTACTGGTATGCTTCAAGCGACTGGGCAAGGTCGTGGTGCTACAATTATGGCCATTTTACAAGGTGCAATTATCATTCCAGTATTATTTATTATGAATGCTTTGTTTGGACTAACAGGTGTCATTTGGTCATTATTAATTGCTGAGTCACTTTGTGCTTTAGCAGCAATGTTAATCGTCTATTTATTACGTGATCGTTTGACAGTTGATACATCTGAATTAATAGAAGGTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35508","NCBI_taxonomy_name":"Staphylococcus aureus","NCBI_taxonomy_id":"1280"}}}},"ARO_accession":"3000026","ARO_id":"36035","ARO_name":"mepA","CARD_short_name":"mepA","ARO_description":"MepA is an efflux protein regulated by MepR and part of the MepRAB cluster. Its presence in Staphylococcus aureus led to multidrug resistance, while it has also been shown to decrease tigecycline susceptibility.","ARO_category":{"36251":{"category_aro_accession":"3000112","category_aro_cvterm_id":"36251","category_aro_name":"multidrug and toxic compound extrusion (MATE) transporter","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Multidrug and toxic compound extrusion (MATE) transporters utilize the cationic gradient across the membrane as an energy source. Although there is a diverse substrate specificity, almost all MATE transporters recognize fluoroquinolones. Arciflavine, ethidium and aminoglycosides are also good substrates.","category_aro_class_name":"AMR Gene Family"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"378":{"model_id":"378","model_name":"TEM-214","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"2126":{"protein_sequence":{"accession":"AJO16044.1","sequence":"MSIQHFRVALFPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"KP050491.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTTTTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001391","ARO_id":"37791","ARO_name":"TEM-214","CARD_short_name":"TEM-214","ARO_description":"TEM-214 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"379":{"model_id":"379","model_name":"OXA-148","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1679":{"protein_sequence":{"accession":"ACX31140.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDKKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKASTTEVFKWNGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVKSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"GQ853679.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATAAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAAGCACCACAGAAGTATTTAAGTGGAACGGGCAAAAAAGGCTGTTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGAAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001453","ARO_id":"37853","ARO_name":"OXA-148","CARD_short_name":"OXA-148","ARO_description":"OXA-148 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"380":{"model_id":"380","model_name":"CTX-M-147","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1272":{"protein_sequence":{"accession":"AHA80961.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAVAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTESTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"KF513180.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGTCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAATCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGACTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002005","ARO_id":"38405","ARO_name":"CTX-M-147","CARD_short_name":"CTX-M-147","ARO_description":"CTX-M-147 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"381":{"model_id":"381","model_name":"QnrS1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"5325":{"protein_sequence":{"accession":"ABF47469.1","sequence":"METYNHTYRHHNFSHKDLSDLTFTACTFIRSDFRRANLRDTTFVNCKFIEQGDIEGCHFDVADLRDASFQQCQLAMANFSNANCYGIEFRACDLKGANFSRTNFAHQVSNRMYFCSAFISGCNLSYANMERVCLEKCELFENRWIGTNLAGASLKESDLSRGVFSEDVWGQFSLQGANLCHAELDGLDPRKVDTSGIKIAAWQQELILEALGIVVYPD"},"dna_sequence":{"accession":"DQ485529.1","fmin":"0","fmax":"657","strand":"+","sequence":"ATGGAAACCTACAATCATACATATCGGCACCACAACTTTTCACATAAAGACTTAAGTGATCTCACCTTCACCGCTTGCACATTCATTCGCAGCGACTTTCGACGTGCTAACTTGCGTGATACGACATTCGTCAACTGCAAGTTCATTGAACAGGGTGATATCGAAGGCTGCCACTTTGATGTCGCAGATCTTCGTGATGCAAGTTTCCAACAATGCCAACTTGCGATGGCAAACTTCAGTAATGCCAATTGCTACGGTATAGAGTTCCGTGCGTGTGATTTAAAAGGTGCCAACTTTTCCCGAACAAACTTTGCCCATCAAGTGAGTAATCGTATGTACTTTTGCTCAGCATTTATTTCTGGATGTAATCTTTCCTATGCCAATATGGAGAGGGTTTGTTTAGAAAAATGTGAGTTGTTTGAAAATCGCTGGATAGGAACGAACCTAGCGGGTGCATCACTGAAAGAGTCAGACTTAAGTCGAGGTGTTTTTTCCGAAGATGTCTGGGGGCAATTTAGCCTACAGGGTGCCAATTTATGCCACGCCGAACTCGACGGTTTAGATCCCCGCAAAGTCGATACATCAGGTATCAAAATTGCAGCCTGGCAGCAAGAACTGATTCTCGAAGCACTGGGTATTGTTGTTTATCCTGACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35711","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Bovismorbificans","NCBI_taxonomy_id":"58097"}}}},"ARO_accession":"3002790","ARO_id":"39224","ARO_name":"QnrS1","CARD_short_name":"QnrS1","ARO_description":"QnrS1 is a plasmid-mediated quinolone resistance protein found in Shigella flexneri.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"382":{"model_id":"382","model_name":"QnrB61","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"721":{"protein_sequence":{"accession":"BAN04737.1","sequence":"MTLALVGEKIDRNRFTSEKVENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNVSALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGTQVLGATFSGSDLSGGEFSTFDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDNYQASLLMERLGIAVIG"},"dna_sequence":{"accession":"AB734053.1","fmin":"2303","fmax":"2948","strand":"+","sequence":"ATGACTCTGGCATTAGTTGGCGAAAAAATTGACAGAAATCGCTTCACCAGTGAGAAAGTTGAAAATAGTACATTTTTTAACTGCGATTTTTCAGGTGCCGACCTGAGCGGCACTGAATTTATCGGCTGCCAGTTCTATGATCGCGAAAGTCAGAAAGGATGCAATTTTAGTCGCGCAATGCTGAAAGATGCCATTTTCAAAAGCTGTGATTTATCAATGGCAGATTTCCGCAACGTCAGCGCATTGGGCATTGAAATTCGCCACTGCCGCGCACAAGGCGCAGATTTCCGCGGTGCAAGCTTTATGAATATGATCACCACGCGCACCTGGTTTTGCAGCGCATATATCACTAATACCAATCTAAGCTACGCCAATTTTTCGAAAGTCGTGTTGGAAAAGTGTGAGCTATGGGAAAACCGCTGGATGGGGACTCAGGTACTGGGTGCGACGTTCAGTGGTTCAGATCTCTCCGGCGGCGAGTTTTCGACTTTCGACTGGCGAGCAGCAAACTTCACACATTGCGATCTGACCAATTCGGAGTTAGGTGACTTAGATATTCGGGGTGTTGATTTACAAGGCGTTAAGTTAGACAACTACCAGGCATCGTTGCTCATGGAGCGGCTTGGCATCGCTGTGATTGGTTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39584","NCBI_taxonomy_name":"Citrobacter braakii","NCBI_taxonomy_id":"57706"}}}},"ARO_accession":"3002774","ARO_id":"39208","ARO_name":"QnrB61","CARD_short_name":"QnrB61","ARO_description":"QnrB61 is a plasmid-mediated quinolone resistance protein found in Citrobacter braakii.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"384":{"model_id":"384","model_name":"APH(2'')-IVa","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"729":{"protein_sequence":{"accession":"AAC14693.1","sequence":"MRTYTFDQVEKAIEQLYPDFTINTIEISGEGNDCIAYEINRDFIFKFPKHSRGSTNLFNEVNILKRIHNKLPLPIPEVVFTGMPSETYQMSFAGFTKIKGVPLTPLLLNNLPKQSQNQAAKDLARFLSELHSINISGFKSNLVLDFREKINEDNKKIKKLLSRELKGPQMKKVDDFYRDILENEIYFKYYPCLIHNDFSSDHILFDTEKNTICGIIDFGDAAISDPDNDFISLMEDDEEYGMEFVSKILNHYKHKDIPTVLEKYRMKEKYWSFEKIIYGKEYGYMDWYEEGLNEIRSIKIK"},"dna_sequence":{"accession":"AF016483.1","fmin":"0","fmax":"906","strand":"+","sequence":"ATGAGAACTTATACTTTCGACCAGGTAGAAAAGGCAATAGAGCAGTTATATCCTGATTTTACTATCAATACAATAGAGATTTCAGGAGAAGGCAATGACTGTATTGCATATGAAATAAACAGGGATTTCATTTTTAAATTTCCAAAGCATTCAAGAGGATCTACTAATCTTTTTAATGAAGTAAATATACTCAAAAGAATCCACAATAAATTACCCCTCCCCATTCCGGAGGTGGTTTTTACAGGAATGCCATCAGAAACGTACCAAATGTCTTTCGCAGGTTTTACAAAAATTAAAGGAGTACCATTGACACCTCTTCTACTCAATAATCTGCCGAAGCAATCTCAAAATCAGGCAGCTAAGGACCTGGCCCGATTTCTAAGTGAACTTCACAGCATAAACATCTCTGGATTCAAAAGTAATCTGGTATTAGATTTTCGAGAGAAGATAAATGAAGATAATAAAAAAATCAAAAAGTTACTATCCAGGGAATTAAAGGGTCCCCAGATGAAGAAAGTGGATGATTTTTACAGGGATATTCTAGAGAACGAAATCTACTTCAAATACTATCCTTGTCTTATTCATAACGATTTTAGCAGTGATCATATTTTATTTGATACCGAAAAAAATACTATTTGTGGAATAATCGATTTTGGAGATGCAGCTATTTCTGATCCCGACAATGATTTTATAAGTTTGATGGAAGATGATGAAGAATACGGCATGGAATTTGTATCAAAAATATTGAACCATTACAAACATAAGGATATACCGACAGTTTTGGAAAAATATAGGATGAAAGAAAAATACTGGTCGTTCGAAAAGATTATCTATGGAAAGGAATATGGTTATATGGATTGGTATGAAGAGGGATTAAATGAAATCAGAAGCATTAAAATTAAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36767","NCBI_taxonomy_name":"Enterococcus casseliflavus","NCBI_taxonomy_id":"37734"}}}},"ARO_accession":"3002637","ARO_id":"39037","ARO_name":"APH(2'')-IVa","CARD_short_name":"APH(2'')-IVa","ARO_description":"APH(2'')-IVa is a chromosomal-encoded aminoglycoside phosphotransferase in E. casseliflavus.","ARO_category":{"36267":{"category_aro_accession":"3000128","category_aro_cvterm_id":"36267","category_aro_name":"APH(2'')","category_aro_description":"A category of aminoglycoside O-phosphotransferase enzymes with modification regiospecificity based at the 2''-hydroxyl group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics, specifically kanamycin, tobramycin and amikacin, by the ATP-dependent phosphorylation of the 3'-hydroxyl group of the compound.","category_aro_class_name":"AMR Gene Family"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"40942":{"category_aro_accession":"3004015","category_aro_cvterm_id":"40942","category_aro_name":"gentamicin A","category_aro_description":"Gentamicin A is part of a complex of broad spectrum aminoglycoside antibiotics. Gentamicin inhibits protein synthesis, resulting in bacterial cell death.","category_aro_class_name":"Antibiotic"},"46133":{"category_aro_accession":"3007382","category_aro_cvterm_id":"46133","category_aro_name":"gentamicin","category_aro_description":"Gentamicin is a commonly used aminoglycoside antibiotic derived from members of the Micromonospora genus of bacteria. It acts by binding the 30S ribosomal subunit, thus inhibiting protein synthesis. Gentamicin is typically used to treat Gram-negative infections of the repiratory and urinary tract, as well as infections of the bone and soft tissue. It also exhibits considerable nephrotoxicity and ototoxicity. Gentamicin is administered as a mixture of gentamicin type C (which makes about around 80% of the complex) and types A, B, and X (distributed in the remaining 20% of the complex).","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"385":{"model_id":"385","model_name":"OXA-46","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1536":{"protein_sequence":{"accession":"AFP97030.1","sequence":"MAIRFFTILLSTFFLTSFVYAQEHVVIRSDWKKFFSDLQAEGAIVIADERQAKHTLSVFDQERAAKRYSPASTFKIPHTLFALDADAVRDEFQVFRWDGVNRSFAGHNQDQDLRSAMRNSTVWVYELFAKDIGEDKARRYLKQIDYGNVDPSTIKGDYWIDGNLKISAHEQILFLRKLYRNQLPFKVEHQRLVKDLMITEAGRSWILRAKTGWEGRFGWWVGWIEWPTGPVFFALNIDTPNRTDDLFKREAIARAILRSIDALPPN"},"dna_sequence":{"accession":"JX131372.1","fmin":"1478","fmax":"2279","strand":"+","sequence":"ATGGCAATCCGATTCTTCACCATACTGCTATCCACCTTCTTTCTTACCTCATTCGTGTATGCGCAAGAACATGTGGTAATCCGTTCGGACTGGAAAAAGTTCTTCAGCGACCTCCAGGCCGAAGGTGCAATCGTTATTGCAGACGAACGTCAAGCGAAGCATACTTTATCGGTTTTTGATCAAGAGCGAGCGGCAAAGCGTTACTCGCCAGCTTCAACCTTCAAGATACCCCACACACTTTTTGCACTTGATGCAGACGCCGTTCGTGATGAGTTCCAGGTTTTTCGATGGGACGGCGTTAACCGAAGCTTTGCAGGTCACAATCAAGACCAAGATTTGCGATCAGCGATGCGAAATTCTACGGTTTGGGTTTATGAGCTGTTTGCAAAAGATATCGGAGAGGACAAAGCAAGACGTTATTTAAAGCAAATTGATTATGGCAACGTCGATCCTTCGACAATCAAGGGCGATTACTGGATAGATGGAAATCTTAAAATCTCAGCGCACGAACAGATTTTGTTTCTCAGAAAACTCTATCGAAATCAGTTACCATTTAAGGTGGAGCACCAGCGCTTGGTGAAAGATCTCATGATTACGGAAGCCGGGCGCAGTTGGATACTACGCGCAAAGACCGGCTGGGAAGGCAGGTTTGGCTGGTGGGTAGGGTGGATTGAATGGCCAACAGGCCCCGTATTCTTTGCGCTGAATATTGATACGCCAAACAGAACGGACGATCTTTTCAAAAGAGAGGCCATCGCACGGGCAATCCTTCGTTCTATTGACGCATTGCCACCCAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3001797","ARO_id":"38197","ARO_name":"OXA-46","CARD_short_name":"OXA-46","ARO_description":"OXA-46 is a beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46509":{"category_aro_accession":"3007720","category_aro_cvterm_id":"46509","category_aro_name":"OXA-46-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-46.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"386":{"model_id":"386","model_name":"LEN-8","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"6133":{"protein_sequence":{"accession":"CEP30258.1","sequence":"MRYVRLCVISLLATLPLVVYAGPQPLEQIKQSESQLPGRVGMVEMDLASGRTLAAWRADERFPMVSTFKVLLCGAVLARVDAGLEQLDRRIHYRQQDLVDYSPVSEKHLVDGMTIGELCAAAITLSDNSAGNLLLATVGGPAGLTAFLRQIGDNVTHLDRWETALNEALPGDARDTTTPASMAATLRKLLTAQHLSARSQQQLLQWMVDDRVAGPLIRAVLPPGWFIADKTGAGERGARGIVALLGPDGKPERIVVIYLRDTPASMAERNQHIAGIGAALIEHWQR"},"dna_sequence":{"accession":"CEGG01000030.1","fmin":"7354","fmax":"8215","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGTGTTATCTCCCTGTTAGCCACCCTGCCACTGGTGGTATACGCCGGTCCACAGCCGCTTGAGCAGATTAAACAAAGCGAAAGCCAGCTGCCGGGCCGCGTGGGGATGGTGGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCGATGAACGCTTTCCCATGGTGAGCACCTTTAAAGTGCTGCTGTGCGGCGCGGTGCTGGCGCGGGTGGATGCCGGGCTCGAACAACTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGTCGACGGGATGACGATCGGCGAACTCTGCGCCGCCGCCATCACCCTGAGCGATAACAGCGCTGGCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCGGGATTAACTGCTTTTCTGCGCCAGATCGGTGACAACGTCACCCATCTTGACCGCTGGGAAACGGCACTGAATGAGGCGCTTCCCGGCGACGCGCGCGACACCACCACCCCGGCCAGCATGGCCGCCACGCTGCGCAAACTACTGACCGCGCAGCATCTGAGCGCCCGTTCGCAACAGCAACTCCTGCAGTGGATGGTGGACGATCGGGTTGCCGGCCCGCTGATCCGCGCCGTGCTGCCGCCGGGCTGGTTTATCGCCGACAAAACCGGGGCTGGCGAACGGGGTGCGCGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAACCGGAGCGCATTGTGGTGATCTATCTGCGGGATACCCCGGCGAGTATGGCCGAGCGTAATCAACATATCGCCGGGATCGGCGCAGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42612","NCBI_taxonomy_name":"Klebsiella variicola","NCBI_taxonomy_id":"244366"}}}},"ARO_accession":"3002458","ARO_id":"38858","ARO_name":"LEN-8","CARD_short_name":"LEN-8","ARO_description":"LEN-8 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36236":{"category_aro_accession":"3000097","category_aro_cvterm_id":"36236","category_aro_name":"LEN beta-lactamase","category_aro_description":"LEN beta-lactamases are chromosomal class A beta-lactamases that confer resistance to ampicillin, amoxicillin, carbenicillin, and ticarcillin but not to extended-spectrum beta-lactams.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"387":{"model_id":"387","model_name":"mdtA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"725"}},"model_sequences":{"sequence":{"15":{"protein_sequence":{"accession":"AAC75135.2","sequence":"MKGSYKSRWVIVIVVVIAAIAAFWFWQGRNDSRSAAPGATKQAQQSPAGGRRGMRSGPLAPVQAATAVEQAVPRYLTGLGTITAANTVTVRSRVDGQLIALHFQEGQQVKAGDLLAEIDPSQFKVALAQAQGQLAKDKATLANARRDLARYQQLAKTNLVSRQELDAQQALVSETEGTIKADEASVASAQLQLDWSRITAPVDGRVGLKQVDVGNQISSGDTTGIVVITQTHPIDLVFTLPESDIATVVQAQKAGKPLVVEAWDRTNSKKLSEGTLLSLDNQIDATTGTIKVKARFNNQDDALFPNQFVNARMLVDTEQNAVVIPTAALQMGNEGHFVWVLNSENKVSKHLVTPGIQDSQKVVIRAGISAGDRVVTDGIDRLTEGAKVEVVEAQSATTPEEKATSREYAKKGARS"},"dna_sequence":{"accession":"U00096.1","fmin":"2154015","fmax":"2155263","strand":"+","sequence":"ATGAAAGGTAGTTATAAATCCCGTTGGGTAATCGTAATCGTGGTGGTTATCGCCGCCATCGCCGCATTCTGGTTCTGGCAAGGCCGCAATGACTCCCGGAGTGCAGCCCCAGGGGCGACGAAACAAGCGCAGCAATCGCCAGCGGGTGGTCGACGTGGTATGCGTTCCGGCCCATTAGCCCCGGTTCAGGCGGCGACCGCCGTAGAACAGGCAGTTCCGCGTTACCTCACCGGGCTTGGCACCATTACCGCCGCTAATACCGTTACGGTGCGCAGCCGCGTGGACGGCCAACTGATAGCGTTACATTTCCAGGAAGGCCAGCAGGTCAAAGCAGGCGATTTACTGGCAGAAATTGACCCCAGCCAGTTCAAAGTTGCATTAGCACAAGCCCAGGGCCAACTGGCAAAAGATAAAGCCACGCTTGCCAACGCCCGCCGTGACCTGGCGCGTTATCAACAACTGGCAAAAACCAATCTCGTTTCCCGCCAGGAGCTGGATGCCCAACAGGCGCTGGTCAGTGAAACCGAAGGCACCATTAAGGCTGATGAAGCAAGCGTTGCCAGCGCGCAGCTGCAACTCGACTGGAGCCGGATTACCGCACCAGTCGATGGTCGCGTTGGTCTCAAGCAGGTTGATGTTGGTAACCAAATCTCCAGTGGTGATACCACCGGGATCGTGGTGATCACCCAGACGCATCCTATCGATTTAGTCTTTACCCTGCCGGAAAGCGATATCGCTACCGTAGTGCAGGCGCAGAAAGCCGGAAAACCGCTGGTGGTAGAAGCCTGGGATCGCACCAACTCGAAGAAATTAAGTGAAGGCACGCTGTTAAGTCTAGATAACCAAATCGATGCCACTACCGGTACGATTAAAGTGAAAGCACGCTTTAATAATCAGGATGATGCGCTGTTTCCCAATCAGTTTGTTAACGCGCGCATGTTAGTCGACACCGAACAAAACGCCGTAGTGATCCCAACAGCCGCCCTGCAAATGGGCAATGAAGGCCATTTTGTCTGGGTGCTGAATAGCGAAAACAAGGTCAGCAAACATCTGGTGACGCCGGGCATTCAGGACAGTCAGAAAGTGGTGATCCGTGCAGGTATTTCTGCGGGCGATCGCGTGGTGACAGACGGCATTGATCGCCTGACCGAAGGGGCGAAAGTGGAAGTGGTGGAAGCCCAGAGCGCCACTACTCCGGAAGAGAAAGCCACCAGCCGCGAATACGCGAAAAAAGGAGCACGCTCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36849","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. MG1655","NCBI_taxonomy_id":"511145"}}}},"ARO_accession":"3000792","ARO_id":"37172","ARO_name":"mdtA","CARD_short_name":"mdtA","ARO_description":"MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"36250":{"category_aro_accession":"3000111","category_aro_cvterm_id":"36250","category_aro_name":"novobiocin","category_aro_description":"Novobiocin is an aminocoumarin antibiotic produced by Streptomyces spheroides and Streptomyces niveus, and binds DNA gyrase subunit B inhibiting ATP-dependent DNA supercoiling.","category_aro_class_name":"Antibiotic"},"36242":{"category_aro_accession":"3000103","category_aro_cvterm_id":"36242","category_aro_name":"aminocoumarin antibiotic","category_aro_description":"Aminocoumarin antibiotics bind DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"388":{"model_id":"388","model_name":"QnrB71","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"406":{"protein_sequence":{"accession":"AGL43632.1","sequence":"MTLALVGEKIGRNRFTGEKVENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNVSALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGTQVLGATFSGSDLSGGEFSTFDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDNYQASLLMERLGIAVIG"},"dna_sequence":{"accession":"KC580660.1","fmin":"0","fmax":"645","strand":"+","sequence":"ATGACTCTGGCATTAGTTGGCGAAAAAATTGGCAGAAATCGCTTCACCGGTGAGAAAGTTGAAAATAGTACATTTTTTAACTGCGATTTTTCAGGTGCCGACCTGAGCGGCACTGAATTTATCGGCTGCCAGTTCTATGATCGCGAAAGTCAGAAAGGATGCAATTTTAGTCGCGCAATGCTGAAAGATGCCATTTTCAAAAGCTGTGATTTATCAATGGCAGATTTCCGCAACGTCAGCGCATTGGGCATTGAAATTCGCCACTGCCGCGCACAAGGCGCAGATTTCCGCGGTGCAAGCTTTATGAATATGATCACCACGCGCACCTGGTTTTGCAGCGCATATATCACTAATACCAATCTAAGCTACGCCAATTTTTCGAAAGTCGTGTTGGAAAAGTGTGAGCTATGGGAAAACCGCTGGATGGGGACTCAGGTACTGGGTGCGACGTTCAGTGGTTCAGATCTCTCCGGCGGCGAGTTTTCGACTTTCGACTGGCGAGCAGCAAACTTCACACATTGCGATCTGACCAATTCGGAGTTAGGTGACTTAGATATTCGGGGTGTTGATTTACAAGGCGTTAAGTTAGACAACTACCAGGCATCGTTGCTCATGGAGCGGCTTGGCATCGCTGTGATTGGTTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39584","NCBI_taxonomy_name":"Citrobacter braakii","NCBI_taxonomy_id":"57706"}}}},"ARO_accession":"3002783","ARO_id":"39217","ARO_name":"QnrB71","CARD_short_name":"QnrB71","ARO_description":"QnrB71 is a plasmid-mediated quinolone resistance protein found in Citrobacter braakii.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"391":{"model_id":"391","model_name":"VIM-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1577":{"protein_sequence":{"accession":"ABR10840.1","sequence":"MFKLLSKLLVYLTASIMAIASPLAFSVDSSGEYPTVSEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEVEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSASVLYGGCAIYELSRTSAGNVADADLAEWPTSIERIQQHYPEAQFVIPGHGLPGGLDLLKHTTNVVKAHTNRSVVE"},"dna_sequence":{"accession":"EF614235.1","fmin":"2948","fmax":"3749","strand":"+","sequence":"ATGTTCAAACTTTTGAGTAAGTTATTGGTCTATTTGACCGCGTCTATCATGGCTATTGCGAGTCCGCTCGCTTTTTCCGTAGATTCTAGCGGTGAGTATCCGACAGTCAGCGAAATTCCGGTCGGGGAGGTCCGGCTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCAGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAGAAGCAAATTGGACTTCCTGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGTAGAGGGGAACGAGATTCCCACGCACTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAACTCTTCTATCCTGGTGCTGCGCATTCGACCGACAACTTAGTTGTGTACGTCCCGTCTGCGAGTGTGCTCTATGGTGGTTGTGCGATTTATGAGTTGTCACGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCATTGAGCGGATTCAACAACACTACCCGGAAGCACAGTTCGTCATTCCGGGGCACGGCCTGCCGGGCGGTCTAGACTTGCTCAAGCACACAACGAATGTTGTAAAAGCGCACACAAATCGCTCAGTCGTTGAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002272","ARO_id":"38672","ARO_name":"VIM-2","CARD_short_name":"VIM-2","ARO_description":"VIM-2 is a beta-lactamase found in Pseudomonas spp.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"393":{"model_id":"393","model_name":"QnrS5","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"254":{"protein_sequence":{"accession":"AEG74319.1","sequence":"METYRHTYRHHNFSHKDLSALTFTACTFIRSDFRRANLRDTTFVNCKFIEQGDIEGCHFDVADLRDASFQQCQLAMANFSNANCYGIEFRACDLKGANFSRTNFAHQVSNRMYFCSAFITGCTLSYANMERVCLERCELFENRWIGTHLAGASLKESDLSRGVFSEDVWGQFSLQGANLCHAELDGLDPRKVDTSGIKIAAWQQEQLLEALGIVVFPD"},"dna_sequence":{"accession":"HQ631377.1","fmin":"0","fmax":"657","strand":"+","sequence":"ATGGAAACCTACCGTCACACATATCGGCACCACAACTTTTCACATAAAGACTTAAGTGCTCTCACCTTCACTGCTTGCACATTTATTCGCAGCGACTTTCGACGAGCTAACTTGCGCGATACGACATTCGTCAACTGCAAGTTCATTGAACAGGGTGATATCGAAGGCTGCCACTTTGATGTCGCAGATCTTCGTGATGCAAGTTTCCAACAATGCCAACTGGCGATGGCAAACTTCAGTAACGCCAATTGCTACGGTATTGAGTTCCGTGCGTGTGATTTAAAAGGTGCCAACTTTTCCCGAACAAACTTTGCCCATCAAGTGAGTAATCGTATGTACTTTTGCTCAGCCTTTATTACAGGATGTACTCTTTCCTATGCCAATATGGAGAGGGTTTGTTTAGAAAGATGTGAGTTGTTTGAAAATCGCTGGATAGGAACTCATCTAGCGGGTGCATCATTGAAAGAGTCAGACTTAAGTCGAGGTGTTTTTTCCGAAGATGTCTGGGGGCAATTTAGCCTACAGGGTGCCAATTTATGCCACGCCGAACTAGACGGTTTAGATCCCCGCAAAGTCGATACATCAGGTATCAAAATTGCAGCTTGGCAGCAAGAACAGCTTCTCGAAGCACTGGGTATTGTTGTTTTTCCTGACTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36957","NCBI_taxonomy_name":"Aeromonas sobria","NCBI_taxonomy_id":"646"}}}},"ARO_accession":"3002794","ARO_id":"39228","ARO_name":"QnrS5","CARD_short_name":"QnrS5","ARO_description":"QnrS5 is a plasmid-mediated quinolone resistance protein found in Aeromonas sobria.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"394":{"model_id":"394","model_name":"OXA-130","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1601":{"protein_sequence":{"accession":"ACD84988.1","sequence":"MNIKALLLITSAIFISACSPYIVTTNPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNTDIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"EU547445.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTACTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATACAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001651","ARO_id":"38051","ARO_name":"OXA-130","CARD_short_name":"OXA-130","ARO_description":"OXA-130 is a beta-lactamase found in A. baumannii.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"396":{"model_id":"396","model_name":"sul3","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4494":{"protein_sequence":{"accession":"ACJ63260.1","sequence":"MSKIFGIVNITTDSFSDGGLYLDTDKAIEHALHLVEDGADVIDLGAASSNPDTTEVGVVEEIKRLKPVIKALKEKGISISVDTFKPEVQSFCIEQKVDFINDIQGFPYPEIYSGLAKSDCKLVLMHSVQRIGAATKVETNPEEVFTSMMEFFKERIAALVEAGVKRERIILDPGMGFFLGSNPETSILVLKRFPEIQEAFNLQVMIAVSRKSFLGKITGTDVKSRLAPTLAAEMYAYKKGADYLRTHDVKSLSDALKISKALG"},"dna_sequence":{"accession":"FJ196385.1","fmin":"8531","fmax":"9323","strand":"-","sequence":"ATGAGCAAGATTTTTGGAATCGTAAATATAACCACCGATAGTTTTTCCGATGGAGGACTTTATTTAGATACAGATAAGGCAATTGAGCATGCTCTGCATTTGGTTGAAGATGGAGCAGATGTGATTGATTTGGGAGCCGCTTCCAGTAATCCTGATACAACTGAAGTGGGCGTTGTGGAAGAAATCAAAAGACTCAAACCTGTCATTAAGGCTTTAAAAGAAAAAGGCATTTCTATTTCTGTTGATACATTTAAACCTGAGGTTCAGAGTTTTTGCATAGAACAAAAGGTTGATTTTATTAATGATATTCAAGGTTTTCCTTATCCTGAGATTTATTCAGGCTTGGCAAAGTCAGATTGCAAACTTGTGTTGATGCACTCCGTTCAGCGAATTGGTGCAGCTACTAAAGTTGAAACGAATCCGGAAGAGGTTTTTACTTCCATGATGGAATTTTTTAAAGAAAGAATTGCTGCTTTAGTTGAGGCTGGTGTAAAGCGTGAACGAATTATTCTTGATCCGGGTATGGGCTTCTTTTTAGGCTCTAATCCAGAAACATCTATTCTTGTTTTGAAGCGTTTCCCTGAAATTCAAGAAGCTTTTAATTTGCAAGTAATGATTGCAGTGTCACGGAAATCATTCTTAGGTAAAATAACTGGAACCGATGTGAAATCTCGTTTAGCACCAACTCTTGCAGCAGAAATGTATGCATACAAAAAAGGTGCAGATTATCTCCGCACCCATGATGTTAAGTCTTTATCAGATGCCTTGAAAATATCCAAAGCCCTAGGTTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000413","ARO_id":"36552","ARO_name":"sul3","CARD_short_name":"sul3","ARO_description":"Sul3 is a sulfonamide resistant dihydropteroate synthase similar to Sul1 and Sul2. Its resistance gene was found encoded in E. coli plasmid DNA of sulfonamide resistant isolates.","ARO_category":{"41402":{"category_aro_accession":"3004238","category_aro_cvterm_id":"41402","category_aro_name":"sulfonamide resistant sul","category_aro_description":"The sul genes encode forms of dihydropteroate synthase that confer resistance to sulfonamide.","category_aro_class_name":"AMR Gene Family"},"36463":{"category_aro_accession":"3000324","category_aro_cvterm_id":"36463","category_aro_name":"sulfadiazine","category_aro_description":"Sulfadiazine is a potent inhibitor of dihydropteroate synthase, interfering with the tetrahydrofolic biosynthesis pathway. Tetrahydrofolic acid is essential for folate synthesis, a precursor to many nucleotides and amino acids.","category_aro_class_name":"Antibiotic"},"36464":{"category_aro_accession":"3000325","category_aro_cvterm_id":"36464","category_aro_name":"sulfadimidine","category_aro_description":"Sulfadimidine is an alkaline sulfonamide antibiotic that inhibits dihydropteroate synthase, and enzyme in the tetrahydrofolic acid biosynthesis pathway. This interferes with the production of folate, which is a precursor to many amino acids and nucleotides.","category_aro_class_name":"Antibiotic"},"36466":{"category_aro_accession":"3000327","category_aro_cvterm_id":"36466","category_aro_name":"sulfadoxine","category_aro_description":"Sulfadoxine is an inhibitor of dihydropteroate synthase, interfering with the tetrahydrofolic biosynthesis pathway. Tetrahydrofolic acid is essential for folate synthesis, a precursor to many nucleotides and amino acids.","category_aro_class_name":"Antibiotic"},"36468":{"category_aro_accession":"3000329","category_aro_cvterm_id":"36468","category_aro_name":"sulfamethoxazole","category_aro_description":"Sulfamethoxazole is a sulfonamide antibiotic usually taken with trimethoprim, a diaminopyrimidine antibiotic. Sulfamethoxazole inhibits dihydropteroate synthase, essential to tetrahydrofolic acid biosynthesis. This pathway generates compounds used in the synthesis of many amino acids and nucleotides.","category_aro_class_name":"Antibiotic"},"36469":{"category_aro_accession":"3000330","category_aro_cvterm_id":"36469","category_aro_name":"sulfisoxazole","category_aro_description":"Sulfisoxazole is an inhibitor of dihydropteroate synthase, interfering with the tetrahydrofolic biosynthesis pathway. Tetrahydrofolic acid is essential for folate synthesis, a precursor to many nucleotides and amino acids.","category_aro_class_name":"Antibiotic"},"37027":{"category_aro_accession":"3000683","category_aro_cvterm_id":"37027","category_aro_name":"sulfacetamide","category_aro_description":"Sulfacetamide is a very soluable sulfonamide antibiotic previously used to treat urinary tract infections. Its relatively low activity and toxicity to those with Stevens-Johnson syndrome have reduced its use and availability.","category_aro_class_name":"Antibiotic"},"37028":{"category_aro_accession":"3000684","category_aro_cvterm_id":"37028","category_aro_name":"mafenide","category_aro_description":"Mafenide is a sulfonamide used topically for treating burns.","category_aro_class_name":"Antibiotic"},"37042":{"category_aro_accession":"3000698","category_aro_cvterm_id":"37042","category_aro_name":"sulfasalazine","category_aro_description":"Sulfasalazine is a derivative of the early sulfonamide sulfapyridine (salicylazosulfapyridine). It was developed to increase water solubility and is taken orally for ulcerative colitis.","category_aro_class_name":"Antibiotic"},"37043":{"category_aro_accession":"3000699","category_aro_cvterm_id":"37043","category_aro_name":"sulfamethizole","category_aro_description":"Sulfamethizole is a short-acting sulfonamide that inhibits dihydropteroate synthetase.","category_aro_class_name":"Antibiotic"},"36421":{"category_aro_accession":"3000282","category_aro_cvterm_id":"36421","category_aro_name":"sulfonamide antibiotic","category_aro_description":"Sulfonamides are broad spectrum, synthetic antibiotics that contain the sulfonamide group. Sulfonamides inhibit dihydropteroate synthase, which catalyzes the conversion of p-aminobenzoic acid to dihydropteroic acid as part of the tetrahydrofolic acid biosynthetic pathway. Tetrahydrofolic acid is essential for folate synthesis, a precursor of many nucleotides and amino acids. Many sulfamides are taken with trimethoprim, an inhibitor of dihydrofolate reductase, also disturbing the trihydrofolic acid synthesis pathway.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"397":{"model_id":"397","model_name":"OXA-357","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1611":{"protein_sequence":{"accession":"AGZ83153.1","sequence":"MYKKALIAATSILFLSSCSSNTVKQHQIHSISANKNSEEIKSLFDQAQTTGVLVIKRGQTEEIYGNDLKRASTDYVPASTFKMLNALIGLEHHKVTTTEVFKWDGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMSKEVKRIGFGNADIGSKVDNFWLVGPLKISPEQETQFAYKLANKTLPFSKNVQEQVQSMVFIEEKNGSKIYAKSGWGWDVEPQVGWLTGWVVQPQGEIVAFSLNLEMKKGTPSSIRKEIAYKGLEQLGVL"},"dna_sequence":{"accession":"KF421160.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGTATAAAAAAGCCCTTATCGCTGCAACAAGTATCCTATTTTTATCCTCCTGTTCTTCCAATACGGTAAAACAACATCAAATACACTCTATTTCTGCCAATAAAAATTCAGAAGAAATTAAATCACTGTTTGATCAGGCACAGACCACGGGTGTTTTGGTGATTAAGCGAGGGCAAACAGAAGAAATTTATGGAAATGATCTTAAAAGAGCATCAACCGACTATGTTCCCGCCTCTACCTTTAAAATGTTAAATGCTTTAATTGGACTTGAACATCATAAGGTAACTACAACTGAAGTATTTAAATGGGATGGGCAGAAACGTTTATTTCCTGACTGGGAAAAGGACATGACACTGGGTGATGCCATGAAAGCTTCTGCGATTCCAGTTTATCAAGAACTAGCTCGTCGTATTGGACTTGATCTTATGTCTAAAGAGGTAAAACGTATTGGTTTCGGTAATGCGGACATTGGTTCAAAAGTAGATAATTTTTGGCTTGTAGGTCCACTTAAAATTTCACCTGAGCAAGAAACCCAATTTGCTTATAAATTAGCCAATAAAACTCTTCCATTTAGTAAAAATGTACAAGAACAAGTCCAATCAATGGTGTTCATAGAAGAAAAAAATGGAAGTAAGATTTATGCCAAAAGTGGGTGGGGATGGGATGTTGAACCACAAGTTGGTTGGTTAACAGGCTGGGTCGTTCAACCACAAGGAGAAATTGTCGCATTCTCACTTAATTTAGAAATGAAAAAAGGAACTCCCAGCTCTATTCGCAAAGAAATTGCTTATAAAGGCTTAGAACAACTCGGTGTTTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39094","NCBI_taxonomy_name":"Acinetobacter calcoaceticus","NCBI_taxonomy_id":"471"}}}},"ARO_accession":"3001544","ARO_id":"37944","ARO_name":"OXA-357","CARD_short_name":"OXA-357","ARO_description":"OXA-357 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46495":{"category_aro_accession":"3007706","category_aro_cvterm_id":"46495","category_aro_name":"OXA-213-like beta-lactamase","category_aro_description":"OXA-213-like enzymes have been identified to be intrinsic to A. calcoaceticus and have been subsequently detected in A. pittii. Phylogenetic analysis of OXA-213-like proteins identified two distinct subgroups within the OXA family. The first group was linked to A. pittii and the second group to A. calcoaceticus. The carbapenemase activity of these OXAs may be related to the species-dependent effect.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"398":{"model_id":"398","model_name":"TEM-71","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1574":{"protein_sequence":{"accession":"AAL03985.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGASKRGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AF203816.1","fmin":"210","fmax":"1071","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCAGTAAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3000937","ARO_id":"37317","ARO_name":"TEM-71","CARD_short_name":"TEM-71","ARO_description":"TEM-71 is an extended-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"399":{"model_id":"399","model_name":"MIR-16","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"1581":{"protein_sequence":{"accession":"AIT76114.1","sequence":"MMTKSLSCALLLSVASAAFAAPMSEKQLAEVVERTVTPLMNAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEIALGDPVAKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDTASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMSYEQAMTTRVFKPLKLDHTWINVPKAEEAHYAWGYREGKAVHVSPGMLDAEAYGVKTNVKDMASWVIANMKPDSLQAPSLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVGGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILDALQ"},"dna_sequence":{"accession":"KM087861.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGACAAAATCCCTAAGCTGTGCCCTGCTGCTCAGCGTCGCCAGCGCTGCATTCGCCGCACCGATGTCCGAAAAACAGCTGGCTGAGGTGGTGGAACGTACCGTTACGCCGCTGATGAACGCGCAGGCCATTCCGGGTATGGCGGTGGCGGTAATTTATCAGGGTCAGCCACACTACTTTACCTTCGGTAAAGCCGATGTTGCGGCGAACAAACCCGTCACCCCGCAAACCCTGTTTGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTACTGGGCGGCGATGCCATTGCCCGGGGTGAAATAGCGCTGGGCGATCCGGTAGCAAAATACTGGCCTGAGCTCACGGGCAAGCAGTGGCAGGGCATTCGCATGCTGGATCTGGCAACCTATACCGCAGGCGGTCTGCCGTTACAGGTGCCGGATGAGGTCACGGATACCGCCTCTCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCGGGCACCACGCGTCTTTACGCTAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTCAAACCTTCCGGCATGAGCTATGAGCAGGCCATGACGACGCGGGTCTTTAAACCCCTCAAGCTGGACCATACATGGATTAACGTCCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGATACCGTGAGGGTAAAGCGGTCCACGTTTCGCCAGGGATGCTGGACGCGGAAGCCTATGGCGTAAAAACTAACGTGAAGGATATGGCGAGCTGGGTGATAGCCAACATGAAGCCGGATTCTCTTCAGGCTCCCTCACTCAAGCAAGGCATTGCTCTGGCGCAGTCTCGCTACTGGCGCGTGGGGGCTATGTATCAGGGGTTAGGCTGGGAGATGCTCAACTGGCCGGTCGATGCCAAAACCGTCGTCGGAGGCAGTGATAACAAGGTGGCGCTGGCACCATTGCCCGTGGCAGAAGTGAATCCACCCGCGCCTCCGGTCAAGGCCTCCTGGGTCCATAAAACAGGCTCGACGGGCGGGTTTGGCAGCTACGTGGCATTTATTCCTGAAAAGCAGCTCGGCATTGTGATGCTCGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCGTATCCTCGACGCGCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36926","NCBI_taxonomy_name":"Enterobacter asburiae","NCBI_taxonomy_id":"61645"}}}},"ARO_accession":"3002181","ARO_id":"38581","ARO_name":"MIR-16","CARD_short_name":"MIR-16","ARO_description":"MIR-16 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36197":{"category_aro_accession":"3000058","category_aro_cvterm_id":"36197","category_aro_name":"MIR beta-lactamase","category_aro_description":"MIR beta-lactamases are plasmid-mediated beta-lactamases that confer resistance to oxyimino- and alpha-methoxy beta-lactams.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"400":{"model_id":"400","model_name":"PDC-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"1308":{"protein_sequence":{"accession":"ACQ82807.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALTQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"FJ666065.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGACCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTATGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36804","NCBI_taxonomy_name":"Pseudomonas aeruginosa PAO1","NCBI_taxonomy_id":"208964"}}}},"ARO_accession":"3002497","ARO_id":"38897","ARO_name":"PDC-1","CARD_short_name":"PDC-1","ARO_description":"PDC-1 is a beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"401":{"model_id":"401","model_name":"ACT-22","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1911":{"protein_sequence":{"accession":"AHM76774.1","sequence":"MMKKSLCCALLLSTSCAALAAPMSETQLAKVVARTVTPLMKAQSIPGMAVAVIYQGQPHYFTFGKADVAANTPVTAQTLFELGSISKTFTGVLGGDAIARGEISLSDPVTKYWPELTGKQWQGVRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQSWQPQWAPGTTRLYANASIGLFGALAVKPSGMRFEQAMTERVLKPLNLNHTWINVPKAEEQHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVKDMASWVVANMAPDGVQDASLKQGMALAQSRYWRTGSMYQGLGWEMLNWPVEAKTVVEGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKKLGIVMLANKSYPNPARVEAAYRILSALQ"},"dna_sequence":{"accession":"KF992027.1","fmin":"700","fmax":"1846","strand":"+","sequence":"ATGATGAAAAAATCCCTGTGCTGCGCCCTGCTGCTCAGCACCTCCTGCGCTGCATTAGCCGCACCTATGTCAGAAACACAGCTGGCGAAGGTCGTGGCACGTACCGTTACGCCCCTGATGAAAGCGCAGTCTATTCCGGGTATGGCGGTCGCCGTGATCTATCAGGGCCAGCCGCACTACTTCACCTTCGGCAAGGCCGATGTCGCAGCGAACACACCCGTCACTGCACAAACGCTGTTTGAGCTGGGCTCAATCAGCAAAACCTTCACCGGCGTTCTGGGTGGCGATGCTATTGCTCGCGGTGAAATTTCGCTGAGCGATCCGGTGACCAAATACTGGCCTGAGCTGACCGGCAAACAGTGGCAGGGCGTTCGCATGCTGGACCTGGCAACCTATACTGCCGGTGGCCTGCCGTTACAGGTGCCCGATGAGGTTACCGATAATGCCTCGCTGCTGCGTTTTTACCAGTCCTGGCAACCACAGTGGGCGCCAGGCACCACGCGTCTTTATGCGAATGCCAGCATCGGTCTGTTTGGGGCTCTGGCGGTGAAACCTTCTGGCATGCGCTTTGAGCAGGCGATGACAGAGCGGGTCCTGAAGCCGCTTAACCTGAACCATACGTGGATTAACGTTCCGAAGGCAGAAGAACAGCATTACGCCTGGGGTTATCGTGACGGTAAAGCGGTTCACGTTTCGCCGGGCATGCTCGATGCCGAAGCGTATGGCGTGAAAACCAACGTGAAGGATATGGCGAGCTGGGTAGTGGCTAACATGGCCCCCGATGGCGTACAGGATGCCTCACTGAAGCAGGGCATGGCGCTTGCACAGTCTCGCTACTGGCGCACAGGCTCGATGTACCAGGGCCTGGGCTGGGAGATGCTCAACTGGCCGGTAGAAGCCAAAACCGTGGTGGAGGGCAGCGACAACAAAGTAGCGCTTGCGCCGTTGCCCGTGGCAGAAGTGAACCCTCCTGCTCCACCGGTAAAAGCGTCATGGGTACATAAAACAGGCTCGACGGGCGGATTTGGCAGCTACGTGGCATTTATCCCTGAGAAGAAACTCGGCATTGTTATGCTGGCGAACAAGAGCTACCCGAACCCGGCGCGCGTGGAAGCGGCATACCGTATTCTGAGCGCTCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3001843","ARO_id":"38243","ARO_name":"ACT-22","CARD_short_name":"ACT-22","ARO_description":"ACT-22 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"403":{"model_id":"403","model_name":"dfrA8","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"568":{"protein_sequence":{"accession":"AHV80711.1","sequence":"MIELHAILAATANGCIGKDNALPWPPLKGDLARFKKLTMGKVVIMGRKTYESLPVKLEGRTCIVMTRQALELPGVRDANGAIFVNNVSDAMRFAQEESVGDVAYVIGGAEIFKRLALMITQIELTFVKRLYEGDTYVDLAEMVKDYEQNGMEEHDLHTYFTYRKKELTE"},"dna_sequence":{"accession":"KJ174469.1","fmin":"710","fmax":"1220","strand":"+","sequence":"ATGATCGAGCTTCATGCCATTTTAGCTGCCACCGCCAATGGTTGCATTGGGAAGGACAACGCACTTCCCTGGCCACCACTAAAAGGCGATCTGGCCAGATTCAAAAAATTGACCATGGGGAAGGTGGTCATTATGGGGCGCAAGACCTATGAGAGCTTGCCCGTCAAATTAGAAGGTCGCACCTGCATCGTTATGACGCGCCAAGCGCTGGAGCTTCCGGGTGTTCGTGACGCTAACGGCGCTATCTTCGTGAACAACGTCAGCGACGCCATGCGGTTCGCTCAAGAAGAGAGCGTGGGCGATGTGGCCTACGTCATTGGTGGCGCTGAGATATTCAAGCGACTTGCCTTGATGATCACGCAGATTGAATTGACCTTTGTTAAGCGACTGTACGAAGGCGACACCTACGTTGATCTGGCCGAAATGGTCAAAGACTACGAGCAGAATGGCATGGAAGAACATGACCTTCACACTTACTTCACTTACCGTAAAAAGGAGCTTACAGAATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35732","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Typhimurium","NCBI_taxonomy_id":"90371"}}}},"ARO_accession":"3002863","ARO_id":"39297","ARO_name":"dfrA8","CARD_short_name":"dfrA8","ARO_description":"dfrA8 is a transposon-encoded dihydrofolate reductase found in Salmonella enterica.","ARO_category":{"37617":{"category_aro_accession":"3001218","category_aro_cvterm_id":"37617","category_aro_name":"trimethoprim resistant dihydrofolate reductase dfr","category_aro_description":"Alternative dihydropteroate synthase dfr present on plasmids produces alternate proteins that are less sensitive to trimethoprim from inhibiting its role in folate synthesis, thus conferring trimethoprim resistance.","category_aro_class_name":"AMR Gene Family"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"404":{"model_id":"404","model_name":"OXA-217","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1455":{"protein_sequence":{"accession":"AEO44980.1","sequence":"MNIKALLLITSAIFISACSPYIVSANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTAVFKWDGQKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"JN603240.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGTCTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACTACAGCAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTAGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001489","ARO_id":"37889","ARO_name":"OXA-217","CARD_short_name":"OXA-217","ARO_description":"OXA-217 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"405":{"model_id":"405","model_name":"OXA-202","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1454":{"protein_sequence":{"accession":"ADX07747.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDVKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAMPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"HQ734813.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGTAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATGCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAACAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001667","ARO_id":"38067","ARO_name":"OXA-202","CARD_short_name":"OXA-202","ARO_description":"OXA-202 is a beta-lactamase found in A. baumannii.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"406":{"model_id":"406","model_name":"ACC-4","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"8175":{"protein_sequence":{"accession":"ABP49606.1","sequence":"MQNTLKLLSVITCLAATVQGALAANIDESKIKDTVDDLIQPLMQKNNIPGMSVAVTVNGKNYIYNYGLAAKQPQQPVTENTLFEVGSLSKTFAATLASYAQVSGKLSLDQSVSHYVPELRGSSFDHVSVLNVGTHTSGLQLFMPEDIKNTTQLMAYLKAWKPADAAGTHRVYSNIGTGLLGMIAAKSLGVSYEDAIEKTLLPQLGMHHSYLKVPADQMENYAWGYNKKDEPVHGNMEILGNEAYGIKTTSSDLLRYVQANMGQLKLDANAKMQQALTATHTGYFKSGEITQDLMWEQLPYPVSLPNLLTGNDMAMTKSVATPIVPPLPPQENVWINKTGSTNGFGAYIAFVPAKKMGIVMLANKNYSIDQRVTVAYKILSSLEGNK"},"dna_sequence":{"accession":"EF504260.2","fmin":"1994","fmax":"3155","strand":"-","sequence":"ATGCAGAACACATTGAAGCTGTTATCCGTGATTACCTGTCTGGCAGCAACTGTCCAAGGTGCTCTGGCTGCTAATATCGATGAGAGCAAAATTAAAGACACCGTTGATGACCTGATCCAGCCGCTGATGCAGAAGAATAATATTCCCGGTATGTCGGTCGCAGTGACCGTCAACGGTAAAAACTACATTTATAACTATGGGTTAGCGGCAAAACAGCCTCAGCAGCCGGTTACGGAAAATACGTTATTTGAAGTGGGTTCGCTGAGTAAAACGTTTGCTGCCACCTTGGCGTCCTATGCGCAGGTGAGCGGTAAGCTGTCTTTGGATCAAAGCGTTAGCCATTACGTTCCAGAGTTGCGTGGCAGCAGCTTTGACCACGTTAGCGTACTCAATGTGGGCACGCATACCTCAGGCCTACAGCTATTTATGCCGGAAGATATTAAAAATACCACACAGCTGATGGCTTATCTAAAAGCATGGAAACCTGCCGATGCGGCTGGAACCCATCGCGTTTATTCCAATATCGGTACTGGTTTGCTAGGGATGATTGCGGCGAAAAGTCTGGGTGTGAGCTATGAAGATGCGATTGAGAAAACCCTCCTTCCTCAGTTAGGCATGCATCACAGCTACTTGAAGGTTCCGGCTGACCAGATGGAAAACTATGCGTGGGGCTACAACAAGAAAGATGAGCCAGTGCACGGGAATATGGAGATTTTGGGTAACGAAGCTTATGGTATCAAAACCACCTCCAGCGACTTGTTACGCTACGTGCAAGCCAATATGGGGCAGTTAAAGCTTGATGCTAATGCCAAGATGCAACAGGCTCTGACAGCCACCCACACCGGCTATTTCAAATCGGGTGAGATTACTCAGGATCTGATGTGGGAGCAGCTGCCATATCCGGTTTCTCTGCCGAATTTGCTCACCGGTAACGATATGGCGATGACGAAAAGCGTGGCTACGCCGATTGTTCCGCCGTTACCGCCACAGGAAAATGTGTGGATTAATAAGACCGGATCAACTAACGGCTTCGGTGCCTATATTGCGTTTGTTCCTGCTAAGAAGATGGGGATCGTGATGCTGGCTAACAAAAACTACTCAATCGATCAGCGAGTGACGGTGGCGTATAAAATCCTGAGCTCATTGGAAGGGAATAAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001818","ARO_id":"38218","ARO_name":"ACC-4","CARD_short_name":"ACC-4","ARO_description":"ACC-4 is a beta-lactamase found in Escherichia coli.","ARO_category":{"36212":{"category_aro_accession":"3000073","category_aro_cvterm_id":"36212","category_aro_name":"ACC beta-lactamase","category_aro_description":"ACC beta-lactamases or Ambler class C beta-lactamases are AmpC beta-lactamases. They possess an interesting resistance phenotype due to their low activity against cephamycins.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"35980":{"category_aro_accession":"0000063","category_aro_cvterm_id":"35980","category_aro_name":"cefuroxime","category_aro_description":"Cefuroxime is a second-generation cephalosporin antibiotic with increased stability with beta-lactamases than first-generation cephalosporins. Cefuroxime is active against Gram-positive organisms but less active against methicillin-resistant strains.","category_aro_class_name":"Antibiotic"},"36689":{"category_aro_accession":"3000550","category_aro_cvterm_id":"36689","category_aro_name":"aztreonam","category_aro_description":"Aztreonam was the first monobactam discovered, and is greatly effective against Gram-negative bacteria while inactive against Gram-positive bacteria. Artreonam is a poor substrate for beta-lactamases, and may even act as an inhibitor. In Gram-negative bacteria, Aztreonam interferes with filamentation, inhibiting cell division and leading to cell death.","category_aro_class_name":"Antibiotic"},"36989":{"category_aro_accession":"3000645","category_aro_cvterm_id":"36989","category_aro_name":"cefotaxime","category_aro_description":"Cefotaxime is a semisynthetic cephalosporin taken parenterally. It is resistant to most beta-lactamases and active against Gram-negative rods and cocci due to its aminothiazoyl and methoximino functional groups.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"407":{"model_id":"407","model_name":"OXA-352","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1213":{"protein_sequence":{"accession":"AGW83450.1","sequence":"MYKKALIVATSILFLSACSSNTVKQHQIHSISANKNSEEIKSLFDQAQTTGVLVIKRGQTEEIYGNDLKRASTDYIPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMSKEVKRIGFGNANIGSKVDDFWLVGPLKITPQQETQFAYQLAHKTLPFSKNVQEQVQSMVFIEEKNGRKIYAKSGWGWDIEPQVGWLTGWVVQPQGEIVAFSLNLEMKKGTPSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"KF297581.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGTATAAAAAAGCCCTTATCGTTGCAACAAGTATCCTATTTTTATCCGCCTGTTCTTCCAATACGGTAAAACAACATCAAATACATTCTATTTCTGCCAATAAAAATTCAGAAGAAATTAAATCACTATTTGATCAAGCACAGACCACGGGTGTTTTGGTGATTAAGCGAGGGCAAACAGAAGAAATTTATGGCAATGATCTTAAAAGAGCATCAACCGACTATATTCCCGCCTCTACCTTTAAAATGTTAAATGCTTTAATTGGACTTGAACATCATAAGGCAACTACAACTGAAGTATTTAAATGGGATGGGCAAAAACGTTTATTTCCTGATTGGGAAAAGGACATGACACTGGGTGATGCCATGAAAGCTTCTGCAATCCCAGTTTACCAAGAATTAGCCCGACGTATTGGTCTGGATCTTATGTCCAAAGAGGTGAAACGAATTGGTTTCGGTAATGCTAACATTGGCTCAAAAGTAGATGATTTCTGGCTTGTTGGCCCTCTAAAAATTACACCTCAACAAGAAACCCAATTTGCTTATCAATTAGCCCATAAAACGCTTCCATTTAGCAAAAATGTACAAGAACAAGTTCAATCAATGGTGTTCATAGAAGAAAAAAATGGACGTAAAATTTATGCAAAAAGCGGTTGGGGATGGGATATTGAGCCACAAGTTGGTTGGTTAACAGGCTGGGTCGTTCAACCACAAGGAGAAATTGTGGCATTCTCACTTAATTTAGAAATGAAAAAAGGAACTCCTAGCTCTATTCGCAAAGAAATTGCTTATAAAGGCTTAGAACAACTGGGTATCTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39094","NCBI_taxonomy_name":"Acinetobacter calcoaceticus","NCBI_taxonomy_id":"471"}}}},"ARO_accession":"3001539","ARO_id":"37939","ARO_name":"OXA-352","CARD_short_name":"OXA-352","ARO_description":"OXA-352 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46495":{"category_aro_accession":"3007706","category_aro_cvterm_id":"46495","category_aro_name":"OXA-213-like beta-lactamase","category_aro_description":"OXA-213-like enzymes have been identified to be intrinsic to A. calcoaceticus and have been subsequently detected in A. pittii. Phylogenetic analysis of OXA-213-like proteins identified two distinct subgroups within the OXA family. The first group was linked to A. pittii and the second group to A. calcoaceticus. The carbapenemase activity of these OXAs may be related to the species-dependent effect.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"408":{"model_id":"408","model_name":"OXA-380","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4501":{"protein_sequence":{"accession":"AHL30280.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDDKAEKIKNLFNEAHTTGVLVIHQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEIFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSLKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"KF986261.1","fmin":"44","fmax":"869","strand":"-","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGACAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCATCAAGGTCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAATATTTAAGTGGGACGGGCAAAAAAGGCTGTTCCCAGAATGGGAAAAGGACATGACCCTAGGTGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCTAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001566","ARO_id":"37966","ARO_name":"OXA-380","CARD_short_name":"OXA-380","ARO_description":"OXA-380 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"410":{"model_id":"410","model_name":"AAC(3)-IIIb","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"5232":{"protein_sequence":{"accession":"KSC15183.1","sequence":"MTPASFVTRASLAADLASLGLAPGDAVMVHAAVSKVGRLLDGPDTIISALSDAVGPEGTVLAYADWEARYEELADEHGRVPVQWRDHIPPFDPQRSRAIRDNGVLPEFLRTTPGALRSGNPGASVVALGAKAEWFTADHPLDYGYGEGSPLAKLVAAGGRVLMLGAPLDTLTLLHHAEHLADIPGKRIKRIEVPFATPTGTQWRMIEEFDTGDPIVAGLAEDYFAGIVTEFLASGQGRQGLIGAAPSVLVDAAAITAFGVTWLEKRFGTPSP"},"dna_sequence":{"accession":"LLLC01000048.1","fmin":"352","fmax":"1171","strand":"-","sequence":"ATGACGCCCGCCTCCTTCGTCACGCGCGCCTCGCTCGCCGCCGACCTTGCCAGCCTTGGCCTTGCTCCCGGCGACGCCGTGATGGTCCACGCTGCCGTCAGCAAGGTTGGCCGCCTGCTCGACGGCCCCGATACGATCATCAGCGCCCTCTCCGACGCCGTCGGCCCGGAGGGCACGGTCCTCGCCTATGCCGATTGGGAAGCGCGCTACGAGGAACTGGCGGACGAGCACGGGCGCGTACCGGTGCAATGGCGCGATCATATCCCGCCTTTCGATCCGCAGCGCTCGCGCGCCATCCGCGACAATGGCGTGCTGCCGGAATTCCTGCGGACGACGCCGGGCGCACTGCGCAGCGGCAATCCCGGCGCTTCGGTGGTGGCGCTCGGCGCAAAGGCGGAATGGTTCACCGCCGATCACCCGCTCGACTACGGCTATGGCGAGGGCTCGCCACTGGCCAAGCTGGTCGCCGCCGGTGGCAGGGTGCTGATGCTCGGAGCACCGCTCGACACGCTGACCCTGCTGCACCATGCCGAGCATCTGGCTGATATCCCCGGCAAGCGGATCAAGCGGATCGAGGTGCCGTTCGCGACACCTACAGGCACGCAATGGCGCATGATCGAGGAGTTCGACACCGGCGATCCGATCGTCGCAGGGCTGGCCGAGGACTATTTCGCGGGAATCGTGACCGAATTCCTCGCCAGCGGCCAGGGTCGGCAAGGGTTGATCGGCGCCGCTCCCTCGGTGCTGGTCGATGCCGCAGCGATCACCGCCTTCGGCGTCACCTGGCTCGAAAAACGGTTCGGTACGCCCTCGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002537","ARO_id":"38937","ARO_name":"AAC(3)-IIIb","CARD_short_name":"AAC(3)-IIIb","ARO_description":"AAC(3)-IIIb is an aminoglycoside acetyltransferase in P. aeruginosa.","ARO_category":{"36461":{"category_aro_accession":"3000322","category_aro_cvterm_id":"36461","category_aro_name":"AAC(3)","category_aro_description":"A category of aminoglycoside N-acetyltransferase enzymes with modification regiospecificity based at the 3-amino group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics through acetylation of the 3-amino group of the compound.","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"37001":{"category_aro_accession":"3000657","category_aro_cvterm_id":"37001","category_aro_name":"paromomycin","category_aro_description":"An aminoglycoside antibiotic used for the treatment of parasitic infections. It is similar to neomycin sharing a similar spectrum of activity, but its hydroxyl group at the 6'-position instead of an amino group makes it resistant to AAC(6') modifying enzymes.","category_aro_class_name":"Antibiotic"},"37002":{"category_aro_accession":"3000658","category_aro_cvterm_id":"37002","category_aro_name":"lividomycin","category_aro_description":"Lividomycins are aminoglycosidic antibiotics produced by Streptomyces lividus. They contain 2-amino-2,3-dideoxy-D-glucose.","category_aro_class_name":"Antibiotic"},"46129":{"category_aro_accession":"3007379","category_aro_cvterm_id":"46129","category_aro_name":"5-episisomicin","category_aro_description":"5-episosomicin is a semisynthetic aminoglycoside antibiotic similar to sisomicin.","category_aro_class_name":"Antibiotic"},"46133":{"category_aro_accession":"3007382","category_aro_cvterm_id":"46133","category_aro_name":"gentamicin","category_aro_description":"Gentamicin is a commonly used aminoglycoside antibiotic derived from members of the Micromonospora genus of bacteria. It acts by binding the 30S ribosomal subunit, thus inhibiting protein synthesis. Gentamicin is typically used to treat Gram-negative infections of the repiratory and urinary tract, as well as infections of the bone and soft tissue. It also exhibits considerable nephrotoxicity and ototoxicity. Gentamicin is administered as a mixture of gentamicin type C (which makes about around 80% of the complex) and types A, B, and X (distributed in the remaining 20% of the complex).","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"411":{"model_id":"411","model_name":"QnrB11","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"146":{"protein_sequence":{"accession":"ABS30107.1","sequence":"MMTLALVGEKIDRNRFTGAKVENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAILKDAIFKSCDLSMADFRNVSALGIEIRHCRAQGSDFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGTQVLGATFSGSDLSGGEFSSFDWRAANFTHCDLTNSELGDLDVRGVDLQGVKLDSYQASLILERLGIAVMG"},"dna_sequence":{"accession":"EF653270.1","fmin":"0","fmax":"648","strand":"+","sequence":"ATGATGACTCTGGCGTTAGTTGGCGAAAAAATTGACAGAAACAGATTCACTGGTGCGAAAGTTGAAAATAGCACATTTTTCAACTGTGATTTTTCGGGCGCCGACCTCAGCGGCACTGAGTTTATTGGCTGCCAGTTCTATGATCGAGAAAGCCAGAAAGGGTGTAATTTTAGTCGCGCTATCCTGAAAGATGCCATTTTCAAAAGTTGTGATCTCTCCATGGCGGATTTCAGGAATGTGAGCGCGCTGGGAATCGAAATTCGCCACTGCCGCGCACAAGGTTCAGATTTTCGCGGCGCAAGCTTTATGAATATGATTACCACACGCACCTGGTTTTGTAGCGCCTATATCACCAATACCAACTTAAGCTACGCCAACTTTTCAAAAGTCGTACTGGAAAAGTGCGAGCTGTGGGAAAACCGTTGGATGGGTACTCAGGTACTGGGGGCGACGTTCAGTGGTTCGGATCTTTCCGGCGGTGAGTTTTCGTCGTTCGACTGGCGGGCCGCAAACTTTACGCACTGTGATTTGACCAATTCAGAACTGGGCGATCTCGATGTCCGGGGTGTTGATTTGCAAGGCGTCAAACTGGACAGCTACCAGGCATCGTTGATCCTGGAACGTCTTGGTATCGCTGTCATGGGTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002725","ARO_id":"39159","ARO_name":"QnrB11","CARD_short_name":"QnrB11","ARO_description":"QnrB11 is a plasmid-mediated quinolone resistance protein found in Citrobacter freundii.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"412":{"model_id":"412","model_name":"OXA-117","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6040":{"protein_sequence":{"accession":"ACV49885.1","sequence":"MNIKALLLITSAIFISACSPYIVSANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTEWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"GQ423625.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGTCTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACTACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTAGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGAATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001442","ARO_id":"37842","ARO_name":"OXA-117","CARD_short_name":"OXA-117","ARO_description":"OXA-117 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"413":{"model_id":"413","model_name":"OXA-144","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1369":{"protein_sequence":{"accession":"ACY56711.1","sequence":"MNIKALLLITSAIFISACSPYIVSANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQEVQDEVQSILFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"FJ872530.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGTCTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACTACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTAGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAGAAGTCCAAGATGAAGTGCAATCCATTCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3002480","ARO_id":"38880","ARO_name":"OXA-144","CARD_short_name":"OXA-144","ARO_description":"OXA-144 is a beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"414":{"model_id":"414","model_name":"OXA-377","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1612":{"protein_sequence":{"accession":"AHL30277.1","sequence":"MNIKTLLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEVHTKGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"KF986258.1","fmin":"14","fmax":"839","strand":"+","sequence":"ATGAACATTAAAACACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGTACACACTAAGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001563","ARO_id":"37963","ARO_name":"OXA-377","CARD_short_name":"OXA-377","ARO_description":"OXA-377 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"415":{"model_id":"415","model_name":"TEM-33","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4506":{"protein_sequence":{"accession":"ADL13944.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMLSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"GU371926.1","fmin":"50304","fmax":"51165","strand":"-","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGCTGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000903","ARO_id":"37283","ARO_name":"TEM-33","CARD_short_name":"TEM-33","ARO_description":"TEM-33 is an inhibitor-resistant beta-lactamase that has been found in clinical isolates.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"416":{"model_id":"416","model_name":"OXA-204","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1605":{"protein_sequence":{"accession":"AFU91598.1","sequence":"MRVLALSAVFLVASIIGMPAVAKEWQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGHRRDIATWNRDHNLITAMKYSVVPVYQEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISATEQISFLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYSTRIEPKIGWWVGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP"},"dna_sequence":{"accession":"JQ809466.1","fmin":"5374","fmax":"6172","strand":"+","sequence":"ATGCGTGTATTAGCCTTATCGGCTGTGTTTTTGGTGGCATCGATTATCGGAATGCCTGCGGTAGCAAAGGAATGGCAAGAAAACAAAAGTTGGAATGCTCACTTTACTGAACATAAATCACAGGGCGTAGTTGTGCTCTGGAATGAGAATAAGCAGCAAGGATTTACCAATAATCTTAAACGGGCGAACCAAGCATTTTTACCCGCATCTACCTTTAAAATTCCCAATAGCTTGATCGCCCTCGATTTGGGCGTGGTTAAGGATGAACACCAAGTCTTTAAGTGGGATGGACATCGGCGCGATATCGCCACTTGGAATCGCGATCATAATCTAATCACCGCGATGAAATATTCAGTTGTGCCTGTTTATCAAGAATTTGCCCGCCAAATTGGCGAGGCACGTATGAGCAAGATGCTACATGCTTTCGATTATGGTAATGAGGACATTTCGGGCAATGTAGACAGTTTCTGGCTCGATGGTGGTATTCGAATTTCGGCCACTGAGCAAATCAGCTTTTTAAGAAAGCTGTATCACAATAAGTTACACGTATCGGAGCGCAGCCAGCGTATTGTCAAACAAGCCATGCTGACCGAAGCCAATGGCGACTATATTATTCGGGCTAAAACGGGATACTCGACTAGAATCGAACCTAAGATTGGCTGGTGGGTCGGTTGGGTTGAACTGGATGATAATGTGTGGTTTTTTGCGATGAATATGGATATGCCCACATCGGATGGTTTAGGGCTGCGCCAAGCCATCACAAAAGAAGTGCTCAAACAGGAAAAAATTATTCCCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001788","ARO_id":"38188","ARO_name":"OXA-204","CARD_short_name":"OXA-204","ARO_description":"OXA-204 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46510":{"category_aro_accession":"3007721","category_aro_cvterm_id":"46510","category_aro_name":"OXA-48-like beta-lactamase","category_aro_description":"OXA-48-type beta-lactamases are now routinely encountered in bacterial infections caused by carbapenam-resistant Enterobacterales. OXA-48-like proteins confer resistance to penicillin (which is efficiently hydrolyzed) and carbapenam antibiotics (which is more slowly broken down). The spectrum of activity of these variants varies, with some hydrolyzing expanded-spectrum oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"417":{"model_id":"417","model_name":"QnrB6","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"610":{"protein_sequence":{"accession":"ABP87778.1","sequence":"MTPLLYKKTGTNMALALVGEKIDRNRFTGEKIENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNASALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGAQVLGATFSGSDLSGGEFSTFDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDNYQASLLMERLGIAVIG"},"dna_sequence":{"accession":"EF520349.1","fmin":"0","fmax":"681","strand":"+","sequence":"ATGACGCCATTACTGTATAAAAAAACAGGTACAAATATGGCTCTGGCACTCGTTGGCGAAAAAATTGACAGAAACCGTTTCACCGGTGAGAAAATTGAAAATAGTACATTTTTTAACTGTGATTTTTCAGGTGCCGACCTGAGCGGCACTGAATTTATCGGCTGTCAGTTCTATGATCGTGAAAGCCAGAAAGGGTGCAATTTTAGTCGTGCGATGCTGAAAGATGCCATTTTTAAAAGCTGTGATTTATCCATGGCGGATTTTCGCAATGCCAGTGCGCTGGGCATTGAAATTCGCCACTGCCGCGCACAAGGCGCAGATTTCCGCGGCGCAAGCTTTATGAATATGATCACCACGCGCACCTGGTTTTGTAGCGCATATATCACGAATACCAATCTAAGCTACGCCAATTTTTCGAAAGTCGTGTTGGAAAAGTGTGAGCTGTGGGAAAACCGTTGGATGGGTGCCCAGGTACTGGGCGCGACGTTCAGTGGTTCAGATCTCTCCGGCGGCGAGTTTTCGACTTTCGACTGGCGAGCAGCAAACTTCACACATTGCGATCTGACCAATTCGGAGTTGGGTGACTTAGATATTCGGGGCGTTGATTTACAAGGCGTTAAGCTGGACAACTACCAGGCGTCGTTGCTCATGGAGCGGCTTGGCATCGCGGTGATTGGTTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36950","NCBI_taxonomy_name":"Pantoea agglomerans","NCBI_taxonomy_id":"549"}}}},"ARO_accession":"3002720","ARO_id":"39154","ARO_name":"QnrB6","CARD_short_name":"QnrB6","ARO_description":"QnrB6 is a plasmid-mediated quinolone resistance protein found in Pantoea agglomerans.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"418":{"model_id":"418","model_name":"OXA-325","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"888":{"protein_sequence":{"accession":"AGW16407.1","sequence":"MYKKALIVATSILFLSACSSNTVKQHQIHTISANKNSEEIKSLFDQAQTTGVLVIKRGQTEEIYGNDLKRASTDYIPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMSKEVKRIGFGNANIGSKVDDFWLVGPLKITPQQETQFAYQLAHKTLPFSKNVQEQVQSMVFIEEKNGRKIYAKSGWGWDVEPQVGWLTGWVVQPQGEIVAFSLNLEMKKGTPSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"KF203099.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGTATAAAAAAGCCCTTATCGTTGCAACAAGTATTCTATTTTTATCCGCCTGTTCTTCCAATACGGTAAAACAACATCAAATACATACTATTTCTGCCAATAAAAATTCAGAAGAAATTAAATCACTTTTTGATCAAGCACAGACCACGGGAGTTTTGGTGATTAAGCGAGGGCAAACAGAAGAAATTTATGGCAATGATCTTAAAAGAGCATCAACCGACTATATTCCCGCCTCTACCTTTAAAATGTTAAATGCTTTAATTGGACTTGAACATCATAAGGCAACTACAACTGAAGTATTTAAATGGGATGGGCAAAAACGTTTATTTCCTGATTGGGAAAAGGACATGACACTGGGTGATGCCATGAAAGCTTCTGCAATCCCAGTTTACCAAGAATTAGCCCGACGAATTGGTCTGGATCTTATGTCCAAAGAGGTGAAACGAATTGGTTTCGGTAATGCTAACATTGGCTCAAAAGTAGATGATTTCTGGCTTGTTGGCCCTCTAAAAATTACACCTCAACAAGAAACCCAATTTGCTTATCAATTAGCCCATAAAACTCTTCCATTTAGCAAAAATGTACAAGAACAAGTTCAATCAATGGTGTTCATAGAAGAAAAAAATGGACGTAAAATTTATGCCAAAAGTGGTTGGGGATGGGATGTGGAACCACAAGTTGGTTGGTTAACAGGCTGGGTCGTTCAACCACAAGGAGAAATTGTCGCATTCTCACTTAATTTAGAAATGAAAAAAGGAACTCCTAGCTCTATTCGCAAAGAAATTGCTTATAAAGGCTTAGAACAACTGGGTATCTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39094","NCBI_taxonomy_name":"Acinetobacter calcoaceticus","NCBI_taxonomy_id":"471"}}}},"ARO_accession":"3001513","ARO_id":"37913","ARO_name":"OXA-325","CARD_short_name":"OXA-325","ARO_description":"OXA-325 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46495":{"category_aro_accession":"3007706","category_aro_cvterm_id":"46495","category_aro_name":"OXA-213-like beta-lactamase","category_aro_description":"OXA-213-like enzymes have been identified to be intrinsic to A. calcoaceticus and have been subsequently detected in A. pittii. Phylogenetic analysis of OXA-213-like proteins identified two distinct subgroups within the OXA family. The first group was linked to A. pittii and the second group to A. calcoaceticus. The carbapenemase activity of these OXAs may be related to the species-dependent effect.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"419":{"model_id":"419","model_name":"SLB-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"3312":{"protein_sequence":{"accession":"AAT90846.1","sequence":"MLSLPSYSHEVEPTSTTIQSVTSSLEGQLSISKLADGVYLHHSYKNVSNFGLVEANGLVVIKDKQAFIIDTPWTDNDTQKLVDWITQQGFIPVASISTHSHQDRAGGIGYLNRQGITTTVSETTQQILTENDKTTAKSTFTGMQYIMKTDLVEVYDLGAGHTKDNLVVWLPTQQILFGGCLIKSLNSSTLGYTGEADLQQWPLTIAKVQAQFPQVKIVVPGHGQVGDKALLEHTIELLIPKNETVNSSS"},"dna_sequence":{"accession":"AY590118.1","fmin":"0","fmax":"750","strand":"+","sequence":"ATGCTCAGCTTACCTAGCTATAGTCATGAAGTAGAGCCCACATCGACAACAATCCAATCAGTAACATCCAGCCTTGAAGGCCAATTAAGTATTTCCAAGCTTGCCGATGGCGTGTACTTACATCACTCCTATAAAAATGTCAGTAATTTCGGTTTAGTCGAAGCCAACGGCCTTGTAGTGATTAAGGATAAACAAGCATTTATTATTGATACCCCGTGGACCGACAACGATACCCAAAAATTAGTTGACTGGATAACTCAGCAAGGTTTTATCCCCGTCGCCAGTATTTCAACCCATTCACATCAAGATCGGGCTGGCGGTATCGGTTACCTTAATCGCCAAGGTATTACGACTACAGTGTCCGAAACGACTCAACAAATTTTAACCGAAAATGATAAAACTACCGCTAAAAGTACTTTTACAGGCATGCAATACATTATGAAAACGGATTTAGTCGAAGTGTATGACTTAGGTGCAGGGCATACCAAAGACAACCTAGTGGTATGGCTGCCGACACAGCAAATCTTATTTGGTGGGTGTTTAATAAAATCGCTTAACTCAAGCACATTAGGTTACACAGGTGAAGCGGACTTACAGCAGTGGCCCTTAACTATCGCCAAGGTACAAGCCCAATTTCCTCAAGTAAAAATAGTCGTACCCGGTCATGGACAGGTTGGCGATAAAGCGCTACTTGAGCATACTATCGAGTTACTAATACCAAAAAATGAAACAGTTAATAGCAGCAGTTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40161","NCBI_taxonomy_name":"Shewanella livingstonensis","NCBI_taxonomy_id":"150120"}}}},"ARO_accession":"3003556","ARO_id":"40159","ARO_name":"SLB-1","CARD_short_name":"SLB-1","ARO_description":"This enzyme breaks the beta-lactam antibiotic ring open and deactivates the molecule's antibacterial properties.","ARO_category":{"40158":{"category_aro_accession":"3003555","category_aro_cvterm_id":"40158","category_aro_name":"SHW beta-lactamase","category_aro_description":"This family of sublcass B1 beta-lactamases were discovered in species of the Shewanella genus.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"420":{"model_id":"420","model_name":"CTX-M-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1916":{"protein_sequence":{"accession":"CAA63262.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAVAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVDGTMSLAELSAAALQYSDNVAMNKLISHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGDYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTNGL"},"dna_sequence":{"accession":"X92506.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGTCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGAAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGTGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACTTGGTTAACTATAATCCGATTGCGGAAAAGCACGTCGATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTTCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGTAATCTGACGCTGGGTAAAGCATTGGGTGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGACTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCAACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001864","ARO_id":"38264","ARO_name":"CTX-M-1","CARD_short_name":"CTX-M-1","ARO_description":"CTX-M-1 is a beta-lactamase found in the Enterobacteriaceae family.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"421":{"model_id":"421","model_name":"TEM-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1724":{"protein_sequence":{"accession":"CAA38429.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDKLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"X54606.1","fmin":"214","fmax":"1075","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATAAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3000874","ARO_id":"37254","ARO_name":"TEM-2","CARD_short_name":"TEM-2","ARO_description":"TEM-2 is a broad-spectrum beta-lactamase.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"422":{"model_id":"422","model_name":"FOX-10","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"951":{"protein_sequence":{"accession":"AGE45503.1","sequence":"MQQRRAFALLTLGSLLLAPCTYASGEAPLTAAVDGIIQPMLKAYRIPGMAVAVLKDGKAHYFNYGVANRESGQRVSEQTLFEIGSVSKTLTATLGAYAAVKGGFELDDKVSQHAPWLKGSALDGVTMAELATYSAGGLPLQFPDEVDSNDKMRTYYRSWSPVYPAGTHRQYSNPSISLFGHLAANSLGQPFEQLMSQTLLPKLGLHHTYIQVPESAMVNYAYGYSKEDKPVRVTPGVLAAEAYGIKTGSADLLKFAEANMGYQGDAAVKSAIALTHTGFYSVGDMTQGLGWESYAYPVTEQTLLAGNAPAVSFQANPVTRFAVPKAMGEQRLYNKTGSTGGFGAYVAFVPARGIAIVMLANRNYPIEARVKAAHAILSQLAE"},"dna_sequence":{"accession":"JX049131.1","fmin":"0","fmax":"1149","strand":"+","sequence":"ATGCAACAACGGCGTGCGTTCGCGCTACTGACGCTGGGTAGCCTGCTGTTAGCCCCTTGTACTTATGCCAGCGGGGAGGCTCCGTTGACCGCCGCTGTGGACGGCATTATCCAGCCGATGCTCAAGGCGTATCGGATCCCGGGGATGGCGGTCGCCGTACTGAAAGATGGCAAAGCCCACTATTTCAACTATGGGGTTGCCAACCGGGAGAGTGGCCAGCGCGTCAGCGAGCAGACCCTGTTCGAGATTGGCTCGGTCAGCAAGACCCTGACTGCGACCCTCGGTGCCTATGCCGCGGTCAAGGGGGGCTTTGAGCTGGATGACAAGGTGAGCCAGCACGCCCCCTGGCTCAAAGGTTCCGCCTTGGATGGTGTGACCATGGCCGAGCTTGCCACCTACAGTGCGGGTGGTTTGCCGCTGCAGTTCCCCGATGAGGTGGATTCGAATGACAAGATGCGCACTTACTATCGGAGCTGGTCACCGGTTTATCCGGCGGGGACCCATCGCCAGTATTCCAACCCCAGCATCAGCCTGTTTGGTCACCTGGCCGCAAATAGTCTGGGCCAGCCATTTGAGCAACTGATGAGCCAGACCCTGCTGCCCAAGCTGGGTTTGCACCACACCTATATCCAGGTACCGGAGTCGGCTATGGTGAACTATGCCTACGGCTATTCGAAGGAAGATAAGCCCGTCCGGGTCACTCCGGGCGTGCTGGCAGCCGAGGCTTACGGGATCAAGACCGGCTCGGCGGATCTGCTGAAGTTTGCCGAGGCAAACATGGGGTATCAGGGAGATGCCGCGGTAAAAAGCGCGATCGCGCTGACCCACACCGGTTTCTACTCGGTGGGAGACATGACCCAGGGACTGGGCTGGGAGAGTTACGCCTATCCGGTGACCGAGCAGACATTGCTGGCGGGTAACGCACCGGCGGTGAGCTTCCAGGCCAATCCGGTTACGCGCTTTGCGGTGCCCAAGGCGATGGGCGAGCAGCGGCTCTATAACAAGACGGGCTCGACTGGCGGCTTTGGCGCCTATGTGGCGTTCGTGCCCGCCAGAGGGATCGCCATCGTCATGCTGGCCAATCGCAACTATCCCATCGAGGCCAGGGTGAAGGCGGCTCACGCCATCCTGAGTCAGTTGGCCGAGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002162","ARO_id":"38562","ARO_name":"FOX-10","CARD_short_name":"FOX-10","ARO_description":"FOX-10 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36206":{"category_aro_accession":"3000067","category_aro_cvterm_id":"36206","category_aro_name":"FOX beta-lactamase","category_aro_description":"FOX beta-lactamases are plasmid-encoded AmpC-type beta-lactamase which conferred resistance to broad-spectrum cephalosporins and cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"423":{"model_id":"423","model_name":"DHA-16","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1012":{"protein_sequence":{"accession":"AIT76105.1","sequence":"MKKSLSATLVSALLAFSAPGFSAADNVAAVVDSTIKPLMAQQDIPGMAVAVSVKGKPYYFNYGFADVQAKQPVTENTLFELGSVSKTFTGVLGAVSVAKKETSLNDPAVKYQPELTQPQWKGITLLDLATYTAGGLPLQVPEAVKSSEDLLHFYQQWQPSWQPGKMRLYANSSIGLFGALTATAAGMPYEQLLTARILAPLGLSHTFITVPESAQSQYAYGYKNNQPVRVTGGPLDAESYGVKSASKDMLRWAEINMSPSRAGNADLEMAMYLAQTRYYKTAAINQGLGWEMYDWPQQKDMIINGVTNEVALQPHPVTDNQVQPYNRASWVHKTGATTGFGAYVAFIPEKQVAIVILANKNYPNTERVKAAQAILSALE"},"dna_sequence":{"accession":"KM087852.1","fmin":"0","fmax":"1140","strand":"+","sequence":"ATGAAAAAATCGTTATCTGCAACACTGGTTTCCGCCCTGCTGGCCTTTTCTGCCCCGGGGTTCTCTGCCGCTGATAATGTCGCGGCAGTCGTCGACAGCACCATTAAACCGCTGATGGCACAGCAGGATATCCCCGGGATGGCGGTTGCTGTCTCCGTAAAGGGAAAACCGTATTACTTCAACTATGGTTTTGCGGATGTGCAGGCAAAACAGCCGGTCACTGAAAATACACTATTTGAACTCGGATCTGTAAGTAAAACTTTCACAGGTGTGCTGGGTGCGGTTTCCGTGGCGAAAAAAGAGACGTCGCTGAATGACCCGGCAGTCAAATACCAGCCTGAACTGACACAGCCGCAGTGGAAAGGGATCACATTACTGGATCTGGCCACCTATACCGCAGGCGGGCTGCCGTTACAGGTGCCGGAAGCGGTGAAAAGCAGTGAGGATCTGCTGCATTTCTATCAGCAGTGGCAGCCGTCATGGCAACCGGGAAAGATGCGTCTGTATGCGAACAGCAGTATCGGCCTGTTCGGTGCGCTGACCGCGACAGCGGCGGGAATGCCTTATGAGCAGCTGCTGACCGCACGTATCCTGGCGCCGCTGGGGTTATCACATACCTTTATTACTGTACCGGAAAGTGCGCAAAGTCAGTATGCATACGGTTATAAAAACAATCAGCCGGTACGGGTGACGGGGGGACCGCTCGATGCGGAATCTTACGGGGTAAAATCCGCCTCAAAAGATATGCTGCGCTGGGCAGAAATCAATATGTCGCCGTCACGGGCGGGCAATGCGGATCTGGAAATGGCGATGTATCTCGCACAGACCCGTTACTATAAAACGGCGGCAATCAACCAGGGACTGGGCTGGGAGATGTATGACTGGCCGCAGCAGAAAGATATGATCATTAACGGCGTGACCAATGAAGTGGCATTGCAGCCGCATCCGGTAACGGATAATCAGGTTCAGCCGTATAACCGCGCTTCCTGGGTACATAAAACAGGAGCAACAACCGGTTTCGGTGCTTATGTGGCCTTTATTCCGGAAAAACAGGTGGCGATTGTGATTCTGGCAAATAAAAACTACCCGAATACCGAAAGAGTCAAAGCCGCACAGGCTATTTTGAGTGCACTGGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36917","NCBI_taxonomy_name":"Morganella morganii","NCBI_taxonomy_id":"582"}}}},"ARO_accession":"3002147","ARO_id":"38547","ARO_name":"DHA-16","CARD_short_name":"DHA-16","ARO_description":"DHA-16 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36207":{"category_aro_accession":"3000068","category_aro_cvterm_id":"36207","category_aro_name":"DHA beta-lactamase","category_aro_description":"DHA beta-lactamases are plasmid-mediated AmpC \u03b2-lactamases that confer resistance to cephamycins and oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"424":{"model_id":"424","model_name":"SHV-36","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1392":{"protein_sequence":{"accession":"AAL82592.1","sequence":"MRYVRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AF467947.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGCATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001094","ARO_id":"37474","ARO_name":"SHV-36","CARD_short_name":"SHV-36","ARO_description":"SHV-36 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"425":{"model_id":"425","model_name":"TEM-182","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1570":{"protein_sequence":{"accession":"ADP20705.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMISTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRLEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDELNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"HQ317449.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATTAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTTGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACTAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36927","NCBI_taxonomy_name":"Haemophilus parainfluenzae","NCBI_taxonomy_id":"729"}}}},"ARO_accession":"3001373","ARO_id":"37773","ARO_name":"TEM-182","CARD_short_name":"TEM-182","ARO_description":"TEM-182 is a beta-lactamase found in clinical isolates of H. parainfluenzae.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"426":{"model_id":"426","model_name":"aadK","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4533":{"protein_sequence":{"accession":"CAB14620.1","sequence":"MRSEQEMMDIFLDFALNDERIRLVTLEGSRTNRNIPPDNFQDYDISYFVTDVESFKENDQWLEIFGKRIMMQKPEDMELFPPELGNWFSYIILFEDGNKLDLTLIPIREAEDYFANNDGLVKVLLDKDSFINYKVTPNDRQYWIKRPTAREFDDCCNEFWMVSTYVVKGLARNEILFAIDHLNEIVRPNLLRMMAWHIASQKGYSFSMGKNYKFMKRYLSNKEWEELMSTYSVNGYQEMWKSLFTCYALFRKYSKAVSEGLAYKYPDYDEGITKYTEGIYCSVK"},"dna_sequence":{"accession":"AL009126.1","fmin":"2735681","fmax":"2736536","strand":"-","sequence":"ATGCGAAGTGAGCAGGAAATGATGGACATTTTTTTGGACTTTGCTTTGAACGATGAGAGAATCCGATTGGTCACTTTGGAAGGGTCACGTACAAACAGAAATATCCCTCCTGACAACTTCCAAGATTATGACATCTCGTATTTTGTAACTGATGTAGAATCTTTTAAAGAAAATGATCAGTGGCTCGAAATCTTTGGGAAGCGCATTATGATGCAAAAACCAGAAGATATGGAGCTTTTTCCTCCCGAATTAGGTAATTGGTTTTCATACATTATTCTTTTTGAGGATGGCAACAAATTAGATCTAACCCTTATTCCAATTCGTGAAGCAGAAGATTATTTTGCTAATAACGATGGTTTGGTTAAGGTATTGCTTGATAAGGATTCGTTCATCAACTATAAAGTGACCCCAAATGATCGCCAATACTGGATAAAAAGGCCGACTGCAAGGGAATTTGATGATTGCTGTAATGAGTTCTGGATGGTTTCGACTTACGTAGTAAAAGGACTAGCAAGAAATGAAATCCTTTTTGCCATTGACCATTTAAATGAAATTGTACGTCCTAATTTATTGAGAATGATGGCCTGGCATATCGCATCTCAGAAAGGGTATTCATTTAGTATGGGGAAGAACTATAAATTTATGAAGCGGTACCTTTCAAATAAAGAATGGGAGGAACTCATGTCTACATATTCTGTGAATGGGTATCAGGAAATGTGGAAGTCTTTATTTACTTGCTATGCATTATTTAGAAAGTATTCAAAAGCTGTATCAGAAGGTCTTGCATATAAGTATCCTGATTACGATGAAGGTATTACTAAGTATACGGAAGGTATTTATTGCTCAGTAAAGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39579","NCBI_taxonomy_name":"Bacillus subtilis subsp. subtilis str. 168","NCBI_taxonomy_id":"224308"}}}},"ARO_accession":"3002627","ARO_id":"39027","ARO_name":"aadK","CARD_short_name":"aadK","ARO_description":"aadK is a chromosomal-encoded aminoglycoside nucleotidyltransferase gene in B. subtilis and Bacillus spp. This enzyme confers low-level resistance to streptomycin.","ARO_category":{"36364":{"category_aro_accession":"3000225","category_aro_cvterm_id":"36364","category_aro_name":"ANT(6)","category_aro_description":"A category of aminoglycoside O-nucleotidyltransferase enzymes with modification regiospecificity based at the 6-hydroxyl group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics, specifically streptomycin, by transfer of an AMP group from an ATP substrate to the 6-hydroxyl group of the compound.","category_aro_class_name":"AMR Gene Family"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"427":{"model_id":"427","model_name":"OCH-7","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1900":{"protein_sequence":{"accession":"CAC17627.1","sequence":"MRKSTTLLIGFLTTAAIIPNSGALAASKVNDGDLRRIVDETVRPLMAEQKIPGMAVAITIDGKSHFFGYGVASKESGQKVTEDTIFEIGSVSKTFTAMLGGYGLATGAFSLSDPATKWAPELAGSSFDKITMRDLGTYTPGGLPLQFPDAVTDDSSMLAYFKKWKPDYPAGTQRRYSNPSIGLFGYLAARSMDKPFDVLMEQKLLPAFGLKNTFINVPASQMKNYAYGYSKANKPIRVSGGALDAQAYGIKTTALDLARFVELNIDSSSLEPDFQKAVAATHTGYYHVGANNQGLGWEFYNYPTALKTLLAGNSSDMALKSHKIEKFDTPRQPSADVWLNKTGSTNGFGAYAAFIPAKKTGIVLLANRNYPIDERVKAAYRILQALDNKQ"},"dna_sequence":{"accession":"AJ295345.1","fmin":"0","fmax":"1173","strand":"+","sequence":"ATGAGAAAATCTACGACACTTTTGATCGGTTTCCTCACCACTGCCGCTATTATCCCGAATAGCGGCGCGCTGGCTGCGAGCAAGGTGAATGATGGCGACTTGCGCCGTATTGTCGATGAAACGGTGCGCCCGCTCATGGCCGAGCAGAAAATCCCCGGCATGGCGGTTGCCATAACCATCGACGGCAAGAGCCACTTCTTCGGTTATGGTGTGGCATCGAAAGAAAGCGGGCAAAAAGTCACTGAAGACACGATTTTCGAGATCGGTTCGGTCAGCAAGACCTTCACTGCAATGCTTGGCGGTTACGGGCTGGCGACAGGCGCGTTCTCCCTGTCCGATCCCGCGACCAAATGGGCTCCTGAACTGGCAGGCAGCAGCTTCGACAAGATCACCATGCGTGATCTTGGGACCTACACGCCGGGCGGATTGCCCCTCCAGTTTCCCGATGCTGTCACCGATGACAGTTCGATGCTGGCATATTTCAAGAAATGGAAGCCGGACTATCCGGCAGGGACGCAGCGTCGCTATTCGAATCCCAGCATCGGCCTGTTCGGCTATCTGGCGGCACGAAGCATGGACAAGCCGTTCGACGTTTTGATGGAGCAAAAGCTTCTGCCTGCATTCGGCCTGAAGAACACCTTCATCAATGTGCCGGCAAGCCAGATGAAGAACTACGCCTACGGCTATTCCAAAGCCAACAAGCCGATCCGGGTATCGGGCGGGGCGCTGGATGCACAAGCCTATGGCATCAAGACCACCGCGCTTGATCTTGCCCGCTTCGTCGAACTGAACATCGACAGCTCATCTCTGGAGCCTGATTTCCAGAAAGCCGTCGCCGCAACGCATACCGGTTACTACCATGTCGGAGCGAACAATCAGGGACTTGGCTGGGAGTTCTACAACTATCCGACTGCGCTCAAGACACTTCTTGCCGGCAATTCGTCGGACATGGCGCTGAAGTCGCACAAAATCGAGAAATTCGATACACCTCGCCAACCGTCAGCTGATGTGTGGCTCAACAAGACAGGCTCAACCAACGGCTTTGGCGCTTATGCGGCCTTTATTCCTGCGAAGAAGACCGGAATTGTTCTGCTTGCCAACCGGAATTATCCGATCGATGAGCGCGTAAAGGCTGCCTATCGGATATTGCAGGCGCTCGACAACAAGCAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37077","NCBI_taxonomy_name":"Brucella anthropi","NCBI_taxonomy_id":"529"}}}},"ARO_accession":"3002520","ARO_id":"38920","ARO_name":"OCH-7","CARD_short_name":"OCH-7","ARO_description":"OCH-7 beta-lactamase is an Ambler class C chromosomal-encoded beta-lactamase in Brucella anthropi.","ARO_category":{"36233":{"category_aro_accession":"3000094","category_aro_cvterm_id":"36233","category_aro_name":"OCH beta-lactamase","category_aro_description":"OCH beta-lactamases are Ambler class C chromosomal-encoded beta-lactamases in Brucella anthropi.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"428":{"model_id":"428","model_name":"OXY-2-7","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1618":{"protein_sequence":{"accession":"CAA88908.1","sequence":"MIKSSWRKIAMLAAAVPLLLASGALWASTDAIHQKLTDLEKRSGGRLGVALINTADNSQILYRGDERFAMCSTSKVMAAAAVLKQSESNKEVVNKRLEINAADLVVWSPITEKHLQSGMTLAELSAATLQYSDNTAMNLIIGYLGGPEKVTAFARSIGDATFRLDRTEPTLNTAIPGDERDTSTPLAMAESLRKLTLGDALGEQQRAQLVTWLKGNTTGGQSIRAGLPESWVVGDKTGAGDYGTTNDIAVIWPEDHAPLVLVTYFTQPQQDAKNRKEVLAAAAKIVTEGL"},"dna_sequence":{"accession":"Z49084.1","fmin":"311","fmax":"1184","strand":"+","sequence":"ATGATAAAAAGTTCGTGGCGTAAAATTGCAATGCTAGCCGCCGCCGTTCCGCTGCTGCTGGCGAGCGGCGCACTGTGGGCCAGTACCGATGCTATCCATCAGAAGCTGACAGATCTCGAGAAGCGTTCAGGCGGCAGGTTGGGCGTGGCGCTAATCAACACGGCAGATAATTCTCAAATCTTATATCGCGGCGACGAGCGTTTTGCCATGTGCAGCACCAGTAAAGTGATGGCCGCCGCCGCGGTATTAAAACAGAGCGAAAGCAATAAAGAGGTGGTAAATAAAAGGCTGGAGATTAACGCAGCCGATTTGGTGGTCTGGAGTCCGATTACCGAAAAACATCTCCAGAGCGGAATGACGCTGGCTGAGCTAAGCGCGGCGACGCTGCAATATAGCGACAATACGGCGATGAATCTGATCATCGGCTACCTTGGCGGGCCGGAAAAAGTCACCGCCTTCGCCCGCAGTATCGGCGATGCCACCTTTCGTCTCGATCGTACGGAGCCCACGCTGAATACCGCCATCCCGGGCGATGAGCGTGATACCAGCACGCCGCTGGCGATGGCTGAAAGCCTACGCAAGCTGACGCTTGGCGATGCGCTGGGCGAACAGCAACGCGCCCAGTTAGTCACCTGGCTGAAAGGCAATACCACCGGCGGGCAAAGCATTCGCGCGGGCCTGCCTGAAAGCTGGGTGGTCGGCGATAAAACCGGCGCCGGAGATTACGGCACCACCAATGATATTGCGGTTATCTGGCCGGAAGATCACGCTCCGCTGGTATTAGTCACCTACTTTACCCAGCCGCAGCAGGATGCGAAAAACCGCAAAGAGGTGTTAGCCGCAGCGGCAAAAATCGTGACCGAAGGGCTTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3002402","ARO_id":"38802","ARO_name":"OXY-2-7","CARD_short_name":"OXY-2-7","ARO_description":"OXY-2-7 is a beta-lactamase found in Klebsiella oxytoca.","ARO_category":{"38788":{"category_aro_accession":"3002388","category_aro_cvterm_id":"38788","category_aro_name":"OXY beta-lactamase","category_aro_description":"OXY beta-lactamases are chromosomal class A beta-lactamases that are found in Klebsiella oxytoca. At constitutive low levels, OXY beta-lactamases confer resistance to aminopenicillins and carboxypenicillins. At high induced levels,  OXY beta-lactamases confer resistance to penicillins, cephalosporins and aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"429":{"model_id":"429","model_name":"mdsA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"770"}},"model_sequences":{"sequence":{"5279":{"protein_sequence":{"accession":"AAL19306.1","sequence":"MRRTFKIMLIAGVIAAIGGVIYMAGEALWDKDNAVGPPASAPPPPSVPVAKALSRTLAPTAEFTGFLAAPETVELRSRVGGTLDAISVPEGRLVSRGQLLFQIDPRPFEVALDTAVAQLRQAEVLARQAQADFDRIQRLVASGAVSRKNADDVTATRNARQAQMQSAKAAVAAARLELSWTRITAPIAGRVDRILVTRGNLVSGGVAGNATLLTTIVSHNPMYVYFDIDEATWLKALRHTRSDKNPPVVNMGLTTDNGLPYQGVLDFMGNQMNRSTGTIRARAVIPDPDGMLSPGLFARISLPIGEPRETVLIDDLAVSADQGKNYVLIVGKENQVEYRPVELGQMVDGFRVVTQGVLPGEKIILKGLVRPGMTVAPRLVPMRQNVTDKQTATLTKADGDSAPKAVRQ"},"dna_sequence":{"accession":"AE006468.2","fmin":"397057","fmax":"398284","strand":"-","sequence":"ATGCGTAGAACATTCAAAATTATGTTGATAGCCGGCGTCATCGCCGCCATCGGGGGCGTGATTTACATGGCCGGCGAAGCACTATGGGATAAAGACAACGCCGTCGGCCCCCCGGCCAGCGCGCCGCCTCCACCGTCGGTACCGGTTGCTAAAGCCCTTAGCCGTACACTCGCGCCTACGGCGGAATTCACCGGTTTTCTGGCCGCGCCGGAAACCGTGGAGCTGCGTTCGCGCGTGGGAGGAACCCTTGACGCCATCAGCGTTCCGGAAGGACGTCTGGTAAGCCGCGGACAACTGCTGTTCCAGATCGATCCGCGCCCGTTCGAGGTCGCCCTCGACACCGCCGTCGCGCAATTACGTCAGGCTGAAGTACTGGCCCGCCAGGCGCAGGCGGATTTCGATCGCATTCAACGACTGGTCGCCAGCGGCGCCGTATCACGTAAAAACGCTGACGATGTCACCGCCACGCGTAATGCGCGACAGGCGCAGATGCAATCGGCCAAAGCCGCCGTCGCCGCAGCGCGCCTTGAACTCTCCTGGACCCGTATTACCGCGCCCATTGCCGGACGCGTTGACCGCATACTGGTGACCCGGGGCAATCTGGTCAGCGGCGGCGTAGCGGGTAACGCCACGCTTCTGACGACTATCGTGTCTCACAATCCCATGTATGTGTATTTCGATATTGACGAAGCCACCTGGCTGAAGGCGTTACGGCATACCCGCTCCGACAAAAATCCACCGGTAGTCAACATGGGGTTAACCACCGATAACGGGCTGCCTTATCAGGGCGTACTCGACTTTATGGGCAATCAGATGAACCGCAGCACCGGCACTATCCGGGCACGCGCCGTGATTCCTGACCCCGACGGAATGCTTTCTCCCGGCCTGTTTGCCCGAATCAGTTTGCCCATCGGCGAGCCGCGGGAAACCGTGCTGATTGACGATCTGGCGGTGAGCGCCGATCAGGGCAAAAACTATGTGCTGATCGTCGGCAAGGAGAATCAGGTGGAGTATCGTCCGGTTGAGTTGGGACAAATGGTCGATGGATTCCGCGTCGTTACACAGGGAGTACTGCCGGGAGAAAAAATCATCCTCAAGGGGCTGGTGCGTCCTGGCATGACCGTTGCGCCACGTCTGGTGCCGATGCGGCAGAATGTGACCGACAAACAGACCGCGACATTGACTAAAGCGGACGGCGACAGTGCGCCGAAGGCGGTGCGCCAATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35734","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Typhimurium str. LT2","NCBI_taxonomy_id":"99287"}}}},"ARO_accession":"3000789","ARO_id":"37169","ARO_name":"mdsA","CARD_short_name":"mdsA","ARO_description":"MdsA is the membrane fusion protein of the multidrug and metal efflux complex MdsABC.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"430":{"model_id":"430","model_name":"OXA-87","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"981":{"protein_sequence":{"accession":"ABC84263.1","sequence":"MNIKTLLLITSTIFISACSPYIVTANPNHSTSKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASIEYVPASTFKMLNALIGLEHHKATTTEIFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSLKAQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"DQ348075.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAACACTCTTACTTATAACAAGCACTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCACTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGATCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAATATTTAAGTGGGACGGGCAAAAAAGGCTGTTCCCAGAATGGGAAAAGGACATGACCCTAGGTGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCTAAAAGCCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001704","ARO_id":"38104","ARO_name":"OXA-87","CARD_short_name":"OXA-87","ARO_description":"OXA-87 is a beta-lactamase found in Acinetobacter spp.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"433":{"model_id":"433","model_name":"ACT-25","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"861":{"protein_sequence":{"accession":"AHL39338.1","sequence":"MMKKSLCCALLLGLSCSALAAPVSEKQLAEVVANTVTPLMKAQSVPGMAVAVIYQGKSHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMPYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPEKVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVVEGSDSKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANKSYPNPARVEAAYHILKALQ"},"dna_sequence":{"accession":"KJ207208.1","fmin":"539","fmax":"1685","strand":"+","sequence":"ATGATGAAAAAATCCCTTTGCTGCGCCCTGCTGCTGGGCCTCTCTTGCTCTGCTCTCGCCGCGCCAGTATCAGAAAAACAGCTGGCGGAGGTGGTCGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCTGTTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGAAAATCGCACTATTACACGTTTGGCAAGGCCGATATCGCGGCGAATAAACCCGTTACGCCTCAGACCCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGCGTTTTAGGTGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTGACAGGCAAGCAGTGGCAGGGTATTCGTATGCTGGATCTCGCCACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGCGCGCTGGCGGTCAAACCTTCTGGCATGCCCTATGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTTCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGAATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCGGAGAAGGTTGCCGATGCCTCACTTAAGCAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGGTCGAAGGCAGCGACAGTAAGGTAGCGCTGGCGCCATTACCCGTGGCAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGTTCTACTGGCGGATTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCAAGGCGCTTCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3001845","ARO_id":"38245","ARO_name":"ACT-25","CARD_short_name":"ACT-25","ARO_description":"ACT-25 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"434":{"model_id":"434","model_name":"LEN-16","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"1347":{"protein_sequence":{"accession":"AAU89706.1","sequence":"MRYVRLCVISLLATLPLAVYAGPQPLEQIKQSESQLSGRVGMVEMDLASGRTLAAWRADERFPMVSTFKVLLCGAVLARVDAGLEQLDRRIHYRQQDLVDYSPVSEKHLTDGMTIGELCAAAITLSDNSAGNLLLATVGGPAGLTAFLRQIGDNVTRLDRWETALNEALPGDARDTTTPASMAATLRKLLTAQHLSARSQQQLLQWMVDDRVAGPLIRAVLPPGWFIADKTGAGERGARGIVALLGPDGKPERIVVIYLRDTPASMAERNQHIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AY743416.1","fmin":"67","fmax":"928","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGTGTTATCTCCCTGTTAGCCACCCTGCCACTGGCGGTATACGCCGGTCCACAGCCGCTTGAGCAGATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTGGGGATGGTGGAAATGGATCTGGCCAGCGGCCGCACGCTGGCGGCCTGGCGCGCCGATGAACGCTTTCCCATGGTGAGCACCTTTAAAGTGCTGCTGTGCGGCGCGGTGCTGGCGCGGGTGGATGCCGGGCTCGAACAACTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTACCGACGGGATGACGATCGGCGAACTCTGCGCCGCCGCCATCACCCTGAGCGATAACAGCGCTGGCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCGGGATTAACTGCCTTTCTGCGCCAGATCGGTGACAACGTCACCCGTCTTGACCGCTGGGAAACGGCACTGAATGAGGCGCTTCCCGGCGACGCGCGCGACACCACCACCCCGGCCAGCATGGCCGCCACGCTGCGCAAACTACTGACCGCGCAGCATCTGAGCGCCCGTTCGCAACAGCAACTCCTGCAGTGGATGGTGGACGATCGGGTTGCCGGCCCGCTGATCCGCGCCGTGCTGCCGCCGGGCTGGTTTATCGCCGACAAAACCGGGGCTGGCGAACGGGGTGCGCGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAACCGGAGCGCATTGTGGTGATCTATCTGCGGGATACCCCGGCGAGTATGGCCGAGCGTAATCAACATATCGCCGGGATCGGCGCAGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002464","ARO_id":"38864","ARO_name":"LEN-16","CARD_short_name":"LEN-16","ARO_description":"LEN-16 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36236":{"category_aro_accession":"3000097","category_aro_cvterm_id":"36236","category_aro_name":"LEN beta-lactamase","category_aro_description":"LEN beta-lactamases are chromosomal class A beta-lactamases that confer resistance to ampicillin, amoxicillin, carbenicillin, and ticarcillin but not to extended-spectrum beta-lactams.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"435":{"model_id":"435","model_name":"OKP-A-9","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"1919":{"protein_sequence":{"accession":"CAJ19607.1","sequence":"MRYVRLCLISLIAALPLAVFASPPPLEQITRSESQLAGRVGYVEMDLASGRTLAAWRASERFPLMSTFKALLCGAVLARVDAGDEQLDRRIRYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAGNLLLKSVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDVRDTTTPASMAATLRKLLTSHALSDRSQQQLLQWMVDDQVAGPLIRAVLPAGWFIADKTGAGERGSRGIVALLGPNGKAERIVVIYLRDTPATMAERNQQIAKIGAALIEHWQR"},"dna_sequence":{"accession":"AM051148.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGCCTTATCTCCCTGATTGCCGCCCTGCCACTGGCGGTATTCGCCAGCCCTCCGCCGCTTGAGCAAATTACACGCAGCGAAAGTCAGCTGGCGGGCCGCGTGGGCTATGTTGAAATGGATCTGGCGAGCGGCCGCACGCTGGCCGCCTGGCGCGCCAGTGAGCGCTTTCCGCTGATGAGCACCTTTAAAGCGCTGCTCTGCGGCGCGGTGCTGGCCCGGGTGGATGCCGGAGACGAACAGCTGGATCGGCGGATCCGCTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGCCGACGGGATGACCGTTGGCGAACTCTGCGCCGCCGCCATCACCATGAGCGACAACAGCGCCGGCAATCTGCTGTTGAAGAGCGTTGGCGGCCCCGCGGGATTGACCGCTTTTCTGCGCCAGATCGGTGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAGCTCAATGAAGCGCTTCCCGGCGACGTGCGCGACACCACCACCCCAGCCAGCATGGCCGCCACCCTGCGCAAGCTGCTAACCAGCCACGCGCTGAGCGACCGTTCGCAGCAGCAGCTGCTGCAGTGGATGGTGGACGACCAGGTGGCCGGTCCGCTGATCCGCGCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAAACCGGGGCCGGCGAGCGGGGCTCACGCGGCATTGTCGCCCTGCTCGGCCCGAACGGCAAAGCGGAGCGCATCGTGGTGATCTATCTGCGGGATACGCCGGCGACCATGGCCGAGCGTAACCAGCAGATCGCCAAAATAGGCGCGGCGCTGATCGAGCACTGGCAGCGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002426","ARO_id":"38826","ARO_name":"OKP-A-9","CARD_short_name":"OKP-A-9","ARO_description":"OKP-A-9 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"38817":{"category_aro_accession":"3002417","category_aro_cvterm_id":"38817","category_aro_name":"OKP beta-lactamase","category_aro_description":"OKP beta-lactamases are chromosomal class A beta-lactamase that confer resistance to penicillins and early cephalosporins in Klebsiella pneumoniae. OKP beta-lactamases can be subdivided into two groups: OKP-A and OKP-B which diverge by about 4.2%.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"436":{"model_id":"436","model_name":"OXY-4-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1939":{"protein_sequence":{"accession":"AAL78161.1","sequence":"MLKSSWRKSALMAAAVPLLLASGSLWASADTLQQKLADLEKRSGGRLGVALINTADDSQTLYRGDERFAMCSTGKVMAAAAVLKQSESHPDVVNKRLEIKKSDLVVWSPITEKHLQSGMTLAELSAAALQYSDNTAMNKIIGYLGGPEKVTAFAQSIGDVTFRLDRMEPALNSAIPGDKRDTTTPLAMAESLRKLTLGNALGEQQRAQLVTWLKGNTTGGQSIRAGLPASWAVGDKTGGGDYGTTNDIAVIWPENHAPLVLVTYFTQPQQDAKSRKEVLAAAAKIVTEGL"},"dna_sequence":{"accession":"AY077481.1","fmin":"185","fmax":"1058","strand":"+","sequence":"ATGTTGAAAAGTTCGTGGCGTAAAAGCGCCCTGATGGCCGCCGCCGTTCCGCTACTGCTGGCGAGCGGTTCATTATGGGCCAGTGCCGATACTCTCCAGCAGAAGCTGGCTGATTTAGAAAAACGTTCCGGCGGTCGGCTGGGCGTGGCGCTGATTAACACGGCAGATGATTCGCAGACCCTCTATCGCGGCGACGAACGTTTTGCCATGTGCAGCACCGGTAAAGTGATGGCCGCCGCCGCGGTGTTAAAACAGAGCGAAAGCCATCCCGATGTGGTGAATAAAAGGCTGGAGATTAAAAAATCGGATTTAGTGGTCTGGAGCCCGATTACCGAAAAACATCTGCAAAGCGGAATGACCCTGGCGGAACTCAGCGCTGCGGCGCTGCAGTATAGCGACAATACCGCGATGAATAAGATTATCGGTTACCTTGGCGGGCCGGAAAAAGTCACCGCATTCGCCCAGAGCATCGGTGACGTTACTTTTCGTCTCGATCGGATGGAGCCGGCGCTGAACAGCGCGATTCCCGGTGATAAGCGCGATACCACCACCCCATTGGCGATGGCCGAAAGTCTGCGTAAGCTGACGCTGGGCAATGCGCTGGGCGAACAGCAGCGCGCCCAGTTAGTGACATGGCTGAAAGGCAATACCACCGGCGGGCAAAGCATTCGTGCAGGCCTGCCCGCAAGCTGGGCGGTCGGGGATAAAACCGGCGGCGGAGATTACGGCACCACCAACGATATCGCGGTGATCTGGCCGGAAAATCATGCTCCGCTGGTGCTAGTGACCTATTTTACCCAACCGCAGCAGGATGCGAAAAGCCGCAAAGAGGTGCTAGCCGCGGCGGCGAAAATCGTGACCGAAGGGCTTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3002410","ARO_id":"38810","ARO_name":"OXY-4-1","CARD_short_name":"OXY-4-1","ARO_description":"OXY-4-1 is a beta-lactamase found in Klebsiella oxytoca.","ARO_category":{"38788":{"category_aro_accession":"3002388","category_aro_cvterm_id":"38788","category_aro_name":"OXY beta-lactamase","category_aro_description":"OXY beta-lactamases are chromosomal class A beta-lactamases that are found in Klebsiella oxytoca. At constitutive low levels, OXY beta-lactamases confer resistance to aminopenicillins and carboxypenicillins. At high induced levels,  OXY beta-lactamases confer resistance to penicillins, cephalosporins and aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"437":{"model_id":"437","model_name":"SHV-69","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1317":{"protein_sequence":{"accession":"ABA06590.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLTDGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"DQ174308.1","fmin":"4","fmax":"865","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTACCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGGATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001123","ARO_id":"37503","ARO_name":"SHV-69","CARD_short_name":"SHV-69","ARO_description":"SHV-69 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"438":{"model_id":"438","model_name":"VIM-6","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"936":{"protein_sequence":{"accession":"AAN84550.1","sequence":"MFKLLSKLLVYLTASIMAIASPLAFSVDSSGEYPTVSEIPVGEVRLYQIADGVWSHIATRSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEVEGSEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSASVLYGGCAIYELSRTSAGNVADADLAEWPTSIERIQQHYPEAQFVIPGHGLPGGLDLLKHTTNVVKAHTNRSVVE"},"dna_sequence":{"accession":"AY165025.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGTTCAAACTTTTGAGTAAGTTATTGGTCTATTTGACCGCGTCTATCATGGCTATTGCGAGTCCGCTCGCTTTTTCCGTAGATTCTAGCGGTGAGTATCCGACAGTCAGCGAAATTCCGGTCGGGGAGGTCCGGCTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCGGTCGTTTGATGGCGCAGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAGAAGCAAATTGGACTTCCTGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGTAGAGGGGAGCGAGATTCCCACGCACTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAACTCTTCTATCCTGGTGCTGCGCATTCGACCGACAACTTAGTTGTGTACGTCCCGTCTGCGAGTGTGCTCTATGGTGGTTGTGCGATTTATGAGTTGTCACGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCATTGAGCGGATTCAACAACACTACCCGGAAGCACAGTTCGTCATTCCGGGGCACGGCCTGCCGGGCGGTCTAGACTTGCTCAAGCACACAACGAATGTTGTAAAAGCGCACACAAATCGCTCAGTCGTTGAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36803","NCBI_taxonomy_name":"Pseudomonas putida","NCBI_taxonomy_id":"303"}}}},"ARO_accession":"3002276","ARO_id":"38676","ARO_name":"VIM-6","CARD_short_name":"VIM-6","ARO_description":"VIM-6 is a beta-lactamase found in Pseudomonas spp.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"439":{"model_id":"439","model_name":"SHV-83","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"8139":{"protein_sequence":{"accession":"CAJ47138.2","sequence":"KRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AM176558.2","fmin":"0","fmax":"861","strand":"+","sequence":"AAGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGGATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001137","ARO_id":"37517","ARO_name":"SHV-83","CARD_short_name":"SHV-83","ARO_description":"SHV-83 is a broad-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"441":{"model_id":"441","model_name":"OXA-54","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"893":{"protein_sequence":{"accession":"AAR89917.1","sequence":"MRVLALSAVLVVASIVGMPAMANEWQEKPSWNTHFSEHKAQGVIVLWNENKQQGFTNNLKRANQAFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGQTRDIAAWNRDHDLITAMKYSVVPVYQEFARQIGQARMSKMLHAFDYGNEDISGNLDSFWLDGGIRISATEQVAFLRKLYHNKLHVSERSQRIVKQAMLTEANSDYIIRAKTGYSTRIEPQIGWWVGWVELDDNVWFFAMNMDMPTADGLGLRQAITKEVLKQEKIIP"},"dna_sequence":{"accession":"AY500137.1","fmin":"0","fmax":"798","strand":"+","sequence":"ATGCGTGTGTTAGCCTTATCGGCTGTATTAGTGGTGGCATCGATTGTTGGCATGCCGGCGATGGCAAACGAATGGCAGGAAAAACCGAGTTGGAATACTCATTTTTCGGAACATAAAGCGCAGGGTGTGATAGTGCTTTGGAACGAGAACAAACAGCAAGGATTTACCAATAATCTTAAGCGGGCAAACCAAGCATTTTTACCCGCATCGACCTTTAAAATCCCCAATAGCTTGATTGCCTTGGATTTAGGTGTCGTGAAGGATGAGCATCAAGTCTTTAAATGGGATGGACAGACTCGGGATATCGCGGCGTGGAATCGCGACCATGACTTAATCACTGCGATGAAATACTCGGTCGTGCCCGTGTATCAAGAGTTTGCGCGCCAAATTGGGCAGGCGCGCATGAGTAAAATGTTGCACGCATTTGATTATGGCAATGAAGATATTTCGGGCAATCTAGACAGCTTTTGGCTCGATGGCGGCATTCGGATTTCGGCAACGGAGCAAGTCGCATTTCTACGAAAGCTGTATCATAACAAGTTGCATGTATCAGAACGCAGTCAGCGTATCGTCAAGCAAGCCATGCTTACCGAGGCTAATAGTGACTACATAATCCGCGCTAAAACCGGATACTCGACCAGAATTGAGCCTCAGATCGGTTGGTGGGTCGGTTGGGTTGAACTCGATGATAATGTGTGGTTCTTCGCGATGAATATGGATATGCCTACGGCTGATGGTTTAGGGCTACGTCAAGCCATCACTAAAGAAGTGCTTAAACAGGAAAAGATAATTCCATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36933","NCBI_taxonomy_name":"Shewanella oneidensis","NCBI_taxonomy_id":"70863"}}}},"ARO_accession":"3001812","ARO_id":"38212","ARO_name":"OXA-54","CARD_short_name":"OXA-54","ARO_description":"OXA-54 is a beta-lactamase found in Shewanella spp.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46510":{"category_aro_accession":"3007721","category_aro_cvterm_id":"46510","category_aro_name":"OXA-48-like beta-lactamase","category_aro_description":"OXA-48-type beta-lactamases are now routinely encountered in bacterial infections caused by carbapenam-resistant Enterobacterales. OXA-48-like proteins confer resistance to penicillin (which is efficiently hydrolyzed) and carbapenam antibiotics (which is more slowly broken down). The spectrum of activity of these variants varies, with some hydrolyzing expanded-spectrum oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"443":{"model_id":"443","model_name":"OKP-B-10","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"795":{"protein_sequence":{"accession":"CAJ19619.1","sequence":"MRYVRLCLISLIAALPLAVFASPQPLEQIKISESQLAGRVGYVEMDLASGRTLAAWRASERFPLMSTFKVLLCGAVLARVDAGDEQLDRRIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNTAGNLLLKIVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDVRDTTTPANMATTLRKLLTTPSLSARSQQQLLQWMVDDRVAGPLIRAVLPAGWFIADKTGAGERGSRGIVALLGPDGKAERIVVIYLRDTAATMAERNQQIAVIGAALIEHWQR"},"dna_sequence":{"accession":"AM051160.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGCCTTATCTCCCTGATTGCCGCCCTGCCACTGGCGGTATTCGCCAGCCCTCAGCCGCTTGAGCAGATTAAAATCAGCGAAAGTCAGCTGGCGGGCCGGGTGGGCTATGTTGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCAGTGAGCGCTTTCCGCTGATGAGCACCTTTAAAGTGCTGCTCTGCGGCGCGGTGCTGGCCCGGGTGGATGCCGGCGACGAACAGCTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGCCGACGGGATGACCGTTGGCGAACTCTGCGCCGCCGCCATCACCATGAGCGACAACACCGCCGGCAATCTGCTGTTGAAGATCGTCGGCGGCCCCGCGGGATTGACCGCTTTTCTGCGCCAGATCGGTGACAACGTCACCCGTCTTGACCGCTGGGAAACGGAACTCAATGAGGCGCTTCCCGGCGACGTGCGCGACACCACCACCCCGGCCAACATGGCCACCACCCTGCGCAAGCTGCTAACCACCCCCTCTCTGAGCGCCCGTTCGCAGCAGCAGCTGCTGCAGTGGATGGTTGACGACCGGGTGGCCGGCCCGTTGATCCGCGCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAAACCGGGGCCGGTGAGCGGGGCTCACGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAAGCGGAGCGTATCGTGGTGATCTATCTGCGGGATACCGCAGCGACCATGGCCGAACGTAACCAGCAGATCGCCGTGATAGGCGCGGCGCTGATCGAGCACTGGCAGCGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002443","ARO_id":"38843","ARO_name":"OKP-B-10","CARD_short_name":"OKP-B-10","ARO_description":"OKP-B-10 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"38817":{"category_aro_accession":"3002417","category_aro_cvterm_id":"38817","category_aro_name":"OKP beta-lactamase","category_aro_description":"OKP beta-lactamases are chromosomal class A beta-lactamase that confer resistance to penicillins and early cephalosporins in Klebsiella pneumoniae. OKP beta-lactamases can be subdivided into two groups: OKP-A and OKP-B which diverge by about 4.2%.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"444":{"model_id":"444","model_name":"AAC(6')-Ib-Suzhou","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"83":{"protein_sequence":{"accession":"ABU55430.1","sequence":"MTEHDLAMLYEWLNRSHIVEWWGGEEARPTLADVQEQYLPSVLAQESVTPYIAMLNGEPIGYAQSYVALGSGDGWWEEETDPGVRGIDQLLANASQLGKGLGTKLVRALVELLFNDPEVTKIQTDPSPSNLRAIRCYEKAGFERQGTVTTPDGPAVYMVQTRQAFERTRMDA"},"dna_sequence":{"accession":"EU085533.1","fmin":"0","fmax":"519","strand":"+","sequence":"ATGACTGAGCATGACCTTGCGATGCTCTATGAGTGGCTAAATCGATCTCATATCGTCGAGTGGTGGGGCGGAGAAGAAGCACGCCCGACACTTGCTGACGTACAGGAACAGTACTTGCCAAGCGTTTTAGCGCAAGAGTCCGTCACTCCATACATTGCAATGCTGAATGGAGAGCCGATTGGGTATGCCCAGTCGTACGTTGCTCTTGGAAGCGGGGACGGATGGTGGGAAGAAGAAACCGATCCAGGAGTACGCGGAATAGACCAGTTACTGGCGAATGCATCACAACTGGGCAAAGGCTTGGGAACCAAGCTGGTTCGAGCTCTGGTTGAGTTGCTGTTCAATGATCCCGAGGTCACCAAGATCCAAACGGACCCGTCGCCGAGCAACTTGCGAGCGATCCGATGCTACGAGAAAGCGGGGTTTGAGAGGCAAGGTACCGTAACCACCCCAGATGGTCCAGCCGTGTACATGGTTCAAACACGCCAGGCATTCGAGCGAACACGCATGGATGCCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3002591","ARO_id":"38991","ARO_name":"AAC(6')-Ib-Suzhou","CARD_short_name":"AAC_6_IB_Su","ARO_description":"AAC(6')-Ib-Suzhou is an aminoglycoside acetyltransferase in E. cloacae and K. pneumoniae.","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"A category of aminoglycoside N-acetyltransferase enzymes with modification regiospecificity based at the 6'-amino group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics through acetylation of the 6-amino group of the compound.","category_aro_class_name":"AMR Gene Family"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"445":{"model_id":"445","model_name":"TEM-22","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1725":{"protein_sequence":{"accession":"CAA76795.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDKLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVKYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGGSERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"Y17583.1","fmin":"213","fmax":"1071","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATAAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTAAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGGCAGTGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGG","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3000893","ARO_id":"37273","ARO_name":"TEM-22","CARD_short_name":"TEM-22","ARO_description":"TEM-22 is an extended-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"446":{"model_id":"446","model_name":"catB8","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"5451":{"protein_sequence":{"accession":"AAM92461.1","sequence":"MKNYFNSPFKGELLSEQVKNPNIRVGRYSYYSGYYHGHSFDECARYLLPDRDDVDKLIIGSFCSIGSGASFIMAGNQGHRHDWASSFPFFYMQEEPAFSRALDAFQRAGDTVIGNDVWIGSEAMIMPGIKIGDGAVIGSRSLVTKDVEPYAIIGGNPAKQIKKRFSDEEISLLMEMEWWNWPLDKIKTAMPLLCSSNIFGLHKYWREFAV"},"dna_sequence":{"accession":"AY123251.1","fmin":"811","fmax":"1444","strand":"+","sequence":"ATGAAAAACTACTTTAACAGCCCTTTCAAAGGGGAACTTCTTTCTGAGCAAGTGAAAAATCCAAATATCAGAGTAGGCCGGTATAGCTATTACTCTGGCTACTATCACGGGCACTCATTTGATGAATGCGCGCGATACTTGCTTCCAGATCGTGATGACGTTGATAAATTGATCATTGGCAGCTTTTGTTCTATAGGAAGCGGGGCTTCCTTCATCATGGCTGGCAATCAGGGGCATCGGCATGACTGGGCATCATCCTTCCCCTTCTTCTATATGCAAGAGGAGCCTGCTTTCTCAAGAGCACTCGACGCCTTCCAAAGAGCAGGTGATACCGTCATTGGCAATGATGTCTGGATAGGCTCGGAGGCAATGATTATGCCTGGCATCAAAATTGGAGACGGTGCCGTGATAGGTAGTCGCTCGTTGGTGACAAAAGATGTAGAGCCTTATGCCATCATCGGGGGAAATCCCGCAAAGCAAATTAAGAAGCGCTTCTCCGATGAGGAAATCTCATTGCTCATGGAGATGGAGTGGTGGAACTGGCCACTAGATAAAATTAAGACAGCAATGCCTCTGCTGTGCTCGTCAAATATTTTTGGTCTGCATAAGTATTGGCGCGAGTTTGCCGTCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35731","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Typhi","NCBI_taxonomy_id":"90370"}}}},"ARO_accession":"3002680","ARO_id":"39114","ARO_name":"catB8","CARD_short_name":"catB8","ARO_description":"catB8 is a plasmid or integron-encoded variant of the cat gene found in Klebsiella pneumoniae, Salmonella typhi and Pseudomonas aeruginosa.","ARO_category":{"36261":{"category_aro_accession":"3000122","category_aro_cvterm_id":"36261","category_aro_name":"chloramphenicol acetyltransferase (CAT)","category_aro_description":"Inactivates chloramphenicol by addition of an acyl group. CAT is used to describe many variants of the chloramphenicol acetyltransferase gene in a range of organisms including Acinetobacter calcoaceticus, Agrobacterium tumefaciens, Alkalihalobacillus clausii, Bacillus subtilis, Campylobacter coli, Enterococcus faecalis, Enterococcus faecium, Lactococcus lactis, Listeria monocytogenes, Listonella anguillarum, Morganella morganii, Photobacterium damselae subsp. piscicida, Proteus mirabilis, Salmonella typhi, Serratia marcescens, Shigella flexneri, Staphylococcus aureus, Staphylococcus haemolyticus, Staphylococcus intermedius, Streptococcus agalactiae, Streptococcus suis and Streptomyces acrimycini.","category_aro_class_name":"AMR Gene Family"},"36521":{"category_aro_accession":"3000382","category_aro_cvterm_id":"36521","category_aro_name":"azidamfenicol","category_aro_description":"Azidamfenicol is a water soluble derivative of chloramphenicol, sharing the same mode of action of inhibiting peptide synthesis by interacting with the 23S RNA of the 50S ribosomal subunit.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36595":{"category_aro_accession":"3000456","category_aro_cvterm_id":"36595","category_aro_name":"thiamphenicol","category_aro_description":"Derivative of Chloramphenicol. The nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3).","category_aro_class_name":"Antibiotic"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"447":{"model_id":"447","model_name":"SHV-67","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1237":{"protein_sequence":{"accession":"ABA06589.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWCADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"DQ174307.1","fmin":"4","fmax":"865","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGTGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACATCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001122","ARO_id":"37502","ARO_name":"SHV-67","CARD_short_name":"SHV-67","ARO_description":"SHV-67 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"448":{"model_id":"448","model_name":"dfrG","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"750":{"protein_sequence":{"accession":"BAE15963.1","sequence":"MKVSLIAAMDKNRVIGKENDIPWRIPKDWEYVKNTTKGHPIILGRKNLESIGRALPDRRNIILTRDKGFTFNGCEIVHSIEDVFELCKNEEEIFIFGGEQIYNLFFPYVEKMYITKIHHEFEGDTFFPEVNYEEWNEVFAQKGIKNDKNPYNYYFHVYERKNLLS"},"dna_sequence":{"accession":"AB205645.1","fmin":"1012","fmax":"1510","strand":"+","sequence":"ATGAAAGTTTCTTTGATTGCTGCGATGGATAAGAATAGAGTGATTGGCAAAGAGAATGACATTCCTTGGAGGATTCCCAAGGACTGGGAATATGTTAAAAATACTACAAAGGGACATCCGATAATATTAGGTAGGAAGAACCTTGAATCAATCGGAAGAGCCTTACCTGACAGAAGAAATATTATTCTGACGAGAGATAAGGGGTTTACCTTTAATGGTTGTGAAATTGTTCATTCAATAGAAGATGTTTTTGAGTTATGTAAAAACGAAGAAGAAATTTTTATTTTCGGAGGAGAACAGATTTATAATTTGTTTTTCCCTTATGTTGAGAAAATGTACATCACAAAAATACATCATGAATTCGAAGGAGATACTTTTTTTCCAGAAGTGAATTATGAGGAATGGAATGAGGTATTTGCCCAAAAAGGGATAAAGAATGATAAAAATCCGTATAACTACTATTTTCATGTATATGAAAGAAAAAACTTATTGAGTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35508","NCBI_taxonomy_name":"Staphylococcus aureus","NCBI_taxonomy_id":"1280"}}}},"ARO_accession":"3002868","ARO_id":"39302","ARO_name":"dfrG","CARD_short_name":"dfrG","ARO_description":"dfrG is a plasmid-encoded dihydrofolate reductase found in Staphylococcus aureus.","ARO_category":{"37617":{"category_aro_accession":"3001218","category_aro_cvterm_id":"37617","category_aro_name":"trimethoprim resistant dihydrofolate reductase dfr","category_aro_description":"Alternative dihydropteroate synthase dfr present on plasmids produces alternate proteins that are less sensitive to trimethoprim from inhibiting its role in folate synthesis, thus conferring trimethoprim resistance.","category_aro_class_name":"AMR Gene Family"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"449":{"model_id":"449","model_name":"SHV-133","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1144":{"protein_sequence":{"accession":"BAI94487.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDGVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AB551737.1","fmin":"14","fmax":"875","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATGGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGCATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATATATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001177","ARO_id":"37557","ARO_name":"SHV-133","CARD_short_name":"SHV-133","ARO_description":"SHV-133 is a beta-lactamase.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"450":{"model_id":"450","model_name":"OXA-51","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8229":{"protein_sequence":{"accession":"CAC83905.2","sequence":"MNIKTLLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEVHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"AJ309734.2","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAACACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGTACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001612","ARO_id":"38012","ARO_name":"OXA-51","CARD_short_name":"OXA-51","ARO_description":"OXA-51 is a beta-lactamase found in A. baumannii.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"40512":{"category_aro_accession":"3003821","category_aro_cvterm_id":"40512","category_aro_name":"BAL30072","category_aro_description":"BAL30072 is a monocyclic beta-lactam antibiotic belonging to the sulfactams. BAL30072 was found to trigger the spheroplasting and lysis of Escherichia coli rather than the formation of extensive filaments.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"451":{"model_id":"451","model_name":"LRA-5","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"4540":{"protein_sequence":{"accession":"ACH59002.1","sequence":"MKTIFGKRRQSAVVLITLIAILLASGQPYQSSQVRGAACLPDIIFDEPSQGPEKNEAISMLTERLSSIINAAGGDIGIAVIHVETGHTTAIQGTTQLPLYSVFKLPLAIAVLKEIEENRLQLDRKVRVTPADVAPGWTANAAMWRRPIDRTVAQLIEVSIIRSDNTSSDKLLQLVGGPAAVTHRMRALGFPNIEIVSTVREFSENRTRPNTGSAEDLARLLVQLQKGELLQPQHSALLLGFMHRATTGTERLRGSLPVGTPVADKTGTGDAGVVTNDVGIITLPKGQGHLAIAVLISGSKLSPAAQEKLIAEIARAAYDAHVSRAE"},"dna_sequence":{"accession":"EU408358.1","fmin":"27458","fmax":"28439","strand":"-","sequence":"ATGAAAACTATCTTTGGTAAGCGTAGGCAATCAGCCGTAGTGCTCATCACTTTAATTGCAATTCTCCTTGCTTCGGGCCAGCCCTACCAAAGCTCTCAGGTGAGGGGGGCCGCGTGCCTTCCAGACATCATTTTTGACGAGCCATCTCAAGGCCCGGAAAAGAACGAAGCCATCTCCATGCTGACTGAACGGCTGAGTTCAATCATCAATGCGGCAGGCGGTGATATCGGAATAGCCGTCATCCACGTCGAGACGGGCCATACCACCGCAATTCAAGGAACAACGCAGTTACCTCTCTACAGTGTCTTCAAACTGCCACTTGCGATTGCGGTGCTCAAGGAGATCGAAGAAAACCGACTTCAGCTCGACAGGAAAGTCCGTGTCACGCCCGCGGATGTTGCGCCGGGCTGGACAGCGAATGCTGCTATGTGGCGCCGGCCCATCGACCGAACTGTCGCTCAACTAATAGAAGTGTCAATCATACGAAGCGACAACACATCGAGCGATAAGCTGCTTCAACTAGTCGGTGGGCCGGCTGCAGTGACGCACCGCATGCGCGCTCTGGGTTTTCCCAACATCGAGATCGTGTCGACGGTACGCGAGTTCTCCGAGAATCGGACCAGACCAAATACTGGGTCGGCGGAGGACCTTGCGCGCTTGCTGGTTCAGCTGCAAAAAGGCGAACTGCTACAGCCACAACATTCCGCTTTGCTTTTGGGTTTTATGCACCGAGCGACGACGGGAACAGAGCGCTTGCGAGGCAGTCTGCCGGTCGGCACTCCTGTAGCTGACAAGACGGGCACCGGCGATGCGGGAGTCGTTACAAACGATGTGGGAATCATCACACTACCAAAAGGACAAGGGCATCTGGCTATCGCGGTGCTTATAAGTGGATCAAAACTGTCACCCGCGGCACAAGAAAAGCTCATTGCCGAAATTGCACGAGCCGCTTATGACGCTCACGTTTCTCGTGCGGAGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39088","NCBI_taxonomy_name":"uncultured bacterium BLR5","NCBI_taxonomy_id":"506522"}}}},"ARO_accession":"3002483","ARO_id":"38883","ARO_name":"LRA-5","CARD_short_name":"LRA-5","ARO_description":"LRA-5 is a beta-lactamase isolated from soil samples in Alaska.","ARO_category":{"41392":{"category_aro_accession":"3004228","category_aro_cvterm_id":"41392","category_aro_name":"class A LRA beta-lactamase","category_aro_description":"Beta-lactamases that are part of the LRA gene family and are classified as Class A beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"452":{"model_id":"452","model_name":"QnrVC4","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"530":{"protein_sequence":{"accession":"ADI55014.1","sequence":"MDKTDQLYVQADFSHQDMSGQYFKNCKFFCCSFKRANLRDTQFVDCSFIERGELEGCDFSYSDLRDASFKNCSLSMSYFKGANCFGIEFRECDLKGANFAQASFMNQVSNRMYFCSAYITGCNLSYANFERQCIEKCDLFENRWIGANLSGASFKESDLSRGVFSEGCWSQCRLQGCDLSHSELYGLDPRKVDLTGVKICSWQQEQLLEQLGLIVVPD"},"dna_sequence":{"accession":"GQ891757.1","fmin":"2004","fmax":"2661","strand":"+","sequence":"ATGGATAAAACAGACCAGTTATATGTACAAGCAGACTTTTCACATCAAGACATGAGTGGTCAGTATTTTAAAAATTGCAAATTTTTCTGCTGTTCCTTTAAACGAGCGAACCTCCGCGATACACAATTTGTAGATTGTTCTTTCATTGAACGAGGTGAATTAGAGGGGTGTGATTTTTCTTACTCGGATCTTAGAGATGCATCTTTTAAAAACTGCAGTCTTTCAATGTCGTATTTCAAAGGTGCAAATTGTTTTGGTATCGAGTTCAGAGAATGCGATTTAAAGGGTGCCAATTTTGCTCAAGCTAGCTTCATGAATCAGGTATCGAACAGAATGTATTTTTGTTCAGCTTATATAACAGGTTGTAATCTTTCATACGCCAACTTTGAAAGGCAGTGTATCGAAAAGTGTGATTTGTTTGAGAATAGATGGATTGGCGCAAATCTGAGTGGTGCATCATTTAAAGAGTCTGATTTAAGTCGGGGAGTATTTTCTGAAGGGTGTTGGAGCCAGTGTAGGTTGCAAGGTTGTGATTTGAGCCACTCGGAGTTGTATGGTTTAGACCCTCGGAAAGTTGACCTTACAGGTGTAAAAATCTGTTCGTGGCAGCAAGAACAACTTTTAGAGCAATTAGGTTTAATAGTAGTTCCTGACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36936","NCBI_taxonomy_name":"Aeromonas caviae","NCBI_taxonomy_id":"648"}}}},"ARO_accession":"3002801","ARO_id":"39235","ARO_name":"QnrVC4","CARD_short_name":"QnrVC4","ARO_description":"QnrVC4 is an integron-mediated quinolone resistance protein found in Aeromonas punctata.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"453":{"model_id":"453","model_name":"mtrE","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"910"}},"model_sequences":{"sequence":{"400":{"protein_sequence":{"accession":"CAA64891.1","sequence":"MNTTLKTTLTSVAAAFALSACTMIPQYEQPKVEVAETFQNDTSVSSIRAVDLGWHDYFADPRLQKLIDIALERNTSLRTAVLNSEIYRKQYMIERNNLLPTLAANANGSRQGSLSGGNVSSSYNVGLGAASYELDLFGRVRSSSEAALQGYFASVANRDAAHLSLIATVAKAYFNERYAEEAMSLAQRVLKTREETYNAVRIAVQGRRDFRRRPAPAEALIESAKADYAHAARSREQARNALATLINRPIPEDLPAGLPLDKQFFVEKLPAGLSSEVLLDRPDIRAAEHALKQANANIGAARAAFFPSIRLTGSVGTGSVELGGLFKSGTGVWAFAPSITLPIFTWGTNKANLDVAKLRQQAQIVAYESAVQSAFQDVANALAAREQLDKAYDALSKQSRASKEALRLVGLRYKHGVSGALDLLDAERSSYSAEGAALSAQLTRAENLADLYKALGGGLKRDTQTGK"},"dna_sequence":{"accession":"X95635.1","fmin":"259","fmax":"1663","strand":"+","sequence":"ATGAATACTACATTGAAAACTACCTTGACCTCTGTTGCAGCAGCCTTTGCATTGTCTGCCTGCACCATGATTCCTCAATACGAGCAGCCCAAAGTCGAAGTTGCGGAAACCTTCCAAAACGACACATCGGTTTCTTCCATCCGCGCGGTTGATTTGGGTTGGCATGACTATTTTGCCGACCCGCGCCTGCAAAAGCTGATCGACATCGCACTCGAGCGCAATACCAGTTTGCGTACAGCCGTATTGAACAGCGAAATCTACCGCAAACAATACATGATCGAGCGCAACAACCTCCTGCCCACGCTTGCCGCCAATGCGAACGGCTCGCGCCAAGGCAGCTTGAGCGGCGGCAATGTCAGCAGCAGCTACAATGTCGGACTGGGTGCGGCATCTTACGAACTCGATCTGTTCGGGCGCGTGCGCAGCAGCAGCGAAGCAGCACTGCAAGGCTATTTTGCCAGCGTTGCCAACCGCGATGCGGCACATTTGAGTCTGATTGCCACCGTTGCCAAAGCCTATTTCAACGAGCGTTATGCCGAAGAAGCGATGTCTTTGGCGCAGCGTGTCTTGAAAACGCGCGAGGAAACCTACAATGCTGTCCGAATTGCGGTACAAGGCAGGCGTGATTTCCGCCGTCGCCCTGCGCCAGCAGAAGCCTTGATTGAATCTGCCAAAGCCGATTATGCCCATGCCGCGCGCAGCCGCGAACAGGCGCGCAATGCCTTGGCAACCTTGATTAACCGTCCGATACCCGAAGACCTGCCCGCCGGTTTGCCGTTGGACAAGCAGTTTTTTGTTGAAAAACTGCCTGCCGGTTTGAGTTCCGAAGTATTGCTCGACCGTCCCGACATCCGCGCCGCCGAACACGCGCTCAAACAGGCAAACGCCAATATCGGTGCGGCGCGCGCCGCCTTTTTCCCGTCCATCCGCCTGACCGGAAGCGTCGGTACGGGTTCTGTCGAATTGGGCGGGCTGTTCAAAAGCGGCACGGGCGTTTGGGCGTTCGCGCCGTCTATTACCCTGCCGATTTTTACTTGGGGAACGAACAAGGCGAACCTTGATGTGGCAAAACTGCGCCAACAGGCACAAATTGTTGCCTATGAATCCGCCGTCCAATCCGCCTTTCAAGACGTGGCAAACGCATTGGCGGCGCGCGAGCAGCTGGATAAAGCCTATGACGCTTTAAGCAAACAAAGCCGCGCCTCTAAAGAAGCGTTGCGCTTGGTCGGACTGCGTTACAAACACGGCGTATCCGGCGCGCTCGATTTGCTCGATGCGGAACGCAGCAGCTATTCGGCGGAAGGTGCGGCTTTGTCGGCACAACTGACCCGCGCCGAAAACCTTGCCGATTTGTACAAGGCGCTCGGCGGCGGATTGAAACGGGATACCCAAACCGGCAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36806","NCBI_taxonomy_name":"Neisseria gonorrhoeae","NCBI_taxonomy_id":"485"}}}},"ARO_accession":"3000812","ARO_id":"37192","ARO_name":"mtrE","CARD_short_name":"mtrE","ARO_description":"MtrE is an outer membrane exporter protein that is part of the MtrCDE multidrug efflux complex.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"454":{"model_id":"454","model_name":"KPC-4","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"5884":{"protein_sequence":{"accession":"ACA34343.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVRWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGGYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"EU447304.1","fmin":"14","fmax":"896","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCGGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGGGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002314","ARO_id":"38714","ARO_name":"KPC-4","CARD_short_name":"KPC-4","ARO_description":"KPC-4 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"455":{"model_id":"455","model_name":"vanC","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"150":{"protein_sequence":{"accession":"AAA24786.1","sequence":"MKKIAVLFGGNSPEYSVSLTSAASVIQAIDPLKYEVMTIGIAPTMDWYWYQGNLANVRNDTWLEDHKNCHQLTFSSQGFILGEKRIVPDVLFPVLHGKYGEDGCIQGLLELMNLPYVGCHVAASALCMNKWLLHQLADTMGIASAPTLLLSRYENDPATIDRFIQDHGFPIFIKPNEAGSSKGITKVTDKTALQSALTTAFAYGSTVLIQKAIAGIEIGCGILGNEQLTIGACDAISLVDGFFDFEEKYQLISATITVPAPLPLALESQIKEQAQLLYRNLGLTGLARIDFFVTNQGAIYLNEINTMPGFTGHSRYPAMMAEVGLSYEILVEQLIALAEEDKR"},"dna_sequence":{"accession":"AF162694.1","fmin":"1410","fmax":"2442","strand":"+","sequence":"ATGAAAAAAATTGCCGTTTTATTTGGAGGGAATTCTCCAGAATACTCAGTGTCACTAACCTCAGCAGCAAGTGTGATCCAAGCTATTGACCCGCTGAAATATGAAGTAATGACCATTGGCATCGCACCAACAATGGATTGGTATTGGTATCAAGGAAACCTCGCGAATGTTCGCAATGATACTTGGCTAGAAGATCACAAAAACTGTCACCAGCTGACTTTTTCTAGCCAAGGATTTATATTAGGAGAAAAACGAATCGTCCCTGATGTCCTCTTTCCAGTCTTGCATGGGAAGTATGGCGAGGATGGCTGTATCCAAGGACTGCTTGAACTAATGAACCTGCCTTATGTTGGTTGCCATGTCGCTGCCTCCGCATTATGTATGAACAAATGGCTCTTGCATCAACTTGCTGATACCATGGGAATCGCTAGTGCTCCCACTTTGCTTTTATCCCGCTATGAAAACGATCCTGCCACAATCGATCGTTTTATTCAAGACCATGGATTCCCGATCTTTATCAAGCCGAATGAAGCCGGTTCTTCAAAAGGGATCACAAAAGTAACTGACAAAACAGCGCTCCAATCTGCATTAACGACTGCTTTTGCTTACGGTTCTACTGTGTTGATCCAAAAGGCGATAGCGGGTATTGAAATTGGCTGCGGCATCTTAGGAAATGAGCAATTGACGATTGGTGCTTGTGATGCGATTTCTCTTGTCGACGGTTTTTTTGATTTTGAAGAGAAATACCAATTAATCAGCGCCACGATCACTGTCCCAGCACCATTGCCTCTCGCGCTTGAATCACAGATCAAGGAGCAGGCACAGCTGCTTTATCGAAACTTGGGATTGACGGGTCTGGCTCGAATCGATTTTTTCGTCACCAATCAAGGAGCGATTTATTTAAACGAAATCAACACCATGCCGGGATTTACTGGGCACTCCCGCTACCCAGCTATGATGGCGGAAGTCGGGTTATCCTACGAAATATTAGTAGAGCAATTGATTGCACTGGCAGAGGAGGACAAACGATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36781","NCBI_taxonomy_name":"Enterococcus gallinarum","NCBI_taxonomy_id":"1353"}}}},"ARO_accession":"3000368","ARO_id":"36507","ARO_name":"vanC","CARD_short_name":"vanC","ARO_description":"VanC is a D-Ala-D-Ala ligase homolog that synthesizes D-Ala-D-Ser, an alternative substrate for peptidoglycan synthesis that reduces vancomycin binding affinity. It is specific to Enterococcus gallinarum and E. casseliflavus, providing intrinsic resistance.","ARO_category":{"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"39340":{"category_aro_accession":"3002906","category_aro_cvterm_id":"39340","category_aro_name":"Van ligase","category_aro_description":"Van ligases synthesize alternative substrates for peptidoglycan synthesis that reduce vancomycin binding affinity.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"456":{"model_id":"456","model_name":"adeR","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"480"}},"model_sequences":{"sequence":{"711":{"protein_sequence":{"accession":"ADM92605.1","sequence":"MFDHSFSFDCQDKVILVVEDDYDIGDIIENYLKREGMSVIRAMNGKQAIELHASQPIDLILLDIKLPELNGWEVLNKIRQKAQTPVIMLTALDQDIDKVMALRIGADDFVVKPFNPNEVVARVQAVLRRTQFANKATNKNKLYKNIEIDTDTHSVYIHSENKKILLNLTLTEYKIISFMIDQPHKVFTRGELMNHCMNDSDALERTVDSHVSKLRKKLEEQGIFQMLINVRGVGYRLDNPLAVKDDA"},"dna_sequence":{"accession":"HM440348.1","fmin":"0","fmax":"744","strand":"+","sequence":"ATGTTTGATCATTCTTTTTCTTTTGATTGCCAAGATAAAGTTATTCTTGTGGTAGAAGATGACTACGATATTGGCGACATTATTGAAAATTATTTAAAACGTGAAGGCATGAGTGTTATTCGGGCCATGAATGGAAAGCAAGCGATTGAATTGCACGCTAGCCAACCCATCGATTTAATCTTACTTGATATTAAATTACCCGAATTAAACGGTTGGGAAGTATTAAATAAAATACGCCAAAAAGCTCAGACTCCCGTGATCATGTTGACGGCGCTAGATCAAGATATTGATAAAGTTATGGCATTACGCATAGGTGCAGATGACTTTGTGGTGAAGCCTTTTAACCCAAATGAAGTCGTCGCTAGAGTTCAGGCAGTCCTAAGACGTACTCAGTTTGCAAACAAAGCAACTAATAAAAATAAACTCTATAAAAATATTGAAATTGATACCGACACTCATAGCGTTTATATACACTCTGAGAATAAGAAGATCTTGCTTAATCTGACGCTGACTGAATATAAAATTATTTCATTCATGATTGATCAGCCTCATAAAGTTTTTACGCGCGGAGAGCTTATGAATCACTGCATGAATGATAGCGATGCACTAGAGCGAACCGTAGATAGCCATGTGAGTAAGCTGAGAAAAAAACTAGAAGAACAAGGCATATTTCAAATGTTAATTAATGTGCGTGGCGTGGGATATAGACTAGATAATCCCCTAGCTGTAAAAGATGATGCCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3000553","ARO_id":"36692","ARO_name":"adeR","CARD_short_name":"adeR","ARO_description":"AdeR is a positive regulator of AdeABC efflux system. AdeR inactivation leads to susceptibility to aminoglycoside antibiotics.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"457":{"model_id":"457","model_name":"OXA-93","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1428":{"protein_sequence":{"accession":"ABF47916.1","sequence":"MNIKALLLITSTIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALISLEHHKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"DQ519087.1","fmin":"38","fmax":"863","strand":"+","sequence":"ATGAACATTAAAGCCCTCTTACTTATAACAAGCACTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTCTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCAGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGACGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001628","ARO_id":"38028","ARO_name":"OXA-93","CARD_short_name":"OXA-93","ARO_description":"OXA-93 is a beta-lactamase found in A. baumannii.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"459":{"model_id":"459","model_name":"CTX-M-94","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"788":{"protein_sequence":{"accession":"ADK11041.1","sequence":"MMRKSVRRAMLMTTACVSLLLASVPLCAQANDVQQKLAALEKSSGGRLGVALINTADNTQTLYRADERFAMCSTSKVMAAAAVLKQSETQKGLLSQRVEIKPSDLINYNPIAEKHVNGTMTLGELSAAALQYSDNTAMNKLIAHLGGPDKVTAFARTIGDDTFRLDRTEPTLNTAIPGDPRDTTTPLAMAQALRNLTLGNALGDTQRAQLVMWLKGNTTGAASIQAGLPTSWVVGDKTGSGGYGTTNDIAVIWPEGRAPLVLVTYFTQSEPKAESRRDVLAAAARIVTDGY"},"dna_sequence":{"accession":"HM167760.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGATGAGAAAAAGCGTAAGGCGGGCGATGTTAATGACGACAGCCTGTGTTTCGCTGCTGTTGGCCAGTGTGCCGCTGTGTGCCCAGGCGAACGATGTTCAACAAAAGCTCGCGGCGCTGGAGAAAAGCAGCGGGGGACGACTGGGTGTGGCGTTGATTAACACCGCCGATAACACGCAGACGCTCTACCGCGCCGACGAGCGTTTTGCCATGTGCAGCACCAGTAAAGTGATGGCGGCAGCGGCGGTGCTTAAGCAAAGTGAAACGCAAAAGGGCTTGTTGAGTCAGCGGGTTGAAATTAAGCCCTCAGACTTGATTAACTACAACCCCATTGCGGAAAAACACGTCAATGGCACGATGACATTAGGGGAGTTGAGCGCGGCGGCGCTACAGTACAGCGATAATACTGCCATGAATAAGCTGATTGCCCATCTCGGGGGGCCGGATAAAGTGACGGCATTTGCCCGTACGATTGGCGATGACACGTTCCGGCTCGATCGTACCGAGCCGACGCTCAACACCGCGATCCCCGGCGACCCGCGCGATACCACCACGCCGTTAGCGATGGCGCAGGCTCTGCGCAATCTGACGTTGGGCAATGCCCTGGGTGACACTCAGCGTGCGCAGCTGGTGATGTGGCTGAAAGGCAACACCACCGGCGCTGCCAGCATTCAGGCAGGGCTACCCACATCGTGGGTTGTCGGGGATAAAACCGGCAGCGGCGGTTATGGTACGACGAATGATATCGCGGTTATTTGGCCGGAAGGTCGCGCGCCGCTCGTTCTGGTGACTTACTTCACCCAGTCGGAGCCGAAGGCAGAGAGCCGTCGTGACGTGCTCGCTGCTGCCGCCAGAATTGTCACCGACGGTTATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001954","ARO_id":"38354","ARO_name":"CTX-M-94","CARD_short_name":"CTX-M-94","ARO_description":"CTX-M-94 is a beta-lactamase found in Escherichia coli.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"460":{"model_id":"460","model_name":"CMY-29","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"8209":{"protein_sequence":{"accession":"ABS12248.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQFPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGELAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"EF685371.2","fmin":"0","fmax":"1143","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGTTCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGAGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAA","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002040","ARO_id":"38440","ARO_name":"CMY-29","CARD_short_name":"CMY-29","ARO_description":"CMY-29 is a beta-lactamase found in the Enterobacteriaceae family.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"461":{"model_id":"461","model_name":"OXA-13","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1523":{"protein_sequence":{"accession":"AAC46344.1","sequence":"MKTFAAYVITACLSSTALASSITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNNLARASKEYLPASTFKIPSAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLSLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLFLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKGTEVYFFAFNMDIDNENKLPLRKSIPTKIMASEGIIGG"},"dna_sequence":{"accession":"U59183.1","fmin":"939","fmax":"1740","strand":"+","sequence":"ATGAAAACATTTGCCGCATATGTAATTACTGCGTGTCTTTCAAGTACGGCATTAGCTAGTTCAATTACAGAAAATACGTCTTGGAACAAAGAGTTCTCTGCCGAAGCCGTCAATGGTGTTTTCGTGCTTTGTAAAAGTAGCAGTAAATCCTGCGCTACCAATAACTTAGCTCGTGCATCAAAGGAATATCTTCCAGCATCAACATTTAAGATCCCCAGCGCAATTATCGGCCTAGAAACTGGTGTCATAAAGAATGAGCATCAGGTTTTCAAATGGGACGGAAAGCCAAGAGCCATGAAACAATGGGAAAGAGACTTGAGCTTAAGAGGGGCAATACAAGTTTCAGCGGTTCCCGTATTTCAACAAATCGCCAGAGAAGTTGGCGAAGTAAGAATGCAGAAATACCTTAAAAAATTTTCATATGGCAACCAGAATATCAGTGGTGGCATTGACAAATTCTGGTTGGAGGGTCAGCTAAGAATTTCCGCAGTTAATCAAGTGGAGTTTCTAGAGTCTCTATTTTTAAATAAATTGTCAGCATCAAAAGAAAATCAGCTAATAGTAAAAGAGGCTTTGGTAACGGAGGCTGCGCCTGAATATCTTGTGCATTCAAAAACTGGTTTTTCTGGTGTGGGAACTGAGTCAAATCCTGGTGTCGCATGGTGGGTTGGTTGGGTTGAGAAGGGAACAGAGGTTTACTTTTTCGCCTTTAACATGGATATAGACAACGAAAATAAGTTGCCGCTAAGAAAATCCATTCCCACCAAAATCATGGCAAGTGAGGGCATCATTGGTGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3001408","ARO_id":"37808","ARO_name":"OXA-13","CARD_short_name":"OXA-13","ARO_description":"OXA-13 is a beta-lactamase found in P. aeruginosa.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46486":{"category_aro_accession":"3007697","category_aro_cvterm_id":"46486","category_aro_name":"OXA-10-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-10.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"463":{"model_id":"463","model_name":"CTX-M-30","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"2043":{"protein_sequence":{"accession":"AAP43508.1","sequence":"MVKKSLRQFTLMATAAVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVDGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGDYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"AY292654.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTCATGGCGACGGCAGCCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGGGTGGCATTGATTAACACTGCGGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTGGTTAACTATAATCCGATTGCGGAAAAGCACGTCGATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGCAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCAGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGACTATGGCACCACCAACGATATCGCGGTGATTTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGTGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3001892","ARO_id":"38292","ARO_name":"CTX-M-30","CARD_short_name":"CTX-M-30","ARO_description":"CTX-M-30 is a beta-lactamase found in Citrobacter freundii.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"464":{"model_id":"464","model_name":"NDM-13","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1918":{"protein_sequence":{"accession":"BAQ02518.1","sequence":"MELPNIMHPVAKLSTALAAALMLSGCMPGEIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTNDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGLVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR"},"dna_sequence":{"accession":"LC012596.1","fmin":"3585","fmax":"4398","strand":"+","sequence":"ATGGAATTGCCCAATATTATGCACCCGGTCGCGAAGCTGAGCACCGCATTAGCCGCTGCATTGATGCTGAGCGGGTGCATGCCCGGTGAAATCCGCCCGACGATTGGCCAGCAAATGGAAACTGGCGACCAACGGTTTGGCGATCTGGTTTTCCGCCAGCTCGCACCGAATGTCTGGCAGCACACTTCCTATCTCGACATGCCGGGTTTCGGGGCAGTCGCTTCCAACGGTTTGATCGTCAGGGATGGCGGCCGCGTGCTGGTGGTCGATACCGCCTGGACCAATGACCAGACCGCCCAGATCCTCAACTGGATCAAGCAGGAGATCAACCTGCCGGTCGCGCTGGCGGTGGTGACTCACGCGCATCAGGACAAGATGGGCGGTATGGACGCGCTGCATGCGGCGGGGATTGCGACTTATGCCAATGCGTTGTCGAACCAGCTTGCCCCGCAAGAGGGGCTGGTTGCGGCGCAACACAGCCTGACTTTCGCCGCCAATGGCTGGGTCGAACCAGCAACCGCGCCCAACTTTGGCCCGCTCAAGGTATTTTACCCCGGCCCCGGCCACACCAGTGACAATATCACCGTTGGGATCGACGGCACCGACATCGCTTTTGGTGGCTGCCTGATCAAGGACAGCAAGGCCAAGTCGCTCGGCAATCTCGGTGATGCCGACACTGAGCACTACGCCGCGTCAGCGCGCGCGTTTGGTGCGGCGTTCCCCAAGGCCAGCATGATCGTGATGAGCCATTCCGCCCCCGATAGCCGCGCCGCAATCACTCATACGGCCCGCATGGCCGACAAGCTGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3003182","ARO_id":"39759","ARO_name":"NDM-13","CARD_short_name":"NDM-13","ARO_description":"Beta-lactamase found in Escherichia coli clinical isolates in Nepal.","ARO_category":{"36196":{"category_aro_accession":"3000057","category_aro_cvterm_id":"36196","category_aro_name":"NDM beta-lactamase","category_aro_description":"NDM beta-lactamases or New Delhi metallo-beta-lactamases are class B beta-lactamases that confer resistance to a broad range of antibiotics including carbapenems, cephalosporins and penicillins.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"466":{"model_id":"466","model_name":"CTX-M-76","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1821":{"protein_sequence":{"accession":"CAQ42486.1","sequence":"MMTQSIRRSMLTVMATLPLLFSSATLHAQTNSVQQQLEALEKSSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKQSESDKHLLNQRVEIKKSDLVNYNPIAEKHVNGTMTLAELGAAALQYSDNTAMNKLIAHLGGPDKVTAFARSLGDETFRLDRTEPTLNTAIPGDPRDTTTPLAMAQTLKNLTLGKALAETQRAQLVTWLKGNTTGSASIRAGLPKSWGVGDKTGSGDYGTTNDIAVIWPENHAPLVLVTYFTQPEQKAESRRDVLAAAAKIVTHGF"},"dna_sequence":{"accession":"AM982520.1","fmin":"5548","fmax":"6424","strand":"+","sequence":"ATGATGACTCAGAGCATTCGCCGCTCAATGTTAACGGTGATGGCGACGCTACCCCTGCTATTTAGCAGCGCAACGCTGCACGCGCAGACGAACAGCGTGCAACAGCAGCTGGAAGCCCTGGAGAAAAGTTCGGGAGGTCGGCTTGGCGTTGCGCTGATTAACACCGCCGATAATTCGCAGATTCTCTACCGTGCCGATGAACGTTTTGCGATGTGCAGTACCAGTAAGGTGATGGCGGCCGCGGCGGTGCTTAAACAGAGCGAGAGCGATAAGCACCTGTTAAATCAGCGCGTTGAAATCAAGAAGAGCGACCTGGTTAACTACAATCCCATTGCGGAGAAACACGTTAACGGCACGATGACGCTGGCTGAGCTTGGCGCAGCGGCGCTGCAGTATAGCGACAATACTGCCATGAATAAGCTGATTGCCCATCTGGGTGGGCCCGATAAAGTGACGGCGTTTGCTCGCTCGTTGGGTGATGAGACCTTCCGTCTGGACAGAACCGAGCCCACGCTCAATACCGCCATTCCAGGCGACCCGCGTGATACCACCACGCCGCTCGCGATGGCGCAGACCCTGAAAAATCTGACGCTGGGTAAAGCGCTGGCGGAAACTCAGCGGGCACAGTTGGTGACGTGGCTTAAGGGCAATACTACCGGTAGCGCGAGCATTCGGGCGGGTCTGCCGAAATCATGGGGAGTGGGCGATAAAACCGGCAGCGGAGATTATGGCACCACCAACGATATCGCGGTTATCTGGCCGGAAAACCACGCACCGCTGGTTCTGGTGACCTACTTTACCCAACCGGAGCAGAAGGCGGAAAGCCGTCGGGATGTTCTGGCTGCGGCGGCGAAAATCGTAACCCACGGTTTCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36928","NCBI_taxonomy_name":"Kluyvera ascorbata","NCBI_taxonomy_id":"51288"}}}},"ARO_accession":"3001937","ARO_id":"38337","ARO_name":"CTX-M-76","CARD_short_name":"CTX-M-76","ARO_description":"CTX-M-76 is a beta-lactamase found in Kluyvera spp.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"467":{"model_id":"467","model_name":"CARB-3","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1506":{"protein_sequence":{"accession":"AAB19430.2","sequence":"MLLYKMCDNQNYGVTYMKFLLAFSLLIPSVVFASSSKFQQVEQDVKAIEVSLSARIGVSVLDTQNGEYWDYNGNQRFPLTSTFKTIACAKLLYDAEQGKVNPNSTVEIKKADLVTYSPVIEKQVGQAITLDDACFATMTTSDNTAANIILSAVGGPKGVTDFLRQIGDKETRLDRIEPDLNEGKLGDLRDTTTPKAIASTLNKLLFGSALSEMNQKKLESWMVNNQVTGNLLRSVLPAGWNIADRSGAGGFGARSITAVVWSEHQAPIIVSIYLAQTQASMAERNDAIVKIGHSIFDVYTSQSR"},"dna_sequence":{"accession":"S46063.1","fmin":"121","fmax":"1036","strand":"+","sequence":"ATGCTTTTATATAAAATGTGTGACAATCAAAATTATGGGGTTACTTACATGAAGTTTTTATTGGCATTTTCGCTTTTAATACCATCCGTGGTTTTTGCAAGTAGTTCAAAGTTTCAGCAAGTTGAACAAGACGTTAAGGCAATTGAAGTTTCTCTTTCTGCTCGTATAGGTGTTTCCGTTCTTGATACTCAAAATGGAGAATATTGGGATTACAATGGCAATCAGCGCTTCCCGTTAACAAGTACTTTTAAAACAATAGCTTGCGCTAAATTACTATATGATGCTGAGCAAGGAAAAGTTAATCCCAATAGTACAGTCGAGATTAAGAAAGCAGATCTTGTGACCTATTCCCCTGTAATAGAAAAGCAAGTAGGGCAGGCAATCACACTCGATGATGCGTGCTTCGCAACTATGACTACAAGTGATAATACTGCGGCAAATATCATCCTAAGTGCTGTAGGTGGCCCCAAAGGCGTTACTGATTTTTTAAGACAAATTGGGGACAAAGAGACTCGTCTAGACCGTATTGAGCCTGATTTAAATGAAGGTAAGCTCGGTGATTTGAGGGATACGACAACTCCTAAGGCAATAGCCAGTACTTTGAATAAACTTTTATTTGGTTCCGCGCTATCTGAAATGAACCAGAAAAAATTAGAGTCTTGGATGGTGAACAATCAAGTCACTGGTAATTTACTACGTTCAGTATTGCCGGCGGGATGGAACATTGCGGATCGCTCAGGTGCTGGCGGATTTGGTGCTCGGAGTATTACAGCAGTTGTGTGGAGTGAGCATCAAGCCCCAATTATTGTGAGCATCTATCTAGCTCAAACACAGGCTTCAATGGCAGAGCGAAATGATGCGATTGTTAAAATTGGTCATTCAATTTTTGACGTTTATACATCACAGTCGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002242","ARO_id":"38642","ARO_name":"CARB-3","CARD_short_name":"CARB-3","ARO_description":"CARB-3 is a beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36230":{"category_aro_accession":"3000091","category_aro_cvterm_id":"36230","category_aro_name":"CARB beta-lactamase","category_aro_description":"CARB beta-lactamases are class A lactamases that can hydrolyze carbenicillin. Many of the PSE beta-lactamases have been renamed as CARB-lactamases with the notable exception of PSE-2 which is now OXA-10.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"468":{"model_id":"468","model_name":"Erm(37)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"582":{"protein_sequence":{"accession":"CCP44758.1","sequence":"MSALGRSRRAWGWHRLHDEWAARVVSAAAVRPGELVFDIGAGEGALTAHLVRAGARVVAVELHPRRVGVLRERFPGITVVHADAASIRLPGRPFRVVANPPYGISSRLLRTLLAPNSGLVAADLVLQRALVCKFASRNARRFTLTVGLMLPRRAFLPPPHVDSAVLVVRRRKCGDWQGR"},"dna_sequence":{"accession":"AL123456.1","fmin":"2231679","fmax":"2232219","strand":"+","sequence":"GTGTCCGCCCTCGGACGGTCGCGACGGGCATGGGGCTGGCACCGGCTCCATGACGAATGGGCAGCGCGGGTAGTCAGCGCGGCCGCAGTGCGGCCCGGTGAGCTCGTGTTTGACATCGGCGCCGGCGAAGGGGCACTGACGGCGCATCTAGTGCGAGCGGGGGCGCGGGTGGTCGCCGTGGAGTTGCACCCGCGACGAGTCGGTGTCCTCCGCGAGCGATTCCCTGGCATTACCGTGGTGCACGCGGACGCCGCCTCGATCCGGTTGCCCGGCCGGCCGTTCCGGGTTGTGGCGAACCCGCCGTACGGGATTTCGTCCCGCCTGCTGCGGACGCTGCTGGCACCCAACAGCGGGCTTGTCGCGGCCGATCTCGTGCTGCAGCGAGCCCTCGTATGTAAATTCGCTTCTCGCAACGCGCGAAGGTTCACCCTGACCGTCGGCCTCATGCTGCCACGGCGCGCGTTCCTGCCACCGCCGCATGTGGATTCCGCGGTGCTCGTCGTCCGCCGCCGGAAGTGCGGTGACTGGCAGGGGCGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3000392","ARO_id":"36531","ARO_name":"Erm(37)","CARD_short_name":"Erm(37)","ARO_description":"Erm(37) is found in Mycobacterium species and confers the MLSb phenotype. In addition to methylation of A2058 this Erm methylates adjacent adenosines (A2057 and A2059) as well.","ARO_category":{"36699":{"category_aro_accession":"3000560","category_aro_cvterm_id":"36699","category_aro_name":"Erm 23S ribosomal RNA methyltransferase","category_aro_description":"Erm proteins are part of the RNA methyltransferase family and methylate A2058 (E. coli nomenclature) of the 23S ribosomal RNA conferring degrees of resistance to Macrolides, Lincosamides and Streptogramin b. This is called the MLSb phenotype.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35946":{"category_aro_accession":"0000027","category_aro_cvterm_id":"35946","category_aro_name":"roxithromycin","category_aro_description":"Roxithromycin is a semi-synthetic, 14-carbon ring macrolide antibiotic derived from erythromycin. It is used to treat respiratory tract, urinary and soft tissue infections. Roxithromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35974":{"category_aro_accession":"0000057","category_aro_cvterm_id":"35974","category_aro_name":"telithromycin","category_aro_description":"Telithromycin is a semi-synthetic derivative of erythromycin. It is a 14-membered macrolide and is the first ketolide antibiotic to be used in clinics. Telithromycin binds the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"35982":{"category_aro_accession":"0000065","category_aro_cvterm_id":"35982","category_aro_name":"clarithromycin","category_aro_description":"Clarithromycin is a methyl derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome and is used to treat pharyngitis, tonsillitis, acute maxillary sinusitis, acute bacterial exacerbation of chronic bronchitis, pneumonia (especially atypical pneumonias associated with Chlamydia pneumoniae or TWAR), and skin structure infections.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"36284":{"category_aro_accession":"3000145","category_aro_cvterm_id":"36284","category_aro_name":"tylosin","category_aro_description":"Tylosin is a 16-membered macrolide, naturally produced by Streptomyces fradiae. It interacts with the bacterial ribosome 50S subunit to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"36295":{"category_aro_accession":"3000156","category_aro_cvterm_id":"36295","category_aro_name":"spiramycin","category_aro_description":"Spiramycin is a 16-membered macrolide and is natural product produced by Streptomyces ambofaciens. It binds to the 50S subunit of bacterial ribosomes and inhibits peptidyl transfer activity to disrupt protein synthesis.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"36315":{"category_aro_accession":"3000176","category_aro_cvterm_id":"36315","category_aro_name":"dirithromycin","category_aro_description":"Dirithromycin is an oxazine derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome to inhibit bacterial protein synthesis.","category_aro_class_name":"Antibiotic"},"36722":{"category_aro_accession":"3000583","category_aro_cvterm_id":"36722","category_aro_name":"pristinamycin IA","category_aro_description":"Pristinamycin IA is a type B streptogramin antibiotic produced by Streptomyces pristinaespiralis. It binds to the P site of the 50S subunit of the bacterial ribosome, preventing the extension of protein chains.","category_aro_class_name":"Antibiotic"},"36723":{"category_aro_accession":"3000584","category_aro_cvterm_id":"36723","category_aro_name":"quinupristin","category_aro_description":"Quinupristin is a type B streptogramin and a semisynthetic derivative of pristinamycin 1A. It is a component of the drug Synercid and interacts with the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"virginiamycin M1","category_aro_description":"Virginiamycin M1 is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37016":{"category_aro_accession":"3000672","category_aro_cvterm_id":"37016","category_aro_name":"madumycin II","category_aro_description":"Madumycin II is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37017":{"category_aro_accession":"3000673","category_aro_cvterm_id":"37017","category_aro_name":"griseoviridin","category_aro_description":"Griseoviridin is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"37019":{"category_aro_accession":"3000675","category_aro_cvterm_id":"37019","category_aro_name":"pristinamycin IB","category_aro_description":"Pristinamycin IB is a class B streptogramin similar to pristinamycin IA, the former containing a N-methyl-4-(methylamino)phenylalanine instead of a N-methyl-4-(dimethylamino)phenylalanine in its class A streptogramin counterpart (one less methyl group).","category_aro_class_name":"Antibiotic"},"37021":{"category_aro_accession":"3000677","category_aro_cvterm_id":"37021","category_aro_name":"virginiamycin S2","category_aro_description":"Virginiamycin S2 is a streptogramin B antibiotic.","category_aro_class_name":"Antibiotic"},"37022":{"category_aro_accession":"3000678","category_aro_cvterm_id":"37022","category_aro_name":"pristinamycin IC","category_aro_description":"Pristinamycin IC is a class B streptogramin derived from virginiamycin S1.","category_aro_class_name":"Antibiotic"},"37023":{"category_aro_accession":"3000679","category_aro_cvterm_id":"37023","category_aro_name":"vernamycin C","category_aro_description":"Vernamycin C is a streptogramin B antibiotic.","category_aro_class_name":"Antibiotic"},"37024":{"category_aro_accession":"3000680","category_aro_cvterm_id":"37024","category_aro_name":"patricin A","category_aro_description":"Patricin A is a streptogramin B antibiotic.","category_aro_class_name":"Antibiotic"},"37025":{"category_aro_accession":"3000681","category_aro_cvterm_id":"37025","category_aro_name":"patricin B","category_aro_description":"Patricin B is a streptogramin B antibiotic.","category_aro_class_name":"Antibiotic"},"37026":{"category_aro_accession":"3000682","category_aro_cvterm_id":"37026","category_aro_name":"ostreogrycin B3","category_aro_description":"Ostreogrycin B3 is a derivative of pristinamycin IA, with an additional 3-hydroxy group on its 4-oxopipecolic acid.","category_aro_class_name":"Antibiotic"},"37247":{"category_aro_accession":"3000867","category_aro_cvterm_id":"37247","category_aro_name":"oleandomycin","category_aro_description":"Oleandomycin is a 14-membered macrolide produced by Streptomyces antibioticus. It is ssimilar to erythromycin, and contains a desosamine amino sugar and an oleandrose sugar. It targets the 50S ribosomal subunit to prevent protein synthesis.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35952":{"category_aro_accession":"0000034","category_aro_cvterm_id":"35952","category_aro_name":"streptogramin A antibiotic","category_aro_description":"Streptogramin A antibiotics are cyclic polyketide peptide hybrids that bind to the ribosomal peptidyl transfer centre. Structural variation arises from substituting a proline for its desaturated derivative and by its substitution for Ala or Cys. Used alone, streptogramin A antibiotics are bacteriostatic, but is bactericidal when used with streptogramin B antibiotics.","category_aro_class_name":"Drug Class"},"35967":{"category_aro_accession":"0000050","category_aro_cvterm_id":"35967","category_aro_name":"streptogramin B antibiotic","category_aro_description":"Streptogramin B antibiotics are are cyclic hepta- or hexa-depsipeptides.  Type B streptogramins block the peptide exit tunnel of the 50S bacterial ribosome. The general composition of group B streptogramins is 3-hydroxypicolinic acid-L-Thr-D-aminobutyric acid (or D-Ala)-L-Pro-L-Phe (or 4-N-,N-(dimethylamino)-L-Phe)-X-L-phenylglycine. Used alone, streptogramin B antibiotics are bacteriostatic, but is bactericidal when used with streptogramin A antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"469":{"model_id":"469","model_name":"SHV-49","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1067":{"protein_sequence":{"accession":"AAS98184.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMISTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AY528718.1","fmin":"413","fmax":"1274","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATAAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTACTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001106","ARO_id":"37486","ARO_name":"SHV-49","CARD_short_name":"SHV-49","ARO_description":"SHV-49 is an inhibitor-resistant beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"470":{"model_id":"470","model_name":"OXA-4","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1690":{"protein_sequence":{"accession":"AET05998.1","sequence":"MKNTIHINFAIFLIIANIIYSSASASTDISTVASPLFEGTEGCFLLYDVSTNAEIAQFNKAKCATQMAPDSTFKIALSLMAFDAEIIDQKTIFKWDKTPKGMEIWNSNHTPKTWMQFSVVWVSQEITQKIGLNKIKNYLKDFDYGNQDFSGDKERNNGLTEAWLESSLKISPEEQIQFLRKIINHNLPVKNSAIENTIENMYLQDLENSTKLYGKTGAGFTANRTLQNGWFEGFIISKSGHKYVFVSALTGNLGSNLTSSIKAKKNAITILNTLNL"},"dna_sequence":{"accession":"JN129451.1","fmin":"1036","fmax":"1867","strand":"+","sequence":"ATGAAAAACACAATACATATCAACTTCGCTATTTTTTTAATAATTGCAAATATTATCTACAGCAGCGCCAGTGCATCAACAGATATCTCTACTGTTGCATCTCCATTATTTGAAGGAACTGAAGGTTGTTTTTTACTTTACGATGTATCCACAAACGCTGAAATTGCTCAATTCAATAAAGCAAAGTGTGCAACGCAAATGGCACCAGATTCAACTTTCAAGATCGCATTATCACTTATGGCATTTGATGCGGAAATAATAGATCAGAAAACCATATTCAAATGGGATAAAACCCCCAAAGGAATGGAGATCTGGAACAGCAATCATACACCAAAGACGTGGATGCAATTTTCTGTTGTTTGGGTTTCGCAAGAAATAACCCAAAAAATTGGATTAAATAAAATCAAGAATTATCTCAAAGATTTTGATTATGGAAATCAAGACTTCTCTGGAGATAAAGAAAGAAACAACGGATTAACAGAAGCATGGCTCGAAAGTAGCTTAAAAATTTCACCAGAAGAACAAATTCAATTCCTGCGTAAAATTATTAATCACAATCTCCCAGTTAAAAACTCAGCCATAGAAAACACCATAGAGAACATGTATCTACAAGATCTGGAGAATAGTACAAAACTGTATGGGAAAACTGGTGCAGGATTCACAGCAAATAGAACCTTACAAAACGGATGGTTTGAAGGGTTTATTATAAGCAAATCAGGACATAAATATGTTTTTGTGTCCGCACTTACAGGAAACTTGGGGTCGAATTTAACATCAAGCATAAAAGCCAAGAAAAATGCGATCACCATTCTAAACACACTAAATTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3001399","ARO_id":"37799","ARO_name":"OXA-4","CARD_short_name":"OXA-4","ARO_description":"OXA-4 is a beta-lactamase found in Enterobacteriaceae and P. aeruginosa.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46485":{"category_aro_accession":"3007696","category_aro_cvterm_id":"46485","category_aro_name":"OXA-1-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-1.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"471":{"model_id":"471","model_name":"TEM-151","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"998":{"protein_sequence":{"accession":"ABI74448.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMVSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDHWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERDRQIAEIGGSLIKHW"},"dna_sequence":{"accession":"DQ834729.1","fmin":"205","fmax":"1066","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGGTGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATCATTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAGATAGACAGATCGCTGAGATAGGTGGCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001018","ARO_id":"37398","ARO_name":"TEM-151","CARD_short_name":"TEM-151","ARO_description":"TEM-151 is a CMT-type, inhibitor-resistant, extended-spectrum beta-lactamase found in E. coli.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"472":{"model_id":"472","model_name":"TEM-128","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1720":{"protein_sequence":{"accession":"AAR89359.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGEHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AY368237.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGAGCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000990","ARO_id":"37370","ARO_name":"TEM-128","CARD_short_name":"TEM-128","ARO_description":"TEM-128 is a broad-spectrum beta-lactamase found in E. coli.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"474":{"model_id":"474","model_name":"dfrD","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"683":{"protein_sequence":{"accession":"AAA85213.1","sequence":"MKISLIVAMDKKRVIGKDNDIPWRISSDWEYVKNTTKGHAIILGRKNLQSIGRALPDRRNIILTRDKNFNFKDCEIAHSIEAAFKLCENEEEVFIFGGEQIYVMFLPYVEKMYVTKIHHEFEGDTFFPVVNFDDWKEVSVEKGIKDEKNPYDYYFHIYERIR"},"dna_sequence":{"accession":"U43152.1","fmin":"93","fmax":"582","strand":"+","sequence":"TTGAAAATTTCTTTAATTGTTGCGATGGATAAGAAAAGAGTAATCGGCAAGGATAACGACATTCCATGGAGAATTTCTAGTGATTGGGAATATGTAAAAAACACTACAAAAGGACATGCAATCATATTAGGTAGAAAGAACCTTCAATCAATCGGAAGGGCTTTACCTGACAGAAGAAATATTATTTTGACTAGAGATAAAAACTTTAACTTTAAGGATTGTGAAATTGCCCATTCAATAGAAGCTGCATTTAAGTTATGCGAAAATGAAGAAGAGGTTTTCATTTTCGGGGGAGAACAGATATATGTTATGTTCTTGCCTTATGTCGAGAAAATGTACGTTACAAAAATTCATCATGAATTCGAAGGAGATACATTTTTTCCAGTAGTTAATTTTGACGATTGGAAAGAAGTATCTGTTGAAAAAGGAATAAAAGATGAAAAGAATCCTTACGATTATTATTTTCATATATATGAGAGAATTCGTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36757","NCBI_taxonomy_name":"Listeria monocytogenes","NCBI_taxonomy_id":"1639"}}}},"ARO_accession":"3002866","ARO_id":"39300","ARO_name":"dfrD","CARD_short_name":"dfrD","ARO_description":"dfrD is a plasmid-encoded dihydrofolate reductase found in Listeria monocytogenes.","ARO_category":{"37617":{"category_aro_accession":"3001218","category_aro_cvterm_id":"37617","category_aro_name":"trimethoprim resistant dihydrofolate reductase dfr","category_aro_description":"Alternative dihydropteroate synthase dfr present on plasmids produces alternate proteins that are less sensitive to trimethoprim from inhibiting its role in folate synthesis, thus conferring trimethoprim resistance.","category_aro_class_name":"AMR Gene Family"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"475":{"model_id":"475","model_name":"OXA-106","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1202":{"protein_sequence":{"accession":"ABV31686.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDKKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWNGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"EF650032.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATAAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGAACGGGCAAAAAAGGCTGTTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001637","ARO_id":"38037","ARO_name":"OXA-106","CARD_short_name":"OXA-106","ARO_description":"OXA-106 is a beta-lactamase found in A. baumannii.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"476":{"model_id":"476","model_name":"amrB","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1750"}},"model_sequences":{"sequence":{"5203":{"protein_sequence":{"accession":"CAH35802.1","sequence":"MARFFIDRPVFAWVISLFIMLGGIFAIRALPVAQYPDIAPPVVSLYATYPGASAQVVEESVTAVIEREMNGVPGLLYTSATSSAGQASLSLTFKQGVSADLAAVDVQNRLKIVEARLPEPVRRDGISIEKAADNAQIIVSLTSEDGRLSGVELGEYASANVLQALRRVEGVGKVQFWGAEYAMRIWPDPVKMAALGLTASDIASAVRAHNARVTIGDVGRSAVPDSAPIAATVLADAPLTTPDAFGAIALRARADGSTLYLRDVARIEFGGNDYNYPSFVNGKTATGMGIKLAPGSNAVATEKRVRATMEELAKFFPPGVKYQIPYETASFVRVSMSKVVTTLVEAGVLVFAVMFLFMQNFRATLIPTLVVPVALLGTFGAMLAAGFSINVLTMFGMVLAIGILVDDAIVVVENVERLMVEEKLPPYEATVKAMKQISGAIVGITVVLTSVFVPMAFFGGAVGNIYRQFAFALAVSIGFSAFLALSLTPALCATLLKPVADDHHEKDGFFGWFNRFVARSTHRYTRRVGRVLERPLRWLVVYGALTAAAALLITKLPAAFLPDEDQGNFMVMVIRPQGTPLAETMQSVRRVEEYVRTHSPSAYTFALGGYNLYGEGPNGGMIFVTMKDWKERKRARDQVQAIIAEINAHFAGTPNTMVFAINMPALPDLGLTGGFDFRLQDRGGLGYGAFVAAREKLLAEGRKDPVLTDLMFAGTQDAPQLKLDIDRAKASALGVSMEEINATLAVMFGSDYIGDFMHGSQVRRVIVQADGRHRLDAADVTKLRVRNAKGEMVPLAAFATLHWTMGPPQLTRYNGFPSFTINGAASAGHSSGEAMAAIERIASTLPAGTGYAWSGQSYEERLSGAQAPMLFALSVLVVFLALAALYESWSIPFAVMLVVPLGVIGAVAGVTLRGMPNDIYFKVGLIATIGLSAKNAILIVEVAKDLVAQRMSLADAALEAARLRLRPIVMTSLAFGVGVLPLAFATGAASGAQIAIGTGVLGGVISATLFAIFLVPLFFVCVGRVFDVVPRRRGGAQAALEAK"},"dna_sequence":{"accession":"BX571965.1","fmin":"2147817","fmax":"2150949","strand":"-","sequence":"ATGGCTCGTTTCTTCATCGATCGCCCGGTGTTCGCATGGGTGATCTCCTTGTTCATCATGCTGGGCGGCATCTTCGCGATCCGCGCGCTGCCCGTCGCGCAGTATCCGGACATCGCGCCGCCCGTCGTCAGCCTCTATGCGACGTATCCGGGCGCGTCCGCGCAGGTCGTCGAGGAATCGGTCACCGCCGTGATCGAGCGCGAGATGAACGGCGTGCCCGGCCTGCTGTACACGTCGGCGACGAGCAGCGCCGGCCAGGCGTCGCTGTCGCTCACGTTCAAGCAGGGCGTGAGCGCCGATCTCGCGGCCGTCGACGTGCAGAACCGCCTGAAAATCGTCGAGGCGCGGCTGCCCGAGCCCGTGCGGCGCGACGGCATCTCGATCGAGAAGGCGGCCGACAACGCGCAGATCATCGTGTCGCTCACGTCGGAGGACGGACGGTTATCGGGCGTGGAGCTCGGCGAATACGCGTCGGCGAACGTGTTGCAGGCGCTGCGGCGCGTCGAGGGCGTCGGCAAGGTGCAGTTCTGGGGCGCCGAGTATGCGATGCGGATCTGGCCGGACCCCGTGAAGATGGCGGCGCTCGGCCTGACGGCGTCCGATATCGCGTCGGCCGTGCGCGCGCACAACGCGCGCGTGACGATCGGCGACGTCGGCCGCAGCGCGGTGCCCGACAGCGCGCCGATCGCGGCGACCGTGCTCGCCGACGCGCCGCTCACGACGCCCGACGCGTTCGGCGCGATCGCGCTGCGCGCGCGCGCCGACGGCTCGACGCTGTACCTGCGCGACGTCGCGAGAATCGAGTTCGGCGGCAACGATTACAACTACCCGTCGTTCGTGAACGGCAAGACGGCGACGGGCATGGGCATCAAGCTCGCGCCCGGTTCGAATGCGGTCGCCACCGAAAAGCGCGTGCGCGCGACGATGGAGGAGCTCGCGAAGTTCTTTCCGCCGGGCGTCAAGTACCAGATTCCGTACGAGACGGCGTCGTTCGTGCGCGTGTCGATGAGCAAGGTCGTCACGACGCTCGTCGAGGCGGGCGTGCTCGTGTTCGCGGTGATGTTCCTCTTCATGCAGAACTTCCGCGCGACGCTGATTCCGACGCTCGTCGTGCCCGTCGCGCTGCTCGGCACGTTCGGCGCGATGCTCGCCGCGGGCTTCTCGATCAACGTGCTGACGATGTTCGGGATGGTGCTCGCGATCGGCATCCTCGTCGACGACGCGATCGTCGTCGTCGAGAACGTCGAGCGGCTGATGGTCGAGGAGAAGCTGCCGCCGTACGAGGCCACCGTGAAGGCGATGAAGCAGATCAGCGGCGCGATCGTCGGGATCACCGTCGTGCTCACGTCGGTGTTCGTGCCGATGGCGTTCTTCGGCGGCGCGGTCGGCAACATCTACCGGCAGTTCGCGTTCGCGCTGGCGGTGTCGATCGGCTTCTCGGCGTTTCTCGCGCTGTCGCTCACGCCGGCGCTCTGCGCGACGCTGCTCAAGCCCGTCGCCGACGACCATCACGAGAAGGACGGCTTCTTCGGCTGGTTCAACCGTTTCGTCGCGCGCTCGACGCACCGCTACACGCGGCGCGTCGGGCGGGTGCTCGAGCGCCCGCTGCGCTGGCTCGTCGTCTACGGCGCGCTGACGGCCGCCGCCGCGCTGCTGATCACGAAGCTGCCGGCCGCGTTCCTGCCCGACGAGGATCAGGGCAACTTCATGGTGATGGTGATTCGCCCGCAGGGCACGCCGCTCGCCGAGACGATGCAGAGCGTGCGGCGCGTCGAGGAATACGTGCGCACGCATTCGCCGAGCGCGTACACGTTCGCGCTCGGCGGCTACAACCTGTACGGCGAAGGGCCGAACGGCGGGATGATCTTCGTCACGATGAAGGACTGGAAGGAGCGCAAGCGGGCGCGGGACCAGGTGCAGGCGATCATCGCGGAGATCAACGCGCATTTCGCCGGCACGCCGAACACGATGGTGTTCGCGATCAACATGCCGGCGCTGCCGGACCTCGGCCTGACGGGCGGCTTCGACTTCCGGCTGCAGGACCGCGGCGGGCTCGGCTACGGCGCGTTCGTCGCCGCGCGCGAGAAGCTGCTCGCCGAGGGGCGCAAGGACCCCGTCCTGACCGATTTGATGTTCGCCGGCACGCAGGACGCGCCGCAGCTGAAGCTCGACATCGATCGCGCGAAGGCGTCGGCGCTCGGCGTATCGATGGAGGAAATCAACGCGACGCTCGCTGTGATGTTCGGCTCGGACTACATCGGCGATTTCATGCACGGCTCGCAGGTGCGCCGCGTGATCGTGCAGGCGGACGGGCGGCACCGGCTCGACGCCGCCGACGTGACGAAGCTGCGCGTGCGCAACGCGAAGGGCGAGATGGTGCCGCTCGCGGCGTTCGCGACGCTGCACTGGACGATGGGCCCGCCGCAGTTGACGCGCTACAACGGCTTTCCGTCGTTTACGATCAACGGCGCGGCGTCGGCCGGGCACAGCAGCGGCGAGGCGATGGCGGCGATCGAGCGGATCGCGTCGACGCTGCCCGCCGGCACCGGCTACGCGTGGTCCGGCCAGTCGTACGAGGAGCGGCTGTCGGGCGCGCAGGCGCCGATGCTGTTCGCGCTGTCGGTGCTCGTCGTGTTCCTCGCGCTCGCGGCGCTGTACGAGAGCTGGTCGATTCCGTTCGCGGTGATGCTCGTCGTGCCGCTCGGCGTGATCGGCGCGGTCGCGGGCGTCACGCTGCGCGGGATGCCGAACGACATCTATTTCAAGGTGGGGCTGATCGCGACGATCGGTTTGTCCGCGAAGAACGCGATCCTGATCGTCGAGGTCGCGAAGGATCTGGTCGCGCAGCGCATGTCGCTCGCCGACGCGGCGCTCGAGGCCGCGCGGCTGCGGCTGCGGCCGATCGTGATGACCTCGCTCGCGTTCGGCGTCGGCGTGCTGCCGCTCGCGTTCGCGACGGGCGCCGCATCCGGCGCGCAGATCGCGATCGGCACGGGGGTGCTCGGCGGCGTGATCAGCGCGACGCTGTTCGCGATCTTCCTCGTCCCGCTCTTTTTCGTCTGCGTCGGGCGCGTGTTCGACGTCGTTCCGCGCCGCCGAGGCGGCGCGCAAGCGGCACTGGAGGCCAAGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41211","NCBI_taxonomy_name":"Burkholderia pseudomallei K96243","NCBI_taxonomy_id":"272560"}}}},"ARO_accession":"3002983","ARO_id":"39417","ARO_name":"amrB","CARD_short_name":"amrB","ARO_description":"amrB is the membrane fusion protein of the AmrAB-OprM multidrug efflux complex.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"477":{"model_id":"477","model_name":"catP","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"571":{"protein_sequence":{"accession":"AAB51421.1","sequence":"MVFEKIDKNSWNRKEYFDHYFASVPCTYSMTVKVDITQIKEKGMKLYPAMLYYIAMIVNRHSEFRTAINQDGELGIYDEMIPSYTIFHNDTETFSSLWTECKSDFKSFLADYESDTQRYGNNHRMEGKPNAPENIFNVSMIPWSTFDGFNLNLQKGYDYLIPIFTMGKYYKEDNKIILPLAIQVHHAVCDGFHICRFVNELQELINS"},"dna_sequence":{"accession":"U15027.1","fmin":"0","fmax":"624","strand":"+","sequence":"ATGGTATTTGAAAAAATTGATAAAAATAGTTGGAACAGAAAAGAGTATTTTGACCACTACTTTGCAAGTGTACCTTGTACATACAGCATGACCGTTAAAGTGGATATCACACAAATAAAGGAAAAGGGAATGAAACTATATCCTGCAATGCTTTATTATATTGCAATGATTGTAAACCGCCATTCAGAGTTTAGGACGGCAATCAATCAAGATGGTGAATTGGGGATATATGATGAGATGATACCAAGCTATACAATATTTCACAATGATACTGAAACATTTTCCAGCCTTTGGACTGAGTGTAAGTCTGACTTTAAATCATTTTTAGCAGATTATGAAAGTGATACGCAACGGTATGGAAACAATCATAGAATGGAAGGAAAGCCAAATGCTCCGGAAAACATTTTTAATGTATCTATGATACCGTGGTCAACCTTCGATGGCTTTAATCTGAATTTGCAGAAAGGATATGATTATTTGATTCCTATTTTTACTATGGGGAAATATTATAAAGAAGATAACAAAATTATACTTCCTTTGGCAATTCAAGTTCATCACGCAGTATGTGACGGATTTCACATTTGCCGTTTTGTAAACGAATTGCAGGAATTGATAAATAGTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36812","NCBI_taxonomy_name":"Clostridium perfringens","NCBI_taxonomy_id":"1502"}}}},"ARO_accession":"3002686","ARO_id":"39120","ARO_name":"catP","CARD_short_name":"catP","ARO_description":"catP is a transposon and chromosome-encoded variant of the cat gene found in Clostridium perfringens and Neisseria meningitidis.","ARO_category":{"36261":{"category_aro_accession":"3000122","category_aro_cvterm_id":"36261","category_aro_name":"chloramphenicol acetyltransferase (CAT)","category_aro_description":"Inactivates chloramphenicol by addition of an acyl group. CAT is used to describe many variants of the chloramphenicol acetyltransferase gene in a range of organisms including Acinetobacter calcoaceticus, Agrobacterium tumefaciens, Alkalihalobacillus clausii, Bacillus subtilis, Campylobacter coli, Enterococcus faecalis, Enterococcus faecium, Lactococcus lactis, Listeria monocytogenes, Listonella anguillarum, Morganella morganii, Photobacterium damselae subsp. piscicida, Proteus mirabilis, Salmonella typhi, Serratia marcescens, Shigella flexneri, Staphylococcus aureus, Staphylococcus haemolyticus, Staphylococcus intermedius, Streptococcus agalactiae, Streptococcus suis and Streptomyces acrimycini.","category_aro_class_name":"AMR Gene Family"},"36521":{"category_aro_accession":"3000382","category_aro_cvterm_id":"36521","category_aro_name":"azidamfenicol","category_aro_description":"Azidamfenicol is a water soluble derivative of chloramphenicol, sharing the same mode of action of inhibiting peptide synthesis by interacting with the 23S RNA of the 50S ribosomal subunit.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36595":{"category_aro_accession":"3000456","category_aro_cvterm_id":"36595","category_aro_name":"thiamphenicol","category_aro_description":"Derivative of Chloramphenicol. The nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3).","category_aro_class_name":"Antibiotic"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"478":{"model_id":"478","model_name":"AAC(3)-IIa","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"560"}},"model_sequences":{"sequence":{"4266":{"protein_sequence":{"accession":"CAA31895.1","sequence":"MHTQKAITEALQKLGVQSGDLLMVHASLKSIGPVEGGAETVVAALRSAVGPTGTVMGYASWDRSPYEETLNGARLDDNARRTWPPFDPATAGTYRGFGLLNQFLVQAPGARRSAHPDASMVAVGPLAETLTEPHELGHALGEGSPNERFVRLGGKALLLGAPLNSVTALHYAEAVADIPNKRWVTYEMPMPGRDGEVAWKTASDYDSNGILDCFAIEGKQDAVETIANAYVKLGRHREGVVGFAQCYLFDAQDIVTFGVTYLEKHFGTTPIVPAHEAIERSCEPSG"},"dna_sequence":{"accession":"X13543.1","fmin":"185","fmax":"1046","strand":"+","sequence":"ATGCATACGCAGAAGGCAATAACGGAGGCGCTTCAAAAACTCGGAGTCCAATCCGGTGACCTGTTGATGGTGCATGCCTCACTTAAATCGATTGGTCCGGTCGAAGGAGGAGCGGAGACGGTCGTCGCCGCGTTACGCTCCGCGGTTGGGCCGACTGGCACTGTGATGGGATACGCATCGTGGGACCGATCACCCTACGAGGAGACTCTGAATGGCGCTCGGTTGGATGACAATGCCCGCCGTACCTGGCCGCCGTTCGATCCCGCAACGGCCGGGACTTACCGTGGGTTCGGCCTGCTGAATCAGTTTCTGGTTCAAGCCCCCGGCGCGCGGCGCAGCGCGCACCCCGATGCATCGATGGTCGCGGTTGGTCCGCTGGCTGAAACGCTGACGGAGCCTCACGAACTCGGTCACGCCTTGGGGGAAGGGTCGCCCAACGAGCGGTTCGTCCGCCTTGGCGGGAAGGCCCTGCTGTTGGGTGCGCCGCTAAACTCCGTTACCGCATTGCACTACGCCGAGGCGGTTGCCGATATACCCAATAAACGGTGGGTGACGTATGAGATGCCGATGCCTGGAAGAGACGGTGAAGTCGCCTGGAAAACGGCATCGGATTACGATTCAAACGGCATTCTCGATTGCTTTGCTATCGAAGGAAAGCAGGATGCGGTCGAAACTATAGCAAATGCTTACGTGAAGCTCGGTCGCCATCGAGAAGGTGTCGTGGGCTTTGCCCAGTGCTACCTGTTCGACGCGCAGGACATCGTGACGTTCGGCGTCACCTATCTTGAGAAGCATTTCGGAACCACTCCGATCGTGCCTGCGCACGAAGCCATCGAGCGCTCTTGCGAGCCTTCAGGTTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39505","NCBI_taxonomy_name":"Plasmid pWP113a","NCBI_taxonomy_id":"28425"}}}},"ARO_accession":"3002533","ARO_id":"38933","ARO_name":"AAC(3)-IIa","CARD_short_name":"AAC(3)-IIa","ARO_description":"AAC(3)-IIa is a plasmid-encoded aminoglycoside acetyltransferase in K. pneumoniae, E. cloacae, Actinobacillus pleuropneumoniae, S. typhimurium, Citrobacter freundii, and P. aeruginosa.","ARO_category":{"36461":{"category_aro_accession":"3000322","category_aro_cvterm_id":"36461","category_aro_name":"AAC(3)","category_aro_description":"A category of aminoglycoside N-acetyltransferase enzymes with modification regiospecificity based at the 3-amino group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics through acetylation of the 3-amino group of the compound.","category_aro_class_name":"AMR Gene Family"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"46127":{"category_aro_accession":"3007377","category_aro_cvterm_id":"46127","category_aro_name":"6'-N-ethylnetilmicin","category_aro_description":"6'-N-ethylnetilmicin is an aminoglycoside antibiotic and a derivative of netilmicin.","category_aro_class_name":"Antibiotic"},"46128":{"category_aro_accession":"3007378","category_aro_cvterm_id":"46128","category_aro_name":"2'-N-ethylnetilmicin","category_aro_description":"2'-N-ethylnetilmicin is an aminoglycoside antibiotic and a derivative of netilmicin.","category_aro_class_name":"Antibiotic"},"46133":{"category_aro_accession":"3007382","category_aro_cvterm_id":"46133","category_aro_name":"gentamicin","category_aro_description":"Gentamicin is a commonly used aminoglycoside antibiotic derived from members of the Micromonospora genus of bacteria. It acts by binding the 30S ribosomal subunit, thus inhibiting protein synthesis. Gentamicin is typically used to treat Gram-negative infections of the repiratory and urinary tract, as well as infections of the bone and soft tissue. It also exhibits considerable nephrotoxicity and ototoxicity. Gentamicin is administered as a mixture of gentamicin type C (which makes about around 80% of the complex) and types A, B, and X (distributed in the remaining 20% of the complex).","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"479":{"model_id":"479","model_name":"IMP-29","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1015":{"protein_sequence":{"accession":"AFG25462.1","sequence":"MSKLFVFLIFLFCSITAAAESLPDLKIEKLDEGVYVHTSFEEVNGWGVVPKHGLVVLVNTEAYLIDTPFTAKDTEKLVTWFVERGYKIKGSISSHFHSDSTGGIEWLNSQSIPTYASELTNELLKKGGKVQAKNSFSGVSYWLVKKKIEVFYPGPGHTPDNVVVWLPENRVLFGGCFVKPYGLGNLDDANVEAWPHSAEILMSRYGNAKLVVPSHSDIGNASLLKLTWEQAVKGLKESKKPSQPSN"},"dna_sequence":{"accession":"JQ041634.1","fmin":"1122","fmax":"1863","strand":"+","sequence":"ATGAGCAAGTTATTTGTATTCCTTATTTTTTTGTTTTGTAGCATTACTGCCGCAGCAGAGTCTTTGCCAGATTTAAAAATTGAGAAGCTCGACGAAGGCGTTTATGTTCATACTTCGTTTGAAGAAGTTAACGGTTGGGGTGTTGTTCCTAAACATGGCTTGGTGGTTCTTGTAAATACTGAGGCCTATCTGATTGACACTCCATTTACGGCTAAAGATACTGAAAAGTTAGTCACTTGGTTTGTGGAACGCGGCTATAAAATAAAAGGCAGTATTTCCTCTCATTTTCATAGCGACAGCACAGGCGGAATAGAGTGGCTTAATTCTCAATCTATCCCCACGTATGCATCTGAATTAACAAATGAACTTCTTAAAAAAGGCGGTAAAGTACAAGCTAAAAATTCATTTAGCGGAGTTAGCTATTGGCTAGTTAAGAAAAAGATTGAAGTTTTTTATCCTGGTCCAGGGCACACTCCAGATAACGTAGTGGTTTGGCTACCTGAAAATAGAGTTTTGTTCGGTGGTTGTTTTGTTAAACCGTACGGTCTTGGAAATCTCGATGACGCAAATGTTGAAGCATGGCCACATTCTGCTGAAATATTAATGTCTAGGTATGGTAATGCAAAACTGGTTGTTCCAAGCCATAGTGACATCGGAAATGCGTCGCTCTTGAAGCTTACATGGGAGCAGGCTGTTAAAGGGCTAAAAGAAAGTAAAAAACCATCACAGCCAAGTAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002220","ARO_id":"38620","ARO_name":"IMP-29","CARD_short_name":"IMP-29","ARO_description":"IMP-29 is a beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"480":{"model_id":"480","model_name":"GES-9","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"871":{"protein_sequence":{"accession":"AAY43207.1","sequence":"MRFIHALLLAGIAHSAYASEKLTFKTDLEKLEREKAAQIGVAIVDPQGEIVAGHRMAQRFAMCSTFKFPLAALVFERIDSGTERGDRKLSYGPDMIVEWSPATERFLASGHMTVLEAAQAAVQLSDNGATNLLLREIGGPAAMTQYFRKIGDSVSRLDRKEPEMGDNTPGDLRDTTTPIAMARTVAKVLYGGALTSTSTHTIERWLIGNQTGDATLRAGFPKDWVVGEKTGTCANGSRNDIGFFKAQERDYAVAVYTTAPKLSAVERDELVASVGQVITQLILSTDK"},"dna_sequence":{"accession":"AY920928.1","fmin":"2689","fmax":"3553","strand":"+","sequence":"ATGCGCTTCATTCACGCACTATTACTGGCAGGGATCGCTCACTCTGCATATGCGTCGGAAAAATTAACCTTCAAGACCGATCTTGAGAAGCTAGAGCGCGAAAAAGCAGCTCAGATCGGTGTTGCGATCGTCGATCCCCAAGGAGAGATCGTCGCGGGCCACCGAATGGCGCAGCGTTTTGCAATGTGCTCAACGTTCAAGTTTCCGCTAGCCGCGCTGGTCTTTGAAAGAATTGACTCAGGCACCGAGCGGGGGGATCGAAAACTTTCATATGGGCCGGACATGATCGTCGAATGGTCTCCTGCCACGGAGCGGTTTCTAGCATCGGGACACATGACGGTTCTCGAGGCAGCGCAAGCTGCGGTGCAGCTTAGCGACAATGGGGCTACTAACCTCTTACTGAGAGAAATTGGCGGACCTGCTGCAATGACGCAGTATTTTCGTAAAATTGGCGACTCTGTGAGTCGGCTAGACCGGAAAGAGCCGGAGATGGGCGACAACACACCTGGCGACCTCAGAGATACAACTACGCCTATTGCTATGGCACGTACTGTGGCCAAAGTCCTCTATGGCGGCGCACTGACGTCCACCTCGACCCACACCATTGAGAGGTGGCTGATCGGAAACCAAACGGGAGACGCGACACTACGAGCGGGTTTTCCTAAAGATTGGGTTGTTGGAGAGAAAACTGGTACCTGCGCCAACGGGAGCCGGAACGACATTGGTTTTTTTAAAGCCCAGGAGAGAGATTACGCTGTAGCGGTGTATACAACGGCCCCGAAACTATCGGCCGTAGAACGTGACGAATTAGTTGCCTCTGTCGGTCAAGTTATTACACAACTCATCCTGAGCACGGACAAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002338","ARO_id":"38738","ARO_name":"GES-9","CARD_short_name":"GES-9","ARO_description":"GES-9 is a beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36205":{"category_aro_accession":"3000066","category_aro_cvterm_id":"36205","category_aro_name":"GES beta-lactamase","category_aro_description":"GES beta-lactamases or Guiana extended-spectrum beta-lactamases are related to the other plasmid-located class A beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"481":{"model_id":"481","model_name":"VIM-30","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1083":{"protein_sequence":{"accession":"AET05999.1","sequence":"MFKLLSKLLVYLTASIMAIASPLAFSVDSSGEYPTVNEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEVEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSASVLYGGCAIYELSRTSAGNVADADLAEWPTSIERIQQHYPEAQFVIPGHGLPGGLDLLKHTTNVVKAHTNRSVVE"},"dna_sequence":{"accession":"JN129451.1","fmin":"87","fmax":"888","strand":"+","sequence":"ATGTTCAAACTTTTGAGTAAGTTATTGGTCTATTTGACCGCGTCTATCATGGCTATTGCGAGTCCGCTCGCTTTTTCCGTAGATTCTAGCGGTGAGTATCCGACAGTCAACGAAATTCCGGTCGGGGAGGTCCGGCTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCAGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAGAAGCAAATTGGACTTCCTGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGTAGAGGGGAACGAGATTCCCACGCACTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAACTCTTCTATCCTGGTGCTGCGCATTCGACCGACAACTTAGTTGTGTACGTCCCGTCTGCGAGTGTGCTCTATGGTGGTTGTGCGATTTATGAGTTGTCACGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCATTGAGCGGATTCAACAACACTACCCGGAAGCACAGTTCGTCATTCCGGGGCACGGCCTGCCGGGCGGTCTAGACTTGCTCAAGCACACAACGAATGTTGTAAAAGCGCACACAAATCGCTCAGTCGTTGAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002300","ARO_id":"38700","ARO_name":"VIM-30","CARD_short_name":"VIM-30","ARO_description":"VIM-30 is a beta-lactamase found in the Enterobacteriaceae family.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"482":{"model_id":"482","model_name":"LEN-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"776":{"protein_sequence":{"accession":"CAA28198.1","sequence":"MRYVRLCVISLLATLPLVVYAGPQPLEQIKQSESQLSGRVGMVEMDLANGRTLAAWRADERFPMVSTFKVLLCGAVLARVDAGLEQLDRRIHYRQQDLVDYSPVSEKHLVDGMTIGELCAAAITLSDNSAGNLLLATVGGPAGLTAFLRQIGDNVTRLDRWETALNEALPGDARDTTTPASMAATLRKLLTAQHLSARSQQQLLQWMVDDRVAGPLIRAVLPPGWFIADKTGAGERGARGIVALLGPDGKPERIVVIYLRDTPASMAERNQHIAGIGQR"},"dna_sequence":{"accession":"X04515.1","fmin":"285","fmax":"1125","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGTGTTATCTCCCTGTTAGCCACCCTGCCACTGGTGGTATACGCCGGTCCACAGCCGCTTGAGCAGATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTGGGGATGGTGGAAATGGATCTGGCCAACGGCCGCACGCTGGCCGCCTGGCGCGCCGATGAACGCTTTCCCATGGTGAGCACCTTTAAAGTGCTGCTGTGCGGCGCGGTGCTGGCGCGGGTGGATGCCGGGCTCGAACAACTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGTCGACGGGATGACGATCGGCGAACTCTGCGCCGCCGCCATCACCCTGAGCGATAACAGCGCTGGCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCGGGATTAACTGCCTTTCTGCGCCAGATCGGTGACAACGTCACCCGTCTTGACCGCTGGGAAACGGCACTGAATGAGGCGCTTCCCGGCGACGCGCGCGACACCACCACCCCGGCCAGCATGGCCGCCACGCTGCGCAAACTACTGACCGCGCAGCATCTGAGCGCCCGTTCGCAACAGCAACTCCTGCAGTGGATGGTGGACGATCGGGTTGCCGGCCCGCTGATCCGCGCCGTGCTGCCGCCGGGCTGGTTTATCGCCGACAAAACCGGGGCTGGCGAACGGGGTGCGCGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAACCGGAGCGCATTGTGGTGATCTATCTGCGGGATACCCCGGCGAGTATGGCCGAGCGTAATCAACATATCGCCGGGATCGGCCAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002454","ARO_id":"38854","ARO_name":"LEN-1","CARD_short_name":"LEN-1","ARO_description":"LEN-1 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36236":{"category_aro_accession":"3000097","category_aro_cvterm_id":"36236","category_aro_name":"LEN beta-lactamase","category_aro_description":"LEN beta-lactamases are chromosomal class A beta-lactamases that confer resistance to ampicillin, amoxicillin, carbenicillin, and ticarcillin but not to extended-spectrum beta-lactams.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"483":{"model_id":"483","model_name":"GES-7","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"8194":{"protein_sequence":{"accession":"AAP22974.1","sequence":"MRFIHALLLAGIAHSAYASEKLTFKTDLEKLEREKAAQIGVAIVDPQGEIVAGHRMAQRFAMCSTFKFPLAALVFERIDSGTERGDRKLSYGPDMIVKWSPATERFLASGHMTVLEAAQAAVQLSDNGATNLLLREIGGPAAMTQYFRKIGDSVSRLDRKEPEMGDNTPGDLRDTTTPIAMARTVAKVLYGGALTSTSTHTIERWLIGNQTGDATLRAGFPKDWVVGEKTGTCANGGRNDIGFFKAQERDYAVAVYTTAPKLSAVERDELVASVGQVITQLILSTDK"},"dna_sequence":{"accession":"AY260546.3","fmin":"4477","fmax":"5341","strand":"+","sequence":"ATGCGCTTCATTCACGCACTATTACTGGCAGGGATCGCTCACTCTGCATATGCATCGGAAAAATTAACCTTCAAGACCGATCTTGAGAAGCTAGAGCGCGAAAAAGCAGCTCAGATCGGTGTTGCGATCGTCGATCCCCAAGGAGAGATCGTCGCGGGCCACCGAATGGCGCAGCGTTTTGCAATGTGCTCAACGTTCAAGTTTCCGCTAGCCGCGCTGGTCTTTGAAAGAATTGACTCAGGCACCGAGCGGGGGGATCGAAAACTTTCATATGGGCCGGACATGATCGTCAAATGGTCTCCTGCCACGGAGCGGTTTCTAGCATCGGGACACATGACGGTTCTCGAGGCAGCGCAAGCTGCGGTGCAGCTTAGCGACAATGGGGCTACTAACCTCTTACTGAGAGAAATTGGCGGACCTGCTGCAATGACGCAGTATTTTCGTAAAATTGGCGACTCTGTGAGTCGGCTAGACCGGAAAGAGCCGGAGATGGGCGACAACACACCTGGCGACCTCAGAGATACAACTACGCCTATTGCTATGGCACGTACTGTGGCTAAAGTCCTCTATGGCGGCGCACTGACGTCCACCTCGACCCACACCATTGAGAGGTGGCTGATCGGAAACCAAACGGGAGACGCGACACTACGAGCGGGTTTTCCTAAAGATTGGGTTGTTGGAGAGAAAACTGGTACCTGCGCCAACGGGGGCCGGAACGACATTGGTTTTTTTAAAGCCCAGGAGAGAGATTACGCTGTAGCGGTGTATACAACGGCCCCGAAACTATCGGCCGTAGAACGTGACGAATTAGTTGCCTCTGTCGGTCAAGTTATTACACAACTCATCCTGAGCACGGACAAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002336","ARO_id":"38736","ARO_name":"GES-7","CARD_short_name":"GES-7","ARO_description":"GES-7 is a beta-lactamase found in Enterobacter cloacae.","ARO_category":{"36205":{"category_aro_accession":"3000066","category_aro_cvterm_id":"36205","category_aro_name":"GES beta-lactamase","category_aro_description":"GES beta-lactamases or Guiana extended-spectrum beta-lactamases are related to the other plasmid-located class A beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"484":{"model_id":"484","model_name":"QnrB49","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"214":{"protein_sequence":{"accession":"AFD54601.1","sequence":"MTPLLYKKTGTNMALALVGEKIDRNRFTGEKIENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNASALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGTQVLGATFSGSDLSGGEFSTFDWRAANFTHCDLTNSELGDLDIRRVDLQGVKLDNYQASLLMERLGIAIIG"},"dna_sequence":{"accession":"JQ582718.1","fmin":"0","fmax":"681","strand":"+","sequence":"ATGACGCCATTACTGTATAAAAAAACAGGTACAAATATGGCACTGGCACTCGTTGGCGAAAAAATTGACAGAAACCGCTTCACCGGTGAGAAAATTGAAAATAGTACATTTTTTAACTGTGATTTTTCAGGTGCCGACCTGAGCGGCACTGAATTTATCGGCTGTCAGTTCTATGATCGTGAAAGCCAGAAAGGGTGCAATTTTAGTCGTGCGATGCTGAAAGATGCCATTTTTAAAAGCTGTGATTTATCCATGGCGGATTTTCGCAATGCCAGTGCGCTTGGCATTGAAATTCGCCACTGTCGTGCGCAAGGCGCAGATTTTCGCGGCGCAAGTTTTATGAATATGATCACTACTCGCACCTGGTTTTGCAGTGCATATATCACTAACACAAATCTAAGCTACGCCAATTTTTCGAAAGTAGTGTTGGAAAAGTGTGAGCTGTGGGAAAACCGTTGGATGGGGACCCAGGTACTGGGCGCGACGTTCAGTGGTTCAGATCTCTCCGGCGGCGAGTTTTCGACTTTCGACTGGCGAGCAGCAAACTTCACACATTGCGATCTGACCAATTCGGAGTTGGGTGACTTAGATATTCGGCGCGTTGATTTACAAGGCGTTAAGTTGGACAACTACCAGGCATCGTTGCTCATGGAACGTCTTGGCATCGCGATTATTGGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002764","ARO_id":"39198","ARO_name":"QnrB49","CARD_short_name":"QnrB49","ARO_description":"QnrB49 is a plasmid-mediated quinolone resistance protein found in Citrobacter freundii.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"485":{"model_id":"485","model_name":"TEM-191","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"5591":{"protein_sequence":{"accession":"APY23677.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGKRGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"KY432484.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTAAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001051","ARO_id":"37431","ARO_name":"TEM-191","CARD_short_name":"TEM-191","ARO_description":"TEM-191 is a beta-lactamase.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"440":{"model_id":"440","model_name":"MexA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"650"}},"model_sequences":{"sequence":{"5500":{"protein_sequence":{"accession":"AAG03814.1","sequence":"MQRTPAMRVLVPALLVAISALSGCGKSEAPPPAQTPEVGIVTLEAQTVTLNTELPGRTNAFRIAEVRPQVNGIILKRLFKEGSDVKAGQQLYQIDPATYEADYQSAQANLASTQEQAQRYKLLVADQAVSKQQYADANAAYLQSKAAVEQARINLRYTKVLSPISGRIGRSAVTEGALVTNGQANAMATVQQLDPIYVDVTQPSTALLRLRRELASGQLERAGDNAAKVSLKLEDGSQYPLEGRLEFSEVSVDEGTGSVTIRAVFPNPNNELLPGMFVHAQLQEGVKQKAILAPQQGVTRDLKGQATALVVNAQNKVELRVIKADRVIGDKWLVTEGLNAGDKIITEGLQFVQPGVEVKTVPAKNVASAQKADAAPAKTDSKG"},"dna_sequence":{"accession":"AE004091.2","fmin":"472023","fmax":"473175","strand":"+","sequence":"ATGCAACGAACGCCAGCCATGCGTGTACTGGTTCCGGCCCTGCTGGTCGCGATTTCGGCCCTTTCCGGGTGCGGAAAAAGCGAGGCGCCGCCGCCGGCGCAAACGCCGGAGGTCGGGATCGTGACCCTGGAAGCGCAGACGGTGACCCTGAATACCGAGCTGCCGGGCCGGACCAATGCGTTCCGCATCGCCGAGGTGCGTCCCCAGGTGAACGGCATCATCCTCAAGCGCCTGTTCAAGGAAGGCAGCGACGTCAAGGCCGGGCAGCAGCTCTACCAGATCGACCCCGCCACCTACGAGGCCGACTACCAGAGCGCCCAGGCCAACCTGGCTTCGACCCAGGAACAGGCCCAGCGCTACAAGCTGCTGGTCGCCGACCAGGCCGTGAGCAAGCAGCAGTACGCCGACGCCAATGCCGCCTACCTGCAGTCCAAGGCGGCGGTGGAGCAGGCGCGGATCAACCTGCGCTACACCAAGGTGCTGTCGCCGATCTCCGGCCGCATCGGCCGTTCCGCGGTGACCGAAGGCGCCCTGGTGACCAACGGCCAGGCCAACGCGATGGCCACCGTGCAACAGCTCGACCCGATCTACGTCGACGTCACCCAGCCGTCCACCGCCCTGCTGCGCCTGCGCCGCGAACTGGCCAGCGGCCAGTTGGAGCGCGCCGGCGACAACGCGGCGAAGGTCTCCCTGAAGCTGGAGGACGGTAGCCAATACCCGCTGGAAGGTCGCCTCGAATTCTCCGAGGTTTCCGTCGACGAAGGCACCGGCTCGGTCACCATCCGCGCCGTGTTCCCCAACCCGAACAACGAGCTGCTGCCCGGCATGTTCGTTCACGCGCAGTTGCAGGAAGGCGTCAAGCAGAAGGCCATCCTCGCTCCGCAGCAAGGCGTGACCCGCGACCTCAAGGGCCAGGCTACCGCGCTGGTGGTGAACGCGCAGAACAAGGTCGAGCTGCGGGTGATCAAGGCCGACCGGGTGATCGGCGACAAGTGGCTGGTTACCGAAGGCCTGAACGCCGGCGACAAGATCATTACCGAAGGCCTGCAGTTCGTGCAGCCGGGTGTCGAGGTGAAGACCGTGCCGGCGAAGAATGTCGCGTCCGCGCAGAAGGCCGACGCCGCTCCGGCGAAAACCGACAGCAAGGGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36804","NCBI_taxonomy_name":"Pseudomonas aeruginosa PAO1","NCBI_taxonomy_id":"208964"}}}},"ARO_accession":"3000377","ARO_id":"36516","ARO_name":"MexA","CARD_short_name":"MexA","ARO_description":"MexA is the membrane fusion protein of the MexAB-OprM multidrug efflux complex.","ARO_category":{"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"458":{"model_id":"458","model_name":"tet(B)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"325":{"protein_sequence":{"accession":"BAC67143.1","sequence":"MNSSTKIALAITLLDAMGIGLIMPVLPTLLREFIASEDIANHFGVLLALYALMQVIFAPWLGKMSDRFGRRPVLLLSLIGASLDYLLLAFSSALWMLYLGRLLSGITGATGAVAASVIADTTSASQRVKWFGWLGASFGLGLIAGPIIGGFAGEISPHSPFFIAALLNIVTFLVVMFWFRETKNTRDNTDTEVGVETQSNSVYITLFKTMPILLIIYFSAQLIGQIPATVWVLFTENRFGWNSMMVGFSLAGLGLLHSVFQAFVAGRIATKWGEKTAVLLGFIADSSAFAFLAFISEGWLVFPVLILLAGGGIALPALQGVMSIQTKSHQQGALQGLLVSLNNATGVIGPLLFAVIYNHSLPIWDGWIWIIGLAFYCIIILLSMTFMLTPQAQGSKQETSA"},"dna_sequence":{"accession":"AB089595.1","fmin":"0","fmax":"1206","strand":"+","sequence":"ATGAATAGTTCGACAAAGATCGCATTGGCAATTACGTTACTCGATGCCATGGGGATTGGCCTTATCATGCCAGTCTTGCCAACGTTATTACGTGAATTTATTGCTTCGGAAGATATCGCTAACCACTTTGGCGTATTGCTTGCACTTTATGCGTTAATGCAGGTTATCTTTGCTCCTTGGCTTGGAAAAATGTCTGACCGATTTGGTCGGCGCCCAGTGCTGTTGTTGTCATTAATAGGCGCATCGCTGGATTACTTATTGCTGGCTTTTTCAAGTGCGCTTTGGATGCTGTATTTAGGCCGTTTGCTTTCAGGGATCACAGGAGCTACTGGGGCTGTCGCGGCATCGGTCATTGCCGATACCACCTCAGCTTCTCAACGCGTGAAGTGGTTCGGTTGGTTAGGGGCAAGTTTTGGGCTTGGTTTAATAGCGGGGCCTATTATTGGTGGTTTTGCAGGAGAGATTTCACCGCATAGTCCCTTTTTTATCGCTGCGTTGCTAAATATTGTCACTTTCCTTGTGGTTATGTTTTGGTTCCGTGAAACCAAAAATACACGTGATAATACAGATACCGAAGTAGGGGTTGAGACGCAATCGAATTCGGTATACATCACTTTATTTAAAACGATGCCCATTTTGTTGATTATTTATTTTTCAGCGCAATTGATAGGCCAAATTCCCGCAACGGTGTGGGTGCTATTTACCGAAAATCGTTTTGGATGGAATAGCATGATGGTTGGCTTTTCATTAGCGGGTCTTGGTCTTTTACACTCAGTATTCCAAGCCTTTGTGGCAGGAAGAATAGCCACTAAATGGGGCGAAAAAACGGCAGTACTGCTCGGATTTATTGCAGATAGTAGTGCATTTGCCTTTTTAGCGTTTATATCTGAAGGTTGGTTAGTTTTCCCTGTTTTAATTTTATTGGCTGGTGGTGGGATCGCTTTACCTGCATTACAGGGAGTGATGTCTATCCAAACAAAGAGTCATCAGCAAGGTGCTTTACAGGGATTATTGGTGAGCCTTAACAATGCAACCGGTGTTATTGGCCCATTACTGTTTGCTGTTATTTATAATCATTCACTACCAATTTGGGATGGCTGGATTTGGATTATTGGTTTAGCGTTTTACTGTATTATTATCCTGCTATCGATGACCTTCATGTTAACCCCTCAAGCTCAGGGGAGTAAACAGGAGACAAGTGCTTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39591","NCBI_taxonomy_name":"Gram-negative bacterium TC71","NCBI_taxonomy_id":"203855"}}}},"ARO_accession":"3000166","ARO_id":"36305","ARO_name":"tet(B)","CARD_short_name":"tet(B)","ARO_description":"Tet(B) is a tetracycline efflux protein expressed in many Gram-negative bacteria. It confers resistance to tetracycline, doxycycline, and minocycline, but not tigecycline.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"402":{"model_id":"402","model_name":"tet(Y)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"3343":{"protein_sequence":{"accession":"AAC72341.1","sequence":"MSKSLITALIVVALDAIGLGLIMPVVPALLNEFVPAEQTAFHYGVFLSLYAFMQVFCAPVLGRLSDRYGRRIILLVSFLGATIDYSIMAAAPVLWVLYIGRIISGVTGATGAIAASIIADTTKQEERARWFGFMGACFGAGMIAGPAIGGVLGDISVHAPFVAGALLNAIAFCLVAFLLPKTPSQPPEGQPAKINLFEGFRFNFAVQGLASFFALFFLMQLIGQAPAALWVIYGEQRLNWDIGTAGVSLAVFGAAHTFVQAVLTGTLSKRLGDRGVLLLGMGADMCGFLLLAFITQSWMVLPAIFMLATGGIGMPALQAIISGLVCDEKQGALQGTLTGLTNITSIIGPVGFTTLYGLTAGQWDGWVWLVAASLYLIAIPLLRQSASLLRS"},"dna_sequence":{"accession":"AF070999.1","fmin":"1679","fmax":"2855","strand":"+","sequence":"ATGTCAAAATCACTTATAACCGCACTCATTGTTGTCGCGCTTGATGCGATTGGTTTGGGATTAATCATGCCGGTGGTTCCGGCTTTATTAAATGAATTTGTACCGGCAGAGCAAACAGCATTTCACTATGGTGTTTTTTTATCGCTTTATGCGTTTATGCAGGTCTTTTGCGCGCCCGTTTTAGGGCGGTTATCTGACCGCTATGGACGGCGGATTATTTTGCTGGTTTCATTTTTAGGTGCCACGATTGATTATAGCATAATGGCGGCAGCGCCTGTTTTATGGGTGCTTTATATCGGCCGGATTATCTCAGGTGTTACCGGAGCAACTGGTGCAATCGCGGCATCAATTATCGCTGATACAACTAAACAGGAAGAACGTGCGCGTTGGTTTGGTTTTATGGGGGCGTGTTTTGGTGCAGGTATGATTGCAGGGCCTGCTATTGGCGGTGTTCTTGGTGATATATCTGTGCATGCGCCCTTTGTGGCAGGGGCTCTTCTCAATGCAATTGCCTTTTGTTTGGTGGCTTTCTTGTTGCCCAAAACGCCGTCACAACCGCCTGAAGGACAGCCAGCCAAAATCAATTTGTTTGAAGGCTTTCGCTTCAATTTTGCAGTTCAGGGACTTGCCAGCTTTTTTGCGTTGTTTTTTCTTATGCAGCTGATTGGGCAGGCGCCCGCCGCTTTGTGGGTGATTTATGGCGAACAGCGCTTGAATTGGGATATTGGCACAGCAGGTGTGTCGCTGGCCGTTTTTGGTGCAGCACATACATTCGTACAAGCTGTTTTAACCGGCACTCTTTCAAAGCGACTGGGTGACCGCGGTGTGTTGCTGCTTGGAATGGGCGCTGATATGTGCGGGTTTTTATTGCTGGCTTTTATCACGCAAAGCTGGATGGTTCTGCCGGCAATTTTTATGCTGGCCACAGGCGGCATTGGTATGCCTGCTTTGCAGGCCATTATTTCAGGTCTTGTTTGCGATGAAAAACAAGGTGCTTTACAGGGAACTTTAACGGGGTTGACGAATATAACCTCGATTATCGGGCCGGTCGGATTTACGACGCTTTATGGCTTAACCGCGGGGCAGTGGGATGGTTGGGTTTGGCTCGTCGCAGCAAGCCTTTATCTTATTGCTATACCATTATTGCGCCAGTCAGCCAGTTTATTGCGATCTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36774","NCBI_taxonomy_name":"IncQ plasmid pIE1120","NCBI_taxonomy_id":"77644"}}}},"ARO_accession":"3000182","ARO_id":"36321","ARO_name":"tet(Y)","CARD_short_name":"tet(Y)","ARO_description":"TetY is a tetracycline efflux pump found in Gram-negative bacteria (Aeromonas and Escherichia). It is associated with plasmid DNA.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"336":{"model_id":"336","model_name":"tlrB conferring tylosin resistance","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"546":{"protein_sequence":{"accession":"AAD12162.1","sequence":"MRKNVVRYLRCPHCAAPLRSSDRTLRCENGHTFDVARQGYVNLLRRPTKLAADTTDMVAARAALLDSGHYAPLTERLAGTAGRAAGAGAPDCVVDIGGGTGHHLARVLEEFEDAEGLLLDMSKPAVRRAARAHPRASSAVADVWDTLPLRDGAAAMALNVFAPRNPPEIRRILRPGGTLLVVTPQQDHLAELVDALGLLRVRDHKEGRLAEQLAPHFEAVGQERLRTTLRLDHDALGRVVAMGPSSWHQDPDELARRIAELPGIHEVTLSVTFTVCRPLP"},"dna_sequence":{"accession":"AF055922.1","fmin":"1787","fmax":"2630","strand":"+","sequence":"ATGCGGAAGAACGTCGTGCGATATCTGCGCTGTCCGCACTGCGCAGCCCCTCTGCGGTCATCCGACCGCACCCTCCGCTGCGAAAACGGGCACACCTTCGACGTCGCCCGGCAGGGCTATGTGAATCTGCTCAGACGCCCGACGAAGCTCGCCGCCGACACCACCGACATGGTCGCCGCCCGGGCCGCGCTGCTGGACAGCGGGCATTACGCGCCGCTGACCGAGCGGCTGGCCGGGACGGCCGGGCGCGCGGCGGGCGCCGGGGCACCGGACTGCGTCGTGGACATCGGCGGGGGCACCGGTCACCATCTCGCCCGTGTCCTGGAGGAGTTCGAGGACGCCGAGGGACTCCTGCTGGACATGTCCAAGCCGGCCGTGCGCAGGGCCGCCCGCGCCCATCCCCGGGCCAGCTCCGCCGTCGCCGACGTATGGGACACACTTCCGCTGCGGGACGGGGCCGCCGCGATGGCCCTCAACGTCTTCGCCCCGCGCAACCCGCCGGAGATCCGCAGGATCCTCCGCCCCGGCGGCACCCTGCTGGTCGTCACGCCCCAGCAGGACCACCTCGCCGAACTCGTGGACGCGCTGGGGCTGTTGCGCGTACGGGACCACAAGGAGGGCCGGCTGGCCGAACAGCTCGCGCCGCACTTCGAGGCCGTCGGGCAGGAGCGGCTGCGGACCACTCTCCGCCTCGATCACGACGCGCTCGGCCGGGTGGTCGCCATGGGGCCCAGTTCCTGGCACCAGGACCCGGATGAACTGGCGCGGCGGATCGCGGAGTTGCCCGGCATCCACGAGGTCACGCTCTCGGTCACCTTCACCGTCTGCCGCCCTCTGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36838","NCBI_taxonomy_name":"Streptomyces fradiae","NCBI_taxonomy_id":"1906"}}}},"ARO_accession":"3001299","ARO_id":"37698","ARO_name":"tlrB conferring tylosin resistance","CARD_short_name":"Sfra_tlrB_TYL","ARO_description":"TlrB is a methyltransferase found in Streptomyces fradiae and confers resistance to mycinamicin, tylosin and lincosamides. Specifically, this enzyme adds a methyl group to guanosine 748 (E. coli numbering). TlrB is found in the tylosin biosynthetic cluster and is one mechanism by which S. fradiae protects itself from self-destruction when producing this macrolide.","ARO_category":{"37697":{"category_aro_accession":"3001298","category_aro_cvterm_id":"37697","category_aro_name":"non-erm 23S ribosomal RNA methyltransferase (G748)","category_aro_description":"Non-erm 23S ribosomal RNA methyltransferases modify guanosine 748 (E. coli numbering) to confer resistance to some macrolides and lincosamides.","category_aro_class_name":"AMR Gene Family"},"36284":{"category_aro_accession":"3000145","category_aro_cvterm_id":"36284","category_aro_name":"tylosin","category_aro_description":"Tylosin is a 16-membered macrolide, naturally produced by Streptomyces fradiae. It interacts with the bacterial ribosome 50S subunit to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"276":{"model_id":"276","model_name":"tetR","model_type":"protein overexpression model","model_type_id":"41091","model_description":"Protein Overexpression Models (POM) are similar to Protein Variant Models (PVM) in that they include a protein reference sequence, a curated BLASTP bitscore cut-off, and mapped resistance variants. Whereas PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, reporting only those with curated mutations conferring AMR, POMs are restricted to regulatory proteins and report both wild-type sequences and\/or sequences with mutations leading to overexpression of efflux complexes. The former lead to efflux of antibiotics at basal levels, while the latter can confer clinical resistance. POMs include a protein reference sequence (often from wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Perfect RGI match is 100% identical to the wild-type reference protein sequence along its entire length, a Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value may or may not contain at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off may or may not contain at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"2710":"H64Y","2711":"N82H","2712":"T103I"},"Curated-R":{"2710":"H64Y","2711":"N82H","2712":"T103I"},"clinical":{"2710":"H64Y","2711":"N82H","2712":"T103I"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"2090":{"protein_sequence":{"accession":"CAD09823.1","sequence":"MMSRLDKSKVINSALELLNEVGIEGLTTRKLAQKLGVEQPTLYWHVKNKRALLDALAIEMLDRHHTHFCPLEGESWQDFLRNNAKSFRCALLSHRDGAKVHLGTRPTEKQYETLENQLAFLCQQGFSLENALYALSAVGHFTLGCVLEDQEHQVAKEERETPTTDSMPPLLRQAIELFDHQGAEPAFLFGLELIICGLEKQLKCESGS"},"dna_sequence":{"accession":"AL513383.1","fmin":"179218","fmax":"179845","strand":"+","sequence":"ATGATGTCTAGATTAGATAAAAGTAAAGTGATTAACAGCGCATTAGAGCTGCTTAATGAGGTCGGAATCGAAGGTTTAACAACCCGTAAACTCGCCCAGAAGCTAGGTGTAGAGCAGCCTACATTGTATTGGCATGTAAAAAATAAGCGGGCTTTGCTCGACGCCTTAGCCATTGAGATGTTAGATAGGCACCATACTCACTTTTGCCCTTTAGAAGGGGAAAGCTGGCAAGATTTTTTACGTAATAACGCTAAAAGTTTTAGATGTGCTTTACTAAGTCATCGCGATGGAGCAAAAGTACATTTAGGTACACGGCCTACAGAAAAACAGTATGAAACTCTCGAAAATCAATTAGCCTTTTTATGCCAACAAGGTTTTTCACTAGAGAATGCATTATATGCACTCAGCGCTGTGGGGCATTTTACTTTAGGTTGCGTATTGGAAGATCAAGAGCATCAAGTCGCTAAAGAAGAAAGGGAAACACCTACTACTGATAGTATGCCGCCATTATTACGACAAGCTATCGAATTATTTGATCACCAAGGTGCAGAGCCAGCCTTCTTATTCGGCCTTGAATTGATCATATGCGGATTAGAAAAACAACTTAAATGTGAAAGTGGGTCTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35776","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Typhi str. CT18","NCBI_taxonomy_id":"220341"}}}},"ARO_accession":"3003479","ARO_id":"40072","ARO_name":"tetR","CARD_short_name":"tetR","ARO_description":"TetR is the repressor of the tetracycline resistance element; its N-terminal region forms a helix-turn-helix structure and binds DNA. Binding of tetracycline to TetR reduces the repressor affinity for the tetracycline resistance gene (tetA) promoter operator sites. Mutations arise within tetR results in lower affinity for tetracyclin.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"395":{"model_id":"395","model_name":"blaF","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"3317":{"protein_sequence":{"accession":"AAA19882.1","sequence":"MTGLSRRNVLIGSLVAAAAVGAGVGGAAPAFAAPIDDQLAELERRDNVLIGLYAANLQSGRRITHRLDEMFAMCSTFKGYAAARVLQMAEHGEISLDNRVFVDADALVPNSPVTEARAGAEMTLAELCQAALQRSDNTAANLLLKTIGGPAAVTAFARSVGDERTRLDRWEVELNSAIPGDPRDTSTAAALAVGYRAILAGDALSPPQRGLLEDWMRANQTSSMRAGLPEGWTTADKTGSGDYGSTNDAGIAFGPDGQRLLLVMMTRSQAHDPKAENLRPLIGELTALVLPSLL"},"dna_sequence":{"accession":"L25634.1","fmin":"1273","fmax":"2158","strand":"+","sequence":"ATGACCGGACTATCGCGACGCAACGTTCTGATCGGTTCGCTCGTGGCGGCAGCTGCCGTCGGTGCCGGCGTCGGTGGCGCCGCACCGGCATTCGCGGCACCGATCGATGACCAGCTGGCGGAACTGGAGCGTCGGGACAACGTCCTGATCGGCTTGTACGCAGCCAATCTGCAGTCTGGGCGGAGGATCACGCACCGTCTCGACGAGATGTTCGCGATGTGCTCGACGTTCAAGGGCTACGCCGCTGCGCGGGTGCTGCAGATGGCCGAGCACGGCGAGATCTCACTGGACAACCGGGTCTTCGTCGATGCGGATGCGCTCGTGCCGAACTCACCCGTCACCGAGGCACGTGCCGGTGCCGAGATGACGTTGGCCGAGCTGTGCCAGGCGGCGCTGCAGCGCAGTGACAACACCGCGGCGAACCTGCTGCTGAAGACCATTGGCGGGCCTGCGGCTGTCACCGCCTTCGCCCGCAGCGTCGGCGATGAGCGCACCCGCCTGGACCGCTGGGAGGTAGAGCTGAACTCCGCGATACCCGGGGACCCGAGGGACACCAGCACCGCTGCGGCGCTGGCGGTCGGATACCGCGCGATTCTGGCCGGTGACGCACTGAGCCCGCCGCAGCGCGGCCTGTTGGAAGACTGGATGCGGGCCAATCAGACCTCGAGCATGCGTGCCGGGCTTCCGGAGGGCTGGACCACCGCGGACAAAACCGGCAGCGGCGATTACGGCAGCACCAACGACGCCGGAATCGCTTTCGGACCCGACGGACAACGGTTGCTGTTGGTGATGATGACGCGATCGCAGGCCCATGACCCCAAGGCCGAGAACCTGCGACCGCTCATCGGTGAGCTGACGGCGCTGGTGCTGCCGTCCTTACTCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36886","NCBI_taxonomy_name":"Mycolicibacterium fortuitum","NCBI_taxonomy_id":"1766"}}}},"ARO_accession":"3003562","ARO_id":"40169","ARO_name":"blaF","CARD_short_name":"blaF","ARO_description":"Class A beta-lactamase found in Mycolicibacterium fortuitum.","ARO_category":{"41397":{"category_aro_accession":"3004233","category_aro_cvterm_id":"41397","category_aro_name":"blaF family beta-lactamase","category_aro_description":"Class A Beta-lactamases first isolated from Mycolicibacterium fortuitum.","category_aro_class_name":"AMR Gene Family"},"35981":{"category_aro_accession":"0000064","category_aro_cvterm_id":"35981","category_aro_name":"amoxicillin","category_aro_description":"Amoxicillin is a moderate-spectrum, bacteriolytic, beta-lactam antibiotic used to treat bacterial infections caused by susceptible microorganisms. A derivative of penicillin, it has a wider range of treatment but remains relatively ineffective against Gram-negative bacteria. It is commonly taken with clavulanic acid, a beta-lactamase inhibitor. Like other beta-lactams, amoxicillin interferes with the synthesis of peptidoglycan.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"473":{"model_id":"473","model_name":"mphF","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"5078":{"protein_sequence":{"accession":"CAJ98570.1","sequence":"MLHDTDRILKLAREAGLELAPGSLRLNEMGLDFQVAFGRDGDAVEWVLRMPRRTDVACAAVKEAKILDYFRSRLPVAVPDWKVFSDDLIAYPSLPGNPGLTFDASTYETTWHFDQNSPVYVETLGAALAQLHGLDTDDAISAGLSNLSIDAVRENWTRDLETVEKSFEVPAARLALWRAWLADLSFWPTHAASVHGDLYVGHVMVKSDGTVCGIIDWSEAHIGDPGIDLAGHLKVFGEASLRDLLGHYEAAGGQTWPRIVEHCKMLQSAEGIRYAMFALKTGSAEHLEGAQGLLSAPGI"},"dna_sequence":{"accession":"AM260957.1","fmin":"4186","fmax":"5086","strand":"+","sequence":"ATGCTGCACGACACGGACCGAATACTGAAGCTGGCCAGGGAGGCAGGCTTGGAGCTTGCGCCCGGTTCCCTTAGGCTCAACGAAATGGGCCTCGATTTCCAAGTTGCTTTCGGCAGGGATGGGGACGCTGTAGAGTGGGTTTTGCGGATGCCGCGCCGGACGGACGTGGCATGTGCGGCAGTCAAGGAAGCGAAGATACTCGACTATTTCCGCAGTCGGCTGCCAGTCGCTGTGCCGGACTGGAAGGTCTTTAGCGATGATCTCATCGCCTACCCCTCCCTGCCGGGCAATCCGGGGCTGACATTTGACGCCTCGACCTATGAGACGACCTGGCACTTTGACCAGAATTCTCCGGTCTATGTTGAAACGCTGGGCGCGGCGCTCGCGCAATTGCATGGGCTCGACACCGACGATGCAATTAGCGCGGGGCTAAGCAATCTCAGTATCGATGCCGTACGAGAGAACTGGACGCGCGATCTCGAAACTGTCGAGAAAAGCTTTGAGGTACCGGCAGCAAGACTTGCCCTCTGGCGCGCTTGGCTTGCTGACTTGTCATTCTGGCCTACCCATGCCGCCTCAGTGCACGGCGATCTTTATGTCGGGCATGTCATGGTCAAATCGGACGGTACTGTCTGCGGGATAATCGACTGGAGTGAGGCTCATATCGGCGATCCTGGAATCGATCTGGCTGGACATCTCAAGGTGTTCGGCGAAGCTAGCCTGCGCGACCTCCTCGGTCACTACGAGGCGGCGGGGGGACAAACCTGGCCGCGTATAGTTGAGCATTGCAAGATGCTGCAGAGCGCCGAGGGCATCCGATATGCTATGTTCGCCCTTAAGACGGGCAGCGCAGAGCATCTGGAGGGTGCCCAGGGGCTTTTGTCGGCGCCAGGGATTTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36791","NCBI_taxonomy_name":"uncultured bacterium","NCBI_taxonomy_id":"77133"}}}},"ARO_accession":"3003071","ARO_id":"39606","ARO_name":"mphF","CARD_short_name":"mphF","ARO_description":"mphF is a macrolide phosphotransferase and resistance gene identified on the IncP plasmid pRSB111.","ARO_category":{"36472":{"category_aro_accession":"3000333","category_aro_cvterm_id":"36472","category_aro_name":"macrolide phosphotransferase (MPH)","category_aro_description":"Macrolide phosphotransferases (MPH) are enzymes encoded by macrolide phosphotransferase genes (mph genes). These enzymes phosphorylate macrolides in GTP dependent manner at 2'-OH of desosamine sugar thereby inactivating them. Characterized MPH's are differentiated based on their substrate specificity.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35946":{"category_aro_accession":"0000027","category_aro_cvterm_id":"35946","category_aro_name":"roxithromycin","category_aro_description":"Roxithromycin is a semi-synthetic, 14-carbon ring macrolide antibiotic derived from erythromycin. It is used to treat respiratory tract, urinary and soft tissue infections. Roxithromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35982":{"category_aro_accession":"0000065","category_aro_cvterm_id":"35982","category_aro_name":"clarithromycin","category_aro_description":"Clarithromycin is a methyl derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome and is used to treat pharyngitis, tonsillitis, acute maxillary sinusitis, acute bacterial exacerbation of chronic bronchitis, pneumonia (especially atypical pneumonias associated with Chlamydia pneumoniae or TWAR), and skin structure infections.","category_aro_class_name":"Antibiotic"},"36284":{"category_aro_accession":"3000145","category_aro_cvterm_id":"36284","category_aro_name":"tylosin","category_aro_description":"Tylosin is a 16-membered macrolide, naturally produced by Streptomyces fradiae. It interacts with the bacterial ribosome 50S subunit to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"486":{"model_id":"486","model_name":"cmlB","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"8399":{"protein_sequence":{"accession":"AAD22144.1","sequence":"MRSKNCNWRYSLAVTVLLLSPFDLLASLGMDMYLPAVPFMPHALGTTAGTIQLTLTTYLVMIGAGQLLFGPLSDRLGRRPVLLAGGAAYVAASIGLVVTSSAGVFLGFRILQACGASACLVATFATVRDIYAGRKESNVIYGLLGSMLAMVPAIGPLLGAVIDTWFGWRAIFAFLGLGMIAALTAAWRLWPETRVQRPAALQWSQLLLPIKHLNFWLYTVCYAAGMGSFFVFFSIAPGLMMGRQGMSQFGFSLLFATVAIAMMLAARFMGRVIAKWGSLSALRMGMGCLIAGAVLLVITELWIPQSVLGFIAPMWLVGVGVATAVSVAPNGALRGFDHIAGAVTAVYFCLGGLLLGSVGTLIISLLPRDTAWPVIAYCLVLATIVLGLSCVSRARDLRGHGEYDAVART"},"dna_sequence":{"accession":"AF034958.3","fmin":"2641","fmax":"3871","strand":"+","sequence":"GTGCGCTCAAAGAACTGTAATTGGCGGTATTCCCTTGCCGTCACTGTGTTGTTGTTATCACCTTTCGATTTACTGGCATCACTCGGCATGGACATGTACTTGCCAGCGGTGCCTTTCATGCCACATGCTCTTGGTACGACAGCGGGCACAATTCAGCTTACGCTGACAACGTATTTGGTCATGATAGGGGCCGGTCAGCTTTTGTTTGGGCCACTGTCGGACCGGCTGGGACGTCGTCCCGTGCTACTGGCGGGCGGTGCCGCCTACGTTGCGGCCTCAATCGGCCTCGTCGTCACGTCATCGGCTGGAGTATTTCTGGGTTTTCGGATTCTCCAAGCTTGTGGTGCCTCGGCATGCCTTGTTGCCACATTTGCAACAGTGCGTGATATCTACGCAGGTCGCAAGGAAAGTAACGTCATCTACGGCTTGCTTGGCTCTATGCTTGCTATGGTTCCGGCGATAGGCCCATTGCTGGGAGCGGTCATAGACACCTGGTTCGGGTGGCGGGCGATCTTTGCGTTCTTGGGATTGGGAATGATCGCTGCATTGACAGCAGCGTGGCGGCTCTGGCCTGAGACCCGGGTGCAGCGACCAGCAGCTTTGCAATGGTCACAACTTCTGCTTCCCATCAAGCACCTTAACTTCTGGTTGTACACAGTGTGTTATGCCGCAGGAATGGGCAGCTTCTTCGTCTTCTTCTCCATAGCGCCCGGATTGATGATGGGTAGGCAAGGCATGTCCCAGTTTGGCTTCAGTCTGTTGTTCGCAACAGTGGCAATTGCGATGATGCTTGCGGCCCGCTTCATGGGGCGCGTAATCGCCAAGTGGGGCAGCCTGAGTGCCTTGCGAATGGGGATGGGCTGCCTGATAGCAGGCGCAGTCTTGCTTGTCATCACCGAGCTATGGATTCCGCAGTCCGTGTTGGGCTTTATTGCCCCAATGTGGCTAGTGGGCGTCGGCGTCGCGACAGCGGTATCCGTTGCACCCAATGGTGCGCTTCGAGGGTTCGACCATATTGCAGGAGCCGTTACGGCAGTCTACTTCTGCTTGGGGGGGCTGCTGCTGGGGAGTGTTGGAACGCTCATCATTTCGCTGTTGCCGCGCGACACGGCCTGGCCAGTTATCGCGTATTGTTTGGTTCTTGCAACAATCGTGCTTGGACTGTCGTGTGTTTCCCGAGCGAGAGACCTTCGCGGTCACGGGGAGTATGATGCGGTTGCACGCACATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36770","NCBI_taxonomy_name":"Klebsiella aerogenes","NCBI_taxonomy_id":"548"}}}},"ARO_accession":"3002698","ARO_id":"39132","ARO_name":"cmlB","CARD_short_name":"cmlB","ARO_description":"cmlB is a plasmid-encoded chloramphenicol exporter that is found in Klebsiella aerogenes.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"487":{"model_id":"487","model_name":"macB","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1280"}},"model_sequences":{"sequence":{"539":{"protein_sequence":{"accession":"AAV85982.1","sequence":"MSLIECKNINRYFGSGENRVHILKDISLSIEKGDFVAIIGQSGSGKSTLMNILGCLDTAGSGSYRIDGIETAKMQPDELAALRRERFGFIFQRYNLLSSLTARDNVALPAVYMGMGGKERSARADKLLQDLGLASKEGNKPGELSGGQQQRVSIARALMNGGEIIFADEPTGALDTASGKNVMEIIRRLHEAGHTVIMVTHDPGIAANANRVIEIRDGEIISDTSKNPEIPASNVGRIQEKASWSFYYDQFVEAFRMSVQAVLAHKMRSLLTMLGIIIGIASVVSVVALGNGSQKKILEDISSMGTNTISIFPGRGFGDRRSGKIKTLTIDDAKIIAKQSYVASATPMTSSGGTLTYRNTDLTASLYGVGEQYFDVRGLKLETGRLFDENDVKEDAQVVVIDQNVKDKLFADSDPLGKTILFRKRPLTVIGVMKKDENAFGNSDVLMLWSPYTTVMHQITGESHTNSITVKIKDNANTRVAEKGLAELLKARHGTEDFFMNNSDSIRQMVESTTGTMKLLISSIALISLVVGGIGVMNIMLVSVTERTKEIGIRMAIGARRGNILQQFLIEAVLICIIGGLVGVGLSAAVSLVFNHFVTDFPMDISAASVIGAVACSTGIGIAFGFMPANKAAKLNPIDALAQD"},"dna_sequence":{"accession":"AY768532.1","fmin":"0","fmax":"1935","strand":"+","sequence":"ATGAGCTTGATCGAATGTAAAAACATCAACCGCTATTTCGGCAGCGGCGAGAACCGCGTCCATATTTTGAAAGACATCAGCCTGTCGATAGAGAAGGGTGATTTTGTCGCCATCATCGGGCAGTCCGGTTCGGGCAAGTCCACGCTGATGAACATACTCGGTTGTTTGGATACCGCCGGTTCCGGTTCGTACCGAATCGACGGCATCGAAACTGCCAAAATGCAGCCTGACGAACTGGCGGCATTGCGGCGCGAACGCTTCGGTTTCATCTTCCAACGCTACAACCTCTTAAGCTCGCTGACCGCAAGGGACAACGTCGCGCTGCCAGCCGTGTATATGGGTATGGGAGGCAAAGAGCGTTCCGCGCGGGCGGACAAACTCTTGCAGGATTTGGGTTTGGCAAGTAAAGAGGGCAACAAGCCCGGCGAACTCTCGGGCGGACAGCAGCAGCGCGTCTCCATCGCCCGCGCCCTGATGAACGGCGGAGAAATCATCTTCGCCGACGAGCCGACCGGCGCACTCGATACCGCCAGCGGCAAAAATGTGATGGAAATCATCCGCAGGCTGCACGAAGCCGGGCATACCGTCATTATGGTCACGCACGACCCCGGCATTGCCGCCAATGCCAACCGCGTCATCGAAATCCGGGACGGCGAAATCATTTCCGACACCTCGAAAAATCCCGAAATCCCCGCAAGCAATGTCGGGAGGATTCAGGAAAAAGCCTCGTGGTCGTTTTATTACGACCAGTTTGTCGAAGCCTTCAGAATGTCGGTGCAAGCAGTATTGGCGCACAAAATGCGTTCGCTTCTGACCATGCTCGGCATCATCATCGGTATCGCTTCGGTTGTCTCCGTCGTCGCGCTGGGCAACGGGTCGCAGAAAAAAATCCTCGAAGACATCAGTTCGATGGGGACGAACACCATCAGCATCTTCCCCGGGCGCGGCTTCGGCGACAGGCGCAGCGGCAAAATCAAAACCCTGACCATAGACGACGCAAAAATCATCGCCAAACAAAGCTATGTTGCTTCCGCCACGCCCATGACTTCGAGCGGCGGCACGCTGACCTACCGCAATACCGACCTGACCGCTTCTTTGTACGGCGTGGGCGAACAATATTTCGACGTGCGCGGGCTGAAGCTGGAAACGGGGCGGCTGTTTGATGAGAACGATGTGAAAGAAGACGCGCAAGTCGTCGTCATCGACCAAAATGTCAAAGACAAACTCTTTGCGGACTCGGATCCGTTGGGTAAAACCATTTTGTTCAGGAAACGCCCCTTGACCGTCATCGGCGTGATGAAAAAAGACGAAAACGCTTTCGGCAATTCCGACGTGCTGATGCTTTGGTCGCCCTATACGACGGTGATGCACCAAATCACAGGCGAGAGCCACACCAACTCCATCACCGTCAAAATCAAAGACAATGCCAATACCCGGGTTGCCGAAAAAGGGCTGGCCGAGCTGCTCAAAGCACGGCACGGCACGGAAGACTTCTTTATGAACAACAGCGACAGCATCAGGCAGATGGTCGAAAGCACCACCGGTACGATGAAGCTGCTGATTTCCTCCATCGCCCTGATTTCATTGGTAGTCGGCGGCATCGGCGTGATGAACATTATGCTGGTGTCCGTTACCGAGCGCACCAAAGAAATCGGCATACGGATGGCAATCGGCGCGCGGCGCGGCAATATTTTGCAGCAGTTTTTGATTGAGGCGGTGTTAATCTGCATCATCGGAGGCTTGGTCGGCGTAGGTTTGTCCGCCGCCGTCAGCCTCGTGTTCAATCATTTTGTAACCGATTTCCCGATGGACATTTCGGCGGCATCCGTTATCGGGGCGGTCGCCTGTTCGACCGGAATCGGCATCGCGTTCGGCTTTATGCCTGCCAATAAGGCAGCCAAACTCAATCCGATAGACGCATTGGCGCAGGATTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36806","NCBI_taxonomy_name":"Neisseria gonorrhoeae","NCBI_taxonomy_id":"485"}}}},"ARO_accession":"3000535","ARO_id":"36674","ARO_name":"macB","CARD_short_name":"macB","ARO_description":"MacB is an ATP-binding cassette (ABC) transporter that exports macrolides with 14- or 15- membered lactones. It forms an antibiotic efflux complex with MacA and TolC. macB corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.","ARO_category":{"36002":{"category_aro_accession":"0010001","category_aro_cvterm_id":"36002","category_aro_name":"ATP-binding cassette (ABC) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding\/hydrolysis to transport substrates across cell membranes.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"488":{"model_id":"488","model_name":"SHV-156","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1558":{"protein_sequence":{"accession":"AFQ23962.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQPERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTTFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"JX121123.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCCGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACATCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTACCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001195","ARO_id":"37575","ARO_name":"SHV-156","CARD_short_name":"SHV-156","ARO_description":"SHV-156 is a beta-lactamase.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"490":{"model_id":"490","model_name":"TEM-188","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"2034":{"protein_sequence":{"accession":"AEL17198.1","sequence":"MSIQHFRVALIPFFAAFCFPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGASKRGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"JN211012.1","fmin":"213","fmax":"1074","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCTTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCAGTAAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35672","NCBI_taxonomy_name":"Salmonella enterica","NCBI_taxonomy_id":"28901"}}}},"ARO_accession":"3001048","ARO_id":"37428","ARO_name":"TEM-188","CARD_short_name":"TEM-188","ARO_description":"TEM-188 is an extended-spectrum beta-lactamase.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"392":{"model_id":"392","model_name":"TUS-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"1163":{"protein_sequence":{"accession":"AAN63648.1","sequence":"MYHYFSSLFVLIFSTLVYPQSDKLKIEPLNDHMYVYTTYQVFQGVEYSSNALYVVTDEGVILIDTPWDKDQYAPLVEHIRREHNKEIKWVITTHFHEDRSGGLDYFNKAGAETYTYALTNEILKQRNEPQATFTFGSTKQFNLGKEKIEVYFLGEGHSKDNTVVWFPEEAILYGGCLIKSAEATTIGNIVDGNVEAWPTTIKAVKRKFKKAKVIIPGHDAWNQSGHLENTARILSAYQAQKLKNNKQL"},"dna_sequence":{"accession":"AF441287.1","fmin":"260","fmax":"1007","strand":"+","sequence":"ATGTACCACTACTTTAGCAGTTTATTTGTACTGATTTTTTCTACTTTGGTCTATCCTCAATCGGATAAATTAAAAATTGAGCCGTTGAACGATCATATGTATGTCTATACGACCTACCAAGTATTTCAAGGCGTCGAATATTCTTCCAATGCTTTATATGTAGTGACGGATGAAGGAGTAATTCTCATTGATACCCCTTGGGATAAAGATCAGTACGCCCCTTTAGTAGAACACATCAGACGTGAACATAACAAAGAAATAAAATGGGTCATTACCACTCACTTCCACGAAGATCGTTCGGGTGGACTTGATTACTTCAATAAAGCTGGAGCAGAAACCTATACTTATGCTTTGACCAACGAAATCTTAAAACAGCGCAATGAACCACAAGCGACTTTTACTTTTGGTTCAACAAAGCAGTTCAACTTGGGCAAAGAAAAAATAGAGGTCTATTTCTTAGGAGAAGGTCATAGTAAAGATAATACGGTGGTTTGGTTTCCAGAAGAAGCGATTTTATACGGTGGTTGTTTGATTAAAAGTGCAGAGGCAACGACTATCGGCAATATCGTCGATGGCAATGTAGAGGCTTGGCCTACGACAATCAAAGCCGTAAAGCGCAAATTCAAAAAGGCCAAAGTGATTATTCCAGGGCATGATGCCTGGAATCAATCCGGTCATCTTGAAAATACAGCCCGTATCTTATCGGCTTATCAGGCACAAAAATTAAAGAACAACAAGCAATTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39073","NCBI_taxonomy_name":"Myroides odoratus DSM 2801","NCBI_taxonomy_id":"929704"}}}},"ARO_accession":"3000844","ARO_id":"37224","ARO_name":"TUS-1","CARD_short_name":"TUS-1","ARO_description":"TUS-1 is a chromosome-encoded beta-lactamase from Myroides odoratus and Myroides odoratimimus.","ARO_category":{"41369":{"category_aro_accession":"3004205","category_aro_cvterm_id":"41369","category_aro_name":"TUS beta-lactamase","category_aro_description":"TUS beta-lactamases are Class B beta-lactamases that can hydrolyze a variety of beta-lactams, such as cephems and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35981":{"category_aro_accession":"0000064","category_aro_cvterm_id":"35981","category_aro_name":"amoxicillin","category_aro_description":"Amoxicillin is a moderate-spectrum, bacteriolytic, beta-lactam antibiotic used to treat bacterial infections caused by susceptible microorganisms. A derivative of penicillin, it has a wider range of treatment but remains relatively ineffective against Gram-negative bacteria. It is commonly taken with clavulanic acid, a beta-lactamase inhibitor. Like other beta-lactams, amoxicillin interferes with the synthesis of peptidoglycan.","category_aro_class_name":"Antibiotic"},"35995":{"category_aro_accession":"0000078","category_aro_cvterm_id":"35995","category_aro_name":"piperacillin","category_aro_description":"Piperacillin is an acetylureidopenicillin and has an extended spectrum of targets relative to other beta-lactam antibiotics. It inhibits cell wall synthesis in bacteria, and is usually taken with the beta-lactamase inhibitor tazobactam to overcome penicillin-resistant bacteria.","category_aro_class_name":"Antibiotic"},"40523":{"category_aro_accession":"3003832","category_aro_cvterm_id":"40523","category_aro_name":"ticarcillin","category_aro_description":"Ticarcillin is a carboxypenicillin used for the treatment of Gram-negative bacteria, particularly P. aeruginosa. Ticarcillin's antibiotic properties arise from its ability to prevent cross-linking of peptidoglycan during cell wall synthesis, when the bacteria try to divide, causing cell death.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"442":{"model_id":"442","model_name":"OpmD","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"920"}},"model_sequences":{"sequence":{"5356":{"protein_sequence":{"accession":"AAG07595.1","sequence":"MKRSYPNLSRLALALAVGTGLAACSVGPDYQRPQSPPPRVASEHLGEFSGERREAPWWSFFDDPQLVRLVDQALARNHDIREARANLRSARALFDDRWLDQLPQVTSQAGYSRSIEQQLDYDGEPRRRLAESYRAGFDAQWEIDLFGRLGRLSDAALARAEAADADLRLVRLSIAADTARAYFEIQGYQRRLDVARAQVRSWRDTLELTRSSLQLGSGLPEDVENAQANLLRSEAAIPPLTTALESARYRLDVLRGEAPGSGAPILDGGAAAPLAKNLPLGDVDRLILQRPDVVSAERQLAASTEDVGAATAELYPRLDLGGFIGFFALRSGDLGSASRAFELAPSVSWPAFRLGNVRARLRAVEAQSDAALARYQRSLLLAQEDVGNALNQLAEHQRRLVALFQSATHGANALEIANERYRAGAGSYLAVLENQRALYQIREELAQAETASFVNVIALYKALGWGSGDLAPGAGQLAAGETAGANR"},"dna_sequence":{"accession":"AE004091.2","fmin":"4710620","fmax":"4712084","strand":"+","sequence":"ATGAAGCGCTCCTACCCGAACCTTTCGCGCCTGGCGCTGGCCCTGGCGGTCGGCACCGGCCTGGCCGCCTGCAGCGTCGGCCCCGACTACCAGCGTCCGCAGTCGCCGCCGCCACGCGTCGCCAGCGAGCACCTCGGCGAGTTCTCCGGCGAGCGGCGGGAAGCGCCCTGGTGGAGTTTCTTCGACGATCCGCAACTGGTGCGCCTGGTCGACCAGGCGCTGGCGCGCAACCACGACATCCGCGAGGCCCGCGCCAACCTGCGCAGCGCCCGCGCGCTGTTCGACGACCGCTGGCTCGACCAGTTGCCGCAGGTCACCAGCCAGGCCGGCTACAGCCGCAGCATCGAACAACAGCTGGACTACGACGGCGAGCCGCGCCGGCGCCTGGCGGAGAGCTACCGCGCCGGCTTCGACGCGCAGTGGGAAATCGACCTGTTCGGCCGCCTCGGCCGACTTTCCGACGCCGCCTTGGCCCGCGCCGAAGCGGCCGACGCCGACCTCCGGCTGGTACGCCTGAGCATCGCCGCCGACACCGCCCGCGCCTACTTCGAGATCCAGGGCTACCAGCGCCGGCTGGACGTGGCGCGCGCCCAGGTGCGCAGTTGGCGCGACACCCTGGAGCTGACCCGCAGCAGCCTGCAACTGGGCAGCGGCCTGCCGGAGGACGTGGAGAACGCCCAGGCCAACCTGCTGCGCAGCGAAGCGGCGATTCCGCCACTGACGACCGCGCTGGAGAGCGCCCGCTATCGCCTCGACGTGCTGCGCGGCGAGGCACCCGGCAGCGGCGCGCCGATCCTCGACGGCGGCGCCGCCGCGCCATTGGCGAAGAACCTGCCGCTGGGCGACGTCGACCGCCTGATCCTCCAGCGCCCCGACGTAGTCAGCGCCGAGCGGCAACTGGCAGCGAGCACCGAAGACGTCGGCGCGGCCACCGCCGAACTCTATCCGCGCCTCGACCTGGGCGGCTTCATCGGTTTCTTCGCCCTGCGCAGCGGCGACCTCGGCAGCGCCTCGCGCGCCTTCGAACTGGCGCCCAGCGTCAGTTGGCCGGCGTTCCGCCTGGGCAACGTGCGGGCCCGCCTGCGCGCCGTCGAGGCGCAGTCCGACGCCGCGCTGGCGCGCTACCAGCGCTCCCTGCTGCTGGCCCAGGAGGACGTCGGCAACGCGCTCAACCAACTGGCCGAACACCAGCGTCGGCTGGTCGCCCTGTTCCAGTCCGCGACCCATGGCGCGAACGCCCTGGAGATCGCCAACGAACGCTACCGCGCCGGCGCCGGCAGCTACCTGGCGGTGCTGGAGAACCAGCGCGCGCTGTACCAGATCCGCGAGGAACTGGCGCAGGCGGAGACCGCCTCGTTCGTCAACGTCATCGCGCTCTACAAGGCGCTCGGCTGGGGCAGCGGCGACCTGGCGCCGGGCGCCGGCCAACTGGCCGCCGGCGAAACCGCCGGGGCCAACCGTTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36804","NCBI_taxonomy_name":"Pseudomonas aeruginosa PAO1","NCBI_taxonomy_id":"208964"}}}},"ARO_accession":"3000809","ARO_id":"37189","ARO_name":"OpmD","CARD_short_name":"OpmD","ARO_description":"OpmD is the outer membrane channel protein of the efflux complex MexGHI-OpmD.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35963":{"category_aro_accession":"0000045","category_aro_cvterm_id":"35963","category_aro_name":"acriflavine","category_aro_description":"Acriflavine is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"43746":{"category_aro_accession":"3005386","category_aro_cvterm_id":"43746","category_aro_name":"disinfecting agents and antiseptics","category_aro_description":"Disinfectants that can also interact with antimicrobial resistance mechanisms, e.g. molecule efflux, and thus are the targets of disinfectant resistance.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"491":{"model_id":"491","model_name":"PER-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"898":{"protein_sequence":{"accession":"CAA63714.1","sequence":"MNVITKCVFTASALLMLGLSSFVVSAQSPLLKEQIETIVTGKKATVGVAVWGPDDLEPLLLNPFEKFPMQSVFKLHLAMLVLHQVDQGKLDLNQSVTVNRAAVLQNTWSPMMKDHQGDEFTVAVQQLLQYSVSHSDNVACDLLFELVGGPQALHAYIQSLGVKEAAVVANEAQMHADDQVQYQNWTSMKAAAQVLQKFEQKKQLSETSQALLWKWMVETTTGPQRLKGLLPAGTIVAHKTGTSGVRAGKTAATNDAGVIMLPDGRPLLVAVFVKDSAESERTNEAIIAQVAQAAYQFELKKLSAVSPD"},"dna_sequence":{"accession":"X93314.1","fmin":"0","fmax":"927","strand":"+","sequence":"ATGAATGTCATCACAAAATGTGTTTTCACCGCTTCTGCTCTGCTGATGCTTGGCTTAAGTTCATTTGTAGTATCAGCCCAATCCCCTTTGTTAAAAGAGCAGATTGAAACCATAGTGACGGGTAAAAAGGCCACTGTAGGTGTAGCAGTGTGGGGGCCTGACGATCTGGAACCTTTGTTGCTGAATCCATTTGAAAAGTTTCCGATGCAAAGTGTGTTTAAACTGCATTTAGCTATGTTAGTTCTGCATCAGGTCGATCAGGGGAAACTGGATTTAAATCAGTCTGTTACTGTTAATCGTGCTGCAGTATTACAAAATACCTGGTCGCCAATGATGAAAGATCATCAGGGCGATGAATTTACTGTTGCAGTACAGCAGTTACTGCAGTATTCGGTGTCACACAGCGACAATGTGGCCTGCGATTTGTTATTTGAACTGGTGGGCGGGCCGCAAGCTTTGCATGCTTATATCCAGTCTTTAGGCGTTAAAGAAGCTGCCGTGGTAGCAAATGAAGCGCAAATGCATGCGGATGATCAGGTGCAATATCAAAACTGGACGTCGATGAAAGCCGCAGCACAAGTTCTGCAAAAGTTTGAACAGAAAAAGCAGTTGTCTGAAACCTCTCAGGCCTTGTTATGGAAATGGATGGTTGAAACCACCACAGGACCACAGCGGTTAAAAGGCTTGTTACCTGCTGGTACTATAGTGGCGCATAAAACCGGTACTTCGGGCGTCAGAGCAGGAAAAACTGCGGCGACTAATGATGCGGGCGTCATTATGTTGCCTGATGGACGGCCTTTATTGGTGGCGGTATTTGTCAAGGATTCGGCTGAATCAGAACGAACCAATGAAGCTATTATTGCGCAGGTTGCGCAAGCGGCTTATCAGTTTGAGCTGAAAAAACTCTCTGCAGTGAGTCCGGATTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35732","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Typhimurium","NCBI_taxonomy_id":"90371"}}}},"ARO_accession":"3002364","ARO_id":"38764","ARO_name":"PER-2","CARD_short_name":"PER-2","ARO_description":"PER-2 is a beta-lactamase found in Salmonella typhimurium.","ARO_category":{"36195":{"category_aro_accession":"3000056","category_aro_cvterm_id":"36195","category_aro_name":"PER beta-lactamase","category_aro_description":"PER beta-lactamases are plasmid-mediated extended spectrum beta-lactamases found in the Enterobacteriaceae family.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"493":{"model_id":"493","model_name":"TEM-84","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1328":{"protein_sequence":{"accession":"AAL29436.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERDRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AF427130.1","fmin":"208","fmax":"1069","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAGATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000951","ARO_id":"37331","ARO_name":"TEM-84","CARD_short_name":"TEM-84","ARO_description":"TEM-84 is an inhibitor-resistant beta-lactamase found in E. coli.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"494":{"model_id":"494","model_name":"KPC-14","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1971":{"protein_sequence":{"accession":"AFV48348.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"JX524191.1","fmin":"395","fmax":"1271","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002324","ARO_id":"38724","ARO_name":"KPC-14","CARD_short_name":"KPC-14","ARO_description":"KPC-14 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"495":{"model_id":"495","model_name":"CMY-28","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1547":{"protein_sequence":{"accession":"ABQ51091.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGELAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDNKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"EF561644.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGAGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAACAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002039","ARO_id":"38439","ARO_name":"CMY-28","CARD_short_name":"CMY-28","ARO_description":"CMY-28 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"409":{"model_id":"409","model_name":"vanR gene in vanL cluster","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"287":{"protein_sequence":{"accession":"ABX54691.1","sequence":"MTDRIVVVDDEQEIANLITTFLENEGFQVTTFYKGEDFLTYIARESISLAILDVMLPDIDGFRILQEIRKNFYFPVLMLTAKEENMDKIMGLTLGADDYITKPFNPIEVVARVKTQLRRVQKYNRKVENESVIEFNKDGLTLKKDSHQVFLFDKEITVTPIEFNLLLYLFEHQGVVVSSEELFEAVWKEKYLENNNTIMAHIARLREKLDEQPRKPKFIKTVWGVGYIIEK"},"dna_sequence":{"accession":"EU250284.1","fmin":"4730","fmax":"5426","strand":"+","sequence":"ATGACGGATAGAATAGTTGTTGTGGATGATGAACAAGAGATAGCCAATTTGATTACAACTTTTTTAGAAAATGAAGGGTTTCAAGTAACAACCTTTTATAAAGGAGAAGATTTTTTGACTTATATAGCTAGAGAGTCAATTTCTTTAGCTATATTAGATGTCATGCTACCTGATATTGATGGGTTTCGAATCTTGCAAGAAATTAGAAAGAATTTTTATTTTCCGGTATTAATGCTTACAGCTAAGGAAGAAAATATGGACAAGATTATGGGACTAACCTTGGGAGCGGATGATTATATTACTAAACCATTTAACCCAATAGAAGTAGTTGCCCGGGTAAAAACACAACTAAGACGAGTCCAAAAGTATAACCGGAAAGTGGAAAATGAATCAGTCATAGAGTTTAACAAAGACGGACTAACGCTAAAAAAAGACAGTCATCAAGTATTTTTATTTGATAAAGAAATAACTGTAACACCTATTGAATTCAATTTGCTTTTATATTTATTTGAACACCAAGGAGTGGTTGTTAGTTCAGAAGAACTATTTGAAGCTGTTTGGAAAGAGAAATATTTAGAAAATAATAACACAATCATGGCACACATTGCTCGCTTAAGGGAAAAATTAGACGAACAGCCACGCAAACCTAAATTCATAAAAACCGTATGGGGGGTAGGATATATTATTGAAAAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35918","NCBI_taxonomy_name":"Enterococcus faecalis","NCBI_taxonomy_id":"1351"}}}},"ARO_accession":"3002927","ARO_id":"39361","ARO_name":"vanR gene in vanL cluster","CARD_short_name":"vanR_in_vanL_cl","ARO_description":"Also known as vanRL, is a vanR variant found in the vanL gene cluster.","ARO_category":{"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"36713":{"category_aro_accession":"3000574","category_aro_cvterm_id":"36713","category_aro_name":"vanR","category_aro_description":"VanR is a OmpR-family transcriptional activator in the VanSR regulatory system. When activated by VanS, it promotes cotranscription of VanA, VanH, and VanX.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"389":{"model_id":"389","model_name":"tet(W)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"5145":{"protein_sequence":{"accession":"CAA10975.1","sequence":"MKIINIGILAHVDAGKTTLTESLLYASGAISEPGSVEKGTTRTDTMFLERQRGITIQAAVTSFQWHRCKVNIVDTPGHMDFLAEVYRSLAVLDGAILVISAKDGVQAQTRILFHALRKMNIPTVIFINKIDQAGVDLQSVVQSVRDKLSADIIIKQTVSLSPEIVLEENTDIEAWDAVIENNDELLEKYIAGEPISREKLAREEQQRVQDASLFPVYHGSAKNGLGIQPLMDAVTGLFQPIGEQGGAALCGSVFKVEYTDCGQRRVYLRLYSGTLRLRDTVALAGREKLKITEMRIPSKGEIVRTDTAYQGEIVILPSDSVRLNDVLGDQTRLPRKRWREDPLPMLRTTIAPKTAAQRERLLDALTQLADTDPLLRCEVDSITHEIILSFLGRVQLEVVSALLSEKYKLETVVKEPSVIYMERPLKAASHTIHIEVPPNPFWASIGLSVTPLSLGSGVQYESRVSLGYLNQSFQNAVRDGIRYGLEQGLFGWNVTDCKICFEYGLYYSPVSTPADFRSLAPIVLEQALKESGTQLLEPYLSFILYAPQEYLSRAYHDAPKYCATIETAQVKKDEVVFTGEIPARCIQAYRTDLAFYTNGRSVCLTELKGYQAAVGQPVIQPRRPNSRLDKVRHMFQKVM"},"dna_sequence":{"accession":"AJ222769.3","fmin":"3686","fmax":"5606","strand":"+","sequence":"ATGAAAATAATCAATATTGGAATTCTTGCCCATGTAGACGCTGGAAAGACGACCTTGACGGAGAGCCTGCTATATGCCAGCGGAGCCATTTCAGAACCGGGGAGCGTCGAAAAAGGGACAACGAGGACGGACACCATGTTTTTGGAGCGGCAGCGTGGGATTACCATTCAAGCGGCAGTCACTTCCTTCCAGTGGCACAGATGTAAAGTTAACATTGTGGATACGCCCGGCCACATGGATTTTTTGGCGGAGGTGTACCGCTCTTTGGCTGTTTTAGATGGGGCCATCTTGGTGATCTCCGCTAAAGATGGCGTGCAGGCCCAGACCCGTATTCTGTTCCATGCCCTGCGGAAAATGAACATTCCCACCGTTATCTTTATCAACAAGATCGACCAGGCTGGCGTTGATTTGCAGAGCGTGGTTCAGTCTGTTCGGGATAAGCTCTCCGCCGATATTATCATCAAGCAGACGGTGTCGCTGTCCCCGGAAATAGTCCTGGAGGAAAATACCGACATAGAAGCATGGGATGCGGTCATCGAAAATAACGATGAATTATTGGAAAAGTATATCGCAGGAGAACCAATCAGCCGGGAAAAACTTGCGCGGGAGGAACAGCAGCGGGTTCAAGACGCCTCCCTGTTCCCAGTCTATCATGGCAGCGCCAAAAATGGCCTTGGCATTCAACCGTTGATGGATGCGGTGACAGGGCTGTTCCAACCGATTGGGGAACAGGGGGGCGCCGCCCTATGCGGCAGCGTTTTCAAGGTTGAGTACACCGATTGCGGCCAGCGGCGTGTCTATCTACGGTTATACAGCGGAACGCTGCGCCTGCGGGATACGGTGGCCCTGGCCGGGAGAGAAAAGCTGAAAATCACAGAGATGCGTATTCCATCCAAAGGGGAAATTGTTCGGACAGACACCGCTTATCAGGGTGAAATTGTTATCCTTCCCAGCGACAGCGTGAGGTTAAACGATGTATTAGGGGACCAAACCCGGCTCCCTCGTAAAAGGTGGCGCGAGGACCCCCTCCCCATGCTGCGGACGACGATTGCGCCGAAAACGGCAGCGCAAAGAGAACGGCTGCTGGACGCTCTTACGCAACTTGCGGATACTGACCCGCTTTTGCGTTGCGAAGTGGATTCCATCACCCATGAGATCATTCTTTCTTTTTTGGGCCGGGTGCAGTTGGAGGTTGTTTCCGCTTTGCTGTCGGAAAAATACAAGCTTGAAACAGTGGTAAAGGAACCCTCCGTCATTTATATGGAGCGGCCGCTCAAAGCAGCCAGCCACACCATCCATATCGAGGTGCCGCCCAACCCGTTTTGGGCATCCATAGGACTGTCTGTTACACCACTCTCGCTTGGCTCCGGTGTACAATACGAGAGCCGGGTTTCGCTGGGATACTTGAACCAGAGTTTTCAAAACGCTGTCAGGGATGGTATCCGTTACGGGCTGGAGCAGGGCTTGTTCGGCTGGAACGTAACGGACTGTAAGATTTGCTTTGAATACGGGCTTTATTACAGTCCGGTCAGCACGCCGGCGGACTTCCGCTCATTGGCCCCGATTGTATTGGAACAGGCATTGAAGGAATCGGGGACGCAGCTGCTGGAACCTTATCTCTCCTTCATCCTCTATGCGCCCCAGGAATACCTTTCCAGGGCTTATCATGATGCACCGAAATACTGTGCCACCATCGAAACGGCCCAGGTAAAAAAGGATGAAGTTGTCTTTACTGGCGAGATTCCCGCCCGCTGTATACAGGCATACCGTACTGATCTGGCCTTTTACACCAACGGGCGGAGCGTATGCCTTACAGAGCTGAAAGGATATCAGGCCGCTGTCGGTCAGCCGGTCATCCAGCCCCGCCGTCCAAACAGCCGCCTGGACAAGGTGCGCCATATGTTTCAGAAGGTAATGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36793","NCBI_taxonomy_name":"Butyrivibrio fibrisolvens","NCBI_taxonomy_id":"831"}}}},"ARO_accession":"3000194","ARO_id":"36333","ARO_name":"tet(W)","CARD_short_name":"tet(W)","ARO_description":"Tet(W) is a ribosomal protection protein. It is associated with both conjugative and non conjugative DNA and has been found strains of Clostridioides difficile.","ARO_category":{"35921":{"category_aro_accession":"0000002","category_aro_cvterm_id":"35921","category_aro_name":"tetracycline-resistant ribosomal protection protein","category_aro_description":"A family of proteins known to bind to the 30S ribosomal subunit. This interaction prevents tetracycline and tetracycline derivatives from inhibiting ribosomal function. Thus, these proteins confer elevated resistance to tetracycline derivatives as a ribosomal protection protein.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35986":{"category_aro_accession":"0000069","category_aro_cvterm_id":"35986","category_aro_name":"doxycycline","category_aro_description":"Doxycycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36291":{"category_aro_accession":"3000152","category_aro_cvterm_id":"36291","category_aro_name":"minocycline","category_aro_description":"Minocycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36667":{"category_aro_accession":"3000528","category_aro_cvterm_id":"36667","category_aro_name":"chlortetracycline","category_aro_description":"Chlortetracycline was an early, first-generation tetracycline antibiotic developed in the 1940's. It inhibits bacterial protein synthesis by binding to the 30S subunit of bacterial ribosomes, preventing the aminoacyl-tRNA from binding to the ribosome.","category_aro_class_name":"Antibiotic"},"37011":{"category_aro_accession":"3000667","category_aro_cvterm_id":"37011","category_aro_name":"demeclocycline","category_aro_description":"Demeclocycline is a tetracycline analog with 7-chloro and 6-methyl groups. Due to its fast absorption and slow excretion, it maintains higher effective blood levels compared to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37012":{"category_aro_accession":"3000668","category_aro_cvterm_id":"37012","category_aro_name":"oxytetracycline","category_aro_description":"Oxytetracycline is a derivative of tetracycline with a 5-hydroxyl group. Its activity is similar to other tetracyclines.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"496":{"model_id":"496","model_name":"KPC-16","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"792":{"protein_sequence":{"accession":"AGJ01153.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAASQRQQLVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"KC465199.1","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGTTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGTCGCAGCGGCAGCAGCTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002326","ARO_id":"38726","ARO_name":"KPC-16","CARD_short_name":"KPC-16","ARO_description":"KPC-16 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"497":{"model_id":"497","model_name":"OXA-79","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1693":{"protein_sequence":{"accession":"ABV71246.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDVKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGGDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"EU019534.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGTAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAACAAAATATACGCAAAAAGTGGTTGGGGAGGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001633","ARO_id":"38033","ARO_name":"OXA-79","CARD_short_name":"OXA-79","ARO_description":"OXA-79 is a beta-lactamase found in A. baumannii.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"498":{"model_id":"498","model_name":"QnrB17","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"388":{"protein_sequence":{"accession":"CAP45902.1","sequence":"MTPLLYKKTGTNMALALVGEKIDRNRFTGEKIENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNSSALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGAQVLGATFSGSDLSGGEFSTFDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDNYQASLLMERLGIAVIG"},"dna_sequence":{"accession":"AM919398.1","fmin":"0","fmax":"681","strand":"+","sequence":"ATGACGCCATTACTGTATAAAAAAACAGGTACAAATATGGCTCTGGCACTCGTTGGCGAAAAAATTGACAGAAACCGTTTCACCGGTGAGAAAATTGAAAATAGTACATTTTTTAACTGTGATTTTTCAGGTGCCGACCTGAGCGGCACTGAATTTATCGGCTGTCAGTTCTATGATCGTGAAAGCCAGAAAGGGTGCAATTTTAGTCGTGCGATGCTGAAAGATGCCATTTTTAAAAGCTGTGATTTATCCATGGCGGATTTTCGCAATTCCAGTGCGCTGGGCATTGAAATTCGCCACTGCCGCGCACAAGGCGCAGATTTCCGCGGCGCAAGCTTTATGAATATGATCACCACGCGCACCTGGTTTTGTAGCGCATATATCACGAATACCAATCTAAGCTACGCCAATTTTTCGAAAGTCGTGTTGGAAAAGTGTGAGCTGTGGGAAAACCGTTGGATGGGTGCCCAGGTACTGGGCGCGACGTTCAGTGGTTCAGATCTCTCCGGCGGCGAGTTTTCGACTTTCGACTGGCGAGCAGCGAACTTCACACATTGCGATCTGACCAATTCGGAGTTGGGTGACTTAGATATTCGGGGCGTTGATTTACAAGGCGTTAAGCTGGACAACTACCAGGCGTCGTTGCTCATGGAGCGGCTTGGCATCGCGGTGATTGGTTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002732","ARO_id":"39166","ARO_name":"QnrB17","CARD_short_name":"QnrB17","ARO_description":"QnrB17 is a plasmid-mediated quinolone resistance protein found in Citrobacter freundii.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"500":{"model_id":"500","model_name":"OXA-164","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1125":{"protein_sequence":{"accession":"ADK34116.1","sequence":"MKLLKILSLVCLSISIGACAEHSMSRAKTSTIPQVNNSIIDQNVQALFNEISADAVFVTYDGQNIKKYGTHLDRAKTAYIPASTFKIANALIGLENHKATSTEIFKWDGKPRFLKAWDKDFTLGEAMQASTVPVYQELARRIGPSLMQSELQRIGYGNMQIGTEVDQFWLKGPLTITPIQEVKFVYDLAQGQLPFKPEVQQQVKEMLYVERRGENRLYAKSGWGMAVDPQVGWYVGFVEKADGQVVAFALNMQMKAGDDIALRKQLSLDVLDKLGVFHYL"},"dna_sequence":{"accession":"GU831575.1","fmin":"0","fmax":"843","strand":"+","sequence":"ATGAAATTATTAAAAATATTGAGTTTAGTTTGCTTAAGCATAAGTATTGGGGCTTGTGCTGAGCATAGTATGAGTCGAGCAAAAACAAGTACAATTCCACAAGTGAATAACTCAATCATCGATCAGAATGTTCAAGCGCTTTTTAATGAAATCTCAGCTGATGCTGTGTTTGTCACATATGATGGTCAAAATATTAAAAAATATGGCACGCATTTAGACCGAGCAAAAACAGCTTATATTCCTGCATCTACATTTAAAATTGCCAATGCACTAATTGGTTTAGAAAATCATAAAGCAACATCTACAGAAATATTTAAGTGGGATGGAAAGCCACGTTTTTTAAAAGCATGGGACAAAGATTTTACTTTGGGCGAAGCCATGCAAGCATCTACAGTGCCTGTATATCAAGAATTGGCACGTCGTATTGGTCCAAGCTTAATGCAAAGTGAATTGCAACGTATTGGTTATGGCAATATGCAAATAGGCACGGAAGTTGATCAATTTTGGTTGAAAGGGCCTTTGACAATTACACCTATACAAGAAGTAAAGTTTGTGTATGATTTAGCCCAAGGGCAATTGCCTTTTAAACCTGAAGTTCAGCAACAAGTGAAAGAGATGTTGTATGTAGAGCGCAGAGGGGAGAATCGTCTATATGCTAAAAGTGGCTGGGGAATGGCTGTAGACCCGCAAGTGGGTTGGTATGTGGGTTTTGTTGAAAAGGCAGATGGGCAAGTGGTGGCATTTGCTTTAAATATGCAAATGAAAGCTGGTGATGATATTGCTCTACGTAAACAATTGTCTTTAGATGTGCTAGATAAGTTGGGTGTTTTTCATTATTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001662","ARO_id":"38062","ARO_name":"OXA-164","CARD_short_name":"OXA-164","ARO_description":"OXA-164 is a beta-lactamase found in A. baumannii.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46517":{"category_aro_accession":"3007728","category_aro_cvterm_id":"46517","category_aro_name":"OXA-58-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-58.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"501":{"model_id":"501","model_name":"AAC(3)-VIIIa","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"12":{"protein_sequence":{"accession":"AAA26685.1","sequence":"MDEKELIERAGGPVTRGRLVRDLEALGVGAGDTVMVHTRMSAIGYVVGGPQTVIDAVRDAVGADGTLMAYCGWNDAPPYDLAEWPPAWREAARAEWPAYDPLLSEADRGNGRVPEALRHQPGAVRSRHPDASFVAVGPAAHPLMDDHPWDDPHGPDSPLARLAGAGGRVLLLGAPLDTLTLLHHAEARAEAPGKRFVAYEQPVTVGGRRVWRRFRDVDTSRGVPYGRVVPEGVVPFTVIAQDMLAAGIGRTGRVAAAPVHLFEAADVVRFGVEWIESRMGGAAGGA"},"dna_sequence":{"accession":"M55426.1","fmin":"465","fmax":"1326","strand":"+","sequence":"GTGGACGAGAAGGAACTGATCGAGCGCGCCGGCGGCCCCGTCACCCGCGGCCGGCTCGTGCGCGACCTCGAGGCACTCGGCGTCGGCGCCGGCGACACCGTCATGGTGCACACCCGCATGTCGGCGATCGGCTACGTCGTGGGCGGCCCGCAGACCGTGATCGACGCCGTCCGCGACGCCGTCGGCGCCGACGGCACCCTCATGGCCTACTGCGGCTGGAACGACGCCCCGCCCTACGACCTCGCCGAGTGGCCCCCCGCGTGGCGGGAGGCCGCACGAGCCGAGTGGCCCGCCTACGACCCGCTGCTCAGCGAGGCCGACCGGGGCAACGGCCGGGTCCCCGAGGCCCTGCGCCACCAGCCCGGCGCGGTCCGCAGCCGGCACCCCGACGCGAGCTTCGTCGCGGTCGGGCCGGCCGCCCACCCGCTCATGGACGACCACCCCTGGGACGACCCGCACGGACCGGACAGCCCGCTCGCCCGGCTCGCCGGGGCCGGCGGACGGGTACTGCTGCTCGGCGCCCCGCTGGACACCCTGACGCTGCTGCACCACGCGGAGGCACGGGCCGAGGCCCCCGGCAAGCGGTTCGTCGCGTACGAGCAGCCCGTGACCGTCGGCGGGCGACGGGTCTGGCGGCGCTTCCGCGACGTCGACACCAGCCGAGGCGTTCCCTACGGGCGGGTGGTGCCCGAGGGGGTCGTGCCGTTCACCGTCATCGCCCAGGACATGCTCGCAGCCGGGATCGGCCGGACCGGCCGGGTCGCCGCCGCCCCCGTCCACCTCTTCGAGGCCGCCGACGTGGTCCGCTTCGGCGTCGAGTGGATCGAGAGCCGGATGGGGGGCGCGGCCGGCGGGGCGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36838","NCBI_taxonomy_name":"Streptomyces fradiae","NCBI_taxonomy_id":"1906"}}}},"ARO_accession":"3002542","ARO_id":"38942","ARO_name":"AAC(3)-VIIIa","CARD_short_name":"AAC(3)-VIIIa","ARO_description":"AAC(3)-VIIIa is a chromosomal-encoded aminoglycoside acetyltransferase in Streptomyces fradiae.","ARO_category":{"36461":{"category_aro_accession":"3000322","category_aro_cvterm_id":"36461","category_aro_name":"AAC(3)","category_aro_description":"A category of aminoglycoside N-acetyltransferase enzymes with modification regiospecificity based at the 3-amino group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics through acetylation of the 3-amino group of the compound.","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"502":{"model_id":"502","model_name":"aadA17","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"8152":{"protein_sequence":{"accession":"ACK43806.1","sequence":"MRVAVTIEISNQLSEVLSVIERHLEPTLLAVHLYGSAVDGGLKPHSDIDLLVTVTVRLDETTRRALINDLLETSASPGESEILRAVEVTIVVHDDIIPWRYPAKRELQFGEWQRNDILAGIFEPATIDIDLAILLTKAREHSVALVGPAAEEFFDPVPEQDLFEALRETLKLWNSQPDWAGDERNVVLTLSRIWYSAITGKIAPKDVAADWAIKRLPAQYQPVLLEAKQAYLGQKEDHLASRADHLEEFIRFVKGEIIKSVGK"},"dna_sequence":{"accession":"FJ460181.2","fmin":"1790","fmax":"2582","strand":"+","sequence":"ATGAGGGTAGCGGTGACCATCGAAATTTCGAACCAACTATCAGAGGTGCTAAGCGTCATCGAGCGCCATCTCGAACCGACGTTGCTGGCCGTACATTTGTACGGCTCCGCAGTGGATGGCGGCCTGAAGCCACACAGTGATATTGATTTGCTGGTTACGGTGACCGTAAGGCTTGATGAAACAACGCGGCGAGCTTTGATCAACGACCTTTTGGAAACTTCGGCTTCCCCTGGAGAGAGCGAGATTCTCCGCGCTGTAGAAGTCACCATTGTTGTGCACGACGACATCATTCCGTGGCGTTATCCAGCTAAGCGCGAACTGCAATTTGGAGAATGGCAGCGCAATGACATTCTTGCAGGTATCTTCGAGCCAGCCACGATCGACATTGATCTAGCTATCCTGCTTACAAAAGCAAGAGAACATAGCGTTGCCTTGGTAGGTCCGGCAGCGGAGGAATTCTTTGACCCGGTTCCTGAACAGGATCTATTCGAGGCGCTGAGGGAAACCTTGAAGCTATGGAACTCGCAGCCCGACTGGGCCGGCGATGAGCGAAATGTAGTGCTTACGTTGTCCCGCATTTGGTACAGCGCAATAACCGGCAAAATCGCGCCGAAGGATGTCGCTGCCGACTGGGCAATAAAACGCCTACCTGCCCAGTATCAGCCCGTCTTACTTGAAGCTAAGCAAGCTTATCTGGGACAAAAAGAAGATCACTTGGCCTCACGCGCAGATCACTTGGAAGAATTTATTCGCTTTGTGAAAGGCGAGATCATCAAGTCAGTTGGTAAATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39526","NCBI_taxonomy_name":"Aeromonas media","NCBI_taxonomy_id":"651"}}}},"ARO_accession":"3002617","ARO_id":"39017","ARO_name":"aadA17","CARD_short_name":"aadA17","ARO_description":"aadA17 is an integron-encoded aminoglycoside nucleotidyltransferase gene in Aeromonas media.","ARO_category":{"41439":{"category_aro_accession":"3004275","category_aro_cvterm_id":"41439","category_aro_name":"ANT(3'')","category_aro_description":"A category of aminoglycoside O-nucleotidyltransferase enzymes with modification regiospecificity based at the 3''-hydroxyl group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics by transfer of an AMP group from an ATP substrate to the 3''-hydroxyl group of the compound.","category_aro_class_name":"AMR Gene Family"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"503":{"model_id":"503","model_name":"CTX-M-69","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1353":{"protein_sequence":{"accession":"ABY91281.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAVAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPNAESRRDVLASAAKIVTNGL"},"dna_sequence":{"accession":"EU402393.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGTGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAACGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCAACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001930","ARO_id":"38330","ARO_name":"CTX-M-69","CARD_short_name":"CTX-M-69","ARO_description":"CTX-M-69 is a beta-lactamase found in Escherichia coli.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"504":{"model_id":"504","model_name":"TEM-52","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1802":{"protein_sequence":{"accession":"CAA73933.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVKYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTTPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGASERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"Y13612.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTAAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGACGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCAGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3000921","ARO_id":"37301","ARO_name":"TEM-52","CARD_short_name":"TEM-52","ARO_description":"TEM-52 is an extended-spectrum beta-lactamase found in Klebsiella pneumoniae and Salmonella enterica.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"506":{"model_id":"506","model_name":"IMP-5","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1191":{"protein_sequence":{"accession":"AAK27847.1","sequence":"MSKLFVFFMFLFCSITAAAESLPDLKIEKLDEGVYVHTSFEEVNGWGVVPKHGLVVLVNTEAYLIDTPFTAKDTEKLVTWFVERGYKIKGSISSHFHSDSTGGIEWLNSQSIPTYASELTNELLKKDGKVQAKNSFSGASYWLVKKKIEVFYPGPGHTPDNVVVWLPENRVLFGGCFVKPYGLGNLGDANVEAWPKSAKLLMSKYGKAKLVVPSHSEVGDASLLKRTLEQAVKGLNESKKPSKPSN"},"dna_sequence":{"accession":"AF290912.1","fmin":"0","fmax":"741","strand":"+","sequence":"ATGAGCAAGTTATTTGTATTCTTTATGTTTTTGTTTTGTAGCATTACTGCCGCAGCAGAGTCTTTGCCAGATTTAAAAATTGAGAAGCTTGACGAAGGCGTTTATGTTCATACTTCGTTTGAAGAAGTTAACGGTTGGGGTGTTGTTCCTAAACACGGCTTGGTGGTTCTTGTAAATACTGAGGCCTATCTGATTGACACTCCATTTACGGCTAAAGATACTGAAAAGTTAGTCACTTGGTTTGTGGAACGCGGCTATAAAATAAAAGGCAGTATTTCCTCTCATTTTCATAGCGACAGCACGGGCGGAATAGAGTGGCTTAATTCTCAATCTATCCCCACGTATGCATCTGAATTAACAAATGAACTTCTTAAAAAAGACGGTAAAGTACAAGCTAAAAATTCATTTAGCGGAGCTAGCTATTGGCTAGTTAAGAAAAAGATTGAAGTTTTTTATCCTGGTCCAGGGCACACTCCAGATAACGTAGTGGTTTGGCTACCTGAAAATAGAGTTTTGTTCGGTGGTTGTTTTGTTAAACCGTACGGTCTAGGTAATTTGGGTGACGCAAATGTAGAAGCTTGGCCAAAGTCCGCCAAATTATTAATGTCCAAATATGGTAAGGCAAAACTGGTAGTTCCAAGTCACAGTGAAGTTGGAGACGCATCACTCTTGAAACGTACGTTAGAACAGGCGGTTAAAGGGTTAAACGAAAGTAAAAAACCATCAAAACCAAGTAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3002196","ARO_id":"38596","ARO_name":"IMP-5","CARD_short_name":"IMP-5","ARO_description":"IMP-5 is a beta-lactamase found in Acinetobacter baumannii.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"507":{"model_id":"507","model_name":"rosB","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1080"}},"model_sequences":{"sequence":{"4555":{"protein_sequence":{"accession":"AAC60780.1","sequence":"MHHSTPLITTIVGGLVLAFLLGSLAHRLRSSPLVGYLAAGVLAGPFTPGFVADTSLAPELAEIGVILLMFGVGLHFSLKDLLAVKAIAIPGAVAQIAVATLLGMGLSHLLGWDLMTGFVFGLCLSTASTVVLLRALEERQLIDSQRGQIAIGRSIVEDLAMVLTLVLLPAFAGVMGNETTSLSQLFTELAITIGKVIAFITLMIVVGRRLVPWILAKTASTGSRELFTLAVLVLALGIAYGAVGLFDVSFALGAFFAGMVLNESELSHRAAQDTLPLRDAFAVLFFVSVGMLFDPMILLREPLAVLASLAIIIFGKSAAAFILVRMFGHSNVYSTHHFCPWRKSVNLPFILAGLGISLGLMSEHGRNLVLAGAILSIMLNPLLFTLLDRYLAKNETMEDLILEEAVEEEKQIPGRFVQSCTVSRLWSGGSLLGAKLHAEGIPLVVIENSRPRVEALREQGINAVLGNAASADIMSLARLDCALVIILTIPNGYEAGEIVASARIKRPDLEIIARAHYDDEVVYISVRGANQVVMGEREIANSMLNMLKIETLTEEDKRPLCPI"},"dna_sequence":{"accession":"U46859.1","fmin":"22365","fmax":"24057","strand":"-","sequence":"ATGCACCACTCAACACCCTTAATTACCACGATCGTCGGAGGCCTTGTTCTCGCCTTCCTCTTGGGCTCCTTGGCTCACCGCCTGCGCTCATCACCACTGGTGGGGTACCTTGCCGCAGGGGTGCTGGCCGGGCCATTTACGCCAGGTTTCGTTGCTGATACCTCATTAGCACCAGAACTGGCTGAAATTGGTGTTATCTTGTTGATGTTTGGTGTCGGACTTCACTTCTCACTTAAAGACCTCCTCGCAGTAAAAGCCATCGCCATACCCGGTGCTGTGGCACAAATTGCCGTTGCCACCTTACTCGGAATGGGACTGTCTCATTTATTAGGCTGGGATTTGATGACAGGTTTTGTCTTCGGTCTTTGTCTATCAACAGCAAGTACCGTGGTATTACTACGAGCTCTAGAAGAACGGCAACTCATAGATAGCCAGCGGGGGCAAATTGCTATCGGTCGGTCGATTGTCGAAGATTTGGCGATGGTACTCACATTGGTGCTATTACCAGCCTTTGCCGGCGTGATGGGTAACGAAACCACCAGTCTCAGCCAGTTATTCACTGAACTAGCAATAACCATCGGTAAAGTCATTGCCTTCATTACGCTGATGATTGTTGTCGGTCGTCGTTTGGTCCCCTGGATACTGGCTAAAACCGCCAGTACCGGTTCCCGTGAGCTATTTACCTTGGCAGTGCTGGTATTAGCGCTTGGTATTGCTTACGGCGCTGTAGGGCTGTTCGACGTATCCTTTGCTCTCGGTGCATTCTTCGCAGGAATGGTATTGAATGAATCAGAGCTCAGCCACCGTGCGGCGCAAGATACCTTACCGCTACGTGATGCATTTGCCGTACTGTTCTTCGTTTCAGTTGGGATGTTGTTCGACCCAATGATTTTGCTACGTGAACCATTAGCTGTACTGGCTTCACTAGCTATCATTATCTTCGGCAAATCAGCAGCAGCGTTTATATTAGTGCGGATGTTTGGTCACTCAAACGTGTACAGCACTCACCATTTCTGTCCCTGGCGCAAATCGGTGAATTTGCCCTTTATTCTCGCCGGGCTTGGAATTTCTCTCGGTTTAATGTCTGAGCATGGCCGTAATCTGGTGCTGGCGGGCGCAATTTTATCAATTATGCTCAACCCGCTACTGTTTACATTATTAGATCGCTATTTGGCTAAAAACGAGACGATGGAAGATCTGATTCTGGAAGAGGCAGTCGAAGAGGAAAAGCAGATACCCGGTAGATTTGTGCAATCATGCACTGTTAGTCGGTTATGGTCGGGTGGGAGTTTATTAGGTGCAAAACTGCACGCGGAAGGTATTCCATTAGTGGTCATTGAGAACTCTCGACCAAGAGTTGAGGCGCTACGTGAACAAGGCATTAATGCGGTATTAGGCAATGCTGCAAGTGCAGATATTATGTCGCTGGCTCGTTTGGATTGTGCCCTGGTTATTATACTGACCATACCGAATGGCTACGAAGCTGGGGAAATTGTCGCCTCCGCCAGAATTAAACGGCCAGACCTTGAGATAATTGCTCGCGCGCATTATGACGACGAAGTGGTTTATATCTCGGTACGTGGCGCGAACCAGGTTGTGATGGGCGAACGTGAAATTGCCAACAGTATGCTTAATATGTTGAAGATAGAAACGCTGACCGAAGAAGACAAACGCCCGCTTTGCCCAATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39589","NCBI_taxonomy_name":"Yersinia enterocolitica (type O:8)","NCBI_taxonomy_id":"34054"}}}},"ARO_accession":"3003049","ARO_id":"39483","ARO_name":"rosB","CARD_short_name":"rosB","ARO_description":"rosB is part of an efflux pump\/potassium antiporter system (RosAB) in Yersinia that confers resistance to cationic antimicrobial peptides such as polymyxin B.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"36593":{"category_aro_accession":"3000454","category_aro_cvterm_id":"36593","category_aro_name":"polymyxin B","category_aro_description":"Polymyxin B is mixture of mostly polymyxins B1 and B2, mainly used for resistant gram-negative infections. They are polypeptides with cationic detergent action on cell membranes.","category_aro_class_name":"Antibiotic"},"36969":{"category_aro_accession":"3000625","category_aro_cvterm_id":"36969","category_aro_name":"polymyxin B1","category_aro_description":"Polymyxin B1 is in the family of polymyxin lipopeptides with a 6-methyloctanoic acid acyl group. These antibiotics disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36970":{"category_aro_accession":"3000626","category_aro_cvterm_id":"36970","category_aro_name":"polymyxin B2","category_aro_description":"Polymyxin B2 is in the family of polymyxin lipopeptides with a 6-methylheptanoic acid acyl group. These antibiotics disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36971":{"category_aro_accession":"3000627","category_aro_cvterm_id":"36971","category_aro_name":"polymyxin B3","category_aro_description":"Polymyxin B3 is in the family of polymyxin lipopeptides with an octanoic acid acyl group. These antibiotics disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36972":{"category_aro_accession":"3000628","category_aro_cvterm_id":"36972","category_aro_name":"polymyxin B4","category_aro_description":"Polymyxin B4 is in the family of polymyxin lipopeptides with a heptanoic acid acyl group. These antibiotics disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"508":{"model_id":"508","model_name":"tetA(P)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"30":{"protein_sequence":{"accession":"AAA20116.1","sequence":"MVNKLSAYKTYLLFSAITAMCFSLVATVMMVYHIEIVHLNPLQLILVGTTLELACFIFEIPTAIVADVYSRKLSIVIGGVLTGVGFILEGSISSFVFVLVAQIVWGLGSTFISGSLEAWIAEEEKNKDLDEIYIKGAQAGQIGAFIGIVLSTVIANFSVRLPIIVSGVLFIILALFLWLYMPENNFKPSAPGDLNTFKKMVYTFKSGLKFVKSKSIIMILLAVTLFYGLSSEGYDRLSNAHFLQDTTLPKLGNLSSVTWFGIFGILGMILSFIVMHFMAKNLKNEDNRKNGKLLLCINILYISSMLIFALTRNFSLMLIAYLATNTFRIINKPIFSAWLNGHIDDNSRATVLSINGQMNSLGQILGGPIIGIIATNISVSIGIVCTSLLVTPVLVLYIVAMIIDKKVDDRVGGIDYEENN"},"dna_sequence":{"accession":"L20800.1","fmin":"1062","fmax":"2325","strand":"+","sequence":"ATGGTTAATAAACTTTCAGCATATAAAACTTATTTATTATTTTCAGCTATTACAGCAATGTGTTTTTCGTTAGTAGCTACAGTTATGATGGTGTATCACATTGAAATAGTTCATTTAAATCCACTTCAGCTTATACTTGTTGGAACTACTTTGGAATTAGCATGCTTTATATTTGAAATTCCTACAGCTATAGTTGCAGATGTGTATAGTCGTAAACTATCTATTGTTATTGGGGGAGTTTTAACAGGAGTGGGATTTATTTTAGAAGGTTCTATTTCTAGTTTTGTTTTCGTACTTGTAGCACAGATTGTATGGGGATTAGGGTCTACTTTTATCAGTGGCTCGCTTGAAGCTTGGATTGCGGAAGAAGAGAAGAATAAAGATTTAGATGAAATTTATATAAAGGGAGCACAAGCAGGGCAGATAGGAGCATTTATTGGAATAGTACTAAGCACTGTAATAGCTAATTTCTCTGTAAGGCTTCCTATTATAGTTAGTGGAGTTTTATTTATAATTCTTGCATTATTTTTATGGTTATATATGCCAGAAAATAATTTTAAACCATCTGCTCCTGGGGATTTAAATACATTCAAAAAGATGGTATATACATTTAAATCTGGTCTTAAATTTGTAAAAAGTAAATCTATAATTATGATTTTACTTGCAGTAACTTTATTTTATGGATTATCAAGTGAAGGTTATGATAGACTTTCTAATGCGCATTTTTTACAAGATACTACACTTCCTAAACTTGGAAACCTTAGTTCAGTGACTTGGTTTGGAATTTTTGGAATTTTAGGAATGATATTGAGCTTCATAGTAATGCATTTTATGGCAAAGAATCTTAAGAATGAGGATAATAGGAAAAATGGAAAACTATTATTATGCATAAATATACTTTATATATCGTCTATGTTGATATTTGCTCTTACAAGAAACTTTAGTTTAATGTTAATAGCTTATTTGGCAACAAATACCTTTAGAATTATAAATAAACCTATATTCAGTGCGTGGTTAAATGGGCATATAGATGATAATTCTAGAGCTACTGTGCTTTCTATAAATGGACAAATGAATTCCTTAGGTCAAATTTTAGGTGGACCGATTATAGGAATCATAGCTACAAATATTTCAGTAAGTATTGGTATAGTATGTACTTCGTTATTAGTAACACCGGTATTAGTGTTATATATTGTTGCTATGATAATTGATAAAAAGGTGGATGATAGAGTTGGAGGTATTGATTATGAAGAAAATAATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36812","NCBI_taxonomy_name":"Clostridium perfringens","NCBI_taxonomy_id":"1502"}}}},"ARO_accession":"3000180","ARO_id":"36319","ARO_name":"tetA(P)","CARD_short_name":"tetA(P)","ARO_description":"TetA(P) is a inner membrane tetracycline efflux protein found on the same operon as the ribosomal protection protein TetB(P). It is found in Clostridium, a Gram-positive bacterium.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"509":{"model_id":"509","model_name":"FOX-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"870":{"protein_sequence":{"accession":"CAA54602.1","sequence":"MQQRRAFALLTLGSLLLAPCTYARGEAPLTAAVDGIIQPMLKEYRIPGMAVAVLKDGKAHYFNYGVANRESGQRVSEQTLFEIGSVSKTLTATLGAYAAVKGGFELDDKVSQHAPWLKGSAFDGVTMAELATYSAGGLPLQFPDEVDSNDKMRTYYRHWSPVYPAGTHRQYSNPSIGLFGHLAANSLGQPFEQLMSQTLLPKLGLHHTYIQVPESAIANYAYGYSKEDKPVRVTPGVLAAEAYGIKTGSADLLKFTEANMGYQGDAALKTRIALTHTGFYSVGDMTQGLGWESYAYPLTEQALLAGNSPAVSFQANPVTRFAVPKAMGEQRLYNKTGSTGGFGAYVAFVPARGIAIVMLANRNYPIEARVKAAHAILSQLAE"},"dna_sequence":{"accession":"X77455.1","fmin":"700","fmax":"1849","strand":"+","sequence":"ATGCAACAACGACGTGCGTTCGCGCTACTGACGCTGGGTAGCCTGCTGCTAGCCCCTTGTACTTATGCCCGCGGGGAGGCTCCGCTGACCGCCGCTGTGGACGGCATTATCCAGCCGATGCTCAAGGAGTATCGGATCCCGGGGATGGCGGTCGCCGTGCTGAAAGATGGCAAGGCCCACTATTTCAACTATGGGGTTGCCAACCGCGAGAGTGGTCAGCGCGTCAGCGAGCAGACCCTGTTCGAGATTGGCTCGGTCAGCAAGACCCTGACCGCGACCCTCGGTGCCTATGCTGCGGTCAAGGGGGGCTTTGAGCTGGATGACAAGGTGAGCCAGCACGCCCCCTGGCTCAAAGGTTCCGCCTTTGATGGTGTGACCATGGCCGAGCTTGCCACCTACAGTGCGGGTGGTTTGCCGCTGCAGTTCCCCGATGAGGTGGATTCGAATGACAAGATGCGCACTTACTATCGGCACTGGTCACCGGTTTATCCGGCGGGGACCCATCGCCAGTATTCCAACCCCAGCATAGGCCTGTTTGGTCACCTGGCCGCAAATAGTCTGGGCCAGCCATTTGAGCAACTGATGAGCCAGACCCTGCTGCCCAAGCTGGGTTTGCACCACACCTATATTCAGGTGCCGGAGTCGGCCATAGCGAACTATGCCTACGGCTATTCGAAGGAAGATAAGCCCGTCCGGGTCACTCCGGGCGTGCTGGCGGCCGAGGCTTACGGGATCAAGACCGGCTCGGCGGATCTGCTGAAGTTTACCGAGGCCAACATGGGGTATCAGGGAGATGCCGCGCTAAAAACGCGGATCGCGCTGACCCATACCGGTTTCTACTCGGTGGGAGACATGACTCAGGGGCTGGGTTGGGAGAGCTACGCCTATCCGTTGACCGAGCAGGCGCTGCTGGCGGGCAACTCCCCGGCGGTGAGCTTCCAGGCCAATCCGGTTACGCGCTTTGCGGTGCCCAAAGCGATGGGCGAGCAGCGGCTCTATAACAAGACGGGCTCGACTGGCGGCTTTGGCGCCTATGTGGCGTTCGTGCCCGCCAGAGGGATCGCCATCGTCATGCTGGCCAATCGCAACTATCCCATCGAGGCCAGGGTGAAGGCGGCTCACGCCATCCTGAGTCAGTTGGCCGAGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002155","ARO_id":"38555","ARO_name":"FOX-1","CARD_short_name":"FOX-1","ARO_description":"FOX-1 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36206":{"category_aro_accession":"3000067","category_aro_cvterm_id":"36206","category_aro_name":"FOX beta-lactamase","category_aro_description":"FOX beta-lactamases are plasmid-encoded AmpC-type beta-lactamase which conferred resistance to broad-spectrum cephalosporins and cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"510":{"model_id":"510","model_name":"CTX-M-9","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1706":{"protein_sequence":{"accession":"AAF05311.2","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTAGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"AF174129.1","fmin":"6335","fmax":"7211","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAGCTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCACAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGCAGGTGATAAGACCGGCAGCGGCGACTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001872","ARO_id":"38272","ARO_name":"CTX-M-9","CARD_short_name":"CTX-M-9","ARO_description":"CTX-M-9 is a beta-lactamase found in the Enterobacteriaceae family.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"511":{"model_id":"511","model_name":"dfrA3","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"69":{"protein_sequence":{"accession":"AAA25550.1","sequence":"MLISLIAALAHNNLIGKDNLIPWHLPADLRHFKAVTLGKPVVMGRRTFESIGRPLPGRRNVVVSRNPQWQAEGVEVAPSLDAALALLTDCEEAMIIGGGQLYAEALPRADRLYLTYIDAQLNGDTHFPDYLSLGWQELERSTHPADDKNSYACEFVTLSRQR"},"dna_sequence":{"accession":"J03306.1","fmin":"0","fmax":"489","strand":"+","sequence":"ATGTTGATTTCTTTGATTGCAGCTTTGGCTCATAACAACTTGATTGGCAAAGATAATCTTATTCCATGGCATCTACCTGCCGATCTGCGTCATTTCAAAGCTGTCACCCTGGGGAAACCTGTGGTGATGGGACGTCGCACCTTTGAGTCGATCGGGCGGCCATTGCCAGGACGGCGCAATGTTGTCGTTAGTCGCAATCCCCAATGGCAGGCCGAAGGGGTGGAGGTGGCTCCCTCGCTGGATGCGGCTCTGGCGCTATTAACCGACTGTGAGGAAGCGATGATCATCGGTGGCGGGCAACTCTATGCCGAGGCTCTGCCCCGAGCGGATCGCTTGTATCTAACCTACATTGACGCTCAGTTGAACGGTGATACCCATTTCCCGGATTACCTATCGCTTGGGTGGCAGGAGTTGGAGCGGTCAACGCATCCTGCTGACGATAAGAACAGCTATGCCTGCGAATTTGTTACCTTGAGTCGTCAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36820","NCBI_taxonomy_name":"Plasmid pAZ1","NCBI_taxonomy_id":"2525"}}}},"ARO_accession":"3003105","ARO_id":"39679","ARO_name":"dfrA3","CARD_short_name":"dfrA3","ARO_description":"dfrA3 is an integron-encoded dihydrofolate reductase found in Escherichia coli.","ARO_category":{"37617":{"category_aro_accession":"3001218","category_aro_cvterm_id":"37617","category_aro_name":"trimethoprim resistant dihydrofolate reductase dfr","category_aro_description":"Alternative dihydropteroate synthase dfr present on plasmids produces alternate proteins that are less sensitive to trimethoprim from inhibiting its role in folate synthesis, thus conferring trimethoprim resistance.","category_aro_class_name":"AMR Gene Family"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"512":{"model_id":"512","model_name":"CTX-M-82","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1088":{"protein_sequence":{"accession":"ABB59946.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFPMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"DQ256091.1","fmin":"98","fmax":"974","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTCCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001943","ARO_id":"38343","ARO_name":"CTX-M-82","CARD_short_name":"CTX-M-82","ARO_description":"CTX-M-82 is a beta-lactamase found in the Enterobacteriaceae family.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"513":{"model_id":"513","model_name":"CARB-19","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1019":{"protein_sequence":{"accession":"AIL92328.1","sequence":"MKKLFLLAGLMVCSTVSYASKLNEDISLIEKQTSGRIGVSVWDTQTDERWDYRGDERFPLMSTFKTLACATMLSDMDSGKLNKNATAKIDERNIVVWSPVMDKLAGQSTRIEHACEAAMLMSDNTAANLVLNEIGGPKAVTLFLRSIGDKATRLDRLEPRLNEAKPGDKRDTTTPNAMVNTLHTLMEDNALSYESRTQLKIWMQDNKVSDSLMRSVLPKGWSIADRSGAGNYGSRGISAMIWKDNYKPVYISIYVTDTDLSLQARDQLIAQISQLILEHYKES"},"dna_sequence":{"accession":"KJ934267.1","fmin":"0","fmax":"852","strand":"+","sequence":"ATGAAAAAGTTATTCCTGTTGGCTGGGCTGATGGTTTGCTCAACTGTTAGTTACGCCTCCAAATTAAACGAAGACATATCCCTCATCGAGAAACAAACATCTGGGCGAATTGGAGTGTCAGTCTGGGATACACAAACGGACGAGCGTTGGGATTATCGCGGAGACGAACGTTTCCCATTAATGAGCACATTCAAAACGTTAGCGTGTGCCACCATGCTAAGCGATATGGACAGCGGCAAACTCAACAAAAATGCTACAGCGAAAATCGATGAACGCAATATTGTGGTTTGGTCTCCGGTGATGGATAAACTGGCTGGACAAAGCACACGTATCGAACACGCTTGTGAGGCCGCCATGTTGATGAGCGACAACACCGCCGCGAACTTAGTGCTAAATGAAATTGGTGGTCCTAAAGCGGTCACGCTGTTTTTGCGATCTATTGGCGACAAAGCAACGCGACTTGACCGATTGGAACCCCGTTTGAATGAAGCAAAACCGGGCGATAAGCGAGACACCACAACGCCTAACGCCATGGTAAACACCCTACATACCTTGATGGAAGATAACGCCCTATCTTACGAGTCACGCACACAGCTGAAAATCTGGATGCAAGATAACAAAGTATCGGATTCTCTCATGCGCTCCGTTCTACCAAAAGGCTGGTCGATTGCAGACCGCTCTGGCGCAGGTAACTACGGTTCACGCGGCATTAGCGCGATGATCTGGAAAGACAACTACAAGCCGGTTTACATCAGTATTTACGTCACAGACACCGACCTTTCGCTTCAAGCTCGCGATCAACTGATCGCGCAAATCAGCCAACTGATTTTAGAGCACTACAAAGAAAGTTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39615","NCBI_taxonomy_name":"Vibrio parahaemolyticus","NCBI_taxonomy_id":"670"}}}},"ARO_accession":"3003175","ARO_id":"39752","ARO_name":"CARB-19","CARD_short_name":"CARB-19","ARO_description":"CARB-19 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36230":{"category_aro_accession":"3000091","category_aro_cvterm_id":"36230","category_aro_name":"CARB beta-lactamase","category_aro_description":"CARB beta-lactamases are class A lactamases that can hydrolyze carbenicillin. Many of the PSE beta-lactamases have been renamed as CARB-lactamases with the notable exception of PSE-2 which is now OXA-10.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"514":{"model_id":"514","model_name":"LEN-10","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"5592":{"protein_sequence":{"accession":"CDA01504.1","sequence":"MRYVRLCVISLLATLPLAVDAGPQPLEQIKQSESQLSGRVGMVEMDLASGRTLAAWRADERFPMVSTFKVLLCGAVLARVDAGLEQLDRRIHYRQQDLVDYSPVSEKHLTDGMTIGELCAAAITLSDNSAGNLLLATVGGPAGLTAFLRQIGDNVTRLDRWETALNEALPGDARDTTTPASMAATLRKLLTAQHLSARSQQQLLQWMVDDRVAGPLIRAVLPPGWFIADKTGAGERGARGIVALLGPDGKPERIVVLYLRDTPASMAERNQHIAGIGAALIEHWQR"},"dna_sequence":{"accession":"CBBA010000184.1","fmin":"3395","fmax":"4256","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGTGTTATCTCCCTGTTAGCCACCCTGCCACTGGCGGTAGACGCCGGTCCACAGCCGCTTGAGCAGATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTGGGGATGGTGGAAATGGATCTGGCCAGCGGCCGCACGCTGGCGGCCTGGCGCGCCGATGAACGCTTTCCCATGGTGAGCACCTTTAAAGTGCTGCTGTGCGGCGCGGTGCTGGCGCGGGTGGATGCCGGGCTCGAACAACTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTACCGACGGGATGACGATCGGCGAACTCTGCGCCGCCGCCATCACCCTGAGCGATAACAGCGCTGGCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCGGGATTAACTGCCTTTCTGCGCCAGATCGGTGACAACGTCACCCGTCTTGACCGCTGGGAAACGGCACTGAATGAGGCGCTTCCCGGCGACGCGCGCGACACCACCACCCCGGCCAGCATGGCCGCCACGCTGCGCAAACTACTGACCGCGCAGCATCTGAGCGCCCGTTCGCAACAGCAACTCCTGCAGTGGATGGTGGACGATCGGGTTGCCGGCCCGCTGATCCGCGCCGTGCTGCCGCCGGGCTGGTTTATCGCCGACAAAACCGGGGCTGGCGAACGGGGTGCGCGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAACCGGAGCGCATTGTGGTGCTCTATCTGCGGGATACCCCGGCGAGTATGGCCGAGCGTAATCAACATATCGCCGGGATCGGCGCAGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42760","NCBI_taxonomy_name":"Klebsiella variicola CAG:634","NCBI_taxonomy_id":"1263083"}}}},"ARO_accession":"3002460","ARO_id":"38860","ARO_name":"LEN-10","CARD_short_name":"LEN-10","ARO_description":"LEN-10 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36236":{"category_aro_accession":"3000097","category_aro_cvterm_id":"36236","category_aro_name":"LEN beta-lactamase","category_aro_description":"LEN beta-lactamases are chromosomal class A beta-lactamases that confer resistance to ampicillin, amoxicillin, carbenicillin, and ticarcillin but not to extended-spectrum beta-lactams.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3665":{"model_id":"3665","model_name":"NDM-24","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"5938":{"protein_sequence":{"accession":"AWU66463.1","sequence":"MELPNIMHPVAKLSTALAAALMLSGCMPGEIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLLVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR"},"dna_sequence":{"accession":"MH450215.1","fmin":"0","fmax":"813","strand":"+","sequence":"ATGGAATTGCCCAATATTATGCACCCGGTCGCGAAGCTGAGCACCGCATTAGCCGCTGCATTGATGCTGAGCGGGTGCATGCCCGGTGAAATCCGCCCGACGATTGGCCAGCAAATGGAAACTGGCGACCAACGGTTTGGCGATCTGGTTTTCCGCCAGCTCGCACCGAATGTCTGGCAGCACACTTCCTATCTCGACATGCCGGGTTTCGGGGCAGTCGCTTCCAACGGTTTGATCGTCAGGGATGGCGGCCGCGTGCTGTTGGTCGATACCGCCTGGACCGATGACCAGACCGCCCAGATCCTCAACTGGATCAAGCAGGAGATCAACCTGCCGGTCGCGCTGGCGGTGGTGACTCACGCGCATCAGGACAAGATGGGCGGTATGGACGCGCTGCATGCGGCGGGGATTGCGACTTATGCCAATGCGTTGTCGAACCAGCTTGCCCCGCAAGAGGGGATGGTTGCGGCGCAACACAGCCTGACTTTCGCCGCCAATGGCTGGGTCGAACCAGCAACCGCGCCCAACTTTGGCCCGCTCAAGGTATTTTACCCCGGCCCCGGCCACACCAGTGACAATATCACCGTTGGGATCGACGGCACCGACATCGCTTTTGGTGGCTGCCTGATCAAGGACAGCAAGGCCAAGTCGCTCGGCAATCTCGGTGATGCCGACACTGAGCACTACGCCGCGTCAGCGCGCGCGTTTGGTGCGGCGTTCCCCAAGGCCAGCATGATCGTGATGAGCCATTCCGCCCCCGATAGCCGCGCCGCAATCACTCATACGGCCCGCATGGCCGACAAGCTGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36946","NCBI_taxonomy_name":"Providencia stuartii","NCBI_taxonomy_id":"588"}}}},"ARO_accession":"3004867","ARO_id":"43005","ARO_name":"NDM-24","CARD_short_name":"NDM-24","ARO_description":"A class B New Delhi metallo-beta-lactamase.","ARO_category":{"36196":{"category_aro_accession":"3000057","category_aro_cvterm_id":"36196","category_aro_name":"NDM beta-lactamase","category_aro_description":"NDM beta-lactamases or New Delhi metallo-beta-lactamases are class B beta-lactamases that confer resistance to a broad range of antibiotics including carbapenems, cephalosporins and penicillins.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"517":{"model_id":"517","model_name":"QnrD2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"33":{"protein_sequence":{"accession":"AHY03238.1","sequence":"MEKHFINEKFSRDQFTGNRVKNIAFSNCDFSGVDLTDTEFVDCSFYDRNSLEGCDFNRAKLKNASFKSCDLSMSNFKNISALGLEISECLAQGADFRGANFMNMITTRSWFCSAYITKTNLSYANFSRVILEKCELWENRWNGTVITGAVFRGSDLSCGEFSSFDWSLADFTGCDLTGGALGELDARRTNLDGVKLDGEQAFQLVESLGVIVHR"},"dna_sequence":{"accession":"KJ158441.1","fmin":"2732","fmax":"3377","strand":"+","sequence":"ATGGAAAAGCACTTTATCAATGAAAAGTTTTCACGAGATCAATTTACGGGGAATAGAGTTAAAAATATTGCCTTTTCAAATTGTGATTTTTCAGGGGTTGATTTAACTGATACTGAATTTGTTGATTGTAGTTTTTACGACAGGAATAGCTTGGAAGGGTGTGATTTTAATAGAGCCAAACTAAAAAACGCTAGCTTTAAAAGCTGCGATTTATCAATGAGTAATTTTAAAAACATTAGCGCCTTAGGTCTTGAGATTAGTGAGTGTTTAGCTCAAGGAGCTGATTTTCGAGGGGCTAATTTTATGAATATGATAACTACAAGGTCATGGTTTTGTAGTGCTTATATAACCAAGACAAATCTTAGTTACGCTAATTTTTCTAGAGTCATATTAGAAAAGTGCGAACTGTGGGAAAATCGCTGGAATGGCACTGTGATAACTGGCGCCGTGTTTCGTGGCTCCGATCTTTCTTGTGGGGAGTTTTCATCGTTTGATTGGTCTTTGGCTGATTTTACTGGTTGTGATTTAACGGGTGGGGCGCTTGGCGAGCTTGATGCAAGACGAACTAATTTAGATGGCGTGAAGTTGGATGGAGAACAGGCGTTTCAGCTTGTTGAGAGTTTAGGTGTTATTGTTCACCGATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35743","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Hadar","NCBI_taxonomy_id":"149385"}}}},"ARO_accession":"3002789","ARO_id":"39223","ARO_name":"QnrD2","CARD_short_name":"QnrD2","ARO_description":"QnrD2 is a plasmid-mediated quinolone resistance protein found in Salmonella enterica.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"519":{"model_id":"519","model_name":"VIM-26","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1963":{"protein_sequence":{"accession":"CBY80143.1","sequence":"MLKVISSLLVYMTASVMAVASPLAHSGEPSGEYPTVNEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEAEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSANVLYGGCAVLELSSTSAGNVADADLAEWPTSVERIQKHYPEAEVVIPGHGLPGGLDLLQHTANVVKAHKNRSVAE"},"dna_sequence":{"accession":"FR748153.1","fmin":"259","fmax":"1060","strand":"+","sequence":"ATGTTAAAAGTTATTAGTAGTTTATTGGTCTACATGACCGCGTCTGTCATGGCTGTCGCAAGTCCGTTAGCCCATTCCGGGGAGCCGAGTGGTGAGTATCCGACAGTCAACGAAATTCCGGTCGGAGAGGTCCGACTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCGGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAAAAGCAAATTGGACTTCCCGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGCAGAGGGGAACGAGATTCCCACGCATTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAGCTCTTCTATCCTGGTGCTGCGCATTCGACCGACAATCTGGTTGTATACGTCCCGTCAGCGAACGTGCTATACGGTGGTTGTGCCGTTCTTGAGTTGTCAAGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCGTTGAGCGGATTCAAAAACACTACCCGGAAGCAGAGGTCGTCATTCCCGGGCACGGTCTACCGGGCGGTCTAGACTTGCTCCAGCACACAGCGAACGTTGTCAAAGCACACAAAAATCGCTCAGTCGCCGAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002296","ARO_id":"38696","ARO_name":"VIM-26","CARD_short_name":"VIM-26","ARO_description":"VIM-26 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"521":{"model_id":"521","model_name":"OXA-386","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4559":{"protein_sequence":{"accession":"AHL30273.1","sequence":"MKIKALLLITSAIFISACSPYIVSANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"KF986254.1","fmin":"34","fmax":"859","strand":"-","sequence":"ATGAAGATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGTCTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACTACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTAGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001572","ARO_id":"37972","ARO_name":"OXA-386","CARD_short_name":"OXA-386","ARO_description":"OXA-386 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"523":{"model_id":"523","model_name":"OXA-75","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"5352":{"protein_sequence":{"accession":"CAP01453.1","sequence":"MNIQALLLITSAIFISACSPYIVTANPNYSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRIGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGISSSVRKEITYRGLEQLGIL"},"dna_sequence":{"accession":"CU468230.2","fmin":"1959577","fmax":"1960402","strand":"+","sequence":"ATGAACATTCAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATTACAGTGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATAGGCCTTGAGCACCATAAGGCAACCACTACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTATTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAACAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATATCTAGCTCTGTTCGAAAAGAGATTACTTATAGAGGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35534","NCBI_taxonomy_name":"Acinetobacter baumannii SDF","NCBI_taxonomy_id":"509170"}}}},"ARO_accession":"3001620","ARO_id":"38020","ARO_name":"OXA-75","CARD_short_name":"OXA-75","ARO_description":"OXA-75 is a beta-lactamase found in A. baumannii.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"524":{"model_id":"524","model_name":"dfrA25","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"49":{"protein_sequence":{"accession":"ABB71176.1","sequence":"MAARAKNGVIGCGPDIPWSAKGEQLLFKALTYNQWLLVGRKTFESMGPLPNRKYAVVTRSNWTAANENVVVFPSIDEAMGRLGEITDHVIVAGGGEIYHETIPMASTLHVSTIDVEPEGDVFFPNIPGKFDVVFEQQFTSNINYCYQIWQKG"},"dna_sequence":{"accession":"DQ267940.1","fmin":"53","fmax":"512","strand":"+","sequence":"ATGGCTGCAAGAGCGAAAAATGGCGTAATCGGTTGCGGTCCTGACATTCCTTGGTCTGCCAAAGGGGAACAGCTTCTTTTCAAAGCACTGACCTATAACCAATGGCTTTTGGTAGGGCGCAAAACATTTGAGTCTATGGGGCCGCTGCCCAATAGGAAATACGCGGTTGTTACCCGCTCAAACTGGACAGCGGCTAATGAAAACGTAGTGGTTTTCCCGTCGATTGACGAAGCGATGGGTAGATTAGGCGAGATCACTGACCATGTCATCGTCGCCGGTGGTGGAGAAATCTACCATGAAACGATACCCATGGCCTCTACTCTGCATGTGTCGACAATCGACGTTGAGCCAGAGGGAGACGTTTTCTTTCCGAACATTCCTGGGAAGTTTGATGTCGTTTTTGAGCAACAATTTACATCAAACATTAACTATTGCTATCAAATCTGGCAAAAGGGTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35709","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Agona","NCBI_taxonomy_id":"58095"}}}},"ARO_accession":"3003020","ARO_id":"39454","ARO_name":"dfrA25","CARD_short_name":"dfrA25","ARO_description":"dfrA25 is an integron-encoded dihydrofolate reductase found in Salmonella agona.","ARO_category":{"37617":{"category_aro_accession":"3001218","category_aro_cvterm_id":"37617","category_aro_name":"trimethoprim resistant dihydrofolate reductase dfr","category_aro_description":"Alternative dihydropteroate synthase dfr present on plasmids produces alternate proteins that are less sensitive to trimethoprim from inhibiting its role in folate synthesis, thus conferring trimethoprim resistance.","category_aro_class_name":"AMR Gene Family"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"525":{"model_id":"525","model_name":"CMY-13","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"8156":{"protein_sequence":{"accession":"AAQ16660.2","sequence":"MMKKSLCCALLLTASFSTFASAKTEQQIADIVNRTITPLMQEQAIPGMAVAIIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGISLLHLATYTAGGLPLQIPDDVTDKAALLRFYQNWQPQWAPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSNVTDMARWVQVNMDASRVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"AY339625.2","fmin":"3640","fmax":"4786","strand":"-","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACGTTTGCCTCCGCCAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCATTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCAGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTACTGATAAAGCCGCATTACTGCGTTTTTATCAAAACTGGCAGCCGCAATGGGCCCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACAGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAACCTGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAACGTTACCGATATGGCACGCTGGGTTCAGGTCAACATGGACGCCAGCCGCGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGTAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCGGCAGTGAAAGCCTCATGGGTGCATAAAACGGGATCCACTGGAGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002024","ARO_id":"38424","ARO_name":"CMY-13","CARD_short_name":"CMY-13","ARO_description":"CMY-13 is a beta-lactamase found in Escherichia coli.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"526":{"model_id":"526","model_name":"ACT-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1812":{"protein_sequence":{"accession":"CAJ28994.1","sequence":"MMMTKSLCCALLLSTSCSVLATPMSEKQLAEVVERTVTPLMKAQAIPGMAVAVIYEGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMSYEQAITTRVFKPLKLDHTWINVPKAEEAHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVQDMASWVMVNMKPDSLQDNSLRKGLTLAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVEGSDNKVALAPLPAREVNPPAPPVNASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILSAL"},"dna_sequence":{"accession":"AM076977.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGATGACTAAATCCCTTTGCTGCGCCCTGCTGCTCAGCACCTCCTGCTCGGTATTGGCTACCCCGATGTCAGAAAAACAGCTGGCTGAGGTGGTGGAACGGACCGTTACGCCGCTGATGAAAGCGCAGGCCATTCCGGGTATGGCGGTGGCGGTGATTTATGAGGGTCAGCCGCACTACTTCACCTTCGGTAAAGCCGATGTTGCGGCGAACAAACCTGTCACTCCACAAACCTTGTTCGAACTGGGTTCTATAAGTAAAACCTTCACCGGCGTACTCGGTGGCGATGCCATTGCTCGCGGTGAAATATCGCTGGGCGATCCGGTGACAAAATACTGGCCTGAGCTGACAGGCAAGCAGTGGCAGGGGATCCGCATGCTGGATCTGGCAACCTATACCGCAGGAGGTTTGCCGTTACAGGTACCGGATGAGGTCACGGATAACGCCTCTCTGTTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCGGGCACCACGCGTCTTTACGCCAATGCCAGCATCGGTCTTTTTGGCGCGCTGGCGGTCAAACCTTCCGGCATGAGCTATGAGCAGGCCATAACGACGCGGGTCTTTAAGCCGCTCAAGCTGGACCATACGTGGATTAACGTTCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGATACCGCGACGGTAAAGCGGTACACGTTTCGCCAGGAATGCTGGACGCTGAAGCCTATGGCGTAAAAACCAACGTGCAGGATATGGCAAGCTGGGTGATGGTCAACATGAAGCCGGACTCCCTTCAGGATAATTCACTCAGGAAAGGCCTTACCCTGGCGCAGTCTCGCTACTGGCGCGTGGGGGCCATGTATCAGGGGTTAGGCTGGGAAATGCTTAACTGGCCGGTCGATGCCAAAACCGTGGTTGAAGGTAGCGACAATAAGGTGGCACTGGCACCGCTGCCTGCGAGAGAAGTGAATCCACCGGCGCCCCCGGTCAACGCATCCTGGGTCCATAAAACAGGCTCTACCGGCGGGTTTGGCAGCTACGTGGCATTTATTCCTGAAAAGCAGCTCGGTATTGTGATGCTGGCAAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCGTATTTTGAGCGCGCTGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36926","NCBI_taxonomy_name":"Enterobacter asburiae","NCBI_taxonomy_id":"61645"}}}},"ARO_accession":"3001822","ARO_id":"38222","ARO_name":"ACT-2","CARD_short_name":"ACT-2","ARO_description":"ACT-2 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"527":{"model_id":"527","model_name":"SHV-38","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1561":{"protein_sequence":{"accession":"AAL79576.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPVGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AY079099.1","fmin":"148","fmax":"1009","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGTAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGGATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001096","ARO_id":"37476","ARO_name":"SHV-38","CARD_short_name":"SHV-38","ARO_description":"SHV-38 is an extended-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"528":{"model_id":"528","model_name":"OCH-8","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1979":{"protein_sequence":{"accession":"ABF50909.1","sequence":"MRKSTTLLIGFLTTAAIIPNNGALATSKANDGDLRRIVDETVRPLMAEQKIPGMAVAITIDGKSHFFGYGVASKESGQKVTEDTIFEIGSVSKTFTAMLGGYGLATGAFSLSDPATKWAPELAGSSFDKITMLDLGTYTPGGLPLQFPDAVTDDSSMLAYFKKWKPDYPAGTQRRYSNPSIGLFGYLAARSMDKPFDVLMEQKLLPAFGLKNTFINVPESQMKNYAYGYSKANKPIRVSGGALDAQAYGIKTTALDLARFVELNIDSSSLEPDFQKAVAATHTGYYHVGANNQGLGWEFYNYPTALKTLLAGNSSDMALKSHKIEKFDTPRQPSADVLINKTGSTNGFGAYAAFIPAKKIGIVLLANRNYPIDERVKAAYRILQALDNKQ"},"dna_sequence":{"accession":"DQ489307.1","fmin":"1070","fmax":"2243","strand":"+","sequence":"ATGAGAAAATCTACGACACTTTTGATCGGTTTCCTCACCACTGCCGCTATTATCCCGAATAATGGCGCGCTGGCTACGAGCAAGGCGAATGATGGCGACTTGCGCCGTATTGTCGATGAAACGGTGCGCCCGCTCATGGCCGAGCAGAAAATCCCCGGCATGGCGGTTGCCATAACCATCGACGGCAAGAGCCACTTCTTCGGTTATGGTGTGGCATCGAAAGAAAGCGGGCAAAAAGTCACTGAAGACACGATTTTCGAGATCGGTTCGGTCAGCAAGACCTTCACTGCAATGCTTGGCGGTTACGGGCTGGCGACAGGCGCGTTCTCCCTGTCCGATCCCGCGACCAAATGGGCTCCTGAACTGGCAGGCAGCAGCTTCGACAAGATCACCATGCTTGATCTTGGGACCTACACGCCGGGCGGATTGCCCCTCCAGTTTCCCGATGCTGTCACCGATGACAGTTCGATGCTGGCATATTTCAAGAAATGGAAACCCGATTATCCGGCAGGGACGCAGCGTCGTTATTCGAATCCCAGCATCGGCCTGTTCGGCTATCTGGCGGCACGAAGCATGGACAAGCCGTTCGACGTTTTGATGGAGCAAAAGCTTCTGCCTGCATTCGGCCTGAAGAACACCTTCATCAATGTGCCGGAAAGCCAGATGAAGAACTACGCCTACGGCTATTCCAAAGCCAACAAGCCGATCCGGGTATCGGGCGGGGCGCTGGATGCACAAGCCTATGGCATCAAGACCACCGCGCTTGATCTTGCCCGCTTCGTCGAACTGAACATCGACAGCTCATCTCTGGAGCCTGATTTCCAGAAAGCCGTCGCCGCAACGCATACCGGTTACTACCATGTCGGAGCGAACAATCAGGGACTTGGCTGGGAGTTCTACAACTATCCGACTGCGCTCAAGACACTTCTTGCCGGCAATTCGTCGGACATGGCGCTGAAGTCGCACAAAATCGAGAAATTCGATACACCTCGCCAACCGTCAGCTGATGTGCTGATCAATAAGACAGGCTCAACCAACGGCTTTGGCGCTTATGCGGCCTTTATTCCTGCGAAGAAGATCGGAATTGTTCTGCTTGCCAACCGGAATTATCCGATCGATGAGCGCGTAAAGGCTGCCTATCGGATATTGCAGGCGCTCGACAACAAGCAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37077","NCBI_taxonomy_name":"Brucella anthropi","NCBI_taxonomy_id":"529"}}}},"ARO_accession":"3002521","ARO_id":"38921","ARO_name":"OCH-8","CARD_short_name":"OCH-8","ARO_description":"OCH-8 beta-lactamase is an Ambler class C chromosomal-encoded beta-lactamases in Brucella anthropi.","ARO_category":{"36233":{"category_aro_accession":"3000094","category_aro_cvterm_id":"36233","category_aro_name":"OCH beta-lactamase","category_aro_description":"OCH beta-lactamases are Ambler class C chromosomal-encoded beta-lactamases in Brucella anthropi.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"529":{"model_id":"529","model_name":"SHV-185","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"2023":{"protein_sequence":{"accession":"AIS67768.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVMIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"KM233164.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGATGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3003152","ARO_id":"39729","ARO_name":"SHV-185","CARD_short_name":"SHV-185","ARO_description":"SHV-185 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"530":{"model_id":"530","model_name":"VIM-11","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"8189":{"protein_sequence":{"accession":"AAT36613.1","sequence":"MFKLLSKLLVYLTASIMAIASPLAFSVDSSGEYPTVSEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEVEGSEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSASVLYGGCAIYELSRTSAGNVADADLAEWPTSIERIQQHYPEAQFVIPGHGLPGGLDLLKHTTNVVKAHTNRSVVE"},"dna_sequence":{"accession":"AY605049.2","fmin":"127","fmax":"928","strand":"+","sequence":"ATGTTCAAACTTTTGAGTAAGTTATTGGTCTATTTGACCGCGTCTATCATGGCTATTGCGAGTCCGCTCGCTTTTTCCGTAGATTCTAGCGGTGAGTATCCGACAGTCAGCGAAATTCCGGTCGGGGAGGTCCGGCTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCAGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAGAAGCAAATTGGACTTCCTGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGTAGAGGGGAGCGAGATTCCCACGCACTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAACTCTTCTATCCTGGTGCTGCGCATTCGACCGACAACTTAGTTGTGTACGTCCCGTCTGCGAGTGTGCTCTATGGTGGTTGTGCGATTTATGAGTTGTCACGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCATTGAGCGGATTCAACAACACTACCCGGAAGCACAGTTCGTCATTCCGGGGCACGGCCTGCCGGGCGGTCTAGACTTGCTCAAGCACACAACGAATGTTGTAAAAGCGCACACAAATCGCTCAGTCGTTGAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002281","ARO_id":"38681","ARO_name":"VIM-11","CARD_short_name":"VIM-11","ARO_description":"VIM-11 is a beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"532":{"model_id":"532","model_name":"CTX-M-47","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"825":{"protein_sequence":{"accession":"AAV97952.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGRRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"AY847143.1","fmin":"82","fmax":"958","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAAGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGACTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001909","ARO_id":"38309","ARO_name":"CTX-M-47","CARD_short_name":"CTX-M-47","ARO_description":"CTX-M-47 is a beta-lactamase found in the Enterobacteriaceae family.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"533":{"model_id":"533","model_name":"CARB-16","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4562":{"protein_sequence":{"accession":"CCW43444.1","sequence":"MDVRKHKASFFSVVITFLCLTLSLNANATDSVLEAVTNAETELGARIGLAVHDLETGKRWEHKSNERFPLSSTFKTLACANVLQRVDLGKERIDRVVRFSESNLVTYSPVTEKHVGKKGMSLAELCQATLSTSDNSAANFILQAIGGPKALTKFLRSIGDDTTRLDRWETELNEAVPGDKRDTTTPIAMVTTLEKLLIDETLSIKSRQQLESWLKGNEVGDALFRKGVPSDWIVADRTGAGGYGSRAITAVMWPPNRKPIVAALYITETDASFEERNAVIAKIGEQIAKTVLMENSRN"},"dna_sequence":{"accession":"HF953351.1","fmin":"2461","fmax":"3358","strand":"-","sequence":"ATGGACGTACGTAAACACAAGGCTAGTTTTTTTAGCGTAGTAATTACTTTTTTATGTCTCACGCTATCATTAAATGCTAATGCAACAGACTCAGTACTTGAAGCGGTTACCAATGCTGAAACTGAATTAGGCGCTAGAATTGGTCTAGCTGTGCATGATTTGGAAACGGGAAAACGTTGGGAACATAAATCTAATGAACGTTTTCCTCTAAGTAGCACCTTTAAAACACTTGCCTGTGCAAACGTTCTTCAAAGAGTTGATCTAGGTAAAGAAAGAATTGATAGAGTTGTGAGATTCTCTGAAAGCAATCTCGTTACATACTCACCTGTAACAGAAAAACATGTGGGTAAAAAAGGGATGTCGCTCGCAGAGCTGTGTCAGGCCACATTATCAACCAGTGATAATTCAGCTGCCAATTTTATTCTACAAGCGATTGGTGGACCTAAGGCTCTAACGAAATTTTTGCGTTCCATTGGCGACGATACTACGCGCCTTGATCGCTGGGAAACAGAACTTAACGAAGCGGTGCCTGGAGATAAGCGAGACACGACAACACCAATTGCAATGGTAACGACACTTGAAAAGTTACTAATTGACGAAACACTATCTATCAAATCTCGTCAACAACTAGAATCTTGGCTTAAAGGTAATGAGGTTGGCGATGCATTGTTTCGTAAAGGCGTTCCAAGTGACTGGATAGTAGCAGATAGAACAGGCGCTGGTGGTTATGGGTCGCGTGCTATTACTGCGGTGATGTGGCCTCCAAATCGCAAGCCTATCGTAGCCGCTCTATACATTACAGAGACAGACGCCTCGTTTGAAGAAAGAAATGCTGTCATTGCAAAAATTGGTGAGCAAATAGCGAAGACAGTATTAATGGAGAATAGCCGTAACTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39652","NCBI_taxonomy_name":"Psychrobacter maritimus","NCBI_taxonomy_id":"256325"}}}},"ARO_accession":"3002255","ARO_id":"38655","ARO_name":"CARB-16","CARD_short_name":"CARB-16","ARO_description":"CARB-16 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36230":{"category_aro_accession":"3000091","category_aro_cvterm_id":"36230","category_aro_name":"CARB beta-lactamase","category_aro_description":"CARB beta-lactamases are class A lactamases that can hydrolyze carbenicillin. Many of the PSE beta-lactamases have been renamed as CARB-lactamases with the notable exception of PSE-2 which is now OXA-10.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"536":{"model_id":"536","model_name":"TEM-95","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"933":{"protein_sequence":{"accession":"CAC67290.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGAKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AJ308558.1","fmin":"181","fmax":"1042","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGAGCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000962","ARO_id":"37342","ARO_name":"TEM-95","CARD_short_name":"TEM-95","ARO_description":"TEM-95 is a broad-spectrum beta-lactamase found in E. coli.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"537":{"model_id":"537","model_name":"OXA-120","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1203":{"protein_sequence":{"accession":"CCJ32595.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDDKAEKIKNLFNEAHTTGVLVIHQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEIFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"HE963768.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGACAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCATCAAGGTCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAATATTTAAGTGGGACGGGCAAAAAAGGCTGTTCCCAGAATGGGAAAAGGACATGACCCTAGGTGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001672","ARO_id":"38072","ARO_name":"OXA-120","CARD_short_name":"OXA-120","ARO_description":"OXA-120 is a beta-lactamase found in A. baumannii.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"539":{"model_id":"539","model_name":"QnrB59","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"574":{"protein_sequence":{"accession":"AFR46590.1","sequence":"MLSLLYKNTGIDMTLALVGEKIDRNRFTSEKVENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNVSALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGTQVLGATFSGSDLSGGEFSTFDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDNYQASLLMERLGIAIIG"},"dna_sequence":{"accession":"JX259320.1","fmin":"0","fmax":"681","strand":"+","sequence":"ATGTTGTCATTACTGTATAAAAACACAGGCATAGATATGACTCTGGCATTAGTTGGCGAAAAAATTGACAGAAATCGCTTCACCAGTGAGAAAGTTGAAAATAGTACATTTTTTAACTGCGATTTTTCAGGTGCCGACCTGAGCGGCACTGAATTTATCGGCTGCCAGTTCTATGATCGCGAAAGTCAGAAAGGATGCAATTTTAGTCGCGCAATGCTGAAAGATGCCATTTTCAAAAGCTGTGATTTATCAATGGCAGATTTCCGCAACGTCAGCGCATTGGGCATTGAAATTCGCCACTGCCGCGCACAAGGCGCAGATTTCCGCGGTGCAAGCTTTATGAATATGATCACCACACGCACCTGGTTTTGCAGCGCATATATCACTAATACCAATCTAAGCTACGCCAATTTTTCGAAAGTCGTGTTGGAAAAGTGTGAGCTATGGGAAAACCGCTGGATGGGGACTCAGGTACTGGGTGCGACGTTCAGTGGTTCAGATCTCTCCGGCGGCGAGTTTTCGACTTTCGACTGGCGAGCAGCAAACTTCACACATTGCGATCTGACCAATTCGGAGTTAGGTGACTTAGATATTCGGGGTGTTGATTTACAAGGCGTTAAGTTAGACAACTACCAGGCATCGTTGCTCATGGAGCGGCTTGGCATCGCGATTATTGGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002772","ARO_id":"39206","ARO_name":"QnrB59","CARD_short_name":"QnrB59","ARO_description":"QnrB59 is a plasmid-mediated quinolone resistance protein found in Citrobacter freundii.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"540":{"model_id":"540","model_name":"emrY","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"900"}},"model_sequences":{"sequence":{"65":{"protein_sequence":{"accession":"BAA11237.1","sequence":"MAITKSTPAPLTGGTLWCVTIALSLATFMQMLDSTISNVAIPTISGFLGASTDEGTWVITSFGVANAIAIPVTGRLAQRIGELRLFLLSVTFFSLSSLMCSLSTNLDVLIFFRVVQGLMAGPLIPLSQSLLLRNYPPEKRTFALALWSMTVIIAPICGPILGGYICDNFSWGWIFLINVPMGIIVLTLCLTLLKGRETETSPVKMNLPGLTLLVLGVGGLQIMLDKGRDLDWFNSSTIIILTVVSVISLISLVIWESTSENPILDLSLFKSRNFTIGIVSITCAYLFYSGAIVLMPQLLQETMGYNAIWAGLAYAPIGIMPLLISPLIGRYGNKIDMRLLVTFSFLMYAVCYYWRSVTFMPTIDFTGIILPQFFQGFAVACFFLPLTTISFSGLPDNKFANASSMSNFFRTLSGSVGTSLTMTLWGRRESLHHSQLTATIDQFNPVFNSSSQIMDKYYGSLSGVLNEINNEITQQSLSISANEIFRMAAIAFILLTVLVWFAKPPFTAKGVG"},"dna_sequence":{"accession":"D78168.1","fmin":"1591","fmax":"3130","strand":"+","sequence":"ATGGCAATCACTAAATCAACTCCGGCACCATTAACCGGTGGGACGTTATGGTGCGTCACTATTGCATTGTCATTAGCGACATTTATGCAAATGTTGGATTCCACTATTTCTAACGTCGCAATACCGACAATATCTGGCTTTCTGGGAGCATCAACAGACGAAGGCACCTGGGTTATCACCTCGTTTGGTGTAGCAAATGCCATTGCGATCCCTGTTACTGGCAGGTTGGCACAAAGAATAGGCGAATTAAGATTATTTTTACTTTCAGTCACTTTTTTTTCGCTGTCTTCATTAATGTGTAGCCTATCGACCAATCTTGATGTGCTGATATTTTTTAGAGTCGTTCAGGGGTTAATGGCGGGGCCGTTAATTCCACTGTCACAGAGTTTATTATTAAGGAATTATCCGCCAGAAAAAAGAACATTTGCTCTGGCATTATGGTCAATGACCGTGATTATCGCTCCGATATGTGGACCGATATTGGGCGGTTATATTTGTGATAACTTTAGCTGGGGTTGGATATTTTTAATCAATGTCCCTATGGGGATTATCGTCCTGACATTATGCTTAACCTTACTTAAAGGAAGAGAAACTGAGACTTCACCGGTCAAAATGAATCTACCAGGACTGACCCTGTTAGTGCTCGGTGTTGGTGGCTTGCAAATTATGCTTGATAAAGGGCGCGATCTGGATTGGTTCAACTCGAGTACAATAATAATATTAACAGTAGTATCAGTTATTTCTCTGATCTCTTTAGTCATTTGGGAGTCGACCTCAGAGAACCCGATTCTTGATCTCAGTTTGTTTAAGTCCCGTAACTTCACCATTGGTATTGTGAGTATCACATGCGCGTATTTATTTTACTCTGGAGCGATCGTCCTTATGCCGCAGTTACTCCAGGAAACGATGGGGTATAATGCGATATGGGCCGGACTTGCTTATGCGCCCATCGGCATCATGCCACTATTAATTTCACCTTTGATAGGACGTTATGGCAACAAAATAGACATGCGGTTGTTAGTGACATTTAGTTTTTTGATGTATGCGGTTTGCTATTACTGGCGTTCTGTGACATTTATGCCAACGATTGATTTTACAGGCATCATTTTGCCGCAGTTTTTTCAGGGATTCGCCGTTGCCTGTTTCTTTTTACCCTTAACAACGATTTCGTTTTCAGGCTTGCCAGATAATAAATTTGCCAATGCCTCGAGTATGAGTAATTTTTTTCGTACCTTGTCAGGATCAGTTGGTACGTCGTTGACAATGACGCTGTGGGGACGACGCGAATCGTTACACCATAGTCAGTTGACAGCAACCATCGATCAATTTAACCCCGTGTTTAATTCATCGTCACAAATTATGGATAAATATTATGGTTCGCTTTCAGGAGTTCTTAATGAAATTAATAATGAAATAACCCAGCAGTCACTTTCTATTTCTGCAAATGAGATTTTCCGTATGGCGGCTATTGCTTTTATCTTACTTACGGTTTTGGTTTGGTTTGCGAAACCGCCGTTTACAGCGAAAGGCGTTGGGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000254","ARO_id":"36393","ARO_name":"emrY","CARD_short_name":"emrY","ARO_description":"emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"541":{"model_id":"541","model_name":"TEM-133","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"844":{"protein_sequence":{"accession":"AAS19171.1","sequence":"MSIQHFRVALIPFFAAFCFPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVKYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDSWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AY528425.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCTTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTAAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATAGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3000997","ARO_id":"37377","ARO_name":"TEM-133","CARD_short_name":"TEM-133","ARO_description":"TEM-133 is an extended-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"542":{"model_id":"542","model_name":"adeH","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"900"}},"model_sequences":{"sequence":{"4253":{"protein_sequence":{"accession":"CAJ77855.1","sequence":"MVITSKQNWLLSSLMGSLLLAGCSLAPEYQPAKVIVPVKFKESDPKLEDNNWKIAQPADQQTRGEWWRIYNDAQLNELEQQAIAGNQNLKAVAANIQASRALRSAAQAERLPSIDAGFGPTRQKPSPASLGLDDNAHTSAQTLWRAQANVSYELDLFGRVASSVNAATADLQQQEALYQSALLALQADVAQGYFLIRQLDTEQAIYNRTIKLLGETRDLMQLRFKNGLVSELDVSRAQTELATAQTTALNIARNRASAEHALAVLLGKPPADFNLAVQPLTANSIRLPAGLPSTLLERRPDIAAAERAMAADNARIGIARAAFFPKLSLTGALGYESSSLSELGKWSSRTFLLGPVAGTILSLPLFDGGQRKAGVAQARAAYEESVANYRQTVLNAFREVENGLSDQRILDQQIQAQNQALSSSRHANQLSHLRYREGAISYLDVIDSDRTILQQEQLAAQLKGSQIIASINLIRALGGGWSS"},"dna_sequence":{"accession":"CT025802.2","fmin":"0","fmax":"1452","strand":"+","sequence":"TTGGTGATTACATCAAAACAAAACTGGTTGTTGTCCTCACTCATGGGAAGCCTGCTCCTTGCAGGCTGCTCATTGGCCCCAGAATATCAACCTGCAAAAGTTATAGTGCCAGTCAAATTCAAAGAATCTGACCCCAAACTTGAAGATAATAACTGGAAGATTGCCCAACCTGCTGATCAGCAAACTCGTGGTGAATGGTGGCGCATTTACAATGATGCTCAACTGAATGAACTTGAACAGCAAGCTATCGCGGGCAACCAGAACCTAAAAGCGGTGGCAGCAAATATTCAGGCTTCACGTGCATTACGTTCGGCAGCTCAAGCTGAACGCTTACCAAGTATTGATGCCGGATTTGGGCCAACCCGCCAAAAGCCGTCTCCGGCTTCACTCGGTTTAGATGACAATGCACATACTTCGGCTCAAACCTTATGGCGAGCTCAAGCCAATGTTTCATATGAGCTCGATTTATTTGGTCGTGTAGCAAGTAGTGTCAACGCAGCAACAGCGGATCTACAGCAACAAGAGGCACTATATCAGTCGGCACTTTTAGCTCTACAAGCGGATGTAGCTCAAGGTTATTTTCTGATACGTCAACTTGATACCGAACAGGCAATTTATAACCGTACAATCAAATTATTAGGTGAAACACGAGATTTAATGCAGCTTCGTTTTAAAAACGGACTGGTCAGTGAATTAGATGTTTCTCGTGCACAAACCGAACTTGCTACCGCACAAACCACTGCCCTAAATATTGCTCGTAACAGAGCCAGTGCAGAACATGCGCTTGCAGTCTTATTAGGAAAACCACCAGCAGACTTTAACTTGGCAGTTCAACCTTTAACTGCAAATAGTATCCGTCTCCCTGCCGGTTTGCCGTCAACTTTACTTGAAAGACGACCCGATATTGCGGCTGCAGAGCGTGCAATGGCAGCAGATAATGCGCGTATTGGAATTGCTCGTGCAGCATTTTTCCCAAAACTCAGTCTTACAGGAGCTTTAGGTTATGAATCTTCAAGTTTAAGCGAGTTGGGTAAATGGTCGAGTCGGACTTTTTTACTAGGACCTGTCGCTGGTACTATTTTGTCGTTACCTTTATTTGATGGTGGACAACGTAAAGCAGGCGTTGCTCAAGCAAGAGCGGCTTATGAGGAAAGCGTCGCCAACTATAGACAAACTGTACTGAATGCATTTCGCGAAGTTGAAAATGGTTTATCTGATCAAAGAATTCTCGATCAGCAAATTCAGGCTCAAAACCAAGCACTCTCCTCTTCTCGTCATGCCAATCAACTTTCTCATTTACGTTATCGAGAAGGTGCTATTAGCTATCTTGATGTCATTGATTCTGACCGCACTATTTTGCAACAAGAACAATTAGCAGCTCAGCTGAAAGGCAGCCAAATCATTGCAAGCATCAATTTAATCCGTGCTTTAGGGGGCGGTTGGAGTAGTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35535","NCBI_taxonomy_name":"Acinetobacter baumannii AYE","NCBI_taxonomy_id":"509173"}}}},"ARO_accession":"3000779","ARO_id":"37159","ARO_name":"adeH","CARD_short_name":"adeH","ARO_description":"AdeH is the outer membrane channel protein of the AdeFGH multidrug efflux complex.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"543":{"model_id":"543","model_name":"TEM-106","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1153":{"protein_sequence":{"accession":"AAM52207.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVKYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTTPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AY101578.1","fmin":"214","fmax":"1075","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTAAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGACGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000969","ARO_id":"37349","ARO_name":"TEM-106","CARD_short_name":"TEM-106","ARO_description":"TEM-106 is an extended-spectrum beta-lactamase found in E. coli.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"544":{"model_id":"544","model_name":"AAC(6')-Is","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"669":{"protein_sequence":{"accession":"AAD03491.1","sequence":"MNIMPISESQLSDWLALRSLLWPDHEDAHLLEMRHVLKQTDTLQLLVYSETQLAIAMLEASIRHEYVNGTQTSPVAFLEGIYVLPEYRRSGIATQLVQCVEEWAKQFACTEFASDAALENTISHAMHRALGFHETERVVYFKKNIG"},"dna_sequence":{"accession":"AF031327.1","fmin":"0","fmax":"441","strand":"+","sequence":"ATGAATATTATGCCGATATCTGAATCACAATTATCAGATTGGCTAGCATTAAGAAGCTTACTCTGGCCTGATCATGAAGATGCGCATTTATTGGAAATGCGCCACGTACTTAAACAAACCGATACTTTACAGTTATTGGTGTATTCGGAAACGCAACTTGCGATAGCAATGTTGGAAGCATCGATCCGACATGAATATGTGAATGGTACACAAACCTCACCCGTGGCTTTTCTTGAAGGGATTTATGTATTGCCTGAATATCGACGTTCAGGCATTGCGACCCAGTTGGTTCAGTGCGTAGAGGAATGGGCGAAACAATTTGCATGTACAGAGTTCGCTTCAGATGCAGCGCTTGAAAATACGATCAGTCATGCAATGCATCGGGCTTTGGGTTTTCATGAAACTGAACGCGTGGTGTACTTTAAGAAAAATATCGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39513","NCBI_taxonomy_name":"Acinetobacter variabilis","NCBI_taxonomy_id":"70346"}}}},"ARO_accession":"3002562","ARO_id":"38962","ARO_name":"AAC(6')-Is","CARD_short_name":"AAC(6')-Is","ARO_description":"AAC(6')-Is is a chromosomal-encoded aminoglycoside acetyltransferase in Acinetobacter variabilis.","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"A category of aminoglycoside N-acetyltransferase enzymes with modification regiospecificity based at the 6'-amino group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics through acetylation of the 6-amino group of the compound.","category_aro_class_name":"AMR Gene Family"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"46128":{"category_aro_accession":"3007378","category_aro_cvterm_id":"46128","category_aro_name":"2'-N-ethylnetilmicin","category_aro_description":"2'-N-ethylnetilmicin is an aminoglycoside antibiotic and a derivative of netilmicin.","category_aro_class_name":"Antibiotic"},"46129":{"category_aro_accession":"3007379","category_aro_cvterm_id":"46129","category_aro_name":"5-episisomicin","category_aro_description":"5-episosomicin is a semisynthetic aminoglycoside antibiotic similar to sisomicin.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"545":{"model_id":"545","model_name":"GES-22","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1415":{"protein_sequence":{"accession":"AFU25739.1","sequence":"MRFIHALLLAGIAHSAYASEKLTFKTDLEKLEREKAAQIGVAIVDPQGEIVAGHRMAQRFAMCSTFKFPLAALVFERIDSGTERGDRKLSYGPDMIVEWSPATERFLASGHMTVLEAAQAAVQLSDNGATNLLLREIGGPAAMTQYFRKIGDSVSRLDRKEPELGDNTPGDLRDTTTPIAMARTVAKVLYGGALTSTSTHTIERWLIGNQTGDATLRAGFPKDWVVGEKTGTCANGARNDIGFFKAQERDYAVAVYTTAPKLSAVERDELVASVGQVITQLILSTDK"},"dna_sequence":{"accession":"JX023441.1","fmin":"37","fmax":"901","strand":"+","sequence":"ATGCGCTTCATTCACGCACTATTACTGGCAGGGATCGCTCACTCTGCATATGCGTCGGAAAAATTAACCTTCAAGACCGATCTTGAGAAGCTAGAGCGCGAAAAAGCAGCTCAGATCGGTGTTGCGATCGTCGATCCCCAAGGAGAGATCGTCGCGGGCCACCGAATGGCGCAGCGTTTTGCAATGTGCTCAACGTTCAAGTTTCCGCTAGCCGCGCTGGTCTTTGAAAGAATTGACTCAGGCACCGAGCGGGGGGATCGAAAACTTTCATATGGGCCGGACATGATCGTCGAATGGTCTCCTGCCACGGAGCGGTTTCTAGCATCGGGACACATGACGGTTCTCGAGGCAGCGCAAGCTGCGGTGCAGCTTAGCGACAATGGGGCTACTAACCTCTTACTGAGAGAAATTGGCGGACCTGCTGCAATGACGCAGTATTTTCGTAAAATTGGCGACTCTGTGAGTCGGCTAGACCGGAAAGAGCCGGAGCTGGGCGACAACACACCTGGCGACCTCAGAGATACAACTACGCCTATTGCTATGGCACGTACTGTGGCTAAAGTCCTCTATGGCGGCGCACTGACGTCCACCTCGACCCACACCATTGAGAGGTGGCTGATCGGAAACCAAACGGGAGACGCGACACTACGAGCGGGTTTTCCTAAAGATTGGGTTGTTGGAGAGAAAACTGGTACCTGCGCCAACGGGGCCCGGAACGACATTGGTTTTTTTAAAGCCCAGGAGAGAGATTACGCTGTAGCGGTGTATACAACGGCCCCGAAACTATCGGCCGTAGAACGTGACGAATTAGTTGCCTCTGTCGGTCAAGTTATTACACAACTCATCCTGAGCACGGACAAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3002351","ARO_id":"38751","ARO_name":"GES-22","CARD_short_name":"GES-22","ARO_description":"GES-22 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36205":{"category_aro_accession":"3000066","category_aro_cvterm_id":"36205","category_aro_name":"GES beta-lactamase","category_aro_description":"GES beta-lactamases or Guiana extended-spectrum beta-lactamases are related to the other plasmid-located class A beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"546":{"model_id":"546","model_name":"TLA-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"3315":{"protein_sequence":{"accession":"AAD37403.1","sequence":"MTVPISIIFWGNIMKKHLVVIAFCVLFASASAFAAKGTDSLKSSIEKYLKDKKAKVGVAVLGIEDNFKLNVNEKHHYPMQSTYKFHLALAVLDKLDKENISIDKKLFVKKSELLPNTWSPLRDKYPDGNVDLSISEILKATVSRSDNNGCDILFRFVGGTNKVHNFISKLGVKNISIKATEEEMHKAWNVQYTNWTTPDATVQLLKKFYKNEILSKNSYDYLLNTMIETTTGPKRLKGLLPDGTVVAHKTGSSDTNDKGITAATNDIGIITLPNGKHFAIAVYVSDSSEKSDVNEKIIAEICKSVWDYLVKDGK"},"dna_sequence":{"accession":"AF148067.1","fmin":"213","fmax":"1158","strand":"+","sequence":"ATGACAGTTCCTATCAGTATTATTTTTTGGGGGAATATAATGAAAAAACATCTTGTTGTAATTGCATTTTGTGTGCTTTTTGCTTCTGCTTCTGCTTTTGCGGCTAAAGGTACGGATTCGCTTAAAAGCAGTATTGAAAAATATCTTAAAGATAAAAAAGCTAAAGTGGGTGTTGCCGTTTTGGGAATTGAAGATAATTTTAAATTGAACGTTAACGAAAAGCATCACTATCCTATGCAGAGCACTTATAAGTTCCATCTTGCATTGGCTGTGCTCGATAAACTTGATAAGGAGAATATTTCCATTGACAAGAAGCTTTTTGTAAAAAAATCGGAGCTTCTGCCGAATACTTGGAGTCCGCTAAGAGATAAATATCCCGATGGAAATGTGGATTTATCCATAAGCGAAATTCTGAAAGCTACCGTTTCGCGTAGCGATAATAACGGTTGTGATATTCTCTTCAGATTTGTTGGTGGAACAAATAAAGTCCACAATTTTATTAGCAAGCTTGGCGTTAAGAATATTTCTATCAAAGCTACAGAAGAAGAAATGCACAAGGCATGGAATGTACAATATACCAATTGGACAACTCCCGACGCTACCGTTCAGCTCTTAAAGAAGTTCTACAAAAATGAAATACTCTCAAAAAATAGTTACGACTATTTGCTTAATACTATGATTGAAACTACTACCGGACCGAAACGACTCAAAGGACTTTTGCCCGATGGAACTGTTGTTGCTCATAAAACCGGAAGCTCCGATACTAACGATAAAGGCATTACTGCTGCCACAAATGATATCGGTATTATTACTCTGCCGAACGGTAAACACTTTGCCATTGCTGTTTATGTGTCGGATTCAAGCGAAAAGAGCGATGTTAACGAAAAGATTATTGCCGAAATTTGCAAAAGCGTTTGGGATTATCTAGTTAAGGATGGGAAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3003202","ARO_id":"39786","ARO_name":"TLA-1","CARD_short_name":"TLA-1","ARO_description":"TLA-1 is a beta-lactamase found in plasmids of clinical isolates of Escherichia coli strain R170 in Latin America. It preferentially hydrolyzed cephaloridine, cefotaxime, cephalothin, benzylpenicillin, and ceftazidime. The enzyme was markedly inhibited by sulbactam, tazobactam, and clavulanic acid.","ARO_category":{"39785":{"category_aro_accession":"3003201","category_aro_cvterm_id":"39785","category_aro_name":"TLA beta-lactamase","category_aro_description":"The TLA beta-lactamases are resistant to expanded-spectrum cephalosporins, and aztreonam but was susceptible to amikacin, cefotetan, and imipenem.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"547":{"model_id":"547","model_name":"arr-5","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"250"}},"model_sequences":{"sequence":{"567":{"protein_sequence":{"accession":"ABV26707.1","sequence":"MTVDWIPISHDNYHQVRGPFYHGTKAELAIGDLISTGFISHFERDRALKHVYFSALMEPAIWGAELAVALSGSDGPGHIYIIEPTGPFEDDPNLTNKRFPGNPTQSYRTCHPLKIVGILREWERHSPEALKTMLDSLADLKRRGLAIIEE"},"dna_sequence":{"accession":"EF660563.1","fmin":"392","fmax":"845","strand":"+","sequence":"ATGACGGTAGACTGGATCCCCATTTCGCACGACAACTACCATCAAGTGCGTGGCCCGTTTTATCACGGAACAAAAGCCGAACTCGCCATTGGCGACTTAATTTCAACCGGATTTATTTCTCACTTTGAGCGGGACAGAGCACTAAAGCATGTGTACTTTTCCGCGCTGATGGAGCCAGCAATCTGGGGGGCCGAGCTCGCTGTAGCACTCTCTGGCTCTGACGGGCCAGGCCATATTTACATCATTGAGCCAACCGGCCCGTTTGAAGACGACCCCAATCTCACAAACAAACGATTCCCTGGCAATCCAACACAGTCCTATCGCACATGCCACCCACTTAAAATTGTTGGCATACTGCGGGAGTGGGAGCGCCATTCTCCTGAAGCATTGAAGACCATGCTAGATTCTCTGGCAGACCTCAAGCGACGCGGCTTGGCCATCATTGAAGAATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002850","ARO_id":"39284","ARO_name":"arr-5","CARD_short_name":"arr-5","ARO_description":"arr-5 is an integron-encoded ribosyltransferase found in Pseudomonas aeruginosa.","ARO_category":{"36529":{"category_aro_accession":"3000390","category_aro_cvterm_id":"36529","category_aro_name":"rifampin ADP-ribosyltransferase (Arr)","category_aro_description":"Enzyme responsible for the ADP-ribosylative inactivation of rifampin at the 23-OH position using NAD+.","category_aro_class_name":"AMR Gene Family"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36656":{"category_aro_accession":"3000517","category_aro_cvterm_id":"36656","category_aro_name":"rifaximin","category_aro_description":"Rifaximin is a semi-synthetic rifamycin used to treat traveller's diarrhea. Rifaximin inhibits RNA synthesis by binding to the beta subunit of bacterial RNA polymerase.","category_aro_class_name":"Antibiotic"},"36669":{"category_aro_accession":"3000530","category_aro_cvterm_id":"36669","category_aro_name":"rifabutin","category_aro_description":"Rifabutin is a semisynthetic rifamycin used in tuberculosis therapy. It inhibits DNA-dependent RNA synthesis.","category_aro_class_name":"Antibiotic"},"36673":{"category_aro_accession":"3000534","category_aro_cvterm_id":"36673","category_aro_name":"rifapentine","category_aro_description":"Rifapentine is a semisynthetic rifamycin that inhibits DNA-dependent RNA synthesis. It is often used in the treatment of tuberculosis and leprosy.","category_aro_class_name":"Antibiotic"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"548":{"model_id":"548","model_name":"QnrB3","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"277":{"protein_sequence":{"accession":"ABC17629.1","sequence":"MTPLLYKKTGTNMALALVGEKIDRNRFTGEKIENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCKFSRAMLKDAIFKSCDLSMADFRNSSALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGAQVLGATFSGSDLSGGEFSTFDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDNYQASLLMERLGIAVIG"},"dna_sequence":{"accession":"DQ303920.1","fmin":"0","fmax":"681","strand":"+","sequence":"ATGACGCCATTACTGTATAAAAAAACAGGTACAAATATGGCTCTGGCACTCGTTGGCGAAAAAATTGACAGAAACCGTTTCACCGGTGAGAAAATTGAAAATAGTACATTTTTTAACTGTGATTTTTCAGGTGCCGACCTGAGCGGCACTGAATTTATCGGCTGTCAGTTCTATGATCGTGAAAGCCAGAAAGGGTGCAAATTTAGTCGTGCGATGCTGAAAGATGCCATTTTTAAAAGCTGTGATTTATCCATGGCGGATTTTCGCAATTCCAGTGCGCTGGGCATTGAAATTCGCCACTGCCGCGCACAAGGCGCAGATTTCCGCGGCGCAAGCTTTATGAATATGATCACCACGCGCACCTGGTTTTGTAGCGCATATATCACGAATACCAATCTAAGCTACGCCAATTTTTCGAAAGTCGTGTTGGAAAAGTGTGAGCTGTGGGAAAACCGTTGGATGGGTGCCCAGGTACTGGGCGCGACGTTCAGTGGTTCGGATCTCTCCGGCGGCGAGTTTTCGACTTTCGACTGGCGAGCAGCAAACTTCACACATTGCGATCTGACCAATTCGGAGTTGGGTGACTTAGATATTCGGGGCGTTGATTTACAAGGCGTTAAGCTGGACAACTACCAGGCGTCGTTGCTCATGGAGCGGCTTGGCATCGCGGTGATTGGTTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002716","ARO_id":"39150","ARO_name":"QnrB3","CARD_short_name":"QnrB3","ARO_description":"QnrB3 is a plasmid-mediated quinolone resistance protein found in Escherichia coli.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"549":{"model_id":"549","model_name":"TEM-107","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1240":{"protein_sequence":{"accession":"AAM52215.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVKYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDHWEPELNEAIPNDERDTTTPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGASERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AY101764.1","fmin":"206","fmax":"1067","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTAAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCATTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGACGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCAGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3000970","ARO_id":"37350","ARO_name":"TEM-107","CARD_short_name":"TEM-107","ARO_description":"TEM-107 is an extended-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"550":{"model_id":"550","model_name":"CMY-71","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1267":{"protein_sequence":{"accession":"AFK08538.1","sequence":"MMKKSLCCALLLTAPFSTFAAAKTEQQIADTVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADITNNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGISLLHLATYTAGGLPLQIPDDVTDKAALLRFYQNWQPQWAPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKAVHVSPGQLDAEAYGVKSSVIDMARWVQVNMDASRVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKKLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"JQ711184.1","fmin":"1026","fmax":"2172","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCCCTTTCTCCACGTTTGCCGCAGCCAAAACAGAACAACAGATTGCCGATACCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCACCAATAACCACCCAGTCACGCAGCAAACTCTGTTTGAGCTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCAGCCTGCTGCACTTAGCCACCTACACGGCAGGCGGCCTGCCGCTGCAGATCCCCGATGACGTTACGGATAAAGCCGCATTACTGCGTTTTTATCAAAACTGGCAGCCGCAATGGGCCCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACAGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGGCTGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGTCAACATGGACGCCAGCCGCGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGGTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGTAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGATCCACTGGAGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAAACTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002084","ARO_id":"38484","ARO_name":"CMY-71","CARD_short_name":"CMY-71","ARO_description":"CMY-71 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"551":{"model_id":"551","model_name":"CTX-M-117","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"906":{"protein_sequence":{"accession":"AET99223.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIQGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"JN227085.1","fmin":"351","fmax":"1227","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCAGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001977","ARO_id":"38377","ARO_name":"CTX-M-117","CARD_short_name":"CTX-M-117","ARO_description":"CTX-M-117 is a beta-lactamase found in Escherichia coli.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"552":{"model_id":"552","model_name":"QnrB28","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"191":{"protein_sequence":{"accession":"ADM52188.1","sequence":"MTLALVSEKIDRNRFTGEKVENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNVSALGIEIRHCRAQGSDFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGTQVAGATFSGSDLSGGEFSAFDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDSYQAALLMERLGIAVIG"},"dna_sequence":{"accession":"HM439643.1","fmin":"0","fmax":"645","strand":"+","sequence":"ATGACTCTGGCATTAGTTAGCGAAAAAATTGACAGAAACCGCTTCACCGGGGAAAAAGTTGAAAACAGTACTTTTTTTAACTGTGATTTTTCAGGGGCCGATCTTAGCGGCACTGAATTTATCGGCTGTCAGTTTTATGATCGCGAAAGCCAGAAAGGGTGTAATTTTAGTCGCGCAATGCTGAAAGATGCCATTTTTAAAAGTTGCGATTTATCCATGGCGGATTTTCGCAACGTCAGTGCCCTGGGAATTGAAATTCGCCACTGCCGCGCGCAGGGTTCAGATTTTCGCGGCGCGAGTTTTATGAACATGATCACCACGCGGACCTGGTTTTGCAGCGCATACATCACGAATACCAATCTAAGCTACGCCAACTTTTCGAAGGTTGTCCTGGAAAAGTGCGAGCTGTGGGAAAACCGCTGGATGGGAACTCAGGTAGCGGGTGCAACGTTCAGTGGATCAGATCTCTCGGGAGGTGAATTTTCAGCGTTCGACTGGCGGGCCGCAAATTTCACGCACTGTGATTTGACCAATTCAGAACTGGGTGATTTAGATATTCGGGGTGTAGATTTACAAGGCGTCAAATTGGATAGCTATCAGGCAGCGTTGCTGATGGAGCGGCTTGGCATCGCGGTGATTGGTTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002743","ARO_id":"39177","ARO_name":"QnrB28","CARD_short_name":"QnrB28","ARO_description":"QnrB28 is a plasmid-mediated quinolone resistance protein found in Citrobacter freundii.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"553":{"model_id":"553","model_name":"VIM-35","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1500":{"protein_sequence":{"accession":"AGC50805.1","sequence":"MLKVISSLLVYMTASVMAVASPLAHSGEPSGEYPTVNEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEAEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSANVLYGGCAVHELSSTSAGNVTDADLAEWPTSVERIQKHYPEAEVVIPGHGLPGGLDLLQHTANVVKAHKNRSVAE"},"dna_sequence":{"accession":"JX982634.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGTTAAAAGTTATTAGTAGTTTATTGGTCTACATGACCGCGTCTGTCATGGCTGTCGCAAGTCCGTTAGCCCATTCCGGGGAGCCGAGTGGTGAGTATCCGACAGTCAACGAAATTCCGGTCGGAGAGGTCCGACTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCGGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAAAAGCAAATTGGACTTCCCGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGCAGAGGGGAACGAGATTCCCACGCATTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAGCTCTTCTATCCTGGTGCTGCGCATTCGACCGACAATCTGGTTGTATACGTCCCGTCAGCGAACGTGCTATACGGTGGTTGTGCCGTTCATGAGTTGTCAAGCACGTCTGCGGGGAACGTGACCGATGCCGATCTGGCTGAATGGCCCACCTCCGTTGAGCGGATTCAAAAACACTACCCGGAAGCAGAGGTCGTCATTCCCGGGCACGGTCTACCGGGCGGTCTAGACTTGCTCCAGCACACAGCGAACGTTGTCAAAGCACACAAAAATCGCTCAGTCGCCGAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3002305","ARO_id":"38705","ARO_name":"VIM-35","CARD_short_name":"VIM-35","ARO_description":"VIM-35 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"554":{"model_id":"554","model_name":"OXA-163","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1045":{"protein_sequence":{"accession":"ADY06444.1","sequence":"MRVLALSAVFLVASIIGMPAVAKEWQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGQTRDIATWNRDHNLITAMKYSVVPVYQEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISATEQISFLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYDTKIGWWVGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP"},"dna_sequence":{"accession":"HQ700343.1","fmin":"0","fmax":"786","strand":"+","sequence":"ATGCGTGTATTAGCCTTATCGGCTGTGTTTTTGGTGGCATCGATTATCGGAATGCCTGCGGTAGCAAAGGAATGGCAAGAAAACAAAAGTTGGAATGCTCACTTTACTGAACATAAATCACAGGGCGTAGTTGTGCTCTGGAATGAGAATAAGCAGCAAGGATTTACCAATAATCTTAAACGGGCGAACCAAGCATTTTTACCCGCATCTACCTTTAAAATTCCCAATAGCTTGATCGCCCTCGATTTGGGCGTGGTTAAGGATGAACACCAAGTCTTTAAGTGGGATGGACAGACGCGCGATATCGCCACTTGGAATCGCGATCATAATCTAATCACCGCGATGAAATATTCAGTTGTGCCTGTTTATCAAGAATTTGCCCGCCAAATTGGCGAGGCACGTATGAGCAAGATGCTACATGCTTTCGATTATGGTAATGAGGACATTTCGGGCAATGTAGACAGTTTCTGGCTCGACGGTGGTATTCGAATTTCGGCCACGGAGCAAATCAGCTTTTTAAGAAAGCTGTATCACAATAAGTTACACGTATCGGAGCGCAGCCAGCGTATTGTCAAACAAGCCATGCTGACCGAAGCCAATGGCGACTATATTATTCGGGCTAAAACTGGATACGATACTAAGATTGGCTGGTGGGTCGGTTGGGTTGAACTTGATGATAATGTGTGGTTTTTTGCGATGAATATGGATATGCCCACATCGGATGGTTTAGGGCTGCGCCAAGCCATCACAAAAGAAGTGCTCAAACAGGAAAAAATTATTCCCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3001783","ARO_id":"38183","ARO_name":"OXA-163","CARD_short_name":"OXA-163","ARO_description":"OXA-163 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46510":{"category_aro_accession":"3007721","category_aro_cvterm_id":"46510","category_aro_name":"OXA-48-like beta-lactamase","category_aro_description":"OXA-48-type beta-lactamases are now routinely encountered in bacterial infections caused by carbapenam-resistant Enterobacterales. OXA-48-like proteins confer resistance to penicillin (which is efficiently hydrolyzed) and carbapenam antibiotics (which is more slowly broken down). The spectrum of activity of these variants varies, with some hydrolyzing expanded-spectrum oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"555":{"model_id":"555","model_name":"OXA-133","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1833":{"protein_sequence":{"accession":"ACE63186.1","sequence":"MNKYFTCYVVASLFFSGCTVQHNLINETQSQIVQGHNQVIHQYFDEKNTSGVLVIQTDKKINLYGNALSRANTEYVPASTFKMLNALIGLENQKTDINEIFKWKGEKRSFTTWEKDMTLGEAMKLSAVPVYQELARRIGLDLMQKEVERIDFGNAEIGQQVDNFWLIGPLKVTPIQEVEFVSQLAHTQLPFSEKVQANVKNMLLLEENNGYKIFGKTGWAMDIKPQVGWLTGWVEQPDGKIVAFALNMEMRSEMPASIRNELLMKSLKQLNII"},"dna_sequence":{"accession":"EU571228.1","fmin":"822","fmax":"1644","strand":"+","sequence":"ATGAATAAATATTTTACTTGCTATGTGGTTGCTTCTCTTTTTTTTTCTGGTTGTACGGTTCAGCATAATTTAATAAATGAAACCCAGAGTCAGATTGTTCAAGGACATAATCAGGTGATTCATCAATACTTTGATGAAAAAAACACCTCAGGTGTGCTGGTTATTCAAACAGATAAAAAAATTAATTTGTATGGTAATGCTCTAAGCCGCGCAAATACAGAATATGTGCCAGCCTCTACATTTAAAATGTTGAATGCCCTGATCGGATTGGAGAACCAGAAAACGGATATTAATGAAATATTTAAATGGAAGGGCGAGAAAAGGTCATTTACCACTTGGGAAAAAGACATGACACTAGGAGAAGCCATGAAGCTTTCTGCAGTCCCAGTCTATCAGGAACTTGCAAGACGTATCGGTCTTGATCTCATGCAAAAAGAAGTAGAACGTATTGATTTCGGTAATGCTGAAATTGGACAGCAGGTTGACAATTTCTGGTTGATAGGCCCATTAAAGGTCACGCCTATTCAAGAGGTAGAGTTTGTTTCTCAATTGGCACATACACAGCTTCCATTTAGTGAAAAAGTGCAGGCTAATGTAAAAAATATGCTACTTCTAGAAGAGAATAATGGCTACAAGATTTTTGGAAAGACTGGTTGGGCAATGGATATAAAACCACAAGTGGGCTGGTTGACCGGCTGGGTTGAGCAGCCAGATGGAAAAATTGTCGCTTTTGCATTAAATATGGAAATGCGGTCAGAAATGCCTGCATCTATACGTAATGAATTATTGATGAAATCATTAAAACAGCTGAATATTATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39672","NCBI_taxonomy_name":"Acinetobacter radioresistens","NCBI_taxonomy_id":"40216"}}}},"ARO_accession":"3001702","ARO_id":"38102","ARO_name":"OXA-133","CARD_short_name":"OXA-133","ARO_description":"OXA-133 is a beta-lactamase found in A. radioresistens.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46499":{"category_aro_accession":"3007710","category_aro_cvterm_id":"46499","category_aro_name":"OXA-23-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases, specifically imipenem, derived from OXA-23, first identified in Acinetobacter baumannii.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"557":{"model_id":"557","model_name":"SHV-9","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1717":{"protein_sequence":{"accession":"AAB37395.2","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLRTVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRNVLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGASKRGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"S82452.1","fmin":"120","fmax":"978","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTACTCCGGACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAACGTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTAGCAAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001068","ARO_id":"37448","ARO_name":"SHV-9","CARD_short_name":"SHV-9","ARO_description":"SHV-9 is an extended-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"558":{"model_id":"558","model_name":"qacB","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"990"}},"model_sequences":{"sequence":{"307":{"protein_sequence":{"accession":"AAQ10694.1","sequence":"MISFFTKTTDMMTSKKRWAALVVLAVSLFVVTMDMTILIMALPELVRELEPSGTQQLWIVDIYSLVLAGFIIPLSAFADKWGRKKALLTGFALFGLVSLAIFFAESAEFVIAIRFLLGIAGALIMPTTLSMIRVIFENPKERATALAVWSIVSSIGAVFGPIIGGALLEQFSWHSAFLINVPFAIIAVVAGLFLLPESKLSKEKSHSWDIPSTILSIAGMIGLVWSIKEFSKEGLADIIPWVVIVLAITMIVIFVKRNLSSSDPMLDVRLFKKRSFSAGTIAAFMTMFAMTSVLLLASQWLQVVEELSPFKAGLYLLPMAIGAMVFAPIAPGLAARFGPKIVLPSGIGIAAIGMFIMYFFGHPLSYSTMALALILVEAGTASLAVASALIMLETPTSKAGNAAAVEESMYDLGNVFGVAVLGSLSSMLYRVFLDISSFSSKGIVGDLAHVAEESVVGAVEVAKATGIKQLANEAVTSFNDAFVATALVGGIIMIIISIVVYLLIPKSLDITKQK"},"dna_sequence":{"accession":"AF535087.1","fmin":"28","fmax":"1573","strand":"+","sequence":"ATGATTTCATTTTTTACAAAAACTACTGATATGATGACATCAAAAAAAAGATGGGCTGCACTAGTAGTATTAGCTGTTAGTTTGTTTGTTGTTACAATGGATATGACAATATTAATTATGGCTTTACCGGAATTAGTAAGAGAGTTAGAGCCTTCTGGTACCCAACAGTTATGGATAGTTGATATATACTCTCTTGTTTTAGCTGGCTTTATAATTCCATTGAGTGCCTTTGCTGATAAATGGGGAAGAAAAAAAGCATTATTAACTGGATTTGCTTTATTTGGCCTCGTTTCATTAGCTATATTTTTCGCAGAAAGTGCAGAGTTCGTAATAGCTATTCGATTTTTACTTGGTATTGCAGGTGCTTTAATAATGCCAACTACCCTTTCAATGATAAGAGTAATTTTTGAAAACCCTAAAGAAAGGGCCACTGCATTAGCTGTATGGTCAATCGTTTCATCGATAGGTGCTGTTTTTGGACCAATTATCGGAGGAGCTTTACTTGAGCAATTTTCATGGCACTCGGCATTTTTAATTAATGTACCGTTTGCGATAATAGCAGTTGTAGCAGGTTTATTTTTATTACCAGAGTCTAAGTTATCAAAAGAAAAGTCTCACTCGTGGGATATTCCTTCTACAATTTTATCAATTGCAGGCATGATTGGACTGGTATGGAGTATCAAAGAATTTTCAAAAGAAGGACTAGCAGATATTATTCCATGGGTTGTAATAGTATTAGCAATTACCATGATAGTGATATTTGTTAAACGTAATTTATCAAGTTCTGATCCAATGTTAGACGTAAGACTTTTTAAAAAGAGATCATTTTCAGCTGGTACAATTGCTGCATTTATGACAATGTTTGCAATGACATCTGTTTTGTTATTAGCTTCACAATGGTTACAGGTTGTGGAAGAACTTTCTCCTTTTAAAGCTGGCTTATACCTATTACCTATGGCAATAGGAGCTATGGTGTTTGCACCAATTGCACCCGGATTAGCGGCGCGATTTGGACCGAAAATAGTGTTACCTTCCGGAATTGGAATTGCAGCCATTGGCATGTTTATTATGTATTTCTTTGGTCATCCATTATCATATTCTACAATGGCTTTAGCATTAATTTTAGTTGAAGCTGGTACGGCTTCACTAGCAGTTGCATCTGCTCTAATAATGTTAGAAACACCTACATCAAAAGCAGGTAATGCAGCTGCTGTTGAAGAGTCTATGTATGACCTTGGAAATGTTTTTGGTGTAGCAGTACTTGGTAGCCTATCTTCTATGCTTTATCGTGTATTTTTAGATATTTCATCTTTTTCATCAAAAGGTATAGTTGGAGATTTAGCTCATGTAGCTGAAGAATCTGTAGTGGGCGCTGTCGAAGTAGCTAAAGCTACGGGGATAAAACAGCTTGCAAACGAGGCTGTAACATCATTTAATGATGCTTTTGTAGCAACTGCTTTAGTAGGTGGGATTATCATGATTATCATTTCAATAGTTGTCTATTTGTTAATTCCCAAATCACTTGATATAACTAAACAAAAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35508","NCBI_taxonomy_name":"Staphylococcus aureus","NCBI_taxonomy_id":"1280"}}}},"ARO_accession":"3003047","ARO_id":"39481","ARO_name":"qacB","CARD_short_name":"qacB","ARO_description":"qacB is a subunit of the qac multidrug efflux pump.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"560":{"model_id":"560","model_name":"OXA-77","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1538":{"protein_sequence":{"accession":"AAX51233.1","sequence":"MNIKALLLITSAIFISACSPYIVSANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKNMTLGDAMKASAIPVYQDLPRRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"AY949202.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATCACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGTCTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACTACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTACCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001622","ARO_id":"38022","ARO_name":"OXA-77","CARD_short_name":"OXA-77","ARO_description":"OXA-77 is a beta-lactamase found in A. baumannii.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"561":{"model_id":"561","model_name":"OKP-B-8","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"1920":{"protein_sequence":{"accession":"CAJ19616.1","sequence":"MRYVRLCLISLIAALPLAVFASPQPLEQIKISESQLAGRVGYVEMDLASGRTLAAWRASERFPLMSTFKVLLCGAVLARVDAGDEQLDRRIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNTAGNLLLKIVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDVRDTTTPASMATTLRKLLTTPSLSARSQQQLLQWMVDDRVAGPLIRAVLPAGWFIADKTGAGERGSRGIVALLGPDGKAERIVVIYLRDTAATMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AM051157.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATGTTCGTCTGTGCCTTATCTCCCTGATTGCCGCCCTGCCACTGGCGGTATTCGCCAGCCCTCAGCCGCTTGAGCAGATTAAAATCAGCGAAAGTCAGCTGGCGGGCCGGGTGGGCTATGTTGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCAGTGAGCGCTTTCCGCTGATGAGCACCTTTAAAGTGCTGCTCTGCGGCGCGGTGCTGGCCCGGGTGGATGCCGGCGACGAACAGCTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGCCGACGGGATGACCGTTGGCGAACTCTGCGCCGCCGCCATCACCATGAGCGACAACACCGCCGGCAATCTGCTGTTGAAGATCGTCGGCGGCCCCGCGGGATTGACCGCTTTTCTGCGCCAGATCGGTGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTCAATGAGGCGCTTCCCGGCGACGTGCGCGACACCACCACCCCGGCCAGCATGGCCACCACCCTGCGCAAGTTGCTAACCACCCCCTCTCTGAGCGCCCGTTCGCAGCAGCAGCTGCTGCAGTGGATGGTGGACGACCGGGTGGCCGGCCCGTTGATCCGCGCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAAACCGGGGCCGGTGAGCGGGGCTCACGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAAGCGGAGCGTATCGTGGTGATCTATCTGCGGGATACCGCGGCGACCATGGCCGAACGTAACCAGCAGATCGCCGGGATAGGCGCGGCGCTGATCGAGCACTGGCAGCGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002441","ARO_id":"38841","ARO_name":"OKP-B-8","CARD_short_name":"OKP-B-8","ARO_description":"OKP-B-8 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"38817":{"category_aro_accession":"3002417","category_aro_cvterm_id":"38817","category_aro_name":"OKP beta-lactamase","category_aro_description":"OKP beta-lactamases are chromosomal class A beta-lactamase that confer resistance to penicillins and early cephalosporins in Klebsiella pneumoniae. OKP beta-lactamases can be subdivided into two groups: OKP-A and OKP-B which diverge by about 4.2%.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"562":{"model_id":"562","model_name":"TEM-187","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1956":{"protein_sequence":{"accession":"ADM61585.1","sequence":"MSIQHFRVALIPFFAAFCFPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDHWEPELNEAIPNDERDTTMPVAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYMTGSQATMDERNRQIAEIGASLIKH"},"dna_sequence":{"accession":"HM246246.1","fmin":"211","fmax":"1069","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCTTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATCATTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGTAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACATGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3001047","ARO_id":"37427","ARO_name":"TEM-187","CARD_short_name":"TEM-187","ARO_description":"TEM-187 is an extended-spectrum beta-lactamase found in P. mirabilis.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"563":{"model_id":"563","model_name":"OKP-B-6","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"8278":{"protein_sequence":{"accession":"CAP12355.2","sequence":"MRYVRLCLISLIAALPLAVFASPQPLEQIKISESQLAGRVGYVEMDLASGRTLAAWRASERFPLMSTFKVLLCGAVLARVDAGDEQLDRRIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAGNLLLKSVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDVRDTTTPASMATTLRKLLTTPSLSARSQQQLLQWMVDDRVAGPLIRAVLPAGWFIADKTGAGERGSRGIVALLGPDGKAERIVVIYLRDTAATMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AM850917.2","fmin":"17","fmax":"878","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGCCTTATCTCCCTGATTGCCGCCCTGCCACTGGCGGTATTCGCCAGCCCTCAGCCGCTTGAGCAGATTAAAATCAGCGAAAGTCAGCTGGCGGGCCGGGTGGGCTATGTTGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCAGTGAGCGCTTTCCGCTGATGAGCACCTTTAAAGTGCTGCTCTGCGGCGCGGTGCTGGCCCGGGTGGATGCCGGCGACGAACAGCTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGCCGACGGGATGACCGTTGGCGAACTCTGCGCCGCCGCCATCACCATGAGCGACAACAGCGCCGGCAATCTGCTGTTGAAGAGCGTCGGCGGCCCCGCGGGATTGACCGCTTTTCTGCGCCAGATCGGTGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTCAATGAGGCGCTTCCCGGCGACGTGCGCGACACCACCACCCCGGCCAGCATGGCCACCACCCTGCGCAAGTTGCTAACCACCCCCTCTCTGAGCGCCCGTTCGCAGCAGCAGCTGCTGCAGTGGATGGTGGACGACCGGGTGGCCGGCCCGTTGATCCGCGCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAAACCGGGGCCGGTGAGCGGGGCTCACGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAAGCGGAGCGTATCGTGGTGATCTATCTGCGGGATACCGCAGCGACCATGGCCGAACGTAACCAGCAGATCGCCGGGATAGGCGCGGCGCTGATCGAGCACTGGCAGCGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002439","ARO_id":"38839","ARO_name":"OKP-B-6","CARD_short_name":"OKP-B-6","ARO_description":"OKP-B-6 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"38817":{"category_aro_accession":"3002417","category_aro_cvterm_id":"38817","category_aro_name":"OKP beta-lactamase","category_aro_description":"OKP beta-lactamases are chromosomal class A beta-lactamase that confer resistance to penicillins and early cephalosporins in Klebsiella pneumoniae. OKP beta-lactamases can be subdivided into two groups: OKP-A and OKP-B which diverge by about 4.2%.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"564":{"model_id":"564","model_name":"IMP-22","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"8251":{"protein_sequence":{"accession":"ABC88434.1","sequence":"MKKLFVLCVFLFCSITAAGESLPDLKIEKLEEGVYVHTSFEEVNGWGVVSKHGLVILVNTDAYLIDTPFTAKDTEKLVTWFVERGYKIKGSISSHFHSDSTGGIEWLNSQSIPTYASELTNDLLKQNGKVQAKNSFSGVSYWLVKNKIEVFYPGPGHTQDNVVVWLPEKKILFGGCFVKPYGLGNLDDANVVAWPHSAEILMSRYGNAKLVVPSHSDIGDASLLKLTWEQAVKGLKESKKPSEPSN"},"dna_sequence":{"accession":"DQ361087.2","fmin":"356","fmax":"1097","strand":"+","sequence":"ATGAAGAAATTATTTGTTTTATGTGTGTTTTTGTTTTGTAGCATTACTGCCGCAGGAGAGTCTTTGCCCGATTTAAAAATTGAAAAGCTTGAAGAAGGTGTTTATGTTCATACATCGTTTGAAGAAGTTAATGGTTGGGGCGTTGTTTCTAAACACGGTTTGGTTATTCTTGTGAATACTGACGCCTATCTGATTGACACTCCATTCACGGCTAAAGATACTGAAAAGTTAGTCACCTGGTTTGTGGAGCGCGGCTATAAAATCAAAGGTAGCATTTCCTCACATTTCCATAGCGACAGCACGGGTGGAATAGAGTGGCTTAATTCTCAATCAATTCCCACGTATGCATCTGAATTAACAAATGACCTTCTTAAACAAAACGGTAAGGTACAAGCTAAAAACTCATTTAGCGGAGTTAGTTATTGGTTAGTTAAAAATAAAATTGAAGTTTTCTATCCCGGCCCCGGGCACACTCAAGATAACGTAGTGGTTTGGTTGCCTGAAAAGAAAATTTTATTTGGTGGGTGCTTTGTTAAACCGTACGGTCTTGGAAATCTCGATGACGCAAATGTTGTAGCATGGCCACATTCTGCTGAAATATTAATGTCTAGGTATGGTAATGCAAAACTGGTTGTTCCAAGCCATAGTGACATCGGAGATGCGTCGCTCTTGAAGCTTACATGGGAGCAGGCTGTTAAAGGGCTAAAAGAAAGTAAAAAACCATCAGAGCCAAGTAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36937","NCBI_taxonomy_name":"Pseudomonas fluorescens","NCBI_taxonomy_id":"294"}}}},"ARO_accession":"3002213","ARO_id":"38613","ARO_name":"IMP-22","CARD_short_name":"IMP-22","ARO_description":"IMP-22 is a beta-lactamase found in Pseudomonas spp.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"565":{"model_id":"565","model_name":"SHV-82","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"8206":{"protein_sequence":{"accession":"CAJ47137.2","sequence":"MRYVRLCIISLLATLPLAVHTSPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AM176557.2","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACACCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001136","ARO_id":"37516","ARO_name":"SHV-82","CARD_short_name":"SHV-82","ARO_description":"SHV-82 is a broad-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"566":{"model_id":"566","model_name":"OXA-32","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1761":{"protein_sequence":{"accession":"AAK58418.1","sequence":"MAIRIFAILFSIFSLATFAHAQEGTLERSDWRKFFSEFQAKGTIVVADERQADRAMLVFDPVRSKKRYSPASTFKIPHTLFALDAGAVRDEFQIFRWDGVNRGFAGHNQDQDLRSAMRNSTVWVYELFAKEIGDDKARRYLKKIDYGNADPSTSNGDYWIEGSIAISAQEQIAFLRKLYRNELPFRVEHQRLVKDLMIVEAGRNWILRAKTGWEGRMGWWVGWVEWPTGSVFFALNIDTPNRMDDLFKREAIVRAILRSIEALPPNPAVNSDAAR"},"dna_sequence":{"accession":"AF315351.1","fmin":"672","fmax":"1500","strand":"+","sequence":"ATGGCAATCCGAATCTTCGCGATACTTTTCTCCATTTTTTCTCTTGCCACTTTCGCGCATGCGCAAGAAGGCACGCTAGAACGTTCTGACTGGAGGAAGTTTTTCAGCGAATTTCAAGCCAAAGGCACGATAGTTGTGGCAGACGAACGCCAAGCGGATCGTGCCATGTTGGTTTTTGATCCTGTGCGATCGAAGAAACGCTACTCGCCTGCATCGACATTCAAGATACCTCATACACTTTTTGCACTTGATGCAGGCGCTGTTCGTGATGAGTTCCAGATTTTTCGATGGGACGGCGTTAACAGGGGCTTTGCAGGCCACAATCAAGACCAAGATTTGCGATCAGCAATGCGGAATTCTACTGTTTGGGTGTATGAGCTATTTGCAAAGGAAATTGGTGATGACAAAGCTCGGCGCTATTTGAAGAAAATCGACTATGGCAACGCCGATCCTTCGACAAGTAATGGCGATTACTGGATAGAAGGCAGCATTGCAATCTCGGCGCAGGAGCAAATTGCATTTCTCAGGAAGCTCTATCGTAACGAGCTGCCCTTTCGGGTAGAACATCAGCGCTTGGTCAAGGATCTCATGATTGTGGAAGCCGGTCGCAACTGGATACTGCGTGCAAAGACGGGCTGGGAAGGCCGTATGGGTTGGTGGGTAGGATGGGTTGAGTGGCCGACTGGCTCCGTATTCTTCGCACTGAATATTGATACGCCAAACAGAATGGATGATCTTTTCAAGAGGGAGGCAATCGTGCGGGCAATCCTTCGCTCTATTGAAGCGTTACCGCCCAACCCGGCAGTCAACTCGGACGCAGCGCGATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3001426","ARO_id":"37826","ARO_name":"OXA-32","CARD_short_name":"OXA-32","ARO_description":"OXA-32 is a beta-lactamase found in P. aeruginosa.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46493":{"category_aro_accession":"3007704","category_aro_cvterm_id":"46493","category_aro_name":"OXA-2-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-2.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"567":{"model_id":"567","model_name":"CTX-M-41","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1667":{"protein_sequence":{"accession":"AAY43008.1","sequence":"MMRKSVRRAMLMTTACVSLLLASVPLCAQANDVQQKLAALEKSSGGRLGVALINTADNTQTLYRADERFAMCSTSKVMAAAAVLKQSETQKGLLSQRVEIKPSDLVNYNPIAEKHVNGTMTFGELIAAALQYSDNTAMNKLIAHLGGPDKVTAFARTIGDDTFRLDRTEPTLNTAIPGDPRDTTTPLAMAQALRNLTLGNALGDTQRAQLVMWLKGNTTGAASIQAGLPTSWVVGDKTGSGGYGTTNDIAVIWPEGRAPLVLVTYFTQSEPKAESRRDVLAAAARIVTDGY"},"dna_sequence":{"accession":"DQ023162.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGATGAGAAAAAGCGTAAGGCGGGCGATGTTAATGACGACAGCCTGTGTTTCGCTGCTGTTGGCCAGTGTGCCGCTGTGTGCCCAGGCGAACGATGTTCAACAAAAGCTCGCGGCGCTGGAGAAAAGCAGCGGGGGACGACTGGGTGTGGCGTTGATTAACACCGCCGATAACACGCAGACGCTCTACCGCGCCGACGAGCGTTTTGCCATGTGCAGCACCAGTAAAGTGATGGCGGCAGCGGCGGTGCTTAAGCAAAGTGAAACGCAAAAGGGCTTGTTGAGTCAGCGGGTTGAAATTAAGCCCTCAGACTTGGTTAACTACAACCCCATTGCGGAAAAACACGTCAATGGCACGATGACATTCGGGGAGTTGATCGCGGCGGCGCTACAGTACAGCGATAATACTGCCATGAATAAGCTGATTGCCCATCTCGGGGGGCCGGATAAAGTGACGGCATTTGCCCGTACGATTGGCGATGACACGTTCCGGCTCGATCGTACCGAGCCGACGCTCAACACCGCGATCCCCGGCGACCCGCGCGATACCACCACGCCGTTAGCGATGGCGCAGGCTCTGCGCAATCTGACGTTGGGCAATGCCCTGGGTGACACTCAGCGTGCGCAGCTGGTGATGTGGCTGAAAGGCAACACCACCGGCGCTGCCAGCATTCAGGCAGGGCTACCCACATCGTGGGTTGTCGGGGATAAAACCGGCAGCGGCGGTTATGGTACGACGAATGATATCGCGGTTATTTGGCCGGAAGGTCGCGCGCCGCTCGTTCTGGTGACTTACTTCACCCAGTCGGAGCCGAAGGCAGAGAGCCGTCGTGACGTGCTCGCTGCTGCCGCCAGAATTGTCACCGACGGTTATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3001903","ARO_id":"38303","ARO_name":"CTX-M-41","CARD_short_name":"CTX-M-41","ARO_description":"CTX-M-41 is a beta-lactamase found in Proteus mirabilis.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"568":{"model_id":"568","model_name":"CTX-M-20","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1168":{"protein_sequence":{"accession":"CAC95175.1","sequence":"MMTQSIRRSMLTVMATLPLLFSSATLHAQANSVQQQLEALEKSSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKQSESDKHLLNQRVEIKKSDLVNYNPIAEKHVNGTMTLAELGAAALQYSDNTAMNKLIAHLGGPDKVTAFARSLGDETFRLDRTEPTLNTAIPGDPRDTTTPLAMAQTLKNLTLGKALAETQRAQLVTWLKGNTTGSASIRAGLPKSWVVGDKTGSGDYGTTNDIAVIWPENHAPLVLVTYFTQPEQKAESRRDFLAAAAKIVTHGF"},"dna_sequence":{"accession":"AJ416344.1","fmin":"303","fmax":"1179","strand":"+","sequence":"ATGATGACTCAGAGCATTCGCCGCTCAATGTTAACGGTGATGGCGACGCTACCCCTGCTATTTAGCAGCGCAACGCTGCATGCGCAGGCGAACAGCGTGCAACAGCAGCTGGAAGCCCTGGAGAAAAGTTCGGGAGGTCGGCTTGGCGTTGCGCTGATTAACACCGCCGATAATTCGCAGATTCTCTACCGTGCCGATGAACGTTTTGCGATGTGCAGTACCAGTAAGGTGATGGCGGCCGCGGCGGTGCTTAAACAGAGCGAGAGCGATAAGCACCTGCTAAATCAGCGCGTTGAAATCAAGAAGAGCGACCTGGTTAACTACAATCCCATTGCGGAGAAACACGTTAACGGCACGATGACGCTGGCTGAGCTTGGCGCAGCGGCGCTGCAGTATAGCGACAATACTGCCATGAATAAGCTGATTGCCCATCTGGGTGGTCCCGATAAAGTGACGGCGTTTGCTCGCTCGTTGGGTGATGAGACCTTCCGTCTGGACAGAACCGAGCCCACGCTCAATACCGCCATTCCAGGCGACCCGCGTGATACCACCACGCCGCTCGCGATGGCGCAGACCCTGAAAAATCTGACGCTGGGTAAAGCGCTGGCGGAAACTCAGCGGGCACAGTTGGTGACGTGGCTTAAGGGCAATACTACCGGTAGCGCGAGCATTCGGGCGGGTCTGCCGAAATCATGGGTAGTGGGCGATAAAACCGGCAGCGGAGATTATGGCACCACCAACGATATCGCGGTTATCTGGCCGGAAAACCACGCACCGCTGGTTCTGGTGACCTACTTTACCCAACCGGAGCAGAAGGCGGAAAGCCGTCGGGATTTTCTGGCTGCGGCGGCGAAAATCGTAACCCACGGTTTCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3001882","ARO_id":"38282","ARO_name":"CTX-M-20","CARD_short_name":"CTX-M-20","ARO_description":"CTX-M-20 is a beta-lactamase found in the Enterobacteriaceae family.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"569":{"model_id":"569","model_name":"OXA-228","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"2005":{"protein_sequence":{"accession":"AFM55001.1","sequence":"MKFKMKGLFCVILSSLAFSGCVYDSKLQRPVISERVTEIPLLFNQAQTQAVFVTYDGIHLKSYGNDLSRAKTEYIPASTFKMLNALIGLQNAKATNTEVFHWNGEKRAFSAWEKDMTLAEAMQASAVPVYQELARRIGLELMREEVKRVGFGNAEIGQQVDNFWLVGPLKISPEQEVQFAYQLAMKQLPFDSNVQQQVKDMLYIERRGDSKLYAKSGWGMDVEPQVGWYTGWVEQPNGKVTAFALNMNMQAGNDPAERKQLTLSILDKLGLFFYLR"},"dna_sequence":{"accession":"JQ422053.1","fmin":"99","fmax":"930","strand":"+","sequence":"ATGAAGTTTAAAATGAAAGGTTTATTTTGTGTCATCCTCAGTAGTTTGGCATTTTCAGGTTGTGTTTATGATTCAAAATTACAACGCCCAGTCATATCAGAGCGAGTAACTGAGATTCCTTTATTATTTAATCAAGCACAGACTCAAGCTGTGTTTGTTACTTATGATGGGATTCATCTAAAAAGTTATGGTAATGATCTAAGCCGAGCAAAGACTGAATATATTCCTGCATCTACATTTAAGATGTTGAATGCTTTAATTGGCTTGCAAAATGCAAAAGCAACCAATACTGAAGTATTTCATTGGAATGGTGAAAAGCGCGCTTTTTCAGCATGGGAAAAAGATATGACTTTGGCAGAAGCGATGCAGGCTTCAGCTGTTCCTGTATATCAAGAGCTTGCTCGACGTATTGGCTTGGAATTGATGCGTGAAGAAGTGAAGCGTGTAGGTTTTGGCAATGCGGAGATTGGTCAGCAAGTCGATAATTTTTGGTTGGTGGGTCCTTTAAAAATCTCCCCTGAACAAGAAGTTCAATTTGCCTATCAACTGGCAATGAAGCAATTGCCTTTTGATTCAAATGTACAGCAACAAGTCAAAGATATGCTTTATATCGAGAGACGTGGTGACAGTAAACTGTATGCTAAAAGTGGTTGGGGAATGGATGTTGAACCTCAAGTGGGTTGGTATACGGGATGGGTTGAACAACCCAATGGCAAGGTGACTGCATTTGCGTTAAATATGAACATGCAAGCAGGTAATGATCCAGCTGAACGTAAACAATTAACCTTAAGTATTTTGGACAAATTGGGTCTATTTTTTTATTTAAGATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39090","NCBI_taxonomy_name":"Acinetobacter bereziniae","NCBI_taxonomy_id":"106648"}}}},"ARO_accession":"3001691","ARO_id":"38091","ARO_name":"OXA-228","CARD_short_name":"OXA-228","ARO_description":"OXA-228 is a beta-lactamase found in A. bereziniae.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46498":{"category_aro_accession":"3007709","category_aro_cvterm_id":"46498","category_aro_name":"OXA-229-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-229.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"571":{"model_id":"571","model_name":"clbA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"4248":{"protein_sequence":{"accession":"AGZ55247.1","sequence":"MQQKNKYIRIQEFLKQNKFPDFRMNQIKNAVFQGRINHFNEITVLPKSLRKLLIEEFGESILNIAPLKVQHSEQVTKVLFEISGDEKIETVNMKYKAGWESFCISSQCGCHFGCKFCATGDIGLKRNLTSDEMTDQILYFHLKGHSIDSISFMGMGEALANVQVFDALHVLTNPELFALSPRRLSISTIGIIPGIKKITQDYPQVNLTFSLHSPFNEQRSKLMPINERYPLLEVMDTLDEHIRVTSRKVYIAYIMLPGVNDSIDHANEVVNLLRSRYKRGNLFHVNIIRYNPTVSSPMRFEEVNEKQVVNFYKKLKSAGINVTVRSQFGIDIDAACGQLYGNYQKNKNQ"},"dna_sequence":{"accession":"CP006845.1","fmin":"539695","fmax":"540745","strand":"+","sequence":"ATGCAACAAAAAAACAAGTATATAAGAATCCAAGAGTTCCTGAAGCAAAATAAATTTCCTGATTTTAGAATGAATCAAATCAAAAATGCTGTATTCCAAGGGAGAATAAATCATTTCAATGAAATAACGGTTCTTCCTAAATCCCTGAGAAAATTGTTAATAGAGGAGTTCGGAGAGTCGATTTTAAATATTGCTCCTTTAAAAGTGCAGCATTCTGAGCAAGTAACAAAAGTCTTATTTGAAATTTCCGGAGACGAAAAAATAGAAACGGTTAATATGAAATATAAAGCCGGTTGGGAGTCATTTTGTATATCCTCGCAGTGCGGCTGTCATTTCGGCTGTAAATTTTGTGCAACAGGAGATATTGGTTTAAAACGCAATTTAACGTCAGATGAAATGACTGACCAAATTTTGTACTTTCACTTAAAAGGACATTCAATTGACAGTATTTCTTTTATGGGAATGGGAGAAGCATTAGCGAATGTACAAGTTTTTGATGCTTTACATGTGCTTACAAATCCGGAGTTGTTTGCTTTAAGCCCTCGCAGGTTATCTATTTCGACTATAGGTATTATTCCGGGCATTAAAAAAATCACTCAGGATTATCCGCAGGTCAACCTGACGTTTTCATTACATTCTCCTTTTAATGAACAGCGAAGCAAGTTAATGCCGATTAATGAACGCTACCCGTTATTGGAGGTAATGGACACATTAGATGAGCATATACGTGTGACCTCAAGAAAAGTTTATATTGCTTATATTATGCTGCCGGGAGTTAATGATTCTATTGATCATGCGAATGAAGTAGTAAATCTTTTAAGAAGCAGATATAAGAGAGGGAACTTGTTCCATGTAAACATCATTAGATATAACCCGACTGTTAGTTCACCTATGAGATTTGAAGAAGTAAATGAGAAACAAGTTGTAAACTTCTATAAAAAATTAAAGTCAGCAGGAATTAACGTGACCGTCAGAAGTCAATTTGGTATTGATATAGATGCTGCTTGCGGACAATTATATGGAAATTATCAAAAAAATAAGAACCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41528","NCBI_taxonomy_name":"Bacillus amyloliquefaciens CC178","NCBI_taxonomy_id":"1412898"}}}},"ARO_accession":"3002814","ARO_id":"39248","ARO_name":"clbA","CARD_short_name":"clbA","ARO_description":"clbA is a plasmid-encoded cfr gene found in Bacillus velezensis (Bacillus amyloliquefaciens subsp. plantarum).","ARO_category":{"36341":{"category_aro_accession":"3000202","category_aro_cvterm_id":"36341","category_aro_name":"Cfr 23S ribosomal RNA methyltransferase","category_aro_description":"Cfr genes produce enzymes which catalyze the methylation of the 23S rRNA subunit at position 8 of adenine-2503. Methylation of 23S rRNA at this site confers resistance to some classes of antibiotics, including streptogramins, chloramphenicols, florfenicols, linezolids and clindamycin.","category_aro_class_name":"AMR Gene Family"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"36521":{"category_aro_accession":"3000382","category_aro_cvterm_id":"36521","category_aro_name":"azidamfenicol","category_aro_description":"Azidamfenicol is a water soluble derivative of chloramphenicol, sharing the same mode of action of inhibiting peptide synthesis by interacting with the 23S RNA of the 50S ribosomal subunit.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36595":{"category_aro_accession":"3000456","category_aro_cvterm_id":"36595","category_aro_name":"thiamphenicol","category_aro_description":"Derivative of Chloramphenicol. The nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3).","category_aro_class_name":"Antibiotic"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"virginiamycin M1","category_aro_description":"Virginiamycin M1 is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37015":{"category_aro_accession":"3000671","category_aro_cvterm_id":"37015","category_aro_name":"tiamulin","category_aro_description":"Tiamulin is a pleuromutilin derivative currently used in veterinary medicine. It binds to the 23 rRNA of the 50S ribosomal subunit to inhibit protein translation.","category_aro_class_name":"Antibiotic"},"37016":{"category_aro_accession":"3000672","category_aro_cvterm_id":"37016","category_aro_name":"madumycin II","category_aro_description":"Madumycin II is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37017":{"category_aro_accession":"3000673","category_aro_cvterm_id":"37017","category_aro_name":"griseoviridin","category_aro_description":"Griseoviridin is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35952":{"category_aro_accession":"0000034","category_aro_cvterm_id":"35952","category_aro_name":"streptogramin A antibiotic","category_aro_description":"Streptogramin A antibiotics are cyclic polyketide peptide hybrids that bind to the ribosomal peptidyl transfer centre. Structural variation arises from substituting a proline for its desaturated derivative and by its substitution for Ala or Cys. Used alone, streptogramin A antibiotics are bacteriostatic, but is bactericidal when used with streptogramin B antibiotics.","category_aro_class_name":"Drug Class"},"36218":{"category_aro_accession":"3000079","category_aro_cvterm_id":"36218","category_aro_name":"oxazolidinone antibiotic","category_aro_description":"Oxazolidinones are a class of synthetic antibiotics discovered the the 1980's.  They inhibit protein synthesis by binding to domain V of the 23S rRNA of the 50S subunit of bacterial ribosomes.  Linezolid is the only member of this class currently in clinical use.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"37014":{"category_aro_accession":"3000670","category_aro_cvterm_id":"37014","category_aro_name":"pleuromutilin antibiotic","category_aro_description":"Pleuromutilins are natural fungal products that target bacterial protein translation by binding the the 23S rRNA, blocking the ribosome P site at the 50S subunit. They are mostly used for agriculture and veterinary purposes.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"572":{"model_id":"572","model_name":"OXA-137","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"799":{"protein_sequence":{"accession":"ABW76138.1","sequence":"MSKKNFILIFIFVILTSCKNTEKISNETTLIDNIFTNSNAEGTLVIYNLNDDKYIIHNKERAEQRFYPASTFKIYNSLIGLNEKAVKDVDEVFYKYNGEKVFLESWAKDSNLRYAIKNSQVPAYKELARRIGLKKMKENIEKLDFGNKSIGDSVDTFWLEGPLEISAMEQIKLLTKLAQNELPYPIEIQKAVSDITILEQTYNYTLHGKTGLADSKNMTTEPIGWFVGWLEENDNIYVFALNIDNINSDDLAKRINIVKESLKALNLLK"},"dna_sequence":{"accession":"EU086834.1","fmin":"88","fmax":"898","strand":"+","sequence":"ATGTCTAAAAAAAATTTTATATTAATATTTATTTTTGTTATTTTAACATCTTGTAAAAATACAGAAAAAATATCAAATGAAACTACATTAATAGATAATATATTTACTAATAGCAATGCTGAAGGAACATTAGTTATATATAATTTAAATGATGATAAATATATAATTCATAATAAAGAAAGAGCTGAACAAAGATTTTATCCAGCATCAACATTTAAAATATATAATAGTTTAATAGGCTTAAATGAAAAAGCAGTTAAAGATGTAGATGAAGTATTTTATAAATATAATGGCGAAAAAGTTTTTCTTGAATCTTGGGCTAAGGACTCTAATTTAAGATATGCAATTAAAAATTCGCAAGTACCGGCATATAAAGAATTAGCAAGAAGAATAGGTCTTAAAAAGATGAAAGAGAATATAGAAAAACTAGATTTTGGTAATAAAAGTATAGGTGATAGTGTAGATACTTTTTGGCTTGAAGGACCTTTGGAAATAAGTGCGATGGAGCAAATTAAATTATTAACTAAATTAGCTCAAAATGAATTACCGTATCCTATAGAAATACAAAAAGCTGTTTCTGATATTACTATACTAGAGCAAACTTACAATTATACGCTTCATGGAAAAACTGGATTAGCTGATTCTAAAAACATGACAACTGAGCCTATTGGTTGGTTCGTAGGCTGGCTTGAAGAAAATGATAATATATATGTCTTTGCTTTAAATATTGATAATATAAATTCAGATGACCTTGCAAAAAGGATAAATATAGTAAAAGAAAGTTTAAAAGCATTAAATTTATTAAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36935","NCBI_taxonomy_name":"Brachyspira pilosicoli","NCBI_taxonomy_id":"52584"}}}},"ARO_accession":"3001767","ARO_id":"38167","ARO_name":"OXA-137","CARD_short_name":"OXA-137","ARO_description":"OXA-137 is a beta-lactamase found in Brachyspira spp.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46521":{"category_aro_accession":"3007732","category_aro_cvterm_id":"46521","category_aro_name":"OXA-63-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-63.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"573":{"model_id":"573","model_name":"OXA-136","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"2000":{"protein_sequence":{"accession":"ABW76134.1","sequence":"MSKKNFILIFIFVILISCKNTEKISNETTLIDNIFTNSNAEGTLVIYNLNDDKYIIHNKERAEQRFYPASTFKIYNSLIGLNEKAVKDVDEVFYKYNGEKVFLESWAKDSNLRYAIKNSQVPAYKELARRIGLKKMKENIEKLDFGNKSIGDSVDTFWLEGPLEISAMEQVKLLTKLAQNELPYPIEIQKAVSDITILEQTYNYTLHGKTGLADSKNMTTEPIGWFVGWLEENDNIYVFALNIDNINSDDLAKRINIVKESLKALNLLK"},"dna_sequence":{"accession":"EU086830.1","fmin":"88","fmax":"898","strand":"+","sequence":"ATGTCTAAAAAAAATTTTATATTAATATTTATTTTTGTTATTTTAATATCTTGTAAAAATACAGAAAAAATATCAAATGAAACTACATTAATAGATAATATATTTACTAATAGCAATGCTGAAGGAACATTAGTTATATATAATTTAAATGATGATAAATATATAATTCATAATAAAGAAAGAGCTGAACAAAGATTTTATCCAGCATCAACATTTAAAATATATAATAGTTTAATAGGCTTAAATGAAAAAGCAGTTAAAGATGTAGATGAAGTATTTTATAAATATAATGGCGAAAAAGTTTTTCTTGAATCTTGGGCTAAGGACTCTAATTTAAGATATGCAATTAAAAATTCGCAAGTACCGGCATATAAAGAATTAGCAAGAAGAATAGGTCTTAAAAAGATGAAAGAGAATATAGAAAAACTAGATTTTGGTAATAAAAGTATAGGTGATAGTGTAGATACTTTTTGGCTTGAAGGACCTTTGGAAATAAGTGCGATGGAGCAAGTTAAATTATTAACTAAATTAGCTCAAAATGAATTACCGTATCCTATAGAAATACAAAAAGCTGTTTCTGATATTACTATACTAGAGCAAACTTACAATTATACGCTTCATGGAAAAACTGGATTAGCTGATTCTAAAAACATGACAACTGAGCCTATTGGTTGGTTCGTAGGCTGGCTTGAAGAAAATGATAATATATATGTCTTTGCTTTAAATATTGATAATATCAATTCAGATGACCTTGCAAAAAGGATAAATATAGTAAAAGAAAGTTTAAAAGCATTAAATTTATTAAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36935","NCBI_taxonomy_name":"Brachyspira pilosicoli","NCBI_taxonomy_id":"52584"}}}},"ARO_accession":"3001765","ARO_id":"38165","ARO_name":"OXA-136","CARD_short_name":"OXA-136","ARO_description":"OXA-136 is a beta-lactamase found in Brachyspira spp.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46521":{"category_aro_accession":"3007732","category_aro_cvterm_id":"46521","category_aro_name":"OXA-63-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-63.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"574":{"model_id":"574","model_name":"AAC(6')-Ia","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"547":{"protein_sequence":{"accession":"AAA98298.1","sequence":"MNYQIVNIAECSNYQLEAANILTEAFNDLGNNSWPDMTSATKEVKECIESPNLCFGLLINNSLVGWIGLRPMYKETWELHPLVVRPDYQNKGIGKILLKELENRAREQGIIGIALGTDDEYYRTSLSLITITEDNIFDSIKNIKNINKHPYEFYQKNGYYIVGIIPNANGKNKPDIWMWKSLIKE"},"dna_sequence":{"accession":"M18967.1","fmin":"756","fmax":"1314","strand":"+","sequence":"ATGAATTATCAAATTGTGAATATTGCGGAATGCAGCAATTATCAGTTAGAAGCAGCAAATATACTAACAGAAGCGTTCAATGATCTTGGTAACAATTCATGGCCAGATATGACGAGTGCAACAAAAGAAGTAAAAGAATGTATTGAGAGTCCAAACCTTTGTTTCGGTCTGCTAATAAATAACTCCTTAGTTGGCTGGATAGGCTTAAGGCCAATGTACAAGGAAACCTGGGAATTGCATCCATTGGTTGTCAGACCAGATTATCAAAATAAAGGTATTGGCAAGATCCTGCTTAAGGAATTAGAAAACAGAGCTAGAGAGCAAGGTATTATTGGAATCGCTTTAGGAACAGATGATGAATACTATAGAACAAGTCTCTCTTTAATAACTATAACAGAAGATAATATATTTGATTCAATAAAAAATATTAAAAATATTAATAAACATCCATATGAGTTTTATCAGAAGAATGGTTATTATATTGTTGGAATAATTCCAAATGCCAATGGTAAAAACAAACCAGATATTTGGATGTGGAAAAGTTTAATCAAAGAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39508","NCBI_taxonomy_name":"Plasmid R","NCBI_taxonomy_id":"2508"}}}},"ARO_accession":"3002545","ARO_id":"38945","ARO_name":"AAC(6')-Ia","CARD_short_name":"AAC(6')-Ia","ARO_description":"AAC(6')-Ia is an aminoglycoside acetyltransferase encoded by plasmids, transposons, integrons in Citrobacter diversus, E. coli, K. pneumoniae, Shigella sonnei, and P. aeruginosa.","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"A category of aminoglycoside N-acetyltransferase enzymes with modification regiospecificity based at the 6'-amino group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics through acetylation of the 6-amino group of the compound.","category_aro_class_name":"AMR Gene Family"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"46128":{"category_aro_accession":"3007378","category_aro_cvterm_id":"46128","category_aro_name":"2'-N-ethylnetilmicin","category_aro_description":"2'-N-ethylnetilmicin is an aminoglycoside antibiotic and a derivative of netilmicin.","category_aro_class_name":"Antibiotic"},"46129":{"category_aro_accession":"3007379","category_aro_cvterm_id":"46129","category_aro_name":"5-episisomicin","category_aro_description":"5-episosomicin is a semisynthetic aminoglycoside antibiotic similar to sisomicin.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"575":{"model_id":"575","model_name":"AAC(3)-Ib","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"224":{"protein_sequence":{"accession":"AAA88422.1","sequence":"MLWSSNDVTQQGSRPKTKLGGSMSIIATVKIGPDEISAMRAVLDLFGKEFEDIPTYSDRQPTNEYLANLLHSETFIALAAFDRGTAIGGLAAYVLPKFEQARSEIYIYDLAVASSHRRLGVATALISHLKRVAVELGAYVIYVQADYGDDPAVALYTKLGVREDVMHFDIDPRTAT"},"dna_sequence":{"accession":"L06157.1","fmin":"554","fmax":"1085","strand":"+","sequence":"ATGTTATGGAGCAGCAACGATGTTACGCAGCAGGGCAGTCGCCCTAAAACAAAGTTAGGTGGCTCAATGAGCATCATTGCAACCGTCAAGATCGGCCCTGACGAAATTTCAGCCATGAGGGCTGTGCTCGATCTCTTCGGCAAAGAGTTTGAGGACATTCCAACCTACTCTGATCGCCAGCCGACCAATGAGTATCTTGCCAATCTTCTGCACAGCGAGACGTTCATCGCGCTCGCTGCTTTTGACCGCGGAACAGCAATAGGTGGGCTCGCCGCCTACGTTCTACCCAAGTTCGAGCAAGCGCGAAGCGAGATCTACATTTATGACTTGGCAGTCGCTTCCAGCCATCGAAGGCTAGGAGTCGCAACTGCCCTGATTAGCCACCTGAAGCGTGTGGCGGTTGAACTTGGCGCGTATGTAATCTATGTGCAAGCAGACTACGGTGACGATCCGGCAGTCGCTCTCTACACAAAGCTTGGAGTTCGGGAAGACGTCATGCACTTCGACATTGATCCAAGAACCGCCACCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002530","ARO_id":"38930","ARO_name":"AAC(3)-Ib","CARD_short_name":"AAC(3)-Ib","ARO_description":"AAC(3)-Ib is an integron-encoded aminoglycoside acetyltransferase in P. aeruginosa.","ARO_category":{"36461":{"category_aro_accession":"3000322","category_aro_cvterm_id":"36461","category_aro_name":"AAC(3)","category_aro_description":"A category of aminoglycoside N-acetyltransferase enzymes with modification regiospecificity based at the 3-amino group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics through acetylation of the 3-amino group of the compound.","category_aro_class_name":"AMR Gene Family"},"35922":{"category_aro_accession":"0000003","category_aro_cvterm_id":"35922","category_aro_name":"astromicin","category_aro_description":"Astromicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Astromicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"46133":{"category_aro_accession":"3007382","category_aro_cvterm_id":"46133","category_aro_name":"gentamicin","category_aro_description":"Gentamicin is a commonly used aminoglycoside antibiotic derived from members of the Micromonospora genus of bacteria. It acts by binding the 30S ribosomal subunit, thus inhibiting protein synthesis. Gentamicin is typically used to treat Gram-negative infections of the repiratory and urinary tract, as well as infections of the bone and soft tissue. It also exhibits considerable nephrotoxicity and ototoxicity. Gentamicin is administered as a mixture of gentamicin type C (which makes about around 80% of the complex) and types A, B, and X (distributed in the remaining 20% of the complex).","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"576":{"model_id":"576","model_name":"MIR-5","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"1978":{"protein_sequence":{"accession":"AJO16037.1","sequence":"MMTKSLSCALLLSVASSAFAAPMSEKQLAEVVERTVTPLMNAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEIALGDPVAKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDTASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMSYEQAMTTRVFKPLKLDHTWINVPKAEEAHYAWGYREGKAVHVSPGMLDAEAYGVKTNVKDMASWLIANMKPDSLQAPSLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVGGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILDALQ"},"dna_sequence":{"accession":"KP050484.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGACAAAATCCCTAAGCTGTGCCCTGCTGCTCAGCGTCGCCAGTTCTGCATTCGCCGCACCGATGTCCGAAAAACAGCTGGCTGAGGTGGTGGAACGTACCGTTACGCCGCTGATGAACGCGCAGGCCATTCCGGGTATGGCGGTGGCGGTAATTTATCAGGGTCAGCCACACTACTTTACCTTCGGTAAAGCCGATGTTGCGGCGAACAAACCCGTCACCCCGCAAACCCTGTTTGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTACTGGGCGGCGATGCCATTGCCCGGGGTGAAATAGCGCTGGGCGATCCGGTAGCAAAATACTGGCCTGAGCTCACGGGCAAGCAGTGGCAGGGCATTCGCATGCTGGATCTGGCAACCTATACCGCAGGCGGTCTGCCGTTACAGGTGCCGGATGAGGTCACGGATACCGCCTCTCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCGGGCACCACGCGTCTTTACGCTAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTTAAACCTTCCGGCATGAGCTATGAGCAGGCCATGACGACGCGGGTCTTTAAACCCCTCAAGCTGGACCATACCTGGATTAACGTCCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGATACCGTGAGGGTAAAGCGGTCCACGTTTCGCCAGGGATGCTGGACGCGGAAGCCTATGGCGTAAAAACTAACGTGAAGGATATGGCGAGCTGGCTGATAGCCAACATGAAGCCGGATTCTCTTCAGGCTCCCTCACTCAAGCAAGGCATTGCTCTGGCGCAGTCTCGCTACTGGCGCGTGGGGGCTATGTATCAGGGGTTAGGCTGGGAGATGCTCAACTGGCCGGTCGATGCCAAAACCGTCGTCGGAGGCAGTGATAACAAGGTGGCGCTGGCACCATTGCCCGTGGCAGAAGTGAATCCACCCGCGCCGCCGGTCAAGGCCTCCTGGGTCCATAAAACAGGCTCGACGGGCGGGTTTGGCAGCTACGTGGCATTTATTCCTGAAAAGCAGCTCGGCATTGTGATGCTGGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCGTATCCTCGACGCGCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36926","NCBI_taxonomy_name":"Enterobacter asburiae","NCBI_taxonomy_id":"61645"}}}},"ARO_accession":"3002170","ARO_id":"38570","ARO_name":"MIR-5","CARD_short_name":"MIR-5","ARO_description":"MIR-5 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36197":{"category_aro_accession":"3000058","category_aro_cvterm_id":"36197","category_aro_name":"MIR beta-lactamase","category_aro_description":"MIR beta-lactamases are plasmid-mediated beta-lactamases that confer resistance to oxyimino- and alpha-methoxy beta-lactams.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"577":{"model_id":"577","model_name":"QnrB65","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"115":{"protein_sequence":{"accession":"AGL43626.1","sequence":"MTLALVGEKIDRNRFTGEKVENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRANLKDAIFKSCDLSMADFRNINALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGTQVLGATFSGSDLSGGEFSSFDWRAANVTHCDLTNSELGDLDIRGVDLQGVKLDSYQASLLLERLGIAVMG"},"dna_sequence":{"accession":"KC580654.1","fmin":"0","fmax":"645","strand":"+","sequence":"ATGACTCTGGCGTTAGTTGGCGAAAAAATTGACAGAAACAGGTTCACCGGTGAGAAAGTCGAAAATAGCACATTTTTCAACTGTGATTTTTCGGGTGCCGACCTTAGCGGTACTGAATTTATTGGCTGCCAGTTTTATGATCGAGAAAGCCAGAAAGGGTGTAATTTTAGTCGCGCTAACCTGAAGGATGCCATTTTCAAAAGTTGTGATCTCTCCATGGCGGATTTCAGAAATATCAATGCGCTGGGAATCGAAATTCGCCACTGCCGGGCACAAGGGGCAGATTTTCGCGGCGCAAGCTTTATGAATATGATCACCACCCGCACCTGGTTTTGTAGCGCCTATATCACCAATACCAACTTAAGCTACGCCAACTTTTCTAAAGTCGTACTGGAAAAGTGCGAGCTGTGGGAAAACCGCTGGATGGGTACTCAGGTGCTGGGCGCAACGTTCAGTGGATCAGACCTCTCTGGCGGCGAGTTTTCATCCTTCGACTGGCGAGCAGCAAACGTTACGCACTGTGATTTGACCAATTCGGAACTGGGCGATTTAGATATCCGTGGGGTTGATTTGCAAGGCGTCAAACTGGACAGCTACCAGGCATCGTTGCTCCTGGAACGTCTTGGCATCGCTGTCATGGGTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002777","ARO_id":"39211","ARO_name":"QnrB65","CARD_short_name":"QnrB65","ARO_description":"QnrB65 is a plasmid-mediated quinolone resistance protein found in Citrobacter freundii.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"578":{"model_id":"578","model_name":"SHV-11","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1062":{"protein_sequence":{"accession":"CAA66729.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"X98101.1","fmin":"73","fmax":"934","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACATCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001070","ARO_id":"37450","ARO_name":"SHV-11","CARD_short_name":"SHV-11","ARO_description":"SHV-11 is a broad-spectrum beta-lactamase found in E. coli, Klebsiella pneumoniae, Proteus mirabilis, and Shigella dysenteriae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"579":{"model_id":"579","model_name":"vgaA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1050"}},"model_sequences":{"sequence":{"5183":{"protein_sequence":{"accession":"AAA26684.1","sequence":"MKIMLEGLNIKHYVQDRLLLNINRLKIYQNDRIGLIGKNGSGKTTLLHILYKKIVPEEGIVKQFSHCELIPQLKLIESTKSGGEVTRNYIRQALDKNPELLLADEPTTNLDNNYIEKLEQDLKNWHGAFIIVSHDRAFLDNLCTTIWEIDEGRITEYKGNYSNYVEQKELERHREELEYEKYEKEKKRLEKAINIKEQKAQRATKKPKNLSLSEGKIKGAKPYFAGKQKKLRKTVKSLETRLEKLESVEKRNELPPLKMDLVNLESVKNRTIIRGEDVSGTIEGRVLWKAKSFSIRGGDKMAIIGSNGTGKTTFIKKIVHGNPGISLSPSVKIGYFSQKIDTLELDKSILENVQSSSQQNETLIRTILARMHFFRDDVYKPISVLSGGERVKVALTKVFLSEVNTLVLDEPTNFLDMEAIEAFESLLKEYNGSIIFVSHDRKFIEKVATRIMTIDNKEIKIFDGTYEQFKQAEKPTRNIKEDKKLLLETKITEVLSRLSIEPSEELEQEFQNLINEKRNLDK"},"dna_sequence":{"accession":"M90056.1","fmin":"908","fmax":"2477","strand":"+","sequence":"ATGAAAATAATGTTAGAGGGACTTAATATAAAACATTATGTTCAAGATCGTTTATTGTTGAACATAAATCGCCTAAAGATTTATCAGAATGATCGTATTGGTTTAATTGGTAAAAATGGAAGTGGAAAAACAACGTTACTTCACATATTATATAAAAAAATTGTGCCTGAAGAAGGTATTGTAAAACAATTTTCACATTGTGAACTTATTCCTCAATTGAAGCTCATAGAATCAACTAAAAGTGGTGGTGAAGTAACACGAAACTATATTCGGCAAGCGCTTGATAAAAATCCAGAACTGCTATTAGCAGATGAACCAACAACTAACTTAGATAATAACTATATAGAAAAATTAGAACAGGATTTAAAAAATTGGCATGGAGCATTTATTATAGTTTCACATGATCGCGCTTTTTTAGATAACTTGTGTACTACTATATGGGAAATTGACGAGGGAAGAATAACTGAATATAAGGGGAATTATAGTAACTATGTTGAACAAAAAGAATTAGAAAGACATCGAGAAGAATTAGAATATGAAAAATATGAAAAAGAAAAGAAACGATTGGAAAAAGCTATAAATATAAAAGAACAGAAAGCTCAACGAGCAACTAAAAAACCGAAAAACTTAAGTTTATCTGAAGGCAAAATAAAAGGAGCAAAGCCATACTTTGCAGGTAAGCAAAAGAAGTTACGAAAAACTGTAAAATCTCTAGAAACCAGACTAGAAAAACTTGAAAGCGTCGAAAAGAGAAACGAACTTCCTCCACTTAAAATGGATTTAGTGAACTTAGAAAGTGTAAAAAATAGAACTATAATACGTGGTGAAGATGTCTCGGGTACAATTGAAGGACGGGTATTGTGGAAAGCAAAAAGTTTTAGTATTCGCGGAGGAGACAAGATGGCAATTATCGGATCTAATGGTACAGGAAAGACAACGTTTATTAAAAAAATTGTGCATGGGAATCCTGGTATTTCATTATCGCCATCTGTCAAAATCGGTTATTTTAGCCAAAAAATAGATACATTAGAATTAGATAAGAGCATTTTAGAAAATGTTCAATCTTCTTCACAACAAAATGAAACTCTTATTCGAACTATTCTAGCTAGAATGCATTTTTTTAGAGATGATGTTTATAAACCAATAAGTGTCTTAAGTGGTGGAGAGCGAGTTAAAGTAGCACTAACTAAAGTATTCTTAAGTGAAGTTAATACGTTGGTACTAGATGAACCAACAAACTTTCTTGATATGGAAGCTATAGAGGCGTTTGAATCTTTGTTAAAGGAATATAATGGCAGTATAATCTTTGTATCTCACGATCGTAAATTTATCGAAAAAGTAGCCACTCGAATAATGACAATTGATAATAAAGAAATAAAAATATTTGATGGCACATATGAACAATTTAAACAAGCTGAAAAGCCAACAAGGAATATTAAAGAAGATAAAAAACTTTTACTTGAGACAAAAATTACAGAAGTACTCAGTCGATTGAGTATTGAACCTTCGGAAGAATTAGAACAAGAGTTTCAAAACTTAATAAATGAAAAAAGAAATTTGGATAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35508","NCBI_taxonomy_name":"Staphylococcus aureus","NCBI_taxonomy_id":"1280"}}}},"ARO_accession":"3002829","ARO_id":"39263","ARO_name":"vgaA","CARD_short_name":"vgaA","ARO_description":"vgaA is an ABC-F subfamily protein expressed in staphylococci that confers resistance to streptogramin A antibiotics and related compounds. It is associated with plasmid DNA.","ARO_category":{"36252":{"category_aro_accession":"3000113","category_aro_cvterm_id":"36252","category_aro_name":"vga-type ABC-F protein","category_aro_description":"Vga-type plasmid-borne ABC-F proteins, expressed in staphylococci that confer resistance to streptogramin A antibiotics through ribosomal protection.","category_aro_class_name":"AMR Gene Family"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"virginiamycin M1","category_aro_description":"Virginiamycin M1 is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35952":{"category_aro_accession":"0000034","category_aro_cvterm_id":"35952","category_aro_name":"streptogramin A antibiotic","category_aro_description":"Streptogramin A antibiotics are cyclic polyketide peptide hybrids that bind to the ribosomal peptidyl transfer centre. Structural variation arises from substituting a proline for its desaturated derivative and by its substitution for Ala or Cys. Used alone, streptogramin A antibiotics are bacteriostatic, but is bactericidal when used with streptogramin B antibiotics.","category_aro_class_name":"Drug Class"},"37014":{"category_aro_accession":"3000670","category_aro_cvterm_id":"37014","category_aro_name":"pleuromutilin antibiotic","category_aro_description":"Pleuromutilins are natural fungal products that target bacterial protein translation by binding the the 23S rRNA, blocking the ribosome P site at the 50S subunit. They are mostly used for agriculture and veterinary purposes.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"580":{"model_id":"580","model_name":"TEM-110","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1566":{"protein_sequence":{"accession":"AAL68923.1","sequence":"MSIQHFRVALIPFFAAFCFPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYMTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AY072920.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCTTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACATGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3000973","ARO_id":"37353","ARO_name":"TEM-110","CARD_short_name":"TEM-110","ARO_description":"TEM-110 is a broad-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"581":{"model_id":"581","model_name":"QnrB19","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"484":{"protein_sequence":{"accession":"AGK90303.1","sequence":"MTLALVGEKIDRNRFTGEKVENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNVSALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGTQVLGATFSGSDLSGGEFSTFDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDSYQASLLMERLGIAVIG"},"dna_sequence":{"accession":"JX298080.1","fmin":"433","fmax":"1078","strand":"+","sequence":"ATGACTCTGGCATTAGTTGGCGAAAAAATTGACAGAAATCGCTTCACCGGTGAGAAAGTTGAAAATAGTACATTTTTTAACTGCGATTTTTCAGGTGCCGACCTGAGCGGCACTGAATTTATCGGCTGCCAGTTCTATGATCGCGAAAGTCAGAAAGGGTGCAATTTTAGTCGCGCAATGCTGAAAGATGCCATTTTCAAAAGCTGTGATTTATCAATGGCAGATTTCCGCAACGTCAGTGCCTTGGGCATTGAAATTCGCCACTGCCGCGCACAAGGCGCAGATTTCCGCGGTGCAAGCTTTATGAATATGATCACCACGCGCACCTGGTTTTGCAGCGCATATATCACTAATACTAATCTAAGCTACGCCAATTTTTCGAAAGTCGTGTTGGAAAAGTGTGAGCTGTGGGAAAACCGCTGGATGGGGACTCAGGTACTGGGTGCGACGTTCAGTGGTTCAGATCTCTCCGGCGGCGAGTTTTCGACTTTCGACTGGCGAGCAGCAAACTTCACACATTGCGATCTGACCAATTCGGAGTTAGGTGACTTAGATATTCGGGGTGTTGATTTACAAGGCGTTAAGTTAGACAGCTACCAGGCATCGTTGCTCATGGAGCGGCTTGGCATCGCTGTGATTGGTTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002734","ARO_id":"39168","ARO_name":"QnrB19","CARD_short_name":"QnrB19","ARO_description":"QnrB19 is a plasmid-mediated quinolone resistance protein found in Escherichia coli.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"582":{"model_id":"582","model_name":"FOX-7","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1355":{"protein_sequence":{"accession":"CAG28256.1","sequence":"MQQRRAFALLTLGSLLLAPCTYARGEAPLTAAVDGIIQPMLKEYRIPGMAVAVLKDGKAHYFNYGVANRESGQRVSEQTLFEIGSVSKTLTATLGAYAAVKGGFELDDKVSQHAPWLKGSAFDGVTMAELATYSAGGLPLQFPDEVDSNDKMRTYYRHWSPVYPAGTHRQYSNPSIGLFGHLAANSLGQPFEQLMSQTLLPKLGLHHTYIQVPESAIANYAYGYSKEDKPVRATPGVLAAEAYGIKTGSADLLKFTEANMGYQGDAALKSAIALTHTGFYSVGDMTQGLGWESYAYPLTEQALLAGNSPAVSFQANPVTRFAVPKAMGEQRLYNKTGSTGGFGAYVAFVPARGIAIVMLANRNYPIEARVKAAHAILSQLAE"},"dna_sequence":{"accession":"AJ703795.1","fmin":"0","fmax":"1149","strand":"+","sequence":"ATGCAACAACGACGTGCGTTCGCGCTACTGACGCTGGGTAGCCTGCTGCTAGCCCCTTGTACTTATGCCCGCGGGGAGGCTCCGCTGACCGCCGCTGTGGACGGCATTATCCAGCCGATGCTCAAGGAGTATCGGATCCCGGGGATGGCGGTCGCCGTGCTGAAAGATGGCAAGGCCCACTATTTCAACTATGGGGTTGCCAACCGCGAGAGTGGTCAGCGCGTCAGCGAGCAGACCCTGTTCGAGATTGGCTCGGTCAGCAAGACCCTGACCGCGACCCTCGGTGCCTATGCTGCGGTCAAGGGGGGCTTTGAGCTGGATGACAAGGTGAGCCAGCACGCCCCCTGGCTCAAAGGTTCCGCCTTTGATGGTGTGACCATGGCCGAGCTTGCCACCTACAGTGCGGGTGGTTTGCCGCTGCAGTTCCCCGATGAGGTGGATTCGAATGACAAGATGCGCACTTACTATCGGCACTGGTCACCGGTTTATCCGGCGGGGACCCATCGCCAGTATTCCAACCCCAGCATAGGCCTGTTTGGTCACCTGGCCGCAAATAGTCTGGGCCAGCCATTTGAGCAACTGATGAGCCAGACCCTGCTGCCCAAGCTGGGTTTGCACCACACCTATATTCAGGTGCCGGAGTCGGCCATAGCGAACTATGCCTACGGCTATTCGAAGGAAGATAAGCCCGTCCGGGCCACTCCGGGCGTGCTGGCGGCCGAGGCTTACGGGATCAAGACCGGCTCGGCGGATCTGCTGAAGTTTACCGAGGCCAACATGGGGTATCAGGGAGATGCCGCGCTAAAAAGCGCGATCGCGCTGACCCATACCGGTTTCTACTCGGTGGGAGACATGACTCAGGGGCTGGGTTGGGAGAGCTACGCCTATCCGTTGACCGAGCAGGCGCTGCTGGCGGGCAACTCCCCGGCGGTGAGCTTCCAGGCCAATCCGGTTACGCGCTTTGCGGTGCCCAAAGCGATGGGCGAGCAGCGGCTCTATAACAAGACGGGCTCGACTGGCGGCTTTGGCGCCTATGTGGCGTTCGTGCCCGCCAGAGGGATCGCCATCGTCATGCTGGCCAATCGCAACTATCCCATCGAGGCCAGGGTGAAGGCGGCTCACGCCATCCTGAGTCAGTTGGCCGAGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002160","ARO_id":"38560","ARO_name":"FOX-7","CARD_short_name":"FOX-7","ARO_description":"FOX-7 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36206":{"category_aro_accession":"3000067","category_aro_cvterm_id":"36206","category_aro_name":"FOX beta-lactamase","category_aro_description":"FOX beta-lactamases are plasmid-encoded AmpC-type beta-lactamase which conferred resistance to broad-spectrum cephalosporins and cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"583":{"model_id":"583","model_name":"SHV-100","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1542":{"protein_sequence":{"accession":"CAQ03505.1","sequence":"MRFIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIESESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AM941846.1","fmin":"0","fmax":"900","strand":"+","sequence":"ATGCGTTTTATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACATCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGAGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATCGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001338","ARO_id":"37738","ARO_name":"SHV-100","CARD_short_name":"SHV-100","ARO_description":"SHV-100 is a beta-lactamase found in Klebsiella pneumoniae. It differs from SHV-1 by a 35SESQLSGRVGMIE36 insertion.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"584":{"model_id":"584","model_name":"aadA21","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"195":{"protein_sequence":{"accession":"AAN87151.1","sequence":"MRVAVTIEISNQLSEVLSVIERHLESTLLAVHLYGSAVDGGLKPYSDIDLLVTVTVRLDETTRRALINDLLETSASPGESEILRAVEVTIVVHDDIIPWRYPAKRELQFGEWQRNDILAGIFEPATIDIDLAILLTKAREHSVALVGPAAEELFDPVPEQDLFEALNETLTLWNSPPDWAGDERNVVLTLSRIWYSAVTGKIAPKDVARDWAMERLPAQYQPVILEARQAYLGQEEDRLASRADQLEEFVHYVKGEITKVVGK"},"dna_sequence":{"accession":"AY171244.1","fmin":"46","fmax":"838","strand":"+","sequence":"ATGAGGGTAGCGGTGACCATCGAAATTTCGAACCAACTATCAGAGGTGCTAAGCGTCATTGAGCGCCATCTGGAATCAACGTTGCTGGCCGTGCATTTGTACGGCTCCGCAGTGGATGGCGGCCTGAAGCCATACAGCGATATTGATTTGCTGGTTACGGTGACCGTAAGGCTTGATGAAACAACGCGGCGAGCTTTGATCAACGACCTTTTGGAAACTTCGGCTTCCCCTGGAGAGAGCGAGATTCTCCGCGCTGTAGAAGTCACCATTGTTGTGCACGACGACATCATTCCGTGGCGTTATCCAGCTAAGCGCGAACTGCAATTTGGAGAATGGCAGCGCAATGACATTCTTGCAGGTATCTTCGAGCCAGCCACGATCGACATTGATCTGGCTATCTTGCTGACAAAAGCAAGAGAACATAGCGTTGCCTTGGTAGGTCCAGCGGCGGAGGAACTCTTTGATCCGGTTCCTGAACAGGATCTATTTGAGGCGCTAAATGAAACCTTAACGCTATGGAACTCGCCGCCCGACTGGGCTGGCGATGAGCGAAATGTAGTGCTTACGTTGTCCCGCATTTGGTACAGCGCAGTAACCGGCAAAATCGCGCCGAAGGATGTCGCTCGCGACTGGGCAATGGAGCGCCTGCCGGCCCAGTATCAGCCCGTCATACTTGAAGCTAGACAGGCTTATCTTGGACAAGAAGAAGATCGCTTGGCCTCGCGCGCAGATCAGTTGGAAGAATTTGTCCACTACGTGAAAGGCGAGATCACCAAGGTAGTCGGCAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35732","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Typhimurium","NCBI_taxonomy_id":"90371"}}}},"ARO_accession":"3002618","ARO_id":"39018","ARO_name":"aadA21","CARD_short_name":"aadA21","ARO_description":"aadA21 is an integron-encoded aminoglycoside nucleotidyltransferase gene in Salmonella spp.","ARO_category":{"41439":{"category_aro_accession":"3004275","category_aro_cvterm_id":"41439","category_aro_name":"ANT(3'')","category_aro_description":"A category of aminoglycoside O-nucleotidyltransferase enzymes with modification regiospecificity based at the 3''-hydroxyl group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics by transfer of an AMP group from an ATP substrate to the 3''-hydroxyl group of the compound.","category_aro_class_name":"AMR Gene Family"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"585":{"model_id":"585","model_name":"NDM-7","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1183":{"protein_sequence":{"accession":"AFQ31613.1","sequence":"MELPNIMHPVAKLSTALAAALMLSGCMPGEIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMNALHAAGIATYANALSNQLAPQEGLVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR"},"dna_sequence":{"accession":"JX262694.1","fmin":"0","fmax":"813","strand":"+","sequence":"ATGGAATTGCCCAATATTATGCACCCGGTCGCGAAGCTGAGCACCGCATTAGCCGCTGCATTGATGCTGAGCGGGTGCATGCCCGGTGAAATCCGCCCGACGATTGGCCAGCAAATGGAAACTGGCGACCAACGGTTTGGCGATCTGGTTTTCCGCCAGCTCGCACCGAATGTCTGGCAGCACACTTCCTATCTCGACATGCCGGGTTTCGGGGCAGTCGCTTCCAACGGTTTGATCGTCAGGGATGGCGGCCGCGTGCTGGTGGTCGATACCGCCTGGACCGATGACCAGACCGCCCAGATCCTCAACTGGATCAAGCAGGAGATCAACCTGCCGGTCGCGCTGGCGGTGGTGACTCACGCGCATCAGGACAAGATGGGCGGTATGAACGCGCTGCATGCGGCGGGGATTGCGACTTATGCCAATGCGTTGTCGAACCAGCTTGCCCCGCAAGAGGGGCTGGTTGCGGCGCAACACAGCCTGACTTTCGCCGCCAATGGCTGGGTCGAACCAGCAACCGCGCCCAACTTTGGCCCGCTCAAGGTATTTTACCCCGGCCCCGGCCACACCAGTGACAATATCACCGTTGGGATCGACGGCACCGACATCGCTTTTGGTGGCTGCCTGATCAAGGACAGCAAGGCCAAGTCGCTCGGCAATCTCGGTGATGCCGACACTGAGCACTACGCCGCGTCAGCGCGCGCGTTTGGTGCGGCGTTCCCCAAGGCCAGCATGATCGTGATGAGCCATTCCGCCCCCGATAGCCGCGCCGCAATCACTCATACGGCCCGCATGGCCGACAAGCTGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002357","ARO_id":"38757","ARO_name":"NDM-7","CARD_short_name":"NDM-7","ARO_description":"NDM-7 is a beta-lactamase found in Escherichia coli.","ARO_category":{"36196":{"category_aro_accession":"3000057","category_aro_cvterm_id":"36196","category_aro_name":"NDM beta-lactamase","category_aro_description":"NDM beta-lactamases or New Delhi metallo-beta-lactamases are class B beta-lactamases that confer resistance to a broad range of antibiotics including carbapenems, cephalosporins and penicillins.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"586":{"model_id":"586","model_name":"VIM-20","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1654":{"protein_sequence":{"accession":"ACV13198.1","sequence":"MFKLLSKLLVYLTASIMAIASPLAFSVDSSGEYPTVSEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEVEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSASVLYGGCAIYELSRTSAGNVADADLAEWPTSIERIQQRYPEAQFVIPGHGLPGGLDLLKHTTNVVKAHTNRSVVE"},"dna_sequence":{"accession":"GQ414736.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGTTCAAACTTTTGAGTAAGTTATTGGTCTATTTGACCGCGTCTATCATGGCTATTGCGAGTCCGCTCGCTTTTTCCGTAGATTCTAGCGGTGAGTATCCGACAGTCAGCGAAATTCCGGTCGGGGAGGTCCGGCTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCAGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAGAAGCAAATTGGACTTCCTGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGTAGAGGGGAACGAGATTCCCACGCACTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAACTCTTCTATCCTGGTGCTGCGCATTCGACCGACAACTTAGTTGTGTACGTCCCGTCTGCGAGTGTGCTCTATGGTGGTTGTGCGATTTATGAGTTGTCACGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCATTGAGCGGATTCAACAACGCTACCCGGAAGCACAGTTCGTCATTCCGGGGCACGGCCTGCCGGGCGGTCTAGACTTGCTCAAGCACACAACGAATGTTGTAAAAGCGCACACAAATCGCTCAGTCGTTGAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002290","ARO_id":"38690","ARO_name":"VIM-20","CARD_short_name":"VIM-20","ARO_description":"VIM-20 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"587":{"model_id":"587","model_name":"TEM-73","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"3324":{"protein_sequence":{"accession":"CAB65358.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMLSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSSGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AJ012256.1","fmin":"208","fmax":"1069","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGCTGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTAGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3000939","ARO_id":"37319","ARO_name":"TEM-73","CARD_short_name":"TEM-73","ARO_description":"TEM-73 is an inhibitor-resistant beta-lactamase that has been found in clinical isolates.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"588":{"model_id":"588","model_name":"OKP-A-7","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"1750":{"protein_sequence":{"accession":"CAJ19605.1","sequence":"MRCVRLCLISLIAALPLAVFASPQPLEQITLSESQLAGRVGYVEMDLASGRTLAAWRASERFPLMSTFKVLLCGAVLARVDAGDERLDRRIRYPQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAGNLLLKSVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDVRDTTTPASMAATLRKLLTSHALSDRSQQQLLQWMVDDQVAGPLIRAVLPAGWFIADKTGAGERGSRGIVALLGPNGKAERIVVIYLRDTPAAMAERNQQIAKIGAALIEHWQR"},"dna_sequence":{"accession":"AM051146.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTGTGTTCGCCTGTGCCTTATCTCCCTGATTGCCGCCCTGCCACTGGCGGTATTCGCCAGCCCTCAGCCGCTCGAACAAATTACACTCAGCGAAAGTCAGCTGGCGGGCCGCGTGGGCTATGTTGAAATGGATCTGGCGAGCGGCCGCACGCTGGCCGCCTGGCGCGCCAGTGAGCGCTTTCCGCTGATGAGCACCTTTAAAGTGCTGCTCTGCGGCGCGGTGCTGGCCCGGGTGGATGCCGGAGACGAACGGCTGGATCGGCGGATCCGCTACCCCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGCCGACGGGATGACCGTTGGCGAACTCTGCGCCGCCGCCATCACCATGAGCGACAACAGCGCCGGCAATCTGCTGTTGAAGAGCGTTGGCGGCCCCGCGGGATTGACCGCTTTTCTGCGCCAGATCGGTGATAACGTCACCCGCCTTGACCGCTGGGAAACGGAGCTCAATGAGGCGCTTCCCGGCGACGTGCGCGACACCACCACCCCAGCCAGCATGGCCGCCACCCTGCGCAAGCTGCTAACCAGCCACGCGCTGAGCGACCGTTCGCAGCAGCAGCTGCTGCAGTGGATGGTGGACGACCAGGTGGCCGGTCCGCTGATCCGCGCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAAACCGGGGCCGGCGAGCGGGGCTCACGCGGCATTGTCGCCCTGCTCGGCCCGAACGGCAAAGCGGAGCGCATCGTGGTGATCTATCTGCGGGATACGCCGGCGGCCATGGCCGAGCGTAACCAGCAGATCGCCAAAATAGGCGCGGCGCTGATCGAGCACTGGCAGCGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002424","ARO_id":"38824","ARO_name":"OKP-A-7","CARD_short_name":"OKP-A-7","ARO_description":"OKP-A-7 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"38817":{"category_aro_accession":"3002417","category_aro_cvterm_id":"38817","category_aro_name":"OKP beta-lactamase","category_aro_description":"OKP beta-lactamases are chromosomal class A beta-lactamase that confer resistance to penicillins and early cephalosporins in Klebsiella pneumoniae. OKP beta-lactamases can be subdivided into two groups: OKP-A and OKP-B which diverge by about 4.2%.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"589":{"model_id":"589","model_name":"TEM-145","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8234":{"protein_sequence":{"accession":"AAZ14083.2","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLMRSALPAGWFIADKSGAGERGSHGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"DQ105528.2","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCAGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTATGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCACGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAAGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001012","ARO_id":"37392","ARO_name":"TEM-145","CARD_short_name":"TEM-145","ARO_description":"TEM-145 is an inhibitor-resistant beta-lactamase found in E. coli.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"590":{"model_id":"590","model_name":"IND-6","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"8287":{"protein_sequence":{"accession":"CAJ32373.2","sequence":"MKRRIQFFMVSMMLTPLFSAQVKDFVIEPPIKKNLYIYKTFGVFGGKEYSANSVYLVTKTGVVLFDVPWEKAQYQSLMDTIKKRHNLPVVAVFATHSHDDRAGDLSFFNNKGIKTYATPKTNQFLKRDGKATSTELIKPGKPYRFGGEEFVVDFLGEGHTADNVVVWFPKYKVLDGGCLVKSNSATDLGYIKEANLEQWPKTMHKLKTKYSEAVLIIPGHDEWKGGGHVEHTLELLDKK"},"dna_sequence":{"accession":"AM087455.2","fmin":"291","fmax":"1011","strand":"+","sequence":"ATGAAAAGAAGAATTCAGTTCTTTATGGTTTCAATGATGCTTACCCCATTATTCAGTGCCCAGGTAAAAGATTTTGTAATTGAACCGCCAATAAAAAAGAACTTATATATTTATAAAACTTTCGGAGTGTTCGGGGGAAAAGAATATTCTGCCAATTCAGTGTATCTTGTCACCAAAACCGGGGTTGTTTTATTTGATGTTCCCTGGGAAAAAGCGCAATACCAAAGCCTGATGGATACCATCAAAAAACGTCATAATTTACCTGTTGTTGCGGTATTTGCGACACATTCCCATGATGACCGGGCAGGAGATTTAAGCTTTTTCAATAATAAAGGAATTAAAACCTATGCTACTCCTAAAACCAATCAATTTCTGAAAAGAGACGGAAAGGCTACTTCTACAGAGCTCATTAAGCCCGGAAAACCTTACCGCTTTGGCGGAGAGGAATTTGTAGTGGATTTTCTTGGTGAAGGGCATACTGCCGATAATGTAGTGGTATGGTTTCCAAAATATAAAGTGCTGGATGGCGGCTGCCTTGTAAAAAGCAATTCAGCTACCGATTTAGGGTATATCAAAGAAGCTAATCTAGAGCAATGGCCTAAAACCATGCATAAACTGAAAACAAAATATTCAGAAGCAGTATTAATTATTCCCGGACATGATGAATGGAAAGGCGGCGGGCACGTTGAACATACTTTGGAGCTGCTGGATAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36916","NCBI_taxonomy_name":"Chryseobacterium indologenes","NCBI_taxonomy_id":"253"}}}},"ARO_accession":"3002262","ARO_id":"38662","ARO_name":"IND-6","CARD_short_name":"IND-6","ARO_description":"IND-6 is a beta-lactamase found in Chryseobacterium indologenes.","ARO_category":{"36199":{"category_aro_accession":"3000060","category_aro_cvterm_id":"36199","category_aro_name":"IND beta-lactamase","category_aro_description":"IND beta-lactamases are class B carbapenem-hydrolyzing beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"591":{"model_id":"591","model_name":"CTX-M-122","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1167":{"protein_sequence":{"accession":"AFA51700.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARSIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAERRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"JN790863.1","fmin":"232","fmax":"1108","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCTCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGACTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGCGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001981","ARO_id":"38381","ARO_name":"CTX-M-122","CARD_short_name":"CTX-M-122","ARO_description":"CTX-M-122 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"592":{"model_id":"592","model_name":"lmrB","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"900"}},"model_sequences":{"sequence":{"4568":{"protein_sequence":{"accession":"KIX81495.1","sequence":"METTAKASQQYKVMPIMISLLLAGFIGMFSETALNIALTDLMKELNITAATVQWLTTGYLLVLGILVPVSGLLLQWFTTRQLFTVSLIFSILGTFIAALAPSFSFLLAARIVQALGTGLLLPLMFNTILVIFPPHKRGAAMGTIGLVIMFAPAIGPTFSGLVLEHLNWHWIFWISLPFLVLALVFGIAYMQNVSETTKPKIDVLSIILSTIGFGGIVFGFSNAGEGSGGWSSPTVIVSLIVGVVGLILFSIRQLTMKQPMMNLRAFKYPMFILGVIMVFICMMVILSSMLLLPMYLQGGLVLTAFASGLVLLPGGILNGFMSPVTGRLFDKYGPKWLVIPGFVIVTVVLWFFSNVTTTSTAVLIIILHTCLMIGISMIMMPAQTNGLNQLPREFYPDGTAIMNTLQQMAGAIGTAVAVSIMAAGQHDYMSTVKNPADPAVIPQALTAGVQHAFVFAMIVAIIGLIGAFFMKRVKVDH"},"dna_sequence":{"accession":"JYFL01000006.1","fmin":"112069","fmax":"113503","strand":"-","sequence":"TTGGAAACAACAGCTAAAGCATCTCAGCAATACAAAGTGATGCCGATTATGATTTCCTTGCTGTTGGCCGGTTTTATCGGCATGTTCAGTGAAACAGCGCTGAATATTGCGTTAACCGACCTTATGAAGGAATTGAACATTACAGCGGCAACCGTCCAATGGTTAACGACGGGCTACCTGCTTGTACTCGGTATCCTTGTTCCTGTTTCAGGACTGCTGTTGCAGTGGTTCACAACAAGACAGCTTTTTACCGTGTCACTTATCTTTTCAATTTTAGGTACATTCATTGCGGCGCTTGCGCCGAGCTTCTCGTTTTTATTAGCGGCAAGGATCGTTCAGGCACTTGGAACCGGTCTTTTACTGCCGCTGATGTTTAACACAATCTTGGTGATTTTCCCGCCTCATAAACGGGGTGCCGCAATGGGAACGATCGGGCTTGTCATTATGTTCGCGCCCGCCATCGGCCCAACTTTCTCAGGATTGGTTCTGGAGCATCTCAACTGGCACTGGATTTTCTGGATCTCTCTTCCATTCCTTGTGCTGGCGCTTGTTTTCGGTATCGCATATATGCAAAATGTATCTGAAACGACAAAGCCGAAAATCGATGTATTGTCTATCATCCTGTCGACGATTGGCTTCGGCGGCATTGTATTCGGATTCAGCAACGCGGGTGAAGGCTCCGGGGGATGGTCCAGCCCGACTGTTATCGTGTCGCTGATTGTCGGCGTTGTCGGCCTTATCTTATTTTCAATCCGCCAGCTGACAATGAAGCAGCCTATGATGAACCTCCGTGCGTTCAAATACCCGATGTTTATTTTGGGTGTGATCATGGTGTTCATTTGTATGATGGTCATTCTGTCATCTATGCTGCTTCTGCCGATGTATCTGCAAGGCGGCTTAGTCCTCACTGCATTTGCATCTGGTCTTGTTCTCTTGCCGGGCGGTATTTTAAATGGATTTATGTCCCCTGTTACAGGCCGCTTGTTCGATAAATACGGGCCGAAATGGCTTGTCATTCCGGGATTTGTGATTGTCACCGTTGTACTATGGTTCTTCTCAAATGTCACGACCACTTCAACAGCTGTGCTGATTATCATCCTGCACACCTGCTTGATGATCGGGATTTCTATGATCATGATGCCTGCACAGACAAACGGTTTAAACCAACTGCCGCGTGAATTTTATCCAGACGGCACCGCCATTATGAACACGCTGCAGCAAATGGCCGGCGCTATCGGAACAGCGGTTGCGGTCAGCATTATGGCTGCAGGCCAGCATGATTATATGAGTACAGTTAAAAACCCTGCCGATCCGGCAGTCATCCCGCAAGCTTTGACAGCAGGCGTACAGCACGCATTTGTGTTTGCAATGATTGTTGCCATTATCGGTTTAATTGGCGCTTTCTTTATGAAACGCGTTAAAGTAGATCATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36833","NCBI_taxonomy_name":"Bacillus subtilis","NCBI_taxonomy_id":"1423"}}}},"ARO_accession":"3002813","ARO_id":"39247","ARO_name":"lmrB","CARD_short_name":"lmrB","ARO_description":"lmrB is a chromosomally-encoded efflux pump that confers resistance to lincosamides in Bacillus subtilis.","ARO_category":{"36002":{"category_aro_accession":"0010001","category_aro_cvterm_id":"36002","category_aro_name":"ATP-binding cassette (ABC) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding\/hydrolysis to transport substrates across cell membranes.","category_aro_class_name":"AMR Gene Family"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35965":{"category_aro_accession":"0000047","category_aro_cvterm_id":"35965","category_aro_name":"puromycin","category_aro_description":"Puromycin is an aminonucleoside antibiotic, derived from Streptomyces alboniger, that causes premature chain termination during ribosomal protein translation.","category_aro_class_name":"Antibiotic"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"36174":{"category_aro_accession":"3000034","category_aro_cvterm_id":"36174","category_aro_name":"nucleoside antibiotic","category_aro_description":"Nucleoside antibiotics are made of modified nucleosides and nucleotides with wide-ranging activities and means of antibacterial effects. This drug class includes aminonucleoside antibiotics, which contain an amino group.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"593":{"model_id":"593","model_name":"abeS","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"175"}},"model_sequences":{"sequence":{"4569":{"protein_sequence":{"accession":"ACJ59254.1","sequence":"MSYLYLAIAIACEVIATSALKASQGFTVPIPSIITVVGYAVAFYLLSLTLKTIPIGIAYAIWSGAGIILISAIGWIFYKQHLDLAACIGLALMIAGIVIINVFSKNTHL"},"dna_sequence":{"accession":"CP001172.1","fmin":"1249018","fmax":"1249348","strand":"-","sequence":"ATGTCTTATCTTTATTTAGCAATTGCGATTGCTTGTGAAGTTATTGCAACTTCAGCATTAAAAGCATCTCAAGGTTTTACTGTTCCAATTCCGTCTATTATTACAGTTGTGGGTTATGCAGTTGCTTTTTATTTATTATCTCTTACGCTCAAAACAATTCCAATCGGGATTGCCTATGCCATTTGGTCAGGCGCAGGTATTATTTTAATTTCTGCAATTGGCTGGATATTTTACAAACAACATTTAGACTTAGCTGCCTGCATTGGTTTAGCTTTAATGATCGCAGGCATTGTGATTATTAATGTGTTTTCTAAAAACACCCATCTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35595","NCBI_taxonomy_name":"Acinetobacter baumannii AB307-0294","NCBI_taxonomy_id":"557600"}}}},"ARO_accession":"3000768","ARO_id":"37148","ARO_name":"abeS","CARD_short_name":"abeS","ARO_description":"AbeS in an efflux pump of the SMR family of transporters found in Acinetobacter baumannii.","ARO_category":{"36004":{"category_aro_accession":"0010003","category_aro_cvterm_id":"36004","category_aro_name":"small multidrug resistance (SMR) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Small multidrug resistance (SMR) proteins are a relatively small family of transporters, restricted to prokaryotic cells. They are also the smallest multidrug transporters, with only four transmembrane alpha-helices and no significant extramembrane domain.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"36250":{"category_aro_accession":"3000111","category_aro_cvterm_id":"36250","category_aro_name":"novobiocin","category_aro_description":"Novobiocin is an aminocoumarin antibiotic produced by Streptomyces spheroides and Streptomyces niveus, and binds DNA gyrase subunit B inhibiting ATP-dependent DNA supercoiling.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"36242":{"category_aro_accession":"3000103","category_aro_cvterm_id":"36242","category_aro_name":"aminocoumarin antibiotic","category_aro_description":"Aminocoumarin antibiotics bind DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"594":{"model_id":"594","model_name":"QnrB41","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"645":{"protein_sequence":{"accession":"AEL31272.1","sequence":"MTPLLYKKTGTNMALALVGDKIDRNRFTGEKIENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNSSALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGAQVLGATFSGSDLSGGEFSTFDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDNYQASLLMERLGIAVIGS"},"dna_sequence":{"accession":"JN166690.1","fmin":"0","fmax":"681","strand":"+","sequence":"ATGACGCCATTACTGTATAAAAAAACAGGTACAAATATGGCTCTGGCACTCGTTGGCGATAAAATTGACAGAAACCGTTTCACCGGTGAGAAAATTGAAAATAGTACATTTTTTAACTGTGATTTTTCAGGTGCCGACCTGAGCGGCACTGAATTTATCGGCTGTCAGTTCTATGATCGTGAAAGCCAGAAAGGGTGCAATTTTAGTCGTGCGATGCTGAAAGATGCCATTTTTAAAAGCTGTGATTTATCCATGGCGGATTTTCGCAATTCCAGTGCGCTGGGCATTGAAATTCGCCACTGCCGCGCACAAGGCGCAGATTTCCGCGGCGCAAGCTTTATGAATATGATCACTACTCGCACCTGGTTTTGCAGCGCATATATCACTAACACAAATCTAAGCTACGCCAATTTTTCGAAAGTCGTGCTGGAAAAATGTGAGCTGTGGGAAAACCGTTGGATGGGTGCCCAGGTACTGGGCGCGACGTTCAGTGGTTCAGATCTTTCCGGCGGCGAGTTTTCGACTTTCGACTGGCGAGCAGCAAACTTCACACATTGCGATCTGACCAATTCGGAGTTGGGTGACTTAGATATTCGGGGCGTTGATTTACAAGGCGTTAAGCTGGACAACTACCAGGCGTCGTTGCTCATGGAGCGACTTGGCATCGCGGTGATTGGTAGC","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002756","ARO_id":"39190","ARO_name":"QnrB41","CARD_short_name":"QnrB41","ARO_description":"QnrB41 is a plasmid-mediated quinolone resistance protein found in Citrobacter freundii.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"595":{"model_id":"595","model_name":"SHV-75","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"8231":{"protein_sequence":{"accession":"CAJ47130.2","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPHNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AM176550.2","fmin":"30","fmax":"891","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACATCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGCATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001129","ARO_id":"37509","ARO_name":"SHV-75","CARD_short_name":"SHV-75","ARO_description":"SHV-75 is a broad-spectrum beta-lactamase that is found in clinical isolates.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"596":{"model_id":"596","model_name":"ROB-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"1386":{"protein_sequence":{"accession":"CAA37052.1","sequence":"MLNKLKIGTLLLLTLTACSPNSVHSVTSNPQPASAPVQQSATQATFQQTLANLEQQYQARIGVYVWDTETGHSLSYRADERFAYASTFKALLAGAVLQSLPEKDLNRTISYSQKDLVSYSPETQKYVGKGMTIAQLCEAAVRFSDNSATNLLLKELGGVEQYQRILRQLGDNVTHTNRLEPDLNQAKPNDIRDTSTPKQMAMNLNAYLLGNTLTESQKTILWNWLDNNATGNPLIRAATPTSWKVYDKSGAGKYGVRNDIAVVRIPNRKPIVMAIMSTQFTEEAKFNNKLVEDAAKQVFHTLQLN"},"dna_sequence":{"accession":"X52872.1","fmin":"220","fmax":"1138","strand":"+","sequence":"ATGTTAAATAAGTTAAAAATCGGCACATTATTATTGCTGACATTAACGGCTTGTTCGCCCAATTCTGTTCATTCGGTAACGTCTAATCCGCAGCCTGCTAGTGCGCCTGTGCAACAATCAGCCACACAAGCCACCTTTCAACAGACTTTGGCGAATTTGGAACAGCAGTATCAAGCCCGAATTGGCGTTTATGTATGGGATACAGAAACGGGACATTCTTTGTCTTATCGTGCAGATGAACGCTTTGCTTATGCGTCCACTTTCAAGGCGTTGTTGGCTGGGGCGGTGTTGCAATCGCTGCCTGAAAAAGATTTAAATCGTACCATTTCATATAGCCAAAAAGATTTGGTTAGTTATTCTCCCGAAACCCAAAAATACGTTGGCAAAGGCATGACGATTGCCCAATTATGTGAAGCAGCCGTGCGGTTTAGCGACAACAGCGCGACCAATTTGCTGCTCAAAGAATTGGGTGGCGTGGAACAATATCAACGTATTTTGCGACAATTAGGCGATAACGTAACCCATACCAATCGGCTAGAACCCGATTTAAATCAAGCCAAACCCAACGATATTCGTGATACGAGTACACCCAAACAAATGGCGATGAATTTAAATGCGTATTTATTGGGCAACACATTAACCGAATCGCAAAAAACGATTTTGTGGAATTGGTTGGACAATAACGCAACAGGCAATCCATTGATTCGCGCTGCTACGCCAACATCGTGGAAAGTGTACGATAAAAGCGGGGCGGGTAAATATGGTGTACGCAATGATATTGCGGTGGTTCGCATACCAAATCGCAAACCGATTGTGATGGCAATCATGAGTACGCAATTTACCGAAGAAGCCAAATTCAACAATAAATTAGTAGAAGATGCAGCAAAGCAAGTATTTCATACTTTACAGCTCAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39540","NCBI_taxonomy_name":"Mannheimia haemolytica","NCBI_taxonomy_id":"75985"}}}},"ARO_accession":"3002995","ARO_id":"39429","ARO_name":"ROB-1","CARD_short_name":"ROB-1","ARO_description":"ROB-1 is a beta-lactamase found in Pasteurella and Haemophilus.","ARO_category":{"39428":{"category_aro_accession":"3002994","category_aro_cvterm_id":"39428","category_aro_name":"ROB beta-lactamase","category_aro_description":"ROB beta-lactamases are a class A beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"598":{"model_id":"598","model_name":"dfrA16","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"8224":{"protein_sequence":{"accession":"AAK60186.1","sequence":"MKLSLMAAKSKNGIIGNGPDIPWSAKGEQLLFKAITYNQWLLVGRKTFESMGALPNRKYAVVTRSNFSTNDEGVMVFSSIQDALINLEEITDHVIVSGGGEIYKSLISKVDTLHISTVDIERDGDIVFPEIPDTFKLVFEQDFESNINYCYQIWQKS"},"dna_sequence":{"accession":"AF174129.3","fmin":"1351","fmax":"1825","strand":"+","sequence":"GTGAAGTTATCACTAATGGCTGCCAAGTCGAAGAACGGTATTATCGGTAATGGACCAGATATTCCATGGAGCGCCAAAGGCGAGCAACTTCTATTTAAGGCAATTACATATAATCAATGGCTTTTAGTTGGACGCAAAACTTTTGAGTCAATGGGCGCTCTCCCAAATCGAAAGTATGCAGTTGTAACTCGCTCTAATTTTTCTACGAATGATGAGGGTGTAATGGTTTTCTCCTCAATTCAGGATGCCTTAATAAATTTAGAGGAAATCACGGATCATGTTATCGTTTCTGGTGGTGGTGAAATATACAAAAGCTTGATTTCCAAAGTAGATACTTTGCATATTTCAACAGTCGACATCGAGCGAGATGGAGACATAGTTTTTCCTGAAATCCCAGATACATTCAAGTTGGTATTTGAGCAAGATTTCGAGTCTAACATTAACTATTGTTATCAAATCTGGCAAAAGAGTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3003014","ARO_id":"39448","ARO_name":"dfrA16","CARD_short_name":"dfrA16","ARO_description":"dfrA16 is an integron-encoded dihydrofolate reductase found in Salmonella enterica.","ARO_category":{"37617":{"category_aro_accession":"3001218","category_aro_cvterm_id":"37617","category_aro_name":"trimethoprim resistant dihydrofolate reductase dfr","category_aro_description":"Alternative dihydropteroate synthase dfr present on plasmids produces alternate proteins that are less sensitive to trimethoprim from inhibiting its role in folate synthesis, thus conferring trimethoprim resistance.","category_aro_class_name":"AMR Gene Family"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"599":{"model_id":"599","model_name":"OKP-A-3","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"1447":{"protein_sequence":{"accession":"CAJ19599.1","sequence":"MRYVRLCLISLIAALPLAVFASPPPLEQITRSESQLAGRVGYVEMDLASGRTLAAWRASERFPLMSTFKVLLCGAVLARVDAGDEQLDRRIRYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAGNLLLKSVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDVRDTTTPASMAATLRKLLTSHALSDRSQQQLLQWMVDDQVAGPLIRAVLPAGWFIADKTGAGERGSRGIVALLGPNGKAERIVVIYLRDTPATMAERNQQIAKIGAALIEHWQR"},"dna_sequence":{"accession":"AM051140.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGCCTTATCTCCCTGATTGCCGCCCTGCCACTGGCGGTATTCGCCAGCCCTCCGCCGCTTGAGCAAATTACACGCAGCGAAAGTCAGCTGGCGGGCCGCGTGGGCTATGTTGAAATGGATCTGGCGAGCGGCCGCACGCTGGCCGCCTGGCGCGCCAGTGAGCGCTTTCCGCTGATGAGCACCTTTAAAGTGCTGCTCTGCGGCGCGGTGCTGGCCCGGGTGGATGCCGGAGACGAACAGCTGGATCGGCGGATCCGCTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGCCGACGGGATGACCGTTGGCGAACTCTGCGCCGCCGCCATCACCATGAGCGACAACAGCGCCGGCAATCTGCTGTTGAAGAGCGTTGGCGGCCCCGCGGGATTGACCGCTTTTCTGCGCCAGATCGGTGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAGCTCAATGAAGCGCTTCCCGGCGACGTGCGCGACACCACCACCCCAGCCAGCATGGCCGCCACCCTGCGCAAGCTGCTAACCAGCCACGCGCTGAGCGACCGTTCGCAGCAGCAGCTGCTGCAGTGGATGGTGGACGACCAGGTGGCCGGTCCGCTGATCCGCGCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAAACCGGGGCCGGCGAGCGGGGCTCACGCGGCATTGTCGCCCTGCTCGGCCCGAACGGCAAAGCGGAGCGCATCGTGGTGATCTATCTGCGGGATACGCCGGCGACCATGGCCGAGCGTAACCAGCAGATCGCCAAAATAGGCGCGGCGCTGATCGAGCACTGGCAGCGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002420","ARO_id":"38820","ARO_name":"OKP-A-3","CARD_short_name":"OKP-A-3","ARO_description":"OKP-A-3 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"38817":{"category_aro_accession":"3002417","category_aro_cvterm_id":"38817","category_aro_name":"OKP beta-lactamase","category_aro_description":"OKP beta-lactamases are chromosomal class A beta-lactamase that confer resistance to penicillins and early cephalosporins in Klebsiella pneumoniae. OKP beta-lactamases can be subdivided into two groups: OKP-A and OKP-B which diverge by about 4.2%.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"600":{"model_id":"600","model_name":"CMY-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"821":{"protein_sequence":{"accession":"CAA62957.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"X91840.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002013","ARO_id":"38413","ARO_name":"CMY-2","CARD_short_name":"CMY-2","ARO_description":"CMY-2 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35927":{"category_aro_accession":"0000008","category_aro_cvterm_id":"35927","category_aro_name":"cefoxitin","category_aro_description":"Cefoxitin is a cephamycin antibiotic often grouped with the second generation cephalosporins. Cefoxitin is bactericidal and acts by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. Cefoxitin's 7-alpha-methoxy group and 3' leaving group make it a poor substrate for most beta-lactamases.","category_aro_class_name":"Antibiotic"},"35975":{"category_aro_accession":"0000058","category_aro_cvterm_id":"35975","category_aro_name":"cefazolin","category_aro_description":"Cefazolin, also known as cefazoline or cephazolin, is a first generation cephalosporin antibiotic. It is administered parenterally, and is active against a broad spectrum of bacteria.","category_aro_class_name":"Antibiotic"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"35979":{"category_aro_accession":"0000062","category_aro_cvterm_id":"35979","category_aro_name":"ceftriaxone","category_aro_description":"Ceftriaxone is a third-generation cephalosporin antibiotic. The presence of an aminothiazolyl sidechain increases ceftriazone's resistance to beta-lactamases. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"35987":{"category_aro_accession":"0000070","category_aro_cvterm_id":"35987","category_aro_name":"ertapenem","category_aro_description":"Ertapenem is a carbapenem antibiotic and is highly resistant to beta-lactamases like other carbapenems. It inhibits bacterial cell wall synthesis.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"36990":{"category_aro_accession":"3000646","category_aro_cvterm_id":"36990","category_aro_name":"cefixime","category_aro_description":"Cefixime is a cephalosporin resistant to most beta-lactamases. It is active against many enterobacteria, but activity against staphylococci is poor.","category_aro_class_name":"Antibiotic"},"37084":{"category_aro_accession":"3000704","category_aro_cvterm_id":"37084","category_aro_name":"cefalotin","category_aro_description":"Cefalotin is a semisynthetic cephalosporin antibiotic activate against staphylococci. It is resistant to staphylococci beta-lactamases but hydrolyzed by enterobacterial beta-lactamases.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"601":{"model_id":"601","model_name":"dfrA20","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"342":{"protein_sequence":{"accession":"CAE53424.1","sequence":"MGIKYSLIVAIGKHREMGADNDLLWHLPRDMQFFKETTTGHAVVMGRKSWESIPQKYRPLPNRLNFVLTRDKNYSAEGATVIYDLKEVAQHLEGKNLTCFIIGGAQIYQLALETGLLNEMYVTQVHNTFEEADTFFPFVNWGEWEEEDILEQDKDEKHLYSFNIKKFTR"},"dna_sequence":{"accession":"AJ605332.1","fmin":"1303","fmax":"1813","strand":"+","sequence":"ATGGGTATTAAATATAGCTTAATTGTTGCAATTGGGAAACACCGAGAAATGGGTGCTGACAATGATTTGCTTTGGCACTTACCAAGAGATATGCAATTTTTTAAGGAAACGACAACGGGTCACGCTGTTGTAATGGGAAGAAAAAGTTGGGAATCTATTCCTCAGAAGTACAGACCGCTTCCAAATCGTTTAAACTTCGTTTTAACACGAGATAAAAACTATAGTGCAGAAGGTGCAACAGTGATTTATGATTTAAAAGAAGTCGCACAACATCTTGAAGGAAAAAACTTAACATGCTTCATTATTGGTGGTGCTCAAATCTACCAACTGGCCTTAGAAACAGGACTTTTAAATGAAATGTATGTCACACAAGTACATAACACATTTGAAGAAGCTGACACCTTTTTCCCTTTTGTAAATTGGGGAGAATGGGAAGAAGAAGATATTTTAGAACAAGATAAAGATGAAAAACATCTTTATTCATTTAATATAAAGAAATTTACGCGTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36867","NCBI_taxonomy_name":"Pasteurella multocida","NCBI_taxonomy_id":"747"}}}},"ARO_accession":"3003016","ARO_id":"39450","ARO_name":"dfrA20","CARD_short_name":"dfrA20","ARO_description":"dfrA20 is a plasmid-encoded dihydrofolate reductase found in Pasteurella multocida.","ARO_category":{"37617":{"category_aro_accession":"3001218","category_aro_cvterm_id":"37617","category_aro_name":"trimethoprim resistant dihydrofolate reductase dfr","category_aro_description":"Alternative dihydropteroate synthase dfr present on plasmids produces alternate proteins that are less sensitive to trimethoprim from inhibiting its role in folate synthesis, thus conferring trimethoprim resistance.","category_aro_class_name":"AMR Gene Family"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"602":{"model_id":"602","model_name":"VIM-16","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1251":{"protein_sequence":{"accession":"ACB54703.1","sequence":"MFKLLSKLLVYLTASIMAIASPLAFSVDSSGEYPTVSEIPVGEVRLYQIADGVWLHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEVEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSASVLYGGCAIYELSRTSAGNVADADLAEWPTSIERIQQHYPEAQFVIPGHGLPGGLDLLKHTTNVVKAHTNRSVVE"},"dna_sequence":{"accession":"EU419746.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGTTCAAACTTTTGAGTAAGTTATTGGTCTATTTGACCGCGTCTATCATGGCTATTGCGAGTCCGCTCGCTTTTTCCGTAGATTCTAGCGGTGAGTATCCGACAGTCAGCGAAATTCCGGTCGGGGAGGTCCGGCTTTACCAGATTGCCGATGGTGTTTGGTTGCATATCGCAACGCAGTCGTTTGATGGCGCAGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAGAAGCAAATTGGACTTCCTGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGTAGAGGGGAACGAGATTCCCACGCACTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAACTCTTCTATCCTGGTGCTGCGCATTCGACCGACAACTTAGTTGTGTACGTCCCGTCTGCGAGTGTGCTCTATGGTGGTTGTGCGATTTATGAGTTGTCACGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCATTGAGCGGATTCAACAACACTACCCGGAAGCACAGTTCGTCATTCCGGGGCACGGCCTGCCGGGCGGTCTAGACTTGCTCAAGCACACAACGAATGTTGTAAAAGCGCACACAAATCGCTCAGTCGTTGAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002286","ARO_id":"38686","ARO_name":"VIM-16","CARD_short_name":"VIM-16","ARO_description":"VIM-16 is a beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"603":{"model_id":"603","model_name":"mdtG","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"4574":{"protein_sequence":{"accession":"ABV18113.1","sequence":"MSPCENDTPINWKRNLIVAWLGCFLTGAAFSLVMPFLPLYVEQLGVTGHSALNMWSGIVFSITFLFSAIASPFWGGLADRKGRKLMLLRSALGMGIVMVLMGLAQNIWQFLILRALLGLLGGFVPNANALIATQVPRNKSGWALGTLSTGGVSGALLGPMAGGLLADSYGLRPVFFITASVLILCFFVTLFCIREKFQPVSKKEMLHMREVVTSLKNPKLVLSLFVTTLIIQVATGSIAPILTLYVRELAGNVSNVAFISGMIASVPGVAALLSAPRLGKLGDRIGPEKILITALIFSVLLLIPMSYVQTPLQLGILRFLLGAADGALLPAVQTLLVYNSSNQIAGRIFSYNQSFRDIGNVTGPLMGAAISANYGFRAVFLVTAGVVLFNAVYSWNSLRRRRIPQVSN"},"dna_sequence":{"accession":"CP000800.1","fmin":"1191727","fmax":"1192954","strand":"-","sequence":"ATGTCACCCTGTGAAAATGACACCCCTATAAACTGGAAACGAAACCTGATCGTCGCCTGGCTAGGCTGTTTTCTTACCGGGGCCGCCTTCAGTCTGGTAATGCCCTTCTTACCCCTCTACGTTGAGCAGCTTGGTGTTACCGGCCACTCCGCCCTGAATATGTGGTCCGGTATTGTCTTCAGCATTACATTTTTATTTTCGGCCATCGCCTCACCGTTTTGGGGTGGACTCGCCGACCGTAAAGGTCGAAAACTCATGCTATTACGCTCTGCTCTCGGCATGGGCATCGTGATGGTGTTGATGGGACTGGCACAAAATATCTGGCAGTTTTTGATCCTACGGGCGCTTCTTGGGTTACTTGGCGGATTTGTCCCCAACGCTAATGCTCTTATCGCCACACAAGTACCGCGTAATAAAAGCGGCTGGGCGCTGGGTACGCTCTCCACAGGCGGCGTTAGTGGTGCGTTGCTCGGCCCAATGGCTGGCGGCCTGCTCGCCGATAGCTACGGCTTACGTCCGGTATTCTTTATTACCGCCAGTGTGCTCATACTCTGCTTTTTCGTCACCCTGTTTTGCATCAGAGAAAAATTCCAGCCGGTCAGCAAAAAAGAGATGCTGCACATGCGGGAAGTGGTGACATCACTTAAAAACCCGAAACTGGTACTCAGCCTGTTTGTCACTACGTTAATCATCCAGGTGGCGACGGGCTCAATTGCCCCCATTCTGACGCTGTATGTCCGCGAACTGGCGGGTAACGTCAGTAACGTCGCCTTTATCAGTGGCATGATCGCCTCGGTGCCAGGCGTGGCGGCTCTGCTAAGTGCACCACGACTCGGCAAACTTGGCGATCGAATCGGACCCGAAAAGATCCTGATTACAGCGCTGATCTTTTCTGTACTGCTGTTGATCCCAATGTCTTACGTTCAGACGCCATTGCAACTTGGGATTTTACGTTTTTTGCTCGGTGCCGCCGATGGTGCACTACTCCCCGCCGTACAGACACTGTTGGTTTACAACTCGAGCAACCAGATCGCCGGGCGTATCTTCAGCTATAACCAATCGTTTCGTGATATTGGCAACGTTACCGGACCATTGATGGGAGCAGCGATTTCAGCGAACTACGGTTTCAGAGCGGTATTTCTCGTCACCGCTGGCGTAGTGTTATTCAACGCAGTCTATTCATGGAACAGTCTACGTCGTCGTCGAATACCCCAGGTATCGAACTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41529","NCBI_taxonomy_name":"Escherichia coli O139:H28 str. E24377A","NCBI_taxonomy_id":"331111"}}}},"ARO_accession":"3001329","ARO_id":"37728","ARO_name":"mdtG","CARD_short_name":"mdtG","ARO_description":"The MdtG protein, also named YceE, appears to be a member of the major facilitator superfamily of transporters, and it has been reported, when overexpressed, to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35944":{"category_aro_accession":"0000025","category_aro_cvterm_id":"35944","category_aro_name":"fosfomycin","category_aro_description":"Fosfomycin (also known as phosphomycin and phosphonomycin) is a broad-spectrum antibiotic produced by certain Streptomyces species. It is effective on gram positive and negative bacteria as it targets the cell wall, an essential feature shared by both bacteria. Its specific target is MurA (MurZ in E.coli), which attaches phosphoenolpyruvate (PEP) to UDP-N-acetylglucosamine, a step of commitment to cell wall synthesis. In the active site of MurA, the active cysteine molecule is alkylated which stops the catalytic reaction.","category_aro_class_name":"Antibiotic"},"45731":{"category_aro_accession":"3007149","category_aro_cvterm_id":"45731","category_aro_name":"phosphonic acid antibiotic","category_aro_description":"A group of antibiotics derived from phosphonic acids.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"604":{"model_id":"604","model_name":"OXA-385","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4575":{"protein_sequence":{"accession":"AHL30272.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALISLEHHKATATEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"KF986253.1","fmin":"15","fmax":"840","strand":"-","sequence":"ATGAACATTAAAGCCCTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTCTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCAGCCTTGAGCACCATAAGGCAACCGCCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGACGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGCCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001571","ARO_id":"37971","ARO_name":"OXA-385","CARD_short_name":"OXA-385","ARO_description":"OXA-385 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"605":{"model_id":"605","model_name":"OXA-96","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1617":{"protein_sequence":{"accession":"ABF47919.1","sequence":"MKLLKILSLVCLSISIGACAEHSMSRAKTSTIPQVNNSIIDQNVQALFNEISADAVFVTYDGQNIKKYGTHLDRAKTAYIPASTFKIANALIGLENHKATSTEIFKWDGKPRFFKAWDKDFTLGEAMQASTVPVYQELARRIGPSLMQSELQRIGYGNMQMGTEVDQFWLKGPLTITPIQEVKFVYDLAQGQLPFKPEVQQQVKEMLYVERRGENRLYAKSGWGMAVDPQVGWYVGFVEKADGQVVAFALNMQMKAGDDIALRKQLSLDVLDKLGVFHYL"},"dna_sequence":{"accession":"DQ519090.1","fmin":"62","fmax":"905","strand":"+","sequence":"ATGAAATTATTAAAAATATTGAGTTTAGTTTGCTTAAGCATAAGTATTGGGGCTTGTGCTGAGCATAGTATGAGTCGAGCAAAAACAAGTACAATTCCACAAGTGAATAACTCAATCATCGATCAGAATGTTCAAGCGCTTTTTAATGAAATCTCAGCTGATGCTGTGTTTGTCACATATGATGGTCAAAATATTAAAAAATATGGCACGCATTTAGACCGAGCAAAAACAGCTTATATTCCTGCATCTACATTTAAAATTGCCAATGCACTAATTGGTTTAGAAAATCATAAAGCAACATCTACAGAAATATTTAAGTGGGATGGAAAGCCACGTTTTTTTAAAGCATGGGACAAAGATTTTACTTTGGGCGAAGCCATGCAAGCATCTACAGTGCCTGTATATCAAGAATTGGCACGTCGTATTGGTCCAAGCTTAATGCAAAGTGAATTGCAACGTATTGGTTATGGCAATATGCAAATGGGCACGGAAGTTGATCAATTTTGGTTGAAAGGGCCTTTGACAATTACACCTATACAAGAAGTAAAGTTTGTGTATGATTTAGCCCAAGGGCAATTGCCTTTTAAACCTGAAGTTCAGCAACAAGTGAAAGAGATGTTGTATGTAGAGCGCAGAGGGGAGAATCGTCTATATGCTAAAAGTGGCTGGGGAATGGCTGTAGACCCGCAAGTGGGTTGGTATGTGGGTTTTGTTGAAAAGGCAGATGGGCAAGTGGTGGCATTTGCTTTAAATATGCAAATGAAAGCTGGTGATGATATTGCTCTACGTAAACAATTGTCTTTAGATGTGCTAGATAAGTTGGGTGTTTTTCATTATTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001631","ARO_id":"38031","ARO_name":"OXA-96","CARD_short_name":"OXA-96","ARO_description":"OXA-96 is a beta-lactamase found in A. baumannii.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46517":{"category_aro_accession":"3007728","category_aro_cvterm_id":"46517","category_aro_name":"OXA-58-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-58.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"606":{"model_id":"606","model_name":"IMI-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1277":{"protein_sequence":{"accession":"ABA00479.1","sequence":"MSLNVKPSRIAILFSSCLVSISFFSQANTKGIDEIKNLETDFNGRIGVYALDTGSGKSFSYKANERFPLCSSFKGFLAAAVLKGSQDNQLNLNQIVNYNTRSLEFYSPITTKYKDNGMSLGDMAAAALQYSDNGATNIILERYIGGPEGMTKFMRSIGDKDFRLDRWELDLNTAIPGDERDTSTPAAVAKSLKTLALGNILNEREKETYQTWLKGNTTGAARIRASVPSDWVVGDKTGSCGAYGTANDYAVVWPKNRAPLIISVYTTKNEKEAKHEDKVIAEASRIAIDNLK"},"dna_sequence":{"accession":"DQ173429.1","fmin":"0","fmax":"879","strand":"+","sequence":"ATGTCACTTAATGTAAAACCAAGTAGAATAGCCATCTTGTTTAGCTCTTGTTTAGTTTCAATATCATTTTTCTCACAGGCCAATACAAAGGGAATCGATGAGATTAAAAACCTTGAAACAGATTTCAATGGTAGAATTGGTGTCTACGCTTTAGACACTGGCTCAGGTAAATCATTTTCGTACAAAGCAAATGAACGATTTCCATTATGTAGTTCTTTCAAAGGTTTTTTAGCTGCTGCTGTATTAAAAGGCTCTCAAGATAATCAACTAAATCTTAATCAGATCGTGAATTATAATACAAGAAGTTTAGAGTTCTATTCACCCATCACAACTAAATATAAAGATAATGGAATGTCATTAGGTGATATGGCTGCTGCCGCTTTACAATATAGCGACAATGGTGCTACTAATATTATTCTTGAACGATATATCGGTGGTCCTGAGGGTATGACTAAATTCATGCGGTCGATTGGAGATAAAGATTTTAGACTCGATCGTTGGGAGTTAGATCTAAACACAGCAATTCCTGGCGATGAACGTGACACATCTACACCTGCAGCAGTAGCTAAGAGCCTGAAAACCCTTGCTCTGGGTAACATACTTAATGAGCGTGAAAAGGAAACCTATCAGACATGGTTAAAGGGTAACACAACCGGTGCAGCGCGTATTCGTGCTAGCGTACCAAGCGATTGGGTAGTTGGCGATAAAACTGGTAGTTGCGGAGCATACGGTACGGCAAATGATTATGCGGTAGTCTGGCCAAAGAACCGAGCTCCTCTTATAATTTCTGTATACACTACAAAAAACGAAAAAGAAGCCAAGCATGAGGATAAAGTAATCGCAGAAGCTTCAAGAATCGCAATTGATAACCTTAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36926","NCBI_taxonomy_name":"Enterobacter asburiae","NCBI_taxonomy_id":"61645"}}}},"ARO_accession":"3001859","ARO_id":"38259","ARO_name":"IMI-2","CARD_short_name":"IMI-2","ARO_description":"IMI-2 is a beta-lactamase found in Enterobacteriaceae.","ARO_category":{"36027":{"category_aro_accession":"3000018","category_aro_cvterm_id":"36027","category_aro_name":"IMI beta-lactamase","category_aro_description":"IMI beta-lactamases are a group of TEM-1-like beta-lactamase that are known to hydrolyze imipenem. IMI beta-lactamases are inhibited by clavulanic acid and tazobactam.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"607":{"model_id":"607","model_name":"TEM-201","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1884":{"protein_sequence":{"accession":"AFS44742.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETVVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGGQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"JX310327.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGGTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGGGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001378","ARO_id":"37778","ARO_name":"TEM-201","CARD_short_name":"TEM-201","ARO_description":"TEM-201 is a beta-lactamase found in Enterobacteriaceae.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"608":{"model_id":"608","model_name":"OXA-361","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"2010":{"protein_sequence":{"accession":"AHA11124.1","sequence":"MKILILLPLFSCLGLTACSLPVSSSPSQITSIQSTQAIAQLFDQAQSAGVLVIQRGQQIQVYGNDLSRANTEYVPASTFKMLNALIGLQHGKATTNEIFKWDGKKRSFSAWEKDMTLGQAMQASAVPVYQELARRIGLELMQQEVQCIQFGNQQIGQQVDNFWLVGPLKVTPKQEVQFVSALAREQLAFDPQVQQQVKVMLLLQEQQAYRLYAKSGWGMDVEPQVGWLTGWVKTPQAEIVAFSLNMQMRNGMDPAIRLEILQQALAELGLYPKAEG"},"dna_sequence":{"accession":"KF460531.1","fmin":"0","fmax":"831","strand":"+","sequence":"ATGAAAATTCTGATTTTGCTGCCTTTATTTAGTTGCTTGGGACTGACGGCGTGTAGTCTGCCCGTTTCATCCTCCCCCTCTCAGATCACTTCAATTCAATCGACTCAAGCCATTGCCCAATTATTTGATCAGGCGCAAAGCGCTGGCGTTTTAGTGATTCAGCGTGGTCAACAGATACAGGTTTATGGTAATGATTTAAGTCGTGCAAATACCGAATATGTTCCAGCCTCTACTTTCAAAATGCTCAATGCCCTGATTGGTCTACAACATGGTAAAGCCACAACCAATGAAATTTTTAAATGGGATGGCAAGAAACGCAGTTTTTCAGCTTGGGAAAAAGACATGACTCTCGGCCAAGCCATGCAAGCGTCTGCTGTACCCGTTTATCAGGAACTGGCACGTCGTATTGGCCTTGAACTGATGCAACAGGAAGTACAATGCATCCAATTTGGTAATCAGCAGATTGGTCAACAGGTCGATAACTTCTGGCTGGTAGGCCCTTTGAAAGTTACTCCAAAACAGGAAGTCCAATTTGTTTCTGCGTTGGCCCGAGAGCAACTGGCCTTTGATCCTCAAGTCCAGCAGCAAGTCAAAGTCATGTTACTGCTACAGGAGCAGCAAGCTTATCGACTATATGCCAAATCTGGTTGGGGCATGGATGTGGAACCGCAAGTCGGCTGGCTCACCGGCTGGGTTAAAACACCGCAAGCCGAGATCGTGGCATTTTCACTGAATATGCAGATGCGAAATGGTATGGATCCGGCGATCCGCCTTGAAATTTTGCAGCAGGCTTTGGCCGAATTAGGGCTTTATCCAAAAGCAGAAGGATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36948","NCBI_taxonomy_name":"Acinetobacter lwoffii","NCBI_taxonomy_id":"28090"}}}},"ARO_accession":"3001548","ARO_id":"37948","ARO_name":"OXA-361","CARD_short_name":"OXA-361","ARO_description":"OXA-361 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46489":{"category_aro_accession":"3007700","category_aro_cvterm_id":"46489","category_aro_name":"OXA-134-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-134.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"609":{"model_id":"609","model_name":"emrK","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"173":{"protein_sequence":{"accession":"BAA11236.1","sequence":"MELEDMISTDDAYVTGNADPISAQVSGSVTVVNHKDTNYVRQGDILVSLDKTDATIALNKAKNNLANIVRQTNKLYLQDKQYSAEVASARIQYQQSLEDYNRRVPLAKQGVISKETLEHTKDTLISSKAALNAAIQAYKANKALVMNTPLNRQPQVVEAADATKEAWLALKRTDIKSPVTGYIAQRSVQVGETVSPGQSLMAVVPARQMWVNANFKETQLTDVRIGQSVNIISDLYGENVVFHGRVTGINMGTGNAFSLLPAQNATGNWIKIVQRVPVEVSLDPKELMEHPLRIGLSMTATIDTKNEDIAEMPELASTVTSMPAYTSKALVIDTSPIEKEISNIISHNGQL"},"dna_sequence":{"accession":"D78168.1","fmin":"536","fmax":"1592","strand":"+","sequence":"ATGGAATTAGAAGACATGATTAGTACAGATGACGCCTATGTCACGGGGAATGCAGATCCAATTTCTGCACAAGTCTCAGGTAGTGTCACTGTCGTTAATCATAAAGATACGAACTACGTTCGACAAGGTGACATTTTAGTTTCACTGGATAAAACTGATGCCACTATCGCACTCAATAAAGCTAAAAATAATCTGGCAAATATTGTTCGGCAAACGAATAAACTATACTTACAGGATAAACAATACAGTGCCGAAGTCGCTTCAGCACGTATTCAGTATCAACAATCTTTAGAAGATTATAACCGTCGAGTGCCGTTAGCGAAGCAGGGGGTTATTTCAAAAGAAACGCTGGAGCATACCAAAGATACGTTAATAAGTAGCAAAGCGGCATTGAATGCCGCTATCCAGGCTTATAAAGCGAATAAAGCTTTAGTAATGAACACACCATTAAACCGTCAGCCACAAGTCGTTGAAGCGGCGGATGCAACTAAAGAAGCCTGGTTGGCGCTTAAACGTACGGATATTAAGAGTCCGGTTACCGGCTATATTGCCCAGAGAAGTGTTCAGGTCGGCGAAACAGTGAGCCCCGGACAATCGTTAATGGCTGTCGTACCGGCACGTCAAATGTGGGTTAATGCCAACTTTAAAGAAACACAACTCACGGATGTACGGATTGGTCAATCGGTCAATATTATCAGCGATCTTTATGGTGAAAATGTTGTGTTTCATGGTCGGGTGACAGGGATCAATATGGGAACCGGCAATGCGTTCTCCTTATTACCTGCACAAAATGCGACAGGGAACTGGATCAAAATCGTTCAGCGTGTACCGGTTGAAGTTTCTCTTGATCCAAAAGAACTCATGGAACACCCCTTGCGTATTGGTTTATCGATGACAGCAACTATTGATACGAAGAACGAAGACATTGCCGAGATGCCTGAGCTGGCTTCAACCGTGACCTCCATGCCGGCTTATACCAGTAAGGCTTTAGTTATCGATACCAGTCCGATAGAAAAAGAAATTAGCAACATTATTTCGCATAATGGACAACTTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000206","ARO_id":"36345","ARO_name":"emrK","CARD_short_name":"emrK","ARO_description":"emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC, it mediates multidrug efflux.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"610":{"model_id":"610","model_name":"SHV-153","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1312":{"protein_sequence":{"accession":"AFQ23959.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGASERGARGIVALLGPNNKAERIVVIYLRDTPASMVERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"JX121120.1","fmin":"0","fmax":"858","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTACTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTAGCGAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGTCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGC","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001192","ARO_id":"37572","ARO_name":"SHV-153","CARD_short_name":"SHV-153","ARO_description":"SHV-153 is a beta-lactamase.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"611":{"model_id":"611","model_name":"OXA-328","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1132":{"protein_sequence":{"accession":"AGW16410.1","sequence":"MYKKALIVATSLLFLSACSSNTVTQHQIHSISANKNSEEIKSLFDQAQTTGVLVIKRGKTEEIYGNDLKRASTAYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPDWEKDMTLGNAMKASAIPVYQELAQRIGLDLMSKEVKRIGFGNANIGSKVDNFWLVGPLKITPQQETQFAYQLAHKTLPFSKNVQEQVQSMVFIEEKNGSKIYAKSGWGWDVEPQVGWLTGWVVQPQGEIVAFSLNLEMKKGTPSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"KF203102.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGTATAAAAAAGCCCTTATCGTTGCAACAAGCCTCCTATTTTTATCCGCCTGTTCTTCCAATACAGTAACACAACATCAAATACACTCTATCTCTGCCAATAAAAATTCAGAAGAAATTAAATCACTGTTTGATCAAGCACAGACCACGGGAGTCTTGGTAATTAAGCGAGGGAAAACAGAAGAAATTTATGGCAATGATCTTAAAAGAGCATCAACCGCCTATGTTCCCGCCTCTACCTTTAAAATGTTAAATGCTTTAATTGGACTTGAACATCATAAGGCAACTACAACTGAAGTATTTAAATGGGATGGGCAAAAACGTTTATTTCCTGATTGGGAAAAGGACATGACACTGGGTAATGCCATGAAAGCTTCTGCAATTCCAGTTTACCAAGAATTAGCCCAACGAATTGGACTTGACCTTATGTCTAAAGAGGTAAAAAGAATTGGTTTCGGTAATGCTAACATTGGTTCAAAAGTAGATAATTTTTGGCTTGTTGGCCCTCTAAAAATTACGCCTCAACAAGAAACCCAATTTGCTTATCAATTAGCCCATAAAACGCTTCCATTTAGCAAAAATGTACAAGAACAAGTTCAATCAATGGTGTTCATAGAGGAAAAAAATGGAAGTAAAATTTATGCCAAAAGTGGTTGGGGATGGGATGTTGAACCACAAGTTGGTTGGTTAACAGGCTGGGTCGTTCAACCACAAGGAGAAATTGTCGCATTCTCACTTAATTTAGAAATGAAAAAAGGAACTCCTAGCTCTATTCGCAAAGAAATTGCTTATAAAGGCTTAGAACAACTGGGTATCTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39094","NCBI_taxonomy_name":"Acinetobacter calcoaceticus","NCBI_taxonomy_id":"471"}}}},"ARO_accession":"3001516","ARO_id":"37916","ARO_name":"OXA-328","CARD_short_name":"OXA-328","ARO_description":"OXA-328 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46495":{"category_aro_accession":"3007706","category_aro_cvterm_id":"46495","category_aro_name":"OXA-213-like beta-lactamase","category_aro_description":"OXA-213-like enzymes have been identified to be intrinsic to A. calcoaceticus and have been subsequently detected in A. pittii. Phylogenetic analysis of OXA-213-like proteins identified two distinct subgroups within the OXA family. The first group was linked to A. pittii and the second group to A. calcoaceticus. The carbapenemase activity of these OXAs may be related to the species-dependent effect.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"612":{"model_id":"612","model_name":"PDC-7","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"1849":{"protein_sequence":{"accession":"ACQ82812.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"FJ666070.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGACGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAACTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTATGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002506","ARO_id":"38906","ARO_name":"PDC-7","CARD_short_name":"PDC-7","ARO_description":"PDC-7 is a extended-spectrum beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"613":{"model_id":"613","model_name":"VEB-4","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1498":{"protein_sequence":{"accession":"ABM54868.1","sequence":"MKIVKRILLVLLSLFFTIVYSNAQADNLTLKIENVLKAKNARIGVAIFNSNEKDTLKINNDFHFPMQSVMKFPIALAVLSEIDKGNLSFEQKIEITPQDLLPKMWSPIKEEFPNGTTLTIEQILNYTVSESDNIGCDILLKLIGGTDSVQKFLNANHFTDISIKANEEQMHKDWNTQYQNWATPTAMNKLLIDTYNNKNQLLSKKSYDFIWKIMRETTTGSNRLKGQLPKNTIVAHKTGTSGINNGIAAATNDVGVITLPNGQLIFISVFVAESKETSEINEKIISDIAKITWNYYLNK"},"dna_sequence":{"accession":"EF136375.1","fmin":"0","fmax":"900","strand":"+","sequence":"ATGAAAATCGTAAAAAGGATATTATTAGTATTGTTAAGTTTATTTTTTACAATTGTGTATTCAAATGCTCAAGCTGACAACTTAACTTTGAAAATTGAGAATGTTTTAAAGGCAAAAAATGCCAGAATAGGAGTAGCAATATTCAACAGCAATGAGAAGGATACTTTGAAGATTAATAACGACTTCCATTTCCCGATGCAAAGCGTTATGAAATTTCCGATTGCTTTAGCCGTTTTGTCTGAGATAGATAAAGGGAATCTTTCTTTTGAACAAAAAATAGAGATTACCCCTCAAGACCTTTTGCCTAAAATGTGGAGTCCGATTAAAGAGGAATTCCCTAATGGAACAACTTTGACGATTGAACAAATACTAAATTATACAGTATCAGAGAGCGACAATATTGGTTGTGATATTTTGCTAAAATTAATCGGAGGAACTGATTCTGTTCAAAAATTCTTGAATGCTAATCATTTCACTGATATTTCAATCAAAGCAAACGAAGAACAAATGCACAAGGATTGGAATACCCAATATCAAAATTGGGCAACCCCAACAGCGATGAACAAACTGTTAATAGATACTTATAATAATAAGAACCAATTACTTTCTAAAAAAAGTTATGATTTTATTTGGAAAATTATGAGAGAAACAACAACAGGAAGTAACCGATTAAAAGGACAATTACCAAAGAATACAATTGTTGCTCATAAAACAGGGACTTCCGGAATAAATAATGGAATTGCAGCAGCCACTAATGATGTTGGGGTAATTACTTTACCGAATGGACAATTAATTTTTATAAGCGTATTTGTTGCAGAGTCCAAAGAAACTTCGGAAATTAATGAAAAGATTATTTCAGACATTGCAAAAATAACGTGGAATTACTATTTGAATAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3002373","ARO_id":"38773","ARO_name":"VEB-4","CARD_short_name":"VEB-4","ARO_description":"VEB-4 is a beta-lactamase found in Proteus mirabilis.","ARO_category":{"36182":{"category_aro_accession":"3000043","category_aro_cvterm_id":"36182","category_aro_name":"VEB beta-lactamase","category_aro_description":"VEB beta-lactamases or Vietnamese extended-spectrum beta-lactamases are class A beta-lactamases that confer high-level resistance to oxyimino cephalosporins and to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"614":{"model_id":"614","model_name":"SFB-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"3311":{"protein_sequence":{"accession":"AAT90847.1","sequence":"MISAPSFAHENEQQTDQSNTDAVKKPQQQPTELFLSPLVPDVYLHQSYKQVSGFGLVESNGLVVVQNKQAFIIDTPWTDSDTAKLVDWITQQGLTVTASISTHSHQDRAGGIGYLNSQGIATWVSDKTQRLLTANKLSTASHTFRTKQHTLQQQLIEVYDLGAGHTVDNLLVWLPKQQILFGGCLIKSLSSRTLGYTGEADLEQWPLTVAKVQAQFIQAKIVVPGHGKIGDTSLLSHTIDLLTQ"},"dna_sequence":{"accession":"AY590119.1","fmin":"0","fmax":"735","strand":"+","sequence":"ATGATAAGTGCACCTTCATTTGCCCATGAAAACGAACAACAAACAGATCAAAGCAACACCGATGCAGTAAAAAAGCCACAGCAGCAACCCACTGAACTCTTCCTATCGCCTCTCGTGCCAGATGTGTATTTACACCAGTCATATAAACAGGTCAGCGGCTTTGGATTAGTTGAGTCTAATGGCTTAGTGGTGGTGCAAAACAAGCAGGCGTTTATTATTGATACTCCCTGGACAGATAGCGATACCGCCAAGCTTGTGGATTGGATTACCCAGCAAGGTTTAACCGTTACAGCCAGTATATCGACTCATTCACATCAAGACCGCGCAGGTGGAATTGGCTACCTTAACAGCCAAGGCATCGCCACTTGGGTGTCAGATAAAACCCAACGCCTATTAACCGCCAACAAACTCAGCACTGCAAGCCACACATTTAGAACTAAGCAACACACACTTCAGCAGCAACTCATTGAAGTGTATGATCTGGGCGCTGGCCACACGGTCGATAACCTGTTGGTGTGGCTGCCTAAGCAACAGATTTTATTCGGCGGCTGTTTAATAAAATCACTGAGTTCACGCACTCTTGGTTATACCGGTGAAGCAGACCTAGAGCAATGGCCGCTGACGGTGGCAAAAGTACAAGCACAATTTATTCAGGCAAAAATAGTCGTACCTGGGCATGGCAAAATAGGTGATACTTCACTGCTAAGCCATACCATAGACTTGTTAACACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40162","NCBI_taxonomy_name":"Shewanella frigidimarina","NCBI_taxonomy_id":"56812"}}}},"ARO_accession":"3003557","ARO_id":"40160","ARO_name":"SFB-1","CARD_short_name":"SFB-1","ARO_description":"This enzyme breaks the beta-lactam antibiotic ring open and deactivates the molecule's antibacterial properties.","ARO_category":{"40158":{"category_aro_accession":"3003555","category_aro_cvterm_id":"40158","category_aro_name":"SHW beta-lactamase","category_aro_description":"This family of sublcass B1 beta-lactamases were discovered in species of the Shewanella genus.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"615":{"model_id":"615","model_name":"OXA-211","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"970":{"protein_sequence":{"accession":"AEV91550.1","sequence":"MKTLQLALIALITTFGSACTTIPPSVETAKNHQQQSAQQQIQQAFDQLQTTGVIVIKDKHGLHSYGNDLSRAQTPYVPASTFKMLNALIGLEHGKATSTEVFKWDGQKRSFPAWEKDMTLGQAMQASAVPVYQELARRIGLDLMKKEVQRIGYGNQQIGTVVDNFWLVGPLQITPVQEVLFVEKLANTQLAFKPDVQHTVQDMLLIEQKPNYKLYAKSGWGMDLEPQVGWWTGWVETATSEKVYFALNMHMKTGISASVREQLVKQSLTALGII"},"dna_sequence":{"accession":"JN861779.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAAAACTTTACAGTTGGCTCTCATCGCCCTCATTACAACCTTCGGTTCCGCATGTACCACAATACCCCCCTCCGTAGAAACAGCTAAAAATCACCAGCAACAAAGTGCTCAGCAGCAGATCCAACAGGCCTTCGATCAACTCCAAACCACGGGGGTGATTGTCATTAAGGATAAGCATGGCTTACACAGCTACGGCAATGACTTGAGCCGTGCTCAGACACCCTATGTACCCGCCTCTACCTTTAAAATGCTGAATGCCTTAATCGGACTAGAACATGGTAAAGCAACCAGCACCGAGGTATTTAAATGGGATGGTCAAAAGCGCAGCTTCCCTGCTTGGGAAAAAGACATGACTTTAGGGCAAGCCATGCAAGCATCTGCCGTTCCCGTTTATCAGGAGCTAGCACGGCGCATTGGCCTAGACCTGATGAAAAAAGAAGTGCAACGCATTGGATATGGCAATCAACAGATTGGCACCGTTGTCGATAATTTTTGGTTAGTCGGTCCACTGCAAATTACGCCTGTTCAAGAAGTCCTTTTTGTAGAGAAGCTGGCCAATACACAACTCGCTTTTAAGCCAGATGTGCAACATACCGTACAAGACATGCTGCTGATTGAACAAAAACCGAATTATAAACTCTACGCCAAATCTGGTTGGGGCATGGACCTAGAACCGCAAGTGGGCTGGTGGACAGGCTGGGTCGAAACAGCAACAAGTGAAAAAGTGTATTTTGCTTTGAATATGCATATGAAAACGGGAATTTCAGCCAGCGTACGTGAGCAACTGGTCAAACAAAGTCTGACAGCACTGGGGATAATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39092","NCBI_taxonomy_name":"Acinetobacter johnsonii","NCBI_taxonomy_id":"40214"}}}},"ARO_accession":"3001710","ARO_id":"38110","ARO_name":"OXA-211","CARD_short_name":"OXA-211","ARO_description":"OXA-211 is a beta-lactamase found in Acinetobacter spp.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46494":{"category_aro_accession":"3007705","category_aro_cvterm_id":"46494","category_aro_name":"OXA-211-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-211.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"616":{"model_id":"616","model_name":"NDM-8","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1270":{"protein_sequence":{"accession":"BAM84089.1","sequence":"MELPNIMHPVAKLSTALAAALMLSGCMPGEIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMGALHAAGIATYANALSNQLAPQEGLVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR"},"dna_sequence":{"accession":"AB744718.1","fmin":"0","fmax":"813","strand":"+","sequence":"ATGGAATTGCCCAATATTATGCACCCGGTCGCGAAGCTGAGCACCGCATTAGCCGCTGCATTGATGCTGAGCGGGTGCATGCCCGGTGAAATCCGCCCGACGATTGGCCAGCAAATGGAAACTGGCGACCAACGGTTTGGCGATCTGGTTTTCCGCCAGCTCGCACCGAATGTCTGGCAGCACACTTCCTATCTCGACATGCCGGGTTTCGGGGCAGTCGCTTCCAACGGTTTGATCGTCAGGGATGGCGGCCGCGTGCTGGTGGTCGATACCGCCTGGACCGATGACCAGACCGCCCAGATCCTCAACTGGATCAAGCAGGAGATCAACCTGCCGGTCGCGCTGGCGGTGGTGACTCACGCGCATCAGGACAAGATGGGCGGTATGGGCGCGCTGCATGCGGCGGGGATTGCGACTTATGCCAATGCGTTGTCGAACCAGCTTGCCCCGCAAGAGGGGCTGGTTGCGGCGCAACACAGCCTGACTTTCGCCGCCAATGGCTGGGTCGAACCAGCAACCGCGCCCAACTTTGGCCCGCTCAAGGTATTTTACCCCGGCCCCGGCCACACCAGTGACAATATCACCGTTGGGATCGACGGCACCGACATCGCTTTTGGTGGCTGCCTGATCAAGGACAGCAAGGCCAAGTCGCTCGGCAATCTCGGTGATGCCGACACTGAGCACTACGCCGCGTCAGCGCGCGCGTTTGGTGCGGCGTTCCCCAAGGCCAGCATGATCGTGATGAGCCATTCCGCCCCCGATAGCCGCGCCGCAATCACTCATACGGCCCGCATGGCCGACAAGCTGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002358","ARO_id":"38758","ARO_name":"NDM-8","CARD_short_name":"NDM-8","ARO_description":"NDM-8 is a beta-lactamase found in Escherichia coli.","ARO_category":{"36196":{"category_aro_accession":"3000057","category_aro_cvterm_id":"36196","category_aro_name":"NDM beta-lactamase","category_aro_description":"NDM beta-lactamases or New Delhi metallo-beta-lactamases are class B beta-lactamases that confer resistance to a broad range of antibiotics including carbapenems, cephalosporins and penicillins.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"617":{"model_id":"617","model_name":"OXA-147","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1602":{"protein_sequence":{"accession":"ACO72579.1","sequence":"MKTFAAYVITACLSSTALASSITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNNLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLSLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFLLEGQLRISAVNQVEFLESLFLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKGTEVYFFAFNMDIDNENKLPLRKSIPTKIMASEGIIGG"},"dna_sequence":{"accession":"FJ848783.1","fmin":"1270","fmax":"2071","strand":"+","sequence":"ATGAAAACATTTGCCGCATATGTAATTACTGCGTGTCTTTCAAGTACGGCATTAGCTAGTTCAATTACAGAAAATACGTCTTGGAACAAAGAGTTCTCTGCCGAAGCCGTCAATGGTGTTTTCGTGCTTTGTAAAAGTAGCAGTAAATCCTGCGCTACCAATAACTTAGCTCGTGCATCAAAGGAATATCTTCCAGCATCAACATTTAAGATCCCCAACGCAATTATCGGCCTAGAAACTGGTGTCATAAAGAATGAGCATCAGGTTTTCAAATGGGACGGAAAGCCAAGAGCCATGAAACAATGGGAAAGAGACTTGAGCTTAAGAGGGGCAATACAAGTTTCAGCGGTTCCCGTATTTCAACAAATCGCCAGAGAAGTTGGCGAAGTAAGAATGCAGAAATACCTTAAAAAATTTTCATATGGCAACCAGAATATCAGTGGTGGCATTGACAAATTCTTGTTGGAGGGTCAGCTAAGAATTTCCGCAGTTAATCAAGTGGAGTTTCTAGAGTCTCTATTTTTAAATAAATTGTCAGCATCAAAAGAAAATCAGCTAATAGTAAAAGAGGCTTTGGTAACGGAGGCTGCGCCTGAATATCTTGTGCATTCAAAAACTGGTTTTTCTGGTGTGGGAACTGAGTCAAATCCTGGTGTCGCATGGTGGGTTGGTTGGGTTGAGAAGGGAACAGAGGTTTACTTTTTCGCCTTTAACATGGATATAGACAACGAAAATAAGTTGCCGCTAAGAAAATCCATTCCCACCAAAATCATGGCAAGTGAGGGCATCATTGGTGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3001801","ARO_id":"38201","ARO_name":"OXA-147","CARD_short_name":"OXA-147","ARO_description":"OXA-147 is a beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46486":{"category_aro_accession":"3007697","category_aro_cvterm_id":"46486","category_aro_name":"OXA-10-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-10.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"618":{"model_id":"618","model_name":"emeA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"720"}},"model_sequences":{"sequence":{"3290":{"protein_sequence":{"accession":"BAC11911.1","sequence":"MTKKNSMMYLAISNLFLVFLGVGLVIPVIPQLKEEMHFSGTTMGMMISIFAIAQLITSPIAGVLSDKIGRKKMIATGMLVFSISELLFGLAQAKSGFYISRGLGGIAAALLMPSVTAFVADMTTISERPKAMGLVSAAISGGFIIGPGVGGFIIGPGVGGFIAYLGIRAPFFAAAFLAFIGFILTLTVLKEPEKRILAAVEAKKGSFMDILRNPMFTSLFVIILISSFGLQAFESIYSIMATINFGFTTSEIAIVITVSGILALICQLFFFDAIVQKIGEMGLIQLTFFASAIFIAVIAFTKNNLVVVFSTFIVFLAFDLFRPAVTTYLSKHAGDQQGTINGLNSTFTSFGNILGPMAAGALFDINHFFPYYVSAVILLGTGFLSLFLNRNKM"},"dna_sequence":{"accession":"AB091338.1","fmin":"173","fmax":"1355","strand":"+","sequence":"ATGACGAAAAAAAATAGTATGATGTACTTAGCAATTTCTAACTTATTTCTTGTTTTTCTAGGCGTAGGCCTAGTCATTCCCGTAATTCCCCAATTAAAAGAAGAAATGCATTTTTCTGGTACCACAATGGGAATGATGATTTCTATTTTTGCGATTGCCCAATTAATCACATCGCCAATCGCAGGTGTCCTTTCGGATAAAATTGGTCGGAAAAAAATGATTGCGACGGGCATGTTGGTGTTTTCAATTTCTGAGTTATTATTTGGTTTAGCCCAAGCGAAAAGCGGTTTTTATATTTCTCGTGGTTTAGGTGGGATTGCCGCCGCGTTATTAATGCCGTCAGTGACAGCCTTTGTGGCAGATATGACCACGATTTCTGAACGTCCGAAAGCGATGGGGCTTGTGTCAGCTGCAATTAGTGGTGGTTTTATTATCGGACCAGGAGTTGGTGGTTTTATTATCGGACCAGGAGTTGGTGGTTTTATTGCTTATTTAGGAATTCGCGCTCCATTTTTTGCGGCCGCATTTTTAGCGTTTATTGGTTTTATTTTGACATTAACTGTTTTGAAGGAGCCAGAGAAACGAATTTTAGCCGCTGTTGAAGCGAAAAAAGGTTCATTTATGGATATTTTAAGAAATCCAATGTTTACCTCATTATTTGTGATTATCTTAATTTCCTCTTTTGGCCTGCAAGCGTTCGAATCTATTTATAGTATTATGGCGACCATTAATTTTGGCTTTACCACAAGTGAAATAGCAATCGTGATTACGGTTAGTGGTATTTTAGCGTTGATTTGTCAGCTGTTTTTCTTTGATGCAATCGTCCAAAAAATAGGTGAAATGGGTTTAATCCAATTAACCTTTTTTGCAAGTGCCATTTTTATTGCCGTGATTGCCTTTACAAAAAATAATTTAGTTGTTGTATTTTCAACGTTTATTGTCTTTTTAGCGTTTGACTTGTTTAGACCAGCAGTAACTACTTATTTATCCAAACATGCTGGAGATCAACAAGGAACCATCAACGGACTAAATTCGACATTTACAAGTTTTGGTAATATTTTAGGACCAATGGCAGCAGGAGCTTTATTTGATATCAATCACTTTTTCCCTTATTATGTTTCAGCAGTAATTCTGTTAGGAACGGGCTTTTTATCGTTATTTTTAAATCGAAATAAGATGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40154","NCBI_taxonomy_name":"Enterococcus faecalis ATCC 29212","NCBI_taxonomy_id":"1201292"}}}},"ARO_accession":"3003551","ARO_id":"40153","ARO_name":"emeA","CARD_short_name":"emeA","ARO_description":"A multidrug efflux pump from Enterococcus faecalis. There exist efflux activity of several antimicrobial agents such as DAPI, Hoechst 33342 and acriflavine. Efflux of DAPI via EmeA was strongly inhibited by reserpine.","ARO_category":{"36251":{"category_aro_accession":"3000112","category_aro_cvterm_id":"36251","category_aro_name":"multidrug and toxic compound extrusion (MATE) transporter","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Multidrug and toxic compound extrusion (MATE) transporters utilize the cationic gradient across the membrane as an energy source. Although there is a diverse substrate specificity, almost all MATE transporters recognize fluoroquinolones. Arciflavine, ethidium and aminoglycosides are also good substrates.","category_aro_class_name":"AMR Gene Family"},"35963":{"category_aro_accession":"0000045","category_aro_cvterm_id":"35963","category_aro_name":"acriflavine","category_aro_description":"Acriflavine is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish.","category_aro_class_name":"Antibiotic"},"43746":{"category_aro_accession":"3005386","category_aro_cvterm_id":"43746","category_aro_name":"disinfecting agents and antiseptics","category_aro_description":"Disinfectants that can also interact with antimicrobial resistance mechanisms, e.g. molecule efflux, and thus are the targets of disinfectant resistance.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"619":{"model_id":"619","model_name":"SHV-30","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"918":{"protein_sequence":{"accession":"AAT75225.1","sequence":"MRYFRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGSVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGASERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AY661885.1","fmin":"48","fmax":"909","strand":"+","sequence":"ATGCGTTATTTTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCAGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTAGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGGATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3001088","ARO_id":"37468","ARO_name":"SHV-30","CARD_short_name":"SHV-30","ARO_description":"SHV-30 is an extended-spectrum beta-lactamase found in Enterobacter cloacae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"620":{"model_id":"620","model_name":"OXA-320","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1840":{"protein_sequence":{"accession":"AGR55864.1","sequence":"MKNTIHINFAIFLIIANIIYSSASASTDISTVASPLFEGTEGCFLLYDASTNAEIAQFNKAKCATQMAPDSTFKIALSLMAFDAEIIDQKTIFKWDKTPKGMEIWNSNHTPKTWMQFSVVWVSQEITQKIGLNKIKNYLKDFDYGNQDFSGDKERNNGLTEAWLESSLKISPEEQIQFLRKIINHNLPVKNSAIENTIENMYLQDLDNSTKLYGKTGAGFTANRTLQNGWFEGFIISKSGHKYVFVSALTGNLGSNLTSSIKAKKIAITILNTLNL"},"dna_sequence":{"accession":"KF151169.1","fmin":"0","fmax":"831","strand":"+","sequence":"ATGAAAAACACAATACATATCAACTTCGCTATTTTTTTAATAATTGCAAATATTATCTACAGCAGCGCCAGTGCATCAACAGATATCTCTACTGTTGCATCTCCATTATTTGAAGGAACTGAAGGTTGTTTTTTACTTTACGATGCATCCACAAACGCTGAAATTGCTCAATTCAATAAAGCAAAGTGTGCAACGCAAATGGCACCAGATTCAACTTTCAAGATCGCATTATCACTTATGGCATTTGATGCGGAAATAATAGATCAGAAAACCATATTCAAATGGGATAAAACCCCCAAAGGAATGGAGATCTGGAACAGCAATCATACACCAAAGACGTGGATGCAATTTTCTGTTGTTTGGGTTTCGCAAGAAATAACCCAAAAAATTGGATTAAATAAAATCAAGAATTATCTCAAAGATTTTGATTATGGAAATCAAGACTTCTCTGGAGATAAAGAAAGAAACAACGGATTAACAGAAGCATGGCTCGAAAGTAGCTTAAAAATTTCACCAGAAGAACAAATTCAATTCCTGCGTAAAATTATTAATCACAATCTCCCAGTTAAAAACTCAGCCATAGAAAACACCATAGAGAACATGTATCTACAAGATCTGGATAATAGTACAAAACTGTATGGGAAAACTGGTGCAGGATTCACAGCAAATAGAACCTTACAAAACGGATGGTTTGAAGGGTTTATTATAAGCAAATCAGGACATAAATATGTTTTTGTGTCCGCACTTACAGGAAACTTGGGGTCGAATTTAACATCAAGCATAAAAGCCAAGAAAATTGCGATCACCATTCTAAACACACTAAATTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3001793","ARO_id":"38193","ARO_name":"OXA-320","CARD_short_name":"OXA-320","ARO_description":"OXA-320 is a beta-lactamase found in Proteus mirabilis.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46485":{"category_aro_accession":"3007696","category_aro_cvterm_id":"46485","category_aro_name":"OXA-1-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-1.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"621":{"model_id":"621","model_name":"ErmF","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"593":{"protein_sequence":{"accession":"AAA88675.1","sequence":"MTKKKLPVRFTGQHFTIDKVLIKDAIRQANISNQDTVLDIGAGKGFLTVHLLKIANNVVAIENDTALVEHLRKLFSDARNVQVVGCDFRNFAVPKFPFKVVSNIPYGITSDIFKILMFESLGNFLGGSIVLQLEPTQKLFSRKLYNPYTVFYHTFFDLKLVYEVGPESFLPPPTVKSALLNIKRKHLFFDFKFKAKYLAFISYLLEKPDLSVKTALKSIFRKSQVRSISEKFGLNLNAQIVCLSPSQWLNCFLEMLEVVPEKFHPS"},"dna_sequence":{"accession":"M17124.1","fmin":"1181","fmax":"1982","strand":"+","sequence":"ATGACAAAAAAGAAATTGCCCGTTCGTTTTACGGGTCAGCACTTTACTATTGATAAAGTGCTAATAAAAGATGCAATAAGACAAGCAAATATAAGTAATCAGGATACGGTTTTAGATATTGGGGCAGGCAAGGGGTTTCTTACTGTTCATTTATTAAAAATCGCCAACAATGTTGTTGCTATTGAAAACGACACAGCTTTGGTTGAACATTTACGAAAATTATTTTCTGATGCCCGAAATGTTCAAGTTGTCGGTTGTGATTTTAGGAATTTTGCAGTTCCGAAATTTCCTTTCAAAGTGGTGTCAAATATTCCTTATGGCATTACTTCCGATATTTTCAAAATCCTGATGTTTGAGAGTCTTGGAAATTTTCTGGGAGGTTCCATTGTCCTTCAATTAGAACCTACACAAAAGTTATTTTCGAGGAAGCTTTACAATCCATATACCGTTTTCTATCATACTTTTTTTGATTTGAAACTTGTCTATGAGGTAGGTCCTGAAAGTTTCTTGCCACCGCCAACTGTCAAATCAGCCCTGTTAAACATTAAAAGAAAACACTTATTTTTTGATTTTAAGTTTAAAGCCAAATACTTAGCATTTATTTCCTATCTGTTAGAGAAACCTGATTTATCTGTAAAAACAGCTTTAAAGTCGATTTTCAGGAAAAGTCAGGTCAGGTCAATTTCGGAAAAATTCGGTTTAAACCTTAATGCTCAAATTGTTTGTTTGTCTCCAAGTCAATGGTTAAACTGTTTTTTGGAAATGCTGGAAGTTGTCCCTGAAAAATTTCATCCTTCGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35916","NCBI_taxonomy_name":"Bacteroides fragilis","NCBI_taxonomy_id":"817"}}}},"ARO_accession":"3000498","ARO_id":"36637","ARO_name":"ErmF","CARD_short_name":"ErmF","ARO_description":"ErmF confers the MLSb phenotype.","ARO_category":{"36699":{"category_aro_accession":"3000560","category_aro_cvterm_id":"36699","category_aro_name":"Erm 23S ribosomal RNA methyltransferase","category_aro_description":"Erm proteins are part of the RNA methyltransferase family and methylate A2058 (E. coli nomenclature) of the 23S ribosomal RNA conferring degrees of resistance to Macrolides, Lincosamides and Streptogramin b. This is called the MLSb phenotype.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35946":{"category_aro_accession":"0000027","category_aro_cvterm_id":"35946","category_aro_name":"roxithromycin","category_aro_description":"Roxithromycin is a semi-synthetic, 14-carbon ring macrolide antibiotic derived from erythromycin. It is used to treat respiratory tract, urinary and soft tissue infections. Roxithromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35974":{"category_aro_accession":"0000057","category_aro_cvterm_id":"35974","category_aro_name":"telithromycin","category_aro_description":"Telithromycin is a semi-synthetic derivative of erythromycin. It is a 14-membered macrolide and is the first ketolide antibiotic to be used in clinics. Telithromycin binds the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"35982":{"category_aro_accession":"0000065","category_aro_cvterm_id":"35982","category_aro_name":"clarithromycin","category_aro_description":"Clarithromycin is a methyl derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome and is used to treat pharyngitis, tonsillitis, acute maxillary sinusitis, acute bacterial exacerbation of chronic bronchitis, pneumonia (especially atypical pneumonias associated with Chlamydia pneumoniae or TWAR), and skin structure infections.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"36284":{"category_aro_accession":"3000145","category_aro_cvterm_id":"36284","category_aro_name":"tylosin","category_aro_description":"Tylosin is a 16-membered macrolide, naturally produced by Streptomyces fradiae. It interacts with the bacterial ribosome 50S subunit to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"36295":{"category_aro_accession":"3000156","category_aro_cvterm_id":"36295","category_aro_name":"spiramycin","category_aro_description":"Spiramycin is a 16-membered macrolide and is natural product produced by Streptomyces ambofaciens. It binds to the 50S subunit of bacterial ribosomes and inhibits peptidyl transfer activity to disrupt protein synthesis.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"36315":{"category_aro_accession":"3000176","category_aro_cvterm_id":"36315","category_aro_name":"dirithromycin","category_aro_description":"Dirithromycin is an oxazine derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome to inhibit bacterial protein synthesis.","category_aro_class_name":"Antibiotic"},"36722":{"category_aro_accession":"3000583","category_aro_cvterm_id":"36722","category_aro_name":"pristinamycin IA","category_aro_description":"Pristinamycin IA is a type B streptogramin antibiotic produced by Streptomyces pristinaespiralis. It binds to the P site of the 50S subunit of the bacterial ribosome, preventing the extension of protein chains.","category_aro_class_name":"Antibiotic"},"36723":{"category_aro_accession":"3000584","category_aro_cvterm_id":"36723","category_aro_name":"quinupristin","category_aro_description":"Quinupristin is a type B streptogramin and a semisynthetic derivative of pristinamycin 1A. It is a component of the drug Synercid and interacts with the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"virginiamycin M1","category_aro_description":"Virginiamycin M1 is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37016":{"category_aro_accession":"3000672","category_aro_cvterm_id":"37016","category_aro_name":"madumycin II","category_aro_description":"Madumycin II is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37017":{"category_aro_accession":"3000673","category_aro_cvterm_id":"37017","category_aro_name":"griseoviridin","category_aro_description":"Griseoviridin is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"37019":{"category_aro_accession":"3000675","category_aro_cvterm_id":"37019","category_aro_name":"pristinamycin IB","category_aro_description":"Pristinamycin IB is a class B streptogramin similar to pristinamycin IA, the former containing a N-methyl-4-(methylamino)phenylalanine instead of a N-methyl-4-(dimethylamino)phenylalanine in its class A streptogramin counterpart (one less methyl group).","category_aro_class_name":"Antibiotic"},"37021":{"category_aro_accession":"3000677","category_aro_cvterm_id":"37021","category_aro_name":"virginiamycin S2","category_aro_description":"Virginiamycin S2 is a streptogramin B antibiotic.","category_aro_class_name":"Antibiotic"},"37022":{"category_aro_accession":"3000678","category_aro_cvterm_id":"37022","category_aro_name":"pristinamycin IC","category_aro_description":"Pristinamycin IC is a class B streptogramin derived from virginiamycin S1.","category_aro_class_name":"Antibiotic"},"37023":{"category_aro_accession":"3000679","category_aro_cvterm_id":"37023","category_aro_name":"vernamycin C","category_aro_description":"Vernamycin C is a streptogramin B antibiotic.","category_aro_class_name":"Antibiotic"},"37024":{"category_aro_accession":"3000680","category_aro_cvterm_id":"37024","category_aro_name":"patricin A","category_aro_description":"Patricin A is a streptogramin B antibiotic.","category_aro_class_name":"Antibiotic"},"37025":{"category_aro_accession":"3000681","category_aro_cvterm_id":"37025","category_aro_name":"patricin B","category_aro_description":"Patricin B is a streptogramin B antibiotic.","category_aro_class_name":"Antibiotic"},"37026":{"category_aro_accession":"3000682","category_aro_cvterm_id":"37026","category_aro_name":"ostreogrycin B3","category_aro_description":"Ostreogrycin B3 is a derivative of pristinamycin IA, with an additional 3-hydroxy group on its 4-oxopipecolic acid.","category_aro_class_name":"Antibiotic"},"37247":{"category_aro_accession":"3000867","category_aro_cvterm_id":"37247","category_aro_name":"oleandomycin","category_aro_description":"Oleandomycin is a 14-membered macrolide produced by Streptomyces antibioticus. It is ssimilar to erythromycin, and contains a desosamine amino sugar and an oleandrose sugar. It targets the 50S ribosomal subunit to prevent protein synthesis.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35952":{"category_aro_accession":"0000034","category_aro_cvterm_id":"35952","category_aro_name":"streptogramin A antibiotic","category_aro_description":"Streptogramin A antibiotics are cyclic polyketide peptide hybrids that bind to the ribosomal peptidyl transfer centre. Structural variation arises from substituting a proline for its desaturated derivative and by its substitution for Ala or Cys. Used alone, streptogramin A antibiotics are bacteriostatic, but is bactericidal when used with streptogramin B antibiotics.","category_aro_class_name":"Drug Class"},"35967":{"category_aro_accession":"0000050","category_aro_cvterm_id":"35967","category_aro_name":"streptogramin B antibiotic","category_aro_description":"Streptogramin B antibiotics are are cyclic hepta- or hexa-depsipeptides.  Type B streptogramins block the peptide exit tunnel of the 50S bacterial ribosome. The general composition of group B streptogramins is 3-hydroxypicolinic acid-L-Thr-D-aminobutyric acid (or D-Ala)-L-Pro-L-Phe (or 4-N-,N-(dimethylamino)-L-Phe)-X-L-phenylglycine. Used alone, streptogramin B antibiotics are bacteriostatic, but is bactericidal when used with streptogramin A antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"622":{"model_id":"622","model_name":"DHA-7","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1865":{"protein_sequence":{"accession":"ADQ00385.1","sequence":"MKKSLSATLISALLAFSAPGFSAADNVAAVVDSTIKPLMAQQDIPGMAVAVSVKGKPYYFNYGFADIQAKQPVTENTLFELGSVSKTFTGVLGAVSVAKKEMALNDPAAKYQPELALPQWKGITLLDLATYTAGGLPLQVPDAVKSRADLLNFYQQWQPSRKPGDMRLYANSSIGLFGALTANAAGMPYEQLLTARILAPLGLSHTFITVPESAQSQYAYGYKNKKPVRVSPGQLDAESYGVKSASKDMLRWAEMNMEPSRAGNADLEMAMYLAQTRYYKTAAINQGLGWEMYDWPQQKDMIINGVTNEVALQPHPVTDNQVQPYNRASWVHKTGATTGSGAYVAFIPEKQVAIVILANKNYPNTERVKAAQAILSALE"},"dna_sequence":{"accession":"HQ456945.1","fmin":"0","fmax":"1140","strand":"+","sequence":"ATGAAAAAATCGTTATCTGCAACACTGATTTCCGCTCTGCTGGCGTTTTCCGCCCCGGGGTTTTCTGCCGCTGATAATGTCGCGGCGGTGGTGGACAGCACCATTAAACCGCTGATGGCACAGCAGGATATTCCCGGGATGGCGGTTGCCGTCTCCGTAAAGGGTAAGCCCTATTATTTCAATTATGGTTTTGCCGATATTCAGGCAAAACAGCCGGTCACTGAAAATACACTATTTGAGCTCGGATCTGTAAGTAAAACTTTCACAGGTGTGCTGGGTGCGGTTTCTGTGGCGAAAAAAGAGATGGCGCTGAATGATCCGGCGGCAAAATACCAGCCGGAGCTGGCTCTGCCGCAGTGGAAGGGGATCACATTGCTGGATCTGGCTACCTATACCGCAGGCGGACTGCCGTTACAGGTGCCGGATGCGGTAAAAAGCCGTGCGGATCTGCTGAATTTCTATCAGCAGTGGCAGCCGTCCCGGAAACCGGGCGATATGCGTCTGTATGCAAACAGCAGTATCGGCCTGTTTGGTGCTCTGACCGCAAACGCGGCGGGGATGCCGTATGAGCAGTTGCTGACTGCACGGATCCTGGCACCGCTGGGGTTATCTCACACCTTTATTACTGTGCCGGAAAGTGCGCAAAGCCAGTATGCGTACGGTTATAAAAACAAAAAACCGGTCCGCGTGTCGCCGGGACAGCTTGATGCGGAATCTTACGGCGTGAAATCCGCCTCAAAAGATATGCTGCGCTGGGCGGAAATGAATATGGAGCCGTCACGGGCCGGTAATGCGGATCTGGAAATGGCAATGTATCTCGCCCAGACCCGCTACTATAAAACCGCCGCGATTAACCAGGGGCTGGGCTGGGAAATGTATGACTGGCCGCAGCAGAAAGATATGATCATTAACGGTGTGACCAACGAGGTCGCATTGCAGCCGCATCCGGTAACAGACAACCAGGTTCAGCCGTATAACCGTGCTTCCTGGGTGCATAAAACGGGCGCAACAACTGGTTCCGGCGCCTATGTCGCCTTTATTCCGGAAAAACAGGTGGCGATTGTGATTCTGGCGAATAAAAACTACCCGAATACCGAAAGAGTCAAAGCTGCACAGGCTATTTTGAGTGCACTGGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3002136","ARO_id":"38536","ARO_name":"DHA-7","CARD_short_name":"DHA-7","ARO_description":"DHA-7 is a beta-lactamase found in the Enterobacteriaceae family.","ARO_category":{"36207":{"category_aro_accession":"3000068","category_aro_cvterm_id":"36207","category_aro_name":"DHA beta-lactamase","category_aro_description":"DHA beta-lactamases are plasmid-mediated AmpC \u03b2-lactamases that confer resistance to cephamycins and oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"623":{"model_id":"623","model_name":"OXA-68","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"2014":{"protein_sequence":{"accession":"AAW81339.1","sequence":"MNIKALLLITSAIFISACSPYIVSANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQEVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"AY750910.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGTCTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACTACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTAGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAGAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001616","ARO_id":"38016","ARO_name":"OXA-68","CARD_short_name":"OXA-68","ARO_description":"OXA-68 is a beta-lactamase found in A. baumannii.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"625":{"model_id":"625","model_name":"QnrB46","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"8169":{"protein_sequence":{"accession":"ADW54092.1","sequence":"MTPLLYKKTGTNMALALVGEKIDRNRFTGEKIENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNASALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKAVLEKCELWENRWMGAQVLGATFSGSDLSGGEFSTFDWRAANFTHCDLTNSELGDLDIRRVDLQGVKLDNYQASLLMERLGIAIIG"},"dna_sequence":{"accession":"HQ704413.2","fmin":"0","fmax":"681","strand":"+","sequence":"ATGACGCCATTACTGTATAAGAAAACAGGAACAAATATGGCTCTAGCGCTCGTGGGCGAAAAAATTGACAGAAACCGTTTCACCGGTGAAAAAATTGAAAATAGTACATTTTTTAACTGTGATTTTTCAGGAGCGGACCTGAGCGGCACTGAGTTTATCGGCTGCCAATTTTATGATCGTGAAAGCCAGAAAGGCTGTAATTTTAGCCGTGCGATGTTAAAGGATGCTATTTTTAAAAGCTGCGATTTATCCATGGCCGATTTTCGCAATGCAAGCGCCCTGGGTATTGAGATTCGTCATTGTAGGGCTCAGGGTGCAGATTTTCGCGGCGCAAGCTTTATGAACATGATTACCACGCGAACTTGGTTCTGCAGCGCGTATATCACGAATACGAATCTGTCTTATGCCAATTTTTCGAAAGCAGTGTTGGAGAAGTGTGAATTATGGGAAAACCGTTGGATGGGTGCCCAGGTACTGGGCGCGACGTTCAGTGGTTCAGATCTCTCCGGCGGCGAGTTTTCAACTTTCGACTGGCGAGCAGCAAACTTTACACATTGCGATCTCACAAATTCGGAGTTGGGTGACTTAGATATTCGTCGGGTTGATTTACAAGGCGTTAAGTTGGACAACTACCAGGCTTCGTTGCTCATGGAGCGACTTGGCATCGCGATAATTGGATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002761","ARO_id":"39195","ARO_name":"QnrB46","CARD_short_name":"QnrB46","ARO_description":"QnrB46 is a plasmid-mediated quinolone resistance protein found in Escherichia coli.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"628":{"model_id":"628","model_name":"catB10","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"6208":{"protein_sequence":{"accession":"ACL13298.1","sequence":"MTNYFESPFKGKLLADQVKNPNIKVGRYSYYSGYYHGHSFDECARFLLPDRNDIDQLIVGSFCSIGTGASFIMAGNQGHRYDWASSFPFFYMKEEPAFSGALDAFQKAGDTVIGSDVWIGSEAMIMPGINVGHGAVIGSRALVTKDVEPYTIVGGNPAKPIKKRFSDEEIAMLLKMNWWDWPTEKIEEAMPLLCSSNIVGLHRYWQGFAV"},"dna_sequence":{"accession":"FJ495083.1","fmin":"732","fmax":"1365","strand":"+","sequence":"ATGACCAACTATTTTGAAAGTCCATTTAAAGGCAAACTGCTGGCCGACCAGGTAAAGAACCCGAACATCAAAGTCGGACGGTATAGCTATTATTCCGGCTATTACCATGGCCATTCGTTTGACGAGTGCGCTCGCTTTCTCTTGCCAGATCGCAATGACATCGACCAACTGATCGTTGGTAGCTTCTGTTCCATCGGCACGGGCGCCTCCTTCATCATGGCCGGAAATCAGGGGCACCGTTATGACTGGGCGTCTTCTTTTCCCTTCTTCTACATGAAAGAGGAGCCAGCATTCTCGGGCGCACTTGATGCATTCCAAAAAGCCGGTGACACAGTCATCGGAAGTGATGTCTGGATAGGCTCTGAGGCCATGATCATGCCCGGCATCAACGTCGGTCATGGCGCTGTGATTGGAAGCCGCGCTTTGGTCACGAAAGATGTGGAGCCGTACACTATCGTTGGCGGAAATCCCGCCAAACCGATCAAGAAACGCTTCTCCGACGAGGAGATCGCCATGCTTTTGAAAATGAATTGGTGGGATTGGCCAACTGAAAAAATTGAGGAAGCAATGCCTTTGCTATGCTCATCCAACATCGTTGGGCTGCATCGATACTGGCAAGGCTTTGCCGTCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3003110","ARO_id":"39686","ARO_name":"catB10","CARD_short_name":"catB10","ARO_description":"catB10 is an integron-encoded variant of the cat gene found in P. aeruginosa.","ARO_category":{"36261":{"category_aro_accession":"3000122","category_aro_cvterm_id":"36261","category_aro_name":"chloramphenicol acetyltransferase (CAT)","category_aro_description":"Inactivates chloramphenicol by addition of an acyl group. CAT is used to describe many variants of the chloramphenicol acetyltransferase gene in a range of organisms including Acinetobacter calcoaceticus, Agrobacterium tumefaciens, Alkalihalobacillus clausii, Bacillus subtilis, Campylobacter coli, Enterococcus faecalis, Enterococcus faecium, Lactococcus lactis, Listeria monocytogenes, Listonella anguillarum, Morganella morganii, Photobacterium damselae subsp. piscicida, Proteus mirabilis, Salmonella typhi, Serratia marcescens, Shigella flexneri, Staphylococcus aureus, Staphylococcus haemolyticus, Staphylococcus intermedius, Streptococcus agalactiae, Streptococcus suis and Streptomyces acrimycini.","category_aro_class_name":"AMR Gene Family"},"36521":{"category_aro_accession":"3000382","category_aro_cvterm_id":"36521","category_aro_name":"azidamfenicol","category_aro_description":"Azidamfenicol is a water soluble derivative of chloramphenicol, sharing the same mode of action of inhibiting peptide synthesis by interacting with the 23S RNA of the 50S ribosomal subunit.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36595":{"category_aro_accession":"3000456","category_aro_cvterm_id":"36595","category_aro_name":"thiamphenicol","category_aro_description":"Derivative of Chloramphenicol. The nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3).","category_aro_class_name":"Antibiotic"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"629":{"model_id":"629","model_name":"VIM-28","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"854":{"protein_sequence":{"accession":"AEI25539.1","sequence":"MLKVISSLLVYMTASVMAVASPLAHSGEPSGEYPTVNEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEAEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSANVLYGGCAVLELSRTSAGNVADADLAEWPTSVERIQKHYPEAEVVIPGHGLPGGLDLLQHTANVVKAHKNRSVAE"},"dna_sequence":{"accession":"JF900599.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGTTAAAAGTTATTAGTAGTTTATTGGTCTACATGACCGCGTCTGTCATGGCTGTCGCAAGTCCGTTAGCCCATTCCGGGGAGCCGAGTGGTGAGTATCCGACAGTCAACGAAATTCCGGTCGGAGAGGTCCGACTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCGGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAAAAGCAAATTGGACTTCCCGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGCAGAGGGGAACGAGATTCCCACGCATTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAGCTCTTCTATCCTGGTGCTGCGCATTCGACCGACAATCTGGTTGTATACGTCCCGTCAGCGAACGTGCTATACGGTGGTTGTGCCGTTCTTGAGTTGTCACGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCGTTGAGCGGATTCAAAAACACTACCCGGAAGCAGAGGTCGTCATTCCCGGGCACGGTCTACCGGGCGGTCTAGACTTGCTCCAGCACACAGCGAACGTTGTCAAAGCACACAAAAATCGCTCAGTCGCCGAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002298","ARO_id":"38698","ARO_name":"VIM-28","CARD_short_name":"VIM-28","ARO_description":"VIM-28 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"630":{"model_id":"630","model_name":"adeJ","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"2000"}},"model_sequences":{"sequence":{"1":{"protein_sequence":{"accession":"AAX14802.1","sequence":"MAQFFIHRPIFAWVIALVIMLAGILTLTKMPIAQYPTIAPPTVTIAATYPGASAETVENTVTQIIEQQMNGLDGLRYISSNSAGNGQASIQLNFEQGVDPDIAQVQVQNKLQSATALLPEDVQRQGVTVTKSGASFLQVIAFYSPDNNLSDSDIKDYVNSSIKEPLSRVAGVGEVQVFGGSYAMRIWLDPAKLTSYQLTPSDIATALQAQNSQVAVGQLGGAPAVQGQVLNATVNAQSLLQTPEQFKNIFLKNTASGAEVRLKDVARVELGSDNYQFDSKFNGKPAAGLAIKIATGANALDTAEAVEQRLSELRKNYPTGLADKLAYDTTPFIRLSIESVVHTLIEAVILVFIVMFLFLQNWRATIIPTLAVPVVVLGTFAVINIFGFSINTLTMFAMVLAIGLLVDDAIVVVENVERVMSEDHTDPVTATSRSMQQISGALVGITSVLTAVFVPMAFFGGTTGVIYRQFSITLVTAMVLSLIVALTFTPALCATILKQHDPNKEPSNNIFARFFRSFNNGFDRMSHSYQNGVSRMLKGKIFSGVLYAVVVALLVFLFQKLPSSFLPEEDQGVVMTLVQLPPNATLDRTGKVIDTMTNFFMNEKDTVESIFTVSGFSFTGVGQNAGIGFVKLKDWSKRTTPETQIGSLIQRGMALNMIIKDASYVMPLQLPAMPELGVTAGFNLQLKDSSGQGHEKLIAARNTILGLASQDKRLVGVRPNGQEDTPQYQINVDQAQAGAMGVSIAEINNTMRIAWGGSYINDFVDRGRVKKVYVQGDAGSRMMPEDLNKWYVRNNKGEMVPFSAFATGEWTYGSPRLERYNGVSSVNIQGTPAPGVSSGDAMKAMEEIIGKLPSMGLQGFDYEWTGLSLEERESGAQAPFLYALSLLIVFLCLAALYESWSIPFSVLLVVPLGVIGAIVLTYLGMIIKGDPNLSNNIYFQVAIIAVIGLSAKNAILIVEFAKELQEKGEDLLDATLHAAKMRLRPIIMTTLAFGFGVLPLALSTGAGAGSQHSVGFGVLGGVLSATFLGIFFIPVFYVWIRSMFKYKPKTINTQEHKS"},"dna_sequence":{"accession":"AY769962.1","fmin":"2434","fmax":"5611","strand":"+","sequence":"ATGGCACAATTTTTTATTCATCGCCCCATATTTGCGTGGGTGATTGCATTAGTCATTATGTTGGCGGGTATTCTTACGCTAACAAAAATGCCTATTGCACAATATCCAACGATTGCACCACCAACCGTAACGATTGCTGCGACTTATCCTGGTGCATCGGCTGAAACAGTTGAAAATACTGTAACCCAGATCATTGAACAACAAATGAATGGTCTTGATGGCTTACGTTATATTTCATCTAACAGTGCTGGTAATGGTCAGGCATCTATTCAATTAAACTTTGAACAAGGTGTTGACCCTGATATTGCACAGGTTCAAGTTCAAAACAAATTGCAATCTGCAACTGCGCTTTTACCTGAAGATGTACAACGTCAAGGTGTAACAGTTACTAAATCTGGTGCGAGCTTCTTGCAAGTTATTGCATTCTATTCACCAGATAACAACCTGTCAGACTCTGACATTAAAGACTACGTAAACTCGTCAATTAAAGAACCGCTTAGCCGTGTTGCCGGTGTTGGTGAGGTACAGGTCTTCGGTGGCTCATACGCAATGCGTATCTGGCTTGATCCAGCTAAATTAACAAGCTATCAACTTACTCCTAGTGATATTGCAACTGCCTTACAAGCGCAGAACTCGCAAGTTGCCGTAGGTCAGTTAGGTGGTGCTCCGGCTGTACAAGGTCAAGTTCTTAACGCAACAGTAAATGCACAAAGCTTATTGCAGACTCCTGAACAGTTTAAAAATATCTTCTTAAAGAACACAGCATCAGGTGCTGAGGTTCGATTAAAAGATGTTGCTCGCGTAGAATTAGGTTCGGATAACTATCAATTCGACTCGAAGTTTAACGGTAAACCGGCAGCTGGTCTTGCAATTAAAATTGCAACAGGTGCTAACGCACTCGACACAGCCGAAGCAGTTGAACAACGTTTATCTGAACTACGTAAGAACTATCCAACAGGTCTTGCAGATAAACTGGCTTATGACACGACTCCATTTATCCGTCTTTCAATTGAAAGTGTAGTACACACATTAATTGAAGCCGTGATTTTGGTATTCATTGTCATGTTCCTATTCTTACAAAACTGGCGTGCAACGATTATTCCAACGCTTGCAGTTCCAGTAGTTGTATTAGGTACATTTGCGGTCATTAATATCTTTGGCTTCTCAATTAACACCTTAACCATGTTCGCTATGGTATTGGCAATCGGTCTTCTGGTCGACGACGCCATTGTTGTAGTCGAAAACGTTGAACGTGTGATGAGTGAAGACCATACCGATCCGGTTACGGCCACTTCTCGCTCAATGCAGCAGATTTCTGGTGCGTTAGTAGGTATTACCAGCGTATTGACAGCGGTATTCGTACCAATGGCTTTCTTTGGTGGTACAACAGGTGTAATTTACCGCCAGTTCTCGATTACCCTTGTAACTGCAATGGTTCTGTCGTTAATTGTAGCGTTGACGTTCACACCGGCACTTTGTGCAACTATCTTGAAACAGCATGATCCTAATAAAGAACCAAGCAATAATATCTTTGCGCGTTTCTTTAGAAGCTTTAACAATGGTTTTGACCGCATGTCGCATAGCTACCAAAATGGTGTTAGCCGCATGCTTAAAGGCAAAATCTTCTCTGGCGTGCTCTATGCTGTTGTAGTTGCCCTTTTAGTCTTCTTGTTCCAAAAACTCCCGTCTTCATTCTTACCAGAAGAAGATCAGGGTGTGGTCATGACACTTGTACAATTACCACCAAATGCAACGCTTGACCGTACCGGTAAAGTGATTGATACCATGACTAACTTCTTTATGAATGAAAAAGATACCGTGGAATCTATTTTCACTGTTTCTGGTTTCTCATTCACAGGTGTTGGTCAAAACGCGGGTATTGGCTTCGTTAAGTTGAAAGACTGGAGCAAACGTACGACACCAGAAACTCAAATTGGTTCATTGATTCAGCGTGGTATGGCATTAAATATGATCATTAAAGATGCATCATACGTTATGCCGTTACAGCTTCCAGCAATGCCTGAACTTGGTGTAACTGCCGGATTTAACTTGCAGCTTAAAGATTCAAGTGGTCAAGGCCATGAGAAACTGATTGCAGCTCGTAACACGATTTTAGGTTTGGCATCACAAGATAAACGTCTTGTAGGTGTGCGTCCAAATGGTCAGGAAGATACTCCTCAGTATCAAATTAATGTAGATCAGGCTCAAGCTGGTGCTATGGGCGTTAGTATTGCCGAAATCAACAATACAATGCGTATTGCATGGGGTGGCTCATACATTAACGATTTCGTTGACCGTGGTCGTGTGAAAAAAGTTTATGTTCAAGGTGATGCGGGCAGCCGTATGATGCCTGAAGACTTAAACAAATGGTATGTACGTAATAACAAAGGTGAGATGGTTCCATTCTCGGCATTTGCTACAGGCGAATGGACGTATGGTTCTCCACGTCTCGAACGTTATAACGGCGTGTCATCGGTTAACATTCAAGGTACACCTGCACCTGGCGTGAGCTCTGGTGATGCCATGAAAGCAATGGAAGAAATTATTGGTAAGTTACCATCTATGGGCTTACAAGGTTTCGACTATGAGTGGACAGGCTTATCACTTGAAGAACGTGAGTCTGGTGCTCAAGCGCCGTTCTTATACGCACTTTCATTGTTAATCGTATTCCTTTGCTTGGCTGCACTATATGAAAGCTGGTCAATTCCGTTCTCGGTTTTACTTGTGGTACCACTTGGTGTCATTGGTGCAATCGTATTGACCTACTTGGGCATGATTATTAAAGGAGATCCAAATCTCTCAAATAACATTTACTTCCAGGTAGCGATTATTGCGGTTATCGGTCTTTCTGCAAAAAATGCGATCTTGATTGTTGAATTCGCAAAAGAATTGCAGGAAAAAGGTGAAGATCTACTTGATGCAACCTTACATGCTGCAAAAATGCGTTTACGTCCAATTATCATGACCACCCTTGCCTTCGGTTTCGGTGTACTTCCACTTGCACTTTCAACAGGTGCCGGTGCAGGAAGTCAGCACTCTGTAGGCTTTGGTGTACTTGGTGGCGTACTCAGCGCGACGTTCTTAGGAATCTTCTTTATCCCTGTATTCTATGTGTGGATTCGTAGTATGTTTAAGTACAAACCAAAAACCATAAACACTCAGGAGCATAAATCGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3000781","ARO_id":"37161","ARO_name":"adeJ","CARD_short_name":"adeJ","ARO_description":"AdeJ is a RND efflux protein that acts as the inner membrane transporter of the AdeIJK efflux complex. It has 57% identity with E. coli AcrB.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36309":{"category_aro_accession":"3000170","category_aro_cvterm_id":"36309","category_aro_name":"imipenem","category_aro_description":"Imipenem is a broad-spectrum antibiotic and is usually taken with cilastatin, which prevents hydrolysis of imipenem by renal dehydropeptidase-I. It is resistant to hydrolysis by most other beta-lactamases. Notable exceptions are the KPC beta-lactamases and Ambler Class B enzymes.","category_aro_class_name":"Antibiotic"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"40523":{"category_aro_accession":"3003832","category_aro_cvterm_id":"40523","category_aro_name":"ticarcillin","category_aro_description":"Ticarcillin is a carboxypenicillin used for the treatment of Gram-negative bacteria, particularly P. aeruginosa. Ticarcillin's antibiotic properties arise from its ability to prevent cross-linking of peptidoglycan during cell wall synthesis, when the bacteria try to divide, causing cell death.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"631":{"model_id":"631","model_name":"TEM-21","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1077":{"protein_sequence":{"accession":"CAA76794.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDKLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVKYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLRNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGASERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"Y17582.1","fmin":"0","fmax":"858","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATAAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTAAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCGCAACATGGGGGATCATGTAACCCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCAGTGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGG","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3000892","ARO_id":"37272","ARO_name":"TEM-21","CARD_short_name":"TEM-21","ARO_description":"TEM-21 is an extended-spectrum beta-lactamase found in many species of Gram-negative bacteria.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"633":{"model_id":"633","model_name":"OXA-355","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1460":{"protein_sequence":{"accession":"AGW83453.1","sequence":"MKFKMKGLFCVILSSLAFSGCVYDSKLQRPVISERETEIPLLFNQAQTQAVFVTYDGIHLKSYGNDLSRAKTEYIPASTFKMLNALIGLQNAKATNTEVFHWNGEKRAFSAWEKDMTLAEAMQASAVPVYQELARRIGLELMREEVKRVGFGNAEIGQQVDNFWLVGPLKISPEQEVQFAYQLAMKQLPFDRNVQQQVKDMLYIERRGDSKLYAKSGWGMDVEPQVGWYTGWVEQPNGKVTAFALNMNMQAGDDPAERKQLTLSILDKLGLFFYLR"},"dna_sequence":{"accession":"KF297584.1","fmin":"0","fmax":"831","strand":"+","sequence":"ATGAAGTTTAAAATGAAAGGTTTATTTTGTGTCATCCTCAGTAGTTTGGCATTTTCAGGTTGTGTTTATGATTCAAAACTACAACGCCCAGTCATATCAGAGCGAGAAACTGAGATTCCTTTATTATTTAATCAAGCACAGACTCAAGCTGTGTTTGTTACTTATGATGGGATTCATCTAAAAAGTTATGGTAATGATCTAAGCCGAGCAAAGACTGAATATATTCCTGCATCTACATTTAAGATGTTGAATGCTTTAATTGGCTTGCAAAATGCAAAAGCAACCAATACTGAAGTATTTCATTGGAATGGTGAAAAGCGCGCTTTTTCAGCATGGGAAAAAGATATGACTTTGGCAGAAGCGATGCAGGCTTCAGCTGTTCCCGTATATCAGGAGCTTGCTCGACGTATTGGCTTGGAATTGATGCGTGAAGAAGTGAAGCGTGTAGGTTTTGGTAATGCAGAGATTGGTCAGCAAGTCGATAATTTTTGGTTGGTGGGTCCTTTAAAAATCTCCCCTGAACAAGAAGTTCAATTTGCCTATCAACTGGCGATGAAGCAATTACCTTTTGATCGAAATGTACAGCAACAAGTCAAAGATATGCTTTATATCGAGAGACGTGGTGACAGTAAACTGTATGCTAAAAGTGGTTGGGGAATGGATGTTGAACCTCAAGTGGGTTGGTATACGGGATGGGTTGAACAACCCAATGGCAAGGTGACTGCATTTGCGTTAAATATGAACATGCAAGCAGGTGATGATCCAGCTGAACGTAAACAATTAACCTTAAGTATTTTGGACAAATTGGGTCTATTTTTTTATTTAAGATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39090","NCBI_taxonomy_name":"Acinetobacter bereziniae","NCBI_taxonomy_id":"106648"}}}},"ARO_accession":"3001542","ARO_id":"37942","ARO_name":"OXA-355","CARD_short_name":"OXA-355","ARO_description":"OXA-355 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46498":{"category_aro_accession":"3007709","category_aro_cvterm_id":"46498","category_aro_name":"OXA-229-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-229.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"634":{"model_id":"634","model_name":"smeF","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"890"}},"model_sequences":{"sequence":{"509":{"protein_sequence":{"accession":"CAC14596.1","sequence":"MEVIPMKSASLFLSIAATLALAGCSTLAPKNTAVAPAIPAQWPAEAAQGEVADVAAVGWRDFFTDARLQQVIEQSLQNNRDLRVAVLNVERARGQYRVQRADRVPGVAVTGQMDRRGTDAGVTEQFSAGVGVAEFELDLFGRVRNLSEAALQQYFAVAANRRNAQLSLVAETATAWLTYGADAQRLKIADATLKTYEDSLRLAEARHERGGSSALELTQTRTLVETARTDAARLRGQLAQDRNALALLAGGQLDPALLPDSIEPQLLALAPPPAGLPSDVLLQRPDIMAAEHQLLAANANIGAARAAFFPSISLTGSIGSGSSELSNLFDSGTRVWSFLPKITLPIFQGGKLRANLAIANADRDIALAQYEKSIQVGFRETADALALNVSLDEQVSSQQRLVEAAEQANRLSQARYDAGLDSFVTLLDARRTAYNAQQTQLQAQLAQQANRITLYKVLGGGWHERG"},"dna_sequence":{"accession":"AJ252200.1","fmin":"4493","fmax":"5894","strand":"+","sequence":"ATGGAAGTGATCCCCATGAAAAGTGCATCCCTGTTCCTCTCCATTGCCGCCACGCTCGCGCTGGCCGGCTGCTCCACCCTGGCGCCGAAGAACACCGCCGTCGCTCCGGCGATTCCTGCGCAGTGGCCGGCCGAGGCCGCGCAGGGCGAGGTGGCCGATGTCGCCGCCGTCGGCTGGCGCGATTTCTTCACCGATGCGCGCCTGCAGCAGGTGATCGAGCAGTCGCTGCAGAACAACCGCGACCTGCGCGTGGCCGTGCTCAATGTCGAGCGCGCGCGTGGCCAGTACCGCGTGCAGCGCGCCGATCGCGTGCCCGGCGTGGCCGTGACCGGCCAGATGGACCGCCGTGGTACCGATGCCGGTGTCACCGAGCAGTTCAGCGCGGGCGTGGGTGTGGCCGAGTTCGAGCTGGACCTGTTCGGTCGCGTGCGCAACCTCAGCGAGGCGGCGCTGCAGCAGTACTTCGCCGTGGCTGCCAACCGCCGCAACGCGCAGCTGAGCCTGGTGGCCGAGACCGCCACCGCGTGGCTGACCTATGGGGCTGATGCGCAGCGGCTGAAGATCGCCGATGCCACGCTGAAGACCTACGAGGATTCGCTGCGCTTGGCCGAGGCCCGCCACGAACGCGGCGGCAGTTCGGCGCTGGAGCTGACCCAGACCCGTACCTTGGTCGAGACCGCACGCACCGATGCCGCGCGCCTGCGCGGCCAGCTGGCCCAGGACCGCAACGCACTGGCGCTGCTGGCCGGTGGCCAGCTCGATCCGGCACTGCTGCCGGACAGCATCGAACCGCAGCTGCTGGCGCTGGCCCCGCCGCCGGCCGGCCTGCCCAGCGACGTGCTGCTGCAGCGCCCGGACATCATGGCCGCCGAACACCAGCTGCTGGCCGCCAATGCCAACATCGGTGCGGCACGCGCAGCGTTCTTCCCGAGCATCTCGCTGACCGGCAGCATCGGCAGCGGCTCCAGCGAACTGTCCAACCTGTTCGACAGCGGCACCCGTGTGTGGAGCTTCCTGCCGAAGATCACCCTGCCGATCTTCCAGGGCGGCAAGCTGCGCGCCAACCTGGCCATCGCCAACGCGGATCGTGATATCGCACTGGCGCAGTACGAGAAGTCGATCCAGGTGGGATTCCGCGAAACGGCCGATGCGCTGGCGTTGAATGTCAGCCTGGATGAGCAGGTGAGTTCACAGCAGCGCCTGGTGGAAGCGGCCGAACAGGCCAATCGCCTGTCGCAGGCACGCTACGACGCGGGGCTGGACAGCTTTGTCACCCTGCTTGACGCGCGGCGTACCGCCTACAACGCGCAGCAGACCCAGCTGCAGGCGCAGTTGGCGCAGCAGGCCAACCGCATCACCCTGTACAAGGTGCTGGGCGGCGGCTGGCACGAGCGCGGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37076","NCBI_taxonomy_name":"Stenotrophomonas maltophilia","NCBI_taxonomy_id":"40324"}}}},"ARO_accession":"3003057","ARO_id":"39491","ARO_name":"smeF","CARD_short_name":"smeF","ARO_description":"smeF is an outer membrane multidrug efflux protein of the smeDEF complex in Stenotrophomonas maltophilia.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"635":{"model_id":"635","model_name":"OXA-332","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1532":{"protein_sequence":{"accession":"AGW16414.1","sequence":"MYKKALIVATSILFLSACSSNTVKQHQIHSISANKNSEEIKSLFDQAQTTGVLVIKRGQTEEIYGNDLKRASTAYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMSKEVKRIGFGNANIGSKVDNFWLVGPLKITPQQETQFAYQLAHKTLPFSKDVQEQVQSMVFIEEKNGSKIYAKSGWGWDVEPQVGWLTGWVVQPQGEIVAFSLNLEMKKGTPSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"KF203106.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGTATAAAAAAGCCCTTATCGTTGCAACAAGTATTCTATTTTTATCCGCCTGTTCTTCCAATACGGTAAAACAACATCAAATACACTCTATTTCTGCCAATAAAAATTCAGAAGAAATTAAATCACTATTTGATCAGGCACAAACCACGGGTGTTTTGGTGATTAAGCGAGGACAAACAGAAGAAATTTATGGCAATGATCTTAAAAGAGCATCAACCGCCTATGTTCCCGCCTCTACCTTTAAAATGTTAAATGCTTTAATTGGACTTGAACATCATAAGGCAACTACAACTGAAGTATTTAAATGGGATGGGCAAAAACGTTTATTTCCTGATTGGGAAAAGGACATGACACTGGGTGATGCCATGAAAGCTTCTGCGATTCCAGTTTACCAAGAATTAGCCCGACGAATTGGCCTTGACCTTATGTCCAAAGAGGTGAAAAGAATTGGTTTCGGTAATGCTAACATTGGTTCAAAAGTAGATAATTTTTGGCTCGTTGGCCCTCTAAAAATTACACCTCAACAAGAAACCCAATTTGCTTATCAATTAGCCCATAAAACGCTTCCATTTAGCAAAGATGTACAAGAACAAGTTCAATCAATGGTGTTCATAGAGGAAAAAAATGGAAGTAAAATTTATGCCAAAAGTGGTTGGGGATGGGATGTTGAACCACAAGTTGGTTGGCTAACAGGCTGGGTCGTTCAACCACAAGGAGAAATTGTGGCATTCTCACTTAATTTAGAAATGAAAAAAGGAACTCCTAGCTCTATTCGCAAAGAAATTGCTTATAAAGGCTTAGAACAACTGGGTATCTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39094","NCBI_taxonomy_name":"Acinetobacter calcoaceticus","NCBI_taxonomy_id":"471"}}}},"ARO_accession":"3001520","ARO_id":"37920","ARO_name":"OXA-332","CARD_short_name":"OXA-332","ARO_description":"OXA-332 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46495":{"category_aro_accession":"3007706","category_aro_cvterm_id":"46495","category_aro_name":"OXA-213-like beta-lactamase","category_aro_description":"OXA-213-like enzymes have been identified to be intrinsic to A. calcoaceticus and have been subsequently detected in A. pittii. Phylogenetic analysis of OXA-213-like proteins identified two distinct subgroups within the OXA family. The first group was linked to A. pittii and the second group to A. calcoaceticus. The carbapenemase activity of these OXAs may be related to the species-dependent effect.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"636":{"model_id":"636","model_name":"CFE-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"902":{"protein_sequence":{"accession":"BAC76072.1","sequence":"MMKKSICCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAIIYQGKPYYFTWGKADIANNRPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTQYWPELTGKQWQGISLLHLATYTAGGLPLQVPDDVTDKAALLRFYQNWQPQWAPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTTRVLQPLKLAHTWITVPQSEQKDYALGYREGKPVHVSPGQLDAEAYGVKSSVVDMTRWVQANMDASQVQEKTLQQGIKLAQSRYWRIGDMYQGLGWEMLNWPVKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPARVEAAWRILEKLQ"},"dna_sequence":{"accession":"AB107899.1","fmin":"1007","fmax":"2153","strand":"+","sequence":"ATGATGAAAAAATCGATATGCTGCGCGCTGCTGCTGACAGCCTCTTTTTCCACCTTTGCCGCCGCAAAAACAGAACAACAAATTGCCGATATCGTTAACCGCACCATCACACCGCTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCGATTATCTACCAGGGAAAACCTTATTACTTTACCTGGGGTAAAGCTGATATCGCCAATAACCGTCCAGTCACTCAGCAAACGCTGTTTGAACTCGGCTCGGTCAGTAAAACGTTCAACGGCGTGCTGGGCGGCGATGCTATCGCTCGCGGCGAAATCAAGCTCAGCGATCCGGTCACGCAATACTGGCCTGAGCTGACGGGTAAGCAGTGGCAGGGTATCAGCCTGCTGCACTTAGCGACCTACACGGCAGGCGGCCTGCCGCTTCAGGTTCCCGACGACGTCACGGATAAAGCCGCCTTACTGCGTTTTTATCAAAACTGGCAGCCACAATGGGCACCGGGCGCTAAACGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCACTGGCGGTGAAACCTTCAGGCATGAGCTACGAAGAGGCGATGACCACCCGCGTCCTGCAGCCCTTAAAACTGGCGCATACATGGATTACGGTTCCACAGAGCGAACAAAAAGATTATGCATTGGGCTATCGCGAAGGAAAGCCTGTGCATGTATCCCCTGGCCAACTTGATGCCGAAGCCTATGGGGTAAAATCAAGCGTTGTCGATATGACCCGCTGGGTCCAGGCCAACATGGATGCCAGCCAGGTTCAGGAGAAAACGCTCCAGCAGGGAATCAAGCTTGCGCAGTCACGTTACTGGCGTATTGGCGATATGTACCAGGGTCTGGGCTGGGAGATGCTGAACTGGCCGGTGAAAGCCGACTCAATAATTAACGGTAGCGACAGCAAAGTGGCGCTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCGCCTGCTGTGAAAGCATCATGGGTGCATAAAACGGGCTCCACTGGCGGATTCGGCAGCTACGTTGCTTTCGTTCCAGAAAAAAACCTTGGCATTGTGATGCTGGCAAACAAGAGCTATCCAAACCCTGCTCGCGTCGAGGCCGCCTGGCGCATTCTTGAAAAACTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001856","ARO_id":"38256","ARO_name":"CFE-1","CARD_short_name":"CFE-1","ARO_description":"CFE-1 is a beta-lactamase found in Escherichia coli.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"637":{"model_id":"637","model_name":"OXY-6-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"983":{"protein_sequence":{"accession":"CAI43423.1","sequence":"MLKSSWRKSALMAAAVPLLLASGSLWASADAIQQKLADLEKRSGGRLGVALINTADDSQTLYRGDERFAMCSTGKVMAAAAVLKQSESHPDVVNKRLEIKKSDLVVWSPITEKHLQSGMTLAELSAAALQYSDNTAMNKMISYLGGPEKVTAFAQSIGDVTFRLDRTEPALNSAIPGDKRDTTTPLAMAESLRKLTLGNALGEQQRAQLVTWLKGNTTGGQSIRAGLPASWAVGDKTGAGDYGTTNDIAVIWPENHAPLVLVTYFTQPQQDAKSRKEVLAAAAKIVTEGL"},"dna_sequence":{"accession":"AJ871875.1","fmin":"0","fmax":"873","strand":"+","sequence":"ATGTTGAAAAGTTCGTGGCGTAAAAGCGCCCTGATGGCCGCCGCCGTTCCGCTGCTGCTGGCGAGCGGTTCATTATGGGCCAGTGCCGATGCTATCCAGCAAAAGCTGGCTGATTTAGAAAAACGGTCCGGTGGCCGGCTGGGCGTGGCGCTGATTAACACGGCGGATGATTCGCAAACCCTTTATCGCGGCGACGAACGTTTTGCCATGTGCAGCACCGGTAAAGTGATGGCCGCCGCCGCGGTGTTAAAGCAGAGCGAAAGCCATCCCGATGTGGTGAATAAAAGGCTGGAGATTAAAAAATCGGATTTAGTGGTCTGGAGCCCGATTACCGAAAAACATCTGCAAAGCGGAATGACCCTGGCGGAACTCAGCGCGGCGGCGCTGCAGTACAGCGACAATACCGCGATGAATAAGATGATTAGCTACCTTGGCGGACCGGAAAAGGTGACCGCATTCGCCCAGAGCATCGGGGACGTTACTTTTCGTCTCGATCGTACGGAGCCGGCGCTGAACAGCGCGATACCCGGCGATAAGCGCGATACCACCACCCCGTTGGCGATGGCCGAAAGCCTGCGCAAGCTGACGCTGGGCAATGCGCTGGGCGAACAGCAGCGCGCCCAGTTAGTGACGTGGCTAAAAGGCAATACCACCGGCGGGCAAAGCATTCGCGCAGGCCTGCCCGCAAGCTGGGCGGTCGGGGATAAAACCGGCGCCGGAGATTACGGCACCACCAACGATATCGCGGTGATCTGGCCGGAAAATCATGCCCCGCTGGTGTTAGTGACCTATTTTACCCAGCCGCAGCAGGATGCGAAAAGCCGCAAAGAGGTGTTAGCCGCGGCGGCGAAAATCGTGACCGAAGGGCTGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3002414","ARO_id":"38814","ARO_name":"OXY-6-2","CARD_short_name":"OXY-6-2","ARO_description":"OXY-6-2 is a beta-lactamase found in Klebsiella oxytoca.","ARO_category":{"38788":{"category_aro_accession":"3002388","category_aro_cvterm_id":"38788","category_aro_name":"OXY beta-lactamase","category_aro_description":"OXY beta-lactamases are chromosomal class A beta-lactamases that are found in Klebsiella oxytoca. At constitutive low levels, OXY beta-lactamases confer resistance to aminopenicillins and carboxypenicillins. At high induced levels,  OXY beta-lactamases confer resistance to penicillins, cephalosporins and aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"638":{"model_id":"638","model_name":"ACT-16","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1341":{"protein_sequence":{"accession":"BAM34463.1","sequence":"MMKKSLCCALLLGLSCSALAAPVSEKQLAEVVANTVTPLMKAQSVPGMAVAVIYQGKSHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMPYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPEKVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVVEGSDSKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANKSYPNPARVEAAYHILEAL"},"dna_sequence":{"accession":"AB737978.1","fmin":"0","fmax":"1140","strand":"+","sequence":"ATGATGAAAAAATCCCTTTGCTGCGCCCTGCTGCTGGGCCTCTCTTGCTCTGCTCTCGCCGCGCCAGTATCAGAAAAACAGCTGGCGGAGGTGGTCGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCTGTTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGAAAATCGCACTATTACACGTTTGGCAAGGCCGATATCGCGGCGAATAAACCCGTTACGCCTCAGACCCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGCGTTTTAGGTGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTGACGGGCAAGCAGTGGCAGGGTATTCGTATGCTGGATCTCGCCACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTCAAACCTTCTGGCATGCCCTATGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTTCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGAATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCGGAGAAGGTTGCCGATGCCTCACTTAAGCAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGGTCGAAGGCAGCGACAGTAAGGTAGCGCTGGCGCCGTTACCCGTGGCAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGTTCTACCGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCGAGGCGCTA","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3001827","ARO_id":"38227","ARO_name":"ACT-16","CARD_short_name":"ACT-16","ARO_description":"ACT-16 is a beta-lactamase found in Enterobacteriaceae.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"641":{"model_id":"641","model_name":"CARB-6","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1736":{"protein_sequence":{"accession":"AAD19217.1","sequence":"MKFLLAFSLLIPSVVFASSSKFQQVEQDVKAIEVSLSARIGVSVLDTQNGEYWDYNGNQRFPLTSTFKTIACAKLLYDAEQGKVNPNSTVEIKKADLVTYSPVIEKQVGQAITLDDACFATMTTSDNTAANIILSAVGGPKGVTDFLRQIGDKETRLDRIEPDLNEGKLGDLRDTTTPKAIASTLNQLLFGSTLSEASQKKLESWMVNNQVTGNLLRSVLPVKWSIADRSGAGGFGARSITAIVWSEEKKTIIVSIYLAQTEASMAERNDAIVKIGRSIFEVYTSQSR"},"dna_sequence":{"accession":"AF030945.1","fmin":"95","fmax":"962","strand":"+","sequence":"ATGAAGTTTTTATTGGCATTTTCGCTTTTAATACCATCCGTGGTTTTTGCAAGTAGTTCAAAGTTTCAGCAAGTTGAACAAGACGTTAAGGCAATTGAAGTTTCTCTTTCTGCTCGTATAGGTGTTTCCGTTCTTGATACTCAAAATGGAGAATATTGGGATTACAATGGCAATCAGCGCTTCCCGTTAACAAGTACTTTTAAAACAATAGCTTGCGCTAAATTACTATATGATGCTGAGCAAGGAAAAGTTAATCCCAATAGTACAGTCGAGATTAAGAAAGCAGATCTTGTGACCTATTCCCCTGTAATAGAAAAGCAAGTAGGGCAGGCAATCACACTCGATGATGCGTGCTTCGCAACTATGACTACAAGTGATAATACTGCGGCAAATATCATCCTAAGTGCTGTAGGTGGCCCCAAAGGCGTTACTGATTTTTTAAGACAAATTGGGGACAAAGAGACTCGTCTAGACCGTATTGAGCCTGATTTAAATGAAGGTAAGCTCGGTGATTTGAGGGATACGACAACTCCTAAGGCAATAGCCAGCACGTTAAATCAATTATTATTTGGTTCCACATTATCTGAAGCTAGTCAGAAAAAATTAGAGTCTTGGATGGTGAACAATCAAGTTACGGGTAATTTATTGAGGTCAGTATTGCCAGTGAAGTGGAGTATTGCTGATCGCTCAGGAGCAGGTGGATTTGGTGCTAGGAGTATTACAGCGATTGTGTGGAGTGAAGAAAAAAAAACGATTATCGTAAGTATTTATCTAGCTCAAACCGAGGCTTCAATGGCAGAACGAAATGATGCGATAGTTAAAATTGGTCGTTCAATTTTTGAAGTTTATACATCACAGTCGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36789","NCBI_taxonomy_name":"Vibrio cholerae","NCBI_taxonomy_id":"666"}}}},"ARO_accession":"3002245","ARO_id":"38645","ARO_name":"CARB-6","CARD_short_name":"CARB-6","ARO_description":"CARB-6 is a beta-lactamase found in Vibrio cholerae.","ARO_category":{"36230":{"category_aro_accession":"3000091","category_aro_cvterm_id":"36230","category_aro_name":"CARB beta-lactamase","category_aro_description":"CARB beta-lactamases are class A lactamases that can hydrolyze carbenicillin. Many of the PSE beta-lactamases have been renamed as CARB-lactamases with the notable exception of PSE-2 which is now OXA-10.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"642":{"model_id":"642","model_name":"aadA25","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"3329":{"protein_sequence":{"accession":"AET15272.1","sequence":"MREAVTIEISNQLSEVLSVIERHLESTLLAVHLYGSAVDGGLKPYSDIDLLVTVAVKLDETTRRALLNDLMEASAFPGESETLRAIEVTLVVHDDIIPWRYPAKRELQFGEWQRNDILAGIFEPAMIDIDLAILLTKAREHSVALVGPAAEELFDPVPEQDLFEALNETLTLWNSPPDWAGDERNVVLTLSRIWYSAITGKIAPKDVAADWAIKRLPAQYQPVLLEARQAYLGQEEDRLASRADQLEEFVHYVKGEITKVVGK"},"dna_sequence":{"accession":"CP003022.1","fmin":"336788","fmax":"337580","strand":"+","sequence":"ATGAGGGAAGCGGTGACCATCGAAATTTCGAACCAACTATCAGAGGTGCTAAGCGTCATTGAGCGCCATCTGGAATCAACGTTGCTGGCCGTGCATTTGTACGGCTCCGCAGTGGATGGCGGCCTGAAGCCATACAGCGATATTGATTTGTTGGTTACTGTGGCCGTAAAGCTTGATGAAACGACGCGGCGAGCATTGCTCAATGATCTTATGGAGGCTTCGGCTTTCCCTGGCGAGAGCGAGACGCTCCGCGCTATAGAAGTCACCCTTGTCGTGCATGACGACATCATCCCGTGGCGTTATCCGGCTAAGCGCGAGCTGCAATTTGGAGAATGGCAGCGCAATGACATTCTTGCGGGTATCTTCGAGCCAGCCATGATCGACATTGATCTGGCTATCTTGCTGACAAAAGCAAGAGAACATAGCGTTGCCTTGGTAGGTCCAGCGGCGGAGGAACTCTTTGATCCGGTTCCTGAACAGGATCTATTTGAGGCGCTAAATGAAACCTTAACGCTATGGAACTCGCCGCCCGACTGGGCTGGCGATGAGCGAAATGTAGTGCTTACGTTGTCCCGCATTTGGTACAGCGCAATAACCGGCAAAATCGCGCCGAAGGATGTCGCTGCCGACTGGGCAATAAAACGCCTACCTGCCCAGTATCAGCCCGTCTTACTTGAAGCTAGACAGGCTTATCTTGGACAAGAAGAAGATCGCTTGGCCTCGCGCGCAGATCAGTTGGAAGAATTTGTTCACTACGTGAAAGGCGAGATCACCAAGGTAGTCGGCAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39783","NCBI_taxonomy_name":"Pasteurella multocida 36950","NCBI_taxonomy_id":"1075089"}}}},"ARO_accession":"3003197","ARO_id":"39780","ARO_name":"aadA25","CARD_short_name":"aadA25","ARO_description":"Streptomycin\/spectinomycin resistance gene found in Pasteurella multocida isolated from bovine respiratory tract.","ARO_category":{"41439":{"category_aro_accession":"3004275","category_aro_cvterm_id":"41439","category_aro_name":"ANT(3'')","category_aro_description":"A category of aminoglycoside O-nucleotidyltransferase enzymes with modification regiospecificity based at the 3''-hydroxyl group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics by transfer of an AMP group from an ATP substrate to the 3''-hydroxyl group of the compound.","category_aro_class_name":"AMR Gene Family"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"643":{"model_id":"643","model_name":"OXY-2-5","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1467":{"protein_sequence":{"accession":"CAG34107.1","sequence":"MIKSSWRKIAMLAAAVPLLLASGALWASTDAIHQKLTDLEKRSGGRLGVALINTADNSQILYRGDERFAMCSTSKVMAAAAVLKQSESNKEVVNKRLEINAADLVVWSPITEKHLQSGMTLAELSAATLQYSDNTAMNLIIGYLGGPEKVTAFARSIGDATFRLDRTESTLNTAIPGDERDTSTPLAMAESLRKLTLGDALGEQQRAQLVTWLKGNTTGGQSIRAGLPESWVVGDKTGSGDYGTTNDIAVIWPEDHAPLVLVTYFTQPQQDAKNRKEVLAAAAKIVTEGL"},"dna_sequence":{"accession":"AJ746227.1","fmin":"94","fmax":"967","strand":"+","sequence":"ATGATAAAAAGTTCGTGGCGTAAAATTGCAATGCTAGCCGCCGCCGTTCCGCTGCTGCTGGCGAGCGGCGCACTGTGGGCCAGTACCGATGCTATCCATCAGAAGCTGACAGATCTCGAGAAGCGTTCAGGCGGCAGGTTGGGCGTGGCGCTAATCAACACGGCAGATAATTCTCAAATCTTATATCGCGGCGACGAGCGTTTTGCCATGTGCAGCACCAGTAAAGTGATGGCCGCCGCCGCGGTATTAAAACAGAGCGAAAGCAATAAAGAGGTGGTAAATAAAAGGCTGGAGATTAACGCAGCCGATTTGGTGGTCTGGAGCCCGATTACCGAAAAACATCTCCAGAGCGGAATGACGCTGGCTGAGCTAAGCGCGGCGACGCTGCAATATAGCGACAATACGGCGATGAATCTGATCATCGGCTACCTTGGCGGGCCGGAAAAAGTCACCGCCTTCGCCCGCAGTATCGGCGATGCCACCTTTCGTCTCGATCGTACGGAGTCCACGCTGAATACCGCCATCCCGGGCGATGAGCGTGATACCAGCACGCCGCTGGCGATGGCTGAAAGCCTGCGCAAGCTGACGCTTGGCGATGCGCTGGGCGAACAGCAACGCGCCCAGTTAGTCACCTGGCTGAAAGGCAATACCACCGGCGGGCAAAGCATTCGCGCGGGCCTGCCTGAAAGCTGGGTGGTCGGCGATAAAACCGGCTCCGGAGATTACGGCACCACCAATGATATTGCGGTTATCTGGCCGGAAGATCACGCTCCGCTGGTATTAGTCACCTACTTTACCCAGCCGCAGCAGGATGCGAAAAACCGCAAAGAGGTGTTAGCCGCAGCGGCAAAAATCGTGACCGAAGGGCTTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3002400","ARO_id":"38800","ARO_name":"OXY-2-5","CARD_short_name":"OXY-2-5","ARO_description":"OXY-2-5 is a beta-lactamase found in Klebsiella oxytoca.","ARO_category":{"38788":{"category_aro_accession":"3002388","category_aro_cvterm_id":"38788","category_aro_name":"OXY beta-lactamase","category_aro_description":"OXY beta-lactamases are chromosomal class A beta-lactamases that are found in Klebsiella oxytoca. At constitutive low levels, OXY beta-lactamases confer resistance to aminopenicillins and carboxypenicillins. At high induced levels,  OXY beta-lactamases confer resistance to penicillins, cephalosporins and aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"644":{"model_id":"644","model_name":"OXY-2-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1059":{"protein_sequence":{"accession":"CAI43414.1","sequence":"MIKSSWRKIAMLAAAVPLLLASGALWASTDAIHQKLTDLEKRSGGRLGVALINTADNSQILYRGDERFAMCSTSKVMAAAAVLKQSESNKEVVNKRLEINAADLVVWSPITEKHLQSGMTLAELSAATLQYSDNTAMNLIIGYLGGPEKVTAFAHSIGDATFRLDRTEPTLNTAIPGDERDTSTPLAMAESLRKLTLGDALGEQQRAQLVTWLKGNTTGGQSIRAGLPESWVVGDKTGAGDYGTTNDIAVIWPEDHAPLVLVTYFTQPQQDAKNRKEVLAAAAKIVTEGL"},"dna_sequence":{"accession":"AJ871866.1","fmin":"0","fmax":"873","strand":"+","sequence":"ATGATAAAAAGTTCGTGGCGTAAAATTGCAATGCTAGCCGCCGCCGTTCCGCTGCTGCTGGCGAGCGGCGCACTGTGGGCCAGTACCGATGCTATCCATCAGAAGCTGACAGATCTCGAGAAGCGTTCAGGCGGCAGGTTGGGCGTGGCGCTAATCAACACGGCAGATAATTCTCAAATCTTATATCGCGGCGACGAGCGTTTTGCCATGTGCAGCACCAGTAAAGTGATGGCCGCCGCCGCGGTATTAAAACAGAGCGAAAGCAATAAAGAGGTGGTAAATAAAAGGCTGGAGATTAACGCAGCCGATTTGGTGGTCTGGAGTCCGATTACCGAAAAACATCTCCAGAGCGGAATGACGCTGGCTGAGCTAAGCGCGGCGACGCTGCAATATAGCGACAATACGGCGATGAATCTGATCATCGGCTACCTTGGCGGGCCGGAAAAAGTCACCGCCTTCGCCCACAGTATCGGCGATGCCACCTTTCGTCTCGATCGTACGGAGCCCACGCTGAATACCGCCATCCCGGGCGATGAGCGTGATACCAGCACGCCGCTGGCGATGGCTGAAAGCCTACGCAAGCTGACGCTTGGCGATGCGCTGGGCGAACAGCAACGCGCCCAGTTAGTCACCTGGCTGAAAGGCAATACCACCGGCGGGCAAAGCATTCGCGCGGGCCTGCCTGAAAGCTGGGTGGTCGGCGATAAAACCGGCGCCGGAGATTACGGCACCACCAATGATATTGCGGTTATCTGGCCGGAAGATCACGCTCCGCTGGTATTAGTCACCTACTTTACCCAGCCGCAGCAGGATGCGAAAAACCGCAAAGAGGTGTTAGCCGCAGCGGCAAAAATCGTGACCGAAGGGCTTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3002396","ARO_id":"38796","ARO_name":"OXY-2-1","CARD_short_name":"OXY-2-1","ARO_description":"OXY-2-1 is a beta-lactamase found in Klebsiella oxytoca.","ARO_category":{"38788":{"category_aro_accession":"3002388","category_aro_cvterm_id":"38788","category_aro_name":"OXY beta-lactamase","category_aro_description":"OXY beta-lactamases are chromosomal class A beta-lactamases that are found in Klebsiella oxytoca. At constitutive low levels, OXY beta-lactamases confer resistance to aminopenicillins and carboxypenicillins. At high induced levels,  OXY beta-lactamases confer resistance to penicillins, cephalosporins and aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"645":{"model_id":"645","model_name":"mecR1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1100"}},"model_sequences":{"sequence":{"5486":{"protein_sequence":{"accession":"ABQ47844.1","sequence":"MLSSFLMLSIISSLLTICVIFLVRMLYIKYTQNIMSHKIWLLVLVSTLIPLIPFYKISNFTFSKDMMNRNVSDTTSSVSHMLDGQQSSVTKDLAINVNQFETSNITYMILLIWVFGSLLCLFYMIKAFRQIDVIKSSSLESSYLNERLKVCQSKMQFYKKHITISYSSNIDNPMVFGLVKSQIVLPTVVVETMNDKEIEYIILHELSHVKSHDLIFNQLYVVFKMIFWFNPALYISKTMMDNDCEKVCDRNVLKILNRHEHIRYGESILKCSILKSQHINNVAAQYLLGFNSNIKERVKYIALYDSMPKPNRNKRIVAYIVCSISLLIQAPLLSAHVQQDKYETNVSYKKLNQLAPYFKGFDGSFVLYNEREQAYSIYNEPESKQRYSPNSTYKIYLALMAFDQNLLSLNHTEQQWDKHQYPFKEWNQDQNLNSSMKYSVNWYYENLNKHLRQDEVKSYLDLIEYGNEEISGNENYWNESSLKISAIEQVNLLKNMKQHNMHFDNKAIEKVENSMTLKQKDTYKYVGKTGTGIVNHKEANGWFVGYVETKDNTYYFATHLKGEDNANGEKAQQISERILKEMELI"},"dna_sequence":{"accession":"CP000703.1","fmin":"40848","fmax":"42606","strand":"+","sequence":"GTGTTATCATCTTTTTTAATGTTAAGTATAATCAGTTCATTGCTCACGATATGTGTAATTTTTTTAGTGAGAATGCTCTATATAAAATATACTCAAAATATTATGTCACATAAGATTTGGTTATTAGTGCTCGTCTCCACGTTAATTCCATTAATACCATTTTACAAAATATCGAATTTTACATTTTCAAAAGATATGATGAATCGAAATGTATCTGACACGACTTCTTCGGTTAGTCATATGTTAGATGGTCAACAATCATCTGTTACGAAAGACTTAGCAATTAATGTTAATCAGTTTGAGACCTCAAATATAACGTATATGATTCTTTTGATATGGGTATTTGGTAGTTTGTTGTGCTTATTTTATATGATTAAGGCATTCCGACAAATTGATGTTATTAAAAGTTCGTCATTGGAATCGTCATATCTTAATGAACGACTTAAAGTATGTCAAAGTAAGATGCAGTTCTACAAAAAGCATATAACAATTAGTTATAGTTCAAACATTGATAATCCGATGGTATTTGGTTTAGTGAAATCCCAAATTGTACTACCAACTGTCGTAGTCGAAACCATGAATGACAAAGAAATTGAATATATTATTCTACATGAACTATCACATGTGAAAAGTCATGACTTAATATTCAACCAGCTTTATGTTGTTTTTAAAATGATATTCTGGTTTAATCCTGCACTATATATAAGTAAAACAATGATGGACAATGACTGTGAAAAAGTATGTGATAGAAACGTTTTAAAAATTTTGAATCGCCATGAACATATACGTTATGGTGAATCGATATTAAAATGCTCTATTTTAAAATCTCAGCACATAAATAATGTGGCAGCACAATATTTACTAGGTTTTAATTCAAATATTAAAGAACGTGTTAAGTATATTGCACTTTATGATTCAATGCCTAAACCTAATCGAAACAAGCGTATTGTTGCGTATATTGTATGTAGTATATCGCTTTTAATACAAGCACCGTTACTATCTGCACATGTTCAACAAGACAAATATGAAACAAATGTATCATATAAAAAATTAAATCAACTAGCTCCGTATTTCAAAGGATTTGATGGAAGTTTTGTGCTTTATAATGAACGGGAGCAAGCTTATTCTATTTATAATGAACCAGAAAGTAAACAACGATATTCACCTAATTCTACTTACAAAATTTATTTAGCGTTAATGGCATTCGACCAAAATTTACTCTCATTAAATCATACTGAACAACAATGGGATAAACATCAATATCCATTTAAAGAATGGAACCAAGATCAAAATTTAAATTCTTCAATGAAATATTCAGTAAATTGGTATTACGAAAATTTAAACAAACATTTAAGACAAGATGAGGTTAAATCTTATTTAGATCTAATTGAATATGGTAATGAAGAAATATCAGGGAATGAAAATTATTGGAATGAATCTTCATTAAAAATTTCTGCAATAGAACAGGTTAATTTGTTGAAAAATATGAAACAACATAACATGCATTTTGATAATAAGGCTATTGAAAAAGTTGAAAATAGTATGACTTTGAAACAAAAAGATACTTATAAATATGTAGGTAAAACTGGAACAGGAATCGTGAATCACAAAGAAGCAAATGGATGGTTCGTAGGTTATGTTGAAACGAAAGATAATACGTATTATTTTGCTACACATTTAAAAGGCGAAGACAATGCGAATGGCGAAAAAGCACAACAAATTTCTGAGCGTATTTTAAAAGAAATGGAATTAATATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35519","NCBI_taxonomy_name":"Staphylococcus aureus subsp. aureus JH9","NCBI_taxonomy_id":"359786"}}}},"ARO_accession":"3000215","ARO_id":"36354","ARO_name":"mecR1","CARD_short_name":"mecR1","ARO_description":"mecR1 is a transmembrane spanning and signal transducing protein which in response to interaction with beta-lactam antibiotics results in upregulation of the mecA\/mecR1\/mecI operon.","ARO_category":{"37589":{"category_aro_accession":"3001208","category_aro_cvterm_id":"37589","category_aro_name":"methicillin resistant PBP2","category_aro_description":"In methicillin sensitive S. aureus (MSSA), beta-lactams bind to native penicillin-binding proteins (PBPs) and disrupt synthesis of the cell membrane's peptidoglycan layer. In methicillin resistant S. aureus (MRSA), foreign PBP2a acquired by lateral gene transfer is able to perform peptidoglycan synthesis in the presence of beta-lactams.","category_aro_class_name":"AMR Gene Family"},"35934":{"category_aro_accession":"0000015","category_aro_cvterm_id":"35934","category_aro_name":"methicillin","category_aro_description":"Derived from penicillin to combat penicillin-resistance, methicillin is insensitive to beta-lactamases (also known as penicillinases) secreted by many penicillin-resistant bacteria. Methicillin is bactericidal, and acts by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"646":{"model_id":"646","model_name":"OXA-349","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"889":{"protein_sequence":{"accession":"AGW83447.1","sequence":"MYKKALIAATSILFLSSCSSNTVKQHQIHSISANKNSEEIKSLFDQAQTTGVLVIKRGQTEEIYGNDLKRAPTAYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMSKEVKRVGFGNASIGSKVDNFWLVGPLKITPQQETQFAYQLALKTLPFSQDVQEQVQSMVFIEEKNGSKIYAKSGWGWDVEPQVGWLTGWIVQPQGEIVAFSLNLEMKKGTPSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"KF297578.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGTATAAAAAAGCCCTTATCGCTGCAACAAGTATCCTATTTTTATCCTCCTGTTCTTCCAATACGGTAAAACAACATCAAATACACTCTATTTCTGCCAATAAAAATTCAGAAGAAATTAAATCACTGTTTGATCAGGCACAGACCACGGGTGTTTTGGTGATTAAGCGAGGGCAAACAGAAGAAATTTATGGCAATGATCTTAAAAGAGCACCAACCGCCTATGTTCCCGCCTCAACCTTTAAAATGTTAAATGCTTTAATTGGACTTGAACATCATAAGGCAACTACAACTGAAGTATTTAAATGGGATGGGCAAAAACGTTTATTTCCTGATTGGGAAAAGGACATGACACTGGGTGATGCCATGAAAGCTTCTGCGATTCCAGTTTACCAAGAATTAGCCCGACGAATTGGTCTAGATCTTATGTCTAAAGAGGTGAAACGAGTTGGTTTTGGTAATGCTAGCATTGGTTCAAAAGTAGATAATTTTTGGCTTGTTGGCCCTCTAAAAATTACACCTCAACAAGAAACCCAATTTGCTTATCAATTAGCCCTTAAAACGCTTCCATTTAGCCAAGATGTACAAGAACAAGTTCAATCAATGGTGTTCATAGAGGAAAAAAATGGAAGTAAAATTTATGCCAAAAGTGGTTGGGGATGGGATGTTGAACCACAAGTTGGTTGGTTAACAGGCTGGATCGTTCAACCACAAGGAGAAATTGTCGCATTCTCACTTAATTTAGAAATGAAAAAAGGAACTCCTAGCTCTATTCGCAAAGAAATTGCTTATAAAGGCTTAGAACAACTGGGTATTTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39094","NCBI_taxonomy_name":"Acinetobacter calcoaceticus","NCBI_taxonomy_id":"471"}}}},"ARO_accession":"3001536","ARO_id":"37936","ARO_name":"OXA-349","CARD_short_name":"OXA-349","ARO_description":"OXA-349 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46495":{"category_aro_accession":"3007706","category_aro_cvterm_id":"46495","category_aro_name":"OXA-213-like beta-lactamase","category_aro_description":"OXA-213-like enzymes have been identified to be intrinsic to A. calcoaceticus and have been subsequently detected in A. pittii. Phylogenetic analysis of OXA-213-like proteins identified two distinct subgroups within the OXA family. The first group was linked to A. pittii and the second group to A. calcoaceticus. The carbapenemase activity of these OXAs may be related to the species-dependent effect.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"647":{"model_id":"647","model_name":"TEM-89","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1727":{"protein_sequence":{"accession":"AAK71474.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDKLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVKYSPVTEKHLTDGMTVRELCSAAITMGDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGASERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEI"},"dna_sequence":{"accession":"AY039040.1","fmin":"188","fmax":"1022","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATAAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTAAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGGGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCAGTGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATA","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3000956","ARO_id":"37336","ARO_name":"TEM-89","CARD_short_name":"TEM-89","ARO_description":"TEM-89 is an inhibitor-resistant, extended-spectrum beta-lactamase that has been found in clinical isolates.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"648":{"model_id":"648","model_name":"GES-4","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1784":{"protein_sequence":{"accession":"BAD08689.1","sequence":"MRFIHALLLAGIAHSAYASEKLTFKTDLEKLEREKAAQIGVAIVDPQGEIVAGHRTAQRFAMCSTFKFPLAALVFERIDSGTERGDRKLSYGPDMIVKWSPATERFLASGHMTVLEAAQAAVQLSDNGATNLLLREIGGPAAMTQYFRKIGDSVSRLDRKEPEMSDNTPGDLRDTTTPIAMARTVAKVLYGGALTSTSTHTIERWLIGNQTGDATLRAGFPKDWVVGEKTGTCANGGRNDIGFFKAQERDYAVAVYTTAPKLSAVERDELVASVGQVITQLILSTDK"},"dna_sequence":{"accession":"AB116260.1","fmin":"1329","fmax":"2193","strand":"+","sequence":"ATGCGCTTCATTCACGCACTATTACTGGCAGGGATCGCTCACTCTGCATATGCGTCGGAAAAATTAACCTTCAAGACCGATCTTGAGAAGCTAGAGCGCGAAAAAGCAGCTCAGATCGGTGTTGCGATCGTCGATCCCCAAGGAGAGATCGTCGCGGGCCACCGAACGGCGCAGCGCTTTGCAATGTGCTCAACGTTCAAGTTTCCGCTAGCCGCGCTGGTCTTTGAAAGAATTGACTCAGGCACCGAGCGGGGGGATCGAAAACTTTCATATGGGCCGGACATGATCGTCAAATGGTCTCCTGCCACGGAGCGGTTTCTAGCATCGGGACACATGACGGTTCTCGAGGCAGCGCAAGCTGCGGTGCAGCTTAGCGACAATGGGGCTACTAACCTCTTACTGAGAGAAATTGGCGGACCTGCTGCAATGACGCAGTATTTTCGTAAAATTGGCGACTCTGTGAGTCGGCTAGACCGGAAAGAGCCGGAGATGAGCGACAACACACCTGGCGACCTCAGAGATACAACTACGCCTATTGCTATGGCACGTACTGTGGCTAAAGTCCTCTATGGCGGCGCACTGACGTCCACCTCGACCCACACCATTGAGAGGTGGCTGATCGGAAACCAAACGGGAGACGCGACACTACGAGCGGGTTTTCCTAAAGATTGGGTTGTTGGAGAGAAAACTGGTACCTGCGCCAACGGGGGCCGGAACGACATTGGTTTTTTTAAAGCCCAGGAGAGAGATTACGCTGTAGCGGTGTATACAACGGCCCCGAAACTATCGGCCGTAGAACGTGACGAATTAGTTGCCTCTGTCGGTCAAGTTATTACACAACTCATCCTGAGCACGGACAAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002333","ARO_id":"38733","ARO_name":"GES-4","CARD_short_name":"GES-4","ARO_description":"GES-4 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36205":{"category_aro_accession":"3000066","category_aro_cvterm_id":"36205","category_aro_name":"GES beta-lactamase","category_aro_description":"GES beta-lactamases or Guiana extended-spectrum beta-lactamases are related to the other plasmid-located class A beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"649":{"model_id":"649","model_name":"OXA-115","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1999":{"protein_sequence":{"accession":"ABS71123.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDVKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAILVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWVVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"EU029998.1","fmin":"575","fmax":"1400","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGTAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCTAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGGTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAACAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001440","ARO_id":"37840","ARO_name":"OXA-115","CARD_short_name":"OXA-115","ARO_description":"OXA-115 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"650":{"model_id":"650","model_name":"aadA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"5220":{"protein_sequence":{"accession":"AAO49597.1","sequence":"MREAVIAEVSTQLSEVVGVIERHLEPTLLAVHLYGSAVDGGLKPHSDIDLLVTVTVRLDETTRRALINDLLETSASPGESEILRAVEVTIVVHDDIIPWRYPAKRELQFGEWQRNDILAGIFEPATIDIDLAILLTKAREHSVALVGPAAEELFDPVPEQDLFEALNETLTLWNSPPDWAGDERNVVLTLSRIWYSAVTGKIAPKDVAADWAMERLPAQYQPVILEARQAYLGQEEDRLASRADQLEEFVHYVKGEITKVVGK"},"dna_sequence":{"accession":"AF550679.1","fmin":"80976","fmax":"81768","strand":"-","sequence":"ATGAGGGAAGCGGTGATCGCCGAAGTATCGACTCAACTATCAGAGGTAGTTGGCGTCATCGAGCGCCATCTCGAACCGACGTTGCTGGCCGTACATTTGTACGGCTCCGCAGTGGATGGCGGCCTGAAGCCACACAGTGATATTGATTTGCTGGTTACGGTGACCGTAAGGCTTGATGAAACAACGCGGCGAGCTTTGATCAACGACCTTTTGGAAACTTCGGCTTCCCCTGGAGAGAGCGAGATTCTCCGCGCTGTAGAAGTCACCATTGTTGTGCACGACGACATCATTCCGTGGCGTTATCCAGCTAAGCGCGAACTGCAATTTGGAGAATGGCAGCGCAATGACATTCTTGCAGGTATCTTCGAGCCAGCCACGATCGACATTGATCTGGCTATCTTGCTGACAAAAGCAAGAGAACATAGCGTTGCCTTGGTAGGTCCAGCGGCGGAGGAACTCTTTGATCCGGTTCCTGAACAGGATCTATTTGAGGCGCTAAATGAAACCTTAACGCTATGGAACTCGCCGCCCGACTGGGCTGGCGATGAGCGAAATGTAGTGCTTACGTTGTCCCGCATTTGGTACAGCGCAGTAACCGGCAAAATCGCGCCGAAGGATGTCGCTGCCGACTGGGCAATGGAGCGCCTGCCGGCCCAGTATCAGCCCGTCATACTTGAAGCTAGACAGGCTTATCTTGGACAAGAAGAAGATCGCTTGGCCTCGCGCGCAGATCAGTTGGAAGAATTTGTCCACTACGTGAAAGGCGAGATCACCAAGGTAGTCGGCAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002601","ARO_id":"39001","ARO_name":"aadA","CARD_short_name":"aadA","ARO_description":"ANT(3'')-Ia is an aminoglycoside nucleotidyltransferase gene encoded by plasmids, transposons, integrons in Enterobacteriaceae, A. baumannii, P. aeruginosa and Vibrio cholerae.","ARO_category":{"41439":{"category_aro_accession":"3004275","category_aro_cvterm_id":"41439","category_aro_name":"ANT(3'')","category_aro_description":"A category of aminoglycoside O-nucleotidyltransferase enzymes with modification regiospecificity based at the 3''-hydroxyl group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics by transfer of an AMP group from an ATP substrate to the 3''-hydroxyl group of the compound.","category_aro_class_name":"AMR Gene Family"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"652":{"model_id":"652","model_name":"tcr3","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"950"}},"model_sequences":{"sequence":{"332":{"protein_sequence":{"accession":"BAA07390.1","sequence":"MGMANATSQTGEAVADEAGGPAGFTHRQIITALSGLLLAVLLAALDQTIVSTALRTIGDQLHGQTVQAWVITGYLVSSTIAMPFYGKLSDIYGRKPLYLAAIAVFIVGSAACAMANSMETLAIARVLQGFGGAGLMSLPTAVIADLAPVRERGRYFSYLMMAWVAASVLGPLVGGLFAGAGEILGVTGWRWAFLINVPLGLVALLSVRKALNLPHRRVDHPIDFRGALTLALCLVPLLIVAEEGLDWGWGSARSLTLFAVSLIGLVLFVLAERARGLEAMVPLRLFRRGGITMATAVNFTIGVGIFGTVSTLPLFLQLVQGRSATVAGLVIIPVMTGAIVSQTICAKIIKKWNRYKKPAIVGLGSMAGALLSLSAAGADTPLAVIVVIAAWLGFGIGLSQTVITLAIQSSAPKSELGVANAASGLFRQLGGTSGAAVFMSVLFGVAAGRLDGADPDEAVRRALSDPGSTGGLSASAVDAFTSGFDTMFLVGGLILAVGFLLTFPLRELRDEE"},"dna_sequence":{"accession":"D38215.1","fmin":"0","fmax":"1539","strand":"+","sequence":"ATGGGAATGGCGAACGCCACCTCGCAGACCGGCGAGGCCGTCGCGGACGAGGCCGGCGGCCCCGCCGGCTTCACTCACCGCCAGATCATCACCGCGCTGTCCGGGCTCCTGTTGGCCGTGCTGCTCGCCGCACTCGACCAGACGATCGTCTCCACCGCGCTGCGTACGATCGGCGACCAACTGCACGGCCAGACCGTCCAGGCCTGGGTGATCACCGGCTACCTGGTCAGCTCCACGATCGCGATGCCGTTCTACGGCAAGCTGTCCGACATCTACGGCCGCAAGCCGCTCTATCTGGCGGCGATCGCGGTCTTCATCGTCGGCTCGGCGGCCTGCGCGATGGCGAACTCGATGGAGACGCTGGCGATCGCCCGCGTCCTCCAGGGCTTCGGCGGCGCCGGGCTGATGTCGCTGCCGACGGCCGTCATCGCCGACCTCGCCCCGGTGCGCGAGCGCGGGCGCTACTTCTCGTACCTGATGATGGCCTGGGTGGCGGCCAGTGTGCTCGGCCCGCTCGTCGGGGGCCTGTTCGCGGGCGCCGGCGAGATCCTCGGGGTGACCGGCTGGCGCTGGGCCTTCCTGATCAACGTGCCGCTCGGTCTCGTGGCGCTGCTCAGCGTGCGCAAGGCGCTCAACCTGCCGCACCGCAGGGTGGACCACCCGATCGACTTCCGGGGGGCGCTCACCCTGGCGCTCTGCCTGGTGCCGCTGCTGATCGTGGCGGAGGAGGGCCTCGACTGGGGCTGGGGATCGGCGCGTTCGCTGACGCTGTTCGCCGTCTCGCTGATCGGCCTGGTGCTGTTCGTGCTCGCCGAGCGGGCCCGCGGGCTGGAGGCGATGGTCCCGCTGCGGCTGTTCCGGCGCGGTGGCATCACGATGGCCACGGCCGTCAACTTCACCATCGGCGTCGGCATCTTCGGTACGGTCTCCACCCTGCCGCTGTTCCTGCAGCTGGTGCAGGGGCGCAGTGCCACCGTCGCCGGACTGGTGATCATCCCGGTGATGACCGGGGCGATCGTCTCCCAGACGATCTGCGCCAAGATCATCAAGAAGTGGAACCGCTACAAGAAGCCCGCGATCGTGGGCCTCGGCTCGATGGCCGGAGCACTGCTGTCGCTCTCCGCCGCGGGCGCGGACACCCCGCTCGCGGTGATCGTGGTGATCGCGGCCTGGCTGGGCTTCGGCATCGGGCTCTCCCAGACCGTCATCACCCTGGCGATCCAGAGCTCGGCGCCCAAGTCCGAGCTGGGCGTGGCCAACGCCGCCTCCGGGCTGTTCCGCCAGCTCGGCGGCACGAGCGGCGCCGCCGTCTTCATGTCGGTGCTGTTCGGCGTCGCCGCCGGCAGGCTCGACGGGGCCGACCCGGACGAGGCCGTGCGCCGTGCGCTCTCCGACCCGGGCTCCACCGGCGGCCTGAGCGCCTCGGCGGTCGACGCCTTCACCTCGGGCTTCGACACGATGTTCCTGGTCGGCGGCCTGATCCTTGCGGTGGGCTTCCTGCTCACCTTCCCGCTGCGGGAACTGCGCGACGAGGAGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36813","NCBI_taxonomy_name":"Kitasatospora aureofaciens","NCBI_taxonomy_id":"1894"}}}},"ARO_accession":"3002893","ARO_id":"39327","ARO_name":"tcr3","CARD_short_name":"tcr3","ARO_description":"tcr3 is a tetracycline efflux pump that confers self-resistance to Kitasatospora aureofaciens.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"531":{"model_id":"531","model_name":"SAT-3","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"673":{"protein_sequence":{"accession":"CAA88265.1","sequence":"MTPQSMRELVICRASDADVLQLARCDFSFEVTAELEEPFDDMRSVPVKPPYLKNYGFDADELVEHMNNSAGALFVARADNCLVGYLAVSQSWNEYAVIDDIAVDVPYRGSGVSRLLMDAAVDWARNVPSAGVRLETQSVNLAACRFYRRYGFRLGGYDRYLYRGLHPGSREVALFWYLSF"},"dna_sequence":{"accession":"Z48231.1","fmin":"220","fmax":"763","strand":"+","sequence":"ATGACGCCACAGTCAATGCGTGAATTGGTCATCTGTCGTGCAAGCGATGCCGACGTTCTTCAGCTTGCGCGGTGCGATTTCTCTTTCGAGGTCACAGCTGAGCTCGAAGAGCCGTTCGATGACATGCGGTCCGTTCCAGTCAAGCCGCCCTACCTCAAGAACTATGGCTTTGATGCCGATGAGTTGGTCGAGCATATGAACAACTCTGCTGGGGCGTTGTTTGTGGCTCGGGCGGACAATTGCCTTGTTGGCTACTTGGCCGTGTCTCAAAGCTGGAACGAATATGCCGTCATCGATGATATCGCGGTCGATGTGCCCTATCGGGGGAGTGGCGTTTCGCGCTTGCTGATGGATGCAGCTGTGGACTGGGCACGAAATGTGCCGTCGGCAGGCGTACGTCTGGAGACGCAGTCCGTTAATCTCGCCGCATGTCGCTTTTACCGACGATACGGTTTCCGGTTAGGTGGTTATGATCGCTACCTGTATCGTGGCCTGCATCCGGGCAGCCGAGAGGTAGCTCTGTTCTGGTATTTGAGTTTTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002898","ARO_id":"39332","ARO_name":"SAT-3","CARD_short_name":"SAT-3","ARO_description":"SAT-3 is a plasmid-mediated streptothricin acetyltransferase and streptothricin resistance determinant. Originally described from an E. coli plasmid gene by Tietze and Brevet, 1995.","ARO_category":{"37249":{"category_aro_accession":"3000869","category_aro_cvterm_id":"37249","category_aro_name":"streptothricin acetyltransferase (SAT)","category_aro_description":"AcetylCoA dependent acetyltransferase that acetylate streptothricins such as nourseothricin at position 16 (beta position of beta-lysine).","category_aro_class_name":"AMR Gene Family"},"35931":{"category_aro_accession":"0000012","category_aro_cvterm_id":"35931","category_aro_name":"streptothricin","category_aro_description":"Streptothricins are a group of N-glycoside antibiotics that include a carbamoylated D-glucosamine to which are attached a series of L-beta-lysine residues at position 2 and a streptolidine at position 1.  Streptothricins vary by the number of beta-lysine residues (from 1 (nourseothricin) to 7) and target protein synthesis in bacteria and eukaryotes.","category_aro_class_name":"Antibiotic"},"36174":{"category_aro_accession":"3000034","category_aro_cvterm_id":"36174","category_aro_name":"nucleoside antibiotic","category_aro_description":"Nucleoside antibiotics are made of modified nucleosides and nucleotides with wide-ranging activities and means of antibacterial effects. This drug class includes aminonucleoside antibiotics, which contain an amino group.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"640":{"model_id":"640","model_name":"tet(31)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"3344":{"protein_sequence":{"accession":"CAC80727.1","sequence":"MIGKLIMMNRYITIALLITFLDATGMGLIMPVLPTLLEEFSVKESIATHYGFILAIYALMQVIFAPILGQLSDKFGRKPVLILSLIGAVCDYTLLSFSSALWMLYLGRMIAGISAATGAVAASMVADHTKKAERTKWFGKLGAAFGAGLIAGPAIGGFIGQYSAHFPFIIAAILNAIALIMVIILFPKEQSRPKEIEQDQSKIHEKTTINAPLIHILKPVLLLLMLFFTVQLIGQIPASTWVLFTEYRFEWNTFNIGLSLAGLGLMHIIFQAFVAGYIASRWKNETVFILGFILDASAFLLLAFISQVWLVIPTLILLAGGGIALPALQGLISIKTADEHQGKIQGIMVSLTNITGIIGPPIFAFSFAKTVTNWDGTLWLIGAVLYSILLGLYFLYQKIRAYKQLKSQTA"},"dna_sequence":{"accession":"AJ250203.1","fmin":"1650","fmax":"2883","strand":"+","sequence":"ATGATAGGGAAGCTTATAATGATGAATCGCTATATCACAATCGCCCTCTTAATTACCTTCCTAGATGCAACAGGAATGGGCTTAATCATGCCTGTATTACCAACACTTTTAGAAGAGTTCTCTGTCAAAGAGTCTATCGCCACTCATTATGGTTTTATCCTCGCAATCTATGCGCTGATGCAAGTTATTTTTGCACCAATATTAGGACAACTCTCGGATAAATTTGGCAGAAAACCGGTCTTGATTCTCTCATTAATAGGCGCTGTTTGTGATTACACCCTACTCTCATTTTCTAGCGCCTTATGGATGCTCTATCTAGGGAGAATGATTGCCGGCATTTCTGCTGCAACAGGAGCCGTAGCAGCATCAATGGTCGCAGATCACACAAAAAAAGCAGAGAGAACTAAATGGTTTGGAAAGTTAGGCGCAGCTTTTGGGGCGGGACTCATTGCCGGACCCGCTATTGGTGGATTTATCGGACAATATTCTGCACATTTCCCCTTTATCATTGCCGCAATTTTAAATGCCATTGCTCTTATCATGGTCATTATCCTCTTCCCTAAAGAGCAATCACGCCCAAAAGAAATCGAGCAAGATCAATCTAAAATTCATGAAAAAACCACCATCAATGCCCCGCTAATTCATATTCTCAAACCCGTTTTGCTACTTCTCATGCTGTTTTTTACAGTACAACTCATCGGACAAATCCCTGCATCAACTTGGGTTCTATTTACTGAGTACCGTTTTGAGTGGAATACCTTTAACATTGGTTTATCCCTTGCAGGGCTAGGGTTAATGCATATTATCTTTCAGGCTTTTGTCGCAGGATATATCGCATCTCGCTGGAAAAATGAAACCGTATTTATTCTCGGATTTATACTAGATGCGAGCGCATTCTTATTACTGGCCTTTATCTCTCAAGTTTGGCTGGTAATTCCTACATTGATCTTATTAGCAGGAGGAGGCATCGCCTTACCGGCATTACAAGGATTAATCTCTATAAAGACAGCAGATGAACATCAAGGAAAGATACAAGGTATCATGGTTAGCCTCACTAATATTACCGGAATAATTGGACCGCCCATTTTTGCATTTTCCTTTGCAAAAACGGTTACAAACTGGGATGGCACACTTTGGCTAATCGGTGCTGTACTCTATAGCATTTTATTAGGTCTCTATTTTCTCTATCAAAAGATACGCGCCTATAAACAACTTAAGTCTCAAACTGCTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40299","NCBI_taxonomy_name":"Aeromonas salmonicida subsp. salmonicida","NCBI_taxonomy_id":"29491"}}}},"ARO_accession":"3000476","ARO_id":"36615","ARO_name":"tet(31)","CARD_short_name":"tet(31)","ARO_description":"Tet31 is a tetracycline efflux pump found in Aeromonas salmonicida, a Gram-negative bacteria. It has also been shown to be expressed in Gallibacterium anatis.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"516":{"model_id":"516","model_name":"eptA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"4556":{"protein_sequence":{"accession":"BAE78116.1","sequence":"MLKRLLKRPSLNLLAWLLLAAFYISICLNIAFFKQVLQALPLDSLHNVLVFLSMPVVAFSVINIVLTLSSFLWLNRPLACLFILVGAAAQYFIMTYGIVIDRSMIANIIDTTPAESYALMTPQMLLTLGFSGVLAALIACWIKIKPATSRLRSVLFRGANILVSVLLILLVAALFYKDYASLFRNNKELVKSLSPSNSIVASWSWYSHQRLANLPLVRIGEDAHRNPLMQNEKRKNLTILIVGETSRAENFSLNGYPRETNPRLAKDNVVYFPNTASCGTATAVSVPCMFSDMPREHYKEELAQHQEGVLDIIQRAGINVLWNDNDGGCKGACDRVPHQNVTALNLPDQCINGECYDEVLFHGLEEYINNLQGDGVIVLHTIGSHGPTYYNRYPPQFRKFTPTCDTNEIQTCTKEQLVNTYDNTLVYVDYIVDKAINLLKEHQDKFTTSLVYLSDHGESLGENGIYLHGLPYAIAPDSQKQVPMLLWLSEDYQKRYQVDQNCLQKQAQTQHYSQDNLFSTLLGLTGVETKYYQAADDILQTCRRVSE"},"dna_sequence":{"accession":"AP009048.1","fmin":"4338624","fmax":"4340268","strand":"-","sequence":"ATGTTGAAGCGCCTACTAAAAAGACCCTCTTTGAATTTACTCGCCTGGCTATTGTTGGCCGCTTTTTATATCTCTATCTGCCTGAATATTGCCTTTTTTAAACAGGTGTTGCAGGCGCTGCCGCTGGATTCGCTGCATAACGTACTGGTTTTCTTGTCGATGCCGGTCGTCGCTTTCAGCGTGATTAATATTGTCCTGACACTAAGCTCTTTCTTATGGCTTAATCGACCACTGGCCTGCCTGTTTATTCTGGTTGGCGCGGCTGCACAATATTTCATAATGACTTACGGCATCGTCATCGACCGCTCGATGATTGCCAATATTATTGATACCACTCCGGCAGAAAGTTATGCGCTGATGACACCGCAAATGTTATTAACGCTGGGATTCAGCGGCGTGCTTGCTGCGCTGATTGCCTGCTGGATAAAAATCAAACCTGCCACCTCGCGTCTGCGCAGTGTTCTTTTCCGTGGAGCCAATATTCTGGTTTCTGTACTACTGATTTTGCTGGTCGCCGCACTGTTTTATAAAGACTACGCCTCGTTGTTCCGCAATAACAAAGAGCTGGTGAAATCCTTAAGCCCCTCTAACAGCATTGTTGCCAGCTGGTCATGGTACTCCCATCAGCGACTGGCAAATCTGCCGCTGGTGCGAATTGGTGAAGACGCGCACCGCAACCCGTTAATGCAGAACGAAAAACGTAAAAATTTGACCATCCTGATTGTCGGCGAAACCTCGCGGGCGGAGAACTTCTCCCTCAACGGCTACCCGCGTGAAACTAACCCGCGGCTGGCGAAAGATAACGTGGTCTATTTCCCTAATACCGCATCTTGCGGCACGGCAACGGCAGTTTCAGTACCGTGCATGTTCTCGGATATGCCGCGTGAGCACTACAAAGAAGAGCTGGCACAGCACCAGGAAGGCGTGCTGGATATCATTCAGCGAGCGGGCATCAACGTGCTGTGGAATGACAACGATGGCGGCTGTAAAGGTGCCTGCGACCGCGTGCCTCACCAGAACGTCACCGCGCTGAATCTACCTGATCAGTGCATCAACGGCGAATGCTATGACGAAGTGCTGTTCCACGGGCTTGAAGAGTACATCAATAACCTGCAAGGTGATGGCGTGATTGTCTTACACACCATCGGCAGCCACGGTCCGACCTATTACAACCGCTATCCGCCTCAGTTCAGGAAATTTACCCCAACCTGCGACACCAATGAGATCCAGACCTGTACCAAAGAGCAACTGGTGAACACTTACGACAACACGCTGGTTTACGTCGACTATATTGTTGATAAAGCGATTAATCTGCTGAAAGAACATCAGGATAAATTTACCACCAGCCTGGTTTATCTTTCTGACCACGGTGAATCGTTAGGTGAAAATGGCATCTATCTGCACGGTCTGCCTTATGCCATCGCCCCGGATAGCCAAAAACAGGTGCCGATGCTGCTGTGGCTGTCGGAGGATTATCAAAAACGGTATCAGGTTGACCAGAACTGCCTGCAAAAACAGGCGCAAACGCAACACTATTCACAAGACAATTTATTCTCCACGCTATTGGGATTAACTGGCGTTGAGACGAAGTATTACCAGGCTGCGGATGATATTCTGCAAACTTGCAGGAGAGTGAGTGAATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36839","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. W3110","NCBI_taxonomy_id":"316407"}}}},"ARO_accession":"3003576","ARO_id":"40186","ARO_name":"eptA","CARD_short_name":"eptA","ARO_description":"PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine, resulting in a less negative cell membrane and decreased binding of polymyxin B.","ARO_category":{"41433":{"category_aro_accession":"3004269","category_aro_cvterm_id":"41433","category_aro_name":"pmr phosphoethanolamine transferase","category_aro_description":"This family of phosphoethanolamine transferase catalyze the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine to lipid A, which impedes the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36593":{"category_aro_accession":"3000454","category_aro_cvterm_id":"36593","category_aro_name":"polymyxin B","category_aro_description":"Polymyxin B is mixture of mostly polymyxins B1 and B2, mainly used for resistant gram-negative infections. They are polypeptides with cationic detergent action on cell membranes.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"492":{"model_id":"492","model_name":"Clostridium butyricum catB","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"174":{"protein_sequence":{"accession":"AAA73865.1","sequence":"MNFNLIDINHWSRKPYFEHYLNNVKCTYSMTANIEITDLLYEIKLKNIKFYPTLIYMIATVVNNHKEFRICFDHKGSLGYWDSMNPSYTIFHKENETFSSIWTEYNKSFLRFYSDYLDDIKNYGNIMKFTPKSNEPDNTFSVSSIPWVSFTGFNLNVYNEGTYLIPIFTAGKYFKQENKIFIPISIQVHHAICDGYHASRFINEMQELAFSFQEWLENK"},"dna_sequence":{"accession":"M93113.1","fmin":"0","fmax":"660","strand":"+","sequence":"ATGAATTTTAATTTAATAGATATTAATCATTGGAGTAGAAAGCCATACTTTGAACATTATTTAAACAATGTGAAATGTACTTACAGTATGACTGCCAATATAGAAATAACTGATTTATTGTATGAAATTAAACTTAAAAATATTAAATTTTATCCTACACTTATTTATATGATTGCAACTGTGGTTAATAATCATAAAGAATTCCGTATTTGTTTTGATCATAAAGGTAGTTTAGGATATTGGGATAGCATGAATCCAAGCTATACTATTTTTCATAAAGAAAACGAAACATTTTCAAGTATTTGGACGGAATATAACAAAAGTTTTTTACGTTTTTATAGTGATTATCTTGACGATATAAAAAACTATGGAAATATCATGAAGTTTACTCCGAAATCAAATGAACCTGACAATACATTTTCTGTATCAAGTATTCCTTGGGTGAGTTTTACAGGATTTAACTTGAATGTTTATAATGAAGGAACATATTTAATTCCTATTTTTACTGCAGGAAAGTATTTCAAACAAGAAAATAAAATATTTATTCCTATATCAATACAAGTACATCATGCTATCTGTGACGGTTATCATGCTAGTAGATTTATTAATGAAATGCAAGAATTAGCATTTAGTTTTCAAGAATGGTTAGAAAATAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36845","NCBI_taxonomy_name":"Clostridium butyricum","NCBI_taxonomy_id":"1492"}}}},"ARO_accession":"3002674","ARO_id":"39108","ARO_name":"Clostridium butyricum catB","CARD_short_name":"Cbut_catB","ARO_description":"catB is a chromosome-encoded variant of the cat gene found in Clostridium butyricum.","ARO_category":{"36261":{"category_aro_accession":"3000122","category_aro_cvterm_id":"36261","category_aro_name":"chloramphenicol acetyltransferase (CAT)","category_aro_description":"Inactivates chloramphenicol by addition of an acyl group. CAT is used to describe many variants of the chloramphenicol acetyltransferase gene in a range of organisms including Acinetobacter calcoaceticus, Agrobacterium tumefaciens, Alkalihalobacillus clausii, Bacillus subtilis, Campylobacter coli, Enterococcus faecalis, Enterococcus faecium, Lactococcus lactis, Listeria monocytogenes, Listonella anguillarum, Morganella morganii, Photobacterium damselae subsp. piscicida, Proteus mirabilis, Salmonella typhi, Serratia marcescens, Shigella flexneri, Staphylococcus aureus, Staphylococcus haemolyticus, Staphylococcus intermedius, Streptococcus agalactiae, Streptococcus suis and Streptomyces acrimycini.","category_aro_class_name":"AMR Gene Family"},"36521":{"category_aro_accession":"3000382","category_aro_cvterm_id":"36521","category_aro_name":"azidamfenicol","category_aro_description":"Azidamfenicol is a water soluble derivative of chloramphenicol, sharing the same mode of action of inhibiting peptide synthesis by interacting with the 23S RNA of the 50S ribosomal subunit.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36595":{"category_aro_accession":"3000456","category_aro_cvterm_id":"36595","category_aro_name":"thiamphenicol","category_aro_description":"Derivative of Chloramphenicol. The nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3).","category_aro_class_name":"Antibiotic"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"653":{"model_id":"653","model_name":"AAC(3)-VIIa","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"694":{"protein_sequence":{"accession":"AAA88552.1","sequence":"MDELALLKRSDGPVTRTRLARDLTALGLGDGDTVMFHTRMSAVGYVAGGPETVIGALRDVVGERGTLMVTCGWNDAPPYDFTDWPQTWQDARRAEHPAYDPVLSEADHNNGRLPEALRRRPGAVRSRHPDASFAALGAAATALTADHPWDDPHGPDSPLARLVAMGGRVLLLGAPLEALTLLHHAEALADAPGKRFVDYEQPILVDGERVWRRFHDIDSEDGAFDYSALVPEGTEAFEIIGRDMRAAGIGRRGTVGAADSHLFEARDVVDFGVAWMEEKLGRERGPGG"},"dna_sequence":{"accession":"M22999.1","fmin":"492","fmax":"1359","strand":"+","sequence":"ATGGACGAACTCGCCTTGCTCAAGCGCTCCGACGGCCCGGTCACCCGGACCCGCCTCGCCCGGGACCTGACCGCGCTCGGCCTCGGCGACGGGGACACCGTGATGTTCCATACGCGGATGTCCGCCGTCGGCTACGTGGCAGGCGGCCCGGAGACGGTCATCGGAGCCCTCCGCGACGTCGTGGGAGAGCGGGGAACCCTGATGGTGACCTGCGGCTGGAACGACGCCCCGCCGTACGACTTCACCGACTGGCCGCAGACCTGGCAGGACGCCCGTCGGGCGGAGCACCCGGCGTACGACCCCGTGCTGAGCGAGGCTGACCACAACAACGGGCGCCTCCCGGAAGCGCTGCGCCGCCGGCCCGGAGCCGTCCGCAGCCGTCACCCCGACGCGAGCTTCGCGGCGCTCGGCGCGGCGGCCACCGCGTTGACGGCCGACCATCCGTGGGACGACCCGCACGGCCCTGACAGCCCGCTGGCGCGGCTGGTCGCGATGGGCGGCCGGGTGCTGCTGCTGGGCGCCCCGCTGGAGGCGCTCACGCTCCTGCACCACGCCGAGGCGCTGGCCGACGCGCCCGGTAAGCGGTTCGTGGACTACGAGCAGCCGATCCTCGTCGACGGGGAGCGGGTCTGGCGGCGGTTCCACGACATCGACTCGGAGGACGGGGCGTTCGACTACTCCGCCCTCGTGCCCGAGGGAACGGAAGCGTTCGAGATCATCGGACGGGACATGCGTGCCGCGGGCATCGGCCGCAGGGGAACGGTCGGGGCGGCCGACAGCCATCTCTTCGAAGCCCGTGACGTGGTCGACTTCGGTGTGGCCTGGATGGAGGAGAAGCTGGGCCGGGAAAGGGGGCCCGGCGGATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36773","NCBI_taxonomy_name":"Streptomyces rimosus","NCBI_taxonomy_id":"1927"}}}},"ARO_accession":"3002541","ARO_id":"38941","ARO_name":"AAC(3)-VIIa","CARD_short_name":"AAC(3)-VIIa","ARO_description":"AAC(3)-VIIa is a chromosomal-encoded aminoglycoside acetyltransferase in Streptomyces rimosus.","ARO_category":{"36461":{"category_aro_accession":"3000322","category_aro_cvterm_id":"36461","category_aro_name":"AAC(3)","category_aro_description":"A category of aminoglycoside N-acetyltransferase enzymes with modification regiospecificity based at the 3-amino group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics through acetylation of the 3-amino group of the compound.","category_aro_class_name":"AMR Gene Family"},"37001":{"category_aro_accession":"3000657","category_aro_cvterm_id":"37001","category_aro_name":"paromomycin","category_aro_description":"An aminoglycoside antibiotic used for the treatment of parasitic infections. It is similar to neomycin sharing a similar spectrum of activity, but its hydroxyl group at the 6'-position instead of an amino group makes it resistant to AAC(6') modifying enzymes.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"654":{"model_id":"654","model_name":"dfrA26","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"111":{"protein_sequence":{"accession":"CAL48457.1","sequence":"MADEEYDPLLDDDMEDAKVAVIAARAQNGCIGRHGKLPWKLPGDLKYFRERTWGKPIIMGRKTWESLNGALPGRTNIVVTRQQGYEAEGARVVDSIEEAISLAQSIALIEAVDEIMVLGGGEIYTQALPQADILYLTEVHASVDGDAFFPDVDLSQYQETQRQDFEPSGGNPYPFSFVVYQRT"},"dna_sequence":{"accession":"AM403715.1","fmin":"302","fmax":"854","strand":"+","sequence":"ATGGCTGATGAAGAATACGACCCGCTACTCGATGACGACATGGAAGATGCCAAAGTCGCCGTCATTGCTGCCCGTGCGCAAAACGGTTGCATTGGTCGCCACGGCAAGCTGCCGTGGAAGCTGCCCGGTGACCTGAAATACTTCCGTGAGCGCACCTGGGGCAAGCCCATCATCATGGGGCGCAAAACCTGGGAATCACTCAATGGTGCCTTGCCGGGGCGCACCAACATCGTGGTAACGCGTCAACAAGGTTATGAAGCCGAAGGTGCTCGCGTGGTCGATAGCATCGAAGAAGCCATTAGCTTGGCACAGTCTATCGCCTTAATCGAAGCCGTTGATGAAATCATGGTGCTGGGCGGCGGCGAAATCTATACCCAAGCCTTACCGCAAGCCGACATTCTCTATCTCACCGAAGTACACGCCTCGGTCGACGGCGATGCCTTCTTCCCCGACGTGGACCTCAGCCAATATCAAGAAACCCAACGCCAGGACTTCGAGCCATCGGGCGGCAACCCTTACCCGTTTAGCTTTGTGGTCTATCAGCGGACGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002857","ARO_id":"39291","ARO_name":"dfrA26","CARD_short_name":"dfrA26","ARO_description":"dfrA26 is an integron-encoded dihydrofolate reductase found in Escherichia coli.","ARO_category":{"37617":{"category_aro_accession":"3001218","category_aro_cvterm_id":"37617","category_aro_name":"trimethoprim resistant dihydrofolate reductase dfr","category_aro_description":"Alternative dihydropteroate synthase dfr present on plasmids produces alternate proteins that are less sensitive to trimethoprim from inhibiting its role in folate synthesis, thus conferring trimethoprim resistance.","category_aro_class_name":"AMR Gene Family"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"655":{"model_id":"655","model_name":"OXA-243","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1928":{"protein_sequence":{"accession":"AFQ90085.1","sequence":"MTVRLSSTALGAALSLSALAGAPAQAAVLCTVVADAADGRIVYQQGTQQACAARYTPASTFKLPIALMGADAGILTGPHAPVWNYQPGYPDWGGDAWRQPTDPARWIKYSVVWYSQLTARALGQERFQRYASAFHYGNEDVSGEPGKHNGLDGAWINSSLRISPLEQLAFLRKLVNRQLPLKAAAYDLAENLFEVGEAGGWHLYGKTGTGSPGSNGVYTAANAYGWFVGWARKDGRQLVFARLVQDEQATKPNAGLRARDDLMRDWPAMADAPRK"},"dna_sequence":{"accession":"JX206446.1","fmin":"0","fmax":"828","strand":"+","sequence":"ATGACCGTTCGCCTCTCTTCGACCGCTCTCGGCGCGGCCCTTTCCCTGTCCGCGCTGGCCGGCGCCCCCGCCCAGGCGGCCGTCCTGTGCACCGTGGTGGCCGACGCCGCCGACGGCCGCATCGTGTACCAGCAGGGCACGCAGCAGGCCTGCGCCGCGCGCTACACGCCGGCCTCGACCTTCAAGCTGCCCATCGCCCTGATGGGCGCGGACGCCGGCATCCTGACGGGCCCGCACGCGCCGGTCTGGAACTACCAGCCCGGCTACCCCGACTGGGGCGGCGACGCCTGGCGCCAGCCCACGGATCCGGCGCGCTGGATCAAGTATTCGGTGGTCTGGTATTCGCAGCTGACCGCCCGGGCGCTGGGGCAGGAACGCTTCCAGCGCTATGCCTCGGCCTTCCATTACGGCAACGAGGACGTCTCGGGCGAACCCGGCAAACACAACGGCCTGGACGGCGCATGGATCAACTCGTCGCTGCGGATTTCTCCGTTGGAACAACTGGCGTTCTTGCGCAAGCTGGTCAACCGGCAATTGCCGCTCAAGGCGGCGGCCTACGACCTGGCCGAGAACCTGTTCGAGGTCGGCGAAGCCGGCGGCTGGCACCTGTATGGCAAGACCGGCACCGGCTCGCCTGGCAGCAACGGCGTCTACACGGCGGCCAACGCCTACGGCTGGTTCGTCGGCTGGGCACGCAAGGACGGCCGCCAGCTGGTGTTCGCCCGCCTGGTGCAGGACGAGCAGGCCACCAAGCCCAACGCCGGCCTGCGCGCCCGCGACGACCTGATGCGCGACTGGCCCGCCATGGCCGACGCGCCGCGCAAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36941","NCBI_taxonomy_name":"Achromobacter xylosoxidans","NCBI_taxonomy_id":"85698"}}}},"ARO_accession":"3001610","ARO_id":"38010","ARO_name":"OXA-243","CARD_short_name":"OXA-243","ARO_description":"OXA-243 is a beta-lactamase found in Achromobacter xylosoxidans.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"656":{"model_id":"656","model_name":"OXA-219","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1528":{"protein_sequence":{"accession":"AEL17179.1","sequence":"MNIKTLLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEVHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWVVGPLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"JN215211.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAACACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGTACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGGTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001668","ARO_id":"38068","ARO_name":"OXA-219","CARD_short_name":"OXA-219","ARO_description":"OXA-219 is a beta-lactamase found in A. baumannii.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"520":{"model_id":"520","model_name":"AcrS","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"380"}},"model_sequences":{"sequence":{"4558":{"protein_sequence":{"accession":"AAC76296.1","sequence":"MAKRTKAEALKTRQELIETAIAQFAQHGVSKTTLNDIADAANVTRGAIYWHFENKTQLFNEMWLQQPSLRELIQEHLTAGLEHDPFQQLREKLIVGLQYIAKIPRQQALLKILYHKCEFNDEMLAEGVIREKMGFNPQTLREVLQACQQQGCVANNLDLDVVMIIIDGAFSGIVQNWLMNMAGYDLYKQAPALVDNVLRMFMPDENITKLIHQTNELSVM"},"dna_sequence":{"accession":"U00096.1","fmin":"3412802","fmax":"3413465","strand":"-","sequence":"ATGGCAAAAAGAACCAAAGCCGAAGCTCTGAAGACCCGGCAAGAACTGATTGAAACTGCCATCGCCCAGTTTGCGCAGCATGGCGTAAGCAAGACGACGCTCAACGACATTGCCGACGCCGCTAACGTTACGCGTGGCGCTATCTACTGGCACTTCGAAAACAAGACTCAACTGTTTAATGAGATGTGGTTGCAACAGCCTTCATTGCGGGAGTTAATCCAGGAACACTTGACGGCTGGATTAGAGCATGACCCGTTTCAACAATTGCGTGAAAAATTGATTGTCGGCTTGCAATATATTGCCAAAATTCCCCGCCAGCAGGCGTTGCTGAAAATCTTATATCACAAATGTGAATTTAATGATGAGATGCTGGCCGAGGGAGTGATACGCGAAAAGATGGGCTTTAATCCGCAGACTCTCCGCGAAGTATTGCAGGCGTGTCAGCAACAAGGTTGTGTAGCAAATAACCTCGATTTAGATGTTGTGATGATTATTATTGATGGTGCCTTCAGCGGAATTGTTCAAAACTGGTTAATGAATATGGCGGGTTATGATCTTTATAAACAAGCCCCCGCTCTGGTCGATAACGTATTAAGAATGTTCATGCCAGATGAAAACATAACGAAATTAATTCATCAAACGAATGAATTAAGTGTCATGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36849","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. MG1655","NCBI_taxonomy_id":"511145"}}}},"ARO_accession":"3000656","ARO_id":"37000","ARO_name":"AcrS","CARD_short_name":"AcrS","ARO_description":"AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"37084":{"category_aro_accession":"3000704","category_aro_cvterm_id":"37084","category_aro_name":"cefalotin","category_aro_description":"Cefalotin is a semisynthetic cephalosporin antibiotic activate against staphylococci. It is resistant to staphylococci beta-lactamases but hydrolyzed by enterobacterial beta-lactamases.","category_aro_class_name":"Antibiotic"},"37250":{"category_aro_accession":"3000870","category_aro_cvterm_id":"37250","category_aro_name":"triclosan","category_aro_description":"Triclosan is a common antibacterial agent added to many consumer products as a biocide.  It is an inhibitor of fatty acid biosynthesis by blocking enoyl-carrier protein reductase (FabI).","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"43746":{"category_aro_accession":"3005386","category_aro_cvterm_id":"43746","category_aro_name":"disinfecting agents and antiseptics","category_aro_description":"Disinfectants that can also interact with antimicrobial resistance mechanisms, e.g. molecule efflux, and thus are the targets of disinfectant resistance.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"556":{"model_id":"556","model_name":"vanY gene in vanB cluster","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"50"}},"model_sequences":{"sequence":{"3457":{"protein_sequence":{"accession":"AAB05624.1","sequence":"MEKSNYHSNVNHHKRHMKQSGEKRAFLWAFIISFTVCTLFLGWRLVSVLEATQLPPIPATHTGSGTGVAENPEENTLATAKEQGDEQEWSLILVNRQNPIPAQYDVELEQLSNGERIDIRISPYLQDLFDAARADGVYPIVASGYRTTEKQQEIMDEKVAEYKAKGYTSAQAKAEAETWVAVPGTSEHQLGLAVDINADGIHSTGNEVYRWLDENSYRFGFIRRYPPDKTEITGVSNEPWHYRYVGIEAATKIYHQGLCLEEYLNTEK"},"dna_sequence":{"accession":"U35369.1","fmin":"2358","fmax":"3165","strand":"+","sequence":"ATGGAAAAAAGCAACTATCATTCCAATGTGAATCATCACAAACGGCATATGAAACAATCTGGGGAAAAACGGGCTTTTCTATGGGCGTTCATTATCTCGTTCACAGTCTGCACGCTGTTTTTGGGGTGGAGATTGGTTTCCGTATTGGAGGCAACACAGCTACCGCCCATCCCTGCAACTCATACAGGCAGCGGGACTGGTGTAGCGGAGAATCCAGAGGAAAACACTCTTGCCACCGCCAAAGAACAGGGAGATGAACAGGAATGGAGCCTGATTTTAGTGAACAGGCAGAACCCCATCCCCGCCCAGTACGATGTGGAACTTGAGCAGCTGTCAAATGGTGAGCGGATAGACATTCGGATTTCTCCCTACCTCCAGGATTTGTTTGATGCCGCAAGAGCTGATGGAGTTTACCCGATTGTCGCATCCGGATACCGGACAACAGAAAAACAGCAAGAAATCATGGATGAAAAAGTCGCCGAATACAAGGCGAAAGGCTACACCTCTGCACAGGCTAAAGCGGAAGCAGAAACTTGGGTGGCCGTGCCGGGAACAAGCGAGCATCAGCTTGGTCTTGCTGTGGATATCAATGCGGATGGAATTCATTCAACCGGCAACGAGGTTTACAGATGGCTGGATGAAAACAGCTATCGCTTTGGTTTTATTCGCCGCTACCCGCCAGACAAGACAGAGATAACCGGTGTGAGCAACGAGCCGTGGCATTACCGATATGTCGGCATCGAAGCTGCCACAAAGATATACCACCAAGGGCTTTGCCTTGAGGAATATTTAAACACAGAAAAATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35918","NCBI_taxonomy_name":"Enterococcus faecalis","NCBI_taxonomy_id":"1351"}}}},"ARO_accession":"3002956","ARO_id":"39390","ARO_name":"vanY gene in vanB cluster","CARD_short_name":"vanY_in_vanB_cl","ARO_description":"Also known as vanYB, is a vanY variant found in the vanB gene cluster.","ARO_category":{"36216":{"category_aro_accession":"3000077","category_aro_cvterm_id":"36216","category_aro_name":"vanY","category_aro_description":"VanY is a D,D-carboxypeptidase that cleaves removes the terminal D-Ala from peptidoglycan for the addition of D-Lactate. The D-Ala-D-Lac peptidoglycan subunits have reduced binding affinity with vancomycin compared to D-Ala-D-Ala.","category_aro_class_name":"AMR Gene Family"},"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"559":{"model_id":"559","model_name":"vanXY gene in vanE cluster","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"125"}},"model_sequences":{"sequence":{"106":{"protein_sequence":{"accession":"AAL27443.1","sequence":"MKKNYLRLINENNEIKDSERPSHLVQAPFAQTNILVDPMVAIQLEKLIKTTGLDSQIITIDGYRSKETQQALWDETIQEKGLEFAHKYVAKPGCSEHEIGLAVDLGLATKENDFIRPSFTDSPIVDKFLKHMTDFGFILRYQKGKESITNINYEPWHFRYVGTPHSSIMVQQNWVLEEYIEFIESIRGTAYEA"},"dna_sequence":{"accession":"FJ872411.1","fmin":"40765","fmax":"41347","strand":"+","sequence":"ATGAAAAAAAATTATCTACGATTGATTAATGAAAACAATGAAATAAAAGACTCTGAGAGACCAAGTCACCTTGTTCAGGCTCCGTTTGCACAAACAAATATACTAGTTGATCCTATGGTAGCGATACAGCTAGAAAAACTAATAAAGACAACAGGTCTTGATAGCCAAATTATTACCATTGATGGCTATCGTTCAAAGGAGACACAGCAAGCACTTTGGGATGAGACGATTCAAGAAAAAGGGCTTGAATTTGCGCACAAATATGTGGCAAAGCCTGGATGTAGTGAACATGAAATTGGTTTAGCAGTGGATTTGGGGTTAGCTACGAAAGAAAATGATTTTATTCGCCCAAGTTTCACTGATAGTCCGATTGTTGATAAATTTTTAAAGCATATGACAGATTTCGGCTTTATCTTAAGATATCAAAAAGGAAAAGAATCTATTACCAATATAAACTATGAACCATGGCATTTCAGGTATGTAGGGACACCCCATAGTTCGATTATGGTACAGCAAAACTGGGTATTAGAAGAATACATTGAATTCATTGAGTCAATAAGAGGAACTGCTTATGAAGCATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35918","NCBI_taxonomy_name":"Enterococcus faecalis","NCBI_taxonomy_id":"1351"}}}},"ARO_accession":"3002967","ARO_id":"39401","ARO_name":"vanXY gene in vanE cluster","CARD_short_name":"vanXY_in_vanE","ARO_description":"Also known as vanXY, is a vanXY variant found in the vanE gene cluster.","ARO_category":{"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"36635":{"category_aro_accession":"3000496","category_aro_cvterm_id":"36635","category_aro_name":"vanXY","category_aro_description":"VanXY is a protein with both D,D-carboxypeptidase and D,D-dipeptidase activity, found in Enterococcus gallinarum. It cleaves and removes the terminal D-Ala of peptidoglycan subunits for the incorporation of D-Ser by VanC. D-Ala-D-Ser has low binding affinity with vancomycin.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"534":{"model_id":"534","model_name":"vanV gene in vanB cluster","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"200"}},"model_sequences":{"sequence":{"4564":{"protein_sequence":{"accession":"AAO82019.1","sequence":"MFTEKFCADGICFIMRAKNEIDHIFSELYSVPNCLQKPYFKLKVQELLLFLCMPLVICTPILIGFAILIPYLCFKNLEKRSIVNRLRAEQKENQQKQVVLALLIHSELFDSGFR"},"dna_sequence":{"accession":"AE016830.1","fmin":"2211932","fmax":"2212277","strand":"-","sequence":"TTGTTTACAGAAAAATTCTGCGCTGATGGAATCTGCTTTATTATGCGGGCGAAAAATGAAATTGACCATATTTTTTCAGAACTTTACTCTGTACCGAATTGCCTGCAAAAGCCTTATTTTAAGCTGAAAGTTCAGGAATTGCTTTTGTTTTTGTGTATGCCCCTCGTGATTTGTACACCTATCTTAATTGGCTTTGCAATTCTCATTCCGTATCTCTGCTTTAAGAATTTGGAAAAACGAAGCATTGTGAATCGGCTGCGGGCAGAGCAAAAAGAGAACCAGCAGAAACAAGTCGTTCTTGCTCTGCTGATTCACTCGGAACTGTTTGATTCGGGTTTTCGTTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37592","NCBI_taxonomy_name":"Enterococcus faecalis V583","NCBI_taxonomy_id":"226185"}}}},"ARO_accession":"3004254","ARO_id":"41418","ARO_name":"vanV gene in vanB cluster","CARD_short_name":"vanV_in_vanB_cl","ARO_description":"Also known as vanVB, is a vanV variant found in the vanB gene cluster. It is found in some but not all vanB operons in E. faecalis, suggesting the existence of varied gene compositions in vanB operons.","ARO_category":{"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"39350":{"category_aro_accession":"3002916","category_aro_cvterm_id":"39350","category_aro_name":"vanV","category_aro_description":"vanV is an accessory protein of van operons, first identified in the vanB operon. It is not required for vancomycin resistance.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"657":{"model_id":"657","model_name":"SHV-142","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1711":{"protein_sequence":{"accession":"AEX99752.1","sequence":"MRYIRLCIISLLAALPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"JQ029959.1","fmin":"28","fmax":"889","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCGCCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGCATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATATATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001184","ARO_id":"37564","ARO_name":"SHV-142","CARD_short_name":"SHV-142","ARO_description":"SHV-142 is a beta-lactamase.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"658":{"model_id":"658","model_name":"CMY-104","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1546":{"protein_sequence":{"accession":"AGR82311.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNHTITPLMQKQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGISLLHLATYTAGGLPLQIPDDVTDKAALLRFYQNWQPQWTPSTKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQSEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASQVQEKTLQQGIELAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPARVDAAWRILEKLQ"},"dna_sequence":{"accession":"KF150216.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACGTTTGCCGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCACACCATCACCCCGTTGATGCAGAAGCAGGCTATTCCGGGGATGGCCGTTGCAGTTATCTACCAGGGTAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGACGCTATCGCCCGCGGTGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCAGCCTGCTGCACTTAGCCACCTATACGGCAGGTGGCCTGCCGCTGCAGATCCCCGATGACGTTACGGATAAAGCCGCATTACTGCGCTTTTATCAAAACTGGCAGCCACAATGGACTCCGAGCACTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGTATGAGCTACGAAGAGGCGATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAAAGCGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGACGCCAGCCAGGTTCAGGAAAAAACACTCCAGCAGGGCATTGAGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGTTGAAAGCTGATTCGATCATCAACGGTAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTACATAAAACGGGATCCACTGGTGGATTTGGCAGCTACGTTGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGCCCGCGTCGATGCAGCCTGGCGTATTCTTGAAAAACTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39654","NCBI_taxonomy_name":"Citrobacter sp. OTESBL0707","NCBI_taxonomy_id":"1367686"}}}},"ARO_accession":"3002116","ARO_id":"38516","ARO_name":"CMY-104","CARD_short_name":"CMY-104","ARO_description":"CMY-104 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"659":{"model_id":"659","model_name":"AAC(6')-29b","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"250"}},"model_sequences":{"sequence":{"5898":{"protein_sequence":{"accession":"WP_064190969.1","sequence":"MSVSILPVKEQDAADWLALRNLLWLADDHASEIEQYFSGGFEEPAEVLIARDATGAAVGHVELSIRHDLEELQGIKTGYIEGLYVAPSHRSTDLVRRFLRESEKWALEQGCSAFASDRSDRVITHRKFAGSAV"},"dna_sequence":{"accession":"NG_048576.1","fmin":"100","fmax":"502","strand":"+","sequence":"TTGAGCGTTTCGATCTTACCTGTGAAAGAACAAGACGCTGCCGACTGGCTAGCGCTGCGGAATCTTCTTTGGCTCGCGGATGATCACGCCTCGGAGATTGAGCAGTACTTCTCTGGTGGATTTGAGGAGCCTGCAGAAGTGCTCATCGCCCGTGATGCTACCGGCGCGGCTGTTGGGCATGTCGAACTCTCGATAAGACATGACTTGGAAGAACTCCAAGGAATCAAGACCGGCTACATCGAAGGCCTTTATGTGGCCCCAAGCCATCGATCAACAGACCTTGTGAGGCGTTTCTTGCGTGAGTCCGAGAAGTGGGCCCTAGAACAAGGGTGCAGCGCATTTGCCTCAGACAGAAGTGATCGGGTCATCACGCACCGCAAGTTCGCAGGCAGCGCCGTCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002584","ARO_id":"38984","ARO_name":"AAC(6')-29b","CARD_short_name":"AAC(6')-29b","ARO_description":"AAC(6')-29b is an integron-encoded aminoglycoside acetyltransferase in P. aeruginosa.","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"A category of aminoglycoside N-acetyltransferase enzymes with modification regiospecificity based at the 6'-amino group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics through acetylation of the 6-amino group of the compound.","category_aro_class_name":"AMR Gene Family"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"661":{"model_id":"661","model_name":"VIM-5","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"855":{"protein_sequence":{"accession":"AAN52134.1","sequence":"MLKVISSLLVYMTASVMAVASPLAHSGEPSGEYPTVNEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRKAGVATYASPSTRRLAEAEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSANVLYGGCAVLALSRTSAGNVADADLAEWPTSVERIQKHYPEAEVVIPGHGLPGGLDLLQHTANVVTAHKNRSVAE"},"dna_sequence":{"accession":"AY144612.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGTTAAAAGTTATTAGTAGTTTATTGGTCTACATGACCGCGTCTGTCATGGCTGTAGCTAGTCCGTTAGCCCATTCCGGGGAGCCGAGTGGTGAGTATCCGACAGTCAACGAAATTCCGGTCGGAGAGGTCCGGCTTTACCAGATTGCTGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCGGTCTACCCATCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCCCTTCTCGCGGAGATTGAGAAGCAAATTGGACTTCCCGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGAAGGCTGGAGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGCAGAGGGGAACGAGATTCCCACGCACTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAGCTCTTCTATCCCGGTGCTGCGCATTCGACCGACAATCTGGTTGTATACGTCCCGTCAGCGAACGTGCTATACGGTGGTTGTGCCGTTCTTGCGTTGTCACGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCGTTGAGCGGATTCAAAAACACTACCCGGAAGCAGAGGTCGTCATTCCCGGGCACGGTCTACCGGGCGGTCTAGACTTGCTCCAGCACACAGCGAACGTTGTCACAGCACACAAAAATCGCTCAGTCGCCGAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002275","ARO_id":"38675","ARO_name":"VIM-5","CARD_short_name":"VIM-5","ARO_description":"VIM-5 is a beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"662":{"model_id":"662","model_name":"TEM-162","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1882":{"protein_sequence":{"accession":"ABO64442.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPKTLVKVKDAENQLGARVGYIELDLNSGKILESFRPEKRFPMMSTFKVLLCGAVLSRIDAGQEQLGRRIHYSQSDVVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPVAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"EF468463.1","fmin":"66","fmax":"927","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCTTTTTGCCTTCCTGTTTTTGCTCACCCAAAAACGCTGGTGAAAGTAAAAGATGCTGAAAATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAAAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTATTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAGTGACGTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGTAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36938","NCBI_taxonomy_name":"Acinetobacter haemolyticus","NCBI_taxonomy_id":"29430"}}}},"ARO_accession":"3001028","ARO_id":"37408","ARO_name":"TEM-162","CARD_short_name":"TEM-162","ARO_description":"TEM-162 is a beta-lactamase found in Acinetobacter haemolyticus.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"663":{"model_id":"663","model_name":"ACT-36","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1660":{"protein_sequence":{"accession":"AJG06170.1","sequence":"MMKKSLCCALLLGISCSALAAPVSEKQLAEVVANTITPLMKAQSIPGMAVAVIYQGKPHYYTFGKADIAASKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNAALLRFYQNWQPQWKPGTTRLYANASIGLFGALTVKPSGMGYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPENVADASLKQGISLAQSRYWRIGSMYQGLGWEMLNWPVEANTVIEGSDSKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANKSYPNPARVEAAYHILDALQ"},"dna_sequence":{"accession":"KM926621.1","fmin":"751","fmax":"1897","strand":"+","sequence":"ATGATGAAAAAATCTCTTTGCTGCGCCCTGCTGCTCGGCATCTCTTGCTCTGCTCTCGCCGCGCCAGTGTCAGAAAAACAGCTGGCGGAGGTGGTCGCGAATACGATTACCCCGCTGATGAAAGCCCAGTCGATTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGTAAACCGCACTATTACACGTTTGGCAAAGCCGATATCGCGGCCAGCAAACCCGTTACGCCTCAGACTCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGGGTTTTAGGAGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTGACGGGCAAGCAGTGGCAGGGGATTCGTATGCTGGATCTCGCAACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAATGCCGCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGTATCGGTCTTTTTGGCGCGCTGACGGTCAAACCTTCCGGCATGGGCTATGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTTCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGAATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCGGAGAACGTTGCTGATGCCTCACTTAAGCAGGGCATCTCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCTGTGGAGGCCAACACGGTGATCGAGGGCAGCGACAGTAAGGTGGCGCTGGCACCGCTGCCCGTGGCAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGCTCTACTGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCGACGCGCTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3003171","ARO_id":"39748","ARO_name":"ACT-36","CARD_short_name":"ACT-36","ARO_description":"ACT-36 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"664":{"model_id":"664","model_name":"CMY-43","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1508":{"protein_sequence":{"accession":"ACJ05361.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFAALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"FJ360626.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGCCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002054","ARO_id":"38454","ARO_name":"CMY-43","CARD_short_name":"CMY-43","ARO_description":"CMY-43 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"665":{"model_id":"665","model_name":"TEM-10","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"2029":{"protein_sequence":{"accession":"AAC72362.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDSWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGKRGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AF093512.1","fmin":"197","fmax":"1058","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATAGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTAAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36917","NCBI_taxonomy_name":"Morganella morganii","NCBI_taxonomy_id":"582"}}}},"ARO_accession":"3000882","ARO_id":"37262","ARO_name":"TEM-10","CARD_short_name":"TEM-10","ARO_description":"TEM-10 is an extended-spectrum beta-lactamase round in Morganella morganii.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"666":{"model_id":"666","model_name":"CTX-M-34","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1028":{"protein_sequence":{"accession":"AAR99493.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTVDVQQKLAELEQQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSCDYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"AY515297.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGTGGACGTACAGCAAAAACTTGCCGAATTAGAGCAGCAGTCGGGAGGAAGGCTGGGTGTGGCATTGATTAACACGGCGGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTCGAGATCAAAAAATCTGACCTGGTTAACTATAATCCGATTGCGGAAAAACACGTCAATGGGACGATGTCACTGGCTGAGCTCAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTTACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCTGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACGCTGCGTAATCTGACGCTGGGTAAAGCATTGGGTGACAGCCAACGGGCGCAGCTGGTGACGTGGATGAAAGGCAATACTACCGGTGCAGCGAGTATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCTGTGACTATGGTACCACCAACGATATCGCGGTGATTTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCCCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001896","ARO_id":"38296","ARO_name":"CTX-M-34","CARD_short_name":"CTX-M-34","ARO_description":"CTX-M-34 is a beta-lactamase found in the Enterobacteriaceae family.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"667":{"model_id":"667","model_name":"ACT-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"8151":{"protein_sequence":{"accession":"AAC45086.2","sequence":"MMMTKSLCCALLLSTSCSVLATPMSEKQLAEVVERTVTPLMKAQAIPGMAVAVIYEGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVKDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMSYEQAITTRVFKPLKLDHTWINVPKAEEAHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVQDMASWVMVNMKPDSLQDNSLRKGLTLAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVEGSDNKVALAPLPAREVNPPAPPVNASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILSAL"},"dna_sequence":{"accession":"U58495.2","fmin":"27","fmax":"1173","strand":"+","sequence":"ATGATGATGACTAAATCCCTTTGCTGCGCCCTGCTGCTCAGCACCTCCTGCTCGGTATTGGCTACCCCGATGTCAGAAAAACAGCTGGCTGAGGTGGTGGAACGGACCGTTACGCCGCTGATGAAAGCGCAGGCCATTCCGGGTATGGCGGTGGCGGTGATTTATGAGGGTCAGCCGCACTACTTCACCTTCGGTAAAGCCGATGTTGCGGCGAACAAACCTGTCACTCCACAAACCTTGTTCGAACTGGGTTCTATAAGTAAAACCTTCACCGGCGTACTCGGTGGCGATGCCATTGCTCGCGGTGAAATATCGCTGGGCGATCCGGTGACAAAATACTGGCCTGAGCTGACAGGCAAGCAGTGGCAGGGGATCCGCATGCTGGATCTGGCAACCTATACCGCAGGAGGTTTGCCGTTACAGGTACCGGATGAGGTCAAGGATAACGCCTCTCTGTTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCGGGCACCACGCGTCTTTACGCCAATGCCAGCATCGGTCTTTTTGGCGCGCTGGCGGTCAAACCTTCCGGCATGAGCTATGAGCAGGCCATAACGACGCGGGTCTTTAAGCCGCTCAAGCTGGACCATACGTGGATTAACGTTCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGATACCGCGACGGTAAAGCAGTACACGTTTCGCCAGGAATGCTGGACGCTGAAGCCTATGGCGTAAAAACCAACGTGCAGGATATGGCAAGCTGGGTGATGGTCAACATGAAGCCGGACTCCCTTCAGGATAATTCACTCAGGAAAGGCCTTACCCTGGCGCAGTCTCGCTACTGGCGCGTGGGGGCCATGTATCAGGGGTTAGGCTGGGAAATGCTTAACTGGCCGGTCGATGCCAAAACCGTGGTTGAAGGTAGCGACAATAAGGTTGCACTGGCACCGCTGCCTGCGAGAGAAGTGAATCCACCAGCGCCCCCGGTCAACGCATCCTGGGTCCATAAAACAGGCTCTACCGGCGGGTTTGGCAGCTACGTGGCATTTATTCCTGAAAAGCAGCTCGGTATTGTGATGCTGGCAAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCGTATTTTGAGCGCGCTGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001821","ARO_id":"38221","ARO_name":"ACT-1","CARD_short_name":"ACT-1","ARO_description":"ACT-1 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"668":{"model_id":"668","model_name":"CTX-M-65","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1029":{"protein_sequence":{"accession":"ABN69105.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAVAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAERRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"EF418608.1","fmin":"9","fmax":"885","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGTCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGACTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGCGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001926","ARO_id":"38326","ARO_name":"CTX-M-65","CARD_short_name":"CTX-M-65","ARO_description":"CTX-M-65 is a beta-lactamase found in Escherichia coli.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"669":{"model_id":"669","model_name":"MIR-12","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"1269":{"protein_sequence":{"accession":"AIT76116.1","sequence":"MMTKSLSCALLLSVTSSAFAAPMSEKQLAEVVERTVTPLMNAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEVALGDPVAKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDTASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMSYEQAMTTRVFKPLKLDHTWINVPKAEEAHYAWGYREGKAVHVSPGMLDAEAYGVKTNVKDMASWLIANMKPDSLQAPSLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVGGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILDALQ"},"dna_sequence":{"accession":"KM087863.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGACAAAATCCCTAAGCTGTGCCCTGCTGCTCAGCGTCACCAGCTCTGCATTCGCCGCACCGATGTCCGAAAAACAGCTGGCTGAGGTGGTGGAACGTACCGTTACGCCGCTGATGAACGCGCAGGCCATTCCGGGTATGGCGGTGGCGGTAATTTATCAGGGTCAGCCACACTACTTTACCTTCGGTAAAGCCGATGTTGCGGCGAACAAACCCGTCACCCCGCAAACCCTGTTTGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTACTGGGCGGCGATGCCATTGCCCGGGGTGAAGTAGCGCTGGGCGATCCGGTAGCAAAATACTGGCCTGAGCTCACGGGCAAGCAGTGGCAGGGCATTCGCATGCTGGATCTGGCAACCTATACCGCAGGCGGTCTGCCGTTACAGGTGCCGGATGAGGTCACGGATACCGCCTCTCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCGGGCACCACGCGTCTTTACGCTAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTCAAACCTTCCGGCATGAGCTATGAGCAGGCCATGACGACGCGGGTCTTTAAACCCCTCAAGCTGGACCATACATGGATTAACGTCCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGATACCGTGAGGGTAAAGCGGTCCACGTTTCGCCAGGGATGCTGGACGCGGAAGCCTATGGCGTAAAAACTAACGTGAAGGATATGGCGAGCTGGCTGATAGCCAACATGAAGCCGGATTCTCTTCAGGCTCCCTCACTCAAGCAAGGCATTGCTCTGGCGCAGTCTCGCTACTGGCGCGTGGGGGCTATGTATCAGGGGTTGGGCTGGGAGATGCTCAACTGGCCGGTCGATGCCAAAACCGTCGTCGGAGGCAGTGATAACAAGGTGGCGCTGGCACCATTGCCCGTGGCAGAAGTGAATCCACCCGCGCCGCCGGTCAAGGCCTCCTGGGTCCATAAAACAGGCTCGACGGGCGGGTTTGGCAGCTACGTGGCATTTATTCCTGAAAAGCAGCTCGGCATTGTGATGCTGGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCGTATCCTCGACGCGCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3002177","ARO_id":"38577","ARO_name":"MIR-12","CARD_short_name":"MIR-12","ARO_description":"MIR-12 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36197":{"category_aro_accession":"3000058","category_aro_cvterm_id":"36197","category_aro_name":"MIR beta-lactamase","category_aro_description":"MIR beta-lactamases are plasmid-mediated beta-lactamases that confer resistance to oxyimino- and alpha-methoxy beta-lactams.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"670":{"model_id":"670","model_name":"IND-3","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"8190":{"protein_sequence":{"accession":"AAG29761.2","sequence":"MKKRIQFFMVSMMLSSLFSAQVKDFVIEPPIKKNLHIYKTFGVFGGKEYSANSVYLVTQKGVVLFDVPWEKVQYQSLMDTIQKRHNLPVIAVFATHSHDDRAGDLSFFNNKGIKTYATSKTNEFLKKDGKATSTEIIKTGKPYRIGGEEFVVDFLGEGHTADNVVVWFPKYNVLDGGCLVKSKAATDLGYIKEANVEQWPKTINKLKSKYSKASLVIPGHDEWKGGGHVKHTLELLNKK"},"dna_sequence":{"accession":"AF219131.2","fmin":"0","fmax":"720","strand":"+","sequence":"ATGAAAAAAAGAATTCAGTTCTTTATGGTTTCAATGATGCTAAGTTCATTATTCAGTGCCCAGGTAAAAGATTTTGTCATCGAACCACCGATTAAAAAGAATTTACATATTTACAAAACTTTTGGTGTATTCGGAGGTAAAGAATATTCTGCCAATTCAGTATATCTTGTTACCCAAAAAGGAGTTGTCTTATTTGACGTCCCGTGGGAAAAGGTACAGTACCAAAGCCTGATGGATACCATCCAAAAACGCCACAATTTACCCGTAATAGCTGTGTTTGCCACTCACTCCCATGATGACCGTGCCGGAGATCTGAGCTTTTTTAACAACAAAGGAATTAAAACCTACGCTACTTCCAAAACCAATGAATTCCTGAAAAAAGACGGAAAAGCAACATCCACAGAGATCATTAAGACCGGAAAGCCATATCGCATAGGAGGTGAGGAATTTGTGGTTGATTTTCTTGGAGAAGGGCATACTGCTGATAATGTAGTGGTATGGTTTCCCAAATACAACGTCCTGGATGGCGGATGCCTTGTAAAAAGTAAAGCTGCAACCGATCTTGGATATATTAAGGAAGCCAATGTAGAGCAATGGCCCAAGACCATCAATAAACTGAAATCCAAATATTCAAAAGCAAGCCTGGTTATTCCCGGACATGATGAATGGAAAGGTGGAGGCCATGTAAAACATACTCTTGAACTTCTTAACAAAAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36916","NCBI_taxonomy_name":"Chryseobacterium indologenes","NCBI_taxonomy_id":"253"}}}},"ARO_accession":"3002259","ARO_id":"38659","ARO_name":"IND-3","CARD_short_name":"IND-3","ARO_description":"IND-3 is a beta-lactamase found in Chryseobacterium indologenes.","ARO_category":{"36199":{"category_aro_accession":"3000060","category_aro_cvterm_id":"36199","category_aro_name":"IND beta-lactamase","category_aro_description":"IND beta-lactamases are class B carbapenem-hydrolyzing beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"671":{"model_id":"671","model_name":"CTX-M-137","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"785":{"protein_sequence":{"accession":"BAO37256.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"AB900900.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATTGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001994","ARO_id":"38394","ARO_name":"CTX-M-137","CARD_short_name":"CTX-M-137","ARO_description":"CTX-M-137 is a beta-lactamase found in Escherichia coli.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"672":{"model_id":"672","model_name":"CMY-27","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1442":{"protein_sequence":{"accession":"ACA30421.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYACGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"EU515250.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGTGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002038","ARO_id":"38438","ARO_name":"CMY-27","CARD_short_name":"CMY-27","ARO_description":"CMY-27 is a beta-lactamase found in the Enterobacteriaceae family.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"673":{"model_id":"673","model_name":"IMP-48","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1111":{"protein_sequence":{"accession":"AIT76110.1","sequence":"MKKLFVLCVFFFCNIAVAEESLPDLKIEKLEEGVYVHTSFEEVKGWSVVTKHGLVVLVKNDAYLIDTPTTAKDTEKLVNWFVERGYKIKGSISTHFHGDSTAGIEWLNSQSIPTYASELTNELLKKDNKVQAKHSFNGVSYSLIKNKIEVFYPGPGHTQDNVVVWLPEKKILFGGCFVKPDGLGYLGDANLEAWPKSAKILMSKYGKAKLVVSSHSDIGDVSLLKRTWEQAVKGLNESKKSSQPSD"},"dna_sequence":{"accession":"KM087857.1","fmin":"0","fmax":"741","strand":"+","sequence":"ATGAAAAAATTATTTGTTTTATGTGTATTCTTCTTCTGCAACATTGCAGTTGCAGAAGAATCTTTGCCTGATTTAAAAATTGAGAAGCTTGAAGAAGGCGTTTATGTTCATACTTCGTTTGAAGAAGTTAAAGGTTGGAGTGTGGTCACTAAACACGGTTTGGTGGTTCTTGTGAAAAATGACGCCTATCTGATTGATACTCCAACTACTGCTAAAGATACTGAAAAATTAGTCAATTGGTTTGTTGAGCGGGGCTATAAAATCAAAGGCAGTATTTCCACACATTTCCATGGTGACAGTACGGCTGGAATAGAGTGGCTTAATTCTCAATCTATCCCCACATATGCTTCTGAATTAACAAATGAACTTCTTAAAAAAGACAATAAGGTACAAGCTAAACACTCTTTTAATGGGGTTAGTTATTCACTAATTAAAAACAAAATTGAAGTTTTTTATCCAGGCCCAGGGCACACTCAAGATAACGTAGTGGTTTGGTTACCTGAAAAGAAAATTTTATTCGGTGGTTGCTTTGTTAAACCGGACGGTCTTGGCTATTTGGGGGACGCAAATTTAGAAGCTTGGCCAAAGTCCGCTAAAATATTAATGTCTAAATATGGTAAAGCAAAACTAGTTGTGTCGAGTCATAGTGATATTGGAGATGTATCACTCTTGAAACGTACATGGGAGCAGGCTGTTAAAGGGCTGAATGAAAGTAAAAAATCATCACAGCCAAGCGACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002239","ARO_id":"38639","ARO_name":"IMP-48","CARD_short_name":"IMP-48","ARO_description":"IMP-48 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"674":{"model_id":"674","model_name":"OXA-15","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1834":{"protein_sequence":{"accession":"AAB05874.1","sequence":"MAIRIFAILFSIFSLATFAHAQEGTLERSDWRKFFSEFQAKGTIVVADERQADRAMLVFDPVRSKKRYSPASTFKIPHTLFALDAGAVRDEFQIFRWDGVNRGFAGHNQDQDLRSAMRNSTVWVYELFAKEIGDDKARRYLKKIDYGNAGPSTSNGDYWIEGSLAISAQEQIAFLRKLYRNELPFRVEHQRLVKDLMIVEAGRNWILRAKTGWEGRMGWWVGWVEWPTGSVFFALNIDTPNRMDDLFKREAIVRAILRSIEALPPNPAVNSDAAR"},"dna_sequence":{"accession":"U63835.1","fmin":"127","fmax":"955","strand":"+","sequence":"ATGGCAATCCGAATCTTCGCGATACTTTTCTCCATTTTTTCTCTTGCCACTTTCGCGCATGCGCAAGAAGGCACGCTAGAACGTTCTGACTGGAGGAAGTTTTTCAGCGAATTTCAAGCCAAAGGCACGATAGTTGTGGCAGACGAACGCCAAGCGGATCGTGCCATGTTGGTTTTTGATCCTGTGCGATCGAAGAAACGCTACTCGCCTGCATCGACATTCAAGATACCTCATACACTTTTTGCACTTGATGCAGGCGCTGTTCGTGATGAGTTCCAGATTTTTCGATGGGACGGCGTTAACAGGGGCTTTGCAGGCCACAATCAAGACCAAGATTTGCGATCAGCAATGCGGAATTCTACTGTTTGGGTGTATGAGCTATTTGCAAAGGAAATTGGTGATGACAAAGCTCGGCGCTATTTGAAGAAAATCGACTATGGCAACGCCGGTCCTTCGACAAGTAATGGCGATTACTGGATAGAAGGCAGCCTTGCAATCTCGGCGCAGGAGCAAATTGCATTTCTCAGGAAGCTCTATCGTAACGAGCTGCCCTTTCGGGTAGAACATCAGCGCTTGGTCAAGGATCTCATGATTGTGGAAGCCGGTCGCAACTGGATACTGCGTGCAAAGACGGGCTGGGAAGGCCGTATGGGTTGGTGGGTAGGATGGGTTGAGTGGCCGACTGGCTCCGTATTCTTCGCACTGAATATTGATACGCCAAACAGAATGGATGATCTTTTCAAGAGGGAGGCAATCGTGCGGGCAATCCTTCGCTCTATTGAAGCGTTACCGCCCAACCCGGCAGTCAACTCGGACGCTGCGCGATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3001410","ARO_id":"37810","ARO_name":"OXA-15","CARD_short_name":"OXA-15","ARO_description":"OXA-15 is a beta-lactamase found in P. aeruginosa.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46493":{"category_aro_accession":"3007704","category_aro_cvterm_id":"46493","category_aro_name":"OXA-2-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-2.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"675":{"model_id":"675","model_name":"OXA-25","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1210":{"protein_sequence":{"accession":"AAG35607.1","sequence":"MKKFILPIFSISILVSLSACSSIKTKSEDNFHISSQQHEKAIKSYFDEAQTQGVIIIKEGKNLSTYGNALARANKEYVPASTFKMLNALIGLENHKATTNEIFKWDGKKRTYPMWEKDMTLGEAMALSAVPVYQELARRTGLELMQKEVKRVNFGNTNIGTQVDNFWLVGPLKITPVQEVNFADDLAHNRLPFKLETQEEVEKMLLIKEVNGSKIYAKSGWGMGVTPQVGWLTGWVEQANGKKIPFSLNLEMKEGMSGSIRNEITYKLLENLGII"},"dna_sequence":{"accession":"AF201826.1","fmin":"21","fmax":"849","strand":"+","sequence":"ATGAAAAAATTTATACTTCCTATATTCAGCATTTCTATTCTAGTTTCTCTCAGTGCATGTTCATCTATTAAAACTAAATCTGAAGATAATTTTCATATTTCTTCTCAGCAACATGAAAAAGCTATTAAAAGCTATTTTGATGAAGCTCAAACACAGGGTGTAATTATTATTAAAGAGGGTAAAAATCTTAGCACCTATGGTAATGCTCTTGCACGAGCAAATAAAGAATATGTCCCTGCATCAACATTTAAGATGCTAAATGCTTTAATCGGGCTAGAAAATCATAAAGCAACAACAAATGAGATTTTCAAATGGGATGGTAAAAAAAGAACTTATCCTATGTGGGAGAAAGATATGACTTTAGGTGAGGCAATGGCATTGTCAGCAGTTCCAGTATATCAAGAGCTTGCAAGACGGACTGGCCTAGAGCTAATGCAGAAAGAAGTAAAGCGGGTTAATTTTGGAAATACAAATATTGGAACACAGGTCGATAATTTTTGGTTAGTTGGCCCCCTTAAAATTACACCAGTACAAGAAGTTAATTTTGCCGATGACCTTGCACATAACCGATTACCTTTTAAATTAGAAACTCAAGAAGAAGTTGAAAAAATGCTTCTAATTAAAGAAGTAAATGGTAGTAAGATTTATGCAAAAAGTGGATGGGGAATGGGTGTTACTCCACAGGTAGGTTGGTTGACTGGTTGGGTGGAGCAAGCTAATGGAAAAAAAATCCCCTTTTCGCTCAACTTAGAAATGAAAGAAGGAATGTCTGGTTCTATTCGTAATGAAATTACTTATAAGTTGCTAGAAAATCTTGGAATCATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001420","ARO_id":"37820","ARO_name":"OXA-25","CARD_short_name":"OXA-25","ARO_description":"OXA-25 is a beta-lactamase found in A. baumannii.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46500":{"category_aro_accession":"3007711","category_aro_cvterm_id":"46500","category_aro_name":"OXA-24-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-24.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"676":{"model_id":"676","model_name":"AAC(6')-Ih","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"456":{"protein_sequence":{"accession":"AAC41391.1","sequence":"MNIMPISESQLSDWLALRCLLWPDHEDVHLQEMRQLITQAHRLQLLAYTDTQQAIAMLEASIRYEYVNGTQTSPVAFLEGIFVLPEYRRSGIATGLVQQVEIWAKQFACTEFASDAALDNQISHAMHQALGFHETERVVYFKKNIG"},"dna_sequence":{"accession":"L29044.1","fmin":"351","fmax":"792","strand":"+","sequence":"ATGAATATTATGCCGATATCTGAATCACAATTATCAGATTGGTTAGCATTAAGATGCTTACTTTGGCCTGATCATGAAGATGTGCATTTACAGGAAATGCGCCAACTGATCACACAGGCACATCGTTTACAATTATTGGCTTATACCGACACCCAACAAGCAATTGCCATGTTGGAAGCTTCAATTCGGTATGAATATGTGAATGGCACACAAACATCGCCTGTGGCTTTTTTGGAAGGGATTTTTGTATTGCCTGAATATCGTCGTTCAGGTATCGCAACGGGGTTGGTTCAACAAGTGGAAATTTGGGCGAAACAGTTTGCATGTACAGAGTTTGCTTCGGATGCAGCGTTGGATAATCAGATCAGCCACGCCATGCATCAAGCACTCGGTTTTCATGAAACTGAACGTGTGGTGTATTTTAAGAAAAATATCGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3002555","ARO_id":"38955","ARO_name":"AAC(6')-Ih","CARD_short_name":"AAC(6')-Ih","ARO_description":"AAC(6')-Ih is a plasmid-encoded aminoglycoside acetyltransferase in A. baumannii.","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"A category of aminoglycoside N-acetyltransferase enzymes with modification regiospecificity based at the 6'-amino group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics through acetylation of the 6-amino group of the compound.","category_aro_class_name":"AMR Gene Family"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"46128":{"category_aro_accession":"3007378","category_aro_cvterm_id":"46128","category_aro_name":"2'-N-ethylnetilmicin","category_aro_description":"2'-N-ethylnetilmicin is an aminoglycoside antibiotic and a derivative of netilmicin.","category_aro_class_name":"Antibiotic"},"46129":{"category_aro_accession":"3007379","category_aro_cvterm_id":"46129","category_aro_name":"5-episisomicin","category_aro_description":"5-episosomicin is a semisynthetic aminoglycoside antibiotic similar to sisomicin.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"677":{"model_id":"677","model_name":"OXA-171","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1755":{"protein_sequence":{"accession":"ADK35875.1","sequence":"MNKYFTCYVVASLFLSGCTVQHNLINETPSQIVQGHNQVIHQYFDEKNTSGVLVIQTDKKINLYGNALSRANTEYVPASTFKMLNALIGLENQKTDINEIFKWKGEKRSFTAWEKDMTLGEAMKLSAVPVYQELARRIGLDLMQKEVKRIGFGNAEIGQQVDNFWLVGPLKVTPIQEVEFVSQLAHTQLPFSEKVQANVKNMLLLEESNGYKIFGKTGWAMDIKPQVGWLTGWVEQPDGKIVAFALNMEMRSEMPASTRNELLMKSLKQLNII"},"dna_sequence":{"accession":"HM488992.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGAATAAATATTTTACTTGCTATGTGGTTGCTTCTCTTTTTCTTTCTGGTTGTACGGTTCAGCATAATTTAATAAATGAAACCCCGAGTCAGATTGTTCAAGGACATAATCAGGTGATTCATCAATACTTTGATGAAAAAAACACCTCAGGTGTGCTGGTTATTCAAACAGATAAAAAAATTAATCTATATGGTAATGCTCTAAGCCGCGCAAATACAGAATATGTGCCAGCCTCTACATTTAAAATGTTGAATGCCCTGATCGGATTGGAGAACCAGAAAACGGATATTAATGAAATATTTAAATGGAAGGGCGAGAAAAGGTCATTTACCGCTTGGGAAAAAGACATGACACTAGGAGAAGCCATGAAGCTTTCTGCAGTCCCAGTCTATCAGGAACTTGCGCGACGTATCGGTCTTGATCTCATGCAAAAAGAAGTAAAACGTATTGGTTTCGGTAATGCTGAAATTGGACAGCAGGTTGATAATTTCTGGTTGGTAGGACCATTAAAGGTTACGCCTATTCAAGAGGTAGAGTTTGTTTCCCAATTAGCACATACACAGCTTCCATTTAGTGAAAAAGTGCAGGCTAATGTAAAAAATATGCTTCTTTTAGAAGAGAGTAATGGCTACAAAATTTTTGGAAAGACTGGTTGGGCAATGGATATAAAACCACAAGTGGGCTGGTTGACCGGCTGGGTTGAGCAGCCAGATGGAAAAATTGTCGCTTTTGCATTAAATATGGAAATGCGGTCAGAAATGCCGGCATCTACACGTAATGAATTATTGATGAAATCATTAAAACAGCTGAATATTATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001471","ARO_id":"37871","ARO_name":"OXA-171","CARD_short_name":"OXA-171","ARO_description":"OXA-171 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46499":{"category_aro_accession":"3007710","category_aro_cvterm_id":"46499","category_aro_name":"OXA-23-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases, specifically imipenem, derived from OXA-23, first identified in Acinetobacter baumannii.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"678":{"model_id":"678","model_name":"PDC-10","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"1385":{"protein_sequence":{"accession":"ACQ82815.1","sequence":"MRDTRFPCLCGIAASTLLFAATPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"FJ666073.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCGCCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTATGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002509","ARO_id":"38909","ARO_name":"PDC-10","CARD_short_name":"PDC-10","ARO_description":"PDC-10 is a extended-spectrum beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"679":{"model_id":"679","model_name":"SHV-108","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"899":{"protein_sequence":{"accession":"ADR80606.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLAIVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"HM751100.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCATCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTAGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001157","ARO_id":"37537","ARO_name":"SHV-108","CARD_short_name":"SHV-108","ARO_description":"SHV-108 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"680":{"model_id":"680","model_name":"CMY-54","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1036":{"protein_sequence":{"accession":"ADK55604.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHVSPGQLELDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"HM544039.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002065","ARO_id":"38465","ARO_name":"CMY-54","CARD_short_name":"CMY-54","ARO_description":"CMY-54 is a beta-lactamase found in the Enterobacteriaceae family.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"681":{"model_id":"681","model_name":"TEM-120","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1072":{"protein_sequence":{"accession":"AAO85882.1","sequence":"MSIQHFRVALIPFFAAFCFPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGASERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AY243512.1","fmin":"208","fmax":"1069","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCTTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCAGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3000982","ARO_id":"37362","ARO_name":"TEM-120","CARD_short_name":"TEM-120","ARO_description":"TEM-120 is an extended-spectrum beta-lactamase found in Klebsiella oxytoca.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"682":{"model_id":"682","model_name":"QnrS4","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"212":{"protein_sequence":{"accession":"ACJ24509.1","sequence":"METYNHTYRHHNFSHKDLSDLTFTACTFIRSDFRRANLRDTTFVNCKFIEQGDIEGCHFDAADLRDASFQQCQLAMANFSNANCYGIEFRACDLKGANFSRTNFAHQVSNRMYFCSAFISGCNLSYANMERVCLEKCELFENRWIGTNLAGASLKESDLSRGVFSEDVWGQFSLQGANLCHAELDGLDPRKVDTSGIKIAAWQQELILEALGIVVYPD"},"dna_sequence":{"accession":"FJ418153.1","fmin":"0","fmax":"657","strand":"+","sequence":"ATGGAAACCTACAATCATACATATCGGCACCACAACTTTTCACATAAAGACTTAAGTGATCTCACCTTCACCGCTTGCACATTCATTCGCAGCGACTTTCGACGTGCTAACTTGCGTGATACGACATTCGTCAACTGCAAGTTCATTGAACAGGGTGATATCGAAGGCTGCCACTTTGATGCCGCAGATCTTCGTGATGCAAGTTTCCAACAATGCCAACTTGCGATGGCAAACTTCAGTAATGCCAATTGCTACGGTATAGAGTTCCGTGCGTGTGATTTAAAAGGTGCCAACTTTTCCCGAACAAACTTTGCCCATCAAGTGAGTAATCGTATGTACTTTTGCTCAGCATTTATTTCTGGATGTAATCTTTCCTATGCCAATATGGAGAGGGTTTGTTTAGAAAAATGTGAGTTGTTTGAAAATCGCTGGATAGGAACGAACCTAGCGGGTGCATCACTGAAAGAGTCAGACTTAAGTCGAGGTGTTTTTTCCGAAGATGTCTGGGGGCAATTTAGCCTACAGGGTGCCAATTTATGCCACGCCGAACTCGACGGTTTAGATCCCCGCAAAGTCGATACATCAGGTATCAAAATTGCAGCCTGGCAGCAAGAACTGATTCTCGAAGCACTGGGTATTGTTGTTTATCCTGACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35767","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Stanley","NCBI_taxonomy_id":"192953"}}}},"ARO_accession":"3002793","ARO_id":"39227","ARO_name":"QnrS4","CARD_short_name":"QnrS4","ARO_description":"QnrS4 is a plasmid-mediated quinolone resistance protein found in Salmonella enterica.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"683":{"model_id":"683","model_name":"CMY-75","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1587":{"protein_sequence":{"accession":"AFK73434.1","sequence":"MMKKSICCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAIIYEGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWRGISLLHLATYTAGGLPLQIPDDVTDKAELLRFYQNWQPQWTPGAKRLYANSSIGLFGALVVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQSEQKNYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIELAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"JQ733572.1","fmin":"1027","fmax":"2173","strand":"+","sequence":"ATGATGAAAAAATCGATATGCTGCGCGCTGCTGCTGACAGCCTCTTTCTCCACGTTTGCTGCCGCAAAAACAGAACAACAAATTGCCGATATCGTTAACCGCACCATCACACCACTGATGCAGGAGCAGGCTATTCCGGGCATGGCCGTGGCAATTATCTACGAGGGGAAACCTTATTACTTTACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAATTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGACGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCGGGGTATCAGCCTGCTGCACTTAGCCACCTATACAGCGGGTGGCCTGCCGCTGCAGATCCCCGATGACGTTACGGATAAAGCCGAATTACTGCGCTTTTATCAAAACTGGCAACCACAATGGACTCCGGGCGCTAAGCGTCTTTATGCTAACTCCAGCATTGGTCTGTTTGGTGCGCTGGTGGTAAAACCTTCAGGTATGAGCTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAAAGCGAACAAAAAAATTATGCCTGGGGCTATCGCGAAGGGAAGCCTGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATCGATATGGCCCGCTGGGTTCAGGCCAACATGGACGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGAGCTTGCGCAGTCTCGCTACTGGCGTATTGGTGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCAGCACCTGCCGTGAAAGCCTCATGGGTGCATAAAACGGGATCCACAGGTGGATTTGGCAGCTACGTTGCCTTCGTTCCAGAAAAAAACCTTGGCATAGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGCGTCGAGGCGGCCTGGCGCATTCTTGAAAAACTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002088","ARO_id":"38488","ARO_name":"CMY-75","CARD_short_name":"CMY-75","ARO_description":"CMY-75 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"684":{"model_id":"684","model_name":"SHV-37","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1475":{"protein_sequence":{"accession":"AAL82593.1","sequence":"MRYIRLCIISLLAALPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITVSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQHIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AF467948.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCGCCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCGTGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGGGACAATGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCATATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001095","ARO_id":"37475","ARO_name":"SHV-37","CARD_short_name":"SHV-37","ARO_description":"SHV-37 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"685":{"model_id":"685","model_name":"OXA-239","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1529":{"protein_sequence":{"accession":"AFN65709.1","sequence":"MNKYFTCYVVASLFLSGCTVQHNLINETPSQIVQGHNQVIHQYFDEKNTSGVLVIQTDKKINLYGNALSRANTEYVPASTFKMLNALIGLENQKTDINEIFKWKGEKRLFTAWEKDMTLGEAMKLSAVPVYQELARRIGLDLMQKEVKRIGFGNAEIGQQVDNFWLVGPLKVTPIQEVEFVSQLAHTQLPFSEKVQANVKNMLLLEESNGYKIFGKTGWAMNIKSQVGWLTGWVEQPDGKIVAFALNMEMRSEMPASIRNELLMKSLKQLNII"},"dna_sequence":{"accession":"JQ837239.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGAATAAATATTTTACTTGCTATGTGGTTGCTTCTCTTTTTCTTTCTGGTTGTACGGTTCAGCATAATTTAATAAATGAAACCCCGAGTCAGATTGTTCAAGGACATAATCAGGTGATTCATCAATACTTTGATGAAAAAAACACCTCAGGTGTGCTGGTTATTCAAACAGATAAAAAAATTAATCTATATGGTAATGCTCTAAGCCGCGCAAATACAGAATATGTGCCAGCCTCTACATTTAAAATGTTGAATGCCCTGATCGGATTGGAGAACCAGAAAACGGATATTAATGAAATATTTAAATGGAAGGGCGAGAAAAGGTTATTTACCGCTTGGGAAAAAGACATGACACTAGGAGAAGCCATGAAGCTTTCTGCAGTCCCAGTCTATCAGGAACTTGCGCGACGTATCGGTCTTGATCTCATGCAAAAAGAAGTAAAACGTATTGGTTTCGGTAATGCTGAAATTGGACAGCAGGTTGATAATTTCTGGTTGGTAGGACCATTAAAGGTTACGCCTATTCAAGAGGTAGAGTTTGTTTCCCAATTAGCACATACACAGCTTCCATTTAGTGAAAAAGTGCAGGCTAATGTAAAAAATATGCTTCTTTTAGAAGAGAGTAATGGCTACAAAATTTTTGGAAAGACTGGTTGGGCAATGAATATAAAATCACAAGTGGGCTGGTTGACCGGCTGGGTTGAGCAGCCAGATGGAAAAATTGTCGCTTTTGCATTAAATATGGAAATGCGGTCAGAAATGCCGGCATCTATACGTAATGAATTATTGATGAAATCATTAAAACAGCTGAATATTATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39095","NCBI_taxonomy_name":"Acinetobacter sp. enrichment culture clone 8407","NCBI_taxonomy_id":"1182652"}}}},"ARO_accession":"3001498","ARO_id":"37898","ARO_name":"OXA-239","CARD_short_name":"OXA-239","ARO_description":"OXA-239 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46499":{"category_aro_accession":"3007710","category_aro_cvterm_id":"46499","category_aro_name":"OXA-23-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases, specifically imipenem, derived from OXA-23, first identified in Acinetobacter baumannii.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"686":{"model_id":"686","model_name":"OXA-162","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"967":{"protein_sequence":{"accession":"ADG27454.1","sequence":"MRVLALSAVFLVASIIGMPAVAKEWQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGQTRDIATWNRDHNLITAMKYSVVPVYQEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISATEQISFLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYSARIEPKIGWWVGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP"},"dna_sequence":{"accession":"HM015773.1","fmin":"2126","fmax":"2924","strand":"+","sequence":"ATGCGTGTATTAGCCTTATCGGCTGTGTTTTTGGTGGCATCGATTATCGGAATGCCTGCGGTAGCAAAGGAATGGCAAGAAAACAAAAGTTGGAATGCTCACTTTACTGAACATAAATCACAGGGCGTAGTTGTGCTCTGGAATGAGAATAAGCAGCAAGGATTTACCAATAATCTTAAACGGGCGAACCAAGCATTTTTACCCGCATCTACCTTTAAAATTCCCAATAGCTTGATCGCCCTCGATTTGGGCGTGGTTAAGGATGAACACCAAGTCTTTAAGTGGGATGGACAGACGCGCGATATCGCCACTTGGAATCGCGATCATAATCTAATCACCGCGATGAAATATTCAGTTGTGCCTGTTTATCAAGAATTTGCCCGCCAAATTGGCGAGGCACGTATGAGCAAGATGCTACATGCTTTCGATTATGGTAATGAGGACATTTCGGGCAATGTAGACAGTTTCTGGCTCGACGGTGGTATTCGAATTTCGGCCACGGAGCAAATCAGCTTTTTAAGAAAGCTGTATCACAATAAGTTACACGTATCGGAGCGCAGCCAGCGTATTGTCAAACAAGCCATGCTGACCGAAGCCAATGGTGACTATATTATTCGGGCTAAAACTGGATACTCGGCTAGAATCGAACCTAAGATTGGCTGGTGGGTCGGTTGGGTTGAACTTGATGATAATGTGTGGTTTTTTGCGATGAATATGGATATGCCCACATCGGATGGTTTAGGGCTGCGCCAAGCCATCACAAAAGAAGTGCTCAAACAGGAAAAAATTATTCCCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001776","ARO_id":"38176","ARO_name":"OXA-162","CARD_short_name":"OXA-162","ARO_description":"OXA-162 is a beta-lactamase found in Enterobacteriaceae.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46510":{"category_aro_accession":"3007721","category_aro_cvterm_id":"46510","category_aro_name":"OXA-48-like beta-lactamase","category_aro_description":"OXA-48-type beta-lactamases are now routinely encountered in bacterial infections caused by carbapenam-resistant Enterobacterales. OXA-48-like proteins confer resistance to penicillin (which is efficiently hydrolyzed) and carbapenam antibiotics (which is more slowly broken down). The spectrum of activity of these variants varies, with some hydrolyzing expanded-spectrum oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"687":{"model_id":"687","model_name":"APH(3')-Vc","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"470":{"protein_sequence":{"accession":"AAB21326.1","sequence":"MYAMLRRKYQHYEWTSVNEGDSGASVYRLAGQQPELYVKFAPREPENSAFDLAGEADRLTWLTRHGIPVPCIVECGGDDTSVFLVTEAVTGVSAAEEWPEHQRFAVVEAMADLARTLHELPVGGCPFDRSLAVTVAEARHNLREGLVDLDDLQEEHANWSGDQLLAELDRTRPEKEDLVLCHGDLCPNNVLLDPETCRVTGMIDVGRLGRADRHADLALAARELEIDEDPWFGPEYAQRFLERYGAHHVDENKMAFYQLLDEFF"},"dna_sequence":{"accession":"S81599.1","fmin":"281","fmax":"1076","strand":"+","sequence":"ATGTACGCCATGTTGCGCCGGAAATACCAGCACTACGAATGGACCTCCGTGAACGAAGGAGATTCGGGCGCCTCCGTTTACCGCCTCGCCGGACAGCAGCCCGAGCTCTATGTGAAATTCGCTCCGCGCGAACCGGAAAATTCCGCGTTCGACCTGGCGGGCGAGGCCGACCGGCTCACCTGGCTCACCCGCCACGGCATCCCGGTTCCGTGCATTGTCGAGTGCGGCGGCGACGACACCTCGGTTTTCCTCGTCACCGAGGCCGTCACCGGCGTATCGGCCGCCGAGGAGTGGCCGGAGCACCAGCGCTTCGCCGTCGTCGAGGCGATGGCCGACCTCGCCCGCACCCTGCACGAACTGCCCGTTGGTGGCTGCCCCTTCGATCGCAGCCTGGCGGTGACGGTTGCCGAAGCCCGCCACAACCTACGCGAGGGCCTCGTGGACCTGGACGACCTCCAAGAGGAGCACGCCAACTGGTCCGGTGACCAGCTTCTCGCCGAGCTCGACCGAACGCGGCCCGAGAAAGAGGATCTGGTCCTCTGCCACGGGGACCTGTGCCCCAACAACGTGCTGCTCGATCCCGAGACATGCCGAGTCACCGGAATGATCGATGTGGGCCGCCTCGGCCGCGCCGATCGCCACGCCGACCTGGCCCTCGCCGCCCGCGAGCTGGAGATCGACGAGGATCCCTGGTTTGGCCCCGAGTACGCCCAGCGGTTCCTCGAACGCTACGGCGCGCACCACGTCGACGAGAACAAGATGGCCTTTTACCAGCTGCTCGACGAGTTTTTCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39506","NCBI_taxonomy_name":"Micromonospora chalcea","NCBI_taxonomy_id":"1874"}}}},"ARO_accession":"3002651","ARO_id":"39051","ARO_name":"APH(3')-Vc","CARD_short_name":"APH(3')-Vc","ARO_description":"APH(3')-Vc is a chromosomal-encoded aminoglycoside phosphotransferase in M. chalcea.","ARO_category":{"36265":{"category_aro_accession":"3000126","category_aro_cvterm_id":"36265","category_aro_name":"APH(3')","category_aro_description":"A category of aminoglycoside O-phosphotransferase enzymes with modification regiospecificity based at the 3'-hydroxyl group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics, specifically kanamycin and neomycin, by the ATP-dependent phosphorylation of the 3'-hydroxyl group of the compound.","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35940":{"category_aro_accession":"0000021","category_aro_cvterm_id":"35940","category_aro_name":"ribostamycin","category_aro_description":"Ribostamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Ribostamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"37001":{"category_aro_accession":"3000657","category_aro_cvterm_id":"37001","category_aro_name":"paromomycin","category_aro_description":"An aminoglycoside antibiotic used for the treatment of parasitic infections. It is similar to neomycin sharing a similar spectrum of activity, but its hydroxyl group at the 6'-position instead of an amino group makes it resistant to AAC(6') modifying enzymes.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"688":{"model_id":"688","model_name":"MOX-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1039":{"protein_sequence":{"accession":"CAB82578.1","sequence":"MQQRQSILWGALATLMWAGLAHAGETSPVDPLRPVVDASIRPLLKEHRIPGMAVAVLKDGKAHYFNYGVADRERAVGVSEQTLFEIGSVSKPLTATLGAYAVVKGAMQLDDKASRHAPWLKGSAFDSITMGELATYSAGGLPLQFPEEVDSLEKMQAYYRQWTPAYSPGSHRQYSNPSIGLFGHLAASSMKQPFAQLMEQTLLPGLGLHHTYVNVPKQAMASYAYGYSKEDKPIRVSPGMLADEAYGIKTSSADLLRFVKANISGVHDKALQQAISLTHKGHYSVGGMTQGLGWESYAYPVSEQTLLAGNSAKVILEANPTAAPRESGSQMLFNKTGSTSGFGAYVAFVPAKGIGIVMLANRNYPIPARVKAAHAILTQLAR"},"dna_sequence":{"accession":"AJ276453.1","fmin":"4619","fmax":"5768","strand":"+","sequence":"ATGCAACAACGACAATCCATCCTGTGGGGCGCTCTGGCCACCCTGATGTGGGCCGGTCTGGCCCATGCAGGTGAGACTTCACCGGTCGATCCCCTGCGCCCCGTGGTGGATGCCAGCATCCGGCCGCTGCTCAAGGAGCACAGGATCCCGGGCATGGCGGTGGCCGTGCTCAAGGATGGCAAGGCCCACTATTTCAACTACGGTGTGGCCGATCGGGAGCGCGCAGTCGGTGTCAGCGAGCAGACCCTGTTCGAGATAGGCTCCGTGAGCAAGCCCCTGACCGCGACCCTAGGAGCCTATGCGGTGGTCAAGGGAGCGATGCAACTGGATGACAAGGCGAGCCGGCACGCCCCCTGGCTCAAGGGATCCGCCTTTGACAGCATCACCATGGGGGAGCTGGCTACCTACAGCGCGGGCGGCTTGCCGCTGCAATTCCCCGAGGAGGTGGATTCGCTCGAGAAGATGCAGGCCTACTACCGCCAGTGGACCCCAGCCTACTCGCCGGGTTCCCATCGCCAGTACTCTAACCCCAGCATAGGGCTGTTCGGCCACCTGGCGGCGAGCAGCATGAAGCAGCCGTTTGCCCAGTTGATGGAGCAGACGCTCCTGCCGGGGCTTGGCCTGCACCACACCTATGTCAATGTGCCGAAGCAGGCCATGGCGAGTTATGCCTATGGCTATTCGAAAGAGGACAAGCCCATCAGGGTCAGCCCCGGCATGCTGGCGGACGAGGCCTACGGCATCAAGACCAGCTCGGCGGATCTGCTGCGCTTTGTGAAGGCCAACATCAGCGGGGTTCATGACAAGGCGTTGCAGCAGGCCATCTCCCTGACCCACAAAGGGCACTACTCGGTAGGCGGGATGACCCAGGGACTGGGTTGGGAGAGTTACGCCTATCCCGTCAGCGAGCAGACATTGCTGGCGGGCAATTCGGCCAAGGTGATCCTCGAAGCCAATCCGACGGCGGCGCCCCGGGAGTCGGGGAGCCAGATGCTCTTCAACAAGACCGGCTCGACCAGCGGCTTCGGCGCCTATGTGGCCTTCGTGCCGGCCAAAGGGATCGGCATCGTCATGCTGGCCAACCGCAACTATCCTATCCCGGCCAGGGTGAAAGCGGCCCACGCCATCCTGACGCAACTGGCCAGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002183","ARO_id":"38583","ARO_name":"MOX-2","CARD_short_name":"MOX-2","ARO_description":"MOX-2 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36222":{"category_aro_accession":"3000083","category_aro_cvterm_id":"36222","category_aro_name":"MOX beta-lactamase","category_aro_description":"MOX beta-lactamases are plasmid-mediated AmpC-type beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"689":{"model_id":"689","model_name":"CTX-M-123","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1254":{"protein_sequence":{"accession":"AFA51701.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"JN790864.1","fmin":"238","fmax":"1114","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001982","ARO_id":"38382","ARO_name":"CTX-M-123","CARD_short_name":"CTX-M-123","ARO_description":"CTX-M-123 is a beta-lactamase found in Escherichia coli.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"690":{"model_id":"690","model_name":"OXA-347","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4583":{"protein_sequence":{"accession":"AET35493.1","sequence":"MKNILFVVFISMIFLFVCCNTTTNKNIIETEISDFDKILDSFQVNGSILIYDNDKNTFYSNDFDWAKNGKLPASTFKIPNSIIAVELGIIENDTTILKWNGEQRKMDIWEKDLSFKDAFRISCVPCYQEIARKIGTIKMKEYLEKFEYKNMIFDSLTIDNFWLEGNSKISQKQQIDFLRKFYFSKFPISDRTIKIVKNIMEIERTENYILSGKTGLSSIEEKYNGWFVGYVETKSNVYFFATNVIPTDGLNVDDFISSRINVTKNALKQMNIMK"},"dna_sequence":{"accession":"JN086160.1","fmin":"1582","fmax":"2407","strand":"-","sequence":"ATGAAAAATATTTTATTTGTAGTTTTTATTTCAATGATATTTTTATTTGTTTGCTGTAACACAACAACGAATAAAAACATAATTGAAACAGAAATTTCTGATTTTGACAAAATTTTAGATAGTTTTCAAGTAAATGGTTCAATTCTAATTTATGATAACGACAAGAATACTTTTTACTCAAATGACTTTGATTGGGCTAAAAACGGAAAATTACCTGCATCAACATTCAAAATTCCAAATTCTATAATTGCTGTTGAATTAGGCATTATTGAAAATGATACAACTATTTTAAAATGGAATGGCGAGCAGAGAAAAATGGATATTTGGGAAAAAGATTTATCATTTAAAGATGCTTTTAGAATTTCCTGTGTTCCTTGCTATCAGGAAATTGCAAGGAAAATCGGAACAATTAAAATGAAAGAATATTTAGAAAAATTTGAGTATAAAAATATGATTTTTGACAGTTTAACGATTGACAATTTTTGGCTTGAAGGAAATTCAAAAATATCTCAAAAACAACAAATCGACTTTTTAAGGAAATTCTATTTTTCAAAATTTCCAATTTCTGATAGGACAATAAAGATTGTCAAAAATATTATGGAAATTGAGCGAACTGAAAATTACATTTTAAGCGGTAAGACTGGATTAAGTTCGATAGAAGAAAAATATAATGGTTGGTTTGTTGGTTATGTTGAAACAAAATCTAATGTTTATTTTTTTGCAACAAATGTAATTCCGACAGACGGATTGAATGTTGATGATTTTATTTCATCGAGAATTAATGTAACAAAAAATGCGTTAAAGCAAATGAATATAATGAAATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36791","NCBI_taxonomy_name":"uncultured bacterium","NCBI_taxonomy_id":"77133"}}}},"ARO_accession":"3001777","ARO_id":"38177","ARO_name":"OXA-347","CARD_short_name":"OXA-347","ARO_description":"OXA-347 is a beta-lactamase found in Enterobacteriaceae.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"692":{"model_id":"692","model_name":"TEM-159","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1646":{"protein_sequence":{"accession":"ABM54869.1","sequence":"MSIQHFRVALIPFFAAFCFPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMISTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTTPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"EF136376.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCTTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATTAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGACGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3001025","ARO_id":"37405","ARO_name":"TEM-159","CARD_short_name":"TEM-159","ARO_description":"TEM-159 is an inhibitor-resistant beta-lactamase found in Proteus mirabilis.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"693":{"model_id":"693","model_name":"OXA-22","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8222":{"protein_sequence":{"accession":"AAD12233.1","sequence":"MKRRHAAIGALLAALATFAHAEHPICTIVADAATGKAVLHEGKCDERVTPASTFKLALAVMGFDHGFLKDEHTPVEHFRHGDPDWGGEAWHQPIDPALWLKYSVVWYSQRITHAMGAQTFQAYVRKLGYGNMDVSGDPGKNNGMDRSWITSSLKISPEEQVGLMRRIVNRQLPVSAHTYEMLDRTVQTWQVPGGWAVQGKTGTAGPAPGNTSPDGTWDQAHAYGWFVGWARKGDKTYVFANLIQDDKVEPTSGGIRSRDALFARLSEVLAFAGH"},"dna_sequence":{"accession":"AF064820.3","fmin":"951","fmax":"1776","strand":"+","sequence":"ATGAAACGCCGCCACGCCGCCATCGGCGCCCTGCTTGCCGCGCTTGCCACCTTTGCCCACGCCGAGCACCCGATCTGCACGATCGTGGCCGATGCCGCCACGGGCAAGGCCGTCTTGCATGAAGGCAAGTGCGACGAGCGCGTGACGCCCGCTTCCACCTTCAAGCTGGCGCTGGCCGTCATGGGCTTCGACCACGGCTTCCTCAAAGATGAGCACACCCCGGTTGAGCACTTCAGGCACGGTGACCCCGACTGGGGCGGCGAAGCCTGGCACCAGCCGATCGACCCGGCGCTGTGGCTCAAGTATTCGGTGGTCTGGTATTCGCAGCGCATTACGCATGCGATGGGCGCGCAGACCTTCCAGGCCTACGTGCGCAAGCTTGGCTACGGCAACATGGATGTGAGCGGCGATCCGGGCAAGAACAACGGCATGGACCGCTCGTGGATCACCTCGTCGCTGAAGATTTCGCCGGAAGAGCAAGTCGGCTTGATGCGCCGGATCGTCAACCGGCAGTTGCCGGTGTCGGCGCACACCTACGAGATGCTCGACCGTACCGTGCAGACCTGGCAGGTGCCCGGCGGCTGGGCGGTGCAGGGCAAGACGGGCACTGCCGGTCCGGCGCCGGGCAACACGTCGCCCGATGGCACGTGGGATCAGGCACACGCTTACGGCTGGTTTGTCGGCTGGGCCAGGAAGGGCGACAAGACCTACGTATTCGCCAACCTGATCCAGGACGACAAGGTTGAGCCGACGTCGGGCGGTATCCGCTCGCGCGATGCGCTGTTTGCTCGCCTGTCGGAAGTGCTGGCCTTTGCTGGGCACTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36921","NCBI_taxonomy_name":"Ralstonia pickettii","NCBI_taxonomy_id":"329"}}}},"ARO_accession":"3001417","ARO_id":"37817","ARO_name":"OXA-22","CARD_short_name":"OXA-22","ARO_description":"OXA-22 is a beta-lactamase found in Ralstonia pickettii.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46497":{"category_aro_accession":"3007708","category_aro_cvterm_id":"46497","category_aro_name":"OXA-22-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-22.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"694":{"model_id":"694","model_name":"CTX-M-40","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4239":{"protein_sequence":{"accession":"AAV28215.2","sequence":"MRHRVKRMMLMTTACISLLLGSAPLYAQANDVQQKLAALEKSSGGRLGVALIDTADNAQTLYRADERFAMCSTSKVMAAAAVLKQSETQKNVLSQKVEIKSSDLINYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAHLGGPDKVTAFARAIGDDTFRLDRTEPTLNTAIPGDPRDTTTPLAMAQTLRHLTLGSALGETQRAQLVTWLKGNTTGAASIQAGLPTSWVVGDKTGSGDYGTTNDIAVIWPEGRAPLILVTYFTQPEQKAESRRDVLAAAAKIVTDGY"},"dna_sequence":{"accession":"AY750914.2","fmin":"206","fmax":"1079","strand":"+","sequence":"ATGAGACATCGCGTTAAGCGGATGATGCTAATGACAACGGCCTGTATTTCGCTGTTGCTGGGGAGTGCGCCGCTGTATGCGCAGGCGAACGACGTTCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGGGGGCGGTTGGGAGTGGCGCTGATTGACACCGCCGATAACGCACAGACGCTCTACCGCGCCGACGAGCGCTTTGCCATGTGCAGCACCAGTAAGGTGATGGCAGCCGCGGCGGTGCTCAAGCAAAGTGAAACGCAAAAGAACGTGTTGAGTCAGAAGGTTGAGATTAAATCCTCGGACCTGATTAACTACAATCCCATCGCTGAAAAACACGTCAACGGCACGATGACGCTGGCGGAATTGAGCGCCGCGGCGTTGCAGTACAGCGATAATACGGCCATGAACAAGCTGATTGCCCATCTTGGGGGGCCGGATAAAGTGACGGCGTTTGCCCGTGCGATTGGGGATGACACCTTCCGGCTCGATCGTACTGAGCCGACGCTCAACACCGCGATCCCCGGCGACCCGCGCGATACCACCACGCCATTAGCGATGGCGCAGACGCTTCGCCATCTGACGTTGGGCAGTGCCTTAGGTGAAACTCAGCGTGCGCAACTGGTAACGTGGCTGAAAGGCAACACCACCGGTGCTGCCAGCATTCAGGCTGGGCTACCCACATCGTGGGTTGTCGGGGATAAAACCGGCAGCGGTGATTATGGTACGACGAATGACATCGCCGTCATCTGGCCGGAAGGGCGTGCGCCGCTTATTCTGGTCACTTACTTCACCCAACCGGAGCAGAAGGCAGAAAGTCGTCGTGACGTGCTCGCGGCTGCCGCGAAAATCGTCACCGACGGTTATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001902","ARO_id":"38302","ARO_name":"CTX-M-40","CARD_short_name":"CTX-M-40","ARO_description":"CTX-M-40 is a beta-lactamase found in Escherichia coli.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"695":{"model_id":"695","model_name":"CMY-66","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"783":{"protein_sequence":{"accession":"AEZ49849.1","sequence":"MMKKSICCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAIIYEGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWRGISLLHLATYTAGGLPLQIPDDITDKAALLRFYQNWQPQWTPGAKRLYANSSIGLFGALVVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQSEQKNYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASLVQEKTLQQGIELAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPARVEAAWRILEKLQ"},"dna_sequence":{"accession":"JN714478.1","fmin":"1034","fmax":"2180","strand":"+","sequence":"ATGATGAAAAAATCGATATGCTGCGCACTGCTGCTGACAGCCTCTTTCTCCACGTTTGCTGCCGCAAAAACAGAACAACAAATTGCCGATATCGTTAACCGCACCATCACACCACTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTGGCGATTATCTACGAGGGGAAACCTTATTACTTTACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGACGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCGGGGTATCAGCCTGCTGCACTTAGCCACCTATACAGCGGGTGGCCTGCCGCTGCAGATCCCCGATGACATTACGGATAAAGCCGCATTACTGCGCTTTTATCAAAACTGGCAACCACAATGGACTCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGTGCGCTGGTGGTAAAACCTTCAGGTATGAGCTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAAAGCGAACAAAAAAATTATGCCTGGGGCTATCGCGAAGGGAAGCCTGTACACGTTTCTCCGGGGCAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATCGATATGGCCCGCTGGGTTCAGGCCAACATGGACGCCAGCCTCGTTCAGGAGAAAACGCTCCAGCAGGGCATTGAGCTTGCGCAGTCTCGCTACTGGCGTATTGGTGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCAGCACCTGCCGTGAAAGCCTCATGGGTGCATAAAACAGGATCCACAGGCGGATTTGGCAGCTACGTTGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTAATGTTGGCAAACAAAAGCTACCCCAACCCGGCTCGCGTCGAGGCGGCCTGGCGCATTCTTGAAAAACTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002079","ARO_id":"38479","ARO_name":"CMY-66","CARD_short_name":"CMY-66","ARO_description":"CMY-66 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"696":{"model_id":"696","model_name":"cfrA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"4584":{"protein_sequence":{"accession":"CAL64019.1","sequence":"MNFNNKTKYGKIQEFLRSNNEPDYRIKQITNAIFKQRISRFEDMKVLPKLLREDLINNFGETVLNIKLLAEQNSEQVTKVLFEVSKNERVETVNMKYKAGWESFCISSQCGCNFGCKFCATGDIGLKKNLTVDEITDQVLYFHLLGHQIDSISFMGMGEALANRQVFDALDSFTDPNLFALSPRRLSISTIGIIPSIKKITQEYPQVNLTFSLHSPYSEERSKLMPINDRYPIDEVMNILDEHIRLTSRKVYIAYIMLPGVNDSLEHANEVVSLLKSRYKSGKLYHVNLIRYNPTISAPEMYGEANEGQVEAFYKVLKSAGIHVTIRSQFGIDIDAACGQLYGNYQNSQ"},"dna_sequence":{"accession":"AM408573.1","fmin":"10027","fmax":"11077","strand":"-","sequence":"ATGAATTTTAATAATAAAACAAAGTATGGTAAAATACAGGAATTTTTAAGAAGTAATAATGAGCCTGATTATAGAATAAAACAAATAACCAATGCGATTTTTAAACAAAGAATTAGTCGATTTGAGGATATGAAGGTTCTTCCAAAATTACTTAGGGAGGATTTAATAAATAATTTTGGAGAAACAGTTTTGAATATCAAGCTCTTAGCAGAGCAAAATTCAGAGCAAGTTACGAAAGTGCTTTTTGAAGTATCAAAGAATGAGAGAGTAGAAACGGTAAACATGAAGTATAAAGCAGGTTGGGAGTCATTTTGTATATCATCACAATGCGGATGTAATTTTGGGTGTAAATTTTGTGCTACAGGCGACATTGGATTGAAAAAAAACCTAACTGTAGATGAGATAACAGATCAAGTTTTATACTTCCATTTATTAGGTCATCAAATTGATAGCATTTCTTTTATGGGAATGGGTGAAGCTCTAGCCAACCGTCAAGTATTTGATGCTCTTGATTCGTTTACGGATCCTAATTTATTTGCATTAAGTCCTCGTAGACTTTCTATATCAACGATTGGTATTATACCTAGTATCAAAAAAATAACCCAGGAATATCCTCAAGTAAATCTTACATTTTCATTACACTCACCTTATAGTGAGGAACGCAGCAAATTGATGCCAATAAATGATAGATACCCAATAGATGAGGTAATGAATATACTCGATGAACATATAAGATTAACTTCAAGGAAAGTATATATAGCTTATATCATGTTGCCTGGTGTAAATGATTCTCTTGAGCATGCAAACGAAGTTGTTAGCCTTCTTAAAAGTCGCTATAAATCAGGGAAGTTATATCATGTAAATTTGATACGATACAATCCTACAATAAGTGCACCTGAGATGTATGGAGAAGCAAACGAAGGGCAGGTAGAAGCCTTTTACAAAGTTTTGAAGTCTGCTGGTATCCATGTCACAATTAGAAGTCAATTTGGGATTGATATTGACGCTGCTTGTGGTCAATTATATGGTAATTATCAAAATAGCCAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40034","NCBI_taxonomy_name":"Staphylococcus warneri","NCBI_taxonomy_id":"1292"}}}},"ARO_accession":"3003441","ARO_id":"40028","ARO_name":"cfrA","CARD_short_name":"cfrA","ARO_description":"CfrA is a chloramphenicol-florfenicol resistance gene and methyltransferase enzyme. Methylation of position 8 of A2503 in 23S rRNA confers resistance to chloramphenicol antibiotics first identified by Schwarz 2000 as cfr from Mammaliicoccus sciuri. Additional Oxazolidinone resistance mediated by the cfr gene in a human isolated was first reported from Colombia in linezolid- and methicillin-resistant Staphylococcus aureus.","ARO_category":{"36341":{"category_aro_accession":"3000202","category_aro_cvterm_id":"36341","category_aro_name":"Cfr 23S ribosomal RNA methyltransferase","category_aro_description":"Cfr genes produce enzymes which catalyze the methylation of the 23S rRNA subunit at position 8 of adenine-2503. Methylation of 23S rRNA at this site confers resistance to some classes of antibiotics, including streptogramins, chloramphenicols, florfenicols, linezolids and clindamycin.","category_aro_class_name":"AMR Gene Family"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"36521":{"category_aro_accession":"3000382","category_aro_cvterm_id":"36521","category_aro_name":"azidamfenicol","category_aro_description":"Azidamfenicol is a water soluble derivative of chloramphenicol, sharing the same mode of action of inhibiting peptide synthesis by interacting with the 23S RNA of the 50S ribosomal subunit.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36595":{"category_aro_accession":"3000456","category_aro_cvterm_id":"36595","category_aro_name":"thiamphenicol","category_aro_description":"Derivative of Chloramphenicol. The nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3).","category_aro_class_name":"Antibiotic"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"virginiamycin M1","category_aro_description":"Virginiamycin M1 is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37015":{"category_aro_accession":"3000671","category_aro_cvterm_id":"37015","category_aro_name":"tiamulin","category_aro_description":"Tiamulin is a pleuromutilin derivative currently used in veterinary medicine. It binds to the 23 rRNA of the 50S ribosomal subunit to inhibit protein translation.","category_aro_class_name":"Antibiotic"},"37016":{"category_aro_accession":"3000672","category_aro_cvterm_id":"37016","category_aro_name":"madumycin II","category_aro_description":"Madumycin II is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37017":{"category_aro_accession":"3000673","category_aro_cvterm_id":"37017","category_aro_name":"griseoviridin","category_aro_description":"Griseoviridin is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35952":{"category_aro_accession":"0000034","category_aro_cvterm_id":"35952","category_aro_name":"streptogramin A antibiotic","category_aro_description":"Streptogramin A antibiotics are cyclic polyketide peptide hybrids that bind to the ribosomal peptidyl transfer centre. Structural variation arises from substituting a proline for its desaturated derivative and by its substitution for Ala or Cys. Used alone, streptogramin A antibiotics are bacteriostatic, but is bactericidal when used with streptogramin B antibiotics.","category_aro_class_name":"Drug Class"},"36218":{"category_aro_accession":"3000079","category_aro_cvterm_id":"36218","category_aro_name":"oxazolidinone antibiotic","category_aro_description":"Oxazolidinones are a class of synthetic antibiotics discovered the the 1980's.  They inhibit protein synthesis by binding to domain V of the 23S rRNA of the 50S subunit of bacterial ribosomes.  Linezolid is the only member of this class currently in clinical use.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"37014":{"category_aro_accession":"3000670","category_aro_cvterm_id":"37014","category_aro_name":"pleuromutilin antibiotic","category_aro_description":"Pleuromutilins are natural fungal products that target bacterial protein translation by binding the the 23S rRNA, blocking the ribosome P site at the 50S subunit. They are mostly used for agriculture and veterinary purposes.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"697":{"model_id":"697","model_name":"Erm(42)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"11":{"protein_sequence":{"accession":"CBY77552.1","sequence":"MNKNTKIKNKNFNIKDSQNFLHNTKLVEDLLFKSNITKEDFVVEIGPGKGIITKALSKICKAVNAIEFDSVLADKLSHEFKSSNVSIIEADFLKYNLPDHNYKVFSNIPFNITASILNKLLDSENPPLDTFLIMQYEPFLKYAGAPSYKESYKSLLYKPFFKTNILHSFSKFDFKPAPNANIILGQFSYKDFTDINLEDRHAWKDFLAFVFLEKGVTFKEKTKRIFSYKQQKIILKESRINDDSNISNWSYEFWLKMFKLYNSNMVSKDKKVLVNNSYKRMLEHESSLEKIHRNRKQNNRK"},"dna_sequence":{"accession":"FR734406.1","fmin":"0","fmax":"906","strand":"+","sequence":"ATGAATAAAAACACTAAAATAAAAAACAAAAATTTCAACATTAAAGACTCACAGAATTTTTTGCATAATACTAAATTAGTCGAAGATTTGCTTTTTAAAAGCAATATAACTAAGGAGGATTTTGTTGTTGAGATTGGGCCTGGAAAAGGCATAATAACCAAGGCATTAAGCAAAATCTGCAAAGCCGTTAATGCTATTGAGTTCGATAGTGTATTGGCTGATAAGTTGAGCCATGAATTTAAAAGTTCAAATGTGTCTATTATTGAAGCCGATTTTTTAAAATACAATTTACCAGACCATAATTATAAAGTTTTTTCAAACATTCCATTTAACATAACGGCAAGTATTTTAAATAAATTGTTAGATAGTGAGAACCCACCCTTAGATACTTTTTTAATTATGCAATATGAACCTTTTTTAAAGTATGCGGGTGCACCATCTTACAAGGAGTCTTATAAATCTTTATTATATAAACCATTTTTCAAAACTAACATATTGCATAGCTTTAGCAAATTTGATTTTAAGCCAGCTCCAAACGCAAACATTATTTTGGGCCAATTTTCTTATAAAGACTTTACAGATATAAACCTTGAAGACAGGCATGCTTGGAAAGATTTTTTAGCCTTTGTCTTTTTAGAAAAGGGAGTTACATTTAAAGAAAAAACAAAACGAATTTTTAGTTATAAGCAACAAAAAATAATTTTAAAAGAAAGCCGAATTAATGATGATTCAAATATAAGTAATTGGAGTTATGAATTTTGGCTAAAAATGTTTAAACTCTATAATTCGAACATGGTAAGCAAGGATAAAAAAGTTTTAGTTAACAATTCGTATAAAAGAATGTTAGAACATGAGTCTAGTTTAGAAAAGATTCATAGAAATAGAAAGCAAAATAACAGAAAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36867","NCBI_taxonomy_name":"Pasteurella multocida","NCBI_taxonomy_id":"747"}}}},"ARO_accession":"3003106","ARO_id":"39680","ARO_name":"Erm(42)","CARD_short_name":"Erm(42)","ARO_description":"Erm42 confers MLSb phenotype in Pasteurella multocida.","ARO_category":{"36699":{"category_aro_accession":"3000560","category_aro_cvterm_id":"36699","category_aro_name":"Erm 23S ribosomal RNA methyltransferase","category_aro_description":"Erm proteins are part of the RNA methyltransferase family and methylate A2058 (E. coli nomenclature) of the 23S ribosomal RNA conferring degrees of resistance to Macrolides, Lincosamides and Streptogramin b. This is called the MLSb phenotype.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"698":{"model_id":"698","model_name":"TEM-205","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1957":{"protein_sequence":{"accession":"AGZ20205.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRIDAGQEQLGRRIHYSQNDLVKYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDSWEPELNEAIPNDERDTTTPVAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"KC900516.1","fmin":"0","fmax":"858","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTATTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTAAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACGCGCCTTGATAGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGACGCCTGTAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGG","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3001382","ARO_id":"37782","ARO_name":"TEM-205","CARD_short_name":"TEM-205","ARO_description":"TEM-205 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"699":{"model_id":"699","model_name":"QnrS9","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"632":{"protein_sequence":{"accession":"AHF20043.1","sequence":"METYNHTYRHHNFSHKDLSDLTFTACTFIRSDFRRANLRDTTFVNCKFIEQGDIEGCHFDVADLRDASFQQCQLAMANFSNANCYGIEFRACDLKGANFFRTNFAHQVSNRMYFCSAFISGCNLSYANMERVCLEKCELFENRWIGTNLAGASLKESDLSRGVFSEDVWGQFSLQGANLCHAELDGLDPRKVDTSGIKIAAWQQELILEALGIVVYPD"},"dna_sequence":{"accession":"KF732714.1","fmin":"0","fmax":"657","strand":"+","sequence":"ATGGAAACCTACAATCATACATATCGGCACCACAACTTTTCACATAAAGACTTAAGTGATCTCACCTTCACCGCTTGCACATTCATTCGCAGCGACTTTCGACGTGCTAACTTGCGTGATACGACATTCGTCAACTGCAAGTTCATTGAACAGGGTGATATCGAAGGCTGCCACTTTGATGTCGCAGATCTTCGTGATGCAAGTTTCCAACAATGCCAACTTGCGATGGCAAACTTCAGTAATGCCAATTGCTACGGTATAGAGTTCCGTGCGTGTGATTTAAAAGGTGCCAACTTTTTCCGAACAAACTTTGCCCATCAAGTGAGTAATCGTATGTACTTTTGCTCAGCATTTATTTCTGGATGTAATCTTTCCTATGCCAATATGGAGAGGGTTTGTTTAGAAAAATGTGAGTTGTTTGAAAATCGCTGGATAGGAACGAACCTAGCGGGTGCATCACTGAAAGAGTCAGACTTAAGTCGAGGTGTTTTTTCCGAAGATGTCTGGGGGCAATTTAGCCTACAGGGTGCCAATTTATGCCACGCCGAACTCGACGGTTTAGATCCCCGCAAAGTCGATACATCAGGTATCAAAATTGCAGCCTGGCAGCAAGAACTGATTCTCGAAGCACTGGGTATTGTTGTTTATCCTGACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002798","ARO_id":"39232","ARO_name":"QnrS9","CARD_short_name":"QnrS9","ARO_description":"QnrS9 is a plasmid-mediated quinolone resistance protein found in Klebsiella pneumoniae.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"700":{"model_id":"700","model_name":"ACT-31","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1342":{"protein_sequence":{"accession":"AIT76096.1","sequence":"MMKKSLCCALLLGLSCSALAAPVSEKQLAEVVANTVTPLMKAQSVPGMAVAVIYQGKSHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMPYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPEKVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVVEGSDSKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANKSYPNPARVEAAYHILDALQ"},"dna_sequence":{"accession":"KM087843.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCTCTTTGCTGCGCCCTGCTGCTGGGCCTCTCTTGCTCTGCTCTCGCCGCGCCAGTATCAGAAAAACAGCTGGCGGAGGTGGTCGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCTGTTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGAAAATCGCACTATTACACGTTTGGCAAGGCCGATATCGCGGCGAATAAACCCGTTACGCCTCAGACCCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGCGTTTTAGGTGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTGACAGGCAAGCAGTGGCAGGGTATTCGTATGCTGGATCTCGCCACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGCGCGCTGGCGGTCAAACCTTCTGGCATGCCCTATGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTTCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTTCGCGTTTCGCCGGGAATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCGGAGAAGGTTGCCGATGCCTCACTTAAGCAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGGTCGAAGGCAGCGACAGTAAGGTAGCGCTGGCGCCGTTACCCGTGGCAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGTTCTACTGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATAAAAGCTACCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCGACGCGCTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3001851","ARO_id":"38251","ARO_name":"ACT-31","CARD_short_name":"ACT-31","ARO_description":"ACT-31 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"701":{"model_id":"701","model_name":"SHV-129","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"986":{"protein_sequence":{"accession":"ADE08533.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGASKRGARGIVALLGPNNKAERIVVIYLRDTPASMAELDQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"GU827715.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTAGCAAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCTCGATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001176","ARO_id":"37556","ARO_name":"SHV-129","CARD_short_name":"SHV-129","ARO_description":"SHV-129 is an extended-spectrum beta-lactamase that has been found in clinical isolates.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"702":{"model_id":"702","model_name":"CTX-M-98","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1030":{"protein_sequence":{"accession":"ADO17948.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAVAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGGYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"HM755448.1","fmin":"244","fmax":"1120","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGTCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGGCTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001957","ARO_id":"38357","ARO_name":"CTX-M-98","CARD_short_name":"CTX-M-98","ARO_description":"CTX-M-98 is a beta-lactamase found in Escherichia coli.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"703":{"model_id":"703","model_name":"cmlv","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"82":{"protein_sequence":{"accession":"AAB36568.1","sequence":"MPSPSAEPTTSTPTPDAGPAASPRMPLAVYILGLSAFALGTSEFMLSGLVPPIAEDMNVSIPRAGLLISAFAIGMVVGAPLLAVATLRLPRKTTLIALITVFGLRQMAGALAPNYAVLFASRVISALPCAGFWAVGAAVAIAMVPVGSRARALAVMIGGLSIANVLRVPAGAFLGEHLGWASAFWAVGLASAIALVGVVTRIPRIPLPETRPRPLKNEVAIYRDRQVLLSIAVTALAAGGVFCAFSYLAPLLTDVSGLDEAWVSGVLGLFGIGAVVGTTIGGRVADAHLFGVLLTGISASTVFLVALALFASNPAATIVLTFLLGVSAFYTAPALNARMFNVAGAAPTLAGATTTAAFNLGNTGGPWLGGTVIDANLGFASTAWAGAAMTVLGLGTAALALRLTKRPAPGHVVARSRGAGGTTPSEPARGKATSSC"},"dna_sequence":{"accession":"U09991.1","fmin":"27","fmax":"1338","strand":"+","sequence":"ATGCCGTCTCCCTCCGCCGAGCCCACGACATCCACCCCGACCCCCGACGCCGGGCCCGCCGCATCCCCCCGGATGCCCCTGGCCGTCTACATCCTCGGACTGTCCGCGTTCGCGCTCGGGACGAGCGAATTCATGCTCTCCGGCCTCGTGCCGCCCATCGCGGAGGACATGAACGTCTCCATCCCCCGCGCCGGACTCCTCATCTCGGCGTTCGCGATCGGCATGGTCGTCGGCGCACCGCTCCTCGCCGTCGCCACCCTCCGGCTCCCCCGCAAGACCACCCTCATCGCCCTCATCACCGTCTTCGGCCTGCGCCAGATGGCCGGCGCCCTCGCCCCCAACTACGCGGTCCTCTTCGCCTCCCGCGTGATCAGCGCCCTGCCCTGCGCGGGCTTCTGGGCGGTCGGCGCGGCGGTGGCCATCGCGATGGTCCCGGTCGGCTCACGGGCCCGGGCGCTGGCGGTCATGATCGGCGGCCTCTCCATCGCCAACGTCCTGCGCGTCCCCGCCGGCGCCTTCCTCGGCGAGCACCTCGGCTGGGCCTCCGCCTTCTGGGCCGTCGGCCTCGCCTCCGCCATCGCGCTCGTCGGCGTCGTCACCCGCATCCCCCGCATCCCGCTCCCCGAGACCAGGCCCCGCCCTCTCAAGAACGAGGTCGCCATCTACCGCGACCGCCAGGTCCTCCTGTCGATCGCGGTCACGGCCCTCGCGGCGGGCGGCGTCTTCTGCGCCTTCTCGTACCTCGCGCCGCTGCTCACCGACGTCTCCGGCCTCGACGAGGCCTGGGTCTCCGGCGTCCTCGGCCTCTTCGGCATCGGCGCCGTCGTCGGTACGACGATCGGCGGCCGGGTCGCCGACGCGCACCTCTTCGGCGTGCTGCTCACCGGCATCTCCGCCTCCACCGTCTTCCTCGTGGCCCTGGCCCTGTTCGCCTCGAACCCGGCCGCCACGATCGTGCTGACCTTCCTCCTCGGCGTCTCGGCCTTCTACACGGCCCCGGCCCTCAACGCCCGCATGTTCAACGTCGCCGGCGCCGCCCCCACCCTCGCGGGCGCCACCACCACCGCCGCCTTCAACCTCGGCAACACGGGCGGCCCCTGGCTCGGCGGCACGGTCATCGACGCGAACCTCGGCTTCGCCTCGACGGCCTGGGCGGGCGCGGCGATGACGGTCCTGGGCCTGGGAACGGCGGCCCTGGCCCTCCGCCTGACCAAGCGCCCGGCCCCCGGCCACGTGGTCGCCCGGAGCAGAGGGGCGGGCGGGACCACCCCGTCCGAACCGGCCAGGGGGAAGGCCACGTCGAGCTGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36896","NCBI_taxonomy_name":"Streptomyces venezuelae ATCC 10712","NCBI_taxonomy_id":"953739"}}}},"ARO_accession":"3002700","ARO_id":"39134","ARO_name":"cmlv","CARD_short_name":"cmlv","ARO_description":"cmlv is a chromosome-encoded chloramphenicol phoshotransferase that is found in Streptomyces venezuelae.","ARO_category":{"36388":{"category_aro_accession":"3000249","category_aro_cvterm_id":"36388","category_aro_name":"chloramphenicol phosphotransferase","category_aro_description":"ATP-dependent kinase modifies the C-3 hydroxyl group of chloramphenicol.  Source is the chloramphenicol producer Streptomyces venezuelae.","category_aro_class_name":"AMR Gene Family"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"705":{"model_id":"705","model_name":"CMY-116","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1098":{"protein_sequence":{"accession":"AIT76093.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAIIYEGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWRGISLLHLATYTAGGLPLQIPDDITDKAALLRFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQSEQKNYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIELAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPVPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"KM087840.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCACTGCTGCTGACAGCCTCTTTCTCCACGTTTGCTGCCGCAAAAACAGAACAACAAATTGCCGATATCGTTAACCGCACCATCACACCACTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTGGCGATTATCTACGAGGGGAAACCTTATTACTTTACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGACGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCGGGGTATCAGCCTGCTGCACTTAGCCACCTATACAGCGGGTGGCCTGCCGCTGCAGATCCCCGATGACATTACGGATAAAGCCGCATTACTGCGCTTTTATCAAAACTGGCAACCACAATGGACTCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGTGCGCTAGCGGTGAAACCTTCAGGTATGAGCTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAAAGCGAACAAAAAAACTATGCCTGGGGCTATCGCGAAGGGAAGCCTGTGCACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATCGATATGGCCCGCTGGGTTCAGGCCAACATGGACGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGAGCTTGCGCAGTCTCGCTACTGGCGTATTGGTGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCAGTACCTGCCGTGAAAGCCTCATGGGTGCATAAAACGGGATCCACAGGTGGATTTGGCAGCTACGTTGCCTTCGTTCCAGAAAAAAACCTTGGCATAGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGCGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002127","ARO_id":"38527","ARO_name":"CMY-116","CARD_short_name":"CMY-116","ARO_description":"CMY-116 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"706":{"model_id":"706","model_name":"APH(7'')-Ia","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"600":{"protein_sequence":{"accession":"CAA27276.1","sequence":"MTQESLLLLDRIDSDDSYASLRNDQEFWEPLARRALEELGLPVPPVLRVPGESTNPVLVGEPDPVIKLFGEHWCGPESLASESEAYAVLADAPVPVPRLLGRGELRPGTGAWPWPYLVMSRMTGTTWRSAMDGTTDRNALLALARELGRVLGRLHRVPLTGNTVLTPHSEVFPELLRERRAATVEDHRGWGYLSPRLLDRLEDWLPDVDTLLAGREPRFVHGDLHGTNIFVDLAATEVTGIVDFTDVYAGDSRYSLVQLHLNAFRGDREILAALLDGAQWKRTEDFARELLAFTFLHDFEVFEETPLDLSGFTDPEELAQFLWGPPDTAPGA"},"dna_sequence":{"accession":"X03615.1","fmin":"231","fmax":"1230","strand":"+","sequence":"GTGACACAAGAATCCCTGTTACTTCTCGACCGTATTGATTCGGATGATTCCTACGCGAGCCTGCGGAACGACCAGGAATTCTGGGAGCCGCTGGCCCGCCGAGCCCTGGAGGAGCTCGGGCTGCCGGTGCCGCCGGTGCTGCGGGTGCCCGGCGAGAGCACCAACCCCGTACTGGTCGGCGAGCCCGACCCGGTGATCAAGCTGTTCGGCGAGCACTGGTGCGGTCCGGAGAGCCTCGCGTCGGAGTCGGAGGCGTACGCGGTCCTGGCGGACGCCCCGGTGCCGGTGCCCCGCCTCCTCGGCCGCGGCGAGCTGCGGCCCGGCACCGGAGCCTGGCCGTGGCCCTACCTGGTGATGAGCCGGATGACCGGCACCACCTGGCGGTCCGCGATGGACGGCACGACCGACCGGAACGCGCTGCTCGCCCTGGCCCGCGAACTCGGCCGGGTGCTCGGCCGGCTGCACAGGGTGCCGCTGACCGGGAACACCGTGCTCACCCCCCATTCCGAGGTCTTCCCGGAACTGCTGCGGGAACGCCGCGCGGCGACCGTCGAGGACCACCGCGGGTGGGGCTACCTCTCGCCCCGGCTGCTGGACCGCCTGGAGGACTGGCTGCCGGACGTGGACACGCTGCTGGCCGGCCGCGAACCCCGGTTCGTCCACGGCGACCTGCACGGGACCAACATCTTCGTGGACCTGGCCGCGACCGAGGTCACCGGGATCGTCGACTTCACCGACGTCTATGCGGGAGACTCCCGCTACAGCCTGGTGCAACTGCATCTCAACGCCTTCCGGGGCGACCGCGAGATCCTGGCCGCGCTGCTCGACGGGGCGCAGTGGAAGCGGACCGAGGACTTCGCCCGCGAACTGCTCGCCTTCACCTTCCTGCACGACTTCGAGGTGTTCGAGGAGACCCCGCTGGATCTCTCCGGCTTCACCGATCCGGAGGAACTGGCGCAGTTCCTCTGGGGGCCGCCGGACACCGCCCCCGGCGCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36900","NCBI_taxonomy_name":"Streptomyces hygroscopicus","NCBI_taxonomy_id":"1912"}}}},"ARO_accession":"3002661","ARO_id":"39061","ARO_name":"APH(7'')-Ia","CARD_short_name":"APH(7'')-Ia","ARO_description":"APH(7'')-Ia is a chromosomal-encoded aminoglycoside phosphotransferase in S. hygroscopicus.","ARO_category":{"36293":{"category_aro_accession":"3000154","category_aro_cvterm_id":"36293","category_aro_name":"APH(7'')","category_aro_description":"A category of aminoglycoside O-phosphotransferase enzymes with modification regiospecificity based at the 7''-hydroxyl group of the respective antibiotic. These enzymes are characterized by enzymatic antibiotic inactivation, specifically of hygromycin, by the ATP-dependent phosphorylation of the 7''-hydroxyl group of the compound.","category_aro_class_name":"AMR Gene Family"},"36353":{"category_aro_accession":"3000214","category_aro_cvterm_id":"36353","category_aro_name":"hygromycin B","category_aro_description":"Hygromycin B is an aminoglycoside antibiotic used to treat different types of bacterial infections. Hygromycin B works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Hygromycin B has also been shown to interact with eukaryotic cells.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"707":{"model_id":"707","model_name":"AIM-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1033":{"protein_sequence":{"accession":"CAQ53840.1","sequence":"MKRRFTLLGSVVALALSSTALASDAPASRGCADDAGWNDPAMPLKVYGNTWYVGTCGISALLVTSDAGHILVDAATPQAGPQILANIRALGFRPEDVRAIVFSHEHFDHAGSLAELQKATGAPVYARAPAIDTLKRGLPDRTDPQFEVAEPVAPVANIVTLADDGVVSVGPLALTAVASPGHTPGGTSWTWRSCEGDDCRQMVYADSLTAISDDVFRYSDDAAHPGYLAAFRNTLARVAALDCDILVTPHPSASGLWNRIGPRAAAPLMDTTACRRYAQGARQRLEKRLAEEAATSPSSGARP"},"dna_sequence":{"accession":"AM998375.1","fmin":"1172","fmax":"2084","strand":"+","sequence":"ATGAAACGTCGCTTCACCCTGCTGGGCAGCGTAGTCGCCCTCGCCCTCTCATCCACAGCCCTCGCCTCCGATGCGCCCGCCTCCAGGGGCTGCGCCGACGATGCCGGCTGGAACGATCCGGCAATGCCCCTGAAGGTGTACGGAAACACCTGGTACGTTGGCACCTGCGGCATCAGTGCGCTGCTGGTCACTTCCGACGCGGGCCATATCCTGGTCGATGCCGCCACGCCGCAGGCGGGCCCACAGATCCTGGCCAACATCCGCGCACTCGGTTTCAGGCCGGAGGACGTGCGCGCCATCGTGTTCTCGCACGAGCATTTCGACCATGCCGGCAGCCTCGCCGAACTGCAGAAGGCCACGGGTGCACCGGTGTACGCGCGCGCGCCCGCGATCGACACGCTGAAGCGCGGCCTGCCGGACCGCACCGACCCGCAATTCGAGGTGGCCGAACCCGTTGCGCCGGTCGCCAACATCGTCACCCTGGCCGACGACGGCGTGGTGAGCGTCGGCCCGCTGGCCCTGACGGCGGTCGCCTCGCCTGGCCACACCCCGGGTGGCACCAGTTGGACCTGGCGCTCCTGCGAAGGCGACGACTGTCGCCAGATGGTCTACGCCGACAGCCTGACGGCGATCTCGGACGACGTCTTCCGCTACAGCGACGACGCCGCGCATCCCGGCTACCTGGCGGCATTCCGCAACACCCTCGCACGGGTCGCAGCGCTCGACTGCGACATCCTGGTCACCCCGCACCCCTCGGCCAGCGGCCTGTGGAACCGGATCGGCCCGAGGGCCGCCGCACCGCTGATGGACACCACCGCCTGCCGCCGCTACGCGCAGGGCGCGAGGCAGCGGCTGGAGAAGCGCCTGGCCGAGGAAGCCGCCACCTCCCCCTCCAGCGGCGCGCGGCCTTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3000853","ARO_id":"37233","ARO_name":"AIM-1","CARD_short_name":"AIM-1","ARO_description":"AIM-1 is an Ambler class B beta-lactamase that hydrolyzes most beta-lactams except aztreonam and ceftazidime. It was isolated from Pseudomonas aeruginosa and was the first subclass B3 mobile-elements encoded beta-lactamase discovered.","ARO_category":{"41380":{"category_aro_accession":"3004216","category_aro_cvterm_id":"41380","category_aro_name":"AIM beta-lactamase","category_aro_description":"A subclass B3 family of beta-lactamases that confer resistance to a range of beta-lactam antibiotics including penams, cephamycins, and cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"708":{"model_id":"708","model_name":"CTX-M-49","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1010":{"protein_sequence":{"accession":"AAV97954.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGRRLGVPLIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"AY847145.1","fmin":"81","fmax":"957","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAAGGCGGCTGGGCGTCCCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGACTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001911","ARO_id":"38311","ARO_name":"CTX-M-49","CARD_short_name":"CTX-M-49","ARO_description":"CTX-M-49 is a beta-lactamase found in the Enterobacteriaceae family.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"709":{"model_id":"709","model_name":"TEM-213","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1246":{"protein_sequence":{"accession":"AHA58207.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEFSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"KF663615.1","fmin":"0","fmax":"858","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTTCTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACGCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGG","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3001390","ARO_id":"37790","ARO_name":"TEM-213","CARD_short_name":"TEM-213","ARO_description":"TEM-213 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"710":{"model_id":"710","model_name":"dfrB6","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"150"}},"model_sequences":{"sequence":{"430":{"protein_sequence":{"accession":"ADO00942.1","sequence":"MDQGSNEVINPVAGQFASPSNATFGMGDRVRKKSGAAWQGQIVGWYSTKLTPEGYAVESEAHPGSVQIYPVAALERVN"},"dna_sequence":{"accession":"GU060319.1","fmin":"624","fmax":"861","strand":"+","sequence":"ATGGACCAAGGTAGCAATGAAGTCATTAATCCAGTCGCTGGCCAGTTTGCGTCCCCATCGAACGCCACGTTTGGTATGGGAGATCGCGTGCGCAAGAAATCTGGCGCCGCCTGGCAAGGTCAGATTGTCGGGTGGTACAGCACAAAGTTGACCCCTGAAGGCTACGCTGTCGAGTCTGAGGCTCACCCTGGCTCGGTGCAGATTTATCCTGTTGCCGCGCTTGAACGCGTCAACTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36791","NCBI_taxonomy_name":"uncultured bacterium","NCBI_taxonomy_id":"77133"}}}},"ARO_accession":"3003023","ARO_id":"39457","ARO_name":"dfrB6","CARD_short_name":"dfrB6","ARO_description":"dfrB6 is an integron-encoded dihydrofolate reductase found in Salmonella enterica.","ARO_category":{"37617":{"category_aro_accession":"3001218","category_aro_cvterm_id":"37617","category_aro_name":"trimethoprim resistant dihydrofolate reductase dfr","category_aro_description":"Alternative dihydropteroate synthase dfr present on plasmids produces alternate proteins that are less sensitive to trimethoprim from inhibiting its role in folate synthesis, thus conferring trimethoprim resistance.","category_aro_class_name":"AMR Gene Family"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"711":{"model_id":"711","model_name":"SHV-62","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"8207":{"protein_sequence":{"accession":"CAI30651.2","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKYLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AJ866285.2","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAATACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCAGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001117","ARO_id":"37497","ARO_name":"SHV-62","CARD_short_name":"SHV-62","ARO_description":"SHV-62 is a broad-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"712":{"model_id":"712","model_name":"catB2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"5222":{"protein_sequence":{"accession":"AAP15294.1","sequence":"MTNYFESPFKGKLLTEQVKNPNIKVGRYSYYSGYYHGHSFDDCARYLLPDRDDVDQLIIGSFCSIGSGAAFIMAGNQGHRYDWVSSFPFFYMNEEPAFAKSVDAFQRAGDTVIGSDVWIGSEAMIMPGIKIGHGAVIGSRALVTKDVEPYTIVGGNPAKSIRKRFSEEEISMLLDMAWWDWPLEQIKEAMPFLCSSGIASLYRRWQGTSA"},"dna_sequence":{"accession":"AY232670.1","fmin":"3524","fmax":"4157","strand":"-","sequence":"ATGACGAATTATTTTGAGAGTCCCTTCAAAGGGAAGCTTCTGACTGAGCAGGTGAAGAATCCGAACATCAAGGTAGGGCGGTATAGCTACTATTCCGGCTATTACCATGGGCACTCGTTTGATGATTGTGCTCGCTACCTTCTACCAGACCGTGATGACGTTGATCAGCTGATTATCGGCAGCTTCTGCTCCATCGGATCAGGCGCAGCTTTTATTATGGCTGGGAATCAAGGCCACCGATATGATTGGGTCTCTTCTTTCCCTTTCTTCTACATGAACGAGGAGCCCGCGTTTGCAAAATCAGTCGATGCATTCCAGCGGGCTGGCGACACAGTTATAGGAAGTGATGTGTGGATCGGTTCGGAGGCCATGATCATGCCCGGGATCAAGATCGGGCATGGAGCGGTGATAGGTAGCCGCGCTTTGGTTACCAAAGACGTGGAACCCTACACCATAGTGGGGGGAAACCCTGCAAAGTCGATTAGGAAGCGCTTTTCTGAAGAAGAAATTTCTATGCTTTTAGATATGGCTTGGTGGGATTGGCCGCTGGAACAAATCAAGGAAGCAATGCCTTTTCTTTGTTCGTCTGGCATTGCCAGCCTGTATCGTCGCTGGCAAGGCACAAGCGCCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36867","NCBI_taxonomy_name":"Pasteurella multocida","NCBI_taxonomy_id":"747"}}}},"ARO_accession":"3002675","ARO_id":"39109","ARO_name":"catB2","CARD_short_name":"catB2","ARO_description":"catB2 is a plasmid-encoded variant of the cat gene found in Escherichia coli, Salmonella enteritidis and Pasteurella multocida.","ARO_category":{"36261":{"category_aro_accession":"3000122","category_aro_cvterm_id":"36261","category_aro_name":"chloramphenicol acetyltransferase (CAT)","category_aro_description":"Inactivates chloramphenicol by addition of an acyl group. CAT is used to describe many variants of the chloramphenicol acetyltransferase gene in a range of organisms including Acinetobacter calcoaceticus, Agrobacterium tumefaciens, Alkalihalobacillus clausii, Bacillus subtilis, Campylobacter coli, Enterococcus faecalis, Enterococcus faecium, Lactococcus lactis, Listeria monocytogenes, Listonella anguillarum, Morganella morganii, Photobacterium damselae subsp. piscicida, Proteus mirabilis, Salmonella typhi, Serratia marcescens, Shigella flexneri, Staphylococcus aureus, Staphylococcus haemolyticus, Staphylococcus intermedius, Streptococcus agalactiae, Streptococcus suis and Streptomyces acrimycini.","category_aro_class_name":"AMR Gene Family"},"36521":{"category_aro_accession":"3000382","category_aro_cvterm_id":"36521","category_aro_name":"azidamfenicol","category_aro_description":"Azidamfenicol is a water soluble derivative of chloramphenicol, sharing the same mode of action of inhibiting peptide synthesis by interacting with the 23S RNA of the 50S ribosomal subunit.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36595":{"category_aro_accession":"3000456","category_aro_cvterm_id":"36595","category_aro_name":"thiamphenicol","category_aro_description":"Derivative of Chloramphenicol. The nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3).","category_aro_class_name":"Antibiotic"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"713":{"model_id":"713","model_name":"CTX-M-81","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8133":{"protein_sequence":{"accession":"ABV57756.3","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLEQSETQKQLLNQPVEIQPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDHTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"EU136031.3","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTGAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCCAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACCATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACCATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGACTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001942","ARO_id":"38342","ARO_name":"CTX-M-81","CARD_short_name":"CTX-M-81","ARO_description":"CTX-M-81 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"714":{"model_id":"714","model_name":"dfrB1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"175"}},"model_sequences":{"sequence":{"6212":{"protein_sequence":{"accession":"AAA82255.1","sequence":"MERSSNEVSNPVAGNFVFPSNATFGMGDRVRKKSGAAWQGQIVGWYCTNLTPEGYAVESEAHPGSVQIYPVAALERIN"},"dna_sequence":{"accession":"U36276.1","fmin":"716","fmax":"953","strand":"+","sequence":"ATGGAACGAAGTAGCAATGAAGTCAGTAATCCAGTTGCTGGCAATTTTGTATTCCCATCGAACGCCACGTTTGGTATGGGAGATCGCGTGCGCAAGAAATCCGGCGCCGCCTGGCAAGGTCAGATTGTCGGGTGGTACTGCACAAATTTGACCCCCGAAGGCTACGCCGTCGAGTCTGAGGCTCACCCAGGCTCAGTACAGATTTATCCTGTTGCGGCGCTTGAACGCATCAACTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002864","ARO_id":"39298","ARO_name":"dfrB1","CARD_short_name":"dfrB1","ARO_description":"A plasmid-associated trimethoprim-resistant dihydrofolate reductase detected in Bordetella bronchispetica on pKBB958.","ARO_category":{"37617":{"category_aro_accession":"3001218","category_aro_cvterm_id":"37617","category_aro_name":"trimethoprim resistant dihydrofolate reductase dfr","category_aro_description":"Alternative dihydropteroate synthase dfr present on plasmids produces alternate proteins that are less sensitive to trimethoprim from inhibiting its role in folate synthesis, thus conferring trimethoprim resistance.","category_aro_class_name":"AMR Gene Family"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"715":{"model_id":"715","model_name":"PDC-3","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"1541":{"protein_sequence":{"accession":"ACQ82808.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"FJ666066.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTATGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002500","ARO_id":"38900","ARO_name":"PDC-3","CARD_short_name":"PDC-3","ARO_description":"PDC-3 is a extended-spectrum beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35927":{"category_aro_accession":"0000008","category_aro_cvterm_id":"35927","category_aro_name":"cefoxitin","category_aro_description":"Cefoxitin is a cephamycin antibiotic often grouped with the second generation cephalosporins. Cefoxitin is bactericidal and acts by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. Cefoxitin's 7-alpha-methoxy group and 3' leaving group make it a poor substrate for most beta-lactamases.","category_aro_class_name":"Antibiotic"},"35975":{"category_aro_accession":"0000058","category_aro_cvterm_id":"35975","category_aro_name":"cefazolin","category_aro_description":"Cefazolin, also known as cefazoline or cephazolin, is a first generation cephalosporin antibiotic. It is administered parenterally, and is active against a broad spectrum of bacteria.","category_aro_class_name":"Antibiotic"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"35979":{"category_aro_accession":"0000062","category_aro_cvterm_id":"35979","category_aro_name":"ceftriaxone","category_aro_description":"Ceftriaxone is a third-generation cephalosporin antibiotic. The presence of an aminothiazolyl sidechain increases ceftriazone's resistance to beta-lactamases. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"36990":{"category_aro_accession":"3000646","category_aro_cvterm_id":"36990","category_aro_name":"cefixime","category_aro_description":"Cefixime is a cephalosporin resistant to most beta-lactamases. It is active against many enterobacteria, but activity against staphylococci is poor.","category_aro_class_name":"Antibiotic"},"37084":{"category_aro_accession":"3000704","category_aro_cvterm_id":"37084","category_aro_name":"cefalotin","category_aro_description":"Cefalotin is a semisynthetic cephalosporin antibiotic activate against staphylococci. It is resistant to staphylococci beta-lactamases but hydrolyzed by enterobacterial beta-lactamases.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"716":{"model_id":"716","model_name":"QnrB32","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"405":{"protein_sequence":{"accession":"AEL00450.1","sequence":"MALALVGEKIDRNRFTGEKIENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNASALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNSNLSYANFSKVVLEKCELWENRWMGAQVLGATFSGSDLSGGEFSTFDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDNYQASLLMERLGIAIIG"},"dna_sequence":{"accession":"JN173054.1","fmin":"36","fmax":"681","strand":"+","sequence":"ATGGCTCTGGCACTCGTTGGCGAAAAAATTGACAGAAACCGTTTCACCGGTGAGAAAATTGAAAATAGTACATTTTTTAACTGTGATTTTTCAGGTGCCGACCTAAGTGGTACTGAATTTATCGGCTGTCAGTTCTATGATCGTGAAAGCCAGAAAGGGTGCAATTTTAGTCGTGCAATGCTAAAAGATGCCATTTTTAAAAGCTGTGATTTATCCATGGCGGATTTTCGCAATGCCAGTGCGCTGGGCATTGAAATTCGCCACTGCCGCGCACAAGGCGCAGATTTCCGCGGCGCAAGCTTTATGAATATGATCACTACACGCACCTGGTTTTGCAGCGCATATATCACTAACTCAAATCTAAGCTACGCCAATTTTTCGAAAGTCGTGCTGGAAAAGTGTGAGCTGTGGGAAAACCGTTGGATGGGTGCCCAGGTACTGGGCGCGACGTTCAGTGGTTCAGATCTCTCCGGCGGCGAGTTTTCGACTTTCGACTGGCGAGCAGCAAACTTCACACATTGCGATCTGACCAATTCGGAGTTGGGTGACTTAGATATTCGGGGCGTTGATTTACAAGGCGTTAAGTTGGACAACTACCAGGCATCGTTGCTCATGGAACGTCTTGGCATCGCGATTATTGGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002747","ARO_id":"39181","ARO_name":"QnrB32","CARD_short_name":"QnrB32","ARO_description":"QnrB32 is a plasmid-mediated quinolone resistance protein found in Citrobacter freundii.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"717":{"model_id":"717","model_name":"CTX-M-100","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"784":{"protein_sequence":{"accession":"CBW46935.1","sequence":"MMRKSVRRAMLMTTACVSLLLASVPLCAQANDVQQKLAALEKSSGGRLGVALINTADNTQTLYRADERFAMCSTSKVMAAAAVLKQSETQKGLLSQRVEIKPSDLINYNPIAEKHVNGTMTFGELSAAALQYSDNTAMNKLIAHLGGPDKVTAFARTIGDDTFRLDRTEPTLNTAIPGDPRDTTTPLAMAQALRNLTLGNALGDTQRAQLVMWLKGNTTGAASIQAGLPTSWVVGDKTGSGGYGTTNDIAVIWPEGRAPLVLVTYFTQSEPKAESRRDVLAAAARIVTDGY"},"dna_sequence":{"accession":"FR682582.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGATGAGAAAAAGCGTAAGGCGGGCGATGTTAATGACGACAGCCTGTGTTTCGCTGCTGTTGGCCAGTGTGCCGCTGTGTGCCCAGGCGAACGATGTTCAACAAAAGCTCGCGGCGCTGGAGAAAAGCAGCGGGGGACGACTGGGTGTGGCGTTGATTAACACCGCCGATAACACGCAGACGCTCTACCGCGCCGACGAGCGTTTTGCCATGTGCAGCACCAGTAAAGTGATGGCGGCAGCGGCGGTGCTTAAGCAAAGTGAAACGCAAAAGGGCTTGTTGAGTCAGCGGGTTGAAATTAAGCCCTCAGACTTGATTAACTACAACCCCATTGCGGAAAAACACGTCAATGGCACGATGACATTCGGGGAGTTGAGCGCGGCGGCGCTACAGTACAGCGATAATACTGCCATGAATAAGCTGATTGCCCATCTCGGGGGGCCGGATAAAGTGACGGCATTTGCCCGTACGATTGGCGATGACACGTTCCGGCTCGATCGTACCGAGCCGACGCTCAACACCGCGATCCCCGGCGACCCGCGCGATACCACCACGCCGTTAGCGATGGCGCAGGCTCTGCGCAATCTGACGTTGGGCAATGCCCTGGGTGACACTCAGCGTGCGCAGCTGGTGATGTGGCTGAAAGGCAACACCACCGGCGCTGCCAGCATTCAGGCAGGGCTACCCACATCGTGGGTTGTCGGGGATAAAACCGGCAGCGGCGGTTATGGTACGACGAATGATATCGCGGTTATTTGGCCGGAAGGTCGCGCGCCGCTCGTTCTGGTGACTTACTTCACCCAGTCGGAGCCGAAGGCAGAGAGCCGTCGTGACGTGCTCGCTGCTGCCGCCAGAATTGTCACCGACGGTTATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001959","ARO_id":"38359","ARO_name":"CTX-M-100","CARD_short_name":"CTX-M-100","ARO_description":"CTX-M-100 is a beta-lactamase found in Escherichia coli.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"718":{"model_id":"718","model_name":"LRA-8","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"858":{"protein_sequence":{"accession":"ACH58988.1","sequence":"MSKSSLKGLVLLALVAAIAAPSWAARKEKPAAKAPPCEQCAVWNADQEPFKIWGNTYYVGVKGLSSVLVTSDWGHVLLDGGLPESAPKIAANIEKLGFKVTDVKAILSSHVHADHAGGIAELQRRSGAKVYQRRPSDQVLRTGKPDPGDPQLARAGPIPPVENVWVVHDEELLGLGPTRFTVVATPGHTPGGTSWAWESCEGAQCLKIVYADSLNAVSAEGFRFTASTTYPNVLQDLEQSFKRVESLPCDVIVSVHPEQSDFFPRMAKRVDGKPESIKDPEGCKRYVAGARERLALRVASEKQGS"},"dna_sequence":{"accession":"EU408349.1","fmin":"107","fmax":"1025","strand":"+","sequence":"ATGTCGAAATCTTCCCTGAAGGGTCTGGTTCTTCTGGCTCTGGTGGCAGCCATCGCGGCCCCGTCGTGGGCGGCGCGCAAGGAAAAACCGGCCGCAAAGGCGCCGCCGTGCGAGCAGTGCGCGGTGTGGAACGCGGACCAGGAGCCGTTCAAGATCTGGGGCAACACGTACTACGTGGGCGTGAAGGGCCTGTCGTCCGTGCTCGTGACCTCCGACTGGGGCCACGTGCTCCTCGACGGCGGACTGCCCGAGTCCGCGCCGAAGATCGCCGCGAACATCGAGAAGCTCGGCTTCAAGGTCACGGACGTGAAGGCGATCCTGAGCTCGCACGTCCACGCGGATCACGCCGGCGGCATCGCCGAGCTGCAGCGGCGCAGCGGCGCCAAGGTGTACCAGCGCCGCCCGAGCGACCAGGTGCTGCGCACGGGCAAGCCCGATCCCGGCGATCCGCAGCTCGCGCGCGCCGGTCCGATCCCGCCGGTGGAGAACGTGTGGGTCGTGCACGACGAGGAGCTCCTCGGGCTCGGCCCCACGCGCTTCACGGTGGTGGCCACGCCGGGCCACACGCCCGGCGGCACCAGCTGGGCCTGGGAGTCCTGCGAAGGGGCGCAGTGCCTGAAGATCGTGTACGCCGACAGCCTCAACGCGGTGTCCGCCGAGGGGTTCCGCTTCACCGCGAGCACTACCTATCCGAACGTGCTGCAGGACTTGGAGCAGAGCTTCAAGCGCGTCGAGTCGTTGCCGTGCGACGTGATCGTGTCCGTGCATCCCGAGCAGTCCGACTTTTTCCCGCGCATGGCGAAGCGTGTGGACGGCAAGCCCGAGTCGATCAAGGACCCGGAAGGCTGCAAGCGCTATGTGGCCGGCGCACGCGAGCGTCTCGCGCTGCGCGTCGCCAGCGAGAAGCAAGGCTCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39082","NCBI_taxonomy_name":"uncultured bacterium BLR8","NCBI_taxonomy_id":"506524"}}}},"ARO_accession":"3002487","ARO_id":"38887","ARO_name":"LRA-8","CARD_short_name":"LRA-8","ARO_description":"LRA-8 is a beta-lactamase isolated from soil samples in Alaska.","ARO_category":{"41390":{"category_aro_accession":"3004226","category_aro_cvterm_id":"41390","category_aro_name":"subclass B3 LRA beta-lactamase","category_aro_description":"Beta-lactamases that are part of the LRA gene family and are classified as B3 (metallo-) beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"719":{"model_id":"719","model_name":"CMY-33","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1914":{"protein_sequence":{"accession":"ACA97847.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"EU496816.1","fmin":"0","fmax":"1140","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002044","ARO_id":"38444","ARO_name":"CMY-33","CARD_short_name":"CMY-33","ARO_description":"CMY-33 is a beta-lactamase found in Escherichia coli.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"720":{"model_id":"720","model_name":"BcI","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"350"}},"model_sequences":{"sequence":{"1622":{"protein_sequence":{"accession":"CAA29819.1","sequence":"MKNKRMLKIGICVGILGLSITSLEAFTGESLQVEAKEKTGQVKHKNQATHKEFSQLEKKFDARLGVYAIDTGTNQTISYRPNERFAFASTYKALAAGVLLQQNSIDSLNEVITYTKEDLVDYSPVTEKHVDTGMKLGEIAEAAVRSSDNTAGNILFNKIGGPKGYEKALRHMGDRITMSNRFETELNEAIPGDIRDTSTAKAIATNLKAFTVGNALPAEKRKILTEWMKGNATGDKLIRAGIPTDWVVGDKSGAGSYGTRNDIAVVWPPNRAPIIIAILSSKDEKEAIYDNQLIAEATKVIVKALR"},"dna_sequence":{"accession":"X06599.1","fmin":"272","fmax":"1193","strand":"+","sequence":"TTGAAAAATAAGAGGATGCTAAAAATAGGAATATGCGTTGGTATATTAGGTTTAAGTATTACAAGCCTAGAAGCTTTTACAGGAGAGTCACTGCAAGTTGAAGCGAAAGAAAAGACTGGACAAGTGAAACACAAAAATCAGGCAACGCATAAAGAGTTCTCTCAACTTGAGAAAAAATTTGATGCTCGATTAGGTGTATATGCGATTGATACTGGTACAAATCAAACAATCTCTTATCGACCTAACGAAAGATTTGCCTTCGCATCAACATACAAGGCTTTAGCCGCGGGAGTATTACTACAGCAAAACTCAATTGATTCATTAAATGAAGTAATCACATATACGAAAGAAGACTTAGTGGATTATTCACCTGTTACAGAGAAACATGTAGATACTGGAATGAAACTAGGAGAAATTGCAGAGGCAGCTGTTCGTTCAAGTGATAATACTGCAGGGAACATTTTATTTAATAAAATAGGAGGACCGAAAGGATATGAAAAAGCGCTTAGGCATATGGGGGATCGGATTACTATGTCTAATCGCTTTGAAACAGAATTAAACGAAGCTATTCCAGGAGACATTCGTGACACTAGTACAGCGAAAGCTATTGCTACGAATCTTAAAGCTTTTACGGTCGGAAATGCACTTCCAGCTGAAAAACGTAAAATTCTTACAGAGTGGATGAAAGGAAATGCTACAGGGGACAAACTTATTCGTGCAGGCATACCAACTGACTGGGTAGTTGGAGATAAATCAGGTGCTGGTAGTTACGGGACAAGAAATGATATTGCTGTCGTTTGGCCTCCAAATAGAGCACCAATTATCATCGCAATTTTATCTAGTAAAGATGAGAAAGAGGCAATCTATGATAATCAACTCATTGCAGAGGCAACTAAAGTTATAGTTAAGGCTCTTAGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36751","NCBI_taxonomy_name":"Bacillus cereus","NCBI_taxonomy_id":"1396"}}}},"ARO_accession":"3002877","ARO_id":"39311","ARO_name":"BcI","CARD_short_name":"BcI","ARO_description":"Bacillus cereus beta-lactamase I is a class A beta-lactamase that breaks down a number of penicillins and cephalosporins in the Bacillus cereus strain 569\/H\/9.","ARO_category":{"45667":{"category_aro_accession":"3007100","category_aro_cvterm_id":"45667","category_aro_name":"class A Bacillus cereus Bc beta-lactamase","category_aro_description":"Class A Bacillus cereus Bc beta-lactamases are enzymes that break down beta-lactam antibiotics, particularly penicillins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"721":{"model_id":"721","model_name":"OXA-28","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"887":{"protein_sequence":{"accession":"AAF72942.1","sequence":"MKTFAAYVITACLSSTALASSITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNNLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLSLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFGLEGQLRISAVNQVEFLESLFLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKGTEVYFFAFNMDIDNENKLPLRKSIPTKIMASEGIIGG"},"dna_sequence":{"accession":"AF231133.1","fmin":"1345","fmax":"2146","strand":"+","sequence":"ATGAAAACATTTGCCGCATATGTAATTACTGCGTGTCTTTCAAGTACGGCATTAGCTAGTTCAATTACAGAAAATACGTCTTGGAACAAAGAGTTCTCTGCCGAAGCCGTCAATGGTGTTTTCGTGCTTTGTAAAAGTAGCAGTAAATCCTGCGCTACCAATAACTTAGCTCGTGCATCAAAGGAATATCTTCCAGCATCAACATTTAAGATCCCCAACGCAATTATCGGCCTAGAAACTGGTGTCATAAAGAATGAGCATCAGGTTTTCAAATGGGACGGAAAGCCAAGAGCCATGAAACAATGGGAAAGAGACTTGAGCTTAAGAGGGGCAATACAAGTTTCAGCGGTTCCCGTATTTCAACAAATCGCCAGAGAAGTTGGCGAAGTAAGAATGCAGAAATACCTTAAAAAATTTTCATATGGCAACCAGAATATCAGTGGTGGCATTGACAAATTCGGGTTGGAGGGTCAGCTAAGAATTTCCGCAGTTAATCAAGTGGAGTTTCTAGAGTCTCTATTTTTAAATAAATTGTCAGCATCAAAAGAAAATCAGCTAATAGTAAAAGAGGCTTTGGTAACGGAGGCTGCGCCTGAATATCTTGTGCATTCAAAAACTGGTTTTTCTGGTGTGGGAACTGAGTCAAATCCTGGTGTCGCATGGTGGGTTGGTTGGGTTGAGAAGGGAACAGAGGTTTACTTTTTCGCCTTTAACATGGATATAGACAACGAAAATAAGTTGCCGCTAAGAAAATCCATTCCCACCAAAATCATGGCAAGTGAGGGCATCATTGGTGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3001423","ARO_id":"37823","ARO_name":"OXA-28","CARD_short_name":"OXA-28","ARO_description":"OXA-28 is a beta-lactamase found in P. aeruginosa.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46486":{"category_aro_accession":"3007697","category_aro_cvterm_id":"46486","category_aro_name":"OXA-10-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-10.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"723":{"model_id":"723","model_name":"SHV-72","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"8162":{"protein_sequence":{"accession":"CAJ47127.2","sequence":"MRYFRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPVGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADRTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AM176547.2","fmin":"30","fmax":"891","strand":"+","sequence":"ATGCGTTATTTTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGTAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAGGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGGATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001126","ARO_id":"37506","ARO_name":"SHV-72","CARD_short_name":"SHV-72","ARO_description":"SHV-72 is an inhibitor-resistant beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"724":{"model_id":"724","model_name":"AAC(6')-Ij","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"494":{"protein_sequence":{"accession":"AAC41392.1","sequence":"MNIMPVSESLMADWLGLRKLLWPDHDEAHLQEMQRLLQQTQSLQLLAYSDTQQAIAMLEASIRYEYVNGTQTSPVAFLEGIYVLPDYRRSGIATHLVQQVEAWAKPFGCIEFASDAALDNRISHAMHQALGFHETERVVYFKKHIG"},"dna_sequence":{"accession":"L29045.1","fmin":"259","fmax":"700","strand":"+","sequence":"ATGAATATTATGCCTGTATCTGAATCCCTGATGGCAGATTGGTTAGGATTGAGAAAACTGCTCTGGCCTGATCATGACGAGGCACATTTACAGGAAATGCAGCGGCTACTTCAACAGACACAAAGCTTACAGCTACTCGCATATTCAGATACTCAACAAGCGATTGCCATGCTAGAAGCATCGATTCGATATGAATATGTAAATGGCACGCAAACTTCACCAGTTGCATTTCTTGAAGGGATTTATGTCCTTCCTGATTATCGGCGTTCAGGCATCGCAACACATCTGGTTCAACAAGTAGAAGCGTGGGCAAAACCGTTTGGATGTATTGAATTTGCCTCGGATGCAGCCCTCGATAATCGTATTAGCCATGCGATGCATCAGGCGCTTGGTTTTCATGAAACTGAACGTGTGGTTTATTTCAAGAAACACATTGGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39510","NCBI_taxonomy_name":"Acinetobacter genomosp. 13","NCBI_taxonomy_id":"72607"}}}},"ARO_accession":"3002557","ARO_id":"38957","ARO_name":"AAC(6')-Ij","CARD_short_name":"AAC(6')-Ij","ARO_description":"AAC(6')-Ij is a chromosomal-encoded aminoglycoside acetyltransferase in Acinetobacter genomosp. 13.","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"A category of aminoglycoside N-acetyltransferase enzymes with modification regiospecificity based at the 6'-amino group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics through acetylation of the 6-amino group of the compound.","category_aro_class_name":"AMR Gene Family"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"46128":{"category_aro_accession":"3007378","category_aro_cvterm_id":"46128","category_aro_name":"2'-N-ethylnetilmicin","category_aro_description":"2'-N-ethylnetilmicin is an aminoglycoside antibiotic and a derivative of netilmicin.","category_aro_class_name":"Antibiotic"},"46129":{"category_aro_accession":"3007379","category_aro_cvterm_id":"46129","category_aro_name":"5-episisomicin","category_aro_description":"5-episosomicin is a semisynthetic aminoglycoside antibiotic similar to sisomicin.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"725":{"model_id":"725","model_name":"GES-11","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1745":{"protein_sequence":{"accession":"ACS44714.1","sequence":"MRFIHALLLAGIAHSAYASEKLTFKTDLEKLEREKAAQIGVAIVDPQGEIVAGHRMAQRFAMCSTFKFPLAALVFERIDSGTERGDRKLSYGPDMIVEWSPATERFLASGHMTVLEAAQAAVQLSDNGATNLLLREIGGPAAMTQYFRKIGDSVSRLDRKEPEMGDNTPGDLRDTTTPIAMARTVAKVLYGGALTSTSTHTIERWLIGNQTGDATLRAGFPKDWVVGEKTGTCANGARNDIGFFKAQERDYAVAVYTTAPKLSAVERDELVASVGQVITQLILSTDK"},"dna_sequence":{"accession":"FJ854362.1","fmin":"701","fmax":"1565","strand":"+","sequence":"ATGCGCTTCATTCACGCACTATTACTGGCAGGGATCGCTCACTCTGCATATGCGTCGGAAAAATTAACCTTCAAGACCGATCTTGAGAAGCTAGAGCGCGAAAAAGCAGCTCAGATCGGTGTTGCGATCGTCGATCCCCAAGGAGAGATCGTCGCGGGCCACCGAATGGCGCAGCGTTTTGCAATGTGCTCAACGTTCAAGTTTCCGCTAGCCGCGCTGGTCTTTGAAAGAATTGACTCAGGCACCGAGCGGGGGGATCGAAAACTTTCATATGGGCCGGACATGATCGTCGAATGGTCTCCTGCCACGGAGCGGTTTCTAGCATCGGGACACATGACGGTTCTCGAGGCAGCGCAAGCTGCGGTGCAGCTTAGCGACAATGGGGCTACTAACCTCTTACTGAGAGAAATTGGCGGACCTGCTGCAATGACGCAGTATTTTCGTAAAATTGGCGACTCTGTGAGTCGGCTAGACCGGAAAGAGCCGGAGATGGGCGACAACACACCTGGCGACCTCAGAGATACAACTACGCCTATTGCTATGGCACGTACTGTGGCTAAAGTCCTCTATGGCGGCGCACTGACGTCCACCTCGACCCACACCATTGAGAGGTGGCTGATCGGAAACCAAACGGGAGACGCGACACTACGAGCGGGTTTTCCTAAAGATTGGGTTGTTGGAGAGAAAACTGGTACCTGCGCCAACGGGGCCCGGAACGACATTGGTTTTTTTAAAGCCCAGGAGAGAGATTACGCTGTAGCGGTGTATACAACGGCCCCGAAACTATCGGCCGTAGAACGTGACGAATTAGTTGCCTCTGTCGGTCAAGTTATTACACAACTCATCCTGAGCACGGACAAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3002340","ARO_id":"38740","ARO_name":"GES-11","CARD_short_name":"GES-11","ARO_description":"GES-11 is a beta-lactamase found in Acinetobacter baumannii.","ARO_category":{"36205":{"category_aro_accession":"3000066","category_aro_cvterm_id":"36205","category_aro_name":"GES beta-lactamase","category_aro_description":"GES beta-lactamases or Guiana extended-spectrum beta-lactamases are related to the other plasmid-located class A beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"726":{"model_id":"726","model_name":"PC1 beta-lactamase (blaZ)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4586":{"protein_sequence":{"accession":"ABX30738.1","sequence":"MKKLIFLIVIALVLSACNSNSSHAKELNDLEKKYNAHIGVYALDTKSGKEVKFNSDKRFAYASTSKAINSAILLEQVPYNKLNKKVHINKDDIVAYSPILEKYVGKDIALKELIEASMKYSDNTANNKIINEIGGIKKIKKRLKKLGDKVTNPVRYEIELNYYSPKSKKDTSTPAAFGKTLNKLIANGKLSKKNKNFLLDLMLNNKNGDTLIKDGIPKDYKVADKSGQAITYASRNDVAFVYPKGQSEPIVLVIFTNKDNKSDKPNDKLISETAKSVMKEF"},"dna_sequence":{"accession":"CP000732.1","fmin":"9682","fmax":"10528","strand":"-","sequence":"TTGAAAAAGTTAATATTTTTAATTGTAATTGCTTTAGTTTTAAGTGCATGTAATTCAAACAGTTCACATGCCAAAGAGTTAAATGATTTAGAAAAAAAATATAATGCTCATATTGGTGTTTATGCTTTAGATACTAAAAGTGGTAAGGAAGTAAAATTTAATTCAGATAAGAGATTTGCCTATGCTTCGACTTCAAAAGCGATAAATAGTGCTATTTTGTTAGAACAAGTACCTTATAATAAGTTAAATAAAAAAGTACATATTAACAAAGATGATATAGTTGCTTATTCTCCTATTTTAGAAAAATATGTAGGAAAAGATATCGCTTTAAAAGAACTTATTGAGGCTTCAATGAAGTACAGTGATAATACAGCAAACAATAAAATTATAAACGAAATCGGTGGAATCAAAAAAATTAAAAAACGTTTAAAAAAATTGGGAGATAAAGTAACAAATCCAGTTAGATATGAAATAGAATTAAATTACTATTCACCAAAGAGCAAAAAAGATACTTCAACGCCTGCTGCTTTCGGCAAGACTTTAAATAAACTTATCGCAAATGGAAAATTAAGCAAAAAAAATAAAAATTTCTTACTTGATTTAATGTTAAATAATAAAAACGGAGACACTTTAATTAAAGATGGTATTCCAAAAGACTATAAAGTTGCTGATAAAAGTGGTCAAGCAATAACATATGCTTCTAGAAATGATGTTGCTTTTGTTTATCCTAAGGGCCAATCTGAACCTATTGTTTTAGTCATTTTTACGAATAAAGACAATAAAAGTGATAAGCCAAATGATAAGTTGATAAGTGAAACCGCCAAGAGTGTAATGAAGGAATTTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35526","NCBI_taxonomy_name":"Staphylococcus aureus subsp. aureus USA300_TCH959","NCBI_taxonomy_id":"450394"}}}},"ARO_accession":"3000621","ARO_id":"36963","ARO_name":"PC1 beta-lactamase (blaZ)","CARD_short_name":"PC1_blaZ","ARO_description":"The blaZ beta-lactamase is found in Bacillus subtilis and Staphylococcus aureus.","ARO_category":{"41361":{"category_aro_accession":"3004197","category_aro_cvterm_id":"41361","category_aro_name":"BlaZ beta-lactamase","category_aro_description":"BlaZ beta-lactamases are Class A beta-lactamases. These beta-lactamases are responsible for penicillin resistance in Staphylococcus aureus.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"727":{"model_id":"727","model_name":"ErmS","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"290":{"protein_sequence":{"accession":"AAA26742.1","sequence":"MARAPRSPHPARSRETSRAHPPYGTRADRAPGRGRDRDRSPDSPGNTSSRDGGRSPDRARRELSQNFLARRAVAERVARLVRPAPGGLLLEVGAGRGVLTEALAPYCGRLVAHEIDPRLLPALRDRFGGPHHAHVRISGGDFLAAPVPREPFALAGNIPYSRTAGIVDWALRARTLTSATFVTQLEYARKRTGDYGRWSLLTVRTWPRHEWRLLGRVSRREFRPVPRVDSGILRIERRERPLLPSAALGDYHRMVELGFSGVGGSLYASLRRAHRAGPLDAAFRAARLDRSVVVAYVTPEQWLTVFRTLRPVRSRPAGR"},"dna_sequence":{"accession":"M19269.1","fmin":"459","fmax":"1419","strand":"+","sequence":"GTGGCCCGTGCACCCCGATCGCCCCACCCTGCCCGCTCGCGGGAGACCTCCCGCGCCCACCCGCCGTACGGCACCCGTGCGGATCGCGCCCCCGGCCGTGGCCGTGACCGTGACCGCAGCCCCGACAGCCCCGGCAACACCAGCAGCCGCGACGGCGGCCGCAGCCCCGACCGCGCGCGGCGCGAGCTCTCGCAGAACTTCCTCGCCCGCCGGGCCGTCGCCGAGCGCGTCGCGCGCCTGGTCCGGCCGGCCCCCGGCGGTCTGTTGCTGGAGGTCGGCGCCGGGCGCGGCGTCCTGACCGAGGCGCTGGCCCCGTACTGCGGGCGGCTGGTCGCCCACGAGATCGACCCCCGTCTGCTGCCGGCGCTGCGCGACCGGTTCGGCGGCCCGCACCATGCCCATGTGCGGATCAGCGGCGGCGACTTCCTGGCAGCCCCCGTCCCCCGTGAGCCGTTCGCCCTCGCGGGGAACATCCCCTACTCCCGGACCGCGGGAATCGTGGACTGGGCGCTGCGGGCGCGCACGCTCACCTCGGCGACCTTCGTCACCCAGCTCGAGTACGCCCGCAAGCGGACCGGCGACTATGGACGCTGGAGCCTGCTGACGGTGCGGACCTGGCCCCGCCACGAGTGGCGGCTGCTCGGCAGGGTCTCCCGCCGGGAGTTCCGGCCGGTGCCCCGCGTGGACTCGGGCATCCTCCGGATCGAGCGGCGCGAGCGGCCCCTGCTGCCGTCCGCCGCCCTCGGCGACTACCACCGCATGGTGGAGCTGGGTTTCTCCGGCGTGGGCGGATCGCTGTACGCATCGCTGCGCCGGGCCCACCGGGCGGGGCCGCTCGACGCCGCGTTCCGTGCCGCGCGGCTGGACCGCTCCGTCGTCGTCGCGTATGTCACACCGGAGCAGTGGCTCACGGTCTTCCGCACGTTGCGGCCCGTCCGCAGCCGACCGGCCGGACGGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36838","NCBI_taxonomy_name":"Streptomyces fradiae","NCBI_taxonomy_id":"1906"}}}},"ARO_accession":"3001304","ARO_id":"37703","ARO_name":"ErmS","CARD_short_name":"ErmS","ARO_description":"ErmS is a methyltransferase found in the tylosin producer Streptomyces fradiae. Like other Erm enzymes, it catalyzes the methylation of A2058 of the 23S ribosomal RNA. Specifically, this enzyme transfers two methyl groups. The gene is found within the tylosin biosynthetic cluster and is responsible for self-resistance.","ARO_category":{"36699":{"category_aro_accession":"3000560","category_aro_cvterm_id":"36699","category_aro_name":"Erm 23S ribosomal RNA methyltransferase","category_aro_description":"Erm proteins are part of the RNA methyltransferase family and methylate A2058 (E. coli nomenclature) of the 23S ribosomal RNA conferring degrees of resistance to Macrolides, Lincosamides and Streptogramin b. This is called the MLSb phenotype.","category_aro_class_name":"AMR Gene Family"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"36284":{"category_aro_accession":"3000145","category_aro_cvterm_id":"36284","category_aro_name":"tylosin","category_aro_description":"Tylosin is a 16-membered macrolide, naturally produced by Streptomyces fradiae. It interacts with the bacterial ribosome 50S subunit to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"37022":{"category_aro_accession":"3000678","category_aro_cvterm_id":"37022","category_aro_name":"pristinamycin IC","category_aro_description":"Pristinamycin IC is a class B streptogramin derived from virginiamycin S1.","category_aro_class_name":"Antibiotic"},"37627":{"category_aro_accession":"3001228","category_aro_cvterm_id":"37627","category_aro_name":"carbomycin","category_aro_description":"Produced by Streptomyces halstedii and Streptomyces thermotolerans.","category_aro_class_name":"Antibiotic"},"37629":{"category_aro_accession":"3001230","category_aro_cvterm_id":"37629","category_aro_name":"niddamycin","category_aro_description":"Produced by Streptomyces caelestis.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35967":{"category_aro_accession":"0000050","category_aro_cvterm_id":"35967","category_aro_name":"streptogramin B antibiotic","category_aro_description":"Streptogramin B antibiotics are are cyclic hepta- or hexa-depsipeptides.  Type B streptogramins block the peptide exit tunnel of the 50S bacterial ribosome. The general composition of group B streptogramins is 3-hydroxypicolinic acid-L-Thr-D-aminobutyric acid (or D-Ala)-L-Pro-L-Phe (or 4-N-,N-(dimethylamino)-L-Phe)-X-L-phenylglycine. Used alone, streptogramin B antibiotics are bacteriostatic, but is bactericidal when used with streptogramin A antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"728":{"model_id":"728","model_name":"TEM-192","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1158":{"protein_sequence":{"accession":"AEQ59620.1","sequence":"MPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPIMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYT"},"dna_sequence":{"accession":"JF949915.1","fmin":"1","fmax":"754","strand":"+","sequence":"ATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATAATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACG","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001052","ARO_id":"37432","ARO_name":"TEM-192","CARD_short_name":"TEM-192","ARO_description":"TEM-192 is a beta-lactamase.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"729":{"model_id":"729","model_name":"CTX-M-8","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"826":{"protein_sequence":{"accession":"AAF04388.1","sequence":"MMRHRVKRMMLMTTACISLLLGSAPLYAQANDVQQKLAALEKSSGGRLGVALIDTADNAQTLYRADERFAMCSTSKVMAAAAVLKQSETQKKVLSQKVEIKSSDLINYNPITEKHVNGTMTLAELSAAALQYSDNTAMNKLIAHLGGPDKVTAFARAIGDNTFRLDRTEPTLNTAIPGDPRDTTTPLAMAQTLRNLTLGSALGETQRAQLVTWLKGNTTGAASIQAGLPTSWVVGDKTGSGDYGTTNDIAVIWPEGRAPLILVTYFTQPEQKAESRRDVLAAAAKIVTDGY"},"dna_sequence":{"accession":"AF189721.1","fmin":"273","fmax":"1149","strand":"+","sequence":"ATGATGAGACATCGCGTTAAGCGGATGATGCTAATGACAACGGCCTGTATTTCGCTGTTGCTGGGGAGTGCGCCGCTGTATGCGCAGGCGAACGACGTTCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGGGGGCGGTTGGGAGTGGCGCTGATTGACACCGCCGATAACGCACAGACGCTCTACCGCGCCGATGAGCGCTTTGCCATGTGCAGCACCAGTAAGGTGATGGCGGCAGCGGCTGTGCTCAAGCAAAGTGAAACGCAAAAGAAGGTGTTGAGTCAGAAGGTTGAGATTAAATCTTCAGACCTGATTAACTACAATCCCATTACTGAAAAACACGTCAACGGCACGATGACGCTGGCGGAATTGAGCGCCGCGGCGTTGCAGTACAGCGACAATACGGCCATGAACAAGCTGATTGCCCATCTTGGGGGGCCGGATAAAGTGACGGCGTTTGCCCGTGCGATTGGGGATAACACCTTCCGGCTCGATCGTACTGAGCCGACGCTCAACACCGCGATCCCCGGCGACCCGCGCGATACCACCACGCCATTAGCGATGGCGCAGACGCTTCGCAATCTGACGTTGGGCAGTGCCTTAGGTGAAACTCAGCGTGCGCAACTGGTAACGTGGCTGAAAGGCAATACCACCGGCGCTGCCAGCATTCAGGCTGGGCTACCCACATCGTGGGTTGTCGGGGATAAAACCGGCAGCGGTGATTATGGTACGACGAATGACATCGCCGTTATCTGGCCGGAAGGGCGTGCGCCGCTTATTCTGGTCACTTACTTCACCCAGCCAGAGCAGAAGGCAGAAAGTCGTCGTGACGTACTCGCGGCTGCCGCGAAAATCGTCACCGACGGTTATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36919","NCBI_taxonomy_name":"Citrobacter amalonaticus","NCBI_taxonomy_id":"35703"}}}},"ARO_accession":"3001871","ARO_id":"38271","ARO_name":"CTX-M-8","CARD_short_name":"CTX-M-8","ARO_description":"CTX-M-8 is a beta-lactamase found in the Enterobacteriaceae family.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"730":{"model_id":"730","model_name":"AAC(6')-IIc","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"313":{"protein_sequence":{"accession":"AAD46626.1","sequence":"MSANNAAIVLRVMAENDLPMLHAWLNRPHIVEWWGGEDERPTLDEVLEHYSPEVLAKQAVVPYIAMLDDEPIGYAQSYIALGSGDGWWEDETDPGVRGIDQSLANPSQLNKGLGTKLVRSLVELLFSDPAVTKIQTDPSPSNHRAIRCYEKAGFVQEKNILTPDGPAVYMVQTRQAFESLRTVQSFKIKGKWS"},"dna_sequence":{"accession":"AF162771.1","fmin":"61","fmax":"643","strand":"+","sequence":"ATGTCCGCCAACAATGCCGCAATAGTTCTACGAGTCATGGCCGAGAACGATCTGCCAATGCTCCATGCTTGGCTGAACCGCCCCCACATAGTCGAGTGGTGGGGCGGCGAGGATGAACGCCCAACTCTTGACGAAGTCTTAGAACACTATTCGCCCGAAGTTCTGGCAAAGCAAGCTGTAGTGCCTTACATCGCAATGCTAGATGACGAACCCATCGGCTACGCCCAATCCTACATCGCACTTGGAAGTGGCGATGGATGGTGGGAAGACGAAACTGATCCAGGGGTCCGCGGGATTGACCAGTCTTTGGCTAATCCATCACAGTTAAACAAGGGGTTGGGTACAAAGCTCGTACGCTCGCTCGTTGAACTCCTGTTTAGCGACCCGGCCGTAACGAAAATCCAAACCGATCCATCTCCTAGCAACCATCGCGCCATTCGCTGCTACGAGAAGGCCGGGTTCGTTCAAGAAAAAAACATCCTCACACCTGACGGCCCTGCGGTGTACATGGTCCAAACACGCCAGGCGTTCGAAAGCCTGCGCACTGTTCAAAGCTTCAAAATCAAGGGGAAGTGGTCATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002596","ARO_id":"38996","ARO_name":"AAC(6')-IIc","CARD_short_name":"AAC(6')-IIc","ARO_description":"AAC(6')-IIc is an aminoglycoside acetyltransferase encoded by plasmids and integrons in E. cloacae.","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"A category of aminoglycoside N-acetyltransferase enzymes with modification regiospecificity based at the 6'-amino group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics through acetylation of the 6-amino group of the compound.","category_aro_class_name":"AMR Gene Family"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"46128":{"category_aro_accession":"3007378","category_aro_cvterm_id":"46128","category_aro_name":"2'-N-ethylnetilmicin","category_aro_description":"2'-N-ethylnetilmicin is an aminoglycoside antibiotic and a derivative of netilmicin.","category_aro_class_name":"Antibiotic"},"46129":{"category_aro_accession":"3007379","category_aro_cvterm_id":"46129","category_aro_name":"5-episisomicin","category_aro_description":"5-episosomicin is a semisynthetic aminoglycoside antibiotic similar to sisomicin.","category_aro_class_name":"Antibiotic"},"46133":{"category_aro_accession":"3007382","category_aro_cvterm_id":"46133","category_aro_name":"gentamicin","category_aro_description":"Gentamicin is a commonly used aminoglycoside antibiotic derived from members of the Micromonospora genus of bacteria. It acts by binding the 30S ribosomal subunit, thus inhibiting protein synthesis. Gentamicin is typically used to treat Gram-negative infections of the repiratory and urinary tract, as well as infections of the bone and soft tissue. It also exhibits considerable nephrotoxicity and ototoxicity. Gentamicin is administered as a mixture of gentamicin type C (which makes about around 80% of the complex) and types A, B, and X (distributed in the remaining 20% of the complex).","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"731":{"model_id":"731","model_name":"IMP-11","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1746":{"protein_sequence":{"accession":"BAB72072.1","sequence":"MKKLFVLCIFLFCSITAAGASLPDLKIEKLEEGVYVHTSFEEVNGWGVVSKHGLVVLVNTDAYLIDTPFTAKDTEKLVNWFVERGYKIKGSISSHFHSDSTGGIEWLNSQSIPTYASVLTNELLKKDGKVQAKNSFSGVSYWLVKNKIEVFYPGPGHTQDNVVVWLPKNKILFGGCFVKPYGLGNLDDANVEAWPHSAEKLISKYGNAKLVVPSHSDIGDASLLKLTWEQAVKGLNESKKSNTVH"},"dna_sequence":{"accession":"AB074436.1","fmin":"16","fmax":"754","strand":"+","sequence":"ATGAAAAAACTATTTGTTTTATGTATATTTTTGTTTTGTAGCATTACTGCCGCAGGAGCGTCTTTGCCTGATTTAAAAATTGAGAAGCTTGAAGAGGGTGTTTATGTTCATACATCGTTTGAAGAAGTTAACGGCTGGGGTGTTGTTTCTAAACACGGTTTGGTGGTTCTTGTAAATACTGACGCCTATCTGATTGACACTCCATTTACTGCTAAAGATACTGAAAAGTTAGTCAATTGGTTTGTGGAGCGCGGCTATAAAATCAAAGGCAGTATTTCCTCACATTTCCATAGCGACAGCACGGGTGGAATAGAGTGGCTTAATTCTCAATCTATTCCCACGTATGCATCTGTATTAACAAATGAACTTCTCAAAAAAGACGGTAAGGTGCAAGCTAAAAACTCATTTAGCGGAGTTAGCTATTGGCTAGTTAAAAATAAAATTGAAGTTTTTTATCCAGGCCCAGGGCACACTCAAGATAACGTAGTGGTTTGGCTACCTAAAAATAAAATCTTATTTGGTGGTTGTTTTGTTAAACCATATGGTCTTGGTAATCTAGATGACGCAAATGTTGAAGCATGGCCACATTCGGCTGAAAAATTAATATCTAAGTATGGTAATGCAAAACTGGTTGTTCCAAGCCATAGTGACATAGGAGATGCGTCGCTCTTGAAGCTTACGTGGGAACAGGCGGTAAAAGGGCTTAATGAAAGCAAAAAAAGTAACACTGTTCATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3002202","ARO_id":"38602","ARO_name":"IMP-11","CARD_short_name":"IMP-11","ARO_description":"IMP-11 is a beta-lactamase found in Pseudomonas and Acinetobacter spp.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"732":{"model_id":"732","model_name":"OXA-237","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1456":{"protein_sequence":{"accession":"AFH36331.1","sequence":"MKTLILLPLLSCLSLTACSLPVSNSSSQITSTQSIQTIAKLFDQAQSSGVLVIQRGPHLQVYGNDLSRAHTEYIPASTFKILNALIGLQHGKATTNEIFKWDGKKRSFAAWEKDMTLGQAMQASAVPVYQELARRIGLELMQQEVQRIRFGNQQIGQHIDNFWLVGPLKITPEQEVEFASALAQEQLAFDPQVQQQVKAMLLLQERQGYRLYAKSGWGMDVEPQVGWLTGWIETPQDEIVAFSLNMQMQSNMDPAIRLKILQQALAELALYPKAEG"},"dna_sequence":{"accession":"JQ820241.1","fmin":"0","fmax":"831","strand":"+","sequence":"ATGAAAACTCTTATTTTGTTGCCTTTACTTAGTTGCTTGAGCCTGACAGCCTGTAGCTTGCCTGTTTCAAATTCGTCCTCTCAAATCACTTCAACTCAATCTATTCAAACCATTGCCAAATTATTTGATCAGGCACAAAGCTCTGGCGTTTTAGTAATTCAACGGGGCCCACATCTACAGGTCTATGGCAATGATTTGAGTCGTGCACATACCGAATATATTCCTGCTTCAACCTTTAAAATACTCAATGCCCTGATTGGCCTGCAACATGGTAAAGCCACGACCAATGAAATCTTTAAATGGGATGGCAAGAAGCGCAGTTTTGCAGCCTGGGAAAAAGACATGACTCTCGGCCAAGCCATGCAAGCTTCTGCTGTACCCGTCTATCAGGAACTGGCACGTCGCATTGGTCTGGAACTAATGCAACAGGAAGTGCAACGCATTCGATTTGGTAATCAGCAGATTGGTCAGCATATCGACAACTTCTGGTTAGTCGGACCTTTGAAAATCACCCCGGAACAAGAAGTCGAATTTGCCTCTGCGCTTGCTCAAGAGCAACTTGCCTTTGATCCTCAAGTCCAGCAACAAGTCAAAGCCATGTTACTGTTACAGGAGCGACAAGGTTATCGACTATATGCCAAATCTGGTTGGGGTATGGATGTGGAGCCGCAAGTCGGCTGGCTCACCGGCTGGATCGAAACACCTCAGGACGAAATCGTGGCATTTTCACTGAATATGCAGATGCAAAGTAATATGGATCCGGCGATCCGTCTTAAAATTTTGCAGCAGGCCTTGGCCGAATTAGCGCTTTATCCGAAAGCTGAAGGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001678","ARO_id":"38078","ARO_name":"OXA-237","CARD_short_name":"OXA-237","ARO_description":"OXA-237 is a beta-lactamase found in A. baumannii.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46489":{"category_aro_accession":"3007700","category_aro_cvterm_id":"46489","category_aro_name":"OXA-134-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-134.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3666":{"model_id":"3666","model_name":"NDM-25","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"5939":{"protein_sequence":{"accession":"AYF56302.1","sequence":"MELPNIMHPVAKLSTALAAALMLSGCMPGEIRPTIGQQMETGDQRFGDLVFRQLSPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR"},"dna_sequence":{"accession":"MH986670.1","fmin":"0","fmax":"813","strand":"+","sequence":"ATGGAATTGCCCAATATTATGCACCCGGTCGCGAAGCTGAGCACCGCATTAGCCGCTGCATTGATGCTGAGCGGGTGCATGCCCGGTGAAATCCGCCCGACGATTGGCCAGCAAATGGAAACTGGCGACCAACGGTTTGGCGATCTGGTTTTCCGCCAGCTCTCACCGAATGTCTGGCAGCACACTTCCTATCTCGACATGCCGGGTTTCGGGGCAGTCGCTTCCAACGGTTTGATCGTCAGGGATGGCGGCCGCGTGCTGGTGGTCGATACCGCCTGGACCGATGACCAGACCGCCCAGATCCTCAACTGGATCAAGCAGGAGATCAACCTGCCGGTCGCGCTGGCGGTGGTGACTCACGCGCATCAGGACAAGATGGGCGGTATGGACGCGCTGCATGCGGCGGGGATTGCGACTTATGCCAATGCGTTGTCGAACCAGCTTGCCCCGCAAGAGGGGATGGTTGCGGCGCAACACAGCCTGACTTTCGCCGCCAATGGCTGGGTCGAACCAGCAACCGCGCCCAACTTTGGCCCGCTCAAGGTATTTTACCCCGGCCCCGGCCACACCAGTGACAATATCACCGTTGGGATCGACGGCACCGACATCGCTTTTGGTGGCTGCCTGATCAAGGACAGCAAGGCCAAGTCGCTCGGCAATCTCGGTGATGCCGACACTGAGCACTACGCCGCGTCAGCGCGCGCGTTTGGTGCGGCGTTCCCCAAGGCCAGCATGATCGTGATGAGCCATTCCGCCCCCGATAGCCGCGCCGCAATCACTCATACGGCCCGCATGGCCGACAAGCTGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3004868","ARO_id":"43006","ARO_name":"NDM-25","CARD_short_name":"NDM-25","ARO_description":"A class B New Delhi metallo-beta-lactamase.","ARO_category":{"36196":{"category_aro_accession":"3000057","category_aro_cvterm_id":"36196","category_aro_name":"NDM beta-lactamase","category_aro_description":"NDM beta-lactamases or New Delhi metallo-beta-lactamases are class B beta-lactamases that confer resistance to a broad range of antibiotics including carbapenems, cephalosporins and penicillins.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"735":{"model_id":"735","model_name":"TEM-30","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"930":{"protein_sequence":{"accession":"CAD24670.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSSGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AJ437107.1","fmin":"208","fmax":"1069","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTAGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000900","ARO_id":"37280","ARO_name":"TEM-30","CARD_short_name":"TEM-30","ARO_description":"TEM-30 is an inhibitor-resistant beta-lactamase found in E. coli. Confers resistance to amoxycilllin-clavulanic acid, ticarcillin-clavulanic acid, kanamycin, neomycin, and intermediate resistance to mezlocillin and piperacillin.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35981":{"category_aro_accession":"0000064","category_aro_cvterm_id":"35981","category_aro_name":"amoxicillin","category_aro_description":"Amoxicillin is a moderate-spectrum, bacteriolytic, beta-lactam antibiotic used to treat bacterial infections caused by susceptible microorganisms. A derivative of penicillin, it has a wider range of treatment but remains relatively ineffective against Gram-negative bacteria. It is commonly taken with clavulanic acid, a beta-lactamase inhibitor. Like other beta-lactams, amoxicillin interferes with the synthesis of peptidoglycan.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"37084":{"category_aro_accession":"3000704","category_aro_cvterm_id":"37084","category_aro_name":"cefalotin","category_aro_description":"Cefalotin is a semisynthetic cephalosporin antibiotic activate against staphylococci. It is resistant to staphylococci beta-lactamases but hydrolyzed by enterobacterial beta-lactamases.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"736":{"model_id":"736","model_name":"arr-7","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"250"}},"model_sequences":{"sequence":{"603":{"protein_sequence":{"accession":"CAZ48628.1","sequence":"MPNDWIPTSHENCSLVPGPFYHGTKAKLAIGDLLSPGHPSHFEQGRRLKHIYFAALMEPAIWGAELAMSLSRQEGRGYIYIVEPLGPFEDDPNLTNKKFPGNPTKSYRTSESLRIVEVVEDWQGHSPDVLQGMLASLEDLQRRGLAIIED"},"dna_sequence":{"accession":"FN397623.1","fmin":"1188","fmax":"1641","strand":"+","sequence":"ATGCCGAATGACTGGATTCCCACCTCGCACGAAAACTGCTCGCTCGTGCCGGGGCCGTTCTACCACGGCACCAAAGCAAAACTCGCAATAGGTGACTTGCTTTCGCCTGGACACCCGTCTCACTTTGAGCAAGGCCGTAGGCTCAAACACATCTATTTTGCCGCACTGATGGAGCCAGCCATCTGGGGTGCTGAGCTTGCAATGTCATTGTCACGCCAAGAGGGGCGCGGTTACATTTACATTGTTGAACCGCTCGGGCCGTTTGAGGACGACCCAAACCTTACAAACAAAAAATTTCCGGGCAATCCAACCAAGTCCTACCGCACCAGTGAGTCGCTACGGATTGTGGAGGTAGTAGAGGACTGGCAAGGCCACTCACCGGATGTGCTGCAGGGCATGTTGGCATCACTGGAGGATCTTCAGCGTCGCGGCCTCGCAATCATTGAGGACTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002852","ARO_id":"39286","ARO_name":"arr-7","CARD_short_name":"arr-7","ARO_description":"arr-7 is an integron-encoded ribosyltransferase found in Pseudomonas aeruginosa.","ARO_category":{"36529":{"category_aro_accession":"3000390","category_aro_cvterm_id":"36529","category_aro_name":"rifampin ADP-ribosyltransferase (Arr)","category_aro_description":"Enzyme responsible for the ADP-ribosylative inactivation of rifampin at the 23-OH position using NAD+.","category_aro_class_name":"AMR Gene Family"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36656":{"category_aro_accession":"3000517","category_aro_cvterm_id":"36656","category_aro_name":"rifaximin","category_aro_description":"Rifaximin is a semi-synthetic rifamycin used to treat traveller's diarrhea. Rifaximin inhibits RNA synthesis by binding to the beta subunit of bacterial RNA polymerase.","category_aro_class_name":"Antibiotic"},"36669":{"category_aro_accession":"3000530","category_aro_cvterm_id":"36669","category_aro_name":"rifabutin","category_aro_description":"Rifabutin is a semisynthetic rifamycin used in tuberculosis therapy. It inhibits DNA-dependent RNA synthesis.","category_aro_class_name":"Antibiotic"},"36673":{"category_aro_accession":"3000534","category_aro_cvterm_id":"36673","category_aro_name":"rifapentine","category_aro_description":"Rifapentine is a semisynthetic rifamycin that inhibits DNA-dependent RNA synthesis. It is often used in the treatment of tuberculosis and leprosy.","category_aro_class_name":"Antibiotic"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"738":{"model_id":"738","model_name":"AAC(6')-Iae","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"583":{"protein_sequence":{"accession":"BAD14386.1","sequence":"MKYNIVNIKDSEKYITQAAEILFDVFSHINFDSWPSLQKATETVIECISAENICIGILINDELCGWVGLREMYKKTWELHPMVIKKKHQNKGFGKILIFETEKKAKERNLEGIVLGTDDETFRTTLSMSELNNENIFHEIKNIKNLKNHPFEFYEKCGYSIIGVIPNANGKNKPDILMWKNIM"},"dna_sequence":{"accession":"AB104852.1","fmin":"1934","fmax":"2486","strand":"+","sequence":"ATGAAATACAACATTGTTAATATTAAAGATTCTGAAAAGTATATAACGCAAGCTGCAGAAATTCTATTTGATGTATTTTCACACATAAATTTCGATTCTTGGCCGTCACTCCAAAAGGCTACAGAAACTGTAATAGAATGTATTAGCGCCGAAAACATTTGTATTGGCATTTTAATAAACGATGAATTGTGTGGTTGGGTTGGATTAAGAGAAATGTATAAAAAAACTTGGGAACTACATCCAATGGTTATTAAGAAAAAACATCAAAATAAGGGATTTGGTAAAATACTAATTTTTGAAACAGAAAAGAAAGCGAAAGAAAGAAATTTAGAAGGAATTGTACTTGGAACAGACGATGAAACATTTAGAACTACATTATCAATGTCAGAATTAAATAATGAAAATATATTCCATGAAATTAAAAATATAAAAAATCTAAAAAATCATCCATTTGAATTTTATGAAAAATGTGGTTACAGTATTATTGGTGTGATTCCTAATGCAAATGGGAAAAATAAACCTGATATATTAATGTGGAAAAATATAATGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002573","ARO_id":"38973","ARO_name":"AAC(6')-Iae","CARD_short_name":"AAC(6')-Iae","ARO_description":"AAC(6')-Iae is an integron-encoded aminoglycoside acetyltransferase in P. aeruginosa and S. enterica.","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"A category of aminoglycoside N-acetyltransferase enzymes with modification regiospecificity based at the 6'-amino group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics through acetylation of the 6-amino group of the compound.","category_aro_class_name":"AMR Gene Family"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"46128":{"category_aro_accession":"3007378","category_aro_cvterm_id":"46128","category_aro_name":"2'-N-ethylnetilmicin","category_aro_description":"2'-N-ethylnetilmicin is an aminoglycoside antibiotic and a derivative of netilmicin.","category_aro_class_name":"Antibiotic"},"46129":{"category_aro_accession":"3007379","category_aro_cvterm_id":"46129","category_aro_name":"5-episisomicin","category_aro_description":"5-episosomicin is a semisynthetic aminoglycoside antibiotic similar to sisomicin.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"739":{"model_id":"739","model_name":"LRA-18","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"1673":{"protein_sequence":{"accession":"ACH58997.1","sequence":"MLKRIRLPQLALALAALFPLAAYAAPDAAALRQAVDAAVGPVMAQFDVPGMAVAVTVDGQPHFFNYGVAARDSKQPVTEATIFELGSNSKTFTATLAAYAQAQGKLALDDHPGKYVPQLQGSALDGATLLHLGTYTAGGFPLQIPDNLKTREQLFSYFQHWKPDAAPGKQRNYSNPSIGLFGHIAGLALGGGFADAAERDLFPQLGLQHTYIRVPQSAMAHYAWGYSKDQAVRVQPDLFDSEAYGVKSTAADMIRYVQLQIDPSRLAAPMRRAVQATHTGYFKAGPMTQGLGWESYPYPVSLEQLLQGNSTDMAWKPQPVQAIQPVQTAAPALYNKTGSTRGFGSYVAFVPSQKIGIVLLANRAYPNDARIKLAYAILNQLAPAAN"},"dna_sequence":{"accession":"EU408355.1","fmin":"24321","fmax":"25482","strand":"+","sequence":"ATGTTGAAACGTATCCGCTTGCCCCAACTGGCGCTGGCCCTTGCGGCGCTGTTCCCCTTGGCCGCCTACGCGGCGCCGGACGCCGCCGCGCTGCGCCAGGCCGTCGACGCGGCAGTCGGCCCCGTCATGGCGCAGTTCGATGTGCCGGGCATGGCGGTCGCCGTCACGGTCGATGGCCAGCCGCACTTTTTCAATTACGGCGTCGCCGCGCGCGACAGCAAGCAACCCGTGACGGAAGCGACCATCTTTGAGTTGGGTTCGAACAGCAAGACTTTTACGGCCACCCTGGCGGCCTATGCCCAGGCGCAAGGCAAACTGGCGCTGGACGATCACCCCGGCAAGTATGTGCCGCAATTGCAGGGCAGTGCGCTCGATGGCGCCACCTTGCTGCACCTCGGCACCTACACGGCGGGCGGCTTTCCGTTGCAAATTCCGGACAACCTGAAAACCCGGGAGCAGTTGTTCAGTTACTTTCAGCACTGGAAACCGGACGCGGCGCCGGGCAAGCAGCGTAACTATTCCAATCCCAGCATCGGCCTATTCGGCCATATTGCCGGCCTGGCGCTCGGTGGCGGCTTTGCCGACGCGGCGGAGCGCGACTTGTTCCCGCAACTGGGTTTGCAACACACTTACATCCGCGTGCCGCAGTCAGCCATGGCCCATTACGCGTGGGGCTATTCGAAAGACCAGGCGGTCCGTGTCCAGCCTGATTTGTTCGATAGTGAAGCCTATGGCGTGAAATCCACGGCGGCCGACATGATCCGCTACGTGCAACTGCAAATCGACCCGTCGCGCCTGGCCGCACCGATGCGGCGCGCGGTGCAAGCGACCCATACCGGCTACTTCAAGGCCGGCCCGATGACGCAGGGACTGGGATGGGAATCGTACCCGTATCCCGTCAGCCTGGAGCAACTGTTGCAGGGCAATTCCACCGACATGGCGTGGAAGCCGCAGCCAGTCCAGGCAATACAACCAGTGCAGACCGCGGCCCCGGCCCTGTACAACAAGACCGGTTCCACGCGGGGCTTCGGCAGCTATGTCGCCTTTGTCCCGTCGCAAAAAATTGGTATCGTGCTGCTGGCCAACCGGGCTTATCCGAACGATGCGCGGATCAAGCTGGCGTATGCGATCTTGAATCAGCTGGCCCCGGCGGCAAATTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39683","NCBI_taxonomy_name":"uncultured bacterium BLR18","NCBI_taxonomy_id":"506518"}}}},"ARO_accession":"3002492","ARO_id":"38892","ARO_name":"LRA-18","CARD_short_name":"LRA-18","ARO_description":"LRA-18 is a beta-lactamase isolated from soil samples in Alaska.","ARO_category":{"41395":{"category_aro_accession":"3004231","category_aro_cvterm_id":"41395","category_aro_name":"class C LRA beta-lactamase","category_aro_description":"Beta-lactamases that are part of the LRA gene family and are classified as Class C beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"740":{"model_id":"740","model_name":"QnrB21","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"609":{"protein_sequence":{"accession":"ACM50952.1","sequence":"MTLALVGEKIDRNRFTGEKVENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAILKDAIFKSCDLSMADFRNVSALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKAVLEKCELWENRWMGTQVLGATLSGSDLSGGEFSSFDWRTANFTHCDLTNSELGDLDIRGVDLQGVKLDSYQAALLMERLGIAVIG"},"dna_sequence":{"accession":"FJ611948.1","fmin":"0","fmax":"645","strand":"+","sequence":"ATGACTCTGGCATTAGTTGGCGAAAAAATTGACAGAAACCGCTTCACCGGTGAAAAAGTTGAAAATAGCACTTTTTTTAACTGTGATTTTTCGGGTGCCGACCTTAGCGGTACTGAATTTATCGGCTGTCAGTTCTATGATCGAGAAAGCCAGAAAGGGTGCAATTTCAGTCGCGCAATACTGAAAGATGCCATTTTTAAAAGCTGTGATTTATCCATGGCGGATTTTCGCAACGTCAGTGCGTTGGGCATAGAAATTCGCCACTGCCGCGCACAGGGTGCAGATTTTCGCGGCGCAAGTTTCATGAATATGATCACCACGCGCACCTGGTTTTGCAGCGCATATATCACTAATACCAATCTAAGCTACGCCAACTTTTCGAAGGCCGTGCTTGAAAAGTGCGAATTGTGGGAAAATCGCTGGATGGGAACTCAGGTACTGGGTGCGACGTTGAGTGGTTCCGATCTCTCCGGTGGCGAGTTTTCGTCGTTCGACTGGCGGACGGCAAATTTCACGCACTGTGATTTGACCAATTCAGAACTGGGTGATTTAGATATTCGGGGCGTCGATTTACAAGGTGTCAAATTGGACAGCTATCAGGCCGCATTGCTCATGGAACGTCTTGGCATCGCTGTGATTGGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002736","ARO_id":"39170","ARO_name":"QnrB21","CARD_short_name":"QnrB21","ARO_description":"QnrB21 is a plasmid-mediated quinolone resistance protein found in Escherichia coli.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"741":{"model_id":"741","model_name":"CfxA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"1354":{"protein_sequence":{"accession":"AAB17891.1","sequence":"MEKNRKKQIVVLSIALVCIFILVFSLFHKSATKDSANPPLTNVLTDSISQIVSACPGEIGVAVIVNNRDTVKVNNKSVYPMMSVFKVHQALALCNDFDNKGISLDTLVNINRDKLDPKTWSPMLKDYSGPVISLTVRDLLRYTLTQSDNNASNLMFKDMVNVAQTDSFIATLIPRSSFQIAYTEEEMSADHNKAYSNYTSPLGAAMLMNRLFTEGLIDDEKQSFIKNTLKECKTGVDRIAAPLLDKEGVVIAHKTGSGYVNENGVLAAHNDVAYICLPNNISYTLAVFVKDFKGNKSQASQYVAHISAVVYSLLMQTSVKS"},"dna_sequence":{"accession":"U38243.1","fmin":"149","fmax":"1115","strand":"+","sequence":"ATGGAAAAAAACAGAAAAAAACAAATCGTAGTTTTGAGTATAGCTTTAGTTTGCATTTTCATCTTGGTATTTTCATTGTTCCATAAATCAGCGACAAAAGATAGCGCAAATCCTCCTTTAACAAATGTTTTGACTGATAGCATTTCTCAAATTGTCTCAGCTTGTCCTGGCGAAATTGGTGTGGCGGTTATTGTTAATAACAGAGATACGGTTAAGGTCAATAATAAGAGTGTTTATCCTATGATGAGTGTGTTTAAGGTTCATCAGGCATTAGCTCTTTGTAATGACTTTGACAATAAAGGAATTTCACTTGATACCTTAGTAAATATAAATAGGGATAAACTTGACCCAAAGACTTGGAGTCCTATGCTGAAAGATTATTCAGGGCCAGTCATATCATTGACAGTGAGAGATTTGCTGCGTTATACTCTTACTCAGAGTGACAACAATGCAAGCAACCTTATGTTTAAGGATATGGTTAATGTCGCTCAAACAGATAGTTTTATAGCCACACTCATTCCTCGTTCAAGTTTTCAGATAGCTTATACGGAAGAGGAAATGTCGGCTGACCATAACAAGGCTTACTCTAACTATACATCTCCTCTTGGTGCTGCAATGTTGATGAATCGTTTGTTTACTGAAGGTCTTATCGATGATGAGAAACAAAGTTTCATTAAGAATACGTTAAAAGAATGCAAAACAGGTGTAGATAGGATAGCAGCTCCACTTCTTGATAAAGAAGGGGTTGTTATAGCGCATAAGACAGGTTCAGGTTATGTTAATGAAAATGGTGTTCTTGCAGCTCACAATGATGTTGCCTATATATGTCTGCCTAATAATATCAGTTATACCTTAGCGGTATTTGTTAAGGATTTCAAGGGAAATAAATCACAAGCGTCACAATATGTTGCGCATATATCAGCTGTAGTATATTCTTTATTAATGCAAACTTCAGTAAAATCTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39546","NCBI_taxonomy_name":"Phocaeicola vulgatus","NCBI_taxonomy_id":"821"}}}},"ARO_accession":"3003001","ARO_id":"39435","ARO_name":"CfxA","CARD_short_name":"CfxA","ARO_description":"CfxA beta-lactamase is a class A beta-lactamase found in Bacteroides vulgatus.","ARO_category":{"39434":{"category_aro_accession":"3003000","category_aro_cvterm_id":"39434","category_aro_name":"CfxA beta-lactamase","category_aro_description":"CfxA beta-lactamases are class A beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35927":{"category_aro_accession":"0000008","category_aro_cvterm_id":"35927","category_aro_name":"cefoxitin","category_aro_description":"Cefoxitin is a cephamycin antibiotic often grouped with the second generation cephalosporins. Cefoxitin is bactericidal and acts by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. Cefoxitin's 7-alpha-methoxy group and 3' leaving group make it a poor substrate for most beta-lactamases.","category_aro_class_name":"Antibiotic"},"40928":{"category_aro_accession":"3004001","category_aro_cvterm_id":"40928","category_aro_name":"cefmetazole","category_aro_description":"Cefmetazole is a semi-synthetic cephamycin antibiotic with broad spectrum antibiotic activity against both gram-positive and gram-negative bacteria, that disrupt cell wall synthesis through binding to PBPs causing cell lysis.","category_aro_class_name":"Antibiotic"},"40931":{"category_aro_accession":"3004004","category_aro_cvterm_id":"40931","category_aro_name":"cefotetan","category_aro_description":"Cefotetan is a cephamycin-class beta-lactam antibiotic that is highly resistant to beta-lactamases and effective against a wide range of gram-negative and gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"40941":{"category_aro_accession":"3004014","category_aro_cvterm_id":"40941","category_aro_name":"flomoxef","category_aro_description":"Flomoxef is an oxacephem antibiotic which was effective in preventing the growth of all ESBL-producing strains and is widely active against Gram-positive, Gram-negative, and anaerobic bacteria. It is sometimes classified as a second-generation or fourth-generation cephalosporin.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"742":{"model_id":"742","model_name":"AAC(3)-Id","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"223":{"protein_sequence":{"accession":"AAR21614.1","sequence":"MSVEIIHLTGNDVALLQSINAMFGEAFNDQDSYARNKPSSSYLQKLLSTSSFIALAAVDEQKVIGAIAAYELQKFEQQRSEIYIYDLAVAATRRREGIATALIKKLKAIGAARGAYVIYVQADKGVEDQPAIELYKKLGTIEDVFHFDIAVEQSKNHA"},"dna_sequence":{"accession":"AY458224.1","fmin":"706","fmax":"1183","strand":"+","sequence":"GTGTCAGTCGAAATCATCCATCTCACTGGAAACGATGTTGCGTTGTTGCAGTCAATAAATGCCATGTTCGGCGAGGCATTCAACGACCAAGATAGTTATGCCCGCAACAAGCCGTCATCAAGCTATCTTCAAAAACTGCTTAGCACTTCTAGTTTTATTGCGTTGGCTGCGGTTGACGAGCAAAAAGTCATTGGCGCTATCGCCGCGTATGAGTTGCAAAAATTCGAGCAGCAAAGAAGCGAGATTTATATCTACGATCTCGCTGTAGCGGCAACCCGCCGCAGAGAAGGCATAGCTACAGCTCTAATTAAAAAACTCAAGGCTATAGGCGCAGCGCGTGGAGCTTATGTGATTTACGTCCAAGCTGATAAAGGCGTAGAAGACCAACCAGCCATAGAGCTCTATAAAAAACTAGGAACCATCGAAGACGTATTTCATTTCGACATTGCGGTTGAGCAGAGTAAAAATCATGCCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35735","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Newport","NCBI_taxonomy_id":"108619"}}}},"ARO_accession":"3002529","ARO_id":"38929","ARO_name":"AAC(3)-Id","CARD_short_name":"AAC(3)-Id","ARO_description":"AAC(3)-Id is an aminoglycoside acetyltransferase encoded by genomic islands and integrons in S. enterica, P. mirabilis and Vibrio fluvialis.","ARO_category":{"36461":{"category_aro_accession":"3000322","category_aro_cvterm_id":"36461","category_aro_name":"AAC(3)","category_aro_description":"A category of aminoglycoside N-acetyltransferase enzymes with modification regiospecificity based at the 3-amino group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics through acetylation of the 3-amino group of the compound.","category_aro_class_name":"AMR Gene Family"},"35922":{"category_aro_accession":"0000003","category_aro_cvterm_id":"35922","category_aro_name":"astromicin","category_aro_description":"Astromicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Astromicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"46133":{"category_aro_accession":"3007382","category_aro_cvterm_id":"46133","category_aro_name":"gentamicin","category_aro_description":"Gentamicin is a commonly used aminoglycoside antibiotic derived from members of the Micromonospora genus of bacteria. It acts by binding the 30S ribosomal subunit, thus inhibiting protein synthesis. Gentamicin is typically used to treat Gram-negative infections of the repiratory and urinary tract, as well as infections of the bone and soft tissue. It also exhibits considerable nephrotoxicity and ototoxicity. Gentamicin is administered as a mixture of gentamicin type C (which makes about around 80% of the complex) and types A, B, and X (distributed in the remaining 20% of the complex).","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"743":{"model_id":"743","model_name":"arr-3","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"250"}},"model_sequences":{"sequence":{"707":{"protein_sequence":{"accession":"ACD56151.1","sequence":"MVKDWIPISHDNYKQVQGPFYHGTKANLAIGDLLTTGFISHFEDGRILKHIYFSALMEPAVWGAELAMSLSGLEGRGYIYIVEPTGPFEDDPNLTNKRFPGNPTQSYRTCEPLRIVGVVEDWEGHPVELIRGMLDSLEDLKRRGLHVIED"},"dna_sequence":{"accession":"EU675686.1","fmin":"1956","fmax":"2409","strand":"+","sequence":"ATGGTAAAAGATTGGATTCCCATCTCTCATGATAATTACAAGCAGGTGCAAGGACCGTTCTATCATGGAACCAAAGCCAATTTGGCGATTGGTGACTTGCTAACCACAGGGTTCATCTCTCATTTCGAGGACGGTCGTATTCTTAAGCACATCTACTTTTCAGCCTTGATGGAGCCAGCAGTTTGGGGAGCTGAACTTGCTATGTCACTGTCTGGCCTCGAGGGTCGCGGCTACATATACATAGTTGAGCCAACAGGACCGTTCGAAGACGATCCGAATCTTACGAACAAAAGATTTCCCGGTAATCCAACACAGTCCTATAGAACCTGCGAACCCTTGAGAATTGTTGGCGTTGTTGAAGACTGGGAGGGGCATCCTGTTGAATTAATAAGGGGAATGTTGGATTCGTTGGAGGACTTAAAGCGCCGTGGTTTACACGTCATTGAAGACTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002848","ARO_id":"39282","ARO_name":"arr-3","CARD_short_name":"arr-3","ARO_description":"arr-3 is a plasmid-encoded ribosyltransferase found in Vibrio fluvialis.","ARO_category":{"36529":{"category_aro_accession":"3000390","category_aro_cvterm_id":"36529","category_aro_name":"rifampin ADP-ribosyltransferase (Arr)","category_aro_description":"Enzyme responsible for the ADP-ribosylative inactivation of rifampin at the 23-OH position using NAD+.","category_aro_class_name":"AMR Gene Family"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36656":{"category_aro_accession":"3000517","category_aro_cvterm_id":"36656","category_aro_name":"rifaximin","category_aro_description":"Rifaximin is a semi-synthetic rifamycin used to treat traveller's diarrhea. Rifaximin inhibits RNA synthesis by binding to the beta subunit of bacterial RNA polymerase.","category_aro_class_name":"Antibiotic"},"36669":{"category_aro_accession":"3000530","category_aro_cvterm_id":"36669","category_aro_name":"rifabutin","category_aro_description":"Rifabutin is a semisynthetic rifamycin used in tuberculosis therapy. It inhibits DNA-dependent RNA synthesis.","category_aro_class_name":"Antibiotic"},"36673":{"category_aro_accession":"3000534","category_aro_cvterm_id":"36673","category_aro_name":"rifapentine","category_aro_description":"Rifapentine is a semisynthetic rifamycin that inhibits DNA-dependent RNA synthesis. It is often used in the treatment of tuberculosis and leprosy.","category_aro_class_name":"Antibiotic"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"745":{"model_id":"745","model_name":"CMY-40","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1266":{"protein_sequence":{"accession":"ACA30422.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGISLLHLATYTAGGLPLQIPDDVTDKAALLRFYQNWQPQWTPGAKRLYANSSIGLFGTLAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQSEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMAHWVQANMDASHVQEKTLQQGIELAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGYTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"EU515251.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAACCGCACCATCACACCGCTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCGGTTATCTACCAGGGAAAACCCTATTATTTTACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGACGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCAGTCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTACGGATAAAGCCGCATTACTGCGCTTTTATCAAAACTGGCAACCACAATGGACTCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGCACGCTGGCGGTGAAACCCTCCGGTATGAGCTACGAAGAGGCGATGACCAGACGCGTTCTGCAGCCATTAAAGCTGGCGCATACCTGGATTACGGTTCCACAGAGCGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAACCTGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATCGATATGGCCCACTGGGTACAGGCCAACATGGACGCCAGCCACGTTCAGGAGAAAACGCTCCAACAGGGCATTGAGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCCGATTCGATCATCAACGGCAGCGACAGCAAAGTAGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTACACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002051","ARO_id":"38451","ARO_name":"CMY-40","CARD_short_name":"CMY-40","ARO_description":"CMY-40 is a beta-lactamase found in the Enterobacteriaceae family.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"746":{"model_id":"746","model_name":"AAC(2')-Ib","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"350"}},"model_sequences":{"sequence":{"85":{"protein_sequence":{"accession":"AAC44793.1","sequence":"MPFQDVSAPVRGGILHTARLVHTSDLDQETREGARRMVIEAFEGDFSDADWEHALGGMHAFICHHGALIAHAAVVQRRLLYRDTALRCGYVEAVAVREDWRGQGLATAVMDAVEQVLRGAYQLGALSASDTARGMYLSRGWLPWQGPTSVLQPAGVTRTPEDDEGLFVLPVGLPAGMELDTTAEITCDWRDGDVW"},"dna_sequence":{"accession":"U41471.1","fmin":"264","fmax":"852","strand":"+","sequence":"GTGCCTTTCCAGGATGTCAGCGCGCCCGTTCGAGGCGGGATCCTGCACACCGCTCGACTCGTCCACACCTCCGATCTCGATCAGGAGACTCGAGAGGGCGCCCGCCGCATGGTCATCGAGGCGTTCGAGGGTGATTTCAGCGACGCCGACTGGGAGCACGCGCTCGGTGGCATGCACGCCTTCATCTGTCACCACGGCGCTCTGATCGCGCATGCCGCGGTGGTCCAGCGCCGGCTGCTCTACCGCGACACCGCGCTGCGCTGCGGGTACGTGGAAGCCGTGGCGGTGCGCGAAGATTGGCGCGGCCAAGGCCTGGCCACCGCCGTCATGGACGCGGTCGAACAGGTGCTGCGCGGCGCCTACCAGCTCGGCGCCCTCAGTGCGTCCGACACAGCCAGAGGCATGTACCTCTCTCGCGGGTGGCTGCCGTGGCAGGGGCCGACCTCGGTGCTGCAGCCGGCCGGCGTGACGCGTACACCCGAGGACGACGAGGGACTGTTCGTGCTGCCCGTCGGTCTCCCGGCGGGAATGGAACTCGACACCACAGCCGAGATCACCTGCGACTGGCGCGACGGGGACGTCTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36886","NCBI_taxonomy_name":"Mycolicibacterium fortuitum","NCBI_taxonomy_id":"1766"}}}},"ARO_accession":"3002524","ARO_id":"38924","ARO_name":"AAC(2')-Ib","CARD_short_name":"AAC(2')-Ib","ARO_description":"AAC(2')-Ib is a chromosomal-encoded aminoglycoside acetyltransferase in Mycolicibacterium fortuitum and A. baumannii.","ARO_category":{"36480":{"category_aro_accession":"3000341","category_aro_cvterm_id":"36480","category_aro_name":"AAC(2')","category_aro_description":"A category of aminoglycoside N-acetyltransferase enzymes with modification regiospecificity based at the 2'-amino group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics through acetylation of the 2-amino group of the compound.","category_aro_class_name":"AMR Gene Family"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"46127":{"category_aro_accession":"3007377","category_aro_cvterm_id":"46127","category_aro_name":"6'-N-ethylnetilmicin","category_aro_description":"6'-N-ethylnetilmicin is an aminoglycoside antibiotic and a derivative of netilmicin.","category_aro_class_name":"Antibiotic"},"46133":{"category_aro_accession":"3007382","category_aro_cvterm_id":"46133","category_aro_name":"gentamicin","category_aro_description":"Gentamicin is a commonly used aminoglycoside antibiotic derived from members of the Micromonospora genus of bacteria. It acts by binding the 30S ribosomal subunit, thus inhibiting protein synthesis. Gentamicin is typically used to treat Gram-negative infections of the repiratory and urinary tract, as well as infections of the bone and soft tissue. It also exhibits considerable nephrotoxicity and ototoxicity. Gentamicin is administered as a mixture of gentamicin type C (which makes about around 80% of the complex) and types A, B, and X (distributed in the remaining 20% of the complex).","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"747":{"model_id":"747","model_name":"QnrA4","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"553":{"protein_sequence":{"accession":"AAZ04783.1","sequence":"MDIIDKVFQQEDFSRQDLSDSRFRRCRFYQCDFSHCQLRDASFEDCSFIESGAVEGCHFSYADLRDASFKACRLSLANFSGANCFGIEFRECDLKGANFSRARFYNQISHKMYFCSAYISGCNLAYANLNGQCLEKCELFENNWSNANLSGASLMGSDLSRGTFSRDCWQQVNLRGCDLTFADLDGLDPRRVNLEGVKICAWQQEQLLEPLGVIVLPD"},"dna_sequence":{"accession":"DQ058662.1","fmin":"0","fmax":"657","strand":"+","sequence":"ATGGATATTATTGATAAAGTTTTTCAGCAAGAGGATTTCTCACGCCAGGATTTGAGTGACAGCCGTTTTCGCCGCTGCCGCTTTTATCAGTGTGACTTCAGCCATTGCCAGCTAAGGGATGCCAGTTTCGAGGATTGCAGTTTCATTGAAAGCGGCGCCGTCGAAGGGTGCCACTTCAGCTATGCCGATCTGCGCGATGCCAGTTTCAAGGCCTGCCGCCTGTCTTTGGCCAATTTCAGCGGCGCCAACTGCTTTGGCATAGAGTTCAGGGAGTGCGATCTCAAGGGCGCCAATTTTTCCCGGGCCCGTTTTTACAATCAAATCAGCCATAAGATGTACTTCTGCTCGGCTTATATCTCAGGCTGCAACCTGGCCTATGCCAATTTGAACGGCCAATGCCTGGAAAAGTGCGAGCTGTTTGAAAACAACTGGAGCAATGCCAACCTCAGCGGCGCTTCCTTGATGGGCTCCGACCTCAGCCGCGGCACCTTCTCCCGCGACTGCTGGCAGCAGGTAAACCTGCGGGGCTGTGACCTGACCTTTGCCGATCTGGATGGGCTCGATCCCAGACGGGTCAACCTCGAAGGGGTCAAGATCTGTGCCTGGCAGCAGGAGCAACTGCTGGAACCCTTGGGAGTCATAGTGCTGCCGGATTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36891","NCBI_taxonomy_name":"Shewanella algae","NCBI_taxonomy_id":"38313"}}}},"ARO_accession":"3002710","ARO_id":"39144","ARO_name":"QnrA4","CARD_short_name":"QnrA4","ARO_description":"QnrA4 is a plasmid-mediated quinolone resistance protein found in Shewanella algae.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"748":{"model_id":"748","model_name":"cmeB","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"2090"}},"model_sequences":{"sequence":{"166":{"protein_sequence":{"accession":"ABS43151.1","sequence":"MFSKFFIERPVFASVVAIIISLAGVIGLTNLPIEQYPSLTPPTVKVSATYTGADAQTIASTVASPIEDAINGADNMIYMDSTSSSSGTMSLTVYFDIGTDPDQATIDVNNRISAATAKMPDAVKKLGVTVRKTSSATLAAISMYSSDGSMSAVDVYNYIALNVLDELKRVPGVGDANAIGNRNYSLRIWLKPDLLNKFKITATDVISAVNDQNAQYATGKIGEEPVTQKSPYVYSITMQGRLQNPSEFENIILRTNDDGSFLRLKDIADVEIGSQQYSSQGRLNGNDAVPIIINLQSGANALHTAELVQAKMQELSKNFPKGLTYKIPYDTTKFVIESIKEVIKTFIEALILVIIVMYMFLKNFRATLIPMIAVPVSLLGTFAGLYVLGFSINLLTLFALILAIGIVVDDAIIVVENIDRILHENEQISVKDAAIQAMQEVSSPVISIVLVLCAVFIPVSFISGFVGEIQRQFALTLAISVTISGFVALTLTPSLCALFLRRNEGEPFKFVRKFNDFFDWSTSVFSAGVAYILKRTIRFVLIFCIMLGTIFYLNKAVPNSLVPEEDQGLMIGIINLPSASALHRTISEVDHISQEVLKTNGIKDAMAMIGFDLFTSSLKENAAAMFIGLQDWKDRNVSADKIAMELNKKFAFDRNASSIFIGLPPIPGLSITGGFEMYVQNKSGKSYDQIQKDVNKLVAAANQRKELSRVRTTLDTTFPQYKLIIDRDKLKHYNLNMQDVFNTMNATIGTYYVNDFSMLGKNFQVNIRAKGDFRNTQDALKNIFVRSNDGKMIPLDSFLTLQRSSGPDDVKRFNLFPAAQVQGQPAPGYTSGQAIEAIAQVAKETLGDDYSIAWSGSAYQEVSSKGTASYAFALGMIFVFLILAAQYERWLIPLAVVTAVPFAVFGSFLLVYLRGFSNDIYFQTGLLLLIGLSAKNAILIVEFAMEERFKKGKGVFEAAVAAAKLRFRPIIMTSLAFTFGVLPMIFATGAGSASRHSLGTGLIGGMIAASTLAIFFVPLFFYLLENFNEWLDKKRGKIHE"},"dna_sequence":{"accession":"CP000768.1","fmin":"1406494","fmax":"1409617","strand":"+","sequence":"ATGTTTTCTAAATTTTTTATCGAAAGACCTGTTTTTGCCTCAGTTGTTGCAATTATCATTTCTTTAGCTGGAGTCATAGGTCTTACAAATTTACCTATAGAACAATACCCTTCTTTAACCCCTCCTACAGTTAAGGTAAGTGCAACTTACACAGGAGCTGATGCACAAACCATTGCTTCAACAGTTGCAAGTCCTATCGAAGATGCAATCAATGGTGCAGATAATATGATTTATATGGATTCGACTTCAAGTTCTTCAGGAACTATGAGTTTGACCGTTTATTTTGATATTGGCACAGATCCTGATCAAGCCACCATAGATGTTAATAATAGAATTTCAGCTGCAACTGCAAAAATGCCAGATGCAGTTAAAAAACTTGGAGTAACTGTTAGAAAAACTTCTTCGGCAACCCTAGCTGCAATTTCTATGTATTCAAGTGATGGCTCAATGAGTGCAGTGGATGTATACAATTACATCGCCTTAAATGTTTTAGATGAGTTAAAAAGGGTTCCAGGAGTTGGAGATGCAAACGCTATAGGAAATCGTAATTATTCTTTAAGAATTTGGCTAAAACCTGATTTGTTAAATAAATTTAAAATCACAGCTACTGATGTAATTTCTGCGGTTAACGATCAAAATGCCCAATACGCAACTGGTAAAATTGGCGAAGAACCTGTAACTCAAAAATCTCCTTATGTTTATTCAATCACCATGCAAGGAAGATTGCAAAATCCTAGCGAATTTGAAAACATTATTTTAAGAACAAATGATGATGGATCATTTTTAAGACTTAAAGATATAGCTGATGTGGAAATAGGATCACAACAATACAGCTCACAAGGACGATTAAATGGTAATGATGCGGTTCCGATTATAATCAATCTTCAATCAGGAGCAAATGCATTACATACAGCAGAACTTGTCCAGGCTAAAATGCAAGAACTTTCAAAAAATTTCCCAAAAGGTTTAACATATAAAATTCCTTACGACACAACAAAATTTGTGATAGAATCAATCAAAGAAGTAATTAAAACTTTTATTGAAGCTCTAATTTTAGTTATCATTGTTATGTATATGTTCTTAAAAAATTTCCGCGCAACACTTATTCCTATGATAGCTGTACCTGTTTCATTGTTAGGAACTTTTGCTGGACTTTATGTTTTAGGCTTTAGTATTAACCTACTTACGCTTTTTGCCTTAATTTTAGCCATAGGGATTGTTGTAGATGATGCGATTATAGTTGTGGAAAATATCGACAGGATTTTACACGAGAATGAACAAATAAGCGTAAAAGATGCTGCTATCCAAGCGATGCAAGAAGTTAGCTCTCCAGTCATTTCAATTGTTCTTGTGCTTTGTGCTGTTTTTATACCGGTTTCTTTTATATCAGGCTTTGTTGGAGAAATTCAAAGACAATTTGCTCTTACCTTAGCTATATCTGTAACCATATCAGGTTTTGTTGCTCTTACCTTAACACCTTCTTTATGCGCACTCTTTTTGCGACGTAATGAAGGAGAGCCATTTAAATTTGTAAGGAAATTCAATGATTTTTTTGATTGGAGCACTTCTGTATTTAGCGCAGGAGTAGCATATATTTTAAAAAGAACCATTCGTTTTGTTTTAATTTTTTGTATCATGCTTGGGACAATTTTTTATCTTAATAAAGCTGTGCCAAATTCTTTAGTTCCTGAAGAAGATCAAGGTTTGATGATTGGCATTATTAACCTTCCTTCAGCTTCAGCACTCCATAGAACAATCTCAGAAGTTGATCACATAAGTCAAGAAGTTTTAAAAACTAATGGAATTAAAGATGCAATGGCTATGATAGGATTTGATCTTTTTACAAGTTCACTCAAAGAAAACGCTGCTGCAATGTTTATAGGCTTGCAAGATTGGAAAGATAGAAATGTGAGTGCTGATAAAATCGCCATGGAGCTTAATAAAAAATTTGCCTTTGATCGCAATGCTTCAAGTATATTTATAGGCTTACCTCCTATACCTGGATTAAGTATCACAGGTGGTTTTGAAATGTATGTTCAAAACAAAAGTGGAAAAAGCTATGATCAAATTCAAAAAGATGTAAATAAACTTGTTGCTGCAGCCAACCAAAGAAAAGAACTATCAAGAGTAAGAACAACCCTTGATACAACTTTCCCTCAATACAAGCTTATAATTGATAGAGATAAATTAAAACACTACAATCTTAACATGCAAGATGTTTTTAACACGATGAATGCAACTATAGGCACTTATTATGTTAATGATTTTTCTATGCTAGGTAAAAACTTCCAAGTAAATATCCGCGCAAAAGGTGATTTTAGAAATACACAAGATGCATTAAAAAATATTTTTGTAAGATCAAATGATGGAAAAATGATACCACTTGATTCTTTCTTAACTTTACAAAGAAGTTCAGGGCCTGATGATGTAAAACGATTCAACCTTTTCCCAGCAGCACAAGTTCAAGGTCAACCCGCACCAGGTTATACTTCAGGTCAAGCTATAGAAGCGATTGCTCAAGTAGCAAAAGAAACTTTAGGGGATGATTATTCCATAGCTTGGAGTGGATCAGCTTATCAAGAAGTTTCTAGTAAAGGAACAGCAAGTTATGCTTTTGCTTTAGGTATGATATTTGTATTTTTAATTCTAGCTGCTCAATATGAAAGGTGGCTTATACCTTTAGCAGTTGTAACAGCTGTGCCTTTTGCAGTATTTGGATCATTTTTATTGGTATATTTAAGAGGGTTTAGTAATGATATATATTTTCAAACAGGACTTTTGCTCTTGATTGGACTTTCAGCTAAAAATGCTATCTTGATCGTAGAATTTGCAATGGAAGAGCGCTTTAAAAAAGGCAAAGGAGTTTTTGAAGCAGCTGTTGCAGCAGCAAAACTTCGTTTTCGTCCTATCATAATGACTTCTTTGGCGTTTACTTTTGGGGTCTTACCAATGATTTTTGCAACAGGAGCAGGAAGTGCTTCAAGACACTCTTTAGGAACAGGGCTTATTGGTGGAATGATCGCAGCATCAACTTTAGCGATATTCTTTGTGCCTTTATTTTTCTATCTTTTAGAAAATTTTAATGAATGGCTAGATAAAAAAAGAGGTAAGATTCATGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37595","NCBI_taxonomy_name":"Campylobacter jejuni subsp. doylei 269.97","NCBI_taxonomy_id":"360109"}}}},"ARO_accession":"3000784","ARO_id":"37164","ARO_name":"cmeB","CARD_short_name":"cmeB","ARO_description":"CmeB is the inner membrane transporter the CmeABC multidrug efflux complex.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"36989":{"category_aro_accession":"3000645","category_aro_cvterm_id":"36989","category_aro_name":"cefotaxime","category_aro_description":"Cefotaxime is a semisynthetic cephalosporin taken parenterally. It is resistant to most beta-lactamases and active against Gram-negative rods and cocci due to its aminothiazoyl and methoximino functional groups.","category_aro_class_name":"Antibiotic"},"37139":{"category_aro_accession":"3000759","category_aro_cvterm_id":"37139","category_aro_name":"fusidic acid","category_aro_description":"Fusidic acid is the only commercially available fusidane, a group of steroid-like antibiotics. It is most active against Gram-positive bacteria, and acts by inhibiting elongation factor G to  block protein synthesis.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"45735":{"category_aro_accession":"3007153","category_aro_cvterm_id":"45735","category_aro_name":"fusidane antibiotic","category_aro_description":"A group of antibiotics possessing steroid rings or steroid-like structures.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"749":{"model_id":"749","model_name":"SHV-97","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"922":{"protein_sequence":{"accession":"ABN49114.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGKRGARGIVALLGPNNKAERIVVIYLRDSPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"EF373973.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGATGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCAAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATTCGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35918","NCBI_taxonomy_name":"Enterococcus faecalis","NCBI_taxonomy_id":"1351"}}}},"ARO_accession":"3001149","ARO_id":"37529","ARO_name":"SHV-97","CARD_short_name":"SHV-97","ARO_description":"SHV-97 is a beta-lactamase found in Enterococcus faecalis.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"750":{"model_id":"750","model_name":"SHV-172","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1313":{"protein_sequence":{"accession":"AHA80958.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKADRIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"KF513177.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGATCGCATTGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001356","ARO_id":"37756","ARO_name":"SHV-172","CARD_short_name":"SHV-172","ARO_description":"SHV-172 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"751":{"model_id":"751","model_name":"TEM-217","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1572":{"protein_sequence":{"accession":"CDN33426.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVMYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"HG934763.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATGTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3001394","ARO_id":"37794","ARO_name":"TEM-217","CARD_short_name":"TEM-217","ARO_description":"TEM-217 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"754":{"model_id":"754","model_name":"CTX-M-48","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"908":{"protein_sequence":{"accession":"AAV97953.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTNAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"AY847144.1","fmin":"81","fmax":"957","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAATGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGACTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001910","ARO_id":"38310","ARO_name":"CTX-M-48","CARD_short_name":"CTX-M-48","ARO_description":"CTX-M-48 is a beta-lactamase found in the Enterobacteriaceae family.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"755":{"model_id":"755","model_name":"KPC-9","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"8408":{"protein_sequence":{"accession":"ACM91559.1","sequence":"RLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGAYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKYSEAVIAAAARLALEGLG"},"dna_sequence":{"accession":"FJ624872.1","fmin":"2","fmax":"854","strand":"+","sequence":"CGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGCGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGTACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGC","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002319","ARO_id":"38719","ARO_name":"KPC-9","CARD_short_name":"KPC-9","ARO_description":"KPC-9 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"757":{"model_id":"757","model_name":"CMY-80","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"762":{"protein_sequence":{"accession":"AFK73449.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEPQIADIVNRTITPLMQEQAIPGMAVAVIYQGKSYYFTWGKADITNNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGISLLHLATYTAGGLPLQIPDDVTDKAALLRFYQNWQPQWAPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWIKVPQSEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQVNMDASRVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"JQ733577.1","fmin":"1026","fmax":"2172","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCATTCTCCACGTTTGCCGCCGCCAAAACAGAACCACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAATCCTATTATTTCACCTGGGGTAAAGCCGATATCACCAATAACCACCCAGTCACGCAGCAAACTCTGTTTGAGCTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCAGCCTGCTGCACTTAGCCACCTACACGGCAGGCGGCCTGCCGCTGCAGATCCCCGATGACGTTACGGATAAAGCCGCATTACTGCGTTTTTATCAAAACTGGCAGCCGCAATGGGCCCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTAAAGTTCCGCAAAGCGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCTGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGTCAACATGGACGCCAGCCGCGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGTAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGATCCACTGGAGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGTATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002093","ARO_id":"38493","ARO_name":"CMY-80","CARD_short_name":"CMY-80","ARO_description":"CMY-80 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"758":{"model_id":"758","model_name":"OXA-198","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8284":{"protein_sequence":{"accession":"ADT70779.1","sequence":"MHKHMSKLFIAFLAFLLSVPAAAEDQTLAELFAQQGIDGTIVISSLHNGKTFIHNDPRAKQRFSTASTFKILNTLISLEEKAISGKDDVLKWDGHIYDFPDWNRDQTLESAFKVSCVWCYQALARQVGAEKYRNYLRKSVYGELREPFEETTFWLDGSLQISAIEQVNFLKKVHLRTLPFSASSYETLRQIMLIEQTPAFTLRAKTGWATRVKPQVGWYVGHVETPTDVWFFATNIEVRDEKDLPLRQKLTRKALQAKGIIE"},"dna_sequence":{"accession":"HQ634775.2","fmin":"3012","fmax":"3801","strand":"+","sequence":"ATGCATAAACACATGAGTAAGCTCTTCATCGCTTTTTTAGCCTTTCTGCTGTCGGTGCCAGCAGCCGCTGAAGACCAGACACTTGCCGAGCTCTTTGCCCAACAAGGCATTGACGGGACTATAGTGATTTCGTCGCTACACAACGGAAAGACATTTATCCACAACGATCCCCGCGCAAAACAGAGATTCTCGACAGCATCCACGTTCAAGATACTGAACACGCTGATCTCGCTCGAAGAAAAAGCCATCTCTGGAAAAGACGATGTGCTGAAATGGGACGGGCATATTTACGATTTTCCAGATTGGAATCGTGACCAGACGCTAGAAAGTGCGTTCAAGGTTTCCTGTGTCTGGTGTTATCAGGCGCTTGCACGCCAGGTCGGCGCGGAGAAGTATCGAAATTATTTACGCAAGTCAGTTTACGGAGAATTACGCGAGCCTTTTGAGGAAACAACATTCTGGCTTGATGGTTCACTTCAAATCAGCGCAATTGAACAAGTGAATTTCCTCAAGAAAGTTCATCTGCGCACTCTCCCATTCAGTGCATCGTCCTACGAAACGCTACGACAAATCATGCTTATCGAGCAAACGCCGGCTTTTACGCTGCGGGCCAAGACAGGCTGGGCAACAAGAGTAAAGCCGCAAGTTGGCTGGTATGTGGGCCATGTCGAAACTCCAACGGATGTATGGTTCTTTGCCACGAATATTGAAGTCCGTGACGAAAAAGACTTGCCCTTACGTCAGAAGCTAACGCGAAAAGCATTACAAGCAAAGGGGATCATCGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3001805","ARO_id":"38205","ARO_name":"OXA-198","CARD_short_name":"OXA-198","ARO_description":"OXA-198 is a beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46492":{"category_aro_accession":"3007703","category_aro_cvterm_id":"46492","category_aro_name":"OXA-198-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-198.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"759":{"model_id":"759","model_name":"OCH-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1504":{"protein_sequence":{"accession":"CAC17622.1","sequence":"MRTSTTLLIGFLTTAAVIPNNGALAASKVNDGDLRRIVDETVRPLMAEQKIPGMAVAITIDGKSHFFGYGVASKESGQKVTEDTIFEIGSVSKTFTAMLGGYGLATGAFSLSDPATKWAPELAGSSFDKITMLDLGTYTPGGLPLQFPDAVTDDSSMLAYFKNWKPDYPAGTQRRYSNPSIGLFGYLAARSMDKPFDVLMEQKLLPAFGLKNTFINVPESQMKNYAYGYSKANKPIRVSGGALDAQAYGIKTTALDLARFVELNIDSSSLELDFQKAVAATHTGYYHVGANNQGLGWEFYNYPTALKTLLAGNSSDMALKSHKIEKFDTPRQPSADVWLNKTGSTNGFGAYAAFIPAKKTGIVLLANRNYPIDERIKAAYRILQALDNKQ"},"dna_sequence":{"accession":"AJ295340.1","fmin":"0","fmax":"1173","strand":"+","sequence":"ATGAGAACATCTACGACACTTTTGATCGGTTTCCTCACCACTGCCGCTGTTATCCCGAATAACGGCGCGCTGGCTGCGAGCAAGGTGAATGATGGCGACTTGCGCCGTATTGTCGATGAAACGGTGCGCCCGCTCATGGCCGAGCAGAAAATCCCCGGCATGGCCGTCGCTATAACCATCGACGGCAAGAGCCACTTCTTCGGTTATGGTGTGGCATCGAAGGAAAGCGGGCAAAAAGTCACCGAAGACACGATTTTCGAGATCGGCTCGGTCAGCAAGACCTTCACTGCAATGCTCGGCGGCTACGGGCTTGCGACCGGCGCGTTCTCCCTGTCCGATCCCGCGACCAAATGGGCTCCCGAACTGGCAGGCAGCAGCTTCGACAAGATCACCATGCTTGATCTTGGGACCTACACGCCGGGCGGATTGCCCCTCCAGTTTCCCGATGCTGTCACCGATGACAGTTCGATGCTGGCATATTTCAAGAACTGGAAACCCGATTACCCGGCAGGGACGCAGCGTCGCTATTCGAATCCCAGCATCGGCCTGTTCGGCTATCTGGCGGCACGAAGCATGGACAAGCCGTTCGACGTTTTGATGGAGCAAAAGCTTCTGCCTGCATTCGGCCTGAAGAACACCTTCATCAATGTGCCGGAAAGCCAGATGAAGAACTACGCCTACGGCTATTCCAAAGCCAACAAGCCGATCCGGGTATCGGGCGGGGCGCTGGATGCACAAGCCTATGGCATCAAGACCACCGCGCTTGATCTTGCCCGCTTCGTCGAACTGAACATCGACAGCTCATCTCTGGAGCTTGATTTCCAGAAAGCCGTCGCCGCAACGCATACCGGTTACTACCATGTCGGAGCGAACAATCAGGGACTTGGCTGGGAGTTCTACAACTATCCGACTGCGCTCAAGACACTTCTTGCCGGCAATTCGTCGGACATGGCGCTGAAGTCGCACAAAATCGAGAAATTCGATACACCTCGCCAACCGTCAGCTGATGTGTGGCTCAACAAGACAGGCTCAACCAACGGCTTTGGCGCTTATGCGGCCTTTATTCCTGCGAAGAAGACCGGAATTGTTCTGCTTGCCAACCGGAATTATCCGATCGATGAGCGCATAAAGGCTGCCTATCGGATATTGCAGGCGCTCGACAACAAGCAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37077","NCBI_taxonomy_name":"Brucella anthropi","NCBI_taxonomy_id":"529"}}}},"ARO_accession":"3002515","ARO_id":"38915","ARO_name":"OCH-2","CARD_short_name":"OCH-2","ARO_description":"OCH-2 beta-lactamase is an Ambler class C chromosomal-encoded beta-lactamase in Brucella anthropi.","ARO_category":{"36233":{"category_aro_accession":"3000094","category_aro_cvterm_id":"36233","category_aro_name":"OCH beta-lactamase","category_aro_description":"OCH beta-lactamases are Ambler class C chromosomal-encoded beta-lactamases in Brucella anthropi.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"760":{"model_id":"760","model_name":"TEM-6","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1002":{"protein_sequence":{"accession":"CAA41038.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVKYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDHWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"X57972.1","fmin":"339","fmax":"1200","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTAAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCATTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000878","ARO_id":"37258","ARO_name":"TEM-6","CARD_short_name":"TEM-6","ARO_description":"TEM-6 is an extended-spectrum beta-lactamase found in E. coli.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"761":{"model_id":"761","model_name":"GES-13","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1905":{"protein_sequence":{"accession":"ACZ54536.1","sequence":"MRFIHALLLAGIAHSAYASEKLTFKTDLEKLEREKAAQIGVAIVDPQGEIVAGHRMAQRFAMCSTFKFPLAALVFERIDSGTERGDRKLSYGPDMIVKWSPATERFLASGHMTVLEAAQAAVQLSDNGATNLLLREIGGPAAMTQYFRKIGDSVSRLDRKEPEMNDNTPGDLRDTTTPIAMARTVAKVLYGGALTSTSTHTIERWLIGNQTGDATLRAGFPKDWVVGEKTGTCANGGRNDIGFFKAQERDYAVAVYTTAPKLSAVERDELVASVGQVITQLILSTDK"},"dna_sequence":{"accession":"GU169702.1","fmin":"608","fmax":"1472","strand":"+","sequence":"ATGCGCTTCATTCACGCACTATTACTGGCAGGGATCGCTCACTCTGCATATGCGTCGGAAAAATTAACCTTCAAGACCGATCTTGAGAAGCTAGAGCGCGAAAAAGCAGCTCAGATCGGTGTTGCGATCGTCGATCCCCAAGGAGAGATCGTCGCGGGCCACCGAATGGCGCAGCGTTTTGCAATGTGCTCAACGTTCAAGTTTCCGCTAGCCGCGCTGGTCTTTGAAAGAATTGACTCAGGCACCGAGCGGGGGGATCGAAAACTTTCATATGGGCCGGACATGATCGTCAAATGGTCTCCTGCCACGGAGCGGTTTCTAGCATCGGGACACATGACGGTTCTCGAGGCAGCGCAAGCTGCGGTGCAGCTTAGCGACAATGGGGCTACTAACCTCTTACTGAGAGAAATTGGCGGACCTGCTGCAATGACGCAGTATTTTCGTAAAATTGGCGACTCTGTGAGTCGGCTAGACCGGAAAGAGCCGGAGATGAACGACAACACACCTGGCGACCTCAGAGATACAACTACGCCTATTGCTATGGCACGTACTGTGGCTAAAGTCCTCTATGGCGGCGCACTGACGTCCACCTCGACCCACACCATTGAGAGGTGGCTGATCGGAAACCAAACGGGAGACGCGACACTACGAGCGGGTTTTCCTAAAGATTGGGTTGTTGGAGAGAAAACTGGTACCTGCGCCAACGGGGGCCGGAACGACATTGGTTTTTTTAAAGCCCAGGAGAGAGATTACGCTGTAGCGGTGTATACAACGGCCCCGAAACTATCGGCCGTAGAACGTGACGAATTAGTTGCCTCTGTCGGTCAAGTTATTACACAACTCATCCTGAGCACGGACAAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002342","ARO_id":"38742","ARO_name":"GES-13","CARD_short_name":"GES-13","ARO_description":"GES-13 is a beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36205":{"category_aro_accession":"3000066","category_aro_cvterm_id":"36205","category_aro_name":"GES beta-lactamase","category_aro_description":"GES beta-lactamases or Guiana extended-spectrum beta-lactamases are related to the other plasmid-located class A beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"762":{"model_id":"762","model_name":"CTX-M-55","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1552":{"protein_sequence":{"accession":"ABI34705.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAVAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"DQ885477.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGTGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001917","ARO_id":"38317","ARO_name":"CTX-M-55","CARD_short_name":"CTX-M-55","ARO_description":"CTX-M-55 is a beta-lactamase found in the Enterobacteriaceae family.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"35979":{"category_aro_accession":"0000062","category_aro_cvterm_id":"35979","category_aro_name":"ceftriaxone","category_aro_description":"Ceftriaxone is a third-generation cephalosporin antibiotic. The presence of an aminothiazolyl sidechain increases ceftriazone's resistance to beta-lactamases. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"764":{"model_id":"764","model_name":"FOX-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1031":{"protein_sequence":{"accession":"CAA71325.1","sequence":"MQQRRALALLTLGSLLLAPCTYASGEAPLTAAVDGIIQPMLKEYRIPGMAVAVLKDGKAHYFNYGVANRESGQRVSEQTLFEIGSVSKTLTATLGAYAAVKGGFELDDKVSHHAPWLKGSAFDGVTMAELATYSAGGLPLQFPDEVDSNDKMQTYYRSWSPVYPAGTHRQYSNPSIGLFGHLAANSLGQPFEKLMSQTLLPKLGLHHTYIQVPESAMANYAYGYSKEDKPIRVTPGVLAAEAYGIKTGSADLLKFVEANMGYQGDAALKSAIALTHTGFYSVGDMTQGLGWESYAYPVTEQALLAGNSPAVSFQANPVTRFAVPKAMGEQRLYNKTGSTGGFGAYVAFVPARGIAIVMLANRNYPIEARVKAAHAILSQLAE"},"dna_sequence":{"accession":"Y10282.1","fmin":"0","fmax":"1149","strand":"+","sequence":"ATGCAACAACGACGTGCGCTCGCGCTACTGACGCTGGGTAGCCTGCTGCTAGCCCCTTGTACTTATGCCAGCGGGGAGGCTCCGCTGACCGCCGCTGTGGACGGCATTATCCAGCCGATGCTCAAGGAGTATCGGATCCCGGGGATGGCGGTCGCCGTGCTGAAAGATGGCAAGGCCCACTATTTCAACTATGGGGTTGCCAACCGCGAGAGTGGCCAGCGCGTCAGCGAGCAGACGCTGTTCGAGATTGGCTCGGTCAGCAAGACCCTGACCGCGACCCTCGGTGCCTATGCTGCGGTCAAGGGGGGCTTTGAGCTGGATGACAAGGTGAGCCACCACGCCCCTTGGCTCAAAGGTTCCGCTTTCGATGGTGTGACTATGGCCGAGCTTGCCACCTACAGTGCGGGTGGTTTGCCGCTGCAGTTCCCTGATGAGGTGGATTCGAATGACAAGATGCAAACTTACTATCGGAGCTGGTCACCGGTTTATCCGGCGGGGACCCATCGCCAGTATTCCAACCCCAGCATAGGCCTGTTTGGTCACCTGGCCGCAAATAGTCTGGGCCAGCCATTTGAGAAACTGATGAGCCAGACCCTGCTGCCCAAGCTTGGTTTGCACCACACCTATATCCAGGTGCCGGAGTCGGCCATGGCGAACTATGCCTACGGCTATTCGAAGGAAGATAAGCCCATCCGGGTCACTCCGGGCGTACTGGCGGCCGAGGCTTACGGGATCAAAACCGGCTCGGCGGATCTGCTGAAGTTTGTCGAGGCAAACATGGGGTATCAGGGAGATGCCGCGCTAAAAAGCGCGATCGCGCTGACCCACACCGGTTTCTACTCGGTGGGAGACATGACCCAGGGACTGGGCTGGGAGAGCTACGCCTATCCGGTGACCGAGCAGGCGTTGCTGGCGGGCAACTCCCCGGCGGTGAGCTTCCAGGCCAATCCGGTTACGCGCTTTGCGGTGCCCAAAGCGATGGGCGAGCAGCGGCTCTATAACAAGACGGGCTCGACCGGCGGCTTTGGCGCCTATGTGGCGTTCGTGCCCGCCAGAGGGATCGCCATCGTCATGCTGGCCAATCGCAACTATCCCATCGAGGCCAGGGTGAAGGCGGCTCACGCCATCCTGAGTCAGTTGGCCGAGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002156","ARO_id":"38556","ARO_name":"FOX-2","CARD_short_name":"FOX-2","ARO_description":"FOX-2 is a beta-lactamase found in Escherichia coli.","ARO_category":{"36206":{"category_aro_accession":"3000067","category_aro_cvterm_id":"36206","category_aro_name":"FOX beta-lactamase","category_aro_description":"FOX beta-lactamases are plasmid-encoded AmpC-type beta-lactamase which conferred resistance to broad-spectrum cephalosporins and cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"765":{"model_id":"765","model_name":"QnrB7","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"8172":{"protein_sequence":{"accession":"ABW03156.3","sequence":"MALALVGEKIDRNRFTGEKIENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNASALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGAQVLGATFSGSDLSGGEFTTFDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDNYQASLLMERLGIAIIG"},"dna_sequence":{"accession":"EU043311.3","fmin":"0","fmax":"645","strand":"+","sequence":"ATGGCTCTGGCACTCGTTGGCGAAAAAATTGACAGAAACCGTTTCACCGGTGAGAAAATTGAAAATAGTACATTTTTTAACTGTGATTTTTCAGGTGCCGACCTAAGTGGTACTGAATTTATCGGCTGTCAGTTCTATGATCGTGAAAGCCAGAAAGGGTGCAATTTTAGTCGTGCAATGCTGAAAGATGCCATTTTTAAAAGCTGTGATTTATCCATGGCGGATTTTCGCAATGCCAGTGCGCTGGGCATTGAAATTCGCCACTGCCGCGCACAAGGCGCAGATTTCCGCGGCGCAAGCTTTATGAATATGATCACTACACGCACCTGGTTTTGCAGCGCATATATCACTAACACAAATCTAAGCTACGCCAATTTTTCGAAAGTCGTGCTGGAAAAGTGTGAGCTGTGGGAAAACCGTTGGATGGGTGCCCAGGTACTGGGCGCGACGTTCAGTGGTTCAGATCTCTCCGGCGGCGAGTTTACGACTTTCGACTGGCGAGCAGCAAACTTCACACATTGCGATCTGACCAATTCGGAGTTGGGTGACTTAGATATTCGGGGCGTTGATTTACAAGGCGTTAAGTTGGACAACTACCAGGCATCGTTGCTCATGGAACGTCTTGGCATCGCGATTATTGGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3002721","ARO_id":"39155","ARO_name":"QnrB7","CARD_short_name":"QnrB7","ARO_description":"QnrB7 is a plasmid-mediated quinolone resistance protein found in Enterobacter cloacae.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"766":{"model_id":"766","model_name":"SHV-102","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1697":{"protein_sequence":{"accession":"ABS72342.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAAERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"EU024485.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTACTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGCCGAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACCCCAGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001151","ARO_id":"37531","ARO_name":"SHV-102","CARD_short_name":"SHV-102","ARO_description":"SHV-102 is an extended spectrum beta-lactamase found in E. coli.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"767":{"model_id":"767","model_name":"OXA-207","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1836":{"protein_sequence":{"accession":"AFK28473.1","sequence":"MKKFILPIFSISILVSLSACSSIKTKSEDNFHISSQQHEKAIKSYFDEAQTQGVIIIKEGKNLSTYGNALARANKEYVPASTFKMLNALIGLENHKATTNEIFKWDGKKRTYPMWEKDMTLGEAMALSAVPVYQELARRTGLELMQKEVKRVNFGNTNIGTQVDNFWLVGPLKITPVQEVNFADDLAHNRLPFKLETQEEVKKMLLIKEVNGSKIYAKSGWVMGVTPQVGWLTGWVEQANGKKIPFSLNLEMKEGMSGSIRNEITYKSLENLGII"},"dna_sequence":{"accession":"JQ838185.1","fmin":"0","fmax":"828","strand":"+","sequence":"ATGAAAAAATTTATACTTCCTATATTCAGCATTTCTATTCTAGTTTCTCTCAGTGCATGTTCATCTATTAAAACTAAATCTGAAGATAATTTTCATATTTCTTCTCAGCAACATGAAAAAGCTATTAAAAGCTATTTTGATGAAGCTCAAACACAGGGTGTAATTATTATTAAAGAGGGTAAAAATCTTAGCACCTATGGTAATGCTCTTGCACGAGCAAATAAAGAATATGTCCCTGCATCAACATTTAAGATGCTAAATGCTTTAATCGGGCTAGAAAATCATAAAGCAACAACAAATGAGATTTTCAAATGGGATGGTAAAAAAAGAACTTATCCTATGTGGGAGAAAGATATGACTTTAGGTGAGGCAATGGCATTGTCAGCAGTTCCAGTATATCAAGAGCTTGCAAGACGGACTGGCCTAGAGCTAATGCAGAAAGAAGTAAAGCGGGTTAATTTTGGAAATACAAATATTGGAACACAGGTCGATAATTTTTGGTTAGTTGGCCCCCTTAAAATTACACCAGTACAAGAAGTTAATTTTGCCGATGACCTTGCACATAACCGATTACCTTTTAAATTAGAAACTCAAGAAGAAGTTAAAAAAATGCTTCTAATTAAAGAAGTAAATGGTAGTAAGATTTATGCAAAAAGTGGATGGGTAATGGGTGTTACTCCACAGGTAGGTTGGTTGACTGGTTGGGTGGAGCAAGCTAATGGAAAAAAAATCCCCTTTTCGCTCAACTTAGAAATGAAAGAAGGAATGTCTGGTTCTATTCGTAATGAAATTACTTATAAGTCGCTAGAAAATCTTGGAATCATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3001485","ARO_id":"37885","ARO_name":"OXA-207","CARD_short_name":"OXA-207","ARO_description":"OXA-207 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46500":{"category_aro_accession":"3007711","category_aro_cvterm_id":"46500","category_aro_name":"OXA-24-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-24.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"768":{"model_id":"768","model_name":"SHV-43","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1947":{"protein_sequence":{"accession":"AAL40899.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHFADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLSAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AY065991.1","fmin":"6","fmax":"867","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACATTTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGTCTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACACCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGAGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATCGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001101","ARO_id":"37481","ARO_name":"SHV-43","CARD_short_name":"SHV-43","ARO_description":"SHV-43 is a broad-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"769":{"model_id":"769","model_name":"KPC-11","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1710":{"protein_sequence":{"accession":"ADH95186.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVLWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"HM066995.1","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCTGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002321","ARO_id":"38721","ARO_name":"KPC-11","CARD_short_name":"KPC-11","ARO_description":"KPC-11 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"770":{"model_id":"770","model_name":"SHV-57","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1715":{"protein_sequence":{"accession":"AAO66446.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETERNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AY223863.1","fmin":"170","fmax":"1031","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTACTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACGGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001113","ARO_id":"37493","ARO_name":"SHV-57","CARD_short_name":"SHV-57","ARO_description":"SHV-57 is an extended-spectrum beta-lactamase found in E. coli.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"771":{"model_id":"771","model_name":"CMY-24","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1195":{"protein_sequence":{"accession":"ABN69070.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVYVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"EF415650.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTATACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002035","ARO_id":"38435","ARO_name":"CMY-24","CARD_short_name":"CMY-24","ARO_description":"CMY-24 is a beta-lactamase found in the Enterobacteriaceae family.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"772":{"model_id":"772","model_name":"LEN-6","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"960":{"protein_sequence":{"accession":"AAP93848.1","sequence":"MISLLATLPLAVDAGPQPLEQIKQSESQLSGRVGMVEMDLASGRTLAAWRADERFPMVSTFKVLLCGAVLARVDAGLEQLDRRIHYRQQDLVDYSPVSEKHLVDGMTIGELCAAAITLSDNSAGNLLLATVGGPAGLTAFLRQIGDNVTRLDRWETE"},"dna_sequence":{"accession":"AY265890.1","fmin":"1","fmax":"472","strand":"+","sequence":"ATTATCTCCCTGTTAGCCACCCTGCCACTGGCGGTAGACGCCGGTCCACAGCCGCTTGAGCAGATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTGGGGATGGTGGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCGATGAACGCTTTCCCATGGTGAGCACCTTTAAAGTGCTGCTGTGCGGCGCGGTGCTGGCGCGGGTGGATGCCGGGCTCGAACAACTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGTCGACGGGATGACGATCGGCGAACTCTGCGCCGCCGCCATCACCCTGAGCGATAACAGCGCTGGCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCGGGATTAACTGCCTTTCTGCGCCAGATCGGTGACAACGTCACCCGTCTTGACCGCTGGGAAACGGAA","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002476","ARO_id":"38876","ARO_name":"LEN-6","CARD_short_name":"LEN-6","ARO_description":"LEN-6 is a beta-lactamase. From the Pasteur Institute list of LEN beta-lactamases.","ARO_category":{"36236":{"category_aro_accession":"3000097","category_aro_cvterm_id":"36236","category_aro_name":"LEN beta-lactamase","category_aro_description":"LEN beta-lactamases are chromosomal class A beta-lactamases that confer resistance to ampicillin, amoxicillin, carbenicillin, and ticarcillin but not to extended-spectrum beta-lactams.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"773":{"model_id":"773","model_name":"OCH-4","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1659":{"protein_sequence":{"accession":"CAC17624.1","sequence":"MRKSTTLLIGFLTTAAIIPNNGALATSKANDGDLRRIVDETVRPLMAEQKIPGMAVAITIDGKSHFFGYGVASKESGQKVTEDTIFEIGSVSKTFTAMLGGYGLATGAFSLSDPATKWAPELAGSSFDKITMRDLGTYTPGGLPLQFPDAVTDDSSMLAYFKKWKPDYPAGTQRRYSNPSIGLFGYLAARSMDKPFDVLMEQKLLPAFGLKNTFINVPASQMKNYAYGYSKANKPIRVSGGALDAQAYGIKTTALDLARFVELNIDSSSLEPDFQKAVAATHTGYYHVGANNQGLGWEFYNYPTALKTLLAGNSSDMALKSHKIEKFDTPRQPSADVLINKTGSTNGFGAYAAFIPAKKIGIVLLANRNYPIDERVKAAYRILQALDNKQ"},"dna_sequence":{"accession":"AJ295342.1","fmin":"0","fmax":"1173","strand":"+","sequence":"ATGAGAAAATCTACGACACTTTTGATCGGTTTCCTCACCACTGCCGCTATTATCCCGAATAATGGCGCGCTGGCTACGAGCAAGGCGAATGATGGCGACTTGCGCCGTATTGTCGATGAAACGGTGCGCCCGCTCATGGCCGAGCAGAAAATCCCCGGCATGGCCGTCGCTATAACCATCGACGGCAAGAGCCACTTCTTCGGTTATGGTGTGGCATCGAAAGAAAGCGGGCAAAAAGTCACTGAAGACACGATTTTCGAGATCGGTTCGGTCAGCAAGACCTTCACTGCAATGCTTGGCGGTTACGGGCTGGCGACAGGCGCGTTCTCCCTGTCCGATCCCGCGACCAAATGGGCTCCTGAACTGGCAGGCAGCAGCTTCGACAAGATCACCATGCGTGATCTTGGGACCTACACGCCGGGCGGATTGCCCCTCCAGTTTCCCGATGCTGTCACCGATGACAGTTCGATGCTGGCATATTTCAAGAAATGGAAGCCGGACTATCCGGCAGGCACGCAGCGTCGCTATTCGAATCCCAGCATCGGCCTGTTCGGCTATCTGGCGGCACGAAGCATGGACAAGCCGTTCGACGTTTTGATGGAGCAAAAGCTTCTGCCTGCATTCGGCCTGAAGAACACCTTCATCAATGTGCCGGCAAGCCAGATGAAGAACTACGCCTACGGATATTCCAAAGCCAACAAGCCGATCCGGGTATCGGGCGGGGCGCTGGATGCACAAGCCTATGGCATCAAGACCACCGCGCTTGATCTTGCCCGCTTCGTCGAACTGAACATCGACAGCTCATCTCTGGAGCCTGATTTCCAGAAAGCCGTCGCCGCAACGCATACCGGTTACTACCATGTCGGAGCGAACAATCAGGGACTTGGCTGGGAGTTCTACAACTATCCGACTGCGCTCAAGACACTTCTTGCCGGCAATTCGTCGGACATGGCGCTGAAGTCGCACAAAATCGAGAAATTCGATACACCTCGCCAACCGTCAGCTGATGTGCTGATCAATAAGACAGGCTCAACCAACGGCTTTGGCGCTTATGCGGCCTTTATTCCTGCGAAGAAGATCGGAATTGTTCTGCTTGCCAACCGGAATTATCCGATCGATGAGCGCGTAAAGGCTGCCTATCGGATATTGCAGGCGCTCGACAACAAGCAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37077","NCBI_taxonomy_name":"Brucella anthropi","NCBI_taxonomy_id":"529"}}}},"ARO_accession":"3002517","ARO_id":"38917","ARO_name":"OCH-4","CARD_short_name":"OCH-4","ARO_description":"OCH-4 beta-lactamase is an Ambler class C chromosomal-encoded beta-lactamases in Brucella anthropi.","ARO_category":{"36233":{"category_aro_accession":"3000094","category_aro_cvterm_id":"36233","category_aro_name":"OCH beta-lactamase","category_aro_description":"OCH beta-lactamases are Ambler class C chromosomal-encoded beta-lactamases in Brucella anthropi.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"775":{"model_id":"775","model_name":"CMY-113","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"863":{"protein_sequence":{"accession":"AIT76089.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAIIYEGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWRGISLLHLATYTAGGLPLQIPDDVTDKAELLRFYQNWQPQWTPGAKRLYANSSIGLFGALVVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQSEQKNYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASLVQEKTLQQGIELAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPARVEAAWRILEKLQ"},"dna_sequence":{"accession":"KM087836.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCACTGCTGCTGACAGCCTCTTTCTCCACGTTTGCTGCCGCAAAAACAGAACAACAAATTGCCGATATCGTTAACCGCACCATCACACCACTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTGGCGATTATCTACGAGGGGAAACCTTATTACTTTACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGACGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCGGGGTATCAGCCTGCTGCACTTAGCCACCTATACAGCGGGTGGCCTGCCGCTGCAGATCCCCGATGACGTTACGGATAAAGCCGAATTACTGCGCTTTTATCAAAACTGGCAACCACAATGGACTCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGTGCGCTGGTGGTAAAACCTTCAGGTATGAGCTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAAAGCGAACAAAAAAATTATGCCTGGGGCTATCGCGAAGGGAAGCCTGTACACGTTTCTCCGGGGCAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATCGATATGGCCCGCTGGGTTCAGGCCAACATGGACGCCAGCCTCGTTCAGGAGAAAACGCTCCAGCAGGGCATTGAGCTTGCGCAGTCTCGCTACTGGCGTATTGGTGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCAGCACCTGCCGTGAAAGCCTCATGGGTGCATAAAACAGGATCCACAGGCGGATTTGGCAGCTACGTTGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTAATGTTGGCAAACAAAAGCTACCCCAACCCGGCTCGCGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002124","ARO_id":"38524","ARO_name":"CMY-113","CARD_short_name":"CMY-113","ARO_description":"CMY-113 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"783":{"model_id":"783","model_name":"NDM-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4450":{"protein_sequence":{"accession":"CAZ39946.1","sequence":"MELPNIMHPVAKLSTALAAALMLSGCMPGEIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR"},"dna_sequence":{"accession":"FN396876.1","fmin":"2406","fmax":"3219","strand":"-","sequence":"ATGGAATTGCCCAATATTATGCACCCGGTCGCGAAGCTGAGCACCGCATTAGCCGCTGCATTGATGCTGAGCGGGTGCATGCCCGGTGAAATCCGCCCGACGATTGGCCAGCAAATGGAAACTGGCGACCAACGGTTTGGCGATCTGGTTTTCCGCCAGCTCGCACCGAATGTCTGGCAGCACACTTCCTATCTCGACATGCCGGGTTTCGGGGCAGTCGCTTCCAACGGTTTGATCGTCAGGGATGGCGGCCGCGTGCTGGTGGTCGATACCGCCTGGACCGATGACCAGACCGCCCAGATCCTCAACTGGATCAAGCAGGAGATCAACCTGCCGGTCGCGCTGGCGGTGGTGACTCACGCGCATCAGGACAAGATGGGCGGTATGGACGCGCTGCATGCGGCGGGGATTGCGACTTATGCCAATGCGTTGTCGAACCAGCTTGCCCCGCAAGAGGGGATGGTTGCGGCGCAACACAGCCTGACTTTCGCCGCCAATGGCTGGGTCGAACCAGCAACCGCGCCCAACTTTGGCCCGCTCAAGGTATTTTACCCCGGCCCCGGCCACACCAGTGACAATATCACCGTTGGGATCGACGGCACCGACATCGCTTTTGGTGGCTGCCTGATCAAGGACAGCAAGGCCAAGTCGCTCGGCAATCTCGGTGATGCCGACACTGAGCACTACGCCGCGTCAGCGCGCGCGTTTGGTGCGGCGTTCCCCAAGGCCAGCATGATCGTGATGAGCCATTCCGCCCCCGATAGCCGCGCCGCAATCACTCATACGGCCCGCATGGCCGACAAGCTGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3000589","ARO_id":"36728","ARO_name":"NDM-1","CARD_short_name":"NDM-1","ARO_description":"NDM-1 is a metallo-beta-lactamase isolated from Klebsiella pneumoniae with nearly complete resistance to all beta-lactam antibiotics.","ARO_category":{"36196":{"category_aro_accession":"3000057","category_aro_cvterm_id":"36196","category_aro_name":"NDM beta-lactamase","category_aro_description":"NDM beta-lactamases or New Delhi metallo-beta-lactamases are class B beta-lactamases that confer resistance to a broad range of antibiotics including carbapenems, cephalosporins and penicillins.","category_aro_class_name":"AMR Gene Family"},"35987":{"category_aro_accession":"0000070","category_aro_cvterm_id":"35987","category_aro_name":"ertapenem","category_aro_description":"Ertapenem is a carbapenem antibiotic and is highly resistant to beta-lactamases like other carbapenems. It inhibits bacterial cell wall synthesis.","category_aro_class_name":"Antibiotic"},"35990":{"category_aro_accession":"0000073","category_aro_cvterm_id":"35990","category_aro_name":"meropenem","category_aro_description":"Meropenem is an ultra-broad spectrum injectable antibiotic used to treat a wide variety of infections, including meningitis and pneumonia. It is a beta-lactam and belongs to the subgroup of carbapenem, similar to imipenem and ertapenem.","category_aro_class_name":"Antibiotic"},"36309":{"category_aro_accession":"3000170","category_aro_cvterm_id":"36309","category_aro_name":"imipenem","category_aro_description":"Imipenem is a broad-spectrum antibiotic and is usually taken with cilastatin, which prevents hydrolysis of imipenem by renal dehydropeptidase-I. It is resistant to hydrolysis by most other beta-lactamases. Notable exceptions are the KPC beta-lactamases and Ambler Class B enzymes.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"778":{"model_id":"778","model_name":"IMP-25","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1986":{"protein_sequence":{"accession":"ACB41775.1","sequence":"MSKLSVFFIFLFCSIATAAESLPDLKIEKLDEGVYVHTSFEEVNGWGVVPKHGLVVLVNAEAYLIDTPFTAKDTEKLVTWFVERGYKIKGSISSHFHSDSTGGIEWLNSRSIPTYASELTNELLKKDGKVQATNSFSGVNYWLVKNKIEVFYPGPGHTPDNVVVWLPERKILFGGCFIKPYGLGNLSDANIEAWPKSAKLLKSKYGKAKLVVPGHSEVGDASLLKLTLEQAVKGLNESKKPSKPSN"},"dna_sequence":{"accession":"EU541448.1","fmin":"0","fmax":"741","strand":"+","sequence":"ATGAGCAAGTTATCTGTATTCTTTATATTTTTGTTTTGCAGCATTGCTACCGCAGCAGAGTCTTTGCCAGATTTAAAAATTGAAAAGCTTGATGAAGGCGTTTATGTTCATACTTCGTTTGAAGAAGTTAACGGGTGGGGCGTTGTTCCTAAACATGGTTTGGTGGTTCTTGTAAATGCTGAGGCTTACCTAATTGACACTCCATTTACGGCTAAAGATACTGAAAAGTTAGTCACTTGGTTTGTGGAGCGTGGCTATAAAATAAAAGGCAGCATTTCCTCTCATTTTCATAGCGACAGCACGGGCGGAATAGAGTGGCTTAATTCTCGATCTATCCCCACGTATGCATCTGAATTAACAAATGAACTGCTTAAAAAAGACGGTAAGGTTCAAGCCACAAATTCATTTAGCGGAGTTAACTATTGGCTAGTTAAAAATAAAATTGAAGTTTTTTATCCAGGCCCGGGACACACTCCAGATAACGTAGTGGTTTGGTTGCCTGAAAGGAAAATATTATTCGGTGGTTGTTTTATTAAACCGTACGGTTTAGGCAATTTGAGTGACGCAAATATAGAAGCTTGGCCAAAGTCCGCCAAATTATTAAAGTCCAAATATGGTAAGGCAAAACTGGTTGTTCCAGGTCACAGTGAAGTTGGAGACGCATCACTCTTGAAACTTACATTAGAGCAGGCGGTTAAAGGGTTAAACGAAAGTAAAAAACCATCAAAACCAAGCAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002216","ARO_id":"38616","ARO_name":"IMP-25","CARD_short_name":"IMP-25","ARO_description":"IMP-25 is a beta-lactamase found in Serratia marcescens.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"779":{"model_id":"779","model_name":"OXA-350","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1053":{"protein_sequence":{"accession":"AGW83448.1","sequence":"MYKKALIVTTSILFLSACSSNSVKQNQIHSISANKNSEEIKSLFDQAQTTGVLVIKRGQTEEIYGNDLKRASTAYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMSKEVKRIGFGNANIGSKVDDFWLVGPLKITPQQETQFAYQLAHKTLPFSKNVQEQVQSMVFIEEKNGSKIYAKSGWGWDVEPQVGWLTGWVVQPQGEIVAFSLNLEMNKGTPSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"KF297579.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGTATAAAAAAGCCCTTATCGTTACAACAAGTATCCTATTTTTATCCGCCTGTTCTTCTAATTCAGTAAAACAAAATCAAATACATTCTATTTCTGCCAATAAAAATTCAGAAGAAATTAAATCACTGTTTGATCAGGCACAGACCACGGGTGTTTTGGTTATTAAGCGAGGGCAAACAGAAGAAATTTATGGAAATGATCTTAAAAGAGCATCAACCGCCTATGTTCCCGCTTCTACCTTTAAAATGTTAAATGCTTTAATTGGACTTGAACATCATAAGGCAACTACAACTGAAGTATTTAAATGGGATGGGCAAAAGCGTTTATTTCCTGATTGGGAAAAGGACATGACACTGGGTGATGCCATGAAAGCTTCTGCAATTCCAGTTTACCAAGAATTAGCCCGACGTATTGGTCTGGATCTTATGTCCAAAGAGGTGAAACGAATTGGTTTCGGTAATGCTAACATTGGCTCAAAAGTAGATGATTTCTGGCTTGTTGGGCCTCTAAAAATTACACCTCAACAAGAAACCCAATTTGCTTATCAATTAGCCCATAAAACTCTTCCATTTAGCAAAAATGTACAAGAACAAGTTCAATCAATGGTGTTCATAGAAGAAAAAAATGGAAGTAAAATTTATGCCAAAAGTGGTTGGGGATGGGATGTTGAACCACAAGTTGGTTGGTTAACAGGTTGGGTCGTTCAACCACAAGGAGAAATTGTCGCATTCTCACTTAATTTAGAAATGAACAAAGGAACTCCTAGCTCTATTCGCAAAGAAATTGCTTATAAAGGCTTAGAACAACTGGGTATCTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39094","NCBI_taxonomy_name":"Acinetobacter calcoaceticus","NCBI_taxonomy_id":"471"}}}},"ARO_accession":"3001537","ARO_id":"37937","ARO_name":"OXA-350","CARD_short_name":"OXA-350","ARO_description":"OXA-350 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46495":{"category_aro_accession":"3007706","category_aro_cvterm_id":"46495","category_aro_name":"OXA-213-like beta-lactamase","category_aro_description":"OXA-213-like enzymes have been identified to be intrinsic to A. calcoaceticus and have been subsequently detected in A. pittii. Phylogenetic analysis of OXA-213-like proteins identified two distinct subgroups within the OXA family. The first group was linked to A. pittii and the second group to A. calcoaceticus. The carbapenemase activity of these OXAs may be related to the species-dependent effect.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"780":{"model_id":"780","model_name":"CARB-9","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1973":{"protein_sequence":{"accession":"AAP22374.1","sequence":"MKSLLVFALLMPSVVFASSSKFQSVEQEIKGIESSLSARIGVAILDTQNGESWDYNGDQRFPLTSTFKTIACAKLLYDAEHGKVNLNSTVEVKKADLVTYSPVLEKQVGKPITLSDACFATMTTSDNTAANIVINAVGDPKSITDFLRQIGDKETRLDRVEPELNEGKLGDLRDTTTPNAITSTLNQLLFGSTLSEASQKKLESWMVNNQVTGNLLRSVLPVTWSIADRSGAGGFGARSITAIVWSEEKKPIIVSIYLAQTEASMAERNDAIVKIGRSIFEVYTSQSR"},"dna_sequence":{"accession":"AY248038.1","fmin":"2072","fmax":"2939","strand":"+","sequence":"ATGAAGTCTTTGTTGGTATTTGCGCTTTTAATGCCATCTGTAGTTTTTGCAAGCAGTTCAAAATTTCAATCAGTTGAACAAGAAATTAAGGGAATTGAGTCTTCACTCTCTGCTCGTATAGGAGTTGCCATTTTGGATACTCAAAATGGCGAAAGCTGGGATTATAATGGTGATCAACGATTTCCATTAACAAGTACTTTCAAAACAATAGCTTGTGCTAAGTTGCTGTATGATGCAGAGCATGGGAAAGTTAATCTCAATAGTACAGTTGAGGTTAAGAAAGCAGATCTTGTTACGTATTCGCCTGTATTAGAAAAGCAAGTAGGTAAACCAATAACGCTCTCTGATGCATGCTTTGCTACTATGACAACAAGCGACAATACAGCAGCCAATATTGTTATAAATGCTGTGGGTGATCCTAAAAGCATTACTGATTTTCTGAGACAAATTGGTGACAAAGAAACTCGTCTAGATCGTGTCGAGCCTGAGCTCAATGAAGGTAAACTCGGTGATTTGAGGGATACGACAACGCCTAATGCAATAACCAGCACGTTAAATCAATTATTATTTGGTTCCACATTATCTGAAGCTAGTCAGAAAAAATTAGAGTCTTGGATGGTGAACAATCAAGTTACGGGTAATTTATTGAGGTCAGTATTGCCAGTGACGTGGAGTATTGCTGATCGCTCAGGGGCAGGTGGATTTGGTGCTAGGAGTATTACAGCGATTGTGTGGAGTGAAGAAAAAAAACCGATTATCGTAAGTATTTATCTAGCTCAAACCGAGGCTTCAATGGCAGAACGAAATGATGCGATAGTTAAGATTGGTCGTTCAATTTTTGAAGTTTATACATCACAGTCGCGTTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36920","NCBI_taxonomy_name":"Vibrio cholerae non-O1\/non-O139","NCBI_taxonomy_id":"156539"}}}},"ARO_accession":"3002248","ARO_id":"38648","ARO_name":"CARB-9","CARD_short_name":"CARB-9","ARO_description":"CARB-9 is a beta-lactamase found in Vibrio cholerae.","ARO_category":{"36230":{"category_aro_accession":"3000091","category_aro_cvterm_id":"36230","category_aro_name":"CARB beta-lactamase","category_aro_description":"CARB beta-lactamases are class A lactamases that can hydrolyze carbenicillin. Many of the PSE beta-lactamases have been renamed as CARB-lactamases with the notable exception of PSE-2 which is now OXA-10.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"781":{"model_id":"781","model_name":"QnrB25","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"73":{"protein_sequence":{"accession":"ADN94685.1","sequence":"MALALVGEKIDRNRFTGEKVENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAILKDAIFKSCDLSMADFRNVSALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITSTNLSYANFSKAVLEKCELWENRWMGTQVLGATLSGSDLSGGEFSSFDWRTANFTHCDLTNSELGDLDIRGVDLQGVKLDSYQAALLMERLGIAIIG"},"dna_sequence":{"accession":"HQ172108.1","fmin":"0","fmax":"645","strand":"+","sequence":"ATGGCTCTGGCGTTAGTTGGCGAAAAAATTGACAGAAACCGCTTCACCGGTGAAAAAGTTGAAAATAGCACTTTTTTTAACTGTGATTTTTCGGGTGCCGACCTTAGCGGTACTGAATTTATCGGCTGTCAGTTCTATGATCGAGAAAGCCAGAAAGGGTGCAATTTCAGTCGCGCAATACTGAAAGATGCCATTTTTAAAAGCTGTGATTTATCCATGGCGGATTTTCGCAATGTCAGTGCGTTGGGCATAGAAATTCGCCACTGCCGCGCACAGGGTGCAGATTTTCGCGGCGCAAGTTTCATGAATATGATCACCACGCGCACCTGGTTTTGCAGCGCATATATCACTAGTACCAATCTAAGCTACGCCAACTTTTCGAAGGCCGTGCTTGAAAAGTGCGAATTGTGGGAAAATCGCTGGATGGGAACTCAGGTGCTGGGTGCGACGTTGAGTGGTTCCGATCTCTCCGGTGGCGAGTTTTCGTCGTTCGACTGGCGGACGGCAAATTTCACGCACTGTGATTTGACCAATTCAGAACTGGGTGATTTAGATATTCGGGGCGTCGATTTACAAGGTGTCAAATTGGACAGCTATCAGGCCGCATTGCTCATGGAACGTCTTGGCATCGCTATCATTGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002740","ARO_id":"39174","ARO_name":"QnrB25","CARD_short_name":"QnrB25","ARO_description":"QnrB25 is a plasmid-mediated quinolone resistance protein found in Citrobacter freundii.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"782":{"model_id":"782","model_name":"OXA-63","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1615":{"protein_sequence":{"accession":"AAU88145.1","sequence":"MSKKNFILIFIFVILISCKNTEKISNETTLIDNIFTNSNAEGTLVIYNLNDDKYIIHNKERAEQRFYPASTFKIYNSLIGLNEKAVKDVDEVFYKLMAKSFLESWAKDSNLRYAIKNSQVPAYKELARRIGIKKMKENIEKLDFGNKSIGDSVDTFWLEGPLEISAMEQVKLLTKLAQNELQYPIEIQKAISDITITRANLHITLHGKTGLADSKNMTTEPIGWFVGWLEENDNIYVFALNIDNINSDDLAKRINIVKESLKALNLLK"},"dna_sequence":{"accession":"AY619003.1","fmin":"703","fmax":"1510","strand":"+","sequence":"ATGTCTAAAAAAAATTTTATATTAATATTTATTTTTGTTATTTTAATATCTTGTAAAAATACAGAAAAAATATCAAATGAAACTACATTAATAGATAATATATTTACTAATAGCAATGCTGAAGGAACATTAGTTATATATAATTTAAATGATGATAAATATATAATTCATAATAAAGAAAGAGCTGAACAAAGATTTTATCCAGCATCAACATTTAAAATATATAATAGTTTAATAGGCTTAAATGAAAAAGCAGTTAAAGATGTAGATGAAGTATTTTATAAATTAATGGCGAAAAGTTTTCTCGAATCTTGGGCTAAAGACTCTAATTTAAGATATGCAATTAAAAATTCGCAAGTACCGGCATATAAAGAATTAGCAAGAAGAATAGGTATTAAAAAGATGAAAGAGAATATAGAAAAACTAGATTTTGGTAATAAAAGTATAGGTGATAGTGTAGATACTTTTTGGCTTGAAGGACCTTTGGAAATAAGTGCGATGGAGCAAGTTAAATTATTAACTAAATTAGCTCAAAATGAATTACAGTATCCTATAGAAATACAAAAAGCTATTTCTGATATTACTATTACTAGAGCAAACTTACATATTACGCTTCATGGAAAAACTGGATTAGCTGATTCTAAAAACATGACAACTGAGCCTATTGGTTGGTTCGTAGGCTGGCTTGAAGAAAATGATAATATATACGTCTTTGCTTTAAATATTGATAATATCAATTCAGATGACCTTGCAAAAAGGATAAATATAGTAAAAGAAAGTTTAAAAGCATTAAATTTATTAAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36935","NCBI_taxonomy_name":"Brachyspira pilosicoli","NCBI_taxonomy_id":"52584"}}}},"ARO_accession":"3001764","ARO_id":"38164","ARO_name":"OXA-63","CARD_short_name":"OXA-63","ARO_description":"OXA-63 is a beta-lactamase found in Brachyspira spp.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46521":{"category_aro_accession":"3007732","category_aro_cvterm_id":"46521","category_aro_name":"OXA-63-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-63.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"784":{"model_id":"784","model_name":"AAC(6')-Iv","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"81":{"protein_sequence":{"accession":"AAD03494.1","sequence":"MKIMPISESQLSDWLVLRCLLWPDHEEQHLQEMRQLITQAHCLQLLAYTDTQQAIAMLEASIRYEYVNGTQTSPVAFLEGIYVLPEYRRSGIATGLVQHVEIWAKQFSCTEFASDAALDNQITHAMHQALGFQETERVVYFKKNIG"},"dna_sequence":{"accession":"AF031330.1","fmin":"0","fmax":"441","strand":"+","sequence":"ATGAAGATTATGCCGATATCTGAATCACAATTATCAGATTGGCTAGTATTGAGATGCTTACTCTGGCCTGATCATGAGGAACAGCATTTACAGGAAATGCGTCAACTGATCACACAGGCACATTGCTTACAATTATTGGCTTATACCGACACCCAACAAGCAATTGCCATGCTGGAAGCTTCAATTCGATATGAATATGTGAATGGCACACAGACATCACCTGTGGCTTTTCTTGAAGGGATTTATGTATTGCCTGAATATCGCCGTTCAGGTATCGCAACGGGTTTGGTTCAGCATGTCGAAATCTGGGCCAAACAGTTTTCATGCACAGAGTTTGCCTCAGATGCAGCGCTGGATAATCAGATCACCCATGCAATGCATCAAGCACTCGGTTTTCAAGAAACTGAACGTGTGGTGTATTTTAAGAAAAATATTGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39517","NCBI_taxonomy_name":"Acinetobacter sp. 631","NCBI_taxonomy_id":"70349"}}}},"ARO_accession":"3002566","ARO_id":"38966","ARO_name":"AAC(6')-Iv","CARD_short_name":"AAC(6')-Iv","ARO_description":"AAC(6')-Iv is a chromosomal-encoded aminoglycoside acetyltransferase in Acinetobacter sp.","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"A category of aminoglycoside N-acetyltransferase enzymes with modification regiospecificity based at the 6'-amino group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics through acetylation of the 6-amino group of the compound.","category_aro_class_name":"AMR Gene Family"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"46128":{"category_aro_accession":"3007378","category_aro_cvterm_id":"46128","category_aro_name":"2'-N-ethylnetilmicin","category_aro_description":"2'-N-ethylnetilmicin is an aminoglycoside antibiotic and a derivative of netilmicin.","category_aro_class_name":"Antibiotic"},"46129":{"category_aro_accession":"3007379","category_aro_cvterm_id":"46129","category_aro_name":"5-episisomicin","category_aro_description":"5-episosomicin is a semisynthetic aminoglycoside antibiotic similar to sisomicin.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"785":{"model_id":"785","model_name":"OXY-2-9","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1770":{"protein_sequence":{"accession":"ACV44455.1","sequence":"MIKSSWRKIAMLAAVPLLLASGALWASTDAIHQKLTDLEKRSGGRLGVALINTADNSQILYRGDERFAMCSTSKVMAAAAVLKQSESNKEVVNKRLEINAADLVVWSPITEKHLQSGMTLAELSAATLQYSDNTAMNLIIGYLGGPEKVTAFARSIGDATFRLDRTEPTLNTAIPGDERDTSTPLAMAESLRKLTLGDALGEQQRAQLVTWLKGNTTGGQSIRAGLPESWVVGDKTGTGDYGTTNDIAVIWPEDHAPLVLVTYFTQPQQDAKNRKEVLAAAAKIVTEGL"},"dna_sequence":{"accession":"FJ785625.1","fmin":"131","fmax":"1001","strand":"+","sequence":"ATGATAAAAAGTTCGTGGCGTAAAATTGCAATGCTAGCCGCCGTTCCGCTGCTGCTGGCGAGCGGCGCACTGTGGGCCAGTACCGATGCTATCCATCAGAAGCTGACAGATCTCGAGAAGCGTTCAGGCGGCAGGTTGGGCGTGGCGCTAATCAACACGGCAGATAATTCTCAAATCTTATATCGCGGCGACGAGCGTTTTGCCATGTGCAGCACCAGTAAAGTGATGGCCGCCGCCGCGGTATTAAAACAGAGCGAAAGCAATAAAGAGGTGGTAAATAAAAGGCTGGAGATTAACGCAGCCGATTTGGTGGTCTGGAGTCCGATTACCGAAAAACATCTCCAGAGCGGAATGACGCTGGCTGAGCTAAGCGCGGCGACGCTGCAATATAGCGACAATACGGCGATGAATCTGATCATCGGCTACCTTGGCGGGCCGGAAAAAGTCACCGCCTTCGCCCGCAGTATCGGCGATGCCACCTTTCGTCTCGATCGTACGGAGCCCACGCTGAATACCGCCATCCCGGGCGATGAGCGTGATACCAGCACGCCGCTGGCGATGGCTGAAAGCCTACGCAAGCTGACGCTTGGCGATGCGCTGGGCGAACAGCAACGCGCCCAGTTAGTCACCTGGCTGAAAGGCAATACCACCGGCGGGCAAAGCATTCGCGCGGGCCTGCCTGAAAGCTGGGTGGTCGGCGATAAAACCGGCACCGGAGATTACGGCACCACCAATGATATTGCGGTTATCTGGCCGGAAGATCACGCTCCGCTGGTATTAGTCACCTACTTTACCCAGCCGCAGCAGGATGCGAAAAACCGCAAAGAGGTGTTAGCCGCAGCGGCAAAAATCGTGACCGAAGGGCTTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3002404","ARO_id":"38804","ARO_name":"OXY-2-9","CARD_short_name":"OXY-2-9","ARO_description":"OXY-2-9 is a beta-lactamase found in Klebsiella oxytoca.","ARO_category":{"38788":{"category_aro_accession":"3002388","category_aro_cvterm_id":"38788","category_aro_name":"OXY beta-lactamase","category_aro_description":"OXY beta-lactamases are chromosomal class A beta-lactamases that are found in Klebsiella oxytoca. At constitutive low levels, OXY beta-lactamases confer resistance to aminopenicillins and carboxypenicillins. At high induced levels,  OXY beta-lactamases confer resistance to penicillins, cephalosporins and aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"787":{"model_id":"787","model_name":"dfrA23","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"8173":{"protein_sequence":{"accession":"CAG34233.2","sequence":"MPTVEIIVAVDPVGGFGRNGQIPWTCKEDMKRFTTISKEIRVCVMGKNTYKDMLDMQMKKEGAEERIKEKGILPERESYVVSSTLKPEDVIGATVVPDLRAVLNQYHDSDQRIAVIGGEKLYVQALASATKVHMTVMHKPYNCDRTLPMSYIDKKFVAGQGSITIQTAVDGETHPVKFITYERARP"},"dna_sequence":{"accession":"AJ746361.2","fmin":"6742","fmax":"7303","strand":"-","sequence":"ATGCCAACAGTTGAGATTATTGTTGCAGTTGATCCTGTTGGGGGATTTGGCCGGAATGGCCAAATCCCTTGGACGTGCAAGGAAGACATGAAGCGCTTCACCACCATATCCAAAGAGATTCGAGTGTGTGTGATGGGGAAGAACACATACAAAGACATGCTCGATATGCAAATGAAGAAGGAAGGCGCTGAAGAACGAATCAAAGAGAAGGGAATTCTTCCGGAGCGCGAATCTTACGTCGTGTCCTCGACTTTGAAGCCCGAGGACGTCATTGGAGCCACGGTAGTTCCGGACCTACGTGCGGTGCTCAATCAATATCACGACAGCGATCAACGAATAGCTGTCATTGGTGGAGAAAAGCTGTACGTGCAAGCCCTCGCATCTGCCACAAAAGTCCACATGACGGTAATGCACAAGCCATATAACTGCGATCGGACGTTGCCGATGTCATACATCGACAAAAAGTTTGTTGCAGGTCAAGGGTCTATCACCATTCAAACTGCGGTAGATGGTGAGACCCATCCCGTGAAGTTCATCACATATGAGCGCGCTCGGCCGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35732","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Typhimurium","NCBI_taxonomy_id":"90371"}}}},"ARO_accession":"3003019","ARO_id":"39453","ARO_name":"dfrA23","CARD_short_name":"dfrA23","ARO_description":"dfrA23 is an integron-encoded dihydrofolate reductase found in Salmonella enterica.","ARO_category":{"37617":{"category_aro_accession":"3001218","category_aro_cvterm_id":"37617","category_aro_name":"trimethoprim resistant dihydrofolate reductase dfr","category_aro_description":"Alternative dihydropteroate synthase dfr present on plasmids produces alternate proteins that are less sensitive to trimethoprim from inhibiting its role in folate synthesis, thus conferring trimethoprim resistance.","category_aro_class_name":"AMR Gene Family"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"788":{"model_id":"788","model_name":"SHV-46","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"919":{"protein_sequence":{"accession":"AAO53445.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLNSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGASKRGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AY210887.1","fmin":"111","fmax":"972","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGAACAGCCAACGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTAGCAAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAATCAACAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3001104","ARO_id":"37484","ARO_name":"SHV-46","CARD_short_name":"SHV-46","ARO_description":"SHV-46 is an extended-spectrum beta-lactamase found in Klebsiella oxytoca.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"789":{"model_id":"789","model_name":"IMP-43","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"791":{"protein_sequence":{"accession":"BAM98935.1","sequence":"MKKLSVFFMFLFCSIAASGEALPDLKIEKLDEGVYVHTSFEEVNGWGVFPKHGLVVLVNTDAYLIDTPFTAKDTEKLVTWFVERGYKIKGSISSHFHSDSTGGIEWLNSQSIPTYASELTNELLKKDGKVQAKNSFSGASYWLVKKKIEIFYPGPGHTPDNVVVWLPEHRVLFGGCFVKPYGLGNLGDANLEAWPKSAKLLVSKYGKAKLVVPSHSEVGDASLLKRTLEQAVKGLNESKKLSKPSN"},"dna_sequence":{"accession":"AB777500.1","fmin":"2034","fmax":"2775","strand":"+","sequence":"ATGAAAAAGTTATCAGTATTCTTTATGTTTTTGTTTTGTAGCATTGCTGCCTCAGGAGAGGCTTTGCCAGATTTAAAAATTGAGAAGCTTGACGAAGGCGTTTATGTTCATACTTCGTTTGAGGAAGTTAACGGCTGGGGCGTGTTTCCTAAACACGGCTTGGTGGTTCTTGTAAATACTGACGCTTATTTGATTGACACTCCATTTACAGCTAAAGATACTGAAAAGTTAGTTACTTGGTTTGTAGAGCGCGGCTATAAAATAAAAGGCAGTATCTCCTCTCATTTTCATAGCGACAGCACGGGCGGAATAGAGTGGCTTAATTCTCAATCTATTCCAACATATGCATCTGAATTAACAAATGAACTTCTTAAAAAAGACGGTAAGGTACAAGCTAAAAATTCATTTAGCGGAGCCAGCTATTGGTTAGTTAAGAAAAAGATTGAAATTTTTTATCCTGGCCCAGGGCACACTCCAGATAACGTAGTGGTTTGGCTACCTGAACATAGAGTTTTGTTTGGTGGTTGTTTTGTTAAACCGTATGGTCTAGGTAATTTGGGTGACGCAAATTTAGAAGCTTGGCCAAAGTCTGCCAAATTATTAGTGTCCAAATATGGTAAGGCAAAACTGGTTGTTCCAAGTCACAGTGAAGTTGGAGATGCATCACTCTTGAAACGTACATTAGAACAGGCTGTTAAAGGATTAAACGAAAGTAAAAAGCTATCAAAACCAAGTAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002234","ARO_id":"38634","ARO_name":"IMP-43","CARD_short_name":"IMP-43","ARO_description":"IMP-43 is a beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"790":{"model_id":"790","model_name":"CMY-32","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1858":{"protein_sequence":{"accession":"ACA97846.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHVSPEQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"EU496815.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGAACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002043","ARO_id":"38443","ARO_name":"CMY-32","CARD_short_name":"CMY-32","ARO_description":"CMY-32 is a beta-lactamase found in Escherichia coli.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"791":{"model_id":"791","model_name":"SHV-14","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1471":{"protein_sequence":{"accession":"AAG17550.1","sequence":"MRYFRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGSVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AF226622.1","fmin":"54","fmax":"915","strand":"+","sequence":"ATGCGTTATTTTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCAGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001073","ARO_id":"37453","ARO_name":"SHV-14","CARD_short_name":"SHV-14","ARO_description":"SHV-14 is an broad-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"792":{"model_id":"792","model_name":"OXY-1-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1938":{"protein_sequence":{"accession":"CAA82916.1","sequence":"MLKSSWRKTALMAAAAVPLLLASGSLWASADAIQQKLADLEKRSGGRLGVALINTADDSQTLYRGDERFAMCSTGKVMAAAAVLKQSESNPEVVNKRLEIKKSDLVVWSPITEKHLQSGMTLAELSAAALQYSDNTAMNKMISYLGGPEKVTAFAQSIGDVTFRLDRTEPALNSAIPGDKRDTTTPLAMAESLRKLTLGNALGEQQRAQLVTWLKGNTTGGQSIRAGLPASWAVGDKTGAGDYGTTNDIAVIWPENHAPLVLVTYFTQPQQDAKSRKEVLAAAAKIVTEGL"},"dna_sequence":{"accession":"Z30177.1","fmin":"348","fmax":"1224","strand":"+","sequence":"ATGTTGAAAAGTTCGTGGCGTAAAACCGCCCTGATGGCCGCCGCCGCCGTTCCGCTGCTGCTGGCGAGCGGTTCATTATGGGCCAGTGCCGATGCTATCCAGCAAAAGCTGGCTGATTTAGAAAAACGTTCCGGCGGTCGGCTGGGCGTAGCGCTGATTAACACGGCAGATGATTCGCAAACCCTCTATCGCGGCGATGAACGTTTTGCCATGTGCAGCACCGGTAAAGTGATGGCCGCCGCCGCGGTGTTAAAACAGAGCGAAAGCAATCCAGAGGTGGTGAATAAAAGGCTGGAGATTAAAAAATCGGATTTAGTGGTCTGGAGCCCGATCACCGAAAAACATCTGCAAAGCGGAATGACCCTGGCGGAACTCAGCGCGGCGGCGCTGCAGTACAGCGACAATACCGCGATGAATAAGATGATTAGCTACCTTGGCGGACCGGAAAAGGTGACCGCATTCGCCCAGAGTATCGGGGATGTCACTTTTCGTCTCGATCGTACGGAGCCGGCGCTGAACAGCGCGATTCCCGGCGATAAGCGCGATACCACCACCCCGTTGGCGATGGCCGAAAGCCTGCGCAAGCTGACGCTGGGCAATGCGCTGGGCGAACAGCAGCGCGCCCAGTTAGTGACGTGGCTAAAAGGCAATACCACCGGCGGGCAAAGCATTCGCGCAGGCCTGCCCGCAAGCTGGGCGGTCGGGGATAAAACCGGCGCCGGAGATTACGGCACCACCAACGATATCGCGGTGATCTGGCCGGAAAATCATGCCCCGCTGGTGCTGGTGACCTATTTTACCCAGCCGCAGCAGGATGCGAAAAGCCGCAAAGAGGTGTTAGCCGCGGCGGCAAAAATCGTCACCGAAGGGCTTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3002389","ARO_id":"38789","ARO_name":"OXY-1-1","CARD_short_name":"OXY-1-1","ARO_description":"OXY-1-1 is a beta-lactamase found in Klebsiella oxytoca.","ARO_category":{"38788":{"category_aro_accession":"3002388","category_aro_cvterm_id":"38788","category_aro_name":"OXY beta-lactamase","category_aro_description":"OXY beta-lactamases are chromosomal class A beta-lactamases that are found in Klebsiella oxytoca. At constitutive low levels, OXY beta-lactamases confer resistance to aminopenicillins and carboxypenicillins. At high induced levels,  OXY beta-lactamases confer resistance to penicillins, cephalosporins and aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"793":{"model_id":"793","model_name":"IMP-34","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"8228":{"protein_sequence":{"accession":"BAP75826.1","sequence":"MSKLSVFFIFLFCSIATAAESLPDLKIEKLDEGVYVHTSFEEVNGWGVVPKHGLVVLVNAEAYLIDTPFTAKDTEKLVTWFVERGYKIKGSISSHFHSDSTGGIGWLNSRSIPTYASELTNELLKKDGKVQATNSFSGVNYWLVKNKIEVFYPGPGHTPDNVVVWLPERKILFGGCFIKPYGLGNLGDANIEAWPKSAKLLKSKYGKAKLVVPSHSEVGDASLLKLTLEQAVKGLNESKKPSKPSN"},"dna_sequence":{"accession":"AB715422.2","fmin":"27225","fmax":"27966","strand":"+","sequence":"ATGAGCAAGTTATCTGTATTCTTTATATTTTTGTTTTGCAGCATTGCTACCGCAGCAGAGTCTTTGCCAGATTTAAAAATTGAAAAGCTTGATGAAGGCGTTTATGTTCATACTTCGTTTGAAGAAGTTAACGGGTGGGGCGTTGTTCCTAAACATGGTTTGGTGGTTCTTGTAAATGCTGAGGCTTATTTAATTGACACTCCATTTACGGCTAAAGATACTGAAAAGTTAGTCACTTGGTTTGTGGAGCGTGGCTATAAAATAAAAGGCAGTATTTCCTCTCATTTTCATAGCGACAGCACGGGCGGAATAGGGTGGCTTAATTCTCGATCTATCCCCACGTATGCATCTGAATTAACAAATGAACTGCTTAAAAAAGACGGTAAGGTTCAAGCCACAAATTCATTTAGCGGAGTTAACTATTGGCTAGTTAAAAATAAAATTGAAGTTTTTTATCCAGGCCCGGGACACACTCCAGATAACGTAGTGGTTTGGCTGCCTGAAAGGAAAATATTATTCGGTGGTTGTTTTATTAAACCGTACGGTTTAGGCAATTTGGGTGACGCAAATATAGAAGCTTGGCCAAAGTCCGCCAAATTATTAAAGTCCAAATATGGTAAGGCAAAACTGGTTGTTCCAAGTCACAGTGAAGTTGGAGACGCATCACTCTTGAAACTTACATTAGAGCAGGCGGTTAAAGGATTAAACGAAAGTAAAAAACCATCAAAACCAAGCAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3002225","ARO_id":"38625","ARO_name":"IMP-34","CARD_short_name":"IMP-34","ARO_description":"IMP-34 is a beta-lactamase found in Klebsiella spp.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"795":{"model_id":"795","model_name":"OXA-324","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"807":{"protein_sequence":{"accession":"AGW16406.1","sequence":"MYKKTLIVTTSILFLSACSSNSVKQHQIHSMSANKNSEEIKSLFDQAQTTGVLVIKRGKTEEIYGNDLKRASTAYVPASTFKMLNALIGLEHHKATATEVFKWDGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMSKEVKRIGFGNANIGSKVDNFWLVGPLKITPQQETQFAYQLAHKTLPFSKDVQEQVQSMVFIEEKNGSKIYAKSGWGWDVEPQVGWLTGWVVQPQGEIVAFSLNLEMKKGTPSSIRKEIAYKGLEQLAIL"},"dna_sequence":{"accession":"KF203098.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGTATAAAAAAACCCTTATCGTTACAACAAGTATCCTATTTTTATCCGCCTGTTCTTCTAATTCAGTAAAACAACATCAAATACACTCTATGTCTGCCAATAAAAATTCAGAAGAAATTAAATCACTGTTTGATCAAGCACAAACCACGGGTGTTTTGGTAATTAAGCGAGGGAAAACAGAAGAAATTTATGGCAATGATCTTAAAAGAGCATCAACCGCCTATGTTCCCGCCTCTACCTTTAAAATGTTAAATGCTTTAATTGGACTTGAACACCATAAGGCAACTGCAACTGAAGTGTTTAAATGGGATGGGCAAAAACGTTTATTTCCTGATTGGGAAAAAGACATGACGCTGGGCGATGCCATGAAAGCTTCTGCTATTCCAGTTTATCAAGAATTAGCCCGACGAATTGGACTTGACCTTATGTCTAAAGAGGTAAAAAGAATTGGTTTCGGTAATGCTAACATTGGTTCAAAAGTAGATAATTTTTGGCTTGTTGGCCCTCTAAAAATTACGCCTCAACAAGAAACCCAATTTGCTTATCAATTAGCCCATAAAACGCTTCCATTTAGCAAAGATGTACAAGAACAAGTTCAATCAATGGTGTTCATAGAGGAAAAAAATGGAAGTAAAATTTATGCCAAAAGTGGTTGGGGATGGGATGTTGAACCACAAGTTGGTTGGTTAACAGGTTGGGTCGTTCAACCACAAGGAGAAATTGTGGCATTCTCACTTAATTTAGAAATGAAAAAAGGAACTCCTAGCTCTATTCGCAAAGAAATTGCTTATAAAGGCTTAGAACAACTGGCTATCCTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39094","NCBI_taxonomy_name":"Acinetobacter calcoaceticus","NCBI_taxonomy_id":"471"}}}},"ARO_accession":"3001512","ARO_id":"37912","ARO_name":"OXA-324","CARD_short_name":"OXA-324","ARO_description":"OXA-324 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46495":{"category_aro_accession":"3007706","category_aro_cvterm_id":"46495","category_aro_name":"OXA-213-like beta-lactamase","category_aro_description":"OXA-213-like enzymes have been identified to be intrinsic to A. calcoaceticus and have been subsequently detected in A. pittii. Phylogenetic analysis of OXA-213-like proteins identified two distinct subgroups within the OXA family. The first group was linked to A. pittii and the second group to A. calcoaceticus. The carbapenemase activity of these OXAs may be related to the species-dependent effect.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"796":{"model_id":"796","model_name":"iri","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"900"}},"model_sequences":{"sequence":{"474":{"protein_sequence":{"accession":"AAB41059.1","sequence":"MSDVIIVGAGPTGLMLAGELRLQGVDVVVVDKDEEPTQFVRALGIHVRSIEIMEQRGLLDKFLAHGRKYPLGGFFAGISKPAPAHLDTAHGYVLGIPQPEIDRILAEHATEVGADIQRGKRVVAIRQDTDNVAAELSDGTTLHARYLVGCDGGRSTVRKLRSTSVFPASRTSADTLIGEMDVTMPADELAAVVAEIRETHKRFGVGPAGNGAFRVVVPAAEVADGRATPTTLDDIKQQLLAIAGTDFGVHSPRWLSRFGDATRLADDYRRDRVFLAGDAAHIHPPMGGQGLNLGVQDAFNLGWKLAAEINGWAPVGLLDTYESERRPVAADVLDNTRAQAELISTAAGPQAVRRLISELMEFEDVKRYLTEKITAISIRYDFGEGDDLLGRRLRNIALTRGNLYDLMRSGRGLLLDQGGQLSVDGWSDRADHIVDTSTELEAPAVLLRPDGHVAWIGDAQAELDTQLSTWFGRSARDRA"},"dna_sequence":{"accession":"U56415.1","fmin":"279","fmax":"1719","strand":"+","sequence":"ATGAGTGACGTCATCATTGTCGGTGCTGGACCAACTGGATTGATGCTGGCAGGTGAGCTCCGGCTACAGGGCGTCGATGTCGTCGTCGTGGACAAGGACGAGGAGCCGACTCAGTTCGTCCGTGCCCTCGGCATCCATGTGCGCAGCATCGAAATCATGGAGCAGCGCGGGTTGCTGGACAAGTTCCTCGCGCACGGCCGCAAGTATCCGCTCGGTGGATTCTTCGCGGGGATCAGCAAACCGGCACCCGCGCACCTCGATACTGCGCACGGGTACGTCCTGGGCATACCTCAGCCCGAGATCGACAGGATTCTTGCCGAACATGCCACCGAAGTCGGCGCGGACATTCAGCGAGGGAAGCGCGTCGTCGCGATCCGTCAAGATACCGACAACGTCGCAGCGGAATTGTCCGACGGCACAACACTTCACGCGCGGTACCTTGTAGGCTGCGACGGCGGCCGCAGCACTGTTCGGAAGCTGAGATCGACGTCGGTATTCCCGGCGAGCCGTACGAGCGCCGACACGTTGATCGGCGAAATGGACGTGACCATGCCTGCTGATGAACTGGCCGCCGTTGTCGCCGAAATCCGGGAAACGCACAAACGATTCGGAGTCGGTCCCGCCGGCAACGGTGCTTTTCGTGTCGTGGTCCCTGCGGCCGAAGTTGCCGACGGTCGCGCAACACCGACCACCCTCGACGACATCAAACAACAGCTACTGGCCATTGCCGGTACCGACTTCGGTGTGCACTCGCCGCGGTGGCTCTCGCGCTTCGGCGACGCCACTCGTCTGGCGGACGACTACCGGCGCGACCGGGTGTTTCTCGCCGGCGACGCCGCACACATCCACCCACCGATGGGCGGTCAAGGTCTCAATCTCGGTGTGCAGGACGCCTTCAACCTCGGCTGGAAGCTCGCCGCCGAGATCAACGGCTGGGCACCGGTGGGCCTGCTCGACACGTACGAATCGGAACGGCGTCCGGTGGCTGCCGACGTGCTGGACAACACGCGCGCCCAGGCCGAGTTGATCTCCACCGCTGCCGGACCACAAGCGGTGCGGCGCTTGATCTCCGAGCTGATGGAATTCGAAGACGTCAAGCGCTATTTGACCGAGAAGATCACTGCGATCTCGATTCGCTACGATTTCGGCGAAGGCGACGACCTACTCGGTCGGAGGCTGCGGAACATCGCGTTGACGCGCGGCAACCTGTACGACCTGATGCGATCCGGCCGCGGACTTCTTCTCGACCAGGGTGGCCAACTGTCCGTCGATGGTTGGAGCGATCGCGCCGACCATATCGTTGACACAAGCACTGAATTGGAAGCTCCGGCTGTCCTGCTTCGGCCGGACGGTCATGTGGCATGGATCGGGGATGCGCAGGCGGAGTTGGATACTCAGCTGTCCACATGGTTCGGCCGGTCGGCGAGGGACCGCGCGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36897","NCBI_taxonomy_name":"Rhodococcus hoagii","NCBI_taxonomy_id":"43767"}}}},"ARO_accession":"3002884","ARO_id":"39318","ARO_name":"iri","CARD_short_name":"iri","ARO_description":"iri is a monooxygenase that confers resistance to rifampin found in Rhodococcus hoagii.","ARO_category":{"36584":{"category_aro_accession":"3000445","category_aro_cvterm_id":"36584","category_aro_name":"rifampin monooxygenase","category_aro_description":"Enzyme responsible for the decolorization of rifampin by monoxygenation.","category_aro_class_name":"AMR Gene Family"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36656":{"category_aro_accession":"3000517","category_aro_cvterm_id":"36656","category_aro_name":"rifaximin","category_aro_description":"Rifaximin is a semi-synthetic rifamycin used to treat traveller's diarrhea. Rifaximin inhibits RNA synthesis by binding to the beta subunit of bacterial RNA polymerase.","category_aro_class_name":"Antibiotic"},"36669":{"category_aro_accession":"3000530","category_aro_cvterm_id":"36669","category_aro_name":"rifabutin","category_aro_description":"Rifabutin is a semisynthetic rifamycin used in tuberculosis therapy. It inhibits DNA-dependent RNA synthesis.","category_aro_class_name":"Antibiotic"},"36673":{"category_aro_accession":"3000534","category_aro_cvterm_id":"36673","category_aro_name":"rifapentine","category_aro_description":"Rifapentine is a semisynthetic rifamycin that inhibits DNA-dependent RNA synthesis. It is often used in the treatment of tuberculosis and leprosy.","category_aro_class_name":"Antibiotic"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"797":{"model_id":"797","model_name":"TEM-55","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"2037":{"protein_sequence":{"accession":"ABB97007.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAEPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"DQ286729.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGAACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000924","ARO_id":"37304","ARO_name":"TEM-55","CARD_short_name":"TEM-55","ARO_description":"TEM-55 is a broad-spectrum beta-lactamase found in E. coli.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"798":{"model_id":"798","model_name":"cmeC","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"960"}},"model_sequences":{"sequence":{"492":{"protein_sequence":{"accession":"BAO79432.1","sequence":"MNKIISISAIASFTLLISACSLSPNLNIPEANYSIDNKLGALSWEKENNSSITKNWWKDFDDENLNKVVDLALKNNNDLKLAFIHMEQAAAQLGIDFSSLLPKFDGSASGSRAKTAINAPSNRTGEVSYGNDFKMGLNLSYEIDLWGKYRDTYRASKSSFKASEYDYEAARLSVISNTVQTYFNLVNAYENENALKEAYESAKEIYRINDEKFQVGAVGEYELAQARANLESMALQYNEAKLNKENYLKALKILTSNDLNDILYKNQSYQVFNLKEFDIPTGISSTILLQRPDIGSSLEKLTQQNYLVGVARTAFLPSLSLTGLLGFESGDLDTLVKGGSKTWNIGGNFTLPIFHWGEIYQNVNLAKLNKDEAFVNYQNTLITAFGEIRYALVARKTIRLQYDNAQASEQSYKRIYEIAKERYDIGEMSLQDYLEARQNWLNAAVAFNNTKYSYANSIIDVIKAFGGGFEQSEDTSKNIKEESKNLDMSFRE"},"dna_sequence":{"accession":"AB894099.1","fmin":"4218","fmax":"5697","strand":"+","sequence":"ATGAATAAAATAATTTCAATTAGTGCTATAGCAAGTTTTACTCTTTTGATTTCAGCTTGCTCTTTAAGTCCAAATTTAAATATTCCCGAAGCAAACTATAGCATTGATAATAAGCTTGGAGCCTTATCTTGGGAAAAAGAAAACAATAGCTCTATCACAAAAAATTGGTGGAAAGATTTTGATGATGAAAATTTAAATAAAGTGGTTGATTTAGCACTTAAAAATAATAATGATTTAAAACTTGCCTTCATACACATGGAACAAGCTGCTGCTCAATTAGGTATAGATTTTAGCAGTTTGTTGCCAAAATTTGATGGTAGCGCAAGCGGTAGTCGTGCAAAAACAGCTATAAATGCTCCAAGCAATCGAACTGGGGAAGTAAGTTACGGTAATGATTTTAAAATGGGGCTTAATTTAAGCTATGAAATCGATCTTTGGGGAAAATATCGCGATACATATCGTGCCTCAAAATCAAGCTTTAAAGCAAGTGAGTATGATTATGAAGCTGCAAGACTTTCTGTTATTTCAAATACGGTTCAAACTTATTTTAATCTTGTAAATGCTTATGAAAATGAAAATGCTCTTAAAGAAGCCTATGAATCTGCAAAAGAAATTTATAGGATTAATGATGAAAAATTTCAAGTTGGTGCTGTAGGTGAATATGAACTTGCTCAAGCAAGAGCCAACTTAGAAAGTATGGCTTTGCAATATAATGAAGCAAAATTAAATAAAGAAAATTACCTTAAAGCTTTAAAAATTTTAACTTCAAATGATTTAAATGACATACTTTACAAAAATCAAAGCTATCAAGTTTTTAATCTTAAAGAATTTGACATTCCAACTGGAATTTCAAGCACCATCTTGCTTCAACGTCCAGATATTGGCTCTTCTTTAGAAAAATTAACTCAGCAAAATTATCTTGTTGGAGTAGCTCGCACGGCTTTCTTACCTAGCCTTTCTTTAACAGGATTATTGGGATTTGAAAGTGGGGATTTAGATACCTTGGTTAAAGGAGGTTCTAAGACTTGGAATATAGGTGGAAACTTTACTCTGCCTATTTTTCATTGGGGTGAAATTTACCAAAATGTAAATTTAGCTAAGCTTAATAAAGATGAAGCTTTTGTAAATTATCAAAATACTTTGATTACTGCTTTTGGAGAAATTCGCTATGCTTTAGTAGCTAGAAAAACTATACGCTTACAATACGATAATGCACAAGCAAGCGAACAATCTTACAAAAGAATCTATGAAATTGCTAAAGAACGCTATGATATAGGAGAAATGTCTTTGCAAGATTATTTAGAAGCACGTCAAAATTGGCTTAATGCTGCCGTTGCTTTTAATAATACTAAATATTCTTATGCCAATTCCATAATAGATGTAATCAAAGCATTTGGTGGAGGATTTGAGCAAAGTGAAGATACGAGTAAAAATATAAAAGAAGAATCAAAAAATTTAGATATGTCTTTTAGAGAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39578","NCBI_taxonomy_name":"Campylobacter jejuni subsp. jejuni","NCBI_taxonomy_id":"32022"}}}},"ARO_accession":"3000785","ARO_id":"37165","ARO_name":"cmeC","CARD_short_name":"cmeC","ARO_description":"CmeC is the outer membrane channel protein of the CmeABC multidrug efflux complex.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"36989":{"category_aro_accession":"3000645","category_aro_cvterm_id":"36989","category_aro_name":"cefotaxime","category_aro_description":"Cefotaxime is a semisynthetic cephalosporin taken parenterally. It is resistant to most beta-lactamases and active against Gram-negative rods and cocci due to its aminothiazoyl and methoximino functional groups.","category_aro_class_name":"Antibiotic"},"37139":{"category_aro_accession":"3000759","category_aro_cvterm_id":"37139","category_aro_name":"fusidic acid","category_aro_description":"Fusidic acid is the only commercially available fusidane, a group of steroid-like antibiotics. It is most active against Gram-positive bacteria, and acts by inhibiting elongation factor G to  block protein synthesis.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"45735":{"category_aro_accession":"3007153","category_aro_cvterm_id":"45735","category_aro_name":"fusidane antibiotic","category_aro_description":"A group of antibiotics possessing steroid rings or steroid-like structures.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"799":{"model_id":"799","model_name":"CTX-M-31","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"786":{"protein_sequence":{"accession":"CAD99181.1","sequence":"MMTQSIRRSMLTVMATLPLLFSSATLHAQANSVQQQLEALEKSSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKQSESDKHLLNQRVEIKKSDLVNYNPIAEKHVNGTMTLAELGAAALQYSDNTAMNKLIAHLGGPDKVTAFARSLGDESFRLDRTEPTLNTAIPGDPRDTTTPLAMAQTLKNLTLGKALAETQRAQLVTWLKGNTTGSASIRAGLPKSWVVGDKTGSGDYGTTNDIAVIWPENHAPLVLVTYFTQPEQKAESRRDILAAAAKIVTHGF"},"dna_sequence":{"accession":"AJ567481.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGATGACTCAGAGCATTCGCCGCTCAATGTTAACGGTGATGGCGACGCTACCCCTGCTATTTAGCAGCGCAACGCTGCATGCGCAGGCGAACAGCGTGCAACAGCAGCTGGAAGCCCTGGAGAAAAGTTCGGGAGGTCGGCTTGGCGTTGCGCTGATTAACACCGCCGATAATTCGCAGATTCTCTACCGTGCCGATGAACGTTTTGCGATGTGCAGTACCAGTAAGGTGATGGCGGCCGCGGCGGTGCTTAAACAGAGCGAGAGCGATAAGCACCTGCTAAATCAGCGCGTTGAAATCAAGAAGAGCGACCTGGTTAACTACAATCCCATTGCGGAGAAACACGTTAACGGCACGATGACGCTGGCTGAGCTTGGCGCAGCGGCGCTGCAGTATAGCGACAATACTGCCATGAATAAGCTGATTGCCCATCTGGGTGGTCCCGATAAAGTGACGGCGTTTGCTCGCTCGTTGGGTGATGAGTCCTTCCGTCTGGACAGAACCGAGCCCACGCTCAATACCGCCATTCCAGGCGACCCGCGTGATACCACCACGCCGCTCGCGATGGCGCAGACCCTGAAAAATCTGACGCTGGGTAAAGCGCTGGCGGAAACTCAGCGGGCACAGTTGGTGACGTGGCTTAAGGGCAATACTACCGGTAGCGCGAGCATTCGGGCGGGTCTGCCGAAATCATGGGTAGTGGGCGATAAAACCGGCAGCGGAGATTATGGCACCACCAACGATATCGCGGTTATCTGGCCGGAAAACCACGCACCGCTGGTTCTGGTGACCTACTTTACCCAACCGGAGCAGAAGGCGGAAAGCCGTCGGGATATTCTGGCTGCGGCGGCGAAAATCGTAACCCACGGTTTCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36924","NCBI_taxonomy_name":"Providencia sp. 4440","NCBI_taxonomy_id":"235468"}}}},"ARO_accession":"3001893","ARO_id":"38293","ARO_name":"CTX-M-31","CARD_short_name":"CTX-M-31","ARO_description":"CTX-M-31 is a beta-lactamase found in the Enterobacteriaceae family.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"800":{"model_id":"800","model_name":"CTX-M-87","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1479":{"protein_sequence":{"accession":"ACB41777.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAVAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTELTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"EU545409.1","fmin":"80","fmax":"956","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGTCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACTTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGACTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001947","ARO_id":"38347","ARO_name":"CTX-M-87","CARD_short_name":"CTX-M-87","ARO_description":"CTX-M-87 is a beta-lactamase found in Escherichia coli.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"801":{"model_id":"801","model_name":"mfpA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"350"}},"model_sequences":{"sequence":{"4588":{"protein_sequence":{"accession":"CCP46182.1","sequence":"MQQWVDCEFTGRDFRDEDLSRLHTERAMFSECDFSGVNLAESQHRGSAFRNCTFERTTLWHSTFAQCSMLGSVFVACRLRPLTLDDVDFTLAVLGGNDLRGLNLTGCRLRETSLVDTDLRKCVLRGADLSGARTTGARLDDADLRGATVDPVLWRTASLVGARVDVDQAVAFAAAHGLCLAGG"},"dna_sequence":{"accession":"AL123456.1","fmin":"3773015","fmax":"3773567","strand":"-","sequence":"TTGCAGCAGTGGGTTGATTGCGAATTCACCGGTCGAGACTTCCGCGACGAGGACCTTAGCCGCCTGCACACCGAACGGGCGATGTTCAGCGAATGCGATTTCAGCGGCGTGAATCTGGCCGAGTCACAACACCGAGGGTCGGCGTTTCGTAATTGCACCTTCGAACGGACGACACTGTGGCACAGCACATTTGCCCAGTGCAGCATGTTGGGCTCGGTCTTCGTGGCTTGCCGGCTGCGGCCGCTGACGTTGGACGACGTGGATTTCACGCTCGCCGTGCTCGGCGGAAATGATCTGCGTGGTCTCAACTTGACCGGCTGCCGGTTGCGAGAGACCAGCCTGGTGGATACCGACTTGCGCAAGTGCGTGCTGCGCGGCGCCGACCTCAGTGGTGCCCGTACCACGGGCGCCCGGCTGGATGACGCCGACTTGCGGGGCGCGACCGTGGACCCGGTATTGTGGCGGACCGCGTCGTTGGTGGGTGCGCGTGTCGACGTCGACCAAGCCGTGGCCTTTGCGGCGGCGCACGGGCTGTGCTTGGCAGGGGGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3003035","ARO_id":"39469","ARO_name":"mfpA","CARD_short_name":"mfpA","ARO_description":"mfpA is a qnr homolog and a pentapeptide repeat protein that confers resistance to fluoroquinolones in Mycolicibacterium smegmatis.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"802":{"model_id":"802","model_name":"QnrA3","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"510":{"protein_sequence":{"accession":"AAZ04782.1","sequence":"MDIIDKVFQQEDFSRQDLSDSRFRRCRFYQCDFSHCQLRDASFEDCSFIESGAVEGCHFSYADLRDASFKACRLSLANFSGANCFGIEFRECDLKGANFSRARFYNQISHKMYFCSAYISGCNLAYANLSGQCLEKCELFENNWSNANLSGASLMGSDLSRGTFSRDCWQQVNLRGCDLTFADLDGLDPRRVNLEGVKICAWQQEQLLEPLGVIVLPD"},"dna_sequence":{"accession":"DQ058661.1","fmin":"0","fmax":"657","strand":"+","sequence":"ATGGATATTATTGATAAAGTTTTTCAGCAAGAGGATTTCTCACGCCAGGATTTGAGTGACAGTCGTTTTCGCCGCTGCCGCTTTTATCAGTGTGACTTCAGCCATTGCCAGCTAAGGGATGCCAGTTTCGAGGATTGCAGTTTCATTGAAAGCGGCGCCGTCGAAGGGTGCCACTTCAGCTATGCCGATCTGCGCGATGCCAGTTTCAAGGCCTGCCGCCTGTCTTTGGCCAATTTCAGCGGTGCCAACTGCTTTGGCATAGAGTTCAGGGAGTGCGATCTCAAGGGCGCCAATTTTTCCCGGGCCCGTTTTTACAATCAAATCAGCCATAAGATGTACTTCTGCTCGGCTTATATCTCAGGCTGCAACCTGGCCTATGCCAATTTGAGCGGCCAATGCCTGGAAAAGTGCGAGCTGTTTGAAAACAACTGGAGCAATGCCAACCTCAGCGGCGCTTCCTTGATGGGCTCCGACCTCAGCCGCGGCACCTTCTCCCGCGACTGCTGGCAACAGGTAAACCTGCGGGGCTGTGACCTGACCTTTGCCGATCTGGATGGGCTCGATCCCAGACGGGTCAACCTCGAAGGGGTCAAGATCTGTGCCTGGCAGCAGGAGCAACTGCTGGAACCCTTGGGAGTCATAGTGCTGCCGGATTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36891","NCBI_taxonomy_name":"Shewanella algae","NCBI_taxonomy_id":"38313"}}}},"ARO_accession":"3002709","ARO_id":"39143","ARO_name":"QnrA3","CARD_short_name":"QnrA3","ARO_description":"QnrA3 is a plasmid-mediated quinolone resistance protein found in Shewanella algae.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"803":{"model_id":"803","model_name":"cphA4","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"1409":{"protein_sequence":{"accession":"AAP69912.1","sequence":"MMKGWMKCTLAGAVVLMASFWGGSVRAAGISLKQVSGPVYVVEDNYYVKENSVVYFGAKGVTVVGATWTPDTARELHKLIKRVSSKPVLEVINTNYHTDRVGGNAYWKSIGAKVVATRQTRDLMKSDWAEIVAFTRKGLPEYPDLPLVLPNVVHDGDFTLQEGKVRAFYAGPAHTPDGIFVYFPDEQVLYGNCILKEKLGNLSFANVKAYPQTIERLKAMKLPIKTVIGGHDSPLHGPELIDHYEELIKAAAAV"},"dna_sequence":{"accession":"AY227050.1","fmin":"130","fmax":"895","strand":"+","sequence":"ATGATGAAAGGTTGGATGAAGTGCACATTAGCCGGGGCCGTGGTGCTGATGGCGAGTTTCTGGGGTGGCAGCGTGCGGGCGGCGGGGATCTCCCTTAAGCAGGTGAGTGGCCCTGTGTATGTGGTTGAAGATAACTACTACGTAAAGGAAAACTCCGTGGTCTATTTCGGGGCCAAGGGGGTGACGGTGGTGGGGGCGACCTGGACGCCGGATACCGCCCGCGAGCTGCACAAGCTGATCAAACGGGTCAGCAGCAAGCCGGTGCTGGAGGTGATCAACACCAACTACCACACCGATCGGGTGGGCGGTAATGCCTACTGGAAGTCCATCGGGGCCAAGGTGGTGGCGACGCGCCAGACCCGGGATCTGATGAAGAGCGACTGGGCCGAGATTGTCGCCTTTACCCGCAAGGGGCTGCCGGAGTATCCGGATCTGCCGCTGGTGCTGCCCAACGTGGTGCACGATGGCGACTTCACCCTGCAAGAGGGCAAGGTGCGCGCTTTCTACGCGGGCCCGGCCCATACGCCGGACGGCATCTTTGTCTACTTCCCTGACGAGCAGGTGCTTTATGGCAACTGCATCCTCAAGGAGAAGCTGGGCAACCTGAGCTTTGCCAATGTGAAGGCCTATCCGCAGACCATCGAGCGGCTTAAAGCGATGAAGTTGCCGATCAAGACGGTGATTGGNGGTCACGACTCGCCGCTGCATGGCCCCGAGCTGATTGATCACTACGAGGAGCTGATCAAGGCGGCCGCCGCAGTCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36947","NCBI_taxonomy_name":"Aeromonas allosaccharophila","NCBI_taxonomy_id":"656"}}}},"ARO_accession":"3003100","ARO_id":"39666","ARO_name":"cphA4","CARD_short_name":"cphA4","ARO_description":"CphA4 is an Ambler Class B MBL; subclass B2 originally isolated from Aeromonas allosaccharophila. This enzyme has specific activity against carbapenems and is active as a mono-zinc protein.","ARO_category":{"36720":{"category_aro_accession":"3000581","category_aro_cvterm_id":"36720","category_aro_name":"CphA beta-lactamase","category_aro_description":"CphA is an Ambler Class B MBL; subclass B2 originally isolated from Aeromonas hydrophilia.  This enzyme has specific activity against carbapenems and is active as a mono-zinc protein.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"804":{"model_id":"804","model_name":"tetB(P)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"473":{"protein_sequence":{"accession":"AAA20117.1","sequence":"MKKIINIGIVAHVDAGKTTITENLLYYSGAIKSVGRVDLGNTQTDSMELERKRGITIKSSTISFNWNNVKVNIIDTPGHVDFISEVERSLNSLDGAILVISGVEGIQSQTRILFDTLKELNIPTIIFVNKLDRIGANFNKVFEEIKKNMSNKVVRLQEVYDVGSKAVYIKKLFDTCIINDDAINVLSDLDEAFLERYIGGIEPDKEEIQEKLSLYAREGSLYPVFCGAAAIGLGIEDLLDGICSYFPFASNDCESDLSGVVFKIERTSKNEKKVYVRLFGGKISVRDKIQVPNKEIAEKVKKINRLENGGVVEAQRIEAGDIGILYGLTSFQVGDVIGISNDKIKNISIAKPALKTTISAIDKEKNPELFKALTLLAEEDPLLAFAMNDIDKEIYVNLFGEVQMEILSSMLDDLYGIKVEFSNIETIYKETPKGFGASIMHMQEDLNPFWATVGLEIEPAGRGEGLRYISNVSVGSLPKSFQNAIEEAVIKTSKQGLFGWEVTDVKVTLSCGEFFSPASTPADFRNVTPMVFMEALYKAQTVLLEPLHEFELKIPQNALSKAVWDLETMRATFDNPIVIGDEFSIKGLIPVENSKEYKMKIASYTEGRGMFVTKFYGYKEASAEFSKARKKTTYDPLNKKEYLLHKLNAIRD"},"dna_sequence":{"accession":"L20800.1","fmin":"2308","fmax":"4267","strand":"+","sequence":"ATGAAGAAAATAATTAATATAGGAATCGTAGCACACGTGGATGCAGGAAAAACAACTATAACAGAAAACTTATTATATTATAGTGGAGCTATAAAATCAGTTGGAAGAGTTGATTTAGGCAATACACAGACGGATTCTATGGAGCTTGAGCGTAAGAGAGGAATTACCATTAAATCGTCAACCATATCTTTTAATTGGAATAATGTTAAGGTGAATATTATTGATACTCCAGGACATGTGGATTTTATTTCGGAAGTTGAACGTTCATTAAATAGCTTAGATGGAGCAATACTAGTTATATCAGGAGTAGAGGGGATTCAGTCACAAACAAGAATATTATTTGACACATTAAAGGAGTTAAATATTCCAACAATAATTTTTGTAAATAAGCTAGATAGAATTGGGGCAAATTTCAACAAAGTATTTGAAGAAATAAAGAAGAATATGTCCAATAAAGTAGTTAGATTACAAGAAGTATATGATGTAGGAAGCAAAGCTGTTTATATAAAAAAACTATTTGATACATGCATAATAAATGATGATGCTATTAATGTTTTATCAGACTTAGACGAAGCATTTTTAGAAAGATATATTGGTGGAATAGAACCTGATAAAGAAGAAATACAAGAAAAGCTTTCATTATATGCAAGAGAAGGAAGTCTATATCCAGTATTTTGTGGTGCTGCAGCAATTGGACTTGGAATTGAAGATTTATTAGATGGAATTTGTAGTTATTTTCCATTTGCAAGTAATGATTGTGAAAGTGATTTATCTGGGGTAGTATTTAAAATCGAAAGAACAAGTAAAAATGAAAAGAAGGTTTATGTAAGATTATTTGGAGGAAAAATATCTGTAAGAGATAAAATTCAAGTACCTAATAAGGAGATAGCAGAAAAAGTAAAGAAAATTAATAGGTTAGAAAATGGGGGAGTTGTTGAAGCACAGAGGATAGAAGCAGGGGATATAGGTATTTTATATGGACTTACAAGTTTCCAAGTGGGAGATGTTATTGGAATTTCAAATGATAAAATTAAAAATATATCTATAGCTAAACCAGCATTAAAAACAACAATTTCTGCAATTGATAAAGAAAAAAATCCAGAGCTATTTAAAGCATTAACATTACTTGCAGAGGAAGATCCACTACTCGCCTTCGCGATGAATGACATAGATAAAGAAATTTATGTCAACTTATTCGGTGAAGTTCAAATGGAAATACTAAGTTCCATGTTAGATGATTTATATGGAATAAAAGTAGAGTTTTCGAATATTGAGACTATCTATAAGGAAACACCTAAAGGTTTTGGAGCGTCAATAATGCATATGCAGGAAGACTTAAATCCATTTTGGGCGACAGTAGGCTTAGAAATAGAACCAGCAGGGAGAGGCGAAGGTCTTAGGTATATTTCTAATGTTTCAGTAGGGTCATTGCCAAAATCTTTTCAAAATGCAATTGAAGAAGCAGTTATTAAGACAAGTAAACAAGGATTATTTGGATGGGAGGTTACAGATGTAAAAGTCACTCTTAGCTGTGGTGAATTTTTTAGTCCAGCCAGCACTCCAGCAGATTTTAGAAATGTGACACCTATGGTATTCATGGAAGCATTATATAAAGCACAAACTGTTTTATTAGAGCCATTACATGAGTTTGAGTTAAAGATTCCTCAAAATGCTTTAAGCAAAGCGGTATGGGATTTAGAAACTATGAGGGCAACCTTTGATAATCCTATTGTTATAGGGGATGAATTCTCAATAAAGGGATTAATTCCAGTAGAAAATTCAAAAGAATATAAAATGAAAATAGCTTCATATACAGAAGGTAGAGGAATGTTTGTGACAAAATTTTATGGGTATAAGGAAGCTTCAGCTGAATTTTCAAAAGCACGCAAAAAAACAACGTATGATCCATTGAATAAAAAAGAGTATTTGCTTCATAAACTAAACGCAATTAGAGATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36812","NCBI_taxonomy_name":"Clostridium perfringens","NCBI_taxonomy_id":"1502"}}}},"ARO_accession":"3000195","ARO_id":"36334","ARO_name":"tetB(P)","CARD_short_name":"tetB(P)","ARO_description":"TetB(P) is a tetracycline ribosomal protection protein found on the same operon as tetA(P), a tetracycline efflux protein.","ARO_category":{"35921":{"category_aro_accession":"0000002","category_aro_cvterm_id":"35921","category_aro_name":"tetracycline-resistant ribosomal protection protein","category_aro_description":"A family of proteins known to bind to the 30S ribosomal subunit. This interaction prevents tetracycline and tetracycline derivatives from inhibiting ribosomal function. Thus, these proteins confer elevated resistance to tetracycline derivatives as a ribosomal protection protein.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35986":{"category_aro_accession":"0000069","category_aro_cvterm_id":"35986","category_aro_name":"doxycycline","category_aro_description":"Doxycycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36291":{"category_aro_accession":"3000152","category_aro_cvterm_id":"36291","category_aro_name":"minocycline","category_aro_description":"Minocycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36667":{"category_aro_accession":"3000528","category_aro_cvterm_id":"36667","category_aro_name":"chlortetracycline","category_aro_description":"Chlortetracycline was an early, first-generation tetracycline antibiotic developed in the 1940's. It inhibits bacterial protein synthesis by binding to the 30S subunit of bacterial ribosomes, preventing the aminoacyl-tRNA from binding to the ribosome.","category_aro_class_name":"Antibiotic"},"37011":{"category_aro_accession":"3000667","category_aro_cvterm_id":"37011","category_aro_name":"demeclocycline","category_aro_description":"Demeclocycline is a tetracycline analog with 7-chloro and 6-methyl groups. Due to its fast absorption and slow excretion, it maintains higher effective blood levels compared to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37012":{"category_aro_accession":"3000668","category_aro_cvterm_id":"37012","category_aro_name":"oxytetracycline","category_aro_description":"Oxytetracycline is a derivative of tetracycline with a 5-hydroxyl group. Its activity is similar to other tetracyclines.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"806":{"model_id":"806","model_name":"SHV-150","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1064":{"protein_sequence":{"accession":"AFQ23956.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVVLLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"JX121117.1","fmin":"0","fmax":"858","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGCATTGTCGTCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGC","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001189","ARO_id":"37569","ARO_name":"SHV-150","CARD_short_name":"SHV-150","ARO_description":"SHV-150 is a beta-lactamase.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"807":{"model_id":"807","model_name":"OKP-B-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"8216":{"protein_sequence":{"accession":"CAG25813.2","sequence":"MRYVRLCLISLIAALPLAVFASPQPLEQIKISEGQLAGRVGYVEMDLASGRMLAAWRASERFPLMSTFKVLLCGAVLARVDAGDEQLDRRIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAGNLLLKSVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDVRDTTTPASMATTLRKLLTTPSLSARSQQQLLQWMVDDRVAGPLIRAVLPAGWFIADKTGAGERGSRGIVALLGPDGKAERIVVIYLRDTAATMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AJ635402.2","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGCCTTATCTCCCTGATTGCCGCCCTGCCACTGGCGGTATTCGCCAGCCCTCAGCCGCTTGAGCAGATTAAAATCAGCGAAGGTCAGCTGGCGGGCCGGGTGGGCTATGTTGAAATGGATCTGGCCAGCGGCCGCATGCTGGCCGCCTGGCGCGCCAGTGAGCGCTTTCCGCTGATGAGCACCTTTAAAGTGCTGCTCTGCGGCGCGGTGCTGGCCCGGGTGGATGCCGGCGACGAACAGCTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCCGTCAGCGAAAAACACCTTGCCGACGGGATGACCGTTGGCGAACTCTGCGCCGCCGCCATCACCATGAGCGACAACAGCGCCGGCAATCTGCTGTTGAAGAGCGTCGGCGGCCCCGCGGGATTGACCGCTTTTCTGCGCCAGATCGGTGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTCAATGAGGCGCTTCCCGGCGACGTGCGCGACACCACCACCCCGGCCAGCATGGCCACCACCCTGCGCAAGTTGCTAACCACCCCCTCTCTGAGCGCCCGTTCGCAGCAGCAGCTGCTGCAGTGGATGGTGGACGACCGGGTGGCCGGCCCGTTGATCCGCGCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAAACCGGGGCCGGTGAGCGGGGCTCACGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAAGCGGAGCGTATCGTGGTGATCTATCTGCGGGATACCGCGGCGACCATGGCCGAACGTAACCAGCAGATCGCCGGGATAGGCGCGGCGCTGATCGAGCACTGGCAGCGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002434","ARO_id":"38834","ARO_name":"OKP-B-1","CARD_short_name":"OKP-B-1","ARO_description":"OKP-B-1 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"38817":{"category_aro_accession":"3002417","category_aro_cvterm_id":"38817","category_aro_name":"OKP beta-lactamase","category_aro_description":"OKP beta-lactamases are chromosomal class A beta-lactamase that confer resistance to penicillins and early cephalosporins in Klebsiella pneumoniae. OKP beta-lactamases can be subdivided into two groups: OKP-A and OKP-B which diverge by about 4.2%.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"808":{"model_id":"808","model_name":"TEM-171","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1244":{"protein_sequence":{"accession":"ADA79630.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRIDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"GQ149347.1","fmin":"5269","fmax":"6130","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTATTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001037","ARO_id":"37417","ARO_name":"TEM-171","CARD_short_name":"TEM-171","ARO_description":"TEM-171 is a beta-lactamase.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"809":{"model_id":"809","model_name":"lnuB","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"5197":{"protein_sequence":{"accession":"CAB41414.1","sequence":"MLKQKELIANVKNLTESDERITACMMYGSFTKGEGDQYSDIEFYIFLKHSITSNFDSSNWLFDVAPYLMLYKNEYGTEVVIFDNLIRGEFHFLSEKDMNIIPSFKDSGYIPDTKAMLIYDETGQLENYLSEISGARPNRLTEENANFLLCNFSNLWLMGINVLKRGEYARSLELLSQLQKNTLQLIRMAEKNADNWLNMSKNLEKEISLENYKKFAKTTARLDKVELFEAYKNSLLLVMDLQSHLIEQYNLKVTHDILERLLNYISE"},"dna_sequence":{"accession":"AJ238249.1","fmin":"126","fmax":"930","strand":"+","sequence":"ATGTTAAAACAAAAAGAATTAATTGCAAACGTTAAGAATCTTACTGAGTCAGATGAACGAATTACAGCTTGTATGATGTATGGATCGTTTACCAAAGGAGAAGGTGACCAATACTCTGATATAGAGTTCTATATATTTTTGAAACATAGTATAACCTCGAACTTTGATTCATCCAACTGGTTGTTTGACGTAGCTCCGTACTTGATGCTTTATAAAAATGAGTACGGAACAGAGGTAGTTATTTTTGATAATCTTATACGTGGGGAATTTCATTTCCTTTCTGAAAAAGATATGAACATAATCCCCTCGTTTAAAGATTCAGGTTATATTCCTGATACGAAGGCTATGCTTATTTACGATGAAACAGGGCAATTAGAAAATTATTTATCAGAGATAAGTGGTGCAAGACCAAATAGACTTACTGAAGAAAATGCTAATTTTTTGTTGTGTAATTTCTCTAATCTATGGTTGATGGGAATCAACGTTCTAAAAAGAGGAGAATATGCTCGTTCATTAGAACTCTTATCACAACTTCAAAAAAATACACTACAACTTATACGTATGGCAGAAAAAAATGCTGATAATTGGCTAAACATGAGTAAAAACCTTGAAAAAGAAATTAGCCTTGAAAATTATAAAAAATTTGCAAAGACCACTGCTCGATTAGATAAGGTAGAATTATTTGAAGCCTATAAAAATTCTTTGCTATTAGTTATGGATTTGCAAAGTCACCTTATTGAACAATACAACTTAAAAGTTACACATGACATTTTAGAAAGATTGTTGAATTACATTAGTGAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36779","NCBI_taxonomy_name":"Enterococcus faecium","NCBI_taxonomy_id":"1352"}}}},"ARO_accession":"3002836","ARO_id":"39270","ARO_name":"lnuB","CARD_short_name":"lnuB","ARO_description":"lnuB is a plasmid-mediated nucleotidyltransferase found in Streptococcus lutetiensis.","ARO_category":{"36360":{"category_aro_accession":"3000221","category_aro_cvterm_id":"36360","category_aro_name":"lincosamide nucleotidyltransferase (LNU)","category_aro_description":"Resistance to the lincosamide antibiotic by ATP-dependent modification of the 3' and\/or 4'-hydroxyl groups of the methylthiolincosamide sugar.","category_aro_class_name":"AMR Gene Family"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"810":{"model_id":"810","model_name":"mecC","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1250"}},"model_sequences":{"sequence":{"5248":{"protein_sequence":{"accession":"CCC86795.1","sequence":"MKKIYISVLVLLLIMIIITWLFKDDDIEKTISSIEKGNYNEVYKNSSEKSKLAYGEEEIVDRNKKIYKDLSVNNLKITNHEIKKTGKDKKQVDVKYNIYTKYGTIRRNTQLNFIYEDKHWKLDWRPDVIVPGLKNGQKINIETLKSERGKIKDRNGIELAKTGNTYEIGIVPNKTPKEKYDDIARDLQIDTKAITNKVNQKWVQPDSFVPIKKINKQDEYIDKLIKSYNLQINTIKSRVYPLNEATVHLLGYVGPINSDELKSKQFRNYSKNTVIGKKGLERLYDKQLQNTDGFKVSIANTYDNKPLDTLLEKKAENGKDLHLTIDARVQESIYKHMKNDDGSGTALQPKTGEILALVSTPSYDVYPFMNGLSNNDYRKLTNNKKEPLLNKFQITTSPGSTQKILTSIIALKENKLDKNTNFDIYGKGWQKDASWGNYNITRFKVVDGNIDLKQAIESSDNIFFARIALALGAKKFEQGMQDLGIGENIPSDYPFYKAQISNSNLKNEILLADSGYGQGEILVNPIQILSIYSALENNGNIQNPHVLRKTKSQIWKKDIIPKKDIDILTNGMERVVNKTHRDDIYKNYARIIGKSGTAELKMNQGETGRQIGWFVSYNKNNPNMLMAINVKDVQNKGMASYNATISGKVYDDLYDNGKTQFDIDQ"},"dna_sequence":{"accession":"FR821779.1","fmin":"35680","fmax":"37678","strand":"-","sequence":"ATGAAAAAAATTTATATTAGTGTGCTAGTTCTTTTACTAATTATGATTATAATAACTTGGTTATTCAAAGATGACGATATTGAGAAAACAATTAGTTCTATTGAAAAAGGAAACTATAACGAAGTATATAAAAATAGTTCAGAAAAATCTAAACTGGCATATGGAGAAGAAGAAATTGTAGATAGGAATAAAAAAATTTACAAAGATTTAAGTGTCAATAACTTAAAAATTACTAATCATGAAATTAAAAAAACTGGAAAAGATAAAAAGCAAGTTGATGTTAAATATAACATATATACAAAATATGGAACTATACGACGTAATACACAATTAAACTTTATTTATGAAGATAAGCATTGGAAATTAGATTGGAGACCAGACGTAATAGTACCTGGTTTGAAAAATGGACAGAAAATTAATATAGAAACATTAAAATCAGAGCGAGGCAAAATAAAAGATAGAAATGGTATAGAATTAGCTAAAACTGGAAATACATATGAAATCGGTATTGTCCCTAACAAAACACCCAAAGAAAAATATGATGATATTGCTCGTGACTTACAAATTGATACAAAAGCTATAACCAATAAAGTTAATCAAAAATGGGTTCAGCCAGATTCATTTGTACCAATTAAAAAGATAAATAAACAAGATGAATATATAGACAAATTAATTAAATCATACAATTTACAAATAAACACTATAAAAAGCCGTGTTTATCCATTGAACGAAGCAACAGTACACCTTTTAGGTTATGTGGGTCCAATTAATTCTGACGAGTTAAAAAGTAAGCAATTTAGAAACTATAGCAAAAATACTGTTATTGGAAAAAAAGGCTTAGAACGCCTCTATGATAAACAATTGCAAAACACTGATGGTTTTAAGGTATCCATTGCAAATACTTATGACAATAAACCTTTAGACACATTATTGGAGAAAAAGGCTGAAAACGGAAAAGATCTTCATTTAACTATAGATGCTAGAGTACAAGAAAGTATTTATAAACATATGAAAAATGACGATGGATCTGGTACAGCATTACAACCAAAAACTGGAGAAATTTTAGCTTTGGTAAGTACCCCATCGTACGATGTTTATCCATTCATGAATGGATTAAGCAATAATGACTACCGTAAATTAACTAACAATAAAAAAGAGCCTTTGCTCAACAAATTTCAAATCACTACATCACCAGGTTCAACCCAAAAAATATTAACATCTATTATAGCCTTAAAAGAAAATAAACTAGACAAAAATACTAATTTTGATATTTATGGTAAGGGTTGGCAAAAAGATGCATCATGGGGGAATTATAATATCACAAGATTTAAAGTAGTAGACGGCAATATCGATTTAAAGCAAGCAATAGAATCATCAGACAACATATTTTTTGCCCGCATTGCATTAGCATTAGGAGCCAAAAAATTTGAGCAAGGTATGCAAGATTTGGGAATCGGTGAAAATATCCCGAGTGATTATCCCTTTTATAAAGCACAAATCTCAAATAGTAATTTAAAAAATGAAATATTATTAGCAGATTCAGGATATGGCCAAGGCGAGATACTAGTAAACCCTATACAAATTTTATCAATATACAGTGCTTTAGAAAATAACGGAAATATACAAAATCCTCATGTTTTACGTAAAACAAAATCTCAAATATGGAAAAAAGATATTATACCTAAAAAAGACATAGATATATTAACTAATGGTATGGAACGTGTAGTTAATAAAACACATAGGGATGATATATACAAAAATTATGCCCGAATTATTGGTAAATCTGGCACAGCAGAATTAAAAATGAATCAAGGGGAAACTGGAAGACAAATAGGTTGGTTTGTTTCATATAATAAAAATAATCCTAATATGTTAATGGCGATTAATGTTAAAGACGTTCAAAATAAAGGGATGGCCAGCTATAATGCTACTATATCTGGAAAAGTTTATGATGATTTGTATGATAATGGAAAAACTCAATTTGATATAGATCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42590","NCBI_taxonomy_name":"Staphylococcus aureus subsp. aureus LGA251","NCBI_taxonomy_id":"985006"}}}},"ARO_accession":"3001209","ARO_id":"37590","ARO_name":"mecC","CARD_short_name":"mecC","ARO_description":"A foreign PBP2a acquired by lateral gene transfer that able to perform peptidoglycan synthesis in the presence of beta-lactams.","ARO_category":{"37589":{"category_aro_accession":"3001208","category_aro_cvterm_id":"37589","category_aro_name":"methicillin resistant PBP2","category_aro_description":"In methicillin sensitive S. aureus (MSSA), beta-lactams bind to native penicillin-binding proteins (PBPs) and disrupt synthesis of the cell membrane's peptidoglycan layer. In methicillin resistant S. aureus (MRSA), foreign PBP2a acquired by lateral gene transfer is able to perform peptidoglycan synthesis in the presence of beta-lactams.","category_aro_class_name":"AMR Gene Family"},"35934":{"category_aro_accession":"0000015","category_aro_cvterm_id":"35934","category_aro_name":"methicillin","category_aro_description":"Derived from penicillin to combat penicillin-resistance, methicillin is insensitive to beta-lactamases (also known as penicillinases) secreted by many penicillin-resistant bacteria. Methicillin is bactericidal, and acts by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"632":{"model_id":"632","model_name":"basR","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"4374":"L157Q","4375":"L71R"},"Curated-R":{"4374":"L157Q","4375":"L71R"},"clinical":{"4374":"L157Q","4375":"L71R"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"375"}},"model_sequences":{"sequence":{"5429":{"protein_sequence":{"accession":"AAG08162.1","sequence":"MRILLAEDDLLLGDGIRAGLRLEGDTVEWVTDGVAAENALVTDEFDLLVLDIGLPRRSGLDILRNLRHQGLLTPVLLLTARDKVADRVAGLDSGADDYLTKPFDLDELQARVRALTRRTTGRALPQLVHGELRLDPATHQVTLSGQAVELAPREYALLRLLLENSGKVLSRNQLEQSLYGWSGDVESNAIEVHVHHLRRKLGNQLIRTVRGIGYGIDQPAP"},"dna_sequence":{"accession":"AE004091.2","fmin":"5364070","fmax":"5364736","strand":"+","sequence":"ATGAGAATACTGCTGGCCGAGGACGACCTGCTGCTCGGCGACGGCATCCGCGCCGGGCTGCGCCTGGAAGGCGATACCGTGGAATGGGTGACCGACGGCGTGGCCGCGGAGAACGCGCTGGTCACCGACGAGTTCGACCTGCTGGTGCTCGACATCGGACTGCCGCGCCGCAGCGGCCTGGACATCCTGCGCAACCTGCGTCACCAGGGCCTGCTCACCCCGGTGCTGCTGCTCACCGCGCGGGACAAGGTGGCCGACCGGGTCGCCGGGCTCGACAGCGGTGCCGACGACTACCTGACCAAGCCCTTCGATCTCGACGAACTGCAGGCACGGGTGCGCGCCCTGACCCGCCGCACCACCGGTCGCGCCCTGCCGCAACTGGTGCACGGCGAGCTGCGCCTGGACCCGGCGACCCACCAGGTGACCCTGTCCGGGCAGGCGGTGGAACTGGCGCCGCGCGAATACGCACTGCTGCGCCTGCTGCTGGAGAACAGCGGCAAGGTGCTCTCGCGCAACCAACTGGAGCAGAGCCTCTACGGCTGGAGCGGCGACGTCGAGAGCAACGCCATCGAAGTCCACGTCCACCACCTGCGGCGCAAGCTCGGCAACCAGTTGATCCGCACCGTCCGCGGCATCGGCTACGGCATCGACCAGCCGGCGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36804","NCBI_taxonomy_name":"Pseudomonas aeruginosa PAO1","NCBI_taxonomy_id":"208964"}}}},"ARO_accession":"3003582","ARO_id":"40192","ARO_name":"basR","CARD_short_name":"basR","ARO_description":"Response regulator for Lipid A modification genes; two-component system involved in polymyxin resistance that senses high extracellular Fe(2+).","ARO_category":{"41433":{"category_aro_accession":"3004269","category_aro_cvterm_id":"41433","category_aro_name":"pmr phosphoethanolamine transferase","category_aro_description":"This family of phosphoethanolamine transferase catalyze the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine to lipid A, which impedes the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36593":{"category_aro_accession":"3000454","category_aro_cvterm_id":"36593","category_aro_name":"polymyxin B","category_aro_description":"Polymyxin B is mixture of mostly polymyxins B1 and B2, mainly used for resistant gram-negative infections. They are polypeptides with cationic detergent action on cell membranes.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"805":{"model_id":"805","model_name":"MexC","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"52":{"protein_sequence":{"accession":"AAB41956.1","sequence":"MADLRAIGRIGALAMAIALAGCGPAEERQEAAEMVLPVEVLTVQAEPLALSSELPGRIEPVRVAEVRARVAGIVVRKRFEEGADVKAGDLLFQIDPAPLKAAVSRAEGELARNRAVLFEAQARVRRYEPLVKIQAVSQQDFDTATADLRSAEAATRSAQADLETARLNLGYASVTAPISGRIGRALVTEGALVGQGEATLMARIQQLDPIYADFTQTAAEALRLRDALKKGTLAAGDSQALTLRVEGTPYERQGALQFADVAVDRGTGQIALRGKFANPDGVLLPGMYVRVRTPQGIDNQAILVPQRAVHRSSDGSAQVMVVGADERAESRSVGTGVMQGSRWQITEGLEPGDRVIVGGLAAVQPGVKIVPKPDGAQAQAQSPAPQQ"},"dna_sequence":{"accession":"U57969.1","fmin":"294","fmax":"1458","strand":"+","sequence":"ATGGCTGATTTGCGTGCAATAGGAAGGATCGGGGCGTTGGCTATGGCCATCGCGTTGGCGGGTTGTGGGCCGGCGGAAGAGCGACAGGAGGCCGCCGAAATGGTGTTGCCGGTGGAGGTCCTGACGGTGCAGGCCGAGCCCCTGGCGCTGAGTTCGGAACTGCCTGGGCGGATCGAACCGGTGCGGGTCGCCGAGGTGCGCGCGCGGGTGGCCGGCATCGTCGTGCGGAAGCGCTTCGAGGAGGGCGCCGACGTCAAGGCTGGCGACCTGCTGTTCCAGATCGATCCGGCACCGCTGAAGGCTGCGGTGTCGCGCGCCGAGGGTGAGCTGGCGCGGAACCGCGCGGTGCTGTTCGAGGCGCAGGCGCGGGTGCGTCGCTACGAGCCGCTGGTGAAGATCCAGGCGGTCAGCCAGCAGGACTTCGATACCGCCACCGCCGACCTGCGCAGCGCCGAGGCGGCGACCCGCTCGGCCCAGGCCGACCTGGAGACCGCGCGCCTGAACCTCGGCTACGCCTCGGTCACTGCGCCGATCTCCGGGCGCATCGGCCGCGCGCTGGTGACCGAGGGCGCGCTGGTCGGGCAGGGCGAGGCGACGCTGATGGCGCGCATCCAGCAGCTCGATCCGATCTATGCGGATTTCACCCAGACCGCGGCCGAGGCCCTGCGCCTGCGCGACGCCCTGAAGAAAGGCACCTTGGCCGCCGGCGACAGCCAGGCGCTGACCCTGCGCGTCGAAGGGACGCCCTACGAGCGCCAGGGCGCGTTGCAGTTCGCCGACGTGGCGGTGGATCGCGGCACCGGCCAGATCGCCCTGCGCGGCAAGTTCGCCAACCCCGACGGGGTCCTGCTGCCGGGCATGTACGTGCGCGTACGTACGCCCCAGGGCATCGACAACCAGGCGATCCTGGTGCCGCAACGGGCCGTGCACCGCTCCAGCGACGGCAGCGCCCAGGTGATGGTGGTGGGCGCCGACGAGCGCGCCGAGTCGCGCAGCGTCGGTACCGGCGTCATGCAGGGTTCGCGCTGGCAGATCACCGAGGGCCTGGAGCCGGGTGACCGGGTCATAGTCGGCGGCCTGGCTGCGGTGCAGCCGGGGGTGAAGATCGTGCCGAAGCCGGATGGTGCCCAGGCGCAAGCCCAGTCACCTGCGCCGCAACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3000800","ARO_id":"37180","ARO_name":"MexC","CARD_short_name":"MexC","ARO_description":"MexC is the membrane fusion protein of the MexCD-OprJ multidrug efflux complex.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36250":{"category_aro_accession":"3000111","category_aro_cvterm_id":"36250","category_aro_name":"novobiocin","category_aro_description":"Novobiocin is an aminocoumarin antibiotic produced by Streptomyces spheroides and Streptomyces niveus, and binds DNA gyrase subunit B inhibiting ATP-dependent DNA supercoiling.","category_aro_class_name":"Antibiotic"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"37007":{"category_aro_accession":"3000663","category_aro_cvterm_id":"37007","category_aro_name":"ofloxacin","category_aro_description":"Ofloxacin is a 6-fluoro, 7-piperazinyl quinolone with a methyl-substituted oxazine ring. It has a broad spectrum of activity including many enterobacteria and mycoplasma but most anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"46133":{"category_aro_accession":"3007382","category_aro_cvterm_id":"46133","category_aro_name":"gentamicin","category_aro_description":"Gentamicin is a commonly used aminoglycoside antibiotic derived from members of the Micromonospora genus of bacteria. It acts by binding the 30S ribosomal subunit, thus inhibiting protein synthesis. Gentamicin is typically used to treat Gram-negative infections of the repiratory and urinary tract, as well as infections of the bone and soft tissue. It also exhibits considerable nephrotoxicity and ototoxicity. Gentamicin is administered as a mixture of gentamicin type C (which makes about around 80% of the complex) and types A, B, and X (distributed in the remaining 20% of the complex).","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36242":{"category_aro_accession":"3000103","category_aro_cvterm_id":"36242","category_aro_name":"aminocoumarin antibiotic","category_aro_description":"Aminocoumarin antibiotics bind DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling.","category_aro_class_name":"Drug Class"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"704":{"model_id":"704","model_name":"OprJ","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"850"}},"model_sequences":{"sequence":{"385":{"protein_sequence":{"accession":"AAB41958.1","sequence":"MRKPAFGVSALLIALTLGACSMAPTYERPAAPVADSWSGAAAQRQGAAIDTLDWKSFIVDAELRRLVDMALDNIRSLRQTLLDIEAARAQYRIQRADRVPGLNAAATGNRQRQPADLSAGNRSEVASSYQVGLALPEYELDLFGRVKSLTDAALQQYLASEEAARAARIALVAEVSQAYLSYDGALRRLALTRQTLVSREYSFALIDQRRAAGAATALDYQEALGLVEQARAEQERNLRQKQQAFNALVLLLGSDDAAQAIPRSPGQRPKLLQDIAPGTPSELIERRPDILAAEHRLRARNADIGAARAAFFPRISLTGSFGTSSAEMSGLFDGGSRSCSFLPTLTLPIFDGGRNRANLSLAEARKDSAVAAYEGTIQTAFREVADALAASDTLRREEKALRALANSSNEALKLAKARYESGVDNHLRYLDAQRSSFLNEIAFIDGSTQRQIALVDLFRALGGGWDEGRSLVVHRGGRS"},"dna_sequence":{"accession":"U57969.1","fmin":"4622","fmax":"6062","strand":"+","sequence":"ATGCGCAAACCTGCTTTCGGCGTATCGGCGCTGCTGATCGCCCTGACCCTCGGCGCCTGCTCCATGGCGCCGACCTACGAACGTCCCGCCGCGCCGGTGGCCGACAGCTGGAGCGGCGCCGCCGCCCAGCGCCAGGGCGCGGCGATCGACACGCTGGATTGGAAGAGTTTCATCGTCGATGCCGAACTACGCCGCCTGGTGGACATGGCCCTGGATAACATCCGCTCGCTGCGCCAGACCCTCCTGGATATCGAGGCGGCCCGCGCGCAGTACCGAATCCAGCGCGCCGACCGGGTTCCGGGCCTGAATGCCGCTGCCACCGGCAACCGCCAGCGGCAGCCGGCCGACCTGTCCGCCGGCAATCGCTCGGAAGTGGCCAGCAGCTACCAGGTCGGGCTGGCCCTGCCGGAGTACGAACTGGACCTCTTCGGTCGGGTCAAGAGCCTGACCGACGCAGCCCTGCAACAGTACCTGGCCAGCGAGGAGGCAGCGCGCGCGGCACGGATCGCCCTGGTCGCCGAGGTCAGCCAGGCCTACCTGAGCTACGACGGCGCCCTGCGGCGCCTGGCGCTGACCCGTCAGACCCTGGTCAGCCGCGAGTATTCCTTCGCCCTGATCGACCAGCGCCGCGCGGCCGGCGCCGCCACCGCGCTGGACTACCAGGAAGCCCTTGGCCTGGTGGAGCAGGCGCGCGCCGAGCAGGAGCGCAACCTGCGGCAGAAACAGCAGGCATTCAACGCGCTGGTGTTGCTGCTGGGTAGCGACGATGCCGCGCAGGCGATTCCGCGGAGTCCGGGGCAGCGGCCGAAGCTGCTGCAGGACATCGCTCCCGGCACGCCGTCCGAGCTGATCGAGCGACGTCCGGACATCCTTGCCGCCGAACATCGTTTGCGGGCGCGCAACGCGGATATCGGCGCGGCGCGCGCGGCGTTCTTCCCGCGCATCAGCCTGACCGGCAGCTTCGGCACCTCCAGCGCGGAAATGTCCGGCCTGTTCGATGGCGGCTCGCGCTCCTGTAGCTTCCTGCCGACGTTGACGCTGCCGATCTTCGATGGCGGGCGCAACCGTGCCAACCTGAGCCTGGCCGAGGCGCGCAAGGATTCGGCGGTGGCCGCCTACGAGGGGACCATCCAGACCGCTTTCCGCGAGGTCGCCGACGCCCTGGCGGCCAGCGATACCCTGCGTCGCGAAGAGAAGGCCCTGCGCGCCCTGGCGAACAGCAGCAACGAAGCCCTGAAGCTGGCCAAGGCACGCTACGAGAGTGGCGTCGACAACCACCTGCGCTACCTCGATGCGCAGCGCAGCAGCTTCCTCAACGAGATCGCCTTCATCGACGGCAGCACCCAGCGGCAGATCGCCCTGGTCGACCTGTTCCGCGCGCTCGGCGGAGGCTGGGACGAGGGACGGAGCCTGGTGGTACATCGAGGCGGCAGGAGTTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3000802","ARO_id":"37182","ARO_name":"OprJ","CARD_short_name":"OprJ","ARO_description":"OprJ is the outer membrane channel component of the MexCD-OprJ multidrug efflux complex.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36250":{"category_aro_accession":"3000111","category_aro_cvterm_id":"36250","category_aro_name":"novobiocin","category_aro_description":"Novobiocin is an aminocoumarin antibiotic produced by Streptomyces spheroides and Streptomyces niveus, and binds DNA gyrase subunit B inhibiting ATP-dependent DNA supercoiling.","category_aro_class_name":"Antibiotic"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"37007":{"category_aro_accession":"3000663","category_aro_cvterm_id":"37007","category_aro_name":"ofloxacin","category_aro_description":"Ofloxacin is a 6-fluoro, 7-piperazinyl quinolone with a methyl-substituted oxazine ring. It has a broad spectrum of activity including many enterobacteria and mycoplasma but most anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"46133":{"category_aro_accession":"3007382","category_aro_cvterm_id":"46133","category_aro_name":"gentamicin","category_aro_description":"Gentamicin is a commonly used aminoglycoside antibiotic derived from members of the Micromonospora genus of bacteria. It acts by binding the 30S ribosomal subunit, thus inhibiting protein synthesis. Gentamicin is typically used to treat Gram-negative infections of the repiratory and urinary tract, as well as infections of the bone and soft tissue. It also exhibits considerable nephrotoxicity and ototoxicity. Gentamicin is administered as a mixture of gentamicin type C (which makes about around 80% of the complex) and types A, B, and X (distributed in the remaining 20% of the complex).","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36242":{"category_aro_accession":"3000103","category_aro_cvterm_id":"36242","category_aro_name":"aminocoumarin antibiotic","category_aro_description":"Aminocoumarin antibiotics bind DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling.","category_aro_class_name":"Drug Class"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"811":{"model_id":"811","model_name":"TEM-26","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"5840":{"protein_sequence":{"accession":"WP_047028173.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVKYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDSWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"NG_050256.1","fmin":"100","fmax":"961","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTAAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATAGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39773","NCBI_taxonomy_name":"Enterobacter kobei","NCBI_taxonomy_id":"208224"}}}},"ARO_accession":"3000896","ARO_id":"37276","ARO_name":"TEM-26","CARD_short_name":"TEM-26","ARO_description":"TEM-26 is an extended-spectrum beta-lactamase that has been found in clinical isolates.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"812":{"model_id":"812","model_name":"CMY-10","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1114":{"protein_sequence":{"accession":"AAK31368.1","sequence":"MQQRQSILWGAVATLMWAGLAHAGEASPVDPLRPVVDASIQPLLKEHRIPGMAVAVLKDGKAHYFNYGVANRESGAGVSEQTLFEIGSVSKTLTATLGAYAVVKGAMQLDDKASRHAPWLKGSAFDSITMGELATYSAGGLPLQFPEEVDSSEKMRAYYRQWAPVYSPGSHRQYSNPSIGLFGHLAASSLKQPFAPLMEQTLLPGLGMHHTYVNVPKQAMASYAYGYSKEDKPIRVNPGMLADEAYGIKTSSADLLRFVKANIGGVDDKALQQAISLTHQGHYSVGGMTQGLGWESYAYPVTEQTLLAGNSAKVILEANPTAAPRESGSQVLFNKTGSTNGFGAYVAFVPARGIGIVMLANRNYPIEARIKAAHAILAQLAG"},"dna_sequence":{"accession":"AF357597.1","fmin":"250","fmax":"1399","strand":"+","sequence":"ATGCAACAACGACAATCCATCCTGTGGGGGGCCGTGGCCACCCTGATGTGGGCCGGTCTGGCCCATGCAGGTGAGGCTTCACCGGTCGATCCCCTGCGCCCCGTGGTGGATGCCAGCATCCAGCCGCTGCTCAAGGAGCACAGGATCCCGGGCATGGCGGTGGCCGTGCTCAAGGATGGCAAGGCCCACTACTTCAATTACGGGGTGGCCAACCGGGAGAGCGGGGCCGGCGTCAGCGAGCAGACCCTGTTCGAGATAGGATCCGTGAGCAAGACCCTGACTGCGACCCTGGGGGCCTATGCGGTGGTCAAGGGAGCGATGCAGCTGGATGACAAGGCGAGCCGGCACGCGCCCTGGCTCAAGGGATCCGCCTTTGACAGCATCACCATGGGGGAGCTTGCCACCTACAGCGCCGGAGGCCTGCCACTGCAATTCCCCGAGGAGGTGGATTCATCCGAGAAGATGCGCGCCTACTACCGCCAGTGGGCCCCTGTCTATTCGCCGGGCTCCCATCGCCAGTACTCCAACCCCAGCATAGGGCTGTTCGGCCACCTGGCGGCGAGCAGCCTGAAGCAGCCGTTTGCCCCCTTGATGGAGCAGACCCTGCTGCCCGGGCTCGGCATGCACCACACCTATGTCAATGTGCCGAAGCAGGCCATGGCGAGTTATGCCTATGGCTATTCGAAAGAGGACAAGCCCATCCGTGTCAACCCTGGCATGCTGGCGGACGAGGCCTATGGCATCAAGACCAGCTCGGCGGATCTGCTGCGTTTTGTGAAGGCCAACATCGGCGGGGTTGATGACAAGGCGTTGCAGCAGGCCATCTCCCTGACCCACCAAGGGCATTACTCGGTAGGCGGGATGACCCAGGGGCTGGGTTGGGAGAGTTACGCCTATCCCGTCACCGAGCAGACATTGCTGGCGGGCAATTCGGCCAAGGTGATCCTCGAAGCCAATCCGACGGCGGCGCCCCGGGAGTCGGGGAGCCAGGTGCTCTTCAACAAGACCGGCTCGACCAATGGCTTTGGCGCCTATGTGGCCTTCGTGCCGGCCAGGGGGATCGGCATCGTCATGCTGGCCAATCGCAACTACCCCATCGAGGCGCGCATCAAGGCGGCCCACGCCATCCTGGCGCAGTTGGCCGGTTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36770","NCBI_taxonomy_name":"Klebsiella aerogenes","NCBI_taxonomy_id":"548"}}}},"ARO_accession":"3002021","ARO_id":"38421","ARO_name":"CMY-10","CARD_short_name":"CMY-10","ARO_description":"CMY-10 is a beta-lactamase found in Klebsiella aerogenes.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"813":{"model_id":"813","model_name":"OXA-216","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1373":{"protein_sequence":{"accession":"CCA94649.1","sequence":"MNIKALLLITSAISISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKDMTLGDAIKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"FR865168.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTCTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATAAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001488","ARO_id":"37888","ARO_name":"OXA-216","CARD_short_name":"OXA-216","ARO_description":"OXA-216 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"814":{"model_id":"814","model_name":"TEM-113","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1795":{"protein_sequence":{"accession":"AAS89983.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDKLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVKYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTTPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGASERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AY589494.1","fmin":"193","fmax":"1054","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATAAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTAAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGACGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCAGTGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACGATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3000976","ARO_id":"37356","ARO_name":"TEM-113","CARD_short_name":"TEM-113","ARO_description":"TEM-113 is an extended-spectrum beta-lactamase found in Proteus mirabilis.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"722":{"model_id":"722","model_name":"vanR gene in vanA cluster","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"3275":{"protein_sequence":{"accession":"AAA65953.1","sequence":"MSDKILIVDDEHEIADLVELYLKNENYTVFKYYTAKEALECIDKSEIDLAILDIMLPGTSGLTICQKIRDKHTYPIIMLTGKDTEVDKITGLTIGADDYITKPFRPLELIARVKAQLRRYKKFSGVKEQNENVIVHSGLVINVNTHECYLNEKQLSLTPTEFSILRILCENKGNVVSSELLFHEIWGDEYFSKSNNTITVHIRHLREKMNDTIDNPKYIKTVWGVGYKIEK"},"dna_sequence":{"accession":"M97297.1","fmin":"3975","fmax":"4671","strand":"+","sequence":"ATGAGCGATAAAATACTTATTGTGGATGATGAACATGAAATTGCCGATTTGGTTGAATTATACTTAAAAAACGAGAATTATACGGTTTTCAAATACTATACCGCCAAAGAAGCATTGGAATGTATAGACAAGTCTGAGATTGACCTTGCCATATTGGACATCATGCTTCCCGGCACAAGCGGCCTTACTATCTGTCAAAAAATAAGGGACAAGCACACCTATCCGATTATCATGCTGACCGGGAAAGATACAGAGGTAGATAAAATTACAGGGTTAACAATCGGCGCGGATGATTATATAACGAAGCCCTTTCGCCCACTGGAGTTAATTGCTCGGGTAAAGGCCCAGTTGCGCCGATACAAAAAATTCAGTGGAGTAAAGGAGCAGAACGAAAATGTTATCGTCCACTCCGGCCTTGTCATTAATGTTAACACCCATGAGTGTTATCTGAACGAGAAGCAGTTATCCCTTACTCCCACCGAGTTTTCAATACTGCGAATCCTCTGTGAAAACAAGGGGAATGTGGTTAGCTCCGAGCTGCTATTTCATGAGATATGGGGCGACGAATATTTCAGCAAGAGCAACAACACCATCACCGTGCATATCCGGCATTTGCGCGAAAAAATGAACGACACCATTGATAATCCGAAATATATAAAAACGGTATGGGGGGTTGGTTATAAAATTGAAAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36779","NCBI_taxonomy_name":"Enterococcus faecium","NCBI_taxonomy_id":"1352"}}}},"ARO_accession":"3002919","ARO_id":"39353","ARO_name":"vanR gene in vanA cluster","CARD_short_name":"vanR_in_vanA_cl","ARO_description":"Also known as vanRA, is a vanR variant found in the vanA gene cluster.","ARO_category":{"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"36713":{"category_aro_accession":"3000574","category_aro_cvterm_id":"36713","category_aro_name":"vanR","category_aro_description":"VanR is a OmpR-family transcriptional activator in the VanSR regulatory system. When activated by VanS, it promotes cotranscription of VanA, VanH, and VanX.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"35948":{"category_aro_accession":"0000029","category_aro_cvterm_id":"35948","category_aro_name":"teicoplanin","category_aro_description":"Teicoplanin is a glycopeptide antibiotic used in the prophylaxis and treatment of serious infections caused by Gram-positive bacteria. Teicoplanin has a unique acyl-aliphatic chain, and binds to cell wall precursors to inhibit transglycosylation  and transpeptidation.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"753":{"model_id":"753","model_name":"SMB-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1239":{"protein_sequence":{"accession":"BAL14456.1","sequence":"MKIIASLILAAFASVAQAQDRDWSSPQQPFTIYGNTHYVGTGGISAVLLSSPQGHILVDGTTEKGAQVVAANIRAMGFKLSDVKYILSTHSHEDHAGGISAMQKLTGATVLAGAANVDTLRTGVSPKSDPQFGSLSNFPGSAKVRAVADGELVKLGPLAVKAHATPGHTEGGITWTWQSCEQGKCKDVVFADSLTAVSADSYRFSDHPEVVASLRGSFEAVEKLSCDIAIAAHPEVNDMWTRQQRAAKEGNSAYVDNGACRAIAAAGRKRLETRLASEKR"},"dna_sequence":{"accession":"AB636283.1","fmin":"0","fmax":"843","strand":"+","sequence":"ATGAAAATCATCGCTTCCCTGATCCTGGCGGCGTTTGCGTCTGTTGCGCAGGCGCAGGATCGTGATTGGAGCTCGCCGCAGCAGCCATTCACCATCTACGGCAATACCCATTACGTCGGCACCGGCGGCATCAGTGCGGTGCTGCTGTCCTCACCGCAAGGCCATATCCTGGTCGATGGCACCACCGAGAAGGGCGCGCAGGTTGTGGCTGCCAATATCCGTGCCATGGGCTTCAAGCTGTCGGACGTGAAGTACATCCTCAGCACCCATTCGCATGAGGACCATGCGGGCGGCATCTCGGCCATGCAGAAGCTGACCGGCGCTACGGTGCTGGCGGGGGCTGCGAATGTGGATACCTTGCGCACCGGTGTCTCGCCCAAGAGCGATCCGCAATTCGGCTCGCTGTCGAACTTCCCCGGCTCGGCAAAAGTGCGCGCGGTGGCTGATGGGGAGCTGGTGAAACTGGGGCCGCTGGCTGTCAAGGCCCATGCCACGCCGGGGCATACCGAGGGCGGCATCACCTGGACCTGGCAGTCCTGCGAACAGGGCAAGTGCAAGGACGTGGTCTTCGCGGACAGCCTGACTGCAGTTTCCGCCGACAGCTATCGTTTCTCCGATCATCCGGAAGTGGTGGCGTCGCTGCGCGGCAGCTTTGAGGCGGTGGAGAAGCTGTCCTGCGATATCGCGATTGCCGCCCATCCGGAAGTGAACGATATGTGGACGCGCCAGCAGCGCGCGGCAAAAGAGGGGAATTCGGCTTACGTGGATAACGGCGCTTGCCGCGCCATCGCGGCAGCCGGCCGCAAACGGCTTGAAACCCGCCTGGCCAGCGAGAAACGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36783","NCBI_taxonomy_name":"Serratia marcescens","NCBI_taxonomy_id":"615"}}}},"ARO_accession":"3000854","ARO_id":"37234","ARO_name":"SMB-1","CARD_short_name":"SMB-1","ARO_description":"SMB-1 can hydrolyze a variety of beta-lactams, including penicillins, cephalosporins, and carbapenems. It was identified in Serratia marcescens.","ARO_category":{"41381":{"category_aro_accession":"3004217","category_aro_cvterm_id":"41381","category_aro_name":"SMB beta-lactamase","category_aro_description":"SMB beta-lactamases are a subclass B3 beta-lactamases that hydrolyze a variety of beta-lactams, including penicillins, cephalosporins, and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"815":{"model_id":"815","model_name":"GOB-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1110":{"protein_sequence":{"accession":"AAF04458.1","sequence":"MRNFATLFFMFICLGLNAQVVKEPENMPKEWNQAYEPFRIAGNLYYVGTYDLASYLIVTDKGNILINTGTAESLPIIKANIQKLGFNYKDIKILLLTQAHYDHTGALQDFKTETAAKFYADKADVDVLRTGGKSDYEMGKYGVTFKPVTPDKTLKDQDKIKLGNITLTLLHHPGHTKGSCSFIFETKDEKRKYRVLIANMPSVIVDKKFSEVTAYPNIQSDYAYTFGVMKKLDFDIWVASHASQFDLHEKRKEGDPYNPQLFMDKQSYFQNLNDLEKSYLDKIKKDSQDK"},"dna_sequence":{"accession":"AF090141.1","fmin":"242","fmax":"1115","strand":"+","sequence":"ATGAGAAATTTTGCTACACTGTTTTTCATGTTCATTTGCTTGGGCTTGAATGCTCAGGTAGTAAAAGAACCTGAAAATATGCCCAAAGAATGGAACCAGGCTTATGAACCATTCAGAATTGCAGGTAATTTATATTACGTAGGAACCTATGATTTGGCTTCTTACCTTATTGTGACAGACAAAGGCAATATTCTCATTAATACAGGAACGGCAGAATCGCTTCCAATAATAAAAGCAAATATCCAAAAGCTCGGGTTTAATTATAAAGACATTAAGATCTTGCTGCTTACTCAGGCTCACTACGACCATACAGGTGCATTACAGGATTTTAAAACAGAAACCGCTGCAAAATTCTATGCCGATAAAGCAGATGTTGATGTCCTGAGAACAGGGGGGAAGTCCGATTATGAAATGGGAAAATATGGTGTGACATTTAAACCTGTTACTCCGGATAAAACATTGAAAGATCAGGATAAAATAAAACTGGGAAATATAACCCTGACTTTGCTTCATCATCCGGGACATACAAAAGGTTCCTGTAGTTTTATTTTTGAAACAAAAGACGAGAAGAGAAAATATAGAGTTTTGATAGCTAATATGCCCTCCGTTATTGTTGATAAGAAATTTTCTGAAGTTACCGCATATCCAAATATTCAGTCCGATTATGCTTATACCTTTGGTGTTATGAAAAAGCTGGATTTTGATATTTGGGTGGCCTCCCATGCAAGTCAGTTCGATCTCCATGAAAAACGTAAAGAAGGAGATCCGTACAATCCGCAATTGTTTATGGATAAGCAAAGCTATTTCCAAAACCTTAATGATTTGGAAAAAAGCTATCTCGACAAAATAAAAAAAGATTCCCAAGATAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36960","NCBI_taxonomy_name":"Elizabethkingia meningoseptica","NCBI_taxonomy_id":"238"}}}},"ARO_accession":"3000850","ARO_id":"37230","ARO_name":"GOB-1","CARD_short_name":"GOB-1","ARO_description":"GOB-1 confers resistance to cephalosporins in Elizabethkingia (Chryseobacterium) meningoseptica.","ARO_category":{"41376":{"category_aro_accession":"3004212","category_aro_cvterm_id":"41376","category_aro_name":"GOB beta-lactamase","category_aro_description":"The GOB family of beta-lactamases have been discovered in the Elizabethkingia meningoseptica and are classified as subclass B3 beta-lactamase. They confer resistance to cephalosporins, penicillins, and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"816":{"model_id":"816","model_name":"OXA-3","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1051":{"protein_sequence":{"accession":"AAC41449.1","sequence":"MAIRIFAILFSTFVFGTFAHAQEGMRERSDWRKFFSEFQAKGTIVVADERQTDRVILVFDQVRSEKRYSPASTFKIPHTLFALDAGAARDEFQVFRWDGIKRSFAAHNQDQDLRSAMRNSTVWIYELFAKEIGEDKARRYLKQIDYGNADPSTSNGDYWIDGNLAIAAQEQIAFLRKLYHNELPFRVEHQRLVKDLMIVEAGRNWILRAKTGWEGRIGWWVGWVEWPTGPVFFALNIDTPNRMDDLFKREAIVRAILRSIEALPPNPAVNSDAAR"},"dna_sequence":{"accession":"L07945.1","fmin":"60","fmax":"888","strand":"+","sequence":"ATGGCAATCCGAATCTTTGCAATACTTTTCTCCACTTTTGTTTTTGGCACGTTCGCGCATGCACAAGAAGGCATGCGCGAACGTTCTGACTGGCGGAAGTTTTTCAGCGAATTTCAAGCCAAAGGCACGATAGTTGTGGCAGACGAACGCCAAACAGATCGTGTCATATTGGTTTTTGATCAGGTGCGGTCAGAGAAACGCTACTCGCCGGCCTCGACATTCAAGATTCCACATACACTTTTTGCACTTGACGCAGGCGCTGCACGTGATGAGTTTCAAGTTTTCCGATGGGACGGCATCAAAAGAAGCTTTGCAGCTCACAACCAAGACCAAGACTTGCGATCAGCAATGCGGAATTCTACTGTCTGGATTTATGAGCTATTTGCAAAAGAGATCGGTGAAGACAAGGCTCGACGCTATTTGAAGCAAATCGACTATGGCAACGCCGATCCTTCGACAAGTAATGGCGATTACTGGATAGATGGCAATCTTGCTATCGCGGCACAAGAACAGATTGCATTTCTCAGGAAGCTCTATCATAACGAGTTGCCCTTTCGGGTAGAACATCAGCGCTTGGTCAAGGACCTCATGATTGTGGAAGCCGGTCGCAACTGGATACTGCGCGCAAAGACGGGCTGGGAAGGCCGCATTGGTTGGTGGGTAGGATGGGTTGAGTGGCCGACTGGCCCCGTATTCTTCGCACTGAATATTGATACGCCAAACAGGATGGATGACCTTTTCAAAAGGGAGGCAATAGTGCGGGCAATCCTTCGCTCTATCGAAGCGTTGCCGCCCAACCCGGCAGTCAACTCGGACGCAGCGCGATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3001398","ARO_id":"37798","ARO_name":"OXA-3","CARD_short_name":"OXA-3","ARO_description":"OXA-3 is a beta-lactamase found in P. aeruginosa.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46493":{"category_aro_accession":"3007704","category_aro_cvterm_id":"46493","category_aro_name":"OXA-2-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-2.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"817":{"model_id":"817","model_name":"CTX-M-158","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1902":{"protein_sequence":{"accession":"AIT97310.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAVAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVDGTMSLAELSVAALQYSDNVAMNKLISHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGDYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTNGL"},"dna_sequence":{"accession":"KM211691.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGTCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGAAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGTGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACTTGGTTAACTATAATCCGATTGCGGAAAAGCACGTCGATGGGACGATGTCACTGGCTGAGCTTAGCGTGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTTCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGTAATCTGACGCTGGGTAAAGCATTGGGTGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGACTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCAACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3003166","ARO_id":"39743","ARO_name":"CTX-M-158","CARD_short_name":"CTX-M-158","ARO_description":"CTX-M-158 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"818":{"model_id":"818","model_name":"SHV-141","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1634":{"protein_sequence":{"accession":"AFC60795.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGSVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGASERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"JQ388884.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCAGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTAGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGGATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001183","ARO_id":"37563","ARO_name":"SHV-141","CARD_short_name":"SHV-141","ARO_description":"SHV-141 is a broad-spectrum beta-lactamase.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"819":{"model_id":"819","model_name":"CTX-M-68","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1274":{"protein_sequence":{"accession":"ABV81082.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLHAQTVDVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDDTFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGDYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"EU177100.1","fmin":"4","fmax":"880","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTATTAGGAAGTGTGCCGCTGCATGCGCAAACGGTGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGAAGGCTGGGTGTGGCATTGATTAACACGGCGGATAATTCGCAAATACTTTATCGTGCTGATGAGCGTTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTAAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTCGAGATCAAAAAATCTGACCTGGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTCAGCGCGGCCGCGCTACAGTACAGCGATAATGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGATGACACGTTCCGTCTCGACCGCACCGAGCCGACGTTAAACACCGCCATTCCTGGCGATCCGCGTGATACCACTTCACCTCGGGCGATGGCGCAAACGCTGCGTAATCTGACGCTGGGTAAAGCGTTGGGCGACAGCCAACGGGCGCAGCTGGTGACGTGGATGAAAGGCAATACTACCGGTGCCGCGAGTATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGACTATGGTACCACCAACGATATCGCGGTGATTTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36940","NCBI_taxonomy_name":"Klebsiella sp. ARS06-441","NCBI_taxonomy_id":"474576"}}}},"ARO_accession":"3001929","ARO_id":"38329","ARO_name":"CTX-M-68","CARD_short_name":"CTX-M-68","ARO_description":"CTX-M-68 is a beta-lactamase found in the Enterobacteriaceae family.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"820":{"model_id":"820","model_name":"mdtB","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1800"}},"model_sequences":{"sequence":{"215":{"protein_sequence":{"accession":"AAC75136.1","sequence":"MQVLPPSSTGGPSRLFIMRPVATTLLMVAILLAGIIGYRALPVSALPEVDYPTIQVVTLYPGASPDVMTSAVTAPLERQFGQMSGLKQMSSQSSGGASVITLQFQLTLPLDVAEQEVQAAINAATNLLPSDLPNPPVYSKVNPADPPIMTLAVTSTAMPMTQVEDMVETRVAQKISQISGVGLVTLSGGQRPAVRVKLNAQAIAALGLTSETVRTAITGANVNSAKGSLDGPSRAVTLSANDQMQSAEEYRQLIIAYQNGAPIRLGDVATVEQGAENSWLGAWANKEQAIVMNVQRQPGANIISTADSIRQMLPQLTESLPKSVKVTVLSDRTTNIRASVDDTQFELMMAIALVVMIIYLFLRNIPATIIPGVAVPLSLIGTFAVMVFLDFSINNLTLMALTIATGFVVDDAIVVIENISRYIEKGEKPLAAALKGAGEIGFTIISLTFSLIAVLIPLLFMGDIVGRLFREFAITLAVAILISAVVSLTLTPMMCARMLSQESLRKQNRFSRASEKMFDRIIAAYGRGLAKVLNHPWLTLSVALSTLLLSVLLWVFIPKGFFPVQDNGIIQGTLQAPQSSSFANMAQRQRQVADVILQDPAVQSLTSFVGVDGTNPSLNSARLQINLKPLDERDDRVQKVIARLQTAVDKVPGVDLFLQPTQDLTIDTQVSRTQYQFTLQATSLDALSTWVPQLMEKLQQLPQLSDVSSDWQDKGLVAYVNVDRDSASRLGISMADVDNALYNAFGQRLISTIYTQANQYRVVLEHNTENTPGLAALDTIRLTSSDGGVVPLSSIAKIEQRFAPLSINHLDQFPVTTISFNVPDNYSLGDAVQAIMDTEKTLNLPVDITTQFQGSTLAFQSALGSTVWLIVAAVVAMYIVLGILYESFIHPITILSTLPTAGVGALLALLIAGSELDVIAIIGIILLIGIVKKNAIMMIDFALAAEREQGMSPREAIYQACLLRFRPILMTTLAALLGALPLMLSTGVGAELRRPLGIGMVGGLIVSQVLTLFTTPVIYLLFDRLALWTKSRFARHEEEA"},"dna_sequence":{"accession":"U00096.1","fmin":"2155262","fmax":"2158385","strand":"+","sequence":"ATGCAGGTGTTACCCCCGAGCAGCACAGGCGGCCCGTCGCGCCTGTTTATTATGCGTCCTGTGGCCACCACGCTGCTGATGGTGGCGATCTTACTCGCCGGGATTATCGGTTATCGCGCCCTGCCCGTTTCGGCGCTGCCGGAAGTGGACTATCCGACCATTCAGGTGGTCACGCTCTACCCAGGTGCCAGCCCGGATGTCATGACCTCTGCCGTTACCGCGCCGCTAGAACGCCAGTTCGGGCAGATGTCTGGCCTGAAACAGATGTCGTCGCAAAGTTCCGGCGGTGCGTCAGTTATCACTTTGCAGTTCCAGCTAACATTACCGCTCGATGTCGCCGAGCAGGAAGTGCAGGCCGCGATTAACGCTGCGACCAACTTGTTGCCGAGCGATCTGCCTAACCCGCCGGTTTACAGCAAAGTGAACCCGGCAGATCCGCCGATCATGACGCTCGCCGTCACCTCAACCGCCATGCCGATGACGCAAGTGGAAGATATGGTGGAAACCCGCGTCGCGCAGAAAATCTCGCAGATTTCCGGCGTCGGCCTGGTGACGCTTTCCGGCGGTCAGCGTCCGGCTGTTCGCGTCAAACTTAACGCTCAGGCGATTGCCGCCCTCGGCCTGACCAGCGAAACCGTGCGCACCGCCATTACCGGCGCTAACGTTAACTCGGCAAAAGGTAGCCTCGACGGCCCTTCCCGTGCGGTCACGCTTTCCGCGAACGACCAGATGCAATCCGCCGAAGAGTATCGCCAGCTAATCATCGCCTACCAGAACGGCGCGCCAATTCGTCTGGGCGATGTCGCAACTGTAGAGCAAGGTGCAGAAAACAGCTGGCTCGGCGCGTGGGCGAACAAAGAACAGGCCATTGTGATGAATGTTCAGCGCCAGCCCGGTGCTAACATTATCTCCACCGCCGACAGCATTCGGCAGATGCTGCCACAGCTCACTGAGAGTCTGCCGAAATCGGTGAAGGTGACAGTGCTTTCCGATCGCACCACCAATATCCGCGCATCCGTCGATGATACTCAGTTTGAATTGATGATGGCTATCGCGCTGGTAGTCATGATTATCTACCTGTTTTTGCGCAATATTCCGGCGACCATCATTCCCGGTGTTGCTGTACCGCTGTCGTTAATCGGCACTTTCGCGGTTATGGTGTTTCTCGATTTTTCAATCAATAACCTGACACTGATGGCGTTAACTATCGCCACCGGATTCGTGGTCGATGACGCCATCGTGGTGATCGAAAACATTTCCCGCTATATCGAAAAAGGCGAAAAACCGTTGGCGGCGGCGCTCAAGGGCGCAGGTGAAATCGGCTTTACCATTATCTCGCTGACCTTCTCACTGATTGCGGTGTTGATCCCACTGCTGTTTATGGGCGATATCGTCGGGCGACTGTTCCGCGAATTTGCTATTACCCTGGCGGTAGCGATTTTGATCTCAGCGGTGGTGTCGCTGACCCTGACACCGATGATGTGCGCGCGGATGCTCAGCCAGGAGTCGTTGCGTAAACAGAACCGCTTCTCCCGTGCCTCGGAAAAAATGTTCGACAGGATAATCGCCGCCTATGGTCGTGGACTGGCGAAAGTGCTGAATCATCCGTGGCTGACCTTAAGCGTGGCACTCAGCACGCTGCTGCTTAGCGTGCTGCTGTGGGTGTTCATTCCGAAAGGTTTCTTCCCGGTACAGGACAATGGCATTATTCAGGGCACTTTGCAGGCACCGCAATCCAGCTCCTTTGCCAATATGGCCCAGCGACAACGCCAGGTCGCGGACGTGATTTTGCAGGATCCGGCAGTGCAAAGCCTGACCTCATTTGTTGGCGTTGATGGCACTAACCCGTCGCTGAACAGTGCACGTTTACAAATCAACCTCAAACCGTTGGATGAACGTGATGATCGGGTGCAAAAAGTCATCGCCCGTCTGCAAACGGCGGTAGATAAAGTGCCGGGCGTCGATCTCTTCCTGCAACCAACGCAGGATCTGACTATTGATACTCAGGTCAGCCGCACCCAGTACCAGTTTACCTTGCAGGCCACGTCACTGGATGCGCTCAGTACCTGGGTGCCACAGTTGATGGAAAAACTCCAGCAACTGCCACAGCTTTCTGATGTCTCCAGCGACTGGCAGGACAAAGGGCTGGTGGCGTATGTCAATGTTGATCGCGACAGCGCCAGCCGTCTGGGGATCAGCATGGCGGATGTCGATAACGCCCTGTACAACGCGTTTGGTCAGCGGCTGATTTCCACTATTTATACTCAGGCCAACCAGTATCGCGTGGTGCTGGAGCACAACACCGAAAATACCCCAGGCCTCGCGGCGCTGGATACCATTCGCCTGACCAGCAGCGACGGCGGCGTGGTGCCGCTAAGCTCAATTGCCAAAATTGAGCAGCGTTTTGCGCCGCTCTCCATCAACCATCTGGATCAGTTCCCGGTAACGACCATCTCCTTTAACGTGCCGGATAACTATTCGCTGGGCGATGCGGTGCAGGCGATTATGGACACCGAAAAGACGCTGAATCTGCCGGTGGATATCACCACGCAGTTCCAGGGCAGCACCCTCGCCTTCCAGTCGGCGCTGGGCAGCACTGTCTGGCTGATTGTCGCGGCGGTGGTGGCGATGTATATCGTGCTCGGCATTCTGTACGAGAGCTTTATTCACCCGATCACCATTCTCTCGACGCTACCCACCGCAGGGGTTGGCGCACTGCTGGCGTTGCTGATTGCTGGTAGCGAACTGGATGTGATTGCGATTATCGGCATTATTTTGCTGATCGGTATCGTGAAGAAGAACGCCATCATGATGATCGACTTCGCGCTGGCTGCTGAGCGCGAGCAAGGCATGTCGCCGCGCGAGGCAATCTACCAGGCTTGTCTGTTGCGTTTTCGTCCGATCCTGATGACCACTCTGGCGGCTCTGCTTGGCGCGCTGCCGCTGATGTTGAGTACCGGGGTCGGCGCGGAACTGCGTCGTCCGTTAGGTATCGGCATGGTCGGCGGTCTGATTGTCAGCCAGGTGCTGACGCTGTTTACCACGCCGGTGATTTATTTGCTGTTCGACCGCCTGGCATTGTGGACCAAAAGCCGCTTTGCCCGTCATGAAGAGGAGGCGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36849","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. MG1655","NCBI_taxonomy_id":"511145"}}}},"ARO_accession":"3000793","ARO_id":"37173","ARO_name":"mdtB","CARD_short_name":"mdtB","ARO_description":"MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"36250":{"category_aro_accession":"3000111","category_aro_cvterm_id":"36250","category_aro_name":"novobiocin","category_aro_description":"Novobiocin is an aminocoumarin antibiotic produced by Streptomyces spheroides and Streptomyces niveus, and binds DNA gyrase subunit B inhibiting ATP-dependent DNA supercoiling.","category_aro_class_name":"Antibiotic"},"36242":{"category_aro_accession":"3000103","category_aro_cvterm_id":"36242","category_aro_name":"aminocoumarin antibiotic","category_aro_description":"Aminocoumarin antibiotics bind DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"822":{"model_id":"822","model_name":"QnrD1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"746":{"protein_sequence":{"accession":"ACG70184.1","sequence":"MEKHFINEKFSRDQFTGNRVKNIAFSNCDFSGVDLTDTEFVDCSFYDRNSLEGCDFNRAKLKNASFKSCDLSMSNFKNISALGLEISECLAQGADFRGANFMNMITTRSWFCSAYITKTNLSYANFSRVILEKCELWENRWNGTVITGAVFRGSDLSCGEFSSFDWSLADFTGCDLTGGALGELDARRINLDGVKLDGEQALQLVESLGVIVHR"},"dna_sequence":{"accession":"FJ228229.1","fmin":"553","fmax":"1198","strand":"+","sequence":"ATGGAAAAGCACTTTATCAATGAAAAGTTTTCACGAGATCAATTTACGGGGAATAGAGTTAAAAATATTGCCTTTTCAAATTGTGATTTTTCAGGGGTTGATTTAACTGATACTGAATTTGTTGATTGTAGTTTTTACGACAGGAATAGCTTGGAAGGGTGTGATTTTAATAGAGCCAAACTAAAAAACGCTAGCTTTAAAAGCTGCGATTTATCAATGAGTAATTTTAAAAACATTAGCGCCTTAGGTCTTGAAATTAGTGAGTGTTTAGCTCAAGGAGCTGATTTTCGAGGGGCTAATTTTATGAATATGATAACTACAAGGTCATGGTTTTGTAGTGCTTATATAACCAAGACAAATCTTAGTTACGCTAATTTTTCTAGAGTCATATTAGAAAAGTGCGAACTGTGGGAAAATCGCTGGAATGGCACTGTGATAACTGGCGCCGTGTTTCGTGGCTCCGATCTTTCTTGTGGGGAGTTTTCATCGTTTGATTGGTCTTTGGCTGATTTTACTGGTTGTGATTTAACGGGTGGGGCGCTTGGCGAGCTTGATGCAAGGCGAATTAATTTAGATGGAGTGAAGTTGGATGGAGAGCAGGCGCTTCAGCTTGTTGAGAGTTTAGGTGTTATTGTTCACCGATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35711","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Bovismorbificans","NCBI_taxonomy_id":"58097"}}}},"ARO_accession":"3002788","ARO_id":"39222","ARO_name":"QnrD1","CARD_short_name":"QnrD1","ARO_description":"QnrD1 is a plasmid-mediated quinolone resistance protein found in Salmonella enterica.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"824":{"model_id":"824","model_name":"vanD","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"350"}},"model_sequences":{"sequence":{"179":{"protein_sequence":{"accession":"AAM09849.1","sequence":"MYKLKIAVLFGGCSEEHDVSVKSAMEVAANINKEKYQPFYIGITKSGAWKLCDKPCRDWENYAGYPAVISPDRRIHGLLIQKDGGYESQPVDVVLPMIHGKFGEDGTIQGLLELSGIPYVGCDIQSSVICMDKSLAYMVVKNAGIEVPGFRVLQKGDSLEAETLSYPVFVKPARSGSSFGVNKVCRAEELQAAVTEAGKYDSKILVEEAVSGSEVGCAILGNGNDLITGEVDQIELKHGFFKIHQEAQPEKGSENAVIRVPAALPDEVREQIQETAKKIYRVLGCRGLARIDLFLREDGSIVLNEVNTMPGFTSYSRYPRMMTAAGFTLSEILDRLIGLSLRR"},"dna_sequence":{"accession":"AY082011.1","fmin":"5900","fmax":"6932","strand":"+","sequence":"ATGTATAAGCTTAAAATTGCAGTCCTGTTTGGAGGCTGCTCAGAGGAACATGATGTTTCAGTGAAATCTGCGATGGAGGTTGCAGCAAATATAAACAAGGAAAAATACCAGCCGTTTTATATTGGAATCACAAAATCCGGCGCATGGAAACTATGCGATAAGCCCTGCCGGGACTGGGAGAACTATGCGGGATACCCGGCTGTGATTTCTCCGGACAGAAGGATCCATGGCCTGCTGATACAAAAGGACGGCGGATATGAGAGCCAGCCTGTAGACGTGGTGCTTCCGATGATTCATGGAAAATTTGGCGAGGACGGAACCATACAGGGTCTGCTTGAGCTGTCCGGCATTCCTTATGTGGGATGCGACATTCAAAGTTCTGTAATCTGTATGGATAAGTCGCTCGCTTATATGGTTGTGAAAAATGCGGGAATTGAGGTACCTGGGTTTCGAGTTCTACAAAAGGGGGACAGCCTGGAAGCAGAGACGCTCTCGTATCCGGTCTTTGTAAAGCCTGCCCGTTCCGGCTCCTCTTTTGGCGTGAATAAGGTATGCCGGGCAGAGGAACTGCAGGCAGCGGTCACAGAGGCGGGTAAGTATGACAGCAAAATATTGGTTGAGGAGGCCGTTTCCGGGAGTGAGGTAGGATGTGCCATACTGGGAAACGGAAACGATCTCATCACCGGCGAGGTCGATCAGATTGAATTGAAACACGGGTTTTTTAAGATCCATCAGGAAGCACAGCCGGAAAAGGGGTCTGAAAATGCTGTGATTAGAGTTCCAGCCGCCCTGCCGGATGAAGTTAGGGAGCAGATTCAGGAAACGGCGAAGAAGATTTACCGGGTACTTGGCTGCAGAGGTCTGGCCCGCATTGATTTGTTTTTACGGGAGGATGGAAGCATTGTCCTGAATGAAGTGAACACCATGCCCGGATTTACTTCCTATAGCCGTTATCCACGCATGATGACAGCAGCAGGGTTTACGCTTTCTGAAATATTGGACCGCTTGATTGGACTTTCACTTAGGAGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36779","NCBI_taxonomy_name":"Enterococcus faecium","NCBI_taxonomy_id":"1352"}}}},"ARO_accession":"3000005","ARO_id":"36014","ARO_name":"vanD","CARD_short_name":"vanD","ARO_description":"VanD is a D-Ala-D-Ala ligase homolog similar to VanA, and can synthesize D-Ala-D-Lac, an alternative substrate for peptidoglycan synthesis that reduces vancomycin binding affinity. It is associated with both vancomycin and teicoplanin resistance.","ARO_category":{"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"39340":{"category_aro_accession":"3002906","category_aro_cvterm_id":"39340","category_aro_name":"Van ligase","category_aro_description":"Van ligases synthesize alternative substrates for peptidoglycan synthesis that reduce vancomycin binding affinity.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"35948":{"category_aro_accession":"0000029","category_aro_cvterm_id":"35948","category_aro_name":"teicoplanin","category_aro_description":"Teicoplanin is a glycopeptide antibiotic used in the prophylaxis and treatment of serious infections caused by Gram-positive bacteria. Teicoplanin has a unique acyl-aliphatic chain, and binds to cell wall precursors to inhibit transglycosylation  and transpeptidation.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"825":{"model_id":"825","model_name":"SHV-20","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1314":{"protein_sequence":{"accession":"AAF34334.1","sequence":"MLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEAFPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGASERGARGIVALLGPNNKAERIVVIYLRDTPASMAERN"},"dna_sequence":{"accession":"AF117744.1","fmin":"0","fmax":"780","strand":"+","sequence":"CTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTACTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGTTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTAGCGAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAAT","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001078","ARO_id":"37458","ARO_name":"SHV-20","CARD_short_name":"SHV-20","ARO_description":"SHV-20 is a broad-spectrum beta-lactamase that has been found in clinical isolates.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"786":{"model_id":"786","model_name":"vanH gene in vanO cluster","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"200"}},"model_sequences":{"sequence":{"576":{"protein_sequence":{"accession":"AHA41499.1","sequence":"MSYRDLGLIDSEVIAERRVRALDDSSPSAVPTTGVRVFGCGHDEAVLFREMGTRLGITPSITEEAISETNAELARGNRCISVSHKTQIDNSTLLALSRVGVEYISTRSVGYNHIDVEFAASIGISVGNVDYSPDSVGDYTLMLMLMTVRHAKSIVRRADTHDYRLNDTRGRELRDLTVGVIGTGRIGTAVIDRLQGFGCRVLAHDSGPHASADYVPLDELLRQSDIVTLHTPLTADTHHLLDRQRIDQMKHGAYIVNTGRGPLLDTEALLSALESGRLGGAALDVVEGEEGIFYADCRNRLIENKALVRLQRLPNVLISPHSAYYTDHALNDTVENSLVNCLNFESGRTA"},"dna_sequence":{"accession":"KF478993.1","fmin":"490","fmax":"1543","strand":"+","sequence":"ATGTCCTACAGAGACCTGGGTTTGATCGACAGCGAAGTGATCGCGGAGCGACGCGTCCGAGCGCTCGACGATTCGTCACCCTCGGCCGTCCCGACCACTGGGGTCAGAGTTTTCGGATGCGGTCACGACGAAGCCGTTTTGTTCCGCGAGATGGGAACCCGCCTCGGGATAACGCCAAGCATCACCGAGGAAGCGATCAGTGAAACCAACGCTGAACTGGCGCGTGGCAACCGATGCATCAGCGTGAGCCACAAGACGCAGATCGACAATTCCACGCTGCTGGCGCTGAGCCGAGTCGGAGTGGAGTACATCTCCACCAGAAGCGTCGGGTACAACCACATCGACGTGGAATTCGCGGCGAGCATCGGCATCTCGGTCGGCAACGTCGACTACTCGCCCGACAGCGTGGGCGACTACACACTGATGTTGATGCTGATGACCGTACGCCACGCGAAATCAATTGTCCGCCGCGCCGATACGCATGATTACCGGCTGAATGACACGCGCGGCAGGGAGCTGCGCGACTTGACCGTCGGGGTGATCGGAACAGGGCGCATCGGCACAGCAGTCATCGACCGGCTGCAGGGATTTGGCTGCCGCGTGCTGGCACATGACAGCGGGCCTCACGCCTCCGCCGACTACGTTCCGCTCGATGAACTGCTGCGGCAGAGCGACATTGTCACGCTCCACACTCCACTCACCGCGGACACACACCATCTCCTCGATCGCCAACGCATCGACCAGATGAAGCACGGCGCGTACATCGTCAACACGGGTCGCGGACCGCTGCTCGATACCGAGGCCCTCCTCTCCGCATTGGAGAGCGGCCGGTTGGGCGGCGCGGCGCTCGATGTCGTCGAAGGAGAGGAAGGGATCTTCTACGCCGACTGCAGGAACAGGCTCATCGAGAACAAGGCCCTGGTGCGGCTACAGCGCCTGCCGAATGTGCTGATCAGTCCGCACTCCGCCTACTACACAGACCACGCCCTGAACGACACCGTCGAAAACAGCCTCGTCAACTGCCTGAACTTTGAAAGTGGGAGAACAGCATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36897","NCBI_taxonomy_name":"Rhodococcus hoagii","NCBI_taxonomy_id":"43767"}}}},"ARO_accession":"3002948","ARO_id":"39382","ARO_name":"vanH gene in vanO cluster","CARD_short_name":"vanH_in_vanO_cl","ARO_description":"Also known as vanHO, is a vanH variant in the vanO gene cluster.","ARO_category":{"36015":{"category_aro_accession":"3000006","category_aro_cvterm_id":"36015","category_aro_name":"vanH","category_aro_description":"VanH is a D-specific alpha-ketoacid dehydrogenase that synthesizes D-lactate. D-lactate is incorporated into the end of the peptidoglycan subunits, decreasing vancomycin binding affinity.","category_aro_class_name":"AMR Gene Family"},"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"774":{"model_id":"774","model_name":"tet(37)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"200"}},"model_sequences":{"sequence":{"24":{"protein_sequence":{"accession":"AAN28721.1","sequence":"MVRYYSNIVGKYGIPVQNALKKLAGIHIDYICSTHGPVWHENVEKVVNLYDRMSKYETDPGLVICYGTMYGNTEDRTPSMYEYIWIKENREAKVVSSFAANIYLGWGR"},"dna_sequence":{"accession":"AF540889.1","fmin":"0","fmax":"327","strand":"+","sequence":"ATGGTTCGCTATTACTCTAACATTGTAGGTAAATACGGTATTCCAGTTCAGAATGCACTGAAGAAACTTGCAGGTATTCACATTGATTATATCTGTTCAACACATGGTCCTGTATGGCATGAGAACGTTGAAAAGGTGGTGAACCTGTATGATCGTATGTCGAAATATGAGACTGATCCAGGCTTGGTTATCTGCTACGGAACGATGTATGGGAACACAGAGGATCGCACACCGTCGATGTATGAATATATATGGATAAAAGAGAATCGAGAAGCTAAGGTTGTTTCATCATTTGCAGCTAATATTTATTTAGGATGGGGGCGGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36791","NCBI_taxonomy_name":"uncultured bacterium","NCBI_taxonomy_id":"77133"}}}},"ARO_accession":"3002871","ARO_id":"39305","ARO_name":"tet(37)","CARD_short_name":"tet(37)","ARO_description":"tet(37) is a chromosome-encoded oxidoreductase isolated from an uncultured bacterium that confers resistance to tetracycline.","ARO_category":{"36176":{"category_aro_accession":"3000036","category_aro_cvterm_id":"36176","category_aro_name":"tetracycline inactivation enzyme","category_aro_description":"Enzymes or other gene products which hydroxylate tetracycline and other tetracycline derivatives. Hydroxylation inactivates tetracycline-like antibiotics, thus conferring resistance to these compounds.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"776":{"model_id":"776","model_name":"tet(X)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"79":{"protein_sequence":{"accession":"AAA27471.1","sequence":"MTMRIDTDKQMNLLSDKNVAIIGGGPVGLTMAKLLQQNGIDVSVYERDNDREARIFGGTLDLHKGSGQEAMKKAGLLQTYYDLALPMGVNIADKKGNILSTKNVKPENRFDNPEINRNDLRAILLNSLENDTVIWDRKLVMLEPGKKKWTLTFENKPSETADLVILANGGMSKVRKFVTDTEVEETGTFNIQADIHQPEINCPGFFQLCNGNRLMASHQGNLLFANPNNNGALHFGISFKTPDEWKNQTQVDFQNRNSVVDFLLKEFSDWDERYKELIHTTLSFVGLATRIFPLEKPWKSKRPLPITMIGDAAHLMPPFAGQGVNSGLVDALILSDNLADGKFNSIEEAVKNYEQQMFMYGKEAQEESTQNEIEMFKPDFTFQQLLNV"},"dna_sequence":{"accession":"M37699.1","fmin":"585","fmax":"1752","strand":"+","sequence":"ATGACAATGCGAATAGATACAGACAAACAAATGAATTTACTTAGTGATAAGAACGTTGCAATAATTGGTGGTGGACCCGTTGGACTGACTATGGCAAAATTATTACAGCAAAACGGCATAGACGTTTCAGTTTACGAAAGAGACAACGACCGAGAGGCAAGAATTTTTGGTGGAACCCTTGACCTACACAAAGGTTCAGGTCAGGAAGCAATGAAAAAAGCGGGATTGTTACAAACTTATTATGACTTAGCCTTACCAATGGGTGTAAATATTGCTGATAAAAAAGGCAATATTTTATCCACAAAAAATGTAAAGCCCGAAAATCGATTTGACAATCCTGAAATAAACAGAAATGACTTAAGGGCTATCTTGTTGAATAGTTTAGAAAACGACACGGTTATTTGGGATAGAAAACTTGTTATGCTTGAACCTGGTAAGAAGAAGTGGACACTAACTTTTGAGAATAAACCGAGTGAAACAGCAGATTTGGTTATTCTTGCCAATGGCGGGATGTCCAAGGTAAGAAAATTTGTTACCGACACGGAAGTTGAAGAAACAGGTACTTTCAATATACAAGCCGATATTCATCAACCAGAGATAAACTGTCCTGGATTTTTTCAGCTATGCAATGGAAACCGGCTAATGGCATCTCACCAAGGTAATTTATTATTTGCTAACCCCAATAATAATGGTGCATTGCATTTTGGAATAAGTTTTAAAACACCTGATGAATGGAAAAACCAAACGCAGGTAGATTTTCAAAACAGAAATAGTGTCGTTGATTTTCTTCTGAAAGAATTTTCCGATTGGGACGAACGCTACAAAGAATTGATTCATACGACGTTGTCATTTGTAGGATTGGCTACACGGATATTTCCTTTAGAAAAGCCTTGGAAAAGCAAGCGCCCATTACCCATAACAATGATTGGGGATGCCGCACATTTGATGCCGCCTTTTGCAGGGCAGGGAGTAAATAGTGGGTTGGTGGATGCCTTGATATTGTCTGATAATCTAGCCGATGGAAAATTTAATAGCATTGAAGAGGCTGTTAAAAATTATGAACAGCAAATGTTTATGTATGGCAAAGAAGCACAAGAAGAATCAACTCAAAACGAAATTGAAATGTTTAAACCCGACTTTACGTTTCAGCAATTGTTAAATGTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35916","NCBI_taxonomy_name":"Bacteroides fragilis","NCBI_taxonomy_id":"817"}}}},"ARO_accession":"3000205","ARO_id":"36344","ARO_name":"tet(X)","CARD_short_name":"tet(X)","ARO_description":"Tet(X) is a flavin-dependent monooxygenase conferring resistance to tetracycline antibiotics. Tet(X) hydroxylates position 11a of the tetraketide group thus inactivating the antibiotic.","ARO_category":{"36176":{"category_aro_accession":"3000036","category_aro_cvterm_id":"36176","category_aro_name":"tetracycline inactivation enzyme","category_aro_description":"Enzymes or other gene products which hydroxylate tetracycline and other tetracycline derivatives. Hydroxylation inactivates tetracycline-like antibiotics, thus conferring resistance to these compounds.","category_aro_class_name":"AMR Gene Family"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35986":{"category_aro_accession":"0000069","category_aro_cvterm_id":"35986","category_aro_name":"doxycycline","category_aro_description":"Doxycycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36291":{"category_aro_accession":"3000152","category_aro_cvterm_id":"36291","category_aro_name":"minocycline","category_aro_description":"Minocycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36667":{"category_aro_accession":"3000528","category_aro_cvterm_id":"36667","category_aro_name":"chlortetracycline","category_aro_description":"Chlortetracycline was an early, first-generation tetracycline antibiotic developed in the 1940's. It inhibits bacterial protein synthesis by binding to the 30S subunit of bacterial ribosomes, preventing the aminoacyl-tRNA from binding to the ribosome.","category_aro_class_name":"Antibiotic"},"37011":{"category_aro_accession":"3000667","category_aro_cvterm_id":"37011","category_aro_name":"demeclocycline","category_aro_description":"Demeclocycline is a tetracycline analog with 7-chloro and 6-methyl groups. Due to its fast absorption and slow excretion, it maintains higher effective blood levels compared to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37012":{"category_aro_accession":"3000668","category_aro_cvterm_id":"37012","category_aro_name":"oxytetracycline","category_aro_description":"Oxytetracycline is a derivative of tetracycline with a 5-hydroxyl group. Its activity is similar to other tetracyclines.","category_aro_class_name":"Antibiotic"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"827":{"model_id":"827","model_name":"QnrB55","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"389":{"protein_sequence":{"accession":"AHE41343.1","sequence":"MTLALVGEKIDRNRFTGEKVENSTFFNCDFSGADLSGTEFIGCQLYDRESQKGCNFSRANLKDAIFKSCDLSMADFRNINALGIEIRHCRAQGSDFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGTQVLGATFSGSDLSGGEFSSFDWRAANVTHCDLTNSELGDLDIRGVDLQGVKLDSYQASLLLERLGIAVMG"},"dna_sequence":{"accession":"KF730650.1","fmin":"0","fmax":"645","strand":"+","sequence":"ATGACTCTGGCGTTAGTTGGCGAAAAAATTGACAGAAACAGGTTCACCGGTGAAAAAGTTGAAAATAGCACATTTTTCAACTGTGATTTTTCGGGTGCCGACCTGAGCGGCACTGAATTTATTGGCTGCCAGTTATATGATCGAGAAAGTCAGAAAGGATGTAATTTTAGTCGCGCTAACCTGAAAGATGCCATTTTCAAAAGTTGTGATCTCTCCATGGCTGATTTCAGGAATATCAATGCGCTGGGAATCGAAATTCGCCACTGCCGGGCACAAGGGTCAGATTTTCGCGGCGCAAGTTTTATGAATATGATCACCACCCGCACCTGGTTTTGTAGCGCCTATATCACCAATACCAACTTAAGCTACGCCAACTTTTCAAAAGTCGTACTGGAAAAGTGCGAGCTGTGGGAAAACCGCTGGATGGGTACTCAGGTGCTGGGCGCAACGTTCAGTGGATCAGACCTCTCTGGCGGCGAGTTTTCATCCTTCGACTGGCGAGCAGCAAACGTTACGCACTGTGATTTGACCAATTCGGAACTGGGCGATTTAGATATCCGCGGGGTTGATTTGCAAGGCGTCAAACTGGACAGCTACCAGGCATCGTTGCTCCTGGAACGTCTTGGTATCGCTGTCATGGGTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39585","NCBI_taxonomy_name":"Raoultella terrigena","NCBI_taxonomy_id":"577"}}}},"ARO_accession":"3002768","ARO_id":"39202","ARO_name":"QnrB55","CARD_short_name":"QnrB55","ARO_description":"QnrB55 is a plasmid-mediated quinolone resistance protein found in Raoultella terrigena.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"828":{"model_id":"828","model_name":"TEM-83","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1249":{"protein_sequence":{"accession":"AAL29435.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMLSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRCEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDEQNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AF427129.1","fmin":"208","fmax":"1069","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGTTGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATCGTTGTGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACAAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000950","ARO_id":"37330","ARO_name":"TEM-83","CARD_short_name":"TEM-83","ARO_description":"TEM-83 is an inhibitor-resistant beta-lactamase found in E. coli.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"829":{"model_id":"829","model_name":"DHA-17","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1089":{"protein_sequence":{"accession":"AIT76103.1","sequence":"MKKSLSATLISALLAFSAPGFSAADNVAVVVDSTIKPLMAQQDIPGMAVAVSVKGKPYYFNYGFADIQAKQPVTENTLFELGSVSKTFTGVLGAVSVAKKEMALNDPAAKYQPELALPQWKGITLLDLATYTAGGLPLQVPDAVKSRADLLNFYQQWQPSRKPGDMRLYANSSIGLFGALTANAAGMPYEQLLTARILAPLGLSHTFITVPESAQSQYAYGYKNKKPVRVSPGQLDAESYGVKSASKDMLRWAEMNMEPSRAGNADLEMAMYLAQTRYYKTAAINQGLGWEMYDWPQQKDMIINGVTNEVALQPHPVTDNQVQPYNRASWVHKTGATTGFGAYVAFIPEKQVAIVILANKNYPNTERVKAAQAILSALE"},"dna_sequence":{"accession":"KM087850.1","fmin":"0","fmax":"1140","strand":"+","sequence":"ATGAAAAAATCGTTATCTGCAACACTGATTTCCGCTCTGCTGGCGTTTTCCGCCCCGGGGTTTTCTGCCGCTGATAATGTCGCGGTGGTGGTGGACAGCACCATTAAACCGCTGATGGCACAGCAGGATATTCCCGGGATGGCGGTTGCCGTCTCCGTAAAGGGTAAGCCCTATTATTTCAATTATGGTTTTGCCGATATTCAGGCAAAACAGCCGGTCACTGAAAATACACTATTTGAGCTCGGATCTGTAAGTAAAACTTTCACAGGTGTGCTGGGTGCGGTTTCTGTGGCGAAAAAAGAGATGGCGCTGAATGATCCGGCGGCAAAATACCAGCCGGAGCTGGCTCTGCCGCAGTGGAAGGGGATCACATTGCTGGATCTGGCTACCTATACCGCAGGCGGACTGCCGTTACAGGTGCCGGATGCGGTAAAAAGCCGTGCGGATCTGCTGAATTTCTATCAGCAGTGGCAGCCGTCCCGGAAACCGGGCGATATGCGTCTGTATGCAAACAGCAGTATCGGCCTGTTTGGTGCTCTGACCGCAAACGCGGCGGGGATGCCGTATGAGCAGTTGCTGACTGCACGGATCCTGGCACCGCTGGGGTTATCTCACACCTTTATTACTGTGCCGGAAAGTGCGCAAAGCCAGTATGCGTACGGTTATAAAAACAAAAAACCGGTCCGCGTGTCGCCGGGACAGCTTGATGCGGAATCTTACGGCGTGAAATCCGCCTCAAAAGATATGCTGCGCTGGGCGGAAATGAATATGGAGCCGTCACGGGCCGGTAATGCGGATCTGGAAATGGCAATGTATCTTGCACAGACCCGCTACTATAAAACCGCCGCGATTAACCAGGGGCTGGGCTGGGAAATGTATGACTGGCCGCAGCAGAAAGATATGATCATTAACGGCGTGACCAACGAGGTCGCATTGCAGCCGCACCCGGTAACAGACAACCAGGTTCAGCCGTATAACCGTGCTTCCTGGGTGCATAAAACGGGGGCAACAACTGGTTTCGGCGCCTATGTGGCCTTTATTCCGGAAAAACAGGTGGCGATTGTGATTCTGGCGAATAAAAACTACCCGAATACCGAAAGAGTCAAAGCCGCACAGGCTATTTTGAGTGCACTGGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36917","NCBI_taxonomy_name":"Morganella morganii","NCBI_taxonomy_id":"582"}}}},"ARO_accession":"3002148","ARO_id":"38548","ARO_name":"DHA-17","CARD_short_name":"DHA-17","ARO_description":"DHA-17 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36207":{"category_aro_accession":"3000068","category_aro_cvterm_id":"36207","category_aro_name":"DHA beta-lactamase","category_aro_description":"DHA beta-lactamases are plasmid-mediated AmpC \u03b2-lactamases that confer resistance to cephamycins and oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"830":{"model_id":"830","model_name":"SHV-157","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1635":{"protein_sequence":{"accession":"AFQ23963.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVMLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"JX121124.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAATGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCAGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCAGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001196","ARO_id":"37576","ARO_name":"SHV-157","CARD_short_name":"SHV-157","ARO_description":"SHV-157 is a beta-lactamase.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"831":{"model_id":"831","model_name":"OKP-B-13","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"1041":{"protein_sequence":{"accession":"AAV80715.1","sequence":"MRYIRLCLISLIAALPLAVFASPQPLEQIKISESQLAGRVGYVEMDLASGRTLAAWRASERFPLMSTFKVLLCGAVLARVDAGDEQLDRRIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNTAGNLLLKIVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDVRDTTTPASMATTLRKLLTTPSLSARSQQQLLQWMVDDRVAGPLIRAVLPAGWFIADKTGAGERGSRGIVALLGPDGKAERIVVIYLRDTAATMAERNQQIAVIGAALIEHWQR"},"dna_sequence":{"accession":"AY825330.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGCCTTATCTCCCTGATTGCCGCCCTGCCACTGGCGGTATTCGCCAGCCCTCAGCCGCTTGAGCAGATTAAAATCAGCGAAAGTCAGCTGGCGGGCCGGGTGGGCTATGTTGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCAGTGAGCGCTTTCCGCTGATGAGCACCTTTAAAGTGCTGCTCTGCGGCGCGGTGCTGGCCCGGGTGGATGCCGGCGACGAACAGCTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGCCGACGGGATGACCGTTGGCGAACTCTGCGCCGCCGCCATCACCATGAGCGACAACACCGCCGGCAATCTGCTGTTGAAGATCGTCGGCGGCCCCGCGGGATTGACCGCTTTTCTGCGCCAGATCGGTGACAACGTCACCCGTCTTGACCGCTGGGAAACGGAACTCAATGAGGCGCTTCCCGGCGACGTGCGCGACACCACCACCCCGGCCAGCATGGCCACCACCCTGCGCAAGCTGCTAACCACCCCCTCTCTGAGCGCCCGTTCGCAGCAGCAGCTGCTGCAGTGGATGGTTGACGACCGGGTGGCCGGCCCGTTGATCCGCGCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAAACCGGGGCCGGTGAGCGGGGCTCACGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAAGCGGAGCGTATCGTGGTGATCTATCTGCGGGATACCGCAGCGACCATGGCCGAACGTAACCAGCAGATCGCCGTGATAGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002446","ARO_id":"38846","ARO_name":"OKP-B-13","CARD_short_name":"OKP-B-13","ARO_description":"OKP-B-13 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"38817":{"category_aro_accession":"3002417","category_aro_cvterm_id":"38817","category_aro_name":"OKP beta-lactamase","category_aro_description":"OKP beta-lactamases are chromosomal class A beta-lactamase that confer resistance to penicillins and early cephalosporins in Klebsiella pneumoniae. OKP beta-lactamases can be subdivided into two groups: OKP-A and OKP-B which diverge by about 4.2%.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"832":{"model_id":"832","model_name":"SHV-161","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"2022":{"protein_sequence":{"accession":"AFQ23967.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGSVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"JX121128.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCAGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001200","ARO_id":"37580","ARO_name":"SHV-161","CARD_short_name":"SHV-161","ARO_description":"SHV-161 is a beta-lactamase.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"833":{"model_id":"833","model_name":"CfxA5","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"1669":{"protein_sequence":{"accession":"AAV37206.1","sequence":"MEKNRKKQIVVLSIALVCIFILVFSLFHKSATKDSANPPLTNVLTDSISQIVSACPGEIGVAVIVNNRDTVKVNNKSVYPMMSVFKVHQALALCNDFDNKGISLDTLVNINRDKLDPKTWSPMLKDYSGPVISLTVRDLLRYTLTQSDNNASNLMFKDMVNVAQTDSFIATLIPRSSFQIAYTEEEMSADHNKAYSNYTSPLGAAMLMNRLFTEGLIDDEKQSFIKNTLKECKTGVDRIAAPLLDKEGVVIAHKTGSGCVNENGVLAAHNDVAYICLPNNISYTLAVFVKDFKGNESQASQYVAHISAVVYSLLMQTSVKS"},"dna_sequence":{"accession":"AY769934.1","fmin":"27","fmax":"993","strand":"+","sequence":"ATGGAAAAAAACAGAAAAAAACAAATCGTAGTTTTGAGTATAGCTTTAGTTTGCATTTTCATCTTGGTATTTTCATTGTTCCATAAATCAGCGACAAAAGATAGCGCAAATCCTCCTTTAACAAATGTTTTGACTGATAGCATTTCTCAAATTGTCTCAGCTTGTCCTGGCGAAATTGGTGTGGCGGTTATTGTTAATAACAGAGATACGGTTAAGGTCAATAATAAGAGTGTTTATCCTATGATGAGTGTGTTTAAGGTTCATCAGGCATTAGCTCTTTGTAATGACTTTGACAATAAAGGAATTTCACTTGATACCTTAGTAAATATAAATAGGGATAAACTTGACCCAAAGACTTGGAGTCCTATGCTGAAAGATTATTCAGGGCCAGTCATATCATTGACAGTGAGAGATTTGCTGCGTTATACTCTTACTCAGAGTGACAACAATGCAAGCAACCTTATGTTTAAGGATATGGTTAATGTCGCTCAAACAGATAGTTTTATAGCCACACTCATTCCTCGTTCAAGTTTTCAGATAGCTTATACGGAAGAGGAAATGTCGGCTGACCATAACAAGGCTTACTCTAACTATACATCTCCTCTTGGTGCTGCAATGTTGATGAATCGTTTGTTTACTGAAGGTCTTATCGATGATGAGAAACAAAGTTTCATTAAGAATACGTTAAAAGAATGCAAAACAGGTGTAGATAGGATAGCAGCTCCACTTCTTGATAAAGAAGGGGTTGTTATAGCGCATAAGACAGGTTCAGGTTGTGTTAATGAAAATGGTGTTCTTGCAGCTCACAATGATGTTGCCTATATATGTCTGCCTAATAATATCAGTTATACCTTAGCGGTATTTGTTAAGGATTTCAAGGGAAATGAATCACAAGCGTCACAATATGTTGCGCATATATCAGCTGTAGTATATTCTTTATTAATGCAAACTTCAGTAAAATCTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39660","NCBI_taxonomy_name":"Parabacteroides distasonis","NCBI_taxonomy_id":"823"}}}},"ARO_accession":"3003096","ARO_id":"39649","ARO_name":"CfxA5","CARD_short_name":"CfxA5","ARO_description":"CfxA5 beta-lactamase is a class A beta-lactamase found in Bacteroides distasonis.","ARO_category":{"39434":{"category_aro_accession":"3003000","category_aro_cvterm_id":"39434","category_aro_name":"CfxA beta-lactamase","category_aro_description":"CfxA beta-lactamases are class A beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"834":{"model_id":"834","model_name":"FosA3","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"200"}},"model_sequences":{"sequence":{"540":{"protein_sequence":{"accession":"AEG78825.1","sequence":"MLQGLNHLTLAVSDLASSLAFYQQLPGMRLHASWDSGAYLSCGALWLCLSLDEQRRKTPPQESDYTHYAFSVAEEEFAGVVALLAQAGAEVWKDNRSEGASYYFLDPDGHKLELHVGNLAQRLAACRERPYKGMVFFD"},"dna_sequence":{"accession":"JF411006.1","fmin":"951","fmax":"1368","strand":"+","sequence":"ATGCTGCAGGGATTGAATCATCTGACGCTGGCGGTCAGCGATCTGGCGTCAAGCCTGGCATTTTATCAGCAGTTACCTGGAATGCGCCTGCACGCCAGCTGGGATAGCGGAGCCTATCTCTCCTGTGGGGCGCTGTGGCTGTGCTTGTCGCTGGATGAGCAGCGGCGTAAAACGCCCCCTCAGGAAAGCGACTATACCCACTACGCCTTCAGCGTGGCGGAAGAAGAGTTTGCCGGGGTGGTGGCTCTGCTGGCGCAGGCGGGGGCTGAGGTATGGAAAGATAACCGCAGTGAAGGGGCGTCTTACTATTTTCTCGACCCTGACGGCCATAAGCTGGAGCTGCATGTGGGGAATCTGGCGCAGCGGCTGGCCGCCTGTCGCGAACGCCCCTACAAGGGGATGGTCTTTTTTGATTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002872","ARO_id":"39306","ARO_name":"FosA3","CARD_short_name":"FosA3","ARO_description":"An enzyme that confers resistance to fosfomycin in Escherichia coli by breaking the epoxide ring of the molecule. It depends on the cofactors Manganese (II) and Potassium and uses Glutathione (GSH) as the nucleophilic molecule.","ARO_category":{"36272":{"category_aro_accession":"3000133","category_aro_cvterm_id":"36272","category_aro_name":"fosfomycin thiol transferase","category_aro_description":"Catalyzes the addition of a thiol group from a nucleophilic molecule to fosfomycin.","category_aro_class_name":"AMR Gene Family"},"35944":{"category_aro_accession":"0000025","category_aro_cvterm_id":"35944","category_aro_name":"fosfomycin","category_aro_description":"Fosfomycin (also known as phosphomycin and phosphonomycin) is a broad-spectrum antibiotic produced by certain Streptomyces species. It is effective on gram positive and negative bacteria as it targets the cell wall, an essential feature shared by both bacteria. Its specific target is MurA (MurZ in E.coli), which attaches phosphoenolpyruvate (PEP) to UDP-N-acetylglucosamine, a step of commitment to cell wall synthesis. In the active site of MurA, the active cysteine molecule is alkylated which stops the catalytic reaction.","category_aro_class_name":"Antibiotic"},"45731":{"category_aro_accession":"3007149","category_aro_cvterm_id":"45731","category_aro_name":"phosphonic acid antibiotic","category_aro_description":"A group of antibiotics derived from phosphonic acids.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"835":{"model_id":"835","model_name":"APH(3')-Ib","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"329":{"protein_sequence":{"accession":"AAA26412.1","sequence":"MNDIDREEPCAAAAVPESMAAHVMGYKWARDKVGQSGCAVYRLHSKSGGSDLFLKHGKDAFADDVTDEMVRLRWLAGHISVPSVVSFVRTPNQAWLLTTAIHGKTAYQVLKSDFGARLVVVDALAAFMRRLHAIPVSECSVQQWTTHAGLPERGSIEAGVVDVDDFDKEREGWTAEQVWEAMHRLLPLAPDPVVTHGDFSLDNLLIVEGKVVGCIDVGRAGIADRYQDLAVLWNCLEEFEPSLQERLVAQYGIADPDRRKLQFHLLLDELF"},"dna_sequence":{"accession":"M20305.1","fmin":"778","fmax":"1594","strand":"+","sequence":"GTGAACGATATTGATCGAGAAGAGCCCTGCGCAGCCGCTGCCGTGCCCGAGAGCATGGCGGCTCACGTGATGGGATACAAATGGGCGCGTGATAAGGTTGGTCAGTCCGGCTGCGCGGTCTATCGGCTGCATAGCAAGTCAGGCGGCTCCGACTTGTTTCTGAAGCACGGCAAAGATGCTTTTGCCGACGACGTGACTGATGAAATGGTGAGATTGCGTTGGCTGGCGGGGCACATTTCTGTGCCCTCCGTTGTAAGCTTCGTTCGCACGCCCAATCAGGCATGGCTCCTGACAACAGCAATACATGGAAAAACGGCATATCAAGTGCTGAAATCGGATTTCGGAGCCCGTCTCGTTGTTGTTGACGCATTGGCGGCGTTCATGCGCCGACTGCATGCGATCCCAGTGAGCGAATGCTCCGTTCAACAGTGGACCACGCATGCAGGCTTGCCCGAGCGCGGGAGTATCGAGGCGGGGGTTGTTGATGTCGATGACTTCGATAAGGAGCGCGAAGGGTGGACGGCCGAACAGGTTTGGGAGGCGATGCATCGCCTCCTACCGCTCGCGCCGGACCCAGTCGTGACGCACGGCGATTTTTCACTCGATAATCTACTTATCGTCGAAGGTAAGGTAGTCGGCTGCATCGACGTTGGGCGGGCTGGTATTGCTGATCGATACCAAGACCTTGCCGTGTTATGGAACTGTCTTGAGGAGTTCGAACCTTCGCTTCAGGAGAGGCTTGTTGCGCAATATGGCATTGCCGATCCGGATAGGCGCAAGCTGCAATTTCATCTCCTGCTGGACGAACTTTTCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39529","NCBI_taxonomy_name":"Plasmid RP4","NCBI_taxonomy_id":"2503"}}}},"ARO_accession":"3002642","ARO_id":"39042","ARO_name":"APH(3')-Ib","CARD_short_name":"APH(3')-Ib","ARO_description":"APH(3')-Ib is a plasmid-encoded aminoglycoside phosphotransferase in E. coli.","ARO_category":{"36265":{"category_aro_accession":"3000126","category_aro_cvterm_id":"36265","category_aro_name":"APH(3')","category_aro_description":"A category of aminoglycoside O-phosphotransferase enzymes with modification regiospecificity based at the 3'-hydroxyl group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics, specifically kanamycin and neomycin, by the ATP-dependent phosphorylation of the 3'-hydroxyl group of the compound.","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35940":{"category_aro_accession":"0000021","category_aro_cvterm_id":"35940","category_aro_name":"ribostamycin","category_aro_description":"Ribostamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Ribostamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"37001":{"category_aro_accession":"3000657","category_aro_cvterm_id":"37001","category_aro_name":"paromomycin","category_aro_description":"An aminoglycoside antibiotic used for the treatment of parasitic infections. It is similar to neomycin sharing a similar spectrum of activity, but its hydroxyl group at the 6'-position instead of an amino group makes it resistant to AAC(6') modifying enzymes.","category_aro_class_name":"Antibiotic"},"37002":{"category_aro_accession":"3000658","category_aro_cvterm_id":"37002","category_aro_name":"lividomycin","category_aro_description":"Lividomycins are aminoglycosidic antibiotics produced by Streptomyces lividus. They contain 2-amino-2,3-dideoxy-D-glucose.","category_aro_class_name":"Antibiotic"},"46133":{"category_aro_accession":"3007382","category_aro_cvterm_id":"46133","category_aro_name":"gentamicin","category_aro_description":"Gentamicin is a commonly used aminoglycoside antibiotic derived from members of the Micromonospora genus of bacteria. It acts by binding the 30S ribosomal subunit, thus inhibiting protein synthesis. Gentamicin is typically used to treat Gram-negative infections of the repiratory and urinary tract, as well as infections of the bone and soft tissue. It also exhibits considerable nephrotoxicity and ototoxicity. Gentamicin is administered as a mixture of gentamicin type C (which makes about around 80% of the complex) and types A, B, and X (distributed in the remaining 20% of the complex).","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"836":{"model_id":"836","model_name":"TEM-68","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1327":{"protein_sequence":{"accession":"CAB92324.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGASKRGSRGIIAALGPDGKPSRIVVIYMTGSQATMDELNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AJ239002.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCAGTAAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACATGACGGGGAGTCAGGCAACTATGGATGAACTAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3000935","ARO_id":"37315","ARO_name":"TEM-68","CARD_short_name":"TEM-68","ARO_description":"TEM-68 is an inhibitor resistant, extended-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"837":{"model_id":"837","model_name":"vatH","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"8208":{"protein_sequence":{"accession":"ACX92987.1","sequence":"MAEKLKGPNSNEMYPIAGNKSVQFVKPSLTRPNIIVGEFTYYDSKNGELFEDQVLYHYEIIGDRLIIGKFCSIGPGVTFIMNGANHRMDGSTYPFNIFGHGWEKHTPTLDMLPLKGDTIVGNDVWIGLDATIMPGVKIGDGAIIAAKSVVTKDVDPSTIVGGNPAKQIKKRFSESKIQELLKIKWWDFEDQVISDNIDAILSLDVEALNNISKEND"},"dna_sequence":{"accession":"GQ205627.2","fmin":"3036","fmax":"3687","strand":"+","sequence":"ATGGCAGAAAAATTAAAAGGACCCAACTCAAATGAAATGTATCCGATTGCCGGAAATAAAAGTGTTCAATTTGTTAAACCGTCATTAACAAGGCCCAATATTATAGTTGGTGAGTTCACTTATTATGATAGCAAGAACGGAGAGCTTTTTGAGGATCAAGTTCTGTATCATTATGAAATTATAGGGGATCGACTGATCATCGGGAAATTTTGTTCAATCGGTCCTGGAGTCACTTTTATTATGAATGGAGCTAATCATCGCATGGATGGCTCCACTTATCCATTTAATATCTTTGGGCATGGGTGGGAAAAGCATACACCTACACTAGATATGCTGCCTTTAAAGGGGGATACTATTGTTGGTAATGACGTATGGATTGGACTAGATGCTACAATTATGCCAGGCGTAAAAATAGGAGACGGCGCGATTATTGCAGCCAAATCTGTAGTAACAAAAGACGTTGACCCCTCCACAATTGTTGGTGGTAATCCTGCAAAACAAATAAAGAAACGATTTTCGGAGTCAAAAATTCAAGAACTATTAAAGATAAAATGGTGGGATTTTGAAGACCAGGTTATTAGCGATAATATTGATGCTATTCTAAGTTTGGATGTTGAAGCGCTTAATAATATTTCTAAAGAAAATGATTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36779","NCBI_taxonomy_name":"Enterococcus faecium","NCBI_taxonomy_id":"1352"}}}},"ARO_accession":"3002845","ARO_id":"39279","ARO_name":"vatH","CARD_short_name":"vatH","ARO_description":"vatH is a plasmid-mediated acetyltransferase found in Enterococcus faecium.","ARO_category":{"36592":{"category_aro_accession":"3000453","category_aro_cvterm_id":"36592","category_aro_name":"streptogramin vat acetyltransferase","category_aro_description":"vat (Virginiamycin acetyltransferases) enzymes catalyze the transfer of an acetyl group from acetyl-CoA to the secondary alcohol of streptogramin A compounds, thus inactivating virginiamycin-like antibiotics and conferring resistance to these compounds.","category_aro_class_name":"AMR Gene Family"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"virginiamycin M1","category_aro_description":"Virginiamycin M1 is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37016":{"category_aro_accession":"3000672","category_aro_cvterm_id":"37016","category_aro_name":"madumycin II","category_aro_description":"Madumycin II is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37017":{"category_aro_accession":"3000673","category_aro_cvterm_id":"37017","category_aro_name":"griseoviridin","category_aro_description":"Griseoviridin is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35952":{"category_aro_accession":"0000034","category_aro_cvterm_id":"35952","category_aro_name":"streptogramin A antibiotic","category_aro_description":"Streptogramin A antibiotics are cyclic polyketide peptide hybrids that bind to the ribosomal peptidyl transfer centre. Structural variation arises from substituting a proline for its desaturated derivative and by its substitution for Ala or Cys. Used alone, streptogramin A antibiotics are bacteriostatic, but is bactericidal when used with streptogramin B antibiotics.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"838":{"model_id":"838","model_name":"CTX-M-102","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"946":{"protein_sequence":{"accession":"ADY02546.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQREQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGGYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"HQ398215.1","fmin":"244","fmax":"1120","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGAGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGGCTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001961","ARO_id":"38361","ARO_name":"CTX-M-102","CARD_short_name":"CTX-M-102","ARO_description":"CTX-M-102 is a beta-lactamase found in Escherichia coli.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"839":{"model_id":"839","model_name":"CMY-44","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1586":{"protein_sequence":{"accession":"ACJ65711.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVAPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"FJ437066.1","fmin":"0","fmax":"1134","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCACCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002055","ARO_id":"38455","ARO_name":"CMY-44","CARD_short_name":"CMY-44","ARO_description":"CMY-44 is a beta-lactamase found in Escherichia coli.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"840":{"model_id":"840","model_name":"CMY-20","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"8195":{"protein_sequence":{"accession":"AAX58682.2","sequence":"MKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGISLLHLATYTAGGLPLQIPDDVTDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDNKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"AY960293.2","fmin":"0","fmax":"1143","strand":"+","sequence":"ATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCCGAACTGACAGGCAAACAGTGGCAGGGTATCAGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTACGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGTTTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAACAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTCCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002031","ARO_id":"38431","ARO_name":"CMY-20","CARD_short_name":"CMY-20","ARO_description":"CMY-20 is a beta-lactamase found in Escherichia coli.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"841":{"model_id":"841","model_name":"CTX-M-14","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8283":{"protein_sequence":{"accession":"AAF72530.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"AF252622.2","fmin":"1740","fmax":"2616","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGACTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001877","ARO_id":"38277","ARO_name":"CTX-M-14","CARD_short_name":"CTX-M-14","ARO_description":"CTX-M-14 is a beta-lactamase found in the Enterobacteriaceae family.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"843":{"model_id":"843","model_name":"QnrB14","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"255":{"protein_sequence":{"accession":"ABX72044.1","sequence":"MTPLLYKKTGTNMALALVGEKIDRNRFTGEKIDNSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNASALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGAQVLGATFSGSDLSGGEFSTFDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDNYQASLLTERLGIAIIG"},"dna_sequence":{"accession":"EU273757.1","fmin":"0","fmax":"681","strand":"+","sequence":"ATGACGCCATTACTGTATAAAAAAACAGGTACAAATATGGCTCTGGCACTCGTCGGCGAAAAAATTGACAGAAACCGTTTCACCGGTGAGAAAATTGATAATAGTACATTTTTTAACTGTGATTTTTCAGGTGCCGACCTGAGCGGCACTGAATTTATCGGCTGTCAGTTCTATGATCGTGAAAGCCAGAAAGGGTGCAATTTTAGTCGTGCGATGCTGAAAGATGCCATTTTTAAAAGCTGTGATCTATCCATGGCGGATTTTCGCAATGCCAGTGCGCTGGGCATTGAAATTCGCCACTGCCGCGCACAAGGCGCAGATTTCCGCGGCGCAAGTTTTATGAATATGATCACTACTCGCACCTGGTTTTGTAGTGCATATATCACTAACACAAATCTAAGCTACGCCAATTTTTCGAAAGTCGTGCTGGAAAAGTGTGAGCTGTGGGAAAACCGTTGGATGGGTGCCCAGGTACTGGGCGCGACGTTCAGTGGTTCAGATCTCTCCGGCGGCGAGTTTTCGACTTTCGACTGGCGAGCAGCAAACTTCACACATTGCGATCTGACCAATTCGGAGTTGGGGGACTTAGATATTCGGGGCGTTGATTTACAGGGCGTTAAGTTGGACAACTACCAGGCATCGTTGCTCACGGAACGTCTTGGCATCGCGATTATTGGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002728","ARO_id":"39163","ARO_name":"QnrB14","CARD_short_name":"QnrB14","ARO_description":"QnrB14 is a plasmid-mediated quinolone resistance protein found in Citrobacter freundii.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"844":{"model_id":"844","model_name":"CMY-117","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1178":{"protein_sequence":{"accession":"AIT76097.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAIIYEGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWRGISLLHLATYTAGGLPLQIPDDITDKAALLRFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQSEQKNYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHAQEKTLQQGIELAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPVPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPARVEAAWRILEKLQ"},"dna_sequence":{"accession":"KM087844.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCACTGCTGCTGACAGCCTCTTTCTCCACGTTTGCTGCCGCAAAAACAGAACAACAAATTGCCGATATCGTTAACCGCACCATCACACCACTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTGGCGATTATCTACGAGGGGAAACCTTATTACTTTACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGACGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCGGGGTATCAGCCTGCTGCACTTAGCCACCTATACAGCGGGTGGCCTGCCGCTGCAGATCCCCGATGACATTACGGATAAAGCCGCATTACTGCGCTTTTATCAAAACTGGCAACCACAATGGACTCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGTGCGCTGGCGGTGAAACCTTCAGGTATGAGCTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAAAGCGAACAAAAAAACTATGCCTGGGGCTATCGCGAAGGGAAGCCTGTGCACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATCGATATGGCCCGCTGGGTTCAGGCCAACATGGACGCCAGCCACGCTCAGGAGAAAACGCTCCAGCAGGGCATTGAGCTTGCGCAGTCTCGCTACTGGCGTATTGGTGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCAGTACCTGCCGTGAAAGCCTCATGGGTGCATAAAACGGGATCCACAGGTGGATTTGGCAGCTACGTTGCCTTCGTTCCAGAAAAAAACCTTGGCATAGTGATGCTGGCAAACAAAAGCTATCCTAACCCGGCTCGCGTAGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002128","ARO_id":"38528","ARO_name":"CMY-117","CARD_short_name":"CMY-117","ARO_description":"CMY-117 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"845":{"model_id":"845","model_name":"TEM-163","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1955":{"protein_sequence":{"accession":"ACF32746.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDEQNRQIAEIGASLIKLW"},"dna_sequence":{"accession":"EU815939.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACAAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCTTTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001029","ARO_id":"37409","ARO_name":"TEM-163","CARD_short_name":"TEM-163","ARO_description":"TEM-163 is an inhibitor resistant beta-lactamase found in E. coli.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"846":{"model_id":"846","model_name":"DHA-12","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1983":{"protein_sequence":{"accession":"CDL68900.1","sequence":"MKKSLSATLISALLAFSAPGFSAADNVAAVVDSTIKPLMAQQDIPGMAVAVSVKGKPYYFNYGFADVEAKQPVTENTLFELGSVSKTFTGVLGAVSVAKKEMSLNDPAAKYRPELTQPQWKGITLLDLATYTAGGLPLQVPDAVKSRADLLHFYQQWQPSWKPGDMRLYANSSIGLFGALTANAAGMPYEQLLTTRILSPLGLSHTFITVPESAQSQYAYGYKNKKPVRVSPGQLDAESYGVKSASKDMLRWAEMNMEPSRAGNADLEMAMYLAQTRYYKTAAINQGLGWEMYDWPQQKDMIVNGVTNEVALQPHPVTDNQVQPYNRASWVHKTGATTGFGAYVAFIPEKQVAIVILANKNYPNTERVKAAQAILSALE"},"dna_sequence":{"accession":"HG798963.1","fmin":"0","fmax":"1140","strand":"+","sequence":"ATGAAAAAATCGTTATCTGCAACACTGATTTCTGCCCTGCTGGCGTTTTCCGCCCCGGGGTTTTCCGCCGCTGACAATGTCGCGGCGGTGGTGGACAGCACCATTAAACCGCTGATGGCACAGCAGGATATTCCCGGGATGGCAGTTGCTGTTTCCGTAAAGGGCAAGCCCTATTATTTCAACTATGGTTTTGCCGATGTTGAGGCAAAACAGCCGGTCACTGAAAATACACTATTTGAGCTCGGATCTGTAAGTAAAACTTTCACAGGTGTGCTGGGTGCAGTTTCCGTGGCGAAAAAAGAGATGTCCCTGAATGACCCGGCGGCAAAATACCGGCCTGAACTGACACAACCGCAGTGGAAGGGGATCACATTGCTCGATCTGGCTACTTATACCGCAGGCGGGCTGCCGTTACAGGTGCCGGACGCGGTGAAAAGCCGTGCGGATCTGTTGCATTTCTATCAGCAGTGGCAGCCGTCATGGAAACCGGGCGATATGCGTCTGTATGCAAACAGCAGTATCGGCCTGTTTGGTGCTCTGACCGCCAACGCCGCAGGAATGCCGTATGAGCAGTTGCTGACCACGCGTATCCTGTCTCCGCTGGGGTTATCACACACCTTTATTACCGTGCCGGAAAGCGCGCAAAGCCAGTATGCGTACGGCTATAAAAACAAAAAACCGGTCCGCGTGTCGCCGGGACAGCTTGATGCAGAATCTTACGGGGTGAAATCCGCCTCAAAAGATATGCTGCGCTGGGCGGAAATGAATATGGAACCGTCACGGGCCGGTAATGCGGATCTGGAAATGGCAATGTATCTTGCACAGACCCGCTACTATAAAACCGCCGCGATTAACCAGGGGCTGGGCTGGGAAATGTATGATTGGCCGCAGCAGAAGGACATGATCGTGAACGGCGTGACCAATGAAGTCGCATTGCAGCCGCATCCGGTAACCGACAATCAGGTGCAGCCGTACAACCGCGCTTCCTGGGTGCATAAAACGGGGGCGACAACCGGTTTCGGCGCCTATGTGGCCTTTATTCCGGAAAAACAGGTGGCGATTGTGATCCTGGCGAATAAAAACTACCCGAATACCGAAAGAGTCAAAGCTGCACAGGCTATTTTGAGTGCACTGGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3002143","ARO_id":"38543","ARO_name":"DHA-12","CARD_short_name":"DHA-12","ARO_description":"DHA-12 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36207":{"category_aro_accession":"3000068","category_aro_cvterm_id":"36207","category_aro_name":"DHA beta-lactamase","category_aro_description":"DHA beta-lactamases are plasmid-mediated AmpC \u03b2-lactamases that confer resistance to cephamycins and oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"847":{"model_id":"847","model_name":"CTX-M-108","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8429":{"protein_sequence":{"accession":"AEM44651.1","sequence":"VKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRAEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVT"},"dna_sequence":{"accession":"JF274245.1","fmin":"1","fmax":"862","strand":"+","sequence":"GTTAAAAAATCACTGCGTCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGCTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACC","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39657","NCBI_taxonomy_name":"Shigella sp. SH223","NCBI_taxonomy_id":"1074434"}}}},"ARO_accession":"3001968","ARO_id":"38368","ARO_name":"CTX-M-108","CARD_short_name":"CTX-M-108","ARO_description":"CTX-M-108 is a beta-lactamase found in Shigella spp.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"848":{"model_id":"848","model_name":"OKP-A-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"8192":{"protein_sequence":{"accession":"CAG25815.2","sequence":"MRYVRLCLFSLIAALPLAVFASPQPLEQVTRSESQLAGRVGYVEMDLASGRTLAAWRASERFPLMSTFKVLLCGAVLARVDAGDEQLDRRIRYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAGNLLLKSVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDVRDTTTPASMAATLRKLLTSHTLSARSQQQLLQWMVDDQVAGPLIRAVLPAGWFIADKTGAGERGSRGIVALLGPNGKAERIVVIYLRDTPATMAERNQQIARIGAALIEHWQR"},"dna_sequence":{"accession":"AJ635404.2","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGCCTTTTCTCCCTGATTGCCGCCCTGCCACTGGCGGTATTCGCCAGCCCTCAGCCGCTCGAGCAAGTTACACGCAGCGAAAGTCAGCTGGCGGGCCGCGTGGGCTATGTTGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCAGTGAGCGCTTTCCGCTGATGAGCACCTTTAAAGTGCTGCTCTGCGGCGCGGTGCTGGCCCGGGTGGATGCCGGAGACGAACAGCTGGATCGGCGGATCCGCTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGCCGACGGGATGACCGTTGGCGAACTCTGCGCCGCCGCCATCACCATGAGCGACAACAGCGCCGGCAATCTGCTGTTGAAGAGCGTTGGCGGCCCCGCGGGATTGACCGCTTTTCTGCGCCAGATCGGTGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAGCTCAATGAAGCGCTTCCCGGCGACGTGCGCGACACCACCACCCCAGCCAGCATGGCCGCCACCCTGCGCAAGCTGCTAACCAGCCACACTCTGAGCGCCCGTTCGCAGCAGCAGCTGCTGCAGTGGATGGTGGACGACCAGGTAGCCGGTCCGCTGATCCGCGCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAAACCGGGGCCGGCGAGCGGGGCTCACGTGGCATTGTCGCCCTGCTCGGCCCGAACGGCAAAGCGGAGCGCATCGTGGTGATCTATCTGCGGGATACGCCGGCGACCATGGCCGAGCGTAACCAGCAGATCGCCAGAATAGGCGCGGCGCTGATCGAGCACTGGCAGCGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002419","ARO_id":"38819","ARO_name":"OKP-A-2","CARD_short_name":"OKP-A-2","ARO_description":"OKP-A-2 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"38817":{"category_aro_accession":"3002417","category_aro_cvterm_id":"38817","category_aro_name":"OKP beta-lactamase","category_aro_description":"OKP beta-lactamases are chromosomal class A beta-lactamase that confer resistance to penicillins and early cephalosporins in Klebsiella pneumoniae. OKP beta-lactamases can be subdivided into two groups: OKP-A and OKP-B which diverge by about 4.2%.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"849":{"model_id":"849","model_name":"OXA-138","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8254":{"protein_sequence":{"accession":"ACD45467.1","sequence":"MNIKTLLLITSAIFISACSPYIVTANPNHSASKSDVKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWVVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"EU670845.2","fmin":"1594","fmax":"2419","strand":"+","sequence":"ATGAACATTAAAACCCTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGTAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGGTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAACAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36949","NCBI_taxonomy_name":"Acinetobacter nosocomialis","NCBI_taxonomy_id":"106654"}}}},"ARO_accession":"3001655","ARO_id":"38055","ARO_name":"OXA-138","CARD_short_name":"OXA-138","ARO_description":"OXA-138 is a beta-lactamase found in A. baumannii.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"850":{"model_id":"850","model_name":"OXA-26","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1929":{"protein_sequence":{"accession":"AAG35608.1","sequence":"MKKFILPIFSISILVSLSACSSIKTKSEDNFHISSQQHEKAIKSYFDEAQTQGVIIIKEGKNLSTYGNALARANKEYVPASTFKMLNALIGLENHKATTNEIFKWDGKKRTYPMWEKDMTLGEAMALSAVPVYQELARRTGLELMQKEVKRVNFGNTNIGTQVDNFWLVGPLKITPVQEVNFADDLAHNRLPFKLETQEEVKKMLLIKEVNGSKIYAKSGWGMGVTPQVGWLTGWVEQANGKKIPFSLNLEMKEGMTGSIRNEITYKSLENLGII"},"dna_sequence":{"accession":"AF201827.1","fmin":"21","fmax":"849","strand":"+","sequence":"ATGAAAAAATTTATACTTCCTATATTCAGCATTTCTATTCTAGTTTCTCTCAGTGCATGTTCATCTATTAAAACTAAATCTGAAGATAATTTTCATATTTCTTCTCAGCAACATGAAAAAGCTATTAAAAGCTATTTTGATGAAGCTCAAACACAGGGTGTAATTATTATTAAAGAGGGTAAAAATCTTAGCACCTATGGTAATGCTCTTGCACGAGCAAATAAAGAATATGTCCCTGCATCAACATTTAAGATGCTAAATGCTTTAATCGGGCTAGAAAATCATAAAGCAACAACAAATGAGATTTTCAAATGGGATGGTAAAAAAAGAACTTATCCTATGTGGGAGAAAGATATGACTTTAGGTGAGGCAATGGCATTGTCAGCAGTTCCAGTATATCAAGAGCTTGCAAGACGGACTGGCCTAGAGCTAATGCAGAAAGAAGTAAAGCGGGTTAATTTTGGAAATACAAATATTGGAACACAGGTCGATAATTTTTGGTTAGTTGGCCCCCTTAAAATTACACCAGTACAAGAAGTTAATTTTGCCGATGACCTTGCACATAACCGATTACCTTTTAAATTAGAAACTCAAGAAGAAGTTAAAAAAATGCTTCTAATTAAAGAAGTAAATGGTAGTAAGATTTATGCAAAAAGTGGATGGGGAATGGGTGTTACTCCACAGGTAGGTTGGTTGACTGGTTGGGTGGAGCAAGCTAATGGAAAAAAAATCCCCTTTTCGCTCAACTTAGAAATGAAAGAAGGAATGACTGGTTCTATTCGTAATGAAATTACTTATAAGTCGCTAGAAAATCTTGGAATCATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001421","ARO_id":"37821","ARO_name":"OXA-26","CARD_short_name":"OXA-26","ARO_description":"OXA-26 is a beta-lactamase found in A. baumannii.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46500":{"category_aro_accession":"3007711","category_aro_cvterm_id":"46500","category_aro_name":"OXA-24-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-24.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"852":{"model_id":"852","model_name":"QnrB62","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"757":{"protein_sequence":{"accession":"AFY16910.1","sequence":"MTPLLYKNTGIDMTLALVGEKIDRNRFTGEKVENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNVSALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGTQVLGATFSGSDLSGGEFSTFDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDNYQASLLMERLGIAIIG"},"dna_sequence":{"accession":"JX987101.1","fmin":"0","fmax":"681","strand":"+","sequence":"ATGACGCCATTACTGTATAAAAACACAGGCATAGATATGACTCTGGCATTAGTTGGCGAAAAAATTGACAGAAATCGCTTCACCGGTGAGAAAGTTGAAAATAGTACATTTTTTAACTGCGATTTTTCAGGTGCCGACCTGAGCGGCACTGAATTTATCGGCTGCCAGTTCTATGATCGCGAAAGTCAAAAAGGATGCAATTTTAGTCGCGCAATGCTGAAAGATGCCATTTTCAAAAGCTGTGATTTATCAATGGCAGATTTCCGCAACGTCAGCGCATTGGGCATTGAAATTCGCCACTGCCGCGCACAAGGCGCAGATTTCCGCGGTGCAAGCTTTATGAATATGATCACCACGCGCACCTGGTTTTGCAGCGCATATATCACTAATACCAATCTAAGCTACGCCAATTTTTCGAAAGTCGTGTTGGAAAAGTGTGAGCTATGGGAAAACCGCTGGATGGGGACTCAGGTACTGGGTGCGACGTTTAGTGGTTCAGATCTCTCCGGTGGCGAGTTTTCGACTTTCGACTGGCGAGCAGCAAACTTCACACATTGCGATCTGACCAATTCGGAGTTAGGTGACTTAGATATTCGGGGTGTTGATTTACAAGGCGTTAAGTTAGACAACTACCAGGCATCGTTGCTCATGGAGCGACTTGGCATCGCGATTATTGGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002775","ARO_id":"39209","ARO_name":"QnrB62","CARD_short_name":"QnrB62","ARO_description":"QnrB62 is a plasmid-mediated quinolone resistance protein found in Citrobacter freundii.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"853":{"model_id":"853","model_name":"OXA-160","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8188":{"protein_sequence":{"accession":"ADB28891.1","sequence":"MKKFILPIFSISILVSLSACSSIKTKSEDNFHISSQQHEKAIKSYFDEAQTQGVIIIKEGKNLSTYGNALARANKEYVPASTFKMLNALIGLENHKATTNEIFKWDGKKRTYPMWEKDMTLGEAMALSAVPVYQELARRTGLELMQKEVKRVNFGNTNIGTQVDNFWLVGPLKITPVQEVNFADDLAHNRLPFKLETQEEVKKMLLIKEVNGSKIYAKSGWGMGVTSQVGWLTGWVEQANGKKIPFSLNLEMKEGMSGSIRNEITYKSLENLGII"},"dna_sequence":{"accession":"GU199038.2","fmin":"1195","fmax":"2023","strand":"+","sequence":"ATGAAAAAATTTATACTTCCTATATTCAGCATTTCTATTCTAGTTTCTCTCAGTGCATGTTCATCTATTAAAACTAAATCTGAAGATAATTTTCATATTTCTTCTCAGCAACATGAAAAAGCTATTAAAAGCTATTTTGATGAAGCTCAAACACAGGGTGTAATTATTATTAAAGAGGGTAAAAATCTTAGCACCTATGGTAATGCTCTTGCACGAGCAAATAAAGAATATGTCCCTGCATCAACATTTAAGATGCTAAATGCTTTAATCGGGCTAGAAAATCATAAAGCAACAACAAATGAGATTTTCAAATGGGATGGTAAAAAAAGAACTTATCCTATGTGGGAGAAAGATATGACTTTAGGTGAGGCAATGGCATTGTCAGCAGTTCCAGTATATCAAGAGCTTGCAAGACGGACTGGCCTAGAGCTAATGCAGAAAGAAGTAAAGCGGGTTAATTTTGGAAATACAAATATTGGAACACAGGTCGATAATTTTTGGTTAGTTGGCCCCCTTAAAATTACACCAGTACAAGAAGTTAATTTTGCCGATGACCTTGCACATAACCGATTACCTTTTAAATTAGAAACTCAAGAAGAAGTTAAAAAAATGCTTCTAATTAAAGAAGTAAATGGTAGTAAGATTTATGCAAAAAGTGGATGGGGAATGGGTGTTACTTCACAGGTAGGTTGGTTGACTGGTTGGGTGGAGCAAGCTAATGGAAAAAAAATCCCCTTTTCGCTCAACTTAGAAATGAAAGAAGGAATGTCTGGTTCTATTCGTAATGAAATTACTTATAAGTCGCTAGAAAATCTTGGAATCATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001663","ARO_id":"38063","ARO_name":"OXA-160","CARD_short_name":"OXA-160","ARO_description":"OXA-160 is a beta-lactamase found in A. baumannii.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46500":{"category_aro_accession":"3007711","category_aro_cvterm_id":"46500","category_aro_name":"OXA-24-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-24.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"854":{"model_id":"854","model_name":"CMY-58","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1362":{"protein_sequence":{"accession":"ADY19254.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHVSPGQLDAEAYCVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"HQ185697.1","fmin":"1267","fmax":"2413","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATTGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002072","ARO_id":"38472","ARO_name":"CMY-58","CARD_short_name":"CMY-58","ARO_description":"CMY-58 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"855":{"model_id":"855","model_name":"TEM-142","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1490":{"protein_sequence":{"accession":"ABD60314.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVKYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGANERGSRGIIAALGPDGKPSRIVVIYMTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"DQ388882.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTAAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCAATGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACATGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001005","ARO_id":"37385","ARO_name":"TEM-142","CARD_short_name":"TEM-142","ARO_description":"TEM-142 is an beta-lactamase found in E. coli.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"856":{"model_id":"856","model_name":"mepR","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"250"}},"model_sequences":{"sequence":{"5491":{"protein_sequence":{"accession":"BAB56495.1","sequence":"MEFTYSYLFRMISHEMKQKADQKLEQFDITNEQGHTLGYLYAHQQDGLTQNDIAKALQRTGPTVSNLLRNLERKKLIYRYVDAQDTRRKNIGLTTSGIKLVEAFTSIFDEMEQTLVSQLSEEENEQMKANLTKMLSSLQ"},"dna_sequence":{"accession":"BA000017.4","fmin":"379931","fmax":"380351","strand":"+","sequence":"ATGGAATTCACTTATTCGTATTTATTTAGAATGATTAGTCATGAGATGAAACAAAAGGCTGATCAAAAGTTAGAGCAATTTGATATTACAAATGAGCAAGGTCATACGTTAGGTTATCTTTATGCACATCAACAAGATGGACTGACACAAAATGATATTGCTAAAGCATTACAACGAACAGGTCCAACTGTCAGTAATTTATTAAGGAACCTTGAACGTAAAAAGCTGATCTATCGCTATGTCGATGCACAAGATACGAGAAGAAAGAATATAGGACTGACTACCTCTGGGATTAAACTTGTAGAAGCATTCACTTCGATATTTGATGAAATGGAGCAAACACTCGTATCGCAGTTATCTGAAGAAGAAAATGAACAAATGAAAGCAAACTTAACTAAAATGTTATCTAGTTTACAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35513","NCBI_taxonomy_name":"Staphylococcus aureus subsp. aureus Mu50","NCBI_taxonomy_id":"158878"}}}},"ARO_accession":"3000746","ARO_id":"37126","ARO_name":"mepR","CARD_short_name":"mepR","ARO_description":"MepR is an upstream repressor of MepA in Staphylococcus aureus. It is part of the mepRAB operon.","ARO_category":{"36251":{"category_aro_accession":"3000112","category_aro_cvterm_id":"36251","category_aro_name":"multidrug and toxic compound extrusion (MATE) transporter","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Multidrug and toxic compound extrusion (MATE) transporters utilize the cationic gradient across the membrane as an energy source. Although there is a diverse substrate specificity, almost all MATE transporters recognize fluoroquinolones. Arciflavine, ethidium and aminoglycosides are also good substrates.","category_aro_class_name":"AMR Gene Family"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"3302":{"model_id":"3302","model_name":"tet(56)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"5229":{"protein_sequence":{"accession":"ARB93503.1","sequence":"MSKNIKILVIGAGVAGPAVCYWLRRFGFSPVLIEKYASIRKGGQALDVRGIATHIAREMGIYDQICEMRTRIERGRFVDSSGKVLHEEQGEKFGFRQDDEVEILRGDLVEILMKTIADVPCYFNQSIISIEQNADNVTVIFMDGRIEQYDLVIAADGIHSAIRRMIFEKNEYQLIHLGAYLSTFTIPNYLGLSHIDLECEANNKLVSINSDNNPEIARAGFMFRSQHLLNDIRDEQEQKQFLRDTFRDFGWETQNILNRMPESNDFYFDAITQVKMNSWTKGRIALVGDAGYCPSPLSGQGNNLAFVGAYILAGELKVANGNYTRAFTRYNALLRSFVDANQKFGVWVSESFLVKDEVSKEIAEERSNKILAMIKSISNGITLPQYESS"},"dna_sequence":{"accession":"CP020412.2","fmin":"3537848","fmax":"3539018","strand":"-","sequence":"ATGTCTAAAAATATCAAAATTCTCGTCATTGGCGCTGGTGTAGCTGGCCCTGCTGTTTGTTATTGGCTAAGAAGGTTTGGTTTTTCTCCTGTTTTGATTGAAAAATATGCGTCTATTAGAAAAGGGGGTCAGGCACTGGATGTTCGTGGCATAGCAACTCATATCGCCAGAGAAATGGGTATCTATGATCAAATATGTGAGATGCGCACGCGAATAGAGCGCGGTCGCTTTGTAGACTCATCGGGTAAAGTGCTGCATGAAGAACAGGGTGAGAAATTCGGGTTTAGGCAAGATGACGAAGTCGAAATTCTCCGTGGTGATTTGGTTGAAATCCTGATGAAAACAATTGCTGATGTCCCTTGTTATTTCAATCAATCCATTATTAGCATTGAGCAGAATGCTGATAACGTTACCGTTATTTTCATGGATGGCAGGATTGAACAATATGATCTGGTGATCGCTGCAGATGGGATTCACTCTGCTATAAGGCGCATGATTTTTGAAAAAAATGAATATCAGTTAATTCACCTTGGCGCATATCTCAGTACATTTACCATTCCAAATTACCTTGGCTTGAGTCACATAGATCTGGAATGTGAGGCTAATAATAAATTAGTCTCAATAAATAGCGATAACAATCCTGAAATAGCAAGAGCAGGATTTATGTTCCGTTCCCAGCATCTCCTGAATGACATCCGTGATGAGCAGGAACAAAAGCAATTCCTACGTGATACTTTTCGCGATTTTGGCTGGGAAACACAAAATATTTTAAATCGAATGCCAGAAAGCAATGATTTTTATTTTGATGCGATTACGCAAGTAAAAATGAATAGTTGGACCAAAGGTCGAATAGCGCTTGTCGGTGATGCAGGCTATTGTCCTTCTCCGTTATCTGGCCAAGGGAATAATTTGGCATTCGTTGGAGCATATATACTGGCGGGAGAATTAAAAGTTGCTAATGGAAATTATACCCGAGCGTTTACTCGTTATAATGCACTGCTACGTTCCTTCGTTGATGCCAATCAAAAATTTGGTGTTTGGGTCAGTGAATCATTCCTTGTAAAAGATGAAGTTTCCAAGGAAATTGCAGAAGAACGCTCGAACAAAATCCTAGCCATGATAAAATCAATTTCGAATGGGATTACCTTACCTCAATATGAATCATCATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42547","NCBI_taxonomy_name":"Legionella longbeachae","NCBI_taxonomy_id":"450"}}}},"ARO_accession":"3004603","ARO_id":"42545","ARO_name":"tet(56)","CARD_short_name":"tet(56)","ARO_description":"A tetracycline inactivating enzyme. A flavoenzyme capable of degrading tetracycline antibiotics.","ARO_category":{"36176":{"category_aro_accession":"3000036","category_aro_cvterm_id":"36176","category_aro_name":"tetracycline inactivation enzyme","category_aro_description":"Enzymes or other gene products which hydroxylate tetracycline and other tetracycline derivatives. Hydroxylation inactivates tetracycline-like antibiotics, thus conferring resistance to these compounds.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"37012":{"category_aro_accession":"3000668","category_aro_cvterm_id":"37012","category_aro_name":"oxytetracycline","category_aro_description":"Oxytetracycline is a derivative of tetracycline with a 5-hydroxyl group. Its activity is similar to other tetracyclines.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"858":{"model_id":"858","model_name":"IND-14","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1908":{"protein_sequence":{"accession":"ADK38716.1","sequence":"MKKRIQFFMVSMMLSPLFSAQVKDFVIEPPIKKNLHIYKTFGVFGGKEYSANSVYLVTQKGVVLFDVPWEKVQYQSLMDTIQKRHNLPVIAVFATHSHDDRAGDLSFFNNKGIKTYATAKTNEFLKKDGKATSTEIIKTGKPYRIGGEEFVVDFLGEGHTADNVVVWFPKYNVLDGGCLVKSKAATDLGYIKEANVEQWPKTINKLKSKYSKASLVIPGHDEWKGGGHIEHTLELLNKK"},"dna_sequence":{"accession":"HM367709.1","fmin":"7","fmax":"727","strand":"+","sequence":"ATGAAAAAAAGAATTCAGTTCTTTATGGTTTCAATGATGCTAAGTCCATTATTCAGTGCCCAGGTAAAAGATTTTGTCATCGAACCACCGATTAAAAAGAATTTACATATTTACAAAACTTTTGGTGTATTCGGAGGTAAAGAATATTCTGCCAATTCAGTATATCTTGTTACCCAAAAAGGAGTTGTCTTATTTGATGTTCCGTGGGAAAAGGTACAGTACCAAAGCCTGATGGATACCATCCAAAAACGCCACAATTTACCCGTAATAGCGGTGTTTGCCACTCACTCCCATGATGACCGTGCCGGAGATCTGAGCTTTTTTAACAACAAAGGAATTAAAACCTACGCTACTGCCAAAACCAATGAGTTCCTGAAAAAAGACGGAAAAGCAACATCCACAGAGATCATTAAGACCGGAAAACCTTATCGCATAGGAGGTGAGGAATTTGTGGTTGATTTTCTTGGAGAAGGGCATACTGCTGATAATGTAGTGGTATGGTTTCCCAAATATAACGTCCTGGATGGCGGATGCCTTGTAAAAAGTAAAGCTGCAACCGATCTTGGATATATTAAGGAAGCCAATGTAGAGCAATGGCCCAAGACCATCAATAAACTGAAATCCAAATATTCAAAAGCAAGCCTGGTTATTCCCGGACATGATGAATGGAAAGGTGGAGGCCATATAGAGCATACTCTTGAACTTCTTAACAAAAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36916","NCBI_taxonomy_name":"Chryseobacterium indologenes","NCBI_taxonomy_id":"253"}}}},"ARO_accession":"3002269","ARO_id":"38669","ARO_name":"IND-14","CARD_short_name":"IND-14","ARO_description":"IND-14 is a beta-lactamase found in Escherichia coli.","ARO_category":{"36199":{"category_aro_accession":"3000060","category_aro_cvterm_id":"36199","category_aro_name":"IND beta-lactamase","category_aro_description":"IND beta-lactamases are class B carbapenem-hydrolyzing beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"860":{"model_id":"860","model_name":"TEM-42","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8426":{"protein_sequence":{"accession":"CAA66659.1","sequence":"QHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDKLGVRVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGASKRGSRGIIAALGPDGKPSRIVVIYMTGSQATMDERNRQIAEIGASLIK"},"dna_sequence":{"accession":"X98047.1","fmin":"0","fmax":"843","strand":"+","sequence":"CAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATAAGTTGGGTGTACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCAGTAAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACATGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAG","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3000911","ARO_id":"37291","ARO_name":"TEM-42","CARD_short_name":"TEM-42","ARO_description":"TEM-42 is an extended-spectrum beta-lactamase that has been found in clinical isolates.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"861":{"model_id":"861","model_name":"OXA-215","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1295":{"protein_sequence":{"accession":"AEV91554.1","sequence":"MKLSKLYTLTVLIGFGLSGVACQHIHTPVSFNQIENDQTKQIASLFENVQTTGVLITFDGQAYKAYGNDLNRAKTAYIPASTFKILNALIGIEHDKTSPNEVFKWDGQKRAFESWEKDLTLAEAMQASAVPVYQALAQRIGLDLMAKEVKRVGFGNTRIGTQVDNFWLIGPLKITPIEEAQFAYRLAKQELPFTPKTQQQVIDMLLVDEIRGTKVYAKSGWGMDITPQVGWWTGWIEDPNGKVIAFSLNMEMNQPTHAAARKEIVYQALTQLKLL"},"dna_sequence":{"accession":"JN861783.1","fmin":"0","fmax":"828","strand":"+","sequence":"ATGAAGCTATCAAAATTATACACCCTCACTGTGCTCATAGGATTTGGATTAAGCGGTGTCGCCTGCCAGCATATCCATACTCCAGTCTCGTTCAATCAAATTGAAAACGATCAAACAAAGCAGATCGCTTCCTTGTTTGAGAATGTTCAAACAACAGGTGTTCTAATTACCTTTGATGGACAGGCGTATAAAGCATACGGTAATGATCTGAATCGTGCCAAAACTGCGTATATCCCAGCATCTACTTTCAAAATATTAAATGCTTTGATTGGCATTGAACATGATAAAACTTCACCAAATGAAGTATTTAAGTGGGATGGTCAGAAGCGTGCTTTTGAAAGTTGGGAAAAAGATCTGACTTTAGCTGAAGCCATGCAAGCTTCTGCTGTACCTGTTTATCAAGCGCTTGCCCAGAGAATCGGATTGGATTTGATGGCAAAGGAAGTCAAAAGAGTCGGCTTCGGTAATACACGCATCGGAACACAAGTTGATAACTTCTGGCTCATTGGACCTTTAAAGATCACGCCAATCGAAGAAGCTCAATTTGCTTACAGGCTTGCGAAACAGGAGTTACCGTTTACCCCAAAAACACAACAGCAAGTGATTGATATGCTGCTGGTGGATGAAATACGGGGAACTAAAGTTTACGCCAAAAGTGGTTGGGGAATGGATATTACTCCGCAAGTAGGATGGTGGACTGGATGGATTGAAGATCCGAACGGAAAAGTGATCGCTTTTTCTCTCAATATGGAAATGAATCAACCTACACATGCAGCTGCACGTAAAGAAATTGTTTATCAGGCACTTACGCAATTGAAATTATTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36938","NCBI_taxonomy_name":"Acinetobacter haemolyticus","NCBI_taxonomy_id":"29430"}}}},"ARO_accession":"3001714","ARO_id":"38114","ARO_name":"OXA-215","CARD_short_name":"OXA-215","ARO_description":"OXA-215 is a beta-lactamase found in Acinetobacter spp.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46496":{"category_aro_accession":"3007707","category_aro_cvterm_id":"46496","category_aro_name":"OXA-214-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-214.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"862":{"model_id":"862","model_name":"IMP-16","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"836":{"protein_sequence":{"accession":"CAE48334.1","sequence":"MKKLFVLCIFLFCSITAAGESLPDLKIEKLEDGVYVHTSFEEVNGWGVVTKHGLVFLVNTDAYLIDTPFAAKDTEKLVNWFVERGYKIKGSISSHFHSDSSGGIEWLNSQSIPTYASELTNELLKKNGKVQAKNSFSGVSYWLLKNKIEIFYPGPGHTQDNVVVWLPEKKILFGGCFVKPYGLGNLDDANVEAWPHSAEILMSRYGNAKLVVPSHSDVGDASLLKLTWEQAVKGLKESKKPSQPSN"},"dna_sequence":{"accession":"AJ584652.1","fmin":"1043","fmax":"1784","strand":"+","sequence":"ATGAAAAAATTATTTGTTTTATGTATCTTTTTGTTTTGTAGCATTACTGCCGCAGGAGAGTCTTTGCCTGATTTAAAAATTGAGAAGCTTGAAGACGGTGTTTATGTTCATACATCGTTTGAAGAAGTTAACGGTTGGGGTGTTGTTACTAAACACGGTTTGGTGTTTCTTGTAAACACAGACGCCTATCTGATTGACACTCCATTTGCTGCTAAAGACACTGAAAAGTTAGTAAATTGGTTTGTGGAGCGCGGTTATAAAATAAAAGGCAGTATTTCCTCACATTTTCATAGCGACAGCTCGGGTGGAATAGAATGGCTTAACTCTCAATCTATTCCCACGTATGCATCTGAATTAACAAACGAACTTCTTAAAAAGAACGGTAAGGTGCAAGCTAAAAACTCATTTAGCGGAGTTAGTTATTGGCTACTTAAAAATAAAATTGAAATTTTTTATCCGGGCCCTGGGCACACTCAAGATAACGTAGTGGTTTGGTTGCCTGAAAAGAAAATTTTATTTGGTGGGTGTTTTGTTAAACCGTACGGTCTTGGAAATCTCGATGATGCAAATGTTGAAGCGTGGCCACATTCTGCTGAAATATTAATGTCTAGGTATGGTAATGCAAAACTGGTTGTTCCAAGCCATAGTGACGTCGGAGATGCGTCGCTCTTGAAGCTTACATGGGAGCAGGCTGTTAAAGGGCTAAAAGAAAGTAAAAAACCATCACAGCCAAGTAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002207","ARO_id":"38607","ARO_name":"IMP-16","CARD_short_name":"IMP-16","ARO_description":"IMP-16 is a beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"863":{"model_id":"863","model_name":"PER-7","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1309":{"protein_sequence":{"accession":"AEI54993.1","sequence":"MNVIIKAVVTASTLLMVSFSSFETSAQSPLLKEQIESIVIGKKATVGVAVWGPDDLEPLLINPFEKFPMQSVFKLHLAMLVLHQVDQGKLDLNQTVIVNRAKVLQNTWAPIMKAYQGDQFSVPVQQLLQYSVSHSDNVACDLLFELVGGPAALHDYIQSMGIKETAVVANEAQMHADDQVQYQNWTSMKGAAEILKKFEQKTQLSETSQALLWKWMVETTTGPERLKGLLPAGTVVAHKTGTSGVRAGKTAATNDLGIILLPDGRPLLVAVFVKDSAESSRTNEAIIAQVAQAAYQFELKKLSALSPN"},"dna_sequence":{"accession":"HQ713678.1","fmin":"5756","fmax":"6683","strand":"+","sequence":"ATGAATGTCATTATAAAAGCTGTAGTTACTGCCTCGACGCTACTGATGGTATCTTTTAGTTCATTCGAAACCTCAGCGCAATCCCCACTGTTAAAAGAGCAAATTGAATCCATAGTCATTGGAAAAAAAGCCACTGTAGGCGTTGCAGTGTGGGGGCCTGACGATCTGGAACCTTTACTGATTAATCCTTTTGAAAAATTCCCAATGCAAAGTGTATTTAAATTGCATTTAGCTATGTTGGTACTGCATCAGGTTGATCAGGGAAAGTTGGATTTAAATCAGACCGTTATCGTAAACAGGGCTAAGGTTTTACAGAATACCTGGGCTCCGATAATGAAAGCGTATCAGGGAGACCAGTTTAGTGTTCCAGTGCAGCAACTGCTGCAATACTCGGTCTCGCACAGCGATAACGTGGCCTGTGATTTGTTATTTGAACTGGTTGGTGGACCAGCTGCTTTGCATGACTATATCCAGTCTATGGGTATAAAGGAGACCGCTGTGGTCGCAAATGAAGCGCAGATGCACGCCGATGATCAGGTGCAGTATCAAAACTGGACCTCGATGAAGGGGGCCGCAGAGATCCTGAAAAAGTTTGAGCAAAAAACACAGCTGTCTGAAACCTCGCAGGCTTTGTTATGGAAGTGGATGGTCGAAACCACCACAGGACCAGAGCGGTTAAAAGGTTTGTTACCAGCTGGTACTGTGGTCGCACATAAAACTGGTACTTCGGGTGTCAGAGCCGGGAAAACTGCGGCCACTAATGATTTAGGTATCATTCTGTTGCCTGATGGACGGCCCTTGCTGGTTGCTGTTTTTGTGAAAGACTCAGCCGAGTCAAGCCGAACCAATGAAGCTATCATTGCGCAGGTTGCTCAGGCTGCGTATCAATTTGAATTGAAAAAGCTTTCTGCCCTAAGCCCAAATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3002369","ARO_id":"38769","ARO_name":"PER-7","CARD_short_name":"PER-7","ARO_description":"PER-7 is a beta-lactamase found in Acinetobacter baumannii.","ARO_category":{"36195":{"category_aro_accession":"3000056","category_aro_cvterm_id":"36195","category_aro_name":"PER beta-lactamase","category_aro_description":"PER beta-lactamases are plasmid-mediated extended spectrum beta-lactamases found in the Enterobacteriaceae family.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"864":{"model_id":"864","model_name":"CMY-61","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1701":{"protein_sequence":{"accession":"AEM97673.1","sequence":"MMNRYAAALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"JF460795.1","fmin":"0","fmax":"1143","strand":"+","sequence":"ATGATGAATCGTTATGCTGCAGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002074","ARO_id":"38474","ARO_name":"CMY-61","CARD_short_name":"CMY-61","ARO_description":"CMY-61 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"865":{"model_id":"865","model_name":"OXA-244","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"2006":{"protein_sequence":{"accession":"AGC60012.1","sequence":"MRVLALSAVFLVASIIGMPAVAKEWQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGQTRDIATWNRDHNLITAMKYSVVPVYQEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISATEQISFLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYSTGIEPKIGWWVGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP"},"dna_sequence":{"accession":"JX438000.1","fmin":"0","fmax":"798","strand":"+","sequence":"ATGCGTGTATTAGCCTTATCGGCTGTGTTTTTGGTGGCATCGATTATCGGAATGCCTGCGGTAGCAAAGGAATGGCAAGAAAACAAAAGTTGGAATGCTCACTTTACTGAACATAAATCACAGGGCGTAGTTGTGCTCTGGAATGAGAATAAGCAGCAAGGATTTACCAATAATCTTAAACGGGCGAACCAAGCATTTTTACCCGCATCTACCTTTAAAATTCCCAATAGCTTGATCGCCCTCGATTTGGGCGTGGTTAAGGATGAACACCAAGTCTTTAAGTGGGATGGACAGACGCGCGATATCGCCACTTGGAATCGCGATCATAATCTAATCACCGCGATGAAATATTCAGTTGTGCCTGTTTATCAAGAATTTGCCCGCCAAATTGGCGAGGCACGTATGAGCAAGATGCTACATGCTTTCGATTATGGTAATGAGGACATTTCGGGCAATGTAGACAGTTTCTGGCTCGACGGTGGTATTCGAATTTCGGCCACGGAGCAAATCAGCTTTTTAAGAAAGCTGTATCACAATAAGTTACACGTATCGGAGCGCAGCCAGCGTATTGTCAAACAAGCCATGCTGACCGAAGCCAATGGTGACTATATTATTCGGGCTAAAACTGGATACTCGACTGGAATCGAACCTAAGATTGGCTGGTGGGTCGGTTGGGTTGAACTTGATGATAATGTGTGGTTTTTTGCGATGAATATGGATATGCCCACATCGGATGGTTTAGGGCTGCGCCAAGCCATCACAAAAGAAGTGCTCAAACAGGAAAAAATTATTCCCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001786","ARO_id":"38186","ARO_name":"OXA-244","CARD_short_name":"OXA-244","ARO_description":"OXA-244 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46510":{"category_aro_accession":"3007721","category_aro_cvterm_id":"46510","category_aro_name":"OXA-48-like beta-lactamase","category_aro_description":"OXA-48-type beta-lactamases are now routinely encountered in bacterial infections caused by carbapenam-resistant Enterobacterales. OXA-48-like proteins confer resistance to penicillin (which is efficiently hydrolyzed) and carbapenam antibiotics (which is more slowly broken down). The spectrum of activity of these variants varies, with some hydrolyzing expanded-spectrum oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"866":{"model_id":"866","model_name":"adeB","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"2000"}},"model_sequences":{"sequence":{"4257":{"protein_sequence":{"accession":"AAL14440.1","sequence":"MSQFFIRRPVFAWVIAIFIIIFGLLSIPKLPIARFPSVAPPQVNISATYPGATAKTINDSVVTLIERELSGVKNLLYYSATTDTSGTAEITATFKPGTDVEMAQVDVQNKIKAVEARLPQVVRQQGLQVEASSSGFLMLVGINSPNNQYSEVDLSDYLVRNVVEELKRVEGVGKVQSFGAEKAMRIWVDPNKLVSYGLSISDVNNAIRENNVEIAPGRLGDLPAEKGQLITIPLSAQGQLSSLEQFKNISLKSKTNGSVIKLSDVANVEIGSQAYNFAILENGKPATAAAIQLSPGANAVKTAEVVRAKIEELKLNLPEGMEFSIPYDTAPFVKISIEKVIHTLLEAMVLVFIVMYLFLHNVRYTLIPAIVAPIALLGTFTVMLLAGFSINVLTMFGMVLAIGIIVDDAIVVVENVERIMATEGLSPKDATSKAMKEITSPIIGITLVLAAVFLPMAFASGSVGVIYKQFTLTMSVSILFSALLALILTPALCATILKPIDGHHQKKGFFAWFDRSFDKVTKKYELMLLKIIKHTVPMMVIFLVITGITFTGMKYWPTAFMPEEDQGWFMTSFQLPSDATAERTRNVVNQFENNLKDNPDVKSNTTILGWGFSGAGQNVAVAFTTLKDFKERTSSASKMTSDVNSSMANSTEGETMAVLPPAIDELGTFSGFSLRLQDRANLGMPALLAAQDELMAMAAKNKKFYMVWNEGLPQGDNISLKIDREKLSAFGVKFSDVSDIISTSMGSMYINDFPNQGRMQQVIVQVEAKSRMQLKDILNLKVMGSSGQLVSLSEVVTPQWNKAPQQYNRYNGRPSLSIAGIPNFDTSSGEAMREMEQLIAKLPKGIGYEWTGISLQEKQSESQMAFLLGLSMLVVFLVLAALYESWAIPLSVMLVVPLGIFGAIIAIMSRGLMNDVFFKIGLITIIGLSAKNAILIVEFAKMLKEEGMSLIEATVAAAKLRLRPILMTSLAFTCGVIPLVIASGASSETQHALGTGVFGGMISATILAIFFVPVFFIFILGAVEKLFSSKKKISS"},"dna_sequence":{"accession":"AF370885.1","fmin":"4628","fmax":"7736","strand":"+","sequence":"ATGTCACAATTTTTTATTCGTCGTCCCGTTTTTGCTTGGGTTATTGCGATCTTCATTATTATATTTGGATTGCTGAGCATTCCTAAACTGCCAATTGCACGTTTTCCAAGTGTGGCCCCGCCACAGGTGAATATTAGTGCGACTTATCCTGGTGCTACAGCTAAAACCATTAACGATAGCGTTGTAACCTTAATTGAGCGCGAATTATCGGGTGTAAAAAATCTACTCTACTATAGTGCGACAACAGATACCTCCGGTACAGCAGAGATTACGGCTACGTTTAAACCAGGCACAGATGTGGAAATGGCTCAGGTTGACGTTCAAAATAAAATCAAGGCTGTAGAAGCTCGCTTACCGCAAGTTGTACGTCAGCAAGGTTTACAGGTTGAGGCTTCATCGTCCGGATTTTTAATGCTGGTCGGGATTAACTCTCCAAATAATCAATATTCCGAAGTTGATTTGAGTGATTATTTGGTTCGAAATGTTGTAGAAGAGCTAAAACGTGTCGAAGGTGTAGGGAAGGTTCAATCTTTCGGTGCCGAGAAAGCTATGCGTATTTGGGTCGACCCGAATAAGCTTGTTTCTTACGGTTTATCGATTAGTGATGTGAATAATGCCATTCGTGAAAATAATGTCGAAATTGCACCCGGCCGACTTGGTGATTTACCAGCTGAAAAAGGCCAGCTCATTACTATTCCATTGTCTGCTCAAGGGCAATTGTCTAGTCTCGAGCAATTTAAAAATATTAGCTTAAAAAGTAAAACTAACGGTAGCGTAATTAAGTTATCTGATGTTGCCAATGTAGAAATAGGCTCACAGGCATATAACTTTGCCATTTTGGAAAATGGTAAGCCTGCTACCGCGGCAGCAATTCAATTAAGCCCGGGTGCTAACGCCGTGAAAACTGCCGAAGTTGTTCGAGCAAAAATTGAAGAGTTGAAGCTAAATTTACCGGAAGGCATGGAGTTTAGTATTCCTTACGACACCGCGCCGTTTGTCAAAATTTCAATTGAAAAGGTAATTCATACATTACTTGAAGCCATGGTTCTGGTTTTCATTGTGATGTATCTATTTTTACATAATGTCCGCTATACGCTTATTCCAGCGATTGTGGCGCCTATTGCCTTACTCGGTACTTTTACCGTGATGTTGCTTGCCGGCTTTTCAATTAACGTACTCACCATGTTCGGTATGGTGCTTGCCATCGGGATTATTGTCGACGATGCCATTGTCGTGGTTGAAAACGTCGAAAGGATTATGGCGACAGAAGGATTATCGCCTAAAGATGCAACCTCTAAAGCAATGAAAGAGATTACCAGCCCGATTATTGGTATTACGCTGGTATTGGCGGCAGTATTTTTACCTATGGCATTTGCGAGTGGTTCTGTAGGGGTAATCTATAAACAGTTTACCTTGACCATGTCGGTATCTATTTTATTTTCAGCGCTATTGGCACTTATTTTAACACCGGCACTTTGTGCCACGATTTTAAAACCAATCGATGGGCATCACCAGAAGAAGGGCTTCTTTGCATGGTTTGACCGTAGTTTCGATAAAGTCACTAAAAAGTATGAATTGATGCTGCTTAAAATCATCAAACATACAGTTCCAATGATGGTGATCTTTTTAGTAATTACCGGTATTACCTTTACCGGAATGAAATATTGGCCAACAGCATTTATGCCAGAGGAAGATCAAGGTTGGTTCATGACTTCGTTCCAGCTACCTTCAGATGCAACCGCTGAGCGTACTCGGAATGTAGTCAATCAATTTGAAAATAATTTGAAAGACAATCCCGATGTAAAAAGTAATACCACCATTTTGGGATGGGGTTTTAGTGGCGCAGGACAAAATGTAGCTGTGGCTTTTACGACACTTAAAGACTTCAAAGAGCGGACTAGCTCTGCATCTAAGATGACAAGCGACGTTAATTCTTCTATGGCGAACAGTACGGAAGGCGAGACTATGGCCGTGTTACCACCCGCTATTGATGAGTTAGGTACTTTTTCAGGTTTCAGTTTACGTTTACAAGACCGCGCTAACTTAGGTATGCCTGCTTTACTGGCTGCTCAAGATGAACTTATGGCAATGGCAGCCAAGAATAAAAAGTTCTATATGGTTTGGAATGAAGGGTTGCCACAAGGTGACAATATTTCTTTAAAAATTGACCGTGAAAAGCTTAGTGCATTTGGTGTTAAGTTTTCTGATGTTTCAGACATCATTTCTACATCAATGGGTTCAATGTATATCAATGACTTCCCTAATCAAGGACGTATGCAACAAGTCATTGTACAGGTTGAGGCTAAATCACGTATGCAATTGAAAGATATCTTGAATCTGAAAGTCATGGGTTCAAGCGGTCAATTAGTCTCGTTATCAGAAGTTGTAACGCCACAATGGAATAAGGCACCACAACAATATAATCGTTATAACGGACGACCATCTTTGAGTATTGCTGGTATTCCTAACTTCGATACGTCATCGGGTGAAGCAATGCGTGAAATGGAACAACTGATTGCGAAATTACCGAAAGGTATTGGCTACGAGTGGACAGGTATTTCCTTACAGGAAAAGCAGTCTGAATCACAAATGGCCTTTTTACTTGGTTTATCCATGTTAGTTGTCTTCCTTGTCTTGGCTGCACTCTATGAAAGCTGGGCAATTCCACTTTCTGTGATGCTAGTTGTGCCACTCGGTATTTTTGGAGCAATCATTGCCATTATGTCTAGGGGGTTAATGAATGATGTGTTCTTCAAAATCGGGCTAATTACCATTATTGGTCTATCGGCAAAGAATGCGATTTTGATTGTTGAATTTGCGAAAATGCTGAAAGAAGAAGGCATGAGTTTGATTGAAGCCACTGTTGCCGCAGCCAAACTTCGCTTACGGCCAATTCTGATGACATCACTTGCATTTACGTGTGGTGTAATTCCTTTGGTGATTGCCTCAGGTGCAAGTTCAGAAACTCAACATGCTTTAGGCACAGGGGTTTTTGGCGGCATGATTTCAGCCACCATTCTGGCTATTTTCTTTGTTCCCGTGTTTTTTATCTTCATTTTGGGTGCAGTAGAAAAGCTATTTTCCTCTAAGAAAAAAATCTCATCTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3000775","ARO_id":"37155","ARO_name":"adeB","CARD_short_name":"adeB","ARO_description":"AdeB is the multidrug transporter of the adeABC efflux system.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"867":{"model_id":"867","model_name":"OXA-175","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"801":{"protein_sequence":{"accession":"ADI58619.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDVKAEKIRNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWVVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"HM113561.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGTAAAAGCAGAGAAAATTAGAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGGTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAACAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001659","ARO_id":"38059","ARO_name":"OXA-175","CARD_short_name":"OXA-175","ARO_description":"OXA-175 is a beta-lactamase found in A. baumannii.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"868":{"model_id":"868","model_name":"DHA-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"5901":{"protein_sequence":{"accession":"CAA76196.1","sequence":"MKKSLSATLISALLAFSAPGFSAADNVAAVVDSTIKPLMAQQDIPGMAVAVSVKGKPYYFNYGFADIQAKQPVTENTLFELGSVSKTFTGVLGAVSVAKKEMALNDPAAKYQPELALPQWKGITLLDLATYTAGGLPLQVPDAVKSRADLLNFYQQWQPSRKPGDMRLYANSSIGLFGALTANAAGMPYEQLLTARILAPLGLSHTFITVPESAQSQYAYGYKNKKPVRVSPGQLDAESYGVKSASKDMLRWAEMNMEPSRAGNADLEMAMYLAQTRYYKTAAINQGLGWEMYDWPQQKDMIINGVTNEVALQPHPVTDNQVQPYNRASWVHKTGATTGFGAYVAFIPEKQVAIVILANKNYPNTERVKAAQAILSALE"},"dna_sequence":{"accession":"Y16410.1","fmin":"986","fmax":"2126","strand":"+","sequence":"ATGAAAAAATCGTTATCTGCAACACTGATTTCCGCTCTGCTGGCGTTTTCCGCCCCGGGGTTTTCTGCCGCTGATAATGTCGCGGCGGTGGTGGACAGCACCATTAAACCGCTGATGGCACAGCAGGATATTCCCGGGATGGCGGTTGCCGTCTCCGTAAAGGGTAAGCCCTATTATTTCAATTATGGTTTTGCCGATATTCAGGCAAAACAGCCGGTCACTGAAAATACACTATTTGAGCTCGGATCTGTAAGTAAAACTTTCACAGGTGTGCTGGGTGCGGTTTCTGTGGCGAAAAAAGAGATGGCGCTGAATGATCCGGCGGCAAAATACCAGCCGGAGCTGGCTCTGCCGCAGTGGAAGGGGATCACATTGCTGGATCTGGCTACCTATACCGCAGGCGGACTGCCGTTACAGGTGCCGGATGCGGTAAAAAGCCGTGCGGATCTGCTGAATTTCTATCAGCAGTGGCAGCCGTCCCGGAAACCGGGCGATATGCGTCTGTATGCAAACAGCAGTATCGGCCTGTTTGGTGCTCTGACCGCAAACGCGGCGGGGATGCCGTATGAGCAGTTGCTGACTGCACGGATCCTGGCACCGCTGGGGTTATCTCACACCTTTATTACTGTGCCGGAAAGTGCGCAAAGCCAGTATGCGTACGGTTATAAAAACAAAAAACCGGTCCGCGTGTCGCCGGGACAGCTTGATGCGGAATCTTACGGCGTGAAATCCGCCTCAAAAGATATGCTGCGCTGGGCGGAAATGAATATGGAGCCGTCACGGGCCGGTAATGCGGATCTGGAAATGGCAATGTATCTCGCCCAGACCCGCTACTATAAAACCGCCGCGATTAACCAGGGGCTGGGCTGGGAAATGTATGACTGGCCGCAGCAGAAAGATATGATCATTAACGGTGTGACCAACGAGGTCGCATTGCAGCCGCATCCGGTAACAGACAACCAGGTTCAGCCGTATAACCGTGCTTCCTGGGTGCATAAAACGGGCGCAACAACTGGTTTCGGCGCCTATGTCGCCTTTATTCCGGAAAAACAGGTGGCGATTGTGATTCTGGCGAATAAAAACTACCCGAATACCGAAAGAGTCAAAGCTGCACAGGCTATTTTGAGTGCACTGGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35750","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Enteritidis","NCBI_taxonomy_id":"149539"}}}},"ARO_accession":"3002132","ARO_id":"38532","ARO_name":"DHA-1","CARD_short_name":"DHA-1","ARO_description":"DHA-1 is a class C beta-lactamase found in Morganella morganii and Salmonella enterica.","ARO_category":{"36207":{"category_aro_accession":"3000068","category_aro_cvterm_id":"36207","category_aro_name":"DHA beta-lactamase","category_aro_description":"DHA beta-lactamases are plasmid-mediated AmpC \u03b2-lactamases that confer resistance to cephamycins and oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"869":{"model_id":"869","model_name":"CRP","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"4752":{"protein_sequence":{"accession":"BAE77933.1","sequence":"MVLGKPQTDPTLEWFLSHCHIHKYPSKSKLIHQGEKAETLYYIVKGSVAVLIKDEEGKEMILSYLNQGDFIGELGLFEEGQERSAWVRAKTACEVAEISYKKFRQLIQVNPDILMRLSAQMARRLQVTSEKVGNLAFLDVTGRIAQTLLNLAKQPDAMTHPDGMQIKITRQEIGQIVGCSRETVGRILKMLEDQNLISAHGKTIVVYGTR"},"dna_sequence":{"accession":"AP009048.1","fmin":"4153663","fmax":"4154296","strand":"-","sequence":"ATGGTGCTTGGCAAACCGCAAACAGACCCGACTCTCGAATGGTTCTTGTCTCATTGCCACATTCATAAGTACCCATCCAAGAGCAAGCTTATTCACCAGGGTGAAAAAGCGGAAACGCTGTACTACATCGTTAAAGGCTCTGTGGCAGTGCTGATCAAAGACGAAGAGGGTAAAGAAATGATCCTCTCCTATCTGAATCAGGGTGATTTTATTGGCGAACTGGGCCTGTTTGAAGAGGGCCAGGAACGTAGCGCATGGGTACGTGCGAAAACCGCCTGTGAAGTGGCTGAAATTTCGTACAAAAAATTTCGCCAATTGATTCAGGTAAACCCGGACATTCTGATGCGTTTGTCTGCACAGATGGCGCGTCGTCTGCAAGTCACTTCAGAGAAAGTGGGCAACCTGGCGTTCCTCGACGTGACGGGCCGCATTGCACAGACTCTGCTGAATCTGGCAAAACAACCAGACGCTATGACTCACCCGGACGGTATGCAAATCAAAATTACCCGTCAGGAAATTGGTCAGATTGTCGGCTGTTCTCGTGAAACCGTGGGACGCATTCTGAAGATGCTGGAAGATCAGAACCTGATCTCCGCACACGGTAAAACCATCGTCGTTTACGGCACTCGTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36839","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. W3110","NCBI_taxonomy_id":"316407"}}}},"ARO_accession":"3000518","ARO_id":"36657","ARO_name":"CRP","CARD_short_name":"CRP","ARO_description":"CRP is a global regulator that represses MdtEF multidrug efflux pump expression.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35930":{"category_aro_accession":"0000011","category_aro_cvterm_id":"35930","category_aro_name":"cloxacillin","category_aro_description":"Cloxacillin is a semisynthetic, isoxazolyl penicillin derivative in the beta-lactam class of antibiotics. It interferes with peptidogylcan synthesis and is commonly used for treating penicillin-resistant Staphylococcus aureus infections.","category_aro_class_name":"Antibiotic"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"872":{"model_id":"872","model_name":"vatC","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"211":{"protein_sequence":{"accession":"AAC61671.1","sequence":"MKWQNQQGPNPEEIYPIEGNKHVQFIKPSITKPNILVGEYSYYDSKDGESFESQVLYHYELIGDKLILGKFCSIGPGTTFIMNGANHRMDGSTFPFNLFGNGWEKHTPTLEDLPYKGNTEIGNDVWIGRDVTIMPGVKIGNGAIIAAKSVVTKNVDPYSVVGGNPSRLIKIRFSKEKIAALLKVRWWDLEIETINENIDCILNGDIKKVKRS"},"dna_sequence":{"accession":"AF015628.1","fmin":"1306","fmax":"1945","strand":"+","sequence":"ATGAAATGGCAAAATCAGCAAGGCCCCAATCCAGAAGAAATATACCCTATAGAAGGTAATAAACATGTTCAATTTATTAAACCATCTATAACAAAGCCCAATATTTTAGTTGGGGAATATTCATATTACGATAGTAAAGATGGTGAATCTTTTGAAAGCCAAGTTCTTTATCACTATGAATTGATTGGGGATAAACTAATATTAGGGAAGTTTTGTTCTATTGGACCCGGAACGACATTTATAATGAATGGGGCTAATCATCGTATGGATGGTTCAACATTTCCATTCAATCTTTTCGGAAATGGTTGGGAGAAGCATACCCCTACATTGGAAGACCTTCCTTATAAGGGTAACACGGAAATTGGGAACGATGTTTGGATTGGACGAGATGTGACAATTATGCCCGGTGTAAAAATAGGAAACGGGGCTATTATTGCAGCAAAATCGGTTGTGACAAAGAACGTTGATCCTTATTCAGTTGTTGGCGGTAATCCTTCACGATTAATTAAGATAAGGTTTTCCAAGGAAAAAATCGCAGCATTACTAAAAGTAAGGTGGTGGGACCTAGAGATAGAGACGATAAATGAAAATATTGATTGCATCCTGAATGGTGATATAAAAAAGGTTAAAAGAAGTTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36766","NCBI_taxonomy_name":"Staphylococcus cohnii","NCBI_taxonomy_id":"29382"}}}},"ARO_accession":"3002842","ARO_id":"39276","ARO_name":"vatC","CARD_short_name":"vatC","ARO_description":"vatC is a plasmid-mediated acetyltransferase found in Staphylococcus cohnii.","ARO_category":{"36592":{"category_aro_accession":"3000453","category_aro_cvterm_id":"36592","category_aro_name":"streptogramin vat acetyltransferase","category_aro_description":"vat (Virginiamycin acetyltransferases) enzymes catalyze the transfer of an acetyl group from acetyl-CoA to the secondary alcohol of streptogramin A compounds, thus inactivating virginiamycin-like antibiotics and conferring resistance to these compounds.","category_aro_class_name":"AMR Gene Family"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"virginiamycin M1","category_aro_description":"Virginiamycin M1 is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37016":{"category_aro_accession":"3000672","category_aro_cvterm_id":"37016","category_aro_name":"madumycin II","category_aro_description":"Madumycin II is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37017":{"category_aro_accession":"3000673","category_aro_cvterm_id":"37017","category_aro_name":"griseoviridin","category_aro_description":"Griseoviridin is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35952":{"category_aro_accession":"0000034","category_aro_cvterm_id":"35952","category_aro_name":"streptogramin A antibiotic","category_aro_description":"Streptogramin A antibiotics are cyclic polyketide peptide hybrids that bind to the ribosomal peptidyl transfer centre. Structural variation arises from substituting a proline for its desaturated derivative and by its substitution for Ala or Cys. Used alone, streptogramin A antibiotics are bacteriostatic, but is bactericidal when used with streptogramin B antibiotics.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"873":{"model_id":"873","model_name":"KPC-19","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"954":{"protein_sequence":{"accession":"AIH07017.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKYSEAVIAAAARLALEGLGVTGQ"},"dna_sequence":{"accession":"KJ775801.1","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGTACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCACGGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39097","NCBI_taxonomy_name":"Klebsiella pneumoniae subsp. pneumoniae","NCBI_taxonomy_id":"72407"}}}},"ARO_accession":"3002329","ARO_id":"38729","ARO_name":"KPC-19","CARD_short_name":"KPC-19","ARO_description":"KPC-19 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"875":{"model_id":"875","model_name":"dfrA19","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"716":{"protein_sequence":{"accession":"CAC81324.1","sequence":"MSHPQLELIVAVDSKLGFGKGGKIPWKCKEDMARFTRISKEIRVCVIGKHTYTDMRDMQLEKDGAEERIKEKGILPERESFVISSTLKQEDVIGATVVPDLRAVINLYENTDQRIAVIGGEKLYIQALSSATKLHMTIIPREFDCDRFIPVDPIQNNFHIDSSASETVEATVDETQERIHFATYVRNNQ"},"dna_sequence":{"accession":"AJ310778.1","fmin":"7003","fmax":"7573","strand":"+","sequence":"ATGAGTCACCCACAACTTGAGCTAATAGTCGCTGTGGATTCTAAGTTGGGATTCGGGAAAGGCGGCAAGATTCCATGGAAATGCAAAGAAGACATGGCGCGATTTACGCGGATTTCTAAAGAGATCCGCGTGTGCGTTATAGGGAAACACACGTATACTGACATGCGTGACATGCAGTTAGAAAAGGATGGCGCCGAGGAGCGAATCAAGGAGAAAGGAATTCTCCCCGAACGCGAATCGTTCGTGATCTCCTCGACGTTAAAACAAGAAGATGTCATAGGCGCTACTGTCGTTCCTGATCTTCGTGCTGTGATCAACCTGTATGAGAATACCGATCAACGCATTGCTGTCATTGGTGGGGAGAAGTTGTACATTCAAGCTCTTTCATCAGCAACGAAACTGCACATGACCATAATTCCAAGAGAGTTCGACTGTGATCGATTTATTCCTGTTGATCCGATCCAGAACAATTTTCACATTGATTCCAGTGCCAGCGAGACTGTGGAGGCAACCGTTGATGAGACTCAAGAGCGCATTCACTTTGCTACTTACGTGCGTAACAATCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35732","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Typhimurium","NCBI_taxonomy_id":"90371"}}}},"ARO_accession":"3003015","ARO_id":"39449","ARO_name":"dfrA19","CARD_short_name":"dfrA19","ARO_description":"dfrA19 is an integron-encoded dihydrofolate reductase found in Klebsiella pneumoniae.","ARO_category":{"37617":{"category_aro_accession":"3001218","category_aro_cvterm_id":"37617","category_aro_name":"trimethoprim resistant dihydrofolate reductase dfr","category_aro_description":"Alternative dihydropteroate synthase dfr present on plasmids produces alternate proteins that are less sensitive to trimethoprim from inhibiting its role in folate synthesis, thus conferring trimethoprim resistance.","category_aro_class_name":"AMR Gene Family"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"876":{"model_id":"876","model_name":"smeE","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"2070"}},"model_sequences":{"sequence":{"564":{"protein_sequence":{"accession":"CAC14595.1","sequence":"MARFFIDRPIFAWVIAIIIMLAGGLALFKLPVSMYPNVAPPAVEISATYPGASAKVVEDSVTQIIEQNMKGLDGLIYFSSNSSSNGQATITLTFESGTNPDIAQVQVQNKLQLAMPLLPQEVQRQGINVAKSSSGFLNAIAFVSENGSMDANDIADYVGSNVVDRLSRVPGVGNIQVFGGKYAMRIWLDPNKLHTYGLSVPEVTAAIKAQNAQVAIGQLGGAPSVKGQQLNATINAQSRLQTPEQFRNIIVRGAQDGAELRLGDVARVELGAESYDFVTRYNGQPASGLAVTLATGANALDTAAGVDAALEDMKGFFPAGLKAEIPYDTTPFVRVSIKGVVQTLIEAIVLVFVVMYLFLQNFRATLIPTIAVPVVLLGTFGVLAMLGFSVNMLTMFAMVLAIGLLVDDAIVVVENVERIMSEEGLSPLEATRKSMGQITGALVGIGLVLSAVFVPMAFMSGSTGVIYRQFSATIVSAMALSVLVAIVLTPALCATMLKPLKKGEHHVAHRGLAGRFFNGFNRGFDRTSESYQRGVRGIIHRPWRFMGIVAALFVLMGVLFVRLPSSFLPNEDQGVLMALVQAPVGATQERTLESIAALENHFLQNEKDAVDSVFSVQGFSFAGMGQNAGMAFVKLKDWSERDADNGVMPITGRAMAALGQIKDAFIFAFPPPAIPELGTASGYTFFLKDNSGQGHEALVAARNQLLGLAAGSKKLANVRPNGQEDTPQFRIDIDAAKATSLGLSIDQINGTLAAAWGSSYIDDFVDRGRVKRVFVQADQAFRMVPEDFDLWSVKNDKGEMVPFSAFATKHWDYGSPRLERYNGVSAMEIQGEPAPGVASGDAMAEIEQLAKQLPAGFGIEWTAMSYQERQAGSQTPLLYTLSLMIVFLCLAAMYESWSVPTAVLLAAPLGILGAVLANTFKGLERDIYFQVAMLTTVGLTSKNAILIVEFAKENLEKGASLIESIMHAVRDRLRPIVMTSLAFGMGVVPLAISTGAGSGAKQAIGTGVLGGMIVGTVLGVFFVPLFFVVVQRVFKRRSTT"},"dna_sequence":{"accession":"AJ252200.1","fmin":"1278","fmax":"4401","strand":"+","sequence":"ATGGCACGCTTTTTCATCGATCGACCCATCTTTGCGTGGGTGATCGCCATCATCATCATGCTCGCCGGCGGCCTGGCGCTGTTCAAGCTGCCGGTCTCGATGTACCCCAACGTCGCACCGCCGGCGGTGGAAATCAGCGCCACCTACCCGGGTGCATCGGCCAAGGTGGTCGAGGACTCGGTGACGCAGATCATCGAGCAGAACATGAAGGGCCTTGATGGCCTGATCTACTTCTCCTCCAACAGCTCGTCCAACGGCCAGGCCACCATCACCCTGACCTTCGAGAGCGGCACCAACCCGGATATCGCCCAGGTGCAGGTGCAGAACAAGCTGCAGCTGGCCATGCCGCTGCTGCCGCAGGAAGTGCAGCGGCAGGGCATCAACGTGGCCAAGTCCAGCTCGGGCTTCCTGAACGCCATCGCGTTCGTGTCCGAGAACGGCAGCATGGACGCCAACGACATCGCCGACTACGTCGGTTCCAATGTCGTCGACCGCCTGAGCCGCGTGCCGGGCGTGGGCAACATCCAGGTGTTCGGTGGCAAGTACGCCATGCGCATCTGGCTGGACCCGAACAAGCTGCATACCTATGGCCTGTCGGTGCCGGAAGTGACCGCCGCGATCAAGGCGCAGAACGCCCAGGTGGCGATCGGCCAGCTCGGCGGTGCGCCGTCGGTGAAGGGCCAGCAGCTCAACGCCACCATCAACGCGCAGTCGCGCCTGCAGACCCCGGAACAGTTCCGAAACATCATCGTGCGCGGTGCGCAGGACGGTGCCGAGCTGCGCCTGGGTGATGTCGCCCGCGTCGAGCTGGGTGCCGAGTCCTACGACTTCGTCACCCGCTACAACGGCCAGCCGGCCAGTGGCCTGGCGGTCACCCTGGCCACCGGCGCCAACGCGCTGGATACCGCGGCCGGTGTGGATGCCGCGCTGGAAGACATGAAGGGCTTCTTCCCGGCCGGCCTGAAGGCCGAGATCCCGTACGACACCACCCCGTTCGTGCGCGTGTCGATCAAGGGCGTGGTGCAGACCCTGATCGAAGCGATCGTGCTGGTGTTCGTGGTGATGTACCTGTTCCTGCAGAACTTCCGCGCCACGCTGATCCCGACCATCGCCGTGCCGGTGGTGCTGCTGGGTACCTTCGGCGTGCTGGCGATGCTGGGCTTCTCGGTGAACATGCTGACCATGTTCGCGATGGTGCTGGCGATCGGCCTGCTGGTGGACGATGCCATCGTGGTGGTGGAGAACGTCGAGCGCATCATGTCCGAGGAAGGGCTGTCGCCGCTCGAAGCGACCCGCAAGTCGATGGGCCAGATCACCGGTGCGCTGGTGGGTATCGGCCTGGTGCTGTCGGCGGTGTTCGTGCCGATGGCCTTCATGAGCGGCTCCACCGGCGTGATCTATCGCCAGTTCTCGGCCACGATTGTCTCTGCGATGGCGTTGTCGGTGCTGGTGGCGATCGTGCTGACCCCGGCACTGTGCGCGACCATGCTCAAGCCGCTGAAGAAGGGTGAGCACCACGTCGCCCACCGTGGCCTGGCCGGTCGCTTCTTCAATGGCTTCAACCGTGGCTTCGATCGCACCAGCGAAAGCTACCAGCGCGGCGTGCGCGGCATCATCCACCGTCCGTGGCGCTTCATGGGCATCGTGGCGGCCTTGTTCGTGCTGATGGGCGTGCTGTTCGTGCGCCTGCCCAGCTCGTTCCTGCCCAACGAAGACCAGGGTGTGCTGATGGCGCTGGTGCAGGCGCCGGTCGGTGCCACCCAGGAACGCACGCTGGAATCGATCGCGGCACTGGAAAACCACTTCCTGCAGAACGAGAAGGATGCGGTGGACTCGGTGTTCTCCGTGCAGGGCTTCAGCTTCGCCGGCATGGGCCAGAACGCGGGCATGGCGTTCGTCAAGCTGAAGGACTGGAGCGAGCGTGACGCCGACAATGGCGTGATGCCGATCACCGGACGTGCGATGGCGGCCCTGGGCCAGATCAAGGATGCCTTCATCTTCGCCTTCCCGCCGCCGGCCATTCCGGAGCTGGGGACCGCCTCGGGCTACACCTTCTTCCTGAAGGACAACAGCGGCCAGGGCCACGAGGCACTGGTGGCCGCGCGCAACCAGCTGCTCGGCCTGGCCGCAGGCAGCAAGAAGCTGGCCAACGTACGCCCGAACGGCCAGGAAGACACGCCGCAGTTCCGCATCGACATCGACGCGGCCAAGGCGACCTCGCTGGGACTGTCGATCGACCAGATCAACGGCACGCTGGCGGCCGCGTGGGGCAGCTCGTACATCGATGACTTCGTCGATCGTGGCCGCGTCAAGCGCGTGTTCGTGCAGGCCGACCAGGCGTTCCGCATGGTGCCGGAGGACTTCGATCTCTGGTCCGTGAAGAACGACAAGGGTGAGATGGTGCCGTTCAGCGCCTTCGCTACCAAGCACTGGGACTACGGTTCGCCGCGCCTGGAACGCTACAACGGTGTGTCGGCAATGGAAATCCAGGGCGAACCGGCCCCGGGTGTCGCCTCCGGTGATGCCATGGCCGAGATCGAACAGCTGGCCAAGCAGCTGCCGGCGGGTTTCGGCATCGAATGGACGGCGATGTCCTACCAGGAACGCCAGGCCGGCTCGCAGACGCCGCTGCTGTACACGCTGTCGCTGATGATCGTGTTCCTGTGCCTGGCCGCGATGTATGAAAGCTGGAGCGTACCGACCGCGGTGCTGCTGGCGGCCCCGCTGGGTATCCTCGGCGCGGTGCTGGCCAACACCTTCAAGGGCCTGGAGCGCGACATCTACTTCCAGGTGGCGATGCTGACCACGGTGGGCCTGACCAGCAAGAACGCGATCCTGATCGTCGAGTTCGCCAAGGAAAACCTGGAAAAGGGCGCCAGCCTGATCGAGTCGATCATGCACGCCGTGCGCGACCGCCTGCGCCCGATCGTGATGACCTCGCTCGCCTTCGGCATGGGCGTGGTACCGCTGGCGATCTCCACCGGTGCCGGCTCCGGCGCCAAGCAGGCGATCGGCACCGGCGTGCTCGGCGGCATGATCGTCGGCACCGTGCTCGGCGTGTTCTTCGTGCCGCTGTTCTTCGTGGTGGTGCAGCGCGTGTTCAAGCGCAGATCCACGACGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37076","NCBI_taxonomy_name":"Stenotrophomonas maltophilia","NCBI_taxonomy_id":"40324"}}}},"ARO_accession":"3003056","ARO_id":"39490","ARO_name":"smeE","CARD_short_name":"smeE","ARO_description":"smeE is the RND protein of the efflux complex smeDEF in Stenotrophomonas maltophilia.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"877":{"model_id":"877","model_name":"SHV-124","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1851":{"protein_sequence":{"accession":"ACV32634.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLDQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGASKRGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQ"},"dna_sequence":{"accession":"GQ390806.1","fmin":"0","fmax":"813","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGATCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTACTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTAGCAAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAATCAG","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001171","ARO_id":"37551","ARO_name":"SHV-124","CARD_short_name":"SHV-124","ARO_description":"SHV-124 is a beta-lactamase that has been found in clinical isolates.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"878":{"model_id":"878","model_name":"CTX-M-142","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1105":{"protein_sequence":{"accession":"AGW25368.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTANVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"KF240809.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGAACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002000","ARO_id":"38400","ARO_name":"CTX-M-142","CARD_short_name":"CTX-M-142","ARO_description":"CTX-M-142 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"879":{"model_id":"879","model_name":"TEM-185","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1799":{"protein_sequence":{"accession":"AEG64812.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMLSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRREPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"JF795538.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGCTGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATCGTCGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001374","ARO_id":"37774","ARO_name":"TEM-185","CARD_short_name":"TEM-185","ARO_description":"TEM-185 is a beta-lactamase found in E. coli.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"880":{"model_id":"880","model_name":"APH(6)-Ib","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"118":{"protein_sequence":{"accession":"CAA29136.1","sequence":"MSTSKLVEIPEPLAASYARAFGEEGQAWIAALPALVEELLDRWELTADGASASGEASLVLPVLRTDGTRAVLKLQLPREETSAAITGLRTWNGHGVVRLLDHDPRSSTMLLERLDASRTLASVEDDDAAMGVLAGLLARLVSVPAPRGLRGLGDIAGAMLEEVPRAVAALADPADRRLLNDWASAVAELVGEPGDRMLHWDLHYGNVLAAEREPWLAIDPEPLAGDPGFDLWPALDSRWDDIVAQRDVVRVVRRRFDLLTEVLGLDRARAAGWTYGRLLQNALWDIEDGSAALDPAAVTLAQALRGH"},"dna_sequence":{"accession":"X05648.1","fmin":"381","fmax":"1305","strand":"+","sequence":"ATGAGCACGTCAAAACTGGTGGAGATCCCGGAACCCCTGGCGGCGTCGTACGCCCGCGCCTTCGGCGAGGAGGGACAGGCATGGATCGCCGCCCTGCCCGCGCTGGTCGAGGAATTACTGGACCGCTGGGAGCTGACGGCGGACGGCGCCTCCGCGTCGGGCGAGGCCTCCCTCGTGCTGCCGGTGCTGCGCACCGACGGCACCCGCGCCGTCCTCAAGCTCCAGCTGCCCAGGGAGGAGACCTCCGCCGCCATCACCGGACTGCGCACCTGGAACGGGCACGGCGTCGTGCGGCTGCTCGACCACGACCCGCGCAGCAGCACCATGCTCCTGGAGCGGCTGGACGCGTCCCGCACGCTGGCCTCGGTCGAGGACGACGACGCCGCCATGGGCGTACTCGCCGGGCTGCTGGCCCGGCTGGTGTCCGTCCCCGCGCCGCGGGGGCTGCGCGGCCTCGGCGACATCGCCGGCGCCATGCTGGAGGAGGTGCCGCGGGCGGTCGCGGCGCTGGCCGACCCGGCCGACCGGCGGCTGCTGAACGACTGGGCGTCGGCGGTGGCCGAACTGGTCGGCGAACCCGGCGACCGGATGCTGCACTGGGACCTGCACTACGGCAACGTCCTCGCCGCCGAGCGCGAACCCTGGCTCGCCATCGACCCCGAACCGCTCGCCGGTGACCCCGGCTTCGACCTGTGGCCCGCCCTGGACAGCCGGTGGGACGACATCGTCGCACAGCGGGACGTCGTACGCGTCGTGCGACGCCGCTTCGACCTGCTGACCGAGGTCCTCGGCCTGGACCGGGCACGGGCGGCCGGCTGGACGTACGGCAGGCTGCTGCAGAACGCCCTGTGGGACATCGAGGACGGCAGTGCCGCCCTCGACCCCGCCGCCGTCACGCTCGCACAGGCGCTGCGGGGCCACTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36901","NCBI_taxonomy_name":"Streptomyces glaucescens","NCBI_taxonomy_id":"1907"}}}},"ARO_accession":"3002658","ARO_id":"39058","ARO_name":"APH(6)-Ib","CARD_short_name":"APH(6)-Ib","ARO_description":"APH(6)-Ib is a chromosomal-encoded aminoglycoside phosphotransferase in S. glaucescens.","ARO_category":{"36290":{"category_aro_accession":"3000151","category_aro_cvterm_id":"36290","category_aro_name":"APH(6)","category_aro_description":"A category of aminoglycoside O-phosphotransferase enzymes with modification regiospecificity based at the 6-hydroxyl group of the respective antibiotic. These enzymes are characterized by enzymatic antibiotic inactivation, specifically of streptomycin, by the ATP-dependent phosphorylation of the 6-hydroxyl group of the compound.","category_aro_class_name":"AMR Gene Family"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"881":{"model_id":"881","model_name":"ErmC","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"501":{"protein_sequence":{"accession":"AAA98296.1","sequence":"MNEKNIKHSQNFITSKHNIDKIMTNIRLNEHDNIFEIGSGKGHFTLELVQRCNFVTAIEIDHKLCKTTENKLVDHDNFQVLNKDILQFKFPKNQSYKIFGNIPYNISTDIIRKIVFDSIADEIYLIVEYGFAKRLLNTKRSFALFLMAEVDISILSMVPREYFHPKPKVNSSLIRLNRKKSRISHKDKQKYNYFVMKWVNKEYKKIFTKNQFNNSLKHAGIDDLNNISFEQFLSLFNSYKLFNK"},"dna_sequence":{"accession":"M12730.1","fmin":"779","fmax":"1514","strand":"+","sequence":"ATGAACGAGAAAAATATAAAACACAGTCAAAACTTTATTACTTCAAAACATAATATAGATAAAATAATGACAAATATAAGATTAAATGAACATGATAATATCTTTGAAATCGGCTCAGGAAAAGGGCATTTTACCCTTGAATTAGTACAGAGGTGTAATTTCGTAACTGCCATTGAAATAGACCATAAATTATGCAAAACTACAGAAAATAAACTTGTTGATCACGATAATTTCCAAGTTTTAAACAAGGATATATTGCAGTTTAAATTTCCTAAAAACCAATCCTATAAAATATTTGGTAATATACCTTATAACATAAGTACGGATATAATACGCAAAATTGTTTTTGATAGTATAGCTGATGAGATTTATTTAATCGTGGAATACGGGTTTGCTAAAAGATTATTAAATACAAAACGCTCATTCGCATTATTTTTAATGGCAGAAGTTGATATTTCTATATTAAGTATGGTTCCAAGAGAATATTTTCATCCTAAACCTAAAGTGAATAGCTCACTTATCAGATTAAATAGAAAAAAATCAAGAATATCACACAAAGATAAACAGAAGTATAATTATTTCGTTATGAAATGGGTTAACAAAGAATACAAGAAAATATTTACAAAAAATCAATTTAACAATTCCTTAAAACATGCAGGAATTGACGATTTAAACAATATTAGCTTTGAACAATTCTTATCTCTTTTCAATAGCTATAAATTATTTAATAAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36868","NCBI_taxonomy_name":"Staphylococcus epidermidis","NCBI_taxonomy_id":"1282"}}}},"ARO_accession":"3000250","ARO_id":"36389","ARO_name":"ErmC","CARD_short_name":"ErmC","ARO_description":"ErmC is a methyltransferase that catalyzes the methylation of A2058 of the 23S ribosomal RNA in two steps. Expression of ErmC is inducible by erythromycin. The leader peptide causes attenuation of the mRNA and stabilizes the structure preventing further translation. When erythromycin is present, it binds the leader peptide causing a change in conformation allowing for the expression of ErmC.","ARO_category":{"36699":{"category_aro_accession":"3000560","category_aro_cvterm_id":"36699","category_aro_name":"Erm 23S ribosomal RNA methyltransferase","category_aro_description":"Erm proteins are part of the RNA methyltransferase family and methylate A2058 (E. coli nomenclature) of the 23S ribosomal RNA conferring degrees of resistance to Macrolides, Lincosamides and Streptogramin b. This is called the MLSb phenotype.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35946":{"category_aro_accession":"0000027","category_aro_cvterm_id":"35946","category_aro_name":"roxithromycin","category_aro_description":"Roxithromycin is a semi-synthetic, 14-carbon ring macrolide antibiotic derived from erythromycin. It is used to treat respiratory tract, urinary and soft tissue infections. Roxithromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35974":{"category_aro_accession":"0000057","category_aro_cvterm_id":"35974","category_aro_name":"telithromycin","category_aro_description":"Telithromycin is a semi-synthetic derivative of erythromycin. It is a 14-membered macrolide and is the first ketolide antibiotic to be used in clinics. Telithromycin binds the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"35982":{"category_aro_accession":"0000065","category_aro_cvterm_id":"35982","category_aro_name":"clarithromycin","category_aro_description":"Clarithromycin is a methyl derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome and is used to treat pharyngitis, tonsillitis, acute maxillary sinusitis, acute bacterial exacerbation of chronic bronchitis, pneumonia (especially atypical pneumonias associated with Chlamydia pneumoniae or TWAR), and skin structure infections.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"36284":{"category_aro_accession":"3000145","category_aro_cvterm_id":"36284","category_aro_name":"tylosin","category_aro_description":"Tylosin is a 16-membered macrolide, naturally produced by Streptomyces fradiae. It interacts with the bacterial ribosome 50S subunit to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"36295":{"category_aro_accession":"3000156","category_aro_cvterm_id":"36295","category_aro_name":"spiramycin","category_aro_description":"Spiramycin is a 16-membered macrolide and is natural product produced by Streptomyces ambofaciens. It binds to the 50S subunit of bacterial ribosomes and inhibits peptidyl transfer activity to disrupt protein synthesis.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"36315":{"category_aro_accession":"3000176","category_aro_cvterm_id":"36315","category_aro_name":"dirithromycin","category_aro_description":"Dirithromycin is an oxazine derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome to inhibit bacterial protein synthesis.","category_aro_class_name":"Antibiotic"},"36722":{"category_aro_accession":"3000583","category_aro_cvterm_id":"36722","category_aro_name":"pristinamycin IA","category_aro_description":"Pristinamycin IA is a type B streptogramin antibiotic produced by Streptomyces pristinaespiralis. It binds to the P site of the 50S subunit of the bacterial ribosome, preventing the extension of protein chains.","category_aro_class_name":"Antibiotic"},"36723":{"category_aro_accession":"3000584","category_aro_cvterm_id":"36723","category_aro_name":"quinupristin","category_aro_description":"Quinupristin is a type B streptogramin and a semisynthetic derivative of pristinamycin 1A. It is a component of the drug Synercid and interacts with the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"virginiamycin M1","category_aro_description":"Virginiamycin M1 is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37016":{"category_aro_accession":"3000672","category_aro_cvterm_id":"37016","category_aro_name":"madumycin II","category_aro_description":"Madumycin II is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37017":{"category_aro_accession":"3000673","category_aro_cvterm_id":"37017","category_aro_name":"griseoviridin","category_aro_description":"Griseoviridin is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"37019":{"category_aro_accession":"3000675","category_aro_cvterm_id":"37019","category_aro_name":"pristinamycin IB","category_aro_description":"Pristinamycin IB is a class B streptogramin similar to pristinamycin IA, the former containing a N-methyl-4-(methylamino)phenylalanine instead of a N-methyl-4-(dimethylamino)phenylalanine in its class A streptogramin counterpart (one less methyl group).","category_aro_class_name":"Antibiotic"},"37021":{"category_aro_accession":"3000677","category_aro_cvterm_id":"37021","category_aro_name":"virginiamycin S2","category_aro_description":"Virginiamycin S2 is a streptogramin B antibiotic.","category_aro_class_name":"Antibiotic"},"37022":{"category_aro_accession":"3000678","category_aro_cvterm_id":"37022","category_aro_name":"pristinamycin IC","category_aro_description":"Pristinamycin IC is a class B streptogramin derived from virginiamycin S1.","category_aro_class_name":"Antibiotic"},"37023":{"category_aro_accession":"3000679","category_aro_cvterm_id":"37023","category_aro_name":"vernamycin C","category_aro_description":"Vernamycin C is a streptogramin B antibiotic.","category_aro_class_name":"Antibiotic"},"37024":{"category_aro_accession":"3000680","category_aro_cvterm_id":"37024","category_aro_name":"patricin A","category_aro_description":"Patricin A is a streptogramin B antibiotic.","category_aro_class_name":"Antibiotic"},"37025":{"category_aro_accession":"3000681","category_aro_cvterm_id":"37025","category_aro_name":"patricin B","category_aro_description":"Patricin B is a streptogramin B antibiotic.","category_aro_class_name":"Antibiotic"},"37026":{"category_aro_accession":"3000682","category_aro_cvterm_id":"37026","category_aro_name":"ostreogrycin B3","category_aro_description":"Ostreogrycin B3 is a derivative of pristinamycin IA, with an additional 3-hydroxy group on its 4-oxopipecolic acid.","category_aro_class_name":"Antibiotic"},"37247":{"category_aro_accession":"3000867","category_aro_cvterm_id":"37247","category_aro_name":"oleandomycin","category_aro_description":"Oleandomycin is a 14-membered macrolide produced by Streptomyces antibioticus. It is ssimilar to erythromycin, and contains a desosamine amino sugar and an oleandrose sugar. It targets the 50S ribosomal subunit to prevent protein synthesis.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35952":{"category_aro_accession":"0000034","category_aro_cvterm_id":"35952","category_aro_name":"streptogramin A antibiotic","category_aro_description":"Streptogramin A antibiotics are cyclic polyketide peptide hybrids that bind to the ribosomal peptidyl transfer centre. Structural variation arises from substituting a proline for its desaturated derivative and by its substitution for Ala or Cys. Used alone, streptogramin A antibiotics are bacteriostatic, but is bactericidal when used with streptogramin B antibiotics.","category_aro_class_name":"Drug Class"},"35967":{"category_aro_accession":"0000050","category_aro_cvterm_id":"35967","category_aro_name":"streptogramin B antibiotic","category_aro_description":"Streptogramin B antibiotics are are cyclic hepta- or hexa-depsipeptides.  Type B streptogramins block the peptide exit tunnel of the 50S bacterial ribosome. The general composition of group B streptogramins is 3-hydroxypicolinic acid-L-Thr-D-aminobutyric acid (or D-Ala)-L-Pro-L-Phe (or 4-N-,N-(dimethylamino)-L-Phe)-X-L-phenylglycine. Used alone, streptogramin B antibiotics are bacteriostatic, but is bactericidal when used with streptogramin A antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"883":{"model_id":"883","model_name":"LRA-17","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"4751":{"protein_sequence":{"accession":"ACH58994.1","sequence":"MSIFRTILFVSILLLTSLANSPHATAQVTNTDRPEWSKPYKPFRIAGNIYYVGTYDLACYLITTPQGHILINAALAGTVDQVKANVEALGFKFSDIKILLISQAHFDHVGGLAAIQKMTGAKVMIDDQDAPVVEDGGNSDYIYGGKGVGSLFAPVHVDRKLHDHDNITLGGTQLEMLHHPGHTKGSCSYLLTVKDEHRSYRVLIANIPYMLSEVTLPGMPTYPNVGKDFMYTYGAMRKLQFDIWVAAHSSQFGLQDVRKETDGYNPGAFGDKKKYLTTIDKTEDIYKEHFKGGK"},"dna_sequence":{"accession":"EU408354.1","fmin":"3570","fmax":"4455","strand":"-","sequence":"ATGTCGATATTCAGAACCATACTTTTTGTATCCATACTATTACTGACCTCACTCGCAAATAGCCCGCATGCCACAGCACAGGTAACCAACACAGACAGGCCCGAATGGTCTAAACCCTACAAGCCATTCCGCATCGCAGGCAATATATACTACGTAGGCACTTATGACCTGGCCTGCTACCTCATCACCACGCCGCAGGGGCATATACTCATTAATGCTGCGCTGGCCGGCACGGTAGACCAGGTCAAGGCTAATGTGGAAGCGCTGGGATTTAAGTTCAGCGATATCAAGATACTGCTCATCTCGCAGGCGCACTTTGATCATGTGGGCGGCCTTGCAGCCATACAGAAGATGACAGGCGCCAAAGTGATGATAGACGATCAGGATGCGCCGGTGGTGGAAGATGGCGGCAATTCAGACTATATCTATGGCGGCAAGGGTGTAGGCAGCCTGTTCGCGCCCGTGCATGTAGACCGCAAGCTGCACGACCATGATAACATAACCCTCGGCGGTACGCAGTTGGAAATGCTGCATCATCCCGGCCATACCAAAGGTTCATGCAGCTACCTGCTCACCGTAAAGGATGAGCACCGCAGCTATCGTGTGCTGATAGCGAATATACCTTACATGCTGTCTGAGGTTACGTTGCCGGGCATGCCCACATATCCCAATGTCGGTAAAGACTTTATGTATACCTATGGCGCTATGAGGAAGCTGCAGTTTGATATATGGGTAGCTGCGCACTCCAGCCAGTTTGGCCTGCAAGACGTGCGCAAAGAGACCGACGGCTACAACCCCGGTGCATTTGGCGACAAAAAGAAATACTTAACCACCATCGACAAGACGGAGGATATATATAAGGAGCACTTTAAGGGAGGGAAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39086","NCBI_taxonomy_name":"uncultured bacterium BLR17","NCBI_taxonomy_id":"506517"}}}},"ARO_accession":"3002512","ARO_id":"38912","ARO_name":"LRA-17","CARD_short_name":"LRA-17","ARO_description":"LRA-17 is a beta-lactamase isolated from soil samples in Alaska.","ARO_category":{"41390":{"category_aro_accession":"3004226","category_aro_cvterm_id":"41390","category_aro_name":"subclass B3 LRA beta-lactamase","category_aro_description":"Beta-lactamases that are part of the LRA gene family and are classified as B3 (metallo-) beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"884":{"model_id":"884","model_name":"CTX-M-99","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1108":{"protein_sequence":{"accession":"ADL27532.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTESTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAERRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"HM803271.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAATCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGACTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGCGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001958","ARO_id":"38358","ARO_name":"CTX-M-99","CARD_short_name":"CTX-M-99","ARO_description":"CTX-M-99 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"885":{"model_id":"885","model_name":"TEM-63","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1161":{"protein_sequence":{"accession":"AAK17194.1","sequence":"MSIQHFRVALIPFFAAFCFPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVKYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDSWEPELNEAIPNDERDTTTPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AF332513.1","fmin":"103","fmax":"964","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCTTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTAAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATAGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGACGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGGCCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000931","ARO_id":"37311","ARO_name":"TEM-63","CARD_short_name":"TEM-63","ARO_description":"TEM-63 is an extended-spectrum beta-lactamase found in E. coli.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"886":{"model_id":"886","model_name":"IND-10","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1672":{"protein_sequence":{"accession":"ADA13241.1","sequence":"MKKSIQFFIVSMLLSPFANAQVKDFVIEPPIKSNLYIYKTFGVFGGKEYSANAAYLKTKKGVILFDVPWEKVQYQSLMDTIKKRHNLPVIAVFATHSHDDRAGDLSFFNNKGIKKYATLKTNEFLKKDGKATSTEIIQTGKPYHIGGEEFVVDFLGEGHTADNVVVWFPKYNVLDGGCLVKSNSATDLGYIKEANVEQWPKTMNKLKTKYSKATLIIPGHDEWKGGGHVEHTLELLNKK"},"dna_sequence":{"accession":"GU206353.1","fmin":"18","fmax":"738","strand":"+","sequence":"ATGAAAAAAAGCATTCAATTTTTTATTGTTTCCATGTTGTTGAGCCCTTTTGCCAATGCACAGGTAAAAGATTTTGTAATTGAGCCACCTATTAAATCCAATCTATATATTTACAAGACTTTTGGAGTATTCGGAGGTAAAGAATATTCTGCCAATGCAGCCTATCTTAAGACTAAAAAAGGTGTAATTCTGTTTGATGTACCCTGGGAAAAAGTACAGTATCAAAGCCTGATGGATACCATCAAAAAACGTCATAACTTACCGGTAATTGCCGTATTTGCTACGCATTCCCATGATGACCGTGCAGGAGACTTAAGCTTTTTCAATAATAAAGGCATTAAGAAGTATGCTACCCTGAAAACCAATGAGTTTCTGAAGAAAGATGGAAAAGCAACATCCACAGAGATCATCCAAACCGGAAAACCTTATCACATTGGCGGAGAAGAATTTGTGGTCGATTTTCTTGGTGAAGGACATACTGCTGATAATGTAGTGGTATGGTTTCCAAAATATAATGTTTTGGATGGCGGATGTCTTGTAAAAAGTAATTCTGCTACTGACTTAGGATACATTAAAGAAGCCAATGTAGAACAATGGCCCAAGACGATGAATAAATTAAAAACCAAATATTCAAAAGCCACATTAATTATTCCCGGGCATGATGAATGGAAAGGGGGTGGACATGTTGAACACACTTTAGAGCTTTTGAACAAAAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36916","NCBI_taxonomy_name":"Chryseobacterium indologenes","NCBI_taxonomy_id":"253"}}}},"ARO_accession":"3002266","ARO_id":"38666","ARO_name":"IND-10","CARD_short_name":"IND-10","ARO_description":"IND-10 is a beta-lactamase found in Escherichia coli.","ARO_category":{"36199":{"category_aro_accession":"3000060","category_aro_cvterm_id":"36199","category_aro_name":"IND beta-lactamase","category_aro_description":"IND beta-lactamases are class B carbapenem-hydrolyzing beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"887":{"model_id":"887","model_name":"SHV-33","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1148":{"protein_sequence":{"accession":"AFN82060.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLSAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"JX268631.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGTCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001091","ARO_id":"37471","ARO_name":"SHV-33","CARD_short_name":"SHV-33","ARO_description":"SHV-33 is an broad-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"888":{"model_id":"888","model_name":"Erm(36)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"197":{"protein_sequence":{"accession":"AAL68827.1","sequence":"MPTYRGGRHEHGQNFLTDHTTIDRLSRLVGDSTGPIVEIGPGQGRLTRELQKLGRSLTAVEIDSRLADRLASASQFREQKHVTVVNADFLHWPLPTTPYVVVGNVPFHLTTAILRRLLHDGAWTQVVLLVQWEVARRRAGIGGSSMMTAQWWPWIDFSLHGRVPRSAFKPAPSVDGGLLEMTRRPDPLLSPDARESYRQFVHDVFTSRGRGIGEILANVSSSLGKRGALQLLKSEGIRSSSLPKDLSAEQWARLFTSASPTKSAKTGRNAHPAHSARRQGR"},"dna_sequence":{"accession":"AF462611.1","fmin":"0","fmax":"846","strand":"+","sequence":"ATGCCCACTTACCGTGGCGGCCGACATGAGCACGGCCAGAACTTCCTCACTGACCACACCACGATCGACCGGCTCTCACGGCTGGTAGGCGACTCGACCGGTCCGATCGTCGAGATCGGCCCGGGCCAGGGCAGGCTCACAAGAGAGCTGCAGAAGCTCGGCCGGTCCCTGACTGCTGTCGAGATCGACAGCCGGCTGGCGGACCGACTTGCATCGGCCAGTCAGTTCCGCGAGCAGAAACACGTAACCGTCGTCAACGCAGACTTCCTTCACTGGCCGCTACCGACCACTCCGTATGTGGTGGTCGGCAACGTTCCGTTCCACCTGACCACAGCCATCCTGCGCAGACTGCTGCACGATGGAGCATGGACCCAGGTGGTCCTGCTCGTGCAGTGGGAAGTGGCCCGCCGGCGTGCCGGCATCGGTGGTAGCAGCATGATGACCGCGCAGTGGTGGCCTTGGATCGACTTCAGCTTGCACGGGCGCGTGCCCCGGTCGGCGTTCAAGCCAGCCCCGAGCGTGGACGGTGGCCTCTTGGAGATGACTCGTCGTCCGGACCCATTGCTCAGCCCAGACGCGAGAGAGTCCTACCGACAGTTCGTCCATGACGTTTTCACCAGTAGGGGCAGGGGTATCGGCGAGATCCTGGCTAACGTATCCAGCTCACTCGGAAAGCGGGGAGCGCTCCAGTTGTTGAAGAGCGAGGGGATTCGCTCCTCGTCCCTGCCCAAAGATCTCTCAGCGGAGCAGTGGGCTCGCCTCTTTACCAGCGCGTCGCCTACGAAGAGTGCCAAAACCGGAAGGAACGCACACCCCGCCCACTCCGCACGGCGGCAAGGTCGATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36878","NCBI_taxonomy_name":"Micrococcus luteus","NCBI_taxonomy_id":"1270"}}}},"ARO_accession":"3000605","ARO_id":"36744","ARO_name":"Erm(36)","CARD_short_name":"Erm(36)","ARO_description":"ErmD confers MLSb phenotype.","ARO_category":{"36699":{"category_aro_accession":"3000560","category_aro_cvterm_id":"36699","category_aro_name":"Erm 23S ribosomal RNA methyltransferase","category_aro_description":"Erm proteins are part of the RNA methyltransferase family and methylate A2058 (E. coli nomenclature) of the 23S ribosomal RNA conferring degrees of resistance to Macrolides, Lincosamides and Streptogramin b. This is called the MLSb phenotype.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35946":{"category_aro_accession":"0000027","category_aro_cvterm_id":"35946","category_aro_name":"roxithromycin","category_aro_description":"Roxithromycin is a semi-synthetic, 14-carbon ring macrolide antibiotic derived from erythromycin. It is used to treat respiratory tract, urinary and soft tissue infections. Roxithromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35974":{"category_aro_accession":"0000057","category_aro_cvterm_id":"35974","category_aro_name":"telithromycin","category_aro_description":"Telithromycin is a semi-synthetic derivative of erythromycin. It is a 14-membered macrolide and is the first ketolide antibiotic to be used in clinics. Telithromycin binds the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"35982":{"category_aro_accession":"0000065","category_aro_cvterm_id":"35982","category_aro_name":"clarithromycin","category_aro_description":"Clarithromycin is a methyl derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome and is used to treat pharyngitis, tonsillitis, acute maxillary sinusitis, acute bacterial exacerbation of chronic bronchitis, pneumonia (especially atypical pneumonias associated with Chlamydia pneumoniae or TWAR), and skin structure infections.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"36284":{"category_aro_accession":"3000145","category_aro_cvterm_id":"36284","category_aro_name":"tylosin","category_aro_description":"Tylosin is a 16-membered macrolide, naturally produced by Streptomyces fradiae. It interacts with the bacterial ribosome 50S subunit to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"36295":{"category_aro_accession":"3000156","category_aro_cvterm_id":"36295","category_aro_name":"spiramycin","category_aro_description":"Spiramycin is a 16-membered macrolide and is natural product produced by Streptomyces ambofaciens. It binds to the 50S subunit of bacterial ribosomes and inhibits peptidyl transfer activity to disrupt protein synthesis.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"36315":{"category_aro_accession":"3000176","category_aro_cvterm_id":"36315","category_aro_name":"dirithromycin","category_aro_description":"Dirithromycin is an oxazine derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome to inhibit bacterial protein synthesis.","category_aro_class_name":"Antibiotic"},"36722":{"category_aro_accession":"3000583","category_aro_cvterm_id":"36722","category_aro_name":"pristinamycin IA","category_aro_description":"Pristinamycin IA is a type B streptogramin antibiotic produced by Streptomyces pristinaespiralis. It binds to the P site of the 50S subunit of the bacterial ribosome, preventing the extension of protein chains.","category_aro_class_name":"Antibiotic"},"36723":{"category_aro_accession":"3000584","category_aro_cvterm_id":"36723","category_aro_name":"quinupristin","category_aro_description":"Quinupristin is a type B streptogramin and a semisynthetic derivative of pristinamycin 1A. It is a component of the drug Synercid and interacts with the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"virginiamycin M1","category_aro_description":"Virginiamycin M1 is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37016":{"category_aro_accession":"3000672","category_aro_cvterm_id":"37016","category_aro_name":"madumycin II","category_aro_description":"Madumycin II is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37017":{"category_aro_accession":"3000673","category_aro_cvterm_id":"37017","category_aro_name":"griseoviridin","category_aro_description":"Griseoviridin is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"37019":{"category_aro_accession":"3000675","category_aro_cvterm_id":"37019","category_aro_name":"pristinamycin IB","category_aro_description":"Pristinamycin IB is a class B streptogramin similar to pristinamycin IA, the former containing a N-methyl-4-(methylamino)phenylalanine instead of a N-methyl-4-(dimethylamino)phenylalanine in its class A streptogramin counterpart (one less methyl group).","category_aro_class_name":"Antibiotic"},"37021":{"category_aro_accession":"3000677","category_aro_cvterm_id":"37021","category_aro_name":"virginiamycin S2","category_aro_description":"Virginiamycin S2 is a streptogramin B antibiotic.","category_aro_class_name":"Antibiotic"},"37022":{"category_aro_accession":"3000678","category_aro_cvterm_id":"37022","category_aro_name":"pristinamycin IC","category_aro_description":"Pristinamycin IC is a class B streptogramin derived from virginiamycin S1.","category_aro_class_name":"Antibiotic"},"37023":{"category_aro_accession":"3000679","category_aro_cvterm_id":"37023","category_aro_name":"vernamycin C","category_aro_description":"Vernamycin C is a streptogramin B antibiotic.","category_aro_class_name":"Antibiotic"},"37024":{"category_aro_accession":"3000680","category_aro_cvterm_id":"37024","category_aro_name":"patricin A","category_aro_description":"Patricin A is a streptogramin B antibiotic.","category_aro_class_name":"Antibiotic"},"37025":{"category_aro_accession":"3000681","category_aro_cvterm_id":"37025","category_aro_name":"patricin B","category_aro_description":"Patricin B is a streptogramin B antibiotic.","category_aro_class_name":"Antibiotic"},"37026":{"category_aro_accession":"3000682","category_aro_cvterm_id":"37026","category_aro_name":"ostreogrycin B3","category_aro_description":"Ostreogrycin B3 is a derivative of pristinamycin IA, with an additional 3-hydroxy group on its 4-oxopipecolic acid.","category_aro_class_name":"Antibiotic"},"37247":{"category_aro_accession":"3000867","category_aro_cvterm_id":"37247","category_aro_name":"oleandomycin","category_aro_description":"Oleandomycin is a 14-membered macrolide produced by Streptomyces antibioticus. It is ssimilar to erythromycin, and contains a desosamine amino sugar and an oleandrose sugar. It targets the 50S ribosomal subunit to prevent protein synthesis.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35952":{"category_aro_accession":"0000034","category_aro_cvterm_id":"35952","category_aro_name":"streptogramin A antibiotic","category_aro_description":"Streptogramin A antibiotics are cyclic polyketide peptide hybrids that bind to the ribosomal peptidyl transfer centre. Structural variation arises from substituting a proline for its desaturated derivative and by its substitution for Ala or Cys. Used alone, streptogramin A antibiotics are bacteriostatic, but is bactericidal when used with streptogramin B antibiotics.","category_aro_class_name":"Drug Class"},"35967":{"category_aro_accession":"0000050","category_aro_cvterm_id":"35967","category_aro_name":"streptogramin B antibiotic","category_aro_description":"Streptogramin B antibiotics are are cyclic hepta- or hexa-depsipeptides.  Type B streptogramins block the peptide exit tunnel of the 50S bacterial ribosome. The general composition of group B streptogramins is 3-hydroxypicolinic acid-L-Thr-D-aminobutyric acid (or D-Ala)-L-Pro-L-Phe (or 4-N-,N-(dimethylamino)-L-Phe)-X-L-phenylglycine. Used alone, streptogramin B antibiotics are bacteriostatic, but is bactericidal when used with streptogramin A antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"889":{"model_id":"889","model_name":"CMY-74","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1509":{"protein_sequence":{"accession":"AFU25632.1","sequence":"MMKKSICCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAIIYQGKPYYFTWGKADIANNRPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTHYWPELTGKQWQGISLLHLATYTAGGLPLQVPDDVTDKAALLRFYQNWQPQWAPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTKRVLHPLKLAHTWITVPQSEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMTRWVQANMDASQVQEKTLQQGIELAQSRYWRVGDMYQGLGWEMLNWPVKADSIISGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"JX440349.1","fmin":"1026","fmax":"2172","strand":"+","sequence":"ATGATGAAAAAATCGATATGCTGCGCGCTGCTGCTGACAGCTTCTTTCTCCACGTTTGCCGCCGCCAAAACAGAACAACAAATTGCCGATATCGTTAACCGCACCATCACACCGCTGATGCAGGAGCAGGCAATTCCGGGCATGGCCGTTGCGATTATCTATCAGGGGAAACCTTATTACTTTACCTGGGGTAAAGCCGATATCGCCAATAACCGTCCAGTCACTCAACAAACGCTGTTTGAACTCGGATCGGTCAGTAAAACGTTCAACGGCGTGCTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGCATTACTGGCCTGAACTGACTGGTAAGCAGTGGCAGGGTATCAGCCTGCTGCACTTAGCCACCTACACGGCAGGCGGCCTGCCGCTTCAGGTTCCGGACGACGTTACGGATAAAGCCGCGTTACTACGCTTTTATCAAAACTGGCAGCCGCAATGGGCCCCAGGCGCTAAACGTCTTTATGCTAACTCCAGCATTGGTCTGTTTGGCGCCCTGGCGGTGAAACCCTCAGGCATGAGCTACGAAGAGGCGATGACCAAACGCGTCCTGCACCCCTTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAGCGAACAAAAAGATTATGCCTGGGGTTATCGCGAAGGAAAGCCAGTGCATGTATCCCCTGGCCAACTTGATGCCGAAGCCTACGGGGTGAAATCGAGCGTTATCGATATGACCCGTTGGGTTCAGGCCAACATGGACGCCAGCCAGGTTCAGGAGAAAACGCTCCAGCAGGGCATCGAGCTTGCGCAGTCACGTTACTGGCGTGTTGGCGATATGTACCAGGGCCTGGGCTGGGAGATGCTGAACTGGCCGGTGAAAGCCGACTCGATAATTAGCGGTAGCGACAGCAAAGTGGCACTGGCAGCGCTTCCTGCCGTTGAGGTAAACCCGCCCGCGCCTGCCGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGCGGATTCGGCAGCTACGTTGCTTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAATAAGAGCTACCCAAACCCTGTTCGCGTCGAGGCCGCCTGGCGCATTCTTGAAAAACTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39584","NCBI_taxonomy_name":"Citrobacter braakii","NCBI_taxonomy_id":"57706"}}}},"ARO_accession":"3002087","ARO_id":"38487","ARO_name":"CMY-74","CARD_short_name":"CMY-74","ARO_description":"CMY-74 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"890":{"model_id":"890","model_name":"SHV-53","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"8428":{"protein_sequence":{"accession":"AAT01223.1","sequence":"IISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLISQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNN"},"dna_sequence":{"accession":"AY590467.1","fmin":"1","fmax":"727","strand":"+","sequence":"ATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGATCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGCATTGTCGCCCTGCTTGGCCCGAATAAC","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001110","ARO_id":"37490","ARO_name":"SHV-53","CARD_short_name":"SHV-53","ARO_description":"SHV-53 is a beta-lactamase that has been found in clinical isolates.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"891":{"model_id":"891","model_name":"QnrB37","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"679":{"protein_sequence":{"accession":"AEL00459.1","sequence":"MTLALVGEKIDRNRFTGEKVENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAILKDAIFKSCDLSMADFRNVSALGIEIRHCRAQGSDFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGTQVLGATFSGSDLSGGEFSSFDWRAANVTHCDLTNSELGDLDVRGVDLQGVKLDSYQASLILERLGIAVIG"},"dna_sequence":{"accession":"JN173059.1","fmin":"35","fmax":"680","strand":"+","sequence":"ATGACTCTTGCGTTAGTTGGCGAAAAAATTGACAGAAACAGGTTCACCGGTGAGAAAGTCGAAAATAGCACATTTTTCAACTGTGATTTTTCGGGTGCCGACCTTAGCGGTACTGAGTTTATTGGCTGCCAATTTTATGATCGAGAGAGCCAGAAAGGGTGTAATTTTAGCCGCGCTATCCTGAAAGATGCCATTTTCAAAAGTTGCGATCTCTCCATGGCGGATTTCAGGAATGTGAGTGCGCTGGGAATCGAAATTCGCCACTGCCGCGCACAAGGTTCAGATTTTCGCGGCGCAAGCTTTATGAATATGATTACCACACGCACCTGGTTTTGTAGCGCCTATATCACCAATACCAACTTAAGCTACGCCAACTTTTCAAAAGTCGTACTGGAAAAGTGCGAGCTGTGGGAAAACCGCTGGATGGGAACTCAGGTACTGGGGGCGACGTTCAGTGGTTCAGATCTTTCCGGCGGTGAGTTTTCGTCGTTCGACTGGCGAGCCGCAAACGTTACGCACTGTGATTTGACCAATTCAGAACTGGGCGATCTCGATGTCCGGGGTGTTGATTTGCAAGGAGTCAAACTGGACAGCTACCAGGCATCGTTGATCCTGGAACGTCTTGGCATCGCTGTCATTGGTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002752","ARO_id":"39186","ARO_name":"QnrB37","CARD_short_name":"QnrB37","ARO_description":"QnrB37 is a plasmid-mediated quinolone resistance protein found in Citrobacter freundii.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"892":{"model_id":"892","model_name":"APH(6)-Ic","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"404":{"protein_sequence":{"accession":"CAA25854.1","sequence":"MERWRLLRDGELLTTHSSWILPVRQGDMPAMLKVARIPDEEAGYRLLTWWDGQGAARVFASAAGALLMERASGAGDLAQIAWSGQDDEACRILCDTAARLHAPRSGPPPDLHPLQEWFQPLFRLAAEHAALAPAASVARQLLAAPREVCPLHGDLHHENVLDFGDRGWLAIDPHGLLGERTFDYANIFTNPDLSDPGRPLAILPGRLEARLSIVVATTGFEPERLLRWIIAWTGLSAAWFIGDGDGEGEGAAIDLAVNAMARRLLD"},"dna_sequence":{"accession":"X01702.1","fmin":"484","fmax":"1285","strand":"+","sequence":"ATGGAGCGCTGGCGCCTGCTGCGCGACGGCGAGCTGCTCACCACCCACTCGAGCTGGATACTTCCCGTCCGCCAGGGGGACATGCCGGCGATGCTGAAGGTCGCGCGCATTCCCGATGAAGAGGCCGGTTACCGCCTGTTGACCTGGTGGGACGGGCAGGGCGCCGCCCGAGTCTTCGCCTCGGCGGCGGGCGCTCTGCTCATGGAGCGCGCGTCCGGGGCCGGGGACCTTGCACAGATAGCGTGGTCCGGCCAGGACGACGAGGCTTGCAGGATCCTCTGCGACACCGCCGCTCGTCTGCACGCGCCGCGGTCCGGACCGCCGCCCGATCTCCATCCGCTACAGGAATGGTTCCAGCCGCTTTTCCGGTTGGCCGCTGAGCACGCGGCACTTGCGCCCGCCGCCAGCGTAGCGCGCCAACTTCTGGCGGCGCCGCGCGAGGTGTGCCCGCTCCACGGCGACCTGCACCACGAGAACGTGCTCGACTTCGGCGACCGCGGCTGGCTGGCCATCGACCCGCACGGACTGCTCGGCGAGCGCACCTTCGACTATGCCAACATCTTCACGAATCCCGATCTCAGCGACCCCGGTCGCCCGCTTGCGATCCTGCCGGGCAGGCTGGAGGCTCGACTCAGCATTGTGGTCGCGACGACCGGGTTTGAGCCCGAACGGCTTCTTCGCTGGATCATTGCATGGACGGGCTTGTCGGCAGCCTGGTTCATCGGCGACGGCGACGGCGAGGGCGAGGGCGCTGCGATTGATCTGGCCGTAAACGCCATGGCACGCCGGTTGCTTGACTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002659","ARO_id":"39059","ARO_name":"APH(6)-Ic","CARD_short_name":"APH(6)-Ic","ARO_description":"APH(6)-Ic is a transposon-encoded aminoglycoside phosphotransferase in S. enterica, P. aeruginosa and E. coli.","ARO_category":{"36290":{"category_aro_accession":"3000151","category_aro_cvterm_id":"36290","category_aro_name":"APH(6)","category_aro_description":"A category of aminoglycoside O-phosphotransferase enzymes with modification regiospecificity based at the 6-hydroxyl group of the respective antibiotic. These enzymes are characterized by enzymatic antibiotic inactivation, specifically of streptomycin, by the ATP-dependent phosphorylation of the 6-hydroxyl group of the compound.","category_aro_class_name":"AMR Gene Family"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"894":{"model_id":"894","model_name":"CMY-90","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1444":{"protein_sequence":{"accession":"CCK86743.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAIIYEGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWRGISLLHLATYTAGGLPLQIPGDVTDKAELLRFYQNWQPQWTPGAKRLYANSSIGLFGALAVKSSGMSYEEAMTRRVLQPLKLAHTWITVPQSEQKNYAWGYLEGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIELAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPARVEAAWRILEKLQ"},"dna_sequence":{"accession":"HE819404.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCGCTGCTGCTGACAGCCTCTTTCTCCACGTTTGCTGCCGCAAAAACAGAACAACAAATTGCCGATATCGTTAACCGCACCATCACACCACTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTGGCGATTATCTACGAGGGGAAACCTTATTACTTTACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGACGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCGGGGTATCAGCCTGCTGCACTTAGCCACCTATACAGCGGGTGGCCTGCCGCTGCAGATCCCCGGTGACGTTACGGATAAAGCCGAATTACTGCGCTTTTATCAAAACTGGCAACCACAATGGACTCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGTGCGCTGGCGGTGAAATCTTCAGGTATGAGCTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAAAGCGAACAAAAAAACTATGCCTGGGGCTATCTCGAAGGGAAGCCTGTGCACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATCGATATGGCCCGCTGGGTTCAGGCCAACATGGACGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGAGCTTGCGCAGTCTCGCTACTGGCGTATTGGTGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCAGCACCTGCCGTGAAAGCCTCATGGGTGCATAAAACAGGATCCACAGGCGGATTTGGCAGCTACGTTGCTTTCGTTCCAGAAAAAAACCTTGGCATCGTAATGTTGGCAAACAAAAGCTACCCCAACCCGGCTCGCGTCGAGGCGGCCTGGCGCATTCTTGAAAAACTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002103","ARO_id":"38503","ARO_name":"CMY-90","CARD_short_name":"CMY-90","ARO_description":"CMY-90 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"895":{"model_id":"895","model_name":"SHV-122","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"4356":{"protein_sequence":{"accession":"ADR80609.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDPPGGTELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"HM751103.1","fmin":"0","fmax":"864","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCCGCCTGGGGGAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATCGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001169","ARO_id":"37549","ARO_name":"SHV-122","CARD_short_name":"SHV-122","ARO_description":"SHV-122 is a beta-lactamase that has been found in clinical isolates.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"896":{"model_id":"896","model_name":"CTX-M-131","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4241":{"protein_sequence":{"accession":"AEW46676.3","sequence":"MMTQSIRRSMLTVMATLPLLFSSATLHAQANSVQQQLEALEKSSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKQSESDKHLLNQRVEIKKSDLVNYNPIAEKHVNGTMTLAELGAAALQYSDNTAMNKLIAHLGGPDKVTAFARSLGDETFRLDRTEPTLNTAIPGDPRDTTTPLAMAQTLKNLTLGKALAETQRAQLVTWLKGNTTGSASIRAGLPKSWVVGDKTGSGGYGTTNDIAVIWPENHAPLVLVTYFTQPEQKAESRRDILAAAAKIVTHGF"},"dna_sequence":{"accession":"JN969893.3","fmin":"2530","fmax":"3406","strand":"+","sequence":"ATGATGACTCAGAGCATTCGCCGCTCAATGTTAACGGTGATGGCGACGCTACCCCTGCTATTTAGCAGCGCAACGCTGCATGCGCAGGCGAACAGCGTGCAACAGCAGCTGGAAGCCCTGGAGAAAAGTTCGGGAGGTCGGCTTGGCGTTGCGCTGATTAACACCGCCGATAATTCGCAGATTCTCTACCGTGCCGATGAACGTTTTGCGATGTGCAGTACCAGTAAGGTGATGGCGGCCGCGGCGGTGCTTAAACAGAGCGAGAGCGATAAGCACCTGCTAAATCAGCGCGTTGAAATCAAGAAGAGCGACCTGGTTAACTACAATCCCATTGCGGAGAAACACGTTAACGGCACGATGACGCTGGCTGAGCTTGGCGCAGCGGCGCTGCAGTATAGCGACAATACTGCCATGAATAAGCTGATTGCCCATCTGGGTGGTCCCGATAAAGTGACGGCGTTTGCTCGCTCGTTGGGTGATGAGACCTTCCGTCTGGACAGAACCGAGCCCACGCTCAATACCGCCATTCCAGGCGACCCGCGTGATACCACCACGCCGCTCGCGATGGCGCAGACCCTGAAAAATCTGACGCTGGGTAAAGCGCTGGCGGAAACTCAGCGGGCACAGTTGGTGACGTGGCTTAAGGGCAATACTACCGGTAGCGCGAGCATTCGGGCGGGTCTGCCGAAATCATGGGTAGTGGGCGATAAAACCGGCAGCGGAGGTTATGGCACCACCAACGATATCGCGGTTATCTGGCCGGAAAACCACGCACCGCTGGTTCTGGTGACCTACTTTACCCAACCGGAGCAGAAGGCGGAAAGCCGTCGGGATATTCTGGCTGCGGCGGCGAAAATCGTAACCCACGGTTTCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36944","NCBI_taxonomy_name":"Providencia rettgeri","NCBI_taxonomy_id":"587"}}}},"ARO_accession":"3001990","ARO_id":"38390","ARO_name":"CTX-M-131","CARD_short_name":"CTX-M-131","ARO_description":"CTX-M-131 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"897":{"model_id":"897","model_name":"OXA-383","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4750":{"protein_sequence":{"accession":"AHL30281.1","sequence":"MNIKTLLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEVHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"KF986262.1","fmin":"27","fmax":"852","strand":"-","sequence":"ATGAACATTAAAACACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGTACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001569","ARO_id":"37969","ARO_name":"OXA-383","CARD_short_name":"OXA-383","ARO_description":"OXA-383 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"898":{"model_id":"898","model_name":"VEB-9","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"3589":{"protein_sequence":{"accession":"AAK14293.1","sequence":"MKIVKRILLVLLSLFFTVVYSNAQTDNLTLKIENVLKAKNARIGVAIFNSNEKDTLKINNDFHFPMQSVMKFPIALAVLSEIDKGNLSFEQKIEITPQDLLPKTWSPIKEEFPNGTTLTIEQILNYTVSESDNIGCDILLKLIGGTDSVQKFLNANHFTDISIKANEEQMHKDWNTQYQNWATPTAMNKLLIDTYNNKNQLLSKKSYDFIWKIMRETTTGSNRLKGQLPKNTIVAHKTGTSGINNGIAAATNDVGVITLPNGQLIFISVFVAESKETSEINEKIISDIAKITWNYYLNK"},"dna_sequence":{"accession":"AF324833.1","fmin":"0","fmax":"900","strand":"+","sequence":"ATGAAAATCGTAAAAAGGATATTATTAGTATTGTTAAGTTTATTTTTTACAGTTGTGTATTCAAATGCTCAAACTGACAACTTAACTTTGAAAATTGAGAATGTTTTAAAGGCAAAAAATGCCAGAATAGGAGTAGCAATATTCAACAGCAATGAGAAGGATACTTTGAAGATTAATAACGACTTCCATTTCCCGATGCAAAGCGTTATGAAATTTCCGATTGCTTTAGCCGTTTTGTCTGAGATAGATAAAGGGAATCTTTCTTTTGAACAAAAAATAGAGATTACCCCTCAAGACCTTTTGCCTAAAACGTGGAGTCCGATTAAAGAGGAATTCCCTAATGGAACAACTTTGACGATTGAACAAATACTAAATTATACAGTATCAGAGAGCGACAATATTGGTTGTGATATTTTGCTAAAATTAATCGGAGGAACTGATTCTGTTCAAAAATTCTTGAATGCTAATCATTTCACTGATATTTCAATCAAAGCAAACGAAGAACAAATGCACAAGGATTGGAATACCCAATATCAAAATTGGGCAACCCCAACAGCGATGAACAAACTGTTAATAGATACTTATAATAATAAGAACCAATTACTTTCTAAAAAAAGTTATGATTTTATTTGGAAAATTATGAGAGAAACAACAACAGGAAGTAACCGATTAAAAGGACAATTACCAAAGAATACAATTGTTGCTCATAAAACAGGGACTTCCGGAATAAATAATGGAATTGCAGCAGCCACTAATGATGTTGGGGTAATTACTTTACCGAATGGACAATTAATTTTTATAAGCGTATTTGTTGCAGAGTCCAAAGAAACTTCGGAAATTAATGAAAAGATTATTTCAGACATTGCAAAAATAACGTGGAATTACTATTTGAATAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002378","ARO_id":"38778","ARO_name":"VEB-9","CARD_short_name":"VEB-9","ARO_description":"VEB-9 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36182":{"category_aro_accession":"3000043","category_aro_cvterm_id":"36182","category_aro_name":"VEB beta-lactamase","category_aro_description":"VEB beta-lactamases or Vietnamese extended-spectrum beta-lactamases are class A beta-lactamases that confer high-level resistance to oxyimino cephalosporins and to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"899":{"model_id":"899","model_name":"OXA-94","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1466":{"protein_sequence":{"accession":"ABF47917.1","sequence":"MNIQALLLITSAIFISACSPYIVSANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPHGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"DQ519088.1","fmin":"8","fmax":"833","strand":"+","sequence":"ATGAACATTCAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGTCTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCATGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001629","ARO_id":"38029","ARO_name":"OXA-94","CARD_short_name":"OXA-94","ARO_description":"OXA-94 is a beta-lactamase found in A. baumannii.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"901":{"model_id":"901","model_name":"LCR-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"775":{"protein_sequence":{"accession":"CAA40146.1","sequence":"MLKSTLLAFGLFIALSARAENQAIAKLFLRAGVDGTIVIESLTTGQRLVHNDPRAQQRYPAASTFKVLNTLIALEEGAISGENQIFHWNGTQYSIANWNQDQTLDSAFKVSCVWCYQQIALRVGALKYPAYIQQTNYGHLLEPFNGTEFWLDGSLTISAEEQVAFLRQVVERKLPFKASSYDSLKKVMFADENAQYRLYAKTGWATRMTPSVGWYVGYVEAKDDVWLFALNLATRDANDLPLRTQIAKDALKAIGAFPTK"},"dna_sequence":{"accession":"X56809.1","fmin":"111","fmax":"894","strand":"+","sequence":"ATGCTAAAGAGCACCCTTCTGGCCTTTGGTCTCTTTATTGCGCTCTCAGCGCGTGCAGAGAACCAGGCAATCGCCAAGCTTTTCCTGAGGGCAGGGGTCGATGGGACCATCGTCATCGAGTCTCTAACCACCGGACAGCGCTTGGTTCACAACGATCCTCGTGCGCAACAACGATACCCGGCAGCTTCCACGTTCAAGGTACTCAATACCTTGATTGCTCTCGAAGAGGGCGCCATTTCAGGTGAGAACCAGATCTTTCACTGGAACGGTACCCAGTATTCGATTGCGAATTGGAACCAGGACCAGACTCTAGACAGTGCGTTTAAAGTGAGTTGTGTCTGGTGCTACCAGCAGATTGCCCTTCGAGTGGGGGCACTCAAGTACCCAGCCTATATTCAACAGACAAACTATGGTCATTTACTGGAACCCTTCAATGGAACGGAGTTTTGGCTGGATGGCTCTTTGACGATCAGCGCGGAAGAACAGGTTGCCTTTCTCCGACAGGTTGTTGAGCGAAAACTACCGTTCAAGGCGAGCAGCTATGATTCCCTGAAGAAAGTCATGTTCGCCGATGAGAATGCCCAGTATCGCCTTTATGCAAAAACAGGTTGGGCGACCCGCATGACTCCCTCGGTGGGTTGGTATGTTGGCTATGTTGAAGCAAAGGACGATGTTTGGCTGTTTGCCCTGAATCTTGCTACCCGCGACGCGAATGACCTGCCCCTACGAACGCAGATAGCCAAAGACGCGCTGAAGGCGATAGGTGCGTTTCCTACGAAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002997","ARO_id":"39431","ARO_name":"LCR-1","CARD_short_name":"LCR-1","ARO_description":"LCR-1 is a class D beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"39430":{"category_aro_accession":"3002996","category_aro_cvterm_id":"39430","category_aro_name":"LCR beta-lactamase","category_aro_description":"LCR beta-lactamases are a class D beta-lactamase that hydrolyze a variety of penams and some cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"902":{"model_id":"902","model_name":"OXA-92","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1427":{"protein_sequence":{"accession":"ABC61637.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDDKAEKIKNLFNEAHTTGVLVIHQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGEKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGSVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"DQ335566.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGACAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCATCAAGGTCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAATGGGATGGGGAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTCTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATCGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001632","ARO_id":"38032","ARO_name":"OXA-92","CARD_short_name":"OXA-92","ARO_description":"OXA-92 is a beta-lactamase found in A. baumannii.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"903":{"model_id":"903","model_name":"APH(2'')-Ig","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"4749":{"protein_sequence":{"accession":"AGV10818.1","sequence":"MCEFSSPQIPITDIENAMERIGSPVRELRRLDAGDDSEVLLCNGLFVIKIPKRPSVRVTQQREFAVYSFLKQYDLPALIPEVIFQCSEFNVMSFIPGENFGFQEYALLSEKEKEALASDMAIFLRRLHGISVPLSEKPFCEIFEDKRKRYLEDQEQLLEVLENRKLLNAPLQKNIQTIYEHIGQNQELFNYAACLVHNDFSSSNMVFRHNRLYGVIDFGDVIVGDPDNDFLCLLDCSMDDFGKDFGRKVLRHYGHRNPQLAERKAEINDAYWPIQQVLLGVQREDRSLFCKGYRELLAIDPDAFIL"},"dna_sequence":{"accession":"CP004067.1","fmin":"43007","fmax":"43928","strand":"-","sequence":"ATGTGTGAATTTAGTAGTCCGCAAATTCCAATAACGGATATTGAGAATGCCATGGAACGGATCGGAAGTCCGGTGAGAGAACTCCGCCGCTTGGATGCGGGGGATGACAGCGAAGTGCTGCTTTGCAATGGGCTGTTTGTCATCAAAATCCCCAAACGGCCATCTGTGCGCGTGACACAGCAAAGAGAATTTGCAGTATACTCCTTTCTCAAACAGTATGATTTACCTGCCTTGATTCCGGAAGTGATTTTTCAATGCAGCGAATTTAATGTTATGTCGTTTATCCCCGGAGAAAACTTTGGCTTTCAAGAATATGCTTTGCTTTCAGAAAAGGAAAAAGAAGCGCTTGCTTCAGATATGGCGATATTTTTGCGGAGATTGCATGGTATATCGGTGCCGCTTTCAGAGAAACCGTTCTGTGAAATCTTCGAAGATAAACGCAAAAGATATTTGGAAGACCAAGAACAGCTGCTTGAAGTGCTCGAAAACCGAAAACTCTTGAATGCACCACTCCAGAAAAATATCCAGACGATATACGAGCATATCGGTCAGAATCAGGAACTGTTTAACTATGCGGCCTGTTTAGTTCACAATGATTTTAGCTCTTCCAATATGGTGTTCAGACATAATCGTCTGTATGGCGTGATCGATTTTGGAGATGTAATTGTCGGCGATCCGGACAATGATTTTTTATGCCTTCTGGATTGCAGCATGGATGACTTTGGGAAAGATTTCGGGCGAAAGGTTTTAAGGCATTATGGCCATCGGAATCCACAATTAGCAGAAAGAAAAGCAGAAATCAATGATGCTTACTGGCCGATACAGCAAGTCCTGCTTGGTGTTCAGAGAGAAGATCGGTCGCTTTTCTGTAAGGGATACCGTGAACTTCTAGCCATAGACCCAGATGCTTTCATTTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39528","NCBI_taxonomy_name":"Campylobacter coli CVM N29710","NCBI_taxonomy_id":"1273173"}}}},"ARO_accession":"3002669","ARO_id":"39069","ARO_name":"APH(2'')-Ig","CARD_short_name":"APH(2'')-Ig","ARO_description":"APH('')-Ig is a plasmid-encoded aminoglycoside phosphotransferase in Campylobacter coli.","ARO_category":{"36267":{"category_aro_accession":"3000128","category_aro_cvterm_id":"36267","category_aro_name":"APH(2'')","category_aro_description":"A category of aminoglycoside O-phosphotransferase enzymes with modification regiospecificity based at the 2''-hydroxyl group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics, specifically kanamycin, tobramycin and amikacin, by the ATP-dependent phosphorylation of the 3'-hydroxyl group of the compound.","category_aro_class_name":"AMR Gene Family"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"40942":{"category_aro_accession":"3004015","category_aro_cvterm_id":"40942","category_aro_name":"gentamicin A","category_aro_description":"Gentamicin A is part of a complex of broad spectrum aminoglycoside antibiotics. Gentamicin inhibits protein synthesis, resulting in bacterial cell death.","category_aro_class_name":"Antibiotic"},"46133":{"category_aro_accession":"3007382","category_aro_cvterm_id":"46133","category_aro_name":"gentamicin","category_aro_description":"Gentamicin is a commonly used aminoglycoside antibiotic derived from members of the Micromonospora genus of bacteria. It acts by binding the 30S ribosomal subunit, thus inhibiting protein synthesis. Gentamicin is typically used to treat Gram-negative infections of the repiratory and urinary tract, as well as infections of the bone and soft tissue. It also exhibits considerable nephrotoxicity and ototoxicity. Gentamicin is administered as a mixture of gentamicin type C (which makes about around 80% of the complex) and types A, B, and X (distributed in the remaining 20% of the complex).","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"904":{"model_id":"904","model_name":"rmtB","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"5521":{"protein_sequence":{"accession":"CAP07796.1","sequence":"MNINDALTSILASKKYRALCPDTVRRILTEEWGRHKSPKQTVEAARTRLHGICGAYVTPESLKAAAAALSAGDVKKALSLHASTKERLAELDTLYDFIFSAETPRRVLDIACGLNPLALYERGIASVWGCDIHQGLGDVITPFAREKDWDFTFALQDVLCAPPAEAGDLALIFKLLPLLEREQAGSAMALLQSLNTPRMAVSFPTRSLGGRGKGMEANYAAWFEGGLPAEFEIEDKKTIGTELIYLIKKNG"},"dna_sequence":{"accession":"AM886293.1","fmin":"116479","fmax":"117235","strand":"+","sequence":"ATGAACATCAACGATGCCCTCACCTCCATCCTGGCCTCAAAAAAATACCGCGCCCTTTGCCCGGATACCGTGCGGCGCATCCTGACTGAGGAATGGGGGCGGCATAAATCCCCCAAACAGACCGTAGAGGCTGCACGCACCCGGCTGCATGGAATTTGCGGGGCATATGTCACCCCGGAATCGCTCAAGGCTGCTGCCGCCGCGCTTTCTGCGGGCGATGTAAAAAAGGCATTGTCGCTGCATGCCTCCACCAAGGAGCGACTGGCCGAGCTGGATACCCTGTACGATTTTATCTTTTCAGCCGAAACTCCCCGCCGCGTGCTGGATATCGCCTGCGGTCTTAACCCCTTGGCGCTATACGAGCGCGGCATTGCATCCGTGTGGGGCTGTGATATCCACCAGGGATTGGGGGATGTCATCACCCCCTTTGCTAGGGAAAAAGATTGGGATTTTACCTTTGCCCTGCAGGATGTGCTGTGTGCGCCGCCCGCCGAAGCCGGCGACCTGGCGCTGATTTTTAAGCTTTTGCCCCTGCTGGAGCGGGAGCAGGCCGGTTCTGCCATGGCACTTTTACAATCCCTCAATACCCCGCGCATGGCTGTCAGCTTTCCCACGCGTAGTTTAGGCGGGCGTGGAAAAGGCATGGAGGCGAACTACGCCGCATGGTTCGAGGGCGGCTTGCCCGCCGAGTTTGAGATTGAGGATAAAAAGACCATCGGAACAGAACTTATATACTTGATAAAAAAGAATGGATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000860","ARO_id":"37240","ARO_name":"rmtB","CARD_short_name":"rmtB","ARO_description":"RmtB is a 16S rRNA methyltransferase that targets mature or nearly mature 30S subunits. It transfers a methyl group from S-adenosyl-L-methionine to N7-G1405 of the 16S rRNA, an aminoglycoside binding site.","ARO_category":{"41435":{"category_aro_accession":"3004271","category_aro_cvterm_id":"41435","category_aro_name":"16S rRNA methyltransferase (G1405)","category_aro_description":"Methyltransferases that methylate the G1405 position of 16S rRNA, which is part of an aminoglycoside binding site.","category_aro_class_name":"AMR Gene Family"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36997":{"category_aro_accession":"3000653","category_aro_cvterm_id":"36997","category_aro_name":"G418","category_aro_description":"A gentamicin class aminoglycoside antibiotic often used in mammalian cell culture work as a selectable marker for the neo cassette (APH3').","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"46133":{"category_aro_accession":"3007382","category_aro_cvterm_id":"46133","category_aro_name":"gentamicin","category_aro_description":"Gentamicin is a commonly used aminoglycoside antibiotic derived from members of the Micromonospora genus of bacteria. It acts by binding the 30S ribosomal subunit, thus inhibiting protein synthesis. Gentamicin is typically used to treat Gram-negative infections of the repiratory and urinary tract, as well as infections of the bone and soft tissue. It also exhibits considerable nephrotoxicity and ototoxicity. Gentamicin is administered as a mixture of gentamicin type C (which makes about around 80% of the complex) and types A, B, and X (distributed in the remaining 20% of the complex).","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"905":{"model_id":"905","model_name":"CTX-M-93","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"2045":{"protein_sequence":{"accession":"ADN26580.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTQNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGGYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"HQ166709.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCAGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGGCTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001953","ARO_id":"38353","ARO_name":"CTX-M-93","CARD_short_name":"CTX-M-93","ARO_description":"CTX-M-93 is a beta-lactamase found in Escherichia coli.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"906":{"model_id":"906","model_name":"CARB-21","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1264":{"protein_sequence":{"accession":"AGQ93789.1","sequence":"MVRVFTRYSLLNIAKVRIKTKRTKNTRMKKLFLLVGLMVCSTVSYASKLNEDISLIEKQTSGRIGVSVWDTQMDERWDYRGDERFPLMSTFKTLACATMLSDMDSGKLNKNATARIDERNIVVWSPVMDKLAGQSTRIEHACEAAMLMSDNTAANLVLNEIGGPKAVTLFLRSIGDKATRLDRLEPRLNEAKPGDKRDTTTPNAMVNTLHTLMEDNALSYESRTQLKIWMQDNKVSDSLMRSVLPKGWSIADRSGAGNYGSRGISAMIWKDNYKPVYISIYVTDTDLSLQARDQLIAQISQLILEHYKES"},"dna_sequence":{"accession":"CP006005.1","fmin":"1728735","fmax":"1729668","strand":"+","sequence":"GTGGTTAGAGTATTCACTCGTTATAGTTTGCTTAACATCGCCAAAGTGCGAATCAAAACCAAAAGAACGAAGAACACACGCATGAAAAAGTTATTCCTGTTGGTTGGGCTGATGGTTTGCTCAACTGTTAGTTACGCTTCCAAATTAAACGAAGACATCTCCCTCATCGAGAAACAAACATCTGGGCGAATTGGAGTGTCAGTCTGGGATACACAAATGGACGAGCGTTGGGATTATCGCGGAGACGAACGTTTCCCATTAATGAGCACATTCAAAACGTTAGCGTGTGCCACCATGCTAAGCGACATGGACAGCGGCAAACTCAACAAAAATGCCACAGCGAGAATCGATGAACGCAATATTGTGGTTTGGTCTCCGGTGATGGATAAACTGGCTGGACAAAGCACGCGTATCGAACACGCTTGTGAAGCCGCCATGTTGATGAGCGACAACACCGCCGCAAACTTAGTGCTAAATGAAATTGGTGGTCCTAAAGCGGTCACGCTGTTTTTGCGCTCTATTGGCGACAAAGCAACGCGACTTGACCGATTGGAGCCCCGTTTGAACGAAGCAAAACCGGGCGACAAGCGAGACACCACAACGCCTAACGCCATGGTAAACACCCTACACACCTTGATGGAAGATAACGCCCTATCTTACGAGTCACGCACACAGCTGAAAATCTGGATGCAAGACAACAAAGTATCGGATTCTCTCATGCGCTCTGTTCTACCAAAAGGCTGGTCGATTGCAGACCGCTCTGGCGCAGGTAACTACGGTTCACGCGGCATTAGCGCGATGATTTGGAAAGACAACTACAAGCCGGTTTACATCAGTATTTACGTCACAGATACTGACCTTTCGCTTCAAGCTCGCGATCAACTGATCGCGCAAATCAGCCAACTGATTTTAGAGCACTACAAAGAAAGTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39775","NCBI_taxonomy_name":"Vibrio parahaemolyticus O1:Kuk str. FDA_R31","NCBI_taxonomy_id":"1338034"}}}},"ARO_accession":"3003176","ARO_id":"39753","ARO_name":"CARB-21","CARD_short_name":"CARB-21","ARO_description":"CARB-21 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36230":{"category_aro_accession":"3000091","category_aro_cvterm_id":"36230","category_aro_name":"CARB beta-lactamase","category_aro_description":"CARB beta-lactamases are class A lactamases that can hydrolyze carbenicillin. Many of the PSE beta-lactamases have been renamed as CARB-lactamases with the notable exception of PSE-2 which is now OXA-10.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"907":{"model_id":"907","model_name":"fexA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"490":{"protein_sequence":{"accession":"CAD70268.1","sequence":"MKKDSKSKEMIQSEKRGSTRLLMMVLSLSVLVGAITADLVNPVLPLISKDLEASKSQVSWIVSGIALVLAIGVPIYGRISDFFELRKLYIFAIMILASGSLLCAIAPNLPLLVLGRMVQGAGMSAIPVLSIIAISKVFPQGKRGGALGIIAGSIGVGTAAGPIFGGVVGQYLGWNALFWFTFLLAIMIVIGAYYALPTIKPAESVGSNKNFDFIGGLFLGLTVGLLLFGITQGETSGFSSFSSLTSLIGSVVALVGFIWRIVTAENPFVPPVLFNNKDYVNTVIIAFFSMFAYFAVLVFVPLLVVEVNGLSSGQAGMILLPGGVAVAILSPFVGRLSDRFGDKRLIITGMTLMGLSTLFLSTYASGASPLLVSVGVLGVGIAFAFTNSPANNAAVSALDADKVGVGMGIFQGALYLGAGTGAGMIGALLSARRDATEPINPLYILDAMSYSDAFLAATGAILIALIAGLGLKKRG"},"dna_sequence":{"accession":"AJ549214.1","fmin":"176","fmax":"1604","strand":"+","sequence":"ATGAAAAAGGATAGTAAATCTAAAGAAATGATTCAATCTGAAAAAAGGGGTTCTACTAGGCTTTTAATGATGGTACTCTCCCTATCTGTACTTGTAGGTGCAATTACGGCTGATTTAGTCAATCCCGTACTTCCACTAATAAGCAAAGATTTAGAAGCTTCGAAATCTCAAGTGAGTTGGATAGTTAGTGGTATTGCACTTGTTCTTGCGATTGGAGTTCCGATTTATGGTCGAATCTCAGACTTTTTTGAGTTACGAAAGCTATATATCTTTGCCATTATGATTCTGGCAAGTGGTAGTCTTTTATGTGCAATTGCCCCGAACCTCCCATTGTTGGTTTTGGGAAGAATGGTTCAGGGTGCTGGGATGTCCGCAATTCCAGTTCTATCAATCATTGCAATTTCGAAGGTTTTCCCACAAGGAAAACGTGGGGGAGCTTTGGGAATTATCGCAGGAAGTATTGGTGTTGGAACTGCTGCTGGTCCAATATTTGGTGGAGTAGTTGGTCAATATTTAGGGTGGAATGCCTTGTTTTGGTTCACATTTTTGTTAGCCATTATGATTGTTATTGGTGCCTACTACGCGTTACCGACAATTAAACCGGCAGAATCCGTAGGAAGCAATAAGAACTTTGATTTCATTGGTGGTTTATTCCTCGGCCTCACAGTAGGATTACTCCTTTTTGGCATCACTCAAGGAGAAACTTCTGGTTTTTCTTCGTTCTCATCGTTAACTAGCCTAATTGGTTCTGTTGTAGCTTTGGTGGGATTTATTTGGAGAATTGTTACCGCAGAAAATCCATTTGTACCACCTGTCCTGTTCAATAACAAGGATTATGTCAATACGGTCATAATTGCATTTTTTTCGATGTTTGCTTATTTCGCTGTTCTTGTGTTCGTCCCATTACTAGTCGTTGAGGTGAATGGACTCTCTTCTGGACAGGCTGGAATGATATTGTTGCCAGGTGGTGTGGCTGTTGCAATCTTATCTCCCTTCGTTGGCCGTCTTTCTGATCGATTTGGGGATAAACGTCTGATAATTACTGGGATGACTCTGATGGGGCTGTCTACCTTATTCTTGTCCACCTATGCATCTGGTGCTTCACCTCTGTTAGTTTCCGTGGGGGTCCTCGGAGTAGGGATTGCTTTTGCATTCACGAATTCTCCCGCAAATAACGCCGCAGTAAGTGCACTCGATGCAGACAAGGTTGGTGTCGGAATGGGGATTTTCCAAGGTGCTTTGTACCTTGGAGCAGGAACTGGAGCAGGTATGATTGGAGCATTATTATCCGCTCGACGTGATGCTACTGAGCCGATAAATCCATTATATATATTGGACGCTATGTCCTACTCAGATGCGTTCCTTGCAGCTACAGGGGCAATACTCATTGCCTTAATAGCTGGATTAGGTTTAAAAAAGCGTGGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39555","NCBI_taxonomy_name":"Mammaliicoccus lentus","NCBI_taxonomy_id":"42858"}}}},"ARO_accession":"3002704","ARO_id":"39138","ARO_name":"fexA","CARD_short_name":"fexA","ARO_description":"fexA is a plasmid-encoded chloramphenicol exporter that is found in Mammaliicoccus lentus.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36600":{"category_aro_accession":"3000461","category_aro_cvterm_id":"36600","category_aro_name":"florfenicol","category_aro_description":"Florfenicol is a fluorine derivative of chloramphenicol, where the nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3) and the hydroxyl group (-OH), by a fluorine group (-F). The action mechanism is the same as chloramphenicol's, where the antibiotic binds to the 23S RNA of the 50S subunit of bacterial ribosomes to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"908":{"model_id":"908","model_name":"CTX-M-139","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"866":{"protein_sequence":{"accession":"AFY98865.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLFAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"KC107824.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTTTGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001997","ARO_id":"38397","ARO_name":"CTX-M-139","CARD_short_name":"CTX-M-139","ARO_description":"CTX-M-139 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"909":{"model_id":"909","model_name":"OXA-5","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1844":{"protein_sequence":{"accession":"CAA41211.1","sequence":"MKTIAAYLVLVFYASTALSESISENLAWNKEFSSESVHGVFVLCKSSSNSCTTNNAARASTAYIPASTFKIPNALIGLETGAIKDERQVFKWDGKPRAMKQWEKDLKLRGAIQVSAVPVFQQIAREVGEIRMQKYLNLFSYGNANIGGGIDKFWLEGQLRISAFNQVKFLESLYLNNLPASKANQLIVKEAIVTEATPEYIVHSKTGYSGVGTESSPGVAWWVGWVEKGTEVYFFAFNMDIDNESKLPSRKSISTKIMASEGIIIGG"},"dna_sequence":{"accession":"X58272.1","fmin":"79","fmax":"883","strand":"+","sequence":"ATGAAAACCATAGCCGCATATTTAGTTCTAGTTTTTTATGCAAGCACCGCGCTCTCAGAGTCTATTTCTGAAAATTTGGCGTGGAATAAAGAATTTTCTAGTGAATCCGTACATGGCGTTTTTGTACTTTGTAAAAGTAGTAGCAATTCCTGTACTACAAATAATGCGGCACGTGCATCTACAGCCTATATTCCAGCATCAACATTCAAAATTCCTAATGCTCTAATAGGTCTTGAAACCGGCGCCATAAAAGATGAACGGCAGGTTTTCAAATGGGACGGCAAGCCCAGAGCCATGAAGCAATGGGAAAAAGACTTAAAGCTAAGGGGCGCTATACAGGTTTCTGCTGTTCCGGTATTTCAACAAATTGCCAGAGAAGTTGGCGAAATAAGAATGCAAAAATACCTTAACCTGTTTTCATACGGCAACGCCAATATAGGGGGAGGCATTGACAAATTCTGGCTAGAAGGTCAGCTTAGAATCTCAGCATTCAATCAAGTTAAATTTTTAGAGTCGCTCTACCTGAATAATTTGCCAGCATCAAAAGCAAACCAACTAATAGTAAAAGAGGCAATAGTTACAGAAGCAACTCCAGAATATATAGTTCATTCAAAAACTGGGTATTCCGGTGTTGGCACAGAATCAAGTCCTGGTGTCGCTTGGTGGGTTGGTTGGGTAGAGAAAGGAACTGAGGTTTACTTTTTTGCTTTTAACATGGACATAGACAATGAGAGTAAATTGCCGTCAAGAAAATCCATTTCAACGAAAATCATGGCAAGTGAAGGCATCATCATTGGTGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3001400","ARO_id":"37800","ARO_name":"OXA-5","CARD_short_name":"OXA-5","ARO_description":"OXA-5 is a beta-lactamase found in P. aeruginosa and Enterobacteriaceae.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46512":{"category_aro_accession":"3007723","category_aro_cvterm_id":"46512","category_aro_name":"OXA-5-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-5.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"911":{"model_id":"911","model_name":"CMY-50","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"822":{"protein_sequence":{"accession":"CBI75447.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAIIYEGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWRGISLLHLATYTAGGLPLQIPDEVTDKAALLRFYQNWQPQWTPGAKRLYANSSIGLFGALAVQPSGMSYEEAMTRRVLQPLKLAHTWITVPQSEQKNYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIELAQSRYWCIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"FN645444.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCGCTGCTGCTGACAGCCTCTTTCTCCACGTTTGCTGCCGCAAAAACAGAACAACAAATTGCCGATATCGTTAACCGCACCATCACACCACTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTGGCGATTATCTACGAGGGGAAACCTTATTACTTTACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGTTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGACGCTATCGCCCGCGGCGAAATTAAGCTCAGCGACCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCGGGGTATCAGCCTGCTACACTTAGCCACCTATACAGCGGGTGGCCTGCCGCTGCAGATCCCCGATGAAGTTACGGATAAAGCCGCATTACTGCGCTTTTATCAAAACTGGCAACCACAATGGACTCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGTGCGCTGGCGGTGCAACCTTCAGGTATGAGCTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAAAGCGAACAAAAAAATTATGCCTGGGGCTATCGCGAAGGGAAGCCTGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATCGATATGGCCCGCTGGGTTCAGGCCAACATGGACGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGAGCTTGCGCAGTCTCGCTACTGGTGTATTGGTGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCAGCACCTGCCGTGAAAGCCTCATGGGTGCATAAAACAGGATCCACAGGCGGATTTGGCAGCTACGTTGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTAATGTTGGCAAACAAAAGCTACCCTAACCCGGTCCGCGTAGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002061","ARO_id":"38461","ARO_name":"CMY-50","CARD_short_name":"CMY-50","ARO_description":"CMY-50 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"912":{"model_id":"912","model_name":"LEN-13","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"6135":{"protein_sequence":{"accession":"ADC58623.1","sequence":"MRYVRLCVISLLATLPLAVDAGPQPLEQIKQSESQLSGRVGMVEMDLASGRTLAAWRADERFPMVSTFKVLLCGAVLARVDAGLEQLDRRIHYRQQDLVDYSPVSEKHLVDGMTIGELCAAAITLSDNSAGNLLLATVGGPAGLTAFLRQIGDNVTRLDRWETALNEALPGDARDTTTPASMAATLRKLLTAQHLSARSQQQLLQWMVDDRVAGPLIRAVLPPGWFIADKTGAGERGARGIVALLGPDGKPERIVVLYLRDTPASMAERNQHIAGIGAALIEHWQR"},"dna_sequence":{"accession":"CP001891.1","fmin":"2841996","fmax":"2842857","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGTGTTATCTCCCTGTTAGCCACCCTGCCACTGGCGGTAGACGCCGGTCCACAGCCGCTTGAGCAGATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTGGGGATGGTGGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCGATGAACGCTTTCCCATGGTGAGCACCTTTAAAGTGCTGCTGTGCGGCGCGGTGCTGGCGCGGGTGGATGCCGGGCTCGAACAACTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGTCGACGGGATGACGATCGGCGAACTCTGCGCCGCCGCCATCACCCTGAGCGATAACAGCGCTGGCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCGGGATTAACTGCCTTTCTGCGCCAGATCGGTGACAACGTCACCCGTCTTGACCGCTGGGAAACGGCACTGAATGAGGCGCTTCCCGGCGACGCGCGCGACACCACCACCCCGGCCAGCATGGCCGCCACGCTGCGCAAACTACTGACCGCGCAGCATCTGAGCGCCCGTTCGCAACAGCAACTCCTGCAGTGGATGGTGGACGATCGGGTTGCCGGCCCGCTGATCCGCGCCGTGCTGCCGCCGGGCTGGTTTATCGCCGACAAAACCGGGGCTGGCGAACGGGGTGCGCGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAACCGGAGCGCATTGTGGTGCTCTATCTGCGGGATACCCCGGCGAGTATGGCCGAGCGTAATCAACATATCGCCGGGATCGGCGCAGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43310","NCBI_taxonomy_name":"Klebsiella variicola At-22","NCBI_taxonomy_id":"640131"}}}},"ARO_accession":"3002463","ARO_id":"38863","ARO_name":"LEN-13","CARD_short_name":"LEN-13","ARO_description":"LEN-13 is a beta-lactamase found in Klebsiella pneumoniae and Klebsiella variicola.","ARO_category":{"36236":{"category_aro_accession":"3000097","category_aro_cvterm_id":"36236","category_aro_name":"LEN beta-lactamase","category_aro_description":"LEN beta-lactamases are chromosomal class A beta-lactamases that confer resistance to ampicillin, amoxicillin, carbenicillin, and ticarcillin but not to extended-spectrum beta-lactams.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"913":{"model_id":"913","model_name":"OXY-6-4","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1141":{"protein_sequence":{"accession":"CAI43425.1","sequence":"MLKSSWRKSALMAAAAVPLLLASGSLWASADAIQQKLANLEKRSGGRLGVALINTADDSQTLYRGDERFAMCSTGKVMAAAAVLKQSESHPDVVNKRLEIKKSDLVVWSPITEKHLQSGMTLAELSAAALQYSDNTAMNKMISYLGGPEKVTAFAQSIGDVTFRLDRTEPALNSAIPGDKRDTTTPLAMAESLRKLTLGNALGEQQRAQLVTWLKGNTTGGQSIRAGLPASWAVGDKTGAGDYGTTNDIAVIWPENHAPLVLVTYFTQPQQDAKSRKEVLAAAAKIVTEGL"},"dna_sequence":{"accession":"AJ871877.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGTTGAAAAGTTCGTGGCGTAAAAGCGCCCTGATGGCCGCCGCCGCCGTTCCGCTGCTGCTGGCGAGCGGTTCATTATGGGCCAGTGCCGATGCTATCCAGCAAAAGCTGGCTAATTTAGAAAAACGGTCCGGTGGCCGGCTGGGCGTGGCGCTGATTAACACGGCGGATGATTCGCAAACCCTTTATCGCGGCGACGAACGTTTTGCCATGTGCAGCACCGGTAAAGTGATGGCCGCCGCCGCGGTGTTAAAGCAGAGCGAAAGCCATCCCGATGTGGTGAATAAAAGGCTGGAGATTAAAAAATCGGATTTAGTGGTCTGGAGCCCGATTACCGAAAAACATCTGCAAAGCGGAATGACCCTGGCGGAACTCAGCGCGGCGGCGCTGCAGTACAGCGACAATACCGCGATGAATAAGATGATTAGCTACCTTGGCGGACCGGAAAAGGTGACCGCATTCGCCCAGAGCATCGGGGACGTTACTTTTCGTCTCGATCGTACGGAGCCGGCGCTGAACAGCGCGATACCCGGCGATAAGCGCGATACCACCACCCCGTTGGCGATGGCCGAAAGCCTGCGCAAGCTGACGCTGGGCAATGCGCTGGGCGAACAGCAGCGCGCCCAGTTAGTGACGTGGCTAAAAGGCAATACCACCGGCGGGCAAAGCATTCGCGCAGGCCTGCCCGCAAGCTGGGCGGTCGGGGATAAAACCGGCGCCGGAGATTACGGCACCACCAACGATATCGCGGTGATCTGGCCGGAAAATCATGCCCCGCTGGTGTTAGTGACCTATTTTACCCAGCCGCAGCAGGATGCGAAAAGCCGCAAAGAGGTGTTAGCCGCGGCGGCGAAAATCGTGACCGAAGGGCTGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3002416","ARO_id":"38816","ARO_name":"OXY-6-4","CARD_short_name":"OXY-6-4","ARO_description":"OXY-6-4 is a beta-lactamase found in Klebsiella oxytoca.","ARO_category":{"38788":{"category_aro_accession":"3002388","category_aro_cvterm_id":"38788","category_aro_name":"OXY beta-lactamase","category_aro_description":"OXY beta-lactamases are chromosomal class A beta-lactamases that are found in Klebsiella oxytoca. At constitutive low levels, OXY beta-lactamases confer resistance to aminopenicillins and carboxypenicillins. At high induced levels,  OXY beta-lactamases confer resistance to penicillins, cephalosporins and aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"914":{"model_id":"914","model_name":"ANT(6)-Ia","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"5528":{"protein_sequence":{"accession":"AHE40557.1","sequence":"MRSEKEMMDLVLSLAEQDERIRIVTLEGSRANINIPKDEFQDYDITYFVSDIEPFISNDDWLNQFGNIIMMQKPEDMELFPPEEKGFSYLMLFDDYNKIDLTLLPLEELDNYLKGDKLIKVLIDKDCRIKRDIVPTDIDYHVRKPSAREYDDCCNEFWNVTPYVIKGLCRKEILFAIDHLNQILRFELLRMMSWKVGIKTEFSLSVGKNYKYINKYIDEDLWNRLLSTYRMDSYENIWKSLFICHQLFREVSKEVAELLGFDYPEYGKNITRYTEDMYKKYVENDYF"},"dna_sequence":{"accession":"KF648874.1","fmin":"60996","fmax":"61860","strand":"-","sequence":"ATGAGATCAGAAAAAGAAATGATGGATTTAGTACTTTCTTTAGCAGAACAGGATGAACGTATTCGAATTGTGACCCTTGAGGGGTCACGCGCAAATATTAATATACCTAAAGATGAATTTCAGGATTATGATATTACATATTTTGTAAGTGATATAGAACCGTTTATATCTAATGATGACTGGCTTAATCAATTTGGGAATATAATAATGATGCAAAAGCCGGAGGATATGGAATTATTCCCACCTGAAGAAAAGGGATTTTCCTATCTTATGCTATTTGATGATTACAATAAAATTGATCTTACCTTATTGCCCTTGGAAGAGTTAGATAATTACCTAAAGGGCGATAAATTAATAAAGGTTCTAATTGATAAAGATTGTAGAATTAAAAGGGACATAGTTCCGACTGATATAGATTATCATGTAAGAAAGCCAAGCGCAAGGGAGTATGATGATTGCTGCAATGAATTTTGGAATGTAACACCTTATGTTATTAAAGGATTGTGCCGCAAAGAGATACTGTTTGCAATCGATCATCTGAACCAGATTCTACGGTTTGAACTACTTAGGATGATGTCGTGGAAGGTTGGGATAAAGACAGAATTTTCATTAAGTGTTGGGAAAAATTATAAGTATATTAACAAATACATTGATGAAGATCTATGGAATAGATTATTATCTACATATCGCATGGATTCCTATGAAAATATTTGGAAGTCATTATTTATATGCCACCAATTGTTCAGGGAAGTGTCCAAAGAGGTAGCAGAACTACTGGGGTTTGATTATCCAGAGTATGGTAAGAACATAACAAGATATACCGAGGACATGTATAAAAAATATGTTGAAAATGACTATTTTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39580","NCBI_taxonomy_name":"Exiguobacterium sp. S3-2","NCBI_taxonomy_id":"1389960"}}}},"ARO_accession":"3002626","ARO_id":"39026","ARO_name":"ANT(6)-Ia","CARD_short_name":"ANT(6)-Ia","ARO_description":"ANT(6)-Ia is an aminoglycoside nucleotidyltransferase gene encoded by plasmids and chromosomes in Staphylococcus epidermidis, E. faecium, Streptococcus suis, S. aureus, E. faecalis and Streptococcus mitis.","ARO_category":{"36364":{"category_aro_accession":"3000225","category_aro_cvterm_id":"36364","category_aro_name":"ANT(6)","category_aro_description":"A category of aminoglycoside O-nucleotidyltransferase enzymes with modification regiospecificity based at the 6-hydroxyl group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics, specifically streptomycin, by transfer of an AMP group from an ATP substrate to the 6-hydroxyl group of the compound.","category_aro_class_name":"AMR Gene Family"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"915":{"model_id":"915","model_name":"SHV-106","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"2019":{"protein_sequence":{"accession":"CAQ03506.1","sequence":"MRFIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGASERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AM941847.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTTTATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACATCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGAGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTAGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATCGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001155","ARO_id":"37535","ARO_name":"SHV-106","CARD_short_name":"SHV-106","ARO_description":"SHV-106 is an extended-spectrum beta-lactamase that has been found in clinical isolates.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"916":{"model_id":"916","model_name":"OXA-36","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1842":{"protein_sequence":{"accession":"AAG24866.1","sequence":"MFSLATFAHAQEGTLERSDWRKFFSEFQAKGTIVVADERQADRAMLVFDPVRSKKRYSPASTFKIPHTLFALDAGAVRDEFQIFRWDGVNRGFAGHNQDQDLRSAMRNSTVWVYELFAKEIGDDKARRYLKKIDYGNAYPSTSNGDYWIEGSLAISAQEQIAFLRKLYRNELPFRVEHQRLVKDLMIVEAGRNWILRAKTGWEGRMGWWVGWVEWPTGSVFFALNIDTPNRMDDLFKREAIVRAIL"},"dna_sequence":{"accession":"AF300985.1","fmin":"1","fmax":"739","strand":"+","sequence":"ATTTTTTCTCTTGCCACTTTCGCGCATGCGCAAGAAGGCACGCTAGAACGTTCTGACTGGAGGAAGTTTTTCAGCGAATTTCAAGCCAAAGGCACGATAGTTGTGGCAGACGAACGCCAAGCGGATCGTGCCATGTTGGTTTTTGATCCTGTGCGATCGAAGAAACGCTACTCGCCTGCATCGACATTCAAGATACCTCATACACTTTTTGCACTTGATGCAGGCGCTGTTCGTGATGAGTTCCAGATTTTTCGATGGGACGGCGTTAACAGGGGCTTTGCAGGCCACAATCAAGACCAAGATTTGCGATCAGCAATGCGGAATTCTACTGTTTGGGTGTATGAGCTATTTGCAAAGGAAATTGGTGATGACAAAGCTCGGCGCTATTTGAAGAAAATCGACTATGGCAACGCCTATCCTTCGACAAGTAATGGCGATTACTGGATAGAAGGCAGCCTTGCAATCTCGGCGCAGGAGCAAATTGCATTTCTCAGGAAGCTCTATCGTAACGAGCTGCCCTTTCGGGTAGAACATCAGCGCTTGGTCAAGGATCTCATGATTGTGGAAGCCGGTCGCAACTGGATACTGCGTGCAAAGACGGGCTGGGAAGGCCGTATGGGTTGGTGGGTAGGATGGGTTGAGTGGCCGACTGGCTCCGTATTCTTCGCACTGAATATTGATACGCCAAACAGAATGGATGATCTTTTCAAGAGGGAGGCAATCGTGCGGGCAATCCTT","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3001430","ARO_id":"37830","ARO_name":"OXA-36","CARD_short_name":"OXA-36","ARO_description":"OXA-36 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"917":{"model_id":"917","model_name":"SHV-186","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"832":{"protein_sequence":{"accession":"AIS67769.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMTATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERCARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"KM233165.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGACCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGTGTGCGCGCGGCATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3003153","ARO_id":"39730","ARO_name":"SHV-186","CARD_short_name":"SHV-186","ARO_description":"SHV-186 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"918":{"model_id":"918","model_name":"TEM-49","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1726":{"protein_sequence":{"accession":"CAA71324.1","sequence":"MSIQHFRVALIPFFAAFCFPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGASKRGSRGIIAALGPDGKPSRIVVIYMTGGQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"Y10281.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCTTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCAGTAAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACATGACGGGGGGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000918","ARO_id":"37298","ARO_name":"TEM-49","CARD_short_name":"TEM-49","ARO_description":"TEM-49 extended-spectrum beta-lactamase found in E. coli.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"919":{"model_id":"919","model_name":"PER-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4747":{"protein_sequence":{"accession":"CAA79968.1","sequence":"MNVIIKAVVTASTLLMVSFSSFETSAQSPLLKEQIESIVIGKKATVGVAVWGPDDLEPLLINPFEKFPMQSVFKLHLAMLVLHQVDQGKLDLNQTVIVNRAKVLQNTWAPIMKAYQGDEFSVPVQQLLQYSVSHSDNVACDLLFELVGGPAALHDYIQSMGIKETAVVANEAQMHADDQVQYQNWTSMKGAAEILKKFEQKTQLSETSQALLWKWMVETTTGPERLKGLLPAGTVVAHKTGTSGIKAGKTAATNDLGIILLPDGRPLLVAVFVKDSAESSRTNEAIIAQVAQTAYQFELKKLSALSPN"},"dna_sequence":{"accession":"Z21957.1","fmin":"284","fmax":"1211","strand":"-","sequence":"ATGAATGTCATTATAAAAGCTGTAGTTACTGCCTCGACGCTACTGATGGTATCTTTTAGTTCATTCGAAACCTCAGCGCAATCCCCACTGTTAAAAGAGCAAATTGAATCCATAGTCATTGGAAAAAAAGCCACTGTAGGCGTTGCAGTGTGGGGGCCTGACGATCTGGAACCTTTACTGATTAATCCTTTTGAAAAATTCCCAATGCAAAGTGTATTTAAATTGCATTTAGCTATGTTGGTACTGCATCAGGTTGATCAGGGAAAGTTGGATTTAAATCAGACCGTTATCGTAAACAGGGCTAAGGTTTTACAGAATACCTGGGCTCCGATAATGAAAGCGTATCAGGGAGACGAGTTTAGTGTTCCAGTGCAGCAACTGCTGCAATACTCGGTCTCGCACAGCGATAACGTGGCCTGTGATTTGTTATTTGAACTGGTTGGTGGACCAGCTGCTTTGCATGACTATATCCAGTCTATGGGTATAAAGGAGACCGCTGTGGTCGCAAATGAAGCGCAGATGCACGCCGATGATCAGGTGCAGTATCAAAACTGGACCTCGATGAAAGGTGCTGCAGAGATCCTGAAAAAGTTTGAGCAAAAAACACAGCTGTCTGAAACCTCGCAGGCTTTGTTATGGAAGTGGATGGTCGAAACCACCACAGGACCAGAGCGGTTAAAAGGTTTGTTACCAGCTGGTACTGTGGTCGCACATAAAACTGGTACTTCGGGTATCAAAGCCGGAAAAACTGCGGCCACTAATGATTTAGGTATCATTCTGTTGCCTGATGGACGGCCCTTGCTGGTTGCTGTTTTTGTGAAAGACTCAGCCGAGTCAAGCCGAACCAATGAAGCTATCATTGCGCAGGTTGCTCAGACTGCGTATCAATTTGAATTGAAAAAGCTTTCTGCCCTAAGCCCAAATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002363","ARO_id":"38763","ARO_name":"PER-1","CARD_short_name":"PER-1","ARO_description":"PER-1 is a beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36195":{"category_aro_accession":"3000056","category_aro_cvterm_id":"36195","category_aro_name":"PER beta-lactamase","category_aro_description":"PER beta-lactamases are plasmid-mediated extended spectrum beta-lactamases found in the Enterobacteriaceae family.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"920":{"model_id":"920","model_name":"TEM-152","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1074":{"protein_sequence":{"accession":"ABI74447.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMVSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDHWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGKRGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERDRQIAEIGASLIKHW"},"dna_sequence":{"accession":"DQ834728.1","fmin":"205","fmax":"1066","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGGTGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATCATTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTAAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAGATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001019","ARO_id":"37399","ARO_name":"TEM-152","CARD_short_name":"TEM-152","ARO_description":"TEM-152 is a CMT-type, inhibitor-resistant, extended-spectrum beta-lactamase found in E. coli.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"921":{"model_id":"921","model_name":"OKP-A-11","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"8242":{"protein_sequence":{"accession":"CAP12353.2","sequence":"MRYVRLCLISLIAALPLAAFASPPPLEQVTRSESQLAGRVGYVEMDLASGRTLAAWRASERFPLMSTFKVLLCGAVLARVDAGDEQLDRRIRYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAGNLLLKSVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDVRDTTTPASMAATLRKLLTSHALSARSQQQLLQWMVDDQVAGPLIRAVLPAGWFIADKTGAGERGSRGIVALLGPNGKAERIVVIYLRDTPATMAERNQQIARIGAALIEHWQR"},"dna_sequence":{"accession":"AM850915.2","fmin":"19","fmax":"880","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGCCTTATCTCCCTGATTGCCGCCCTGCCACTGGCGGCATTCGCCAGCCCTCCGCCGCTCGAGCAAGTTACACGCAGCGAAAGTCAGCTGGCGGGCCGCGTGGGCTATGTTGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCAGTGAGCGCTTTCCGCTGATGAGCACCTTTAAAGTGCTGCTCTGCGGCGCGGTGCTGGCCCGGGTGGATGCCGGAGACGAACAGCTGGATCGGCGGATCCGCTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGCCGACGGGATGACCGTTGGCGAACTCTGCGCCGCCGCCATCACCATGAGCGACAACAGCGCCGGCAATCTGCTGTTGAAGAGCGTTGGCGGCCCCGCGGGATTGACCGCTTTTCTGCGCCAGATCGGTGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAGCTCAATGAGGCGCTTCCCGGCGACGTGCGCGACACCACCACCCCAGCCAGCATGGCCGCCACCCTGCGCAAGCTGCTAACCAGCCACGCGCTGAGCGCCCGTTCGCAGCAGCAGCTGCTGCAGTGGATGGTGGACGACCAGGTGGCCGGTCCGCTGATCCGCGCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAAACCGGGGCCGGCGAGCGGGGCTCACGCGGCATTGTCGCCCTGCTCGGCCCGAACGGCAAAGCGGAGCGCATCGTGGTGATCTATCTGCGGGATACGCCGGCGACCATGGCCGAGCGTAACCAGCAGATCGCCAGAATAGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002428","ARO_id":"38828","ARO_name":"OKP-A-11","CARD_short_name":"OKP-A-11","ARO_description":"OKP-A-11 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"38817":{"category_aro_accession":"3002417","category_aro_cvterm_id":"38817","category_aro_name":"OKP beta-lactamase","category_aro_description":"OKP beta-lactamases are chromosomal class A beta-lactamase that confer resistance to penicillins and early cephalosporins in Klebsiella pneumoniae. OKP beta-lactamases can be subdivided into two groups: OKP-A and OKP-B which diverge by about 4.2%.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"923":{"model_id":"923","model_name":"VIM-25","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1890":{"protein_sequence":{"accession":"ADO50679.1","sequence":"MLKVISSLLVYMTASVMAVASPLAHSGEPSGEYPTVNEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRKAGVATYASPSTRRLAEAEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSANVLYGGCAVLALSRTSAGNVADADLAEWPTSVERIQKHYPEAQFVIPGHGLPGGLDLLKHTTNVVKAHTNRSVVE"},"dna_sequence":{"accession":"HM750249.1","fmin":"90","fmax":"891","strand":"+","sequence":"ATGTTAAAAGTTATTAGTAGTTTATTGGTCTACATGACCGCGTCTGTCATGGCTGTAGCTAGTCCGTTAGCCCATTCCGGGGAGCCGAGTGGTGAGTATCCGACAGTCAACGAAATTCCGGTCGGAGAGGTCCGGCTTTACCAGATTGCTGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCGGTCTACCCATCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCCCTTCTCGCGGAGATTGAGAAGCAAATTGGACTTCCCGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGAAGGCTGGAGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGCAGAGGGGAACGAGATTCCCACGCACTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAGCTCTTCTATCCCGGTGCTGCGCATTCGACCGACAATCTGGTTGTATACGTCCCGTCAGCGAACGTGCTATACGGTGGTTGTGCCGTTCTTGCGTTGTCACGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCGTTGAGCGGATTCAAAAACACTACCCGGAAGCACAGTTCGTCATTCCGGGGCACGGCCTGCCGGGCGGTCTAGACTTGCTCAAGCACACAACGAATGTTGTAAAAGCGCACACAAATCGCTCAGTCGTTGAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3002295","ARO_id":"38695","ARO_name":"VIM-25","CARD_short_name":"VIM-25","ARO_description":"VIM-25 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"925":{"model_id":"925","model_name":"AAC(3)-IIb","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"10":{"protein_sequence":{"accession":"AAA26548.1","sequence":"MNTIESITADLHGLGVRPGDLIMVHASLKAVGPVEGGAASVVSALRAAVGSAGTLMGYASWDRSPYEETLNGARMDEELRRRWPPFDLATSGTYPGFGLLNRFLLEAPDARRSAHPDASMVAVGPLAATLTEPHRLGQALGEGSPLERFVGHGGKVLLLGAPLDSVTVLHYAEAIAPIPNKRRVTYEMPMLGPDGRVRWELAEDFDSNGILDCFAVDGKPDAVETIAKAYVELGRHREGIVGRAPSYLFEAQDIVSFGVTYLEQHFGAP"},"dna_sequence":{"accession":"M97172.1","fmin":"655","fmax":"1465","strand":"+","sequence":"ATGAACACGATCGAATCGATCACGGCGGACCTGCACGGACTGGGCGTCCGGCCCGGCGACCTGATCATGGTCCATGCATCGCTGAAAGCCGTCGGCCCGGTCGAGGGAGGTGCGGCCTCGGTGGTGTCGGCCCTTCGCGCCGCGGTCGGGTCCGCAGGGACCCTGATGGGTTATGCCTCATGGGACCGCTCGCCCTATGAGGAGACGCTGAACGGCGCGCGGATGGACGAAGAACTGCGCCGCCGGTGGCCACCCTTCGATCTGGCCACATCCGGTACCTATCCCGGCTTCGGCCTGCTCAACCGGTTTCTGCTTGAGGCGCCCGACGCACGGCGCAGCGCGCATCCCGACGCCTCCATGGTCGCGGTCGGCCCCCTTGCCGCCACGCTGACAGAGCCGCACCGGCTTGGGCAGGCGCTGGGCGAAGGCTCGCCGCTGGAGCGCTTCGTCGGGCATGGCGGAAAGGTCCTGCTTCTGGGAGCGCCGCTCGACTCCGTCACCGTGCTGCATTACGCCGAGGCCATCGCCCCCATCCCGAACAAACGCCGCGTGACCTATGAAATGCCGATGCTCGGCCCGGATGGCAGGGTCCGATGGGAGCTGGCCGAGGATTTCGACAGCAACGGCATTCTCGATTGCTTCGCGGTCGATGGGAAGCCGGATGCCGTCGAGACGATCGCCAAGGCTTATGTCGAACTGGGCCGGCATCGGGAAGGCATCGTCGGTCGCGCACCCTCCTATCTGTTTGAAGCGCAGGATATCGTCTCGTTCGGCGTCACCTATCTCGAACAGCATTTCGGCGCGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36783","NCBI_taxonomy_name":"Serratia marcescens","NCBI_taxonomy_id":"615"}}}},"ARO_accession":"3002534","ARO_id":"38934","ARO_name":"AAC(3)-IIb","CARD_short_name":"AAC(3)-IIb","ARO_description":"AAC(3)-IIb is an aminoglycoside acetyltransferase in E. coli, A. faecalis and S. marcescens.","ARO_category":{"36461":{"category_aro_accession":"3000322","category_aro_cvterm_id":"36461","category_aro_name":"AAC(3)","category_aro_description":"A category of aminoglycoside N-acetyltransferase enzymes with modification regiospecificity based at the 3-amino group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics through acetylation of the 3-amino group of the compound.","category_aro_class_name":"AMR Gene Family"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"46127":{"category_aro_accession":"3007377","category_aro_cvterm_id":"46127","category_aro_name":"6'-N-ethylnetilmicin","category_aro_description":"6'-N-ethylnetilmicin is an aminoglycoside antibiotic and a derivative of netilmicin.","category_aro_class_name":"Antibiotic"},"46128":{"category_aro_accession":"3007378","category_aro_cvterm_id":"46128","category_aro_name":"2'-N-ethylnetilmicin","category_aro_description":"2'-N-ethylnetilmicin is an aminoglycoside antibiotic and a derivative of netilmicin.","category_aro_class_name":"Antibiotic"},"46133":{"category_aro_accession":"3007382","category_aro_cvterm_id":"46133","category_aro_name":"gentamicin","category_aro_description":"Gentamicin is a commonly used aminoglycoside antibiotic derived from members of the Micromonospora genus of bacteria. It acts by binding the 30S ribosomal subunit, thus inhibiting protein synthesis. Gentamicin is typically used to treat Gram-negative infections of the repiratory and urinary tract, as well as infections of the bone and soft tissue. It also exhibits considerable nephrotoxicity and ototoxicity. Gentamicin is administered as a mixture of gentamicin type C (which makes about around 80% of the complex) and types A, B, and X (distributed in the remaining 20% of the complex).","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"926":{"model_id":"926","model_name":"KPC-15","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"2049":{"protein_sequence":{"accession":"AGF70638.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVRWSPISEKYLTTGMTVLELSAAAVQYSDNAAANLLLKELGGPAKLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGGYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKYSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"KC433553.1","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCGGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTTTTGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCAAACTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGGGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGTACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002325","ARO_id":"38725","ARO_name":"KPC-15","CARD_short_name":"KPC-15","ARO_description":"KPC-15 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"927":{"model_id":"927","model_name":"OXA-381","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1933":{"protein_sequence":{"accession":"AHL30285.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDKKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGFEHHKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKVSAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"KJ135344.1","fmin":"14","fmax":"839","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATAAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATAGGCTTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGTTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001567","ARO_id":"37967","ARO_name":"OXA-381","CARD_short_name":"OXA-381","ARO_description":"OXA-381 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"928":{"model_id":"928","model_name":"carA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1050"}},"model_sequences":{"sequence":{"90":{"protein_sequence":{"accession":"AAC32027.1","sequence":"MSTAQLALHDITKRYQDHVVLDRIGFTIKPGEKVGVIGDNGSGKSTLIKLIAGREQPDNGAVTVVAPGGVGYLAQTLELPLEATVQDAVDLALADLRELEEGMRRTEAELAERPYQTGQDPELAGLLESYAALVDRYQARGGYEADSRVEIALHGLGLPGLERGRRLGTLSGGERSRLALAATLASEPELLLLDEPTNDLDDRAVDWLEEHLRKHKGTVVAVTHDRLFLDRLTTTILEIDSGKVMRYGNGYEGYLAAKAAERQRRLLEYEQWRAELDRSRDLIASNVARLDAIPRKLPFAVFGAGQFRMRGRGHGAMVRIRNAKERVARLTENPVAPPPEPLTFTAEITTEAAQSRETVAELTGVRVGDRLSVDSLHLGPGERLLVTGPNGAGKTTLLRVLSGELEPDSGSLLVSGRVGHLRQEQTPWRPGMTVLQAFSSGRAGDIDEHTEALLSLGLFSPDDLRQRVQDLSYGQRRRIELARLVTEPVDLLLLDEPTNHLSPALVEELEEALTGYQGTVVVVTHDRRMRSRFNGAHLTLQDGRVAEFTAA"},"dna_sequence":{"accession":"M80346.1","fmin":"0","fmax":"1656","strand":"+","sequence":"GTGTCGACAGCGCAACTAGCTCTGCATGACATCACCAAGCGTTACCAGGACCACGTCGTACTCGACCGGATCGGCTTCACCATCAAGCCGGGCGAGAAGGTCGGTGTCATCGGGGACAACGGATCCGGCAAGTCCACGCTGATCAAGCTCATCGCCGGGCGGGAACAGCCGGACAACGGTGCGGTGACGGTGGTCGCGCCCGGTGGCGTCGGCTATCTGGCCCAGACACTGGAGCTGCCGCTGGAGGCCACGGTCCAGGACGCCGTCGATCTGGCCCTGGCCGACCTGCGGGAGCTGGAGGAGGGCATGCGCCGGACCGAGGCCGAGCTGGCCGAACGGCCCTACCAAACGGGCCAAGACCCCGAACTCGCCGGCCTCCTGGAGAGTTACGCCGCGCTGGTGGACCGGTATCAGGCCCGCGGCGGCTACGAGGCCGACTCCCGCGTGGAGATCGCGCTGCACGGGCTCGGGCTGCCCGGGCTGGAACGCGGCCGGCGGCTGGGCACCCTGTCCGGCGGCGAGCGCTCGCGCCTCGCCCTGGCGGCGACGCTGGCCTCGGAACCCGAACTGCTGCTGTTGGACGAGCCGACCAACGACCTGGACGACCGGGCCGTGGACTGGCTGGAGGAACACCTGCGCAAGCACAAAGGCACCGTTGTCGCCGTTACCCACGACCGGCTCTTCCTCGACCGGCTCACCACCACGATCCTGGAGATCGACTCCGGCAAGGTGATGCGCTACGGCAACGGCTACGAGGGCTACCTGGCAGCCAAGGCGGCGGAACGGCAGCGCAGGCTGCTTGAGTACGAGCAGTGGCGCGCCGAGCTGGACCGCAGCCGCGACCTGATCGCGTCCAACGTGGCGCGTCTGGACGCCATCCCACGCAAGCTGCCCTTCGCCGTCTTCGGCGCCGGCCAGTTCCGGATGCGCGGGCGGGGCCATGGTGCGATGGTGCGGATCCGCAACGCCAAGGAACGCGTCGCGCGGCTGACCGAAAACCCGGTCGCGCCGCCGCCCGAGCCGCTCACCTTCACCGCGGAGATCACCACCGAGGCCGCGCAGTCCCGGGAGACGGTGGCCGAACTCACCGGCGTCCGGGTCGGCGACCGGCTCAGCGTCGACTCCCTGCACCTCGGGCCCGGTGAACGGCTGCTGGTCACCGGCCCCAACGGGGCGGGCAAGACGACGCTGCTGCGGGTGCTCTCCGGGGAGCTGGAACCCGACAGCGGATCCCTGCTGGTGTCGGGCCGGGTGGGACACCTGAGGCAGGAACAGACACCATGGCGGCCGGGTATGACGGTGCTTCAGGCGTTCAGCAGCGGACGGGCCGGTGACATCGACGAGCACACCGAGGCGCTGCTCTCCCTCGGGCTGTTCAGCCCGGACGACCTCCGCCAGCGTGTGCAGGACCTGTCGTACGGGCAGCGGCGCCGCATCGAGCTTGCCCGGCTGGTGACGGAGCCGGTCGACCTGCTGCTGCTGGACGAACCCACCAACCACCTCTCGCCCGCGCTCGTCGAGGAACTGGAGGAGGCGCTGACCGGTTATCAGGGCACGGTCGTCGTCGTCACCCACGACCGGCGCATGCGGTCCCGCTTCAACGGCGCCCATCTGACGCTGCAGGACGGGCGCGTCGCCGAGTTCACCGCCGCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36843","NCBI_taxonomy_name":"Streptomyces thermotolerans","NCBI_taxonomy_id":"80858"}}}},"ARO_accession":"3002817","ARO_id":"39251","ARO_name":"carA","CARD_short_name":"carA","ARO_description":"carA is an ABC-F subfamily protein involved in macrolide resistance. It is found in Streptomyces thermotolerans.","ARO_category":{"45630":{"category_aro_accession":"3007068","category_aro_cvterm_id":"45630","category_aro_name":"Miscellaneous ABC-F subfamily ATP-binding cassette ribosomal protection proteins","category_aro_description":"ABC-F subfamily ATP-binding cassette ribosomal protection proteins of unknown, unclear or miscellaneous classification which nevertheless confer resistance to antibiotics through ribosomal protection and not through antibiotic efflux. These proteins should be further reviewed to elucidate associated genes, their function, origin and classification.","category_aro_class_name":"AMR Gene Family"},"37627":{"category_aro_accession":"3001228","category_aro_cvterm_id":"37627","category_aro_name":"carbomycin","category_aro_description":"Produced by Streptomyces halstedii and Streptomyces thermotolerans.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"929":{"model_id":"929","model_name":"GES-10","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1670":{"protein_sequence":{"accession":"ACS73598.1","sequence":"MRFIHALLLAGTAHSAYASEKLTFKTDLEKLEREKAAQIGVAIVDPQGEIVAGHRTAQRFAMCSTFKFPLAALVFERIDSGTERGDRKLSYGPDMIVEWSPATERFLASGHMTVLEAAQAAVQLCDNGATNLLLREIGGPAAMTQYFRKIGDSVSRLDRKEPEMGDNTPGDLRDTTTPIAMARTVAKVLYGGALTSTSTHTIERWLIGNQTGDATLRAGFPKDWVVGEKTGTCANGGRNDIGFFKAQERDYAVAVYTTAPKLSAVERDELVASVGQVITQLILSTDK"},"dna_sequence":{"accession":"FJ820124.1","fmin":"1123","fmax":"1987","strand":"+","sequence":"ATGCGCTTCATTCACGCACTATTACTGGCAGGGACCGCTCACTCTGCATATGCGTCGGAAAAATTAACCTTCAAGACCGATCTTGAGAAGCTAGAGCGCGAAAAAGCAGCTCAGATCGGTGTTGCGATCGTCGATCCCCAAGGAGAGATCGTCGCGGGCCACCGAACGGCGCAGCGCTTTGCAATGTGCTCAACGTTCAAGTTTCCGCTAGCCGCGCTGGTCTTTGAAAGAATTGACTCAGGCACCGAGCGGGGGGATCGAAAACTTTCATATGGGCCGGACATGATCGTCGAATGGTCTCCTGCCACGGAGCGGTTTCTAGCATCGGGACACATGACGGTTCTCGAGGCAGCGCAAGCTGCGGTGCAGCTTTGCGACAATGGGGCTACTAACCTCTTACTGAGAGAAATTGGCGGACCTGCTGCAATGACGCAGTATTTTCGTAAAATTGGCGACTCTGTGAGTCGGCTAGACCGGAAAGAGCCGGAGATGGGCGACAACACACCTGGCGACCTCAGAGATACAACTACGCCTATTGCTATGGCACGTACTGTGGCTAAAGTCCTCTATGGCGGCGCACTGACGTCCACCTCGACCCACACCATTGAGAGGTGGCTGATCGGAAACCAAACGGGAGACGCGACACTACGAGCGGGTTTTCCTAAAGATTGGGTTGTTGGAGAGAAAACTGGTACCTGCGCCAACGGGGGCCGGAACGACATTGGTTTTTTTAAAGCCCAGGAGAGAGATTACGCTGTAGCGGTGTATACAACGGCCCCGAAACTATCGGCCGTAGAACGTGACGAATTAGTTGCCTCTGTCGGTCAAGTTATTACACAACTCATCCTGAGCACGGACAAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36791","NCBI_taxonomy_name":"uncultured bacterium","NCBI_taxonomy_id":"77133"}}}},"ARO_accession":"3002339","ARO_id":"38739","ARO_name":"GES-10","CARD_short_name":"GES-10","ARO_description":"GES-10 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36205":{"category_aro_accession":"3000066","category_aro_cvterm_id":"36205","category_aro_name":"GES beta-lactamase","category_aro_description":"GES beta-lactamases or Guiana extended-spectrum beta-lactamases are related to the other plasmid-located class A beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"948":{"model_id":"948","model_name":"mecI","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"200"}},"model_sequences":{"sequence":{"4247":{"protein_sequence":{"accession":"BAB41258.1","sequence":"MDNKTYEISSAEWEVMNIIWMKKYASANNIIEEIQMQKDWSPKTIRTLITRLYKKGFIDRKKDNKIFQYYSLVEESDIKYKTSKNFINKVYKGGFNSLVLNFVEKEDLSQDEIEELRNILNKK"},"dna_sequence":{"accession":"BA000018.3","fmin":"48893","fmax":"49265","strand":"+","sequence":"ATGGATAATAAAACGTATGAAATATCATCTGCAGAATGGGAAGTTATGAATATCATTTGGATGAAAAAATATGCAAGTGCGAATAATATAATAGAAGAAATACAAATGCAAAAGGACTGGAGTCCAAAAACCATTCGTACACTTATAACGAGATTGTATAAAAAGGGATTTATAGATCGTAAAAAAGACAATAAAATTTTTCAATATTACTCTCTTGTAGAAGAAAGTGATATAAAATATAAAACATCTAAAAACTTTATCAATAAAGTATACAAAGGCGGTTTCAATTCACTTGTCTTAAACTTTGTAGAAAAAGAAGATCTATCACAAGATGAAATAGAAGAATTGAGAAATATATTGAATAAAAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35514","NCBI_taxonomy_name":"Staphylococcus aureus subsp. aureus N315","NCBI_taxonomy_id":"158879"}}}},"ARO_accession":"3000124","ARO_id":"36263","ARO_name":"mecI","CARD_short_name":"mecI","ARO_description":"mecI acts as a repressor of transcription of the mecA\/mecR1\/mecI operon.","ARO_category":{"37589":{"category_aro_accession":"3001208","category_aro_cvterm_id":"37589","category_aro_name":"methicillin resistant PBP2","category_aro_description":"In methicillin sensitive S. aureus (MSSA), beta-lactams bind to native penicillin-binding proteins (PBPs) and disrupt synthesis of the cell membrane's peptidoglycan layer. In methicillin resistant S. aureus (MRSA), foreign PBP2a acquired by lateral gene transfer is able to perform peptidoglycan synthesis in the presence of beta-lactams.","category_aro_class_name":"AMR Gene Family"},"35934":{"category_aro_accession":"0000015","category_aro_cvterm_id":"35934","category_aro_name":"methicillin","category_aro_description":"Derived from penicillin to combat penicillin-resistance, methicillin is insensitive to beta-lactamases (also known as penicillinases) secreted by many penicillin-resistant bacteria. Methicillin is bactericidal, and acts by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"931":{"model_id":"931","model_name":"OXA-316","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1609":{"protein_sequence":{"accession":"AGU69254.1","sequence":"MNIQALLLITSAIFISACSPYIVSANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMEASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPHGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"KF057033.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTCAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGTCTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGGAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCATGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001687","ARO_id":"38087","ARO_name":"OXA-316","CARD_short_name":"OXA-316","ARO_description":"OXA-316 is a beta-lactamase found in A. baumannii.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"932":{"model_id":"932","model_name":"GES-8","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"790":{"protein_sequence":{"accession":"AAK18183.1","sequence":"MRFIHALLLAGIAHSAYASEKLTFKTDLEKLEREKAAQIGVAIVDPQGEIVAGHRMAQRFAMCSTFKFPLAALVFERIDSGTERGDRKLSYGPDMIVEWSPATERFLASGHMTVLEAAQLAVQLSDNGATNLLLREIGGPAAMTQYFRKIGDSVSRLDRKEPEMGDNTPGDLRDTTTPIAMARTVAKVLYGGALTSTSTHTIERWLIGNQTGDATLRAGFPKDWVVGEKTGTCANGGRNDIGFFKAQERDYAVAVYTTAPKLSAVERDELVASVGQVITQLILSTDK"},"dna_sequence":{"accession":"AF329699.1","fmin":"372","fmax":"1236","strand":"+","sequence":"ATGCGCTTCATTCACGCACTATTACTGGCAGGGATCGCTCACTCTGCATATGCATCGGAAAAATTAACCTTCAAGACCGATCTTGAGAAGCTAGAGCGCGAAAAAGCAGCTCAGATCGGTGTTGCGATCGTCGATCCCCAAGGAGAGATCGTCGCGGGCCACCGAATGGCGCAGCGTTTTGCAATGTGCTCAACGTTCAAGTTTCCGCTAGCCGCGCTGGTCTTTGAAAGAATTGACTCAGGCACCGAGCGGGGGGATCGAAAACTTTCATATGGGCCGGACATGATCGTCGAATGGTCTCCTGCCACGGAGCGGTTTCTAGCATCGGGACACATGACGGTTCTCGAGGCAGCGCAACTGGCGGTGCAGCTTAGCGACAATGGGGCTACTAACCTCTTACTGAGAGAAATTGGCGGACCTGCTGCAATGACGCAGTATTTTCGTAAAATTGGCGACTCTGTGAGTCGGCTAGACCGGAAAGAGCCGGAGATGGGCGACAACACACCTGGCGACCTCAGAGATACAACTACGCCTATTGCTATGGCACGTACTGTGGCTAAAGTCCTCTATGGCGGCGCACTGACGTCCACCTCGACCCACACCATTGAGAGGTGGCTGATCGGAAACCAAACGGGAGACGCGACACTACGAGCGGGTTTTCCTAAAGATTGGGTTGTTGGAGAGAAAACTGGTACCTGCGCCAACGGGGGCCGGAACGACATTGGTTTTTTTAAAGCCCAGGAGAGAGATTACGCTGTAGCGGTGTATACAACGGCCCCGAAACTATCGGCCGTAGAACGTGACGAATTAGTTGCCTCTGTCGGTCAAGTTATTACACAACTCATCCTGAGCACGGACAAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002337","ARO_id":"38737","ARO_name":"GES-8","CARD_short_name":"GES-8","ARO_description":"GES-8 is a beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36205":{"category_aro_accession":"3000066","category_aro_cvterm_id":"36205","category_aro_name":"GES beta-lactamase","category_aro_description":"GES beta-lactamases or Guiana extended-spectrum beta-lactamases are related to the other plasmid-located class A beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"933":{"model_id":"933","model_name":"OKP-A-14","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"1120":{"protein_sequence":{"accession":"ACL68095.1","sequence":"MRYIRLCLFSLIAALPLAVFASPPPLEQITRSESQLAGRVGYVEMDLASGRTLAAWRASERFPLMSTFKVLLCGAVLARVDAGDEQLDRRIRYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAGNLLLKSVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDVRDTTTPASMATTLRKLLTSHTLSARSQQQLLQWMVDDQVAGPLIRAVLPAGWFIADKTGAGERGSRGIVALLGPNGKAERIVVIYLRDTPATIAERNQQIARIGAALIEHWQR"},"dna_sequence":{"accession":"FJ534512.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGCCTTTTCTCCCTGATTGCCGCCCTGCCACTGGCGGTATTCGCCAGCCCTCCGCCGCTTGAGCAAATTACACGCAGCGAAAGTCAGCTGGCGGGCCGCGTGGGCTATGTTGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCAGTGAGCGCTTTCCGCTGATGAGCACCTTTAAAGTGCTGCTCTGCGGCGCGGTGCTGGCCCGGGTGGATGCCGGAGACGAACAGCTGGATCGGCGGATCCGCTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGCCGACGGGATGACCGTTGGCGAACTCTGCGCCGCCGCCATCACCATGAGCGACAACAGCGCCGGCAATCTGCTGTTGAAGAGCGTTGGCGGCCCCGCGGGATTGACCGCTTTTTTGCGCCAGATCGGTGACAACGTCACCCGCCTCGACCGCTGGGAAACGGAGCTCAATGAAGCGCTTCCCGGCGACGTGCGCGACACCACCACCCCAGCCAGCATGGCCACCACCCTGCGCAAGCTGCTAACCAGCCACACTCTGAGCGCCCGTTCGCAGCAGCAGCTGCTGCAGTGGATGGTGGACGACCAGGTAGCCGGTCCGCTGATCCGCGCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAAACCGGGGCCGGCGAGCGGGGCTCACGTGGCATTGTCGCCCTGCTCGGCCCGAACGGCAAAGCGGAGCGCATCGTGGTGATCTATCTGCGGGATACGCCGGCGACCATAGCCGAGCGTAACCAGCAGATCGCCAGAATAGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002431","ARO_id":"38831","ARO_name":"OKP-A-14","CARD_short_name":"OKP-A-14","ARO_description":"OKP-A-14 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"38817":{"category_aro_accession":"3002417","category_aro_cvterm_id":"38817","category_aro_name":"OKP beta-lactamase","category_aro_description":"OKP beta-lactamases are chromosomal class A beta-lactamase that confer resistance to penicillins and early cephalosporins in Klebsiella pneumoniae. OKP beta-lactamases can be subdivided into two groups: OKP-A and OKP-B which diverge by about 4.2%.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"934":{"model_id":"934","model_name":"IMP-8","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"8171":{"protein_sequence":{"accession":"AAK13430.1","sequence":"MKKLFVLCVCFLCSITAAGAALPDLKIEKLEEGVYVHTSFEEVNGWGVVSKHGLVVLVNTDAYLIDTPFTATDTEKLVNWFVERGYKIKGTISSHFHSDSTGGIEWLNSQSIPTYASELTNELLKKDGKVQAKNSFSGVSYWLVKNKIEVFYPGPGHTQDNVVVWLPEKKILFGGCFVKPDGLGNLGDANLEAWPKSAKILMSKYGKAKLVVSSHSEIGDASLLKRTWEQAVKGLNESKKPSQPSN"},"dna_sequence":{"accession":"AF322577.2","fmin":"2081","fmax":"2822","strand":"+","sequence":"ATGAAGAAATTATTTGTTTTATGTGTATGCTTCCTTTGTAGCATTACTGCCGCAGGAGCGGCTTTGCCTGATTTAAAAATCGAGAAGCTTGAAGAAGGTGTTTATGTTCATACATCGTTCGAAGAAGTTAACGGTTGGGGTGTTGTTTCTAAACACGGTTTGGTGGTTCTTGTAAACACTGACGCCTATCTGATTGACACTCCATTTACTGCTACAGATACTGAAAAGTTAGTCAATTGGTTTGTGGAGCGCGGCTATAAAATCAAAGGCACTATTTCCTCACATTTCCATAGCGACAGCACAGGGGGAATAGAGTGGCTTAATTCTCAATCTATTCCCACGTATGCATCTGAATTAACAAATGAACTTCTTAAAAAAGACGGTAAGGTGCAAGCTAAAAACTCATTTAGCGGAGTTAGTTATTGGCTAGTTAAAAATAAAATTGAAGTTTTTTATCCCGGCCCGGGGCACACTCAAGATAACGTAGTGGTTTGGTTACCTGAAAAGAAAATTTTATTCGGTGGTTGTTTTGTTAAACCGGACGGTCTTGGTAATTTGGGTGACGCAAATTTAGAAGCTTGGCCAAAGTCCGCCAAAATATTAATGTCTAAATATGGTAAAGCAAAACTGGTTGTTTCAAGTCATAGTGAAATTGGGGACGCATCACTCTTGAAACGTACATGGGAACAGGCTGTTAAAGGGCTAAATGAAAGTAAAAAACCATCACAGCCAAGTAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002199","ARO_id":"38599","ARO_name":"IMP-8","CARD_short_name":"IMP-8","ARO_description":"IMP-8 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"935":{"model_id":"935","model_name":"OXA-314","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1458":{"protein_sequence":{"accession":"AGU69252.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"KF057031.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGACGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCATTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001685","ARO_id":"38085","ARO_name":"OXA-314","CARD_short_name":"OXA-314","ARO_description":"OXA-314 is a beta-lactamase found in A. baumannii.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"936":{"model_id":"936","model_name":"OKP-A-13","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"1040":{"protein_sequence":{"accession":"ACL68096.1","sequence":"MRYIRLCLFSLIAALPLAVFASPPPLEQITRSESQLAGRVGYVEMDLASGRTLAAWRASERFPLMSTFKVLLCGAVLARVDAGDEQLDRRIRYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAGNLLLKSVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDVRDTTTPASMAATLRKLLTSHTLSARSQQQLLQWMVDDQVAGPLIRAVLPAGWFIADKTGAGERGSRGIVALLGPNGKAERIVVIYLRDTPATMAERNQQIARIGAALIEHWQR"},"dna_sequence":{"accession":"FJ534513.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGCCTTTTCTCCCTGATTGCCGCCCTGCCACTGGCGGTATTCGCCAGCCCTCCGCCGCTTGAGCAAATTACACGCAGCGAAAGTCAGCTGGCGGGCCGCGTGGGCTATGTTGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCAGTGAGCGCTTTCCGCTGATGAGCACCTTTAAAGTGCTGCTCTGCGGCGCGGTGCTGGCCCGGGTGGATGCCGGAGACGAACAGCTGGATCGGCGGATCCGCTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGCCGACGGGATGACCGTTGGCGAACTCTGCGCCGCCGCCATCACCATGAGCGACAACAGCGCCGGCAATCTGCTGTTGAAGAGCGTTGGCGGCCCCGCGGGATTGACCGCTTTTTTGCGCCAGATCGGTGACAACGTCACCCGCCTCGACCGCTGGGAAACGGAGCTCAATGAAGCGCTTCCCGGCGACGTGCGCGACACCACCACCCCAGCCAGCATGGCCGCCACCCTGCGCAAGCTGCTAACCAGCCACACTCTGAGCGCCCGTTCGCAGCAGCAGCTGCTGCAGTGGATGGTGGACGACCAGGTAGCCGGTCCGCTGATCCGCGCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAAACCGGGGCCGGCGAGCGGGGCTCACGTGGCATTGTCGCCCTGCTCGGCCCGAACGGCAAAGCGGAGCGCATCGTGGTGATCTATCTGCGGGATACGCCGGCGACCATGGCCGAGCGTAACCAGCAGATCGCCAGAATAGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002430","ARO_id":"38830","ARO_name":"OKP-A-13","CARD_short_name":"OKP-A-13","ARO_description":"OKP-A-13 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"38817":{"category_aro_accession":"3002417","category_aro_cvterm_id":"38817","category_aro_name":"OKP beta-lactamase","category_aro_description":"OKP beta-lactamases are chromosomal class A beta-lactamase that confer resistance to penicillins and early cephalosporins in Klebsiella pneumoniae. OKP beta-lactamases can be subdivided into two groups: OKP-A and OKP-B which diverge by about 4.2%.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"937":{"model_id":"937","model_name":"OXA-242","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1838":{"protein_sequence":{"accession":"AFO55202.1","sequence":"MNIKTLLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEVHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQRNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"JX025022.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAACACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGTACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACGCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCCTTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAAGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001680","ARO_id":"38080","ARO_name":"OXA-242","CARD_short_name":"OXA-242","ARO_description":"OXA-242 is a beta-lactamase found in A. baumannii.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"938":{"model_id":"938","model_name":"QnrB70","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"370":{"protein_sequence":{"accession":"AGL43631.1","sequence":"MTLVLVGEKIDRNRFTGEKVENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNVSALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGTQVLGATFSGSDLSGGEFSTFDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDNYQASLLMERLGIAVIG"},"dna_sequence":{"accession":"KC580659.1","fmin":"0","fmax":"645","strand":"+","sequence":"ATGACTCTGGTATTAGTAGGCGAAAAAATTGACAGAAATCGCTTCACCGGTGAGAAAGTTGAAAATAGTACATTTTTTAACTGCGATTTTTCAGGTGCCGACCTGAGCGGCACTGAATTTATCGGCTGCCAGTTCTATGATCGCGAAAGTCAGAAAGGATGCAATTTTAGTCGCGCAATGCTGAAAGATGCCATTTTCAAAAGCTGTGATTTATCAATGGCAGATTTCCGCAACGTCAGCGCATTGGGCATTGAAATTCGCCACTGCCGCGCACAAGGCGCAGATTTCCGCGGTGCAAGCTTTATGAATATGATCACCACGCGCACCTGGTTTTGCAGCGCATATATCACTAATACCAATCTAAGCTACGCCAATTTTTCGAAAGTCGTGTTGGAAAAGTGTGAGCTATGGGAAAACCGCTGGATGGGGACTCAGGTACTGGGTGCGACGTTTAGTGGTTCAGATCTCTCCGGTGGCGAGTTTTCGACTTTCGACTGGCGAGCAGCAAACTTCACACATTGCGATCTGACCAATTCGGAGTTAGGTGACTTAGATATTCGGGGTGTTGATTTACAAGGCGTTAAGTTAGACAACTACCAGGCATCGTTGCTCATGGAGCGGCTTGGCATCGCTGTGATTGGTTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39584","NCBI_taxonomy_name":"Citrobacter braakii","NCBI_taxonomy_id":"57706"}}}},"ARO_accession":"3002782","ARO_id":"39216","ARO_name":"QnrB70","CARD_short_name":"QnrB70","ARO_description":"QnrB70 is a plasmid-mediated quinolone resistance protein found in Citrobacter freundii.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"939":{"model_id":"939","model_name":"CTX-M-113","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1901":{"protein_sequence":{"accession":"AEM44653.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKRSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"JF274247.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCGGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGACTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36955","NCBI_taxonomy_name":"Shigella sp. SH284","NCBI_taxonomy_id":"1074436"}}}},"ARO_accession":"3001973","ARO_id":"38373","ARO_name":"CTX-M-113","CARD_short_name":"CTX-M-113","ARO_description":"CTX-M-113 is a beta-lactamase found in Shigella spp.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"940":{"model_id":"940","model_name":"TEM-125","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1489":{"protein_sequence":{"accession":"AAT46414.1","sequence":"MSIQHFRVALIPFLAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMLSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDSREPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERDRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AY628176.1","fmin":"75","fmax":"936","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTCTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGCTAAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAACAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATAGTCGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAGATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000987","ARO_id":"37367","ARO_name":"TEM-125","CARD_short_name":"TEM-125","ARO_description":"TEM-125 is a CMT-type, inhibitor-resistant, extended-spectrum beta-lactamase found in E. coli.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"941":{"model_id":"941","model_name":"GES-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1593":{"protein_sequence":{"accession":"AAF27723.1","sequence":"MRFIHALLLAGIAHSAYASEKLTFKTDLEKLEREKAAQIGVAIVDPQGEIVAGHRMAQRFAMCSTFKFPLAALVFERIDSGTERGDRKLSYGPDMIVEWSPATERFLASGHMTVLEAAQAAVQLSDNGATNLLLREIGGPAAMTQYFRKIGDSVSRLDRKEPEMGDNTPGDLRDTTTPIAMARTVAKVLYGGALTSTSTHTIERWLIGNQTGDATLRAGFPKDWVVGEKTGTCANGGRNDIGFFKAQERDYAVAVYTTAPKLSAVERDELVASVGQVITQLILSTDK"},"dna_sequence":{"accession":"AF156486.1","fmin":"1331","fmax":"2195","strand":"+","sequence":"ATGCGCTTCATTCACGCACTATTACTGGCAGGGATCGCTCACTCTGCATATGCGTCGGAAAAATTAACCTTCAAGACCGATCTTGAGAAGCTAGAGCGCGAAAAAGCAGCTCAGATCGGTGTTGCGATCGTCGATCCCCAAGGAGAGATCGTCGCGGGCCACCGAATGGCGCAGCGTTTTGCAATGTGCTCAACGTTCAAGTTTCCGCTAGCCGCGCTGGTCTTTGAAAGAATTGACTCAGGCACCGAGCGGGGGGATCGAAAACTTTCATATGGGCCGGACATGATCGTCGAATGGTCTCCTGCCACGGAGCGGTTTCTAGCATCGGGACACATGACGGTTCTCGAGGCAGCGCAAGCTGCGGTGCAGCTTAGCGACAATGGGGCTACTAACCTCTTACTGAGAGAAATTGGCGGACCTGCTGCAATGACGCAGTATTTTCGTAAAATTGGCGACTCTGTGAGTCGGCTAGACCGGAAAGAGCCGGAGATGGGCGACAACACACCTGGCGACCTCAGAGATACAACTACGCCTATTGCTATGGCACGTACTGTGGCTAAAGTCCTCTATGGCGGCGCACTGACGTCCACTTCGACCCACACCATTGAGAGGTGGCTGATCGGAAACCAAACGGGAGACGCGACACTACGAGCGGGTTTTCCTAAAGATTGGGTTGTTGGAGAGAAAACTGGTACCTGCGCCAACGGGGGCCGGAACGACATTGGTTTTTTTAAAGCCCAGGAGAGAGATTACGCTGTAGCGGTGTATACAACGGCCCCGAAACTATCGGCCGTAGAACGTGACGAATTAGTTGCCTCTGTCGGTCAAGTTATTACACAACTCATCCTGAGCACGGACAAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002330","ARO_id":"38730","ARO_name":"GES-1","CARD_short_name":"GES-1","ARO_description":"GES-1 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36205":{"category_aro_accession":"3000066","category_aro_cvterm_id":"36205","category_aro_name":"GES beta-lactamase","category_aro_description":"GES beta-lactamases or Guiana extended-spectrum beta-lactamases are related to the other plasmid-located class A beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"942":{"model_id":"942","model_name":"OXA-104","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1122":{"protein_sequence":{"accession":"ABQ52429.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"EF581285.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGAACATTAAAGCGCTGCTGCTGATTACCAGCGCGATTTTTATTAGCGCGTGCAGCCCGTATATTGTGACCGCGAACCCGAACCATAGCGCGAGCAAAAGCGATGAAAAAGCGGAAAAAATTAAAAACCTGTTTAACGAAGCGCATACCACCGGCGTGCTGGTGATTCAGCAGGGCCAGACCCAGCAGAGCTATGGCAACGATCTGGCGCGCGCGAGCACCGAATATGTGCCGGCGAGCACCTTTAAAATGCTGAACGCGCTGATTGGCCTGGAACATCATAAAGCGACCACCACCGAAGTGTTTAAATGGGATGGCAAAAAACGCCTGTTTCCGGAATGGGAAAAAAACATGACCCTGGGCGATGCGATGAAAGCGAGCGCGATTCCGGTGTATCAGGATCTGGCGCGCCGCATTGGCCTGGAACTGATGAGCAACGAAGTGAAACGCGTGGGCTATGGCAACGCGGATATTGGCACCCAGGTGGATAACTTTTGGCTGGTGGGCCCGCTGAAAATTACCCCGCAGCAGGAAGCGCAGTTTGCGTATAAACTGGCGAACAAAACCCTGCCGTTTAGCCAGAAAGTGCAGGATGAAGTGCAGAGCATGCTGTTTATTGAAGAAAAAAACGGCAACAAAATTTATGCGAAAAGCGGCTGGGGCTGGGATGTGGATCCGCAGGTGGGCTGGCTGACCGGCTGGGTGGTGCAGCCGCAGGGCAACATTGTGGCGTTTAGCCTGAACCTGGAAATGAAAAAAGGCATTCCGAGCAGCGTGCGCAAAGAAATTACCTATAAAAGCCTGGAACAGCTGGGCATTCTG","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001636","ARO_id":"38036","ARO_name":"OXA-104","CARD_short_name":"OXA-104","ARO_description":"OXA-104 is a beta-lactamase found in A. baumannii.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"944":{"model_id":"944","model_name":"bcrB","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"370"}},"model_sequences":{"sequence":{"585":{"protein_sequence":{"accession":"AAA99505.1","sequence":"MAKKAKYPDVPIRFSETFSDTNLYIVLLIGVPLYGVITSYLFNREYAESTLKNLLTIPVSRISLIVSKLVLLLIWIMMLTLIAWVLTLLFGLIGQFEGLSSAVLIEGFKQFMIGGALLFFLVSPIIFVTLLFKNYVPTIIFTIIISMVSIMVYGTEYSALFPWSAVWVIASGTFFPEYPPEYSFISVAATTVLGLAATIVYFKKIDIH"},"dna_sequence":{"accession":"L20573.1","fmin":"1317","fmax":"1944","strand":"+","sequence":"TTGGCTAAAAAAGCCAAGTACCCTGATGTACCGATTCGCTTCAGTGAGACCTTTTCCGATACCAACCTGTATATTGTGCTTTTGATCGGAGTCCCGTTGTATGGTGTGATTACATCATATTTATTCAATCGGGAATACGCTGAAAGCACGCTAAAGAATCTATTGACGATTCCTGTTTCAAGAATCAGCCTGATTGTCAGCAAATTGGTTCTGCTTCTCATTTGGATCATGATGCTGACGTTAATCGCCTGGGTGCTGACGCTGCTGTTCGGGCTGATCGGTCAGTTTGAAGGGCTCAGTTCGGCGGTTTTAATTGAAGGGTTTAAACAATTTATGATAGGCGGGGCACTTCTTTTCTTCCTGGTCAGTCCGATTATATTTGTGACACTGCTGTTTAAAAACTACGTGCCCACCATTATCTTTACGATCATTATATCAATGGTCAGCATTATGGTATACGGCACGGAATACAGCGCTTTATTCCCTTGGTCAGCGGTATGGGTGATCGCTTCGGGTACGTTCTTTCCGGAATATCCGCCCGAATATTCTTTTATCAGTGTTGCCGCCACAACCGTTCTTGGATTAGCCGCGACAATCGTTTACTTTAAAAAAATCGATATTCATTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36834","NCBI_taxonomy_name":"Bacillus licheniformis","NCBI_taxonomy_id":"1402"}}}},"ARO_accession":"3002988","ARO_id":"39422","ARO_name":"bcrB","CARD_short_name":"bcrB","ARO_description":"bcrB is an ABC transporter found in Bacillus licheniformis that confers bacitracin resistance.","ARO_category":{"36002":{"category_aro_accession":"0010001","category_aro_cvterm_id":"36002","category_aro_name":"ATP-binding cassette (ABC) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding\/hydrolysis to transport substrates across cell membranes.","category_aro_class_name":"AMR Gene Family"},"35959":{"category_aro_accession":"0000041","category_aro_cvterm_id":"35959","category_aro_name":"bacitracin","category_aro_description":"Bacitracin is a mixture of related cyclic polypeptides produced by organisms of the licheniformis group of Bacillus subtilis var Tracy. Bacitracin interferes with the dephosphorylation of the C55-isoprenyl pyrophosphate, a molecule which carries the building blocks of the peptidoglycan bacterial cell wall outside of the inner membrane.","category_aro_class_name":"Antibiotic"},"36973":{"category_aro_accession":"3000629","category_aro_cvterm_id":"36973","category_aro_name":"bacitracin A","category_aro_description":"Bacitracin A is the primary component of bacitracin. It contains many uncommon amino acids and interferes with bacterial cell wall synthesis.","category_aro_class_name":"Antibiotic"},"36974":{"category_aro_accession":"3000630","category_aro_cvterm_id":"36974","category_aro_name":"bacitracin B","category_aro_description":"Bacitracin B is a component of bacitracin, an antibiotic mixture that interferes with bacterial cell wall synthesis. It differs from Bacitracin A with a valine instead of an isoleucine in its peptide.","category_aro_class_name":"Antibiotic"},"36975":{"category_aro_accession":"3000631","category_aro_cvterm_id":"36975","category_aro_name":"bacitracin F","category_aro_description":"Bacitracin F is a component of bacitracin, an antibiotic mixture that interferes with bacterial cell wall synthesis. It is formed when the thiazoline ring of bacitracin A is oxidatively deaminated.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"946":{"model_id":"946","model_name":"QnrB48","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"177":{"protein_sequence":{"accession":"AFH88686.1","sequence":"MALALVGEKIDRNRFTGEKIENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNASALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGAQVLGATFSGSDLSGGEFSTFDWRAANFTHCDLTNSELGGLDIRGVDLQGVKLDNYQASLLMERLGIAIIG"},"dna_sequence":{"accession":"JQ762640.1","fmin":"36","fmax":"681","strand":"+","sequence":"ATGGCTCTGGCACTCGTTGGCGAAAAAATTGACAGGAACCGCTTCACCGGTGAGAAAATTGAAAATAGTACATTTTTTAACTGTGATTTTTCAGGTGCCGACCTGAGCGGCACTGAATTTATCGGCTGTCAGTTCTATGATCGTGAAAGCCAGAAAGGGTGCAATTTTAGTCGTGCGATGCTGAAAGATGCCATTTTTAAAAGCTGTGATTTATCCATGGCGGATTTTCGCAATGCCAGTGCGCTTGGCATTGAAATTCGCCACTGTCGTGCGCAAGGCGCAGATTTTCGCGGCGCAAGCTTTATGAATATGATCACCACACGCACCTGGTTTTGCAGCGCATATATAACTAACACAAATCTAAGCTACGCCAATTTTTCGAAAGTCGTGCTGGAAAAATGTGAGCTGTGGGAAAACCGTTGGATGGGTGCCCAGGTACTGGGCGCGACGTTCAGTGGTTCAGATCTTTCCGGCGGCGAGTTTTCGACTTTCGACTGGCGAGCAGCAAACTTCACACATTGCGATCTGACCAATTCGGAGTTGGGTGGCTTAGATATTCGGGGCGTTGATTTACAAGGCGTTAAGTTGGACAACTACCAGGCATCGTTGCTCATGGAACGTCTTGGCATCGCGATTATTGGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002763","ARO_id":"39197","ARO_name":"QnrB48","CARD_short_name":"QnrB48","ARO_description":"QnrB48 is a plasmid-mediated quinolone resistance protein found in Citrobacter freundii.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"947":{"model_id":"947","model_name":"OXA-100","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8236":{"protein_sequence":{"accession":"CAJ77817.2","sequence":"MNIKALLLITSTIFISACSPYIVTANPNHSTSKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEIFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"AM231720.2","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCACTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCACTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAATATTTAAGTGGGACGGGCAAAAAAGGCTGTTCCCAGAATGGGAAAAGGACATGACCCTAGGTGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACGCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001438","ARO_id":"37838","ARO_name":"OXA-100","CARD_short_name":"OXA-100","ARO_description":"OXA-100 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"949":{"model_id":"949","model_name":"CTX-M-77","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1904":{"protein_sequence":{"accession":"CAQ42480.1","sequence":"MMTQSIRRSMLTVMATLPLLFSSATLHAQTNSVQQQLKALEKSSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKQSESDKHLLNQRVEIKKSDLVNYNPIAEKHVNGTMTLAELGAAALQYSDNTAMNKLIAHLGGPDKVTAFARSLGDETFRLDRTEPTLNTAIPGDPRDTTTPLAMAQTLKNLTLGKALAETQRAQLVTWLKGNTTGSASIQAGLPKSWVVGDKTGSGDYGTTNDIAIIWPENHAPLVLVTYFTQPEQKAESRRDVLAAAAKIVTRGF"},"dna_sequence":{"accession":"AM982521.1","fmin":"1911","fmax":"2787","strand":"+","sequence":"ATGATGACTCAGAGCATTCGCCGCTCAATGTTAACGGTGATGGCGACGCTACCCCTGCTATTTAGCAGCGCAACGCTGCATGCGCAGACGAACAGCGTGCAACAGCAGCTGAAAGCCCTGGAGAAAAGTTCGGGAGGTCGGCTTGGCGTTGCGCTGATTAACACCGCCGATAATTCGCAGATTCTCTACCGTGCCGATGAACGTTTTGCGATGTGCAGTACCAGTAAGGTGATGGCGGCCGCGGCGGTGCTTAAACAGAGCGAGAGCGATAAGCACCTGCTAAATCAGCGCGTTGAAATCAAGAAGAGCGACCTGGTTAACTACAATCCCATTGCGGAGAAACACGTTAACGGCACGATGACGCTGGCTGAGCTTGGCGCAGCGGCGCTGCAGTATAGCGACAATACTGCCATGAATAAGCTGATTGCCCATCTGGGTGGGCCCGATAAAGTGACGGCGTTTGCTCGCTCGTTGGGTGATGAGACCTTCCGTCTGGACAGAACCGAGCCCACGCTCAATACCGCCATTCCAGGCGACCCGCGTGATACCACCACGCCGCTCGCGATGGCGCAGACCCTGAAAAATCTGACGCTGGGTAAAGCGCTGGCGGAAACCCAGCGGGCACAGTTGGTGACGTGGCTTAAGGGCAATACTACCGGTAGCGCGAGCATTCAGGCGGGTCTGCCGAAATCATGGGTAGTGGGCGATAAAACCGGCAGCGGAGATTATGGCACCACCAACGATATCGCGATTATCTGGCCGGAAAACCACGCACCGCTGGTTCTGGTGACCTACTTTACCCAACCGGAGCAGAAGGCGGAAAGCCGTCGGGATGTTCTGGCTGCGGCGGCGAAAATCGTAACCCGCGGTTTCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36928","NCBI_taxonomy_name":"Kluyvera ascorbata","NCBI_taxonomy_id":"51288"}}}},"ARO_accession":"3001938","ARO_id":"38338","ARO_name":"CTX-M-77","CARD_short_name":"CTX-M-77","ARO_description":"CTX-M-77 is a beta-lactamase found in Kluyvera spp.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"950":{"model_id":"950","model_name":"ErmX","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"5163":{"protein_sequence":{"accession":"AAA98484.1","sequence":"MSAYGQGRHEHGQNFLTNHKIINSIIDLVKQTSGPIIEIGPGSGALTHPMAHLGRAITAVEVDAKLAAKITQETSSAAVEVVHDDFLNFRLPATPCVIVGNIPFHLTTAILRKLLHAPAWTDAVLLMQWEVARRRAGVGATTMMTAQWSPWFTFHLGSRVPRSAFRPQPNVDGGILVIRRVGDPKIPIEQRKAFQAMVHTVFTARGRGIGEILRRQGCFHHVQKHNHGCAREESTPRPYLPDCYTNDWIDLFQVTGSSLPHHRPISPSGSSQRPPQRKNRSRRR"},"dna_sequence":{"accession":"M36726.1","fmin":"295","fmax":"1150","strand":"+","sequence":"ATGTCTGCATACGGACAGGGCCGTCACGAGCATGGCCAAAATTTTCTCACCAACCACAAGATCATCAACTCCATCATCGACCTTGTGAAACAAACCTCCGGCCCCATCATTGAGATCGGACCAGGAAGCGGTGCCCTCACTCACCCGATGGCCCACTTGGGGAGGGCGATAACGGCAGTTGAAGTGGACGCAAAACTAGCTGCCAAAATCACACAAGAAACCTCCTCGGCGGCGGTCGAAGTGGTCCATGATGATTTCCTTAACTTCCGGTTACCCGCCACTCCCTGCGTCATTGTGGGAAACATTCCCTTTCACCTCACCACTGCCATTCTTCGAAAGTTGCTGCATGCGCCAGCATGGACTGACGCTGTACTCCTCATGCAGTGGGAAGTCGCTCGCCGCCGGGCCGGGGTAGGCGCAACGACGATGATGACGGCTCAGTGGTCCCCATGGTTCACATTTCACCTGGGTTCTCGGGTACCAAGGTCTGCTTTCCGGCCACAGCCAAACGTTGACGGGGGGATCTTAGTGATCCGCCGGGTGGGTGACCCGAAGATTCCGATAGAGCAGCGCAAAGCCTTTCAGGCGATGGTGCACACCGTTTTCACTGCCCGGGGACGCGGGATAGGGGAAATTCTCCGAAGGCAGGGTTGTTTTCATCACGTTCAGAAACATAATCATGGTTGCGCTCGCGAGGAATCGACCCCGCGACCCTACCTCCCAGATTGCTACACCAACGACTGGATCGATCTCTTCCAGGTGACTGGTTCCTCTCTACCTCACCATCGACCCATTTCACCATCGGGAAGTAGTCAACGACCTCCTCAACGGAAAAACCGAAGCCGGCGGCGTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36836","NCBI_taxonomy_name":"Plasmid pNG2","NCBI_taxonomy_id":"2609"}}}},"ARO_accession":"3000596","ARO_id":"36735","ARO_name":"ErmX","CARD_short_name":"ErmX","ARO_description":"ErmX is a rRNA methyltransferase that protects the ribosome from inactivation due to antibiotic binding.","ARO_category":{"36699":{"category_aro_accession":"3000560","category_aro_cvterm_id":"36699","category_aro_name":"Erm 23S ribosomal RNA methyltransferase","category_aro_description":"Erm proteins are part of the RNA methyltransferase family and methylate A2058 (E. coli nomenclature) of the 23S ribosomal RNA conferring degrees of resistance to Macrolides, Lincosamides and Streptogramin b. This is called the MLSb phenotype.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35946":{"category_aro_accession":"0000027","category_aro_cvterm_id":"35946","category_aro_name":"roxithromycin","category_aro_description":"Roxithromycin is a semi-synthetic, 14-carbon ring macrolide antibiotic derived from erythromycin. It is used to treat respiratory tract, urinary and soft tissue infections. Roxithromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35974":{"category_aro_accession":"0000057","category_aro_cvterm_id":"35974","category_aro_name":"telithromycin","category_aro_description":"Telithromycin is a semi-synthetic derivative of erythromycin. It is a 14-membered macrolide and is the first ketolide antibiotic to be used in clinics. Telithromycin binds the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"35982":{"category_aro_accession":"0000065","category_aro_cvterm_id":"35982","category_aro_name":"clarithromycin","category_aro_description":"Clarithromycin is a methyl derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome and is used to treat pharyngitis, tonsillitis, acute maxillary sinusitis, acute bacterial exacerbation of chronic bronchitis, pneumonia (especially atypical pneumonias associated with Chlamydia pneumoniae or TWAR), and skin structure infections.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"36284":{"category_aro_accession":"3000145","category_aro_cvterm_id":"36284","category_aro_name":"tylosin","category_aro_description":"Tylosin is a 16-membered macrolide, naturally produced by Streptomyces fradiae. It interacts with the bacterial ribosome 50S subunit to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"36295":{"category_aro_accession":"3000156","category_aro_cvterm_id":"36295","category_aro_name":"spiramycin","category_aro_description":"Spiramycin is a 16-membered macrolide and is natural product produced by Streptomyces ambofaciens. It binds to the 50S subunit of bacterial ribosomes and inhibits peptidyl transfer activity to disrupt protein synthesis.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"36315":{"category_aro_accession":"3000176","category_aro_cvterm_id":"36315","category_aro_name":"dirithromycin","category_aro_description":"Dirithromycin is an oxazine derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome to inhibit bacterial protein synthesis.","category_aro_class_name":"Antibiotic"},"36722":{"category_aro_accession":"3000583","category_aro_cvterm_id":"36722","category_aro_name":"pristinamycin IA","category_aro_description":"Pristinamycin IA is a type B streptogramin antibiotic produced by Streptomyces pristinaespiralis. It binds to the P site of the 50S subunit of the bacterial ribosome, preventing the extension of protein chains.","category_aro_class_name":"Antibiotic"},"36723":{"category_aro_accession":"3000584","category_aro_cvterm_id":"36723","category_aro_name":"quinupristin","category_aro_description":"Quinupristin is a type B streptogramin and a semisynthetic derivative of pristinamycin 1A. It is a component of the drug Synercid and interacts with the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"virginiamycin M1","category_aro_description":"Virginiamycin M1 is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37016":{"category_aro_accession":"3000672","category_aro_cvterm_id":"37016","category_aro_name":"madumycin II","category_aro_description":"Madumycin II is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37017":{"category_aro_accession":"3000673","category_aro_cvterm_id":"37017","category_aro_name":"griseoviridin","category_aro_description":"Griseoviridin is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"37019":{"category_aro_accession":"3000675","category_aro_cvterm_id":"37019","category_aro_name":"pristinamycin IB","category_aro_description":"Pristinamycin IB is a class B streptogramin similar to pristinamycin IA, the former containing a N-methyl-4-(methylamino)phenylalanine instead of a N-methyl-4-(dimethylamino)phenylalanine in its class A streptogramin counterpart (one less methyl group).","category_aro_class_name":"Antibiotic"},"37021":{"category_aro_accession":"3000677","category_aro_cvterm_id":"37021","category_aro_name":"virginiamycin S2","category_aro_description":"Virginiamycin S2 is a streptogramin B antibiotic.","category_aro_class_name":"Antibiotic"},"37022":{"category_aro_accession":"3000678","category_aro_cvterm_id":"37022","category_aro_name":"pristinamycin IC","category_aro_description":"Pristinamycin IC is a class B streptogramin derived from virginiamycin S1.","category_aro_class_name":"Antibiotic"},"37023":{"category_aro_accession":"3000679","category_aro_cvterm_id":"37023","category_aro_name":"vernamycin C","category_aro_description":"Vernamycin C is a streptogramin B antibiotic.","category_aro_class_name":"Antibiotic"},"37024":{"category_aro_accession":"3000680","category_aro_cvterm_id":"37024","category_aro_name":"patricin A","category_aro_description":"Patricin A is a streptogramin B antibiotic.","category_aro_class_name":"Antibiotic"},"37025":{"category_aro_accession":"3000681","category_aro_cvterm_id":"37025","category_aro_name":"patricin B","category_aro_description":"Patricin B is a streptogramin B antibiotic.","category_aro_class_name":"Antibiotic"},"37026":{"category_aro_accession":"3000682","category_aro_cvterm_id":"37026","category_aro_name":"ostreogrycin B3","category_aro_description":"Ostreogrycin B3 is a derivative of pristinamycin IA, with an additional 3-hydroxy group on its 4-oxopipecolic acid.","category_aro_class_name":"Antibiotic"},"37247":{"category_aro_accession":"3000867","category_aro_cvterm_id":"37247","category_aro_name":"oleandomycin","category_aro_description":"Oleandomycin is a 14-membered macrolide produced by Streptomyces antibioticus. It is ssimilar to erythromycin, and contains a desosamine amino sugar and an oleandrose sugar. It targets the 50S ribosomal subunit to prevent protein synthesis.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35952":{"category_aro_accession":"0000034","category_aro_cvterm_id":"35952","category_aro_name":"streptogramin A antibiotic","category_aro_description":"Streptogramin A antibiotics are cyclic polyketide peptide hybrids that bind to the ribosomal peptidyl transfer centre. Structural variation arises from substituting a proline for its desaturated derivative and by its substitution for Ala or Cys. Used alone, streptogramin A antibiotics are bacteriostatic, but is bactericidal when used with streptogramin B antibiotics.","category_aro_class_name":"Drug Class"},"35967":{"category_aro_accession":"0000050","category_aro_cvterm_id":"35967","category_aro_name":"streptogramin B antibiotic","category_aro_description":"Streptogramin B antibiotics are are cyclic hepta- or hexa-depsipeptides.  Type B streptogramins block the peptide exit tunnel of the 50S bacterial ribosome. The general composition of group B streptogramins is 3-hydroxypicolinic acid-L-Thr-D-aminobutyric acid (or D-Ala)-L-Pro-L-Phe (or 4-N-,N-(dimethylamino)-L-Phe)-X-L-phenylglycine. Used alone, streptogramin B antibiotics are bacteriostatic, but is bactericidal when used with streptogramin A antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"951":{"model_id":"951","model_name":"ACT-15","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1262":{"protein_sequence":{"accession":"AFU25653.1","sequence":"MMKKSLCCALLLGISCSALATPVSEKQLAEVVANTVTPLMKAQSVPGMAVAVIYQGKPHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKSGTTRLYANASIGLFGALAVKPSGMPYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPENVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVVEGSDSKVALAPLPVVEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANTSYPNPARVEAAYHILEALQ"},"dna_sequence":{"accession":"JX440356.1","fmin":"754","fmax":"1900","strand":"+","sequence":"ATGATGAAAAAATCCCTTTGCTGCGCCCTGCTGCTCGGCATTTCTTGCTCTGCTCTCGCCACGCCAGTGTCAGAAAAACAGCTGGCGGAGGTGGTCGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCTGTTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGAAAACCGCACTATTACACGTTTGGCAAGGCCGATATCGCGGCGAATAAACCCGTTACGCCTCAGACCCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGCGTTTTAGGTGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTGACGGGCAAGCAGTGGCAGGGTATTCGTATGCTGGATCTCGCCACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGTCTGGCACAACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTCAAACCTTCTGGCATGCCCTATGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTGCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGTATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCGGAGAACGTTGCTGATGCCTCACTTAAGCAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGGTCGAGGGCAGCGACAGTAAGGTAGCGCTGGCGCCGTTGCCCGTGGTAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGCTCTACTGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATACAAGCTATCCGAACCCGGCACGTGTTGAGGCGGCATACCATATCCTCGAGGCGCTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3001837","ARO_id":"38237","ARO_name":"ACT-15","CARD_short_name":"ACT-15","ARO_description":"ACT-15 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"952":{"model_id":"952","model_name":"sul2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4745":{"protein_sequence":{"accession":"AAL59753.1","sequence":"MNKSLIIFGIVNITSDSFSDGGRYLAPDAAIAQARKLMAEGADVIDLGPASSNPDAAPVSSDTEIARIAPVLDALKADGIPVSLDSYQPATQAYALSRGVAYLNDIRGFPDAAFYPQLAKSSAKLVVMHSVQDGQADRREAPAGDIMDHIAAFFDARIAALTGAGIKRNRLVLDPGMGFFLGAAPETSLSVLARFDELRLRFDLPVLLSVSRKSFLRALTGRGPGDVGAATLAAELAAAAGGADFIRTHEPRPLRDGLAVLAALKETARIR"},"dna_sequence":{"accession":"AY055428.1","fmin":"20268","fmax":"21084","strand":"-","sequence":"ATGAATAAATCGCTCATCATTTTCGGCATCGTCAACATAACCTCGGACAGTTTCTCCGATGGAGGCCGGTATCTGGCGCCAGACGCAGCCATTGCGCAGGCGCGTAAGCTGATGGCCGAGGGGGCAGATGTGATCGACCTCGGTCCGGCATCCAGCAATCCCGACGCCGCGCCTGTTTCGTCCGACACAGAAATCGCGCGTATCGCGCCGGTGCTGGACGCGCTCAAGGCAGATGGCATTCCCGTCTCGCTCGACAGTTATCAACCCGCGACGCAAGCCTATGCCTTGTCGCGTGGTGTGGCCTATCTCAATGATATTCGCGGTTTTCCAGACGCTGCGTTCTATCCGCAATTGGCGAAATCATCTGCCAAACTCGTCGTTATGCATTCGGTGCAAGACGGGCAGGCAGATCGGCGCGAGGCACCCGCTGGCGACATCATGGATCACATTGCGGCGTTCTTTGACGCGCGCATCGCGGCGCTGACGGGTGCCGGTATCAAACGCAACCGCCTTGTCCTTGATCCCGGCATGGGGTTTTTTCTGGGGGCTGCTCCCGAAACCTCGCTCTCGGTGCTGGCGCGGTTCGATGAATTGCGGCTGCGCTTCGATTTGCCGGTGCTTCTGTCTGTTTCGCGCAAATCCTTTCTGCGCGCGCTCACAGGCCGTGGTCCGGGGGATGTCGGGGCCGCGACACTCGCTGCAGAGCTTGCCGCCGCCGCAGGTGGAGCTGACTTCATCCGCACACACGAGCCGCGCCCCTTGCGCGACGGGCTGGCGGTATTGGCGGCGCTGAAAGAAACCGCAAGAATTCGTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36789","NCBI_taxonomy_name":"Vibrio cholerae","NCBI_taxonomy_id":"666"}}}},"ARO_accession":"3000412","ARO_id":"36551","ARO_name":"sul2","CARD_short_name":"sul2","ARO_description":"Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria, usually found on small plasmids.","ARO_category":{"41402":{"category_aro_accession":"3004238","category_aro_cvterm_id":"41402","category_aro_name":"sulfonamide resistant sul","category_aro_description":"The sul genes encode forms of dihydropteroate synthase that confer resistance to sulfonamide.","category_aro_class_name":"AMR Gene Family"},"36463":{"category_aro_accession":"3000324","category_aro_cvterm_id":"36463","category_aro_name":"sulfadiazine","category_aro_description":"Sulfadiazine is a potent inhibitor of dihydropteroate synthase, interfering with the tetrahydrofolic biosynthesis pathway. Tetrahydrofolic acid is essential for folate synthesis, a precursor to many nucleotides and amino acids.","category_aro_class_name":"Antibiotic"},"36464":{"category_aro_accession":"3000325","category_aro_cvterm_id":"36464","category_aro_name":"sulfadimidine","category_aro_description":"Sulfadimidine is an alkaline sulfonamide antibiotic that inhibits dihydropteroate synthase, and enzyme in the tetrahydrofolic acid biosynthesis pathway. This interferes with the production of folate, which is a precursor to many amino acids and nucleotides.","category_aro_class_name":"Antibiotic"},"36466":{"category_aro_accession":"3000327","category_aro_cvterm_id":"36466","category_aro_name":"sulfadoxine","category_aro_description":"Sulfadoxine is an inhibitor of dihydropteroate synthase, interfering with the tetrahydrofolic biosynthesis pathway. Tetrahydrofolic acid is essential for folate synthesis, a precursor to many nucleotides and amino acids.","category_aro_class_name":"Antibiotic"},"36468":{"category_aro_accession":"3000329","category_aro_cvterm_id":"36468","category_aro_name":"sulfamethoxazole","category_aro_description":"Sulfamethoxazole is a sulfonamide antibiotic usually taken with trimethoprim, a diaminopyrimidine antibiotic. Sulfamethoxazole inhibits dihydropteroate synthase, essential to tetrahydrofolic acid biosynthesis. This pathway generates compounds used in the synthesis of many amino acids and nucleotides.","category_aro_class_name":"Antibiotic"},"36469":{"category_aro_accession":"3000330","category_aro_cvterm_id":"36469","category_aro_name":"sulfisoxazole","category_aro_description":"Sulfisoxazole is an inhibitor of dihydropteroate synthase, interfering with the tetrahydrofolic biosynthesis pathway. Tetrahydrofolic acid is essential for folate synthesis, a precursor to many nucleotides and amino acids.","category_aro_class_name":"Antibiotic"},"37027":{"category_aro_accession":"3000683","category_aro_cvterm_id":"37027","category_aro_name":"sulfacetamide","category_aro_description":"Sulfacetamide is a very soluable sulfonamide antibiotic previously used to treat urinary tract infections. Its relatively low activity and toxicity to those with Stevens-Johnson syndrome have reduced its use and availability.","category_aro_class_name":"Antibiotic"},"37028":{"category_aro_accession":"3000684","category_aro_cvterm_id":"37028","category_aro_name":"mafenide","category_aro_description":"Mafenide is a sulfonamide used topically for treating burns.","category_aro_class_name":"Antibiotic"},"37042":{"category_aro_accession":"3000698","category_aro_cvterm_id":"37042","category_aro_name":"sulfasalazine","category_aro_description":"Sulfasalazine is a derivative of the early sulfonamide sulfapyridine (salicylazosulfapyridine). It was developed to increase water solubility and is taken orally for ulcerative colitis.","category_aro_class_name":"Antibiotic"},"37043":{"category_aro_accession":"3000699","category_aro_cvterm_id":"37043","category_aro_name":"sulfamethizole","category_aro_description":"Sulfamethizole is a short-acting sulfonamide that inhibits dihydropteroate synthetase.","category_aro_class_name":"Antibiotic"},"36421":{"category_aro_accession":"3000282","category_aro_cvterm_id":"36421","category_aro_name":"sulfonamide antibiotic","category_aro_description":"Sulfonamides are broad spectrum, synthetic antibiotics that contain the sulfonamide group. Sulfonamides inhibit dihydropteroate synthase, which catalyzes the conversion of p-aminobenzoic acid to dihydropteroic acid as part of the tetrahydrofolic acid biosynthetic pathway. Tetrahydrofolic acid is essential for folate synthesis, a precursor of many nucleotides and amino acids. Many sulfamides are taken with trimethoprim, an inhibitor of dihydrofolate reductase, also disturbing the trihydrofolic acid synthesis pathway.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"954":{"model_id":"954","model_name":"APH(3')-IIb","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"159":{"protein_sequence":{"accession":"CAA62365.1","sequence":"MHDAATSMPPQAPSTWADYLAGYRWRGQGEGCSAATVHRLEAARRPTLFVKQEVLSAHAELPAEIARLRWLHGAGIDCPQVLNETQSDGRQWLLMSAMPGDTLSALAQRDELEPERLVRLVAAALRRLHDLDPAACPFDHRLERRLDTVRQRVEAGLVDEADFDDDHRGRSATELYRLLLDRRPAVEDLVVAHGDACLPNLLAEGRRFSGFIDCGRLGVADRHQDLALAARDIEAELGAAWAEAFLVEYGGDIDGERLAYFRLLDEFF"},"dna_sequence":{"accession":"X90856.1","fmin":"387","fmax":"1194","strand":"+","sequence":"ATGCATGATGCAGCCACCTCCATGCCGCCGCAGGCTCCCTCAACCTGGGCCGACTACCTTGCCGGCTACCGCTGGCGAGGGCAGGGCGAAGGATGTTCCGCGGCCACGGTCCACCGCCTGGAGGCTGCGCGGCGGCCGACCCTGTTCGTCAAGCAGGAAGTGCTGTCCGCACATGCCGAGCTGCCCGCCGAAATCGCCCGCCTGCGCTGGCTGCACGGTGCCGGCATCGACTGCCCGCAGGTGCTGAACGAAACCCAGAGCGACGGCCGGCAATGGCTGCTGATGAGCGCAATGCCGGGGGACACGCTGTCCGCGCTGGCGCAGCGCGACGAGCTGGAGCCCGAGCGCCTGGTGCGCCTGGTGGCCGCCGCCCTGCGCCGGCTGCACGATCTCGATCCGGCCGCCTGTCCCTTCGATCATCGCCTGGAACGGCGTCTGGACACCGTGCGCCAGCGGGTCGAGGCCGGGCTGGTGGACGAGGCGGACTTCGACGACGACCATCGCGGTCGCAGCGCCACGGAGCTGTACCGCCTGCTGCTCGACCGGCGTCCGGCGGTCGAAGACCTGGTGGTCGCCCACGGCGACGCCTGCCTGCCCAACCTCTTGGCGGAGGGCCGGCGCTTCAGCGGCTTCATCGATTGCGGGCGGCTCGGCGTCGCCGACCGGCACCAGGACCTGGCCCTGGCCGCGCGGGACATCGAGGCCGAACTCGGCGCGGCCTGGGCCGAGGCCTTCCTCGTCGAATACGGCGGCGATATCGACGGCGAACGGCTGGCGTACTTCAGGCTATTGGACGAGTTCTTCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002645","ARO_id":"39045","ARO_name":"APH(3')-IIb","CARD_short_name":"APH(3')-IIb","ARO_description":"APH(3')-IIb is a chromosomal-encoded aminoglycoside phosphotransferase in P. aeruginosa.","ARO_category":{"36265":{"category_aro_accession":"3000126","category_aro_cvterm_id":"36265","category_aro_name":"APH(3')","category_aro_description":"A category of aminoglycoside O-phosphotransferase enzymes with modification regiospecificity based at the 3'-hydroxyl group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics, specifically kanamycin and neomycin, by the ATP-dependent phosphorylation of the 3'-hydroxyl group of the compound.","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35940":{"category_aro_accession":"0000021","category_aro_cvterm_id":"35940","category_aro_name":"ribostamycin","category_aro_description":"Ribostamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Ribostamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35943":{"category_aro_accession":"0000024","category_aro_cvterm_id":"35943","category_aro_name":"butirosin","category_aro_description":"Butirosin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Butirosin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"37001":{"category_aro_accession":"3000657","category_aro_cvterm_id":"37001","category_aro_name":"paromomycin","category_aro_description":"An aminoglycoside antibiotic used for the treatment of parasitic infections. It is similar to neomycin sharing a similar spectrum of activity, but its hydroxyl group at the 6'-position instead of an amino group makes it resistant to AAC(6') modifying enzymes.","category_aro_class_name":"Antibiotic"},"46133":{"category_aro_accession":"3007382","category_aro_cvterm_id":"46133","category_aro_name":"gentamicin","category_aro_description":"Gentamicin is a commonly used aminoglycoside antibiotic derived from members of the Micromonospora genus of bacteria. It acts by binding the 30S ribosomal subunit, thus inhibiting protein synthesis. Gentamicin is typically used to treat Gram-negative infections of the repiratory and urinary tract, as well as infections of the bone and soft tissue. It also exhibits considerable nephrotoxicity and ototoxicity. Gentamicin is administered as a mixture of gentamicin type C (which makes about around 80% of the complex) and types A, B, and X (distributed in the remaining 20% of the complex).","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"955":{"model_id":"955","model_name":"SHV-96","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"841":{"protein_sequence":{"accession":"ABN49112.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDARVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"EF373971.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGATGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGCTCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001148","ARO_id":"37528","ARO_name":"SHV-96","CARD_short_name":"SHV-96","ARO_description":"SHV-96 is a beta-lactamase found in Acinetobacter baumannii.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"956":{"model_id":"956","model_name":"TEM-88","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1652":{"protein_sequence":{"accession":"AAK14792.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVKYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTTPAAMATTLRKLLTDELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGASERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AY027590.1","fmin":"112","fmax":"973","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTAAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGACGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGACGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCAGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3000955","ARO_id":"37335","ARO_name":"TEM-88","CARD_short_name":"TEM-88","ARO_description":"TEM-88 is an extended-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"958":{"model_id":"958","model_name":"OXA-418","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"2112":{"protein_sequence":{"accession":"AIN56719.1","sequence":"MKFKMKGLFCVILSSLAFSGCVYDSKLQRPVISERETEIPLLFNQAQTQAVFVTYDGIHLKSYGNDLSRAKTEYIPASTFKMLNALIGLQNAKATNTEVFHWNGEKRAFSAWEKDMTLAEAMQASAVPVYQELARRIGLELMREEVKRVGFGNAEIGQQVDNFWLVGPLKISPEQEVQFAYQLAMKQLPFDRNVQQQVKNMLYIERRGDSKLYAKSGWGMDVKPQVGWYTGWVEQPNGKVTAFALNMNMQAGDDPAERKQLTLSILDKLGLFFYLR"},"dna_sequence":{"accession":"KJ997966.1","fmin":"0","fmax":"831","strand":"+","sequence":"ATGAAGTTTAAAATGAAAGGTTTATTTTGTGTCATCCTCAGTAGTTTGGCATTTTCAGGTTGTGTTTATGATTCAAAACTACAACGCCCAGTCATATCAGAGCGAGAAACTGAGATTCCTTTATTATTTAATCAAGCACAGACTCAAGCTGTGTTTGTTACTTATGATGGGATTCATCTAAAAAGTTATGGTAATGATCTAAGCCGAGCAAAGACTGAATATATTCCTGCATCTACATTTAAGATGTTGAATGCTTTAATTGGATTGCAAAATGCAAAAGCAACCAATACTGAAGTATTTCATTGGAATGGTGAAAAGCGCGCTTTTTCAGCATGGGAAAAAGATATGACTTTGGCAGAAGCGATGCAGGCTTCAGCTGTTCCCGTATATCAGGAGCTTGCTCGACGTATTGGCTTGGAGTTGATGCGTGAAGAAGTGAAGCGTGTAGGTTTTGGCAATGCGGAGATTGGTCAGCAAGTCGATAATTTTTGGTTGGTGGGTCCTTTAAAAATCTCCCCTGAACAAGAAGTTCAATTTGCCTATCAACTGGCGATGAAGCAATTACCTTTTGATCGAAATGTACAGCAACAAGTCAAAAATATGCTTTATATCGAGAGACGTGGTGACAGTAAACTGTATGCTAAAAGTGGTTGGGGAATGGATGTTAAACCTCAAGTGGGTTGGTATACGGGATGGGTTGAACAACCCAATGGCAAGGTGACTGCATTTGCGTTAAATATGAACATGCAAGCAGGTGATGATCCAGCTGAACGTAAACAATTAACCTTAAGTATTTTGGACAAATTGGGTCTATTTTTTTATTTAAGATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39090","NCBI_taxonomy_name":"Acinetobacter bereziniae","NCBI_taxonomy_id":"106648"}}}},"ARO_accession":"3002496","ARO_id":"38896","ARO_name":"OXA-418","CARD_short_name":"OXA-418","ARO_description":"OXA-418 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46498":{"category_aro_accession":"3007709","category_aro_cvterm_id":"46498","category_aro_name":"OXA-229-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-229.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"959":{"model_id":"959","model_name":"OXA-64","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1692":{"protein_sequence":{"accession":"AAW81336.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDEKGEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"AY750907.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGGAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001613","ARO_id":"38013","ARO_name":"OXA-64","CARD_short_name":"OXA-64","ARO_description":"OXA-64 is a beta-lactamase found in A. baumannii.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"960":{"model_id":"960","model_name":"TEM-137","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1155":{"protein_sequence":{"accession":"CAL08007.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDSWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGRRGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AM286274.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATAGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTAGGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36790","NCBI_taxonomy_name":"Shigella sonnei","NCBI_taxonomy_id":"624"}}}},"ARO_accession":"3001001","ARO_id":"37381","ARO_name":"TEM-137","CARD_short_name":"TEM-137","ARO_description":"TEM-137 is an extended-spectrum beta-lactamase found in Shigella sonnei.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"961":{"model_id":"961","model_name":"SHV-93","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1877":{"protein_sequence":{"accession":"ABN49110.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGTVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIDDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"EF373969.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCACAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACATCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGACGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGATGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001145","ARO_id":"37525","ARO_name":"SHV-93","CARD_short_name":"SHV-93","ARO_description":"SHV-93 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"962":{"model_id":"962","model_name":"OXA-356","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1533":{"protein_sequence":{"accession":"AGW83454.1","sequence":"MKFKMKGLFCVILSSLAFSGCVYDSKLQRPVISERETEIPLLFNQAQTQAVFVTYDGIHLKSYGNDLSRAKTEYIPASTFKMLNALIGLQNAKATNTEIFHWNGEKRAFSAWEKDMTLAEAMQASAVPVYQELARRIGLELMREEVKRVGFGNAEIGQQVDNFWLVGPLKISPEQEVQFAYQLAMKQLPFDRNVQQQVKDMLYIERRGDSKLYAKSGWGMDVEPQVGWYTGWVEQPNGKVTAFALNMNMQAGDDPAERKQLTLSILDKLGLFFYLR"},"dna_sequence":{"accession":"KF297585.1","fmin":"0","fmax":"831","strand":"+","sequence":"ATGAAGTTTAAAATGAAAGGTTTATTTTGTGTCATCCTCAGTAGTTTGGCATTTTCAGGTTGTGTTTATGATTCAAAACTACAACGCCCAGTCATATCAGAGCGAGAAACTGAGATTCCTTTATTATTTAATCAAGCACAGACTCAAGCTGTGTTTGTTACTTATGATGGGATTCATCTAAAAAGTTATGGTAATGATCTAAGCCGAGCAAAGACTGAATATATTCCTGCATCTACATTTAAGATGTTGAATGCTTTAATTGGCTTGCAAAATGCAAAAGCAACCAATACTGAAATATTTCATTGGAATGGTGAAAAGCGCGCTTTTTCAGCATGGGAAAAAGATATGACTTTGGCAGAAGCGATGCAGGCTTCAGCTGTTCCCGTATATCAGGAGCTTGCTCGACGTATTGGCTTGGAATTGATGCGTGAAGAAGTGAAGCGTGTAGGTTTCGGCAATGCGGAGATTGGTCAGCAAGTCGATAATTTTTGGTTGGTGGGTCCTTTAAAAATCTCCCCTGAACAAGAAGTTCAATTTGCCTATCAACTGGCAATGAAGCAATTACCTTTTGATCGAAATGTACAGCAACAAGTCAAAGATATGCTTTATATCGAGAGACGTGGTGACAGTAAACTGTATGCTAAAAGTGGTTGGGGAATGGATGTTGAACCTCAAGTGGGTTGGTATACGGGATGGGTTGAACAACCCAATGGCAAGGTGACTGCATTTGCGTTAAATATGAACATGCAAGCAGGTGATGATCCAGCTGAACGTAAACAATTAACCTTAAGTATTTTGGACAAATTGGGTCTATTTTTTTATTTAAGATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39090","NCBI_taxonomy_name":"Acinetobacter bereziniae","NCBI_taxonomy_id":"106648"}}}},"ARO_accession":"3001543","ARO_id":"37943","ARO_name":"OXA-356","CARD_short_name":"OXA-356","ARO_description":"OXA-356 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46498":{"category_aro_accession":"3007709","category_aro_cvterm_id":"46498","category_aro_name":"OXA-229-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-229.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"963":{"model_id":"963","model_name":"CMY-69","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1022":{"protein_sequence":{"accession":"AGE45504.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALPALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"JX049132.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGCCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002082","ARO_id":"38482","ARO_name":"CMY-69","CARD_short_name":"CMY-69","ARO_description":"CMY-69 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"964":{"model_id":"964","model_name":"OXA-129","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1450":{"protein_sequence":{"accession":"CAP69660.1","sequence":"MKTIAAYLVLVFFAGTALSESISENLAWNKEFSSESVHGVFVLCKSSSNSCTTNNATRASTAYIPASTFKIPNALIGLETGAIKDARQVFKWDGKPRAMKQWEKDLTLRGAIQVSAVPVFQQIARDIGKKRMQKYLNLFSYGNANIGGGIDKFWLEGQLRISAVNQVKFLESLYLNNLPASKANQLIVKEAIVTEATPEYIVHSKTGYSGVGTESNPGVAWWVGWVEKGTEVYFFAFNMDIDNESKLPSRKSIPTKIMASEGIIIGG"},"dna_sequence":{"accession":"AM932669.1","fmin":"698","fmax":"1502","strand":"+","sequence":"ATGAAAACCATAGCCGCATATTTAGTTCTAGTATTTTTTGCAGGCACTGCACTTTCAGAGTCTATTTCTGAAAATTTAGCTTGGAATAAAGAATTTTCCAGTGAATCAGTGCATGGTGTTTTTGTACTTTGTAAAAGCAGTAGTAATTCCTGTACAACAAATAATGCAACACGTGCATCTACGGCCTATATTCCAGCATCAACATTCAAAATTCCCAATGCTCTCATAGGCCTTGAAACCGGCGCCATAAAAGATGCGCGGCAGGTTTTCAAATGGGACGGCAAGCCCAGAGCCATGAAGCAATGGGAAAAAGACTTAACGCTAAGGGGCGCTATACAAGTTTCTGCTGTTCCGGTATTTCAACAAATTGCCAGAGACATTGGCAAAAAAAGAATGCAAAAATACCTTAACCTTTTTTCATATGGCAACGCCAATATAGGCGGAGGCATTGACAAATTTTGGCTAGAAGGTCAGCTTAGAATCTCAGCAGTCAATCAAGTTAAATTTTTAGAGTCGCTTTACCTAAATAATTTGCCAGCATCTAAAGCAAACCAACTTATAGTAAAAGAGGCAATAGTTACAGAAGCAACTCCAGAATATATAGTGCATTCAAAAACCGGGTATTCCGGTGTGGGCACAGAATCAAATCCTGGTGTCGCTTGGTGGGTTGGTTGGGTAGAAAAAGGAACTGAGGTTTACTTTTTTGCATTTAACATGGACATAGACAATGAGAGTAAGTTGCCGTCAAGAAAATCCATTCCAACGAAAATCATGGCAAGTGAAGGTATCATCATTGGTGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35739","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Bredeney","NCBI_taxonomy_id":"134047"}}}},"ARO_accession":"3001811","ARO_id":"38211","ARO_name":"OXA-129","CARD_short_name":"OXA-129","ARO_description":"OXA-129 is a beta-lactamase found in Salmonella enterica.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46512":{"category_aro_accession":"3007723","category_aro_cvterm_id":"46512","category_aro_name":"OXA-5-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-5.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"965":{"model_id":"965","model_name":"OXA-333","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1610":{"protein_sequence":{"accession":"AGW16415.1","sequence":"MKNLQLGLIVLITTFGSACTTISPSVETAKNQHQQSAQQQIQQAFNQLQTTGVIVIKDKHGLHSYGNDLSRAQTPYVPASTFKILNALIGLEHGKATSTEVFKWDGQKRSFPTWEKDMTLGQAIQASAVPVYQELARRIGLDLMQKEVQRIGYGNQQIGTVVDNFWLVGPLQITPVQEVLFVEKLANIQLAFKPDVQHTVQDMLLIEQKANYELYAKSGWGMDLEPQVGWWTGWVETATGEKVYFALNMHMKTGISASVREQLVKQSLTALGII"},"dna_sequence":{"accession":"KF203107.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAAAAATTTACAGTTGGGACTCATCGTCCTCATTACAACCTTCGGTTCCGCGTGTACCACAATAAGCCCCTCCGTAGAAACAGCTAAAAACCAACATCAGCAAAGCGCGCAGCAGCAGATCCAACAGGCCTTCAATCAACTCCAAACCACTGGGGTGATTGTCATTAAGGATAAGCACGGTTTACACAGCTACGGCAATGACTTGAGCCGTGCTCAGACACCCTATGTACCCGCCTCTACCTTTAAAATATTAAATGCCTTAATCGGACTAGAACATGGTAAGGCAACCAGCACCGAGGTATTTAAATGGGATGGTCAAAAGCGTAGTTTCCCTACTTGGGAAAAAGACATGACTTTAGGGCAAGCCATACAAGCATCTGCCGTTCCCGTTTATCAGGAGCTTGCACGGCGCATTGGTCTAGACCTAATGCAAAAAGAAGTGCAGCGCATTGGATATGGCAATCAACAGATTGGCACCGTTGTCGATAATTTTTGGTTAGTCGGTCCACTGCAAATTACGCCTGTTCAAGAAGTCCTTTTTGTAGAGAAGCTGGCCAATATACAACTCGCTTTTAAGCCAGATGTGCAACATACCGTACAAGACATGCTGCTGATTGAACAAAAAGCGAATTATGAACTCTACGCCAAATCTGGTTGGGGCATGGACCTAGAACCGCAAGTGGGCTGGTGGACAGGCTGGGTCGAAACAGCAACAGGTGAAAAAGTGTATTTTGCTTTGAATATGCATATGAAAACGGGAATTTCAGCCAGCGTACGTGAGCAACTGGTCAAACAAAGTCTGACAGCACTGGGGATAATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39092","NCBI_taxonomy_name":"Acinetobacter johnsonii","NCBI_taxonomy_id":"40214"}}}},"ARO_accession":"3001521","ARO_id":"37921","ARO_name":"OXA-333","CARD_short_name":"OXA-333","ARO_description":"OXA-333 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46494":{"category_aro_accession":"3007705","category_aro_cvterm_id":"46494","category_aro_name":"OXA-211-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-211.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"967":{"model_id":"967","model_name":"AAC(6')-Isa","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"705":{"protein_sequence":{"accession":"BAD10948.2","sequence":"MELRGDDVVLRPVADGEGEVLDRIVREPEVAAWWSPPEDFAGMLAIVFEGEVVGAIQFYEETDPEFHHAGIDVFLTARHQGKGLGTDAVRTLARWLVAERGHHRLTIDPAAANTAAIRSYRKVGFRPVGIMRAYGRDHRTGRWQDALLMDLLADELT"},"dna_sequence":{"accession":"AB116646.1","fmin":"429","fmax":"903","strand":"+","sequence":"ATGGAGCTGCGCGGGGACGACGTCGTACTGCGACCGGTGGCCGACGGCGAGGGCGAGGTGCTCGACCGGATCGTGCGGGAGCCGGAGGTGGCGGCGTGGTGGTCGCCCCCGGAGGACTTCGCGGGCATGCTCGCCATCGTCTTCGAGGGCGAGGTCGTCGGAGCGATCCAGTTCTACGAGGAGACCGACCCCGAATTCCACCACGCCGGCATCGACGTCTTCCTGACGGCACGCCACCAGGGGAAGGGGCTGGGCACCGACGCGGTGCGCACGCTGGCCCGGTGGCTGGTGGCGGAACGCGGCCACCACCGGCTGACCATCGACCCCGCCGCCGCCAACACCGCGGCGATCCGCAGCTACCGCAAGGTCGGGTTCCGGCCGGTGGGCATCATGCGGGCGTACGGGCGCGACCACCGGACGGGACGCTGGCAGGACGCGCTGCTCATGGACCTGCTCGCCGACGAACTGACCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39514","NCBI_taxonomy_name":"Streptomyces albulus","NCBI_taxonomy_id":"68570"}}}},"ARO_accession":"3002563","ARO_id":"38963","ARO_name":"AAC(6')-Isa","CARD_short_name":"AAC(6')-Isa","ARO_description":"AAC(6')-Isa is a plasmid-encoded aminoglycoside acetyltransferase in Streptomyces albulus.","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"A category of aminoglycoside N-acetyltransferase enzymes with modification regiospecificity based at the 6'-amino group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics through acetylation of the 6-amino group of the compound.","category_aro_class_name":"AMR Gene Family"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"46128":{"category_aro_accession":"3007378","category_aro_cvterm_id":"46128","category_aro_name":"2'-N-ethylnetilmicin","category_aro_description":"2'-N-ethylnetilmicin is an aminoglycoside antibiotic and a derivative of netilmicin.","category_aro_class_name":"Antibiotic"},"46129":{"category_aro_accession":"3007379","category_aro_cvterm_id":"46129","category_aro_name":"5-episisomicin","category_aro_description":"5-episosomicin is a semisynthetic aminoglycoside antibiotic similar to sisomicin.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"968":{"model_id":"968","model_name":"MIR-15","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"1503":{"protein_sequence":{"accession":"AIT76104.1","sequence":"MMTKSLSCALLLSVASAAFAAPMSEKQLAEVVERTVTPLINAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEIALGDPVAKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDTASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMSYEQAMTTRVFKPLKLDHTWINVPKAEEAHYAWGYREGKAVHVSPGMLDAEAYGVKTNVKDMASWVIANMKPDSLQAPSLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVGGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILDALQ"},"dna_sequence":{"accession":"KM087851.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGACAAAATCCCTAAGCTGTGCCCTGCTGCTCAGCGTCGCCAGCGCTGCATTCGCCGCACCGATGTCCGAAAAACAGCTGGCTGAGGTGGTGGAACGTACCGTTACGCCGCTGATAAACGCGCAGGCCATTCCGGGTATGGCGGTGGCGGTAATTTATCAGGGTCAGCCACACTACTTTACCTTCGGTAAAGCCGATGTTGCGGCGAACAAACCCGTCACCCCGCAAACCCTGTTTGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTACTGGGCGGCGATGCCATTGCCCGGGGTGAAATAGCGCTGGGCGATCCGGTAGCAAAATACTGGCCTGAGCTCACGGGCAAGCAGTGGCAGGGCATTCGCATGCTGGATCTGGCAACCTACACCGCAGGCGGTCTGCCGTTACAGGTGCCGGATGAGGTCACGGATACCGCTTCTCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCGGGCACCACGCGTCTTTACGCTAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTTAAACCTTCCGGCATGAGCTATGAGCAGGCCATGACGACGCGGGTCTTTAAACCCCTCAAGCTGGACCATACCTGGATTAACGTCCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGATACCGTGAGGGTAAAGCGGTCCACGTTTCGCCAGGGATGCTGGACGCGGAAGCCTATGGCGTAAAAACTAACGTGAAGGATATGGCGAGCTGGGTGATAGCCAACATGAAGCCGGATTCTCTTCAGGCTCCCTCACTCAAGCAAGGCATTGCTCTGGCGCAGTCTCGCTACTGGCGCGTGGGGGCTATGTATCAGGGGTTGGGCTGGGAGATGCTCAACTGGCCGGTCGATGCCAAAACCGTCGTCGGAGGCAGTGATAACAAGGTGGCGCTGGCACCATTGCCCGTGGCAGAAGTGAATCCACCCGCGCCGCCGGTTAAGGCCTCCTGGGTCCATAAAACAGGCTCGACGGGTGGGTTTGGCAGCTACGTGGCATTTATTCCTGAAAAGCAGCTCGGCATTGTGATGCTGGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCGTATCCTCGACGCGCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39773","NCBI_taxonomy_name":"Enterobacter kobei","NCBI_taxonomy_id":"208224"}}}},"ARO_accession":"3002180","ARO_id":"38580","ARO_name":"MIR-15","CARD_short_name":"MIR-15","ARO_description":"MIR-15 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36197":{"category_aro_accession":"3000058","category_aro_cvterm_id":"36197","category_aro_name":"MIR beta-lactamase","category_aro_description":"MIR beta-lactamases are plasmid-mediated beta-lactamases that confer resistance to oxyimino- and alpha-methoxy beta-lactams.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"969":{"model_id":"969","model_name":"VEB-8","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1805":{"protein_sequence":{"accession":"AGH33739.1","sequence":"MKIVKRILLVLLSLFFTVEYSNAQTDNLTLKIENVLKAKNARIGVAIFNSNEKDTLKINNDFHFPMQSVMKFPIALAVLSEIDKGNLSFEQKIEITPQDLLPKMWSPIKEEFPNGTTLTIEQILNYTVSESDNIGCDILLKLIGGTDSVQKFLNANHFTDISIKANEEQMHKDWNTQYQNWATPTAMNKLLIDTYNNKNQLLSKKSYDFIWKIMRETTAGSNRLKGQLPKNTIVAHKTGTSGINNGIAAATNDVGVITLPNGQLIFISVFVAESKETSEINEKIISDIAKITWNYYLNK"},"dna_sequence":{"accession":"JX679208.1","fmin":"0","fmax":"900","strand":"+","sequence":"ATGAAAATCGTAAAAAGGATATTATTAGTATTGTTAAGTTTATTTTTTACAGTTGAGTATTCAAATGCTCAAACTGACAACTTAACTTTGAAAATTGAGAATGTTTTAAAGGCAAAAAATGCCAGAATAGGAGTAGCAATATTCAACAGCAATGAGAAGGATACTTTGAAGATTAATAACGACTTCCATTTCCCGATGCAAAGCGTTATGAAATTTCCGATTGCTTTAGCCGTTTTGTCTGAGATAGATAAAGGGAATCTTTCTTTTGAACAAAAAATAGAGATTACCCCTCAAGACCTTTTGCCTAAAATGTGGAGTCCGATTAAAGAGGAATTCCCTAATGGAACAACTTTGACGATTGAACAAATACTAAATTATACAGTATCAGAGAGCGACAATATTGGTTGTGATATTTTGCTAAAATTAATCGGAGGAACTGATTCTGTTCAAAAATTCTTGAATGCTAATCATTTCACTGATATTTCAATCAAAGCAAACGAAGAACAAATGCACAAGGATTGGAATACCCAATATCAAAATTGGGCAACCCCAACAGCGATGAACAAACTGTTAATAGATACTTATAATAATAAGAACCAATTACTTTCTAAAAAAAGTTATGATTTTATTTGGAAAATTATGAGAGAAACAACAGCAGGAAGTAACCGATTAAAAGGACAATTACCAAAGAATACAATTGTTGCTCATAAAACAGGGACTTCCGGAATAAATAATGGAATTGCAGCAGCCACTAATGATGTTGGGGTAATTACTTTACCGAATGGACAATTAATTTTTATAAGCGTATTTGTTGCAGAGTCCAAAGAAACTTCGGAAATTAATGAAAAGATTATTTCAGACATTGCAAAAATAACGTGGAATTACTATTTGAATAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002377","ARO_id":"38777","ARO_name":"VEB-8","CARD_short_name":"VEB-8","ARO_description":"VEB-8 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36182":{"category_aro_accession":"3000043","category_aro_cvterm_id":"36182","category_aro_name":"VEB beta-lactamase","category_aro_description":"VEB beta-lactamases or Vietnamese extended-spectrum beta-lactamases are class A beta-lactamases that confer high-level resistance to oxyimino cephalosporins and to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"870":{"model_id":"870","model_name":"otr(B)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"900"}},"model_sequences":{"sequence":{"697":{"protein_sequence":{"accession":"AAD04032.1","sequence":"MSSANPGPAGTADQAGGAFTHRQILTAMSGLLLAVFLAALDQTVIATAMRTIADDLHGQTEQAWATTGYLIASVLAMPFYGKLSDIYGRKPMYLISIVVFIGGSVLCGTAGSMWELALFRAVQGLGGGGLMSLPTAVVADLAPVRERGRYFAFLQMAWVVASVAGPLAGGFFAEAGQVFGIDGWRWVFLLNVPLGLLALVTVRKALNLPHERREHRMDVLGAAALALFLVPLLIVAEQGRTWGWGSPAALALFALGAAGLAVFIPVELRRGDEAILPLGLFRRGSIALCSAVNFTIGVGIFGTVTTLPLFLQMVQGRTPTQAGLVVIPFMLGTIASQMVSGKLIASSGRFKKLAIVGLGSMAGALLAMATTGATTPMWGIVLIVLWLGVGIGLSQTVITSPMQNSAPKSQLGVANGASGLCRQIGGSTGIAVLFSVMFAVALGRLADLLHTPRYERLLTDPAITGDPANHRFLDMAESGQGAGINLDDTSLLNGIDARLMQPVTDSFAHGFHIMFLAGGVVLLAGFVMTWFLRELQEETAPEEERPAESGAGAKNGPLPASDA"},"dna_sequence":{"accession":"AF079900.1","fmin":"39","fmax":"1731","strand":"+","sequence":"GTGTCATCCGCAAATCCGGGCCCGGCGGGCACGGCGGACCAGGCAGGCGGGGCGTTCACGCATCGGCAGATCCTGACGGCCATGTCGGGACTGCTGCTGGCCGTGTTCCTCGCGGCCCTGGACCAGACGGTCATCGCCACCGCGATGCGCACCATCGCGGACGACCTCCACGGCCAGACCGAGCAGGCATGGGCGACGACGGGCTACCTCATCGCCTCCGTCCTGGCGATGCCGTTCTACGGCAAGCTGTCCGACATCTACGGGCGCAAGCCCATGTACCTGATCTCCATCGTGGTGTTCATCGGCGGCTCGGTGCTGTGCGGCACGGCCGGCTCGATGTGGGAGCTGGCCCTCTTCCGGGCCGTCCAGGGACTGGGCGGCGGCGGGCTGATGTCCCTGCCCACCGCGGTGGTCGCCGACCTCGCCCCGGTGCGCGAGCGCGGCCGCTACTTCGCCTTCCTCCAGATGGCGTGGGTGGTCGCCAGCGTCGCGGGCCCGCTGGCGGGCGGCTTCTTCGCGGAGGCGGGCCAGGTCTTCGGCATCGACGGCTGGCGCTGGGTGTTCCTGCTCAACGTACCGCTGGGCCTGCTGGCCCTGGTCACCGTGCGCAAGGCCCTGAACCTGCCGCACGAACGGCGCGAGCACCGCATGGACGTACTGGGCGCGGCGGCGCTGGCGCTGTTCCTGGTGCCCCTGCTGATCGTCGCCGAACAGGGCCGGACCTGGGGCTGGGGCTCGCCGGCCGCCCTCGCCCTCTTCGCGCTCGGCGCGGCCGGGCTGGCGGTCTTCATCCCCGTCGAGCTGCGGCGCGGCGACGAGGCCATCCTGCCGCTGGGGCTCTTCCGGCGCGGCAGCATCGCGCTGTGCTCCGCGGTCAACTTCACCATCGGCGTCGGCATCTTCGGCACGGTCACCACCCTGCCGCTGTTCCTCCAGATGGTGCAGGGGCGGACCCCGACCCAGGCCGGACTGGTGGTCATCCCGTTCATGCTGGGCACCATCGCCTCGCAGATGGTCTCCGGCAAGCTCATCGCGTCCTCGGGCCGGTTCAAGAAACTGGCGATCGTGGGCCTGGGCTCGATGGCCGGGGCGCTGCTGGCCATGGCCACCACCGGCGCGACGACCCCGATGTGGGGCATCGTCCTGATCGTCCTCTGGCTCGGCGTCGGCATCGGCCTGTCCCAGACCGTCATCACCTCGCCCATGCAGAACTCGGCCCCCAAGAGCCAGCTCGGCGTGGCGAACGGCGCCTCCGGCCTGTGCCGGCAGATCGGCGGCTCCACCGGCATCGCGGTTCTGTTCTCCGTGATGTTCGCGGTGGCGCTCGGCCGCCTCGCCGACCTGCTGCACACCCCGCGCTACGAGCGCCTCCTGACGGACCCGGCGATCACCGGCGACCCCGCCAACCACCGCTTCCTTGACATGGCCGAGTCCGGGCAGGGCGCGGGGATCAACCTTGACGACACGTCCCTGCTGAACGGCATCGACGCCCGGCTGATGCAGCCGGTGACGGATTCCTTCGCCCACGGCTTCCACATCATGTTCCTCGCCGGCGGCGTGGTGCTGCTGGCCGGGTTCGTCATGACCTGGTTCCTGCGCGAACTCCAGGAGGAGACCGCGCCGGAGGAGGAGCGGCCGGCCGAGAGCGGCGCCGGGGCGAAGAACGGGCCGCTGCCCGCGTCGGACGCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36773","NCBI_taxonomy_name":"Streptomyces rimosus","NCBI_taxonomy_id":"1927"}}}},"ARO_accession":"3002892","ARO_id":"39326","ARO_name":"otr(B)","CARD_short_name":"otr(B)","ARO_description":"otr(B) is a tetracycline resistance efflux pump found in Streptomyces rimosus.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"910":{"model_id":"910","model_name":"rphA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1500"}},"model_sequences":{"sequence":{"7":{"protein_sequence":{"accession":"AIA08936.1","sequence":"MSGRLVVDLQDVDAAGLAEVGGKGAHLGELSRIDGVRVPSGFCVTTHAFRRIMAEAPESGELLDRLSRVDEGDQEAVRSLAARLRQVVGATPLPDEVAAAVTGALARHGERSAYAVRSSATAEDLPTASFAGQQDTYLNVVGTEEILRHVSRCWASLFTERAVTYRGRQGVDHRTVHMGVVVQRMVVPRASGILFTADPVTGDRRTATVDAGFGLGEALVSGLVDPDVLTVRHGEVVARTIAAKRRALHAVQGGGTRETPIEERRQREPVLTDDQAVELVALGRRIEAHFGSPQDIEWCLDDDGFHIVQSRPITTLFPVPERDDDVFRVYLSVGHQQMMTDAMKPLGLSMWRLTALAPMYEAGGRLFVDATARLAVPGSRATLLDVVGRGDPLTRDALETVLENGEFEPTPAETDGGAPPAGDGAEPDEADPSIVTELIERSRRSLAELEREIGTKSGPALFAFLREAFEEHKRVVGDPLNIRAIMAGMEATWWLNDRLEEWLGEKNAADTLTLSAPDNVTSEMGLELLDVADVVRTHPEVVAFLEGVEDDGFLDELPKVPGGAEARDAFEAYLDRYGMRCVGEIDITXPPVRERPSALVPVVLDHVRAFGPGAAARRFEDGRRRALAKEREVLERLRDLPDGERRADAARRMIRQVRAFAGYREYPKYAIVSRSFVYRQALLREADELVRAGVLADREDVHYLTFDEFEEAVRVRRVDERLVRRRKDAFRSYQALTPPRVLTSEGVALSGAYRRDDVPEGALAGLAVSAGTVEGRARVVLDMAEADLEAGDILVTRFTDPSWSPLFVGIAGLVTEVGGLMTHGAVIAREYGLAAVVGVERATRLIRDGQRIRVHGTEGYIELLS"},"dna_sequence":{"accession":"KJ151292.1","fmin":"294","fmax":"2892","strand":"+","sequence":"ATGAGCGGGCGTCTGGTCGTGGATCTTCAGGACGTCGACGCGGCGGGGCTCGCCGAGGTCGGCGGCAAGGGCGCCCACCTGGGCGAGCTGTCCCGGATCGACGGGGTCCGGGTGCCGTCCGGGTTCTGTGTGACGACGCACGCCTTCCGGCGGATCATGGCGGAGGCACCCGAGAGCGGGGAACTCCTCGACCGGCTGTCCCGCGTGGACGAGGGCGACCAGGAGGCGGTCCGATCCCTCGCCGCCCGTCTACGGCAGGTCGTCGGGGCGACGCCCCTCCCGGACGAGGTGGCGGCGGCCGTCACCGGGGCGCTCGCCCGGCACGGTGAGCGGTCCGCGTACGCCGTACGGTCCAGCGCGACGGCCGAGGACCTGCCGACCGCGTCGTTCGCCGGCCAGCAGGACACGTACCTGAACGTCGTCGGCACCGAGGAGATCCTCCGGCACGTCAGCCGGTGCTGGGCCTCCCTGTTCACCGAGCGGGCGGTGACCTACCGCGGGCGTCAGGGCGTCGACCACCGTACGGTCCACATGGGCGTGGTCGTGCAGCGGATGGTCGTGCCGCGGGCGTCCGGCATCCTGTTCACCGCCGACCCGGTGACGGGAGACCGCCGCACGGCGACCGTGGACGCCGGTTTCGGTCTCGGCGAGGCCCTGGTGTCGGGGCTGGTCGACCCGGACGTCCTCACGGTGCGGCACGGCGAGGTCGTCGCGCGGACGATCGCCGCGAAGCGGCGCGCCCTGCACGCCGTGCAGGGCGGTGGGACGCGCGAGACCCCGATCGAGGAACGGCGGCAGCGCGAACCGGTACTGACGGACGATCAGGCCGTGGAGCTGGTCGCGCTCGGGCGGCGGATCGAGGCGCACTTCGGCAGCCCGCAGGACATCGAGTGGTGCCTGGACGACGACGGCTTCCACATCGTGCAGAGCCGGCCGATCACCACGCTGTTCCCCGTGCCCGAGCGGGACGACGACGTCTTCCGCGTCTATCTCTCGGTCGGCCACCAGCAGATGATGACCGACGCCATGAAGCCCCTGGGCCTCTCGATGTGGCGGCTGACGGCCCTGGCACCGATGTACGAGGCCGGCGGGCGGCTGTTCGTCGACGCCACCGCCCGGCTGGCGGTGCCCGGGAGCCGTGCCACTCTCCTGGACGTCGTCGGCCGTGGCGACCCGCTGACCCGGGACGCGCTCGAAACGGTCCTGGAGAACGGCGAGTTCGAGCCGACGCCGGCGGAGACGGACGGAGGCGCGCCGCCCGCCGGTGACGGGGCCGAACCGGACGAGGCCGATCCTTCCATCGTCACCGAGCTGATCGAGCGCAGCCGGCGCTCCCTCGCCGAGCTGGAGCGGGAGATCGGCACGAAGAGCGGTCCCGCCCTGTTCGCGTTCCTGCGGGAGGCGTTCGAGGAGCACAAGCGGGTGGTCGGCGATCCGCTGAACATCCGCGCGATCATGGCGGGCATGGAGGCCACCTGGTGGCTGAACGACCGGCTGGAGGAGTGGCTCGGCGAGAAGAACGCCGCCGACACGCTCACGCTGTCCGCCCCCGACAACGTGACCTCGGAGATGGGGCTGGAGCTGCTCGACGTCGCCGACGTGGTCCGCACGCACCCGGAGGTGGTGGCCTTCCTGGAGGGCGTCGAGGACGACGGCTTCCTGGACGAGCTGCCCAAGGTCCCCGGTGGCGCCGAGGCCCGGGACGCCTTCGAGGCATACCTGGACCGGTACGGCATGCGCTGCGTCGGCGAGATCGACATCACGNGGCCCCCGGTGCGGGAACGGCCCAGCGCGCTCGTGCCGGTCGTCCTCGACCACGTGCGCGCCTTCGGGCCCGGCGCCGCCGCGCGCCGCTTCGAGGACGGCCGGCGCAGGGCGCTCGCGAAGGAGCGTGAGGTGCTGGAGCGGCTGCGGGACCTGCCGGACGGGGAGCGCAGGGCCGACGCGGCGCGCCGGATGATCCGGCAGGTCCGCGCGTTCGCCGGCTACCGGGAGTACCCGAAGTACGCGATCGTCAGCCGCTCCTTCGTCTACCGTCAGGCCCTGCTGCGGGAGGCCGACGAGCTGGTGCGGGCCGGCGTCCTCGCCGACCGGGAGGACGTCCACTACCTGACGTTCGACGAGTTCGAGGAGGCCGTCCGCGTGCGCCGGGTGGACGAGCGGCTGGTGCGGCGCCGCAAGGACGCCTTCCGTTCGTACCAGGCGCTGACCCCGCCCCGCGTCCTCACCTCGGAGGGTGTGGCCCTCTCCGGGGCGTACCGGCGCGACGACGTGCCGGAAGGGGCGCTGGCGGGTCTCGCGGTGTCCGCGGGGACCGTGGAGGGCCGGGCCCGGGTGGTCCTCGACATGGCGGAGGCCGATCTGGAGGCGGGCGACATCCTGGTCACGCGGTTCACGGACCCCAGCTGGTCACCGCTGTTCGTCGGGATCGCGGGCCTGGTGACGGAGGTGGGCGGTCTGATGACCCATGGCGCGGTGATCGCCCGCGAGTACGGTCTGGCGGCCGTGGTCGGGGTGGAGCGGGCCACCCGGCTGATCCGGGACGGGCAGCGCATCCGGGTGCACGGGACGGAGGGCTATATCGAGCTTCTGTCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39689","NCBI_taxonomy_name":"Streptomyces sp. WAC4747","NCBI_taxonomy_id":"1501383"}}}},"ARO_accession":"3000444","ARO_id":"36583","ARO_name":"rphA","CARD_short_name":"rphA","ARO_description":"The enzymatic inactivation of rifampin by phosphorylation at the 21-OH position.","ARO_category":{"41087":{"category_aro_accession":"3004040","category_aro_cvterm_id":"41087","category_aro_name":"rifampin phosphotransferase","category_aro_description":"Enzymes, protein or other gene products that inactivate rifampin (rifamycin) antibiotics through phosphorylation of the antibiotic at the 21-OH position.","category_aro_class_name":"AMR Gene Family"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36656":{"category_aro_accession":"3000517","category_aro_cvterm_id":"36656","category_aro_name":"rifaximin","category_aro_description":"Rifaximin is a semi-synthetic rifamycin used to treat traveller's diarrhea. Rifaximin inhibits RNA synthesis by binding to the beta subunit of bacterial RNA polymerase.","category_aro_class_name":"Antibiotic"},"36669":{"category_aro_accession":"3000530","category_aro_cvterm_id":"36669","category_aro_name":"rifabutin","category_aro_description":"Rifabutin is a semisynthetic rifamycin used in tuberculosis therapy. It inhibits DNA-dependent RNA synthesis.","category_aro_class_name":"Antibiotic"},"36673":{"category_aro_accession":"3000534","category_aro_cvterm_id":"36673","category_aro_name":"rifapentine","category_aro_description":"Rifapentine is a semisynthetic rifamycin that inhibits DNA-dependent RNA synthesis. It is often used in the treatment of tuberculosis and leprosy.","category_aro_class_name":"Antibiotic"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"945":{"model_id":"945","model_name":"tet(40)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"5150":{"protein_sequence":{"accession":"CAM12479.1","sequence":"MFAKNSKAYSVYLLFRFVCSLAVSMSTVLSIVYHLEVVQLDAFQLVLVGTVQEASCFLFEMPTGVVADLYSRRRSVLIGMFLYGLGFLMEGALPWFAPVLLAQVVWGCGDTFITGALEAWIASEEEDKPIDKVFLRGSQMGQIGGVLGVVLGTLLGNINLQMPLILGGSLCLLLGLVMVRIMPETNFSPAIEERQGLLKDFVCLFKLNLGFVKGAPVLLALLAITLCGGLASEGFDRLSTAHFLDDTVIPVIGPLNSVTWFGVISLIGNGLGILASQLLIARMEKKGTVSRTSVVMSTSAGYILFLVLFAVGRSFWFMLLVFLLAGLMRTIKEPVLAAWMNDHVDEKMRATVFSTSGQLDSFGQIIGGPIVGLVAQQVSIPWGLVCTAFLLLPALFLVPVAGKKRD"},"dna_sequence":{"accession":"AM419751.1","fmin":"14210","fmax":"15431","strand":"+","sequence":"ATGTTTGCTAAAAATTCAAAGGCATATTCTGTCTACCTGCTGTTCCGATTTGTCTGTTCCCTGGCGGTTTCTATGTCCACAGTGCTTTCCATCGTGTACCACCTGGAGGTGGTGCAGCTGGATGCTTTCCAGCTTGTCCTGGTAGGGACGGTTCAGGAGGCCTCCTGCTTTCTGTTCGAGATGCCCACCGGTGTGGTGGCGGATTTGTATAGCCGTCGGCGCTCGGTGCTGATTGGAATGTTCCTCTACGGCCTGGGCTTTCTGATGGAGGGTGCGCTACCGTGGTTCGCGCCGGTTCTGCTGGCCCAGGTTGTCTGGGGTTGCGGTGATACCTTCATCACCGGCGCTCTGGAGGCGTGGATTGCCTCGGAGGAAGAGGACAAACCCATAGACAAGGTGTTCCTGCGGGGCAGTCAAATGGGGCAAATCGGCGGCGTTCTGGGCGTGGTGCTGGGCACACTGCTGGGAAACATAAACCTGCAAATGCCTCTCATCTTGGGGGGCAGTTTGTGCTTGTTGTTGGGGCTGGTGATGGTTCGCATCATGCCAGAAACCAACTTCTCCCCTGCTATTGAGGAACGGCAGGGCTTGCTTAAAGACTTTGTCTGCCTGTTCAAGCTCAACCTGGGCTTTGTGAAAGGCGCACCTGTGTTGCTGGCGCTCTTAGCAATCACACTATGCGGGGGACTTGCCAGTGAAGGCTTTGACCGGCTCTCCACCGCTCATTTTCTGGATGACACGGTAATACCCGTTATCGGGCCGCTGAACAGCGTCACTTGGTTCGGTGTTATCAGTCTTATCGGCAACGGCTTAGGTATTCTGGCTTCTCAGTTGCTCATCGCCCGCATGGAGAAAAAAGGGACTGTCAGCCGAACCAGTGTGGTCATGTCCACCAGCGCCGGGTATATCCTGTTCCTGGTTCTCTTCGCGGTGGGGCGGAGCTTTTGGTTCATGTTGTTGGTGTTCCTGCTGGCGGGGCTTATGCGCACCATCAAGGAGCCTGTGCTGGCCGCCTGGATGAACGACCATGTGGATGAGAAAATGCGCGCCACAGTCTTTTCCACCAGCGGACAGCTGGACTCTTTCGGGCAGATCATCGGCGGGCCTATTGTGGGGCTGGTAGCCCAGCAGGTGTCCATACCCTGGGGGCTGGTCTGTACCGCTTTCCTGCTGTTGCCCGCGCTGTTCTTAGTGCCGGTGGCGGGAAAGAAGCGGGATTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36791","NCBI_taxonomy_name":"uncultured bacterium","NCBI_taxonomy_id":"77133"}}}},"ARO_accession":"3000567","ARO_id":"36706","ARO_name":"tet(40)","CARD_short_name":"tet(40)","ARO_description":"Tet40 is a tetracycline efflux pump found in the Gram-positive Clostridium. It is similar to tetA(P).","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"900":{"model_id":"900","model_name":"tet(C)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"5826":{"protein_sequence":{"accession":"AAK97755.1","sequence":"MKSNNALIVILGTVTLDAVGIGLVMPVLPGLLRDIVHSDSIASHYGVLLALYALMQFLCAPVLGALSDRFGRRPVLLASLLGATIDYAIMATTPVLWILYAGRIVAGITGATGAVAGAYIADITDGEDRARHFGLMSACFGVGMVAGPVAGGLLGAISLHAPFLAAAVLNGLNLLLGCFLMQESHKGERRPMPLRAFNPVSSFRWARGMTIVAALMTVFFIMQLVGQVPAALWVIFGEDRFRWSATMIGLSLAVFGILHALAQAFVTGPATKRFGEKQAIIAGMAADALGYVLLAFATRGWMAFPIMILLASGGIGMPALQAMLSRQVDDDHQGQLQGSLAALTSLTSIIGPLIVTAIYAASASTWNGLAWIVGAALYLVCLPALRRGAWSRATST"},"dna_sequence":{"accession":"AY043299.1","fmin":"3984","fmax":"5175","strand":"-","sequence":"ATGAAATCTAACAATGCGCTCATCGTCATCCTCGGCACCGTCACCCTGGATGCTGTAGGCATAGGCTTGGTTATGCCGGTACTGCCGGGCCTCTTGCGGGATATCGTCCATTCCGACAGCATCGCCAGTCACTATGGCGTGCTGCTAGCGCTATATGCGTTGATGCAATTTCTATGCGCACCCGTTCTCGGAGCACTGTCCGACCGCTTTGGCCGCCGCCCAGTCCTGCTCGCTTCGCTACTTGGAGCCACTATCGACTACGCGATCATGGCGACCACACCCGTCCTGTGGATCCTCTACGCCGGACGCATCGTGGCCGGCATCACCGGCGCCACAGGTGCGGTTGCTGGCGCCTATATCGCCGACATCACCGATGGGGAAGATCGGGCTCGCCACTTCGGGCTCATGAGCGCTTGTTTCGGCGTGGGTATGGTGGCAGGCCCCGTGGCCGGGGGACTGTTGGGCGCCATCTCCTTGCATGCACCATTCCTTGCGGCGGCGGTGCTCAACGGCCTCAACCTACTACTGGGCTGCTTCCTAATGCAGGAGTCGCATAAGGGAGAGCGTCGACCGATGCCCTTGAGAGCCTTCAACCCAGTCAGCTCCTTCCGGTGGGCGCGGGGCATGACTATCGTCGCCGCACTTATGACTGTCTTCTTTATCATGCAACTCGTAGGACAGGTGCCGGCAGCGCTCTGGGTCATTTTCGGCGAGGACCGCTTTCGCTGGAGCGCGACGATGATCGGCCTGTCGCTTGCGGTATTCGGAATCTTGCACGCCCTCGCTCAAGCCTTCGTCACTGGTCCCGCCACCAAACGTTTCGGCGAGAAGCAGGCCATTATCGCCGGCATGGCGGCCGACGCGCTGGGCTACGTCTTGCTGGCGTTCGCGACGCGAGGCTGGATGGCCTTCCCCATTATGATTCTTCTCGCTTCCGGCGGCATCGGGATGCCCGCGTTGCAGGCCATGCTGTCCAGGCAGGTAGATGACGACCATCAGGGACAGCTTCAAGGATCGCTCGCGGCTCTTACCAGCCTAACTTCGATCATTGGACCGCTGATCGTCACGGCGATTTATGCCGCCTCGGCGAGCACATGGAACGGGTTGGCATGGATTGTAGGCGCCGCCCTATACCTTGTCTGCCTCCCCGCGTTGCGTCGCGGTGCATGGAGCCGGGCCACCTCGACCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36795","NCBI_taxonomy_name":"Aeromonas salmonicida","NCBI_taxonomy_id":"645"}}}},"ARO_accession":"3000167","ARO_id":"36306","ARO_name":"tet(C)","CARD_short_name":"tet(C)","ARO_description":"Tet(C) is a tetracycline efflux pump found in many species of Gram-negative bacteria. It is typically found in plasmid DNA.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"957":{"model_id":"957","model_name":"tet(G)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"730"}},"model_sequences":{"sequence":{"239":{"protein_sequence":{"accession":"AAD25538.1","sequence":"MRSSAIIALLIVGLDAIGLGLIMPVLPTLLRELVPAEQVAGHYGALLSLYALMQVVCAPLLGQFSDGYGRRPVLLASLAGAAVDYTIMASAPVLWVLYIGRLISGITGATGAVAASTIADSTGEGSRARWFGYMGACYGTGMIAGPALGGMLGGISAHAPFIAAALLNGFAFLLACIFLKETNRSHGETGKLVRIEPFVLFRLDDALRGLTALFAVFFTIQLIGQVPAALWVIYGEDRFQWDTTTVGLSLAAFGATHAIFQAFVTGPLSSRLGERRTLLFGMAADATGFILLAFATQGWMVFPILLLLAAGGVGMPALQAMLSNNVSSNKQGALQGTLTSLTNLSSIAGPLGFTALYSATIGAWTGWVWIVGAILYLICLPILRRPFATSL"},"dna_sequence":{"accession":"AF133139.1","fmin":"0","fmax":"1176","strand":"+","sequence":"GTGCGCAGCTCTGCCATCATTGCCCTGCTGATCGTCGGTCTCGACGCCATAGGACTCGGCCTCATAATGCCGGTCCTTCCGACGCTTCTGCGCGAGCTTGTGCCGGCAGAGCAGGTCGCTGGTCACTATGGTGCTTTGCTGTCGCTCTATGCGTTGATGCAGGTCGTCTGCGCCCCTCTACTTGGGCAATTTTCAGATGGTTACGGTCGGCGTCCGGTGCTTCTGGCTTCTCTTGCGGGGGCCGCAGTCGATTACACGATTATGGCATCAGCGCCGGTCTTATGGGTGCTGTATATTGGCCGGCTCATTTCTGGCATCACGGGAGCAACCGGAGCTGTAGCTGCCTCAACCATTGCCGATTCGACAGGGGAAGGGTCTCGCGCACGCTGGTTCGGCTACATGGGAGCCTGTTATGGGACAGGCATGATTGCCGGGCCAGCACTTGGTGGCATGCTCGGTGGTATTTCTGCTCATGCTCCGTTTATCGCCGCTGCCCTTCTAAACGGCTTCGCGTTCCTGCTTGCCTGCATTTTTCTCAAGGAGACTAATCGCAGCCATGGCGAGACCGGAAAACTGGTCCGCATCGAACCATTCGTTCTGTTCCGGCTGGATGATGCATTGCGTGGACTAACCGCGCTTTTCGCAGTTTTCTTCACTATTCAACTGATCGGCCAAGTGCCTGCGGCCCTATGGGTCATATATGGCGAGGACCGTTTTCAGTGGGACACCACGACCGTTGGTTTGTCGCTCGCGGCGTTTGGAGCAACACATGCGATCTTCCAAGCGTTTGTTACCGGCCCTCTTTCAAGCCGGCTTGGAGAGCGGCGCACATTACTGTTTGGCATGGCTGCGGATGCGACTGGCTTCATTCTTCTAGCTTTTGCCACGCAGGGATGGATGGTGTTCCCGATTCTGCTGCTGCTTGCCGCCGGGGGCGTTGGCATGCCGGCCTTGCAGGCAATGCTCTCAAACAATGTCAGCAGTAACAAGCAAGGAGCTCTACAGGGAACGCTTACAAGCCTCACCAATCTAAGCTCTATCGCGGGACCGCTTGGCTTCACGGCACTCTATTCTGCCACCATAGGAGCATGGACCGGTTGGGTTTGGATTGTCGGCGCGATCCTCTATTTAATATGTCTGCCAATACTACGCAGACCTTTCGCAACTTCATTGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36778","NCBI_taxonomy_name":"Pseudomonas sp.","NCBI_taxonomy_id":"306"}}}},"ARO_accession":"3000174","ARO_id":"36313","ARO_name":"tet(G)","CARD_short_name":"tet(G)","ARO_description":"TetG is a tetracycline efflux protein found in Gram-negative bacteria. The encoding gene is found in both chromosomal and plasmid DNA where it is frequently linked to the floR, sul1, and cmlA9 genes which encode proteins that can confer florfenicol\/chloramphenicol, sulfamethoxazole, and chloramphenicol resistance, respectively.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"842":{"model_id":"842","model_name":"ugd","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"4591":{"protein_sequence":{"accession":"AAC75089.1","sequence":"MKITISGTGYVGLSNGLLIAQNHEVVALDILPSRVAMLNDRISPIVDKEIQQFLQSDKIHFNATLDKNEAYRDADYVIIATPTDYDPKTNYFNTSSVESVIKDVVEINPYAVMVIKSTVPVGFTAAMHKKYRTENIIFSPEFLREGKALYDNLHPSRIVIGERSERAERFAALLQEGAIKQNIPMLFTDSTEAEAIKLFANTYLAMRVAYFNELDSYAESLGLNSRQIIEGVCLDPRIGNHYNNPSFGYGGYCLPKDTKQLLANYQSVPNNLISAIVDANRTRKDFIADAILSRKPQVVGIYRLIMKSGSDNFRASSIQGIMKRIKAKGVEVIIYEPVMKEDSFFNSRLERDLATFKQQADVIISNRMAEELKDVADKVYTRDLFGSD"},"dna_sequence":{"accession":"U00096.1","fmin":"2098446","fmax":"2099613","strand":"-","sequence":"ATGAAAATCACCATTTCCGGTACTGGCTATGTAGGCTTGTCAAACGGGCTTCTAATCGCACAAAATCATGAGGTTGTGGCATTAGATATTTTACCGTCACGCGTTGCTATGCTGAATGATCGGATATCTCCTATTGTTGATAAGGAAATTCAGCAGTTTTTGCAATCAGATAAAATACACTTTAATGCCACATTAGATAAAAATGAAGCCTACCGGGATGCTGATTATGTCATCATCGCCACTCCAACCGACTATGATCCTAAAACTAATTATTTCAATACATCCAGTGTAGAATCAGTAATTAAAGACGTAGTTGAGATAAATCCTTATGCGGTTATGGTCATCAAATCAACGGTTCCCGTTGGTTTTACCGCAGCGATGCATAAGAAATATCGCACTGAAAATATTATATTCTCCCCGGAATTTCTCCGTGAGGGTAAAGCCCTTTACGATAATCTCCATCCTTCACGTATTGTCATCGGTGAGCGTTCAGAACGCGCAGAACGTTTCGCTGCTCTGTTACAGGAAGGCGCGATTAAGCAAAATATCCCGATGCTGTTTACCGACTCCACTGAAGCAGAAGCGATTAAACTTTTTGCAAACACCTACCTGGCGATGCGCGTGGCGTACTTTAACGAACTGGATAGCTATGCAGAAAGTTTAGGTCTGAATTCCCGTCAAATAATCGAAGGCGTTTGTCTCGACCCACGTATTGGCAACCATTACAACAATCCGTCGTTTGGTTATGGTGGTTATTGTCTGCCGAAAGATACCAAGCAGTTACTGGCGAACTACCAGTCTGTGCCGAATAACCTGATCTCGGCAATTGTCGATGCTAACCGCACGCGTAAAGATTTTATTGCCGATGCCATTTTGTCACGCAAGCCGCAAGTGGTGGGTATTTATCGTCTGATTATGAAGAGCGGTTCAGATAACTTCCGTGCGTCTTCTATTCAGGGGATTATGAAACGTATCAAGGCGAAAGGTGTTGAAGTGATCATCTACGAGCCAGTGATGAAAGAAGACTCATTCTTCAACTCTCGCCTGGAACGTGATCTCGCCACCTTCAAACAACAAGCCGACGTCATTATCTCTAACCGAATGGCAGAAGAGCTTAAGGATGTGGCAGATAAGGTATACACCCGCGATCTCTTTGGCAGCGACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36849","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. MG1655","NCBI_taxonomy_id":"511145"}}}},"ARO_accession":"3003577","ARO_id":"40187","ARO_name":"ugd","CARD_short_name":"ugd","ARO_description":"PmrE is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A, which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin.","ARO_category":{"41433":{"category_aro_accession":"3004269","category_aro_cvterm_id":"41433","category_aro_name":"pmr phosphoethanolamine transferase","category_aro_description":"This family of phosphoethanolamine transferase catalyze the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine to lipid A, which impedes the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36593":{"category_aro_accession":"3000454","category_aro_cvterm_id":"36593","category_aro_name":"polymyxin B","category_aro_description":"Polymyxin B is mixture of mostly polymyxins B1 and B2, mainly used for resistant gram-negative infections. They are polypeptides with cationic detergent action on cell membranes.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"882":{"model_id":"882","model_name":"RCP-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"3306":{"protein_sequence":{"accession":"CAA33795.1","sequence":"MRFTATVLSRVATGLALGLSMATASLAETPVEALSETVARIEEQLGARVGLSLMETGTGWSWSHREDELFLMNSTVKVPVCGAILARWDAGRLSLSDALPVRKADLVPYAPVTETRVGGNMTLDELCLAAIDMSDNVAANILIGHLGGPEAVTQFFRSVGDPTSRLDRIEPKLNDFASGDERDTTSPAAMSETLRALLLGDVLSPEARGKLAEWMRHGGVTGALLRAEAEDAWLILDKSGSGSHTRNLVAVIQPEGGAPWIATMFISDTDAEFEVRNEALKDLGRAVVAVVRE"},"dna_sequence":{"accession":"X15791.1","fmin":"1375","fmax":"2257","strand":"+","sequence":"ATGCGGTTCACCGCTACCGTCCTGTCGCGTGTCGCGACAGGGCTCGCTCTCGGCCTGTCCATGGCCACGGCCTCCCTCGCCGAAACGCCTGTCGAGGCGCTCTCCGAAACCGTCGCCCGGATCGAGGAACAGCTCGGCGCCCGCGTCGGCCTCTCGCTCATGGAGACCGGCACGGGTTGGTCCTGGTCTCACCGCGAGGACGAGCTTTTCCTCATGAACAGCACGGTCAAGGTGCCGGTCTGCGGCGCCATCCTCGCGCGTTGGGACGCGGGCAGGCTGTCGCTCTCCGATGCGCTGCCGGTGCGCAAGGCCGACCTCGTGCCCTACGCGCCCGTCACGGAGACGCGGGTCGGCGGCAACATGACCCTCGACGAGCTCTGCCTCGCGGCGATCGACATGAGCGACAATGTGGCGGCGAACATCCTGATCGGGCATCTCGGGGGGCCGGAGGCGGTGACGCAGTTCTTCCGCAGCGTCGGCGACCCGACGAGCCGTCTCGACCGCATCGAGCCCAAGCTGAACGACTTCGCTTCTGGAGACGAGCGGGACACCACGAGCCCGGCCGCCATGTCCGAGACGCTGCGAGCGCTGCTGCTGGGCGACGTGCTGTCTCCGGAGGCCCGCGGGAAGCTGGCGGAGTGGATGCGCCACGGCGGCGTGACCGGCGCATTGCTGCGCGCCGAGGCCGAGGACGCCTGGCTGATCCTCGACAAGTCGGGCAGCGGAAGCCACACGCGCAACCTCGTCGCGGTGATCCAGCCTGAAGGCGGAGCGCCCTGGATCGCGACCATGTTCATCTCGGATACGGACGCGGAGTTCGAGGTTCGCAACGAGGCGCTCAAAGATCTGGGTAGGGCGGTGGTCGCGGTTGTTCGCGAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40171","NCBI_taxonomy_name":"Rhodobacter capsulatus","NCBI_taxonomy_id":"1061"}}}},"ARO_accession":"3003563","ARO_id":"40170","ARO_name":"RCP-1","CARD_short_name":"RCP-1","ARO_description":"RCP is a class A beta-lactamase found in Rhodopseudomonas capsulata.","ARO_category":{"41399":{"category_aro_accession":"3004235","category_aro_cvterm_id":"41399","category_aro_name":"RCP beta-lactamase","category_aro_description":"A family of class A beta-lactamases that have been discovered in the Rhodobacter genus.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"970":{"model_id":"970","model_name":"OKP-B-18","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"1201":{"protein_sequence":{"accession":"CAP12358.1","sequence":"MRYVRLCLISLIAALPLAVFASPQPLEQIKISEGQLAGRVGYVEMDLASGRTLAAWRASERFPLMSTFKVLLCGAVLARVDAGDEQLDRRIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAGNLLLKIVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDVRDTTTPASMATTLRKLLTTPSLSARSQQQLLQWMVDDQVAGPLIRAVLPAGWFIADKTGAGERGSRGIVALLGPDGKAERIVVIYLRDTAATMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AM850920.1","fmin":"40","fmax":"901","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGCCTTATCTCCCTGATTGCCGCCCTGCCACTGGCGGTATTCGCCAGCCCTCAGCCGCTTGAGCAGATTAAAATCAGCGAAGGTCAGCTGGCGGGCCGGGTGGGCTATGTTGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCAGTGAGCGCTTTCCGCTGATGAGCACCTTTAAAGTGCTGCTCTGCGGCGCGGTGCTGGCCCGGGTGGATGCCGGCGACGAACAGCTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGCCGACGGGATGACCGTTGGCGAACTCTGCGCCGCCGCCATCACCATGAGCGACAACAGCGCCGGCAATCTGCTGTTGAAGATCGTCGGCGGCCCTGCGGGATTGACCGCTTTTCTGCGCCAGATCGGTGACAACGTCACCCGTCTTGACCGCTGGGAAACGGAACTCAATGAGGCGCTTCCCGGCGACGTGCGCGACACCACCACCCCGGCCAGCATGGCCACCACCCTGCGCAAGCTGCTAACCACCCCCTCTCTGAGCGCCCGCTCGCAGCAGCAGCTGCTGCAGTGGATGGTTGACGACCAGGTGGCCGGCCCGTTGATCCGCGCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAAACCGGGGCCGGTGAGCGGGGCTCACGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAAGCGGAGCGTATCGTGGTGATCTATCTGCGGGATACCGCAGCGACCATGGCCGAACGTAACCAGCAGATCGCCGGGATAGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002451","ARO_id":"38851","ARO_name":"OKP-B-18","CARD_short_name":"OKP-B-18","ARO_description":"OKP-B-18 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"38817":{"category_aro_accession":"3002417","category_aro_cvterm_id":"38817","category_aro_name":"OKP beta-lactamase","category_aro_description":"OKP beta-lactamases are chromosomal class A beta-lactamase that confer resistance to penicillins and early cephalosporins in Klebsiella pneumoniae. OKP beta-lactamases can be subdivided into two groups: OKP-A and OKP-B which diverge by about 4.2%.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"971":{"model_id":"971","model_name":"cmlA4","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"656":{"protein_sequence":{"accession":"AAF27726.1","sequence":"MRSKNFSWRYSLAATVLLLSPFDLLASLGMDMYLPAVPFMPNALGTTASTVQLTLATYLVMIGAGQLLFGPLSDRLGRRPVLLGGGLAYVVASMGLAFTSLAEVFLGLRILQACGASACLVSTFATVRDIYAGREESNVIYGILGSMLAMVPAVGPLLGALVDMWLGWRAIFAFLGLGMIAASAAAWRFWPETRVQRVTGLQWSQLLLPVKCLNFWLYTLCYAAGMGSFFVFFFIAPGLIMGRQGVSQLGFSLLFATVAIAMVFTARFMGRVIPKWGSPSVLRMGMGCLIAGAVLLAITEIWASQSVLGFIAPMWLVGIGVATAVSVAPNGALQGFDHVAGTVTAVYFCLGGVLLGSIGTLIISLLPRNTAWPVVVYCLTLATVVLGLSCVSRAKGSRGQGEHDVVALQSAESTSNPNR"},"dna_sequence":{"accession":"AF156486.1","fmin":"3648","fmax":"4908","strand":"+","sequence":"GTGCGCTCAAAAAACTTTAGTTGGCGGTACTCCCTTGCCGCCACGGTGTTGTTGTTATCACCGTTCGATTTGCTGGCATCACTCGGCATGGACATGTACTTGCCGGCAGTGCCTTTTATGCCAAACGCGCTTGGCACGACAGCGAGCACAGTTCAGCTTACGCTGGCAACGTACTTGGTCATGATCGGTGCCGGTCAGCTCTTGTTTGGACCGCTATCGGACCGACTGGGGCGCCGCCCCGTTCTACTGGGAGGTGGCCTCGCCTACGTTGTGGCGTCAATGGGCCTCGCTTTTACGTCATTGGCTGAAGTCTTTCTGGGGCTTCGGATTCTTCAGGCTTGTGGTGCCTCGGCGTGCCTTGTTTCCACGTTTGCAACAGTACGTGACATTTACGCAGGTCGCGAGGAAAGTAACGTCATTTACGGCATACTCGGATCCATGCTGGCCATGGTCCCGGCGGTAGGCCCATTGCTCGGAGCGCTCGTCGACATGTGGCTTGGGTGGCGGGCTATCTTTGCGTTTCTAGGTTTGGGCATGATCGCTGCATCTGCAGCAGCGTGGCGATTCTGGCCAGAAACCCGGGTGCAACGAGTTACGGGCTTGCAATGGTCGCAGCTGCTACTCCCCGTTAAGTGCCTGAACTTCTGGTTGTACACGTTGTGTTACGCCGCTGGAATGGGTAGCTTCTTCGTCTTTTTCTTCATTGCGCCCGGACTAATAATGGGCAGGCAAGGTGTGTCTCAGCTTGGCTTCAGCCTGCTGTTTGCCACAGTGGCAATTGCCATGGTGTTTACGGCTCGTTTTATGGGGCGTGTGATACCCAAGTGGGGCAGCCCAAGTGTCTTGCGAATGGGAATGGGATGCCTGATAGCTGGAGCAGTATTGCTTGCCATCACCGAAATATGGGCTTCGCAGTCCGTGTTAGGCTTTATTGCTCCGATGTGGCTAGTGGGTATTGGTGTCGCCACAGCGGTATCTGTGGCACCCAATGGCGCTCTTCAAGGATTCGACCATGTTGCTGGAACGGTCACGGCAGTTTACTTCTGCTTGGGCGGTGTACTGCTAGGAAGCATCGGAACGTTGATCATTTCGCTGTTGCCGCGCAACACGGCTTGGCCGGTTGTCGTGTACTGTTTGACCCTTGCAACAGTCGTGCTCGGTCTGTCTTGTGTTTCCCGAGCGAAGGGCTCTCGCGGCCAGGGGGAGCATGATGTGGTCGCGCTACAAAGTGCGGAAAGTACGTCAAATCCCAATCGTTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002694","ARO_id":"39128","ARO_name":"cmlA4","CARD_short_name":"cmlA4","ARO_description":"cmlA4 is a plasmid-encoded chloramphenicol exporter that is found in Klebsiella pneumoniae.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"972":{"model_id":"972","model_name":"CMY-23","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1115":{"protein_sequence":{"accession":"ABF06441.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHVSPGQLDAGAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"DQ463751.1","fmin":"75","fmax":"1221","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGCCGGAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35671","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Senftenberg","NCBI_taxonomy_id":"28150"}}}},"ARO_accession":"3002034","ARO_id":"38434","ARO_name":"CMY-23","CARD_short_name":"CMY-23","ARO_description":"CMY-23 is a beta-lactamase found in the Enterobacteriaceae family.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"973":{"model_id":"973","model_name":"OXA-378","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4743":{"protein_sequence":{"accession":"AHL30278.1","sequence":"MNIQALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQIQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRIGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"KF986259.1","fmin":"16","fmax":"841","strand":"-","sequence":"ATGAACATTCAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATTCAACAAGGCCAAATTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACTACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTATTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001564","ARO_id":"37964","ARO_name":"OXA-378","CARD_short_name":"OXA-378","ARO_description":"OXA-378 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"974":{"model_id":"974","model_name":"lmrC","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1050"}},"model_sequences":{"sequence":{"5185":{"protein_sequence":{"accession":"ABX00624.1","sequence":"MADASIVCTNLSFSWPDETPVFDGLSFALGAGRCGLVGPNGAGKSTLLRLAVGELTPTAGSITAQGHVGYLPQSLPLIDGTVDEALEIASIRAALHAIESGDVDEAHFTTVGDHWDIEERTTIVLDRLGLGDVSLDRPLRSLSGGQVLAIGLAAQLLKRPDVLILDEPTNNLDLAARQRLYQVVEEWKGALLVVSHDRELLDRVDTIAELQASELRLYGGNFTAYTEAVELEQENVQRAVRGAEQELRRHKREAQAAQERAQRRASNAKRNKASSGVPRIHAGALQRQAQESAGRAASVHQDRVSQAKAKLDEASQGMREEARLAITLPQTSVPAGRTVLTCHEANVRYGERTLFTGSGVDLGIRGPERIALLGPNGSGKSTLLKLIAGELEPSSGTVTAPTDRVSYLSQRLDLLDLDASVLDNLRRFAPHLQDGEVRYRLAQFLFRGDRVHRTAGWLSGGERLRATLACVLSTDPAPQLLLLDEPTNNLDLNSAAQLENALNAFQGAFVVVSHDQAFLRAIGVSRWLRLADGTLEEIAEADDAWPHRDK"},"dna_sequence":{"accession":"EU124663.1","fmin":"32695","fmax":"34348","strand":"-","sequence":"ATGGCTGACGCGAGTATTGTCTGCACCAATCTCTCCTTCTCCTGGCCCGACGAGACGCCGGTCTTCGACGGGTTGTCCTTTGCCCTCGGCGCCGGCCGTTGCGGCCTCGTGGGCCCCAATGGCGCGGGAAAGTCCACACTGTTGCGGCTCGCCGTAGGGGAACTCACCCCTACCGCAGGCTCGATCACCGCGCAGGGACATGTCGGGTACCTGCCGCAGTCCCTGCCGCTGATCGACGGCACCGTCGACGAGGCCCTGGAGATCGCCTCCATCCGGGCGGCTCTGCATGCCATCGAGTCAGGTGACGTGGACGAGGCGCACTTCACCACTGTGGGCGATCACTGGGACATCGAGGAACGCACCACGATCGTCCTGGACCGTCTGGGTCTCGGCGACGTGTCCCTTGACCGCCCGCTTCGCTCCCTCAGCGGCGGCCAGGTCCTCGCCATCGGCCTGGCCGCGCAGCTCCTGAAGCGACCCGACGTGCTGATCCTCGACGAACCCACCAACAACCTTGACCTGGCCGCCCGGCAGCGGCTCTACCAGGTCGTCGAAGAGTGGAAGGGGGCCCTCCTCGTCGTCAGCCACGACCGGGAGCTCCTGGACCGCGTAGACACCATCGCCGAGCTGCAGGCATCCGAACTCCGCCTCTACGGTGGCAACTTCACCGCCTACACGGAAGCCGTCGAGCTGGAACAGGAGAACGTGCAGCGCGCGGTGCGCGGGGCGGAGCAGGAGTTGCGCCGCCACAAGCGCGAGGCGCAGGCGGCCCAGGAGCGGGCCCAGCGCCGGGCCAGCAACGCCAAGCGCAACAAGGCTTCGTCGGGGGTGCCCCGTATCCACGCGGGCGCCCTTCAGCGACAGGCTCAGGAATCGGCGGGCCGCGCCGCCTCGGTGCACCAGGACCGGGTGTCCCAGGCCAAGGCCAAGCTGGACGAGGCCAGTCAGGGGATGCGTGAGGAAGCGCGCCTGGCGATCACCCTTCCGCAGACCTCGGTCCCGGCCGGACGCACCGTGTTGACGTGCCATGAGGCCAATGTCCGGTACGGGGAACGGACGTTGTTCACCGGCTCGGGCGTCGACCTCGGGATCCGCGGGCCGGAGCGGATCGCGCTGCTCGGGCCCAACGGCTCGGGCAAGTCAACGCTGTTGAAGCTGATCGCCGGCGAGCTCGAACCCTCCTCGGGGACGGTCACGGCGCCGACGGACCGGGTGTCCTATCTCTCGCAGCGCCTCGATCTGCTCGACTTGGACGCCAGCGTCCTGGACAACCTGCGCCGTTTCGCCCCGCATCTGCAGGACGGCGAAGTCCGCTACCGCCTGGCGCAGTTCCTCTTCCGCGGCGACCGAGTTCATCGCACCGCCGGATGGCTCTCCGGCGGTGAGCGGCTGCGCGCGACCCTGGCGTGTGTCCTGTCCACGGACCCTGCCCCTCAGCTGCTCCTGCTGGACGAGCCGACGAACAACCTCGACCTCAACAGTGCCGCCCAGCTGGAGAACGCGCTCAACGCCTTCCAGGGCGCCTTCGTAGTCGTCAGCCACGACCAGGCGTTCCTGCGCGCCATCGGTGTCTCGCGCTGGCTGCGCCTGGCGGACGGAACCCTGGAGGAGATCGCGGAGGCGGACGACGCGTGGCCTCATCGGGATAAGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36862","NCBI_taxonomy_name":"Streptomyces lincolnensis","NCBI_taxonomy_id":"1915"}}}},"ARO_accession":"3002881","ARO_id":"39315","ARO_name":"lmrC","CARD_short_name":"lmrC","ARO_description":"lmrC is an ABC-F subfamily protein that confers resistance to lincosamides in Streptomyces lincolnensis and Lactococcus lactis. It can dimerize with lmrD.","ARO_category":{"45630":{"category_aro_accession":"3007068","category_aro_cvterm_id":"45630","category_aro_name":"Miscellaneous ABC-F subfamily ATP-binding cassette ribosomal protection proteins","category_aro_description":"ABC-F subfamily ATP-binding cassette ribosomal protection proteins of unknown, unclear or miscellaneous classification which nevertheless confer resistance to antibiotics through ribosomal protection and not through antibiotic efflux. These proteins should be further reviewed to elucidate associated genes, their function, origin and classification.","category_aro_class_name":"AMR Gene Family"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"37630":{"category_aro_accession":"3001231","category_aro_cvterm_id":"37630","category_aro_name":"celesticetin","category_aro_description":"Produced by Streptomyces caelestis, which also produces the macrolide niddamycin.","category_aro_class_name":"Antibiotic"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"975":{"model_id":"975","model_name":"QnrB1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"4449":{"protein_sequence":{"accession":"ABC86904.2","sequence":"MALALVGEKIDRNRFTGEKIENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNSSALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWIGAQVLGATFSGSDLSGGEFSTFDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDNYQASLLMERLGIAVIG"},"dna_sequence":{"accession":"DQ351241.1","fmin":"36","fmax":"681","strand":"+","sequence":"ATGGCTCTGGCACTCGTTGGCGAAAAAATTGACAGAAACCGTTTCACCGGTGAGAAAATTGAAAATAGTACATTTTTTAACTGTGATTTTTCAGGTGCCGACCTGAGCGGCACTGAATTTATCGGCTGTCAGTTCTATGATCGTGAAAGCCAGAAAGGGTGCAATTTTAGTCGTGCGATGCTGAAAGATGCCATTTTTAAAAGCTGTGATTTATCCATGGCGGATTTTCGCAATTCCAGTGCGCTGGGCATTGAAATTCGCCACTGCCGCGCACAAGGCGCAGATTTCCGCGGCGCAAGCTTTATGAATATGATCACCACGCGCACCTGGTTTTGTAGCGCATATATCACGAATACCAATCTAAGCTACGCCAATTTTTCGAAAGTCGTGTTGGAAAAGTGTGAGCTGTGGGAAAACCGTTGGATAGGTGCCCAGGTACTGGGCGCGACGTTCAGTGGTTCAGATCTCTCCGGCGGCGAGTTTTCGACTTTCGACTGGCGAGCAGCAAACTTCACACATTGCGATCTGACCAATTCGGAGTTGGGTGACTTAGATATTCGGGGCGTTGATTTACAAGGCGTTAAGTTGGACAACTACCAGGCATCGTTGCTCATGGAGCGACTTGGCATCGCGGTGATTGGTTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002714","ARO_id":"39148","ARO_name":"QnrB1","CARD_short_name":"QnrB1","ARO_description":"QnrB1 is a plasmid-mediated quinolone resistance protein found in Klebsiella pneumoniae.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"976":{"model_id":"976","model_name":"CTX-M-61","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"2044":{"protein_sequence":{"accession":"ABN09669.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAVAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVDGTMSLAELSAAALQYSDNVAMNKLISHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGDYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"EF219142.1","fmin":"10","fmax":"886","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGTCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGAAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGTGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACTTGGTTAACTATAATCCGATTGCGGAAAAGCACGTCGATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTTCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGTAATCTGACGCTGGGTAAAGCATTGGGTGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGACTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35732","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Typhimurium","NCBI_taxonomy_id":"90371"}}}},"ARO_accession":"3001922","ARO_id":"38322","ARO_name":"CTX-M-61","CARD_short_name":"CTX-M-61","ARO_description":"CTX-M-61 is a beta-lactamase found in the Enterobacteriaceae family.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"871":{"model_id":"871","model_name":"CGB-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"956":{"protein_sequence":{"accession":"ABS29619.1","sequence":"MKKSIPFFIISMLLSPLANAQDTQVRDFVIEPQIQPNFYIYKTFGVFGGKEYSTNAVYLVTKKGVVLFDVPWQKTQYQSLMDTIQKRHHLPVIAVFATHSHEDRAGDLSFYNKKGIKTYATAKTNEILKKEGKATSTEIIKTGKPYRIGGEEFVVDFLGEGHTADNVVVWFPKYKILDGGCLVKSKAAADLGYTGEANVAQWPKTMEKLKSKYAQATLIIPGHDEWKGGGHVEHTLDLLNKK"},"dna_sequence":{"accession":"EF672680.1","fmin":"0","fmax":"729","strand":"+","sequence":"ATGAAAAAAAGCATTCCGTTTTTTATTATTTCGATGTTGCTAAGCCCATTGGCAAACGCCCAGGACACACAGGTAAGAGATTTTGTAATTGAGCCTCAAATTCAACCTAACTTTTATATTTACAAAACTTTCGGAGTATTCGGAGGGAAAGAATATTCTACCAATGCCGTGTATCTGGTAACTAAAAAAGGAGTTGTCCTGTTTGATGTTCCATGGCAGAAAACCCAATACCAAAGTCTGATGGATACCATTCAAAAACGTCATCATCTGCCGGTTATTGCGGTATTTGCCACCCATTCTCATGAAGACAGAGCGGGAGATTTAAGCTTTTATAATAAGAAAGGAATCAAAACCTACGCTACAGCAAAAACCAATGAAATTTTAAAGAAAGAAGGAAAAGCAACTTCTACAGAAATTATAAAAACCGGTAAACCTTACCGTATTGGCGGTGAAGAATTTGTAGTAGACTTTCTTGGTGAAGGTCATACGGCGGATAATGTAGTGGTTTGGTTTCCCAAATATAAGATACTGGACGGAGGCTGCCTTGTAAAAAGTAAAGCAGCAGCCGATCTTGGCTACACCGGCGAAGCCAACGTTGCACAATGGCCAAAAACAATGGAAAAGTTAAAATCCAAATACGCTCAGGCAACCCTGATCATTCCCGGACATGATGAATGGAAAGGCGGCGGCCATGTAGAGCACACACTTGATCTTTTAAATAAAAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39078","NCBI_taxonomy_name":"Chryseobacterium gleum","NCBI_taxonomy_id":"250"}}}},"ARO_accession":"3000841","ARO_id":"37221","ARO_name":"CGB-1","CARD_short_name":"CGB-1","ARO_description":"CGB-1 is an Ambler class B beta-lactamase that mediates resistance for carbapenems in Chryseobacterium gleum.","ARO_category":{"41367":{"category_aro_accession":"3004203","category_aro_cvterm_id":"41367","category_aro_name":"CGB beta-lactamase","category_aro_description":"CGB beta-lactamases are Class B beta-lactamases found in Chryseobacterium gleu that can hydrolyze penicillins; narrow- and expanded-spectrum cephalosporins; and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"966":{"model_id":"966","model_name":"vanS gene in vanC cluster","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"565":{"protein_sequence":{"accession":"AAF86642.1","sequence":"MKNRNPLIRKLLTQYFVTTGILLAFLVMIPLVIRFIAGTRTWYGTEPIYYILRFFADRWLFCVAIGALLIWFGTTIYYMTKAIGYLNETIQATTQLIEEPSKRITLSSHLIDVQEEMNQLREKSLQDQRAAKEAEQRKNDLIVYLAHDLRTPLTSVIGYLTLLKEEPQLSNAMRNRYTEIALQKAQRLELLISEFFEITRFNLTTIVLQTETTDLSLMLEQLTFEFLPLLEEKNLNWQLNLQKNVLATVDTEKIARVFDNLIRNAINYSYPDSPLLLELVESDSIHIRLTNRGKTIPEEMIGRLFEPFYRMDSSRATATSGTGLGLPIAKEILLASGGDISAESKDETIIFNVRLPKPANN"},"dna_sequence":{"accession":"AF162694.1","fmin":"5877","fmax":"6963","strand":"+","sequence":"TTGAAAAATAGAAATCCTTTGATCCGAAAGCTCTTGACCCAATACTTCGTCACCACTGGAATCTTGCTGGCATTCCTTGTAATGATTCCATTAGTCATTCGCTTTATTGCCGGAACCCGGACTTGGTATGGAACGGAACCTATCTACTATATCTTACGTTTTTTTGCGGATCGCTGGTTGTTTTGTGTTGCGATTGGCGCTTTACTGATATGGTTTGGTACCACCATTTACTATATGACCAAAGCCATCGGTTATTTGAATGAAACGATCCAAGCCACGACTCAACTGATAGAAGAACCATCCAAACGCATCACTTTATCGAGCCATCTGATTGATGTTCAAGAGGAAATGAATCAACTGCGGGAGAAAAGTCTGCAAGATCAACGTGCCGCTAAAGAAGCGGAACAGCGGAAAAATGATTTGATCGTTTATCTCGCCCACGATTTGCGGACGCCTCTGACAAGTGTCATAGGTTATCTGACTCTTCTAAAAGAAGAACCACAATTATCCAATGCGATGCGGAATCGTTACACGGAGATTGCTTTACAAAAAGCCCAACGGCTGGAACTATTGATCAGTGAATTCTTCGAGATCACACGCTTCAATTTGACCACGATCGTTTTGCAGACAGAAACGACTGATTTAAGTTTAATGCTTGAACAGCTGACCTTTGAGTTTTTACCTCTCTTGGAAGAAAAGAATCTAAATTGGCAACTCAACTTACAAAAAAATGTTCTTGCAACAGTAGACACCGAAAAAATAGCTCGTGTCTTTGATAATCTCATTCGCAATGCCATCAACTACAGCTATCCAGATTCGCCTTTACTTCTTGAATTGGTCGAATCAGACAGTATTCACATTCGTCTGACGAATCGTGGAAAAACAATTCCAGAAGAGATGATCGGACGTCTCTTTGAACCTTTCTATCGCATGGATTCTTCCCGAGCTACAGCCACAAGCGGAACTGGTCTTGGTCTTCCGATTGCAAAAGAGATTCTGTTAGCATCTGGCGGGGATATCTCGGCAGAAAGCAAAGACGAAACCATCATTTTCAACGTTCGCTTGCCAAAACCTGCCAACAACTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36781","NCBI_taxonomy_name":"Enterococcus gallinarum","NCBI_taxonomy_id":"1353"}}}},"ARO_accession":"3002933","ARO_id":"39367","ARO_name":"vanS gene in vanC cluster","CARD_short_name":"vanS_in_vanC_cl","ARO_description":"Also known as vanSC, is a vanS variant found in the vanC gene cluster.","ARO_category":{"36210":{"category_aro_accession":"3000071","category_aro_cvterm_id":"36210","category_aro_name":"vanS","category_aro_description":"VanS is similar to histidine protein kinases like EnvZ and acts as a response regulator by activating VanR. VanS is required for high level transcription of other van glycopeptide resistance genes.","category_aro_class_name":"AMR Gene Family"},"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"977":{"model_id":"977","model_name":"OXA-112","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1752":{"protein_sequence":{"accession":"ABV31692.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDDKAEKIKNLFNEAHTTGVLVIHQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGEKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFPLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"EF650038.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGACAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCATCAAGGTCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAATGGGATGGGGAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTCTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCCCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001643","ARO_id":"38043","ARO_name":"OXA-112","CARD_short_name":"OXA-112","ARO_description":"OXA-112 is a beta-lactamase found in A. baumannii.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"978":{"model_id":"978","model_name":"OXA-134","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1922":{"protein_sequence":{"accession":"ADM47435.1","sequence":"MKILIFLPLLSCLGLTACSLPVSSLPSQSISTQAIASLFDQAQSSGVLVIQRDQQVQVYGNDLNRANTEYVPASTFKMLNALIGLQHGKATTNEIFKWDGKKRSFTAWEKDMTLGQAMQASAVPVYQELARRIGLELMQQEVQRIQFGNQQIGQQVDNFWLVGPLKVTPKQEVQFVSALAREQLAFDPQVQQQVKAMLFLQERKAYRLYVKSGWGMDVEPQVGWLTGWVETPQAEIVAFSLNMQMQNGIDPAIRLEILQQALAELGLYPKAEG"},"dna_sequence":{"accession":"HQ122933.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGAAAATTTTGATTTTTCTGCCTTTACTGAGTTGCTTGGGCCTGACAGCATGTAGCCTACCCGTTTCATCTCTCCCATCTCAAAGCATTTCGACTCAAGCGATTGCCAGCTTATTTGATCAGGCGCAAAGCTCTGGTGTTTTAGTGATTCAGCGTGATCAACAAGTACAGGTCTATGGCAATGATTTAAATCGTGCAAATACCGAATATGTTCCCGCCTCTACTTTTAAAATGCTCAATGCTCTGATTGGCCTGCAACATGGCAAAGCCACAACCAATGAAATTTTTAAATGGGATGGCAAGAAACGCAGCTTTACCGCCTGGGAAAAAGACATGACGCTCGGCCAAGCCATGCAAGCTTCTGCGGTACCGGTCTATCAAGAGCTGGCGCGTCGTATTGGTCTGGAATTAATGCAACAGGAAGTACAACGCATCCAATTTGGTAATCAGCAGATTGGTCAACAGGTCGATAACTTCTGGTTGGTAGGCCCTTTGAAAGTTACTCCAAAACAGGAAGTCCAATTTGTTTCTGCGTTGGCCCGAGAGCAACTGGCCTTTGATCCTCAAGTCCAGCAACAAGTCAAAGCCATGTTATTTTTACAGGAGCGGAAAGCTTATCGACTATATGTCAAATCCGGTTGGGGCATGGATGTGGAACCGCAAGTCGGCTGGCTCACCGGCTGGGTTGAAACACCGCAGGCTGAAATCGTGGCATTTTCACTCAATATGCAGATGCAAAATGGTATAGATCCGGCGATCCGCCTTGAAATTTTGCAGCAGGCTTTGGCCGAATTAGGGCTTTATCCAAAAGCTGAAGGATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36948","NCBI_taxonomy_name":"Acinetobacter lwoffii","NCBI_taxonomy_id":"28090"}}}},"ARO_accession":"3001695","ARO_id":"38095","ARO_name":"OXA-134","CARD_short_name":"OXA-134","ARO_description":"OXA-134 is a beta-lactamase found in A. lwoffii.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46489":{"category_aro_accession":"3007700","category_aro_cvterm_id":"46489","category_aro_name":"OXA-134-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-134.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"979":{"model_id":"979","model_name":"TEM-96","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1004":{"protein_sequence":{"accession":"AAM22276.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLGRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AY092401.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGGTCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGGGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000963","ARO_id":"37343","ARO_name":"TEM-96","CARD_short_name":"TEM-96","ARO_description":"TEM-96 is a beta-lactamase found in E. coli.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"980":{"model_id":"980","model_name":"y56 beta-lactamase","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"3318":{"protein_sequence":{"accession":"AAX55643.1","sequence":"MKHSSLRRALLLAGITLPLVNFSLPTWAAAIPGSLDKQLAALEHSANGRLGIAMINTGNGTKILYRGARRFPFCSTFKFMLAAAVLGQSQSQPNLLNKHINYHESDLLSYAPITRKNLAHGMTVSELCAATIQYSDNTAANLLLKELGGLAAVNQFARSIGDQMFRLDRWEPDLNTALPNDPRDTTTPAAMAASINKLVLGDALHPAQRSQLTAWLKGNTTGDATIRAGAPTDWIVGDKTGSGDYGTTNDIAVLWPTKGAPIVLVVYFTQREKDAKPRRDVLASATKIILSQIS"},"dna_sequence":{"accession":"AY954728.1","fmin":"11","fmax":"896","strand":"+","sequence":"ATGAAGCACTCTTCGCTACGGCGTGCGCTATTATTAGCCGGTATTACCCTGCCCTTAGTCAATTTTTCGCTGCCAACCTGGGCCGCTGCGATTCCGGGGTCATTAGACAAGCAATTGGCAGCACTTGAGCACAGTGCTAACGGTCGTTTAGGCATTGCGATGATTAATACCGGCAATGGCACCAAAATTCTGTATCGCGGAGCTCGACGTTTCCCATTCTGTAGTACTTTTAAGTTTATGTTAGCCGCTGCTGTATTGGGTCAAAGCCAATCTCAGCCGAATTTGCTCAATAAGCATATCAATTACCATGAGAGTGATTTGTTATCTTATGCCCCCATCACGCGTAAAAATCTGGCGCATGGTATGACAGTTTCTGAATTATGTGCGGCTACCATTCAATATAGCGATAACACGGCCGCGAATTTATTACTTAAAGAGTTGGGTGGTTTAGCGGCTGTTAATCAGTTTGCTCGCAGTATTGGCGATCAGATGTTCAGGTTAGACCGCTGGGAACCGGATTTAAACACCGCACTACCTAATGACCCACGTGATACCACCACTCCTGCGGCTATGGCAGCTAGTATAAATAAATTGGTATTGGGTGATGCATTGCACCCTGCCCAACGAAGCCAACTCACGGCATGGCTGAAAGGAAACACCACCGGGGATGCCACGATTCGCGCGGGTGCCCCTACTGACTGGATTGTGGGTGACAAAACAGGTAGTGGCGATTACGGAACCACCAATGATATTGCGGTACTTTGGCCGACGAAAGGTGCACCGATTGTTTTAGTGGTGTATTTCACGCAACGTGAAAAAGATGCGAAGCCACGTCGCGATGTATTGGCCTCTGCGACCAAAATAATTTTGTCGCAAATATCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40164","NCBI_taxonomy_name":"Yersinia enterocolitica","NCBI_taxonomy_id":"630"}}}},"ARO_accession":"3003558","ARO_id":"40163","ARO_name":"y56 beta-lactamase","CARD_short_name":"Yent_y56","ARO_description":"Class A beta-lactamase found in Yersinia enterocolitica biovar 1A.","ARO_category":{"41354":{"category_aro_accession":"3004190","category_aro_cvterm_id":"41354","category_aro_name":"BlaA beta-lactamase","category_aro_description":"BlaA beta-lactamases are Class A beta-lactamases first identified in Yersinia enterocolitica and have the ability to hydrolize penicilins and cephalosporins.","category_aro_class_name":"AMR Gene Family"},"40523":{"category_aro_accession":"3003832","category_aro_cvterm_id":"40523","category_aro_name":"ticarcillin","category_aro_description":"Ticarcillin is a carboxypenicillin used for the treatment of Gram-negative bacteria, particularly P. aeruginosa. Ticarcillin's antibiotic properties arise from its ability to prevent cross-linking of peptidoglycan during cell wall synthesis, when the bacteria try to divide, causing cell death.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"981":{"model_id":"981","model_name":"OXA-86","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"895":{"protein_sequence":{"accession":"AAZ78361.1","sequence":"MNIKTLLLITSTIFISACSPYIVTANPNHSTSKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASIEYVPASTFKMLNALIGLEHHKATTTEIFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSLKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"DQ149247.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAACACTCTTACTTATAACAAGCACTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCACTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGATCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAATATTTAAGTGGGACGGGCAAAAAAGGCTGTTCCCAGAATGGGAAAAGGACATGACCCTAGGTGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCTAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001703","ARO_id":"38103","ARO_name":"OXA-86","CARD_short_name":"OXA-86","ARO_description":"OXA-86 is a beta-lactamase found in Acinetobacter spp.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"982":{"model_id":"982","model_name":"TEM-153","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1156":{"protein_sequence":{"accession":"AGA83484.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVKYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTTPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTVSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"KC149518.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTAAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGACGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGTGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001369","ARO_id":"37769","ARO_name":"TEM-153","CARD_short_name":"TEM-153","ARO_description":"TEM-153 is a beta-lactamase found in Enterobacteriaceae.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"983":{"model_id":"983","model_name":"GES-20","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1259":{"protein_sequence":{"accession":"AEZ05108.1","sequence":"MRFIHALLLAAIAHSAYASEKLTFKTDLEKLEREKAAQIGVAIVDPQGEIVAGHRMAQRFAMCSTFKFPLAALVFERIDSGTERGDRKLSYGPDMIVEWSPATERFLASGHMTVLEAAQAAVQLSDNGATNLLLREIGGPAAMTQYFRKIGDSVSRLDRKEPEMSDNTPGDLRDTTTPIAMARTVAKVLYGGALTSTSTHTIERWLIGNQTGDATLRAGFPKDWVVGEKTGTCANGGRNDIGFFKAQERDYAVAVYTTAPKLSAVERDELVASVGQVITQLILSTDK"},"dna_sequence":{"accession":"JN596280.1","fmin":"2847","fmax":"3711","strand":"+","sequence":"ATGCGCTTCATTCACGCACTATTACTGGCAGCGATCGCTCACTCTGCATATGCGTCGGAAAAATTAACCTTCAAGACCGATCTTGAGAAGCTAGAGCGCGAAAAAGCAGCTCAGATCGGTGTTGCGATCGTCGATCCCCAAGGAGAGATCGTCGCGGGCCACCGAATGGCGCAGCGTTTTGCAATGTGCTCAACGTTCAAGTTTCCGCTAGCCGCGCTGGTCTTTGAAAGAATTGACTCAGGCACCGAGCGGGGGGATCGAAAACTTTCATATGGGCCGGACATGATCGTCGAATGGTCTCCTGCCACGGAGCGGTTTCTAGCATCGGGACACATGACGGTTCTCGAGGCAGCGCAAGCTGCGGTGCAGCTTAGCGACAATGGGGCTACTAACCTCTTACTGAGAGAAATTGGCGGACCTGCTGCAATGACGCAGTATTTTCGTAAAATTGGCGACTCTGTGAGTCGGCTAGACCGGAAAGAGCCGGAGATGAGCGACAACACACCTGGCGACCTCAGAGATACAACTACGCCTATTGCTATGGCACGTACTGTGGCTAAAGTCCTCTATGGCGGCGCACTGACGTCCACCTCGACCCACACCATTGAGAGGTGGCTGATCGGAAACCAAACGGGAGACGCGACACTACGAGCGGGTTTTCCTAAAGATTGGGTTGTTGGAGAGAAAACTGGTACCTGCGCCAACGGGGGCCGGAACGACATTGGTTTTTTTAAAGCCCAGGAGAGAGATTACGCTGTAGCGGTGTATACAACGGCCCCGAAACTATCGGCCGTAGAACGTGACGAATTAGTTGCCTCTGTCGGTCAAGTTATTACACAACTCATCCTGAGCACGGACAAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002349","ARO_id":"38749","ARO_name":"GES-20","CARD_short_name":"GES-20","ARO_description":"GES-20 is a beta-lactamase found in the Enterobacteriaceae family.","ARO_category":{"36205":{"category_aro_accession":"3000066","category_aro_cvterm_id":"36205","category_aro_name":"GES beta-lactamase","category_aro_description":"GES beta-lactamases or Guiana extended-spectrum beta-lactamases are related to the other plasmid-located class A beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"985":{"model_id":"985","model_name":"ErmA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"5170":{"protein_sequence":{"accession":"CAA26964.1","sequence":"MNQKNPKDTQNFITSKKHVKEILNHTNISKQDNVIEIGSGKGHFTKELVKMSRSVTAIEIDGGLCQVTKEAVNPSENIKVIQTDILKFSFPKHINYKIYGNIPYNISTDIVKRITFESQAKYSYLIVEKGFAKRLQNLQRALGLLLMVEMDIKMLKKVPPLYFHPKPSVDSVLIVLERHQPLISKKDYKKYRSFVYKWVNREYRVLFTKNQFRQALKHANVTNINKLSKEQFLSIFNSYKLFH"},"dna_sequence":{"accession":"X03216.1","fmin":"4550","fmax":"5282","strand":"-","sequence":"ATGAACCAGAAAAACCCTAAAGACACGCAAAATTTTATTACTTCTAAAAAGCATGTAAAAGAAATATTGAATCACACGAATATCAGTAAACAAGACAACGTAATAGAAATCGGATCAGGAAAAGGACATTTTACCAAAGAGCTAGTCAAAATGAGTCGATCAGTTACTGCTATAGAAATTGATGGAGGCTTATGTCAAGTGACTAAAGAAGCGGTAAACCCCTCTGAGAATATAAAAGTGATTCAAACGGATATTCTAAAATTTTCCTTCCCAAAACATATAAACTATAAGATATATGGTAATATTCCTTATAACATCAGTACGGATATTGTCAAAAGAATTACCTTTGAAAGTCAGGCTAAATATAGCTATCTTATCGTTGAGAAGGGATTTGCGAAAAGATTGCAAAATCTGCAACGAGCTTTGGGTTTACTATTAATGGTGGAGATGGATATAAAAATGCTCAAAAAAGTACCACCACTATATTTTCATCCTAAGCCAAGTGTAGACTCTGTATTGATTGTTCTTGAACGACATCAACCATTGATTTCAAAGAAGGACTACAAAAAGTATCGATCTTTTGTTTATAAGTGGGTAAACCGTGAATATCGTGTTCTTTTCACTAAAAACCAATTCCGACAGGCTTTGAAGCATGCAAATGTCACTAATATTAATAAACTATCGAAGGAACAATTTCTTTCTATTTTCAATAGTTACAAATTGTTTCACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35508","NCBI_taxonomy_name":"Staphylococcus aureus","NCBI_taxonomy_id":"1280"}}}},"ARO_accession":"3000347","ARO_id":"36486","ARO_name":"ErmA","CARD_short_name":"ErmA","ARO_description":"ErmA confers the MLSb phenotype. Similar to ErmC, Expression of ErmA is inducible by erythromycin. The leader peptide causes attenuation of the mRNA and stabilizes the structure preventing further translation. When erythromycin is present, it binds the leader peptide causing a change in conformation allowing for the expression of ErmA.","ARO_category":{"36699":{"category_aro_accession":"3000560","category_aro_cvterm_id":"36699","category_aro_name":"Erm 23S ribosomal RNA methyltransferase","category_aro_description":"Erm proteins are part of the RNA methyltransferase family and methylate A2058 (E. coli nomenclature) of the 23S ribosomal RNA conferring degrees of resistance to Macrolides, Lincosamides and Streptogramin b. This is called the MLSb phenotype.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35946":{"category_aro_accession":"0000027","category_aro_cvterm_id":"35946","category_aro_name":"roxithromycin","category_aro_description":"Roxithromycin is a semi-synthetic, 14-carbon ring macrolide antibiotic derived from erythromycin. It is used to treat respiratory tract, urinary and soft tissue infections. Roxithromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35974":{"category_aro_accession":"0000057","category_aro_cvterm_id":"35974","category_aro_name":"telithromycin","category_aro_description":"Telithromycin is a semi-synthetic derivative of erythromycin. It is a 14-membered macrolide and is the first ketolide antibiotic to be used in clinics. Telithromycin binds the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"35982":{"category_aro_accession":"0000065","category_aro_cvterm_id":"35982","category_aro_name":"clarithromycin","category_aro_description":"Clarithromycin is a methyl derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome and is used to treat pharyngitis, tonsillitis, acute maxillary sinusitis, acute bacterial exacerbation of chronic bronchitis, pneumonia (especially atypical pneumonias associated with Chlamydia pneumoniae or TWAR), and skin structure infections.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"36284":{"category_aro_accession":"3000145","category_aro_cvterm_id":"36284","category_aro_name":"tylosin","category_aro_description":"Tylosin is a 16-membered macrolide, naturally produced by Streptomyces fradiae. It interacts with the bacterial ribosome 50S subunit to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"36295":{"category_aro_accession":"3000156","category_aro_cvterm_id":"36295","category_aro_name":"spiramycin","category_aro_description":"Spiramycin is a 16-membered macrolide and is natural product produced by Streptomyces ambofaciens. It binds to the 50S subunit of bacterial ribosomes and inhibits peptidyl transfer activity to disrupt protein synthesis.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"36315":{"category_aro_accession":"3000176","category_aro_cvterm_id":"36315","category_aro_name":"dirithromycin","category_aro_description":"Dirithromycin is an oxazine derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome to inhibit bacterial protein synthesis.","category_aro_class_name":"Antibiotic"},"36722":{"category_aro_accession":"3000583","category_aro_cvterm_id":"36722","category_aro_name":"pristinamycin IA","category_aro_description":"Pristinamycin IA is a type B streptogramin antibiotic produced by Streptomyces pristinaespiralis. It binds to the P site of the 50S subunit of the bacterial ribosome, preventing the extension of protein chains.","category_aro_class_name":"Antibiotic"},"36723":{"category_aro_accession":"3000584","category_aro_cvterm_id":"36723","category_aro_name":"quinupristin","category_aro_description":"Quinupristin is a type B streptogramin and a semisynthetic derivative of pristinamycin 1A. It is a component of the drug Synercid and interacts with the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"virginiamycin M1","category_aro_description":"Virginiamycin M1 is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37016":{"category_aro_accession":"3000672","category_aro_cvterm_id":"37016","category_aro_name":"madumycin II","category_aro_description":"Madumycin II is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37017":{"category_aro_accession":"3000673","category_aro_cvterm_id":"37017","category_aro_name":"griseoviridin","category_aro_description":"Griseoviridin is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"37019":{"category_aro_accession":"3000675","category_aro_cvterm_id":"37019","category_aro_name":"pristinamycin IB","category_aro_description":"Pristinamycin IB is a class B streptogramin similar to pristinamycin IA, the former containing a N-methyl-4-(methylamino)phenylalanine instead of a N-methyl-4-(dimethylamino)phenylalanine in its class A streptogramin counterpart (one less methyl group).","category_aro_class_name":"Antibiotic"},"37021":{"category_aro_accession":"3000677","category_aro_cvterm_id":"37021","category_aro_name":"virginiamycin S2","category_aro_description":"Virginiamycin S2 is a streptogramin B antibiotic.","category_aro_class_name":"Antibiotic"},"37022":{"category_aro_accession":"3000678","category_aro_cvterm_id":"37022","category_aro_name":"pristinamycin IC","category_aro_description":"Pristinamycin IC is a class B streptogramin derived from virginiamycin S1.","category_aro_class_name":"Antibiotic"},"37023":{"category_aro_accession":"3000679","category_aro_cvterm_id":"37023","category_aro_name":"vernamycin C","category_aro_description":"Vernamycin C is a streptogramin B antibiotic.","category_aro_class_name":"Antibiotic"},"37024":{"category_aro_accession":"3000680","category_aro_cvterm_id":"37024","category_aro_name":"patricin A","category_aro_description":"Patricin A is a streptogramin B antibiotic.","category_aro_class_name":"Antibiotic"},"37025":{"category_aro_accession":"3000681","category_aro_cvterm_id":"37025","category_aro_name":"patricin B","category_aro_description":"Patricin B is a streptogramin B antibiotic.","category_aro_class_name":"Antibiotic"},"37026":{"category_aro_accession":"3000682","category_aro_cvterm_id":"37026","category_aro_name":"ostreogrycin B3","category_aro_description":"Ostreogrycin B3 is a derivative of pristinamycin IA, with an additional 3-hydroxy group on its 4-oxopipecolic acid.","category_aro_class_name":"Antibiotic"},"37247":{"category_aro_accession":"3000867","category_aro_cvterm_id":"37247","category_aro_name":"oleandomycin","category_aro_description":"Oleandomycin is a 14-membered macrolide produced by Streptomyces antibioticus. It is ssimilar to erythromycin, and contains a desosamine amino sugar and an oleandrose sugar. It targets the 50S ribosomal subunit to prevent protein synthesis.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35952":{"category_aro_accession":"0000034","category_aro_cvterm_id":"35952","category_aro_name":"streptogramin A antibiotic","category_aro_description":"Streptogramin A antibiotics are cyclic polyketide peptide hybrids that bind to the ribosomal peptidyl transfer centre. Structural variation arises from substituting a proline for its desaturated derivative and by its substitution for Ala or Cys. Used alone, streptogramin A antibiotics are bacteriostatic, but is bactericidal when used with streptogramin B antibiotics.","category_aro_class_name":"Drug Class"},"35967":{"category_aro_accession":"0000050","category_aro_cvterm_id":"35967","category_aro_name":"streptogramin B antibiotic","category_aro_description":"Streptogramin B antibiotics are are cyclic hepta- or hexa-depsipeptides.  Type B streptogramins block the peptide exit tunnel of the 50S bacterial ribosome. The general composition of group B streptogramins is 3-hydroxypicolinic acid-L-Thr-D-aminobutyric acid (or D-Ala)-L-Pro-L-Phe (or 4-N-,N-(dimethylamino)-L-Phe)-X-L-phenylglycine. Used alone, streptogramin B antibiotics are bacteriostatic, but is bactericidal when used with streptogramin A antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"987":{"model_id":"987","model_name":"CTX-M-4","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1512":{"protein_sequence":{"accession":"CAA74573.1","sequence":"MMTQSIRRSMLTVMATLPLLFSSATLHAQANSVQQQLEALEKSSGGRLGVAQINTADNSQILYVADERFAMCSTSKVMAAAAVLKQSESDKHLLNQRVEIRASDLVNYNPIAEKHVNGTMTLAELGAGALQYSDNTAMNKLIAHLGGPDKVTAFARSLGDETFRLDRTEPTLNSAIPGDPRDTTTPLAMAQTLKNLTLGKALAETQRAQLVTWLKGNTTGSASIRAGMPKSWGVGDKTGSGDYGTTNDIAVIWPENHAPLVLVTYFTQPEQKAESRRDILAAAAKIVTHGF"},"dna_sequence":{"accession":"Y14156.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGATGACTCAGAGCATTCGCCGCTCAATGTTAACGGTGATGGCGACGCTACCCCTGCTATTTAGCAGCGCAACGCTGCATGCGCAGGCGAACAGCGTGCAACAGCAGCTGGAAGCCCTGGAGAAAAGTTCGGGAGGTCGGCTTGGCGTTGCGCAGATTAACACCGCCGATAATTCGCAGATTCTCTACGTGGCCGATGAGCGTTTTGCGATGTGCAGTACCAGTAAGGTGATGGCGGCCGCGGCGGTGCTTAAACAGAGCGAGAGCGATAAGCACCTGCTAAATCAGCGCGTTGAAATCAGAGCAAGCGACCTGGTTAACTACAATCCCATTGCGGAGAAACACGTTAACGGCACGATGACGCTGGCTGAGCTTGGCGCAGGCGCCCTGCAGTATAGCGACAATACTGCCATGAATAAGCTGATTGCCCATCTGGGTGGGCCCGATAAAGTGACGGCGTTTGCTCGCTCGTTGGGTGATGAGACCTTCCGTCTGGACAGAACCGAGCCCACGCTCAATAGCGCCATTCCAGGCGACCCGCGTGATACCACCACGCCGCTCGCGATGGCGCAGACCCTGAAAAATCTGACGCTGGGTAAAGCGCTGGCGGAAACTCAGCGGGCACAGTTGGTGACGTGGCTTAAGGGCAATACTACCGGTAGCGCGAGCATTCGGGCGGGTATGCCGAAATCATGGGGAGTGGGCGATAAAACCGGCAGCGGAGATTATGGCACCACCAACGATATCGCGGTTATCTGGCCGGAAAACCACGCACCGCTGGTTCTGGTGACCTACTTTACCCAACCGGAGCAGAAGGCGGAAAGCCGTCGGGATATTCTGGCTGCGGCGGCGAAAATCGTAACCCACGGTTTCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35732","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Typhimurium","NCBI_taxonomy_id":"90371"}}}},"ARO_accession":"3001867","ARO_id":"38267","ARO_name":"CTX-M-4","CARD_short_name":"CTX-M-4","ARO_description":"CTX-M-4 is a beta-lactamase found in Salmonella typhimurium.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"989":{"model_id":"989","model_name":"ErmG","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"590":{"protein_sequence":{"accession":"AAC37034.1","sequence":"MNKVNIKDSQNFITSKYHIEKIMNCISLDEKDNIFEIGAGKGHFTAELVKRCNFVTAIEIDSKLCEVTRNKLLNYPNYQIVNDDILKFTFPSHNPYKIFGSIPYNISTNIIRKIVFESSATISYLIVEYGFAKMLLDTNRSLALLLMAEVDISILAKIPRYYFHPKPKVDSTLIVLKRKPAKMAFKERKKYETFVMKWVNKEYEKLFTKNQFNKALKHARIYDINNISFEQFVSLFNSYKIFNG"},"dna_sequence":{"accession":"L42817.1","fmin":"201","fmax":"936","strand":"+","sequence":"ATGAACAAAGTAAATATAAAAGATAGTCAAAATTTTATTACTTCAAAATATCACATAGAAAAAATAATGAATTGCATAAGTTTAGATGAAAAAGATAACATCTTTGAAATAGGTGCAGGGAAAGGTCATTTTACTGCTGAATTGGTAAAGAGATGTAATTTTGTTACGGCGATAGAAATTGATTCTAAATTATGTGAGGTAACTCGTAATAAGCTCTTAAATTATCCTAACTATCAAATAGTAAATGATGATATACTGAAATTTACATTTCCTAGCCACAATCCATATAAAATATTTGGCAGCATACCTTACAACATAAGCACAAATATAATTCGAAAAATTGTTTTTGAAAGTTCAGCCACAATAAGTTATTTAATAGTGGAATATGGTTTTGCTAAAATGTTATTAGATACAAACAGATCACTAGCATTGCTGTTAATGGCAGAGGTAGATATTTCTATATTAGCAAAAATTCCTAGGTATTATTTCCATCCAAAACCTAAAGTGGATAGCACATTAATTGTATTAAAAAGAAAGCCAGCAAAAATGGCATTTAAAGAGAGAAAAAAATATGAAACTTTTGTAATGAAATGGGTTAACAAAGAGTACGAAAAACTGTTTACAAAAAATCAATTTAATAAAGCTTTAAAACATGCGAGAATATATGATATAAACAATATTAGTTTCGAACAATTTGTATCGCTATTTAATAGTTATAAAATATTTAACGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39568","NCBI_taxonomy_name":"Bacteroides thetaiotaomicron","NCBI_taxonomy_id":"818"}}}},"ARO_accession":"3000522","ARO_id":"36661","ARO_name":"ErmG","CARD_short_name":"ErmG","ARO_description":"ErmG is a rRNA adenine N-6-methyltransferase that protects the ribosome from inactivation due to antibiotic binding.","ARO_category":{"36699":{"category_aro_accession":"3000560","category_aro_cvterm_id":"36699","category_aro_name":"Erm 23S ribosomal RNA methyltransferase","category_aro_description":"Erm proteins are part of the RNA methyltransferase family and methylate A2058 (E. coli nomenclature) of the 23S ribosomal RNA conferring degrees of resistance to Macrolides, Lincosamides and Streptogramin b. This is called the MLSb phenotype.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35946":{"category_aro_accession":"0000027","category_aro_cvterm_id":"35946","category_aro_name":"roxithromycin","category_aro_description":"Roxithromycin is a semi-synthetic, 14-carbon ring macrolide antibiotic derived from erythromycin. It is used to treat respiratory tract, urinary and soft tissue infections. Roxithromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35974":{"category_aro_accession":"0000057","category_aro_cvterm_id":"35974","category_aro_name":"telithromycin","category_aro_description":"Telithromycin is a semi-synthetic derivative of erythromycin. It is a 14-membered macrolide and is the first ketolide antibiotic to be used in clinics. Telithromycin binds the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"35982":{"category_aro_accession":"0000065","category_aro_cvterm_id":"35982","category_aro_name":"clarithromycin","category_aro_description":"Clarithromycin is a methyl derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome and is used to treat pharyngitis, tonsillitis, acute maxillary sinusitis, acute bacterial exacerbation of chronic bronchitis, pneumonia (especially atypical pneumonias associated with Chlamydia pneumoniae or TWAR), and skin structure infections.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"36284":{"category_aro_accession":"3000145","category_aro_cvterm_id":"36284","category_aro_name":"tylosin","category_aro_description":"Tylosin is a 16-membered macrolide, naturally produced by Streptomyces fradiae. It interacts with the bacterial ribosome 50S subunit to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"36295":{"category_aro_accession":"3000156","category_aro_cvterm_id":"36295","category_aro_name":"spiramycin","category_aro_description":"Spiramycin is a 16-membered macrolide and is natural product produced by Streptomyces ambofaciens. It binds to the 50S subunit of bacterial ribosomes and inhibits peptidyl transfer activity to disrupt protein synthesis.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"36315":{"category_aro_accession":"3000176","category_aro_cvterm_id":"36315","category_aro_name":"dirithromycin","category_aro_description":"Dirithromycin is an oxazine derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome to inhibit bacterial protein synthesis.","category_aro_class_name":"Antibiotic"},"36722":{"category_aro_accession":"3000583","category_aro_cvterm_id":"36722","category_aro_name":"pristinamycin IA","category_aro_description":"Pristinamycin IA is a type B streptogramin antibiotic produced by Streptomyces pristinaespiralis. It binds to the P site of the 50S subunit of the bacterial ribosome, preventing the extension of protein chains.","category_aro_class_name":"Antibiotic"},"36723":{"category_aro_accession":"3000584","category_aro_cvterm_id":"36723","category_aro_name":"quinupristin","category_aro_description":"Quinupristin is a type B streptogramin and a semisynthetic derivative of pristinamycin 1A. It is a component of the drug Synercid and interacts with the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"virginiamycin M1","category_aro_description":"Virginiamycin M1 is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37016":{"category_aro_accession":"3000672","category_aro_cvterm_id":"37016","category_aro_name":"madumycin II","category_aro_description":"Madumycin II is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37017":{"category_aro_accession":"3000673","category_aro_cvterm_id":"37017","category_aro_name":"griseoviridin","category_aro_description":"Griseoviridin is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"37019":{"category_aro_accession":"3000675","category_aro_cvterm_id":"37019","category_aro_name":"pristinamycin IB","category_aro_description":"Pristinamycin IB is a class B streptogramin similar to pristinamycin IA, the former containing a N-methyl-4-(methylamino)phenylalanine instead of a N-methyl-4-(dimethylamino)phenylalanine in its class A streptogramin counterpart (one less methyl group).","category_aro_class_name":"Antibiotic"},"37021":{"category_aro_accession":"3000677","category_aro_cvterm_id":"37021","category_aro_name":"virginiamycin S2","category_aro_description":"Virginiamycin S2 is a streptogramin B antibiotic.","category_aro_class_name":"Antibiotic"},"37022":{"category_aro_accession":"3000678","category_aro_cvterm_id":"37022","category_aro_name":"pristinamycin IC","category_aro_description":"Pristinamycin IC is a class B streptogramin derived from virginiamycin S1.","category_aro_class_name":"Antibiotic"},"37023":{"category_aro_accession":"3000679","category_aro_cvterm_id":"37023","category_aro_name":"vernamycin C","category_aro_description":"Vernamycin C is a streptogramin B antibiotic.","category_aro_class_name":"Antibiotic"},"37024":{"category_aro_accession":"3000680","category_aro_cvterm_id":"37024","category_aro_name":"patricin A","category_aro_description":"Patricin A is a streptogramin B antibiotic.","category_aro_class_name":"Antibiotic"},"37025":{"category_aro_accession":"3000681","category_aro_cvterm_id":"37025","category_aro_name":"patricin B","category_aro_description":"Patricin B is a streptogramin B antibiotic.","category_aro_class_name":"Antibiotic"},"37026":{"category_aro_accession":"3000682","category_aro_cvterm_id":"37026","category_aro_name":"ostreogrycin B3","category_aro_description":"Ostreogrycin B3 is a derivative of pristinamycin IA, with an additional 3-hydroxy group on its 4-oxopipecolic acid.","category_aro_class_name":"Antibiotic"},"37247":{"category_aro_accession":"3000867","category_aro_cvterm_id":"37247","category_aro_name":"oleandomycin","category_aro_description":"Oleandomycin is a 14-membered macrolide produced by Streptomyces antibioticus. It is ssimilar to erythromycin, and contains a desosamine amino sugar and an oleandrose sugar. It targets the 50S ribosomal subunit to prevent protein synthesis.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35952":{"category_aro_accession":"0000034","category_aro_cvterm_id":"35952","category_aro_name":"streptogramin A antibiotic","category_aro_description":"Streptogramin A antibiotics are cyclic polyketide peptide hybrids that bind to the ribosomal peptidyl transfer centre. Structural variation arises from substituting a proline for its desaturated derivative and by its substitution for Ala or Cys. Used alone, streptogramin A antibiotics are bacteriostatic, but is bactericidal when used with streptogramin B antibiotics.","category_aro_class_name":"Drug Class"},"35967":{"category_aro_accession":"0000050","category_aro_cvterm_id":"35967","category_aro_name":"streptogramin B antibiotic","category_aro_description":"Streptogramin B antibiotics are are cyclic hepta- or hexa-depsipeptides.  Type B streptogramins block the peptide exit tunnel of the 50S bacterial ribosome. The general composition of group B streptogramins is 3-hydroxypicolinic acid-L-Thr-D-aminobutyric acid (or D-Ala)-L-Pro-L-Phe (or 4-N-,N-(dimethylamino)-L-Phe)-X-L-phenylglycine. Used alone, streptogramin B antibiotics are bacteriostatic, but is bactericidal when used with streptogramin A antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"990":{"model_id":"990","model_name":"FOX-9","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1515":{"protein_sequence":{"accession":"AEK78851.1","sequence":"MQQRRAFALLTLGSLLLAPCTYASGEAPLTVTVDGIIQPMLKAYRIPGMAVAVLKDGKAHYFNYGVANRESGQRVSEQTLFEIGSVSKTLTATLGAYAAVKGGFELDDKVSQHAPWLKGSAFDGVTMAELATYSAGGLPLQFPEEVDSNDKMRTYYRSWSPVYPAGTHRQYANTSIGLFGYLAANSLGQSFEQLMSQTLLPKLGLHHTYIQVPESAMANYAYGYSKEEKPIRVTPGMLAAEAYGIKTGSADLLKFAEANMGYQGDAAVKSAIALTHTGFYSVGDMTQGLGWESYDYPVTEQVLLADNSPAVSFQANPVTRFAVPKAMGEQRLYNKTGSTGGFGAYVAFVPARGIAIVMLANRNYPIEARVKAAHAILSQLAE"},"dna_sequence":{"accession":"JF896803.1","fmin":"0","fmax":"1149","strand":"+","sequence":"ATGCAACAACGACGTGCGTTCGCGCTACTGACGCTGGGTAGCCTGCTGTTAGCCCCTTGTACCTATGCCAGCGGGGAGGCCCCGCTGACCGTCACTGTGGACGGCATTATCCAGCCGATGCTCAAGGCGTATCGGATCCCGGGGATGGCGGTCGCCGTACTGAAAGATGGCAAGGCCCACTATTTCAACTATGGGGTTGCCAACCGCGAGAGTGGTCAGCGCGTCAGCGAGCAGACCCTGTTCGAGATTGGCTCGGTCAGCAAAACCCTGACCGCGACCCTTGGCGCTTATGCAGCGGTCAAGGGAGGCTTTGAGCTGGATGACAAGGTGAGCCAGCACGCCCCCTGGCTGAAAGGTTCCGCCTTTGATGGGGTGACCATGGCCGAGCTTGCCACCTACAGTGCGGGTGGTTTGCCGCTGCAGTTCCCCGAAGAGGTGGATTCGAATGACAAGATGCGCACTTACTATCGGAGTTGGTCACCGGTTTATCCGGCGGGGACCCACCGTCAGTACGCCAATACCAGTATCGGTCTGTTCGGCTATCTGGCTGCCAACTCCCTGGGCCAGTCATTTGAGCAACTGATGAGCCAGACCCTGCTGCCCAAGCTGGGTTTGCACCACACCTATATCCAGGTGCCGGAGTCGGCCATGGCGAACTATGCCTACGGCTATTCGAAGGAAGAGAAGCCCATCCGGGTCACTCCGGGCATGCTGGCGGCCGAGGCTTACGGGATCAAGACCGGTTCGGCGGATCTGCTGAAGTTTGCCGAGGCAAACATGGGGTATCAGGGAGATGCCGCGGTAAAAAGCGCGATCGCGCTGACCCACACCGGTTTCTACTCGGTGGGAGACATGACTCAGGGGCTGGGCTGGGAGAGTTACGACTATCCCGTCACCGAGCAGGTGCTGCTGGCGGACAACTCACCAGCGGTGAGCTTCCAGGCCAATCCGGTTACGCGTTTTGCTGTGCCCAAAGCGATGGGCGAGCAGCGGCTCTATAACAAGACGGGCTCGACCGGCGGCTTTGGCGCCTATGTGGCGTTCGTGCCCGCCAGAGGGATAGCCATCGTCATGCTGGCCAATCGCAACTATCCCATCGAGGCCAGGGTGAAGGCGGCTCACGCCATCCTGAGTCAGTTGGCCGAGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002163","ARO_id":"38563","ARO_name":"FOX-9","CARD_short_name":"FOX-9","ARO_description":"FOX-9 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36206":{"category_aro_accession":"3000067","category_aro_cvterm_id":"36206","category_aro_name":"FOX beta-lactamase","category_aro_description":"FOX beta-lactamases are plasmid-encoded AmpC-type beta-lactamase which conferred resistance to broad-spectrum cephalosporins and cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"991":{"model_id":"991","model_name":"EreA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"650"}},"model_sequences":{"sequence":{"5833":{"protein_sequence":{"accession":"AAO38247.1","sequence":"MTWRTTRTLLQPQKLDFNEFEILTSVIEGARIVGIGEGAHFVAEFSLARASLIRYLVERHEFNAIGLECGAIQASRLSEWLNSTAGAHELERFSDTLTFSVYGSVLIWLKSYLRESGRKLQLVGIDLPNTLNPRDDLAQLAEIIQLIDHLMKPHVDMLTHLLASIDGQSAVISSAKWGELETARQEKAISGVTRLKLRLASLAPVLKKHVNSDLFRKASDRIESIEYTLETLRIMKTFFDGTSLEGDTSVRDSYMAGVVDGMVRANPDVKIILLAHNNHLQKTPVSFSGELTAVPMGQHLAERVNYRAIAFTHLGPTVPEMHFPSPKSPLGFSVVTTPADAIREDSMEQYVIDACGTENSCLTLTDAPMEAKRMRSQSASVETKLSEAFDAIVCVTSAGKDSLVAL"},"dna_sequence":{"accession":"AY183453.1","fmin":"2729","fmax":"3950","strand":"+","sequence":"ATGACATGGAGAACGACCAGAACACTTTTACAGCCTCAAAAGCTGGACTTCAATGAGTTTGAGATTCTTACTTCCGTAATTGAGGGCGCCCGAATTGTCGGCATTGGCGAGGGCGCTCATTTTGTCGCGGAGTTTTCACTGGCTAGAGCTAGTCTTATCCGCTATTTGGTCGAAAGGCATGAGTTTAATGCGATTGGTTTGGAATGTGGGGCGATTCAGGCATCCCGGTTATCTGAATGGCTCAACTCAACAGCCGGTGCTCATGAACTTGAGCGATTTTCGGATACCCTGACCTTTTCTGTGTATGGCTCAGTGCTGATCTGGCTGAAATCATATCTCCGCGAATCAGGAAGAAAACTGCAGTTAGTCGGAATCGACTTACCCAACACCCTGAACCCAAGGGACGACCTAGCGCAATTGGCCGAAATTATCCAGCTCATCGATCACCTCATGAAACCGCACGTTGATATGTTGACTCACTTGTTGGCGTCCATTGATGGCCAGTCGGCGGTTATTTCATCGGCAAAATGGGGGGAGCTAGAAACGGCTCGGCAGGAGAAAGCTATCTCAGGGGTAACCAGATTGAAGCTCCGCTTGGCGTCGCTTGCCCCCGTCCTGAAAAAACACGTCAACAGCGATTTGTTCCGAAAAGCCTCTGATCGAATAGAGTCGATAGAGTATACGTTGGAAACCTTGCGTATAATGAAAACTTTCTTCGATGGTACCTCTCTTGAGGGAGATACTTCCGTACGTGACTCGTATATGGCGGGCGTAGTAGATGGAATGGTTCGAGCGAATCCGGATGTGAAGATAATTCTGCTGGCGCACAACAATCATCTACAAAAAACTCCAGTCTCCTTTTCAGGCGAGCTTACGGCTGTTCCCATGGGGCAGCACCTCGCAGAGAGGGTGAATTACCGTGCGATTGCATTCACCCATCTTGGACCCACCGTGCCGGAAATGCATTTCCCATCGCCAAAAAGTCCTCTTGGATTCTCTGTTGTGACCACGCCTGCCGATGCAATCCGTGAGGATAGTATGGAACAGTATGTCATCGACGCCTGTGGTACGGAGAATTCATGTCTGACATTGACAGATGCCCCCATGGAAGCAAAGCGAATGCGGTCTCAAAGCGCCTCTGTAGAAACGAAATTGAGCGAGGCATTTGATGCCATCGTCTGTGTTACAAGCGCCGGCAAGGACAGCCTGGTTGCCCTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000361","ARO_id":"36500","ARO_name":"EreA","CARD_short_name":"EreA","ARO_description":"EreA is an erythromycin esterase that hydrolyses the drug's lactone ring.","ARO_category":{"36459":{"category_aro_accession":"3000320","category_aro_cvterm_id":"36459","category_aro_name":"macrolide esterase","category_aro_description":"Hydrolytic enzymes that cleave the macrocycle lactone ring of macrolide antibiotics.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35946":{"category_aro_accession":"0000027","category_aro_cvterm_id":"35946","category_aro_name":"roxithromycin","category_aro_description":"Roxithromycin is a semi-synthetic, 14-carbon ring macrolide antibiotic derived from erythromycin. It is used to treat respiratory tract, urinary and soft tissue infections. Roxithromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35982":{"category_aro_accession":"0000065","category_aro_cvterm_id":"35982","category_aro_name":"clarithromycin","category_aro_description":"Clarithromycin is a methyl derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome and is used to treat pharyngitis, tonsillitis, acute maxillary sinusitis, acute bacterial exacerbation of chronic bronchitis, pneumonia (especially atypical pneumonias associated with Chlamydia pneumoniae or TWAR), and skin structure infections.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"992":{"model_id":"992","model_name":"SHV-66","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1150":{"protein_sequence":{"accession":"ABA06588.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADQRFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGASKRGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"DQ174306.1","fmin":"4","fmax":"865","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATCAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTAGCAAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001121","ARO_id":"37501","ARO_name":"SHV-66","CARD_short_name":"SHV-66","ARO_description":"SHV-66 is an extended-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"993":{"model_id":"993","model_name":"AAC(6')-Ib9","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"463":{"protein_sequence":{"accession":"AAD02244.1","sequence":"MLRSSSRPKTKLGITKYSIVTNSNDSVTLRLMTEHDLAMLYEWLNRSHIVEWWGGEEARPTLADVQEQYLPSVLAQESVTPYIAMLNGEPIGYAQSYVALGSGDGWWEEETDPGVRGIDQSLANASQLGKGLGTKLVRALVELLFNDPEVTKIQTDPSPSNLRAIRCYEKAGFERQGTVTTPDGPAVYMVQTRQAFERTRSDA"},"dna_sequence":{"accession":"AF043381.1","fmin":"251","fmax":"863","strand":"+","sequence":"ATGTTACGCAGCAGCAGTCGCCCTAAAACAAAGTTAGGCATCACAAAGTACAGCATCGTGACCAACAGCAACGATTCCGTCACACTGCGCCTCATGACTGAGCATGACCTTGCGATGCTCTATGAGTGGCTAAATCGATCTCATATCGTCGAGTGGTGGGGCGGAGAAGAAGCACGCCCGACACTTGCTGACGTACAGGAACAGTACTTGCCAAGCGTTTTAGCGCAAGAGTCCGTCACTCCATACATTGCAATGCTGAATGGAGAGCCGATTGGGTATGCCCAGTCGTACGTTGCTCTTGGAAGCGGGGACGGATGGTGGGAAGAAGAAACCGATCCAGGAGTACGCGGAATAGACCAGTCACTGGCGAATGCATCACAACTGGGCAAAGGCTTGGGAACCAAGCTGGTTCGAGCTCTGGTTGAGTTGCTGTTCAATGATCCCGAGGTCACCAAGATCCAAACGGACCCGTCGCCGAGCAACTTGCGAGCGATCCGATGCTACGAGAAAGCGGGGTTTGAGAGGCAAGGTACCGTAACCACCCCAGATGGTCCAGCCGTGTACATGGTTCAAACACGCCAGGCATTCGAGCGAACACGCAGTGATGCCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002580","ARO_id":"38980","ARO_name":"AAC(6')-Ib9","CARD_short_name":"AAC(6')-Ib9","ARO_description":"AAC(6')-Ib9 is an integron-encoded aminoglycoside acetyltransferase in P. aeruginosa.","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"A category of aminoglycoside N-acetyltransferase enzymes with modification regiospecificity based at the 6'-amino group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics through acetylation of the 6-amino group of the compound.","category_aro_class_name":"AMR Gene Family"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"994":{"model_id":"994","model_name":"SHV-77","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"8138":{"protein_sequence":{"accession":"CAJ47132.2","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVALCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AM176552.2","fmin":"30","fmax":"891","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGCGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACATCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001131","ARO_id":"37511","ARO_name":"SHV-77","CARD_short_name":"SHV-77","ARO_description":"SHV-77 is a broad-spectrum beta-lactamase found in Klebsiella pneumoniae and E. coli.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"986":{"model_id":"986","model_name":"baeS","model_type":"protein overexpression model","model_type_id":"41091","model_description":"Protein Overexpression Models (POM) are similar to Protein Variant Models (PVM) in that they include a protein reference sequence, a curated BLASTP bitscore cut-off, and mapped resistance variants. Whereas PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, reporting only those with curated mutations conferring AMR, POMs are restricted to regulatory proteins and report both wild-type sequences and\/or sequences with mutations leading to overexpression of efflux complexes. The former lead to efflux of antibiotics at basal levels, while the latter can confer clinical resistance. POMs include a protein reference sequence (often from wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Perfect RGI match is 100% identical to the wild-type reference protein sequence along its entire length, a Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value may or may not contain at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off may or may not contain at least one curated mutation from amongst the mapped resistance variants.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"850"},"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"13134":"D89V"},"Curated-R":{"13134":"D89V"},"clinical":{"13134":"D89V"}}},"model_sequences":{"sequence":{"8725":{"protein_sequence":{"accession":"ADF62939.1","sequence":"MKFWRPGITGKLFLAIFATCIVLLITMHWAVRLSFERGFIDYIKHGNEQRLQGLSDALSEQYAQHGNWRFLRNNDRFIFQILRSLEHDSGDDRPGPGMPPHGWRTQFWVIDQDMRTLVGPRAPIPPDGTRRAIKVNNATVGWVIASPVERLTRNTDINFDRQQRRASWLIVILSTLLAALATFPLARGLLAPVKRLVEGTHKLAAGDFSTRVDTRSQDELGKLAQDFNQLASTLEKNQQMRRDFMADISHELRTPLAVLRGELEAIQDGVRKFTPESVASLQAEVGTLTKLVDDLHQLSMSDEGALAYQKAPVDVINILEVISGAFRERFASRNLTIDLSLPDSAVVFGDKDRLMQLFNNLLENSLRYTDSGGGLHISGKQENGRFALTFADSAPGVQDAQLEKLFERFYRTEGSRNRASGGSGLGLAICVNIVEAHNGTLRAAHSPFGGVSITVELPLERDLSREA"},"dna_sequence":{"accession":"CP001918.1","fmin":"3478459","fmax":"3479863","strand":"+","sequence":"ATGAAATTCTGGCGTCCGGGCATTACCGGTAAGCTCTTTCTGGCAATTTTTGCCACCTGTATTGTCCTGCTGATCACCATGCACTGGGCCGTACGGCTCAGCTTTGAGCGCGGTTTTATCGATTACATTAAGCATGGTAATGAGCAGCGCCTGCAGGGTTTGAGCGATGCACTGAGCGAGCAGTATGCCCAGCACGGGAACTGGCGTTTTTTACGCAACAATGACCGTTTTATCTTCCAGATCCTGCGCTCGCTGGAGCACGATAGCGGCGATGACCGCCCCGGCCCGGGCATGCCACCCCATGGCTGGCGCACCCAGTTCTGGGTGATCGACCAGGATATGCGCACGCTGGTTGGCCCTCGTGCGCCCATCCCCCCGGACGGCACCCGGCGGGCAATCAAAGTGAATAACGCTACCGTCGGCTGGGTTATCGCCTCGCCAGTGGAACGCCTGACGCGCAACACCGATATCAACTTCGATCGTCAGCAGCGCCGGGCCAGTTGGCTGATCGTCATCCTCTCCACGCTGCTGGCCGCGCTTGCCACCTTCCCGCTGGCGCGGGGCCTGCTCGCCCCGGTGAAAAGGCTGGTGGAAGGCACGCATAAACTGGCCGCCGGGGATTTTTCCACCCGCGTGGACACGCGCAGCCAGGATGAGCTGGGCAAGCTGGCGCAGGATTTTAACCAGCTCGCCAGTACGCTGGAGAAAAACCAGCAGATGCGGCGCGATTTTATGGCCGATATTTCACACGAGCTGCGCACCCCGCTGGCAGTGCTGCGCGGCGAACTGGAGGCCATTCAGGACGGCGTGCGCAAGTTCACGCCCGAATCCGTGGCTTCGCTGCAGGCGGAAGTGGGTACGCTGACCAAACTGGTAGACGATCTGCACCAGCTCTCTATGTCAGACGAAGGGGCGCTGGCCTACCAGAAAGCACCGGTGGACGTAATCAACATTCTGGAGGTCATCAGCGGGGCTTTCCGCGAACGTTTTGCCAGCCGCAACCTGACCATTGACCTCTCCCTGCCGGACAGCGCGGTGGTGTTTGGCGATAAAGATCGTCTGATGCAGCTCTTCAACAACCTGCTGGAAAACAGCCTGCGATACACCGACAGCGGTGGCGGACTACACATCTCCGGCAAACAGGAAAACGGCCGCTTCGCCCTCACCTTTGCCGACTCCGCTCCCGGCGTGCAGGATGCGCAGCTGGAAAAACTGTTTGAACGTTTTTATCGCACCGAAGGCTCCCGCAACCGTGCCAGCGGCGGCTCCGGGCTGGGACTGGCGATTTGCGTTAATATCGTCGAGGCGCACAATGGCACCCTGCGTGCCGCCCATTCGCCTTTTGGCGGGGTTAGCATTACAGTAGAGTTACCGCTGGAACGGGATTTATCGAGAGAAGCATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37608","NCBI_taxonomy_name":"Enterobacter cloacae subsp. cloacae ATCC 13047","NCBI_taxonomy_id":"716541"}}}},"ARO_accession":"3000829","ARO_id":"37209","ARO_name":"baeS","CARD_short_name":"baeS","ARO_description":"BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity, BaeS is not necessary for overexpressed BaeR to confer resistance.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36250":{"category_aro_accession":"3000111","category_aro_cvterm_id":"36250","category_aro_name":"novobiocin","category_aro_description":"Novobiocin is an aminocoumarin antibiotic produced by Streptomyces spheroides and Streptomyces niveus, and binds DNA gyrase subunit B inhibiting ATP-dependent DNA supercoiling.","category_aro_class_name":"Antibiotic"},"46133":{"category_aro_accession":"3007382","category_aro_cvterm_id":"46133","category_aro_name":"gentamicin","category_aro_description":"Gentamicin is a commonly used aminoglycoside antibiotic derived from members of the Micromonospora genus of bacteria. It acts by binding the 30S ribosomal subunit, thus inhibiting protein synthesis. Gentamicin is typically used to treat Gram-negative infections of the repiratory and urinary tract, as well as infections of the bone and soft tissue. It also exhibits considerable nephrotoxicity and ototoxicity. Gentamicin is administered as a mixture of gentamicin type C (which makes about around 80% of the complex) and types A, B, and X (distributed in the remaining 20% of the complex).","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36242":{"category_aro_accession":"3000103","category_aro_cvterm_id":"36242","category_aro_name":"aminocoumarin antibiotic","category_aro_description":"Aminocoumarin antibiotics bind DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"996":{"model_id":"996","model_name":"CMY-77","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1739":{"protein_sequence":{"accession":"AFU25644.1","sequence":"MMKKSLCCALLLTAPLSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADITNNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGISLLHLATYTAGGLPLQIPDDVTDKAALLRFYQNWQPQWAPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKAVHVSPGQLDAEAYGVKSSVIDMARWVQVNMDASRVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"JX440353.1","fmin":"1026","fmax":"2172","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCCCTTTATCCACGTTTGCCGCCGCCAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCTGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCACCAATAACCACCCAGTCACGCAGCAAACTCTGTTTGAGCTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCAGCCTGCTGCACTTAGCCACCTACACGGCAGGCGGCCTGCCGCTGCAGATCCCCGATGACGTTACGGATAAAGCCGCATTACTGCGTTTTTATCAAAACTGGCAGCCGCAATGGGCCCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACAGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGGCTGTACACGTTTCTCCGGGACAACTTGATGCCGAAGCCTATGGCGTGAAATCCAGTGTTATTGATATGGCCCGCTGGGTTCAGGTCAACATGGACGCCAGCCGCGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGTGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCAATCATCAACGGTAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCTGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGATCCACTGGAGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39655","NCBI_taxonomy_name":"Citrobacter sp. W1065","NCBI_taxonomy_id":"1236704"}}}},"ARO_accession":"3002090","ARO_id":"38490","ARO_name":"CMY-77","CARD_short_name":"CMY-77","ARO_description":"CMY-77 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"997":{"model_id":"997","model_name":"VIM-31","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1165":{"protein_sequence":{"accession":"AFK24647.1","sequence":"MFKLLSKLLVYLTASIMAIASPLAFSVDSSGEYPTVSEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEVEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSASVLYGGCAIHELSRTSAGNVADADLAEWPTSIERIQQRYPEAQFVIPGHGLPGGLDLLKHTTNVVKAHTNRSVVE"},"dna_sequence":{"accession":"JN982330.1","fmin":"245","fmax":"1046","strand":"+","sequence":"ATGTTCAAACTTTTGAGTAAGTTATTGGTCTATTTGACCGCGTCTATCATGGCTATTGCGAGTCCGCTCGCTTTTTCCGTAGATTCTAGCGGTGAGTATCCGACAGTCAGCGAAATTCCGGTCGGGGAGGTCCGGCTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCAGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAGAAGCAAATTGGACTTCCTGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGTAGAGGGGAACGAGATTCCCACGCACTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAACTCTTCTATCCTGGTGCTGCGCATTCGACCGACAACTTAGTTGTGTACGTCCCGTCTGCGAGTGTGCTCTATGGTGGTTGTGCGATTCATGAGTTGTCACGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCATTGAGCGGATTCAACAACGCTACCCGGAAGCACAGTTCGTCATTCCGGGGCACGGCCTGCCGGGCGGTCTAGACTTGCTCAAGCACACAACGAATGTTGTAAAAGCGCACACAAATCGCTCAGTCGTTGAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3002301","ARO_id":"38701","ARO_name":"VIM-31","CARD_short_name":"VIM-31","ARO_description":"VIM-31 is a beta-lactamase found in Enterobacter cloacae.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"998":{"model_id":"998","model_name":"SHV-134","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1231":{"protein_sequence":{"accession":"ADM25824.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLREIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGASKRGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"HM559945.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCGAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTAGCAAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001178","ARO_id":"37558","ARO_name":"SHV-134","CARD_short_name":"SHV-134","ARO_description":"SHV-134 is an extended-spectrum beta-lactamase.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"999":{"model_id":"999","model_name":"LEN-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"1580":{"protein_sequence":{"accession":"AAK69830.1","sequence":"MRYVRLCVISLLATLPLAVDAGPQPLEQIKQSESQLSGRVGMVEMDLASGRTLAAWRADERFPMVSTFKVLLCGAVLARVDAGVEQLDRRIHYRQQDLVDYSPVSEKHLVDGMTIGELCAAAITLSDNSAGNLLLATVGGPAGLTAFLRQIGDNVTRLDRWETALNEALPGDARDTTTPASMAATLRKLLTAQHLSARSQQQLLQWMVDDRVAGPLIRAVLPPGWFIADKTGAGERGARGIVALLGPDGKPERIVVIYLRDTPASMAERNQHIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AY037780.1","fmin":"88","fmax":"949","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGTGTTATCTCCCTGTTAGCCACCCTGCCACTGGCGGTAGACGCCGGTCCACAGCCGCTTGAGCAGATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTGGGGATGGTGGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCGATGAACGCTTTCCCATGGTGAGCACCTTTAAAGTGCTGCTGTGCGGCGCGGTGCTGGCGCGGGTGGATGCAGGGGTCGAACAACTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGTCGACGGGATGACGATCGGCGAACTCTGCGCCGCCGCCATCACCCTGAGCGATAACAGCGCTGGCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCGGGATTAACTGCCTTTTTGCGCCAGATCGGTGACAACGTCACCCGTCTTGACCGCTGGGAAACGGCACTGAATGAGGCGCTTCCCGGCGACGCGCGCGACACCACCACCCCGGCCAGCATGGCCGCCACGCTGCGCAAACTACTGACCGCGCAGCATCTGAGCGCCCGTTCGCAACAGCAACTCCTGCAGTGGATGGTGGACGATCGGGTTGCCGGCCCGCTGATCCGCGCCGTGCTGCCGCCGGGCTGGTTTATCGCCGACAAAACCGGGGCTGGCGAACGGGGTGCGCGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAACCGGAGCGCATTGTGGTGATCTATCTGCGGGATACCCCGGCGAGTATGGCCGAGCGTAATCAACATATCGCCGGGATCGGCGCAGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002455","ARO_id":"38855","ARO_name":"LEN-2","CARD_short_name":"LEN-2","ARO_description":"LEN-2 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36236":{"category_aro_accession":"3000097","category_aro_cvterm_id":"36236","category_aro_name":"LEN beta-lactamase","category_aro_description":"LEN beta-lactamases are chromosomal class A beta-lactamases that confer resistance to ampicillin, amoxicillin, carbenicillin, and ticarcillin but not to extended-spectrum beta-lactams.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1000":{"model_id":"1000","model_name":"AAC(6')-Ib-Hangzhou","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"29":{"protein_sequence":{"accession":"ACL37342.1","sequence":"MTEHDLVMLYEWLNRSHIVEWWGGEEARPTLADVQEQYLPSVLAQESVTPYIAMLNGEPIGYAQSYVALGSGDGWWEEETDPGVRGIDQSLANASQLGKGLGTKLVRALVELLFNDPEVTKIQTDPSPSNLRAIRCYEKAGFERQGTVTTPDGPAVYMVQTRQAFERTRSDA"},"dna_sequence":{"accession":"FJ503047.1","fmin":"0","fmax":"519","strand":"+","sequence":"ATGACTGAGCATGACCTTGTGATGCTCTATGAGTGGCTAAATCGATCTCATATCGTCGAGTGGTGGGGCGGAGAAGAAGCACGCCCGACACTTGCTGACGTACAGGAACAGTACTTGCCAAGCGTTTTAGCGCAAGAGTCCGTCACTCCATACATTGCAATGCTGAATGGAGAGCCGATTGGGTATGCCCAGTCGTACGTTGCTCTTGGAAGCGGGGACGGATGGTGGGAAGAAGAAACCGATCCAGGAGTACGCGGAATAGACCAGTCACTGGCGAATGCATCACAACTGGGCAAAGGCTTGGGAACCAAGCTGGTTCGAGCTCTGGTTGAGTTGCTGTTCAATGATCCCGAGGTCACCAAGATCCAAACGGACCCGTCGCCGAGCAACTTGCGAGCGATCCGATGCTACGAGAAAGCGGGGTTTGAGAGGCAAGGTACCGTAACCACCCCAGATGGTCCAGCCGTGTACATGGTTCAAACACGCCAGGCATTCGAGCGAACACGCAGTGATGCCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3002592","ARO_id":"38992","ARO_name":"AAC(6')-Ib-Hangzhou","CARD_short_name":"AAC6_IB_HZ","ARO_description":"AAC(6')-Ib-Hangzhou is an aminoglycoside acetyltransferase in A. baumannii.","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"A category of aminoglycoside N-acetyltransferase enzymes with modification regiospecificity based at the 6'-amino group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics through acetylation of the 6-amino group of the compound.","category_aro_class_name":"AMR Gene Family"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1002":{"model_id":"1002","model_name":"AAC(6')-Ib4","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"401":{"protein_sequence":{"accession":"AAL38577.1","sequence":"MTNSNDSVTLRLMTEHDLAMLYEWLNRSHIVEWWGGEEARPTLADVQEQYLPSVLAQESVTPYIAMLNGEPIGYAQSYVALGSGDGWWEEETDPGVRGIDQSLANASQLGKGLGTKLVRALVELLFNDPEVTKIQTDPSPSNLRAIRCYEKAGFERQGTVTTPDGPAVYMVQTRQAFERTRSDA"},"dna_sequence":{"accession":"AF445082.1","fmin":"2788","fmax":"3343","strand":"+","sequence":"GTGACCAACAGCAACGATTCCGTCACACTGCGCCTCATGACTGAGCATGACCTTGCGATGCTCTATGAGTGGCTAAATCGATCTCATATCGTCGAGTGGTGGGGCGGAGAAGAAGCACGCCCGACACTTGCTGACGTACAGGAACAGTACTTGCCAAGCGTTTTAGCGCAAGAGTCCGTCACTCCATACATTGCAATGCTGAATGGAGAGCCGATTGGGTATGCCCAGTCGTACGTTGCTCTTGGAAGCGGGGACGGATGGTGGGAAGAAGAAACCGATCCAGGAGTACGCGGAATAGACCAGTCACTGGCGAATGCATCACAACTGGGCAAAGGCTTGGGAACCAAGCTGGTTCGAGCTCTGGTTGAGTTGCTGTTCAATGATCCCGAGGTCACCAAGATCCAAACGGACCCGTCGCCGAGCAACTTGCGAGCGATCCGATGCTACGAGAAAGCGGGGTTTGAGAGGCAAGGTACCGTAACCACCCCAGATGGTCCAGCCGTGTACATGGTTCAAACACGCCAGGCATTCGAGCGAACACGCAGTGATGCCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3002577","ARO_id":"38977","ARO_name":"AAC(6')-Ib4","CARD_short_name":"AAC(6')-Ib4","ARO_description":"AAC(6')-Ib4 is an aminoglycoside acetyltransferase in Serratia spp.","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"A category of aminoglycoside N-acetyltransferase enzymes with modification regiospecificity based at the 6'-amino group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics through acetylation of the 6-amino group of the compound.","category_aro_class_name":"AMR Gene Family"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1003":{"model_id":"1003","model_name":"OXA-18","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1206":{"protein_sequence":{"accession":"AAB58555.1","sequence":"MQRSLSMSGKRHFIFAVSFVISTVCLTFSPANAAQKLSCTLVIDEASGDLLHREGSCDKAFAPMSTFKLPLAIMGYDADILLDATTPRWDYKPEFNGYKSQQKPTDPTIWLKDSIVWYSQELTRRLGESRFSDYVQRFDYGNKDVSGDPGKHNGLTHAWLASSLKISPEEQVRFLRRFLRGELPVSEDALEMTKAVVPHFEAGDWDVQGKTGTGSLSDAKGGKAPIGWFIGWATRDDRRVVFARLTVGARKGEQPAGPAARDEFLNTLPALSENF"},"dna_sequence":{"accession":"U85514.1","fmin":"149","fmax":"977","strand":"+","sequence":"ATGCAACGGAGCCTGTCCATGAGCGGAAAAAGACATTTCATCTTTGCAGTATCATTTGTTATTTCAACGGTTTGCCTTACGTTCTCCCCGGCAAATGCCGCACAAAAACTGTCCTGCACGCTTGTTATCGACGAGGCGAGCGGCGACCTGCTGCACCGGGAAGGCAGTTGCGACAAGGCTTTTGCGCCGATGTCGACGTTCAAACTGCCTTTGGCCATCATGGGCTACGATGCCGATATCCTGCTCGACGCCACCACGCCGCGCTGGGATTACAAGCCGGAATTCAACGGCTACAAATCGCAGCAGAAGCCGACCGATCCGACCATCTGGCTGAAGGATTCCATCGTCTGGTATTCGCAGGAGCTGACGCGCCGCCTCGGCGAAAGCCGCTTTTCCGATTACGTGCAGCGCTTCGATTACGGCAACAAGGATGTTTCCGGCGATCCCGGCAAGCATAACGGCCTGACCCATGCCTGGCTCGCCTCGTCGCTGAAGATCTCGCCGGAGGAGCAGGTGCGTTTCCTGCGTCGTTTCCTGCGCGGCGAATTGCCGGTCTCCGAGGACGCGTTGGAGATGACGAAAGCCGTCGTGCCGCATTTCGAGGCCGGCGATTGGGACGTGCAGGGCAAGACCGGCACCGGTTCGCTTTCCGATGCCAAGGGCGGCAAGGCGCCGATCGGCTGGTTCATCGGCTGGGCGACACGCGACGACCGCCGCGTCGTCTTCGCCCGCCTAACGGTCGGGGCGAGGAAGGGCGAGCAGCCGGCCGGGCCCGCCGCTCGCGACGAGTTCCTCAACACCCTGCCGGCCCTGTCGGAAAACTTCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3001413","ARO_id":"37813","ARO_name":"OXA-18","CARD_short_name":"OXA-18","ARO_description":"OXA-18 is a beta-lactamase found in P. aeruginosa and Rickettsia.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1007":{"model_id":"1007","model_name":"OKP-A-8","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"1830":{"protein_sequence":{"accession":"CAJ19606.1","sequence":"MRYVRLCLISLIAALPLAAFASPPPLEQVTRSESQLAGRVGYVEMDLASGRTLAAWRASERFPLMSTFKVLLCGAVLARVDAGDEQLDRRIRYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAGNLLLKSVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDVRDTTTPASMAATLRKLLTSHTLSARSQQQLLQWMVDDQVAGPLIRAVLPAGWFIADKTGAGERGSRGIVALLGPNGKAERIVVIYLRDTPATMAERNQQIARIGAALIEHWQR"},"dna_sequence":{"accession":"AM051147.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGCCTTATCTCCCTGATTGCCGCCCTGCCACTGGCGGCATTCGCCAGCCCTCCGCCGCTCGAGCAAGTTACACGCAGCGAAAGTCAGCTGGCGGGCCGCGTGGGCTATGTTGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCAGTGAGCGCTTTCCGCTGATGAGCACCTTTAAAGTGCTGCTCTGCGGCGCGGTGCTGGCCCGGGTGGATGCCGGAGACGAACAGCTGGATCGGCGGATCCGCTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGCCGACGGGATGACCGTTGGCGAACTCTGCGCCGCCGCCATCACCATGAGCGACAACAGCGCCGGCAATCTGCTGTTGAAGAGCGTTGGCGGCCCCGCGGGATTGACCGCTTTTCTGCGCCAGATCGGTGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAGCTCAATGAAGCGCTTCCCGGCGACGTGCGCGACACCACCACCCCAGCCAGCATGGCCGCCACCCTGCGCAAGCTGCTAACCAGCCACACTCTGAGCGCCCGTTCGCAGCAGCAGCTGCTGCAGTGGATGGTGGACGACCAGGTAGCCGGTCCGCTGATCCGCGCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAAACCGGGGCCGGCGAGCGGGGCTCACGCGGCATTGTCGCCCTGCTCGGCCCGAACGGCAAAGCGGAGCGCATCGTGGTGATCTATCTGCGGGATACGCCGGCGACCATGGCCGAGCGTAACCAGCAGATCGCCAGAATAGGCGCGGCGCTGATCGAGCACTGGCAGCGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002425","ARO_id":"38825","ARO_name":"OKP-A-8","CARD_short_name":"OKP-A-8","ARO_description":"OKP-A-8 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"38817":{"category_aro_accession":"3002417","category_aro_cvterm_id":"38817","category_aro_name":"OKP beta-lactamase","category_aro_description":"OKP beta-lactamases are chromosomal class A beta-lactamase that confer resistance to penicillins and early cephalosporins in Klebsiella pneumoniae. OKP beta-lactamases can be subdivided into two groups: OKP-A and OKP-B which diverge by about 4.2%.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1008":{"model_id":"1008","model_name":"BEL-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1193":{"protein_sequence":{"accession":"AAZ04368.1","sequence":"MKLLLYPLLLFLVIPAFAQADFEHAISDLEAHNQAKIGVALVSENGNLIQGYRANERFAMCSTFKLPLAALVLSRIDAGEENPERKLHYDSAFLEEYAPAAKRYVATGYMTVTEAIQSALQLSDNAAANLLLKEVGGPPLLTKYFRSLGDKVSRLDRIEPTLNTNTPGDERDTTTPMSMAQTVSKLIFGDTLTYKSKGQLRRLLIGNQTGDKTIRAGLPDSWVTGDKTGSCANGGRNDVAFFITTAGKKYVLSVYTNAPELQGEERALLIASVAKLARQYVVH"},"dna_sequence":{"accession":"DQ089809.1","fmin":"1005","fmax":"1857","strand":"+","sequence":"ATGAAACTGCTGCTCTACCCGTTATTGCTGTTCCTTGTCATTCCAGCCTTTGCCCAGGCGGACTTTGAACATGCCATTTCAGATCTTGAGGCGCACAATCAAGCCAAGATCGGAGTGGCCCTAGTTAGTGAAAATGGCAACCTGATTCAAGGGTATCGTGCGAATGAAAGGTTCGCGATGTGCTCAACTTTCAAGTTGCCGTTGGCCGCTCTTGTTCTGAGTCGCATTGACGCTGGGGAAGAGAATCCTGAGCGCAAGCTTCATTACGATTCCGCGTTCCTTGAAGAGTACGCCCCAGCCGCAAAACGGTATGTGGCAACTGGATATATGACTGTAACTGAGGCAATTCAATCCGCCCTCCAACTCAGCGACAATGCCGCAGCTAACCTGCTGTTAAAAGAGGTTGGCGGCCCACCTTTATTGACAAAGTATTTCCGTAGCCTGGGTGATAAAGTAAGTCGCCTTGATCGTATTGAACCGACTTTGAACACCAATACGCCCGGCGATGAAAGAGATACAACAACGCCCATGTCCATGGCACAGACTGTGTCAAAGCTGATTTTTGGAGACACGTTGACATATAAATCCAAGGGGCAGCTAAGGCGATTACTCATCGGCAATCAGACCGGGGACAAAACCATTCGAGCTGGCTTGCCTGATTCATGGGTAACGGGTGACAAGACAGGCTCGTGTGCGAATGGCGGCCGTAACGATGTGGCGTTTTTTATAACCACTGCCGGAAAAAAATATGTTCTTTCTGTATATACCAATGCACCTGAATTGCAAGGCGAGGAAAGGGCGTTATTAATTGCTTCTGTAGCAAAGTTAGCACGTCAATATGTTGTTCACTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002385","ARO_id":"38785","ARO_name":"BEL-1","CARD_short_name":"BEL-1","ARO_description":"BEL-1 is a beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"38784":{"category_aro_accession":"3002384","category_aro_cvterm_id":"38784","category_aro_name":"BEL beta-lactamase","category_aro_description":"BEL beta-lactamases are class A expanded-spectrum beta-lactamases that are inhibited by clavulanic acid. They are chromosomally encoded and hydrolyze most cephalosporins and aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1009":{"model_id":"1009","model_name":"IND-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1595":{"protein_sequence":{"accession":"AAD20273.1","sequence":"MKKSIRFFIVSILLSPFASAQVKDFVIEPPIKNNLHIYKTFGVFGGKEYSANSMYLVTKKGVVLFDVPWEKIQYQSLMDTIKKRHNLPVVAVFATHSHDDRAGDLSFFNNKGIKTYATAKTNEFLKKDGKATSTEIIKTGKPYRIGGEEFVVDFLGEGHTADNVVVWFPKYNVLDGGCLVKSNSATDLGYIKEANVEQWPKTINKLKAKYSKATLIIPGHDEWKGGGHVEHTLELLNKK"},"dna_sequence":{"accession":"AF099139.1","fmin":"505","fmax":"1225","strand":"+","sequence":"ATGAAAAAAAGCATCCGTTTTTTTATTGTTTCGATATTGTTGAGCCCTTTTGCAAGTGCACAGGTAAAAGATTTTGTAATAGAACCACCCATCAAAAATAACCTGCATATTTATAAAACTTTTGGAGTATTTGGTGGTAAAGAATATTCTGCAAATTCAATGTATCTGGTTACTAAAAAAGGAGTTGTTCTCTTTGATGTTCCATGGGAAAAAATACAGTACCAAAGCCTCATGGATACCATTAAAAAACGTCATAATTTACCGGTTGTAGCGGTATTTGCCACACACTCCCATGATGACCGCGCCGGTGACCTTAGTTTTTTCAATAATAAAGGGATTAAAACATATGCAACTGCCAAAACCAACGAGTTCTTGAAAAAAGACGGAAAAGCAACATCCACAGAAATCATCAAAACCGGAAAACCGTACCGCATTGGCGGAGAAGAATTTGTGGTAGATTTTCTTGGTGAAGGGCATACTGCTGATAATGTAGTGGTATGGTTCCCTAAATACAATGTATTGGATGGTGGCTGTCTTGTAAAAAGTAATTCAGCTACTGATTTAGGATATATTAAGGAAGCCAATGTAGAACAGTGGCCCAAAACTATAAATAAATTAAAAGCCAAATATTCTAAAGCAACATTAATTATTCCGGGACATGATGAATGGAAAGGCGGTGGACATGTTGAACACACTTTAGAACTTCTGAATAAAAAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36916","NCBI_taxonomy_name":"Chryseobacterium indologenes","NCBI_taxonomy_id":"253"}}}},"ARO_accession":"3002256","ARO_id":"38656","ARO_name":"IND-1","CARD_short_name":"IND-1","ARO_description":"IND-1 is a beta-lactamase found in Chryseobacterium indologenes.","ARO_category":{"36199":{"category_aro_accession":"3000060","category_aro_cvterm_id":"36199","category_aro_name":"IND beta-lactamase","category_aro_description":"IND beta-lactamases are class B carbapenem-hydrolyzing beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1010":{"model_id":"1010","model_name":"TEM-209","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1001":{"protein_sequence":{"accession":"AGW25367.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLDARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"KF240808.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGATGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001386","ARO_id":"37786","ARO_name":"TEM-209","CARD_short_name":"TEM-209","ARO_description":"TEM-209 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1011":{"model_id":"1011","model_name":"TEM-29","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"2036":{"protein_sequence":{"accession":"CAA76796.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDHWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"Y17584.1","fmin":"0","fmax":"858","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCATTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGG","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000899","ARO_id":"37279","ARO_name":"TEM-29","CARD_short_name":"TEM-29","ARO_description":"TEM-29 is an extended-spectrum beta-lactamase that has been found in clinical isolates.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1012":{"model_id":"1012","model_name":"KPC-5","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"8232":{"protein_sequence":{"accession":"ABY91240.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVRWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"EU400222.2","fmin":"2159","fmax":"3041","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCGGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002315","ARO_id":"38715","ARO_name":"KPC-5","CARD_short_name":"KPC-5","ARO_description":"KPC-5 is a beta-lactamase found in Klebsiella pneumoniae and Pseudomonas aeruginosa.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1013":{"model_id":"1013","model_name":"APH(2'')-IIIa","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"181":{"protein_sequence":{"accession":"AAB49832.1","sequence":"MKQNKLHYTTMIMTQFPDISIQSVESLGEGFRNYAILVNGDWVFRFPKSQQGADELNKEIQLLPLLVGCVKVNIPQYVYIGKRSDGNPFVGYRKVQGQILGEDGMAVFPDDAKDRLALQLAEFMNELSAFPVETAISAGVPVTNLKNKILLLSEAVEDQVFPLLDESLRDYLTLRFQSYMTHPVYTRYTPRLIHGDLSPDHFLTNLNSRQTPLTGIIDFGDAAISDPDYDYVYLLEDCGELFTRQVMAYRGEVDLDTHIRKVSLFVTFDQVSYLLEGLRARDQDWISEGLELLEEDKANNFGANSA"},"dna_sequence":{"accession":"U51479.1","fmin":"0","fmax":"921","strand":"+","sequence":"ATGAAACAAAATAAACTTCACTATACCACAATGATAATGACTCAGTTCCCAGATATAAGCATACAATCCGTCGAGTCGCTTGGTGAGGGCTTTAGGAATTACGCGATCCTCGTCAATGGAGATTGGGTTTTTCGTTTTCCCAAGAGTCAACAAGGTGCAGACGAATTGAACAAAGAAATCCAATTGCTACCTCTGTTGGTCGGTTGTGTTAAGGTGAATATTCCACAGTATGTATATATCGGAAAGCGAAGTGATGGAAATCCCTTCGTGGGCTACCGTAAAGTCCAAGGCCAAATCTTGGGTGAAGACGGGATGGCCGTTTTTCCCGATGATGCAAAAGATCGACTGGCGCTGCAACTTGCTGAGTTCATGAATGAGCTAAGCGCATTTCCTGTTGAAACTGCCATATCAGCCGGGGTTCCTGTTACAAACCTGAAAAATAAAATTCTCTTGCTATCGGAAGCTGTGGAGGATCAGGTGTTCCCTCTTCTTGATGAGTCTTTAAGGGACTATCTCACGCTGCGCTTCCAATCCTATATGACTCATCCGGTATATACACGATATACGCCGAGACTAATTCACGGCGATTTGTCACCTGATCATTTTTTGACGAATTTGAATTCACGTCAGACCCCATTAACAGGCATTATCGATTTTGGTGATGCCGCAATAAGTGATCCCGATTATGATTATGTATACCTTTTGGAAGATTGCGGCGAGCTGTTTACTCGGCAAGTGATGGCTTATAGAGGCGAGGTTGACTTGGATACTCACATCAGAAAAGTCTCCTTGTTCGTAACGTTCGATCAAGTCAGTTACCTGTTAGAAGGCTTAAGGGCAAGGGATCAGGACTGGATTTCTGAAGGGTTAGAGCTTTTGGAAGAGGATAAGGCCAACAATTTTGGTGCGAACAGTGCTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36781","NCBI_taxonomy_name":"Enterococcus gallinarum","NCBI_taxonomy_id":"1353"}}}},"ARO_accession":"3002636","ARO_id":"39036","ARO_name":"APH(2'')-IIIa","CARD_short_name":"APH(2'')-IIIa","ARO_description":"APH(2'')-IIIa is a plasmid-encoded aminoglycoside phosphotransferase in Enterococcus gallinarum.","ARO_category":{"36267":{"category_aro_accession":"3000128","category_aro_cvterm_id":"36267","category_aro_name":"APH(2'')","category_aro_description":"A category of aminoglycoside O-phosphotransferase enzymes with modification regiospecificity based at the 2''-hydroxyl group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics, specifically kanamycin, tobramycin and amikacin, by the ATP-dependent phosphorylation of the 3'-hydroxyl group of the compound.","category_aro_class_name":"AMR Gene Family"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"40942":{"category_aro_accession":"3004015","category_aro_cvterm_id":"40942","category_aro_name":"gentamicin A","category_aro_description":"Gentamicin A is part of a complex of broad spectrum aminoglycoside antibiotics. Gentamicin inhibits protein synthesis, resulting in bacterial cell death.","category_aro_class_name":"Antibiotic"},"46133":{"category_aro_accession":"3007382","category_aro_cvterm_id":"46133","category_aro_name":"gentamicin","category_aro_description":"Gentamicin is a commonly used aminoglycoside antibiotic derived from members of the Micromonospora genus of bacteria. It acts by binding the 30S ribosomal subunit, thus inhibiting protein synthesis. Gentamicin is typically used to treat Gram-negative infections of the repiratory and urinary tract, as well as infections of the bone and soft tissue. It also exhibits considerable nephrotoxicity and ototoxicity. Gentamicin is administered as a mixture of gentamicin type C (which makes about around 80% of the complex) and types A, B, and X (distributed in the remaining 20% of the complex).","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1014":{"model_id":"1014","model_name":"SHV-25","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"8205":{"protein_sequence":{"accession":"AAF37209.2","sequence":"MRYIRLCIISLLAALPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITVSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AF208796.2","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCGCCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCGTGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001083","ARO_id":"37463","ARO_name":"SHV-25","CARD_short_name":"SHV-25","ARO_description":"SHV-25 is a broad-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1015":{"model_id":"1015","model_name":"evgA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"390"}},"model_sequences":{"sequence":{"5466":{"protein_sequence":{"accession":"BAB36671.1","sequence":"MNAIIIDDHPLAIAAIRNLLIKNDIEILAELTEGGSAVQRVETLKPDIVIIDVDIPGVNGIQVLETLRKRQYSGIIIIVSAKNDHFYGKHCADAGANGFVSKKEGMNNIIAAIEAAKNGYCYFPFSLNRFVGSLTSDQQKLDSLSKQEISVMRYILDGKDNNDIAEKMFISNKTVSTYKSRLMEKLECKSLMDLYTFAQRNKIG"},"dna_sequence":{"accession":"BA000007.3","fmin":"3212025","fmax":"3212640","strand":"+","sequence":"ATGAACGCAATAATTATTGATGACCATCCTCTTGCTATCGCAGCAATTCGTAATTTATTGATCAAAAACGATATTGAAATCTTAGCAGAGTTGACTGAAGGCGGAAGTGCCGTTCAGCGGGTGGAAACACTTAAGCCTGATATCGTCATCATTGATGTCGATATCCCCGGAGTTAACGGTATCCAGGTGTTAGAAACGCTGAGGAAGCGCCAATATAGCGGAATTATTATTATCGTCTCCGCTAAAAATGACCATTTTTACGGGAAACATTGTGCTGATGCTGGCGCTAATGGTTTCGTGAGTAAAAAAGAAGGCATGAACAATATCATTGCGGCTATTGAAGCTGCAAAAAATGGCTACTGCTATTTCCCCTTCTCTCTCAACCGGTTTGTTGGAAGTTTAACGTCCGACCAGCAAAAACTCGACTCCTTATCGAAACAAGAAATTAGTGTCATGCGGTATATTCTTGATGGCAAGGATAATAATGACATTGCTGAAAAAATGTTCATCAGCAACAAAACTGTCAGCACTTATAAAAGTCGCCTGATGGAAAAATTAGAATGTAAATCACTGATGGATCTTTACACATTCGCACAACGTAACAAAATCGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36747","NCBI_taxonomy_name":"Escherichia coli O157:H7 str. Sakai","NCBI_taxonomy_id":"386585"}}}},"ARO_accession":"3000832","ARO_id":"37212","ARO_name":"evgA","CARD_short_name":"evgA","ARO_description":"EvgA, when phosphorylated, is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner, it can be phosphorylated in the absence of EvgS when overexpressed.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35930":{"category_aro_accession":"0000011","category_aro_cvterm_id":"35930","category_aro_name":"cloxacillin","category_aro_description":"Cloxacillin is a semisynthetic, isoxazolyl penicillin derivative in the beta-lactam class of antibiotics. It interferes with peptidogylcan synthesis and is commonly used for treating penicillin-resistant Staphylococcus aureus infections.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1016":{"model_id":"1016","model_name":"OXA-255","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8157":{"protein_sequence":{"accession":"AGK07369.1","sequence":"MKKFILPIFSISTLLSLSACSTIQNKFEKTSDISDQQHEKAIKSYFDEAQTQGVIIIKEGKNIRIYGNNLVRAHTEYVPASTFKMLNALIGLENHKATTTEIFKWDGKKRSYPMWEKDMTLGDAMALSAVPVYQELARRTGLDLMQKEVKRVGFGNMSIGTQVNNFWLVGPLKITPIQEANFADDLANNRLPFKLETQEEVKKMLLIKEVNGSKIYAKSGWGMDVTPQVGWLTGWVEKSNGEKVPFSLNLEMKQGMSGSIRNEITYKSLENLGII"},"dna_sequence":{"accession":"KC479325.2","fmin":"668","fmax":"1496","strand":"+","sequence":"ATGAAAAAATTTATACTTCCTATCTTCAGCATTTCTACTCTACTTTCTCTCAGTGCATGCTCAACTATTCAAAATAAATTTGAAAAAACTTCTGATATTTCTGATCAGCAACATGAAAAAGCCATTAAAAGCTATTTTGATGAAGCTCAAACACAAGGTGTAATAATTATTAAAGAGGGAAAGAATATTAGAATCTATGGTAATAACCTGGTACGAGCACATACAGAATATGTCCCTGCGTCAACATTTAAGATGCTAAATGCCTTAATTGGATTAGAAAATCATAAAGCTACAACAACTGAGATTTTCAAATGGGATGGTAAAAAAAGATCTTATCCTATGTGGGAAAAAGATATGACTTTAGGTGATGCCATGGCACTTTCAGCAGTTCCTGTATATCAAGAACTTGCAAGACGGACTGGCTTAGATCTAATGCAAAAAGAAGTTAAACGGGTTGGTTTTGGTAATATGAGCATCGGGACACAAGTTAATAACTTCTGGTTAGTTGGCCCCCTCAAGATTACACCAATACAAGAGGCTAATTTTGCCGATGATCTTGCGAATAATCGATTACCCTTTAAATTAGAAACTCAAGAAGAAGTAAAAAAAATGCTTCTGATTAAAGAAGTCAATGGTAGTAAAATTTATGCGAAAAGTGGATGGGGAATGGATGTGACCCCTCAAGTAGGTTGGTTAACAGGTTGGGTAGAAAAATCTAATGGCGAAAAAGTTCCCTTTTCTCTAAACCTAGAAATGAAGCAAGGAATGTCTGGTTCTATTCGTAATGAAATTACTTATAAATCATTAGAAAATTTAGGGATTATATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3001690","ARO_id":"38090","ARO_name":"OXA-255","CARD_short_name":"OXA-255","ARO_description":"OXA-255 is a beta-lactamase found in A. baumannii.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46490":{"category_aro_accession":"3007701","category_aro_cvterm_id":"46490","category_aro_name":"OXA-143-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-143.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1017":{"model_id":"1017","model_name":"CTX-M-86","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1413":{"protein_sequence":{"accession":"ACI29348.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPFAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"FJ214369.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGTTTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGACTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35709","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Agona","NCBI_taxonomy_id":"58095"}}}},"ARO_accession":"3001946","ARO_id":"38346","ARO_name":"CTX-M-86","CARD_short_name":"CTX-M-86","ARO_description":"CTX-M-86 is a beta-lactamase found in Salmonella enterica.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1018":{"model_id":"1018","model_name":"APH(3')-IIc","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"194":{"protein_sequence":{"accession":"ADQ43421.1","sequence":"MEASNPFTDGLRLPRAWQEALADAHIERQSIGVSRADVARVHRPGQTDAFLKSEVIDAFSELGDEIARLRWLQAQGQSAPTVIATTEEGGRRWLLMSALPGRDLASSPELAPRRVAELLADALRGLHAVPVANCPFDQQLASRLQAAQARVEAGLVDADDFDDERLGQSPQQVFAELRATRPAHEDLVVSQGDACLPNLTVTDGRFTGFIDCGRLGVADRYQDLALAARSLVHNFGESRCVAALFQRYGAVPDERRLAFYRLLDEFF"},"dna_sequence":{"accession":"HQ424460.1","fmin":"1","fmax":"805","strand":"+","sequence":"ATGGAAGCTTCCAATCCCTTCACTGATGGCCTGCGGCTGCCGCGCGCATGGCAGGAAGCGTTGGCCGATGCGCACATCGAGCGGCAGTCGATCGGCGTGTCGCGCGCGGATGTCGCGCGGGTGCATCGTCCCGGGCAGACCGACGCCTTCCTGAAATCGGAAGTGATCGATGCCTTCAGTGAACTGGGTGATGAGATCGCCCGGCTGCGTTGGCTGCAGGCGCAGGGGCAGTCGGCGCCGACGGTGATTGCCACGACCGAGGAGGGCGGTCGGCGCTGGTTGTTGATGAGCGCGTTGCCCGGCCGCGACTTGGCCTCCTCGCCGGAGCTCGCGCCGAGACGGGTGGCAGAACTGCTGGCTGACGCACTGCGTGGCCTGCATGCCGTGCCTGTAGCCAACTGCCCGTTCGACCAGCAGTTGGCATCGCGCCTGCAGGCCGCACAGGCACGCGTCGAGGCGGGGCTGGTCGATGCCGATGACTTCGACGACGAGCGGCTGGGCCAGAGCCCGCAGCAGGTTTTCGCCGAGCTGCGCGCTACCCGGCCCGCTCATGAAGACCTGGTGGTCAGTCAGGGCGATGCCTGCCTGCCCAACCTGACGGTGACCGATGGGCGGTTCACTGGCTTCATCGATTGTGGCCGGTTGGGCGTGGCCGACCGCTATCAGGACCTGGCCCTGGCCGCGCGCAGCCTGGTCCACAATTTCGGGGAGAGCCGCTGTGTCGCCGCGCTGTTCCAGCGCTACGGTGCGGTCCCTGATGAGCGGCGGCTTGCATTCTATCGGTTGCTTGACGAGTTTTTCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37076","NCBI_taxonomy_name":"Stenotrophomonas maltophilia","NCBI_taxonomy_id":"40324"}}}},"ARO_accession":"3002646","ARO_id":"39046","ARO_name":"APH(3')-IIc","CARD_short_name":"APH(3')-IIc","ARO_description":"APH(3')-IIc is a chromosomal-encoded aminoglycoside phosphotransferase in S. maltophilia.","ARO_category":{"36265":{"category_aro_accession":"3000126","category_aro_cvterm_id":"36265","category_aro_name":"APH(3')","category_aro_description":"A category of aminoglycoside O-phosphotransferase enzymes with modification regiospecificity based at the 3'-hydroxyl group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics, specifically kanamycin and neomycin, by the ATP-dependent phosphorylation of the 3'-hydroxyl group of the compound.","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35940":{"category_aro_accession":"0000021","category_aro_cvterm_id":"35940","category_aro_name":"ribostamycin","category_aro_description":"Ribostamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Ribostamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35943":{"category_aro_accession":"0000024","category_aro_cvterm_id":"35943","category_aro_name":"butirosin","category_aro_description":"Butirosin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Butirosin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"37001":{"category_aro_accession":"3000657","category_aro_cvterm_id":"37001","category_aro_name":"paromomycin","category_aro_description":"An aminoglycoside antibiotic used for the treatment of parasitic infections. It is similar to neomycin sharing a similar spectrum of activity, but its hydroxyl group at the 6'-position instead of an amino group makes it resistant to AAC(6') modifying enzymes.","category_aro_class_name":"Antibiotic"},"46133":{"category_aro_accession":"3007382","category_aro_cvterm_id":"46133","category_aro_name":"gentamicin","category_aro_description":"Gentamicin is a commonly used aminoglycoside antibiotic derived from members of the Micromonospora genus of bacteria. It acts by binding the 30S ribosomal subunit, thus inhibiting protein synthesis. Gentamicin is typically used to treat Gram-negative infections of the repiratory and urinary tract, as well as infections of the bone and soft tissue. It also exhibits considerable nephrotoxicity and ototoxicity. Gentamicin is administered as a mixture of gentamicin type C (which makes about around 80% of the complex) and types A, B, and X (distributed in the remaining 20% of the complex).","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1019":{"model_id":"1019","model_name":"IMP-21","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1867":{"protein_sequence":{"accession":"BAD89802.1","sequence":"MKKLFVLCIFLFCSITAAGASLPDLKIEKLEEGVYVHTSFEEVNGWGVASKHGLVVLVNTDAYLIDTPFTAKDTEKLVNWFVERGYKIKGSISSHFHSDSTGGIEWLNSQSIPTYASVLTNELLKKDGKVQAKNSFSGVSYWLVKNKIEVFYPGPGHTQDNVVVWLPKNKILFGGCFVKPYGLGNLDDANVEAWPHSAEKLISKYGNAKLVVPSHSDIGDASLLKLTWEQAVKGLNESKKSNTVH"},"dna_sequence":{"accession":"AB204557.1","fmin":"0","fmax":"738","strand":"+","sequence":"ATGAAAAAACTATTTGTTTTATGTATATTTTTGTTTTGTAGCATTACTGCCGCAGGAGCGTCTTTGCCTGATTTAAAAATTGAGAAGCTTGAAGAGGGTGTTTATGTTCATACATCGTTTGAAGAAGTTAACGGCTGGGGTGTTGCTTCTAAACACGGTTTGGTGGTTCTTGTAAATACTGACGCCTATCTGATTGACACTCCATTTACTGCTAAAGATACTGAAAAGTTAGTCAATTGGTTTGTGGAGCGCGGCTATAAAATCAAAGGCAGTATTTCCTCACATTTCCATAGCGACAGCACGGGTGGAATAGAGTGGCTTAATTCTCAATCTATTCCCACGTATGCATCTGTATTAACAAATGAACTTCTCAAAAAAGACGGTAAGGTGCAAGCTAAAAACTCATTTAGCGGAGTTAGCTATTGGCTAGTTAAAAATAAAATTGAAGTTTTTTATCCAGGCCCAGGGCACACTCAAGATAACGTAGTGGTTTGGCTACCTAAAAATAAAATCTTATTTGGTGGTTGTTTTGTTAAACCATATGGTCTTGGTAATCTAGATGACGCAAATGTTGAAGCATGGCCACATTCGGCTGAAAAATTAATATCTAAGTATGGTAATGCAAAACTGGTTGTTCCAAGCCATAGTGACATAGGAGATGCGTCGCTCTTGAAGCTTACGTGGGAACAGGCGGTAAAAGGGCTTAATGAAAGCAAAAAAAGTAACACTGTTCATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002212","ARO_id":"38612","ARO_name":"IMP-21","CARD_short_name":"IMP-21","ARO_description":"IMP-21 is a beta-lactamase found in Pseudomonas and Acinetobacter spp.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1020":{"model_id":"1020","model_name":"OXA-241","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1759":{"protein_sequence":{"accession":"AFO55201.1","sequence":"MNIKALLLITSAIFISACSPYIVIANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLAHASTEYVPASTFKMLNALIGLEHHKTTTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"JX025021.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCCCTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGATTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTCTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCATGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGACAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGACGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCATTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001679","ARO_id":"38079","ARO_name":"OXA-241","CARD_short_name":"OXA-241","ARO_description":"OXA-241 is a beta-lactamase found in A. baumannii.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1021":{"model_id":"1021","model_name":"CTX-M-54","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8155":{"protein_sequence":{"accession":"ABC18328.3","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEQTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGDYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"DQ303459.3","fmin":"2174","fmax":"3050","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCAGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGACTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001916","ARO_id":"38316","ARO_name":"CTX-M-54","CARD_short_name":"CTX-M-54","ARO_description":"CTX-M-54 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1022":{"model_id":"1022","model_name":"TEM-28","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1958":{"protein_sequence":{"accession":"AAC32891.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDHWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGKRGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"U37195.1","fmin":"75","fmax":"936","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCATTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTAAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000898","ARO_id":"37278","ARO_name":"TEM-28","CARD_short_name":"TEM-28","ARO_description":"TEM-28 is an extended-spectrum beta-lactamase found in E. coli.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1023":{"model_id":"1023","model_name":"IMP-14","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1985":{"protein_sequence":{"accession":"AAT49068.1","sequence":"MKKLFVLCVFFFCNIAVAEESLPDLKIEKLEEGVYVHTSFEEVKGWSVVTKHGLVVLVKNDAYLIDTPITAKDTEKLVNWFVERGYKIKGSISTHFHGDSTAGIEWLNSQSIPTYASELTNELLKKDNKVQAKHSFNGVSYSLIKNKIEVFYPGPGHTQDNVVVWLPEKKILFGGCFVKPDGLGYLGDANLEAWPKSAKILMSKYGKAKLVVSSHSDIGDVSLLKRTWEQAVKGLNESKKSSQPSD"},"dna_sequence":{"accession":"AY553332.1","fmin":"113","fmax":"854","strand":"+","sequence":"ATGAAAAAATTATTTGTTTTATGTGTATTCTTCTTCTGCAACATTGCAGTTGCAGAAGAATCTTTGCCTGATTTAAAAATTGAGAAGCTTGAAGAAGGCGTTTATGTTCATACTTCGTTTGAAGAAGTTAAAGGTTGGAGTGTGGTCACTAAACACGGTTTGGTGGTTCTTGTGAAAAATGACGCCTATCTGATTGATACTCCAATTACTGCTAAAGATACTGAAAAATTAGTCAATTGGTTTGTTGAGCGGGGCTATAAAATCAAAGGCAGTATTTCAACACATTTCCATGGTGACAGTACGGCTGGAATAGAGTGGCTTAATTCTCAATCTATCCCCACATATGCTTCTGAATTAACAAATGAACTTCTTAAAAAAGACAATAAGGTACAAGCTAAACACTCTTTTAATGGGGTTAGTTATTCACTAATTAAAAACAAAATTGAAGTTTTTTATCCAGGCCCAGGGCACACTCAAGATAACGTAGTGGTTTGGTTACCTGAAAAGAAAATTTTATTCGGTGGTTGCTTTGTTAAACCGGACGGTCTTGGCTATTTGGGGGACGCAAATTTAGAAGCTTGGCCAAAGTCCGCTAAAATATTAATGTCTAAATATGGTAAAGCAAAACTAGTTGTGTCGAGTCATAGTGATATTGGAGATGTATCACTCTTGAAACGTACATGGGAGCAGGCTGTTAAAGGGCTGAATGAAAGTAAAAAATCATCACAGCCAAGCGACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002205","ARO_id":"38605","ARO_name":"IMP-14","CARD_short_name":"IMP-14","ARO_description":"IMP-14 is a beta-lactamase found in Pseudomonas and Acinetobacter spp.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1024":{"model_id":"1024","model_name":"AAC(6')-Ib-SK","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"360":{"protein_sequence":{"accession":"BAD11815.1","sequence":"MRAHRSCCIRRRGLGHNAGVELNGEKVLLRPVLDSDVKKLDKIVREPEVAAWWSTPDDYEEMLAITLDGEVIGAVQYEEEEDPEFRHAGIDIFLTASRHGLGLGTDTVRTVARWLIDERGHHRITIDPAVANAGAIRSYSKVGFKPVGVMRSYARDHTSGVWQDALLMDLLAEELV"},"dna_sequence":{"accession":"AB164230.1","fmin":"35","fmax":"566","strand":"+","sequence":"ATGCGGGCACATCGGAGCTGCTGCATCCGCAGGCGCGGGCTCGGGCACAATGCAGGAGTGGAACTGAACGGTGAGAAAGTGCTGCTGCGGCCCGTGCTCGACAGCGATGTGAAGAAGCTCGACAAGATCGTCAGAGAACCCGAGGTGGCCGCTTGGTGGTCGACCCCCGATGACTACGAGGAGATGCTCGCCATCACCCTCGACGGCGAGGTCATCGGGGCAGTGCAGTACGAGGAGGAGGAAGACCCCGAGTTCCGCCACGCGGGCATCGACATCTTCCTCACGGCGAGTCGGCACGGCCTCGGCCTCGGCACGGACACCGTCCGCACCGTGGCACGTTGGCTGATCGACGAGCGGGGACACCACCGGATCACCATCGACCCGGCGGTGGCGAACGCGGGCGCGATCCGCAGCTACAGCAAGGTGGGCTTCAAGCCGGTCGGCGTCATGCGGTCATACGCCCGTGACCACACGAGCGGCGTGTGGCAGGACGCCCTGCTGATGGACCTGCTGGCCGAAGAGCTGGTCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39523","NCBI_taxonomy_name":"Streptomyces kanamyceticus","NCBI_taxonomy_id":"1967"}}}},"ARO_accession":"3002593","ARO_id":"38993","ARO_name":"AAC(6')-Ib-SK","CARD_short_name":"AAC(6')-Ib-SK","ARO_description":"AAC(6')-Ib-SK is a chromosomal-encoded aminoglycoside acetyltransferase in Streptomyces kanamyceticus.","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"A category of aminoglycoside N-acetyltransferase enzymes with modification regiospecificity based at the 6'-amino group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics through acetylation of the 6-amino group of the compound.","category_aro_class_name":"AMR Gene Family"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1025":{"model_id":"1025","model_name":"TEM-136","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1073":{"protein_sequence":{"accession":"AAV83795.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDSWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGTGKRGSRGIIAALGPDGKPSRIVVIYTTGGQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AY826417.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATAGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAACCGGTAAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGGGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001000","ARO_id":"37380","ARO_name":"TEM-136","CARD_short_name":"TEM-136","ARO_description":"TEM-136 is an extended-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1026":{"model_id":"1026","model_name":"SHV-74","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"8225":{"protein_sequence":{"accession":"CAJ47129.2","sequence":"MRYIRLCIISLLATLPLTVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AM176549.2","fmin":"30","fmax":"891","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGACGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACATCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGCATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001128","ARO_id":"37508","ARO_name":"SHV-74","CARD_short_name":"SHV-74","ARO_description":"SHV-74 is a broad-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1028":{"model_id":"1028","model_name":"SHV-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1469":{"protein_sequence":{"accession":"ACR66323.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"FJ668814.1","fmin":"76","fmax":"937","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGCATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001059","ARO_id":"37439","ARO_name":"SHV-1","CARD_short_name":"SHV-1","ARO_description":"SHV-1 is a broad-spectrum beta-lactamase found in Klebsiella spp., as well as Acinetobacter spp., E. coli., Raoultella terrigena, and Yersinia pestis.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1029":{"model_id":"1029","model_name":"CMY-102","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1360":{"protein_sequence":{"accession":"AHA80103.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNCTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGISLLHLATYTAGGLPLQIPDDVTDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"KF526115.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATTGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCAGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTACGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTAGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002114","ARO_id":"38514","ARO_name":"CMY-102","CARD_short_name":"CMY-102","ARO_description":"CMY-102 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1031":{"model_id":"1031","model_name":"APH(6)-Id","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"467":{"protein_sequence":{"accession":"AAC23556.1","sequence":"MFMPPVFPAHWHVSQPVLIADTFSSLVWKVSLPDGTPAIVKGLKPIEDIADELRGADYLVWRNGRGAVRLLGRENNLMLLEYAGERMLSHIVAEHGDYQATEIAAELMAKLYAASEEPLPSALLPIRDRFAALFQRARDDQNAGCQTDYVHAAIIADQMMSNASELRGLHGDLHHENIMFSSRGWLVIDPVGLVGEVGFGAANMFYDPADRDDLCLDPRRIAQMADAFSRALDVDPRRLLDQAYAYGCLSAAWNADGEQEQRDLAIAAAIKQVRQTSY"},"dna_sequence":{"accession":"AF024602.1","fmin":"3155","fmax":"3992","strand":"+","sequence":"ATGTTCATGCCGCCTGTTTTTCCTGCTCATTGGCACGTTTCGCAACCTGTTCTCATTGCGGACACCTTTTCCAGCCTCGTTTGGAAAGTTTCATTGCCAGACGGGACTCCTGCAATCGTCAAGGGATTGAAACCTATAGAAGACATTGCTGATGAACTGCGCGGGGCCGACTATCTGGTATGGCGCAATGGGAGGGGAGCAGTCCGGTTGCTCGGTCGTGAGAACAATCTGATGTTGCTCGAATATGCCGGGGAGCGAATGCTCTCTCACATCGTTGCCGAGCACGGCGACTACCAGGCGACCGAAATTGCAGCGGAACTAATGGCGAAGCTGTATGCCGCATCTGAGGAACCCCTGCCTTCTGCCCTTCTCCCGATCCGGGATCGCTTTGCAGCTTTGTTTCAGCGGGCGCGCGATGATCAAAACGCAGGTTGTCAAACTGACTACGTCCACGCGGCGATTATAGCCGATCAAATGATGAGCAATGCCTCGGAACTGCGTGGGCTACATGGCGATCTGCATCATGAAAACATCATGTTCTCCAGTCGCGGCTGGCTGGTGATAGATCCCGTCGGTCTGGTCGGTGAAGTGGGCTTTGGCGCCGCCAATATGTTCTACGATCCGGCTGACAGAGACGACCTTTGTCTCGATCCTAGACGCATTGCACAGATGGCGGACGCATTCTCTCGTGCGCTGGACGTCGATCCGCGTCGCCTGCTCGACCAGGCGTACGCTTATGGGTGCCTTTCCGCAGCTTGGAACGCGGATGGAGAACAGGAGCAACGCGATCTAGCTATCGCGGCCGCGATCAAGCAGGTGCGACAGACGTCATACTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002660","ARO_id":"39060","ARO_name":"APH(6)-Id","CARD_short_name":"APH(6)-Id","ARO_description":"APH(6)-Id is an aminoglycoside phosphotransferase encoded by plasmids, integrative conjugative elements and chromosomal genomic islands in K. pneumoniae, Salmonella spp., E. coli, Shigella flexneri, Providencia alcalifaciens, Pseudomonas spp., V. cholerae, Edwardsiella tarda, Pasteurella multocida and Aeromonas bestiarum.","ARO_category":{"36290":{"category_aro_accession":"3000151","category_aro_cvterm_id":"36290","category_aro_name":"APH(6)","category_aro_description":"A category of aminoglycoside O-phosphotransferase enzymes with modification regiospecificity based at the 6-hydroxyl group of the respective antibiotic. These enzymes are characterized by enzymatic antibiotic inactivation, specifically of streptomycin, by the ATP-dependent phosphorylation of the 6-hydroxyl group of the compound.","category_aro_class_name":"AMR Gene Family"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1032":{"model_id":"1032","model_name":"OXA-365","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"976":{"protein_sequence":{"accession":"AHI63011.1","sequence":"MNIKTLLLITSAIFISACSPYIVSANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEMTYKSLEQLGIL"},"dna_sequence":{"accession":"KF885217.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAACACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGTCTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATGACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001552","ARO_id":"37952","ARO_name":"OXA-365","CARD_short_name":"OXA-365","ARO_description":"OXA-365 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1034":{"model_id":"1034","model_name":"QnrA7","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"8202":{"protein_sequence":{"accession":"ACV83303.2","sequence":"MDIIDKVFQQEDFSRQDLSDSRFRRCRFYQCDFSHCQLRDASFEDCSFIESGAVEGCHFSYADLRDASFKACRLSLANFSGANCFGIEFRECDLKGANFSRARFYNQISHKMYFCSAYISGCNLAYANLSGQCLEKCELFENNWSNANLSGASLMGSDLSHGTFSRDCWQQVNLRGCDLTFADLDGLDPRRVNLEGVKICAWQQEQLLEPLGVIVLPD"},"dna_sequence":{"accession":"GQ463707.3","fmin":"0","fmax":"657","strand":"+","sequence":"ATGGATATTATTGATAAAGTTTTTCAGCAAGAGGATTTCTCACGCCAGGATTTGAGCGACAGCCGTTTTCGCCGCTGCCGCTTTTATCAGTGTGACTTCAGCCATTGCCAGCTAAGGGATGCCAGTTTCGAGGATTGCAGTTTCATTGAAAGCGGCGCCGTCGAAGGGTGCCACTTCAGCTATGCCGATCTGCGCGATGCCAGTTTCAAGGCCTGCCGCCTGTCTTTGGCCAATTTCAGCGGTGCCAACTGCTTTGGCATAGAGTTCAGGGAGTGCGATCTCAAGGGCGCCAATTTTTCCCGGGCCCGTTTTTACAATCAAATCAGCCATAAGATGTACTTCTGCTCGGCTTATATCTCAGGCTGTAACCTGGCCTATGCCAATTTGAGCGGCCAATGCCTGGAAAAGTGCGAGCTGTTTGAAAACAACTGGAGCAATGCCAACCTCAGCGGCGCTTCCTTGATGGGCTCCGACCTCAGCCACGGCACCTTCTCCCGCGACTGCTGGCAACAGGTAAACCTGCGGGGCTGTGACCTGACCTTTGCCGATCTGGATGGGCTCGACCCCAGACGGGTCAACCTCGAAGGGGTCAAGATCTGTGCCTGGCAGCAGGAGCAACTGCTGGAACCCTTGGGAGTCATAGTGCTGCCGGATTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36891","NCBI_taxonomy_name":"Shewanella algae","NCBI_taxonomy_id":"38313"}}}},"ARO_accession":"3002713","ARO_id":"39147","ARO_name":"QnrA7","CARD_short_name":"QnrA7","ARO_description":"QnrA7 is a plasmid-mediated quinolone resistance protein found in Shewanella algae.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1037":{"model_id":"1037","model_name":"cmlA1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"8347":{"protein_sequence":{"accession":"AAA26057.1","sequence":"MSSKNFSWRYSLAATVLLLSPFDLLASLGMDMYLPAVPFMPNALGTTASTIQLTLTTYLVMIGAGQLLFGPLSDRLGRRPVLLGGGLAYVVASMGLALTSSAEVFLGLRILQACGASACLVSTFATVRDIYAGREESNVIYGILGSMLAMVPAVGPLLGALVDMWLGWRAIFAFLGLGMIAASAAAWRFWPETRVQRVAGLQWSQLLLPVKCLNFWLYTLCYAAGMGSFFVFFSIAPGLMMGRQGVSQLGFSLLFATVAIAMVFTARFMGRVIPKWGSPSVLRMGMGCLIAGAVLLAITEIWALQSVLGFIAPMWLVGIGVATAVSVAPNGALRGFDHVAGTVTAVYFCLGGVLLGSIGTLIISLLPRNTAWPVVVYCLTLATVVLGLSCVSRVKGSRGQGEHDVVALQSAGSTSNPNR"},"dna_sequence":{"accession":"M64556.1","fmin":"600","fmax":"1860","strand":"+","sequence":"GTGAGCTCAAAAAACTTTAGTTGGCGGTACTCCCTTGCCGCCACGGTGTTGTTGTTATCACCGTTCGATTTATTGGCATCACTCGGCATGGACATGTACTTGCCAGCAGTGCCGTTTATGCCAAACGCGCTTGGTACGACAGCGAGCACAATTCAGCTTACGCTGACAACGTACTTGGTCATGATTGGTGCCGGTCAGCTCTTGTTTGGACCGCTATCGGACCGACTGGGGCGCCGCCCCGTTCTACTGGGAGGTGGCCTCGCCTACGTTGTGGCGTCAATGGGCCTCGCTCTTACGTCATCGGCTGAAGTCTTTCTGGGGCTTCGGATTCTTCAGGCTTGTGGTGCCTCGGCGTGCCTTGTTTCCACATTTGCAACAGTACGTGACATTTACGCAGGTCGCGAGGAAAGTAATGTCATTTACGGCATACTCGGATCCATGCTGGCCATGGTCCCGGCGGTAGGCCCATTGCTCGGAGCGCTCGTCGACATGTGGCTTGGGTGGCGGGCTATCTTTGCGTTTCTAGGTTTGGGCATGATCGCTGCATCTGCAGCAGCGTGGCGATTCTGGCCTGAAACCCGGGTGCAACGAGTTGCGGGCTTGCAATGGTCGCAGCTGCTACTCCCCGTTAAGTGCCTGAACTTCTGGTTGTACACGTTGTGTTACGCCGCTGGAATGGGTAGCTTCTTCGTCTTTTTCTCCATTGCGCCCGGACTAATGATGGGCAGGCAAGGTGTGTCTCAGCTTGGCTTCAGCCTGCTGTTCGCCACAGTGGCAATTGCCATGGTGTTTACGGCTCGTTTTATGGGGCGTGTGATACCCAAGTGGGGCAGCCCAAGTGTCTTGCGAATGGGAATGGGATGCCTGATAGCTGGAGCAGTATTGCTTGCCATCACCGAAATATGGGCTTTGCAGTCCGTGTTAGGCTTTATTGCTCCAATGTGGCTAGTGGGTATTGGTGTCGCCACAGCGGTATCTGTGGCGCCCAATGGCGCTCTTCGAGGATTCGACCATGTTGCTGGAACGGTCACGGCAGTCTACTTCTGCTTGGGCGGTGTACTGCTAGGAAGCATCGGAACGTTGATCATTTCGCTGTTGCCGCGCAACACGGCTTGGCCGGTTGTCGTGTACTGTTTGACCCTTGCAACAGTCGTGCTCGGTCTGTCTTGTGTTTCCCGAGTGAAGGGCTCTCGCGGCCAGGGGGAGCATGATGTGGTCGCGCTACAAAGTGCGGGAAGTACATCAAATCCCAATCGTTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002693","ARO_id":"39127","ARO_name":"cmlA1","CARD_short_name":"cmlA1","ARO_description":"cmlA1 is a plasmid or transposon-encoded chloramphenicol exporter that is found in Pseudomonas aeruginosa and Klebsiella pneumoniae.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1038":{"model_id":"1038","model_name":"cmlB1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"731":{"protein_sequence":{"accession":"CAL30186.1","sequence":"MRSKDFSWRYSLAATLLLLSPFDLLASLGMDMYLPVVPFMAGALGAGAGTIQLTLTVYLVLLGAGQLLFGPLSDLLGRRPVLLGGGITYILASFGLAAASSPEVFLSFRILQACGASACLVSTFATVRDIYSGSEESNVIYGLLGSMLAMVPAIGPLLGALVDAWLGWRAIFGLLGIAMIGAVTAAWRFWPETRRQRTADLQWSQLLLPVKCLNFWLYTLCYSAGMGSFFVFFSTAPWLMMGRQALSQLSFSLLFATVAIAMMATARIMGRLIPRWGSLNTLRVGMGCLVVGALLLAVGETLIPNSVLGFIAPMWLVGVGIATAASVAPNGALRGFDHIAGTATAVYFCLGGLLLGGIGTFIIALLPSDTTWPIIAYCLILAIAVLCLSCFNPNRHHPSDDEHDSLATQDIGRSQSGHGHD"},"dna_sequence":{"accession":"AM296481.1","fmin":"775","fmax":"2041","strand":"+","sequence":"GTGCGCTCTAAAGATTTTTCTTGGCGGTATTCTCTTGCCGCCACGCTATTACTGTTATCACCATTCGACTTGTTGGCATCACTCGGCATGGATATGTATCTGCCTGTGGTGCCTTTCATGGCCGGTGCACTCGGTGCCGGTGCAGGGACGATCCAGCTGACGTTGACGGTATACCTGGTTTTGCTTGGAGCCGGTCAGCTTCTCTTTGGCCCGTTATCGGATCTGCTGGGGCGCCGCCCGGTATTACTCGGTGGTGGAATTACCTATATTTTGGCTTCATTCGGACTCGCCGCAGCTTCATCACCAGAAGTTTTCCTGAGCTTCCGTATTCTTCAAGCCTGCGGTGCTTCGGCATGTCTCGTGTCCACTTTCGCGACCGTACGCGACATATATTCGGGCAGCGAGGAAAGCAACGTTATCTATGGCTTGCTCGGCTCTATGCTTGCGATGGTTCCAGCAATAGGCCCATTGTTAGGAGCGCTGGTCGACGCTTGGCTGGGGTGGCGAGCAATCTTTGGTTTGCTGGGAATCGCAATGATAGGTGCTGTTACCGCAGCTTGGCGATTCTGGCCCGAGACCCGGCGGCAGCGAACGGCAGATTTACAGTGGTCACAGCTATTGCTTCCTGTGAAATGCCTGAACTTCTGGCTGTACACCCTCTGCTACAGCGCGGGAATGGGCAGTTTCTTTGTCTTCTTCTCGACTGCCCCTTGGCTAATGATGGGCAGGCAAGCGTTATCGCAACTTAGCTTCAGCTTGCTGTTTGCGACAGTGGCCATCGCGATGATGGCTACAGCGCGGATCATGGGACGGCTGATTCCCCGATGGGGAAGCCTGAACACTTTACGAGTTGGAATGGGTTGCCTAGTGGTCGGGGCACTGTTGCTTGCTGTCGGCGAGACACTCATACCAAACTCGGTGCTTGGCTTCATCGCCCCAATGTGGCTCGTCGGTGTTGGCATTGCCACTGCGGCCTCGGTGGCACCCAATGGTGCACTTCGAGGGTTTGATCACATCGCTGGAACCGCCACAGCAGTCTACTTCTGCTTGGGTGGGTTACTGCTAGGTGGTATCGGTACTTTCATCATTGCACTTTTACCAAGTGATACCACATGGCCGATCATTGCTTATTGCCTAATCCTCGCAATAGCAGTGCTTTGTCTATCCTGCTTCAACCCCAACAGGCACCATCCCAGCGATGACGAGCATGATTCGCTTGCGACGCAAGACATCGGCCGCTCGCAATCGGGCCATGGTCATGATTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36800","NCBI_taxonomy_name":"Bordetella bronchiseptica","NCBI_taxonomy_id":"518"}}}},"ARO_accession":"3002699","ARO_id":"39133","ARO_name":"cmlB1","CARD_short_name":"cmlB1","ARO_description":"cmlB1 is a plasmid-encoded chloramphenicol exporter that is found in Bordetella bronchiseptica.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1039":{"model_id":"1039","model_name":"dfrB3","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"150"}},"model_sequences":{"sequence":{"392":{"protein_sequence":{"accession":"ACR57831.1","sequence":"MDQHNNGVSTLVAGQFALPSHATFGLGDRVRKKSGAAWQGQVVGWYCTKLTPEGYAVESESHPGSVQIYPVAALERVA"},"dna_sequence":{"accession":"GQ150744.1","fmin":"122","fmax":"359","strand":"+","sequence":"ATGGACCAACACAACAATGGAGTCAGTACTCTAGTTGCTGGCCAGTTTGCGCTCCCATCGCACGCCACGTTTGGCCTGGGAGATCGCGTGCGCAAGAAATCTGGCGCCGCTTGGCAGGGTCAAGTTGTCGGGTGGTACTGCACAAAACTGACCCCTGAAGGCTATGCCGTCGAGTCCGAGTCTCACCCCGGTTCAGTACAGATTTATCCTGTGGCTGCGCTTGAACGCGTGGCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3003022","ARO_id":"39456","ARO_name":"dfrB3","CARD_short_name":"dfrB3","ARO_description":"dfrB3 is an integron-encoded dihydrofolate reductase found in Klebsiella oxytoca.","ARO_category":{"37617":{"category_aro_accession":"3001218","category_aro_cvterm_id":"37617","category_aro_name":"trimethoprim resistant dihydrofolate reductase dfr","category_aro_description":"Alternative dihydropteroate synthase dfr present on plasmids produces alternate proteins that are less sensitive to trimethoprim from inhibiting its role in folate synthesis, thus conferring trimethoprim resistance.","category_aro_class_name":"AMR Gene Family"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1040":{"model_id":"1040","model_name":"OXA-95","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1539":{"protein_sequence":{"accession":"ABF47918.1","sequence":"MNIKALFLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"DQ519089.1","fmin":"8","fmax":"833","strand":"+","sequence":"ATGAACATTAAAGCACTCTTCCTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001630","ARO_id":"38030","ARO_name":"OXA-95","CARD_short_name":"OXA-95","ARO_description":"OXA-95 is a beta-lactamase found in A. baumannii.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1043":{"model_id":"1043","model_name":"SHV-76","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"8230":{"protein_sequence":{"accession":"CAJ47131.2","sequence":"MRYIRLCIISLLAALPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVEDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AM176551.2","fmin":"30","fmax":"891","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCGCCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGTGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGAAGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATCGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001130","ARO_id":"37510","ARO_name":"SHV-76","CARD_short_name":"SHV-76","ARO_description":"SHV-76 is a broad-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1044":{"model_id":"1044","model_name":"CTX-M-22","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1334":{"protein_sequence":{"accession":"AAL86924.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGDYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTNGL"},"dna_sequence":{"accession":"AY080894.1","fmin":"3","fmax":"879","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGACTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCAACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001884","ARO_id":"38284","ARO_name":"CTX-M-22","CARD_short_name":"CTX-M-22","ARO_description":"CTX-M-22 is a beta-lactamase found in the Enterobacteriaceae family.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1046":{"model_id":"1046","model_name":"vgaD","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"519":{"protein_sequence":{"accession":"ACX92986.2","sequence":"MLILEANHIEKSINDRKLLDVTHLQIHYEDRIGVVGRNGSGKTTLLSILAGEIEADKGEVKTSASRYFLPQLKETDTFRSGGEITKSYIDKALAMKAEILFADEPTTNLDTHNIKELEKHFSRYRGAIILVSHNRYFLDQICTKIWEIEDGEVKEIHGNYTSYVKQKELLRRQQQEEYEKYITKKKQLERAVTMKEQKAQKMIKPPSKQMGTSESRIWKMQHATKQKKMHQNIKALETRVEKLERVKKPKDYPAVKMKLSNQDQIQGRNVLRVKDLSVSFGNHVLWTDASFTIKGGEKAAIIGNNGVGKTTLLKQILERVPAVTISPAAKIGYFSQNLDTLDTHVSILENVMSTAIQDETTVRTVLARLHFYREDVYKEVQVLSGGERVKVAFAKLFVSDYNTLILDEPTNYLDIDAIEALEELLINYEGAVLFVSHDCRFVQNIASKIIELSDQKVIEFLGSYKAFRERSQETERDYMKEELLKIEIKLTQMISEMNDEASNELEKEFQMLIHERNQLRNQVNN"},"dna_sequence":{"accession":"GQ205627.1","fmin":"1393","fmax":"2971","strand":"+","sequence":"ATGCTCATTCTTGAAGCGAATCATATTGAAAAATCTATAAATGACCGGAAACTTTTAGATGTTACTCATCTACAAATTCATTATGAGGATCGGATTGGTGTAGTTGGTCGTAATGGAAGCGGGAAAACGACATTATTATCTATATTGGCTGGTGAAATAGAAGCAGATAAAGGTGAAGTGAAAACAAGTGCAAGTCGCTACTTTTTACCTCAATTGAAGGAGACGGATACTTTCAGAAGTGGTGGTGAGATAACAAAAAGCTATATTGACAAAGCATTAGCGATGAAGGCGGAAATATTGTTTGCCGACGAACCAACTACAAACCTTGATACCCACAATATAAAAGAACTTGAAAAGCATTTCAGTCGATATCGGGGGGCAATCATTCTTGTATCACATAACCGGTATTTTTTAGATCAAATTTGTACAAAAATATGGGAAATTGAAGATGGAGAAGTGAAAGAAATTCACGGTAACTATACAAGTTATGTAAAACAAAAAGAACTACTTCGTCGACAGCAACAAGAGGAATATGAAAAATATATAACGAAGAAAAAGCAACTGGAGCGAGCTGTTACCATGAAAGAACAAAAGGCGCAAAAAATGATTAAGCCTCCTTCTAAACAAATGGGTACTTCTGAATCTCGAATATGGAAGATGCAGCATGCGACTAAACAAAAGAAAATGCATCAAAATATTAAGGCTCTTGAAACACGTGTTGAAAAACTAGAGCGTGTGAAAAAACCAAAAGATTATCCGGCTGTCAAAATGAAGTTGTCTAACCAAGATCAAATACAGGGGCGCAATGTACTTCGGGTAAAAGACTTATCTGTTTCCTTTGGGAATCATGTGCTTTGGACAGATGCTTCTTTTACCATTAAAGGCGGGGAGAAGGCTGCCATTATTGGCAATAATGGGGTCGGTAAAACAACATTGTTGAAACAAATTTTAGAAAGGGTACCAGCGGTAACAATATCACCCGCAGCAAAAATCGGCTATTTTAGCCAGAATTTGGATACGCTTGATACGCATGTGTCGATCTTAGAAAATGTCATGTCCACCGCTATTCAAGATGAAACTACTGTACGGACTGTTCTCGCAAGATTACATTTCTACCGGGAGGATGTTTATAAGGAAGTTCAAGTCCTAAGTGGTGGGGAACGTGTGAAGGTTGCTTTTGCAAAACTATTTGTTAGCGACTATAATACGTTGATTCTGGATGAACCAACAAATTATTTAGACATTGATGCCATAGAAGCGTTAGAGGAGCTCCTAATTAACTATGAGGGGGCAGTACTATTTGTATCTCATGATTGTCGTTTCGTTCAAAATATTGCATCCAAAATTATTGAACTATCCGACCAGAAGGTTATAGAGTTTCTTGGAAGCTATAAAGCGTTTAGAGAAAGATCTCAAGAGACAGAGCGTGACTATATGAAGGAAGAACTTCTTAAAATTGAGATCAAACTCACTCAAATGATTAGTGAAATGAATGACGAGGCATCAAATGAATTAGAAAAAGAATTCCAAATGTTGATTCATGAACGTAATCAGTTAAGAAATCAAGTAAACAATTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36779","NCBI_taxonomy_name":"Enterococcus faecium","NCBI_taxonomy_id":"1352"}}}},"ARO_accession":"3002832","ARO_id":"39266","ARO_name":"vgaD","CARD_short_name":"vgaD","ARO_description":"vgaD is an ABC-F subfamily protein expressed in Enterococcus faecium that confers resistance to streptogramin A antibiotics and related compounds. It is associated with plasmid DNA.","ARO_category":{"36252":{"category_aro_accession":"3000113","category_aro_cvterm_id":"36252","category_aro_name":"vga-type ABC-F protein","category_aro_description":"Vga-type plasmid-borne ABC-F proteins, expressed in staphylococci that confer resistance to streptogramin A antibiotics through ribosomal protection.","category_aro_class_name":"AMR Gene Family"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35952":{"category_aro_accession":"0000034","category_aro_cvterm_id":"35952","category_aro_name":"streptogramin A antibiotic","category_aro_description":"Streptogramin A antibiotics are cyclic polyketide peptide hybrids that bind to the ribosomal peptidyl transfer centre. Structural variation arises from substituting a proline for its desaturated derivative and by its substitution for Ala or Cys. Used alone, streptogramin A antibiotics are bacteriostatic, but is bactericidal when used with streptogramin B antibiotics.","category_aro_class_name":"Drug Class"},"37014":{"category_aro_accession":"3000670","category_aro_cvterm_id":"37014","category_aro_name":"pleuromutilin antibiotic","category_aro_description":"Pleuromutilins are natural fungal products that target bacterial protein translation by binding the the 23S rRNA, blocking the ribosome P site at the 50S subunit. They are mostly used for agriculture and veterinary purposes.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1047":{"model_id":"1047","model_name":"catS","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"6245":{"protein_sequence":{"accession":"CAA52904.1","sequence":"FTNIPCTYSMTVKLDITQIKKKRMKLYPAMLYYLATIVNRHSEFRTAINQEGELGIYDEMIPSYTIFHEDTETFSNLWTPYIPDFEAFSMAYANDMQRYGSNYGMIGKPDIPENVFNVSMIPWSTFDSFNLNLQKGYDYLIPIFTMGKYYRDDEKIILPLAIQV"},"dna_sequence":{"accession":"X74948.1","fmin":"0","fmax":"492","strand":"+","sequence":"TTTACGAATATACCTTGCACATACAGTATGACTGTTAAATTGGATATTACACAAATAAAAAAGAAACGAATGAAATTATACCCTGCGATGCTTTATTATCTTGCAACGATTGTAAACCGTCATTCAGAGTTTAGAACGGCAATTAATCAGGAGGGTGAACTGGGAATATATGACGAGATGATACCCAGCTATACCATATTCCATGAGGACACAGAGACATTTTCCAACCTTTGGACACCATACATACCAGATTTTGAAGCATTTTCTATGGCGTATGCGAATGATATGCAAAGGTATGGAAGCAATTATGGAATGATAGGAAAACCAGATATACCAGAAAATGTTTTTAATGTATCGATGATACCATGGTCAACCTTCGATAGCTTTAATCTGAATTTGCAGAAAGGATATGATTATTTGATTCCTATTTTTACGATGGGGAAATATTACAGAGATGATGAAAAAATCATACTTCCTCTCGCCATCCAAGTT","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36764","NCBI_taxonomy_name":"Streptococcus pyogenes","NCBI_taxonomy_id":"1314"}}}},"ARO_accession":"3002688","ARO_id":"39122","ARO_name":"catS","CARD_short_name":"catS","ARO_description":"catS is a chromosome-encoded variant of the cat gene found in Streptococcus pyogenes.","ARO_category":{"36261":{"category_aro_accession":"3000122","category_aro_cvterm_id":"36261","category_aro_name":"chloramphenicol acetyltransferase (CAT)","category_aro_description":"Inactivates chloramphenicol by addition of an acyl group. CAT is used to describe many variants of the chloramphenicol acetyltransferase gene in a range of organisms including Acinetobacter calcoaceticus, Agrobacterium tumefaciens, Alkalihalobacillus clausii, Bacillus subtilis, Campylobacter coli, Enterococcus faecalis, Enterococcus faecium, Lactococcus lactis, Listeria monocytogenes, Listonella anguillarum, Morganella morganii, Photobacterium damselae subsp. piscicida, Proteus mirabilis, Salmonella typhi, Serratia marcescens, Shigella flexneri, Staphylococcus aureus, Staphylococcus haemolyticus, Staphylococcus intermedius, Streptococcus agalactiae, Streptococcus suis and Streptomyces acrimycini.","category_aro_class_name":"AMR Gene Family"},"36521":{"category_aro_accession":"3000382","category_aro_cvterm_id":"36521","category_aro_name":"azidamfenicol","category_aro_description":"Azidamfenicol is a water soluble derivative of chloramphenicol, sharing the same mode of action of inhibiting peptide synthesis by interacting with the 23S RNA of the 50S ribosomal subunit.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36595":{"category_aro_accession":"3000456","category_aro_cvterm_id":"36595","category_aro_name":"thiamphenicol","category_aro_description":"Derivative of Chloramphenicol. The nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3).","category_aro_class_name":"Antibiotic"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1048":{"model_id":"1048","model_name":"QnrB33","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"468":{"protein_sequence":{"accession":"AEL00451.1","sequence":"MTLALVSEKIDRNRFTGEKVENSTFFNCDFSGADLSSTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNASALGIEIRHCRAQGSDFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGTQVAGATFSGSDLSGGEFSAFDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDSYQAALLMERLGIAVIG"},"dna_sequence":{"accession":"JN173055.1","fmin":"35","fmax":"680","strand":"+","sequence":"ATGACTCTGGCATTAGTTAGCGAAAAAATTGACAGAAACCGCTTCACCGGGGAAAAAGTTGAAAACAGTACTTTTTTTAACTGTGATTTTTCAGGGGCCGATCTTAGCAGCACTGAATTTATCGGCTGTCAGTTTTATGATCGCGAAAGCCAGAAAGGGTGTAATTTTAGTCGCGCAATGCTGAAAGATGCCATTTTTAAAAGTTGCGATTTATCCATGGCGGATTTTCGCAACGCCAGTGCCCTGGGAATTGAAATTCGCCACTGCCGCGCGCAGGGTTCAGATTTTCGCGGCGCGAGTTTTATGAACATGATCACCACGCGGACCTGGTTTTGCAGCGCATACATCACGAATACCAATCTAAGCTACGCCAACTTTTCGAAGGTTGTCCTGGAAAAGTGCGAGCTGTGGGAAAACCGCTGGATGGGAACTCAGGTAGCGGGTGCAACGTTCAGTGGATCAGATCTCTCGGGCGGTGAATTTTCAGCGTTCGACTGGCGGGCCGCAAATTTCACGCACTGTGATTTGACCAATTCAGAACTGGGTGATTTAGATATTCGGGGTGTAGATTTACAAGGCGTCAAATTGGATAGCTATCAGGCAGCGTTGCTGATGGAGCGGCTTGGCATCGCGGTGATTGGTTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39584","NCBI_taxonomy_name":"Citrobacter braakii","NCBI_taxonomy_id":"57706"}}}},"ARO_accession":"3002748","ARO_id":"39182","ARO_name":"QnrB33","CARD_short_name":"QnrB33","ARO_description":"QnrB33 is a plasmid-mediated quinolone resistance protein found in Citrobacter braakii.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1049":{"model_id":"1049","model_name":"MOX-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"8161":{"protein_sequence":{"accession":"BAA02563.2","sequence":"MQQRQSILWGAVATLMWAGLAHAGEASPVDPLRPVVDASIQPLLKEHRIPGMAVAVLKDGKAHYFNYGVANRESGASVSEQTLFEIGSVSKTLTATLGAYAVVKGAMQLDDKASRHAPWLKGSVFDSITMGELATYSAGGLPLQFPEEVDSSEKMRAYYRQWAPVYSPGSHRQYSNPSIGLFGHLAASSLKQPFAQLMEQTLLPGLGMHHTYVNVPKQAMASYAYGYSKEDKPIRVNPGMLADEAYGIKTSSADLLAFVKANIGGVDDKALQQAISLTHKGHYSVGGMTQGLGWESYAYPVTEQTLLAGNSAKVILEANPTAAPRESGSQVLFNKTGSSNGFGAYVAFVPARGIGIVMLANRNYPIPARVKAAHAILAQLAG"},"dna_sequence":{"accession":"D13304.2","fmin":"232","fmax":"1381","strand":"+","sequence":"ATGCAACAACGACAATCCATCCTGTGGGGGGCCGTGGCCACCCTGATGTGGGCCGGTCTGGCCCATGCAGGTGAGGCTTCACCGGTCGATCCCCTGCGCCCCGTGGTGGATGCCAGCATCCAGCCGCTGCTCAAGGAGCACAGGATCCCGGGCATGGCGGTGGCCGTGCTCAAGGATGGCAAGGCCCACTATTTCAATTACGGGGTGGCCAACCGGGAGAGCGGGGCCAGCGTCAGCGAGCAGACCCTGTTCGAGATAGGATCCGTGAGCAAGACCCTGACTGCGACCCTGGGGGCCTATGCGGTGGTCAAGGGAGCGATGCAGCTGGATGACAAGGCGAGCCGGCACGCGCCCTGGCTCAAGGGATCCGTCTTTGACAGCATCACCATGGGGGAGCTTGCCACCTACAGCGCCGGAGGCCTGCCACTGCAATTCCCCGAGGAGGTGGATTCATCCGAGAAGATGCGCGCCTACTACCGCCAGTGGGCCCCTGTCTATTCGCCGGGCTCCCATCGCCAGTACTCCAACCCCAGCATAGGGCTGTTCGGCCACCTGGCGGCGAGCAGCCTGAAGCAGCCATTTGCCCAGTTGATGGAGCAGACCCTGCTGCCCGGGCTCGGCATGCACCACACCTATGTCAATGTGCCGAAGCAGGCCATGGCGAGTTATGCCTATGGCTATTCGAAAGAGGACAAGCCCATCCGGGTCAACCCTGGCATGCTGGCGGACGAGGCCTACGGCATCAAGACCAGCTCGGCGGATCTGCTCGCCTTCGTGAAGGCCAACATCGGCGGGGTTGATGACAAGGCGTTGCAGCAGGCCATCTCCCTGACCCACAAAGGGCATTACTCGGTAGGCGGGATGACCCAGGGGCTGGGTTGGGAGAGTTACGCCTATCCCGTCACCGAGCAGACATTGCTGGCGGGCAATTCGGCCAAGGTGATCCTCGAAGCCAATCCGACGGCGGCTCCCCGGGAGTCGGGGAGCCAGGTGCTCTTCAACAAGACCGGCTCGAGCAATGGCTTTGGCGCCTATGTGGCCTTCGTGCCGGCCAGGGGGATCGGCATCGTCATGCTGGCCAATCGCAACTATCCCATCCCGGCCAGGGTGAAGGCGGCCCACGCCATCCTGGCGCAGTTGGCCGGTTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002182","ARO_id":"38582","ARO_name":"MOX-1","CARD_short_name":"MOX-1","ARO_description":"MOX-1 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36222":{"category_aro_accession":"3000083","category_aro_cvterm_id":"36222","category_aro_name":"MOX beta-lactamase","category_aro_description":"MOX beta-lactamases are plasmid-mediated AmpC-type beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1051":{"model_id":"1051","model_name":"LEN-12","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"5845":{"protein_sequence":{"accession":"PXK69226.1","sequence":"MRYVRLCVISLLATLPLAVYAGPQPLEQIKQSESQLSGRVGMVEMDLASGRTLAAWRADERFPMVSTFKVLLCGAVLARVDAGLEQLDRRIHYRQQDLVDYSPVSEKHLVDGMTIGELCAAAITLSDNSAGNLLLATVGGPAGLTAFLRQIGDNVTRLDRWETALNEALPGDARDTTTPASMAATLRKLLTAQHLSARSQQQLLQWMVDDRVAGPLIRAVLPAGWFIADKTGAGERGARGIVALLGPDGKPERIVVIYLRDTPASMAERNQHIAGIGAALIEHWQR"},"dna_sequence":{"accession":"QIXO01000012.1","fmin":"30208","fmax":"31069","strand":"-","sequence":"ATGCGTTATGTTCGCCTGTGTGTTATCTCCCTGTTAGCCACCCTGCCACTGGCGGTATACGCCGGTCCACAGCCGCTTGAGCAGATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTGGGGATGGTGGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCGATGAACGCTTTCCCATGGTGAGCACCTTTAAAGTGCTGCTGTGCGGCGCGGTGCTGGCGCGGGTGGATGCCGGGCTCGAACAACTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGTCGACGGGATGACGATCGGCGAACTCTGCGCCGCCGCCATCACCCTGAGCGATAACAGCGCTGGCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCGGGATTAACTGCCTTTCTGCGCCAGATCGGTGACAACGTCACCCGTCTTGACCGCTGGGAAACGGCACTGAATGAGGCGCTTCCCGGCGACGCGCGCGACACCACCACCCCGGCCAGCATGGCCGCCACGCTGCGCAAACTACTGACCGCGCAGCATCTGAGCGCCCGTTCGCAACAGCAACTCCTGCAGTGGATGGTGGACGATCGGGTTGCCGGCCCGCTGATCCGCGCCGTGCTGCCGGCGGGCTGGTTTATCGCCGACAAAACCGGGGCTGGCGAACGGGGTGCGCGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAACCGGAGCGCATTGTGGTGATCTATCTGCGGGATACCCCGGCGAGTATGGCCGAGCGTAATCAACATATCGCCGGGATCGGCGCAGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42612","NCBI_taxonomy_name":"Klebsiella variicola","NCBI_taxonomy_id":"244366"}}}},"ARO_accession":"3002462","ARO_id":"38862","ARO_name":"LEN-12","CARD_short_name":"LEN-12","ARO_description":"LEN-12 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36236":{"category_aro_accession":"3000097","category_aro_cvterm_id":"36236","category_aro_name":"LEN beta-lactamase","category_aro_description":"LEN beta-lactamases are chromosomal class A beta-lactamases that confer resistance to ampicillin, amoxicillin, carbenicillin, and ticarcillin but not to extended-spectrum beta-lactams.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1052":{"model_id":"1052","model_name":"OXA-206","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1757":{"protein_sequence":{"accession":"BAL15076.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDVKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAISVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"AB634250.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGTAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTTCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAACAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001484","ARO_id":"37884","ARO_name":"OXA-206","CARD_short_name":"OXA-206","ARO_description":"OXA-206 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1053":{"model_id":"1053","model_name":"SHV-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1234":{"protein_sequence":{"accession":"AAD37413.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGASERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AF148851.1","fmin":"5","fmax":"866","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTACTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTAGCGAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001060","ARO_id":"37440","ARO_name":"SHV-2","CARD_short_name":"SHV-2","ARO_description":"SHV-2 is an extended-spectrum beta-lactamase found in E. coli., Klebsiella pneumoniae, and Shigella flexneri.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1056":{"model_id":"1056","model_name":"VIM-19","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1499":{"protein_sequence":{"accession":"ACY29468.1","sequence":"MLKVISSLLVYMTASVMAVASPLAHSGEPSGEYPTVNEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEAEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSAKVLYGGCAVHELSRTSAGNVADADLAEWPTSVERIQKHYPEAEVVIPGHGLPGGLDLLQHTANVVKAHKNRSVAE"},"dna_sequence":{"accession":"FJ822963.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGTTAAAAGTTATTAGTAGTTTATTGGTCTACATGACCGCGTCTGTCATGGCTGTCGCAAGTCCGTTAGCCCATTCCGGGGAGCCGAGTGGTGAGTATCCGACAGTCAACGAAATTCCGGTCGGAGAGGTCCGACTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCGGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAAAAGCAAATTGGACTTCCCGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGCAGAGGGGAACGAGATTCCCACGCATTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAGCTCTTCTATCCTGGTGCTGCGCATTCGACCGACAATCTGGTTGTATACGTCCCGTCAGCGAAAGTGCTATACGGTGGTTGTGCCGTTCATGAGTTGTCACGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCGTTGAGCGGATTCAAAAACACTACCCGGAAGCAGAGGTCGTCATTCCCGGGCACGGTCTACCGGGCGGTCTAGACTTGCTCCAGCACACAGCGAACGTTGTCAAAGCACACAAAAATCGCTCAGTCGCCGAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002289","ARO_id":"38689","ARO_name":"VIM-19","CARD_short_name":"VIM-19","ARO_description":"VIM-19 is a beta-lactamase found in the Enterobacteriaceae family.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1057":{"model_id":"1057","model_name":"CTX-M-114","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1980":{"protein_sequence":{"accession":"ACU00153.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKAMAVAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"GQ351346.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGCGATGGCCGTGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36944","NCBI_taxonomy_name":"Providencia rettgeri","NCBI_taxonomy_id":"587"}}}},"ARO_accession":"3001974","ARO_id":"38374","ARO_name":"CTX-M-114","CARD_short_name":"CTX-M-114","ARO_description":"CTX-M-114 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1058":{"model_id":"1058","model_name":"VIM-27","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"2041":{"protein_sequence":{"accession":"ADX78234.1","sequence":"MLKVISSLLVYMTASVMAVASPLAHSGEPSGEYPTVNEIPVGEVRLYQIADGVWSHISTQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEAEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSANVLYGGCAVHELSSTSAGNVADADLAEWPTSVERIQKHYPEAEVVIPGHGLPGGLDLLQHTANVVKAHKNRSVAE"},"dna_sequence":{"accession":"HQ858608.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGTTAAAAGTTATTAGTAGTTTATTGGTCTACATGACCGCGTCTGTCATGGCTGTCGCAAGTCCGTTAGCCCATTCCGGGGAGCCGAGTGGTGAGTATCCGACAGTCAACGAAATTCCGGTCGGAGAGGTCCGACTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCTCAACGCAGTCGTTTGATGGCGCGGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAAAAGCAAATTGGACTTCCCGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGCAGAGGGGAACGAGATTCCCACGCATTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAGCTCTTCTATCCTGGTGCTGCGCATTCGACCGACAATCTGGTTGTATACGTCCCGTCAGCGAACGTGCTATACGGTGGTTGTGCCGTTCATGAGTTGTCAAGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCGTTGAGCGGATTCAAAAACACTACCCGGAAGCAGAGGTCGTCATTCCCGGGCACGGTCTACCGGGCGGTCTAGACTTGCTCCAGCACACAGCGAACGTTGTCAAAGCACACAAAAATCGCTCAGTCGCCGAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002297","ARO_id":"38697","ARO_name":"VIM-27","CARD_short_name":"VIM-27","ARO_description":"VIM-27 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1059":{"model_id":"1059","model_name":"APH(9)-Ib","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"4738":{"protein_sequence":{"accession":"AAB66655.1","sequence":"MEDLPENLDQESLFQGLREFGISTTSASYAPLGFGDYHWHITGDDGQRWFATVSDLEHKEHCGHGAPAALRGLRRAMDTAVHLREQGGLPFVVAPRTTSDGASLVPLDSRYALTVFPHVSARPGEFGQKLTERERDQVLVLLAELHGQAPPKCTPTTDMVPTGLDGVHTALAEPSGTWTGGPFSEPARELLAEHEATLRGRMAEFGELVARVRGRGAPLVVTHGEPHPGNLILGEDGYVLVDWDTVGLAIPERDLSLISDDPAALARYTELTGHTPDPAALALYRLRWSLLDVAEFVEWFRGEHQRTSDTEAAWQSFAETLDHLNSEVPS"},"dna_sequence":{"accession":"U70376.2","fmin":"7525","fmax":"8518","strand":"-","sequence":"ATGGAAGATCTTCCTGAGAACCTGGACCAGGAAAGCCTATTTCAGGGACTACGAGAATTCGGTATCTCCACGACCAGTGCGTCGTACGCGCCGCTCGGCTTCGGCGACTATCACTGGCACATCACCGGTGACGACGGGCAGCGGTGGTTCGCCACCGTCTCCGACCTCGAACACAAGGAGCACTGCGGGCACGGTGCCCCGGCGGCACTGCGAGGTCTGCGGAGAGCCATGGACACCGCGGTGCACTTGCGTGAGCAGGGCGGCCTGCCGTTCGTGGTGGCACCCCGGACCACGAGTGACGGCGCTTCACTGGTCCCGCTGGACTCGCGGTACGCGTTGACCGTATTTCCCCATGTCTCGGCCCGACCCGGGGAGTTCGGCCAGAAGCTGACGGAGCGGGAGCGGGACCAGGTGCTGGTGCTGCTCGCAGAATTGCACGGCCAGGCACCGCCGAAGTGCACCCCGACCACCGACATGGTGCCGACCGGACTGGATGGCGTGCACACCGCGCTGGCCGAGCCGTCCGGAACCTGGACGGGCGGGCCGTTCTCCGAGCCGGCCCGCGAGTTGCTGGCCGAGCACGAGGCGACGCTCCGCGGGCGGATGGCGGAGTTCGGCGAACTGGTGGCGCGGGTACGGGGCCGCGGCGCCCCGCTGGTCGTCACACACGGCGAGCCGCACCCGGGGAACCTGATCCTTGGTGAGGACGGCTATGTGCTGGTGGACTGGGACACGGTGGGCCTCGCGATACCCGAACGGGACCTCTCCCTGATCTCGGACGACCCGGCAGCTCTCGCCCGCTACACCGAACTGACCGGGCACACGCCCGACCCGGCCGCGCTGGCGCTCTACCGGCTGCGGTGGAGCCTGCTGGACGTCGCCGAGTTCGTCGAGTGGTTCCGCGGGGAACACCAGCGCACCTCCGACACCGAAGCCGCTTGGCAGAGCTTCGCCGAGACTCTCGACCATCTGAACTCCGAAGTACCGAGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39531","NCBI_taxonomy_name":"Streptomyces netropsis","NCBI_taxonomy_id":"55404"}}}},"ARO_accession":"3002663","ARO_id":"39063","ARO_name":"APH(9)-Ib","CARD_short_name":"APH(9)-Ib","ARO_description":"APH(9)-Ib is a chromosomal-encoded aminoglycoside phosphotransferase in S. flavopersicus.","ARO_category":{"36292":{"category_aro_accession":"3000153","category_aro_cvterm_id":"36292","category_aro_name":"APH(9)","category_aro_description":"A category of aminoglycoside O-phosphotransferase enzymes with modification regiospecificity based at the 9-hydroxyl group of the respective antibiotic. These enzymes are characterized by enzymatic antibiotic inactivation, specifically of spectinomycin, by the ATP-dependent phosphorylation of the 9-hydroxyl group of the compound.","category_aro_class_name":"AMR Gene Family"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1060":{"model_id":"1060","model_name":"SHV-103","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1772":{"protein_sequence":{"accession":"ABS72351.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNRAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"EU032604.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAGAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001152","ARO_id":"37532","ARO_name":"SHV-103","CARD_short_name":"SHV-103","ARO_description":"SHV-103 is a beta-lactamase that has been found in clinical isolates.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1061":{"model_id":"1061","model_name":"OXY-2-10","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1140":{"protein_sequence":{"accession":"ACV44456.1","sequence":"MIKSSWRKIAMLAAAVPLLLASGALWASTDAIHQKLTDLEKRSGGRLGVALINTADNSQILYRGDERFAMCSTSKVMAAAAVLKQSESNKEVVNKRLEINAADLVVWSPITEKHLQSGMTLAELSAATLQYSDNTAMNLIIGYLGGPEKVTAFARSIGDATFRLDRTEPTLNTAIPGDERDTSTPLAMAESLRKLTLGDALGEQQRAQLVTWLKGNTTGGQSIRAGLPESWVVGDKTGAGDYGTTNDIAVIWPENHAPLVLVTYFTQPQQDAKNRKEVLAAATKIVTEGL"},"dna_sequence":{"accession":"FJ785626.1","fmin":"131","fmax":"1004","strand":"+","sequence":"ATGATAAAAAGTTCGTGGCGTAAAATTGCAATGCTAGCCGCCGCCGTTCCGCTGCTGCTGGCGAGCGGCGCACTGTGGGCCAGTACCGATGCTATCCATCAGAAGCTGACAGATCTCGAGAAGCGTTCAGGCGGCAGGTTGGGCGTGGCGCTAATCAACACGGCAGATAATTCTCAAATCTTATATCGCGGCGACGAGCGTTTTGCCATGTGCAGCACCAGTAAAGTGATGGCCGCCGCCGCGGTATTAAAACAGAGCGAAAGCAATAAAGAGGTGGTAAATAAAAGGCTGGAGATTAACGCAGCCGATTTGGTGGTCTGGAGTCCGATTACCGAAAAACATCTCCAGAGCGGAATGACGCTGGCTGAGCTAAGCGCGGCGACGCTGCAATATAGCGACAATACGGCGATGAATCTGATCATCGGCTACCTTGGCGGGCCGGAAAAAGTCACCGCCTTCGCCCGCAGTATCGGCGATGCCACCTTTCGTCTCGATCGTACGGAGCCCACGCTGAATACCGCCATCCCGGGCGATGAGCGTGATACCAGCACGCCGCTGGCGATGGCTGAAAGCCTGCGCAAGCTGACGCTTGGCGATGCGCTGGGCGAACAGCAACGCGCCCAGTTAGTCACCTGGCTGAAAGGCAATACCACCGGCGGGCAAAGCATTCGCGCGGGCCTGCCTGAAAGCTGGGTGGTCGGCGATAAAACCGGTGCCGGAGATTACGGCACCACCAATGATATTGCGGTTATCTGGCCGGAAAATCACGCTCCGCTGGTATTAGTCACCTACTTTACCCAGCCGCAGCAGGATGCGAAAAACCGCAAAGAGGTGTTAGCCGCAGCGACAAAAATCGTGACCGAAGGGCTTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3002405","ARO_id":"38805","ARO_name":"OXY-2-10","CARD_short_name":"OXY-2-10","ARO_description":"OXY-2-10 is a beta-lactamase. From the Pasteur Institute (Genopole) list of OXY beta-lactamases.","ARO_category":{"38788":{"category_aro_accession":"3002388","category_aro_cvterm_id":"38788","category_aro_name":"OXY beta-lactamase","category_aro_description":"OXY beta-lactamases are chromosomal class A beta-lactamases that are found in Klebsiella oxytoca. At constitutive low levels, OXY beta-lactamases confer resistance to aminopenicillins and carboxypenicillins. At high induced levels,  OXY beta-lactamases confer resistance to penicillins, cephalosporins and aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1062":{"model_id":"1062","model_name":"SHV-71","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"8237":{"protein_sequence":{"accession":"CAJ47126.2","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKYLADGMTVGELCAAAITMSDNSAANLLLATVGGPVGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AM176546.2","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAATACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGTAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGGATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001125","ARO_id":"37505","ARO_name":"SHV-71","CARD_short_name":"SHV-71","ARO_description":"SHV-71 is a broad-spectrum beta-lactamase found in Klebsiella pneumoniae and Shigella.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1063":{"model_id":"1063","model_name":"QnrB73","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"513":{"protein_sequence":{"accession":"AGT59159.1","sequence":"MSLALVSEKIDRNRFTGEKVENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNVSALGIEIRHCRAQGSDFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGTQVAGATFSGSDLSGGEFSAFDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDSYQAALLMERLGIAIIG"},"dna_sequence":{"accession":"KF443075.1","fmin":"0","fmax":"645","strand":"+","sequence":"ATGAGTCTGGCACTAGTTAGCGAAAAAATTGACAGAAACCGCTTCACCGGGGAAAAAGTTGAAAACAGTACTTTTTTTAACTGTGATTTTTCAGGGGCCGATCTTAGCGGCACTGAATTTATCGGCTGTCAGTTTTATGATCGCGAAAGCCAGAAAGGGTGTAATTTTAGTCGCGCAATGCTGAAAGATGCCATTTTTAAAAGTTGCGATTTATCCATGGCGGATTTTCGCAACGTCAGTGCTCTGGGAATTGAAATTCGCCACTGCCGCGCGCAGGGTTCAGATTTTCGCGGCGCGAGTTTTATGAACATGATCACCACGCGGACCTGGTTTTGCAGCGCATACATCACGAATACCAATCTAAGCTACGCCAACTTTTCGAAGGTTGTCCTGGAAAAGTGCGAGCTGTGGGAAAATCGCTGGATGGGAACTCAGGTAGCGGGTGCAACGTTCAGTGGATCAGATCTCTCGGGCGGTGAATTTTCAGCGTTCGACTGGCGGGCCGCAAACTTCACGCACTGTGATTTGACCAATTCAGAACTGGGTGATTTAGATATTCGGGGTGTAGATTTACAAGGCGTCAAATTGGATAGCTATCAGGCAGCGTTGCTGATGGAGCGGCTTGGCATCGCGATTATTGGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002785","ARO_id":"39219","ARO_name":"QnrB73","CARD_short_name":"QnrB73","ARO_description":"QnrB73 is a plasmid-mediated quinolone resistance protein found in Citrobacter freundii.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1064":{"model_id":"1064","model_name":"CTX-M-141","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1027":{"protein_sequence":{"accession":"AGN11769.1","sequence":"MMTQSIRRSMLTVMATLPLLFSSATLHAQANSVQQQLEALEKSSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKQSESDKHLLNQRVEIKKSDLVNYNPIAEKHVNGTMTLAELGAAALQYSDNTAMNKLIAHLGGPDKVTAFARSLGDETFRLDRTEPTLNTAIPGDPRDTTTPLAMAQTLKNLTLGKALAETQREQLVTWLKGNTTGSASIRAGLPKSWVVGDKTGSGDYGTTNDIAVIWPENHAPLVLVTYFTQPEQKAESRRDILAAAAKIVTHGF"},"dna_sequence":{"accession":"KC964871.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGATGACTCAGAGCATTCGCCGCTCAATGTTAACGGTGATGGCGACGCTACCCCTGCTATTTAGCAGCGCAACGCTGCATGCGCAGGCGAACAGCGTGCAACAGCAGCTGGAAGCCCTGGAGAAAAGTTCGGGAGGTCGGCTTGGCGTTGCGCTGATTAACACCGCCGATAATTCGCAGATTCTCTACCGTGCCGATGAACGTTTTGCGATGTGCAGTACCAGTAAGGTGATGGCGGCCGCGGCGGTGCTTAAACAGAGCGAGAGCGATAAGCACCTGCTAAATCAGCGCGTTGAAATCAAGAAGAGCGACCTGGTTAACTACAATCCCATTGCGGAGAAACACGTTAACGGCACGATGACGCTGGCTGAGCTTGGCGCAGCGGCGCTGCAGTATAGCGACAATACTGCCATGAATAAGCTGATTGCCCATCTGGGTGGTCCCGATAAAGTGACGGCGTTTGCTCGCTCGTTGGGTGATGAGACCTTCCGTCTGGACAGAACCGAGCCCACGCTCAATACCGCCATTCCAGGCGACCCGCGTGATACCACCACGCCGCTCGCGATGGCGCAGACCCTGAAAAATCTGACGCTGGGTAAAGCGCTGGCGGAAACTCAGCGGGAACAGTTGGTGACGTGGCTTAAGGGCAATACTACCGGTAGCGCGAGCATTCGGGCGGGTCTGCCGAAATCATGGGTAGTGGGCGATAAAACCGGCAGCGGAGATTATGGCACCACCAACGATATCGCGGTTATCTGGCCGGAAAACCACGCACCGCTGGTTCTGGTGACCTACTTTACCCAACCGGAGCAGAAGGCGGAAAGCCGTCGGGATATTCTGGCTGCGGCGGCGAAAATCGTAACCCACGGTTTCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001999","ARO_id":"38399","ARO_name":"CTX-M-141","CARD_short_name":"CTX-M-141","ARO_description":"CTX-M-141 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1065":{"model_id":"1065","model_name":"OXA-384","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4737":{"protein_sequence":{"accession":"AHL30282.1","sequence":"MNIQALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRIGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNSEMKKGISSSVRKEITYRSLEQLGIL"},"dna_sequence":{"accession":"KF986263.1","fmin":"90","fmax":"915","strand":"-","sequence":"ATGAACATTCAAGCCCTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATAGGCCTTGAGCACCATAAGGCAACCACTACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTATTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAACAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTCAGAAATGAAAAAAGGAATATCTAGCTCTGTTCGAAAAGAGATTACTTATAGAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001570","ARO_id":"37970","ARO_name":"OXA-384","CARD_short_name":"OXA-384","ARO_description":"OXA-384 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1066":{"model_id":"1066","model_name":"TEM-118","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8422":{"protein_sequence":{"accession":"AAN05029.1","sequence":"FFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDHWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYMTGSQATMDERNR"},"dna_sequence":{"accession":"AY130285.1","fmin":"0","fmax":"783","strand":"+","sequence":"TTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATCATTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACATGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGA","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3000981","ARO_id":"37361","ARO_name":"TEM-118","CARD_short_name":"TEM-118","ARO_description":"TEM-118 is an extended-spectrum beta-lactamase that has been found in clinical isolates.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1068":{"model_id":"1068","model_name":"AAC(6')-Ib3","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"141":{"protein_sequence":{"accession":"ACS44715.1","sequence":"MTNSNDSVTLRLMTEHDLAMLYEWLNRSHIVEWWGGEEARPTLADVQEQYLPSVLAQESVTPYIAMLNGEPIGYAQSYVALGSGDGWWEEETDPGVRGIDQLLANASQLGKGLGTKLVRALVELLFNDPEVTKIQTDPSPSNLRAIRCYEKAGFERQGTVTTPDGPAVYMVQTRQAFERTRSDA"},"dna_sequence":{"accession":"FJ854362.1","fmin":"1702","fmax":"2257","strand":"+","sequence":"GTGACCAACAGCAACGATTCCGTCACACTGCGCCTCATGACTGAGCATGACCTTGCGATGCTCTATGAGTGGCTAAATCGATCTCATATTGTCGAGTGGTGGGGCGGAGAAGAAGCACGCCCGACACTTGCTGACGTACAGGAACAGTACTTGCCAAGCGTTTTAGCGCAAGAGTCCGTCACTCCATACATTGCAATGCTGAATGGAGAGCCGATTGGGTATGCCCAGTCGTACGTTGCTCTTGGAAGCGGGGACGGATGGTGGGAAGAAGAAACCGATCCAGGAGTACGCGGAATAGACCAGTTACTGGCGAATGCATCACAACTGGGCAAAGGCTTGGGAACCAAGCTGGTTCGAGCTCTGGTTGAGTTGCTGTTCAATGATCCCGAGGTCACCAAGATCCAAACGGACCCGTCGCCGAGCAACTTGCGAGCGATCCGATGCTACGAGAAAGCGGGGTTTGAGAGGCAAGGTACCGTAACCACCCCAGATGGTCCAGCCGTGTACATGGTTCAAACACGCCAGGCATTCGAGCGAACACGCAGTGATGCCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3002576","ARO_id":"38976","ARO_name":"AAC(6')-Ib3","CARD_short_name":"AAC(6')-Ib3","ARO_description":"AAC(6')-Ib3 is an integron-encoded aminoglycoside acetyltransferase in P. aeruginosa.","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"A category of aminoglycoside N-acetyltransferase enzymes with modification regiospecificity based at the 6'-amino group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics through acetylation of the 6-amino group of the compound.","category_aro_class_name":"AMR Gene Family"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1069":{"model_id":"1069","model_name":"IMP-35","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1556":{"protein_sequence":{"accession":"AFO59566.1","sequence":"MKKIFVLFVFLFCSITAAGESLPDIKIEKLDEDVYVHTSFEEDNGWGVITKHGLVVLVNTDAYIIDTPFTAKDTEKLVRWFVGRGYKIKGSISSHFHSDSAGGIEWLNSQSIPTYASKLTNELLKKNGNAQAENSFSGVSYWLVKHKIEVFYPGPGHTQDNVVVWLPEKKILFGGCFIKPDGLGYLGDANLEAWPKSAETLMSKYGNAKLVVSSHSEIGGASLLKRTWEQAVKGLKESKKPSQPNN"},"dna_sequence":{"accession":"JF816544.1","fmin":"0","fmax":"741","strand":"+","sequence":"ATGAAAAAAATATTTGTGTTATTTGTATTTTTGTTTTGCAGTATTACTGCCGCCGGAGAGTCTTTGCCTGATATAAAAATTGAGAAACTTGACGAAGATGTTTATGTTCATACTTCTTTTGAAGAAGATAACGGCTGGGGTGTTATTACTAAACACGGCTTGGTGGTTCTTGTAAATACTGATGCCTATATAATTGACACTCCATTTACAGCTAAAGATACTGAAAAATTAGTCCGCTGGTTTGTGGGGCGTGGTTATAAAATCAAAGGCAGTATTTCCTCACATTTTCATAGCGATAGCGCAGGTGGAATTGAGTGGCTTAATTCTCAATCTATCCCCACATATGCATCTAAATTAACAAATGAGCTTCTTAAAAAGAACGGTAATGCGCAAGCCGAAAACTCATTTAGTGGCGTTAGCTATTGGCTAGTTAAACATAAAATTGAAGTTTTCTATCCAGGACCAGGGCACACTCAGGATAATGTAGTGGTTTGGTTGCCTGAAAAGAAAATTTTATTTGGCGGTTGTTTTATTAAGCCGGACGGTCTTGGTTATTTGGGAGACGCAAATCTAGAAGCATGGCCTAAGTCCGCAGAAACATTAATGTCTAAGTATGGTAATGCAAAACTGGTTGTTTCGAGTCATAGTGAAATTGGGGGCGCATCACTATTGAAGCGCACTTGGGAGCAGGCTGTTAAGGGGCTAAAAGAAAGTAAAAAACCATCACAGCCAAATAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002226","ARO_id":"38626","ARO_name":"IMP-35","CARD_short_name":"IMP-35","ARO_description":"IMP-35 is a beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1070":{"model_id":"1070","model_name":"sul1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"340":{"protein_sequence":{"accession":"AEJ33969.1","sequence":"MVTVFGILNLTEDSFFDESRRLDPAGAVTAAIEMLRVGSDVVDVGPAASHPDARPVSPADEIRRIAPLLDALSDQMHRVSIDSFQPETQRYALKRGVGYLNDIQGFPDPALYPDIAEADCRLVVMHSAQRDGIATRTGHLRPEDALDEIVRFFEARVSALRRSGVAADRLILDPGMGFFLSPAPETSLHVLSNLQKLKSALGLPLLVSVSRKSFLGATVGLPVKDLGPASLAAELHAIGNGADYVRTHAPGDLRSAITFSETLAKFRSRDARDRGLDHA"},"dna_sequence":{"accession":"JF969163.1","fmin":"1053","fmax":"1893","strand":"+","sequence":"ATGGTGACGGTGTTCGGCATTCTGAATCTCACCGAGGACTCCTTCTTCGATGAGAGCCGGCGGCTAGACCCCGCCGGCGCTGTCACCGCGGCGATCGAAATGCTGCGAGTCGGATCAGACGTCGTGGATGTCGGACCGGCCGCCAGCCATCCGGACGCGAGGCCTGTATCGCCGGCCGATGAGATCAGACGTATTGCGCCGCTCTTAGACGCCCTGTCCGATCAGATGCACCGTGTTTCAATCGACAGCTTCCAACCGGAAACCCAGCGCTATGCGCTCAAGCGCGGCGTGGGCTACCTGAACGATATCCAAGGATTTCCTGACCCTGCGCTCTATCCCGATATTGCTGAGGCGGACTGCAGGCTGGTGGTTATGCACTCAGCGCAGCGGGATGGCATCGCCACCCGCACCGGTCACCTTCGACCCGAAGACGCGCTCGACGAGATTGTGCGGTTCTTCGAGGCGCGGGTTTCCGCCTTGCGACGGAGCGGGGTCGCTGCCGACCGGCTCATCCTCGATCCGGGGATGGGATTTTTCTTGAGCCCCGCACCGGAAACATCGCTGCACGTGCTGTCGAACCTTCAAAAGCTGAAGTCGGCGTTGGGGCTTCCGCTATTGGTCTCGGTGTCGCGGAAATCCTTCTTGGGCGCCACCGTTGGCCTTCCTGTAAAGGATCTGGGTCCAGCGAGCCTTGCGGCGGAACTTCACGCGATCGGCAATGGCGCTGACTACGTCCGCACCCACGCGCCTGGAGATCTGCGAAGCGCAATCACCTTCTCGGAAACCCTCGCGAAATTTCGCAGTCGCGACGCCAGAGACCGAGGGTTAGATCATGCCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39525","NCBI_taxonomy_name":"Vibrio fluvialis","NCBI_taxonomy_id":"676"}}}},"ARO_accession":"3000410","ARO_id":"36549","ARO_name":"sul1","CARD_short_name":"sul1","ARO_description":"Sul1 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria. It is linked to other resistance genes of class 1 integrons.","ARO_category":{"41402":{"category_aro_accession":"3004238","category_aro_cvterm_id":"41402","category_aro_name":"sulfonamide resistant sul","category_aro_description":"The sul genes encode forms of dihydropteroate synthase that confer resistance to sulfonamide.","category_aro_class_name":"AMR Gene Family"},"36463":{"category_aro_accession":"3000324","category_aro_cvterm_id":"36463","category_aro_name":"sulfadiazine","category_aro_description":"Sulfadiazine is a potent inhibitor of dihydropteroate synthase, interfering with the tetrahydrofolic biosynthesis pathway. Tetrahydrofolic acid is essential for folate synthesis, a precursor to many nucleotides and amino acids.","category_aro_class_name":"Antibiotic"},"36464":{"category_aro_accession":"3000325","category_aro_cvterm_id":"36464","category_aro_name":"sulfadimidine","category_aro_description":"Sulfadimidine is an alkaline sulfonamide antibiotic that inhibits dihydropteroate synthase, and enzyme in the tetrahydrofolic acid biosynthesis pathway. This interferes with the production of folate, which is a precursor to many amino acids and nucleotides.","category_aro_class_name":"Antibiotic"},"36466":{"category_aro_accession":"3000327","category_aro_cvterm_id":"36466","category_aro_name":"sulfadoxine","category_aro_description":"Sulfadoxine is an inhibitor of dihydropteroate synthase, interfering with the tetrahydrofolic biosynthesis pathway. Tetrahydrofolic acid is essential for folate synthesis, a precursor to many nucleotides and amino acids.","category_aro_class_name":"Antibiotic"},"36468":{"category_aro_accession":"3000329","category_aro_cvterm_id":"36468","category_aro_name":"sulfamethoxazole","category_aro_description":"Sulfamethoxazole is a sulfonamide antibiotic usually taken with trimethoprim, a diaminopyrimidine antibiotic. Sulfamethoxazole inhibits dihydropteroate synthase, essential to tetrahydrofolic acid biosynthesis. This pathway generates compounds used in the synthesis of many amino acids and nucleotides.","category_aro_class_name":"Antibiotic"},"36469":{"category_aro_accession":"3000330","category_aro_cvterm_id":"36469","category_aro_name":"sulfisoxazole","category_aro_description":"Sulfisoxazole is an inhibitor of dihydropteroate synthase, interfering with the tetrahydrofolic biosynthesis pathway. Tetrahydrofolic acid is essential for folate synthesis, a precursor to many nucleotides and amino acids.","category_aro_class_name":"Antibiotic"},"37027":{"category_aro_accession":"3000683","category_aro_cvterm_id":"37027","category_aro_name":"sulfacetamide","category_aro_description":"Sulfacetamide is a very soluable sulfonamide antibiotic previously used to treat urinary tract infections. Its relatively low activity and toxicity to those with Stevens-Johnson syndrome have reduced its use and availability.","category_aro_class_name":"Antibiotic"},"37028":{"category_aro_accession":"3000684","category_aro_cvterm_id":"37028","category_aro_name":"mafenide","category_aro_description":"Mafenide is a sulfonamide used topically for treating burns.","category_aro_class_name":"Antibiotic"},"37042":{"category_aro_accession":"3000698","category_aro_cvterm_id":"37042","category_aro_name":"sulfasalazine","category_aro_description":"Sulfasalazine is a derivative of the early sulfonamide sulfapyridine (salicylazosulfapyridine). It was developed to increase water solubility and is taken orally for ulcerative colitis.","category_aro_class_name":"Antibiotic"},"37043":{"category_aro_accession":"3000699","category_aro_cvterm_id":"37043","category_aro_name":"sulfamethizole","category_aro_description":"Sulfamethizole is a short-acting sulfonamide that inhibits dihydropteroate synthetase.","category_aro_class_name":"Antibiotic"},"36421":{"category_aro_accession":"3000282","category_aro_cvterm_id":"36421","category_aro_name":"sulfonamide antibiotic","category_aro_description":"Sulfonamides are broad spectrum, synthetic antibiotics that contain the sulfonamide group. Sulfonamides inhibit dihydropteroate synthase, which catalyzes the conversion of p-aminobenzoic acid to dihydropteroic acid as part of the tetrahydrofolic acid biosynthetic pathway. Tetrahydrofolic acid is essential for folate synthesis, a precursor of many nucleotides and amino acids. Many sulfamides are taken with trimethoprim, an inhibitor of dihydrofolate reductase, also disturbing the trihydrofolic acid synthesis pathway.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1071":{"model_id":"1071","model_name":"DHA-22","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1554":{"protein_sequence":{"accession":"AIT76109.1","sequence":"MKKSLSATLISALLAFSAPGFSAADNVAAVVDSAIKPLMAQQDIPGMAVAVSVKGKPYYFNYGFADIQAKQPVTENTLFELGSVSKTFTGVLGAVSVAKKEMALNDLAAKYQPELALPQWKGITLLDLATYTAGGLPLQVPDAVKSRADLLNFYQQWQPSRKPGDMRLYANSSIGLFGALTANAAGMPYEQLLTARILAPLGLSHTFITVPESAQSQYAYGYKNKKPVRVSPGQLDAESYGVKSASKDMLRWAEMNMEPSRAGNADLEMAMYLAQTRYYKTAAINQGLGWEMYDWPQQKDMIINGVTNEVALQPHPVTDNQVQPYNRASWVHKTGATTGFGAYVAFIPEKQVAIVILANKNYPNTERVKAAQAILSALE"},"dna_sequence":{"accession":"KM087856.1","fmin":"0","fmax":"1140","strand":"+","sequence":"ATGAAAAAATCGTTATCTGCAACACTGATTTCCGCTCTGCTGGCGTTTTCCGCCCCGGGGTTTTCTGCCGCTGATAATGTCGCGGCGGTGGTGGACAGCGCCATTAAACCGCTGATGGCACAGCAGGATATTCCCGGGATGGCGGTTGCCGTCTCCGTAAAGGGTAAGCCCTATTATTTCAATTATGGTTTTGCCGATATTCAGGCAAAACAGCCGGTCACTGAAAATACACTATTTGAGCTCGGATCTGTAAGTAAAACTTTCACAGGTGTGCTGGGTGCAGTTTCTGTGGCGAAAAAAGAGATGGCGCTGAATGATCTGGCGGCAAAATACCAGCCGGAGCTGGCTCTGCCGCAGTGGAAGGGGATCACATTGCTGGATCTGGCTACCTATACCGCAGGCGGACTGCCGTTACAGGTGCCGGATGCGGTAAAAAGCCGTGCGGATCTGCTGAATTTCTATCAGCAGTGGCAGCCGTCCCGGAAACCGGGCGATATGCGTCTGTATGCAAACAGCAGTATCGGCCTGTTTGGTGCTCTGACCGCAAACGCGGCGGGGATGCCGTATGAGCAGTTGCTGACTGCACGGATCCTGGCACCGCTGGGGTTATCTCACACCTTTATTACTGTGCCGGAAAGTGCGCAAAGCCAGTATGCGTACGGTTATAAAAACAAAAAACCGGTCCGCGTGTCGCCGGGACAGCTTGATGCGGAATCTTACGGCGTGAAATCCGCCTCAAAAGATATGCTGCGCTGGGCGGAAATGAATATGGAGCCGTCACGGGCCGGTAATGCGGATCTGGAAATGGCAATGTATCTTGCACAGACCCGCTACTATAAAACCGCCGCGATTAACCAGGGGCTGGGCTGGGAAATGTATGACTGGCCGCAGCAGAAAGATATGATCATTAACGGCGTGACCAACGAGGTCGCATTGCAGCCGCACCCGGTAACAGACAACCAGGTTCAGCCGTATAACCGTGCTTCCTGGGTGCATAAAACGGGGGCAACAACTGGTTTCGGCGCCTATGTGGCCTTTATTCCGGAAAAACAGGTGGCGATTGTGATTCTGGCGAATAAAAACTACCCGAATACCGAAAGAGTCAAAGCCGCACAGGCTATTTTGAGTGCACTGGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002153","ARO_id":"38553","ARO_name":"DHA-22","CARD_short_name":"DHA-22","ARO_description":"DHA-22 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36207":{"category_aro_accession":"3000068","category_aro_cvterm_id":"36207","category_aro_name":"DHA beta-lactamase","category_aro_description":"DHA beta-lactamases are plasmid-mediated AmpC \u03b2-lactamases that confer resistance to cephamycins and oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1072":{"model_id":"1072","model_name":"OXA-37","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1134":{"protein_sequence":{"accession":"AAG33665.1","sequence":"MIIRFLALLFSAVVLVSLGHAQDKTHESSNWGKYFSDFNAKGTIVVVDERTNGNSTSVYNESRAQQRYSPASTFKIPHTLFALDAGAVRDEFHVFRWDGAKRSFAGHNQDQNLRSAMRNSTVWVYQLFAKEIGENKARSYLEKLNYGNADPSTKSGDYWIDGNLAISANEQISILKKLYRNELPFRVEHQRLVKDLMIVEAKRDWILRAKTGWDGQMGWWVGWVEWPTGPVFFALNIDTPNRMEDLHKREAIARAILQSVNALPPN"},"dna_sequence":{"accession":"AY007784.1","fmin":"1122","fmax":"1923","strand":"+","sequence":"TTGATAATCCGATTTCTAGCACTGCTTTTCTCAGCTGTTGTACTTGTCTCTCTTGGTCATGCACAAGATAAAACGCATGAGAGCTCTAATTGGGGGAAATACTTTAGTGATTTCAACGCTAAAGGTACAATAGTTGTAGTAGATGAACGCACAAACGGTAATTCCACATCGGTTTATAATGAATCCCGGGCTCAGCAGCGCTATTCGCCTGCGTCCACATTCAAGATTCCGCATACCCTTTTTGCGCTGGATGCAGGGGCGGTTCGCGATGAGTTTCATGTTTTTCGATGGGACGGCGCTAAAAGAAGCTTTGCAGGTCACAATCAAGACCAAAACCTACGATCGGCAATGCGCAATTCTACCGTTTGGGTCTATCAACTATTCGCAAAAGAAATAGGCGAAAACAAAGCACGAAGCTACCTAGAAAAATTAAATTACGGCAATGCAGACCCCTCGACCAAGAGCGGTGACTACTGGATAGATGGAAATCTTGCAATTTCAGCAAATGAACAAATTTCCATCCTAAAGAAGCTTTATCGAAATGAGCTTCCTTTTAGGGTAGAGCACCAACGCTTGGTTAAAGACTTGATGATTGTCGAAGCCAAACGTGATTGGATACTACGTGCCAAAACAGGCTGGGATGGTCAAATGGGTTGGTGGGTCGGTTGGGTAGAGTGGCCTACAGGCCCAGTATTTTTTGCGTTAAATATCGACACGCCAAACAGGATGGAAGACCTTCATAAACGAGAGGCAATTGCGCGTGCTATTCTTCAATCCGTCAATGCTTTGCCACCCAACTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001431","ARO_id":"37831","ARO_name":"OXA-37","CARD_short_name":"OXA-37","ARO_description":"OXA-37 is a beta-lactamase found in A. baumannii.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1073":{"model_id":"1073","model_name":"OKP-B-19","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"8280":{"protein_sequence":{"accession":"CAP12359.2","sequence":"MRYVRLCLISLIAALPLAVFASPQPLEQIKISEGQLAGRVGYVEMDLASGRMLAAWRASERFPLMSTFKVLLCGAVLARVDAGDEQLDRRIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNTAGNLLLKIVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDVRDTTTPASMATTLRKLLTTPSLSARSQQQLLQWMVDDRVAGPLIRAVLPAGWFIADKTGAGERGSRGIVALLGPDGKAERIVVIYLRDTPATMVERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AM850921.2","fmin":"24","fmax":"885","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGCCTTATCTCCCTGATTGCCGCCCTGCCACTGGCGGTATTCGCCAGCCCTCAGCCGCTTGAGCAGATTAAAATCAGCGAAGGTCAGCTGGCGGGCCGGGTGGGCTATGTTGAAATGGATCTGGCCAGCGGCCGCATGCTGGCCGCCTGGCGCGCCAGTGAGCGCTTTCCGCTGATGAGCACCTTTAAAGTGCTGCTCTGCGGCGCTGTGCTGGCCCGGGTGGATGCCGGCGACGAACAGCTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGCCGACGGGATGACCGTTGGCGAACTCTGCGCCGCCGCCATCACCATGAGCGACAACACCGCCGGCAATCTGCTGTTGAAGATCGTCGGCGGCCCCGCGGGATTGACCGCTTTTCTGCGCCAGATCGGTGACAACGTCACCCGTCTTGACCGCTGGGAAACGGAACTCAATGAGGCGCTTCCCGGCGACGTGCGCGACACCACCACCCCGGCCAGCATGGCCACCACCCTGCGCAAGCTGCTAACCACCCCCTCTCTGAGCGCCCGTTCGCAGCAGCAGCTGCTGCAGTGGATGGTTGACGACCGGGTGGCCGGCCCGTTGATCCGCGCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAAACCGGGGCCGGTGAGCGGGGCTCACGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAAGCGGAGCGTATCGTGGTGATCTATCTGCGTGATACCCCGGCGACCATGGTCGAGCGTAACCAGCAGATCGCCGGGATAGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002452","ARO_id":"38852","ARO_name":"OKP-B-19","CARD_short_name":"OKP-B-19","ARO_description":"OKP-B-19 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"38817":{"category_aro_accession":"3002417","category_aro_cvterm_id":"38817","category_aro_name":"OKP beta-lactamase","category_aro_description":"OKP beta-lactamases are chromosomal class A beta-lactamase that confer resistance to penicillins and early cephalosporins in Klebsiella pneumoniae. OKP beta-lactamases can be subdivided into two groups: OKP-A and OKP-B which diverge by about 4.2%.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1074":{"model_id":"1074","model_name":"LEN-3","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"8409":{"protein_sequence":{"accession":"AAN05030.1","sequence":"VISLLATLPLVVYAGPQPLEQIKQSESQLSGRVGMVEMDLASGRTLAAWRADERFPMVSTFKVLLCGAVLARVDAGLEQLDRRIHYRQQDLVDYSPVSEKHLVDGMTIGELCAAAITLSDNSAGNLLLATVGGPAGLTAFLRQIGDNVTRLDRWETALNEALPGDARDTTTPASMAATLRKLLTAQHLSARSQQQLLQWMVDDRVAGPLIRAVLPPGWFIADKTGAGERGARGIVALLGPDGKPERIVVIYLRDTPASMAERNQQIAGIGAALI"},"dna_sequence":{"accession":"AY130286.1","fmin":"1","fmax":"823","strand":"+","sequence":"GTTATCTCCCTGTTAGCCACCCTGCCACTGGTGGTATACGCCGGTCCACAGCCGCTTGAGCAGATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTGGGGATGGTGGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCGATGAACGCTTTCCCATGGTGAGCACCTTTAAAGTGCTGCTGTGCGGCGCGGTGCTGGCGCGGGTGGATGCCGGGCTCGAACAACTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGTCGACGGGATGACGATCGGCGAACTCTGCGCCGCCGCCATCACCCTGAGCGATAACAGCGCTGGCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCGGGATTAACTGCCTTTCTGCGCCAGATCGGTGACAACGTCACCCGTCTTGACCGCTGGGAAACGGCACTGAATGAGGCGCTTCCCGGCGACGCGCGCGACACCACCACCCCGGCCAGCATGGCCGCCACGCTGCGCAAACTACTGACCGCGCAGCATCTGAGCGCCCGTTCGCAACAGCAACTCCTGCAGTGGATGGTGGACGATCGGGTTGCCGGCCCGCTGATCCGCGCCGTGCTGCCGCCGGGCTGGTTTATCGCCGACAAAACCGGGGCTGGCGAACGGGGTGCGCGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAACCGGAGCGCATTGTGGTGATCTATCTGCGGGATACCCCGGCGAGTATGGCCGAGCGTAATCAACAAATCGCCGGGATCGGCGCGGCGCTGATC","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002475","ARO_id":"38875","ARO_name":"LEN-3","CARD_short_name":"LEN-3","ARO_description":"LEN-3 is a beta-lactamase. From the Pasteur Institute list of LEN beta-lactamases.","ARO_category":{"36236":{"category_aro_accession":"3000097","category_aro_cvterm_id":"36236","category_aro_name":"LEN beta-lactamase","category_aro_description":"LEN beta-lactamases are chromosomal class A beta-lactamases that confer resistance to ampicillin, amoxicillin, carbenicillin, and ticarcillin but not to extended-spectrum beta-lactams.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1075":{"model_id":"1075","model_name":"TEM-20","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1800":{"protein_sequence":{"accession":"CAA76793.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTTPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGASERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"Y17581.1","fmin":"78","fmax":"936","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGACGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCAGTGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGG","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3000891","ARO_id":"37271","ARO_name":"TEM-20","CARD_short_name":"TEM-20","ARO_description":"TEM-20 is an extended-spectrum beta-lactamase found in several species of Gram-negative bacteria.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1076":{"model_id":"1076","model_name":"IMP-37","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1632":{"protein_sequence":{"accession":"AFP97028.1","sequence":"MKKLFVLCVCFFCSITAAGAALPDLKIEKLEEGVFVHTSFEEVNGWGVVTKHGLVVLVNTDAYLIDTPFTATDTEKLVNWFVERGYEIKGTISSHFHSDSTGGIEWLNSQSIPTYASELTNELLKKSGKVQAKYSFSEVSYWLVKNKIEVFYPGPGHTQDNLVVWLPESKILFGGCFIKPHGLGNLGDANLEAWPKSAKILMSKYGKAKLVVSSHSEKGDASLMKRTWEQALKGLKESKKTSSQSTAS"},"dna_sequence":{"accession":"JX131372.1","fmin":"96","fmax":"843","strand":"+","sequence":"ATGAAGAAATTATTTGTTTTATGTGTATGCTTCTTTTGTAGCATTACTGCCGCAGGAGCGGCTTTACCTGATTTAAAAATCGAGAAGCTTGAAGAAGGTGTTTTTGTTCATACATCGTTCGAAGAGGTTAACGGTTGGGGGGTTGTTACTAAACACGGTTTAGTGGTGCTTGTAAACACAGACGCCTATCTAATTGACACTCCATTTACTGCTACAGACACTGAAAAATTAGTCAATTGGTTTGTGGAGCGCGGCTATGAAATCAAAGGCACTATTTCATCACATTTCCATAGCGACAGCACAGGAGGAATAGAGTGGCTTAATTCTCAATCTATTCCCACGTATGCATCTGAATTAACAAATGAACTTTTGAAAAAATCCGGTAAGGTACAAGCTAAATATTCATTTAGCGAAGTTAGCTATTGGCTAGTTAAAAATAAAATTGAAGTTTTCTACCCTGGCCCAGGTCACACTCAAGATAACCTAGTGGTTTGGTTGCCTGAAAGTAAAATTTTATTCGGTGGTTGCTTTATTAAACCTCACGGTCTTGGCAATTTAGGTGACGCAAATTTAGAAGCTTGGCCAAAGTCCGCCAAAATATTAATGTCTAAATATGGCAAAGCAAAGCTTGTTGTTTCAAGTCATAGTGAAAAAGGGGACGCATCACTAATGAAACGTACATGGGAACAAGCCCTTAAAGGGCTTAAAGAAAGTAAAAAAACATCATCACAAAGTACAGCATCGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002228","ARO_id":"38628","ARO_name":"IMP-37","CARD_short_name":"IMP-37","ARO_description":"IMP-37 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1077":{"model_id":"1077","model_name":"OXA-420","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"2012":{"protein_sequence":{"accession":"BAP28835.1","sequence":"MKLLKILSLVCLSISIGACAEHSMSRAKTSTIPQVNNSIIDQNVQALFNEISADAVFVTYDGQNIKKYGTHLDRAKTAYIPASTFKIANALIGLENHKATSTEIFKWDGKPRFFKAWDKDFTLGEAMQASTVPVYQELARRIGPSLMQSELQRIGYGNMQIGTEVDQFWLKGPLTITPIQEVKFVYDLAQGQLPFKPEVQQQVKEMLYVERRGENRLYAKSGWGMAVDPQVGWYVGFVEKADGQVVAFALNMQMKDGDDIALRKQLSLDVLDKLGVFHYL"},"dna_sequence":{"accession":"AB983359.1","fmin":"2425","fmax":"3268","strand":"+","sequence":"ATGAAATTATTAAAAATATTGAGTTTAGTTTGCTTAAGCATAAGTATTGGGGCTTGTGCTGAGCATAGTATGAGTCGAGCAAAAACAAGTACAATTCCACAAGTGAATAACTCAATCATCGATCAGAATGTTCAAGCGCTTTTTAATGAAATCTCAGCTGATGCTGTGTTTGTTACATATGATGGTCAAAATATTAAAAAATATGGCACGCATTTAGACCGAGCAAAAACAGCTTATATTCCTGCATCTACATTTAAAATTGCCAATGCACTAATTGGTTTAGAAAATCATAAAGCAACATCTACAGAAATATTTAAGTGGGATGGAAAGCCACGTTTTTTTAAAGCATGGGACAAAGATTTTACTTTGGGCGAAGCCATGCAAGCATCTACAGTGCCTGTATATCAAGAATTGGCACGTCGTATTGGTCCAAGCTTAATGCAAAGTGAATTGCAACGTATTGGTTATGGCAATATGCAAATAGGCACGGAAGTTGATCAATTTTGGTTGAAAGGGCCTTTGACAATTACACCTATACAAGAAGTAAAGTTTGTTTATGATTTAGCCCAAGGGCAATTGCCTTTTAAACCTGAAGTTCAGCAACAAGTGAAAGAGATGTTGTATGTAGAGCGCAGAGGGGAGAATCGTCTATATGCTAAAAGTGGCTGGGGAATGGCTGTAGACCCGCAAGTGGGTTGGTATGTGGGTTTTGTTGAAAAGGCAGATGGGCAAGTGGTGGCATTTGCTTTAAATATGCAAATGAAAGATGGTGATGATATTGCTCTACGTAAACAATTGTCTTTAGATGTGCTAGATAAGTTGGGTGTTTTTCATTATTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3003116","ARO_id":"39693","ARO_name":"OXA-420","CARD_short_name":"OXA-420","ARO_description":"OXA-420 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46517":{"category_aro_accession":"3007728","category_aro_cvterm_id":"46517","category_aro_name":"OXA-58-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-58.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1078":{"model_id":"1078","model_name":"VIM-4","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1891":{"protein_sequence":{"accession":"CAJ32502.1","sequence":"MLKVISSLLVYMTASVMAVASPLAHSGEPSGEYPTVNEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEAEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSANVLYGGCAVHELSRTSAGNVADADLAEWPTSVERIQKHYPEAEVVIPGHGLPGGLDLLQHTANVVKAHKNRSVAE"},"dna_sequence":{"accession":"AM087411.1","fmin":"127","fmax":"928","strand":"+","sequence":"ATGTTAAAAGTTATTAGTAGTTTATTGGTCTACATGACCGCGTCTGTCATGGCTGTCGCAAGTCCGTTAGCCCATTCCGGGGAGCCGAGTGGTGAGTATCCGACAGTCAACGAAATTCCGGTCGGAGAGGTCCGACTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCGGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAAAAGCAAATTGGACTTCCCGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGCAGAGGGGAACGAGATTCCCACGCATTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAGCTCTTCTATCCTGGTGCTGCGCATTCGACCGACAATCTGGTTGTATACGTCCCGTCAGCGAACGTGCTATACGGTGGTTGTGCCGTTCATGAGTTGTCACGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCGTTGAGCGGATTCAAAAACACTACCCGGAAGCAGAGGTCGTCATTCCCGGGCACGGTCTACCGGGCGGTCTAGACTTGCTCCAGCACACAGCGAACGTTGTCAAAGCACACAAAAATCGCTCAGTCGCCGAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002274","ARO_id":"38674","ARO_name":"VIM-4","CARD_short_name":"VIM-4","ARO_description":"VIM-4 is a beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1079":{"model_id":"1079","model_name":"OXA-161","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"881":{"protein_sequence":{"accession":"ACT09125.1","sequence":"MAIRIFAILFSIFSLATFAHAQEGTLERSDWRKFFSEFQAKGTIVVADERQADRAMLVFDPVRSKKRYSPASTFKIPHTLFALDAGAVRDEFQIFRWDGVNRGFAGHNQDQDLRSAMRNSTVWVYELFAKEIGDDKARRYLKKIDYGDADPSTSNGDYWIEGSLAISAQEQIAFLRKLYRNELPFRVEHQRLVKDLMIVEAGRNWILRAKTGWEGRMGWWVGWVEWPTGSVFFALNIDTPNRMDDLFKREAIVRAILRSIEALPPNPAVNSDAAR"},"dna_sequence":{"accession":"GQ202693.1","fmin":"1171","fmax":"1999","strand":"+","sequence":"ATGGCAATCCGAATCTTCGCGATACTTTTCTCCATTTTTTCTCTTGCCACTTTCGCGCATGCGCAAGAAGGCACGCTAGAACGTTCTGACTGGAGGAAGTTTTTCAGCGAATTTCAAGCCAAAGGCACGATAGTTGTGGCAGACGAACGCCAAGCGGATCGTGCCATGTTGGTTTTTGATCCTGTGCGATCGAAGAAACGCTACTCGCCTGCATCGACATTCAAGATACCTCATACACTTTTTGCACTTGATGCAGGCGCTGTTCGTGATGAGTTCCAGATTTTTCGATGGGACGGCGTTAACAGGGGCTTTGCAGGCCACAATCAAGACCAAGATTTGCGATCAGCAATGCGGAATTCTACTGTTTGGGTGTATGAGCTATTTGCAAAGGAAATTGGTGATGACAAAGCTCGGCGCTATTTGAAGAAAATCGACTATGGCGACGCCGATCCTTCGACAAGTAATGGCGATTACTGGATAGAAGGCAGCCTTGCAATCTCGGCGCAGGAGCAAATTGCATTTCTCAGGAAGCTCTATCGTAACGAGCTGCCCTTTCGGGTAGAACATCAGCGCTTGGTCAAGGATCTCATGATTGTGGAAGCCGGTCGCAACTGGATACTGCGTGCAAAGACGGGCTGGGAAGGCCGTATGGGTTGGTGGGTAGGATGGGTTGAGTGGCCGACTGGCTCCGTATTCTTCGCACTGAATATTGATACGCCAAACAGAATGGATGATCTTTTCAAGAGGGAGGCAATCGTGCGGGCAATCCTTCGCTCTATTGAAGCGTTACCGCCCAACCCGGCAGTCAACTCGGACGCTGCGCGATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3001799","ARO_id":"38199","ARO_name":"OXA-161","CARD_short_name":"OXA-161","ARO_description":"OXA-161 is a beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46493":{"category_aro_accession":"3007704","category_aro_cvterm_id":"46493","category_aro_name":"OXA-2-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-2.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1080":{"model_id":"1080","model_name":"SHV-158","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1712":{"protein_sequence":{"accession":"AFQ23964.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLAAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"JX121125.1","fmin":"0","fmax":"858","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACATCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGTATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGC","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001197","ARO_id":"37577","ARO_name":"SHV-158","CARD_short_name":"SHV-158","ARO_description":"SHV-158 is a beta-lactamase.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1081":{"model_id":"1081","model_name":"IMP-30","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1174":{"protein_sequence":{"accession":"ABF70513.1","sequence":"MSKLSVFFIFLFCSIATAAESLPDLKIEKLDEGVYVHTSFKEVNGWGVVPKHGLVVLVNAEAYLIDTPFTAKDTEKLVTWFVERGYKIKGSISSHFHSDSTGGIEWLNSRSIPTYASELTNELLKKDGKVQATNSFSGVNYWLVKNKIEVFYPGPGHTPDNVVVWLPERKILFGGCFIKPYGLGNLGDANIEAWPKSAKLLKSKYGKAKLVVPSHSEVGDASLLKLTLEQAVKGLNESKKPSKPSN"},"dna_sequence":{"accession":"DQ522237.1","fmin":"1075","fmax":"1816","strand":"+","sequence":"ATGAGCAAGTTATCTGTATTCTTTATATTTTTGTTTTGCAGCATTGCTACCGCAGCAGAGTCTTTGCCAGATTTAAAAATTGAAAAGCTTGATGAAGGCGTTTATGTTCATACTTCGTTTAAAGAAGTTAACGGGTGGGGCGTTGTTCCTAAACATGGTTTGGTGGTTCTTGTAAATGCTGAGGCTTACCTAATTGACACTCCATTTACGGCTAAAGATACTGAAAAGTTAGTCACTTGGTTTGTGGAGCGTGGCTATAAAATAAAAGGCAGCATTTCCTCTCATTTTCATAGCGACAGCACGGGCGGAATAGAGTGGCTTAATTCTCGATCTATCCCCACGTATGCATCTGAATTAACAAATGAACTGCTTAAAAAAGACGGTAAGGTTCAAGCCACAAATTCATTTAGCGGAGTTAACTATTGGCTAGTTAAAAATAAAATTGAAGTTTTTTATCCAGGCCCGGGACACACTCCAGATAACGTAGTGGTTTGGTTGCCTGAAAGGAAAATATTATTCGGTGGTTGTTTTATTAAACCGTACGGTTTAGGCAATTTGGGTGACGCAAATATAGAAGCTTGGCCAAAGTCCGCCAAATTATTAAAGTCCAAATATGGTAAGGCAAAACTGGTTGTTCCAAGTCACAGTGAAGTTGGAGACGCATCACTCTTGAAACTTACATTAGAGCAGGCGGTTAAAGGGTTAAACGAAAGTAAAAAACCATCAAAACCAAGCAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002221","ARO_id":"38621","ARO_name":"IMP-30","CARD_short_name":"IMP-30","ARO_description":"IMP-30 is a beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1082":{"model_id":"1082","model_name":"CTX-M-7","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1432":{"protein_sequence":{"accession":"CAA06312.1","sequence":"MMTQSIRRSMLTVMATLPLLFSSATLHAQANSVQQQLEALEKSSGGRLGVALINTADNSQILYVADERFAMCSTSKVMAAAAVLKQSESDKHLLNQRVEIRASDLVNYNPIAEKHVNGTMTLAQLGAGALQYSDNTAMNKLIAHLGGPDKVTAFARSLGDETFRLDRTEPTLNSAIPGDPRDTTTPLAMAQTLKNLTLGKALAETQRAQLVTWLKGNTTGSASIRAGLPKSWGVGDKTGSGDYGTTNDIAVIWPENHAPLVLVTYFTQPEQKAESRRDVLAAAAKIVTHGF"},"dna_sequence":{"accession":"AJ005045.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGATGACTCAGAGCATTCGCCGCTCAATGTTAACGGTGATGGCGACGCTACCCCTGCTATTTAGCAGCGCAACGCTGCATGCGCAGGCGAACAGCGTGCAACAGCAGCTGGAAGCCCTGGAGAAAAGTTCGGGAGGTCGGCTTGGCGTTGCGCTGATTAACACCGCCGATAATTCGCAGATTCTCTACGTGGCCGATGAGCGTTTTGCGATGTGCAGTACCAGTAAGGTGATGGCGGCCGCGGCGGTGCTTAAACAGAGCGAGAGCGATAAGCACCTGCTAAATCAGCGCGTTGAAATCAGAGCAAGCGACCTGGTTAACTACAATCCGATTGCGGAGAAACACGTTAACGGCACGATGACGCTGGCTCAGCTTGGCGCCGGCGCCCTGCAGTATAGCGACAATACTGCCATGAATAAGCTGATTGCCCATCTGGGTGGGCCCGATAAAGTGACGGCGTTTGCTCGCTCATTGGGTGATGAGACCTTCCGTCTGGACAGAACCGAGCCCACGCTCAATAGCGCCATTCCAGGCGACCCGCGTGATACCACCACGCCGCTCGCGATGGCGCAGACCCTGAAAAATCTGACGCTGGGCAAAGCGCTGGCGGAAACTCAGCGGGCACAGTTGGTGACGTGGCTTAAGGGCAATACTACCGGTAGCGCGAGCATTCGGGCGGGTCTGCCGAAATCATGGGGAGTGGGCGATAAAACCGGCAGCGGAGATTATGGCACCACCAACGATATCGCGGTTATCTGGCCGGAAAACCACGCACCGCTGGTTCTGGTGACCTACTTTACCCAACCGGAGCAGAAGGCGGAAAGCCGTCGGGATGTTCTGGCTGCGGCGGCGAAAATCGTAACCCACGGTTTCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35732","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Typhimurium","NCBI_taxonomy_id":"90371"}}}},"ARO_accession":"3001870","ARO_id":"38270","ARO_name":"CTX-M-7","CARD_short_name":"CTX-M-7","ARO_description":"CTX-M-7 is a beta-lactamase found in Salmonella typhimurium.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1083":{"model_id":"1083","model_name":"OXA-323","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"2008":{"protein_sequence":{"accession":"AGW16405.1","sequence":"MYKKALIVATSILFLSACSSNTVKQNQIHSISANKNSEEIKSLFDQAQTTGVLVIKRGQTEEIYGNDLKRASTAYVPASTFKMLNALIGLEHHKATITEVFKWDGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMSKEVKRIGFGNANIGSKVDNFWLVGPLKITPQQETQFAYQLAHKTLPFSQDVQEQVQSMVFIEEKNGSKIYAKSGWGWDVEPQVGWLTGWVVQPQGEIVAFSLNLEMKKGTPSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"KF203097.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGTATAAAAAAGCCCTTATCGTTGCAACAAGTATCCTATTTTTATCCGCCTGTTCTTCCAATACGGTAAAACAAAATCAAATACATTCTATTTCTGCCAATAAAAATTCAGAAGAAATTAAATCACTATTTGATCAAGCACAGACCACGGGTGTTTTGGTGATTAAGCGAGGACAAACAGAAGAAATTTATGGCAATGATCTTAAAAGAGCATCAACCGCCTATGTTCCCGCCTCTACCTTTAAAATGTTAAATGCTTTAATTGGACTTGAACATCATAAGGCAACTATAACTGAAGTGTTTAAATGGGATGGACAAAAACGCTTATTTCCTGATTGGGAAAAGGACATGACACTGGGCGATGCCATGAAAGCTTCTGCGATTCCAGTTTACCAAGAATTAGCCCGACGAATTGGTCTAGATCTTATGTCCAAAGAGGTGAAACGAATTGGTTTTGGTAATGCTAACATTGGTTCAAAAGTAGATAATTTTTGGCTTGTTGGCCCTCTAAAAATTACACCTCAACAAGAAACCCAATTTGCTTATCAATTAGCCCATAAAACGCTTCCATTTAGCCAAGATGTACAAGAACAAGTTCAATCAATGGTGTTCATAGAGGAAAAAAATGGAAGTAAAATTTATGCCAAAAGTGGTTGGGGATGGGATGTTGAACCGCAAGTTGGTTGGTTAACAGGCTGGGTCGTTCAACCACAAGGAGAAATTGTGGCATTTTCACTTAATTTAGAAATGAAAAAAGGAACTCCTAGCTCTATTCGCAAAGAAATTGCTTATAAAGGCTTAGAACAACTGGGTATTTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39094","NCBI_taxonomy_name":"Acinetobacter calcoaceticus","NCBI_taxonomy_id":"471"}}}},"ARO_accession":"3001511","ARO_id":"37911","ARO_name":"OXA-323","CARD_short_name":"OXA-323","ARO_description":"OXA-323 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46495":{"category_aro_accession":"3007706","category_aro_cvterm_id":"46495","category_aro_name":"OXA-213-like beta-lactamase","category_aro_description":"OXA-213-like enzymes have been identified to be intrinsic to A. calcoaceticus and have been subsequently detected in A. pittii. Phylogenetic analysis of OXA-213-like proteins identified two distinct subgroups within the OXA family. The first group was linked to A. pittii and the second group to A. calcoaceticus. The carbapenemase activity of these OXAs may be related to the species-dependent effect.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1084":{"model_id":"1084","model_name":"LEN-5","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"874":{"protein_sequence":{"accession":"AAU25807.1","sequence":"MRYIRLCVISLLATLPLAVYAGPQPLEQIKQSESQLSGRVGMVEMDLASGRTLAAWRADERFPMVSTFKVLLCGAVLARVDAGLEQLDRRIHYRQQDLVDYSPVSEKHLTDGMTIGELCAAAITLSDNSAGNLLLATVGGPAGLTAFLRQIGDNVTRLDRWETALNEALPGDARDTTTPASMAATLRKLLTAQHLSARSQQQLLQWMVDDRVAGPLIRAVLPPGWFIADKTGAGERGARGIVALLGPDGKPERIVVIYLRDTPASMAERNQHIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AY633109.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTGTTATCTCCCTGTTAGCCACCCTGCCACTGGCGGTATACGCCGGTCCACAGCCGCTTGAGCAGATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTGGGGATGGTGGAAATGGATCTGGCCAGCGGCCGCACGCTGGCGGCCTGGCGCGCCGATGAACGCTTTCCCATGGTGAGCACCTTTAAAGTGCTGCTGTGCGGCGCGGTGCTGGCGCGGGTGGATGCCGGGCTCGAACAACTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTACCGACGGGATGACGATCGGCGAACTTTGCGCCGCCGCCATCACCCTGAGCGATAACAGCGCTGGCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCGGGATTAACTGCCTTTCTGCGCCAGATCGGTGACAACGTCACCCGCCTTGACCGCTGGGAAACGGCACTGAATGAGGCGCTTCCCGGCGACGCGCGCGACACCACCACCCCGGCCAGCATGGCCGCCACGCTGCGCAAACTACTGACCGCGCAGCATCTGAGCGCCCGTTCGCAACAGCAACTCCTGCAGTGGATGGTGGACGATCGGGTTGCCGGCCCGCTGATCCGCGCCGTGCTGCCGCCGGGCTGGTTTATCGCCGACAAAACCGGGGCTGGCGAACGGGGTGCGCGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAACCGGAGCGCATTGTGGTGATCTATCTGCGGGATACCCCGGCGAGTATGGCCGAGCGTAATCAACATATCGCCGGGATCGGCGCAGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002456","ARO_id":"38856","ARO_name":"LEN-5","CARD_short_name":"LEN-5","ARO_description":"LEN-5 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36236":{"category_aro_accession":"3000097","category_aro_cvterm_id":"36236","category_aro_name":"LEN beta-lactamase","category_aro_description":"LEN beta-lactamases are chromosomal class A beta-lactamases that confer resistance to ampicillin, amoxicillin, carbenicillin, and ticarcillin but not to extended-spectrum beta-lactams.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1085":{"model_id":"1085","model_name":"OKP-B-5","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"8269":{"protein_sequence":{"accession":"CAP12356.2","sequence":"MRYVRLCLISLIAALPLAVFASPQPLEQIKISESQLAGRVGYVEMDLASGRTLAAWRASERFPLMSTFKVLLCGAVLARVDAGDEQLDRRIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNTAGNLLLKIVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDVRDTTTPASMATTLRKLLTTPSLSARSQQQLLQWMVDDRVAGPLIRAVLPAGWFIADKTGAGERGSRGIVALLGPDGKAERIVVIYLRDTPATMVERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AM850918.2","fmin":"24","fmax":"885","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGCCTTATCTCCCTGATTGCCGCCCTGCCACTGGCGGTATTCGCCAGCCCTCAGCCGCTTGAGCAGATTAAAATCAGCGAAAGTCAGCTGGCGGGCCGGGTGGGCTATGTTGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCAGTGAGCGCTTTCCGCTGATGAGCACCTTTAAAGTGCTGCTCTGCGGCGCGGTGCTGGCCCGGGTGGATGCCGGCGACGAACAGCTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGCCGACGGGATGACCGTTGGCGAACTCTGCGCCGCCGCCATCACCATGAGCGACAACACCGCCGGCAATCTGCTGTTGAAGATCGTCGGCGGCCCCGCGGGATTGACCGCTTTTCTGCGCCAGATCGGTGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTCAATGAGGCGCTTCCCGGCGACGTGCGCGACACCACCACCCCGGCCAGCATGGCCACCACCCTGCGCAAGCTGCTAACCACCCCCTCTCTGAGCGCCCGTTCGCAGCAGCAGCTGCTGCAGTGGATGGTTGACGACCGGGTGGCCGGCCCGTTGATCCGCGCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAAACCGGGGCCGGTGAGCGGGGCTCACGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAAGCGGAGCGTATCGTGGTGATCTATCTGCGTGATACCCCGGCGACCATGGTCGAGCGTAACCAGCAGATCGCCGGGATAGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002438","ARO_id":"38838","ARO_name":"OKP-B-5","CARD_short_name":"OKP-B-5","ARO_description":"OKP-B-5 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"38817":{"category_aro_accession":"3002417","category_aro_cvterm_id":"38817","category_aro_name":"OKP beta-lactamase","category_aro_description":"OKP beta-lactamases are chromosomal class A beta-lactamase that confer resistance to penicillins and early cephalosporins in Klebsiella pneumoniae. OKP beta-lactamases can be subdivided into two groups: OKP-A and OKP-B which diverge by about 4.2%.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1086":{"model_id":"1086","model_name":"CMY-41","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1345":{"protein_sequence":{"accession":"BAG14343.1","sequence":"MMKKSICCALLLTASFSTFAATKTEQQIADIVNRTITPLMQEQAIPGMAVAIIYEEKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWRGISLLHLATYTAGGLPLQIPDEVTDKAALLRFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQSEQKNYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIELAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPARVEAAWRILEKLQ"},"dna_sequence":{"accession":"AB429270.1","fmin":"14","fmax":"1160","strand":"+","sequence":"ATGATGAAAAAATCGATATGCTGCGCGCTGCTGCTGACAGCCTCTTTCTCCACGTTTGCTGCCACAAAAACAGAACAACAAATTGCCGATATCGTTAACCGCACCATCACACCACTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTGGCGATTATCTACGAGGAGAAACCTTATTACTTTACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAATTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGACGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCGGGGTATCAGCCTGCTGCACTTAGCCACCTATACAGCGGGTGGCCTACCGCTGCAGATCCCCGATGAAGTTACGGATAAAGCCGCATTACTGCGCTTTTATCAAAACTGGCAACCACAATGGACTCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGTGCGCTGGCGGTGAAACCTTCAGGTATGAGCTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAAAGCGAACAAAAAAATTATGCCTGGGGCTATCGCGAAGGGAAGCCTGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATCGATATGGCCCGCTGGGTTCAGGCCAACATGGACGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGAGCTTGCGCAGTCTCGTTACTGGCGTATTGGTGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCAGCACCTGCCGTGAAAGCCTCATGGGTGCATAAAACGGGATCCACAGGTGGATTTGGCAGCTACGTTGCCTTCGTTCCAGAAAAAAACCTTGGCATAGTGATGCTGGCAAACAAAAGCTACCCCAACCCGGCTCGCGTCGAGGCGGCCTGGCGCATTCTTGAAAAACTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002052","ARO_id":"38452","ARO_name":"CMY-41","CARD_short_name":"CMY-41","ARO_description":"CMY-41 is a beta-lactamase found in the Enterobacteriaceae family.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1087":{"model_id":"1087","model_name":"OXA-253","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8256":{"protein_sequence":{"accession":"AGK07368.1","sequence":"MKKFILPIFSISILLSLSACSSIQTKFEDTSDISDQQQGKAIKSYFDEAQTQGVIIIKEGKNISTYGNNLARAHTEYVPASTFKMLNALIGLENHKATTTEIFKWDGKKRSYPMWEKDMTLGDAMALSAVPVYQELARRTGLDLMQKEVKRVGFGNMNIGTQVDNFWLVGPLKITPIQEVNFADDLANNRLPFKLETQEEVKKMLLIKEVNGSKIYAKSGWGMDVIPQVGWLTGWVEKSNGEKVPFSLNLEMKQGMSGSIRNEITYKSLENLGII"},"dna_sequence":{"accession":"KC479324.2","fmin":"575","fmax":"1403","strand":"+","sequence":"ATGAAAAAATTTATACTTCCTATCTTCAGCATTTCTATTCTACTTTCTCTCAGTGCATGCTCATCTATTCAAACTAAATTTGAAGATACTTCTGATATTTCTGATCAGCAACAAGGAAAAGCCATTAAAAGCTATTTTGATGAAGCTCAAACACAAGGTGTAATCATTATTAAAGAGGGAAAGAATATTAGTACCTATGGTAATAACCTGGCACGAGCACATACAGAATATGTCCCTGCATCAACATTTAAGATGCTAAATGCCTTAATTGGATTAGAAAATCATAAAGCTACAACAACTGAGATTTTCAAATGGGATGGTAAAAAAAGATCTTATCCTATGTGGGAAAAAGATATGACTTTAGGTGATGCCATGGCACTTTCAGCAGTTCCTGTATATCAAGAACTTGCAAGACGGACTGGTTTAGACCTAATGCAAAAAGAAGTCAAACGGGTTGGTTTTGGTAATATGAACATTGGAACACAAGTTGATAACTTCTGGTTGGTTGGCCCGCTTAAAATTACACCAATACAAGAGGTTAATTTTGCCGACGATCTCGCTAATAATCGATTACCCTTTAAATTAGAAACTCAAGAAGAAGTAAAAAAAATGCTTCTGATTAAAGAAGTCAATGGTAGTAAAATTTATGCGAAAAGCGGATGGGGAATGGATGTAATCCCTCAGGTAGGTTGGTTAACAGGTTGGGTAGAAAAATCTAATGGCGAAAAAGTTCCCTTTTCTCTAAACCTAGAAATGAAGCAAGGAATGTCTGGTTCTATTCGTAATGAAATTACTTATAAGTCATTAGAAAATTTAGGGATTATATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001689","ARO_id":"38089","ARO_name":"OXA-253","CARD_short_name":"OXA-253","ARO_description":"OXA-253 is a beta-lactamase found in A. baumannii.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46490":{"category_aro_accession":"3007701","category_aro_cvterm_id":"46490","category_aro_name":"OXA-143-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-143.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1089":{"model_id":"1089","model_name":"CMY-14","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"8235":{"protein_sequence":{"accession":"CAD88479.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYARGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEINPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"AJ555825.2","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCCGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGATAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3002025","ARO_id":"38425","ARO_name":"CMY-14","CARD_short_name":"CMY-14","ARO_description":"CMY-14 is a beta-lactamase found in Proteus mirabilis.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1090":{"model_id":"1090","model_name":"TEM-169","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1075":{"protein_sequence":{"accession":"ACP18864.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMLSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRGEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"FJ873740.1","fmin":"0","fmax":"858","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGCTGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTGGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGG","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35655","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Infantis","NCBI_taxonomy_id":"595"}}}},"ARO_accession":"3001035","ARO_id":"37415","ARO_name":"TEM-169","CARD_short_name":"TEM-169","ARO_description":"TEM-169 is an extended spectrum beta-lactamase.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1091":{"model_id":"1091","model_name":"IMP-6","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1278":{"protein_sequence":{"accession":"BAB15941.1","sequence":"MSKLSVFFIFLFCSIATAAESLPDLKIEKLDEGVYVHTSFEEVNGWGVVPKHGLVVLVNAEAYLIDTPFTAKDTEKLVTWFVERGYKIKGSISSHFHSDSTGGIEWLNSRSIPTYASELTNELLKKDGKVQATNSFSGVNYWLVKNKIEVFYPGPGHTPDNVVVWLPERKILFGGCFIKPYGLGNLGDANIEAWPKSAKLLKSKYGKAKLVVPGHSEVGDASLLKLTLEQAVKGLNESKKPSKPSN"},"dna_sequence":{"accession":"AB040994.1","fmin":"0","fmax":"741","strand":"+","sequence":"ATGAGCAAGTTATCTGTATTCTTTATATTTTTGTTTTGCAGCATTGCTACCGCAGCAGAGTCTTTGCCAGATTTAAAAATTGAAAAGCTTGATGAAGGCGTTTATGTTCATACTTCGTTTGAAGAAGTTAACGGGTGGGGCGTTGTTCCTAAACATGGTTTGGTGGTTCTTGTAAATGCTGAGGCTTACCTAATTGACACTCCATTTACGGCTAAAGATACTGAAAAGTTAGTCACTTGGTTTGTGGAGCGTGGCTATAAAATAAAAGGCAGCATTTCCTCTCATTTTCATAGCGACAGCACGGGCGGAATAGAGTGGCTTAATTCTCGATCTATCCCCACGTATGCATCTGAATTAACAAATGAACTGCTTAAAAAAGACGGTAAGGTTCAAGCCACAAATTCATTTAGCGGAGTTAACTATTGGCTAGTTAAAAATAAAATTGAAGTTTTTTATCCAGGCCCGGGACACACTCCAGATAACGTAGTGGTTTGGTTGCCTGAAAGGAAAATATTATTCGGTGGTTGTTTTATTAAACCGTACGGTTTAGGCAATTTGGGTGACGCAAATATAGAAGCTTGGCCAAAGTCCGCCAAATTATTAAAGTCCAAATATGGTAAGGCAAAACTGGTTGTTCCAGGTCACAGTGAAGTTGGAGACGCATCACTCTTGAAACTTACATTAGAGCAGGCGGTTAAAGGGTTAAACGAAAGTAAAAAACCATCAAAACCAAGCAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36783","NCBI_taxonomy_name":"Serratia marcescens","NCBI_taxonomy_id":"615"}}}},"ARO_accession":"3002197","ARO_id":"38597","ARO_name":"IMP-6","CARD_short_name":"IMP-6","ARO_description":"IMP-6 is a beta-lactamase found in Serratia marcescens.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1093":{"model_id":"1093","model_name":"AAC(6')-31","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"325"}},"model_sequences":{"sequence":{"267":{"protein_sequence":{"accession":"CAK55557.1","sequence":"MTEHDLPMLHDWLNRPHIVEWWGGEETRPTLAEVLEQYLPSALAKESVTPYIAMLDEEPIGYAQSYIALGSGDGWWEDETDPGVRGIDQSLANPSQLGKGLGTKLVCALVEMLFKDAEVTKIQTDPSPNNLRAIRCYEKAGFVAQRTINTPDGPAVYMVQTRQAFEQARSAV"},"dna_sequence":{"accession":"AM283489.1","fmin":"2655","fmax":"3174","strand":"+","sequence":"ATGACCGAGCACGACCTTCCGATGCTCCATGACTGGCTAAATCGGCCTCACATCGTTGAGTGGTGGGGCGGAGAAGAAACACGTCCAACACTTGCTGAAGTGCTGGAGCAATACCTACCAAGCGCCCTGGCGAAAGAGTCCGTCACTCCCTACATCGCAATGCTGGATGAAGAACCGATTGGGTACGCTCAGTCGTACATTGCACTCGGAAGCGGTGACGGATGGTGGGAAGACGAAACCGATCCAGGAGTACGCGGAATAGACCAGTCTCTGGCGAATCCATCGCAGCTGGGCAAGGGCTTGGGAACCAAGCTCGTTTGCGCGCTCGTTGAGATGCTGTTCAAAGACGCTGAGGTAACCAAGATCCAAACGGACCCGTCGCCGAACAACTTACGCGCAATCCGGTGCTACGAGAAGGCGGGTTTTGTGGCGCAAAGAACCATAAACACCCCAGATGGACCGGCCGTATACATGGTTCAAACACGTCAGGCGTTCGAGCAGGCGCGCAGTGCTGTCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36803","NCBI_taxonomy_name":"Pseudomonas putida","NCBI_taxonomy_id":"303"}}}},"ARO_accession":"3002585","ARO_id":"38985","ARO_name":"AAC(6')-31","CARD_short_name":"AAC(6')-31","ARO_description":"AAC(6')-31 is an integron-encoded aminoglycoside acetyltransferase in Pseudomonas putida, A. baumannii and K. pneumoniae.","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"A category of aminoglycoside N-acetyltransferase enzymes with modification regiospecificity based at the 6'-amino group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics through acetylation of the 6-amino group of the compound.","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"46133":{"category_aro_accession":"3007382","category_aro_cvterm_id":"46133","category_aro_name":"gentamicin","category_aro_description":"Gentamicin is a commonly used aminoglycoside antibiotic derived from members of the Micromonospora genus of bacteria. It acts by binding the 30S ribosomal subunit, thus inhibiting protein synthesis. Gentamicin is typically used to treat Gram-negative infections of the repiratory and urinary tract, as well as infections of the bone and soft tissue. It also exhibits considerable nephrotoxicity and ototoxicity. Gentamicin is administered as a mixture of gentamicin type C (which makes about around 80% of the complex) and types A, B, and X (distributed in the remaining 20% of the complex).","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1094":{"model_id":"1094","model_name":"CARB-17","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"862":{"protein_sequence":{"accession":"AIL92326.1","sequence":"MKKLFLLVGLMVCSTVSYASKLNEDISLIEKQTSGRIGVSVWDTQTDERWDYRGDERFPLMSTFKTLACATMLSDMDSGKLNKNATARIDERNIVVWSPVMDKLTGQSTRIEHACEAAMLMSDNTAANLVLNEIGGPKAVTLFLRSIGDKATRLDRLEPRLNEAKPGDKRDTTTPNAMVNTLHTLMEDNALSYESRTQLKIWMQDNKVSDSLMRSVLPKGWSIADRSGAGNYGSRGISAMIWKDNYKPVYISIYVTDTDLSLQARDQLIAQISQLILEHYKES"},"dna_sequence":{"accession":"KJ934265.1","fmin":"0","fmax":"852","strand":"+","sequence":"ATGAAAAAGTTATTCCTGTTGGTTGGGCTGATGGTTTGCTCAACTGTTAGTTACGCCTCCAAATTAAACGAAGACATCTCCCTCATCGAGAAACAAACATCTGGGCGAATTGGAGTGTCAGTCTGGGATACACAAACGGACGAGCGTTGGGATTATCGCGGAGACGAACGCTTCCCATTAATGAGCACATTCAAAACGTTAGCGTGTGCCACCATGCTAAGCGACATGGACAGCGGCAAACTCAACAAAAATGCCACAGCGAGAATCGATGAACGCAATATTGTGGTTTGGTCTCCGGTGATGGATAAACTGACTGGACAAAGCACACGTATCGAACACGCTTGTGAAGCCGCCATGTTGATGAGCGACAACACCGCCGCGAACTTAGTGCTAAATGAAATTGGTGGTCCTAAAGCGGTCACACTGTTTTTGCGCTCTATTGGCGACAAAGCAACGCGACTTGACCGATTGGAACCCCGTTTGAATGAAGCAAAACCGGGCGACAAGCGAGATACCACAACGCCTAACGCCATGGTAAACACCCTACATACCTTGATGGAAGATAACGCCCTATCTTACGAGTCACGCACACAGCTGAAAATCTGGATGCAAGACAACAAAGTATCGGATTCGCTCATGCGCTCTGTTCTGCCAAAAGGCTGGTCGATTGCAGACCGCTCTGGCGCAGGTAACTACGGTTCACGCGGCATTAGCGCGATGATCTGGAAAGACAACTACAAGCCAGTTTACATCAGTATTTACGTCACAGACACCGACCTTTCGCTTCAAGCTCGCGATCAACTGATCGCGCAAATCAGCCAACTGATTTTAGAGCACTACAAAGAAAGTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39615","NCBI_taxonomy_name":"Vibrio parahaemolyticus","NCBI_taxonomy_id":"670"}}}},"ARO_accession":"3002254","ARO_id":"38654","ARO_name":"CARB-17","CARD_short_name":"CARB-17","ARO_description":"CARB-17 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36230":{"category_aro_accession":"3000091","category_aro_cvterm_id":"36230","category_aro_name":"CARB beta-lactamase","category_aro_description":"CARB beta-lactamases are class A lactamases that can hydrolyze carbenicillin. Many of the PSE beta-lactamases have been renamed as CARB-lactamases with the notable exception of PSE-2 which is now OXA-10.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1095":{"model_id":"1095","model_name":"SHV-59","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1791":{"protein_sequence":{"accession":"AAV66328.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSVANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTLASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AY790341.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACCCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGTCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATCGTGGTGATTTATCTGCGGGATACGCTGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001114","ARO_id":"37494","ARO_name":"SHV-59","CARD_short_name":"SHV-59","ARO_description":"SHV-59 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1096":{"model_id":"1096","model_name":"TEM-79","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"851":{"protein_sequence":{"accession":"AAF05611.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSGGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AF190692.1","fmin":"208","fmax":"1069","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTGGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000946","ARO_id":"37326","ARO_name":"TEM-79","CARD_short_name":"TEM-79","ARO_description":"TEM-79 is an inhibitor-resistant beta-lactamase found in E. coli.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1097":{"model_id":"1097","model_name":"Erm(38)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"4238":{"protein_sequence":{"accession":"AAN86837.2","sequence":"MSTPHHGRHELGQNFLSDRRVIADIVEIVSRTNGPIIEIGAGDGALTIPLQRLARPLTAVEVDARRARRLAQRTARSAPGPASRPTEVVAADFLRYPLPRSPHVVVGNLPFHLTTAILRRLLHGPGWTTAVLLMQWEVARRRAAVGGATMMTAQWWPWFEFGLARKVSAASFTPRPAVDAGLLTITRRSRPLVDVADRARYQALVHRVFTGRGHGMAQILQRLPTPVPRTWLRANGIAPNSLPRQLSAAQWAALFEQTRLTGAQRVDRPRDVQHGRAHRRRGGEVDRPATHHKQTGPVVGQRQPQRGRDADADPDDQRTAPPVTRHHQGERRDEDQADHQDRPLTGEHLAGEFLWRHASFDSSASTTLVSRKARVNGPTPPGLGDT"},"dna_sequence":{"accession":"AY154657.2","fmin":"62","fmax":"1223","strand":"+","sequence":"GTGTCCACACCACATCACGGCCGGCACGAGCTCGGCCAGAACTTCCTGTCCGATCGGCGCGTCATCGCCGATATCGTCGAAATCGTCTCGCGCACAAACGGTCCGATCATCGAGATCGGGGCGGGCGACGGCGCGCTGACCATACCCTTGCAACGACTCGCCCGCCCGCTCACCGCCGTCGAGGTCGACGCGCGGCGCGCGCGGCGGTTGGCGCAGCGCACCGCGAGATCCGCCCCGGGGCCTGCCTCGCGGCCCACCGAGGTCGTCGCCGCCGACTTCCTGCGCTACCCACTGCCCCGCTCACCCCACGTGGTCGTGGGCAACCTGCCGTTCCACCTCACCACCGCGATCCTGCGGCGACTGCTGCACGGTCCGGGCTGGACCACGGCCGTGCTGCTCATGCAGTGGGAGGTGGCCCGCCGACGCGCCGCGGTGGGCGGCGCCACCATGATGACCGCCCAGTGGTGGCCGTGGTTCGAATTCGGCCTTGCCCGAAAGGTTTCCGCGGCGAGCTTCACGCCGCGGCCCGCGGTCGACGCCGGACTGCTCACCATCACGCGCCGCAGCCGGCCGCTGGTCGACGTCGCGGACCGGGCGCGTTACCAGGCGCTGGTGCACCGCGTGTTCACCGGACGCGGACACGGCATGGCGCAGATCCTGCAACGGTTGCCCACGCCGGTGCCCCGCACTTGGTTGCGGGCCAACGGGATAGCACCGAACTCCCTGCCCCGCCAGTTGTCCGCGGCGCAGTGGGCGGCGCTGTTCGAGCAGACGCGTCTAACTGGTGCCCAACGGGTCGATCGTCCACGCGATGTACAGCACGGCCGCGCTCACCGTCGCCGTGGTGGCGAAGTCGATCGCCCGGCTACGCACCACAAGCAGACCGGCCCGGTCGTCGGTCAGCGCCAACCGCAGCGCGGCCGCGACGCCGACGCCGATCCCGATGACCAGCGCACCGCGCCGCCAGTAACCCGCCACCACCAGGGCGAACGCCGCGATGAAGATCAGGCCGACCACCAGGATCGGCCATTGACCGGCGAACACCTTGCGGGCGAATTCCTTTGGCGTCACGCCAGTTTCGACTCTTCGGCTTCGACGACGTTGGTCAGCAGGAAGGCGCGGGTCAACGGGCCCACGCCACCGGGGTTGGGCGACACGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36871","NCBI_taxonomy_name":"Mycolicibacterium smegmatis","NCBI_taxonomy_id":"1772"}}}},"ARO_accession":"3000601","ARO_id":"36740","ARO_name":"Erm(38)","CARD_short_name":"Erm(38)","ARO_description":"ErmD confers MLSb phenotype.","ARO_category":{"36699":{"category_aro_accession":"3000560","category_aro_cvterm_id":"36699","category_aro_name":"Erm 23S ribosomal RNA methyltransferase","category_aro_description":"Erm proteins are part of the RNA methyltransferase family and methylate A2058 (E. coli nomenclature) of the 23S ribosomal RNA conferring degrees of resistance to Macrolides, Lincosamides and Streptogramin b. This is called the MLSb phenotype.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35946":{"category_aro_accession":"0000027","category_aro_cvterm_id":"35946","category_aro_name":"roxithromycin","category_aro_description":"Roxithromycin is a semi-synthetic, 14-carbon ring macrolide antibiotic derived from erythromycin. It is used to treat respiratory tract, urinary and soft tissue infections. Roxithromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35974":{"category_aro_accession":"0000057","category_aro_cvterm_id":"35974","category_aro_name":"telithromycin","category_aro_description":"Telithromycin is a semi-synthetic derivative of erythromycin. It is a 14-membered macrolide and is the first ketolide antibiotic to be used in clinics. Telithromycin binds the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"35982":{"category_aro_accession":"0000065","category_aro_cvterm_id":"35982","category_aro_name":"clarithromycin","category_aro_description":"Clarithromycin is a methyl derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome and is used to treat pharyngitis, tonsillitis, acute maxillary sinusitis, acute bacterial exacerbation of chronic bronchitis, pneumonia (especially atypical pneumonias associated with Chlamydia pneumoniae or TWAR), and skin structure infections.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"36284":{"category_aro_accession":"3000145","category_aro_cvterm_id":"36284","category_aro_name":"tylosin","category_aro_description":"Tylosin is a 16-membered macrolide, naturally produced by Streptomyces fradiae. It interacts with the bacterial ribosome 50S subunit to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"36295":{"category_aro_accession":"3000156","category_aro_cvterm_id":"36295","category_aro_name":"spiramycin","category_aro_description":"Spiramycin is a 16-membered macrolide and is natural product produced by Streptomyces ambofaciens. It binds to the 50S subunit of bacterial ribosomes and inhibits peptidyl transfer activity to disrupt protein synthesis.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"36315":{"category_aro_accession":"3000176","category_aro_cvterm_id":"36315","category_aro_name":"dirithromycin","category_aro_description":"Dirithromycin is an oxazine derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome to inhibit bacterial protein synthesis.","category_aro_class_name":"Antibiotic"},"36722":{"category_aro_accession":"3000583","category_aro_cvterm_id":"36722","category_aro_name":"pristinamycin IA","category_aro_description":"Pristinamycin IA is a type B streptogramin antibiotic produced by Streptomyces pristinaespiralis. It binds to the P site of the 50S subunit of the bacterial ribosome, preventing the extension of protein chains.","category_aro_class_name":"Antibiotic"},"36723":{"category_aro_accession":"3000584","category_aro_cvterm_id":"36723","category_aro_name":"quinupristin","category_aro_description":"Quinupristin is a type B streptogramin and a semisynthetic derivative of pristinamycin 1A. It is a component of the drug Synercid and interacts with the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"virginiamycin M1","category_aro_description":"Virginiamycin M1 is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37016":{"category_aro_accession":"3000672","category_aro_cvterm_id":"37016","category_aro_name":"madumycin II","category_aro_description":"Madumycin II is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37017":{"category_aro_accession":"3000673","category_aro_cvterm_id":"37017","category_aro_name":"griseoviridin","category_aro_description":"Griseoviridin is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"37019":{"category_aro_accession":"3000675","category_aro_cvterm_id":"37019","category_aro_name":"pristinamycin IB","category_aro_description":"Pristinamycin IB is a class B streptogramin similar to pristinamycin IA, the former containing a N-methyl-4-(methylamino)phenylalanine instead of a N-methyl-4-(dimethylamino)phenylalanine in its class A streptogramin counterpart (one less methyl group).","category_aro_class_name":"Antibiotic"},"37021":{"category_aro_accession":"3000677","category_aro_cvterm_id":"37021","category_aro_name":"virginiamycin S2","category_aro_description":"Virginiamycin S2 is a streptogramin B antibiotic.","category_aro_class_name":"Antibiotic"},"37022":{"category_aro_accession":"3000678","category_aro_cvterm_id":"37022","category_aro_name":"pristinamycin IC","category_aro_description":"Pristinamycin IC is a class B streptogramin derived from virginiamycin S1.","category_aro_class_name":"Antibiotic"},"37023":{"category_aro_accession":"3000679","category_aro_cvterm_id":"37023","category_aro_name":"vernamycin C","category_aro_description":"Vernamycin C is a streptogramin B antibiotic.","category_aro_class_name":"Antibiotic"},"37024":{"category_aro_accession":"3000680","category_aro_cvterm_id":"37024","category_aro_name":"patricin A","category_aro_description":"Patricin A is a streptogramin B antibiotic.","category_aro_class_name":"Antibiotic"},"37025":{"category_aro_accession":"3000681","category_aro_cvterm_id":"37025","category_aro_name":"patricin B","category_aro_description":"Patricin B is a streptogramin B antibiotic.","category_aro_class_name":"Antibiotic"},"37026":{"category_aro_accession":"3000682","category_aro_cvterm_id":"37026","category_aro_name":"ostreogrycin B3","category_aro_description":"Ostreogrycin B3 is a derivative of pristinamycin IA, with an additional 3-hydroxy group on its 4-oxopipecolic acid.","category_aro_class_name":"Antibiotic"},"37247":{"category_aro_accession":"3000867","category_aro_cvterm_id":"37247","category_aro_name":"oleandomycin","category_aro_description":"Oleandomycin is a 14-membered macrolide produced by Streptomyces antibioticus. It is ssimilar to erythromycin, and contains a desosamine amino sugar and an oleandrose sugar. It targets the 50S ribosomal subunit to prevent protein synthesis.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35952":{"category_aro_accession":"0000034","category_aro_cvterm_id":"35952","category_aro_name":"streptogramin A antibiotic","category_aro_description":"Streptogramin A antibiotics are cyclic polyketide peptide hybrids that bind to the ribosomal peptidyl transfer centre. Structural variation arises from substituting a proline for its desaturated derivative and by its substitution for Ala or Cys. Used alone, streptogramin A antibiotics are bacteriostatic, but is bactericidal when used with streptogramin B antibiotics.","category_aro_class_name":"Drug Class"},"35967":{"category_aro_accession":"0000050","category_aro_cvterm_id":"35967","category_aro_name":"streptogramin B antibiotic","category_aro_description":"Streptogramin B antibiotics are are cyclic hepta- or hexa-depsipeptides.  Type B streptogramins block the peptide exit tunnel of the 50S bacterial ribosome. The general composition of group B streptogramins is 3-hydroxypicolinic acid-L-Thr-D-aminobutyric acid (or D-Ala)-L-Pro-L-Phe (or 4-N-,N-(dimethylamino)-L-Phe)-X-L-phenylglycine. Used alone, streptogramin B antibiotics are bacteriostatic, but is bactericidal when used with streptogramin A antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1098":{"model_id":"1098","model_name":"vanB","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"350"}},"model_sequences":{"sequence":{"107":{"protein_sequence":{"accession":"AHH83938.1","sequence":"MNRIKVAIIFGGCSEEHDVSVKSAIEIAANIDTEKFDPHYIGITKNGVWKLCKKPCTEWEADSLPAILSPDRKTHGLLVMKESEYETRRIDVAFPVLHGKCGEDGAIQGLFVLSGIPYVGCDIQSSAACMDKSLAYILTKNAGIAVPEFQMIDKGDKPEAGALTYPVFVKPARSGSSFGVTKVNGTEELNAAIEAAGQYDGKILIEQAISGCEVGCAVMGNEDDLIVGEVDQIRLSHGIFRIHQENEPEKGSENAMITVPADIPVEERNRVQETAKKVYRVLGCRGLARVDLFLQEDGGIVLNEVNTLPGFTSYSRYPRMMAAAGITLPALIDSLITLALKR"},"dna_sequence":{"accession":"KF823969.1","fmin":"5110","fmax":"6139","strand":"+","sequence":"ATGAATAGAATAAAAGTCGCAATCATCTTCGGCGGTTGCTCGGAGGAACATGATGTGTCGGTAAAATCCGCAATAGAAATTGCTGCGAACATTGATACGGAAAAATTCGATCCGCACTACATCGGAATTACAAAAAACGGTGTATGGAAGCTATGCAAGAAGCCATGTACGGAATGGGAAGCCGACAGTCTCCCCGCCATACTCTCCCCGGATAGGAAAACGCATGGGCTGCTTGTCATGAAAGAAAGCGAATACGAAACACGGCGTATTGATGTGGCTTTCCCGGTTTTGCATGGCAAATGCGGGGAGGATGGTGCGATACAGGGGCTGTTTGTATTGTCTGGTATCCCCTATGTGGGCTGTGATATTCAAAGCTCCGCAGCTTGCATGGACAAATCACTGGCCTACATTCTTACAAAAAATGCGGGCATCGCCGTTCCCGAATTTCAAATGATTGATAAAGGTGACAAGCCGGAGGCGGGTGCGCTTACCTACCCTGTCTTTGTGAAGCCGGCACGGTCAGGTTCGTCCTTTGGCGTAACCAAAGTAAACGGTACGGAAGAACTTAACGCTGCGATAGAAGCGGCAGGACAATATGATGGAAAAATCTTAATTGAGCAAGCGATTTCGGGCTGTGAGGTCGGGTGTGCGGTCATGGGGAACGAGGATGATTTGATTGTCGGCGAAGTGGATCAAATCCGGCTGAGCCACGGTATCTTCCGCATCCATCAGGAAAACGAGCCGGAAAAAGGCTCAGAAAATGCGATGATTACAGTTCCCGCAGACATTCCGGTCGAGGAACGAAATCGGGTGCAGGAAACGGCAAAGAAAGTATATCGGGTGCTTGGATGCAGAGGGCTTGCCCGTGTTGATCTTTTTTTGCAGGAGGATGGCGGCATCGTTCTAAATGAGGTCAATACCCTGCCCGGTTTTACATCGTACAGCCGCTACCCACGTATGATGGCCGCCGCAGGAATCACGCTTCCTGCACTGATTGACAGCCTGATTACATTGGCGTTAAAGAGGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36779","NCBI_taxonomy_name":"Enterococcus faecium","NCBI_taxonomy_id":"1352"}}}},"ARO_accession":"3000013","ARO_id":"36022","ARO_name":"vanB","CARD_short_name":"vanB","ARO_description":"VanB is a D-Ala-D-Ala ligase homolog similar to VanA, and can synthesize D-Ala-D-Lac, an alternative substrate for peptidoglycan synthesis that reduces vancomycin binding affinity. It has been isolated from VREs. It is associated with vancomycin resistance, but not teicoplanin resistance.","ARO_category":{"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"39340":{"category_aro_accession":"3002906","category_aro_cvterm_id":"39340","category_aro_name":"Van ligase","category_aro_description":"Van ligases synthesize alternative substrates for peptidoglycan synthesis that reduce vancomycin binding affinity.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1099":{"model_id":"1099","model_name":"OXA-48","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8249":{"protein_sequence":{"accession":"AAP70012.1","sequence":"MRVLALSAVFLVASIIGMPAVAKEWQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGQTRDIATWNRDHNLITAMKYSVVPVYQEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISATEQISFLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYSTRIEPKIGWWVGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP"},"dna_sequence":{"accession":"AY236073.2","fmin":"2187","fmax":"2985","strand":"+","sequence":"ATGCGTGTATTAGCCTTATCGGCTGTGTTTTTGGTGGCATCGATTATCGGAATGCCTGCGGTAGCAAAGGAATGGCAAGAAAACAAAAGTTGGAATGCTCACTTTACTGAACATAAATCACAGGGCGTAGTTGTGCTCTGGAATGAGAATAAGCAGCAAGGATTTACCAATAATCTTAAACGGGCGAACCAAGCATTTTTACCCGCATCTACCTTTAAAATTCCCAATAGCTTGATCGCCCTCGATTTGGGCGTGGTTAAGGATGAACACCAAGTCTTTAAGTGGGATGGACAGACGCGCGATATCGCCACTTGGAATCGCGATCATAATCTAATCACCGCGATGAAATATTCAGTTGTGCCTGTTTATCAAGAATTTGCCCGCCAAATTGGCGAGGCACGTATGAGCAAGATGCTACATGCTTTCGATTATGGTAATGAGGACATTTCGGGCAATGTAGACAGTTTCTGGCTCGACGGTGGTATTCGAATTTCGGCCACGGAGCAAATCAGCTTTTTAAGAAAGCTGTATCACAATAAGTTACACGTATCGGAGCGCAGCCAGCGTATTGTCAAACAAGCCATGCTGACCGAAGCCAATGGTGACTATATTATTCGGGCTAAAACTGGATACTCGACTAGAATCGAACCTAAGATTGGCTGGTGGGTCGGTTGGGTTGAACTTGATGATAATGTGTGGTTTTTTGCGATGAATATGGATATGCCCACATCGGATGGTTTAGGGCTGCGCCAAGCCATCACAAAAGAAGTGCTCAAACAGGAAAAAATTATTCCCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001782","ARO_id":"38182","ARO_name":"OXA-48","CARD_short_name":"OXA-48","ARO_description":"OXA-48 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46510":{"category_aro_accession":"3007721","category_aro_cvterm_id":"46510","category_aro_name":"OXA-48-like beta-lactamase","category_aro_description":"OXA-48-type beta-lactamases are now routinely encountered in bacterial infections caused by carbapenam-resistant Enterobacterales. OXA-48-like proteins confer resistance to penicillin (which is efficiently hydrolyzed) and carbapenam antibiotics (which is more slowly broken down). The spectrum of activity of these variants varies, with some hydrolyzing expanded-spectrum oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"40522":{"category_aro_accession":"3003831","category_aro_cvterm_id":"40522","category_aro_name":"temocillin","category_aro_description":"Temocillin is a beta-lactamase resistant carboxypenicillin. It is primarily used for the treatment of multiple drug resistant, Gram-negative bacteria, specifically Enterobacteriaceae.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1100":{"model_id":"1100","model_name":"OXA-245","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"805":{"protein_sequence":{"accession":"AGC60013.1","sequence":"MRVLALSAVFLVASIIGMPAVAKEWQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGQTRDIATWNRDHNLITAMKYSVVPVYQYFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISATEQISFLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYSTRIEPKIGWWVGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP"},"dna_sequence":{"accession":"JX438001.1","fmin":"0","fmax":"798","strand":"+","sequence":"ATGCGTGTATTAGCCTTATCGGCTGTGTTTTTGGTGGCATCGATTATCGGAATGCCTGCGGTAGCAAAGGAATGGCAAGAAAACAAAAGTTGGAATGCTCACTTTACTGAACATAAATCACAGGGCGTAGTTGTGCTCTGGAATGAGAATAAGCAGCAAGGATTTACCAATAATCTTAAACGGGCGAACCAAGCATTTTTACCCGCATCTACCTTTAAAATTCCCAATAGCTTGATCGCCCTCGATTTGGGCGTGGTTAAGGATGAACACCAAGTCTTTAAGTGGGATGGACAGACGCGCGATATCGCCACTTGGAATCGCGATCATAATCTAATCACCGCGATGAAATATTCAGTTGTGCCTGTTTATCAATACTTTGCCCGCCAAATTGGCGAGGCACGTATGAGCAAGATGCTACATGCTTTCGATTATGGTAATGAGGACATTTCGGGCAATGTAGACAGTTTCTGGCTCGACGGTGGTATTCGAATTTCGGCCACGGAGCAAATCAGCTTTTTAAGAAAGCTGTATCACAATAAGTTACACGTATCGGAGCGCAGCCAGCGTATTGTCAAACAAGCCATGCTGACCGAAGCCAATGGTGACTATATTATTCGGGCTAAAACTGGATACTCGACTAGAATCGAACCTAAGATTGGCTGGTGGGTCGGTTGGGTTGAACTTGATGATAATGTGTGGTTTTTTGCGATGAATATGGATATGCCCACATCGGATGGTTTAGGGCTGCGCCAAGCCATCACAAAAGAAGTGCTCAAACAGGAAAAAATTATTCCCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001787","ARO_id":"38187","ARO_name":"OXA-245","CARD_short_name":"OXA-245","ARO_description":"OXA-245 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46510":{"category_aro_accession":"3007721","category_aro_cvterm_id":"46510","category_aro_name":"OXA-48-like beta-lactamase","category_aro_description":"OXA-48-type beta-lactamases are now routinely encountered in bacterial infections caused by carbapenam-resistant Enterobacterales. OXA-48-like proteins confer resistance to penicillin (which is efficiently hydrolyzed) and carbapenam antibiotics (which is more slowly broken down). The spectrum of activity of these variants varies, with some hydrolyzing expanded-spectrum oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1101":{"model_id":"1101","model_name":"CTX-M-21","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1255":{"protein_sequence":{"accession":"CAD08929.1","sequence":"MVTKRVQRMMFAGGAGIPLLLGSAPFYAQTSAGQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"AJ416346.1","fmin":"556","fmax":"1432","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGGGGGGGCGGGCATTCCGCTGCTGTTGGGCAGCGCGCCGTTTTATGCGCAGACGAGTGCGGGGCAGCAAAAGCTGGCGGCGCTGGAAAAAAGCAGCGGAGGGCGGTTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGACTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001883","ARO_id":"38283","ARO_name":"CTX-M-21","CARD_short_name":"CTX-M-21","ARO_description":"CTX-M-21 is a beta-lactamase found in the Enterobacteriaceae family.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1102":{"model_id":"1102","model_name":"QnrB29","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"235":{"protein_sequence":{"accession":"ADM52193.1","sequence":"MTPLLYKKTGTNMALALVGEKIDRNRFTGEKIENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMVDFRNASALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGAQVLGATFSGSDLSGGEFSTFDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDNYQASLLMERLGIAVIG"},"dna_sequence":{"accession":"HM439649.1","fmin":"0","fmax":"681","strand":"+","sequence":"ATGACGCCATTACTGTATAAAAAAACAGGTACAAATATGGCACTGGCACTCGTTGGCGAAAAAATTGACAGAAACCGCTTCACCGGTGAGAAAATTGAAAATAGTACATTTTTTAACTGTGATTTTTCAGGTGCCGACCTGAGCGGCACTGAATTTATCGGCTGTCAGTTCTATGATCGTGAAAGCCAGAAAGGGTGCAATTTTAGTCGTGCGATGCTGAAAGATGCCATTTTTAAAAGCTGTGATTTATCCATGGTGGATTTTCGCAATGCCAGTGCGCTTGGCATTGAAATTCGCCACTGTCGTGCGCAAGGCGCAGATTTCCGCGGCGCAAGCTTTATGAATATGATCACTACTCGCACCTGGTTTTGCAGCGCATATATCACTAACACAAATCTAAGCTACGCCAATTTTTCGAAAGTCGTGCTGGAAAAATGTGAGCTGTGGGAAAACCGTTGGATGGGTGCCCAGGTACTGGGCGCGACGTTCAGTGGTTCAGATCTTTCCGGCGGCGAGTTTTCGACTTTCGACTGGCGAGCAGCAAACTTCACACATTGCGATCTGACCAATTCGGAGTTGGGTGACTTAGATATTCGGGGCGTTGATTTACAAGGCGTTAAGTTGGACAACTACCAGGCATCGTTGCTCATGGAACGTCTTGGCATCGCGGTGATTGGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002744","ARO_id":"39178","ARO_name":"QnrB29","CARD_short_name":"QnrB29","ARO_description":"QnrB29 is a plasmid-mediated quinolone resistance protein found in Citrobacter freundii.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1103":{"model_id":"1103","model_name":"CMY-17","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1895":{"protein_sequence":{"accession":"AAS13399.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVAFAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"AY513266.1","fmin":"164","fmax":"1310","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTTGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002028","ARO_id":"38428","ARO_name":"CMY-17","CARD_short_name":"CMY-17","ARO_description":"CMY-17 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1104":{"model_id":"1104","model_name":"acrB","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1900"}},"model_sequences":{"sequence":{"5485":{"protein_sequence":{"accession":"AAC73564.1","sequence":"MPNFFIDRPIFAWVIAIIIMLAGGLAILKLPVAQYPTIAPPAVTISASYPGADAKTVQDTVTQVIEQNMNGIDNLMYMSSNSDSTGTVQITLTFESGTDADIAQVQVQNKLQLAMPLLPQEVQQQGVSVEKSSSSFLMVVGVINTDGTMTQEDISDYVAANMKDAISRTSGVGDVQLFGSQYAMRIWMNPNELNKFQLTPVDVITAIKAQNAQVAAGQLGGTPPVKGQQLNASIIAQTRLTSTEEFGKILLKVNQDGSRVLLRDVAKIELGGENYDIIAEFNGQPASGLGIKLATGANALDTAAAIRAELAKMEPFFPSGLKIVYPYDTTPFVKISIHEVVKTLVEAIILVFLVMYLFLQNFRATLIPTIAVPVVLLGTFAVLAAFGFSINTLTMFGMVLAIGLLVDDAIVVVENVERVMAEEGLPPKEATRKSMGQIQGALVGIAMVLSAVFVPMAFFGGSTGAIYRQFSITIVSAMALSVLVALILTPALCATMLKPIAKGDHGEGKKGFFGWFNRMFEKSTHHYTDSVGGILRSTGRYLVLYLIIVVGMAYLFVRLPSSFLPDEDQGVFMTMVQLPAGATQERTQKVLNEVTHYYLTKEKNNVESVFAVNGFGFAGRGQNTGIAFVSLKDWADRPGEENKVEAITMRATRAFSQIKDAMVFAFNLPAIVELGTATGFDFELIDQAGLGHEKLTQARNQLLAEAAKHPDMLTSVRPNGLEDTPQFKIDIDQEKAQALGVSINDINTTLGAAWGGSYVNDFIDRGRVKKVYVMSEAKYRMLPDDIGDWYVRAADGQMVPFSAFSSSRWEYGSPRLERYNGLPSMEILGQAAPGKSTGEAMELMEQLASKLPTGVGYDWTGMSYQERLSGNQAPSLYAISLIVVFLCLAALYESWSIPFSVMLVVPLGVIGALLAATFRGLTNDVYFQVGLLTTIGLSAKNAILIVEFAKDLMDKEGKGLIEATLDAVRMRLRPILMTSLAFILGVMPLVISTGAGSGAQNAVGTGVMGGMVTATVLAIFFVPVFFVVVRRRFSRKNEDIEHSHTVDHH"},"dna_sequence":{"accession":"U00096.3","fmin":"481253","fmax":"484403","strand":"-","sequence":"ATGCCTAATTTCTTTATCGATCGCCCGATTTTTGCGTGGGTGATCGCCATTATCATCATGTTGGCAGGGGGGCTGGCGATCCTCAAACTGCCGGTGGCGCAATATCCTACGATTGCACCGCCGGCAGTAACGATCTCCGCCTCCTACCCCGGCGCTGATGCGAAAACAGTGCAGGACACGGTGACACAGGTTATCGAACAGAATATGAACGGTATCGATAACCTGATGTACATGTCCTCTAACAGTGACTCCACGGGTACCGTGCAGATCACCCTGACCTTTGAGTCTGGTACTGATGCGGATATCGCGCAGGTTCAGGTGCAGAACAAACTGCAGCTGGCGATGCCGTTGCTGCCGCAAGAAGTTCAGCAGCAAGGGGTGAGCGTTGAGAAATCATCCAGCAGCTTCCTGATGGTTGTCGGCGTTATCAACACCGATGGCACCATGACGCAGGAGGATATCTCCGACTACGTGGCGGCGAATATGAAAGATGCCATCAGCCGTACGTCGGGCGTGGGTGATGTTCAGTTGTTCGGTTCACAGTACGCGATGCGTATCTGGATGAACCCGAATGAGCTGAACAAATTCCAGCTAACGCCGGTTGATGTCATTACCGCCATCAAAGCGCAGAACGCCCAGGTTGCGGCGGGTCAGCTCGGTGGTACGCCGCCGGTGAAAGGCCAACAGCTTAACGCCTCTATTATTGCTCAGACGCGTCTGACCTCTACTGAAGAGTTCGGCAAAATCCTGCTGAAAGTGAATCAGGATGGTTCCCGCGTGCTGCTGCGTGACGTCGCGAAGATTGAGCTGGGTGGTGAGAACTACGACATCATCGCAGAGTTTAACGGCCAACCGGCTTCCGGTCTGGGGATCAAGCTGGCGACCGGTGCAAACGCGCTGGATACCGCTGCGGCAATCCGTGCTGAACTGGCGAAGATGGAACCGTTCTTCCCGTCGGGTCTGAAAATTGTTTACCCATACGACACCACGCCGTTCGTGAAAATCTCTATTCACGAAGTGGTTAAAACGCTGGTCGAAGCGATCATCCTCGTGTTCCTGGTTATGTATCTGTTCCTGCAGAACTTCCGCGCGACGTTGATTCCGACCATTGCCGTACCGGTGGTATTGCTCGGGACCTTTGCCGTCCTTGCCGCCTTTGGCTTCTCGATAAACACGCTAACAATGTTCGGGATGGTGCTCGCCATCGGCCTGTTGGTGGATGACGCCATCGTTGTGGTAGAAAACGTTGAGCGTGTTATGGCGGAAGAAGGTTTGCCGCCAAAAGAAGCTACCCGTAAGTCGATGGGGCAGATTCAGGGCGCTCTGGTCGGTATCGCGATGGTACTGTCGGCGGTATTCGTACCGATGGCCTTCTTTGGCGGTTCTACTGGTGCTATCTATCGTCAGTTCTCTATTACCATTGTTTCAGCAATGGCGCTGTCGGTACTGGTGGCGTTGATCCTGACTCCAGCTCTTTGTGCCACCATGCTGAAACCGATTGCCAAAGGCGATCACGGGGAAGGTAAAAAAGGCTTCTTCGGCTGGTTTAACCGCATGTTCGAGAAGAGCACGCACCACTACACCGACAGCGTAGGCGGTATTCTGCGCAGTACGGGGCGTTACCTGGTGCTGTATCTGATCATCGTGGTCGGCATGGCCTATCTGTTCGTGCGTCTGCCAAGCTCCTTCTTGCCAGATGAGGACCAGGGCGTGTTTATGACCATGGTTCAGCTGCCAGCAGGTGCAACGCAGGAACGTACACAGAAAGTGCTCAATGAGGTAACGCATTACTATCTGACCAAAGAAAAGAACAACGTTGAGTCGGTGTTCGCCGTTAACGGCTTCGGCTTTGCGGGACGTGGTCAGAATACCGGTATTGCGTTCGTTTCCTTGAAGGACTGGGCCGATCGTCCGGGCGAAGAAAACAAAGTTGAAGCGATTACCATGCGTGCAACACGCGCTTTCTCGCAAATCAAAGATGCGATGGTTTTCGCCTTTAACCTGCCCGCAATCGTGGAACTGGGTACTGCAACCGGCTTTGACTTTGAGCTGATTGACCAGGCTGGCCTTGGTCACGAAAAACTGACTCAGGCGCGTAACCAGTTGCTTGCAGAAGCAGCGAAGCACCCTGATATGTTGACCAGCGTACGTCCAAACGGTCTGGAAGATACCCCGCAGTTTAAGATTGATATCGACCAGGAAAAAGCGCAGGCGCTGGGTGTTTCTATCAACGACATTAACACCACTCTGGGCGCTGCATGGGGCGGCAGCTATGTGAACGACTTTATCGACCGCGGTCGTGTGAAGAAAGTTTATGTCATGTCAGAAGCGAAATACCGTATGCTGCCGGATGATATCGGCGACTGGTATGTTCGTGCTGCTGATGGTCAGATGGTGCCATTCTCGGCGTTCTCCTCTTCTCGTTGGGAGTACGGTTCGCCGCGTCTGGAACGTTACAACGGCCTGCCATCCATGGAAATCTTAGGCCAGGCGGCACCGGGTAAAAGTACCGGTGAAGCAATGGAGCTGATGGAACAACTGGCGAGCAAACTGCCTACCGGTGTTGGCTATGACTGGACGGGGATGTCCTATCAGGAACGTCTCTCCGGCAACCAGGCACCTTCACTGTACGCGATTTCGTTGATTGTCGTGTTCCTGTGTCTGGCGGCGCTGTACGAGAGCTGGTCGATTCCGTTCTCCGTTATGCTGGTCGTTCCGCTGGGGGTTATCGGTGCGTTGCTGGCTGCCACCTTCCGTGGCCTGACCAATGACGTTTACTTCCAGGTAGGCCTGCTCACAACCATTGGGTTGTCGGCGAAGAACGCGATCCTTATCGTCGAATTCGCCAAAGACTTGATGGATAAAGAAGGTAAAGGTCTGATTGAAGCGACGCTTGATGCGGTGCGGATGCGTTTACGTCCGATCCTGATGACCTCGCTGGCGTTTATCCTCGGCGTTATGCCGCTGGTTATCAGTACTGGTGCTGGTTCCGGCGCGCAGAACGCAGTAGGTACCGGTGTAATGGGCGGGATGGTGACCGCAACGGTACTGGCAATCTTCTTCGTTCCGGTATTCTTTGTGGTGGTTCGCCGCCGCTTTAGCCGCAAGAATGAAGATATCGAGCACAGCCATACTGTCGATCATCATTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36849","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. MG1655","NCBI_taxonomy_id":"511145"}}}},"ARO_accession":"3000216","ARO_id":"36355","ARO_name":"acrB","CARD_short_name":"acrB","ARO_description":"Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug\/proton antiporter.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35963":{"category_aro_accession":"0000045","category_aro_cvterm_id":"35963","category_aro_name":"acriflavine","category_aro_description":"Acriflavine is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"37084":{"category_aro_accession":"3000704","category_aro_cvterm_id":"37084","category_aro_name":"cefalotin","category_aro_description":"Cefalotin is a semisynthetic cephalosporin antibiotic activate against staphylococci. It is resistant to staphylococci beta-lactamases but hydrolyzed by enterobacterial beta-lactamases.","category_aro_class_name":"Antibiotic"},"37250":{"category_aro_accession":"3000870","category_aro_cvterm_id":"37250","category_aro_name":"triclosan","category_aro_description":"Triclosan is a common antibacterial agent added to many consumer products as a biocide.  It is an inhibitor of fatty acid biosynthesis by blocking enoyl-carrier protein reductase (FabI).","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"43746":{"category_aro_accession":"3005386","category_aro_cvterm_id":"43746","category_aro_name":"disinfecting agents and antiseptics","category_aro_description":"Disinfectants that can also interact with antimicrobial resistance mechanisms, e.g. molecule efflux, and thus are the targets of disinfectant resistance.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1105":{"model_id":"1105","model_name":"AAC(3)-VIa","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"659":{"protein_sequence":{"accession":"AAA16194.1","sequence":"MTDPRKNGDLHEPATAPATPWSKSELVRQLRDLGVRSGDMVMPHVSLRAVGPLADGPQTLVDALIEAVGPTGNILAFVSWRDSPYEQTLGHDAPPAAIAQSWPAFDPDHAPAYPGFGAINEFIRTYPGCRRTAHPDASMAAIGPDAAWLVAPHEMGAAYGPRSPIARFLAHAGKILSIGAGPDAVTALHYAEAVARIEGKRRVTYSMPLLREGKRVWVTTSDWDSNGILDEYAAPDGPDAVERIARDYLARTRVAQGPVGGAQSRLIDAADIVSFGIEWLEARHAAPAAAALKPKQRRD"},"dna_sequence":{"accession":"M88012.1","fmin":"192","fmax":"1092","strand":"+","sequence":"ATGACTGATCCCCGCAAAAACGGCGATTTGCACGAACCCGCGACGGCACCCGCGACGCCCTGGTCCAAAAGCGAGCTGGTCCGGCAATTGCGCGACCTCGGCGTGCGCTCAGGCGATATGGTGATGCCGCATGTGTCGTTGCGCGCCGTCGGGCCGCTGGCGGACGGACCGCAGACACTTGTCGATGCGCTGATCGAGGCCGTCGGCCCCACCGGGAATATTCTCGCCTTCGTCTCGTGGCGCGATTCGCCCTATGAACAGACGCTGGGTCATGATGCGCCGCCCGCCGCCATCGCCCAAAGCTGGCCTGCGTTCGACCCCGACCATGCGCCCGCCTACCCCGGCTTTGGCGCGATCAACGAATTTATCCGAACCTATCCGGGGTGTCGGCGCACGGCCCATCCCGACGCATCGATGGCGGCGATCGGGCCCGATGCGGCGTGGCTGGTGGCGCCGCACGAGATGGGCGCCGCTTATGGCCCCCGCTCGCCGATCGCGCGTTTTCTCGCCCACGCAGGAAAAATCCTGTCGATCGGCGCCGGGCCCGATGCAGTCACCGCGCTCCATTATGCCGAAGCGGTGGCGCGGATCGAGGGCAAGCGCCGCGTCACTTATTCGATGCCCTTACTGCGCGAAGGCAAGCGCGTCTGGGTCACCACGTCCGACTGGGATTCGAACGGCATCCTCGACGAATATGCCGCGCCCGACGGCCCCGACGCGGTCGAACGGATCGCCCGCGACTATCTCGCCCGCACCAGGGTTGCGCAAGGCCCGGTCGGCGGCGCGCAATCCCGGCTGATCGACGCGGCCGATATCGTTTCCTTCGGCATCGAATGGCTCGAGGCGCGCCACGCCGCGCCAGCGGCGGCAGCGCTGAAGCCGAAACAACGCCGCGACTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3002540","ARO_id":"38940","ARO_name":"AAC(3)-VIa","CARD_short_name":"AAC(3)-VIa","ARO_description":"AAC(3)-VIa is a plasmid-encoded aminoglycoside acetyltransferase in E. cloacae, S. enterica and E. coli.","ARO_category":{"36461":{"category_aro_accession":"3000322","category_aro_cvterm_id":"36461","category_aro_name":"AAC(3)","category_aro_description":"A category of aminoglycoside N-acetyltransferase enzymes with modification regiospecificity based at the 3-amino group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics through acetylation of the 3-amino group of the compound.","category_aro_class_name":"AMR Gene Family"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"46127":{"category_aro_accession":"3007377","category_aro_cvterm_id":"46127","category_aro_name":"6'-N-ethylnetilmicin","category_aro_description":"6'-N-ethylnetilmicin is an aminoglycoside antibiotic and a derivative of netilmicin.","category_aro_class_name":"Antibiotic"},"46133":{"category_aro_accession":"3007382","category_aro_cvterm_id":"46133","category_aro_name":"gentamicin","category_aro_description":"Gentamicin is a commonly used aminoglycoside antibiotic derived from members of the Micromonospora genus of bacteria. It acts by binding the 30S ribosomal subunit, thus inhibiting protein synthesis. Gentamicin is typically used to treat Gram-negative infections of the repiratory and urinary tract, as well as infections of the bone and soft tissue. It also exhibits considerable nephrotoxicity and ototoxicity. Gentamicin is administered as a mixture of gentamicin type C (which makes about around 80% of the complex) and types A, B, and X (distributed in the remaining 20% of the complex).","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1106":{"model_id":"1106","model_name":"NDM-5","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1025":{"protein_sequence":{"accession":"AEN03071.1","sequence":"MELPNIMHPVAKLSTALAAALMLSGCMPGEIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLLVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGLVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR"},"dna_sequence":{"accession":"JN104597.1","fmin":"114","fmax":"927","strand":"+","sequence":"ATGGAATTGCCCAATATTATGCACCCGGTCGCGAAGCTGAGCACCGCATTAGCCGCTGCATTGATGCTGAGCGGGTGCATGCCCGGTGAAATCCGCCCGACGATTGGCCAGCAAATGGAAACTGGCGACCAACGGTTTGGCGATCTGGTTTTCCGCCAGCTCGCACCGAATGTCTGGCAGCACACTTCCTATCTCGACATGCCGGGTTTCGGGGCAGTCGCTTCCAACGGTTTGATCGTCAGGGATGGCGGCCGCGTGCTGTTGGTCGATACCGCCTGGACCGATGACCAGACCGCCCAGATCCTCAACTGGATCAAGCAGGAGATCAACCTGCCGGTCGCGCTGGCGGTGGTGACTCACGCGCATCAGGACAAGATGGGCGGTATGGACGCGCTGCATGCGGCGGGGATTGCGACTTATGCCAATGCGTTGTCGAACCAGCTTGCCCCGCAAGAGGGGCTGGTTGCGGCGCAACACAGCCTGACTTTCGCCGCCAATGGCTGGGTCGAACCAGCAACCGCGCCCAACTTTGGCCCGCTCAAGGTATTTTACCCCGGCCCCGGCCACACCAGTGACAATATCACCGTTGGGATCGACGGCACCGACATCGCTTTTGGTGGCTGCCTGATCAAGGACAGCAAGGCCAAGTCGCTCGGCAATCTCGGTGATGCCGACACTGAGCACTACGCCGCGTCAGCGCGCGCGTTTGGTGCGGCGTTCCCCAAGGCCAGCATGATCGTGATGAGCCATTCCGCCCCCGATAGCCGCGCCGCAATCACTCATACGGCCCGCATGGCCGACAAGCTGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000467","ARO_id":"36606","ARO_name":"NDM-5","CARD_short_name":"NDM-5","ARO_description":"New Delhi beta-lactamase NDM-5.","ARO_category":{"36196":{"category_aro_accession":"3000057","category_aro_cvterm_id":"36196","category_aro_name":"NDM beta-lactamase","category_aro_description":"NDM beta-lactamases or New Delhi metallo-beta-lactamases are class B beta-lactamases that confer resistance to a broad range of antibiotics including carbapenems, cephalosporins and penicillins.","category_aro_class_name":"AMR Gene Family"},"35927":{"category_aro_accession":"0000008","category_aro_cvterm_id":"35927","category_aro_name":"cefoxitin","category_aro_description":"Cefoxitin is a cephamycin antibiotic often grouped with the second generation cephalosporins. Cefoxitin is bactericidal and acts by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. Cefoxitin's 7-alpha-methoxy group and 3' leaving group make it a poor substrate for most beta-lactamases.","category_aro_class_name":"Antibiotic"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"35987":{"category_aro_accession":"0000070","category_aro_cvterm_id":"35987","category_aro_name":"ertapenem","category_aro_description":"Ertapenem is a carbapenem antibiotic and is highly resistant to beta-lactamases like other carbapenems. It inhibits bacterial cell wall synthesis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1107":{"model_id":"1107","model_name":"PDC-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"1468":{"protein_sequence":{"accession":"ACQ82806.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTVTLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"FJ666064.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGACGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGTCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAACTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTATGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002498","ARO_id":"38898","ARO_name":"PDC-2","CARD_short_name":"PDC-2","ARO_description":"PDC-2 is a extended-spectrum beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1110":{"model_id":"1110","model_name":"LEN-19","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"8274":{"protein_sequence":{"accession":"CAP12347.2","sequence":"MRYVRLCVISLLATLPLAVYAGPQPLEQIKQSESQLSGRVGMVEMDLASGRTLAAWRADERFPMVSTFKVLLCGAVLARVDAGLEQLDRRIHYRQQDLVDYSPVSEKHLTDGMTVGELCAAAITLSDNSAGNLLLATVGGPAGLTAFLRQIGDNVTRLDRWETALNEALPGDARDTTTPASMAATLRKLLTAQHLSARSQQQLLQWMVDDRVAGPLIRAVLPPGWFIADKTGAGERGARGIVALLGPDGKPERIVVIYLRDTPASMAERNQHIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AM850909.2","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGTGTTATCTCCCTGTTAGCCACCCTGCCACTGGCGGTATACGCCGGTCCACAGCCGCTTGAGCAGATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTGGGGATGGTGGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCGATGAACGCTTTCCCATGGTGAGCACCTTTAAAGTGCTGCTGTGCGGCGCGGTGCTGGCGCGGGTGGATGCCGGGCTCGAACAACTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTACCGACGGGATGACGGTCGGCGAACTCTGCGCCGCCGCCATCACCCTGAGCGATAACAGCGCTGGCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCGGGATTAACTGCCTTTCTGCGCCAGATCGGTGACAACGTCACCCGTCTTGACCGCTGGGAAACGGCACTGAATGAGGCGCTTCCCGGCGACGCGCGCGACACCACCACCCCGGCCAGCATGGCCGCCACGCTGCGCAAACTACTGACCGCGCAGCATCTGAGCGCCCGTTCGCAACAGCAACTCCTGCAGTGGATGGTGGACGATCGGGTTGCCGGCCCGCTGATCCGCGCCGTGCTGCCGCCGGGCTGGTTTATCGCCGACAAAACCGGGGCTGGCGAACGGGGTGCGCGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAACCGGAGCGCATTGTGGTGATCTATCTGCGGGATACCCCGGCGAGTATGGCCGAGCGTAATCAACATATCGCCGGGATCGGCGCAGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002466","ARO_id":"38866","ARO_name":"LEN-19","CARD_short_name":"LEN-19","ARO_description":"LEN-19 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36236":{"category_aro_accession":"3000097","category_aro_cvterm_id":"36236","category_aro_name":"LEN beta-lactamase","category_aro_description":"LEN beta-lactamases are chromosomal class A beta-lactamases that confer resistance to ampicillin, amoxicillin, carbenicillin, and ticarcillin but not to extended-spectrum beta-lactams.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1111":{"model_id":"1111","model_name":"AAC(6')-Ig","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"396":{"protein_sequence":{"accession":"AAA21889.1","sequence":"MNIKPASEASLKDWLELRNKLWSDSEASHLQEMHQLLAEKYALQLLAYSDHQAIAMLEASIRFEYVNGTETSPVGFLEGIYVLPAHRRSGVATMLIRQAEVWAKQFSCTEFASDAALDNVISHAMHRSLGFQETEKVVYFSKKID"},"dna_sequence":{"accession":"L09246.1","fmin":"543","fmax":"981","strand":"+","sequence":"ATGAATATTAAACCTGCATCAGAAGCTTCACTCAAAGATTGGTTAGAATTAAGAAATAAATTGTGGAGTGATTCGGAAGCTTCTCATTTACAAGAGATGCATCAATTATTAGCCGAAAAATATGCCCTACAATTATTGGCCTATTCCGATCACCAAGCTATTGCGATGTTAGAAGCCTCAATTCGGTTTGAATATGTGAATGGGACTGAGACTTCTCCTGTGGGTTTTTTGGAAGGTATTTACGTACTTCCGGCACATCGTCGCTCGGGCGTTGCAACGATGCTTATTCGACAGGCCGAAGTGTGGGCAAAACAATTTTCTTGCACTGAATTTGCATCTGATGCTGCATTGGACAATGTAATTAGTCATGCTATGCATCGTTCATTAGGTTTTCAAGAAACTGAAAAAGTCGTTTATTTTAGTAAAAAAATAGATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36938","NCBI_taxonomy_name":"Acinetobacter haemolyticus","NCBI_taxonomy_id":"29430"}}}},"ARO_accession":"3002554","ARO_id":"38954","ARO_name":"AAC(6')-Ig","CARD_short_name":"AAC(6')-Ig","ARO_description":"AAC(6')-Ig is a chromosomal-encoded aminoglycoside acetyltransferase in Acinetobacter haemolyticus.","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"A category of aminoglycoside N-acetyltransferase enzymes with modification regiospecificity based at the 6'-amino group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics through acetylation of the 6-amino group of the compound.","category_aro_class_name":"AMR Gene Family"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"46128":{"category_aro_accession":"3007378","category_aro_cvterm_id":"46128","category_aro_name":"2'-N-ethylnetilmicin","category_aro_description":"2'-N-ethylnetilmicin is an aminoglycoside antibiotic and a derivative of netilmicin.","category_aro_class_name":"Antibiotic"},"46129":{"category_aro_accession":"3007379","category_aro_cvterm_id":"46129","category_aro_name":"5-episisomicin","category_aro_description":"5-episosomicin is a semisynthetic aminoglycoside antibiotic similar to sisomicin.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1112":{"model_id":"1112","model_name":"OXA-58","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"5914":{"protein_sequence":{"accession":"ACC58995.1","sequence":"MKLLKILSLVCLSISIGACAEHSMSRAKTSTIPQVNNSIIDQNVQALFNEISADAVFVTYDGQNIKKYGTHLDRAKTAYIPASTFKIANALIGLENHKATSTEIFKWDGKPRFFKAWDKDFTLGEAMQASTVPVYQELARRIGPSLMQSELQRIGYGNMQIGTEVDQFWLKGPLTITPIQEVKFVYDLAQGQLPFKPEVQQQVKEMLYVERRGENRLYAKSGWGMAVDPQVGWYVGFVEKADGQVVAFALNMQMKAGDDIALRKQLSLDVLDKLGVFHYL"},"dna_sequence":{"accession":"CP000864.1","fmin":"13383","fmax":"14226","strand":"+","sequence":"ATGAAATTATTAAAAATATTGAGTTTAGTTTGCTTAAGCATAAGTATTGGGGCTTGTGCTGAGCATAGTATGAGTCGAGCAAAAACAAGTACAATTCCACAAGTGAATAACTCAATCATCGATCAGAATGTTCAAGCGCTTTTTAATGAAATCTCAGCTGATGCTGTGTTTGTCACATATGATGGTCAAAATATTAAAAAATATGGCACGCATTTAGACCGAGCAAAAACAGCTTATATTCCTGCATCTACATTTAAAATTGCCAATGCACTAATTGGTTTAGAAAATCATAAAGCAACATCTACAGAAATATTTAAGTGGGATGGAAAGCCACGTTTTTTTAAAGCATGGGACAAAGATTTTACTTTGGGCGAAGCCATGCAAGCATCTACAGTGCCTGTATATCAAGAATTGGCACGTCGTATTGGTCCAAGCTTAATGCAAAGTGAATTGCAACGTATTGGTTATGGCAATATGCAAATAGGCACGGAAGTTGATCAATTTTGGTTGAAAGGGCCTTTGACAATTACACCTATACAAGAAGTAAAGTTTGTGTATGATTTAGCCCAAGGGCAATTGCCTTTTAAACCTGAAGTTCAGCAACAAGTGAAAGAGATGTTGTATGTAGAGCGCAGAGGGGAGAATCGTCTATATGCTAAAAGTGGCTGGGGAATGGCTGTAGACCCGCAAGTGGGTTGGTATGTGGGTTTTGTTGAAAAGGCAGATGGGCAAGTGGTGGCATTTGCTTTAAATATGCAAATGAAAGCTGGTGATGATATTGCTCTACGTAAACAATTGTCTTTAGATGTGCTAGATAAGTTGGGTGTTTTTCATTATTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35523","NCBI_taxonomy_name":"Acinetobacter baumannii ACICU","NCBI_taxonomy_id":"405416"}}}},"ARO_accession":"3001611","ARO_id":"38011","ARO_name":"OXA-58","CARD_short_name":"OXA-58","ARO_description":"OXA-58 is a beta-lactamase found in A. baumannii.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46517":{"category_aro_accession":"3007728","category_aro_cvterm_id":"46517","category_aro_name":"OXA-58-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-58.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1113":{"model_id":"1113","model_name":"ANT(6)-Ib","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"60":{"protein_sequence":{"accession":"CBH51824.1","sequence":"MKMRTEKQIYDTILNFAKADDRIRVVTLEGSRTNINIIPDDFQDYDITFFVTDMQSFINSDEWLNVFGERLIMQKPEDMELFPKEEKGYSYLMLFWDGVKIDLTLLPLEVLDEYFTWDKLVKLLLDKDNRVTNIPVPTDEDYYIEHPTARSFDDCCNEFWNTVTYVVKGLCRKEILFAIDHLNNIVRMELLRMISWKVGIEQGYSFSLGKNYKFLERYISPELWKKILATYNMGSYTEMWKSLELCMGIFRMVSKEVAQCLNYLYPDYDKNISNYVIRQKEKYQR"},"dna_sequence":{"accession":"FN594949.1","fmin":"27481","fmax":"28339","strand":"+","sequence":"ATGAAAATGAGAACAGAGAAACAAATATATGATACTATACTTAATTTTGCTAAAGCAGATGATAGAATTAGGGTGGTTACTTTAGAAGGTTCAAGAACAAATATTAATATTATACCAGATGATTTTCAAGATTATGATATTACTTTTTTTGTCACAGACATGCAGAGTTTTATTAATAGTGATGAGTGGCTTAATGTTTTTGGAGAGAGACTTATTATGCAAAAACCCGAGGATATGGAATTGTTTCCAAAAGAAGAAAAAGGGTATTCATATCTTATGTTATTTTGGGACGGAGTTAAAATAGATTTGACATTATTGCCATTAGAAGTTTTAGATGAATATTTTACTTGGGATAAATTAGTAAAATTATTATTAGATAAGGATAATCGTGTTACTAATATACCAGTACCTACAGATGAAGATTATTATATAGAACATCCGACAGCACGTTCTTTTGATGATTGCTGTAATGAATTTTGGAATACTGTAACATATGTAGTGAAAGGATTATGTCGAAAGGAAATTTTATTTGCAATCGACCATTTAAATAATATTGTGCGTATGGAATTACTGCGAATGATTTCATGGAAGGTTGGAATAGAGCAAGGTTATAGTTTTAGTCTAGGAAAAAACTATAAATTTTTAGAACGATATATTTCACCTGAATTATGGAAGAAAATTCTTGCTACATATAATATGGGGTCATATACAGAAATGTGGAAATCTTTAGAATTATGTATGGGAATTTTTAGAATGGTATCAAAAGAAGTGGCACAATGTTTAAATTATTTATATCCAGATTATGATAAAAATATTAGTAATTATGTTATAAGACAAAAAGAAAAATATCAAAGATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36889","NCBI_taxonomy_name":"Campylobacter fetus subsp. fetus","NCBI_taxonomy_id":"32019"}}}},"ARO_accession":"3002629","ARO_id":"39029","ARO_name":"ANT(6)-Ib","CARD_short_name":"ANT(6)-Ib","ARO_description":"ANT(6)-Ib is an aminoglycoside nucleotidyltransferase gene encoded by transferable pathogenicity islands in C. fetus subsp. fetus and B. subtilis.","ARO_category":{"36364":{"category_aro_accession":"3000225","category_aro_cvterm_id":"36364","category_aro_name":"ANT(6)","category_aro_description":"A category of aminoglycoside O-nucleotidyltransferase enzymes with modification regiospecificity based at the 6-hydroxyl group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics, specifically streptomycin, by transfer of an AMP group from an ATP substrate to the 6-hydroxyl group of the compound.","category_aro_class_name":"AMR Gene Family"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1114":{"model_id":"1114","model_name":"ACT-17","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1418":{"protein_sequence":{"accession":"AHM76771.1","sequence":"MMKKSLCCALLLGISCSALATPVSEKQLAEVVANTVTPLMKAQSVPGMAVAVIYQGKPHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMPYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPENVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVVEGSDSKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANTSYPNPARVEAAYHILEALQ"},"dna_sequence":{"accession":"KF992026.1","fmin":"753","fmax":"1899","strand":"+","sequence":"ATGATGAAAAAATCCCTTTGCTGCGCCCTGCTGCTCGGCATCTCTTGCTCTGCTCTCGCCACGCCAGTGTCAGAAAAACAGCTGGCGGAGGTGGTCGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCTGTTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGAAAACCGCACTATTACACGTTTGGCAAGGCCGATATCGCGGCGAATAAACCCGTTACGCCTCAGACCCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGCGTTTTAGGTGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTGACGGGCAAGCAGTGGCAGGGTATTCGTATGCTGGATCTCGCCACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTCAAACCTTCTGGCATGCCCTATGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTGCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGATGGTAAAGCGGTGCGTGTTTCGCCGGGTATGCTAGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCGGAGAACGTTGCTGATGCCTCACTTAAGCAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGGTCGAGGGCAGCGACAGTAAGGTAGCGCTGGCGCCGTTGCCCGTGGCAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGCTCTACTGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATACAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCGAGGCGCTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3001838","ARO_id":"38238","ARO_name":"ACT-17","CARD_short_name":"ACT-17","ARO_description":"ACT-17 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1115":{"model_id":"1115","model_name":"OXA-435","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"2121":{"protein_sequence":{"accession":"AJT57878.1","sequence":"MNKYFTCYVVASLFLSGCTVQHNLINETPSQIVQGHNQVIHQYFDEKNTSGVLVIQTDKKINLYGNALSRANTEYVPASTFKMLNALIGLENQKTDINEIFKWKGEKRSFTAWEKDMTLGEAMKLSAVPVYQELARRIGLDLMQKEVKRIGFGNAEIGQQVDNFWLVGPLKVTPIQEVEFVSQLAHTQLPFSEKVQANVKNMLLLEESNGYKIFGKTGWAMDIKPQVGWLSGWVEQPDGKIVAFALNMEMRSEMPASIRNELLMKSLKQLNII"},"dna_sequence":{"accession":"KP144324.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGAATAAATATTTTACTTGCTATGTGGTTGCTTCTCTTTTTCTTTCTGGTTGTACGGTTCAGCATAATTTAATAAATGAAACCCCGAGTCAGATTGTTCAAGGACATAATCAGGTGATTCATCAATACTTTGATGAAAAAAACACCTCAGGTGTGCTGGTTATTCAAACAGATAAAAAAATTAATCTATATGGTAATGCTCTAAGCCGCGCAAATACAGAATATGTGCCAGCCTCTACATTTAAAATGTTGAATGCCCTGATCGGATTGGAGAACCAGAAAACGGATATTAATGAAATATTTAAATGGAAGGGCGAGAAAAGGTCATTTACCGCTTGGGAAAAAGACATGACACTAGGAGAAGCCATGAAGCTTTCTGCAGTCCCAGTCTATCAGGAACTTGCGCGACGTATCGGTCTTGATCTCATGCAAAAAGAAGTAAAACGTATTGGTTTCGGTAATGCTGAAATTGGACAGCAGGTTGATAATTTCTGGTTGGTAGGACCATTAAAGGTTACGCCTATTCAAGAGGTAGAGTTTGTTTCCCAATTAGCACATACACAGCTTCCATTTAGTGAAAAAGTGCAGGCTAATGTAAAAAATATGCTTCTTTTAGAAGAGAGTAATGGCTACAAAATTTTTGGAAAGACTGGTTGGGCAATGGATATAAAACCACAAGTGGGCTGGTTGTCCGGCTGGGTTGAGCAGCCAGATGGAAAAATTGTCGCTTTTGCATTAAATATGGAAATGCGGTCAGAAATGCCGGCATCTATACGTAATGAATTATTGATGAAATCATTAAAACAGCTGAATATTATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3003162","ARO_id":"39739","ARO_name":"OXA-435","CARD_short_name":"OXA-435","ARO_description":"OXA-435 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46499":{"category_aro_accession":"3007710","category_aro_cvterm_id":"46499","category_aro_name":"OXA-23-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases, specifically imipenem, derived from OXA-23, first identified in Acinetobacter baumannii.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1116":{"model_id":"1116","model_name":"arr-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"250"}},"model_sequences":{"sequence":{"480":{"protein_sequence":{"accession":"AAC64366.1","sequence":"MVKDWIPISHDNYKQVQGPFYHGTKANLAIGDLLTTGFISHFEDGRILKHIYFSALMEPAVWGAELAMSLSGLEGRGYIYIVEPTGPFEDDPNLTNKKFPGNPTQSYRTCEPLRIVGVVEDWEGHPVELIRGMLDSLEDLKRRGLHVIED"},"dna_sequence":{"accession":"AF078527.1","fmin":"4387","fmax":"4840","strand":"+","sequence":"ATGGTAAAAGATTGGATTCCCATCTCTCATGATAATTACAAGCAGGTGCAAGGACCGTTCTATCATGGAACCAAAGCCAATTTGGCGATTGGTGACTTGCTAACCACAGGGTTCATCTCTCATTTCGAGGACGGTCGTATTCTTAAGCACATCTACTTTTCAGCCTTGATGGAGCCAGCAGTTTGGGGAGCTGAACTTGCTATGTCACTGTCTGGCCTCGAGGGTCGCGGCTACATATACATAGTTGAGCCAACAGGACCGTTCGAAGACGATCCGAATCTTACGAACAAAAAATTTCCCGGTAATCCAACACAGTCCTATAGAACCTGCGAACCCTTGAGAATTGTTGGCGTTGTTGAAGACTGGGAGGGGCATCCTGTTGAATTAATAAGGGGAATGTTGGATTCGTTAGAGGACTTAAAGCGCCGTGGTTTACACGTCATTGAAGACTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002847","ARO_id":"39281","ARO_name":"arr-2","CARD_short_name":"arr-2","ARO_description":"arr-2 is an integron-encoded ribosyltransferase found in Pseudomonas aeruginosa.","ARO_category":{"36529":{"category_aro_accession":"3000390","category_aro_cvterm_id":"36529","category_aro_name":"rifampin ADP-ribosyltransferase (Arr)","category_aro_description":"Enzyme responsible for the ADP-ribosylative inactivation of rifampin at the 23-OH position using NAD+.","category_aro_class_name":"AMR Gene Family"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36656":{"category_aro_accession":"3000517","category_aro_cvterm_id":"36656","category_aro_name":"rifaximin","category_aro_description":"Rifaximin is a semi-synthetic rifamycin used to treat traveller's diarrhea. Rifaximin inhibits RNA synthesis by binding to the beta subunit of bacterial RNA polymerase.","category_aro_class_name":"Antibiotic"},"36669":{"category_aro_accession":"3000530","category_aro_cvterm_id":"36669","category_aro_name":"rifabutin","category_aro_description":"Rifabutin is a semisynthetic rifamycin used in tuberculosis therapy. It inhibits DNA-dependent RNA synthesis.","category_aro_class_name":"Antibiotic"},"36673":{"category_aro_accession":"3000534","category_aro_cvterm_id":"36673","category_aro_name":"rifapentine","category_aro_description":"Rifapentine is a semisynthetic rifamycin that inhibits DNA-dependent RNA synthesis. It is often used in the treatment of tuberculosis and leprosy.","category_aro_class_name":"Antibiotic"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1117":{"model_id":"1117","model_name":"ErmD","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"240":{"protein_sequence":{"accession":"AAA22597.1","sequence":"MKKKNHKYRGKKLNRGESPNFSGQHLMHNKKLIEEIVDRANISIDDTVLELGAGKGALTTVLSQKAGKVLAVENDSKFVDILTRKTAQHSNTKIIHQDIMKIHLPKEKFVVVSNIPYAITTPIMKMLLNNPASGFQKGIIVMEKGAAKRFTSKFIKNSYVLAWRMWFDIGIVREISKEHFSPPPKVDSAMVRITRKKDAPLSHKHYIAFRGLAEYALKEPNIPLCVRLRGIFTPRQMKHLRKSLKINNEKTVGTLTENQWAVIFNTMTQYVMHHKWPRANKRKPGEI"},"dna_sequence":{"accession":"L08389.1","fmin":"390","fmax":"1254","strand":"+","sequence":"ATGAAGAAAAAAAATCATAAGTACAGAGGAAAAAAGTTAAACCGCGGGGAATCTCCGAATTTTTCCGGACAGCATTTGATGCATAATAAAAAATTAATTGAAGAAATTGTGGATCGGGCAAATATTAGCATAGACGATACGGTTTTAGAGTTAGGAGCGGGAAAAGGGGCTTTGACAACTGTGCTAAGTCAAAAAGCCGGTAAGGTATTGGCAGTGGAAAACGATTCTAAATTCGTTGATATACTCACACGTAAAACAGCACAGCATTCAAATACGAAAATTATTCATCAAGATATCATGAAGATTCATTTACCAAAAGAAAAGTTTGTGGTGGTCTCTAATATTCCCTATGCCATCACAACTCCCATCATGAAAATGCTCTTGAACAATCCTGCAAGCGGATTTCAAAAAGGGATCATCGTAATGGAAAAAGGGGCTGCTAAACGTTTCACATCAAAATTCATTAAAAATTCCTATGTTTTAGCTTGGAGAATGTGGTTTGATATTGGCATTGTCAGAGAAATATCGAAAGAGCATTTTTCTCCCCCTCCAAAAGTGGACTCGGCAATGGTCAGAATAACACGAAAAAAAGACGCGCCTCTATCACATAAACATTATATTGCGTTTCGGGGACTTGCCGAATACGCGCTAAAGGAGCCGAATATCCCTCTCTGTGTTCGTTTACGCGGAATTTTTACCCCGCGTCAAATGAAACACTTAAGAAAAAGTCTAAAAATCAACAATGAAAAAACCGTTGGAACGCTCACCGAAAACCAATGGGCGGTTATTTTTAACACGATGACTCAATATGTAATGCATCACAAATGGCCAAGAGCAAATAAGCGAAAACCCGGAGAAATATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36786","NCBI_taxonomy_name":"Bacillus anthracis","NCBI_taxonomy_id":"1392"}}}},"ARO_accession":"3000495","ARO_id":"36634","ARO_name":"ErmD","CARD_short_name":"ErmD","ARO_description":"ErmD confers MLSb phenotype.","ARO_category":{"36699":{"category_aro_accession":"3000560","category_aro_cvterm_id":"36699","category_aro_name":"Erm 23S ribosomal RNA methyltransferase","category_aro_description":"Erm proteins are part of the RNA methyltransferase family and methylate A2058 (E. coli nomenclature) of the 23S ribosomal RNA conferring degrees of resistance to Macrolides, Lincosamides and Streptogramin b. This is called the MLSb phenotype.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35946":{"category_aro_accession":"0000027","category_aro_cvterm_id":"35946","category_aro_name":"roxithromycin","category_aro_description":"Roxithromycin is a semi-synthetic, 14-carbon ring macrolide antibiotic derived from erythromycin. It is used to treat respiratory tract, urinary and soft tissue infections. Roxithromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35974":{"category_aro_accession":"0000057","category_aro_cvterm_id":"35974","category_aro_name":"telithromycin","category_aro_description":"Telithromycin is a semi-synthetic derivative of erythromycin. It is a 14-membered macrolide and is the first ketolide antibiotic to be used in clinics. Telithromycin binds the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"35982":{"category_aro_accession":"0000065","category_aro_cvterm_id":"35982","category_aro_name":"clarithromycin","category_aro_description":"Clarithromycin is a methyl derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome and is used to treat pharyngitis, tonsillitis, acute maxillary sinusitis, acute bacterial exacerbation of chronic bronchitis, pneumonia (especially atypical pneumonias associated with Chlamydia pneumoniae or TWAR), and skin structure infections.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"36284":{"category_aro_accession":"3000145","category_aro_cvterm_id":"36284","category_aro_name":"tylosin","category_aro_description":"Tylosin is a 16-membered macrolide, naturally produced by Streptomyces fradiae. It interacts with the bacterial ribosome 50S subunit to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"36295":{"category_aro_accession":"3000156","category_aro_cvterm_id":"36295","category_aro_name":"spiramycin","category_aro_description":"Spiramycin is a 16-membered macrolide and is natural product produced by Streptomyces ambofaciens. It binds to the 50S subunit of bacterial ribosomes and inhibits peptidyl transfer activity to disrupt protein synthesis.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"36315":{"category_aro_accession":"3000176","category_aro_cvterm_id":"36315","category_aro_name":"dirithromycin","category_aro_description":"Dirithromycin is an oxazine derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome to inhibit bacterial protein synthesis.","category_aro_class_name":"Antibiotic"},"36722":{"category_aro_accession":"3000583","category_aro_cvterm_id":"36722","category_aro_name":"pristinamycin IA","category_aro_description":"Pristinamycin IA is a type B streptogramin antibiotic produced by Streptomyces pristinaespiralis. It binds to the P site of the 50S subunit of the bacterial ribosome, preventing the extension of protein chains.","category_aro_class_name":"Antibiotic"},"36723":{"category_aro_accession":"3000584","category_aro_cvterm_id":"36723","category_aro_name":"quinupristin","category_aro_description":"Quinupristin is a type B streptogramin and a semisynthetic derivative of pristinamycin 1A. It is a component of the drug Synercid and interacts with the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"virginiamycin M1","category_aro_description":"Virginiamycin M1 is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37016":{"category_aro_accession":"3000672","category_aro_cvterm_id":"37016","category_aro_name":"madumycin II","category_aro_description":"Madumycin II is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37017":{"category_aro_accession":"3000673","category_aro_cvterm_id":"37017","category_aro_name":"griseoviridin","category_aro_description":"Griseoviridin is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"37019":{"category_aro_accession":"3000675","category_aro_cvterm_id":"37019","category_aro_name":"pristinamycin IB","category_aro_description":"Pristinamycin IB is a class B streptogramin similar to pristinamycin IA, the former containing a N-methyl-4-(methylamino)phenylalanine instead of a N-methyl-4-(dimethylamino)phenylalanine in its class A streptogramin counterpart (one less methyl group).","category_aro_class_name":"Antibiotic"},"37021":{"category_aro_accession":"3000677","category_aro_cvterm_id":"37021","category_aro_name":"virginiamycin S2","category_aro_description":"Virginiamycin S2 is a streptogramin B antibiotic.","category_aro_class_name":"Antibiotic"},"37022":{"category_aro_accession":"3000678","category_aro_cvterm_id":"37022","category_aro_name":"pristinamycin IC","category_aro_description":"Pristinamycin IC is a class B streptogramin derived from virginiamycin S1.","category_aro_class_name":"Antibiotic"},"37023":{"category_aro_accession":"3000679","category_aro_cvterm_id":"37023","category_aro_name":"vernamycin C","category_aro_description":"Vernamycin C is a streptogramin B antibiotic.","category_aro_class_name":"Antibiotic"},"37024":{"category_aro_accession":"3000680","category_aro_cvterm_id":"37024","category_aro_name":"patricin A","category_aro_description":"Patricin A is a streptogramin B antibiotic.","category_aro_class_name":"Antibiotic"},"37025":{"category_aro_accession":"3000681","category_aro_cvterm_id":"37025","category_aro_name":"patricin B","category_aro_description":"Patricin B is a streptogramin B antibiotic.","category_aro_class_name":"Antibiotic"},"37026":{"category_aro_accession":"3000682","category_aro_cvterm_id":"37026","category_aro_name":"ostreogrycin B3","category_aro_description":"Ostreogrycin B3 is a derivative of pristinamycin IA, with an additional 3-hydroxy group on its 4-oxopipecolic acid.","category_aro_class_name":"Antibiotic"},"37247":{"category_aro_accession":"3000867","category_aro_cvterm_id":"37247","category_aro_name":"oleandomycin","category_aro_description":"Oleandomycin is a 14-membered macrolide produced by Streptomyces antibioticus. It is ssimilar to erythromycin, and contains a desosamine amino sugar and an oleandrose sugar. It targets the 50S ribosomal subunit to prevent protein synthesis.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35952":{"category_aro_accession":"0000034","category_aro_cvterm_id":"35952","category_aro_name":"streptogramin A antibiotic","category_aro_description":"Streptogramin A antibiotics are cyclic polyketide peptide hybrids that bind to the ribosomal peptidyl transfer centre. Structural variation arises from substituting a proline for its desaturated derivative and by its substitution for Ala or Cys. Used alone, streptogramin A antibiotics are bacteriostatic, but is bactericidal when used with streptogramin B antibiotics.","category_aro_class_name":"Drug Class"},"35967":{"category_aro_accession":"0000050","category_aro_cvterm_id":"35967","category_aro_name":"streptogramin B antibiotic","category_aro_description":"Streptogramin B antibiotics are are cyclic hepta- or hexa-depsipeptides.  Type B streptogramins block the peptide exit tunnel of the 50S bacterial ribosome. The general composition of group B streptogramins is 3-hydroxypicolinic acid-L-Thr-D-aminobutyric acid (or D-Ala)-L-Pro-L-Phe (or 4-N-,N-(dimethylamino)-L-Phe)-X-L-phenylglycine. Used alone, streptogramin B antibiotics are bacteriostatic, but is bactericidal when used with streptogramin A antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1118":{"model_id":"1118","model_name":"OXA-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8744":{"protein_sequence":{"accession":"CAA30246.1","sequence":"MAIRIFAILFSIFSLATFAHAQEGTLERSDWRKFFSEFQAKGTIVVADERQADRAMLVFDPVRSKKRYSPASTFKIPHTLFALDAGAVRDEFQIFRWDGVNRGFAGHNQDQDLRSAMRNSTVWVYELFAKEIGDDKARRYLKKIDYGNADPSTSNGDYWIEGSLAISAQEQIAFLRKLYRNELPFRVEHQRLVKDLMIVEAGRNWILRAKTGWEGRMGWWVGWVEWPTGSVFFALNIDTPNRMDDLFKREAIVRAILRSIEALPPNPAVNSDAAR"},"dna_sequence":{"accession":"X07260.1","fmin":"700","fmax":"1528","strand":"+","sequence":"ATGGCAATCCGAATCTTCGCGATACTTTTCTCCATTTTTTCTCTTGCCACTTTCGCGCATGCGCAAGAAGGCACGCTAGAACGTTCTGACTGGAGGAAGTTTTTCAGCGAATTTCAAGCCAAAGGCACGATAGTTGTGGCAGACGAACGCCAAGCGGATCGTGCCATGTTGGTTTTTGATCCTGTGCGATCGAAGAAACGCTACTCGCCTGCATCGACATTCAAGATACCTCATACACTTTTTGCACTTGATGCAGGCGCTGTTCGTGATGAGTTCCAGATTTTTCGATGGGACGGCGTTAACAGGGGCTTTGCAGGCCACAATCAAGACCAAGATTTGCGATCAGCAATGCGGAATTCTACTGTTTGGGTGTATGAGCTATTTGCAAAGGAAATTGGTGATGACAAAGCTCGGCGCTATTTGAAGAAAATCGACTATGGCAACGCCGATCCTTCGACAAGTAATGGCGATTACTGGATAGAAGGCAGCCTTGCAATCTCGGCGCAGGAGCAAATTGCATTTCTCAGGAAGCTCTATCGTAACGAGCTGCCCTTTCGGGTAGAACATCAGCGCTTGGTCAAGGATCTCATGATTGTGGAAGCCGGTCGCAACTGGATACTGCGTGCAAAGACGGGCTGGGAAGGCCGTATGGGTTGGTGGGTAGGATGGGTTGAGTGGCCGACTGGCTCCGTATTCTTCGCACTGAATATTGATACGCCAAACAGAATGGATGATCTTTTCAAGAGGGAGGCAATCGTGCGGGCAATCCTTCGCTCTATTGAAGCGTTACCGCCCAACCCGGCAGTCAACTCGGACGCTGCGCGATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35732","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Typhimurium","NCBI_taxonomy_id":"90371"}}}},"ARO_accession":"3001397","ARO_id":"37797","ARO_name":"OXA-2","CARD_short_name":"OXA-2","ARO_description":"OXA-2 is a beta-lactamase found in the Enterobacteriaceae family.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46493":{"category_aro_accession":"3007704","category_aro_cvterm_id":"46493","category_aro_name":"OXA-2-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-2.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"35981":{"category_aro_accession":"0000064","category_aro_cvterm_id":"35981","category_aro_name":"amoxicillin","category_aro_description":"Amoxicillin is a moderate-spectrum, bacteriolytic, beta-lactam antibiotic used to treat bacterial infections caused by susceptible microorganisms. A derivative of penicillin, it has a wider range of treatment but remains relatively ineffective against Gram-negative bacteria. It is commonly taken with clavulanic acid, a beta-lactamase inhibitor. Like other beta-lactams, amoxicillin interferes with the synthesis of peptidoglycan.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1120":{"model_id":"1120","model_name":"IMI-7","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"2107":{"protein_sequence":{"accession":"AIS19858.1","sequence":"MSLNVKPSRIAILFSSCLVSISFFSQANTKGIDEIKDLEKDFNGRIGVYALDTGSGKSFSYKANERFPLCSSFKGFLAAAVLKGSQDNQLNLNQIVNYNTRSLEFHSPITTKYKDNGMSLGDMAAAALQYSDNGATNIILERYIGGPEGMTKFMRSIGDKDFRLDRWELDLNTAIPGDERDTSTPAAVAKSLKTLALGNILNEREKETYQTWLKGNTTGAARIRASVPSDWVVGDKTGSCGAYGTANDYAVVWPKNRAPLIISVYTTKNEKEAKHEDKVIAEASRIAIDNLK"},"dna_sequence":{"accession":"KM103296.1","fmin":"0","fmax":"879","strand":"+","sequence":"ATGTCACTTAATGTAAAACCAAGTAGAATAGCCATCTTGTTTAGCTCTTGTTTAGTTTCAATATCATTTTTCTCACAGGCCAATACAAAGGGCATCGATGAGATTAAAGACCTTGAAAAAGATTTCAATGGTAGAATTGGTGTCTACGCTTTAGACACTGGCTCAGGCAAATCATTTTCATACAAAGCAAATGAACGATTTCCATTATGTAGTTCTTTCAAAGGTTTTTTAGCTGCTGCTGTATTAAAAGGCTCTCAAGATAATCAACTAAATCTTAATCAGATCGTGAATTATAATACAAGAAGTTTAGAGTTCCATTCACCCATCACAACTAAATATAAAGATAATGGAATGTCATTAGGTGATATGGCTGCTGCAGCTTTACAATATAGCGACAATGGTGCTACTAATATTATCCTTGAACGATATATCGGTGGTCCTGAGGGTATGACTAAATTCATGCGGTCGATTGGAGATAAAGATTTTAGACTCGATCGTTGGGAGTTAGATCTAAACACAGCTATTCCTGGCGATGAACGTGACACATCTACACCTGCAGCAGTAGCTAAGAGCCTGAAAACCCTTGCACTGGGTAACATACTCAATGAGCGTGAAAAGGAAACCTATCAGACATGGTTAAAGGGTAACACAACCGGTGCAGCGCGTATTCGTGCTAGCGTACCAAGCGATTGGGTAGTTGGCGATAAAACTGGTAGTTGCGGTGCATACGGTACGGCAAATGATTATGCGGTAGTCTGGCCAAAGAACCGAGCTCCTCTTATAATTTCTGTTTACACTACAAAAAACGAAAAAGAAGCCAAGCATGAGGATAAAGTAATCGCAGAAGCTTCAAGAATCGCAATTGATAACCTTAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3003177","ARO_id":"39754","ARO_name":"IMI-7","CARD_short_name":"IMI-7","ARO_description":"IMI-7 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36027":{"category_aro_accession":"3000018","category_aro_cvterm_id":"36027","category_aro_name":"IMI beta-lactamase","category_aro_description":"IMI beta-lactamases are a group of TEM-1-like beta-lactamase that are known to hydrolyze imipenem. IMI beta-lactamases are inhibited by clavulanic acid and tazobactam.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1121":{"model_id":"1121","model_name":"APH(3')-VIa","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"368":{"protein_sequence":{"accession":"CAA30578.1","sequence":"MELPNIIQQFIGNSVLEPNKIGQSPSDVYSFNRNNETFFLKRSSTLYTETTYSVSREAKMLSWLSEKLKVPELIMTFQDEQFEFMITKAINAKPISALFLTDQELLAIYKEALNLLNSIAIIDCPFISNIDHRLKESKFFIDNQLLDDIDQDDFDTELWGDHKTYLSLWNELTETRVEERLVFSHGDITDSNIFIDKFNEIYFLDLGRAGLADEFVDISFVERCLREDASEETAKIFLKHLKNDRPDKRNYFLKLDELN"},"dna_sequence":{"accession":"X07753.1","fmin":"102","fmax":"882","strand":"+","sequence":"ATGGAATTGCCCAATATTATTCAACAATTTATCGGAAACAGCGTTTTAGAGCCAAATAAAATTGGTCAGTCGCCATCGGATGTTTATTCTTTTAATCGAAATAATGAAACTTTTTTTCTTAAGCGATCTAGCACTTTATATACAGAGACCACATACAGTGTCTCTCGTGAAGCGAAAATGTTGAGTTGGCTCTCTGAGAAATTAAAGGTGCCTGAACTCATCATGACTTTTCAGGATGAGCAGTTTGAATTCATGATCACTAAAGCGATCAATGCAAAACCAATTTCAGCGCTTTTTTTAACAGACCAAGAATTGCTTGCTATCTATAAGGAGGCACTCAATCTGTTAAATTCAATTGCTATTATTGATTGTCCATTTATTTCAAACATTGATCATCGGTTAAAAGAGTCAAAATTTTTTATTGATAACCAACTCCTTGACGATATAGATCAAGATGATTTTGACACTGAATTATGGGGAGACCATAAAACTTACCTAAGTCTATGGAATGAGTTAACCGAGACTCGTGTTGAAGAAAGATTGGTTTTTTCTCATGGCGATATCACGGATAGTAATATTTTTATAGATAAATTCAATGAAATTTATTTTTTAGATCTTGGTCGTGCTGGGTTAGCAGATGAATTTGTAGATATATCCTTTGTTGAACGTTGCCTAAGAGAGGATGCATCGGAGGAAACTGCGAAAATATTTTTAAAGCATTTAAAAAATGATAGACCTGACAAAAGGAATTATTTTTTAAAACTTGATGAATTGAATTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3002652","ARO_id":"39052","ARO_name":"APH(3')-VIa","CARD_short_name":"APH(3')-VIa","ARO_description":"APH(3')-VIa is a plasmid-encoded aminoglycoside phosphotransferase in A. baumannii.","ARO_category":{"36265":{"category_aro_accession":"3000126","category_aro_cvterm_id":"36265","category_aro_name":"APH(3')","category_aro_description":"A category of aminoglycoside O-phosphotransferase enzymes with modification regiospecificity based at the 3'-hydroxyl group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics, specifically kanamycin and neomycin, by the ATP-dependent phosphorylation of the 3'-hydroxyl group of the compound.","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35940":{"category_aro_accession":"0000021","category_aro_cvterm_id":"35940","category_aro_name":"ribostamycin","category_aro_description":"Ribostamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Ribostamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35943":{"category_aro_accession":"0000024","category_aro_cvterm_id":"35943","category_aro_name":"butirosin","category_aro_description":"Butirosin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Butirosin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"37001":{"category_aro_accession":"3000657","category_aro_cvterm_id":"37001","category_aro_name":"paromomycin","category_aro_description":"An aminoglycoside antibiotic used for the treatment of parasitic infections. It is similar to neomycin sharing a similar spectrum of activity, but its hydroxyl group at the 6'-position instead of an amino group makes it resistant to AAC(6') modifying enzymes.","category_aro_class_name":"Antibiotic"},"46133":{"category_aro_accession":"3007382","category_aro_cvterm_id":"46133","category_aro_name":"gentamicin","category_aro_description":"Gentamicin is a commonly used aminoglycoside antibiotic derived from members of the Micromonospora genus of bacteria. It acts by binding the 30S ribosomal subunit, thus inhibiting protein synthesis. Gentamicin is typically used to treat Gram-negative infections of the repiratory and urinary tract, as well as infections of the bone and soft tissue. It also exhibits considerable nephrotoxicity and ototoxicity. Gentamicin is administered as a mixture of gentamicin type C (which makes about around 80% of the complex) and types A, B, and X (distributed in the remaining 20% of the complex).","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1122":{"model_id":"1122","model_name":"OXA-180","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1293":{"protein_sequence":{"accession":"ADM26745.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKDMTLGDAIKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"HM570036.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATAAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001474","ARO_id":"37874","ARO_name":"OXA-180","CARD_short_name":"OXA-180","ARO_description":"OXA-180 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1123":{"model_id":"1123","model_name":"FOX-8","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1434":{"protein_sequence":{"accession":"ADK73994.1","sequence":"MQQRRAFALLTLGSLLLAPCTYASGEAPLTATVDGIIQPMLKEYRIPGIAVAVLKDGKAHYFNYGVANRESGQRVSEQTLFEIGSVSKTLTATLGAYAAVKGGFVLDDKVSQHAPWLKGSALDGVTMAELATYSAGGLPLQFPDKVDSNDKMQTYYRSWSPVYPAGTHRQYSNPSIGLFGHLAANSLGQPFEQLMSQTLLPKLGLHHTYIQVPESAMANYAYGYSKEDKPIRVTPGVLAAEAYGIKTGSADLLKFAEANMGYQGDALVKSAIALTHTGFYSVGEMTQGLGWESYDYPVTEQVLLAGNSPAVSLQANPVTRFAVPKAMGEQRLYNKTGSTGGFGAYVAFVPARGIAIVMLANRNYPIEARVKAAHAILSQLAE"},"dna_sequence":{"accession":"HM565917.1","fmin":"0","fmax":"1149","strand":"+","sequence":"ATGCAACAACGACGTGCGTTCGCGCTACTGACGCTGGGTAGCCTGCTGCTAGCCCCTTGTACTTATGCCAGCGGGGAGGCCCCGCTGACCGCCACTGTGGACGGCATTATCCAGCCGATGCTCAAGGAGTATCGGATCCCGGGGATAGCGGTCGCCGTACTGAAAGATGGCAAGGCCCACTATTTCAACTATGGGGTTGCCAACCGCGAGAGTGGCCAGCGCGTCAGCGAGCAGACCCTGTTCGAGATTGGCTCGGTCAGCAAGACCCTGACCGCGACCCTCGGTGCCTATGCTGCGGTCAAGGGGGGCTTTGTGCTGGATGACAAGGTGAGCCAGCACGCCCCCTGGCTCAAAGGTTCCGCCTTGGATGGTGTGACCATGGCCGAGCTTGCCACCTACAGTGCGGGTGGTTTGCCGCTGCAGTTCCCCGATAAGGTGGATTCGAATGACAAGATGCAAACTTACTATCGGAGCTGGTCACCGGTTTATCCGGCAGGGACTCATCGCCAGTATTCCAACCCCAGCATAGGCCTGTTTGGTCACCTGGCCGCAAATAGTCTGGGCCAGCCATTTGAGCAACTGATGAGCCAGACCCTGCTGCCCAAGCTGGGTTTGCACCACACCTATATCCAGGTGCCGGAGTCGGCCATGGCGAACTATGCCTACGGCTATTCGAAGGAAGATAAGCCCATCCGGGTCACTCCGGGCGTGCTGGCGGCCGAGGCTTACGGGATCAAGACCGGCTCGGCGGATCTGCTGAAGTTTGCCGAGGCAAACATGGGGTATCAGGGAGATGCCCTGGTAAAAAGCGCAATCGCGCTGACCCACACCGGTTTCTACTCGGTGGGGGAAATGACCCAGGGGCTGGGCTGGGAGAGTTACGACTATCCCGTCACCGAGCAGGTGCTGCTGGCGGGCAACTCCCCGGCGGTGAGCCTCCAGGCCAATCCGGTTACGCGCTTTGCGGTGCCCAAAGCGATGGGCGAGCAGCGGCTCTATAACAAGACGGGCTCGACTGGCGGCTTTGGCGCCTATGTGGCGTTCGTGCCCGCCAGAGGGATCGCCATCGTCATGCTGGCCAATCGCAACTATCCCATCGAGGCCAGGGTGAAGGCGGCTCACGCCATCCTGAGTCAGTTGGCCGAGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002161","ARO_id":"38561","ARO_name":"FOX-8","CARD_short_name":"FOX-8","ARO_description":"FOX-8 is a beta-lactamase found in the Enterobacteriaceae family.","ARO_category":{"36206":{"category_aro_accession":"3000067","category_aro_cvterm_id":"36206","category_aro_name":"FOX beta-lactamase","category_aro_description":"FOX beta-lactamases are plasmid-encoded AmpC-type beta-lactamase which conferred resistance to broad-spectrum cephalosporins and cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1124":{"model_id":"1124","model_name":"TEM-186","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1883":{"protein_sequence":{"accession":"AET99222.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNNERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"JN227084.1","fmin":"308","fmax":"1169","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACAACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001046","ARO_id":"37426","ARO_name":"TEM-186","CARD_short_name":"TEM-186","ARO_description":"TEM-186 is a beta-lactamase.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1125":{"model_id":"1125","model_name":"OKP-B-11","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"877":{"protein_sequence":{"accession":"CAJ19620.1","sequence":"MRYVRLCLISLITALPLAVFASPQPLEQIKISESQLAGRVGYVEMDLASGRTLATWRASERFPLMSTFKVLLCGAVLARVDAGDEQLDRRIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAGNLLLKIVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDVRDTTTPASMATTLRKLLTTPSLSARSQQQLLQWMVDDRVAGPLIRAVLPAGWFIADKTGAGERGSRGIVALLGPDGKAERIVVIYLRDTPATMVERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AM051161.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGCCTTATCTCCCTGATTACCGCCCTGCCACTGGCGGTATTCGCCAGCCCTCAGCCGCTTGAGCAGATTAAAATCAGCGAAAGTCAGCTGGCGGGCCGGGTGGGCTATGTTGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCACCTGGCGCGCCAGTGAGCGCTTTCCGCTGATGAGCACCTTTAAAGTGCTGCTCTGCGGCGCGGTGCTGGCCCGGGTGGATGCCGGCGACGAACAGCTGGATCGGCGGATTCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGCCGACGGGATGACCGTTGGCGAACTCTGCGCCGCCGCCATCACCATGAGCGACAACAGCGCCGGCAATCTGCTGTTGAAGATCGTCGGCGGCCCTGCGGGATTGACCGCTTTTCTGCGCCAGATCGGTGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTCAATGAGGCGCTTCCCGGCGACGTGCGCGACACCACCACCCCGGCCAGCATGGCCACCACCCTGCGCAAGCTGCTAACCACCCCCTCTCTGAGCGCCCGTTCGCAGCAGCAGCTGCTGCAGTGGATGGTGGACGACCGAGTGGCCGGCCCGTTGATCCGCGCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAAACCGGGGCCGGTGAGCGGGGCTCACGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAAGCGGAGCGTATCGTGGTGATCTATCTGCGTGATACCCCGGCGACCATGGTCGAGCGTAACCAGCAGATCGCCGGGATAGGCGCGGCGCTGATCGAACACTGGCAGCGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002444","ARO_id":"38844","ARO_name":"OKP-B-11","CARD_short_name":"OKP-B-11","ARO_description":"OKP-B-11 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"38817":{"category_aro_accession":"3002417","category_aro_cvterm_id":"38817","category_aro_name":"OKP beta-lactamase","category_aro_description":"OKP beta-lactamases are chromosomal class A beta-lactamase that confer resistance to penicillins and early cephalosporins in Klebsiella pneumoniae. OKP beta-lactamases can be subdivided into two groups: OKP-A and OKP-B which diverge by about 4.2%.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1126":{"model_id":"1126","model_name":"OXA-184","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"1604":{"protein_sequence":{"accession":"AFO09968.1","sequence":"MKKILLLFSLFYSFALANDKLKDFFKDYNTSGVFITFDGKHYASNNFKRAKEPFSPASTFKIFNALIALDNGVVKDTKEIFYHYKGEKVFLPSWKQDASLSSAIKRSQVPAFKELARKIGLKTMQESLNKLSYGNTKISKIDTFWLDNSLQISAKNQADLLFKLSQNSLPFSKKSQEEVKKIILFKEDKIQKIYAKTGFNDGINLAWIVGFIESKNKILSFALNVDIKNIKNLKIREELLEKYIYSLN"},"dna_sequence":{"accession":"JQ396378.1","fmin":"0","fmax":"747","strand":"+","sequence":"TTGAAAAAAATACTTTTACTTTTTAGTCTTTTTTACTCTTTTGCTTTGGCAAATGATAAATTAAAAGATTTTTTTAAAGACTACAATACAAGCGGAGTTTTTATAACTTTTGATGGAAAACATTATGCAAGTAATAATTTTAAAAGAGCTAAAGAACCTTTTTCTCCTGCTTCGACTTTTAAAATTTTTAATGCTTTAATTGCGCTTGATAATGGTGTAGTTAAAGATACAAAGGAAATTTTTTATCATTATAAGGGTGAAAAAGTATTTTTGCCCTCTTGGAAACAAGATGCTAGTTTAAGCTCAGCCATAAAACGCTCTCAAGTGCCTGCTTTTAAAGAATTGGCAAGAAAAATAGGACTTAAAACCATGCAAGAAAGCTTAAATAAACTTTCCTATGGAAATACAAAAATTTCAAAAATCGATACCTTTTGGTTGGATAATTCTTTACAAATTTCTGCAAAAAATCAAGCTGATTTGCTTTTTAAACTTTCACAAAATTCTTTACCTTTTTCCAAGAAAAGTCAAGAAGAAGTTAAAAAAATTATTCTTTTTAAAGAAGATAAAATCCAAAAAATTTATGCTAAAACAGGTTTTAATGATGGTATAAATTTGGCTTGGATTGTTGGATTTATAGAGAGTAAAAACAAAATTTTATCTTTTGCCTTAAATGTTGATATAAAGAACATTAAAAATCTTAAAATAAGAGAAGAATTGCTAGAAAAATATATTTATTCTTTAAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36772","NCBI_taxonomy_name":"Campylobacter jejuni","NCBI_taxonomy_id":"197"}}}},"ARO_accession":"3001476","ARO_id":"37876","ARO_name":"OXA-184","CARD_short_name":"OXA-184","ARO_description":"OXA-184 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46491":{"category_aro_accession":"3007702","category_aro_cvterm_id":"46491","category_aro_name":"OXA-184-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-184.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1127":{"model_id":"1127","model_name":"CTX-M-64","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8154":{"protein_sequence":{"accession":"BAF63422.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"AB284167.2","fmin":"225","fmax":"1101","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36790","NCBI_taxonomy_name":"Shigella sonnei","NCBI_taxonomy_id":"624"}}}},"ARO_accession":"3001925","ARO_id":"38325","ARO_name":"CTX-M-64","CARD_short_name":"CTX-M-64","ARO_description":"CTX-M-64 is a beta-lactamase found in Shigella sonnei.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1128":{"model_id":"1128","model_name":"OXA-23","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"885":{"protein_sequence":{"accession":"AAV65289.1","sequence":"MNKYFTCYVVASLFLSGCTVQHNLINETPSQIVQGHNQVIHQYFDEKNTSGVLVIQTDKKINLYGNALSRANTEYVPASTFKMLNALIGLENQKTDINEIFKWKGEKRSFTAWEKDMTLGEAMKLSAVPVYQELARRIGLDLMQKEVKRIGFGNAEIGQQVDNFWLVGPLKVTPIQEVEFVSQLAHTQLPFSEKVQANVKNMLLLEESNGYKIFGKTGWAMDIKPQVGWLTGWVEQPDGKIVAFALNMEMRSEMPASIRNELLMKSLKQLNII"},"dna_sequence":{"accession":"AY795964.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGAATAAATATTTTACTTGCTATGTGGTTGCTTCTCTTTTTCTTTCTGGTTGTACGGTTCAGCATAATTTAATAAATGAAACCCCGAGTCAGATTGTTCAAGGACATAATCAGGTGATTCATCAATACTTTGATGAAAAAAACACCTCAGGTGTGCTGGTTATTCAAACAGATAAAAAAATTAATCTATATGGTAATGCTCTAAGCCGCGCAAATACAGAATATGTGCCAGCCTCTACATTTAAAATGTTGAATGCCCTGATCGGATTGGAGAACCAGAAAACGGATATTAATGAAATATTTAAATGGAAGGGCGAGAAAAGGTCATTTACCGCTTGGGAAAAAGACATGACACTAGGAGAAGCCATGAAGCTTTCTGCAGTCCCAGTCTATCAGGAACTTGCGCGACGTATCGGTCTTGATCTCATGCAAAAAGAAGTAAAACGTATTGGTTTCGGTAATGCTGAAATTGGACAGCAGGTTGATAATTTCTGGTTGGTAGGACCATTAAAGGTTACGCCTATTCAAGAGGTAGAGTTTGTTTCCCAATTAGCACATACACAGCTTCCATTTAGTGAAAAAGTGCAGGCTAATGTAAAAAATATGCTTCTTTTAGAAGAGAGTAATGGCTACAAAATTTTTGGAAAGACTGGTTGGGCAATGGATATAAAACCACAAGTGGGCTGGTTGACCGGCTGGGTTGAGCAGCCAGATGGAAAAATTGTCGCTTTTGCATTAAATATGGAAATGCGGTCAGAAATGCCGGCATCTATACGTAATGAATTATTGATGAAATCATTAAAACAGCTGAATATTATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001418","ARO_id":"37818","ARO_name":"OXA-23","CARD_short_name":"OXA-23","ARO_description":"OXA-23 is a beta-lactamase found in A. baumannii.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46499":{"category_aro_accession":"3007710","category_aro_cvterm_id":"46499","category_aro_name":"OXA-23-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases, specifically imipenem, derived from OXA-23, first identified in Acinetobacter baumannii.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1129":{"model_id":"1129","model_name":"CMY-19","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"761":{"protein_sequence":{"accession":"BAE48233.1","sequence":"MQQRQSILWGAVATLMWAGLAHAGEASPVDPLRPVVDASIQPLLKEHRIPGMAVAVLKDGKAHYFNYGVANRESGASVSEQTLFDIGSVSKTLTATLGAYAVVKGAMQLDDKASRHAPWLKGSVFDSITMGELATYSAGGLPLQFPEEVDSSEKMRAYYRQWAPVYSPGSHRQYSNPSIGLFGHLAASSLKQPFAQLMEQTLLPGLGMHHTYVNVPKQAMASYAYGYSKEDKPIRVNPGMLADEAYGIKTSSADLLAFVKANIGGVDDKALQQAISLTHKGHYSVGGMTQGLGWESYAYPVTEQTLLAGNSAKVSLEANPTAAPRESGSQVLFNKTGSTNGFGAYVAFVPARGIGIVMLANRNYPIPARVKAAHAILAQLAG"},"dna_sequence":{"accession":"AB194410.1","fmin":"0","fmax":"1149","strand":"+","sequence":"ATGCAACAACGACAATCCATCCTGTGGGGGGCCGTGGCCACCCTGATGTGGGCCGGTCTGGCCCATGCAGGTGAGGCTTCACCGGTCGATCCCCTGCGCCCCGTGGTGGATGCCAGCATCCAGCCGCTGCTCAAGGAGCACAGGATCCCGGGCATGGCGGTGGCCGTGCTCAAGGATGGCAAGGCCCACTATTTCAATTACGGGGTGGCCAACCGGGAGAGCGGGGCCAGCGTCAGCGAGCAGACCCTGTTCGATATAGGATCCGTGAGCAAGACCCTGACTGCGACCCTGGGGGCCTATGCGGTGGTCAAGGGAGCGATGCAGCTGGATGACAAGGCGAGCCGGCACGCGCCCTGGCTCAAGGGATCCGTCTTTGACAGCATCACCATGGGGGAGCTTGCCACCTACAGCGCCGGAGGCCTGCCACTGCAATTCCCCGAGGAGGTGGATTCATCCGAGAAGATGCGCGCCTACTACCGCCAGTGGGCCCCTGTCTATTCGCCGGGCTCCCATCGCCAGTACTCCAACCCCAGCATAGGGCTGTTCGGCCACCTGGCGGCGAGCAGCCTGAAGCAGCCATTTGCCCAGTTGATGGAGCAGACCCTGCTGCCCGGGCTCGGCATGCACCACACCTATGTCAATGTGCCGAAGCAGGCCATGGCGAGTTATGCCTATGGCTATTCGAAAGAGGACAAGCCCATCCGGGTCAACCCTGGCATGCTGGCGGACGAGGCCTACGGCATCAAGACCAGCTCGGCGGATCTGCTCGCCTTCGTGAAGGCCAACATCGGCGGGGTTGATGACAAGGCGTTGCAGCAGGCCATCTCCCTGACCCACAAAGGGCATTACTCGGTAGGCGGGATGACCCAGGGGCTGGGTTGGGAGAGTTACGCCTATCCCGTCACCGAGCAGACATTGCTGGCGGGCAATTCGGCCAAGGTGAGCCTCGAAGCCAATCCGACGGCGGCTCCCCGGGAGTCGGGGAGCCAGGTGCTCTTCAACAAGACCGGCTCGACCAATGGCTTTGGCGCCTATGTGGCCTTCGTGCCGGCCAGGGGGATCGGCATCGTCATGCTGGCCAATCGCAACTATCCCATCCCGGCCAGGGTGAAGGCGGCCCACGCCATCCTGGCGCAGTTGGCCGGTTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002030","ARO_id":"38430","ARO_name":"CMY-19","CARD_short_name":"CMY-19","ARO_description":"CMY-19 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1130":{"model_id":"1130","model_name":"PDC-9","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"2018":{"protein_sequence":{"accession":"ACQ82814.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAVEAPADRLKALVDAAVQPVMKANDIPGLTVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDRAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"FJ666072.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGTCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGACCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCGGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAACTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTATGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002508","ARO_id":"38908","ARO_name":"PDC-9","CARD_short_name":"PDC-9","ARO_description":"PDC-9 is a extended-spectrum beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1131":{"model_id":"1131","model_name":"AAC(3)-Ic","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"47":{"protein_sequence":{"accession":"CAD53575.1","sequence":"MISTQTKITRLNSQDVGVMRAMLGMFGEAFEDAENYCRAQPSDSYLQDLLCGSGFIAIAALQGQEVIGGLAAYVLPKFEQQRKEIYIYDLGVQGAYRRRGIATALINELQRIAHDIGAYVIFVQADYGDDPAVALYTKLGIREDVMHFDIEPQPAA"},"dna_sequence":{"accession":"AJ511268.1","fmin":"1294","fmax":"1765","strand":"+","sequence":"ATGATCTCTACTCAAACCAAGATTACCCGCCTCAACTCTCAAGACGTTGGTGTAATGCGGGCAATGCTAGGCATGTTCGGCGAGGCTTTTGAGGACGCTGAGAACTATTGCCGCGCTCAACCAAGCGACAGTTACCTACAAGACTTACTGTGTGGCTCTGGCTTCATCGCAATCGCTGCGTTACAGGGGCAAGAGGTCATCGGTGGGCTCGCCGCGTATGTGCTCCCAAAGTTTGAACAACAGCGCAAAGAAATCTATATCTACGACTTAGGCGTGCAGGGAGCCTATCGCCGACGAGGCATCGCCACAGCCTTGATCAATGAACTCCAGCGTATCGCACATGATATTGGCGCTTATGTAATTTTTGTCCAGGCTGACTATGGGGACGATCCTGCGGTAGCGCTCTACACAAAACTCGGTATCCGGGAGGACGTGATGCACTTTGACATAGAACCTCAACCTGCTGCCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002531","ARO_id":"38931","ARO_name":"AAC(3)-Ic","CARD_short_name":"AAC(3)-Ic","ARO_description":"AAC(3)-Ic is an integron-encoded aminoglycoside acetyltransferase in P. aeruginosa.","ARO_category":{"36461":{"category_aro_accession":"3000322","category_aro_cvterm_id":"36461","category_aro_name":"AAC(3)","category_aro_description":"A category of aminoglycoside N-acetyltransferase enzymes with modification regiospecificity based at the 3-amino group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics through acetylation of the 3-amino group of the compound.","category_aro_class_name":"AMR Gene Family"},"35922":{"category_aro_accession":"0000003","category_aro_cvterm_id":"35922","category_aro_name":"astromicin","category_aro_description":"Astromicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Astromicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"46133":{"category_aro_accession":"3007382","category_aro_cvterm_id":"46133","category_aro_name":"gentamicin","category_aro_description":"Gentamicin is a commonly used aminoglycoside antibiotic derived from members of the Micromonospora genus of bacteria. It acts by binding the 30S ribosomal subunit, thus inhibiting protein synthesis. Gentamicin is typically used to treat Gram-negative infections of the repiratory and urinary tract, as well as infections of the bone and soft tissue. It also exhibits considerable nephrotoxicity and ototoxicity. Gentamicin is administered as a mixture of gentamicin type C (which makes about around 80% of the complex) and types A, B, and X (distributed in the remaining 20% of the complex).","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1027":{"model_id":"1027","model_name":"tet(H)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"780"}},"model_sequences":{"sequence":{"732":{"protein_sequence":{"accession":"CAA75663.1","sequence":"MNKSIIIILLITVLDAIGIGLIMPVLPTLLNEFVSENSLATHYGVLLALYATMQVIFAPILGRLSDKYGRKPILLFSLLGAALDYLLMAFSTTLWMLYIGRIIAGITGATGAVCASAMSDVTPAKNRTRYFGFLGGAFGVGLIIGPMLGGLLGDISAHMPFIFAAISHSILLILSLLFFRETQKREALVANRTPENQTASNTVTVFFKKSLYFWLATYFIIQLIGQIPATIWVLFTQYRFDWNTTSIGMSLAVLGVLHIFFQAIVAGKLAQKWGEKTTIMISMSIDMMGCLLLAWIGHVWVILPALICLAAGGMGQPALQGYLSKSVDDNAQGKLQGTLVSLTNITGIIGPLLFAFIYSYSVAYWDGLLWLMGAILYAMLLITAYFHQRKTTPKAVISTP"},"dna_sequence":{"accession":"Y15510.1","fmin":"0","fmax":"1203","strand":"+","sequence":"ATGAATAAATCAATTATTATTATACTGCTGATCACCGTATTAGATGCCATTGGTATCGGGCTTATCATGCCAGTACTCCCTACTCTATTAAATGAATTTGTCAGTGAAAATTCACTGGCAACCCATTACGGTGTGCTATTAGCGCTCTATGCTACCATGCAGGTTATTTTTGCTCCTATTCTAGGACGACTGTCTGATAAATACGGCAGAAAACCCATCTTGCTGTTTTCCCTTTTAGGCGCGGCACTCGACTATCTTTTAATGGCATTCTCAACCACACTTTGGATGCTCTATATTGGGCGCATCATTGCGGGGATCACAGGCGCAACAGGTGCCGTATGTGCATCAGCGATGAGTGATGTGACTCCCGCTAAAAATCGAACTCGCTATTTTGGTTTCTTAGGTGGTGCTTTTGGTGTTGGCCTTATTATCGGCCCAATGCTAGGGGGATTATTAGGTGATATCAGTGCTCATATGCCATTTATTTTTGCCGCTATTTCACACTCGATATTATTAATACTCTCTTTGCTCTTTTTCCGAGAAACACAAAAAAGAGAAGCGCTTGTTGCCAATAGGACACCTGAAAACCAAACTGCCTCAAATACAGTCACTGTTTTTTTTAAGAAAAGCCTCTACTTTTGGTTAGCAACCTATTTTATTATCCAGCTTATCGGGCAAATTCCTGCCACCATCTGGGTGCTGTTTACACAATATCGTTTTGATTGGAACACAACTTCTATCGGTATGTCTTTGGCGGTTCTGGGTGTATTACATATTTTCTTTCAGGCGATTGTCGCTGGGAAATTGGCACAAAAATGGGGCGAAAAAACCACCATTATGATCAGTATGTCTATTGATATGATGGGCTGTTTATTATTAGCGTGGATAGGCCACGTTTGGGTCATCTTACCAGCATTAATTTGCTTAGCGGCAGGAGGTATGGGGCAACCCGCATTACAAGGTTATTTATCAAAATCTGTCGATGATAATGCGCAAGGGAAATTACAAGGTACTCTGGTGAGCCTAACCAATATTACCGGGATCATTGGTCCCCTTTTATTTGCCTTTATTTATAGTTATAGCGTCGCTTATTGGGATGGTCTGTTATGGCTGATGGGGGCAATACTTTATGCTATGTTGCTTATTACCGCTTATTTTCACCAAAGAAAAACCACACCTAAAGCTGTTATTTCAACCCCTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36867","NCBI_taxonomy_name":"Pasteurella multocida","NCBI_taxonomy_id":"747"}}}},"ARO_accession":"3000175","ARO_id":"36314","ARO_name":"tet(H)","CARD_short_name":"tet(H)","ARO_description":"TetH is a tetracycline efflux protein expressed in Gram-negative bacteria (Actinobacillus, Acinetobacter, Gallibacterium, Histophilus, Mannheimia, Moraxella, Pasteurella, and Psychrobacter). Its gene is linked to the resistance genes sul2, and strA, which confer resistance to sulfamethoxazole and streptomycin, respectively.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1092":{"model_id":"1092","model_name":"tet(39)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"161":{"protein_sequence":{"accession":"AAW66497.1","sequence":"MKKSLSVILITIFLDAVGIGLIMPILPELLRSLAGAEAGGVHYGALLAVYALMQFIFAPILGALSDRFGRRPVLIISIAGATADYLLMAAAPSLLWLYIGRIFAGITGANMAVATAYVSDITPAHERAKRFGLLGAVFGIGFIAGPVIGGVLGEWNLHAPFFAAAFMNGINLIMTAVLLKESKHSNKMTEKVQEQSILKKLSYLITQPNMAPLLGIFLIITLVSQVPATLWVIYGQDRYGWSIFIAGVSLASYGICHSIAQAFAIAPMVKRFGEKNTLLCGIACDAIGLLLLSIAVEEWVPFALLPLFALGGVAVPALQAMMSRGISDERQGELQGLLSSFNSLGAIIGPVLVTSLYFMTQASAPGMVWALAAILYVITLPLLLKYRLNKYSGVP"},"dna_sequence":{"accession":"AY743590.1","fmin":"0","fmax":"1188","strand":"+","sequence":"GTGAAGAAATCATTGAGCGTGATTTTAATCACTATATTTCTGGATGCTGTTGGGATTGGTTTAATTATGCCGATCTTGCCTGAATTATTACGGTCATTGGCTGGAGCTGAAGCAGGCGGTGTTCACTATGGTGCTTTATTAGCTGTGTATGCTCTGATGCAGTTCATTTTTGCACCTATCCTTGGAGCGTTGAGTGACCGATTTGGACGTCGACCTGTATTAATTATTTCAATTGCTGGTGCAACGGCTGATTATCTCCTAATGGCTGCTGCTCCTTCTCTATTGTGGCTATATATTGGTCGTATTTTTGCGGGAATTACAGGTGCCAACATGGCTGTTGCAACAGCTTATGTTTCAGATATTACTCCAGCCCATGAGCGTGCAAAAAGGTTTGGTCTCCTTGGAGCTGTCTTTGGTATTGGGTTTATAGCGGGTCCGGTAATAGGTGGAGTTTTGGGTGAATGGAACTTACATGCACCGTTCTTTGCTGCTGCTTTTATGAATGGGATTAATTTAATAATGACAGCAGTCTTATTAAAAGAATCAAAACACAGCAATAAAATGACTGAGAAGGTTCAGGAGCAATCAATATTAAAGAAATTATCCTATTTGATCACTCAACCTAATATGGCTCCATTGCTTGGTATCTTTTTAATTATCACATTGGTTTCACAAGTCCCCGCAACTTTATGGGTTATCTATGGGCAGGATCGTTATGGCTGGAGTATATTTATTGCAGGTGTTTCCCTTGCTAGTTATGGAATATGCCATTCTATTGCACAGGCTTTTGCTATCGCCCCTATGGTAAAGAGGTTTGGAGAGAAAAATACGTTGTTATGTGGAATAGCTTGCGATGCAATTGGTTTACTTCTTTTATCTATTGCTGTTGAAGAATGGGTGCCTTTTGCGTTGTTACCATTGTTTGCCCTTGGTGGAGTAGCCGTTCCTGCTTTGCAAGCAATGATGTCCAGAGGTATTAGTGATGAAAGACAAGGTGAATTACAAGGGCTATTAAGCAGTTTTAATAGTCTGGGGGCTATAATTGGTCCTGTATTAGTTACTAGCCTCTATTTTATGACTCAGGCATCAGCTCCTGGAATGGTATGGGCATTAGCTGCAATACTTTATGTAATCACCCTACCCTTATTGCTTAAGTATCGCCTGAATAAATATTCTGGAGTTCCATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36811","NCBI_taxonomy_name":"Acinetobacter sp. LUH5605","NCBI_taxonomy_id":"309867"}}}},"ARO_accession":"3000566","ARO_id":"36705","ARO_name":"tet(39)","CARD_short_name":"tet(39)","ARO_description":"Tet39 is a tetracycline efflux pump found in Gram-negative bacteria, including Brevundimonas, Stenotrophomonas, Enterobacter, Alcaligenes, Acinetobacter, and Providencia.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1067":{"model_id":"1067","model_name":"MexE","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"5525":{"protein_sequence":{"accession":"AAG05881.1","sequence":"MEQSSHFSWRYPLALAAVLVLSACGKAPETTQGMAAPKVSVAEVIEQPLNEWDEFTGRLEAPESVELRPRVSGYIDRVAFHEGALVKKGDLLFQIDPRPFEAEVKRLEAQLQQARAAQARSVNEAQRGERLRASNAISAELADARTTAAQEAKAAVAATQAQLDAARLNLSFTRITAPIDGRVSRAEVTAGNLVNSGETLLTTLVSTDKVYAYFDADERVFLKYVELARQAGRDTRSESPVYLGLSSEDGNPHLGRLDFLDNQVNPRTGTIRGRAVFDNAKGEFTPGLYVRLKLVGSKTYAATLIKDEAVGTDLGKKFVLVLDGDNKTVYRTVEMGPKLEGLRIVRSGLSKGDRIVVNGLQRVRPGMQVDPQKVEMASADTLATLARLRQSVGDSEPPKVAASKDNATRNEPRG"},"dna_sequence":{"accession":"AE004091.2","fmin":"2808742","fmax":"2809987","strand":"+","sequence":"ATGGAACAGTCATCCCACTTCTCCTGGCGCTACCCCCTCGCACTCGCGGCCGTACTGGTCCTGAGCGCCTGCGGCAAGGCCCCGGAAACCACCCAAGGCATGGCGGCGCCCAAGGTCAGCGTCGCCGAAGTCATCGAACAACCGCTGAACGAGTGGGACGAATTCACCGGCCGCCTGGAGGCCCCGGAGTCGGTGGAGCTGCGCCCGCGGGTGTCGGGCTACATCGACCGCGTGGCCTTCCATGAAGGCGCACTGGTGAAGAAAGGCGACCTGCTGTTCCAGATCGACCCGCGCCCGTTCGAGGCCGAGGTCAAGCGCCTCGAAGCCCAGCTGCAACAGGCCCGCGCGGCCCAGGCGCGGAGCGTCAACGAAGCCCAGCGCGGCGAACGCCTGCGCGCCAGCAACGCGATCTCCGCGGAACTCGCCGACGCCCGCACCACCGCCGCCCAGGAAGCCAAGGCGGCGGTCGCCGCGACCCAGGCGCAACTGGACGCGGCGCGCCTGAACCTGAGCTTCACCCGGATCACCGCGCCGATCGACGGTCGCGTCAGCCGCGCCGAGGTCACCGCCGGCAACCTGGTCAACTCCGGGGAGACCCTGCTCACCACCCTGGTCAGCACCGACAAGGTCTACGCCTACTTCGACGCCGACGAGCGCGTGTTCCTCAAGTACGTCGAGCTGGCCCGCCAGGCCGGTCGCGACACGCGCAGCGAGAGCCCGGTGTACCTCGGCCTGAGCAGCGAGGACGGCAACCCGCACCTGGGCCGGCTGGACTTCCTCGACAACCAGGTCAACCCGCGTACCGGCACCATCCGCGGCCGCGCCGTGTTCGACAACGCCAAGGGCGAGTTCACCCCGGGCCTCTACGTGCGCCTGAAGCTGGTCGGCAGCAAGACCTACGCCGCCACCCTGATCAAGGACGAAGCGGTCGGCACCGACCTGGGCAAGAAGTTCGTGCTGGTCCTGGATGGCGACAACAAGACCGTCTACCGCACCGTCGAGATGGGACCGAAGCTGGAGGGCCTGCGCATCGTCCGCAGCGGCCTGAGCAAGGGCGACCGGATCGTCGTGAATGGCCTGCAGCGGGTCCGCCCGGGCATGCAGGTGGATCCGCAGAAGGTCGAGATGGCCAGCGCCGACACCCTGGCCACCCTCGCGCGCCTGCGGCAGTCGGTCGGCGACAGCGAACCACCGAAGGTGGCGGCGTCCAAGGACAACGCCACTCGCAACGAGCCGCGCGGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36804","NCBI_taxonomy_name":"Pseudomonas aeruginosa PAO1","NCBI_taxonomy_id":"208964"}}}},"ARO_accession":"3000803","ARO_id":"37183","ARO_name":"MexE","CARD_short_name":"MexE","ARO_description":"MexE is the membrane fusion protein of the MexEF-OprN multidrug efflux complex.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1041":{"model_id":"1041","model_name":"MexS","model_type":"protein overexpression model","model_type_id":"41091","model_description":"Protein Overexpression Models (POM) are similar to Protein Variant Models (PVM) in that they include a protein reference sequence, a curated BLASTP bitscore cut-off, and mapped resistance variants. Whereas PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, reporting only those with curated mutations conferring AMR, POMs are restricted to regulatory proteins and report both wild-type sequences and\/or sequences with mutations leading to overexpression of efflux complexes. The former lead to efflux of antibiotics at basal levels, while the latter can confer clinical resistance. POMs include a protein reference sequence (often from wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Perfect RGI match is 100% identical to the wild-type reference protein sequence along its entire length, a Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value may or may not contain at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off may or may not contain at least one curated mutation from amongst the mapped resistance variants.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"660"},"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"7573":"V104A","7574":"F253L","7575":"D44E","7576":"S60F","7577":"F185L","7578":"V73A","7579":"L270Q","7580":"C245G","7581":"A166P","7582":"S60P","7583":"L263Q"},"Curated-R":{"7573":"V104A","7574":"F253L","7575":"D44E","7576":"S60F","7577":"F185L","7578":"V73A","7579":"L270Q","7580":"C245G","7581":"A166P","7582":"S60P","7583":"L263Q"},"clinical":{"7573":"V104A","7574":"F253L","7575":"D44E","7576":"S60F","7577":"F185L","7578":"V73A","7579":"L270Q","7580":"C245G","7581":"A166P","7582":"S60P","7583":"L263Q"}}},"model_sequences":{"sequence":{"667":{"protein_sequence":{"accession":"ADT64081.1","sequence":"MSRVIRFHQFGPPEVLKCEELPTPAPAAGEVLVRVQAIGVSWKDVLWRQNLAPEQAALPSGLGFELAGEVLAVGAGVGDLPLGSRVASFPAHTPDHYPAYGDVVLMPRAALAVYPEVLTPVEASVYYTGLLVAYFGLVDLAGLKAGQTVLITEAARMYGPVSIQLAKALGARVIASTKSAEEREFLREQGADKVVVTDEQDLVLEVERFTEGKGVNVILDELGGPQMTLLGDVSATRGKLVLYGCNGGNESAFPACAAFKKHLQFYRHCLMDFTGHPEMGLERNDESVSKALAHIEQLTRDRLLKPVVDRVFEFDQVVEAHRYMETCPKRGRVVIHVAD"},"dna_sequence":{"accession":"HQ433550.1","fmin":"0","fmax":"1020","strand":"+","sequence":"ATGTCCCGAGTGATCCGTTTTCATCAGTTTGGCCCGCCAGAGGTCCTCAAATGCGAAGAGCTGCCGACCCCGGCGCCGGCCGCAGGGGAAGTCCTGGTGCGTGTCCAGGCGATCGGCGTGAGCTGGAAGGATGTGCTCTGGCGTCAGAACCTGGCCCCGGAGCAGGCTGCGCTGCCGTCCGGTCTCGGCTTCGAACTGGCCGGCGAGGTGCTGGCGGTCGGCGCCGGCGTCGGCGACCTGCCGCTGGGTTCCCGCGTGGCCAGTTTCCCCGCCCATACCCCCGATCATTATCCGGCCTATGGCGACGTGGTGCTGATGCCGCGCGCGGCCCTGGCGGTCTACCCCGAGGTACTCACCCCGGTGGAGGCCAGCGTCTACTACACCGGCCTGCTGGTGGCCTATTTCGGCCTGGTCGACCTGGCCGGGTTGAAGGCCGGGCAGACCGTGCTGATCACCGAGGCGGCGCGCATGTACGGGCCGGTCTCGATCCAGTTGGCCAAGGCTCTCGGCGCGCGGGTGATCGCTTCCACCAAGTCCGCCGAGGAGCGCGAGTTCCTCCGCGAGCAGGGCGCCGACAAGGTGGTGGTGACCGACGAGCAGGACCTGGTCCTGGAAGTCGAGCGCTTCACCGAGGGCAAGGGCGTCAATGTCATCCTCGACGAATTGGGCGGTCCGCAGATGACCCTGCTCGGCGATGTCTCCGCCACCCGCGGCAAGCTGGTGCTGTATGGCTGCAACGGCGGCAACGAGTCGGCGTTCCCGGCCTGCGCCGCGTTCAAGAAGCACCTGCAGTTCTACCGCCACTGCCTGATGGATTTCACCGGTCATCCGGAGATGGGCCTGGAACGCAACGACGAGTCGGTGAGCAAGGCCCTCGCGCACATCGAGCAACTGACCCGCGATCGCCTGCTCAAACCGGTGGTCGACCGGGTATTCGAGTTCGACCAGGTGGTCGAGGCGCACCGCTACATGGAAACCTGTCCAAAGCGCGGCCGGGTGGTGATCCACGTCGCCGATTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39594","NCBI_taxonomy_name":"Pseudomonas aeruginosa PAK","NCBI_taxonomy_id":"1009714"}}}},"ARO_accession":"3000813","ARO_id":"37193","ARO_name":"MexS","CARD_short_name":"MexS","ARO_description":"MexS is a suppressor of MexT, which is an activator of the multidrug pump MexEF-OprN. Mutations in MexS lead to multidrug resistance.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"988":{"model_id":"988","model_name":"tet(J)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"770"}},"model_sequences":{"sequence":{"413":{"protein_sequence":{"accession":"AAD12753.1","sequence":"MNKSIIIILLVTVLDAIGIGLIMPVLPTLLNEFVSENRLANHYGILLALYATMQVIFAPILGKLSDKYGRKPILLISLLGAALDYLLMACPTSLWMLYIGRIIAGITGATGAVCASAMTDVTHPHERTRYFGFLGGAFGVGLIIGPMLGGLLGEISAHTPFIFAAISHSLLFIFSLLCFQETQTTKISTEISALNQDTAPHSTTGFIKKSLFFWLIAYFIIQLIGQIPATIWVLFTQVRFAWHTTEVGLSLAFLGVLHIFFQAVLAGKLAQKWGERNTVIISMSIDAFGCLLLAWISHVWVMLPALICLAAGGMGQPALQGYLSKSVDHHVQGQLQGTLVSLTNITGIVGPLLFSFIYSYSVEYWDGLLWFIGAMLYSGLLVASYFKQKSPILKKFPS"},"dna_sequence":{"accession":"AF038993.1","fmin":"0","fmax":"1197","strand":"+","sequence":"ATGAATAAATCAATTATTATCATACTGCTTGTCACAGTATTAGATGCCATTGGTATTGGCCTTATCATGCCAGTACTACCAACACTATTAAACGAGTTTGTGAGCGAAAACAGACTCGCCAATCATTACGGTATATTATTAGCACTCTATGCGACGATGCAGGTGATCTTCGCACCTATTTTAGGAAAATTATCAGATAAATATGGCAGAAAACCTATTTTATTAATTTCGCTATTGGGTGCCGCATTAGATTACCTATTAATGGCTTGCCCCACCTCATTATGGATGCTCTACATTGGACGAATAATTGCGGGTATAACAGGAGCCACTGGTGCAGTATGCGCATCAGCAATGACTGATGTAACTCATCCTCATGAAAGAACACGCTATTTCGGTTTTTTGGGTGGTGCATTTGGTGTGGGTTTAATTATTGGCCCCATGTTAGGGGGATTACTCGGTGAGATCAGCGCCCATACGCCATTTATCTTTGCGGCTATTTCTCATTCGTTATTATTTATATTTTCATTACTTTGTTTCCAAGAAACTCAAACCACAAAAATTTCGACTGAAATATCCGCATTAAATCAGGATACAGCGCCTCACTCTACCACTGGTTTTATTAAAAAGAGTCTCTTTTTTTGGCTTATTGCCTATTTTATTATTCAACTAATAGGGCAAATTCCGGCCACTATTTGGGTGCTATTCACACAAGTTCGTTTCGCTTGGCACACTACTGAAGTAGGTTTATCTCTTGCATTTCTTGGTGTATTACATATTTTTTTTCAAGCGGTTCTCGCAGGAAAACTGGCGCAAAAATGGGGAGAACGCAACACGGTTATCATTAGCATGTCAATTGATGCATTTGGTTGCTTATTATTAGCCTGGATAAGCCATGTTTGGGTTATGCTTCCCGCTTTAATCTGTTTAGCTGCGGGAGGAATGGGACAACCTGCTTTACAAGGATATTTATCAAAATCTGTTGATCATCATGTTCAAGGACAGTTACAAGGAACGTTAGTCAGTCTAACGAATATAACTGGGATTGTCGGCCCGTTACTCTTCTCTTTTATTTATAGTTACAGCGTTGAATATTGGGATGGCTTATTGTGGTTTATTGGTGCAATGCTTTACAGTGGGTTACTTGTAGCCAGTTATTTTAAACAGAAATCACCAATATTAAAAAAATTTCCCTCATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3000177","ARO_id":"36316","ARO_name":"tet(J)","CARD_short_name":"tet(J)","ARO_description":"TetJ is a tetracycline efflux protein expressed in Gram-negative bacteria (Escherichia, Morganella, and Proteus).","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1006":{"model_id":"1006","model_name":"tet(V)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"770"}},"model_sequences":{"sequence":{"4742":{"protein_sequence":{"accession":"AAB84282.1","sequence":"MRSPRPVAGWRVLAPFRIREYRLLIAAVTLSIFAEGMWSVVMALQVIAIDNDPASLSLVATCLGVGLVAFVLVGGITADRINQRTIIIAVEVVNFVTVAVISALALLGVLKIWHMAVAAGILGIAAAFFFPAYSAILPRILPPEQLLAANGVEGVVRPVFQRSVGPAVAGMVIGATMPSIGAVVVAVLFALGLALLVATRPPAQPASEHHERPHVLRDLREGFAFVLKTPWLLWTVLFASMFVLVVLGPIEVLLPFIAQDRFADGARAYGFILAFFGIGSAMGALTVSSRRMPRRYLTTMMLMWGLGSIPLVIVGYTSSFPLMAAATFVIGVTDGAGMVIWGTLLQRRVPTEMLGRVSSLDFFVSLAFMPLSFAIVGPLSKVVSMEVIFATAGLVPVAIAAVAFTAARMHRDEVANPLL"},"dna_sequence":{"accession":"AF030344.1","fmin":"461","fmax":"1721","strand":"-","sequence":"GTGCGCTCGCCGCGTCCGGTCGCAGGCTGGCGCGTACTCGCACCGTTCCGGATCCGCGAGTACCGCCTGCTGATCGCCGCGGTCACGCTGTCGATCTTCGCCGAGGGCATGTGGTCTGTGGTCATGGCGCTGCAGGTGATCGCGATCGACAACGATCCGGCGTCACTGTCGCTGGTCGCGACGTGCCTCGGTGTCGGCCTGGTCGCGTTCGTCCTCGTCGGCGGCATCACCGCGGACCGGATCAACCAGCGCACCATCATCATTGCCGTCGAGGTGGTCAACTTCGTCACGGTCGCGGTGATCTCCGCGCTGGCCCTGCTGGGCGTGCTGAAGATCTGGCACATGGCCGTTGCCGCAGGCATTCTCGGCATCGCGGCGGCGTTCTTCTTCCCGGCCTACAGCGCGATCCTGCCGCGCATCCTGCCGCCCGAACAGCTGCTGGCCGCCAACGGTGTCGAGGGCGTGGTACGCCCGGTGTTCCAGCGTTCGGTGGGCCCCGCGGTGGCCGGCATGGTCATCGGTGCAACGATGCCGTCGATCGGCGCGGTCGTGGTGGCGGTGCTGTTCGCGCTCGGCCTGGCGCTGCTGGTCGCGACCCGTCCGCCCGCCCAGCCCGCCTCCGAGCACCATGAGCGCCCGCACGTATTGCGGGACCTGCGTGAAGGTTTCGCCTTCGTCCTGAAGACACCGTGGCTGCTGTGGACCGTGCTGTTCGCGAGCATGTTCGTGCTCGTCGTGCTGGGACCCATCGAGGTGCTGCTGCCGTTCATCGCACAGGACCGCTTCGCCGACGGCGCCCGCGCCTACGGTTTCATCCTGGCGTTCTTCGGTATCGGCAGTGCGATGGGCGCGCTGACGGTGTCGTCGCGGCGCATGCCGCGCCGCTATCTCACGACCATGATGCTGATGTGGGGTCTCGGCTCGATTCCCCTTGTGATCGTGGGATATACATCGTCGTTCCCGCTGATGGCCGCTGCGACGTTCGTCATCGGCGTCACCGACGGCGCTGGCATGGTGATCTGGGGAACGCTGCTGCAACGGCGTGTGCCCACCGAGATGCTGGGCCGCGTGTCGAGCCTGGACTTCTTCGTATCGCTGGCGTTCATGCCGTTGTCATTCGCGATCGTGGGTCCGCTGTCGAAGGTGGTCTCGATGGAGGTGATCTTCGCGACGGCGGGTCTGGTGCCCGTGGCGATCGCGGCCGTGGCGTTCACCGCGGCGCGCATGCACCGTGACGAGGTGGCGAACCCACTGCTGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36769","NCBI_taxonomy_name":"Mycolicibacterium smegmatis MC2 155","NCBI_taxonomy_id":"246196"}}}},"ARO_accession":"3000181","ARO_id":"36320","ARO_name":"tet(V)","CARD_short_name":"tet(V)","ARO_description":"TetV is a tetracycline efflux protein that has been found in Mycolicibacterium smegmatis and Mycolicibacterium fortuitum.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1050":{"model_id":"1050","model_name":"AAC(6')-Ii","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"172":{"protein_sequence":{"accession":"AAB63533.1","sequence":"MIISEFDRNNPVLKDQLSDLLRLTWPEEYGDSSAEEVEEMMNPERIAVAAVDQDELVGFIGAIPQYGITGWELHPLVVESSRRKNQIGTRLVNYLEKEVASRGGITIYLGTDDLDHGTTLSQTDLYVHTFDKVASIQNLREHPYEFYEKLGYKIVGVLPNANGWDKPDIWMAKTIIPRPDSQ"},"dna_sequence":{"accession":"L12710.1","fmin":"0","fmax":"549","strand":"+","sequence":"ATGATAATCAGTGAATTTGACCGTAATAATCCAGTATTGAAAGATCAGCTTTCTGATTTACTGAGACTGACTTGGCCGGAAGAATATGGAGACAGCTCGGCAGAAGAAGTAGAAGAAATGATGAATCCAGAACGAATCGCGGTAGCAGCGGTAGACCAAGATGAGTTAGTAGGATTTATTGGTGCAATCCCTCAATACGGTATCACAGGTTGGGAATTGCATCCATTAGTTGTAGAAAGCTCCCGACGAAAGAACCAAATAGGTACTCGATTAGTCAATTACTTAGAAAAAGAAGTAGCTTCCAGAGGAGGAATCACGATTTATTTAGGTACGGATGATTTAGACCATGGAACAACGTTAAGTCAAACGGACCTGTATGTGCATACATTTGATAAAGTGGCTTCCATCCAGAACCTTCGTGAACATCCGTATGAATTCTATGAAAAATTAGGTTATAAAATCGTAGGTGTCTTACCAAATGCAAATGGCTGGGACAAACCGGATATTTGGATGGCAAAAACGATTATTCCTCGACCAGATTCTCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36779","NCBI_taxonomy_name":"Enterococcus faecium","NCBI_taxonomy_id":"1352"}}}},"ARO_accession":"3002556","ARO_id":"38956","ARO_name":"AAC(6')-Ii","CARD_short_name":"AAC(6')-Ii","ARO_description":"AAC(6')-Ii is a chromosomal-encoded aminoglycoside acetyltransferase in Enterococcus spp.","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"A category of aminoglycoside N-acetyltransferase enzymes with modification regiospecificity based at the 6'-amino group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics through acetylation of the 6-amino group of the compound.","category_aro_class_name":"AMR Gene Family"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"46128":{"category_aro_accession":"3007378","category_aro_cvterm_id":"46128","category_aro_name":"2'-N-ethylnetilmicin","category_aro_description":"2'-N-ethylnetilmicin is an aminoglycoside antibiotic and a derivative of netilmicin.","category_aro_class_name":"Antibiotic"},"46129":{"category_aro_accession":"3007379","category_aro_cvterm_id":"46129","category_aro_name":"5-episisomicin","category_aro_description":"5-episosomicin is a semisynthetic aminoglycoside antibiotic similar to sisomicin.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1132":{"model_id":"1132","model_name":"OXA-88","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1058":{"protein_sequence":{"accession":"ABD48715.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDKKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"DQ392963.1","fmin":"8","fmax":"833","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATAAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001626","ARO_id":"38026","ARO_name":"OXA-88","CARD_short_name":"OXA-88","ARO_description":"OXA-88 is a beta-lactamase found in A. baumannii.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1133":{"model_id":"1133","model_name":"SHV-109","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"985":{"protein_sequence":{"accession":"ACM04459.1","sequence":"MRYIRRCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDMPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"EU418913.1","fmin":"16","fmax":"877","strand":"+","sequence":"ATGCGTTATATTCGCCGGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAACTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGCATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATATGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001158","ARO_id":"37538","ARO_name":"SHV-109","CARD_short_name":"SHV-109","ARO_description":"SHV-109 is a broad-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1136":{"model_id":"1136","model_name":"MIR-6","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"764":{"protein_sequence":{"accession":"AFJ79785.1","sequence":"MMTKSLSCALLLSVTSAAFAAPMSETQLAEVVERTVTPLMNAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTSTGVLGGDAIARGEIALGDPVAKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDTASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMSYEQAMTTRVFKPLKLDHTWINVPKAEEAHYAWGYREGKAVHVSPGMLDAEAYGVKTNVKDMASWLIANMKPDSLQAPSLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVGGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILDALQ"},"dna_sequence":{"accession":"JQ664733.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGACAAAATCCCTAAGCTGTGCCCTGCTGCTCAGCGTCACCAGCGCTGCATTCGCCGCACCGATGTCCGAAACACAGCTGGCTGAGGTGGTGGAACGTACCGTTACGCCGCTGATGAACGCGCAGGCCATTCCGGGTATGGCGGTGGCGGTAATTTATCAGGGTCAGCCACACTACTTTACCTTCGGTAAAGCCGATGTTGCGGCGAACAAACCCGTCACCCCGCAAACCCTGTTTGAGCTGGGCTCTATAAGTAAAACCTCCACCGGCGTACTGGGCGGCGATGCCATTGCCCGGGGTGAAATAGCGCTGGGCGATCCGGTAGCAAAATACTGGCCTGAGCTCACGGGCAAGCAGTGGCAGGGCATTCGCATGCTGGATCTGGCAACCTATACCGCAGGCGGTCTGCCGTTACAGGTGCCGGATGAGGTCACGGATACCGCTTCTCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCGGGCACCACGCGTCTTTACGCTAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTTAAACCTTCCGGCATGAGCTATGAGCAGGCCATGACGACGCGGGTCTTTAAACCCCTCAAGCTGGACCATACCTGGATTAACGTCCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGATACCGTGAGGGTAAAGCGGTCCACGTTTCGCCAGGGATGCTGGACGCGGAAGCCTATGGCGTAAAAACTAACGTGAAGGATATGGCGAGCTGGCTGATAGCCAACATGAAGCCGGATTCTCTTCAGGCTCCCTCACTCAAGCAAGGCATTGCTCTGGCGCAGTCTCGCTACTGGCGCGTGGGGGCTATGTATCAGGGGCTGGGCTGGGAGATGCTCAACTGGCCGGTCGATGCCAAAACCGTCGTCGGAGGCAGTGATAACAAGGTGGCGCTGGCACCATTGCCCGTGGCAGAAGTGAATCCACCCGCGCCGCCGGTCAAAGCCTCCTGGGTCCATAAAACAGGCTCGACGGGCGGGTTTGGCAGCTACGTGGCATTTATTCCTGAAAAGCAGCTCGGCATTGTGATGCTGGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCGTATCCTCGACGCGCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3002171","ARO_id":"38571","ARO_name":"MIR-6","CARD_short_name":"MIR-6","ARO_description":"MIR-6 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36197":{"category_aro_accession":"3000058","category_aro_cvterm_id":"36197","category_aro_name":"MIR beta-lactamase","category_aro_description":"MIR beta-lactamases are plasmid-mediated beta-lactamases that confer resistance to oxyimino- and alpha-methoxy beta-lactams.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1137":{"model_id":"1137","model_name":"TEM-90","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1804":{"protein_sequence":{"accession":"AAK30619.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTGGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AF351241.1","fmin":"89","fmax":"950","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGGTGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000957","ARO_id":"37337","ARO_name":"TEM-90","CARD_short_name":"TEM-90","ARO_description":"TEM-90 is a broad-spectrum beta-lactamase found in E. coli.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1139":{"model_id":"1139","model_name":"dfrA12","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"5110":{"protein_sequence":{"accession":"ADG84870.1","sequence":"MNSESVRIYLVAAMGANRVIGNGPNIPWKIPGEQKIFRRLTEGKVVVMGRKTFESIGKPLPNRHTLVISRQANYRATGCVVVSTLSHAIALASELGNELYVAGGAEIYTLALPHAHGVFLSEVHQTFEGDAFFPMLNETEFELVSTETIQAVIPYTHSVYARRNG"},"dna_sequence":{"accession":"GU585907.1","fmin":"21605","fmax":"22103","strand":"-","sequence":"ATGAACTCGGAATCAGTACGCATTTATCTCGTTGCTGCGATGGGAGCCAATCGGGTTATTGGCAATGGTCCTAATATCCCCTGGAAAATTCCGGGTGAGCAGAAGATTTTTCGCAGACTCACTGAGGGAAAAGTCGTTGTCATGGGGCGAAAGACCTTTGAGTCTATCGGCAAGCCTCTACCGAACCGTCACACATTGGTAATCTCACGCCAAGCTAACTACCGCGCCACTGGCTGCGTAGTTGTTTCAACGCTGTCGCACGCTATCGCTTTGGCATCCGAACTCGGCAATGAACTCTACGTCGCGGGCGGAGCTGAGATATACACTCTGGCACTACCTCACGCCCACGGCGTGTTTCTATCTGAGGTACATCAAACCTTCGAGGGTGACGCCTTCTTCCCAATGCTCAACGAAACAGAATTCGAGCTTGTCTCAACCGAAACCATTCAAGCTGTAATTCCGTACACCCACTCCGTTTATGCGCGTCGAAACGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002858","ARO_id":"39292","ARO_name":"dfrA12","CARD_short_name":"dfrA12","ARO_description":"dfrA12 is an integron-encoded dihydrofolate reductase found in Vibrio cholerae.","ARO_category":{"37617":{"category_aro_accession":"3001218","category_aro_cvterm_id":"37617","category_aro_name":"trimethoprim resistant dihydrofolate reductase dfr","category_aro_description":"Alternative dihydropteroate synthase dfr present on plasmids produces alternate proteins that are less sensitive to trimethoprim from inhibiting its role in folate synthesis, thus conferring trimethoprim resistance.","category_aro_class_name":"AMR Gene Family"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1140":{"model_id":"1140","model_name":"CMY-86","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1197":{"protein_sequence":{"accession":"AHL39327.1","sequence":"MMKKSLCCALLLTAPFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADITNNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGISLLHLATYTAGGLPLQIPDDVTDKAALLRFYQNWQPQWAPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQSEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQVNMDASRVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEVAWHILEKLQ"},"dna_sequence":{"accession":"KJ207204.1","fmin":"579","fmax":"1725","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCCCTTTCTCCACGTTTGCCGCAGCCAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCACCAATAACCACCCAGTCACGCAGCAAACTCTGTTTGAGCTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCAGCCTGCTGCACTTAGCCACCTACACGGCAGGCGGCCTGCCGCTGCAGATCCCCGATGACGTTACGGATAAAGCCGCATTACTGCGTTTTTATCAAAACTGGCAGCCGCAATGGGCCCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACAGTTCCGCAAAGCGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCTGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGTCAACATGGACGCCAGCCGCGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGTAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGATCCACTGGAGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGTGGCCTGGCACATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002099","ARO_id":"38499","ARO_name":"CMY-86","CARD_short_name":"CMY-86","ARO_description":"CMY-86 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1141":{"model_id":"1141","model_name":"OXA-169","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1525":{"protein_sequence":{"accession":"ADK35873.1","sequence":"MNKYFTCYVVASLFLSGCTVQHNLINETPSQIVQGHNQVIHQYFDERNTSGVLVIQTDKKINLYGNALSRANTEYVPASTFKMLNALIGLENQKTDINEIFKWKGEKRSFTAWEKDMTLGEAMKLSAVPVYQELARRIGLDLMQKEVKRIGFGNAEIGQQVDNFWLVGPLKVTPIQEVEFVSQLAHTQLPFSEKVQANVKNMLLLEESNGYKIFGKTGWAMDIKPQVGWLTGWVEQPDGKIVAFALNMEMRSEMPASIRNELLMKSLKQLNII"},"dna_sequence":{"accession":"HM488990.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGAATAAATATTTTACTTGCTATGTGGTTGCTTCTCTTTTTCTTTCTGGTTGTACGGTTCAGCATAATTTAATAAATGAAACCCCGAGTCAGATTGTTCAAGGACATAATCAGGTGATTCATCAATACTTTGATGAAAGAAACACCTCAGGTGTGCTGGTTATTCAAACAGATAAAAAAATTAATCTATATGGTAATGCTCTAAGCCGCGCAAATACAGAATATGTGCCAGCCTCTACATTTAAAATGTTGAATGCCCTGATCGGATTGGAGAACCAGAAAACGGATATTAATGAAATATTTAAATGGAAGGGCGAGAAAAGGTCATTTACCGCTTGGGAAAAAGACATGACACTAGGAGAAGCCATGAAGCTTTCTGCAGTCCCAGTCTATCAGGAACTTGCGCGACGTATCGGTCTTGATCTCATGCAAAAAGAAGTAAAACGTATTGGTTTCGGTAATGCTGAAATTGGACAGCAGGTTGATAATTTCTGGTTGGTAGGACCATTAAAGGTTACGCCTATTCAAGAGGTAGAGTTTGTTTCCCAATTAGCACATACACAGCTTCCATTTAGTGAAAAAGTGCAGGCTAATGTAAAAAATATGCTTCTTTTAGAAGAGAGTAATGGCTACAAAATTTTTGGAAAGACTGGTTGGGCAATGGATATAAAACCACAAGTGGGCTGGTTGACCGGCTGGGTTGAGCAGCCAGATGGAAAAATTGTCGCTTTTGCATTAAATATGGAAATGCGGTCAGAAATGCCGGCATCTATACGTAATGAATTATTGATGAAATCATTAAAACAGCTGAATATTATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001469","ARO_id":"37869","ARO_name":"OXA-169","CARD_short_name":"OXA-169","ARO_description":"OXA-169 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46499":{"category_aro_accession":"3007710","category_aro_cvterm_id":"46499","category_aro_name":"OXA-23-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases, specifically imipenem, derived from OXA-23, first identified in Acinetobacter baumannii.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1142":{"model_id":"1142","model_name":"dfrA17","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"291":{"protein_sequence":{"accession":"ABG91835.1","sequence":"MKISLISAVSENGVIGSGPDIPWSVKGEQLLFKALTYNQWLLVGRKTFDSMGVLPNRKYAVVSKNGISSSNENVLVFPSIENALKELSKVTDHVYVSGGGQIYNSLIEKADIIHLSTVHVEVEGDIKFPIMPENFNLVFEQFFMSNINYTYQIWKKG"},"dna_sequence":{"accession":"DQ838665.1","fmin":"0","fmax":"474","strand":"+","sequence":"TTGAAAATATCATTGATTTCTGCAGTGTCAGAAAATGGCGTAATCGGTAGTGGTCCTGATATCCCGTGGTCAGTAAAAGGTGAGCAACTACTCTTTAAAGCGCTCACATATAATCAATGGCTCCTTGTCGGAAGAAAAACATTTGACTCTATGGGTGTTCTTCCAAATCGCAAATATGCAGTAGTGTCAAAGAACGGAATTTCAAGCTCAAATGAAAACGTCCTAGTTTTTCCTTCAATAGAAAATGCTTTGAAAGAGCTATCAAAAGTTACAGATCATGTATATGTCTCTGGCGGGGGTCAAATCTATAATAGCCTTATTGAAAAAGCAGATATAATTCATTTGTCTACTGTTCACGTTGAAGTCGAAGGTGATATCAAATTCCCTATAATGCCTGAGAATTTCAATTTGGTTTTTGAACAGTTTTTTATGTCTAATATAAATTATACATACCAGATTTGGAAAAAAGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002860","ARO_id":"39294","ARO_name":"dfrA17","CARD_short_name":"dfrA17","ARO_description":"dfrA17 is an integron-encoded dihydrofolate reductase found in Escherichia coli.","ARO_category":{"37617":{"category_aro_accession":"3001218","category_aro_cvterm_id":"37617","category_aro_name":"trimethoprim resistant dihydrofolate reductase dfr","category_aro_description":"Alternative dihydropteroate synthase dfr present on plasmids produces alternate proteins that are less sensitive to trimethoprim from inhibiting its role in folate synthesis, thus conferring trimethoprim resistance.","category_aro_class_name":"AMR Gene Family"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1143":{"model_id":"1143","model_name":"OXA-7","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"894":{"protein_sequence":{"accession":"CAA53242.1","sequence":"MKTFAAYVITACLSSTALASSITENTFWNKEFSAEAVNGVFVLCKSSSKLACATNNLARASKEYLPASTFKIPNAIIGLETGVIKNEHQIFKWDGKPRAMKQWERDLSLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLFLNKLSASKENQLIVKEALVTEAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKGAEVYFFAFNMDIDNENKLPLRKSIPTKIMASEGIIGG"},"dna_sequence":{"accession":"X75562.1","fmin":"134","fmax":"935","strand":"+","sequence":"ATGAAAACATTTGCCGCATATGTAATTACTGCGTGTCTTTCAAGTACGGCATTAGCTAGTTCAATTACAGAAAATACGTTTTGGAACAAAGAGTTCTCTGCCGAAGCCGTCAATGGTGTTTTCGTGCTTTGTAAAAGTAGCAGTAAATTAGCCTGCGCTACCAATAACTTAGCTCGTGCATCAAAGGAATATCTTCCAGCATCAACATTTAAGATCCCCAACGCAATTATCGGCCTAGAAACTGGTGTCATAAAGAATGAGCATCAGATTTTCAAATGGGACGGAAAGCCAAGAGCCATGAAACAATGGGAAAGAGACTTGAGCTTAAGAGGGGCAATACAAGTTTCAGCGGTTCCCGTATTTCAACAAATCGCCAGAGAAGTTGGCGAAGTAAGAATGCAGAAATATCTTAAAAAATTTTCATATGGTAACCAGAATATCAGTGGTGGCATTGACAAATTCTGGTTGGAGGGTCAGCTTAGAATTTCCGCAGTTAATCAAGTGGAGTTTCTAGAGTCTCTATTTTTAAATAAATTGTCAGCATCAAAAGAAAATCAGCTAATAGTAAAAGAGGCTTTGGTAACGGAGGCGCCTGAATATCTTGTGCATTCAAAAACTGGTTTTTCTGGTGTGGGAACTGAGTCAAATCCTGGTGTCGCATGGTGGGTTGGTTGGGTTGAGAAGGGAGCAGAGGTTTACTTTTTCGCCTTTAACATGGATATAGACAACGAAAATAAGTTGCCGCTAAGAAAATCCATTCCCACCAAAATCATGGCAAGTGAGGGCATCATTGGTGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001402","ARO_id":"37802","ARO_name":"OXA-7","CARD_short_name":"OXA-7","ARO_description":"OXA-7 is a beta-lactamase found in P. aeruginosa and Enterobacteriaceae.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46486":{"category_aro_accession":"3007697","category_aro_cvterm_id":"46486","category_aro_name":"OXA-10-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-10.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1004":{"model_id":"1004","model_name":"vanR gene in vanD cluster","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"122":{"protein_sequence":{"accession":"AAM09851.1","sequence":"MNEKILVVDDEKELADLVEVYLKNDGYTVYKFYNGRDALNCIESVELDLAILDIMLPDIDGFQICQKIREKFYFPVIMLTAKVEDGDKIMGLSVADDYITKPFNPLEVVARVKAQLRQYMRYKQPCIKQEAERTEYDIRGMTISKSSHKCILFGKEIQLTPTEFSILWYLCERQGTVVSTEELFEAVWGERYFDSNNTVMAHIGRLREKMKEPSRNPKFIKTVWGVGYTIEK"},"dna_sequence":{"accession":"AY082011.1","fmin":"0","fmax":"699","strand":"+","sequence":"ATGAATGAAAAAATCTTAGTGGTTGACGATGAAAAAGAGTTGGCCGACTTAGTTGAAGTGTACCTGAAAAACGATGGATATACCGTTTATAAATTTTATAATGGCAGGGACGCATTAAATTGCATTGAATCCGTGGAACTGGATTTAGCCATACTGGATATCATGCTCCCGGATATTGACGGTTTTCAAATCTGCCAGAAAATCCGGGAGAAGTTCTACTTCCCTGTTATCATGCTGACAGCGAAAGTAGAAGATGGGGATAAAATCATGGGGCTGTCCGTTGCAGATGATTATATTACGAAGCCGTTTAATCCGCTGGAAGTGGTTGCGAGGGTAAAGGCACAGCTAAGGCAGTACATGCGGTACAAGCAGCCCTGCATAAAGCAGGAGGCTGAACGCACGGAATACGATATCCGGGGGATGACAATCAGCAAGAGCAGCCATAAGTGTATCTTGTTTGGAAAGGAAATTCAACTGACACCAACGGAATTTTCGATCCTTTGGTATCTGTGCGAGCGTCAGGGAACGGTAGTTTCTACGGAGGAATTATTCGAGGCAGTATGGGGCGAGCGGTATTTTGACAGCAATAATACCGTGATGGCGCATATTGGGCGTCTCAGAGAGAAAATGAAGGAACCGTCAAGAAACCCGAAGTTCATAAAAACCGTGTGGGGAGTTGGATATACCATTGAAAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36779","NCBI_taxonomy_name":"Enterococcus faecium","NCBI_taxonomy_id":"1352"}}}},"ARO_accession":"3002923","ARO_id":"39357","ARO_name":"vanR gene in vanD cluster","CARD_short_name":"vanR_in_vanD_cl","ARO_description":"Also known as vanRD, is a mutated vanR variant found in the vanD gene cluster that caused constitutive expression of vanD peptidoglycan synthesis.","ARO_category":{"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"36713":{"category_aro_accession":"3000574","category_aro_cvterm_id":"36713","category_aro_name":"vanR","category_aro_description":"VanR is a OmpR-family transcriptional activator in the VanSR regulatory system. When activated by VanS, it promotes cotranscription of VanA, VanH, and VanX.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"35948":{"category_aro_accession":"0000029","category_aro_cvterm_id":"35948","category_aro_name":"teicoplanin","category_aro_description":"Teicoplanin is a glycopeptide antibiotic used in the prophylaxis and treatment of serious infections caused by Gram-positive bacteria. Teicoplanin has a unique acyl-aliphatic chain, and binds to cell wall precursors to inhibit transglycosylation  and transpeptidation.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1030":{"model_id":"1030","model_name":"vanZ gene in vanA cluster","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"250"}},"model_sequences":{"sequence":{"3280":{"protein_sequence":{"accession":"AAA65959.1","sequence":"MGKILSRGLLALYLVTLIWLVLFKLQYNILSVFNYHQRSLNLTPFTATGNFREMIDNVIIFIPFGLLLNVNFKEIGFLPKFAFVLVLSLTFEIIQFIFAIGATDITDVITNTVGGFLGLKLYGLSNKHMNQKKLDRVIIFVGILLLVLLLVYRTHLRINYV"},"dna_sequence":{"accession":"M97297.1","fmin":"10115","fmax":"10601","strand":"+","sequence":"TTGGGAAAAATATTATCTAGAGGATTGCTAGCTTTATATTTAGTGACACTAATCTGGTTAGTGTTATTCAAATTACAATACAATATTTTATCAGTATTTAATTATCATCAAAGAAGTCTTAACTTGACTCCATTTACTGCTACTGGGAATTTCAGAGAGATGATAGATAATGTTATAATCTTTATTCCATTTGGCTTGCTTTTGAATGTCAATTTTAAAGAAATCGGATTTTTACCTAAGTTTGCTTTTGTACTGGTTTTAAGTCTTACTTTTGAAATAATTCAATTTATCTTCGCTATTGGAGCGACAGACATAACAGATGTAATTACAAATACTGTTGGAGGCTTTCTTGGACTGAAATTATATGGTTTAAGCAATAAGCATATGAATCAAAAAAAATTAGACAGAGTTATTATTTTTGTAGGTATACTTTTGCTCGTATTATTGCTCGTTTACCGTACCCATTTAAGAATAAATTACGTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36779","NCBI_taxonomy_name":"Enterococcus faecium","NCBI_taxonomy_id":"1352"}}}},"ARO_accession":"3002962","ARO_id":"39396","ARO_name":"vanZ gene in vanA cluster","CARD_short_name":"vanZ_in_vanA_cl","ARO_description":"Also known as vanZA, is a vanZ variant found in the vanA gene cluster.","ARO_category":{"36255":{"category_aro_accession":"3000116","category_aro_cvterm_id":"36255","category_aro_name":"vanZ","category_aro_description":"VanZ is a teicoplanin resistance gene that is an accessory protein. VanZ prevents the incorporation of the terminal D-Ala into peptidoglycan subunits.","category_aro_class_name":"AMR Gene Family"},"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"35948":{"category_aro_accession":"0000029","category_aro_cvterm_id":"35948","category_aro_name":"teicoplanin","category_aro_description":"Teicoplanin is a glycopeptide antibiotic used in the prophylaxis and treatment of serious infections caused by Gram-positive bacteria. Teicoplanin has a unique acyl-aliphatic chain, and binds to cell wall precursors to inhibit transglycosylation  and transpeptidation.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1045":{"model_id":"1045","model_name":"ErmO-srmA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"5447":{"protein_sequence":{"accession":"CAA11706.1","sequence":"MARPTQRARTLSQNFLADRAAAAHVARLTAPDRRHPPLVLEVGAGKGALTEPLARRSRELHAYEIDSRLVPGLRTRFAAAPHVRVVAGDFLAARPPRTPFSVAGNVPFSRTADIVDWCLGAPALTDATLITQLEYARKRTGDYGRWTLLTVRTWPHHEWRLVGRVSRYGFRPAPRVDAGVLRIERRATPLLTGAAQHGWRDLVELGFSGVGGSLHASLRRAHPRRRVDAAFRAARLDPGVLVGEVAPARWLRLHEELAS"},"dna_sequence":{"accession":"AJ223970.1","fmin":"20","fmax":"800","strand":"+","sequence":"ATGGCCCGCCCCACCCAGCGTGCGCGCACGCTCTCGCAGAACTTCCTCGCCGACCGCGCCGCCGCCGCACACGTCGCCCGGCTGACCGCCCCCGACCGTCGGCACCCGCCGCTCGTCCTGGAAGTGGGCGCCGGCAAGGGCGCCCTCACCGAGCCGCTCGCCCGCCGCAGCCGGGAGCTGCACGCCTACGAGATCGACTCCAGGCTCGTCCCCGGGCTGCGCACCCGTTTCGCCGCCGCACCCCATGTCCGCGTGGTCGCCGGTGACTTCCTCGCCGCGCGGCCTCCGCGCACGCCGTTCTCCGTCGCCGGGAACGTGCCCTTCTCCCGCACGGCGGACATCGTCGACTGGTGCCTCGGCGCGCCGGCCCTCACCGACGCCACCCTGATCACCCAGCTCGAGTACGCACGCAAACGCACCGGCGACTACGGCCGTTGGACCCTGCTGACGGTACGGACCTGGCCCCACCACGAGTGGCGCCTGGTGGGACGCGTGAGCCGCTACGGCTTCCGGCCGGCGCCCCGCGTCGACGCGGGCGTCCTCCGTATCGAGCGCCGCGCCACCCCGCTGCTCACCGGTGCCGCCCAGCACGGCTGGCGGGACCTGGTCGAGCTGGGCTTCTCCGGAGTCGGCGGCTCGCTGCACGCGTCCCTGCGCCGGGCACACCCCAGGCGCCGGGTGGACGCGGCGTTCCGGGCGGCCCGGCTGGACCCCGGGGTGCTCGTCGGCGAGGTGGCGCCGGCGCGGTGGCTGCGGCTGCACGAGGAGCTGGCGTCGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36864","NCBI_taxonomy_name":"Streptomyces ambofaciens","NCBI_taxonomy_id":"1889"}}}},"ARO_accession":"3001303","ARO_id":"37702","ARO_name":"ErmO-srmA","CARD_short_name":"ErmO-srmA","ARO_description":"ErmO (gene srmA) is a methyltransferase found in the spiramycin producer Streptomyces ambofaciens. Like other Erm enzymes, it catalyzes the methylation of A2058 of the 23S ribosomal RNA. Specifically, this enzyme transfers only one methyl group. The gene is responsible for self-resistance to spiramycin.","ARO_category":{"36699":{"category_aro_accession":"3000560","category_aro_cvterm_id":"36699","category_aro_name":"Erm 23S ribosomal RNA methyltransferase","category_aro_description":"Erm proteins are part of the RNA methyltransferase family and methylate A2058 (E. coli nomenclature) of the 23S ribosomal RNA conferring degrees of resistance to Macrolides, Lincosamides and Streptogramin b. This is called the MLSb phenotype.","category_aro_class_name":"AMR Gene Family"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"36295":{"category_aro_accession":"3000156","category_aro_cvterm_id":"36295","category_aro_name":"spiramycin","category_aro_description":"Spiramycin is a 16-membered macrolide and is natural product produced by Streptomyces ambofaciens. It binds to the 50S subunit of bacterial ribosomes and inhibits peptidyl transfer activity to disrupt protein synthesis.","category_aro_class_name":"Antibiotic"},"37627":{"category_aro_accession":"3001228","category_aro_cvterm_id":"37627","category_aro_name":"carbomycin","category_aro_description":"Produced by Streptomyces halstedii and Streptomyces thermotolerans.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1109":{"model_id":"1109","model_name":"CAU-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"760":{"protein_sequence":{"accession":"CAC87665.1","sequence":"MKRLILAAAASLLALASAAHADDMPANWTKPTKPYRVVGNIYYVGTEGISSWLITSSEGHVVLDGGPNAETGKLVERNITALGFQLADVKILINTHAHYDHAGGLAQLKADTGAKLWISRDDAPAMAAGHHIGDNIYGPTPMPAAKPDRSFGDQTKLKLGEIAMVAHLTPGHTIGCTSWTTAVVEKGRPLTVTFPCSLSVAGNVLVGNKTHRTIVADYRASFAKLRAIPTDVMLPAHEEQGNLLAKRQKQLRGDPNAFVDPGELARFVDASEAAFNKELARQQAAGPNR"},"dna_sequence":{"accession":"AJ308331.1","fmin":"0","fmax":"870","strand":"+","sequence":"ATGAAGCGCCTGATCCTGGCCGCCGCTGCGTCGCTGTTGGCTCTGGCCTCGGCGGCCCACGCCGACGACATGCCGGCCAACTGGACCAAGCCGACCAAGCCCTACCGTGTGGTCGGCAACATCTATTACGTCGGCACCGAGGGCATCTCGTCCTGGCTGATCACGTCGTCCGAGGGCCATGTGGTGCTGGACGGCGGGCCGAACGCCGAGACGGGCAAGCTGGTCGAGCGCAACATCACGGCGCTGGGCTTCCAGCTTGCGGACGTGAAGATCCTGATCAACACCCACGCCCACTACGATCACGCCGGCGGTCTGGCGCAGTTGAAGGCCGACACCGGCGCCAAGCTGTGGATCTCGCGCGACGACGCCCCGGCCATGGCGGCGGGCCACCACATCGGCGACAATATCTATGGCCCAACGCCGATGCCGGCCGCCAAGCCCGACAGGAGCTTCGGCGACCAGACCAAGCTGAAGCTGGGCGAGATCGCCATGGTCGCCCACCTGACGCCGGGCCACACCATTGGCTGCACCAGCTGGACCACGGCCGTGGTCGAGAAGGGGCGGCCGCTGACCGTCACCTTCCCGTGCTCGCTGTCGGTGGCAGGCAATGTGCTCGTGGGCAACAAGACCCACCGGACCATCGTCGCCGACTATCGCGCCAGCTTCGCCAAGCTGCGCGCCATTCCTACCGACGTGATGCTGCCCGCGCACGAAGAGCAGGGGAACCTGCTGGCCAAGCGCCAGAAGCAGCTGCGCGGTGATCCCAACGCCTTTGTCGACCCAGGCGAGCTTGCCCGGTTCGTCGACGCCTCCGAAGCCGCCTTCAACAAGGAGCTCGCGCGCCAGCAGGCGGCGGGGCCCAACCGATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39075","NCBI_taxonomy_name":"Caulobacter vibrioides","NCBI_taxonomy_id":"155892"}}}},"ARO_accession":"3000855","ARO_id":"37235","ARO_name":"CAU-1","CARD_short_name":"CAU-1","ARO_description":"CAU-1 is a B3 metallo-beta-lactamase that is encoded by the Caulobacter crescentus chromosome.","ARO_category":{"41382":{"category_aro_accession":"3004218","category_aro_cvterm_id":"41382","category_aro_name":"CAU beta-lactamase","category_aro_description":"CAU beta-lactamases are a subclass B3 family.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1119":{"model_id":"1119","model_name":"EBR-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"2046":{"protein_sequence":{"accession":"AAN32638.1","sequence":"MKKLFSLIALIGSFAFGQIKPIQIDPINNNLFVYQTFNSFNGVEYNANGMYLVTNKGIVLFDVPWQKSQYQELNDMLQEKYNLPVIAVFATHSHDDRAGDLSFYNELNIPTYATSLTNSKLKKEGKATSKFEIELGKTYKFGNEKFVFEYFGEGHTSDNVVVWFPKYKVLNGGCLIKGADAVNLGYTGEANVVEWPKTVHKLVAKHPTIKQVIPGHDNWKATGHIENTFKLLEKK"},"dna_sequence":{"accession":"AF416700.1","fmin":"56","fmax":"764","strand":"+","sequence":"ATGAAGAAATTATTTTCACTTATTGCATTGATAGGAAGTTTTGCATTTGGTCAAATAAAACCAATTCAAATTGATCCGATTAATAACAATCTATTTGTTTATCAAACATTCAATTCGTTTAATGGTGTTGAGTACAATGCAAATGGAATGTATTTGGTAACGAATAAAGGAATTGTTTTATTTGATGTTCCTTGGCAAAAATCGCAGTATCAAGAGTTAAATGATATGTTACAAGAAAAGTATAATTTGCCAGTTATCGCTGTCTTTGCAACACATTCGCATGATGATAGAGCAGGGGATTTGAGTTTTTATAATGAGTTGAATATTCCTACTTATGCAACTTCTTTAACCAATTCTAAATTAAAAAAAGAAGGAAAAGCGACTTCTAAATTTGAGATTGAATTAGGTAAAACATACAAGTTTGGTAACGAAAAATTTGTTTTTGAATATTTTGGAGAAGGACATACTTCTGATAATGTTGTGGTGTGGTTTCCGAAATATAAAGTGTTGAACGGAGGTTGTTTGATAAAGGGTGCTGATGCTGTAAATTTAGGTTACACAGGCGAAGCTAATGTTGTTGAATGGCCAAAAACAGTACACAAACTAGTTGCAAAACATCCAACGATTAAACAAGTTATTCCAGGCCATGATAATTGGAAAGCTACTGGACATATCGAAAATACTTTTAAACTTTTAGAAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39071","NCBI_taxonomy_name":"Empedobacter brevis","NCBI_taxonomy_id":"247"}}}},"ARO_accession":"3000842","ARO_id":"37222","ARO_name":"EBR-1","CARD_short_name":"EBR-1","ARO_description":"EBR-1 is an Ambler class B beta-lactamase found in Empedobacter brevis and is known to mediate the hydrolysis of penicillins, cephalosporins, and carbapenems efficiently but not aztreonam.","ARO_category":{"41368":{"category_aro_accession":"3004204","category_aro_cvterm_id":"41368","category_aro_name":"EBR beta-lactamase","category_aro_description":"EBR beta-lactamases are Class B beta-lactamases first isolated from Empedobacter brevis and are able to hydrolyze penicillins, cephalosporins, and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1145":{"model_id":"1145","model_name":"CTX-M-124","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1333":{"protein_sequence":{"accession":"AFH88134.1","sequence":"MMTQSIRRSMLTVMATLPLLFSSATLHAQANSVQQQLEALEKSSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKQSESDKHLLNQRVEIKKSDLVNYNPIAEKHVNGTMTLAELGAAALQYSDNTAMNKLIAHLGGPDKVTAFARSLGDETFRLDRTEPTLNTAIPGDPRDTTTPLAMAQTLKNLTLGKALAETQRAQLVTWLKGNTTGSASIRAGLPKSWVVGDKTGSGDYGTTNDIAIIWPENHAPLVLVTYFTQPEQKAESRRDVLAAAAKIVTHGF"},"dna_sequence":{"accession":"JQ429324.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGATGACTCAGAGCATTCGCCGCTCAATGTTAACGGTGATGGCGACGCTACCCCTGCTATTTAGCAGCGCAACGCTGCATGCGCAGGCGAACAGCGTGCAACAGCAGCTGGAAGCCCTGGAGAAAAGTTCGGGAGGTCGGCTTGGCGTTGCGCTGATTAACACCGCCGATAATTCGCAGATTCTCTACCGTGCCGATGAACGTTTTGCGATGTGCAGTACCAGTAAGGTGATGGCGGCCGCGGCGGTGCTTAAACAGAGCGAGAGCGATAAGCACCTGCTAAATCAGCGCGTTGAAATCAAGAAGAGCGACCTGGTTAACTACAATCCCATTGCTGAGAAACACGTTAACGGCACTATGACGCTGGCTGAGCTTGGCGCAGCGGCGCTGCAGTATAGCGACAATACTGCCATGAATAAGCTGATTGCCCATCTGGGTGGGCCCGATAAAGTGACGGCGTTTGCTCGCTCGTTGGGTGATGAGACCTTCCGTCTGGACAGAACCGAGCCCACGCTCAATACCGCCATTCCAGGCGACCCGCGTGATACCACCACGCCGCTCGCGATGGCGCAGACCCTGAAAAATCTGACGCTGGGTAAAGCGCTGGCGGAAACTCAGCGGGCACAGTTGGTGACGTGGCTTAAGGGCAATACTACCGGTAGCGCGAGCATTCGGGCGGGTCTGCCGAAATCATGGGTAGTGGGCGATAAAACCGGCAGCGGAGATTATGGCACCACCAACGATATCGCGATTATCTGGCCGGAAAACCACGCACCGCTGGTTCTGGTGACCTACTTTACCCAACCGGAGCAGAAGGCGGAAAGCCGTCGGGATGTTCTGGCTGCGGCGGCGAAAATCGTAACCCACGGTTTCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001983","ARO_id":"38383","ARO_name":"CTX-M-124","CARD_short_name":"CTX-M-124","ARO_description":"CTX-M-124 is a beta-lactamase found in Escherichia coli.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1146":{"model_id":"1146","model_name":"TEM-156","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1400":{"protein_sequence":{"accession":"CAQ00120.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNIGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AM941159.1","fmin":"208","fmax":"1069","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATAGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3001022","ARO_id":"37402","ARO_name":"TEM-156","CARD_short_name":"TEM-156","ARO_description":"TEM-156 is a TEM beta-lactamase.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1147":{"model_id":"1147","model_name":"CMY-63","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1859":{"protein_sequence":{"accession":"AET07387.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADITNNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGISLLHLATYTAGGLPLQIPDDVTDKAALLRFYQNWQPQWAPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKAVHVSPGQLDAEAYGVKSSVIDMARWVQVNMDASRVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKKLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"HQ650104.1","fmin":"63","fmax":"1209","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCATTCTCCACGTTTGCCGCCGCCAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCACCAATAACCACCCAGTCACGCAGCAAACTCTGTTTGAGCTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCAGCCTGCTGCACTTAGCCACCTACACGGCAGGCGGCCTGCCGCTGCAGATCCCCGATGACGTTACGGATAAAGCCGCATTACTGCGTTTTTATCAAAACTGGCAGCCGCAATGGGCCCCGGGCGCTAAGAGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGTATGAGCTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACAGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGGCTGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGTGTTATTGATATGGCCCGCTGGGTTCAGGTCAACATGGACGCCAGCCGCGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCAATCATCAACGGTAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCTGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGATCCACTGGAGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAAACTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002076","ARO_id":"38476","ARO_name":"CMY-63","CARD_short_name":"CMY-63","ARO_description":"CMY-63 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1148":{"model_id":"1148","model_name":"OXA-363","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"890":{"protein_sequence":{"accession":"AHA11126.1","sequence":"MKTLIFLPLLNCLSLTACTLPVSSSPSHITSTQSTQAIAQLFDQAQSSGVLVIQRGQQIQVYGNDLSRADTEYVPASTFKMLNALIGLQHGKATTNEIFKWDGKKRSFSAWEKDMTLGQAMQASAVPVYQELARRIGLELMQQEVQRIQFGNQQIGQQVDNFWLVGPLKITPKQEVEFVSALAREQLAFDPQVQQQVKAMLLLQERKAYRLYAKSGWGMDVEPQVGWLTGWVETPQAEIVAFSLNMQMQNGMDPAIRLEILQQALAELGLYPKAEG"},"dna_sequence":{"accession":"KF460533.1","fmin":"0","fmax":"831","strand":"+","sequence":"ATGAAAACTCTGATTTTTCTGCCTTTACTTAATTGCTTGAGCCTGACGGCGTGTACCTTACCCGTTTCATCTTCCCCATCTCATATCACTTCGACTCAATCGACTCAAGCCATTGCCCAATTATTTGATCAGGCGCAAAGCTCTGGCGTTTTAGTGATTCAGCGTGGTCAACAGATACAGGTCTATGGCAATGATTTAAGCCGTGCAGATACCGAATATGTTCCCGCCTCTACTTTTAAAATGCTCAATGCCCTGATTGGCCTGCAACATGGCAAAGCCACAACCAATGAAATTTTTAAATGGGATGGTAAGAAACGTAGTTTTTCAGCCTGGGAAAAAGACATGACTCTCGGCCAAGCCATGCAAGCTTCTGCTGTACCCGTCTATCAGGAACTGGCGCGTCGTATTGGCCTTGAACTGATGCAACAGGAAGTACAACGCATCCAATTTGGTAATCAGCAGATTGGTCAGCAAGTCGATAATTTCTGGTTGGTAGGCCCTTTGAAAATCACTCCAAAACAGGAGGTCGAATTTGTCTCGGCTCTAGCCCGAGAGCAGCTTGCCTTTGATCCACAAGTCCAGCAGCAAGTCAAAGCCATGTTACTTTTACAGGAGCGGAAAGCTTATCGACTATATGCCAAATCTGGTTGGGGCATGGATGTGGAACCACAAGTCGGCTGGCTCACCGGCTGGGTTGAAACACCGCAGGCTGAAATCGTGGCATTTTCGCTGAATATGCAGATGCAAAATGGTATGGATCCGGCAATCCGCCTTGAAATTTTACAGCAGGCTTTGGCCGAATTAGGGCTTTATCCAAAAGCTGAAGGATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36948","NCBI_taxonomy_name":"Acinetobacter lwoffii","NCBI_taxonomy_id":"28090"}}}},"ARO_accession":"3001550","ARO_id":"37950","ARO_name":"OXA-363","CARD_short_name":"OXA-363","ARO_description":"OXA-363 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46489":{"category_aro_accession":"3007700","category_aro_cvterm_id":"46489","category_aro_name":"OXA-134-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-134.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1149":{"model_id":"1149","model_name":"AER-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"901":{"protein_sequence":{"accession":"AAC09015.1","sequence":"MYVLSVEKPTLRNKFAAGIGVVLVCVVASFIPTPVFALDTTKLIQAVQSEESALHARVGMTVFDSNTGTTWNYRGDERFPLNSTHKTFSCAALLAKVDGKSLSLGQSVSISKEMLVTYSPITEKSLSPETVTFGKICQAAVSYSDNTAANVVFDAIGGATGFNAYMRSIGDEETQLDRKEPELNEGTPGDVRDTTTPNAMVNSLRKILLGDALSASSRSQLTQWMLDDQVAGALLRASLPSDWKIADKTGAGGYGSRSIVAVIWPPSKQPLVVGIYITQTKASMQASNQAIARIGVVLKDTVAP"},"dna_sequence":{"accession":"U14748.1","fmin":"324","fmax":"1239","strand":"+","sequence":"ATGTACGTACTTTCCGTGGAGAAACCTACATTGAGAAACAAATTTGCGGCCGGAATAGGCGTCGTGCTTGTATGTGTCGTTGCCTCGTTTATTCCAACCCCAGTATTCGCCCTAGACACCACGAAGCTGATCCAAGCCGTCCAGTCGGAAGAGAGCGCCTTGCATGCCCGAGTCGGCATGACCGTGTTTGACTCAAACACTGGAACGACTTGGAACTATCGGGGCGATGAGCGGTTTCCATTGAACAGTACGCACAAGACGTTTTCCTGTGCAGCTTTGCTCGCGAAGGTCGATGGGAAGTCCCTCTCTCTGGGCCAATCCGTATCGATCAGCAAGGAAATGCTGGTCACCTATTCGCCGATTACGGAAAAGTCGCTGTCACCCGAAACCGTTACCTTCGGCAAGATTTGTCAGGCAGCGGTGAGCTATAGCGATAACACAGCCGCAAACGTCGTCTTTGATGCCATTGGAGGAGCAACCGGATTCAACGCATACATGCGGTCTATCGGCGATGAAGAAACCCAGCTTGATCGCAAAGAACCCGAGTTGAACGAAGGTACGCCGGGCGATGTGCGTGACACCACCACTCCCAACGCCATGGTCAATAGTCTTAGGAAGATACTTCTTGGCGACGCGTTGTCAGCATCATCCCGATCCCAGCTGACGCAATGGATGCTGGACGATCAGGTTGCTGGTGCGCTCCTGCGTGCCTCACTGCCATCCGATTGGAAGATCGCCGACAAGACCGGCGCGGGGGGTTACGGCTCACGCTCGATCGTCGCAGTAATCTGGCCGCCATCGAAGCAGCCACTGGTGGTTGGCATCTATATCACGCAAACCAAAGCATCCATGCAGGCCAGCAATCAGGCGATTGCAAGGATAGGAGTGGTGCTGAAGGATACGGTCGCTCCTTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36810","NCBI_taxonomy_name":"Aeromonas hydrophila","NCBI_taxonomy_id":"644"}}}},"ARO_accession":"3002481","ARO_id":"38881","ARO_name":"AER-1","CARD_short_name":"AER-1","ARO_description":"AER-1 is a beta-lactamase found in Aeromonas hydrophila.","ARO_category":{"36228":{"category_aro_accession":"3000089","category_aro_cvterm_id":"36228","category_aro_name":"AER beta-lactamase","category_aro_description":"AER beta-lactamases are capable of hydrolyzing arbenicillin.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1150":{"model_id":"1150","model_name":"QnrVC5","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"572":{"protein_sequence":{"accession":"AEM62764.1","sequence":"MDKTDQLYVQADFSHQDMSGQYFKNCKFFCCSFKRANLRDTQFVDCSFIERGELEGCDFSYSDLRDASFKNCSLSMSYFKGANCFGIEFRECDLKGANFSQASFMNQVSNRMYFCSAYITGCNLSYANFERQCIEKCDLFENRWIGANLSGASFKESDLSRGVFSEGCWSQCRLQGCDLSHSELYGLDPRKVDLTGVKICSWQQEQLLEQLGLIVVPD"},"dna_sequence":{"accession":"JN408080.1","fmin":"0","fmax":"657","strand":"+","sequence":"ATGGATAAAACAGACCAGTTATATGTACAAGCAGACTTTTCACATCAAGACATGAGTGGTCAGTATTTTAAAAATTGCAAATTTTTCTGCTGTTCCTTTAAACGAGCGAACCTCCGCGATACACAATTTGTAGATTGTTCTTTCATTGAACGAGGTGAATTAGAGGGGTGTGATTTTTCTTACTCGGATCTTAGAGATGCATCTTTTAAAAACTGCAGTCTTTCAATGTCGTATTTCAAAGGTGCAAATTGTTTTGGTATCGAGTTCAGAGAATGCGATTTAAAGGGTGCCAATTTTTCTCAAGCTAGCTTCATGAATCAGGTATCGAACAGAATGTATTTTTGTTCAGCTTATATAACAGGTTGTAATCTTTCATACGCCAACTTTGAAAGGCAGTGTATCGAAAAGTGTGATTTGTTTGAGAATAGATGGATTGGCGCAAATCTGAGTGGTGCATCATTTAAAGAGTCTGATTTAAGTCGGGGAGTATTTTCTGAAGGGTGTTGGAGCCAGTGTAGGTTGCAAGGTTGTGATTTGAGCCACTCGGAGTTGTATGGTTTAGACCCTCGGAAAGTTGACCTTACAGGTGTAAAAATCTGTTCGTGGCAGCAAGAACAACTTTTAGAGCAATTAGGTTTAATAGTAGTTCCTGACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39525","NCBI_taxonomy_name":"Vibrio fluvialis","NCBI_taxonomy_id":"676"}}}},"ARO_accession":"3002802","ARO_id":"39236","ARO_name":"QnrVC5","CARD_short_name":"QnrVC5","ARO_description":"QnrVC5 is an integron-mediated quinolone resistance protein found in Vibrio fluvialis.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1151":{"model_id":"1151","model_name":"OXA-240","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1684":{"protein_sequence":{"accession":"AFN20670.1","sequence":"MKTFAAYVIIACLSSTALAGSITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDGKPRAMNQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGIIGG"},"dna_sequence":{"accession":"JX089628.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGAAAACATTTGCCGCATATGTAATTATCGCGTGTCTTTCGAGTACGGCATTAGCTGGTTCAATTACAGAAAATACGTCTTGGAACAAAGAGTTCTCTGCCGAAGCCGTCAATGGTGTCTTCGTGCTTTGTAAAAGTAGCAGTAAATCCTGCGCTACCAATGACTTAGCTCGTGCATCAAAGGAATATCTTCCAGCATCAACATTTAAGATCCCCAACGCAATTATCGGCCTAGAAACTGGTGTCATAAAGAATGAGCATCAGGTTTTCAAATGGGACGGAAAGCCAAGAGCCATGAATCAATGGGAAAGAGACTTGACCTTAAGAGGGGCAATACAAGTTTCAGCTGTTCCCGTATTTCAACAAATCGCCAGAGAAGTTGGCGAAGTAAGAATGCAGAAATACCTTAAAAAATTTTCCTATGGCAACCAGAATATCAGTGGTGGCATTGACAAATTCTGGTTGGAAGGCCAGCTTAGAATTTCCGCAGTTAATCAAGTGGAGTTTCTAGAGTCTCTATATTTAAATAAATTGTCAGCATCTAAAGAAAACCAGCTAATAGTAAAAGAGGCTTTGGTAACGGAGGCGGCACCTGAATATCTAGTGCATTCAAAAACTGGTTTTTCTGGTGTGGGAACTGAGTCAAATCCTGGTGTCGCATGGTGGGTTGGGTGGGTTGAGAAGGAGACAGAGGTTTACTTTTTCGCCTTTAACATGGATATAGACAACGAAAGTAAGTTGCCGCTAAGAAAATCCATTCCCACCAAAATCATGGAAAGTGAGGGCATCATTGGTGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3001499","ARO_id":"37899","ARO_name":"OXA-240","CARD_short_name":"OXA-240","ARO_description":"OXA-240 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46486":{"category_aro_accession":"3007697","category_aro_cvterm_id":"46486","category_aro_name":"OXA-10-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-10.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1152":{"model_id":"1152","model_name":"CTX-M-39","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1431":{"protein_sequence":{"accession":"AAX54694.1","sequence":"MMRKSVRRAMLMTTACVSLLLASVPLCAQANDVQQKLAALEKSSGGRLGVALINTADNTQTLYRADERFAMCSTSKVMAAAAVLKQSETQKGLLSQRVEIKPSDLINYNPIAEKHVNGTMTFGELSAAALQYSDNTAMNKLIAHLGGPDKVTAFARTIGDDTFRLDRTEPTLNTAIPGDPRDTTTPLAMAQALRNLTLGNALGDTQRAQLVMWLKGNTTGAASIQAGLPTSWVVGDKTGSGDYGTTNDIAVIWPEGRAPLVLVTYFTQSEPKAESRRDVLAAAARIVTDGY"},"dna_sequence":{"accession":"AY954516.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGATGAGAAAAAGCGTAAGGCGGGCGATGTTAATGACGACAGCCTGTGTTTCGCTGCTGTTGGCCAGTGTGCCGCTGTGTGCCCAGGCGAACGATGTTCAACAAAAGCTCGCGGCGCTGGAGAAAAGCAGCGGGGGACGACTGGGTGTGGCGTTGATTAACACCGCCGATAACACGCAGACGCTCTACCGCGCCGACGAGCGTTTTGCCATGTGCAGCACCAGTAAAGTGATGGCGGCAGCGGCGGTGCTTAAGCAAAGTGAAACGCAAAAGGGCTTGTTGAGTCAGCGGGTTGAAATTAAGCCCTCAGACTTGATTAACTACAACCCCATTGCGGAAAAACACGTCAATGGCACGATGACATTCGGGGAGTTGAGCGCGGCGGCGCTACAGTACAGCGATAATACTGCCATGAATAAGCTGATTGCCCATCTCGGGGGGCCGGATAAAGTGACGGCATTTGCCCGTACGATTGGCGATGACACGTTCCGGCTCGATCGTACCGAGCCGACGCTCAACACCGCGATCCCCGGCGACCCGCGCGATACCACCACGCCGTTAGCGATGGCGCAGGCTCTGCGCAATCTGACGTTGGGCAATGCCCTGGGTGACACTCAGCGTGCGCAGCTGGTGATGTGGCTGAAAGGCAACACCACCGGCGCTGCCAGCATTCAGGCAGGGCTACCCACATCGTGGGTTGTCGGGGATAAAACCGGCAGCGGCGATTATGGTACGACGAATGATATCGCGGTTATTTGGCCGGAAGGTCGCGCGCCGCTCGTTCTGGTGACTTACTTCACCCAGTCGGAGCCGAAGGCAGAGAGCCGTCGTGACGTGCTCGCTGCTGCCGCCAGAATTGTCACCGACGGTTATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001901","ARO_id":"38301","ARO_name":"CTX-M-39","CARD_short_name":"CTX-M-39","ARO_description":"CTX-M-39 is a beta-lactamase found in Escherichia coli.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1153":{"model_id":"1153","model_name":"KPC-3","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1192":{"protein_sequence":{"accession":"AAL05630.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKYSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"AF395881.1","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGTACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002313","ARO_id":"38713","ARO_name":"KPC-3","CARD_short_name":"KPC-3","ARO_description":"KPC-3 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1154":{"model_id":"1154","model_name":"TEM-146","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8177":{"protein_sequence":{"accession":"AAZ14084.2","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLPDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSHGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"DQ105529.2","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTCCGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCACGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001013","ARO_id":"37393","ARO_name":"TEM-146","CARD_short_name":"TEM-146","ARO_description":"TEM-146 is a beta-lactamase found in E. coli.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1156":{"model_id":"1156","model_name":"Erm(31)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"249":{"protein_sequence":{"accession":"AAC69327.1","sequence":"MAFSPQGGRHELGQNFLVDRSVIDEIDGLVARTKGPILEIGPGDGALTLPLSRHGRPITAVELDGRRAQRLGARTPGHVTVVHHDFLQYPLPRNPHVVVGNVPFHLTTAIMRRLLDAQHWHTAVLLVQWEVARRRAGVGGSTLLTAGWAPWYEFDLHSRVPARAFRPMPGVDGGVLAIRRRSAPLVGQVKTYQDFVRQVFTGKGNGLKEILRRTGRISQRDLATWLRRNEISPHALPKDLKPGQWASLWELTGGTADGSFDGTAGGGAAGSHGAARVGAGHPGGRVSASRRGVPQARRGRGHAVRSSTGTEPRWGRGRAESA"},"dna_sequence":{"accession":"AF079138.1","fmin":"153","fmax":"1122","strand":"+","sequence":"ATGGCATTTTCCCCGCAGGGCGGCCGACACGAGCTCGGTCAGAACTTCCTCGTCGACCGGTCAGTGATCGACGAGATCGACGGCCTGGTGGCCAGGACCAAGGGTCCGATACTGGAGATCGGTCCGGGTGACGGCGCCCTGACCCTGCCGCTGAGCAGGCACGGCAGGCCGATCACCGCCGTCGAGCTCGACGGCCGGCGCGCGCAGCGCCTCGGTGCCCGCACCCCCGGTCATGTGACCGTGGTGCACCACGACTTCCTGCAGTACCCGCTGCCGCGCAACCCGCATGTGGTCGTCGGCAACGTCCCCTTCCATCTGACGACGGCGATCATGCGGCGGCTGCTCGACGCCCAGCACTGGCACACCGCCGTCCTCCTCGTCCAGTGGGAGGTCGCCCGGCGCCGGGCCGGCGTCGGCGGGTCGACGCTGCTGACGGCCGGCTGGGCGCCCTGGTACGAGTTCGACCTGCACTCCCGGGTCCCCGCGCGGGCCTTCCGTCCGATGCCGGGCGTGGACGGAGGAGTACTGGCCATCCGGCGGCGGTCCGCGCCGCTCGTGGGCCAGGTGAAGACGTACCAGGACTTCGTACGCCAGGTGTTCACCGGCAAGGGGAACGGGCTGAAGGAGATCCTGCGGCGGACCGGGCGGATCTCGCAGCGGGACCTGGCGACCTGGCTGCGGAGGAACGAGATCTCGCCGCACGCGCTGCCCAAGGACCTGAAGCCCGGGCAGTGGGCGTCGCTGTGGGAGCTGACCGGCGGCACGGCCGACGGATCCTTCGACGGTACGGCGGGCGGTGGCGCGGCCGGATCGCACGGGGCGGCTCGGGTCGGGGCCGGTCACCCGGGCGGCCGGGTGTCCGCGAGCCGGCGGGGCGTGCCGCAGGCGCGGCGCGGCCGGGGGCATGCGGTACGGAGCTCCACGGGGACCGAGCCGAGGTGGGGCAGGGGGCGGGCGGAGAGCGCGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36873","NCBI_taxonomy_name":"Streptomyces venezuelae","NCBI_taxonomy_id":"54571"}}}},"ARO_accession":"3000598","ARO_id":"36737","ARO_name":"Erm(31)","CARD_short_name":"Erm(31)","ARO_description":"Erm(31) confers a MLSb resistant phenotype. Along with erm(30), these genes are responsible for self-resistance in the pikromycin\/narbomycin\/methymycin\/neomethymycin producer, Streptomyces venezuelae.","ARO_category":{"36699":{"category_aro_accession":"3000560","category_aro_cvterm_id":"36699","category_aro_name":"Erm 23S ribosomal RNA methyltransferase","category_aro_description":"Erm proteins are part of the RNA methyltransferase family and methylate A2058 (E. coli nomenclature) of the 23S ribosomal RNA conferring degrees of resistance to Macrolides, Lincosamides and Streptogramin b. This is called the MLSb phenotype.","category_aro_class_name":"AMR Gene Family"},"37625":{"category_aro_accession":"3001226","category_aro_cvterm_id":"37625","category_aro_name":"narbomycin","category_aro_description":"Produced by Streptomyces narbonensis.","category_aro_class_name":"Antibiotic"},"37631":{"category_aro_accession":"3001232","category_aro_cvterm_id":"37631","category_aro_name":"methymycin","category_aro_description":"Produced by Streptomyces venezuelae ATCC 15439.","category_aro_class_name":"Antibiotic"},"37632":{"category_aro_accession":"3001233","category_aro_cvterm_id":"37632","category_aro_name":"pikromycin","category_aro_description":"Produced by Streptomyces venezuelae ATCC 15439.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1157":{"model_id":"1157","model_name":"vanG","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"250"}},"model_sequences":{"sequence":{"300":{"protein_sequence":{"accession":"ABA71731.1","sequence":"MQNKKIAVIFGGNSTEYEVSLQSASAVFENINTNKFDIIPIGITRSGEWYHYTGEKEKILNNTWFEDSKNLCPVVVSQNRSVKGFLEIASDKYRIIKVDLVFPVLHGKNGEDGTLQGIFELAGIPVVGCDTLSSALCMDKDRAHKLVSLAGISVPKSVTFKRFNEEAAMKEIEANLTYPLFIKPVRAGSSFGITKVIEKQELDAAIELAFEHDTEVIVEETINGFEVGCAVLGIDELIVGRVDEIELSSGFFDYTEKYTLKSSKIYMPARIDAEAEKRIQEAAVTIYKALGCSGFSRVDMFYTPSGEIVFNEVNTIPGFTSHSRYPNMMKGIGLSFSQMLDKLIGLYVE"},"dna_sequence":{"accession":"DQ212986.1","fmin":"5984","fmax":"7034","strand":"+","sequence":"ATGCAAAATAAAAAAATAGCAGTTATTTTTGGAGGCAATTCAACAGAGTACGAGGTGTCATTGCAATCGGCATCCGCTGTTTTTGAAAATATCAATACCAATAAATTTGACATAATTCCAATAGGAATTACAAGAAGTGGTGAATGGTATCACTATACGGGAGAAAAGGAGAAAATCCTAAACAATACTTGGTTTGAAGATAGCAAAAATCTATGCCCTGTTGTCGTTTCCCAAAATCGTTCCGTTAAAGGCTTTTTAGAAATTGCTTCAGACAAATACCGTATTATAAAAGTTGATTTGGTATTCCCCGTATTGCATGGCAAAAACGGCGAAGATGGTACTTTGCAGGGCATATTTGAATTGGCAGGAATACCTGTTGTTGGCTGCGATACACTCTCATCAGCTCTTTGTATGGATAAGGACAGGGCACATAAACTCGTTAGCCTTGCGGGTATATCTGTTCCTAAATCGGTAACATTCAAACGCTTTAACGAAGAAGCAGCGATGAAAGAGATTGAAGCGAATTTAACTTATCCGCTGTTTATTAAACCTGTTCGTGCAGGCTCTTCCTTTGGAATAACAAAAGTAATTGAAAAGCAAGAGCTTGATGCTGCCATAGAGTTGGCATTTGAACACGATACAGAAGTCATCGTTGAAGAAACAATAAACGGCTTTGAAGTCGGTTGTGCCGTACTTGGCATAGATGAGCTCATTGTTGGCAGAGTTGATGAAATCGAACTGTCAAGCGGCTTTTTTGATTATACAGAGAAATATACGCTTAAATCTTCAAAGATATATATGCCTGCAAGGATTGATGCCGAAGCAGAAAAACGGATACAAGAAGCGGCTGTAACCATATATAAAGCTCTGGGCTGTTCGGGTTTTTCCAGAGTGGATATGTTTTATACACCGTCTGGCGAAATTGTATTTAATGAGGTAAACACAATACCAGGCTTTACCTCGCACAGTCGCTATCCAAATATGATGAAAGGCATTGGTCTATCGTTCTCCCAAATGTTGGATAAGCTGATAGGTCTGTATGTGGAATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35918","NCBI_taxonomy_name":"Enterococcus faecalis","NCBI_taxonomy_id":"1351"}}}},"ARO_accession":"3002909","ARO_id":"39343","ARO_name":"vanG","CARD_short_name":"vanG","ARO_description":"VanG is a D-Ala-D-Ala ligase homolog that can synthesize D-Ala-D-Ser, an alternative substrate for peptidoglycan synthesis that reduces vancomycin binding affinity in Enterococcus faecalis.","ARO_category":{"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"39340":{"category_aro_accession":"3002906","category_aro_cvterm_id":"39340","category_aro_name":"Van ligase","category_aro_description":"Van ligases synthesize alternative substrates for peptidoglycan synthesis that reduce vancomycin binding affinity.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1158":{"model_id":"1158","model_name":"SHV-22","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1474":{"protein_sequence":{"accession":"AAF34336.1","sequence":"MLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDKVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGASKRGARGIVALLGPNNKAERIVVIYLRDTPASMAERN"},"dna_sequence":{"accession":"AF117746.1","fmin":"0","fmax":"780","strand":"+","sequence":"CTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTACTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAAGGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTAGCAAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAAT","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001080","ARO_id":"37460","ARO_name":"SHV-22","CARD_short_name":"SHV-22","ARO_description":"SHV-22 is a broad-spectrum beta-lactamase that has been found in clinical isolates.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1159":{"model_id":"1159","model_name":"TEM-129","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1796":{"protein_sequence":{"accession":"CAG34105.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDKLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVKYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDSWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AJ746225.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATAAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTAAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATAGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3000993","ARO_id":"37373","ARO_name":"TEM-129","CARD_short_name":"TEM-129","ARO_description":"TEM-129 is an extended-spectrum beta-lactamase found in Klebsiella oxytoca.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1160":{"model_id":"1160","model_name":"QnrB34","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"512":{"protein_sequence":{"accession":"AEL00452.1","sequence":"MMTLALVGEKIDRNRFTGAKVENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAILKDAIFKSCDLSMAGFRNVSALGIEIRHCRAQGSDFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGTQVLGATFSGSDLSGGEFSSFDWRAANFTHCDLTNSELGDLDVRGVDLQGVKLDSYQASLILERLGIAVIG"},"dna_sequence":{"accession":"JN173056.1","fmin":"35","fmax":"683","strand":"+","sequence":"ATGATGACTCTGGCGTTAGTTGGCGAAAAAATTGACAGAAACAGATTCACTGGTGCGAAAGTTGAAAATAGCACATTTTTCAACTGTGATTTTTCGGGTGCCGACCTCAGCGGTACTGAGTTTATTGGCTGCCAGTTCTATGATCGAGAGAGCCAGAAAGGGTGTAATTTTAGTCGCGCTATCCTGAAAGATGCCATTTTCAAAAGTTGTGATCTCTCCATGGCGGGTTTCAGGAATGTGAGCGCGCTGGGAATCGAAATTCGCCACTGCCGCGCACAAGGTTCAGATTTTCGCGGCGCAAGCTTTATGAATATGATTACCACACGCACCTGGTTTTGTAGCGCCTATATCACCAATACCAACTTAAGCTACGCCAACTTTTCAAAAGTCGTACTGGAAAAGTGCGAGCTGTGGGAAAACCGTTGGATGGGTACTCAGGTACTGGGGGCGACGTTCAGTGGTTCAGATCTTTCCGGCGGTGAGTTTTCGTCGTTCGACTGGCGGGCCGCAAACTTTACGCACTGTGATTTGACCAATTCAGAACTGGGCGATCTCGATGTCCGGGGTGTTGATTTGCAAGGCGTCAAACTGGACAGCTACCAGGCATCGTTGATCCTGGAACGTCTTGGCATCGCTGTCATTGGTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39583","NCBI_taxonomy_name":"Citrobacter werkmanii","NCBI_taxonomy_id":"67827"}}}},"ARO_accession":"3002749","ARO_id":"39183","ARO_name":"QnrB34","CARD_short_name":"QnrB34","ARO_description":"QnrB34 is a plasmid-mediated quinolone resistance protein found in Citrobacter werkmanii.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1161":{"model_id":"1161","model_name":"lsaB","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"5173":{"protein_sequence":{"accession":"CAE18141.1","sequence":"MSMIHVQNLTFSYPSSFDNIFEDVSFQIDTDWKLGFIGRNGRGKTTLFNLLLDKFEYRGKIISSVDFNYFPYPVEDKSKYTHEILEEICPQAEDWEFLREIAYLNVDAEAMYRPFETLSNGEQTKVLLVALFLNEGQFLLIDEPTNHLDTEARKTVSNYLRKKKGNILISHDRNFLDGSVDHILSINRADIEVQSGNYSSWKLNFDRQQGHEQATNERLQKDIGRLEQSTKRSAGWSNRVEASKNGTTNSGSKLDKGFVGHKAAKMMKRSKNLEARQQKSIEEKSKLLKNIEKTESLQFEPVEYKSKELIQLTDVSVIYDGQVVNKPISFNVEQGDRIVLDGKNGSGKSSILKLILGDPIQYTGTLNTGSNLITSYVQQDTSHLKGMLADFIEENEIDESLFKAILRKLDFDRVQFEKDISHYSGGQKKKLLIAKSLCEKAHLYIWDEPLNFIDIYSRMQIEELIQTFNPTMVFVEHDQTFQETISTKIIKI"},"dna_sequence":{"accession":"AJ579365.1","fmin":"4149","fmax":"5628","strand":"+","sequence":"ATGTCAATGATACATGTACAAAATTTAACTTTCTCTTATCCGAGTAGTTTTGATAATATCTTTGAAGATGTAAGCTTTCAAATTGATACAGATTGGAAGCTTGGATTTATTGGTCGAAATGGACGAGGGAAAACAACCCTTTTTAATTTATTACTAGATAAATTTGAATATAGGGGGAAAATCATTTCTTCGGTCGATTTTAACTACTTCCCATATCCAGTAGAAGATAAAAGTAAGTATACACATGAAATTTTAGAAGAAATATGCCCTCAAGCTGAGGACTGGGAATTTCTTCGAGAAATAGCTTATTTAAATGTGGATGCCGAAGCCATGTACCGTCCTTTTGAAACTTTATCAAACGGTGAACAAACAAAGGTATTGCTTGTTGCTCTATTTTTAAACGAAGGACAATTTTTATTAATTGATGAACCAACAAATCATTTAGATACTGAAGCTCGTAAGACGGTTTCGAATTACTTGAGGAAGAAAAAAGGGAATATTTTAATTTCTCATGACCGTAACTTTTTAGATGGCAGTGTTGATCATATCTTGTCTATAAATAGAGCAGATATTGAGGTTCAAAGTGGAAATTATTCCTCATGGAAGTTGAACTTTGACCGACAGCAGGGACATGAACAAGCAACAAATGAACGCTTGCAGAAGGATATTGGAAGGTTAGAACAATCTACAAAACGTTCGGCTGGTTGGTCTAACCGAGTCGAAGCTTCAAAAAATGGAACAACGAATTCTGGTTCTAAATTGGACAAAGGTTTTGTAGGACATAAAGCAGCAAAAATGATGAAACGATCTAAGAACCTTGAGGCTCGACAGCAAAAATCGATTGAAGAAAAGTCAAAGCTTCTAAAAAACATTGAAAAAACGGAGTCCCTACAGTTTGAACCAGTGGAATATAAATCGAAGGAACTCATTCAATTAACAGATGTGTCTGTCATATATGATGGGCAAGTTGTCAACAAACCAATAAGTTTTAATGTTGAACAAGGAGATAGAATTGTACTGGATGGAAAGAACGGCAGTGGAAAAAGTAGTATTTTAAAATTAATCTTAGGCGATCCAATACAGTATACAGGCACGTTAAATACGGGTTCTAACCTGATAACTTCTTATGTTCAGCAAGACACCTCTCATTTAAAGGGGATGCTAGCTGACTTTATTGAAGAAAATGAGATTGATGAATCGTTGTTTAAGGCCATCCTGAGAAAGCTAGATTTTGACCGAGTACAGTTTGAAAAAGATATATCTCATTATTCAGGTGGTCAGAAGAAAAAATTGCTTATCGCTAAAAGTTTATGTGAAAAAGCTCACCTATATATTTGGGATGAACCATTAAACTTTATTGATATTTACTCTCGAATGCAAATTGAAGAGCTTATTCAAACCTTTAATCCGACTATGGTTTTTGTTGAACATGACCAGACCTTCCAAGAGACAATATCAACAAAAATAATAAAAATATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36794","NCBI_taxonomy_name":"Mammaliicoccus sciuri","NCBI_taxonomy_id":"1296"}}}},"ARO_accession":"3003111","ARO_id":"39687","ARO_name":"lsaB","CARD_short_name":"lsaB","ARO_description":"LsaB is an ABC-F subfamily protein expressed in Mammaliicoccus sciuri. It confers resistance to clindamycin.","ARO_category":{"41696":{"category_aro_accession":"3004472","category_aro_cvterm_id":"41696","category_aro_name":"lsa-type ABC-F protein","category_aro_description":"A subgroup of the ABC-F protein subfamily of ATP-binding cassette proteins. lsa-type ABC-F proteins confer resistance to streptogramin, lincosamide and pleuromutilin antibiotics through antibiotic target protection of the ribosome.","category_aro_class_name":"AMR Gene Family"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"37716":{"category_aro_accession":"3001317","category_aro_cvterm_id":"37716","category_aro_name":"pleuromutilin","category_aro_description":"Pleuromutilin is a natural product antibiotic produced by Clitopilus passeckerianus. Related antibiotics of clinical significance, such as tiamulin and retapamulin, are semi-synthetic derivatives of this compound.","category_aro_class_name":"Antibiotic"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"37014":{"category_aro_accession":"3000670","category_aro_cvterm_id":"37014","category_aro_name":"pleuromutilin antibiotic","category_aro_description":"Pleuromutilins are natural fungal products that target bacterial protein translation by binding the the 23S rRNA, blocking the ribosome P site at the 50S subunit. They are mostly used for agriculture and veterinary purposes.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1162":{"model_id":"1162","model_name":"aadA15","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"116":{"protein_sequence":{"accession":"ABD58917.1","sequence":"MREAVIAEVSTQLSEVVGVIERHLEPTLLAVHLYGSAVDGGLKPHSDIDLLVTVTVRLDETTRRALINDLLETSASPGESEILRAVEVTIVVHDDIIPWRYPAKRELQFGEWQRNDILAGIFEPATIDIDLAILLTKAREHSVALVGPAAEELFDPVPEQDLFEALNETLTLWNSPPDWAGDERNVVLTLSRIWYSAITGKIAPKDVAADWAIKRLPAQYQPVLLEAKQAYLGQKEDHLASRADHLEEFIRFVKGEIIKSVGK"},"dna_sequence":{"accession":"DQ393783.1","fmin":"1799","fmax":"2591","strand":"+","sequence":"ATGAGGGAAGCGGTGATCGCCGAAGTATCGACTCAACTATCAGAGGTAGTTGGCGTCATCGAGCGCCATCTCGAACCGACGTTGCTGGCCGTCCATTTGTACGGCTCCGCAGTGGATGGCGGCCTGAAGCCACACAGTGATATTGATTTGCTGGTTACGGTGACCGTAAGGCTTGATGAAACAACGCGGCGAGCTTTGATCAACGACCTTTTGGAAACTTCGGCTTCCCCTGGAGAGAGCGAGATTCTCCGCGCTGTAGAAGTCACCATTGTTGTGCACGACGACATCATTCCGTGGCGTTATCCAGCTAAGCGCGAACTGCAATTTGGAGAATGGCAGCGCAATGACATTCTTGCAGGTATCTTCGAGCCAGCCACGATCGACATTGATCTGGCTATCTTGCTGACAAAAGCAAGAGAACATAGCGTTGCCTTGGTAGGTCCAGCGGCGGAGGAACTCTTTGATCCGGTTCCTGAACAGGATCTATTTGAGGCGCTAAATGAAACCTTAACGCTATGGAACTCGCCGCCCGACTGGGCCGGCGATGAGCGAAATGTAGTGCTTACGTTGTCCCGCATTTGGTACAGCGCAATAACCGGCAAAATCGCGCCGAAGGATGTCGCTGCCGACTGGGCAATAAAACGCCTACCTGCCCAGTATCAGCCCGTCTTACTTGAAGCTAAGCAAGCTTATCTGGGACAAAAAGAAGATCACTTGGCCTCACGCGCAGATCACTTGGAAGAATTTATTCGCTTTGTGAAAGGCGAGATCATCAAGTCAGTTGGTAAATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002615","ARO_id":"39015","ARO_name":"aadA15","CARD_short_name":"aadA15","ARO_description":"aadA15 is an integron-encoded aminoglycoside nucleotidyltransferase gene in P. aeruginosa.","ARO_category":{"41439":{"category_aro_accession":"3004275","category_aro_cvterm_id":"41439","category_aro_name":"ANT(3'')","category_aro_description":"A category of aminoglycoside O-nucleotidyltransferase enzymes with modification regiospecificity based at the 3''-hydroxyl group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics by transfer of an AMP group from an ATP substrate to the 3''-hydroxyl group of the compound.","category_aro_class_name":"AMR Gene Family"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1163":{"model_id":"1163","model_name":"CMY-94","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1626":{"protein_sequence":{"accession":"AGC54798.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVASAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"JX514368.1","fmin":"271","fmax":"1417","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATCGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002107","ARO_id":"38507","ARO_name":"CMY-94","CARD_short_name":"CMY-94","ARO_description":"CMY-94 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1164":{"model_id":"1164","model_name":"MIR-9","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"875":{"protein_sequence":{"accession":"AIT76113.1","sequence":"MMTKSLSCALLLSVASSAFAAPMSEKQLAEVVERTVTPLMNAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEIALGDPVAKYWPELTGKQWQSIRMLDLATYTAGGLPLQVPDEVTDTASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMSYEQAMTTRVFKPLKLDHTWINVPKAEEAHYAWGYREGKAVHVSPGMLDAEAYGVKTNVKDMASWVIANMKPDSLQAPSLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVGGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILDALQ"},"dna_sequence":{"accession":"KM087860.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGACAAAATCCCTAAGCTGTGCCCTGCTGCTCAGCGTCGCCAGTTCTGCATTCGCCGCACCGATGTCCGAAAAACAGCTGGCTGAGGTGGTGGAACGTACCGTTACGCCGCTGATGAACGCGCAGGCCATTCCGGGTATGGCGGTGGCGGTAATTTATCAGGGTCAGCCACACTACTTTACCTTCGGTAAAGCCGATGTTGCGGCGAACAAACCCGTCACCCCGCAAACCCTGTTTGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTACTGGGCGGCGATGCCATTGCCCGGGGTGAAATAGCGCTGGGCGATCCGGTAGCAAAATACTGGCCTGAGCTCACGGGCAAGCAGTGGCAGAGCATTCGCATGCTGGATCTGGCAACCTATACCGCAGGCGGTCTGCCGTTACAGGTGCCGGATGAGGTCACGGATACCGCCTCTCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCGGGCACCACGCGTCTTTACGCTAACGCCAGCATCGGTCTTTTTGGTGCGTTGGCGGTTAAACCTTCCGGCATGAGCTATGAGCAGGCCATGACGACGCGGGTCTTTAAACCCCTCAAGCTGGACCATACCTGGATTAACGTCCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGATACCGTGAGGGTAAAGCGGTCCACGTTTCGCCAGGGATGCTGGACGCGGAAGCCTATGGCGTAAAAACTAACGTGAAGGATATGGCGAGCTGGGTGATAGCCAACATGAAGCCGGATTCTCTTCAGGCTCCCTCACTCAAGCAAGGCATTGCTCTGGCGCAGTCTCGCTACTGGCGCGTGGGGGCTATGTATCAGGGGTTGGGCTGGGAGATGCTCAACTGGCCGGTCGATGCCAAAACCGTCGTCGGAGGCAGTGATAACAAGGTGGCGCTGGCACCATTGCCCGTGGCAGAAGTGAATCCACCCGCACCGCCGGTCAAGGCCTCCTGGGTCCATAAAACAGGCTCGACGGGCGGGTTTGGCAGCTACGTGGCATTTATTCCTGAAAAGCAGCTCGGCATTGTGATGCTGGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCGTATCCTTGACGCGCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36926","NCBI_taxonomy_name":"Enterobacter asburiae","NCBI_taxonomy_id":"61645"}}}},"ARO_accession":"3002174","ARO_id":"38574","ARO_name":"MIR-9","CARD_short_name":"MIR-9","ARO_description":"MIR-9 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36197":{"category_aro_accession":"3000058","category_aro_cvterm_id":"36197","category_aro_name":"MIR beta-lactamase","category_aro_description":"MIR beta-lactamases are plasmid-mediated beta-lactamases that confer resistance to oxyimino- and alpha-methoxy beta-lactams.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1165":{"model_id":"1165","model_name":"OKP-A-4","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"1520":{"protein_sequence":{"accession":"CAJ19601.1","sequence":"MRYVRLCLFSLIAALPLAVFASPPPLEQITRSESQLAGRVGYVEMDLASGRTLAAWRASERFPLMSTFKVLLCGAVLARVDAGDEQLDRRIRYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAGNLLLKSVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDVRDTTTPASMAATLRKLLTSHTLSARSQQQLLQWMVDDQVAGPLIRAVLPAGWFIADKTGAGERGSRGIVALLGPNGKAERIVVIYLRDTPATMAERNQQIARIGAALIEHWQR"},"dna_sequence":{"accession":"AM051142.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGCCTTTTCTCCCTGATTGCCGCCCTGCCACTGGCGGTATTCGCCAGCCCTCCGCCACTTGAGCAAATTACACGCAGCGAAAGTCAGCTGGCGGGCCGCGTGGGCTATGTTGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCAGTGAGCGCTTTCCGCTGATGAGCACCTTTAAAGTGCTGCTCTGCGGCGCGGTGCTGGCCCGGGTGGATGCCGGAGACGAACAGCTGGATCGGCGGATCCGCTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGCCGACGGGATGACCGTTGGCGAACTCTGCGCCGCCGCCATCACCATGAGCGACAACAGCGCCGGCAATCTGCTGTTGAAGAGCGTTGGCGGCCCCGCGGGATTGACCGCTTTTCTGCGCCAGATCGGTGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAGCTCAATGAAGCGCTTCCCGGCGACGTGCGCGACACCACCACCCCAGCCAGCATGGCCGCCACCCTGCGCAAGCTGCTAACCAGCCACACTCTGAGCGCCCGTTCGCAGCAGCAGCTGCTGCAGTGGATGGTGGACGACCAGGTAGCCGGTCCGCTGATCCGCGCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAAACCGGGGCCGGCGAGCGGGGCTCACGTGGCATTGTCGCCCTGCTCGGCCCGAACGGCAAAGCGGAGCGCATCGTGGTGATCTATCTGCGGGATACGCCGGCGACCATGGCCGAGCGTAACCAGCAGATCGCCAGAATAGGCGCGGCGCTGATCGAGCACTGGCAGCGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002421","ARO_id":"38821","ARO_name":"OKP-A-4","CARD_short_name":"OKP-A-4","ARO_description":"OKP-A-4 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"38817":{"category_aro_accession":"3002417","category_aro_cvterm_id":"38817","category_aro_name":"OKP beta-lactamase","category_aro_description":"OKP beta-lactamases are chromosomal class A beta-lactamase that confer resistance to penicillins and early cephalosporins in Klebsiella pneumoniae. OKP beta-lactamases can be subdivided into two groups: OKP-A and OKP-B which diverge by about 4.2%.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1167":{"model_id":"1167","model_name":"norB","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"900"}},"model_sequences":{"sequence":{"4734":{"protein_sequence":{"accession":"CCQ22388.1","sequence":"MTSTAYKGTNKLIVGIVFGVITFWLFAQSMVNIVPAVQSDLGISSDLLSIAISLTALFSGIFIVVAGGMADKFGRVKLTYIGLILSIIGSLLLVVTQGSTLLIIGRIIQGLSAACIMPATLALMKTYFDGADRQRALSYWSIGSWGGSGICSFAGGAIATYMGWRWIFIISIVFALLGMLLIKGTPESKVVQNTKAKFDSFGLVLFVIAMVCLNLIITRGATFGWTSPITITMLVVFLVSAGLFFRVELRQANGFIDFSLFKNKAYTGATLSNFLLNAAAGTLVVANTYVQIGRGFTAFQSGLLSIGYLVCVLGMIRIGEKILQRVGARKPMILGSGITAVGIALMALTFIPGTLYTVLVFIGFALFGIGLGMYATPSTDTAISNAPEDKVGVASGIYKMASSLGGSFGVAISATIYGVIALSGNIDLAAMVGLLTNVGFCVVSLISVAITTPSAKKALELKAAKE"},"dna_sequence":{"accession":"HE999704.1","fmin":"2734780","fmax":"2736181","strand":"-","sequence":"ATGACTTCAACAGCGTATAAAGGTACAAATAAACTAATCGTTGGAATTGTTTTCGGGGTTATCACGTTTTGGCTTTTTGCTCAATCTATGGTGAATATTGTTCCGGCCGTGCAATCTGACCTTGGAATTTCCTCTGATTTACTTAGTATTGCCATCAGTTTAACCGCGCTATTTTCAGGTATTTTTATCGTTGTAGCAGGTGGGATGGCTGACAAATTTGGTCGTGTGAAATTAACTTATATCGGACTTATTCTTAGTATCATCGGTTCACTGCTACTTGTTGTCACTCAAGGGTCGACGCTACTTATTATCGGCCGGATTATTCAAGGTCTTTCAGCTGCTTGTATTATGCCAGCAACCCTTGCCTTAATGAAAACTTATTTTGACGGGGCAGATAGACAAAGAGCACTTAGTTACTGGTCAATTGGCTCATGGGGCGGATCAGGTATTTGTTCGTTCGCAGGTGGCGCTATCGCAACATATATGGGCTGGCGCTGGATTTTCATTATTTCCATCGTATTCGCACTGCTTGGAATGCTACTTATTAAAGGTACTCCAGAAAGTAAAGTCGTTCAAAATACAAAAGCAAAATTTGATTCATTTGGTCTTGTTCTTTTTGTTATCGCAATGGTTTGTTTGAACCTTATTATTACTCGTGGCGCAACATTTGGCTGGACAAGCCCAATTACTATTACAATGCTCGTTGTTTTCCTAGTTTCTGCGGGATTATTCTTCCGAGTGGAACTGCGACAAGCAAACGGATTTATTGATTTCTCGTTATTTAAAAATAAAGCTTATACAGGCGCAACACTTTCGAACTTCTTGCTAAACGCAGCAGCTGGAACACTGGTTGTCGCAAACACTTATGTGCAAATTGGTCGCGGTTTTACGGCGTTCCAATCCGGTTTACTTTCTATCGGATATCTTGTCTGTGTGCTCGGAATGATTCGCATCGGTGAAAAAATTCTTCAACGTGTTGGTGCGCGTAAACCAATGATTTTAGGCTCTGGTATTACGGCTGTTGGTATTGCACTAATGGCGCTGACGTTTATTCCGGGAACCCTTTATACAGTGCTTGTATTTATCGGTTTTGCTTTATTCGGGATTGGACTTGGCATGTATGCGACTCCTTCAACAGATACAGCCATTTCTAATGCTCCAGAAGATAAAGTCGGAGTAGCATCTGGTATTTACAAAATGGCAAGTTCGCTAGGTGGCTCATTCGGCGTGGCGATATCTGCTACGATTTATGGTGTGATTGCACTTTCAGGAAATATTGATTTAGCCGCAATGGTGGGGCTTTTAACGAACGTCGGTTTTTGTGTCGTTTCACTTATTTCCGTTGCTATAACAACACCATCTGCGAAAAAAGCGCTCGAATTAAAAGCCGCAAAAGAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36757","NCBI_taxonomy_name":"Listeria monocytogenes","NCBI_taxonomy_id":"1639"}}}},"ARO_accession":"3000421","ARO_id":"36560","ARO_name":"norB","CARD_short_name":"norB","ARO_description":"NorB is a multidrug efflux pump in Staphylococcus aureus that confers resistance to fluoroquinolones and other structurally unrelated antibiotics like tetracycline. It shares 30% similarity with NorB, and is a structural homolog of Blt of Bacillus subtilis. It is regulated by mgrA, also known as NorR.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1168":{"model_id":"1168","model_name":"NDM-9","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8233":{"protein_sequence":{"accession":"AGU91756.1","sequence":"MELPNIMHPVAKLSTALAAALMLSGCMPGEIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQKGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR"},"dna_sequence":{"accession":"KC999080.2","fmin":"379","fmax":"1192","strand":"+","sequence":"ATGGAATTGCCCAATATTATGCACCCGGTCGCGAAGCTGAGCACCGCATTAGCCGCTGCATTGATGCTGAGCGGGTGCATGCCCGGTGAAATCCGCCCGACGATTGGCCAGCAAATGGAAACTGGCGACCAACGGTTTGGCGATCTGGTTTTCCGCCAGCTCGCACCGAATGTCTGGCAGCACACTTCCTATCTCGACATGCCGGGTTTCGGGGCAGTCGCTTCCAACGGTTTGATCGTCAGGGATGGCGGCCGCGTGCTGGTGGTCGATACCGCCTGGACCGATGACCAGACCGCCCAGATCCTCAACTGGATCAAGCAGGAGATCAACCTGCCGGTCGCGCTGGCGGTGGTGACTCACGCGCATCAGGACAAGATGGGCGGTATGGACGCGCTGCATGCGGCGGGGATTGCGACTTATGCCAATGCGTTGTCGAACCAGCTTGCCCCGCAAAAGGGGATGGTTGCGGCGCAACACAGCCTGACTTTCGCCGCCAATGGCTGGGTCGAACCAGCAACCGCGCCCAACTTTGGCCCGCTCAAGGTATTTTACCCCGGCCCCGGCCACACCAGTGACAATATCACCGTTGGGATCGACGGCACCGACATCGCTTTTGGTGGCTGCCTGATCAAGGACAGCAAGGCCAAGTCGCTCGGCAATCTCGGTGATGCCGACACTGAGCACTACGCCGCGTCAGCGCGCGCGTTTGGTGCGGCGTTCCCCAAGGCCAGCATGATCGTGATGAGCCATTCCGCCCCCGATAGCCGCGCCGCAATCACTCATACGGCCCGCATGGCCGACAAGCTGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39097","NCBI_taxonomy_name":"Klebsiella pneumoniae subsp. pneumoniae","NCBI_taxonomy_id":"72407"}}}},"ARO_accession":"3002359","ARO_id":"38759","ARO_name":"NDM-9","CARD_short_name":"NDM-9","ARO_description":"NDM-9 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"45729":{"category_aro_accession":"3007147","category_aro_cvterm_id":"45729","category_aro_name":"taniborbactam","category_aro_description":"Taniborbactam is a broad-spectrum beta-lactamase inhibitor. As of 2022, it is in phase III clinical trials in combination with cefepime and is the only beta-lactamase inhibitor exhibiting activity against all four classes of beta-lactamase.","category_aro_class_name":"Adjuvant"},"36196":{"category_aro_accession":"3000057","category_aro_cvterm_id":"36196","category_aro_name":"NDM beta-lactamase","category_aro_description":"NDM beta-lactamases or New Delhi metallo-beta-lactamases are class B beta-lactamases that confer resistance to a broad range of antibiotics including carbapenems, cephalosporins and penicillins.","category_aro_class_name":"AMR Gene Family"},"35976":{"category_aro_accession":"0000059","category_aro_cvterm_id":"35976","category_aro_name":"cefepime","category_aro_description":"Cefepime (INN) is a fourth-generation cephalosporin antibiotic developed in 1994. It contains an aminothiazolyl group that decreases its affinity with beta-lactamases. Cefepime shows high binding affinity with penicillin-binding proteins and has an extended spectrum of activity against Gram-positive and Gram-negative bacteria, with greater activity against both Gram-negative and Gram-positive organisms than third-generation agents.","category_aro_class_name":"Antibiotic"},"45730":{"category_aro_accession":"3007148","category_aro_cvterm_id":"45730","category_aro_name":"cefepime-taniborbactam","category_aro_description":"An antibiotic cocktail containing the beta-lactam antibiotic cefepime and the beta-lactamase inhibitor taniborbactam. As of 2022, this antibiotic-adjuvant mixture is in phase III clinical trials for the treatment of various bacterial infections.","category_aro_class_name":"Antibiotic+Adjuvant"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1169":{"model_id":"1169","model_name":"OXA-360","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1932":{"protein_sequence":{"accession":"AGZ83156.1","sequence":"MKILILLPLLSCLSLTACSFAVSNSPSQITSTQSIQAIVKLFDQAQSSGVLVIQRGPHLQVYGNELSRAHTEYVPASTFKMLNALIGLQHGKATTNEIFKWDRKKRSFAAWEKDMTLGQAMQASAVPVYQELARRIGLELMQQEVQRIQFGNQQIGQHIDNFWLVGPLKVTPKQEVKFASALAQEQLAFDPRFQQQVKTMLLLQERQAYRLYAKSGWGMDVEPQVGWLTGWIETPQDEIVAFSLNMQMQSNMDPAIRLKILQQALAELGLYPKAEG"},"dna_sequence":{"accession":"KF421163.1","fmin":"0","fmax":"831","strand":"+","sequence":"ATGAAAATTCTTATTTTGTTGCCTTTACTCAGTTGCTTGAGCCTGACAGCCTGTAGCTTCGCTGTTTCAAATTCGCCCTCTCAAATCACTTCAACTCAATCTATTCAAGCTATTGTAAAGTTATTTGATCAGGCACAAAGCTCTGGCGTTTTAGTAATTCAACGGGGTCCACATCTACAAGTCTATGGCAATGAGTTGAGTCGTGCACATACCGAATATGTTCCTGCTTCAACCTTTAAAATGCTTAATGCTCTGATTGGCCTGCAACATGGTAAAGCTACGACCAATGAAATTTTTAAATGGGATCGCAAGAAGCGCAGTTTTGCAGCCTGGGAAAAAGACATGACTCTCGGCCAAGCCATGCAAGCTTCTGCTGTACCGGTCTATCAGGAACTGGCACGTCGCATTGGTCTGGAATTAATGCAACAGGAAGTGCAACGCATCCAATTTGGTAATCAGCAGATTGGTCAGCATATCGACAACTTCTGGTTGGTCGGACCTTTGAAAGTTACTCCAAAACAGGAAGTCAAATTTGCCTCTGCGCTTGCTCAAGAGCAACTTGCCTTTGATCCTCGGTTTCAGCAGCAAGTTAAAACCATGTTACTGTTACAGGAGCGACAAGCTTATCGACTATATGCCAAATCTGGTTGGGGTATGGATGTGGAGCCGCAAGTCGGCTGGCTCACCGGCTGGATCGAAACACCTCAGGACGAAATTGTGGCATTTTCACTGAATATGCAGATGCAAAGTAATATGGATCCGGCGATCCGCCTTAAAATTTTGCAGCAGGCCTTGGCCGAATTAGGGCTTTATCCCAAAGCTGAAGGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39096","NCBI_taxonomy_name":"Acinetobacter schindleri","NCBI_taxonomy_id":"108981"}}}},"ARO_accession":"3001547","ARO_id":"37947","ARO_name":"OXA-360","CARD_short_name":"OXA-360","ARO_description":"OXA-360 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46489":{"category_aro_accession":"3007700","category_aro_cvterm_id":"46489","category_aro_name":"OXA-134-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-134.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1170":{"model_id":"1170","model_name":"CMY-46","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1738":{"protein_sequence":{"accession":"CBH19182.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADITNNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGISLLHLATYTAGGLPLQIPDDVTDKAALLRFYQNWQPQWAPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPKNEQKDYAWGYREGKAVHVSPGQLDAEAYGVKSSVIDMARWVQVNMDASRVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"FN556186.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCATTCTCCACGTTTGCCGCCGCCAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCTGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCACCAATAACCACCCAGTCACGCAGCAAACTCTGTTTGAGCTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCAGCCTGCTGCACTTAGCCACCTACACGGCAGGCGGCCTGCCGCTGCAGATCCCCGATGACGTTACGGATAAAGCCGCATTACTGCGTTTTTATCAAAACTGGCAGCCGCAATGGGCCCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACAGTTCCGAAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGGCTGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGTCAACATGGACGCCAGCCGCGTTCAGGAGAAAACACTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGTAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGATCCACTGGAGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002057","ARO_id":"38457","ARO_name":"CMY-46","CARD_short_name":"CMY-46","ARO_description":"CMY-46 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1172":{"model_id":"1172","model_name":"OXA-194","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1925":{"protein_sequence":{"accession":"AEB98920.1","sequence":"MNIKALFLITSAIFISACSPYIVTANPNHSASKSDVKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWVVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"HQ425492.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGAACATTAAAGCCCTCTTCCTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGTAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGGTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAACAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTA","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36949","NCBI_taxonomy_name":"Acinetobacter nosocomialis","NCBI_taxonomy_id":"106654"}}}},"ARO_accession":"3001479","ARO_id":"37879","ARO_name":"OXA-194","CARD_short_name":"OXA-194","ARO_description":"OXA-194 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1173":{"model_id":"1173","model_name":"TEM-54","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1959":{"protein_sequence":{"accession":"AAD22539.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSLGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AF104442.1","fmin":"193","fmax":"1054","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCTCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000923","ARO_id":"37303","ARO_name":"TEM-54","CARD_short_name":"TEM-54","ARO_description":"TEM-54 is an inhibitor-resistant beta-lactamase found in E. coli.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1174":{"model_id":"1174","model_name":"QnrB22","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"689":{"protein_sequence":{"accession":"ACS71746.1","sequence":"MMTLALVGEKIDRNRFTGEKVENSTFFNCDFSGADLCGTEFIGCQFYDRESQKGCNFSRANLKDAIFKSCDLSMADFRNINALGIEIRHCRAQGSDFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGTQVLGATFSGSDLSGGEFSSFDWRAANVTHCDLTNSELGDLDIRVVDLQGVKLDSYQASLLLERLGIAVMG"},"dna_sequence":{"accession":"FJ981621.1","fmin":"0","fmax":"648","strand":"+","sequence":"ATGATGACTCTGGCGTTAGTTGGCGAAAAAATTGACAGAAACAGGTTCACCGGTGAAAAAGTCGAAAATAGCACATTTTTCAACTGTGATTTTTCGGGTGCCGACCTTTGCGGTACTGAATTTATTGGCTGCCAGTTTTATGATCGAGAAAGCCAGAAAGGGTGTAATTTTAGTCGCGCTAACCTGAAGGATGCCATTTTCAAAAGTTGTGATCTCTCCATGGCGGATTTCAGAAATATCAATGCGCTGGGAATCGAAATTCGCCACTGCCGGGCACAAGGGTCAGATTTTCGCGGCGCAAGCTTTATGAATATGATCACCACCCGCACCTGGTTTTGTAGCGCTTATATCACCAATACCAACTTAAGCTACGCCAACTTTTCTAAAGTCGTACTGGAAAAGTGCGAGCTGTGGGAGAACCGCTGGATGGGTACTCAGGTGCTGGGCGCAACGTTCAGTGGATCAGACCTCTCTGGCGGCGAGTTTTCATCCTTCGACTGGCGAGCAGCAAACGTAACGCACTGTGATTTGACCAATTCGGAACTGGGCGATTTAGATATCCGGGTAGTTGATTTGCAAGGCGTCAAACTGGACAGCTACCAGGCATCGTTGCTCCTGGAACGTCTTGGTATCGCTGTCATGGGTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39583","NCBI_taxonomy_name":"Citrobacter werkmanii","NCBI_taxonomy_id":"67827"}}}},"ARO_accession":"3002737","ARO_id":"39171","ARO_name":"QnrB22","CARD_short_name":"QnrB22","ARO_description":"QnrB22 is a plasmid-mediated quinolone resistance protein found in Citrobacter werkmanii.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1177":{"model_id":"1177","model_name":"KPC-12","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1786":{"protein_sequence":{"accession":"ADZ75467.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELEMNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"HQ641421.1","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGATGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002322","ARO_id":"38722","ARO_name":"KPC-12","CARD_short_name":"KPC-12","ARO_description":"KPC-12 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1178":{"model_id":"1178","model_name":"CMY-81","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"823":{"protein_sequence":{"accession":"AFK73452.1","sequence":"MMKKSICCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAIIYEGKPYYFTWGKADIVNNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWRGISLLHLATYTAGGLPLQIPDYVTDKAELLRFYQNWQPQWTPGAKRLYANSSIGLFGALVVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQSEQKNYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIELAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPARVEAAWRILEKLQ"},"dna_sequence":{"accession":"JQ733578.1","fmin":"1007","fmax":"2153","strand":"+","sequence":"ATGATGAAAAAATCGATATGCTGCGCGCTGCTGCTGACAGCCTCTTTCTCCACGTTTGCTGCCGCAAAAACAGAACAACAAATTGCCGATATCGTTAACCGCACCATCACACCACTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTGGCGATTATCTACGAGGGGAAACCTTATTACTTTACCTGGGGTAAAGCCGATATCGTCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGACGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCGGGGTATCAGCCTGCTGCACTTAGCCACCTATACAGCGGGTGGCCTGCCGCTGCAGATCCCCGATTACGTTACGGATAAAGCCGAATTACTGCGCTTTTATCAAAACTGGCAACCACAATGGACTCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGTGCGCTGGTGGTAAAACCTTCAGGTATGAGCTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAAAGCGAACAAAAAAATTATGCCTGGGGCTATCGCGAAGGGAAGCCTGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATCGATATGGCCCGCTGGGTTCAGGCCAACATGGACGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGAGCTTGCGCAGTCTCGCTACTGGCGTATTGGTGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCAGCACCTGCCGTGAAAGCCTCATGGGTGCATAAAACAGGATCCACAGGCGGATTTGGCAGCTACGTTGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTAATGTTGGCAAACAAAAGCTACCCCAACCCGGCTCGCGTCGAGGCGGCCTGGCGCATTCTTGAAAAACTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002094","ARO_id":"38494","ARO_name":"CMY-81","CARD_short_name":"CMY-81","ARO_description":"CMY-81 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1179":{"model_id":"1179","model_name":"IMP-4","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1785":{"protein_sequence":{"accession":"AAK13078.1","sequence":"MSKLSVFFIFLFCSIATAAEPLPDLKIEKLDEGVYVHTSFEEVNGWGVVPKHGLVVLVDAEAYLIDTPFTAKDTEKLVTWFVERGYKIKGSISSHFHSDSTGGIEWLNSQSIPTYASELTNELLKKDGKVQAKNSFGGVNYWLVKNKIEVFYPGPGHTPDNLVVWLPERKILFGGCFIKPYGLGNLGDANLEAWPKSAKLLISKYGKAKLVVPSHSEAGDASLLKLTLEQAVKGLNESKKPSKLSN"},"dna_sequence":{"accession":"AF244145.1","fmin":"0","fmax":"741","strand":"+","sequence":"ATGAGCAAGTTATCTGTATTCTTTATATTTTTGTTTTGTAGCATTGCTACCGCAGCAGAGCCTTTGCCAGATTTAAAAATTGAAAAACTTGATGAAGGCGTTTATGTTCATACTTCGTTTGAAGAAGTTAACGGGTGGGGCGTTGTTCCTAAACATGGTTTGGTTGTTCTTGTAGATGCTGAAGCTTATCTAATTGACACTCCATTTACGGCTAAAGATACTGAAAAGTTAGTCACTTGGTTTGTGGAACGTGGCTATAAAATAAAAGGCAGTATTTCCTCTCATTTTCATAGTGACAGCACGGGCGGAATAGAGTGGCTTAATTCTCAATCCATCCCCACGTATGCGTCTGAATTAACTAATGAGCTGCTTAAAAAAGACGGTAAGGTTCAAGCTAAAAATTCATTTGGCGGGGTTAACTATTGGCTAGTTAAAAATAAAATTGAAGTTTTTTATCCAGGCCCAGGACACACTCCAGATAACCTAGTAGTTTGGCTGCCTGAAAGGAAAATATTATTCGGTGGTTGTTTTATTAAACCGTACGGTCTAGGTAATTTGGGTGACGCAAATTTAGAAGCTTGGCCAAAGTCCGCTAAATTATTAATATCCAAATATGGTAAGGCAAAACTGGTTGTTCCAAGTCACAGTGAAGCTGGAGACGCATCACTCTTGAAACTTACATTAGAGCAGGCGGTTAAAGGGTTAAACGAAAGTAAAAAACCATCAAAACTAAGCAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3002195","ARO_id":"38595","ARO_name":"IMP-4","CARD_short_name":"IMP-4","ARO_description":"IMP-4 is a beta-lactamase found in Acinetobacter baumannii.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1180":{"model_id":"1180","model_name":"mdsC","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"940"}},"model_sequences":{"sequence":{"5482":{"protein_sequence":{"accession":"AAL19304.1","sequence":"MRTALIRMISKHNDGNGIMKITFTGYRQTATLATLAFVTTLAGCTMAPKHERPASPTAMVYPYATSTVSGAPDAADIGWRDFFHDPLLQELIAIALRNNRDLRKAGLNVEAARALYRIQRAEMLPTLGIATAMDASRTPADLSVMDESEINRRYEAAGATTAWELDLWGRVRSLSDQALAAYMALDETYIAARMSLVSEVASAWLTLRADRELLRLTEDTLAAQKSSYTLTTQLARTGNATQLDLRMAEIALRSAEINRAAYTRQLARDRNALELLLGQPLTPELSRRLNEAVTLTEGAIPTTLPGGLPSDLLVRRPDIRAAEYRLRGANARIGAARAAFFPTISLTGSAGTASASLSGLFEPGSGSWRFLPQITLPLFHGGALRADLDRAHVQKQIEIARYENVIQQAFRDVADGLAGQRTLNDQVQSEQRAVEASQIAYELAGLRFQEGVDDYLTLLDTHRMLYGAQQRLVRTRLMQQLNIINLYKALGGGWREYSEKKQG"},"dna_sequence":{"accession":"AE006468.2","fmin":"392419","fmax":"393931","strand":"-","sequence":"GTGAGAACCGCGTTGATTCGCATGATCAGCAAGCATAATGATGGGAATGGCATAATGAAGATCACTTTTACAGGCTATCGGCAGACCGCCACGCTGGCGACGCTTGCTTTCGTCACCACGCTTGCTGGCTGTACGATGGCGCCGAAGCACGAACGCCCCGCATCGCCGACTGCGATGGTCTATCCCTACGCAACGTCAACCGTTTCTGGCGCGCCGGATGCCGCTGACATTGGCTGGCGTGATTTCTTCCACGATCCGCTTCTACAGGAACTGATTGCGATCGCGTTACGCAATAATCGGGATTTACGCAAGGCAGGGCTCAATGTTGAAGCCGCCCGGGCGTTATACCGCATTCAGCGCGCGGAGATGCTGCCGACGCTCGGCATCGCCACCGCCATGGACGCCAGTCGCACTCCCGCCGATCTCAGCGTCATGGACGAGTCTGAGATTAACCGACGCTACGAGGCGGCTGGGGCGACGACGGCCTGGGAACTGGATCTCTGGGGGCGAGTGCGAAGCCTTAGCGACCAGGCATTAGCCGCCTATATGGCGCTTGATGAGACGTACATTGCGGCGCGAATGAGCCTGGTTTCCGAAGTCGCCAGCGCCTGGCTGACGCTACGGGCTGACCGGGAGCTGCTGCGCTTAACCGAGGATACGCTGGCCGCGCAAAAAAGTTCATACACATTGACGACCCAGCTTGCCCGGACAGGTAACGCCACACAGCTCGATCTGCGTATGGCGGAGATCGCGCTGCGTTCTGCCGAAATCAATCGCGCGGCGTATACGCGACAGTTGGCGCGGGATCGTAACGCGCTGGAATTGCTGTTGGGCCAGCCGCTCACGCCTGAACTGTCGCGTCGACTAAACGAAGCGGTCACGCTTACAGAAGGCGCGATCCCGACCACACTGCCAGGCGGATTACCGTCAGATCTGCTGGTACGCCGCCCGGATATTCGCGCCGCCGAGTACAGGCTGCGCGGCGCAAACGCCCGGATAGGCGCAGCGCGCGCCGCCTTCTTCCCGACCATCAGCCTGACAGGCTCGGCGGGAACGGCCAGCGCGTCTCTTAGCGGACTCTTTGAACCGGGATCGGGAAGCTGGCGTTTTCTACCGCAAATCACCTTGCCTCTCTTTCACGGCGGCGCATTACGCGCTGACCTGGATAGGGCGCATGTCCAAAAACAGATTGAAATCGCCAGGTATGAAAACGTTATTCAGCAAGCCTTTCGCGACGTGGCGGATGGTCTGGCGGGACAGCGTACGCTGAATGACCAGGTGCAATCAGAACAACGCGCGGTTGAAGCCAGTCAAATCGCCTATGAGCTGGCCGGACTCCGTTTTCAGGAAGGCGTCGATGACTACCTTACGCTGCTTGATACCCATCGTATGCTTTATGGCGCACAACAGCGCCTGGTACGCACACGTCTCATGCAACAGTTAAATATCATTAACCTGTATAAAGCATTAGGCGGCGGTTGGCGGGAATACAGTGAGAAAAAGCAAGGTTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35734","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Typhimurium str. LT2","NCBI_taxonomy_id":"99287"}}}},"ARO_accession":"3000791","ARO_id":"37171","ARO_name":"mdsC","CARD_short_name":"mdsC","ARO_description":"MdsC is the outer membrane channel of the multidrug and metal efflux complex MdsABC.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1181":{"model_id":"1181","model_name":"cmeA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"710"}},"model_sequences":{"sequence":{"431":{"protein_sequence":{"accession":"ABS43901.1","sequence":"MKLFQKNTILVLGVVFLLTACSKEEAPKIQMPPQPVTTMSAKSEDLPLNFTYPAKLVSDYDVIIKPQVSGVIVNKLFKAGDKVKRGQTLFIIEQAKFKASVDSAYGQALMAKATFENASKDFNRSEALFSKNAISQKEYDSSLATFNNAKASLASARAQLANARIDLDHTEIKAPFDGTIGDALVNIGDYVSTSTTELVRVTNLNPIYADFFISDTDKLNLVRNTQSGKWDLDSIHANLNLNGETVQGKLYFIDSVIDANSGTVKAKAVFDNNNSTLLPGAFATITSEGFIQKNGFKVPQIAIKQDQNDVYVLLVKNGKVEKSSVHISYQNNEYAIIDKGLQNGDKIILDNFKKIQVGSEVKEIGAQ"},"dna_sequence":{"accession":"CP000768.1","fmin":"1405391","fmax":"1406495","strand":"+","sequence":"ATGAAATTATTTCAAAAAAATACTATTTTAGTTTTAGGTGTTGTGTTTTTACTCACTGCTTGCAGCAAAGAAGAAGCGCCAAAAATACAAATGCCGCCTCAACCTGTAACAACCATGAGTGCTAAATCTGAAGATTTACCACTTAATTTTACCTATCCTGCCAAACTTGTCAGTGATTATGATGTTATTATAAAACCTCAAGTTAGCGGTGTGATAGTAAATAAACTTTTTAAGGCTGGAGATAAGGTAAAAAGAGGACAAACATTATTTATTATAGAACAAGCCAAATTTAAAGCTAGCGTTGATTCAGCCTACGGACAAGCGTTAATGGCTAAAGCAACTTTCGAAAATGCAAGTAAAGATTTTAATCGCTCTGAGGCTCTTTTTAGCAAAAACGCAATCTCTCAAAAAGAATACGACTCTTCTCTTGCTACATTTAATAATGCAAAAGCTAGTCTAGCAAGTGCTAGAGCACAGCTTGCAAATGCAAGAATTGATCTAGATCATACCGAAATAAAAGCTCCTTTTGATGGTACTATAGGAGATGCTTTAGTTAATATAGGAGATTATGTAAGCACTTCAACAACTGAACTAGTTAGAGTTACAAATTTAAATCCTATTTACGCAGATTTCTTTATTTCAGATACAGATAAACTAAATTTAGTCCGCAATACTCAAAGTGGAAAATGGGATTTAGACAGCATTCATGCAAATTTAAATCTTAACGGAGAAACTGTTCAAGGCAAACTTTATTTTATTGATTCTGTTATAGATGCCAATAGTGGAACAGTAAAAGCCAAAGCTGTATTTGATAACAACAACTCGACACTTTTACCAGGTGCTTTTGCAACGATTACCTCAGAAGGTTTTATACAAAAAAATGGCTTTAAGGTACCTCAAATAGCTATTAAACAAGATCAAAATGATGTTTATGTTCTTCTTGTTAAAAATGGAAAAGTAGAAAAATCTTCTGTACATATAAGCTACCAAAACAATGAATACGCTATTATTGACAAAGGATTGCAAAATGGCGATAAAATCATTTTGGATAATTTTAAAAAAATTCAAGTTGGTAGCGAAGTTAAAGAAATTGGAGCACAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37595","NCBI_taxonomy_name":"Campylobacter jejuni subsp. doylei 269.97","NCBI_taxonomy_id":"360109"}}}},"ARO_accession":"3000783","ARO_id":"37163","ARO_name":"cmeA","CARD_short_name":"cmeA","ARO_description":"CmeA is the membrane fusion protein of the CmeABC multidrug efflux complex.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"36989":{"category_aro_accession":"3000645","category_aro_cvterm_id":"36989","category_aro_name":"cefotaxime","category_aro_description":"Cefotaxime is a semisynthetic cephalosporin taken parenterally. It is resistant to most beta-lactamases and active against Gram-negative rods and cocci due to its aminothiazoyl and methoximino functional groups.","category_aro_class_name":"Antibiotic"},"37139":{"category_aro_accession":"3000759","category_aro_cvterm_id":"37139","category_aro_name":"fusidic acid","category_aro_description":"Fusidic acid is the only commercially available fusidane, a group of steroid-like antibiotics. It is most active against Gram-positive bacteria, and acts by inhibiting elongation factor G to  block protein synthesis.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"45735":{"category_aro_accession":"3007153","category_aro_cvterm_id":"45735","category_aro_name":"fusidane antibiotic","category_aro_description":"A group of antibiotics possessing steroid rings or steroid-like structures.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1182":{"model_id":"1182","model_name":"CTX-M-105","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1184":{"protein_sequence":{"accession":"ADY02554.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAVAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQREQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGGYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"HQ833651.1","fmin":"244","fmax":"1120","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGTCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGAGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGGCTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001965","ARO_id":"38365","ARO_name":"CTX-M-105","CARD_short_name":"CTX-M-105","ARO_description":"CTX-M-105 is a beta-lactamase found in Escherichia coli.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1184":{"model_id":"1184","model_name":"OXA-182","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8277":{"protein_sequence":{"accession":"ADK92148.1","sequence":"MKKFILPIFSISILLSLSACSSIQTKFEDTFHISNQKHEKAIKSYFDEAQTQGVIIIKEGKNISSYGNNLVRAHTEYVPASTFKMLNALIGLENHKATTNEIFKWDGKKRSYPMWEKDMTLGEAMALSAVPVYQDLARRIGLNLMQKEVKRVGFGNMNIGTQVDNFWLIGPLKITPIQEVNFADDLANNRLPFKLETQEEVKKMLLIKEVNGSKIYAKSGWGMDVSPQVGWLTGWVEKSNGEKVSFSLNIEMKQGMSGSIRNEITYKSLENLGII"},"dna_sequence":{"accession":"HM640278.2","fmin":"0","fmax":"828","strand":"+","sequence":"ATGAAAAAATTTATACTTCCTATCTTCAGCATTTCTATTCTACTTTCTCTCAGTGCATGCTCATCTATTCAAACTAAATTTGAAGATACTTTTCATATTTCTAATCAGAAACATGAAAAAGCTATTAAAAGCTATTTTGATGAAGCTCAAACACAAGGTGTAATTATTATTAAGGAAGGTAAAAATATTAGCTCCTATGGTAATAACCTTGTACGAGCACATACAGAATATGTCCCTGCATCAACATTTAAGATGCTAAATGCTTTAATCGGACTAGAAAATCATAAAGCGACAACAAATGAGATTTTTAAATGGGATGGTAAAAAAAGATCTTATCCTATGTGGGAGAAAGATATGACTTTGGGTGAGGCCATGGCACTTTCAGCTGTTCCTGTATATCAAGATCTTGCGAGACGGATTGGCTTAAATCTCATGCAAAAAGAAGTTAAACGCGTTGGTTTTGGTAATATGAACATTGGAACACAAGTTGATAATTTCTGGTTGATTGGTCCTCTTAAGATTACACCAATACAAGAAGTGAATTTTGCCGATGATCTTGCGAATAATCGATTACCCTTTAAATTAGAAACTCAAGAAGAAGTAAAAAAGATGCTTCTGATTAAAGAAGTCAATGGTAGTAAAATTTATGCTAAAAGCGGATGGGGAATGGATGTAAGCCCACAAGTAGGTTGGTTAACAGGTTGGGTAGAAAAATCTAATGGAGAAAAAGTTTCCTTTTCTTTAAATATAGAAATGAAGCAAGGAATGTCTGGTTCTATTCGTAATGAGATTACTTATAAGTCGTTAGAAAATTTAGGGATCATCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001709","ARO_id":"38109","ARO_name":"OXA-182","CARD_short_name":"OXA-182","ARO_description":"OXA-182 is a beta-lactamase found in Acinetobacter spp.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46490":{"category_aro_accession":"3007701","category_aro_cvterm_id":"46490","category_aro_name":"OXA-143-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-143.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1185":{"model_id":"1185","model_name":"OXA-176","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"882":{"protein_sequence":{"accession":"ADI58620.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDVKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDSKKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWVVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"HM113562.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGTAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATAGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGGTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAACAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001660","ARO_id":"38060","ARO_name":"OXA-176","CARD_short_name":"OXA-176","ARO_description":"OXA-176 is a beta-lactamase found in A. baumannii.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1186":{"model_id":"1186","model_name":"OXA-327","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1052":{"protein_sequence":{"accession":"AGW16409.1","sequence":"MYKKALIVATSILFLSACSSNTVKQHQIHSISANKNSEEIKSLFDQAQTTGVLVIKRGQTEEIYGNDLKRASTAYVPASTFKMLNALIGLEHHKATTTEVFKWNGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMSKEVKRIGFGNANIGSKVDNFWLVGPLKITPQQETQFAYQLAHKTLPFSQDVQEQVQSMVFIEEKNGSKIYAKSGWGWDVEPQVGWLTGWVVQPQGEIVAFSLNLEMKKGTPSSIRKEIAYKGLEQLGVL"},"dna_sequence":{"accession":"KF203101.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGTACAAAAAAGCCCTTATCGTTGCAACAAGTATCCTATTTTTATCCGCCTGTTCTTCCAATACGGTAAAACAACATCAAATACACTCTATTTCTGCCAATAAAAATTCAGAAGAAATTAAATCACTGTTTGATCAAGCACAGACCACGGGAGTTTTGGTGATTAAGCGAGGGCAAACAGAAGAAATTTATGGCAATGATCTTAAAAGAGCATCAACCGCCTATGTTCCCGCCTCTACCTTTAAAATGTTAAATGCTTTAATTGGACTTGAACATCATAAGGCAACTACAACTGAAGTGTTTAAATGGAATGGACAAAAACGCTTATTTCCTGATTGGGAAAAGGACATGACATTGGGCGATGCCATGAAAGCTTCTGCGATTCCAGTTTACCAAGAATTAGCCCGACGAATTGGTCTAGATCTTATGTCCAAAGAGGTGAAACGAATTGGTTTTGGTAATGCTAACATTGGTTCAAAAGTAGATAATTTTTGGCTTGTTGGCCCTCTAAAAATTACACCTCAACAAGAAACCCAATTTGCTTATCAATTAGCCCATAAAACGCTTCCATTTAGCCAAGATGTACAAGAACAAGTTCAATCAATGGTGTTCATAGAGGAAAAAAATGGAAGTAAAATTTATGCCAAAAGTGGTTGGGGATGGGATGTTGAACCGCAAGTTGGTTGGTTAACAGGTTGGGTCGTTCAACCACAAGGAGAAATTGTCGCATTCTCACTTAATTTAGAAATGAAAAAAGGAACTCCTAGCTCTATTCGCAAAGAAATTGCTTATAAAGGATTAGAACAACTCGGTGTTTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39094","NCBI_taxonomy_name":"Acinetobacter calcoaceticus","NCBI_taxonomy_id":"471"}}}},"ARO_accession":"3001515","ARO_id":"37915","ARO_name":"OXA-327","CARD_short_name":"OXA-327","ARO_description":"OXA-327 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46495":{"category_aro_accession":"3007706","category_aro_cvterm_id":"46495","category_aro_name":"OXA-213-like beta-lactamase","category_aro_description":"OXA-213-like enzymes have been identified to be intrinsic to A. calcoaceticus and have been subsequently detected in A. pittii. Phylogenetic analysis of OXA-213-like proteins identified two distinct subgroups within the OXA family. The first group was linked to A. pittii and the second group to A. calcoaceticus. The carbapenemase activity of these OXAs may be related to the species-dependent effect.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1187":{"model_id":"1187","model_name":"OXA-248","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1050":{"protein_sequence":{"accession":"CCJ32596.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDDKAEKIKNLFNEAHTTGVLVIHQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGEKRLFPEWEKNMTLGDAMKASAMPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"HE963769.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGACAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCATCAAGGTCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAATGGGATGGGGAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATGCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTCTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001673","ARO_id":"38073","ARO_name":"OXA-248","CARD_short_name":"OXA-248","ARO_description":"OXA-248 is a beta-lactamase found in A. baumannii.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1188":{"model_id":"1188","model_name":"ErmV","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"420":{"protein_sequence":{"accession":"AAB51440.1","sequence":"MARPSRVSRALSQNFLADRAAAGQLARLAAPHGLPVPLLLEVGAGKGALTELLAPRCRSLLAYEIDPRLVPVLRSRFADAPHVRVLGEDFLRARAPRTPFSVAGNVPFSRTAAVVAWCLRAPHLTDATLLTQLEYARRRTGDYGSWTRLTVLTWPRHEWRLAGRVGRRSFRPVPRVDAGIVRIERRRTPLLAPGADAGWRELVDLGFSGAGGSLHASLRRARPRRRVDAAFRAAGLDRDVLVGEVPPWTWLRLHEVLGS"},"dna_sequence":{"accession":"U59450.1","fmin":"396","fmax":"1176","strand":"+","sequence":"ATGGCCCGCCCCAGTCGCGTATCCCGCGCGCTCTCGCAGAACTTCCTCGCCGACCGCGCCGCCGCCGGACAGCTCGCCCGGCTCGCCGCGCCCCACGGCCTCCCCGTCCCGCTGCTGCTCGAAGTCGGCGCGGGCAAAGGCGCGTTGACCGAGCTGCTCGCCCCGCGCTGTCGCAGTCTCCTCGCCTACGAGATCGACCCACGGCTCGTCCCCGTCCTGCGCTCGCGCTTCGCGGACGCCCCGCACGTCCGCGTCCTCGGCGAGGACTTCCTGCGCGCCAGGGCGCCGCGCACCCCGTTCTCCGTCGCCGGGAACGTCCCCTTCTCCCGTACCGCCGCCGTCGTCGCGTGGTGTCTGCGGGCCCCGCACCTCACCGACGCCACCCTGCTCACCCAGCTGGAGTACGCCCGCAGACGCACCGGCGACTACGGCAGCTGGACGCGGCTGACCGTGCTGACTTGGCCCCGCCACGAGTGGCGGCTCGCCGGGCGGGTCGGGCGCCGCAGCTTCCGTCCCGTGCCCCGGGTGGACGCGGGGATCGTCCGTATCGAGCGGCGTCGCACCCCGCTGCTCGCGCCCGGTGCCGACGCCGGCTGGCGGGAGCTGGTCGACCTCGGCTTCTCCGGGGCCGGCGGCTCCCTGCACGCCTCGCTGCGGCGGGCCCGCCCGAGACGGCGGGTGGACGCGGCGTTCCGCGCGGCGGGGCTCGACCGGGACGTCCTGGTGGGGGAGGTGCCGCCGTGGACGTGGCTGAGGCTGCACGAGGTGCTGGGCTCGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39570","NCBI_taxonomy_name":"Streptomyces viridochromogenes","NCBI_taxonomy_id":"1938"}}}},"ARO_accession":"3002824","ARO_id":"39258","ARO_name":"ErmV","CARD_short_name":"ErmV","ARO_description":"ErmV is a plasmid-mediated methyltransferase found in Streptomyces viridochromogenes.","ARO_category":{"36699":{"category_aro_accession":"3000560","category_aro_cvterm_id":"36699","category_aro_name":"Erm 23S ribosomal RNA methyltransferase","category_aro_description":"Erm proteins are part of the RNA methyltransferase family and methylate A2058 (E. coli nomenclature) of the 23S ribosomal RNA conferring degrees of resistance to Macrolides, Lincosamides and Streptogramin b. This is called the MLSb phenotype.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"36284":{"category_aro_accession":"3000145","category_aro_cvterm_id":"36284","category_aro_name":"tylosin","category_aro_description":"Tylosin is a 16-membered macrolide, naturally produced by Streptomyces fradiae. It interacts with the bacterial ribosome 50S subunit to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"37247":{"category_aro_accession":"3000867","category_aro_cvterm_id":"37247","category_aro_name":"oleandomycin","category_aro_description":"Oleandomycin is a 14-membered macrolide produced by Streptomyces antibioticus. It is ssimilar to erythromycin, and contains a desosamine amino sugar and an oleandrose sugar. It targets the 50S ribosomal subunit to prevent protein synthesis.","category_aro_class_name":"Antibiotic"},"37621":{"category_aro_accession":"3001222","category_aro_cvterm_id":"37621","category_aro_name":"chalcomycin","category_aro_description":"Produced by Streptomyces bikiniensis.","category_aro_class_name":"Antibiotic"},"37626":{"category_aro_accession":"3001227","category_aro_cvterm_id":"37626","category_aro_name":"kitasamycin","category_aro_description":"Kitasamycin is a macrolide antibiotic and is produced by Streptoverticillium kitasatoense. The drug has antimicrobial activity against a wide spectrum of pathogens.","category_aro_class_name":"Antibiotic"},"37627":{"category_aro_accession":"3001228","category_aro_cvterm_id":"37627","category_aro_name":"carbomycin","category_aro_description":"Produced by Streptomyces halstedii and Streptomyces thermotolerans.","category_aro_class_name":"Antibiotic"},"37630":{"category_aro_accession":"3001231","category_aro_cvterm_id":"37630","category_aro_name":"celesticetin","category_aro_description":"Produced by Streptomyces caelestis, which also produces the macrolide niddamycin.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1189":{"model_id":"1189","model_name":"vatB","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"3345":{"protein_sequence":{"accession":"AAA86871.1","sequence":"MKYGPDPNSIYPHEEIKSVCFIKNTITNPNIIVGDYTYYSDVNGAEKFEEHVTHHYEFRGDKLVIGKFCAIAEGIEFIMNGANHRMNSITTYPFNIMGNGWEKATPSLEDLPFKGDTVVGNDVWIGQNVTVMPGIQIGDGAIVAANSVVTKDVPPYRIIGGNPSRIIKKRFEDELIDYLLQIKWWDWSAQKIFSNLETLCSSDLEKIKSIRD"},"dna_sequence":{"accession":"U19459.1","fmin":"66","fmax":"705","strand":"+","sequence":"ATGAAATATGGCCCTGATCCAAATAGCATATATCCACATGAAGAAATAAAAAGTGTTTGTTTTATTAAAAATACAATTACCAATCCAAATATTATAGTTGGAGATTATACTTACTATTCCGATGTTAACGGAGCTGAAAAATTTGAAGAACATGTGACACATCATTATGAATTTAGGGGTGATAAACTTGTAATTGGCAAGTTTTGTGCAATAGCTGAAGGTATAGAATTTATTATGAATGGAGCAAACCATAGAATGAATTCAATAACAACTTATCCTTTTAATATAATGGGAAATGGTTGGGAAAAAGCAACTCCATCTCTTGAAGATTTACCATTTAAGGGAGATACTGTTGTTGGAAATGATGTGTGGATTGGTCAGAATGTTACTGTTATGCCAGGAATTCAAATAGGAGATGGAGCAATTGTTGCTGCGAATTCAGTTGTTACAAAAGATGTACCACCATATCGTATTATTGGTGGAAATCCGAGTAGAATTATAAAGAAAAGGTTTGAAGATGAATTGATAGATTATTTATTGCAAATAAAATGGTGGGATTGGTCAGCACAAAAAATATTTTCTAATCTTGAAACACTTTGTAGCTCTGATTTAGAGAAAATAAAATCTATTCGAGATTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35508","NCBI_taxonomy_name":"Staphylococcus aureus","NCBI_taxonomy_id":"1280"}}}},"ARO_accession":"3002841","ARO_id":"39275","ARO_name":"vatB","CARD_short_name":"vatB","ARO_description":"vatB is a plasmid-mediated acetyltransferase found in Staphylococcus aureus.","ARO_category":{"36592":{"category_aro_accession":"3000453","category_aro_cvterm_id":"36592","category_aro_name":"streptogramin vat acetyltransferase","category_aro_description":"vat (Virginiamycin acetyltransferases) enzymes catalyze the transfer of an acetyl group from acetyl-CoA to the secondary alcohol of streptogramin A compounds, thus inactivating virginiamycin-like antibiotics and conferring resistance to these compounds.","category_aro_class_name":"AMR Gene Family"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"virginiamycin M1","category_aro_description":"Virginiamycin M1 is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37016":{"category_aro_accession":"3000672","category_aro_cvterm_id":"37016","category_aro_name":"madumycin II","category_aro_description":"Madumycin II is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37017":{"category_aro_accession":"3000673","category_aro_cvterm_id":"37017","category_aro_name":"griseoviridin","category_aro_description":"Griseoviridin is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35952":{"category_aro_accession":"0000034","category_aro_cvterm_id":"35952","category_aro_name":"streptogramin A antibiotic","category_aro_description":"Streptogramin A antibiotics are cyclic polyketide peptide hybrids that bind to the ribosomal peptidyl transfer centre. Structural variation arises from substituting a proline for its desaturated derivative and by its substitution for Ala or Cys. Used alone, streptogramin A antibiotics are bacteriostatic, but is bactericidal when used with streptogramin B antibiotics.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1190":{"model_id":"1190","model_name":"OXA-354","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1378":{"protein_sequence":{"accession":"AGW83452.1","sequence":"MYKKALIVATSILFLSACSSNSVKQHQIHSISANKNSEEIKSLFDQAQTTGVLVIKRGQTEEIYGNDLKRASTDYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMSKEVKRIGFGNANIGSKVDDFWLVGPLKITPQQETQFAYQLAHKMLPFSKDVQEQVQSMVFIEEKNGRKIYAKSGWGWDIEPQVGWLTGWVVQPQGEIVAFSLNLEMKKGTPSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"KF297583.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGTATAAAAAAGCCCTTATCGTTGCAACAAGTATCCTATTTTTATCCGCCTGTTCTTCTAATTCAGTAAAACAACATCAAATACACTCTATTTCTGCCAATAAAAATTCAGAAGAAATTAAATCACTGTTTGATCAGGCACAAACCACGGGTGTTTTGGTGATTAAGCGAGGACAAACAGAAGAAATTTATGGCAATGATCTTAAAAGAGCATCAACAGACTATGTTCCCGCCTCTACCTTTAAAATGTTAAATGCTTTAATTGGACTTGAACATCATAAGGCAACTACAACTGAAGTATTTAAATGGGATGGGCAGAAACGTTTATTTCCTGATTGGGAAAAGGACATGACACTGGGTGATGCCATGAAAGCTTCTGCAATCCCAGTTTACCAAGAATTAGCCCGACGAATTGGTCTGGATCTTATGTCTAAAGAGGTAAAGCGAATTGGTTTCGGTAATGCTAACATTGGCTCAAAAGTAGATGATTTCTGGCTTGTTGGTCCTCTAAAAATTACACCTCAACAAGAAACCCAATTTGCTTATCAATTAGCCCATAAAATGCTTCCATTTAGTAAAGATGTACAAGAACAAGTTCAATCAATGGTGTTCATAGAAGAAAAAAATGGACGTAAAATTTATGCAAAAAGCGGTTGGGGATGGGATATTGAGCCACAAGTTGGTTGGTTAACAGGCTGGGTCGTTCAACCACAAGGAGAAATTGTGGCATTCTCACTTAATTTAGAAATGAAAAAAGGAACTCCTAGCTCTATTCGCAAAGAAATTGCTTATAAAGGCTTAGAACAACTGGGTATCTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39094","NCBI_taxonomy_name":"Acinetobacter calcoaceticus","NCBI_taxonomy_id":"471"}}}},"ARO_accession":"3001541","ARO_id":"37941","ARO_name":"OXA-354","CARD_short_name":"OXA-354","ARO_description":"OXA-354 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46495":{"category_aro_accession":"3007706","category_aro_cvterm_id":"46495","category_aro_name":"OXA-213-like beta-lactamase","category_aro_description":"OXA-213-like enzymes have been identified to be intrinsic to A. calcoaceticus and have been subsequently detected in A. pittii. Phylogenetic analysis of OXA-213-like proteins identified two distinct subgroups within the OXA family. The first group was linked to A. pittii and the second group to A. calcoaceticus. The carbapenemase activity of these OXAs may be related to the species-dependent effect.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1191":{"model_id":"1191","model_name":"mdtM","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"4730":{"protein_sequence":{"accession":"AAC77293.1","sequence":"MPRFFTRHAATLFFPMALILYDFAAYLSTDLIQPGIINVVRDFNADVSLAPAAVSLYLAGGMALQWLLGPLSDRIGRRPVLITGALIFTLACAATMFTTSMTQFLIARAIQGTSICFIATVGYVTVQEAFGQTKGIKLMAIITSIVLIAPIIGPLSGAALMHFMHWKVLFAIIAVMGFISFVGLLLAMPETVKRGAVPFSAKSVLRDFRNVFCNRLFLFGAATISLSYIPMMSWVAVSPVILIDAGSLTTSQFAWTQVPVFGAVIVANAIVARFVKDPTEPRFIWRAVPIQLVGLSLLIVGNLLSPHVWLWSVLGTSLYAFGIGLIFPTLFRFTLFSNKLPKGTVSASLNMVILMVMSVSVEIGRWLWFNGGRLPFHLLAVVAGVIVVFTLAGLLNRVRQHQAAELVEEQ"},"dna_sequence":{"accession":"U00096.3","fmin":"4567286","fmax":"4568519","strand":"-","sequence":"ATGCCACGTTTTTTTACCCGCCATGCCGCCACGCTGTTTTTCCCGATGGCGTTGATTTTGTATGACTTTGCTGCGTATCTGTCGACGGATCTGATCCAGCCTGGGATCATTAATGTGGTACGTGATTTTAATGCCGATGTCAGTCTGGCCCCTGCTGCCGTCAGTCTCTATCTTGCTGGCGGTATGGCGTTACAGTGGCTGCTGGGGCCGCTTTCCGACAGAATTGGCCGCAGGCCGGTGCTGATTACCGGGGCGCTAATTTTTACCCTTGCCTGCGCCGCGACAATGTTCACAACGTCTATGACACAGTTTCTTATCGCGCGTGCAATTCAGGGCACCAGTATCTGTTTTATTGCCACCGTTGGTTATGTCACGGTGCAGGAGGCGTTCGGACAGACAAAAGGGATCAAGTTGATGGCGATTATCACCTCCATCGTACTGATTGCGCCGATTATCGGCCCGCTTTCCGGCGCAGCTCTGATGCACTTTATGCACTGGAAAGTCCTTTTTGCCATCATTGCGGTTATGGGTTTTATCTCATTTGTTGGCTTACTGTTGGCGATGCCAGAGACGGTGAAGCGCGGCGCGGTTCCGTTTAGCGCCAAAAGCGTCTTGCGCGATTTTCGTAATGTCTTTTGCAATCGGCTGTTCCTCTTTGGCGCAGCAACCATCTCTTTAAGCTATATCCCGATGATGAGCTGGGTGGCTGTCTCGCCGGTGATCCTTATCGATGCAGGCAGCTTAACAACTTCGCAGTTCGCCTGGACACAGGTTCCGGTGTTCGGCGCGGTGATTGTTGCGAATGCCATCGTGGCGCGTTTTGTTAAAGATCCGACCGAACCGCGGTTTATCTGGCGTGCCGTACCCATTCAACTGGTCGGCCTCTCGCTGTTGATTGTCGGCAATCTGCTGTCGCCGCACGTCTGGCTGTGGTCGGTGCTGGGCACCAGTCTGTATGCTTTCGGGATTGGTTTGATTTTCCCGACCTTATTCCGCTTTACGCTGTTTTCCAATAAGTTACCGAAAGGGACCGTCTCCGCATCGCTAAATATGGTGATCCTGATGGTGATGTCGGTCTCGGTCGAAATCGGCCGCTGGCTATGGTTTAACGGCGGTCGCTTGCCGTTTCATCTGTTAGCCGTTGTGGCGGGCGTTATCGTCGTTTTCACCCTGGCGGGATTGCTCAATCGCGTGCGCCAGCATCAGGCAGCCGAGCTAGTGGAGGAGCAGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36849","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. MG1655","NCBI_taxonomy_id":"511145"}}}},"ARO_accession":"3001214","ARO_id":"37613","ARO_name":"mdtM","CARD_short_name":"mdtM","ARO_description":"Multidrug resistance protein MdtM.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35963":{"category_aro_accession":"0000045","category_aro_cvterm_id":"35963","category_aro_name":"acriflavine","category_aro_description":"Acriflavine is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish.","category_aro_class_name":"Antibiotic"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35965":{"category_aro_accession":"0000047","category_aro_cvterm_id":"35965","category_aro_name":"puromycin","category_aro_description":"Puromycin is an aminonucleoside antibiotic, derived from Streptomyces alboniger, that causes premature chain termination during ribosomal protein translation.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"36174":{"category_aro_accession":"3000034","category_aro_cvterm_id":"36174","category_aro_name":"nucleoside antibiotic","category_aro_description":"Nucleoside antibiotics are made of modified nucleosides and nucleotides with wide-ranging activities and means of antibacterial effects. This drug class includes aminonucleoside antibiotics, which contain an amino group.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"43746":{"category_aro_accession":"3005386","category_aro_cvterm_id":"43746","category_aro_name":"disinfecting agents and antiseptics","category_aro_description":"Disinfectants that can also interact with antimicrobial resistance mechanisms, e.g. molecule efflux, and thus are the targets of disinfectant resistance.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1192":{"model_id":"1192","model_name":"VEB-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"5481":{"protein_sequence":{"accession":"CAM88398.1","sequence":"MKIVKRILLVLLSLFFTIVYSNAQTDNLTLKIENVLKAKNARIGVAIFNSNEKDTLKINNDFHFPMQSVMKFPIALAVLSEIDKGNLSFEQKIEITPQDLLPKTWSPIKEEFPNGTTLTIEQILNYTVSESDNIGCDILLKLIGGTDSVQKFLNANHFTDISIKANEEQMHKDWNTQYQNWATPTAMNKLLIDTYNNKNQLLSKKSYDFIWKIMRETTTGSNRLKGQLPKNTIVAHKTGTSGINNGIAAATNDVGVITLPNGQLIFISVFVAESKETSEINEKIISDIAKITWNYYLNK"},"dna_sequence":{"accession":"CU459141.1","fmin":"3660736","fmax":"3661636","strand":"-","sequence":"ATGAAAATCGTAAAAAGGATATTATTAGTATTGTTAAGTTTATTTTTTACAATTGTGTATTCAAATGCTCAAACTGACAACTTAACTTTGAAAATTGAGAATGTTTTAAAGGCAAAAAATGCCAGAATAGGAGTAGCAATATTCAACAGCAATGAGAAGGATACTTTGAAGATTAATAACGACTTCCATTTCCCGATGCAAAGCGTTATGAAATTTCCGATTGCTTTAGCCGTTTTGTCTGAGATAGATAAAGGGAATCTTTCTTTTGAACAAAAAATAGAGATTACCCCTCAAGACCTTTTGCCTAAAACGTGGAGTCCGATTAAAGAGGAATTCCCTAATGGAACAACTTTGACGATTGAACAAATACTAAATTATACAGTATCAGAGAGCGACAATATTGGTTGTGATATTTTGCTAAAATTAATCGGAGGAACTGATTCTGTTCAAAAATTCTTGAATGCTAATCATTTCACTGATATTTCAATCAAAGCAAACGAAGAACAAATGCACAAGGATTGGAATACCCAATATCAAAATTGGGCAACCCCAACAGCGATGAACAAACTGTTAATAGATACTTATAATAATAAGAACCAATTACTTTCTAAAAAAAGTTATGATTTTATTTGGAAAATTATGAGAGAAACAACAACAGGAAGTAACCGATTAAAAGGACAATTACCAAAGAATACAATTGTTGCTCATAAAACAGGGACTTCCGGAATAAATAATGGAATTGCAGCAGCCACTAATGATGTTGGGGTAATTACTTTACCGAATGGACAATTAATTTTTATAAGCGTATTTGTTGCAGAGTCCAAAGAAACTTCGGAAATTAATGAAAAGATTATTTCAGACATTGCAAAAATAACGTGGAATTACTATTTGAATAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35535","NCBI_taxonomy_name":"Acinetobacter baumannii AYE","NCBI_taxonomy_id":"509173"}}}},"ARO_accession":"3002370","ARO_id":"38770","ARO_name":"VEB-1","CARD_short_name":"VEB-1","ARO_description":"VEB-1 is a beta-lactamase found in Escherichia coli and Pseudomonas aeruginosa.","ARO_category":{"36182":{"category_aro_accession":"3000043","category_aro_cvterm_id":"36182","category_aro_name":"VEB beta-lactamase","category_aro_description":"VEB beta-lactamases or Vietnamese extended-spectrum beta-lactamases are class A beta-lactamases that confer high-level resistance to oxyimino cephalosporins and to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1193":{"model_id":"1193","model_name":"ErmH","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"63":{"protein_sequence":{"accession":"AAC32026.1","sequence":"MAALLKRILRRRMAEKRSGRGRMAAARTTGAQSRKTAQRSGRSEADRRRRVHGQNFLVDRETVQRFVRFADPDPGEVVLEVGAGNGAITRELARLCRRVVAYEIDRHFADRLREATAEDPRIEVVAGDFLKTSQPKVPFSVVGNIPFGNTADIVDWCLNARRLRTTTLVTQLEYARKRTGGYRRWSRLTVATWPEVEWRMGERISRRWFRPVPAVDSAVLRLERRPVPLIPPGLMHDFRDLVETGFTGKGGSLDASLRRRFPARRVAAGFRRARLEQGVVVAYVTPGQWITLFEELHGR"},"dna_sequence":{"accession":"M16503.1","fmin":"243","fmax":"1143","strand":"+","sequence":"ATGGCTGCGCTCCTGAAGCGCATACTTAGGAGACGCATGGCTGAAAAGAGGTCAGGACGCGGGCGCATGGCCGCAGCGCGTACAACCGGAGCTCAGTCGCGTAAAACGGCACAGCGGTCGGGCCGGAGTGAGGCTGACCGTAGAAGAAGAGTCCACGGGCAGAATTTCCTCGTCGACCGGGAAACAGTACAACGGTTTGTGCGTTTCGCCGATCCGGACCCCGGGGAGGTCGTTCTCGAGGTCGGTGCCGGTAATGGTGCGATCACGCGCGAGCTGGCGCGATTATGCCGACGAGTGGTGGCGTATGAGATCGACCGGCACTTCGCGGACCGATTACGTGAGGCGACCGCCGAGGATCCGCGGATCGAGGTCGTCGCCGGCGACTTCCTGAAGACCTCGCAGCCCAAGGTCCCGTTCTCCGTGGTCGGCAACATCCCGTTCGGCAACACCGCGGACATAGTGGACTGGTGCCTGAACGCGCGGCGGCTGCGTACGACCACCCTGGTCACCCAGCTCGAATACGCCCGCAAGCGCACCGGCGGCTATCGGCGCTGGTCACGGCTCACCGTGGCCACCTGGCCCGAGGTGGAGTGGCGGATGGGCGAGCGGATCAGCCGCCGCTGGTTCCGGCCCGTCCCCGCCGTCGACTCCGCGGTACTGCGACTGGAACGGCGACCGGTGCCGCTGATCCCACCCGGTCTGATGCACGACTTCCGGGACCTGGTGGAGACCGGGTTCACGGGAAAGGGCGGTTCGCTGGACGCCTCGCTGCGCCGGCGCTTCCCGGCCCGGCGGGTGGCCGCCGGGTTCCGCAGGGCCCGCCTGGAGCAGGGCGTGGTCGTCGCCTACGTCACCCCGGGCCAATGGATCACACTCTTCGAGGAACTCCACGGGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36843","NCBI_taxonomy_name":"Streptomyces thermotolerans","NCBI_taxonomy_id":"80858"}}}},"ARO_accession":"3002823","ARO_id":"39257","ARO_name":"ErmH","CARD_short_name":"ErmH","ARO_description":"ErmH is a plasmid-mediated methyltransferase found in Streptomyces thermotolerans.","ARO_category":{"36699":{"category_aro_accession":"3000560","category_aro_cvterm_id":"36699","category_aro_name":"Erm 23S ribosomal RNA methyltransferase","category_aro_description":"Erm proteins are part of the RNA methyltransferase family and methylate A2058 (E. coli nomenclature) of the 23S ribosomal RNA conferring degrees of resistance to Macrolides, Lincosamides and Streptogramin b. This is called the MLSb phenotype.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"37022":{"category_aro_accession":"3000678","category_aro_cvterm_id":"37022","category_aro_name":"pristinamycin IC","category_aro_description":"Pristinamycin IC is a class B streptogramin derived from virginiamycin S1.","category_aro_class_name":"Antibiotic"},"37247":{"category_aro_accession":"3000867","category_aro_cvterm_id":"37247","category_aro_name":"oleandomycin","category_aro_description":"Oleandomycin is a 14-membered macrolide produced by Streptomyces antibioticus. It is ssimilar to erythromycin, and contains a desosamine amino sugar and an oleandrose sugar. It targets the 50S ribosomal subunit to prevent protein synthesis.","category_aro_class_name":"Antibiotic"},"37627":{"category_aro_accession":"3001228","category_aro_cvterm_id":"37627","category_aro_name":"carbomycin","category_aro_description":"Produced by Streptomyces halstedii and Streptomyces thermotolerans.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35967":{"category_aro_accession":"0000050","category_aro_cvterm_id":"35967","category_aro_name":"streptogramin B antibiotic","category_aro_description":"Streptogramin B antibiotics are are cyclic hepta- or hexa-depsipeptides.  Type B streptogramins block the peptide exit tunnel of the 50S bacterial ribosome. The general composition of group B streptogramins is 3-hydroxypicolinic acid-L-Thr-D-aminobutyric acid (or D-Ala)-L-Pro-L-Phe (or 4-N-,N-(dimethylamino)-L-Phe)-X-L-phenylglycine. Used alone, streptogramin B antibiotics are bacteriostatic, but is bactericidal when used with streptogramin A antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1194":{"model_id":"1194","model_name":"OXA-16","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8404":{"protein_sequence":{"accession":"AAB97924.1","sequence":"IACLSSTALAGSITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQITREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEDQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGIIGG"},"dna_sequence":{"accession":"AF043100.1","fmin":"1","fmax":"775","strand":"+","sequence":"ATCGCGTGTCTTTCGAGTACGGCATTAGCTGGTTCAATTACAGAAAATACGTCTTGGAACAAAGAGTTCTCTGCCGAAGCCGTCAATGGTGTCTTCGTGCTTTGTAAAAGTAGCAGTAAATCCTGCGCTACCAATGACTTAGCTCGTGCATCAAAGGAATATCTTCCAGCATCAACATTTAAGATCCCCAACGCAATTATCGGCCTAGAAACTGGTGTCATAAAGAATGAGCATCAGGTTTTCAAATGGGACGGAAAGCCAAGAGCCATGAAGCAATGGGAAAGAGACTTGACCTTAAGAGGGGCAATACAAGTTTCAGCTGTTCCCGTATTTCAACAAATCACCAGAGAAGTTGGCGAAGTAAGAATGCAGAAATACCTTAAAAAATTTTCCTATGGCAACCAGAATATCAGTGGTGGCATTGACAAATTCTGGTTGGAAGACCAGCTTAGAATTTCCGCAGTTAATCAAGTGGAGTTTCTAGAGTCTCTATATTTAAATAAATTGTCAGCATCTAAAGAAAACCAGCTAATAGTAAAAGAGGCTTTGGTAACGGAGGCGGCACCTGAATATCTAGTGCATTCAAAAACTGGTTTTTCTGGTGTGGGAACTGAGTCAAATCCTGGTGTCGCATGGTGGGTTGGGTGGGTTGAGAAGGAGACAGAGGTTTACTTTTTCGCCTTTAACATGGATATAGACAACGAAAGTAAGTTGCCGCTAAGAAAATCCATTCCCACCAAAATCATGGAAAGTGAGGGCATCATTGGTGGCTAA","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3001411","ARO_id":"37811","ARO_name":"OXA-16","CARD_short_name":"OXA-16","ARO_description":"OXA-16 is a beta-lactamase found in P. aeruginosa.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1195":{"model_id":"1195","model_name":"SHV-55","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"8263":{"protein_sequence":{"accession":"CAI10727.2","sequence":"MRFIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGASKRGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AJ863560.2","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTTTATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACATCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGAGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTAGCAAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATCGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001111","ARO_id":"37491","ARO_name":"SHV-55","CARD_short_name":"SHV-55","ARO_description":"SHV-55 is an extended-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1196":{"model_id":"1196","model_name":"OXA-71","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1057":{"protein_sequence":{"accession":"AAW81342.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKTTTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"AY750913.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCCCTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTCTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGACAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGACGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCATTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001619","ARO_id":"38019","ARO_name":"OXA-71","CARD_short_name":"OXA-71","ARO_description":"OXA-71 is a beta-lactamase found in A. baumannii.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1199":{"model_id":"1199","model_name":"SHV-168","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1233":{"protein_sequence":{"accession":"AFW16978.1","sequence":"MRYFRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPVGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"JX870080.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATTTTCGCCTGTGTATTATCTCTCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGTAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGGATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001352","ARO_id":"37752","ARO_name":"SHV-168","CARD_short_name":"SHV-168","ARO_description":"SHV-168 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1200":{"model_id":"1200","model_name":"msrA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"5179":{"protein_sequence":{"accession":"CAA36304.1","sequence":"MEQYTIKFNQINHKLTDLRSLNIDHLYAYQFEKIALIGGNGTGKTTLLNMIAQKTKPESGTVETNGEIQYFEQLNMDVENDFNTLDGSLMSELHIPMHTTDSMSGGEKAKYKLRNVISNYSPILLLDEPTNHLDKIGKDYLNNILKYYYGTLIIVSHDRALIDQIADTIWDIQEDGTIRVFKGNYTQYQNQYEQEQLEQQRKYEQYISEKQRLSQASKAKRNQAQQMAQASSKQKNKSIAPDRLSASKEKGTVEKAAQKQAKHIEKRMEHLEEVEKPQSYHEFNFPQNKIYDIHNNYPIIAQNLTLVKGSQKLLTQVRFQIPYGKNIALVGANGVGKTTLLEAIYHQIEGIDCSPKVQMAYYRQLAYEDMRDVSLLQYLMDETDSSESFSRAILNNLGLNEALERSCNVLSGGERTKLSLAVLFSTKANMLILDEPTNFLDIKTLEALEMFMNKYPGIILFTSHDTRFVKHVSDKKWELTGQSIHDIT"},"dna_sequence":{"accession":"X52085.1","fmin":"342","fmax":"1809","strand":"+","sequence":"ATGGAACAATATACAATTAAATTTAACCAAATCAATCATAAATTGACAGATTTACGATCACTTAACATCGATCATCTTTATGCTTACCAATTTGAAAAAATAGCACTTATTGGGGGTAATGGTACTGGTAAAACCACATTACTAAATATGATTGCTCAAAAAACAAAACCAGAATCTGGAACAGTTGAAACGAATGGCGAAATTCAATATTTTGAACAGCTTAACATGGATGTGGAAAATGATTTTAACACGTTAGACGGTAGTTTAATGAGTGAACTCCATATACCTATGCATACAACCGACAGTATGAGTGGTGGTGAAAAAGCAAAATATAAATTACGTAATGTCATATCAAATTATAGTCCGATATTACTTTTAGATGAACCTACAAATCACTTGGATAAAATTGGTAAAGATTATCTGAATAATATTTTAAAATATTACTATGGTACTTTAATTATAGTAAGTCACGATAGAGCACTTATAGACCAAATTGCTGACACAATTTGGGATATACAAGAAGATGGCACAATAAGAGTGTTTAAAGGTAATTACACACAGTATCAAAATCAATATGAACAAGAACAGTTAGAACAACAACGTAAATATGAACAGTATATAAGTGAAAAACAAAGATTGTCCCAAGCCAGTAAAGCTAAACGAAATCAAGCGCAACAAATGGCACAAGCATCATCAAAACAAAAAAATAAAAGTATAGCACCAGATCGTTTAAGTGCATCAAAAGAAAAAGGCACGGTTGAGAAGGCTGCTCAAAAACAAGCTAAGCATATTGAAAAAAGAATGGAACATTTGGAAGAAGTTGAAAAACCACAAAGTTATCATGAATTCAATTTTCCACAAAATAAAATTTATGATATCCATAATAATTATCCAATCATTGCACAAAATCTAACATTGGTTAAAGGAAGTCAAAAACTGCTAACACAAGTACGATTCCAAATACCATATGGCAAAAATATAGCGCTCGTAGGTGCAAATGGTGTAGGTAAGACAACTTTACTTGAAGCTATTTACCACCAAATAGAGGGAATTGATTGTTCTCCTAAAGTGCAAATGGCATACTATCGTCAACTTGCTTATGAAGACATGCGTGACGTTTCATTATTGCAATATTTAATGGATGAAACGGATTCATCAGAATCATTCAGTAGAGCTATTTTAAATAACTTGGGTTTAAATGAAGCACTTGAGCGTTCTTGTAATGTTTTGAGTGGTGGGGAAAGAACGAAATTATCGTTAGCAGTATTATTTTCAACGAAAGCGAATATGTTAATTTTGGATGAACCAACTAATTTTTTAGATATTAAAACATTAGAAGCATTAGAAATGTTTATGAATAAATATCCTGGAATCATTTTGTTTACATCACATGATACAAGGTTTGTTAAACATGTATCAGATAAAAAATGGGAATTAACAGGACAATCTATTCATGATATAACTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36868","NCBI_taxonomy_name":"Staphylococcus epidermidis","NCBI_taxonomy_id":"1282"}}}},"ARO_accession":"3000251","ARO_id":"36390","ARO_name":"msrA","CARD_short_name":"msrA","ARO_description":"MsrA is an ABC-F subfamily ribosomal protection protein expressed in Staphylococcus species which confers resistance to erythromycin and streptogramin B antibiotics through antibiotic target protection mechanisms. It is associated with plasmid DNA.","ARO_category":{"41695":{"category_aro_accession":"3004471","category_aro_cvterm_id":"41695","category_aro_name":"msr-type ABC-F protein","category_aro_description":"msr-type ABC-F subfamily ribosomal protection proteins expression in Staphylococci species and confer resistance to erythromycin and streptogramin B antibiotics through antibiotic target protection mechanisms.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"36723":{"category_aro_accession":"3000584","category_aro_cvterm_id":"36723","category_aro_name":"quinupristin","category_aro_description":"Quinupristin is a type B streptogramin and a semisynthetic derivative of pristinamycin 1A. It is a component of the drug Synercid and interacts with the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35967":{"category_aro_accession":"0000050","category_aro_cvterm_id":"35967","category_aro_name":"streptogramin B antibiotic","category_aro_description":"Streptogramin B antibiotics are are cyclic hepta- or hexa-depsipeptides.  Type B streptogramins block the peptide exit tunnel of the 50S bacterial ribosome. The general composition of group B streptogramins is 3-hydroxypicolinic acid-L-Thr-D-aminobutyric acid (or D-Ala)-L-Pro-L-Phe (or 4-N-,N-(dimethylamino)-L-Phe)-X-L-phenylglycine. Used alone, streptogramin B antibiotics are bacteriostatic, but is bactericidal when used with streptogramin A antibiotics.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1201":{"model_id":"1201","model_name":"CARB-22","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4727":{"protein_sequence":{"accession":"BAC61820.1","sequence":"MKKLFLLVGLMVCSTVSYASKLNEDISLIEKQTSGRIGVSVWDTQTDKRWDYRGDERFPLMSTFKTLACATMLSDMDSGKLNKNATAKIDERNIVVWSPVMDKLAGQSTRIEHACEAAMLMSDNTAANLVLNEIGGPKAVTQFLRSIGDKATRLDRLEPRLNEAKPGDKRDTTTPNAMVNTLHTLMEDNALSYESRTQLKIWMQDNKVSDSLMRSVLPKGWSIADRSGAGNYGSRGISAMIWKDNYKPVYISIYVTDTDLSLQARDQLIAQISQLILEHYKES"},"dna_sequence":{"accession":"BA000032.2","fmin":"476707","fmax":"477559","strand":"-","sequence":"ATGAAAAAGTTATTCCTGTTGGTTGGGCTGATGGTTTGCTCAACTGTTAGTTACGCCTCCAAATTAAACGAAGACATCTCCCTCATCGAGAAACAAACATCTGGGCGAATTGGAGTGTCAGTCTGGGATACACAAACGGACAAGCGTTGGGATTATCGCGGAGACGAACGTTTCCCATTAATGAGCACATTCAAAACGTTAGCGTGTGCCACCATGCTAAGCGACATGGACAGCGGCAAACTCAACAAAAATGCCACAGCGAAAATCGATGAACGCAATATTGTGGTTTGGTCTCCGGTGATGGATAAACTGGCTGGACAAAGCACACGCATCGAACACGCTTGTGAAGCCGCCATGTTGATGAGCGACAACACCGCCGCGAACTTAGTGTTAAATGAAATTGGTGGTCCTAAAGCGGTCACGCAGTTTTTGCGATCTATTGGCGACAAAGCAACGCGACTTGACCGATTGGAACCCCGTTTGAATGAAGCAAAACCGGGCGACAAGCGAGACACCACAACGCCTAACGCCATGGTAAACACCCTACACACCTTGATGGAAGATAACGCCCTATCTTACGAGTCACGCACACAGCTGAAAATCTGGATGCAAGACAACAAAGTATCGGATTCTCTCATGCGCTCTGTTCTGCCAAAAGGCTGGTCGATTGCAGACCGCTCTGGCGCAGGTAACTACGGTTCACGCGGCATTAGCGCGATGATCTGGAAAGACAACTACAAGCCGGTTTACATCAGTATTTACGTCACAGACACAGACCTTTCGCTTCAAGCTCGCGATCAACTGATCGCGCAAATCAGCCAACTGATTTTAGAGCACTACAAAGAAAGTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39776","NCBI_taxonomy_name":"Vibrio parahaemolyticus RIMD 2210633","NCBI_taxonomy_id":"223926"}}}},"ARO_accession":"3003151","ARO_id":"39728","ARO_name":"CARB-22","CARD_short_name":"CARB-22","ARO_description":"CARB-22 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36230":{"category_aro_accession":"3000091","category_aro_cvterm_id":"36230","category_aro_name":"CARB beta-lactamase","category_aro_description":"CARB beta-lactamases are class A lactamases that can hydrolyze carbenicillin. Many of the PSE beta-lactamases have been renamed as CARB-lactamases with the notable exception of PSE-2 which is now OXA-10.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1202":{"model_id":"1202","model_name":"CTX-M-28","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1780":{"protein_sequence":{"accession":"CAD70280.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTNGL"},"dna_sequence":{"accession":"AJ549244.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGTCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCAACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001890","ARO_id":"38290","ARO_name":"CTX-M-28","CARD_short_name":"CTX-M-28","ARO_description":"CTX-M-28 is a beta-lactamase found in Salmonella enterica.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1205":{"model_id":"1205","model_name":"VIM-39","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1807":{"protein_sequence":{"accession":"AGS82586.1","sequence":"MLKVISSLLVYMTASVMAVASPLAHSGEPSGEYPAVNEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEAEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSANVLYGGCAVLELSSTSAGNVADADLAEWPTSVERIQKHYPEAEVVIPGHGLPGGLDLLQHTANVVKAHKNRSVAE"},"dna_sequence":{"accession":"KF131539.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGTTAAAAGTTATTAGTAGTTTATTGGTCTACATGACCGCGTCTGTCATGGCTGTCGCAAGTCCGTTAGCCCATTCCGGGGAGCCGAGTGGTGAGTATCCGGCAGTCAACGAAATTCCGGTCGGAGAGGTCCGACTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCGGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAAAAGCAAATTGGACTTCCCGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGCAGAGGGGAACGAGATTCCCACGCATTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAGCTCTTCTATCCTGGTGCTGCGCATTCGACCGACAATCTGGTTGTATACGTCCCGTCAGCGAACGTGCTATACGGTGGTTGTGCCGTTCTTGAGTTGTCAAGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCGTTGAGCGGATTCAAAAACACTACCCGGAAGCAGAGGTCGTCATTCCCGGGCACGGTCTACCGGGCGGTCTAGACTTGCTCCAGCACACAGCGAACGTTGTCAAAGCACACAAAAATCGCTCAGTCGCCGAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002309","ARO_id":"38709","ARO_name":"VIM-39","CARD_short_name":"VIM-39","ARO_description":"VIM-39 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1207":{"model_id":"1207","model_name":"DHA-13","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"770":{"protein_sequence":{"accession":"AIT76108.1","sequence":"MKKSLSATLISALLAFSAPGFSAADNVAAVVDSTIKPLMAQQDIPGMAVAVSVKGKPYYFNYGFADVQAKQPVTENTLFELGSVSKTFTGVLGAVSVAKKEMALNDPAAKYQPELALPQWKGITLLDLATYTAGGLPLQVPDAVKSRADLLNFYQQWQPSWKPGDMRLYANSSIGLFGALTANAAGMPYEQLLTARILAPLGLSHTFITVPESAQSQYAYGYKNKKPVRVSPGQLDAESYGVKSASKDMLRWAEMNMEPSRAGNADLEMAMYLAQTRYYKTAAINQGLGWEMYDWPQQKDMIINGVTNEVALQPHPVTDNQVQPYNRASWVHKTGATTGFGAYVAFIPEKQVAIVILANKNYPNTERVKAAQAILSALE"},"dna_sequence":{"accession":"KM087855.1","fmin":"0","fmax":"1140","strand":"+","sequence":"ATGAAAAAATCGTTATCTGCAACACTGATTTCCGCTCTGCTGGCGTTTTCCGCCCCGGGGTTTTCTGCCGCTGATAATGTCGCGGCGGTGGTGGACAGCACCATTAAACCGCTGATGGCACAGCAGGATATTCCCGGGATGGCGGTTGCCGTCTCCGTAAAGGGTAAGCCCTATTATTTCAATTACGGTTTTGCCGATGTTCAGGCAAAACAGCCTGTCACTGAAAATACACTATTTGAGCTCGGATCTGTAAGTAAAACTTTCACAGGTGTGCTGGGTGCGGTTTCCGTGGCGAAAAAAGAGATGGCGCTGAATGATCCGGCGGCAAAATATCAGCCGGAGCTGGCTCTGCCGCAGTGGAAGGGGATCACGCTGCTGGATCTGGCCACCTATACCGCAGGCGGGCTGCCGTTACAGGTACCGGATGCGGTGAAAAGCCGTGCGGATCTGCTGAATTTCTATCAGCAGTGGCAGCCATCATGGAAACCGGGCGATATGCGTCTGTATGCAAACAGCAGTATCGGCCTGTTTGGTGCTCTGACCGCCAACGCGGCGGGGATGCCGTATGAGCAGTTGCTGACTGCACGGATCCTGGCACCGCTGGGGTTATCTCACACCTTTATTACTGTGCCGGAAAGTGCGCAAAGCCAGTATGCGTACGGTTATAAAAACAAAAAACCGGTCCGCGTGTCGCCGGGACAGCTTGATGCGGAATCTTACGGCGTGAAATCCGCCTCAAAAGATATGCTGCGCTGGGCGGAAATGAATATGGAGCCGTCACGGGCCGGTAATGCGGATCTGGAAATGGCAATGTATCTTGCACAGACCCGCTACTATAAAACCGCCGCGATTAACCAGGGGCTGGGCTGGGAAATGTATGACTGGCCGCAGCAGAAAGATATGATCATTAACGGCGTGACCAACGAGGTCGCATTGCAGCCGCACCCGGTAACAGACAACCAGGTTCAGCCGTATAACCGTGCTTCCTGGGTGCATAAAACGGGGGCAACAACTGGTTTCGGCGCCTATGTGGCCTTTATTCCGGAAAAACAGGTGGCGATTGTGATTCTGGCGAATAAAAACTACCCGAATACCGAAAGAGTCAAAGCCGCACAGGCTATTTTGAGTGCACTGGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36917","NCBI_taxonomy_name":"Morganella morganii","NCBI_taxonomy_id":"582"}}}},"ARO_accession":"3002144","ARO_id":"38544","ARO_name":"DHA-13","CARD_short_name":"DHA-13","ARO_description":"DHA-13 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36207":{"category_aro_accession":"3000068","category_aro_cvterm_id":"36207","category_aro_name":"DHA beta-lactamase","category_aro_description":"DHA beta-lactamases are plasmid-mediated AmpC \u03b2-lactamases that confer resistance to cephamycins and oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1208":{"model_id":"1208","model_name":"SHV-173","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1390":{"protein_sequence":{"accession":"AHA80959.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDQASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"KF513178.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCAGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACATCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGCATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001357","ARO_id":"37757","ARO_name":"SHV-173","CARD_short_name":"SHV-173","ARO_description":"SHV-173 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1209":{"model_id":"1209","model_name":"QnrB45","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"5843":{"protein_sequence":{"accession":"WP_063866109.1","sequence":"MALALVGEKIDRNRFTGEKIENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRTMLKDAIFKSCDLSMADFRNASALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGAQVLGATFSGSDLSGGEFSTFDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDNYQASLLMERLGIAVIG"},"dna_sequence":{"accession":"NG_050508.1","fmin":"36","fmax":"681","strand":"+","sequence":"ATGGCTCTGGCACTCGTTGGCGAAAAAATTGACAGAAACCGCTTCACCGGTGAGAAAATTGAAAATAGTACATTTTTTAACTGTGATTTTTCAGGTGCCGACCTGAGCGGCACTGAATTTATCGGCTGTCAGTTCTATGATCGTGAAAGCCAGAAAGGGTGCAATTTTAGTCGTACGATGCTGAAAGATGCCATTTTTAAAAGCTGTGATTTATCCATGGCGGATTTTCGCAATGCCAGTGCGCTTGGCATTGAAATTCGCCACTGTCGTGCGCAAGGCGCAGATTTCCGCGGCGCAAGCTTTATGAATATGATCACTACTCGCACCTGGTTTTGTAGTGCATATATCACTAACACAAATCTAAGCTACGCCAATTTTTCGAAAGTCGTGCTGGAAAAGTGTGAGCTGTGGGAAAACCGTTGGATGGGTGCCCAGGTACTGGGCGCGACGTTCAGTGGTTCAGATCTCTCCGGCGGCGAGTTTTCGACTTTCGACTGGCGAGCAGCAAACTTCACACATTGCGATCTGACCAATTCGGAGTTGGGTGACTTAGATATTCGGGGCGTTGATTTACAAGGCGTTAAGTTGGACAACTACCAGGCATCGTTGCTCATGGAACGTCTTGGCATCGCGGTGATTGGTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002760","ARO_id":"39194","ARO_name":"QnrB45","CARD_short_name":"QnrB45","ARO_description":"QnrB45 is a plasmid-mediated quinolone resistance protein found in Escherichia coli.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1210":{"model_id":"1210","model_name":"novA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1190"}},"model_sequences":{"sequence":{"8215":{"protein_sequence":{"accession":"AAF67494.2","sequence":"MKSALSTWKPSDRPPDPTLPEPPAQLRRIFRLFRPYRGRLAVVGLLVGASSLVAVASPFMLREILDTAIPQGRTGLLSLLALGMILTAVLSSVFGVVQTLISTTVGQRVMHDLRTAVYAQLQRMPLAFFTRTRTGEVQSRIANDIGGMQATVTSTATSLVSNLTAVIATVVAMLALDWRLTVVSLLLLPVFVWISRRVGRERKRITLQRQKQMATMAATVTESLSVSGILLGRTMGRADSLTRSFAEESERLVDLEVRSNMAGRWRMSVIGIVMAAMPAVIYWAAGFVLQSGGTVVSIGTLVAFVSLQQGLFRPAVSLLATGVQMQTSLALFQRIFEYLDLPVDITEPERPVALDKVRGEVRFDGVDFSYEEKDGNTLHGLDLTVPAGGSLAVVGPTGSGKSTLSYLVPRLYDVTGGRVLLDGVDVRDLAFDTLARAVGVVSQETYLFHASVADNLRFAKPDATDEEIEKAARAAQIHEHIVTLPDGYDTLVGERGYRFSGGEKQRLAIARTILRDPPVLVLDEATSALDTRTEHAVQQAIDSLSEGRTTITIAHRLSTVRDADQIVVLDAGRIAERGTHEELIDRDGRYAALVRRDGAPAPAPVPARDERVGAA"},"dna_sequence":{"accession":"AF170880.4","fmin":"0","fmax":"1848","strand":"+","sequence":"ATGAAGTCCGCACTCTCGACCTGGAAGCCCTCGGACCGGCCGCCGGATCCGACACTGCCCGAGCCGCCGGCCCAGCTGCGCCGCATCTTCCGGCTCTTCCGCCCGTACCGCGGCAGGCTCGCCGTCGTCGGCCTGCTCGTCGGCGCCTCGTCGCTGGTGGCCGTCGCCTCGCCGTTCATGCTGCGCGAGATCCTCGACACCGCGATCCCGCAGGGCCGCACCGGGCTGCTCAGCCTGCTCGCCCTCGGCATGATCCTGACCGCCGTCCTCAGCAGCGTCTTCGGCGTCGTCCAGACCCTCATCTCCACGACGGTCGGCCAGCGCGTCATGCACGACCTGCGCACCGCCGTCTACGCGCAGCTCCAGCGCATGCCCCTCGCGTTCTTCACCCGCACCCGCACCGGTGAGGTCCAGTCCCGGATAGCCAACGACATCGGCGGCATGCAGGCGACCGTCACCTCAACCGCCACGTCGCTGGTCTCCAACCTCACCGCCGTCATCGCCACCGTCGTCGCGATGCTCGCGCTGGACTGGCGGCTGACCGTCGTCTCGCTGCTCCTGCTGCCGGTGTTCGTCTGGATCAGCCGCCGCGTCGGCCGTGAGCGCAAACGGATCACCCTGCAACGGCAGAAGCAGATGGCCACGATGGCCGCCACGGTCACGGAGTCGCTGTCGGTCAGCGGCATCCTCCTCGGCCGCACGATGGGGCGCGCCGACTCGCTCACCAGATCCTTCGCCGAGGAGTCCGAGCGACTCGTCGACCTGGAGGTCCGCTCCAACATGGCCGGGCGGTGGCGGATGTCCGTCATCGGCATCGTCATGGCCGCCATGCCCGCCGTCATCTACTGGGCGGCCGGCTTCGTCCTCCAGTCCGGCGGCACGGTCGTCTCCATCGGCACACTCGTCGCCTTCGTCTCCCTCCAGCAGGGCCTCTTCCGCCCGGCCGTGAGCCTGCTCGCCACCGGCGTGCAGATGCAGACGTCCCTCGCGCTCTTCCAGCGCATCTTCGAATATCTCGACCTGCCCGTCGACATCACCGAACCCGAGCGTCCGGTGGCCCTCGACAAGGTCCGGGGCGAAGTGCGCTTCGACGGCGTCGACTTCAGTTACGAGGAGAAGGACGGCAACACCCTCCACGGCCTGGATCTGACCGTCCCGGCCGGCGGCAGCCTCGCCGTCGTCGGTCCCACCGGATCGGGCAAGTCGACCCTGAGCTATCTCGTGCCGCGTCTGTACGACGTGACGGGCGGCCGGGTCCTGCTCGACGGCGTCGACGTACGCGACCTGGCCTTCGACACCCTCGCCCGCGCGGTGGGCGTCGTGTCGCAGGAGACGTATCTCTTCCACGCCTCCGTCGCCGACAACCTCCGCTTCGCCAAACCGGACGCGACGGACGAGGAGATCGAGAAGGCGGCCAGGGCCGCCCAGATCCACGAGCACATCGTCACCCTGCCCGACGGGTACGACACACTGGTCGGCGAGCGCGGATACCGGTTCTCCGGCGGCGAGAAACAGCGCCTCGCGATCGCCCGCACCATCCTGCGCGACCCGCCCGTCCTCGTGCTGGACGAGGCGACGAGCGCGCTCGACACCCGTACCGAACACGCGGTCCAGCAGGCCATCGACTCCCTCTCCGAGGGCCGTACGACCATCACCATCGCCCACCGGCTCTCCACGGTGCGCGACGCCGACCAGATCGTCGTCCTCGACGCCGGTCGCATAGCCGAGCGCGGCACGCACGAGGAGCTGATCGACCGGGACGGCAGGTACGCGGCGCTCGTCCGCCGGGACGGCGCGCCGGCGCCCGCGCCCGTGCCCGCCCGGGACGAGCGCGTGGGCGCCGCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39503","NCBI_taxonomy_name":"Streptomyces niveus","NCBI_taxonomy_id":"193462"}}}},"ARO_accession":"3002522","ARO_id":"38922","ARO_name":"novA","CARD_short_name":"novA","ARO_description":"A type III ABC transporter, identified on the novobiocin biosynthetic gene cluster, involved in the transport and resistance of novobiocin.","ARO_category":{"36002":{"category_aro_accession":"0010001","category_aro_cvterm_id":"36002","category_aro_name":"ATP-binding cassette (ABC) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding\/hydrolysis to transport substrates across cell membranes.","category_aro_class_name":"AMR Gene Family"},"36250":{"category_aro_accession":"3000111","category_aro_cvterm_id":"36250","category_aro_name":"novobiocin","category_aro_description":"Novobiocin is an aminocoumarin antibiotic produced by Streptomyces spheroides and Streptomyces niveus, and binds DNA gyrase subunit B inhibiting ATP-dependent DNA supercoiling.","category_aro_class_name":"Antibiotic"},"36242":{"category_aro_accession":"3000103","category_aro_cvterm_id":"36242","category_aro_name":"aminocoumarin antibiotic","category_aro_description":"Aminocoumarin antibiotics bind DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1211":{"model_id":"1211","model_name":"VIM-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1962":{"protein_sequence":{"accession":"AAN63496.1","sequence":"MLKVISSLLVYMTASVMAVASPLAHSGEPSGEYPTVNEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEAEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSANVLYGGCAVHELSSTSAGNVADADLAEWPTSVERIQKHYPEAEVVIPGHGLPGGLDLLQHTANVVKAHKNRSVAE"},"dna_sequence":{"accession":"AF317511.1","fmin":"187","fmax":"988","strand":"+","sequence":"ATGTTAAAAGTTATTAGTAGTTTATTGGTCTACATGACCGCGTCTGTCATGGCTGTCGCAAGTCCGTTAGCCCATTCCGGGGAGCCGAGTGGTGAGTATCCGACAGTCAACGAAATTCCGGTCGGAGAGGTCCGACTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCGGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAAAAGCAAATTGGACTTCCCGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGCAGAGGGGAACGAGATTCCCACGCATTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAGCTCTTCTATCCTGGTGCTGCGCATTCGACCGACAATCTGGTTGTATACGTCCCGTCAGCGAACGTGCTATACGGTGGTTGTGCCGTTCATGAGTTGTCAAGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCGTTGAGCGGATTCAAAAACACTACCCGGAAGCAGAGGTCGTCATTCCCGGGCACGGTCTACCGGGCGGTCTAGACTTGCTCCAGCACACAGCGAACGTTGTCAAAGCACACAAAAATCGCTCAGTCGCCGAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002271","ARO_id":"38671","ARO_name":"VIM-1","CARD_short_name":"VIM-1","ARO_description":"VIM-1 is a beta-lactamase found in Pseudomonas spp.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1212":{"model_id":"1212","model_name":"OXA-141","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1124":{"protein_sequence":{"accession":"ABQ15112.1","sequence":"MAIRIFAILFSIFSLATFAHAQEGTLERSDWRKFFSEFQAKGTIVVADERQADRAMLVFDPVRSKKRYSPASTFKIPHTLFALDAGAVRDEFQIFRWDGVNRGFAGHNQDQDLRSAMRNSTVWVYELFAKEIGDDKARRYLKKIDYGNADPSTSNGDYWIESSLAISAQEQIAFLRKLYRNELPFRVEHQRLVKDLMIVEAGRNWILRAKTGWEGRMGWWVGWVEWPTGSVFFALNIDTPNRMDDLFKREAIVRAILRSIEALPPNPAVNSDAAR"},"dna_sequence":{"accession":"EF552405.1","fmin":"12","fmax":"840","strand":"+","sequence":"ATGGCAATCCGAATCTTCGCGATACTTTTCTCCATTTTTTCTCTTGCCACTTTCGCGCATGCGCAAGAAGGCACGCTAGAACGTTCTGACTGGAGGAAGTTTTTCAGCGAATTTCAAGCCAAAGGCACGATAGTTGTGGCAGACGAACGCCAAGCGGATCGTGCCATGTTGGTTTTTGATCCTGTGCGATCGAAGAAACGCTACTCGCCTGCATCGACATTCAAGATACCTCATACACTTTTTGCACTTGATGCAGGCGCTGTTCGTGATGAGTTCCAGATTTTTCGATGGGACGGCGTTAACAGGGGCTTTGCAGGCCACAATCAAGACCAAGATTTGCGATCAGCAATGCGGAATTCTACTGTTTGGGTGTATGAGCTATTTGCAAAGGAAATTGGTGATGACAAAGCTCGGCGCTATTTGAAGAAAATCGACTATGGCAACGCCGATCCTTCGACAAGTAATGGCGATTACTGGATAGAAAGCAGCCTTGCAATCTCGGCGCAGGAGCAAATTGCATTTCTCAGGAAGCTCTATCGTAACGAGCTGCCCTTTCGGGTAGAACATCAGCGCTTGGTCAAGGATCTCATGATTGTGGAAGCCGGTCGCAACTGGATACTGCGTGCAAAGACGGGCTGGGAAGGCCGTATGGGTTGGTGGGTAGGATGGGTTGAGTGGCCGACTGGCTCCGTATTCTTCGCACTGAATATTGATACGCCAAACAGAATGGATGATCTTTTCAAGAGGGAGGCAATCGTGCGGGCAATCCTTCGCTCTATTGAAGCGTTACCGCCCAACCCGGCAGTCAACTCGGACGCTGCGCGATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3001802","ARO_id":"38202","ARO_name":"OXA-141","CARD_short_name":"OXA-141","ARO_description":"OXA-141 is a beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46493":{"category_aro_accession":"3007704","category_aro_cvterm_id":"46493","category_aro_name":"OXA-2-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-2.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3304":{"model_id":"3304","model_name":"erm(40)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"8336":{"protein_sequence":{"accession":"AAS76623.1","sequence":"MSSKNQGRHEHGQNFLCDRRVVADIVKIVSHTTGSIVEIGAGDGALTVPMQRLGRPLTAIEIDRRRAERLARRTTAHVVTADFLRYRLPPTEHVVVGNLPFHLTTAILRRLLHSPAWTDAVLLMQWEVARRRAAVGGATMMTAQWWPWFEFGLARKVSADAFRPRPSVDAGLLTITRRREPLIDGADRRRYQALVHAVFTGRGRGVAQIVGPRVPRHWLRHNGITPSALPRDLTAAQWAALFEVTSEAKRC"},"dna_sequence":{"accession":"AY570506.1","fmin":"2034","fmax":"2790","strand":"+","sequence":"GTGTCATCCAAAAATCAAGGCCGGCATGAGCACGGCCAGAATTTTCTGTGCGACCGTCGCGTGGTCGCCGACATCGTCAAAATCGTCTCGCACACAACAGGTTCCATCGTCGAGATCGGCGCCGGAGACGGTGCGCTGACCGTCCCGATGCAGCGGCTCGGGCGGCCGTTGACGGCCATCGAGATCGACCGTCGACGAGCAGAGCGCCTGGCTCGCCGTACCACGGCGCATGTCGTCACCGCCGATTTCCTGCGCTACCGCCTGCCACCCACCGAGCACGTGGTGGTGGGCAACCTGCCGTTCCACCTGACCACCGCGATTTTGCGGCGGCTGCTGCACAGCCCGGCATGGACCGACGCGGTGCTGCTCATGCAGTGGGAGGTGGCGCGCCGCCGCGCCGCGGTCGGCGGCGCAACGATGATGACCGCGCAGTGGTGGCCGTGGTTCGAATTCGGCTTGGCCCGTAAGGTTTCCGCCGACGCGTTCCGTCCCCGCCCGAGCGTGGACGCCGGGTTGCTGACCATCACGCGGCGCCGGGAACCGCTGATCGACGGCGCCGACCGCCGGCGCTACCAGGCGCTGGTCCATGCAGTGTTCACCGGGCGCGGCCGCGGTGTGGCGCAGATTGTGGGTCCACGAGTCCCGCGGCACTGGTTGCGCCACAACGGCATCACACCGTCGGCGCTGCCGAGGGATCTCACGGCCGCGCAGTGGGCAGCTCTGTTCGAGGTGACGAGCGAGGCGAAGCGGTGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42568","NCBI_taxonomy_name":"Mycolicibacterium mageritense","NCBI_taxonomy_id":"53462"}}}},"ARO_accession":"3004606","ARO_id":"42567","ARO_name":"erm(40)","CARD_short_name":"erm(40)","ARO_description":"erm(40) is an adenine RNA methylase and confers intrinsic resistance in Mycobacteria.","ARO_category":{"36699":{"category_aro_accession":"3000560","category_aro_cvterm_id":"36699","category_aro_name":"Erm 23S ribosomal RNA methyltransferase","category_aro_description":"Erm proteins are part of the RNA methyltransferase family and methylate A2058 (E. coli nomenclature) of the 23S ribosomal RNA conferring degrees of resistance to Macrolides, Lincosamides and Streptogramin b. This is called the MLSb phenotype.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35982":{"category_aro_accession":"0000065","category_aro_cvterm_id":"35982","category_aro_name":"clarithromycin","category_aro_description":"Clarithromycin is a methyl derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome and is used to treat pharyngitis, tonsillitis, acute maxillary sinusitis, acute bacterial exacerbation of chronic bronchitis, pneumonia (especially atypical pneumonias associated with Chlamydia pneumoniae or TWAR), and skin structure infections.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"36295":{"category_aro_accession":"3000156","category_aro_cvterm_id":"36295","category_aro_name":"spiramycin","category_aro_description":"Spiramycin is a 16-membered macrolide and is natural product produced by Streptomyces ambofaciens. It binds to the 50S subunit of bacterial ribosomes and inhibits peptidyl transfer activity to disrupt protein synthesis.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1214":{"model_id":"1214","model_name":"TEM-134","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"925":{"protein_sequence":{"accession":"AAS79107.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDKLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVKYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDHWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGASERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AY574271.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATAAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTAAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATCATTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCAGTGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36934","NCBI_taxonomy_name":"Citrobacter koseri","NCBI_taxonomy_id":"545"}}}},"ARO_accession":"3000998","ARO_id":"37378","ARO_name":"TEM-134","CARD_short_name":"TEM-134","ARO_description":"TEM-134 is an extended-spectrum beta-lactamase found in Citrobacter koseri.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1215":{"model_id":"1215","model_name":"FosC","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"481":{"protein_sequence":{"accession":"CAA83855.1","sequence":"MMTSIMFSMLSDITRIFVEQGLRVYPFQSSALLGVDEEGRVTLHARQLATAMASGYMPLLTGDLLLRGEQEAQVFSSDNIAPLLAADFEVRRVLYYSDVAGVYDQGNALVPWVGNANAACMEACVGASSMTDLTGGMRNKFMQQRQLARLGVVSEVLSFECFDRVHLSLCGLRQFGTVFLSE"},"dna_sequence":{"accession":"Z33413.1","fmin":"386","fmax":"935","strand":"+","sequence":"ATGATGACATCGATCATGTTTTCGATGTTGTCGGACATCACGCGGATTTTTGTCGAGCAGGGGCTACGGGTCTATCCCTTTCAAAGCAGTGCCTTGCTGGGCGTCGATGAAGAGGGGCGTGTCACGCTTCATGCGCGCCAGCTGGCAACGGCCATGGCATCGGGTTACATGCCCTTGCTCACTGGGGATCTGCTGCTGCGCGGCGAGCAGGAGGCGCAGGTCTTTTCAAGTGACAATATCGCCCCGTTGCTCGCTGCGGACTTCGAAGTGCGTCGGGTCTTGTATTACTCCGATGTGGCCGGTGTCTACGACCAGGGCAATGCCTTGGTCCCTTGGGTTGGCAATGCCAACGCCGCGTGCATGGAGGCTTGTGTGGGGGCGTCGTCGATGACGGACCTGACCGGTGGCATGCGCAACAAGTTCATGCAGCAGCGCCAGTTGGCACGCCTGGGCGTGGTTTCGGAGGTCTTGTCATTCGAGTGCTTCGACAGGGTGCATCTGTCGTTGTGCGGGTTGCGTCAATTTGGAACCGTGTTCTTGAGCGAGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37078","NCBI_taxonomy_name":"Pseudomonas syringae","NCBI_taxonomy_id":"317"}}}},"ARO_accession":"3000380","ARO_id":"36519","ARO_name":"FosC","CARD_short_name":"FosC","ARO_description":"FosC is an enzyme that phosphorylates fosfomycin to confer resistance.","ARO_category":{"41409":{"category_aro_accession":"3004245","category_aro_cvterm_id":"41409","category_aro_name":"fosC phosphotransferase family","category_aro_description":"The fosC family of phosphotransferases phosphorylate fosfomycin to confer resistance and have been found in various bacterial isolates.","category_aro_class_name":"AMR Gene Family"},"35944":{"category_aro_accession":"0000025","category_aro_cvterm_id":"35944","category_aro_name":"fosfomycin","category_aro_description":"Fosfomycin (also known as phosphomycin and phosphonomycin) is a broad-spectrum antibiotic produced by certain Streptomyces species. It is effective on gram positive and negative bacteria as it targets the cell wall, an essential feature shared by both bacteria. Its specific target is MurA (MurZ in E.coli), which attaches phosphoenolpyruvate (PEP) to UDP-N-acetylglucosamine, a step of commitment to cell wall synthesis. In the active site of MurA, the active cysteine molecule is alkylated which stops the catalytic reaction.","category_aro_class_name":"Antibiotic"},"45731":{"category_aro_accession":"3007149","category_aro_cvterm_id":"45731","category_aro_name":"phosphonic acid antibiotic","category_aro_description":"A group of antibiotics derived from phosphonic acids.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1216":{"model_id":"1216","model_name":"SHV-119","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1387":{"protein_sequence":{"accession":"AIG51284.1","sequence":"MRHIRLCIISLLATLPLAVQASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"KJ776406.1","fmin":"16","fmax":"877","strand":"+","sequence":"ATGCGTCATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACAAGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTTACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001340","ARO_id":"37740","ARO_name":"SHV-119","CARD_short_name":"SHV-119","ARO_description":"SHV-119 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1217":{"model_id":"1217","model_name":"OXA-139","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"966":{"protein_sequence":{"accession":"CAQ51348.1","sequence":"MKKFILPIFSISILVSLSACSSIKTKSEDNFHISSQQHEKAIKSYFDEAQTQGVIIIKEGKNLSTYGNALARANKEYVPASTFKMLIALIGLENHKATTNEIFKWDGKKRTYPMWEKDMTLGEAMALSAVPVYQELARRTGLELMQKEVKRVNFGNTNIGTQVDNFWLVGPLKITPVQEVNFADDLAHNRLPFKLETQEEVKKMLLIKEVNGSKIYAKSGWGMGVTPQVGWLTGWVEQANGKKIPFSLNLEMKEGMSGSIRNEITYKSLENLGII"},"dna_sequence":{"accession":"AM991978.1","fmin":"0","fmax":"828","strand":"+","sequence":"ATGAAAAAATTTATACTTCCTATATTCAGCATTTCTATTCTAGTTTCTCTCAGTGCATGTTCATCTATTAAAACTAAATCTGAAGATAATTTTCATATTTCTTCTCAGCAACATGAAAAAGCTATTAAAAGCTATTTTGATGAAGCTCAAACACAGGGTGTAATTATTATTAAAGAGGGTAAAAATCTTAGCACCTATGGTAATGCTCTTGCACGAGCAAATAAAGAATATGTCCCTGCATCAACATTTAAGATGCTAATTGCTTTAATCGGGCTAGAAAATCATAAAGCAACAACAAATGAGATTTTCAAATGGGATGGTAAAAAAAGAACTTATCCTATGTGGGAGAAAGATATGACTTTAGGTGAGGCAATGGCATTGTCAGCAGTTCCAGTATATCAAGAGCTTGCAAGACGGACTGGCCTAGAGCTAATGCAGAAAGAAGTAAAGCGGGTTAATTTTGGAAATACAAATATTGGAACACAGGTCGATAATTTTTGGTTAGTTGGCCCCCTTAAAATTACACCAGTACAAGAAGTTAATTTTGCCGATGACCTTGCACATAACCGATTACCTTTTAAATTAGAAACTCAAGAAGAAGTTAAAAAAATGCTTCTAATTAAAGAAGTAAATGGTAGTAAGATTTATGCAAAAAGTGGATGGGGAATGGGTGTTACTCCACAGGTAGGTTGGTTGACTGGTTGGGTGGAGCAAGCTAATGGAAAAAAAATCCCCTTTTCGCTCAACTTAGAAATGAAAGAAGGAATGTCTGGTTCTATTCGTAATGAAATTACTTATAAGTCGCTAGAAAATCTTGGAATCATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001451","ARO_id":"37851","ARO_name":"OXA-139","CARD_short_name":"OXA-139","ARO_description":"OXA-139 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46500":{"category_aro_accession":"3007711","category_aro_cvterm_id":"46500","category_aro_name":"OXA-24-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-24.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1218":{"model_id":"1218","model_name":"TEM-219","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1649":{"protein_sequence":{"accession":"AIS39742.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVFIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"KM114268.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTATTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3003157","ARO_id":"39734","ARO_name":"TEM-219","CARD_short_name":"TEM-219","ARO_description":"TEM-219 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1220":{"model_id":"1220","model_name":"OCH-5","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1734":{"protein_sequence":{"accession":"CAC17625.1","sequence":"MRKSTTLLIGFLTTAAIIPNNGALAASKANDGDLRRIVDETVRPLMAEQKIPGMAVAITIDGKSHFFGYGVASKESGQKVTEDTIFEIGSVSKTFTAMLGGYGLATGAFSLSDPATKWAPELAGSSFDKITMLDLGTYTPGGLPLQFPDAVTDDSSMLAYFKKWRPDYPAGTQHRYSNPSIGLFGYLAARSMDKPFDVLMEQKLLPAFGLKNTFINVPESQMKNYAYGYSKANKPIRVSGGTLDAQAYGIKTTALDLARFVELNIDSSSLEPDFQKAVAATHTGYYHVDANNQGLGWEFYNYPTALKTLLAGNSSDMALKSHKIEKFDTPRQPSADVLINKTGSTNGFGAYAAFIPAKKIGIVVLANRNYPIDERVKAAYRILQALDNKQ"},"dna_sequence":{"accession":"AJ295343.1","fmin":"0","fmax":"1173","strand":"+","sequence":"ATGAGAAAATCTACGACACTTTTGATCGGTTTCCTCACCACTGCCGCTATTATCCCGAATAACGGCGCGCTGGCTGCGAGCAAGGCGAATGATGGCGACTTGCGCCGTATTGTCGATGAAACGGTGCGCCCGCTCATGGCCGAGCAGAAAATCCCCGGCATGGCGGTTGCCATAACCATCGACGGCAAGAGCCACTTCTTCGGTTATGGTGTGGCATCGAAGGAAAGCGGGCAAAAAGTCACTGAAGACACGATTTTCGAGATCGGCTCGGTCAGCAAGACCTTCACTGCAATGCTTGGCGGCTACGGGCTGGCGACGGGCGCGTTCTCCCTGTCCGATCCCGCGACCAAATGGGCTCCTGAACTGGCAGGCAGCAGCTTCGACAAGATCACCATGCTTGATCTTGGGACCTACACGCCGGGCGGATTGCCCCTCCAGTTTCCCGATGCTGTCACCGATGACAGTTCGATGCTGGCATATTTCAAGAAATGGAGGCCGGACTATCCGGCAGGCACGCAGCATCGCTATTCGAATCCCAGCATCGGCCTGTTCGGCTATCTGGCGGCACGAAGCATGGACAAGCCGTTCGACGTTTTGATGGAGCAAAAGCTTCTGCCTGCATTCGGCCTGAAGAACACCTTCATCAATGTGCCGGAAAGCCAGATGAAGAACTACGCCTACGGCTATTCCAAAGCCAACAAGCCGATCCGGGTATCGGGCGGGACGCTGGATGCACAAGCCTATGGCATCAAGACCACCGCGCTTGATCTTGCCCGCTTCGTCGAACTGAACATTGACAGCTCATCTCTGGAGCCTGATTTCCAGAAAGCCGTCGCCGCAACACACACGGGTTACTACCATGTCGATGCGAACAATCAGGGACTTGGCTGGGAGTTCTACAACTATCCGACTGCGCTCAAGACACTTCTTGCCGGCAATTCGTCGGACATGGCGCTGAAGTCGCACAAAATCGAGAAATTCGATACACCTCGCCAACCGTCAGCTGATGTGCTGATCAATAAGACAGGCTCAACCAACGGCTTTGGCGCTTATGCGGCCTTTATTCCTGCGAAGAAGATCGGAATTGTTGTGCTTGCCAACCGGAATTATCCGATCGATGAGCGCGTAAAGGCTGCCTATCGGATATTGCAGGCGCTCGACAACAAGCAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37077","NCBI_taxonomy_name":"Brucella anthropi","NCBI_taxonomy_id":"529"}}}},"ARO_accession":"3002518","ARO_id":"38918","ARO_name":"OCH-5","CARD_short_name":"OCH-5","ARO_description":"OCH-5 beta-lactamase is an Ambler class C chromosomal-encoded beta-lactamases in Brucella anthropi.","ARO_category":{"36233":{"category_aro_accession":"3000094","category_aro_cvterm_id":"36233","category_aro_name":"OCH beta-lactamase","category_aro_description":"OCH beta-lactamases are Ambler class C chromosomal-encoded beta-lactamases in Brucella anthropi.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1221":{"model_id":"1221","model_name":"OXA-231","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8258":{"protein_sequence":{"accession":"AFG29918.1","sequence":"MKKFILPILSISTLLSVSACSSIQTKFEDTFHTSNQQHEKAIKSYFDEAQTQGVIIIKKGKNISTYGNNLTRAHTEYVPASTFKMLNALIGLENHKATTTEIFKWDGKKRSYPMWEKDMTLGDAMALSAVPVYQELARRTGLDLMQKEVKRVGFGNMNIGTQVDNFWLVGPLKITPIQEVNFADDFANNRLPFKLETQEEVKKMLLIKEFNGSKIYAKSGWGMAVTPQVGWLTGWVEKSNGEKVAFSLNIEMKQGMPGSIRNEITYKSLENLGII"},"dna_sequence":{"accession":"JQ326200.2","fmin":"193","fmax":"1021","strand":"+","sequence":"ATGAAAAAATTTATACTTCCTATTCTCAGCATTTCTACTCTACTTTCTGTCAGTGCATGCTCATCTATTCAAACTAAATTTGAAGACACTTTTCATACTTCTAATCAGCAACATGAAAAAGCCATTAAAAGCTATTTTGATGAAGCTCAAACACAGGGTGTAATCATTATTAAAAAGGGAAAAAATATTAGTACCTATGGTAATAACCTGACACGAGCACATACAGAATATGTCCCTGCATCAACATTTAAGATGCTAAATGCCTTAATTGGACTAGAAAATCATAAAGCTACAACAACTGAGATTTTCAAATGGGACGGTAAAAAGAGATCTTATCCCATGTGGGAAAAAGATATGACTTTAGGTGATGCCATGGCACTTTCAGCAGTTCCTGTATATCAAGAACTTGCAAGACGGACTGGCTTAGACCTAATGCAAAAAGAAGTTAAACGGGTTGGTTTTGGTAATATGAACATTGGAACACAAGTTGATAACTTCTGGTTGGTTGGCCCCCTCAAGATTACACCAATACAAGAGGTTAATTTTGCCGATGATTTTGCAAATAATCGATTACCCTTTAAATTAGAGACTCAAGAAGAAGTTAAAAAAATGCTTCTGATTAAAGAATTCAATGGTAGTAAAATTTATGCAAAAAGCGGCTGGGGAATGGCTGTAACCCCTCAAGTAGGTTGGTTAACAGGTTGGGTAGAAAAATCTAATGGAGAAAAAGTTGCCTTTTCTCTAAACATAGAAATGAAGCAAGGAATGCCTGGTTCTATTCGTAATGAAATTACTTATAAATCATTAGAGAATTTAGGGATTATATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001670","ARO_id":"38070","ARO_name":"OXA-231","CARD_short_name":"OXA-231","ARO_description":"OXA-231 is a beta-lactamase found in A. baumannii.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46490":{"category_aro_accession":"3007701","category_aro_cvterm_id":"46490","category_aro_name":"OXA-143-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-143.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1224":{"model_id":"1224","model_name":"Erm(30)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"4725":{"protein_sequence":{"accession":"AAC69328.1","sequence":"MAMRDSIPRRADRDTLRRELGQNFLQDDRAVRNLVTHVEGDGRNVLEIGPGKGAITEELVRSFDTVTVVEMDPHWAAHVRRKFEGERVTVFQGDFLDFRIPRDIDTVVGNVPFGITTQILRSLLESTNWQSAALIVQWEVARKRAGRSGGSLLTTSWAPWYEFAVHDRVRASSFRPMPRVDGGVLTIRRRPQPLLPESASRAFQNFAEAVFTGPGRGLAEILRRHIPKRTYRSLADRHGIPDGGLPKDLTLTQWIALFQASQPSYAPGAPGTRMPGQGGGAGGRDYDSETSRAAVPGSRRYGPTRGGEPCAPRAQVRQTKGRQGARGSSYGRRTGR"},"dna_sequence":{"accession":"AF079138.1","fmin":"1282","fmax":"2293","strand":"-","sequence":"ATGGCAATGCGCGACTCCATACCGAGGCGAGCGGACCGCGACACCCTTCGCCGCGAATTAGGCCAGAACTTCCTTCAGGACGACAGAGCCGTGCGCAATCTCGTCACGCATGTCGAGGGGGACGGTAGGAACGTTCTCGAAATCGGCCCCGGAAAGGGCGCGATAACCGAGGAGTTGGTGCGCTCCTTCGACACCGTGACGGTCGTGGAGATGGACCCGCACTGGGCCGCGCATGTGCGGCGGAAATTCGAAGGGGAGAGGGTCACCGTATTCCAGGGTGATTTCCTCGACTTCCGCATTCCGCGCGATATCGACACCGTCGTCGGAAACGTTCCCTTCGGCATCACGACCCAGATTCTCCGGAGTCTCCTGGAATCGACGAACTGGCAGTCGGCGGCCCTGATAGTGCAGTGGGAGGTCGCCCGCAAACGCGCCGGTCGCAGCGGCGGATCGCTCCTCACGACCTCCTGGGCCCCCTGGTACGAGTTCGCGGTCCACGACCGCGTCCGCGCCTCGTCGTTCCGTCCGATGCCCCGCGTCGACGGCGGCGTCCTGACGATCAGGCGACGCCCCCAGCCCCTGCTGCCCGAGAGCGCGAGCCGCGCCTTCCAGAACTTCGCCGAAGCCGTCTTCACCGGCCCCGGACGGGGCCTCGCGGAGATCCTCCGGCGCCACATCCCCAAGCGGACCTACCGTTCCCTCGCCGACCGCCACGGAATTCCGGACGGCGGACTGCCGAAGGACCTCACGCTCACCCAATGGATCGCCCTTTTCCAGGCCTCCCAGCCGAGTTACGCGCCGGGGGCGCCCGGCACGCGCATGCCGGGCCAGGGCGGTGGCGCCGGCGGCAGGGACTATGACTCGGAGACGAGCAGGGCCGCCGTGCCCGGGAGCCGCAGATACGGCCCCACGCGCGGCGGCGAACCCTGCGCACCCCGCGCACAGGTCCGGCAGACCAAGGGCCGCCAGGGCGCGCGAGGCTCGTCGTACGGACGCCGCACGGGCCGTTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36873","NCBI_taxonomy_name":"Streptomyces venezuelae","NCBI_taxonomy_id":"54571"}}}},"ARO_accession":"3001265","ARO_id":"37664","ARO_name":"Erm(30)","CARD_short_name":"Erm(30)","ARO_description":"Erm(30) confers a MLSb resistant phenotype. Along with erm(31), these genes are responsible for self-resistance in the pikromycin\/narbomycin\/methymycin\/neomethymycin producer, Streptomyces venezuelae.","ARO_category":{"36699":{"category_aro_accession":"3000560","category_aro_cvterm_id":"36699","category_aro_name":"Erm 23S ribosomal RNA methyltransferase","category_aro_description":"Erm proteins are part of the RNA methyltransferase family and methylate A2058 (E. coli nomenclature) of the 23S ribosomal RNA conferring degrees of resistance to Macrolides, Lincosamides and Streptogramin b. This is called the MLSb phenotype.","category_aro_class_name":"AMR Gene Family"},"37625":{"category_aro_accession":"3001226","category_aro_cvterm_id":"37625","category_aro_name":"narbomycin","category_aro_description":"Produced by Streptomyces narbonensis.","category_aro_class_name":"Antibiotic"},"37631":{"category_aro_accession":"3001232","category_aro_cvterm_id":"37631","category_aro_name":"methymycin","category_aro_description":"Produced by Streptomyces venezuelae ATCC 15439.","category_aro_class_name":"Antibiotic"},"37632":{"category_aro_accession":"3001233","category_aro_cvterm_id":"37632","category_aro_name":"pikromycin","category_aro_description":"Produced by Streptomyces venezuelae ATCC 15439.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1225":{"model_id":"1225","model_name":"TEM-178","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1492":{"protein_sequence":{"accession":"CAA65888.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGSTSGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGSQELTAFLHNMGDHVTRLDRWEPELNEAIPNDEADTTMPAAMATTLRKLLTGELLTLASRQQLIDWMADKVAGPLLRSALPAGWFIADKSGARERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"X97254.1","fmin":"153","fmax":"1011","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTTCGACGAGTGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGATCGCAAGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGGCTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCCGTGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATCGGTGCTTCCCTTATCAAACATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36783","NCBI_taxonomy_name":"Serratia marcescens","NCBI_taxonomy_id":"615"}}}},"ARO_accession":"3001043","ARO_id":"37423","ARO_name":"TEM-178","CARD_short_name":"TEM-178","ARO_description":"TEM-178 is an inhibitor-resistant, extended-spectrum beta-lactamase.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1226":{"model_id":"1226","model_name":"adeG","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"6249":{"protein_sequence":{"accession":"CAJ77857.1","sequence":"MSFSRKQFALSAIFVAILATGGSFMLLHENADAKAAPTAAQQAATVDVAPVVSKTITDWQEYSGRLEAIDQVDIRPQVSGKLIAVHFKDGSLVKKGDLLFTIDPRPFEAELNRAKAQLASAEAQVTYTASNLSRIQRLIQSNAVSRQELDLAENDARSANANLQAARAAVQSARLNLEYTRITAPVSGRISRAEVTVGNVVSAGNGAQVLTSLVSVSRLYASFDVDEQTYLKYISNQRNSAQVPVYMGLANETGFTREGTINSIDNNLNTTSGTIRVRATFDNPNGVLLPGLYARIRLGGGQPRPAILISPTAVGVDQDKRFVVVVDAKNQTAYREVKLGAQQDGLQIVNSGLQAGDRIVVNGLQRIRPGDPVTPHLVPMPNSQITASATPPQPQPTDKTSTPAKG"},"dna_sequence":{"accession":"CT025800.2","fmin":"0","fmax":"1221","strand":"+","sequence":"ATGTCATTTTCCCGCAAACAGTTTGCACTGTCTGCCATCTTTGTCGCTATTTTAGCAACCGGTGGCAGTTTTATGTTGTTACATGAAAATGCCGATGCAAAAGCTGCACCAACCGCTGCCCAACAAGCTGCTACTGTTGATGTAGCCCCAGTAGTAAGCAAAACCATTACCGATTGGCAAGAATATTCCGGTCGTTTAGAAGCAATTGATCAAGTTGATATTCGGCCTCAAGTTTCAGGAAAACTTATTGCCGTACATTTCAAAGATGGAAGCCTCGTTAAAAAAGGTGATTTACTTTTCACAATCGACCCTCGTCCTTTTGAAGCAGAACTGAACCGTGCAAAAGCCCAACTTGCTTCAGCTGAAGCACAGGTAACATATACCGCAAGCAATCTTTCGCGTATTCAACGTCTCATTCAGAGTAATGCTGTTTCTCGCCAAGAACTGGATTTAGCCGAAAATGATGCACGTTCAGCGAATGCTAACCTACAAGCCGCTAGAGCTGCTGTCCAATCTGCACGTTTAAATCTAGAATACACCCGTATTACAGCACCTGTCAGCGGCCGGATTTCACGAGCTGAAGTCACCGTTGGTAATGTAGTTTCTGCAGGTAACGGCGCACAGGTTTTAACAAGTTTAGTGTCTGTATCCCGCCTTTATGCATCTTTCGATGTTGATGAACAAACTTACCTGAAATATATCAGTAATCAGCGTAATTCAGCACAAGTACCTGTCTATATGGGACTTGCCAATGAAACAGGCTTTACTCGTGAAGGTACAATCAACTCAATCGATAACAATCTGAATACAACCTCAGGTACGATCCGTGTTCGCGCAACTTTTGACAATCCAAACGGTGTTTTATTACCAGGCCTATATGCACGAATTCGTTTAGGTGGAGGCCAACCTCGCCCAGCGATTCTGATTAGTCCAACCGCGGTTGGTGTCGACCAAGATAAACGTTTTGTCGTAGTAGTAGATGCGAAAAATCAAACTGCTTATCGCGAAGTAAAACTCGGTGCCCAACAAGATGGCTTGCAAATCGTAAATAGCGGATTACAAGCGGGTGATCGTATTGTAGTGAATGGTTTACAACGGATTCGTCCGGGTGACCCTGTTACACCGCATCTCGTCCCTATGCCAAATTCACAAATCACTGCTAGCGCTACTCCTCCTCAACCTCAGCCAACAGATAAAACATCAACTCCGGCAAAAGGTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35535","NCBI_taxonomy_name":"Acinetobacter baumannii AYE","NCBI_taxonomy_id":"509173"}}}},"ARO_accession":"3000778","ARO_id":"37158","ARO_name":"adeG","CARD_short_name":"adeG","ARO_description":"AdeG is the inner membrane transporter of the AdeFGH multidrug efflux complex.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1227":{"model_id":"1227","model_name":"aadA2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"3404":{"protein_sequence":{"accession":"AAF27727.1","sequence":"MTIEISNQLSEVLSVIERHLESTLLAVHLYGSAVDGGLKPYSDIDLLVTVAVKLDETTRRALLNDLMEASAFPGESETLRAIEVTLVVHDDIIPWRYPAKRELQFGEWQRNDILAGIFEPAMIDIDLAILLTKAREHSVALVGPAAEEFFDPVPEQDLFEALRETLKLWNSQPDWAGDERNVVLTLSRIWYSAITGKIAPKDVAADWAIKRLPAQYQPVLLEAKQAYLGQKEDHLASRADHLEEFIRFVKGEIIKSVGK"},"dna_sequence":{"accession":"AF156486.1","fmin":"5012","fmax":"5792","strand":"+","sequence":"GTGACCATCGAAATTTCGAACCAACTATCAGAGGTGCTAAGCGTCATTGAGCGCCATCTGGAATCAACGTTGCTGGCCGTGCATTTGTACGGCTCCGCAGTGGATGGCGGCCTGAAGCCATACAGCGATATTGATTTGTTGGTTACTGTGGCCGTAAAGCTTGATGAAACGACGCGGCGAGCATTGCTCAATGACCTTATGGAGGCTTCGGCTTTCCCTGGCGAGAGCGAGACGCTCCGCGCTATAGAAGTCACCCTTGTCGTGCATGACGACATCATCCCGTGGCGTTATCCGGCTAAGCGCGAGCTGCAATTTGGAGAATGGCAGCGCAATGACATTCTTGCGGGTATCTTCGAGCCAGCCATGATCGACATTGATCTAGCTATCCTGCTTACAAAAGCAAGAGAACATAGCGTTGCCTTGGTAGGTCCGGCAGCGGAGGAATTCTTTGACCCGGTTCCTGAACAGGATCTATTCGAGGCGCTGAGGGAAACCTTGAAGCTATGGAACTCGCAGCCCGACTGGGCCGGCGATGAGCGAAATGTAGTGCTTACGTTGTCCCGCATTTGGTACAGCGCAATAACCGGCAAAATCGCGCCGAAGGATGTCGCTGCCGACTGGGCAATAAAACGCCTACCTGCCCAGTATCAGCCCGTCTTACTTGAAGCTAAGCAAGCTTATCTGGGACAAAAAGAAGATCACTTGGCCTCACGCGCAGATCACTTGGAAGAATTTATTCGCTTTGTGAAAGGCGAGATCATCAAGTCAGTTGGTAAATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002602","ARO_id":"39002","ARO_name":"aadA2","CARD_short_name":"aadA2","ARO_description":"aadA2 is an aminoglycoside nucleotidyltransferase gene encoded by plasmids and integrons in K. pneumoniae, Salmonella spp., Corynebacterium glutamicum, C. freundii and Aeromonas spp.","ARO_category":{"41439":{"category_aro_accession":"3004275","category_aro_cvterm_id":"41439","category_aro_name":"ANT(3'')","category_aro_description":"A category of aminoglycoside O-nucleotidyltransferase enzymes with modification regiospecificity based at the 3''-hydroxyl group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics by transfer of an AMP group from an ATP substrate to the 3''-hydroxyl group of the compound.","category_aro_class_name":"AMR Gene Family"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1228":{"model_id":"1228","model_name":"CMY-30","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"8164":{"protein_sequence":{"accession":"ABS12249.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHGSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"EF685372.2","fmin":"0","fmax":"1143","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGGTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAA","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002041","ARO_id":"38441","ARO_name":"CMY-30","CARD_short_name":"CMY-30","ARO_description":"CMY-30 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1229":{"model_id":"1229","model_name":"CTX-M-6","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1863":{"protein_sequence":{"accession":"CAA06311.1","sequence":"MMTQSIRRSMLTVMATLPLLFSSATLHAQANSVQQQLEALEKSSGGRLGVALINTADNSQILYLADERFAMCSTSKVMAAAAVLKQSESDKHLLNQRVEIKASDLVNYNPIAEKHVNGTMTLAELGAGALQYSDNTAMNKLIAHLGGPDKVTAFARSLGDETFRLDRTEPTLNSAIPGDPRDTTTPLAMAQTLKNLTLGKALAETQRAQLVTWLKGNTTGSASIRAGLPKCWVVGDKTGSGDYGTTNDIAVIWPENHAPLVLVTYFTQPEQKAESRRDVLAAAAKIVTHGF"},"dna_sequence":{"accession":"AJ005044.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGATGACTCAGAGCATTCGCCGCTCAATGTTAACGGTGATGGCGACGCTACCCCTGCTATTTAGCAGCGCAACGCTGCATGCGCAGGCGAACAGCGTGCAACAGCAGCTGGAAGCCCTGGAGAAAAGTTCGGGAGGTCGGCTTGGCGTTGCGCTGATTAACACCGCCGATAATTCGCAGATTCTCTACCTGGCCGATGAGCGTTTTGCGATGTGCAGTACCAGTAAGGTGATGGCGGCCGCGGCGGTGCTTAAACAGAGCGAGAGCGATAAGCACCTGCTAAATCAGCGCGTTGAAATCAAGGCGAGCGACCTGGTTAACTACAATCCCATTGCGGAGAAACACGTTAACGGCACGATGACGCTGGCTGAGCTTGGCGCAGGCGCCCTGCAGTATAGCGACAATACTGCCATGAATAAGCTGATTGCCCATCTGGGTGGGCCCGATAAAGTGACGGCGTTTGCCCGCTCGTTGGGTGATGAGACCTTCCGTCTGGACAGAACCGAGCCCACGCTCAATAGCGCCATTCCAGGCGACCCGCGTGATACCACCACGCCGCTCGCGATGGCGCAGACCCTGAAAAATCTGACGCTGGGTAAAGCGCTGGCGGAAACTCAGCGGGCACAGTTGGTGACGTGGCTTAAGGGCAATACTACCGGTAGCGCGAGCATTCGGGCGGGTCTGCCGAAATGTTGGGTAGTGGGCGATAAAACCGGCAGCGGAGATTATGGCACCACCAACGATATCGCGGTTATCTGGCCGGAAAACCACGCACCGCTGGTTCTGGTGACCTACTTTACCCAACCGGAGCAGAAGGCGGAAAGCCGTCGGGATGTTCTGGCTGCGGCGGCGAAAATCGTAACCCACGGTTTCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35732","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Typhimurium","NCBI_taxonomy_id":"90371"}}}},"ARO_accession":"3001869","ARO_id":"38269","ARO_name":"CTX-M-6","CARD_short_name":"CTX-M-6","ARO_description":"CTX-M-6 is a beta-lactamase found in Salmonella typhimurium.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1230":{"model_id":"1230","model_name":"CTX-M-33","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4724":{"protein_sequence":{"accession":"AAO88912.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYSPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"AY238472.1","fmin":"12","fmax":"888","strand":"-","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAGTCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001895","ARO_id":"38295","ARO_name":"CTX-M-33","CARD_short_name":"CTX-M-33","ARO_description":"CTX-M-33 is a beta-lactamase found in Salmonella enterica.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1231":{"model_id":"1231","model_name":"mel","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"5180":{"protein_sequence":{"accession":"AAL73129.1","sequence":"MEKYNNWKLKFYTIWAGQAVSLITSAILQMAIIFYLTEKTGSAMVLSMASLLGFLPYAVFGPAIGVLVDRHDRKKIMIGADLIIAAAGSVLTIVAFYMELPVWMVMIVLFIRSIGTAFHTPALNAVTPLLVPEEQLTKCAGYSQSLQSISYIVSPAVAALLYSVWELNAIIAIDVLGAVIASITVAIVRIPKLGDRVQSLDPNFIREMQEGMAVLRQNKGLFALLLVGTLYMFVYMPINALFPLISMDYFNGTPVHISITEISFASGMLIGGLLLGLFGNYQKRILLITASIFMMGISLTISGLLPQSGFFIFVVCCAIMGLSVPFYSGVQTALFQEKIKPEYLGRVFSLTGSIMSLAMPIGLILSALFADRIGVNHWFLLSGTLIICIAIVCPMINEIRKLDLK"},"dna_sequence":{"accession":"AF227521.1","fmin":"3269","fmax":"4487","strand":"+","sequence":"ATGGAAAAATACAACAATTGGAAACTTAAGTTTTATACAATATGGGCAGGGCAAGCAGTATCATTAATCACTAGTGCCATCTTGCAAATGGCGATTATTTTTTACCTTACAGAAAAAACTGGATCCGCGATGGTCTTGTCTATGGCTTCACTATTAGGTTTTTTACCCTATGCGGTCTTTGGACCTGCAATTGGTGTGCTAGTGGATCGTCATGATAGGAAGAAGATAATGATTGGTGCTGATTTAATTATCGCAGCAGCTGGTTCGGTGCTTACTATTGTTGCATTCTATATGGAGCTACCTGTCTGGATGGTTATGATAGTATTGTTTATCCGTAGCATTGGAACAGCTTTTCACACCCCGGCTCTCAATGCGGTTACGCCACTTTTAGTACCAGAAGAACAGCTTACGAAATGTGCAGGCTATAGTCAGTCTTTGCAGTCTATAAGCTATATTGTTAGTCCGGCGGTTGCAGCACTCTTATACTCCGTTTGGGAACTAAATGCTATTATTGCCATCGATGTATTGGGTGCTGTGATTGCATCTATTACGGTAGCAATTGTACGTATTCCTAAGCTGGGTGATCGCGTGCAAAGTTTGGACCCAAATTTCATAAGAGAAATGCAAGAAGGAATGGCTGTACTACGGCAAAATAAAGGATTATTTGCTTTATTACTCGTTGGAACATTATATATGTTTGTTTATATGCCAATTAATGCACTATTCCCTTTAATTAGCATGGATTACTTTAATGGAACACCTGTGCATATTTCTATTACGGAAATTTCCTTTGCATCTGGAATGTTGATAGGGGGTCTATTATTAGGGTTATTTGGGAATTACCAAAAGCGAATCTTATTAATAACGGCATCCATTTTTATGATGGGGATAAGCTTAACCATTTCAGGATTACTTCCCCAAAGTGGATTTTTCATTTTTGTAGTCTGCTGTGCAATAATGGGGCTTTCTGTTCCGTTTTACAGCGGTGTGCAAACAGCTCTTTTTCAGGAGAAAATTAAGCCTGAATATTTAGGACGTGTATTTTCTTTAACTGGAAGTATCATGTCTCTTGCTATGCCAATTGGATTAATTCTTTCTGCACTCTTTGCTGATAGAATCGGTGTAAATCATTGGTTTTTACTATCAGGTACTTTAATTATTTGCATTGCAATAGTTTGCCCAATGATAAATGAGATTAGAAAATTAGATTTAAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36764","NCBI_taxonomy_name":"Streptococcus pyogenes","NCBI_taxonomy_id":"1314"}}}},"ARO_accession":"3000616","ARO_id":"36910","ARO_name":"mel","CARD_short_name":"mel","ARO_description":"Mel, a homolog of MsrA, is an ABC-F subfamily protein associated with macrolide resistance. It is expressed on the same operon as mefA and mefE, both MFS-type efflux proteins that confer macrolide resistance.","ARO_category":{"41695":{"category_aro_accession":"3004471","category_aro_cvterm_id":"41695","category_aro_name":"msr-type ABC-F protein","category_aro_description":"msr-type ABC-F subfamily ribosomal protection proteins expression in Staphylococci species and confer resistance to erythromycin and streptogramin B antibiotics through antibiotic target protection mechanisms.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35974":{"category_aro_accession":"0000057","category_aro_cvterm_id":"35974","category_aro_name":"telithromycin","category_aro_description":"Telithromycin is a semi-synthetic derivative of erythromycin. It is a 14-membered macrolide and is the first ketolide antibiotic to be used in clinics. Telithromycin binds the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1232":{"model_id":"1232","model_name":"cmeR","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"5477":{"protein_sequence":{"accession":"CAL34518.1","sequence":"MNSNRTPSQKVLARQEKIKAVALELFLTKGYQETSLSDIIKLSGGSYSNIYDGFKSKEGLFFEILDDICKKHFHLIYSKTQEIENGTLKEILTSFGLAFIEIFNQPEAVAFGKIIYSQVYDKDRHLANWIENNQQNFSYNILMGFFKQQNNSYMKKNAEKLAVLFCTMLKEPYHHLNVLINAPLKNKKEQKEHVEFVVNVFLNGINSSKA"},"dna_sequence":{"accession":"AL111168.1","fmin":"336915","fmax":"337548","strand":"-","sequence":"ATGAACTCAAATAGAACACCATCACAAAAAGTTTTAGCCAGACAAGAAAAAATCAAAGCAGTGGCCTTAGAGCTTTTTTTAACAAAAGGATACCAAGAAACAAGTTTGAGTGATATTATTAAATTATCTGGAGGATCTTATTCTAATATTTATGATGGTTTTAAAAGTAAAGAAGGGCTATTCTTTGAAATTTTAGATGACATATGTAAAAAACACTTTCATCTTATTTATTCCAAAACACAAGAAATTGAAAATGGCACTTTAAAAGAAATTTTAACTTCTTTTGGTTTAGCTTTTATAGAAATTTTCAATCAACCAGAAGCTGTAGCTTTTGGTAAAATTATCTATTCTCAAGTTTATGACAAAGATAGACATCTTGCCAATTGGATAGAAAATAATCAACAAAATTTTTCCTATAACATACTTATGGGTTTTTTCAAGCAACAAAATAATTCTTATATGAAAAAAAATGCAGAAAAACTTGCTGTTCTTTTTTGCACTATGTTAAAAGAACCTTATCATCATCTTAATGTTTTAATTAACGCTCCTTTGAAAAATAAAAAAGAACAAAAAGAACATGTTGAATTTGTTGTAAATGTTTTTCTAAATGGAATCAATAGCTCCAAAGCTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36956","NCBI_taxonomy_name":"Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819","NCBI_taxonomy_id":"192222"}}}},"ARO_accession":"3000526","ARO_id":"36665","ARO_name":"cmeR","CARD_short_name":"cmeR","ARO_description":"CmeR is a repressor for the CmeABC multidrug efflux pump, binding to the cmeABC promoter region.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"36989":{"category_aro_accession":"3000645","category_aro_cvterm_id":"36989","category_aro_name":"cefotaxime","category_aro_description":"Cefotaxime is a semisynthetic cephalosporin taken parenterally. It is resistant to most beta-lactamases and active against Gram-negative rods and cocci due to its aminothiazoyl and methoximino functional groups.","category_aro_class_name":"Antibiotic"},"37139":{"category_aro_accession":"3000759","category_aro_cvterm_id":"37139","category_aro_name":"fusidic acid","category_aro_description":"Fusidic acid is the only commercially available fusidane, a group of steroid-like antibiotics. It is most active against Gram-positive bacteria, and acts by inhibiting elongation factor G to  block protein synthesis.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"45735":{"category_aro_accession":"3007153","category_aro_cvterm_id":"45735","category_aro_name":"fusidane antibiotic","category_aro_description":"A group of antibiotics possessing steroid rings or steroid-like structures.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1234":{"model_id":"1234","model_name":"MIR-13","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"1348":{"protein_sequence":{"accession":"AIT76115.1","sequence":"MMTKSLSCALLLSVTSSAFAAPMSEKQLAEVVERTVTPLMNAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEIALGDPVAKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDTASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMSYEQAMTTRVFKPLKLDHTWINVPKAEEAHYAWGYREGKAVHVSPGMLNAEAYGVKTNVKDMASWVIANMKPDSLQAPSLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVGGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILDALQ"},"dna_sequence":{"accession":"KM087862.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGACAAAATCCCTAAGCTGTGCCCTGCTGCTCAGCGTCACCAGCTCTGCATTCGCCGCACCGATGTCCGAAAAACAGCTGGCTGAGGTGGTGGAACGTACCGTTACGCCGCTGATGAACGCGCAGGCCATTCCGGGTATGGCGGTGGCGGTAATTTATCAGGGTCAGCCACACTACTTTACCTTCGGTAAAGCCGATGTTGCGGCGAACAAACCCGTCACCCCGCAAACCCTGTTTGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTACTGGGCGGCGATGCCATTGCCCGGGGTGAAATAGCGCTGGGCGATCCGGTTGCAAAATACTGGCCTGAGCTCACGGGCAAGCAGTGGCAGGGCATTCGCATGCTGGATCTGGCAACCTATACCGCAGGCGGTCTGCCGTTACAGGTGCCGGATGAGGTCACGGATACCGCCTCTCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCGGGCACCACGCGTCTTTACGCTAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTTAAACCTTCCGGCATGAGCTATGAGCAGGCCATGACGACGCGGGTCTTTAAACCCCTCAAGCTGGACCATACCTGGATTAACGTCCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGATACCGTGAGGGTAAAGCGGTCCACGTTTCGCCAGGGATGCTGAACGCAGAAGCCTATGGCGTAAAAACTAACGTGAAGGATATGGCGAGCTGGGTGATAGCCAACATGAAGCCGGATTCTCTTCAGGCTCCCTCACTCAAGCAAGGCATTGCTCTGGCGCAGTCTCGCTACTGGCGCGTGGGGGCCATGTATCAGGGGTTGGGCTGGGAGATGCTCAACTGGCCGGTCGATGCCAAAACCGTCGTCGGAGGCAGTGATAACAAGGTGGCGCTGGCACCATTGCCCGTGGCAGAAGTGAATCCACCCGCGCCGCCGGTTAAGGCCTCCTGGGTCCATAAAACAGGCTCGACGGGTGGGTTTGGCAGCTACGTGGCATTTATTCCTGAAAAGCAGCTCGGCATTGTGATGCTGGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCGTATCCTCGACGCGCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36926","NCBI_taxonomy_name":"Enterobacter asburiae","NCBI_taxonomy_id":"61645"}}}},"ARO_accession":"3002178","ARO_id":"38578","ARO_name":"MIR-13","CARD_short_name":"MIR-13","ARO_description":"MIR-13 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36197":{"category_aro_accession":"3000058","category_aro_cvterm_id":"36197","category_aro_name":"MIR beta-lactamase","category_aro_description":"MIR beta-lactamases are plasmid-mediated beta-lactamases that confer resistance to oxyimino- and alpha-methoxy beta-lactams.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1235":{"model_id":"1235","model_name":"AAC(6')-Ib'","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"4753":{"protein_sequence":{"accession":"AAT74613.1","sequence":"MTNSNDSVTLRLMTEHDLAMLYEWLNRSHIVEWWGGEEARPTLADVQEQYLPSVLAQESVTPYIAMLNGEPIGYAQSYVALGSGDGWWEEETDPGVRGIDQSLANASQLGKGLGTKLVRALVELLFNDPEVTKIQTDPSPSNLRAIRCYEKAGFERQGTVTTPDGPAVYMVQTRQAFERTRSVA"},"dna_sequence":{"accession":"AY660529.1","fmin":"121","fmax":"676","strand":"+","sequence":"GTGACCAACAGCAACGATTCCGTCACACTGCGCCTCATGACTGAGCATGACCTTGCGATGCTCTATGAGTGGCTAAATCGATCTCATATCGTCGAGTGGTGGGGCGGAGAAGAAGCACGCCCGACACTTGCTGACGTACAGGAACAGTACTTGCCAAGCGTTTTAGCGCAAGAGTCCGTCACTCCATACATTGCAATGCTGAATGGAGAGCCGATTGGGTATGCCCAGTCGTACGTTGCTCTTGGAAGCGGGGACGGATGGTGGGAAGAAGAAACCGATCCAGGAGTACGCGGAATAGACCAGTCACTGGCGAATGCATCACAACTGGGCAAAGGCTTGGGAACCAAGCTGGTTCGAGCTCTGGTTGAGTTGCTGTTCAATGATCCCGAGGTCACCAAGATCCAAACGGACCCGTCGCCGAGCAACTTGCGAGCGATCCGATGCTACGAGAAAGCGGGGTTTGAGAGGCAAGGTACCGTAACCACCCCAGATGGTCCAGCCGTGTACATGGTTCAAACACGCCAGGCATTCGAGCGAACACGCAGTGTTGCCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3003676","ARO_id":"40308","ARO_name":"AAC(6')-Ib'","CARD_short_name":"AAC(6')-Ib'","ARO_description":"AAC(6')-Ib' is an aminoglycoside acetyltransferase encoded by plasmids, transposons, integrons in P. aeruginosa and P. fluorescens.","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"A category of aminoglycoside N-acetyltransferase enzymes with modification regiospecificity based at the 6'-amino group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics through acetylation of the 6-amino group of the compound.","category_aro_class_name":"AMR Gene Family"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1236":{"model_id":"1236","model_name":"CMY-53","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"958":{"protein_sequence":{"accession":"ADQ38362.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGICLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIELAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPARVEAAWRILEKLQ"},"dna_sequence":{"accession":"HQ336940.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCTGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGAGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAATAAAAGCTATCCTAACCCTGCCCGCGTCGAGGCGGCCTGGCGTATTCTTGAAAAACTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002064","ARO_id":"38464","ARO_name":"CMY-53","CARD_short_name":"CMY-53","ARO_description":"CMY-53 is a beta-lactamase found in Escherichia coli.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1238":{"model_id":"1238","model_name":"OXA-397","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1535":{"protein_sequence":{"accession":"AIT76118.1","sequence":"MKLLKILSLVCLSISIGACAEHSMSRAKTSTIPQVNNSIIDQNVQALFNEISADAVFVTYDGQNIKKYGTHLDRAKTAYIPASTFKIANALIGLENHKATSTEIFKWDGKPRFFKAWDKDFTLGEAMQASAVPVYQELARRIGPSLMQSELQRIGYGNMQIGTEVDQFWLKGPLTITPIQEVKFVYDLAQGQLPFKPEVQQQVKEMLYVERRGENRLYAKSGWGMAVDPQVGWYVGFVEKADGQVVAFALNMQMKAGDDIALRKQLSLDVLDKLGVFHYL"},"dna_sequence":{"accession":"KM087865.1","fmin":"0","fmax":"843","strand":"+","sequence":"ATGAAATTATTAAAAATATTGAGTTTAGTTTGCTTAAGCATAAGTATTGGGGCTTGTGCTGAGCATAGTATGAGTCGAGCAAAAACAAGTACAATTCCACAAGTGAATAACTCAATCATCGATCAGAATGTTCAAGCGCTTTTTAATGAAATCTCAGCTGATGCTGTGTTTGTCACATATGATGGTCAAAATATTAAAAAATATGGCACGCATTTAGACCGAGCAAAAACAGCTTATATTCCTGCATCTACATTTAAAATTGCCAATGCACTAATTGGTTTAGAAAATCATAAAGCAACATCTACAGAAATATTTAAGTGGGATGGAAAGCCACGTTTTTTTAAAGCATGGGACAAAGATTTTACTTTGGGCGAAGCCATGCAAGCATCTGCAGTGCCTGTATATCAAGAATTGGCACGTCGTATTGGTCCAAGCTTAATGCAAAGTGAATTGCAACGTATTGGTTATGGCAATATGCAAATAGGCACGGAAGTTGATCAATTTTGGTTGAAAGGGCCTTTGACAATTACACCTATACAAGAAGTAAAGTTTGTGTATGATTTAGCCCAAGGGCAATTGCCTTTTAAACCTGAAGTTCAGCAACAAGTGAAAGAGATGTTGTATGTAGAGCGCAGAGGGGAGAATCGTCTATATGCTAAAAGTGGCTGGGGAATGGCTGTAGACCCGCAAGTGGGTTGGTATGTGGGTTTTGTTGAAAAGGCAGATGGGCAAGTGGTGGCATTTGCTTTAAATATGCAAATGAAAGCTGGTGATGATATTGCTCTACGTAAACAATTGTCTTTAGATGTGCTAGATAAGTTGGGTGTTTTTCATTATTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001583","ARO_id":"37983","ARO_name":"OXA-397","CARD_short_name":"OXA-397","ARO_description":"OXA-397 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46517":{"category_aro_accession":"3007728","category_aro_cvterm_id":"46517","category_aro_name":"OXA-58-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-58.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1239":{"model_id":"1239","model_name":"SHV-81","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"8204":{"protein_sequence":{"accession":"CAJ47136.2","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGSPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AM176556.2","fmin":"25","fmax":"886","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACATCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCAGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001135","ARO_id":"37515","ARO_name":"SHV-81","CARD_short_name":"SHV-81","ARO_description":"SHV-81 is a broad-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1241":{"model_id":"1241","model_name":"TEM-144","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1645":{"protein_sequence":{"accession":"CAJ17558.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDCWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGKRGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AM049399.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATTGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTAAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35667","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Derby","NCBI_taxonomy_id":"28144"}}}},"ARO_accession":"3001007","ARO_id":"37387","ARO_name":"TEM-144","CARD_short_name":"TEM-144","ARO_description":"TEM-144 is an extended-spectrum beta-lactamase found in Salmonella enterica.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1242":{"model_id":"1242","model_name":"aadA6\/aadA10","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"409":{"protein_sequence":{"accession":"CAJ32491.1","sequence":"MSNAVPAEISVQLSLALNAIERHLESTLLAVHLYGSALDGGLKPYSDIDLLVTVAARLDETVRQALVVDLLEISASPGQSEALRALEVTIVVHGDVVPWRYPARRELQFGEWQRKDILAGIFEPATTDVDLAILLTKVRQHSLALAGSAAEDFFNPVPEGDLFKALSDTLKLWNSQPDWEGDERNVVLTLSRIWYSAATGKIAPKDIVANWAMERLPDQHKPVLLEARQAYLGQGEDCLASRADQLAAFVHFVKHEATKLLSAMPVMSKTKLDALST"},"dna_sequence":{"accession":"AM087405.1","fmin":"1748","fmax":"2582","strand":"+","sequence":"ATGAGTAACGCAGTACCCGCCGAGATTTCGGTACAGCTATCACTGGCTCTCAACGCCATCGAGCGTCATCTGGAATCAACGTTGCTGGCCGTGCATTTGTACGGCTCTGCACTGGACGGTGGCCTGAAGCCATACAGTGATATTGATTTGCTGGTTACTGTGGCTGCACGGCTCGATGAGACTGTCCGACAAGCCCTGGTCGTAGATCTCTTGGAAATTTCTGCCTCCCCTGGCCAAAGTGAGGCTCTCCGCGCCTTGGAAGTTACCATCGTCGTGCATGGTGATGTTGTCCCTTGGCGTTATCCGGCCAGACGGGAACTGCAATTCGGGGAGTGGCAGCGTAAGGACATTCTTGCGGGCATCTTCGAGCCCGCCACAACCGATGTTGATCTGGCTATTCTGCTAACTAAAGTAAGGCAGCATAGCCTTGCATTGGCAGGTTCGGCCGCAGAGGATTTCTTTAACCCAGTTCCGGAAGGCGATCTATTCAAGGCATTGAGCGACACTCTGAAACTATGGAATTCGCAGCCGGATTGGGAAGGCGATGAGCGGAATGTAGTGCTTACCTTGTCTCGCATTTGGTACAGCGCAGCAACCGGCAAGATCGCACCGAAGGATATCGTTGCCAACTGGGCAATGGAGCGTCTGCCAGATCAACATAAGCCCGTACTGCTTGAAGCCCGGCAGGCTTATCTTGGACAAGGAGAAGATTGCTTGGCCTCACGCGCGGATCAGTTGGCGGCGTTCGTTCACTTCGTGAAACATGAAGCCACTAAATTGCTTAGTGCCATGCCAGTGATGTCTAAAACAAAGTTAGATGCACTAAGCACATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002622","ARO_id":"39022","ARO_name":"aadA6\/aadA10","CARD_short_name":"aadA6\/aadA10","ARO_description":"aadA6\/aadA10 is an integron-encoded aminoglycoside nucleotidyltransferase gene cassette in P. aeruginosa.","ARO_category":{"41439":{"category_aro_accession":"3004275","category_aro_cvterm_id":"41439","category_aro_name":"ANT(3'')","category_aro_description":"A category of aminoglycoside O-nucleotidyltransferase enzymes with modification regiospecificity based at the 3''-hydroxyl group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics by transfer of an AMP group from an ATP substrate to the 3''-hydroxyl group of the compound.","category_aro_class_name":"AMR Gene Family"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1243":{"model_id":"1243","model_name":"mphA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"5188":{"protein_sequence":{"accession":"BAA03776.1","sequence":"MTVVTTADTSQLYALAARHGLKLHGPLTVNELGLDYRIVIATVDDGRRWVLRIPRRAEVSAKVEPEARVLAMLKNRLPFAVPDWRVANAELVAYPMLEDSTAMVIQPGSSTPDWVVPQDSEVFAESFATALAALHAVPISAAVDAGMLIRTPTQARQKVADDVDRVRREFVVNDKRLHRWQRWLDDDSSWPDFSVVVHGDLYVGHVLIDNTERVSGMIDWSEARVDDPAIDMAAHLMVFGEEGLAKLLLTYEAAGGRVWPRLAHHIAERLAFGAVTYALFALDSGNEEYLAAAKAQLAAAE"},"dna_sequence":{"accession":"D16251.1","fmin":"1625","fmax":"2531","strand":"-","sequence":"ATGACCGTAGTCACGACCGCCGATACCTCCCAACTGTACGCACTTGCAGCCCGACATGGGCTCAAGCTCCATGGCCCGCTGACTGTCAATGAGCTTGGGCTCGACTATAGGATCGTGATCGCCACCGTCGACGATGGACGTCGGTGGGTGCTGCGCATCCCGCGCCGAGCCGAGGTAAGCGCGAAGGTCGAACCAGAGGCGCGGGTGCTGGCAATGCTCAAGAATCGCCTGCCGTTCGCGGTGCCGGACTGGCGCGTGGCCAACGCCGAGCTCGTTGCCTATCCCATGCTCGAAGACTCGACTGCGATGGTCATCCAGCCTGGTTCGTCCACGCCCGACTGGGTCGTGCCGCAGGACTCGGAGGTCTTCGCGGAGAGCTTCGCGACCGCGCTCGCCGCCCTGCATGCCGTCCCCATTTCCGCCGCCGTGGATGCGGGGATGCTCATCCGTACACCGACGCAGGCCCGTCAGAAGGTGGCCGACGACGTTGACCGCGTCCGACGCGAGTTCGTGGTGAACGACAAGCGCCTCCACCGGTGGCAGCGCTGGCTCGACGACGATTCGTCGTGGCCAGATTTCTCCGTGGTGGTGCATGGCGATCTCTACGTGGGCCATGTGCTCATCGACAACACGGAGCGCGTCAGCGGGATGATCGACTGGAGCGAGGCCCGCGTTGATGACCCTGCCATCGACATGGCCGCGCACCTTATGGTCTTTGGTGAAGAGGGGCTCGCGAAGCTCCTCCTCACGTATGAAGCGGCCGGTGGCCGGGTGTGGCCGCGGCTCGCCCACCACATCGCGGAGCGCCTTGCGTTCGGGGCGGTCACCTACGCACTCTTCGCCCTCGACTCGGGTAACGAAGAGTACCTCGCTGCGGCGAAGGCGCAGCTCGCCGCAGCGGAATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000316","ARO_id":"36455","ARO_name":"mphA","CARD_short_name":"mphA","ARO_description":"The mphA gene encodes for resistance enzyme MPH(2')-I which preferentially inactivate 14-membered macrolides (e.g.erythromycin, telithromycin, roxithromycin) over 16-membered macrolides (e.g.tylosin, spiramycin). It phosphorylates macrolides at 2'-OH hydroxyl of desosamine sugar of macrolides in a GTP-dependent manner.","ARO_category":{"36472":{"category_aro_accession":"3000333","category_aro_cvterm_id":"36472","category_aro_name":"macrolide phosphotransferase (MPH)","category_aro_description":"Macrolide phosphotransferases (MPH) are enzymes encoded by macrolide phosphotransferase genes (mph genes). These enzymes phosphorylate macrolides in GTP dependent manner at 2'-OH of desosamine sugar thereby inactivating them. Characterized MPH's are differentiated based on their substrate specificity.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35946":{"category_aro_accession":"0000027","category_aro_cvterm_id":"35946","category_aro_name":"roxithromycin","category_aro_description":"Roxithromycin is a semi-synthetic, 14-carbon ring macrolide antibiotic derived from erythromycin. It is used to treat respiratory tract, urinary and soft tissue infections. Roxithromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35974":{"category_aro_accession":"0000057","category_aro_cvterm_id":"35974","category_aro_name":"telithromycin","category_aro_description":"Telithromycin is a semi-synthetic derivative of erythromycin. It is a 14-membered macrolide and is the first ketolide antibiotic to be used in clinics. Telithromycin binds the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"35982":{"category_aro_accession":"0000065","category_aro_cvterm_id":"35982","category_aro_name":"clarithromycin","category_aro_description":"Clarithromycin is a methyl derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome and is used to treat pharyngitis, tonsillitis, acute maxillary sinusitis, acute bacterial exacerbation of chronic bronchitis, pneumonia (especially atypical pneumonias associated with Chlamydia pneumoniae or TWAR), and skin structure infections.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"36315":{"category_aro_accession":"3000176","category_aro_cvterm_id":"36315","category_aro_name":"dirithromycin","category_aro_description":"Dirithromycin is an oxazine derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome to inhibit bacterial protein synthesis.","category_aro_class_name":"Antibiotic"},"37247":{"category_aro_accession":"3000867","category_aro_cvterm_id":"37247","category_aro_name":"oleandomycin","category_aro_description":"Oleandomycin is a 14-membered macrolide produced by Streptomyces antibioticus. It is ssimilar to erythromycin, and contains a desosamine amino sugar and an oleandrose sugar. It targets the 50S ribosomal subunit to prevent protein synthesis.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1244":{"model_id":"1244","model_name":"OXY-5-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"2017":{"protein_sequence":{"accession":"CAI43417.1","sequence":"MLKSSWRKTALMAAAVPLLLASGSLWASADAIQQKLADLEKHSGGRLGVALINTADDSQTLYRGDERFAMCSTGKVMAAAAVLKQSESNPEVVNKRLEIKKADLVVWSPITEKHLQSGMTLAELSAAALQYSDNTAMNKIIGYLGGPEKVTAFAQSIGDVTFRLDRMEPALNSAIPGDKRDTTTPLAMAESLRKLTLGNALGEQQRAQLVTWLKGNTTGGQSIRAGLPASWAVGDKTGAGDYGTTNDIAVIWPENHAPLVLVTYFTQPQQDAKSRKEVLAAAAKIVTEGL"},"dna_sequence":{"accession":"AJ871869.1","fmin":"0","fmax":"873","strand":"+","sequence":"ATGTTGAAAAGTTCGTGGCGTAAAACCGCCCTGATGGCCGCCGCCGTTCCGCTGCTGCTGGCGAGCGGTTCATTATGGGCCAGTGCCGATGCTATCCAGCAAAAGCTGGCTGATTTAGAAAAACATTCCGGCGGTCGGCTGGGCGTAGCGCTGATTAATACGGCAGATGATTCGCAAACCCTCTATCGCGGCGATGAACGGTTTGCCATGTGCAGCACCGGTAAAGTGATGGCCGCCGCCGCGGTGTTAAAACAGAGCGAAAGCAATCCAGAGGTAGTGAATAAAAGGCTGGAGATTAAAAAAGCGGATTTAGTAGTCTGGAGCCCGATTACCGAAAAACATCTGCAAAGCGGAATGACCCTGGCGGAACTCAGCGCGGCGGCGCTGCAGTACAGCGACAATACCGCGATGAATAAGATTATCGGTTACCTTGGCGGGCCGGAAAAAGTCACCGCATTCGCCCAGAGTATCGGTGACGTTACTTTTCGTCTCGATCGCATGGAGCCGGCGCTGAACAGCGCGATTCCCGGCGATAAGCGCGATACCACCACCCCGTTGGCGATGGCCGAAAGCCTGCGCAAGCTGACGCTGGGCAATGCGCTGGGCGAACAGCAGCGCGCCCAGTTAGTGACGTGGCTAAAAGGCAATACCACCGGCGGGCAAAGCATTCGCGCAGGCCTGCCCGCAAGCTGGGCGGTCGGGGATAAAACCGGCGCCGGAGATTACGGCACCACCAACGATATTGCGGTGATCTGGCCGGAAAATCATGCCCCGCTGGTGCTGGTGACCTATTTTACCCAGCCGCAGCAGGATGCGAAAAGCCGCAAAGAGGTGTTAGCCGCGGCGGCAAAAATCGTCACCGAAGGGCTTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3002411","ARO_id":"38811","ARO_name":"OXY-5-1","CARD_short_name":"OXY-5-1","ARO_description":"OXY-5-1 is a beta-lactamase found in Klebsiella oxytoca.","ARO_category":{"38788":{"category_aro_accession":"3002388","category_aro_cvterm_id":"38788","category_aro_name":"OXY beta-lactamase","category_aro_description":"OXY beta-lactamases are chromosomal class A beta-lactamases that are found in Klebsiella oxytoca. At constitutive low levels, OXY beta-lactamases confer resistance to aminopenicillins and carboxypenicillins. At high induced levels,  OXY beta-lactamases confer resistance to penicillins, cephalosporins and aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1245":{"model_id":"1245","model_name":"TEM-114","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1879":{"protein_sequence":{"accession":"AAS89984.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDKLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDSWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGTGKRGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AY589495.1","fmin":"181","fmax":"1042","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATAAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATAGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAACCGGTAAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36770","NCBI_taxonomy_name":"Klebsiella aerogenes","NCBI_taxonomy_id":"548"}}}},"ARO_accession":"3000977","ARO_id":"37357","ARO_name":"TEM-114","CARD_short_name":"TEM-114","ARO_description":"TEM-114 is an extended-spectrum beta-lactamase found in Klebsiella aerogenes.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1246":{"model_id":"1246","model_name":"AAC(2')-Ic","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"4719":{"protein_sequence":{"accession":"CCP42991.1","sequence":"MHTQVHTARLVHTADLDSETRQDIRQMVTGAFAGDFTETDWEHTLGGMHALIWHHGAIIAHAAVIQRRLIYRGNALRCGYVEGVAVRADWRGQRLVSALLDAVEQVMRGAYQLGALSSSARARRLYASRGWLPWHGPTSVLAPTGPVRTPDDDGTVFVLPIDISLDTSAELMCDWRAGDVW"},"dna_sequence":{"accession":"AL123456.3","fmin":"314308","fmax":"314854","strand":"-","sequence":"GTGCACACCCAGGTACACACGGCCCGCCTGGTCCACACCGCCGATCTTGACAGCGAGACCCGCCAGGACATCCGTCAGATGGTCACCGGCGCGTTTGCCGGTGACTTCACCGAGACCGACTGGGAGCACACGCTGGGTGGGATGCACGCCCTGATCTGGCATCACGGGGCGATCATCGCGCATGCCGCGGTGATCCAGCGGCGACTGATCTACCGCGGCAACGCGCTGCGCTGCGGGTACGTCGAAGGCGTTGCGGTGCGGGCGGACTGGCGGGGCCAACGCCTGGTGAGCGCGCTGTTGGACGCCGTCGAGCAGGTGATGCGCGGCGCTTACCAGCTCGGAGCGCTCAGTTCCTCGGCGCGGGCCCGCAGACTGTACGCCTCACGCGGCTGGCTGCCCTGGCACGGCCCGACATCGGTACTGGCACCAACCGGTCCAGTCCGTACACCCGATGACGACGGAACGGTGTTCGTCCTGCCCATCGACATCAGCCTGGACACCTCGGCGGAGCTGATGTGCGATTGGCGCGCGGGCGACGTCTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3002525","ARO_id":"38925","ARO_name":"AAC(2')-Ic","CARD_short_name":"AAC(2')-Ic","ARO_description":"AAC(2')-Ic is a chromosomal-encoded aminoglycoside acetyltransferase in M. tuberculosis and Mycobacterium tuberculosis variant bovis.","ARO_category":{"36480":{"category_aro_accession":"3000341","category_aro_cvterm_id":"36480","category_aro_name":"AAC(2')","category_aro_description":"A category of aminoglycoside N-acetyltransferase enzymes with modification regiospecificity based at the 2'-amino group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics through acetylation of the 2-amino group of the compound.","category_aro_class_name":"AMR Gene Family"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"46127":{"category_aro_accession":"3007377","category_aro_cvterm_id":"46127","category_aro_name":"6'-N-ethylnetilmicin","category_aro_description":"6'-N-ethylnetilmicin is an aminoglycoside antibiotic and a derivative of netilmicin.","category_aro_class_name":"Antibiotic"},"46133":{"category_aro_accession":"3007382","category_aro_cvterm_id":"46133","category_aro_name":"gentamicin","category_aro_description":"Gentamicin is a commonly used aminoglycoside antibiotic derived from members of the Micromonospora genus of bacteria. It acts by binding the 30S ribosomal subunit, thus inhibiting protein synthesis. Gentamicin is typically used to treat Gram-negative infections of the repiratory and urinary tract, as well as infections of the bone and soft tissue. It also exhibits considerable nephrotoxicity and ototoxicity. Gentamicin is administered as a mixture of gentamicin type C (which makes about around 80% of the complex) and types A, B, and X (distributed in the remaining 20% of the complex).","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1247":{"model_id":"1247","model_name":"CMY-72","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1346":{"protein_sequence":{"accession":"AFU25641.1","sequence":"MMKKSICCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAIIYEGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWRGISLLHLATYTAGGLPLQIPDDVTDKAELLRFYQNWQPQWTPGAKRLYANSSIGLFGALAVKSSGMSYEEAMTRRVLQPLKLAHTWITVPQSEQKNYAWGYLEGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIELAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPARVEAAWRILEKLQ"},"dna_sequence":{"accession":"JX440352.1","fmin":"1027","fmax":"2173","strand":"+","sequence":"ATGATGAAAAAATCGATATGCTGCGCGCTGCTGCTGACAGCCTCTTTCTCCACGTTTGCTGCCGCAAAAACAGAACAACAAATTGCCGATATCGTTAACCGCACCATCACACCACTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTGGCGATTATCTACGAGGGGAAACCTTATTACTTTACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGACGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCGGGGTATCAGCCTGCTGCACTTAGCCACCTATACAGCGGGTGGCCTGCCGCTGCAGATCCCCGATGACGTTACGGATAAAGCCGAATTACTGCGCTTTTATCAAAACTGGCAACCACAATGGACTCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGTGCGCTGGCGGTGAAATCTTCAGGTATGAGCTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAAAGCGAACAAAAAAACTATGCCTGGGGCTATCTCGAAGGGAAGCCTGTGCACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATCGATATGGCCCGCTGGGTTCAGGCCAACATGGACGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGAGCTTGCGCAGTCTCGCTACTGGCGTATTGGTGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCAGCACCTGCCGTGAAAGCCTCATGGGTGCATAAAACGGGATCCACAGGTGGATTTGGCAGCTACGTTGCCTTCGTTCCAGAAAAAAACCTTGGCATAGTGATGCTGGCAAACAAAAGCTATCCTAACCCGGCTCGCGTAGAGGCGGCCTGGCGCATTCTTGAAAAACTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002085","ARO_id":"38485","ARO_name":"CMY-72","CARD_short_name":"CMY-72","ARO_description":"CMY-72 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1248":{"model_id":"1248","model_name":"H-NS","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"240"}},"model_sequences":{"sequence":{"5476":{"protein_sequence":{"accession":"BAB35162.1","sequence":"MSEALKILNNIRTLRAQARECTLETLEEMLEKLEVVVNERREEESAAAAEVEERTRKLQQYREMLIADGIDPNELLNSLAAVKSGTKAKRAQRPAKYSYVDENGETKTWTGQGRTPAVIKKAMDEQGKSLDDFLIKQ"},"dna_sequence":{"accession":"BA000007.3","fmin":"1737690","fmax":"1738104","strand":"-","sequence":"ATGAGCGAAGCACTTAAAATTCTGAACAACATCCGTACTCTTCGTGCGCAGGCAAGAGAATGTACACTTGAAACGCTGGAAGAAATGCTGGAAAAATTAGAAGTTGTTGTTAACGAACGTCGCGAAGAAGAAAGCGCGGCTGCTGCTGAAGTTGAAGAGCGCACTCGTAAACTGCAGCAATATCGCGAAATGCTGATCGCTGACGGTATTGACCCGAACGAGCTGCTGAATAGCCTTGCCGCCGTTAAATCTGGCACCAAAGCTAAACGTGCTCAGCGTCCGGCAAAATATAGCTACGTTGACGAAAACGGCGAAACTAAAACCTGGACTGGCCAGGGCCGTACTCCAGCTGTAATCAAAAAAGCAATGGATGAGCAAGGTAAATCCCTCGACGATTTCCTGATCAAGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36747","NCBI_taxonomy_name":"Escherichia coli O157:H7 str. Sakai","NCBI_taxonomy_id":"386585"}}}},"ARO_accession":"3000676","ARO_id":"37020","ARO_name":"H-NS","CARD_short_name":"H-NS","ARO_description":"H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE, mdtE, and emrK as well as nearby genes of many RND-type multidrug exporters.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35930":{"category_aro_accession":"0000011","category_aro_cvterm_id":"35930","category_aro_name":"cloxacillin","category_aro_description":"Cloxacillin is a semisynthetic, isoxazolyl penicillin derivative in the beta-lactam class of antibiotics. It interferes with peptidogylcan synthesis and is commonly used for treating penicillin-resistant Staphylococcus aureus infections.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1249":{"model_id":"1249","model_name":"FOX-5","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1276":{"protein_sequence":{"accession":"AAG12974.1","sequence":"MQQRRAFALLTLGSLLLAPCTYASGEAPLTAAVDGIIQPMLKAYRIPGMAVAVLKDGKAHYFNYGVANRESGQRVSEQTLFEIGSVSKTLTATLGAYAAVKGGFELDDKVSQHAPWLKGSALDGVTMAELATYSAGGLPLQFPDEVDSNDKMRTYYRSWSPVYPAGTHRQYSNPSIGLFGHLAANSLGQPFEQLMSQTLLPKLGLHHTYIQVPESAMVNYAYGYSKEDKPVRVTPGVLAAEAYGIKTGSADLLKFAEANMGYQGDAAVKSAIALTHTGFYSVGDMTQGLGWESYAYPVTEQTLLAGNAPAVSFQANPVTRFAVPKAMGEQRLYNKTGSTGGFGAYVAFVPARGIAIVMLANRNYPIEARVKAAHAILSQLAE"},"dna_sequence":{"accession":"AY007369.1","fmin":"0","fmax":"1149","strand":"+","sequence":"ATGCAACAACGGCGTGCGTTCGCGCTACTGACGCTGGGTAGCCTGCTGTTAGCCCCTTGTACTTATGCCAGCGGGGAGGCTCCGTTGACCGCCGCTGTGGACGGCATTATCCAGCCGATGCTCAAGGCGTATCGGATCCCGGGGATGGCGGTCGCCGTACTGAAAGATGGCAAAGCCCACTATTTCAACTATGGGGTTGCCAACCGGGAGAGTGGCCAGCGCGTCAGCGAGCAGACCCTGTTCGAGATTGGCTCGGTCAGCAAGACCCTGACTGCGACCCTCGGTGCCTATGCCGCGGTCAAGGGGGGCTTTGAGCTGGATGACAAGGTGAGCCAGCACGCCCCCTGGCTCAAAGGTTCCGCCTTGGATGGTGTGACCATGGCCGAGCTTGCCACCTACAGTGCGGGTGGTTTGCCGCTGCAGTTCCCCGATGAGGTGGATTCGAATGACAAGATGCGCACTTACTATCGGAGCTGGTCACCGGTTTATCCGGCGGGGACCCATCGCCAGTATTCCAACCCCAGCATCGGCCTGTTTGGTCACCTGGCCGCAAATAGTCTGGGCCAGCCATTTGAGCAACTGATGAGCCAGACCCTGCTGCCCAAGCTGGGTTTGCACCACACCTATATCCAGGTACCGGAGTCGGCTATGGTGAACTATGCCTACGGCTATTCGAAGGAAGATAAGCCCGTCCGGGTCACTCCGGGCGTGCTGGCAGCCGAGGCTTACGGGATCAAGACCGGCTCGGCGGATCTGCTGAAGTTTGCCGAGGCAAACATGGGGTATCAGGGAGATGCCGCGGTAAAAAGCGCGATCGCGCTGACCCACACCGGTTTCTACTCGGTGGGAGACATGACCCAGGGACTGGGCTGGGAGAGTTACGCCTATCCGGTGACCGAGCAGACATTGCTGGCGGGTAACGCACCGGCGGTGAGCTTCCAGGCCAATCCGGTTACGCGCTTTGCGGTGCCCAAGGCGATGGGCGAGCAGCGGCTCTATAACAAGACGGGCTCGACTGGCGGCTTTGGCGCCTATGTGGCGTTCGTGCCCGCCAGAGGGATCGCCATCGTCATGCTGGCCAATCGCAACTATCCCATCGAGGCCAGGGTGAAGGCGGCTCACGCCATCCTGAGTCAGTTGGCCGAGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002159","ARO_id":"38559","ARO_name":"FOX-5","CARD_short_name":"FOX-5","ARO_description":"FOX-5 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36206":{"category_aro_accession":"3000067","category_aro_cvterm_id":"36206","category_aro_name":"FOX beta-lactamase","category_aro_description":"FOX beta-lactamases are plasmid-encoded AmpC-type beta-lactamase which conferred resistance to broad-spectrum cephalosporins and cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1250":{"model_id":"1250","model_name":"CTX-M-96","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"950":{"protein_sequence":{"accession":"CAG28417.1","sequence":"MVKKSLRQFTLMATAAVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPSLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDILASAAKIVTDGL"},"dna_sequence":{"accession":"AJ704396.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAGCCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCGGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTCGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAGTCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTGGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCAGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATTTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATATATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001956","ARO_id":"38356","ARO_name":"CTX-M-96","CARD_short_name":"CTX-M-96","ARO_description":"CTX-M-96 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1251":{"model_id":"1251","model_name":"CTX-M-157","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1819":{"protein_sequence":{"accession":"AIS67613.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTAPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"KM211510.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGCGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3003165","ARO_id":"39742","ARO_name":"CTX-M-157","CARD_short_name":"CTX-M-157","ARO_description":"CTX-M-157 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1252":{"model_id":"1252","model_name":"ceoB","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"2030"}},"model_sequences":{"sequence":{"121":{"protein_sequence":{"accession":"AAB58161.1","sequence":"MNISKFFIDRPIFAGVLSVIILLGGVIAMFLLPISEYPEVVPPSVIVKAQYPGANPKVIAETVASPLEEQINGVENMLYMQSQANSDGNMTITVTFKLGTDPDKATQLVQNRVNQALPRLPEDVQRLGITTVKSSPTLTMVVHLISPDNRYDMTYLRNYALINVKDRLSRIQGVGQVQLWGSGDYAMRVWLDPQKVAQRGLSAEDVVQAIREQNVQVAAGVIGASPSLPGTPLQLSVNARGRLQTEDEFGDIVVKTTPDGGVTHLRDIARIQLDASEYGLRSLLDNKPAVAMAINQSPGANSLQISDEVRKTMAELKQDMPAGVDYKIVYDPTQFVRSSIKAVVHTLLEAIALVVIVVIVFLQTWRASLIPLIAVPVSIIGTFSLLLAFGYSINALSLFGMVLAIGIVVDDAIVVVENVERNIENGMNARQATYKAMQEVSGPIIAIALTLVAVFVPLAFMSGLTGQFYKQFAMTIAISTVISAFNSLTLSPALSAILLKGHGDKEDWLTRVMNRVLGGFFRGFNKVFHRGAENYGRGVRGVLSRKTLMLGVYLVLVGATVLVSKVVPGGFVPAQDKEYLIAFAQLPNGASLDRTEKVIRDMGSIALKQPGVESAVAFPGLSVNGFTNSSSAGIVFVTLKPFAERHGKALSAGAIAGALNQKYGAMKDSFVAVFPPPPVLGLGTLGGFKMQIEDRGAVGYAKLSDATNDFIKRAQQAPELGPLFTSYQINVPQLNVDLDRVKAKQLGVPVTDVFNTMQVYLGSLYVNDFNRFGRVYQVRVQADAPFRQRADDILQLKTRNDKGEMVPLSSLVTVTPTFGPEMVVRYNGYTAADINGGPAPGFSSGQAQAAVERIADETLPRGVRFEWTDLTYQQILAGDSAMWVFPISVLLVFLVLAALYESLTLPLAVILIVPMSILSALTGVWLTQGDNNIFTQIGLMVLVGLSAKNAILIVEFARELEHDGRTPLEAAIEASRLRLRPILMTSIAFIMGVVPLVTSTGAGSEMRHAMGVAVFFGMLGVTLFGLI"},"dna_sequence":{"accession":"U97042.1","fmin":"1263","fmax":"4347","strand":"+","sequence":"ATGAACATTTCCAAATTCTTTATCGACCGGCCGATCTTTGCAGGAGTCCTATCGGTGATCATCCTGCTCGGCGGGGTGATCGCGATGTTCCTGCTGCCGATTTCGGAATATCCGGAAGTCGTGCCGCCTTCGGTGATCGTGAAGGCGCAGTACCCGGGCGCGAACCCGAAAGTGATCGCCGAGACGGTCGCGTCGCCACTTGAAGAGCAGATCAACGGCGTCGAGAACATGCTCTACATGCAGTCGCAGGCGAACAGCGACGGCAACATGACGATCACCGTCACGTTCAAGCTGGGCACCGATCCGGACAAGGCCACGCAGCTCGTGCAGAACCGCGTGAACCAGGCGCTGCCGCGCTTGCCGGAAGACGTGCAGCGGCTCGGCATCACCACGGTGAAGAGCTCGCCGACGCTGACGATGGTGGTCCACCTGATCTCGCCGGACAACCGCTACGACATGACCTACCTGCGCAACTACGCGCTGATCAACGTGAAGGATCGCCTGTCGCGGATCCAGGGCGTCGGCCAGGTGCAGCTGTGGGGTTCGGGCGACTACGCGATGCGCGTGTGGCTCGATCCGCAGAAGGTCGCGCAGCGCGGGCTGTCGGCCGAGGACGTCGTGCAGGCGATCCGCGAGCAGAACGTGCAGGTCGCGGCCGGCGTGATCGGCGCATCGCCGTCGCTGCCCGGCACGCCGCTGCAGCTGTCGGTGAACGCGCGCGGCCGTCTGCAGACGGAAGACGAATTCGGCGACATCGTCGTGAAGACGACGCCGGATGGCGGCGTCACGCACCTGCGCGACATCGCGCGGATCCAGCTCGACGCGTCCGAGTACGGGCTGCGCTCGCTGCTCGACAACAAGCCGGCCGTCGCGATGGCGATCAACCAGTCGCCGGGCGCGAACTCGCTGCAGATCTCGGACGAAGTGCGCAAGACGATGGCCGAACTGAAGCAGGACATGCCGGCGGGCGTCGACTACAAGATCGTCTATGACCCGACGCAGTTCGTGCGCTCGTCGATCAAGGCCGTCGTGCACACGCTGCTCGAAGCGATCGCGCTGGTCGTGATCGTCGTGATCGTGTTCCTGCAGACCTGGCGCGCGTCGCTGATTCCGCTGATCGCGGTGCCGGTGTCGATCATCGGCACGTTCTCGCTGCTGCTCGCGTTCGGGTATTCGATCAACGCGTTGTCGCTGTTCGGGATGGTGCTCGCGATCGGGATCGTGGTCGACGATGCGATCGTCGTCGTCGAGAACGTCGAGCGCAACATCGAGAACGGGATGAACGCGCGGCAGGCGACCTACAAGGCGATGCAGGAAGTGAGCGGGCCGATCATCGCGATCGCGCTGACGCTGGTCGCCGTGTTCGTGCCGCTCGCGTTCATGTCGGGCCTGACCGGCCAGTTCTACAAGCAGTTCGCGATGACCATCGCGATCTCGACGGTGATCTCGGCGTTCAACTCGCTGACGCTGTCGCCGGCGCTGTCCGCGATCCTGCTGAAGGGGCACGGCGACAAGGAAGACTGGCTCACGCGTGTGATGAACCGCGTGCTCGGCGGCTTCTTCCGCGGCTTCAACAAGGTGTTCCATCGCGGGGCGGAGAACTACGGCCGCGGCGTGCGCGGCGTGCTGTCGCGCAAGACGCTGATGCTCGGCGTGTATCTCGTGCTGGTGGGCGCGACGGTGCTCGTGTCGAAGGTCGTGCCGGGCGGCTTCGTGCCCGCGCAGGACAAGGAATACCTGATCGCGTTCGCGCAGCTGCCGAACGGTGCGTCGCTCGACCGCACCGAGAAGGTGATCCGCGACATGGGTTCGATCGCGCTGAAGCAGCCGGGCGTCGAGAGCGCGGTCGCGTTCCCGGGGCTGTCGGTGAACGGCTTCACCAACAGCTCGAGCGCGGGCATCGTGTTCGTCACGCTCAAGCCGTTCGCGGAACGGCACGGCAAGGCGCTGTCGGCCGGCGCCATCGCGGGTGCGCTGAACCAGAAGTACGGCGCGATGAAGGATTCGTTCGTCGCGGTGTTCCCGCCGCCGCCGGTGCTCGGCCTCGGTACGCTCGGCGGGTTCAAGATGCAGATCGAGGATCGCGGCGCGGTCGGCTACGCGAAGCTGTCGGATGCGACCAACGACTTCATCAAGCGCGCGCAGCAGGCGCCTGAACTCGGCCCGCTGTTCACGAGCTACCAGATCAACGTGCCGCAGCTCAACGTCGATCTCGACCGCGTGAAGGCGAAGCAGCTCGGCGTGCCGGTGACCGACGTGTTCAACACGATGCAGGTGTATCTGGGTTCGCTGTACGTGAACGACTTCAACCGCTTCGGACGCGTGTACCAGGTGCGCGTGCAGGCCGATGCGCCGTTCCGCCAGCGCGCGGACGACATCCTGCAACTGAAGACGCGCAACGACAAGGGCGAGATGGTGCCGCTGTCGTCGCTGGTCACCGTGACGCCGACGTTCGGCCCGGAAATGGTCGTGCGCTACAACGGCTACACGGCGGCCGACATCAACGGCGGCCCGGCGCCCGGCTTCTCGTCGGGGCAGGCGCAGGCCGCGGTCGAGCGCATCGCCGACGAGACGCTGCCGCGCGGCGTGCGCTTCGAGTGGACCGACCTCACGTACCAGCAGATCCTCGCGGGCGATTCGGCGATGTGGGTGTTCCCGATCAGCGTGCTGCTCGTGTTCCTCGTGCTCGCCGCGCTGTATGAAAGCCTGACGCTGCCGCTCGCGGTGATCCTGATCGTGCCGATGAGCATTCTGTCGGCGCTGACGGGCGTGTGGCTCACGCAGGGCGACAACAACATCTTCACGCAGATCGGCCTGATGGTGCTGGTGGGGCTGTCGGCGAAGAACGCGATCCTGATCGTCGAATTCGCGCGCGAGCTCGAACACGACGGCAGGACGCCGCTCGAGGCCGCGATCGAGGCGAGCCGGCTGCGGCTGCGCCCGATCCTGATGACGTCGATCGCTTTCATCATGGGCGTGGTGCCGCTCGTCACGTCGACCGGCGCGGGTTCGGAAATGCGTCATGCGATGGGGGTCGCGGTGTTCTTCGGGATGCTCGGCGTGACGCTGTTCGGGCTGATCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36822","NCBI_taxonomy_name":"Burkholderia cepacia","NCBI_taxonomy_id":"292"}}}},"ARO_accession":"3003010","ARO_id":"39444","ARO_name":"ceoB","CARD_short_name":"ceoB","ARO_description":"ceoB is a cytoplasmic membrane component of the CeoAB-OpcM efflux pump.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1253":{"model_id":"1253","model_name":"GES-23","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1481":{"protein_sequence":{"accession":"AGT20529.1","sequence":"MRFIHALLLAGIAHSAYASEKLTFKTDLEKLEREKAAQIGVAIVDPQGELVAGHRMAQRFAMCSTFKFPLAALVFERIDSGTERGDRKLSYGPDMIVEWSPATERFLASGHMTVLEAAQAAVQLSDNGATNLLLREIGGPAAMTQYFRKIGDSVSRLDRKEPEMGDNTPGDLRDTTTPIAMARTVAKVLYGGALTSTSTHTIERWLIGNQTGDATLRAGFPKDWVVGEKTGTCANGGRNDIGFFKAQERDYAVAVYTTAPKLSAVERDELVASVGQVITQLILSTDK"},"dna_sequence":{"accession":"KF179354.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGCTTCATCCACGCCCTGCTGCTGGCCGGCATCGCCCACAGCGCCTACGCCAGCGAGAAGCTGACCTTCAAGACCGACCTGGAGAAGCTGGAGCGCGAGAAGGCCGCCCAGATCGGCGTGGCCATCGTGGACCCGCAGGGCGAGCTGGTGGCCGGCCACCGCATGGCCCAGCGCTTCGCCATGTGCAGCACCTTCAAGTTCCCGCTGGCCGCCCTGGTGTTCGAGCGCATCGACAGCGGCACCGAGCGCGGCGACCGCAAGCTGAGCTACGGCCCGGACATGATCGTGGAGTGGAGCCCGGCCACCGAGCGCTTCCTGGCCAGCGGCCACATGACCGTGCTGGAGGCCGCCCAGGCCGCCGTGCAGCTGAGCGACAACGGCGCCACCAACCTGCTGCTGCGCGAGATCGGCGGCCCGGCCGCCATGACCCAGTACTTCCGCAAGATCGGCGACAGCGTGAGCCGCCTGGACCGCAAGGAGCCGGAGATGGGCGACAACACCCCGGGCGACCTGCGCGACACCACCACCCCGATCGCCATGGCCCGCACCGTGGCCAAGGTGCTGTACGGCGGCGCCCTGACCAGCACCAGCACCCACACCATCGAGCGCTGGCTGATCGGCAACCAGACCGGCGACGCCACCCTGCGCGCCGGCTTCCCGAAGGACTGGGTGGTGGGCGAGAAGACCGGCACCTGCGCCAACGGCGGCCGCAACGACATCGGCTTCTTCAAGGCCCAGGAGCGCGACTACGCCGTGGCCGTGTACACCACCGCCCCGAAGCTGAGCGCCGTGGAGCGCGACGAGCTGGTGGCCAGCGTGGGCCAGGTGATCACCCAGCTGATCCTGAGCACCGACAAG","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002352","ARO_id":"38752","ARO_name":"GES-23","CARD_short_name":"GES-23","ARO_description":"GES-23 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36205":{"category_aro_accession":"3000066","category_aro_cvterm_id":"36205","category_aro_name":"GES beta-lactamase","category_aro_description":"GES beta-lactamases or Guiana extended-spectrum beta-lactamases are related to the other plasmid-located class A beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1254":{"model_id":"1254","model_name":"CTX-M-46","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"768":{"protein_sequence":{"accession":"AAV97956.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTNAVQQKLAALEKSSGGRLGVPLIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"AY847147.1","fmin":"81","fmax":"957","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAATGCGGTGCAACAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCCCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGACTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001908","ARO_id":"38308","ARO_name":"CTX-M-46","CARD_short_name":"CTX-M-46","ARO_description":"CTX-M-46 is a beta-lactamase found in the Enterobacteriaceae family.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1255":{"model_id":"1255","model_name":"OXA-119","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1043":{"protein_sequence":{"accession":"AAN41427.1","sequence":"MAIRFLTILLSTFFLTSFVHAQEHVLERSDWKKFFSDLRAEGAIVISDERQAEHALLVFGQERAAKRYSPASTFKLPHTLFALDADAVRDEFQVFRWDGVKRSFAGHNQDQDLRSAMRNSAVWVYELFAKEIGEDKARRYLKQIDYGNADPSTIKGDYWIDGNLEISAHEQISFLRKLYRNQLPFQVEHQRLVKDLMITEAGRNWILRAKTGWEGRFGWWVGWVEWPTGPVFFALNIDTPNRTDDLFKREAIARAILRSIDALPPN"},"dna_sequence":{"accession":"AY139598.1","fmin":"1486","fmax":"2287","strand":"+","sequence":"ATGGCAATCCGATTCCTCACCATACTGCTATCTACTTTTTTTCTTACCTCATTCGTGCATGCGCAAGAACACGTGCTAGAGCGTTCTGACTGGAAGAAGTTCTTCAGCGACCTCCGGGCCGAAGGTGCAATCGTTATTTCAGACGAACGTCAAGCGGAGCATGCTTTATTGGTTTTTGGTCAAGAGCGAGCAGCAAAGCGTTACTCGCCTGCTTCAACCTTCAAGCTTCCACACACACTTTTTGCACTCGATGCAGACGCCGTTCGTGATGAGTTCCAGGTTTTTCGATGGGACGGCGTTAAACGGAGCTTTGCGGGCCATAATCAAGACCAAGACTTGCGATCAGCGATGCGAAATTCTGCGGTCTGGGTTTATGAGCTATTTGCAAAAGAGATCGGAGAGGACAAAGCAAGACGCTATTTAAAGCAAATTGATTATGGCAACGCCGACCCTTCGACAATCAAGGGCGATTACTGGATAGATGGCAATCTTGAAATCTCAGCGCACGAACAGATTTCGTTTCTCAGAAAACTCTATCGAAATCAGCTGCCATTTCAGGTGGAACATCAGCGCTTGGTCAAAGATCTCATGATTACGGAAGCCGGGCGCAATTGGATACTACGCGCAAAGACCGGCTGGGAAGGCAGGTTTGGCTGGTGGGTAGGGTGGGTGGAGTGGCCAACCGGTCCCGTATTCTTCGCGCTGAATATTGATACGCCAAACAGAACGGATGATCTTTTCAAAAGAGAGGCAATCGCGCGGGCAATCCTTCGCTCTATCGACGCATTGCCGCCCAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36791","NCBI_taxonomy_name":"uncultured bacterium","NCBI_taxonomy_id":"77133"}}}},"ARO_accession":"3001775","ARO_id":"38175","ARO_name":"OXA-119","CARD_short_name":"OXA-119","ARO_description":"OXA-119 is a beta-lactamase found in Enterobacteriaceae.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46509":{"category_aro_accession":"3007720","category_aro_cvterm_id":"46509","category_aro_name":"OXA-46-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-46.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1256":{"model_id":"1256","model_name":"bmr","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"86":{"protein_sequence":{"accession":"AAA22277.1","sequence":"MEKKNITLTILLTNLFIAFLGIGLVIPVTPTIMNELHLSGTAVGYMVACFAITQLIVSPIAGRWVDRFGRKIMIVIGLLFFSVSEFLFGIGKTVEMLFISRMLGGISAPFIMPGVTAFIADITTIKTRPKALGYMSAAISTGFIIGPGIGGFLAEVHSRLPFFFAAAFALLAAILSILTLREPERNPENQEIKGQKTGFKRIFAPMYFIAFLIILISSFGLASFESLFALFVDHKFGFTASDIAIMITGGAIVGAITQVVLFDRFTRWFGEIHLIRYSLILSTSLVFLLTTVHSYVAILLVTVTVFVGFDLMRPAVTTYLSKIAGNEQGFAGGMNSMFTSIGNVFGPIIGGMLFDIDVNYPFYFATVTLAIGIALTIAWKAPAHLKAST"},"dna_sequence":{"accession":"M33768.1","fmin":"194","fmax":"1364","strand":"+","sequence":"ATGGAGAAGAAAAATATTACCTTAACTATATTATTAACCAATTTATTTATTGCTTTTTTGGGGATCGGGCTTGTGATTCCAGTAACGCCGACCATTATGAATGAATTGCATTTATCGGGGACCGCGGTCGGCTATATGGTTGCCTGCTTCGCTATTACACAGCTCATTGTCTCACCAATAGCCGGACGATGGGTTGATCGCTTCGGGCGCAAGATCATGATCGTAATCGGCCTGTTGTTCTTTAGTGTGTCGGAGTTTTTGTTCGGCATTGGAAAAACAGTTGAGATGTTATTTATCTCCCGTATGCTGGGCGGTATCAGCGCACCGTTCATTATGCCCGGGGTCACGGCTTTTATTGCAGATATCACGACCATTAAAACACGGCCAAAAGCGCTCGGTTATATGTCAGCCGCTATTTCAACAGGATTTATTATCGGCCCCGGCATCGGGGGATTTTTAGCAGAAGTCCATTCCCGGCTGCCTTTTTTCTTTGCGGCAGCTTTTGCACTGTTAGCAGCCATTTTATCAATCCTCACGCTGCGCGAGCCGGAACGAAACCCTGAAAATCAGGAAATAAAAGGACAGAAGACAGGCTTTAAACGAATTTTTGCCCCCATGTATTTCATAGCTTTTCTCATTATCTTAATTTCGTCTTTTGGTTTAGCATCATTTGAATCTTTATTTGCATTATTCGTGGATCATAAATTCGGATTTACGGCCAGCGACATTGCCATTATGATTACAGGAGGAGCGATTGTTGGCGCCATTACGCAAGTCGTCTTATTCGACCGCTTCACAAGATGGTTTGGCGAAATTCATTTAATTCGGTACAGCTTAATTCTCTCGACGAGTCTGGTATTCTTGCTGACAACGGTACATTCATATGTTGCGATTCTGCTGGTGACAGTCACCGTATTTGTCGGATTTGATCTCATGCGGCCTGCGGTAACGACTTACCTGTCAAAGATTGCGGGAAATGAACAGGGGTTTGCCGGCGGTATGAATTCAATGTTTACAAGTATCGGCAATGTATTCGGGCCTATTATCGGCGGAATGCTGTTCGATATAGATGTAAACTATCCTTTCTACTTTGCAACGGTCACCTTAGCCATAGGGATTGCACTGACCATTGCTTGGAAAGCGCCTGCACATCTTAAAGCCAGCACGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36833","NCBI_taxonomy_name":"Bacillus subtilis","NCBI_taxonomy_id":"1423"}}}},"ARO_accession":"3003007","ARO_id":"39441","ARO_name":"bmr","CARD_short_name":"bmr","ARO_description":"bmr is an MFS antibiotic efflux pump that confers resistance to multiple drugs including acridine dyes, fluoroquinolone antibiotics, chloramphenicol, and puromycin.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35963":{"category_aro_accession":"0000045","category_aro_cvterm_id":"35963","category_aro_name":"acriflavine","category_aro_description":"Acriflavine is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish.","category_aro_class_name":"Antibiotic"},"35965":{"category_aro_accession":"0000047","category_aro_cvterm_id":"35965","category_aro_name":"puromycin","category_aro_description":"Puromycin is an aminonucleoside antibiotic, derived from Streptomyces alboniger, that causes premature chain termination during ribosomal protein translation.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36174":{"category_aro_accession":"3000034","category_aro_cvterm_id":"36174","category_aro_name":"nucleoside antibiotic","category_aro_description":"Nucleoside antibiotics are made of modified nucleosides and nucleotides with wide-ranging activities and means of antibacterial effects. This drug class includes aminonucleoside antibiotics, which contain an amino group.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"43746":{"category_aro_accession":"3005386","category_aro_cvterm_id":"43746","category_aro_name":"disinfecting agents and antiseptics","category_aro_description":"Disinfectants that can also interact with antimicrobial resistance mechanisms, e.g. molecule efflux, and thus are the targets of disinfectant resistance.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1257":{"model_id":"1257","model_name":"QnrB68","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"236":{"protein_sequence":{"accession":"AGL43629.1","sequence":"MTLALVGEKIDRNRFTGEKVENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNVSALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGTQVMGATFSGSDLSGGEFSTFDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDNYQASLLMERLGIAVIG"},"dna_sequence":{"accession":"KC580657.1","fmin":"0","fmax":"645","strand":"+","sequence":"ATGACTCTGGCATTAGTTGGCGAAAAAATTGACAGAAATCGCTTCACCGGTGAGAAAGTTGAAAATAGTACATTTTTTAACTGCGATTTTTCAGGTGCCGACCTGAGCGGCACTGAATTTATCGGCTGCCAGTTCTATGATCGCGAAAGTCAGAAAGGATGCAATTTTAGTCGCGCAATGCTGAAAGATGCCATTTTCAAAAGCTGTGATTTATCAATGGCAGATTTCCGCAACGTCAGCGCATTGGGCATTGAAATTCGCCACTGCCGCGCACAAGGCGCAGATTTCCGCGGTGCAAGCTTTATGAATATGATCACCACGCGCACCTGGTTTTGCAGCGCATATATCACTAATACCAATCTAAGCTACGCCAATTTTTCGAAAGTCGTGTTGGAAAAGTGTGAGCTATGGGAAAACCGCTGGATGGGGACTCAGGTAATGGGTGCGACGTTTAGTGGTTCAGATCTCTCCGGTGGCGAGTTTTCGACTTTCGACTGGCGAGCAGCAAACTTCACACATTGCGATCTGACCAATTCGGAGTTAGGTGACTTAGATATTCGGGGTGTTGATTTACAAGGCGTTAAGTTAGACAACTACCAGGCATCGTTGCTCATGGAGCGGCTTGGCATCGCTGTGATTGGTTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39584","NCBI_taxonomy_name":"Citrobacter braakii","NCBI_taxonomy_id":"57706"}}}},"ARO_accession":"3002780","ARO_id":"39214","ARO_name":"QnrB68","CARD_short_name":"QnrB68","ARO_description":"QnrB68 is a plasmid-mediated quinolone resistance protein found in Citrobacter braakii.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1258":{"model_id":"1258","model_name":"OXA-55","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"979":{"protein_sequence":{"accession":"AAR03105.1","sequence":"MNKGLHRKRLSKRLLLPMLLCLLAQQTQAVAAEQTKVSDVCSEVTAEGWQEVRRWDKLFESAGVKGSLLLWDQKRSLGLSNNLSRAAEGFIPASTFKLPSSLIALETGAVRDETSRFSWDGKVREIAVWNRDQSFRTAMKYSVVPVYQQLAREIGPKVMAAMVRQLEYGNQDIGGQADSFWLDGQLRITAFQQVDFLRQLHDNKLPVSERSQRIVKQMMLTEASTDYIIRAKTGYGVRRTPAIGWWVGWLELDDNTVYFAVNLDLASASQLPLRQQLVKQVLKQEQLLP"},"dna_sequence":{"accession":"AY343493.1","fmin":"76","fmax":"946","strand":"+","sequence":"ATGAATAAAGGTTTGCACAGAAAGCGCCTGAGTAAGCGTTTGCTGCTGCCCATGTTGCTGTGTTTATTGGCTCAACAAACGCAGGCTGTGGCAGCTGAGCAGACCAAGGTCAGTGACGTCTGCTCTGAGGTCACGGCTGAGGGTTGGCAAGAGGTACGCCGCTGGGACAAGCTGTTCGAATCCGCAGGAGTTAAAGGCAGTTTGCTGCTTTGGGATCAAAAGCGTTCTTTGGGGCTCTCCAACAATCTAAGTCGCGCCGCCGAAGGCTTTATTCCGGCTTCCACCTTCAAGCTCCCCTCCAGCCTTATTGCGTTGGAAACCGGGGCGGTGCGCGATGAAACCAGTCGTTTTAGCTGGGACGGAAAGGTTCGCGAAATTGCCGTCTGGAACAGGGACCAGAGTTTTCGCACCGCAATGAAGTACTCTGTGGTGCCTGTATATCAGCAGTTGGCCAGGGAGATAGGCCCCAAAGTGATGGCAGCTATGGTGCGGCAGCTGGAATATGGCAATCAGGATATCGGTGGCCAAGCGGACAGCTTCTGGCTCGACGGCCAACTGAGAATTACAGCATTTCAACAAGTGGATTTTCTAAGGCAACTGCATGACAACAAGTTGCCTGTGTCCGAGCGCAGCCAGCGAATTGTCAAACAGATGATGCTGACCGAAGCGAGTACTGACTATATTATTCGCGCCAAGACAGGCTATGGTGTGCGGCGTACGCCGGCCATAGGTTGGTGGGTCGGTTGGTTGGAGTTGGACGACAACACTGTCTATTTCGCCGTTAACCTGGATCTGGCCTCGGCCAGCCAGTTACCGTTGCGCCAACAACTGGTGAAACAGGTGCTCAAGCAGGAACAGCTGCTGCCTTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36891","NCBI_taxonomy_name":"Shewanella algae","NCBI_taxonomy_id":"38313"}}}},"ARO_accession":"3001813","ARO_id":"38213","ARO_name":"OXA-55","CARD_short_name":"OXA-55","ARO_description":"OXA-55 is a beta-lactamase found in Shewanella spp.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46516":{"category_aro_accession":"3007727","category_aro_cvterm_id":"46516","category_aro_name":"OXA-55-like beta-lactamase","category_aro_description":"A subfamily of carbapanem-hydrolyzing class D OXA beta-lactamases derived from OXA-55.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1259":{"model_id":"1259","model_name":"SHV-31","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"8197":{"protein_sequence":{"accession":"AAP33454.2","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGKRGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AY277255.2","fmin":"66","fmax":"927","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCAAACGGGGTGCGCGCGGCATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001089","ARO_id":"37469","ARO_name":"SHV-31","CARD_short_name":"SHV-31","ARO_description":"SHV-31 is an extended-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1260":{"model_id":"1260","model_name":"APH(3')-IVa","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"237":{"protein_sequence":{"accession":"CAA27061.1","sequence":"MNESTRNWPEELLELLGQTELTVNKIGYSGDHVYHVKEYRGTPAFLKIAPSVWWRTLRPEIEALAWLDGKLPVPKILYTAEHGGMDYLLMEALGGKDGSHETIQAKRKLFVKLYAEGLRSVHGLDIRECPLSNGLEKKLRDAKRIVDESLVDPADIKEEYDCTPEELYGLLLESKPVTEDLVFAHGDYCAPNLIIDGEKLSGFIDLGRAGVADRYQDISLAIRSLRHDYGDDRYKALFLELYGLDGLDEDKVRYYIRLDEFF"},"dna_sequence":{"accession":"X03364.1","fmin":"0","fmax":"789","strand":"+","sequence":"ATGAACGAAAGTACGCGTAATTGGCCGGAGGAACTTCTTGAGCTTCTCGGGCAGACGGAACTAACCGTCAACAAAATCGGATATTCCGGAGATCACGTCTATCACGTGAAAGAGTACAGGGGCACCCCCGCATTTCTGAAAATCGCCCCCAGTGTATGGTGGAGAACGCTCCGGCCCGAAATTGAAGCGCTCGCTTGGCTGGACGGGAAGCTCCCGGTTCCCAAAATTTTGTACACGGCCGAACACGGCGGGATGGACTACTTGCTGATGGAGGCGCTAGGCGGAAAAGACGGCTCCCACGAAACGATCCAGGCGAAGCGGAAACTGTTTGTGAAGCTGTACGCGGAAGGGCTCCGAAGCGTGCATGGCCTCGATATCCGCGAATGTCCGCTGTCGAACGGGCTGGAGAAGAAGCTCCGGGATGCGAAAAGAATAGTCGATGAGAGCCTGGTGGACCCGGCCGATATAAAAGAGGAGTACGATTGCACGCCGGAGGAATTGTACGGGCTATTGCTTGAGAGTAAGCCGGTAACCGAAGATCTGGTTTTTGCGCACGGAGATTACTGTGCTCCGAATCTGATTATCGACGGTGAGAAGCTGTCGGGATTTATCGATCTCGGACGTGCGGGCGTGGCGGACCGTTATCAGGACATCAGCCTGGCGATCCGCAGCCTCCGGCACGATTACGGCGACGACCGCTACAAAGCGCTCTTCCTGGAACTTTACGGGCTGGACGGGCTTGACGAGGACAAGGTCCGGTATTACATCCGGCTGGATGAATTTTTTTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36858","NCBI_taxonomy_name":"Niallia circulans","NCBI_taxonomy_id":"1397"}}}},"ARO_accession":"3002648","ARO_id":"39048","ARO_name":"APH(3')-IVa","CARD_short_name":"APH(3')-IVa","ARO_description":"APH(3')-IVa is a chromosomal-encoded aminoglycoside phosphotransferase in Niallia circulans.","ARO_category":{"36265":{"category_aro_accession":"3000126","category_aro_cvterm_id":"36265","category_aro_name":"APH(3')","category_aro_description":"A category of aminoglycoside O-phosphotransferase enzymes with modification regiospecificity based at the 3'-hydroxyl group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics, specifically kanamycin and neomycin, by the ATP-dependent phosphorylation of the 3'-hydroxyl group of the compound.","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35940":{"category_aro_accession":"0000021","category_aro_cvterm_id":"35940","category_aro_name":"ribostamycin","category_aro_description":"Ribostamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Ribostamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35943":{"category_aro_accession":"0000024","category_aro_cvterm_id":"35943","category_aro_name":"butirosin","category_aro_description":"Butirosin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Butirosin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"37001":{"category_aro_accession":"3000657","category_aro_cvterm_id":"37001","category_aro_name":"paromomycin","category_aro_description":"An aminoglycoside antibiotic used for the treatment of parasitic infections. It is similar to neomycin sharing a similar spectrum of activity, but its hydroxyl group at the 6'-position instead of an amino group makes it resistant to AAC(6') modifying enzymes.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1261":{"model_id":"1261","model_name":"rosA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"770"}},"model_sequences":{"sequence":{"4717":{"protein_sequence":{"accession":"AAC60781.1","sequence":"MTDRSETELPPSVNTQPFDNTKVKRTSFSILGAISVSHLLNDMIQSLILAIYPLLQAEFSLSFAQIGLITLTYQLTASLLQPLIGLYTDKHPQPYSLPIGMGFTLSGILLLAVATTFPGGFTWHAALVGTGSSVFHPESSRVAARLPVAATVWLSLFLGGRQFRQRLGPLLAAILIAPYGKGNVGWFSLAALLAIVVLLQVSKWYQQQQRATYGKVVKVSSAKILPKKTVISALAILMVLIFSKYFYLTSISSYYTFYLMHKFGVSVQNAQIHLFVFLFAVAAGTIIGGPLGDRIGRKYVIWGSILGVAPFTLILPYVSLYWTGVLTVIIGLILASAFSAILVYAQELIPGKVGMVSGLFFGFAFGMGGLGAAVLGYVADLTSIELVYQICAFLPLLGIITVFLPNIEDK"},"dna_sequence":{"accession":"U46859.1","fmin":"24294","fmax":"25527","strand":"-","sequence":"ATGACCGATCGTTCTGAGACGGAGCTCCCTCCCTCCGTCAATACCCAGCCCTTCGATAATACCAAGGTAAAACGCACCTCTTTCTCTATATTAGGTGCTATTAGCGTATCTCACTTACTTAACGATATGATCCAGTCGCTGATTCTGGCGATTTATCCGCTATTACAAGCCGAGTTTTCGCTGAGTTTTGCGCAGATTGGATTAATCACCCTCACTTATCAGCTTACCGCCTCATTATTACAGCCACTTATTGGTCTTTATACCGATAAGCATCCGCAGCCCTATTCACTGCCGATTGGCATGGGTTTCACCTTATCAGGTATCTTGCTGCTTGCGGTTGCCACGACTTTCCCAGGTGGTTTTACATGGCATGCGGCATTAGTCGGAACCGGTTCTTCGGTCTTCCACCCAGAATCCTCACGCGTAGCCGCTAGGCTACCGGTGGCCGCCACGGTATGGCTCAGTCTATTTTTGGGTGGGAGGCAATTTCGGCAGCGCCTTGGCCCACTATTAGCCGCGATCCTTATCGCACCTTACGGTAAAGGCAATGTAGGTTGGTTTTCACTCGCGGCACTGCTGGCTATTGTGGTGCTGTTGCAGGTCAGTAAATGGTATCAGCAACAACAAAGAGCAACCTATGGCAAAGTAGTAAAAGTCTCATCGGCCAAAATACTGCCTAAAAAGACGGTTATTAGCGCCCTAGCTATCTTAATGGTGCTGATATTCTCTAAATACTTCTACTTGACCAGTATTAGTAGCTATTACACCTTTTATTTGATGCATAAGTTTGGTGTTTCGGTACAAAATGCCCAAATACATTTATTTGTCTTCTTATTCGCAGTGGCCGCTGGCACCATCATTGGCGGCCCTCTTGGCGATAGGATAGGTCGAAAGTATGTTATTTGGGGGTCAATATTGGGCGTTGCGCCATTTACCCTTATTTTACCCTACGTTTCTCTGTATTGGACCGGGGTTTTAACCGTGATCATTGGCCTTATCCTTGCCTCTGCCTTCTCGGCAATACTGGTGTATGCGCAAGAGCTTATTCCGGGTAAAGTGGGCATGGTATCCGGTCTATTCTTCGGTTTTGCTTTCGGTATGGGGGGGTTAGGTGCGGCTGTACTAGGGTATGTTGCTGATTTAACCAGTATTGAACTGGTTTATCAAATATGCGCCTTCTTACCATTACTGGGGATAATTACGGTCTTCCTGCCCAATATAGAAGATAAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39589","NCBI_taxonomy_name":"Yersinia enterocolitica (type O:8)","NCBI_taxonomy_id":"34054"}}}},"ARO_accession":"3003048","ARO_id":"39482","ARO_name":"rosA","CARD_short_name":"rosA","ARO_description":"rosA is part of an efflux pump\/potassium antiporter system (RosAB) in Yersinia that confers resistance to cationic antimicrobial peptides such as polymyxin B.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"36593":{"category_aro_accession":"3000454","category_aro_cvterm_id":"36593","category_aro_name":"polymyxin B","category_aro_description":"Polymyxin B is mixture of mostly polymyxins B1 and B2, mainly used for resistant gram-negative infections. They are polypeptides with cationic detergent action on cell membranes.","category_aro_class_name":"Antibiotic"},"36969":{"category_aro_accession":"3000625","category_aro_cvterm_id":"36969","category_aro_name":"polymyxin B1","category_aro_description":"Polymyxin B1 is in the family of polymyxin lipopeptides with a 6-methyloctanoic acid acyl group. These antibiotics disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36970":{"category_aro_accession":"3000626","category_aro_cvterm_id":"36970","category_aro_name":"polymyxin B2","category_aro_description":"Polymyxin B2 is in the family of polymyxin lipopeptides with a 6-methylheptanoic acid acyl group. These antibiotics disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36971":{"category_aro_accession":"3000627","category_aro_cvterm_id":"36971","category_aro_name":"polymyxin B3","category_aro_description":"Polymyxin B3 is in the family of polymyxin lipopeptides with an octanoic acid acyl group. These antibiotics disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36972":{"category_aro_accession":"3000628","category_aro_cvterm_id":"36972","category_aro_name":"polymyxin B4","category_aro_description":"Polymyxin B4 is in the family of polymyxin lipopeptides with a heptanoic acid acyl group. These antibiotics disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1262":{"model_id":"1262","model_name":"SHV-149","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"915":{"protein_sequence":{"accession":"AFQ23955.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESRLSGSVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTASLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"JX121116.1","fmin":"0","fmax":"858","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCGGCTGTCGGGCAGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTCTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGCATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGC","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001188","ARO_id":"37568","ARO_name":"SHV-149","CARD_short_name":"SHV-149","ARO_description":"SHV-149 is a beta-lactamase.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1263":{"model_id":"1263","model_name":"QnrB56","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"425":{"protein_sequence":{"accession":"AFR46587.1","sequence":"MTPLLYKNTGIDMTLALVGEKIDRNRFTGEKVENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNVSALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGTQVLGATFSGSDLSGGEFSTFDWRAGNFTHCDLTNSELGDLDIRGVDLQGVKLDSYQASLLMERLGIAIIG"},"dna_sequence":{"accession":"JX259317.1","fmin":"0","fmax":"681","strand":"+","sequence":"ATGACGCCATTACTGTATAAAAACACAGGCATAGATATGACTCTGGCATTAGTTGGCGAAAAAATTGACAGAAACCGCTTCACCGGTGAGAAAGTTGAAAATAGTACATTTTTTAACTGCGATTTTTCAGGTGCCGACCTGAGCGGCACTGAATTTATCGGCTGCCAGTTCTATGATCGCGAAAGTCAGAAAGGGTGCAATTTTAGTCGCGCAATGCTGAAAGATGCCATTTTCAAAAGCTGTGATTTATCAATGGCAGATTTCCGCAACGTCAGCGCATTGGGCATTGAAATTCGCCACTGCCGCGCACAAGGCGCAGATTTTCGCGGTGCAAGCTTTATGAATATGATCACCACGCGTACCTGGTTTTGCAGCGCATATATCACTAATACCAATCTAAGCTACGCCAATTTTTCGAAAGTCGTGTTGGAAAAGTGTGAGCTATGGGAAAACCGCTGGATGGGGACTCAGGTACTGGGTGCGACGTTCAGTGGTTCAGATCTCTCCGGCGGCGAGTTTTCGACTTTCGACTGGCGAGCAGGAAACTTCACACATTGCGATCTGACCAATTCGGAGTTAGGTGACTTAGATATTCGGGGTGTTGATTTACAAGGCGTTAAGTTAGACAGCTACCAGGCATCGTTGCTCATGGAGCGGCTTGGCATCGCGATTATTGGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002769","ARO_id":"39203","ARO_name":"QnrB56","CARD_short_name":"QnrB56","ARO_description":"QnrB56 is a plasmid-mediated quinolone resistance protein found in Citrobacter freundii.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1264":{"model_id":"1264","model_name":"smeC","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"900"}},"model_sequences":{"sequence":{"155":{"protein_sequence":{"accession":"AAD51346.1","sequence":"MKPMLLRALAAATMTTVLGGCVSMAPHYQRPEAPVPAQFGNAAIGAAEPALAMPAWRDVFLEPRLQQVIALALQNNRDLRVAVLQVEKERAQYRIQRAALLPSVDASGSVTRSRVSDANSETGVTQVTESDAVQVGISSWELDLFGRIRSLKNEALQNWLASAENQRAVRTSLVAEVATAWLALAADEQSLAFTQQTLDSQHQTLQRTEARHAQGLASGLDLSQVQTSVEAARGALAKLQAQQAQDRDALQLLVGAPLDPALLPTAQALDGSVALAPLPANLPSSVLLQRPDVLSAEHALQAANADIGAARAAFFPTLALTANYGHSSTALSTLFSAGTRGWSFAPSITAPIFHAGALKASLDASKIGKDIGIAQYEKAIQQAFSEVADALATRDHLTAQLDAQRALVADSQRSYTLADARYRTGLDGYLQSLDAQRSLYAAQQDLIALQQQEAGNRVTLFKVLGGGADAR"},"dna_sequence":{"accession":"AF173226.1","fmin":"6913","fmax":"8329","strand":"+","sequence":"ATGAAGCCGATGCTGCTGCGCGCCCTGGCGGCCGCAACGATGACCACCGTGCTGGGCGGCTGCGTGAGCATGGCCCCGCACTACCAGCGTCCCGAGGCACCGGTGCCGGCGCAGTTCGGCAATGCTGCCATCGGCGCGGCCGAACCGGCACTGGCGATGCCGGCCTGGCGCGACGTGTTCCTGGAACCGCGCCTGCAGCAGGTCATCGCGCTGGCGCTGCAGAACAACCGCGATCTGCGCGTGGCGGTGCTGCAGGTGGAGAAGGAGCGCGCGCAGTACCGCATCCAGCGCGCGGCACTGCTGCCGTCGGTGGATGCCAGCGGCAGTGTCACCCGTTCGCGGGTGAGCGATGCCAACAGCGAGACCGGCGTCACCCAGGTGACCGAATCCGATGCCGTGCAGGTGGGCATCAGCAGCTGGGAGCTGGACCTGTTCGGGCGTATCCGCAGCTTGAAGAACGAGGCGCTGCAGAACTGGCTGGCCAGCGCCGAGAACCAGCGCGCCGTGCGCACCAGCCTGGTGGCTGAAGTGGCGACGGCGTGGCTGGCGCTGGCGGCCGACGAGCAGTCGCTGGCATTCACGCAACAGACGCTGGACAGCCAGCACCAGACCCTGCAGCGCACCGAGGCCCGCCATGCACAGGGGCTGGCCTCGGGCCTGGACCTGTCGCAGGTGCAGACCAGCGTGGAAGCCGCGCGCGGGGCGCTGGCGAAGCTGCAGGCCCAGCAGGCGCAGGATCGCGATGCATTGCAGCTGTTGGTGGGGGCACCGCTGGATCCGGCCCTGCTGCCAACCGCGCAGGCGCTGGATGGCAGCGTCGCATTGGCGCCGCTGCCCGCCAACCTGCCGTCCAGCGTGTTGCTGCAGCGCCCGGACGTGCTGTCCGCCGAGCATGCATTGCAGGCAGCCAACGCCGATATCGGTGCCGCGCGCGCCGCATTCTTTCCGACGCTGGCGTTGACCGCCAACTACGGCCACAGTTCCACCGCGTTGTCGACGCTGTTCTCGGCCGGCACCCGTGGCTGGTCGTTCGCGCCCAGCATCACCGCGCCGATCTTCCATGCCGGTGCACTGAAGGCCTCGCTGGATGCCTCGAAGATCGGCAAGGACATCGGCATCGCGCAGTACGAGAAGGCGATCCAGCAGGCCTTCAGTGAGGTGGCCGATGCGCTGGCCACGCGCGATCACCTGACCGCGCAGCTGGACGCGCAACGCGCGTTGGTGGCTGACAGCCAGCGCAGCTACACCTTGGCCGATGCGCGCTACCGCACCGGACTGGATGGCTACCTGCAGTCGTTGGATGCGCAGCGCAGCCTGTATGCCGCGCAGCAGGACCTGATCGCCCTGCAGCAGCAGGAGGCGGGCAACCGGGTGACGTTGTTCAAGGTGCTGGGTGGTGGCGCGGACGCGCGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37076","NCBI_taxonomy_name":"Stenotrophomonas maltophilia","NCBI_taxonomy_id":"40324"}}}},"ARO_accession":"3003053","ARO_id":"39487","ARO_name":"smeC","CARD_short_name":"smeC","ARO_description":"smeC is an outer membrane multidrug efflux protein of the smeABC complex in Stenotrophomonas maltophilia.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1265":{"model_id":"1265","model_name":"MIR-4","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"8148":{"protein_sequence":{"accession":"ABN69112.2","sequence":"MMTKSLSCALLLSVASAAFAAPMFEKQLAEVVERTVTPLMNAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEIALGDPVAKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDTASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMSYEQAMTTRVFKPLKLDHTWINVPKAEEAHYAWGYREGKAVHVSPGMLDAEAYGVKTNVKDMASWLIANMKPDSLHAPSLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVGGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILDALQ"},"dna_sequence":{"accession":"EF417572.2","fmin":"29","fmax":"1175","strand":"+","sequence":"ATGATGACAAAATCCCTAAGCTGTGCCCTGCTGCTCAGCGTCGCCAGCGCTGCATTCGCCGCACCGATGTTCGAAAAACAGCTGGCTGAGGTGGTGGAACGTACCGTTACGCCGCTGATGAACGCGCAGGCCATTCCGGGTATGGCGGTGGCGGTAATTTATCAGGGTCAGCCACACTACTTTACCTTCGGTAAAGCCGATGTTGCGGCGAACAAACCCGTCACCCCGCAAACCCTGTTTGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTACTGGGCGGCGATGCCATTGCCCGGGGTGAAATAGCGCTGGGCGATCCGGTAGCAAAATACTGGCCTGAGCTCACGGGCAAGCAGTGGCAGGGCATTCGCATGCTGGATCTGGCAACCTATACCGCAGGCGGTCTGCCGTTACAGGTGCCGGATGAGGTCACGGATACCGCCTCTCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCGGGCACCACGCGTCTTTACGCTAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTCAAACCTTCCGGCATGAGCTATGAGCAGGCCATGACGACGCGGGTCTTTAAACCCCTCAAGCTGGACCATACCTGGATTAACGTCCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGATACCGTGAGGGTAAAGCGGTCCACGTTTCGCCAGGGATGCTGGACGCGGAAGCCTATGGCGTAAAAACTAACGTGAAGGATATGGCGAGCTGGCTGATAGCCAACATGAAGCCGGATTCTCTTCACGCTCCCTCACTCAAGCAAGGCATTGCTCTGGCGCAGTCTCGCTACTGGCGCGTGGGTGCTATGTATCAGGGGTTAGGCTGGGAGATGCTCAACTGGCCGGTCGATGCCAAAACCGTCGTCGGAGGCAGTGATAACAAGGTGGCGCTGGCACCATTGCCCGTGGCAGAAGTGAATCCACCCGCGCCGCCGGTCAAAGCCTCCTGGGTCCATAAAACAGGCTCGACGGGCGGGTTTGGCAGCTACGTGGCATTTATTCCTGAAAAGCAGCTAGGCATTGTGATGCTGGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCGTATCCTCGACGCGCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002167","ARO_id":"38567","ARO_name":"MIR-4","CARD_short_name":"MIR-4","ARO_description":"MIR-4 is a beta-lactamase found in Escherichia coli.","ARO_category":{"36197":{"category_aro_accession":"3000058","category_aro_cvterm_id":"36197","category_aro_name":"MIR beta-lactamase","category_aro_description":"MIR beta-lactamases are plasmid-mediated beta-lactamases that confer resistance to oxyimino- and alpha-methoxy beta-lactams.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1266":{"model_id":"1266","model_name":"ANT(4')-IIa","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"190":{"protein_sequence":{"accession":"AAA25717.1","sequence":"MHLTITYWIDRLREAYPHAVAILLKGSYARGEASAWSDIDFDVLVSDEEVEEYRTWIEPVGERLVHISVAVEWVTGWERDSADPSSWSYGLPTQETTQLLWAADENIRRRLDRPFKVHPAAEPEVEDTVEALGKIRNAMVRGDDLAVYQAAQVVGKLIPTLLVPINPPTYARFAREAIDRILAFPNVPEGFAADWLTCMGLVDRRTHDPQPTRPNEWCAARSRFCRRMRTSSVRISRGCWKQDWYLRISART"},"dna_sequence":{"accession":"M98270.1","fmin":"0","fmax":"759","strand":"+","sequence":"ATGCACCTCACCATTACCTACTGGATCGATCGTCTGCGAGAAGCGTATCCCCATGCGGTCGCGATTTTGCTGAAGGGAAGCTATGCCCGGGGCGAGGCGAGTGCGTGGAGCGATATCGATTTCGATGTGCTCGTGAGCGACGAGGAAGTGGAGGAGTATCGCACCTGGATCGAGCCTGTGGGCGAGCGGCTGGTGCATATCTCGGTCGCGGTGGAGTGGGTCACCGGGTGGGAGCGCGATTCGGCAGATCCATCGAGTTGGAGTTATGGCCTGCCTACGCAGGAGACCACCCAGCTGCTTTGGGCAGCTGATGAGAATATTCGCCGACGTCTCGATCGACCGTTCAAGGTGCATCCGGCCGCCGAACCAGAGGTGGAAGACACGGTAGAAGCGCTCGGGAAGATCCGGAATGCGATGGTTCGGGGTGACGACCTTGCGGTCTATCAAGCTGCGCAGGTCGTGGGGAAATTGATTCCGACACTCCTGGTTCCCATCAATCCGCCCACGTACGCACGGTTCGCACGCGAGGCGATCGACAGGATTCTCGCCTTCCCGAATGTACCCGAAGGGTTCGCGGCCGATTGGCTGACGTGCATGGGTCTGGTCGATCGGCGGACGCACGATCCACAGCCGACGCGGCCGAACGAATGGTGCGCGGCACGATCTCGCTTCTGCCGGCGGATGCGGACATCGTCGGTGAGGATATCGCGCGGTTGCTGGAAGCAGGATTGGTACTTGCGTATATCGGCCAGAACGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002624","ARO_id":"39024","ARO_name":"ANT(4')-IIa","CARD_short_name":"ANT(4')-IIa","ARO_description":"ANT(4')-IIa is a plasmid-encoded aminoglycoside nucleotidyltransferase in P. aeruginosa and Enterobacteriaceae.","ARO_category":{"36368":{"category_aro_accession":"3000229","category_aro_cvterm_id":"36368","category_aro_name":"ANT(4')","category_aro_description":"A category of aminoglycoside O-nucleotidyltransferase enzymes with modification regiospecificity based at the 4'-hydroxyl group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics by transfer of an AMP group from an ATP substrate to the 4-hydroxyl group of the compound.","category_aro_class_name":"AMR Gene Family"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1267":{"model_id":"1267","model_name":"QnrB40","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"6131":{"protein_sequence":{"accession":"WP_063866081.1","sequence":"MTLALVGEKIDRNRFTGEKVENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLRDAIFKSCDLSMADFRNVSALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGTQVLGTTFSGSDLSGGEFSTFDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDNYQASLLMERLGIAVIG"},"dna_sequence":{"accession":"NG_050503.1","fmin":"15","fmax":"660","strand":"+","sequence":"ATGACTCTGGCATTAGTTGGCGAAAAAATTGACAGAAATCGCTTCACTGGTGAGAAAGTTGAAAATAGTACATTTTTTAACTGCGATTTTTCAGGTGCCGACCTGAGCGGCACTGAATTTATCGGCTGCCAGTTCTATGATCGCGAAAGTCAGAAAGGATGCAATTTTAGTCGCGCAATGCTGAGAGATGCCATTTTCAAAAGCTGTGATTTATCAATGGCAGATTTCCGCAACGTCAGCGCATTGGGCATTGAAATTCGCCACTGCCGCGCACAAGGCGCAGATTTCCGCGGTGCAAGCTTTATGAATATGATCACCACGCGCACCTGGTTTTGCAGCGCATATATCACTAATACCAATCTAAGCTACGCCAATTTTTCGAAAGTCGTGTTGGAAAAGTGTGAGCTATGGGAAAACCGCTGGATGGGGACTCAGGTACTGGGTACGACGTTCAGTGGTTCAGATCTCTCCGGCGGCGAGTTTTCGACTTTCGACTGGCGAGCAGCAAACTTCACACATTGCGATCTGACCAATTCGGAGTTAGGTGACTTAGATATTCGGGGTGTTGATTTACAAGGCGTTAAGTTAGACAACTACCAGGCATCGTTGCTCATGGAGCGGCTTGGCATCGCTGTGATTGGTTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39584","NCBI_taxonomy_name":"Citrobacter braakii","NCBI_taxonomy_id":"57706"}}}},"ARO_accession":"3002755","ARO_id":"39189","ARO_name":"QnrB40","CARD_short_name":"QnrB40","ARO_description":"QnrB40 is a plasmid-mediated quinolone resistance protein found in Citrobacter braakii.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1268":{"model_id":"1268","model_name":"CMY-115","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1020":{"protein_sequence":{"accession":"AIT76092.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAIIYKGKPYYFTWGKADIANNHPVTQHTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWRGISLLHLATYTAGGLPLQIPDDITDKAALLRFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQSEQKNYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMAHWVQANMDASHVQEKTLQQGIELAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPARVEAAWRILEKLQ"},"dna_sequence":{"accession":"KM087839.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCACTGCTGCTGACAGCCTCTTTCTCCACGTTTGCTGCCGCAAAAACAGAACAACAAATTGCCGATATCGTTAACCGCACCATCACACCACTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTGGCGATTATCTACAAGGGGAAACCTTATTACTTTACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCATACGCTGTTTGAGCTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGACGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCGGGGTATCAGCCTGCTGCACTTAGCCACCTATACAGCGGGTGGCCTGCCGCTGCAGATCCCCGATGACATTACGGATAAAGCCGCATTACTGCGCTTTTATCAAAACTGGCAACCACAATGGACTCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGTGCGCTGGCGGTGAAACCTTCAGGTATGAGCTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAAAGCGAACAAAAAAACTATGCCTGGGGCTATCGCGAAGGGAAGCCTGTGCACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATCGATATGGCCCACTGGGTTCAGGCCAACATGGACGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGAGCTTGCGCAGTCTCGCTACTGGCGTATTGGTGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCAGCACCTGCCGTGAAAGCCTCATGGGTGCATAAAACAGGATCCACAGGCGGATTTGGCAGCTACGTTGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTAATGTTGGCAAACAAAAGCTATCCCAACCCGGCTCGCGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002126","ARO_id":"38526","ARO_name":"CMY-115","CARD_short_name":"CMY-115","ARO_description":"CMY-115 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1269":{"model_id":"1269","model_name":"OXA-192","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1756":{"protein_sequence":{"accession":"ADZ54048.1","sequence":"MSKKNFILIFIFVILISCKNTEKTSNETTLIDNIFTNSNAEGTLVIYNLNDDKYIIHNKERAEQRFYPASTFKIYNSLIGLNEKAVKDVDEVFYKYNGEKVFLESWAKDSNLRYAIKNSQVPAYKELARRIGLEKMKENIEKLDFGNKNIGDSVDTFWLEGPLEISAMEQVKLLTKLAQNELPYPIEIQKAVSDITILEQTDNYTLHGKTGLADSENMTTEPIGWLVGWLEENNNIYVFALNIDNINSDDLAKRINIVKESLKALNLLK"},"dna_sequence":{"accession":"JF273470.1","fmin":"0","fmax":"810","strand":"+","sequence":"ATGTCTAAAAAAAATTTTATATTAATATTTATTTTTGTTATTTTAATATCTTGTAAAAATACAGAAAAAACATCAAATGAAACTACATTAATAGATAATATATTTACTAATAGCAATGCTGAAGGAACATTAGTTATATATAATTTAAATGATGATAAATACATAATTCATAATAAAGAAAGAGCTGAACAAAGATTTTATCCAGCATCAACATTTAAAATATATAATAGTTTAATAGGCTTAAATGAAAAAGCAGTTAAAGATGTAGATGAAGTATTTTATAAATATAATGGCGAAAAAGTTTTTCTTGAATCTTGGGCTAAGGACTCTAATTTAAGATATGCAATTAAAAATTCACAAGTACCGGCATATAAAGAATTAGCAAGAAGAATAGGGCTTGAAAAGATGAAAGAGAATATAGAAAAACTAGATTTTGGTAATAAAAATATAGGTGATAGTGTAGATACTTTTTGGCTTGAAGGACCTTTGGAAATAAGTGCGATGGAGCAAGTTAAATTATTAACTAAATTAGCTCAAAATGAATTGCCGTATCCTATAGAAATACAAAAAGCTGTTTCTGATATTACTATACTAGAGCAAACTGACAATTATACGCTTCATGGAAAAACTGGATTAGCTGATTCTGAAAACATGACAACTGAGCCTATTGGTTGGTTAGTAGGCTGGCTTGAAGAAAATAATAATATATACGTCTTTGCTTTAAATATTGATAATATCAATTCAGATGACCTTGCAAAAAGGATAAATATAGTAAAAGAAAGTTTAAAAGCATTAAATTTATTAAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36935","NCBI_taxonomy_name":"Brachyspira pilosicoli","NCBI_taxonomy_id":"52584"}}}},"ARO_accession":"3001766","ARO_id":"38166","ARO_name":"OXA-192","CARD_short_name":"OXA-192","ARO_description":"OXA-192 is a beta-lactamase found in Brachyspira spp.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46521":{"category_aro_accession":"3007732","category_aro_cvterm_id":"46521","category_aro_name":"OXA-63-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-63.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1270":{"model_id":"1270","model_name":"QnrS3","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"8406":{"protein_sequence":{"accession":"ABU52984.1","sequence":"ETYNHTYRHRNFSHKDLSDLTFTACTFIRSDFRRANLRDTTFVNCKFIEQGDIEGCHFDVADLRDASFQQCQLAMANFSNANCYGIEFRACDLKGANFSRTNFAHQVSNRMYFCSAFISGCNLSYANMERVCLEKCELFENRWIGTNLAGASLKESDLSRGVFSEDVWGQFSLQGANLCHAELDGLDPRKVDTSGIKIAAWQQELILEALGIVVYPD"},"dna_sequence":{"accession":"EU077611.1","fmin":"2","fmax":"656","strand":"+","sequence":"GAAACCTACAATCATACATATCGGCACCGCAACTTTTCACATAAAGACTTAAGTGATCTCACCTTCACCGCTTGCACATTCATTCGCAGCGACTTTCGACGTGCTAACTTGCGTGATACGACATTCGTCAACTGCAAGTTCATTGAACAGGGTGATATCGAAGGCTGCCACTTTGATGTCGCAGATCTTCGTGATGCAAGTTTCCAACAATGCCAACTTGCGATGGCAAACTTCAGTAATGCCAATTGCTACGGTATAGAGTTCCGTGCGTGTGATTTAAAAGGTGCCAACTTTTCCCGAACAAACTTTGCCCATCAAGTGAGTAATCGTATGTACTTTTGCTCAGCATTTATTTCTGGATGTAATCTTTCCTATGCCAATATGGAGAGGGTTTGTTTAGAAAAATGTGAGTTGTTTGAAAATCGCTGGATAGGAACGAACCTAGCGGGTGCATCACTGAAAGAGTCAGACTTAAGTCGAGGTGTTTTTTCCGAAGATGTCTGGGGGCAATTTAGCCTACAGGGTGCCAATTTATGCCACGCCGAACTCGACGGTTTAGATCCCCGCAAAGTCGATACATCAGGTATCAAAATTGCAGCCTGGCAGCAAGAACTGATTCTCGAAGCACTGGGTATTGTTGTTTATCCTGACTAA","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002792","ARO_id":"39226","ARO_name":"QnrS3","CARD_short_name":"QnrS3","ARO_description":"QnrS3 is a plasmid-mediated quinolone resistance protein found in Escherichia coli.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1271":{"model_id":"1271","model_name":"AAC(6')-Iw","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"139":{"protein_sequence":{"accession":"AAD03495.1","sequence":"MKIMPISEALLADWLQLRILLWPDHEDAHLLEMRQLLTRTDSLQLLAYSETQQPIAMLEASIRHEYVNGTQTSPVAFLEGIYVLPEHRRSGIATQLVQQVEQWAKQYACTEFASDAAIDNTISHAMHQALGFHETERVVYFKKNIS"},"dna_sequence":{"accession":"AF031331.1","fmin":"0","fmax":"441","strand":"+","sequence":"ATGAAAATTATGCCTATATCTGAAGCATTATTGGCAGATTGGTTACAATTAAGAATTTTGCTGTGGCCTGATCATGAAGATGCGCATTTATTGGAAATGCGTCAGTTACTTACACGAACAGATAGTTTGCAGTTATTGGCATATTCAGAAACGCAACAGCCGATTGCGATGTTAGAAGCATCCATTCGACATGAATATGTGAACGGTACACAAACCTCACCTGTGGCGTTTCTGGAAGGGATTTATGTCCTGCCTGAGCACCGACGTTCAGGTATTGCCACTCAATTGGTTCAACAAGTAGAACAATGGGCAAAACAATATGCATGTACTGAATTTGCTTCAGATGCAGCAATTGATAATACCATCAGTCATGCAATGCATCAGGCTTTAGGTTTTCATGAAACTGAACGCGTGGTTTATTTCAAGAAAAATATCAGTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39518","NCBI_taxonomy_name":"Acinetobacter sp. 640","NCBI_taxonomy_id":"70350"}}}},"ARO_accession":"3002567","ARO_id":"38967","ARO_name":"AAC(6')-Iw","CARD_short_name":"AAC(6')-Iw","ARO_description":"AAC(6')-Iw is a chromosomal-encoded aminoglycoside acetyltransferase in Acinetobacter sp.","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"A category of aminoglycoside N-acetyltransferase enzymes with modification regiospecificity based at the 6'-amino group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics through acetylation of the 6-amino group of the compound.","category_aro_class_name":"AMR Gene Family"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"46128":{"category_aro_accession":"3007378","category_aro_cvterm_id":"46128","category_aro_name":"2'-N-ethylnetilmicin","category_aro_description":"2'-N-ethylnetilmicin is an aminoglycoside antibiotic and a derivative of netilmicin.","category_aro_class_name":"Antibiotic"},"46129":{"category_aro_accession":"3007379","category_aro_cvterm_id":"46129","category_aro_name":"5-episisomicin","category_aro_description":"5-episosomicin is a semisynthetic aminoglycoside antibiotic similar to sisomicin.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1272":{"model_id":"1272","model_name":"CTX-M-67","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1187":{"protein_sequence":{"accession":"ABS90365.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYSPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"EF581888.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAGTCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGACTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001928","ARO_id":"38328","ARO_name":"CTX-M-67","CARD_short_name":"CTX-M-67","ARO_description":"CTX-M-67 is a beta-lactamase found in Escherichia coli.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1274":{"model_id":"1274","model_name":"VIM-10","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"2040":{"protein_sequence":{"accession":"AAS13761.1","sequence":"MFKLLSKLLVYLTASIMAIASPLAFSVDSSGEYPTVSEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEVEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSASVLYGGCAIYELSRTSAGNVADADLAEWPTSIERIQQHYPEAQYVIPGHGLPGGLDLLKHTTNVVKAHTNRSVVE"},"dna_sequence":{"accession":"AY524989.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGTTCAAACTTTTGAGTAAGTTATTGGTCTATTTGACCGCGTCTATCATGGCTATTGCGAGTCCGCTCGCTTTTTCCGTAGATTCTAGCGGTGAGTATCCGACAGTCAGCGAAATTCCGGTCGGGGAGGTCCGGCTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCAGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAGAAGCAAATTGGACTTCCTGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGTAGAGGGGAACGAGATTCCCACGCACTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAACTCTTCTATCCTGGTGCTGCGCATTCGACCGACAACTTAGTTGTGTACGTCCCGTCTGCGAGTGTGCTCTATGGTGGTTGTGCGATTTATGAGTTGTCACGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCATTGAGCGGATTCAACAACACTACCCGGAAGCACAGTACGTCATTCCGGGGCACGGCCTGCCGGGCGGTCTAGACTTGCTCAAGCACACAACGAATGTTGTAAAAGCGCACACAAATCGCTCAGTCGTTGAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002280","ARO_id":"38680","ARO_name":"VIM-10","CARD_short_name":"VIM-10","ARO_description":"VIM-10 is a beta-lactamase found in Pseudomonas spp.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1275":{"model_id":"1275","model_name":"ErmT","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"367":{"protein_sequence":{"accession":"AAA98096.1","sequence":"MNKKNIKDSQNFITSKHHINEILRNVHLNTNDNIIEIGSGKGHFSFELAKRCNYVTAIEIDPKLCRITKNKLIEYENFQVINKDILQFKFPKNKSYKIFGNIPYNISTDIIRKIVFESTATESYLIVEYGFAKRLLNTNRSLALFLMTEVDISILSKIPREYFHPKPRVNSSLIVLKRHPSKISLKDRKQYENFVMKWVNKEYIKLFSKNQFYQALKYARIDDLNNISFEQFLSLFNSYKLFNR"},"dna_sequence":{"accession":"M64090.1","fmin":"0","fmax":"735","strand":"+","sequence":"ATGAACAAAAAAAATATAAAAGATAGTCAAAACTTTATTACTTCAAAGCATCATATAAATGAAATTTTGAGAAATGTACATTTAAATACAAATGATAATATTATTGAGATTGGTTCAGGGAAAGGTCATTTCTCGTTTGAATTAGCTAAAAGGTGTAATTATGTAACCGCCATTGAAATAGATCCTAAATTATGTAGGATAACTAAAAACAAACTTATTGAATATGAGAACTTCCAGGTTATCAATAAAGATATTTTACAATTTAAGTTTCCTAAAAATAAGTCATATAAGATATTTGGAAATATACCCTACAATATAAGTACAGATATAATTCGAAAAATTGTTTTTGAAAGCACAGCTACAGAAAGTTATTTAATAGTGGAATATGGATTTGCTAAAAGGTTGCTAAATACAAATCGTTCACTAGCACTATTTTTAATGACAGAAGTTGATATATCCATATTAAGTAAAATCCCTAGAGAATACTTTCATCCAAAACCTAGAGTTAATAGCTCGTTAATTGTATTAAAAAGACACCCTTCAAAAATATCACTCAAAGATAGAAAACAATATGAAAATTTTGTTATGAAATGGGTTAACAAAGAATACATAAAACTATTTTCCAAAAACCAATTTTATCAAGCCTTAAAATATGCAAGAATTGACGATTTAAACAATATTAGCTTTGAACAATTCTTGTCTCTTTTCAATAGCTATAAATTATTTAATAGATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36841","NCBI_taxonomy_name":"Plasmid pGT633","NCBI_taxonomy_id":"28406"}}}},"ARO_accession":"3000595","ARO_id":"36734","ARO_name":"ErmT","CARD_short_name":"ErmT","ARO_description":"ErmT confers MLSb phenotype.","ARO_category":{"36699":{"category_aro_accession":"3000560","category_aro_cvterm_id":"36699","category_aro_name":"Erm 23S ribosomal RNA methyltransferase","category_aro_description":"Erm proteins are part of the RNA methyltransferase family and methylate A2058 (E. coli nomenclature) of the 23S ribosomal RNA conferring degrees of resistance to Macrolides, Lincosamides and Streptogramin b. This is called the MLSb phenotype.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35946":{"category_aro_accession":"0000027","category_aro_cvterm_id":"35946","category_aro_name":"roxithromycin","category_aro_description":"Roxithromycin is a semi-synthetic, 14-carbon ring macrolide antibiotic derived from erythromycin. It is used to treat respiratory tract, urinary and soft tissue infections. Roxithromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35974":{"category_aro_accession":"0000057","category_aro_cvterm_id":"35974","category_aro_name":"telithromycin","category_aro_description":"Telithromycin is a semi-synthetic derivative of erythromycin. It is a 14-membered macrolide and is the first ketolide antibiotic to be used in clinics. Telithromycin binds the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"35982":{"category_aro_accession":"0000065","category_aro_cvterm_id":"35982","category_aro_name":"clarithromycin","category_aro_description":"Clarithromycin is a methyl derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome and is used to treat pharyngitis, tonsillitis, acute maxillary sinusitis, acute bacterial exacerbation of chronic bronchitis, pneumonia (especially atypical pneumonias associated with Chlamydia pneumoniae or TWAR), and skin structure infections.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"36284":{"category_aro_accession":"3000145","category_aro_cvterm_id":"36284","category_aro_name":"tylosin","category_aro_description":"Tylosin is a 16-membered macrolide, naturally produced by Streptomyces fradiae. It interacts with the bacterial ribosome 50S subunit to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"36295":{"category_aro_accession":"3000156","category_aro_cvterm_id":"36295","category_aro_name":"spiramycin","category_aro_description":"Spiramycin is a 16-membered macrolide and is natural product produced by Streptomyces ambofaciens. It binds to the 50S subunit of bacterial ribosomes and inhibits peptidyl transfer activity to disrupt protein synthesis.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"36315":{"category_aro_accession":"3000176","category_aro_cvterm_id":"36315","category_aro_name":"dirithromycin","category_aro_description":"Dirithromycin is an oxazine derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome to inhibit bacterial protein synthesis.","category_aro_class_name":"Antibiotic"},"36722":{"category_aro_accession":"3000583","category_aro_cvterm_id":"36722","category_aro_name":"pristinamycin IA","category_aro_description":"Pristinamycin IA is a type B streptogramin antibiotic produced by Streptomyces pristinaespiralis. It binds to the P site of the 50S subunit of the bacterial ribosome, preventing the extension of protein chains.","category_aro_class_name":"Antibiotic"},"36723":{"category_aro_accession":"3000584","category_aro_cvterm_id":"36723","category_aro_name":"quinupristin","category_aro_description":"Quinupristin is a type B streptogramin and a semisynthetic derivative of pristinamycin 1A. It is a component of the drug Synercid and interacts with the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"virginiamycin M1","category_aro_description":"Virginiamycin M1 is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37016":{"category_aro_accession":"3000672","category_aro_cvterm_id":"37016","category_aro_name":"madumycin II","category_aro_description":"Madumycin II is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37017":{"category_aro_accession":"3000673","category_aro_cvterm_id":"37017","category_aro_name":"griseoviridin","category_aro_description":"Griseoviridin is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"37019":{"category_aro_accession":"3000675","category_aro_cvterm_id":"37019","category_aro_name":"pristinamycin IB","category_aro_description":"Pristinamycin IB is a class B streptogramin similar to pristinamycin IA, the former containing a N-methyl-4-(methylamino)phenylalanine instead of a N-methyl-4-(dimethylamino)phenylalanine in its class A streptogramin counterpart (one less methyl group).","category_aro_class_name":"Antibiotic"},"37021":{"category_aro_accession":"3000677","category_aro_cvterm_id":"37021","category_aro_name":"virginiamycin S2","category_aro_description":"Virginiamycin S2 is a streptogramin B antibiotic.","category_aro_class_name":"Antibiotic"},"37022":{"category_aro_accession":"3000678","category_aro_cvterm_id":"37022","category_aro_name":"pristinamycin IC","category_aro_description":"Pristinamycin IC is a class B streptogramin derived from virginiamycin S1.","category_aro_class_name":"Antibiotic"},"37023":{"category_aro_accession":"3000679","category_aro_cvterm_id":"37023","category_aro_name":"vernamycin C","category_aro_description":"Vernamycin C is a streptogramin B antibiotic.","category_aro_class_name":"Antibiotic"},"37024":{"category_aro_accession":"3000680","category_aro_cvterm_id":"37024","category_aro_name":"patricin A","category_aro_description":"Patricin A is a streptogramin B antibiotic.","category_aro_class_name":"Antibiotic"},"37025":{"category_aro_accession":"3000681","category_aro_cvterm_id":"37025","category_aro_name":"patricin B","category_aro_description":"Patricin B is a streptogramin B antibiotic.","category_aro_class_name":"Antibiotic"},"37026":{"category_aro_accession":"3000682","category_aro_cvterm_id":"37026","category_aro_name":"ostreogrycin B3","category_aro_description":"Ostreogrycin B3 is a derivative of pristinamycin IA, with an additional 3-hydroxy group on its 4-oxopipecolic acid.","category_aro_class_name":"Antibiotic"},"37247":{"category_aro_accession":"3000867","category_aro_cvterm_id":"37247","category_aro_name":"oleandomycin","category_aro_description":"Oleandomycin is a 14-membered macrolide produced by Streptomyces antibioticus. It is ssimilar to erythromycin, and contains a desosamine amino sugar and an oleandrose sugar. It targets the 50S ribosomal subunit to prevent protein synthesis.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35952":{"category_aro_accession":"0000034","category_aro_cvterm_id":"35952","category_aro_name":"streptogramin A antibiotic","category_aro_description":"Streptogramin A antibiotics are cyclic polyketide peptide hybrids that bind to the ribosomal peptidyl transfer centre. Structural variation arises from substituting a proline for its desaturated derivative and by its substitution for Ala or Cys. Used alone, streptogramin A antibiotics are bacteriostatic, but is bactericidal when used with streptogramin B antibiotics.","category_aro_class_name":"Drug Class"},"35967":{"category_aro_accession":"0000050","category_aro_cvterm_id":"35967","category_aro_name":"streptogramin B antibiotic","category_aro_description":"Streptogramin B antibiotics are are cyclic hepta- or hexa-depsipeptides.  Type B streptogramins block the peptide exit tunnel of the 50S bacterial ribosome. The general composition of group B streptogramins is 3-hydroxypicolinic acid-L-Thr-D-aminobutyric acid (or D-Ala)-L-Pro-L-Phe (or 4-N-,N-(dimethylamino)-L-Phe)-X-L-phenylglycine. Used alone, streptogramin B antibiotics are bacteriostatic, but is bactericidal when used with streptogramin A antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1276":{"model_id":"1276","model_name":"OXA-210","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"884":{"protein_sequence":{"accession":"AEE61368.1","sequence":"MAIRIFAILFSIFSLATFAHAQEGTLERSDWRKFFSEFQAKGTIVVADERQADRAMLVFDPVRSKKRYSPASTFKIPHTLFALDAGAVRDEFQIFRWDGVNRGFAGHNQDQDLRSAMRNSTVWVYELFAKEIGDDKARRYLKKIDYGNADPSTSNGDCWIEGSLAISAQEQIAFLRKLYRNELPFRVEHQRLVKDLMIVEAGRNWILRAKTGWEGRMGWWVGWVEWPTGSVFFALNIDTPNRMDDLFKREAIVRAILRSIEALPPNPAVNSDAAR"},"dna_sequence":{"accession":"JF795487.1","fmin":"0","fmax":"828","strand":"+","sequence":"ATGGCAATCCGAATCTTCGCGATACTTTTCTCCATTTTTTCTCTTGCCACTTTCGCGCATGCGCAAGAAGGCACGCTAGAACGTTCTGACTGGAGGAAGTTTTTCAGCGAATTTCAAGCCAAAGGCACGATAGTTGTGGCAGACGAACGCCAAGCGGATCGTGCCATGTTGGTTTTTGATCCTGTGCGATCGAAGAAACGCTACTCGCCTGCATCGACATTCAAGATACCTCATACACTTTTTGCACTTGATGCAGGCGCTGTTCGTGATGAGTTCCAGATTTTTCGATGGGACGGCGTTAACAGGGGCTTTGCAGGCCACAATCAAGACCAAGATTTGCGATCAGCAATGCGGAATTCTACTGTTTGGGTGTATGAGCTATTTGCAAAGGAAATTGGTGATGACAAAGCTCGGCGCTATTTGAAGAAAATCGACTATGGCAACGCCGATCCTTCGACAAGTAATGGCGATTGCTGGATAGAAGGCAGCCTTGCAATCTCGGCGCAGGAGCAAATTGCATTTCTCAGGAAGCTCTATCGTAACGAGCTGCCCTTTCGGGTAGAACATCAGCGCTTGGTCAAGGATCTCATGATTGTGGAAGCCGGTCGCAACTGGATACTGCGTGCAAAGACGGGCTGGGAAGGCCGTATGGGTTGGTGGGTAGGATGGGTTGAGTGGCCGACTGGCTCCGTATTCTTCGCACTGAATATTGATACGCCAAACAGAATGGATGATCTTTTCAAGAGGGAGGCAATCGTGCGGGCAATCCTTCGCTCTATTGAAGCGTTACCGCCCAACCCGGCAGTCAACTCGGACGCTGCGCGATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3001487","ARO_id":"37887","ARO_name":"OXA-210","CARD_short_name":"OXA-210","ARO_description":"OXA-210 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46493":{"category_aro_accession":"3007704","category_aro_cvterm_id":"46493","category_aro_name":"OXA-2-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-2.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1277":{"model_id":"1277","model_name":"GES-16","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"835":{"protein_sequence":{"accession":"ADJ94120.1","sequence":"MRFIHALLLAGIAHSAYASEKLTFKTDLEKLEREKAAEIGVAIVDPQGEIVAGHRMAQRFAMCSTFKFPLAALVFERIDSGTERGDRKLSYGPDMIVEWSPATERFLASGHMTVLEAAQAAVQLSDNGATNLLLREIGGPAAMTQYFRKIGDSVSRLDRKEPEMSDNTPGDLRDTTTPIAMARTVAKVLYGGALTSTSTHTIERWLIGNQTGDATLRAGFPKDWVVGEKTGTCANGGRNDIGFFKAQERDYAVAVYTTAPKLSAVERDELVASVGQVITQLILSTDK"},"dna_sequence":{"accession":"HM173356.1","fmin":"511","fmax":"1375","strand":"+","sequence":"ATGCGCTTCATTCACGCACTATTACTGGCAGGGATCGCTCACTCTGCATATGCGTCGGAAAAATTAACCTTCAAGACCGATCTTGAGAAGCTAGAGCGCGAAAAAGCAGCTGAGATCGGTGTTGCGATCGTCGATCCCCAAGGAGAGATCGTCGCGGGCCACCGAATGGCGCAGCGTTTTGCAATGTGCTCAACGTTCAAGTTTCCGCTAGCCGCGCTGGTCTTTGAAAGAATTGACTCAGGCACCGAGCGGGGGGATCGAAAACTTTCATATGGGCCGGACATGATCGTCGAATGGTCTCCTGCCACGGAGCGGTTTCTAGCATCGGGACACATGACGGTTCTCGAGGCAGCGCAAGCTGCGGTGCAGCTTAGCGACAATGGGGCTACTAACCTCTTACTGAGAGAAATTGGCGGACCTGCTGCAATGACGCAGTATTTTCGTAAAATTGGCGACTCTGTGAGTCGGCTAGACCGGAAAGAGCCGGAGATGAGCGACAACACACCTGGCGACCTCAGAGATACAACTACGCCTATTGCTATGGCACGTACTGTGGCTAAAGTCCTCTATGGCGGCGCACTGACGTCCACCTCGACCCACACCATTGAGAGGTGGCTGATCGGAAACCAAACGGGAGACGCGACGCTACGAGCGGGTTTTCCTAAAGATTGGGTTGTTGGAGAGAAAACTGGTACCTGCGCCAACGGGGGCCGGAACGACATTGGTTTTTTTAAAGCCCAGGAGAGAGATTACGCTGTAGCGGTGTATACAACGGCCCCGAAACTATCGGCCGTAGAACGTGACGAATTAGTTGCCTCTGTCGGTCAAGTTATTACACAACTCATCCTGAGCACGGACAAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36783","NCBI_taxonomy_name":"Serratia marcescens","NCBI_taxonomy_id":"615"}}}},"ARO_accession":"3002345","ARO_id":"38745","ARO_name":"GES-16","CARD_short_name":"GES-16","ARO_description":"GES-16 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36205":{"category_aro_accession":"3000066","category_aro_cvterm_id":"36205","category_aro_name":"GES beta-lactamase","category_aro_description":"GES beta-lactamases or Guiana extended-spectrum beta-lactamases are related to the other plasmid-located class A beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1278":{"model_id":"1278","model_name":"TEM-45","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1495":{"protein_sequence":{"accession":"CAA64682.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMLSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDEQNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"X95401.1","fmin":"208","fmax":"1069","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGTTGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACAAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000914","ARO_id":"37294","ARO_name":"TEM-45","CARD_short_name":"TEM-45","ARO_description":"TEM-45 is an inhibitor-resistant beta-lactamase found in E. coli.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1279":{"model_id":"1279","model_name":"TEM-104","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"995":{"protein_sequence":{"accession":"AAM61952.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIVEIGASLIKHW"},"dna_sequence":{"accession":"AF516719.1","fmin":"214","fmax":"1075","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGTCGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3000967","ARO_id":"37347","ARO_name":"TEM-104","CARD_short_name":"TEM-104","ARO_description":"TEM-104 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1280":{"model_id":"1280","model_name":"QnrB12","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"176":{"protein_sequence":{"accession":"CAO82104.1","sequence":"MMTLALVGEKIDRNRFTGAKVENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAILKDAIFKSCDLSMADFRNVSALGIEIRHCRAQGSDFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGTQVLGATFSGSDLSGGEFSSFDWRAANFTHCDLTNSELGDLDVRGVDLQGVKLDSYQASLILERLGIAVIG"},"dna_sequence":{"accession":"AM774474.1","fmin":"2431","fmax":"3079","strand":"+","sequence":"ATGATGACTCTGGCATTAGTTGGCGAAAAAATTGACAGAAACAGATTCACTGGTGCGAAAGTTGAAAATAGCACATTTTTCAACTGTGATTTTTCGGGTGCCGACCTCAGCGGCACTGAGTTTATTGGCTGTCAGTTCTATGATCGAGAGAGCCAGAAAGGGTGTAATTTTAGTCGCGCTATCCTGAAAGATGCCATTTTCAAAAGTTGTGATCTCTCCATGGCGGATTTCAGGAATGTGAGCGCGCTGGGAATCGAAATTCGCCACTGCCGCGCACAAGGTTCAGATTTTCGCGGCGCAAGCTTTATGAATATGATTACCACACGCACCTGGTTTTGTAGCGCCTATATCACCAATACCAACTTAAGCTACGCCAACTTTTCAAAAGTCGTACTGGAAAAGTGCGAGCTGTGGGAAAACCGTTGGATGGGTACTCAGGTACTGGGGGCGACGTTCAGTGGTTCAGATCTTTCCGGCGGTGAGTTTTCGTCGTTCGACTGGCGGGCCGCAAACTTTACGCACTGTGATTTGACCAATTCAGAACTGGGCGATCTCGATGTCCGGGGTGTTGATTTGCAAGGCGTCAAACTGGACAGCTACCAGGCATCGTTGATCCTGGAACGTCTTGGCATCGCTGTCATTGGTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39583","NCBI_taxonomy_name":"Citrobacter werkmanii","NCBI_taxonomy_id":"67827"}}}},"ARO_accession":"3002726","ARO_id":"39160","ARO_name":"QnrB12","CARD_short_name":"QnrB12","ARO_description":"QnrB12  is a plasmid-mediated quinolone resistance protein found in Citrobacter werkmanii.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1281":{"model_id":"1281","model_name":"OXA-110","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1600":{"protein_sequence":{"accession":"ABV31690.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDDKAEKIKNLFNEAHTTGVLVIHQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGEKRLFPEWEKNMTLGDAMKASALPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"EF650036.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGACAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCATCAAGGTCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAATGGGATGGGGAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTCTTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTCTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001641","ARO_id":"38041","ARO_name":"OXA-110","CARD_short_name":"OXA-110","ARO_description":"OXA-110 is a beta-lactamase found in A. baumannii.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1283":{"model_id":"1283","model_name":"KPC-6","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1437":{"protein_sequence":{"accession":"ACB71165.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGGYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"EU555534.1","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGGGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002316","ARO_id":"38716","ARO_name":"KPC-6","CARD_short_name":"KPC-6","ARO_description":"KPC-6 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1284":{"model_id":"1284","model_name":"IND-15","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1987":{"protein_sequence":{"accession":"BAJ14288.1","sequence":"MKKSIQLLMMSMFLSPLINAQVKDFVIEPPVKPNLYLYKSFGVFGGKEYSANAVYLTTKKGVVLFDVPWQKEQYQTLMDTIQKRHHLPVIAVFATHSHDDRAGDLSFYNQKGIKTYATAKTNELLKKDGKATSTEIIKTGKPYKIGGEEFMVDFLGEGHTVDNVVVRFPKYKVLDGGCLVKSRTATDLGYTGEANVKQWPETMRKLKMKYAQATLVIPGHDEWKGGGHVQHTLDLLDKNKKPE"},"dna_sequence":{"accession":"AB563173.1","fmin":"32","fmax":"764","strand":"+","sequence":"ATGAAAAAAAGTATTCAGCTTTTGATGATGTCAATGTTTTTAAGCCCATTGATCAATGCCCAGGTTAAAGATTTTGTAATTGAGCCGCCTGTTAAACCCAACCTGTATCTTTATAAAAGTTTCGGAGTTTTCGGGGGTAAAGAATATTCTGCCAATGCTGTATATCTTACCACTAAGAAAGGAGTGGTCTTATTTGATGTCCCATGGCAAAAGGAACAATATCAAACCCTTATGGACACTATACAAAAGCGTCATCACCTTCCTGTAATTGCTGTATTTGCCACCCACTCTCATGATGACAGAGCGGGCGATCTAAGCTTTTACAATCAAAAAGGAATTAAAACATATGCGACCGCCAAGACCAATGAACTGTTGAAAAAAGACGGAAAAGCAACCTCAACCGAAATTATAAAAACAGGAAAACCTTACAAAATTGGTGGTGAAGAATTTATGGTAGACTTTCTTGGAGAAGGACATACAGTTGATAATGTTGTTGTACGGTTCCCCAAATATAAAGTACTGGACGGAGGATGTCTTGTAAAAAGCAGGACAGCCACTGACCTGGGATATACCGGTGAAGCAAACGTAAAACAATGGCCGGAAACCATGCGAAAACTAAAAATGAAATATGCTCAGGCTACTCTGGTAATCCCGGGACACGACGAATGGAAAGGCGGTGGTCATGTACAGCATACTCTGGATCTTCTGGATAAGAATAAAAAGCCGGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36916","NCBI_taxonomy_name":"Chryseobacterium indologenes","NCBI_taxonomy_id":"253"}}}},"ARO_accession":"3002270","ARO_id":"38670","ARO_name":"IND-15","CARD_short_name":"IND-15","ARO_description":"IND-15 is a beta-lactamase found in Escherichia coli.","ARO_category":{"36199":{"category_aro_accession":"3000060","category_aro_cvterm_id":"36199","category_aro_name":"IND beta-lactamase","category_aro_description":"IND beta-lactamases are class B carbapenem-hydrolyzing beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1286":{"model_id":"1286","model_name":"SHV-34","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1235":{"protein_sequence":{"accession":"AAK64187.1","sequence":"MRYFRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGSVGMIEMDLASGRTLTAWRADGRFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGASERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AY036620.1","fmin":"88","fmax":"949","strand":"+","sequence":"ATGCGTTATTTTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCAGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGGACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTAGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGGATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001092","ARO_id":"37472","ARO_name":"SHV-34","CARD_short_name":"SHV-34","ARO_description":"SHV-34 is an extended-spectrum beta-lactamase found in E. coli.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1287":{"model_id":"1287","model_name":"CTX-M-110","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1665":{"protein_sequence":{"accession":"AEM44648.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEEHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGNL"},"dna_sequence":{"accession":"JF274242.1","fmin":"1","fmax":"877","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAGAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGACTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGAATCTC","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36952","NCBI_taxonomy_name":"Shigella sp. SH165","NCBI_taxonomy_id":"1074431"}}}},"ARO_accession":"3001970","ARO_id":"38370","ARO_name":"CTX-M-110","CARD_short_name":"CTX-M-110","ARO_description":"CTX-M-110 is a beta-lactamase found in Shigella spp.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1288":{"model_id":"1288","model_name":"OXA-82","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1846":{"protein_sequence":{"accession":"ABV71248.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDVKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWVVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"EU019536.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGTAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCAAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGGTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAACAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001635","ARO_id":"38035","ARO_name":"OXA-82","CARD_short_name":"OXA-82","ARO_description":"OXA-82 is a beta-lactamase found in A. baumannii.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1289":{"model_id":"1289","model_name":"OKP-B-7","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"1831":{"protein_sequence":{"accession":"CAJ19615.1","sequence":"MRYVRLCLISLIAALPLAVFASPQPLEQIKISESQLAGRVGYVEMDLASGRTLAAWRASERFPLMSTFKVLLCGAVLARVDAGDEQLDRRIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAGNLLLKIVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDVRDTTTPASMATTLRKLLTTPSLSARSQQQLLQWMVDDRVAGPLIRAVLPAGWFIADKTGAGERGSRGIVALLGPDGKAERIVVIYLRDTAATMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AM051156.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGCCTTATCTCCCTGATTGCCGCCCTGCCACTGGCGGTATTCGCCAGCCCTCAGCCGCTTGAGCAGATTAAAATCAGCGAAAGTCAGCTGGCGGGCCGGGTGGGCTATGTTGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCAGTGAGCGCTTTCCGCTGATGAGCACCTTTAAAGTGCTGCTCTGCGGCGCGGTGCTGGCCCGGGTGGATGCCGGCGACGAACAGCTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGCCGACGGGATGACCGTTGGCGAACTCTGCGCCGCCGCCATCACCATGAGCGACAACAGCGCCGGCAATCTGCTGTTGAAGATCGTCGGCGGCCCCGCGGGATTGACAGCTTTTCTGCGCCAGATCGGTGACAACGTCACCCGTCTTGATCGCTGGGAAACGGAACTCAATGAGGCGCTTCCCGGCGACGTGCGCGACACCACCACCCCGGCCAGCATGGCCACCACCCTGCGCAAGCTGCTAACCACCCCCTCTCTGAGCGCCCGTTCGCAGCAGCAGCTGCTGCAGTGGATGGTTGACGACCGGGTGGCCGGCCCGTTGATCCGCGCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAAACCGGGGCCGGTGAGCGGGGCTCACGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAAGCGGAGCGTATCGTGGTGATCTATCTGCGGGATACCGCAGCGACCATGGCCGAACGTAACCAGCAGATCGCCGGGATAGGCGCGGCGCTGATCGAGCACTGGCAGCGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002440","ARO_id":"38840","ARO_name":"OKP-B-7","CARD_short_name":"OKP-B-7","ARO_description":"OKP-B-7 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"38817":{"category_aro_accession":"3002417","category_aro_cvterm_id":"38817","category_aro_name":"OKP beta-lactamase","category_aro_description":"OKP beta-lactamases are chromosomal class A beta-lactamase that confer resistance to penicillins and early cephalosporins in Klebsiella pneumoniae. OKP beta-lactamases can be subdivided into two groups: OKP-A and OKP-B which diverge by about 4.2%.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1290":{"model_id":"1290","model_name":"TEM-141","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1399":{"protein_sequence":{"accession":"AAX56615.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVEDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AY956335.1","fmin":"38","fmax":"899","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAGAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3001004","ARO_id":"37384","ARO_name":"TEM-141","CARD_short_name":"TEM-141","ARO_description":"TEM-141 is a broad-spectrum beta-lactamase found in Enterobacter cloacae.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1291":{"model_id":"1291","model_name":"TEM-177","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1401":{"protein_sequence":{"accession":"CBJ06718.1","sequence":"MSIKHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDKLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVKYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDSWEPELNEAIPNDERDTTTPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGTGKRGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"FN652295.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTAAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATAAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTAAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATAGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGACGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAACCGGTAAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3001042","ARO_id":"37422","ARO_name":"TEM-177","CARD_short_name":"TEM-177","ARO_description":"TEM-177 is an extended-spectrum beta-lactamase.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1292":{"model_id":"1292","model_name":"CTX-M-109","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8420":{"protein_sequence":{"accession":"AEM44654.1","sequence":"VKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSRILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTK"},"dna_sequence":{"accession":"JF274248.1","fmin":"0","fmax":"864","strand":"-","sequence":"GTTAAAAAATCACTGCGTCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCGAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCAAA","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39658","NCBI_taxonomy_name":"Shigella sp. SH361","NCBI_taxonomy_id":"1074437"}}}},"ARO_accession":"3001969","ARO_id":"38369","ARO_name":"CTX-M-109","CARD_short_name":"CTX-M-109","ARO_description":"CTX-M-109 is a beta-lactamase found in Shigella spp.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1293":{"model_id":"1293","model_name":"OXA-197","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"883":{"protein_sequence":{"accession":"AEB98923.1","sequence":"MNIKALFLITSAIFISACSPYIVTANPNHSASKSDVKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWVVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEIAYKSLEQLGIL"},"dna_sequence":{"accession":"HQ425495.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGAACATTAAAGCCCTCTTCCTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGTAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGGTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAACAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTGCTTATAAAAGCTTAGAACAATTAGGTATTTTA","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36949","NCBI_taxonomy_name":"Acinetobacter nosocomialis","NCBI_taxonomy_id":"106654"}}}},"ARO_accession":"3001482","ARO_id":"37882","ARO_name":"OXA-197","CARD_short_name":"OXA-197","ARO_description":"OXA-197 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1138":{"model_id":"1138","model_name":"tet(D)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"5131":{"protein_sequence":{"accession":"AAL75563.1","sequence":"MNKPAVIALVITLLDAMGIGLIMPVLPSLLREYLPEADVANHYGILLALYAVMQVCFAPLLGRWSDKLGRRPVLLLSLAGAAFDYTLLALSNVLWMLYLGRIISGITGATGAVAASVVADSTAVSERTAWFGRLGAAFGAGLIAGPAIGGLAGDISPHLPFVIAAILNACTFLMVFFIFKPAVQTEEKPAEQKQESAGISFITLLKPLALLLFVFFTAQLIGQIPATVWVLFTESRFAWDSAAVGFSLAGLGAMHALFQAVVAGALAKRLSEKTIIFAGFIADATAFLLMSAITSGWMVYPVLILLAGGGIALPALQGIISAGASAANQGKLQGVLVSLTNLTGVAGPLLFAFIFSQTQQSADGTVWLIGTALYGLLLAICLLIRKPAPVAATC"},"dna_sequence":{"accession":"AF467077.1","fmin":"163","fmax":"1348","strand":"+","sequence":"ATGAATAAACCCGCTGTCATCGCGCTGGTGATTACACTGCTGGACGCGATGGGAATTGGTCTGATCATGCCGGTATTACCGTCACTGCTGCGGGAATATCTCCCGGAAGCGGATGTGGCAAACCATTACGGCATTCTGCTGGCGCTGTATGCGGTGATGCAGGTCTGTTTTGCTCCGCTGCTGGGCAGATGGTCAGATAAGCTGGGGCGCAGACCGGTGCTGCTGTTATCCCTGGCGGGTGCCGCGTTTGATTACACACTGCTGGCACTGTCCAATGTGCTGTGGATGTTGTATCTCGGGCGGATTATCTCCGGGATCACTGGTGCCACCGGCGCGGTTGCGGCTTCGGTAGTGGCGGACAGCACGGCGGTCAGCGAGCGTACCGCCTGGTTCGGCCGTCTCGGTGCGGCCTTTGGTGCCGGGCTGATTGCCGGGCCGGCTATCGGCGGACTGGCGGGGGATATCTCACCGCATCTGCCGTTTGTCATTGCGGCAATACTGAATGCCTGCACCTTTCTGATGGTCTTTTTTATCTTTAAACCGGCGGTACAGACAGAAGAAAAACCGGCGGAGCAGAAACAAGAAAGCGCAGGTATCAGCTTTATCACACTGCTTAAACCTCTGGCGCTGTTGCTGTTTGTCTTTTTTACCGCGCAGCTTATCGGGCAGATCCCGGCCACTGTCTGGGTATTGTTTACGGAGAGCCGCTTTGCCTGGGACAGCGCGGCGGTCGGTTTTTCACTGGCGGGACTCGGGGCGATGCATGCACTGTTTCAGGCGGTGGTTGCCGGGGCGCTGGCAAAACGGCTGAGTGAGAAAACCATTATTTTCGCCGGATTTATTGCCGATGCCACCGCGTTTTTACTGATGTCTGCTATCACTTCCGGATGGATGGTGTATCCGGTCCTGATCCTGCTGGCAGGCGGCGGAATTGCACTGCCTGCATTGCAGGGCATTATCTCTGCCGGGGCATCGGCGGCAAATCAGGGAAAACTACAGGGTGTGCTGGTCAGCCTGACCAATCTGACCGGCGTGGCGGGCCCGCTGCTGTTTGCTTTTATTTTCAGTCAGACACAGCAGAGTGCGGACGGTACGGTGTGGCTGATTGGCACGGCACTGTACGGTCTGCTGCTGGCAATCTGTCTGCTGATCAGAAAACCGGCACCGGTGGCGGCCACCTGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42476","NCBI_taxonomy_name":"Shigella flexneri Y","NCBI_taxonomy_id":"424720"}}}},"ARO_accession":"3000168","ARO_id":"36307","ARO_name":"tet(D)","CARD_short_name":"tet(D)","ARO_description":"TetD is a tetracycline efflux pump found exclusively in Gram-negative bacteria.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1295":{"model_id":"1295","model_name":"catII","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"742":{"protein_sequence":{"accession":"CAA37806.1","sequence":"MNFTRIDLNTWNRREHFALYRQQIKCGFSLTTKLDITAFRTALAETDYKFYPVMIYLISRVVNQFPEFRMAMKDNALIYWDQTDPVFTVFHKETETFSALFCRYCPDISEFMAGYNAVMAEYQHNTALFPQGALPENHLNISSLPWVSFDGFNLNITGNDDYFAPVFTMAKFQQEDNRVLLPVSVQVHHAVCDGFHAARFINTLQMMCDNILK"},"dna_sequence":{"accession":"X53797.1","fmin":"133","fmax":"775","strand":"+","sequence":"ATGAATTTTACCAGAATTGATCTGAACACCTGGAACCGCAGAGAACATTTTGCTCTTTATCGTCAGCAGATAAAATGCGGATTCAGCCTGACCACAAAACTCGATATTACAGCTTTTCGTACCGCACTGGCGGAAACGGATTATAAATTTTATCCGGTGATGATTTATCTGATCTCCCGGGTTGTTAATCAGTTTCCGGAGTTCCGGATGGCAATGAAAGATAATGCACTGATTTACTGGGATCAGACCGATCCTGTATTTACTGTTTTTCATAAAGAGACTGAAACATTTTCTGCGCTCTTCTGCCGTTATTGTCCGGATATCAGTGAATTTATGGCGGGCTATAATGCGGTGATGGCAGAATATCAGCATAATACTGCATTGTTCCCGCAGGGAGCGTTACCAGAGAACCACCTGAATATATCATCATTACCCTGGGTGAGTTTTGACGGATTTAACCTGAATATCACCGGTAATGATGATTATTTTGCTCCGGTGTTTACTATGGCGAAATTTCAGCAGGAAGATAACCGCGTATTATTACCTGTTTCTGTACAGGTACATCATGCCGTTTGTGATGGCTTTCATGCAGCCAGGTTTATTAATACACTTCAGATGATGTGTGATAACATACTGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36768","NCBI_taxonomy_name":"Haemophilus influenzae","NCBI_taxonomy_id":"727"}}}},"ARO_accession":"3002684","ARO_id":"39118","ARO_name":"catII","CARD_short_name":"catII","ARO_description":"catII is a plasmid-encoded variant of the cat gene found in Haemophilus influenzae, Agrobacterium tumefaciens and Escherichia coli.","ARO_category":{"36261":{"category_aro_accession":"3000122","category_aro_cvterm_id":"36261","category_aro_name":"chloramphenicol acetyltransferase (CAT)","category_aro_description":"Inactivates chloramphenicol by addition of an acyl group. CAT is used to describe many variants of the chloramphenicol acetyltransferase gene in a range of organisms including Acinetobacter calcoaceticus, Agrobacterium tumefaciens, Alkalihalobacillus clausii, Bacillus subtilis, Campylobacter coli, Enterococcus faecalis, Enterococcus faecium, Lactococcus lactis, Listeria monocytogenes, Listonella anguillarum, Morganella morganii, Photobacterium damselae subsp. piscicida, Proteus mirabilis, Salmonella typhi, Serratia marcescens, Shigella flexneri, Staphylococcus aureus, Staphylococcus haemolyticus, Staphylococcus intermedius, Streptococcus agalactiae, Streptococcus suis and Streptomyces acrimycini.","category_aro_class_name":"AMR Gene Family"},"36521":{"category_aro_accession":"3000382","category_aro_cvterm_id":"36521","category_aro_name":"azidamfenicol","category_aro_description":"Azidamfenicol is a water soluble derivative of chloramphenicol, sharing the same mode of action of inhibiting peptide synthesis by interacting with the 23S RNA of the 50S ribosomal subunit.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36595":{"category_aro_accession":"3000456","category_aro_cvterm_id":"36595","category_aro_name":"thiamphenicol","category_aro_description":"Derivative of Chloramphenicol. The nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3).","category_aro_class_name":"Antibiotic"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1296":{"model_id":"1296","model_name":"OKP-B-12","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"6221":{"protein_sequence":{"accession":"CAG25831.1","sequence":"TALPLAVFASPQPLEQIKISEGQLAGRVGYVEMDLASGRMLAAWRASERFPLMSTFKVLLCGAVLARVDAGDEQLDRRIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAGNLLLKSVGGPAGLTTFLRQIGDNVTRLDRWETELNEALPGDVRDTTTPASMATTLRKLLTTPSLSARSQQQLLQWMVDDQVAGPLIRAVLPAGWFIADKTGAGERGSRGIVALLGPDGKAERIVVIYLRDTAATMAERNQQIAG"},"dna_sequence":{"accession":"AJ635420.1","fmin":"0","fmax":"789","strand":"+","sequence":"ACCGCCCTGCCACTGGCGGTATTCGCCAGCCCTCAGCCGCTTGAGCAGATTAAAATCAGCGAAGGTCAGCTGGCGGGCCGGGTGGGCTATGTTGAAATGGATCTGGCCAGCGGCCGCATGCTGGCCGCCTGGCGCGCCAGTGAGCGCTTTCCGCTGATGAGCACCTTTAAAGTGCTGCTCTGCGGCGCTGTGCTGGCCCGGGTGGATGCCGGCGACGAACAGCTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGCCGACGGGATGACCGTTGGCGAACTCTGCGCCGCCGCCATCACCATGAGCGATAACAGCGCCGGCAATCTGCTGTTGAAGAGCGTCGGCGGCCCCGCGGGATTGACCACTTTTCTGCGCCAGATCGGTGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTCAATGAGGCGCTTCCCGGCGACGTGCGCGACACCACCACCCCGGCCAGCATGGCCACCACCCTGCGCAAGTTGCTAACCACCCCCTCTCTGAGCGCCCGTTCGCAGCAGCAGCTGCTGCAGTGGATGGTGGACGACCAGGTGGCCGGCCCGTTGATCCGCGCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAAACCGGGGCCGGTGAGCGGGGCTCACGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAAGCGGAGCGTATCGTGGTGATCTATCTGCGGGATACCGCTGCGACCATGGCCGAACGTAACCAGCAGATCGCCGGG","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002445","ARO_id":"38845","ARO_name":"OKP-B-12","CARD_short_name":"OKP-B-12","ARO_description":"OKP-B-12 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"38817":{"category_aro_accession":"3002417","category_aro_cvterm_id":"38817","category_aro_name":"OKP beta-lactamase","category_aro_description":"OKP beta-lactamases are chromosomal class A beta-lactamase that confer resistance to penicillins and early cephalosporins in Klebsiella pneumoniae. OKP beta-lactamases can be subdivided into two groups: OKP-A and OKP-B which diverge by about 4.2%.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1297":{"model_id":"1297","model_name":"CTX-M-80","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8241":{"protein_sequence":{"accession":"ABW86620.2","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTVDVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGDYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"EU202673.2","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACCGTGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGACTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001941","ARO_id":"38341","ARO_name":"CTX-M-80","CARD_short_name":"CTX-M-80","ARO_description":"CTX-M-80 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1298":{"model_id":"1298","model_name":"lsaA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"5171":{"protein_sequence":{"accession":"AAO43110.1","sequence":"MSKIELKQLSFAYDNQEALLFDQANITMDTNWKLGLIGRNGRGKTTLLRLLQKQLDYQGEILHQVDFVYFPQTVAEEQQLTYYVLQEVTSFEQWKLERELTLLNVDPEVLWRPFSSLSGGEKTKVLLGLLFIEENAFPLIDEPTNHLDLAGRQQVAEYLKKKKHGFILVSHDRAFVDEVVDHILAIEKSQLTLYQGDFSIYEEQKKLRDAFELAENEKIKKEVNRLKETARKKAEWSMNREGDKYGNAKEKGSGAIFDTGAIGARAARVMKRSKHIQQRAETQLAEKEKLLKDLEYIDPLSMDYQPTHHKTLLTVEELRLGYEKNWLFTPISFSINAGEIVGITGKNGSGKSSLIQYLLGDFSGDSEGEATLAHQLTISYVRQDYEDNQGTLSEFAEKNQLDYTQFLNNLRKLGMERAVFTNRIEQMSMGQRKKVEVAKSLSQSAELYIWDEPLNYLDVFNHQQLEALILSVRPAMLVIEHDAHFMKKITDKKIALKS"},"dna_sequence":{"accession":"AY225127.1","fmin":"40","fmax":"1537","strand":"+","sequence":"ATGTCGAAAATTGAACTAAAACAACTATCTTTTGCCTATGATAATCAAGAAGCGTTGCTTTTTGATCAGGCAAATATCACGATGGATACCAATTGGAAATTAGGATTGATTGGCCGCAATGGCCGTGGGAAAACAACCTTATTAAGATTGTTACAAAAGCAGTTGGATTACCAAGGAGAGATTCTTCATCAAGTCGATTTCGTCTATTTTCCACAAACAGTTGCAGAAGAACAACAGCTCACTTATTATGTCTTACAAGAGGTGACTTCTTTTGAACAGTGGAAATTAGAACGAGAATTAACGCTTTTAAACGTTGATCCTGAAGTTTTATGGCGGCCCTTTTCTTCTTTATCAGGCGGCGAAAAGACGAAAGTTTTATTAGGTCTTCTTTTTATTGAAGAAAATGCCTTTCCTTTAATTGACGAGCCAACAAATCATTTAGATCTAGCTGGCAGACAACAAGTGGCTGAATATTTGAAGAAAAAGAAACACGGGTTTATTTTAGTCAGCCACGATCGGGCATTTGTTGATGAAGTGGTTGATCATATTTTGGCGATTGAAAAAAGTCAATTGACACTGTATCAAGGGGATTTTTCTATTTATGAAGAGCAAAAAAAATTAAGAGATGCTTTTGAACTAGCAGAAAATGAAAAAATCAAAAAAGAAGTCAATCGCTTGAAAGAAACCGCTCGTAAAAAAGCGGAATGGTCGATGAACCGTGAAGGTGATAAGTACGGCAATGCTAAAGAAAAAGGGAGCGGGGCGATTTTTGATACAGGAGCCATTGGTGCCCGGGCAGCGCGCGTAATGAAGCGCTCGAAACACATTCAACAACGTGCCGAAACACAATTAGCAGAAAAAGAAAAACTATTAAAAGATCTTGAGTATATTGATCCTTTGTCAATGGATTATCAGCCAACGCATCACAAAACATTATTGACGGTGGAAGAGCTTCGTCTAGGCTACGAGAAAAATTGGCTATTTACGCCAATTTCTTTTTCAATAAACGCGGGAGAAATTGTCGGAATAACAGGAAAAAATGGCTCAGGAAAATCGAGCTTGATTCAGTATTTGTTGGGGGATTTTTCTGGAGATTCAGAAGGAGAAGCCACTCTGGCTCACCAATTAACCATTTCTTATGTGCGCCAAGATTATGAAGACAATCAAGGAACTTTATCCGAATTTGCAGAGAAAAATCAGTTAGATTACACCCAATTTTTAAATAACTTACGAAAACTTGGGATGGAGCGCGCCGTTTTCACTAATCGAATTGAACAAATGAGTATGGGGCAACGGAAAAAAGTCGAAGTAGCCAAATCATTGTCTCAATCAGCTGAACTTTATATTTGGGATGAACCCCTTAATTACTTGGATGTGTTTAATCATCAACAATTAGAAGCGCTAATCTTATCTGTGAGGCCTGCAATGCTAGTGATTGAGCATGATGCACATTTCATGAAGAAAATAACGGATAAAAAAATTGCCTTGAAATCATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40154","NCBI_taxonomy_name":"Enterococcus faecalis ATCC 29212","NCBI_taxonomy_id":"1201292"}}}},"ARO_accession":"3000300","ARO_id":"36439","ARO_name":"lsaA","CARD_short_name":"lsaA","ARO_description":"LsaA is an ABC-F subfamily protein expressed in Enterococcus faecalis. It confers resistance to clindamycin, quinupristin-dalfopristin, and dalfopristin.","ARO_category":{"41696":{"category_aro_accession":"3004472","category_aro_cvterm_id":"41696","category_aro_name":"lsa-type ABC-F protein","category_aro_description":"A subgroup of the ABC-F protein subfamily of ATP-binding cassette proteins. lsa-type ABC-F proteins confer resistance to streptogramin, lincosamide and pleuromutilin antibiotics through antibiotic target protection of the ribosome.","category_aro_class_name":"AMR Gene Family"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"36723":{"category_aro_accession":"3000584","category_aro_cvterm_id":"36723","category_aro_name":"quinupristin","category_aro_description":"Quinupristin is a type B streptogramin and a semisynthetic derivative of pristinamycin 1A. It is a component of the drug Synercid and interacts with the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"37716":{"category_aro_accession":"3001317","category_aro_cvterm_id":"37716","category_aro_name":"pleuromutilin","category_aro_description":"Pleuromutilin is a natural product antibiotic produced by Clitopilus passeckerianus. Related antibiotics of clinical significance, such as tiamulin and retapamulin, are semi-synthetic derivatives of this compound.","category_aro_class_name":"Antibiotic"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35952":{"category_aro_accession":"0000034","category_aro_cvterm_id":"35952","category_aro_name":"streptogramin A antibiotic","category_aro_description":"Streptogramin A antibiotics are cyclic polyketide peptide hybrids that bind to the ribosomal peptidyl transfer centre. Structural variation arises from substituting a proline for its desaturated derivative and by its substitution for Ala or Cys. Used alone, streptogramin A antibiotics are bacteriostatic, but is bactericidal when used with streptogramin B antibiotics.","category_aro_class_name":"Drug Class"},"35967":{"category_aro_accession":"0000050","category_aro_cvterm_id":"35967","category_aro_name":"streptogramin B antibiotic","category_aro_description":"Streptogramin B antibiotics are are cyclic hepta- or hexa-depsipeptides.  Type B streptogramins block the peptide exit tunnel of the 50S bacterial ribosome. The general composition of group B streptogramins is 3-hydroxypicolinic acid-L-Thr-D-aminobutyric acid (or D-Ala)-L-Pro-L-Phe (or 4-N-,N-(dimethylamino)-L-Phe)-X-L-phenylglycine. Used alone, streptogramin B antibiotics are bacteriostatic, but is bactericidal when used with streptogramin A antibiotics.","category_aro_class_name":"Drug Class"},"37014":{"category_aro_accession":"3000670","category_aro_cvterm_id":"37014","category_aro_name":"pleuromutilin antibiotic","category_aro_description":"Pleuromutilins are natural fungal products that target bacterial protein translation by binding the the 23S rRNA, blocking the ribosome P site at the 50S subunit. They are mostly used for agriculture and veterinary purposes.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1299":{"model_id":"1299","model_name":"AAC(6')-Ic","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"306":{"protein_sequence":{"accession":"AAA26549.1","sequence":"MIVICDHDNLDAWLALRTALWPSGSPEDHRAEMREILASPHHTAFMARGLDGAFVAFAEVALRYDYVNGCESSPVAFLEGIYTAERARRQGWAARLIAQVQEWAKQQGCSELASDTDIANLDSQRLHAALGFAETERVVFYRKTLG"},"dna_sequence":{"accession":"M94066.1","fmin":"1553","fmax":"1994","strand":"+","sequence":"ATGATCGTCATCTGCGACCACGACAACCTCGACGCCTGGCTGGCGCTGCGCACCGCGCTGTGGCCCTCCGGCTCGCCTGAAGATCACCGCGCGGAAATGCGCGAGATATTGGCTTCGCCGCACCACACCGCGTTTATGGCGCGGGGGCTGGACGGCGCTTTCGTTGCCTTTGCCGAGGTCGCGCTGCGCTACGATTACGTCAACGGCTGCGAATCGTCGCCGGTGGCGTTTTTGGAAGGAATTTATACCGCCGAACGCGCCCGCCGCCAGGGCTGGGCCGCGCGCCTGATCGCGCAGGTGCAGGAGTGGGCGAAGCAACAGGGGTGCAGCGAGCTGGCGTCGGATACCGATATCGCCAATCTGGACTCCCAGCGCCTGCATGCGGCGCTGGGCTTTGCCGAAACGGAGCGAGTAGTGTTTTACCGCAAAACGCTGGGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36783","NCBI_taxonomy_name":"Serratia marcescens","NCBI_taxonomy_id":"615"}}}},"ARO_accession":"3002549","ARO_id":"38949","ARO_name":"AAC(6')-Ic","CARD_short_name":"AAC(6')-Ic","ARO_description":"AAC(6')-Ic is a chromosomal-encoded aminoglycoside acetyltransferase in S. marcescens.","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"A category of aminoglycoside N-acetyltransferase enzymes with modification regiospecificity based at the 6'-amino group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics through acetylation of the 6-amino group of the compound.","category_aro_class_name":"AMR Gene Family"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"46128":{"category_aro_accession":"3007378","category_aro_cvterm_id":"46128","category_aro_name":"2'-N-ethylnetilmicin","category_aro_description":"2'-N-ethylnetilmicin is an aminoglycoside antibiotic and a derivative of netilmicin.","category_aro_class_name":"Antibiotic"},"46129":{"category_aro_accession":"3007379","category_aro_cvterm_id":"46129","category_aro_name":"5-episisomicin","category_aro_description":"5-episosomicin is a semisynthetic aminoglycoside antibiotic similar to sisomicin.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3305":{"model_id":"3305","model_name":"EreD","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"5235":{"protein_sequence":{"accession":"AKO71461.1","sequence":"MKNIKPLTFPFNSENNTSIKQSLFRFREYFDSSTIVGLGENSHFIKEFFTFRHQVIEFLVTECDFDTLAFEFGFSEGLEVDKWIKSQIPFDDLDKLLSHFYYPNEFKDTLLWLRRYNQDNNNQITFLGVDIPKNGGSYFPNFRIVSDYLQRLSIVSSDVLQKILNLAEKFDFYSTSQLALNLSLFDEAEHNELKALLLKVYIRLVTLQPKLESLEFQSILHQVKGLIYMNYNADAMESFITEKGIEGDMGAKDQYMAESIDWFLKNSLGKKIILVAHNAHIQKTPVDFDGFISCYPMGQRLSMTFGEKYKAFAITNLRGETAALYPDNDYQFGFRVDKFPLDSPESDSVEFFMQELSGKECCLIINKSKELKNCSKIRFDSIYLKTEIVDSFDGIFLIEKSTVSEIVD"},"dna_sequence":{"accession":"KP265721.1","fmin":"331","fmax":"1558","strand":"+","sequence":"ATGAAAAATATAAAACCCTTAACTTTTCCGTTTAATTCGGAAAATAATACATCCATAAAACAAAGTCTTTTTCGATTTCGAGAATATTTTGATTCTTCTACAATTGTTGGTTTAGGCGAAAACTCACATTTCATAAAAGAGTTTTTTACATTCAGGCATCAAGTTATTGAGTTTTTAGTAACTGAATGTGATTTTGACACCTTGGCATTTGAGTTTGGTTTTTCTGAAGGATTAGAAGTTGATAAGTGGATAAAATCACAAATTCCATTCGACGATTTGGATAAGTTACTGTCACACTTTTATTATCCAAATGAGTTTAAAGATACTTTGCTATGGCTTCGTCGGTATAATCAAGACAATAATAATCAAATTACCTTTTTAGGTGTGGATATTCCTAAAAATGGAGGTTCTTATTTTCCAAACTTTCGTATTGTATCTGATTATTTGCAAAGACTTTCAATCGTTTCTTCTGATGTCTTACAGAAGATTTTAAATCTTGCTGAGAAATTTGATTTCTATTCGACTTCTCAGCTTGCGTTAAATTTATCGCTTTTTGATGAAGCTGAACATAATGAATTAAAAGCATTGCTATTAAAAGTTTACATTCGTTTGGTCACTCTTCAACCAAAACTGGAAAGTTTAGAGTTTCAATCGATACTTCATCAAGTTAAAGGCTTGATTTATATGAATTATAATGCTGATGCTATGGAAAGCTTCATTACTGAAAAGGGAATTGAGGGAGATATGGGAGCAAAAGACCAGTATATGGCAGAAAGTATTGATTGGTTTTTGAAAAATTCACTTGGTAAAAAGATTATTTTAGTTGCCCACAATGCTCACATTCAAAAAACTCCGGTCGATTTTGACGGATTTATTAGTTGTTATCCAATGGGGCAAAGACTTTCGATGACTTTTGGAGAAAAATACAAAGCATTTGCAATAACTAATCTACGTGGAGAAACTGCCGCATTGTATCCTGATAATGATTATCAATTTGGTTTTAGGGTTGATAAATTTCCACTTGATTCTCCAGAGTCGGATTCTGTTGAATTTTTTATGCAGGAATTATCAGGAAAAGAATGCTGTTTAATAATCAATAAAAGTAAGGAATTAAAAAATTGTAGTAAGATTCGTTTTGATTCTATATATCTAAAAACTGAAATAGTAGATTCTTTTGATGGGATTTTCCTAATAGAAAAATCAACTGTTTCAGAAATAGTGGATTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36951","NCBI_taxonomy_name":"Riemerella anatipestifer","NCBI_taxonomy_id":"34085"}}}},"ARO_accession":"3004608","ARO_id":"42572","ARO_name":"EreD","CARD_short_name":"EreD","ARO_description":"EreD is an erythromycin esterase protein.","ARO_category":{"36459":{"category_aro_accession":"3000320","category_aro_cvterm_id":"36459","category_aro_name":"macrolide esterase","category_aro_description":"Hydrolytic enzymes that cleave the macrocycle lactone ring of macrolide antibiotics.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1303":{"model_id":"1303","model_name":"BEL-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1280":{"protein_sequence":{"accession":"ACV69996.1","sequence":"MKLLLYPLLLFLVIPAFAQADFEHAISDLEAHNQAKIGVALVSENGNLIQGYRANERFAMCSTFKLPLAALVLSRIDAGEENPERKLHYDSAFLEEYAPAAKRYVATGYMTVTEAIQSALQLSDNAAANLLLKEVGGPPLLTKYFRSLGDKVSRFDRIEPTLNTNTPGDERDTTTPMSMAQTVSKLIFGDTLTYKSKGQLRRLLIGNQTGDKTIRAGLPDSWVTGDKTGSCANGGRNDVAFFITTAGKKYVLSVYTNAPELQGEERALLIASVAKLARQYVVH"},"dna_sequence":{"accession":"FJ666063.1","fmin":"0","fmax":"852","strand":"+","sequence":"ATGAAACTGCTGCTCTACCCGTTATTGCTGTTCCTTGTCATTCCAGCCTTTGCCCAGGCGGACTTTGAACATGCCATTTCAGATCTTGAGGCGCACAATCAAGCCAAGATCGGAGTGGCCCTAGTTAGTGAAAATGGCAACCTGATTCAAGGGTATCGTGCGAATGAAAGGTTCGCGATGTGCTCAACTTTCAAGTTGCCGTTGGCCGCTCTTGTTCTGAGTCGCATTGACGCTGGGGAAGAGAATCCTGAGCGCAAGCTTCATTACGATTCCGCGTTCCTTGAAGAGTACGCCCCAGCCGCAAAACGGTATGTGGCAACTGGATATATGACTGTAACTGAGGCAATTCAATCCGCCCTCCAACTCAGCGACAATGCCGCAGCTAACCTGCTGTTAAAAGAGGTTGGCGGCCCACCTTTATTGACAAAGTATTTCCGTAGCCTGGGTGATAAAGTAAGTCGCTTTGATCGTATTGAACCGACTTTGAACACCAATACGCCCGGCGATGAAAGAGATACAACAACGCCCATGTCCATGGCACAGACTGTGTCAAAGCTGATTTTTGGAGACACGTTGACATATAAATCCAAGGGGCAGCTAAGGCGATTACTCATCGGCAATCAGACCGGGGACAAAACCATTCGAGCTGGCTTGCCTGATTCATGGGTAACGGGTGACAAGACAGGCTCGTGTGCGAATGGCGGCCGTAACGATGTGGCGTTTTTTATAACCACTGCCGGAAAAAAATATGTTCTTTCTGTATATACCAATGCACCTGAATTGCAAGGCGAGGAAAGGGCGTTATTAATTGCTTCTGTAGCAAAGTTAGCACGTCAATATGTTGTTCACTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002386","ARO_id":"38786","ARO_name":"BEL-2","CARD_short_name":"BEL-2","ARO_description":"BEL-2 is a beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"38784":{"category_aro_accession":"3002384","category_aro_cvterm_id":"38784","category_aro_name":"BEL beta-lactamase","category_aro_description":"BEL beta-lactamases are class A expanded-spectrum beta-lactamases that are inhibited by clavulanic acid. They are chromosomally encoded and hydrolyze most cephalosporins and aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1304":{"model_id":"1304","model_name":"CTX-M-85","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1336":{"protein_sequence":{"accession":"ACI29347.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTPAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"FJ214368.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCCGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGACTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35772","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Albany","NCBI_taxonomy_id":"211968"}}}},"ARO_accession":"3002495","ARO_id":"38895","ARO_name":"CTX-M-85","CARD_short_name":"CTX-M-85","ARO_description":"CTX-M-85 is a beta-lactamase found in Salmonella enterica.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1306":{"model_id":"1306","model_name":"IND-5","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1093":{"protein_sequence":{"accession":"AAS78754.1","sequence":"MKKRIQFFMVSMMLAPMFNAQVKDFVIEPPIKNNLHIYKTFGVFGGKEYSANSVYLVTKKGVVLFDVPWEKAQYQSLMDTIKKRHNLPVIAVFATHSHDDRAGDLSFFNNKGIKTYATSKTNEFLKKDGKATSTEIIKTGKPYRIGGEEFTVDFLGEGHTADNVVVWFPKYNVLDGGCLVKSNSATDLGYIKEANVEQWPITIDKLKAKYSKATLIIPGHDDWKGGGHVEHTLELLNKK"},"dna_sequence":{"accession":"AY504627.1","fmin":"0","fmax":"720","strand":"+","sequence":"ATGAAAAAAAGAATTCAGTTCTTTATGGTTTCAATGATGCTTGCTCCAATGTTTAATGCGCAGGTAAAGGATTTTGTAATTGAGCCACCCATTAAAAATAACTTACATATTTATAAAACATTTGGAGTATTTGGTGGTAAAGAATATTCTGCCAACTCAGTATATCTTGTCACTAAAAAAGGAGTCGTTTTATTTGATGTTCCCTGGGAAAAAGCACAATACCAAAGCCTGATGGATACAATCAAAAAACGTCATAACCTACCGGTTATTGCTGTATTTGCTACGCATTCCCATGATGACCGCGCTGGAGATCTAAGCTTTTTCAATAATAAAGGGATTAAAACCTATGCTACCAGCAAAACCAATGAGTTTTTGAAAAAAGACGGAAAAGCAACATCCACTGAAATCATAAAAACAGGAAAGCCTTACCGCATTGGAGGCGAAGAATTTACTGTTGATTTTCTGGGTGAAGGGCATACTGCTGATAATGTAGTGGTATGGTTTCCAAAATACAATGTACTGGATGGTGGTTGTCTGGTAAAAAGTAATTCAGCTACTGATTTAGGATATATTAAAGAAGCCAATGTGGAACAATGGCCAATAACCATAGATAAACTGAAGGCTAAATATTCAAAGGCAACATTGATTATTCCAGGACATGATGACTGGAAAGGCGGAGGACATGTTGAGCACACTCTTGAACTTCTTAACAAAAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36916","NCBI_taxonomy_name":"Chryseobacterium indologenes","NCBI_taxonomy_id":"253"}}}},"ARO_accession":"3002261","ARO_id":"38661","ARO_name":"IND-5","CARD_short_name":"IND-5","ARO_description":"IND-5 is a beta-lactamase found in Chryseobacterium indologenes.","ARO_category":{"36199":{"category_aro_accession":"3000060","category_aro_cvterm_id":"36199","category_aro_name":"IND beta-lactamase","category_aro_description":"IND beta-lactamases are class B carbapenem-hydrolyzing beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1171":{"model_id":"1171","model_name":"tet(44)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"410":{"protein_sequence":{"accession":"CBH51823.1","sequence":"MKIINIGILAHVDAGKTTLTESLLYTSGAILELGSVDKGTTRTDTMFLERQRGITIQAAVTSFNWNDYKINIVDTPGHTDFITEVYRSLSVLDGAILVISAKDGVQAQTRILFHALQKMNIPTIIFINKIDQDGINLNNIYQNIKEKLSNDIIVMQNVTLTPEISIKNIIDLDDWDPVISKNDKLLEKYIVGEKLTIQELMYEEYRCVKKGSLFPIYHGSARNNIGTQQLIEAISNLFCSEMNENDSELCGRVFKIEYTDHKQRLVYLRLYSGTLHLRDTIILPEKKKVKLTEIYIPSNGEMIQTKTVCSGDIFIIPNNTLRLNDIIGNEKLLPCNVWNDKTVPILRTRIEPIKIEEREKLLDALTEIADTDPLLRYYVDTITHEIIISFLGTVQLEVICSLLIEKYHINIRIEDPTVIYLEKPLQKADYTIHIEVPPNPFWASIGLSITPLPIGSGIQYESKVSLGYLNQSFQNAVREGINYGLEQGLYGWEVTDCKICFEYGVYYSPVSTPSDFRFLAPIVLEQTLKKAGTQLLEPYLSFILFTPQGYFSRAYKDAQKHCAIIETSQSKNDEVIFTGHIPVRCINEYRNTLTLYTNGQAVFLTELKDYQIATCEPVIQSRRPNNRIDKVRHMFNKKEN"},"dna_sequence":{"accession":"FN594949.1","fmin":"25244","fmax":"27167","strand":"+","sequence":"ATGAAAATAATCAACATTGGTATTCTTGCTCATGTAGATGCAGGAAAGACGACCTTAACGGAAAGTCTGCTTTATACAAGTGGAGCAATTTTAGAATTAGGCAGTGTAGATAAGGGAACAACAAGGACAGATACTATGTTTTTAGAACGTCAGCGTGGAATCACAATTCAGGCAGCAGTTACTTCTTTTAATTGGAATGACTACAAAATCAATATTGTAGATACTCCTGGACATACAGATTTTATAACAGAAGTGTATCGTTCCTTATCTGTTCTTGATGGAGCAATTTTAGTAATTTCTGCTAAAGATGGTGTACAAGCACAAACCCGAATACTATTCCATGCACTTCAAAAAATGAATATACCAACAATTATTTTTATAAATAAAATAGATCAGGATGGAATTAACTTAAATAATATTTATCAAAATATCAAAGAAAAACTTTCAAATGATATTATTGTTATGCAAAATGTAACATTAACTCCAGAAATATCAATTAAAAATATCATTGATTTAGATGATTGGGATCCTGTAATTTCCAAAAATGATAAACTTTTAGAAAAATATATTGTAGGAGAAAAATTGACTATACAAGAATTAATGTATGAAGAATATAGGTGTGTTAAAAAAGGTTCGTTGTTTCCTATATACCATGGAAGTGCTAGAAATAATATAGGGACTCAACAACTTATCGAAGCTATTTCAAATCTTTTTTGTTCTGAAATGAATGAGAATGATTCAGAACTATGTGGAAGAGTTTTTAAAATTGAATATACAGACCATAAGCAAAGATTAGTTTATTTGCGTCTTTATAGTGGAACATTACACTTACGAGATACAATTATATTGCCAGAAAAAAAGAAAGTGAAACTTACAGAAATATATATTCCTTCAAATGGAGAAATGATACAGACAAAAACAGTTTGTTCTGGAGATATTTTTATTATACCTAACAATACATTAAGATTGAACGATATTATAGGAAATGAAAAGCTTTTGCCATGCAATGTATGGAATGACAAGACTGTACCAATACTACGAACAAGAATTGAACCGATAAAAATAGAAGAGAGAGAAAAATTATTGGATGCTCTTACAGAAATTGCAGATACTGATCCTCTTTTACGTTATTATGTTGATACGATAACACATGAAATCATCATTTCTTTTTTAGGAACAGTGCAGTTAGAAGTTATCTGTTCTCTGTTGATTGAAAAATATCACATAAACATAAGAATCGAAGATCCAACCGTAATTTATTTGGAAAAACCATTACAAAAGGCAGATTATACTATTCATATTGAAGTACCACCAAATCCATTTTGGGCATCGATTGGATTATCAATAACTCCACTTCCAATTGGCAGTGGAATACAGTACGAAAGCAAAGTTTCACTCGGTTATTTAAATCAAAGTTTCCAAAATGCAGTAAGAGAAGGTATTAATTATGGACTGGAGCAAGGTTTGTATGGTTGGGAAGTAACAGATTGTAAAATATGTTTTGAATATGGTGTTTATTATAGCCCTGTTAGTACTCCCTCGGATTTTCGCTTTCTTGCCCCAATTGTACTTGAACAAACATTGAAAAAAGCGGGAACGCAATTATTAGAGCCATATCTTTCGTTTATACTTTTTACGCCACAGGGATACTTTTCTCGTGCATATAAAGATGCACAAAAACATTGTGCAATAATTGAAACAAGTCAATCAAAAAATGATGAAGTTATTTTTACAGGACATATTCCTGTACGTTGTATTAATGAATATCGTAATACTTTAACTCTATATACAAATGGGCAAGCAGTTTTTTTGACAGAATTAAAAGATTATCAAATTGCTACTTGTGAACCAGTTATTCAATCACGTAGACCAAATAATCGAATAGATAAAGTACGCCATATGTTTAATAAAAAAGAAAATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36889","NCBI_taxonomy_name":"Campylobacter fetus subsp. fetus","NCBI_taxonomy_id":"32019"}}}},"ARO_accession":"3000556","ARO_id":"36695","ARO_name":"tet(44)","CARD_short_name":"tet(44)","ARO_description":"Tet44 is a tetracycline resistance gene found in Campylobacter fetus, and binds to the ribosome to confer antibiotic resistance as a ribosomal protection protein.","ARO_category":{"35921":{"category_aro_accession":"0000002","category_aro_cvterm_id":"35921","category_aro_name":"tetracycline-resistant ribosomal protection protein","category_aro_description":"A family of proteins known to bind to the 30S ribosomal subunit. This interaction prevents tetracycline and tetracycline derivatives from inhibiting ribosomal function. Thus, these proteins confer elevated resistance to tetracycline derivatives as a ribosomal protection protein.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35986":{"category_aro_accession":"0000069","category_aro_cvterm_id":"35986","category_aro_name":"doxycycline","category_aro_description":"Doxycycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36291":{"category_aro_accession":"3000152","category_aro_cvterm_id":"36291","category_aro_name":"minocycline","category_aro_description":"Minocycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36667":{"category_aro_accession":"3000528","category_aro_cvterm_id":"36667","category_aro_name":"chlortetracycline","category_aro_description":"Chlortetracycline was an early, first-generation tetracycline antibiotic developed in the 1940's. It inhibits bacterial protein synthesis by binding to the 30S subunit of bacterial ribosomes, preventing the aminoacyl-tRNA from binding to the ribosome.","category_aro_class_name":"Antibiotic"},"37011":{"category_aro_accession":"3000667","category_aro_cvterm_id":"37011","category_aro_name":"demeclocycline","category_aro_description":"Demeclocycline is a tetracycline analog with 7-chloro and 6-methyl groups. Due to its fast absorption and slow excretion, it maintains higher effective blood levels compared to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37012":{"category_aro_accession":"3000668","category_aro_cvterm_id":"37012","category_aro_name":"oxytetracycline","category_aro_description":"Oxytetracycline is a derivative of tetracycline with a 5-hydroxyl group. Its activity is similar to other tetracyclines.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1198":{"model_id":"1198","model_name":"mef(B)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"4728":{"protein_sequence":{"accession":"ACJ63262.1","sequence":"MNRIKNWKKQFAVIYTGQAFSILGSAAVQFAVIWWLTIQTESAITLTIASLVAFLPNMLIGPFAGVWIDRYNRRTVMILADGLVAVSSIILGAAFLLVETPPIWFIYIVLFLRGLGNTFHGPAMQAAIPMFVPADMLTKAGGWGNMIQSISNMMGPVLGAALMSFLPISSIMIVDILGAAFAIVCLLFVIIPDITQTNEKMSVLSDMKQGFIAMKANKPLMAVFSPMLLMTILYMPLGSLFPLLARSHFMGEAWHNSIVEFVFAGGLLLSSLVIGVWGGMKRRFFMASLAIGLMGLATLISGALPTSGFWIFVICCFFLGASGTFMNVPVMAYVQESIAPEMMGKVFSLLMTAMTLSMPIGLLVAGPVVEVIGVNTWFFWSGVALIVNAVLCRILTRRYDKVTMKPQVD"},"dna_sequence":{"accession":"FJ196385.1","fmin":"11083","fmax":"12313","strand":"-","sequence":"ATGAACAGAATAAAAAATTGGAAGAAACAATTTGCTGTAATATACACAGGGCAGGCTTTTTCAATCTTGGGTTCTGCCGCAGTGCAGTTCGCTGTTATCTGGTGGCTGACCATCCAGACTGAATCCGCAATCACCTTGACGATTGCATCCTTAGTTGCCTTTCTCCCCAATATGTTAATCGGACCCTTTGCCGGTGTGTGGATCGACCGATACAACCGCCGAACAGTAATGATTTTAGCTGACGGTCTGGTAGCTGTATCCAGCATCATCCTTGGGGCAGCATTTTTACTTGTGGAAACACCCCCTATTTGGTTTATCTACATTGTTTTATTTTTGCGTGGATTGGGGAATACCTTTCACGGTCCAGCTATGCAAGCGGCGATACCCATGTTTGTGCCAGCAGATATGTTGACCAAAGCAGGGGGCTGGGGAAATATGATCCAATCAATATCCAACATGATGGGGCCTGTGCTGGGTGCTGCGCTTATGTCATTTCTACCTATTTCCTCCATTATGATTGTGGATATACTGGGAGCCGCTTTTGCGATAGTTTGCCTCCTATTTGTTATAATTCCAGACATTACGCAAACCAATGAGAAGATGAGTGTATTGTCTGACATGAAGCAGGGCTTTATCGCAATGAAAGCAAATAAACCTTTAATGGCTGTGTTTTCCCCCATGCTGCTGATGACCATACTTTATATGCCATTAGGTTCTCTGTTCCCTCTACTGGCACGCAGCCACTTTATGGGTGAAGCCTGGCACAATAGCATTGTGGAATTTGTCTTTGCAGGTGGATTGCTTCTTTCATCTTTGGTTATCGGTGTATGGGGCGGCATGAAAAGAAGGTTTTTCATGGCATCCTTAGCTATTGGCTTAATGGGTCTGGCTACACTGATTAGCGGAGCGCTACCGACAAGCGGTTTTTGGATATTTGTTATATGCTGCTTCTTCTTGGGCGCCTCTGGCACATTTATGAATGTTCCTGTTATGGCTTATGTTCAAGAAAGCATTGCCCCTGAAATGATGGGCAAGGTGTTTTCCCTTTTGATGACCGCCATGACTCTTTCTATGCCGATAGGCTTACTTGTTGCAGGTCCGGTTGTTGAGGTTATAGGTGTTAATACATGGTTTTTCTGGTCTGGTGTTGCGTTGATAGTAAACGCTGTTCTCTGCCGCATTCTGACACGACGCTATGACAAAGTAACAATGAAACCGCAAGTGGACTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3003107","ARO_id":"39681","ARO_name":"mef(B)","CARD_short_name":"mef(B)","ARO_description":"mef(B) is a macrolide efflux gene located in the vicinity of sul3 in Escherichia coli. There is also a mefB found in Streptococcus agalactiae that confers resistance to macrolides.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1206":{"model_id":"1206","model_name":"QepA1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"900"}},"model_sequences":{"sequence":{"398":{"protein_sequence":{"accession":"AEZ36150.1","sequence":"MSATLHDTAADRRKATRREWIGLAVVALPCLVYAMDLTVLNLALPVLSRELQPSSAQLLWILDIYGFFVAGFLITMGTLGDRIGRRRLLLIGAAFFAFASVLAALADTAALLIAARALLGLAGATIAPSTMALVRNMFHDPRQRQFAIGVWIAAFSLGSAIGPLVGGVLLEFFHWGAVFWLNVPVMLLTLALGPRFLPEYRDPDAGHLDLASVLLSLAAVLLTIYGLKQLAEHGEGLASMAALLAGLAVGALFLRRQGHIAYPLLDLRLFAHALFRAALAAYALAALAMFGVYIFMTQYLQLVLGLSPLQAGLATLPCSLCFVIGSLLSPQLAARWPAARILVVGLSAAAFGFAVLGLGQGLWWLVPATIVKGLGLAPVFTIGNEIIITSAPSERAGAASALSETVSEFSGALGIALFGSVGLVVYRQALTSAALPGLPADALQTAGASLGGAVHLADTLPAWQGAALLAAARAGFTDALQATAWAGAVLVLVAAGLVARLLRKRPALASG"},"dna_sequence":{"accession":"JQ064560.1","fmin":"0","fmax":"1536","strand":"+","sequence":"ATGTCCGCCACGCTCCACGACACCGCAGCGGATCGTCGGAAGGCCACCCGCCGCGAATGGATCGGCCTGGCCGTGGTCGCCCTGCCGTGCCTGGTCTACGCCATGGACCTCACGGTGCTGAACCTGGCGCTGCCGGTGCTCAGCCGTGAACTGCAGCCCTCCAGCGCCCAGCTTCTCTGGATCCTGGACATCTACGGCTTCTTCGTCGCCGGCTTCCTGATCACCATGGGCACGCTGGGCGACCGCATCGGCCGGCGCCGGCTGTTGTTGATCGGCGCGGCGTTCTTCGCATTCGCCTCGGTGCTCGCGGCGCTGGCCGATACCGCCGCGCTGTTGATCGCGGCGCGCGCCTTGCTCGGCCTGGCCGGCGCCACCATCGCGCCGTCCACCATGGCGCTGGTCCGCAACATGTTCCACGACCCGCGCCAGCGCCAGTTCGCCATCGGCGTGTGGATCGCCGCGTTTTCGCTGGGCAGCGCGATCGGTCCGCTGGTCGGCGGCGTGTTGCTGGAGTTCTTCCACTGGGGCGCCGTGTTCTGGCTCAACGTGCCGGTGATGCTGCTGACGCTGGCGCTCGGCCCTCGCTTCCTGCCCGAGTATCGTGATCCGGACGCGGGGCACCTGGACCTGGCCAGCGTGCTGCTGTCGCTGGCGGCGGTGCTGCTGACGATCTACGGGCTCAAGCAGTTGGCCGAGCATGGAGAGGGCCTCGCCTCGATGGCTGCGCTGCTGGCCGGGCTGGCGGTCGGGGCGCTGTTCCTGCGCCGCCAGGGCCACATCGCCTACCCGCTGCTGGACCTGCGGCTGTTCGCGCACGCGCTGTTCCGCGCGGCGCTGGCGGCGTATGCGCTGGCCGCGCTGGCCATGTTCGGCGTCTACATCTTCATGACGCAGTACCTGCAGCTCGTGCTGGGGCTGTCGCCGCTGCAGGCCGGGCTGGCCACGCTGCCCTGCTCCCTGTGCTTCGTCATCGGTTCGCTGTTGTCGCCGCAGCTCGCGGCGCGCTGGCCGGCGGCGCGCATCCTCGTCGTGGGCCTGTCGGCAGCGGCGTTCGGCTTCGCCGTGCTGGGGCTGGGGCAGGGCCTGTGGTGGCTGGTGCCGGCCACGATCGTCAAGGGCCTGGGCCTGGCGCCGGTGTTCACCATCGGCAACGAGATCATCATCACCAGCGCGCCGTCCGAGCGCGCGGGCGCGGCCTCGGCCTTGTCGGAGACGGTGTCCGAATTCAGCGGCGCGCTGGGCATCGCGCTGTTCGGCAGCGTCGGCCTGGTGGTCTACCGGCAGGCGCTGACCAGCGCGGCGCTGCCCGGCCTGCCGGCCGATGCGCTGCAGACGGCCGGTGCCTCGCTCGGGGGCGCCGTGCACCTGGCCGACACCCTGCCGGCGTGGCAGGGCGCGGCCTTGCTGGCGGCCGCACGCGCGGGCTTCACCGATGCGCTGCAGGCCACGGCCTGGGCCGGCGCGGTGCTGGTGCTGGTGGCCGCTGGGCTGGTGGCGCGCCTGCTGCGCAAGCGCCCAGCGCTCGCATCTGGTTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36770","NCBI_taxonomy_name":"Klebsiella aerogenes","NCBI_taxonomy_id":"548"}}}},"ARO_accession":"3000448","ARO_id":"36587","ARO_name":"QepA1","CARD_short_name":"QepA1","ARO_description":"QepA1 is a plasmid-mediated efflux pump in E. coli, shown to contribute to fluoroquinolone resistance. It is regulated by sox genes, also known as global stress regulators.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1223":{"model_id":"1223","model_name":"vph","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"62":{"protein_sequence":{"accession":"CAA26235.1","sequence":"MRIIETHRDLLSRLLPGDTVGGLAVHEGQFHHVVIGSHRVVCFARTRAAADRLPGRADVLRALAGIDLGFRTPQPLSEGGAQGTDEPPYLVLSRIPGAPLEDDVLTSPEVAEAVARQYATLLSGLAAAGDEEKVRAALPEAPANEWQEFATGVRTELFPLMSDGGRERAERELAALDALPHLTSAVVHGDLGGENVLWETVDGVPRMSGVVDWDEVGIGDPAEDLAAIGASYGEELLGRVLALGGWADNGTAERISAIRGTFALQQALYAQRDGDEEELADGLSGYR"},"dna_sequence":{"accession":"X02393.1","fmin":"96","fmax":"960","strand":"+","sequence":"ATGAGAATCATTGAGACGCACCGCGATCTGCTGAGCCGGCTCCTGCCCGGGGACACCGTGGGCGGACTCGCCGTCCACGAGGGGCAGTTCCACCATGTGGTGATCGGATCGCACCGGGTGGTCTGCTTCGCCCGCACCCGGGCGGCCGCCGACCGTCTGCCCGGCAGGGCGGACGTCCTGCGCGCTCTTGCCGGGATCGACCTCGGGTTTCGCACGCCGCAGCCGCTGTCCGAGGGCGGCGCCCAGGGCACGGACGAGCCGCCGTACCTGGTGCTGAGCCGCATTCCCGGAGCACCGTTGGAGGACGATGTGCTCACCAGCCCGGAGGTGGCGGAGGCCGTCGCCCGACAGTACGCGACCCTGCTGTCCGGGCTCGCGGCGGCGGGCGACGAGGAGAAGGTGCGCGCCGCGCTGCCGGAGGCTCCCGCGAACGAGTGGCAGGAGTTCGCCACGGGGGTGCGTACCGAACTGTTCCCGCTGATGTCCGACGGCGGCCGGGAGCGTGCCGAGCGCGAGCTCGCCGCGCTCGACGCCCTGCCCCATCTCACCTCCGCGGTGGTCCACGGTGACCTCGGCGGCGAGAACGTCCTGTGGGAGACGGTGGACGGAGTGCCGCGCATGAGCGGCGTCGTCGACTGGGACGAGGTCGGCATCGGCGACCCGGCTGAGGACCTGGCCGCCATCGGGGCGAGCTACGGCGAGGAACTGCTGGGCCGAGTGCTCGCGCTCGGCGGCTGGGCCGACAACGGAACGGCCGAGCGGATCTCGGCGATCCGAGGCACCTTCGCACTCCAGCAGGCCCTCTACGCGCAGCGCGACGGCGACGAGGAGGAACTCGCCGACGGCCTCAGCGGCTACCGGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39588","NCBI_taxonomy_name":"Streptomyces vinaceus","NCBI_taxonomy_id":"1960"}}}},"ARO_accession":"3003061","ARO_id":"39495","ARO_name":"vph","CARD_short_name":"vph","ARO_description":"vph is a phosphotransferase that confers resistance to viomycin in Streptomyces vinaceus.","ARO_category":{"41425":{"category_aro_accession":"3004261","category_aro_cvterm_id":"41425","category_aro_name":"viomycin phosphotransferase","category_aro_description":"Viomycin family of phosphotransferases confer resistance to viomycin antibiotics.","category_aro_class_name":"AMR Gene Family"},"35937":{"category_aro_accession":"0000018","category_aro_cvterm_id":"35937","category_aro_name":"viomycin","category_aro_description":"Viomycin sulfate (Viocin) is an polypeptide antibiotic used in the treatment of tuberculosis. It is produced by the actinomycete Streptomyces puniceus and binds to the bacterial ribosome, inhibiting prokaryotic protein synthesis and certain forms of RNA splicing.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1282":{"model_id":"1282","model_name":"SIM-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1152":{"protein_sequence":{"accession":"ACT66697.1","sequence":"MRTLLILCLFGTLNTAFAEEAQPDLKIEKIEEGIYLHTSFQEYKGFGIVKKQGLVVLDNHKAYLIDTPASAGDTEKLVNWLEKNDFTVNGSISTHFHDDSTAGIEWLNTKSIPTYASKLTNELLNKNGKTQAKHSFDKESFWLVKNKIEIFYPGPGHTQDNEVVWIPNKKILFGGCFIKPNGLGNLSDANLEAWPGSAKKMISKYSKAKLVIPSHSEIGDASLLKLTWEQAIKGLNESKSKPPLIN"},"dna_sequence":{"accession":"GQ288397.1","fmin":"0","fmax":"741","strand":"+","sequence":"ATGAGAACTTTATTGATTTTATGTTTATTCGGCACTTTAAATACCGCGTTTGCGGAAGAAGCCCAGCCAGATTTAAAAATTGAAAAAATAGAAGAAGGGATCTATCTTCATACATCTTTTCAAGAGTACAAGGGATTCGGCATCGTTAAAAAACAAGGCTTAGTAGTTCTTGACAATCACAAGGCATATCTCATCGACACTCCAGCTTCCGCAGGAGATACTGAAAAGCTAGTAAACTGGCTCGAAAAAAATGATTTCACTGTCAATGGAAGCATTTCAACACATTTCCACGACGACAGTACTGCTGGGATAGAGTGGCTTAATACAAAGTCCATCCCCACATATGCATCTAAATTGACAAATGAATTGCTAAATAAAAATGGCAAAACTCAAGCCAAGCACTCTTTTGATAAAGAGAGCTTTTGGTTGGTCAAAAATAAAATTGAAATTTTTTATCCAGGCCCAGGACACACTCAAGATAACGAAGTTGTCTGGATACCTAATAAAAAAATCCTATTCGGGGGCTGTTTTATAAAACCGAATGGCCTTGGCAATCTAAGTGACGCAAATTTGGAAGCTTGGCCAGGCTCCGCAAAAAAAATGATATCAAAATACAGTAAGGCAAAACTTGTTATCCCAAGCCACAGTGAAATCGGAGACGCATCACTATTGAAACTCACATGGGAACAGGCCATTAAAGGTTTAAATGAAAGCAAATCAAAACCGCCGCTCATTAATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39090","NCBI_taxonomy_name":"Acinetobacter bereziniae","NCBI_taxonomy_id":"106648"}}}},"ARO_accession":"3000846","ARO_id":"37226","ARO_name":"SIM-1","CARD_short_name":"SIM-1","ARO_description":"SIM-1 is an integron-encoded Ambler class B beta-lactamase isolated from Acinetobacter baumannii.","ARO_category":{"41370":{"category_aro_accession":"3004206","category_aro_cvterm_id":"41370","category_aro_name":"SIM beta-lactamase","category_aro_description":"SIM beta-lactamases are Class B beta-lactamases that are capable of hydrolyzing a wide variety of beta-lactams, including penicillins, narrow- to expanded-spectrum cephalosporins, and carbapenem. The SIM family of beta-lactamases appear to be transferable through integrons.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1285":{"model_id":"1285","model_name":"SAT-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"584":{"protein_sequence":{"accession":"BAD95494.1","sequence":"MKISVIPEQVAETLDAENHFIVREVFDVHLSDQGFELSTRSVSPYRKDYISDDDSDEDSACYGAFIDQELVGKIELNSTWNDLASIEHIVVSHTHRGKGVAHSLIEFAKKWALSRQLLGIRLETQTNNVPACNLYAKCGFTLGGIDLFTYKTRPQVSNETAMYWYWFSGAQDDA"},"dna_sequence":{"accession":"AB211124.1","fmin":"0","fmax":"525","strand":"+","sequence":"ATGAAGATTTCGGTGATCCCTGAGCAGGTGGCGGAAACATTGGATGCTGAGAACCATTTCATTGTTCGTGAAGTGTTCGATGTGCACCTATCCGACCAAGGCTTTGAACTATCTACCAGAAGTGTGAGCCCCTACCGGAAGGATTACATCTCGGATGATGACTCTGATGAAGACTCTGCTTGCTATGGCGCATTCATCGACCAAGAGCTTGTCGGGAAGATTGAACTCAACTCAACATGGAACGATCTAGCCTCTATCGAACACATTGTTGTGTCGCACACGCACCGAGGCAAAGGAGTCGCGCACAGTCTCATCGAATTTGCGAAAAAGTGGGCACTAAGCAGACAGCTCCTTGGCATACGATTAGAGACACAAACGAACAATGTACCTGCCTGCAATTTGTACGCAAAATGTGGCTTTACTCTCGGCGGCATTGACCTGTTCACGTATAAAACTAGACCTCAAGTCTCGAACGAAACAGCGATGTACTGGTACTGGTTCTCGGGAGCACAGGATGACGCCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002895","ARO_id":"39329","ARO_name":"SAT-2","CARD_short_name":"SAT-2","ARO_description":"SAT-2 is a plasmid-mediated streptothricin acetyltransferase, which confers resistance to streptothricin, a nucleoside antibiotic. Originally described from an E. coli plasmid sequence by Heim et al., 1989.","ARO_category":{"37249":{"category_aro_accession":"3000869","category_aro_cvterm_id":"37249","category_aro_name":"streptothricin acetyltransferase (SAT)","category_aro_description":"AcetylCoA dependent acetyltransferase that acetylate streptothricins such as nourseothricin at position 16 (beta position of beta-lysine).","category_aro_class_name":"AMR Gene Family"},"35931":{"category_aro_accession":"0000012","category_aro_cvterm_id":"35931","category_aro_name":"streptothricin","category_aro_description":"Streptothricins are a group of N-glycoside antibiotics that include a carbamoylated D-glucosamine to which are attached a series of L-beta-lysine residues at position 2 and a streptolidine at position 1.  Streptothricins vary by the number of beta-lysine residues (from 1 (nourseothricin) to 7) and target protein synthesis in bacteria and eukaryotes.","category_aro_class_name":"Antibiotic"},"36174":{"category_aro_accession":"3000034","category_aro_cvterm_id":"36174","category_aro_name":"nucleoside antibiotic","category_aro_description":"Nucleoside antibiotics are made of modified nucleosides and nucleotides with wide-ranging activities and means of antibacterial effects. This drug class includes aminonucleoside antibiotics, which contain an amino group.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1222":{"model_id":"1222","model_name":"FosA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"200"}},"model_sequences":{"sequence":{"5386":{"protein_sequence":{"accession":"AAG04518.1","sequence":"MLTGLNHLTLAVADLPASIAFYRDLLGFRLEARWDQGAYLELGSLWLCLSREPQYGGPAADYTHYAFGIAAADFARFAAQLRAHGVREWKQNRSEGDSFYFLDPDGHRLEAHVGDLRSRLAACRQAPYAGMRFAD"},"dna_sequence":{"accession":"AE004091.2","fmin":"1221690","fmax":"1222098","strand":"+","sequence":"ATGCTTACCGGTCTCAATCACCTGACCCTGGCGGTCGCCGACCTGCCGGCCAGCATCGCCTTCTACCGCGATCTTCTCGGCTTTCGCCTGGAAGCGCGCTGGGACCAGGGCGCCTATCTCGAACTGGGTTCGCTGTGGCTGTGCCTGTCCCGGGAGCCGCAGTACGGCGGGCCGGCCGCGGACTACACGCACTACGCCTTCGGCATCGCCGCCGCGGATTTCGCCCGCTTCGCCGCGCAGCTGCGCGCGCATGGCGTGCGCGAATGGAAGCAGAACCGCAGCGAGGGCGATTCGTTCTACTTCCTCGACCCGGACGGCCATCGCCTGGAGGCCCACGTCGGCGACCTGCGCAGCCGGCTCGCGGCGTGCCGGCAAGCGCCCTATGCGGGAATGCGTTTCGCCGACTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36804","NCBI_taxonomy_name":"Pseudomonas aeruginosa PAO1","NCBI_taxonomy_id":"208964"}}}},"ARO_accession":"3000149","ARO_id":"36288","ARO_name":"FosA","CARD_short_name":"FosA","ARO_description":"An enzyme that confers resistance to fosfomycin in Serratia marcescens by breaking the epoxide ring of the molecule. It depends on the cofactors Manganese (II) and Potassium and uses Glutathione (GSH) as the nucleophilic molecule. In Pseudomonas aeruginosa, FosA catalyzes the conjugation of glutathione to carbon-1 of fosfomycin, rendering it ineffective as an antibacterial drug.","ARO_category":{"36272":{"category_aro_accession":"3000133","category_aro_cvterm_id":"36272","category_aro_name":"fosfomycin thiol transferase","category_aro_description":"Catalyzes the addition of a thiol group from a nucleophilic molecule to fosfomycin.","category_aro_class_name":"AMR Gene Family"},"35944":{"category_aro_accession":"0000025","category_aro_cvterm_id":"35944","category_aro_name":"fosfomycin","category_aro_description":"Fosfomycin (also known as phosphomycin and phosphonomycin) is a broad-spectrum antibiotic produced by certain Streptomyces species. It is effective on gram positive and negative bacteria as it targets the cell wall, an essential feature shared by both bacteria. Its specific target is MurA (MurZ in E.coli), which attaches phosphoenolpyruvate (PEP) to UDP-N-acetylglucosamine, a step of commitment to cell wall synthesis. In the active site of MurA, the active cysteine molecule is alkylated which stops the catalytic reaction.","category_aro_class_name":"Antibiotic"},"45731":{"category_aro_accession":"3007149","category_aro_cvterm_id":"45731","category_aro_name":"phosphonic acid antibiotic","category_aro_description":"A group of antibiotics derived from phosphonic acids.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1307":{"model_id":"1307","model_name":"OXY-1-6","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"982":{"protein_sequence":{"accession":"CAB42615.1","sequence":"MLKSSWRKTALMAAAAVPLLLASGSLWASADAIQQKLADLEKRSGGRLGVALINTADDSQTLYRGDERFAMCSTGKVMAAAAVLKQSESNPEVVNKRLEIKKSDLVVWSPITEKHLQSGMTLAELSAAALQYSDNTAMNKMISYLGGPEKVTAFAQSIGDVTFRLDRTEPALNSAIPGDKRDTTTPLAMAESLRKLTLGNALGEQQRAQLVTWLKGNTTGGQSIRAGLPASWAVGDKTGAGDYGTTNDIAVIWPENHAPLVPVTYFTQPQQDAKSRKKVLAAAAKIVTEGL"},"dna_sequence":{"accession":"Y17715.1","fmin":"146","fmax":"1022","strand":"+","sequence":"ATGTTGAAAAGTTCGTGGCGTAAAACCGCCCTGATGGCCGCCGCCGCCGTTCCGCTGCTGCTGGCGAGCGGTTCATTATGGGCCAGTGCCGATGCTATCCAGCAAAAGCTGGCTGATTTAGAAAAACGTTCCGGCGGTCGGCTGGGCGTAGCGCTGATTAACACGGCAGATGATTCGCAAACCCTCTATCGCGGCGATGAACGTTTTGCCATGTGCAGCACCGGTAAAGTGATGGCCGCCGCCGCGGTGTTAAAACAGAGCGAAAGCAATCCAGAGGTGGTGAATAAAAGGCTGGAGATTAAAAAATCGGATTTAGTGGTCTGGAGCCCGATCACCGAAAAACATCTGCAAAGCGGAATGACCCTGGCGGAACTCAGCGCGGCGGCGCTGCAGTACAGCGACAATACCGCGATGAATAAGATGATTAGCTACCTTGGCGGACCGGAAAAGGTGACCGCATTCGCCCAGAGTATCGGGGATGTCACTTTTCGTCTCGATCGTACGGAGCCGGCGCTGAACAGCGCGATTCCCGGCGATAAGCGCGATACCACCACCCCGTTGGCGATGGCCGAAAGCCTGCGCAAGCTGACGCTGGGCAATGCGCTGGGCGAACAGCAGCGCGCCCAGTTAGTGACGTGGCTAAAAGGCAATACCACCGGCGGGCAAAGCATTCGCGCAGGCCTGCCCGCAAGCTGGGCGGTCGGGGATAAAACCGGCGCCGGAGATTACGGCACCACCAACGATATTGCGGTGATCTGGCCGGAAAATCATGCCCCGCTGGTGCCGGTGACCTATTTTACCCAGCCGCAGCAAGATGCGAAAAGCCGCAAAAAGGTGTTAGCCGCGGCGGCAAAAATCGTCACCGAAGGGCTTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3002394","ARO_id":"38794","ARO_name":"OXY-1-6","CARD_short_name":"OXY-1-6","ARO_description":"OXY-1-6 is a beta-lactamase found in Klebsiella oxytoca.","ARO_category":{"38788":{"category_aro_accession":"3002388","category_aro_cvterm_id":"38788","category_aro_name":"OXY beta-lactamase","category_aro_description":"OXY beta-lactamases are chromosomal class A beta-lactamases that are found in Klebsiella oxytoca. At constitutive low levels, OXY beta-lactamases confer resistance to aminopenicillins and carboxypenicillins. At high induced levels,  OXY beta-lactamases confer resistance to penicillins, cephalosporins and aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1309":{"model_id":"1309","model_name":"ACT-20","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1853":{"protein_sequence":{"accession":"AHA80105.1","sequence":"MMKKSLCCALLLGLSCSALAAPVSEKQLAEVVANTVTPLMKAQSVPGMAVAVIYQGKSHYYTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMPYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPEKVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVVEGSDSKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANKSYPNPARVEAAYHILEALQ"},"dna_sequence":{"accession":"KF526117.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCCCTTTGCTGCGCCCTGCTGCTGGGCCTCTCTTGCTCTGCTCTCGCCGCGCCAGTATCAGAAAAACAGCTGGCGGAGGTGGTCGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCTGTTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGAAAATCGCACTATTACACGTTCGGTAAAGCCGATGTTGCGGCGAATAAACCCGTTACGCCTCAGACCCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGCGTTTTAGGTGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTGACGGGCAAGCAGTGGCAGGGTATTCGTATGCTGGATCTCGCCACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTCAAACCTTCTGGCATGCCCTATGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTTCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGAATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCGGAGAAGGTTGCCGATGCCTCACTTAAGCAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGGTCGAAGGCAGCGACAGTAAGGTAGCGCTGGCGCCGTTACCCGTGGCAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGTTCTACCGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCGAGGCGCTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39098","NCBI_taxonomy_name":"Enterobacter hormaechei","NCBI_taxonomy_id":"158836"}}}},"ARO_accession":"3001841","ARO_id":"38241","ARO_name":"ACT-20","CARD_short_name":"ACT-20","ARO_description":"ACT-20 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1310":{"model_id":"1310","model_name":"IMP-10","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1671":{"protein_sequence":{"accession":"BAB72069.1","sequence":"MSKLSVFFIFLFCSIATAAESLPDLKIEKLDEGVYVHTSFEEVNGWGVFPKHGLVVLVNAEAYLIDTPFTAKDTEKLVTWFVERGYKIKGSISSHFHSDSTGGIEWLNSRSIPTYASELTNELLKKDGKVQATNSFSGVNYWLVKNKIEVFYPGPGHTPDNVVVWLPERKILFGGCFIKPYGLGNLGDANIEAWPKSAKLLKSKYGKAKLVVPSHSEVGDASLLKLTLEQAVKGLNESKKPSKPSN"},"dna_sequence":{"accession":"AB074433.1","fmin":"16","fmax":"757","strand":"+","sequence":"ATGAGCAAGTTATCTGTATTCTTTATATTTTTGTTTTGCAGCATTGCTACCGCAGCAGAGTCTTTGCCAGATTTAAAAATTGAAAAGCTTGATGAAGGCGTTTATGTTCATACTTCGTTTGAAGAAGTTAACGGGTGGGGCGTTTTTCCTAAACATGGTTTGGTGGTTCTTGTAAATGCTGAGGCTTACCTAATTGACACTCCATTTACGGCTAAAGATACTGAAAAGTTAGTCACTTGGTTTGTGGAGCGTGGCTATAAAATAAAAGGCAGCATTTCCTCTCATTTTCATAGCGACAGCACGGGCGGAATAGAGTGGCTTAATTCTCGATCTATCCCCACGTATGCATCTGAATTAACAAATGAACTGCTTAAAAAAGACGGTAAGGTTCAAGCCACAAATTCATTTAGCGGAGTTAACTATTGGCTAGTTAAAAATAAAATTGAAGTTTTTTATCCAGGCCCGGGACACACTCCAGATAACGTAGTGGTTTGGTTGCCTGAAAGGAAAATATTATTCGGTGGTTGTTTTATTAAACCGTACGGTTTAGGCAATTTGGGTGACGCAAATATAGAAGCTTGGCCAAAGTCCGCCAAATTATTAAAGTCCAAATATGGTAAGGCAAAACTGGTTGTTCCAAGTCACAGTGAAGTTGGAGACGCATCACTCTTGAAACTTACATTAGAGCAGGCGGTTAAAGGGTTAAACGAAAGTAAAAAACCATCAAAACCAAGCAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002201","ARO_id":"38601","ARO_name":"IMP-10","CARD_short_name":"IMP-10","ARO_description":"IMP-10 is a beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1311":{"model_id":"1311","model_name":"OXY-5-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"816":{"protein_sequence":{"accession":"CAI43419.1","sequence":"MLKSSWRKTALMAAAVPLLLASGSLWASADAIQQKLADLEKRSGGRLGVALINTADDSQTLYRGDERFAMCSTGKVMAAAAVLKQSESNPEVVNKRLEIKKADLVVWSPITEKHLQSGMTLAELSAAALQYSDNTAMNKIIGYLGGPEKVTAFALSIGDVTFRLDRMEPALNSAIPGDKRDTTTPLAMAESLRKLTLGNALGEQQRAQLVTWLKGNTTGGQSIRAGLPASWAVGDKTGAGDYGTTNDIAVIWPENHAPLVLVTYFTQPQQDAKSRKEVLAAAAKIVTEGL"},"dna_sequence":{"accession":"AJ871871.1","fmin":"0","fmax":"873","strand":"+","sequence":"ATGTTGAAAAGTTCGTGGCGTAAAACCGCCCTGATGGCCGCCGCCGTTCCGCTGCTGCTGGCGAGCGGTTCATTATGGGCCAGTGCCGATGCTATCCAGCAAAAGCTGGCTGATTTAGAAAAACGTTCCGGCGGTCGGCTGGGCGTAGCGCTGATTAACACGGCAGATGATTCGCAAACCCTCTATCGCGGCGATGAACGGTTTGCCATGTGCAGCACCGGTAAAGTGATGGCCGCCGCCGCGGTGTTAAAACAGAGCGAAAGCAATCCAGAGGTAGTGAATAAAAGGCTGGAGATTAAAAAAGCGGATTTAGTAGTCTGGAGCCCGATTACCGAAAAACATCTGCAAAGCGGAATGACCCTGGCGGAACTCAGCGCGGCGGCGCTGCAGTACAGCGACAATACCGCGATGAATAAGATTATCGGTTACCTTGGCGGGCCGGAAAAAGTCACCGCATTCGCCCTGAGTATCGGTGACGTTACTTTTCGTCTCGATCGCATGGAGCCGGCGCTGAACAGCGCGATTCCCGGCGATAAGCGCGATACCACCACCCCGTTGGCGATGGCCGAAAGCCTGCGCAAGCTGACGCTGGGCAATGCGCTGGGCGAACAGCAGCGCGCCCAGTTAGTGACGTGGCTAAAAGGCAATACCACCGGCGGGCAAAGCATTCGCGCAGGCCTGCCCGCAAGCTGGGCGGTCGGGGATAAAACCGGCGCCGGAGATTACGGCACCACCAACGATATCGCGGTGATCTGGCCGGAAAATCATGCCCCGCTGGTGCTGGTGACCTATTTTACCCAGCCGCAGCAGGATGCGAAAAGCCGCAAAGAGGTGTTAGCCGCGGCGGCAAAAATCGTCACCGAAGGGCTTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3002412","ARO_id":"38812","ARO_name":"OXY-5-2","CARD_short_name":"OXY-5-2","ARO_description":"OXY-5-2 is a beta-lactamase found in Klebsiella oxytoca.","ARO_category":{"38788":{"category_aro_accession":"3002388","category_aro_cvterm_id":"38788","category_aro_name":"OXY beta-lactamase","category_aro_description":"OXY beta-lactamases are chromosomal class A beta-lactamases that are found in Klebsiella oxytoca. At constitutive low levels, OXY beta-lactamases confer resistance to aminopenicillins and carboxypenicillins. At high induced levels,  OXY beta-lactamases confer resistance to penicillins, cephalosporins and aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1312":{"model_id":"1312","model_name":"OXA-111","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1677":{"protein_sequence":{"accession":"ABV31691.1","sequence":"MNIKTLLLITSAIFISACSPYIVSANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEMNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"EF650037.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAACACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGTCTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCATCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGCCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAATGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001642","ARO_id":"38042","ARO_name":"OXA-111","CARD_short_name":"OXA-111","ARO_description":"OXA-111 is a beta-lactamase found in A. baumannii.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1313":{"model_id":"1313","model_name":"adeA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"4256":{"protein_sequence":{"accession":"AAL14439.1","sequence":"MQKHLLLPLFLSIGLILQGCDSKEVAQAEPPPAKVSVLSIQPQSVNFSENLPARVHAFRTAEIRPQVGGIIEKVLFKQGSEVRAGQALYKINSETFEADVNSNRASLNKAEAEVARLKVQLERYEQLLPSNAISKQEVSNAQAQYRQALADVAQMKALLARQNLNLQYATVRAPISGRIGQSFVTEGALVGQGDTNTMATIQQIDKVYVDVKQSVSEYERLQAALQSGELSANSDKTVRITNSHGQPYNVTAKMLFEDINVDPETGDVTFRIEVNNTERKLLPGMYVRVNIDRASIPQALLVPAQAIQRNISGEPQVYVINAQGTAEIRPIEIGQQYEQFYIANKGLKVGDRVVVEGIERIKPNQKLALAAWKAPAVANHASSVETKTSIAEGAQP"},"dna_sequence":{"accession":"AF370885.1","fmin":"3438","fmax":"4629","strand":"+","sequence":"ATGCAAAAGCATCTTTTACTTCCTTTATTTTTATCTATTGGGCTGATATTACAGGGGTGTGATTCAAAAGAAGTCGCTCAAGCTGAGCCACCACCGGCTAAAGTCAGTGTATTAAGCATTCAACCGCAATCGGTAAATTTTAGTGAAAATCTTCCTGCACGTGTACATGCATTCCGTACGGCGGAAATCCGTCCGCAAGTCGGAGGTATCATTGAAAAGGTTCTATTTAAACAAGGTAGTGAAGTTAGAGCAGGGCAAGCCTTATATAAAATTAATTCCGAGACTTTTGAGGCCGATGTAAATAGCAATAGAGCTTCTCTCAATAAAGCTGAAGCTGAGGTGGCAAGACTCAAAGTTCAGTTAGAACGTTATGAGCAGTTATTACCAAGTAATGCAATTAGTAAGCAAGAAGTAAGTAATGCTCAAGCTCAGTATCGTCAGGCTCTAGCCGATGTCGCTCAAATGAAAGCATTGCTGGCCAGACAAAACTTGAATCTGCAATATGCAACAGTTCGAGCGCCTATTTCTGGGCGTATTGGGCAATCTTTTGTCACTGAAGGTGCATTGGTCGGTCAGGGCGATACCAATACGATGGCAACCATTCAACAGATTGATAAAGTCTATGTTGATGTAAAGCAATCGGTTAGTGAGTATGAACGCCTACAGGCTGCGCTACAAAGCGGCGAATTATCAGCAAATAGTGACAAAACCGTTCGTATTACCAATAGCCACGGACAGCCCTATAACGTCACAGCAAAAATGTTGTTTGAAGATATTAATGTTGACCCGGAAACAGGCGATGTCACATTCCGTATTGAAGTTAATAACACTGAACGAAAATTACTTCCGGGCATGTATGTGCGTGTCAATATTGATCGTGCTTCTATTCCTCAAGCGCTATTGGTTCCGGCGCAAGCGATCCAACGTAATATCAGTGGCGAGCCTCAGGTATATGTCATTAACGCCCAAGGGACAGCGGAAATTCGTCCTATCGAAATTGGACAGCAATATGAGCAGTTCTATATCGCTAACAAAGGCTTGAAAGTCGGTGACAGAGTCGTTGTTGAAGGTATTGAACGTATTAAGCCAAATCAAAAATTGGCATTGGCAGCATGGAAAGCACCAGCCGTCGCGAATCATGCTTCAAGTGTAGAAACCAAAACTTCTATAGCTGAAGGGGCACAACCATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3000774","ARO_id":"37154","ARO_name":"adeA","CARD_short_name":"adeA","ARO_description":"AdeA is the membrane fusion protein of the multidrug efflux complex AdeABC.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1314":{"model_id":"1314","model_name":"OXA-214","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1208":{"protein_sequence":{"accession":"AEV91553.1","sequence":"MKLSKLYTLTVLIGFGLSGVACQHIHTPVSFNQIENDQTKQIASLFENVQTTGVLITFDGQAYKAYGNDLNRAKTAYIPASTFKILNALIGIEHDKTSPNEVFKWDGQKRAFESWEKDLTLAEAMQASAVPVYQALAQRIGLDLMAKEVKRVGFGNTRIGTQVDNFWLIGPLKITPIEEAQFAYRLAKQELPFTPKTQQQVIDMLLVDEIRGTKVYAKSGWGMDITPQVGWWTGWIEDPNGKVIAFSLNMEMNQPAHAAARKEIVYQALTQLKLL"},"dna_sequence":{"accession":"JN861782.1","fmin":"0","fmax":"828","strand":"+","sequence":"ATGAAGCTATCAAAATTATACACCCTCACTGTGCTCATAGGATTTGGATTAAGCGGTGTCGCCTGCCAGCATATCCATACTCCAGTCTCGTTCAATCAAATTGAAAACGATCAAACAAAGCAGATCGCTTCCTTGTTTGAGAATGTTCAAACAACAGGTGTTCTAATTACCTTTGATGGACAGGCGTATAAAGCATACGGTAATGATCTGAATCGTGCCAAAACTGCGTATATCCCAGCATCTACTTTCAAAATATTAAATGCTTTGATTGGCATTGAACATGATAAAACTTCACCAAATGAAGTATTTAAGTGGGATGGTCAGAAGCGTGCTTTTGAAAGTTGGGAAAAAGATCTGACTTTAGCTGAAGCCATGCAAGCTTCTGCTGTACCTGTTTATCAAGCGCTTGCCCAGAGAATCGGATTGGATTTGATGGCAAAGGAAGTCAAAAGAGTCGGCTTCGGTAATACACGCATCGGAACACAAGTTGATAACTTCTGGCTCATTGGACCTTTAAAGATCACGCCAATCGAAGAAGCTCAATTTGCTTACAGGCTTGCAAAACAGGAGTTACCGTTTACCCCAAAAACACAACAGCAAGTGATTGATATGCTGTTGGTGGATGAAATACGGGGAACGAAAGTTTACGCCAAAAGTGGTTGGGGAATGGATATTACCCCGCAAGTAGGATGGTGGACTGGATGGATTGAAGATCCGAACGGAAAAGTGATCGCTTTTTCTCTCAATATGGAAATGAATCAACCTGCGCATGCAGCTGCACGTAAAGAAATTGTTTATCAGGCACTTACGCAATTGAAATTATTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36938","NCBI_taxonomy_name":"Acinetobacter haemolyticus","NCBI_taxonomy_id":"29430"}}}},"ARO_accession":"3001713","ARO_id":"38113","ARO_name":"OXA-214","CARD_short_name":"OXA-214","ARO_description":"OXA-214 is a beta-lactamase found in Acinetobacter spp.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46496":{"category_aro_accession":"3007707","category_aro_cvterm_id":"46496","category_aro_name":"OXA-214-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-214.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1315":{"model_id":"1315","model_name":"mdtC","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1800"}},"model_sequences":{"sequence":{"257":{"protein_sequence":{"accession":"AAC75137.1","sequence":"MKFFALFIYRPVATILLSVAITLCGILGFRMLPVAPLPQVDFPVIIVSASLPGASPETMASSVATPLERSLGRIAGVSEMTSSSSLGSTRIILQFDFDRDINGAARDVQAAINAAQSLLPSGMPSRPTYRKANPSDAPIMILTLTSDTYSQGELYDFASTQLAPTISQIDGVGDVDVGGSSLPAVRVGLNPQALFNQGVSLDDVRTAVSNANVRKPQGALEDGTHRWQIQTNDELKTAAEYQPLIIHYNNGGAVRLGDVATVTDSVQDVRNAGMTNAKPAILLMIRKLPEANIIQTVDSIRAKLPELQETIPAAIDLQIAQDRSPTIRASLEEVEQTLIISVALVILVVFLFLRSGRATIIPAVSVPVSLIGTFAAMYLCGFSLNNLSLMALTIATGFVVDDAIVVLENIARHLEAGMKPLQAALQGTREVGFTVLSMSLSLVAVFLPLLLMGGLPGRLLREFAVTLSVAIGISLLVSLTLTPMMCGWMLKASKPREQKRLRGFGRMLVALQQGYGKSLKWVLNHTRLVGVVLLGTIALNIWLYISIPKTFFPEQDTGVLMGGIQADQSISFQAMRGKLQDFMKIIRDDPAVDNVTGFTGGSRVNSGMMFITLKPRDERSETAQQIIDRLRVKLAKEPGANLFLMAVQDIRVGGRQSNASYQYTLLSDDLAALREWEPKIRKKLATLPELADVNSDQQDNGAEMNLVYDRDTMARLGIDVQAANSLLNNAFGQRQISTIYQPMNQYKVVMEVDPRYTQDISALEKMFVINNEGKAIPLSYFAKWQPANAPLSVNHQGLSAASTISFNLPTGKSLSDASAAIDRAMTQLGVPSTVRGSFAGTAQVFQETMNSQVILIIAAIATVYIVLGILYESYVHPLTILSTLPSAGVGALLALELFNAPFSLIALIGIMLLIGIVKKNAIMMVDFALEAQRHGNLTPQEAIFQACLLRFRPIMMTTLAALFGALPLVLSGGDGSELRQPLGITIVGGLVMSQLLTLYTTPVVYLFFDRLRLRFSRKPKQTVTE"},"dna_sequence":{"accession":"U00096.1","fmin":"2158385","fmax":"2161463","strand":"+","sequence":"GTGAAGTTTTTTGCCCTCTTCATTTACCGCCCGGTGGCGACGATTTTACTGTCGGTTGCCATTACCCTGTGCGGCATACTGGGCTTCCGTATGCTGCCGGTCGCCCCGCTGCCGCAGGTCGATTTTCCGGTGATTATCGTCAGCGCCTCGCTGCCCGGTGCGTCACCAGAAACAATGGCGTCTTCCGTTGCCACGCCGCTGGAGCGCTCACTTGGGCGCATTGCCGGAGTCAGTGAAATGACCTCCAGCAGTTCGCTCGGCAGCACGCGTATTATTTTGCAGTTTGATTTTGACCGGGATATCAACGGCGCAGCGCGTGATGTGCAGGCGGCGATCAACGCTGCACAAAGTTTGCTGCCCAGTGGGATGCCCAGCCGCCCGACCTATCGCAAAGCGAACCCGTCGGATGCGCCAATTATGATCCTCACGCTGACGTCCGATACTTATTCGCAGGGTGAACTGTACGATTTCGCCTCGACGCAGCTGGCTCCGACGATTTCGCAAATCGACGGTGTTGGTGATGTCGATGTCGGAGGCAGCTCACTGCCCGCCGTACGCGTCGGGCTGAATCCGCAGGCGCTGTTTAATCAGGGCGTGTCGCTGGACGACGTACGCACCGCCGTCAGCAATGCCAACGTGCGTAAACCGCAGGGCGCGCTGGAAGATGGCACTCACCGCTGGCAGATCCAGACCAATGATGAGCTAAAAACCGCCGCTGAATATCAGCCGTTGATTATTCACTACAACAACGGCGGCGCGGTTCGTCTGGGCGATGTGGCGACGGTGACCGACTCAGTGCAGGATGTGCGCAACGCCGGGATGACCAACGCCAAACCGGCTATTTTACTGATGATCCGCAAACTGCCGGAAGCCAATATTATCCAGACGGTTGACAGCATCCGGGCAAAATTACCGGAGTTGCAGGAAACCATTCCGGCGGCGATTGATCTGCAAATTGCCCAGGATCGCTCCCCCACCATTCGCGCCTCGCTGGAAGAAGTCGAGCAAACGCTGATTATCTCGGTGGCGCTGGTGATTCTGGTGGTGTTTTTATTCCTGCGCTCGGGTCGCGCCACTATTATTCCCGCCGTTTCGGTGCCGGTTTCGCTGATTGGTACGTTTGCGGCGATGTACCTGTGCGGATTCAGTCTCAATAACCTTTCGTTAATGGCGCTCACCATCGCTACTGGTTTCGTGGTGGATGACGCCATCGTGGTGCTGGAAAACATTGCACGTCATCTGGAAGCGGGAATGAAACCGTTGCAAGCCGCACTGCAAGGTACTCGCGAAGTCGGTTTTACGGTGCTGTCGATGAGTCTGTCACTGGTGGCGGTGTTCCTGCCGCTGCTGTTGATGGGCGGATTGCCGGGCCGACTGTTACGCGAATTTGCCGTGACGCTTTCTGTCGCCATTGGTATATCGTTGCTGGTTTCTCTGACATTAACGCCAATGATGTGTGGCTGGATGCTGAAAGCCAGCAAGCCGCGCGAGCAAAAGCGACTGCGTGGTTTTGGTCGCATGTTGGTAGCCCTGCAACAAGGCTACGGCAAGTCACTAAAATGGGTGCTCAATCATACCCGTCTGGTGGGCGTGGTGCTGCTTGGCACCATTGCGCTGAATATCTGGCTGTATATCTCGATCCCGAAAACCTTCTTCCCGGAGCAGGACACTGGCGTGTTGATGGGCGGGATTCAGGCGGATCAGAGTATTTCGTTTCAGGCGATGCGCGGTAAGTTGCAGGATTTCATGAAAATTATCCGTGACGATCCGGCAGTGGATAATGTCACCGGCTTTACAGGCGGTTCGCGAGTGAACAGCGGGATGATGTTTATCACCCTCAAGCCACGCGACGAACGCAGCGAAACGGCGCAGCAAATTATCGACCGTCTGCGCGTAAAACTGGCGAAAGAACCGGGGGCGAATCTGTTCCTGATGGCGGTACAGGATATTCGCGTTGGTGGGCGTCAGTCGAACGCCAGCTACCAGTACACGTTGTTATCCGACGACCTGGCGGCACTGCGAGAATGGGAGCCGAAAATCCGCAAAAAACTGGCGACGTTGCCGGAACTGGCGGACGTGAACTCCGATCAGCAGGATAACGGCGCGGAGATGAATCTGGTTTACGACCGCGACACCATGGCACGGCTGGGAATCGACGTACAAGCCGCCAACAGTCTGTTAAATAACGCCTTCGGTCAGCGGCAAATCTCGACCATTTACCAGCCGATGAACCAGTATAAAGTGGTGATGGAAGTGGATCCGCGCTATACCCAGGACATCAGTGCGCTGGAAAAAATGTTCGTTATCAATAACGAAGGCAAAGCGATCCCGCTGTCGTATTTCGCTAAATGGCAACCGGCGAATGCCCCACTATCGGTGAATCATCAGGGATTATCGGCGGCCTCGACCATTTCGTTTAACCTGCCGACCGGAAAATCGCTCTCGGACGCCAGTGCGGCGATCGATCGCGCAATGACCCAGCTTGGTGTGCCTTCGACGGTGCGCGGCAGTTTTGCCGGCACGGCGCAGGTGTTCCAGGAGACGATGAACTCGCAGGTGATCCTGATTATCGCCGCCATCGCCACGGTGTATATCGTGCTGGGTATCCTTTACGAGAGTTACGTACATCCGCTGACGATTCTCTCCACCCTGCCCTCGGCGGGCGTTGGAGCGCTGTTGGCGCTGGAGCTGTTCAATGCCCCGTTCAGCCTAATCGCCCTGATAGGGATCATGCTATTAATCGGCATCGTGAAGAAAAACGCCATTATGATGGTCGATTTTGCGCTTGAAGCCCAACGGCACGGTAACCTGACGCCGCAGGAAGCTATTTTCCAGGCCTGTCTGCTGCGTTTTCGCCCGATTATGATGACTACCCTGGCGGCGCTGTTTGGTGCGCTGCCGCTGGTATTGTCGGGCGGCGACGGCTCGGAGCTGCGGCAACCCCTGGGGATCACCATTGTCGGCGGACTGGTAATGAGCCAGCTCCTTACGCTGTATACCACGCCGGTGGTGTATCTCTTTTTCGACCGTCTGCGGCTGCGTTTTTCGCGTAAACCTAAACAAACGGTAACCGAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36849","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. MG1655","NCBI_taxonomy_id":"511145"}}}},"ARO_accession":"3000794","ARO_id":"37174","ARO_name":"mdtC","CARD_short_name":"mdtC","ARO_description":"MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB, MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC\/muxB) and 3 loci in Pseudomonas aeruginosa LESB58.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"36250":{"category_aro_accession":"3000111","category_aro_cvterm_id":"36250","category_aro_name":"novobiocin","category_aro_description":"Novobiocin is an aminocoumarin antibiotic produced by Streptomyces spheroides and Streptomyces niveus, and binds DNA gyrase subunit B inhibiting ATP-dependent DNA supercoiling.","category_aro_class_name":"Antibiotic"},"36242":{"category_aro_accession":"3000103","category_aro_cvterm_id":"36242","category_aro_name":"aminocoumarin antibiotic","category_aro_description":"Aminocoumarin antibiotics bind DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1317":{"model_id":"1317","model_name":"CTX-M-3","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1965":{"protein_sequence":{"accession":"CAA71321.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGDYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"Y10278.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGACTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3001866","ARO_id":"38266","ARO_name":"CTX-M-3","CARD_short_name":"CTX-M-3","ARO_description":"CTX-M-3 is a beta-lactamase found in Citrobacter freundii.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35927":{"category_aro_accession":"0000008","category_aro_cvterm_id":"35927","category_aro_name":"cefoxitin","category_aro_description":"Cefoxitin is a cephamycin antibiotic often grouped with the second generation cephalosporins. Cefoxitin is bactericidal and acts by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. Cefoxitin's 7-alpha-methoxy group and 3' leaving group make it a poor substrate for most beta-lactamases.","category_aro_class_name":"Antibiotic"},"35975":{"category_aro_accession":"0000058","category_aro_cvterm_id":"35975","category_aro_name":"cefazolin","category_aro_description":"Cefazolin, also known as cefazoline or cephazolin, is a first generation cephalosporin antibiotic. It is administered parenterally, and is active against a broad spectrum of bacteria.","category_aro_class_name":"Antibiotic"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"35979":{"category_aro_accession":"0000062","category_aro_cvterm_id":"35979","category_aro_name":"ceftriaxone","category_aro_description":"Ceftriaxone is a third-generation cephalosporin antibiotic. The presence of an aminothiazolyl sidechain increases ceftriazone's resistance to beta-lactamases. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"36990":{"category_aro_accession":"3000646","category_aro_cvterm_id":"36990","category_aro_name":"cefixime","category_aro_description":"Cefixime is a cephalosporin resistant to most beta-lactamases. It is active against many enterobacteria, but activity against staphylococci is poor.","category_aro_class_name":"Antibiotic"},"37084":{"category_aro_accession":"3000704","category_aro_cvterm_id":"37084","category_aro_name":"cefalotin","category_aro_description":"Cefalotin is a semisynthetic cephalosporin antibiotic activate against staphylococci. It is resistant to staphylococci beta-lactamases but hydrolyzed by enterobacterial beta-lactamases.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1318":{"model_id":"1318","model_name":"evgS","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"2300"}},"model_sequences":{"sequence":{"178":{"protein_sequence":{"accession":"AAC75429.1","sequence":"MKFLPYIFLLCCGLWSTISFADEDYIEYRGISSNNRVTLDPLRLSNKELRWLASKKNLVIAVHKSQTATLLHTDSQQRVRGINADYLNLLKRALNIKLTLREYADHQKAMDALAEGEVDIVLSHLVTSPPLNNDIAATKPLIITFPALVTTLHDSMRPLTSPKPVNIARVANYPPDEVIHQSFPKATIISFTNLYQALASVSAGHNDYFIGSNIITSSMISRYFTHSLNVVKYYNSPRQYNFFLTRKESVILNEVLNRFVDALTNEVRYEVSQNWLDTGNLAFLNKPLELTEHEKQWIKQHPNLKVLENPYSPPYSMTDENGSVRGVMGDILNIITLQTGLNFSPITVSHNIHAGTQLSPGGWDIIPGAIYSEDRENNVLFAEAFITTPYVFVMQKAPDSEQTLKKGMKVAIPYYYELHSQLKEMYPEVEWIQVDNASAAFHKVKEGELDALVATQLNSRYMIDHYYPNELYHFLIPGVPNASLSFAFPRGEPELKDIINKALNAIPPSEVLRLTEKWIKMPNVTIDTWDLYSEQFYIVTTLSVLLVGSSLLWGFYLLRSVRRRKVIQGDLENQISFRKALSDSLPNPTYVVNWQGNVISHNSAFEHYFTADYYKNAMLPLENSDSPFKDVFSNAHEVTAETKENRTIYTQVFEIDNGIEKRCINHWHTLCNLPASDNAVYICGWQDITETRDLINALEVEKNKAIKATVAKSQFLATMSHEIRTPISSIMGFLELLSGSGLSKEQRVEAISLAYATGQSLLGLIGEILDVDKIESGNYQLQPQWVDIPTLVQNTCHSFGAIAASKSIALSCSSTFPEHYLVKIDPQAFKQVLSNLLSNALKFTTEGAVKITTSLGHIDDNHAVIKMTIMDSGSGLSQEEQQQLFKRYSQTSAGRQQTGSGLGLMICKELIKNMQGDLSLESHPGIGTTFTITIPVEISQQVATVEAKAEQPITLPEKLSILIADDHPTNRLLLKRQLNLLGYDVDEATDGVQALHKVSMQHYDLLITDVNMPNMDGFELTRKLREQNSSLPIWGLTANAQANEREKGLSCGMNLCLFKPLTLDVLKTHLSQLHQVAHIAPQYRHLDIEALKNNTANDLQLMQEILMTFQHETHKDLPAAFQALEAGDNRTFHQCIHRIHGAANILNLQKLINISHQLEITPVSDDSKPEILQLLNSVKEHIAELDQEIAVFCQKND"},"dna_sequence":{"accession":"U00096.1","fmin":"2484373","fmax":"2487967","strand":"+","sequence":"ATGAAGTTTTTACCCTATATTTTTCTTCTCTGTTGTGGTCTTTGGTCGACCATAAGTTTCGCAGACGAAGATTACATCGAATATCGTGGCATCAGTAGTAACAACCGTGTCACACTTGATCCACTACGTCTGAGCAACAAGGAATTACGTTGGTTAGCGAGCAAAAAAAATCTTGTGATTGCAGTACATAAGTCCCAAACGGCTACGTTGTTGCATACCGATTCGCAGCAACGGGTTCGTGGTATTAATGCTGATTATTTAAATCTTTTAAAAAGAGCGTTAAATATCAAATTAACACTCCGGGAATACGCAGATCATCAAAAAGCAATGGACGCGCTTGCAGAAGGTGAAGTCGATATAGTGTTATCACATTTAGTTACTTCGCCGCCTCTTAATAATGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACCCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGTCTCAGCTGGGCACAATGATTACTTTATTGGTAGTAACATCATTACCAGCAGTATGATTTCCCGCTATTTCACTCACTCCTTAAATGTAGTGAAATATTATAACTCGCCGCGTCAATATAATTTTTTCTTGACCAGAAAAGAATCTGTCATTCTTAATGAAGTACTCAATAGATTTGTTGATGCTTTAACAAATGAAGTTCGCTATGAAGTATCACAAAATTGGCTTGATACAGGAAACCTGGCCTTTCTGAACAAACCATTAGAACTCACTGAACATGAAAAACAGTGGATTAAGCAGCATCCCAATTTAAAGGTGCTGGAAAATCCTTACTCGCCCCCCTATTCTATGACGGATGAAAATGGCTCGGTTCGGGGCGTTATGGGGGACATTCTTAATATTATTACCTTGCAAACAGGTTTAAATTTTTCTCCGATCACCGTTTCACACAATATCCATGCTGGAACACAGCTTAGCCCCGGAGGATGGGATATAATACCTGGCGCTATTTATAGTGAAGATCGAGAAAATAATGTTTTATTTGCTGAAGCCTTCATAACAACGCCTTACGTTTTTGTCATGCAAAAAGCGCCTGACAGTGAACAAACATTAAAAAAAGGAATGAAAGTTGCCATTCCATATTATTATGAGCTGCATTCGCAATTAAAAGAGATGTATCCGGAGGTTGAATGGATACAGGTCGATAATGCCAGCGCTGCATTTCACAAGGTTAAGGAAGGTGAACTTGATGCTCTGGTCGCGACACAGCTAAATTCGCGTTACATGATCGATCATTACTATCCTAATGAACTTTATCATTTTCTTATTCCTGGCGTTCCGAATGCATCGCTTTCGTTCGCTTTTCCTCGCGGAGAACCGGAACTTAAGGATATTATTAATAAAGCACTGAATGCAATTCCCCCAAGCGAAGTTCTGCGCCTGACGGAAAAATGGATTAAAATGCCCAATGTGACCATTGACACATGGGACCTATATAGCGAGCAATTTTATATTGTTACGACATTATCCGTTTTATTAGTTGGCAGTAGCCTTTTATGGGGATTCTACCTGTTACGCTCAGTTCGTCGTCGTAAAGTCATTCAGGGTGATTTAGAAAACCAAATATCATTCCGAAAAGCACTCTCGGATTCCTTACCGAATCCAACTTATGTTGTAAACTGGCAAGGTAATGTCATTAGTCATAATAGTGCTTTTGAACATTATTTCACTGCGGATTACTACAAAAATGCAATGTTACCATTAGAAAACAGTGACTCACCCTTTAAAGATGTTTTTTCTAATGCGCATGAAGTCACAGCAGAAACGAAAGAAAATCGAACAATATACACACAGGTATTTGAAATTGATAATGGCATCGAGAAAAGATGCATTAATCACTGGCATACATTATGCAATCTTCCTGCAAGTGACAATGCAGTATATATTTGTGGTTGGCAAGATATTACTGAAACGCGTGATCTAATTAATGCACTCGAGGTAGAAAAAAATAAAGCGATAAAGGCTACCGTAGCAAAAAGTCAGTTTCTGGCAACGATGAGTCACGAAATAAGAACACCAATAAGCTCTATTATGGGCTTCCTGGAACTTCTGTCGGGTTCTGGTCTTAGCAAGGAGCAACGGGTGGAGGCGATTTCACTTGCCTACGCCACCGGACAATCACTCCTCGGCTTAATTGGTGAAATCCTTGATGTCGACAAAATTGAATCGGGTAACTATCAACTTCAACCACAATGGGTCGATATCCCTACTTTAGTCCAGAACACTTGTCACTCTTTCGGTGCGATTGCTGCAAGCAAATCGATCGCATTAAGTTGCAGCAGTACGTTTCCTGAACATTACCTGGTTAAGATCGACCCTCAGGCGTTTAAGCAGGTCTTATCAAATTTACTGAGTAATGCTCTCAAATTTACCACCGAGGGGGCAGTAAAAATTACGACCTCCCTGGGTCACATTGATGACAACCACGCTGTTATCAAAATGACGATTATGGATTCTGGAAGTGGATTATCGCAGGAAGAACAACAACAACTGTTTAAACGCTACAGCCAAACAAGTGCAGGTCGTCAGCAAACAGGTTCTGGTTTAGGCTTAATGATCTGCAAAGAATTAATTAAAAATATGCAGGGCGATTTGTCATTAGAAAGTCATCCAGGCATAGGAACAACATTTACGATCACAATCCCGGTAGAAATTAGCCAGCAAGTGGCGACTGTCGAGGCAAAAGCAGAACAACCCATCACACTACCTGAAAAGTTGAGCATATTAATCGCGGATGATCATCCGACCAACAGGCTATTACTCAAACGCCAGCTAAATCTATTAGGATATGATGTTGATGAAGCCACTGATGGTGTGCAAGCGCTACACAAAGTCAGTATGCAACATTATGATCTGCTTATTACTGACGTTAATATGCCGAATATGGATGGTTTTGAGTTGACTCGCAAACTCCGTGAGCAAAATTCTTCCTTACCCATCTGGGGGCTTACAGCCAACGCACAGGCTAACGAACGTGAAAAAGGGTTAAGTTGCGGCATGAACTTATGTTTGTTCAAACCGTTGACCCTGGATGTACTGAAAACACATTTAAGTCAGTTACACCAAGTTGCGCATATTGCACCTCAGTATCGCCACCTTGATATCGAAGCCCTGAAAAATAATACGGCGAACGATCTACAACTGATGCAGGAGATTCTCATGACTTTCCAGCATGAAACGCATAAAGATCTACCCGCTGCGTTTCAAGCACTAGAAGCTGGCGATAACAGAACTTTCCATCAGTGTATTCATCGCATCCACGGTGCGGCTAACATCCTGAATTTGCAAAAGTTGATTAATATTAGCCATCAGTTAGAAATAACACCTGTTTCAGATGACAGTAAGCCTGAAATTCTTCAGTTGCTGAACTCTGTAAAAGAACACATTGCAGAGCTGGACCAGGAGATTGCTGTTTTCTGTCAGAAAAATGACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36849","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. MG1655","NCBI_taxonomy_id":"511145"}}}},"ARO_accession":"3000833","ARO_id":"37213","ARO_name":"evgS","CARD_short_name":"evgS","ARO_description":"EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35930":{"category_aro_accession":"0000011","category_aro_cvterm_id":"35930","category_aro_name":"cloxacillin","category_aro_description":"Cloxacillin is a semisynthetic, isoxazolyl penicillin derivative in the beta-lactam class of antibiotics. It interferes with peptidogylcan synthesis and is commonly used for treating penicillin-resistant Staphylococcus aureus infections.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1319":{"model_id":"1319","model_name":"SHV-147","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"2021":{"protein_sequence":{"accession":"AFQ23953.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSAFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTSASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"JX121114.1","fmin":"0","fmax":"858","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCGCCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGCATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGTCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGC","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001186","ARO_id":"37566","ARO_name":"SHV-147","CARD_short_name":"SHV-147","ARO_description":"SHV-147 is a beta-lactamase.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1321":{"model_id":"1321","model_name":"mecA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1250"}},"model_sequences":{"sequence":{"227":{"protein_sequence":{"accession":"AGC51118.1","sequence":"MKKIKIVPLILIVVVVGFGIYFYASKDKEINNTIDAIEDKNFKQVYKDSSYISKSDNGEVEMTERPIKIYNSLGVKDINIQDRKIKKVSKNKKRVDAQYKIKTNYGNIDRNVQFNFVKEDGMWKLDWDHSVIIPGMQKDQSIHIENLKSERGKILDRNNVELANTGTAYEIGIVPKNVSKKDYKAIAKELSISEDYIKQQMDQNWVQDDTFVPLKTVKKMDEYLSDFAKKFHLTTNETKSRNYPLEKATSHLLGYVGPINSEELKQKEYKGYKDDAVIGKKGLEKLYDKKLQHEDGYRVTIVDDNSNTIAHTLIEKKKKDGKDIQLTIDAKVQKSIYNNMKNDYGSGTAIHPQTGELLALVSTPSYDVYPFMYGMSNEEYNKLTEDKKEPLLNKFQITTSPGSTQKILTAMIGLNNKTLDDKTSYKIDGKGWQKDKSWGGYNVTRYEVVNGNIDLKQAIESSDNIFFARVALELGSKKFEKGMKKLGVGEDIPSDYPFYNAQISNKNLDNEILLADSGYGQGEILINPVQILSIYSALENNGNINAPHLLKDTKNKVWKKNIISKENINLLTDGMQQVVNKTHKEDIYRSYANLIGKSGTAELKMKQGETGRQIGWFISYDKDNPNMMMAINVKDVQDKGMASYNAKISGKVYDELYENGNKKYDIDE"},"dna_sequence":{"accession":"KC243783.1","fmin":"0","fmax":"2007","strand":"+","sequence":"ATGAAAAAGATAAAAATTGTTCCACTTATTTTAATAGTTGTAGTTGTCGGGTTTGGTATATATTTTTATGCTTCAAAAGATAAAGAAATTAATAATACTATTGATGCAATTGAAGATAAAAATTTCAAACAAGTTTATAAAGATAGCAGTTATATTTCTAAAAGCGATAATGGTGAAGTAGAAATGACTGAACGTCCGATAAAAATATATAATAGTTTAGGCGTTAAAGATATAAACATTCAGGATCGTAAAATAAAAAAAGTATCTAAAAATAAAAAACGAGTAGATGCTCAATATAAAATTAAAACAAACTACGGTAACATTGATCGCAACGTTCAATTTAATTTTGTTAAAGAAGATGGTATGTGGAAGTTAGATTGGGATCATAGCGTCATTATTCCAGGAATGCAGAAAGACCAAAGCATACATATTGAAAATTTAAAATCAGAACGTGGTAAAATTTTAGACCGAAACAATGTGGAATTGGCCAATACAGGAACAGCATATGAGATAGGCATCGTTCCAAAGAATGTATCTAAAAAAGATTATAAAGCAATCGCTAAAGAACTAAGTATTTCTGAAGACTATATCAAACAACAAATGGATCAAAATTGGGTACAAGATGATACCTTCGTTCCACTTAAAACCGTTAAAAAAATGGATGAATATTTAAGTGATTTCGCAAAAAAATTTCATCTTACAACTAATGAAACAAAAAGTCGTAACTATCCTCTAGAAAAAGCGACTTCACATCTATTAGGTTATGTTGGTCCCATTAACTCTGAAGAATTAAAACAAAAAGAATATAAAGGCTATAAAGATGATGCAGTTATTGGTAAAAAGGGACTCGAAAAACTTTACGATAAAAAGCTCCAACATGAAGATGGCTATCGTGTCACAATCGTTGACGATAATAGCAATACAATCGCACATACATTAATAGAGAAAAAGAAAAAAGATGGCAAAGATATTCAACTAACTATTGATGCTAAAGTTCAAAAGAGTATTTATAACAACATGAAAAATGATTATGGCTCAGGTACTGCTATCCACCCTCAAACAGGTGAATTATTAGCACTTGTAAGCACACCTTCATATGACGTCTATCCATTTATGTATGGCATGAGTAACGAAGAATATAATAAATTAACCGAAGATAAAAAAGAACCTCTGCTCAACAAGTTCCAGATTACAACTTCACCAGGTTCAACTCAAAAAATATTAACAGCAATGATTGGGTTAAATAACAAAACATTAGACGATAAAACAAGTTATAAAATCGATGGTAAAGGTTGGCAAAAAGATAAATCTTGGGGTGGTTACAACGTTACAAGATATGAAGTGGTAAATGGTAATATCGACTTAAAACAAGCAATAGAATCATCAGATAACATTTTCTTTGCTAGAGTAGCACTCGAATTAGGCAGTAAGAAATTTGAAAAAGGCATGAAAAAACTAGGTGTTGGTGAAGATATACCAAGTGATTATCCATTTTATAATGCTCAAATTTCAAACAAAAATTTAGATAATGAAATATTATTAGCTGATTCAGGTTACGGACAAGGTGAAATACTGATTAACCCAGTACAGATCCTTTCAATCTATAGCGCATTAGAAAATAATGGCAATATTAACGCACCTCACTTATTAAAAGACACGAAAAACAAAGTTTGGAAGAAAAATATTATTTCCAAAGAAAATATCAATCTATTAACTGATGGTATGCAACAAGTCGTAAATAAAACACATAAAGAAGATATTTATAGATCTTATGCAAACTTAATTGGCAAATCCGGTACTGCAGAACTCAAAATGAAACAAGGAGAAACTGGCAGACAAATTGGGTGGTTTATATCATATGATAAAGATAATCCAAACATGATGATGGCTATTAATGTTAAAGATGTACAAGATAAAGGAATGGCTAGCTACAATGCCAAAATCTCAGGTAAAGTGTATGATGAGCTATATGAGAACGGTAATAAAAAATACGATATAGATGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35508","NCBI_taxonomy_name":"Staphylococcus aureus","NCBI_taxonomy_id":"1280"}}}},"ARO_accession":"3000617","ARO_id":"36911","ARO_name":"mecA","CARD_short_name":"mecA","ARO_description":"A foreign PBP2a acquired by lateral gene transfer that is able to perform peptidoglycan synthesis in the presence of beta-lactams.","ARO_category":{"37589":{"category_aro_accession":"3001208","category_aro_cvterm_id":"37589","category_aro_name":"methicillin resistant PBP2","category_aro_description":"In methicillin sensitive S. aureus (MSSA), beta-lactams bind to native penicillin-binding proteins (PBPs) and disrupt synthesis of the cell membrane's peptidoglycan layer. In methicillin resistant S. aureus (MRSA), foreign PBP2a acquired by lateral gene transfer is able to perform peptidoglycan synthesis in the presence of beta-lactams.","category_aro_class_name":"AMR Gene Family"},"35934":{"category_aro_accession":"0000015","category_aro_cvterm_id":"35934","category_aro_name":"methicillin","category_aro_description":"Derived from penicillin to combat penicillin-resistance, methicillin is insensitive to beta-lactamases (also known as penicillinases) secreted by many penicillin-resistant bacteria. Methicillin is bactericidal, and acts by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1322":{"model_id":"1322","model_name":"SHV-65","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1068":{"protein_sequence":{"accession":"ABA06587.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCTAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"DQ174305.1","fmin":"4","fmax":"865","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACCCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCACCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGCATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001120","ARO_id":"37500","ARO_name":"SHV-65","CARD_short_name":"SHV-65","ARO_description":"SHV-65 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1324":{"model_id":"1324","model_name":"LRA-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"4713":{"protein_sequence":{"accession":"ACH58985.1","sequence":"MMDGIKKKTAAGAAAGSLLMMLGVFATPAAGGEAAFKDCPQCAQWNQQRKPFRIYGNTYFVGTAGLSSILVTSDYGHVLIDGGLAQSAPLIKANIEALGFKLTDVKAILVSHVHPDHAGGVAELQRQSGAQVYALRTAEAVLRTGRLTQDDPQSASKTATITPVPQVWVVQDDQLLGVGALRMRAIATPGHTPGGTSWTWDACEDGNCLKMIYADSLSAVAAGKYRFKDHPEVLQAFASSFSRAESAPCDVLLTPHPDASQLFQRLDPEGGTRAASIKDDTACRRYVQAARDTLARKLASEG"},"dna_sequence":{"accession":"EU408347.1","fmin":"10174","fmax":"11083","strand":"-","sequence":"ATGATGGATGGAATAAAGAAGAAGACGGCGGCCGGCGCTGCAGCAGGTTCACTGCTGATGATGCTGGGTGTTTTTGCCACGCCCGCCGCGGGCGGTGAAGCGGCATTCAAGGATTGCCCGCAGTGCGCCCAGTGGAATCAGCAGCGCAAGCCGTTTCGCATCTACGGTAATACCTATTTCGTCGGCACCGCCGGTCTCAGCTCGATTCTCGTCACCTCCGACTACGGCCATGTGCTGATCGACGGCGGGCTCGCGCAATCCGCGCCGCTCATCAAGGCAAACATCGAAGCACTGGGCTTCAAGCTCACCGATGTAAAGGCCATCCTGGTCTCGCATGTGCATCCAGACCATGCGGGTGGCGTCGCCGAGCTGCAGCGGCAGAGCGGTGCGCAGGTCTATGCATTGCGAACCGCAGAAGCCGTGCTGCGAACGGGCAGGCTCACGCAGGACGATCCCCAATCCGCCAGCAAGACGGCAACCATCACACCGGTGCCGCAGGTCTGGGTGGTGCAGGATGACCAGCTGCTCGGCGTCGGCGCGCTGCGGATGCGGGCCATCGCGACCCCCGGTCACACGCCTGGCGGTACCAGCTGGACCTGGGACGCCTGCGAAGACGGCAACTGCCTGAAGATGATCTATGCAGACAGCCTGTCCGCCGTAGCTGCCGGCAAGTATCGCTTCAAGGATCACCCCGAAGTGCTGCAGGCCTTTGCCAGCAGCTTCTCCCGGGCGGAGTCCGCACCCTGCGATGTACTGCTCACGCCGCATCCGGATGCTTCGCAGTTGTTCCAGCGGCTGGATCCGGAGGGCGGCACCCGGGCAGCCAGCATCAAGGACGACACGGCATGCCGGCGATACGTGCAGGCAGCGCGGGACACGCTTGCCCGGAAACTCGCCAGCGAGGGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39080","NCBI_taxonomy_name":"uncultured bacterium BLR2","NCBI_taxonomy_id":"506520"}}}},"ARO_accession":"3002485","ARO_id":"38885","ARO_name":"LRA-2","CARD_short_name":"LRA-2","ARO_description":"LRA-2 is a beta-lactamase isolated from soil samples in Alaska.","ARO_category":{"41390":{"category_aro_accession":"3004226","category_aro_cvterm_id":"41390","category_aro_name":"subclass B3 LRA beta-lactamase","category_aro_description":"Beta-lactamases that are part of the LRA gene family and are classified as B3 (metallo-) beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1183":{"model_id":"1183","model_name":"tet(Q)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"476":{"protein_sequence":{"accession":"CAA79727.1","sequence":"MRFDNASIVVYYCLIQMNIINLGILAHIDAGKTSVTENLLFASGATEKCGRVDNGDTITDSMDIEKRRGITVRASTTSIIWNGVKCNIIDTPGHMDFIAEVERTFKMLDGAVLILSAKEGIQAQTKLLFNTLQKLQIPTIIFINKIDRDGVNLERLYLDIKTNLSQDVLFMQTVVDGLVYPICSQTYIKEEYKEFVCNHDDNILERYLADSEISPADYWNTIIDLVAKAKVYPVLHGSAMFNIGINELLDAISSFILPPESVSNRLSAYLYKIEHDPKGHKRSFLKIIDGSLRLRDIVRINDSEKFIKIKNLKTIYQGREINVDEVGANDIAIVEDMEDFRIGDYLGTKPCLIQGLSHQHPALKSSVRPDRSEERSKVISALNTLWIEDPSLSFSINSYSDELEISLYGLTQKEIIQTLLEERFSVKVHFDEIKTIYKERPVKKVNKIIQIEVPPNPYWATIGLTLEPLPLGTGLQIESDISYGYLNHSFQNAVFEGIRMSCQSGLHGWEVTDLKVTFTQAEYYSPVSTPADFRQLTPYVFRLALQQSGVDILEPMLYFELQIPQAASSKAITDLQKMMSEIEDISCNNEWCHIKGKVPLNTSKDYASEVSSYTKGLGVFMVKPCGYQITKGDYSDNIRMNEKDKLLFMFQKSMSSK"},"dna_sequence":{"accession":"Z21523.1","fmin":"0","fmax":"1974","strand":"+","sequence":"GTGCGTTTCGACAATGCATCTATTGTAGTATATTATTGCTTAATCCAAATGAATATTATAAATTTAGGAATTCTTGCTCACATTGATGCAGGAAAAACTTCCGTAACCGAGAATCTGCTGTTTGCCAGTGGAGCAACGGAAAAGTGCGGCCGTGTGGATAATGGTGACACCATAACAGACTCTATGGATATAGAGAAACGTAGAGGAATTACTGTTCGGGCTTCTACGACATCTATTATCTGGAATGGAGTGAAATGCAATATCATTGACACTCCGGGACACATGGATTTTATTGCGGAAGTGGAGCGGACATTCAAAATGCTTGATGGAGCAGTCCTCATCTTATCCGCAAAGGAAGGCATACAAGCGCAAACAAAGTTGCTGTTCAATACTTTACAAAAACTGCAAATCCCGACAATTATATTTATCAATAAAATTGACCGTGACGGTGTGAATTTAGAGCGTTTGTATCTGGATATAAAAACAAATCTGTCTCAAGATGTCCTGTTTATGCAAACTGTTGTCGATGGATTGGTTTATCCGATTTGCTCCCAAACATATATAAAGGAAGAATACAAAGAATTTGTATGCAACCATGACGACAATATATTAGAACGATATTTGGCGGATAGCGAAATTTCACCGGCTGATTATTGGAATACGATAATCGATCTTGTGGCAAAAGCCAAAGTCTATCCGGTACTACATGGATCAGCAATGTTCAATATCGGTATCAATGAGTTGTTGGACGCCATCTCTTCTTTTATACTTCCTCCAGAATCAGTCTCAAACAGACTTTCAGCTTATCTCTATAAGATAGAGCATGACCCCAAAGGACATAAAAGAAGTTTTCTAAAAATAATTGACGGAAGTCTGAGACTTCGAGACATTGTAAGAATCAACGATTCGGAAAAATTCATCAAGATTAAAAATCTAAAGACTATTTATCAGGGCAGAGAGATAAATGTTGATGAAGTGGGGGCCAATGATATCGCGATTGTAGAAGATATGGAAGATTTTCGAATCGGAGATTATTTAGGTACTAAACCTTGTTTGATTCAAGGGTTATCTCATCAGCATCCCGCTCTCAAATCCTCCGTCCGGCCAGACAGGTCCGAAGAGAGAAGCAAGGTGATATCCGCTCTGAATACATTGTGGATTGAAGACCCGTCTTTGTCCTTTTCCATAAACTCATATAGTGATGAATTGGAAATCTCGTTATATGGTTTGACACAAAAGGAAATCATACAGACATTGCTGGAAGAACGATTTTCCGTAAAGGTCCATTTTGATGAGATCAAGACTATCTACAAAGAACGACCTGTAAAAAAGGTCAATAAGATTATTCAGATCGAAGTGCCACCCAACCCTTACTGGGCCACAATAGGGCTGACGCTTGAACCCTTGCCGTTAGGGACAGGGTTGCAAATCGAAAGTGACATCTCCTATGGTTATCTGAACCATTCTTTTCAAAATGCCGTTTTTGAAGGGATTCGTATGTCTTGCCAATCTGGTTTACATGGATGGGAAGTGACTGATCTGAAAGTAACTTTTACTCAAGCCGAGTATTATAGCCCGGTAAGTACACCTGCTGATTTCAGACAGCTGACCCCTTATGTCTTCAGGCTGGCCTTGCAACAGTCAGGTGTGGACATTCTCGAACCGATGCTCTATTTTGAGTTGCAGATACCCCAAGCGGCAAGTTCCAAAGCTATTACAGATTTGCAAAAAATGATGTCTGAGATTGAAGACATCAGTTGCAATAATGAGTGGTGTCATATTAAAGGGAAAGTTCCATTAAATACAAGTAAAGACTACGCCTCAGAAGTAAGTTCATACACTAAGGGCTTAGGCGTTTTTATGGTCAAGCCATGCGGGTATCAAATAACAAAAGGCGATTATTCTGATAATATCCGCATGAACGAAAAAGATAAACTTTTATTCATGTTCCAAAAATCAATGTCATCAAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35916","NCBI_taxonomy_name":"Bacteroides fragilis","NCBI_taxonomy_id":"817"}}}},"ARO_accession":"3000191","ARO_id":"36330","ARO_name":"tet(Q)","CARD_short_name":"tet(Q)","ARO_description":"Tet(Q) is a ribosomal protection protein. Its gene is associated with a conjugative transposon and has been found in both Gram-positive and Gram-negative bacteria.","ARO_category":{"35921":{"category_aro_accession":"0000002","category_aro_cvterm_id":"35921","category_aro_name":"tetracycline-resistant ribosomal protection protein","category_aro_description":"A family of proteins known to bind to the 30S ribosomal subunit. This interaction prevents tetracycline and tetracycline derivatives from inhibiting ribosomal function. Thus, these proteins confer elevated resistance to tetracycline derivatives as a ribosomal protection protein.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35986":{"category_aro_accession":"0000069","category_aro_cvterm_id":"35986","category_aro_name":"doxycycline","category_aro_description":"Doxycycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36291":{"category_aro_accession":"3000152","category_aro_cvterm_id":"36291","category_aro_name":"minocycline","category_aro_description":"Minocycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36667":{"category_aro_accession":"3000528","category_aro_cvterm_id":"36667","category_aro_name":"chlortetracycline","category_aro_description":"Chlortetracycline was an early, first-generation tetracycline antibiotic developed in the 1940's. It inhibits bacterial protein synthesis by binding to the 30S subunit of bacterial ribosomes, preventing the aminoacyl-tRNA from binding to the ribosome.","category_aro_class_name":"Antibiotic"},"37011":{"category_aro_accession":"3000667","category_aro_cvterm_id":"37011","category_aro_name":"demeclocycline","category_aro_description":"Demeclocycline is a tetracycline analog with 7-chloro and 6-methyl groups. Due to its fast absorption and slow excretion, it maintains higher effective blood levels compared to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37012":{"category_aro_accession":"3000668","category_aro_cvterm_id":"37012","category_aro_name":"oxytetracycline","category_aro_description":"Oxytetracycline is a derivative of tetracycline with a 5-hydroxyl group. Its activity is similar to other tetracyclines.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1233":{"model_id":"1233","model_name":"tet(32)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"5146":{"protein_sequence":{"accession":"ACH87088.1","sequence":"MKIINIGILAHVDAGKTTLTESLLYTSGAIAEQGNVDKGTTRTDTMILERQRGITIQTAVTSFYWNDYKINIVDTPGHMDFLTEAYRSLSVLDGAVLVISAKDGVQAQTRILFHALQKMDIPTIIFINKIDQNGIDLQCVYQSIKDKLTSDMIVMQEVSLSPKITMTDISDLDKWDMIISGSDELLERYVAEDSLDIQELQYEKCKRTRCCSLFPVYHGSAKDNLGTEKLIEAIIETFITETDDIQSELCGYVFKVEYTERKKRLSYLRLYHGTLHLRDTLLLSKKEKIKITEMCIPSNGEIVPADHACPGEIVILADDTLKLNDILGNEKLLPHKTRIDNPMPLLRTTVEPQKPEQREALLNALAEIADTDPLLHFDIDTVTHEIMLSFLGKVQLEVICSLLEEKYHVGVAMKEPSVIYLERPQKKASCTIHIEVPPNPFWASIGLTVTPLPVGSGTQYKSEVSLGYLNQSFQNAVMEGVRYGMEQGLYGWGVTDCQICFDYGVYYSPVSTPADFRFLAPVVLEQALKKAGTQLLEPYLSFTLFAPQEYLSRAYNDAPKYCAIIESTRLEKDEVIFKGEIPARCIGEYRNDLNFYTNGRSVCITELKGYQETSGEPVFQPRRPNSRLDKIRHMFQKIM"},"dna_sequence":{"accession":"EU722333.1","fmin":"1932","fmax":"3852","strand":"+","sequence":"ATGAAAATAATCAATATCGGCATTCTGGCCCATGTAGACGCAGGAAAAACTACATTGACAGAAAGTCTGCTATACACCAGTGGAGCGATTGCGGAACAGGGAAACGTGGATAAAGGGACCACAAGAACAGACACTATGATTTTGGAACGGCAACGGGGAATTACCATTCAGACAGCGGTTACTTCTTTTTATTGGAATGATTATAAAATCAATATCGTGGACACTCCCGGTCATATGGATTTTTTAACCGAAGCATACCGCTCTTTATCTGTCCTTGACGGAGCTGTTTTAGTCATTTCAGCAAAAGACGGCGTACAGGCACAAACCCGTATATTATTCCATGCGCTTCAGAAAATGGACATTCCGACAATTATCTTTATAAATAAGATAGACCAAAATGGGATCGACCTGCAGTGTGTTTACCAAAGCATTAAAGATAAACTTACCAGTGATATGATTGTCATGCAGGAGGTTTCCCTGTCGCCAAAGATAACCATGACCGATATTTCTGATTTAGACAAATGGGATATGATTATTTCCGGAAGCGATGAACTATTAGAACGATATGTTGCAGAGGATTCTTTGGATATACAGGAATTACAATATGAAAAGTGCAAAAGAACCAGATGCTGCTCTTTGTTTCCTGTTTATCATGGGAGTGCAAAAGACAATTTAGGAACAGAAAAACTGATTGAAGCGATTATAGAAACTTTCATTACAGAAACGGACGATATTCAGTCTGAATTATGTGGATATGTTTTTAAGGTTGAGTATACAGAGCGGAAAAAACGGCTTTCTTATTTACGCCTGTATCATGGGACGCTCCATTTACGGGATACCCTGCTGCTGTCAAAAAAGGAAAAAATAAAGATTACAGAAATGTGTATTCCGTCAAATGGTGAAATCGTCCCGGCTGACCATGCCTGTCCGGGAGAAATTGTTATTTTAGCTGATGATACTTTGAAACTGAACGATATCCTGGGAAATGAAAAACTCCTGCCTCACAAAACACGGATTGATAATCCCATGCCATTACTTCGGACAACGGTAGAGCCGCAAAAGCCGGAGCAAAGGGAAGCCCTGTTAAATGCCCTCGCAGAGATTGCTGATACAGACCCTCTTTTGCATTTTGACATTGATACTGTTACCCATGAGATTATGTTATCTTTTTTGGGAAAAGTACAGTTAGAAGTTATTTGTTCGCTATTAGAAGAAAAATATCATGTGGGCGTGGCTATGAAAGAGCCTTCGGTTATTTATCTGGAAAGACCGCAAAAAAAAGCGAGCTGCACGATTCATATTGAAGTGCCGCCGAATCCGTTTTGGGCATCTATTGGTTTGACTGTAACACCGCTTCCTGTTGGAAGCGGAACACAATATAAAAGCGAGGTATCTCTCGGCTATTTAAACCAAAGTTTTCAAAATGCCGTCATGGAGGGTGTGCGTTATGGAATGGAGCAGGGCTTATATGGCTGGGGAGTGACAGACTGCCAAATTTGTTTTGATTATGGAGTTTATTACAGCCCGGTCAGCACCCCCGCTGATTTTCGTTTTCTTGCGCCTGTCGTGTTGGAGCAGGCATTGAAAAAAGCAGGGACACAACTGTTGGAACCATACCTTTCCTTTACCCTTTTTGCACCGCAGGAATATCTTTCACGGGCTTATAATGATGCACCAAAGTATTGCGCAATCATTGAATCAACCAGACTTGAAAAAGATGAAGTTATTTTTAAGGGTGAAATCCCTGCCCGTTGTATCGGTGAATATAGGAATGATCTGAATTTTTATACAAATGGAAGAAGTGTCTGCATTACAGAATTAAAAGGGTATCAGGAAACTTCCGGCGAGCCTGTATTTCAGCCACGCCGCCCGAACAGCCGTTTAGACAAGATCCGGCATATGTTTCAGAAGATAATGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000196","ARO_id":"36335","ARO_name":"tet(32)","CARD_short_name":"tet(32)","ARO_description":"Tet(32) is a tetracycline resistance gene similar to Tet(O), and binds to the ribosome to confer tetracycline resistance as a ribosomal protection protein.","ARO_category":{"35921":{"category_aro_accession":"0000002","category_aro_cvterm_id":"35921","category_aro_name":"tetracycline-resistant ribosomal protection protein","category_aro_description":"A family of proteins known to bind to the 30S ribosomal subunit. This interaction prevents tetracycline and tetracycline derivatives from inhibiting ribosomal function. Thus, these proteins confer elevated resistance to tetracycline derivatives as a ribosomal protection protein.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35986":{"category_aro_accession":"0000069","category_aro_cvterm_id":"35986","category_aro_name":"doxycycline","category_aro_description":"Doxycycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36291":{"category_aro_accession":"3000152","category_aro_cvterm_id":"36291","category_aro_name":"minocycline","category_aro_description":"Minocycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36667":{"category_aro_accession":"3000528","category_aro_cvterm_id":"36667","category_aro_name":"chlortetracycline","category_aro_description":"Chlortetracycline was an early, first-generation tetracycline antibiotic developed in the 1940's. It inhibits bacterial protein synthesis by binding to the 30S subunit of bacterial ribosomes, preventing the aminoacyl-tRNA from binding to the ribosome.","category_aro_class_name":"Antibiotic"},"37011":{"category_aro_accession":"3000667","category_aro_cvterm_id":"37011","category_aro_name":"demeclocycline","category_aro_description":"Demeclocycline is a tetracycline analog with 7-chloro and 6-methyl groups. Due to its fast absorption and slow excretion, it maintains higher effective blood levels compared to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37012":{"category_aro_accession":"3000668","category_aro_cvterm_id":"37012","category_aro_name":"oxytetracycline","category_aro_description":"Oxytetracycline is a derivative of tetracycline with a 5-hydroxyl group. Its activity is similar to other tetracyclines.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1325":{"model_id":"1325","model_name":"OXA-65","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1767":{"protein_sequence":{"accession":"AAW81337.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"AY750908.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAACAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001614","ARO_id":"38014","ARO_name":"OXA-65","CARD_short_name":"OXA-65","ARO_description":"OXA-65 is a beta-lactamase found in A. baumannii.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1326":{"model_id":"1326","model_name":"OXA-170","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1680":{"protein_sequence":{"accession":"ADK35874.1","sequence":"MNKYFTCYVVASLFLSGCTVQHNLINETPSQIVQGHNQVIHQYFDEKNTSGVLVIQTDKKINLYGNALSRANTEYVPASTFKMLNALIGLENQKTDINEIFKWKGEKRSFTAWEKDMTLGEAMKLSAVPVYQELARRIGLDLMQKEVKRIGFGNAEIGQQVDNFWLVGPLKVTPIQEVEFVSQLAHTQLPFSEKVQANVKNMLLLEKSNGYKIFGKTGWAMDIKPQVGWLTGWVEQPDGKIVAFALNMEMRSEMPASIRNELLMKSLKQLNII"},"dna_sequence":{"accession":"HM488991.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGAATAAATATTTTACTTGCTATGTGGTTGCTTCTCTTTTTCTTTCTGGTTGTACGGTTCAGCATAATTTAATAAATGAAACCCCGAGTCAGATTGTTCAAGGACATAATCAGGTGATTCATCAATACTTTGATGAAAAAAACACCTCAGGTGTGCTGGTTATTCAAACAGATAAAAAAATTAATCTATATGGTAATGCTCTAAGCCGCGCAAATACAGAATATGTGCCAGCCTCTACATTTAAAATGTTGAATGCCCTGATCGGATTGGAGAACCAGAAAACGGATATTAATGAAATATTTAAATGGAAGGGCGAGAAAAGGTCATTTACCGCTTGGGAAAAAGACATGACACTAGGAGAAGCCATGAAGCTTTCTGCAGTCCCAGTCTATCAGGAACTTGCGCGACGTATCGGTCTTGATCTCATGCAAAAAGAAGTAAAACGTATTGGTTTCGGTAATGCTGAAATTGGACAGCAGGTTGATAATTTCTGGTTGGTAGGACCATTAAAGGTTACGCCTATTCAAGAGGTAGAGTTTGTTTCCCAATTAGCACATACACAGCTTCCATTTAGTGAAAAAGTGCAGGCTAATGTAAAAAATATGCTTCTTTTAGAAAAGAGTAATGGCTACAAAATTTTTGGAAAGACTGGTTGGGCAATGGATATAAAACCACAAGTGGGCTGGTTGACCGGCTGGGTTGAGCAGCCAGATGGAAAAATTGTCGCTTTTGCATTAAATATGGAAATGCGGTCAGAAATGCCGGCATCTATACGTAATGAATTATTGATGAAATCATTAAAACAGCTGAATATTATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001470","ARO_id":"37870","ARO_name":"OXA-170","CARD_short_name":"OXA-170","ARO_description":"OXA-170 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46499":{"category_aro_accession":"3007710","category_aro_cvterm_id":"46499","category_aro_name":"OXA-23-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases, specifically imipenem, derived from OXA-23, first identified in Acinetobacter baumannii.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1327":{"model_id":"1327","model_name":"AAC(6')-Iq","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"343":{"protein_sequence":{"accession":"AAC25500.1","sequence":"MDYSICDIAESNELILEAAKILRKSFLDAGNESWVDIKKAIEEVEDCIEHPNLCLGICLDDKLIGWTGLRPMYDKTWELHPMVIKTEYQCRGIGKVLIKELEKRAKGRGIIGIALGTDDEYQKTSLSMIDINERNIFDEIGNIKNVTNHPYEFYKKCGYMIVGIIPNANGKRKPDIWMWKDIS"},"dna_sequence":{"accession":"AF047556.1","fmin":"126","fmax":"678","strand":"+","sequence":"TTGGACTATTCAATATGCGATATAGCGGAATCAAATGAATTAATCCTTGAAGCAGCAAAAATACTTAGGAAAAGCTTTCTTGATGCTGGAAATGAATCATGGGTAGATATCAAAAAGGCTATTGAAGAAGTTGAGGATTGTATAGAACACCCAAATCTATGCTTGGGAATATGTCTGGATGATAAACTGATTGGCTGGACCGGATTAAGGCCGATGTACGATAAGACCTGGGAACTTCATCCCATGGTTATAAAAACTGAGTATCAATGCAGGGGTATTGGGAAAGTCTTAATAAAAGAACTAGAGAAGAGAGCGAAGGGTAGGGGAATTATCGGAATAGCTCTTGGAACTGATGATGAATATCAGAAAACTAGTTTGTCTATGATTGATATAAACGAACGAAACATCTTCGATGAAATCGGGAACATAAAGAACGTTACTAATCATCCATATGAGTTTTATAAGAAATGTGGTTATATGATCGTTGGAATAATCCCTAATGCTAATGGAAAAAGAAAACCAGATATTTGGATGTGGAAAGATATTAGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002560","ARO_id":"38960","ARO_name":"AAC(6')-Iq","CARD_short_name":"AAC(6')-Iq","ARO_description":"AAC(6')-Iq is a aminoglycoside acetyltransferase encoded by plasmids and integrons in K. pneumoniae.","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"A category of aminoglycoside N-acetyltransferase enzymes with modification regiospecificity based at the 6'-amino group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics through acetylation of the 6-amino group of the compound.","category_aro_class_name":"AMR Gene Family"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"46128":{"category_aro_accession":"3007378","category_aro_cvterm_id":"46128","category_aro_name":"2'-N-ethylnetilmicin","category_aro_description":"2'-N-ethylnetilmicin is an aminoglycoside antibiotic and a derivative of netilmicin.","category_aro_class_name":"Antibiotic"},"46129":{"category_aro_accession":"3007379","category_aro_cvterm_id":"46129","category_aro_name":"5-episisomicin","category_aro_description":"5-episosomicin is a semisynthetic aminoglycoside antibiotic similar to sisomicin.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1329":{"model_id":"1329","model_name":"ANT(4')-IIb","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"234":{"protein_sequence":{"accession":"AAM76670.1","sequence":"MQHTIARWVDRLREEYADAVAILLKGSYARGDAATWSDIDFDVLVSTQDVEDYRTWIEPVGDRLVHISAAVEWVTGWERDTVDPSSWSYGLPTQETTRLMWAINDETRRRMDRPYKTHPAAEPEVENTVEALGKIRNAIARGDDLGVYQSAQTVAKLVPTLLIPINPPVTVSHARQAIEAILAFPRVPVGFAADWLTCLGLVEERSARSTAAAAERMVRGVLEMLPTDPDLLGEDIARLMNAGLLEKYVQQ"},"dna_sequence":{"accession":"AY114142.1","fmin":"1060","fmax":"1816","strand":"+","sequence":"GTGCAACATACTATCGCCCGTTGGGTTGATCGCCTTCGCGAGGAGTACGCCGATGCCGTCGCGATTCTACTGAAGGGCAGTTACGCCCGGGGCGATGCTGCGACGTGGAGCGATATCGATTTCGATGTATTGGTAAGCACGCAGGATGTGGAGGATTACCGCACCTGGATAGAGCCGGTCGGCGATCGGCTGGTGCATATCTCGGCGGCGGTCGAGTGGGTCACCGGTTGGGAGCGCGATACCGTCGATCCATCCAGTTGGAGTTACGGCCTGCCAACGCAGGAAACCACCCGACTTATGTGGGCGATTAATGACGAGACTCGGCGGCGCATGGATCGTCCTTACAAAACGCATCCGGCCGCCGAACCCGAGGTGGAGAATACCGTTGAGGCGCTAGGCAAAATTCGCAATGCCATTGCTCGCGGCGATGACCTGGGCGTGTATCAATCCGCACAGACCGTGGCAAAGTTAGTGCCGACATTGTTGATCCCCATCAATCCACCGGTGACCGTGTCGCACGCACGGCAGGCGATCGAGGCGATTCTCGCGTTTCCCCGCGTGCCCGTGGGGTTTGCAGCAGATTGGCTCACCTGCCTCGGATTGGTGGAAGAGCGAAGTGCGCGCTCGACCGCCGCAGCGGCCGAGCGCATGGTTCGTGGCGTGCTCGAAATGCTCCCTACCGATCCCGACCTCCTAGGCGAGGATATCGCCCGATTGATGAACGCCGGGTTGCTCGAGAAATACGTGCAGCAGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002625","ARO_id":"39025","ARO_name":"ANT(4')-IIb","CARD_short_name":"ANT(4')-IIb","ARO_description":"ANT(4')-IIb is a transposon-encoded aminoglycoside nucleotidyltransferase in P. aeruginosa.","ARO_category":{"36368":{"category_aro_accession":"3000229","category_aro_cvterm_id":"36368","category_aro_name":"ANT(4')","category_aro_description":"A category of aminoglycoside O-nucleotidyltransferase enzymes with modification regiospecificity based at the 4'-hydroxyl group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics by transfer of an AMP group from an ATP substrate to the 4-hydroxyl group of the compound.","category_aro_class_name":"AMR Gene Family"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1330":{"model_id":"1330","model_name":"emrR","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"280"}},"model_sequences":{"sequence":{"5286":{"protein_sequence":{"accession":"AAC75731.1","sequence":"MDSSFTPIEQMLKFRASRHEDFPYQEILLTRLCMHMQSKLLENRNKMLKAQGINETLFMALITLESQENHSIQPSELSCALGSSRTNATRIADELEKRGWIERRESDNDRRCLHLQLTEKGHEFLREVLPPQHNCLHQLWSALSTTEKDQLEQITRKLLSRLDQMEQDGVVLEAMS"},"dna_sequence":{"accession":"U00096.3","fmin":"2810769","fmax":"2811300","strand":"+","sequence":"ATGGATAGTTCGTTTACGCCCATTGAACAAATGCTAAAATTTCGCGCCAGCCGCCACGAAGATTTTCCTTATCAGGAGATCCTTCTGACTCGTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTCAGCCTTCTGAATTAAGTTGTGCTCTTGGATCATCCCGTACCAACGCGACGCGTATTGCCGATGAACTGGAAAAACGCGGTTGGATCGAACGTCGTGAAAGCGATAACGATCGCCGCTGCCTGCATCTGCAATTAACGGAAAAAGGTCACGAGTTTTTGCGCGAGGTTTTACCACCGCAGCATAACTGCCTGCATCAACTCTGGTCCGCGCTCAGCACAACAGAAAAAGATCAGCTCGAGCAAATCACCCGCAAATTGCTCTCCCGTCTCGACCAGATGGAACAAGACGGTGTGGTTCTCGAAGCGATGAGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36849","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. MG1655","NCBI_taxonomy_id":"511145"}}}},"ARO_accession":"3000516","ARO_id":"36655","ARO_name":"emrR","CARD_short_name":"emrR","ARO_description":"EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1331":{"model_id":"1331","model_name":"CTX-M-52","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1335":{"protein_sequence":{"accession":"ABB17185.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAVAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTESTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGDYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"DQ223685.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGTGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGTCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGACTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001914","ARO_id":"38314","ARO_name":"CTX-M-52","CARD_short_name":"CTX-M-52","ARO_description":"CTX-M-52 is a beta-lactamase found in Escherichia coli.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1332":{"model_id":"1332","model_name":"APH(3')-IIIa","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"233":{"protein_sequence":{"accession":"AGV10830.1","sequence":"MAKMRISPELKKLIEKYRCVKDTEGMSPAKVYKLVGENENLYLKMTDSRYKGTTYDVEREKDMMLWLEGKLPVPKVLHFERHDGWSNLLMSEADGVLCSEEYEDEQSPEKIIELYAECIRLFHSIDISDCPYTNSLDSRLAELDYLLNNDLADVDCENWEEDTPFKDPRELYDFLKTEKPEEELVFSHGDLGDSNIFVKDGKVSGFIDLGRSGRADKWYDIAFCVRSIREDIGEEQYVELFFDLLGIKPDWEKIKYYILLDELF"},"dna_sequence":{"accession":"CP004067.1","fmin":"52914","fmax":"53709","strand":"+","sequence":"ATGGCTAAAATGAGAATATCACCGGAATTGAAAAAACTGATCGAAAAATACCGCTGCGTAAAAGATACGGAAGGAATGTCTCCTGCTAAGGTATATAAGCTGGTGGGAGAAAATGAAAACCTATATTTAAAAATGACGGACAGCCGGTATAAAGGGACCACCTATGATGTGGAACGGGAAAAGGACATGATGCTATGGCTGGAAGGAAAGCTGCCTGTTCCAAAGGTCCTGCACTTTGAACGGCATGATGGCTGGAGCAATCTGCTCATGAGTGAGGCCGATGGCGTCCTTTGCTCGGAAGAGTATGAAGATGAACAAAGCCCTGAAAAGATTATCGAGCTGTATGCGGAGTGCATCAGGCTCTTTCACTCCATCGACATATCGGATTGTCCCTATACGAATAGCTTAGACAGCCGCTTAGCCGAATTGGATTACTTACTGAATAACGATCTGGCCGATGTGGATTGCGAAAACTGGGAAGAAGACACTCCATTTAAAGATCCGCGCGAGCTGTATGATTTTTTAAAGACGGAAAAGCCCGAAGAGGAACTTGTCTTTTCCCACGGCGACCTGGGAGACAGCAACATCTTTGTGAAAGATGGCAAAGTAAGTGGCTTTATTGATCTTGGGAGAAGCGGCAGGGCGGACAAGTGGTATGACATTGCCTTCTGCGTCCGGTCGATCAGGGAGGATATCGGGGAAGAACAGTATGTCGAGCTATTTTTTGACTTACTGGGGATCAAGCCTGATTGGGAGAAAATAAAATATTATATTTTACTGGATGAATTGTTTTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39528","NCBI_taxonomy_name":"Campylobacter coli CVM N29710","NCBI_taxonomy_id":"1273173"}}}},"ARO_accession":"3002647","ARO_id":"39047","ARO_name":"APH(3')-IIIa","CARD_short_name":"APH(3')-IIIa","ARO_description":"APH(3')-IIIa is a plasmid-encoded aminoglycoside phosphotransferase in S. aureus and Enterococcus spp.","ARO_category":{"36265":{"category_aro_accession":"3000126","category_aro_cvterm_id":"36265","category_aro_name":"APH(3')","category_aro_description":"A category of aminoglycoside O-phosphotransferase enzymes with modification regiospecificity based at the 3'-hydroxyl group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics, specifically kanamycin and neomycin, by the ATP-dependent phosphorylation of the 3'-hydroxyl group of the compound.","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35940":{"category_aro_accession":"0000021","category_aro_cvterm_id":"35940","category_aro_name":"ribostamycin","category_aro_description":"Ribostamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Ribostamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35943":{"category_aro_accession":"0000024","category_aro_cvterm_id":"35943","category_aro_name":"butirosin","category_aro_description":"Butirosin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Butirosin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"37001":{"category_aro_accession":"3000657","category_aro_cvterm_id":"37001","category_aro_name":"paromomycin","category_aro_description":"An aminoglycoside antibiotic used for the treatment of parasitic infections. It is similar to neomycin sharing a similar spectrum of activity, but its hydroxyl group at the 6'-position instead of an amino group makes it resistant to AAC(6') modifying enzymes.","category_aro_class_name":"Antibiotic"},"37002":{"category_aro_accession":"3000658","category_aro_cvterm_id":"37002","category_aro_name":"lividomycin","category_aro_description":"Lividomycins are aminoglycosidic antibiotics produced by Streptomyces lividus. They contain 2-amino-2,3-dideoxy-D-glucose.","category_aro_class_name":"Antibiotic"},"46133":{"category_aro_accession":"3007382","category_aro_cvterm_id":"46133","category_aro_name":"gentamicin","category_aro_description":"Gentamicin is a commonly used aminoglycoside antibiotic derived from members of the Micromonospora genus of bacteria. It acts by binding the 30S ribosomal subunit, thus inhibiting protein synthesis. Gentamicin is typically used to treat Gram-negative infections of the repiratory and urinary tract, as well as infections of the bone and soft tissue. It also exhibits considerable nephrotoxicity and ototoxicity. Gentamicin is administered as a mixture of gentamicin type C (which makes about around 80% of the complex) and types A, B, and X (distributed in the remaining 20% of the complex).","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1334":{"model_id":"1334","model_name":"SHV-126","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"2020":{"protein_sequence":{"accession":"ACV32636.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGKRGARGIVALLGPNNKAERTVVIYLRDTPASMAERNQ"},"dna_sequence":{"accession":"GQ390808.1","fmin":"0","fmax":"813","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTACTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCAAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCACCGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAATCAG","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001173","ARO_id":"37553","ARO_name":"SHV-126","CARD_short_name":"SHV-126","ARO_description":"SHV-126 is a beta-lactamase that has been found in clinical isolates.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1335":{"model_id":"1335","model_name":"QnrB8","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"8143":{"protein_sequence":{"accession":"ABW03157.2","sequence":"MTLALVGEKIDRNRFTGEKVENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAILKDAIFKSCDLSMADFRNVSALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKAVLEKCELWENRWMGTQVLGATLSGSDLSGGEFSSFDWRTANFTHCDLTNSELGDLDIRGVDLQGVKLDNYQAALLMERLGIAVIG"},"dna_sequence":{"accession":"EU043312.2","fmin":"0","fmax":"645","strand":"+","sequence":"ATGACTCTGGCATTAGTTGGCGAAAAAATTGACAGAAACCGCTTCACCGGTGAAAAAGTTGAAAATAGCACTTTTTTTAACTGTGATTTTTCGGGTGCCGACCTTAGCGGTACTGAATTTATCGGCTGTCAGTTCTATGATCGAGAAAGCCAGAAAGGGTGCAATTTCAGTCGCGCAATACTGAAAGATGCCATTTTTAAAAGCTGTGATTTATCCATGGCGGATTTTCGCAACGTCAGTGCGTTGGGCATAGAAATTCGCCACTGCCGCGCACAGGGTGCAGATTTTCGCGGCGCAAGTTTCATGAATATGATCACCACGCGCACCTGGTTTTGCAGCGCATATATCACTAATACCAATCTAAGCTACGCCAACTTTTCGAAGGCCGTGCTTGAAAAGTGCGAATTGTGGGAAAATCGCTGGATGGGAACTCAGGTACTGGGTGCGACGTTGAGTGGTTCCGATCTCTCCGGTGGCGAGTTTTCGTCGTTCGACTGGCGGACGGCAAATTTCACGCACTGTGATTTGACCAATTCAGAACTGGGTGATTTAGATATTCGGGGCGTCGATTTACAAGGTGTCAAATTGGACAACTATCAGGCCGCATTGCTCATGGAACGTCTTGGCATCGCTGTGATTGGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002722","ARO_id":"39156","ARO_name":"QnrB8","CARD_short_name":"QnrB8","ARO_description":"QnrB8 is a plasmid-mediated quinolone resistance protein found in Citrobacter freundii.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1336":{"model_id":"1336","model_name":"BcII","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"1699":{"protein_sequence":{"accession":"AAA22562.1","sequence":"MKNTLLKLGVCVSLLGITPFVSTISSVQAERTVEHKVIKNETGTISISQLNKNVWVHTELGYFSGEAVPSNGLVLNTSKGLVLVDSSWDDKLTKELIEMVEKKFKKRVTDVIITHAHADRIGGMKTLKERGIKAHSTALTAELAKKNGYEEPLGDLQSVTNLKFGNMKVETFYPGKGHTEDNIVVWLPQYQILAGGCLVKSASSKDLGNVADAYVNEWSTSIENVLKRYGNINLVVPGHGEVGDRGLLLHTLDLLK"},"dna_sequence":{"accession":"M19530.1","fmin":"415","fmax":"1186","strand":"+","sequence":"ATGAAAAATACATTATTAAAATTAGGGGTATGTGTTAGTTTACTAGGAATAACTCCATTTGTTAGTACAATTTCTTCTGTACAAGCAGAACGAACGGTAGAGCATAAAGTAATAAAAAATGAGACAGGAACTATTTCGATTTCTCAGTTAAACAAAAATGTATGGGTTCATACGGAGTTAGGTTATTTTAGCGGAGAAGCAGTTCCTTCGAACGGTTTAGTCCTTAATACTTCTAAAGGGTTAGTACTTGTCGATTCTTCTTGGGATGATAAGTTAACGAAGGAATTAATAGAGATGGTAGAAAAGAAATTTAAGAAGCGCGTAACAGATGTCATTATTACACATGCACACGCTGATCGAATTGGTGGAATGAAAACATTGAAAGAAAGGGGCATTAAAGCGCATAGTACAGCGTTAACTGCGGAATTAGCAAAGAAAAATGGATATGAAGAACCACTTGGAGACTTACAAAGCGTTACAAATTTGAAGTTTGGAAATATGAAAGTAGAAACATTTTATCCAGGGAAGGGACATACAGAAGATAATATTGTTGTTTGGTTGCCACAATATCAAATTTTAGCTGGAGGCTGTTTAGTTAAATCTGCGTCCTCTAAAGATTTAGGAAACGTTGCTGATGCGTATGTAAATGAATGGTCCACATCGATTGAAAATGTGCTGAAGCGATATGGAAATATAAATTTAGTAGTGCCTGGTCATGGAGAAGTAGGGGATAGAGGATTACTTTTACATACATTGGATTTGTTGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36751","NCBI_taxonomy_name":"Bacillus cereus","NCBI_taxonomy_id":"1396"}}}},"ARO_accession":"3002878","ARO_id":"39312","ARO_name":"BcII","CARD_short_name":"BcII","ARO_description":"Bacillus cereus beta-lactamase II is a zinc metallo-beta-lactamase that hydrolyzes a large number of penicillins and cephalosporins in the Bacillus cereus strain 5\/B\/6.","ARO_category":{"36716":{"category_aro_accession":"3000577","category_aro_cvterm_id":"36716","category_aro_name":"subclass B1 Bacillus cereus Bc beta-lactamase","category_aro_description":"Subclass B1 Bacillus cereus Bc beta-lactamases are zinc metallo-beta-lactamases that hydrolyze a large number of penicillins and cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1340":{"model_id":"1340","model_name":"mtrC","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"790"}},"model_sequences":{"sequence":{"5879":{"protein_sequence":{"accession":"AAF42063.1","sequence":"MAFYAFKAMRAAALAAAVALVLSSCGKGGDAAQGGQPAGREAPAPVVGVVTVHPQTVALTVELPGRLESLRTADVRAQVGGIIQKRLFQEGSYVRAGQPLYQIDSSTYEAGLESARAQLATAQATLAKADADLARYKPLVAAEAVSRQEYDAAVTAKRSAEAGVKAAQAAIKSAGISLNRSRITAPISGFIGQSKVSEGTLLNAGDATVLATIRQTNPMYVNVTQSASEVMKLRRQIAEGKLLAADGVIAVGIKFDDGTVYPEKGRLLFADPAVNESTGQITLRAAVPNDQNILMPGLYVRVLMDQVAVDNAFVVPQQAVTRGAKDTVMIVNAQGGMEPREVTVAQQQGTNWIVTSGLKDGDKVVVEGISIAGITGAKKVTPKEWASSENQAAAPQSGVQTASEAKPASEAK"},"dna_sequence":{"accession":"AE002098.2","fmin":"1795181","fmax":"1796420","strand":"-","sequence":"ATGGCTTTTTATGCTTTTAAGGCGATGCGTGCGGCCGCGTTGGCTGCCGCCGTTGCATTGGTACTGTCGTCTTGCGGTAAAGGCGGAGACGCGGCGCAGGGCGGGCAGCCTGCTGGTCGGGAAGCCCCTGCGCCCGTCGTCGGTGTCGTAACCGTCCATCCGCAAACCGTCGCATTGACCGTCGAGTTGCCGGGGCGTTTGGAATCGCTGCGTACCGCCGATGTCCGCGCCCAAGTCGGCGGCATCATCCAAAAACGCCTGTTCCAAGAAGGCAGTTATGTCCGTGCCGGACAGCCGCTGTATCAGATCGACAGTTCCACTTATGAAGCAGGTCTGGAAAGCGCGCGCGCGCAACTGGCAACGGCTCAGGCAACGCTTGCCAAAGCGGATGCGGATTTGGCGCGATACAAGCCTTTGGTTGCCGCCGAAGCCGTCAGCCGGCAGGAATACGATGCTGCGGTAACGGCGAAACGTTCTGCCGAGGCAGGCGTTAAAGCGGCGCAGGCGGCAATCAAATCCGCCGGCATCAGCCTGAACCGTTCGCGCATTACCGCGCCGATTTCCGGCTTTATCGGTCAGTCCAAAGTTTCCGAAGGTACGTTGCTGAACGCTGGCGATGCGACCGTACTGGCGACCATCCGCCAAACCAATCCGATGTATGTGAACGTTACCCAGTCTGCATCCGAAGTGATGAAATTGCGCCGTCAGATAGCCGAAGGCAAACTGCTGGCGGCGGATGGTGTGATTGCGGTCGGCATCAAATTTGACGACGGCACAGTTTACCCTGAAAAAGGCCGCCTGCTGTTTGCCGATCCGGCCGTCAACGAATCGACCGGTCAGATTACCCTGCGCGCCGCCGTACCGAACGATCAGAATATCTTGATGCCCGGTCTGTATGTGCGCGTGCTGATGGACCAAGTGGCGGTGGATAACGCATTTGTTGTGCCGCAGCAGGCGGTAACGCGCGGTGCGAAAGATACCGTGATGATTGTGAATGCCCAAGGCGGTATGGAACCCCGCGAGGTAACGGTTGCGCAACAGCAGGGTACGAATTGGATTGTTACGTCGGGTCTGAAGGACGGGGACAAGGTGGTTGTGGAAGGCATCAGTATCGCCGGTATAACGGGTGCGAAAAAGGTAACGCCCAAAGAATGGGCGTCGTCTGAAAACCAAGCCGCCGCGCCTCAATCCGGCGTTCAGACGGCATCTGAAGCCAAACCTGCTTCTGAAGCGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39597","NCBI_taxonomy_name":"Neisseria meningitidis MC58","NCBI_taxonomy_id":"122586"}}}},"ARO_accession":"3000810","ARO_id":"37190","ARO_name":"mtrC","CARD_short_name":"mtrC","ARO_description":"MtrC is the membrane fusion protein of the MtrCDE multidrug efflux complex.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1341":{"model_id":"1341","model_name":"OXA-53","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"812":{"protein_sequence":{"accession":"AAP43641.1","sequence":"MAIQIFAILFSTFVLATFAHAQDGTLERSDWGKFFSDFQAKGTIVVADERQADHAILVFDQARSMKRYSPASTFKIPHTLFALDAGAVRDEFQIFRWDGVKRSFAGHNKDQDLRSAMRNSTVWVYELFAKEIGDGKARRYLKQIGYGNADPSTSHGDYWIEGSLAISAQEQIAFLRKLYQNDLPFRVEHQRLVKDLMIVEAGRNWILRAKTGWEGSMGWWVGWVEWPTGPVFFALNIDTPNRMDDLFKREAIARAILLSIEALPPNPAVHSDAAR"},"dna_sequence":{"accession":"AY289608.1","fmin":"616","fmax":"1444","strand":"+","sequence":"ATGGCAATCCAAATCTTCGCAATACTTTTCTCCACTTTTGTTCTTGCCACTTTTGCACATGCGCAAGATGGCACGCTGGAACGTTCTGACTGGGGGAAATTTTTCAGCGATTTTCAGGCCAAAGGTACGATAGTTGTGGCAGACGAACGCCAAGCGGATCATGCGATATTGGTTTTTGATCAAGCACGGTCAATGAAACGCTACTCGCCTGCGTCGACATTCAAGATTCCACATACACTTTTTGCACTTGATGCAGGCGCCGTTCGCGATGAGTTTCAGATTTTCCGCTGGGACGGCGTCAAAAGGAGCTTTGCAGGTCACAATAAAGACCAAGATTTGCGATCAGCAATGCGAAATTCTACTGTCTGGGTTTATGAGCTATTTGCAAAGGAAATCGGTGATGGCAAGGCTCGACGCTATTTGAAGCAAATCGGCTATGGCAACGCCGATCCTTCGACAAGTCATGGCGATTACTGGATAGAAGGCAGCCTTGCAATCTCAGCACAGGAACAGATCGCGTTTCTCAGAAAGCTCTATCAAAACGATCTGCCCTTTAGGGTGGAACATCAGCGCTTGGTCAAGGATCTGATGATTGTGGAAGCGGGACGCAACTGGATTCTGCGCGCGAAGACGGGCTGGGAAGGCAGCATGGGTTGGTGGGTGGGGTGGGTTGAATGGCCAACCGGTCCCGTATTCTTTGCCTTGAATATCGATACGCCAAACAGAATGGACGATCTTTTCAAGAGGGAAGCAATAGCGCGAGCGATACTTCTCTCTATCGAAGCGTTGCCGCCCAACCCGGCAGTCCACTCGGACGCTGCGCGATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35709","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Agona","NCBI_taxonomy_id":"58095"}}}},"ARO_accession":"3001810","ARO_id":"38210","ARO_name":"OXA-53","CARD_short_name":"OXA-53","ARO_description":"OXA-53 is a beta-lactamase found in Salmonella enterica.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46493":{"category_aro_accession":"3007704","category_aro_cvterm_id":"46493","category_aro_name":"OXA-2-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-2.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1343":{"model_id":"1343","model_name":"OXA-166","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1292":{"protein_sequence":{"accession":"ADK35870.1","sequence":"MNKYFTCYVVASLFLSGCTVQHNLINETPSQIVQGHNQVIHQYFDEKNTSGALVIQTDKKINLYGNALSRANTEYVPASTFKMLNALIGLENQKTDINEIFKWKGEKRSFTAWEKDMTLGEAMKLSAVPVYQELARRIGLDLMQKEVKRIGFGNAEIGQQVDNFWLVGPLKVTPIQEVEFVSQLAHTQLPFSEKVQANVKNMLLLEESNGYKIFGKTGWAMDIKPQVGWLTGWVEQPDGKIVAFALNMEMRSEMPASIRNELLMKSLKQLNII"},"dna_sequence":{"accession":"HM488987.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGAATAAATATTTTACTTGCTATGTGGTTGCTTCTCTTTTTCTTTCTGGTTGTACGGTTCAGCATAATTTAATAAATGAAACCCCGAGTCAGATTGTTCAAGGACATAATCAGGTGATTCATCAATACTTTGATGAAAAAAACACCTCAGGTGCGCTGGTTATTCAAACAGATAAAAAAATTAATCTATATGGTAATGCTCTAAGCCGCGCAAATACAGAATATGTGCCAGCCTCTACATTTAAAATGTTGAATGCCCTGATCGGATTGGAGAACCAGAAAACGGATATTAATGAAATATTTAAATGGAAGGGCGAGAAAAGGTCATTTACCGCTTGGGAAAAAGACATGACACTAGGAGAAGCCATGAAGCTTTCTGCAGTCCCAGTCTATCAGGAACTTGCGCGACGTATCGGTCTTGATCTCATGCAAAAAGAAGTAAAACGTATTGGTTTCGGTAATGCTGAAATTGGACAGCAGGTTGATAATTTCTGGTTGGTAGGACCATTAAAGGTTACGCCTATTCAAGAGGTAGAGTTTGTTTCCCAATTAGCACATACACAGCTTCCATTTAGTGAAAAAGTGCAGGCTAATGTAAAAAATATGCTTCTTTTAGAAGAGAGTAATGGCTACAAAATTTTTGGAAAGACTGGTTGGGCAATGGATATAAAACCACAAGTGGGCTGGTTGACCGGCTGGGTTGAGCAGCCAGATGGAAAAATTGTCGCTTTTGCATTAAATATGGAAATGCGGTCAGAAATGCCGGCATCTATACGTAATGAATTATTGATGAAATCATTAAAACAGCTGAATATTATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001466","ARO_id":"37866","ARO_name":"OXA-166","CARD_short_name":"OXA-166","ARO_description":"OXA-166 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46499":{"category_aro_accession":"3007710","category_aro_cvterm_id":"46499","category_aro_name":"OXA-23-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases, specifically imipenem, derived from OXA-23, first identified in Acinetobacter baumannii.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1346":{"model_id":"1346","model_name":"SHV-94","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1950":{"protein_sequence":{"accession":"ABN49111.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQHLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"EF373970.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGCATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGATGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001146","ARO_id":"37526","ARO_name":"SHV-94","CARD_short_name":"SHV-94","ARO_description":"SHV-94 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1347":{"model_id":"1347","model_name":"OXA-425","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1136":{"protein_sequence":{"accession":"AJA32743.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDVKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTLKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASALPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"KM588353.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGTAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCCTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTCTTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAACAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3003148","ARO_id":"39725","ARO_name":"OXA-425","CARD_short_name":"OXA-425","ARO_description":"OXA-425 is a beta-lactamase found in clinical isolates of Acinetobacter baumannii. It is carbapenem-resistant.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1349":{"model_id":"1349","model_name":"IND-2a","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"838":{"protein_sequence":{"accession":"AAG29760.1","sequence":"MKKSIQLLMMSMFLSPLINAQVKDFVIEPPVKPNLYLYKSFGVFGGKEYSANAVYLTTKKGVVLFDVPWQKEQYQTLMDTIQKRHHLPVIAVFATHSHDDRAGDLSFYNQKGIKTYATAKTNELLKKDGKATSTEIIKTGKPYKIGGEEFMVDFLGEGHTVDNVVVWFPKYKVLDGGCLVKSRTATDLGYTGEANVKQWPETMRKLKTKYAQATLVIPGHEEWKGGGHVQHTLDLLDKNKKPE"},"dna_sequence":{"accession":"AF219130.1","fmin":"0","fmax":"732","strand":"+","sequence":"ATGAAAAAAAGTATTCAGCTTTTGATGATGTCAATGTTTTTAAGCCCATTGATCAATGCCCAGGTTAAAGATTTTGTAATTGAGCCGCCTGTTAAACCCAACCTGTATCTTTATAAAAGTTTCGGAGTTTTCGGGGGTAAAGAATATTCTGCCAATGCTGTATATCTTACCACTAAGAAAGGAGTTGTCTTATTTGATGTCCCATGGCAAAAGGAACAATATCAAACCCTTATGGACACTATACAAAAGCGTCATCACCTTCCTGTAATTGCTGTATTTGCCACCCACTCTCATGATGACAGAGCGGGCGATCTAAGCTTTTACAATCAAAAAGGAATTAAAACATATGCGACCGCCAAGACCAATGAACTGTTGAAAAAAGACGGAAAAGCAACCTCAACCGAAATTATAAAAACAGGAAAACCTTACAAAATTGGTGGTGAAGAATTTATGGTAGACTTTCTTGGAGAAGGACATACAGTTGATAATGTTGTTGTATGGTTCCCCAAATATAAAGTACTGGACGGAGGATGTCTTGTAAAAAGCAGGACAGCCACTGACCTGGGATATACCGGTGAAGCAAACGTAAAACAATGGCCGGAAACCATGCGAAAACTAAAAACGAAATATGCTCAGGCCACTCTGGTAATCCCGGGACACGAGGAATGGAAAGGCGGTGGCCATGTACAGCATACTCTGGATCTTCTGGATAAGAATAAAAAGCCGGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36916","NCBI_taxonomy_name":"Chryseobacterium indologenes","NCBI_taxonomy_id":"253"}}}},"ARO_accession":"3002258","ARO_id":"38658","ARO_name":"IND-2a","CARD_short_name":"IND-2a","ARO_description":"IND-2a is a beta-lactamase found in Chryseobacterium indologenes.","ARO_category":{"36199":{"category_aro_accession":"3000060","category_aro_cvterm_id":"36199","category_aro_name":"IND beta-lactamase","category_aro_description":"IND beta-lactamases are class B carbapenem-hydrolyzing beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1350":{"model_id":"1350","model_name":"TEM-93","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"2039":{"protein_sequence":{"accession":"CAC85660.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTTPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGASKRGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AJ318093.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGACGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCAGTAAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000960","ARO_id":"37340","ARO_name":"TEM-93","CARD_short_name":"TEM-93","ARO_description":"TEM-93 is an extended-spectrum beta-lactamase found in E. coli.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1351":{"model_id":"1351","model_name":"QnrVC1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"8213":{"protein_sequence":{"accession":"ACC54440.2","sequence":"MEKSKQLYNQVNFSHQDLQEHIFSNCTFIHCNFKRSNLRDTQFINCTFIEQGALEGCDFSYADLRDASFKNCQLSMSHFKGANCFGIELRDCDLKGANFSQVSFVNQVSNKMYFCSAYITGCNLSYANFEQQLIEKCDLFENRWIGANLRGASFKESDLSRGVFSEDCWEQFRVQGCDLSHSELYGLDPRKIDLTGVKICSWQQEQLLEQLGVIIVPD"},"dna_sequence":{"accession":"EU436855.2","fmin":"1401","fmax":"2058","strand":"+","sequence":"ATGGAAAAATCAAAGCAATTATATAATCAAGTGAACTTCTCACATCAGGACTTGCAAGAACATATCTTTAGCAATTGTACTTTTATACATTGTAATTTTAAGCGCTCAAACCTCCGAGATACACAGTTCATTAACTGTACTTTCATAGAGCAGGGGGCATTGGAAGGGTGCGATTTTTCTTATGCTGATCTTCGAGATGCTTCATTTAAAAACTGTCAGCTTTCAATGTCCCATTTTAAGGGGGCAAATTGCTTTGGTATTGAACTGAGAGATTGTGATCTTAAAGGAGCAAATTTTAGTCAAGTTAGTTTTGTAAATCAGGTTTCGAATAAAATGTACTTTTGTTCTGCATACATAACAGGTTGTAACTTATCCTATGCCAATTTTGAGCAGCAGCTTATTGAAAAATGTGACCTGTTCGAAAATAGATGGATTGGTGCAAATCTTCGAGGCGCTTCATTTAAAGAATCAGATTTAAGCCGTGGTGTTTTTTCGGAAGACTGCTGGGAACAGTTTAGAGTACAAGGCTGTGATTTAAGCCATTCAGAGCTTTATGGTTTAGATCCTCGAAAGATTGATCTTACGGGTGTAAAAATATGCTCGTGGCAACAGGAACAGTTACTGGAGCAATTAGGGGTAATCATTGTTCCTGACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36789","NCBI_taxonomy_name":"Vibrio cholerae","NCBI_taxonomy_id":"666"}}}},"ARO_accession":"3002799","ARO_id":"39233","ARO_name":"QnrVC1","CARD_short_name":"QnrVC1","ARO_description":"QnrVC1 is an integron-mediated quinolone resistance protein found in Vibrio cholerae.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1352":{"model_id":"1352","model_name":"OXA-251","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1375":{"protein_sequence":{"accession":"AER57903.1","sequence":"MKTFAAYVIIACLSSTALAGSITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQIAREVDEVRMQKYLKNFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLYLNKLSASKENQLTVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGIIGG"},"dna_sequence":{"accession":"JN118546.1","fmin":"1761","fmax":"2562","strand":"+","sequence":"ATGAAAACATTTGCCGCATATGTAATTATCGCGTGTCTTTCGAGTACGGCATTAGCTGGTTCAATTACAGAAAATACGTCTTGGAACAAAGAGTTCTCTGCCGAAGCCGTCAATGGTGTCTTCGTGCTTTGTAAAAGTAGCAGTAAATCCTGCGCTACCAATGACTTAGCTCGTGCATCAAAGGAATATCTTCCAGCATCAACATTTAAGATCCCCAACGCAATTATCGGCCTAGAAACTGGTGTCATAAAGAATGAGCATCAGGTTTTCAAATGGGACGGAAAGCCAAGAGCCATGAAGCAATGGGAAAGAGACTTGACCTTAAGAGGGGCAATACAAGTTTCAGCTGTTCCCGTATTTCAACAAATCGCCAGAGAAGTTGACGAAGTAAGAATGCAGAAATACCTTAAAAACTTTTCCTATGGCAACCAGAATATCAGTGGTGGCATTGACAAATTCTGGTTGGAAGGCCAGCTTAGAATTTCCGCAGTTAATCAAGTGGAGTTTCTAGAGTCTCTATATTTAAATAAATTGTCAGCATCTAAAGAAAACCAGCTAACAGTAAAAGAGGCTTTGGTAACGGAGGCGGCACCTGAATATCTAGTGCATTCAAAAACTGGTTTTTCTGGTGTGGGAACTGAGTCAAATCCTGGTGTCGCATGGTGGGTTGGGTGGGTTGAGAAGGAGACAGAGGTTTACTTTTTCGCCTTTAACATGGATATAGACAACGAAAGTAAGTTGCCGCTAAGAAAATCCATTCCCACCAAAATCATGGAAAGTGAGGGCATCATTGGTGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3001500","ARO_id":"37900","ARO_name":"OXA-251","CARD_short_name":"OXA-251","ARO_description":"OXA-251 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46486":{"category_aro_accession":"3007697","category_aro_cvterm_id":"46486","category_aro_name":"OXA-10-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-10.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1353":{"model_id":"1353","model_name":"GES-5","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1866":{"protein_sequence":{"accession":"AAR97270.1","sequence":"MRFIHALLLAGIAHSAYASEKLTFKTDLEKLEREKAAQIGVAIVDPQGEIVAGHRMAQRFAMCSTFKFPLAALVFERIDSGTERGDRKLSYGPDMIVEWSPATERFLASGHMTVLEAAQAAVQLSDNGATNLLLREIGGPAAMTQYFRKIGDSVSRLDRKEPEMSDNTPGDLRDTTTPIAMARTVAKVLYGGALTSTSTHTIERWLIGNQTGDATLRAGFPKDWVVGEKTGTCANGGRNDIGFFKAQERDYAVAVYTTAPKLSAVERDELVASVGQVITQLILSTDK"},"dna_sequence":{"accession":"AY494717.1","fmin":"0","fmax":"864","strand":"+","sequence":"ATGCGCTTCATTCACGCACTATTACTGGCAGGGATCGCTCACTCTGCATATGCATCGGAAAAATTAACCTTCAAGACCGATCTTGAGAAGCTAGAGCGCGAAAAAGCAGCTCAGATCGGTGTTGCGATCGTCGATCCCCAAGGAGAGATCGTCGCGGGCCACCGAATGGCGCAGCGTTTTGCAATGTGCTCAACGTTCAAGTTTCCGCTAGCCGCGCTGGTCTTTGAAAGAATTGACTCAGGCACCGAGCGGGGGGATCGAAAACTTTCATATGGGCCGGACATGATCGTCGAATGGTCTCCTGCCACGGAGCGGTTTCTAGCATCGGGACACATGACGGTTCTCGAGGCAGCGCAAGCTGCGGTGCAGCTTAGCGACAATGGGGCTACTAACCTCTTACTGAGAGAAATTGGCGGACCTGCTGCAATGACGCAGTATTTTCGTAAAATTGGCGACTCTGTGAGTCGGCTAGACCGGAAAGAGCCGGAGATGAGCGACAACACACCTGGCGACCTCAGAGATACAACTACGCCTATTGCTATGGCACGTACTGTGGCTAAAGTCCTCTATGGCGGCGCACTGACGTCCACCTCGACCCACACCATTGAGAGGTGGCTGATCGGAAACCAAACGGGAGACGCGACACTACGAGCGGGTTTTCCTAAAGATTGGGTTGTTGGAGAGAAAACTGGTACCTGCGCCAACGGGGGCCGGAACGACATTGGTTTTTTTAAAGCCCAGGAGAGAGATTACGCTGTAGCGGTGTATACAACGGCCCCGAAACTATCGGCCGTAGAACGTGACGAATTAGTTGCCTCTGTCGGTCAAGTTATTACACAACTCATCCTGAGCACGGACAAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002334","ARO_id":"38734","ARO_name":"GES-5","CARD_short_name":"GES-5","ARO_description":"GES-5 is a beta-lactamase found in the Enterobacteriaceae family.","ARO_category":{"36205":{"category_aro_accession":"3000066","category_aro_cvterm_id":"36205","category_aro_name":"GES beta-lactamase","category_aro_description":"GES beta-lactamases or Guiana extended-spectrum beta-lactamases are related to the other plasmid-located class A beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1355":{"model_id":"1355","model_name":"TEM-149","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"2032":{"protein_sequence":{"accession":"ABC96711.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVKYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDSWEPELNEAIPNDERDTTTPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGVRGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"DQ369751.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTAAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATAGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGACGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGTGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36770","NCBI_taxonomy_name":"Klebsiella aerogenes","NCBI_taxonomy_id":"548"}}}},"ARO_accession":"3001016","ARO_id":"37396","ARO_name":"TEM-149","CARD_short_name":"TEM-149","ARO_description":"TEM-149 is an extended-spectrum beta-lactamase found in Klebsiella aerogenes.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1356":{"model_id":"1356","model_name":"dfrA22","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"6205":{"protein_sequence":{"accession":"AGY30828.1","sequence":"MNRESVRIYLVAAMGANRVIGNGPDIPWTIPGEQKIFRRLTEGKVVVMGRKTFESIGKPLPSRRTVVLSRQAGYSAAGCAVVSTLSQAIAIAAEHGKELYVAGGAEVYALALPHADGVFLSEVHQTFEGDAFFPVLNAAEFEVVSAETVQATITYTHSVYARRNG"},"dna_sequence":{"accession":"KF525301.1","fmin":"105","fmax":"603","strand":"+","sequence":"ATGAACCGGGAATCGGTCCGCATTTATCTGGTCGCTGCCATGGGTGCCAATCGGGTTATTGGCAATGGCCCCGACATCCCCTGGACAATCCCAGGTGAGCAGAAGATTTTTCGCAGGCTCACCGAGGGCAAAGTGGTCGTGATGGGTCGTAAGACATTTGAGTCCATAGGAAAGCCCTTACCAAGCCGCCGCACAGTGGTGCTCTCCCGCCAAGCTGGTTATAGCGCTGCTGGTTGTGCAGTTGTTTCAACGCTGTCGCAGGCTATTGCCATCGCAGCCGAACACGGCAAAGAACTCTACGTAGCCGGCGGAGCCGAGGTATATGCACTGGCACTACCTCATGCCGACGGCGTCTTTCTATCTGAGGTACATCAAACCTTCGAGGGTGACGCCTTCTTCCCTGTGCTCAACGCAGCAGAATTCGAGGTTGTCTCAGCCGAAACCGTTCAAGCCACTATCACGTACACGCACTCCGTCTATGCACGTCGTAACGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36791","NCBI_taxonomy_name":"uncultured bacterium","NCBI_taxonomy_id":"77133"}}}},"ARO_accession":"3003018","ARO_id":"39452","ARO_name":"dfrA22","CARD_short_name":"dfrA22","ARO_description":"dfrA22 is an integron-encoded dihydrofolate reductase found in Salmonella enterica.","ARO_category":{"37617":{"category_aro_accession":"3001218","category_aro_cvterm_id":"37617","category_aro_name":"trimethoprim resistant dihydrofolate reductase dfr","category_aro_description":"Alternative dihydropteroate synthase dfr present on plasmids produces alternate proteins that are less sensitive to trimethoprim from inhibiting its role in folate synthesis, thus conferring trimethoprim resistance.","category_aro_class_name":"AMR Gene Family"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1357":{"model_id":"1357","model_name":"CTX-M-132","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1861":{"protein_sequence":{"accession":"AFQ94051.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"JX313020.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001991","ARO_id":"38391","ARO_name":"CTX-M-132","CARD_short_name":"CTX-M-132","ARO_description":"CTX-M-132 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1358":{"model_id":"1358","model_name":"VIM-24","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1806":{"protein_sequence":{"accession":"ADL27533.1","sequence":"MFKLLSKLLVYLTASIMAIASPLAFSVDSSGEYPTVSEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEVEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSASVLYGGCAIYELSLTSAGNVADADLAEWPTSIERIQQHYPEAQFVIPGHGLPGGLDLLKHTTNVVKAHTNRSVVE"},"dna_sequence":{"accession":"HM855205.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGTTCAAACTTTTGAGTAAGTTATTGGTCTATTTGACCGCGTCTATCATGGCTATTGCGAGTCCGCTCGCTTTTTCCGTAGATTCTAGCGGTGAGTATCCGACAGTCAGCGAAATTCCGGTCGGGGAGGTCCGGCTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCAGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAGAAGCAAATTGGACTTCCTGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGTAGAGGGGAACGAGATTCCCACGCACTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAACTCTTCTATCCTGGTGCTGCGCATTCGACCGACAACTTAGTTGTGTACGTCCCGTCTGCGAGTGTGCTCTATGGTGGTTGTGCGATTTATGAGTTGTCACTCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCATTGAGCGGATTCAACAACACTACCCGGAAGCACAGTTCGTCATTCCGGGGCACGGCCTGCCGGGCGGTCTAGACTTGCTCAAGCACACAACGAATGTTGTAAAAGCGCACACAAATCGCTCAGTCGTTGAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002294","ARO_id":"38694","ARO_name":"VIM-24","CARD_short_name":"VIM-24","ARO_description":"VIM-24 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1359":{"model_id":"1359","model_name":"OXA-233","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1209":{"protein_sequence":{"accession":"AID67109.1","sequence":"MKTFAAYVIIACLSSTALAGSITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFKIPSAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAFPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGIIGG"},"dna_sequence":{"accession":"KJ657570.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGAAAACATTTGCCGCATATGTAATTATCGCGTGTCTTTCGAGTACGGCATTAGCTGGTTCAATTACAGAAAATACGTCTTGGAACAAAGAGTTCTCTGCCGAAGCCGTCAATGGTGTCTTCGTGCTTTGTAAAAGTAGCAGTAAATCCTGCGCTACCAATGACTTAGCTCGTGCATCAAAGGAATATCTTCCAGCATCAACATTTAAGATCCCCAGCGCAATTATCGGCCTAGAAACTGGTGTCATAAAGAATGAGCATCAGGTTTTCAAATGGGACGGAAAGCCAAGAGCCATGAAGCAATGGGAAAGAGACTTGACCTTAAGAGGGGCAATACAAGTTTCAGCTTTTCCCGTATTTCAACAAATCGCCAGAGAAGTTGGCGAAGTAAGAATGCAGAAATACCTTAAAAAATTTTCCTATGGCAACCAGAATATCAGTGGTGGCATTGACAAATTCTGGTTGGAAGGCCAGCTTAGAATTTCCGCAGTTAATCAAGTGGAGTTTCTAGAGTCTCTATATTTAAATAAATTGTCAGCATCTAAAGAAAACCAGCTAATAGTAAAAGAGGCTTTGGTAACGGAGGCGGCACCTGAATATCTAGTGCATTCAAAAACTGGTTTTTCTGGTGTGGGAACTGAGTCAAATCCTGGTGTCGCATGGTGGGTTGGGTGGGTTGAGAAGGAGACAGAGGTTTACTTTTTCGCCTTTAACATGGATATAGACAACGAAAGTAAGTTGCCGCTAAGAAAATCCATTCCCACCAAAATCATGGAAAGTGAGGGCATCATTGGTGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3001495","ARO_id":"37895","ARO_name":"OXA-233","CARD_short_name":"OXA-233","ARO_description":"OXA-233 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46486":{"category_aro_accession":"3007697","category_aro_cvterm_id":"46486","category_aro_name":"OXA-10-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-10.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1361":{"model_id":"1361","model_name":"OXA-223","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1683":{"protein_sequence":{"accession":"AEL88491.1","sequence":"MNIKTLLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEVHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEYHKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"JN248564.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAACACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGTACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGTACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCCTTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001669","ARO_id":"38069","ARO_name":"OXA-223","CARD_short_name":"OXA-223","ARO_description":"OXA-223 is a beta-lactamase found in A. baumannii.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1362":{"model_id":"1362","model_name":"IMP-31","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1260":{"protein_sequence":{"accession":"AGS82587.1","sequence":"MKKIFVLFVFLFCSITAAGESLPDIKIEKLDEDVYVHTSFEKITGWGVITKHGLVVLVNTDAYIIDTPFTAKDTEKLVRWFVGRGYKIKGSISSHFHSDSAGGIEWLNSQSIPTYASKLTNELLKKNGNAQAENSFSGVSYWLVKHKIEVFYPGPGHTQDNVVVWLPEKKILFGGCFIKPDGLGYLGDANLEAWPKSAETLMSKYGNAKLVVSSHSEIGGASLLKRTWEQAVKGLKESKNHHSPK"},"dna_sequence":{"accession":"KF148593.1","fmin":"0","fmax":"738","strand":"+","sequence":"ATGAAAAAAATATTTGTGTTATTTGTATTTTTGTTTTGCAGTATTACTGCCGCCGGAGAGTCTTTGCCTGATATAAAAATTGAGAAACTTGACGAAGATGTTTATGTTCATACTTCTTTTGAAAAGATAACCGGCTGGGGTGTTATTACTAAACACGGCTTGGTGGTTCTTGTAAATACTGATGCCTATATAATTGACACTCCATTTACAGCTAAAGATACTGAAAAATTAGTCCGCTGGTTTGTGGGGCGTGGTTATAAAATCAAAGGCAGTATTTCCTCACATTTTCATAGCGATAGCGCAGGTGGAATTGAGTGGCTTAATTCTCAATCTATCCCCACATATGCATCTAAATTAACAAATGAGCTTCTTAAAAAGAACGGTAATGCGCAAGCCGAAAACTCATTTAGTGGCGTTAGCTATTGGCTAGTTAAACATAAAATTGAAGTTTTCTATCCAGGACCAGGGCACACTCAGGATAATGTAGTGGTTTGGTTGCCTGAAAAGAAAATTTTATTTGGCGGTTGTTTTATTAAGCCGGACGGTCTTGGTTATTTGGGAGACGCAAATCTAGAAGCATGGCCTAAGTCCGCAGAAACATTAATGTCTAAGTATGGTAATGCAAAACTGGTTGTTTCGAGTCATAGTGAAATTGGGGGCGCATCACTATTGAAGCGCACTTGGGAGCAGGCTGTTAAGGGGCTAAAAGAAAGTAAAAACCATCACAGCCCCAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002222","ARO_id":"38622","ARO_name":"IMP-31","CARD_short_name":"IMP-31","ARO_description":"IMP-31 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1363":{"model_id":"1363","model_name":"CARB-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1855":{"protein_sequence":{"accession":"AAK96394.1","sequence":"MKFLLAFSLLIPSVVFASSSKFQQVEQDVKAIEVSLSARIGVSVLDTQNGEYWDYNGNQRFPLTSTFKTIACAKLLYDAEQGKVNPNSTVEIKKADLVTYSPVIEKQVGQAITLDDACFATMTTSDNTAANIILSAVGGPKGVTDFLRQIGDKETRLDRIEPDLNEGKLGDLRDTTTPKAIASTLNKFLFGSALSEMNQKKLESWMVNNQVTGNLLRSVLPAGWNIADRSGAGGFGARSITAVVWSEHQAPIIVSIYLAQTQASMEERNDAIVKIGHSIFDVYTSQSR"},"dna_sequence":{"accession":"AF313471.1","fmin":"1421","fmax":"2288","strand":"+","sequence":"ATGAAGTTTTTATTGGCATTTTCGCTTTTAATACCATCCGTGGTTTTTGCAAGTAGTTCAAAGTTTCAGCAAGTTGAACAAGACGTTAAGGCAATTGAAGTTTCTCTTTCTGCTCGTATAGGTGTTTCCGTTCTTGATACTCAAAATGGAGAATATTGGGATTACAATGGCAATCAGCGCTTCCCGTTAACAAGTACTTTTAAAACAATAGCTTGCGCTAAATTACTATATGATGCTGAGCAAGGAAAAGTTAATCCCAATAGTACAGTCGAGATTAAGAAAGCAGATCTTGTGACCTATTCCCCTGTAATAGAAAAGCAAGTAGGGCAGGCAATCACACTCGATGATGCGTGCTTCGCAACTATGACTACAAGTGATAATACTGCGGCAAATATCATCCTAAGTGCTGTAGGTGGCCCCAAAGGCGTTACTGATTTTTTAAGACAAATTGGGGACAAAGAGACTCGTCTAGACCGTATTGAGCCTGATTTAAATGAAGGTAAGCTCGGTGATTTGAGGGATACGACAACTCCTAAGGCAATAGCCAGTACTTTGAATAAATTTTTATTTGGTTCCGCGCTATCTGAAATGAACCAGAAAAAATTAGAGTCTTGGATGGTGAACAATCAAGTCACTGGTAATTTACTACGTTCAGTATTGCCGGCGGGATGGAACATTGCGGATCGCTCAGGTGCTGGCGGATTTGGTGCTCGGAGTATTACAGCAGTTGTGTGGAGTGAGCATCAAGCCCCAATTATTGTGAGCATCTATCTAGCTCAAACACAGGCTTCAATGGAAGAGCGAAATGATGCGATTGTTAAAATTGGTCATTCAATTTTTGACGTTTATACATCACAGTCGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002240","ARO_id":"38640","ARO_name":"CARB-1","CARD_short_name":"CARB-1","ARO_description":"CARB-1 is a beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36230":{"category_aro_accession":"3000091","category_aro_cvterm_id":"36230","category_aro_name":"CARB beta-lactamase","category_aro_description":"CARB beta-lactamases are class A lactamases that can hydrolyze carbenicillin. Many of the PSE beta-lactamases have been renamed as CARB-lactamases with the notable exception of PSE-2 which is now OXA-10.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1364":{"model_id":"1364","model_name":"CMY-101","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1281":{"protein_sequence":{"accession":"AHA80102.1","sequence":"MMKKSICCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAIIYQGKPYYFTWGKADIANNRPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTHYWPELTGKQWQGISLLHLATYTAGGLPLQVPDDVTDKAALLRFYQNWQPQWAPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTKRVLHPLKLAHTWITVPQSEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMTRWVQANMDASQVQEKTLQQGIELAQSRYWRIGDMYQGLGWEMLNWPVKADSIISGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"KF526114.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGATATGCTGCGCGCTGCTGCTGACAGCTTCTTTCTCCACGTTTGCCGCCGCCAAAACAGAACAACAAATTGCCGATATCGTTAACCGCACCATCACACCGCTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCGATTATCTATCAGGGGAAACCTTATTACTTTACCTGGGGTAAAGCCGATATCGCCAATAACCGTCCAGTCACGCAACAAACGCTGTTTGAACTCGGATCGGTCAGTAAAACGTTCAACGGCGTGCTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGCATTACTGGCCTGAACTGACTGGTAAGCAGTGGCAGGGTATCAGCCTGCTGCACTTAGCCACCTACACGGCAGGCGGCCTGCCGCTTCAGGTTCCGGACGACGTTACGGATAAAGCCGCGTTACTACGCTTTTATCAAAACTGGCAGCCGCAATGGGCCCCAGGCGCTAAACGTCTTTATGCTAACTCCAGCATTGGTCTGTTTGGCGCCCTGGCGGTGAAACCCTCAGGCATGAGCTACGAAGAGGCGATGACCAAACGCGTCCTGCACCCCTTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAGCGAACAAAAAGATTATGCCTGGGGTTATCGCGAAGGAAAGCCAGTGCATGTATCCCCTGGCCAACTTGATGCCGAAGCATACGGGGTGAAATCGAGCGTTATCGATATGACCCGTTGGGTTCAGGCCAACATGGACGCCAGCCAGGTTCAGGAGAAAACGCTCCAGCAGGGCATCGAGCTTGCGCAGTCACGTTACTGGCGTATTGGCGATATGTACCAGGGCCTGGGTTGGGAGATGCTGAACTGGCCGGTGAAAGCCGACTCGATAATTAGCGGTAGCGACAGCAAAGTGGCACTGGCAGCGCTTCCTGCCGTTGAGGTAAACCCGCCCGCGCCTGCCGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGCGGATTCGGCAGCTACGTTGCTTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAGAGCTACCCAAACCCTGTTCGCGTCGAGGCCGCCTGGCGCATTCTTGAAAAACTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002113","ARO_id":"38513","ARO_name":"CMY-101","CARD_short_name":"CMY-101","ARO_description":"CMY-101 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1365":{"model_id":"1365","model_name":"AAC(6')-I30","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"399":{"protein_sequence":{"accession":"AAP43642.1","sequence":"MAYAFCEIGESNEYIIQAARILTKSFLDIGNDSWPDMKSATKEVEECIEKPNICLGIHENEKLLGWIGLRPMYKLTWELHPLVISTQYQNKGIGRLLINELEKQAKQNGIIGIVLGTDDEYFKTSLSDVDLSGKNILDEIRNIKNIRNHPYEFYQRCGYSIVGVIPDANGKRKPDIWMWKKISD"},"dna_sequence":{"accession":"AY289608.1","fmin":"1523","fmax":"2078","strand":"+","sequence":"ATGGCATATGCGTTCTGCGAAATTGGAGAATCAAATGAATATATTATTCAGGCAGCTAGAATCTTAACGAAATCATTCCTTGATATTGGAAATGATTCCTGGCCTGATATGAAAAGTGCCACCAAAGAAGTTGAAGAATGTATTGAGAAGCCAAACATATGTCTTGGAATACATGAAAACGAAAAACTACTTGGATGGATTGGTCTTAGGCCCATGTACAAATTAACATGGGAATTACATCCCTTGGTAATAAGTACGCAATATCAGAATAAAGGTATTGGAAGACTTCTAATAAATGAATTGGAAAAACAAGCAAAGCAAAATGGAATAATCGGAATAGTATTGGGAACTGACGATGAATACTTTAAGACTTCATTATCAGATGTGGATCTTTCCGGGAAAAATATACTTGATGAGATAAGGAATATTAAAAATATAAGGAATCATCCGTACGAATTCTATCAACGATGTGGTTATTCCATTGTCGGAGTAATACCCGATGCAAATGGCAAAAGAAAGCCAGATATTTGGATGTGGAAGAAGATTAGTGATTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35709","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Agona","NCBI_taxonomy_id":"58095"}}}},"ARO_accession":"3002588","ARO_id":"38988","ARO_name":"AAC(6')-I30","CARD_short_name":"AAC(6')-I30","ARO_description":"AAC(6')-I30 is an integron-encoded aminoglycoside acetyltransferase in S. enterica.","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"A category of aminoglycoside N-acetyltransferase enzymes with modification regiospecificity based at the 6'-amino group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics through acetylation of the 6-amino group of the compound.","category_aro_class_name":"AMR Gene Family"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"46128":{"category_aro_accession":"3007378","category_aro_cvterm_id":"46128","category_aro_name":"2'-N-ethylnetilmicin","category_aro_description":"2'-N-ethylnetilmicin is an aminoglycoside antibiotic and a derivative of netilmicin.","category_aro_class_name":"Antibiotic"},"46129":{"category_aro_accession":"3007379","category_aro_cvterm_id":"46129","category_aro_name":"5-episisomicin","category_aro_description":"5-episosomicin is a semisynthetic aminoglycoside antibiotic similar to sisomicin.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1366":{"model_id":"1366","model_name":"cmx","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"8150":{"protein_sequence":{"accession":"AAG03380.1","sequence":"MPFALYMLALAVFVMGTSEFMLAGLLPAIATELDVSVGTAGLLTSAFAVGMVVGAPVMAAFARRWPPRLTLIVCLLVFAGSHVIGAMTPVFSLLLITRVLSALANAGFLAVALSTATTLVPANQKGRALSILLSGTTIATVVGVPAGALLGTALGWRTTFWAIAILCIPAAVGVIRGVTNNVGRSETSATSPRLRVELSQLATPRLILAMALGALINGGTFAAFTFLAPIVTETAGLAEAWVSVALVMFGIGSFLGVTIAGRLSDQRPGLVLAVGGPLLLTGWIVLAVVASHPVALIVLVLVQGFLSFGVGSTLITRVLYAASGAPTMGGSYATAALNIGAAAGPVLGALGLATGLGLLAPVWVASVLTAIALVIMLLTRRALTKTAAEAN"},"dna_sequence":{"accession":"AF024666.2","fmin":"35934","fmax":"37110","strand":"+","sequence":"ATGCCTTTTGCCCTCTACATGCTTGCCCTGGCGGTCTTCGTCATGGGCACTTCAGAATTCATGCTCGCGGGATTGCTCCCCGCGATCGCGACCGAACTTGACGTCTCGGTCGGCACTGCGGGCCTGCTGACCTCCGCATTCGCAGTCGGTATGGTCGTCGGCGCGCCAGTGATGGCGGCATTCGCTCGCCGTTGGCCACCGCGGCTCACATTGATCGTTTGCCTTCTCGTGTTCGCGGGAAGCCACGTCATCGGAGCGATGACACCAGTGTTCTCTCTCCTGCTCATCACCCGGGTGCTCAGCGCTCTCGCAAACGCAGGATTCCTCGCCGTAGCACTGAGCACGGCCACTACCCTCGTGCCAGCGAACCAGAAGGGGCGTGCACTGTCGATCCTGCTCTCCGGCACGACGATCGCAACCGTCGTGGGCGTCCCCGCCGGGGCACTGCTCGGCACAGCGCTGGGCTGGCGAACGACGTTCTGGGCGATCGCCATCCTCTGTATTCCCGCGGCCGTTGGAGTCATTCGTGGCGTCACGAACAATGTTGGTCGGAGCGAGACTAGCGCGACCTCACCAAGGCTCCGTGTCGAGCTCAGCCAGTTGGCGACGCCGCGGCTCATCCTGGCCATGGCACTCGGAGCGCTGATCAACGGAGGGACCTTTGCGGCATTCACCTTCCTGGCACCCATCGTGACCGAGACCGCGGGCTTGGCCGAAGCGTGGGTGTCCGTCGCGCTGGTGATGTTCGGCATCGGATCGTTCCTTGGCGTCACGATCGCAGGACGACTATCAGATCAACGACCTGGCCTCGTGCTCGCAGTCGGCGGACCGCTATTGCTGACAGGCTGGATCGTGTTGGCAGTGGTCGCATCTCATCCCGTTGCGCTTATCGTCCTCGTCCTCGTTCAGGGATTCCTGTCGTTCGGCGTCGGCAGTACTCTGATCACGCGTGTGCTGTATGCAGCATCGGGTGCGCCAACGATGGGCGGTTCGTACGCAACCGCAGCATTGAATATCGGAGCTGCAGCGGGGCCCGTGCTTGGTGCGCTCGGGCTCGCGACCGGGCTGGGGCTGCTCGCGCCGGTTTGGGTCGCTTCGGTGCTGACAGCGATCGCTCTCGTCATCATGCTTCTCACCAGACGCGCGCTTACGAAGACCGCGGCGGAGGCCAATTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39554","NCBI_taxonomy_name":"Corynebacterium striatum","NCBI_taxonomy_id":"43770"}}}},"ARO_accession":"3002703","ARO_id":"39137","ARO_name":"cmx","CARD_short_name":"cmx","ARO_description":"cmx is a plasmid or transposon-encoded chloramphenicol exporter that is found in Corynebacterium striatum and Pseudomonas aeruginosa.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1367":{"model_id":"1367","model_name":"oleD","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"4240":{"protein_sequence":{"accession":"ABA42119.2","sequence":"MTTQTTPAHIAMFSIAAHGHVNPSLEVIRELVARGHRVTYAIPPVFADKVAATGARPVLYHSTLPGPDADPEAWGSTLLDNVEPFLNDAIQALPQLADAYADDIPDLVLHDITSYPARVLARRWGVPAVSLSPNLVAWKGYEEEVAEPMWREPRQTERGRAYYARFEAWLKENGITEHPDTFASHPPRSLVLIPKALQPHADRVDEDVYTFVGACQGDRAEEGGWQRPAGAEKVVLVSLGSAFTKQPAFYRECVRAFGNLPGWHLVLQIGRKVTPAELGELPDNVEVHDWVPQLAILRQADLFVTHAGAGGSQEGLATATPMIAVPQAVDQFGNADMLQGLGVARKLATEEATADLLRETALALVDDPEVARRLRRIQAEMAQEGGTRRAADLIEAELPARHERQEPVGDRPNGG"},"dna_sequence":{"accession":"DQ195536.2","fmin":"0","fmax":"1248","strand":"+","sequence":"ATGACCACCCAGACCACTCCCGCCCACATCGCCATGTTCTCCATCGCCGCCCACGGCCATGTGAACCCCAGCCTGGAGGTGATCCGTGAACTCGTCGCCCGCGGCCACCGGGTCACGTACGCCATTCCGCCCGTCTTCGCCGACAAGGTGGCCGCCACCGGCGCCCGGCCCGTCCTCTACCACTCCACCCTGCCCGGCCCCGACGCCGACCCGGAGGCATGGGGAAGCACCCTGCTGGACAACGTCGAACCGTTCCTGAACGACGCGATCCAGGCGCTCCCGCAGCTCGCCGATGCCTACGCCGACGACATCCCCGATCTCGTCCTGCACGACATCACCTCCTACCCGGCCCGCGTCCTGGCCCGCCGCTGGGGCGTCCCGGCGGTCTCCCTCTCCCCGAACCTCGTCGCCTGGAAGGGTTACGAGGAGGAGGTCGCCGAGCCGATGTGGCGCGAACCCCGGCAGACCGAGCGCGGACGGGCCTACTACGCCCGGTTCGAGGCATGGCTGAAGGAGAACGGGATCACCGAGCACCCGGACACGTTCGCCAGTCATCCGCCGCGCTCCCTGGTGCTCATCCCGAAGGCGCTCCAGCCGCACGCCGACCGGGTGGACGAAGACGTGTACACCTTCGTCGGCGCCTGCCAGGGAGACCGCGCCGAGGAAGGCGGCTGGCAGCGGCCCGCCGGCGCGGAGAAGGTCGTCCTGGTGTCGCTCGGCTCGGCGTTCACCAAGCAGCCCGCCTTCTACCGGGAGTGCGTGCGCGCCTTCGGGAACCTGCCCGGCTGGCACCTCGTCCTCCAGATCGGCCGGAAGGTGACCCCCGCCGAACTGGGGGAGCTGCCGGACAACGTGGAGGTGCACGACTGGGTGCCGCAGCTCGCGATCCTGCGCCAGGCCGATCTGTTCGTCACCCACGCGGGCGCCGGCGGCAGCCAGGAGGGGCTGGCCACCGCGACGCCCATGATCGCCGTACCGCAGGCCGTCGACCAGTTCGGCAACGCCGACATGCTCCAAGGGCTCGGCGTCGCCCGGAAGCTGGCGACCGAGGAGGCCACCGCCGACCTGCTCCGCGAGACCGCCCTCGCTCTGGTGGACGACCCGGAGGTCGCGCGCCGGCTCCGGCGGATCCAGGCGGAGATGGCCCAGGAGGGCGGCACCCGGCGGGCGGCCGACCTCATCGAGGCCGAACTGCCCGCGCGCCACGAGCGGCAGGAGCCGGTGGGCGACCGACCCAACGGTGGGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36823","NCBI_taxonomy_name":"Streptomyces antibioticus","NCBI_taxonomy_id":"1890"}}}},"ARO_accession":"3000865","ARO_id":"37245","ARO_name":"oleD","CARD_short_name":"oleD","ARO_description":"OleD is a glycotransferase found in Streptomyces antibioticus, a natural producer  of oleandomycin. OleD can glycosylate a wide range of macrolides. Unlike oleI, oleD is not found in the oleandomycin biosynthetic cluster.","ARO_category":{"36604":{"category_aro_accession":"3000465","category_aro_cvterm_id":"36604","category_aro_name":"ole glycosyltransferase","category_aro_description":"OleI and OleD are glycosyltransferases found in Streptomyces antibioticus which is a natural producer of antibiotic oleandomycin. OleI glycosylates antibiotic oleandomycin whereas OleD can glycosylate a wide variety of macrolides.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"36284":{"category_aro_accession":"3000145","category_aro_cvterm_id":"36284","category_aro_name":"tylosin","category_aro_description":"Tylosin is a 16-membered macrolide, naturally produced by Streptomyces fradiae. It interacts with the bacterial ribosome 50S subunit to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1368":{"model_id":"1368","model_name":"abeM","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"850"}},"model_sequences":{"sequence":{"8212":{"protein_sequence":{"accession":"BAD89844.2","sequence":"MSNVTSFRSELKQLFHLMLPILITQFAQAGFGLIDTIMAGHLSAADLAAIAVGVGLWIPVMLLFSGIMIATTPLVAEAKGARNTEQIPVIVRQSLWVAVILGVLAMLILQLMPFFLHVFGVPESLQPKASLFLHAIGLGMPAVTMYAALRGYSEALGHPRPVTVISLLALVVLIPLNMIFMYGLGPIPALGSAGCGFATSILQWLMLITLAGYIYKASAYRNTSIFSRFDKISLTWVKRILQLGLPIGLAVFFEVSIFSTGALVLSPLGEVFIAAHQVAISVTSVLFMIPLSLAIALTIRVGTYYGEKNWASMYQVQKIGLSTAVFFALLTMSFIALGREQIVSVYTQDINVVPVAMYLLWFAMAYQLMDALQVSAAGCLRGMQDTQAPMWITLMAYWVIAFPIGLYLARYTDWGVAGVWLGLIIGLSIACVLLLSRLYLNTKRLSQT"},"dna_sequence":{"accession":"AB204810.2","fmin":"186","fmax":"1533","strand":"+","sequence":"GTGTCGAATGTCACGTCGTTTCGGTCTGAATTAAAACAACTCTTCCATTTAATGTTACCTATTTTAATTACGCAGTTTGCTCAAGCAGGGTTCGGGTTAATTGATACCATTATGGCTGGGCATTTATCTGCCGCAGACTTAGCCGCTATTGCGGTAGGTGTAGGCTTATGGATTCCAGTCATGCTCTTGTTCAGTGGCATCATGATTGCAACCACACCATTAGTTGCCGAAGCAAAAGGCGCTAGAAATACAGAGCAAATTCCAGTGATTGTCCGCCAATCATTATGGGTTGCAGTAATTCTAGGGGTATTGGCAATGCTCATTTTGCAGCTTATGCCATTTTTCTTACATGTGTTTGGCGTACCAGAAAGTTTACAACCTAAAGCCAGTTTATTCTTACATGCAATTGGTTTGGGTATGCCCGCTGTAACCATGTATGCAGCGCTCCGAGGCTATTCCGAAGCATTAGGCCATCCCCGCCCTGTCACGGTCATTAGCTTACTAGCCTTAGTGGTTTTAATCCCGCTTAACATGATTTTTATGTATGGCTTAGGACCAATACCTGCTTTGGGTAGCGCAGGCTGTGGTTTTGCAACATCCATTTTACAGTGGCTGATGCTCATTACGTTAGCAGGCTATATTTATAAGGCTTCGGCTTATCGAAACACATCTATTTTTAGCAGATTCGATAAAATTAGCCTGACTTGGGTTAAAAGAATTTTACAGCTCGGCCTGCCAATTGGTTTAGCTGTGTTTTTTGAAGTGAGTATTTTTAGTACAGGGGCATTGGTCCTTAGCCCTCTAGGGGAAGTCTTTATTGCCGCACACCAAGTAGCAATTTCAGTCACTTCGGTACTGTTTATGATTCCACTTTCTCTTGCCATTGCTTTAACCATTCGCGTGGGGACGTATTATGGTGAAAAGAACTGGGCTTCCATGTACCAAGTACAGAAAATTGGTCTAAGCACAGCAGTATTTTTTGCTCTATTGACCATGTCTTTTATTGCTTTAGGCCGTGAACAAATTGTCTCGGTTTATACTCAAGATATAAATGTTGTGCCGGTTGCCATGTATTTGCTCTGGTTTGCAATGGCATATCAATTAATGGATGCTCTACAAGTCAGCGCTGCCGGCTGTTTAAGAGGTATGCAAGATACTCAGGCACCGATGTGGATCACCTTAATGGCGTATTGGGTAATTGCTTTTCCAATCGGTCTTTATTTAGCGCGTTATACCGATTGGGGCGTAGCTGGTGTGTGGTTAGGTTTAATTATTGGTTTAAGTATTGCCTGTGTTTTATTGCTATCACGACTCTATTTGAATACCAAACGTTTAAGTCAAACCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3000753","ARO_id":"37133","ARO_name":"abeM","CARD_short_name":"abeM","ARO_description":"AbeM is an multidrug efflux pump found in Acinetobacter baumannii.","ARO_category":{"36251":{"category_aro_accession":"3000112","category_aro_cvterm_id":"36251","category_aro_name":"multidrug and toxic compound extrusion (MATE) transporter","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Multidrug and toxic compound extrusion (MATE) transporters utilize the cationic gradient across the membrane as an energy source. Although there is a diverse substrate specificity, almost all MATE transporters recognize fluoroquinolones. Arciflavine, ethidium and aminoglycosides are also good substrates.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35963":{"category_aro_accession":"0000045","category_aro_cvterm_id":"35963","category_aro_name":"acriflavine","category_aro_description":"Acriflavine is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37007":{"category_aro_accession":"3000663","category_aro_cvterm_id":"37007","category_aro_name":"ofloxacin","category_aro_description":"Ofloxacin is a 6-fluoro, 7-piperazinyl quinolone with a methyl-substituted oxazine ring. It has a broad spectrum of activity including many enterobacteria and mycoplasma but most anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"37250":{"category_aro_accession":"3000870","category_aro_cvterm_id":"37250","category_aro_name":"triclosan","category_aro_description":"Triclosan is a common antibacterial agent added to many consumer products as a biocide.  It is an inhibitor of fatty acid biosynthesis by blocking enoyl-carrier protein reductase (FabI).","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"43746":{"category_aro_accession":"3005386","category_aro_cvterm_id":"43746","category_aro_name":"disinfecting agents and antiseptics","category_aro_description":"Disinfectants that can also interact with antimicrobial resistance mechanisms, e.g. molecule efflux, and thus are the targets of disinfectant resistance.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1369":{"model_id":"1369","model_name":"QnrB69","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"278":{"protein_sequence":{"accession":"AGL43630.1","sequence":"MTLALVGEKIDRNRFTGEKVENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAILKDAIFKSCDLSMADFRNVSALGIEIRHCRAQGSDFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGTQVLGATFSGSDLSGGEFSSFDWRAANFTHCDLTNSELGDLDVRGVDLQGVKLDSYQASLILERLGIAVIG"},"dna_sequence":{"accession":"KC580658.1","fmin":"0","fmax":"645","strand":"+","sequence":"ATGACTCTGGCGTTAGTTGGCGAAAAAATTGACAGAAACAGGTTCACCGGTGAGAAAGTCGAAAATAGCACATTTTTCAACTGTGATTTTTCGGGTGCCGACCTTAGCGGTACTGAGTTTATTGGCTGCCAATTTTATGATCGAGAGAGCCAGAAAGGGTGTAATTTTAGCCGCGCTATCCTGAAAGATGCCATTTTCAAAAGTTGCGATCTCTCCATGGCGGATTTCAGAAATGTGAGTGCGCTGGGAATCGAAATTCGCCACTGCCGCGCACAAGGTTCAGATTTTCGCGGCGCAAGCTTTATGAATATGATTACCACACGCACCTGGTTTTGTAGCGCCTATATCACCAATACCAACTTAAGCTACGCCAACTTTTCAAAAGTCGTACTGGAAAAGTGCGAGCTGTGGGAAAACCGCTGGATGGGTACTCAGGTACTTGGCGCAACGTTCAGTGGATCGGACCTCTCTGGCGGCGAGTTTTCATCGTTCGACTGGCGGGCAGCAAACTTTACGCACTGTGATTTGACCAATTCAGAACTGGGCGATCTCGATGTCCGGGGTGTTGATTTGCAAGGCGTTAAACTGGACAGCTACCAGGCATCGTTGATCCTGGAACGTCTTGGCATCGCTGTCATTGGTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002781","ARO_id":"39215","ARO_name":"QnrB69","CARD_short_name":"QnrB69","ARO_description":"QnrB69 is a plasmid-mediated quinolone resistance protein found in Citrobacter freundii.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1370":{"model_id":"1370","model_name":"AAC(6')-Ib10","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"314":{"protein_sequence":{"accession":"AAC46343.1","sequence":"MLRSSSRPKTKLGITKYSIVTNSNDSVTLRLMTEHDLAMLYEWLNRSHIVEWWGGEEARPTLADVQEQYLPSVLAQESVTPYIAMLNGEPIGYAQSYVALGSGDGWWEEETDPGVRGIDQLLANASQLGKGLGTKLVRALVELLFNDPEVTKIQTDPSPSNLRAIRCYEKAGFERQGTVTTPDGPAVYMVQTRQAFERTRSDA"},"dna_sequence":{"accession":"U59183.1","fmin":"247","fmax":"859","strand":"+","sequence":"ATGTTACGCAGCAGCAGTCGCCCTAAAACAAAGTTAGGCATCACAAAGTACAGCATCGTGACCAACAGCAACGATTCCGTCACACTGCGCCTCATGACTGAGCATGACCTTGCGATGCTCTATGAGTGGCTAAATCGATCTCATATCGTCGAGTGGTGGGGCGGAGAAGAAGCACGCCCGACACTTGCTGACGTACAGGAACAGTACTTGCCAAGCGTTTTAGCGCAAGAGTCCGTCACTCCATACATTGCAATGCTGAATGGAGAGCCGATTGGGTATGCCCAGTCGTACGTTGCTCTTGGAAGCGGGGACGGATGGTGGGAAGAAGAAACCGATCCAGGAGTACGCGGAATAGACCAGTTACTGGCGAATGCATCACAACTGGGCAAAGGCTTGGGAACCAAGCTGGTTCGAGCTCTGGTTGAGTTGCTGTTCAATGATCCCGAGGTCACCAAGATCCAAACGGACCCGTCGCCGAGCAACTTGCGAGCGATCCGATGCTACGAGAAAGCGGGGTTTGAGAGGCAAGGTACCGTAACCACCCCAGATGGTCCAGCCGTGTACATGGTTCAAACACGCCAGGCATTCGAGCGAACACGCAGTGATGCCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002581","ARO_id":"38981","ARO_name":"AAC(6')-Ib10","CARD_short_name":"AAC(6')-Ib10","ARO_description":"AAC(6')-Ib10 is an integron-encoded aminoglycoside acetyltransferase in P. aeruginosa.","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"A category of aminoglycoside N-acetyltransferase enzymes with modification regiospecificity based at the 6'-amino group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics through acetylation of the 6-amino group of the compound.","category_aro_class_name":"AMR Gene Family"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1371":{"model_id":"1371","model_name":"CTX-M-26","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1628":{"protein_sequence":{"accession":"AAN75444.1","sequence":"MMRKSVRRAMLMTTACVSLLLASVPLCAQANDVQQKLAALEKSSGGRLGVALINTADNTQTLYRADERFAMCSTSKVMAAAAVLKQSETQKGLLSQRVEIKPSDLINYNPIAEKHVNGTMTFGELSAAALQYSDNTAMNKLIAHLGGPDKVTAFARTIGDDTFRLDRTEPTLNTAIPGDPRDTTTPLAMAQALRNLTLGNALGDTQRAQLVMWLKGNTTGAASIRAGLPTSWVVGDKTGSGDYGTTNDIAVIWPEGRAPLVLVTYFTQSEPKAESRRDVLAAAARIVTDGY"},"dna_sequence":{"accession":"AY157676.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGATGAGAAAAAGCGTAAGGCGGGCGATGTTAATGACGACAGCCTGTGTTTCGCTGCTGTTGGCCAGTGTGCCGCTGTGTGCCCAGGCGAACGATGTTCAACAAAAGCTCGCGGCGCTGGAGAAAAGCAGCGGGGGACGACTGGGTGTGGCGTTGATTAACACCGCCGATAACACGCAGACGCTCTACCGCGCCGACGAGCGTTTTGCCATGTGCAGCACCAGTAAAGTGATGGCGGCAGCGGCGGTGCTTAAGCAAAGTGAAACGCAAAAGGGCTTGTTGAGTCAGCGGGTTGAAATTAAGCCCTCAGACTTGATTAACTACAACCCCATTGCGGAAAAACACGTCAATGGCACGATGACATTCGGGGAGTTGAGCGCGGCGGCGCTACAGTACAGCGATAATACTGCCATGAATAAGCTGATTGCCCATCTCGGGGGGCCGGATAAAGTGACGGCATTTGCCCGTACGATTGGCGATGACACGTTCCGGCTCGATCGTACCGAGCCGACGCTCAACACCGCGATCCCCGGCGACCCGCGCGATACCACCACGCCGTTAGCGATGGCGCAGGCTCTGCGCAATCTGACGTTGGGCAATGCCCTGGGTGACACTCAGCGTGCGCAGCTGGTGATGTGGCTGAAAGGCAACACCACCGGCGCTGCCAGCATTCGGGCAGGGCTACCCACATCGTGGGTTGTCGGGGATAAAACCGGCAGCGGCGATTATGGTACGACGAATGATATCGCGGTTATTTGGCCGGAAGGTCGCGCGCCGCTCGTTCTGGTGACTTACTTCACCCAGTCGGAGCCGAAGGCAGAGAGCCGTCGTGACGTGCTCGCTGCTGCCGCCAGAATTGTCACCGACGGTTATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001888","ARO_id":"38288","ARO_name":"CTX-M-26","CARD_short_name":"CTX-M-26","ARO_description":"CTX-M-26 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1372":{"model_id":"1372","model_name":"ANT(2'')-Ia","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"457":{"protein_sequence":{"accession":"AAC64365.1","sequence":"MDTTQVTLIHKILAAADERNLPLWIGGGWAIDARLGRVTRKHDDIDLTFPGERRGELEAIVEMLGGRVMEELDYGFLAEIGDELLDCEPAWWADEAYEIAEAPQGSCPEAAEGVIAGRPVRCNSWEAIIWDYFYYADEVPPVDWPTKHIESYRLACTSLGAEKVEVLRAAFRSRYAA"},"dna_sequence":{"accession":"AF078527.1","fmin":"3769","fmax":"4303","strand":"+","sequence":"ATGGACACAACGCAGGTCACATTGATACACAAAATTCTAGCTGCGGCAGATGAGCGAAATCTGCCGCTCTGGATCGGTGGGGGCTGGGCGATCGATGCACGGCTAGGGCGTGTAACACGCAAGCACGATGATATTGATCTGACGTTTCCCGGCGAGAGGCGCGGCGAGCTCGAGGCAATAGTTGAAATGCTCGGCGGGCGCGTCATGGAGGAGTTGGACTATGGATTCTTAGCGGAGATCGGGGATGAGTTACTTGACTGCGAACCTGCTTGGTGGGCAGACGAAGCGTATGAAATCGCGGAGGCTCCGCAGGGCTCGTGCCCAGAGGCGGCTGAGGGCGTCATCGCCGGGCGGCCAGTCCGTTGTAACAGCTGGGAGGCGATCATCTGGGATTACTTTTACTATGCCGATGAAGTACCACCAGTGGACTGGCCTACAAAGCACATAGAGTCCTACAGGCTCGCATGCACCTCACTCGGGGCGGAAAAGGTTGAGGTCTTGCGTGCCGCTTTCAGGTCGCGATATGCGGCCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3000230","ARO_id":"36369","ARO_name":"ANT(2'')-Ia","CARD_short_name":"ANT(2'')-Ia","ARO_description":"Plasmid or integron-encoded nucleotidylylation of 2-deoxystreptamine aminoglycosides at the hydroxyl group at position 2'' in P. aeruginosa, K. pneumoniae, Morganella morganii, E. coli, S. typhimurium, C. freundii and A. baumannii.","ARO_category":{"41440":{"category_aro_accession":"3004276","category_aro_cvterm_id":"41440","category_aro_name":"ANT(2'')","category_aro_description":"A category of aminoglycoside O-nucleotidyltransferase enzymes with modification regiospecificity based at the 2''-hydroxyl group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics by transfer of an AMP group from an ATP substrate to the 2''-hydroxyl group of the compound.","category_aro_class_name":"AMR Gene Family"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"46133":{"category_aro_accession":"3007382","category_aro_cvterm_id":"46133","category_aro_name":"gentamicin","category_aro_description":"Gentamicin is a commonly used aminoglycoside antibiotic derived from members of the Micromonospora genus of bacteria. It acts by binding the 30S ribosomal subunit, thus inhibiting protein synthesis. Gentamicin is typically used to treat Gram-negative infections of the repiratory and urinary tract, as well as infections of the bone and soft tissue. It also exhibits considerable nephrotoxicity and ototoxicity. Gentamicin is administered as a mixture of gentamicin type C (which makes about around 80% of the complex) and types A, B, and X (distributed in the remaining 20% of the complex).","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1373":{"model_id":"1373","model_name":"CMY-26","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1361":{"protein_sequence":{"accession":"BAF56185.1","sequence":"MMKKSLCCALLLTASFSTFASAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKTYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQDISLLHLATYTAGGLPLQIPDDVTDKTALLHFYQNWQPQWAPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQSEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSNVTDMARWVQVNMDASRVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"AB300358.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACGTTTGCCTCCGCCAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAAACCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGATATCAGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTACGGATAAAACCGCATTACTGCACTTTTATCAAAACTGGCAGCCGCAATGGGCTCCGGGCGCTAAGAGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGTATGAGCTACGAAGAGGCAATGACCAGACGCGTCCTGCAGCCATTAAAACTGGCGCATACCTGGATTACAGTTCCGCAAAGCGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCTGTACACGTTTCTCCGGGACAACTTGATGCCGAAGCCTATGGCGTGAAATCCAACGTTACCGATATGGCACGCTGGGTTCAGGTCAACATGGACGCCAGCCGCGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGTAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCGGCAGTGAAAGCCTCATGGGTGCATAAAACGGGATCCACTGGTGGATTTGGCAGCTACGTTGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3002037","ARO_id":"38437","ARO_name":"CMY-26","CARD_short_name":"CMY-26","ARO_description":"CMY-26 is a beta-lactamase found in the Enterobacteriaceae family.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1375":{"model_id":"1375","model_name":"CMY-11","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1857":{"protein_sequence":{"accession":"AAK31370.1","sequence":"MQQRQSILWGAVATLMWAGLAHAGEASPVDPLRPVVDASIQPLLKEHRIPGMAVAVLKDGKAHYFNYGVANRESGAGVSEQTLFEIGSVSKTLTATLGAYAVVKGAMQLDDKASRHAPWLKGSAFDSITMGELATYSAGGLPLQFPEEVDSSEKMRAYYRQWAPVYSPGSHRQYSNPSIGLFGHLAASSLKQPFAPLMEQTLLPGLGMHHTYVNVPKQAMASYAYGYSKEDKPIRVNPGMLADEAYGIKTSSADLLRFVKANIGGVDDKALQQAISLTHQGHYSVGGMTQGLGWESYAYPVTEQTLLAGNSAKVSLEANPTAAPRESGSQVLFNKTGSTNGFGAYVAFVPARGIGIVMLANRNYPIEARIKAAHAILAQLAG"},"dna_sequence":{"accession":"AF357599.1","fmin":"253","fmax":"1402","strand":"+","sequence":"ATGCAACAACGACAATCCATCCTGTGGGGGGCCGTGGCCACCCTGATGTGGGCCGGTCTGGCCCATGCAGGTGAGGCTTCACCGGTCGATCCCCTGCGCCCCGTGGTGGATGCCAGCATCCAGCCGCTGCTCAAGGAGCACAGGATCCCGGGCATGGCGGTGGCCGTGCTCAAGGATGGCAAGGCCCACTACTTCAATTACGGGGTGGCCAACCGGGAGAGCGGGGCCGGCGTCAGCGAGCAGACCCTGTTCGAGATAGGATCCGTGAGCAAGACCCTGACTGCGACCCTGGGGGCCTATGCGGTGGTCAAGGGAGCGATGCAGCTGGATGACAAGGCGAGCCGGCACGCGCCCTGGCTCAAGGGATCCGCCTTTGACAGCATCACCATGGGGGAGCTTGCCACCTACAGCGCCGGAGGCCTGCCACTGCAATTCCCCGAGGAGGTGGATTCATCCGAGAAGATGCGCGCCTACTACCGCCAGTGGGCCCCTGTCTATTCGCCGGGCTCCCATCGCCAGTACTCCAACCCCAGCATAGGGCTGTTCGGCCACCTGGCGGCGAGCAGCCTGAAGCAGCCGTTTGCCCCCTTGATGGAGCAGACCCTGCTGCCCGGGCTCGGCATGCACCACACCTATGTCAATGTGCCGAAGCAGGCCATGGCGAGTTATGCCTATGGCTATTCGAAAGAGGACAAGCCCATCCGTGTCAACCCTGGCATGCTGGCGGACGAGGCCTATGGCATCAAGACCAGCTCGGCGGATCTGCTGCGTTTTGTGAAGGCCAACATCGGCGGGGTTGATGACAAGGCGTTGCAGCAGGCCATCTCCCTGACCCACCAAGGGCATTACTCGGTAGGCGGGATGACCCAGGGGCTGGGTTGGGAGAGTTACGCCTATCCCGTCACCGAGCAGACATTGCTGGCGGGCAATTCGGCCAAGGTGAGCCTCGAAGCCAATCCGACGGCGGCGCCCCGGGAGTCGGGGAGCCAGGTGCTCTTCAACAAGACCGGCTCGACCAATGGCTTTGGCGCCTATGTGGCCTTCGTGCCGGCCAGGGGGATCGGCATCGTCATGCTGGCCAATCGCAACTACCCCATCGAGGCGCGCATCAAGGCGGCCCACGCCATCCTGGCGCAGTTGGCCGGTTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002022","ARO_id":"38422","ARO_name":"CMY-11","CARD_short_name":"CMY-11","ARO_description":"CMY-11 is a beta-lactamase found in Escherichia coli.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1376":{"model_id":"1376","model_name":"MOX-6","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1364":{"protein_sequence":{"accession":"ACS44784.1","sequence":"MQQRQSILWGVLPTLMWAGLAHAGDRAATDPLRPVVDASIRPLLKEHRIPGMAVAVLKDGKAHYFNYGVADRERAVGVSEQTLFEIGSVSKTLTATLGAYAVVQGSFELDDKASLFAPWLKGSVFDNITMGELATYSAGGLPLQFPEEVDSLEKMQAYYRQWTPAYSPGSHRQYANPSIGLFGYLAASSMKQPFDRLMEQTILPGLGLYHTYLNVPEQAMGHYAYGYSKEDKPIRVTPGMLADEAYGIKTSSADLLRFVKANISGVDNAAMQQAIDLTHQGQYAVGEMTQGLGWERYAYPVSEQTLLAGNSAAMIYNANPAAPAPAARGHPVLFNKTGSTNGFGAYVAFVPAKGIGIVMLANRNSPIEGTLKAGHAILTQLAR"},"dna_sequence":{"accession":"GQ152601.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCAACAACGACAATCCATCCTGTGGGGCGTTCTGCCCACCCTGATGTGGGCCGGCCTGGCCCATGCAGGTGACAGGGCGGCGACCGATCCCCTGCGCCCCGTGGTGGATGCCAGCATCCGGCCGCTGCTCAAGGAGCACAGGATCCCGGGCATGGCGGTGGCCGTGCTCAAGGATGGCAAGGCCCACTATTTCAACTACGGTGTGGCCGATCGGGAGCGCGCAGTCGGTGTCAGCGAGCAGACCCTGTTCGAGATAGGTTCCGTGAGCAAGACCCTGACCGCGACGCTGGGGGCCTACGCCGTGGTGCAGGGGAGCTTCGAGCTCGATGACAAGGCGAGTCTGTTCGCCCCCTGGCTCAAGGGATCCGTCTTTGACAACATCACCATGGGGGAGCTGGCTACCTACAGCGCGGGCGGCTTGCCGCTGCAATTCCCCGAGGAGGTGGATTCGCTCGAGAAGATGCAGGCCTACTACCGCCAGTGGACCCCAGCCTACTCGCCGGGTTCCCATCGCCAGTACGCCAACCCCAGCATCGGGCTCTTTGGCTATCTGGCGGCGAGCAGCATGAAGCAGCCGTTCGATCGCCTGATGGAGCAGACGATCCTGCCGGGGCTTGGCCTGTACCATACCTACCTCAATGTGCCCGAGCAGGCCATGGGGCACTACGCCTACGGCTACTCGAAGGAGGACAAGCCCATCCGCGTCACTCCCGGCATGCTGGCGGACGAGGCCTACGGCATCAAGACCAGCTCGGCGGATCTGCTGCGCTTTGTGAAGGCCAACATCAGCGGGGTGGATAATGCGGCCATGCAGCAGGCCATCGACCTGACTCACCAGGGGCAGTATGCGGTGGGGGAGATGACCCAGGGACTGGGCTGGGAGCGTTACGCCTATCCCGTCAGCGAGCAGACGCTGCTGGCGGGCAACTCCGCGGCGATGATTTACAATGCGAACCCGGCTGCGCCCGCGCCCGCTGCAAGGGGGCACCCTGTGCTCTTCAACAAGACCGGCTCGACCAACGGCTTCGGGGCCTATGTGGCCTTCGTGCCGGCCAAAGGGATCGGCATCGTCATGCTGGCCAATCGCAACTCTCCCATCGAGGGCACGCTCAAGGCGGGCCACGCCATCCTGACGCAACTGGCCAGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36936","NCBI_taxonomy_name":"Aeromonas caviae","NCBI_taxonomy_id":"648"}}}},"ARO_accession":"3002185","ARO_id":"38585","ARO_name":"MOX-6","CARD_short_name":"MOX-6","ARO_description":"MOX-6 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36222":{"category_aro_accession":"3000083","category_aro_cvterm_id":"36222","category_aro_name":"MOX beta-lactamase","category_aro_description":"MOX beta-lactamases are plasmid-mediated AmpC-type beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1377":{"model_id":"1377","model_name":"CTX-M-60","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1966":{"protein_sequence":{"accession":"CAL80726.1","sequence":"MVKKSLRQFTLMATAAVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAVAAVLKKSESEPSLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGDYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDILASAAKIVTDGL"},"dna_sequence":{"accession":"AM411407.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAGCCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCGGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTCGCGATGTGCAGCACCAGTAAAGTGATGGCCGTGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAGTCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTGGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCAGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGACTATGGCACCACCAACGATATCGCGGTGATTTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATATATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001921","ARO_id":"38321","ARO_name":"CTX-M-60","CARD_short_name":"CTX-M-60","ARO_description":"CTX-M-60 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1378":{"model_id":"1378","model_name":"AAC(3)-IIc","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"616":{"protein_sequence":{"accession":"CAA38525.1","sequence":"MHTRKAITEALQKLGVQTGDLLMVHASLKAIGPVEGGAETVVAALRSAVGPTGTVMGYASWDRSPYEETRNGARLDDKTRRTWPPFDPATAGTYRGFGLLNQFLVQAPGARRSAHPDASMVAVGPLAETLTEPHKLGHALGEGSPVERFVRLGGKALLLGAPLNSVTALHYAEAVADIPNKRRVTYEMPMLGSNGEVAWKTASDYDSNGILDCFAIEGKPDAVETIANAYVKLGRHREGVVGFAQCYLFDAQDIVTFGVTYLEKHFGTTPIVPAHEVAECSCEPSG"},"dna_sequence":{"accession":"X54723.1","fmin":"818","fmax":"1679","strand":"+","sequence":"ATGCATACGCGGAAGGCAATAACGGAGGCGCTTCAAAAACTCGGAGTCCAAACCGGTGACCTATTGATGGTGCATGCCTCACTTAAAGCGATTGGTCCGGTCGAAGGAGGAGCGGAGACGGTCGTTGCCGCGTTACGCTCCGCGGTTGGGCCGACTGGCACTGTGATGGGATACGCATCGTGGGACCGATCACCCTACGAGGAGACTCGTAATGGCGCTCGGTTGGATGACAAAACCCGCCGTACCTGGCCGCCGTTCGATCCCGCAACGGCCGGGACTTACCGTGGGTTCGGCCTGCTGAATCAGTTTCTGGTTCAAGCCCCCGGCGCGCGGCGCAGCGCGCACCCCGATGCATCGATGGTCGCGGTTGGTCCACTGGCTGAAACGCTGACGGAGCCTCACAAGCTCGGTCACGCCTTGGGGGAAGGGTCGCCCGTCGAGCGGTTCGTTCGCCTTGGCGGGAAGGCCCTGCTGTTGGGTGCGCCGCTAAACTCCGTTACCGCATTGCACTACGCCGAGGCGGTTGCCGATATCCCCAACAAACGGCGGGTGACGTATGAGATGCCGATGCTTGGAAGCAACGGCGAAGTCGCCTGGAAAACGGCATCGGATTACGATTCAAACGGCATTCTCGATTGCTTTGCTATCGAAGGAAAGCCGGATGCGGTCGAAACTATAGCAAATGCTTACGTGAAGCTCGGTCGCCATCGAGAAGGTGTCGTGGGCTTTGCTCAGTGCTACCTGTTCGACGCGCAGGACATCGTGACGTTCGGCGTCACCTATCTTGAGAAGCATTTCGGAACCACTCCGATCGTGCCAGCACACGAAGTCGCCGAGTGCTCTTGCGAGCCTTCAGGTTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002535","ARO_id":"38935","ARO_name":"AAC(3)-IIc","CARD_short_name":"AAC(3)-IIc","ARO_description":"AAC(3)-IIc is a plasmid-encoded aminoglycoside acetyltransferase in E. coli and P. aeruginosa.","ARO_category":{"36461":{"category_aro_accession":"3000322","category_aro_cvterm_id":"36461","category_aro_name":"AAC(3)","category_aro_description":"A category of aminoglycoside N-acetyltransferase enzymes with modification regiospecificity based at the 3-amino group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics through acetylation of the 3-amino group of the compound.","category_aro_class_name":"AMR Gene Family"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"46127":{"category_aro_accession":"3007377","category_aro_cvterm_id":"46127","category_aro_name":"6'-N-ethylnetilmicin","category_aro_description":"6'-N-ethylnetilmicin is an aminoglycoside antibiotic and a derivative of netilmicin.","category_aro_class_name":"Antibiotic"},"46128":{"category_aro_accession":"3007378","category_aro_cvterm_id":"46128","category_aro_name":"2'-N-ethylnetilmicin","category_aro_description":"2'-N-ethylnetilmicin is an aminoglycoside antibiotic and a derivative of netilmicin.","category_aro_class_name":"Antibiotic"},"46133":{"category_aro_accession":"3007382","category_aro_cvterm_id":"46133","category_aro_name":"gentamicin","category_aro_description":"Gentamicin is a commonly used aminoglycoside antibiotic derived from members of the Micromonospora genus of bacteria. It acts by binding the 30S ribosomal subunit, thus inhibiting protein synthesis. Gentamicin is typically used to treat Gram-negative infections of the repiratory and urinary tract, as well as infections of the bone and soft tissue. It also exhibits considerable nephrotoxicity and ototoxicity. Gentamicin is administered as a mixture of gentamicin type C (which makes about around 80% of the complex) and types A, B, and X (distributed in the remaining 20% of the complex).","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1379":{"model_id":"1379","model_name":"OXA-313","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1376":{"protein_sequence":{"accession":"AGU69251.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKTTTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIQVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"KF057030.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCCCTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTCTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGACAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGACGCTATGAAAGCTTCCGCTATTCAGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCATTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001684","ARO_id":"38084","ARO_name":"OXA-313","CARD_short_name":"OXA-313","ARO_description":"OXA-313 is a beta-lactamase found in A. baumannii.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1380":{"model_id":"1380","model_name":"TEM-193","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1245":{"protein_sequence":{"accession":"AFC75523.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAAHLFLTTIGGPKELTAFLHNMGDHVTRLDCWGPKLTEAIPHDERDTTMPAAVANTLRKLLTGELLTLASRQQLIDWMEADKVAGPILRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"JN935135.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCCACTTATTTCTGACAACGATCGGAGGACCGAAGGAGCTCACCGCTTTTTTGCACAACATGGGGGATCATGTCACCCGCCTTGATTGTTGGGGACCGAAGCTGACTGAGGCCATACCACACGACGAGCGTGACACCACGATGCCTGCAGCAGTGGCCAACACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCAATTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001053","ARO_id":"37433","ARO_name":"TEM-193","CARD_short_name":"TEM-193","ARO_description":"TEM-193 is a beta-lactamase.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1382":{"model_id":"1382","model_name":"rmtG","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"93":{"protein_sequence":{"accession":"AGE00988.1","sequence":"MRDPLFEKLAASKKYRDVCPDTIARILTECRAKYRREKEIDKAAREKLHGITAAFMTDAEYRRAMEIAVRGGELAELMECHASTRERLPLEETDAVYARLLGAPDESALDLACGLNPAYLQNRYPEMRVTGIDISGQCVRVLRALGVDARLGDLLAENAIPRARYSVALLFKILPLLDRQSAGAARRILEAVNADALICSFPTRSLSGRNVGMAVHYAAWMRDQLPEKWRIERTVETDNELYYVLKEKQDGEAVRGGDSHRESE"},"dna_sequence":{"accession":"JX486113.1","fmin":"0","fmax":"795","strand":"+","sequence":"ATGCGTGATCCGTTGTTTGAAAAGCTGGCGGCTTCGAAGAAATACCGCGATGTGTGTCCGGATACGATCGCGCGCATTTTAACGGAATGCCGCGCGAAGTACCGGCGGGAAAAGGAAATCGATAAAGCGGCGCGCGAAAAGCTGCACGGCATCACCGCTGCGTTCATGACGGATGCGGAATACAGGCGCGCGATGGAAATTGCAGTGCGGGGCGGCGAACTGGCTGAATTGATGGAATGCCACGCCTCCACGCGCGAACGGCTGCCGCTGGAAGAAACAGATGCCGTGTATGCGCGTCTGTTGGGTGCGCCCGACGAATCGGCGCTGGATCTGGCGTGCGGGCTGAATCCCGCGTATCTGCAAAATCGATACCCCGAAATGCGCGTTACCGGAATCGATATCAGCGGCCAATGCGTGCGCGTGCTGCGCGCGCTGGGCGTGGATGCGCGCCTCGGCGATCTGCTTGCGGAGAACGCGATTCCGCGGGCGCGGTATTCCGTCGCGCTGCTGTTTAAAATTCTGCCGCTGCTGGATCGCCAGTCGGCGGGCGCGGCGCGGCGCATCCTGGAAGCGGTGAACGCCGATGCGCTGATCTGTTCGTTCCCCACGCGCAGCCTGTCCGGCAGAAATGTGGGCATGGCGGTGCATTACGCCGCGTGGATGCGGGATCAGCTGCCCGAAAAATGGCGAATCGAACGCACCGTGGAAACGGATAACGAGCTATATTACGTTCTGAAGGAGAAACAGGATGGCGAAGCTGTACGTGGTGGCGACTCCCATCGGGAATCTGAATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002668","ARO_id":"39068","ARO_name":"rmtG","CARD_short_name":"rmtG","ARO_description":"RmtG is a 16S rRNA methyltransferase found in Pseudomonas aeruginosa which methylates G1405 of the 16S rRNA. It confers high level resistance to many aminoglycosides.","ARO_category":{"41435":{"category_aro_accession":"3004271","category_aro_cvterm_id":"41435","category_aro_name":"16S rRNA methyltransferase (G1405)","category_aro_description":"Methyltransferases that methylate the G1405 position of 16S rRNA, which is part of an aminoglycoside binding site.","category_aro_class_name":"AMR Gene Family"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"40942":{"category_aro_accession":"3004015","category_aro_cvterm_id":"40942","category_aro_name":"gentamicin A","category_aro_description":"Gentamicin A is part of a complex of broad spectrum aminoglycoside antibiotics. Gentamicin inhibits protein synthesis, resulting in bacterial cell death.","category_aro_class_name":"Antibiotic"},"46133":{"category_aro_accession":"3007382","category_aro_cvterm_id":"46133","category_aro_name":"gentamicin","category_aro_description":"Gentamicin is a commonly used aminoglycoside antibiotic derived from members of the Micromonospora genus of bacteria. It acts by binding the 30S ribosomal subunit, thus inhibiting protein synthesis. Gentamicin is typically used to treat Gram-negative infections of the repiratory and urinary tract, as well as infections of the bone and soft tissue. It also exhibits considerable nephrotoxicity and ototoxicity. Gentamicin is administered as a mixture of gentamicin type C (which makes about around 80% of the complex) and types A, B, and X (distributed in the remaining 20% of the complex).","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1383":{"model_id":"1383","model_name":"IMI-4","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1435":{"protein_sequence":{"accession":"AHE78014.1","sequence":"MSLNVKPSRIAILFSSCLVSISFFSQANTKGIDEIKDLETDFNGRIGVYALDTGSGKSFSYKANERFPLCSSFKGFLAAAVLKGSQDNQLNLNQIVNYNTRSLEFHSPITTKYKDNGMSLGDMAAAALQYSDNGATNIILERYIGGPEGMTKFMRSIGDKDFRLDRWELDLNTAIPGDERDTSTPAAVAKSLKTLALGNILNEREKETYQTWLKGNTTGAARIRASVPSDWVVGDKTGSCGAYGTANDYAVVWPKNRAPLIISVYTTKYEKEAKHEDKVIAEASRIAIDNLK"},"dna_sequence":{"accession":"KF958750.1","fmin":"0","fmax":"879","strand":"+","sequence":"ATGTCACTTAATGTAAAACCAAGTAGAATAGCCATCTTGTTTAGCTCTTGTTTAGTTTCAATATCATTTTTCTCACAGGCCAATACAAAGGGCATCGATGAGATTAAAGACCTTGAAACAGATTTCAATGGTAGAATTGGTGTCTACGCTTTAGACACTGGCTCAGGCAAATCATTTTCATACAAAGCAAATGAACGATTTCCATTATGTAGTTCTTTCAAAGGTTTTTTAGCTGCTGCTGTATTAAAAGGCTCTCAAGATAATCAACTAAATCTTAATCAGATCGTGAATTATAATACAAGAAGTTTAGAGTTCCATTCACCCATCACAACTAAATATAAAGATAATGGAATGTCATTAGGTGATATGGCTGCTGCAGCTTTACAATATAGCGACAATGGTGCTACTAATATTATCCTTGAACGATATATCGGTGGTCCTGAGGGTATGACTAAATTCATGCGGTCGATTGGAGATAAAGATTTTAGACTCGATCGTTGGGAGTTAGATCTAAACACAGCTATTCCTGGCGATGAACGTGACACATCTACACCTGCAGCAGTAGCTAAGAGCCTGAAAACCCTTGCACTGGGTAACATACTCAATGAGCGTGAAAAGGAAACCTATCAGACATGGTTAAAGGGTAACACAACCGGTGCAGCGCGTATTCGTGCTAGCGTACCAAGCGATTGGGTAGTTGGCGATAAAACTGGTAGTTGCGGTGCATACGGTACGGCAAATGATTATGCGGTAGTCTGGCCAAAGAACCGAGCTCCTCTTATAATTTCTGTATACACTACAAAATACGAAAAAGAAGCCAAGCATGAGGATAAAGTAATCGCAGAAGCTTCAAGAATCGCAATTGATAACCTTAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3001861","ARO_id":"38261","ARO_name":"IMI-4","CARD_short_name":"IMI-4","ARO_description":"IMI-4 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36027":{"category_aro_accession":"3000018","category_aro_cvterm_id":"36027","category_aro_name":"IMI beta-lactamase","category_aro_description":"IMI beta-lactamases are a group of TEM-1-like beta-lactamase that are known to hydrolyze imipenem. IMI beta-lactamases are inhibited by clavulanic acid and tazobactam.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1384":{"model_id":"1384","model_name":"OXA-382","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"2011":{"protein_sequence":{"accession":"AHL30286.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKTDKKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWNGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFTYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"KJ135345.1","fmin":"14","fmax":"839","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAAACTGATAAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGAACGGGCAAAAAAGGCTGTTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGGCTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTACTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001568","ARO_id":"37968","ARO_name":"OXA-382","CARD_short_name":"OXA-382","ARO_description":"OXA-382 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1385":{"model_id":"1385","model_name":"mdsB","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"2090"}},"model_sequences":{"sequence":{"5454":{"protein_sequence":{"accession":"AAL19305.1","sequence":"MKFTHFFIARPIFAIVLSLLMLLAGAIAFLKLPLSEYPAVTPPTVQVSASYPGANPQVIADTVAAPLEQVINGVDGMLYMNTQMAIDGRMVISIAFEQGTDPDMAQIQVQNRVSRALPRLPEEVQRIGVVTEKTSPDMLMVVHLVSPQKRYDSLYLSNFAIRQVRDELARLPGVGDVLVWGAGEYAMRVWLDPAKIANRGLTASDIVTALREQNVQVAAGSVGQQPEASAAFQMTVNTLGRLTSEEQFGEIVVKIGADGEVTRLRDVARVTLGADAYTLRSLLNGEAAPALQIIQSPGANAIDVSNAIRGKMDELQQNFPQDIEYRIAYDPTVFVRASLQSVAITLLEALVLVVLVVVMFLQTWRASIIPLVAVPVSLVGTFALMHLFGFSLNTLSLFGLVLSIGIVVDDAIVVVENVERHISQGKSPGEAAKKAMDEVTGPILSITSVLTAVFIPSAFLAGLQGEFYRQFALTIAISTILSAINSLTLSPALAAILLRPHHDTAKADWLTRLMGTVTGGFFHRFNRFFDSASNRYVSAVRRAVRGSVIVMVLYAGFVGLTWLGFHQVPNGFVPAQDKYYLVGIAQLPSGASLDRTEAVVKQMSAIALAEPGVESVVVFPGLSVNGPVNVPNSALMFAMLKPFDEREDPSLSANAIAGKLMHKFSHIPDGFIGIFPPPPVPGLGATGGFKLQIEDRAELGFEAMTKVQSEIMSKAMQTPELANMLASFQTNAPQLQVDIDRVKAKSMGVSLTDIFETLQINLGSLYVNDFNRFGRAWRVMAQADAPFRMQQEDIGLLKVRNAKGEMIPLSAFVTIMRQSGPDRIIHYNGFPSVDISGGPAPGFSSGQATDAIEKIVRETLPEGMVFEWTDLVYQEKQAGNSALAIFALAVLLAFLILAAQYNSWSLPFAVLLIAPMSLLSAIVGVWVSGGDNNIFTQIGFVVLVGLAAKNAILIVEFARAKEHDGADPLTAVLEASRLRLRPILMTSFAFIAGVVPLVLATGAGAEMRHAMGIAVFAGMLGVTLFGLLLTPVFYVVVRRMALKRENRVDSHDQQA"},"dna_sequence":{"accession":"AE006468.2","fmin":"393893","fmax":"397061","strand":"-","sequence":"ATGAAATTCACCCACTTTTTCATTGCACGCCCCATCTTCGCCATCGTCCTGTCGCTGTTAATGCTGCTGGCTGGCGCTATCGCCTTTTTAAAACTGCCGCTGAGTGAATATCCGGCCGTTACGCCGCCCACGGTACAGGTTAGCGCCAGCTACCCCGGCGCTAACCCGCAAGTGATTGCCGATACGGTAGCCGCGCCGCTGGAACAGGTGATCAACGGCGTTGACGGCATGTTGTATATGAATACCCAGATGGCCATTGATGGTCGCATGGTTATCTCTATCGCCTTCGAACAGGGAACCGATCCTGATATGGCGCAAATTCAGGTGCAAAACCGGGTATCCCGCGCGCTGCCTCGCCTGCCCGAAGAAGTCCAGCGAATTGGCGTTGTAACGGAGAAAACGTCCCCCGATATGTTGATGGTGGTTCATCTTGTCTCGCCGCAAAAACGCTATGACTCGCTTTACCTGTCTAACTTCGCCATCCGGCAGGTTCGCGACGAACTGGCCCGTTTACCCGGCGTCGGCGATGTTCTCGTCTGGGGCGCGGGCGAGTACGCCATGCGCGTCTGGCTGGACCCGGCGAAAATCGCCAACCGCGGTCTTACCGCCAGTGATATCGTTACGGCGTTGCGGGAACAAAACGTACAGGTCGCCGCCGGTTCCGTCGGGCAACAGCCGGAGGCCTCCGCCGCTTTTCAGATGACGGTAAACACGCTGGGCCGCCTGACCAGCGAAGAACAGTTCGGCGAGATTGTGGTAAAAATCGGCGCTGACGGCGAGGTGACGCGTCTGCGTGATGTCGCCCGCGTCACGCTGGGCGCAGATGCCTATACGCTGCGCAGTTTACTGAATGGCGAAGCGGCGCCAGCGTTACAGATTATTCAAAGTCCGGGCGCCAATGCGATTGACGTTTCTAACGCGATTCGCGGCAAAATGGATGAGTTGCAGCAAAACTTCCCGCAGGATATCGAATACCGGATTGCCTATGATCCTACGGTCTTCGTGCGCGCATCGCTACAATCGGTGGCGATTACGTTGCTGGAAGCCCTCGTGCTGGTCGTCCTTGTCGTGGTGATGTTCCTGCAAACCTGGCGGGCGTCCATTATTCCTCTGGTGGCGGTTCCCGTTTCGCTGGTCGGCACCTTTGCCTTGATGCACCTGTTTGGCTTTTCGCTGAATACGCTTTCGCTGTTTGGTTTGGTCCTGTCGATAGGTATCGTTGTCGATGACGCCATCGTTGTGGTCGAAAACGTGGAACGGCATATCTCGCAGGGCAAAAGTCCCGGAGAGGCGGCAAAGAAGGCGATGGATGAAGTCACTGGTCCCATTCTTTCTATTACCTCGGTGCTAACGGCGGTCTTTATCCCTTCCGCATTCCTGGCGGGCCTGCAGGGTGAGTTTTATCGTCAGTTCGCGTTGACCATCGCTATTTCGACCATCCTTTCGGCCATTAACTCGCTGACGCTCTCCCCTGCGCTGGCTGCCATTTTGCTAAGACCGCACCACGATACTGCGAAGGCTGACTGGCTAACGCGGTTGATGGGCACGGTCACTGGCGGTTTTTTCCATCGCTTTAACCGTTTCTTCGACAGCGCGTCGAACCGCTATGTTAGCGCCGTCCGTCGGGCCGTGCGCGGCAGCGTCATTGTGATGGTGCTCTATGCTGGCTTTGTGGGGCTGACCTGGCTTGGCTTCCATCAGGTGCCGAACGGGTTTGTGCCTGCGCAGGATAAATACTATCTCGTCGGCATCGCCCAGCTCCCAAGCGGCGCATCGTTGGATCGCACAGAGGCGGTCGTGAAACAGATGTCCGCTATCGCGCTGGCGGAACCCGGCGTTGAAAGCGTCGTCGTCTTCCCCGGTCTGTCGGTTAACGGCCCGGTAAATGTGCCAAATTCGGCGCTGATGTTCGCCATGCTGAAACCCTTTGACGAGCGTGAAGATCCTTCGCTTTCCGCTAACGCTATCGCCGGAAAGCTAATGCACAAATTTAGCCACATTCCCGACGGATTTATTGGCATCTTCCCGCCACCGCCGGTTCCAGGGCTTGGCGCGACGGGCGGCTTTAAATTGCAGATTGAAGATCGTGCGGAACTGGGATTTGAAGCGATGACAAAGGTGCAAAGCGAGATTATGTCTAAGGCGATGCAGACGCCCGAACTGGCCAATATGCTGGCCAGTTTCCAGACAAACGCCCCGCAATTACAGGTGGATATCGACCGGGTAAAGGCGAAATCAATGGGGGTATCGCTCACCGACATCTTTGAAACGTTGCAAATTAACCTCGGCTCGCTTTACGTCAACGATTTCAACCGATTTGGCCGTGCCTGGCGGGTGATGGCGCAGGCCGATGCGCCATTCCGTATGCAGCAAGAGGATATCGGCCTGCTTAAAGTCCGCAATGCGAAGGGCGAGATGATCCCGCTTAGCGCTTTCGTCACGATTATGCGCCAGTCGGGGCCGGACAGAATCATCCATTACAACGGCTTCCCCTCGGTAGATATTAGCGGTGGACCGGCTCCGGGCTTCTCCTCCGGACAGGCGACGGACGCGATTGAAAAGATCGTGCGTGAAACGTTACCGGAAGGGATGGTCTTCGAATGGACCGATCTGGTTTATCAGGAAAAACAGGCCGGCAACTCTGCGCTTGCTATCTTTGCGCTGGCGGTGCTGCTGGCCTTCCTGATCCTGGCGGCGCAGTACAACAGTTGGTCGCTGCCCTTCGCCGTCCTGCTTATTGCGCCTATGTCATTACTCTCAGCCATTGTCGGCGTGTGGGTATCTGGCGGAGATAACAATATCTTTACGCAGATTGGTTTCGTGGTGCTGGTCGGCCTGGCGGCCAAGAACGCCATTTTGATTGTCGAGTTTGCCCGCGCCAAAGAACACGACGGCGCAGACCCGCTGACCGCCGTACTGGAAGCGTCCCGCCTGCGTCTGCGTCCTATCCTGATGACCTCATTCGCCTTTATCGCAGGTGTAGTACCACTGGTACTCGCGACGGGTGCCGGCGCGGAAATGCGACATGCGATGGGCATCGCCGTGTTTGCCGGCATGTTGGGCGTCACGCTCTTCGGCCTGTTATTGACGCCTGTATTTTACGTGGTGGTTCGCAGGATGGCATTAAAGCGTGAGAACCGCGTTGATTCGCATGATCAGCAAGCATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35734","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Typhimurium str. LT2","NCBI_taxonomy_id":"99287"}}}},"ARO_accession":"3000790","ARO_id":"37170","ARO_name":"mdsB","CARD_short_name":"mdsB","ARO_description":"MdsB is the inner membrane transporter of the multidrug and metal efflux complex MdsABC. mdsB corresponds to 1 locus in Pseudomonas aeruginosa PAO1 (gene name: mexQ) and 2 loci in Pseudomonas aeruginosa LESB58.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1386":{"model_id":"1386","model_name":"ANT(9)-Ia","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"6083":{"protein_sequence":{"accession":"CAA26428.1","sequence":"MSNLINGKIPNQAIQTLKIVKDLFGSSIVGVYLFGSAVNGGLRINSDVDVLVVVNHSLPQLTRKKLTERLMTISGKIGNTDSVRPLEVTVINRSEVVPWQYPPKREFIYGEWLRGEFENGQIQEPSYDPDLAIVLAQARKNSISLFGPDSSSILVSVPLTDIRRAIKDSLPELIEGIKGDERNVILTLARMWQTVTTGEITSKDVAAEWAIPLLPKEHVTLLDIARKGYRGECDDKWEGLYSKVKALVKYMKNSIETSLN"},"dna_sequence":{"accession":"X02588.1","fmin":"330","fmax":"1113","strand":"+","sequence":"ATGAGCAATTTGATTAACGGAAAAATACCAAATCAAGCGATTCAAACATTAAAAATCGTAAAAGATTTATTTGGAAGTTCAATAGTTGGAGTATATCTATTTGGTTCAGCAGTAAATGGTGGTTTACGCATTAACAGCGATGTAGATGTTCTAGTCGTCGTGAATCATAGTTTACCTCAATTAACTCGAAAAAAACTAACAGAAAGACTAATGACTATATCAGGAAAGATTGGAAATACGGATTCTGTTAGACCACTTGAAGTTACGGTTATAAATAGGAGTGAAGTTGTCCCTTGGCAATATCCTCCAAAAAGAGAATTTATATACGGTGAGTGGCTCAGGGGTGAATTTGAGAATGGACAAATTCAGGAACCAAGCTATGATCCTGATTTGGCTATTGTTTTAGCACAAGCAAGAAAGAATAGTATTTCTCTATTTGGTCCTGATTCTTCAAGTATACTTGTCTCCGTACCTTTGACAGATATTCGAAGAGCAATTAAGGATTCTTTGCCAGAACTAATTGAGGGGATAAAAGGTGATGAGCGTAATGTAATTTTAACCCTAGCTCGAATGTGGCAAACAGTGACTACTGGTGAAATTACCTCGAAAGATGTCGCTGCAGAATGGGCTATACCTCTTTTACCTAAAGAGCATGTAACTTTACTGGATATAGCTAGAAAAGGCTATCGGGGAGAGTGTGATGATAAGTGGGAAGGACTATATTCAAAGGTGAAAGCACTCGTTAAGTATATGAAAAATTCTATAGAAACTTCTCTCAATTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35508","NCBI_taxonomy_name":"Staphylococcus aureus","NCBI_taxonomy_id":"1280"}}}},"ARO_accession":"3002630","ARO_id":"39030","ARO_name":"ANT(9)-Ia","CARD_short_name":"ANT(9)-Ia","ARO_description":"ANT(9)-Ia is an aminoglycoside nucleotidyltransferase encoded by plasmids and transposons in S. aureus, Enterococcus spp., Mammaliicoccus sciuri, and E. faecalis.","ARO_category":{"36367":{"category_aro_accession":"3000228","category_aro_cvterm_id":"36367","category_aro_name":"ANT(9)","category_aro_description":"A category of aminoglycoside O-nucleotidyltransferase enzymes with modification regiospecificity based at the 9-hydroxyl group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics, specifically streptomycin, by transfer of an AMP group from an ATP substrate to the 9-hydroxyl group of the compound.","category_aro_class_name":"AMR Gene Family"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1387":{"model_id":"1387","model_name":"OXA-99","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1847":{"protein_sequence":{"accession":"ABI53716.1","sequence":"MNIKTLLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEVHTTGVLVIRQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEMNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"DQ888718.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAACACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGTACACACTACGGGTGTTTTAGTTATCCGACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAATGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001649","ARO_id":"38049","ARO_name":"OXA-99","CARD_short_name":"OXA-99","ARO_description":"OXA-99 is a beta-lactamase found in A. baumannii.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1388":{"model_id":"1388","model_name":"oleB","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1100"}},"model_sequences":{"sequence":{"3347":{"protein_sequence":{"accession":"AAA50325.1","sequence":"MQNAHRSDTGAAALTGTPEKLLPTQPETGSFQVVLDDVVRAPGGRPLLDGVNQSVALGERVGIIGENGSGKSTLLRMLAGVDRPDGGQVLVRAPGGCGYLPQTPDLPPEDTVQDAIDHALAELRSLERGLREAEQALAGAEPEELEGLLGAYGDLLEAFEARDGYAADARVDAAMHGLGLAGITGDRRLGSLSGGEQARLNLACLLAASPQLMLLDEPTNHLDVGALEWLEERLRAHRGSVLVVSHDRVFLERVATALWEVDGERRTVNRHGGGYAGYLQAKAAARRRWEQAYQDWLEDLARQRELARSAADHLATGPRRNTERSNQRHQRNVEKQISARVRNAKERVRRLEENPVPRPPQPMRFRARVEGGGTVGRGGALAELYKVTVGTRLDVPSFTVDPGERILITGHNGAGKSTLLRVLAGDLAPDQGECERPERIGWLPQETEITDRQQSLLAAFAAGLPGIAEEHRGALLGFGLFRPSALGTAVGDLSTGQLRRLALARLLRDPADLLLLDEPTNHLSPALVEDLEEALAHYRGALVVVSHDRMFAQRFTGRRMHMEGGRFVE"},"dna_sequence":{"accession":"L36601.1","fmin":"1420","fmax":"3130","strand":"+","sequence":"ATGCAGAACGCACACCGTTCCGATACCGGCGCCGCGGCGCTCACCGGCACGCCGGAAAAGCTCCTTCCCACGCAACCTGAGACCGGTTCCTTCCAGGTCGTCCTCGACGACGTCGTCCGGGCACCCGGCGGACGGCCGCTGTTGGACGGCGTCAACCAGTCGGTGGCACTCGGCGAGCGCGTCGGCATCATCGGTGAGAACGGATCGGGCAAGTCGACCCTGCTCCGCATGCTCGCCGGCGTGGACCGCCCGGACGGTGGCCAGGTCCTCGTCCGGGCTCCCGGCGGCTGCGGCTACCTCCCCCAGACACCGGACCTGCCCCCGGAGGACACCGTTCAGGACGCCATCGACCACGCCCTCGCCGAACTGCGCTCCCTGGAGCGGGGGTTGCGTGAGGCGGAGCAGGCGCTGGCCGGGGCGGAGCCCGAGGAGCTGGAGGGCCTGCTCGGCGCCTACGGCGACCTGCTGGAGGCGTTCGAGGCCCGCGACGGCTACGCGGCGGACGCCCGTGTCGACGCGGCGATGCACGGCCTCGGTCTGGCGGGCATCACGGGCGACCGGCGGCTCGGCAGCCTCTCCGGAGGTGAGCAGGCGCGTCTCAACCTGGCCTGCCTGCTGGCCGCGTCCCCGCAGCTGATGCTGCTCGACGAACCCACCAACCACCTCGACGTCGGGGCGCTGGAGTGGCTGGAGGAGCGCCTGCGGGCCCACCGCGGCAGCGTGCTGGTCGTCTCGCACGACCGGGTCTTCCTGGAGCGCGTGGCCACCGCCCTGTGGGAGGTGGACGGCGAGCGGCGCACCGTCAACCGGCACGGCGGCGGTTACGCGGGATACCTGCAAGCCAAGGCGGCCGCGCGGCGCCGCTGGGAGCAGGCTTACCAGGACTGGCTGGAGGACCTGGCACGCCAGCGGGAACTGGCCCGCAGCGCCGCCGACCACCTGGCCACCGGCCCGCGGCGCAACACCGAGCGGTCGAACCAGCGCCACCAGCGCAACGTGGAGAAGCAGATCTCCGCGCGGGTCCGCAACGCCAAGGAGCGGGTCCGCCGGCTGGAGGAGAACCCGGTGCCGCGGCCCCCTCAACCCATGCGTTTCCGGGCCCGGGTGGAGGGTGGCGGCACGGTCGGGCGCGGCGGGGCACTCGCCGAGCTGTACAAGGTCACCGTCGGCACGCGGCTCGACGTCCCGTCCTTCACCGTCGACCCCGGTGAGCGCATCCTGATCACGGGGCACAACGGCGCGGGCAAGAGCACCCTGCTGCGCGTGCTGGCCGGTGACCTGGCGCCCGATCAGGGCGAGTGCGAGCGCCCGGAGCGCATCGGCTGGCTGCCGCAGGAGACGGAGATCACCGACCGGCAGCAGAGCCTGCTGGCGGCCTTCGCGGCGGGGCTGCCCGGCATCGCGGAGGAACACCGGGGCGCGCTCCTGGGATTCGGGCTCTTCCGGCCCTCGGCGCTGGGCACCGCGGTGGGAGACCTGTCCACCGGGCAGTTGAGGCGGCTGGCCCTGGCCCGTCTGCTGCGCGACCCGGCGGACCTGCTGCTGCTCGACGAGCCGACGAACCACCTGTCGCCCGCGCTCGTGGAGGACCTGGAGGAGGCGCTGGCGCACTACCGGGGCGCACTGGTCGTGGTCTCCCACGACCGCATGTTCGCGCAGCGGTTCACCGGTCGCCGCATGCACATGGAGGGTGGCCGCTTCGTGGAGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36823","NCBI_taxonomy_name":"Streptomyces antibioticus","NCBI_taxonomy_id":"1890"}}}},"ARO_accession":"3003036","ARO_id":"39470","ARO_name":"oleB","CARD_short_name":"oleB","ARO_description":"oleB is an ABC-F subfamily protein in Streptomyces antibioticus and is involved in oleandomycin secretion.","ARO_category":{"45630":{"category_aro_accession":"3007068","category_aro_cvterm_id":"45630","category_aro_name":"Miscellaneous ABC-F subfamily ATP-binding cassette ribosomal protection proteins","category_aro_description":"ABC-F subfamily ATP-binding cassette ribosomal protection proteins of unknown, unclear or miscellaneous classification which nevertheless confer resistance to antibiotics through ribosomal protection and not through antibiotic efflux. These proteins should be further reviewed to elucidate associated genes, their function, origin and classification.","category_aro_class_name":"AMR Gene Family"},"37247":{"category_aro_accession":"3000867","category_aro_cvterm_id":"37247","category_aro_name":"oleandomycin","category_aro_description":"Oleandomycin is a 14-membered macrolide produced by Streptomyces antibioticus. It is ssimilar to erythromycin, and contains a desosamine amino sugar and an oleandrose sugar. It targets the 50S ribosomal subunit to prevent protein synthesis.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1389":{"model_id":"1389","model_name":"KPC-22","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1112":{"protein_sequence":{"accession":"AIX87991.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPGSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQLVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"KM379100.1","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGGGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGCTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3003180","ARO_id":"39757","ARO_name":"KPC-22","CARD_short_name":"KPC-22","ARO_description":"KPC-22 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1390":{"model_id":"1390","model_name":"arlR","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"410"}},"model_sequences":{"sequence":{"5453":{"protein_sequence":{"accession":"ATC67679.1","sequence":"MTQILIVEDEQNLARFLELELTHENYNVDTEYDGQDGLDKALSHYYDLIILDLMLPSINGLEICRKIRQQQSTPIIIITAKSDTYDKVAGLDYGADDYIVKPFDIEELLARIRAILRRQPQKDIIDVNGITIDKNAFKVTVNGAEIELTKTEYDLLYLLAENKNHVMQREQILNHVWGYNSEVETNVVDVYIRYLRNKLKPYDRDKMIETVRGVGYVIR"},"dna_sequence":{"accession":"CP023390.1","fmin":"1461588","fmax":"1462248","strand":"-","sequence":"ATGACGCAAATTTTAATAGTAGAAGATGAACAAAACTTAGCAAGATTTCTTGAATTGGAACTCACACATGAAAATTACAATGTGGACACAGAGTATGATGGACAAGACGGTTTAGATAAAGCGCTTAGCCATTACTATGATTTAATCATATTAGATTTAATGTTGCCGTCAATTAATGGCTTAGAAATTTGTCGCAAAATTAGACAACAACAATCTACACCTATCATTATAATTACAGCGAAAAGTGATACGTATGACAAAGTTGCTGGGCTTGATTACGGTGCAGACGATTATATAGTTAAGCCGTTTGATATTGAAGAACTTTTAGCAAGAATTCGTGCAATTTTACGTCGTCAGCCACAAAAGGATATTATCGATGTCAACGGTATTACAATTGATAAGAACGCTTTTAAAGTGACGGTAAATGGCGCAGAAATTGAATTAACAAAAACAGAGTATGATTTACTATATCTTCTAGCTGAAAATAAAAACCATGTTATGCAACGGGAACAAATTTTAAATCATGTATGGGGTTATAATAGTGAAGTAGAAACAAATGTCGTAGATGTTTATATAAGATATTTACGAAACAAGTTAAAACCATACGATCGTGACAAAATGATTGAAACAGTTCGTGGCGTTGGGTATGTGATACGATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35525","NCBI_taxonomy_name":"Staphylococcus aureus subsp. aureus str. Newman","NCBI_taxonomy_id":"426430"}}}},"ARO_accession":"3000838","ARO_id":"37218","ARO_name":"arlR","CARD_short_name":"arlR","ARO_description":"ArlR is a response regulator that binds to the norA promoter to activate expression. ArlR must first be phosphorylated by ArlS.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35963":{"category_aro_accession":"0000045","category_aro_cvterm_id":"35963","category_aro_name":"acriflavine","category_aro_description":"Acriflavine is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"43746":{"category_aro_accession":"3005386","category_aro_cvterm_id":"43746","category_aro_name":"disinfecting agents and antiseptics","category_aro_description":"Disinfectants that can also interact with antimicrobial resistance mechanisms, e.g. molecule efflux, and thus are the targets of disinfectant resistance.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1391":{"model_id":"1391","model_name":"CTX-M-92","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1967":{"protein_sequence":{"accession":"ACY74743.1","sequence":"MMTQSIRRSMLTVMATLPLLFSSATLHAQANSVQQQLEALEKSSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKQSESDKHLLNQRVEIKKSDLVNYNPIAEKHVNGTMTLAELGAAALQYSDNTAMNKLIAHLGGPDKVTAFARSLGDETFRLDRTEPTLNTAIPGDPRDTTTPLAMAQTLKNLTLGKALAETQRTQLVTWLKGNTTGSASIRAGLPKSWVVGDKTGSGDYGTTNDIAVIWPENHAPLVLVTYFTQPEQKAESRRDILAAAAKIVTHGF"},"dna_sequence":{"accession":"GU127598.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGATGACTCAGAGCATTCGCCGCTCAATGTTAACGGTGATGGCGACGCTACCCCTGCTATTTAGCAGCGCAACGCTGCATGCGCAGGCGAACAGCGTGCAACAGCAGCTGGAAGCCCTGGAGAAAAGTTCGGGAGGTCGGCTTGGCGTTGCGCTGATTAACACCGCCGATAATTCGCAGATTCTCTACCGTGCCGATGAACGTTTTGCGATGTGCAGTACCAGTAAGGTGATGGCGGCCGCGGCGGTGCTTAAACAGAGCGAGAGCGATAAGCACCTGCTAAATCAGCGCGTTGAAATCAAGAAGAGCGACCTGGTTAACTACAATCCCATTGCGGAGAAACACGTTAACGGCACGATGACGCTGGCTGAGCTTGGCGCAGCGGCGCTGCAGTATAGCGACAATACTGCCATGAATAAGCTGATTGCCCATCTGGGTGGTCCCGATAAAGTGACGGCGTTTGCTCGCTCGTTGGGTGATGAGACCTTCCGTCTGGACAGAACCGAGCCCACGCTCAATACCGCCATTCCAGGCGACCCGCGTGATACCACCACGCCGCTCGCGATGGCGCAGACCCTGAAAAATCTGACGCTGGGTAAAGCGCTGGCGGAAACTCAGCGGACACAGTTGGTGACGTGGCTTAAGGGCAATACTACCGGTAGCGCGAGCATTCGGGCGGGTCTGCCGAAATCATGGGTAGTGGGCGATAAAACCGGCAGCGGAGATTATGGCACCACCAACGATATCGCGGTTATCTGGCCGGAAAACCACGCACCGCTGGTTCTGGTGACCTACTTTACCCAACCGGAGCAGAAGGCGGAAAGCCGTCGGGATATTCTGGCTGCGGCGGCGAAAATCGTAACCCACGGTTTCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001952","ARO_id":"38352","ARO_name":"CTX-M-92","CARD_short_name":"CTX-M-92","ARO_description":"CTX-M-92 is a beta-lactamase found in Escherichia coli.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1392":{"model_id":"1392","model_name":"aadA22","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"238":{"protein_sequence":{"accession":"CAK12750.1","sequence":"MRVAVTIEISNQLSEVLSVIERHLESTLLAVHLYGSAVDGGLKPYSDIDLLVTVTVRLDETTRRALINDLLETSASPGESEILRAVEVTIVVHDDIIPWRYPAKRELQFGEWQRNDILAGIFEPATIDIDLAILLTKAREHSVALVGPAAEELFDPVPEQDLFEALNETLTLWNSPPDWAGDERNVVLTLSRIWYSAVTGKIAPKDVAADWAMERLPAQYQPVILEARQAYLGQEEDRLASRADQLEEFVHYVKGEITKVIGK"},"dna_sequence":{"accession":"AM261837.1","fmin":"73","fmax":"865","strand":"+","sequence":"ATGAGGGTAGCGGTGACCATCGAAATTTCGAACCAACTATCAGAGGTGCTAAGCGTCATTGAGCGCCATCTGGAATCAACGTTGCTGGCCGTGCATTTGTACGGCTCCGCAGTGGATGGCGGCCTGAAGCCATACAGCGATATTGATTTGCTGGTTACGGTGACCGTAAGGCTTGATGAAACAACGCGGCGAGCTTTGATCAACGACCTTTTGGAAACTTCGGCTTCCCCTGGAGAGAGCGAGATTCTCCGCGCTGTAGAAGTCACCATTGTTGTGCACGACGACATCATTCCGTGGCGTTATCCAGCTAAGCGCGAACTGCAATTTGGAGAATGGCAGCGCAATGACATTCTTGCAGGTATCTTCGAGCCAGCCACGATCGACATTGATCTGGCTATCTTGCTGACAAAAGCAAGAGAACATAGCGTTGCCTTGGTAGGTCCAGCGGCGGAGGAACTCTTTGATCCGGTTCCTGAACAGGATCTATTTGAGGCGCTAAATGAAACCTTAACGCTATGGAACTCGCCGCCCGACTGGGCTGGCGATGAGCGAAATGTAGTGCTTACGTTGTCCCGCATTTGGTACAGCGCAGTAACCGGCAAAATCGCGCCGAAGGATGTCGCTGCCGACTGGGCAATGGAGCGCCTGCCGGCCCAGTATCAGCCCGTCATACTTGAAGCTAGACAGGCTTATCTTGGACAAGAAGAAGATCGCTTGGCCTCGCGCGCAGATCAGTTGGAAGAATTTGTCCACTACGTGAAAGGCGAGATCACCAAGGTAATCGGCAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35732","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Typhimurium","NCBI_taxonomy_id":"90371"}}}},"ARO_accession":"3002619","ARO_id":"39019","ARO_name":"aadA22","CARD_short_name":"aadA22","ARO_description":"aadA22 is an aminoglycoside nucleotidyltransferase gene encoded by plasmids and integrons in S. enterica and E. coli.","ARO_category":{"41439":{"category_aro_accession":"3004275","category_aro_cvterm_id":"41439","category_aro_name":"ANT(3'')","category_aro_description":"A category of aminoglycoside O-nucleotidyltransferase enzymes with modification regiospecificity based at the 3''-hydroxyl group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics by transfer of an AMP group from an ATP substrate to the 3''-hydroxyl group of the compound.","category_aro_class_name":"AMR Gene Family"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1394":{"model_id":"1394","model_name":"OXA-257","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1760":{"protein_sequence":{"accession":"AGK07370.1","sequence":"MKFKMKGLFYVILSSLAFSGCVYDSKLQRPVISERETEIPLLFNQAQTQAVFVTYDGIHLKSYGNDLSRAKTEYIPASTFKMLNALIGLQNAKATNTEVFHWNGEKRAFSAWEKDMTLAEAMQASAVPVYQELARRIGLELMREEVKRVGFGNAEIGQQVDNFWLVGPLKISPEQEVQFAYQLAMKQLPFDRNVQQQVKDMLYIERRGDSKLYAKSGWGMDVEPQVGWYTGWVEQPNGKVTAFALNMKMQAGDDLAERKQLTLSILDKLGLFFYLR"},"dna_sequence":{"accession":"KC567681.1","fmin":"1210","fmax":"2041","strand":"+","sequence":"ATGAAGTTTAAAATGAAAGGTTTATTTTATGTCATCCTCAGTAGTTTGGCATTTTCAGGTTGTGTTTATGATTCAAAACTACAACGCCCAGTCATATCAGAGCGAGAAACTGAGATTCCTTTATTATTTAATCAAGCACAGACTCAAGCTGTGTTTGTTACTTATGATGGGATTCATCTAAAAAGTTATGGTAATGATCTAAGCCGAGCAAAGACTGAATATATTCCTGCATCTACATTTAAGATGTTGAATGCTTTAATTGGCTTGCAAAATGCAAAAGCAACCAATACTGAAGTATTTCATTGGAATGGTGAAAAGCGCGCTTTTTCAGCATGGGAAAAAGATATGACTTTGGCAGAAGCGATGCAGGCTTCAGCTGTTCCCGTATATCAGGAGCTTGCTCGACGTATTGGCTTGGAATTGATGCGTGAAGAAGTGAAGCGTGTAGGTTTTGGCAATGCGGAGATTGGTCAGCAAGTCGATAATTTTTGGTTGGTGGGTCCTTTAAAAATCTCCCCTGAACAAGAAGTTCAATTTGCCTATCAACTGGCGATGAAGCAATTACCTTTTGATCGAAATGTACAGCAACAAGTCAAAGATATGCTTTATATCGAGAGACGTGGTGACAGTAAACTGTATGCTAAAAGTGGTTGGGGAATGGATGTTGAACCTCAAGTGGGTTGGTATACGGGATGGGTTGAACAACCCAATGGCAAGGTGACTGCATTTGCGTTAAATATGAAAATGCAAGCAGGTGATGATCTAGCTGAACGTAAACAATTAACCTTAAGTATTTTGGACAAATTGGGTCTATTTTTTTATTTAAGATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39090","NCBI_taxonomy_name":"Acinetobacter bereziniae","NCBI_taxonomy_id":"106648"}}}},"ARO_accession":"3001694","ARO_id":"38094","ARO_name":"OXA-257","CARD_short_name":"OXA-257","ARO_description":"OXA-257 is a beta-lactamase found in A. bereziniae.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46498":{"category_aro_accession":"3007709","category_aro_cvterm_id":"46498","category_aro_name":"OXA-229-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-229.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1396":{"model_id":"1396","model_name":"OXA-11","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1522":{"protein_sequence":{"accession":"CAA80304.1","sequence":"MKTFAAYVIIACLSSTALAGSITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGSQNISGGIDKFWLEDQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGIIGG"},"dna_sequence":{"accession":"Z22590.1","fmin":"154","fmax":"955","strand":"+","sequence":"ATGAAAACATTTGCCGCATATGTAATTATCGCGTGTCTTTCGAGTACGGCATTAGCTGGTTCAATTACAGAAAATACGTCTTGGAACAAAGAGTTCTCTGCCGAAGCCGTCAATGGTGTCTTCGTGCTTTGTAAAAGTAGCAGTAAATCCTGCGCTACCAATGACTTAGCTCGTGCATCAAAGGAATATCTTCCAGCATCAACATTTAAGATCCCCAACGCAATTATCGGCCTAGAAACTGGTGTCATAAAGAATGAGCATCAGGTTTTCAAATGGGACGGAAAGCCAAGAGCCATGAAGCAATGGGAAAGAGACTTGACCTTAAGAGGGGCAATACAAGTTTCAGCTGTTCCCGTATTTCAACAAATCGCCAGAGAAGTTGGCGAAGTAAGAATGCAGAAATACCTTAAAAAATTTTCCTATGGCAGCCAGAATATCAGTGGTGGCATTGACAAATTCTGGTTGGAAGACCAGCTTAGAATTTCCGCAGTTAATCAAGTGGAGTTTCTAGAGTCTCTATATTTAAATAAATTGTCAGCATCTAAAGAAAACCAGCTAATAGTAAAAGAGGCTTTGGTAACGGAGGCGGCACCTGAATATCTAGTGCATTCAAAAACTGGTTTTTCTGGTGTGGGAACTGAGTCAAATCCTGGTGTCGCATGGTGGGTTGGGTGGGTTGAGAAGGAGACAGAGGTTTACTTTTTCGCCTTTAACATGGATATAGACAACGAAAGTAAGTTGCCGCTAAGAAAATCCATTCCCACCAAAATCATGGAAAGTGAGGGCATCATTGGTGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3001406","ARO_id":"37806","ARO_name":"OXA-11","CARD_short_name":"OXA-11","ARO_description":"OXA-11 is a beta-lactamase found in P. aeruginosa.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46486":{"category_aro_accession":"3007697","category_aro_cvterm_id":"46486","category_aro_name":"OXA-10-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-10.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1397":{"model_id":"1397","model_name":"dfrC","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"4707":{"protein_sequence":{"accession":"AAO04716.1","sequence":"MTLSIIVAHDKQRVIGYQNQLPWHLPNDLKHVKQLTTGNTLVMGRKTFNSIGKPLPNRRNVVLTNQASFHHEGVDVINSLDEIKELSGHVFIFGGQTLFEAMIDQVDDMYITVIDGKFQGDTFFPPYTFENWEVESSVEGQLDEKNTIPHTFLHLVRRKGK"},"dna_sequence":{"accession":"AE015929.1","fmin":"1128933","fmax":"1129419","strand":"-","sequence":"ATGACATTATCAATAATTGTCGCTCACGATAAACAAAGAGTCATTGGGTACCAAAATCAATTACCTTGGCACTTACCAAATGATTTAAAGCATGTTAAACAACTGACCACTGGGAATACACTTGTAATGGGACGGAAAACTTTTAATTCTATAGGGAAACCATTGCCAAATAGACGTAACGTCGTACTCACTAACCAAGCTTCATTTCACCATGAAGGGGTAGATGTTATAAACTCTCTTGATGAAATTAAAGAGTTATCTGGTCATGTTTTTATATTTGGAGGACAAACGTTATTCGAGGCAATGATTGACCAGGTAGATGATATGTATATCACAGTAATAGATGGAAAGTTTCAAGGAGACACATTCTTTCCACCATACACATTCGAAAACTGGGAAGTCGAATCTTCAGTAGAAGGTCAACTAGATGAAAAAAATACTATACCGCATACATTCTTACATTTAGTGCGTAGAAAAGGGAAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37591","NCBI_taxonomy_name":"Staphylococcus epidermidis ATCC 12228","NCBI_taxonomy_id":"176280"}}}},"ARO_accession":"3002865","ARO_id":"39299","ARO_name":"dfrC","CARD_short_name":"dfrC","ARO_description":"dfrC is a chromosome-encoded dihydrofolate reductase found in Staphylococcus aureus.","ARO_category":{"37617":{"category_aro_accession":"3001218","category_aro_cvterm_id":"37617","category_aro_name":"trimethoprim resistant dihydrofolate reductase dfr","category_aro_description":"Alternative dihydropteroate synthase dfr present on plasmids produces alternate proteins that are less sensitive to trimethoprim from inhibiting its role in folate synthesis, thus conferring trimethoprim resistance.","category_aro_class_name":"AMR Gene Family"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1398":{"model_id":"1398","model_name":"OXA-108","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1367":{"protein_sequence":{"accession":"ABV31688.1","sequence":"MNIKALLLITSAIFISACSPYIVTTNPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNTDIGTQVDNFWVVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"EF650034.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTACTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATACAGATATCGGTACCCAAGTCGATAATTTTTGGGTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001639","ARO_id":"38039","ARO_name":"OXA-108","CARD_short_name":"OXA-108","ARO_description":"OXA-108 is a beta-lactamase found in A. baumannii.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1399":{"model_id":"1399","model_name":"OXA-315","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1531":{"protein_sequence":{"accession":"AGU69253.1","sequence":"MNIQALLLITSAIFISACSPYIVSANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIPIYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPHGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"KF057032.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTCAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGTCTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCCGATTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCATGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001686","ARO_id":"38086","ARO_name":"OXA-315","CARD_short_name":"OXA-315","ARO_description":"OXA-315 is a beta-lactamase found in A. baumannii.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1400":{"model_id":"1400","model_name":"CTX-M-74","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1668":{"protein_sequence":{"accession":"ACS32293.1","sequence":"MMTQSIRRSMLTVMATLPLLFSSATLHAQANSVQQQLEALEKSSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKQSESDKHLLNQRVEIKKSDLVNYNPIAEKHVNGTMTLAELGAAALQYSDNTAMNKLIAHLGGPDKVTAFARSLGDETFRLDRTETTLNTAIPGDPRDTTTPLAMAQTLKNLTLGKALAETQRAQLVTWLKGNTTGSASIRAGLPKSWVVGDKTGSGDYGTTNDIAVIWPENHAPLVLVTYFTQPEQKAESRRDILAAAAKIVTHGF"},"dna_sequence":{"accession":"GQ149243.1","fmin":"0","fmax":"873","strand":"+","sequence":"ATGATGACCCAGAGCATTCGCCGCAGCATGCTGACCGTGATGGCGACCCTGCCGCTGCTGTTTAGCAGCGCGACCCTGCATGCGCAGGCGAACAGCGTGCAGCAGCAGCTGGAAGCGCTGGAAAAAAGCAGCGGCGGCCGCCTGGGCGTGGCGCTGATTAACACCGCGGATAACAGCCAGATTCTGTATCGCGCGGATGAACGCTTTGCGATGTGCAGCACCAGCAAAGTGATGGCGGCGGCGGCGGTGCTGAAACAGAGCGAAAGCGATAAACATCTGCTGAACCAGCGCGTGGAAATTAAAAAAAGCGATCTGGTGAACTATAACCCGATTGCGGAAAAACATGTGAACGGCACCATGACCCTGGCGGAACTGGGCGCGGCGGCGCTGCAGTATAGCGATAACACCGCGATGAACAAACTGATTGCGCATCTGGGCGGCCCGGATAAAGTGACCGCGTTTGCGCGCAGCCTGGGCGATGAAACCTTTCGCCTGGATCGCACCGAAACCACCCTGAACACCGCGATTCCGGGCGATCCGCGCGATACCACCACCCCGCTGGCGATGGCGCAGACCCTGAAAAACCTGACCCTGGGCAAAGCGCTGGCGGAAACCCAGCGCGCGCAGCTGGTGACCTGGCTGAAAGGCAACACCACCGGCAGCGCGAGCATTCGCGCGGGCCTGCCGAAAAGCTGGGTGGTGGGCGATAAAACCGGCAGCGGCGATTATGGCACCACCAACGATATTGCGGTGATTTGGCCGGAAAACCATGCGCCGCTGGTGCTGGTGACCTATTTTACCCAGCCGGAACAGAAAGCGGAAAGCCGCCGCGATATTCTGGCGGCGGCGGCGAAAATTGTGACCCATGGCTTT","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3001935","ARO_id":"38335","ARO_name":"CTX-M-74","CARD_short_name":"CTX-M-74","ARO_description":"CTX-M-74 is a beta-lactamase found in the Enterobacteriaceae family.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1402":{"model_id":"1402","model_name":"OXA-390","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4706":{"protein_sequence":{"accession":"AHL30283.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDDKAEKIKNLFTEAHTTGVLVIHQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWNGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"KJ135342.1","fmin":"48","fmax":"873","strand":"-","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGACAAAGCAGAGAAAATTAAAAATTTATTTACCGAAGCACACACTACGGGTGTTTTAGTTATCCATCAAGGTCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGAACGGGCAAAAAAGGCTGTTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001576","ARO_id":"37976","ARO_name":"OXA-390","CARD_short_name":"OXA-390","ARO_description":"OXA-390 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1403":{"model_id":"1403","model_name":"OXA-388","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1215":{"protein_sequence":{"accession":"AHL30284.1","sequence":"MNIQALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKYLFNEAHTTGVLVIQQGQIQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRIGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"KJ135343.1","fmin":"14","fmax":"839","strand":"+","sequence":"ATGAACATTCAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAATATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATTCAACAAGGCCAAATTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACTACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTATTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001574","ARO_id":"37974","ARO_name":"OXA-388","CARD_short_name":"OXA-388","ARO_description":"OXA-388 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1404":{"model_id":"1404","model_name":"IMP-3","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1092":{"protein_sequence":{"accession":"BAA77393.1","sequence":"MSKLSVFFIFLFCSIATAAESLPDLKIEKLDEGVYVHTSFEEVNGWGVVPKHGLVVLVNAEAYLIDTPFTAKDTEKLVTWFVERGYKIKGSISSHFHSDSTGGIGWLNSRSIPTYASELTNELLKKDGKVQATNSFSGVNYWLVKNKIEVFYPGPGHTPDNVVVWLPERKILFGGCFIKPYGLGNLGDANIEAWPKSAKLLKSKYGKAKLVVPGHSEVGDASLLKLTLEQAVKGLNESKKPSKPSN"},"dna_sequence":{"accession":"AB010417.1","fmin":"0","fmax":"741","strand":"+","sequence":"ATGAGCAAGTTATCTGTATTCTTTATATTTTTGTTTTGCAGCATTGCTACCGCAGCAGAGTCTTTGCCAGATTTAAAAATTGAAAAGCTTGATGAAGGCGTTTATGTTCATACTTCGTTTGAAGAAGTTAACGGGTGGGGCGTTGTTCCTAAACATGGTTTGGTGGTTCTTGTAAATGCTGAGGCTTATTTAATTGACACTCCATTTACGGCTAAAGATACTGAAAAGTTAGTCACTTGGTTTGTGGAGCGTGGCTATAAAATAAAAGGCAGTATTTCCTCTCATTTTCATAGCGACAGCACGGGCGGAATAGGGTGGCTTAATTCTCGATCTATCCCCACGTATGCATCTGAATTAACAAATGAACTGCTTAAAAAAGACGGTAAGGTTCAAGCCACAAATTCATTTAGCGGAGTTAACTATTGGCTAGTTAAAAATAAAATTGAAGTTTTTTATCCAGGCCCGGGACACACTCCAGATAACGTAGTGGTTTGGCTGCCTGAAAGGAAAATATTATTCGGTGGTTGTTTTATTAAACCGTACGGTTTAGGCAATTTGGGTGACGCAAATATAGAAGCTTGGCCAAAGTCCGCCAAATTATTAAAGTCCAAATATGGTAAGGCAAAACTGGTTGTTCCAGGTCACAGTGAAGTTGGAGACGCATCACTCTTGAAACTTACATTAGAGCAGGCGGTTAAAGGATTAAACGAAAGTAAAAAACCATCAAAACCAAGCAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36870","NCBI_taxonomy_name":"Shigella flexneri","NCBI_taxonomy_id":"623"}}}},"ARO_accession":"3002194","ARO_id":"38594","ARO_name":"IMP-3","CARD_short_name":"IMP-3","ARO_description":"IMP-3 is a beta-lactamase found in Acinetobacter baumannii.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1405":{"model_id":"1405","model_name":"armA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"3397":{"protein_sequence":{"accession":"ADC55560.1","sequence":"MDKNDVVKKILESKKYENLDSDIVEKVVSISEKKYKLKEVENYSKKKLHQIWGSYYSAYPNWDKLLKKYNQGQLSIEDLLKIHSSTNERVATLNDFYTYVFGNIKHVSSILDFGCGFNPLALYQWNENEKIIYHAYDIDRAEIAFLSSIIGKLKTTIKYRFLNKESDVYKGTYDVVFLLKMLPVLKQQDVNILDFLQLFHTQNFVISFPIKSLSGKEKGMEENYQLWFESFTKGWIKILDSKVIGNELVYITSGFQK"},"dna_sequence":{"accession":"GU437214.1","fmin":"0","fmax":"774","strand":"+","sequence":"ATGGATAAGAATGATGTTGTTAAGAAGATACTTGAATCAAAAAAGTACGAAAACCTTGATTCAGATATTGTTGAAAAGGTTGTTTCCATTTCTGAGAAGAAATATAAATTAAAGGAAGTTGAGAATTATTCTAAAAAGAAATTGCATCAAATATGGGGGTCTTACTATTCTGCCTATCCTAATTGGGATAAATTATTAAAAAAGTACAATCAGGGGCAGTTATCAATAGAAGATTTACTAAAGATTCATTCTTCGACGAATGAAAGAGTCGCAACATTAAATGACTTTTACACTTATGTATTTGGAAATATCAAACATGTCTCATCTATTTTAGATTTTGGTTGTGGCTTCAATCCATTAGCTTTATACCAATGGAATGAAAATGAAAAAATAATATATCATGCATACGATATTGATAGAGCTGAGATAGCTTTTTTGAGTAGCATTATTGGGAAGTTAAAGACGACGATAAAGTATAGGTTTTTGAATAAAGAGAGTGATGTCTACAAAGGTACTTATGATGTAGTATTCCTTTTAAAGATGCTTCCTGTGCTAAAACAGCAAGATGTAAATATCTTGGATTTCCTACAGCTTTTTCATACTCAAAACTTTGTAATATCTTTTCCAATAAAGTCTTTATCTGGAAAGGAGAAGGGAATGGAAGAGAATTACCAGCTATGGTTTGAATCTTTTACAAAAGGTTGGATAAAAATCCTTGATTCGAAGGTTATAGGGAATGAGTTAGTATATATTACTAGTGGATTTCAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3000858","ARO_id":"37238","ARO_name":"armA","CARD_short_name":"armA","ARO_description":"ArmA is a 16S rRNA methyltransferase that targets mature or nearly mature 30S subunits. It transfers a methyl group from S-adenosyl-L-methionine to N7-G1405 of the 16S rRNA, an aminoglycoside binding site.","ARO_category":{"41435":{"category_aro_accession":"3004271","category_aro_cvterm_id":"41435","category_aro_name":"16S rRNA methyltransferase (G1405)","category_aro_description":"Methyltransferases that methylate the G1405 position of 16S rRNA, which is part of an aminoglycoside binding site.","category_aro_class_name":"AMR Gene Family"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36997":{"category_aro_accession":"3000653","category_aro_cvterm_id":"36997","category_aro_name":"G418","category_aro_description":"A gentamicin class aminoglycoside antibiotic often used in mammalian cell culture work as a selectable marker for the neo cassette (APH3').","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"46133":{"category_aro_accession":"3007382","category_aro_cvterm_id":"46133","category_aro_name":"gentamicin","category_aro_description":"Gentamicin is a commonly used aminoglycoside antibiotic derived from members of the Micromonospora genus of bacteria. It acts by binding the 30S ribosomal subunit, thus inhibiting protein synthesis. Gentamicin is typically used to treat Gram-negative infections of the repiratory and urinary tract, as well as infections of the bone and soft tissue. It also exhibits considerable nephrotoxicity and ototoxicity. Gentamicin is administered as a mixture of gentamicin type C (which makes about around 80% of the complex) and types A, B, and X (distributed in the remaining 20% of the complex).","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1406":{"model_id":"1406","model_name":"OXA-121","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1290":{"protein_sequence":{"accession":"AGU69248.1","sequence":"MNIKALLLITNAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKTTTTEVFKWDGQKRLCPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"KF057027.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCCCTCTTACTTATAACAAACGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTCTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGACAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATGCCCAGAATGGGAAAAGGACATGACCCTAGGCGACGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCATTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001443","ARO_id":"37843","ARO_name":"OXA-121","CARD_short_name":"OXA-121","ARO_description":"OXA-121 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1407":{"model_id":"1407","model_name":"CMY-62","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1777":{"protein_sequence":{"accession":"AEM97674.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFSALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"JF460796.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTAGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002075","ARO_id":"38475","ARO_name":"CMY-62","CARD_short_name":"CMY-62","ARO_description":"CMY-62 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1408":{"model_id":"1408","model_name":"TEM-124","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1398":{"protein_sequence":{"accession":"AAQ93491.1","sequence":"MSIKHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVKYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTTPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIALGPDGKPSRIVVIYTTGSQATMDEANRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AY327540.1","fmin":"0","fmax":"858","strand":"+","sequence":"ATGAGTATTAAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTAAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGACGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAAGCAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36917","NCBI_taxonomy_name":"Morganella morganii","NCBI_taxonomy_id":"582"}}}},"ARO_accession":"3000986","ARO_id":"37366","ARO_name":"TEM-124","CARD_short_name":"TEM-124","ARO_description":"TEM-124 is an extended-spectrum beta-lactamase found in Morganella morganii.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1409":{"model_id":"1409","model_name":"CMY-6","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1548":{"protein_sequence":{"accession":"CAB36902.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYALGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"AJ011293.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTTGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002017","ARO_id":"38417","ARO_name":"CMY-6","CARD_short_name":"CMY-6","ARO_description":"CMY-6 is a beta-lactamase found in Escherichia coli.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1410":{"model_id":"1410","model_name":"OXA-19","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1681":{"protein_sequence":{"accession":"AAD02245.1","sequence":"MKTFAAYVITACLSSTALASSITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNNLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLSLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEDQLRISAVNQVEFLESLFLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKGTEVYFFAFNMDIDNENKLPLRKSIPTKIMASEGIIGG"},"dna_sequence":{"accession":"AF043381.1","fmin":"943","fmax":"1744","strand":"+","sequence":"ATGAAAACATTTGCCGCATATGTAATTACTGCGTGTCTTTCAAGTACGGCATTAGCTAGTTCAATTACAGAAAATACGTCTTGGAACAAAGAGTTCTCTGCCGAAGCCGTCAATGGTGTTTTCGTGCTTTGTAAAAGTAGCAGTAAATCCTGCGCTACCAATAACTTAGCTCGTGCATCAAAGGAATATCTTCCAGCATCAACATTTAAGATCCCCAACGCAATTATCGGCCTAGAAACTGGTGTCATAAAGAATGAGCATCAGGTTTTCAAATGGGACGGAAAGCCAAGAGCCATGAAACAATGGGAAAGAGACTTGAGCTTAAGAGGGGCAATACAAGTTTCAGCGGTTCCCGTATTTCAACAAATCGCCAGAGAAGTTGGCGAAGTAAGAATGCAGAAATACCTTAAAAAATTTTCATATGGCAACCAGAATATCAGTGGTGGCATTGACAAATTCTGGTTGGAGGATCAGCTAAGAATTTCCGCAGTTAATCAAGTGGAGTTTCTAGAGTCTCTATTTTTAAATAAATTGTCAGCATCAAAAGAAAATCAGCTAATAGTAAAAGAGGCTTTGGTAACGGAGGCTGCGCCTGAATATCTTGTGCATTCAAAAACTGGTTTTTCTGGTGTGGGAACTGAGTCAAATCCTGGTGTCGCATGGTGGGTTGGTTGGGTTGAGAAGGGAACAGAGGTTTACTTTTTCGCCTTTAACATGGATATAGACAACGAAAATAAGTTGCCGCTAAGAAAATCCATTCCCACCAAAATCATGGCAAGTGAGGGCATCATTGGTGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3001414","ARO_id":"37814","ARO_name":"OXA-19","CARD_short_name":"OXA-19","ARO_description":"OXA-19 is a beta-lactamase found in P. aeruginosa.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46486":{"category_aro_accession":"3007697","category_aro_cvterm_id":"46486","category_aro_name":"OXA-10-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-10.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1411":{"model_id":"1411","model_name":"OXA-62","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1537":{"protein_sequence":{"accession":"AAR32134.1","sequence":"MNTIISRRWRAGLWRRLVGAVVLPATLAATPAAYAADVPKAALGRITERADWGKLFAAEGVKGTIVVLDARTQTYQAYDAARAEKRMSPASTYKIFNSLLALDSGALDNERAIIPWDGKPRRIKNWNAAMDLRTAFRVSCLPCYQVVSHKIGRRYAQAKLNEVGYGNRTIGGAPDAYWVDDSLQISAREQVDFVQRLARGTLPFSARSQDIVRQMSIVEATPDYVLHGKTGWFVDKKPDIGWWVGWIERDGNITSVAINIDMLSEADAPKRARIVKAVLKDLKLI"},"dna_sequence":{"accession":"AY423074.1","fmin":"0","fmax":"858","strand":"+","sequence":"ATGAATACGATAATCTCTCGCCGGTGGCGTGCCGGCCTGTGGCGGCGGCTGGTCGGCGCGGTCGTCTTGCCCGCAACGCTCGCCGCCACCCCTGCGGCCTATGCGGCCGACGTGCCGAAAGCCGCGTTGGGGCGCATCACCGAGCGCGCCGACTGGGGCAAGCTGTTCGCCGCGGAGGGCGTGAAGGGCACGATCGTGGTGCTCGACGCACGCACGCAAACCTATCAGGCCTACGACGCCGCACGTGCCGAGAAGCGCATGTCGCCGGCGTCGACCTACAAGATATTCAACAGCCTGCTGGCGCTCGACTCCGGGGCGCTGGACAACGAACGCGCGATCATTCCCTGGGATGGCAAGCCGCGACGCATCAAGAACTGGAACGCGGCGATGGACCTGAGGACCGCGTTTCGCGTGTCATGCCTGCCCTGCTATCAGGTCGTCTCGCACAAGATCGGGCGCCGGTACGCGCAGGCGAAGCTGAACGAGGTCGGGTATGGCAACCGCACCATTGGCGGCGCGCCGGACGCCTATTGGGTCGACGACAGTCTGCAGATTTCGGCGCGTGAGCAGGTGGACTTCGTGCAGCGTCTCGCGCGTGGCACGTTGCCGTTCTCTGCGCGCTCGCAGGACATCGTGCGCCAGATGTCGATCGTCGAAGCCACGCCGGACTATGTGCTTCACGGCAAGACGGGTTGGTTCGTCGACAAGAAGCCCGATATCGGCTGGTGGGTAGGGTGGATCGAGCGCGACGGCAACATCACCAGCGTCGCGATCAACATCGACATGCTGTCGGAGGCGGACGCCCCGAAACGGGCACGCATCGTGAAGGCGGTGCTGAAGGACCTGAAGCTGATCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36932","NCBI_taxonomy_name":"Pandoraea pnomenusa","NCBI_taxonomy_id":"93220"}}}},"ARO_accession":"3001792","ARO_id":"38192","ARO_name":"OXA-62","CARD_short_name":"OXA-62","ARO_description":"OXA-62 is a beta-lactamase found in Pandoraea pnomenusa.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46520":{"category_aro_accession":"3007731","category_aro_cvterm_id":"46520","category_aro_name":"OXA-62-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-62.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1412":{"model_id":"1412","model_name":"SHV-167","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1146":{"protein_sequence":{"accession":"BAM28879.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDADDEQLERKIHYRQQDLVDYSPVSEKYLADGMTVGELCAAAITMSDNSAANLLLATVGGPVGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIE"},"dna_sequence":{"accession":"AB733453.1","fmin":"3","fmax":"849","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGATGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAATACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGTAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAG","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001204","ARO_id":"37584","ARO_name":"SHV-167","CARD_short_name":"SHV-167","ARO_description":"SHV-167 is a beta-lactamase.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1413":{"model_id":"1413","model_name":"OXA-172","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1835":{"protein_sequence":{"accession":"ADI58616.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDVKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAVPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGLDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"HM113558.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGTAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTGTTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAACAAAATATACGCAAAAAGTGGTTGGGGATTGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001656","ARO_id":"38056","ARO_name":"OXA-172","CARD_short_name":"OXA-172","ARO_description":"OXA-172 is a beta-lactamase found in A. baumannii.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1414":{"model_id":"1414","model_name":"QnrB15","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"297":{"protein_sequence":{"accession":"ABX72227.1","sequence":"MTPLLYKKTGTNMALALVGEKIDRNRFTGEKIESSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNANALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGAQVLGATFSGSDLSGGEFSTFDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDNYQASLLMERLGIAIIG"},"dna_sequence":{"accession":"EU302865.1","fmin":"0","fmax":"681","strand":"+","sequence":"ATGACGCCATTACTGTATAAAAAAACAGGTACAAATATGGCTCTGGCACTCGTTGGCGAAAAAATTGACAGAAACCGTTTCACCGGTGAGAAAATTGAAAGTAGTACATTTTTTAACTGTGATTTTTCAGGTGCCGACCTGAGCGGCACTGAATTTATCGGCTGTCAGTTCTATGATCGTGAAAGCCAGAAAGGGTGCAATTTTAGTCGTGCGATGCTGAAAGATGCCATTTTTAAAAGCTGTGATTTATCCATGGCGGATTTTCGCAATGCCAATGCGCTGGGCATTGAAATTCGCCACTGCCGCGCACAAGGCGCAGATTTCCGCGGCGCAAGTTTTATGAATATGATCACTACTCGCACCTGGTTTTGTAGTGCATATATCACTAACACAAATCTAAGCTACGCCAATTTTTCGAAAGTCGTGTTGGAAAAGTGTGAGCTGTGGGAAAACCGTTGGATGGGTGCCCAGGTACTGGGCGCGACGTTCAGTGGTTCAGATCTCTCCGGCGGCGAGTTTTCGACTTTCGACTGGCGAGCAGCAAACTTCACACATTGCGATCTGACCAATTCGGAGTTGGGTGACTTAGATATTCGGGGCGTTGATTTACAAGGCGTTAAGCTGGACAACTACCAGGCGTCGTTGCTCATGGAGCGGCTTGGCATCGCGATTATTGGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002730","ARO_id":"39164","ARO_name":"QnrB15","CARD_short_name":"QnrB15","ARO_description":"QnrB15 is a plasmid-mediated quinolone resistance protein found in Citrobacter freundii.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1415":{"model_id":"1415","model_name":"AAC(2')-Id","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"350"}},"model_sequences":{"sequence":{"228":{"protein_sequence":{"accession":"AAB41701.1","sequence":"MLTQHVSEARTRGAIHTARLIHTSDLDQETRDGARRMVIEAFRDPSGDSDFTDDFTDDDWDHALGGMHALISHHGALIAHGAVVQRRLMYRGPDGRGHALRCGYVEAVAVREDRRGDGLGTAVLDALEQVIRGAYQIGALSASDIARPMYIARGWLSWEGPTSVLTPTEGIVRTPEDDRSLFVLPVDLPDGLELDTAREITCDWRSGDPW"},"dna_sequence":{"accession":"U72743.1","fmin":"385","fmax":"1018","strand":"+","sequence":"GTGCTCACCCAGCATGTCAGTGAGGCTCGCACGCGCGGTGCGATCCACACCGCGCGTCTGATCCACACCTCCGATCTGGACCAGGAAACCCGCGACGGCGCGCGCCGCATGGTGATCGAGGCGTTCCGCGATCCGTCCGGAGACAGTGATTTCACCGACGATTTCACCGACGACGACTGGGACCACGCGCTCGGCGGCATGCACGCGCTGATCTCTCACCACGGTGCGCTCATCGCGCACGGCGCCGTCGTCCAACGTCGGTTGATGTACCGGGGACCCGACGGTAGAGGTCACGCGCTGCGCTGCGGTTACGTCGAGGCCGTCGCGGTGCGCGAGGACCGGCGGGGCGACGGTCTGGGCACCGCCGTGCTCGACGCGCTCGAGCAGGTGATCCGCGGCGCCTATCAGATCGGCGCGCTGAGCGCGTCGGACATCGCCCGGCCGATGTACATTGCCAGGGGCTGGCTGTCGTGGGAGGGTCCGACATCGGTGCTGACCCCCACCGAGGGCATCGTTCGCACCCCTGAGGACGACCGGTCGCTGTTCGTCCTGCCGGTCGATCTCCCGGACGGCCTCGAGTTGGACACCGCGCGCGAGATCACGTGCGACTGGCGCTCCGGCGACCCCTGGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36769","NCBI_taxonomy_name":"Mycolicibacterium smegmatis MC2 155","NCBI_taxonomy_id":"246196"}}}},"ARO_accession":"3002526","ARO_id":"38926","ARO_name":"AAC(2')-Id","CARD_short_name":"AAC(2')-Id","ARO_description":"AAC(2')-Id is a chromosomal-encoded aminoglycoside acetyltransferase in Mycolicibacterium smegmatis.","ARO_category":{"36480":{"category_aro_accession":"3000341","category_aro_cvterm_id":"36480","category_aro_name":"AAC(2')","category_aro_description":"A category of aminoglycoside N-acetyltransferase enzymes with modification regiospecificity based at the 2'-amino group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics through acetylation of the 2-amino group of the compound.","category_aro_class_name":"AMR Gene Family"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"46127":{"category_aro_accession":"3007377","category_aro_cvterm_id":"46127","category_aro_name":"6'-N-ethylnetilmicin","category_aro_description":"6'-N-ethylnetilmicin is an aminoglycoside antibiotic and a derivative of netilmicin.","category_aro_class_name":"Antibiotic"},"46133":{"category_aro_accession":"3007382","category_aro_cvterm_id":"46133","category_aro_name":"gentamicin","category_aro_description":"Gentamicin is a commonly used aminoglycoside antibiotic derived from members of the Micromonospora genus of bacteria. It acts by binding the 30S ribosomal subunit, thus inhibiting protein synthesis. Gentamicin is typically used to treat Gram-negative infections of the repiratory and urinary tract, as well as infections of the bone and soft tissue. It also exhibits considerable nephrotoxicity and ototoxicity. Gentamicin is administered as a mixture of gentamicin type C (which makes about around 80% of the complex) and types A, B, and X (distributed in the remaining 20% of the complex).","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1416":{"model_id":"1416","model_name":"OXA-89","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1139":{"protein_sequence":{"accession":"ABE03012.1","sequence":"MNIKTLLLITSAIFISACSHYIVSANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFTYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"DQ445683.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAACACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACATTATATAGTGTCTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCATCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACTACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTACTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001625","ARO_id":"38025","ARO_name":"OXA-89","CARD_short_name":"OXA-89","ARO_description":"OXA-89 is a beta-lactamase found in A. baumannii.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1417":{"model_id":"1417","model_name":"OXA-131","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1678":{"protein_sequence":{"accession":"ACD84989.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDVKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAVPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNQQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"EU547446.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGTAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTGTTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAACAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCAACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001652","ARO_id":"38052","ARO_name":"OXA-131","CARD_short_name":"OXA-131","ARO_description":"OXA-131 is a beta-lactamase found in A. baumannii.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1418":{"model_id":"1418","model_name":"DHA-6","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1783":{"protein_sequence":{"accession":"ADT91161.1","sequence":"MKKSLSATLISALLAFSAPGFSAADNVAAVVDSTIKPLMAQQDIPGMAVAVSVKGKPYYFNYGFADIQAKQPVTENTLFELGSVSKTFTGVLGAVSVAKKEMALNDPAAKYQPELALPQWKGITLLDLATYTAGGLPLQVPDAVKSRADLLNFYQQWQPSRKPGDMRLYANSSIGLFGALTANAAGMPYEQLLTARILAPLGLSHTFITVPESAQSQYAYGYKNKKPVRVSPGQLDAESYGVKSTSKDMLRWAEMNMEPSRAGNADLEMAMYLAQTRYYKTAAINQGLGWEMYDWPQQKDMIINGVTNEVALQPHPVTDNQVQPYNRASWVHKTGATTGFGAYVAFIPEKQVAIVILANKNYPNTERVKAAQAILSALE"},"dna_sequence":{"accession":"HQ322612.1","fmin":"0","fmax":"1140","strand":"+","sequence":"ATGAAAAAATCGTTATCTGCAACACTGATTTCCGCTCTGCTGGCGTTTTCCGCCCCGGGGTTTTCTGCCGCTGATAATGTCGCGGCGGTGGTGGACAGCACCATTAAACCGCTGATGGCACAGCAGGATATTCCCGGGATGGCGGTTGCCGTCTCCGTAAAGGGTAAGCCCTATTATTTCAATTATGGTTTTGCCGATATTCAGGCAAAACAGCCGGTCACTGAAAATACACTATTTGAGCTCGGATCTGTAAGTAAAACTTTCACAGGTGTGCTGGGTGCGGTTTCTGTGGCGAAAAAAGAGATGGCGCTGAATGATCCGGCGGCAAAATACCAGCCGGAGCTGGCTCTGCCGCAGTGGAAGGGGATCACATTGCTGGATCTGGCTACCTATACCGCAGGCGGACTGCCGTTACAGGTGCCGGATGCGGTAAAAAGCCGTGCGGATCTGCTGAATTTCTATCAGCAGTGGCAGCCGTCCCGGAAACCGGGCGATATGCGTCTGTATGCAAACAGCAGTATCGGCCTGTTTGGTGCTCTGACCGCAAACGCGGCGGGGATGCCGTATGAGCAGTTGCTGACTGCACGGATCCTGGCACCGCTGGGGTTATCTCACACCTTTATTACTGTGCCGGAAAGTGCGCAAAGCCAGTATGCGTACGGTTATAAAAACAAAAAACCGGTCCGCGTGTCGCCGGGACAGCTTGATGCGGAATCTTACGGCGTGAAATCCACCTCAAAAGATATGCTGCGCTGGGCGGAAATGAATATGGAGCCGTCACGGGCCGGTAATGCGGATCTGGAAATGGCAATGTATCTCGCCCAGACCCGCTACTATAAAACCGCCGCGATTAACCAGGGGCTGGGCTGGGAAATGTATGACTGGCCGCAGCAGAAAGATATGATCATTAACGGTGTGACCAACGAGGTCGCATTGCAGCCGCATCCGGTAACAGACAACCAGGTTCAGCCGTATAACCGTGCTTCCTGGGTGCATAAAACGGGCGCAACAACTGGTTTCGGCGCCTATGTCGCCTTTATTCCGGAAAAACAGGTGGCGATTGTGATTCTGGCGAATAAAAACTACCCGAATACCGAAAGAGTCAAAGCTGCACAGGCTATTTTGAGTGCACTGGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002135","ARO_id":"38535","ARO_name":"DHA-6","CARD_short_name":"DHA-6","ARO_description":"DHA-6 is a beta-lactamase found in the Enterobacteriaceae family.","ARO_category":{"36207":{"category_aro_accession":"3000068","category_aro_cvterm_id":"36207","category_aro_name":"DHA beta-lactamase","category_aro_description":"DHA beta-lactamases are plasmid-mediated AmpC \u03b2-lactamases that confer resistance to cephamycins and oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1419":{"model_id":"1419","model_name":"OXA-454","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"2122":{"protein_sequence":{"accession":"BAR45714.1","sequence":"MKTFAAYVIIACLSSTALAGSITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFKIPNAIIGLETGVIENEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLKGQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGIIGG"},"dna_sequence":{"accession":"LC037981.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGAAAACATTTGCCGCATATGTAATTATCGCGTGTCTTTCGAGTACGGCATTAGCTGGTTCAATTACAGAAAATACGTCTTGGAACAAAGAGTTCTCTGCCGAAGCCGTCAATGGTGTCTTCGTGCTTTGTAAAAGTAGCAGTAAATCCTGCGCTACCAATGACTTAGCTCGTGCATCAAAGGAATATCTTCCAGCATCAACATTTAAGATCCCCAACGCAATTATCGGCCTAGAAACTGGTGTCATAGAGAATGAGCATCAGGTTTTCAAATGGGACGGAAAGCCAAGAGCCATGAAGCAATGGGAAAGAGACTTGACCTTAAGAGGGGCAATACAAGTTTCAGCTGTTCCCGTATTTCAACAAATCGCCAGAGAAGTTGGCGAAGTAAGAATGCAGAAATACCTTAAAAAATTTTCCTATGGCAACCAGAATATCAGTGGTGGCATTGACAAATTCTGGTTGAAAGGCCAGCTTAGAATTTCCGCAGTTAATCAAGTGGAGTTTCTAGAGTCTCTATATTTAAATAAATTGTCAGCATCTAAAGAAAACCAGCTAATAGTAAAAGAGGCTTTGGTAACGGAGGCGGCACCTGAATATCTAGTGCATTCAAAAACTGGTTTTTCTGGTGTGGGAACTGAGTCAAATCCTGGTGTCGCATGGTGGGTTGGGTGGGTTGAGAAGGAGACAGAGGTTTACTTTTTCGCCTTTAACATGGATATAGACAACGAAAGTAAGTTGCCGCTAAGAAAATCCATTCCCACCAAAATCATGGAAAGTGAGGGCATCATTGGTGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40276","NCBI_taxonomy_name":"Delftia acidovorans","NCBI_taxonomy_id":"80866"}}}},"ARO_accession":"3003610","ARO_id":"40220","ARO_name":"OXA-454","CARD_short_name":"OXA-454","ARO_description":"OXA-454 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46486":{"category_aro_accession":"3007697","category_aro_cvterm_id":"46486","category_aro_name":"OXA-10-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-10.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1420":{"model_id":"1420","model_name":"aadA5","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"471":{"protein_sequence":{"accession":"AAF17880.1","sequence":"MGEFFPAQVFKQLSHARAVIERHLAATLDTIHLFGSAIDGGLKPDSDIDLLVTVSAAPNDSLRQALMLDLLKVSSPPGDGGTWRPLELTVVARSEVVPWRYPARRELQFGEWLRHDILSGTFEPAVLDHDLAILLTKARQHSLALLGPSAATFFEPVPKEHFSKALFDTIAQWNAESDWKGDERNVVLALARIWYSASTGLIAPKDVAAAWVSERLPAEHRPLICKARAAYLGSEDDDLAMRVEETAAFVRYAKATIERILR"},"dna_sequence":{"accession":"AF137361.1","fmin":"63","fmax":"852","strand":"+","sequence":"ATGGGTGAATTTTTCCCTGCACAAGTTTTCAAGCAGCTGTCCCACGCTCGCGCGGTGATCGAGCGCCATCTGGCTGCGACACTGGACACAATCCACCTGTTCGGATCTGCGATCGATGGAGGGCTGAAGCCGGACAGCGACATAGACTTGCTCGTGACCGTCAGCGCCGCACCTAACGATTCGCTCCGGCAGGCGCTAATGCTCGATTTGCTGAAAGTCTCATCACCGCCAGGCGATGGCGGAACATGGCGACCGCTGGAGCTAACTGTTGTCGCTCGAAGCGAAGTAGTGCCTTGGCGCTATCCGGCGCGGCGTGAGCTTCAGTTCGGTGAGTGGCTCCGCCACGACATCCTTTCCGGAACGTTCGAGCCTGCCGTTCTGGATCACGATCTTGCGATTTTGCTGACCAAGGCGAGGCAACACAGCCTTGCGCTTCTAGGCCCATCCGCAGCCACGTTTTTCGAGCCGGTGCCGAAGGAGCATTTCTCCAAGGCGCTTTTCGACACTATTGCCCAGTGGAATGCAGAGTCGGATTGGAAGGGTGACGAGCGGAACGTCGTTCTTGCTCTTGCTCGCATTTGGTACAGCGCTTCAACTGGTCTCATTGCTCCTAAGGACGTTGCTGCCGCATGGGTATCGGAGCGTTTGCCTGCCGAGCATCGGCCCCTCATCTGCAAGGCACGCGCGGCGTACCTGGGTAGCGAGGACGACGACCTAGCAATGCGCGTCGAAGAGACGGCCGCGTTCGTTCGATATGCCAAAGCAACGATTGAGAGAATCTTGCGTTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002605","ARO_id":"39005","ARO_name":"aadA5","CARD_short_name":"aadA5","ARO_description":"aadA5 is an aminoglycoside nucleotidyltransferase gene encoded by plasmids, transposons and integrons in E. coli, K. pneumoniae, Kluyvera georgiana, P. aeruginosa and E. cloacae.","ARO_category":{"41439":{"category_aro_accession":"3004275","category_aro_cvterm_id":"41439","category_aro_name":"ANT(3'')","category_aro_description":"A category of aminoglycoside O-nucleotidyltransferase enzymes with modification regiospecificity based at the 3''-hydroxyl group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics by transfer of an AMP group from an ATP substrate to the 3''-hydroxyl group of the compound.","category_aro_class_name":"AMR Gene Family"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1421":{"model_id":"1421","model_name":"TEM-85","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1405":{"protein_sequence":{"accession":"CAC43229.1","sequence":"MSIQHFRVALIPFFAAFCFPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDSWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGKRGSRGIIAALGPDGKPSRIVVIYMTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AJ277414.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCTTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATAGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTAAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACATGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3000952","ARO_id":"37332","ARO_name":"TEM-85","CARD_short_name":"TEM-85","ARO_description":"TEM-85 is an extended-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1422":{"model_id":"1422","model_name":"ACC-3","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1910":{"protein_sequence":{"accession":"AAF86697.1","sequence":"MRKKMQNTLKMLSVITCLALTAQGAMASEMDQAKIKDTVDSLIQPLMQKNNIPGMSVAVTLNGKNYIYNYGLASKQPQQPVTDNTLFEVGSLSKTFAATLASYAQVSGKLSLDKSISHYVPELRGSSFDHISVLNAGTHTTGLALFMPEEVKNTDQLMAYLKAWKPADPAGTHRVYSNIGTGLLGMIAAQSMGMTYEDAIEKTLLPKLGMTHTYLNVPADQAENYAWGYNKKNEPIHVNMEVLGNEAYGIRTNASDLIRYVQANMGQLKLDGNSTLQKALTDTHIGYFKSGKITQDLMWEQLPYPVSLPDLLTGNDMAMTKSVATPIVPPLPPQENVWINKTGSTNGFGAYIAFVPAKKMGIVMLANKNYSIDQRVT"},"dna_sequence":{"accession":"AF180958.1","fmin":"0","fmax":"1131","strand":"+","sequence":"ATGCGTAAAAAAATGCAGAACACCTTGAAGATGTTATCCGTGATTACCTGTCTGGCTTTAACGGCTCAGGGTGCCATGGCGTCAGAAATGGATCAGGCCAAAATTAAAGACACCGTTGATAGCCTGATCCAGCCGCTGATGCAGAAGAATAATATTCCGGGCATGTCGGTGGCAGTTACGCTGAACGGTAAAAATTATATTTATAACTATGGCTTAGCCTCCAAACAGCCCCAGCAGCCCGTAACGGACAACACGCTATTTGAAGTTGGCTCGCTGAGCAAAACCTTTGCAGCGACGCTGGCGTCTTATGCACAGGTCAGCGGCAAGTTATCGCTGGATAAAAGCATTAGCCATTATGTTCCAGAACTGCGCGGCAGCAGCTTCGATCACATTAGCGTGCTGAATGCGGGAACGCATACCACAGGTTTAGCGCTGTTCATGCCTGAAGAAGTGAAAAACACCGATCAGCTGATGGCTTATCTGAAAGCGTGGAAACCCGCCGATCCTGCGGGGACTCACCGTGTTTATTCCAATATTGGTACCGGCTTGTTGGGCATGATTGCCGCGCAAAGCATGGGAATGACTTACGAAGATGCGATTGAGAAAACGCTCCTTCCGAAGTTGGGCATGACGCACACCTATCTTAATGTTCCAGCAGACCAAGCGGAAAATTATGCTTGGGGCTATAACAAAAAGAATGAGCCGATCCACGTTAATATGGAAGTGTTGGGCAACGAAGCCTATGGCATTAGAACCAATGCGAGTGACCTGATTCGCTATGTGCAAGCCAATATGGGGCAGCTAAAACTTGATGGAAATTCGACGCTGCAAAAAGCGCTCACCGACACGCATATCGGTTACTTCAAGTCAGGCAAAATCACTCAGGATCTGATGTGGGAACAGCTGCCATATCCGGTATCTCTGCCGGATCTGCTCACTGGCAACGATATGGCGATGACAAAAAGCGTTGCTACGCCGATTGTTCCACCGCTGCCACCACAGGAAAATGTATGGATTAACAAAACCGGTTCCACCAATGGTTTTGGTGCCTACATCGCATTTGTTCCGGCTAAAAAGATGGGTATCGTGATGCTGGCGAACAAGAACTACTCTATCGATCAGCGTGTAACG","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36784","NCBI_taxonomy_name":"Hafnia alvei","NCBI_taxonomy_id":"569"}}}},"ARO_accession":"3001817","ARO_id":"38217","ARO_name":"ACC-3","CARD_short_name":"ACC-3","ARO_description":"ACC-3 is a beta-lactamase found in Hafnia alvei.","ARO_category":{"36212":{"category_aro_accession":"3000073","category_aro_cvterm_id":"36212","category_aro_name":"ACC beta-lactamase","category_aro_description":"ACC beta-lactamases or Ambler class C beta-lactamases are AmpC beta-lactamases. They possess an interesting resistance phenotype due to their low activity against cephamycins.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1423":{"model_id":"1423","model_name":"TEM-15","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"845":{"protein_sequence":{"accession":"CAO98721.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVKYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGASERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AM849805.1","fmin":"262","fmax":"1123","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTAAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCAGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36927","NCBI_taxonomy_name":"Haemophilus parainfluenzae","NCBI_taxonomy_id":"729"}}}},"ARO_accession":"3000886","ARO_id":"37266","ARO_name":"TEM-15","CARD_short_name":"TEM-15","ARO_description":"TEM-15 is an extended-spectrum beta-lactamase that has been found in Haemophilus parainfluenzae.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1424":{"model_id":"1424","model_name":"OXY-2-4","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1384":{"protein_sequence":{"accession":"CAB42614.1","sequence":"MIKSSWRKIAMLAAVPLLLASGALWASTDAIHQKLTDLEKRSGGRLGVALINTADNSQILYRGDERFAMCSTSKVMAAAAVLKQSESNKEVVNKRLEINAADLVVWSPITEKHLQSGMTLAELSAATLQYSDNTAMNLIIGYLGGPEKVTAFARSIGDATFRLDRTEPTLNTAIPGDERDTSTPLAMAESLRKLTLGDALGEQQRAQLVTWLKGNTTGGQSIRAGLPESWVVGDKTGAGDYGTTNDIAVIWPEDHAPLVLVTYFTQPQQDAKNRKEVLAAAAKIVTEGL"},"dna_sequence":{"accession":"Y17714.1","fmin":"146","fmax":"1016","strand":"+","sequence":"ATGATAAAAAGTTCGTGGCGTAAAATTGCAATGCTAGCCGCCGTTCCGCTGCTGCTGGCGAGCGGCGCACTGTGGGCCAGTACCGATGCTATCCATCAGAAGCTGACAGATCTCGAGAAGCGTTCAGGCGGCAGGTTGGGCGTGGCGCTAATCAACACGGCAGATAATTCTCAAATCTTATATCGCGGCGACGAGCGTTTTGCCATGTGCAGCACCAGTAAAGTGATGGCCGCCGCCGCGGTATTAAAACAGAGCGAAAGCAATAAAGAGGTGGTAAATAAAAGGCTGGAGATTAACGCAGCCGATTTGGTGGTCTGGAGTCCGATTACCGAAAAACATCTCCAGAGCGGAATGACGCTGGCTGAGCTAAGCGCGGCGACGCTGCAATATAGCGACAATACGGCGATGAATCTGATCATCGGCTACCTTGGCGGGCCGGAAAAAGTCACCGCCTTCGCCCGCAGTATCGGCGATGCCACCTTTCGTCTCGATCGTACGGAGCCCACGCTGAATACCGCCATCCCGGGCGATGAGCGTGATACCAGCACGCCGCTGGCGATGGCTGAAAGCCTACGCAAGCTGACGCTTGGCGATGCGCTGGGCGAACAGCAACGCGCCCAGTTAGTCACCTGGCTGAAAGGCAATACCACCGGCGGGCAAAGCATTCGCGCGGGCCTGCCTGAAAGCTGGGTGGTCGGCGATAAAACCGGCGCCGGAGATTACGGCACCACCAATGATATTGCGGTTATCTGGCCGGAAGATCACGCTCCGCTGGTATTAGTCACCTACTTTACCCAGCCGCAGCAGGATGCGAAAAACCGCAAAGAAGTGTTAGCCGCAGCGGCAAAAATCGTGACCGAAGGGCTTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3002399","ARO_id":"38799","ARO_name":"OXY-2-4","CARD_short_name":"OXY-2-4","ARO_description":"OXY-2-4 is a beta-lactamase found in Klebsiella oxytoca.","ARO_category":{"38788":{"category_aro_accession":"3002388","category_aro_cvterm_id":"38788","category_aro_name":"OXY beta-lactamase","category_aro_description":"OXY beta-lactamases are chromosomal class A beta-lactamases that are found in Klebsiella oxytoca. At constitutive low levels, OXY beta-lactamases confer resistance to aminopenicillins and carboxypenicillins. At high induced levels,  OXY beta-lactamases confer resistance to penicillins, cephalosporins and aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1425":{"model_id":"1425","model_name":"RbpA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"200"}},"model_sequences":{"sequence":{"356":{"protein_sequence":{"accession":"ADV91011.1","sequence":"MADRVLRGSRLGAVSYETDRNHDLAPRQVARYRTDNGEEFDVPFADDAEIPGTWLCRNGLEGTLIEGDVPEPKKVKPPRTHWDMLLERRSVEELEELLKERLDLIKAKRRGTGS"},"dna_sequence":{"accession":"HQ203032.1","fmin":"0","fmax":"345","strand":"+","sequence":"ATGGCTGATCGTGTCCTGCGGGGCAGTCGCCTCGGAGCCGTGAGCTACGAGACCGACCGCAACCATGACCTGGCGCCGCGTCAGGTCGCCCGCTACCGCACGGATAACGGCGAGGAGTTCGACGTACCTTTCGCCGACGACGCCGAGATCCCCGGTACGTGGCTCTGCCGCAACGGTCTGGAGGGCACCCTCATCGAGGGTGACGTGCCGGAGCCCAAGAAGGTCAAGCCGCCGCGTACGCACTGGGACATGCTGTTGGAGCGCCGGTCCGTCGAGGAGCTCGAAGAGCTGCTCAAGGAGCGTCTCGACCTGATCAAGGCCAAGCGGCGCGGAACCGGAAGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36769","NCBI_taxonomy_name":"Mycolicibacterium smegmatis MC2 155","NCBI_taxonomy_id":"246196"}}}},"ARO_accession":"3000245","ARO_id":"36384","ARO_name":"RbpA","CARD_short_name":"RbpA","ARO_description":"RNA-polymerase binding protein which confers resistance to rifampin.","ARO_category":{"41407":{"category_aro_accession":"3004243","category_aro_cvterm_id":"41407","category_aro_name":"RbpA bacterial RNA polymerase-binding protein","category_aro_description":"RbpA is a family of bacterial RNA polymerase-binding proteins, which acts as a transcription factor and binds to the sigma subunit of RNA polymerase.","category_aro_class_name":"AMR Gene Family"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36656":{"category_aro_accession":"3000517","category_aro_cvterm_id":"36656","category_aro_name":"rifaximin","category_aro_description":"Rifaximin is a semi-synthetic rifamycin used to treat traveller's diarrhea. Rifaximin inhibits RNA synthesis by binding to the beta subunit of bacterial RNA polymerase.","category_aro_class_name":"Antibiotic"},"36669":{"category_aro_accession":"3000530","category_aro_cvterm_id":"36669","category_aro_name":"rifabutin","category_aro_description":"Rifabutin is a semisynthetic rifamycin used in tuberculosis therapy. It inhibits DNA-dependent RNA synthesis.","category_aro_class_name":"Antibiotic"},"36673":{"category_aro_accession":"3000534","category_aro_cvterm_id":"36673","category_aro_name":"rifapentine","category_aro_description":"Rifapentine is a semisynthetic rifamycin that inhibits DNA-dependent RNA synthesis. It is often used in the treatment of tuberculosis and leprosy.","category_aro_class_name":"Antibiotic"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1426":{"model_id":"1426","model_name":"IMP-7","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1357":{"protein_sequence":{"accession":"AAK12087.1","sequence":"MKKLSVFFMFLFCSIAASGEALPDLKIEKLDEGVYVHTSFEEVNGWGVVPKHGLVVLVNTDAYLIDTPFTAKDTEKLVTWFVERGYKIKGSISSHFHSDSTGGIEWLNSQSIPTYASELTNELLKKDGKVQAKNSFSGASYWLVKKKIEIFYPGPGHTPDNVVVWLPEHRVLFGGCFVKPYGLGNLGDANLEAWPKSAKLLVSKYGKAKLVVPSHSEVGDASLLKRTLEQAVKGLNESKKLSKPSN"},"dna_sequence":{"accession":"AF318077.1","fmin":"1147","fmax":"1888","strand":"+","sequence":"ATGAAAAAGTTATCAGTATTCTTTATGTTTTTGTTTTGTAGCATTGCTGCCTCAGGAGAGGCTTTGCCAGATTTAAAAATTGAGAAGCTTGACGAAGGCGTTTATGTTCATACTTCGTTTGAGGAAGTTAACGGCTGGGGCGTGGTTCCTAAACACGGCTTGGTGGTTCTTGTAAATACTGACGCTTATTTGATTGACACTCCATTTACAGCTAAAGATACTGAAAAGTTAGTTACTTGGTTTGTAGAGCGCGGCTATAAAATAAAAGGCAGTATCTCCTCTCATTTTCATAGCGACAGCACGGGCGGAATAGAGTGGCTTAATTCTCAATCTATTCCAACATATGCATCTGAATTAACAAATGAACTTCTTAAAAAAGACGGTAAGGTACAAGCTAAAAATTCATTTAGCGGAGCCAGCTATTGGTTAGTTAAGAAAAAGATTGAAATTTTTTATCCTGGCCCAGGGCACACTCCAGATAACGTAGTGGTTTGGCTACCTGAACATAGAGTTTTGTTTGGTGGTTGTTTTGTTAAACCGTATGGTCTAGGTAATTTGGGTGACGCAAATTTAGAAGCTTGGCCAAAGTCTGCCAAATTATTAGTGTCCAAATATGGTAAGGCAAAACTGGTTGTTCCAAGTCACAGTGAAGTTGGAGATGCATCACTCTTGAAACGTACATTAGAACAGGCTGTTAAAGGATTAAACGAAAGTAAAAAGCTATCAAAACCAAGTAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002198","ARO_id":"38598","ARO_name":"IMP-7","CARD_short_name":"IMP-7","ARO_description":"IMP-7 is a beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1427":{"model_id":"1427","model_name":"acrD","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1900"}},"model_sequences":{"sequence":{"5517":{"protein_sequence":{"accession":"BAA16344.1","sequence":"MANFFIDRPIFAWVLAILLCLTGTLAIFSLPVEQYPDLAPPNVRVTANYPGASAQTLENTVTQVIEQNMTGLDNLMYMSSQSSGTGQASVTLSFKAGTDPDEAVQQVQNQLQSAMRKLPQAVQNQGVTVRKTGDTNILTIAFVSTDGSMDKQDIADYVASNIQDPLSRVNGVGDIDAYGSQYSMRIWLDPAKLNSFQMTAKDVTDAIESQNAQIAVGQLGGTPSVDKQALNATINAQSLLQTPEQFRDITLRVNQDGSEVRLGDVATVEMGAEKYDYLSRFNGKPASGLGVKLASGANEMATAELVLNRLDELAQYFPHGLEYKVAYETTSFVKASIEDVVKTLLEAIALVFLVMYLFLQNFRATLIPTIAVPVVLMGTFSVLYAFGYSVNTLTMFAMVLAIGLLVDDAIVVVENVERIMSEEGLTPREATRKSMGQIQGALVGIAMVLSAVFVPMAFFGGTTGAIYRQFSITIVAAMVLSVLVAMILTPALCATLLKPLKKGEHHGQKGFFAWFNQMFNRNAERYEKGVAKILHRSLRWIVIYVLLLGGMVFLFLRLPTSFLPLEDRGMFTTSVQLPSGSTQQQTLKVVEQIEKYYFTHEKDNIMSVFATVGSGPGGNGQNVARMFIRLKDWSERDSKTGTSFAIIERATKAFNQIKEARVIASSPPAISGLGSSAGFDMELQDHAGAGHDALMAARNQLLALAAENPELTRVRHNGLDDSPQLQIDIDQRKAQALGVAIDDINDTLQTAWGSSYVNDFMDRGRVKKVYVQAAAPYRMLPDDINLWYVRNKDGGMVPFSAFATSRWETGSPRLERYNGYSAVEIVGEAAPGVSTGTAMDIMESLVKQLPNGFGLEWTAMSYQERLSGAQAPALYAISLLVVFLCLAALYESWSVPFSVMLVVPLGVIGALLATWMRGLENDVYFQVGLLTVIGLSAKNAILIVEFANEMNQKGHDLFEATLHACRQRLRPILMTSLAFIFGVLPMATSTGAGSGGQHAVGTGVMGGMISATILAIYFVPLFFVLVRRRFPLKPRPE"},"dna_sequence":{"accession":"AP009048.1","fmin":"2586250","fmax":"2589364","strand":"+","sequence":"ATGGCGAATTTCTTTATTGATCGCCCCATTTTTGCCTGGGTGCTGGCAATCCTGTTGTGTCTGACAGGTACCCTGGCGATTTTTTCATTGCCCGTTGAACAATACCCCGATCTCGCGCCACCGAATGTGCGAGTGACCGCTAACTATCCCGGCGCATCGGCCCAGACGCTGGAAAACACCGTGACCCAGGTTATCGAGCAAAATATGACCGGCCTCGATAATCTCATGTATATGTCATCTCAGAGCAGTGGCACCGGTCAGGCATCTGTCACTTTAAGTTTTAAAGCAGGCACCGATCCGGACGAAGCCGTGCAGCAAGTACAAAACCAGCTGCAATCAGCCATGCGAAAGTTACCGCAGGCGGTGCAAAATCAGGGCGTGACGGTGCGTAAAACCGGCGATACCAACATTCTGACCATTGCCTTCGTCTCTACCGATGGTTCGATGGATAAACAGGATATTGCTGATTATGTTGCCAGTAATATTCAGGACCCGTTAAGCCGCGTGAATGGCGTCGGGGATATCGATGCCTATGGTTCGCAATATTCCATGCGTATCTGGCTGGACCCGGCGAAACTCAACAGTTTCCAGATGACGGCTAAAGATGTCACTGATGCCATTGAGTCACAGAACGCGCAGATTGCGGTTGGGCAACTTGGTGGTACACCTTCCGTCGATAAGCAGGCGCTCAACGCCACCATTAACGCCCAGTCACTGCTGCAAACACCAGAACAGTTCCGCGATATCACCTTGCGGGTCAATCAGGACGGCTCAGAGGTAAGGCTGGGCGATGTCGCCACCGTCGAAATGGGGGCGGAGAAATACGATTATCTTAGCCGCTTCAATGGTAAGCCAGCCTCCGGGCTGGGGGTAAAACTGGCCTCCGGCGCTAACGAAATGGCGACAGCGGAGCTGGTGCTCAATCGTCTCGACGAGCTGGCGCAGTATTTCCCGCATGGACTGGAATACAAGGTGGCGTATGAAACCACCTCGTTTGTTAAAGCCTCCATTGAAGACGTGGTGAAAACGCTGCTGGAAGCTATCGCTCTGGTTTTCCTCGTTATGTATCTGTTCCTGCAAAACTTCCGCGCCACGCTGATACCCACTATCGCCGTGCCGGTGGTGTTGATGGGAACCTTCTCCGTACTTTACGCCTTCGGTTACAGCGTCAACACCTTAACCATGTTCGCGATGGTGCTGGCGATCGGTCTGCTGGTGGATGACGCCATCGTGGTGGTGGAAAACGTCGAACGTATTATGAGTGAGGAAGGACTCACTCCTCGCGAAGCCACACGTAAATCGATGGGGCAGATCCAGGGGGCACTGGTCGGGATTGCGATGGTTCTTTCGGCGGTATTTGTACCAATGGCCTTCTTCGGCGGCACCACCGGTGCCATCTATCGCCAGTTCTCTATTACCATTGTTGCGGCGATGGTGCTGTCAGTACTGGTAGCGATGATCCTCACTCCGGCTCTGTGTGCCACACTACTTAAGCCACTGAAAAAAGGTGAGCATCATGGGCAAAAAGGCTTTTTTGCCTGGTTTAACCAGATGTTTAACCGCAACGCCGAACGCTACGAAAAAGGGGTGGCGAAAATTCTCCACCGTAGCCTGCGCTGGATTGTGATTTATGTCCTGCTGCTTGGCGGCATGGTGTTCCTGTTCCTGCGTTTGCCGACGTCGTTCTTACCGCTGGAAGACCGTGGCATGTTTACTACCTCGGTACAGTTGCCCAGCGGTTCAACGCAACAACAGACCCTGAAAGTCGTTGAGCAAATCGAGAAATACTACTTCACCCATGAAAAAGACAACATCATGTCGGTGTTTGCCACCGTTGGTTCTGGCCCTGGGGGTAACGGGCAAAACGTGGCGCGAATGTTTATCCGCCTGAAAGACTGGAGCGAACGCGACAGTAAGACCGGCACCTCGTTTGCCATTATCGAGCGTGCAACGAAGGCGTTTAACCAAATTAAAGAAGCTCGCGTTATCGCCAGCAGCCCGCCAGCAATTAGCGGTCTTGGTAGTTCTGCAGGTTTTGATATGGAGTTGCAGGACCACGCTGGAGCGGGTCACGATGCGCTGATGGCAGCACGTAATCAGTTGCTGGCGCTGGCGGCGGAAAACCCGGAGCTAACCCGTGTGCGCCATAACGGCCTCGACGACAGTCCGCAGTTGCAGATTGATATCGACCAGCGTAAAGCTCAGGCGCTGGGCGTTGCTATCGACGATATTAACGACACACTGCAAACCGCCTGGGGTTCGAGCTATGTGAATGACTTTATGGATCGCGGTCGCGTGAAGAAAGTCTATGTGCAGGCAGCTGCGCCGTATCGCATGCTGCCAGATGACATCAATCTCTGGTATGTCCGAAATAAAGATGGCGGCATGGTGCCCTTCTCTGCTTTCGCGACCTCACGCTGGGAAACAGGCTCGCCGCGTCTGGAACGCTATAACGGTTATTCTGCGGTTGAGATTGTTGGGGAAGCCGCACCGGGGGTCAGTACCGGTACGGCGATGGATATTATGGAATCGTTAGTGAAGCAGCTGCCAAACGGCTTTGGTCTGGAGTGGACGGCGATGTCGTATCAGGAGCGGCTTTCCGGCGCGCAGGCTCCGGCGCTGTACGCCATTTCCTTGCTGGTGGTATTCCTGTGTCTGGCTGCGTTGTATGAAAGCTGGTCGGTGCCGTTCTCGGTAATGCTGGTCGTGCCGCTGGGGGTAATCGGCGCGCTGCTGGCAACCTGGATGCGCGGGCTGGAAAACGACGTTTACTTCCAGGTGGGCCTGTTAACGGTCATTGGTTTATCGGCGAAAAACGCCATCCTGATCGTCGAGTTTGCTAACGAGATGAACCAAAAAGGCCACGACCTGTTTGAAGCGACGCTCCACGCCTGCCGTCAGCGTTTACGCCCGATTCTGATGACCTCGCTGGCATTTATCTTCGGCGTATTGCCAATGGCAACCAGCACGGGTGCCGGTTCCGGTGGTCAGCATGCGGTGGGTACTGGCGTAATGGGCGGGATGATTTCGGCCACTATTCTGGCTATTTACTTCGTGCCGCTGTTCTTTGTGCTGGTGCGCCGCCGCTTCCCGCTGAAGCCGCGCCCGGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36839","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. W3110","NCBI_taxonomy_id":"316407"}}}},"ARO_accession":"3000491","ARO_id":"36630","ARO_name":"acrD","CARD_short_name":"acrD","ARO_description":"AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole, and is regulated by baeRS and cpxAR.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"46133":{"category_aro_accession":"3007382","category_aro_cvterm_id":"46133","category_aro_name":"gentamicin","category_aro_description":"Gentamicin is a commonly used aminoglycoside antibiotic derived from members of the Micromonospora genus of bacteria. It acts by binding the 30S ribosomal subunit, thus inhibiting protein synthesis. Gentamicin is typically used to treat Gram-negative infections of the repiratory and urinary tract, as well as infections of the bone and soft tissue. It also exhibits considerable nephrotoxicity and ototoxicity. Gentamicin is administered as a mixture of gentamicin type C (which makes about around 80% of the complex) and types A, B, and X (distributed in the remaining 20% of the complex).","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1428":{"model_id":"1428","model_name":"cphA2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"3364":{"protein_sequence":{"accession":"AAB03413.1","sequence":"MMKGWMKCGLAGAVVLMASFWGGSVRAAGMSLTQVSGPVYVVEDNYYVQENSMVYFGAKGVTVVGATWTPDTARELHKLIKRVSRQPVLEVINTNYHTDRAGGNAYWKSIGAKVVSTRQTRDLMKSDWAEIVAFTRKGLPEYPDLPLVLPNVVHEGDFTLQEGKLRAFYAGPAHTPDGIFVYFPDQQVLYGNCILKEKLGNLSFADVKAYPRTLERLKAMKLPIKTVVGGHDSPLHGPELIDHYEALIKAAPQS"},"dna_sequence":{"accession":"U60294.1","fmin":"0","fmax":"765","strand":"+","sequence":"ATGATGAAAGGTTGGATGAAGTGTGGATTGGCCGGGGCCGTGGTGCTGATGGCGAGTTTCTGGGGTGGCAGCGTGCGGGCGGCGGGGATGTCGCTGACGCAGGTGAGCGGCCCTGTCTATGTGGTAGAGGACAATTACTACGTGCAGGAAAACTCCATGGTCTATTTCGGGGCCAAGGGAGTGACTGTTGTAGGGGCGACCTGGACGCCGGATACCGCCCGCGAGCTGCACAAGCTGATCAAACGAGTCAGCCGCCAGCCGGTGCTGGAGGTGATCAACACCAACTACCACACCGACCGGGCGGGCGGTAACGCCTACTGGAAGTCCATCGGGGCCAAGGTGGTATCGACCCGCCAGACCCGGGATCTGATGAAGAGCGACTGGGCCGAGATTGTTGCCTTTACCCGCAAGGGGTTGCCGGAGTACCCGGATCTGCCCCTGGTGCTGCCCAACGTGGTGCACGAGGGCGACTTCACGCTGCAAGAGGGCAAGCTGCGCGCCTTCTATGCGGGCCCGGCCCACACGCCGGATGGCATCTTTGTCTACTTCCCCGACCAGCAGGTGCTCTATGGCAACTGCATCCTCAAGGAGAAGCTGGGCAACCTGAGCTTTGCCGATGTGAAGGCCTATCCGCGCACGCTTGAGCGGCTCAAGGCGATGAAGCTGCCAATCAAGACGGTGGTGGGCGGTCACGACTCGCCGCTGCATGGGCCTGAGCTTATCGATCACTACGAGGCGCTGATCAAGGCCGCACCCCAGTCATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36810","NCBI_taxonomy_name":"Aeromonas hydrophila","NCBI_taxonomy_id":"644"}}}},"ARO_accession":"3003099","ARO_id":"39665","ARO_name":"cphA2","CARD_short_name":"cphA2","ARO_description":"CphA2 is an Ambler Class B MBL; subclass B2 originally isolated from Aeromonas hydrophila. This enzyme has specific activity against carbapenems and is active as a mono-zinc protein.","ARO_category":{"36720":{"category_aro_accession":"3000581","category_aro_cvterm_id":"36720","category_aro_name":"CphA beta-lactamase","category_aro_description":"CphA is an Ambler Class B MBL; subclass B2 originally isolated from Aeromonas hydrophilia.  This enzyme has specific activity against carbapenems and is active as a mono-zinc protein.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1429":{"model_id":"1429","model_name":"SHV-60","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1948":{"protein_sequence":{"accession":"BAF92780.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMTATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AB302939.1","fmin":"8","fmax":"869","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGACCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGCATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001115","ARO_id":"37495","ARO_name":"SHV-60","CARD_short_name":"SHV-60","ARO_description":"SHV-60 is a broad-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1430":{"model_id":"1430","model_name":"SHV-125","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"1942":{"protein_sequence":{"accession":"ACV32635.1","sequence":"MRYIRLNIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQ"},"dna_sequence":{"accession":"GQ390807.1","fmin":"0","fmax":"813","strand":"+","sequence":"ATGCGTTATATTCGCCTGAATATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTACTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAATCAG","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001172","ARO_id":"37552","ARO_name":"SHV-125","CARD_short_name":"SHV-125","ARO_description":"SHV-125 is a beta-lactamase that has been found in clinical isolates.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1431":{"model_id":"1431","model_name":"GES-15","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"771":{"protein_sequence":{"accession":"ACZ98826.1","sequence":"MRFIHALLLAGIAHSAYASEKLTFKTDLEKLEREKAAQIGVAIVDPQGEIVAGHRMAQRFAMCSTFKFPLAALVFERIDSGTERGDRKLSYGPDMIVEWSPATERFLASGHMTVLEAAQAAVQLSDNGATNLLLREIGGPAAMTQYFRKIGDSVSRLDRKESEMSDNTPGDLRDTTTPIAMARTVAKVLYGGALTSTSTHTIERWLIGNQTGDATLRAGFPKDWVVGEKTGTCANGGRNDIGFFKAQERDYAVAVYTTAPKLSAVERDELVASVGQVITQLILSTDK"},"dna_sequence":{"accession":"GU208678.1","fmin":"0","fmax":"864","strand":"+","sequence":"ATGCGCTTCATTCACGCACTATTACTGGCAGGGATCGCTCACTCTGCATATGCGTCGGAAAAATTAACCTTCAAGACCGATCTTGAGAAGCTAGAGCGCGAAAAAGCAGCTCAGATCGGTGTTGCGATCGTCGATCCCCAAGGAGAGATCGTCGCGGGCCACCGAATGGCGCAGCGTTTTGCAATGTGCTCAACGTTCAAGTTTCCGCTAGCCGCGCTGGTCTTTGAAAGAATTGACTCAGGCACCGAGCGGGGGGATCGAAAACTTTCATATGGGCCGGACATGATCGTCGAATGGTCTCCTGCCACGGAGCGGTTTCTAGCATCGGGACACATGACGGTTCTCGAGGCAGCGCAAGCTGCGGTGCAGCTTAGCGACAATGGGGCTACTAACCTCTTACTGAGAGAAATTGGCGGACCTGCTGCAATGACGCAGTATTTTCGTAAAATTGGCGACTCTGTGAGTCGGCTAGACCGGAAAGAGTCGGAGATGAGCGACAACACACCTGGCGACCTCAGAGATACAACTACGCCTATTGCTATGGCACGTACTGTGGCTAAAGTCCTCTATGGCGGCGCACTGACGTCCACCTCGACCCACACCATTGAGAGGTGGCTGATCGGAAACCAAACGGGAGACGCGACACTACGAGCGGGTTTTCCTAAAGATTGGGTTGTTGGAGAGAAAACTGGTACCTGCGCCAACGGGGGCCGGAACGACATTGGTTTTTTTAAAGCCCAGGAGAGAGATTACGCTGTAGCGGTGTATACAACGGCCCCGAAACTATCGGCCGTAGAACGTGACGAATTAGTTGCCTCTGTCGGTCAAGTTATTACACAACTCATCCTGAGCACGGACAAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002344","ARO_id":"38744","ARO_name":"GES-15","CARD_short_name":"GES-15","ARO_description":"GES-15 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36205":{"category_aro_accession":"3000066","category_aro_cvterm_id":"36205","category_aro_name":"GES beta-lactamase","category_aro_description":"GES beta-lactamases or Guiana extended-spectrum beta-lactamases are related to the other plasmid-located class A beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1433":{"model_id":"1433","model_name":"CMY-18","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1974":{"protein_sequence":{"accession":"AAU95778.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGNGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"AY743434.1","fmin":"46","fmax":"1198","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002029","ARO_id":"38429","ARO_name":"CMY-18","CARD_short_name":"CMY-18","ARO_description":"CMY-18 is a beta-lactamase found in the Enterobacteriaceae family.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1434":{"model_id":"1434","model_name":"Erm(35)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"4237":{"protein_sequence":{"accession":"AAK07612.2","sequence":"MTKKKLPVRFTGQHFTIDKVLIKDAIKESNINQHDTVLDIGAGKGFLTVHLLKNVDKVIAIENDVALSQHLRKKFIHAQNVQVVSCDYRNFVVPKVPFKVVSNIPFGITSDIFSSLMFENVEYFLCGSIILQSEPAKKLFSSKVYNPLTVLYHTYYDLKFLYEINPESFLPPPTVKSALLRIERKQISLDIGLKVKYLNFVSYMLQKPDLTVKTAMKSIFRKKQVRSISEKFGVDLNSKIVCLTPNQWKNCFLEMLEVVPEKFHPS"},"dna_sequence":{"accession":"AF319779.2","fmin":"32","fmax":"833","strand":"+","sequence":"ATGACAAAAAAGAAATTGCCCGTTCGTTTTACGGGTCAGCACTTTACTATTGACAAAGTGCTTATTAAAGATGCAATAAAAGAATCAAATATAAATCAACACGATACAGTTTTAGATATTGGAGCTGGTAAGGGTTTTCTAACTGTTCATCTCTTAAAAAATGTCGATAAAGTTATTGCCATTGAAAACGATGTTGCATTAAGTCAACATTTGCGCAAAAAATTCATTCACGCTCAAAACGTTCAAGTGGTTAGTTGTGATTATAGAAATTTTGTGGTTCCGAAAGTTCCATTTAAAGTAGTTTCAAATATTCCTTTTGGTATTACATCTGATATTTTTAGTAGTCTGATGTTTGAAAATGTCGAATATTTTCTATGCGGTTCAATTATCCTTCAGTCAGAACCGGCAAAAAAATTGTTTTCAAGTAAGGTTTATAACCCATTGACAGTACTTTATCATACCTATTATGATTTGAAATTCCTGTATGAGATAAATCCTGAAAGTTTTTTGCCACCACCAACTGTCAAATCAGCACTTTTGAGAATTGAAAGAAAACAGATTTCATTAGATATTGGGCTTAAGGTTAAGTACTTAAATTTTGTTTCGTATATGTTACAAAAACCTGATTTAACAGTCAAAACAGCTATGAAGTCTATTTTTAGAAAAAAACAAGTTAGGTCAATTTCAGAAAAATTTGGAGTTGACCTTAACTCCAAAATTGTCTGTTTGACTCCAAATCAATGGAAGAATTGTTTTTTAGAAATGCTCGAAGTTGTTCCTGAAAAGTTTCATCCGTCATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36798","NCBI_taxonomy_name":"Bacteroides coprosuis DSM 18011","NCBI_taxonomy_id":"679937"}}}},"ARO_accession":"3000604","ARO_id":"36743","ARO_name":"Erm(35)","CARD_short_name":"Erm(35)","ARO_description":"ErmD confers MLSb phenotype.","ARO_category":{"36699":{"category_aro_accession":"3000560","category_aro_cvterm_id":"36699","category_aro_name":"Erm 23S ribosomal RNA methyltransferase","category_aro_description":"Erm proteins are part of the RNA methyltransferase family and methylate A2058 (E. coli nomenclature) of the 23S ribosomal RNA conferring degrees of resistance to Macrolides, Lincosamides and Streptogramin b. This is called the MLSb phenotype.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35946":{"category_aro_accession":"0000027","category_aro_cvterm_id":"35946","category_aro_name":"roxithromycin","category_aro_description":"Roxithromycin is a semi-synthetic, 14-carbon ring macrolide antibiotic derived from erythromycin. It is used to treat respiratory tract, urinary and soft tissue infections. Roxithromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35974":{"category_aro_accession":"0000057","category_aro_cvterm_id":"35974","category_aro_name":"telithromycin","category_aro_description":"Telithromycin is a semi-synthetic derivative of erythromycin. It is a 14-membered macrolide and is the first ketolide antibiotic to be used in clinics. Telithromycin binds the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"35982":{"category_aro_accession":"0000065","category_aro_cvterm_id":"35982","category_aro_name":"clarithromycin","category_aro_description":"Clarithromycin is a methyl derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome and is used to treat pharyngitis, tonsillitis, acute maxillary sinusitis, acute bacterial exacerbation of chronic bronchitis, pneumonia (especially atypical pneumonias associated with Chlamydia pneumoniae or TWAR), and skin structure infections.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"36284":{"category_aro_accession":"3000145","category_aro_cvterm_id":"36284","category_aro_name":"tylosin","category_aro_description":"Tylosin is a 16-membered macrolide, naturally produced by Streptomyces fradiae. It interacts with the bacterial ribosome 50S subunit to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"36295":{"category_aro_accession":"3000156","category_aro_cvterm_id":"36295","category_aro_name":"spiramycin","category_aro_description":"Spiramycin is a 16-membered macrolide and is natural product produced by Streptomyces ambofaciens. It binds to the 50S subunit of bacterial ribosomes and inhibits peptidyl transfer activity to disrupt protein synthesis.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"36315":{"category_aro_accession":"3000176","category_aro_cvterm_id":"36315","category_aro_name":"dirithromycin","category_aro_description":"Dirithromycin is an oxazine derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome to inhibit bacterial protein synthesis.","category_aro_class_name":"Antibiotic"},"36722":{"category_aro_accession":"3000583","category_aro_cvterm_id":"36722","category_aro_name":"pristinamycin IA","category_aro_description":"Pristinamycin IA is a type B streptogramin antibiotic produced by Streptomyces pristinaespiralis. It binds to the P site of the 50S subunit of the bacterial ribosome, preventing the extension of protein chains.","category_aro_class_name":"Antibiotic"},"36723":{"category_aro_accession":"3000584","category_aro_cvterm_id":"36723","category_aro_name":"quinupristin","category_aro_description":"Quinupristin is a type B streptogramin and a semisynthetic derivative of pristinamycin 1A. It is a component of the drug Synercid and interacts with the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"virginiamycin M1","category_aro_description":"Virginiamycin M1 is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37016":{"category_aro_accession":"3000672","category_aro_cvterm_id":"37016","category_aro_name":"madumycin II","category_aro_description":"Madumycin II is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37017":{"category_aro_accession":"3000673","category_aro_cvterm_id":"37017","category_aro_name":"griseoviridin","category_aro_description":"Griseoviridin is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"37019":{"category_aro_accession":"3000675","category_aro_cvterm_id":"37019","category_aro_name":"pristinamycin IB","category_aro_description":"Pristinamycin IB is a class B streptogramin similar to pristinamycin IA, the former containing a N-methyl-4-(methylamino)phenylalanine instead of a N-methyl-4-(dimethylamino)phenylalanine in its class A streptogramin counterpart (one less methyl group).","category_aro_class_name":"Antibiotic"},"37021":{"category_aro_accession":"3000677","category_aro_cvterm_id":"37021","category_aro_name":"virginiamycin S2","category_aro_description":"Virginiamycin S2 is a streptogramin B antibiotic.","category_aro_class_name":"Antibiotic"},"37022":{"category_aro_accession":"3000678","category_aro_cvterm_id":"37022","category_aro_name":"pristinamycin IC","category_aro_description":"Pristinamycin IC is a class B streptogramin derived from virginiamycin S1.","category_aro_class_name":"Antibiotic"},"37023":{"category_aro_accession":"3000679","category_aro_cvterm_id":"37023","category_aro_name":"vernamycin C","category_aro_description":"Vernamycin C is a streptogramin B antibiotic.","category_aro_class_name":"Antibiotic"},"37024":{"category_aro_accession":"3000680","category_aro_cvterm_id":"37024","category_aro_name":"patricin A","category_aro_description":"Patricin A is a streptogramin B antibiotic.","category_aro_class_name":"Antibiotic"},"37025":{"category_aro_accession":"3000681","category_aro_cvterm_id":"37025","category_aro_name":"patricin B","category_aro_description":"Patricin B is a streptogramin B antibiotic.","category_aro_class_name":"Antibiotic"},"37026":{"category_aro_accession":"3000682","category_aro_cvterm_id":"37026","category_aro_name":"ostreogrycin B3","category_aro_description":"Ostreogrycin B3 is a derivative of pristinamycin IA, with an additional 3-hydroxy group on its 4-oxopipecolic acid.","category_aro_class_name":"Antibiotic"},"37247":{"category_aro_accession":"3000867","category_aro_cvterm_id":"37247","category_aro_name":"oleandomycin","category_aro_description":"Oleandomycin is a 14-membered macrolide produced by Streptomyces antibioticus. It is ssimilar to erythromycin, and contains a desosamine amino sugar and an oleandrose sugar. It targets the 50S ribosomal subunit to prevent protein synthesis.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35952":{"category_aro_accession":"0000034","category_aro_cvterm_id":"35952","category_aro_name":"streptogramin A antibiotic","category_aro_description":"Streptogramin A antibiotics are cyclic polyketide peptide hybrids that bind to the ribosomal peptidyl transfer centre. Structural variation arises from substituting a proline for its desaturated derivative and by its substitution for Ala or Cys. Used alone, streptogramin A antibiotics are bacteriostatic, but is bactericidal when used with streptogramin B antibiotics.","category_aro_class_name":"Drug Class"},"35967":{"category_aro_accession":"0000050","category_aro_cvterm_id":"35967","category_aro_name":"streptogramin B antibiotic","category_aro_description":"Streptogramin B antibiotics are are cyclic hepta- or hexa-depsipeptides.  Type B streptogramins block the peptide exit tunnel of the 50S bacterial ribosome. The general composition of group B streptogramins is 3-hydroxypicolinic acid-L-Thr-D-aminobutyric acid (or D-Ala)-L-Pro-L-Phe (or 4-N-,N-(dimethylamino)-L-Phe)-X-L-phenylglycine. Used alone, streptogramin B antibiotics are bacteriostatic, but is bactericidal when used with streptogramin A antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1435":{"model_id":"1435","model_name":"cmlA6","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"728":{"protein_sequence":{"accession":"AAK52606.1","sequence":"MRSKNFSWRYSLAATVLLLSPFDLLASLGMDMYLPAVPFMPNALGTTASTIQLTLTTYLVMIGAGQLLFGPLSDRLGRRPVLLGGGLAYVVASMGLALTSSAEVFLGLRILQACGASACLVSTFATVRDIYAGREESNVIYGILGSMLAIVPAVGPLLGALVDMWLGWRAIFAFLGLGMIAASAAAWRFWPETRVQRVAGLQWSQLLLPVKCLNFWLYTLCYAAGMGSFFVFFSIAPGLMMGRQGVSQLGFSLLFATVAIAMVFTARFMGRVIPKWGSPSVLRMGMGCLIAGAVLLAITEIWALQSVLGFIAPMWLVGIGVATAVSVAPNGALRGFDHVAGTVTAVYFCLGGVLLGSIGTLIISLLPRNTAWPVVVYCLTLATVVLGLSCVSRVKGSRGQGEHDVVALQSAESTSNPNR"},"dna_sequence":{"accession":"AF294653.1","fmin":"2749","fmax":"4009","strand":"+","sequence":"GTGCGCTCAAAAAACTTTAGTTGGCGGTACTCCCTTGCCGCCACGGTGTTGTTGTTATCACCGTTCGATTTATTGGCATCACTCGGCATGGACATGTACTTGCCAGCAGTGCCGTTTATGCCAAACGCGCTTGGTACGACAGCGAGCACAATTCAGCTTACGCTGACAACGTACTTGGTCATGATTGGTGCCGGTCAGCTCTTGTTTGGACCGCTATCGGACCGACTGGGGCGCCGCCCCGTTCTACTGGGAGGTGGCCTCGCCTACGTTGTGGCGTCAATGGGCCTCGCTCTTACGTCATCGGCTGAAGTCTTTCTGGGGCTTCGGATTCTTCAGGCTTGTGGTGCCTCGGCGTGCCTTGTTTCCACATTTGCAACAGTACGTGACATTTACGCAGGTCGCGAGGAAAGTAATGTCATTTACGGCATACTCGGATCCATGCTGGCCATAGTCCCGGCGGTAGGCCCATTGCTCGGAGCGCTCGTCGACATGTGGCTTGGGTGGCGGGCTATCTTTGCGTTTCTAGGTTTGGGCATGATCGCTGCATCTGCAGCAGCGTGGCGATTCTGGCCTGAAACCCGGGTGCAACGAGTTGCGGGCTTGCAATGGTCGCAGCTGCTACTCCCCGTTAAGTGCCTGAACTTCTGGTTGTACACGTTGTGTTACGCCGCTGGAATGGGTAGCTTCTTCGTCTTTTTCTCCATTGCGCCCGGACTAATGATGGGCAGGCAAGGTGTGTCTCAGCTTGGCTTCAGCCTGCTGTTCGCCACAGTGGCAATTGCCATGGTGTTTACGGCTCGTTTTATGGGGCGTGTGATACCCAAGTGGGGCAGCCCAAGTGTCTTGCGAATGGGAATGGGATGCCTGATAGCTGGAGCAGTATTGCTTGCCATCACCGAAATATGGGCTTTGCAGTCCGTGTTAGGCTTTATTGCTCCAATGTGGCTAGTGGGTATTGGTGTCGCCACAGCGGTATCTGTGGCGCCCAATGGCGCTCTTCGAGGATTCGACCATGTTGCTGGAACGGTCACGGCAGTCTACTTCTGCTTGGGCGGTGTACTGCTAGGAAGCATCGGAACGTTGATCATTTCGCTGTTGCCGCGCAACACGGCTTGGCCGGTTGTCGTGTACTGTTTGACCCTTGCAACAGTCGTGCTCGGTCTGTCTTGTGTTTCCCGAGTGAAGGGCTCTCGCGGCCAGGGGGAGCATGATGTGGTCGCGCTACAAAGTGCGGAAAGTACATCAAATCCCAATCGTTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002696","ARO_id":"39130","ARO_name":"cmlA6","CARD_short_name":"cmlA6","ARO_description":"cmlA6 is a plasmid-encoded chloramphenicol exporter that is found in Pseudomonas aeruginosa.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1436":{"model_id":"1436","model_name":"TEM-40","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1247":{"protein_sequence":{"accession":"CBX53726.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMISTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"FR717535.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATAAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000910","ARO_id":"37290","ARO_name":"TEM-40","CARD_short_name":"TEM-40","ARO_description":"TEM-40 is an inhibitor-resistant beta-lactamase that has been found in clinical isolates.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1438":{"model_id":"1438","model_name":"SHV-19","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8843":{"protein_sequence":{"accession":"HBU8935839.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEAFPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"DAGGWD010000033.1","fmin":"85","fmax":"946","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGTTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001077","ARO_id":"37457","ARO_name":"SHV-19","CARD_short_name":"SHV-19","ARO_description":"SHV-19 is a broad-spectrum beta-lactamase that has been found in clinical isolates.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1439":{"model_id":"1439","model_name":"SHV-80","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"8142":{"protein_sequence":{"accession":"CAJ47135.2","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPTGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AM176555.2","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCACAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGCATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001134","ARO_id":"37514","ARO_name":"SHV-80","CARD_short_name":"SHV-80","ARO_description":"SHV-80 is a broad-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1440":{"model_id":"1440","model_name":"CTX-M-103","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1026":{"protein_sequence":{"accession":"CDG50843.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGNGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"HG423149.1","fmin":"39","fmax":"915","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAACGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001962","ARO_id":"38362","ARO_name":"CTX-M-103","CARD_short_name":"CTX-M-103","ARO_description":"CTX-M-103 is a beta-lactamase found in Escherichia coli.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1442":{"model_id":"1442","model_name":"mdtN","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"4705":{"protein_sequence":{"accession":"BAE78084.1","sequence":"MESTPKKAPRSKFPALLVVALALVALVFVIWRVDSAPSTNDAYASADTIDVVPEVSGRIVELAVTDNQAVKQGDLLFRIDPRPYEANLAKAEASLAALDKQIMLTQRSVDAQQFGADSVNATVEKARAAAKQATDTLRRTEPLLKEGFVSAEDVDRARTAQRAAEADLNAVLLQAQSAASAVSGVDALVAQRAAVEADIALTKLHLEMATVRAPFDGRVISLKTSVGQFASAMRPIFTLIDTRHWYVIANFRETDLKNIRSGTPATIRLMSDSGKTFEGKVDSIGYGVLPDDGGLVLGGLPKVSRSINWVRVAQRFPVKIMVDKPDPEMFRIGASAVANLEPQ"},"dna_sequence":{"accession":"AP009048.1","fmin":"4306556","fmax":"4307588","strand":"-","sequence":"ATGGAAAGTACGCCGAAAAAAGCTCCTCGCAGTAAATTCCCTGCTCTGTTAGTGGTTGCGTTGGCGCTGGTTGCCCTTGTTTTCGTTATCTGGCGCGTAGACAGTGCGCCATCAACTAATGACGCTTACGCGTCAGCAGATACCATTGATGTGGTACCGGAAGTCAGCGGCCGCATTGTAGAACTGGCGGTCACCGACAACCAGGCAGTCAAACAGGGCGATTTGCTGTTCCGCATCGACCCGCGCCCGTACGAAGCCAATCTGGCGAAAGCTGAAGCCTCCCTCGCGGCGCTGGATAAGCAAATTATGCTCACCCAGCGTAGCGTTGACGCGCAACAGTTTGGTGCCGACTCGGTTAATGCCACGGTAGAAAAAGCCCGTGCCGCCGCGAAACAGGCCACAGATACATTACGCCGCACCGAGCCATTACTGAAAGAAGGTTTTGTCTCAGCGGAAGATGTTGACCGTGCAAGAACGGCGCAGCGCGCCGCAGAAGCGGATCTTAATGCCGTATTGTTACAGGCGCAGTCAGCCGCCAGCGCCGTCAGCGGCGTGGATGCATTAGTTGCCCAGCGTGCGGCGGTCGAAGCGGATATTGCCCTGACCAAACTGCATCTGGAAATGGCGACCGTTCGCGCGCCGTTTGATGGCCGGGTCATTTCCCTCAAAACCTCCGTCGGGCAATTTGCTTCTGCCATGCGCCCTATTTTTACCCTAATCGACACTCGTCACTGGTATGTGATCGCCAACTTCCGCGAAACCGATCTGAAAAATATTCGCTCAGGTACACCCGCAACGATTCGCCTGATGAGTGACAGCGGCAAAACCTTCGAGGGTAAAGTGGATTCGATTGGCTACGGCGTGCTACCGGATGACGGCGGCCTGGTGCTGGGCGGCCTGCCGAAAGTGTCTCGTTCTATTAACTGGGTCCGCGTTGCCCAGCGTTTTCCGGTCAAAATCATGGTCGATAAACCTGACCCGGAAATGTTCCGCATCGGCGCTTCGGCAGTCGCTAATCTTGAGCCGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36839","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. W3110","NCBI_taxonomy_id":"316407"}}}},"ARO_accession":"3003548","ARO_id":"40150","ARO_name":"mdtN","CARD_short_name":"mdtN","ARO_description":"Multidrug resistance efflux pump. Could be involved in resistance to puromycin, acriflavine and tetraphenylarsonium chloride.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35963":{"category_aro_accession":"0000045","category_aro_cvterm_id":"35963","category_aro_name":"acriflavine","category_aro_description":"Acriflavine is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish.","category_aro_class_name":"Antibiotic"},"35965":{"category_aro_accession":"0000047","category_aro_cvterm_id":"35965","category_aro_name":"puromycin","category_aro_description":"Puromycin is an aminonucleoside antibiotic, derived from Streptomyces alboniger, that causes premature chain termination during ribosomal protein translation.","category_aro_class_name":"Antibiotic"},"36174":{"category_aro_accession":"3000034","category_aro_cvterm_id":"36174","category_aro_name":"nucleoside antibiotic","category_aro_description":"Nucleoside antibiotics are made of modified nucleosides and nucleotides with wide-ranging activities and means of antibacterial effects. This drug class includes aminonucleoside antibiotics, which contain an amino group.","category_aro_class_name":"Drug Class"},"43746":{"category_aro_accession":"3005386","category_aro_cvterm_id":"43746","category_aro_name":"disinfecting agents and antiseptics","category_aro_description":"Disinfectants that can also interact with antimicrobial resistance mechanisms, e.g. molecule efflux, and thus are the targets of disinfectant resistance.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1443":{"model_id":"1443","model_name":"CARB-7","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1814":{"protein_sequence":{"accession":"AAM74565.1","sequence":"MKSLLVFALLMPSVVFASSSKFQSVEQEIKGIESSLSARIGVAILDTQNGESWDYNGDQRFPLTSTFKTIACAKLLYDAEHGKVNLNSTVEIKKADLVTYSPVLEKQVGKPITLSDACLATMTTSDNTAANIVINAVGDPKSITDFLRQIGDKETRLDRVEPELNEGKLGDLRDTTTPNAITSTLNQLLFGSTLSEASQKKLESWMVNNQVTGNLLRSVLPVKWSIADRSGAGGFGARSITAIVWSEEKKPIIVSIYLAQTEASMAERNDAIVKIGRSIFEVYTSQSR"},"dna_sequence":{"accession":"AF409092.1","fmin":"887","fmax":"1754","strand":"+","sequence":"ATGAAGTCTTTGTTGGTATTTGCGCTTTTAATGCCATCTGTAGTTTTTGCAAGCAGTTCAAAATTTCAATCAGTTGAACAAGAAATTAAGGGAATTGAGTCTTCACTCTCTGCTCGTATAGGAGTCGCCATTTTGGATACTCAAAATGGCGAAAGCTGGGATTATAATGGTGATCAACGATTTCCATTAACAAGTACTTTCAAAACAATAGCTTGTGCTAAGTTGCTGTATGATGCAGAGCATGGGAAAGTTAATCTCAATAGTACAGTTGAGATTAAGAAAGCAGATCTTGTTACGTATTCGCCTGTATTAGAAAAGCAAGTAGGTAAACCAATAACGCTCTCTGATGCATGCCTTGCTACTATGACAACAAGCGACAATACAGCAGCCAATATTGTTATAAATGCTGTCGGTGATCCTAAAAGCATTACTGATTTTCTGAGACAAATTGGTGACAAAGAAACTCGTCTAGATCGTGTCGAGCCTGAGCTCAATGAAGGTAAACTCGGTGATTTGAGGGATACGACAACGCCTAATGCAATAACCAGCACGTTAAATCAATTATTATTTGGTTCCACATTATCTGAAGCTAGTCAGAAAAAATTAGAGTCTTGGATGGTGAACAATCAAGTTACGGGTAATTTATTGAGGTCAGTATTGCCAGTGAAGTGGAGTATTGCTGATCGCTCAGGAGCAGGTGGATTTGGTGCTAGGAGTATTACAGCGATTGTGTGGAGTGAAGAAAAAAAACCGATTATCGTAAGTATTTATCTAGCTCAAACCGAGGCTTCAATGGCAGAACGAAATGATGCGATAGTTAAGATTGGTCGTTCAATTTTTGAAGTTTATACATCACAGTCGCGTTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36920","NCBI_taxonomy_name":"Vibrio cholerae non-O1\/non-O139","NCBI_taxonomy_id":"156539"}}}},"ARO_accession":"3002246","ARO_id":"38646","ARO_name":"CARB-7","CARD_short_name":"CARB-7","ARO_description":"CARB-7 is a beta-lactamase found in Vibrio cholerae.","ARO_category":{"36230":{"category_aro_accession":"3000091","category_aro_cvterm_id":"36230","category_aro_name":"CARB beta-lactamase","category_aro_description":"CARB beta-lactamases are class A lactamases that can hydrolyze carbenicillin. Many of the PSE beta-lactamases have been renamed as CARB-lactamases with the notable exception of PSE-2 which is now OXA-10.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1444":{"model_id":"1444","model_name":"IND-12","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1826":{"protein_sequence":{"accession":"ADK25051.1","sequence":"MKKSIQLLMMSMFLSPLINAQVKDFVIEPPVKPNLYLYKSFGVFGGKEYSANAVYLTTKKGVVLFDVPWQKEQYQTLMDTIQKRHHLPVIAVFATHSHDDRAGDLSFYNQKGIKTYATAKTNELLKKDGKATSTEIIKTGKPYKIGGEEFMVDFLGEGHTVDNVVVWFPKYKVLDGGCLVKSRTATDLGYTGEANVKQWPETMRKLKTKYAQATLVIPGHDEWKGGGHVQHSLDLLDKNKKPE"},"dna_sequence":{"accession":"HM245380.1","fmin":"27","fmax":"759","strand":"+","sequence":"ATGAAAAAAAGTATTCAGCTTTTGATGATGTCAATGTTTTTAAGCCCATTGATCAATGCCCAGGTTAAAGATTTTGTAATTGAGCCGCCTGTTAAACCCAACCTGTATCTTTATAAAAGTTTCGGAGTTTTCGGGGGTAAAGAATATTCTGCCAATGCTGTATATCTTACCACTAAGAAAGGAGTTGTCTTATTTGATGTCCCATGGCAAAAGGAACAATATCAAACCCTTATGGACACCATACAAAAGCGTCATCACCTTCCTGTAATTGCTGTATTTGCCACCCACTCTCATGATGACAGAGCGGGTGATCTAAGCTTTTACAATCAAAAAGGAATTAAAACATATGCGACCGCCAAGACCAATGAACTGTTGAAAAAAGACGGAAAAGCAACCTCAACCGAAATTATAAAAACAGGAAAACCTTACAAAATTGGTGGTGAAGAATTTATGGTAGACTTTCTTGGAGAAGGACATACAGTTGATAATGTTGTTGTATGGTTCCCCAAATATAAAGTACTGGACGGAGGATGTCTTGTAAAAAGCAGGACAGCCACTGACCTGGGATATACCGGTGAAGCAAATGTAAAACAATGGCCGGAAACCATGCGAAAACTAAAAACGAAATATGCTCAGGCCACTCTGGTAATCCCGGGACACGACGAATGGAAAGGCGGTGGCCATGTACAGCATTCTCTGGATCTTCTGGATAAGAATAAAAAGCCGGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36916","NCBI_taxonomy_name":"Chryseobacterium indologenes","NCBI_taxonomy_id":"253"}}}},"ARO_accession":"3002268","ARO_id":"38668","ARO_name":"IND-12","CARD_short_name":"IND-12","ARO_description":"IND-12 is a beta-lactamase found in Escherichia coli.","ARO_category":{"36199":{"category_aro_accession":"3000060","category_aro_cvterm_id":"36199","category_aro_name":"IND beta-lactamase","category_aro_description":"IND beta-lactamases are class B carbapenem-hydrolyzing beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1446":{"model_id":"1446","model_name":"PDC-6","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"1771":{"protein_sequence":{"accession":"ACQ82811.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFTATLAGYALTQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"FJ666069.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGACCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTATGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002505","ARO_id":"38905","ARO_name":"PDC-6","CARD_short_name":"PDC-6","ARO_description":"PDC-6 is a beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1447":{"model_id":"1447","model_name":"OKP-A-10","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"794":{"protein_sequence":{"accession":"CAJ19608.1","sequence":"MRCVRLCLIPLIAALPLAVFASPPPLEQITLSESQLAGRVGYVEMDLASGRTLAAWRASERFPLMSTFKVLLCGAVLARVDAGDEQLDRRIRYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAGNLLLKSVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDVRDTTTPASMAATLRKLLTSHALSDRSQQQLLQWMVDDQVAGPLIRAVLPAGWFIADKTGAGERGSRGIVALLGPNGKAERIVMIYLRDTPATMAERNQQIAKIGAALIEHWQR"},"dna_sequence":{"accession":"AM051149.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTGTGTTCGCCTGTGCCTTATCCCCCTGATTGCCGCCCTGCCACTGGCGGTATTCGCCAGCCCTCCGCCGCTTGAGCAAATTACACTCAGCGAAAGTCAGCTGGCGGGCCGCGTGGGCTATGTTGAAATGGATCTGGCGAGCGGCCGCACGCTGGCCGCCTGGCGCGCCAGTGAGCGCTTTCCGCTGATGAGCACCTTTAAAGTGCTGCTCTGCGGCGCGGTGCTGGCCCGGGTGGATGCCGGAGACGAACAGCTGGATCGGCGGATCCGCTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGCCGACGGGATGACCGTTGGCGAACTCTGCGCCGCCGCCATCACCATGAGCGACAACAGCGCCGGCAATCTGCTGTTGAAGAGCGTTGGCGGCCCCGCGGGATTGACCGCTTTTCTGCGCCAGATCGGTGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAGCTCAATGAAGCGCTTCCCGGCGACGTGCGCGACACCACCACCCCAGCCAGCATGGCCGCCACCCTGCGCAAGCTGCTAACCAGCCACGCGCTGAGCGACCGTTCGCAGCAGCAGCTGCTGCAGTGGATGGTGGACGATCAGGTGGCCGGTCCGCTGATCCGCGCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAAACCGGGGCCGGCGAGCGGGGCTCACGCGGCATTGTCGCCCTGCTCGGCCCGAACGGCAAAGCGGAGCGCATCGTGATGATCTATCTGCGGGATACGCCGGCGACCATGGCCGAGCGTAACCAGCAGATCGCCAAAATAGGCGCGGCGCTGATCGAGCACTGGCAGCGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002427","ARO_id":"38827","ARO_name":"OKP-A-10","CARD_short_name":"OKP-A-10","ARO_description":"OKP-A-10 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"38817":{"category_aro_accession":"3002417","category_aro_cvterm_id":"38817","category_aro_name":"OKP beta-lactamase","category_aro_description":"OKP beta-lactamases are chromosomal class A beta-lactamase that confer resistance to penicillins and early cephalosporins in Klebsiella pneumoniae. OKP beta-lactamases can be subdivided into two groups: OKP-A and OKP-B which diverge by about 4.2%.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1448":{"model_id":"1448","model_name":"SHV-26","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1789":{"protein_sequence":{"accession":"AAF36719.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMTATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AF227204.1","fmin":"73","fmax":"934","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGACCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGCATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001084","ARO_id":"37464","ARO_name":"SHV-26","CARD_short_name":"SHV-26","ARO_description":"SHV-26 is an inhibitor-resistant beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1449":{"model_id":"1449","model_name":"OXA-59","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1304":{"protein_sequence":{"accession":"CAG15145.1","sequence":"MKFRHALSSAFVLLGCIAASAHAKTICTAIADAGTGKLLVQDGDCGRRASPASTFKIAISLMGYDAGFLRNEHDPVLPYRDSYIAWGGEAWKQPTDPTRWLKYSVVWYSQQVAHHLGAQRFAQYAKAFGYGNADVSGDPGQNNGLDRAWIGSSLQISPLEQLEFLGKMLNRKLPVSPTAVDMTERIVESTTLADGTVVHGKTGVSYPLLADGTRDWARGSGWFVGWIVRGKQTLVFARLTQDERKQPVSAGIRTREAFLRDLPRLLAAR"},"dna_sequence":{"accession":"AJ632249.1","fmin":"0","fmax":"810","strand":"+","sequence":"ATGAAATTCCGACACGCGCTGTCGAGCGCATTCGTTTTGCTGGGTTGCATCGCCGCGTCGGCGCATGCGAAGACGATCTGCACGGCGATCGCCGATGCGGGCACGGGCAAGCTGCTGGTGCAGGACGGCGATTGCGGCCGCCGCGCATCGCCCGCGTCGACGTTCAAGATCGCGATCAGCCTGATGGGCTACGACGCAGGCTTCCTGCGCAACGAGCATGACCCGGTGCTGCCGTATCGCGACAGTTACATCGCGTGGGGTGGCGAAGCATGGAAGCAGCCGACCGATCCGACGCGCTGGCTCAAGTATTCGGTCGTGTGGTATTCGCAGCAGGTGGCGCACCATCTCGGCGCGCAGCGCTTCGCGCAGTATGCGAAGGCGTTCGGCTACGGCAATGCGGACGTGTCCGGCGATCCCGGCCAGAACAACGGCCTCGATCGCGCGTGGATCGGCTCGTCGCTGCAGATCTCGCCGCTCGAACAATTGGAATTCCTCGGCAAGATGCTCAATCGCAAGCTGCCCGTGTCGCCCACAGCCGTCGACATGACGGAGCGGATCGTCGAATCGACGACGCTTGCCGACGGAACGGTGGTGCACGGCAAGACCGGCGTGTCCTATCCGCTGCTGGCCGACGGCACACGCGACTGGGCGCGTGGATCCGGCTGGTTCGTCGGCTGGATCGTGCGTGGCAAGCAGACGCTGGTGTTCGCGCGCCTCACGCAGGACGAGCGCAAGCAGCCCGTTTCAGCCGGCATACGGACGCGCGAGGCCTTCCTGCGCGACTTGCCCCGGCTTCTCGCCGCGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36923","NCBI_taxonomy_name":"Burkholderia pseudomallei","NCBI_taxonomy_id":"28450"}}}},"ARO_accession":"3001772","ARO_id":"38172","ARO_name":"OXA-59","CARD_short_name":"OXA-59","ARO_description":"OXA-59 is a beta-lactamase found in Burkholderia pseudomallei.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46507":{"category_aro_accession":"3007718","category_aro_cvterm_id":"46507","category_aro_name":"OXA-42-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-42.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1451":{"model_id":"1451","model_name":"MIR-17","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"1658":{"protein_sequence":{"accession":"CEA29752.1","sequence":"MMTKSLSCALLLSVTSAAFAAPMSEKQLAEVVERTVTPLMNAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEVALGDPVAKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDTASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMSYEQAMTTRVFKPLKLDHTWINVPKAEEAHYAWGYREGKAVHVSPGMLDAEAYGVKTNVKDMASWVIANMKPDSLQAPSLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVGGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILDALQ"},"dna_sequence":{"accession":"LN515535.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGACAAAATCCCTAAGCTGTGCCCTGCTGCTCAGCGTCACCAGCGCTGCATTCGCCGCACCGATGTCCGAAAAACAGCTGGCTGAGGTGGTGGAACGTACCGTTACGCCGCTGATGAACGCGCAGGCCATTCCGGGTATGGCGGTGGCGGTAATTTATCAGGGTCAGCCACACTACTTTACCTTCGGTAAAGCCGATGTTGCGGCGAACAAACCCGTCACCCCGCAAACCCTGTTTGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTACTGGGCGGCGATGCCATTGCCCGGGGTGAAGTAGCGCTGGGCGATCCGGTAGCAAAATACTGGCCTGAGCTCACGGGCAAGCAGTGGCAGGGCATTCGCATGCTGGATCTGGCAACCTATACCGCAGGCGGTCTGCCGTTACAGGTGCCGGATGAGGTCACGGATACCGCTTCTCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCGGGCACCACGCGTCTTTACGCTAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTTAAACCTTCCGGCATGAGCTATGAGCAGGCCATGACGACGCGGGTCTTTAAACCCCTCAAGCTGGACCATACCTGGATTAACGTCCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGATACCGTGAGGGTAAAGCGGTCCACGTTTCGCCAGGGATGCTGGACGCGGAAGCCTATGGCGTAAAAACTAACGTGAAGGATATGGCGAGCTGGGTGATAGCCAACATGAAGCCGGATTCTCTTCAGGCTCCCTCACTCAAGCAAGGCATTGCTCTGGCGCAGTCTCGCTACTGGCGCGTGGGGGCTATGTATCAGGGGTTAGGCTGGGAGATGCTCAACTGGCCGGTCGATGCCAAAACCGTCGTCGGAGGCAGTGATAACAAGGTGGCGCTGGCACCATTGCCCGTGGCAGAAGTGAATCCACCCGCGCCGCCGGTCAAGGCCTCCTGGGTCCATAAAACAGGCTCGACGGGCGGGTTTGGCAGCTACGTGGCATTTATTCCTGAAAAGCAGCTCGGCATTGTGATGCTCGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCGTATCCTCGACGCGCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3003173","ARO_id":"39750","ARO_name":"MIR-17","CARD_short_name":"MIR-17","ARO_description":"MIR-17 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36197":{"category_aro_accession":"3000058","category_aro_cvterm_id":"36197","category_aro_name":"MIR beta-lactamase","category_aro_description":"MIR beta-lactamases are plasmid-mediated beta-lactamases that confer resistance to oxyimino- and alpha-methoxy beta-lactams.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1452":{"model_id":"1452","model_name":"TEM-216","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1494":{"protein_sequence":{"accession":"AHJ78622.1","sequence":"MSIQHFRVSLIPFFAAFCLPVFAHPETLVKVKDAEDQLGAPVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"KF944358.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCTCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACCAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001393","ARO_id":"37793","ARO_name":"TEM-216","CARD_short_name":"TEM-216","ARO_description":"TEM-216 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1454":{"model_id":"1454","model_name":"CMY-112","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"781":{"protein_sequence":{"accession":"AIT76090.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAIIYEEKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWRGISLLHLATYTAGGLPLQIPDEVTDKAALLRFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQSEQKNYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIELAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPARVEAAWRILEKLQ"},"dna_sequence":{"accession":"KM087837.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCGCTGCTGCTGACAGCCTCTTTCTCCACGTTTGCTGCCGCAAAAACAGAACAACAAATTGCCGATATCGTTAACCGCACCATCACACCACTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTGGCGATTATCTACGAGGAGAAACCTTATTACTTTACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAATTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGACGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCGGGGTATCAGCCTGCTGCACTTAGCCACCTATACAGCGGGTGGCCTACCGCTGCAGATCCCCGATGAAGTTACGGATAAAGCCGCATTACTGCGCTTTTATCAAAACTGGCAACCACAATGGACTCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGTGCGCTGGCGGTGAAACCTTCAGGTATGAGCTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAAAGCGAACAAAAAAATTATGCCTGGGGCTATCGCGAAGGGAAGCCTGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATCGATATGGCCCGCTGGGTTCAGGCCAACATGGACGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGAGCTTGCGCAGTCTCGTTACTGGCGTATTGGTGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCAGCACCTGCCGTGAAAGCCTCATGGGTGCATAAAACGGGATCCACAGGTGGATTTGGCAGCTACGTTGCCTTCGTTCCAGAAAAAAACCTTGGCATAGTGATGCTGGCAAACAAAAGCTACCCCAACCCGGCTCGCGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002123","ARO_id":"38523","ARO_name":"CMY-112","CARD_short_name":"CMY-112","ARO_description":"CMY-112 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1455":{"model_id":"1455","model_name":"IND-9","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1417":{"protein_sequence":{"accession":"ACZ65153.1","sequence":"MKKSIQFFIVSLLLSPFANAQVKDFVIEPPISKNLYIYKTFGVFGGKEYSANAVYLVTKKGVVLFDVPWEKVQYQSLMDTIKKRHNLPVVAVFATHSHDDRAGDLSFFNKKGIKTYATAKTNELLKKEGKAVSSNIINTGKAYHIGGEEFVVDFIGEGHTVDNVVVWFPKYKVLDGGCLVKSTSATDLGYIKEANVEQWPQTMNTLKSKYSQATLIIPGHDEWKGGGHVEHTLELLNKK"},"dna_sequence":{"accession":"GU186045.1","fmin":"34","fmax":"754","strand":"+","sequence":"ATGAAAAAAAGCATACAGTTTTTTATTGTTTCCCTATTATTAAGTCCGTTTGCTAATGCTCAGGTAAAGGATTTTGTAATAGAACCTCCTATCAGCAAGAACTTATATATTTATAAAACTTTTGGTGTATTCGGAGGAAAAGAATATTCTGCCAACGCTGTTTACCTTGTCACAAAAAAAGGAGTAGTCCTGTTTGATGTTCCCTGGGAAAAAGTTCAGTACCAAAGCTTGATGGATACCATAAAAAAACGTCATAATTTACCTGTAGTGGCAGTATTTGCTACCCATTCTCATGATGACAGAGCCGGAGATTTAAGCTTCTTCAACAAAAAAGGGATTAAGACCTATGCCACGGCAAAAACCAATGAGTTATTGAAAAAAGAAGGTAAAGCGGTGTCCAGCAATATTATAAATACAGGGAAAGCTTATCATATAGGCGGAGAAGAATTTGTGGTTGATTTTATTGGAGAAGGACATACCGTAGATAATGTAGTGGTATGGTTTCCAAAATATAAAGTTCTTGATGGCGGCTGCTTAGTAAAAAGTACTTCTGCAACAGATTTAGGATATATCAAGGAAGCAAACGTTGAACAATGGCCACAAACTATGAATACTTTAAAATCCAAATACTCTCAGGCAACCTTAATCATTCCGGGACATGACGAATGGAAAGGCGGCGGACATGTAGAACATACATTAGAGCTTTTGAATAAAAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36916","NCBI_taxonomy_name":"Chryseobacterium indologenes","NCBI_taxonomy_id":"253"}}}},"ARO_accession":"3002265","ARO_id":"38665","ARO_name":"IND-9","CARD_short_name":"IND-9","ARO_description":"IND-9 is a beta-lactamase found in Escherichia coli.","ARO_category":{"36199":{"category_aro_accession":"3000060","category_aro_cvterm_id":"36199","category_aro_name":"IND beta-lactamase","category_aro_description":"IND beta-lactamases are class B carbapenem-hydrolyzing beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1456":{"model_id":"1456","model_name":"IMP-15","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"772":{"protein_sequence":{"accession":"AAT49070.1","sequence":"MNKLSVFFMFMFCSITAAGESLPDLKIEKLDEGVYVHTSFEEVNGWGVVPKHGLVVLVNTEAYLIDTPFTAKDTEKLVTWFVERGYKIKGSISSHFHSDSTGGIEWLNSQSIPTYASELTNELLKKDGKVQAKNSFSGGSYWLVNNKIEVFYPGPGHTPDNVVVWLPENRVLFGGCFVKPYGLGNLGDANLEAWPKSAKILMSKYGKAKLVVSSHSETGNASLLKLTWEQAVKGLKESKKPSLPSN"},"dna_sequence":{"accession":"AY553333.1","fmin":"113","fmax":"854","strand":"+","sequence":"ATGAACAAGTTATCTGTATTCTTTATGTTTATGTTTTGTAGCATTACTGCCGCAGGAGAGTCTTTGCCAGATTTAAAAATTGAGAAGCTTGACGAAGGTGTTTATGTTCATACTTCGTTTGAAGAAGTTAACGGTTGGGGTGTTGTTCCTAAACACGGCTTGGTGGTTCTTGTAAATACTGAGGCCTATCTGATTGACACTCCATTTACGGCAAAAGATACTGAAAAGTTAGTCACTTGGTTTGTGGAGCGCGGCTATAAAATAAAAGGCAGTATTTCCTCTCATTTTCATAGCGACAGCACGGGCGGAATAGAGTGGCTTAATTCTCAATCTATCCCCACGTATGCATCTGAATTAACAAATGAACTTCTTAAAAAAGACGGTAAGGTACAAGCTAAAAATTCATTTAGCGGAGGTAGCTATTGGCTAGTTAATAATAAGATTGAAGTTTTTTATCCTGGTCCAGGGCACACTCCAGATAACGTAGTGGTTTGGCTACCTGAAAATAGAGTTTTGTTCGGTGGTTGTTTTGTTAAACCGTACGGTCTTGGTAATTTGGGTGACGCAAATTTAGAAGCTTGGCCAAAGTCCGCCAAAATATTAATGTCTAAATATGGTAAAGCAAAGTTGGTTGTTTCAAGTCATAGTGAAACTGGGAACGCATCACTCTTGAAACTTACTTGGGAGCAGGCTGTTAAAGGGCTAAAAGAAAGTAAAAAACCATCACTGCCAAGTAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002206","ARO_id":"38606","ARO_name":"IMP-15","CARD_short_name":"IMP-15","ARO_description":"IMP-15 is a beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1457":{"model_id":"1457","model_name":"CTX-M-13","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8220":{"protein_sequence":{"accession":"AAF72531.1","sequence":"MVTKRMQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTKDNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFAREIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"AF252623.2","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTGACAAAGAGAATGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCAAAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGAGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGACTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001876","ARO_id":"38276","ARO_name":"CTX-M-13","CARD_short_name":"CTX-M-13","ARO_description":"CTX-M-13 is a beta-lactamase found in the Enterobacteriaceae family.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1458":{"model_id":"1458","model_name":"TEM-157","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1491":{"protein_sequence":{"accession":"ABI81768.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRIDAGQEQLGRRIHYSQSDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPVAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"DQ909059.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTCCGAGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTATTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAGTGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGTAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3001023","ARO_id":"37403","ARO_name":"TEM-157","CARD_short_name":"TEM-157","ARO_description":"TEM-157 is an extended-spectrum beta-lactamase found in Enterobacter cloacae.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1459":{"model_id":"1459","model_name":"CTX-M-78","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8196":{"protein_sequence":{"accession":"CAQ42481.2","sequence":"MMRKSVRRAILMTTACVSLLLASVPLYAQANDIQQKLAALEKSSGGRLGVALINTADNTQTLYRADERFAMCSTSKVMAAAAVLKQSETQKDLLSQRVEIKSSDLINYNPIAEKHVNGTMTLGELSAAALQYSDNTAMNKLIAHLGGPGKVTAFARVIGDDTFRLDRTEPTLNTAIPGDPRDTTTPLAMAQTLRNLTLGNALGDTQRAQLVTWLKGNTTGAASIQAGLPTSWVVGDKTGSGDYGTTNDIAVIWPEGRAPLVLVTYFTQPEPKAESRRDVLAAAARIVTDGY"},"dna_sequence":{"accession":"AM982522.2","fmin":"0","fmax":"876","strand":"+","sequence":"ATGATGAGAAAAAGCGTAAGGCGGGCGATATTAATGACGACAGCCTGTGTTTCGCTGCTGTTGGCCAGTGTGCCGCTGTATGCCCAAGCGAACGATATTCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGGGGACGACTGGGTGTGGCGTTGATTAACACCGCCGATAACACGCAGACGCTCTACCGCGCCGACGAGCGTTTTGCTATGTGCAGCACCAGTAAAGTGATGGCGGCGGCGGCGGTGCTTAAGCAAAGTGAAACGCAAAAAGACTTACTGAGTCAGCGGGTTGAAATTAAGTCCTCAGACTTGATTAACTACAACCCAATCGCTGAAAAGCACGTCAATGGCACGATGACACTCGGGGAGCTGAGCGCGGCGGCGCTGCAGTACAGCGATAATACTGCCATGAATAAGCTGATTGCCCATCTCGGGGGGCCGGGTAAAGTGACGGCATTTGCTCGCGTGATTGGCGATGACACTTTCCGGCTCGATCGTACCGAGCCGACGCTCAACACCGCGATCCCCGGCGACCCGCGCGATACCACCACGCCGTTAGCGATGGCGCAGACTCTACGCAATCTCACATTGGGCAATGCCCTGGGTGACACTCAGCGTGCGCAGCTGGTGACGTGGCTGAAAGGCAACACCACCGGCGCTGCCAGCATTCAGGCAGGGCTACCCACATCGTGGGTTGTCGGGGATAAAACCGGCAGCGGCGATTATGGTACGACGAATGATATCGCGGTTATTTGGCCGGAAGGTCGCGCGCCGCTCGTTCTGGTGACTTACTTCACCCAGCCGGAGCCGAAGGCAGAGAGCCGTCGTGACGTGCTCGCTGCTGCCGCCAGAATAGTCACCGACGGTTATTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36929","NCBI_taxonomy_name":"Kluyvera georgiana","NCBI_taxonomy_id":"73098"}}}},"ARO_accession":"3001939","ARO_id":"38339","ARO_name":"CTX-M-78","CARD_short_name":"CTX-M-78","ARO_description":"CTX-M-78 is a beta-lactamase found in Kluyvera georgiana.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1460":{"model_id":"1460","model_name":"FosB3","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"250"}},"model_sequences":{"sequence":{"418":{"protein_sequence":{"accession":"ADX95999.1","sequence":"MIKGINHITYSVSNIAKSIEFYRDILGADILVESETLAYFNLGGIWLALNEEKNIPRSEIKYSYTHIAFTISDNDFEDWYNWLKENEVNILEGRDRDIRDKKSIYFTDLDGHKLELHTGSLEDRLSYYKEAKPHMNFYI"},"dna_sequence":{"accession":"HQ219726.1","fmin":"385","fmax":"805","strand":"+","sequence":"ATGATTAAAGGAATAAATCATATTACTTATTCGGTTTCTAATATAGCTAAATCAATTGAATTTTACAGAGATATTTTAGGGGCTGACATTTTAGTTGAAAGTGAGACCTTGGCCTATTTTAATTTAGGTGGTATATGGTTAGCTTTGAACGAAGAAAAAAATATTCCTAGAAGCGAAATTAAATATTCGTATACTCATATAGCATTTACAATTTCAGATAACGATTTTGAAGATTGGTATAACTGGTTGAAAGAAAATGAAGTAAATATTCTTGAAGGTAGAGATAGAGATATTAGAGATAAAAAATCAATATATTTCACTGATTTAGATGGTCATAAATTAGAATTGCATACAGGAAGTTTAGAAGATAGATTGAGTTATTATAAAGAGGCTAAACCTCATATGAATTTTTATATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36779","NCBI_taxonomy_name":"Enterococcus faecium","NCBI_taxonomy_id":"1352"}}}},"ARO_accession":"3002873","ARO_id":"39307","ARO_name":"FosB3","CARD_short_name":"FosB3","ARO_description":"A thiol transferase that leads to the resistance of fosfomycin in Enterococcus faecium. Contrasting FosA, FosB is dependent on the cofactor Magnesium (II) and uses either bacillithiol to open up the epoxide ring of fosfomycin.","ARO_category":{"36272":{"category_aro_accession":"3000133","category_aro_cvterm_id":"36272","category_aro_name":"fosfomycin thiol transferase","category_aro_description":"Catalyzes the addition of a thiol group from a nucleophilic molecule to fosfomycin.","category_aro_class_name":"AMR Gene Family"},"35944":{"category_aro_accession":"0000025","category_aro_cvterm_id":"35944","category_aro_name":"fosfomycin","category_aro_description":"Fosfomycin (also known as phosphomycin and phosphonomycin) is a broad-spectrum antibiotic produced by certain Streptomyces species. It is effective on gram positive and negative bacteria as it targets the cell wall, an essential feature shared by both bacteria. Its specific target is MurA (MurZ in E.coli), which attaches phosphoenolpyruvate (PEP) to UDP-N-acetylglucosamine, a step of commitment to cell wall synthesis. In the active site of MurA, the active cysteine molecule is alkylated which stops the catalytic reaction.","category_aro_class_name":"Antibiotic"},"45731":{"category_aro_accession":"3007149","category_aro_cvterm_id":"45731","category_aro_name":"phosphonic acid antibiotic","category_aro_description":"A group of antibiotics derived from phosphonic acids.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1345":{"model_id":"1345","model_name":"tet(K)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"850"}},"model_sequences":{"sequence":{"5182":{"protein_sequence":{"accession":"AAB28795.1","sequence":"MFSLYKKFKGLFYSVLFWLCILSFFSVLNEMVLNVSLPDIANHFNTTPGITNWVNTAYMLTFSIGTAVYGKLSDYINIKKLLIIGISLSCLGSLIAFIGHNHFFILIFGRLVQGVGSAAFPSLIMVVVARNITRKKQGKAFGFIGSIVALGEGLGPSIGGIIAHYIHWSYLLILPMITIVTIPFLIKVMVPGKSTKNTLDIVGIVLMSISIICFMLFTTNYNWTFLILFTIFFVIFIKHISRVSNPFINPKLGKNIPFMLGLFSGGLIFSIVAGFISMVPYMMKTIYHVNVATIGNSVIFPGTMSVIVFGYFGGFLVDRKGSLFVFILGSLSISISFLTIAFFVEFSMWLTTFMFIFVMGGLSFTKTVISKIVSSSLSEEEVASGMSLLNFTSFLSEGTGIAIVGGLLSLQLINRKLVLEFINYSSGVYSNILVAMAILIILCCLLTIIVFKRSEKQFE"},"dna_sequence":{"accession":"S67449.1","fmin":"0","fmax":"1380","strand":"+","sequence":"TTGTTTAGTTTATATAAAAAATTTAAAGGTTTGTTTTATAGCGTTTTATTTTGGCTTTGTATTCTTTCATTTTTTAGTGTATTAAATGAAATGGTTTTAAATGTTTCTTTACCTGATATTGCAAATCATTTTAATACTACTCCTGGAATTACAAACTGGGTAAACACTGCATATATGTTAACTTTTTCGATAGGAACAGCAGTATATGGAAAATTATCTGATTATATAAATATAAAAAAATTGTTAATTATTGGTATTAGTTTGAGCTGTCTTGGTTCATTGATTGCTTTTATTGGTCACAATCACTTTTTTATTTTGATTTTTGGTAGGTTAGTACAAGGAGTAGGATCTGCTGCATTCCCTTCACTGATTATGGTGGTTGTAGCTAGAAATATTACAAGAAAAAAACAAGGCAAAGCCTTTGGTTTTATAGGATCAATTGTAGCTTTAGGTGAAGGGTTAGGTCCTTCAATAGGGGGAATAATAGCACATTATATTCATTGGTCTTACCTACTTATACTTCCTATGATTACAATAGTAACTATACCTTTTCTTATTAAAGTAATGGTACCTGGTAAATCAACAAAAAATACATTAGATATCGTAGGTATTGTTTTAATGTCTATAAGTATTATATGTTTTATGTTATTTACGACAAATTATAATTGGACTTTTTTAATACTCTTCACAATCTTTTTTGTGATTTTTATTAAACATATTTCAAGAGTTTCTAACCCTTTTATTAATCCTAAACTAGGGAAAAACATTCCGTTTATGCTTGGTTTGTTTTCTGGTGGGCTAATATTTTCTATAGTAGCTGGTTTTATATCAATGGTGCCTTATATGATGAAAACTATTTATCATGTAAATGTAGCGACAATAGGTAATAGTGTTATTTTTCCTGGAACCATGAGTGTTATTGTTTTTGGTTATTTTGGTGGTTTTTTAGTGGATAGAAAAGGATCATTATTTGTTTTTATTTTAGGATCATTGTCTATCTCTATAAGTTTTTTAACTATTGCATTTTTTGTTGAGTTTAGTATGTGGTTGACTACTTTTATGTTTATATTTGTTATGGGCGGATTATCTTTTACTAAAACAGTTATATCAAAAATAGTATCAAGTAGTCTTTCTGAAGAAGAAGTTGCTTCTGGAATGAGTTTGCTAAATTTCACAAGTTTTTTATCAGAGGGAACAGGTATAGCAATTGTAGGAGGTTTATTGTCACTACAATTGATTAATCGTAAACTAGTTCTGGAATTTATAAATTATTCTTCTGGAGTGTATAGTAATATTCTTGTAGCCATGGCTATCCTTATTATTTTATGTTGTCTTTTGACGATTATTGTATTTAAACGTTCTGAAAAGCAGTTTGAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35508","NCBI_taxonomy_name":"Staphylococcus aureus","NCBI_taxonomy_id":"1280"}}}},"ARO_accession":"3000178","ARO_id":"36317","ARO_name":"tet(K)","CARD_short_name":"tet(K)","ARO_description":"TetK is a tetracycline efflux protein found in both Gram-negative (Haemophilus and Gallibacterium) and Gram-positive (many species, including mycobacteria) bacteria.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1461":{"model_id":"1461","model_name":"SHV-63","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"920":{"protein_sequence":{"accession":"ABY56290.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGENVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTNQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"EU342351.1","fmin":"172","fmax":"1033","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGAAAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAACCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGCATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001118","ARO_id":"37498","ARO_name":"SHV-63","CARD_short_name":"SHV-63","ARO_description":"SHV-63 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1462":{"model_id":"1462","model_name":"LRA-19","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1748":{"protein_sequence":{"accession":"ACH59005.1","sequence":"MNSEMSQTSFKIRILVTCLLSIAQLTMAQQVQVTEPPITNQDWVKPYPPFRIVGNLYYVGTYDLACYLIVTPQGNILINTGLASSAPMIEASIKALGFKFSDTKILLTTQAHYDHVGAMAAIKKSTNAQLMIDEKDSPVMADGGSSDYELFGSTGSTYEPVKADRLLKNGDKITLGGTTLVMLHHPGHTKGSCSFLFDVKDESKSYKVLIANMPSIITSKKFSDIPTYPGIAEDYTYTFDAMKKVHFDIWLSSHASQFGMHSKHKPGEAYNPGVFIDRAGYDKAVGDLEDKFSKKKQADK"},"dna_sequence":{"accession":"EU408359.1","fmin":"3791","fmax":"4694","strand":"+","sequence":"ATGAACTCAGAAATGTCTCAAACTTCTTTTAAAATCAGGATATTGGTGACCTGCCTCCTATCCATTGCCCAGTTAACAATGGCGCAACAAGTACAGGTAACTGAACCCCCGATCACAAATCAGGATTGGGTCAAACCCTATCCTCCATTCCGTATAGTCGGCAATTTGTATTATGTGGGCACTTACGATTTAGCCTGTTACCTCATTGTCACCCCACAGGGGAATATCCTTATCAATACAGGACTCGCTTCCTCCGCGCCTATGATCGAGGCAAGCATCAAAGCATTAGGCTTCAAGTTTTCCGACACGAAAATTCTGTTGACAACCCAGGCCCATTACGATCATGTGGGCGCCATGGCCGCAATTAAAAAGTCAACCAACGCGCAACTTATGATTGATGAAAAAGATTCACCCGTGATGGCTGATGGTGGAAGCTCGGATTATGAATTGTTTGGAAGTACCGGCAGCACCTATGAACCGGTTAAGGCCGATAGGCTTTTAAAGAATGGCGATAAAATAACATTGGGAGGTACCACCCTTGTCATGCTCCATCACCCCGGTCACACCAAAGGCTCATGTAGTTTTCTGTTTGATGTGAAAGACGAGAGCAAATCCTACAAAGTACTTATCGCCAACATGCCATCGATCATCACATCTAAAAAGTTTTCCGACATACCCACATATCCTGGCATTGCCGAAGACTATACCTACACGTTCGATGCAATGAAAAAAGTGCACTTCGATATCTGGCTCTCCTCACATGCTAGTCAGTTTGGGATGCATTCAAAACACAAACCAGGTGAAGCCTACAACCCTGGTGTCTTCATAGACCGGGCCGGATATGACAAGGCTGTGGGTGATCTGGAAGATAAATTTTCAAAAAAGAAGCAGGCGGACAAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39089","NCBI_taxonomy_name":"uncultured bacterium BLR19","NCBI_taxonomy_id":"506519"}}}},"ARO_accession":"3002513","ARO_id":"38913","ARO_name":"LRA-19","CARD_short_name":"LRA-19","ARO_description":"LRA-19 is a beta-lactamase isolated from soil samples in Alaska.","ARO_category":{"41390":{"category_aro_accession":"3004226","category_aro_cvterm_id":"41390","category_aro_name":"subclass B3 LRA beta-lactamase","category_aro_description":"Beta-lactamases that are part of the LRA gene family and are classified as B3 (metallo-) beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1463":{"model_id":"1463","model_name":"GES-19","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1090":{"protein_sequence":{"accession":"AEZ05107.1","sequence":"MRFIHALLLAAIAHSAYASEKLTFKTDLEKLEREKAAQIGVAIVDPQGEIVAGHRMAQRFAMCSTFKFPLAALVFERIDSGTERGDRKLSYGPDMIVEWSPATERFLASGHMTVLEAAQAAVQLSDNGATNLLLREIGGPAAMTQYFRKIGDSVSRLDRKEPEMGDNTPGDLRDTTTPIAMARTVAKVLYGGALTSTSTHTIERWLIGNQTGDATLRAGFPKDWVVGEKTGTCANGARNDIGFFKAQERDYAVAVYTTAPKLSAVERDELVASVGQVITQLILSTDK"},"dna_sequence":{"accession":"JN596280.1","fmin":"1918","fmax":"2782","strand":"+","sequence":"ATGCGCTTCATTCACGCACTATTACTGGCAGCGATCGCTCACTCTGCATATGCGTCGGAAAAATTAACCTTCAAGACCGATCTTGAGAAGCTAGAGCGCGAAAAAGCAGCTCAGATCGGTGTTGCGATCGTCGATCCCCAAGGAGAGATCGTCGCGGGCCACCGAATGGCGCAGCGTTTTGCAATGTGCTCAACGTTCAAGTTTCCGCTAGCCGCGCTGGTCTTTGAAAGAATTGACTCAGGCACCGAGCGGGGGGATCGAAAACTTTCATATGGGCCGGACATGATCGTCGAATGGTCTCCTGCCACGGAGCGGTTTCTAGCATCGGGACACATGACGGTTCTCGAGGCAGCGCAAGCTGCGGTGCAGCTTAGCGACAATGGGGCTACTAACCTCTTACTGAGAGAAATTGGCGGACCTGCTGCAATGACGCAGTATTTTCGTAAAATTGGCGACTCTGTGAGTCGGCTAGACCGGAAAGAGCCGGAGATGGGCGACAACACACCTGGCGACCTCAGAGATACAACTACGCCTATTGCTATGGCACGTACTGTGGCTAAAGTCCTCTATGGCGGCGCACTGACGTCCACCTCGACCCACACCATTGAGAGGTGGCTGATCGGAAACCAAACGGGAGACGCGACACTACGAGCGGGTTTTCCTAAAGATTGGGTTGTTGGAGAGAAAACTGGTACCTGCGCCAACGGGGCCCGGAACGACATTGGTTTTTTTAAAGCCCAGGAGAGAGATTACGCTGTAGCGGTGTATACAACGGCCCCGAAACTATCGGCCGTAGAACGTGACGAATTAGTTGCCTCTGTCGGTCAAGTTATTACACAACTCATCCTGAGCACGGACAAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002348","ARO_id":"38748","ARO_name":"GES-19","CARD_short_name":"GES-19","ARO_description":"GES-19 is a beta-lactamase found in the Enterobacteriaceae family.","ARO_category":{"36205":{"category_aro_accession":"3000066","category_aro_cvterm_id":"36205","category_aro_name":"GES beta-lactamase","category_aro_description":"GES beta-lactamases or Guiana extended-spectrum beta-lactamases are related to the other plasmid-located class A beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1464":{"model_id":"1464","model_name":"aadA7","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"516":{"protein_sequence":{"accession":"BAD00739.1","sequence":"MSEKVPAEISVQLSQALNGIGRHLESTLLAVHLYGSALDGGLKPYSDIDLLVTVAAPLNDAVRQALLVDLLEVSASPGQNKALRALEVTIVVHSDIVPWRYPARRELQFGEWQRKDILAGIFEPATTDSDLAILLTKAKQHSVVLAGSAAKDLFSSVPESDLFKALADTLKLWNSPPDWAGDERNVVLTLSRIWYTAATGKIAPKDVAATWAMARLPAQHQPILLNAKRAYLGQEEDYLPARADQVAALIKFVKYEAVKLLGASQ"},"dna_sequence":{"accession":"AB114632.1","fmin":"655","fmax":"1453","strand":"+","sequence":"ATGAGTGAAAAAGTGCCCGCCGAGATTTCGGTGCAACTATCACAAGCACTCAACGGCATCGGGCGCCACTTGGAGTCGACGTTGCTGGCCGTGCATTTGTACGGCTCCGCACTGGATGGCGGATTGAAACCGTACAGTGATATTGATTTGCTGGTGACTGTAGCTGCACCGCTCAATGATGCCGTGCGGCAAGCCCTGCTCGTCGATCTCTTGGAGGTTTCAGCTTCCCCTGGCCAAAACAAGGCACTCCGCGCCTTGGAAGTGACCATCGTCGTGCACAGTGACATCGTACCTTGGCGTTATCCGGCCAGGCGGGAACTGCAGTTCGGAGAGTGGCAGCGCAAAGACATCCTTGCGGGCATCTTCGAGCCCGCCACAACCGATTCTGACTTGGCGATTCTGCTAACAAAGGCAAAGCAACATAGCGTCGTCTTGGCAGGTTCAGCAGCGAAGGATCTCTTCAGCTCAGTCCCAGAAAGCGATCTATTCAAGGCACTGGCCGATACTCTGAAGCTATGGAACTCGCCGCCAGATTGGGCGGGCGATGAGCGGAATGTAGTGCTTACTTTGTCTCGTATCTGGTACACCGCAGCAACCGGCAAGATCGCGCCAAAGGATGTTGCTGCCACTTGGGCAATGGCACGCTTGCCAGCTCAACATCAGCCCATCCTGTTGAATGCCAAGCGGGCTTATCTTGGGCAAGAAGAAGATTATTTGCCCGCTCGTGCGGATCAGGTGGCGGCGCTCATTAAATTCGTGAAGTATGAAGCAGTTAAACTGCTTGGTGCCAGCCAATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39525","NCBI_taxonomy_name":"Vibrio fluvialis","NCBI_taxonomy_id":"676"}}}},"ARO_accession":"3002607","ARO_id":"39007","ARO_name":"aadA7","CARD_short_name":"aadA7","ARO_description":"aadA7 is an integron-encoded aminoglycoside nucleotidyltransferase gene in V. fluvialis, P. aeruginosa, E. coli, V. cholerae and S. enterica.","ARO_category":{"41439":{"category_aro_accession":"3004275","category_aro_cvterm_id":"41439","category_aro_name":"ANT(3'')","category_aro_description":"A category of aminoglycoside O-nucleotidyltransferase enzymes with modification regiospecificity based at the 3''-hydroxyl group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics by transfer of an AMP group from an ATP substrate to the 3''-hydroxyl group of the compound.","category_aro_class_name":"AMR Gene Family"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1466":{"model_id":"1466","model_name":"SHV-13","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1063":{"protein_sequence":{"accession":"AAD43815.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAAERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AF164577.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGCCGAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001072","ARO_id":"37452","ARO_name":"SHV-13","CARD_short_name":"SHV-13","ARO_description":"SHV-13 is an extended-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1467":{"model_id":"1467","model_name":"LEN-22","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"8179":{"protein_sequence":{"accession":"CAP12350.2","sequence":"MRYVRLCVISLLATLPLAVDAGPQPLEQIKQSESQLSGRVGMVEMDLASGRTLAAWRADERFPMVSTFKVLLCGAVLARVDAGLEQLDRRIHYRQQDLVDYSPVSEKHLVDGMTIGELCAAAITLSDNSAGNLLLATVGGPAGLTAFLRQIGDNVTRLDRWETALNEALPGDARDTTTPASMAATLRKLLTAQHLSPRSQQQLLQWMVDDRVAGPLIRAVLPAGWFIADKTGAGERGARGIVALLGPDGKPERIVVIYLRDTPASMAERNQHIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AM850912.2","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGTGTTATCTCCCTGTTAGCCACCCTGCCACTGGCGGTAGACGCCGGTCCACAGCCGCTTGAGCAGATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTGGGGATGGTGGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCGATGAACGCTTTCCCATGGTGAGCACCTTTAAAGTGCTGCTGTGCGGCGCGGTGCTGGCGCGGGTGGATGCCGGGCTCGAACAACTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGTCGACGGGATGACGATCGGCGAACTCTGCGCCGCCGCCATCACCCTGAGCGATAACAGCGCTGGCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCGGGATTAACTGCCTTTCTGCGCCAGATCGGTGACAACGTCACCCGTCTTGACCGCTGGGAAACGGCACTGAATGAGGCGCTTCCCGGCGACGCGCGCGACACCACCACCCCGGCCAGCATGGCCGCCACGCTGCGCAAACTACTGACCGCGCAGCATCTGAGCCCCCGTTCGCAACAGCAACTCCTGCAGTGGATGGTGGACGATCGGGTTGCCGGCCCGCTGATCCGCGCCGTGCTGCCGGCGGGCTGGTTTATCGCCGACAAGACCGGGGCTGGCGAACGGGGTGCGCGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAACCGGAGCGCATTGTGGTGATCTATCTGCGGGATACCCCGGCGAGTATGGCCGAGCGTAATCAACATATCGCCGGGATCGGCGCAGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002469","ARO_id":"38869","ARO_name":"LEN-22","CARD_short_name":"LEN-22","ARO_description":"LEN-22 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36236":{"category_aro_accession":"3000097","category_aro_cvterm_id":"36236","category_aro_name":"LEN beta-lactamase","category_aro_description":"LEN beta-lactamases are chromosomal class A beta-lactamases that confer resistance to ampicillin, amoxicillin, carbenicillin, and ticarcillin but not to extended-spectrum beta-lactams.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1468":{"model_id":"1468","model_name":"SHV-135","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1311":{"protein_sequence":{"accession":"ADR66517.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLKQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMTATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"HQ637576.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTAAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGACCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGCATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001179","ARO_id":"37559","ARO_name":"SHV-135","CARD_short_name":"SHV-135","ARO_description":"SHV-135 is a beta-lactamase.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1469":{"model_id":"1469","model_name":"facT","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1050"}},"model_sequences":{"sequence":{"687":{"protein_sequence":{"accession":"AFK80333.1","sequence":"MNKAGQAEKPAAAGPPATPETPEPDPKRWLALTVLLVATFMDLLDANIITVAIPSIQRDLGASTFAIQAMTAGYTLSFAVLLITGGRLGDIFGRKRMFLVGVGGFVLASAMCAAAPSTDLLVVARALQGLTAAVMVPQVLALIHVSFAPQEIGRVVSLYASMVGLAIVSGPLIGGALISWNPLDLGWRSIFVVNLPVGVLALVGAAKWMRESSSPHAKRLDIAGMLLIVLGLLLLMVPLTLGRELDWPVWSIVSLVAAAPVLVLFVVYERHKTAKDGSPLVTLSLFKVRAFGAGIGVQLLFSAIPAGFFLSWTLYLQAGLGWSALHTGLTAIPFSLCVPIVGGLAVRRLSPLYGRYCLLAGAVLMLAGILSYAWAADRFGTDITSWHAIPSMLLIGSGMGMLMPPLTALVLREVQPQEAGAASGIINATGQLGAALGVAVIGSLFFAALAGNAGPQAERVAPTVQSVSPRQASDLRDCATEALGQDDLAKVPDICSTLVQGADDGTRDTINGALGEIRAKTFVSTYSETLYWAAGGLVPVTALVLLLPHHRVRREEPAQ"},"dna_sequence":{"accession":"JQ768046.1","fmin":"7760","fmax":"9440","strand":"+","sequence":"ATGAACAAGGCAGGGCAGGCAGAAAAGCCGGCGGCAGCCGGCCCACCTGCCACTCCCGAGACGCCCGAGCCCGACCCGAAGCGGTGGCTCGCGCTGACAGTCCTGCTGGTCGCCACCTTCATGGACCTGCTCGACGCGAACATCATCACCGTGGCCATCCCGAGCATCCAACGCGACCTCGGCGCCTCGACCTTCGCCATCCAGGCGATGACGGCCGGCTACACCCTGAGCTTCGCGGTCCTGCTGATCACCGGCGGCCGGCTCGGCGACATCTTCGGCCGCAAGCGCATGTTCCTCGTCGGCGTCGGCGGCTTCGTCCTCGCGTCCGCGATGTGCGCCGCCGCGCCGAGCACCGACTTACTCGTCGTCGCCCGCGCGCTCCAGGGCCTCACCGCCGCCGTCATGGTGCCCCAGGTGCTCGCGCTCATCCACGTCTCCTTCGCGCCCCAGGAGATCGGCCGCGTCGTCAGCCTGTACGCGAGCATGGTCGGTCTGGCCATCGTCTCCGGGCCCCTCATCGGCGGTGCGCTGATCAGCTGGAACCCGCTGGACCTCGGCTGGCGCAGCATCTTCGTGGTGAACCTGCCGGTCGGCGTGCTCGCCCTGGTCGGCGCCGCGAAGTGGATGCGGGAGTCGAGCTCCCCCCATGCGAAGCGCCTGGACATCGCCGGCATGCTGCTGATCGTGCTCGGCCTGCTGCTGCTCATGGTGCCGCTGACCCTCGGCCGCGAGCTCGACTGGCCGGTGTGGAGCATCGTCTCGCTCGTCGCCGCCGCCCCCGTCCTCGTGCTGTTCGTCGTCTACGAGCGCCACAAGACCGCCAAGGACGGCTCGCCCCTGGTGACGCTGTCCCTGTTCAAGGTCCGCGCGTTCGGCGCCGGCATCGGCGTCCAGCTCCTCTTCAGCGCCATCCCCGCGGGCTTCTTCCTCAGCTGGACCCTCTACCTCCAGGCCGGCCTCGGCTGGTCGGCCCTGCACACGGGCCTGACCGCCATCCCGTTCTCCCTGTGCGTCCCGATCGTCGGCGGTCTCGCCGTCCGCAGGCTCTCGCCGCTCTACGGCCGCTACTGCCTGCTCGCCGGTGCCGTCCTGATGCTCGCGGGCATCCTCTCCTACGCCTGGGCGGCCGACCGCTTCGGCACGGACATCACCTCCTGGCACGCGATCCCGTCCATGCTCCTGATCGGCTCCGGCATGGGCATGCTGATGCCCCCGCTGACGGCGCTGGTGCTCAGGGAGGTCCAGCCGCAGGAGGCCGGCGCCGCCTCCGGCATCATCAACGCCACCGGCCAGCTCGGTGCCGCGCTCGGCGTGGCGGTCATCGGCAGCCTCTTCTTCGCGGCCCTCGCCGGCAACGCCGGGCCGCAGGCCGAACGCGTCGCCCCCACCGTGCAGTCGGTCTCACCCCGGCAGGCCTCCGACCTCCGGGACTGCGCGACCGAGGCGCTGGGCCAGGACGACCTGGCCAAGGTCCCGGACATCTGCTCCACCCTGGTGCAGGGCGCCGACGACGGCACCCGGGATACGATCAATGGCGCGCTCGGCGAGATCCGCGCGAAGACGTTCGTGTCCACCTACAGCGAGACGCTGTACTGGGCGGCCGGTGGCCTCGTCCCGGTCACCGCCCTCGTCCTGCTCCTGCCGCACCACCGCGTCCGGCGGGAGGAACCGGCCCAGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37730","NCBI_taxonomy_name":"Streptomyces sp. WAC05292","NCBI_taxonomy_id":"1194538"}}}},"ARO_accession":"3001313","ARO_id":"37712","ARO_name":"facT","CARD_short_name":"facT","ARO_description":"Efflux protein facT confers resistance to factumycin. The gene has been heterologously expressed in S. coelicolor and its function confirmed. It is possible that this gene can export other kirromycin-like elfamycins, but this has not been tested.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"37619":{"category_aro_accession":"3001220","category_aro_cvterm_id":"37619","category_aro_name":"factumycin","category_aro_description":"Factumycin is a kirromycin-like antibiotic produced by Kitasatospora setae and Streptomyces strains. Its biosynthetic cluster has been characterized which has interesting acetyl transferase domains in trans, or outside of the polyketide synthase domains. Factumycin has specific, rather than broad spectrum,  antibacterial properties, especially targeting various Acinetobacter baumanii strains.","category_aro_class_name":"Antibiotic"},"37618":{"category_aro_accession":"3001219","category_aro_cvterm_id":"37618","category_aro_name":"elfamycin antibiotic","category_aro_description":"Elfamycins are molecules that inhibit bacterial elongation factor Tu (EF-Tu), a key protein which brings aminoacyl-tRNA (aa-tRNA) to the ribosome during protein synthesis. Elfamycins defined by their target (EF-Tu), rather than a conserved chemical backbone. Elfamycins follow two mechanisms to disrupt protein synthesis: 1. kirromycins and enacyloxin fix EF-Tu in the GTP bound conformation and lock EF-Tu onto the ribosome, and 2. pulvomycin and GE2270 cover the binding site of aa-tRNA disallowing EF-Tu from being charged with aa-tRNA. All elfamycins cause increased the affinity of EF-Tu for GTP.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1470":{"model_id":"1470","model_name":"QnrB26","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"114":{"protein_sequence":{"accession":"AEH59666.1","sequence":"MTPLLYKKTGTNMALALVGVKIDRNRFTGEKIENGTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNASALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGAQVLGATFSGSDLSGGEFSTFDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDNYQASLLMERLGIAVIG"},"dna_sequence":{"accession":"HQ386846.1","fmin":"0","fmax":"681","strand":"+","sequence":"ATGACGCCATTACTGTATAAAAAAACAGGTACAAATATGGCTCTGGCACTCGTTGGCGTAAAAATTGACAGAAACCGTTTCACCGGTGAGAAAATTGAAAATGGTACATTTTTTAATTGTGATTTTTCAGGTGCCGACCTGAGCGGCACTGAATTTATCGGCTGTCAGTTCTATGATCGTGAAAGCCAGAAAGGGTGCAATTTTAGTCGTGCGATGCTGAAAGATGCCATTTTTAAAAGCTGTGATTTATCCATGGCGGATTTTCGCAATGCCAGTGCGCTGGGCATTGAAATTCGCCACTGCCGCGCACAAGGCGCAGATTTCCGCGGCGCAAGCTTTATGAATATGATCACCACGCGCACCTGGTTTTGTAGCGCATATATCACGAATACCAATCTAAGCTACGCCAATTTTTCGAAAGTCGTGTTGGAAAAGTGTGAGCTGTGGGAAAACCGTTGGATGGGTGCCCAGGTACTGGGCGCGACGTTCAGTGGTTCAGATCTCTCCGGCGGCGAGTTTTCGACTTTCGACTGGCGAGCAGCGAACTTCACACATTGCGATCTGACCAATTCGGAGTTGGGTGACTTAGATATTCGGGGCGTTGATTTACAAGGCGTTAAGCTGGACAACTACCAGGCGTCGTTGCTCATGGAGCGGCTTGGCATCGCGGTGATTGGTTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36943","NCBI_taxonomy_name":"Proteus vulgaris","NCBI_taxonomy_id":"585"}}}},"ARO_accession":"3002741","ARO_id":"39175","ARO_name":"QnrB26","CARD_short_name":"QnrB26","ARO_description":"QnrB26 is a plasmid-mediated quinolone resistance protein found in Proteus vulgaris.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1471":{"model_id":"1471","model_name":"adeI","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"5374":{"protein_sequence":{"accession":"ACJ41739.1","sequence":"MMSAKLWAPALTACALATSIALVGCSKGSDEKQQAAAAQKMPPAEVGVIVAQPQSVEQSVELSGRTSAYQISEVRPQTSGVILKRLFAEGSYVREGQALYELDSRTNRATLENAKASLLQQQANLASLRTKLNRYKQLVSSNAVSKQEYDDLLGQVNVAEAQVAAAKAQVTNANVDLGYSTIRSPISGQSGRSSVTAGALVTANQTDPLVTIQQLDPIYVDINQSSAELLRLRQQLSKGSLNNSNNTKVKLKLEDGSTYPIEGQLAFSDASVNQDTGTITLRAVFSNPNHLLLPGMYTTAQIVQGVVPNAYLIPQAAITRLPTGQAVAMLVNAKGVVESRPVETSGVQGQNWIVTNGLKAGDKVIVDGVAKVKEGQEVSAKPYQAQPANSQGAAPNAAKPAQSGKPQAEQKAASNA"},"dna_sequence":{"accession":"CP001182.2","fmin":"3283426","fmax":"3284677","strand":"+","sequence":"ATGATGTCGGCTAAGCTTTGGGCACCAGCCCTTACTGCTTGCGCATTAGCAACAAGTATCGCGCTTGTTGGTTGTAGCAAAGGCTCCGATGAGAAACAGCAAGCTGCTGCTGCTCAGAAAATGCCGCCTGCAGAAGTAGGTGTTATTGTTGCTCAACCACAAAGTGTTGAACAAAGCGTTGAGCTTTCAGGCCGTACTTCAGCATATCAAATTTCTGAAGTTCGTCCTCAAACAAGTGGCGTGATTTTAAAACGTTTATTTGCTGAAGGAAGCTATGTTCGTGAAGGTCAGGCGCTTTATGAGCTCGACTCTAGAACGAACCGTGCAACGTTAGAAAATGCAAAAGCATCACTCCTACAACAACAGGCAAATCTAGCTTCACTACGTACCAAGTTAAATCGTTATAAACAACTTGTTTCTAGTAATGCTGTGTCTAAACAGGAATATGATGACTTACTTGGTCAAGTCAATGTTGCAGAAGCACAAGTTGCAGCAGCTAAGGCTCAAGTAACAAATGCAAATGTAGATCTTGGTTATTCTACAATTCGCTCTCCTATTTCTGGCCAATCTGGTCGTTCTTCAGTAACGGCTGGTGCTTTGGTTACTGCAAACCAGACTGACCCGTTGGTAACGATTCAACAATTAGATCCTATCTATGTTGATATTAATCAGTCTAGTGCTGAGTTATTGCGTTTACGTCAACAACTAAGCAAAGGCAGTTTAAATAACAGTAACAACACGAAAGTAAAATTAAAGCTTGAAGATGGTTCTACCTATCCAATCGAAGGGCAACTTGCTTTCTCTGACGCTTCTGTAAACCAAGATACAGGAACAATTACATTACGTGCCGTATTCTCTAACCCGAATCATTTATTGCTTCCGGGTATGTATACCACTGCGCAAATTGTTCAGGGCGTTGTTCCAAATGCTTACCTGATTCCTCAAGCTGCCATTACTCGTTTACCTACAGGACAAGCTGTAGCGATGCTTGTTAATGCTAAAGGGGTTGTTGAGAGCCGTCCTGTTGAAACCTCTGGTGTTCAAGGACAAAACTGGATTGTGACTAACGGCTTAAAAGCCGGCGATAAAGTCATTGTTGATGGTGTTGCCAAAGTTAAAGAAGGGCAAGAAGTATCAGCAAAACCTTATCAAGCTCAACCAGCAAACTCTCAAGGTGCAGCACCAAATGCTGCGAAACCGGCTCAATCAGGTAAACCTCAAGCAGAACAGAAAGCAGCTTCAAATGCATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35531","NCBI_taxonomy_name":"Acinetobacter baumannii AB0057","NCBI_taxonomy_id":"480119"}}}},"ARO_accession":"3000780","ARO_id":"37160","ARO_name":"adeI","CARD_short_name":"adeI","ARO_description":"AdeI is the membrane fusion protein of the AdeIJK multidrug efflux complex.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36309":{"category_aro_accession":"3000170","category_aro_cvterm_id":"36309","category_aro_name":"imipenem","category_aro_description":"Imipenem is a broad-spectrum antibiotic and is usually taken with cilastatin, which prevents hydrolysis of imipenem by renal dehydropeptidase-I. It is resistant to hydrolysis by most other beta-lactamases. Notable exceptions are the KPC beta-lactamases and Ambler Class B enzymes.","category_aro_class_name":"Antibiotic"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"40523":{"category_aro_accession":"3003832","category_aro_cvterm_id":"40523","category_aro_name":"ticarcillin","category_aro_description":"Ticarcillin is a carboxypenicillin used for the treatment of Gram-negative bacteria, particularly P. aeruginosa. Ticarcillin's antibiotic properties arise from its ability to prevent cross-linking of peptidoglycan during cell wall synthesis, when the bacteria try to divide, causing cell death.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1333":{"model_id":"1333","model_name":"vanH gene in vanD cluster","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"200"}},"model_sequences":{"sequence":{"428":{"protein_sequence":{"accession":"AAM09850.1","sequence":"MQEKIDITVFGCERDEAAVFRKLSSEYGVTVSLIEDVVSEHNAKLADGCQCVSVSHKAELSEQLLLALKHAGVKYISTRSIGFNHIDIQAAGQLGMAVGTVAYSPGSVADYTVMLMLMLLRGTKSVLRGTQKQNYCLNDCRGKELQDLTVGVLGTGRIGQAVMERLEGIGCKVLAYDRTHKAGANYVSFCELLKSSDIVTLHVPLAEDTRHMIGREQLEMMKREALLINTARGALVDTAALVAALKEQKIGGAALDVLEGEEGIFYHECTQKTIGHPYLSVLQKMPNVIVTPHTAYHTDRVLVDTVSNTIRNCLNFERSLGNV"},"dna_sequence":{"accession":"AY082011.1","fmin":"4936","fmax":"5908","strand":"+","sequence":"ATGCAGGAAAAAATAGATATTACGGTTTTTGGGTGTGAGCGGGATGAAGCGGCGGTATTCCGTAAACTTTCATCTGAGTATGGCGTCACAGTTTCGCTCATCGAAGATGTCGTATCAGAGCACAATGCAAAATTAGCGGACGGATGCCAGTGTGTCAGCGTAAGCCATAAGGCGGAGCTGTCGGAGCAGCTTCTCCTTGCGCTGAAACACGCAGGAGTGAAATACATCAGTACCCGGAGCATTGGATTCAACCATATTGATATACAGGCTGCAGGTCAGTTGGGTATGGCTGTTGGCACAGTGGCATACTCACCGGGAAGCGTGGCCGATTATACCGTCATGCTGATGCTCATGCTGCTGCGCGGCACAAAGTCGGTTCTACGAGGAACCCAGAAGCAGAATTATTGTCTGAATGACTGCCGTGGAAAAGAACTGCAGGATTTGACGGTTGGCGTCCTGGGAACCGGACGAATCGGACAGGCAGTCATGGAACGCCTGGAGGGAATCGGCTGCAAGGTGTTGGCCTATGACCGAACTCACAAAGCCGGAGCAAATTATGTTTCGTTTTGTGAATTATTGAAGAGCAGCGACATTGTTACGCTGCATGTGCCTCTGGCAGAGGATACCCGCCATATGATTGGGCGCGAGCAGCTAGAGATGATGAAGAGGGAGGCACTTCTGATCAACACGGCACGGGGGGCTTTAGTGGATACGGCTGCACTGGTTGCTGCGCTGAAAGAACAAAAAATCGGCGGAGCCGCCTTAGATGTCCTGGAAGGGGAAGAAGGCATCTTTTACCATGAATGCACACAAAAAACGATAGGGCATCCTTACCTCTCCGTTTTGCAGAAAATGCCCAATGTCATTGTTACGCCGCATACGGCCTATCATACGGATCGGGTACTGGTCGATACCGTGAGCAATACCATCCGAAATTGTCTGAATTTTGAAAGGAGTCTTGGAAATGTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36779","NCBI_taxonomy_name":"Enterococcus faecium","NCBI_taxonomy_id":"1352"}}}},"ARO_accession":"3002944","ARO_id":"39378","ARO_name":"vanH gene in vanD cluster","CARD_short_name":"vanH_in_vanD_cl","ARO_description":"Also known as vanHD, is a vanH variant in the vanD gene cluster.","ARO_category":{"36015":{"category_aro_accession":"3000006","category_aro_cvterm_id":"36015","category_aro_name":"vanH","category_aro_description":"VanH is a D-specific alpha-ketoacid dehydrogenase that synthesizes D-lactate. D-lactate is incorporated into the end of the peptidoglycan subunits, decreasing vancomycin binding affinity.","category_aro_class_name":"AMR Gene Family"},"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"35948":{"category_aro_accession":"0000029","category_aro_cvterm_id":"35948","category_aro_name":"teicoplanin","category_aro_description":"Teicoplanin is a glycopeptide antibiotic used in the prophylaxis and treatment of serious infections caused by Gram-positive bacteria. Teicoplanin has a unique acyl-aliphatic chain, and binds to cell wall precursors to inhibit transglycosylation  and transpeptidation.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1338":{"model_id":"1338","model_name":"Bla1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"1545":{"protein_sequence":{"accession":"AAR20595.1","sequence":"MIVLKNKKMLKIGMCVGILGLSITSLVTFTGGALQVEAKEKTGQVKHKNQATHKEFSQLEKKFDARLGVYAIDTGTNQTIAYRPNERFAFASTYKALAAGVLLQQNSTKKLDEVITYTKEDLVDYSPVTEKHVDTGMTLGEIAEAAVRYSDNTAGNILFHKIGGPKGYEKALRQMGDRVTMSDRFETELNEAIPGDIRDTSTAKAIATNLKAFTAGNALPNHKRNILTKWMKGNATGDKLIRAGVPTNWVVADKSGAGSYGTRNDIAIVWPPNRAPIIIAILSSKDEKGATYDNQLIAEAAEVIVNAFR"},"dna_sequence":{"accession":"AY453161.1","fmin":"500","fmax":"1430","strand":"+","sequence":"ATGATAGTTTTGAAAAACAAGAAAATGCTAAAAATAGGGATGTGTGTTGGTATATTAGGTTTAAGTATTACAAGCCTAGTAACTTTTACAGGAGGTGCATTGCAAGTTGAAGCGAAAGAAAAGACTGGACAAGTGAAACATAAAAATCAGGCGACGCATAAAGAGTTCTCTCAACTTGAGAAAAAATTTGATGCTCGATTAGGTGTATATGCGATTGATACTGGTACAAATCAAACAATCGCTTATCGACCTAACGAAAGGTTTGCCTTTGCATCAACTTACAAGGCTTTAGCGGCAGGGGTATTACTGCAACAGAACTCTACTAAGAAATTAGATGAAGTTATTACTTATACGAAAGAAGACTTAGTGGATTATTCACCTGTTACAGAGAAACATGTAGATACTGGAATGACACTAGGAGAAATTGCGGAGGCTGCTGTTCGTTACAGTGATAATACTGCAGGGAACATTTTATTTCATAAAATAGGCGGACCGAAAGGATATGAAAAAGCGCTTAGACAGATGGGGGACCGGGTTACTATGTCTGATCGTTTTGAAACAGAATTAAACGAGGCTATTCCAGGAGACATTCGTGACACCAGTACAGCGAAAGCAATTGCTACGAATCTTAAAGCTTTTACGGCCGGAAATGCGCTTCCAAATCATAAACGTAACATTCTTACAAAGTGGATGAAAGGAAATGCTACAGGAGACAAACTTATTCGTGCAGGTGTGCCTACTAACTGGGTAGTTGCAGATAAATCAGGAGCTGGAAGTTACGGGACACGAAATGATATTGCTATCGTTTGGCCACCAAATAGAGCACCTATTATCATCGCAATTTTATCTAGTAAAGATGAAAAAGGGGCTACCTATGATAATCAACTCATTGCAGAGGCGGCTGAAGTTATAGTTAATGCTTTTAGGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36786","NCBI_taxonomy_name":"Bacillus anthracis","NCBI_taxonomy_id":"1392"}}}},"ARO_accession":"3000090","ARO_id":"36229","ARO_name":"Bla1","CARD_short_name":"Bla1","ARO_description":"Bla1 is a chromosomal-encoded beta-lactamase, found in Bacillus anthracis, which hydrolyzes penicillins.","ARO_category":{"41393":{"category_aro_accession":"3004229","category_aro_cvterm_id":"41393","category_aro_name":"class A Bacillus anthracis Bla beta-lactamase","category_aro_description":"Beta-lactamases belonging to the Bla genes from Bacillus anthracis that are classified as class A beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1344":{"model_id":"1344","model_name":"MexH","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"650"}},"model_sequences":{"sequence":{"5354":{"protein_sequence":{"accession":"AAG07593.1","sequence":"MQKPVLIASAALICAAVIGIAVYATGSAKKDAGGFAGYPPVKVALASVERRVVPRVFDGVGELEAGRQVQVAAEAAGRITRIAFESGQQVQQGQLLVQLNDAVEQAELIRLKAQLRNAEILHARARKLVERNVASQEQLDNAVAARDMALGAVRQTQALIDQKAIRAPFSGQLGIRRVHLGQYLGVAEPVASLVDARTLKSNFSLDESTSPELKLGQPLEVLVDAYPGRSFPARISAIDPLIGKSRTVQVQALLDNPEGLLAAGMFASIRVSRKADAPSLSVPETAVTYTAYGDTVFVAHQDGDRPLSAKRVSVRIGERWDGRVEILQGLAEGDRVVTSGQINLSDGMAVEPVKEDTLSSAAPPVPVAGR"},"dna_sequence":{"accession":"AE004091.2","fmin":"4706409","fmax":"4707522","strand":"+","sequence":"ATGCAGAAACCCGTCCTGATCGCCAGTGCCGCGCTCATCTGCGCGGCGGTTATCGGCATCGCCGTCTACGCCACCGGCTCGGCGAAGAAAGACGCCGGCGGTTTCGCCGGCTACCCGCCGGTGAAGGTCGCCCTCGCCTCGGTGGAGCGGCGGGTGGTGCCGCGCGTCTTCGATGGCGTCGGCGAGCTGGAGGCCGGTCGCCAGGTCCAGGTGGCCGCCGAAGCGGCAGGACGGATCACCCGCATCGCCTTCGAATCGGGCCAGCAGGTGCAGCAAGGGCAGTTGCTGGTGCAACTCAACGACGCGGTGGAACAGGCCGAGCTGATCCGTCTCAAGGCGCAGTTGCGCAATGCCGAGATCCTCCATGCCCGTGCGCGCAAGCTGGTAGAGCGCAACGTCGCCTCGCAGGAACAGCTGGACAACGCCGTCGCCGCCCGCGACATGGCGCTCGGCGCGGTGCGCCAGACCCAGGCGCTGATCGACCAGAAGGCGATCCGCGCGCCCTTCTCCGGCCAGCTCGGCATCCGCCGCGTGCACCTCGGCCAGTACCTCGGCGTCGCCGAGCCGGTGGCCAGCCTGGTGGATGCGCGGACCCTGAAAAGCAATTTCTCCCTGGACGAAAGCACCAGTCCCGAGCTGAAGCTCGGCCAGCCCCTCGAGGTCCTGGTCGACGCCTATCCGGGGCGCAGCTTCCCGGCGCGCATCAGCGCCATCGACCCGCTGATCGGCAAGTCGCGCACGGTGCAGGTCCAGGCCTTGCTGGACAACCCCGAAGGCCTGCTCGCCGCCGGCATGTTCGCCAGCATCCGGGTCTCGCGCAAAGCCGACGCGCCGTCGCTGAGCGTGCCGGAAACCGCGGTCACCTATACCGCCTACGGCGACACCGTGTTCGTCGCCCACCAGGACGGCGACCGGCCGCTCAGCGCCAAGCGCGTCTCGGTGCGGATCGGCGAGCGCTGGGACGGTCGCGTGGAAATCCTCCAGGGCCTCGCCGAGGGCGACCGGGTAGTGACTTCCGGACAGATCAACCTGAGCGACGGGATGGCCGTGGAACCGGTCAAGGAAGACACCCTGAGCAGTGCCGCGCCCCCCGTGCCGGTCGCCGGCCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36804","NCBI_taxonomy_name":"Pseudomonas aeruginosa PAO1","NCBI_taxonomy_id":"208964"}}}},"ARO_accession":"3000807","ARO_id":"37187","ARO_name":"MexH","CARD_short_name":"MexH","ARO_description":"MexH is the membrane fusion protein of the efflux complex MexGHI-OpmD.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35963":{"category_aro_accession":"0000045","category_aro_cvterm_id":"35963","category_aro_name":"acriflavine","category_aro_description":"Acriflavine is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"43746":{"category_aro_accession":"3005386","category_aro_cvterm_id":"43746","category_aro_name":"disinfecting agents and antiseptics","category_aro_description":"Disinfectants that can also interact with antimicrobial resistance mechanisms, e.g. molecule efflux, and thus are the targets of disinfectant resistance.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1381":{"model_id":"1381","model_name":"CcrA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"1275":{"protein_sequence":{"accession":"AAA22904.1","sequence":"MKTVFILISMLFPVAVMAQKSVKISDDISITQLSDKVYTYVSLAEIEGWGMVPSNGMIVINNHQAALLDTPINDAQTEMLVNWVTDSLHAKVTTFIPNHWHGDCIGGLGYLQRKGVQSYANQMTIDLAKEKGLPVPEHGFTDSLTVSLDGMPLQCYYLGGGHATDNIVVWLPTENILFGGCMLKDNQATSIGNISDADVTAWPKTLDKVKAKFPSARYVVPGHGDYGGTELIEHTKQIVNQYIESTSKP"},"dna_sequence":{"accession":"M63556.1","fmin":"90","fmax":"840","strand":"+","sequence":"ATGAAAACAGTATTTATCCTTATCTCCATGCTTTTCCCTGTCGCAGTTATGGCACAGAAAAGCGTAAAAATATCCGATGACATCAGTATCACCCAACTCTCGGACAAAGTGTACACTTATGTATCCCTCGCCGAAATCGAAGGATGGGGTATGGTACCTTCCAACGGGATGATTGTTATCAACAACCACCAGGCAGCGTTGCTGGACACACCGATCAATGACGCACAAACGGAAATGCTGGTCAACTGGGTGACAGACTCTTTGCATGCCAAAGTCACCACGTTTATCCCGAACCACTGGCACGGCGATTGTATTGGCGGACTGGGTTACCTGCAAAGGAAAGGTGTCCAATCATACGCGAACCAGATGACGATAGACCTCGCCAAGGAAAAAGGGTTGCCCGTACCGGAACATGGATTCACCGATTCACTGACCGTCAGCTTGGACGGCATGCCTCTCCAATGTTATTATTTAGGAGGCGGACATGCGACCGACAATATCGTGGTTTGGCTGCCGACAGAGAATATCCTTTTTGGCGGATGTATGCTTAAAGACAACCAGGCGACAAGCATCGGCAACATCTCGGACGCGGACGTGACGGCATGGCCGAAAACTCTCGATAAGGTAAAAGCCAAGTTCCCCTCGGCCCGTTACGTCGTGCCCGGACATGGCGACTATGGCGGAACCGAACTGATAGAGCATACCAAGCAGATCGTGAACCAATATATAGAAAGCACTTCAAAGCCATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35916","NCBI_taxonomy_name":"Bacteroides fragilis","NCBI_taxonomy_id":"817"}}}},"ARO_accession":"3000578","ARO_id":"36717","ARO_name":"CcrA","CARD_short_name":"CcrA","ARO_description":"CcrA is a CfiA beta-lactamase.","ARO_category":{"41364":{"category_aro_accession":"3004200","category_aro_cvterm_id":"41364","category_aro_name":"CfiA beta-lactamase","category_aro_description":"CfiA beta-lactamases are chromosomal-encoded carbapenemase commonly found in Bacteroides fragilis isolates.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1393":{"model_id":"1393","model_name":"THIN-B","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"1081":{"protein_sequence":{"accession":"CAC33832.1","sequence":"MTLLAKLMLATVATMSAATVQAKTPAPKPDTPVDCDSCKAWNGEVTPFNVFGNTWYVGTAGLSAVLVTSPQGHVLLDGALPQSAPLIIANIAALGFRIEDVKFILNSHAHWDHAGGIAALQAASGATVVASASGALGLQSGTNGKDDPQFQAKPVVHVAKVEKVKVVGEGDAIKLGPLNLTAHMTPGHTPGATTWTWTSCEGQRCLDVVYADSLNPYSSGDFTYTGKGDGPDISASFAASIAKVAALPCDIILSVHPDSTGVLDKAAKRSGEHNPFIDANACRAYAATADAMLTKRLAKERGVALPAAAPAAQHAH"},"dna_sequence":{"accession":"AJ250876.1","fmin":"36","fmax":"987","strand":"+","sequence":"ATGACACTATTGGCGAAGTTGATGCTGGCGACGGTTGCGACCATGTCGGCGGCTACGGTGCAGGCAAAGACACCGGCGCCCAAGCCGGATACCCCTGTCGATTGCGACAGCTGCAAGGCGTGGAACGGGGAAGTCACACCATTCAACGTATTTGGCAATACCTGGTATGTGGGCACGGCCGGCTTGTCCGCCGTGCTGGTGACCAGCCCGCAAGGCCACGTCCTGCTCGACGGCGCGCTGCCGCAATCGGCGCCACTGATCATCGCGAACATCGCGGCGCTGGGTTTCCGCATCGAGGATGTGAAATTCATCCTCAATTCCCACGCGCATTGGGATCACGCCGGCGGCATCGCCGCGCTGCAGGCCGCCAGCGGCGCCACCGTGGTGGCCAGCGCCTCGGGCGCCCTGGGATTGCAAAGCGGCACCAACGGCAAGGATGATCCGCAATTCCAGGCCAAGCCTGTCGTGCATGTGGCAAAGGTGGAGAAGGTCAAGGTGGTGGGCGAGGGCGATGCCATCAAGCTGGGGCCGTTGAACCTGACGGCGCACATGACGCCAGGCCACACGCCAGGCGCCACCACCTGGACCTGGACCTCGTGCGAAGGGCAGCGCTGCCTGGACGTGGTGTATGCCGACAGCCTGAATCCGTATTCCAGCGGCGACTTTACGTACACGGGCAAAGGGGACGGACCCGATATCTCGGCCTCGTTTGCCGCCAGCATCGCCAAGGTGGCGGCCCTGCCGTGCGACATCATTCTTTCCGTGCATCCCGATTCGACGGGCGTGCTGGACAAGGCGGCCAAGCGCAGCGGCGAACACAATCCCTTCATCGATGCGAACGCCTGCCGCGCCTATGCGGCCACGGCGGACGCCATGCTGACGAAACGGCTGGCGAAGGAGCGCGGCGTGGCCCTGCCTGCGGCGGCCCCGGCTGCCCAGCACGCGCACTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39074","NCBI_taxonomy_name":"Janthinobacterium lividum","NCBI_taxonomy_id":"29581"}}}},"ARO_accession":"3000851","ARO_id":"37231","ARO_name":"THIN-B","CARD_short_name":"THIN-B","ARO_description":"THIN-B, isolated from Janthinobacterium lividum, hydrolyzes a broad spectrum of beta-lactams including penicillins, cephalosporins, and carbapenems.","ARO_category":{"41378":{"category_aro_accession":"3004214","category_aro_cvterm_id":"41378","category_aro_name":"THIN-B beta-lactamase","category_aro_description":"Beta-lactamases that are part of the THIN-B family, which is a subclass B3 beta-lactamase family and hydrolyze a broad spectrum of beta-lactams including penicillins, cephalosporins, and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1437":{"model_id":"1437","model_name":"AcrF","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1900"}},"model_sequences":{"sequence":{"700":{"protein_sequence":{"accession":"AAC76298.1","sequence":"MANFFIRRPIFAWVLAIILMMAGALAILQLPVAQYPTIAPPAVSVSANYPGADAQTVQDTVTQVIEQNMNGIDNLMYMSSTSDSAGSVTITLTFQSGTDPDIAQVQVQNKLQLATPLLPQEVQQQGISVEKSSSSYLMVAGFVSDNPGTTQDDISDYVASNVKDTLSRLNGVGDVQLFGAQYAMRIWLDADLLNKYKLTPVDVINQLKVQNDQIAAGQLGGTPALPGQQLNASIIAQTRFKNPEEFGKVTLRVNSDGSVVRLKDVARVELGGENYNVIARINGKPAAGLGIKLATGANALDTAKAIKAKLAELQPFFPQGMKVLYPYDTTPFVQLSIHEVVKTLFEAIMLVFLVMYLFLQNMRATLIPTIAVPVVLLGTFAILAAFGYSINTLTMFGMVLAIGLLVDDAIVVVENVERVMMEDKLPPKEATEKSMSQIQGALVGIAMVLSAVFIPMAFFGGSTGAIYRQFSITIVSAMALSVLVALILTPALCATLLKPVSAEHHENKGGFFGWFNTTFDHSVNHYTNSVGKILGSTGRYLLIYALIVAGMVVLFLRLPSSFLPEEDQGVFLTMIQLPAGATQERTQKVLDQVTDYYLKNEKANVESVFTVNGFSFSGQAQNAGMAFVSLKPWEERNGDENSAEAVIHRAKMELGKIRDGFVIPFNMPAIVELGTATGFDFELIDQAGLGHDALTQARNQLLGMAAQHPASLVSVRPNGLEDTAQFKLEVDQEKAQALGVSLSDINQTISTALGGTYVNDFIDRGRVKKLYVQADAKFRMLPEDVDKLYVRSANGEMVPFSAFTTSHWVYGSPRLERYNGLPSMEIQGEAAPGTSSGDAMALMENLASKLPAGIGYDWTGMSYQERLSGNQAPALVAISFVVVFLCLAALYESWSIPVSVMLVVPLGIVGVLLAATLFNQKNDVYFMVGLLTTIGLSAKNAILIVEFAKDLMEKEGKGVVEATLMAVRMRLRPILMTSLAFILGVLPLAISNGAGSGAQNAVGIGVMGGMVSATLLAIFFVPVFFVVIRRCFKG"},"dna_sequence":{"accession":"U00096.1","fmin":"3415032","fmax":"3418137","strand":"+","sequence":"ATGGCAAACTTTTTTATTCGACGACCGATATTTGCATGGGTGCTGGCCATTATTCTGATGATGGCGGGCGCACTGGCGATCCTACAATTGCCCGTCGCTCAGTATCCAACAATTGCACCGCCTGCGGTTTCTGTTTCAGCAAACTATCCGGGCGCTGATGCGCAGACCGTGCAGGATACGGTGACGCAGGTTATCGAACAGAATATGAACGGTATCGATAACCTGATGTATATGTCCTCCACCAGCGATTCCGCCGGTAGCGTGACAATTACCCTTACCTTCCAGTCCGGGACCGATCCTGATATCGCGCAAGTGCAGGTGCAGAACAAACTCCAGCTCGCCACGCCGTTGCTGCCGCAGGAGGTTCAGCAGCAGGGGATCAGTGTTGAAAAGTCCAGTAGCAGCTATTTGATGGTGGCGGGCTTTGTCTCTGATAACCCAGGCACCACACAGGACGATATCTCGGACTATGTGGCCTCTAACGTTAAAGATACGCTTAGCCGTCTGAATGGCGTCGGTGACGTACAGCTTTTCGGCGCACAGTATGCGATGCGTATCTGGCTGGATGCCGATCTGCTAAACAAATATAAACTGACACCGGTTGATGTGATTAACCAGTTGAAGGTACAGAACGATCAGATCGCTGCCGGACAGTTGGGCGGAACGCCAGCGTTACCAGGGCAACAATTGAACGCCTCGATTATTGCTCAGACGCGGTTTAAAAATCCGGAAGAATTCGGCAAAGTGACCCTGCGCGTAAACAGTGACGGCTCGGTGGTACGCCTGAAAGATGTCGCACGGGTTGAACTTGGCGGTGAAAACTATAACGTTATCGCTCGTATCAACGGAAAACCGGCGGCGGGCCTGGGGATTAAGCTGGCAACCGGCGCGAATGCTCTCGATACCGCGAAAGCCATTAAGGCAAAACTGGCGGAATTACAGCCATTCTTCCCGCAGGGAATGAAGGTTCTCTACCCTTATGACACCACGCCATTCGTCCAGCTTTCTATTCACGAAGTGGTAAAAACGCTGTTCGAAGCCATTATGCTGGTGTTCCTGGTGATGTATCTGTTCTTGCAGAATATGCGAGCAACGCTGATCCCCACCATTGCGGTACCCGTGGTGTTGTTAGGGACGTTTGCCATCCTCGCCGCTTTTGGTTACTCCATCAACACACTAACGATGTTCGGGATGGTGCTTGCCATCGGGCTGCTCGTCGATGATGCGATAGTGGTGGTGGAGAACGTCGAGCGCGTGATGATGGAGGATAAGCTCCCGCCAAAAGAAGCGACGGAAAAATCGATGTCGCAAATTCAGGGCGCACTGGTGGGTATCGCGATGGTGCTGTCAGCGGTATTTATTCCGATGGCATTCTTCGGCGGTTCTACTGGGGCAATTTATCGCCAGTTCTCTATCACCATCGTTTCGGCAATGGCGCTTTCTGTTCTGGTGGCATTGATTCTTACCCCTGCGTTATGTGCAACGCTGCTTAAACCCGTCTCTGCTGAGCATCACGAAAATAAGGGCGGTTTCTTCGGTTGGTTTAATACCACCTTCGATCATAGCGTTAACCACTACACCAACAGCGTCGGCAAAATCCTCGGATCCACAGGACGATATTTACTGATCTATGCGCTGATTGTTGCAGGAATGGTGGTGTTGTTTTTACGTCTTCCGTCTTCCTTCTTACCTGAAGAGGATCAGGGTGTCTTTCTGACCATGATTCAGTTACCCGCTGGCGCGACGCAAGAGCGGACGCAAAAAGTGTTGGATCAAGTTACGGATTACTATCTGAAGAACGAGAAAGCGAACGTTGAAAGTGTCTTTACGGTTAACGGCTTTAGCTTCAGCGGCCAGGCACAAAACGCCGGTATGGCCTTCGTCAGTCTGAAACCGTGGGAAGAGCGTAATGGTGACGAAAACAGTGCGGAAGCGGTAATCCATCGTGCCAAAATGGAATTGGGCAAGATCCGCGACGGTTTTGTCATTCCATTCAATATGCCAGCCATTGTTGAACTGGGCACGGCAACGGGTTTCGACTTTGAGTTAATTGATCAGGCTGGGCTGGGTCACGATGCCCTAACCCAGGCCCGTAACCAGTTGCTTGGTATGGCGGCGCAACATCCTGCCAGCTTAGTCAGCGTGCGCCCTAATGGCCTGGAAGACACCGCGCAGTTTAAACTGGAAGTTGACCAGGAAAAGGCGCAGGCATTAGGTGTTTCACTTTCTGACATCAATCAGACCATTTCAACGGCGCTGGGTGGGACTTACGTTAACGACTTCATCGACCGTGGCCGCGTGAAAAAGTTGTATGTTCAGGCGGATGCCAAATTCCGTATGCTGCCAGAAGATGTCGATAAACTTTATGTCCGCAGCGCCAACGGCGAAATGGTGCCATTCTCGGCCTTTACCACTTCACATTGGGTGTATGGCTCTCCGCGACTGGAACGCTACAACGGTCTGCCGTCAATGGAGATTCAGGGGGAAGCCGCGCCAGGAACCAGTTCCGGCGATGCCATGGCGTTGATGGAAAACCTTGCGTCAAAATTACCTGCGGGCATTGGTTATGACTGGACGGGTATGTCGTATCAGGAACGCTTATCGGGAAACCAGGCTCCCGCTCTGGTAGCAATTTCCTTTGTGGTTGTTTTCCTGTGCCTTGCTGCACTCTATGAAAGCTGGTCAATTCCTGTCTCGGTTATGTTGGTAGTGCCGTTAGGGATTGTCGGCGTGCTGCTGGCGGCGACACTCTTTAATCAAAAAAATGACGTCTACTTTATGGTGGGCTTGCTAACGACAATTGGCTTGTCGGCCAAAAACGCTATTTTGATCGTTGAGTTCGCTAAAGATCTCATGGAGAAAGAGGGTAAAGGTGTTGTTGAAGCGACACTGATGGCAGTACGTATGCGTCTGCGTCCTATCCTGATGACCTCTCTCGCCTTTATTCTCGGCGTATTACCGCTAGCTATCAGTAACGGTGCCGGCAGTGGCGCGCAGAACGCTGTGGGTATCGGGGTAATGGGAGGAATGGTCTCTGCAACGTTGCTGGCAATCTTCTTCGTACCGGTGTTCTTTGTGGTGATCCGCCGTTGCTTTAAAGGATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36849","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. MG1655","NCBI_taxonomy_id":"511145"}}}},"ARO_accession":"3000502","ARO_id":"36641","ARO_name":"AcrF","CARD_short_name":"AcrF","ARO_description":"AcrF is a inner membrane transporter, similar to AcrB.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1445":{"model_id":"1445","model_name":"AcrE","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"675"}},"model_sequences":{"sequence":{"333":{"protein_sequence":{"accession":"AAC76297.1","sequence":"MTKHARFFLLPSFILISAALIAGCNDKGEEKAHVGEPQVTVHIVKTAPLEVKTELPGRTNAYRIAEVRPQVSGIVLNRNFTEGSDVQAGQSLYQIDPATYQANYDSAKGELAKSEAAAAIAHLTVKRYVPLVGTKYISQQEYDQAIADARQADAAVIAAKATVESARINLAYTKVTAPISGRIGKSTVTEGALVTNGQTTELATVQQLDPIYVDVTQSSNDFMRLKQSVEQGNLHKENATSNVELVMENGQTYPLKGTLQFSDVTVDESTGSITLRAVFPNPQHTLLPGMFVRARIDEGVQPDAILIPQQGVSRTPRGDATVLIVNDKSQVEARPVVASQAIGDKWLISEGLKSGDQVIVSGLQKARPGEQVKATTDTPADTASK"},"dna_sequence":{"accession":"U00096.1","fmin":"3413863","fmax":"3415021","strand":"+","sequence":"ATGACGAAACATGCCAGGTTTTTCCTCCTGCCCTCCTTTATTCTGATCTCCGCGGCTTTAATCGCCGGTTGTAACGATAAGGGAGAAGAGAAAGCTCACGTCGGTGAACCGCAGGTTACCGTTCATATTGTAAAAACGGCCCCGTTAGAAGTTAAGACTGAATTACCAGGCCGCACCAATGCTTATCGTATAGCCGAAGTTCGCCCACAGGTTAGCGGGATCGTACTGAATCGCAATTTCACTGAAGGCAGCGATGTGCAAGCAGGCCAGTCCCTGTACCAGATCGATCCCGCGACCTATCAGGCAAATTATGACAGCGCGAAAGGCGAACTGGCGAAAAGTGAAGCCGCCGCCGCCATCGCGCATTTGACGGTAAAACGTTACGTTCCGCTCGTGGGTACGAAATACATCAGCCAGCAGGAGTACGACCAGGCCATTGCTGATGCTCGTCAGGCCGATGCCGCCGTGATTGCCGCAAAAGCCACAGTCGAAAGCGCTCGCATCAATCTTGCTTATACCAAAGTCACTGCGCCAATTAGCGGACGTATCGGCAAATCGACTGTGACCGAAGGCGCTCTTGTCACTAATGGGCAAACGACTGAACTGGCGACTGTCCAGCAGCTCGATCCTATCTACGTTGATGTGACCCAATCCAGCAACGATTTTATGAGGCTGAAGCAATCCGTAGAGCAAGGAAATTTGCATAAGGAAAACGCCACCAGCAACGTAGAGTTGGTCATGGAAAACGGTCAAACCTATCCCCTGAAAGGTACGCTGCAATTCTCCGATGTGACCGTTGATGAAAGCACCGGCTCCATAACCCTACGTGCTGTCTTCCCTAACCCGCAACATACGCTTTTGCCGGGTATGTTTGTGCGTGCACGGATTGATGAAGGCGTCCAACCTGACGCCATTCTTATCCCGCAACAAGGCGTTAGCCGCACACCGCGTGGTGATGCAACCGTGCTGATTGTTAACGATAAAAGTCAGGTTGAAGCGCGCCCTGTCGTTGCCAGTCAGGCGATTGGCGATAAATGGTTGATTAGTGAAGGACTGAAATCTGGCGATCAAGTCATTGTCAGCGGCCTGCAAAAAGCGCGTCCGGGAGAGCAGGTTAAAGCCACTACCGATACCCCCGCAGATACTGCATCGAAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36849","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. MG1655","NCBI_taxonomy_id":"511145"}}}},"ARO_accession":"3000499","ARO_id":"36638","ARO_name":"AcrE","CARD_short_name":"AcrE","ARO_description":"AcrE is a membrane fusion protein, similar to AcrA.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1342":{"model_id":"1342","model_name":"Plasmid-encoded cat (pp-cat)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"486":{"protein_sequence":{"accession":"BAA03718.1","sequence":"MEKKITGYTTVDISQWHRKEHFEAFQSVAQCTYNQTVQLDITAFLKTVKKNKHKFYPAFIHILARLMNAHPEFRMAMKDGELVIWDSVHPCYTVFHEQTETFSSLWSEYHDDFRQFLHIYSQDIACYGENLAYFPKGFIENMFFVSANPWVSFTSFDLNVANMDNFFAPVFTMGKYYTQGDKVLMPLAIQVHHAVCDGFHVGRMLNELQQYCDEWQGGA"},"dna_sequence":{"accession":"D16171.1","fmin":"382","fmax":"1042","strand":"+","sequence":"ATGGAGAAAAAAATCACTGGATATACCACCGTTGATATATCCCAATGGCATCGTAAAGAACATTTTGAGGCATTTCAGTCAGTTGCTCAATGTACCTATAACCAGACCGTTCAGCTGGATATTACGGCTTTCTTAAAAACCGTAAAGAAAAATAAGCACAAATTTTATCCGGCCTTTATTCACATTCTTGCCCGCCTGATGAATGCTCATCCGGAATTCCGTATGGCAATGAAAGACGGTGAGCTGGTGATATGGGATAGTGTTCACCCTTGTTACACCGTATTCCATGAGCAAACTGAAACGTTTTCATCGCTCTGGAGTGAATACCACGACGATTTCCGGCAGTTTCTACACATATATTCGCAAGATATAGCGTGTTACGGTGAAAACCTGGCCTATTTCCCCAAAGGGTTCATTGAGAATATGTTTTTCGTCTCAGCCAATCCCTGGGTGAGTTTCACCAGTTTTGATTTAAACGTGGCCAATATGGACAACTTCTTCGCCCCCGTTTTCACCATGGGCAAATATTATACGCAAGGCGACAAGGTGCTGATGCCGCTGGCGATTCAGGTTCATCATGCCGTTTGTGATGGCTTCCATGTCGGCAGAATGCTTAATGAATTACAACAGTACTGCGATGAGTGGCAGGGCGGGGCGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39539","NCBI_taxonomy_name":"Photobacterium damselae subsp. piscicida","NCBI_taxonomy_id":"38294"}}}},"ARO_accession":"3002689","ARO_id":"39123","ARO_name":"Plasmid-encoded cat (pp-cat)","CARD_short_name":"pp_cat","ARO_description":"Plasmid-encoded cat, or pp-cat, is a plasmid-encoded variant of the cat gene found in Photobacterium damselae subsp. piscicida.","ARO_category":{"36261":{"category_aro_accession":"3000122","category_aro_cvterm_id":"36261","category_aro_name":"chloramphenicol acetyltransferase (CAT)","category_aro_description":"Inactivates chloramphenicol by addition of an acyl group. CAT is used to describe many variants of the chloramphenicol acetyltransferase gene in a range of organisms including Acinetobacter calcoaceticus, Agrobacterium tumefaciens, Alkalihalobacillus clausii, Bacillus subtilis, Campylobacter coli, Enterococcus faecalis, Enterococcus faecium, Lactococcus lactis, Listeria monocytogenes, Listonella anguillarum, Morganella morganii, Photobacterium damselae subsp. piscicida, Proteus mirabilis, Salmonella typhi, Serratia marcescens, Shigella flexneri, Staphylococcus aureus, Staphylococcus haemolyticus, Staphylococcus intermedius, Streptococcus agalactiae, Streptococcus suis and Streptomyces acrimycini.","category_aro_class_name":"AMR Gene Family"},"36521":{"category_aro_accession":"3000382","category_aro_cvterm_id":"36521","category_aro_name":"azidamfenicol","category_aro_description":"Azidamfenicol is a water soluble derivative of chloramphenicol, sharing the same mode of action of inhibiting peptide synthesis by interacting with the 23S RNA of the 50S ribosomal subunit.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36595":{"category_aro_accession":"3000456","category_aro_cvterm_id":"36595","category_aro_name":"thiamphenicol","category_aro_description":"Derivative of Chloramphenicol. The nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3).","category_aro_class_name":"Antibiotic"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1316":{"model_id":"1316","model_name":"Pseudomonas aeruginosa catB6","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"295":{"protein_sequence":{"accession":"CAA11473.1","sequence":"MENYFDSPFKGKLLSEQVTNRNIKVGRYSYYSGYYHGHSFDDCARYLLPDRDDVDKLIIGSFCSIGSGASFIMAGNQGHRHDWVTSFPFFYMQEEPAFSSSTDAFQKAGDTIVGNDVWIGSEAMIMPGIKIGDGAVIGSRSLVTRDVEPYTIIGGNPAKQIKKRFSDEEISLLMEMEWWNWPLDKIKTAMPLLCSSDIFGLHRHWRGIAV"},"dna_sequence":{"accession":"AJ223604.1","fmin":"3017","fmax":"3650","strand":"+","sequence":"ATGGAAAATTACTTTGACAGTCCCTTCAAAGGGAAACTACTTTCAGAGCAAGTGACTAACCGCAACATCAAAGTTGGTCGGTACAGCTACTACTCTGGTTACTATCACGGGCATTCATTTGATGACTGCGCACGATACTTGCTCCCAGACCGTGATGACGTTGACAAACTAATCATCGGCAGCTTTTGCTCCATCGGAAGCGGGGCTTCTTTCATCATGGCGGGCAATCAGGGTCACCGGCATGACTGGGTAACATCTTTCCCTTTCTTCTACATGCAAGAAGAGCCAGCTTTTTCAAGTTCAACGGACGCCTTTCAAAAGGCCGGTGACACCATCGTCGGCAATGATGTCTGGATAGGATCAGAGGCAATGATTATGCCCGGCATCAAGATTGGAGATGGCGCGGTAATAGGCAGCCGATCGTTGGTGACGAGAGATGTAGAACCCTATACCATCATTGGCGGAAACCCTGCAAAGCAAATTAAAAAGCGATTCTCTGACGAGGAGATTTCATTACTCATGGAAATGGAGTGGTGGAACTGGCCGTTAGATAAAATCAAAACAGCTATGCCCCTTCTCTGCTCTTCAGACATTTTTGGTCTGCACAGGCATTGGCGTGGGATTGCCGTCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002678","ARO_id":"39112","ARO_name":"Pseudomonas aeruginosa catB6","CARD_short_name":"Paer_catB6","ARO_description":"catB6 is a plasmid-encoded variant of the cat gene found in Pseudomonas aeruginosa.","ARO_category":{"36261":{"category_aro_accession":"3000122","category_aro_cvterm_id":"36261","category_aro_name":"chloramphenicol acetyltransferase (CAT)","category_aro_description":"Inactivates chloramphenicol by addition of an acyl group. CAT is used to describe many variants of the chloramphenicol acetyltransferase gene in a range of organisms including Acinetobacter calcoaceticus, Agrobacterium tumefaciens, Alkalihalobacillus clausii, Bacillus subtilis, Campylobacter coli, Enterococcus faecalis, Enterococcus faecium, Lactococcus lactis, Listeria monocytogenes, Listonella anguillarum, Morganella morganii, Photobacterium damselae subsp. piscicida, Proteus mirabilis, Salmonella typhi, Serratia marcescens, Shigella flexneri, Staphylococcus aureus, Staphylococcus haemolyticus, Staphylococcus intermedius, Streptococcus agalactiae, Streptococcus suis and Streptomyces acrimycini.","category_aro_class_name":"AMR Gene Family"},"36521":{"category_aro_accession":"3000382","category_aro_cvterm_id":"36521","category_aro_name":"azidamfenicol","category_aro_description":"Azidamfenicol is a water soluble derivative of chloramphenicol, sharing the same mode of action of inhibiting peptide synthesis by interacting with the 23S RNA of the 50S ribosomal subunit.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36595":{"category_aro_accession":"3000456","category_aro_cvterm_id":"36595","category_aro_name":"thiamphenicol","category_aro_description":"Derivative of Chloramphenicol. The nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3).","category_aro_class_name":"Antibiotic"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1472":{"model_id":"1472","model_name":"DHA-18","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1171":{"protein_sequence":{"accession":"AIT76094.1","sequence":"MKKSLSATLISALLAFSAPGFSAADNVAAVVDSTIKPLMAQQDIPGMAVAVSVKGKPYYFNYGFADVQAKQPVTENTLFELGSVSKTFTGVLGAVSVAKKETALNDPAAKYQPELALPQWKGITLLDLATYTAGGLPLQVPDAVKSRADLLNFYQQWQPSWKPGDMRLYANSSIGLFGALTANAAGMPYEQLLTARILAPLGLSHTFITVPESVQSRYAYGYKNKKPVRVSPGQLDAESYGVKSASKDMLRWAEMNMEPSRAGNADLEMAMYLAQTRYYKTAAINQGLGWEMYDWPQQKDMIINGVTNEVALQPHPVTDNQVQPYNRASWVHKTGATTGFGAYVAFIPEKQVAIVILANKNYPNTERVKAAQAILSALE"},"dna_sequence":{"accession":"KM087841.1","fmin":"0","fmax":"1140","strand":"+","sequence":"ATGAAAAAATCGTTATCTGCAACACTGATTTCTGCCCTGCTGGCGTTTTCCGCCCCGGGGTTTTCTGCCGCTGATAATGTCGCAGCGGTGGTGGACAGCACTATTAAACCGCTGATGGCACAGCAGGATATTCCCGGGATGGCGGTTGCCGTATCCGTAAAGGGCAAGCCCTATTATTTTAACTATGGTTTTGCCGATGTTCAGGCAAAACAGCCGGTCACTGAAAATACACTATTTGAGCTCGGATCTGTAAGTAAAACTTTCACAGGTGTGCTGGGTGCGGTTTCTGTGGCGAAAAAAGAGACGGCGCTGAATGATCCGGCGGCAAAATATCAGCCGGAGCTGGCTCTGCCGCAGTGGAAGGGGATCACGCTGCTGGATCTGGCCACCTATACCGCAGGCGGGCTGCCGTTACAGGTACCGGATGCGGTGAAAAGCCGTGCGGATCTGCTGAATTTCTATCAGCAGTGGCAGCCATCATGGAAACCGGGCGATATGCGTCTGTATGCAAACAGCAGTATCGGCCTGTTTGGTGCTCTGACCGCCAATGCGGCGGGGATGCCGTATGAGCAGTTGCTGACCGCGCGGATCCTGGCACCGCTGGGATTATCTCACACCTTTATTACCGTGCCGGAAAGTGTGCAAAGCCGGTATGCGTACGGCTATAAAAACAAAAAACCGGTCCGCGTGTCGCCGGGACAGCTTGATGCGGAATCTTACGGCGTGAAATCCGCCTCAAAAGATATGCTGCGCTGGGCGGAAATGAATATGGAGCCGTCACGGGCCGGTAATGCGGATCTGGAAATGGCAATGTATCTCGCCCAGACCCGCTACTATAAAACCGCCGCGATTAACCAGGGGCTGGGCTGGGAAATGTATGACTGGCCGCAGCAGAAAGATATGATCATTAACGGTGTGACCAACGAGGTCGCATTGCAGCCGCATCCGGTAACAGACAACCAGGTTCAGCCGTATAACCGTGCTTCCTGGGTGCATAAAACGGGGGCAACAACTGGTTTCGGCGCCTATGTGGCCTTTATTCCGGAAAAACAGGTGGCGATTGTGATTCTGGCGAATAAAAACTACCCGAATACCGAAAGAGTCAAAGCTGCACAGGCTATTTTGAGTGCACTGGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36917","NCBI_taxonomy_name":"Morganella morganii","NCBI_taxonomy_id":"582"}}}},"ARO_accession":"3002149","ARO_id":"38549","ARO_name":"DHA-18","CARD_short_name":"DHA-18","ARO_description":"DHA-18 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36207":{"category_aro_accession":"3000068","category_aro_cvterm_id":"36207","category_aro_name":"DHA beta-lactamase","category_aro_description":"DHA beta-lactamases are plasmid-mediated AmpC \u03b2-lactamases that confer resistance to cephamycins and oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1473":{"model_id":"1473","model_name":"CTX-M-44","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1903":{"protein_sequence":{"accession":"BAA07082.1","sequence":"MMTQSIRRSMLTVMATLPLLFSSATLHAQANSVQQQLEALEKSSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKQSESDKHLLNQRVEIKKSDLVNYNPIAEKHVNGTMTLAELGAAALQYSDNTAMNKLIAHLGGPDKVTAFARSLGDETFRLDRTEPTLNTAIPGDPRDTTTPLAMAQTLKNLTLGKALAETQRAQLVTWLKGNTTGSASIRAGLPKSWVVGDKTGSGDYGTTNDIAVIWPENHAPLVLVTYFTQPEQKAERRRDILAAAAKIVTHGF"},"dna_sequence":{"accession":"D37830.1","fmin":"90","fmax":"966","strand":"+","sequence":"ATGATGACTCAGAGCATTCGCCGCTCAATGTTAACGGTGATGGCGACGCTACCCCTGCTATTTAGCAGCGCAACGCTGCATGCGCAGGCGAACAGCGTGCAACAGCAGCTGGAAGCCCTGGAGAAAAGTTCGGGAGGTCGGCTTGGCGTTGCGCTGATTAACACCGCCGATAATTCGCAGATTCTCTACCGTGCCGATGAACGTTTTGCGATGTGCAGTACCAGTAAGGTGATGGCGGCCGCGGCGGTGCTTAAACAGAGCGAGAGCGATAAGCACCTGCTAAATCAGCGCGTTGAAATCAAGAAGAGCGACCTGGTTAACTACAATCCCATTGCGGAGAAACACGTTAACGGCACGATGACGCTGGCTGAGCTTGGCGCAGCGGCGCTGCAGTATAGCGACAATACTGCCATGAATAAGCTGATTGCCCATCTGGGTGGTCCCGATAAAGTGACGGCGTTTGCTCGCTCGTTGGGTGATGAGACCTTCCGTCTGGACAGAACCGAGCCCACGCTCAATACCGCCATTCCAGGCGACCCGCGTGATACCACCACGCCGCTCGCGATGGCGCAGACCCTGAAAAATCTGACGCTGGGTAAAGCGCTGGCGGAAACTCAGCGGGCACAGTTGGTGACGTGGCTTAAGGGCAATACTACCGGTAGCGCGAGCATTCGGGCGGGTCTGCCGAAATCATGGGTAGTGGGCGATAAAACCGGCAGCGGAGATTATGGCACCACCAACGATATCGCGGTTATCTGGCCGGAAAACCACGCACCGCTGGTTCTGGTGACCTACTTTACCCAACCGGAGCAGAAGGCGGAAAGGCGTCGGGATATTCTGGCTGCGGCGGCGAAAATCGTAACCCACGGTTTCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001906","ARO_id":"38306","ARO_name":"CTX-M-44","CARD_short_name":"CTX-M-44","ARO_description":"CTX-M-44 is a beta-lactamase found in the Enterobacteriaceae family.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1475":{"model_id":"1475","model_name":"SHV-99","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1070":{"protein_sequence":{"accession":"CAQ03504.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVGYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AM941845.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGGCTACTCGCCGGTCAGCGAAAAACATCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATCGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001337","ARO_id":"37737","ARO_name":"SHV-99","CARD_short_name":"SHV-99","ARO_description":"SHV-99 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1476":{"model_id":"1476","model_name":"TEM-199","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8407":{"protein_sequence":{"accession":"AFN69127.1","sequence":"QHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDKLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVKYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNIGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGASERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"JX050178.1","fmin":"1","fmax":"853","strand":"+","sequence":"CAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATAAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTAAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATTGGGGATCATGTAACCCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCAGTGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3001058","ARO_id":"37438","ARO_name":"TEM-199","CARD_short_name":"TEM-199","ARO_description":"TEM-199 is a beta-lactamase.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1478":{"model_id":"1478","model_name":"CARB-10","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1856":{"protein_sequence":{"accession":"ACJ61335.1","sequence":"MDVRQHKASFFSVVITFLCLTLSLNANATDSVLEAVTNAETELGARIGLAAHDLETGKRWEHKSNERFPLTSTFKTLACANVLQRVDLGKERIDRVVRFSESNLVTYSPVTEKHVGKKGMSLAELCQATLSTSDNSAANFILQAIGGPKALTKFLRSIGDDTTRLDRWETELNEAVPGDKRDTTTPIAMVTTLEKLLIDETLSIKSRQQLESWLKGNEVGDALFRKGVPSDWIVADRTGAGGYGSRAITAVMWPPNRKPIVAALYITETDASFEERNAVIAKIGEQIAKTVLMENSRN"},"dna_sequence":{"accession":"EU850412.1","fmin":"2269","fmax":"3166","strand":"+","sequence":"ATGGACGTACGTCAACACAAGGCTAGTTTTTTTAGCGTAGTAATTACTTTTTTATGTCTCACGCTATCATTAAATGCTAATGCAACAGACTCAGTACTTGAAGCGGTTACCAATGCTGAAACTGAATTAGGCGCTAGAATTGGTCTAGCTGCGCATGATTTGGAAACGGGAAAACGTTGGGAACATAAATCTAATGAACGTTTTCCTCTAACTAGTACCTTTAAAACACTTGCCTGTGCAAACGTTCTTCAAAGAGTTGATCTAGGTAAAGAAAGAATTGATAGAGTTGTGAGATTCTCTGAAAGCAATCTCGTTACATACTCACCTGTAACAGAAAAACATGTGGGTAAAAAAGGGATGTCGCTCGCAGAGCTGTGTCAGGCCACATTATCAACCAGTGATAATTCAGCTGCCAATTTTATTCTACAAGCGATTGGGGGACCTAAGGCTCTAACGAAATTTTTGCGTTCCATTGGCGACGATACTACGCGCCTTGATCGCTGGGAAACAGAACTTAACGAAGCGGTGCCTGGAGATAAGCGAGACACGACAACACCAATTGCAATGGTAACGACACTTGAAAAGTTACTAATTGACGAAACACTATCTATCAAATCTCGTCAACAACTAGAATCTTGGCTTAAAGGTAATGAGGTTGGCGATGCATTGTTTCGTAAAGGCGTTCCAAGTGACTGGATAGTAGCAGATAGAACAGGCGCTGGTGGTTATGGGTCGCGTGCTATTACTGCGGTGATGTGGCCTCCAAATCGCAAGCCTATCGTAGCCGCTCTATACATTACAGAGACAGACGCCTCGTTTGAAGAAAGAAATGCTGTCATTGCAAAAATTGGTGAGCAAATAGCGAAGACAGTATTAATGGAGAATAGCCGTAACTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3002249","ARO_id":"38649","ARO_name":"CARB-10","CARD_short_name":"CARB-10","ARO_description":"CARB-10 is a beta-lactamase found in Acinetobacter baumannii.","ARO_category":{"36230":{"category_aro_accession":"3000091","category_aro_cvterm_id":"36230","category_aro_name":"CARB beta-lactamase","category_aro_description":"CARB beta-lactamases are class A lactamases that can hydrolyze carbenicillin. Many of the PSE beta-lactamases have been renamed as CARB-lactamases with the notable exception of PSE-2 which is now OXA-10.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1479":{"model_id":"1479","model_name":"IMP-40","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1868":{"protein_sequence":{"accession":"BAM62794.1","sequence":"MSKLSVFFIFLFCSIATAAESLPDLKIEKLDEGVYVHTSFEEVNGWGVFPKHGLVVLVNAEAYLIDTPSTAKDTEKLVTWFVERGYKIKGSISSHFHSDSTGGIEWLNSRSIPTYASELTNELLKKDGKVQATNSFSGVNYWLVKNKIEVFYPGPGHTPDNVVVWLPERKILFGGCFIKPYGLGNLGDANIEAWPKSAKLLKSKYGKAKLVVPSHSEVGDASLLKLTLEQAVKGLNESKKPSKPSN"},"dna_sequence":{"accession":"AB753457.1","fmin":"0","fmax":"741","strand":"+","sequence":"ATGAGCAAGTTATCTGTATTCTTTATATTTTTGTTTTGCAGCATTGCTACCGCAGCAGAGTCTTTGCCAGATTTAAAAATTGAAAAGCTTGATGAAGGCGTTTATGTTCATACTTCGTTTGAAGAAGTTAACGGGTGGGGCGTTTTTCCTAAACATGGTTTGGTGGTTCTTGTAAATGCTGAGGCTTACCTAATTGACACTCCATCTACGGCTAAAGATACTGAAAAGTTAGTCACTTGGTTTGTGGAGCGTGGCTATAAAATAAAAGGCAGCATTTCCTCTCATTTTCATAGCGACAGCACGGGCGGAATAGAGTGGCTTAATTCTCGATCTATCCCCACGTATGCATCTGAATTAACAAATGAACTGCTTAAAAAAGACGGTAAGGTTCAAGCCACAAATTCATTTAGCGGAGTTAACTATTGGCTAGTTAAAAATAAAATTGAAGTTTTTTATCCAGGCCCGGGACACACTCCAGATAACGTAGTGGTTTGGTTGCCTGAAAGGAAAATATTATTCGGTGGTTGTTTTATTAAACCGTACGGTTTAGGCAATTTGGGTGACGCAAATATAGAAGCTTGGCCAAAGTCCGCCAAATTATTAAAGTCCAAATATGGTAAGGCAAAACTGGTTGTTCCAAGTCACAGTGAAGTTGGAGACGCATCACTCTTGAAACTTACATTAGAGCAGGCGGTTAAAGGGTTAAACGAAAGTAAAAAACCATCAAAACCAAGCAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002231","ARO_id":"38631","ARO_name":"IMP-40","CARD_short_name":"IMP-40","ARO_description":"IMP-40 is a beta-lactamase found in Pseudomonas and Acinetobacter spp.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1481":{"model_id":"1481","model_name":"OXY-1-4","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"896":{"protein_sequence":{"accession":"AAL78276.1","sequence":"MLKSSWRKTALMAAAVPLLLASGSLWASADAIQQKLADLEKRSGGRLGVALINTADDSQTLYRGDERFAMCSTGKVMAAAAVLKQSESNPEVVNKRLEIKKSDLVVWSPITEKHLQSGMTLAELSAAALQYSDNTAMNKMISYLGGPEKVTAFAQSIGDVTFRLDRTEPALNSAIPGDKRDTTTPLAMAESLRKLTLGNALGEQQRAQLVTWLKGNTTGGQSIRAGLPASWVVGDKTGAGDYGTTNDIAVIWPENHAPLVLVTYFTQPQQDAKSRKEVLAAAAKIVTEGL"},"dna_sequence":{"accession":"AY077483.1","fmin":"182","fmax":"1055","strand":"+","sequence":"ATGTTGAAAAGTTCGTGGCGTAAAACCGCCCTGATGGCCGCCGCCGTTCCGCTGCTGCTGGCGAGCGGTTCATTATGGGCCAGTGCCGATGCTATCCAGCAAAAGCTGGCTGATTTAGAAAAACGTTCCGGCGGTCGGCTGGGCGTAGCGCTGATTAACACGGCAGATGATTCGCAAACCCTCTATCGCGGCGATGAACGTTTTGCCATGTGCAGCACCGGTAAAGTGATGGCCGCCGCCGCGGTGTTAAAACAGAGCGAAAGCAATCCAGAGGTGGTGAATAAAAGGCTGGAGATTAAAAAATCGGATTTAGTGGTCTGGAGCCCGATCACCGAAAAACATCTGCAAAGCGGAATGACCCTGGCGGAACTCAGCGCGGCGGCGCTGCAGTACAGCGACAATACCGCGATGAATAAGATGATTAGCTACCTTGGCGGACCGGAAAAGGTGACCGCATTCGCCCAGAGTATCGGGGATGTCACTTTTCGTCTCGATCGTACGGAGCCGGCGCTGAACAGCGCGATTCCCGGCGATAAGCGCGATACCACCACCCCGTTGGCGATGGCCGAAAGCCTGCGCAAGCTGACGCTGGGCAATGCGCTGGGCGAACAGCAGCGCGCCCAGTTAGTGACGTGGCTAAAAGGCAATACCACCGGCGGGCAAAGCATTCGCGCAGGCCTGCCCGCAAGCTGGGTGGTCGGGGATAAAACCGGCGCCGGAGATTACGGCACCACCAACGATATCGCGGTGATCTGGCCGGAAAATCATGCCCCGCTGGTGCTGGTGACCTATTTTACCCAGCCGCAGCAGGATGCGAAAAGCCGCAAAGAGGTGTTAGCCGCGGCGGCAAAAATCGTCACCGAAGGGCTTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3002392","ARO_id":"38792","ARO_name":"OXY-1-4","CARD_short_name":"OXY-1-4","ARO_description":"OXY-1-4 is a beta-lactamase found in Klebsiella oxytoca.","ARO_category":{"38788":{"category_aro_accession":"3002388","category_aro_cvterm_id":"38788","category_aro_name":"OXY beta-lactamase","category_aro_description":"OXY beta-lactamases are chromosomal class A beta-lactamases that are found in Klebsiella oxytoca. At constitutive low levels, OXY beta-lactamases confer resistance to aminopenicillins and carboxypenicillins. At high induced levels,  OXY beta-lactamases confer resistance to penicillins, cephalosporins and aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1482":{"model_id":"1482","model_name":"SME-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"1319":{"protein_sequence":{"accession":"CAA82281.1","sequence":"MSNKVNFKTASFLFSVCLALSAFNAHANKSDAAAKQIKKLEEDFDGRIGVFAIDTGSGNTFGYRSDERFPLCSSFKGFLAAAVLERVQQKKLDINQKVKYESRDLEYHSPITTKYKGSGMTLGDMASAALQYSDNGATNIIMERFLGGPEGMTKFMRSIGDNEFRLDRWELELNTAIPGDKRDTSTPKAVANSLNKLALGNVLNAKVKAIYQNWLKGNTTGDARIRASVPADWVVGDKTGSCGAIGTANDYAVIWPKNRAPLIVSIYTTRKSKDDKHSDKTIAEASRIAIQAID"},"dna_sequence":{"accession":"Z28968.1","fmin":"0","fmax":"885","strand":"+","sequence":"ATGTCAAACAAAGTAAATTTTAAAACGGCTTCATTTTTGTTTAGTGTTTGTTTAGCTTTGTCGGCATTTAATGCTCATGCTAACAAAAGTGATGCTGCGGCAAAACAAATAAAAAAATTAGAGGAAGACTTTGATGGGAGGATTGGCGTCTTTGCAATAGATACAGGATCGGGTAATACATTTGGGTATAGATCAGATGAGCGGTTCCCTTTATGCAGTTCATTTAAAGGTTTTTTGGCGGCTGCTGTTTTAGAGAGGGTGCAACAAAAAAAACTAGATATCAACCAAAAGGTTAAATATGAGAGTAGGGATCTAGAATATCATTCACCTATTACAACAAAATATAAAGGCTCAGGTATGACATTAGGTGATATGGCTTCTGCTGCATTGCAATATAGCGACAATGGGGCAACAAATATAATTATGGAACGATTTCTTGGCGGTCCTGAGGGGATGACTAAATTTATGCGTTCTATTGGAGATAATGAGTTTAGGTTAGATCGCTGGGAACTGGAACTTAACACTGCAATCCCAGGAGATAAACGTGACACTTCAACGCCAAAAGCTGTTGCAAATAGTTTGAATAAACTAGCTTTGGGGAATGTTCTCAATGCTAAAGTGAAAGCGATTTATCAAAATTGGTTAAAAGGTAATACAACTGGTGATGCTCGAATTCGTGCTAGTGTTCCTGCTGATTGGGTTGTAGGTGACAAAACTGGGAGCTGTGGGGCTATAGGTACTGCGAATGATTATGCCGTCATTTGGCCTAAAAATAGAGCACCATTAATTGTCTCTATATATACAACACGAAAATCGAAAGATGATAAGCACAGTGATAAAACTATTGCGGAAGCATCACGTATTGCAATTCAGGCAATTGATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36783","NCBI_taxonomy_name":"Serratia marcescens","NCBI_taxonomy_id":"615"}}}},"ARO_accession":"3002379","ARO_id":"38779","ARO_name":"SME-1","CARD_short_name":"SME-1","ARO_description":"SME-1 is a beta-lactamase found in Serratia marcescens.","ARO_category":{"36194":{"category_aro_accession":"3000055","category_aro_cvterm_id":"36194","category_aro_name":"SME beta-lactamase","category_aro_description":"SME beta-lactamases are chromosome-mediated class A beta-lactamases that hydrolyze carbapenems in Serratia marcescens.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1483":{"model_id":"1483","model_name":"AAC(3)-Xa","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"4702":{"protein_sequence":{"accession":"BAA78619.1","sequence":"MDETELLRRSDGPVTRDRIRHDLAALGLVPGDTVMFHTRLSAIGYVSGGPQTVIDALLDVVGPTGTLLVTCGWNDAPPYDFTDWPPAWQEAVRAHHPAFDPRTSEAEHANGRLPEALRRRPGAVRSRHPDVSLAALGASAPALMDAHPWDDPHGPGSPLARLVALGGRVLLLGAPRDTMTLLHHAEALAQAPGKRFVTYEQPIEVAGERVWRTFRDIDSEHGAFDYSSAVPEGQDPFAVIVGSMLAAGIGREGFVGAARSRLFDAAPAVEFGVRWIEEHLNRDR"},"dna_sequence":{"accession":"AB028210.1","fmin":"2710","fmax":"3565","strand":"-","sequence":"ATGGACGAGACGGAACTGCTGCGACGCTCCGACGGGCCCGTGACCCGGGACCGGATCCGGCACGACCTGGCCGCGCTCGGCCTCGTCCCGGGCGACACCGTGATGTTCCATACGCGGCTGTCCGCGATCGGCTACGTCTCCGGAGGCCCCCAGACCGTCATCGACGCCCTGCTGGACGTGGTGGGACCGACCGGCACTCTGTTGGTCACCTGCGGCTGGAACGACGCTCCGCCCTACGACTTCACCGACTGGCCTCCCGCCTGGCAGGAGGCCGTACGCGCCCACCACCCCGCGTTCGACCCGCGGACGAGCGAGGCCGAGCACGCCAACGGCCGCCTTCCGGAGGCCCTGCGCCGCAGACCGGGGGCCGTACGCAGTCGCCACCCCGACGTGAGTCTCGCGGCGCTCGGCGCCTCGGCCCCCGCTCTGATGGACGCCCACCCCTGGGACGATCCGCACGGTCCCGGCAGCCCGCTGGCGCGCCTGGTCGCCCTCGGCGGCCGGGTGCTGCTGCTCGGCGCGCCCCGGGACACGATGACGCTGCTGCACCACGCCGAGGCGCTGGCCCAGGCCCCCGGCAAGCGGTTCGTGACGTACGAGCAGCCCATCGAGGTGGCGGGCGAGCGGGTCTGGCGCACCTTCCGGGACATCGACTCCGAGCACGGTGCGTTCGACTACTCCTCGGCCGTGCCCGAGGGGCAGGACCCCTTCGCGGTGATCGTCGGTTCCATGCTCGCCGCGGGCATCGGACGGGAGGGCTTCGTCGGGGCGGCCAGGAGCCGGCTGTTCGACGCCGCCCCGGCCGTCGAGTTCGGCGTCCGCTGGATCGAGGAGCACCTGAACCGGGACCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36903","NCBI_taxonomy_name":"Streptomyces griseus","NCBI_taxonomy_id":"1911"}}}},"ARO_accession":"3002544","ARO_id":"38944","ARO_name":"AAC(3)-Xa","CARD_short_name":"AAC(3)-Xa","ARO_description":"AAC(3)-Xa is a chromosomal-encoded aminoglycoside acetyltransferase in Streptomyces griseus.","ARO_category":{"36461":{"category_aro_accession":"3000322","category_aro_cvterm_id":"36461","category_aro_name":"AAC(3)","category_aro_description":"A category of aminoglycoside N-acetyltransferase enzymes with modification regiospecificity based at the 3-amino group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics through acetylation of the 3-amino group of the compound.","category_aro_class_name":"AMR Gene Family"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1484":{"model_id":"1484","model_name":"ACT-27","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"941":{"protein_sequence":{"accession":"AHL39340.1","sequence":"MMKKSLCCALLLGISCSALAAPVSEKQLAEVVANTVTPLMKAQSVPGMAVAVIYQGKPHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMPYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPENVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVVEGSDSKVALAPLPVVEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANTSYPNPARVEAAYHILEALQ"},"dna_sequence":{"accession":"KJ207209.1","fmin":"454","fmax":"1600","strand":"+","sequence":"ATGATGAAAAAATCCCTTTGCTGCGCCCTGCTGCTCGGCATCTCTTGCTCTGCTCTCGCCGCGCCAGTGTCAGAAAAACAGCTGGCGGAGGTGGTCGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCTGTTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGAAAACCGCACTATTACACGTTTGGCAAGGCCGATATCGCGGCGAATAAACCCGTTACGCCTCAGACCCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGCGTTTTAGGTGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCAGAGCTGACGGGCAAGCAGTGGCAGGGTATTCGTATGCTGGATCTCGCCACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTCAAACCTTCTGGCATGCCCTATGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTGCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGTATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCGGAGAACGTTGCTGATGCCTCACTTAAGCAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGGTCGAGGGCAGCGACAGTAAGGTAGCGCTGGCGCCGTTGCCCGTGGTAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGCTCTACTGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATACAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCGAGGCGCTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3001847","ARO_id":"38247","ARO_name":"ACT-27","CARD_short_name":"ACT-27","ARO_description":"ACT-27 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1485":{"model_id":"1485","model_name":"MOX-8","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1519":{"protein_sequence":{"accession":"AGH56079.1","sequence":"MQQRQSILWGALATLMWAGLAHAGDKAATDPLRPVVDASIRPLLKEHRIPGMAVAVLKDGKAHYFNYGVADRERAVGVSEQTLFEIGSVSKPLTATLGAYAVVKGAMQLDDKASRHAPWLKGSAFDSITMGELATYSAGGLPLQFPEEVDSLEKMQAYYRQWTPAYSPGSHRQYSNPSIGLFGHLAASSMKQPFAQLMEQTLLPGLGLHHTYVNVPKQAMASYAYGYSKEDKPIRVSPGMLADEAYGIKTSSADLLRFVKANISGVDDKALQQAISLTHKGHYSVGGMTQGLGWESYAYPVSEQTLLAGNSPAMIYNANPAAPAPAAAGHPVLFNKTGSTSGFGAYVAFVPAKGIGIVMLANRNYPIPARVKAAHAILTQLAR"},"dna_sequence":{"accession":"JX173956.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCAACAACGACAATCCATCCTGTGGGGCGCTTTGGCCACCCTGATGTGGGCCGGTCTGGCTCATGCCGGTGACAAGGCGGCGACCGATCCCCTGCGCCCCGTGGTGGATGCCAGCATCCGGCCGCTGCTCAAGGAGCACAGGATCCCGGGCATGGCGGTGGCCGTGCTCAAGGATGGCAAGGCCCACTATTTCAACTACGGTGTGGCCGATCGGGAGCGCGCGGTCGGTGTCAGCGAGCAGACCCTGTTCGAGATAGGCTCCGTGAGCAAGCCCCTGACCGCGACCCTAGGAGCCTATGCGGTGGTCAAGGGAGCGATGCAACTGGATGACAAGGCGAGCCGGCACGCCCCCTGGCTCAAGGGATCCGCCTTTGACAGCATCACCATGGGGGAGCTGGCTACCTACAGCGCGGGCGGCTTGCCGCTGCAATTCCCCGAGGAGGTGGATTCGCTCGAGAAGATGCAGGCCTACTACCGCCAGTGGACCCCAGCCTACTCGCCGGGTTCCCATCGCCAGTACTCTAACCCCAGCATAGGGCTGTTCGGCCACCTGGCGGCGAGCAGCATGAAGCAGCCGTTTGCCCAGTTGATGGAGCAGACGCTCCTGCCGGGGCTTGGCCTGCACCACACCTATGTCAATGTGCCGAAGCAGGCCATGGCGAGTTATGCCTATGGCTATTCGAAAGAGGACAAGCCCATCAGGGTCAGCCCCGGCATGCTGGCGGACGAGGCCTACGGCATCAAGACCAGCTCGGCGGATCTGCTGCGCTTTGTGAAGGCCAACATCAGCGGGGTTGATGACAAGGCGTTGCAGCAGGCCATCTCCCTGACCCACAAAGGGCACTACTCGGTAGGCGGGATGACCCAGGGACTGGGTTGGGAGAGTTACGCCTATCCCGTCAGCGAGCAGACATTGCTGGCGGGCAACTCCCCGGCGATGATTTACAATGCCAACCCGGCGGCGCCCGCGCCCGCTGCGGCAGGGCACCCTGTGCTCTTCAACAAGACCGGCTCGACCAGCGGCTTCGGCGCCTATGTGGCCTTCGTGCCGGCCAAAGGGATCGGCATCGTCATGCTGGCCAACCGCAACTATCCTATCCCGGCCAGGGTGAAAGCGGCCCACGCCATCCTGACGCAACTGGCCAGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36936","NCBI_taxonomy_name":"Aeromonas caviae","NCBI_taxonomy_id":"648"}}}},"ARO_accession":"3002190","ARO_id":"38590","ARO_name":"MOX-8","CARD_short_name":"MOX-8","ARO_description":"MOX-8 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36222":{"category_aro_accession":"3000083","category_aro_cvterm_id":"36222","category_aro_name":"MOX beta-lactamase","category_aro_description":"MOX beta-lactamases are plasmid-mediated AmpC-type beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1486":{"model_id":"1486","model_name":"CARB-12","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1912":{"protein_sequence":{"accession":"BAA02497.1","sequence":"MKFLLVFSLLIPSVVFASSSKFRQVEQDVKAIEVSLSARIGVSVLDTQNGEYWDYNGNQRFPLTSTFKTIACAKLLYDAEQGKVNPNSTVEIKKADLVTYSPVIEKQVGQAITLDDACFATMTTSDNTAANIILSAVGGSKGVTDFLRQIGDKETRLDRIEPDLNEGKLGDLRDTTTPKAIASTLNKFLFGSALSEMNKKKLESWMVNNQVTGNLLRSVLPAGWNIADRSGAGGFGARSITAVVWSEHQAPIIVSIYLAQTQASMAERNDAIVKIGRSIFDVYTSQSR"},"dna_sequence":{"accession":"D13210.1","fmin":"231","fmax":"1098","strand":"+","sequence":"ATGAAGTTTTTATTGGTATTTTCGCTTTTAATACCATCCGTGGTTTTTGCAAGTAGTTCAAAGTTTCGGCAAGTTGAACAAGACGTTAAGGCAATTGAAGTTTCTCTTTCTGCTCGTATAGGTGTTTCCGTTCTTGATACTCAAAATGGAGAATACTGGGATTACAATGGCAATCAGCGCTTCCCGTTGACAAGTACTTTTAAAACAATAGCTTGCGCTAAATTACTATATGATGCTGAGCAAGGAAAAGTTAATCCCAATAGTACAGTCGAGATTAAGAAAGCAGATCTTGTGACCTATTCCCCTGTAATAGAAAAGCAAGTAGGGCAGGCAATCACACTCGATGATGCGTGCTTCGCAACTATGACTACAAGTGATAATACTGCGGCAAATATCATCCTAAGTGCTGTAGGTGGCTCCAAAGGCGTTACTGATTTTTTAAGACAAATTGGGGACAAAGAGACTCGTCTAGACCGTATTGAGCCTGATTTAAATGAAGGTAAGCTCGGTGATTTGAGGGATACGACAACTCCTAAGGCAATAGCCAGTACTTTGAATAAATTTTTATTTGGTTCAGCGCTATCTGAAATGAACAAAAAAAAATTAGAGTCTTGGATGGTGAACAATCAAGTCACTGGTAATTTACTACGTTCAGTATTGCCGGCGGGATGGAACATTGCGGATCGTTCAGGTGCTGGCGGATTTGGTGCTCGGAGTATTACAGCAGTTGTGTGGAGTGAGCATCAAGCCCCAATTATTGTGAGCATCTATCTAGCTCAAACACAGGCTTCAATGGCAGAGCGAAATGATGCGATTGTTAAAATTGGTCGTTCAATTTTTGACGTTTATACATCACAGTCGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3002250","ARO_id":"38650","ARO_name":"CARB-12","CARD_short_name":"CARB-12","ARO_description":"CARB-12 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36230":{"category_aro_accession":"3000091","category_aro_cvterm_id":"36230","category_aro_name":"CARB beta-lactamase","category_aro_description":"CARB beta-lactamases are class A lactamases that can hydrolyze carbenicillin. Many of the PSE beta-lactamases have been renamed as CARB-lactamases with the notable exception of PSE-2 which is now OXA-10.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1487":{"model_id":"1487","model_name":"SHV-48","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"991":{"protein_sequence":{"accession":"AAP03063.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTIGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AY263404.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGATCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTACTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACCCCAGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001105","ARO_id":"37485","ARO_name":"SHV-48","CARD_short_name":"SHV-48","ARO_description":"SHV-48 is a broad-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1488":{"model_id":"1488","model_name":"TEM-75","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8423":{"protein_sequence":{"accession":"AAN05028.1","sequence":"FFAAFCFPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDHWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYMTGSQATMDERNR"},"dna_sequence":{"accession":"AY130284.1","fmin":"0","fmax":"783","strand":"+","sequence":"TTTTTTGCGGCATTTTGCTTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATCATTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACATGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGA","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3000941","ARO_id":"37321","ARO_name":"TEM-75","CARD_short_name":"TEM-75","ARO_description":"TEM-75 is an extended-spectrum beta-lactamase that has been found in clinical isolates.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1489":{"model_id":"1489","model_name":"CMY-37","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"944":{"protein_sequence":{"accession":"BAF36388.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWSELTGKQWQGISLLHLATYTAGGLPLQIPDDVTDKTALLHFYQNWQPQWAPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQSEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASRVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAAIPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPIRVEAAWRILEKLQ"},"dna_sequence":{"accession":"AB280919.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCATTCTCCACGTTTGCCGCCGCCAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGTCAGAACTGACAGGCAAACAGTGGCAGGGTATCAGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTACGGATAAAACCGCATTACTGCACTTTTATCAAAACTGGCAGCCTCAATGGGCTCCGGGCGCTAAGAGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGTATGAGCTACGAAGAGGCAATGACCAGACGCGTCCTGCAGCCATTAAAACTGGCGCATACCTGGATTACAGTTCCGCAGAGCGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCTGTACACGTTTCTCCGGGACAACTTGATGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCACGCTGGGTTCAGGCCAACATGGATGCCAGCCGCGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAGGCTGATTCGATCATCAACGGTAGCGACAGCAAAGTGGCATTGGCAGCGATTCCCGCCGTTGAGGTAAACCCGCCCGCCCCGGCAGTGAAAGCCTCATGGGTGCATAAAACGGGATCCACTGGTGGATTTGGCAGCTACGTTGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTATCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002048","ARO_id":"38448","ARO_name":"CMY-37","CARD_short_name":"CMY-37","ARO_description":"CMY-37 is a beta-lactamase found in Citrobacter freundii.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1490":{"model_id":"1490","model_name":"SHV-107","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"818":{"protein_sequence":{"accession":"CAQ03507.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKAGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AM941848.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACATCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGGCCGGAGCTGGCGAGCGGGGTGCGCGCGGCATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001156","ARO_id":"37536","ARO_name":"SHV-107","CARD_short_name":"SHV-107","ARO_description":"SHV-107 is an inhibitor-resistant beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1491":{"model_id":"1491","model_name":"lnuF","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"8158":{"protein_sequence":{"accession":"CAD91132.1","sequence":"MLQQKMIERFKEACHEDARIIAALMFGSFAIGEGDEFSDIEFAVFIQNNHFENFDQRSWLNAVSPVAAYFPDDFGHHTALFENGIRGEFHFMRKSDIPVISTWQGYGWFPSLEEAVLLDRSGELSRYASALVGSPPKREGAPLVEGLVLNLISLMLFGANLLNRGEYARAWALLSKAHENLLKLVRLHEGATDHWPTPSRALEKDVSEDSYNRYLACTGSAEPKALCVAYHETWKWSLELFRSVAGPLNIELPRIVIAQTKRLLNESATPHNK"},"dna_sequence":{"accession":"AJ561197.2","fmin":"1320","fmax":"2142","strand":"+","sequence":"ATGCTTCAGCAGAAAATGATCGAACGCTTCAAGGAAGCTTGCCATGAGGATGCACGAATAATCGCGGCGCTGATGTTCGGCTCATTTGCTATCGGAGAGGGTGACGAGTTCTCTGATATCGAATTTGCAGTGTTCATCCAGAATAATCATTTTGAAAATTTCGATCAGCGCTCGTGGCTTAATGCTGTAAGTCCGGTTGCAGCTTACTTTCCGGATGACTTCGGCCACCACACCGCGCTTTTTGAAAACGGCATTCGCGGTGAATTCCATTTCATGCGAAAATCGGACATACCGGTCATTTCCACTTGGCAAGGCTACGGGTGGTTTCCCTCGCTTGAGGAGGCTGTTTTGTTGGACCGATCAGGAGAGTTGTCAAGGTACGCGAGTGCTCTCGTGGGCAGTCCCCCGAAACGTGAAGGCGCGCCGCTGGTGGAAGGACTTGTATTGAACCTCATCAGCCTGATGCTCTTTGGGGCAAATCTTTTAAATCGGGGAGAGTATGCTCGCGCCTGGGCTTTGCTCAGCAAAGCACATGAAAACTTACTCAAGTTGGTTCGCCTCCATGAAGGGGCAACAGACCACTGGCCGACACCTTCACGCGCGCTCGAAAAGGATGTCTCGGAGGACTCGTATAATCGCTACCTGGCATGCACAGGCAGCGCGGAACCAAAAGCACTATGTGTAGCCTATCATGAAACGTGGAAGTGGAGTCTCGAATTGTTCAGGAGTGTGGCTGGACCTCTGAATATCGAGCTTCCGAGAATTGTAATTGCGCAGACAAAAAGGTTGCTAAATGAATCTGCGACGCCGCACAACAAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002839","ARO_id":"39273","ARO_name":"lnuF","CARD_short_name":"lnuF","ARO_description":"lnuF is an integron-mediated nucleotidyltransferase found in Escherichia coli.","ARO_category":{"36360":{"category_aro_accession":"3000221","category_aro_cvterm_id":"36360","category_aro_name":"lincosamide nucleotidyltransferase (LNU)","category_aro_description":"Resistance to the lincosamide antibiotic by ATP-dependent modification of the 3' and\/or 4'-hydroxyl groups of the methylthiolincosamide sugar.","category_aro_class_name":"AMR Gene Family"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1492":{"model_id":"1492","model_name":"MOX-3","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1119":{"protein_sequence":{"accession":"ACA30419.1","sequence":"MQQRQSILWGAVATLMWAGLAHAGETSPVDPLRPVVDASIQPLLKEHRIPGMAVAVLKDGKAHYFNYGVADRERAVGVSEQTLFEIGSVSKPLTATLGAYAVVKGAMQLDDKASRHAPWLKGSAFDSITMGELATYSAGGLPLQFPEEVDSLEKMQAYYRQWTPAYSPGSHRQYSNPSIGLFGHLAASSLKQPFAQLMEQTLLPGLGLHHTYVNVPKQAMASYAYGYSKEDKPIRVSPGMLADEAYGIKTSSADLLRFVKANISGVDDKALQQAISLTHKGHYSVGGMTQGLGWERYAYPVSEQTLLAGNSAKVILEANPTAAPRESGSQMLFNKTGSTSGFGAYVAFVPAKGIGIVMLANRNYPIPARVKAAHAILTQLAR"},"dna_sequence":{"accession":"EU515248.1","fmin":"0","fmax":"1149","strand":"+","sequence":"ATGCAACAACGACAATCCATCCTGTGGGGGGCCGTGGCCACCCTGATGTGGGCCGGTCTGGCCCATGCAGGTGAGACTTCACCGGTCGATCCCCTGCGCCCCGTGGTGGATGCCAGCATCCAGCCGCTGCTCAAGGAGCACAGGATCCCGGGCATGGCGGTGGCCGTGCTCAAGGATGGCAAGGCCCACTATTTCAACTACGGTGTGGCCGATCGGGAGCGCGCAGTCGGTGTCAGCGAGCAGACCCTGTTCGAGATAGGCTCCGTGAGCAAGCCCCTGACCGCGACCCTAGGAGCCTATGCGGTGGTCAAGGGAGCGATGCAACTGGATGACAAGGCGAGCCGGCACGCCCCCTGGCTCAAGGGATCCGCCTTTGACAGCATCACCATGGGGGAGCTGGCTACCTACAGCGCGGGCGGCTTGCCGCTGCAATTCCCCGAGGAGGTGGATTCGCTCGAGAAGATGCAGGCCTACTACCGCCAGTGGACCCCAGCCTACTCGCCGGGTTCCCATCGCCAGTACTCTAACCCCAGCATAGGGCTGTTCGGCCACCTGGCGGCGAGCAGCCTGAAGCAGCCGTTTGCCCAGTTGATGGAGCAGACGCTCCTGCCGGGGCTTGGCCTGCACCACACCTATGTCAATGTGCCGAAGCAGGCCATGGCGAGTTATGCCTATGGCTATTCGAAAGAGGACAAGCCCATCAGGGTCAGCCCCGGCATGCTGGCGGACGAGGCCTACGGCATCAAAACCAGCTCGGCGGATCTGCTGCGCTTTGTGAAGGCCAACATCAGCGGGGTTGATGACAAGGCGTTGCAGCAGGCCATCTCCCTGACCCACAAAGGGCACTACTCGGTAGGCGGGATGACCCAGGGACTGGGTTGGGAGCGTTACGCCTATCCCGTCAGCGAGCAGACATTGCTGGCGGGCAATTCGGCCAAGGTGATCCTCGAAGCCAATCCGACGGCGGCGCCCCGGGAGTCGGGGAGCCAGATGCTCTTCAACAAGACCGGCTCGACCAGCGGCTTCGGCGCCTATGTGGCCTTCGTGCCGGCCAAAGGGATCGGCATCGTCATGCTGGCCAACCGCAACTATCCTATCCCGGCCAGGGTGAAAGCGGCCCACGCCATCCTGACGCAACTGGCCAGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36942","NCBI_taxonomy_name":"Aeromonas sp. HCUZ 2422275","NCBI_taxonomy_id":"505724"}}}},"ARO_accession":"3002186","ARO_id":"38586","ARO_name":"MOX-3","CARD_short_name":"MOX-3","ARO_description":"MOX-3 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36222":{"category_aro_accession":"3000083","category_aro_cvterm_id":"36222","category_aro_name":"MOX beta-lactamase","category_aro_description":"MOX beta-lactamases are plasmid-mediated AmpC-type beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1493":{"model_id":"1493","model_name":"PER-6","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1229":{"protein_sequence":{"accession":"ADD80743.1","sequence":"MNVIAKGVFTTTALLMLSLSSWVVSAQSPLLKEQIETIVTGKKATVGVAVWGPDDLEPLLVNPFEKFPMQSVFKMHLAMLVLHQVDQGKLDLNKTVAVNRAAVLQNTWSPMMKDHQGDEFTVTVQQLLQYSVSHSDNVACDLLFELVGGPAALHAYIQSLGIKETEVVANEAQMHADDQVQYKNWTSMKAAAQLLRKFEQKKQLSETSQALLWKWMVETTTGPQRLKGLLPAGTVVAHKTGTSGVRAGKTAATNDIGVIMLPDGRPLLVAVFVKDSAESARTNEAIIAQVAQAAYQFELKKLSAVSPD"},"dna_sequence":{"accession":"GQ396303.1","fmin":"0","fmax":"927","strand":"+","sequence":"ATGAATGTCATCGCAAAAGGTGTTTTTACTACTACAGCTCTGCTGATGTTGAGTTTAAGTTCATGGGTCGTCTCTGCCCAATCCCCGCTGTTAAAAGAGCAAATTGAGACCATAGTGACAGGTAAAAAAGCCACTGTAGGTGTTGCCGTATGGGGCCCTGATGATCTGGAGCCTTTGCTGGTTAATCCTTTTGAGAAATTCCCGATGCAAAGCGTATTTAAGATGCATTTAGCCATGCTGGTTCTGCATCAGGTGGATCAGGGCAAACTGGATTTAAATAAAACTGTTGCTGTTAATCGTGCTGCAGTATTACAAAATACCTGGTCGCCTATGATGAAAGATCATCAAGGCGATGAATTTACCGTTACTGTGCAGCAGTTGCTGCAGTATTCGGTGTCGCACAGTGATAACGTGGCCTGTGATTTATTGTTCGAACTGGTTGGAGGGCCTGCAGCTCTGCATGCTTACATTCAGTCTTTAGGTATTAAAGAAACTGAAGTGGTAGCAAATGAAGCACAAATGCATGCTGATGATCAGGTGCAATATAAAAACTGGACCTCGATGAAAGCAGCAGCGCAACTTTTGCGAAAGTTTGAACAAAAAAAGCAGTTGTCTGAAACCTCTCAGGCTTTATTGTGGAAGTGGATGGTGGAAACCACCACAGGACCACAGCGGTTAAAAGGCCTGTTACCTGCCGGAACTGTAGTAGCGCATAAAACCGGTACGTCCGGTGTCAGAGCAGGAAAAACGGCGGCGACCAATGATATAGGCGTCATTATGTTGCCTGATGGGCGGCCTTTATTGGTGGCGGTATTTGTCAAAGATTCCGCCGAATCAGCAAGAACCAATGAAGCCATTATCGCGCAGGTGGCTCAAGCTGCTTATCAGTTTGAGCTGAAAAAACTCTCCGCAGTAAGTCCGGATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36947","NCBI_taxonomy_name":"Aeromonas allosaccharophila","NCBI_taxonomy_id":"656"}}}},"ARO_accession":"3002368","ARO_id":"38768","ARO_name":"PER-6","CARD_short_name":"PER-6","ARO_description":"PER-6 is a beta-lactamase found in Aeromonas allosaccharophila.","ARO_category":{"36195":{"category_aro_accession":"3000056","category_aro_cvterm_id":"36195","category_aro_name":"PER beta-lactamase","category_aro_description":"PER beta-lactamases are plasmid-mediated extended spectrum beta-lactamases found in the Enterobacteriaceae family.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1494":{"model_id":"1494","model_name":"LAT-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1988":{"protein_sequence":{"accession":"CAA55007.1","sequence":"MMKKSLCSALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDCIARGEIKLSDPVTKYWPELTGKKWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHVSPGRLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"X78117.1","fmin":"141","fmax":"1287","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTCCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAACCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGGAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGACTGTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAAAAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCTTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACGACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001857","ARO_id":"38257","ARO_name":"LAT-1","CARD_short_name":"LAT-1","ARO_description":"LAT-1 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1495":{"model_id":"1495","model_name":"ACT-4","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"8163":{"protein_sequence":{"accession":"ABZ81086.1","sequence":"MMTKSLCCALLLSTSCSVLAAPMSEKQLAEVVERTVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVADNASLLRFYQNWQPQWKPGTTRLYANTSIGLFGALAVKPSGMSYEQAITTRVFKPLKLDHTWINVPKAEEAHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVQDMASWVMVNMKPDSLQDNSLRQGIALAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVEGSDNKVALAPLPAREVNPPAPPVNASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILSAL"},"dna_sequence":{"accession":"EU427302.2","fmin":"1475","fmax":"2618","strand":"+","sequence":"ATGATGACTAAATCCCTTTGCTGCGCCCTGCTGCTCAGCACCTCCTGCTCGGTATTGGCTGCACCGATGTCAGAAAAACAGCTGGCTGAGGTGGTGGAACGGACCGTTACGCCGCTGATGAAAGCGCAGGCCATTCCGGGTATGGCGGTGGCGGTGATTTATCAGGGCCAGCCGCACTACTTTACCTTCGGTAAAGCCGATGTTGCGGCGAACAAACCTGTCACCCCACAAACCTTGTTCGAACTGGGTTCTATAAGTAAAACCTTTACCGGCGTACTGGGTGGCGATGCCATTGCTCGGGGTGAAATATCGCTGGGCGATCCGGTGACAAAATACTGGCCTGAGCTGACGGGCAAGCAGTGGCAGGGGATCCGCATGCTGGATCTGGCAACCTATACCGCAGGCGGTCTGCCGTTACAGGTACCGGATGAGGTCGCGGATAACGCCTCTCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCGGGTACCACGCGTCTTTACGCCAATACCAGCATCGGCCTTTTTGGCGCGCTGGCGGTCAAACCTTCCGGCATGAGCTATGAACAGGCCATAACGACGCGGGTCTTTAAGCCGCTCAAGCTGGACCATACGTGGATTAACGTTCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGATACCGCGACGGTAAAGCGGTACACGTTTCGCCAGGCATGCTGGACGCTGAAGCCTATGGCGTAAAAACCAACGTGCAGGATATGGCAAGCTGGGTGATGGTCAACATGAAGCCGGACTCCCTTCAGGATAATTCACTCAGGCAAGGCATTGCCCTGGCGCAGTCTCGCTACTGGCGCGTAGGGGCCATGTATCAGGGGTTAGGCTGGGAAATGCTTAACTGGCCGGTCGATGCCAAAACCGTGGTTGAAGGTAGCGACAATAAGGTGGCACTGGCACCGCTGCCCGCAAGAGAAGTGAATCCTCCGGCGCCTCCGGTCAACGCGTCCTGGGTCCATAAAACAGGCTCTACCGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGCTCGGCATTGTGATGCTGGCGAATAAAAGCTATCCCAACCCAGCACGCGTTGAGGCGGCTTACCGTATTTTGAGCGCGCTGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36926","NCBI_taxonomy_name":"Enterobacter asburiae","NCBI_taxonomy_id":"61645"}}}},"ARO_accession":"3001829","ARO_id":"38229","ARO_name":"ACT-4","CARD_short_name":"ACT-4","ARO_description":"ACT-4 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1496":{"model_id":"1496","model_name":"OXA-224","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8176":{"protein_sequence":{"accession":"AEQ73521.1","sequence":"MKNTIHINFAIFLIIANIIYSSASASTDISTVASPLFEGTEGCFLLYDVSTNTEIAQFNKAKCATQMAPDSTFKIALSLMAFDAEIIDQKTIFKWDKTPKGMEIWNSNHTPKTWMQFSVVWVSQEITQKIGLNKIKNYLKDFDYGNQDFSGDKERNNGLTEAWLESSLKISPEEQIQFLRKIINHNLPVKNSAIENTIENMYLQDLENSTKLYGKTGAGFTANRTLQNGWFEGFIISKSGHKYVFVSALTGNLGSNLTSSIKAKKNAITILNTLNL"},"dna_sequence":{"accession":"JN596991.2","fmin":"2280","fmax":"3111","strand":"+","sequence":"ATGAAAAACACAATACATATCAACTTCGCTATTTTTTTAATAATTGCAAATATTATCTACAGCAGCGCCAGTGCATCAACAGATATCTCTACTGTTGCATCTCCATTATTTGAAGGAACTGAAGGTTGTTTTTTACTTTACGATGTATCCACAAACACTGAAATTGCTCAATTCAATAAAGCAAAGTGTGCAACGCAAATGGCACCAGATTCAACTTTCAAGATCGCATTATCACTTATGGCATTTGATGCGGAAATAATAGATCAGAAAACCATATTCAAATGGGATAAAACCCCCAAAGGAATGGAGATCTGGAACAGCAATCATACACCAAAGACGTGGATGCAATTTTCTGTTGTTTGGGTTTCGCAAGAAATAACCCAAAAAATTGGATTAAATAAAATCAAGAATTATCTCAAAGATTTTGATTATGGAAATCAAGACTTCTCTGGAGATAAAGAAAGAAACAACGGATTAACAGAAGCATGGCTCGAAAGTAGCTTAAAAATTTCACCAGAAGAACAAATTCAATTCCTGCGTAAAATTATTAATCACAATCTCCCAGTTAAAAACTCAGCCATAGAAAACACCATAGAGAACATGTATCTACAAGATCTGGAGAATAGTACAAAACTGTATGGGAAAACTGGTGCAGGATTCACAGCAAATAGAACCTTACAAAACGGATGGTTTGAAGGGTTTATTATAAGCAAATCAGGACATAAATATGTTTTTGTGTCCGCACTTACAGGAAACTTGGGGTCGAATTTAACATCAAGCATAAAAGCCAAGAAAAATGCGATCACCATTCTAAACACACTAAATTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3001806","ARO_id":"38206","ARO_name":"OXA-224","CARD_short_name":"OXA-224","ARO_description":"OXA-224 is a beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46485":{"category_aro_accession":"3007696","category_aro_cvterm_id":"46485","category_aro_name":"OXA-1-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-1.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1497":{"model_id":"1497","model_name":"dfrA10","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"8272":{"protein_sequence":{"accession":"AHG97174.1","sequence":"MNISLIFANELITRAFGNQGKLPWQFIKEDMQFFQKTTENSVVVMGLNTWRSLPKMKKLGRDFIVISSTITEHEVLNNNIQIFKSFESFLEAFRDTTKPINVIGGVGLLSEAIEHASTVYMSSIHMVKPVHADVYVPVELMNKLYSDFKYPENILWVGDPIDSVYSLSIDKFVRPASLVGVPNDINT"},"dna_sequence":{"accession":"KF976462.2","fmin":"111558","fmax":"112122","strand":"+","sequence":"ATGAATATATCACTTATCTTTGCCAATGAATTAATTACCAGAGCATTCGGTAATCAAGGCAAATTACCTTGGCAATTCATTAAAGAAGATATGCAGTTCTTCCAGAAGACTACAGAAAATTCTGTAGTCGTTATGGGATTAAATACATGGAGATCTCTACCTAAGATGAAGAAGCTTGGTAGAGACTTCATTGTCATATCTTCAACTATCACAGAGCACGAAGTGCTCAACAATAATATCCAAATATTCAAATCATTTGAGAGCTTCTTAGAAGCATTCAGAGACACAACCAAACCAATCAATGTCATTGGTGGTGTTGGTTTATTATCTGAAGCGATAGAACATGCTAGCACTGTTTACATGAGTTCTATTCATATGGTTAAACCTGTTCATGCTGATGTGTATGTACCGGTAGAACTAATGAATAAACTCTATAGTGATTTCAAATATCCAGAAAATATTCTATGGGTAGGTGATCCAATAGATTCTGTGTATAGCTTGTCTATTGATAAGTTTGTTAGACCAGCTTCGCTGGTTGGGGTGCCAAATGATATTAATACGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3003011","ARO_id":"39445","ARO_name":"dfrA10","CARD_short_name":"dfrA10","ARO_description":"dfrA10 is an integron-encoded dihydrofolate reductase found in Klebsiella pneumoniae.","ARO_category":{"37617":{"category_aro_accession":"3001218","category_aro_cvterm_id":"37617","category_aro_name":"trimethoprim resistant dihydrofolate reductase dfr","category_aro_description":"Alternative dihydropteroate synthase dfr present on plasmids produces alternate proteins that are less sensitive to trimethoprim from inhibiting its role in folate synthesis, thus conferring trimethoprim resistance.","category_aro_class_name":"AMR Gene Family"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1498":{"model_id":"1498","model_name":"cphA8","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"1731":{"protein_sequence":{"accession":"AAP97129.1","sequence":"MMKGWIKCTLAGAVVLMASFWGGSVRAAGMSLMQVSGPVYVVEDNYYVKENSMVYFGAKGVTVVGATWTPDTARELHKLIKRVSSKPVLEVINTNYHTDRAGGNAYWKSIGAKVVSTRQTRDLMKSDWAEIVAFTRKGLPEYPDLPLVLPNVVHDGDFKLQEGKVRAFYAGPAHTPDGIFVYFPDQQVFYGNCILKEKLGNLSFANVKEYPQTIERLKAMKLPIKTVIGGHDSPLHGPELIDHYEELIKAATHS"},"dna_sequence":{"accession":"AY261375.1","fmin":"0","fmax":"765","strand":"+","sequence":"ATGATGAAAGGTTGGATAAAGTGCACATTGGCCGGGGCCGTGGTGCTGATGGCGAGTTTCTGGGGTGGCAGCGTGCGGGCGGCGGGGATGTCGCTGATGCAGGTGAGCGGCCCTGTCTATGTTGTTGAAGATAACTACTACGTCAAAGAGAACTCCATGGTCTATTTCGGGGCCAAGGGGGTGACGGTGGTGGGGGCGACCTGGACGCCGGATACCGCCCGCGAGCTGCACAAGCTGATCAAACGGGTCAGCAGCAAACCGGTGCTGGAGGTGATCAACACCAACTACCACACCGACCGAGCGGGCGGTAACGCCTACTGGAAGTCCATCGGGGCCAAGGTGGTATCGACTCGCCAGACCCGGGATCTGATGAAGAGCGACTGGGCCGAGATTGTCGCCTTTACCCGCAAGGGGCTGCCGGAGTATCCGGATCTACCGCTGGTGCTGCCCAACGTGGTGCACGATGGCGACTTCAAGCTGCAAGAGGGCAAGGTGCGCGCCTTCTACGCAGGCCCGGCCCACACGCCGGACGGCATCTTTGTCTACTTCCCCGACCAGCAGGTGTTCTATGGCAACTGCATCCTCAAGGAGAAGCTGGGCAACCTGAGCTTTGCCAATGTGAAGGAGTATCCGCAGACCATCGAGCGGCTCAAGGCGATGAAGCTGCCGATCAAGACGGTAATCGGCGGTCACGACTCACCGCTGCACGGGCCTGAGCTGATTGATCACTATGAAGAGCTGATCAAGGCGGCAACTCATTCATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36957","NCBI_taxonomy_name":"Aeromonas sobria","NCBI_taxonomy_id":"646"}}}},"ARO_accession":"3003104","ARO_id":"39670","ARO_name":"cphA8","CARD_short_name":"cphA8","ARO_description":"cphA8 is an Ambler Class B MBL; subclass B2 originally isolated from Aeromonas sobria. This enzyme has specific activity against carbapenems and is active as a mono-zinc protein.","ARO_category":{"36720":{"category_aro_accession":"3000581","category_aro_cvterm_id":"36720","category_aro_name":"CphA beta-lactamase","category_aro_description":"CphA is an Ambler Class B MBL; subclass B2 originally isolated from Aeromonas hydrophilia.  This enzyme has specific activity against carbapenems and is active as a mono-zinc protein.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1499":{"model_id":"1499","model_name":"VEB-6","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"4701":{"protein_sequence":{"accession":"ACA34904.1","sequence":"MKIVKRILLVLLSLFFTVVYSNAQADNLTLKIENVLKAKNARIGVAIFNSNEKDTLKINNDFHFPMQSVMKFPIALAVLSEIDKGNLSFEQKIEITPQDLLPKMWSPIKEEFPNGTTLTIEQILNYTVSESDNIGCDILLKLIGGTDSVQKFLNANHFTDISIKANEEQMHKDWNTQYQNWATPTAMNKLLIDTYNNKNQLLSKKSYDFIWKIMRETTTGSNRLKGQLPKNTIVAHKTGTSGINNGIAAATNDVGVITLPNGQLIFISVFVAESKETSEINEKIISDIAKITWNYYLNK"},"dna_sequence":{"accession":"EU259884.2","fmin":"6411","fmax":"7311","strand":"-","sequence":"ATGAAAATCGTAAAAAGGATATTATTAGTATTGTTAAGTTTATTTTTTACAGTTGTGTATTCAAATGCTCAAGCTGACAACTTAACTTTGAAAATTGAGAATGTTTTAAAGGCAAAAAATGCCAGAATAGGAGTAGCAATATTCAACAGCAATGAGAAGGATACTTTGAAGATTAATAACGACTTCCATTTCCCGATGCAAAGCGTTATGAAATTTCCGATTGCTTTAGCCGTTTTGTCTGAGATAGATAAAGGGAATCTTTCTTTTGAACAAAAAATAGAGATTACCCCTCAAGACCTTTTGCCTAAAATGTGGAGTCCGATTAAAGAGGAATTCCCTAATGGAACAACTTTGACGATTGAACAAATACTAAATTATACAGTATCAGAGAGCGACAATATTGGTTGTGATATTTTGCTAAAATTAATCGGAGGAACTGATTCTGTTCAAAAATTCTTGAATGCTAATCATTTCACTGATATTTCAATCAAAGCAAACGAAGAACAAATGCACAAGGATTGGAATACCCAATATCAAAATTGGGCAACCCCAACAGCGATGAACAAACTGTTAATAGATACTTATAATAATAAGAACCAATTACTTTCTAAAAAAAGTTATGATTTTATTTGGAAAATTATGAGAGAAACAACAACAGGAAGTAACCGATTAAAAGGACAATTACCAAAGAATACAATTGTTGCTCATAAAACAGGGACTTCCGGAATAAATAATGGAATTGCAGCAGCCACTAATGATGTTGGGGTAATTACTTTACCGAATGGACAATTAATTTTTATAAGCGTATTTGTTGCAGAGTCCAAAGAAACTTCGGAAATTAATGAAAAGATTATTTCAGACATTGCAAAAATAACGTGGAATTACTATTTGAATAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3002374","ARO_id":"38774","ARO_name":"VEB-6","CARD_short_name":"VEB-6","ARO_description":"VEB-6 is a beta-lactamase found in Proteus mirabilis.","ARO_category":{"36182":{"category_aro_accession":"3000043","category_aro_cvterm_id":"36182","category_aro_name":"VEB beta-lactamase","category_aro_description":"VEB beta-lactamases or Vietnamese extended-spectrum beta-lactamases are class A beta-lactamases that confer high-level resistance to oxyimino cephalosporins and to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1500":{"model_id":"1500","model_name":"APH(6)-Ia","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"94":{"protein_sequence":{"accession":"CAA68516.1","sequence":"MSSSDHIHVPDGLAESYSRSGGEEGRAWIAGLPALVARCVDRWELKRDGGVRSGEASLVVPVLRADGTRAALKLQMPREETTAALIGLRAWGGDGMVRLLDHDEESSTMLLERLDGSRTLASVEDDDEAMGVLAGLLNRLHSVPAPPGLRGLGEIAGAMVEEVPSAVDSLADPEDRSRLRGWASAVAELVGEPGDRVLHWDLHYENVLAAEREPWLAIDPEPLVGDPGFDLWPALDTGWERIEATGDARRVVRRRFDLLTESLELDRGRAAGWTLARLLQNTLWDIEDGLTAIAPSQIAVAEALAKP"},"dna_sequence":{"accession":"Y00459.1","fmin":"2824","fmax":"3748","strand":"+","sequence":"ATGAGTTCGTCGGACCACATCCACGTCCCGGACGGCCTGGCCGAGTCGTACAGCAGAAGCGGTGGCGAGGAAGGGCGCGCCTGGATCGCCGGACTTCCCGCTCTCGTCGCGCGATGCGTCGACCGCTGGGAGCTGAAGAGGGACGGCGGCGTCCGCTCCGGTGAGGCCTCCCTCGTGGTGCCGGTGCTGCGTGCTGACGGCACCCGGGCGGCGCTCAAACTCCAGATGCCCCGGGAAGAGACGACGGCCGCGCTGATCGGCCTGCGAGCCTGGGGCGGGGACGGCATGGTGCGGCTGCTCGACCACGACGAGGAGAGCAGCACGATGCTGCTGGAACGCCTGGACGGTTCGCGGACGCTGGCGTCGGTCGAGGACGACGACGAGGCCATGGGCGTCCTCGCCGGGCTGCTGAACCGGCTGCACTCCGTTCCGGCACCTCCGGGGCTGCGGGGTCTGGGAGAGATCGCCGGCGCCATGGTGGAGGAAGTTCCCTCCGCTGTCGACTCGTTGGCGGATCCGGAGGACCGTAGCCGGTTGCGCGGCTGGGCGTCGGCCGTGGCCGAGCTGGTGGGCGAGCCCGGTGACCGCGTCCTGCACTGGGACCTGCACTACGAGAACGTGCTGGCCGCCGAGCGCGAACCGTGGCTGGCCATCGACCCCGAGCCGCTGGTCGGCGACCCGGGGTTCGACCTGTGGCCGGCCCTGGACACCGGTTGGGAGCGGATCGAGGCCACCGGTGACGCGCGGCGGGTGGTCCGGCGGCGCTTCGACCTGCTGACGGAATCGCTGGAGCTGGACCGCGGGAGGGCGGCCGGGTGGACCCTGGCCCGGCTCCTGCAGAACACCCTGTGGGACATCGAGGACGGGCTGACGGCGATCGCCCCCTCCCAGATCGCCGTGGCCGAAGCGCTGGCGAAGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36903","NCBI_taxonomy_name":"Streptomyces griseus","NCBI_taxonomy_id":"1911"}}}},"ARO_accession":"3002657","ARO_id":"39057","ARO_name":"APH(6)-Ia","CARD_short_name":"APH(6)-Ia","ARO_description":"APH(6)-Ia is a chromosomal-encoded aminoglycoside phosphotransferase in S. griseus.","ARO_category":{"36290":{"category_aro_accession":"3000151","category_aro_cvterm_id":"36290","category_aro_name":"APH(6)","category_aro_description":"A category of aminoglycoside O-phosphotransferase enzymes with modification regiospecificity based at the 6-hydroxyl group of the respective antibiotic. These enzymes are characterized by enzymatic antibiotic inactivation, specifically of streptomycin, by the ATP-dependent phosphorylation of the 6-hydroxyl group of the compound.","category_aro_class_name":"AMR Gene Family"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1501":{"model_id":"1501","model_name":"CMY-49","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1975":{"protein_sequence":{"accession":"ACV32310.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAIIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGISLLHLATYTAGGLPLQIPDDVTDKAALLRFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHVTPGQLDAEAYGVKSNVTDMARWIQVNMDASRVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALHTVEVNPPAPAVKASWVHKTGSTGGFGSYVAFIPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"GQ402541.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCATTCTCCACGTTTGCCGCCGCCAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCATTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCAGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTACAGATAAAGCCGCATTACTGCGTTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACAGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGTTACTCCTGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAACGTTACCGATATGGCCCGTTGGATTCAGGTCAACATGGACGCCAGCCGCGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGTAGTGACAGCAAAGTGGCATTGGCAGCGCTTCACACCGTTGAGGTAAACCCGCCCGCCCCGGCAGTGAAAGCCTCATGGGTGCATAAAACGGGATCCACTGGAGGATTTGGCAGCTACGTAGCCTTCATTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002060","ARO_id":"38460","ARO_name":"CMY-49","CARD_short_name":"CMY-49","ARO_description":"CMY-49 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1337":{"model_id":"1337","model_name":"baeR","model_type":"protein overexpression model","model_type_id":"41091","model_description":"Protein Overexpression Models (POM) are similar to Protein Variant Models (PVM) in that they include a protein reference sequence, a curated BLASTP bitscore cut-off, and mapped resistance variants. Whereas PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, reporting only those with curated mutations conferring AMR, POMs are restricted to regulatory proteins and report both wild-type sequences and\/or sequences with mutations leading to overexpression of efflux complexes. The former lead to efflux of antibiotics at basal levels, while the latter can confer clinical resistance. POMs include a protein reference sequence (often from wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Perfect RGI match is 100% identical to the wild-type reference protein sequence along its entire length, a Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value may or may not contain at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off may or may not contain at least one curated mutation from amongst the mapped resistance variants.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"},"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"13135":"S104N"},"Curated-R":{"13135":"S104N"},"clinical":{"13135":"S104N"}}},"model_sequences":{"sequence":{"8726":{"protein_sequence":{"accession":"ADF62940.1","sequence":"MTELPIDENTPRILIVEDEPKLGQLLIDYLRAASYAPSLISHGDQVLPYVRQTPPDLILLDLMLPGTDGLTLCREIRRFSDVPIVMVTAKIEEIDRLLGLEIGADDYICKPYSPREVVARVKTILRRCKPQRELQVLDAESPLIVDESRFQASWRSKLLDLTPAEFRLLKTLSHEPGKVFSREQLLNHLYDDYRVVTDRTIDSHIKNLRRKLEALDAEQSFIRAVYGVGYRWEADACRIA"},"dna_sequence":{"accession":"CP001918.1","fmin":"3479859","fmax":"3480582","strand":"+","sequence":"ATGACCGAATTACCGATTGACGAAAACACGCCACGCATTTTGATTGTGGAAGACGAGCCTAAGCTTGGGCAGTTACTGATCGACTATTTACGTGCGGCCAGCTACGCCCCGTCGCTTATCAGCCATGGCGATCAGGTGTTACCGTACGTGCGCCAGACGCCGCCGGATCTGATCCTGCTGGATTTGATGCTCCCCGGCACGGACGGCCTGACCCTGTGCCGGGAAATTCGTCGCTTCTCCGACGTGCCGATCGTCATGGTGACGGCAAAAATCGAAGAGATCGACCGCCTGCTGGGACTCGAAATTGGCGCGGACGATTACATCTGCAAACCCTACAGCCCGCGTGAAGTGGTCGCCCGCGTGAAAACCATTCTGCGTCGCTGTAAGCCGCAGCGCGAGCTTCAGGTGCTGGACGCCGAAAGCCCGCTGATTGTTGATGAGAGCCGCTTCCAGGCCAGCTGGCGCAGCAAGCTTCTCGATCTCACGCCTGCTGAGTTCCGCCTGCTGAAAACCCTTTCCCACGAGCCGGGGAAAGTGTTCTCTCGCGAGCAGCTGCTCAACCACCTGTATGACGATTACCGCGTGGTGACGGACCGCACCATCGACAGCCACATCAAAAACCTGCGCCGTAAGCTGGAGGCGCTCGACGCCGAACAGTCATTTATTCGCGCGGTGTATGGCGTGGGATACCGCTGGGAAGCGGATGCGTGCAGGATTGCATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37608","NCBI_taxonomy_name":"Enterobacter cloacae subsp. cloacae ATCC 13047","NCBI_taxonomy_id":"716541"}}}},"ARO_accession":"3000828","ARO_id":"37208","ARO_name":"baeR","CARD_short_name":"baeR","ARO_description":"BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36250":{"category_aro_accession":"3000111","category_aro_cvterm_id":"36250","category_aro_name":"novobiocin","category_aro_description":"Novobiocin is an aminocoumarin antibiotic produced by Streptomyces spheroides and Streptomyces niveus, and binds DNA gyrase subunit B inhibiting ATP-dependent DNA supercoiling.","category_aro_class_name":"Antibiotic"},"46133":{"category_aro_accession":"3007382","category_aro_cvterm_id":"46133","category_aro_name":"gentamicin","category_aro_description":"Gentamicin is a commonly used aminoglycoside antibiotic derived from members of the Micromonospora genus of bacteria. It acts by binding the 30S ribosomal subunit, thus inhibiting protein synthesis. Gentamicin is typically used to treat Gram-negative infections of the repiratory and urinary tract, as well as infections of the bone and soft tissue. It also exhibits considerable nephrotoxicity and ototoxicity. Gentamicin is administered as a mixture of gentamicin type C (which makes about around 80% of the complex) and types A, B, and X (distributed in the remaining 20% of the complex).","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36242":{"category_aro_accession":"3000103","category_aro_cvterm_id":"36242","category_aro_name":"aminocoumarin antibiotic","category_aro_description":"Aminocoumarin antibiotics bind DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1502":{"model_id":"1502","model_name":"OXA-209","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4700":{"protein_sequence":{"accession":"AEM66528.1","sequence":"MKKTFILLNLILLVNLNGYCQTKSLKSNEIVKPEFRNILDSLKVKGAILIYDVKNKTYYSNDFSWTKTGIIPASTFKIPNSIIALETGIIKNDSTIFKWNGEKRKFKNWEEDLTFKKAFQVSCVPCYQEIARKIGVKRMKRYLKKLNYRGMVFDTLTIDQFWLEGESKITQMQQIDFLERLYFSKFPISDRTIKIVKNIMEIERTENYILSGKTGLSSIEEKYNGWFVGYVETKSNVYFFATNVIPTDGLNVDDFISSRINVTKNALKQMNIMK"},"dna_sequence":{"accession":"JF268688.1","fmin":"5407","fmax":"6232","strand":"-","sequence":"ATGAAAAAAACATTTATACTTCTGAATCTAATTTTATTAGTAAATCTTAATGGATATTGTCAAACTAAAAGTTTAAAATCAAATGAAATTGTAAAACCTGAATTTAGAAATATATTAGATAGTTTAAAGGTAAAAGGAGCAATTTTAATTTATGATGTAAAAAACAAAACTTATTATTCAAATGATTTTTCTTGGACAAAAACTGGAATAATTCCTGCATCGACTTTCAAAATACCAAATTCAATTATTGCGTTAGAAACAGGAATAATCAAAAATGACTCTACAATTTTTAAATGGAATGGTGAAAAACGCAAATTTAAAAATTGGGAAGAAGATTTGACTTTTAAAAAAGCATTTCAAGTTTCTTGTGTTCCTTGTTATCAAGAAATTGCCAGAAAAATTGGTGTGAAAAGGATGAAAAGATATTTGAAAAAATTAAATTACAGAGGAATGGTTTTCGATACTTTGACGATTGATCAATTTTGGTTAGAAGGAGAATCTAAAATTACTCAAATGCAACAAATAGATTTTTTAGAACGATTATACTTTTCAAAATTTCCAATTTCTGATAGGACAATAAAGATTGTCAAAAATATTATGGAAATTGAGCGAACTGAAAATTACATTTTAAGCGGTAAGACTGGATTAAGTTCGATAGAAGAAAAATATAATGGTTGGTTTGTTGGTTATGTTGAAACAAAATCTAATGTTTATTTTTTTGCAACAAATGTAATTCCGACAGACGGATTGAATGTTGATGATTTTATTTCATCGAGAATTAATGTAACAAAAAATGCGTTAAAGCAAATGAATATAATGAAATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36951","NCBI_taxonomy_name":"Riemerella anatipestifer","NCBI_taxonomy_id":"34085"}}}},"ARO_accession":"3001809","ARO_id":"38209","ARO_name":"OXA-209","CARD_short_name":"OXA-209","ARO_description":"OXA-209 is a beta-lactamase found in Riemerella anatipestifer.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1503":{"model_id":"1503","model_name":"LEN-4","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"8405":{"protein_sequence":{"accession":"AAN05031.1","sequence":"VISLLATLPLAVDAGPQPLEQIKQSESQLSGRVGMVEMDLASGRTLAAWRADERFPMVSTFKVLLCGAVLARVDAGLEQLDRRIHYRQQDLVDYSPVSEKHLTDGMTIGELCAAAITLSDNSAGNLLLATVGGPAGLTAFLRQIGDNVTRLDRWETALNEALPGDARDTTTPASMAATLRKLLTAQHLSARSQQQLLQWMVDDRVAGPLIRAVLPPGWFIADKTGAGERGARGIVALLGPDGKPERIVVIYLRDTPASMAERNQQIAGIGAALI"},"dna_sequence":{"accession":"AY130287.1","fmin":"1","fmax":"823","strand":"+","sequence":"GTTATCTCCCTGTTAGCCACCCTGCCACTGGCGGTAGACGCCGGTCCACAGCCGCTTGAGCAGATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTGGGGATGGTGGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCGATGAACGCTTTCCCATGGTGAGCACCTTTAAAGTGCTGCTGTGCGGCGCGGTGCTGGCGCGGGTGGATGCCGGGCTCGAACAACTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTACCGACGGGATGACGATCGGCGAACTCTGCGCCGCCGCCATCACCCTGAGCGATAACAGCGCTGGCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCGGGATTAACTGCCTTTCTGCGCCAGATCGGTGACAACGTCACCCGTCTTGACCGCTGGGAAACGGCACTGAATGAGGCGCTTCCCGGCGACGCGCGCGACACCACCACCCCGGCCAGCATGGCCGCCACGCTGCGCAAACTACTGACCGCGCAGCATCTGAGCGCCCGTTCGCAACAGCAACTCCTGCAGTGGATGGTGGACGATCGGGTTGCCGGCCCGCTGATCCGCGCCGTGCTGCCGCCGGGCTGGTTTATCGCCGACAAAACCGGGGCTGGCGAACGGGGTGCGCGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAACCGGAGCGCATTGTGGTGATCTATCTGCGGGATACCCCGGCGAGTATGGCCGAGCGTAATCAACAAATCGCCGGGATCGGCGCGGCGCTGATC","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002472","ARO_id":"38872","ARO_name":"LEN-4","CARD_short_name":"LEN-4","ARO_description":"LEN-4 is a beta-lactamase found in Escherichia coli.","ARO_category":{"36236":{"category_aro_accession":"3000097","category_aro_cvterm_id":"36236","category_aro_name":"LEN beta-lactamase","category_aro_description":"LEN beta-lactamases are chromosomal class A beta-lactamases that confer resistance to ampicillin, amoxicillin, carbenicillin, and ticarcillin but not to extended-spectrum beta-lactams.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1504":{"model_id":"1504","model_name":"CMY-108","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1775":{"protein_sequence":{"accession":"AGZ20169.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGISLLHLATYTAGGLPLQIPDDVTDKAALLRFYQNWQPQWAPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQSEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQVNMDASRVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWHILEKLQ"},"dna_sequence":{"accession":"KF564648.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCATTCTCCACGTTTGCCGCCGCCAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCAGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTACTGATAAAGCCGCATTACTGCGTTTTTATCAAAACTGGCAGCCGCAATGGGCCCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACAGTTCCGCAAAGCGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCTGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGTCAACATGGACGCCAGCCGCGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGTAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAGGCCTCATGGGTGCATAAAACGGGATCCACTGGAGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCACATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002120","ARO_id":"38520","ARO_name":"CMY-108","CARD_short_name":"CMY-108","ARO_description":"CMY-108 is a beta-lactamase present in plasmids of clinical Escherichia coli from humans and companion animals in the upper Midwestern USA . Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1506":{"model_id":"1506","model_name":"ACT-12","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1017":{"protein_sequence":{"accession":"AFU25650.1","sequence":"MMKKSLCCALLLSTSCAALAAPLSETQLAKVVERTVTPLMKAQSIPGMAVAVIYQGQPHYFTFGKADVAANTPVTAQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPELTGKQWQGVRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQSWQPQWAPGTTRLYANASIGLFGALAVKPSGMRFEQAMTERVLKPLNLNHTWINVPKAEEQHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVKDMASWVVANMAPDGVQDASLKQGMVLAQSRYWRTGSMYQGLGWEMLNWPVEAKTVVEGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKELGIVMLANKSYPNPARVEAAYRILSALQ"},"dna_sequence":{"accession":"JX440355.1","fmin":"751","fmax":"1897","strand":"+","sequence":"ATGATGAAAAAATCCCTGTGCTGCGCCCTGCTGCTCAGCACCTCCTGCGCTGCATTAGCCGCACCTCTGTCAGAAACACAGCTGGCGAAGGTCGTGGAACGTACCGTTACGCCCCTGATGAAAGCGCAGTCTATTCCGGGTATGGCGGTCGCCGTGATCTATCAGGGCCAGCCGCACTACTTCACCTTCGGCAAGGCCGATGTCGCCGCGAACACACCCGTCACTGCACAAACGCTGTTTGAGCTGGGCTCAATCAGCAAAACCTTCACCGGCGTTCTGGGTGGCGATGCTATTGCTCGCGGTGAAATTTCGCTGGGCGATCCGGTGACCAAATACTGGCCTGAACTGACCGGCAAACAGTGGCAGGGCGTTCGCATGCTGGACCTGGCAACCTATACTGCCGGTGGCCTGCCGTTACAGGTGCCCGATGAGGTTACCGATAATGCCTCGCTGCTGCGTTTTTACCAGTCCTGGCAACCACAGTGGGCGCCAGGCACCACGCGTCTTTATGCGAATGCCAGCATCGGTCTGTTTGGGGCTCTGGCAGTGAAACCTTCTGGCATGCGCTTTGAGCAGGCGATGACGGAGCGGGTCCTGAAGCCGCTTAACCTGAACCATACGTGGATTAACGTTCCGAAGGCAGAAGAACAGCATTACGCCTGGGGTTATCGTGACGGTAAAGCGGTTCACGTTTCGCCGGGCATGCTCGATGCCGAAGCATATGGCGTGAAAACCAACGTGAAGGATATGGCGAGCTGGGTGGTGGCTAACATGGCCCCCGATGGGGTACAGGATGCCTCACTGAAGCAGGGCATGGTGCTTGCACAGTCTCGCTACTGGCGCACAGGCTCGATGTACCAGGGCCTGGGCTGGGAGATGCTCAACTGGCCGGTAGAAGCCAAAACCGTGGTGGAGGGCAGCGACAACAAGGTAGCGCTTGCACCGTTGCCCGTGGCAGAAGTGAACCCTCCGGCTCCACCGGTAAAAGCGTCATGGGTACATAAAACAGGCTCGACGGGCGGATTTGGCAGCTACGTGGCATTTATCCCTGAGAAGGAACTCGGCATCGTTATGCTGGCGAACAAGAGCTACCCGAACCCGGCACGCGTGGAAGCGGCATACCGTATTCTGAGCGCTCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3001834","ARO_id":"38234","ARO_name":"ACT-12","CARD_short_name":"ACT-12","ARO_description":"ACT-12 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1507":{"model_id":"1507","model_name":"smeA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"496":{"protein_sequence":{"accession":"AAD51344.1","sequence":"MSLLRPLSRSPRPLLLPLLLALAACSADRTDAPAMPEVGVIIASAQPLALQQTLPGRAVPFEISEVRPQIGGLIRQRLFTEGQQVKAGQLLYQVDPAPYQAAFDTARGQLAQAEATVLSAQPKAERTRALVSMDAASKQDADDATSALKQAQANVIAARAALQAARINLDYTRVTAPIDGRIGTSSVTAGALVAAGQDTALTTIQRLDPVYLDVTQSSTQMLALRKRLDAGLVKAIDGKAQVKVLLEDGSTYAHEGTLEFVGSAVDPGTGNVKLRAVIPNPDGLLLPGMYLKAVLPMATDARALLVPQKAVVRNERGEPLLRLLDAKDHVVERRVSTGQVVGNQWQITSGLKAGERVIVSNGSAVSLGQQVKAVAPTTAQLAAMPAVDPNGNTDEKSH"},"dna_sequence":{"accession":"AF173226.1","fmin":"2558","fmax":"3755","strand":"+","sequence":"ATGTCTCTCCTGCGCCCGCTGTCCCGTTCCCCGCGTCCCCTGCTGTTGCCCCTGCTGCTGGCCCTGGCGGCCTGTTCGGCGGACAGGACCGACGCCCCGGCCATGCCCGAAGTGGGCGTCATCATCGCCAGCGCGCAGCCGCTGGCACTCCAGCAGACCTTGCCCGGCCGTGCCGTGCCGTTCGAGATCTCCGAGGTGCGGCCGCAGATCGGCGGCCTGATCCGCCAGCGGTTGTTCACCGAAGGCCAGCAGGTCAAGGCAGGGCAGCTGCTGTACCAGGTCGACCCGGCACCGTACCAGGCGGCCTTCGATACCGCCCGCGGGCAGCTGGCGCAGGCCGAGGCCACCGTGTTGTCGGCACAGCCGAAGGCCGAGCGTACCCGCGCGCTGGTGAGCATGGATGCAGCCAGCAAGCAGGACGCCGACGATGCCACCTCGGCGTTGAAGCAGGCGCAGGCCAACGTGATTGCCGCGCGCGCTGCATTGCAGGCTGCCCGCATCAACCTCGACTACACCCGGGTGACCGCCCCCATCGACGGTCGCATCGGCACCTCCAGCGTCACCGCCGGCGCGCTGGTCGCGGCCGGCCAGGATACGGCGTTGACCACCATCCAGCGGCTGGACCCGGTGTACCTGGATGTCACCCAGTCCAGCACGCAGATGCTGGCGCTGCGCAAGCGGCTCGATGCGGGCCTAGTGAAGGCCATCGATGGCAAGGCACAGGTTAAGGTGCTGCTGGAGGACGGCAGCACCTACGCGCATGAAGGCACGTTGGAGTTCGTCGGCAGCGCAGTGGATCCGGGCACCGGAAACGTGAAGCTGCGCGCGGTCATTCCGAACCCGGACGGCCTGCTGTTGCCGGGCATGTACCTGAAGGCGGTGCTGCCGATGGCCACCGACGCGCGTGCCCTGCTGGTGCCGCAGAAGGCAGTGGTGCGCAACGAACGCGGCGAACCGCTGCTGCGCCTGCTCGACGCCAAGGATCATGTGGTCGAGCGCCGCGTCAGCACCGGCCAGGTGGTCGGTAACCAGTGGCAGATCACCAGCGGCCTCAAGGCTGGCGAACGGGTGATCGTCAGCAACGGCAGCGCGGTATCGCTCGGTCAGCAGGTGAAAGCGGTGGCGCCCACGACGGCGCAGTTGGCGGCGATGCCGGCGGTCGATCCGAACGGCAACACCGACGAAAAGTCGCACTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37076","NCBI_taxonomy_name":"Stenotrophomonas maltophilia","NCBI_taxonomy_id":"40324"}}}},"ARO_accession":"3003051","ARO_id":"39485","ARO_name":"smeA","CARD_short_name":"smeA","ARO_description":"smeA is the membrane fusion protein of the smeABC multidrug efflux complex in Stenotrophomonas maltophilia.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1508":{"model_id":"1508","model_name":"QnrA2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"465":{"protein_sequence":{"accession":"ADU33193.1","sequence":"MDIIDKVFQQEDFSRQDLSDSRFRRCRFYQCDFSHCQLRDASFEDCSFIESGAVEGCHFSYADLRDASFKACRLSLANFSGANCFGIEFRECDLKGANFSRARFYNQVSHKMYFCAAYISGCNLAYANLSGQCLEKCELFENNWSNANLSGASLMGSDLSRGTFSRDCWQQVNLRGCDLTFADLDGLDPRRVNLEGVKICAWQQEQLLEPLGIIVLPD"},"dna_sequence":{"accession":"HQ449669.1","fmin":"0","fmax":"657","strand":"+","sequence":"ATGGATATTATCGATAAAGTTTTTCAACAAGAGGATTTCTCACGCCAGGATTTGAGTGACAGCCGTTTTCGCCGCTGCCGCTTCTATCAGTGTGACTTCAGCCACTGTCAGCTAAGGGATGCCAGTTTCGAGGATTGCAGTTTCATTGAAAGCGGCGCCGTTGAAGGGTGCCACTTCAGCTATGCCGATCTGCGCGATGCCAGTTTCAAGGCTTGCCGTCTGTCTTTGGCTAACTTCAGCGGTGCCAACTGCTTTGGCATAGAGTTCAGGGAATGCGATCTCAAGGGCGCCAACTTTTCCCGGGCCCGCTTTTACAATCAAGTCAGCCATAAAATGTACTTTTGTGCGGCTTATATCTCAGGCTGCAACCTGGCCTATGCCAATTTGAGTGGCCAATGCCTGGAAAAGTGCGAGCTGTTTGAAAATAACTGGAGCAATGCCAATCTCAGCGGTGCTTCCTTGATGGGCTCCGACCTCAGCCGCGGCACCTTCTCCCGCGACTGTTGGCAACAGGTCAATCTGCGGGGCTGTGACCTGACCTTTGCCGATCTGGATGGACTCGATCCCAGGCGGGTCAACCTCGAGGGGGTCAAGATCTGTGCCTGGCAACAGGAGCAACTGTTAGAGCCTCTGGGGATAATAGTGCTTCCGGATTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36891","NCBI_taxonomy_name":"Shewanella algae","NCBI_taxonomy_id":"38313"}}}},"ARO_accession":"3002708","ARO_id":"39142","ARO_name":"QnrA2","CARD_short_name":"QnrA2","ARO_description":"QnrA2 is a plasmid-mediated quinolone resistance protein found in Klebsiella oxytoca.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1511":{"model_id":"1511","model_name":"OXA-423","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"978":{"protein_sequence":{"accession":"AIY30332.1","sequence":"MNKYFTCYVVASLFLSGCTVQHNLINETPSQIVQGHNQVIHQYFDEKNTSGVLVIQTDKKINLYGNALSRANTEYVPASTFKMLNALIGLENQKTDINEIFKWKGEKRSFTAWEKDMTLGEAMKLSAAPVYQELARRIGLDLMQKEVKRIGFGNAEIGQQVDNFWLVGPLKVTPIQEVEFVSQLAHTQLPFSEKVQANVKNMLLLEESNGYKIFGKTGWAMDIKPQVGWLTGWVEQPDGKIVAFALNMEMRSEMPASIRNELLMKSLKQLNII"},"dna_sequence":{"accession":"KM433672.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGAATAAATATTTTACTTGCTATGTGGTTGCTTCTCTTTTTCTTTCTGGTTGTACGGTTCAGCATAATTTAATAAATGAAACCCCGAGTCAGATTGTTCAAGGACATAATCAGGTGATTCATCAATACTTTGATGAAAAAAACACCTCAGGTGTGCTGGTTATTCAAACAGATAAAAAAATTAATCTATATGGTAATGCTCTAAGCCGCGCAAATACAGAATATGTGCCAGCCTCTACATTTAAAATGTTGAATGCCCTGATCGGATTGGAGAACCAGAAAACGGATATTAATGAAATATTTAAATGGAAGGGCGAGAAAAGGTCGTTTACCGCTTGGGAAAAAGACATGACACTAGGAGAAGCCATGAAGCTTTCTGCAGCCCCAGTCTATCAGGAACTTGCGCGACGTATCGGTCTTGATCTCATGCAAAAAGAAGTAAAACGTATTGGTTTCGGTAATGCTGAAATTGGACAGCAGGTTGATAATTTCTGGTTGGTAGGACCATTAAAGGTTACGCCTATTCAAGAGGTAGAGTTTGTTTCCCAATTAGCACATACACAGCTTCCATTTAGTGAAAAAGTGCAGGCTAATGTAAAAAATATGCTTCTTTTAGAAGAGAGTAATGGCTACAAAATTTTTGGAAAGACTGGTTGGGCAATGGATATAAAACCACAAGTGGGCTGGTTGACCGGCTGGGTTGAGCAGCCAGATGGAAAAATTGTCGCTTTTGCATTAAATATGGAAATGCGGTCAGAAATGCCGGCATCTATACGTAATGAATTATTGATGAAATCATTAAAACAGCTGAATATTATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3003161","ARO_id":"39738","ARO_name":"OXA-423","CARD_short_name":"OXA-423","ARO_description":"OXA-423 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46499":{"category_aro_accession":"3007710","category_aro_cvterm_id":"46499","category_aro_name":"OXA-23-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases, specifically imipenem, derived from OXA-23, first identified in Acinetobacter baumannii.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1512":{"model_id":"1512","model_name":"SME-3","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"1487":{"protein_sequence":{"accession":"AAS92558.1","sequence":"MSNKVNFKTASFLFSVCLALSAFNAHANKSDAAAKQIKKLEEDFDGRIGVFAIDTGSGNTFGYRSDERFPLCSSFKGFLAAAVLERVQQKKLDINQKVKYESRDLEYYSPITTKYKGSGMTLGDMASAALQYSDNGATNIIMERFLGGPEGMTKFMRSIGDNEFRLDRWELELNTAIPGDKRDTSTPKAVANSLNKLALGNVLNAKVKAIYQNWLKGNTTGDARIRASVPADWVVGDKTGSCGAYGTANDYAVIWPKNRAPLIVSIYTTRKSKDDKHSDKTIAEASRIAIQAID"},"dna_sequence":{"accession":"AY584237.1","fmin":"123","fmax":"1008","strand":"+","sequence":"ATGTCAAACAAAGTAAATTTTAAAACGGCTTCATTTTTGTTTAGTGTTTGTTTAGCTTTGTCGGCATTTAATGCTCATGCTAACAAAAGTGATGCTGCGGCAAAACAAATAAAAAAATTAGAGGAAGACTTTGATGGGAGGATTGGCGTCTTTGCAATAGATACAGGATCGGGTAATACATTTGGGTATAGATCAGATGAGCGGTTCCCTTTATGCAGTTCATTTAAAGGTTTTTTGGCGGCTGCTGTTTTAGAGAGGGTGCAACAAAAAAAACTAGATATCAACCAAAAGGTTAAATATGAGAGTAGGGATCTAGAATATTATTCACCTATTACAACAAAATATAAAGGCTCAGGTATGACATTAGGTGATATGGCTTCTGCTGCATTGCAATATAGCGACAATGGGGCAACAAATATAATTATGGAACGATTTCTTGGCGGTCCTGAGGGGATGACTAAATTTATGCGTTCTATTGGAGATAATGAGTTTAGGTTAGATCGCTGGGAACTGGAACTTAACACTGCAATCCCAGGAGATAAACGTGACACTTCAACGCCAAAAGCTGTTGCAAATAGTTTGAATAAACTAGCTTTGGGGAATGTTCTCAATGCTAAAGTGAAAGCGATTTATCAAAATTGGTTAAAAGGTAATACAACTGGTGATGCTCGAATTCGTGCTAGTGTTCCTGCTGATTGGGTTGTAGGTGACAAAACTGGGAGCTGTGGGGCATATGGTACTGCGAATGATTATGCCGTCATTTGGCCTAAAAATAGAGCACCATTAATTGTCTCTATATATACAACACGAAAATCGAAAGATGATAAGCACAGTGATAAAACTATTGCGGAAGCATCACGTATTGCAATTCAGGCAATTGATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36783","NCBI_taxonomy_name":"Serratia marcescens","NCBI_taxonomy_id":"615"}}}},"ARO_accession":"3002381","ARO_id":"38781","ARO_name":"SME-3","CARD_short_name":"SME-3","ARO_description":"SME-3 is a beta-lactamase found in Serratia marcescens.","ARO_category":{"36194":{"category_aro_accession":"3000055","category_aro_cvterm_id":"36194","category_aro_name":"SME beta-lactamase","category_aro_description":"SME beta-lactamases are chromosome-mediated class A beta-lactamases that hydrolyze carbapenems in Serratia marcescens.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1513":{"model_id":"1513","model_name":"QnrB64","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"74":{"protein_sequence":{"accession":"AGL43625.1","sequence":"MALALVGDKIDRNRFTGEKIENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNASALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGAQVLGATFSGSDLSGGEFSTFDWRAANFTHCDLTNSELGDLDIRRVDLQGVKLDNYQASLLMERLGIAIIG"},"dna_sequence":{"accession":"KC580653.1","fmin":"0","fmax":"645","strand":"+","sequence":"ATGGCTCTGGCACTCGTTGGCGATAAAATTGACAGAAACCGTTTCACCGGTGAGAAAATTGAAAATAGTACATTTTTTAACTGTGATTTTTCAGGTGCCGACCTGAGCGGCACTGAATTTATCGGCTGTCAGTTCTATGATCGTGAAAGCCAGAAAGGGTGCAATTTTAGTCGTGCGATGCTGAAAGATGCCATTTTTAAAAGCTGTGATTTATCCATGGCGGATTTTCGCAATGCCAGTGCGCTGGGCATTGAAATTCGTCACTGCCGCGCACAAGGCGCAGATTTCCGCGGCGCAAGCTTTATGAATATGATCACTACTCGCACCTGGTTTTGCAGCGCATATATCACTAACACAAATCTAAGCTATGCCAATTTTTCGAAAGTCGTGCTGGAAAAATGTGAGCTGTGGGAAAACCGTTGGATGGGTGCCCAGGTACTGGGCGCGACGTTCAGTGGTTCAGATCTCTCCGGCGGCGAGTTTTCGACTTTCGACTGGCGAGCAGCAAACTTCACACATTGCGATCTGACCAATTCGGAGTTGGGTGACTTAGATATTCGGCGCGTTGATTTACAAGGCGTTAAGTTGGACAACTACCAGGCATCGTTGCTCATGGAACGTCTTGGCATCGCGATTATTGGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002776","ARO_id":"39210","ARO_name":"QnrB64","CARD_short_name":"QnrB64","ARO_description":"QnrB64 is a plasmid-mediated quinolone resistance protein found in Citrobacter freundii.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1514":{"model_id":"1514","model_name":"IMP-28","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"913":{"protein_sequence":{"accession":"AFG73659.1","sequence":"MSKLFVFFMFLFCSITAAAESLPDLKIERLDEGVYVHTSFEEVNGWGVVPKHGLVVLVNTEAYLIDTPFTAKDTEKLVTWFVGRGYKIKGSISSHFHSDSTGGIEWLNSQSIPTYASELTNELLKKDGKVQAKNSFGGVSYWLVKNKIEVFYPGPGHTPDNVVVWLPENRVLFGGCFVKPYGLGNLGDANLEAWPKSAKLLMSKYGKAKLVVPSHSEVGDASLLKRTLEHAVKGLNESKKPSKPSN"},"dna_sequence":{"accession":"JQ407409.1","fmin":"1168","fmax":"1909","strand":"+","sequence":"ATGAGCAAGTTATTTGTATTCTTTATGTTTTTGTTTTGTAGCATTACTGCCGCAGCAGAGTCTTTGCCAGATTTAAAAATTGAGAGGCTTGATGAAGGCGTTTATGTTCATACTTCGTTTGAAGAAGTTAACGGTTGGGGTGTTGTTCCTAAACACGGCTTGGTGGTTCTTGTAAATACTGAGGCCTATCTGATTGACACTCCATTTACGGCTAAAGATACTGAAAAGTTAGTCACTTGGTTTGTGGGACGCGGCTATAAAATAAAAGGCAGTATTTCCTCTCATTTTCATAGCGACAGCACGGGCGGAATAGAGTGGCTTAATTCTCAATCTATCCCCACGTATGCATCTGAATTAACAAATGAACTTCTTAAAAAAGACGGTAAGGTACAAGCTAAAAATTCATTTGGCGGAGTTAGCTATTGGCTAGTTAAGAATAAGATTGAAGTTTTTTATCCTGGTCCAGGGCACACTCCAGATAACGTAGTGGTTTGGCTACCTGAAAATAGAGTTTTGTTCGGTGGTTGTTTTGTTAAACCGTACGGTCTTGGTAATTTGGGTGACGCAAATTTAGAAGCTTGGCCAAAGTCCGCCAAATTATTAATGTCCAAATATGGTAAGGCAAAACTGGTTGTTCCAAGTCACAGTGAAGTTGGAGACGCATCACTCTTGAAGCGAACATTAGAACATGCGGTTAAAGGGTTAAATGAAAGTAAAAAACCATCAAAACCAAGTAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3002219","ARO_id":"38619","ARO_name":"IMP-28","CARD_short_name":"IMP-28","ARO_description":"IMP-28 is a beta-lactamase found in Klebsiella oxytoca.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1515":{"model_id":"1515","model_name":"NDM-3","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"859":{"protein_sequence":{"accession":"AFK80349.1","sequence":"MELPNIMHPVAKLSTALAAALMLSGCMPGEIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTNDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR"},"dna_sequence":{"accession":"JQ734687.1","fmin":"0","fmax":"813","strand":"+","sequence":"ATGGAATTGCCCAATATTATGCACCCGGTCGCGAAGCTGAGCACCGCATTAGCCGCTGCATTGATGCTGAGCGGGTGCATGCCCGGTGAAATCCGCCCGACGATTGGCCAGCAAATGGAAACTGGCGACCAACGGTTTGGCGATCTGGTTTTCCGCCAGCTCGCACCGAATGTCTGGCAGCACACTTCCTATCTCGACATGCCGGGTTTCGGGGCAGTCGCTTCCAACGGTTTGATCGTCAGGGATGGCGGCCGCGTGCTGGTGGTCGATACCGCCTGGACCAATGACCAGACCGCCCAGATCCTCAACTGGATCAAGCAGGAGATCAACCTGCCGGTCGCGCTGGCGGTGGTGACTCACGCGCATCAGGACAAGATGGGCGGTATGGACGCGCTGCATGCGGCGGGGATTGCGACTTATGCCAATGCGTTGTCGAACCAGCTTGCCCCGCAAGAGGGGATGGTTGCGGCGCAACACAGCCTGACTTTCGCCGCCAATGGCTGGGTCGAACCAGCAACCGCGCCCAACTTTGGCCCGCTCAAGGTATTTTACCCCGGCCCCGGCCACACCAGTGACAATATCACCGTTGGGATCGACGGCACCGACATCGCTTTTGGTGGCTGCCTGATCAAGGACAGCAAGGCCAAGTCGCTCGGCAATCTCGGTGATGCCGACACTGAGCACTACGCCGCGTCAGCGCGCGCGTTTGGTGCGGCGTTCCCCAAGGCCAGCATGATCGTGATGAGCCATTCCGCCCCCGATAGCCGCGCCGCAATCACTCATACGGCCCGCATGGCCGACAAGCTGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002354","ARO_id":"38754","ARO_name":"NDM-3","CARD_short_name":"NDM-3","ARO_description":"NDM-3 is a beta-lactamase found in the Enterobacteriaceae family.","ARO_category":{"36196":{"category_aro_accession":"3000057","category_aro_cvterm_id":"36196","category_aro_name":"NDM beta-lactamase","category_aro_description":"NDM beta-lactamases or New Delhi metallo-beta-lactamases are class B beta-lactamases that confer resistance to a broad range of antibiotics including carbapenems, cephalosporins and penicillins.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1516":{"model_id":"1516","model_name":"CMY-45","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1663":{"protein_sequence":{"accession":"CBB16411.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLKIPDDVRDKAALLHFYQNWQPQWTPGAKRLYSNSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYARGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTVGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"FN546177.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGAAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACTCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCCGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGTTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3002056","ARO_id":"38456","ARO_name":"CMY-45","CARD_short_name":"CMY-45","ARO_description":"CMY-45 is a beta-lactamase found in Proteus mirabilis.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1517":{"model_id":"1517","model_name":"OXA-33","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8425":{"protein_sequence":{"accession":"AAG23871.1","sequence":"ANIIYSSASASTDISTVASPLFEGTEGCFLLYDVSTNAEIAQFNKAKCATQMAPDSTFKIALSLMAFDAEIIDQKTIFKWDKTPKGMEIWNSNHTPKTWMQFSVVWVSQEITQKIGLNKIKNYLKDFDYGNQDFSGDKERNNGLTEAWLESSLKISPEEQIQFLRKIINHNLPVKNSAIENTIENMYLQDLENSTKLYGKTGAGFTANRTLQNGWFEGFIISKSGHKYVFVSALTGNLGSNLTSSIKAKKNAITIL"},"dna_sequence":{"accession":"AY008291.1","fmin":"0","fmax":"768","strand":"+","sequence":"GCAAATATTATCTACAGCAGCGCCAGTGCATCAACAGATATCTCTACTGTTGCATCTCCATTATTTGAAGGAACTGAAGGTTGTTTTTTACTTTACGATGTATCCACAAACGCTGAAATTGCTCAATTCAATAAAGCAAAGTGTGCAACGCAAATGGCACCAGATTCAACTTTCAAGATCGCATTATCACTTATGGCATTTGATGCGGAAATAATAGATCAGAAAACCATATTCAAATGGGATAAAACCCCCAAAGGAATGGAGATCTGGAACAGCAATCATACACCAAAGACGTGGATGCAATTTTCTGTTGTTTGGGTTTCGCAAGAAATAACCCAAAAAATTGGATTAAATAAAATCAAGAATTATCTCAAAGATTTTGATTATGGAAATCAAGACTTCTCTGGAGATAAAGAAAGAAACAACGGATTAACAGAAGCATGGCTCGAAAGTAGCTTAAAAATTTCACCAGAAGAACAAATTCAATTCCTGCGTAAAATTATTAATCACAATCTCCCAGTTAAAAACTCAGCCATAGAAAACACCATAGAGAACATGTATCTACAAGATCTGGAGAATAGTACAAAACTGTATGGGAAAACTGGTGCAGGATTCACAGCAAATAGAACCTTACAAAACGGATGGTTTGAAGGGTTTATTATAAGCAAATCAGGACATAAATATGTTTTTGTGTCCGCACTTACAGGAAACTTGGGGTCGAATTTAACATCAAGCATAAAAGCCAAGAAAAATGCGATCACCATTCTA","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3001427","ARO_id":"37827","ARO_name":"OXA-33","CARD_short_name":"OXA-33","ARO_description":"OXA-33 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1518":{"model_id":"1518","model_name":"EreA2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"219":{"protein_sequence":{"accession":"AAC78336.1","sequence":"MTWRTTRTLLQPQKLEFNEFEILNPVVEGARIVGIGEGAHFVAEFSLARASLIRYFVERHDFNAIGLECGAIQASRLSEWLNSTAGAHELERFSDTLTFSLYGSVLIWVKSYLRESGRKLQLVGIDLPNTLNPRDDLAQLAEIIQVIDHLMKPHVDALTQLLTSIDGQSAVISSAKWGELETAQQEKAISGVTRLKLRLASLAPVLKNHVNSDFFRKASDRIESIEYTLETLRVMKAFFDGTSLEGDTSVRDSYMAGVVDGMVRANPDVRIILLAHNNHLQKTPVSFSGELTAVPMGQHLAEREEGDYRAIAFTHLGLTVPEMHFPSPDSPLGFSVVTTPADAIREDSVEQYVIDACGKEDSCLTLTDDPMEAKRMRSQSASVETNLSEAFDAIVCVPSAGKDSLVAL"},"dna_sequence":{"accession":"AF099140.1","fmin":"136","fmax":"1363","strand":"+","sequence":"ATGACATGGAGAACGACCAGAACACTTTTACAGCCTCAAAAGCTGGAGTTCAATGAGTTTGAGATTCTTAATCCCGTAGTTGAGGGCGCCCGAATTGTCGGCATTGGCGAGGGTGCTCACTTTGTCGCGGAGTTCTCACTGGCTAGAGCTAGTCTTATTCGCTATTTTGTCGAGAGGCATGATTTTAATGCGATTGGTTTGGAATGTGGGGCGATTCAGGCATCCCGGCTATCTGAATGGCTCAACTCAACAGCCGGTGCTCATGAACTTGAGCGATTTTCGGATACCCTGACCTTTTCTTTGTATGGCTCAGTGCTGATTTGGGTTAAATCATATCTACGCGAATCAGGAAGAAAACTGCAGTTAGTCGGAATCGATTTACCCAACACCTTGAATCCAAGGGACGACCTAGCGCAATTGGCCGAAATTATCCAGGTCATCGACCACCTCATGAAACCCCACGTTGATGCGCTGACTCAGTTGTTGACGTCCATTGATGGCCAGTCGGCGGTTATTTCATCGGCAAAATGGGGGGAGTTGGAAACGGCTCAGCAGGAGAAAGCTATCTCAGGGGTAACCAGATTGAAGCTCCGTTTGGCGTCGCTTGCCCCTGTCCTGAAAAATCACGTCAACAGCGATTTTTTCCGAAAAGCCTCTGATCGAATAGAGTCGATAGAGTATACGTTGGAAACCTTGCGTGTAATGAAAGCTTTCTTCGATGGTACCTCTCTTGAGGGAGATACTTCCGTACGTGACTCGTATATGGCGGGCGTGGTGGATGGAATGGTTCGAGCGAATCCGGATGTAAGGATAATTCTGCTGGCGCACAACAATCATTTACAAAAAACTCCAGTTTCCTTTTCAGGCGAGCTTACGGCTGTTCCCATGGGACAGCATCTCGCAGAGAGGGAGGAGGGGGATTACCGTGCGATTGCATTCACCCATCTTGGACTCACCGTGCCGGAAATGCATTTCCCATCGCCCGACAGTCCTCTTGGATTCTCTGTTGTGACCACGCCTGCCGATGCAATCCGTGAGGATAGTGTGGAACAGTATGTCATCGATGCCTGTGGTAAGGAGGATTCATGCCTGACATTGACAGATGACCCCATGGAAGCAAAGCGAATGCGGTCCCAAAGCGCCTCTGTAGAAACGAATTTGAGCGAGGCATTTGATGCCATCGTCTGCGTTCCCAGCGCCGGCAAGGACAGCCTGGTTGCCCTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36946","NCBI_taxonomy_name":"Providencia stuartii","NCBI_taxonomy_id":"588"}}}},"ARO_accession":"3002826","ARO_id":"39260","ARO_name":"EreA2","CARD_short_name":"EreA2","ARO_description":"EreA2 is an integron-encoded erythromycin esterase that hydrolyses the drug's lactone ring. EreA2 is found in Providencia stuartii.","ARO_category":{"36459":{"category_aro_accession":"3000320","category_aro_cvterm_id":"36459","category_aro_name":"macrolide esterase","category_aro_description":"Hydrolytic enzymes that cleave the macrocycle lactone ring of macrolide antibiotics.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1519":{"model_id":"1519","model_name":"vatE","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"507":{"protein_sequence":{"accession":"AAF86220.1","sequence":"MTIPDANAIYPNSAIKEVVFIKNVIKSPNIEIGDYTYYDDPVNPTDFEKHVTHHYEFLGDKLIIGKFCSIASGIEFIMNGANHVMKGISTYPFNILGGDWQQYTPELTDLPLKGDTVVGNDVWFGQNVTVLPGVKIGDGAIIGANSVVTKDVAPYTIVGGNPIQLIGPRFEPEVIQALENLAWWNKDIEWITANVPKLMQTTPTLELINSLMEK"},"dna_sequence":{"accession":"AF242872.1","fmin":"3579","fmax":"4224","strand":"+","sequence":"ATGACTATACCTGACGCAAATGCAATCTATCCTAACTCAGCCATCAAAGAGGTTGTCTTTATCAAGAACGTGATCAAAAGTCCCAATATTGAAATTGGGGACTACACCTATTATGATGACCCAGTAAATCCCACCGATTTTGAGAAACACGTTACCCATCACTATGAATTTCTAGGCGACAAATTAATCATCGGTAAATTTTGTTCTATCGCCAGTGGCATTGAATTTATCATGAACGGTGCCAACCACGTAATGAAAGGTATTTCGACTTATCCATTTAATATTTTAGGTGGCGATTGGCAACAATACACTCCTGAACTGACTGATTTGCCGTTGAAAGGTGATACTGTAGTCGGAAATGACGTGTGGTTTGGGCAAAATGTGACCGTCCTACCAGGCGTAAAAATAGGTGACGGTGCCATTATCGGAGCAAATAGTGTTGTAACAAAAGACGTCGCTCCATATACAATTGTCGGTGGCAATCCAATTCAACTCATCGGACCAAGATTTGAACCGGAAGTTATTCAAGCATTAGAAAATCTGGCATGGTGGAATAAAGATATTGAATGGATAACTGCTAATGTTCCTAAACTAATGCAAACAACACCCACACTTGAATTGATAAACAGTTTAATGGAAAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36779","NCBI_taxonomy_name":"Enterococcus faecium","NCBI_taxonomy_id":"1352"}}}},"ARO_accession":"3002844","ARO_id":"39278","ARO_name":"vatE","CARD_short_name":"vatE","ARO_description":"vatE is a transposon-mediated acetyltransferase found in Enterococcus faecium.","ARO_category":{"36592":{"category_aro_accession":"3000453","category_aro_cvterm_id":"36592","category_aro_name":"streptogramin vat acetyltransferase","category_aro_description":"vat (Virginiamycin acetyltransferases) enzymes catalyze the transfer of an acetyl group from acetyl-CoA to the secondary alcohol of streptogramin A compounds, thus inactivating virginiamycin-like antibiotics and conferring resistance to these compounds.","category_aro_class_name":"AMR Gene Family"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"virginiamycin M1","category_aro_description":"Virginiamycin M1 is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37016":{"category_aro_accession":"3000672","category_aro_cvterm_id":"37016","category_aro_name":"madumycin II","category_aro_description":"Madumycin II is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37017":{"category_aro_accession":"3000673","category_aro_cvterm_id":"37017","category_aro_name":"griseoviridin","category_aro_description":"Griseoviridin is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35952":{"category_aro_accession":"0000034","category_aro_cvterm_id":"35952","category_aro_name":"streptogramin A antibiotic","category_aro_description":"Streptogramin A antibiotics are cyclic polyketide peptide hybrids that bind to the ribosomal peptidyl transfer centre. Structural variation arises from substituting a proline for its desaturated derivative and by its substitution for Ala or Cys. Used alone, streptogramin A antibiotics are bacteriostatic, but is bactericidal when used with streptogramin B antibiotics.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1520":{"model_id":"1520","model_name":"SHV-85","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1486":{"protein_sequence":{"accession":"ABC54571.1","sequence":"MRYIRLCIISLLATMPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"DQ322460.1","fmin":"15","fmax":"876","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCATGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATCGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001139","ARO_id":"37519","ARO_name":"SHV-85","CARD_short_name":"SHV-85","ARO_description":"SHV-85 is a broad-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1521":{"model_id":"1521","model_name":"VIM-32","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"8290":{"protein_sequence":{"accession":"AEZ49857.1","sequence":"MLKVISSLLVYMTASVMAVASPLAHSGEPSGEYPTVNEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEAAGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSANVLYGGCAVHELSSTSAGNVADADLAEWPTSVERIQKHYPEAEVVIPGHGLPGGLDLLQHTANVVKAHKNRSVAE"},"dna_sequence":{"accession":"JN676230.2","fmin":"1549","fmax":"2350","strand":"+","sequence":"ATGTTAAAAGTTATTAGTAGTTTATTGGTCTACATGACCGCGTCTGTCATGGCTGTCGCAAGTCCGTTAGCCCATTCCGGGGAGCCGAGTGGTGAGTATCCGACAGTCAACGAAATTCCGGTCGGAGAGGTCCGACTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCGGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAAAAGCAAATTGGACTTCCCGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGCAGCGGGGAACGAGATTCCCACGCATTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAGCTCTTCTATCCTGGTGCTGCGCATTCGACCGACAATCTGGTTGTATACGTCCCGTCAGCGAACGTGCTATACGGTGGTTGTGCCGTTCATGAGTTGTCAAGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCGTTGAGCGGATTCAAAAACACTACCCGGAAGCAGAGGTCGTCATTCCCGGGCACGGTCTACCGGGCGGTCTAGACTTGCTCCAGCACACAGCGAACGTTGTCAAAGCACACAAAAATCGCTCAGTCGCCGAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3002302","ARO_id":"38702","ARO_name":"VIM-32","CARD_short_name":"VIM-32","ARO_description":"VIM-32 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1522":{"model_id":"1522","model_name":"IMP-38","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1709":{"protein_sequence":{"accession":"AEN75249.1","sequence":"MSKLSVFFIFLFCSIATAAEPLPDLKIEKLDEGVYVHTSFEEVNGWGVVPKHGLVVLVDAEAYLIDTPFTAKDTEKLVTWFVERGYKIKGSISSHFHSDSTGGIEWLNSQSIPTYASELTNELLKKDGKVQAKNSFGGVNYWLVKNKIEVFYPGPGHTPDNLVVWLPERKILFGGCFIKPYGLGNLGDANLEAWPKSAKLLISKYGKAKLVVPGHSEAGDASLLKLTLEQAVKGLNESKKPSKLSN"},"dna_sequence":{"accession":"HQ875573.1","fmin":"0","fmax":"741","strand":"+","sequence":"ATGAGCAAGTTATCTGTATTCTTTATATTTTTGTTTTGTAGCATTGCTACCGCAGCAGAGCCTTTGCCAGATTTAAAAATTGAAAAACTTGATGAAGGCGTTTATGTTCATACTTCGTTTGAAGAAGTTAACGGGTGGGGCGTTGTTCCTAAACATGGTTTGGTTGTTCTTGTAGATGCTGAAGCTTATCTAATTGACACTCCATTTACGGCTAAAGATACTGAAAAGTTAGTCACTTGGTTTGTGGAACGTGGCTATAAAATAAAAGGCAGTATTTCCTCTCATTTTCATAGTGACAGCACGGGCGGAATAGAGTGGCTTAATTCTCAATCCATCCCCACGTATGCGTCTGAATTAACTAATGAGCTGCTTAAAAAAGACGGTAAGGTTCAAGCTAAAAATTCATTTGGCGGGGTTAACTATTGGCTAGTTAAAAATAAAATTGAAGTTTTTTATCCAGGCCCAGGACACACTCCAGATAACCTAGTAGTTTGGCTGCCTGAAAGGAAAATATTATTCGGTGGTTGTTTTATTAAACCGTACGGTCTAGGTAATTTGGGTGACGCAAATTTAGAAGCTTGGCCAAAGTCCGCTAAATTATTAATATCCAAATATGGTAAGGCAAAACTGGTTGTTCCAGGTCACAGTGAAGCTGGAGACGCATCACTCTTGAAACTTACATTAGAGCAGGCGGTTAAAGGGTTAAACGAAAGTAAAAAACCATCAAAACTAAGCAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002229","ARO_id":"38629","ARO_name":"IMP-38","CARD_short_name":"IMP-38","ARO_description":"IMP-38 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1525":{"model_id":"1525","model_name":"TEM-160","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1798":{"protein_sequence":{"accession":"ABM54870.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDKLGARVGYIELDLNSGKILESFRPEERFPMVSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"EF136377.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATAAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGGTGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3001026","ARO_id":"37406","ARO_name":"TEM-160","CARD_short_name":"TEM-160","ARO_description":"TEM-160 is an inhibitor-resistant beta-lactamase found in Proteus mirabilis.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1526":{"model_id":"1526","model_name":"AAC(6')-Iaa","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"5208":{"protein_sequence":{"accession":"AAL20537.1","sequence":"MDIRQMNRTHLDHWRGLRKQLWPGHPDDAHLADGEEILQADHLASFIAMADGVAIGFADASIRHDYVNGCDSSPVVFLEGIFVLPSFRQRGVAKQLIAAVQRWGTNKGCREMASDTSPENTISQKVHQALGFEETERVIFYRKRC"},"dna_sequence":{"accession":"AE006468.2","fmin":"1707351","fmax":"1707789","strand":"+","sequence":"ATGGACATCAGGCAAATGAACAGAACCCATCTGGATCACTGGCGCGGATTGCGAAAACAGCTCTGGCCTGGTCACCCGGATGACGCCCATCTGGCGGACGGCGAAGAAATTCTGCAAGCCGATCATCTGGCATCATTTATTGCGATGGCAGACGGGGTGGCGATTGGCTTTGCGGATGCCTCAATCCGCCACGATTATGTCAATGGCTGTGACAGTTCGCCCGTGGTTTTCCTTGAAGGTATTTTTGTTCTCCCCTCATTCCGTCAACGCGGCGTAGCGAAACAATTGATTGCAGCGGTGCAACGATGGGGAACGAATAAAGGGTGTCGGGAAATGGCCTCCGATACCTCGCCGGAAAATACAATTTCCCAGAAAGTTCATCAGGCGTTAGGATTTGAGGAAACAGAGCGCGTCATTTTCTACCGAAAGCGTTGTTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35734","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Typhimurium str. LT2","NCBI_taxonomy_id":"99287"}}}},"ARO_accession":"3002571","ARO_id":"38971","ARO_name":"AAC(6')-Iaa","CARD_short_name":"AAC(6')-Iaa","ARO_description":"AAC(6')-Iaa is a chromosomal-encoded aminoglycoside acetyltransferase in S. typhimurium.","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"A category of aminoglycoside N-acetyltransferase enzymes with modification regiospecificity based at the 6'-amino group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics through acetylation of the 6-amino group of the compound.","category_aro_class_name":"AMR Gene Family"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"46128":{"category_aro_accession":"3007378","category_aro_cvterm_id":"46128","category_aro_name":"2'-N-ethylnetilmicin","category_aro_description":"2'-N-ethylnetilmicin is an aminoglycoside antibiotic and a derivative of netilmicin.","category_aro_class_name":"Antibiotic"},"46129":{"category_aro_accession":"3007379","category_aro_cvterm_id":"46129","category_aro_name":"5-episisomicin","category_aro_description":"5-episosomicin is a semisynthetic aminoglycoside antibiotic similar to sisomicin.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1527":{"model_id":"1527","model_name":"SHV-51","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1316":{"protein_sequence":{"accession":"AAP41944.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGLAGLTAFLRQIGDNVTRLDRWETELNEALPADARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AY289548.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACATCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCTCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGCCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001108","ARO_id":"37488","ARO_name":"SHV-51","CARD_short_name":"SHV-51","ARO_description":"SHV-51 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1528":{"model_id":"1528","model_name":"TEM-168","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"999":{"protein_sequence":{"accession":"ACR22829.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYMTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"FJ919776.1","fmin":"208","fmax":"1069","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACATGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001034","ARO_id":"37414","ARO_name":"TEM-168","CARD_short_name":"TEM-168","ARO_description":"TEM-168 is an extended-spectrum beta-lactamase.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1529":{"model_id":"1529","model_name":"TEM-130","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1880":{"protein_sequence":{"accession":"CAI29263.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKPAEDKLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVKYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDSWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGTGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AJ866988.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAACCTGCTGAAGATAAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTAAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATAGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAACCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3000994","ARO_id":"37374","ARO_name":"TEM-130","CARD_short_name":"TEM-130","ARO_description":"TEM-130 is an extended-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1530":{"model_id":"1530","model_name":"OXA-67","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1936":{"protein_sequence":{"accession":"ABF50983.1","sequence":"MNIKALLLITSTIFISACSPYIVTANPNHSTSKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEIFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSLKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"DQ491200.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCACTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCACTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAATATTTAAGTGGGACGGGCAAAAAAGGCTGTTCCCAGAATGGGAAAAGGACATGACCCTAGGTGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCTAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001437","ARO_id":"37837","ARO_name":"OXA-67","CARD_short_name":"OXA-67","ARO_description":"OXA-67 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1531":{"model_id":"1531","model_name":"TEM-81","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1080":{"protein_sequence":{"accession":"AAL29433.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMLSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAVTMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AF427127.1","fmin":"208","fmax":"1069","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGCTGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCGTAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000948","ARO_id":"37328","ARO_name":"TEM-81","CARD_short_name":"TEM-81","ARO_description":"TEM-81 is an inhibitor-resistant beta-lactamase found in E. coli.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1532":{"model_id":"1532","model_name":"OXA-249","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1130":{"protein_sequence":{"accession":"CCJ32597.1","sequence":"MNIKALLLITSAIFISACSPYIVTTNPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIQVYQDLARRIGLELMSKEVKRVGYGNTDIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"HE963770.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTACTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCAAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATACAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001674","ARO_id":"38074","ARO_name":"OXA-249","CARD_short_name":"OXA-249","ARO_description":"OXA-249 is a beta-lactamase found in A. baumannii.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1533":{"model_id":"1533","model_name":"SHV-143","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"4699":{"protein_sequence":{"accession":"AFQ32277.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDLWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"JQ341060.1","fmin":"881","fmax":"1742","strand":"-","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTACTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCTCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001344","ARO_id":"37744","ARO_name":"SHV-143","CARD_short_name":"SHV-143","ARO_description":"SHV-143 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1534":{"model_id":"1534","model_name":"PER-5","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"5839":{"protein_sequence":{"accession":"WP_063864594.1","sequence":"MNVIIKAVVTASTLLMVSFSSFETSAQSPLLKGQIESIVIGKKATVGVAVWGPDDLEPLLINPFEKFPMQSVFKLHLAMLVLHQVDQGKLDLNQTVIVNRAKVLQNTWAPIMKAYQGDEFSVPVQQLLQYSVSHSDNVACDLLFELVGGPAALHDYIQSMGIKETAVVANEAQMHADDQVQYQNWTSMKGAAEILKKFEQKTQLSETSQALLWKWMVETTTGPERLKGLLPAGTVVAHKTGTSGIKAGKTAATNDLGIILLPDGRPLLVAVFVKDSAESSRTNEAIIAQVAQTAYQFELKKLSALSPN"},"dna_sequence":{"accession":"NG_049964.1","fmin":"0","fmax":"927","strand":"+","sequence":"ATGAATGTCATTATAAAAGCTGTAGTTACTGCCTCGACGCTACTGATGGTATCTTTTAGTTCATTCGAAACCTCAGCGCAATCCCCACTGTTAAAAGGGCAAATTGAATCCATAGTCATTGGAAAAAAAGCCACTGTAGGCGTTGCAGTGTGGGGGCCTGACGATCTGGAACCTTTACTGATTAATCCTTTTGAAAAATTCCCAATGCAAAGTGTATTTAAATTGCATTTAGCTATGTTGGTACTGCATCAGGTTGATCAGGGAAAGTTGGATTTAAATCAGACCGTTATCGTAAACAGGGCTAAGGTTTTACAGAATACCTGGGCTCCGATAATGAAAGCGTATCAGGGAGACGAGTTTAGTGTTCCAGTGCAGCAACTGCTGCAATACTCGGTCTCGCACAGCGATAACGTGGCCTGTGATTTGTTATTTGAACTGGTTGGTGGACCAGCTGCTTTGCATGACTATATCCAGTCTATGGGTATAAAGGAGACCGCTGTGGTCGCAAATGAAGCGCAGATGCACGCCGATGATCAGGTGCAGTATCAAAACTGGACCTCGATGAAAGGTGCTGCAGAGATCCTGAAAAAGTTTGAGCAAAAAACACAGCTGTCTGAAACCTCGCAGGCTTTGTTATGGAAGTGGATGGTCGAAACCACCACAGGACCAGAGCGGTTAAAAGGTTTGTTACCAGCTGGTACTGTGGTCGCACATAAAACTGGTACTTCGGGTATCAAAGCCGGAAAAACTGCGGCCACTAATGATTTAGGTATCATTCTGTTGCCTGATGGACGGCCCTTGCTGGTTGCTGTTTTTGTGAAAGACTCAGCCGAGTCAAGCCGAACCAATGAAGCTATCATTGCGCAGGTTGCTCAGACTGCGTATCAATTTGAATTGAAAAAGCTTTCTGCCCTAAGCCCAAATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36944","NCBI_taxonomy_name":"Providencia rettgeri","NCBI_taxonomy_id":"587"}}}},"ARO_accession":"3002367","ARO_id":"38767","ARO_name":"PER-5","CARD_short_name":"PER-5","ARO_description":"PER-5 is a beta-lactamase found in the Enterobacteriaceae family.","ARO_category":{"36195":{"category_aro_accession":"3000056","category_aro_cvterm_id":"36195","category_aro_name":"PER beta-lactamase","category_aro_description":"PER beta-lactamases are plasmid-mediated extended spectrum beta-lactamases found in the Enterobacteriaceae family.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1535":{"model_id":"1535","model_name":"CMY-16","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1815":{"protein_sequence":{"accession":"CAH03679.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYSNSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYARGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"AJ781421.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACTCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCCGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3002027","ARO_id":"38427","ARO_name":"CMY-16","CARD_short_name":"CMY-16","ARO_description":"CMY-16 is a beta-lactamase found in Proteus mirabilis.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1536":{"model_id":"1536","model_name":"OXA-421","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4698":{"protein_sequence":{"accession":"AIZ00987.1","sequence":"MTKKTLFFAIGTMFLSACSFNTVEQHQIQSISTNKNSEKIQSLFDQAQTTGVLIIKRGQTEEVYGNDLKRASTEYVPASTFKMLNALIGLEHHKATPTEVFKWDGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMSKEVKRIDFGNADIGSKIDNFWLVGPLKITPQQEAQFAYELAHKTLPFSKNVQEQVQSMLFIEEKNGRKIYAKSGWGWDVEPQVGWFTGWVVQPQGEIVAFALNLEMKKGIPSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"KM401566.1","fmin":"1211","fmax":"2033","strand":"-","sequence":"ATGACTAAAAAAACTCTTTTCTTTGCCATTGGTACGATGTTTTTATCGGCGTGTTCTTTTAATACCGTAGAACAACATCAAATACAGTCAATTTCTACCAATAAAAACTCAGAGAAAATTCAATCATTGTTTGATCAAGCACAAACTACAGGTGTTTTAATTATAAAACGTGGCCAAACAGAGGAAGTCTATGGTAATGATCTTAAAAGAGCATCAACCGAATATGTTCCCGCCTCTACCTTTAAAATGTTAAATGCTTTGATCGGCCTTGAGCATCATAAAGCAACACCAACTGAAGTATTTAAATGGGATGGGCAAAAGCGTTTATTTCCCGATTGGGAAAAAGACATGACATTAGGCGATGCTATGAAAGCTTCTGCTATTCCAGTTTATCAGGAACTAGCTCGACGAATTGGCCTTGATCTTATGTCTAAAGAGGTAAAGCGTATTGATTTCGGTAATGCTGATATTGGTTCAAAAATAGATAATTTTTGGCTTGTTGGCCCACTTAAAATTACACCTCAACAAGAAGCCCAGTTTGCTTATGAACTAGCCCACAAAACTCTTCCCTTTAGCAAAAATGTGCAAGAACAAGTTCAATCTATGTTGTTCATAGAAGAAAAAAATGGACGAAAAATTTATGCTAAAAGTGGTTGGGGATGGGATGTTGAACCACAAGTTGGTTGGTTTACAGGCTGGGTGGTTCAACCACAAGGAGAAATTGTAGCGTTCGCACTTAATTTAGAAATGAAAAAAGGAATACCTAGTTCTATTCGAAAAGAAATTGCTTATAAAGGATTAGAACAATTAGGTATTTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3003117","ARO_id":"39694","ARO_name":"OXA-421","CARD_short_name":"OXA-421","ARO_description":"OXA-421 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46495":{"category_aro_accession":"3007706","category_aro_cvterm_id":"46495","category_aro_name":"OXA-213-like beta-lactamase","category_aro_description":"OXA-213-like enzymes have been identified to be intrinsic to A. calcoaceticus and have been subsequently detected in A. pittii. Phylogenetic analysis of OXA-213-like proteins identified two distinct subgroups within the OXA family. The first group was linked to A. pittii and the second group to A. calcoaceticus. The carbapenemase activity of these OXAs may be related to the species-dependent effect.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1537":{"model_id":"1537","model_name":"GES-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1172":{"protein_sequence":{"accession":"AAK58421.1","sequence":"MRFIHALLLAGIAHSAYASEKLTFKTDLEKLEREKAAQIGVAIVDPQGEIVAGHRMAQRFAMCSTFKFPLAALVFERIDSGTERGDRKLSYGPDMIVEWSPATERFLASGHMTVLEAAQAAVQLSDNGATNLLLREIGGPAAMTQYFRKIGDSVSRLDRKEPEMNDNTPGDLRDTTTPIAMARTVAKVLYGGALTSTSTHTIERWLIGNQTGDATLRAGFPKDWVVGEKTGTCANGGRNDIGFFKAQERDYAVAVYTTAPKLSAVERDELVASVGQVITQLILSTDK"},"dna_sequence":{"accession":"AF326355.1","fmin":"0","fmax":"864","strand":"+","sequence":"ATGCGCTTCATTCACGCACTATTACTGGCAGGGATCGCTCACTCTGCATATGCGTCGGAAAAATTAACCTTCAAGACCGATCTTGAGAAGCTAGAGCGCGAAAAAGCAGCTCAGATCGGTGTTGCGATCGTCGATCCCCAAGGAGAGATCGTCGCGGGCCACCGAATGGCGCAGCGTTTTGCAATGTGCTCAACGTTCAAGTTTCCGCTAGCCGCGCTGGTCTTTGAAAGAATTGACTCAGGCACCGAGCGGGGGGATCGAAAACTTTCATATGGGCCGGACATGATCGTCGAATGGTCTCCTGCCACGGAGCGGTTTCTAGCATCGGGACACATGACGGTTCTCGAGGCAGCGCAAGCTGCGGTGCAGCTTAGCGACAATGGGGCTACTAACCTCTTACTGAGAGAAATTGGCGGACCTGCTGCAATGACGCAGTATTTTCGTAAAATTGGCGACTCTGTGAGTCGGCTAGACCGGAAAGAGCCGGAGATGAACGACAACACACCTGGCGACCTCAGAGATACAACTACGCCTATTGCTATGGCACGTACTGTGGCTAAAGTCCTCTATGGCGGCGCACTGACGTCCACCTCGACCCACACCATTGAGAGGTGGCTGATCGGAAACCAAACGGGAGACGCGACACTACGAGCGGGTTTTCCTAAAGATTGGGTTGTTGGAGAGAAAACTGGTACCTGCGCCAACGGGGGCCGGAACGACATTGGTTTTTTTAAAGCCCAGGAGAGAGATTACGCTGTAGCGGTGTATACAACGGCCCCGAAACTATCGGCCGTAGAACGTGACGAATTAGTTGCCTCTGTCGGTCAAGTTATTACACAACTCATCCTGAGCACGGACAAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002331","ARO_id":"38731","ARO_name":"GES-2","CARD_short_name":"GES-2","ARO_description":"GES-2 is a beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36205":{"category_aro_accession":"3000066","category_aro_cvterm_id":"36205","category_aro_name":"GES beta-lactamase","category_aro_description":"GES beta-lactamases or Guiana extended-spectrum beta-lactamases are related to the other plasmid-located class A beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1538":{"model_id":"1538","model_name":"SHV-104","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1850":{"protein_sequence":{"accession":"ABX71158.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSASSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"EU274581.1","fmin":"0","fmax":"861","strand":"+","sequence":"TTGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCAGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGCATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001153","ARO_id":"37533","ARO_name":"SHV-104","CARD_short_name":"SHV-104","ARO_description":"SHV-104 is an extended-spectrum beta-lactamase that has been found in clinical isolates.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1539":{"model_id":"1539","model_name":"aadA3","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"8168":{"protein_sequence":{"accession":"AAC14728.1","sequence":"MRVAVTIEISNQLSEVLSVIERHLESTLLAVHLYGSAVDGGLKPYSDIDLLVTVAVKLDETTRRALLNDLMEASAFPGESETLRAIEVTLVVHDDIIPWRYPAKRELQFGEWQRNDILAGIFEPAMIDIDLAILLTKAREHSVALVGPAAEEFFDPVPEQDLFEALRETLKLWNSQPDWAGDERNVVLTLSRIWYSAITGKIAPKDVAADWAIKRLPAQYQPVLLEAKQAYLGQKEDHLASRADHLEEFIHYVKGEITKVVGK"},"dna_sequence":{"accession":"AF047479.2","fmin":"1295","fmax":"2087","strand":"+","sequence":"ATGAGGGTAGCGGTGACCATCGAAATTTCGAACCAACTATCAGAGGTGCTAAGCGTCATTGAGCGCCATCTGGAATCAACGTTGCTGGCCGTGCATTTGTACGGCTCCGCAGTGGATGGCGGCCTGAAGCCATACAGCGATATTGATTTGTTGGTTACTGTGGCCGTAAAGCTTGATGAAACGACGCGGCGAGCATTGCTCAATGACCTTATGGAGGCTTCGGCTTTCCCTGGCGAGAGCGAGACGCTCCGCGCTATAGAAGTCACCCTTGTCGTGCATGACGACATCATCCCGTGGCGTTATCCGGCTAAGCGCGAGCTGCAATTTGGAGAATGGCAGCGCAATGACATTCTTGCGGGTATCTTCGAGCCAGCCATGATCGACATTGATCTAGCTATCCTGCTTACAAAAGCAAGAGAACATAGCGTTGCCTTGGTAGGTCCGGCAGCGGAGGAATTCTTTGACCCGGTTCCTGAACAGGATCTATTCGAGGCGCTGAGGGAAACCTTGAAGCTATGGAACTCGCAGCCCGACTGGGCCGGCGATGAGCGAAATGTAGTGCTTACGTTGTCCCGCATTTGGTACAGCGCAATAACCGGCAAAATCGCGCCGAAGGATGTCGCTGCCGACTGGGCAATAAAACGCCTACCTGCCCAGTATCAGCCCGTCTTACTTGAAGCTAAGCAAGCTTATCTGGGACAAAAAGAAGATCACTTGGCCTCACGCGCAGATCACTTGGAAGAATTTATTCACTACGTGAAAGGCGAGATCACCAAGGTAGTCGGCAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36872","NCBI_taxonomy_name":"Plasmid NR79","NCBI_taxonomy_id":"2468"}}}},"ARO_accession":"3002603","ARO_id":"39003","ARO_name":"aadA3","CARD_short_name":"aadA3","ARO_description":"aadA3 is an aminoglycoside nucleotidyltransferase gene encoded by plasmids, transposons and integrons in E. coli.","ARO_category":{"41439":{"category_aro_accession":"3004275","category_aro_cvterm_id":"41439","category_aro_name":"ANT(3'')","category_aro_description":"A category of aminoglycoside O-nucleotidyltransferase enzymes with modification regiospecificity based at the 3''-hydroxyl group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics by transfer of an AMP group from an ATP substrate to the 3''-hydroxyl group of the compound.","category_aro_class_name":"AMR Gene Family"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1540":{"model_id":"1540","model_name":"rmtC","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"3396":{"protein_sequence":{"accession":"AIA09786.1","sequence":"MKTNDNYIEEVTAKVLTSGKYSTLYPPTVRRVTERLFDRYPPKQLEKEVRKKLHQAYGAYIGGIDGKRLEKKIEKIIHEIPNPTTDEATRTEWEKEICLKILNLHTSTNERTVAYDELYQKIFEVTGVPTSITDAGCALNPFSFPFFTEAGMLGQYIGFDLDKGMIEAIEHSLRTLNAPEGIVVKQGDILSDPSGESDLLLMFKLYTLLDRQEEASGLKILQEWKYKNAVISFPIKTISGRDVGMEENYTVKFENDLVGSDLRIMQKLKLGNEMYFIVSRL"},"dna_sequence":{"accession":"KJ476816.1","fmin":"79","fmax":"925","strand":"+","sequence":"ATGAAAACCAACGATAATTATATCGAAGAAGTAACAGCCAAAGTACTCACAAGTGGTAAATACTCCACACTTTATCCACCAACTGTACGACGTGTAACTGAGAGGCTTTTCGATCGATACCCTCCCAAGCAGCTAGAGAAGGAGGTTCGCAAGAAATTGCATCAAGCATATGGTGCTTATATTGGTGGGATCGATGGGAAAAGGTTGGAGAAGAAGATTGAGAAGATAATTCATGAGATACCAAATCCAACTACGGATGAAGCAACTCGTACGGAGTGGGAAAAAGAGATCTGCCTGAAAATATTGAACTTGCACACTTCAACAAATGAGCGAACGGTGGCTTACGATGAGCTTTACCAAAAGATCTTTGAGGTAACAGGGGTTCCAACAAGTATCACCGATGCAGGTTGCGCTTTGAATCCATTTTCTTTTCCATTCTTTACGGAGGCTGGCATGCTTGGGCAATACATAGGTTTCGATCTTGATAAAGGTATGATCGAAGCGATCGAACACTCGTTGAGAACGCTTAACGCCCCAGAGGGTATTGTTGTCAAACAGGGAGATATATTATCCGATCCGTCAGGCGAGAGTGATCTTCTACTTATGTTCAAGCTATATACTCTACTCGATCGGCAGGAAGAGGCCTCTGGTTTGAAAATTCTTCAAGAGTGGAAATACAAAAATGCTGTGATCTCTTTTCCTATTAAAACTATAAGTGGGAGAGATGTTGGGATGGAAGAGAATTACACTGTTAAGTTCGAGAATGATCTTGTTGGGTCAGATCTGAGAATCATGCAAAAATTGAAATTAGGAAACGAGATGTATTTTATCGTATCGAGATTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3000861","ARO_id":"37241","ARO_name":"rmtC","CARD_short_name":"rmtC","ARO_description":"RmtC is a rRNA methyltransferase found in Proteus mirabilis with high level resistance to similar to aminoglycosides, with the exception of non-4,6-disubstituted deoxystreptamines (streptomycin and neomycin). It has also been isolated in Salmonella enterica ser. Virchow. It is hypothesized to methylate G1405, like related methyltransferases RmtA, RmtB, and ArmA.","ARO_category":{"41435":{"category_aro_accession":"3004271","category_aro_cvterm_id":"41435","category_aro_name":"16S rRNA methyltransferase (G1405)","category_aro_description":"Methyltransferases that methylate the G1405 position of 16S rRNA, which is part of an aminoglycoside binding site.","category_aro_class_name":"AMR Gene Family"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36997":{"category_aro_accession":"3000653","category_aro_cvterm_id":"36997","category_aro_name":"G418","category_aro_description":"A gentamicin class aminoglycoside antibiotic often used in mammalian cell culture work as a selectable marker for the neo cassette (APH3').","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"46133":{"category_aro_accession":"3007382","category_aro_cvterm_id":"46133","category_aro_name":"gentamicin","category_aro_description":"Gentamicin is a commonly used aminoglycoside antibiotic derived from members of the Micromonospora genus of bacteria. It acts by binding the 30S ribosomal subunit, thus inhibiting protein synthesis. Gentamicin is typically used to treat Gram-negative infections of the repiratory and urinary tract, as well as infections of the bone and soft tissue. It also exhibits considerable nephrotoxicity and ototoxicity. Gentamicin is administered as a mixture of gentamicin type C (which makes about around 80% of the complex) and types A, B, and X (distributed in the remaining 20% of the complex).","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1541":{"model_id":"1541","model_name":"ACT-14","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1176":{"protein_sequence":{"accession":"AFU25647.1","sequence":"MMKKSLCCALLLGISCSALAAPVSEKQLAEVVANTVTPLMKAQSIPGMAVAVIYQGKPHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNAALLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMGYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPEKVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVIEGSDSKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYLAFIPEKQIGIVMLANKSYPNPARVEAAYHILDALQ"},"dna_sequence":{"accession":"JX440354.1","fmin":"756","fmax":"1902","strand":"+","sequence":"ATGATGAAAAAATCTCTTTGCTGCGCCCTGCTGCTCGGCATCTCTTGCTCTGCTCTCGCCGCGCCAGTGTCAGAAAAACAGCTGGCGGAGGTGGTCGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCGATTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGTAAACCGCACTATTACACGTTTGGCAAAGCAGATATCGCGGCTAATAAACCCGTTACGCCTCAGACTCTGTTCGAGCTGGGCTCTATAAGTAAAACCTTCACCGGGGTTTTAGGTGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTAACGGGCAAGCAGTGGCAGGGGATTCGTATGCTGGATCTCGCAACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAATGCCGCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGTATCGGTCTTTTTGGCGCGCTGGCGGTCAAACCTTCCGGCATGGGCTATGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTTCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGAATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCGGAGAAGGTTGCTGATGCCTCACTTAAGCAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGATCGAGGGCAGCGACAGTAAGGTGGCGCTGGCACCGCTGCCCGTGGCAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGCTCTACTGGCGGGTTTGGCAGCTACTTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCGACGCGCTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3001836","ARO_id":"38236","ARO_name":"ACT-14","CARD_short_name":"ACT-14","ARO_description":"ACT-14 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1542":{"model_id":"1542","model_name":"amrA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"5442":{"protein_sequence":{"accession":"CAH35803.1","sequence":"MKYEWARTRRLSAALAVAAFVAAGCGKHESEHDAAAPREASVVTVKKTSVPLSVELPGRLDAYRQAEVRARVAGIVTARTYEEGQEVKRGAVLFRIDPAPFKAARDAAAGALEKARAAHLAALDKRRRYDELVRDRAVSERDHTEALADERQAKAAVASARAELARAQLQLDYATVTAPIDGRARRALVTEGALVGQDQATPLTTVEQLDPIYVNFSQPAADVESLRRAVKSGRAAGIAQQDVEVTLVRPDGSTYARKGKLLFADLAVDPSTDTVAMRALFPNPERELLPGAYVRIALDRAVARDAILVPRDALLRTADSATVKVVGQNGKIRDVTVEAAQMKGRDWIVTRGLAGGERVVVVDAAQFEAGTTVKALERGAAAQPASGAAAASAPGRRST"},"dna_sequence":{"accession":"BX571965.1","fmin":"2150965","fmax":"2152165","strand":"-","sequence":"ATGAAATACGAATGGGCACGCACGCGCCGCTTGTCGGCGGCGCTCGCGGTCGCGGCGTTCGTCGCGGCCGGCTGCGGCAAGCACGAAAGCGAGCACGACGCCGCCGCGCCGCGCGAGGCGAGCGTCGTCACGGTGAAGAAGACATCGGTGCCGCTGTCGGTCGAATTGCCGGGCCGGCTCGACGCGTACCGGCAGGCCGAGGTGCGCGCGCGGGTCGCGGGCATCGTGACCGCGCGCACCTACGAGGAAGGGCAGGAAGTCAAGCGCGGCGCGGTGCTGTTCAGGATCGATCCCGCGCCGTTCAAGGCGGCGCGCGACGCGGCCGCGGGCGCGCTCGAGAAGGCGCGGGCCGCGCACCTCGCGGCGCTCGACAAGCGCCGCCGCTATGACGAGCTCGTGCGCGACCGCGCGGTCAGCGAGCGCGACCACACCGAGGCGCTCGCCGACGAACGGCAGGCGAAGGCGGCCGTCGCGTCGGCGCGCGCGGAGCTCGCGCGCGCGCAACTGCAGCTCGATTACGCGACCGTCACCGCGCCGATCGACGGCCGCGCGCGCCGCGCGCTCGTGACCGAAGGCGCGCTCGTCGGCCAGGATCAGGCGACGCCGCTCACGACCGTCGAGCAGCTCGATCCGATCTACGTGAACTTCTCGCAGCCCGCGGCCGACGTCGAATCGCTGCGGCGCGCGGTGAAGAGCGGACGCGCGGCGGGCATCGCGCAGCAGGACGTCGAGGTGACGCTCGTGCGCCCGGACGGCAGCACGTACGCGCGCAAGGGCAAGCTGCTGTTCGCGGATCTTGCCGTCGACCCGTCCACCGACACGGTGGCGATGCGTGCGCTCTTTCCGAACCCGGAGCGCGAACTGCTGCCCGGCGCGTACGTGCGGATCGCGCTCGATCGCGCGGTCGCGCGCGACGCGATCCTCGTGCCGCGCGACGCGCTGCTGCGCACGGCCGACAGCGCGACCGTCAAGGTCGTCGGCCAGAACGGCAAGATACGCGACGTGACGGTCGAGGCCGCGCAGATGAAAGGCCGCGACTGGATCGTCACGCGCGGGCTCGCGGGCGGCGAGCGCGTCGTCGTCGTCGACGCCGCGCAATTCGAAGCAGGCACGACGGTGAAGGCGCTCGAGCGCGGCGCCGCCGCGCAGCCGGCCTCCGGCGCCGCCGCGGCTTCCGCGCCCGGCCGGCGCTCAACCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41211","NCBI_taxonomy_name":"Burkholderia pseudomallei K96243","NCBI_taxonomy_id":"272560"}}}},"ARO_accession":"3002982","ARO_id":"39416","ARO_name":"amrA","CARD_short_name":"amrA","ARO_description":"amrA is the efflux pump subunit of the AmrAB-OprM multidrug efflux complex. amrA corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1543":{"model_id":"1543","model_name":"CMY-22","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1035":{"protein_sequence":{"accession":"ABB72431.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAYWRILEKLQ"},"dna_sequence":{"accession":"DQ256079.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGTACTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002033","ARO_id":"38433","ARO_name":"CMY-22","CARD_short_name":"CMY-22","ARO_description":"CMY-22 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1544":{"model_id":"1544","model_name":"dfrE","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"4696":{"protein_sequence":{"accession":"EOD99669.1","sequence":"MLAAIWAQDEQGVIGKEGKLPWHLPNDLKFFKEKTIHNTLVLGRATFEGMGCRPLPNRTTIVLTSNPDYRAEGVLVMHSVEEILAYADNYEGVTVIGGGSVVFKELIPACDVLYRTMIHETFEGDTFFPEIDWFVWEKVATVPGVVDEKNLYAHDYETYHRNDK"},"dna_sequence":{"accession":"AIIS01000002.1","fmin":"233812","fmax":"234307","strand":"-","sequence":"ATGTTAGCAGCTATTTGGGCCCAAGATGAACAAGGAGTGATTGGTAAAGAAGGCAAATTGCCTTGGCATTTACCCAATGACTTGAAATTTTTCAAGGAAAAAACAATTCATAATACATTGGTCTTAGGACGTGCAACTTTCGAAGGCATGGGATGTCGTCCGCTACCAAATCGAACAACGATTGTCCTAACCAGTAATCCGGATTACCGAGCTGAAGGCGTTTTGGTTATGCATTCCGTAGAGGAAATTCTTGCGTATGCTGACAACTATGAAGGTGTGACCGTTATTGGTGGAGGTTCTGTCGTTTTTAAAGAACTGATTCCCGCATGCGATGTCTTATATCGGACGATGATTCATGAAACGTTTGAAGGCGACACTTTCTTTCCAGAAATCGACTGGTTTGTTTGGGAAAAAGTTGCCACTGTTCCCGGCGTCGTGGACGAGAAAAATCTCTATGCACATGACTATGAAACGTATCATCGAAACGATAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41527","NCBI_taxonomy_name":"Enterococcus faecalis EnGen0074","NCBI_taxonomy_id":"1151194"}}}},"ARO_accession":"3002875","ARO_id":"39309","ARO_name":"dfrE","CARD_short_name":"dfrE","ARO_description":"dfrE is a chromosome-encoded dihydrofolate reductase found in Enterococcus faecalis.","ARO_category":{"37617":{"category_aro_accession":"3001218","category_aro_cvterm_id":"37617","category_aro_name":"trimethoprim resistant dihydrofolate reductase dfr","category_aro_description":"Alternative dihydropteroate synthase dfr present on plasmids produces alternate proteins that are less sensitive to trimethoprim from inhibiting its role in folate synthesis, thus conferring trimethoprim resistance.","category_aro_class_name":"AMR Gene Family"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1546":{"model_id":"1546","model_name":"Erm(43)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"3291":{"protein_sequence":{"accession":"CCF55073.1","sequence":"MNNKNPKDTQNFITSKKCINEILKNIIITADDNIVEIGTGKGHFTKALSKVVKSVIGVEIDKSLYYNLKKDSKLQDNIQLINQDILNFQFPDNKDYKIFGSIPYNISTEIIKKILYESKAEYNYLIVELGFAKRIQDKNKALSLLLLPKMDVEILKVIPNKYFHPKPKVESALILLKKHKPLISAKDEKNYQFFVYKWVNKEYKKLFTKNQFKKALKNANVQNLNKISKQQFISIFYSYKLFN"},"dna_sequence":{"accession":"HE650138.1","fmin":"2186","fmax":"2918","strand":"+","sequence":"ATGAATAACAAAAATCCCAAAGATACGCAGAACTTTATAACCTCTAAGAAATGTATAAATGAAATATTAAAAAATATTATTATTACAGCAGATGATAACATTGTTGAAATTGGAACTGGGAAAGGTCATTTTACGAAAGCTTTATCAAAAGTAGTTAAGTCTGTAATTGGCGTAGAAATCGATAAGTCTTTATATTATAACTTGAAAAAGGATAGTAAACTACAAGATAATATACAACTTATTAATCAAGATATATTAAATTTTCAATTCCCTGATAATAAAGATTATAAAATTTTTGGTAGTATTCCTTATAATATTAGTACTGAAATTATTAAAAAAATACTGTATGAGAGTAAAGCAGAATACAATTATTTAATTGTAGAATTAGGATTTGCTAAACGGATTCAAGATAAAAATAAAGCGTTAAGCCTACTATTATTGCCTAAAATGGATGTTGAAATCTTGAAAGTAATTCCTAACAAATATTTTCATCCCAAACCTAAAGTAGAATCGGCATTAATATTATTAAAAAAACATAAACCTTTAATTTCGGCAAAAGATGAAAAAAATTATCAATTCTTTGTATATAAGTGGGTAAACAAAGAATATAAGAAATTGTTTACAAAAAACCAGTTTAAGAAAGCATTAAAAAATGCAAATGTACAAAACTTAAATAAAATATCGAAACAACAATTTATCTCTATTTTTTATAGTTATAAATTATTTAATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39555","NCBI_taxonomy_name":"Mammaliicoccus lentus","NCBI_taxonomy_id":"42858"}}}},"ARO_accession":"3003205","ARO_id":"39789","ARO_name":"Erm(43)","CARD_short_name":"Erm(43)","ARO_description":"Erm(43) is a macrolide, lincosamide, and streptogramin B resistance gene found in Mammaliicoccus lentus chromosome isolated from human, dog and chicken.","ARO_category":{"36699":{"category_aro_accession":"3000560","category_aro_cvterm_id":"36699","category_aro_name":"Erm 23S ribosomal RNA methyltransferase","category_aro_description":"Erm proteins are part of the RNA methyltransferase family and methylate A2058 (E. coli nomenclature) of the 23S ribosomal RNA conferring degrees of resistance to Macrolides, Lincosamides and Streptogramin b. This is called the MLSb phenotype.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"36722":{"category_aro_accession":"3000583","category_aro_cvterm_id":"36722","category_aro_name":"pristinamycin IA","category_aro_description":"Pristinamycin IA is a type B streptogramin antibiotic produced by Streptomyces pristinaespiralis. It binds to the P site of the 50S subunit of the bacterial ribosome, preventing the extension of protein chains.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35967":{"category_aro_accession":"0000050","category_aro_cvterm_id":"35967","category_aro_name":"streptogramin B antibiotic","category_aro_description":"Streptogramin B antibiotics are are cyclic hepta- or hexa-depsipeptides.  Type B streptogramins block the peptide exit tunnel of the 50S bacterial ribosome. The general composition of group B streptogramins is 3-hydroxypicolinic acid-L-Thr-D-aminobutyric acid (or D-Ala)-L-Pro-L-Phe (or 4-N-,N-(dimethylamino)-L-Phe)-X-L-phenylglycine. Used alone, streptogramin B antibiotics are bacteriostatic, but is bactericidal when used with streptogramin A antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1548":{"model_id":"1548","model_name":"APH(3')-Vb","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"407":{"protein_sequence":{"accession":"AAC32025.1","sequence":"MESTLRRTYPHHTWHLVNEGDSGAFVYRLTGHGPELYAKIAPRTPENSAFHLDGEADRLDWLARHGISVPRVVERGADDTTAWLVTEAVPGAAASEEWPEDERAAVVDAIAEMARTLHELPVSECPFDRRLDVTGEARHNVREGLVDLDDLQEEPAGWTGDQLLAELDLTRPEKEDLVVCHGDLCPNNVLLDPETHRITGLIDVGRLRLATCHADLALAARELAIDEDPWFGPAYAERFLERYGAHHVDQEKMAFYQLLDEFF"},"dna_sequence":{"accession":"M22126.1","fmin":"372","fmax":"1164","strand":"+","sequence":"ATGGAAAGCACGTTGCGCCGGACATACCCGCACCACACTTGGCACCTCGTGAACGAAGGAGACTCGGGCGCCTTCGTCTACCGCCTCACCGGACACGGGCCCGAGCTCTACGCGAAGATCGCCCCCCGCACCCCCGAGAACTCCGCCTTCCACCTCGACGGCGAGGCCGACCGCCTCGACTGGCTCGCCCGCCATGGCATCTCGGTCCCCCGTGTCGTCGAGCGCGGTGCCGACGACACCACCGCCTGGCTCGTCACCGAGGCCGTGCCCGGCGCCGCGGCCTCCGAGGAGTGGCCCGAGGACGAGCGGGCGGCCGTTGTCGACGCGATCGCCGAAATGGCCCGCACCCTCCATGAACTCCCCGTGTCCGAGTGCCCCTTCGACCGCCGCCTCGACGTCACCGGCGAGGCCCGGCACAACGTCCGCGAGGGCCTGGTCGACCTCGACGACCTCCAGGAGGAGCCGGCCGGCTGGACCGGCGACCAACTCCTGGCCGAACTCGACCTGACGCGGCCCGAGAAGGAGGACTTGGTCGTCTGCCATGGCGACCTGTGCCCCAACAACGTGCTGCTCGACCCCGAGACCCACCGGATCACCGGGCTGATCGACGTCGGCCGCCTCCGGCTCGCCACCTGCCACGCCGACCTCGCCCTCGCCGCCCGCGAACTGGCGATCGACGAGGACCCGTGGTTCGGCCCCGCATACGCCGAACGGTTCCTCGAACGGTACGGGGCCCACCACGTCGACCAGGAGAAGATGGCCTTCTACCAGCTGCTCGACGAGTTCTTCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39530","NCBI_taxonomy_name":"Streptomyces ribosidificus","NCBI_taxonomy_id":"80859"}}}},"ARO_accession":"3002650","ARO_id":"39050","ARO_name":"APH(3')-Vb","CARD_short_name":"APH(3')-Vb","ARO_description":"APH(3')-Vb is a chromosomal-encoded aminoglycoside phosphotransferase in Streptomyces ribosidificus.","ARO_category":{"36265":{"category_aro_accession":"3000126","category_aro_cvterm_id":"36265","category_aro_name":"APH(3')","category_aro_description":"A category of aminoglycoside O-phosphotransferase enzymes with modification regiospecificity based at the 3'-hydroxyl group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics, specifically kanamycin and neomycin, by the ATP-dependent phosphorylation of the 3'-hydroxyl group of the compound.","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35940":{"category_aro_accession":"0000021","category_aro_cvterm_id":"35940","category_aro_name":"ribostamycin","category_aro_description":"Ribostamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Ribostamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"37001":{"category_aro_accession":"3000657","category_aro_cvterm_id":"37001","category_aro_name":"paromomycin","category_aro_description":"An aminoglycoside antibiotic used for the treatment of parasitic infections. It is similar to neomycin sharing a similar spectrum of activity, but its hydroxyl group at the 6'-position instead of an amino group makes it resistant to AAC(6') modifying enzymes.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1549":{"model_id":"1549","model_name":"ErmB","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"8354":{"protein_sequence":{"accession":"AAF86219.1","sequence":"MNKNIKYSQNFLTSEKVLNQIIKQLNLKETDTVYEIGTGKGHLTTKLAKISKQVTSIELDSHLFNLSSEKLKLNTRVTLIHQDILQFQFPNKQRYKIVGSIPYNLSTQIIKKVVFESRASDIYLIVEEGFYKRTLDIHRTLGLLLHTQVSIQQLLKLPAECFHPKPKVNSVLIKLTRHTTDVPDKYWKLYTYFVSKWVNREYRQLFTKNQFHQAMKHAKVNNLSTITYEQVLSIFNSYLLFNGRKLIL"},"dna_sequence":{"accession":"AF242872.1","fmin":"2131","fmax":"2878","strand":"+","sequence":"ATGAACAAAAATATAAAATATTCTCAAAACTTTTTAACGAGTGAAAAAGTACTCAACCAAATAATAAAACAATTGAATTTAAAAGAAACCGATACCGTTTACGAAATTGGAACAGGTAAAGGGCATTTAACGACGAAACTGGCTAAAATAAGTAAACAGGTAACGTCTATTGAATTAGACAGTCATCTATTCAACTTATCGTCAGAAAAATTAAAACTGAATACTCGTGTCACTTTAATTCACCAAGATATTCTACAGTTTCAATTCCCTAACAAACAGAGGTATAAAATTGTTGGGAGTATTCCTTACAATTTAAGCACACAAATTATTAAAAAAGTGGTTTTTGAAAGCCGTGCGTCTGACATCTATCTGATTGTTGAAGAAGGATTCTACAAGCGTACCTTGGATATTCACCGAACACTAGGGTTGCTCTTGCACACTCAAGTCTCGATTCAGCAATTGCTTAAGCTGCCAGCGGAATGCTTTCATCCTAAACCAAAAGTAAACAGTGTCTTAATAAAACTTACCCGCCATACCACAGATGTTCCAGATAAATATTGGAAGCTATATACGTACTTTGTTTCAAAATGGGTCAATCGAGAATATCGTCAACTGTTTACTAAAAATCAGTTTCATCAAGCAATGAAACACGCCAAAGTAAACAATTTAAGTACCATTACTTATGAGCAAGTATTGTCTATTTTTAATAGTTATCTATTATTTAACGGGAGGAAATTAATTCTATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36779","NCBI_taxonomy_name":"Enterococcus faecium","NCBI_taxonomy_id":"1352"}}}},"ARO_accession":"3000375","ARO_id":"36514","ARO_name":"ErmB","CARD_short_name":"ErmB","ARO_description":"ErmB confers the MLSb phenotype. Similar to ErmC, expression of ErmB is inducible by erythromycin. The leader peptide causes attenuation of the mRNA and stabilizes the structure preventing further translation. When erythromycin is present, it binds the leader peptide causing a change in conformation allowing for the expression of ErmB.","ARO_category":{"36699":{"category_aro_accession":"3000560","category_aro_cvterm_id":"36699","category_aro_name":"Erm 23S ribosomal RNA methyltransferase","category_aro_description":"Erm proteins are part of the RNA methyltransferase family and methylate A2058 (E. coli nomenclature) of the 23S ribosomal RNA conferring degrees of resistance to Macrolides, Lincosamides and Streptogramin b. This is called the MLSb phenotype.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35946":{"category_aro_accession":"0000027","category_aro_cvterm_id":"35946","category_aro_name":"roxithromycin","category_aro_description":"Roxithromycin is a semi-synthetic, 14-carbon ring macrolide antibiotic derived from erythromycin. It is used to treat respiratory tract, urinary and soft tissue infections. Roxithromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35974":{"category_aro_accession":"0000057","category_aro_cvterm_id":"35974","category_aro_name":"telithromycin","category_aro_description":"Telithromycin is a semi-synthetic derivative of erythromycin. It is a 14-membered macrolide and is the first ketolide antibiotic to be used in clinics. Telithromycin binds the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"35982":{"category_aro_accession":"0000065","category_aro_cvterm_id":"35982","category_aro_name":"clarithromycin","category_aro_description":"Clarithromycin is a methyl derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome and is used to treat pharyngitis, tonsillitis, acute maxillary sinusitis, acute bacterial exacerbation of chronic bronchitis, pneumonia (especially atypical pneumonias associated with Chlamydia pneumoniae or TWAR), and skin structure infections.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"36284":{"category_aro_accession":"3000145","category_aro_cvterm_id":"36284","category_aro_name":"tylosin","category_aro_description":"Tylosin is a 16-membered macrolide, naturally produced by Streptomyces fradiae. It interacts with the bacterial ribosome 50S subunit to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"36295":{"category_aro_accession":"3000156","category_aro_cvterm_id":"36295","category_aro_name":"spiramycin","category_aro_description":"Spiramycin is a 16-membered macrolide and is natural product produced by Streptomyces ambofaciens. It binds to the 50S subunit of bacterial ribosomes and inhibits peptidyl transfer activity to disrupt protein synthesis.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"36315":{"category_aro_accession":"3000176","category_aro_cvterm_id":"36315","category_aro_name":"dirithromycin","category_aro_description":"Dirithromycin is an oxazine derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome to inhibit bacterial protein synthesis.","category_aro_class_name":"Antibiotic"},"36722":{"category_aro_accession":"3000583","category_aro_cvterm_id":"36722","category_aro_name":"pristinamycin IA","category_aro_description":"Pristinamycin IA is a type B streptogramin antibiotic produced by Streptomyces pristinaespiralis. It binds to the P site of the 50S subunit of the bacterial ribosome, preventing the extension of protein chains.","category_aro_class_name":"Antibiotic"},"36723":{"category_aro_accession":"3000584","category_aro_cvterm_id":"36723","category_aro_name":"quinupristin","category_aro_description":"Quinupristin is a type B streptogramin and a semisynthetic derivative of pristinamycin 1A. It is a component of the drug Synercid and interacts with the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"virginiamycin M1","category_aro_description":"Virginiamycin M1 is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37016":{"category_aro_accession":"3000672","category_aro_cvterm_id":"37016","category_aro_name":"madumycin II","category_aro_description":"Madumycin II is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37017":{"category_aro_accession":"3000673","category_aro_cvterm_id":"37017","category_aro_name":"griseoviridin","category_aro_description":"Griseoviridin is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"37019":{"category_aro_accession":"3000675","category_aro_cvterm_id":"37019","category_aro_name":"pristinamycin IB","category_aro_description":"Pristinamycin IB is a class B streptogramin similar to pristinamycin IA, the former containing a N-methyl-4-(methylamino)phenylalanine instead of a N-methyl-4-(dimethylamino)phenylalanine in its class A streptogramin counterpart (one less methyl group).","category_aro_class_name":"Antibiotic"},"37021":{"category_aro_accession":"3000677","category_aro_cvterm_id":"37021","category_aro_name":"virginiamycin S2","category_aro_description":"Virginiamycin S2 is a streptogramin B antibiotic.","category_aro_class_name":"Antibiotic"},"37022":{"category_aro_accession":"3000678","category_aro_cvterm_id":"37022","category_aro_name":"pristinamycin IC","category_aro_description":"Pristinamycin IC is a class B streptogramin derived from virginiamycin S1.","category_aro_class_name":"Antibiotic"},"37023":{"category_aro_accession":"3000679","category_aro_cvterm_id":"37023","category_aro_name":"vernamycin C","category_aro_description":"Vernamycin C is a streptogramin B antibiotic.","category_aro_class_name":"Antibiotic"},"37024":{"category_aro_accession":"3000680","category_aro_cvterm_id":"37024","category_aro_name":"patricin A","category_aro_description":"Patricin A is a streptogramin B antibiotic.","category_aro_class_name":"Antibiotic"},"37025":{"category_aro_accession":"3000681","category_aro_cvterm_id":"37025","category_aro_name":"patricin B","category_aro_description":"Patricin B is a streptogramin B antibiotic.","category_aro_class_name":"Antibiotic"},"37026":{"category_aro_accession":"3000682","category_aro_cvterm_id":"37026","category_aro_name":"ostreogrycin B3","category_aro_description":"Ostreogrycin B3 is a derivative of pristinamycin IA, with an additional 3-hydroxy group on its 4-oxopipecolic acid.","category_aro_class_name":"Antibiotic"},"37247":{"category_aro_accession":"3000867","category_aro_cvterm_id":"37247","category_aro_name":"oleandomycin","category_aro_description":"Oleandomycin is a 14-membered macrolide produced by Streptomyces antibioticus. It is ssimilar to erythromycin, and contains a desosamine amino sugar and an oleandrose sugar. It targets the 50S ribosomal subunit to prevent protein synthesis.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35952":{"category_aro_accession":"0000034","category_aro_cvterm_id":"35952","category_aro_name":"streptogramin A antibiotic","category_aro_description":"Streptogramin A antibiotics are cyclic polyketide peptide hybrids that bind to the ribosomal peptidyl transfer centre. Structural variation arises from substituting a proline for its desaturated derivative and by its substitution for Ala or Cys. Used alone, streptogramin A antibiotics are bacteriostatic, but is bactericidal when used with streptogramin B antibiotics.","category_aro_class_name":"Drug Class"},"35967":{"category_aro_accession":"0000050","category_aro_cvterm_id":"35967","category_aro_name":"streptogramin B antibiotic","category_aro_description":"Streptogramin B antibiotics are are cyclic hepta- or hexa-depsipeptides.  Type B streptogramins block the peptide exit tunnel of the 50S bacterial ribosome. The general composition of group B streptogramins is 3-hydroxypicolinic acid-L-Thr-D-aminobutyric acid (or D-Ala)-L-Pro-L-Phe (or 4-N-,N-(dimethylamino)-L-Phe)-X-L-phenylglycine. Used alone, streptogramin B antibiotics are bacteriostatic, but is bactericidal when used with streptogramin A antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1550":{"model_id":"1550","model_name":"smeR","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"420"}},"model_sequences":{"sequence":{"4694":{"protein_sequence":{"accession":"AAD51348.1","sequence":"MSTSPATSTKILIVEDEPRLASVLRDYLAAAGMASEWVDDGGQVIDAFARYQPDLVLLDLMLPQRDGVDLCRELRASSDVPVIMVTARVEEIDRLLGLEIGADDYICKPFSPREVVARVMAVLRRYRPDPGARANGGLHIDEPAARATWNGKGLDLTPVEYRLLRTLLATPGRIWARDELLDRLYLDHRVVVDRTVDSHVRNLRRKLADAGMEGEPIRSVYGMGYSYEP"},"dna_sequence":{"accession":"AF173226.1","fmin":"351","fmax":"1041","strand":"-","sequence":"ATGAGCACGTCGCCCGCCACGTCCACGAAGATCCTGATCGTCGAGGACGAGCCACGCCTGGCCTCGGTACTGCGCGACTACCTGGCCGCCGCCGGCATGGCCAGCGAGTGGGTGGACGACGGTGGCCAGGTGATCGACGCATTCGCGCGCTACCAGCCCGACCTGGTGCTGCTGGACCTGATGCTGCCGCAGCGCGACGGCGTGGACCTGTGCCGCGAACTGCGTGCCAGCAGCGATGTACCGGTCATCATGGTCACCGCACGGGTGGAAGAGATCGACCGCCTGCTGGGCCTGGAGATCGGCGCCGACGACTACATCTGCAAGCCGTTCAGTCCGCGCGAAGTGGTCGCGCGGGTAATGGCGGTGCTGCGCCGCTACCGCCCGGACCCGGGTGCGCGCGCCAACGGTGGCCTGCACATCGACGAGCCGGCCGCACGCGCCACCTGGAACGGCAAGGGCCTGGACCTGACGCCGGTGGAGTACCGCCTGCTGCGCACGCTGCTGGCCACCCCAGGCCGGATCTGGGCGCGCGATGAACTGCTCGACCGGCTGTACCTGGACCATCGCGTGGTGGTCGACCGCACCGTCGACAGCCATGTGCGCAACCTGCGCCGCAAGCTGGCCGACGCCGGCATGGAAGGCGAGCCGATCCGTTCGGTGTACGGCATGGGCTACAGCTACGAGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37076","NCBI_taxonomy_name":"Stenotrophomonas maltophilia","NCBI_taxonomy_id":"40324"}}}},"ARO_accession":"3003066","ARO_id":"39500","ARO_name":"smeR","CARD_short_name":"smeR","ARO_description":"smeR is the responder component of a two component signal transduction system that includes smeS.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1551":{"model_id":"1551","model_name":"OXA-78","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1616":{"protein_sequence":{"accession":"AAW81358.1","sequence":"MNIKALLLITSAIFISACSPYIVSANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTAVFKWDGQKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGTPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"AY862132.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGTCTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACTACAGCAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTAGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAACACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001645","ARO_id":"38045","ARO_name":"OXA-78","CARD_short_name":"OXA-78","ARO_description":"OXA-78 is a beta-lactamase found in A. baumannii.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1554":{"model_id":"1554","model_name":"norA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"268":{"protein_sequence":{"accession":"AAS68233.1","sequence":"MKKQLFILYFNIFLIFLGIGLVIPVLPVYLKDLGLKGSDLGMLVAAFALSQMIISPFGGTLADKLGKKLIICIGLVFFAVSEFMFAAGQSFTILIISRVLGGFSAGMVMPGVTGMIADISPGADKAKNFGYMSAIINSGFILGPGFGGFLAEISHRLPFYVAGTLGVVAFIMSVLLIHNPQKATTDGFHQYQPELFTKINWKVFITPVILTLVLAFGLSAFETLFSLYTADKVNYTPKDISIAIIGGGVFGALFQVFFFDKFMKYMSELNFIAWSLLYSAIVLVMLVLANGYWTIMIISFVVFIGFDMIRPALTNYFSNIAGKRQGFAGGLNSTFTSMGNFIGPLVAGALFDVNLEFPLYMAIAVSLSGIIIIFIEKGLKSRRKEAN"},"dna_sequence":{"accession":"AY566250.1","fmin":"391","fmax":"1555","strand":"+","sequence":"ATGAAAAAACAATTATTCATTCTTTATTTTAATATATTTCTTATATTTTTAGGGATTGGATTAGTTATTCCTGTACTTCCTGTATATTTGAAGGATTTAGGATTAAAAGGTAGTGACTTAGGAATGCTAGTTGCTGCTTTTGCATTATCACAAATGATTATTTCACCATTTGGTGGGACACTAGCTGATAAATTGGGTAAAAAATTAATTATATGTATCGGTTTAGTATTCTTTGCTGTCTCTGAATTTATGTTCGCAGCCGGTCAAAGTTTTACCATTTTAATCATTTCACGTGTTTTAGGTGGCTTTAGTGCAGGCATGGTCATGCCTGGTGTAACAGGTATGATTGCAGATATTTCTCCAGGAGCTGATAAAGCTAAAAACTTTGGTTACATGTCGGCAATTATTAATTCAGGTTTTATATTAGGACCTGGATTTGGAGGCTTTTTAGCTGAAATTTCACATAGATTACCTTTCTATGTTGCTGGAACATTAGGTGTTGTTGCATTCATTATGTCAGTTTTATTAATTCATAATCCTCAAAAAGCAACTACAGATGGATTCCACCAATATCAACCTGAATTATTCACTAAAATTAATTGGAAAGTATTTATTACTCCAGTCATATTAACACTTGTATTAGCATTTGGTTTATCTGCTTTTGAAACATTATTTTCTTTATATACAGCTGACAAAGTAAATTATACTCCTAAAGATATTTCGATAGCTATTATCGGTGGAGGCGTGTTTGGCGCATTATTCCAAGTATTCTTCTTTGATAAATTTATGAAATATATGAGTGAACTTAATTTTATTGCATGGTCATTACTATATTCAGCCATTGTTCTCGTTATGTTAGTGCTTGCAAACGGTTATTGGACGATTATGATTATTAGCTTTGTTGTTTTTATAGGTTTTGATATGATTAGACCAGCTTTAACCAATTACTTCTCGAATATAGCAGGCAAACGGCAAGGTTTTGCAGGTGGATTGAATTCAACTTTTACCAGTATGGGTAACTTTATAGGTCCTCTTGTAGCTGGTGCATTATTCGATGTTAATTTAGAGTTTCCTTTATATATGGCTATTGCGGTTTCATTAAGTGGAATTATCATTATTTTTATTGAAAAAGGACTTAAGTCACGCCGTAAAGAAGCAAATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36868","NCBI_taxonomy_name":"Staphylococcus epidermidis","NCBI_taxonomy_id":"1282"}}}},"ARO_accession":"3000391","ARO_id":"36530","ARO_name":"norA","CARD_short_name":"norA","ARO_description":"NorA is a multidrug efflux pump in Staphylococcus aureus that confers resistance to fluoroquinolones and other structurally unrelated antibiotics like acriflavine. It shares 30% similarity with NorA, and is a structural homolog of Bmr of Bacillus subtilis. It is regulated by arlRS and mgrA, the latter also known as NorR.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35963":{"category_aro_accession":"0000045","category_aro_cvterm_id":"35963","category_aro_name":"acriflavine","category_aro_description":"Acriflavine is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"43746":{"category_aro_accession":"3005386","category_aro_cvterm_id":"43746","category_aro_name":"disinfecting agents and antiseptics","category_aro_description":"Disinfectants that can also interact with antimicrobial resistance mechanisms, e.g. molecule efflux, and thus are the targets of disinfectant resistance.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1555":{"model_id":"1555","model_name":"SHV-140","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"6223":{"protein_sequence":{"accession":"AEK80394.1","sequence":"KRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYSQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"JN051143.1","fmin":"0","fmax":"861","strand":"+","sequence":"AAGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCCCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATAGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGGATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001182","ARO_id":"37562","ARO_name":"SHV-140","CARD_short_name":"SHV-140","ARO_description":"SHV-140 is a broad-spectrum beta-lactamase.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1556":{"model_id":"1556","model_name":"VIM-13","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1005":{"protein_sequence":{"accession":"ABC94518.1","sequence":"MLKVISSLLFYMTASLMAVASPLAHSGESRGEYPTVSEIPVGEVRLYQIDDGVWSHIATHTFDGVVYPSNGLIVRDGDELLLIDTAWGTKNTVALLAEIEKQIGLPVTRSVSTHFHDDRVGGVDALRAAGVATYASPSTRRLAEAEGNEVPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSANVLYGGCAVLELSRTSAGNVADADLAEWPGSVERIQQHYPEAEVVIPGHGLPGGLDLLQHTANVVKAHTNRSVAE"},"dna_sequence":{"accession":"DQ365886.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGTTAAAAGTTATTAGTAGTTTATTGTTCTACATGACCGCCTCTCTAATGGCTGTAGCTAGTCCGTTAGCCCATTCCGGGGAGTCGAGAGGTGAGTATCCGACAGTCAGCGAAATTCCGGTCGGAGAAGTTCGGCTGTACCAGATTGACGATGGTGTTTGGTCGCATATCGCAACGCATACGTTTGATGGCGTGGTGTACCCGTCCAATGGTCTCATTGTCCGTGATGGCGATGAGTTGCTTTTGATTGATACAGCTTGGGGTACGAAAAACACAGTGGCCCTTCTCGCGGAGATTGAGAAGCAAATTGGACTTCCCGTAACGCGTTCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGAGTTGATGCCCTTAGGGCGGCTGGAGTGGCGACGTACGCATCGCCCTCGACACGCCGTCTAGCCGAGGCAGAGGGGAACGAGGTTCCCACACACTCTCTAGAAGGGCTCTCATCGAGTGGGGACGCAGTGCGTTTCGGTCCAGTAGAGCTCTTCTATCCTGGTGCTGCGCATTCGACCGACAATCTGGTTGTATACGTCCCGTCAGCGAACGTGCTATACGGTGGTTGTGCCGTTCTGGAATTGTCACGCACATCCGCGGGAAACGTGGCCGATGCCGACCTGGCTGAATGGCCCGGTTCCGTTGAGCGGATTCAACAACATTACCCAGAAGCAGAGGTGGTCATTCCCGGGCACGGTCTACCGGGCGGTCTAGACTTGCTCCAGCACACAGCGAACGTTGTCAAAGCACACACAAATCGCTCAGTCGCCGAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002283","ARO_id":"38683","ARO_name":"VIM-13","CARD_short_name":"VIM-13","ARO_description":"VIM-13 is a beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1557":{"model_id":"1557","model_name":"SHV-187","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"917":{"protein_sequence":{"accession":"CEA29750.1","sequence":"MVKRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"LN515533.1","fmin":"0","fmax":"867","strand":"+","sequence":"GTGGTTAAGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGGATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3003154","ARO_id":"39731","ARO_name":"SHV-187","CARD_short_name":"SHV-187","ARO_description":"SHV-187 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1559":{"model_id":"1559","model_name":"mtrA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"8649":{"protein_sequence":{"accession":"AAD44693.1","sequence":"MDILDKLVDLAQLTGSADVQCLLGGQWSVRHETLQCEGLVHIVTAGSGYLCIDGETSPRPVGTGDIVFFPRGLGHVLSHDGKYGESLQPDIRQNGTFMVKQCGNGLDMSLFCARFRYDTHADLMNGLPETVFLNIAHPSLQYVVSMLQLESEKPLTGTVSVVNALPSVLLVLILRAYLEQDKDVELSGVLKGWQDKRLGHLIQKVIDKPEDEWNIDKMVAAANMSRAQLMRRFKSQVGLSPHAFVNHIRLQKGALLLKKTPDSVLEVALSVGFQSETHFGKAFKRQYHVSPGQYRKEGGQK"},"dna_sequence":{"accession":"AF128627.1","fmin":"0","fmax":"906","strand":"+","sequence":"ATGGACATTCTGGACAAACTGGTCGATCTCGCCCAATTGACGGGCAGTGCGGATGTGCAGTGCCTTTTGGGCGGACAATGGTCGGTACGGCATGAAACCTTGCAATGCGAAGGGCTGGTACACATTGTTACGGCGGGCAGCGGTTATCTCTGCATCGACGGCGAAACTTCCCCGCGTCCGGTCGGCACGGGCGATATTGTATTTTTCCCGCGCGGCTTGGGTCATGTGTTGAGCCACGACGGAAAATACGGAGAAAGTTTACAACCGGACATACGACAAAACGGCACATTTATGGTCAAACAGTGCGGCAACGGGCTGGATATGAGCCTGTTTTGCGCCCGTTTCCGCTACGACACCCACGCCGATTTGATGAACGGGCTGCCGGAAACCGTTTTTCTGAACATTGCCCATCCAAGTTTGCAGTATGTGGTTTCAATGCTGCAACTGGAAAGCGAAAAACCTTTGACGGGGACGGTTTCCGTGGTCAACGCATTACCGTCCGTCCTGCTGGTGCTTATCCTGCGCGCCTATCTCGAACAGGATAAGGATGTCGAACTCTCGGGCGTATTGAAAGGTTGGCAGGACAAACGTTTGGGACATTTGATCCAAAAGGTGATAGACAAACCGGAAGACGAATGGAATATTGACAAAATGGTTGCCGCCGCCAATATGTCGCGCGCGCAACTGATGCGCCGCTTCAAAAGCCAAGTCGGACTCAGCCCGCACGCCTTTGTGAACCATATCCGCCTGCAAAAAGGCGCATTGCTGCTGAAGAAAACCCCGGATTCGGTTTTGGAGGTCGCGCTGTCGGTGGGCTTTCAGTCGGAAACGCATTTCGGCAAGGCGTTCAAACGGCAATATCACGTTTCGCCGGGGCAATACCGGAAAGAAGGCGGGCAAAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36806","NCBI_taxonomy_name":"Neisseria gonorrhoeae","NCBI_taxonomy_id":"485"}}}},"ARO_accession":"3000816","ARO_id":"37196","ARO_name":"mtrA","CARD_short_name":"mtrA","ARO_description":"MtrA is a transcriptional activator of the MtrCDE multidrug efflux pump of Neisseria gonorrhoeae.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1560":{"model_id":"1560","model_name":"OKP-B-20","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"8261":{"protein_sequence":{"accession":"CAP12360.2","sequence":"MRYVRLCLISLIAALPLAVFASPQPLEQIKISESQLAGRVGYVEMDLASGRTLAAWRASERFPLMSTFKVLLCGAVLARVDAGDEQLDRRIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNTAGNLLLKIVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDVRDTTTPASMATTLRKLLTTPSLSARSQQQLLQWMVDDRVAGPLIRAVLPAGWFIADKTGAGERGSRGIVALLGPDGKAERIVVIYLRDTAATMVERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AM850922.2","fmin":"24","fmax":"885","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGCCTTATCTCCCTGATTGCCGCCCTGCCACTGGCGGTATTCGCCAGCCCTCAGCCGCTTGAGCAGATTAAAATCAGCGAAAGTCAGCTGGCGGGCCGTGTGGGCTATGTTGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCAGTGAGCGCTTTCCGCTGATGAGCACCTTTAAAGTGCTGCTCTGCGGCGCGGTGCTGGCCCGGGTGGATGCCGGCGACGAACAGCTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGCCGACGGGATGACCGTTGGCGAACTCTGCGCCGCCGCCATCACCATGAGCGACAACACCGCCGGCAATCTGCTGTTGAAGATCGTCGGCGGCCCCGCGGGATTGACCGCTTTTCTGCGCCAGATCGGTGACAACGTCACCCGTCTTGACCGCTGGGAAACGGAACTCAATGAGGCGCTTCCCGGCGACGTGCGCGACACCACCACCCCGGCCAGCATGGCCACCACCCTGCGCAAGCTGCTAACCACCCCCTCTCTGAGCGCCCGTTCGCAGCAGCAGCTGCTGCAGTGGATGGTTGACGACCGGGTGGCCGGCCCGTTGATCCGCGCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAAACCGGGGCCGGTGAGCGGGGCTCACGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAAGCGGAGCGTATCGTGGTGATCTATCTGCGTGATACCGCGGCGACCATGGTCGAGCGTAACCAGCAGATCGCCGGGATAGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002453","ARO_id":"38853","ARO_name":"OKP-B-20","CARD_short_name":"OKP-B-20","ARO_description":"OKP-B-20 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"38817":{"category_aro_accession":"3002417","category_aro_cvterm_id":"38817","category_aro_name":"OKP beta-lactamase","category_aro_description":"OKP beta-lactamases are chromosomal class A beta-lactamase that confer resistance to penicillins and early cephalosporins in Klebsiella pneumoniae. OKP beta-lactamases can be subdivided into two groups: OKP-A and OKP-B which diverge by about 4.2%.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1562":{"model_id":"1562","model_name":"aad(6)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6244":{"protein_sequence":{"accession":"AAU10334.1","sequence":"EGSRANINIPKDEFQDYDITYFVSDIEPFISNDDWLNQFGNIIMMQKPEDMELFPPEEKGFSYLMLFDDYNKIDLTLLPLEELDNYLKGDKLIKVLIDKDCRIKRDIVPTDIDYHVRKPSAREYDDCCNEFWNVTPYVIKGLCRKEILFAIDHFNQIVRHELLRMISWKVGIETGFKLSVGKNYKFIERYISEDLWEKLLSTYRMDSYENIWEALFLCHQLFRAVSGEVAERLHYAYPEYDRNITKYTRDMYKKYTGKTGCLDSTYAADIEERREQ"},"dna_sequence":{"accession":"AY712687.1","fmin":"0","fmax":"831","strand":"+","sequence":"GAGGGGTCACGCGCAAATATTAATATACCTAAAGATGAATTTCAGGATTATGATATTACATATTTTGTAAGTGATATAGAACCGTTTATATCTAATGATGACTGGCTTAATCAATTTGGGAATATAATAATGATGCAAAAGCCGGAGGATATGGAATTATTCCCACCTGAAGAAAAGGGATTTTCCTATCTTATGCTATTTGATGATTACAATAAAATTGATCTTACCTTATTGCCCTTGGAAGAGTTAGATAATTACCTAAAGGGCGATAAATTAATAAAGGTTCTAATTGATAAAGATTGTAGAATTAAAAGGGACATAGTTCCGACTGATATAGATTATCATGTAAGAAAGCCAAGCGCAAGGGAGTATGATGATTGCTGCAATGAATTTTGGAATGTAACACCTTATGTTATTAAAGGATTGTGCCGTAAGGAAATTTTATTTGCTATTGATCATTTTAATCAGATTGTTCGCCATGAGCTGCTGAGAATGATATCATGGAAGGTCGGCATCGAAACAGGCTTTAAATTAAGTGTAGGCAAGAACTATAAGTTTATTGAAAGGTATATATCCGAGGATTTGTGGGAGAAACTTTTGTCCACCTACCGGATGGATTCCTATGAAAACATATGGGAAGCATTATTTCTATGCCATCAATTGTTCAGGGCGGTATCCGGTGAGGTGGCGGAAAGGCTTCATTATGCCTATCCGGAGTATGATAGGAATATAACAAAATATACCAGGGACATGTATAAAAAATACACTGGTAAAACCGGCTGCCTGGATAGCACATATGCCGCTGATATAGAAGAGAGGCGGGAACAGTGA","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39527","NCBI_taxonomy_name":"Streptococcus oralis","NCBI_taxonomy_id":"1303"}}}},"ARO_accession":"3002628","ARO_id":"39028","ARO_name":"aad(6)","CARD_short_name":"aad(6)","ARO_description":"ANT(6)-Ia\/aad(6) is a plasmid-encoded aminoglycoside nucleotidyltransferase gene in E. faecalis and Streptococcus oralis.","ARO_category":{"36364":{"category_aro_accession":"3000225","category_aro_cvterm_id":"36364","category_aro_name":"ANT(6)","category_aro_description":"A category of aminoglycoside O-nucleotidyltransferase enzymes with modification regiospecificity based at the 6-hydroxyl group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics, specifically streptomycin, by transfer of an AMP group from an ATP substrate to the 6-hydroxyl group of the compound.","category_aro_class_name":"AMR Gene Family"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1563":{"model_id":"1563","model_name":"CTX-M-63","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"868":{"protein_sequence":{"accession":"BAD90119.1","sequence":"MRHRVKRMMLMTTACISLLLGSAPLYAQANDVQQKLAALEKSSGGRLGVALIDTADNAQTLYRADERFAMCSTSKVMAAAAVLKQSETQKNVLSQKVEIKSSDLINYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAHLGGPDKVTAFARAIGDDTFRLDRTEPTLNTAIPGDPRDTTTPLAMAQTLRHLTLGSALGETQRAQLVTWLKGNTTGAASIQAGLPTSWVVGDKTGSGDYGTTNDIAVIWPEGRAPLILVTYFTQPEQKAENRRDVLAAAAKIVTDGY"},"dna_sequence":{"accession":"AB205197.1","fmin":"3","fmax":"876","strand":"+","sequence":"ATGAGACATCGCGTTAAGCGGATGATGCTAATGACAACGGCCTGTATTTCGCTGTTGCTGGGGAGTGCGCCGCTGTATGCGCAGGCGAACGACGTTCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGGGGGCGGTTGGGAGTGGCGCTGATTGACACCGCCGATAACGCACAGACGCTCTACCGCGCCGACGAGCGCTTTGCCATGTGCAGCACCAGTAAGGTGATGGCAGCCGCGGCGGTGCTCAAGCAAAGTGAAACGCAAAAGAACGTGTTGAGTCAGAAGGTTGAGATTAAATCCTCGGACCTGATTAACTACAATCCCATCGCTGAAAAACACGTCAACGGCACGATGACGCTGGCGGAATTGAGCGCCGCGGCGTTGCAGTACAGCGATAATACGGCCATGAACAAGCTGATTGCCCATCTTGGGGGGCCGGATAAAGTGACGGCGTTTGCCCGTGCGATTGGGGATGACACCTTCCGGCTCGATCGTACTGAGCCGACGCTCAACACCGCGATCCCCGGCGACCCGCGCGATACCACCACGCCATTAGCGATGGCGCAGACGCTTCGCCATCTGACGTTGGGCAGTGCCTTAGGTGAAACTCAGCGTGCGCAACTGGTAACGTGGCTGAAAGGCAACACCACCGGTGCTGCCAGCATTCAGGCTGGGCTACCCACATCGTGGGTTGTCGGGGATAAAACCGGCAGCGGTGATTATGGTACGACGAATGACATCGCCGTCATCTGGCCGGAAGGGCGTGCGCCGCTTATTCTGGTCACTTACTTCACCCAACCGGAGCAGAAGGCAGAAAATCGTCGTGACGTGCTCGCGGCTGCCGCGAAAATCGTCACCGACGGTTATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001924","ARO_id":"38324","ARO_name":"CTX-M-63","CARD_short_name":"CTX-M-63","ARO_description":"CTX-M-63 is a beta-lactamase found in Salmonella enterica.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1564":{"model_id":"1564","model_name":"QnrB16","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"349":{"protein_sequence":{"accession":"ABV66096.1","sequence":"MTPLLYIKTGTNMALALVGEKIDRNRFTGEKIENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNASALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGTQVLGATFSGSDLSGGEFSTFDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDNYQASLLMERLGIAIIG"},"dna_sequence":{"accession":"EU136183.1","fmin":"0","fmax":"681","strand":"+","sequence":"ATGACGCCATTACTGTATATAAAAACAGGTACAAATATGGCTCTGGCACTCGTTGGCGAAAAAATTGACAGAAACCGCTTCACCGGTGAGAAAATTGAAAATAGTACATTTTTTAACTGTGATTTTTCAGGTGCCGACCTGAGCGGCACTGAATTTATCGGCTGTCAGTTCTATGATCGTGAAAGCCAGAAAGGGTGCAATTTTAGTCGTGCGATGCTGAAAGATGCCATTTTTAAAAGCTGTGATTTATCCATGGCGGATTTTCGCAATGCCAGTGCGCTTGGCATTGAAATTCGCCACTGCCGCGCACAAGGCGCAGATTTCCGCGGCGCAAGCTTTATGAATATGATCACCACGCGCACCTGGTTTTGTAGCGCATATATCACGAATACAAATCTAAGCTACGCCAATTTTTCGAAAGTCGTGCTGGAAAAGTGTGAGCTGTGGGAAAACCGTTGGATGGGTACCCAGGTACTGGGCGCGACGTTCAGTGGTTCAGATCTCTCCGGCGGCGAGTTTTCGACTTTCGACTGGCGAGCAGCAAACTTCACACATTGCGATCTGACCAATTCGGAGTTGGGTGACTTAGATATTCGGGGGGTTGATTTACAAGGCGTTAAGTTGGACAACTACCAGGCATCGTTGCTCATGGAACGTCTTGGCATCGCGATTATTGGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002731","ARO_id":"39165","ARO_name":"QnrB16","CARD_short_name":"QnrB16","ARO_description":"QnrB16 is a plasmid-mediated quinolone resistance protein found in Citrobacter freundii.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1565":{"model_id":"1565","model_name":"ACT-18","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1505":{"protein_sequence":{"accession":"AHM76777.1","sequence":"MMKKSLCCALLLGISCSALAAPVSEKQLAEVVANTITPLMKAQSIPGMAVAVIYQGKPHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNAALLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMGYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPEKVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVIEGSDSKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANKSYPNPARVEAAYHILDALQ"},"dna_sequence":{"accession":"KF992028.1","fmin":"761","fmax":"1907","strand":"+","sequence":"ATGATGAAAAAATCTCTTTGCTGCGCCCTGCTGCTCGGCATCTCTTGCTCTGCTCTCGCCGCGCCAGTGTCAGAAAAACAGCTGGCGGAGGTGGTCGCGAATACGATTACCCCGCTGATGAAAGCCCAGTCGATTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGTAAACCGCACTATTATACGTTTGGCAAAGCCGATATCGCGGCTAATAAACCCGTTACGCCTCAGACTCTGTTCGAGCTGGGCTCTATAAGTAAAACCTTCACCGGGGTTTTAGGTGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTGACGGGCAAGCAGTGGCAGGGGATTCGTATGCTGGATCTCGCAACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAATGCCGCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGTATCGGTCTTTTTGGCGCGCTGGCGGTCAAACCTTCCGGCATGGGCTATGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTTCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGAATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCGGAGAAGGTTGCTGATGCCTCACTTAAGCAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGATCGAGGGCAGCGACAGTAAGGTGGCGCTGGCACCGCTGCCCGTGGCAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGCTCTACTGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCGACGCGCTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3001839","ARO_id":"38239","ARO_name":"ACT-18","CARD_short_name":"ACT-18","ARO_description":"ACT-18 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1567":{"model_id":"1567","model_name":"FosB","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"225"}},"model_sequences":{"sequence":{"5284":{"protein_sequence":{"accession":"AAP08996.1","sequence":"MLRGINHICFSVSNLENSIMFYEKVLEGELLVKGRKLAYFNICGVWIALNEETHIPRNEVHQSYTHIAFSVEQEDFKCLIQRLEENDVHILQGRERDVRDCESIYFVDPDGHKFEFHSGTLQDRLNYYRDEKPHMTFY"},"dna_sequence":{"accession":"AE016877.1","fmin":"1972251","fmax":"1972668","strand":"+","sequence":"TTGTTAAGGGGAATCAATCATATTTGTTTTTCGGTATCTAATTTAGAAAACTCTATTATGTTTTATGAAAAAGTATTAGAAGGAGAATTATTAGTTAAAGGAAGAAAATTGGCTTATTTTAACATATGTGGAGTATGGATAGCGCTTAATGAAGAGACGCATATTCCGAGAAATGAGGTTCATCAATCTTATACGCACATTGCATTTTCTGTTGAACAAGAAGACTTTAAATGTCTAATACAGCGATTAGAAGAAAATGATGTTCATATTTTACAAGGAAGAGAACGTGATGTAAGAGATTGCGAATCTATATACTTTGTTGATCCTGACGGTCATAAATTTGAGTTTCACTCAGGGACACTGCAAGACCGTTTAAATTATTATAGAGATGAGAAACCTCATATGACATTTTATTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40539","NCBI_taxonomy_name":"Bacillus cereus ATCC 14579","NCBI_taxonomy_id":"226900"}}}},"ARO_accession":"3000172","ARO_id":"36311","ARO_name":"FosB","CARD_short_name":"FosB","ARO_description":"A thiol transferase that leads to the resistance of fosfomycin. Contrasting FosA, FosB is dependent on the cofactor Magnesium (II) and uses either bacillithiol or  L-cysteine to open up the epoxide ring of fosfomycin.","ARO_category":{"36272":{"category_aro_accession":"3000133","category_aro_cvterm_id":"36272","category_aro_name":"fosfomycin thiol transferase","category_aro_description":"Catalyzes the addition of a thiol group from a nucleophilic molecule to fosfomycin.","category_aro_class_name":"AMR Gene Family"},"35944":{"category_aro_accession":"0000025","category_aro_cvterm_id":"35944","category_aro_name":"fosfomycin","category_aro_description":"Fosfomycin (also known as phosphomycin and phosphonomycin) is a broad-spectrum antibiotic produced by certain Streptomyces species. It is effective on gram positive and negative bacteria as it targets the cell wall, an essential feature shared by both bacteria. Its specific target is MurA (MurZ in E.coli), which attaches phosphoenolpyruvate (PEP) to UDP-N-acetylglucosamine, a step of commitment to cell wall synthesis. In the active site of MurA, the active cysteine molecule is alkylated which stops the catalytic reaction.","category_aro_class_name":"Antibiotic"},"45731":{"category_aro_accession":"3007149","category_aro_cvterm_id":"45731","category_aro_name":"phosphonic acid antibiotic","category_aro_description":"A group of antibiotics derived from phosphonic acids.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1568":{"model_id":"1568","model_name":"OXA-183","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1526":{"protein_sequence":{"accession":"ADV41666.1","sequence":"MKTFAAYVITACLSSTALASSITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNNLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLSLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGTDKFWLEDQLRISAVNQVEFLESLFLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKGTEVYFFAFNMDIDNENKLPLRKSIPTKIMASEGIIGG"},"dna_sequence":{"accession":"HQ111474.1","fmin":"1056","fmax":"1857","strand":"+","sequence":"ATGAAAACATTTGCCGCATATGTAATTACTGCGTGTCTTTCAAGTACGGCATTAGCTAGTTCAATTACAGAAAATACGTCTTGGAACAAAGAGTTCTCTGCCGAAGCCGTCAATGGTGTTTTCGTGCTTTGTAAAAGTAGCAGTAAATCCTGCGCTACCAATAACTTAGCTCGTGCATCAAAGGAATATCTTCCAGCATCAACATTTAAGATCCCCAACGCAATTATCGGCCTAGAAACTGGTGTCATAAAGAATGAGCATCAGGTTTTCAAATGGGACGGAAAGCCAAGAGCCATGAAACAATGGGAAAGAGACTTGAGCTTAAGAGGGGCAATACAAGTTTCAGCGGTTCCCGTATTTCAACAAATCGCCAGAGAAGTTGGCGAAGTAAGAATGCAGAAATACCTTAAAAAATTTTCATATGGCAACCAGAATATCAGTGGTGGCACTGACAAATTCTGGTTGGAGGATCAGCTAAGAATTTCCGCAGTTAATCAAGTGGAGTTTCTAGAGTCTCTATTTTTAAATAAATTGTCAGCATCAAAAGAAAATCAGCTAATAGTAAAAGAGGCTTTGGTAACGGAGGCTGCGCCTGAATATCTTGTGCATTCAAAAACTGGTTTTTCTGGTGTGGGAACTGAGTCAAATCCTGGTGTCGCATGGTGGGTTGGTTGGGTTGAGAAGGGAACAGAGGTTTACTTTTTCGCCTTTAACATGGATATAGACAACGAAAATAAGTTGCCGCTAAGAAAATCCATTCCCACCAAAATCATGGCAAGTGAGGGCATCATTGGTGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3001475","ARO_id":"37875","ARO_name":"OXA-183","CARD_short_name":"OXA-183","ARO_description":"OXA-183 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46486":{"category_aro_accession":"3007697","category_aro_cvterm_id":"46486","category_aro_name":"OXA-10-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-10.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1572":{"model_id":"1572","model_name":"OXA-205","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1682":{"protein_sequence":{"accession":"AEO92079.1","sequence":"MAIRFLTILLSTFFLTSFVHAQEHVVVRSDWKKFFSDLQAEGAIVIADERQAEHALLVFGQERAAKRYSPASTFKLPHTLFALDAGAVRDEFQVFRWDGVKRSFAGHNQDQDLRSAMRNSAVWVYELFAKEIGEDNARRYLKQIDYGNADPSTIKGNYWIDGNLEISAHEQISFLRKLYRNQLPFQVEHQRLVKYLMITEAGRNWILRAKTGWEGRFGWWIGWVEWPTGPVFFALNIDTPNRTDDLFKREAIARAILRSIDALPPN"},"dna_sequence":{"accession":"JF800667.1","fmin":"657","fmax":"1458","strand":"+","sequence":"ATGGCAATCCGATTCCTCACCATACTGCTATCTACTTTTTTTCTTACCTCATTCGTGCATGCGCAAGAACACGTGGTAGTCCGTTCTGACTGGAAGAAGTTCTTCAGCGACCTCCAGGCCGAAGGTGCAATCGTTATTGCAGACGAACGTCAAGCGGAGCATGCTTTATTGGTTTTTGGTCAAGAGCGAGCAGCAAAGCGTTACTCGCCTGCTTCAACCTTCAAGCTTCCACACACACTTTTTGCACTCGATGCAGGCGCCGTTCGTGATGAGTTCCAGGTTTTTCGATGGGATGGCGTTAAGCGGAGCTTTGCGGGCCACAATCAAGACCAAGACTTGCGATCAGCGATGCGAAATTCTGCGGTCTGGGTTTATGAGCTATTTGCAAAAGAGATCGGAGAGGACAACGCAAGACGCTATTTAAAGCAAATTGACTATGGCAACGCCGACCCTTCGACAATTAAGGGCAATTACTGGATAGATGGCAATCTTGAAATCTCAGCGCACGAACAGATTTCGTTTCTCAGAAAACTTTATCGAAATCAGCTGCCATTTCAGGTGGAACACCAGCGCTTGGTCAAATATCTCATGATTACGGAAGCCGGGCGCAACTGGATACTACGCGCAAAGACTGGCTGGGAAGGCAGGTTTGGCTGGTGGATAGGGTGGGTTGAATGGCCAACCGGTCCCGTATTCTTCGCGCTGAATATTGATACGCCAAACAGAACGGATGATCTTTTCAAAAGAGAGGCAATCGCGCGGGCAATCCTTCGCTCTATCGACGCGTTGCCGCCCAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3001483","ARO_id":"37883","ARO_name":"OXA-205","CARD_short_name":"OXA-205","ARO_description":"OXA-205 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46509":{"category_aro_accession":"3007720","category_aro_cvterm_id":"46509","category_aro_name":"OXA-46-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-46.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1573":{"model_id":"1573","model_name":"SHV-110","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1143":{"protein_sequence":{"accession":"AEK48094.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIDDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"HQ877615.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACATCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGACGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001159","ARO_id":"37539","ARO_name":"SHV-110","CARD_short_name":"SHV-110","ARO_description":"SHV-110 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1575":{"model_id":"1575","model_name":"OXA-91","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1383":{"protein_sequence":{"accession":"ABF47914.1","sequence":"MNIKALLLITSAIFISACSPYIVSANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"DQ519086.1","fmin":"1198","fmax":"2023","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGTCTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACTACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001627","ARO_id":"38027","ARO_name":"OXA-91","CARD_short_name":"OXA-91","ARO_description":"OXA-91 is a beta-lactamase found in A. baumannii.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1576":{"model_id":"1576","model_name":"OXA-17","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8356":{"protein_sequence":{"accession":"ABI63579.1","sequence":"MKTFAAYVIIACLSSTALAGSITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFKIPSAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGIIGG"},"dna_sequence":{"accession":"DQ902344.1","fmin":"2716","fmax":"3517","strand":"+","sequence":"ATGAAAACATTTGCCGCATATGTAATTATCGCGTGTCTTTCGAGTACGGCATTAGCTGGTTCAATTACAGAAAATACGTCTTGGAACAAAGAGTTCTCTGCCGAAGCCGTCAATGGTGTCTTCGTGCTTTGTAAAAGTAGCAGTAAATCCTGCGCTACCAATGACTTAGCTCGTGCATCAAAGGAATATCTTCCAGCATCAACATTTAAGATCCCCAGCGCAATTATCGGCCTAGAAACTGGTGTCATAAAGAATGAGCATCAGGTTTTCAAATGGGACGGAAAGCCAAGAGCCATGAAGCAATGGGAAAGAGACTTGACCTTAAGAGGGGCAATACAAGTTTCAGCTGTTCCCGTATTTCAACAAATCGCCAGAGAAGTTGGCGAAGTAAGAATGCAGAAATACCTTAAAAAATTTTCCTATGGCAACCAGAATATCAGTGGTGGCATTGACAAATTCTGGTTGGAAGGCCAGCTTAGAATTTCCGCAGTTAATCAAGTGGAGTTTCTAGAGTCTCTATATTTAAATAAATTGTCAGCATCTAAAGAAAACCAGCTAATAGTAAAAGAGGCTTTGGTAACGGAGGCGGCACCTGAATATCTAGTGCATTCAAAAACTGGTTTTTCTGGTGTGGGAACTGAGTCAAATCCTGGTGTCGCATGGTGGGTTGGGTGGGTTGAGAAGGAGACAGAGGTTTACTTTTTCGCCTTTAACATGGATATAGACAACGAAAGTAAGTTGCCGCTAAGAAAATCCATTCCCACCAAAATCATGGAAAGTGAGGGCATCATTGGTGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001412","ARO_id":"37812","ARO_name":"OXA-17","CARD_short_name":"OXA-17","ARO_description":"OXA-17 is a beta-lactamase found in P. aeruginosa and Klebsiella pneumoniae.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46486":{"category_aro_accession":"3007697","category_aro_cvterm_id":"46486","category_aro_name":"OXA-10-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-10.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1577":{"model_id":"1577","model_name":"AAC(6')-32","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"310":{"protein_sequence":{"accession":"ABR10839.1","sequence":"MSPSKTPVTLRLMTERDLPMLHAWLNRPHIVEWWGGEEERPTLHEVVKHYLPRVLAEEAVTPYIAMLGDEPIGYAQSYVALGSGDGWWEDETDPGVRGIDQFLSNHTQLNQGLGTKLVQALVELLFSDPTVTKIQTDPAPNNHRAIRCYEKAGFVQQNVITTPDGPAVYMVQTRQAFERVRSAA"},"dna_sequence":{"accession":"EF614235.1","fmin":"2246","fmax":"2801","strand":"+","sequence":"ATGTCCCCGAGCAAAACACCCGTTACCTTGCGCCTCATGACCGAGCGCGACCTACCGATGCTGCATGCATGGCTGAACCGGCCGCACATTGTCGAGTGGTGGGGTGGAGAAGAAGAACGCCCGACTCTTCATGAAGTGGTCAAACACTACCTGCCGAGGGTTTTGGCAGAAGAAGCCGTCACACCATACATCGCGATGTTGGGCGACGAACCCATCGGCTACGCTCAGTCATACGTCGCACTCGGAAGCGGTGATGGATGGTGGGAGGATGAAACCGACCCAGGCGTACGAGGGATAGACCAATTCCTGTCGAACCATACACAGTTGAACCAGGGCCTAGGTACAAAGCTCGTCCAGGCACTCGTTGAACTGCTGTTCTCAGATCCTACCGTGACGAAGATCCAAACCGACCCGGCGCCAAACAACCATCGAGCGATTCGCTGCTACGAGAAAGCTGGCTTTGTTCAGCAAAACGTCATCACCACACCAGACGGCCCAGCCGTCTACATGGTTCAAACCAGGCAGGCCTTCGAGCGTGTGCGCAGTGCTGCCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002586","ARO_id":"38986","ARO_name":"AAC(6')-32","CARD_short_name":"AAC(6')-32","ARO_description":"AAC(6')-32 is an aminoglycoside acetyltransferase encoded by plasmids and integrons in P. aeruginosa.","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"A category of aminoglycoside N-acetyltransferase enzymes with modification regiospecificity based at the 6'-amino group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics through acetylation of the 6-amino group of the compound.","category_aro_class_name":"AMR Gene Family"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"46133":{"category_aro_accession":"3007382","category_aro_cvterm_id":"46133","category_aro_name":"gentamicin","category_aro_description":"Gentamicin is a commonly used aminoglycoside antibiotic derived from members of the Micromonospora genus of bacteria. It acts by binding the 30S ribosomal subunit, thus inhibiting protein synthesis. Gentamicin is typically used to treat Gram-negative infections of the repiratory and urinary tract, as well as infections of the bone and soft tissue. It also exhibits considerable nephrotoxicity and ototoxicity. Gentamicin is administered as a mixture of gentamicin type C (which makes about around 80% of the complex) and types A, B, and X (distributed in the remaining 20% of the complex).","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1578":{"model_id":"1578","model_name":"SHV-123","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1773":{"protein_sequence":{"accession":"ACV32633.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGASKRGARGIVALLGGNIKAERIVVIYLRDTPASMAERNQ"},"dna_sequence":{"accession":"GQ390805.1","fmin":"0","fmax":"813","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTACTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTAGCAAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCGGGAATATCAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAATCAG","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001170","ARO_id":"37550","ARO_name":"SHV-123","CARD_short_name":"SHV-123","ARO_description":"SHV-123 is a beta-lactamase that has been found in clinical isolates.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1579":{"model_id":"1579","model_name":"QnrB9","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"681":{"protein_sequence":{"accession":"ABP88094.1","sequence":"MALALVGEKIDRNRFTGEKIENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNASALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGAQVLGATFSGSDLSGGEFSTFDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDNYQASLLMERLGIAIIG"},"dna_sequence":{"accession":"EF526508.1","fmin":"0","fmax":"645","strand":"+","sequence":"ATGGCTCTGGCACTCGTTGGCGAAAAAATTGACAGAAACCGTTTCACCGGTGAGAAAATTGAAAATAGTACATTTTTTAACTGTGATTTTTCAGGTGCCGACCTAAGTGGTACTGAATTTATCGGCTGTCAGTTCTATGATCGTGAAAGCCAGAAAGGGTGCAATTTTAGTCGTGCAATGCTGAAAGATGCCATTTTTAAAAGCTGTGATTTATCCATGGCGGATTTTCGCAATGCCAGTGCGCTGGGCATTGAAATTCGCCACTGCCGCGCACAAGGCGCAGATTTCCGCGGCGCAAGCTTTATGAATATGATCACTACACGCACCTGGTTTTGCAGCGCATATATCACTAACACAAATCTAAGCTACGCCAATTTTTCGAAAGTCGTGCTGGAAAAGTGTGAGCTGTGGGAAAACCGTTGGATGGGTGCCCAGGTACTGGGCGCGACGTTCAGTGGTTCAGATCTCTCCGGCGGCGAGTTTTCGACTTTCGACTGGCGAGCAGCAAACTTCACACATTGCGATCTGACCAATTCGGAGTTGGGTGACTTAGATATTCGGGGCGTTGATTTACAAGGCGTTAAGTTGGACAACTACCAGGCATCGTTGCTCATGGAACGTCTTGGCATCGCGATTATTGGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002723","ARO_id":"39157","ARO_name":"QnrB9","CARD_short_name":"QnrB9","ARO_description":"QnrB9 is a plasmid-mediated quinolone resistance protein found in Citrobacter freundii.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1580":{"model_id":"1580","model_name":"catIII","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"528":{"protein_sequence":{"accession":"CAA30695.1","sequence":"MNYTKFDVKNWVRREHFEFYRHRLPCGFSLTSKIDITTLKKSLDDSAYKFYPVMIYLIAQAVNQFDELRMAIKDDELIVWDSVDPQFTVFHQETETFSALSCPYSSDIDQFMVNYLSVMERYKSDTKLFPQGVTPENHLNISALPWVNFDSFNLNVANFTDYFAPIITMAKYQQEGDRLLLPLSVQVHHAVCDGFHVARFINRLQELCNSKLK"},"dna_sequence":{"accession":"X07848.1","fmin":"271","fmax":"913","strand":"+","sequence":"ATGAACTATACAAAATTTGATGTAAAAAATTGGGTTCGCCGTGAGCATTTTGAGTTTTATCGGCATCGTTTACCATGTGGTTTTAGCTTAACAAGCAAAATTGATATCACGACGTTAAAAAAGTCATTGGATGATTCAGCGTATAAGTTTTATCCGGTAATGATCTATCTGATTGCTCAGGCCGTGAATCAATTTGATGAGTTGAGAATGGCGATAAAAGATGATGAATTGATCGTATGGGATTCAGTCGACCCACAATTCACCGTATTCCATCAAGAAACAGAGACATTTTCAGCACTGAGTTGCCCATACTCATCCGATATTGATCAATTTATGGTGAATTATTTATCGGTAATGGAACGTTATAAAAGTGATACCAAGTTATTTCCTCAAGGGGTAACACCAGAAAATCATTTAAATATTTCAGCATTACCTTGGGTTAATTTTGATAGCTTTAATTTAAATGTTGCTAATTTTACCGATTATTTTGCACCCATTATAACAATGGCAAAATATCAGCAAGAAGGGGATAGACTGTTATTGCCGCTCTCAGTACAGGTTCATCATGCAGTTTGTGATGGCTTCCATGTTGCACGCTTTATTAATCGGCTACAAGAGTTGTGTAACAGTAAATTAAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39545","NCBI_taxonomy_name":"Plasmid R387","NCBI_taxonomy_id":"2486"}}}},"ARO_accession":"3002685","ARO_id":"39119","ARO_name":"catIII","CARD_short_name":"catIII","ARO_description":"catIII is a plasmid-encoded variant of the cat gene found in Shigella flexneri.","ARO_category":{"36261":{"category_aro_accession":"3000122","category_aro_cvterm_id":"36261","category_aro_name":"chloramphenicol acetyltransferase (CAT)","category_aro_description":"Inactivates chloramphenicol by addition of an acyl group. CAT is used to describe many variants of the chloramphenicol acetyltransferase gene in a range of organisms including Acinetobacter calcoaceticus, Agrobacterium tumefaciens, Alkalihalobacillus clausii, Bacillus subtilis, Campylobacter coli, Enterococcus faecalis, Enterococcus faecium, Lactococcus lactis, Listeria monocytogenes, Listonella anguillarum, Morganella morganii, Photobacterium damselae subsp. piscicida, Proteus mirabilis, Salmonella typhi, Serratia marcescens, Shigella flexneri, Staphylococcus aureus, Staphylococcus haemolyticus, Staphylococcus intermedius, Streptococcus agalactiae, Streptococcus suis and Streptomyces acrimycini.","category_aro_class_name":"AMR Gene Family"},"36521":{"category_aro_accession":"3000382","category_aro_cvterm_id":"36521","category_aro_name":"azidamfenicol","category_aro_description":"Azidamfenicol is a water soluble derivative of chloramphenicol, sharing the same mode of action of inhibiting peptide synthesis by interacting with the 23S RNA of the 50S ribosomal subunit.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36595":{"category_aro_accession":"3000456","category_aro_cvterm_id":"36595","category_aro_name":"thiamphenicol","category_aro_description":"Derivative of Chloramphenicol. The nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3).","category_aro_class_name":"Antibiotic"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1581":{"model_id":"1581","model_name":"ACT-3","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1177":{"protein_sequence":{"accession":"ABL67017.1","sequence":"MMMTKSLCCALLLSTSCSVLATPMSEKQLAEVVERTVTPLMKAQAIPGMAVAVIYEGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMSYEQAITTRVFKPLKLDHTWINVPKAEEAHYAWGYRDGKAIHVSPGMLDAEAYGVKTNVQDMASWVMVNMKPDSLQDNSLRKGLTLAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVEGSDNKVALAPLPAREVNPPAPPVNASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILSAL"},"dna_sequence":{"accession":"EF125013.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGATGACTAAATCCCTTTGCTGCGCCCTGCTGCTCAGCACCTCCTGCTCGGTATTGGCTACCCCGATGTCAGAAAAACAGCTGGCTGAGGTGGTGGAGCGGACCGTTACGCCGCTGATGAAAGCGCAGGCCATTCCGGGTATGGCGGTGGCGGTGATTTATGAGGGTCAGCCGCACTACTTCACCTTCGGTAAAGCCGATGTTGCGGCGAACAAACCTGTCACTCCACAAACCTTGTTCGAACTGGGTTCTATAAGTAAAACCTTCACCGGCGTACTCGGTGGCGATGCCATTGCTCGGGGTGAAATATCGCTGGGCGATCCGGTGACAAAATACTGGCCTGAGCTGACAGGCAAGCAGTGGCAGGGGATCCGCATGCTGGATCTGGCAACCTATACCGCAGGAGGTTTGCCGTTACAGGTACCGGATGAGGTCACGGATAACGCCTCTCTGTTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCGGGCACCACGCGTCTTTACGCCAATGCCAGCATCGGTCTTTTTGGCGCGCTGGCGGTCAAACCTTCCGGCATGAGCTATGAGCAGGCCATAACGACGCGGGTCTTTAAGCCGCTCAAGCTGGACCATACGTGGATTAACGTTCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGATACCGCGACGGTAAAGCGATACACGTTTCGCCAGGAATGCTGGACGCTGAAGCCTATGGCGTAAAAACCAACGTGCAGGATATGGCAAGCTGGGTGATGGTCAACATGAAGCCGGACTCCCTTCAGGATAATTCACTCAGGAAAGGCCTTACCCTGGCGCAGTCTCGCTACTGGCGCGTGGGGGCCATGTATCAGGGGTTAGGCTGGGAAATGCTTAACTGGCCGGTCGATGCCAAAACCGTGGTTGAAGGTAGCGACAATAAGGTTGCACTGGCACCGCTGCCTGCGAGAGAAGTGAATCCACCAGCGCCCCCGGTCAATGCATCCTGGGTCCATAAAACAGGCTCTACCGGCGGGTTTGGCAGCTACGTGGCATTTATTCCTGAAAAGCAGCTCGGTATTGTGATGCTGGCAAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCGTATTTTGAGCGCGCTGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001823","ARO_id":"38223","ARO_name":"ACT-3","CARD_short_name":"ACT-3","ARO_description":"ACT-3 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1582":{"model_id":"1582","model_name":"dfrA5","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"2104":{"protein_sequence":{"accession":"ABB89122.1","sequence":"MKVSLMAAKAKNGVIGCGPHIPWSAKGEQLLFKALTYNQWLLVGRKTFESMGALPNRKYAVVTRSAWTADNDNVIVFPSIEEAMYGLAELTDHVIVSGGGEIYRETLPMASTLHISTIDIEPEGDVFFPNIPNTFEVVFEQHFSSNINYCYQIWQKG"},"dna_sequence":{"accession":"DQ278190.1","fmin":"0","fmax":"474","strand":"+","sequence":"GTGAAAGTATCATTAATGGCTGCAAAAGCGAAAAACGGAGTGATTGGTTGCGGTCCACACATACCCTGGTCCGCGAAAGGAGAGCAGCTACTCTTTAAAGCCTTGACGTACAACCAGTGGCTTTTGGTGGGCCGCAAGACGTTCGAATCTATGGGAGCACTCCCTAATAGGAAATACGCGGTCGTTACTCGCTCAGCCTGGACGGCCGATAATGACAACGTAATAGTATTCCCGTCGATCGAAGAGGCCATGTACGGGCTGGCTGAACTCACCGATCACGTTATAGTGTCTGGTGGCGGGGAGATTTACAGAGAAACATTGCCCATGGCCTCTACGCTCCATATATCGACGATTGATATTGAGCCGGAAGGAGATGTTTTCTTTCCGAATATTCCCAATACCTTCGAAGTTGTTTTTGAGCAACACTTTAGCTCAAACATTAACTATTGCTATCAAATTTGGCAAAAGGGTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35750","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Enteritidis","NCBI_taxonomy_id":"149539"}}}},"ARO_accession":"3002861","ARO_id":"39295","ARO_name":"dfrA5","CARD_short_name":"dfrA5","ARO_description":"dfrA5 is an integron-encoded dihydrofolate reductase found in Vibrio cholerae.","ARO_category":{"37617":{"category_aro_accession":"3001218","category_aro_cvterm_id":"37617","category_aro_name":"trimethoprim resistant dihydrofolate reductase dfr","category_aro_description":"Alternative dihydropteroate synthase dfr present on plasmids produces alternate proteins that are less sensitive to trimethoprim from inhibiting its role in folate synthesis, thus conferring trimethoprim resistance.","category_aro_class_name":"AMR Gene Family"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1583":{"model_id":"1583","model_name":"QnrVC6","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"631":{"protein_sequence":{"accession":"AGH08253.1","sequence":"MEKSKQLYNQVNFSHQDLQEHIFSNCTFIHCNFKRSNLRDTQFINCTFIEQGALEGCDFSYADLRDASFKDCQLSMSHFKGANCFGIELRDCDLKGANFSQVSFVNQVSNKMYFCSAYITGCNLSYANFEQQLIEKCDLFENRWIGANLRGASFKESDLSRGVFSEDCWEQFRVQGCDLSHSELYGLDPRKIDLTGVKICSWQQEQLLEQLGVIIVPD"},"dna_sequence":{"accession":"KC202804.1","fmin":"3874","fmax":"4531","strand":"+","sequence":"ATGGAAAAATCAAAGCAATTATATAATCAAGTGAACTTCTCACATCAGGACTTGCAAGAACATATCTTTAGCAATTGTACTTTTATACATTGTAATTTTAAGCGCTCAAACCTTCGAGATACACAGTTCATTAACTGTACTTTCATAGAGCAGGGGGCACTGGAAGGGTGCGATTTTTCTTATGCTGATCTTCGAGATGCTTCATTTAAAGATTGTCAGCTTTCAATGTCCCATTTTAAGGGGGCAAATTGCTTTGGTATTGAACTGAGAGATTGTGATCTTAAAGGGGCAAATTTTAGCCAAGTTAGTTTTGTAAATCAGGTTTCGAATAAAATGTACTTTTGCTCTGCATACATAACAGGTTGTAACTTATCCTATGCCAATTTTGAGCAGCAGCTTATTGAAAAATGTGACCTGTTCGAAAATAGATGGATTGGTGCAAATCTTCGAGGCGCTTCATTTAAAGAATCAGATTTAAGTCGTGGCGTTTTTTCAGAAGACTGCTGGGAACAGTTTAGAGTACAAGGCTGTGATTTAAGTCATTCAGAGCTTTATGGTTTAGATCCTCGAAAGATTGATCTTACAGGTGTAAAAATATGCTCGTGGCAACAGGAGCAGTTACTGGAGCAATTAGGGGTAATCATTGTTCCTGACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39615","NCBI_taxonomy_name":"Vibrio parahaemolyticus","NCBI_taxonomy_id":"670"}}}},"ARO_accession":"3002803","ARO_id":"39237","ARO_name":"QnrVC6","CARD_short_name":"QnrVC6","ARO_description":"QnrVC6 is an integron-mediated quinolone resistance protein found in Acinetobacter baumannii.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1585":{"model_id":"1585","model_name":"CMY-73","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1423":{"protein_sequence":{"accession":"ACU00152.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVLYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYLPELTGKQWQGISLLHLATYTAGGLPLQIPDDVTDKAALLRFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHVTPGQLDAEAYGVKSNVTDMARWIQVNMDASRVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPTVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"GQ351345.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCATTCTCCACGTTTGCCGCCGCCAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTCTCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTTGCCAGAACTGACAGGCAAGCAGTGGCAGGGTATCAGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTACAGATAAAGCCGCATTACTGCGTTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACAGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGTTACTCCTGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAACGTTACCGATATGGCCCGTTGGATTCAGGTCAACATGGACGCCAGCCGCGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGTGACAGCAAAGTGGCATTGGCAGCGCTTCCCACCGTTGAGGTAAACCCGCCCGCCCCGGCAGTGAAAGCCTCATGGGTGCATAAAACGGGTTCCACTGGTGGATTTGGCAGCTACGTTGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTACAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002086","ARO_id":"38486","ARO_name":"CMY-73","CARD_short_name":"CMY-73","ARO_description":"CMY-73 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1586":{"model_id":"1586","model_name":"CTX-M-32","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"867":{"protein_sequence":{"accession":"CAD89606.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAVAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVDGTMSLAELSAAALQYSDNVAMNKLISHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTNGL"},"dna_sequence":{"accession":"AJ557142.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGTCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGAAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGTGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACTTGGTTAACTATAATCCGATTGCGGAAAAGCACGTCGATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTTCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGTAATCTGACGCTGGGTAAAGCATTGGGTGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCAACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001894","ARO_id":"38294","ARO_name":"CTX-M-32","CARD_short_name":"CTX-M-32","ARO_description":"CTX-M-32 is a beta-lactamase found in Escherichia coli.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1587":{"model_id":"1587","model_name":"OXA-10","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"878":{"protein_sequence":{"accession":"AAG45720.1","sequence":"MKTFAAYVIIACLSSTALAGSITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGIIGG"},"dna_sequence":{"accession":"AF205943.1","fmin":"7511","fmax":"8312","strand":"+","sequence":"ATGAAAACATTTGCCGCATATGTAATTATCGCGTGTCTTTCGAGTACGGCATTAGCTGGTTCAATTACAGAAAATACGTCTTGGAACAAAGAGTTCTCTGCCGAAGCCGTCAATGGTGTCTTCGTGCTTTGTAAAAGTAGCAGTAAATCCTGCGCTACCAATGACTTAGCTCGTGCATCAAAGGAATATCTTCCAGCATCAACATTTAAGATCCCCAACGCAATTATCGGCCTAGAAACTGGTGTCATAAAGAATGAGCATCAGGTTTTCAAATGGGACGGAAAGCCAAGAGCCATGAAGCAATGGGAAAGAGACTTGACCTTAAGAGGGGCAATACAAGTTTCAGCTGTTCCCGTATTTCAACAAATCGCCAGAGAAGTTGGCGAAGTAAGAATGCAGAAATACCTTAAAAAATTTTCCTATGGCAACCAGAATATCAGTGGTGGCATTGACAAATTCTGGTTGGAAGGCCAGCTTAGAATTTCCGCAGTTAATCAAGTGGAGTTTCTAGAGTCTCTATATTTAAATAAATTGTCAGCATCTAAAGAAAACCAGCTAATAGTAAAAGAGGCTTTGGTAACGGAGGCGGCACCTGAATATCTAGTGCATTCAAAAACTGGTTTTTCTGGTGTGGGAACTGAGTCAAATCCTGGTGTCGCATGGTGGGTTGGGTGGGTTGAGAAGGAGACAGAGGTTTACTTTTTCGCCTTTAACATGGATATAGACAACGAAAGTAAGTTGCCGCTAAGAAAATCCATTCCCACCAAAATCATGGAAAGTGAGGGCATCATTGGTGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001405","ARO_id":"37805","ARO_name":"OXA-10","CARD_short_name":"OXA-10","ARO_description":"OXA-10 is a beta-lactamase found in Acinetobacter baumannii and P. aeruginosa.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46486":{"category_aro_accession":"3007697","category_aro_cvterm_id":"46486","category_aro_name":"OXA-10-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-10.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1588":{"model_id":"1588","model_name":"QnrB50","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"298":{"protein_sequence":{"accession":"AFU25656.1","sequence":"MTLALVGEKIDRKRFTGEKVENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNVSALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGTQVLGATFSGSDLSGGEFSTFDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDNYQASLLMERLGIAVIG"},"dna_sequence":{"accession":"JX440357.1","fmin":"135","fmax":"780","strand":"+","sequence":"ATGACTCTGGCATTAGTTGGCGAAAAAATTGACAGAAAGCGCTTCACCGGTGAGAAAGTTGAAAATAGTACATTTTTTAACTGCGATTTTTCAGGTGCCGACCTGAGCGGCACTGAATTTATCGGCTGCCAGTTCTATGATCGCGAAAGTCAGAAAGGATGCAATTTTAGTCGCGCAATGCTGAAAGATGCCATTTTCAAAAGCTGTGATTTATCAATGGCAGATTTCCGCAACGTCAGCGCATTGGGCATTGAAATTCGCCACTGCCGCGCACAAGGCGCAGATTTCCGCGGTGCAAGCTTTATGAATATGATCACCACGCGCACCTGGTTTTGCAGCGCATATATCACTAATACCAATCTAAGCTACGCCAATTTTTCGAAAGTCGTGTTGGAAAAGTGTGAGCTATGGGAAAACCGCTGGATGGGGACTCAGGTACTGGGTGCGACGTTCAGTGGTTCAGATCTCTCCGGCGGCGAGTTTTCGACTTTCGACTGGCGAGCAGCAAACTTCACACATTGCGATCTGACCAATTCGGAGTTAGGTGACTTAGATATTCGGGGTGTTGATTTACAAGGCGTTAAGTTAGACAACTACCAGGCATCGTTGCTCATGGAGCGGCTTGGCATCGCTGTGATTGGTTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002765","ARO_id":"39199","ARO_name":"QnrB50","CARD_short_name":"QnrB50","ARO_description":"QnrB50 is a plasmid-mediated quinolone resistance protein found in Citrobacter freundii.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1589":{"model_id":"1589","model_name":"PER-3","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"984":{"protein_sequence":{"accession":"AAU89132.1","sequence":"MNVIIKAVVTASTLLMVSFSSFETSAQSPLLKEQIESIVIGKKATVGVAVWGPDDLEPLLINPFEKFPMQSVFKLHLAMLVLHQVDQGKLDLNQTVIVNRAKVLQNTWAPIMKAYQGDEFSVPVQQLLQYSVSLSDNVACDLLFELVGGPAALHDYIQSMGIKETAVVANEAQMHADDQVQYQNWTSMKGAAEILKKFEQKTQLSETSQALLWKWMVETTTGPERLKGLLPAGTVVAHKTGTSGIKAGKTAATNDLGIILLPDGRPLLVAVFVKDSAESSRTNEAIIAQVAQTAYQFELKKLSALSPN"},"dna_sequence":{"accession":"AY740681.1","fmin":"7102","fmax":"8029","strand":"+","sequence":"ATGAATGTCATTATAAAAGCTGTAGTTACTGCCTCGACGCTACTGATGGTATCTTTTAGTTCATTCGAAACCTCAGCGCAATCCCCACTGTTAAAAGAGCAAATTGAATCCATAGTCATTGGAAAAAAAGCCACTGTAGGCGTTGCAGTGTGGGGGCCTGACGATCTGGAACCTTTACTGATTAATCCTTTTGAAAAATTCCCAATGCAAAGTGTATTTAAATTGCATTTAGCTATGTTGGTACTGCATCAGGTTGATCAGGGAAAGTTGGATTTAAATCAGACCGTTATCGTAAACAGGGCTAAGGTTTTACAGAATACCTGGGCTCCGATAATGAAAGCGTATCAGGGAGACGAGTTTAGTGTTCCAGTGCAGCAACTGCTGCAATACTCGGTCTCGCTCAGCGATAACGTGGCCTGTGATTTGTTATTTGAACTGGTTGGTGGACCAGCTGCTTTGCATGACTATATCCAGTCTATGGGTATAAAGGAGACCGCTGTGGTCGCAAATGAAGCGCAGATGCACGCCGATGATCAGGTGCAGTATCAAAACTGGACCTCGATGAAAGGTGCTGCAGAGATCCTGAAAAAGTTTGAGCAAAAAACACAGCTGTCTGAAACCTCGCAGGCTTTGTTATGGAAGTGGATGGTCGAAACCACCACAGGACCAGAGCGGTTAAAAGGTTTGTTACCAGCTGGTACTGTGGTCGCACATAAAACTGGTACTTCGGGTATCAAAGCCGGAAAAACTGCGGCCACTAATGATTTAGGTATCATTCTGTTGCCTGATGGACGGCCCTTGCTGGTTGCTGTTTTTGTGAAAGACTCAGCCGAGTCAAGCCGAACCAATGAAGCTATCATTGCGCAGGTTGCTCAGACTGCGTATCAATTTGAATTGAAAAAGCTTTCTGCCCTAAGCCCAAATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36936","NCBI_taxonomy_name":"Aeromonas caviae","NCBI_taxonomy_id":"648"}}}},"ARO_accession":"3002365","ARO_id":"38765","ARO_name":"PER-3","CARD_short_name":"PER-3","ARO_description":"PER-3 is a beta-lactamase found in Aeromonas spp.","ARO_category":{"36195":{"category_aro_accession":"3000056","category_aro_cvterm_id":"36195","category_aro_name":"PER beta-lactamase","category_aro_description":"PER beta-lactamases are plasmid-mediated extended spectrum beta-lactamases found in the Enterobacteriaceae family.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1590":{"model_id":"1590","model_name":"QnrB27","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"156":{"protein_sequence":{"accession":"ADM52186.1","sequence":"MTLALVSEKIDRNRFTGEKVENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNASALGIEIRHCRAQGSDFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGTQVAGATFSGSDLSGGEFSAFDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDSYQAALLMERLGIAVIG"},"dna_sequence":{"accession":"HM439641.1","fmin":"0","fmax":"645","strand":"+","sequence":"ATGACTCTGGCATTAGTTAGCGAAAAAATTGACAGAAACCGCTTCACCGGGGAAAAAGTTGAAAACAGTACTTTTTTTAACTGTGATTTTTCAGGGGCCGATCTTAGCGGCACTGAATTTATCGGCTGTCAGTTTTATGATCGCGAAAGCCAGAAAGGGTGTAATTTTAGTCGCGCAATGCTGAAAGATGCCATTTTTAAAAGTTGCGATTTATCCATGGCGGATTTTCGCAACGCCAGTGCCCTGGGAATTGAAATTCGCCACTGCCGCGCGCAGGGTTCAGATTTTCGCGGCGCGAGTTTTATGAACATGATCACCACGCGGACCTGGTTTTGCAGCGCATACATCACGAATACCAATCTAAGCTACGCCAACTTTTCGAAGGTTGTCCTGGAAAAGTGCGAGCTGTGGGAAAACCGCTGGATGGGAACTCAGGTAGCGGGTGCAACGTTCAGTGGATCAGATCTCTCGGGCGGTGAATTTTCAGCGTTCGACTGGCGGGCCGCAAACTTCACGCACTGTGATTTGACCAATTCAGAACTGGGTGATTTAGATATTCGGGGTGTAGATTTACAAGGCGTCAAATTGGATAGCTATCAGGCAGCGTTGCTGATGGAGCGGCTTGGCATCGCGGTGATTGGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39584","NCBI_taxonomy_name":"Citrobacter braakii","NCBI_taxonomy_id":"57706"}}}},"ARO_accession":"3002742","ARO_id":"39176","ARO_name":"QnrB27","CARD_short_name":"QnrB27","ARO_description":"QnrB27 is a plasmid-mediated quinolone resistance protein found in Citrobacter braakii.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1591":{"model_id":"1591","model_name":"CMY-64","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1915":{"protein_sequence":{"accession":"ADW84690.1","sequence":"MMKKSLCCALLLTASLSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAIAVIYQGKPYYFTWGKADITNNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGISLLHLATYTAGGLPLQIPDDVTDKAALLRFYQNWQPQWAPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKAVHVSPGQLDAEAYGVKSSVIDMARWVQVNMDASRVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"HQ832678.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTATCCACGTTTGCCGCCGCCAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCTATTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCACCAATAACCACCCAGTCACGCAGCAAACTCTGTTTGAGCTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCAGCCTGCTGCACTTAGCCACCTACACGGCAGGCGGCCTGCCGCTGCAGATCCCCGATGACGTTACGGATAAAGCCGCATTACTGCGTTTTTATCAAAACTGGCAGCCGCAATGGGCCCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACAGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGGCTGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGTGTTATTGATATGGCCCGCTGGGTTCAGGTCAACATGGACGCCAGCCGCGTTCAAGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCAATCATCAACGGTAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCTGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGATCCACTGGAGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002077","ARO_id":"38477","ARO_name":"CMY-64","CARD_short_name":"CMY-64","ARO_description":"CMY-64 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1592":{"model_id":"1592","model_name":"dfrA14","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"6119":{"protein_sequence":{"accession":"AHK10285.1","sequence":"MKVSLMAAKAKNGVIGCGPDIPWSAKGEQLLFKALTYNQWLLVGRKTFESMGALPNRKYAVVTRSGWTSNDDNVVVFQSIEEAMDRLAEFTGHVIVSGGGEIYRETLPMASTLHLSTIDIEPEGDVFFPSIPNTFEVVFEQHFTSNINYCYQIWKKG"},"dna_sequence":{"accession":"KF921535.1","fmin":"617","fmax":"1091","strand":"+","sequence":"TTGAAAGTATCATTGATGGCTGCGAAAGCGAAAAACGGCGTGATTGGTTGCGGTCCAGACATACCCTGGTCCGCGAAAGGGGAGCAGCTACTTTTTAAAGCATTGACCTACAATCAGTGGCTTCTGGTGGGTCGCAAGACGTTTGAATCTATGGGCGCACTCCCCAATAGGAAATACGCGGTCGTTACCCGCTCAGGTTGGACATCAAATGATGACAATGTAGTTGTATTTCAGTCAATCGAAGAGGCCATGGACAGGCTAGCTGAATTCACCGGTCACGTTATAGTGTCTGGTGGCGGAGAAATTTACCGAGAAACATTACCCATGGCCTCTACGCTCCACTTATCGACGATCGACATCGAGCCAGAGGGGGATGTTTTCTTCCCGAGTATTCCAAATACCTTCGAAGTTGTTTTTGAGCAACACTTTACTTCAAACATTAACTATTGCTATCAAATTTGGAAAAAGGGTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002859","ARO_id":"39293","ARO_name":"dfrA14","CARD_short_name":"dfrA14","ARO_description":"dfrA14 is an integron-encoded dihydrofolate reductase found in Escherichia coli.","ARO_category":{"37617":{"category_aro_accession":"3001218","category_aro_cvterm_id":"37617","category_aro_name":"trimethoprim resistant dihydrofolate reductase dfr","category_aro_description":"Alternative dihydropteroate synthase dfr present on plasmids produces alternate proteins that are less sensitive to trimethoprim from inhibiting its role in folate synthesis, thus conferring trimethoprim resistance.","category_aro_class_name":"AMR Gene Family"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1593":{"model_id":"1593","model_name":"CMY-99","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1860":{"protein_sequence":{"accession":"AGU59995.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYSNSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYARGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPATAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"KF305673.1","fmin":"17","fmax":"1163","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACTCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCCGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCACCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3002070","ARO_id":"38470","ARO_name":"CMY-99","CARD_short_name":"CMY-99","ARO_description":"CMY-99 is a beta-lactamase found in Proteus mirabilis.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1595":{"model_id":"1595","model_name":"mecB","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1300"}},"model_sequences":{"sequence":{"3282":{"protein_sequence":{"accession":"BAI83385.1","sequence":"MKNKALAILIICICLLIAYNFVKKDEVDKIFDAIELRDSEYLNEHATFLSKSLYDKDQRYKRMDKIDASLGIKEVKVSNVRLVQKKKNKRQYSANLNFRTKYGNFSREGNYSFEKDEITKKWLLDWSPEVIIPGLTDRNQISIETLESFRGKILDRNGIDIAKDGIHYEVGIDIKNLNKKNKKNISKLLSISESTLNKKLKQTWVKEGVFLPLKSYIELDDELKLGIQKYHLTVNQTKGRVYPLREATVHLLGYVGEINAEELKNKKFKDYDEHSIVGKSGIELQYDKQLQNKDGYKVVITSDDALNNDEDVLLEKKPKNGQDIILTIDSKVQRSIYSHLKEDNGSGVAMNPKTGELLALVSYPAYDPYEFMFGISDENYKKIVNDKKEPLLNKFQTTSSPGSTQKLITSIIGLKNGTIDASTSYNIVTKGWQRNSSWGGYEVTRFEEVNGDIDLEKAIAHSDNIFFARATLDMGSEKFIKGMKALDIGRNIPSDYYFQKGQIANPESLKNNFKNEILLADSGYGQGEILISPVQILSIYSSLINEGKMMKPKLFETTKEDIWKNHIISKDDVDILTRSMRKVVTGTHRLDAERNYAQFAGKTGTAELKTSREEGLGAQIGWFVGYDQNNPNMMLGISVKNVENKGMSSYNARKFAEIMDELYENGTKKYEIDR"},"dna_sequence":{"accession":"AB498758.1","fmin":"3737","fmax":"5762","strand":"+","sequence":"ATGAAAAATAAAGCTTTAGCAATTTTAATTATATGTATTTGCCTTTTAATAGCATATAATTTTGTGAAAAAAGATGAAGTTGATAAAATATTTGATGCTATTGAATTAAGGGATTCGGAATATCTGAATGAACATGCGACATTCTTATCTAAAAGTCTTTACGACAAAGATCAGAGATATAAAAGAATGGATAAGATTGATGCTTCTCTTGGTATTAAAGAAGTGAAAGTTAGTAATGTACGACTCGTGCAAAAGAAAAAAAATAAACGTCAATATAGTGCAAATTTAAATTTTAGAACTAAATATGGTAATTTTTCTAGAGAAGGGAACTATTCTTTTGAAAAGGATGAAATAACAAAAAAATGGCTTTTGGATTGGTCACCTGAGGTTATAATACCGGGATTGACTGATAGAAATCAAATCAGTATAGAAACCTTGGAATCTTTCAGAGGGAAAATACTAGACAGAAACGGGATTGATATAGCGAAAGACGGAATTCATTACGAAGTTGGAATAGATATTAAAAATTTAAATAAAAAAAATAAGAAAAATATTTCAAAATTGTTATCAATAAGTGAATCGACACTAAATAAAAAGTTAAAACAAACATGGGTAAAAGAAGGTGTTTTTTTACCTTTAAAATCGTACATAGAGTTGGATGATGAACTTAAATTGGGTATCCAAAAATATCATTTGACGGTTAATCAAACAAAAGGTAGGGTTTATCCATTAAGAGAAGCAACAGTACATCTTTTAGGGTATGTTGGAGAAATTAATGCTGAAGAATTAAAGAATAAAAAGTTTAAGGATTATGATGAACACTCAATCGTAGGAAAAAGTGGTATCGAACTACAATATGATAAACAATTGCAAAATAAAGATGGTTATAAAGTTGTCATAACTAGTGATGATGCATTAAATAATGATGAAGATGTCTTGTTAGAAAAGAAACCAAAAAATGGACAGGACATTATATTAACAATTGATAGCAAAGTACAAAGAAGTATATATAGTCATTTAAAAGAAGATAATGGTTCAGGAGTAGCCATGAATCCTAAAACTGGTGAATTATTAGCTTTAGTTAGTTATCCTGCATATGACCCCTATGAGTTTATGTTCGGCATTTCCGACGAAAACTACAAAAAGATAGTTAATGATAAGAAAGAGCCCCTGTTAAATAAATTTCAGACAACCTCTTCCCCAGGATCTACTCAGAAATTAATAACATCTATCATAGGTTTGAAAAATGGGACTATAGACGCATCAACCAGCTACAACATAGTAACTAAGGGATGGCAGAGAAATTCTTCATGGGGAGGATATGAAGTTACAAGGTTTGAGGAAGTTAATGGAGATATTGATTTAGAAAAAGCGATAGCACATTCTGATAATATATTTTTTGCAAGAGCTACCCTCGATATGGGTTCCGAAAAATTTATTAAGGGCATGAAAGCTTTAGACATTGGGAGAAATATTCCTTCTGATTATTATTTTCAAAAAGGACAAATTGCAAATCCAGAAAGTTTAAAAAATAATTTTAAAAATGAAATATTACTAGCTGATTCAGGATATGGCCAGGGAGAAATACTTATAAGTCCAGTACAAATATTATCTATTTATAGTTCTTTAATTAATGAAGGTAAAATGATGAAACCTAAATTATTTGAAACAACAAAAGAAGATATTTGGAAAAATCATATTATTTCAAAAGATGACGTAGATATATTAACAAGAAGCATGAGAAAAGTAGTTACTGGGACACATAGATTGGATGCAGAAAGAAATTATGCACAGTTTGCTGGAAAAACTGGCACTGCAGAATTGAAAACCTCTAGAGAAGAGGGGTTAGGAGCTCAAATCGGTTGGTTTGTTGGATATGATCAAAATAATCCCAATATGATGTTAGGTATAAGTGTGAAGAATGTAGAGAATAAAGGTATGTCGAGTTATAATGCAAGAAAGTTTGCCGAGATAATGGATGAATTATATGAAAATGGAACGAAAAAATATGAAATAGATAGGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40025","NCBI_taxonomy_name":"Macrococcus caseolyticus","NCBI_taxonomy_id":"69966"}}}},"ARO_accession":"3003440","ARO_id":"40024","ARO_name":"mecB","CARD_short_name":"mecB","ARO_description":"A foreign PBP2 acquired by lateral gene transfer that able to perform peptidoglycan synthesis in the presence of beta-lactams.","ARO_category":{"37589":{"category_aro_accession":"3001208","category_aro_cvterm_id":"37589","category_aro_name":"methicillin resistant PBP2","category_aro_description":"In methicillin sensitive S. aureus (MSSA), beta-lactams bind to native penicillin-binding proteins (PBPs) and disrupt synthesis of the cell membrane's peptidoglycan layer. In methicillin resistant S. aureus (MRSA), foreign PBP2a acquired by lateral gene transfer is able to perform peptidoglycan synthesis in the presence of beta-lactams.","category_aro_class_name":"AMR Gene Family"},"35934":{"category_aro_accession":"0000015","category_aro_cvterm_id":"35934","category_aro_name":"methicillin","category_aro_description":"Derived from penicillin to combat penicillin-resistance, methicillin is insensitive to beta-lactamases (also known as penicillinases) secreted by many penicillin-resistant bacteria. Methicillin is bactericidal, and acts by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1596":{"model_id":"1596","model_name":"OXA-24","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1607":{"protein_sequence":{"accession":"AAM34291.1","sequence":"MKKFILPIFSISILVSLSACSSIKTKSEDNFHISSQQHEKAIKSYFDEAQTQGVIIIKEGKNLSTYGNALARANKEYVPASTFKMLNALIGLENHKATTNEIFKWDGKKRTYPMWEKDMTLGEAMALSAVPVYQELARRTGLELMQKEVKRVNFGNTNIGTQVDNFWLVGPLKITPVQEVNFADDLAHNRLPFKLETQEEVKKMLLIKEVNGSKIYAKSGWGMGVTPQVGWLTGWVEQANGKKIPFSLNLEMKEGMSGSIRNEITYKSLENLGII"},"dna_sequence":{"accession":"AF509241.1","fmin":"0","fmax":"828","strand":"+","sequence":"ATGAAAAAATTTATACTTCCTATATTCAGCATTTCTATTCTAGTTTCTCTCAGTGCATGTTCATCTATTAAAACTAAATCTGAAGATAATTTTCATATTTCTTCTCAGCAACATGAAAAAGCTATTAAAAGCTATTTTGATGAAGCTCAAACACAGGGTGTAATTATTATTAAAGAGGGTAAAAATCTTAGCACCTATGGTAATGCTCTTGCACGAGCAAATAAAGAATATGTCCCTGCATCAACATTTAAGATGCTAAATGCTTTAATCGGGCTAGAAAATCATAAAGCAACAACAAATGAGATTTTCAAATGGGATGGTAAAAAAAGAACTTATCCTATGTGGGAGAAAGATATGACTTTAGGTGAGGCAATGGCATTGTCAGCAGTTCCAGTATATCAAGAGCTTGCAAGACGGACTGGCCTAGAGCTAATGCAGAAAGAAGTAAAGCGGGTTAATTTTGGAAATACAAATATTGGAACACAGGTCGATAATTTTTGGTTAGTTGGCCCCCTTAAAATTACACCAGTACAAGAAGTTAATTTTGCCGATGACCTTGCACATAACCGATTACCTTTTAAATTAGAAACTCAAGAAGAAGTTAAAAAAATGCTTCTAATTAAAGAAGTAAATGGTAGTAAGATTTATGCAAAAAGTGGATGGGGAATGGGTGTTACTCCACAGGTAGGTTGGTTGACTGGTTGGGTGGAGCAAGCTAATGGAAAAAAAATCCCCTTTTCGCTCAACTTAGAAATGAAAGAAGGAATGTCTGGTTCTATTCGTAATGAAATTACTTATAAGTCGCTAGAAAATCTTGGAATCATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001419","ARO_id":"37819","ARO_name":"OXA-24","CARD_short_name":"OXA-24","ARO_description":"OXA-24 is a beta-lactamase found in A. baumannii and P. aeruginosa.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46500":{"category_aro_accession":"3007711","category_aro_cvterm_id":"46500","category_aro_name":"OXA-24-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-24.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"40512":{"category_aro_accession":"3003821","category_aro_cvterm_id":"40512","category_aro_name":"BAL30072","category_aro_description":"BAL30072 is a monocyclic beta-lactam antibiotic belonging to the sulfactams. BAL30072 was found to trigger the spheroplasting and lysis of Escherichia coli rather than the formation of extensive filaments.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1597":{"model_id":"1597","model_name":"SHV-2A","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"833":{"protein_sequence":{"accession":"CAA66730.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGASERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"X98102.1","fmin":"73","fmax":"934","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTACTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGTTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTAGCGAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001061","ARO_id":"37441","ARO_name":"SHV-2A","CARD_short_name":"SHV-2A","ARO_description":"SHV-2A is an extended-spectrum beta-lactamase found in Enterobacter cloacae, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Salmonella enterica.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1598":{"model_id":"1598","model_name":"OXA-101","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1042":{"protein_sequence":{"accession":"CAL85435.1","sequence":"MKTFAAYVITACLSSTALASSITENTFWNKEFSAEAVNGVFVLCKSSSKSCATNNLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLSLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLFLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKGTEVYFFAFNMDIDNENKLPLRKSIPTKIMASEGIIGG"},"dna_sequence":{"accession":"AM412777.1","fmin":"117","fmax":"918","strand":"+","sequence":"ATGAAAACATTTGCCGCATATGTAATTACTGCGTGTCTTTCAAGTACGGCATTAGCTAGTTCAATTACAGAAAATACGTTTTGGAACAAAGAGTTCTCTGCCGAAGCCGTCAATGGTGTTTTCGTGCTTTGTAAAAGTAGCAGTAAATCCTGCGCTACCAATAACTTAGCTCGTGCATCAAAGGAATATCTTCCAGCATCAACATTTAAGATCCCCAACGCAATTATCGGCCTAGAAACTGGTGTCATAAAGAATGAGCATCAGGTTTTCAAATGGGACGGAAAGCCAAGAGCCATGAAACAATGGGAAAGAGACTTGAGCTTAAGAGGGGCAATACAAGTTTCAGCGGTTCCCGTATTTCAACAAATCGCCAGAGAAGTTGGCGAAGTAAGAATGCAGAAATATCTTAAAAAATTTTCATATGGTAACCAGAATATCAGTGGTGGCATTGACAAATTCTGGTTGGAGGGTCAGCTTAGAATTTCCGCAGTTAATCAAGTGGAGTTTCTAGAGTCTCTATTTTTAAATAAATTGTCAGCATCAAAAGAAAATCAGCTAATAGTAAAAGAGGCTTTGGTAACGGAGGCTGCGCCTGAATATCTTGTGCATTCAAAAACTGGTTTTTCTGGTGTGGGAACTGAGTCAAATCCTGGTGTCGCATGGTGGGTTGGTTGGGTTGAGAAGGGAACAGAGGTTTACTTTTTCGCCTTTAACATGGATATAGACAACGAAAATAAGTTGCCGCTAAGAAAATCCATTCCCACCAAAATCATGGCAAGTGAGGGCATCATTGGTGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3001439","ARO_id":"37839","ARO_name":"OXA-101","CARD_short_name":"OXA-101","ARO_description":"OXA-101 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46486":{"category_aro_accession":"3007697","category_aro_cvterm_id":"46486","category_aro_name":"OXA-10-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-10.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1599":{"model_id":"1599","model_name":"SHV-23","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1560":{"protein_sequence":{"accession":"AAF34337.1","sequence":"MLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGEFCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAGTLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGASKRGARGIVALLGPNNKAERIVVIYLRDTPASMAERN"},"dna_sequence":{"accession":"AF117747.1","fmin":"0","fmax":"780","strand":"+","sequence":"CTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAATTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTACTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGGGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTAGCAAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAAT","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001081","ARO_id":"37461","ARO_name":"SHV-23","CARD_short_name":"SHV-23","ARO_description":"SHV-23 is an extended-spectrum beta-lactamase that has been found in clinical isolates.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1601":{"model_id":"1601","model_name":"LRA-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"4688":{"protein_sequence":{"accession":"ACH58980.1","sequence":"MNPPIHRRTLLLAASVLPLASACTAWSAKGPQQDASAQLAALEAASGSRLGVVGFNTATGARVQHRAEERFPFCSTFKLMLAAAVLERSAKEGDLLARRVNYSKGDLVSYSPITEKNVATGMTVAELCAATVQYSDNGAANLLMKILGGPSAVTAFARASGDEVFRLDRWETELNTAIPGDLRDTTTPAAMAASVQRLVLGNALGAAQREQLKTWLLGNTTSTQRFLAGVPAGWKVGDKTGSGSYGTTNDVGVLWPPAGAPLVLAVYLTFPQKEAKGRSDVVASATRIAVSALAS"},"dna_sequence":{"accession":"EU408346.1","fmin":"4825","fmax":"5713","strand":"-","sequence":"ATGAATCCTCCAATCCATCGCCGCACCCTGTTGCTCGCCGCCTCGGTCCTCCCGCTCGCAAGCGCCTGCACCGCGTGGTCCGCCAAGGGGCCGCAGCAAGACGCATCGGCGCAGCTCGCCGCGCTCGAAGCCGCATCGGGCAGCCGGCTCGGTGTGGTCGGTTTCAACACCGCCACCGGCGCGCGCGTGCAGCACCGTGCCGAGGAACGCTTTCCGTTCTGCAGCACCTTCAAGCTCATGCTGGCCGCGGCCGTCCTCGAACGCAGCGCGAAAGAGGGCGACCTGCTCGCGCGCCGCGTCAACTACAGCAAGGGCGACCTGGTCTCCTACTCGCCCATCACCGAAAAGAATGTGGCGACCGGCATGACGGTGGCCGAGCTGTGCGCCGCCACCGTCCAGTACAGCGACAACGGCGCGGCCAACCTGCTGATGAAGATCCTGGGCGGCCCGTCCGCCGTGACGGCCTTTGCGCGTGCCTCCGGCGACGAGGTCTTCAGGCTGGACCGCTGGGAGACCGAACTCAACACCGCCATCCCCGGCGACCTGCGCGACACCACCACGCCCGCGGCCATGGCGGCAAGCGTGCAGCGGCTGGTGCTGGGCAACGCGCTGGGCGCGGCACAGCGCGAGCAGCTCAAGACCTGGTTGCTGGGCAACACCACGAGCACCCAGCGCTTCCTGGCCGGCGTGCCCGCCGGCTGGAAGGTGGGCGACAAGACCGGTTCGGGCTCCTACGGCACCACGAACGACGTGGGCGTGCTGTGGCCGCCGGCCGGCGCGCCGCTGGTGCTGGCGGTCTACCTGACGTTTCCGCAGAAGGAGGCGAAGGGGCGCAGCGATGTGGTTGCGTCGGCGACGCGCATTGCGGTGAGCGCGCTGGCGAGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39079","NCBI_taxonomy_name":"uncultured bacterium BLR1","NCBI_taxonomy_id":"506512"}}}},"ARO_accession":"3002482","ARO_id":"38882","ARO_name":"LRA-1","CARD_short_name":"LRA-1","ARO_description":"LRA-1 is a beta-lactamase isolated from soil samples in Alaska.","ARO_category":{"41392":{"category_aro_accession":"3004228","category_aro_cvterm_id":"41392","category_aro_name":"class A LRA beta-lactamase","category_aro_description":"Beta-lactamases that are part of the LRA gene family and are classified as Class A beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1602":{"model_id":"1602","model_name":"AAC(6')-Iai","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"708":{"protein_sequence":{"accession":"ACI28880.1","sequence":"MKYTIIDIKDSETYITQAAEILFDVFSEISPESWPTLQKAKEDVIECIEGENICIGIIINKELIGWIGLREMYKKTWELHPMVIKKTHHNMGFGKILINEIEKKARERNLEGIVLGTDDETYRTSLSMIELNNENILQEIKNIRNLENHPYEFYKKCGYCIIGVIPNANGKNKPDILMWKNIMEENCG"},"dna_sequence":{"accession":"EU886977.1","fmin":"543","fmax":"1110","strand":"+","sequence":"ATGAAATACACTATTATTGATATTAAAGATTCAGAAACGTACATTACTCAAGCTGCAGAAATATTATTTGATGTATTTTCAGAAATAAGCCCAGAATCATGGCCAACACTCCAAAAAGCAAAAGAAGATGTTATTGAATGTATAGAAGGTGAAAACATTTGCATTGGCATTATAATAAATAAAGAATTAATTGGATGGATTGGATTAAGAGAAATGTATAAAAAAACATGGGAATTACATCCTATGGTTATCAAGAAAACACATCATAATATGGGATTTGGAAAAATACTAATTAATGAAATAGAAAAAAAAGCAAGAGAAAGAAATTTAGAAGGTATTGTACTTGGAACAGATGATGAAACATATAGAACTTCATTATCAATGATTGAATTAAATAATGAAAATATTTTGCAAGAAATAAAGAATATTAGAAATTTAGAAAATCATCCTTATGAATTTTATAAAAAATGTGGATATTGTATTATTGGTGTAATTCCAAACGCAAATGGGAAGAATAAGCCAGATATATTAATGTGGAAAAATATTATGGAAGAAAATTGCGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002575","ARO_id":"38975","ARO_name":"AAC(6')-Iai","CARD_short_name":"AAC(6')-Iai","ARO_description":"AAC(6')-Iai is an aminoglycoside acetyltransferase encoded by plasmids and integrons in P. aeruginosa.","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"A category of aminoglycoside N-acetyltransferase enzymes with modification regiospecificity based at the 6'-amino group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics through acetylation of the 6-amino group of the compound.","category_aro_class_name":"AMR Gene Family"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"46128":{"category_aro_accession":"3007378","category_aro_cvterm_id":"46128","category_aro_name":"2'-N-ethylnetilmicin","category_aro_description":"2'-N-ethylnetilmicin is an aminoglycoside antibiotic and a derivative of netilmicin.","category_aro_class_name":"Antibiotic"},"46129":{"category_aro_accession":"3007379","category_aro_cvterm_id":"46129","category_aro_name":"5-episisomicin","category_aro_description":"5-episosomicin is a semisynthetic aminoglycoside antibiotic similar to sisomicin.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1603":{"model_id":"1603","model_name":"SHV-86","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1564":{"protein_sequence":{"accession":"ABC58727.1","sequence":"MRFIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGASRRGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"DQ328802.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTTTATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTAGCAGGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001140","ARO_id":"37520","ARO_name":"SHV-86","CARD_short_name":"SHV-86","ARO_description":"SHV-86 is an extended-spectrum beta-lactamase that has been found in clinical isolates.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1604":{"model_id":"1604","model_name":"CTX-M-84","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1257":{"protein_sequence":{"accession":"ACI29346.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVAWLKGNTTGAASIRAGLPTSWTVGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"FJ214367.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGGCGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGACTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35667","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Derby","NCBI_taxonomy_id":"28144"}}}},"ARO_accession":"3001945","ARO_id":"38345","ARO_name":"CTX-M-84","CARD_short_name":"CTX-M-84","ARO_description":"CTX-M-84 is a beta-lactamase found in Salmonella enterica.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1605":{"model_id":"1605","model_name":"cphA5","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"1501":{"protein_sequence":{"accession":"AAP69913.1","sequence":"MMKGWIKCGLAGAVVLVASFWGGSVHAAAISLTQVSGPVYVVEDNYYVKENSMVYFGAKGVTIVGATWTPDTARELHKLIKRVNNKPVLEVINTNYHTGQAGGNAYWKSIGAKVVSTRQTRDLMKSDWAEIVAFTRKGLPEYPDLPLVLPNVVHDGDFNLQEGKVRAFYAGPAHTPDGIFVYFPDQQVLYGNCILKEKLGNLSFADVKAYPQTLERLKAMKLPIKIVVGGHDSPLHGPELIDHYQALIKAATHS"},"dna_sequence":{"accession":"AY227051.1","fmin":"0","fmax":"765","strand":"+","sequence":"ATGATGAAAGGTTGGATAAAGTGCGGGCTGGCCGGAGCTGTGGTGCTGGTGGCGAGTTTCTGGGGCGGCAGCGTGCATGCGGCGGCGATCTCCCTCACTCAGGTAAGCGGCCCTGTCTATGTGGTGGAGGATAACTACTACGTCAAAGAGAACTCCATGGTTTATTTCGGAGCCAAGGGAGTGACGATAGTGGGGGCGACCTGGACGCCGGATACCGCCCGCGAGCTGCACAAGCTGATCAAACGGGTCAACAACAAGCCTGTGCTGGAGGTGATCAACACCAACTACCACACCGGACAGGCAGGGGGTAACGCCTACTGGAAGTCCATCGGTGCCAAGGTGGTCTCGACCCGCCAGACCCGGGATCTGATGAAGAGCGACTGGGCCGAGATCGTCGCCTTTACCCGCAAGGGGCTGCCGGAGTACCCGGACTTGCCGCTGGTGCTGCCGAACGTGGTGCACGATGGTGACTTCAATCTGCAAGAGGGCAAGGTGCGCGCCTTCTATGCGGGCCCGGCCCACACGCCGGACGGCATCTTTGTCTACTTCCCTGACCAGCAGGTGCTCTATGGCAACTGCATCCTCAAGGAGAAGCTGGGCAACCTGAGCTTTGCCGATGTGAAGGCGTATCCGCAGACGCTGGAGCGGCTGAAAGCGATGAAGCTGCCCATCAAGATTGTGGTTGGCGGTCACGACTCGCCGCTGCACGGCCCCGAGTTGATTGATCACTACCAGGCGCTGATCAAGGCCGCTACTCACTCATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36795","NCBI_taxonomy_name":"Aeromonas salmonicida","NCBI_taxonomy_id":"645"}}}},"ARO_accession":"3003101","ARO_id":"39667","ARO_name":"cphA5","CARD_short_name":"cphA5","ARO_description":"cphA5 is an Ambler Class B MBL; subclass B2 originally isolated from Aeromonas salmonicida. This enzyme has specific activity against carbapenems and is active as a mono-zinc protein.","ARO_category":{"36720":{"category_aro_accession":"3000581","category_aro_cvterm_id":"36720","category_aro_name":"CphA beta-lactamase","category_aro_description":"CphA is an Ambler Class B MBL; subclass B2 originally isolated from Aeromonas hydrophilia.  This enzyme has specific activity against carbapenems and is active as a mono-zinc protein.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1606":{"model_id":"1606","model_name":"CTX-M-16","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"767":{"protein_sequence":{"accession":"AAK32961.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTAGDKTGSGGYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"AY029068.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAGCTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCACAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGCAGGTGATAAGACCGGCAGCGGCGGCTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001879","ARO_id":"38279","ARO_name":"CTX-M-16","CARD_short_name":"CTX-M-16","ARO_description":"CTX-M-16 is a beta-lactamase found in Escherichia coli.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1609":{"model_id":"1609","model_name":"QnrC","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"508":{"protein_sequence":{"accession":"ACK75961.1","sequence":"MNYSHKTYDQIDFSGQDLSSHHFSHCKFFGCNFNRVNLRDAKFMGCTFIESNDFEGCNFIYADLRDASFMNCMLSMANFQGANCFGLELRECDLKGANFSQANFVNHVSNKMYFCSAYITGCNLSYANFDKQCLEKCDLFENKWVGASLQGASFKESDLSRGSFSDDFWEQCRIQGCDLTHSELNGLEPRKVDLTGVKICSWQQEQLLEQLGVIVIPDKVF"},"dna_sequence":{"accession":"EU917444.1","fmin":"1716","fmax":"2382","strand":"+","sequence":"TTGAATTATTCCCATAAAACGTACGATCAAATTGATTTTTCCGGCCAAGATTTGAGCTCTCATCACTTTTCTCACTGTAAATTTTTTGGTTGTAATTTTAATCGAGTGAATTTACGTGATGCTAAATTCATGGGTTGTACATTTATTGAATCGAATGATTTTGAAGGATGTAATTTTATCTATGCAGACCTACGAGATGCTTCATTTATGAATTGCATGCTTTCAATGGCGAATTTCCAAGGGGCAAACTGTTTTGGCCTTGAATTGAGAGAATGCGATTTAAAAGGTGCTAATTTCTCACAGGCAAACTTTGTTAATCATGTTTCTAACAAAATGTATTTTTGCTCTGCTTACATTACGGGTTGTAATTTGTCTTATGCTAATTTCGATAAGCAATGCCTTGAAAAGTGTGATTTATTTGAAAATAAATGGGTAGGTGCAAGCCTGCAAGGGGCCTCTTTTAAAGAGTCAGACTTAAGTAGGGGATCATTTTCTGATGACTTTTGGGAGCAATGCAGAATTCAGGGGTGTGATCTCACTCATTCAGAATTAAATGGCTTAGAACCTCGTAAAGTGGATTTAACTGGCGTGAAAATTTGTTCATGGCAACAAGAGCAGCTTTTGGAGCAGTTGGGGGTGATTGTTATTCCAGACAAAGTGTTTTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3002787","ARO_id":"39221","ARO_name":"QnrC","CARD_short_name":"QnrC","ARO_description":"QnrC is a plasmid-mediated quinolone resistance protein found in Proteus mirabilis.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1610":{"model_id":"1610","model_name":"OXA-74","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1305":{"protein_sequence":{"accession":"CAH69530.1","sequence":"MKTFAAYVIIACLSSTALAGSITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPVSTFKIPSAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGIIGG"},"dna_sequence":{"accession":"AJ854182.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGAAAACATTTGCCGCATATGTAATTATCGCGTGTCTTTCGAGTACGGCATTAGCTGGTTCAATTACAGAAAATACGTCTTGGAACAAAGAGTTCTCTGCCGAAGCCGTCAATGGTGTCTTCGTGCTTTGTAAAAGTAGCAGTAAATCCTGCGCTACCAATGACTTAGCTCGTGCATCAAAGGAATATCTTCCAGTATCAACATTTAAGATCCCCAGCGCAATTATCGGCCTAGAAACTGGTGTCATAAAGAATGAGCATCAGGTTTTCAAATGGGACGGAAAGCCAAGAGCCATGAAGCAATGGGAAAGAGACTTGACCTTAAGAGGGGCAATACAAGTTTCAGCTGTTCCCGTATTTCAACAAATCGCCAGAGAAGTTGGCGAAGTAAGAATGCAGAAATACCTTAAAAAATTTTCCTATGGCAACCAGAATATCAGTGGTGGCATTGACAAATTCTGGTTGGAAGGCCAGCTTAGAATTTCCGCAGTTAATCAAGTGGAGTTTCTAGAGTCTCTATATTTAAATAAATTGTCAGCATCTAAAGAAAACCAGCTAATAGTAAAAGAGGCTTTGGTAACGGAGGCGGCACCTGAATATCTAGTGCATTCAAAAACTGGTTTTTCTGGTGTGGGAACTGAGTCAAATCCTGGTGTCGCATGGTGGGTTGGGTGGGTTGAGAAGGAGACAGAGGTTTACTTTTTCGCCTTTAACATGGATATAGACAACGAAAGTAAGTTGCCGCTAAGAAAATCCATTCCCACCAAAATCATGGAAAGTGAGGGCATCATTGGTGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3001798","ARO_id":"38198","ARO_name":"OXA-74","CARD_short_name":"OXA-74","ARO_description":"OXA-74 is a beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46486":{"category_aro_accession":"3007697","category_aro_cvterm_id":"46486","category_aro_name":"OXA-10-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-10.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1611":{"model_id":"1611","model_name":"SME-4","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"1565":{"protein_sequence":{"accession":"AHA49908.1","sequence":"MSNKVNFKTASFLFSVCLALSAFNAHANKSDAAAKQIKKLEEDFDGRIGVFAIDTGSGNTFGYRSDERFPLCSSFKGFLAAAVLERVQQKKLDINQKVKYESRDLEYHSPITTKYKGSGMTLGDMASAALQYSDNGATNIIMERFLGGPEGMTKFMRSIGDNEFRLDRWELELNTAIPGDKRDTSTPKAVANSLNKLALGNVLNAKVKAIYQNWLKGNTTGDARIRASVPADWVVGDKTGSCGAYGTANDYAVIWPKNRAPLIVSIYTTRKSKDDKHSDKTIAEASRIAIQAID"},"dna_sequence":{"accession":"KF481967.1","fmin":"0","fmax":"885","strand":"+","sequence":"ATGTCAAACAAAGTAAATTTTAAAACGGCTTCATTTTTGTTTAGTGTTTGTTTAGCTTTGTCGGCATTTAATGCTCATGCTAACAAAAGTGATGCTGCGGCAAAACAAATAAAAAAATTAGAGGAAGACTTTGATGGGAGGATTGGCGTCTTTGCAATAGATACAGGATCGGGTAATACATTTGGGTATAGATCAGATGAGCGGTTCCCTTTATGCAGTTCATTTAAAGGTTTTTTGGCGGCTGCTGTTTTAGAGAGGGTGCAACAAAAAAAACTAGATATCAACCAAAAGGTTAAATATGAGAGTAGGGATCTAGAATATCATTCACCTATTACAACAAAATATAAAGGCTCAGGTATGACATTAGGTGATATGGCTTCTGCTGCATTGCAATATAGCGACAATGGGGCAACAAATATAATTATGGAACGATTTCTTGGCGGTCCTGAGGGGATGACTAAATTTATGCGTTCTATTGGAGATAATGAGTTTAGGTTAGATCGCTGGGAACTGGAACTTAACACTGCAATCCCAGGAGATAAACGTGACACTTCAACGCCAAAAGCTGTTGCAAATAGTTTGAATAAACTAGCTTTGGGGAATGTTCTCAATGCTAAAGTGAAAGCGATTTATCAAAATTGGTTAAAAGGTAATACAACTGGTGATGCTCGAATTCGTGCTAGTGTTCCTGCTGATTGGGTTGTAGGTGACAAAACTGGGAGCTGTGGGGCATATGGTACTGCGAATGATTATGCCGTCATTTGGCCTAAAAATAGAGCACCATTAATTGTCTCTATATATACAACACGAAAATCGAAAGATGATAAGCACAGTGATAAAACTATTGCGGAAGCATCACGTATTGCAATTCAGGCAATTGATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36783","NCBI_taxonomy_name":"Serratia marcescens","NCBI_taxonomy_id":"615"}}}},"ARO_accession":"3002382","ARO_id":"38782","ARO_name":"SME-4","CARD_short_name":"SME-4","ARO_description":"SME-4 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36194":{"category_aro_accession":"3000055","category_aro_cvterm_id":"36194","category_aro_name":"SME beta-lactamase","category_aro_description":"SME beta-lactamases are chromosome-mediated class A beta-lactamases that hydrolyze carbapenems in Serratia marcescens.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1612":{"model_id":"1612","model_name":"ErmR","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"8141":{"protein_sequence":{"accession":"AAU93796.1","sequence":"MAGPQDRPRGRGPSSGRPQRPVGGRSQRDRDRRVLGQNFLRDPATIRRIADAADVDPDGLVVEAGPGEGLLTRELARRAGRVRTYELDQRLARRLSTDLAQETSIEVVHADFLTAPHPEEPFQFVGAIPYGITSAIVDWCLTAPTLTSATLVTQQEFARKRTGDYGRWTALTVTTWPTFEWQYVAKVDRTLFTPVPRVHSAIMRLRRRPQPLLRDAAARSRFADMVEIGFVGKGGSLYRSLTREWPRSKVDSAFARADVHHDEIVAFVHPDQWITLFQLLDGSRGGAARGPGDQRGRRGRPGGGPRPDGRAGGGPRRDAGGRRTGDGRGGRPRPPRGGQA"},"dna_sequence":{"accession":"AY623658.2","fmin":"12449","fmax":"13472","strand":"+","sequence":"ATGGCAGGTCCGCAAGACCGTCCGCGAGGGCGCGGACCCTCCTCCGGTCGCCCGCAGCGGCCGGTGGGCGGCCGCAGCCAGCGCGACCGCGACCGGCGGGTCCTCGGCCAGAACTTCCTGCGCGACCCGGCGACCATCCGGCGCATCGCCGACGCCGCCGACGTCGACCCCGACGGGCTCGTCGTCGAGGCGGGTCCCGGCGAAGGGCTGCTCACCCGCGAGCTCGCCCGACGCGCCGGGCGGGTACGCACCTACGAGCTGGACCAGCGCCTCGCGCGACGACTCTCGACCGACCTGGCCCAGGAGACGAGCATCGAGGTCGTCCACGCCGACTTCCTGACCGCGCCTCACCCCGAGGAGCCGTTCCAGTTCGTCGGCGCGATCCCCTACGGCATCACCTCCGCCATCGTCGACTGGTGCCTGACCGCCCCGACCCTGACGTCGGCGACCCTCGTGACCCAGCAGGAGTTCGCGCGCAAGCGGACGGGTGACTACGGACGGTGGACGGCCCTCACCGTCACCACGTGGCCGACCTTCGAGTGGCAGTACGTCGCCAAGGTCGACCGCACGCTGTTCACACCGGTGCCGCGCGTGCACTCCGCGATCATGCGGCTGCGCCGCCGCCCACAGCCCCTCCTGCGCGACGCGGCGGCGAGGTCGCGCTTCGCGGACATGGTGGAGATCGGCTTCGTCGGCAAGGGCGGCAGCCTCTACCGGTCGCTGACCCGGGAGTGGCCGCGCTCGAAGGTCGACAGCGCGTTCGCGCGCGCCGACGTCCACCACGACGAGATCGTCGCCTTCGTGCACCCCGACCAGTGGATCACGCTGTTCCAGCTCCTCGACGGGTCCCGTGGCGGCGCCGCGCGCGGACCGGGCGACCAGCGGGGGCGGCGCGGCCGCCCAGGCGGAGGCCCCCGGCCGGACGGTCGCGCGGGCGGCGGCCCGCGCCGCGACGCGGGCGGGCGCCGCACGGGTGACGGACGCGGAGGTCGCCCCCGTCCCCCGCGCGGCGGCCAGGCCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40506","NCBI_taxonomy_name":"Aeromicrobium erythreum","NCBI_taxonomy_id":"2041"}}}},"ARO_accession":"3000594","ARO_id":"36733","ARO_name":"ErmR","CARD_short_name":"ErmR","ARO_description":"ErmR is a methyltransferase found in the erythromycin producer Aeromicrobium erythreum. Like other Erm enzymes, it catalyzes the methylation of A2058 of the 23S ribosomal RNA. The gene is found within the erythromycin biosynthetic cluster and is responsible for self-resistance.","ARO_category":{"36699":{"category_aro_accession":"3000560","category_aro_cvterm_id":"36699","category_aro_name":"Erm 23S ribosomal RNA methyltransferase","category_aro_description":"Erm proteins are part of the RNA methyltransferase family and methylate A2058 (E. coli nomenclature) of the 23S ribosomal RNA conferring degrees of resistance to Macrolides, Lincosamides and Streptogramin b. This is called the MLSb phenotype.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35946":{"category_aro_accession":"0000027","category_aro_cvterm_id":"35946","category_aro_name":"roxithromycin","category_aro_description":"Roxithromycin is a semi-synthetic, 14-carbon ring macrolide antibiotic derived from erythromycin. It is used to treat respiratory tract, urinary and soft tissue infections. Roxithromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35974":{"category_aro_accession":"0000057","category_aro_cvterm_id":"35974","category_aro_name":"telithromycin","category_aro_description":"Telithromycin is a semi-synthetic derivative of erythromycin. It is a 14-membered macrolide and is the first ketolide antibiotic to be used in clinics. Telithromycin binds the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"35982":{"category_aro_accession":"0000065","category_aro_cvterm_id":"35982","category_aro_name":"clarithromycin","category_aro_description":"Clarithromycin is a methyl derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome and is used to treat pharyngitis, tonsillitis, acute maxillary sinusitis, acute bacterial exacerbation of chronic bronchitis, pneumonia (especially atypical pneumonias associated with Chlamydia pneumoniae or TWAR), and skin structure infections.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"36284":{"category_aro_accession":"3000145","category_aro_cvterm_id":"36284","category_aro_name":"tylosin","category_aro_description":"Tylosin is a 16-membered macrolide, naturally produced by Streptomyces fradiae. It interacts with the bacterial ribosome 50S subunit to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"36295":{"category_aro_accession":"3000156","category_aro_cvterm_id":"36295","category_aro_name":"spiramycin","category_aro_description":"Spiramycin is a 16-membered macrolide and is natural product produced by Streptomyces ambofaciens. It binds to the 50S subunit of bacterial ribosomes and inhibits peptidyl transfer activity to disrupt protein synthesis.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"36315":{"category_aro_accession":"3000176","category_aro_cvterm_id":"36315","category_aro_name":"dirithromycin","category_aro_description":"Dirithromycin is an oxazine derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome to inhibit bacterial protein synthesis.","category_aro_class_name":"Antibiotic"},"36722":{"category_aro_accession":"3000583","category_aro_cvterm_id":"36722","category_aro_name":"pristinamycin IA","category_aro_description":"Pristinamycin IA is a type B streptogramin antibiotic produced by Streptomyces pristinaespiralis. It binds to the P site of the 50S subunit of the bacterial ribosome, preventing the extension of protein chains.","category_aro_class_name":"Antibiotic"},"36723":{"category_aro_accession":"3000584","category_aro_cvterm_id":"36723","category_aro_name":"quinupristin","category_aro_description":"Quinupristin is a type B streptogramin and a semisynthetic derivative of pristinamycin 1A. It is a component of the drug Synercid and interacts with the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"virginiamycin M1","category_aro_description":"Virginiamycin M1 is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37016":{"category_aro_accession":"3000672","category_aro_cvterm_id":"37016","category_aro_name":"madumycin II","category_aro_description":"Madumycin II is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37017":{"category_aro_accession":"3000673","category_aro_cvterm_id":"37017","category_aro_name":"griseoviridin","category_aro_description":"Griseoviridin is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"37019":{"category_aro_accession":"3000675","category_aro_cvterm_id":"37019","category_aro_name":"pristinamycin IB","category_aro_description":"Pristinamycin IB is a class B streptogramin similar to pristinamycin IA, the former containing a N-methyl-4-(methylamino)phenylalanine instead of a N-methyl-4-(dimethylamino)phenylalanine in its class A streptogramin counterpart (one less methyl group).","category_aro_class_name":"Antibiotic"},"37021":{"category_aro_accession":"3000677","category_aro_cvterm_id":"37021","category_aro_name":"virginiamycin S2","category_aro_description":"Virginiamycin S2 is a streptogramin B antibiotic.","category_aro_class_name":"Antibiotic"},"37022":{"category_aro_accession":"3000678","category_aro_cvterm_id":"37022","category_aro_name":"pristinamycin IC","category_aro_description":"Pristinamycin IC is a class B streptogramin derived from virginiamycin S1.","category_aro_class_name":"Antibiotic"},"37023":{"category_aro_accession":"3000679","category_aro_cvterm_id":"37023","category_aro_name":"vernamycin C","category_aro_description":"Vernamycin C is a streptogramin B antibiotic.","category_aro_class_name":"Antibiotic"},"37024":{"category_aro_accession":"3000680","category_aro_cvterm_id":"37024","category_aro_name":"patricin A","category_aro_description":"Patricin A is a streptogramin B antibiotic.","category_aro_class_name":"Antibiotic"},"37025":{"category_aro_accession":"3000681","category_aro_cvterm_id":"37025","category_aro_name":"patricin B","category_aro_description":"Patricin B is a streptogramin B antibiotic.","category_aro_class_name":"Antibiotic"},"37026":{"category_aro_accession":"3000682","category_aro_cvterm_id":"37026","category_aro_name":"ostreogrycin B3","category_aro_description":"Ostreogrycin B3 is a derivative of pristinamycin IA, with an additional 3-hydroxy group on its 4-oxopipecolic acid.","category_aro_class_name":"Antibiotic"},"37247":{"category_aro_accession":"3000867","category_aro_cvterm_id":"37247","category_aro_name":"oleandomycin","category_aro_description":"Oleandomycin is a 14-membered macrolide produced by Streptomyces antibioticus. It is ssimilar to erythromycin, and contains a desosamine amino sugar and an oleandrose sugar. It targets the 50S ribosomal subunit to prevent protein synthesis.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35952":{"category_aro_accession":"0000034","category_aro_cvterm_id":"35952","category_aro_name":"streptogramin A antibiotic","category_aro_description":"Streptogramin A antibiotics are cyclic polyketide peptide hybrids that bind to the ribosomal peptidyl transfer centre. Structural variation arises from substituting a proline for its desaturated derivative and by its substitution for Ala or Cys. Used alone, streptogramin A antibiotics are bacteriostatic, but is bactericidal when used with streptogramin B antibiotics.","category_aro_class_name":"Drug Class"},"35967":{"category_aro_accession":"0000050","category_aro_cvterm_id":"35967","category_aro_name":"streptogramin B antibiotic","category_aro_description":"Streptogramin B antibiotics are are cyclic hepta- or hexa-depsipeptides.  Type B streptogramins block the peptide exit tunnel of the 50S bacterial ribosome. The general composition of group B streptogramins is 3-hydroxypicolinic acid-L-Thr-D-aminobutyric acid (or D-Ala)-L-Pro-L-Phe (or 4-N-,N-(dimethylamino)-L-Phe)-X-L-phenylglycine. Used alone, streptogramin B antibiotics are bacteriostatic, but is bactericidal when used with streptogramin A antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1613":{"model_id":"1613","model_name":"CMY-38","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1021":{"protein_sequence":{"accession":"CAP60699.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYARGYREGKPVHVSPGQLNAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKNYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"AM931008.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCCGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTAACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAACTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3002049","ARO_id":"38449","ARO_name":"CMY-38","CARD_short_name":"CMY-38","ARO_description":"CMY-38 is a beta-lactamase found in the Enterobacteriaceae family.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1614":{"model_id":"1614","model_name":"TEM-194","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1325":{"protein_sequence":{"accession":"AFC75524.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSRNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANILLTTIGGPKELTAFLHNMRDHVTRLDRWEPELNEAIPHDERDTTMPAPVATTLRTLLTVELLTLASRPRLIDWMEADKVAGPILRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"JN935136.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCGGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACATACTTCTGACAACGATCGGAGGACCGAAGGAGCTCACCGCTTTTTTGCACAACATGAGAGATCATGTCACCCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCACACGACGAGCGTGACACCACGATGCCTGCTCCAGTGGCCACAACGTTGCGCACACTATTAACTGTCGAACTACTTACTCTAGCTTCCCGGCCACGATTAATAGACTGGATGGAGGCGGATAAAGTGGCAGGACCAATTCTGCGCTCGGCCCTTCCGGCCGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001054","ARO_id":"37434","ARO_name":"TEM-194","CARD_short_name":"TEM-194","ARO_description":"TEM-194 is a beta-lactamase.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1615":{"model_id":"1615","model_name":"APH(2'')-IIa","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"696":{"protein_sequence":{"accession":"AAK63040.1","sequence":"MVNLDAEIYEHLNKQIKINELRYLSSGDDSDTFLCNEQYVVKVPKRDSVRISQKRELELYRFLENCKLSYQIPAVVYQSDRFNIMKYIKGERITYEQYHKLSEKEKDALAYDEATFLKELHSIEIDCSVSLFSDALVNKKDKFLQDKKLLISILEKEQLLTDEMLEHIETIYENILSNAVLFKYTPCLVHNDFSANNMIFRNNRLFGVIDFGDFNVGDPDNDFLCLLDCSTDDFGKEFGRKVLKYYQHKAPEVAERKAELNDVYWSIDQIIYGYERKDREMLIKDVSELLQTQAEMFIF"},"dna_sequence":{"accession":"AF337947.1","fmin":"271","fmax":"1171","strand":"+","sequence":"ATGGTTAACTTGGACGCTGAGATATATGAGCACTTAAATAAACAGATAAAAATAAATGAACTCCGTTATTTATCGTCCGGCGATGATAGTGATACTTTTTTGTGTAATGAACAATATGTTGTGAAAGTTCCTAAACGAGATTCTGTTAGAATTTCTCAGAAACGAGAGCTTGAATTGTATCGTTTTTTAGAAAACTGTAAGCTATCTTATCAAATCCCTGCGGTAGTGTATCAAAGTGACCGATTTAATATTATGAAATATATTAAAGGGGAACGTATTACTTATGAGCAGTATCATAAGTTGAGTGAAAAGGAAAAGGATGCCCTTGCATATGATGAAGCGACGTTTTTGAAAGAGTTACATTCCATAGAGATTGATTGTTCTGTCAGTTTGTTTTCAGATGCTCTGGTGAATAAGAAAGATAAGTTTTTGCAAGATAAAAAATTACTTATAAGTATTCTGGAAAAGGAGCAGCTGTTAACTGATGAGATGTTGGAACATATCGAAACAATATATGAAAACATATTAAGCAATGCTGTTTTATTTAAATATACCCCTTGTTTGGTACATAATGATTTCAGTGCAAATAACATGATTTTTAGAAATAATAGACTGTTTGGAGTTATTGATTTTGGCGATTTTAATGTAGGTGACCCGGATAATGATTTTTTGTGCTTGCTGGATTGTAGTACAGATGATTTCGGGAAAGAATTTGGCAGGAAGGTATTAAAATACTATCAGCATAAGGCGCCGGAAGTAGCAGAAAGAAAAGCAGAGCTTAATGATGTATATTGGTCGATAGACCAAATCATTTATGGTTATGAAAGAAAAGATAGGGAAATGTTGATTAAGGATGTTTCTGAATTGCTACAAACACAAGCAGAGATGTTTATATTTTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002635","ARO_id":"39035","ARO_name":"APH(2'')-IIa","CARD_short_name":"APH(2'')-IIa","ARO_description":"APH(2'')-IIa is a chromosomal-encoded aminoglycoside phosphotransferase in E. faecium and E. coli.","ARO_category":{"36267":{"category_aro_accession":"3000128","category_aro_cvterm_id":"36267","category_aro_name":"APH(2'')","category_aro_description":"A category of aminoglycoside O-phosphotransferase enzymes with modification regiospecificity based at the 2''-hydroxyl group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics, specifically kanamycin, tobramycin and amikacin, by the ATP-dependent phosphorylation of the 3'-hydroxyl group of the compound.","category_aro_class_name":"AMR Gene Family"},"40307":{"category_aro_accession":"3003675","category_aro_cvterm_id":"40307","category_aro_name":"plazomicin","category_aro_description":"Plazomicin is a neoglycoside, or next-generation, aminoglycoside, that has been identified as a potentially useful agent to combat drug-resistant bacteria, such as Acinetobacter baumannii and Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1616":{"model_id":"1616","model_name":"CTX-M-152","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1589":{"protein_sequence":{"accession":"AHY20039.1","sequence":"MRKSVRRAILMTTACVSLLLASVPLYAHANDVQQKLAALEKSSGGRLGVALINTADNTQTLYRADERFAMCSTSKVMAAAAVLKQSETQKDLLSQRVEIKSSDLINYNPIAEKHVNGTMTLGELSAAALQYSDNTAMNKLIAHLGGPGKVTAFARAIGDDTFRLDRTEPTLNTAIPGDPRDTTTPLAMAQALRNLTLGNALGDTQRAQLVMWLKGNTTGAASIQAGLPTSWVVGDKTGSGDYGTTNDIAVIWPEGRAPLVLVTYFTQSEPKAESRRDVLAAAARIVTDGY"},"dna_sequence":{"accession":"KJ461948.1","fmin":"3","fmax":"876","strand":"+","sequence":"ATGAGAAAAAGCGTAAGGCGGGCGATATTAATGACGACAGCCTGTGTTTCGCTGCTGTTGGCCAGTGTGCCGCTGTATGCCCACGCGAACGATGTTCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGGGGACGACTGGGTGTGGCGTTGATTAACACCGCCGATAACACGCAGACGCTCTACCGCGCCGACGAGCGTTTTGCTATGTGCAGCACCAGTAAAGTGATGGCGGCGGCGGCGGTGCTTAAGCAAAGTGAAACGCAAAAGGACTTACTGAGTCAGCGGGTTGAAATTAAGTCCTCAGACTTGATTAACTACAACCCAATCGCTGAAAAGCACGTCAATGGCACGATGACACTCGGGGAGCTGAGCGCGGCGGCGCTGCAGTACAGCGATAATACTGCCATGAATAAGCTGATTGCCCATCTCGGGGGGCCGGGTAAAGTGACGGCATTTGCTCGTGCGATTGGCGATGACACTTTCCGGCTCGATCGTACCGAGCCGACGCTCAACACCGCGATCCCCGGCGACCCGCGCGATACCACCACGCCGTTAGCGATGGCGCAGGCTCTGCGCAATCTGACGTTGGGCAATGCCCTGGGTGACACTCAGCGTGCGCAGCTGGTGATGTGGCTGAAAGGCAACACCACCGGCGCTGCCAGCATTCAGGCAGGGCTACCCACATCGTGGGTTGTCGGGGATAAAACCGGCAGCGGCGATTATGGTACGACGAATGATATCGCGGTTATTTGGCCGGAAGGTCGCGCGCCGCTCGTTCTGGTGACTTACTTCACCCAGTCGGAGCCGAAGGCAGAGAGCCGTCGTGACGTGCTCGCTGCTGCCGCCAGAATTGTCACCGACGGTTATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39100","NCBI_taxonomy_name":"Kluyvera sp. MRB7","NCBI_taxonomy_id":"1491392"}}}},"ARO_accession":"3002009","ARO_id":"38409","ARO_name":"CTX-M-152","CARD_short_name":"CTX-M-152","ARO_description":"CTX-M-152 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1617":{"model_id":"1617","model_name":"vanE","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"216":{"protein_sequence":{"accession":"AAL27442.1","sequence":"MKTVAIIFGGVSSEYEVSLKSAVAIIKNMESIDYNVMKIGITEEGHWYLFEGTTDKIKKDRWFLDESCEEIVVDFAKKSFVLKNSKKIIKPDILFPVLHGGYGENGAMQGVFELLDIPYVGCGIGAAAISMNKIMLHQFAEAIGVKSTPSMIIEKGQDLQKVDAFAKIHGFPLYIKPNEAGSSKGISKVERKSDLYKAIDEASKYDSRILIQKEVKGVEIGCGILGNEQLVVGECDQISLVDGFFDYEEKYNLVTAEILLPAKLSIDKKEDIQMKAKKLYRLLGCKGLARIDFFLTDDGEILLNEINTMPGFTEHSRFPMMMNEIGMDYKEIIENLLVLAVENHEKKLSTID"},"dna_sequence":{"accession":"FJ872411.1","fmin":"39735","fmax":"40794","strand":"+","sequence":"ATGAAGACAGTTGCGATTATCTTTGGCGGAGTTTCTTCTGAATATGAAGTTTCACTGAAATCTGCTGTAGCGATTATTAAAAATATGGAATCTATTGATTATAACGTAATGAAAATAGGGATCACCGAAGAAGGTCATTGGTATCTATTTGAAGGAACGACAGACAAAATAAAGAAAGATCGTTGGTTTTTAGATGAAAGCTGTGAAGAAATCGTAGTTGATTTCGCAAAAAAAAGCTTTGTATTGAAAAACAGTAAAAAAATAATCAAGCCTGATATTTTATTCCCAGTTTTACATGGAGGTTATGGTGAGAATGGTGCTATGCAGGGAGTATTTGAGTTATTAGATATTCCATATGTAGGTTGTGGTATCGGAGCTGCAGCAATCTCTATGAATAAAATAATGCTCCATCAATTTGCTGAAGCAATTGGTGTAAAAAGCACCCCTAGTATGATTATAGAAAAGGGACAAGACCTACAAAAAGTCGATGCGTTTGCGAAAATACATGGATTTCCTTTATATATTAAACCGAATGAGGCAGGCTCATCAAAAGGAATTAGCAAGGTAGAACGAAAAAGTGATTTATATAAAGCAATAGACGAAGCTTCAAAATATGATAGTCGTATTTTAATTCAAAAGGAAGTGAAAGGGGTAGAAATTGGTTGTGGTATTTTAGGAAATGAACAATTGGTCGTTGGAGAATGTGACCAAATCAGTCTTGTGGATGGCTTTTTCGATTATGAAGAGAAATACAATTTAGTAACAGCAGAAATTTTGTTACCAGCTAAACTATCAATAGACAAAAAAGAAGATATTCAGATGAAAGCAAAAAAACTATACAGACTATTAGGATGCAAAGGATTAGCGAGAATCGACTTTTTCTTAACTGATGACGGAGAAATTTTATTAAATGAAATCAATACAATGCCTGGTTTTACAGAGCATTCGAGATTTCCAATGATGATGAATGAGATTGGGATGGACTACAAAGAGATTATAGAAAACCTATTAGTATTGGCGGTGGAAAATCATGAAAAAAAATTATCTACGATTGATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35918","NCBI_taxonomy_name":"Enterococcus faecalis","NCBI_taxonomy_id":"1351"}}}},"ARO_accession":"3002907","ARO_id":"39341","ARO_name":"vanE","CARD_short_name":"vanE","ARO_description":"VanE is a D-Ala-D-Ala ligase homolog that can synthesize D-Ala-D-Ser, an alternative substrate for peptidoglycan synthesis that reduces vancomycin binding affinity in Enterococcus faecalis.","ARO_category":{"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"39340":{"category_aro_accession":"3002906","category_aro_cvterm_id":"39340","category_aro_name":"Van ligase","category_aro_description":"Van ligases synthesize alternative substrates for peptidoglycan synthesis that reduce vancomycin binding affinity.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1618":{"model_id":"1618","model_name":"OXA-362","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"809":{"protein_sequence":{"accession":"AHA11125.1","sequence":"MKILILLPLLSCLGLTACTSPVSSFPSHITSTQSTQAIAQLFDQAQSSGVLVIQRGQKVQVYGNDLSRAGTEYVPASTFKMLNALIGLQHGKATTNEIFKWDGKKRSFAAWEKDMTLGEAMQASAVPVYQELARRIGLELMQQEVRRIQFGNQQIGQQVDNFWLVGPLKITPKQEVEFVSALAREQLAFDPQVQQQVKAMLLLQERKAYRLYAKSGWGMDVEPQVGWLTGWVETPQAEIVAFSLNMQMQNGMDPAIRLEILQQALAELGLYPKAEG"},"dna_sequence":{"accession":"KF460532.1","fmin":"0","fmax":"831","strand":"+","sequence":"ATGAAAATTCTGATTTTGCTACCTTTACTGAGTTGCTTGGGCCTGACAGCGTGTACCTCACCTGTTTCATCTTTCCCTTCTCATATCACTTCGACTCAATCGACTCAAGCCATTGCCCAATTATTTGATCAGGCGCAAAGTTCTGGCGTTTTAGTGATTCAGCGTGGTCAAAAAGTACAGGTCTATGGCAATGATTTAAGCCGTGCAGGTACCGAATATGTTCCAGCCTCTACTTTCAAAATGCTCAATGCCCTGATTGGCCTGCAACATGGCAAAGCCACAACCAATGAAATTTTTAAATGGGATGGCAAGAAACGCAGTTTTGCAGCCTGGGAAAAAGACATGACTCTCGGCGAAGCCATGCAAGCTTCTGCTGTACCCGTGTATCAGGAACTGGCACGTCGCATTGGCCTTGAACTGATGCAACAGGAAGTGAGACGTATTCAATTCGGCAATCAGCAGATTGGGCAGCAGGTTGATAACTTCTGGTTGGTAGGCCCTTTGAAAATCACTCCAAAACAGGAGGTCGAATTTGTCTCGGCTCTAGCCCGAGAGCAGCTTGCCTTTGATCCACAAGTCCAGCAGCAAGTCAAAGCCATGTTACTTTTACAGGAGCGGAAAGCTTATCGACTATATGCCAAATCTGGTTGGGGCATGGATGTGGAACCACAAGTCGGCTGGCTCACCGGCTGGGTTGAAACACCGCAGGCTGAAATCGTGGCATTTTCGCTGAATATGCAGATGCAAAATGGTATGGATCCGGCAATCCGCCTTGAAATTTTACAGCAGGCTTTGGCCGAATTAGGGCTTTATCCAAAAGCTGAAGGATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36948","NCBI_taxonomy_name":"Acinetobacter lwoffii","NCBI_taxonomy_id":"28090"}}}},"ARO_accession":"3001549","ARO_id":"37949","ARO_name":"OXA-362","CARD_short_name":"OXA-362","ARO_description":"OXA-362 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46489":{"category_aro_accession":"3007700","category_aro_cvterm_id":"46489","category_aro_name":"OXA-134-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-134.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1619":{"model_id":"1619","model_name":"L1 beta-lactamase","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1909":{"protein_sequence":{"accession":"CAB75346.1","sequence":"MRSTLLAFALSSLALAATLFTFDGAAADASLPQLQAYTVDPSWLQTMAPLQIADHTWQIGTHDLTALLVQTADGLVLIDGGMPQMASYLLTNMKARGTNTGPLRMVLLSHAHTDHAGPVAEIKRRTGAQVVVNAETAVLLARGGSDDLHFGDEITFPPVNADRIVMDREVVKLGGIAFTAHFMPGHTPGSTAWTWTDTRDGKPVRIAYADSLSAPGYQLQGNARYPRLVEDYRRSFATVRGLPCDLLLTPHPGASNWNYAAGSNASEKVLSCKAYADAAEKKFDAQLAKETAGAR"},"dna_sequence":{"accession":"AJ272109.1","fmin":"0","fmax":"888","strand":"+","sequence":"ATGCGTTCTACCCTGCTCGCCTTCGCCCTCTCGTCGCTCGCCCTGGCCGCCACGCTCTTCACCTTCGACGGCGCCGCCGCCGACGCATCGCTGCCACAGCTGCAGGCCTACACGGTGGACCCTTCCTGGCTGCAAACGATGGCGCCGTTGCAGATTGCCGATCACACCTGGCAGATCGGCACGCATGACCTGACGGCACTGCTGGTCCAGACGGCTGATGGCCTCGTCCTGATCGATGGTGGCATGCCGCAAATGGCCTCTTACCTGCTGACCAACATGAAGGCCAGGGGAACCAATACCGGTCCCCTGCGCATGGTCCTGCTCAGCCACGCGCACACCGATCACGCCGGCCCTGTGGCCGAGATCAAGCGCCGCACGGGGGCGCAGGTGGTCGTGAACGCCGAAACCGCAGTGCTGCTGGCCCGAGGCGGCAGCGACGACCTTCATTTCGGCGACGAAATCACGTTTCCACCGGTCAATGCAGACCGCATCGTCATGGATCGGGAGGTCGTCAAGCTGGGCGGCATCGCGTTCACCGCCCATTTCATGCCCGGGCACACGCCGGGGAGCACCGCCTGGACCTGGACCGATACGCGCGATGGCAAGCCGGTGCGCATCGCCTATGCCGACAGCCTGAGCGCGCCGGGCTACCAGCTGCAGGGCAATGCCCGCTATCCCCGCCTGGTTGAGGACTACCGACGCAGCTTCGCTACGGTGCGCGGCCTGCCCTGCGACCTGTTGCTGACCCCGCATCCGGGCGCCAGCAACTGGAACTATGCTGCTGGCAGCAACGCCAGCGAGAAGGTACTGAGCTGCAAAGCCTACGCGGATGCGGCCGAGAAGAAGTTCGACGCGCAGCTGGCCAAGGAAACGGCCGGGGCCCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37076","NCBI_taxonomy_name":"Stenotrophomonas maltophilia","NCBI_taxonomy_id":"40324"}}}},"ARO_accession":"3000582","ARO_id":"36721","ARO_name":"L1 beta-lactamase","CARD_short_name":"L1_BLA","ARO_description":"L1 is an Ambler class B MBL; subclass B3 originally isolated from Stenotrophomonas maltophilia.  It has activity against a broad range of beta-lactams and is only active with two Zn(II) ions in the active site.","ARO_category":{"41379":{"category_aro_accession":"3004215","category_aro_cvterm_id":"41379","category_aro_name":"L1 family beta-lactamase","category_aro_description":"This subclass B3 of beta-lactamses have the ability to hydrolyze cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1620":{"model_id":"1620","model_name":"CTX-M-156","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1741":{"protein_sequence":{"accession":"AIS67612.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPNAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"KM211509.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAACGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3003164","ARO_id":"39741","ARO_name":"CTX-M-156","CARD_short_name":"CTX-M-156","ARO_description":"CTX-M-156 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1621":{"model_id":"1621","model_name":"SHV-45","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"834":{"protein_sequence":{"accession":"AAN39364.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIDDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGASKRGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AF547625.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACATCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGACGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTAGCAAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001103","ARO_id":"37483","ARO_name":"SHV-45","CARD_short_name":"SHV-45","ARO_description":"SHV-45 is an extended-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1505":{"model_id":"1505","model_name":"SAT-4","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"459":{"protein_sequence":{"accession":"AAB53445.1","sequence":"MITEMKAEHLKDIDKPSEPFEVIGKIIPRYENENWTFTELLYEAPYLKSYQDEEDEEDEEADCLEYIDNTDKIIYLYYQDDKCVGKVKLRKNWNRYAYIEDIAVCKDFRGQGIGSALINISIEWAKHKNLHGLMLETQDNNLIACKFYHNCGFKIGSVDTMLYANFENNFEKAVFWYLRF"},"dna_sequence":{"accession":"U01945.1","fmin":"373","fmax":"916","strand":"+","sequence":"GTGATTACAGAAATGAAAGCAGAGCACCTGAAAGATATCGATAAACCCAGCGAACCATTTGAGGTGATAGGTAAGATTATACCGAGGTATGAAAACGAGAATTGGACCTTTACAGAATTACTCTATGAAGCGCCATATTTAAAAAGCTACCAAGACGAAGAGGATGAAGAGGATGAGGAGGCAGATTGCCTTGAATATATTGACAATACTGATAAGATAATATATCTTTACTACCAAGACGATAAATGCGTCGGAAAAGTTAAACTGCGAAAAAATTGGAACCGGTACGCTTATATAGAAGATATCGCCGTATGTAAGGATTTCAGGGGGCAAGGCATAGGCAGCGCGCTTATCAATATATCTATAGAATGGGCAAAGCATAAAAACTTGCATGGACTAATGCTTGAAACCCAGGACAATAACCTTATAGCTTGTAAATTCTATCATAATTGTGGTTTCAAAATCGGCTCCGTCGATACTATGTTATACGCCAACTTTGAAAACAACTTTGAAAAAGCTGTTTTCTGGTATTTAAGGTTTTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36835","NCBI_taxonomy_name":"Campylobacter coli","NCBI_taxonomy_id":"195"}}}},"ARO_accession":"3002897","ARO_id":"39331","ARO_name":"SAT-4","CARD_short_name":"SAT-4","ARO_description":"SAT-4 is a plasmid-mediated streptothricin acetyltransferase and streptothricin (a nucleoside antibiotic) resistant determinant. Originally described from a Campylobacter coli BE\/G4 plasmid gene sequence by Jacob et al, 1994.","ARO_category":{"37249":{"category_aro_accession":"3000869","category_aro_cvterm_id":"37249","category_aro_name":"streptothricin acetyltransferase (SAT)","category_aro_description":"AcetylCoA dependent acetyltransferase that acetylate streptothricins such as nourseothricin at position 16 (beta position of beta-lysine).","category_aro_class_name":"AMR Gene Family"},"35931":{"category_aro_accession":"0000012","category_aro_cvterm_id":"35931","category_aro_name":"streptothricin","category_aro_description":"Streptothricins are a group of N-glycoside antibiotics that include a carbamoylated D-glucosamine to which are attached a series of L-beta-lysine residues at position 2 and a streptolidine at position 1.  Streptothricins vary by the number of beta-lysine residues (from 1 (nourseothricin) to 7) and target protein synthesis in bacteria and eukaryotes.","category_aro_class_name":"Antibiotic"},"36174":{"category_aro_accession":"3000034","category_aro_cvterm_id":"36174","category_aro_name":"nucleoside antibiotic","category_aro_description":"Nucleoside antibiotics are made of modified nucleosides and nucleotides with wide-ranging activities and means of antibacterial effects. This drug class includes aminonucleoside antibiotics, which contain an amino group.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1608":{"model_id":"1608","model_name":"MexT","model_type":"protein overexpression model","model_type_id":"41091","model_description":"Protein Overexpression Models (POM) are similar to Protein Variant Models (PVM) in that they include a protein reference sequence, a curated BLASTP bitscore cut-off, and mapped resistance variants. Whereas PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, reporting only those with curated mutations conferring AMR, POMs are restricted to regulatory proteins and report both wild-type sequences and\/or sequences with mutations leading to overexpression of efflux complexes. The former lead to efflux of antibiotics at basal levels, while the latter can confer clinical resistance. POMs include a protein reference sequence (often from wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Perfect RGI match is 100% identical to the wild-type reference protein sequence along its entire length, a Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value may or may not contain at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off may or may not contain at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"7570":"G258D","7571":"Y138D"},"Curated-R":{"7570":"G258D","7571":"Y138D"},"clinical":{"7570":"G258D","7571":"Y138D"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"5414":{"protein_sequence":{"accession":"AAG05880.1","sequence":"MPVSDPMPLRHLARPRPVSHARLDGEPPRLQPLAPGNEERHEPKRPAPRRSEPADRVRDPDARTQRDPRRRETVPRPAGQPAISAALSRLRTLFDDPLFVRTGRSMEPTARAQEIFAHLSPALDSISTAMSRASEFDPATSTAVFRIGLSDDVEFGLLPPLLRRLRAEAPGFVLVVRRANYLLMPNLLASGEISVGVSYTDELPANAKRKTVRRSKPKILRADSAPGQLTLDDYCARPHALVSFAGDLSGFVDEELEKFGRKRKVVLAVPQFNGLGTLLAGTDIIATVPDYAAQALIAAGGLRAEDPPFETRAFELSMAWRGAQDNDPAERWLRSRISMFIGDPDSL"},"dna_sequence":{"accession":"AE004091.2","fmin":"2807468","fmax":"2808512","strand":"+","sequence":"ATGCCTGTCAGTGATCCTATGCCCCTCCGGCACCTCGCCAGGCCCCGCCCCGTCTCGCACGCAAGGCTTGACGGCGAGCCCCCGCGGTTGCAGCCTCTAGCCCCTGGAAACGAGGAACGCCATGAACCGAAACGACCTGCGCCGCGTCGATCTGAACCTGCTGATCGTGTTCGAGACCCTGATGCACGAACGCAGCGTGACCCGCGCCGCAGAGAAACTGTTCCTCGGCCAGCCGGCCAGCCGGCCATCAGCGCCGCGCTGTCGCGCCTGCGCACGCTGTTCGACGACCCGCTGTTCGTCCGTACCGGACGCAGCATGGAGCCCACCGCGCGAGCCCAGGAAATCTTCGCCCACCTGTCGCCGGCGCTGGATTCCATCTCCACCGCCATGAGTCGCGCCAGCGAGTTCGATCCGGCGACCAGCACCGCGGTGTTCCGCATCGGCCTTTCCGACGACGTCGAGTTCGGCCTGTTGCCGCCCCTGCTCCGCCGCCTGCGCGCGGAGGCGCCGGGGTTCGTCCTCGTCGTGCGCCGCGCCAACTATCTATTGATGCCGAACCTGCTGGCCTCGGGGGAGATCTCGGTGGGCGTCAGCTACACCGACGAACTGCCGGCCAACGCCAAGCGCAAGACCGTGCGCCGCAGCAAGCCGAAGATCCTCCGCGCCGACTCCGCGCCCGGCCAGCTGACCCTCGACGACTATTGCGCGCGACCGCACGCGCTGGTGTCCTTCGCCGGCGACCTCAGCGGCTTCGTCGACGAGGAGCTGGAAAAATTCGGCCGCAAGCGCAAGGTGGTCCTGGCGGTGCCGCAGTTCAACGGCCTCGGCACCCTCCTGGCCGGCACCGACATCATCGCCACCGTGCCCGACTACGCCGCCCAGGCGCTGATCGCCGCCGGCGGCCTACGCGCCGAGGACCCACCGTTCGAGACCCGGGCCTTCGAACTGTCGATGGCTTGGCGCGGCGCCCAGGACAACGATCCGGCCGAACGCTGGCTGCGCTCGCGGATCAGCATGTTCATCGGCGATCCGGACAGTCTCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36804","NCBI_taxonomy_name":"Pseudomonas aeruginosa PAO1","NCBI_taxonomy_id":"208964"}}}},"ARO_accession":"3000814","ARO_id":"37194","ARO_name":"MexT","CARD_short_name":"MexT","ARO_description":"MexT is a LysR-type transcriptional activator that positively regulates the expression of MexEF-OprN, OprD, and MexS.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1523":{"model_id":"1523","model_name":"MexD","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1800"}},"model_sequences":{"sequence":{"335":{"protein_sequence":{"accession":"AAB41957.1","sequence":"MSEFFIKRPNFAWVVALFISLGGLLVISKLPVAQYPNVAPPQITITATYPGASAKVLVDSVTSVLEESLNGAKGLLYFESTNNSNGTAEIVVTFEPGTDPDLAQVDVQNRLKKAEARMPQAVLTQGLQVEQTSAGFLLIYALSYKEGAQRSDTTALGDYAARNINNELRRLPGVGKLQFFSSEAAMRVWIDPQKLVGFGLSIDDVSNAIRGQNVQVPAGAFGSAPGSSAQELTATLAVKGTLDDPQEFGQVVLRANEDGSLVPARRCRAPGTRQGELQHFLATERHAHRGRGYPAVARGQRDPDPTLVKQRLAELSAFFPEDMQYSVPYDTSRFVDVAIEKVIHTLIEAMVLVFLVMFLFLENVRYTLIPSIVVPVCLLGTLMVMYLLGFSVNMMTMFGMVLAIGILVDDAIVVVENVERIMAEEGISPAEATVKAMKQVSGAIVGITLVLSAVFLPLAFMAGSVGVIYQQFSVSLAVSILFSGFLALTFTPALCATLFKPIPEGHHEKRGFFGAFNRGFARVTERYSLLNSKLVARAGRFMLVYAGLVAMLGYFYLRLPEAFVPAEDLGYMVVDVQLPPGASRVRTDATGEELERFLKSREAVASVFLISGFSFSGQGDNAALAFPTFKDWSERGAEQSSAAEIAALNEHFALPDDGTVMAVSPPPINGLGNSGGFALRLMDRSGVGREALLQARDTLLGEIQTNPKFLYAMMEGLAEAPQLRLLIDREKARALGVSFETISGTLSAAFGSEVINDFTNAGRQQRVVIQAEQGNRMTPESVLELYVPNAAGNLVPLSAFVSVKWEEGPVQLVRYNGYPSIRIVGDAAPGFSTGEAMAEMERLASQLPAGIGYEWTGLSYQEKVSAGQATSLFALAILVVFLLLVALYESWSIPLSVMLIVPIGAIGAVLAVMVSGMSNDVYFKVGLITIIGLSAKNAILIVEFAKELWEQGHSLRDAAIEAARLRFRPIIMTSMAFILGVIPLALASGAGAASQRAIGTGVIGGMLSATFLGVLFVPICFVWLLSLLRSKPAPIEQAASAGE"},"dna_sequence":{"accession":"U57969.1","fmin":"1485","fmax":"4617","strand":"+","sequence":"ATGTCCGAATTCTTCATCAAGCGGCCGAACTTCGCCTGGGTGGTGGCCCTGTTCATCTCCCTGGGCGGCCTGCTGGTCATTTCCAAATTGCCGGTAGCGCAGTACCCCAATGTCGCGCCGCCACAGATCACCATCACCGCCACCTATCCCGGCGCCTCGGCGAAGGTGCTGGTGGACTCCGTCACCAGTGTGCTCGAGGAGTCGCTGAACGGCGCCAAGGGCCTGCTCTACTTCGAGTCGACCAACAACTCCAACGGCACCGCCGAGATCGTCGTCACCTTCGAGCCGGGCACCGATCCGGACCTGGCCCAGGTGGACGTGCAGAACCGCCTGAAGAAAGCCGAGGCGCGCATGCCGCAGGCGGTGCTGACCCAGGGCCTGCAGGTCGAGCAGACCAGCGCCGGTTTCCTGCTGATCTATGCGCTCAGCTACAAGGAAGGCGCTCAGCGCAGCGACACCACCGCCCTCGGCGACTACGCCGCGCGCAATATCAACAACGAGCTGCGGCGCCTGCCGGGCGTCGGCAAGCTGCAATTCTTCTCTTCCGAGGCGGCCATGCGGGTCTGGATCGATCCGCAGAAGCTGGTGGGCTTCGGCCTCTCCATCGACGACGTGAGCAATGCCATCCGCGGGCAGAACGTGCAGGTGCCGGCCGGCGCCTTCGGCAGCGCACCGGGCAGTTCCGCGCAGGAGCTGACGGCGACCCTGGCGGTGAAGGGCACCCTGGACGATCCGCAGGAGTTCGGCCAGGTAGTGCTGCGCGCCAACGAGGACGGCTCGCTGGTCCCGGCTCGCCGATGTCGCGCGCCTGGAACTCGGCAAGGAGAGCTACAACATTTCCTCGCGACTGAACGGCACGCCCACCGTGGGCGGGGCTATCCAGCTGTCGCCCGGGGCCAACGCGATCCAGACCCTACCCTGGTGAAACAGCGTCTCGCCGAACTGTCGGCGTTCTTCCCCGAGGACATGCAGTACAGCGTGCCCTACGACACCTCGCGCTTCGTCGACGTGGCCATCGAGAAGGTGATCCACACCCTGATCGAAGCGATGGTCCTGGTGTTCCTGGTGATGTTCCTGTTCCTGGAGAACGTCCGCTACACCCTGATCCCGTCCATCGTGGTGCCGGTGTGCCTGCTGGGTACGCTGATGGTGATGTACCTGCTGGGGTTCTCGGTGAACATGATGACCATGTTCGGCATGGTCCTGGCGATCGGCATCCTGGTGGACGACGCCATCGTGGTGGTGGAGAACGTCGAGCGGATCATGGCGGAGGAGGGGATTTCCCCGGCCGAGGCCACGGTCAAGGCGATGAAGCAGGTATCCGGCGCCATCGTCGGCATCACCCTGGTGCTCTCGGCGGTGTTCCTGCCGCTGGCTTTCATGGCCGGTTCGGTGGGGGTGATCTACCAGCAGTTCTCGGTGTCGCTGGCGGTCTCGATCCTGTTCTCCGGCTTCCTCGCCCTGACCTTCACCCCGGCGCTGTGCGCCACGCTGTTCAAGCCCATTCCCGAAGGGCACCACGAGAAGCGCGGCTTCTTCGGCGCCTTCAACCGTGGCTTCGCCCGCGTCACCGAGCGCTATTCGCTGCTCAACTCGAAGCTGGTGGCGCGCGCCGGACGCTTCATGCTGGTGTACGCCGGCCTGGTGGCCATGCTCGGCTACTTCTACCTGCGCCTGCCGGAAGCCTTCGTGCCGGCGGAAGACCTCGGCTACATGGTGGTCGACGTGCAACTGCCGCCTGGCGCTTCGCGCGTGCGCACCGATGCCACCGGCGAGGAGCTCGAGCGCTTCCTCAAGTCCCGCGAGGCGGTGGCTTCGGTGTTCCTGATCTCGGGCTTCAGCTTCTCCGGCCAGGGCGACAATGCCGCGCTGGCCTTCCCAACCTTCAAGGACTGGTCCGAGCGAGGCGCCGAGCAGTCGTCCGCCGCCGAGATCGCCGCGCTGAACGAGCATTTCGCGCTGCCCGACGATGGCACGGTCATGGCCGTGTCGCCGCCACCGATCAACGGTCTGGGTAACTCCGGCGGCTTCGCATTGCGCCTGATGGACCGTAGCGGGGTCGGCCGCGAAGCGCTGCTGCAGGCTCGCGATACTCTTCTTGGCGAGATCCAGACCAACCCGAAATTCCTTTACGCGATGATGGAAGGACTGGCCGAAGCGCCGCAACTGCGCCTGTTGATCGACCGGGAGAAGGCCCGTGCCCTGGGGGTGAGCTTCGAGACCATCAGCGGCACGCTGTCCGCTGCCTTCGGCTCGGAGGTGATCAACGACTTCACCAATGCGGGGCGCCAACAGCGGGTGGTGATCCAGGCCGAACAGGGCAACCGGATGACCCCGGAAAGCGTGCTCGAGCTATACGTGCCTAACGCTGCTGGCAACCTGGTACCGCTCAGCGCCTTCGTCAGCGTGAAATGGGAAGAGGGACCGGTGCAATTGGTGCGCTATAACGGCTACCCGTCGATCCGCATCGTCGGTGACGCCGCGCCCGGCTTCAGTACCGGCGAAGCCATGGCGGAAATGGAGCGCCTGGCCTCGCAGCTGCCGGCCGGCATCGGCTACGAGTGGACCGGCCTGTCCTATCAGGAGAAGGTCTCCGCCGGGCAGGCCACCAGCCTGTTCGCCCTCGCCATCCTGGTGGTGTTCCTGTTGCTGGTGGCGCTCTACGAGAGCTGGTCGATCCCGCTGTCGGTGATGCTGATCGTGCCGATCGGCGCCATCGGCGCGGTGCTCGCGGTGATGGTCAGCGGTATGTCCAACGACGTGTATTTCAAGGTCGGCCTGATCACCATCATCGGTCTTTCGGCGAAGAACGCGATCCTCATCGTCGAGTTCGCCAAGGAACTCTGGGAACAGGGACATAGCCTGCGCGACGCCGCCATCGAGGCCGCGCGCCTGCGCTTCCGGCCGATCATCATGACTTCCATGGCGTTCATCCTCGGCGTGATACCCCTGGCCCTGGCCAGCGGTGCCGGCGCGGCGAGCCAGCGTGCCATCGGCACCGGAGTGATCGGCGGGATGCTCAGCGCCACCTTCCTCGGCGTGCTGTTCGTACCTATCTGTTTCGTCTGGCTGCTGTCGCTGCTGCGCAGCAAGCCGGCACCCATCGAACAGGCCGCTTCGGCCGGGGAGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3000801","ARO_id":"37181","ARO_name":"MexD","CARD_short_name":"MexD","ARO_description":"MexD is the multidrug inner membrane transporter of the MexCD-OprJ complex.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36250":{"category_aro_accession":"3000111","category_aro_cvterm_id":"36250","category_aro_name":"novobiocin","category_aro_description":"Novobiocin is an aminocoumarin antibiotic produced by Streptomyces spheroides and Streptomyces niveus, and binds DNA gyrase subunit B inhibiting ATP-dependent DNA supercoiling.","category_aro_class_name":"Antibiotic"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"37007":{"category_aro_accession":"3000663","category_aro_cvterm_id":"37007","category_aro_name":"ofloxacin","category_aro_description":"Ofloxacin is a 6-fluoro, 7-piperazinyl quinolone with a methyl-substituted oxazine ring. It has a broad spectrum of activity including many enterobacteria and mycoplasma but most anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"46133":{"category_aro_accession":"3007382","category_aro_cvterm_id":"46133","category_aro_name":"gentamicin","category_aro_description":"Gentamicin is a commonly used aminoglycoside antibiotic derived from members of the Micromonospora genus of bacteria. It acts by binding the 30S ribosomal subunit, thus inhibiting protein synthesis. Gentamicin is typically used to treat Gram-negative infections of the repiratory and urinary tract, as well as infections of the bone and soft tissue. It also exhibits considerable nephrotoxicity and ototoxicity. Gentamicin is administered as a mixture of gentamicin type C (which makes about around 80% of the complex) and types A, B, and X (distributed in the remaining 20% of the complex).","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36242":{"category_aro_accession":"3000103","category_aro_cvterm_id":"36242","category_aro_name":"aminocoumarin antibiotic","category_aro_description":"Aminocoumarin antibiotics bind DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling.","category_aro_class_name":"Drug Class"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1584":{"model_id":"1584","model_name":"tet(41)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"4689":{"protein_sequence":{"accession":"AAP93922.1","sequence":"MKKPMLVILLTVLLDAVGIGLIMPILPALLRSLGGLDAGSVHYGALLAAYALMQFLFSPILGALSDRFGRRPVLLISLAGAAADYLLMAFAPTLAWLYLGRLLAGITGANMAVATAYVTDITPVGQRARRFGLVGAVFGVGFIVGPLLGGSLGEWHLHAPFLAAAMMNALNLVMAFFLLPESRKSRPRAAEKIRLNPFSSLRRLHGKPGLLPLAGIYLVMALVSQAPATLWILYGQDRFGWSMMVAGLSLAGYGACHALSQAFAIGPLVARLGERKALLIGLAADAVGLALLSVATRGWAPFALLPFFAAGGMALPALQALMAHKVDDDHQGELQGTLASMGSLIGVAGPLVATALYAATRDVWPGLVWALAAALYLVVPPLLARSRARDAAP"},"dna_sequence":{"accession":"AY264780.2","fmin":"1824","fmax":"3006","strand":"-","sequence":"TTGAAAAAACCCATGCTGGTTATTTTGTTGACGGTGTTGCTGGATGCGGTGGGCATCGGTCTGATCATGCCTATTCTACCGGCGCTGTTGCGCTCGCTGGGCGGTCTCGATGCCGGCAGCGTGCATTACGGCGCCCTGCTGGCGGCCTATGCGTTGATGCAATTCCTGTTTTCGCCGATCCTCGGCGCGCTGAGCGATCGTTTCGGGCGGCGGCCGGTGCTGTTGATTTCGCTCGCCGGCGCGGCGGCCGACTACCTGCTGATGGCGTTCGCGCCGACGCTGGCCTGGCTCTATCTGGGGCGGTTGCTGGCGGGCATCACCGGCGCCAACATGGCGGTCGCCACCGCTTACGTCACCGATATTACCCCCGTCGGCCAGCGCGCTCGGCGTTTCGGCCTGGTGGGCGCGGTGTTCGGCGTCGGCTTTATCGTCGGCCCGCTGCTCGGCGGATCGCTGGGCGAATGGCATCTGCATGCGCCCTTCCTGGCGGCGGCGATGATGAATGCCCTCAACCTGGTGATGGCGTTTTTCCTGCTGCCCGAATCGCGTAAATCCCGCCCCCGCGCCGCCGAGAAAATTCGCCTTAATCCCTTCTCGTCATTGCGCCGGCTGCACGGCAAGCCTGGCCTGCTGCCGCTGGCCGGCATTTATCTGGTTATGGCGCTGGTTTCGCAGGCGCCGGCCACGCTGTGGATTTTATACGGTCAGGATCGTTTCGGCTGGAGCATGATGGTGGCGGGCCTGTCGCTGGCCGGCTACGGCGCCTGCCACGCGCTGTCGCAGGCCTTTGCCATCGGCCCGCTGGTCGCGCGGCTCGGCGAGCGCAAGGCGCTGCTGATCGGCCTGGCCGCCGACGCCGTGGGCCTGGCGCTGTTGTCTGTCGCCACGCGCGGCTGGGCGCCGTTCGCCCTGCTGCCGTTCTTCGCCGCGGGCGGCATGGCGTTGCCCGCACTGCAGGCGCTGATGGCGCACAAGGTGGACGACGATCATCAGGGCGAGCTGCAAGGGACGCTCGCCAGCATGGGCAGCCTGATCGGCGTCGCGGGGCCGCTGGTGGCGACGGCGCTGTATGCCGCCACGCGCGATGTCTGGCCTGGGCTGGTGTGGGCGTTGGCCGCCGCCCTGTACCTGGTGGTGCCGCCGCTGCTGGCACGCTCACGCGCCAGGGATGCGGCGCCATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36783","NCBI_taxonomy_name":"Serratia marcescens","NCBI_taxonomy_id":"615"}}}},"ARO_accession":"3000569","ARO_id":"36708","ARO_name":"tet(41)","CARD_short_name":"tet(41)","ARO_description":"Tet41 is a tetracycline efflux pump found in Serratia, a Gram-negative bacterium.  It is related to Acinetobacter Tet(39).","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1623":{"model_id":"1623","model_name":"GIM-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"2106":{"protein_sequence":{"accession":"AIY26289.1","sequence":"MKNVLVFLILLVALPALAQGHKPLEVIKIEDGVYLHTSFKNIEGYGLVDSNGLVVLDNNQAYIIDTPWSEEDTKLLLSWATDRGYQVMASISTHSHGDRTAGIKLLNSKSIPTYTSELTKKLLAREGKPVPTHYFKDDEFTLGNGLIELYYPGAGHTEDNIVAWLPKSKILFGGCLVRSHEWEGLGYVGDASISSWADSIKNIVSKKYPIQMVVPGHGKVGSSDILDHTIDLAESASNKLMQPTAEASAD"},"dna_sequence":{"accession":"KM659858.1","fmin":"401","fmax":"1154","strand":"+","sequence":"ATGAAAAATGTATTAGTGTTTTTAATATTACTTGTAGCGTTGCCAGCTTTAGCTCAGGGTCATAAACCGCTAGAAGTTATAAAAATTGAAGATGGAGTATATCTTCATACCTCCTTTAAGAATATTGAAGGCTATGGGTTAGTTGATTCGAATGGGTTGGTAGTTCTGGATAATAATCAAGCCTATATTATCGACACACCTTGGTCTGAAGAAGACACGAAGTTGTTATTATCCTGGGCGACTGACAGGGGATACCAGGTTATGGCTAGCATCTCAACTCATTCTCATGGAGATCGCACTGCTGGTATCAAGTTGCTAAATTCAAAGTCAATTCCTACATACACATCAGAGTTAACTAAAAAGCTTCTTGCCCGTGAAGGAAAGCCGGTTCCTACCCACTACTTTAAAGACGACGAATTCACACTGGGAAATGGGCTTATAGAGCTCTACTATCCAGGTGCTGGGCATACAGAGGATAATATTGTTGCTTGGTTACCCAAAAGCAAAATACTATTTGGTGGCTGCCTCGTGAGGAGTCATGAGTGGGAAGGCTTAGGTTACGTAGGCGACGCCTCAATTAGCTCTTGGGCTGACTCAATTAAAAATATTGTATCGAAAAAATATCCCATTCAAATGGTCGTTCCGGGGCATGGCAAAGTTGGAAGTTCAGATATATTAGATCACACCATTGATCTTGCTGAATCAGCTTCTAACAAATTAATGCAACCGACCGCTGAAGCGTCGGCTGATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3003194","ARO_id":"39771","ARO_name":"GIM-2","CARD_short_name":"GIM-2","ARO_description":"GIM-2 is a metallo-beta-lactamase present on an integron found in clinical isolates of Enterobacter cloacae in Germany.","ARO_category":{"39772":{"category_aro_accession":"3003195","category_aro_cvterm_id":"39772","category_aro_name":"GIM beta-lactamase","category_aro_description":"GIM beta-lactamase enzymes isolated from Pseudomonas aeruginosa, and found to confer broad-spectrum resistance to beta-lactam antibiotics.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1624":{"model_id":"1624","model_name":"lmrD","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1320"}},"model_sequences":{"sequence":{"5589":{"protein_sequence":{"accession":"AYV52072.1","sequence":"MENTKSTRKMSDTTRAIRFFYLYLKRYKLQFAVIMIFIILATWLQVVSPSLLGDAITNLTKYVTDFFTHQHAGQSQDALQQIAQQLSQQMHQTVDWHNVPEVVKSLPQAAQDQITANLPKGTTLETLKTVATSHAASTSTFMKGMWQLLAVYVATGVSMLIYTLLFSRIVAHSTNRMRKGLFGKLERLTISYFDRHQDGDILARFTSDLDNIQNTLNQALVSVISNAAVFVGVIIQIFNKDVTFAWLTVAASPVAILSAVIIIRQSKKATDKQQEEVSQLNAYMDEKISGQKAIIVEGLQEDSINGFLEHNENVKKRTFAAQAWSGMIFPLMNGFQLLSIAIVIFGGTAYVLNDDSMSIATGLGLLVAFVQYVQSYYNPIMQISSNFGQLQLAITGATRLNVMFDEPEEVRPENGKKFDTIKDGIQIENLDFEYLPGKPVLKKVNIDVKKGQMVALVGPTGSGKTTVMNLMNRFYDVNGGAIKFDGTDIREFDLDSLRSNVGIVLQESVLFDGTIADNIKFGKPNATQEEIETVAKTTHIHDFIDSLPDKYETHVSDDESVFSVGQKQQISIARTILTNPELLILDEATSNVDTVTEQQIQWAMEAAIAGRTSFVIAHRLKTILNADKIVVLKDGEVIEEGNHHELVAQGGFYSELYHNQFVFE"},"dna_sequence":{"accession":"CP033607.1","fmin":"310893","fmax":"312888","strand":"+","sequence":"ATGGAAAATACCAAATCAACAAGAAAAATGTCTGACACCACACGTGCCATCCGATTTTTTTACCTCTATCTGAAAAGATATAAACTCCAATTTGCTGTAATTATGATTTTCATCATTTTAGCAACTTGGTTACAGGTTGTTTCTCCATCACTTTTGGGGGACGCCATCACTAATTTGACTAAATATGTGACTGACTTCTTTACACATCAACATGCTGGTCAATCCCAAGATGCACTACAACAAATTGCTCAACAATTAAGCCAACAAATGCACCAAACAGTAGATTGGCACAATGTTCCTGAAGTTGTGAAATCTTTGCCACAAGCAGCACAAGACCAAATCACTGCTAATCTTCCTAAAGGAACAACTTTAGAAACACTTAAAACAGTGGCAACTTCACATGCAGCCAGCACTTCTACATTCATGAAAGGAATGTGGCAATTGCTTGCAGTCTATGTAGCAACAGGTGTATCAATGTTGATTTATACCTTGCTCTTTAGTCGTATCGTTGCTCATTCAACAAATCGCATGCGTAAAGGTTTGTTTGGTAAACTTGAACGTTTGACAATTTCATATTTTGACCGTCATCAAGATGGTGATATCCTTGCTCGTTTCACATCTGACTTGGATAACATTCAAAATACTTTAAACCAAGCACTCGTTTCGGTTATTTCAAATGCTGCGGTCTTTGTGGGTGTCATTATCCAGATTTTCAATAAAGATGTGACATTTGCTTGGTTGACAGTTGCTGCTTCTCCAGTTGCCATTTTATCTGCTGTGATTATCATTCGTCAATCGAAAAAAGCAACAGACAAACAACAAGAAGAAGTTTCACAACTTAATGCCTATATGGATGAAAAAATCTCTGGGCAAAAAGCAATTATCGTTGAAGGTTTACAAGAAGATTCTATTAATGGATTCTTGGAACACAATGAAAATGTTAAAAAACGTACCTTTGCTGCTCAAGCATGGTCTGGTATGATTTTCCCATTGATGAATGGTTTCCAACTTTTATCAATTGCCATTGTTATCTTTGGTGGAACGGCCTATGTTCTTAACGATGATAGCATGTCAATTGCCACAGGTTTAGGGCTTTTGGTTGCCTTTGTTCAATACGTTCAAAGTTACTACAACCCAATCATGCAAATTTCATCAAACTTTGGTCAACTTCAACTTGCCATCACAGGGGCAACTCGTCTGAATGTCATGTTTGATGAACCAGAAGAAGTTCGTCCTGAAAATGGTAAGAAATTTGATACGATTAAAGACGGAATTCAAATCGAAAATCTTGATTTTGAATATCTTCCAGGAAAACCAGTCCTCAAAAAAGTTAATATTGATGTTAAAAAAGGACAAATGGTTGCCCTCGTTGGTCCAACTGGTTCAGGTAAAACAACAGTTATGAACTTGATGAACCGTTTCTACGATGTTAATGGTGGAGCAATTAAATTTGATGGAACTGATATTCGTGAATTTGATTTAGATAGCTTGCGTTCAAATGTCGGAATTGTTTTGCAAGAGTCTGTTCTCTTTGATGGAACGATTGCTGATAATATCAAGTTTGGTAAACCAAATGCTACTCAAGAAGAAATTGAAACAGTGGCTAAGACAACTCACATTCATGATTTCATTGATAGCTTACCTGACAAGTACGAAACACATGTTTCAGATGATGAATCAGTCTTCTCAGTTGGTCAAAAACAACAAATTTCTATCGCACGTACCATTTTGACAAATCCAGAACTTTTGATTTTGGATGAAGCAACTTCAAATGTGGATACAGTAACTGAACAACAAATTCAATGGGCGATGGAAGCTGCTATTGCTGGTCGTACTTCATTCGTTATTGCTCACCGTTTGAAAACAATTCTTAATGCAGATAAGATTGTTGTTCTTAAAGATGGTGAAGTTATCGAAGAAGGAAATCACCATGAACTTGTTGCTCAAGGTGGCTTCTACTCTGAACTTTATCACAATCAATTTGTTTTTGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39577","NCBI_taxonomy_name":"Lactococcus lactis","NCBI_taxonomy_id":"1358"}}}},"ARO_accession":"3002882","ARO_id":"39316","ARO_name":"lmrD","CARD_short_name":"lmrD","ARO_description":"lmrD is a chromosomally-encoded efflux pump that confers resistance to lincosamides in Streptomyces lincolnensis and Lactococcus lactis. It can dimerize with lmrC.","ARO_category":{"36002":{"category_aro_accession":"0010001","category_aro_cvterm_id":"36002","category_aro_name":"ATP-binding cassette (ABC) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding\/hydrolysis to transport substrates across cell membranes.","category_aro_class_name":"AMR Gene Family"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1625":{"model_id":"1625","model_name":"OXA-179","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1126":{"protein_sequence":{"accession":"ADM26744.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIAVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"HM570035.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCCCTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTCTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTGCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001473","ARO_id":"37873","ARO_name":"OXA-179","CARD_short_name":"OXA-179","ARO_description":"OXA-179 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1626":{"model_id":"1626","model_name":"vgaE","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1020"}},"model_sequences":{"sequence":{"562":{"protein_sequence":{"accession":"CBY88983.1","sequence":"MLLFEGTSLKKHIQDRLLFDIDLIQVHEHQRIGLVGRNGTGKTSLLKIITGEELVDGGNVNHFTSVKLVPQFKETRSEKSGGEITQQYLQLAFNEKPGLLILDEPTTHLDTQRIDWLEKKLANYQGAFVVVSHDRTFLNNVCTEIWEIEDGSLNAFKGDYNAYAEQKELIKTQQQIAFEKYEREKKQLEKAIRQKEERAQRATKKPKNLSSSEARITGAKTHYANIQKKLRGSAKALETRLEQLDRIDKVKELPEIKMDILNKESLTNQSVLRAENIKGEVDGRKLWNPFSLYLYGGDKVAIIGKNGTGKTTLLKKIVERDERIAIPEKVRIGYFSQHLTILDDDKTIIENIQLTSSQDETLIRTVLARMHFWDEDVYKKVGILSGGEKVKVALAKLFLSDVNMLVLDEPTNFLDIESLEALETLMKSYHGTILFVTHDRTLVTNIATKIIDIKDGKITVFDGSYEAYEEWLENQTKSNNDDQLLLIETKISDVLGRLSLEPSRELEDEFQRLLKEKKELTKKL"},"dna_sequence":{"accession":"FR772051.1","fmin":"8740","fmax":"10315","strand":"+","sequence":"ATGTTATTATTTGAAGGTACATCATTGAAAAAACACATACAAGACAGATTATTATTTGATATAGATTTAATACAAGTACATGAACATCAGCGAATAGGATTAGTAGGTAGGAATGGAACGGGGAAAACAAGTCTATTAAAAATTATTACAGGTGAAGAACTAGTTGATGGAGGGAATGTTAATCATTTTACCTCTGTAAAATTAGTACCACAATTTAAAGAAACAAGATCGGAGAAAAGTGGTGGAGAAATAACGCAACAATATTTGCAATTAGCATTTAATGAAAAGCCAGGATTATTAATTTTAGATGAACCAACGACTCATTTAGATACACAAAGAATTGATTGGTTAGAAAAGAAATTAGCAAACTATCAAGGAGCATTTGTTGTCGTATCACATGATCGGACATTTCTAAATAATGTGTGTACTGAAATATGGGAAATAGAAGATGGTAGTCTAAACGCGTTTAAAGGGGATTATAATGCTTATGCGGAACAAAAGGAATTAATAAAAACACAGCAGCAGATTGCATTTGAAAAGTACGAACGAGAGAAAAAGCAATTAGAAAAAGCAATACGACAAAAAGAGGAAAGAGCACAGCGAGCAACAAAGAAACCTAAAAATCTGAGTTCTTCAGAGGCAAGAATAACAGGAGCTAAAACCCATTATGCCAATATACAGAAAAAGTTGAGGGGTTCTGCAAAAGCATTAGAAACAAGGTTGGAACAACTGGATAGGATTGACAAGGTGAAAGAACTACCTGAAATTAAGATGGATATATTAAATAAAGAAAGTCTAACAAACCAGTCTGTGTTACGCGCTGAAAACATTAAGGGAGAGGTTGACGGACGTAAGCTTTGGAATCCCTTTAGTTTATATTTATATGGCGGCGATAAAGTTGCTATCATTGGGAAAAATGGCACGGGTAAAACAACCTTACTTAAAAAAATAGTTGAGCGAGATGAAAGAATAGCAATCCCAGAAAAGGTGAGGATAGGTTATTTTTCCCAACACCTCACAATTCTCGATGATGATAAAACAATCATAGAAAATATACAATTGACCTCTAGTCAGGATGAAACATTAATTAGAACAGTTTTAGCAAGAATGCATTTTTGGGATGAAGATGTCTATAAAAAGGTCGGCATATTAAGTGGTGGTGAAAAAGTAAAAGTAGCACTAGCTAAACTATTCTTAAGTGACGTGAATATGCTGGTGTTAGATGAACCTACAAATTTTTTAGATATTGAATCTTTAGAAGCGCTAGAAACATTAATGAAAAGTTATCATGGAACGATTCTATTTGTTACTCACGACCGAACGTTAGTAACAAATATAGCTACAAAAATAATTGATATAAAAGATGGTAAGATAACAGTATTCGATGGATCATACGAAGCATATGAAGAGTGGTTAGAGAATCAAACAAAGTCCAACAATGATGATCAACTTTTACTAATCGAAACTAAAATATCTGACGTTCTGGGTAGGTTGAGTTTGGAGCCTTCACGAGAGTTAGAAGATGAATTTCAAAGATTATTGAAAGAAAAGAAAGAACTGACTAAAAAACTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35536","NCBI_taxonomy_name":"Staphylococcus aureus subsp. aureus ST398","NCBI_taxonomy_id":"523796"}}}},"ARO_accession":"3002833","ARO_id":"39267","ARO_name":"vgaE","CARD_short_name":"vgaE","ARO_description":"vgaE is an ABC-F subfamily protein expressed in staphylococci that confers resistance to streptogramin A antibiotics and related compounds. It is associated with transposon DNA.","ARO_category":{"36252":{"category_aro_accession":"3000113","category_aro_cvterm_id":"36252","category_aro_name":"vga-type ABC-F protein","category_aro_description":"Vga-type plasmid-borne ABC-F proteins, expressed in staphylococci that confer resistance to streptogramin A antibiotics through ribosomal protection.","category_aro_class_name":"AMR Gene Family"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"virginiamycin M1","category_aro_description":"Virginiamycin M1 is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37015":{"category_aro_accession":"3000671","category_aro_cvterm_id":"37015","category_aro_name":"tiamulin","category_aro_description":"Tiamulin is a pleuromutilin derivative currently used in veterinary medicine. It binds to the 23 rRNA of the 50S ribosomal subunit to inhibit protein translation.","category_aro_class_name":"Antibiotic"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35952":{"category_aro_accession":"0000034","category_aro_cvterm_id":"35952","category_aro_name":"streptogramin A antibiotic","category_aro_description":"Streptogramin A antibiotics are cyclic polyketide peptide hybrids that bind to the ribosomal peptidyl transfer centre. Structural variation arises from substituting a proline for its desaturated derivative and by its substitution for Ala or Cys. Used alone, streptogramin A antibiotics are bacteriostatic, but is bactericidal when used with streptogramin B antibiotics.","category_aro_class_name":"Drug Class"},"37014":{"category_aro_accession":"3000670","category_aro_cvterm_id":"37014","category_aro_name":"pleuromutilin antibiotic","category_aro_description":"Pleuromutilins are natural fungal products that target bacterial protein translation by binding the the 23S rRNA, blocking the ribosome P site at the 50S subunit. They are mostly used for agriculture and veterinary purposes.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1627":{"model_id":"1627","model_name":"CTX-M-95","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"869":{"protein_sequence":{"accession":"CBL80615.1","sequence":"MMTQSIRRSMLTVMATLPLLFSSATLHAQTNSVQQQLEALEKSSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAALLKQSESDKHLLNQRVEIKKSDLVNYNPIAEKHVNGTMTLAELGAAALQYSDNTAMNKLIAHLGGPDKVTAFARSLGDETFRLDRTEPTLNTAIPGDPRDTTTPLAMAQTLKNLTLGKALAETQRAQLVTWLKGNTTGSASIQAGLPKSWVVGDKTGSGDYGTTNDIAVIWPENHAPLVLVTYFTQPEQKAESRRDVLAAAAKIVTHGF"},"dna_sequence":{"accession":"FN813245.1","fmin":"1911","fmax":"2787","strand":"+","sequence":"ATGATGACTCAGAGCATTCGCCGCTCAATGTTAACGGTGATGGCGACGCTACCCCTGCTATTTAGCAGCGCAACGCTGCATGCGCAAACGAACAGCGTGCAACAGCAGCTGGAAGCCCTGGAGAAAAGTTCGGGAGGTCGGCTTGGCGTTGCGCTGATTAACACCGCCGATAATTCGCAGATTCTCTACCGTGCCGATGAACGTTTTGCGATGTGCAGTACCAGTAAGGTGATGGCGGCCGCGGCGTTGCTTAAACAGAGCGAGAGCGATAAGCACCTGCTAAATCAGCGCGTTGAAATCAAGAAGAGCGACCTGGTTAACTACAATCCCATTGCGGAGAAACACGTTAACGGCACGATGACGCTGGCTGAGCTTGGCGCAGCGGCGCTGCAGTATAGCGACAATACTGCCATGAATAAGCTGATTGCCCATCTGGGTGGGCCCGATAAAGTGACGGCGTTTGCTCGCTCGTTGGGTGATGAGACCTTCCGTCTGGACAGAACCGAGCCCACGCTCAATACCGCCATTCCAGGCGACCCGCGTGATACTACCACGCCGCTCGCGATGGCGCAGACCCTGAAAAATCTGACGCTGGGTAAAGCGCTGGCGGAAACCCAGCGGGCACAGTTGGTGACGTGGCTTAAGGGCAATACTACCGGTAGCGCGAGCATTCAGGCGGGTCTGCCGAAATCATGGGTAGTGGGCGATAAAACCGGCAGCGGAGATTATGGCACCACCAACGATATCGCGGTTATCTGGCCGGAAAACCACGCACCGCTGGTTCTGGTGACCTACTTTACCCAACCGGAGCAGAAGGCGGAAAGCCGTCGGGATGTTCTGGCTGCGGCAGCGAAAATCGTAACCCACGGTTTCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36928","NCBI_taxonomy_name":"Kluyvera ascorbata","NCBI_taxonomy_id":"51288"}}}},"ARO_accession":"3001955","ARO_id":"38355","ARO_name":"CTX-M-95","CARD_short_name":"CTX-M-95","ARO_description":"CTX-M-95 is a beta-lactamase found in Kluyvera spp.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1628":{"model_id":"1628","model_name":"SHV-154","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1389":{"protein_sequence":{"accession":"AFQ23960.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGSVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGASKRGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"JX121121.1","fmin":"0","fmax":"858","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCAGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTAGCAAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGGATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGC","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001193","ARO_id":"37573","ARO_name":"SHV-154","CARD_short_name":"SHV-154","ARO_description":"SHV-154 is a beta-lactamase.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1629":{"model_id":"1629","model_name":"TEM-197","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1493":{"protein_sequence":{"accession":"AEK48085.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVKYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPVAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGASERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"HQ877606.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTAAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGTAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCAGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001056","ARO_id":"37436","ARO_name":"TEM-197","CARD_short_name":"TEM-197","ARO_description":"TEM-197 is an extended-spectrum beta-lactamase.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1630":{"model_id":"1630","model_name":"IMP-13","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1906":{"protein_sequence":{"accession":"CAD80251.1","sequence":"MKKLFVLCVCFFCSITAAGAALPDLKIEKLEEGVFVHTSFEEVNGWGVVTKHGLVVLVNTDAYLIDTPFTATDTEKLVNWFVERGYEIKGTISSHFHSDSTGGIEWLNSQSIPTYASELTNELLKKSGKVQAKYSFSEVSYWLVKNKIEVFYPGPGHTQDNLVVWLPESKILFGGCFIKPHGLGNLGDANLEAWPKSAKILMSKYGKAKLVVSSHSEKGDASLMKRTWEQALKGLKESKKTSSPSN"},"dna_sequence":{"accession":"AJ550807.1","fmin":"2242","fmax":"2983","strand":"+","sequence":"ATGAAGAAATTATTTGTTTTATGTGTATGCTTCTTTTGTAGCATTACTGCCGCAGGAGCGGCTTTACCTGATTTAAAAATCGAGAAGCTTGAAGAAGGTGTTTTTGTTCATACATCGTTCGAAGAGGTTAACGGTTGGGGGGTTGTTACTAAACACGGTTTAGTGGTGCTTGTAAACACAGACGCCTATCTAATTGACACTCCATTTACTGCTACAGACACTGAAAAATTAGTCAATTGGTTTGTGGAGCGCGGCTATGAAATCAAAGGCACTATTTCATCACATTTCCATAGCGACAGCACAGGAGGAATAGAGTGGCTTAATTCTCAATCTATTCCCACGTATGCATCTGAATTAACAAATGAACTTTTGAAAAAATCCGGTAAGGTACAAGCTAAATATTCATTTAGCGAAGTTAGCTATTGGCTAGTTAAAAATAAAATTGAAGTTTTCTACCCTGGCCCAGGTCACACTCAAGATAACCTAGTGGTTTGGTTGCCTGAAAGTAAAATTTTATTCGGTGGTTGCTTTATTAAACCTCACGGTCTTGGCAATTTAGGTGACGCAAATTTAGAAGCTTGGCCAAAGTCCGCCAAAATATTAATGTCTAAATATGGCAAAGCAAAGCTTGTTGTTTCAAGTCATAGTGAAAAAGGGGACGCATCACTAATGAAACGTACATGGGAACAAGCCCTTAAAGGGCTTAAAGAAAGTAAAAAAACATCATCACCAAGTAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002204","ARO_id":"38604","ARO_name":"IMP-13","CARD_short_name":"IMP-13","ARO_description":"IMP-13 is a beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1631":{"model_id":"1631","model_name":"CTX-M-71","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1513":{"protein_sequence":{"accession":"ACV92002.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSCGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"FJ815436.1","fmin":"195","fmax":"1071","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCTGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001932","ARO_id":"38332","ARO_name":"CTX-M-71","CARD_short_name":"CTX-M-71","ARO_description":"CTX-M-71 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1632":{"model_id":"1632","model_name":"CTX-M-53","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8257":{"protein_sequence":{"accession":"ABB72225.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTVDVQQKLAELEQQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAVAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVIYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"DQ268764.2","fmin":"5891","fmax":"6767","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGTGGACGTACAGCAAAAACTTGCCGAATTAGAGCAGCAGTCGGGAGGAAGGCTGGGTGTGGCATTGATTAACACGGCGGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGTGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTCGAGATCAAAAAATCTGACCTGGTTAACTATAATCCGATTGCGGAAAAACACGTCAATGGGACGATGTCACTGGCTGAGCTCAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTTACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCTGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACGCTGCGTAATCTGACGCTGGGTAAAGCATTGGGTGACAGCCAACGGGCGCAGCTGGTGACGTGGATGAAAGGCAATACTACCGGTGCAGCGAGTATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGTACCACCAACGATATCGCGGTGATTTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCATTTACTTCACCCAGCCCCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35809","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Westhampton","NCBI_taxonomy_id":"356621"}}}},"ARO_accession":"3001915","ARO_id":"38315","ARO_name":"CTX-M-53","CARD_short_name":"CTX-M-53","ARO_description":"CTX-M-53 is a beta-lactamase found in Salmonella enterica.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1633":{"model_id":"1633","model_name":"catQ","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"607":{"protein_sequence":{"accession":"AAA23215.1","sequence":"MKFNLIDIEDWNRKPYFEHYLNAVRCTYSMTANIEITGLLREIKLKGLKLYPTLIYIITTVVNRHKEFRTCFDQKGKLGYWDSMNPSYTVFHKDNETFSSIWTEYDENFPRFYYNYLEDIRNYSDVLNFMPKTGEPANTINVSSIPWVNFTGFNLNIYNDATYLIPIFTLGKYFQQDNKILLPMSVQVHHAVCDGYHISRFFNEAQELASNYETWLGEK"},"dna_sequence":{"accession":"M55620.1","fmin":"0","fmax":"660","strand":"+","sequence":"ATGAAATTTAATTTGATAGATATTGAGGATTGGAATAGAAAGCCATACTTTGAGCATTATTTAAATGCGGTTAGGTGCACTTACAGTATGACTGCAAATATAGAGATAACTGGTTTACTGCGTGAAATTAAACTTAAGGGCCTGAAACTGTACCCTACGCTTATTTATATCATCACAACTGTGGTTAACCGTCACAAGGAGTTCCGCACCTGTTTTGATCAAAAAGGTAAGTTAGGATACTGGGATAGTATGAACCCAAGTTATACTGTCTTTCATAAGGATAACGAAACTTTTTCAAGTATTTGGACAGAGTATGACGAGAACTTCCCACGTTTTTACTATAATTACCTTGAGGATATTAGAAACTATAGCGACGTTTTGAATTTCATGCCTAAGACAGGTGAACCTGCTAATACAATTAATGTGTCCAGCATTCCTTGGGTGAATTTTACCGGATTCAACCTGAATATATACAATGATGCAACATATCTAATCCCTATTTTTACTTTGGGTAAGTATTTTCAGCAGGATAATAAAATTTTATTACCTATGTCTGTACAGGTGCATCATGCGGTTTGCGACGGTTATCATATAAGCAGATTTTTTAATGAGGCACAGGAATTAGCGTCAAATTATGAGACATGGTTAGGAGAAAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36812","NCBI_taxonomy_name":"Clostridium perfringens","NCBI_taxonomy_id":"1502"}}}},"ARO_accession":"3002687","ARO_id":"39121","ARO_name":"catQ","CARD_short_name":"catQ","ARO_description":"catQ is a chromosome-encoded variant of the cat gene found in Clostridium perfringens.","ARO_category":{"36261":{"category_aro_accession":"3000122","category_aro_cvterm_id":"36261","category_aro_name":"chloramphenicol acetyltransferase (CAT)","category_aro_description":"Inactivates chloramphenicol by addition of an acyl group. CAT is used to describe many variants of the chloramphenicol acetyltransferase gene in a range of organisms including Acinetobacter calcoaceticus, Agrobacterium tumefaciens, Alkalihalobacillus clausii, Bacillus subtilis, Campylobacter coli, Enterococcus faecalis, Enterococcus faecium, Lactococcus lactis, Listeria monocytogenes, Listonella anguillarum, Morganella morganii, Photobacterium damselae subsp. piscicida, Proteus mirabilis, Salmonella typhi, Serratia marcescens, Shigella flexneri, Staphylococcus aureus, Staphylococcus haemolyticus, Staphylococcus intermedius, Streptococcus agalactiae, Streptococcus suis and Streptomyces acrimycini.","category_aro_class_name":"AMR Gene Family"},"36521":{"category_aro_accession":"3000382","category_aro_cvterm_id":"36521","category_aro_name":"azidamfenicol","category_aro_description":"Azidamfenicol is a water soluble derivative of chloramphenicol, sharing the same mode of action of inhibiting peptide synthesis by interacting with the 23S RNA of the 50S ribosomal subunit.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36595":{"category_aro_accession":"3000456","category_aro_cvterm_id":"36595","category_aro_name":"thiamphenicol","category_aro_description":"Derivative of Chloramphenicol. The nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3).","category_aro_class_name":"Antibiotic"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1480":{"model_id":"1480","model_name":"EXO-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"3292":{"protein_sequence":{"accession":"AAA26775.1","sequence":"MHPSTSRPSRRTLLTATAGAALAAATLVPGTAHASSGGRGHGSGSVSDAERRLAGLERASGARLGVYAYDTGSGRTVAYRADELFPMCSVFKTLSSAAVLRDLDRNGEFLSRRILYTQDDVEQADGAGPETGKPQNLANAQLTVEELCEVSITASDNCAANLMLRELGGPAAVTRFVRSLGDRVTRLDRWEPELNSAEPGRVTDTTSPRAITRTYGRLVLGDALNPRDRRLLTSWLLANTTSGDRFRAGLPDDWTLGDKTGAGRYGTNNDAGVTWPPGRAPIVLTVLTAKTEQDAARDDGLVADAARVLAETLG"},"dna_sequence":{"accession":"M28303.1","fmin":"242","fmax":"1187","strand":"+","sequence":"GTGCACCCCAGCACTTCCCGTCCCTCCCGCCGCACCCTGTTGACCGCCACGGCGGGCGCAGCCCTGGCCGCCGCCACACTCGTACCCGGTACCGCGCACGCCTCCTCCGGCGGGCGGGGCCACGGTTCCGGTTCCGTCTCCGACGCCGAACGGCGGCTCGCGGGGCTGGAGCGGGCCAGTGGGGCGCGGCTCGGGGTGTACGCGTACGACACGGGGAGCGGGCGGACGGTCGCGTACCGGGCCGACGAGCTGTTCCCGATGTGTTCGGTGTTCAAGACGCTGTCGTCGGCGGCCGTTCTGCGGGACCTCGACCGGAACGGGGAGTTCCTGTCCCGCCGGATCTTGTACACGCAGGACGACGTGGAGCAGGCCGACGGCGCCGGCCCCGAGACAGGCAAGCCGCAGAACCTGGCCAACGCGCAATTGACCGTCGAGGAGTTGTGCGAGGTCTCCATCACCGCCTCCGACAACTGCGCCGCCAACCTCATGCTGCGCGAGCTGGGCGGGCCCGCCGCCGTCACCCGGTTCGTCCGCTCGCTCGGTGACCGGGTCACCCGGCTCGACCGCTGGGAGCCGGAGCTGAACTCCGCCGAGCCCGGCCGCGTCACCGACACCACCTCGCCGCGCGCCATCACCCGCACCTACGGCCGCCTCGTCCTCGGCGACGCCCTGAACCCGCGCGACCGCCGCCTGCTCACCAGCTGGCTCCTGGCCAACACCACGAGCGGCGACCGGTTCCGCGCGGGGCTCCCGGACGACTGGACCCTCGGCGACAAGACCGGCGCCGGCCGCTACGGCACCAACAACGACGCGGGCGTCACCTGGCCCCCCGGCCGCGCGCCGATCGTCCTGACCGTCCTCACGGCCAAGACCGAGCAGGACGCCGCCCGCGACGACGGGCTCGTCGCGGACGCGGCCCGGGTACTGGCGGAGACGCTGGGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40173","NCBI_taxonomy_name":"Streptomyces albus","NCBI_taxonomy_id":"1888"}}}},"ARO_accession":"3003564","ARO_id":"40172","ARO_name":"EXO-1","CARD_short_name":"EXO-1","ARO_description":"Class A beta-lactamase found in Streptomyces albus G.","ARO_category":{"41398":{"category_aro_accession":"3004234","category_aro_cvterm_id":"41398","category_aro_name":"EXO beta-lactamase","category_aro_description":"Beta-lactamases part of this family discovered in Streptomyces albus G.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1509":{"model_id":"1509","model_name":"vanX gene in vanF cluster","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"200"}},"model_sequences":{"sequence":{"8203":{"protein_sequence":{"accession":"AAF36804.1","sequence":"MEKDFVFLDEILHGVRWDSKYATWDNFTGKPVDGYEVNRIAGTYALAVALLEVKKQAAALGYGLLLWDGYRPQRAVNCFLHWSAQPEDGRTKERYYPNIDRIEMVTKGYVASKSSHSRGSAIDLTLYRLDTGALVPMGSGFDFMDERSHHTSKGISSNEAQNRQLLCSIMEYSGFESYVYEWWHYVLRNEPYPSSYFDFPIGGNHLDPFSNFCGTVPLDALSP"},"dna_sequence":{"accession":"AF155139.2","fmin":"6976","fmax":"7648","strand":"+","sequence":"ATGGAAAAAGATTTTGTTTTTTTAGATGAAATATTGCATGGAGTTCGTTGGGACTCCAAATATGCCACATGGGACAATTTCACTGGAAAACCGGTAGACGGATATGAAGTCAATCGCATAGCGGGGACATATGCTTTGGCTGTTGCGCTGCTGGAGGTAAAGAAGCAGGCGGCTGCTCTAGGGTACGGCTTGCTCCTGTGGGATGGCTATCGTCCTCAACGTGCGGTAAACTGTTTCTTGCATTGGTCTGCGCAGCCGGAAGACGGCCGCACAAAAGAAAGATATTATCCCAATATTGATCGGATCGAGATGGTTACAAAGGGATATGTGGCTTCAAAATCAAGCCACAGTCGCGGAAGCGCGATTGACCTTACGCTTTATCGATTGGACACGGGTGCGCTTGTCCCTATGGGGAGCGGCTTCGATTTTATGGATGAACGTTCACATCATACCTCAAAAGGAATTTCAAGTAACGAAGCGCAAAATCGCCAGTTATTATGTTCTATTATGGAATACAGCGGATTTGAATCATATGTATATGAATGGTGGCACTACGTATTAAGAAACGAACCATACCCCAGCAGCTATTTTGATTTTCCCATTGGCGGGAACCATCTAGACCCATTTTCCAACTTTTGTGGGACAGTGCCACTTGATGCGTTGTCGCCCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39542","NCBI_taxonomy_name":"Paenibacillus popilliae ATCC 14706","NCBI_taxonomy_id":"1212764"}}}},"ARO_accession":"3002952","ARO_id":"39386","ARO_name":"vanX gene in vanF cluster","CARD_short_name":"vanX_in_vanF_cl","ARO_description":"Also known as vanXF, is a vanX variant found in the vanF gene cluster.","ARO_category":{"36020":{"category_aro_accession":"3000011","category_aro_cvterm_id":"36020","category_aro_name":"vanX","category_aro_description":"VanX is a D,D-dipeptidase that cleaves D-Ala-D-Ala but not D-Ala-D-Lac, ensuring that the latter dipeptide that has reduced binding affinity with vancomycin is used to synthesize peptidoglycan substrate.","category_aro_class_name":"AMR Gene Family"},"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1547":{"model_id":"1547","model_name":"vanR gene in vanC cluster","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"105":{"protein_sequence":{"accession":"AAF86641.1","sequence":"MSEKIVVVDDEKEIADLVTTFLQNEGFSVQPFYDGTSAIAYIEKEAIDLAVLDVMLPDIDGFQLLQQIRKTHFFPVLMLTAKGEDLDKITGLSLGADDYVTKPFNPLEVVARVKTQLRRYQRYNHSTASPTVEEYEKDGLILKINSHQCILYGKEVFLTPIEFKILLYLFEHQGSVVSSETLFEAVWKEKYLDNNNTVMAHIARLREKLHEEPRKPKLIKTVWGVGYIIEK"},"dna_sequence":{"accession":"AF162694.1","fmin":"5192","fmax":"5888","strand":"+","sequence":"ATGTCAGAAAAAATAGTCGTTGTTGATGATGAAAAAGAAATTGCGGACTTAGTCACGACCTTTTTGCAAAACGAAGGATTTAGTGTGCAGCCGTTTTATGATGGTACTAGTGCCATCGCCTATATTGAAAAAGAAGCCATTGATTTGGCCGTTTTAGATGTCATGTTGCCGGACATTGATGGTTTTCAACTGTTACAGCAGATCCGCAAGACCCATTTTTTCCCAGTGTTGATGCTGACTGCCAAGGGAGAGGATCTAGACAAAATCACTGGATTGAGTTTGGGAGCGGATGACTATGTCACCAAACCTTTTAATCCTTTAGAAGTTGTGGCTCGGGTAAAAACCCAATTGCGGCGCTACCAGCGATACAATCATTCCACTGCTTCTCCAACAGTAGAAGAATATGAAAAAGACGGCTTGATACTCAAAATCAACAGTCATCAATGCATTCTCTACGGCAAAGAAGTTTTCCTGACTCCCATTGAGTTCAAAATATTGCTTTATTTATTTGAGCACCAAGGATCCGTCGTCTCTTCCGAAACACTTTTCGAAGCGGTTTGGAAAGAAAAATATTTAGATAACAATAATACTGTCATGGCACACATTGCTCGTTTAAGAGAAAAATTGCATGAAGAACCTCGTAAACCTAAATTAATCAAAACCGTATGGGGGGTCGGCTATATCATTGAAAAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36781","NCBI_taxonomy_name":"Enterococcus gallinarum","NCBI_taxonomy_id":"1353"}}}},"ARO_accession":"3002922","ARO_id":"39356","ARO_name":"vanR gene in vanC cluster","CARD_short_name":"vanR_in_vanC_cl","ARO_description":"Also known as vanRC, is a vanR variant found in the vanC gene cluster.","ARO_category":{"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"36713":{"category_aro_accession":"3000574","category_aro_cvterm_id":"36713","category_aro_name":"vanR","category_aro_description":"VanR is a OmpR-family transcriptional activator in the VanSR regulatory system. When activated by VanS, it promotes cotranscription of VanA, VanH, and VanX.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1552":{"model_id":"1552","model_name":"MUS-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1597":{"protein_sequence":{"accession":"AAN63647.1","sequence":"MHRILSVITMLICTTLVHAQSDKLKIKQLNDNMYIYTTYQEFQGVTYSSNSMYVLTDEGVILIDTPWDKDQYEPLLEYIRSNHNKEVKWVITTHFHEDRSGGLGYFNSIGAQTYTYALTNEILKERNEPQAQHSFNKEKQFTFGNEKLAVYFLGEGHSLDNTVVWFPKEEVLYGGCLIKSAEATTIGNIADGNVIAWPKTIEAVKQKFKNAKVIIPGHDEWDMTGHIENTERILSAYNQQHSTKND"},"dna_sequence":{"accession":"AF441286.1","fmin":"224","fmax":"965","strand":"+","sequence":"ATGCACAGAATACTTAGTGTCATAACGATGTTAATCTGTACTACATTAGTACACGCTCAATCTGACAAACTAAAAATCAAACAACTCAATGATAATATGTATATATACACTACTTATCAAGAGTTTCAAGGAGTAACATACTCTTCTAATTCGATGTACGTACTGACAGACGAAGGCGTTATTCTAATAGACACACCTTGGGATAAAGATCAGTACGAACCTCTATTAGAGTACATCAGATCGAATCATAACAAAGAGGTTAAATGGGTCATCACTACCCACTTCCACGAAGATCGTTCTGGTGGATTAGGTTACTTTAACAGTATAGGAGCACAGACGTATACCTATGCATTGACCAATGAAATATTAAAAGAACGCAATGAACCACAAGCTCAACATTCTTTTAATAAAGAAAAACAGTTTACCTTTGGCAATGAGAAGTTGGCTGTATACTTTTTAGGAGAAGGACATTCACTAGATAATACCGTAGTCTGGTTTCCAAAAGAAGAAGTATTATACGGAGGATGCCTGATTAAGAGTGCCGAAGCTACCACTATAGGTAATATAGCCGATGGTAACGTGATAGCTTGGCCTAAGACTATCGAAGCCGTAAAACAAAAATTTAAGAATGCTAAAGTCATTATACCAGGACATGATGAATGGGATATGACAGGCCATATCGAGAATACTGAGCGTATATTATCAGCATACAATCAACAACATTCAACTAAAAACGATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39072","NCBI_taxonomy_name":"Myroides odoratimimus","NCBI_taxonomy_id":"76832"}}}},"ARO_accession":"3000843","ARO_id":"37223","ARO_name":"MUS-1","CARD_short_name":"MUS-1","ARO_description":"MUS-1 is a chromosome-encoded beta-lactamase from Myroides odoratus and Myroides odoratimimus.","ARO_category":{"41143":{"category_aro_accession":"3004067","category_aro_cvterm_id":"41143","category_aro_name":"MUS beta-lactamase","category_aro_description":"Subclass B1 (metallo-) beta-lactamases found in Myroides spp., which confer resistance to carbapenam class beta-lactamase antibiotics.","category_aro_class_name":"AMR Gene Family"},"35981":{"category_aro_accession":"0000064","category_aro_cvterm_id":"35981","category_aro_name":"amoxicillin","category_aro_description":"Amoxicillin is a moderate-spectrum, bacteriolytic, beta-lactam antibiotic used to treat bacterial infections caused by susceptible microorganisms. A derivative of penicillin, it has a wider range of treatment but remains relatively ineffective against Gram-negative bacteria. It is commonly taken with clavulanic acid, a beta-lactamase inhibitor. Like other beta-lactams, amoxicillin interferes with the synthesis of peptidoglycan.","category_aro_class_name":"Antibiotic"},"35995":{"category_aro_accession":"0000078","category_aro_cvterm_id":"35995","category_aro_name":"piperacillin","category_aro_description":"Piperacillin is an acetylureidopenicillin and has an extended spectrum of targets relative to other beta-lactam antibiotics. It inhibits cell wall synthesis in bacteria, and is usually taken with the beta-lactamase inhibitor tazobactam to overcome penicillin-resistant bacteria.","category_aro_class_name":"Antibiotic"},"40523":{"category_aro_accession":"3003832","category_aro_cvterm_id":"40523","category_aro_name":"ticarcillin","category_aro_description":"Ticarcillin is a carboxypenicillin used for the treatment of Gram-negative bacteria, particularly P. aeruginosa. Ticarcillin's antibiotic properties arise from its ability to prevent cross-linking of peptidoglycan during cell wall synthesis, when the bacteria try to divide, causing cell death.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1566":{"model_id":"1566","model_name":"vanX gene in vanD cluster","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"200"}},"model_sequences":{"sequence":{"652":{"protein_sequence":{"accession":"AAM09852.1","sequence":"MEKNFVFLDEMLPGIRWDAKYATWDNFTGKPVDGYEVNRIVGTKELGAALRKAQKAAEKLGYGLLLWDGYRPQCAVDCFLTWASLPENNLTKKRYYPNIKRNEMITKGYVASQSSHSRGSAIDLTIFRLDTGMLVPMGGDFDFMDVRSHHAASGLSEEEAGNRERLRDIMERSGFEAYRYEWWHYVLADEPYPDTYFDFCIA"},"dna_sequence":{"accession":"AY082011.1","fmin":"6937","fmax":"7546","strand":"+","sequence":"ATGGAAAAGAACTTTGTCTTTTTGGATGAAATGCTGCCGGGCATCCGGTGGGATGCCAAATATGCCACATGGGACAATTTCACCGGGAAACCGGTAGACGGATACGAGGTAAACCGCATTGTGGGAACGAAAGAGCTTGGTGCCGCTTTACGTAAGGCACAGAAGGCGGCGGAGAAACTGGGATACGGTCTGCTCTTATGGGACGGCTACCGTCCCCAGTGTGCAGTGGACTGCTTTTTGACTTGGGCTTCCCTGCCGGAGAACAATCTGACGAAAAAGCGTTACTACCCAAATATCAAAAGGAACGAGATGATCACGAAAGGGTATGTGGCTTCTCAGTCCAGCCACAGTCGCGGGAGCGCGATTGATCTCACGATTTTTCGTTTGGACACGGGTATGCTTGTGCCAATGGGCGGAGATTTCGACTTTATGGATGTACGGTCGCATCATGCCGCCAGTGGTCTGAGCGAAGAGGAGGCCGGAAACCGTGAGCGCCTGCGTGATATCATGGAGCGCAGCGGATTTGAAGCCTACCGATATGAATGGTGGCATTATGTCTTGGCAGACGAGCCATACCCGGATACATATTTTGATTTTTGCATTGCCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36779","NCBI_taxonomy_name":"Enterococcus faecium","NCBI_taxonomy_id":"1352"}}}},"ARO_accession":"3003070","ARO_id":"39600","ARO_name":"vanX gene in vanD cluster","CARD_short_name":"vanX_in_vanD_cl","ARO_description":"Also known as vanXD, is a vanX variant found in the vanD gene cluster.","ARO_category":{"36020":{"category_aro_accession":"3000011","category_aro_cvterm_id":"36020","category_aro_name":"vanX","category_aro_description":"VanX is a D,D-dipeptidase that cleaves D-Ala-D-Ala but not D-Ala-D-Lac, ensuring that the latter dipeptide that has reduced binding affinity with vancomycin is used to synthesize peptidoglycan substrate.","category_aro_class_name":"AMR Gene Family"},"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"35948":{"category_aro_accession":"0000029","category_aro_cvterm_id":"35948","category_aro_name":"teicoplanin","category_aro_description":"Teicoplanin is a glycopeptide antibiotic used in the prophylaxis and treatment of serious infections caused by Gram-positive bacteria. Teicoplanin has a unique acyl-aliphatic chain, and binds to cell wall precursors to inhibit transglycosylation  and transpeptidation.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1570":{"model_id":"1570","model_name":"OprA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"890"}},"model_sequences":{"sequence":{"315":{"protein_sequence":{"accession":"BAM10414.1","sequence":"MPLSKLSASSLALCLGLLGACSLAPRYQRPEAPIPTTYPAVPASQQAGDRARLDDWQQQFTDPVLRQMIGQALEHNRNLRVAALRIEEARALYGVQASERLPTLEASGRYERERMRGETREAGEVEQRYRVAAGISAFELDFFGRVKNLGDAALADYLASEEAQRSARIALIAEVAGGYVQERALYAQQRLAERTLHARENGLALVRKRYAAGMSTRIDLRSEEMLVESARATHAALVRERSQAVSGLQLLLGDFTGDWQDSQLDLEHLQLQPLPAGLPSELLARRPDIRQAEQQLRAANANIGAARAAFFPSLRLSTDLGSASSGLHGLFRGGSRVWTFSPQMTLPIFDGGRNRANLDLAEVRKDIAVNRYEESIQVAFREVADALSAGDQLELQLRAQRAVRDADRERLQLVRKRYAKGVANYLEMLDAQRSLFDSEQQLIHLRGLRLNNGVALYRALGGGWSQG"},"dna_sequence":{"accession":"AB639410.1","fmin":"0","fmax":"1404","strand":"+","sequence":"ATGCCCCTTTCGAAACTCTCGGCCTCCTCCCTGGCGCTGTGCCTGGGCCTGCTCGGCGCCTGTTCGCTGGCGCCCCGCTACCAGCGCCCGGAGGCGCCGATCCCGACGACCTATCCGGCCGTCCCGGCGAGCCAGCAGGCTGGCGACCGGGCCAGGCTGGACGACTGGCAACAACAGTTCACCGACCCGGTGCTGCGCCAGATGATCGGCCAGGCCCTGGAGCACAACCGCAACCTGCGCGTCGCCGCCCTGCGCATCGAGGAAGCCCGCGCGCTATATGGCGTACAGGCCTCGGAGCGCTTGCCGACGCTGGAGGCCAGCGGTCGCTACGAGCGCGAGCGCATGCGCGGCGAAACCCGCGAGGCCGGCGAGGTCGAACAACGCTATCGGGTCGCAGCCGGCATCAGCGCCTTCGAGCTGGACTTCTTCGGCCGGGTGAAAAACCTCGGCGACGCCGCCCTGGCCGACTACCTGGCCAGCGAGGAGGCCCAGCGCAGCGCGCGGATCGCCCTGATCGCCGAGGTCGCCGGCGGCTACGTGCAGGAACGGGCGCTGTACGCACAGCAACGGCTGGCGGAACGCACCCTGCACGCGCGGGAAAACGGCCTGGCGCTGGTGCGCAAGCGCTACGCCGCCGGGATGAGCACGCGCATCGACCTGCGCAGCGAGGAAATGCTGGTGGAAAGCGCCCGCGCCACCCACGCCGCGCTGGTTCGCGAACGCAGCCAGGCGGTCAGCGGTCTGCAGCTGCTGCTCGGCGACTTCACCGGCGACTGGCAGGATAGCCAGCTGGACCTGGAACACCTCCAGCTGCAGCCACTGCCCGCCGGACTGCCCTCGGAGCTGCTCGCGCGGCGTCCGGACATCCGCCAGGCCGAACAACAACTGCGCGCGGCCAACGCCAACATCGGCGCGGCGCGCGCGGCGTTCTTCCCGAGCCTGCGCCTGAGCACCGACCTGGGCTCGGCCAGTTCAGGCCTGCACGGCCTGTTCAGGGGCGGCAGCCGGGTCTGGACCTTCAGCCCGCAGATGACCCTGCCGATCTTCGACGGCGGACGCAACCGCGCCAATCTCGACCTCGCCGAAGTGCGCAAGGACATCGCCGTCAACCGCTACGAGGAAAGCATCCAGGTCGCCTTCCGCGAGGTCGCCGACGCGCTCAGCGCCGGCGACCAGCTGGAGCTCCAGCTGCGCGCGCAGCGCGCTGTCCGCGACGCCGACCGTGAACGCCTGCAACTGGTACGCAAGCGCTATGCCAAGGGTGTCGCCAATTACCTGGAAATGCTCGACGCCCAGCGCAGCCTGTTCGACTCGGAACAGCAACTGATCCACCTGCGGGGCCTGCGCCTGAACAATGGCGTCGCCCTCTATCGCGCCCTCGGCGGCGGCTGGTCGCAAGGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3003039","ARO_id":"39473","ARO_name":"OprA","CARD_short_name":"OprA","ARO_description":"OprA is an outer membrane factor protein found in Pseudomonas aeruginosa. It is part of the MexXY-OprA complex.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35990":{"category_aro_accession":"0000073","category_aro_cvterm_id":"35990","category_aro_name":"meropenem","category_aro_description":"Meropenem is an ultra-broad spectrum injectable antibiotic used to treat a wide variety of infections, including meningitis and pneumonia. It is a beta-lactam and belongs to the subgroup of carbapenem, similar to imipenem and ertapenem.","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37007":{"category_aro_accession":"3000663","category_aro_cvterm_id":"37007","category_aro_name":"ofloxacin","category_aro_description":"Ofloxacin is a 6-fluoro, 7-piperazinyl quinolone with a methyl-substituted oxazine ring. It has a broad spectrum of activity including many enterobacteria and mycoplasma but most anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"46133":{"category_aro_accession":"3007382","category_aro_cvterm_id":"46133","category_aro_name":"gentamicin","category_aro_description":"Gentamicin is a commonly used aminoglycoside antibiotic derived from members of the Micromonospora genus of bacteria. It acts by binding the 30S ribosomal subunit, thus inhibiting protein synthesis. Gentamicin is typically used to treat Gram-negative infections of the repiratory and urinary tract, as well as infections of the bone and soft tissue. It also exhibits considerable nephrotoxicity and ototoxicity. Gentamicin is administered as a mixture of gentamicin type C (which makes about around 80% of the complex) and types A, B, and X (distributed in the remaining 20% of the complex).","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1571":{"model_id":"1571","model_name":"vanS gene in vanE cluster","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"649":{"protein_sequence":{"accession":"AAL27446.1","sequence":"MKNNLTVQITKKYFYTMIIITTILVILPLVAKMFLSLRVWQGTEFFYPILYILNRSLGVWLIVTPLFIWLIVTYMFFRKMISYLEEMIVATKSLIETPNEKIVLRVELAEFENEINHIRIDSLENKKMAEEAGKKRDDLLTYLAHDLRTPLTSIIGYISLLQNEQTYLELDSTKRKNYIDIISDKANRLEHLLNDFFEIAKTGKSREEVYKEEVDLSLMLSQISSEFLPLLDEKKLEWDFKIEPNVFVQLNINKFERVLDNLIRNAISYSLNDTTIKLTLEKVDEKVVVSVGNITDKVSEKDIDQLFEPFYRGDKSRNTKTGNAGLGLAIAKQIISEHGGTIEAELQNNDFKVSIIL"},"dna_sequence":{"accession":"FJ872411.1","fmin":"44192","fmax":"45266","strand":"+","sequence":"TTGAAAAATAATCTAACAGTGCAGATTACAAAAAAATATTTCTATACAATGATCATAATAACAACTATTCTAGTGATCCTTCCTTTGGTAGCCAAAATGTTTCTTTCTCTTCGAGTATGGCAGGGTACTGAATTTTTTTACCCAATATTATATATTTTAAATAGATCATTAGGAGTCTGGTTGATTGTAACACCGTTATTTATTTGGTTGATAGTGACTTATATGTTCTTTAGAAAAATGATTAGCTATTTAGAGGAAATGATAGTGGCTACTAAGAGTTTAATTGAAACACCGAATGAAAAAATAGTGTTAAGAGTTGAATTAGCAGAGTTTGAGAATGAAATTAATCATATTCGTATAGATAGTTTAGAGAATAAAAAGATGGCCGAAGAAGCAGGAAAAAAAAGAGATGATCTTCTAACCTATTTAGCACATGACTTGAGAACTCCTTTGACGAGTATTATTGGATATATCTCACTACTTCAAAATGAACAAACCTACTTGGAATTAGATTCTACAAAAAGGAAAAATTATATAGACATCATTTCAGACAAAGCTAACAGATTAGAGCATCTGCTCAATGATTTTTTTGAAATTGCAAAAACAGGCAAAAGTAGAGAAGAGGTGTATAAAGAAGAAGTAGATTTAAGCTTGATGTTAAGCCAAATTAGTTCTGAATTTTTGCCTCTTTTAGACGAGAAGAAGCTTGAGTGGGATTTTAAGATTGAACCAAATGTCTTTGTCCAATTAAATATTAATAAATTTGAACGAGTGTTGGATAATCTTATTAGAAATGCTATATCATACTCGCTCAATGATACAACGATAAAACTTACATTAGAGAAAGTAGATGAGAAAGTAGTAGTATCTGTAGGAAATATAACTGATAAGGTATCAGAAAAGGACATAGACCAGCTATTTGAACCATTTTACAGAGGAGATAAATCGAGAAATACAAAAACAGGGAATGCTGGTCTAGGGTTAGCAATTGCCAAACAAATTATTAGTGAGCATGGTGGAACTATCGAGGCAGAACTACAAAATAATGATTTCAAAGTATCAATTATTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35918","NCBI_taxonomy_name":"Enterococcus faecalis","NCBI_taxonomy_id":"1351"}}}},"ARO_accession":"3002935","ARO_id":"39369","ARO_name":"vanS gene in vanE cluster","CARD_short_name":"vanS_in_vanE_cl","ARO_description":"Also known as vanSE, is a vanS variant found in the vanE gene cluster.","ARO_category":{"36210":{"category_aro_accession":"3000071","category_aro_cvterm_id":"36210","category_aro_name":"vanS","category_aro_description":"VanS is similar to histidine protein kinases like EnvZ and acts as a response regulator by activating VanR. VanS is required for high level transcription of other van glycopeptide resistance genes.","category_aro_class_name":"AMR Gene Family"},"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1634":{"model_id":"1634","model_name":"CMY-78","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1817":{"protein_sequence":{"accession":"AFK73443.1","sequence":"MMKKSICCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAIIYEGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWRGISLLHLATYTAGGLPLQIPGDVTDKAELLRFYQNWQPQWTPGAKRLYANSSIGLFGALAVKSSGMSYEEAMTRRVLQPLKLAHTWITVPQSEQKNYAWGYLEGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIELAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPARVEAAWRILEKLQ"},"dna_sequence":{"accession":"JQ733575.1","fmin":"1027","fmax":"2173","strand":"+","sequence":"ATGATGAAAAAATCGATATGCTGCGCGCTGCTGCTGACAGCCTCTTTCTCCACGTTTGCTGCCGCAAAAACAGAACAACAAATTGCCGATATCGTTAACCGCACCATCACACCACTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTGGCGATTATCTACGAGGGGAAACCTTATTACTTTACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGACGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCGGGGTATCAGCCTGCTGCACTTAGCCACCTATACAGCGGGTGGCCTGCCGCTGCAGATCCCCGGTGACGTTACGGATAAAGCCGAATTACTGCGCTTTTATCAAAACTGGCAACCACAATGGACTCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGTGCGCTGGCGGTGAAATCTTCAGGTATGAGCTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAAAGCGAACAAAAAAACTATGCCTGGGGCTATCTCGAAGGGAAGCCTGTGCACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATCGATATGGCCCGCTGGGTTCAGGCCAACATGGACGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGAGCTTGCGCAGTCTCGCTACTGGCGTATTGGTGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCAGCACCTGCCGTGAAAGCCTCATGGGTGCATAAAACAGGATCCACAGGCGGATTTGGCAGCTACGTTGCTTTCGTTCCAGAAAAAAACCTTGGCATCGTAATGTTGGCAAACAAAAGCTACCCCAACCCGGCTCGCGTCGAGGCGGCCTGGCGCATTCTTGAAAAACTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002091","ARO_id":"38491","ARO_name":"CMY-78","CARD_short_name":"CMY-78","ARO_description":"CMY-78 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1636":{"model_id":"1636","model_name":"QnrB57","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"485":{"protein_sequence":{"accession":"AFR46588.1","sequence":"MTPLLYKKTGTNMALALVGEKIDRNRFTGEKIENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNASALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGAQVLGATFSGSDLSGGEFSTFDWRAANFTHCDLTNSELGNLDIRGVDLQGVKLDNYQASLLMERLGIAIIG"},"dna_sequence":{"accession":"JX259318.1","fmin":"0","fmax":"681","strand":"+","sequence":"ATGACGCCATTACTGTATAAAAAAACAGGTACAAATATGGCTCTGGCACTCGTTGGCGAAAAAATTGACAGAAACCGCTTCACCGGTGAGAAAATTGAAAATAGTACATTTTTTAACTGTGATTTTTCAGGTGCCGACCTGAGCGGCACTGAATTTATCGGCTGTCAGTTCTATGATCGTGAAAGCCAGAAAGGGTGCAATTTTAGTCGTGCGATGCTGAAAGATGCCATTTTTAAAAGCTGTGATTTATCCATGGCGGATTTTCGCAATGCCAGTGCGCTTGGCATTGAAATTCGCCACTGTCGTGCGCAAGGCGCAGATTTCCGCGGCGCAAGCTTTATGAATATGATCACTACTCGCACCTGGTTTTGCAGCGCATATATCACTAACACAAATCTAAGCTACGCCAATTTTTCGAAAGTCGTGTTGGAAAAATGTGAGCTGTGGGAAAACCGTTGGATGGGTGCCCAGGTACTGGGCGCGACGTTCAGTGGTTCAGATCTTTCCGGCGGCGAGTTTTCGACTTTCGACTGGCGAGCAGCAAACTTCACACATTGCGATCTGACCAATTCGGAGTTGGGTAACTTAGATATTCGGGGCGTTGATTTACAAGGCGTTAAGTTGGACAACTACCAGGCATCGCTGCTCATGGAACGTCTTGGCATCGCGATTATTGGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002770","ARO_id":"39204","ARO_name":"QnrB57","CARD_short_name":"QnrB57","ARO_description":"QnrB57 is a plasmid-mediated quinolone resistance protein found in Citrobacter freundii.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1637":{"model_id":"1637","model_name":"MOX-7","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1446":{"protein_sequence":{"accession":"ACS44785.1","sequence":"MQQRQSILWGALATLMWAGLVHAGDKAATDPLRPVVDASIRPLLKEHRIPGMAVAVLKDGKAHYFNYGVADRERAVGVSEQTLFEIGSVSKTLTATLGAYAVVQGSFELDDKASLFAPWLKGSVFDNITMGELATYSAGGLPLQFPEEVDSLEKMQAYYRQWTPAYSPGSHRQYANPSIGLFGYLAASSMKQPFDRLMEQTMLPGLGLYHTYLTVPEQAMGHYAYGYSKEDKPIRVTPGMLADEAYGIKTSSADLLRFVKANIGGVDNAAMQQAIDLTHQGQYAVGEMTQGLGWERYAYPVSEQTLLAGNSPAMIYNAIPAVPAPAAAGHPVLFNKTGSTNGFGAYVAFVPAKGIGIVMLANRNSPIEARIKAAHAILTQLAR"},"dna_sequence":{"accession":"GQ152602.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCAACAACGACAATCCATCCTGTGGGGCGCTCTGGCCACCTTGATGTGGGCCGGCTTGGTTCATGCCGGTGACAAGGCGGCGACCGATCCCCTGCGCCCCGTGGTGGATGCCAGCATCCGGCCGCTGCTCAAGGAGCACAGGATCCCGGGCATGGCGGTGGCCGTGCTCAAGGATGGCAAGGCCCACTATTTCAACTACGGTGTGGCCGATCGGGAGCGCGCAGTCGGTGTCAGCGAGCAGACCCTGTTCGAGATAGGTTCCGTGAGCAAGACCCTGACCGCGACGCTGGGGGCCTACGCCGTGGTGCAGGGGAGCTTCGAGCTCGATGACAAGGCGAGTCTGTTCGCCCCCTGGCTCAAGGGATCCGTCTTTGACAACATCACCATGGGGGAGCTGGCTACCTACAGCGCAGGCGGCTTGCCGCTGCAATTCCCCGAGGAGGTGGATTCGCTCGAGAAGATGCAGGCCTACTACCGCCAGTGGACTCCAGCCTACTCGCCGGGTTCCCATCGCCAGTACGCCAACCCCAGCATCGGGCTCTTTGGCTATCTGGCGGCGAGCAGCATGAAGCAGCCGTTCGATCGCCTGATGGAGCAGACGATGCTGCCGGGGCTAGGCCTGTACCATACTTACCTCACTGTGCCCGAGCAGGCCATGGGGCACTACGCCTACGGCTACTCGAAGGAGGACAAGCCGATCCGCGTCACTCCCGGCATGCTGGCGGACGAGGCCTACGGCATCAAGACCAGTTCGGCGGATCTGCTGCGCTTTGTGAAGGCGAACATCGGCGGGGTGGATAATGCGGCCATGCAGCAGGCCATCGACCTGACTCACCAGGGCCAGTATGCGGTGGGGGAGATGACCCAGGGACTGGGCTGGGAGCGTTACGCCTATCCCGTCAGCGAGCAGACGCTGCTGGCGGGCAACTCCCCGGCGATGATTTACAATGCCATCCCGGCTGTGCCCGCGCCCGCTGCGGCAGGCCACCCTGTGCTTTTCAACAAGACCGGCTCGACCAATGGCTTCGGGGCTTATGTGGCCTTCGTGCCGGCCAAAGGGATCGGCATCGTCATGCTGGCCAATCGCAACTCTCCCATCGAGGCGCGCATCAAGGCGGCTCACGCAATCCTGACGCAACTGGCCAGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36936","NCBI_taxonomy_name":"Aeromonas caviae","NCBI_taxonomy_id":"648"}}}},"ARO_accession":"3002189","ARO_id":"38589","ARO_name":"MOX-7","CARD_short_name":"MOX-7","ARO_description":"MOX-7 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36222":{"category_aro_accession":"3000083","category_aro_cvterm_id":"36222","category_aro_name":"MOX beta-lactamase","category_aro_description":"MOX beta-lactamases are plasmid-mediated AmpC-type beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1638":{"model_id":"1638","model_name":"CMY-111","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1992":{"protein_sequence":{"accession":"AHW47897.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHVSPGQLDVEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"KJ155695.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGTCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36783","NCBI_taxonomy_name":"Serratia marcescens","NCBI_taxonomy_id":"615"}}}},"ARO_accession":"3002122","ARO_id":"38522","ARO_name":"CMY-111","CARD_short_name":"CMY-111","ARO_description":"CMY-111 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1639":{"model_id":"1639","model_name":"SHV-84","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"8846":{"protein_sequence":{"accession":"HBU8836957.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADRTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"DAGGVK010000093.1","fmin":"2639","fmax":"3500","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTACTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAGGACCGGAGCTGGCGAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACCCCAGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001138","ARO_id":"37518","ARO_name":"SHV-84","CARD_short_name":"SHV-84","ARO_description":"SHV-84 is an inhibitor-resistant beta-lactamase that has been found in clinical isolates.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1640":{"model_id":"1640","model_name":"MIR-14","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"1425":{"protein_sequence":{"accession":"AIT76117.1","sequence":"MMTKSLSCALLLSVASSAFAAPMSEKQLAEVVERTVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPELTGKQWQGIHMLELATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMSYEQAMTTRIFKPLNLNHTWINVPKTEEAHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVQDMASWVMVNMKPDSLQDSSLRKGIALAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVEGSDNKVALAPLPAREVNPPAPLVNASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILDALQ"},"dna_sequence":{"accession":"KM087864.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGACAAAATCCCTAAGCTGTGCCCTGCTGCTCAGCGTTGCCAGCTCTGCATTCGCCGCACCGATGTCCGAAAAACAGCTGGCTGAGGTGGTGGAACGTACCGTTACGCCGCTGATGAAAGCGCAGGCCATTCCGGGCATGGCGGTGGCGGTGATTTATCAGGGTCAGCCGCACTACTTTACCTTCGGTAAAGCCGATGTTGCGGCAAACAAACCCGTCACCCCACAAACCTTGTTCGAACTGGGTTCTATAAGTAAAACCTTCACCGGCGTACTGGGTGGCGATGCCATTGCTCGCGGTGAAATATCGCTCGGCGATCCGGTGACAAAATACTGGCCTGAACTGACGGGCAAGCAGTGGCAGGGCATTCACATGCTGGAGCTGGCAACCTATACCGCAGGCGGTCTGCCGTTACAGGTACCGGATGAGGTCACGGATAACGCCTCTCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCGGGCACCACGCGTCTTTACGCCAATGCCAGCATCGGTCTTTTTGGCGCGCTGGCGGTTAAACCTTCCGGCATGAGCTATGAGCAGGCCATGACGACGCGAATCTTTAAGCCGCTCAATCTGAACCATACCTGGATTAACGTTCCGAAAACGGAAGAGGCGCATTACGCCTGGGGATACCGCGACGGTAAAGCGGTCCACGTTTCGCCAGGAATGCTGGATGCAGAAGCCTATGGCGTAAAAACCAACGTGCAGGATATGGCAAGCTGGGTGATGGTCAACATGAAGCCGGACTCGCTTCAGGATAGTTCACTCAGGAAAGGCATTGCCCTGGCGCAGTCTCGCTACTGGCGCGTGGGGGCCATGTATCAAGGGTTAGGTTGGGAAATGCTTAACTGGCCGGTCGATGCCAAAACCGTGGTTGAAGGCAGCGACAATAAGGTGGCGCTGGCACCGCTGCCTGCGAGAGAAGTGAATCCACCGGCACCGCTGGTCAACGCGTCCTGGGTCCATAAAACAGGCTCAACCGGCGGGTTTGGCAGCTACGTGGCATTTATTCCTGAAAAACAGCTCGGCATTGTGATGCTGGCGAATAAAAGCTATCCGAACCCTGCCCGCGTTGAGGCGGCATACCGTATCCTCGACGCGCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36926","NCBI_taxonomy_name":"Enterobacter asburiae","NCBI_taxonomy_id":"61645"}}}},"ARO_accession":"3002179","ARO_id":"38579","ARO_name":"MIR-14","CARD_short_name":"MIR-14","ARO_description":"MIR-14 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36197":{"category_aro_accession":"3000058","category_aro_cvterm_id":"36197","category_aro_name":"MIR beta-lactamase","category_aro_description":"MIR beta-lactamases are plasmid-mediated beta-lactamases that confer resistance to oxyimino- and alpha-methoxy beta-lactams.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1641":{"model_id":"1641","model_name":"OXA-203","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1527":{"protein_sequence":{"accession":"ADX07748.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEVHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"HQ998857.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGTTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGTACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCATTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001664","ARO_id":"38064","ARO_name":"OXA-203","CARD_short_name":"OXA-203","ARO_description":"OXA-203 is a beta-lactamase found in A. baumannii.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1642":{"model_id":"1642","model_name":"clbC","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"4249":{"protein_sequence":{"accession":"BAD63613.1","sequence":"MKVVNHATKYERLKHFLNALNEPTYRYKQITEAIFKHRIGAFNKMTTLPKALRESLINEFGPSILTVEPVLETTSQQVTKVLLKVAGNNQVEAVRMHYEAGWESFCISSQCGCGLGCTFCSTGAIGLKQNLSADEMTDQLLYFYLKGHSLDSVSFMGMGEALANVRIFDALNVLVDRQLFALSPRRITVSTVGIIPNIQRMTSSFPQMNLTFSLHSPFHDQRSELMPINNKYPLDQVMNVLDQHIHETGRKVYIAYVMLRGVNDSEKHAEALVKRILNNRYPHLYHVNLIRYNPTVGTPENYGQTIEEKLQTFYRVVKSARIPVTIRSQFGREIDAACGQLYGQYQAKKR"},"dna_sequence":{"accession":"AP006627.1","fmin":"1162417","fmax":"1163470","strand":"+","sequence":"ATGAAAGTTGTCAATCATGCGACAAAATACGAACGATTAAAACATTTTTTGAATGCTTTAAATGAACCAACGTACCGGTATAAACAGATTACTGAAGCGATTTTCAAACATCGTATTGGTGCGTTTAATAAAATGACCACATTGCCAAAAGCACTGAGAGAATCGCTCATAAACGAATTTGGTCCTTCCATCCTTACAGTAGAGCCGGTGCTAGAAACAACGTCTCAACAAGTCACTAAAGTGTTGCTAAAAGTAGCGGGAAACAATCAAGTGGAAGCCGTAAGAATGCATTATGAAGCAGGGTGGGAGTCGTTTTGCATTTCTTCTCAATGTGGCTGTGGGTTAGGGTGTACGTTTTGTTCGACAGGAGCCATTGGGTTAAAACAAAACTTATCAGCAGACGAGATGACAGACCAGTTGCTCTATTTTTATCTGAAGGGGCATTCCTTAGATAGTGTCTCTTTTATGGGCATGGGCGAAGCGCTAGCCAATGTAAGGATATTTGATGCTTTGAATGTGCTTGTCGATCGGCAACTATTTGCATTAAGTCCTAGAAGAATAACGGTCTCTACGGTTGGCATCATACCAAACATCCAAAGAATGACTAGCAGCTTTCCTCAGATGAACCTAACGTTTTCACTGCACTCTCCTTTTCATGATCAGCGCAGCGAGTTGATGCCGATTAACAACAAGTACCCGTTAGACCAGGTAATGAATGTATTGGATCAGCATATTCACGAGACAGGGAGAAAAGTATATATTGCTTATGTCATGCTTCGGGGTGTCAATGATTCGGAGAAACATGCAGAAGCACTTGTTAAACGGATTCTAAACAATCGCTATCCCCATCTCTATCATGTCAATTTGATTCGCTACAATCCGACTGTGGGTACGCCTGAAAACTATGGCCAAACCATAGAAGAGAAACTGCAAACTTTTTACCGTGTCGTAAAATCAGCTCGAATTCCTGTAACGATTCGGAGTCAATTTGGAAGAGAAATTGATGCCGCCTGCGGCCAATTATATGGTCAGTATCAGGCGAAAAAAAGGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39605","NCBI_taxonomy_name":"Alkalihalobacillus clausii KSM-K16","NCBI_taxonomy_id":"66692"}}}},"ARO_accession":"3002816","ARO_id":"39250","ARO_name":"clbC","CARD_short_name":"clbC","ARO_description":"clbC is a plasmid-encoded cfr gene found in Alkalihalobacillus clausii.","ARO_category":{"36341":{"category_aro_accession":"3000202","category_aro_cvterm_id":"36341","category_aro_name":"Cfr 23S ribosomal RNA methyltransferase","category_aro_description":"Cfr genes produce enzymes which catalyze the methylation of the 23S rRNA subunit at position 8 of adenine-2503. Methylation of 23S rRNA at this site confers resistance to some classes of antibiotics, including streptogramins, chloramphenicols, florfenicols, linezolids and clindamycin.","category_aro_class_name":"AMR Gene Family"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"36521":{"category_aro_accession":"3000382","category_aro_cvterm_id":"36521","category_aro_name":"azidamfenicol","category_aro_description":"Azidamfenicol is a water soluble derivative of chloramphenicol, sharing the same mode of action of inhibiting peptide synthesis by interacting with the 23S RNA of the 50S ribosomal subunit.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36595":{"category_aro_accession":"3000456","category_aro_cvterm_id":"36595","category_aro_name":"thiamphenicol","category_aro_description":"Derivative of Chloramphenicol. The nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3).","category_aro_class_name":"Antibiotic"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"virginiamycin M1","category_aro_description":"Virginiamycin M1 is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37015":{"category_aro_accession":"3000671","category_aro_cvterm_id":"37015","category_aro_name":"tiamulin","category_aro_description":"Tiamulin is a pleuromutilin derivative currently used in veterinary medicine. It binds to the 23 rRNA of the 50S ribosomal subunit to inhibit protein translation.","category_aro_class_name":"Antibiotic"},"37016":{"category_aro_accession":"3000672","category_aro_cvterm_id":"37016","category_aro_name":"madumycin II","category_aro_description":"Madumycin II is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37017":{"category_aro_accession":"3000673","category_aro_cvterm_id":"37017","category_aro_name":"griseoviridin","category_aro_description":"Griseoviridin is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35952":{"category_aro_accession":"0000034","category_aro_cvterm_id":"35952","category_aro_name":"streptogramin A antibiotic","category_aro_description":"Streptogramin A antibiotics are cyclic polyketide peptide hybrids that bind to the ribosomal peptidyl transfer centre. Structural variation arises from substituting a proline for its desaturated derivative and by its substitution for Ala or Cys. Used alone, streptogramin A antibiotics are bacteriostatic, but is bactericidal when used with streptogramin B antibiotics.","category_aro_class_name":"Drug Class"},"36218":{"category_aro_accession":"3000079","category_aro_cvterm_id":"36218","category_aro_name":"oxazolidinone antibiotic","category_aro_description":"Oxazolidinones are a class of synthetic antibiotics discovered the the 1980's.  They inhibit protein synthesis by binding to domain V of the 23S rRNA of the 50S subunit of bacterial ribosomes.  Linezolid is the only member of this class currently in clinical use.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"37014":{"category_aro_accession":"3000670","category_aro_cvterm_id":"37014","category_aro_name":"pleuromutilin antibiotic","category_aro_description":"Pleuromutilins are natural fungal products that target bacterial protein translation by binding the the 23S rRNA, blocking the ribosome P site at the 50S subunit. They are mostly used for agriculture and veterinary purposes.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1643":{"model_id":"1643","model_name":"arnA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1200"}},"model_sequences":{"sequence":{"5385":{"protein_sequence":{"accession":"AAG06942.1","sequence":"MTSKAVVFAYHDIGCTGIEALLNAGYEIAAVFTHADDPRENTFYASVARLCAERGIPLHAPEDVNHPLWLERIRQLRPDFLFSFYYRRLLGAELLACAARGAYNLHGSLLPRYRGRAPANWVLVNGETQTGVTLHRMIERADAGPILAQQAVAIDPEDTALSLHGKLRKAAGALLRDSLPLLALGVLPEVEQDESQASHFGRRTPADGLLDWHRPARQLYDLVRAVTQPYPGAFCQVGEQKLIVWSAEVVAGNHGREPGSVLSCDPLRIACGEDSLVLRFGQRGERGLYLAGTQLATELGLVEGARLRGAACSPQRRTRVLILGVNGFIGNHLSERLLRDGRYEVHGMDIGSDAIERLKADPHFHFVEGDIGIHSEWLEYHVKKCDVILPLVAIATPIEYTRNPLRVFELDFEENLRIVRYCVKYGKRVVFPSTSEVYGMCQDPDFDEDRSNLVVGPINKQRWIYSVSKQLLDRVIWAYGQQGLRFTLFRPFNWMGPRLDRLDSARIGSSRAITQLILHLVEGTPIRLVDGGAQKRCFTDVDDGIEALARIIDNRDGRCDGQIVNIGNPDNEASIRQLGEELLRQFEAHPLRAQFPPFAGFREVESRSFYGDGYQDVAHRKPSIDNARRLLDWQPTIELRETIGKTLDFFLHEALREREAQA"},"dna_sequence":{"accession":"AE004091.2","fmin":"3982020","fmax":"3984009","strand":"+","sequence":"ATGACCTCGAAAGCCGTCGTCTTCGCCTACCACGACATCGGTTGCACCGGTATCGAAGCCCTGCTCAATGCCGGCTACGAGATCGCCGCCGTCTTCACCCATGCCGACGACCCACGGGAAAACACCTTCTACGCCTCGGTCGCACGCCTCTGCGCCGAGCGCGGCATTCCGCTGCACGCGCCCGAGGACGTGAACCATCCGCTGTGGCTGGAGCGTATCCGCCAACTGCGCCCGGACTTCCTGTTCTCCTTCTACTACCGCCGCCTGCTCGGCGCCGAGCTGCTCGCCTGCGCCGCACGCGGCGCCTACAACCTGCACGGTTCGCTGCTGCCGCGCTACCGCGGACGCGCCCCGGCGAACTGGGTGCTGGTCAACGGCGAAACGCAGACCGGGGTGACCCTGCATCGCATGATCGAGCGCGCCGACGCCGGGCCGATCCTCGCCCAGCAGGCCGTCGCCATCGACCCCGAGGACACCGCCCTGAGCCTGCACGGCAAGCTGCGCAAGGCCGCCGGCGCCCTGCTGCGCGACAGCCTGCCGCTGCTCGCCCTCGGCGTGCTGCCGGAAGTCGAGCAGGACGAGAGCCAGGCCAGCCACTTCGGCCGGCGCACCCCGGCGGACGGCCTGCTCGACTGGCACAGGCCGGCACGGCAGTTGTACGACCTGGTGCGCGCGGTGACCCAGCCCTACCCTGGCGCCTTCTGCCAGGTCGGCGAACAGAAGCTGATCGTCTGGAGCGCCGAGGTGGTCGCCGGCAACCACGGCCGCGAGCCGGGCAGCGTACTGTCCTGCGACCCGCTGCGGATCGCCTGCGGCGAGGACTCGCTGGTGCTGCGCTTCGGCCAGCGCGGCGAGCGCGGCCTGTACCTGGCCGGCACGCAACTGGCCACCGAGCTGGGCCTGGTCGAGGGCGCGCGCCTGCGTGGCGCGGCATGCAGTCCGCAGCGCCGCACGCGGGTGCTGATCCTCGGGGTCAACGGCTTCATCGGCAACCACCTGTCCGAACGCCTGCTGCGCGACGGTCGCTACGAGGTCCACGGCATGGACATCGGCTCCGACGCCATCGAACGGCTCAAGGCCGACCCGCATTTCCACTTCGTCGAAGGCGACATCGGCATCCATTCGGAGTGGCTCGAATACCATGTGAAGAAATGCGACGTGATCCTGCCGCTGGTGGCCATCGCCACGCCCATCGAGTACACGCGCAACCCGCTGCGGGTGTTCGAACTGGACTTCGAGGAAAACCTGCGGATCGTCCGCTACTGCGTGAAATACGGCAAACGCGTGGTGTTCCCTTCCACCTCCGAGGTCTACGGCATGTGCCAGGACCCGGACTTCGACGAAGACCGCTCGAACCTGGTGGTCGGGCCGATCAACAAGCAGCGCTGGATCTACTCGGTGTCCAAGCAGTTGCTCGACCGGGTGATCTGGGCCTACGGCCAGCAGGGCCTGCGCTTCACCCTGTTCCGTCCGTTCAACTGGATGGGCCCGCGCCTGGACCGCCTGGATTCGGCGCGGATCGGCAGCTCGCGGGCGATCACCCAGCTCATCCTGCACCTGGTCGAAGGCACGCCGATCCGCCTGGTCGACGGCGGCGCGCAGAAGCGCTGCTTCACCGACGTCGACGACGGCATCGAGGCCCTCGCGCGGATCATCGACAACCGCGACGGCCGCTGCGACGGGCAGATCGTCAACATCGGCAACCCGGACAACGAGGCGAGCATCCGCCAGCTCGGCGAGGAACTGCTGCGCCAGTTCGAGGCCCACCCGCTGCGCGCGCAGTTCCCGCCCTTCGCCGGCTTCCGCGAGGTGGAGAGCCGCAGCTTCTACGGCGACGGCTACCAGGACGTGGCCCACCGCAAGCCGAGCATCGACAACGCCCGGCGCCTGCTCGACTGGCAGCCCACCATCGAACTGCGCGAGACCATCGGCAAGACCCTCGACTTCTTCCTCCACGAAGCGCTCCGCGAGCGCGAGGCACAGGCGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36804","NCBI_taxonomy_name":"Pseudomonas aeruginosa PAO1","NCBI_taxonomy_id":"208964"}}}},"ARO_accession":"3002985","ARO_id":"39419","ARO_name":"arnA","CARD_short_name":"arnA","ARO_description":"arnA modifies lipid A with 4-amino-4-deoxy-L-arabinose (Ara4N) which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. arnA is found in E. coli and P. aeruginosa.","ARO_category":{"41433":{"category_aro_accession":"3004269","category_aro_cvterm_id":"41433","category_aro_name":"pmr phosphoethanolamine transferase","category_aro_description":"This family of phosphoethanolamine transferase catalyze the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine to lipid A, which impedes the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36593":{"category_aro_accession":"3000454","category_aro_cvterm_id":"36593","category_aro_name":"polymyxin B","category_aro_description":"Polymyxin B is mixture of mostly polymyxins B1 and B2, mainly used for resistant gram-negative infections. They are polypeptides with cationic detergent action on cell membranes.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1644":{"model_id":"1644","model_name":"SHV-70","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1485":{"protein_sequence":{"accession":"AAY42633.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGVTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"DQ013287.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGAGTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3001124","ARO_id":"37504","ARO_name":"SHV-70","CARD_short_name":"SHV-70","ARO_description":"SHV-70 is an extended-spectrum beta-lactamase found in Enterobacter cloacae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1645":{"model_id":"1645","model_name":"ACT-23","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1990":{"protein_sequence":{"accession":"AGU38146.1","sequence":"MMKKSLCCALLLGISCSALAAPVSEKQLAEVVANTVTPLMKAQSIPGMAVAVIYQGKPHYYTFGKADIAASKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNAALLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMGYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMVPEKVADASLKQGISLAQSRYWRIGSMYQGLGWEMLNWPVEANTVIEGSDSKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANKSYPNPARVEAAYHILDALQ"},"dna_sequence":{"accession":"KF515536.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCTCTTTGCTGCGCCCTGCTGCTCGGCATCTCTTGCTCTGCTCTCGCCGCGCCAGTGTCAGAAAAACAGCTGGCGGAGGTGGTCGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCGATTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGTAAACCGCACTATTACACGTTTGGCAAAGCCGATATCGCGGCCAGCAAACCCGTTACGCCTCAGACTCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGGGTTTTAGGAGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTAACGGGCAAGCAGTGGCAGGGGATTCGTATGCTGGATCTCGCAACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAATGCCGCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGTATCGGTCTTTTTGGCGCGCTGGCGGTCAAACCTTCCGGCATGGGCTATGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTTCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGAATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGTGCCGGAGAAGGTTGCTGATGCCTCACTTAAGCAGGGCATCTCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGATCGAGGGCAGCGACAGTAAGGTGGCGCTGGCACCGCTGCCCGTGGCAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGCTCTACTGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCGACGCGCTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3001828","ARO_id":"38228","ARO_name":"ACT-23","CARD_short_name":"ACT-23","ARO_description":"ACT-23 is a beta-lactamase found in Escherichia coli.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1646":{"model_id":"1646","model_name":"TEM-139","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1322":{"protein_sequence":{"accession":"AAZ23494.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDKLGARVGYIEMDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVKYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGASERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"DQ072853.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATAAGTTGGGTGCACGAGTGGGTTACATCGAGATGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTAAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCAGTGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001003","ARO_id":"37383","ARO_name":"TEM-139","CARD_short_name":"TEM-139","ARO_description":"TEM-139 is an extended-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1648":{"model_id":"1648","model_name":"CTX-M-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8252":{"protein_sequence":{"accession":"AAZ95872.1","sequence":"MMTQSIRRSMLTVMATLPLLFSSATLHAQANSVQQQLEALEKSSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKQSESDKHLLNQRVEIKKSDLVNYNPIAEKHVNGTMTLAELGAAALQYSDNTAMNKLIAHLGGPDKVTAFARSLGDETFRLDRTEPTLNTAIPGDPRDTTTPLAMAQTLKNLTLGKALAETQRAQLVTWLKGNTTGSASIRAGLPKSWVVGDKTGSGDYGTTNDIAVIWPENHAPLVLVTYFTQPEQKAESRRDILAAAAKIVTHGF"},"dna_sequence":{"accession":"DQ125241.2","fmin":"6832","fmax":"7708","strand":"+","sequence":"ATGATGACTCAGAGCATTCGCCGCTCAATGTTAACGGTGATGGCGACGCTACCCCTGCTATTTAGCAGCGCAACGCTGCATGCGCAGGCGAACAGCGTGCAACAGCAGCTGGAAGCCCTGGAGAAAAGTTCGGGAGGTCGGCTTGGCGTTGCGCTGATTAACACCGCCGATAATTCGCAGATTCTCTACCGTGCCGATGAACGTTTTGCGATGTGCAGTACCAGTAAGGTGATGGCGGCCGCGGCGGTGCTTAAACAGAGCGAGAGCGATAAGCACCTGCTAAATCAGCGCGTTGAAATCAAGAAGAGCGACCTGGTTAACTACAATCCCATTGCGGAGAAACACGTTAACGGCACGATGACGCTGGCTGAGCTTGGCGCAGCGGCGCTGCAGTATAGCGACAATACTGCCATGAATAAGCTGATTGCCCATCTGGGTGGTCCCGATAAAGTGACGGCGTTTGCTCGCTCGTTGGGTGATGAGACCTTCCGTCTGGACAGAACCGAGCCCACGCTCAATACCGCCATTCCAGGCGACCCGCGTGATACCACCACGCCGCTCGCGATGGCGCAGACCCTGAAAAATCTGACGCTGGGTAAAGCGCTGGCGGAAACTCAGCGGGCACAGTTGGTGACGTGGCTTAAGGGCAATACTACCGGTAGCGCGAGCATTCGGGCGGGTCTGCCGAAATCATGGGTAGTGGGCGATAAAACCGGCAGCGGAGATTATGGCACCACCAACGATATCGCGGTTATCTGGCCGGAAAACCACGCACCGCTGGTTCTGGTGACCTACTTTACCCAACCGGAGCAGAAGGCGGAAAGCCGTCGGGATATTCTGGCTGCGGCGGCGAAAATCGTAACCCACGGTTTCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001865","ARO_id":"38265","ARO_name":"CTX-M-2","CARD_short_name":"CTX-M-2","ARO_description":"CTX-M-2 is a beta-lactamase found in the Enterobacteriaceae family.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1649":{"model_id":"1649","model_name":"DHA-21","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1480":{"protein_sequence":{"accession":"AIT76100.1","sequence":"MKKSLSATLISALLAFSAPGFSAADNVAAVVDSTIKPLMAQQDIPGMAVAVSVKGKPYYFNYGFADVQAKQPVTENTLFELGSVSKTFTGVLGAVSVAKKEMTLNDPAEKYQPELALPQWKGITLLDLATYTAGGLPLQVPDAVKSRADLLHFYQQWQPSRKPGDMRLYANSSIGLFGALTANAAGMPYEQLLTARILAPLGLSHTFITVPESAQSQYAYGYKNKKPVRVSPGQLDAESYGVKSASKDMLRWAEMNMEPSRAGNADLEMAMYLAQTRYYKTAAINQGLGWEMYDWPQQKDMIINGVTNEVALQPHPVTDNQVQPYNRASWVHKTGATTGFGAYVAFIPEKQVAIVILANKNYPNTERVKAAQAILSALE"},"dna_sequence":{"accession":"KM087847.1","fmin":"0","fmax":"1140","strand":"+","sequence":"ATGAAAAAATCGTTATCTGCAACACTGATTTCCGCTCTGCTGGCGTTTTCCGCCCCGGGGTTTTCTGCCGCTGATAATGTCGCGGCGGTGGTGGACAGCACCATTAAACCGCTGATGGCACAGCAGGATATTCCTGGGATGGCGGTTGCCGTCTCCGTAAAGGGTAAGCCCTATTATTTCAATTACGGTTTTGCCGATGTTCAGGCAAAACAGCCTGTCACTGAAAATACACTATTTGAGCTCGGATCTGTAAGTAAAACTTTCACAGGTGTGCTGGGTGCGGTTTCCGTGGCGAAAAAAGAGATGACGTTGAATGACCCGGCAGAAAAATACCAGCCGGAGCTGGCTCTGCCGCAGTGGAAGGGGATCACACTGCTGGATCTGGCTACCTACACCGCAGGCGGGCTGCCGTTACAGGTGCCGGATGCGGTGAAAAGCCGTGCGGATCTGCTGCATTTCTATCAGCAGTGGCAGCCGTCCCGGAAACCGGGCGATATGCGTCTGTATGCAAACAGCAGTATCGGCCTGTTTGGTGCTCTGACCGCCAACGCGGCGGGGATGCCGTATGAGCAGTTGCTGACTGCACGGATCCTGGCACCGCTGGGGTTATCTCACACCTTTATTACTGTGCCGGAAAGTGCGCAAAGCCAGTATGCGTACGGTTATAAAAACAAAAAACCGGTCCGCGTGTCGCCGGGACAGCTTGATGCGGAATCTTACGGCGTGAAATCCGCCTCAAAAGATATGCTGCGCTGGGCGGAAATGAATATGGAGCCGTCACGGGCCGGTAATGCGGATCTGGAAATGGCAATGTATCTTGCACAGACCCGCTACTATAAAACCGCCGCGATTAACCAGGGGCTGGGCTGGGAAATGTATGACTGGCCGCAGCAGAAAGATATGATCATTAACGGCGTGACCAACGAGGTCGCATTGCAGCCGCACCCGGTAACAGACAACCAGGTTCAGCCGTATAACCGTGCTTCCTGGGTGCATAAAACGGGGGCAACAACGGGTTTCGGCGCCTATGTGGCCTTTATTCCGGAAAAACAGGTGGCGATTGTGATTCTGGCGAATAAAAACTACCCGAATACCGAAAGAGTCAAAGCCGCACAGGCTATTTTGAGTGCACTGGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36917","NCBI_taxonomy_name":"Morganella morganii","NCBI_taxonomy_id":"582"}}}},"ARO_accession":"3002152","ARO_id":"38552","ARO_name":"DHA-21","CARD_short_name":"DHA-21","ARO_description":"DHA-21 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36207":{"category_aro_accession":"3000068","category_aro_cvterm_id":"36207","category_aro_name":"DHA beta-lactamase","category_aro_description":"DHA beta-lactamases are plasmid-mediated AmpC \u03b2-lactamases that confer resistance to cephamycins and oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1650":{"model_id":"1650","model_name":"CMY-15","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"8201":{"protein_sequence":{"accession":"CAD88477.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYARGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKNYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"AJ555823.2","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCCGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAACTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3002026","ARO_id":"38426","ARO_name":"CMY-15","CARD_short_name":"CMY-15","ARO_description":"CMY-15 is a beta-lactamase found in Proteus mirabilis.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1651":{"model_id":"1651","model_name":"AAC(6')-If","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"358":{"protein_sequence":{"accession":"CAA39038.1","sequence":"MDEASLSMWVGLRSQLWPDHSYEDHILDSQHILSCPDKYVSFLAINNQSQAIAFADAAVRHDYVNGCESSPVVYLEGIFVIPEQRGHGVAKLLVAAVQDWGVAKGCTEMASDAALDNHISYQMHQALGFEETERVVFFRKRIAG"},"dna_sequence":{"accession":"X55353.1","fmin":"278","fmax":"713","strand":"+","sequence":"ATGGATGAAGCTTCTTTGAGCATGTGGGTTGGGCTTCGAAGTCAGCTATGGCCAGACCATAGCTATGAAGATCATATTCTGGATAGCCAACACATTTTATCTTGTCCCGATAAATATGTTTCATTCCTGGCAATAAATAACCAGAGTCAGGCAATAGCGTTTGCCGATGCCGCGGTTCGCCATGATTATGTGAATGGTTGTGAAAGCAGTCCGGTGGTTTATCTTGAAGGGATTTTTGTTATTCCGGAGCAGAGAGGCCATGGCGTTGCCAAACTACTGGTTGCAGCCGTACAGGATTGGGGAGTGGCGAAAGGTTGCACCGAGATGGCAAGCGATGCGGCTTTAGATAACCATATATCCTATCAAATGCATCAGGCTTTAGGCTTTGAAGAAACCGAACGCGTGGTATTTTTCAGAAAAAGAATAGCTGGTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3002553","ARO_id":"38953","ARO_name":"AAC(6')-If","CARD_short_name":"AAC(6')-If","ARO_description":"AAC(6')-If is a plasmid-encoded aminoglycoside acetyltransferase in E. cloacae.","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"A category of aminoglycoside N-acetyltransferase enzymes with modification regiospecificity based at the 6'-amino group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics through acetylation of the 6-amino group of the compound.","category_aro_class_name":"AMR Gene Family"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"46128":{"category_aro_accession":"3007378","category_aro_cvterm_id":"46128","category_aro_name":"2'-N-ethylnetilmicin","category_aro_description":"2'-N-ethylnetilmicin is an aminoglycoside antibiotic and a derivative of netilmicin.","category_aro_class_name":"Antibiotic"},"46129":{"category_aro_accession":"3007379","category_aro_cvterm_id":"46129","category_aro_name":"5-episisomicin","category_aro_description":"5-episosomicin is a semisynthetic aminoglycoside antibiotic similar to sisomicin.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1652":{"model_id":"1652","model_name":"IMP-20","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1173":{"protein_sequence":{"accession":"BAD81061.1","sequence":"MKKLFVLCVCFLCSITAAGAALPDLKIEKLEEGVYVHTSFEEVNGWGVFSKHGLVVLVNTDAYLIDTPFTATDTEKLVNWFVERGYKIKGTISSHFHSDSTGGIEWLNSQSIPTYASELTNELLKKDGKVQAKNSFSGVSYWLVKNKIEVFYPGPGHTQDNVVVWLPEKKILFGGCFVKPDGLGNLGDANLEAWPKSAKILMSKYVKAKLVVSSHSEIGDASLLKRTWEQAVKGLNESKKPSQPSN"},"dna_sequence":{"accession":"AB196988.1","fmin":"0","fmax":"741","strand":"+","sequence":"ATGAAGAAATTATTTGTTTTATGTGTATGCTTCCTTTGTAGCATTACTGCCGCAGGAGCGGCTTTGCCTGATTTAAAAATCGAGAAGCTTGAAGAAGGTGTTTATGTTCATACATCGTTCGAAGAAGTTAACGGTTGGGGTGTTTTTTCTAAACACGGTTTGGTGGTTCTTGTAAACACTGACGCCTATCTGATTGACACTCCATTTACTGCTACAGATACTGAAAAGTTAGTCAATTGGTTTGTGGAGCGCGGCTATAAAATCAAAGGCACTATTTCCTCACATTTCCATAGCGACAGCACAGGGGGAATAGAGTGGCTTAATTCTCAATCTATTCCCACGTATGCATCTGAATTAACAAATGAACTTCTTAAAAAAGACGGTAAGGTGCAAGCTAAAAACTCATTTAGCGGAGTTAGTTATTGGCTAGTTAAAAATAAAATTGAAGTTTTTTATCCCGGCCCGGGGCACACTCAAGATAACGTAGTGGTTTGGTTACCTGAAAAGAAAATTTTATTCGGTGGTTGTTTTGTTAAACCGGACGGTCTTGGTAATTTGGGTGACGCAAATTTAGAAGCTTGGCCAAAGTCCGCCAAAATATTAATGTCTAAATATGTTAAAGCAAAACTGGTTGTTTCAAGTCATAGTGAAATTGGGGACGCATCACTCTTGAAACGTACATGGGAACAGGCTGTTAAAGGGCTAAATGAAAGTAAAAAACCATCACAGCCAAGTAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002211","ARO_id":"38611","ARO_name":"IMP-20","CARD_short_name":"IMP-20","ARO_description":"IMP-20 is a beta-lactamase found in Pseudomonas and Acinetobacter spp.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1561":{"model_id":"1561","model_name":"vanT gene in vanG cluster","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"175"}},"model_sequences":{"sequence":{"217":{"protein_sequence":{"accession":"ABA71733.1","sequence":"MTKNESYSGIDYFRFIAALLIVAIHTSPLSSFSETGNFIFTRIVARVAVPFFFMTSGFFLISRYTCNAEKLGAFIKKTTLIYGVAILLYIPINVYNGYFKMDNLLPNIIKDIVFDGTLYHLWYLPASIIGAAIAWYLVKKVHYRKAFLIASILYIIGLFGDSYYGIVKSVSCLNVFYNLIFQLTDYTRNGIFFAPIFFVLGGYISDSQNRLSLKRSIVGFIVCFALMFGEALTLHHFDIQKHDSMYVLLLPSVYCLFNLLLHFRGKRRTGLRTISLIIYIIHPFMIVVIRLFAKLLHLQSLLVENSLVHYIAVCFASVVLAVVITALLSSLKPKKAKHTADTDRAYLEINLNNLEHNVNTLQKAMSPKCELMAVVKAEAYGHGMYEVTTYLEQIGVSSFAVATIDEGIRLRKYGISSEILILGYTSPSRAKELCKYELTQTLIDYRYSLLLNKQGYDIKAHIKIDTGMHRLGFSTEDKDKILAAFSLKHIKVAGIFTHLCAADSLEENDVAFTNKQIGSFYKVLDWLKSSGLNIPKVHIQSSYGLLNYPELECDYIRVGVALYGVLSSTNDKTKLELDLRPVLSLKAKVVLIRKIKQGESVGYSRAFTATRDSLIAILPIGYADGFPRNLSCGNSYVLIGGRQAPIVGKICMDQLAVDVTDIPNVKTGSIATLIGKDGKEEITAPMVAESAESITNELLSRMGHRLNIIRRA"},"dna_sequence":{"accession":"DQ212986.1","fmin":"7787","fmax":"9926","strand":"+","sequence":"ATGACTAAAAACGAAAGCTATTCTGGCATTGATTATTTTAGATTTATTGCAGCCTTATTGATTGTTGCTATTCATACTTCGCCTCTCTCTTCTTTTAGTGAAACAGGCAACTTTATATTTACACGCATTGTAGCCCGTGTAGCCGTTCCGTTCTTTTTTATGACATCTGGATTTTTTCTGATTTCCAGATATACCTGTAATGCCGAAAAGCTGGGAGCTTTTATAAAAAAGACAACCTTAATTTACGGGGTTGCAATACTCTTATACATACCTATCAATGTTTATAACGGTTATTTCAAAATGGACAACCTTTTGCCAAATATCATAAAAGATATTGTATTTGATGGTACTTTATATCACTTGTGGTATCTTCCTGCATCTATTATCGGAGCTGCGATTGCTTGGTATCTGGTAAAGAAAGTTCATTATCGCAAAGCCTTTTTGATAGCTTCTATACTCTATATCATAGGCTTATTTGGAGATAGTTATTATGGAATTGTGAAAAGCGTTTCCTGCTTAAATGTTTTTTACAATCTAATCTTCCAATTAACAGATTACACAAGAAACGGAATATTTTTTGCCCCAATCTTTTTTGTGCTTGGTGGATATATCTCTGATAGTCAAAACAGACTATCGTTAAAAAGAAGTATAGTAGGATTTATAGTTTGTTTTGCCCTTATGTTTGGAGAAGCCCTTACTTTACATCATTTTGATATACAGAAACATGACAGTATGTATGTGCTTTTACTTCCGAGTGTGTATTGCTTATTTAATCTTCTTCTGCACTTTAGAGGAAAACGCCGCACAGGATTACGGACAATATCATTGATTATCTATATCATTCATCCGTTTATGATTGTTGTAATACGATTGTTTGCCAAATTACTGCATCTGCAAAGCCTGCTTGTTGAAAACAGCCTTGTTCATTATATTGCGGTCTGCTTTGCATCGGTAGTATTAGCAGTGGTTATAACAGCGTTATTGAGCAGTCTGAAACCGAAAAAGGCAAAACATACCGCCGATACGGATAGAGCGTATCTGGAAATCAACCTAAATAATTTAGAGCATAATGTAAACACTTTGCAAAAAGCAATGTCACCTAAATGTGAATTGATGGCGGTTGTAAAAGCGGAAGCCTATGGTCACGGTATGTATGAAGTGACGACATATCTTGAGCAGATAGGAGTTTCTTCATTTGCGGTAGCTACCATTGATGAAGGTATCCGATTGAGAAAATATGGCATCTCTAGCGAAATCCTAATTTTAGGCTATACATCGCCTTCAAGGGCAAAAGAACTTTGTAAGTATGAGCTGACACAAACCTTGATAGATTATAGGTATTCGTTGCTTTTGAATAAACAGGGATATGACATTAAAGCACATATTAAAATTGACACAGGTATGCATAGACTTGGATTTAGCACAGAAGATAAGGATAAAATCCTTGCAGCTTTTTCTTTGAAGCACATCAAAGTTGCGGGAATTTTTACACATTTGTGTGCGGCTGACAGCCTTGAAGAAAATGATGTTGCATTTACAAACAAGCAAATAGGCAGTTTCTATAAAGTGCTTGATTGGCTGAAAAGCAGCGGTTTGAATATACCTAAAGTACATATCCAAAGTAGTTATGGATTATTGAATTATCCAGAGCTTGAATGTGATTATATCAGAGTGGGTGTTGCTCTGTATGGTGTTTTAAGCTCTACTAATGACAAAACAAAATTAGAACTTGATTTAAGACCTGTACTTTCTTTGAAAGCAAAAGTTGTTTTAATTCGGAAGATAAAGCAGGGCGAAAGTGTTGGTTATAGCAGGGCTTTTACTGCAACCCGAGATAGTTTAATTGCCATATTACCAATTGGATATGCAGATGGTTTTCCAAGAAATCTGTCTTGTGGAAATAGTTATGTGCTGATTGGTGGACGACAAGCCCCTATTGTCGGAAAAATCTGTATGGATCAACTTGCAGTTGATGTAACAGATATTCCCAATGTTAAGACTGGAAGTATTGCAACGCTGATTGGTAAAGATGGAAAGGAAGAAATTACAGCACCGATGGTAGCTGAAAGTGCAGAAAGCATAACCAATGAATTGTTAAGCCGTATGGGACACAGATTAAATATTATTCGTAGAGCGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35918","NCBI_taxonomy_name":"Enterococcus faecalis","NCBI_taxonomy_id":"1351"}}}},"ARO_accession":"3002972","ARO_id":"39406","ARO_name":"vanT gene in vanG cluster","CARD_short_name":"vanT_in_vanG_cl","ARO_description":"Also known as vanTG, is a vanT variant found in the vanG gene cluster.","ARO_category":{"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"36511":{"category_aro_accession":"3000372","category_aro_cvterm_id":"36511","category_aro_name":"vanT","category_aro_description":"VanT is a membrane bound serine racemase, converting L-serine to D-serine. It is associated with VanC, which incorporated D-serine into D-Ala-D-Ser terminal end of peptidoglycan subunits that have a decreased binding affinity with vancomycin. It was isolated from Enterococcus gallinarum.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1635":{"model_id":"1635","model_name":"vanR gene in vanG cluster","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"246":{"protein_sequence":{"accession":"ABA71727.1","sequence":"MNEKILIVDDEKEIADLIELYLKNDGYKVYKFYNGIDALKCVESEKMDLAILDVMLPDVDGFHICQKIRERYFYPIIMLTAKVEDADKIMGLTIGADDYITKPFNPLEVAARVKTQLRRYVCYNNAADIEKENVLVTEYDINGLVINKNTHKCTLYGKAVTLTPIEFSVLWYLCENRGKVISSEELFENVWGEKFLDNNNTVMAHIGRLREKLKEPARNPKFIKTVWGVGYTIEE"},"dna_sequence":{"accession":"DQ212986.1","fmin":"2258","fmax":"2966","strand":"+","sequence":"ATGAATGAAAAGATTTTAATTGTTGATGATGAAAAAGAGATAGCAGATTTAATTGAGCTTTATCTGAAAAATGACGGTTATAAAGTGTATAAATTTTACAATGGTATAGACGCATTAAAATGTGTGGAATCAGAAAAAATGGATTTGGCAATTTTAGATGTTATGCTTCCTGATGTCGATGGTTTCCATATCTGTCAAAAGATTCGGGAACGATATTTTTATCCAATTATTATGCTGACGGCAAAGGTAGAAGATGCTGATAAGATTATGGGGCTGACGATTGGAGCGGATGATTATATTACAAAGCCATTTAATCCACTAGAGGTTGCTGCAAGGGTCAAGACACAGCTTCGCCGTTATGTATGTTACAATAATGCCGCAGATATAGAAAAAGAAAATGTATTGGTTACGGAATATGATATTAACGGACTTGTCATTAATAAGAATACTCATAAATGCACACTGTATGGAAAGGCAGTCACATTAACCCCGATAGAATTTTCTGTTCTTTGGTATTTGTGTGAAAATAGGGGAAAAGTGATTTCTTCAGAGGAACTTTTTGAAAATGTCTGGGGCGAGAAATTCCTTGATAATAATAATACAGTTATGGCTCATATCGGGAGGTTACGGGAAAAATTGAAAGAACCTGCCAGAAATCCGAAATTTATAAAAACCGTATGGGGAGTGGGATATACCATTGAAGAATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35918","NCBI_taxonomy_name":"Enterococcus faecalis","NCBI_taxonomy_id":"1351"}}}},"ARO_accession":"3002926","ARO_id":"39360","ARO_name":"vanR gene in vanG cluster","CARD_short_name":"vanR_in_vanG_cl","ARO_description":"Also known as vanRG, is a vanR variant found in the vanG gene cluster.","ARO_category":{"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"36713":{"category_aro_accession":"3000574","category_aro_cvterm_id":"36713","category_aro_name":"vanR","category_aro_description":"VanR is a OmpR-family transcriptional activator in the VanSR regulatory system. When activated by VanS, it promotes cotranscription of VanA, VanH, and VanX.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1553":{"model_id":"1553","model_name":"tet(S)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"619":{"protein_sequence":{"accession":"AAA25293.1","sequence":"MKIINIGILAHVDAGKTTLTESLLYSSGAIKELGSVDSGTTKTDTMFLERQRGITIQTAITSFQRENVKVNIVDTPGHMDFLADVYRSLSVLDGAILLISAKDGVQSQTRILFHALRKMNIPIIFFINKIDQNGINLPDVYQDIKDKLSDDIIIKQTVNLNLKPYVIDYTEPEQWETVIVGNDYLLEKYTIGKTLNIAELEKEENERIQSCSLYPVYHGSAKNNIGIKQLIEVITSKLFSPTQLNSDKLCGNVFKVEYSDDGQRLVYVRLYSGTLHLRDSVNISEKEKIKVTEMYTSINGELRQIDKAEPGEIIILKNELLKLNNVLGDKKRLPHREILENPLPMLQTTIEPCKSVQREKLLDALFEISDSDPLLQYYVDTVTHEIVLSFLGEVQMEVTCTLIQEKYHIEIETRKPTVIYMERPLKKSEFTIDIEVPPNPFWASIGLSVTPLPLGSGIQYESLVSLGYLNQSFQNAVMEGIRYGCEQGLYGWKLTDCKICFKYGLYYSPVSTPADFRMLAPIVLEQAFRKSGTELLEPYLSFEIYVPQEYLSRAYNDASKYCANILNTKLKGNEVILIGEIPARCIQEYRNSLTFFTNGRSVCLTELKGYQVTNIKSAFQPRRPNNRIDKVRHMFNKINLH"},"dna_sequence":{"accession":"L09756.1","fmin":"0","fmax":"1926","strand":"+","sequence":"TTGAAAATTATTAATATCGGTATCTTAGCACATGTTGATGCAGGAAAAACTACTTTGACAGAAAGCTTACTATACAGTAGCGGAGCAATTAAAGAGTTAGGAAGTGTAGATAGCGGTACAACGAAAACGGATACTATGTTTTTGGAACGCCAGAGAGGTATTACTATTCAGACCGCAATAACATCTTTTCAACGGGAAAATGTTAAAGTAAATATTGTAGATACTCCTGGACACATGGATTTTTTGGCAGATGTATACCGTTCATTATCTGTTTTGGATGGAGCTATTTTGCTAATCTCTGCAAAAGATGGAGTACAGTCACAAACTCGTATACTATTCCATGCACTTAGAAAGATGAACATACCTATAATATTTTTTATTAACAAAATTGATCAAAATGGAATAAATTTGCCAGATGTTTATCAAGATATTAAGGACAAACTTTCTGACGACATCATAATTAAGCAGACTGTGAATCTAAATTTGAAACCTTATGTAATAGATTATACTGAACCAGAACAATGGGAGACAGTAATTGTGGGAAATGATTATTTATTAGAAAAATATACCATTGGGAAAACATTGAATATTGCAGAACTTGAAAAGGAGGAAAACGAAAGAATTCAAAGTTGCTCCTTATATCCTGTTTATCACGGAAGTGCAAAGAATAATATTGGAATTAAACAACTTATAGAGGTAATTACTAGCAAATTATTTTCACCCACACAACTCAATTCAGATAAACTTTGTGGAAATGTTTTTAAAGTAGAATATTCAGATGATGGTCAACGGCTTGTCTATGTACGTCTTTATAGTGGAACGCTACATTTGCGAGACTCAGTCAATATATCAGAAAAGGAAAAAATAAAAGTTACAGAAATGTATACTTCAATAAATGGAGAATTACGCCAGATAGATAAGGCAGAGCCTGGTGAGATTATTATTTTAAAAAATGAGCTTTTAAAACTAAATAACGTACTTGGAGATAAAAAAAGATTACCACATAGAGAAATTCTTGAGAATCCTCTTCCTATGTTACAAACAACAATTGAACCATGTAAATCAGTACAAAGAGAAAAGTTACTAGATGCACTTTTTGAAATATCCGATAGTGATCCCCTTCTACAATATTATGTAGATACAGTAACTCACGAAATTGTGCTATCTTTTTTAGGTGAGGTCCAAATGGAGGTAACTTGTACTCTGATTCAAGAAAAATATCATATTGAGATAGAAACAAGAAAACCAACTGTCATTTATATGGAAAGACCATTAAAAAAATCTGAATTTACCATTGATATCGAAGTACCTCCAAATCCTTTCTGGGCTTCTATTGGTTTATCTGTAACACCACTTCCTTTGGGTAGTGGCATTCAGTATGAGAGCCTGGTTTCTCTAGGTTATTTAAATCAATCATTTCAAAATGCAGTTATGGAAGGTATACGCTATGGGTGTGAACAAGGATTGTACGGTTGGAAATTAACAGACTGTAAGATCTGTTTTAAGTATGGTCTATATTACAGCCCTGTCAGTACGCCAGCAGATTTCCGAATGCTTGCGCCTATTGTACTAGAGCAGGCTTTTAGAAAGAGTGGTACAGAGTTATTAGAGCCATATCTTAGCTTCGAAATTTATGTACCACAAGAATATCTTTCGAGAGCATATAATGATGCTTCCAAATATTGTGCAAATATTTTAAATACTAAGTTAAAAGGTAACGAGGTCATTCTCATTGGTGAAATTCCAGCCCGTTGTATTCAAGAGTATCGAAACAGTTTAACTTTCTTTACAAATGGACGCAGTGTCTGTTTAACAGAGTTAAAAGGTTATCAGGTTACTAACATTAAGTCTGCTTTCCAACCACGTCGTCCAAATAATAGAATAGACAAAGTAAGGCATATGTTTAATAAAATCAACTTACATTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36757","NCBI_taxonomy_name":"Listeria monocytogenes","NCBI_taxonomy_id":"1639"}}}},"ARO_accession":"3000192","ARO_id":"36331","ARO_name":"tet(S)","CARD_short_name":"tet(S)","ARO_description":"Tet(S) is a ribosomal protection protein found in Gram-positive and Gram-negative strains. It is similar to tet(M) and tet(O).","ARO_category":{"35921":{"category_aro_accession":"0000002","category_aro_cvterm_id":"35921","category_aro_name":"tetracycline-resistant ribosomal protection protein","category_aro_description":"A family of proteins known to bind to the 30S ribosomal subunit. This interaction prevents tetracycline and tetracycline derivatives from inhibiting ribosomal function. Thus, these proteins confer elevated resistance to tetracycline derivatives as a ribosomal protection protein.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35986":{"category_aro_accession":"0000069","category_aro_cvterm_id":"35986","category_aro_name":"doxycycline","category_aro_description":"Doxycycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36291":{"category_aro_accession":"3000152","category_aro_cvterm_id":"36291","category_aro_name":"minocycline","category_aro_description":"Minocycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36667":{"category_aro_accession":"3000528","category_aro_cvterm_id":"36667","category_aro_name":"chlortetracycline","category_aro_description":"Chlortetracycline was an early, first-generation tetracycline antibiotic developed in the 1940's. It inhibits bacterial protein synthesis by binding to the 30S subunit of bacterial ribosomes, preventing the aminoacyl-tRNA from binding to the ribosome.","category_aro_class_name":"Antibiotic"},"37011":{"category_aro_accession":"3000667","category_aro_cvterm_id":"37011","category_aro_name":"demeclocycline","category_aro_description":"Demeclocycline is a tetracycline analog with 7-chloro and 6-methyl groups. Due to its fast absorption and slow excretion, it maintains higher effective blood levels compared to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37012":{"category_aro_accession":"3000668","category_aro_cvterm_id":"37012","category_aro_name":"oxytetracycline","category_aro_description":"Oxytetracycline is a derivative of tetracycline with a 5-hydroxyl group. Its activity is similar to other tetracyclines.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1653":{"model_id":"1653","model_name":"AAC(6')-Ip","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"5237":{"protein_sequence":{"accession":"CAA91010.1","sequence":"MLKKSFLDAGNESWGDIKNAIEEVEECIEHPNICLGICLDDKLIGWTGLRPMYDKTWELHPMVIKTEYQGKGFGKVLLRELETRAKSRGIIGIALGTDDEYQKTSLSMIDINERNIFDEIGNIKNVNNHPYEFYKKCGYMIVGIIPNANGKRKPDIWMWQILARKNSPTIAST"},"dna_sequence":{"accession":"Z54241.1","fmin":"529","fmax":"1051","strand":"+","sequence":"ATGCTTAAGAAAAGCTTTCTTGATGCTGGAAATGAATCATGGGGAGATATTAAAAATGCTATTGAAGAAGTTGAAGAATGTATAGAACATCCAAATATATGCTTGGGAATATGTCTGGATGATAAACTGATTGGATGGACCGGATTAAGGCCGATGTACGATAAGACCTGGGAACTTCATCCCATGGTTATAAAAACTGAATATCAAGGCAAGGGTTTTGGGAAAGTACTACTAAGAGAACTAGAGACGAGAGCGAAGAGTAGGGGAATTATCGGAATAGCTCTTGGAACTGATGACGAATATCAGAAAACTAGTTTGTCTATGATTGATATAAACGAACGAAATATCTTCGATGAAATCGGGAATATAAAGAACGTTAATAATCATCCATATGAGTTTTATAAGAAATGTGGTTATATGATCGTTGGAATAATCCCTAATGCTAATGGAAAAAGAAAACCAGATATATGGATGTGGCAGATATTAGCTAGGAAGAACAGCCCAACAATCGCTTCAACCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002559","ARO_id":"38959","ARO_name":"AAC(6')-Ip","CARD_short_name":"AAC(6')-Ip","ARO_description":"AAC(6')-Ip is an aminoglycoside acetyltransferase encoded by plasmids and integrons in C. freundii, E. coli, E. faecium and Klebsiella aerogenes.","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"A category of aminoglycoside N-acetyltransferase enzymes with modification regiospecificity based at the 6'-amino group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics through acetylation of the 6-amino group of the compound.","category_aro_class_name":"AMR Gene Family"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"46128":{"category_aro_accession":"3007378","category_aro_cvterm_id":"46128","category_aro_name":"2'-N-ethylnetilmicin","category_aro_description":"2'-N-ethylnetilmicin is an aminoglycoside antibiotic and a derivative of netilmicin.","category_aro_class_name":"Antibiotic"},"46129":{"category_aro_accession":"3007379","category_aro_cvterm_id":"46129","category_aro_name":"5-episisomicin","category_aro_description":"5-episosomicin is a semisynthetic aminoglycoside antibiotic similar to sisomicin.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1654":{"model_id":"1654","model_name":"SHV-95","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"2028":{"protein_sequence":{"accession":"ABN49113.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARLQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"EF373972.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGATGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTTGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGAGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3001147","ARO_id":"37527","ARO_name":"SHV-95","CARD_short_name":"SHV-95","ARO_description":"SHV-95 is a beta-lactamase found in Citrobacter freundii.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1655":{"model_id":"1655","model_name":"TEM-117","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"5900":{"protein_sequence":{"accession":"AAN05026.1","sequence":"FFAAFCFPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQA"},"dna_sequence":{"accession":"AY130282.1","fmin":"0","fmax":"762","strand":"+","sequence":"TTTTTTGCGGCATTTTGCTTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCA","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000980","ARO_id":"37360","ARO_name":"TEM-117","CARD_short_name":"TEM-117","ARO_description":"TEM-117 is a beta-lactamase that has been found in clinical isolates.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1656":{"model_id":"1656","model_name":"CTX-M-79","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"769":{"protein_sequence":{"accession":"ABO09821.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAVAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTNGL"},"dna_sequence":{"accession":"EF426798.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGTGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCAACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001940","ARO_id":"38340","ARO_name":"CTX-M-79","CARD_short_name":"CTX-M-79","ARO_description":"CTX-M-79 is a beta-lactamase found in Escherichia coli.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1657":{"model_id":"1657","model_name":"AAC(6')-IIa","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"460":{"protein_sequence":{"accession":"AAM92464.1","sequence":"MSASTPPITLRLMTERDLPMLHDWLNRPHIVEWWGGDEERPTLDEVLEHYLPRAMAEESVTPYIAMLGEEPIGYAQSYVALGSGDGWWEDETDPGVRGIDQSLADPTQLNKGLGTRLVRALVELLFSDPTVTKIQTDPTPNNHRAIRCYEKAGFVREKIITTPDGPAVYMVQTRQAFERKRGVA"},"dna_sequence":{"accession":"AY123251.1","fmin":"2950","fmax":"3505","strand":"+","sequence":"ATGTCCGCGAGCACCCCCCCCATAACTCTTCGCCTCATGACCGAGCGCGACCTGCCGATGCTCCATGATTGGCTCAACCGGCCGCACATCGTTGAGTGGTGGGGTGGTGACGAAGAGCGACCGACTCTTGATGAAGTGCTGGAACACTACCTGCCCAGAGCGATGGCGGAAGAGTCCGTAACACCGTACATCGCAATGCTGGGCGAGGAACCGATCGGCTATGCTCAGTCGTACGTCGCGCTCGGAAGCGGTGATGGCTGGTGGGAAGATGAAACTGATCCAGGAGTGCGAGGAATAGACCAGTCTCTGGCTGACCCGACACAGTTGAACAAAGGCCTAGGAACAAGGCTTGTCCGCGCTCTCGTTGAACTACTGTTCTCGGACCCCACCGTGACGAAGATTCAGACCGACCCGACTCCGAACAACCATCGAGCCATACGCTGCTATGAGAAGGCAGGATTCGTGCGGGAGAAGATCATCACCACGCCTGACGGGCCGGCGGTTTACATGGTTCAAACACGACAAGCCTTCGAGAGAAAGCGCGGTGTTGCCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35731","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Typhi","NCBI_taxonomy_id":"90370"}}}},"ARO_accession":"3002594","ARO_id":"38994","ARO_name":"AAC(6')-IIa","CARD_short_name":"AAC(6')-IIa","ARO_description":"AAC(6')-IIa is an aminoglycoside acetyltransferase encoded by plasmids and integrons in P. aeruginosa and S. enterica.","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"A category of aminoglycoside N-acetyltransferase enzymes with modification regiospecificity based at the 6'-amino group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics through acetylation of the 6-amino group of the compound.","category_aro_class_name":"AMR Gene Family"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"46128":{"category_aro_accession":"3007378","category_aro_cvterm_id":"46128","category_aro_name":"2'-N-ethylnetilmicin","category_aro_description":"2'-N-ethylnetilmicin is an aminoglycoside antibiotic and a derivative of netilmicin.","category_aro_class_name":"Antibiotic"},"46129":{"category_aro_accession":"3007379","category_aro_cvterm_id":"46129","category_aro_name":"5-episisomicin","category_aro_description":"5-episosomicin is a semisynthetic aminoglycoside antibiotic similar to sisomicin.","category_aro_class_name":"Antibiotic"},"46133":{"category_aro_accession":"3007382","category_aro_cvterm_id":"46133","category_aro_name":"gentamicin","category_aro_description":"Gentamicin is a commonly used aminoglycoside antibiotic derived from members of the Micromonospora genus of bacteria. It acts by binding the 30S ribosomal subunit, thus inhibiting protein synthesis. Gentamicin is typically used to treat Gram-negative infections of the repiratory and urinary tract, as well as infections of the bone and soft tissue. It also exhibits considerable nephrotoxicity and ototoxicity. Gentamicin is administered as a mixture of gentamicin type C (which makes about around 80% of the complex) and types A, B, and X (distributed in the remaining 20% of the complex).","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1658":{"model_id":"1658","model_name":"OKP-B-4","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"1599":{"protein_sequence":{"accession":"CAJ19612.1","sequence":"MRYVRLCLISLIAALPLAVFASPQPLEQIKISESQLAGRVGYVEMDLASGRTLAAWRASERFPLMSTFKVLLCGAVLARVDAGDEQLDRRIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAGNLLLKSVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDVRDTTTPASMATTLRKLLTTPSLSARSQQQLLQWMVDDRVAGPLIRAVLPAGWFIADKTGAGERGSRGIVALLGPDGKAERIVVIYLRDTPATMVERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AM051153.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGCCTTATCTCCCTGATTGCCGCCCTGCCACTGGCGGTATTCGCCAGCCCTCAGCCGCTTGAGCAGATTAAAATCAGCGAAAGTCAGCTGGCGGGCCGGGTGGGCTATGTTGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCAGTGAGCGCTTTCCGCTGATGAGCACCTTTAAAGTGCTGCTCTGCGGCGCGGTGCTGGCCCGGGTGGATGCCGGCGACGAACAGCTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGCCGACGGGATGACCGTTGGCGAACTCTGCGCCGCCGCCATCACCATGAGCGACAACAGCGCCGGCAATCTGCTGTTGAAGAGCGTCGGCGGCCCCGCGGGATTGACCGCTTTTCTGCGCCAGATCGGTGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTCAATGAGGCGCTTCCCGGCGACGTGCGCGACACCACCACCCCGGCCAGCATGGCCACCACCCTGCGCAAGTTGCTAACCACCCCCTCTCTGAGCGCCCGTTCGCAGCAGCAGCTGCTGCAGTGGATGGTGGACGACCGGGTGGCCGGCCCGTTGATCCGCGCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAAACCGGGGCCGGTGAGCGGGGCTCACGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAAGCGGAGCGTATCGTGGTGATCTATCTGCGTGATACCCCGGCGACCATGGTCGAGCGTAACCAGCAGATCGCCGGGATAGGCGCGGCGCTGATCGAGCACTGGCAGCGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002437","ARO_id":"38837","ARO_name":"OKP-B-4","CARD_short_name":"OKP-B-4","ARO_description":"OKP-B-4 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"38817":{"category_aro_accession":"3002417","category_aro_cvterm_id":"38817","category_aro_name":"OKP beta-lactamase","category_aro_description":"OKP beta-lactamases are chromosomal class A beta-lactamase that confer resistance to penicillins and early cephalosporins in Klebsiella pneumoniae. OKP beta-lactamases can be subdivided into two groups: OKP-A and OKP-B which diverge by about 4.2%.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1659":{"model_id":"1659","model_name":"OXA-258","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8267":{"protein_sequence":{"accession":"CCE73593.2","sequence":"MTVRLVSRALGAVLFASALTLPARADVLCTLVADAADGRILFQQGTRQDCTQRYTPASTFKLPIALMGADAGILQGPHQPVWNYQPAYPDWGGEAWRQPTDPARWIKYSVVWYSQLTARALGQERFQRYTSAFGYGNADVSGEPGKHNGTDGAWIISSLRISPFEQVDFLRKFVNRQLPVKAAAYDLAENLFEVGEADGWRLYGKTGTGSPGSHGVYTPANAYGWFVGWARKDDRQLVFARLLQDEGATQPNAGLRARDGLMRDWAAMVAAPRK"},"dna_sequence":{"accession":"HE614014.2","fmin":"0","fmax":"825","strand":"+","sequence":"ATGACAGTTCGACTCGTTTCGCGCGCCCTGGGCGCAGTCCTCTTTGCGTCCGCCCTGACCCTGCCCGCCCGGGCGGACGTCCTGTGCACCCTGGTGGCCGACGCCGCCGACGGCCGCATCCTGTTCCAGCAGGGCACGCGGCAGGACTGCACGCAGCGCTACACCCCCGCCTCGACCTTCAAGCTGCCCATCGCCCTGATGGGCGCGGATGCCGGCATCCTGCAGGGCCCGCACCAGCCCGTCTGGAACTACCAGCCCGCTTATCCCGACTGGGGCGGCGAGGCCTGGCGCCAGCCCACCGATCCGGCTCGCTGGATCAAGTATTCGGTGGTCTGGTACTCGCAGTTGACCGCCAGGGCGCTGGGGCAGGAGCGCTTCCAGCGCTACACCTCCGCGTTCGGTTATGGCAACGCGGACGTCTCGGGTGAACCCGGCAAGCACAACGGCACCGATGGCGCGTGGATCATCTCCTCGCTGCGCATTTCGCCGTTTGAGCAGGTGGACTTCCTGCGCAAGTTCGTCAACCGGCAACTGCCCGTCAAGGCGGCTGCCTATGACCTGGCCGAGAACCTGTTCGAGGTCGGCGAAGCCGACGGCTGGCGTCTGTACGGCAAGACCGGAACCGGCTCGCCCGGCAGCCACGGCGTCTACACGCCGGCCAACGCCTATGGCTGGTTCGTCGGCTGGGCGCGCAAGGACGACCGCCAACTGGTGTTTGCCCGCCTGCTGCAGGACGAGGGGGCGACCCAGCCCAATGCCGGCCTGCGCGCCCGCGACGGCCTGATGCGCGACTGGGCCGCCATGGTCGCGGCGCCCCGCAAATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39091","NCBI_taxonomy_name":"Achromobacter ruhlandii","NCBI_taxonomy_id":"72557"}}}},"ARO_accession":"3001503","ARO_id":"37903","ARO_name":"OXA-258","CARD_short_name":"OXA-258","ARO_description":"OXA-258 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1660":{"model_id":"1660","model_name":"OXA-375","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4687":{"protein_sequence":{"accession":"AHL30275.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLVRASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFREWEKDMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"KF986256.1","fmin":"40","fmax":"865","strand":"-","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGTTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCGAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001561","ARO_id":"37961","ARO_name":"OXA-375","CARD_short_name":"OXA-375","ARO_description":"OXA-375 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1661":{"model_id":"1661","model_name":"CARB-8","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1894":{"protein_sequence":{"accession":"AAO59455.1","sequence":"MDVRKHKASFFSVVITFLCLTLSLNANATDSVLEAVTNAETELGARIGLAVHDLETGKRWEHKSNERFPLSSTFKTLACANVLQRVDLGKERIDRVVRFSESNLVTYSPVTEKHVGKKGMSLAELCQATLSTSDNSAANFILQAIGGPKALTKFLRSIGDDTTRLDRWETELNEAVPGDKRDTTTPIAMVTTLEKLLIDETLSIKSRQQLESWLKGNEVGDALFRKGVPSDWIVADRTGAGGYGSRAITAVMWPPNRKPIVAALYITETDASFEERNAVIAKIGEQIAKTILMENSRN"},"dna_sequence":{"accession":"AY178993.1","fmin":"574","fmax":"1471","strand":"+","sequence":"ATGGACGTACGTAAACACAAGGCTAGTTTTTTTAGCGTAGTAATTACTTTTTTATGTCTCACGCTATCATTAAATGCTAATGCAACAGACTCAGTACTTGAAGCGGTTACCAATGCTGAAACTGAATTAGGCGCTAGAATTGGTCTAGCTGTGCATGATTTGGAAACGGGAAAACGTTGGGAACATAAATCTAATGAACGTTTTCCTCTAAGTAGTACCTTTAAAACACTTGCCTGTGCAAACGTTCTTCAAAGAGTTGATCTAGGTAAAGAAAGAATTGATAGAGTTGTGAGATTCTCTGAAAGCAATCTCGTTACATACTCACCTGTAACAGAAAAACATGTGGGTAAAAAAGGGATGTCGCTCGCAGAGCTGTGTCAGGCCACATTATCAACCAGTGATAATTCAGCTGCCAATTTTATTCTACAAGCGATTGGTGGACCTAAGGCTCTAACGAAATTTTTGCGTTCCATTGGCGACGATACTACGCGCCTTGATCGCTGGGAAACAGAACTTAACGAAGCGGTGCCTGGAGATAAGCGAGACACGACAACACCAATTGCAATGGTAACGACACTTGAAAAGTTACTAATTGACGAAACACTATCTATCAAATCTCGTCAACAACTAGAATCTTGGCTTAAAGGTAATGAGGTTGGCGATGCATTGTTTCGTAAAGGCGTTCCAAGTGACTGGATAGTAGCAGATAGAACAGGTGCTGGTGGTTATGGGTCGCGTGCTATTACTGCGGTGATGTGGCCTCCAAATCGCAAGCCTATCGTAGCCGCTCTATACATTACAGAGACAGACGCCTCGTTTGAAGAAAGAAATGCTGTCATTGCAAAAATTGGTGAGCAAATAGCGAAGACAATATTAATGGAGAATAGCCGTAACTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36930","NCBI_taxonomy_name":"Oligella urethralis","NCBI_taxonomy_id":"90245"}}}},"ARO_accession":"3002247","ARO_id":"38647","ARO_name":"CARB-8","CARD_short_name":"CARB-8","ARO_description":"CARB-8 is a beta-lactamase found in Oligella urethralis.","ARO_category":{"36230":{"category_aro_accession":"3000091","category_aro_cvterm_id":"36230","category_aro_name":"CARB beta-lactamase","category_aro_description":"CARB beta-lactamases are class A lactamases that can hydrolyze carbenicillin. Many of the PSE beta-lactamases have been renamed as CARB-lactamases with the notable exception of PSE-2 which is now OXA-10.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1662":{"model_id":"1662","model_name":"OKP-B-17","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"8271":{"protein_sequence":{"accession":"CAP12357.2","sequence":"MRYVRLCLISLIAALPLAVFASPQPLEQIKISEGQLAGRVGYVEMDLASGRTLAAWRASERFPLMSTFKVLLCGAVLARVDAGDEQLDRRIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAGNLLLKSVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDVRDTTTPASMATTLRKLLTTPSLSARSQQQLLQWMVDDRVAGPLIRAVLPAGWFIADKTGAGERGSRGIVALLGPDGKAERIVVIYLRDTPATMVERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AM850919.2","fmin":"24","fmax":"885","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGCCTTATCTCCCTGATTGCCGCCCTGCCACTGGCGGTATTCGCCAGCCCTCAGCCGCTTGAGCAGATTAAAATCAGCGAAGGTCAGCTGGCGGGCCGGGTGGGCTATGTTGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCAGTGAGCGCTTTCCGCTGATGAGCACCTTTAAAGTGCTGCTCTGCGGCGCGGTGCTGGCCCGGGTGGATGCCGGCGACGAACAGCTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGCCGACGGGATGACCGTTGGCGAACTCTGCGCCGCCGCCATCACCATGAGCGACAACAGCGCCGGCAATCTGCTGTTGAAGAGCGTCGGCGGCCCCGCGGGATTGACCGCTTTTCTGCGCCAGATCGGTGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTCAATGAGGCGCTTCCCGGCGACGTGCGCGACACCACCACCCCGGCCAGCATGGCCACCACCCTGCGCAAGCTGCTAACCACCCCCTCTCTGAGCGCCCGTTCGCAGCAGCAGCTGCTGCAGTGGATGGTGGACGACCGGGTGGCCGGCCCGTTGATCCGCGCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAAACCGGGGCCGGTGAGCGGGGCTCACGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAAGCGGAGCGTATCGTGGTGATCTATCTGCGTGATACCCCGGCGACCATGGTCGAGCGTAACCAGCAGATCGCCGGGATAGGCGCGGCGCTGATCGAGCACTGGCAGCGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002450","ARO_id":"38850","ARO_name":"OKP-B-17","CARD_short_name":"OKP-B-17","ARO_description":"OKP-B-17 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"38817":{"category_aro_accession":"3002417","category_aro_cvterm_id":"38817","category_aro_name":"OKP beta-lactamase","category_aro_description":"OKP beta-lactamases are chromosomal class A beta-lactamase that confer resistance to penicillins and early cephalosporins in Klebsiella pneumoniae. OKP beta-lactamases can be subdivided into two groups: OKP-A and OKP-B which diverge by about 4.2%.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1663":{"model_id":"1663","model_name":"ACC-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"856":{"protein_sequence":{"accession":"CAB46491.1","sequence":"MQNTLKLLSVITCLAATVQGALAANIDESKIKDTVDDLIQPLMQKNNIPGMSVAVTVNGKNYIYNYGLAAKQPQQPVTENTLFEVGSLSKTFAATLASYAQVSGKLSLDQSVSHYVPELRGSSFDHVSVLNVGTHTSGLQLFMPEDIKNTTQLMAYLKAWKPADAAGTHRVYSNIGTGLLGMIAAKSLGVSYEDAIEKTLLPQLGMHHSYLKVPADQMENYAWGYNKKDEPVHVNMEILGNEAYGIKTTSSDLLRYVQANMGQLKLDANAKMQQALTATHTGYFKSGEITQDLMWEQLPYPVSLPNLLTGNDMAMTKSVATPIVPPLPPQENVWINKTGSTNGFGAYIAFVPAKKMGIVMLANKNYSIDQRVTVAYKILSSLEGNK"},"dna_sequence":{"accession":"AJ133121.1","fmin":"649","fmax":"1810","strand":"+","sequence":"ATGCAGAACACATTGAAGCTGTTATCCGTGATTACCTGTCTGGCAGCAACTGTCCAAGGTGCTCTGGCTGCTAATATCGATGAGAGCAAAATTAAAGACACCGTTGATGACCTGATCCAGCCGCTGATGCAGAAGAATAATATTCCCGGTATGTCGGTCGCAGTGACCGTCAACGGTAAAAACTACATTTATAACTATGGGTTAGCGGCAAAACAGCCTCAGCAGCCGGTTACGGAAAATACGTTATTTGAAGTGGGTTCGCTGAGTAAAACGTTTGCTGCCACCTTGGCGTCCTATGCGCAGGTGAGCGGTAAGCTGTCTTTGGATCAAAGCGTTAGCCATTACGTTCCAGAGTTGCGTGGCAGCAGCTTTGACCACGTTAGCGTACTCAATGTGGGCACGCATACCTCAGGCCTACAGCTATTTATGCCGGAAGATATTAAAAATACCACACAGCTGATGGCTTATCTAAAAGCATGGAAACCTGCCGATGCGGCTGGAACCCATCGCGTTTATTCCAATATCGGTACTGGTTTGCTAGGGATGATTGCGGCGAAAAGTCTGGGTGTGAGCTATGAAGATGCGATTGAGAAAACCCTCCTTCCTCAGTTAGGCATGCATCACAGCTACTTGAAGGTTCCGGCTGACCAGATGGAAAACTATGCGTGGGGCTACAACAAGAAAGATGAGCCAGTGCACGTGAATATGGAGATTTTGGGTAACGAAGCTTATGGTATCAAAACCACCTCCAGCGACTTGTTACGCTACGTGCAAGCCAATATGGGGCAGTTAAAGCTTGATGCTAATGCCAAGATGCAACAGGCTCTGACAGCCACCCACACCGGCTATTTCAAATCGGGTGAGATTACTCAGGATCTGATGTGGGAGCAGCTGCCATATCCGGTTTCTCTGCCGAATTTGCTCACCGGTAACGATATGGCGATGACGAAAAGCGTGGCTACGCCGATTGTTCCGCCGTTACCGCCACAGGAAAATGTGTGGATTAATAAGACCGGATCAACTAACGGCTTCGGTGCCTATATTGCGTTTGTTCCTGCTAAGAAGATGGGGATCGTGATGCTGGCTAACAAAAACTACTCAATCGATCAGCGAGTGACGGTGGCGTATAAAATCCTGAGCTCATTGGAAGGGAATAAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001815","ARO_id":"38215","ARO_name":"ACC-1","CARD_short_name":"ACC-1","ARO_description":"ACC-1 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36212":{"category_aro_accession":"3000073","category_aro_cvterm_id":"36212","category_aro_name":"ACC beta-lactamase","category_aro_description":"ACC beta-lactamases or Ambler class C beta-lactamases are AmpC beta-lactamases. They possess an interesting resistance phenotype due to their low activity against cephamycins.","category_aro_class_name":"AMR Gene Family"},"35976":{"category_aro_accession":"0000059","category_aro_cvterm_id":"35976","category_aro_name":"cefepime","category_aro_description":"Cefepime (INN) is a fourth-generation cephalosporin antibiotic developed in 1994. It contains an aminothiazolyl group that decreases its affinity with beta-lactamases. Cefepime shows high binding affinity with penicillin-binding proteins and has an extended spectrum of activity against Gram-positive and Gram-negative bacteria, with greater activity against both Gram-negative and Gram-positive organisms than third-generation agents.","category_aro_class_name":"Antibiotic"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"35995":{"category_aro_accession":"0000078","category_aro_cvterm_id":"35995","category_aro_name":"piperacillin","category_aro_description":"Piperacillin is an acetylureidopenicillin and has an extended spectrum of targets relative to other beta-lactam antibiotics. It inhibits cell wall synthesis in bacteria, and is usually taken with the beta-lactamase inhibitor tazobactam to overcome penicillin-resistant bacteria.","category_aro_class_name":"Antibiotic"},"36689":{"category_aro_accession":"3000550","category_aro_cvterm_id":"36689","category_aro_name":"aztreonam","category_aro_description":"Aztreonam was the first monobactam discovered, and is greatly effective against Gram-negative bacteria while inactive against Gram-positive bacteria. Artreonam is a poor substrate for beta-lactamases, and may even act as an inhibitor. In Gram-negative bacteria, Aztreonam interferes with filamentation, inhibiting cell division and leading to cell death.","category_aro_class_name":"Antibiotic"},"36989":{"category_aro_accession":"3000645","category_aro_cvterm_id":"36989","category_aro_name":"cefotaxime","category_aro_description":"Cefotaxime is a semisynthetic cephalosporin taken parenterally. It is resistant to most beta-lactamases and active against Gram-negative rods and cocci due to its aminothiazoyl and methoximino functional groups.","category_aro_class_name":"Antibiotic"},"40931":{"category_aro_accession":"3004004","category_aro_cvterm_id":"40931","category_aro_name":"cefotetan","category_aro_description":"Cefotetan is a cephamycin-class beta-lactam antibiotic that is highly resistant to beta-lactamases and effective against a wide range of gram-negative and gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"40941":{"category_aro_accession":"3004014","category_aro_cvterm_id":"40941","category_aro_name":"flomoxef","category_aro_description":"Flomoxef is an oxacephem antibiotic which was effective in preventing the growth of all ESBL-producing strains and is widely active against Gram-positive, Gram-negative, and anaerobic bacteria. It is sometimes classified as a second-generation or fourth-generation cephalosporin.","category_aro_class_name":"Antibiotic"},"40944":{"category_aro_accession":"3004017","category_aro_cvterm_id":"40944","category_aro_name":"moxalactam","category_aro_description":"Moxalactam (Latamoxef) is a broad spectrum cephalosporin (oxacephem) and beta-lactam antibiotic. Moxalactam binding to PBPs inhibits peptidoglycan cross-linkage in the cell wall, resulting in cell death. Moxalactam is proposed to be effective against meningitides as it passes the blood-brain barrier.","category_aro_class_name":"Antibiotic"},"42781":{"category_aro_accession":"3004726","category_aro_cvterm_id":"42781","category_aro_name":"cefpirome","category_aro_description":"Cefpirome is a fourth generation cephalosporin with activity against methicillin-susceptible Staphylococcus aureus, coagulase-negative staphylococci and viridans group streptococci, and in vitro activity towards Streptococcus pneumoniae.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1664":{"model_id":"1664","model_name":"adeK","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"950"}},"model_sequences":{"sequence":{"674":{"protein_sequence":{"accession":"AAX14803.1","sequence":"MQKVWSISGRSIAVSALALALAACQSMRGPEPVVKTDIPQSYAYNSASGTSIAEQGYKQFFADPRLLEVIDLALANNRDLRTATLNIERAQQQYQITQNNQLPTIGASGSAIRQVSQSRDPNNPYSTYQVGLGVTAYELDFWGRVRSLKDAALDSYLATQSARDSTQISLISQVAQAWLNYSFATANLRLAEQTLKAQLDSYNLNKKRFDVGIDSEVPLRQAQISVETARNDVANYKTQIAQAQNLLNLLVGQPVPQNLLPTQPVKRIAQQNVFTAGLPSDLLNNRPDVKAAEYNLSAAGANIGAAKARLFPTISLTGSAGYASTDLSDLFKSGGFVWSVGPSLDLPIFDWGTRRANVKISETDQKIALSDYEKSVQSAFREVNDALATRANIGERLTAQQRLVEATNRNYTLSNARFRAGIDSYLTVLDAQRSSYAAEQGLLLLQQANLNNQIELYKTLGGGLKANTSDTVVHQPSSAELKKQ"},"dna_sequence":{"accession":"AY769962.1","fmin":"5610","fmax":"7065","strand":"+","sequence":"ATGCAAAAAGTATGGTCTATTTCAGGTCGTAGCATTGCGGTGTCTGCACTTGCGCTTGCTTTGGCAGCTTGTCAAAGCATGCGCGGCCCAGAACCAGTCGTGAAAACCGATATACCACAAAGCTATGCATATAACAGCGCTTCTGGTACGTCTATTGCTGAACAGGGTTATAAACAGTTCTTTGCTGACCCGCGTTTGCTTGAAGTGATTGATTTGGCTCTTGCCAATAACCGTGACTTACGTACAGCAACGCTCAATATTGAACGTGCTCAACAGCAATATCAGATTACACAGAACAACCAGCTTCCAACAATCGGAGCAAGTGGTAGTGCAATTCGTCAGGTTTCTCAAAGCCGTGATCCGAATAACCCCTACTCTACTTATCAAGTAGGTTTGGGTGTAACTGCTTATGAGCTAGATTTCTGGGGTCGTGTTCGTAGCCTCAAAGATGCTGCTTTAGATAGTTATCTTGCAACACAAAGTGCTCGTGATTCGACTCAAATCAGTCTGATTAGCCAAGTTGCTCAAGCATGGTTAAATTATTCGTTTGCAACAGCAAACTTAAGACTGGCAGAGCAAACGCTTAAAGCACAGTTAGATTCTTACAATCTCAACAAAAAACGTTTTGATGTAGGTATTGACAGTGAAGTTCCATTACGTCAAGCACAGATTTCTGTAGAAACTGCGCGTAATGATGTAGCGAACTACAAAACTCAAATTGCTCAAGCACAAAACTTGTTGAACTTGCTTGTAGGCCAACCTGTTCCACAAAACTTGTTACCTACACAACCTGTAAAACGCATTGCTCAACAAAATGTGTTTACTGCCGGTTTACCAAGTGACTTGTTAAATAACCGTCCGGATGTAAAAGCTGCTGAATACAACTTAAGCGCTGCGGGTGCGAATATCGGTGCTGCAAAAGCACGTTTATTCCCAACCATTAGCTTAACGGGTTCGGCTGGTTATGCATCAACTGACTTAAGTGATCTATTTAAGTCTGGTGGTTTTGTATGGTCAGTTGGTCCAAGCTTAGATTTACCAATCTTTGACTGGGGTACACGCCGTGCCAATGTAAAAATTTCTGAAACCGATCAGAAAATTGCATTGTCTGATTATGAAAAATCAGTTCAGTCGGCGTTCCGTGAAGTTAATGACGCGCTTGCAACTCGTGCCAATATTGGTGAGCGTTTAACAGCACAACAACGTCTAGTAGAAGCAACTAACCGCAACTACACACTTTCAAATGCCCGCTTCCGTGCCGGTATTGATAGTTACTTGACTGTTCTTGATGCACAGCGTTCTTCATATGCAGCTGAACAAGGTTTGTTATTGCTTCAACAAGCAAACTTAAACAACCAAATCGAGTTATACAAAACTCTAGGTGGTGGTTTAAAAGCAAATACTTCAGATACAGTGGTTCACCAACCATCTAGTGCTGAACTTAAAAAGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3000782","ARO_id":"37162","ARO_name":"adeK","CARD_short_name":"adeK","ARO_description":"AdeK is the outer membrane factor protein in the adeIJK multidrug efflux complex.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36309":{"category_aro_accession":"3000170","category_aro_cvterm_id":"36309","category_aro_name":"imipenem","category_aro_description":"Imipenem is a broad-spectrum antibiotic and is usually taken with cilastatin, which prevents hydrolysis of imipenem by renal dehydropeptidase-I. It is resistant to hydrolysis by most other beta-lactamases. Notable exceptions are the KPC beta-lactamases and Ambler Class B enzymes.","category_aro_class_name":"Antibiotic"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"40523":{"category_aro_accession":"3003832","category_aro_cvterm_id":"40523","category_aro_name":"ticarcillin","category_aro_description":"Ticarcillin is a carboxypenicillin used for the treatment of Gram-negative bacteria, particularly P. aeruginosa. Ticarcillin's antibiotic properties arise from its ability to prevent cross-linking of peptidoglycan during cell wall synthesis, when the bacteria try to divide, causing cell death.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1665":{"model_id":"1665","model_name":"ramA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"230"}},"model_sequences":{"sequence":{"289":{"protein_sequence":{"accession":"AFK13828.1","sequence":"MINQEAEGESSMTISAQIIDTIVEWIDDNLHQPLRIEEIARHAGYSKWHLQRLFMQYKGESLGRYIRERKLLLAARDLRESDARVYDICLRYGFDSQQTFTRIFTRTFNQPPGAYRKENHSRAH"},"dna_sequence":{"accession":"JQ727668.1","fmin":"0","fmax":"375","strand":"+","sequence":"ATGATCAATCAGGAAGCTGAAGGGGAGAGCAGTATGACCATTTCCGCTCAAATCATCGACACTATCGTCGAGTGGATCGACGATAACCTGCACCAGCCATTACGTATCGAAGAGATTGCCCGCCATGCGGGTTACTCGAAATGGCACCTGCAGCGGCTGTTTATGCAATACAAAGGGGAGAGTCTGGGGCGCTATATCCGTGAACGCAAGCTGCTGCTGGCGGCGCGGGATCTGCGCGAATCAGACGCCCGGGTATACGACATCTGCCTGCGTTACGGGTTTGACTCGCAGCAGACCTTCACTCGCATCTTCACCCGCACGTTCAACCAGCCGCCTGGGGCGTATCGTAAAGAGAACCACAGCCGCGCGCACTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3000823","ARO_id":"37203","ARO_name":"ramA","CARD_short_name":"ramA","ARO_description":"RamA (resistance antibiotic multiple) is a positive regulator of AcrAB-TolC and leads to high level multidrug resistance in Klebsiella pneumoniae, Salmonella enterica, and Enterobacter aerugenes, increasing the expression of both the mar operon as well as AcrAB. RamA also decreases OmpF expression.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"41445":{"category_aro_accession":"3004281","category_aro_cvterm_id":"41445","category_aro_name":"General Bacterial Porin with reduced permeability to beta-lactams","category_aro_description":"These are GBPs that are associated with decreased susceptibility to beta-lactams either through mutations in the porin protein, absence of the porin protein, or expression of the porin protein.","category_aro_class_name":"AMR Gene Family"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"37084":{"category_aro_accession":"3000704","category_aro_cvterm_id":"37084","category_aro_name":"cefalotin","category_aro_description":"Cefalotin is a semisynthetic cephalosporin antibiotic activate against staphylococci. It is resistant to staphylococci beta-lactamases but hydrolyzed by enterobacterial beta-lactamases.","category_aro_class_name":"Antibiotic"},"37250":{"category_aro_accession":"3000870","category_aro_cvterm_id":"37250","category_aro_name":"triclosan","category_aro_description":"Triclosan is a common antibacterial agent added to many consumer products as a biocide.  It is an inhibitor of fatty acid biosynthesis by blocking enoyl-carrier protein reductase (FabI).","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"43746":{"category_aro_accession":"3005386","category_aro_cvterm_id":"43746","category_aro_name":"disinfecting agents and antiseptics","category_aro_description":"Disinfectants that can also interact with antimicrobial resistance mechanisms, e.g. molecule efflux, and thus are the targets of disinfectant resistance.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"},"36383":{"category_aro_accession":"3000244","category_aro_cvterm_id":"36383","category_aro_name":"reduced permeability to antibiotic","category_aro_description":"Reduction in permeability to antibiotic, generally through reduced production of porins, can provide resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1667":{"model_id":"1667","model_name":"TEM-80","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1003":{"protein_sequence":{"accession":"AAM15527.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMLSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAVTMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERDRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AF347054.1","fmin":"208","fmax":"1069","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGCTGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCGTAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAGATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3000947","ARO_id":"37327","ARO_name":"TEM-80","CARD_short_name":"TEM-80","ARO_description":"TEM-80 is an inhibitor-resistant beta-lactamase found in Enterobacter cloacae.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1668":{"model_id":"1668","model_name":"CMY-68","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"945":{"protein_sequence":{"accession":"AEZ49855.1","sequence":"MMKKSICCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGIAVAIIYEGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWRGISLLHLATYTAGGLPLQIPDEVTDKAELLRFYQNWQPQWTPGAKRLYANSSIGLFGALVVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQSEQKNYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIELAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"JN714480.1","fmin":"1039","fmax":"2185","strand":"+","sequence":"ATGATGAAAAAATCGATATGCTGCGCACTGCTGCTGACAGCCTCTTTCTCCACGTTTGCTGCCGCAAAAACAGAACAACAAATTGCCGATATCGTTAACCGCACCATCACACCACTGATGCAGGAGCAGGCTATTCCGGGCATTGCCGTGGCAATTATCTACGAGGGGAAACCTTATTACTTTACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAATTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGACGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCGGGGTATCAGCCTGCTGCACTTAGCCACCTATACAGCGGGTGGCCTGCCGCTGCAGATCCCCGATGAAGTTACGGATAAAGCCGAATTACTGCGCTTTTATCAAAACTGGCAACCACAATGGACTCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGTGCGTTGGTGGTAAAACCTTCAGGTATGAGCTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAAAGCGAACAAAAAAATTATGCCTGGGGCTATCGCGAAGGGAAGCCTGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATCGATATGGCCCGCTGGGTTCAGGCCAACATGGACGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGAGCTTGCGCAGTCTCGCTACTGGCGTATTGGTGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCAGCACCTGCCGTGAAAGCCTCATGGGTGCATAAAACGGGATCCACAGGTGGATTTGGCAGCTACGTTGCCTTCGTTCCAGAAAAAAACCTTGGCATAGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGCGTCGAGGCGGCCTGGCGCATTCTTGAAAAACTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002081","ARO_id":"38481","ARO_name":"CMY-68","CARD_short_name":"CMY-68","ARO_description":"CMY-68 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1672":{"model_id":"1672","model_name":"TEM-211","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1159":{"protein_sequence":{"accession":"AHA80960.1","sequence":"MSIKHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVKYSPVTEKHLTDGMTVRELCSAAITMTDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTTPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGASERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDELNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"KF513179.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTAAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTAAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGACTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGACGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCAGTGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACTAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3001388","ARO_id":"37788","ARO_name":"TEM-211","CARD_short_name":"TEM-211","ARO_description":"TEM-211 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1673":{"model_id":"1673","model_name":"QnrA6","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"3348":{"protein_sequence":{"accession":"AAZ78355.1","sequence":"MDIIDKVFQQEDFSRQDLSDSRFRRCRFYQCDFSHCQLRDASFEDCSFIESGAIEGCHFSYADLRDASFKACRLSLANFSGANCFGIEFRECDLKGANFSRARFYNQISHKMYFCSAYISGCNLAYANLSGQCLEKCELFENNWSNANLSGASLMGSDLSHGTFSRDCWQQVNLRGCDLTFADLDGLDPRRVNLEGVKICAWQQEQLLEPLGVIVLPD"},"dna_sequence":{"accession":"DQ151889.1","fmin":"0","fmax":"657","strand":"+","sequence":"ATGGATATTATTGATAAAGTTTTTCAGCAAGAGGATTTCTCACGCCAGGATTTGAGTGACAGCCGTTTTCGCCGCTGCCGCTTTTATCAGTGTGACTTCAGCCATTGCCAGCTAAGGGATGCCAGTTTCGAGGATTGCAGTTTCATTGAAAGCGGCGCCATCGAAGGGTGCCACTTCAGCTATGCCGATCTGCGCGATGCCAGTTTCAAGGCCTGCCGCCTGTCTTTGGCCAATTTCAGCGGTGCCAACTGCTTTGGCATAGAGTTCAGGGAGTGCGATCTCAAGGGCGCCAATTTTTCCCGGGCCCGTTTTTACAATCAAATCAGCCATAAGATGTACTTCTGCTCGGCTTATATCTCAGGCTGTAACCTGGCCTATGCCAATTTGAGCGGCCAATGCCTGGAAAAGTGCGAGCTGTTTGAAAACAACTGGAGCAATGCCAACCTCAGCGGCGCTTCCTTGATGGGCTCCGACCTCAGCCACGGCACCTTCTCCCGCGACTGCTGGCAACAGGTAAACCTGCGGGGCTGTGACCTGACCTTTGCCGATCTGGATGGGCTCGACCCCAGACGGGTCAACCTCGAAGGGGTCAAGATCTGTGCCTGGCAGCAGGAGCAACTGCTGGAACCCTTGGGAGTAATAGTGCTGCCGGATTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3002712","ARO_id":"39146","ARO_name":"QnrA6","CARD_short_name":"QnrA6","ARO_description":"QnrA6 is a plasmid-mediated quinolone resistance protein found in Proteus mirabilis.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1674":{"model_id":"1674","model_name":"AAC(6')-It","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"736":{"protein_sequence":{"accession":"AAD03492.1","sequence":"MHIMPITESQLSDWLVLRCLLWPDHEDADLQEMRQLITQAHCLQLLAYTNTQKAIGMLEASIRYEYVNGTQTSPVAFLEGIYVLPEYRRSGIATGLVQHVEIWAKQFACTEFASDATLDNQISHAMHRALGFHETERVVYFKKNIG"},"dna_sequence":{"accession":"AF031328.1","fmin":"0","fmax":"441","strand":"+","sequence":"ATGCATATTATGCCGATAACTGAATCACAATTATCAGATTGGCTAGTATTGAGATGCTTACTCTGGCCTGATCATGAAGATGCAGATTTACAGGAAATGCGCCAACTGATCACACAGGCACATTGCTTACAATTATTGGCTTATACCAACACCCAAAAAGCAATTGGCATGTTGGAAGCTTCGATTCGATATGAATATGTGAATGGTACGCAAACCTCACCCGTGGCTTTTCTTGAAGGGATTTATGTATTACCTGAATATCGCCGTTCAGGTATCGCAACAGGTTTGGTTCAGCATGTCGAAATCTGGGCTAAACAGTTTGCATGTACAGAGTTTGCTTCAGACGCAACGCTGGACAATCAGATCAGCCATGCAATGCATCGAGCGCTCGGTTTTCATGAAACTGAACGTGTGGTGTATTTTAAGAAAAATATCGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39515","NCBI_taxonomy_name":"Acinetobacter genomosp. 16BJ","NCBI_taxonomy_id":"70347"}}}},"ARO_accession":"3002564","ARO_id":"38964","ARO_name":"AAC(6')-It","CARD_short_name":"AAC(6')-It","ARO_description":"AAC(6')-It is a chromosomal-encoded aminoglycoside acetyltransferase in Acinetobacter genomosp. 16.","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"A category of aminoglycoside N-acetyltransferase enzymes with modification regiospecificity based at the 6'-amino group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics through acetylation of the 6-amino group of the compound.","category_aro_class_name":"AMR Gene Family"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"46128":{"category_aro_accession":"3007378","category_aro_cvterm_id":"46128","category_aro_name":"2'-N-ethylnetilmicin","category_aro_description":"2'-N-ethylnetilmicin is an aminoglycoside antibiotic and a derivative of netilmicin.","category_aro_class_name":"Antibiotic"},"46129":{"category_aro_accession":"3007379","category_aro_cvterm_id":"46129","category_aro_name":"5-episisomicin","category_aro_description":"5-episosomicin is a semisynthetic aminoglycoside antibiotic similar to sisomicin.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1675":{"model_id":"1675","model_name":"CTX-M-5","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1087":{"protein_sequence":{"accession":"AAC32890.1","sequence":"MMTQSIRRSMLTVMATLPLLFSSATLHAQTNSVQQQLEALEKSSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKQSESDKHLLNQRVEIKKSDLVNYNPIAEKHVNGTMTLAELGAAALQYSDNTAMNKLIAHLGGPDKVTAFARSLGDETFRLDRTEPTLNTAIPGDPRDTTTPLAMAQTLKNLTLGKALAETQRAQLVTWLKGNTTGSASIRAGLPKSWGVGDKTGSGDYGTTNDIAVIWPANHAPLVLVTYFTQPEQKAESRRDVLAAAAKIVTHGF"},"dna_sequence":{"accession":"U95364.1","fmin":"5","fmax":"881","strand":"+","sequence":"ATGATGACTCAGAGCATTCGCCGCTCAATGTTAACGGTGATGGCGACGCTACCCCTGCTATTTAGCAGCGCAACGCTGCACGCGCAGACGAACAGCGTGCAGCAGCAGCTGGAAGCCCTGGAGAAAAGTTCGGGAGGTCGGCTTGGCGTTGCGCTGATTAACACCGCCGATAATTCGCAGATTCTCTACCGTGCCGATGAACGTTTTGCGATGTGCAGTACCAGTAAGGTGATGGCGGCCGCGGCGGTGCTTAAACAGAGCGAGAGCGATAAGCACCTGCTAAATCAGCGCGTTGAAATCAAGAAGAGCGACCTGGTTAACTACAATCCCATTGCGGAGAAACACGTTAACGGCACGATGACGCTGGCTGAGCTTGGCGCAGCGGCGCTGCAGTATAGCGACAATACTGCCATGAATAAGCTGATTGCCCATCTGGGTGGGCCCGATAAAGTGACGGCGTTTGCTCGCTCGTTGGGTGATGAGACCTTCCGTCTGGACAGAACCGAGCCCACGCTCAATACCGCCATTCCAGGCGACCCGCGTGATACCACCACGCCGCTCGCGATGGCGCAGACCCTGAAAAATCTGACGCTGGGTAAAGCGCTGGCGGAAACTCAGCGGGCACAGTTGGTGACGTGGCTTAAGGGCAATACTACCGGTAGCGCGAGCATTCGGGCGGGTCTGCCGAAATCATGGGGAGTGGGCGATAAAACCGGCAGCGGAGATTATGGCACCACCAACGATATCGCGGTTATCTGGCCGGCAAACCACGCACCGCTGGTTCTGGTGACCTACTTTACCCAACCGGAGCAGAAGGCGGAAAGCCGTCGGGATGTTCTGGCTGCGGCGGCGAAAATCGTAACCCACGGTTTCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35732","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Typhimurium","NCBI_taxonomy_id":"90371"}}}},"ARO_accession":"3001868","ARO_id":"38268","ARO_name":"CTX-M-5","CARD_short_name":"CTX-M-5","ARO_description":"CTX-M-5 is a beta-lactamase found in Salmonella typhimurium.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1676":{"model_id":"1676","model_name":"GES-18","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1013":{"protein_sequence":{"accession":"AEX59144.1","sequence":"MRFIHALLLAGIAHSAYASEKLTFKTDLEKLEREKAAQIGVAIVDPQGEIVAGHRMAQRFAMCSTFKFPLAALIFERIDSGTERGDRKLSYGPDMIVEWSPATERFLASGHMTVLEAAQAAVQLSDNGATNLLLREIGGPAAMTQYFRKIGDSVSRLDRKEPEMSDNTPGDLRDTTTPIAMARTVAKVLYGGALTSTSTHTIERWLIGNQTGDATLRAGFPKDWVVGEKTGTCANGGRNDIGFFKAQERDYAVAVYTTAPKLSAVERDELVASVGQVITQLILSTDK"},"dna_sequence":{"accession":"JQ028729.1","fmin":"0","fmax":"864","strand":"+","sequence":"ATGCGCTTCATTCACGCACTATTACTGGCAGGGATCGCTCACTCTGCATATGCGTCGGAAAAATTAACCTTCAAGACCGATCTTGAGAAGCTAGAGCGCGAAAAAGCAGCTCAGATCGGTGTTGCGATCGTCGATCCCCAAGGAGAGATCGTCGCGGGCCACCGAATGGCGCAGCGTTTTGCAATGTGCTCAACGTTCAAGTTTCCGCTAGCCGCGCTGATCTTTGAAAGAATTGACTCAGGCACCGAGCGGGGGGATCGAAAACTTTCATATGGGCCGGACATGATCGTCGAATGGTCTCCTGCCACGGAGCGGTTTCTAGCATCGGGACACATGACGGTTCTCGAGGCAGCGCAAGCTGCGGTGCAGCTTAGCGACAATGGGGCTACTAACCTCTTACTGAGAGAAATTGGCGGACCTGCTGCAATGACGCAGTATTTTCGTAAAATTGGGGACTCTGTGAGTCGGCTAGACCGGAAAGAGCCGGAGATGAGCGACAACACACCTGGCGACCTCAGAGATACAACTACGCCTATTGCTATGGCACGTACTGTGGCTAAAGTCCTCTATGGCGGCGCACTGACGTCCACCTCGACCCACACCATTGAGAGGTGGCTGATCGGAAACCAAACGGGAGACGCGACACTACGAGCGGGTTTTCCTAAAGATTGGGTTGTTGGAGAGAAAACTGGTACCTGCGCCAACGGGGGCCGGAACGACATTGGTTTTTTTAAAGCCCAGGAGAGAGATTACGCTGTAGCGGTGTATACAACGGCCCCGAAACTATCGGCCGTAGAACGTGACGAATTAGTTGCCTCTGTCGGTCAAGTTATTACACAACTCATCCTGAGCACGGACAAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002347","ARO_id":"38747","ARO_name":"GES-18","CARD_short_name":"GES-18","ARO_description":"GES-18 is a beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36205":{"category_aro_accession":"3000066","category_aro_cvterm_id":"36205","category_aro_name":"GES beta-lactamase","category_aro_description":"GES beta-lactamases or Guiana extended-spectrum beta-lactamases are related to the other plasmid-located class A beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1679":{"model_id":"1679","model_name":"OXA-49","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1766":{"protein_sequence":{"accession":"AAP40270.1","sequence":"MNKYFTCYVVASLFLSGCTVQHNLINETPSQIVQGHNQVIHQYFDEKNTSGVLVIQTDKKINLYGNALSRANTEYVPASTFKMLNALIGLENQKTDINEIFKWKGEKRSFTAWEKDMTLGEAMKLSAVPVYQELARRIGLDLMQKEVERIGFGNAEIGQQVDNFWLVGPLKVTPIQEVEFVSQLAHTQLPFSEKVQANVKNMLLLEESNGYKIFGKTGWAAMDIKPQVGWLTGWVEQPDGKIVAFALNMEMRSEMPASIRNELLMKSLKQLNII"},"dna_sequence":{"accession":"AY288523.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAATAAATATTTTACTTGCTATGTGGTTGCTTCTCTTTTTCTTTCTGGTTGTACGGTTCAGCATAATTTAATAAATGAAACCCCGAGTCAGATTGTTCAAGGACATAATCAGGTGATTCATCAATACTTTGATGAAAAAAACACCTCAGGTGTGCTGGTTATTCAAACAGATAAAAAAATTAATCTATATGGTAATGCTCTAAGCCGCGCAAATACAGAATATGTGCCAGCCTCTACATTTAAAATGTTGAATGCCCTGATCGGATTGGAGAACCAGAAAACGGATATTAATGAAATATTTAAATGGAAGGGCGAGAAAAGGTCATTTACCGCTTGGGAAAAAGACATGACACTAGGAGAAGCCATGAAGCTTTCTGCAGTCCCAGTCTATCAGGAACTTGCGCGACGTATCGGTCTTGATCTCATGCAAAAAGAAGTAGAACGTATTGGTTTCGGTAATGCTGAAATTGGACAGCAGGTTGATAATTTCTGGTTGGTAGGACCATTAAAGGTTACGCCTATTCAAGAGGTAGAGTTTGTTTCCCAATTAGCACATACACAGCTTCCATTTAGTGAAAAAGTGCAGGCTAATGTAAAAAATATGCTTCTTTTAGAAGAGAGTAATGGCTACAAAATTTTTGGAAAGACTGGTTGGGCGGCAATGGATATAAAACCACAAGTGGGCTGGTTGACCGGCTGGGTTGAGCAGCCAGATGGAAAAATTGTCGCTTTTGCATTAAATATGGAAATGCGGTCAGAAATGCCGGCATCTATACGTAATGAATTATTGATGAAATCATTAAAACAGCTGAATATTATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001671","ARO_id":"38071","ARO_name":"OXA-49","CARD_short_name":"OXA-49","ARO_description":"OXA-49 is a beta-lactamase found in A. baumannii.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46499":{"category_aro_accession":"3007710","category_aro_cvterm_id":"46499","category_aro_name":"OXA-23-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases, specifically imipenem, derived from OXA-23, first identified in Acinetobacter baumannii.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1680":{"model_id":"1680","model_name":"macA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"760"}},"model_sequences":{"sequence":{"578":{"protein_sequence":{"accession":"AAV85981.1","sequence":"MAKMMKWSAVAAVAAAAVWGGWHYLKPEPQAAYITETVRRGGISRTVSATGEISPSNLVSVGAQASGQIKKLYVKLGQQVKKGDLIAEINSTTQTNTLNMEKSKLETYQAKLVSAQIALGSAEKKYKRQTALWKDDATSKEDLESAQDALAAAKANVAELKALIRQSKISINTAESDLGYTRITATMDGTVVAIPVEEGQTVNAAQSTPTIVQLANLDMMLNKMQIAEGDITKVKAGQDISFTILSEPDTPIKAKLDSVDPGLTTMSSGGYNSSTDTASNAVYYYARSFVPNPDGKLATGMTTQNTVEIDGVKNVLLIPSLTVKNRGGKAFVRVLGADGKAAEREIRTGMRDSMNTEVKSGLKEGDKVVISEITAAEQQESGERALGGPPRR"},"dna_sequence":{"accession":"AY768531.1","fmin":"0","fmax":"1179","strand":"+","sequence":"ATGGCGAAAATGATGAAATGGTCGGCTGTTGCGGCAGTCGCGGCGGCAGCGGTTTGGGGCGGATGGCATTATCTGAAGCCCGAACCGCAGGCTGCTTATATTACGGAAACGGTCAGGCGCGGCGGCATCAGCCGGACGGTTTCCGCGACGGGCGAGATTTCGCCGTCGAATCTGGTATCGGTCGGCGCGCAGGCTTCGGGGCAGATTAAAAAGCTTTATGTCAAACTCGGGCAACAGGTCAAAAAGGGAGATTTGATTGCGGAAATCAATTCGACCACGCAGACCAACACGCTCAATATGGAAAAATCTAAATTGGAAACGTATCAGGCGAAGCTGGTGTCGGCACAGATTGCATTGGGCAGCGCGGAGAAGAAATATAAGCGTCAGACGGCGTTGTGGAAGGATGATGCGACCTCTAAAGAAGATTTGGAAAGCGCGCAGGATGCGCTTGCCGCCGCCAAAGCCAATGTTGCCGAGTTGAAGGCTTTAATCAGACAGAGCAAAATTTCCATCAATACCGCCGAGTCGGATTTGGGCTACACGCGCATTACCGCGACGATGGACGGCACGGTGGTGGCGATTCCCGTGGAAGAGGGGCAAACCGTGAACGCGGCGCAGTCTACGCCGACGATTGTCCAATTGGCGAATCTGGATATGATGTTGAACAAAATGCAGATTGCCGAGGGCGATATTACCAAGGTGAAGGCGGGGCAGGATATTTCGTTTACGATTTTGTCCGAACCGGATACGCCGATTAAGGCGAAGCTCGACAGCGTCGACCCCGGGCTGACCACGATGTCGTCGGGCGGCTACAACAGCAGTACGGATACGGCTTCCAATGCGGTCTATTATTATGCCCGTTCGTTTGTGCCGAATCCGGACGGCAAACTCGCCACGGGGATGACGACGCAGAATACGGTTGAAATCGACGGTGTGAAAAATGTGTTGCTTATTCCGTCGCTGACCGTGAAAAATCGCGGCGGCAAGGCGTTCGTACGCGTGTTGGGTGCGGACGGCAAGGCGGCGGAACGCGAAATCCGGACCGGTATGAGAGACAGTATGAATACCGAAGTGAAAAGCGGGTTGAAAGAGGGGGACAAAGTGGTCATCTCCGAAATAACCGCCGCCGAGCAGCAGGAAAGCGGCGAACGCGCCCTAGGCGGCCCGCCGCGCCGATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36806","NCBI_taxonomy_name":"Neisseria gonorrhoeae","NCBI_taxonomy_id":"485"}}}},"ARO_accession":"3000533","ARO_id":"36672","ARO_name":"macA","CARD_short_name":"macA","ARO_description":"MacA is a membrane fusion protein that forms an antibiotic efflux complex with MacB and TolC. macA corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.","ARO_category":{"36002":{"category_aro_accession":"0010001","category_aro_cvterm_id":"36002","category_aro_name":"ATP-binding cassette (ABC) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding\/hydrolysis to transport substrates across cell membranes.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1681":{"model_id":"1681","model_name":"APH(4)-Ib","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"262":{"protein_sequence":{"accession":"CAA52372.1","sequence":"MLQTSKKKSGHDESWANADAHKWRGERKRDNRKIVLSGTTKLLFVAEEQFQLIPPPSYCVSLVPKLPSNVTQPLFEYCFAPRILFFYALKKMTQHTKLCKLSSLIWREMWAISSRLQWQCVCAARRITMRNGGWKFIEMLSCWSDMVHKHESVLISTLPSFINFLVGPFRSAGAEPGGMHRRVDPPRPLSPALIEAFDGVMQLSGAPSRGVTPTPRGPDALGRITDSRGGSEAGYRFNMCNRAVPSAALPIGEVLDIGEFSGKRTYLAAVHRAREQDLPETELPAVLQPCTGMAHAIAAADLSHTSGFAPFGPQGMGQETPWRDKRDCYFDPQVYYWLSQMGDTLRASVAQGFEKRMLWAEDCPEARHLRIHVKGSNAALPEPGPKTWAGDGSQAVWAGRLRPTQDSRYVVASIFPWRPW"},"dna_sequence":{"accession":"X74325.1","fmin":"645","fmax":"1908","strand":"+","sequence":"ATGCTGCAAACTTCTAAAAAAAAATCTGGGCACGATGAAAGTTGGGCTAACGCTGACGCTCACAAATGGCGTGGCGAAAGGAAGCGAGACAATCGGAAAATTGTTCTCTCGGGCACCACAAAGCTGTTGTTTGTCGCTGAAGAACAATTCCAACTGATTCCGCCGCCTTCCTATTGCGTCAGCCTTGTACCTAAGCTGCCGAGTAACGTCACTCAACCTCTCTTTGAATACTGCTTTGCTCCGCGAATACTTTTCTTCTATGCGCTCAAGAAAATGACACAGCACACCAAGCTCTGCAAACTTTCTTCGCTCATCTGGCGCGAAATGTGGGCCATTTCTTCTCGCCTGCAATGGCAATGCGTCTGTGCGGCGAGGAGAATCACGATGCGGAATGGGGGCTGGAAGTTCATAGAGATGCTGAGTTGTTGGAGCGACATGGTACATAAGCATGAGTCTGTCCTGATTTCCACCCTCCCGTCTTTCATCAACTTTCTCGTCGGACCCTTCCGATCGGCGGGCGCAGAACCAGGCGGTATGCACCGTAGGGTGGACCCACCGCGGCCACTGTCGCCAGCCTTGATCGAGGCCTTCGACGGGGTCATGCAGCTCTCGGGCGCCCCCTCTCGTGGGGTCACACCAACCCCACGAGGGCCAGATGCTTTGGGCCGGATAACAGATAGCCGCGGGGGGTCCGAGGCTGGCTATAGGTTTAATATGTGTAATCGGGCAGTACCATCGGCCGCGCTCCCGATTGGGGAAGTGCTTGACATTGGGGAATTCAGCGGGAAGCGGACCTACCTGGCCGCCGTGCACAGGGCCCGCGAGCAAGACCTGCCTGAAACCGAACTGCCCGCTGTTCTGCAGCCCTGCACGGGCATGGCACATGCGATCGCTGCGGCCGATCTTAGCCACACGAGCGGGTTCGCCCCATTCGGACCGCAAGGAATGGGTCAAGAGACTCCATGGCGTGATAAGCGCGATTGCTATTTCGATCCCCAGGTGTATTATTGGCTCTCTCAAATGGGCGACACCCTACGGGCGTCCGTCGCGCAGGGTTTCGAAAAGCGGATGCTTTGGGCCGAGGACTGCCCCGAAGCCCGGCACCTCCGGATTCACGTAAAGGGGTCCAACGCTGCCCTGCCGGAACCCGGCCCCAAAACGTGGGCGGGGGACGGGAGCCAAGCGGTGTGGGCAGGCCGGCTGCGTCCCACCCAGGATTCCCGGTACGTGGTCGCCAGCATCTTCCCCTGGAGGCCGTGGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36923","NCBI_taxonomy_name":"Burkholderia pseudomallei","NCBI_taxonomy_id":"28450"}}}},"ARO_accession":"3002656","ARO_id":"39056","ARO_name":"APH(4)-Ib","CARD_short_name":"APH(4)-Ib","ARO_description":"APH(4)-Ib is a chromosomal-encoded aminoglycoside phosphotransferase in Pseudomonas pseudomallei.","ARO_category":{"36294":{"category_aro_accession":"3000155","category_aro_cvterm_id":"36294","category_aro_name":"APH(4)","category_aro_description":"A category of aminoglycoside O-phosphotransferase enzymes with modification regiospecificity based at the 4-hydroxyl group of the respective antibiotic. These enzymes are characterized by enzymatic antibiotic inactivation, specifically of hygromycin, by the ATP-dependent phosphorylation of the 4-hydroxyl group of the compound.","category_aro_class_name":"AMR Gene Family"},"36353":{"category_aro_accession":"3000214","category_aro_cvterm_id":"36353","category_aro_name":"hygromycin B","category_aro_description":"Hygromycin B is an aminoglycoside antibiotic used to treat different types of bacterial infections. Hygromycin B works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Hygromycin B has also been shown to interact with eukaryotic cells.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1682":{"model_id":"1682","model_name":"aadA24","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"330":{"protein_sequence":{"accession":"ABG72894.1","sequence":"MTIEISNQLSEVLSVIERHLEPTLLAVHLYGSAVDGGLKPHSDIDLLVTVTVRLDETTRRALINDLLETSASPGESEILRAVEVTIVVHDDIIPWRYPAKRELQFGEWQRNDILAGIFEPATIDIDLAILLTKAREHSVALVGPAAEELFDPVPEQDLFEALNETLTLWNSPPDWAGDERNVVLTLSRIWYSAVTGKIAPKDVAADWAMERLPAQYQPVILEARQAYLGQEEDRLASRADQLEEFVHYVKGEITKVVGK"},"dna_sequence":{"accession":"DQ677333.1","fmin":"0","fmax":"780","strand":"+","sequence":"GTGACCATCGAAATTTCGAACCAACTATCAGAGGTGCTAAGCGTCATTGAGCGCCATCTCGAACCGACGTTGCTGGCCGTACATTTGTACGGCTCCGCAGTGGATGGCGGCCTGAAGCCACACAGTGATATTGATTTGCTGGTTACGGTGACCGTAAGGCTTGATGAAACAACGCGGCGAGCTTTGATCAACGACCTTTTGGAAACTTCGGCTTCCCCTGGAGAGAGCGAGATTCTCCGCGCTGTAGAAGTCACCATTGTTGTGCACGACGACATCATTCCGTGGCGTTATCCAGCTAAGCGCGAACTGCAATTTGGAGAATGGCAGCGCAATGACATTCTTGCAGGTATCTTCGAGCCAGCCACGATCGACATTGATCTGGCTATCTTGCTGACAAAAGCAAGAGAACATAGCGTTGCCTTGGTAGGTCCAGCGGCGGAGGAACTCTTTGATCCGGTTCCTGAACAGGATCTATTTGAGGCGCTAAATGAAACCTTAACGCTATGGAACTCGCCGCCCGACTGGGCTGGCGATGAGCGAAATGTAGTGCTTACGTTGTCCCGCATTTGGTACAGCGCAGTAACCGGCAAAATCGCGCCGAAGGATGTCGCTGCCGACTGGGCAATGGAGCGCCTGCCGGCCCAGTATCAGCCCGTCATACTTGAAGCTAGACAGGCTTATCTTGGACAAGAAGAAGATCGCTTGGCCTCCCGCGCAGATCAGTTGGAAGAATTTGTTCACTACGTGAAAGGCGAGATCACCAAGGTAGTCGGCAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35735","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Newport","NCBI_taxonomy_id":"108619"}}}},"ARO_accession":"3002621","ARO_id":"39021","ARO_name":"aadA24","CARD_short_name":"aadA24","ARO_description":"aadA24 is an integron-encoded aminoglycoside nucleotidyltransferase gene in Salmonella spp.","ARO_category":{"41439":{"category_aro_accession":"3004275","category_aro_cvterm_id":"41439","category_aro_name":"ANT(3'')","category_aro_description":"A category of aminoglycoside O-nucleotidyltransferase enzymes with modification regiospecificity based at the 3''-hydroxyl group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics by transfer of an AMP group from an ATP substrate to the 3''-hydroxyl group of the compound.","category_aro_class_name":"AMR Gene Family"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1683":{"model_id":"1683","model_name":"QnrB67","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"192":{"protein_sequence":{"accession":"AGL43628.1","sequence":"MTLALVCEKIDRNRFTGEKVENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNVSALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGTQVLGATFSGSDLSGGEFSTFDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDNYQASLLMERLGIAVIG"},"dna_sequence":{"accession":"KC580656.1","fmin":"0","fmax":"645","strand":"+","sequence":"ATGACTCTGGCATTAGTTTGCGAAAAAATTGACAGAAATCGCTTCACCGGTGAGAAAGTTGAAAATAGTACATTTTTTAACTGCGATTTTTCAGGTGCCGACCTGAGCGGCACTGAATTTATCGGCTGCCAGTTCTATGATCGCGAAAGTCAGAAAGGATGCAATTTTAGTCGCGCAATGCTGAAAGATGCCATTTTCAAAAGCTGTGATTTATCAATGGCAGATTTCCGCAACGTCAGCGCATTGGGCATTGAAATTCGCCACTGCCGCGCACAAGGCGCAGATTTCCGCGGTGCAAGCTTTATGAATATGATCACCACGCGCACCTGGTTTTGCAGCGCATATATCACTAATACCAATCTAAGCTACGCCAATTTTTCGAAAGTCGTGTTGGAAAAGTGTGAACTATGGGAAAACCGCTGGATGGGGACTCAGGTACTGGGTGCGACGTTCAGTGGTTCAGATCTCTCCGGCGGCGAGTTTTCGACTTTCGACTGGCGAGCAGCAAACTTCACACATTGCGATCTGACTAATTCGGAGTTAGGTGACTTAGATATTCGGGGTGTTGATTTACAAGGCGTTAAGTTAGACAACTACCAGGCATCGTTGCTCATGGAGCGGCTTGGCATCGCTGTGATTGGTTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39584","NCBI_taxonomy_name":"Citrobacter braakii","NCBI_taxonomy_id":"57706"}}}},"ARO_accession":"3002779","ARO_id":"39213","ARO_name":"QnrB67","CARD_short_name":"QnrB67","ARO_description":"QnrB67 is a plasmid-mediated quinolone resistance protein found in Citrobacter braakii.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1684":{"model_id":"1684","model_name":"LEN-18","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"8140":{"protein_sequence":{"accession":"CAP12346.2","sequence":"MRYVRLCVISLLATLPLAVDAGPQPLEQIKQSESQLSGRVGMVEMDLASGRTLAAWRADERFPMVSTFKVLLCGAVLARVDAGLEQLDRRIHYRQQDLVDYSPVSEKHLTDGMTVGELCAAAITLSDNSAGNLLLATVGGPAGLTAFLRQIGDNVTRLDRWETALNEALPGDARDTTTPASMAATLRKLLTAQHLSARSQQQLLQWMVDDRVAGPLIRAVLPPGWFIADKTGAGERGARGIVALLGPDGKPERIVVLYLRDTPASMAERNQHIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AM850908.2","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATGTTCGCCTTTGTGTTATCTCCCTGTTAGCCACCCTGCCACTGGCGGTAGACGCCGGTCCACAGCCGCTTGAGCAGATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTGGGGATGGTGGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCGATGAACGCTTTCCCATGGTGAGCACCTTTAAAGTGCTGCTGTGCGGCGCGGTGCTGGCGCGGGTGGATGCCGGGCTCGAACAACTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTACCGACGGGATGACGGTCGGCGAACTCTGCGCCGCCGCCATCACCCTGAGCGATAACAGCGCTGGCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCGGGATTAACTGCCTTTCTGCGCCAGATCGGTGACAACGTCACCCGTCTTGACCGCTGGGAAACGGCACTGAATGAGGCGCTTCCCGGCGACGCGCGCGACACCACCACCCCGGCCAGCATGGCCGCCACGCTGCGCAAACTACTGACCGCGCAGCATCTGAGCGCCCGTTCGCAACAGCAACTCCTGCAGTGGATGGTGGACGATCGGGTTGCCGGCCCGCTGATCCGCGCCGTGCTGCCGCCGGGCTGGTTTATCGCCGACAAAACCGGGGCTGGCGAACGGGGTGCGCGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAACCGGAGCGCATTGTGGTGCTCTATCTGCGGGATACCCCGGCGAGTATGGCCGAGCGTAATCAACATATCGCCGGGATCGGCGCAGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002465","ARO_id":"38865","ARO_name":"LEN-18","CARD_short_name":"LEN-18","ARO_description":"LEN-18 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36236":{"category_aro_accession":"3000097","category_aro_cvterm_id":"36236","category_aro_name":"LEN beta-lactamase","category_aro_description":"LEN beta-lactamases are chromosomal class A beta-lactamases that confer resistance to ampicillin, amoxicillin, carbenicillin, and ticarcillin but not to extended-spectrum beta-lactams.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1685":{"model_id":"1685","model_name":"SHV-40","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1714":{"protein_sequence":{"accession":"AAN04882.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGGRGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AF535128.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGGGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATCGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001098","ARO_id":"37478","ARO_name":"SHV-40","CARD_short_name":"SHV-40","ARO_description":"SHV-40 is an extended-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1686":{"model_id":"1686","model_name":"OXA-34","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1931":{"protein_sequence":{"accession":"AAK15582.1","sequence":"MAIRIFAILFSIFSLATFAHAQEGTLERSDWRKFFSEFQAKGTIVVADERQADRAMLVFDPVRSKKRYSPASTFKIPHTLFALDAGAVRDEFQIFRWDGVNRGFAGHNQDQDLRSAMRNSTVWVYELFAKEIGDDKARRYLKKIDYGNADPSTSNGDYCIEGSLAISAQEQIAFLRKLYRNELPFRVEHQRLVKDLMIVEAGRNWILRAKTGWEGRMGWWVGWVEWPTGSVFFALNIDTPNRMDDLFKREAIVRAIL"},"dna_sequence":{"accession":"AF350424.1","fmin":"0","fmax":"771","strand":"+","sequence":"ATGGCAATCCGAATCTTCGCGATACTTTTCTCCATTTTTTCTCTTGCCACTTTCGCGCATGCGCAAGAAGGCACGCTAGAACGTTCTGACTGGAGGAAGTTTTTCAGCGAATTTCAAGCCAAAGGCACGATAGTTGTGGCAGACGAACGCCAAGCGGATCGTGCCATGTTGGTTTTTGATCCTGTGCGATCGAAGAAACGCTACTCGCCTGCATCGACATTCAAGATACCTCATACACTTTTTGCACTTGATGCAGGCGCTGTTCGTGATGAGTTCCAGATTTTTCGATGGGACGGCGTTAACAGGGGCTTTGCAGGCCACAATCAAGACCAAGATTTGCGATCAGCAATGCGGAATTCTACTGTTTGGGTGTATGAGCTATTTGCAAAGGAAATTGGTGATGACAAAGCTCGGCGCTATTTGAAGAAAATCGACTATGGCAACGCCGATCCTTCGACAAGTAATGGCGATTACTGTATAGAAGGCAGCCTTGCAATCTCGGCGCAGGAGCAAATTGCATTTCTCAGGAAGCTCTATCGTAACGAGCTGCCCTTTCGGGTAGAACATCAGCGCTTGGTCAAGGATCTCATGATTGTGGAAGCCGGTCGCAACTGGATACTGCGTGCAAAGACGGGCTGGGAAGGCCGTATGGGTTGGTGGGTAGGATGGGTTGAGTGGCCGACTGGCTCCGTATTCTTCGCACTGAATATTGATACGCCAAACAGAATGGATGATCTTTTCAAGAGGGAGGCAATCGTGCGGGCAATCCTT","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3001428","ARO_id":"37828","ARO_name":"OXA-34","CARD_short_name":"OXA-34","ARO_description":"OXA-34 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1688":{"model_id":"1688","model_name":"CTX-M-90","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1782":{"protein_sequence":{"accession":"ACQ99521.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAVAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"FJ907381.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGTCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGACTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36945","NCBI_taxonomy_name":"Salmonella sp. YLD3","NCBI_taxonomy_id":"644616"}}}},"ARO_accession":"3001950","ARO_id":"38350","ARO_name":"CTX-M-90","CARD_short_name":"CTX-M-90","ARO_description":"CTX-M-90 is a beta-lactamase found in Proteus mirabilis.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1690":{"model_id":"1690","model_name":"OXA-317","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1686":{"protein_sequence":{"accession":"AGU69255.1","sequence":"MNIKALLLITSAIFISACSPYIVSANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQEEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"KF057034.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGTCTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACTACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACGCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCCTTTAGCCAAAAAGTCCAAGAAGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001688","ARO_id":"38088","ARO_name":"OXA-317","CARD_short_name":"OXA-317","ARO_description":"OXA-317 is a beta-lactamase found in A. baumannii.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1691":{"model_id":"1691","model_name":"CMY-31","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1776":{"protein_sequence":{"accession":"ABR18736.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHVSPGRLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"EF622224.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACGACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002042","ARO_id":"38442","ARO_name":"CMY-31","CARD_short_name":"CMY-31","ARO_description":"CMY-31 is a beta-lactamase found in the Enterobacteriaceae family.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1693":{"model_id":"1693","model_name":"TEM-143","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1568":{"protein_sequence":{"accession":"AAY85632.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDCWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"DQ075245.1","fmin":"217","fmax":"1078","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATTGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001006","ARO_id":"37386","ARO_name":"TEM-143","CARD_short_name":"TEM-143","ARO_description":"TEM-143 is an extended-spectrum beta-lactamase found in E. coli.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1694":{"model_id":"1694","model_name":"OXA-353","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1300":{"protein_sequence":{"accession":"AGW83451.1","sequence":"MYKKTLIVTTSILFLSACSSNMVKQHQIHSMSANKNSEEIKSLFDQAQTTGVLVIKRGKTEEIYGNDLKRASTAYVPASTFKMLNALIGLEHHKATTTEVFKWNGQKRLFPDWKKDMTLGDAMKASAIPVYQELARRIGLDLMSKEVKRIGFGNANIGSKVDDFWLVGPLKITPQQETQFAYQLAHKTLPFSKNVQEQVQSMVFIEKKNGSKIYAKSGWGWDVEPQVGWLTGWVVQPQGEIVAFSLNLEMKKGTSSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"KF297582.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGTATAAAAAAACCCTTATCGTTACAACAAGTATCCTATTTTTATCCGCCTGTTCTTCCAATATGGTAAAACAACATCAAATACACTCTATGTCTGCCAATAAAAATTCAGAAGAAATTAAATCACTGTTTGATCAAGCACAAACCACGGGTGTTTTGGTAATTAAGCGAGGGAAAACAGAAGAAATTTATGGCAATGATCTTAAAAGAGCATCAACCGCCTATGTTCCCGCCTCTACCTTTAAAATGTTAAATGCTTTAATTGGACTTGAACATCATAAGGCAACTACAACTGAAGTATTTAAATGGAATGGGCAAAAACGTTTATTTCCTGATTGGAAAAAGGACATGACACTGGGCGATGCCATGAAAGCTTCTGCAATTCCAGTTTACCAAGAATTAGCCCGACGAATTGGTCTGGATCTTATGTCCAAAGAGGTGAAACGAATTGGTTTCGGTAATGCTAACATTGGCTCAAAAGTAGATGATTTCTGGCTTGTTGGCCCTCTAAAAATTACACCTCAACAAGAAACCCAATTTGCTTATCAATTAGCCCATAAAACGCTTCCATTTAGCAAAAATGTACAAGAGCAAGTTCAATCAATGGTGTTCATAGAGAAAAAAAATGGAAGTAAAATTTATGCCAAAAGTGGTTGGGGATGGGATGTTGAACCACAAGTTGGTTGGCTAACAGGCTGGGTCGTTCAACCACAAGGAGAAATTGTGGCATTCTCACTTAATTTAGAAATGAAAAAAGGAACTTCTAGCTCTATTCGCAAAGAAATTGCTTATAAAGGCTTAGAACAACTGGGTATCTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39094","NCBI_taxonomy_name":"Acinetobacter calcoaceticus","NCBI_taxonomy_id":"471"}}}},"ARO_accession":"3001540","ARO_id":"37940","ARO_name":"OXA-353","CARD_short_name":"OXA-353","ARO_description":"OXA-353 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46495":{"category_aro_accession":"3007706","category_aro_cvterm_id":"46495","category_aro_name":"OXA-213-like beta-lactamase","category_aro_description":"OXA-213-like enzymes have been identified to be intrinsic to A. calcoaceticus and have been subsequently detected in A. pittii. Phylogenetic analysis of OXA-213-like proteins identified two distinct subgroups within the OXA family. The first group was linked to A. pittii and the second group to A. calcoaceticus. The carbapenemase activity of these OXAs may be related to the species-dependent effect.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1695":{"model_id":"1695","model_name":"DHA-5","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1707":{"protein_sequence":{"accession":"AEL22919.1","sequence":"MKKSLSATLISALLAFSAPGFSAADNVAAVVDSTIKPLMAQQDIPGMAVAVSVKGRPYYFNYGFADVQAKQPVTENTLFELGSVSKTFTGVLGAVSVAKKEMALNDPAAKYQPELALPQWKGITLLDLATYTAGGLPLQVPDAVKSRADLLHFYQQWQPSRKPGDMRLYANSSIGLFGALTANAAGMPYEQLLTARILAPLGLSHTFITVPESAQSQYAYGYKNKKPVRVSPGQLDAESYGVKSASKDMLRWAEMNMEPSRAGNADLEMAMYLAQTRYYKTAAINQGLGWEMYDWPQQKDMIINGVTNEVALQPHPVTDNQVQPYNRASWVHKTGATTGFGAYVAFIPEKQVAIVILANKNYPNTERVKAAQAILSALE"},"dna_sequence":{"accession":"JF273491.1","fmin":"745","fmax":"1885","strand":"+","sequence":"ATGAAAAAATCGTTATCTGCAACACTGATTTCCGCTCTGCTGGCGTTTTCCGCCCCGGGGTTTTCTGCCGCTGATAATGTCGCGGCGGTGGTGGACAGCACCATTAAACCGCTGATGGCACAGCAGGACATTCCCGGGATGGCGGTTGCCGTCTCTGTAAAGGGCAGGCCCTATTATTTCAATTACGGTTTTGCCGATGTTCAGGCAAAACAGCCGGTCACTGAAAATACACTATTTGAGCTCGGATCTGTAAGTAAAACTTTCACAGGTGTGCTGGGTGCGGTTTCTGTGGCGAAAAAAGAGATGGCGCTGAATGATCCGGCGGCAAAATACCAGCCGGAGCTGGCTCTGCCGCAGTGGAAGGGGATCACATTGCTGGATCTGGCTACCTATACCGCAGGCGGACTGCCGTTACAGGTGCCGGATGCGGTAAAAAGCCGTGCGGATCTGCTGCACTTCTATCAGCAGTGGCAGCCGTCCCGGAAACCGGGCGATATGCGTCTGTATGCAAACAGCAGCATCGGCCTGTTTGGTGCTCTGACCGCAAACGCGGCGGGGATGCCGTATGAGCAGTTGCTGACTGCACGGATCCTGGCACCGCTGGGGTTATCTCACACCTTTATTACTGTGCCGGAAAGTGCGCAAAGCCAGTATGCGTACGGTTATAAAAACAAAAAACCGGTCCGCGTGTCGCCGGGACAGCTTGATGCGGAATCTTACGGCGTGAAATCCGCCTCAAAAGATATGCTGCGCTGGGCGGAAATGAATATGGAGCCGTCACGGGCCGGTAATGCGGATCTGGAAATGGCAATGTATCTCGCCCAGACCCGTTACTATAAAACCGCCGCGATTAATCAGGGGCTGGGCTGGGAAATGTATGACTGGCCGCAGCAGAAAGATATGATCATTAACGGCGTGACCAACGAGGTCGCATTGCAGCCGCACCCGGTAACAGACAACCAGGTTCAGCCGTATAACCGTGCTTCCTGGGTGCATAAAACGGGGGCAACAACTGGTTTCGGCGCCTATGTGGCCTTTATTCCGGAAAAACAGGTGGCGATTGTGATTCTGGCGAATAAAAACTACCCGAATACCGAAAGAGTCAAAGCTGCACAGGCTATTTTGAGTGCACTGGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36917","NCBI_taxonomy_name":"Morganella morganii","NCBI_taxonomy_id":"582"}}}},"ARO_accession":"3002138","ARO_id":"38538","ARO_name":"DHA-5","CARD_short_name":"DHA-5","ARO_description":"DHA-5 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36207":{"category_aro_accession":"3000068","category_aro_cvterm_id":"36207","category_aro_name":"DHA beta-lactamase","category_aro_description":"DHA beta-lactamases are plasmid-mediated AmpC \u03b2-lactamases that confer resistance to cephamycins and oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1697":{"model_id":"1697","model_name":"TEM-135","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4683":{"protein_sequence":{"accession":"CAG25427.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTTPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AJ634602.1","fmin":"7839","fmax":"8700","strand":"-","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGACGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35732","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Typhimurium","NCBI_taxonomy_id":"90371"}}}},"ARO_accession":"3000999","ARO_id":"37379","ARO_name":"TEM-135","CARD_short_name":"TEM-135","ARO_description":"TEM-135 is a broad-spectrum beta-lactamase found in Salmonella enterica.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1698":{"model_id":"1698","model_name":"OCH-6","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1811":{"protein_sequence":{"accession":"CAC17626.1","sequence":"MRKSTTLLIGFLTTAAIIPNNGALAASKANDGDLRRIVDETVRPLMAEQKIPGMAVAITIDGKSHFFGYGVASKESGQKVTEDTIFEIGSVSKTFTAMLGGYGLATGAFSLSDPATKWAPELAGSSFDKITMRDLGTYTPGGLPLQFPDAVTDDSSMLAYFKKWKPDYPAGTQRRYSNPSIGLFGYLAARSMDKPFDVLMEQKLLPAFGLKNTFINVPESQMKNYAYGYSKANKPIRVSGGALDAQAYGIKTTALDLARFVELNIDSSSLEPDFQKAVAATHTGYYHVGANNQGLGWEFYNYPTALKTLLAGNSSDMALKSHKIEKFDTPRQPSADVWLNKTGSTNGFGAYAAFIPAKKTGIVLLANRNYPIDERVKAAYRILQALDNKQ"},"dna_sequence":{"accession":"AJ295344.1","fmin":"0","fmax":"1173","strand":"+","sequence":"ATGAGAAAATCTACGACACTTTTGATCGGTTTCCTCACCACTGCCGCTATTATCCCGAATAATGGCGCGCTGGCTGCGAGCAAGGCGAATGATGGCGACTTGCGCCGTATTGTCGATGAAACGGTGCGCCCGCTCATGGCCGAGCAGAAAATCCCCGGCATGGCCGTCGCTATAACCATCGACGGCAAGAGCCACTTCTTCGGTTATGGTGTGGCATCGAAAGAAAGCGGGCAAAAAGTCACTGAAGACACGATTTTCGAGATCGGTTCGGTCAGCAAGACCTTCACTGCAATGCTTGGCGGTTACGGGCTGGCGACAGGCGCGTTCTCCCTGTCCGATCCCGCGACCAAATGGGCTCCTGAACTGGCAGGCAGCAGCTTCGACAAGATCACCATGCGTGATCTTGGGACCTACACGCCGGGCGGATTGCCCCTCCAGTTTCCCGATGCTGTCACCGATGACAGTTCGATGCTGGCATATTTCAAGAAATGGAAGCCGGACTATCCGGCAGGCACGCAGCGTCGCTATTCGAATCCCAGCATCGGCCTGTTCGGCTATCTGGCGGCACGAAGCATGGACAAGCCGTTCGACGTTTTGATGGAGCAAAAGCTTCTGCCTGCATTCGGCCTGAAGAACACCTTCATCAATGTGCCGGAAAGCCAGATGAAGAACTACGCCTACGGCTATTCCAAAGCCAACAAGCCGATCCGGGTATCGGGCGGGGCGCTGGATGCACAAGCCTATGGCATCAAGACCACCGCGCTTGATCTTGCCCGCTTCGTCGAACTGAACATCGACAGCTCATCTCTGGAGCCTGATTTCCAGAAAGCCGTCGCCGCAACGCATACCGGTTACTACCATGTCGGAGCGAACAATCAGGGACTTGGCTGGGAGTTCTACAACTATCCGACTGCGCTCAAGACACTTCTTGCCGGCAATTCGTCGGACATGGCGCTGAAGTCGCACAAAATCGAGAAATTCGATACACCTCGCCAACCGTCAGCTGATGTGTGGCTCAACAAGACAGGCTCAACCAACGGCTTTGGCGCTTATGCGGCCTTTATTCCTGCGAAGAAGACCGGAATTGTTCTGCTTGCCAATCGGAATTATCCGATCGATGAGCGCGTAAAGGCTGCCTATCGGATATTGCAGGCGCTCGACAACAAGCAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37077","NCBI_taxonomy_name":"Brucella anthropi","NCBI_taxonomy_id":"529"}}}},"ARO_accession":"3002519","ARO_id":"38919","ARO_name":"OCH-6","CARD_short_name":"OCH-6","ARO_description":"OCH-6 beta-lactamase is an Ambler class C chromosomal-encoded beta-lactamases in Brucella anthropi.","ARO_category":{"36233":{"category_aro_accession":"3000094","category_aro_cvterm_id":"36233","category_aro_name":"OCH beta-lactamase","category_aro_description":"OCH beta-lactamases are Ambler class C chromosomal-encoded beta-lactamases in Brucella anthropi.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1700":{"model_id":"1700","model_name":"ACT-28","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1018":{"protein_sequence":{"accession":"AHL39333.1","sequence":"MKTKSLCCALLLSTSCSVLAAPMSEKQLSDVVERTVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQHWQPQWKPGATRLYANASIGLFGALAVKPSGMSFEQAMTKRVFKPLKLDHTWINVPKEEEAHYAWGYRDGKAIHVSPGMLDAEAYGVKTNIQDMASWLKANMNPDALPDSTLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVEAKTVVEGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKELGIVMLANKSYPNPARVEAAYRILSALQ"},"dna_sequence":{"accession":"KJ207206.1","fmin":"751","fmax":"1897","strand":"+","sequence":"ATGAAGACAAAATCCCTTTGCTGTGCCCTGCTGCTCAGCACCTCCTGCTCTGTTCTCGCCGCGCCGATGTCAGAGAAACAGCTGTCTGACGTGGTGGAACGTACCGTTACCCCCCTGATGAAAGCGCAAGCCATTCCGGGCATGGCGGTAGCGGTGATTTATCAGGGTCAGCCGCACTACTTTACCTTCGGAAAGGCCGATGTTGCGGCGAACAAACCTGTCACCCCGCAAACCCTGTTTGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTATTAGGTGGCGATGCGATTGCGCGCGGAGAAATATCGCTGGGCGACCCCGTGACAAAGTACTGGCCCGAGCTAACAGGCAAGCAGTGGCAGGGTATTCGCATGTTGGATCTGGCGACCTACACCGCGGGTGGCCTGCCGCTACAGGTGCCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGTTTCTATCAACACTGGCAACCGCAGTGGAAACCAGGCGCAACGCGTCTTTATGCGAACGCCAGCATCGGGCTTTTTGGCGCCCTCGCGGTTAAACCCTCCGGCATGAGCTTTGAACAGGCCATGACGAAGCGGGTCTTCAAGCCACTCAAACTGGACCATACATGGATTAACGTTCCGAAAGAAGAAGAGGCGCATTACGCCTGGGGATACCGTGATGGTAAAGCAATCCACGTTTCACCGGGAATGCTGGATGCCGAAGCGTATGGTGTCAAAACCAACATCCAGGATATGGCGAGCTGGCTGAAGGCCAACATGAACCCTGACGCCCTTCCGGATTCAACGTTGAAACAGGGTATTGCCCTGGCACAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCGGTAGAAGCCAAAACCGTCGTGGAGGGCAGCGATAACAAGGTGGCTCTTGCACCGTTACCGGTGGCAGAAGTGAACCCTCCAGCTCCGCCAGTAAAAGCATCATGGGTACATAAAACAGGCTCGACGGGTGGATTCGGCAGCTATGTCGCATTTATTCCTGAAAAGGAACTCGGCATTGTTATGCTGGCGAACAAGAGCTACCCGAACCCGGCGCGCGTGGAAGCGGCATACCGTATTCTGAGCGCTCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3001848","ARO_id":"38248","ARO_name":"ACT-28","CARD_short_name":"ACT-28","ARO_description":"ACT-28 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1701":{"model_id":"1701","model_name":"Erm(39)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"274":{"protein_sequence":{"accession":"AAR92235.1","sequence":"MSSVHHGRHENGQNFLRDRRVVGDIVRMVSHTAGPIVEIGAGDGALTLPLQRLGRPLTAIEIDLHRARRLADRTTAEVIATDFLRYRLPRTPHVVVGNLPFHLTTAILRRLLHENGWTDAILLVQWEVARRRAGVGGATMMTAQWWPWFEFGLARKVSADAFRPRPSVDAGLLTIQRRAEPLLPWADRRAYQALVHRVFTGRGRGLAQILRPHVHPRWLSANGIHPSALPRALTARQWVALFDAAG"},"dna_sequence":{"accession":"AY487229.1","fmin":"2152","fmax":"2893","strand":"+","sequence":"GTGTCTTCAGTTCATCACGGCCGGCATGAGAACGGCCAGAATTTTCTGCGCGACCGTCGAGTGGTCGGCGACATCGTGAGGATGGTCTCGCACACAGCGGGTCCCATCGTCGAGATCGGGGCCGGAGACGGCGCCCTCACCCTGCCGTTACAGCGGCTGGGCCGACCGTTGACCGCCATCGAGATCGACCTCCACCGTGCCCGACGGCTCGCCGACCGAACCACTGCCGAGGTGATCGCAACCGACTTCCTGCGGTACCGGCTGCCGCGCACGCCGCACGTGGTGGTGGGCAACCTGCCGTTCCATCTGACCACCGCCATCCTCCGGCGCCTACTGCACGAGAACGGCTGGACCGATGCGATCCTGTTGGTGCAGTGGGAGGTGGCTCGACGGCGGGCCGGTGTCGGCGGCGCCACCATGATGACCGCCCAGTGGTGGCCGTGGTTCGAATTCGGCCTGGCGCGAAAGGTTTCGGCCGACGCGTTCCGGCCGCGGCCGAGTGTGGATGCCGGGCTGCTGACCATTCAGCGCCGAGCTGAGCCGCTACTCCCGTGGGCCGACCGTCGTGCGTATCAGGCGCTGGTCCACAGGGTTTTCACCGGGCGCGGGCGTGGTCTGGCCCAGATTCTGCGGCCCCACGTGCACCCACGGTGGCTGTCTGCCAACGGAATTCACCCGTCGGCTCTGCCCAGAGCGCTGACGGCTCGACAGTGGGTGGCGTTGTTCGATGCCGCCGGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36886","NCBI_taxonomy_name":"Mycolicibacterium fortuitum","NCBI_taxonomy_id":"1766"}}}},"ARO_accession":"3000602","ARO_id":"36741","ARO_name":"Erm(39)","CARD_short_name":"Erm(39)","ARO_description":"ErmD confers MLSb phenotype.","ARO_category":{"36699":{"category_aro_accession":"3000560","category_aro_cvterm_id":"36699","category_aro_name":"Erm 23S ribosomal RNA methyltransferase","category_aro_description":"Erm proteins are part of the RNA methyltransferase family and methylate A2058 (E. coli nomenclature) of the 23S ribosomal RNA conferring degrees of resistance to Macrolides, Lincosamides and Streptogramin b. This is called the MLSb phenotype.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35946":{"category_aro_accession":"0000027","category_aro_cvterm_id":"35946","category_aro_name":"roxithromycin","category_aro_description":"Roxithromycin is a semi-synthetic, 14-carbon ring macrolide antibiotic derived from erythromycin. It is used to treat respiratory tract, urinary and soft tissue infections. Roxithromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35974":{"category_aro_accession":"0000057","category_aro_cvterm_id":"35974","category_aro_name":"telithromycin","category_aro_description":"Telithromycin is a semi-synthetic derivative of erythromycin. It is a 14-membered macrolide and is the first ketolide antibiotic to be used in clinics. Telithromycin binds the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"35982":{"category_aro_accession":"0000065","category_aro_cvterm_id":"35982","category_aro_name":"clarithromycin","category_aro_description":"Clarithromycin is a methyl derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome and is used to treat pharyngitis, tonsillitis, acute maxillary sinusitis, acute bacterial exacerbation of chronic bronchitis, pneumonia (especially atypical pneumonias associated with Chlamydia pneumoniae or TWAR), and skin structure infections.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"36284":{"category_aro_accession":"3000145","category_aro_cvterm_id":"36284","category_aro_name":"tylosin","category_aro_description":"Tylosin is a 16-membered macrolide, naturally produced by Streptomyces fradiae. It interacts with the bacterial ribosome 50S subunit to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"36295":{"category_aro_accession":"3000156","category_aro_cvterm_id":"36295","category_aro_name":"spiramycin","category_aro_description":"Spiramycin is a 16-membered macrolide and is natural product produced by Streptomyces ambofaciens. It binds to the 50S subunit of bacterial ribosomes and inhibits peptidyl transfer activity to disrupt protein synthesis.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"36315":{"category_aro_accession":"3000176","category_aro_cvterm_id":"36315","category_aro_name":"dirithromycin","category_aro_description":"Dirithromycin is an oxazine derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome to inhibit bacterial protein synthesis.","category_aro_class_name":"Antibiotic"},"36722":{"category_aro_accession":"3000583","category_aro_cvterm_id":"36722","category_aro_name":"pristinamycin IA","category_aro_description":"Pristinamycin IA is a type B streptogramin antibiotic produced by Streptomyces pristinaespiralis. It binds to the P site of the 50S subunit of the bacterial ribosome, preventing the extension of protein chains.","category_aro_class_name":"Antibiotic"},"36723":{"category_aro_accession":"3000584","category_aro_cvterm_id":"36723","category_aro_name":"quinupristin","category_aro_description":"Quinupristin is a type B streptogramin and a semisynthetic derivative of pristinamycin 1A. It is a component of the drug Synercid and interacts with the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"virginiamycin M1","category_aro_description":"Virginiamycin M1 is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37016":{"category_aro_accession":"3000672","category_aro_cvterm_id":"37016","category_aro_name":"madumycin II","category_aro_description":"Madumycin II is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37017":{"category_aro_accession":"3000673","category_aro_cvterm_id":"37017","category_aro_name":"griseoviridin","category_aro_description":"Griseoviridin is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"37019":{"category_aro_accession":"3000675","category_aro_cvterm_id":"37019","category_aro_name":"pristinamycin IB","category_aro_description":"Pristinamycin IB is a class B streptogramin similar to pristinamycin IA, the former containing a N-methyl-4-(methylamino)phenylalanine instead of a N-methyl-4-(dimethylamino)phenylalanine in its class A streptogramin counterpart (one less methyl group).","category_aro_class_name":"Antibiotic"},"37021":{"category_aro_accession":"3000677","category_aro_cvterm_id":"37021","category_aro_name":"virginiamycin S2","category_aro_description":"Virginiamycin S2 is a streptogramin B antibiotic.","category_aro_class_name":"Antibiotic"},"37022":{"category_aro_accession":"3000678","category_aro_cvterm_id":"37022","category_aro_name":"pristinamycin IC","category_aro_description":"Pristinamycin IC is a class B streptogramin derived from virginiamycin S1.","category_aro_class_name":"Antibiotic"},"37023":{"category_aro_accession":"3000679","category_aro_cvterm_id":"37023","category_aro_name":"vernamycin C","category_aro_description":"Vernamycin C is a streptogramin B antibiotic.","category_aro_class_name":"Antibiotic"},"37024":{"category_aro_accession":"3000680","category_aro_cvterm_id":"37024","category_aro_name":"patricin A","category_aro_description":"Patricin A is a streptogramin B antibiotic.","category_aro_class_name":"Antibiotic"},"37025":{"category_aro_accession":"3000681","category_aro_cvterm_id":"37025","category_aro_name":"patricin B","category_aro_description":"Patricin B is a streptogramin B antibiotic.","category_aro_class_name":"Antibiotic"},"37026":{"category_aro_accession":"3000682","category_aro_cvterm_id":"37026","category_aro_name":"ostreogrycin B3","category_aro_description":"Ostreogrycin B3 is a derivative of pristinamycin IA, with an additional 3-hydroxy group on its 4-oxopipecolic acid.","category_aro_class_name":"Antibiotic"},"37247":{"category_aro_accession":"3000867","category_aro_cvterm_id":"37247","category_aro_name":"oleandomycin","category_aro_description":"Oleandomycin is a 14-membered macrolide produced by Streptomyces antibioticus. It is ssimilar to erythromycin, and contains a desosamine amino sugar and an oleandrose sugar. It targets the 50S ribosomal subunit to prevent protein synthesis.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35952":{"category_aro_accession":"0000034","category_aro_cvterm_id":"35952","category_aro_name":"streptogramin A antibiotic","category_aro_description":"Streptogramin A antibiotics are cyclic polyketide peptide hybrids that bind to the ribosomal peptidyl transfer centre. Structural variation arises from substituting a proline for its desaturated derivative and by its substitution for Ala or Cys. Used alone, streptogramin A antibiotics are bacteriostatic, but is bactericidal when used with streptogramin B antibiotics.","category_aro_class_name":"Drug Class"},"35967":{"category_aro_accession":"0000050","category_aro_cvterm_id":"35967","category_aro_name":"streptogramin B antibiotic","category_aro_description":"Streptogramin B antibiotics are are cyclic hepta- or hexa-depsipeptides.  Type B streptogramins block the peptide exit tunnel of the 50S bacterial ribosome. The general composition of group B streptogramins is 3-hydroxypicolinic acid-L-Thr-D-aminobutyric acid (or D-Ala)-L-Pro-L-Phe (or 4-N-,N-(dimethylamino)-L-Phe)-X-L-phenylglycine. Used alone, streptogramin B antibiotics are bacteriostatic, but is bactericidal when used with streptogramin A antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1702":{"model_id":"1702","model_name":"MIR-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"8186":{"protein_sequence":{"accession":"AAD22636.1","sequence":"MMTKSLSCALLLSVASSAFAAPMSEKQLAEVVERTVTPLMNAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEIALGDPVAKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDTASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMSYEQAMTTRVFKPLKLDHTWINVPKAEEAHFAWGYREGKAVHVSPGMLDAEAYGVKTNVKDMASWLIANMKPDSLQAPSLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVGGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILDALQ"},"dna_sequence":{"accession":"M37839.2","fmin":"927","fmax":"2073","strand":"+","sequence":"ATGATGACAAAATCCCTAAGCTGTGCCCTGCTGCTCAGCGTCGCCAGTTCTGCATTCGCCGCACCGATGTCCGAAAAACAGCTGGCTGAGGTGGTGGAACGTACCGTTACGCCGCTGATGAACGCGCAGGCCATTCCGGGTATGGCGGTGGCGGTAATTTATCAGGGTCAGCCACACTACTTTACCTTCGGTAAAGCCGATGTTGCGGCGAACAAACCCGTCACCCCGCAAACCCTGTTTGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTACTGGGCGGCGATGCCATTGCCCGGGGTGAAATAGCGCTGGGCGATCCGGTAGCAAAATACTGGCCTGAGCTCACGGGCAAGCAGTGGCAGGGCATTCGCATGCTGGATCTGGCAACCTATACCGCAGGCGGTCTGCCGTTACAGGTGCCGGATGAGGTCACGGATACCGCCTCTCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCGGGCACCACGCGTCTTTACGCTAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTTAAACCTTCCGGCATGAGCTATGAGCAGGCCATGACGACGCGGGTCTTTAAACCCCTCAAGCTGGACCATACCTGGATTAACGTCCCGAAAGCGGAAGAGGCGCATTTCGCCTGGGGATACCGTGAGGGTAAAGCGGTCCACGTTTCGCCAGGGATGCTGGACGCGGAAGCCTATGGCGTAAAAACTAACGTGAAGGATATGGCGAGCTGGCTGATAGCCAACATGAAGCCGGATTCTCTTCAGGCTCCCTCACTCAAGCAAGGCATTGCTCTGGCGCAGTCTCGCTACTGGCGCGTGGGGGCTATGTATCAGGGGTTAGGCTGGGAGATGCTCAACTGGCCGGTCGATGCCAAAACCGTCGTCGGAGGCAGTGATAACAAGGTGGCGCTGGCACCATTGCCCGTGGCAGAAGTGAATCCACCCGCGCCGCCGGTCAAGGCCTCCTGGGTCCATAAAACAGGCTCGACGGGCGGGTTTGGCAGCTACGTGGCATTTATTCCTGAAAAGCAGCTCGGCATTGTGATGCTGGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCGTATCCTCGACGCGCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002166","ARO_id":"38566","ARO_name":"MIR-1","CARD_short_name":"MIR-1","ARO_description":"MIR-1 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36197":{"category_aro_accession":"3000058","category_aro_cvterm_id":"36197","category_aro_name":"MIR beta-lactamase","category_aro_description":"MIR beta-lactamases are plasmid-mediated beta-lactamases that confer resistance to oxyimino- and alpha-methoxy beta-lactams.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1703":{"model_id":"1703","model_name":"FosK","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"200"}},"model_sequences":{"sequence":{"8153":{"protein_sequence":{"accession":"BAO79518.1","sequence":"MITGINHITFSVRDLSSSIEFYRDLLGMRLHVTWEAGAYFTAGDTWVCLSVGEPKPANDYTHVAFSVGERELVELHARLKEAGVEEWKQNTSEGNSVYLLDPNGHRIELHCGTLATRLAELEKSPYKRLVWC"},"dna_sequence":{"accession":"AB917040.2","fmin":"736","fmax":"1135","strand":"+","sequence":"ATGATCACTGGTATCAATCACATCACCTTTTCCGTCAGGGACTTGAGCTCTTCAATCGAGTTCTATCGTGACTTGCTGGGAATGAGGCTGCACGTGACCTGGGAAGCAGGTGCTTATTTTACAGCGGGTGATACGTGGGTATGTCTGAGCGTCGGGGAACCTAAACCCGCCAACGACTACACGCATGTGGCATTCAGTGTTGGCGAAAGAGAGCTTGTTGAGCTGCACGCTAGGCTAAAAGAAGCCGGGGTTGAGGAGTGGAAGCAGAATACAAGTGAGGGTAACTCCGTGTATCTGCTTGATCCAAACGGCCATCGCATTGAGCTTCACTGCGGAACGTTGGCAACCCGCTTAGCTGAGTTGGAGAAGTCGCCCTATAAAAGGTTGGTCTGGTGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39070","NCBI_taxonomy_name":"Acinetobacter soli","NCBI_taxonomy_id":"487316"}}}},"ARO_accession":"3003207","ARO_id":"39791","ARO_name":"FosK","CARD_short_name":"FosK","ARO_description":"FosK is a fosfomycin thiol transferase isolated from Acinetobacter soli. It is integrin-mediated. It confers a high level of resistance to fosfomycin.","ARO_category":{"36272":{"category_aro_accession":"3000133","category_aro_cvterm_id":"36272","category_aro_name":"fosfomycin thiol transferase","category_aro_description":"Catalyzes the addition of a thiol group from a nucleophilic molecule to fosfomycin.","category_aro_class_name":"AMR Gene Family"},"35944":{"category_aro_accession":"0000025","category_aro_cvterm_id":"35944","category_aro_name":"fosfomycin","category_aro_description":"Fosfomycin (also known as phosphomycin and phosphonomycin) is a broad-spectrum antibiotic produced by certain Streptomyces species. It is effective on gram positive and negative bacteria as it targets the cell wall, an essential feature shared by both bacteria. Its specific target is MurA (MurZ in E.coli), which attaches phosphoenolpyruvate (PEP) to UDP-N-acetylglucosamine, a step of commitment to cell wall synthesis. In the active site of MurA, the active cysteine molecule is alkylated which stops the catalytic reaction.","category_aro_class_name":"Antibiotic"},"45731":{"category_aro_accession":"3007149","category_aro_cvterm_id":"45731","category_aro_name":"phosphonic acid antibiotic","category_aro_description":"A group of antibiotics derived from phosphonic acids.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1704":{"model_id":"1704","model_name":"CMY-57","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1283":{"protein_sequence":{"accession":"ADP37961.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHVSPGQFDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"HQ285243.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAATTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002068","ARO_id":"38468","ARO_name":"CMY-57","CARD_short_name":"CMY-57","ARO_description":"CMY-57 is a beta-lactamase found in the Enterobacteriaceae family.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1705":{"model_id":"1705","model_name":"SHV-111","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1230":{"protein_sequence":{"accession":"BAF95849.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALSGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AB372881.1","fmin":"8","fmax":"869","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTTCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGGATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001160","ARO_id":"37540","ARO_name":"SHV-111","CARD_short_name":"SHV-111","ARO_description":"SHV-111 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1706":{"model_id":"1706","model_name":"OXA-142","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1204":{"protein_sequence":{"accession":"ABY79006.1","sequence":"MKTFAAYVIIACLSSTALAGSITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFKIPSAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEDQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGIIGG"},"dna_sequence":{"accession":"EU358785.1","fmin":"720","fmax":"1521","strand":"+","sequence":"ATGAAAACATTTGCCGCATATGTAATTATCGCGTGTCTTTCGAGTACGGCATTAGCTGGTTCAATTACAGAAAATACGTCTTGGAACAAAGAGTTCTCTGCCGAAGCCGTCAATGGTGTCTTCGTGCTTTGTAAAAGTAGCAGTAAATCCTGCGCTACCAATGACTTAGCTCGTGCATCAAAGGAATATCTTCCAGCATCAACATTTAAGATCCCCAGCGCAATTATCGGCCTAGAAACTGGTGTCATAAAGAATGAGCATCAGGTTTTCAAATGGGACGGAAAGCCAAGAGCCATGAAGCAATGGGAAAGAGACTTGACCTTAAGAGGGGCAATACAAGTTTCAGCTGTTCCCGTATTTCAACAAATCGCCAGAGAAGTTGGCGAAGTAAGAATGCAGAAATACCTTAAAAAATTTTCCTATGGCAACCAGAATATCAGTGGTGGCATTGACAAATTCTGGTTGGAAGACCAGCTTAGAATTTCCGCAGTTAATCAAGTGGAGTTTCTAGAGTCTCTATATTTAAATAAATTGTCAGCATCTAAAGAAAACCAGCTAATAGTAAAAGAGGCTTTGGTAACGGAGGCGGCACCTGAATATCTAGTGCATTCAAAAACTGGTTTTTCTGGTGTGGGAACTGAGTCAAATCCTGGTGTCGCATGGTGGGTTGGGTGGGTTGAGAAGGAGACAGAGGTTTACTTTTTCGCCTTTAACATGGATATAGACAACGAAAGTAAGTTGCCGCTAAGAAAATCCATTCCCACCAAAATCATGGAAAGTGAGGGCATCATTGGTGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3001803","ARO_id":"38203","ARO_name":"OXA-142","CARD_short_name":"OXA-142","ARO_description":"OXA-142 is a beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46486":{"category_aro_accession":"3007697","category_aro_cvterm_id":"46486","category_aro_name":"OXA-10-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-10.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1707":{"model_id":"1707","model_name":"QnrB4","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"8184":{"protein_sequence":{"accession":"ABC17630.3","sequence":"MTLALVGEKIDRNRFTGEKVENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRANLKDAIFKSCDLSMADFRNINALGIEIRHCRAQGSDFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGTQVLGATFSGSDLSGGEFSSFDWRAANVTHCDLTNSELGDLDIRGVDLQGVKLDSYQASLLLERLGIAVMG"},"dna_sequence":{"accession":"DQ303921.2","fmin":"3","fmax":"648","strand":"+","sequence":"ATGACTCTGGCGTTAGTTGGCGAAAAAATTGACAGAAACAGGTTCACCGGTGAAAAAGTTGAAAATAGCACATTTTTCAACTGTGATTTTTCGGGTGCCGACCTTAGCGGCACTGAATTTATTGGCTGCCAGTTTTATGATCGAGAAAGTCAGAAAGGATGTAATTTTAGTCGCGCTAACCTGAAAGATGCCATTTTCAAAAGTTGTGATCTCTCCATGGCTGATTTCAGGAATATCAATGCGCTGGGAATCGAAATTCGCCACTGCCGGGCACAAGGGTCAGATTTTCGCGGCGCAAGTTTTATGAATATGATCACCACCCGCACCTGGTTTTGTAGCGCCTATATCACCAATACCAACTTAAGCTACGCCAACTTTTCAAAAGTCGTACTGGAAAAGTGCGAGCTGTGGGAAAACCGCTGGATGGGTACTCAGGTGCTGGGCGCAACGTTCAGTGGATCAGACCTCTCTGGCGGCGAGTTTTCATCCTTCGACTGGCGAGCAGCAAACGTTACGCACTGTGATTTGACCAATTCGGAACTGGGCGATTTAGATATCCGCGGGGTTGATTTGCAAGGCGTCAAACTGGACAGCTACCAGGCATCGTTGCTCCTGGAACGTCTTGGTATCGCTGTCATGGGTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002718","ARO_id":"39152","ARO_name":"QnrB4","CARD_short_name":"QnrB4","ARO_description":"QnrB4 is a plasmid-mediated quinolone resistance protein found in Escherichia coli.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1709":{"model_id":"1709","model_name":"TEM-115","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1952":{"protein_sequence":{"accession":"AAN04881.1","sequence":"MSIQHFRVALIPFFAAFCFPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDHWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AF535127.1","fmin":"208","fmax":"1069","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCTTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATCATTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3000978","ARO_id":"37358","ARO_name":"TEM-115","CARD_short_name":"TEM-115","ARO_description":"TEM-115 is an extended-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1711":{"model_id":"1711","model_name":"AQU-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"725"}},"model_sequences":{"sequence":{"1113":{"protein_sequence":{"accession":"BAM76830.1","sequence":"MKQTSPLSSLALSALLLSPLTQAAPADPLVGVVDEVIRPLVKEHRIPGMAVAVFKEGQPHYFNYGVAELATGKKVSEQTLFEIGSVSKTYTATLGAYAVVKGSIGLDDKVSRHAPWLKGSAFDGITMAELATYSAGGLPLQFPDEVESLEQMQAYYRQWTPAYQPGSHRQYSNPSIGLFGYLAASSLQQPFAQLMEQTLLPGLGLHHTYINVPKQAMANYAYGYSKEDKPIRVTPGVLADEAYGIKTSSADLLAFVKANINGVDDKGLQQAIALTHQGRYSVGEMTQGLGWESYPYPVSEQTLLAGNSVQVIMKANPTTAAPKEMGSQRLFNKTGSTNGFGAYVAFVPAKGVGIVMLANRNYPIQERVKAAHSILSKLAP"},"dna_sequence":{"accession":"AB765395.1","fmin":"0","fmax":"1143","strand":"+","sequence":"ATGAAGCAAACCTCACCCTTGTCGTCGCTGGCGCTGAGCGCCCTGCTGCTGTCGCCCCTCACCCAGGCCGCTCCCGCCGATCCGCTGGTCGGGGTAGTGGATGAGGTCATTCGTCCGCTGGTGAAAGAGCACAGGATCCCGGGCATGGCGGTAGCCGTGTTCAAAGAGGGGCAACCCCACTACTTCAACTACGGGGTTGCCGAGCTGGCGACGGGGAAGAAGGTCAGCGAGCAGACCCTGTTCGAGATTGGCTCGGTCAGCAAAACCTATACCGCCACCCTGGGGGCCTACGCCGTGGTCAAGGGGAGCATTGGGCTGGATGACAAGGTGAGCCGGCACGCTCCCTGGCTCAAGGGCTCCGCCTTTGATGGCATCACCATGGCCGAGCTTGCCACTTACAGTGCCGGGGGTCTGCCGCTGCAATTCCCCGACGAGGTGGAATCGCTCGAGCAGATGCAGGCTTACTATCGCCAGTGGACGCCGGCCTATCAACCAGGCAGCCATCGCCAGTACTCCAACCCCAGTATCGGCCTGTTCGGCTATCTGGCGGCGAGCAGTCTGCAGCAGCCGTTTGCCCAGTTGATGGAGCAGACCCTGCTGCCCGGGCTCGGCCTGCATCACACCTATATCAATGTGCCGAAGCAGGCGATGGCGAACTACGCCTATGGCTATTCGAAAGAGGACAAGCCCATCAGGGTCACGCCAGGGGTGCTGGCGGACGAGGCCTACGGCATCAAGACCAGCTCGGCGGATCTGCTCGCCTTCGTGAAGGCCAACATCAACGGGGTGGATGACAAGGGATTGCAGCAGGCCATCGCTTTGACCCACCAGGGGCGCTACTCGGTAGGCGAGATGACCCAGGGGCTGGGCTGGGAGAGTTACCCCTATCCGGTCAGCGAGCAGACGCTGCTGGCGGGCAACTCGGTCCAGGTGATCATGAAGGCCAATCCGACGACGGCCGCGCCGAAGGAGATGGGGAGCCAGCGGCTCTTCAACAAGACCGGCTCGACCAACGGCTTTGGCGCCTATGTGGCCTTCGTGCCGGCCAAGGGAGTGGGCATCGTCATGCTGGCCAACCGCAACTACCCCATCCAGGAGAGGGTAAAGGCGGCCCACTCCATCCTGAGCAAGCTGGCTCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39651","NCBI_taxonomy_name":"Aeromonas dhakensis","NCBI_taxonomy_id":"196024"}}}},"ARO_accession":"3002993","ARO_id":"39427","ARO_name":"AQU-1","CARD_short_name":"AQU-1","ARO_description":"AQU-1 is a chromosomal class C beta-lactamase found in clinical Aeromonas dhakensis isolates.","ARO_category":{"39426":{"category_aro_accession":"3002992","category_aro_cvterm_id":"39426","category_aro_name":"AQU beta-lactamase","category_aro_description":"AQU beta-lactamases are chromosomal class C beta-lactamases that confer resistance to cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1712":{"model_id":"1712","model_name":"IMP-41","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1970":{"protein_sequence":{"accession":"BAM62795.1","sequence":"MKKLFVLCIFLFCSITAAGASLPDLKIEKLEEGVYVHTSFEEVNGWGVFSKHGLVVLVNTDAYLIDTPFTAKDTEKLVNWFVERGYKIKGSISSHFHSDSTGGIEWLNSQSIPTYASVLTNELLKKDGKVQAKNSFSGVSYWLVKNKIEVFYPGPGHTQDNVVVWLPKNKILFGGCFVKPYGLGNLDDANVEAWPHSAEKLISKYGNAKLVVPSHSDIGDASLLKLTWEQAVKGLNESKKSNTVH"},"dna_sequence":{"accession":"AB753458.1","fmin":"0","fmax":"738","strand":"+","sequence":"ATGAAAAAACTATTTGTTTTATGTATATTTTTGTTTTGTAGCATTACTGCCGCAGGAGCGTCTTTGCCTGATTTAAAAATTGAGAAGCTTGAAGAGGGTGTTTATGTTCATACATCGTTTGAAGAAGTTAACGGCTGGGGTGTTTTTTCTAAACACGGTTTGGTGGTTCTTGTAAATACTGACGCCTATCTGATTGACACTCCATTTACTGCTAAAGATACTGAAAAGTTAGTCAATTGGTTTGTGGAGCGCGGCTATAAAATCAAAGGCAGTATTTCCTCACATTTCCATAGCGACAGCACGGGTGGAATAGAGTGGCTTAATTCTCAATCTATTCCCACGTATGCATCTGTATTAACAAATGAACTTCTCAAAAAAGACGGTAAGGTGCAAGCTAAAAACTCATTTAGCGGAGTTAGCTATTGGCTAGTTAAAAATAAAATTGAAGTTTTTTATCCAGGCCCAGGGCACACTCAAGATAACGTAGTGGTTTGGCTACCTAAAAATAAAATCTTATTTGGTGGTTGTTTTGTTAAACCATATGGTCTTGGTAATCTAGATGACGCAAATGTTGAAGCATGGCCACATTCGGCTGAAAAATTAATATCTAAGTATGGTAATGCAAAACTGGTTGTTCCAAGCCATAGTGACATAGGAGATGCGTCGCTCTTGAAGCTTACGTGGGAACAGGCGGTAAAAGGGCTTAATGAAAGCAAAAAAAGTAACACTGTTCATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002232","ARO_id":"38632","ARO_name":"IMP-41","CARD_short_name":"IMP-41","ARO_description":"IMP-41 is a beta-lactamase found in Pseudomonas and Acinetobacter spp.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1714":{"model_id":"1714","model_name":"ErmW","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"493":{"protein_sequence":{"accession":"BAA03402.1","sequence":"MSSIRRRHAAASLDTPAVGGRHELGQNFLVDRGVCTRIAEVVSSTTAHPVLELGAGDGAITRALVAANLPVTALELDPRRVRRLQRTFADGVTVVHGDMLRYDFGPYPHHVVSTVPFSITTPLLRRLIGQRFWHTAVLLVQWEVARKRAGVGGTTMLTAASWPWYEFTLVERVPKTSFDPVPSVDGGILVIERRSAPLLDDRCVGDYQNLVREVYTGPGRGLAAILRTRLPGREVDAWLRRERVDPAALPRDLKAGHWASLYRLYREVGTRPAPAGRSVRARPGSVGPDRSLPPRGLRSGPPRARRRGGGA"},"dna_sequence":{"accession":"D14532.1","fmin":"1038","fmax":"1974","strand":"+","sequence":"ATGTCATCAATCCGGCGCCGGCACGCCGCCGCTTCGCTCGACACCCCTGCCGTGGGCGGCAGGCACGAACTCGGTCAGAACTTCCTCGTCGACCGAGGTGTATGCACAAGGATCGCCGAGGTCGTCTCCTCGACGACGGCCCATCCGGTCCTCGAACTGGGCGCCGGTGACGGTGCCATCACCCGGGCCCTGGTCGCGGCGAATCTCCCGGTCACCGCGCTGGAACTCGACCCCCGGCGGGTCCGGCGGCTCCAGCGGACCTTCGCCGACGGGGTCACCGTCGTGCACGGGGACATGCTCCGGTACGACTTCGGGCCGTACCCGCACCACGTGGTGTCGACCGTGCCGTTCTCCATCACCACGCCGCTGCTCCGGCGCCTGATCGGCCAGCGGTTCTGGCACACCGCGGTGCTGTTGGTGCAGTGGGAGGTGGCCCGTAAGCGGGCCGGTGTGGGCGGCACCACGATGCTCACCGCAGCCAGTTGGCCGTGGTACGAGTTCACCCTGGTGGAGCGGGTGCCGAAGACCTCGTTCGACCCGGTGCCGAGCGTCGACGGCGGCATCCTCGTCATCGAGCGTCGATCCGCGCCGCTGCTCGACGACCGCTGCGTGGGTGACTACCAGAACCTGGTACGCGAGGTGTACACCGGTCCCGGTCGTGGTCTGGCCGCGATTCTCCGTACCCGTCTGCCCGGTCGTGAGGTGGACGCCTGGCTCCGCCGCGAGCGGGTGGACCCGGCGGCCCTGCCCCGCGACCTCAAGGCCGGGCACTGGGCATCCCTCTACCGGCTCTACCGGGAGGTGGGTACTCGGCCCGCCCCTGCCGGCCGGTCCGTCCGGGCCCGGCCCGGATCCGTCGGCCCCGACCGCTCGCTCCCTCCGCGCGGCCTGCGATCCGGTCCGCCGAGGGCTCGACGACGTGGTGGAGGCGCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39571","NCBI_taxonomy_name":"Micromonospora griseorubida","NCBI_taxonomy_id":"28040"}}}},"ARO_accession":"3001306","ARO_id":"37705","ARO_name":"ErmW","CARD_short_name":"ErmW","ARO_description":"ErmW is a methyltransferase found in the mycinamicin producer Micromonospora griseorubida. Like other Erm enzymes, it catalyzes the methylation of A2058 of the 23S ribosomal RNA. The gene is found within the mycinamicin biosynthetic cluster and is responsible for self-resistance.","ARO_category":{"36699":{"category_aro_accession":"3000560","category_aro_cvterm_id":"36699","category_aro_name":"Erm 23S ribosomal RNA methyltransferase","category_aro_description":"Erm proteins are part of the RNA methyltransferase family and methylate A2058 (E. coli nomenclature) of the 23S ribosomal RNA conferring degrees of resistance to Macrolides, Lincosamides and Streptogramin b. This is called the MLSb phenotype.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"37620":{"category_aro_accession":"3001221","category_aro_cvterm_id":"37620","category_aro_name":"josamycin","category_aro_description":"A macrolide antibiotic from Streptomyces narbonensis\u00a0subsp.\u00a0josamyceticus. The drug has antimicrobial activity against a wide spectrum of pathogens.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1715":{"model_id":"1715","model_name":"OXA-73","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1218":{"protein_sequence":{"accession":"AAW22056.1","sequence":"MNKYFTCYVVASLFLSGCTVQHNLINETPSQIVQGHNQVIHQYFDEKNTSGVLVIQTDKKINLYGNALSRANTEYVPASTFKMLNALIGLENQKTDINEIFKWKGEKRSFTAWEKDMTLGEAMKLSAVPVYQELARRIGLDLMQKEVKRIGFGNAEIGQQVDNFWLVGPLKVTPIQEVEFVSQLAHTQLPFSEKVQANVKNMLLLEESNGYKIFGKTGWAMDIKPQVGWLTGWVEQPDGKIVAFALKMEMRSEMPASIRNELLMKSLKQLNII"},"dna_sequence":{"accession":"AY762325.1","fmin":"115","fmax":"937","strand":"+","sequence":"ATGAATAAATATTTTACTTGCTATGTGGTTGCTTCTCTTTTTCTTTCTGGTTGTACGGTTCAGCATAATTTAATAAATGAAACCCCGAGTCAGATTGTTCAAGGACATAATCAGGTGATTCATCAATACTTTGATGAAAAAAACACCTCAGGTGTGCTGGTTATTCAAACAGATAAAAAAATTAATCTATATGGTAATGCTCTAAGCCGCGCAAATACAGAATATGTGCCAGCCTCTACATTTAAAATGTTGAATGCCCTGATCGGATTGGAGAACCAGAAAACGGATATTAATGAAATATTTAAATGGAAGGGCGAGAAAAGGTCATTTACCGCTTGGGAAAAAGACATGACACTAGGAGAAGCCATGAAGCTTTCTGCAGTCCCAGTCTATCAGGAACTTGCGCGACGTATCGGTCTTGATCTCATGCAAAAAGAAGTAAAACGTATTGGTTTCGGTAATGCTGAAATTGGACAGCAGGTTGATAATTTCTGGTTGGTAGGACCATTAAAGGTTACGCCTATTCAAGAGGTAGAGTTTGTTTCCCAATTAGCACATACACAGCTTCCATTTAGTGAAAAAGTGCAGGCTAATGTAAAAAATATGCTTCTTTTAGAAGAGAGTAATGGCTACAAAATTTTTGGAAAGACTGGTTGGGCAATGGATATAAAACCACAAGTGGGCTGGTTGACCGGCTGGGTTGAGCAGCCAGATGGAAAAATTGTCGCTTTTGCATTAAAAATGGAAATGCGGTCAGAAATGCCGGCATCTATACGTAATGAATTATTGATGAAATCATTAAAACAGCTGAATATTATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001785","ARO_id":"38185","ARO_name":"OXA-73","CARD_short_name":"OXA-73","ARO_description":"OXA-73 is a beta-lactamase found in Klebsiella pneumonia.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46499":{"category_aro_accession":"3007710","category_aro_cvterm_id":"46499","category_aro_name":"OXA-23-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases, specifically imipenem, derived from OXA-23, first identified in Acinetobacter baumannii.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1716":{"model_id":"1716","model_name":"OXA-398","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1613":{"protein_sequence":{"accession":"AIT76095.1","sequence":"MNKYFTCYVVASLFLSGCTVQHNLINETPSQIVQGHNQVIHQYFDEKNTSGVLVIQTDKKINLYGNALSRANTEYVPASTFKMLNALIGLENQKTDINEIFKWKGEKRSFTAWEKDMTLGEAMKLSAVPVYQELARRIGLDLMQKEVKRIGFGNAEIGQQVDNFWLVGPLKVTPIQEVEFVSQLAHTQLPFSEKVQANVKNMLLLEESNGYKIFGKTGWAMDIKQQVGWLTGWVEQPDGKIVAFALNMEMRSEMPASIRNELLMKSLKQLNII"},"dna_sequence":{"accession":"KM087842.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGAATAAATATTTTACTTGCTATGTGGTTGCTTCTCTTTTTCTTTCTGGTTGTACGGTTCAGCATAATTTAATAAATGAAACCCCGAGTCAGATTGTTCAAGGACATAATCAGGTGATTCATCAATACTTTGATGAAAAAAACACCTCAGGTGTGCTGGTTATTCAAACAGATAAAAAAATTAATCTATATGGTAATGCTCTAAGCCGCGCAAATACAGAATATGTGCCAGCCTCTACATTTAAAATGTTGAATGCCCTGATCGGATTGGAGAACCAGAAAACGGATATTAATGAAATATTTAAATGGAAGGGCGAGAAAAGGTCATTTACCGCTTGGGAAAAAGACATGACACTAGGAGAAGCCATGAAGCTTTCTGCAGTCCCAGTCTATCAGGAACTTGCGCGACGTATCGGTCTTGATCTCATGCAAAAAGAAGTAAAACGTATTGGTTTCGGTAATGCTGAAATTGGACAGCAGGTTGATAATTTCTGGTTGGTAGGACCATTAAAGGTTACGCCTATTCAAGAGGTAGAGTTTGTTTCCCAATTAGCACATACACAGCTTCCATTTAGTGAAAAAGTGCAGGCTAATGTAAAAAATATGCTTCTTTTAGAAGAGAGTAATGGCTACAAAATTTTTGGAAAGACTGGTTGGGCAATGGATATAAAACAACAAGTGGGCTGGTTGACCGGCTGGGTTGAGCAGCCAGATGGAAAAATTGTCGCTTTTGCATTAAATATGGAAATGCGGTCAGAAATGCCGGCATCTATACGTAATGAATTATTGATGAAATCATTAAAACAGCTGAATATTATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001584","ARO_id":"37984","ARO_name":"OXA-398","CARD_short_name":"OXA-398","ARO_description":"OXA-398 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46499":{"category_aro_accession":"3007710","category_aro_cvterm_id":"46499","category_aro_name":"OXA-23-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases, specifically imipenem, derived from OXA-23, first identified in Acinetobacter baumannii.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1717":{"model_id":"1717","model_name":"OXA-230","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"971":{"protein_sequence":{"accession":"AFM55002.1","sequence":"MKFKMKGLFCVILSSLAFSGCVYDSKLQRPVISERETEIPLLFNQAQTQAVFVTYDGIHLKSYGNDLSRAKTEYIPASTFKMLNALIGLQNGKATNTEVFQWNGEKRAFSAWEKDMTLAEAMQASAVPVYQELARRIGLELMREEVKRVGFGNAEIGQQVDNFWLVGPLKISPEQEVQFAYQLAMKQLPFDRNVQQQVKDMLYIERRGDSKLYAKSGWGMDVEPQVGWYTGWVEQPNGKVTAFALNMNMQAGNDPAERKQLTLSILDKLGLFFYLR"},"dna_sequence":{"accession":"JQ422054.1","fmin":"100","fmax":"931","strand":"+","sequence":"ATGAAGTTTAAAATGAAAGGTTTATTTTGTGTCATCCTCAGTAGTTTGGCATTTTCAGGTTGTGTTTATGATTCAAAACTACAACGCCCAGTCATATCAGAGCGAGAAACTGAGATTCCTTTATTATTTAATCAAGCACAGACTCAAGCTGTGTTTGTTACTTATGATGGGATTCATCTAAAAAGTTATGGTAATGATCTAAGCCGAGCAAAGACTGAATATATTCCTGCATCTACATTTAAGATGTTGAATGCTTTAATTGGCTTGCAAAATGGAAAAGCAACCAATACTGAAGTATTTCAGTGGAATGGTGAAAAGCGTGCTTTTTCAGCATGGGAAAAAGATATGACTTTGGCAGAAGCGATGCAGGCTTCAGCTGTTCCCGTATATCAAGAGCTTGCTCGACGTATTGGCTTGGAATTGATGCGTGAAGAAGTGAAGCGTGTAGGTTTTGGCAATGCGGAGATTGGTCAGCAAGTCGATAATTTTTGGTTGGTGGGTCCTTTAAAAATCTCCCCTGAACAAGAAGTTCAATTTGCCTATCAACTGGCGATGAAGCAATTACCTTTTGATCGAAATGTACAGCAACAAGTCAAAGATATGCTTTATATCGAGAGACGTGGTGACAGTAAACTGTATGCTAAAAGTGGTTGGGGAATGGATGTTGAACCTCAAGTGGGTTGGTATACGGGATGGGTTGAACAACCCAATGGCAAGGTGACTGCATTTGCGTTAAATATGAACATGCAAGCAGGTAATGATCCAGCTGAACGTAAACAATTAACCTTAAGTATTTTGGACAAATTGGGTCTATTTTTTTATTTAAGATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39090","NCBI_taxonomy_name":"Acinetobacter bereziniae","NCBI_taxonomy_id":"106648"}}}},"ARO_accession":"3001693","ARO_id":"38093","ARO_name":"OXA-230","CARD_short_name":"OXA-230","ARO_description":"OXA-230 is a beta-lactamase found in A. bereziniae.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46498":{"category_aro_accession":"3007709","category_aro_cvterm_id":"46498","category_aro_name":"OXA-229-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-229.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1719":{"model_id":"1719","model_name":"ceoA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"730"}},"model_sequences":{"sequence":{"302":{"protein_sequence":{"accession":"AAB58160.1","sequence":"MAILRTSRSRIATAAIVTLAVVGLGTFGAMRVSANAPEKAAAPLPEVDVATVVPQTVTDWQSYSGRLEAVEKVDVRPQVSGTIVAVNFKDGALVKKGDVLFVIDPRPYQAEVDRAAAQLAAAQARNGYAQTDWQRAQRLIGDNAIAKRDYDEKQNAAREAKREPEGRRSRAGNGAHQSRLYAHHRAGVGPRVARGNHARQRRVGRRVGRAADDAGIGVADLRVVRRRRADLPAIHQRRAQRPQGAGRARPRERNRLLAQRRDRFGRQPARHVVRHDPRARPLRQRGRHPGPGPLRTREGGRQRAARGAARRRRGDQHRPGQEVRVRRRPAGPRVVSRSAARDAARQPARDRERAVGRRPRGRERHAARASGRAGEAAHGPDDGRRCAVRAVASTAKPAAPAKADS"},"dna_sequence":{"accession":"U97042.1","fmin":"0","fmax":"1218","strand":"+","sequence":"ATGGCCATCCTACGCACCTCCCGTTCCCGAATCGCGACCGCGGCGATCGTCACGCTCGCCGTCGTCGGCCTCGGCACGTTCGGCGCGATGCGCGTGAGCGCGAACGCCCCCGAGAAAGCGGCGGCGCCGCTGCCCGAAGTCGACGTCGCGACCGTCGTGCCGCAGACCGTGACCGACTGGCAAAGCTATTCGGGCCGCCTCGAGGCGGTCGAGAAAGTCGACGTGCGCCCGCAGGTGTCGGGCACGATCGTCGCGGTGAACTTCAAGGACGGCGCGCTCGTGAAGAAAGGCGACGTGCTGTTCGTGATCGACCCGCGCCCGTACCAGGCGGAAGTCGACCGCGCCGCCGCGCAGCTCGCGGCCGCGCAGGCCCGCAACGGCTACGCGCAGACCGACTGGCAGCGCGCGCAGCGGCTGATCGGCGACAACGCGATCGCGAAGCGCGACTACGACGAGAAGCAGAACGCGGCGCGCGAAGCGAAACGCGAACCTGAAGGCCGCCGAAGCCGCGCTGGAAACGGCGCGCATCAATCTCGGCTATACGCGCATCACCGCGCCGGTGTCGGGCCGCGTGTCGCGCGCGGAAATCACGCTCGGCAACGTCGTGTCGGCCGGCGCGTCGGCCGCGCCGCTGACGACGCTGGTATCGGTGTCGCCGATCTACGCGTCGTTCGACGCCGACGAGCAGACCTACCTGCAATACATCAACGGCGCGCGCAGCGGCCGCAAGGTGCCGGTCGAGCTCGGCCTCGCGAACGAAACCGGCTACTCGCGCAGCGGCGAGATCGATTCGGTCGACAACCGGCTCGACACGTCGTCCGGCACGATCCGCGTGCGCGCCCGCTTCGACAACGCGGACGGCACCCTGGTCCCGGGCCTCTACGCACGCGTGAAGGTGGGCGGCAGCGCGCCGCACGAGGCGCTGCTCGTCGACGACGCGGCGATCAACACCGACCAGGACAAGAAGTTCGTGTTCGTCGTCGACCAGCAGGGCCGCGTGTCGTATCGCGAAGTGCAGCAAGGGATGCAGCACGGCAACCGGCGCGTGATCGTGAGCGGGCTGTCGGCCGGCGACCGCGTGGTCGTGAACGGCACGCAGCGCGTGCGTCCGGGCGAGCAGGTGAAGCCGCACATGGTCCCGATGACGGGCGGCGATGCGCCGTCCGCGCCGTCGCGAGCACCGCGAAGCCGGCCGCACCGGCGAAGGCGGATTCGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36822","NCBI_taxonomy_name":"Burkholderia cepacia","NCBI_taxonomy_id":"292"}}}},"ARO_accession":"3003009","ARO_id":"39443","ARO_name":"ceoA","CARD_short_name":"ceoA","ARO_description":"ceoA is a periplasmic linker subunit of the CeoAB-OpcM efflux pump.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1720":{"model_id":"1720","model_name":"tap","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"75":{"protein_sequence":{"accession":"CAA03986.1","sequence":"MTNTKRGPLLLILFAALTAGAGNGITIVAFPWLVLQHNGSALDASIVAMAGTLPLLVATLIAGAAVDYLGRRRVSMISDLLSALSVAAVPVLALIFGVDAVNVAVLAVLAGLGAFFDPAGMTARETMLPEAAGRAGWTLDHANSVYEAVFNLGYIVGPGIGGLMIATLGGINTMWVTAGAFCCSILAISVLRLEGAGAPDRSVLTEAVLAGIVEGLRFVWYTPVLRTLAIVDLVATGLYMPMESVLFPKYFTDRNEPTELGWVLMALSIGGLLGALGYAVMSRYMSRRATMLTAVITLGVAMTVIAFLPPLPLILVLCAIVGFVYGPIAPIYNYVMQTTAPQHLRGRVVGVMGSLAYAAGPLGLILAGPLADAAGLHATFLALSLPMLLLGVVAVFLPRLRELDLASKP"},"dna_sequence":{"accession":"AJ000283.1","fmin":"619","fmax":"1849","strand":"+","sequence":"ATGACGAACACCAAGCGCGGCCCCTTGCTGCTGATCCTGTTCGCCGCGTTGACGGCCGGCGCCGGCAACGGAATCACCATCGTCGCGTTCCCGTGGCTGGTGTTGCAGCACAACGGATCCGCGCTCGACGCCTCGATCGTCGCGATGGCCGGCACCCTGCCGCTGCTGGTGGCCACACTGATCGCCGGGGCGGCGGTGGATTACCTGGGTCGCCGACGGGTTTCGATGATCTCGGATCTGCTCTCGGCGCTGTCGGTCGCTGCGGTACCCGTGCTGGCCCTGATTTTCGGGGTGGACGCGGTCAATGTCGCGGTGCTGGCGGTCCTGGCGGGGCTGGGAGCGTTCTTCGACCCGGCCGGCATGACAGCGCGCGAGACCATGCTGCCCGAGGCCGCGGGCCGGGCCGGTTGGACGCTGGACCATGCCAACTCGGTGTACGAGGCGGTCTTCAACCTGGGCTACATCGTCGGCCCCGGTATCGGCGGCCTGATGATCGCCACGCTCGGCGGGATCAACACCATGTGGGTGACGGCCGGGGCGTTCTGCTGCTCGATCCTGGCCATCTCGGTGCTGCGACTGGAGGGCGCGGGCGCGCCGGACCGCTCGGTGCTGACCGAGGCCGTTTTGGCGGGCATAGTCGAGGGACTGCGATTCGTCTGGTACACACCGGTATTGCGCACCCTGGCCATCGTCGACCTGGTGGCCACCGGCTTGTACATGCCGATGGAATCGGTCCTTTTTCCGAAGTACTTCACGGACCGGAACGAACCCACCGAACTGGGCTGGGTGCTGATGGCGTTGAGCATCGGCGGACTGTTGGGTGCGCTCGGTTACGCCGTGATGTCCAGGTACATGAGCCGACGGGCCACCATGCTGACCGCCGTGATCACCCTCGGGGTGGCGATGACGGTGATCGCCTTCCTGCCACCGCTGCCGCTGATCCTGGTGCTGTGCGCAATCGTCGGCTTCGTCTACGGACCGATCGCACCCATCTACAACTACGTCATGCAGACCACCGCTCCCCAACACCTGCGTGGCCGCGTGGTCGGGGTGATGGGCTCATTGGCCTACGCCGCGGGCCCGCTCGGGCTGATCCTGGCCGGGCCGCTGGCCGACGCCGCAGGCCTGCACGCGACGTTCCTGGCACTGTCCCTACCGATGCTGTTGCTCGGCGTCGTGGCGGTGTTCCTGCCGCGGCTGCGCGAGCTGGACCTAGCATCGAAACCGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36886","NCBI_taxonomy_name":"Mycolicibacterium fortuitum","NCBI_taxonomy_id":"1766"}}}},"ARO_accession":"3000343","ARO_id":"36482","ARO_name":"tap","CARD_short_name":"tap","ARO_description":"Efflux pump proteins contained within Mycobacterial genomes which confer resistance to a number of different antibiotics including aminoglycosides, and tetracyclines.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1722":{"model_id":"1722","model_name":"TEM-184","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1723":{"protein_sequence":{"accession":"CCA61905.1","sequence":"MSIKHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVKYSPVTEKHLTDGMTVRELCSAAVTMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDSWEPELNEAIPNDERDTTTPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"FR848831.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTAAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTAAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCGTAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATAGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGACGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001375","ARO_id":"37775","ARO_name":"TEM-184","CARD_short_name":"TEM-184","ARO_description":"TEM-184 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1723":{"model_id":"1723","model_name":"IMP-44","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"872":{"protein_sequence":{"accession":"BAM98942.1","sequence":"MKKLFVLCIFLFCSITAAGASLPDLKIEKLEEGVYVHTSFEEVNGWGVFSKHGLVVLVNTDAYLIDTPSTAKDTEKLVNWFVERGYKIKGSISSHFHSDSTGGIEWLNSQSIPTYASVLTNELLKKDGKVQAKNSFSGVSYWLVKNKIEVFYPGPGHTQDNVVVWLPKNKILFGGCFVKPYGLGNLDDANVEAWPHSAEKLISKYGNAKLVVPSHSDIGDASLLKLTWEQAVKGLNESKKSNTVH"},"dna_sequence":{"accession":"AB777501.1","fmin":"1398","fmax":"2136","strand":"+","sequence":"ATGAAAAAACTATTTGTTTTATGTATATTTTTGTTTTGTAGCATTACTGCCGCAGGAGCGTCTTTGCCTGATTTAAAAATTGAGAAGCTTGAAGAGGGTGTTTATGTTCATACATCGTTTGAAGAAGTTAACGGCTGGGGTGTTTTTTCTAAACACGGTTTGGTGGTTCTTGTAAATACTGACGCCTATCTGATTGACACTCCATCTACTGCTAAAGATACTGAAAAGTTAGTCAATTGGTTTGTGGAGCGCGGCTATAAAATCAAAGGCAGTATTTCCTCACATTTCCATAGCGACAGCACGGGTGGAATAGAGTGGCTTAATTCTCAATCTATTCCCACGTATGCATCTGTATTAACAAATGAACTTCTCAAAAAAGACGGTAAGGTGCAAGCTAAAAACTCATTTAGCGGAGTTAGCTATTGGCTAGTTAAAAATAAAATTGAAGTTTTTTATCCAGGCCCAGGGCACACTCAAGATAACGTAGTGGTTTGGCTACCTAAAAATAAAATCTTATTTGGTGGTTGTTTTGTTAAACCATATGGTCTTGGTAATCTAGATGACGCAAATGTTGAAGCATGGCCACATTCGGCTGAAAAATTAATATCTAAGTATGGTAATGCAAAACTGGTTGTTCCAAGCCATAGTGACATAGGAGATGCGTCGCTCTTGAAGCTTACGTGGGAACAGGCGGTAAAAGGGCTTAATGAAAGCAAAAAAAGTAACACTGTTCATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002235","ARO_id":"38635","ARO_name":"IMP-44","CARD_short_name":"IMP-44","ARO_description":"IMP-44 is a beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1725":{"model_id":"1725","model_name":"TEM-101","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"842":{"protein_sequence":{"accession":"AAM18924.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDKLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGASKRGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIVEIGASLIKHW"},"dna_sequence":{"accession":"AF495873.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATAAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCAGTAAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGTCGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000964","ARO_id":"37344","ARO_name":"TEM-101","CARD_short_name":"TEM-101","ARO_description":"TEM-101 is an extended-spectrum beta-lactamase found in E. coli.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1726":{"model_id":"1726","model_name":"FOX-4","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1189":{"protein_sequence":{"accession":"CAB89086.1","sequence":"MQQRRALALLMLGSLLLAPCTYASGEAPLTATVDGIIQPMLKAYRIPGMAVAVLKDGKAHYFNYGVANRESGQRVSEQTLFEIGSVSKTLTATLGAYAAVKGGFELDDKVSQHAPWLKGSAFDGVTMAELATYSAGGLPLQFPDEVDSNDKMQTYYRSWSPVYPAGTHRQYSNPSIGLFGHLAANSLGQPFEQLMSQTLLPKLGLHHTYIQVPESAMANYAYGYSKEDKPIRATPGVLAAEAYGIKTGSADLLKFVEANMGYQGDAALKSAIALTHTGFHSVGEMTQGLGWESYDYPVTEQVLLAGNSPAVSFQANPVTRFAVPKAMGEQRLYNKTGSTGGFGAYVAFVPARGIAIVMLANRNYPIEARVKAAHAILSQLAE"},"dna_sequence":{"accession":"AJ277535.1","fmin":"0","fmax":"1149","strand":"+","sequence":"ATGCAACAACGACGTGCGCTCGCGCTACTGATGCTGGGTAGCCTGCTGTTAGCCCCTTGCACTTATGCCAGCGGGGAGGCCCCGCTGACCGCCACTGTGGACGGCATTATCCAGCCGATGCTCAAGGCGTATCGGATCCCGGGGATGGCGGTCGCTGTACTGAAAGATGGCAAGGCCCACTATTTCAACTATGGGGTTGCCAACCGCGAGAGCGGCCAGCGCGTCAGCGAGCAGACCCTGTTCGAGATTGGCTCGGTCAGCAAGACCCTGACCGCGACCCTTGGCGCCTATGCCGCAGTCAAGGGGGGCTTTGAGCTGGATGACAAGGTGAGCCAGCACGCCCCCTGGCTCAAAGGTTCCGCCTTTGATGGTGTGACCATGGCCGAGCTTGCCACCTACAGTGCGGGTGGTTTGCCGCTGCAGTTCCCCGATGAGGTAGATTCGAATGACAAGATGCAAACTTACTATCGGAGCTGGTCACCGGTTTATCCGGCGGGGACTCATCGCCAGTATTCCAACCCCAGCATAGGCCTGTTTGGTCACCTGGCCGCAAATAGTCTGGGCCAGCCATTTGAGCAACTGATGAGCCAGACCCTGCTGCCCAAACTGGGTTTGCACCACACCTATATCCAGGTGCCGGAGTCGGCCATGGCGAACTATGCCTACGGCTATTCGAAGGAAGATAAGCCTATCCGGGCCACTCCGGGCGTGCTGGCTGCCGAGGCTTACGGGATCAAGACCGGTTCGGCGGATCTGCTGAAGTTTGTCGAGGCCAACATGGGGTATCAGGGAGATGCCGCGCTAAAAAGCGCGATCGCGCTGACCCACACCGGCTTCCATTCGGTGGGGGAAATGACCCAGGGGCTGGGCTGGGAGAGTTACGACTATCCCGTCACCGAGCAGGTGCTGCTGGCGGGCAACTCACCAGCGGTGAGCTTCCAGGCCAATCCGGTTACGCGCTTTGCGGTGCCCAAAGCGATGGGCGAGCAGCGGCTCTATAACAAGACGGGCTCGACTGGTGGCTTTGGCGCCTATGTGGCGTTCGTGCCTGCCAGAGGGATAGCCATCGTCATGCTGGCCAATCGCAACTATCCCATCGAGGCCAGGGTGAAGGCGGCTCACGCCATCCTGAGTCAGTTGGCCGAGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002158","ARO_id":"38558","ARO_name":"FOX-4","CARD_short_name":"FOX-4","ARO_description":"FOX-4 is a beta-lactamase found in Escherichia coli.","ARO_category":{"36206":{"category_aro_accession":"3000067","category_aro_cvterm_id":"36206","category_aro_name":"FOX beta-lactamase","category_aro_description":"FOX beta-lactamases are plasmid-encoded AmpC-type beta-lactamase which conferred resistance to broad-spectrum cephalosporins and cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1727":{"model_id":"1727","model_name":"SHV-73","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"8211":{"protein_sequence":{"accession":"CAJ47128.2","sequence":"MRIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPVGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADRTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AM176548.2","fmin":"16","fmax":"874","strand":"+","sequence":"ATGCGTATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAATTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGTAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAGGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGGATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001127","ARO_id":"37507","ARO_name":"SHV-73","CARD_short_name":"SHV-73","ARO_description":"SHV-73 is a broad-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1728":{"model_id":"1728","model_name":"OXA-42","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1934":{"protein_sequence":{"accession":"CAD32564.1","sequence":"MKFRHALSSAFVLLGCIAASAHAKTICTAIADAGTGKLLVQDGDCGRRASPASTFKIAISLMGYDAGFLRNEHDPVLPYRDSYIAWGGEAWKQPTDPTRWLKYSVVWYSQQVAHHLGAQRFAQYAKAFGYGNADVSGDPGQNNGLDRAWIGSSLQISPLEQLEFLGKMLNRKLPVSPTAVDMTERIVESTTLADGTVVHGKTGVSYPLLADGTRDWARGSGWFVGWIVRGNQTLVFARLTQDERKQPVSAGIRTREAFLRDLPRLLAAR"},"dna_sequence":{"accession":"AJ488302.1","fmin":"0","fmax":"810","strand":"+","sequence":"ATGAAATTCCGACACGCGCTGTCGAGCGCATTCGTTTTGCTGGGTTGCATCGCCGCGTCGGCGCATGCGAAGACGATCTGCACGGCGATCGCCGATGCGGGCACGGGCAAGCTGCTGGTGCAGGACGGCGATTGCGGCCGCCGCGCATCGCCCGCGTCGACGTTCAAGATCGCGATCAGCCTGATGGGCTACGACGCAGGCTTCCTGCGCAACGAGCATGACCCGGTGCTGCCGTATCGCGACAGTTACATCGCGTGGGGTGGCGAAGCATGGAAGCAGCCGACCGATCCGACGCGCTGGCTCAAGTATTCGGTCGTGTGGTATTCGCAGCAGGTGGCGCACCATCTCGGCGCGCAGCGCTTCGCGCAGTATGCGAAGGCGTTCGGCTACGGCAATGCGGACGTGTCCGGCGATCCCGGCCAGAACAACGGCCTCGATCGCGCGTGGATCGGCTCGTCGCTGCAGATCTCGCCGCTCGAACAATTGGAATTCCTCGGCAAGATGCTCAATCGCAAGCTGCCCGTGTCGCCCACAGCCGTCGACATGACGGAGCGGATCGTCGAATCGACGACGCTTGCCGACGGAACGGTGGTGCACGGCAAGACCGGCGTGTCCTATCCGCTGCTGGCCGACGGCACACGCGACTGGGCGCGTGGATCCGGCTGGTTCGTCGGCTGGATCGTGCGTGGCAATCAGACGCTGGTGTTCGCGCGCCTCACGCAGGACGAGCGCAAGCAGCCCGTTTCAGCCGGCATACGGACGCGCGAGGCCTTCCTGCGCGACTTGCCCCGGCTTCTCGCCGCGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36923","NCBI_taxonomy_name":"Burkholderia pseudomallei","NCBI_taxonomy_id":"28450"}}}},"ARO_accession":"3001769","ARO_id":"38169","ARO_name":"OXA-42","CARD_short_name":"OXA-42","ARO_description":"OXA-42 is a beta-lactamase found in Burkholderia pseudomallei.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46507":{"category_aro_accession":"3007718","category_aro_cvterm_id":"46507","category_aro_name":"OXA-42-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-42.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1729":{"model_id":"1729","model_name":"CTX-M-66","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1107":{"protein_sequence":{"accession":"ABQ45409.1","sequence":"MVKKSLRQFTLMATATVTLLLGNVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGDYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"EF576988.1","fmin":"239","fmax":"1115","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAATGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGACTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3001927","ARO_id":"38327","ARO_name":"CTX-M-66","CARD_short_name":"CTX-M-66","ARO_description":"CTX-M-66 is a beta-lactamase found in Proteus mirabilis.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1730":{"model_id":"1730","model_name":"OXA-235","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8262":{"protein_sequence":{"accession":"AFH36330.1","sequence":"MKTLILLPLLSCLSLTACSLPVSNSSSQITSTQSIQTIAKLFDQAQSSGVLVIQRGPHLQVYGNDLSRAHTEYIPASTFKILNALIGLQHGKATTNEIFKWDGKKRSFAAWEKDMTLGQAMQASAVPVYQELARRIGLELMQQEVQRIRFGNQQIGQHIDNFWLVGPLKITPEQEVEFASALAQEQLAFDPQVQQQVKAMLLLQERQDYRLYAKSGWGMDVEPQVGWLTGWIETPQDEIVAFSLNMQMQSNMDPAIRLKILQQALAELALYPKAEG"},"dna_sequence":{"accession":"JQ820240.2","fmin":"590","fmax":"1421","strand":"+","sequence":"ATGAAAACTCTTATTTTGTTGCCTTTACTTAGTTGCTTGAGCCTGACAGCCTGTAGCTTGCCTGTTTCAAATTCGTCCTCTCAAATCACTTCAACTCAATCTATTCAAACCATTGCCAAATTATTTGATCAGGCACAAAGCTCTGGCGTTTTAGTAATTCAACGGGGCCCACATCTACAGGTCTATGGCAATGATTTGAGTCGTGCACATACCGAATATATTCCTGCTTCAACCTTTAAAATACTCAATGCCCTGATTGGCCTGCAACATGGTAAAGCCACGACCAATGAAATCTTTAAATGGGATGGCAAGAAGCGCAGTTTTGCAGCCTGGGAAAAAGACATGACTCTCGGCCAAGCCATGCAAGCTTCTGCTGTACCCGTCTATCAGGAACTGGCACGTCGCATTGGTCTGGAACTAATGCAACAGGAAGTGCAACGCATTCGATTTGGTAATCAGCAGATTGGTCAGCATATCGACAACTTCTGGTTAGTCGGACCTTTGAAAATCACCCCGGAACAAGAAGTCGAATTTGCCTCTGCGCTTGCTCAAGAGCAACTTGCCTTTGATCCTCAAGTCCAGCAACAAGTCAAAGCCATGTTACTGTTACAGGAGCGACAAGATTATCGACTATATGCCAAATCTGGTTGGGGTATGGATGTGGAGCCGCAAGTCGGCTGGCTCACCGGCTGGATCGAAACACCTCAGGACGAAATCGTGGCATTTTCACTGAATATGCAGATGCAAAGTAATATGGATCCGGCGATCCGTCTTAAAATTTTGCAGCAGGCCTTGGCCGAATTAGCGCTTTATCCGAAAGCTGAAGGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001676","ARO_id":"38076","ARO_name":"OXA-235","CARD_short_name":"OXA-235","ARO_description":"OXA-235 is a beta-lactamase found in A. baumannii.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46489":{"category_aro_accession":"3007700","category_aro_cvterm_id":"46489","category_aro_name":"OXA-134-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-134.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1731":{"model_id":"1731","model_name":"mphB","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"6082":{"protein_sequence":{"accession":"BAA12910.1","sequence":"MSKDIKQVIEIAKKHNLFLKEETIQFNESGLDFQAVFAQDNNGIDWVLRLPRREDVMPRTKVEKQALDLVNKYAISFQAPNWIIYTEELIAYKKLDGVPAGTIDHNIGNYIWEIDINNVPELFHKSLGRVLAELHSIPSNKAAALDLVVHTPEEARMSMKQRMDAVRAKFGVGENLWNRWQAWLNDDDMWPKKTGLIHGDVHAGHTMIDKDANVTGLIDWTEAKVTDVSHDFIFNYRAFGEEGLEALILAYKEIGGYYWPKMKEHIIELNAAYPVSIAEFALVSGIEEYEQMAKEALEVQGS"},"dna_sequence":{"accession":"D85892.1","fmin":"1158","fmax":"2067","strand":"+","sequence":"ATGAGTAAAGATATTAAACAAGTAATCGAGATAGCAAAAAAACACAATCTTTTTCTAAAAGAAGAAACGATACAGTTTAATGAATCAGGGCTTGATTTTCAAGCTGTTTTTGCACAAGATAATAATGGAATTGATTGGGTTCTAAGATTGCCTAGACGGGAAGATGTGATGCCTAGAACAAAGGTAGAAAAACAAGCTTTGGATTTGGTAAATAAGTACGCTATATCCTTTCAGGCACCAAACTGGATCATTTACACAGAGGAACTAATAGCTTATAAAAAGTTAGATGGTGTGCCAGCAGGTACGATAGATCATAACATAGGTAACTATATTTGGGAGATAGACATAAATAATGTTCCAGAATTATTTCACAAGTCGCTAGGCAGGGTGTTAGCAGAGCTTCATAGCATACCTAGTAATAAAGCCGCAGCGCTTGATCTTGTAGTACACACACCAGAAGAAGCAAGAATGTCAATGAAGCAGCGTATGGATGCAGTAAGAGCAAAGTTCGGAGTAGGTGAGAATCTATGGAACAGATGGCAAGCGTGGTTGAATGATGATGATATGTGGCCTAAGAAAACTGGACTGATTCATGGAGATGTACATGCCGGACATACTATGATTGATAAGGATGCCAATGTGACTGGATTAATCGATTGGACTGAAGCGAAGGTTACAGATGTTTCGCATGACTTTATTTTCAACTATAGAGCTTTTGGGGAAGAAGGGTTAGAAGCTTTAATTCTCGCTTATAAGGAAATTGGTGGATATTACTGGCCTAAAATGAAAGAGCATATTATCGAACTTAATGCAGCATACCCAGTTTCAATCGCTGAGTTTGCATTAGTGTCTGGAATTGAGGAATATGAGCAGATGGCAAAGGAAGCATTGGAAGTACAAGGTTCGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000318","ARO_id":"36457","ARO_name":"mphB","CARD_short_name":"mphB","ARO_description":"The mphB gene encodes for MPH(2')-II. This enzymes phosphorylates 14-membered and 16-membered macrolides.  It phosphorylates macrolides in GTP- dependent manner at 2'-OH hydroxyl of desosamine sugar of macrolides.","ARO_category":{"36472":{"category_aro_accession":"3000333","category_aro_cvterm_id":"36472","category_aro_name":"macrolide phosphotransferase (MPH)","category_aro_description":"Macrolide phosphotransferases (MPH) are enzymes encoded by macrolide phosphotransferase genes (mph genes). These enzymes phosphorylate macrolides in GTP dependent manner at 2'-OH of desosamine sugar thereby inactivating them. Characterized MPH's are differentiated based on their substrate specificity.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35946":{"category_aro_accession":"0000027","category_aro_cvterm_id":"35946","category_aro_name":"roxithromycin","category_aro_description":"Roxithromycin is a semi-synthetic, 14-carbon ring macrolide antibiotic derived from erythromycin. It is used to treat respiratory tract, urinary and soft tissue infections. Roxithromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35974":{"category_aro_accession":"0000057","category_aro_cvterm_id":"35974","category_aro_name":"telithromycin","category_aro_description":"Telithromycin is a semi-synthetic derivative of erythromycin. It is a 14-membered macrolide and is the first ketolide antibiotic to be used in clinics. Telithromycin binds the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"35982":{"category_aro_accession":"0000065","category_aro_cvterm_id":"35982","category_aro_name":"clarithromycin","category_aro_description":"Clarithromycin is a methyl derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome and is used to treat pharyngitis, tonsillitis, acute maxillary sinusitis, acute bacterial exacerbation of chronic bronchitis, pneumonia (especially atypical pneumonias associated with Chlamydia pneumoniae or TWAR), and skin structure infections.","category_aro_class_name":"Antibiotic"},"36284":{"category_aro_accession":"3000145","category_aro_cvterm_id":"36284","category_aro_name":"tylosin","category_aro_description":"Tylosin is a 16-membered macrolide, naturally produced by Streptomyces fradiae. It interacts with the bacterial ribosome 50S subunit to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"36295":{"category_aro_accession":"3000156","category_aro_cvterm_id":"36295","category_aro_name":"spiramycin","category_aro_description":"Spiramycin is a 16-membered macrolide and is natural product produced by Streptomyces ambofaciens. It binds to the 50S subunit of bacterial ribosomes and inhibits peptidyl transfer activity to disrupt protein synthesis.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"36315":{"category_aro_accession":"3000176","category_aro_cvterm_id":"36315","category_aro_name":"dirithromycin","category_aro_description":"Dirithromycin is an oxazine derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome to inhibit bacterial protein synthesis.","category_aro_class_name":"Antibiotic"},"37247":{"category_aro_accession":"3000867","category_aro_cvterm_id":"37247","category_aro_name":"oleandomycin","category_aro_description":"Oleandomycin is a 14-membered macrolide produced by Streptomyces antibioticus. It is ssimilar to erythromycin, and contains a desosamine amino sugar and an oleandrose sugar. It targets the 50S ribosomal subunit to prevent protein synthesis.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1732":{"model_id":"1732","model_name":"SHV-151","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1145":{"protein_sequence":{"accession":"AFQ23957.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQPSGSVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"JX121118.1","fmin":"0","fmax":"858","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCCGTCGGGCAGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGCATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGC","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001190","ARO_id":"37570","ARO_name":"SHV-151","CARD_short_name":"SHV-151","ARO_description":"SHV-151 is a beta-lactamase.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1733":{"model_id":"1733","model_name":"OXA-415","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1765":{"protein_sequence":{"accession":"AIG94927.1","sequence":"MAIRIFAILFSIFSLATFAHAQEGTLERSDWRKFFSEFQAKGTIVVADERQADRAMLVFDPVRSKKRYSPASTFKIPHTLFALDAGAVRDEFQIFRWDGVNRGFAGHNQDQDLRSAMRNSTVWVYELFAKEIGDDKARRYLKKIDYGNADPSTSNGDYWIEDSLAISAQEQIAFLRKLYRNELPFRVEHQRLVKDLMIVEAGRNWILRAKTGWEGRMGWWVGWVEWPTGSVFFALNIDTPNRMDDLFKREAIVRAILRSIEALPPNPAVNSDAAR"},"dna_sequence":{"accession":"KJ865754.1","fmin":"0","fmax":"828","strand":"+","sequence":"ATGGCAATCCGAATCTTCGCGATACTTTTCTCCATTTTTTCTCTTGCCACTTTCGCGCATGCGCAAGAAGGCACGCTAGAACGTTCTGACTGGAGGAAGTTTTTCAGCGAATTTCAAGCCAAAGGCACGATAGTTGTGGCAGACGAACGCCAAGCGGATCGTGCCATGTTGGTTTTTGATCCTGTGCGATCGAAGAAACGCTACTCGCCTGCATCGACATTCAAGATACCTCATACACTTTTTGCACTTGATGCAGGCGCTGTTCGTGATGAGTTCCAGATTTTTCGATGGGACGGCGTTAACAGGGGCTTTGCAGGCCACAATCAAGACCAAGATTTGCGATCAGCAATGCGGAATTCTACTGTTTGGGTGTATGAGCTATTTGCAAAGGAAATTGGTGATGACAAAGCTCGGCGCTATTTGAAGAAAATCGACTATGGCAACGCCGATCCTTCGACAAGTAATGGCGATTACTGGATAGAAGACAGCCTTGCAATCTCGGCGCAGGAGCAAATTGCATTTCTCAGGAAGCTCTATCGTAACGAGCTGCCCTTTCGGGTAGAACATCAGCGCTTGGTCAAGGATCTCATGATTGTGGAAGCCGGTCGCAACTGGATACTGCGTGCAAAGACGGGCTGGGAAGGCCGTATGGGTTGGTGGGTAGGATGGGTTGAGTGGCCGACTGGCTCCGTATTCTTCGCACTGAATATTGATACGCCAAACAGAATGGATGATCTTTTCAAGAGGGAGGCAATCGTGCGGGCAATCCTTCGCTCTATTGAAGCGTTACCGCCCAACCCGGCAGTCAACTCGGACGCTGCGCGATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3001606","ARO_id":"38006","ARO_name":"OXA-415","CARD_short_name":"OXA-415","ARO_description":"OXA-415 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46493":{"category_aro_accession":"3007704","category_aro_cvterm_id":"46493","category_aro_name":"OXA-2-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-2.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1734":{"model_id":"1734","model_name":"IND-4","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"8199":{"protein_sequence":{"accession":"AAG29765.2","sequence":"MRKNVRIFTVLSLFLINFFNAQARDFVIEQPFGKQLYLYKTFGVFDGKEYSTNALYLVTKKGVVLFDVPWQKTQYQSLMDTIKKRHNLPVIAVFATHSHSDRAGDLSFYNKKGIPTYATAKTNELLKKEGKATSSKLTKIGKKYKIGGEEFTVDFLGEGHTADNVVVWFPKYNVLDGGCLVKSSAAVDLGYTGEANVEQWPATMKKLQAKYPSTAKVIPGHDEWKGNDHVKHTLELLDQQKQ"},"dna_sequence":{"accession":"AF219135.2","fmin":"0","fmax":"729","strand":"+","sequence":"ATGAGGAAAAATGTTAGGATTTTTACTGTGTTGTCTCTGTTCTTAATTAATTTTTTTAATGCGCAGGCCCGTGACTTTGTAATTGAGCAGCCTTTTGGCAAACAACTTTATCTGTATAAAACCTTCGGAGTTTTTGACGGCAAAGAATATTCAACCAATGCGCTTTATCTGGTCACTAAAAAAGGAGTAGTCCTTTTTGATGTCCCATGGCAGAAAACCCAGTATCAAAGTCTTATGGATACGATAAAGAAACGTCATAACTTACCGGTGATCGCTGTATTTGCAACACATTCACACTCAGACAGAGCCGGAGACCTGAGTTTTTACAATAAAAAAGGCATCCCGACCTATGCCACGGCCAAAACCAATGAACTGCTGAAGAAAGAAGGAAAAGCAACTTCCAGTAAATTAACAAAGATTGGAAAGAAATATAAAATAGGCGGTGAAGAATTCACTGTAGACTTCTTAGGTGAAGGTCACACAGCAGATAACGTGGTGGTTTGGTTTCCAAAATATAACGTCCTGGACGGTGGCTGCTTAGTGAAAAGCAGTGCAGCAGTTGATCTTGGATATACAGGAGAAGCTAATGTAGAACAATGGCCGGCAACCATGAAAAAGCTGCAGGCTAAATACCCCTCCACTGCAAAGGTAATTCCGGGACACGACGAGTGGAAAGGCAACGACCATGTAAAACATACACTGGAGCTTTTAGATCAACAAAAACAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36916","NCBI_taxonomy_name":"Chryseobacterium indologenes","NCBI_taxonomy_id":"253"}}}},"ARO_accession":"3002260","ARO_id":"38660","ARO_name":"IND-4","CARD_short_name":"IND-4","ARO_description":"IND-4 is a beta-lactamase found in Chryseobacterium indologenes.","ARO_category":{"36199":{"category_aro_accession":"3000060","category_aro_cvterm_id":"36199","category_aro_name":"IND beta-lactamase","category_aro_description":"IND beta-lactamases are class B carbapenem-hydrolyzing beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1735":{"model_id":"1735","model_name":"vatA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"144":{"protein_sequence":{"accession":"AAA26683.1","sequence":"MNLNNDHGPDPENILPIKGNRNLQFIKPTITNENILVGEYSYYDSKRGESFEDQVLYHYEVIGDKLIIGRFCSIGPGTTFIMNGANHRMDGSTYPFHLFRMGWEKYMPSLKDLPLKGDIEIGNDVWIGRDVTIMPGVKIGDGAIIAAEAVVTKNVAPYSIVGGNPLKFIRKRFSDGVIEEWLALQWWNLDMKIINENLPFIINGDIEMLKRKRKLLDDT"},"dna_sequence":{"accession":"L07778.1","fmin":"0","fmax":"660","strand":"+","sequence":"TTGAATTTAAACAATGACCATGGACCTGATCCCGAAAATATTTTACCGATAAAAGGGAATCGGAATCTTCAATTTATAAAACCTACTATAACGAACGAAAACATTTTGGTGGGGGAATATTCTTATTATGATAGTAAGCGAGGAGAATCCTTTGAAGATCAAGTCTTATATCATTATGAAGTGATTGGAGATAAGTTGATTATAGGAAGATTTTGTTCAATTGGTCCCGGAACAACATTTATTATGAATGGTGCAAACCATCGGATGGATGGATCAACATATCCTTTTCATCTATTCAGGATGGGTTGGGAGAAGTATATGCCTTCCTTAAAAGATCTTCCCTTGAAAGGGGACATTGAAATTGGAAATGATGTATGGATAGGTAGAGATGTAACCATTATGCCTGGGGTGAAAATTGGGGACGGGGCAATCATTGCTGCAGAAGCTGTTGTCACAAAGAATGTTGCTCCCTATTCTATTGTCGGTGGAAATCCCTTAAAATTTATAAGAAAAAGGTTTTCTGATGGAGTTATCGAAGAATGGTTAGCTTTACAATGGTGGAATTTAGATATGAAAATTATTAATGAAAATCTTCCCTTCATAATAAATGGAGATATCGAAATGCTGAAGAGAAAAAGAAAACTTCTAGATGACACTTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35508","NCBI_taxonomy_name":"Staphylococcus aureus","NCBI_taxonomy_id":"1280"}}}},"ARO_accession":"3002840","ARO_id":"39274","ARO_name":"vatA","CARD_short_name":"vatA","ARO_description":"vatA is a plasmid-mediated acetyltransferase found in Staphylococcus aureus.","ARO_category":{"36592":{"category_aro_accession":"3000453","category_aro_cvterm_id":"36592","category_aro_name":"streptogramin vat acetyltransferase","category_aro_description":"vat (Virginiamycin acetyltransferases) enzymes catalyze the transfer of an acetyl group from acetyl-CoA to the secondary alcohol of streptogramin A compounds, thus inactivating virginiamycin-like antibiotics and conferring resistance to these compounds.","category_aro_class_name":"AMR Gene Family"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"virginiamycin M1","category_aro_description":"Virginiamycin M1 is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37016":{"category_aro_accession":"3000672","category_aro_cvterm_id":"37016","category_aro_name":"madumycin II","category_aro_description":"Madumycin II is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37017":{"category_aro_accession":"3000673","category_aro_cvterm_id":"37017","category_aro_name":"griseoviridin","category_aro_description":"Griseoviridin is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35952":{"category_aro_accession":"0000034","category_aro_cvterm_id":"35952","category_aro_name":"streptogramin A antibiotic","category_aro_description":"Streptogramin A antibiotics are cyclic polyketide peptide hybrids that bind to the ribosomal peptidyl transfer centre. Structural variation arises from substituting a proline for its desaturated derivative and by its substitution for Ala or Cys. Used alone, streptogramin A antibiotics are bacteriostatic, but is bactericidal when used with streptogramin B antibiotics.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1736":{"model_id":"1736","model_name":"GES-24","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1555":{"protein_sequence":{"accession":"BAP75641.1","sequence":"MRFIHALLLAGIAHSAYASEKLTFKTDLEKLEREKAAQIGVAIVDPQGEIVAGHRTAQRFAMCSTFKFPLAALVFERIDSGTERGDRKLSYGPDMIVEWSPATERFLASGHMTVLEAAQAAVQLSDNGATNLLLREIGGPAAMTQYFRKIGDSVSRLDRKEPEMSDNTPGDLRDTTTPIAMARTVAKVLYGGALTSTSTHTIERWLIGNQTGDATLRAGFPKDWVVGEKTGTCANGGRNDIGFFKAQERDYAVAVYTTAPKLSAVERDELVASVGQVITQLILSTDK"},"dna_sequence":{"accession":"AB901141.1","fmin":"0","fmax":"864","strand":"+","sequence":"ATGCGCTTCATTCACGCACTATTACTGGCAGGGATCGCTCACTCTGCATATGCGTCGGAAAAATTAACCTTCAAGACCGATCTTGAGAAGCTAGAGCGCGAAAAAGCAGCTCAGATCGGTGTTGCGATCGTCGATCCCCAAGGAGAGATCGTCGCGGGCCACCGAACGGCGCAGCGCTTTGCAATGTGCTCAACGTTCAAGTTTCCGCTAGCCGCGCTGGTCTTTGAAAGAATTGACTCAGGCACCGAGCGGGGGGATCGAAAACTTTCATATGGGCCGGACATGATCGTCGAATGGTCTCCTGCCACGGAGCGGTTTCTAGCATCGGGACACATGACGGTTCTCGAGGCAGCGCAAGCTGCGGTGCAGCTTAGCGACAATGGGGCTACTAACCTCTTACTGAGAGAAATTGGCGGACCTGCTGCAATGACGCAGTATTTTCGTAAAATTGGCGACTCTGTGAGTCGGCTAGACCGGAAAGAGCCGGAGATGAGCGACAACACACCTGGCGACCTCAGAGATACAACTACGCCTATTGCTATGGCACGTACTGTGGCTAAAGTCCTCTATGGCGGCGCACTGACGTCCACCTCGACCCACACCATTGAGAGGTGGCTGATCGGAAACCAAACGGGAGACGCGACACTACGAGCGGGTTTTCCTAAAGATTGGGTTGTTGGAGAGAAAACTGGTACCTGCGCCAACGGGGGCCGGAACGACATTGGTTTTTTTAAAGCCCAGGAGAGAGATTACGCTGTAGCGGTGTATACAACGGCCCCGAAACTATCGGCCGTAGAACGTGACGAATTAGTTGCCTCTGTCGGTCAAGTTATTACACAACTCATCCTGAGCACGGACAAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3002353","ARO_id":"38753","ARO_name":"GES-24","CARD_short_name":"GES-24","ARO_description":"GES-24 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36205":{"category_aro_accession":"3000066","category_aro_cvterm_id":"36205","category_aro_name":"GES beta-lactamase","category_aro_description":"GES beta-lactamases or Guiana extended-spectrum beta-lactamases are related to the other plasmid-located class A beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1737":{"model_id":"1737","model_name":"ANT(4')-Ia","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8650":{"protein_sequence":{"accession":"AAA92254.1","sequence":"MNGPIIMTREERMKIVHEIKERILDKYGDDVKAIGVYGSLGRQTDGPYSDIEMMCVMSTEEAEFSHEWTTGEWKVEVNFDSEEILLDYASQVESDWPLTHGQFFSILPIYDSGGYLEKVYQTAKSVEAQKFHDAICALIVEELFEYAGKWRNIRVQGPTTFLPSLTVQVAMAGAMLIGLHHRICYTTSASVLTEAVKQSDLPSGYDHLCQFVMSGQLSDSEKLLESLENFWNGIQEWTERHGYIVDVSKRIPF"},"dna_sequence":{"accession":"K02551.1","fmin":"240","fmax":"1002","strand":"+","sequence":"GTGAATGGACCAATAATAATGACTAGAGAAGAAAGAATGAAGATTGTTCATGAAATTAAGGAACGAATATTGGATAAATATGGGGATGATGTTAAGGCTATTGGTGTTTATGGCTCTCTTGGTCGTCAGACTGATGGGCCCTATTCGGATATTGAGATGATGTGTGTCATGTCAACAGAGGAAGCAGAGTTCAGCCATGAATGGACAACCGGTGAGTGGAAGGTGGAAGTGAATTTTGATAGCGAAGAGATTCTACTAGATTATGCATCTCAGGTGGAATCAGATTGGCCGCTTACACATGGTCAATTTTTCTCTATTTTGCCGATTTATGATTCAGGTGGATACTTAGAGAAAGTGTATCAAACTGCTAAATCGGTAGAAGCCCAAAAGTTCCACGATGCGATTTGTGCCCTTATCGTAGAAGAGCTGTTTGAATATGCAGGCAAATGGCGTAATATTCGTGTGCAAGGACCGACAACATTTCTACCATCCTTGACTGTACAGGTAGCAATGGCAGGTGCCATGTTGATTGGTCTGCATCATCGCATCTGTTATACGACGAGCGCTTCGGTCTTAACTGAAGCAGTTAAGCAATCAGATCTTCCTTCAGGTTATGACCATCTGTGCCAGTTCGTAATGTCTGGTCAACTTTCCGACTCTGAGAAACTTCTGGAATCGCTAGAGAATTTCTGGAATGGGATTCAGGAGTGGACAGAACGACACGGATATATAGTGGATGTGTCAAAACGCATACCATTTTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"46192","NCBI_taxonomy_name":"Plasmid pTB913","NCBI_taxonomy_id":"2641"}}}},"ARO_accession":"3002623","ARO_id":"39023","ARO_name":"ANT(4')-Ia","CARD_short_name":"ANT(4')-Ia","ARO_description":"ANT(4')-Ia is a plasmid-encoded aminoglycoside nucleotidyltransferase in S. epidermidis, S. aureus, Enterococcus spp. and Bacillus spp.","ARO_category":{"36368":{"category_aro_accession":"3000229","category_aro_cvterm_id":"36368","category_aro_name":"ANT(4')","category_aro_description":"A category of aminoglycoside O-nucleotidyltransferase enzymes with modification regiospecificity based at the 4'-hydroxyl group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics by transfer of an AMP group from an ATP substrate to the 4-hydroxyl group of the compound.","category_aro_class_name":"AMR Gene Family"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1738":{"model_id":"1738","model_name":"CTX-M-45","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1981":{"protein_sequence":{"accession":"BAA28282.1","sequence":"MVTKRVQRMMSAAAACIPLLLGSPTLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTARAGADVASLRWVMRWAKPSGAVGDVAQRQYDRAAGIRAGLPTSWTVGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"D89862.1","fmin":"111","fmax":"981","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTCCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCCCAACGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCTTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGGCGCGGGCTGGCGCAGACGTTGCGTCATTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGCGCAGCCGGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGACTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001907","ARO_id":"38307","ARO_name":"CTX-M-45","CARD_short_name":"CTX-M-45","ARO_description":"CTX-M-45 is a beta-lactamase found in Escherichia coli.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1739":{"model_id":"1739","model_name":"SHV-16","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"8247":{"protein_sequence":{"accession":"AAC98092.2","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKITHRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AF072684.2","fmin":"117","fmax":"993","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCACTCATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTACTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001075","ARO_id":"37455","ARO_name":"SHV-16","CARD_short_name":"SHV-16","ARO_description":"SHV-16 is an extended-spectrum beta-lactamase that has been found in clinical isolates. It differs from SHV-1 by a 163DRWET167 insertion.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1740":{"model_id":"1740","model_name":"TEM-53","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1886":{"protein_sequence":{"accession":"AAD22538.1","sequence":"MSIQHFRVALIPFFAAFCFPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDSWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AF104441.1","fmin":"193","fmax":"1054","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCTTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATAGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3000922","ARO_id":"37302","ARO_name":"TEM-53","CARD_short_name":"TEM-53","ARO_description":"TEM-53 is an extended-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1741":{"model_id":"1741","model_name":"OXA-359","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1763":{"protein_sequence":{"accession":"AGZ83155.1","sequence":"MYKKAFIVATSLLFLSACSSNTVEQHQIYSISANKNSEEIKSLFDQAQTTGVLVIKRGQTEEIYGNDLKRASTEYVPASIFKMLNALIGLEHHKATATEVFKWDGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMSKEVKRIGFGNANIGSKVDNFWLVGPLKITPQQEAQFAYQLAHKTLPFSKDVQEQVQSMVFIEEKNGRKIYAKSGWGWDVEPQVGWLTGWVIQPQGEIVAFSLNLEMKKGTPSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"KF421162.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGTATAAAAAAGCCTTTATCGTTGCAACAAGCCTCCTATTTTTATCTGCCTGTTCTTCTAATACGGTGGAACAACATCAAATATATTCTATTTCTGCCAATAAAAATTCAGAAGAAATTAAATCGCTGTTTGATCAAGCACAGACCACGGGTGTTTTGGTTATTAAGCGAGGGCAAACAGAAGAAATTTATGGCAATGATCTTAAAAGAGCATCAACTGAATATGTTCCAGCTTCTATTTTTAAAATGTTAAATGCTTTAATTGGACTTGAACACCATAAGGCAACTGCAACTGAAGTGTTTAAATGGGATGGGCAAAAACGTTTATTTCCTGATTGGGAAAAAGATATGACGCTGGGCGATGCCATGAAAGCTTCTGCTATTCCGGTCTATCAAGAATTAGCCCGACGAATTGGTCTGGATCTTATGTCTAAAGAGGTGAAACGAATTGGTTTCGGTAATGCCAATATTGGCTCAAAAGTAGATAATTTTTGGCTTGTTGGTCCACTAAAAATCACACCTCAACAAGAAGCCCAGTTTGCTTATCAATTGGCCCATAAAACACTTCCATTTAGCAAAGATGTACAAGAACAAGTTCAATCAATGGTGTTCATAGAGGAAAAGAATGGACGTAAAATTTATGCTAAAAGTGGTTGGGGATGGGATGTTGAACCGCAAGTTGGTTGGTTAACAGGCTGGGTCATTCAACCACAAGGAGAAATTGTCGCATTCTCACTGAATTTAGAAATGAAAAAAGGAACTCCTAGCTCTATTCGCAAAGAAATTGCTTATAAAGGCTTAGAACAACTGGGTATCTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39094","NCBI_taxonomy_name":"Acinetobacter calcoaceticus","NCBI_taxonomy_id":"471"}}}},"ARO_accession":"3001546","ARO_id":"37946","ARO_name":"OXA-359","CARD_short_name":"OXA-359","ARO_description":"OXA-359 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46495":{"category_aro_accession":"3007706","category_aro_cvterm_id":"46495","category_aro_name":"OXA-213-like beta-lactamase","category_aro_description":"OXA-213-like enzymes have been identified to be intrinsic to A. calcoaceticus and have been subsequently detected in A. pittii. Phylogenetic analysis of OXA-213-like proteins identified two distinct subgroups within the OXA family. The first group was linked to A. pittii and the second group to A. calcoaceticus. The carbapenemase activity of these OXAs may be related to the species-dependent effect.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1742":{"model_id":"1742","model_name":"SHV-28","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1946":{"protein_sequence":{"accession":"AAG15384.1","sequence":"MRFIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AF299299.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTTTATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACATCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGAGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATCGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001086","ARO_id":"37466","ARO_name":"SHV-28","CARD_short_name":"SHV-28","ARO_description":"SHV-28 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1743":{"model_id":"1743","model_name":"OXA-338","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1841":{"protein_sequence":{"accession":"AHN07454.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"KF048909.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAATATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGACGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAACGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001526","ARO_id":"37926","ARO_name":"OXA-338","CARD_short_name":"OXA-338","ARO_description":"OXA-338 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1744":{"model_id":"1744","model_name":"cmrA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"699":{"protein_sequence":{"accession":"AAC45805.1","sequence":"MPFAIYVLGLAVFAQGTSEFMLSGLIPDMARDLGVSVPAAGLLTSAFAVGMIIGAPLMAIASMRWPRRRALLTFLITFMLVHVIGALTSSFEVLLVTRIVGALANAGFLAVALGAAMAMVPADMKGRATSVLLGGVTIACVAGVPGGAFLGEIWGWRAAFWAVVVISAPAVVAIMFATPAEPPAESTPNAKRELSSLRSRKLQLMLVLGALINGATFCSFTYMAPTLTDISGFDSRWIPLLLGLFGLGSFIGVSVGGRLADTRPFQLLAVGSAALLTGWIVFALTASHPAVTLVMLFVQGALSFAVGSTLISQVLYAADAAPTLGGSFATAAFNVGAALGPALGGLAIGMGLSYRAPLWTSAALVTLAIVIGAATLSLWRRPASVQETVPA"},"dna_sequence":{"accession":"AF015087.1","fmin":"435","fmax":"1611","strand":"+","sequence":"GTGCCTTTCGCTATCTACGTCCTCGGGCTTGCCGTCTTTGCCCAGGGCACATCCGAATTCATGTTGTCCGGGCTCATACCGGATATGGCCCGCGACCTCGGCGTCTCGGTCCCCGCCGCCGGACTCCTCACCTCCGCCTTCGCGGTCGGGATGATCATCGGCGCTCCGCTGATGGCCATCGCCAGCATGCGGTGGCCCCGGCGACGCGCCCTTTTGACATTCCTCATCACGTTCATGCTGGTCCACGTCATCGGCGCGCTCACCAGCAGCTTCGAGGTCTTGCTGGTCACACGCATCGTCGGCGCCCTCGCCAACGCCGGATTCTTGGCGGTGGCCCTGGGCGCGGCGATGGCGATGGTGCCCGCCGACATGAAAGGGCGCGCAACGTCCGTCCTCCTCGGTGGTGTCACGATCGCATGTGTAGCCGGAGTTCCCGGGGGCGCCTTCCTCGGTGAAATATGGGGCTGGCGTGCAGCGTTCTGGGCTGTCGTCGTCATCTCCGCCCCTGCGGTGGTGGCGATCATGTTCGCCACCCCGGCCGAGCCGCCAGCAGAGTCCACACCGAACGCCAAGCGTGAACTGTCCTCGCTGCGCTCACGCAAGCTCCAGCTGATGCTTGTCCTCGGTGCCCTGATCAACGGCGCAACATTCTGTTCGTTCACCTACATGGCGCCCACTCTCACCGACATCTCCGGTTTCGACTCCCGTTGGATTCCGTTGCTGCTGGGGTTGTTCGGGCTCGGATCGTTCATCGGCGTCAGCGTCGGAGGCAGGCTCGCCGATACCCGGCCGTTCCAACTTCTCGCCGTGGGATCCGCAGCACTGTTGACGGGATGGATCGTCTTCGCTCTCACGGCATCCCACCCTGCGGTGACATTGGTGATGCTGTTCGTGCAGGGCGCTCTGTCCTTCGCGGTCGGCTCGACCTTGATCTCCCAGGTGCTCTACGCCGCCGACGCGGCGCCGACCTTGGGTGGATCGTTCGCGACGGCCGCGTTCAACGTCGGCGCTGCACTGGGCCCGGCCCTCGGCGGGCTGGCGATCGGTATGGGCCTGAGCTACCGCGCCCCGCTCTGGACGAGCGCCGCGCTGGTGACTCTCGCGATCGTCATCGGCGCAGCCACCTTGTCGCTCTGGCGGCGTCCAGCGTCCGTCCAGGAAACCGTCCCAGCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39553","NCBI_taxonomy_name":"Rhodococcus rhodochrous","NCBI_taxonomy_id":"1829"}}}},"ARO_accession":"3002702","ARO_id":"39136","ARO_name":"cmrA","CARD_short_name":"cmrA","ARO_description":"cmrA is a transposon-encoded chloramphenicol exporter that is found in Rhodococcus rhodochrous.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1746":{"model_id":"1746","model_name":"IMP-24","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1907":{"protein_sequence":{"accession":"ABM68358.1","sequence":"MKKLFVLCVCFLCSITAAGAALPDLKIEKLEEGVYVHTSFEEVNGWGVVSKHGLVVLVNTDAYLIDTPFTATDTEKLVNWFVERGYKIKGTISSHFHSDSTGGIEWLNSQSIPTYASELTNELLKKDGKVQAKNSFSGVSYWLVKNKIEVFYPGPGHTQDNVVVWLPEKKILFGGCFVKPDGLGNLGDANLEAWPKSAKILMSKYGKAKLVVSSHSEIGDASLLKRTWEQAVKGLNESRKPSQPSN"},"dna_sequence":{"accession":"EF192154.1","fmin":"0","fmax":"741","strand":"+","sequence":"ATGAAGAAATTATTTGTTTTATGTGTATGCTTCCTTTGTAGCATTACTGCCGCAGGAGCGGCTTTGCCTGATTTAAAAATCGAGAAGCTTGAAGAAGGTGTTTATGTTCATACATCGTTCGAAGAAGTTAACGGTTGGGGTGTTGTTTCTAAACACGGTTTGGTGGTTCTTGTAAACACTGACGCCTATCTGATTGACACTCCATTTACTGCTACAGATACTGAAAAGTTAGTCAATTGGTTTGTGGAGCGCGGCTATAAAATCAAAGGCACTATTTCCTCACATTTCCATAGCGACAGCACAGGGGGAATAGAGTGGCTTAATTCTCAATCTATTCCCACGTATGCATCTGAATTAACAAATGAACTTCTTAAAAAAGACGGTAAGGTGCAAGCTAAAAACTCATTTAGCGGAGTTAGTTATTGGCTAGTTAAAAATAAAATTGAAGTTTTTTATCCCGGCCCGGGGCACACTCAAGATAACGTAGTGGTTTGGTTACCTGAAAAGAAAATTTTATTCGGTGGTTGTTTTGTTAAACCGGACGGTCTTGGTAATTTGGGTGACGCAAATTTAGAAGCTTGGCCAAAGTCCGCCAAAATATTAATGTCTAAATATGGTAAAGCAAAACTGGTTGTTTCAAGTCATAGTGAAATTGGGGACGCATCACTCTTGAAACGTACATGGGAACAGGCTGTTAAAGGGCTAAATGAAAGTAGAAAACCATCACAGCCAAGTAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36783","NCBI_taxonomy_name":"Serratia marcescens","NCBI_taxonomy_id":"615"}}}},"ARO_accession":"3002215","ARO_id":"38615","ARO_name":"IMP-24","CARD_short_name":"IMP-24","ARO_description":"IMP-24 is a beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1747":{"model_id":"1747","model_name":"CMY-103","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1441":{"protein_sequence":{"accession":"AHA80104.1","sequence":"MMKKSICCALLLTASFSTFAATKTEQQIADIVNRTITPLMQEQAIPGMAVAIIYEEKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWRGISLLHLATYTAGGLPLQIPDEVTDKAALLRFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQSEQKNYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQGKTLQQGIELAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPARVEAAWRILEKLQ"},"dna_sequence":{"accession":"KF526116.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGATATGCTGCGCGCTGCTGCTGACAGCCTCTTTCTCCACGTTTGCTGCCACAAAAACAGAACAACAAATTGCCGATATCGTTAACCGCACCATCACACCACTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTGGCGATTATCTACGAGGAGAAACCTTATTACTTTACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAATTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGACGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCGGGGTATCAGCCTGCTGCACTTAGCCACCTATACAGCGGGTGGCCTACCGCTGCAGATCCCCGATGAAGTTACGGATAAAGCCGCATTACTGCGCTTTTATCAAAACTGGCAACCACAATGGACTCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGTGCGCTGGCGGTGAAACCTTCAGGTATGAGCTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAAAGCGAACAAAAAAATTATGCCTGGGGCTATCGCGAAGGGAAGCCTGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATCGATATGGCCCGCTGGGTTCAGGCCAACATGGACGCCAGCCACGTTCAAGGGAAAACGCTCCAGCAGGGCATTGAGCTTGCGCAGTCTCGTTACTGGCGTATTGGTGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCAGCACCTGCCGTGAAAGCCTCATGGGTGCATAAAACGGGATCCACAGGTGGATTTGGCAGCTACGTTGCCTTCGTTCCAGAAAAAAACCTTGGCATAGTGATGCTGGCAAACAAAAGCTACCCCAACCCGGCTCGCGTCGAGGCGGCCTGGCGCATTCTTGAAAAACTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002115","ARO_id":"38515","ARO_name":"CMY-103","CARD_short_name":"CMY-103","ARO_description":"CMY-103 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1748":{"model_id":"1748","model_name":"lsaC","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"960"}},"model_sequences":{"sequence":{"76":{"protein_sequence":{"accession":"AEA37904.1","sequence":"MSTIKIENLTFSYYGYVKPVFENVSFSFDTNWKTGLIGRNGIGKSTLFKLLLNQEVYKGKISKSVDFIKFPPNLSDTSKLGIELYRELISDEEEWKLFRELHLLKVDESLIYRKFETLSKGEQTKILLAILFTREDGFLLIDEPTNHLDMDGRKIVSEYLKNKKGFLLISHDRDFLDGCINHIISINRNSIDVQSGNFTSWYENKLMKDQFEISQNEKLRKDIKRLKEAARQSQIWSDKVENTKNGVKVSGVKPDKGHIGHQSAKMMKKSKNLENRQNKAIEEKQNLLKDIETKESLLLHPLHHHKNPLISVCDLSSYYGKKQILSNISFDIKQGDIVAIYGGNGSGKSTLIKILLGLNHEYSGDVKLASNLKISYVPQDTSNLTGSLNEYIHKQGVDETLCKTILRKLDFARELFEIDMKNYSDGQKKKVLIAVSLSKSAHIFIWDEPLNYLDVISRIQIEEIIKEANPTLIFVEHDKSFVEDIANKIIRL"},"dna_sequence":{"accession":"HM990671.1","fmin":"5192","fmax":"6671","strand":"+","sequence":"ATGTCAACAATTAAAATTGAAAACCTTACTTTCTCATATTATGGCTATGTAAAACCTGTATTTGAAAATGTATCATTTTCATTTGATACGAACTGGAAAACAGGACTAATAGGAAGAAACGGAATTGGGAAATCAACACTATTTAAGCTGCTTCTAAACCAAGAAGTTTATAAGGGGAAAATCAGCAAAAGTGTTGACTTTATTAAATTCCCACCCAATTTAAGTGATACTTCAAAATTAGGGATTGAGTTATATAGAGAACTAATATCAGATGAGGAAGAATGGAAATTATTTAGAGAACTTCATTTGCTAAAGGTAGATGAGAGTCTTATTTACAGAAAGTTTGAAACGCTTTCTAAAGGAGAACAAACAAAAATCCTTTTAGCTATTTTGTTTACAAGAGAAGATGGTTTTTTACTTATAGATGAACCAACAAACCATTTAGATATGGACGGAAGAAAAATTGTCAGTGAATATCTGAAAAATAAAAAAGGTTTTTTGCTTATATCACATGATAGAGATTTTTTAGATGGTTGTATCAATCATATTATTTCTATTAACAGGAATTCTATTGATGTCCAATCAGGAAATTTTACATCGTGGTATGAAAATAAATTGATGAAAGACCAATTTGAGATTAGTCAAAATGAGAAATTAAGAAAAGATATTAAACGATTAAAAGAAGCTGCAAGACAAAGTCAAATTTGGTCTGATAAAGTTGAAAATACTAAAAACGGCGTGAAAGTATCAGGTGTAAAACCAGACAAGGGGCATATAGGTCATCAGTCAGCTAAGATGATGAAAAAATCTAAGAATTTGGAGAATAGACAAAATAAGGCAATAGAAGAAAAACAGAATTTACTAAAAGATATTGAAACAAAGGAAAGTCTATTATTGCATCCGTTACATCACCACAAAAATCCTCTAATATCAGTTTGCGATTTATCATCATATTATGGAAAAAAGCAGATATTAAGTAATATAAGTTTTGATATAAAGCAAGGTGATATAGTGGCTATATATGGGGGTAATGGTAGCGGAAAATCAACCTTGATTAAAATTTTATTAGGTCTAAATCACGAGTATTCAGGTGATGTAAAATTAGCAAGTAATTTAAAAATATCATATGTTCCTCAAGATACATCCAATTTAACAGGTAGCCTAAACGAGTATATTCATAAGCAAGGTGTTGATGAAACATTGTGCAAAACAATTCTTAGAAAATTAGATTTTGCAAGAGAATTATTTGAAATAGATATGAAGAACTATAGCGATGGACAAAAAAAGAAAGTTTTAATTGCTGTAAGTTTGTCAAAGTCAGCTCATATATTTATTTGGGACGAACCACTGAATTATTTAGATGTAATATCAAGAATACAGATTGAGGAAATTATAAAAGAAGCAAATCCTACACTCATATTTGTGGAACACGATAAGAGTTTTGTAGAAGATATAGCGAATAAAATAATACGATTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36847","NCBI_taxonomy_name":"Streptococcus agalactiae","NCBI_taxonomy_id":"1311"}}}},"ARO_accession":"3003112","ARO_id":"39688","ARO_name":"lsaC","CARD_short_name":"lsaC","ARO_description":"LsaC is an ABC-F subfamily protein expressed in Streptococcus agalactiae. It confers resistance to lincomycin, clindamycin, dalfopristin, and tiamulin.","ARO_category":{"41696":{"category_aro_accession":"3004472","category_aro_cvterm_id":"41696","category_aro_name":"lsa-type ABC-F protein","category_aro_description":"A subgroup of the ABC-F protein subfamily of ATP-binding cassette proteins. lsa-type ABC-F proteins confer resistance to streptogramin, lincosamide and pleuromutilin antibiotics through antibiotic target protection of the ribosome.","category_aro_class_name":"AMR Gene Family"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"37716":{"category_aro_accession":"3001317","category_aro_cvterm_id":"37716","category_aro_name":"pleuromutilin","category_aro_description":"Pleuromutilin is a natural product antibiotic produced by Clitopilus passeckerianus. Related antibiotics of clinical significance, such as tiamulin and retapamulin, are semi-synthetic derivatives of this compound.","category_aro_class_name":"Antibiotic"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"37014":{"category_aro_accession":"3000670","category_aro_cvterm_id":"37014","category_aro_name":"pleuromutilin antibiotic","category_aro_description":"Pleuromutilins are natural fungal products that target bacterial protein translation by binding the the 23S rRNA, blocking the ribosome P site at the 50S subunit. They are mostly used for agriculture and veterinary purposes.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1749":{"model_id":"1749","model_name":"IMP-18","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"912":{"protein_sequence":{"accession":"AEQ73520.1","sequence":"MKKLFVLCVFFLCNIAAADDSLPDLKIEKLEKGVYVHTSFEEVKGWGVVTKHGLVVLVKNDAYLIDTPITAKDTEKLVNWFIEHGYRIKGSISTHFHGDSTAGIEWLNSQSISTYASELTNELLKKDNKVQATNSFSGVSYSLIKNKIEVFYPGPGHTQDNVVVWLPEKKILFGGCFVKPDGLGNLGDANLEAWPKSAKILMSKYGKAKLVVSSHSEIGNASLLQRTWEQAVKGLNESKKPLQPSS"},"dna_sequence":{"accession":"JN596991.1","fmin":"482","fmax":"1223","strand":"+","sequence":"ATGAAAAAATTATTTGTTTTATGTGTATTCTTCCTTTGCAACATTGCTGCTGCAGATGATTCTTTGCCTGATTTAAAAATTGAGAAGCTTGAAAAAGGCGTTTATGTTCATACTTCGTTTGAAGAAGTTAAAGGTTGGGGTGTAGTCACAAAACACGGTTTAGTGGTTCTTGTAAAGAATGATGCTTATCTGATAGATACTCCAATTACCGCTAAAGATACTGAAAAATTAGTTAATTGGTTTATTGAGCACGGCTATAGAATCAAAGGCAGTATTTCCACACATTTCCATGGCGACAGTACGGCTGGAATAGAGTGGCTTAATTCTCAATCTATCTCCACGTATGCCTCTGAATTAACAAATGAACTTCTAAAAAAAGACAATAAGGTGCAAGCTACAAATTCTTTTAGTGGAGTTAGTTATTCACTTATCAAAAACAAAATTGAAGTTTTCTATCCAGGTCCAGGACACACTCAAGATAACGTAGTGGTTTGGTTACCTGAAAAGAAAATTTTATTCGGTGGTTGCTTTGTTAAACCGGACGGTCTTGGAAATTTAGGGGATGCAAATTTAGAAGCTTGGCCAAAGTCCGCTAAAATATTAATGTCTAAATATGGTAAAGCAAAACTGGTTGTTTCAAGTCATAGTGAAATTGGAAACGCATCACTCTTGCAACGCACATGGGAGCAGGCTGTTAAAGGGTTAAATGAAAGTAAAAAACCGTTACAGCCAAGTAGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002209","ARO_id":"38609","ARO_name":"IMP-18","CARD_short_name":"IMP-18","ARO_description":"IMP-18 is a beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1750":{"model_id":"1750","model_name":"OXA-254","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1530":{"protein_sequence":{"accession":"BAN10684.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDVKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAITVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"AB781687.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGTAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTACAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAACAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001682","ARO_id":"38082","ARO_name":"OXA-254","CARD_short_name":"OXA-254","ARO_description":"OXA-254 is a beta-lactamase found in A. baumannii.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1751":{"model_id":"1751","model_name":"Erm(33)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"5165":{"protein_sequence":{"accession":"CAC86410.1","sequence":"MNKKNIKDSQNFITSKRNIDKIMTNISLNEHDNIFEIGSGKGHFTLELVQRCNFVTAIEIDHKLCKTTENKLVDHDNFQVLNKDILQFKFPKNQSYNIFGNIPYNISTDIVKRITFESQAKYSYLIVEKGFAKRLQNLQRALGLLLMVEMDIKMLKKVPPLYFHPKPSVDSVLIVLERHQPLISKKDYKKYRSFVYKWVNREYRVLFTKNQFRQALKHANVTNINKLSKEQFLSIFNSYKLFH"},"dna_sequence":{"accession":"AJ313523.1","fmin":"162","fmax":"894","strand":"+","sequence":"ATGAACAAAAAAAATATAAAAGACAGTCAAAACTTTATTACTTCGAAACGTAATATAGATAAAATAATGACAAATATAAGCTTAAATGAACATGATAATATCTTTGAAATTGGCTCAGGAAAAGGGCATTTTACCCTTGAATTAGTACAAAGGTGTAATTTCGTAACTGCTATTGAAATAGACCATAAATTATGCAAGACTACAGAAAATAAACTTGTTGATCACGATAATTTTCAAGTTTTAAACAAGGATATATTGCAGTTTAAATTTCCTAAAAACCAATCCTATAATATATTTGGTAATATTCCTTATAACATCAGTACGGATATTGTCAAAAGAATTACCTTTGAAAGTCAGGCTAAATATAGCTATCTTATCGTTGAGAAGGGATTTGCGAAAAGATTGCAAAATCTGCAACGAGCTTTGGGTTTACTATTAATGGTGGAGATGGATATAAAAATGCTCAAAAAAGTACCACCACTATATTTTCATCCTAAGCCAAGTGTAGACTCTGTATTGATTGTTCTTGAACGACATCAACCATTGATTTCAAAGAAGGACTACAAAAAGTATCGATCTTTTGTTTATAAGTGGGTAAACCGTGAATATCGTGTTCTTTTCACTAAAAACCAATTCCGACAGGCTTTGAAGCATGCAAATGTCACTAATATTAATAAACTATCGAAGGAACAATTTCTTTCTATTTTCAATAGTTACAAATTGTTTCACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36794","NCBI_taxonomy_name":"Mammaliicoccus sciuri","NCBI_taxonomy_id":"1296"}}}},"ARO_accession":"3000599","ARO_id":"36738","ARO_name":"Erm(33)","CARD_short_name":"Erm(33)","ARO_description":"ErmD confers MLSb phenotype.","ARO_category":{"36699":{"category_aro_accession":"3000560","category_aro_cvterm_id":"36699","category_aro_name":"Erm 23S ribosomal RNA methyltransferase","category_aro_description":"Erm proteins are part of the RNA methyltransferase family and methylate A2058 (E. coli nomenclature) of the 23S ribosomal RNA conferring degrees of resistance to Macrolides, Lincosamides and Streptogramin b. This is called the MLSb phenotype.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35946":{"category_aro_accession":"0000027","category_aro_cvterm_id":"35946","category_aro_name":"roxithromycin","category_aro_description":"Roxithromycin is a semi-synthetic, 14-carbon ring macrolide antibiotic derived from erythromycin. It is used to treat respiratory tract, urinary and soft tissue infections. Roxithromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35974":{"category_aro_accession":"0000057","category_aro_cvterm_id":"35974","category_aro_name":"telithromycin","category_aro_description":"Telithromycin is a semi-synthetic derivative of erythromycin. It is a 14-membered macrolide and is the first ketolide antibiotic to be used in clinics. Telithromycin binds the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"35982":{"category_aro_accession":"0000065","category_aro_cvterm_id":"35982","category_aro_name":"clarithromycin","category_aro_description":"Clarithromycin is a methyl derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome and is used to treat pharyngitis, tonsillitis, acute maxillary sinusitis, acute bacterial exacerbation of chronic bronchitis, pneumonia (especially atypical pneumonias associated with Chlamydia pneumoniae or TWAR), and skin structure infections.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"36284":{"category_aro_accession":"3000145","category_aro_cvterm_id":"36284","category_aro_name":"tylosin","category_aro_description":"Tylosin is a 16-membered macrolide, naturally produced by Streptomyces fradiae. It interacts with the bacterial ribosome 50S subunit to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"36295":{"category_aro_accession":"3000156","category_aro_cvterm_id":"36295","category_aro_name":"spiramycin","category_aro_description":"Spiramycin is a 16-membered macrolide and is natural product produced by Streptomyces ambofaciens. It binds to the 50S subunit of bacterial ribosomes and inhibits peptidyl transfer activity to disrupt protein synthesis.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"36315":{"category_aro_accession":"3000176","category_aro_cvterm_id":"36315","category_aro_name":"dirithromycin","category_aro_description":"Dirithromycin is an oxazine derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome to inhibit bacterial protein synthesis.","category_aro_class_name":"Antibiotic"},"36722":{"category_aro_accession":"3000583","category_aro_cvterm_id":"36722","category_aro_name":"pristinamycin IA","category_aro_description":"Pristinamycin IA is a type B streptogramin antibiotic produced by Streptomyces pristinaespiralis. It binds to the P site of the 50S subunit of the bacterial ribosome, preventing the extension of protein chains.","category_aro_class_name":"Antibiotic"},"36723":{"category_aro_accession":"3000584","category_aro_cvterm_id":"36723","category_aro_name":"quinupristin","category_aro_description":"Quinupristin is a type B streptogramin and a semisynthetic derivative of pristinamycin 1A. It is a component of the drug Synercid and interacts with the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"virginiamycin M1","category_aro_description":"Virginiamycin M1 is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37016":{"category_aro_accession":"3000672","category_aro_cvterm_id":"37016","category_aro_name":"madumycin II","category_aro_description":"Madumycin II is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37017":{"category_aro_accession":"3000673","category_aro_cvterm_id":"37017","category_aro_name":"griseoviridin","category_aro_description":"Griseoviridin is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"37019":{"category_aro_accession":"3000675","category_aro_cvterm_id":"37019","category_aro_name":"pristinamycin IB","category_aro_description":"Pristinamycin IB is a class B streptogramin similar to pristinamycin IA, the former containing a N-methyl-4-(methylamino)phenylalanine instead of a N-methyl-4-(dimethylamino)phenylalanine in its class A streptogramin counterpart (one less methyl group).","category_aro_class_name":"Antibiotic"},"37021":{"category_aro_accession":"3000677","category_aro_cvterm_id":"37021","category_aro_name":"virginiamycin S2","category_aro_description":"Virginiamycin S2 is a streptogramin B antibiotic.","category_aro_class_name":"Antibiotic"},"37022":{"category_aro_accession":"3000678","category_aro_cvterm_id":"37022","category_aro_name":"pristinamycin IC","category_aro_description":"Pristinamycin IC is a class B streptogramin derived from virginiamycin S1.","category_aro_class_name":"Antibiotic"},"37023":{"category_aro_accession":"3000679","category_aro_cvterm_id":"37023","category_aro_name":"vernamycin C","category_aro_description":"Vernamycin C is a streptogramin B antibiotic.","category_aro_class_name":"Antibiotic"},"37024":{"category_aro_accession":"3000680","category_aro_cvterm_id":"37024","category_aro_name":"patricin A","category_aro_description":"Patricin A is a streptogramin B antibiotic.","category_aro_class_name":"Antibiotic"},"37025":{"category_aro_accession":"3000681","category_aro_cvterm_id":"37025","category_aro_name":"patricin B","category_aro_description":"Patricin B is a streptogramin B antibiotic.","category_aro_class_name":"Antibiotic"},"37026":{"category_aro_accession":"3000682","category_aro_cvterm_id":"37026","category_aro_name":"ostreogrycin B3","category_aro_description":"Ostreogrycin B3 is a derivative of pristinamycin IA, with an additional 3-hydroxy group on its 4-oxopipecolic acid.","category_aro_class_name":"Antibiotic"},"37247":{"category_aro_accession":"3000867","category_aro_cvterm_id":"37247","category_aro_name":"oleandomycin","category_aro_description":"Oleandomycin is a 14-membered macrolide produced by Streptomyces antibioticus. It is ssimilar to erythromycin, and contains a desosamine amino sugar and an oleandrose sugar. It targets the 50S ribosomal subunit to prevent protein synthesis.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35952":{"category_aro_accession":"0000034","category_aro_cvterm_id":"35952","category_aro_name":"streptogramin A antibiotic","category_aro_description":"Streptogramin A antibiotics are cyclic polyketide peptide hybrids that bind to the ribosomal peptidyl transfer centre. Structural variation arises from substituting a proline for its desaturated derivative and by its substitution for Ala or Cys. Used alone, streptogramin A antibiotics are bacteriostatic, but is bactericidal when used with streptogramin B antibiotics.","category_aro_class_name":"Drug Class"},"35967":{"category_aro_accession":"0000050","category_aro_cvterm_id":"35967","category_aro_name":"streptogramin B antibiotic","category_aro_description":"Streptogramin B antibiotics are are cyclic hepta- or hexa-depsipeptides.  Type B streptogramins block the peptide exit tunnel of the 50S bacterial ribosome. The general composition of group B streptogramins is 3-hydroxypicolinic acid-L-Thr-D-aminobutyric acid (or D-Ala)-L-Pro-L-Phe (or 4-N-,N-(dimethylamino)-L-Phe)-X-L-phenylglycine. Used alone, streptogramin B antibiotics are bacteriostatic, but is bactericidal when used with streptogramin A antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1753":{"model_id":"1753","model_name":"SHV-148","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"829":{"protein_sequence":{"accession":"AFQ23954.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQQ"},"dna_sequence":{"accession":"JX121115.1","fmin":"0","fmax":"858","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGCATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACAA","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001187","ARO_id":"37567","ARO_name":"SHV-148","CARD_short_name":"SHV-148","ARO_description":"SHV-148 is a beta-lactamase.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1754":{"model_id":"1754","model_name":"vanO","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"350"}},"model_sequences":{"sequence":{"675":{"protein_sequence":{"accession":"AHA41500.1","sequence":"MSRLKVGVIFGGASEEHPVSIKSAREVARSLDTEKYEPFWIGITTGGEWKLCDGPDADWENRSARPAVLSPDRSVHGLLVMEQGGYETVRLDLVFPVLHGKLGEDGAIQGLLELAGIPYVGCDIQGSAVCMDKALAYIVAKSAGIATPSFWVVAENEKVDADHLRYPVFVKPARSGSSFGVSKVTREDELPNALSAARQYDSKVLIEEAVAGSEIGCAVMGELFGLITGEVDRVDLSHGFFRIHQEDSPETGSENSTFIVPADISDESRRLVQETAKAIYRTLGCKGLARVDMFLTDDGRVVLNEVNTMPGMTSYSRYPRMMAAAGLPISDMIDRLISMTMHGKKR"},"dna_sequence":{"accession":"KF478993.1","fmin":"1539","fmax":"2580","strand":"+","sequence":"ATGAGCAGATTGAAGGTCGGGGTCATCTTCGGAGGGGCTTCCGAAGAACATCCCGTCTCCATCAAGTCGGCGCGAGAGGTGGCAAGAAGTCTCGACACGGAGAAGTACGAACCGTTCTGGATCGGCATCACGACCGGCGGCGAGTGGAAGCTCTGTGACGGCCCCGACGCGGATTGGGAGAATCGCAGCGCCCGTCCCGCCGTGCTGTCACCCGATCGAAGTGTGCACGGCCTGCTGGTCATGGAGCAGGGGGGCTACGAAACCGTGCGCCTCGACCTCGTCTTCCCCGTACTTCACGGCAAGCTCGGCGAAGACGGCGCGATCCAAGGCCTGTTGGAGCTCGCCGGCATCCCCTACGTCGGCTGCGACATCCAGGGCTCGGCTGTGTGCATGGACAAGGCCCTGGCCTACATCGTGGCCAAGAGCGCGGGAATCGCCACGCCGAGCTTTTGGGTTGTCGCGGAGAACGAGAAGGTCGACGCCGATCACCTTCGCTATCCGGTCTTCGTGAAGCCGGCCCGTTCGGGTTCATCTTTCGGCGTCAGCAAGGTCACCCGAGAAGACGAGCTGCCGAACGCGCTGAGCGCGGCGCGACAGTACGACTCGAAGGTCCTGATCGAAGAAGCCGTGGCCGGCAGCGAGATCGGCTGCGCGGTCATGGGTGAACTATTCGGCCTGATCACTGGGGAGGTGGACCGCGTCGACCTCTCGCACGGATTCTTCAGGATCCACCAGGAGGACTCACCCGAAACCGGATCGGAGAACTCGACGTTCATCGTTCCCGCCGACATCTCCGACGAATCGCGCCGGCTCGTCCAAGAGACCGCCAAGGCCATCTACCGCACCCTGGGCTGCAAGGGACTTGCCCGCGTTGACATGTTCCTCACCGACGACGGACGGGTGGTCCTCAACGAGGTCAACACCATGCCCGGCATGACGTCGTACAGCCGGTACCCGCGGATGATGGCCGCCGCGGGACTGCCGATCTCCGACATGATCGACCGGCTCATCTCGATGACAATGCACGGGAAGAAGCGATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36897","NCBI_taxonomy_name":"Rhodococcus hoagii","NCBI_taxonomy_id":"43767"}}}},"ARO_accession":"3002913","ARO_id":"39347","ARO_name":"vanO","CARD_short_name":"vanO","ARO_description":"VanO is a D-Ala-D-Ala ligase homolog that can synthesize D-Ala-D-Lac, an alternative substrate for peptidoglycan synthesis that reduces vancomycin binding affinity. It is associated with both vancomycin and teicoplanin resistance.","ARO_category":{"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"39340":{"category_aro_accession":"3002906","category_aro_cvterm_id":"39340","category_aro_name":"Van ligase","category_aro_description":"Van ligases synthesize alternative substrates for peptidoglycan synthesis that reduce vancomycin binding affinity.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1755":{"model_id":"1755","model_name":"CTX-M-23","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1411":{"protein_sequence":{"accession":"AAL99990.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAVAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTETTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGDYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTNGL"},"dna_sequence":{"accession":"AF488377.1","fmin":"62","fmax":"938","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGTCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGACGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGTGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACTTGGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGACGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGGGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGACTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCAACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001885","ARO_id":"38285","ARO_name":"CTX-M-23","CARD_short_name":"CTX-M-23","ARO_description":"CTX-M-23 is a beta-lactamase found in the Enterobacteriaceae family.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1756":{"model_id":"1756","model_name":"CMY-93","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1549":{"protein_sequence":{"accession":"AHM76768.1","sequence":"MMKKSICCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAIIYQGKPYYFTWGKADIANNRPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKFSDPVTHYWPELTGKQWQGISLLHLATYTAGGLPLQVPDDVTDKAALLRFYQNWQPQWAPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTKRVLRPLKLAHTWITVPQSEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMTRWVQANMDASQVQEKTLQQGIELAQSRYWRVGDMYQGLGWEMLNWPVKADSIISGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"KF992025.1","fmin":"1026","fmax":"2172","strand":"+","sequence":"ATGATGAAAAAATCGATATGCTGCGCGCTGCTGCTGACAGCTTCGTTCTCCACGTTTGCCGCCGCAAAAACAGAACAACAAATTGCCGATATCGTTAACCGCACCATCACACCGCTGATGCAGGAGCAGGCAATTCCGGGCATGGCCGTTGCGATTATCTATCAGGGGAAACCTTATTACTTTACCTGGGGTAAAGCCGATATCGCCAATAACCGTCCAGTCACTCAACAAACGCTGTTTGAACTCGGATCGGTCAGTAAAACGTTCAACGGTGTGCTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGTTCAGCGATCCGGTCACGCATTACTGGCCTGAACTGACTGGTAAGCAGTGGCAGGGTATCAGCCTGCTGCACTTAGCCACCTACACGGCAGGCGGCCTGCCGCTTCAGGTTCCGGACGACGTTACGGATAAAGCCGCGTTACTACGCTTTTATCAAAACTGGCAGCCGCAATGGGCCCCAGGCGCTAAACGTCTTTATGCTAACTCCAGCATTGGTCTGTTTGGTGCCCTGGCGGTCAAACCCTCAGGCATGAGCTACGAAGAGGCGATGACCAAACGCGTCCTGCGCCCCTTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAGCGAACAAAAAGATTATGCCTGGGGTTATCGCGAAGGAAAGCCAGTGCATGTATCCCCTGGCCAACTTGATGCCGAAGCCTACGGGGTGAAATCGAGCGTTATCGATATGACCCGTTGGGTTCAGGCCAACATGGACGCCAGCCAGGTTCAGGAGAAAACGCTCCAGCAGGGCATCGAGCTTGCGCAGTCACGTTACTGGCGTGTTGGCGATATGTACCAGGGCCTGGGCTGGGAGATGCTGAACTGGCCGGTGAAAGCCGACTCGATAATTAGCGGTAGCGACAGCAAAGTGGCACTGGCAGCGCTTCCTGCCGTTGAGGTAAACCCGCCCGCGCCTGCCGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGCGGATTCGGCAGCTACGTTGCTTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAGAGCTACCCAAACCCTGTTCGCGTCGAGGCCGCCTGGCGCATTCTTGAAAAACTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002106","ARO_id":"38506","ARO_name":"CMY-93","CARD_short_name":"CMY-93","ARO_description":"CMY-93 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1757":{"model_id":"1757","model_name":"emrA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"675"}},"model_sequences":{"sequence":{"411":{"protein_sequence":{"accession":"BAA16547.1","sequence":"MSANAETQTPQQPVKKSGKRKRLLLLLTLLFIIIAVAIGIYWFLVLRHFEETDDAYVAGNQIQIMSQVSGSVTKVWADNTDFVKEGDVLVTLDPTDARQAFEKAKTALASSVRQTHQLMINSKQLQANIEVQKIALAKAQSDYNRRVPLGNANLIGREELQHARDAVTSAQAQLDVAIQQYNANQAMILGTKLEDQPAVQQAATEVRNAWLALERTRIISPMTGYVSRRAVQPGAQISPTTPLMAVVPATNMWVDANFKETQIANMRIGQPVTITTDIYGDDVKYTGKVVGLDMGTGSAFSLLPAQNATGNWIKVVQRLPVRIELDQKQLEQYPLRIGLSTLVSVNTTNRDGQVLANKVRSTPVAVSTAREISLAPVNKLIDDIVKANAG"},"dna_sequence":{"accession":"AP009048.1","fmin":"2810082","fmax":"2811255","strand":"+","sequence":"ATGAGCGCAAATGCGGAGACTCAAACCCCGCAGCAACCGGTAAAGAAGAGCGGCAAACGTAAGCGTCTGCTCCTCCTTCTCACCTTGCTCTTTATAATTATTGCCGTAGCGATAGGGATTTATTGGTTTTTGGTACTGCGTCACTTCGAAGAAACCGATGACGCATACGTGGCAGGGAATCAAATTCAAATTATGTCTCAGGTGTCTGGCAGCGTGACGAAAGTCTGGGCCGATAACACCGATTTTGTAAAAGAAGGCGACGTGCTGGTCACTCTCGACCCGACAGATGCTCGCCAGGCGTTTGAAAAAGCCAAAACTGCACTGGCTTCCAGCGTTCGCCAAACCCACCAGCTGATGATTAACAGCAAGCAGTTGCAGGCGAATATTGAGGTGCAGAAAATCGCCCTCGCGAAAGCACAAAGCGACTACAACCGCCGTGTGCCGCTGGGCAATGCCAACCTGATTGGTCGCGAAGAGCTGCAACACGCCCGCGACGCCGTCACCAGTGCCCAGGCGCAACTGGACGTCGCGATTCAACAATACAATGCCAATCAGGCGATGATTCTGGGGACTAAACTGGAAGATCAGCCAGCCGTGCAACAGGCTGCCACCGAAGTACGTAACGCCTGGCTGGCGCTGGAGCGTACTCGTATTATCAGTCCGATGACCGGTTATGTCTCCCGCCGCGCGGTACAGCCTGGGGCGCAAATTAGCCCAACGACGCCGCTGATGGCGGTCGTTCCAGCCACCAATATGTGGGTGGATGCCAACTTTAAAGAGACGCAGATTGCCAATATGCGTATCGGTCAGCCGGTCACTATCACCACGGATATTTACGGCGATGATGTGAAATACACCGGTAAAGTGGTTGGTCTGGATATGGGCACAGGTAGCGCGTTCTCACTGCTTCCAGCGCAAAATGCGACCGGTAACTGGATCAAAGTCGTTCAGCGTCTGCCTGTGCGTATCGAACTGGACCAGAAACAGCTGGAGCAATATCCGCTGCGTATCGGTTTGTCCACGCTGGTGAGCGTCAATACCACTAACCGTGACGGTCAGGTACTGGCAAATAAAGTACGTTCCACTCCGGTAGCGGTAAGCACCGCGCGTGAAATCAGCCTGGCACCTGTCAATAAACTGATCGACGATATCGTAAAAGCTAACGCTGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36839","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. W3110","NCBI_taxonomy_id":"316407"}}}},"ARO_accession":"3000027","ARO_id":"36036","ARO_name":"emrA","CARD_short_name":"emrA","ARO_description":"EmrA is a membrane fusion protein, providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli, a Gram-negative bacterium.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1758":{"model_id":"1758","model_name":"OXA-326","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"974":{"protein_sequence":{"accession":"AGW16408.1","sequence":"MYKKAFIVATSILFLSACSSNTVKQHQIHSISANKNSEAIKSLFDQAQTTGVLVIKRGQTEEIYGNDLKRASTDYVPASTFKMLNALIGLEHHKVTTTEVFKWDGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMSKEVKRIGFGNANIGSKVDDFWLVGPLKITPQQETQFAYQLAHKTLPFSKNVQEQVQSMVFIEEKNGSKIYAKSGWGWDVEPQVGWLTGWVVQPQGEIVAFSLNLEMKKGTPSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"KF203100.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGTATAAAAAAGCCTTTATCGTTGCAACAAGTATTCTATTTTTATCCGCCTGTTCTTCCAATACGGTAAAACAACATCAAATACACTCTATTTCTGCCAATAAAAATTCAGAAGCAATTAAATCACTGTTTGATCAGGCACAGACCACGGGTGTTTTGGTGATTAAGCGAGGGCAAACAGAAGAAATTTATGGCAATGATCTTAAAAGAGCATCAACAGACTATGTTCCCGCCTCTACCTTTAAAATGTTAAATGCTTTAATTGGACTTGAACATCATAAGGTAACTACAACTGAAGTATTTAAATGGGATGGGCAAAAACGTTTATTTCCTGATTGGGAAAAGGACATGACACTGGGTGATGCCATGAAAGCTTCTGCAATTCCAGTTTACCAAGAATTAGCCCGACGAATTGGTCTGGATCTTATGTCCAAAGAGGTGAAACGAATTGGTTTCGGTAATGCTAACATTGGCTCAAAAGTAGATGATTTCTGGCTTGTTGGCCCTCTAAAAATTACACCTCAACAAGAAACCCAATTTGCTTATCAATTAGCCCATAAAACTCTTCCATTTAGCAAAAATGTACAAGAACAAGTTCAATCAATGGTGTTCATAGAAGAAAAAAATGGAAGTAAAATTTATGCCAAAAGTGGTTGGGGATGGGATGTGGAACCACAAGTTGGTTGGTTAACAGGCTGGGTCGTTCAACCACAAGGAGAAATTGTCGCATTCTCACTTAATTTAGAAATGAAAAAAGGAACTCCTAGCTCTATTCGCAAAGAAATTGCTTATAAAGGCTTAGAACAACTGGGTATCTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39094","NCBI_taxonomy_name":"Acinetobacter calcoaceticus","NCBI_taxonomy_id":"471"}}}},"ARO_accession":"3001514","ARO_id":"37914","ARO_name":"OXA-326","CARD_short_name":"OXA-326","ARO_description":"OXA-326 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46495":{"category_aro_accession":"3007706","category_aro_cvterm_id":"46495","category_aro_name":"OXA-213-like beta-lactamase","category_aro_description":"OXA-213-like enzymes have been identified to be intrinsic to A. calcoaceticus and have been subsequently detected in A. pittii. Phylogenetic analysis of OXA-213-like proteins identified two distinct subgroups within the OXA family. The first group was linked to A. pittii and the second group to A. calcoaceticus. The carbapenemase activity of these OXAs may be related to the species-dependent effect.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1759":{"model_id":"1759","model_name":"vanF","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"350"}},"model_sequences":{"sequence":{"258":{"protein_sequence":{"accession":"AAF36803.1","sequence":"MNRLKIAILFGGCSEEHDVSVKSAKEIANNIDTEKYEPIYIGITRSGVWKMCEKPCMDWDNENCRSAVLSPDKKMHGLLVMRNKGYQIQRIDAVFSVLHGKSGEDGAIQGLFELSSIPYVGCDVQSSAVCMDKSLTYIVAQNAGFGTPEFLILNHGDIPDSNTLTYPVFVKPARSGSSFGVNKVNNEDELDAAIETARQYDSKVLIEQAVPGLEVGCAVLGNGTDLIVGEVDQISLSHGIFRIHQEDQPEKGSENAVVLVPANLSAEKRIKIQETAKAIYKALGCKGLSRVDMFLQENGRIILNEVNTLPGFTAYSRYPRMMAAAGMTLSGLIDHCITLALKG"},"dna_sequence":{"accession":"AF155139.1","fmin":"5939","fmax":"6971","strand":"+","sequence":"TTGAATAGATTAAAAATAGCCATCCTGTTTGGGGGCTGTTCAGAGGAACACGATGTGTCGGTAAAATCGGCGAAAGAGATTGCCAATAACATTGACACGGAAAAATATGAGCCGATATACATCGGAATCACCCGATCCGGCGTCTGGAAAATGTGCGAAAAGCCATGCATGGATTGGGACAACGAAAACTGCCGTTCGGCAGTGCTTTCTCCGGACAAAAAAATGCACGGGCTGCTTGTTATGCGGAATAAAGGATATCAAATCCAACGTATAGACGCGGTATTTTCGGTTTTGCACGGCAAATCGGGTGAAGACGGCGCCATACAAGGTTTATTTGAATTGTCCAGCATCCCCTATGTAGGCTGTGATGTTCAAAGTTCGGCGGTGTGTATGGACAAATCCCTGACATACATTGTGGCCCAAAATGCTGGTTTTGGCACTCCTGAATTTTTGATTTTGAATCATGGCGATATACCGGATTCAAATACCTTAACATATCCTGTTTTTGTTAAACCGGCGCGTTCCGGCTCATCTTTCGGCGTGAATAAAGTCAATAACGAGGACGAATTAGACGCCGCCATTGAAACAGCAAGGCAGTATGACAGTAAAGTCCTGATTGAACAAGCTGTTCCAGGCCTTGAAGTTGGCTGTGCCGTGTTGGGAAACGGTACCGACTTAATCGTTGGCGAAGTGGACCAAATTTCACTTTCGCATGGTATCTTTCGTATTCATCAAGAAGATCAACCAGAAAAAGGCTCCGAAAACGCAGTTGTTTTGGTTCCCGCAAACCTGTCGGCAGAGAAACGCATAAAGATACAAGAGACGGCGAAAGCAATTTATAAGGCGCTCGGCTGTAAAGGTCTTTCTCGTGTTGATATGTTTTTGCAGGAAAACGGACGTATTATACTGAATGAAGTCAATACGTTGCCGGGATTCACGGCATACAGCCGTTATCCCCGTATGATGGCTGCCGCGGGGATGACACTGTCCGGGTTAATTGATCATTGCATCACACTGGCACTCAAAGGATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39542","NCBI_taxonomy_name":"Paenibacillus popilliae ATCC 14706","NCBI_taxonomy_id":"1212764"}}}},"ARO_accession":"3002908","ARO_id":"39342","ARO_name":"vanF","CARD_short_name":"vanF","ARO_description":"VanF is a D-Ala-D-Ala ligase homolog that can synthesize D-Ala-D-Lac, an alternative substrate for peptidoglycan synthesis that reduces vancomycin binding affinity. It is associated with both vancomycin and teicoplanin resistance in Paenibacillus popilliae.","ARO_category":{"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"39340":{"category_aro_accession":"3002906","category_aro_cvterm_id":"39340","category_aro_name":"Van ligase","category_aro_description":"Van ligases synthesize alternative substrates for peptidoglycan synthesis that reduce vancomycin binding affinity.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1760":{"model_id":"1760","model_name":"QnrB35","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"555":{"protein_sequence":{"accession":"AEL00456.1","sequence":"MALALIGEKIDRNRFTGAKVENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAILKDAIFKSCDLSMADFRNVSALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKAVLEKCELWENRWMGTQMLGATLSGSDLSGGEFSSFDWRTANFTHCDLTNSELGDLDIRGVDLQGVKLDSYQAALLMERLGIAVIG"},"dna_sequence":{"accession":"JN173057.1","fmin":"2306","fmax":"2951","strand":"+","sequence":"ATGGCTCTGGCATTAATTGGCGAAAAAATTGACAGAAACCGCTTCACCGGTGCAAAAGTTGAAAATAGCACTTTTTTTAACTGTGATTTTTCGGGCGCCGACCTTAGCGGTACTGAATTTATCGGCTGTCAGTTCTATGATCGAGAAAGCCAGAAAGGGTGCAATTTCAGTCGCGCAATACTGAAAGATGCCATTTTTAAAAGCTGTGATTTATCCATGGCGGATTTTCGCAACGTCAGTGCGTTGGGCATAGAAATTCGCCACTGCCGAGCACAGGGTGCAGATTTTCGCGGCGCAAGTTTCATGAATATGATCACCACGCGCACCTGGTTTTGCAGCGCATATATCACTAATACCAATCTAAGCTATGCCAACTTTTCGAAGGCCGTGCTTGAAAAGTGCGAATTGTGGGAAAATCGCTGGATGGGAACTCAGATGCTGGGTGCGACGTTGAGTGGTTCCGATCTCTCCGGTGGCGAGTTTTCGTCGTTCGACTGGCGGACGGCAAATTTCACGCACTGTGATTTGACCAATTCAGAACTGGGTGATTTAGATATTCGGGGCGTCGATTTACAAGGTGTCAAATTGGACAGCTATCAGGCCGCGTTGCTCATGGAACGTCTTGGCATCGCTGTCATTGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002750","ARO_id":"39184","ARO_name":"QnrB35","CARD_short_name":"QnrB35","ARO_description":"QnrB35 is a plasmid-mediated quinolone resistance protein found in Citrobacter freundii.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1761":{"model_id":"1761","model_name":"OXA-351","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1133":{"protein_sequence":{"accession":"AGW83449.1","sequence":"MYKKALIVAISILFLSACSSNMVKQHQIHSISANKNSEEIKSLFDQAQTTGVLVIKRGQTEEIYGNDLKRASTDYVPASTFKMLNALIGLEHHKATTTEVFKWNGQKRLFPDWEKDMTLSDAMKASAIPVYQELARRIGLDLMSKEVKRIGFGNANIGSKVDDFWLVGPLKITPQQETQFAYQLAHKTLPFSKNVQEQVQSMVFIEEKNGSKIYAKSGWGWDVEPQVGWLTGWVVQPQGEIVAFSLNLEMKKGTPSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"KF297580.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGTATAAAAAAGCCCTTATCGTTGCAATAAGTATCCTATTTTTATCCGCCTGTTCTTCCAATATGGTCAAACAACATCAAATACACTCTATTTCTGCCAATAAAAATTCAGAAGAAATTAAATCACTGTTTGATCAAGCACAGACCACTGGAGTTTTGGTGATTAAGCGAGGGCAAACAGAAGAAATTTATGGCAATGATCTTAAAAGAGCATCAACCGACTATGTTCCCGCCTCTACCTTTAAAATGTTAAATGCTTTAATTGGACTTGAACATCATAAGGCAACTACAACTGAAGTATTTAAATGGAATGGGCAAAAACGTTTATTTCCTGATTGGGAAAAGGACATGACACTGAGCGATGCCATGAAAGCTTCTGCAATTCCAGTTTACCAAGAATTAGCCCGACGGATTGGTCTGGATCTTATGTCCAAAGAGGTGAAACGAATTGGTTTCGGTAATGCTAACATTGGCTCAAAAGTAGATGATTTTTGGCTTGTTGGCCCTCTAAAAATTACACCTCAACAAGAAACCCAATTTGCTTATCAATTAGCCCATAAAACTCTTCCATTTAGCAAAAATGTACAAGAACAAGTTCAATCGATGGTGTTCATAGAGGAAAAAAATGGAAGTAAAATTTATGCCAAAAGTGGTTGGGGATGGGATGTTGAACCGCAAGTTGGTTGGTTAACAGGCTGGGTCGTTCAACCACAAGGAGAAATTGTGGCATTTTCACTTAATTTAGAAATGAAAAAAGGAACTCCTAGCTCTATTCGCAAAGAAATTGCTTATAAAGGCTTAGAACAACTGGGTATTTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39094","NCBI_taxonomy_name":"Acinetobacter calcoaceticus","NCBI_taxonomy_id":"471"}}}},"ARO_accession":"3001538","ARO_id":"37938","ARO_name":"OXA-351","CARD_short_name":"OXA-351","ARO_description":"OXA-351 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46495":{"category_aro_accession":"3007706","category_aro_cvterm_id":"46495","category_aro_name":"OXA-213-like beta-lactamase","category_aro_description":"OXA-213-like enzymes have been identified to be intrinsic to A. calcoaceticus and have been subsequently detected in A. pittii. Phylogenetic analysis of OXA-213-like proteins identified two distinct subgroups within the OXA family. The first group was linked to A. pittii and the second group to A. calcoaceticus. The carbapenemase activity of these OXAs may be related to the species-dependent effect.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1762":{"model_id":"1762","model_name":"aadA16","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"8226":{"protein_sequence":{"accession":"ACF17980.1","sequence":"MSNAVPAEISVQLSQALNVIERHLGSTLLAVHLYGSALDGGLKPCSDIDLLVTVTAQLDETVRQALFVDFLEVSASPGQSEALRALEVTIVVYGDVAPWRYLARRELQFGEWQRKDILAGIFEPATTDVDLAILLTKARQHSLALAGSAAEDFFNSVPESDLFKALADTLKLWNSQPDWAGDERNVVLTLSRIWYSAATGKIAPKDVAANWVMERLPVQHQPVLLEAQQAYLGQGMDCLASRADQLTAFIYFVKHEAASLLGSTPMMSNSSFKPTPLRGAA"},"dna_sequence":{"accession":"EU675686.2","fmin":"3196","fmax":"4042","strand":"+","sequence":"ATGAGCAACGCAGTGCCCGCCGAGATTTCGGTACAGCTATCACAGGCACTCAACGTCATCGAGCGTCATCTGGGATCGACGTTGCTGGCCGTGCATTTGTACGGCTCTGCACTCGACGGTGGCCTGAAGCCATGCAGTGATATTGATTTGCTGGTTACTGTGACTGCACAGCTCGATGAGACTGTGCGGCAGGCTCTGTTCGTAGATTTCCTGGAAGTTTCCGCTTCTCCCGGCCAAAGTGAAGCTCTCCGTGCCTTGGAAGTTACCATCGTCGTGTACGGCGATGTTGCTCCTTGGCGTTATCTAGCCAGACGGGAACTGCAATTCGGGGAGTGGCAGCGCAAGGACATTCTTGCGGGCATCTTCGAGCCCGCGACAACCGATGTTGATCTGGCTATTCTGCTAACTAAAGCAAGGCAACACAGCCTTGCCTTGGCAGGTTCGGCCGCGGAAGATTTCTTCAACTCAGTCCCGGAAAGCGATCTATTCAAAGCACTGGCCGACACCTTGAAACTATGGAACTCACAACCGGATTGGGCAGGCGACGAGCGGAATGTAGTGCTTACTTTGTCTCGCATTTGGTACAGCGCAGCAACCGGCAAGATCGCGCCGAAGGATGTAGCTGCCAACTGGGTAATGGAACGCCTGCCCGTCCAACATCAGCCCGTGCTGCTTGAAGCCCAGCAGGCTTACCTTGGACAAGGGATGGATTGCTTGGCCTCACGCGCTGATCAGTTGACTGCGTTCATTTACTTTGTGAAGCACGAAGCCGCCAGTCTGCTCGGCTCCACGCCAATGATGTCTAACAGTTCATTCAAGCCGACGCCGCTTCGCGGCGCAGCTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002616","ARO_id":"39016","ARO_name":"aadA16","CARD_short_name":"aadA16","ARO_description":"aadA16 is an aminoglycoside nucleotidyltransferase gene encoded by plasmids and integrons in E. coli, V. cholerae and K. pneumoniae.","ARO_category":{"41439":{"category_aro_accession":"3004275","category_aro_cvterm_id":"41439","category_aro_name":"ANT(3'')","category_aro_description":"A category of aminoglycoside O-nucleotidyltransferase enzymes with modification regiospecificity based at the 3''-hydroxyl group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics by transfer of an AMP group from an ATP substrate to the 3''-hydroxyl group of the compound.","category_aro_class_name":"AMR Gene Family"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1763":{"model_id":"1763","model_name":"NDM-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"777":{"protein_sequence":{"accession":"AEA41876.1","sequence":"MELPNIMHPVAKLSTALAAALMLSGCMAGEIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR"},"dna_sequence":{"accession":"JF703135.1","fmin":"0","fmax":"813","strand":"+","sequence":"ATGGAATTGCCCAATATTATGCACCCGGTCGCGAAGCTGAGCACCGCATTAGCCGCTGCATTGATGCTGAGCGGGTGCATGGCCGGTGAAATCCGCCCGACGATTGGCCAGCAAATGGAAACTGGCGACCAACGGTTTGGCGATCTGGTTTTCCGCCAGCTCGCACCGAATGTCTGGCAGCACACTTCCTATCTCGACATGCCGGGTTTCGGGGCAGTCGCTTCCAACGGTTTGATCGTCAGGGATGGCGGCCGCGTGCTGGTGGTCGATACCGCCTGGACCGATGACCAGACCGCCCAGATCCTCAACTGGATCAAGCAGGAGATCAACCTGCCGGTCGCGCTGGCGGTGGTGACTCACGCGCATCAGGACAAGATGGGCGGTATGGACGCGCTGCATGCGGCGGGGATTGCGACTTATGCCAATGCGTTGTCGAACCAGCTTGCCCCGCAAGAGGGGATGGTTGCGGCGCAACACAGCCTGACTTTCGCCGCCAATGGCTGGGTCGAACCAGCAACCGCGCCCAACTTTGGCCCGCTCAAGGTATTTTACCCCGGCCCCGGCCACACCAGTGACAATATCACCGTTGGGATCGACGGCACCGACATCGCTTTTGGTGGCTGCCTGATCAAGGACAGCAAGGCCAAGTCGCTCGGCAATCTCGGTGATGCCGACACTGAGCACTACGCCGCGTCAGCGCGCGCGTTTGGTGCGGCGTTCCCCAAGGCCAGCATGATCGTGATGAGCCATTCCGCCCCCGATAGCCGCGCCGCAATCACTCATACGGCCCGCATGGCCGACAAGCTGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3000590","ARO_id":"36729","ARO_name":"NDM-2","CARD_short_name":"NDM-2","ARO_description":"NDM-2 was isolated from a strain of Acinetobacter baumannii in Germany from a patient hospitalized in Cairo.  A single amino acid substitution (P28R) differentiates this gene from NDM-1 and the two enzymes appear to have an identical spectrum of hydrolysis.","ARO_category":{"36196":{"category_aro_accession":"3000057","category_aro_cvterm_id":"36196","category_aro_name":"NDM beta-lactamase","category_aro_description":"NDM beta-lactamases or New Delhi metallo-beta-lactamases are class B beta-lactamases that confer resistance to a broad range of antibiotics including carbapenems, cephalosporins and penicillins.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1764":{"model_id":"1764","model_name":"OXA-97","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4681":{"protein_sequence":{"accession":"ABO33299.1","sequence":"MKLLKILSLVCLSISIGACAEHSMSRAKTSTIPQVNNSIIDQNVQALFNEISGDAVFVTYDGQNIKKYGTHLDRAKTAYIPASTFKIANALIGLENHKATSTEIFKWDGKPRFFKAWDKDFTLGEAMQASTVPVYQELARRIGPSLMQSELQRIGYGNMQIGTEVDQFWLKGPLTITPIQEVKFVYDLAQGQLPFKPEVQQQVKEMLYVERRGENRLYAKSGWGMAVDPQVGWYVGFVEKADGQVVAFALNMQMKAGDDIALRKQLSLDVLDKLGVFHYL"},"dna_sequence":{"accession":"EF102240.1","fmin":"11722","fmax":"12565","strand":"-","sequence":"ATGAAATTATTAAAAATATTGAGTTTAGTTTGCTTAAGCATAAGTATTGGGGCTTGTGCTGAGCATAGTATGAGTCGAGCAAAAACAAGTACAATTCCACAAGTGAATAACTCAATCATCGATCAGAATGTTCAAGCGCTTTTTAATGAAATCTCAGGTGATGCTGTGTTTGTCACATATGATGGTCAAAATATTAAAAAATATGGCACGCATTTAGACCGAGCAAAAACAGCTTATATTCCTGCATCTACATTTAAAATTGCCAATGCACTAATTGGTTTAGAAAATCATAAAGCAACATCTACAGAAATATTTAAGTGGGATGGAAAGCCACGTTTTTTTAAAGCATGGGACAAAGATTTTACTTTGGGCGAAGCCATGCAAGCATCTACAGTGCCTGTATATCAAGAATTGGCACGTCGTATTGGTCCAAGCTTAATGCAAAGTGAATTGCAACGTATTGGTTATGGCAATATGCAAATAGGCACGGAAGTTGATCAATTTTGGTTGAAAGGGCCTTTGACAATTACACCTATACAAGAAGTAAAGTTTGTGTATGATTTAGCCCAAGGGCAATTGCCTTTTAAACCTGAAGTTCAGCAACAAGTGAAAGAGATGTTGTATGTAGAGCGCAGAGGGGAGAATCGTCTATATGCTAAAAGTGGCTGGGGAATGGCTGTAGACCCGCAAGTGGGTTGGTATGTGGGTTTTGTTGAAAAGGCAGATGGGCAAGTGGTGGCATTTGCTTTAAATATGCAAATGAAAGCTGGTGATGATATTGCTCTACGTAAACAATTGTCTTTAGATGTGCTAGATAAGTTGGGTGTTTTTCATTATTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001647","ARO_id":"38047","ARO_name":"OXA-97","CARD_short_name":"OXA-97","ARO_description":"OXA-97 is a beta-lactamase found in A. baumannii.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46517":{"category_aro_accession":"3007728","category_aro_cvterm_id":"46517","category_aro_name":"OXA-58-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-58.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1765":{"model_id":"1765","model_name":"OXA-56","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1056":{"protein_sequence":{"accession":"AAR32651.1","sequence":"MKTFAAYVITACLSSTALASSITENTFWNKEFSAEAVNGVFVLCKSSSKSCATNNLARASKEYLPASTFKIPNAIIGLETGVIKNEHQIFKWDGKPRAMKQWERDLSLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLFLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKGAEVYFFAFNMDIDNENKLPLRKSIPTKIMASEGIIGG"},"dna_sequence":{"accession":"AY445080.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGAAAACATTTGCCGCATATGTAATTACTGCGTGTCTTTCAAGTACGGCATTAGCTAGTTCAATTACAGAAAATACGTTTTGGAACAAAGAGTTCTCTGCCGAAGCCGTCAATGGTGTTTTCGTGCTTTGTAAAAGTAGCAGTAAATCCTGCGCTACCAATAACTTAGCTCGTGCATCAAAGGAATATCTTCCAGCATCAACATTTAAGATCCCCAACGCAATTATCGGCCTAGAAACTGGTGTCATAAAGAATGAGCATCAGATTTTCAAATGGGACGGAAAGCCAAGAGCCATGAAACAATGGGAAAGAGACTTGAGCTTAAGAGGGGCAATACAAGTTTCAGCGGTTCCCGTATTTCAACAAATCGCCAGAGAAGTTGGCGAAGTAAGAATGCAGAAATATCTTAAAAAATTTTCATATGGTAACCAGAATATCAGTGGTGGCATTGACAAATTCTGGTTGGAGGGTCAGCTTAGAATTTCCGCAGTTAATCAAGTGGAGTTTCTAGAGTCTCTATTTTTAAATAAATTGTCAGCATCAAAAGAAAATCAGCTAATAGTAAAAGAGGCTTTGGTAACGGAGGCTGCGCCTGAATATCTTGTGCATTCAAAAACTGGTTTTTCTGGTGTGGGAACTGAGTCAAATCCTGGTGTCGCATGGTGGGTTGGTTGGGTTGAGAAGGGAGCAGAGGTTTACTTTTTCGCCTTTAACATGGATATAGACAACGAAAATAAGTTGCCGCTAAGAAAATCCATTCCCACCAAAATCATGGCAAGTGAGGGCATCATTGGTGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3001795","ARO_id":"38195","ARO_name":"OXA-56","CARD_short_name":"OXA-56","ARO_description":"OXA-56 is a beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46486":{"category_aro_accession":"3007697","category_aro_cvterm_id":"46486","category_aro_name":"OXA-10-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-10.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1766":{"model_id":"1766","model_name":"VIM-14","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1082":{"protein_sequence":{"accession":"AAT48653.1","sequence":"MLKVISSLLVYMTASVMAVASPLAHSGEPSSEYPTVNEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEAEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSANVLYGGCAVHELSRTSAGNVADADLAEWPTSVERIQKHYPEAEVVIPGHGLPGGLDLLQHTANVVKAHKNRSVAE"},"dna_sequence":{"accession":"AY635904.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGTTAAAAGTTATTAGTAGTTTATTGGTCTACATGACCGCGTCTGTCATGGCTGTCGCAAGTCCGTTAGCCCATTCCGGGGAGCCGAGTAGTGAGTATCCGACAGTCAACGAAATTCCGGTCGGAGAGGTCCGACTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCGGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAAAAGCAAATTGGACTTCCCGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGCAGAGGGGAACGAGATTCCCACGCATTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAGCTCTTCTATCCTGGTGCTGCGCATTCGACCGACAATCTGGTTGTATACGTCCCGTCAGCGAACGTGCTATACGGTGGTTGTGCCGTTCATGAGTTGTCACGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCGTTGAGCGGATTCAAAAACACTACCCGGAAGCAGAGGTCGTCATTCCCGGGCACGGTCTACCGGGCGGTCTAGACTTGCTCCAGCACACAGCGAACGTTGTCAAAGCACACAAAAATCGCTCAGTCGCCGAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002284","ARO_id":"38684","ARO_name":"VIM-14","CARD_short_name":"VIM-14","ARO_description":"VIM-14 is a beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1767":{"model_id":"1767","model_name":"OKP-A-16","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"1287":{"protein_sequence":{"accession":"ACN65418.1","sequence":"MRYVRLCLISLIAALPLVAFASPQPLEQVTRSESQLAGRVGYVEMDLASGRTLAAWRASERFPLMSTFKVLLCGAVLARVDAGDEQLDRRIRYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAGNLLLKSVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDVRDTTTPASMAATLRKLLTSHALSARSQQQLLQWMVDDQVAGPLIRAVLPAGWFIADKTGAGERGSRGIVALLGPNGKAERIVVIYLRDTPATMAERNQQIARIGAALIEHWQR"},"dna_sequence":{"accession":"FJ755840.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGCCTTATCTCCCTGATTGCCGCCCTGCCACTGGTGGCATTCGCCAGCCCTCAGCCGCTCGAGCAAGTTACACGCAGCGAAAGTCAGCTGGCGGGCCGCGTGGGCTATGTTGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCAGTGAGCGCTTTCCGCTGATGAGCACCTTTAAAGTGCTGCTCTGCGGCGCGGTGCTGGCCCGGGTGGATGCCGGAGACGAACAGCTGGATCGGCGGATCCGCTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGCCGACGGGATGACCGTTGGTGAACTCTGCGCCGCCGCCATCACCATGAGCGACAACAGCGCCGGCAATCTGCTGTTGAAGAGCGTTGGCGGCCCCGCGGGATTGACCGCTTTTCTGCGCCAGATCGGTGACAACGTCACCCGACTTGACCGCTGGGAAACGGAGCTCAATGAGGCGCTTCCCGGCGACGTGCGCGACACCACCACCCCAGCCAGCATGGCCGCCACCCTGCGCAAGCTGCTAACCAGCCACGCGCTGAGCGCCCGTTCGCAGCAGCAGCTGCTGCAGTGGATGGTGGACGACCAGGTAGCCGGTCCGCTGATCCGCGCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAAACCGGGGCCGGCGAGCGGGGCTCACGCGGCATTGTCGCCCTGCTCGGCCCGAACGGCAAAGCGGAGCGCATCGTGGTGATCTATCTGCGGGATACGCCGGCGACCATGGCCGAGCGTAACCAGCAGATCGCCAGAATAGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002433","ARO_id":"38833","ARO_name":"OKP-A-16","CARD_short_name":"OKP-A-16","ARO_description":"OKP-A-16 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"38817":{"category_aro_accession":"3002417","category_aro_cvterm_id":"38817","category_aro_name":"OKP beta-lactamase","category_aro_description":"OKP beta-lactamases are chromosomal class A beta-lactamase that confer resistance to penicillins and early cephalosporins in Klebsiella pneumoniae. OKP beta-lactamases can be subdivided into two groups: OKP-A and OKP-B which diverge by about 4.2%.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1768":{"model_id":"1768","model_name":"CTX-M-144","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1185":{"protein_sequence":{"accession":"AHX39588.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAVAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDLRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"KJ020573.1","fmin":"274","fmax":"1150","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGTGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCTGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002002","ARO_id":"38402","ARO_name":"CTX-M-144","CARD_short_name":"CTX-M-144","ARO_description":"CTX-M-144 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1769":{"model_id":"1769","model_name":"CTX-M-115","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"766":{"protein_sequence":{"accession":"AIL54055.1","sequence":"MMTQSIRRSMLTVMATLPLLFSSATLHAQANSVQQQLEALEKSSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKQSESDKHLLNQRVEIKKSDLVNYNPIAEKHVNGTMTLAELGAAALQYSDNTAMNKLIAHLGGPDKVTAFARSLGDETFRLDRTEPTLNTAIPGDPRDTTTPLAMAQTLKNLTLGKALAETQRAQLVTWLKGNTTGSASIRAGLPKSWVVGDKTGSGDYGTTNDIAIIWPENHAPLVLVTYFTQPEQKAESRRDVLAAAAKIVTHSF"},"dna_sequence":{"accession":"KJ911020.1","fmin":"111","fmax":"987","strand":"+","sequence":"ATGATGACTCAGAGCATTCGCCGCTCAATGTTAACGGTGATGGCGACGCTACCCCTGCTATTTAGCAGCGCAACGCTGCATGCGCAGGCGAACAGCGTGCAACAGCAGCTGGAAGCCCTGGAGAAAAGTTCGGGAGGTCGGCTTGGCGTTGCGCTGATTAACACCGCCGATAATTCGCAGATTCTCTACCGTGCCGATGAACGTTTTGCGATGTGCAGTACCAGTAAGGTGATGGCGGCCGCGGCGGTGCTTAAACAGAGCGAGAGCGATAAGCACCTGCTAAATCAGCGCGTTGAAATCAAGAAGAGCGACCTGGTTAACTACAATCCCATTGCTGAGAAACACGTTAACGGCACTATGACGCTGGCTGAGCTTGGCGCAGCGGCGCTGCAGTATAGCGACAATACTGCCATGAATAAGCTGATTGCCCATCTGGGTGGGCCCGATAAAGTGACGGCGTTTGCTCGCTCGTTGGGTGATGAGACCTTCCGTCTGGACAGAACCGAGCCCACGCTCAATACCGCCATTCCAGGCGACCCGCGTGATACCACCACGCCGCTCGCGATGGCGCAGACCCTGAAAAATCTGACGCTGGGTAAAGCGCTGGCGGAAACTCAGCGGGCACAGTTGGTGACGTGGCTTAAGGGCAATACTACCGGTAGCGCGAGCATTCGGGCGGGTCTGCCGAAATCATGGGTAGTGGGCGATAAAACCGGCAGCGGAGATTATGGCACCACCAACGATATCGCGATTATCTGGCCGGAAAACCACGCACCGCTGGTTCTGGTGACCTACTTTACCCAACCGGAGCAGAAGGCGGAAAGCCGTCGGGATGTTCTGGCTGCGGCGGCGAAAATCGTAACCCACAGTTTCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001975","ARO_id":"38375","ARO_name":"CTX-M-115","CARD_short_name":"CTX-M-115","ARO_description":"CTX-M-115 is a beta-lactamase found in Acinetobacter baumannii.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1770":{"model_id":"1770","model_name":"TEM-127","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1644":{"protein_sequence":{"accession":"AAR89358.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDNVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AY368236.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATAATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000989","ARO_id":"37369","ARO_name":"TEM-127","CARD_short_name":"TEM-127","ARO_description":"TEM-127 is a broad-spectrum beta-lactamase found in E. coli.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1771":{"model_id":"1771","model_name":"TEM-19","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"928":{"protein_sequence":{"accession":"AFN21551.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGASERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"JX042489.1","fmin":"141","fmax":"1002","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCAGTGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3000890","ARO_id":"37270","ARO_name":"TEM-19","CARD_short_name":"TEM-19","ARO_description":"TEM-19 is an extended-spectrum beta-lactamase that has been found in clinical isolates.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1772":{"model_id":"1772","model_name":"aadA11","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"13":{"protein_sequence":{"accession":"AAV32840.1","sequence":"MSNAVPAEISVQLSLALNAIERHLESTLLAVHLYGSALDGGLKPYSDIDLLVTVAAQLDETVRQALVVDLLEISASPGQSEALRALEVTIVVHGDVVPWRYPARRELQFGEWQRKDILAGIFEPATTDVDLAILLTKVRQHSLALAGSAAEDFFNPVPEGDLFKALSDTLKLWNSQPDWEGDERNVVLTLSRIWYSAATGKIAPKDIVANWAIERLPDQHKPVLLEARQAYLGQGEDCLASRADQLAAFVHFVKHEATKLLGAMPVMSNNSFKPNPLRGSA"},"dna_sequence":{"accession":"AY758206.1","fmin":"2743","fmax":"3589","strand":"+","sequence":"ATGAGTAACGCAGTACCCGCCGAGATTTCGGTACAGCTATCACTGGCTCTCAACGCCATCGAGCGTCATCTGGAATCAACGTTGCTGGCCGTGCATTTGTACGGCTCTGCACTGGACGGTGGCCTGAAGCCATACAGTGATATTGATTTGCTGGTTACTGTGGCTGCACAGCTCGATGAGACTGTCCGACAAGCCCTGGTCGTAGATCTCTTGGAAATTTCTGCCTCCCCTGGCCAAAGTGAGGCTCTCCGCGCCTTGGAAGTTACCATCGTCGTGCATGGTGATGTTGTCCCTTGGCGTTATCCGGCCAGACGGGAACTGCAATTCGGGGAGTGGCAGCGTAAGGACATTCTTGCGGGCATCTTCGAGCCCGCCACAACCGATGTTGATCTGGCTATTCTGCTAACTAAAGTAAGGCAGCATAGCCTTGCATTGGCAGGTTCGGCCGCAGAGGATTTCTTTAACCCAGTTCCGGAAGGCGATCTATTCAAGGCATTGAGCGACACTCTGAAACTATGGAATTCGCAGCCGGATTGGGAAGGCGATGAGCGGAATGTAGTGCTTACCTTGTCTCGCATTTGGTACAGCGCAGCAACCGGCAAGATCGCACCGAAGGATATCGTTGCCAACTGGGCAATTGAGCGTCTGCCAGATCAACATAAGCCCGTACTGCTTGAAGCCCGGCAGGCTTATCTTGGACAAGGAGAAGATTGCTTGGCCTCACGCGCGGATCAGTTGGCGGCGTTCGTTCACTTCGTGAAACATGAAGCCACTAAATTGCTTGGTGCCATGCCAGTGATGTCTAACAATTCATTCAAGCCGAACCCGCTTCGCGGGTCGGCTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002611","ARO_id":"39011","ARO_name":"aadA11","CARD_short_name":"aadA11","ARO_description":"aadA11 is an integron-encoded aminoglycoside nucleotidyltransferase gene in E. coli and P. aeruginosa.","ARO_category":{"41439":{"category_aro_accession":"3004275","category_aro_cvterm_id":"41439","category_aro_name":"ANT(3'')","category_aro_description":"A category of aminoglycoside O-nucleotidyltransferase enzymes with modification regiospecificity based at the 3''-hydroxyl group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics by transfer of an AMP group from an ATP substrate to the 3''-hydroxyl group of the compound.","category_aro_class_name":"AMR Gene Family"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1774":{"model_id":"1774","model_name":"CTX-M-106","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1271":{"protein_sequence":{"accession":"ADZ31262.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDRTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRHDVLASAARIIAEG"},"dna_sequence":{"accession":"HQ913565.1","fmin":"0","fmax":"870","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAGGACCGGCAGCGGCGACTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAGCCGCCACGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGG","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001966","ARO_id":"38366","ARO_name":"CTX-M-106","CARD_short_name":"CTX-M-106","ARO_description":"CTX-M-106 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1775":{"model_id":"1775","model_name":"QnrS7","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"348":{"protein_sequence":{"accession":"AHE41344.1","sequence":"METYNHTYRHHNFSHKDLSDLTFTACTFIRSDFRRANLRDTTFVNCKFIEQGDIEGCHFDVADLHDASFQQCQLAMANFSNANCYGIEFRACDLKGANFSRTNFAHQVSNRMYFCSAFISGCNLSYANMERVCLEKCELFENRWIGTNLAGASLKESDLSRGVFSEDVWGQFSLQGANLCHAELDGLDPRKVDTSGIKIAAWQQELILEALGIVVYPD"},"dna_sequence":{"accession":"KF730651.1","fmin":"0","fmax":"657","strand":"+","sequence":"ATGGAAACCTACAATCATACATATCGGCACCACAACTTTTCACATAAAGACTTAAGTGATCTCACCTTCACCGCTTGCACATTCATTCGCAGCGACTTTCGACGTGCTAACTTGCGTGATACGACATTCGTCAACTGCAAGTTCATTGAACAGGGTGATATCGAAGGCTGCCACTTTGATGTCGCAGATCTTCATGATGCAAGTTTCCAACAATGCCAACTTGCGATGGCAAACTTCAGTAATGCCAATTGCTACGGTATAGAGTTCCGTGCGTGTGATTTAAAAGGTGCCAACTTTTCCCGAACAAACTTTGCCCATCAAGTGAGTAATCGTATGTACTTTTGCTCAGCATTTATTTCTGGATGTAATCTTTCCTATGCCAATATGGAGAGGGTTTGTTTAGAAAAATGTGAGTTGTTTGAAAATCGCTGGATAGGAACGAACCTAGCGGGTGCATCACTGAAAGAGTCAGACTTAAGTCGAGGTGTTTTTTCCGAAGATGTCTGGGGGCAATTTAGCCTACAGGGTGCCAATTTATGCCACGCCGAACTCGACGGTTTAGATCCCCGCAAAGTCGATACATCAGGTATCAAAATTGCAGCCTGGCAGCAAGAACTGATTCTCGAAGCACTGGGTATTGTTGTTTATCCTGACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002796","ARO_id":"39230","ARO_name":"QnrS7","CARD_short_name":"QnrS7","ARO_description":"QnrS7 is a plasmid-mediated quinolone resistance protein found in Escherichia coli.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1776":{"model_id":"1776","model_name":"SHV-159","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1788":{"protein_sequence":{"accession":"AFQ23965.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVGDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"JX121126.1","fmin":"0","fmax":"858","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACATCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGGCGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGTATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGC","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001198","ARO_id":"37578","ARO_name":"SHV-159","CARD_short_name":"SHV-159","ARO_description":"SHV-159 is a beta-lactamase.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1777":{"model_id":"1777","model_name":"OXA-177","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"968":{"protein_sequence":{"accession":"ADI58621.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDVKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWVVGPLKITPQQEAQFAYKLANKTLPFSQKVQDGVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"HM113563.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGTAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGGTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGGAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAACAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001661","ARO_id":"38061","ARO_name":"OXA-177","CARD_short_name":"OXA-177","ARO_description":"OXA-177 is a beta-lactamase found in A. baumannii.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1778":{"model_id":"1778","model_name":"OKP-A-5","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"1598":{"protein_sequence":{"accession":"CAJ19602.1","sequence":"MRYVRLCLISLIAALPLAVFASPQPLEQITLSESQLAGRVGYVEMDLASGRTLAAWRASERFPLMSTFKVLLCGAVLARVDAGDERLDRRIRYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAGNLLLKSVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDVRDTTTPASMAATLRKLLTSHALSDRSQQQLLQWMVDDQVAGPLIRAVLPAGWFIADKTGAGERGSRGIVALLGPNGKAERIVVIYLRDTPATMAERNQQIARIGAALIEHWQR"},"dna_sequence":{"accession":"AM051143.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGCCTTATCTCCCTGATTGCCGCCCTGCCACTGGCGGTATTCGCCAGCCCTCAGCCGCTCGAACAAATTACACTCAGCGAAAGTCAGCTGGCGGGCCGCGTGGGCTATGTTGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCAGTGAGCGCTTTCCGCTGATGAGCACCTTTAAAGTGCTGCTCTGCGGCGCGGTGCTGGCCCGGGTGGATGCCGGAGACGAACGGCTGGATCGGCGGATCCGCTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGCCGACGGGATGACCGTTGGCGAACTCTGCGCCGCCGCCATCACCATGAGCGACAACAGCGCCGGCAATCTGCTGTTGAAGAGCGTTGGCGGCCCCGCGGGATTGACCGCTTTTCTGCGCCAGATCGGTGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAGCTCAATGAAGCGCTTCCCGGCGACGTGCGCGACACCACCACCCCAGCCAGCATGGCCGCCACCCTGCGCAAGCTGCTAACCAGCCACGCGCTGAGCGACCGTTCGCAGCAGCAGCTGCTGCAGTGGATGGTGGACGACCAGGTGGCCGGTCCGCTGATCCGCGCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAAACCGGGGCCGGCGAGCGGGGCTCACGCGGCATTGTCGCCCTGCTCGGCCCGAACGGCAAAGCGGAGCGCATCGTGGTGATCTATCTGCGGGATACGCCGGCGACCATGGCCGAGCGTAACCAGCAGATCGCCAGAATAGGCGCGGCGCTGATCGAGCACTGGCAGCGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002422","ARO_id":"38822","ARO_name":"OKP-A-5","CARD_short_name":"OKP-A-5","ARO_description":"OKP-A-5 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"38817":{"category_aro_accession":"3002417","category_aro_cvterm_id":"38817","category_aro_name":"OKP beta-lactamase","category_aro_description":"OKP beta-lactamases are chromosomal class A beta-lactamase that confer resistance to penicillins and early cephalosporins in Klebsiella pneumoniae. OKP beta-lactamases can be subdivided into two groups: OKP-A and OKP-B which diverge by about 4.2%.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1779":{"model_id":"1779","model_name":"CTX-M-12","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1008":{"protein_sequence":{"accession":"AAG34108.1","sequence":"MVKKSLRQFTLMATAAVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPSLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGDYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDILASAAKIVTDGL"},"dna_sequence":{"accession":"AF305837.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAGCCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCGGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTCGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAGTCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTGGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCAGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGACTATGGCACCACCAACGATATCGCGGTGATTTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATATATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001875","ARO_id":"38275","ARO_name":"CTX-M-12","CARD_short_name":"CTX-M-12","ARO_description":"CTX-M-12 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1780":{"model_id":"1780","model_name":"OXA-146","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1524":{"protein_sequence":{"accession":"ACI28281.1","sequence":"MNKYFTCYVVASLFLSGCTVQHNLINETPSQIVQGHNQVIHQYFDEKNTSGVLVIQTDKKINLYGNALSRANTEYVPASTFKMLNALIGLENQKTDINEIFKWKGEKRSFTAWEKDMTLGEAMKLSAVPVYQELARRIGLDLMQKEVKRIGFGNAEIGQQVDNFWLVGPLKVTPIQEVEFVSQLAHTQLPFSEKVQANVKNMLLLEESNGYKIFGKTGWAAMDIKPQVGWLTGWVEQPDGKIVAFALNMEMRSEMPASIRNELLMKSLKQLNII"},"dna_sequence":{"accession":"FJ194494.1","fmin":"171","fmax":"996","strand":"+","sequence":"ATGAATAAATATTTTACTTGCTATGTGGTTGCTTCTCTTTTTCTTTCTGGTTGTACGGTTCAGCATAATTTAATAAATGAAACCCCGAGTCAGATTGTTCAAGGACATAATCAGGTGATTCATCAATACTTTGATGAAAAAAACACCTCAGGTGTGCTGGTTATTCAAACAGATAAAAAAATTAATCTATATGGTAATGCTCTAAGCCGCGCAAATACAGAATATGTGCCAGCCTCTACATTTAAAATGTTGAATGCCCTGATCGGATTGGAGAACCAGAAAACGGATATTAATGAAATATTTAAATGGAAGGGCGAGAAAAGGTCATTTACCGCTTGGGAAAAAGACATGACACTAGGAGAAGCCATGAAGCTTTCTGCAGTCCCAGTCTATCAGGAACTTGCGCGACGTATCGGTCTTGATCTCATGCAAAAAGAAGTAAAACGTATTGGTTTCGGTAATGCTGAAATTGGACAGCAGGTTGATAATTTCTGGTTGGTAGGACCATTAAAGGTTACGCCTATTCAAGAGGTAGAGTTTGTTTCCCAATTAGCACATACACAGCTTCCATTTAGTGAAAAAGTGCAGGCTAATGTAAAAAATATGCTTCTTTTAGAAGAGAGTAATGGCTACAAAATTTTTGGAAAGACTGGTTGGGCGGCAATGGATATAAAACCACAAGTGGGCTGGTTGACCGGCTGGGTTGAGCAGCCAGATGGAAAAATTGTCGCTTTTGCATTAAATATGGAAATGCGGTCAGAAATGCCGGCATCTATACGTAATGAATTATTGATGAAATCATTAAAACAGCTGAATATTATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001779","ARO_id":"38179","ARO_name":"OXA-146","CARD_short_name":"OXA-146","ARO_description":"OXA-146 is a beta-lactamase found in Enterobacteriaceae.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46499":{"category_aro_accession":"3007710","category_aro_cvterm_id":"46499","category_aro_name":"OXA-23-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases, specifically imipenem, derived from OXA-23, first identified in Acinetobacter baumannii.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1607":{"model_id":"1607","model_name":"Streptococcus pneumoniae PBP1a conferring resistance to amoxicillin","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"4483":"S575T","4484":"N609D"},"Curated-R":{"4483":"S575T","4484":"N609D"},"clinical":{"4483":"S575T","4484":"N609D"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1350"}},"model_sequences":{"sequence":{"692":{"protein_sequence":{"accession":"AFC91828.1","sequence":"MNKPTILHLIKYLSISFLSLVIAAIVLGGGVFFYYVSKAPSLSESKLVATTSSKIYDNKNQLIADLGSERRVNAQANDIPTDLVKAIVSIEDHRFFDHRGIDTIRILGAFLRNLQSNSLQGGSTLTQQLIKLTYFSTSTSDQTISRKTQEAWLAIQLEQKATKQEILTYYINKVYMSNGNYGMQTAAQNYYGKDLNNLSLPQLALLAGMPQAPNQYDPYSHPEAAQDRRNLVLSEMKNQGYISAEQYEKAVNTPITDGLQSLKSASNYPAYMDNYLKEVINQVEKETGYNLLTTGMDVYTNVDQEAQKHLWDIYNTDEYVAYPDDELQVASTIVDVSNGKVIAQLGARHQSSNVSFGINQAVETNRDWGSTMKPITDYAPALEYGVYDSTATIVHDEPYNYPGTNTPVYNWDRGYFGNITLQYALQQSRNVPAVETLNKVGLNRAKTFLNGLGIDYPSIHYSNAISSNTTESDKKYGASSEKMAAAYAAFANGGTYYKPMYIHKVVFSDGSEKEFSNVGTRAMKETTAYMMTDMMKTVLSYGTGRNAYLAWLPQAGKTGTSNYTDEEIENHIKTSQFVAPDELFAGYTRKYSMAVWTGYSNRLTPLVGNGLTVAAKVYRSMMTYLSEGSNPEDWNIPEGLYRNGEFVFKNGARSTWTQPAPQQPPSTESSSSSSDSSTSQSSSTTPSTNNSTTTDPNNNTQQSNTTPDQQNQNPQPAQP"},"dna_sequence":{"accession":"JN645776.1","fmin":"0","fmax":"2160","strand":"+","sequence":"ATGAACAAACCAACGATTCTGCACCTAATCAAGTATCTGAGCATTAGCTTCTTAAGCTTGGTTATCGCAGCCATTGTCTTAGGCGGAGGAGTTTTTTTCTACTACGTTAGCAAGGCTCCTAGCCTATCCGAGAGTAAACTAGTTGCAACAACTTCTAGTAAAATCTACGACAATAAAAATCAACTCATTGCTGACTTGGGTTCTGAACGCCGCGTCAATGCCCAAGCTAATGATATTCCCACAGATTTGGTTAAGGCAATCGTTTCTATCGAAGACCATCGCTTCTTCGACCACAGGGGGATTGATACCATCCGTATCCTGGGAGCTTTCTTGCGCAATCTGCAAAGCAATTCCCTCCAAGGTGGATCAACTCTCACCCAACAGTTGATTAAGTTGACTTACTTTTCAACTTCGACTTCCGACCAGACTATTTCTCGTAAGACTCAGGAAGCTTGGTTAGCGATTCAGTTAGAACAAAAAGCAACCAAGCAAGAAATCTTGACCTACTATATAAATAAGGTCTACATGTCTAATGGCAACTATGGAATGCAGACAGCAGCTCAAAACTACTATGGTAAAGACCTCAATAATTTAAGTTTACCTCAGTTAGCCTTGCTGGCTGGAATGCCTCAGGCACCAAACCAATATGACCCCTATTCACATCCAGAAGCAGCCCAAGACCGCCGAAACTTGGTCTTATCTGAAATGAAAAATCAAGGCTACATCTCTGCTGAACAGTATGAGAAAGCAGTCAATACACCAATTACTGATGGACTACAAAGTCTCAAATCAGCAAGTAATTACCCTGCTTACATGGATAATTACCTCAAGGAAGTCATCAATCAAGTTGAAAAAGAAACAGGCTATAACCTGCTCACAACTGGGATGGATGTCTACACAAATGTAGACCAAGAAGCTCAAAAACATCTGTGGGATATTTACAATACAGACGAATACGTTGCCTATCCAGACGATGAATTGCAAGTCGCTTCTACCATTGTTGATGTTTCTAACGGTAAAGTCATTGCCCAGCTAGGAGCACGCCATCAGTCAAGTAATGTTTCCTTCGGAATTAACCAAGCAGTAGAAACAAACCGCGACTGGGGATCAACTATGAAACCGATCACAGACTATGCTCCTGCCTTGGAGTACGGTGTCTACGATTCAACTGCTACTATCGTTCACGATGAGCCCTATAACTACCCTGGGACAAATACTCCTGTTTATAACTGGGATAGGGGCTACTTTGGCAACATCACCTTGCAATACGCCCTGCAACAATCGCGAAACGTCCCAGCCGTGGAAACTCTAAACAAGGTCGGACTCAACCGCGCCAAGACTTTCCTAAATGGTCTCGGAATCGACTACCCAAGTATTCACTACTCAAATGCCATTTCAAGTAACACAACCGAATCAGACAAAAAATATGGAGCAAGTAGTGAAAAGATGGCTGCTGCTTACGCTGCCTTTGCAAATGGTGGAACTTACTATAAACCAATGTATATCCATAAAGTCGTCTTTAGTGATGGGAGTGAAAAAGAGTTCTCTAATGTCGGAACTCGTGCCATGAAGGAAACAACAGCCTATATGATGACCGACATGATGAAAACAGTCTTGAGTTATGGAACTGGACGAAATGCCTATCTTGCTTGGCTCCCTCAGGCTGGTAAAACAGGAACCTCTAACTATACAGACGAGGAAATTGAAAACCACATCAAGACCTCTCAATTTGTAGCACCTGACGAACTATTTGCTGGCTATACGCGTAAATATTCAATGGCTGTATGGACAGGCTATTCTAACCGTCTGACACCACTTGTAGGCAATGGCCTTACGGTCGCTGCCAAAGTTTACCGCTCTATGATGACCTACCTGTCTGAAGGAAGCAATCCAGAGGATTGGAATATACCAGAGGGGCTCTACAGAAATGGAGAATTCGTATTTAAAAATGGTGCTCGTTCTACGTGGACTCAACCTGCTCCACAACAACCCCCATCAACTGAAAGTTCAAGCTCATCATCAGATAGTTCAACTTCACAGTCTAGCTCAACCACTCCAAGCACAAATAATAGTACGACTACCGATCCTAACAATAATACGCAACAATCAAATACAACCCCTGATCAACAAAATCAGAATCCTCAACCAGCACAACCATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35917","NCBI_taxonomy_name":"Streptococcus pneumoniae","NCBI_taxonomy_id":"1313"}}}},"ARO_accession":"3003041","ARO_id":"39475","ARO_name":"Streptococcus pneumoniae PBP1a conferring resistance to amoxicillin","CARD_short_name":"Spne_PBP1a_AMX","ARO_description":"PBP1a is a penicillin-binding protein found in Streptococcus pneumoniae.","ARO_category":{"40661":{"category_aro_accession":"3003938","category_aro_cvterm_id":"40661","category_aro_name":"Penicillin-binding protein mutations conferring resistance to beta-lactam antibiotics","category_aro_description":"Mutations in PBP transpeptidases that change the affinity for penicillin thereby conferring resistance to penicillin antibiotics.","category_aro_class_name":"AMR Gene Family"},"35981":{"category_aro_accession":"0000064","category_aro_cvterm_id":"35981","category_aro_name":"amoxicillin","category_aro_description":"Amoxicillin is a moderate-spectrum, bacteriolytic, beta-lactam antibiotic used to treat bacterial infections caused by susceptible microorganisms. A derivative of penicillin, it has a wider range of treatment but remains relatively ineffective against Gram-negative bacteria. It is commonly taken with clavulanic acid, a beta-lactamase inhibitor. Like other beta-lactams, amoxicillin interferes with the synthesis of peptidoglycan.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1773":{"model_id":"1773","model_name":"tet(43)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"4680":{"protein_sequence":{"accession":"ACS83748.1","sequence":"MPPSHHMLRPIEQCSILWNDVRYSNSVRLKEAGMTATTQASAPAARTYLSLRAAWIPLFALCLAFFVEMVDNTLLTIALPTIGRDLGASVTSLQWVTGAYSLTFGGLLLTAGSLADRFGRRRVLQIGLLAFGLISLTVIAVATAGQLIAVRAALGLAAAAMAPITNSLVFRLFEGEDLRRRAMTLMIVVGMSGFILGPLLGGTVLAHASWQWLLLINAPIALIALIGVRLGVPADDAEGLTKDRLDVKGSALSIAAIGLACYTLTSGVEHGWMSAVTWACGIGAAAALMGFVWHERRTDHPMLDLDVFRNRTVRGASIAQVGTSIAMASLMFGLILHFQGAYGWSPMRAGLANLPLILTMILATPVSEGLAKRFGHRIAMLIGAGLLAGSLAGLAWGVGHGYLVIAVFMVTFTLGLRTVMTIAAVGLVGAMPENRTSLGAALNDTAQEVGTSLGMAVIGTLIAVLXTTTLPNGDXSLDLATSYFAGERIAYLFLAVVVGVIAGWGALTLSNSKEMEDVH"},"dna_sequence":{"accession":"GQ244501.1","fmin":"59","fmax":"1619","strand":"-","sequence":"ATGCCCCCATCTCACCACATGTTGCGCCCAATCGAACAATGTTCTATTCTATGGAACGACGTTCGATACTCGAACAGCGTTCGACTGAAGGAGGCCGGTATGACCGCCACAACTCAAGCCTCGGCACCCGCGGCACGTACCTATCTGTCGCTGCGCGCCGCGTGGATTCCGCTCTTCGCGCTCTGCCTCGCGTTCTTCGTGGAGATGGTTGACAACACCCTGCTCACGATCGCGCTGCCGACGATCGGGCGCGACCTCGGCGCGAGCGTCACCTCCTTGCAGTGGGTGACCGGCGCCTATTCGCTGACCTTTGGCGGCCTGTTGCTGACAGCGGGCTCGCTCGCCGACCGCTTTGGCCGGCGCCGCGTGCTGCAGATTGGCCTTCTCGCCTTTGGGCTCATCAGCCTCACGGTGATTGCCGTGGCAACCGCGGGCCAGCTGATCGCGGTGCGCGCTGCGCTCGGCCTCGCCGCCGCCGCGATGGCCCCAATCACCAACTCCCTCGTGTTCAGGCTGTTCGAGGGCGAGGACCTCCGTCGGCGGGCAATGACCCTCATGATCGTCGTCGGCATGAGCGGATTCATCCTTGGCCCGCTACTCGGCGGAACGGTTCTCGCTCACGCCAGCTGGCAGTGGTTGCTGCTTATCAACGCACCCATCGCGCTCATTGCGCTCATCGGCGTTCGCCTTGGCGTGCCTGCGGACGACGCCGAGGGACTCACAAAGGACCGCCTTGACGTGAAGGGCTCGGCACTCAGCATCGCCGCGATCGGCCTCGCTTGCTACACACTCACGAGCGGAGTGGAGCACGGCTGGATGTCTGCCGTCACCTGGGCCTGCGGGATCGGCGCGGCTGCCGCGCTGATGGGATTCGTGTGGCACGAGCGCCGCACCGATCACCCCATGCTGGACCTCGACGTCTTCAGGAACCGCACCGTTCGCGGCGCATCGATCGCCCAGGTAGGCACCTCAATCGCGATGGCTTCGCTGATGTTCGGCCTGATCCTTCACTTCCAGGGCGCGTACGGCTGGAGCCCCATGCGCGCCGGCCTCGCCAACCTGCCGCTCATCCTCACGATGATTCTTGCGACACCGGTCTCTGAGGGCCTCGCGAAGAGGTTCGGCCACCGCATTGCCATGCTCATCGGCGCGGGTCTCCTCGCCGGATCGCTCGCTGGCCTCGCGTGGGGCGTGGGGCATGGSTACCTCGTCATCGCGGTATTCATGGTGACCTTCACCCTCGGTCTCCGCACCGTTATGACGATCGCGGCGGTGGGCCTCGTTGGTGCGATGCCGGAGAACCGCACCTCGCTCGGCGCGGCACTCAACGACACCGCCCAAGAAGTAGGAACAAGCCTCGGCATGGCAGTGATCGGCACGCTCATCGCGGTGCTCGYCACCACGACGCTTCCCAACGGCGACKGGAGCCTCGACCTCGCGACTTCATACTTCGCCGGGGAGCGCATCGCTTATCTGTTCCTTGCCGTCGTAGTCGGAGTGATCGCGGGATGGGGCGCGCTCACGTTGTCCAACTCCAAGGAGATGGAAGACGTCCACTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37082","NCBI_taxonomy_name":"uncultured bacterium AOTet43","NCBI_taxonomy_id":"654983"}}}},"ARO_accession":"3000573","ARO_id":"36712","ARO_name":"tet(43)","CARD_short_name":"tet(43)","ARO_description":"Tet(43) is a tetracycline resistance gene with unknown origins, isolated from metagenomic DNA.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1781":{"model_id":"1781","model_name":"AAC(2')-Ia","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"8144":{"protein_sequence":{"accession":"AAA03550.1","sequence":"MGIEYRSLHTSQLTLSEKEALYDLLIEGFEGDFSHDDFAHTLGGMHVMAFDQQKLVGHVAIIQRHMALDNTPISVGYVEAMVVEQSYRRQGIGRQLMLQTNKIIASCYQLGLLSASDDGQKLYHSVGWQIWKGKLFELKQGSYIRSIEEEGGVMGWKADGEVDFTASLYCDFRGGDQW"},"dna_sequence":{"accession":"L06156.2","fmin":"263","fmax":"800","strand":"+","sequence":"ATGGGCATAGAATACCGCAGTCTGCATACCAGCCAATTGACACTGAGTGAAAAAGAAGCGCTTTACGATTTATTAATTGAAGGTTTTGAAGGCGATTTTTCGCATGACGATTTCGCGCACACTTTAGGTGGAATGCACGTCATGGCTTTTGATCAACAAAAATTGGTTGGTCATGTTGCAATTATTCAACGCCATATGGCCCTAGATAATACGCCTATCTCTGTAGGGTATGTTGAAGCGATGGTAGTTGAACAAAGTTATCGTCGCCAAGGTATTGGGCGGCAATTGATGCTGCAAACCAATAAAATTATAGCTTCGTGTTATCAATTAGGGCTGCTGTCGGCTTCAGATGATGGACAAAAATTGTATCATTCGGTTGGATGGCAAATCTGGAAAGGTAAGTTGTTTGAATTGAAACAAGGGAGCTATATCCGTTCTATTGAAGAAGAAGGCGGAGTCATGGGCTGGAAAGCGGATGGTGAGGTTGATTTTACCGCTTCGCTTTACTGTGATTTTCGTGGCGGTGATCAGTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36946","NCBI_taxonomy_name":"Providencia stuartii","NCBI_taxonomy_id":"588"}}}},"ARO_accession":"3002523","ARO_id":"38923","ARO_name":"AAC(2')-Ia","CARD_short_name":"AAC(2')-Ia","ARO_description":"AAC(2')-Ia is a chromosomal-encoded aminoglycoside acetyltransferase in P. stuartii.","ARO_category":{"36480":{"category_aro_accession":"3000341","category_aro_cvterm_id":"36480","category_aro_name":"AAC(2')","category_aro_description":"A category of aminoglycoside N-acetyltransferase enzymes with modification regiospecificity based at the 2'-amino group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics through acetylation of the 2-amino group of the compound.","category_aro_class_name":"AMR Gene Family"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"46127":{"category_aro_accession":"3007377","category_aro_cvterm_id":"46127","category_aro_name":"6'-N-ethylnetilmicin","category_aro_description":"6'-N-ethylnetilmicin is an aminoglycoside antibiotic and a derivative of netilmicin.","category_aro_class_name":"Antibiotic"},"46133":{"category_aro_accession":"3007382","category_aro_cvterm_id":"46133","category_aro_name":"gentamicin","category_aro_description":"Gentamicin is a commonly used aminoglycoside antibiotic derived from members of the Micromonospora genus of bacteria. It acts by binding the 30S ribosomal subunit, thus inhibiting protein synthesis. Gentamicin is typically used to treat Gram-negative infections of the repiratory and urinary tract, as well as infections of the bone and soft tissue. It also exhibits considerable nephrotoxicity and ototoxicity. Gentamicin is administered as a mixture of gentamicin type C (which makes about around 80% of the complex) and types A, B, and X (distributed in the remaining 20% of the complex).","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1782":{"model_id":"1782","model_name":"TEM-12","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"996":{"protein_sequence":{"accession":"AAA25053.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDSWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"M88143.1","fmin":"367","fmax":"1228","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATAGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3000884","ARO_id":"37264","ARO_name":"TEM-12","CARD_short_name":"TEM-12","ARO_description":"TEM-12 is an extended-spectrum beta-lactamase found in Klebsiella oxytoca.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1783":{"model_id":"1783","model_name":"VIM-36","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1578":{"protein_sequence":{"accession":"AGC50806.1","sequence":"MFKLLSKLLVYLTASIMAIASPLAFSVDSSGEYPTVSEIPVGEVRLYQIADGVWSHIATRSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEVEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSASVLYGGCAIYELSRTSAGNVADADLAEWPTSIERIQQHYPEAQFVIPGHGLPGGLDLLKHTTNVVKAHTNRSVVE"},"dna_sequence":{"accession":"JX982635.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGTTCAAACTTTTGAGTAAGTTATTGGTCTATTTGACCGCGTCTATCATGGCTATTGCGAGTCCGCTCGCTTTTTCCGTAGATTCTAGCGGTGAGTATCCGACAGTCAGCGAAATTCCGGTCGGGGAGGTCCGGCTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCGGTCGTTTGATGGCGCAGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAGAAGCAAATTGGACTTCCTGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGTAGAGGGGAACGAGATTCCCACGCACTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAACTCTTCTATCCTGGTGCTGCGCATTCGACCGACAACTTAGTTGTGTACGTCCCGTCTGCGAGTGTGCTCTATGGTGGTTGTGCGATTTATGAGTTGTCACGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCATTGAGCGGATTCAACAACACTACCCGGAAGCACAGTTCGTCATTCCGGGGCACGGCCTGCCGGGCGGTCTAGACTTGCTCAAGCACACAACGAATGTTGTAAAAGCGCACACAAATCGCTCAGTCGTTGAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002306","ARO_id":"38706","ARO_name":"VIM-36","CARD_short_name":"VIM-36","ARO_description":"VIM-36 is a beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1784":{"model_id":"1784","model_name":"OXA-334","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1687":{"protein_sequence":{"accession":"AGW16416.1","sequence":"MKTVQLCLIVLITTFGSACTTISPSVETAKNQHQQSTQQQIQQAFNQLQTTGVIVIKDKHGLHSYGNDLSRAQTPYVPASTFKMLNALIGLEHGKATRTEVFKWDGQKRSFTAWEKDMTLGQAMQASAVPVYQELARRIGVDLMQKEVQRIGYGNQQIGTVVDNFWLVGPLQITPVQEVLFVEKLANTQLAFKPDVQHTVQDMLLIEQKPNYKLYAKSGWGMDLEPQVGWWAGWVETSTGEKAYFALNMQMKTGISASVREQLVKQSLTALGII"},"dna_sequence":{"accession":"KF203108.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAAAACTGTACAGTTGTGCCTCATCGTCCTCATTACTACCTTCGGTTCCGCATGTACCACAATAAGCCCCTCCGTAGAAACAGCTAAAAACCAACATCAGCAAAGCACGCAGCAGCAGATCCAACAAGCCTTCAATCAACTCCAAACCACGGGGGTGATTGTCATTAAGGATAAACATGGCTTACACAGCTACGGCAATGACTTGAGCCGTGCTCAGACACCCTATGTACCGGCCTCTACCTTTAAAATGCTGAATGCCTTAATCGGACTAGAACATGGTAAAGCAACCAGAACCGAGGTGTTTAAATGGGATGGTCAAAAGCGCAGCTTCACTGCCTGGGAAAAAGACATGACTTTAGGGCAAGCCATGCAAGCATCTGCCGTTCCCGTTTATCAGGAGCTTGCACGGCGCATTGGTGTAGATCTAATGCAAAAAGAAGTACAGCGCATTGGATATGGCAATCAACAGATTGGCACCGTTGTCGATAATTTTTGGTTAGTCGGTCCACTGCAAATTACGCCTGTTCAAGAAGTCCTTTTTGTAGAGAAGCTGGCCAATACGCAACTCGCTTTTAAGCCAGATGTGCAACATACCGTACAAGACATGCTACTGATTGAACAAAAACCGAATTATAAACTCTACGCCAAATCAGGCTGGGGTATGGACCTAGAACCACAAGTGGGCTGGTGGGCAGGCTGGGTCGAAACTTCAACAGGTGAAAAAGCGTATTTTGCTTTGAATATGCAGATGAAAACGGGAATTTCAGCCAGCGTGCGTGAGCAACTGGTCAAACAAAGTCTGACAGCACTGGGGATAATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39092","NCBI_taxonomy_name":"Acinetobacter johnsonii","NCBI_taxonomy_id":"40214"}}}},"ARO_accession":"3001522","ARO_id":"37922","ARO_name":"OXA-334","CARD_short_name":"OXA-334","ARO_description":"OXA-334 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46494":{"category_aro_accession":"3007705","category_aro_cvterm_id":"46494","category_aro_name":"OXA-211-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-211.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1785":{"model_id":"1785","model_name":"TEM-48","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1650":{"protein_sequence":{"accession":"CAA71323.1","sequence":"MSIQHFRVALIPFFAAFCFPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGASKRGSRGIIAALGPDGKPSRIVVIYMTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"Y10280.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCTTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCAGTAAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACATGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3000917","ARO_id":"37297","ARO_name":"TEM-48","CARD_short_name":"TEM-48","ARO_description":"TEM-48 is an extended-spectrum beta-lactamase found Klebsiella pneumoniae.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1786":{"model_id":"1786","model_name":"mexY","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1800"}},"model_sequences":{"sequence":{"414":{"protein_sequence":{"accession":"BAA34300.1","sequence":"MARFFIDRPVFAWVISLLIVLAGVLAIRFLPVAQYPDIAPPVVNVSATYPGASAKVVEEAVTAIIEREMNGAPGLLYTKATSSTGQASLTLTFRQGVNANLAAVEVQNRLKIVESRLPESVRRDGIYVEKAADSIQLIVTLTSSSGRYDAMELGEIASSNVLQALRRVEGVGKVETWGAEYAMRIWPDPAKLTSMNLSASDLVNAVRRHNARLTVGDIGNLGVPDSAPISATVKVDDTLVTPEQFGEIPLAHPRDGGAIRLRDVARVEFGQSEYGFVSRVNQMTATGLAVKMAPGSNAVATAKRIRATLDELSRYFPEGVSYNIPYDTSAFVEISIRKVVSTLLEAMLLVFAVMYLFMQNFRATLIPTLVVPVALLGTFTVMLGLGFSINVLTMFGMVLAIGILVDDAIIVVENVERLMAEEGLSPHDATVKAMRQISGAIVGITVVLVSVFVPMAFFSGAVGNIYRQFAVTLAVSIGFSAFLALSLTPALCATLLRPIDADHHEKRGFFGWFNRAFLRLTGRYRNAVAGILARPIRWMLVYTLVIGVVALLFVRLPQAFLPEEDQGDFMIMVMQPEGTPMAETMANVGDVERYLAEHEPVAYAYAVGGFSLYGDGTSSAMIFATLKDWSERREASQHVGAIVERINQRFAGLPNRTVYAMNSPPLPDLGSTSGFDFRLQDRGGVGYEALVKARDQLLARAAEDPRLANVMFAGQGEAPQIRLDIDRRKAETLGVSMDEINTTLAVMFGSDYIGDFMHGSQVRKVVVQADRRKRLGIDDIGRLHVRNEQGEMGAAGDVRQGRLDPRPAATDPLQRLSLVQPRGPGRAGLQQREAMQAMEQLMQGTARGIRPRVVRPVLRRTPVAGAQAPALFALSVLIVFLALAALYESWSIPLAVILVVPLGVLGALLGVSLRGLPNDIYFKVGLITIIGLSAKNAILIIEVAKDHYQEGMSLLQATLEAARLRLRPIVMTSLAFGFGVVPLALSSGAGIRAQVAIGTGVLGGIVTATVLAVFLVPLFFLVVGRLFRLRKAPRTGNSPQIPTEQA"},"dna_sequence":{"accession":"AB015853.1","fmin":"1330","fmax":"4471","strand":"+","sequence":"ATGGCTCGTTTCTTCATTGACCGGCCGGTCTTCGCCTGGGTGATCTCCCTGCTGATCGTGCTCGCCGGGGTCCTGGCGATCCGCTTCCTGCCGGTCGCCCAGTACCCGGACATCGCGCCGCCGGTGGTCAACGTCAGCGCCACGTATCCCGGCGCCTCGGCCAAGGTGGTCGAGGAAGCGGTGACCGCGATCATCGAGCGCGAGATGAACGGCGCGCCCGGCCTGCTCTACACCAAGGCCACCAGCAGCACCGGCCAGGCCTCGCTGACCCTGACCTTCCGCCAGGGCGTGAACGCGAACCTCGCCGCGGTGGAAGTGCAGAACCGCCTGAAGATCGTCGAGTCGCGCCTGCCCGAATCGGTGCGGCGCGACGGCATCTACGTGGAGAAGGCGGCGGACAGCATCCAGCTGATCGTTACCCTTACCTCCTCCAGCGGCCGCTACGACGCCATGGAGCTGGGCGAGATCGCCTCGTCCAACGTGTTGCAGGCGCTGCGCCGGGTGGAGGGCGTGGGCAAGGTCGAGACCTGGGGCGCCGAGTACGCCATGCGCATCTGGCCCGACCCGGCCAAGCTGACCTCGATGAACCTCAGCGCCAGCGACCTGGTCAACGCCGTGCGCCGGCACAACGCCCGCCTCACCGTGGGCGACATCGGCAACCTCGGGGTCCCCGACTCGGCGCCGATCAGCGCCACGGTGAAGGTCGACGACACCCTGGTGACGCCCGAGCAGTTCGGCGAAATTCCGCTGGCGCATCCGCGCGACGGCGGCGCGATCCGCCTGCGCGACGTGGCCCGCGTCGAGTTCGGCCAGAGCGAGTACGGCTTCGTCTCGCGGGTCAACCAAATGACCGCCACCGGCCTGGCGGTGAAGATGGCGCCCGGCTCCAACGCGGTGGCCACCGCCAAGCGCATCCGCGCCACCCTCGACGAGCTGTCGCGCTACTTCCCGGAGGGCGTGAGCTACAACATCCCCTATGACACCTCGGCGTTCGTCGAGATCTCGATCAGGAAGGTGGTCAGCACCCTGCTCGAGGCGATGCTGCTGGTGTTCGCCGTGATGTACCTGTTCATGCAGAACTTCCGCGCCACCCTGATCCCGACACTGGTGGTGCCGGTGGCCCTGCTGGGCACCTTCACGGTGATGCTCGGCCTGGGCTTCTCGATCAACGTGCTGACCATGTTCGGCATGGTCCTGGCGATCGGCATCCTGGTGGACGACGCGATCATCGTGGTGGAGAACGTCGAGCGGCTGATGGCCGAGGAAGGCCTGTCGCCGCACGACGCCACGGTCAAGGCGATGCGCCAGATCAGCGGGGCCATCGTCGGCATCACCGTAGTGCTGGTCTCGGTGTTCGTGCCGATGGCGTTCTTCAGCGGCGCGGTGGGCAACATCTACCGCCAGTTCGCGGTGACCCTGGCGGTCTCCATCGGCTTCTCGGCGTTCCTCGCGCTGTCGCTGACCCCGGCCCTGTGCGCCACCCTGCTGCGCCCGATCGACGCCGACCACCACGAGAAGCGCGGCTTCTTCGGCTGGTTCAACCGCGCCTTCCTGCGCCTGACCGGACGCTACCGCAACGCGGTGGCCGGCATCCTCGCCCGGCCGATCCGCTGGATGCTGGTCTACACCCTGGTCATCGGCGTGGTCGCCCTGCTCTTCGTGCGCCTGCCGCAGGCGTTCCTGCCGGAAGAGGACCAGGGCGACTTCATGATCATGGTGATGCAGCCCGAAGGCACGCCGATGGCGGAGACCATGGCCAACGTCGGCGACGTCGAGCGCTACCTGGCGGAGCACGAACCGGTGGCCTACGCCTATGCGGTCGGCGGCTTCAGCCTGTACGGCGACGGCACCAGCTCGGCGATGATCTTCGCCACCCTGAAGGACTGGTCGGAACGCCGGGAGGCCAGCCAGCACGTCGGCGCCATCGTCGAGCGCATCAACCAGCGCTTCGCCGGCCTGCCCAACCGTACGGTGTATGCGATGAACTCGCCGCCGCTGCCGGACCTGGGTTCCACCAGCGGCTTCGACTTCCGCCTGCAGGACCGTGGCGGGGTTGGCTACGAGGCCCTGGTCAAGGCCCGCGACCAGTTGCTGGCGCGCGCCGCCGAGGACCCGCGCCTGGCCAACGTGATGTTCGCCGGCCAGGGCGAGGCGCCGCAGATCCGCCTGGACATCGACCGGCGCAAGGCGGAGACCCTTGGCGTGAGCATGGACGAGATCAACACCACCCTGGCGGTGATGTTCGGCTCGGACTACATCGGCGACTTCATGCACGGCAGCCAGGTGCGCAAGGTGGTGGTCCAGGCCGACCGGCGCAAGCGCCTGGGCATCGACGACATCGGCCGGCTTCACGTGCGCAACGAGCAGGGCGAGATGGGTGCCGCTGGCGACGTTCGCCAAGGCCGCCTGGACCCTCGGCCCGCCGCAACTGACCCGCTACAACGGCTATCCCTCGTTCAACCTCGAGGGCCAGGCCGCGCCGGGCTACAGCAGCGCGAAGCCATGCAGGCGATGGAGCAATTGATGCAGGGAACTGCCCGAGGCATTCGCCCACGAGTGGTCCGGCCAGTCCTTCGAAGAACGCCTGTTGCCGGCGCCCAGGCGCCGGCGCTGTTCGCCCTCTCGGTGTTGATCGTGTTCCTCGCCCTGGCCGCCCTCTACGAAAGCTGGTCGATCCCGCTGGCGGTGATCCTGGTGGTGCCGCTGGGCGTACTCGGCGCACTGCTCGGGGTGAGCCTGCGCGGTCTGCCCAACGACATCTACTTCAAGGTCGGCCTGATCACCATCATCGGCCTCTCGGCGAAGAACGCCATCCTCATCATCGAGGTGGCCAAGGACCATTACCAGGAAGGCATGAGCCTGCTGCAGGCGACCCTGGAGGCCGCGCGCCTGCGCCTGCGACCGATCGTCATGACCTCGCTGGCGTTCGGTTTCGGCGTGGTCCCGCTGGCGCTCTCCAGCGGCGCCGGTATCCGCGCCCAGGTCGCCATCGGCACCGGGGTGCTCGGCGGGATCGTCACCGCCACGGTACTCGCGGTGTTCCTGGTACCGCTGTTCTTCCTGGTGGTCGGGCGCCTGTTCCGGTTGCGCAAGGCGCCGCGCACCGGCAACTCGCCCCAGATCCCCACGGAGCAAGCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36804","NCBI_taxonomy_name":"Pseudomonas aeruginosa PAO1","NCBI_taxonomy_id":"208964"}}}},"ARO_accession":"3003033","ARO_id":"39467","ARO_name":"mexY","CARD_short_name":"mexY","ARO_description":"MexY is the RND-type membrane protein of the efflux complex MexXY-OprM.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35963":{"category_aro_accession":"0000045","category_aro_cvterm_id":"35963","category_aro_name":"acriflavine","category_aro_description":"Acriflavine is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35990":{"category_aro_accession":"0000073","category_aro_cvterm_id":"35990","category_aro_name":"meropenem","category_aro_description":"Meropenem is an ultra-broad spectrum injectable antibiotic used to treat a wide variety of infections, including meningitis and pneumonia. It is a beta-lactam and belongs to the subgroup of carbapenem, similar to imipenem and ertapenem.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37007":{"category_aro_accession":"3000663","category_aro_cvterm_id":"37007","category_aro_name":"ofloxacin","category_aro_description":"Ofloxacin is a 6-fluoro, 7-piperazinyl quinolone with a methyl-substituted oxazine ring. It has a broad spectrum of activity including many enterobacteria and mycoplasma but most anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"46133":{"category_aro_accession":"3007382","category_aro_cvterm_id":"46133","category_aro_name":"gentamicin","category_aro_description":"Gentamicin is a commonly used aminoglycoside antibiotic derived from members of the Micromonospora genus of bacteria. It acts by binding the 30S ribosomal subunit, thus inhibiting protein synthesis. Gentamicin is typically used to treat Gram-negative infections of the repiratory and urinary tract, as well as infections of the bone and soft tissue. It also exhibits considerable nephrotoxicity and ototoxicity. Gentamicin is administered as a mixture of gentamicin type C (which makes about around 80% of the complex) and types A, B, and X (distributed in the remaining 20% of the complex).","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"43746":{"category_aro_accession":"3005386","category_aro_cvterm_id":"43746","category_aro_name":"disinfecting agents and antiseptics","category_aro_description":"Disinfectants that can also interact with antimicrobial resistance mechanisms, e.g. molecule efflux, and thus are the targets of disinfectant resistance.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1787":{"model_id":"1787","model_name":"VIM-42","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"2128":{"protein_sequence":{"accession":"AJP08641.1","sequence":"MLKVISSLLVYMTASVMAVASPLAHSGEPSGEYPTVNEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEAEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSANVLYGGCAVHELSSTSAGNVADADLAEWPTSIERIQKHYPEAEVVIPGHGLPGGLDLLQHTANVVKAHKNRSVAE"},"dna_sequence":{"accession":"KP071470.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGTTAAAAGTTATTAGTAGTTTATTGGTCTACATGACCGCGTCTGTCATGGCTGTCGCAAGTCCGTTAGCCCATTCCGGGGAGCCGAGTGGTGAGTATCCGACAGTCAACGAAATTCCGGTCGGAGAGGTCCGACTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCGGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAAAAGCAAATTGGACTTCCCGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGCAGAGGGGAACGAGATTCCCACGCATTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAGCTCTTCTATCCTGGTGCTGCGCATTCGACCGACAATCTGGTTGTATACGTCCCGTCAGCGAACGTGCTATACGGTGGTTGTGCCGTTCATGAGTTGTCAAGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCATTGAGCGGATTCAAAAACACTACCCGGAAGCAGAGGTCGTCATTCCCGGGCACGGTCTACCGGGCGGTCTAGACTTGCTCCAGCACACAGCGAACGTTGTCAAAGCACACAAAAATCGCTCAGTCGCCGAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3003178","ARO_id":"39755","ARO_name":"VIM-42","CARD_short_name":"VIM-42","ARO_description":"VIM-42 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1788":{"model_id":"1788","model_name":"ACT-6","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1972":{"protein_sequence":{"accession":"ACJ05686.1","sequence":"MMTKSLCCALLLSTSCSVLAAPMSEKQLAEVVERTVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMSYEQAITTRVFKPLKLDHTWINVPKAEEAHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVKDMANWVMVNMKPDSLQDSSLKEGITLAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVEGSDNKVALAPLPAREVNPPAPPVNASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILDALQ"},"dna_sequence":{"accession":"FJ237366.1","fmin":"40","fmax":"1186","strand":"+","sequence":"ATGATGACTAAATCCCTTTGCTGCGCCCTGCTGCTCAGCACCTCCTGCTCGGTATTGGCTGCCCCGATGTCAGAAAAACAGCTGGCTGAGGTGGTGGAACGTACCGTTACGCCGCTGATGAAAGCTCAGGCCATTCCGGGTATGGCGGTGGCGGTGATTTATCAGGGTCAGCCGCACTACTTTACCTTCGGTAAAGCCGATGTCGCGGCGAATAAACCCGTCACCCCACAAACCTTATTCGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTACTCGGCGGCGATGCCATTGCTCGCGGTGAAATATCGCTGGGCGATCCGGTGACAAAATACTGGCCTGAGCTGACAGGCAAGCAGTGGCAGGGGATCCGCATGCTGGATCTGGCAACCTATACCGCAGGTGGTTTGCCGTTACAGGTACCGGATGAGGTCACGGATAACGCCTCACTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCGGGCACCACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGCGCGCTGGCGGTCAAACCTTCCGGCATGAGCTATGAGCAGGCCATAACGACGCGGGTCTTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTTCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGATACCGCGACGGTAAGGCGGTACACGTTTCGCCAGGAATGCTGGACGCTGAAGCCTATGGCGTAAAAACCAACGTGAAGGATATGGCAAACTGGGTGATGGTCAACATGAAGCCGGACTCGCTTCAGGATAGTTCACTCAAGGAAGGCATTACCCTGGCGCAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAGGGATTAGGCTGGGAAATGCTTAACTGGCCGGTCGATGCCAAAACCGTGGTTGAAGGTAGCGACAATAAGGTGGCGCTGGCACCGCTGCCTGCGAGAGAAGTGAATCCACCGGCGCCCCCGGTCAATGCGTCATGGGTCCATAAAACAGGCTCTACCGGCGGGTTTGGCAGCTACGTGGCATTTATTCCTGAAAAGCAGCTCGGCATTGTGATGCTGGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCGTATCCTCGACGCGCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001825","ARO_id":"38225","ARO_name":"ACT-6","CARD_short_name":"ACT-6","ARO_description":"ACT-6 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1789":{"model_id":"1789","model_name":"QnrB44","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"5842":{"protein_sequence":{"accession":"WP_063866105.1","sequence":"MALALVGEKIDRNRFTGEKIENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNASALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGAQVLGATFSGSDLSGGEFTTFDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDNYQASLLMERLGIAVIG"},"dna_sequence":{"accession":"NG_050507.1","fmin":"36","fmax":"681","strand":"+","sequence":"ATGGCTCTGGCACTCGTTGGCGAAAAAATTGACAGAAACCGTTTCACCGGTGAGAAAATTGAAAATAGTACATTTTTTAACTGTGATTTTTCAGGTGCCGACCTAAGTGGTACTGAATTTATCGGCTGTCAGTTCTATGATCGTGAAAGCCAGAAAGGGTGCAATTTTAGTCGTGCAATGCTGAAAGATGCCATTTTTAAAAGCTGTGATTTATCCATGGCGGATTTTCGCAATGCCAGTGCGCTGGGCATTGAAATTCGCCACTGCCGCGCACAAGGTGCAGATTTCCGCGGCGCAAGCTTTATGAATATGATCACTACACGCACCTGGTTTTGCAGCGCATATATCACTAACACAAATCTAAGCTACGCCAATTTTTCGAAAGTCGTGCTGGAAAAGTGTGAGCTGTGGGAAAACCGTTGGATGGGTGCCCAGGTACTGGGCGCGACGTTCAGTGGTTCAGATCTCTCCGGCGGCGAGTTTACGACTTTCGACTGGCGAGCAGCAAACTTCACACATTGCGATCTGACCAATTCGGAGTTGGGTGACTTAGATATTCGGGGCGTTGATTTACAAGGCGTTAAGTTGGACAACTACCAGGCATCGTTGCTCATGGAACGTCTTGGCATCGCGGTCATTGGTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002759","ARO_id":"39193","ARO_name":"QnrB44","CARD_short_name":"QnrB44","ARO_description":"QnrB44 is a plasmid-mediated quinolone resistance protein found in Escherichia coli.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1791":{"model_id":"1791","model_name":"TEM-164","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"2033":{"protein_sequence":{"accession":"ABX71157.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQVGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQTAEIGASLIKHW"},"dna_sequence":{"accession":"EU274580.1","fmin":"214","fmax":"1075","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGGTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGACCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001030","ARO_id":"37410","ARO_name":"TEM-164","CARD_short_name":"TEM-164","ARO_description":"TEM-164 is an extended-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1792":{"model_id":"1792","model_name":"DHA-20","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1414":{"protein_sequence":{"accession":"AIT76101.1","sequence":"MKKSLSATLISALLAFSAPGFSAADNVAAVVDSTIKPLMAQQDIPGMAVAVSVKGKPYYFNYGFADVQAKQPVTENTLFELGSVSKTFTGVLGAVSVAKKEMTLNDPAEKYQPELALPQWKGITLLDLATYTAGGLPLQVPDAVKSRADLLNFYQQWQPSRKPGDMRLYANSSIGLFGALTANAAGMPYEQLLTARILAPLGLSHTFITVPESAQSQYAYGYKNKKPVRVSPGQLDAESYGVKSASKDMLRWAEMNMEPSRAGNADLEMAMYLAQTRYYKTAAINQGLGWEMYDWPQQKDMIINGVTNEVALQPHPVTDNQVQPYNRASWVHKTGATTGFGAYVAFIPEKQVAIVILANKNYPNTERVKAAQAILSALE"},"dna_sequence":{"accession":"KM087848.1","fmin":"0","fmax":"1140","strand":"+","sequence":"ATGAAAAAATCGTTATCTGCAACACTGATTTCCGCCCTGCTGGCATTTTCCGCCCCGGGGTTTTCTGCCGCTGATAATGTCGCGGCGGTGGTGGACAGCACCATTAAACCGCTGATGGCACAGCAGGATATTCCCGGGATGGCGGTTGCCGTCTCCGTAAAGGGTAAGCCCTATTATTTCAATTACGGTTTTGCCGATGTTCAGGCAAAACAGCCTGTCACTGAAAATACACTATTTGAGCTCGGATCTGTAAGTAAAACTTTCACAGGTGTGCTGGGTGCGGTTTCCGTGGCGAAAAAAGAGATGACGCTGAATGACCCGGCAGAAAAATACCAGCCGGAGCTGGCTCTGCCGCAGTGGAAGGGGATCACACTGTTGGATCTGGCCACCTACACCGCAGGCGGGCTGCCGTTACAGGTACCGGATGCGGTGAAAAGCCGTGCGGATCTGCTGAATTTCTATCAGCAGTGGCAGCCGTCCCGGAAACCGGGCGATATGCGTCTGTATGCAAACAGCAGTATCGGCCTGTTTGGTGCTCTGACCGCCAACGCAGCGGGGATGCCGTATGAGCAGTTGCTGACTGCACGGATCCTGGCACCGCTGGGGTTATCTCACACCTTTATTACTGTGCCGGAAAGCGCGCAAAGCCAGTATGCGTACGGTTATAAAAACAAAAAACCGGTCCGCGTGTCGCCGGGACAGCTTGATGCGGAATCTTACGGCGTGAAATCCGCCTCAAAAGATATGCTGCGCTGGGCGGAAATGAATATGGAGCCGTCACGGGCCGGTAATGCGGATCTGGAAATGGCAATGTATCTTGCACAGACCCGCTACTATAAAACCGCCGCGATTAACCAGGGGCTGGGCTGGGAAATGTATGACTGGCCGCAGCAGAAAGATATGATCATTAACGGCGTGACCAACGAGGTCGCATTGCAGCCGCACCCGGTAACAGACAACCAGGTTCAGCCGTATAACCGTGCTTCCTGGGTGCATAAAACGGGGGCAACAACCGGTTTCGGCGCCTATGTGGCCTTTATTCCGGAAAAACAGGTGGCGATTGTGATTCTGGCGAATAAAAACTACCCGAATACCGAAAGAGTCAAAGCCGCACAGGCTATTTTGAGTGCACTGGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36934","NCBI_taxonomy_name":"Citrobacter koseri","NCBI_taxonomy_id":"545"}}}},"ARO_accession":"3002151","ARO_id":"38551","ARO_name":"DHA-20","CARD_short_name":"DHA-20","ARO_description":"DHA-20 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36207":{"category_aro_accession":"3000068","category_aro_cvterm_id":"36207","category_aro_name":"DHA beta-lactamase","category_aro_description":"DHA beta-lactamases are plasmid-mediated AmpC \u03b2-lactamases that confer resistance to cephamycins and oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1793":{"model_id":"1793","model_name":"DHA-14","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"827":{"protein_sequence":{"accession":"AIT76107.1","sequence":"MKKSLSATLISALLAFSAPGFSAADNVAAVVDSTIKPLMAQQDIPGMAVAVSVKGKPYYFNYGFADIQAKQPVTENTLFELGSVSKTFTGVLGAVSVAKKEMALNDPAAKYQPELALPQWKGITLLDLATYTAGGLPLQVPDAVKSRADLLHFYQQWQPSRKPGDMRLYANSSIGLFGALTANAAGMPYEQLLTARILAPLGLSHTFITVPESAQSQYAYGYKNKKPVRVSPGQLDAESYGVKSASKDMLRWAEMNMEPSRAGNADLEMAMYLAQTRYYKTAAINQGLGWEMYDWPQQKDMIINGVTNEVALQPHPVTDNQVQPYNRASWVHKTGATTGFGAYVAFIPEKQVAIVILANKNYPNTERVKAAQAILSALE"},"dna_sequence":{"accession":"KM087854.1","fmin":"0","fmax":"1140","strand":"+","sequence":"ATGAAAAAATCGTTATCTGCAACACTGATTTCCGCTCTGCTGGCGTTTTCCGCCCCGGGGTTTTCTGCCGCTGATAATGTCGCGGCGGTGGTGGACAGCACCATTAAACCGCTGATGGCACAGCAGGATATTCCCGGGATGGCGGTTGCCGTCTCCGTAAAGGGTAAGCCCTATTATTTCAATTATGGTTTTGCCGATATTCAGGCAAAACAGCCGGTCACTGAAAATACACTATTTGAGCTCGGATCTGTAAGTAAAACTTTCACAGGTGTGCTGGGTGCGGTTTCTGTGGCGAAAAAAGAGATGGCGCTGAATGATCCGGCGGCAAAATACCAGCCGGAGCTGGCTCTGCCGCAGTGGAAGGGGATCACATTGCTGGATCTGGCTACCTATACCGCAGGCGGACTGCCGTTACAGGTGCCGGATGCGGTAAAAAGCCGTGCGGATCTGCTGCACTTCTATCAGCAGTGGCAGCCGTCCCGGAAACCGGGCGATATGCGTCTGTATGCAAACAGCAGTATCGGCCTGTTTGGTGCTCTGACCGCAAACGCGGCGGGGATGCCGTATGAGCAGTTGCTGACTGCACGGATCCTGGCACCGCTGGGGTTATCTCACACCTTTATTACTGTGCCGGAAAGTGCGCAAAGCCAGTATGCGTACGGTTATAAAAACAAAAAACCGGTCCGCGTGTCGCCGGGACAGCTTGATGCGGAATCTTACGGCGTGAAATCCGCCTCAAAAGATATGCTGCGCTGGGCGGAAATGAATATGGAGCCGTCACGGGCCGGTAATGCGGATCTGGAAATGGCAATGTATCTTGCACAGACCCGCTACTATAAAACCGCCGCGATTAACCAGGGGCTGGGCTGGGAAATGTATGACTGGCCGCAGCAGAAAGATATGATCATTAACGGCGTGACCAACGAGGTCGCATTGCAGCCGCACCCGGTAACAGACAACCAGGTTCAGCCGTATAACCGTGCTTCCTGGGTGCATAAAACGGGGGCAACAACTGGTTTCGGCGCCTATGTGGCCTTTATTCCGGAAAAACAGGTGGCGATTGTGATTCTGGCGAATAAAAACTACCCGAATACCGAAAGAGTCAAAGCCGCACAGGCTATTTTGAGTGCACTGGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36917","NCBI_taxonomy_name":"Morganella morganii","NCBI_taxonomy_id":"582"}}}},"ARO_accession":"3002145","ARO_id":"38545","ARO_name":"DHA-14","CARD_short_name":"DHA-14","ARO_description":"DHA-14 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36207":{"category_aro_accession":"3000068","category_aro_cvterm_id":"36207","category_aro_name":"DHA beta-lactamase","category_aro_description":"DHA beta-lactamases are plasmid-mediated AmpC \u03b2-lactamases that confer resistance to cephamycins and oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1666":{"model_id":"1666","model_name":"vanX gene in vanB cluster","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"200"}},"model_sequences":{"sequence":{"3456":{"protein_sequence":{"accession":"AAB05628.1","sequence":"MENGFLFLDEMLHGVRWDAKYATWDNFTGKPVDGYEVNRIIGTKAVALALREAQIHAARLGYGLLLWDGYRPKSAVDCFLRWAAQPEDNLTKEKYYPNIERAELITKGYVASQSSHSRGSTIDLTLYHLDTGELVSMGSNFDFMDERSHHTAKGIGNAEAQNRRCLRKIMESSGFQSYRFEWWHYKLIDEPYPDTYFNFAVS"},"dna_sequence":{"accession":"U35369.1","fmin":"6004","fmax":"6613","strand":"+","sequence":"ATGGAAAATGGTTTTTTGTTTTTAGATGAAATGTTGCATGGTGTTCGTTGGGATGCCAAGTACGCTACATGGGATAACTTCACGGGAAAACCAGTGGATGGGTATGAGGTGAATCGCATCATCGGCACAAAGGCCGTGGCGCTTGCTCTGCGCGAAGCACAAATCCATGCGGCACGCCTTGGCTACGGCTTGCTTTTATGGGATGGATATCGGCCAAAATCTGCGGTGGACTGTTTCCTGCGTTGGGCGGCGCAGCCGGAGGACAACCTCACAAAAGAAAAATATTACCCCAATATTGAGCGAGCCGAGTTGATTACAAAGGGCTATGTGGCCTCACAATCCAGCCATAGCCGTGGAAGCACAATTGATCTTACGCTCTACCACTTGGATACAGGGGAACTTGTTTCAATGGGAAGCAACTTCGATTTTATGGACGAACGGTCGCACCATACAGCAAAAGGGATAGGGAATGCAGAGGCACAAAATCGAAGATGCTTGCGTAAAATCATGGAAAGCAGCGGATTTCAGTCCTATCGCTTTGAATGGTGGCACTATAAGTTGATTGATGAGCCATACCCCGATACCTATTTTAATTTTGCTGTTTCATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35918","NCBI_taxonomy_name":"Enterococcus faecalis","NCBI_taxonomy_id":"1351"}}}},"ARO_accession":"3002950","ARO_id":"39384","ARO_name":"vanX gene in vanB cluster","CARD_short_name":"vanX_in_vanB_cl","ARO_description":"Also known as vanXB, is a vanX variant found in the vanB gene cluster.","ARO_category":{"36020":{"category_aro_accession":"3000011","category_aro_cvterm_id":"36020","category_aro_name":"vanX","category_aro_description":"VanX is a D,D-dipeptidase that cleaves D-Ala-D-Ala but not D-Ala-D-Lac, ensuring that the latter dipeptide that has reduced binding affinity with vancomycin is used to synthesize peptidoglycan substrate.","category_aro_class_name":"AMR Gene Family"},"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1677":{"model_id":"1677","model_name":"cepA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"3285":{"protein_sequence":{"accession":"AAA21532.1","sequence":"MQKRLIHLSIIFFLLCPALVVAQNSPLETQLKKAIEGKKAEIGIAVIIDGQDTITVNNDIHYPMMSVFKFHQALALADYMHHQKQPLETRLLIKKSDLKPDTYSPLRETYPQGGIEMSIADLLKYTLQQSDNNACDILFNYQGGPDAVNKYLHSLGIRECAVIHTENDMHKNLEFCYQNWTTPLAAAKLLEIFRNENLFDKEYKNFIYQTMVECQTGQDRLIAPLLDKKVTMGHKTGTGDRNAKGQQIGCNDIGFILLPDGHAYSIAVFVKDSEADNRENSEIIAEISRIVYEYVTQQID"},"dna_sequence":{"accession":"U05883.1","fmin":"555","fmax":"1458","strand":"+","sequence":"ATGCAAAAAAGACTTATACATTTATCCATTATCTTCTTTCTGCTATGTCCTGCCCTGGTAGTTGCGCAGAACAGTCCTCTTGAAACTCAACTCAAGAAAGCCATAGAAGGGAAAAAAGCCGAAATAGGAATTGCAGTCATTATCGACGGGCAAGATACGATAACAGTCAATAATGATATTCATTATCCCATGATGAGTGTTTTCAAATTTCATCAGGCATTGGCATTGGCCGATTACATGCATCATCAAAAGCAACCTTTGGAAACCCGATTATTGATTAAAAAGTCGGATTTAAAGCCGGACACCTATAGTCCGCTTCGAGAAACATACCCGCAGGGAGGAATCGAAATGAGCATTGCCGATCTACTGAAATATACGCTTCAGCAAAGTGACAATAATGCCTGCGATATTCTTTTTAATTATCAAGGTGGTCCGGATGCCGTGAATAAGTATCTTCATTCATTGGGAATTCGTGAATGTGCTGTCATCCATACAGAAAACGATATGCATAAAAATCTGGAGTTCTGTTACCAAAACTGGACTACTCCATTAGCAGCCGCCAAATTACTGGAAATATTTCGCAATGAAAACCTTTTTGACAAAGAATACAAGAATTTCATTTATCAAACAATGGTGGAATGTCAGACAGGACAAGACCGCCTGATTGCTCCACTGCTCGATAAAAAAGTAACAATGGGGCATAAAACCGGAACAGGCGACCGTAATGCGAAAGGACAACAGATCGGTTGCAATGACATCGGGTTTATTCTTCTTCCCGACGGACATGCCTATAGTATAGCCGTCTTCGTGAAAGATTCCGAAGCAGATAACAGAGAAAACAGTGAGATTATCGCAGAAATTTCGCGCATCGTTTACGAATACGTAACGCAACAGATAGATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35916","NCBI_taxonomy_name":"Bacteroides fragilis","NCBI_taxonomy_id":"817"}}}},"ARO_accession":"3003559","ARO_id":"40165","ARO_name":"cepA","CARD_short_name":"cepA","ARO_description":"A beta-lactamase found in Bacteroides fragilis producing either low or high levels of the endogenous cephalosporinase activity.","ARO_category":{"41356":{"category_aro_accession":"3004192","category_aro_cvterm_id":"41356","category_aro_name":"CepA beta-lactamase","category_aro_description":"CepA beta-lactamases are Class A beta-lactamases found in Bateroides fragilis and have the ability to hydrolyze cephalosporin.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1687":{"model_id":"1687","model_name":"cphA3","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"475"}},"model_sequences":{"sequence":{"820":{"protein_sequence":{"accession":"AAM63403.1","sequence":"MMKGWIKCTLAGAVVLMASFWGGSVRAAGIELKQVSGPVYVVEDNYYVKENSMVYFGAKGVTVVGATWTPDTARELHKLIKRVSSKPVLEVINTNYHTDRAGGNAYWKSIGAKVVATRQTRDLMKSDWAEIVAFTRKGLPEYPDLPLVLPNVVHDGDFTLQEGKVRAFYAGPAHTPDGIFVYFPDEQVLYGNCILKEKLGNLSFANVKAYPQTIERLKAMKLPIKTVIGGHDSPLHGPELIDHYEELIKAVPQS"},"dna_sequence":{"accession":"AY112998.1","fmin":"196","fmax":"961","strand":"+","sequence":"ATGATGAAAGGTTGGATAAAGTGCACATTGGCCGGGGCCGTGGTGCTGATGGCGAGTTTCTGGGGTGGCAGCGTGCGGGCGGCGGGGATCGAGCTCAAGCAGGTGAGTGGCCCTGTCTATGTTGTTGAAGACAACTACTACGTCAAAGAGAACTCCATGGTCTATTTCGGGGCCAAGGGAGTGACGGTGGTGGGGGCGACCTGGACGCCGGATACTGCTCGCGAGCTGCACAAGCTGATTAAACGGGTCAGCAGCAAGCCGGTGCTGGAGGTGATCAACACCAACTACCACACCGACCGGGCGGGCGGTAACGCCTACTGGAAGTCCATCGGGGCCAAGGTGGTGGCGACGCGCCAGACCCGGGATCTGATGAAGAGCGACTGGGCCGAGATTGTCGCCTTTACCCGCAAGGGGCTGCCGGAGTACCCGGATCTGCCGCTGGTGCTGCCAAACGTGGTGCACGATGGCGACTTCACTCTGCAAGAGGGCAAGGTGCGCGCTTTCTACGCGGGCCCGGCCCACACGCCGGACGGCATCTTTGTCTACTTCCCCGACGAGCAGGTGCTCTATGGCAACTGCATCCTCAAGGAGAAGCTGGGCAACTTGAGTTTTGCCAATGTGAAGGCGTATCCGCAGACCATCGAGCGGCTCAAAGCGATGAAGCTGCCGATCAAGACGGTGATTGGCGGCCACGATTCGCCGCTGCACGGCCCCGAGTTGATTGATCACTATGAAGAGCTGATCAAGGCCGTGCCGCAGTCATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39653","NCBI_taxonomy_name":"Aeromonas veronii bv. sobria","NCBI_taxonomy_id":"114517"}}}},"ARO_accession":"3003093","ARO_id":"39646","ARO_name":"cphA3","CARD_short_name":"cphA3","ARO_description":"CEPH-A3 is an Ambler Class B MBL; subclass B2 originally isolated from Aeromonas veronii. This enzyme has specific activity against carbapenems and is active as a mono-zinc protein.","ARO_category":{"36720":{"category_aro_accession":"3000581","category_aro_cvterm_id":"36720","category_aro_name":"CphA beta-lactamase","category_aro_description":"CphA is an Ambler Class B MBL; subclass B2 originally isolated from Aeromonas hydrophilia.  This enzyme has specific activity against carbapenems and is active as a mono-zinc protein.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1752":{"model_id":"1752","model_name":"MdtK","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"900"}},"model_sequences":{"sequence":{"4682":{"protein_sequence":{"accession":"AML99881.1","sequence":"MNVSTALRQAVVRTPWYAKRKSYKVLFWREITPLAIPIFLENTCVLLMGVLSTFLVSWLGKEAMAGVGLADSFNMVIMAFFAAIDLGTTVVVAFSLGKRDRRRARAAARQSLVIMTLFAVVLAVVIHYFGSEIINIVAGEATPEVKGLALTYLELTVLSYPAAAIALIGSGALRGAGNTKIPLMINGGMNILNIIISSILIYGAFSWQGLGFAGAGLGLTISRYIGAVAIIWVLMIGFNPALRIPLKSYLKPLNFGIIWEVMGIGIPASIESVLFNGSKLLTQMFVAGMGTNVIAGNFIAFSVAALINLPGNALGSASTIITGKRLGTGQIGQAERQLRHVFWMSTIVLTAIAWGTAPFAGLFASFYTQEQDVKEVVKVLLWLNAAFMPIWAAAWVLPSGFKGARDVRFAMWVSMLGMWGCRVVAGYTLGIVLGMGVVGVWLGMFLDWAVRGALFYWRLISGRWLWRYPRVKRE"},"dna_sequence":{"accession":"CP014358.1","fmin":"2161325","fmax":"2162750","strand":"-","sequence":"TTGAACGTCTCCACTGCCTTACGCCAGGCTGTCGTCCGTACGCCCTGGTATGCCAAACGCAAGAGCTACAAAGTGTTGTTCTGGCGTGAAATCACCCCACTTGCTATCCCTATTTTTCTGGAAAATACCTGTGTTTTGCTAATGGGCGTGCTCAGTACTTTTCTCGTCAGTTGGCTGGGCAAGGAAGCAATGGCGGGCGTGGGGCTTGCCGACAGTTTTAATATGGTAATTATGGCTTTTTTTGCGGCTATCGATCTTGGTACTACGGTGGTGGTCGCCTTTAGCCTCGGCAAGCGCGACAGGCGACGCGCAAGGGCGGCGGCGCGCCAGTCGCTGGTGATTATGACGCTATTTGCCGTTGTGCTGGCAGTGGTCATTCATTATTTCGGCAGTGAAATTATTAATATTGTCGCAGGCGAGGCGACGCCAGAAGTAAAGGGGCTGGCGTTAACGTACCTTGAACTGACGGTGCTGAGTTATCCGGCTGCGGCAATTGCGCTAATCGGTAGCGGCGCGCTGCGTGGGGCAGGGAATACGAAAATCCCGTTGATGATTAACGGCGGGATGAACATTCTCAATATTATTATCAGCAGCATCCTGATTTACGGGGCTTTCTCCTGGCAAGGGCTGGGTTTTGCCGGCGCGGGGCTGGGATTAACCATTTCGCGCTACATCGGCGCGGTAGCGATTATTTGGGTGCTGATGATTGGTTTTAATCCGGCGCTGCGCATTCCGCTGAAAAGCTATCTGAAGCCGCTGAATTTCGGCATTATCTGGGAAGTGATGGGTATCGGTATTCCGGCGAGCATTGAATCAGTGCTGTTCAACGGTAGCAAGCTACTGACGCAAATGTTTGTCGCCGGAATGGGCACTAACGTTATTGCGGGTAACTTTATTGCCTTTTCCGTGGCGGCGCTTATCAACCTGCCGGGTAACGCCCTTGGTTCGGCGTCGACTATTATCACCGGTAAGCGTCTTGGTACCGGGCAAATTGGTCAGGCAGAGCGTCAACTGCGCCATGTATTCTGGATGTCGACTATCGTACTTACGGCAATTGCCTGGGGGACGGCGCCGTTTGCGGGTCTGTTTGCCTCATTTTATACCCAGGAGCAGGACGTAAAAGAGGTAGTGAAAGTTCTGCTCTGGCTTAATGCTGCCTTTATGCCAATTTGGGCGGCCGCGTGGGTGTTGCCGTCGGGTTTTAAAGGCGCGCGCGATGTGCGATTTGCGATGTGGGTATCGATGCTGGGGATGTGGGGCTGTCGCGTTGTGGCAGGGTATACGCTTGGTATTGTGCTGGGTATGGGGGTTGTAGGGGTTTGGCTGGGGATGTTTCTTGACTGGGCCGTGCGTGGCGCACTGTTTTACTGGCGTCTGATAAGCGGGCGCTGGCTGTGGAGATACCCGCGCGTAAAGAGGGAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35732","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Typhimurium","NCBI_taxonomy_id":"90371"}}}},"ARO_accession":"3001327","ARO_id":"37726","ARO_name":"MdtK","CARD_short_name":"MdtK","ARO_description":"A multidrug and toxic compound extrusions (MATE) transporter conferring resistance to norfloxacin, doxorubicin and acriflavine.","ARO_category":{"36251":{"category_aro_accession":"3000112","category_aro_cvterm_id":"36251","category_aro_name":"multidrug and toxic compound extrusion (MATE) transporter","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Multidrug and toxic compound extrusion (MATE) transporters utilize the cationic gradient across the membrane as an energy source. Although there is a diverse substrate specificity, almost all MATE transporters recognize fluoroquinolones. Arciflavine, ethidium and aminoglycosides are also good substrates.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1718":{"model_id":"1718","model_name":"DIM-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"8218":{"protein_sequence":{"accession":"AGC92784.1","sequence":"MRTHFTALLLLFSLSSLANDEVPELRIEKVKENIFLHTSYSRVNGFGLVSSNGLVVIDKGNAFIVDTPWSDRDTETLVHWIRKNGYELLGSVSTHWHEDRTAGIKWLNDQSISTYATTSTNHLLKENKKEPAKYTLKGNESTLVDGLIEVFYPGGGHTIDNVVVWLPKSKILFGGCFVRSLDSEGLGYTGEAHIDQWSRSAQNALSRYSEAQIVIPGHGKIGDIALLKHTKSLAETASNKSIQPNANASAD"},"dna_sequence":{"accession":"KC004136.2","fmin":"40","fmax":"796","strand":"+","sequence":"ATGAGAACACATTTTACAGCGTTATTACTTCTATTCAGCTTGTCTTCGCTTGCTAACGACGAGGTACCTGAGCTAAGAATCGAGAAAGTAAAAGAGAACATCTTTTTGCACACATCATACAGTCGTGTGAATGGGTTTGGTTTGGTCAGTTCAAACGGCCTTGTTGTCATAGATAAGGGTAATGCTTTCATTGTTGATACACCTTGGTCAGACCGAGATACAGAAACGCTCGTACATTGGATTCGTAAAAATGGTTATGAGCTACTGGGGAGTGTTTCTACTCATTGGCATGAGGATAGAACCGCAGGAATTAAATGGCTTAATGACCAATCAATTTCTACGTATGCCACGACTTCAACCAACCATCTCTTGAAAGAAAATAAAAAAGAGCCAGCGAAATACACCTTGAAAGGAAATGAGTCCACATTGGTTGACGGCCTTATCGAAGTATTTTATCCAGGAGGTGGTCATACAATAGACAACGTAGTGGTGTGGTTGCCAAAGTCGAAAATCTTATTTGGCGGCTGTTTTGTGCGTAGCCTTGATTCCGAGGGGTTAGGCTACACTGGTGAAGCCCATATTGATCAATGGTCCCGATCAGCTCAGAATGCTCTGTCTAGGTACTCAGAAGCCCAGATAGTAATTCCTGGCCATGGGAAAATCGGGGATATAGCGCTGTTAAAACACACCAAAAGTCTGGCTGAGACAGCCTCTAACAAATCAATCCAGCCGAACGCTAACGCGTCGGCTGATTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39662","NCBI_taxonomy_name":"Enterobacter sp. SL1","NCBI_taxonomy_id":"1284354"}}}},"ARO_accession":"3000848","ARO_id":"37228","ARO_name":"DIM-1","CARD_short_name":"DIM-1","ARO_description":"Dutch imipenemase or DIM-1 is an integron-encoded metallo-beta-lactamase from Pseudomonas stutzeri.","ARO_category":{"41372":{"category_aro_accession":"3004208","category_aro_cvterm_id":"41372","category_aro_name":"DIM beta-lactamase","category_aro_description":"DIM type beta-lactamases were first identified from a carbapenem-resistant Pseudomonas stutzeri strain isolated from a Dutch patient. Encoded in mobile elements, these MBLs significantly hydrolyze broad-spectrum cephalosporins and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1790":{"model_id":"1790","model_name":"vanH gene in vanF cluster","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"200"}},"model_sequences":{"sequence":{"487":{"protein_sequence":{"accession":"AAF36802.1","sequence":"MKNIGITIYGCERDEAEVFNELSPRFGVIPAITSSAVSETNAMLAPGNQCISVGHKSEISESILLALKESGVKYISTRSIGCNHIDVKAAESMGIAVGNVAYSPDSVADYTLMLMLMAIRNAKSIVSRAEKYDFRLDTVPGKELREMTVGVLGTGQIGKAVIERLRGFGCHVLAYGHSKEAAANYVSLNELLQKSDILTIHVPLGTDTYHMIGHEQIEAVKQGAFLINTARGGLVDTGALIKALENGRLGGAALDVLEGEEGLFYFDCTQKPIDNQLLLKLHKMPNVIITPHTAYYTGRALYDTVEKTILNCLEFERRETLE"},"dna_sequence":{"accession":"AF155139.1","fmin":"4978","fmax":"5947","strand":"+","sequence":"ATGAAAAATATCGGCATTACCATTTATGGATGTGAGAGGGACGAGGCTGAAGTGTTCAATGAACTTTCGCCACGCTTTGGTGTCATACCTGCCATTACAAGCTCTGCCGTATCGGAAACCAACGCAATGTTAGCTCCCGGCAATCAATGTATCAGCGTGGGGCACAAATCTGAGATTTCCGAATCCATTCTTCTTGCTCTGAAGGAATCCGGCGTCAAATATATCTCTACCCGAAGTATTGGCTGCAATCACATAGACGTGAAGGCCGCGGAAAGTATGGGTATCGCTGTTGGAAACGTGGCATATTCACCGGATAGCGTTGCCGATTATACATTGATGCTGATGCTGATGGCGATACGAAACGCAAAATCCATTGTGAGCCGTGCGGAAAAATATGATTTCAGATTGGATACTGTCCCTGGAAAAGAATTGCGTGAGATGACGGTTGGCGTGCTGGGAACCGGTCAAATAGGCAAGGCGGTTATTGAGCGACTGCGGGGATTTGGATGTCATGTGCTGGCGTATGGTCACAGCAAAGAGGCGGCGGCCAATTATGTATCCCTCAATGAATTGCTGCAGAAAAGCGACATTCTCACCATTCATGTGCCGCTCGGCACGGACACATATCATATGATTGGTCACGAACAGATTGAAGCAGTGAAACAGGGCGCGTTTCTTATCAATACAGCGCGCGGCGGGCTTGTGGATACCGGCGCGCTGATCAAAGCGTTGGAAAATGGAAGGTTAGGCGGCGCGGCGTTGGATGTGTTGGAAGGAGAAGAAGGGCTTTTCTATTTTGATTGCACACAGAAACCGATTGACAACCAACTATTGCTTAAGCTCCACAAGATGCCAAATGTGATCATCACGCCGCATACGGCGTACTATACCGGACGGGCACTGTATGATACCGTTGAAAAGACAATATTGAACTGTCTGGAATTTGAGAGGAGAGAGACACTTGAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39542","NCBI_taxonomy_name":"Paenibacillus popilliae ATCC 14706","NCBI_taxonomy_id":"1212764"}}}},"ARO_accession":"3002945","ARO_id":"39379","ARO_name":"vanH gene in vanF cluster","CARD_short_name":"vanH_in_vanF_cl","ARO_description":"Also known as vanHF, is a vanH variant in the vanF gene cluster.","ARO_category":{"36015":{"category_aro_accession":"3000006","category_aro_cvterm_id":"36015","category_aro_name":"vanH","category_aro_description":"VanH is a D-specific alpha-ketoacid dehydrogenase that synthesizes D-lactate. D-lactate is incorporated into the end of the peptidoglycan subunits, decreasing vancomycin binding affinity.","category_aro_class_name":"AMR Gene Family"},"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1678":{"model_id":"1678","model_name":"AAC(6')-Ib-cr1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"6152":{"protein_sequence":{"accession":"WP_071846215.1","sequence":"MTNSNDSVTLRHMTEHDLAMLYEWLNRSHIVEWWGGEEARPTLADVQEQYLPSVLAQESVTPYIAMLNGEPIGYAQSYVALGSGDGRWEEETDPGVRGIDQLLANASQLGKGLGTKLVRALVELLFNDPEVTKIQTDPSPSNLRAIRCYEKAGFERQGTVTTPYGPAVYMVQTRQAFERTRSDA"},"dna_sequence":{"accession":"NG_052213.1","fmin":"100","fmax":"655","strand":"+","sequence":"GTGACCAACAGCAACGATTCCGTCACACTGCGCCACATGACTGAGCATGACCTTGCGATGCTCTATGAGTGGCTAAATCGATCTCATATCGTCGAGTGGTGGGGCGGAGAAGAAGCACGCCCGACACTTGCTGACGTACAGGAACAGTACTTGCCAAGCGTTTTAGCGCAAGAGTCCGTCACTCCATACATTGCAATGCTGAATGGAGAGCCGATTGGGTATGCCCAGTCGTACGTTGCTCTTGGAAGCGGGGACGGACGGTGGGAAGAAGAAACCGATCCAGGAGTACGCGGAATAGACCAGTTACTGGCGAATGCATCACAACTGGGCAAAGGCTTGGGAACCAAGCTGGTTCGAGCTCTGGTTGAGTTGCTGTTCAATGATCCCGAGGTCACCAAGATCCAAACGGACCCGTCGCCGAGCAACTTGCGAGCGATCCGATGCTACGAGAAAGCGGGGTTTGAGAGGCAAGGTACCGTAACCACCCCATATGGTCCAGCCGTGTACATGGTTCAAACACGCCAGGCATTCGAGCGAACACGCAGTGATGCCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37076","NCBI_taxonomy_name":"Stenotrophomonas maltophilia","NCBI_taxonomy_id":"40324"}}}},"ARO_accession":"3002547","ARO_id":"38947","ARO_name":"AAC(6')-Ib-cr1","CARD_short_name":"AAC(6')-Ib-cr1","ARO_description":"AAC(6')-Ib-cr is an aminoglycoside acetyltransferase encoded by plasmids, transposons, integrons in Enterobacteriaceae. The aac(6')-Ib-cr variant gene can induce resistance against aminoglycoside and fluoroquinolone simultaneously.","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"A category of aminoglycoside N-acetyltransferase enzymes with modification regiospecificity based at the 6'-amino group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics through acetylation of the 6-amino group of the compound.","category_aro_class_name":"AMR Gene Family"},"43328":{"category_aro_accession":"3005113","category_aro_cvterm_id":"43328","category_aro_name":"AAC(6')-Ib-cr","category_aro_description":"A subfamily of aminoglycoside 6'-N-acetyltransferases, AAC(6'), which doubly confer resistance to aminoglycoside and fluoroquinolone antibiotics through fluoroquinolone-acetylating activity.","category_aro_class_name":"AMR Gene Family"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1794":{"model_id":"1794","model_name":"tmrB","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"375"}},"model_sequences":{"sequence":{"4679":{"protein_sequence":{"accession":"CAB12108.2","sequence":"MIIWINGAFGSGKTQTAFELHRRLNPSYVYDPEKMGFALRSMVPQEIAKDDFQSYPLWRAFNYSLLASLTDTYRGILIVPMTIVHPEYFNEIIGRLRQEGRIVHHFTLMASKETLLKRLRTRAEGKNSWAAKQIDRCVEGLSSPIFEDHIQTDNLSIQDVAENIAARAELPLDPDTRGSLRRFADRLMVKLNHIRIK"},"dna_sequence":{"accession":"AL009126.3","fmin":"339155","fmax":"339749","strand":"-","sequence":"ATGATCATTTGGATAAACGGGGCATTCGGTTCGGGAAAAACACAAACAGCCTTCGAACTGCACAGAAGGCTGAACCCATCTTACGTGTATGATCCCGAGAAAATGGGTTTTGCGCTGCGCTCCATGGTGCCGCAGGAGATCGCAAAGGACGATTTTCAAAGCTATCCTTTATGGCGGGCGTTCAATTACAGTTTGCTAGCTTCTCTGACAGATACATACCGCGGCATCCTTATTGTGCCTATGACGATTGTACACCCTGAATACTTCAATGAGATCATCGGCAGGCTCAGACAGGAAGGCAGGATCGTTCACCACTTTACACTAATGGCTTCAAAGGAAACCTTGTTAAAAAGGCTGCGCACCAGAGCAGAAGGAAAAAACTCATGGGCCGCCAAACAAATTGACCGCTGTGTTGAAGGATTATCATCACCCATTTTTGAGGACCACATTCAAACAGACAACCTGTCGATTCAGGATGTGGCAGAGAACATTGCCGCGAGAGCCGAACTCCCATTAGATCCTGATACAAGAGGCAGCCTCCGAAGGTTCGCCGACAGATTAATGGTAAAGCTGAATCATATCCGCATCAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39579","NCBI_taxonomy_name":"Bacillus subtilis subsp. subtilis str. 168","NCBI_taxonomy_id":"224308"}}}},"ARO_accession":"3003059","ARO_id":"39493","ARO_name":"tmrB","CARD_short_name":"tmrB","ARO_description":"tmrB is an ATP-binding tunicamycin resistance protein found in Bacillus subtilis.","ARO_category":{"41449":{"category_aro_accession":"3004285","category_aro_cvterm_id":"41449","category_aro_name":"tunicamycin resistance protein","category_aro_description":"A grouping of tunicamycin resistance proteins that are homologous to tmrB found in Bacillus subtilis.","category_aro_class_name":"AMR Gene Family"},"35928":{"category_aro_accession":"0000009","category_aro_cvterm_id":"35928","category_aro_name":"tunicamycin","category_aro_description":"Tunicamycin is mixture of homologous nucleoside antibiotics that block the reaction of UDP-N-acetylglucosamine and dolichyl phosphate in the first step of glycoprotein synthesis.","category_aro_class_name":"Antibiotic"},"36174":{"category_aro_accession":"3000034","category_aro_cvterm_id":"36174","category_aro_name":"nucleoside antibiotic","category_aro_description":"Nucleoside antibiotics are made of modified nucleosides and nucleotides with wide-ranging activities and means of antibacterial effects. This drug class includes aminonucleoside antibiotics, which contain an amino group.","category_aro_class_name":"Drug Class"},"36383":{"category_aro_accession":"3000244","category_aro_cvterm_id":"36383","category_aro_name":"reduced permeability to antibiotic","category_aro_description":"Reduction in permeability to antibiotic, generally through reduced production of porins, can provide resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1795":{"model_id":"1795","model_name":"VEB-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1329":{"protein_sequence":{"accession":"AAK29174.1","sequence":"MKIVKRILLVLLSLFFTIVYSNAQADNLTLKIENVLKAKNARIGVAIFNSNEKDTLKINNDFHFPMQSVMKFPIALAVLSEIDKGNLSFEQKIEITPQDLLPKTWSPIKEEFPNGTTLTIEQILNYTVSESDNIGCDILLKLIGGTDSVQKFLNANHFTDISIKANEEQMHKDWNTQYQNWATPTAMNKLLIDTYNNKNQLLSKKSYDFIWKIMRETTTGSNRLKGQLPKNTIVAHKTGTSGINNGIAAATNDVGVITLPNGQLIFISVFVAESKETSEINEKIISDIAKITWNYYLNK"},"dna_sequence":{"accession":"AY027870.1","fmin":"46","fmax":"946","strand":"+","sequence":"ATGAAAATCGTAAAAAGGATATTATTAGTATTGTTAAGTTTATTTTTTACAATTGTGTATTCAAATGCTCAAGCTGACAACTTAACTTTGAAAATTGAGAATGTTTTAAAGGCAAAAAATGCCAGAATAGGAGTAGCAATATTCAACAGCAATGAGAAGGATACTTTGAAGATTAATAACGACTTCCATTTCCCGATGCAAAGCGTTATGAAATTTCCGATTGCTTTAGCCGTTTTGTCTGAGATAGATAAAGGGAATCTTTCTTTTGAACAAAAAATAGAGATTACCCCTCAAGACCTTTTGCCTAAAACGTGGAGTCCGATTAAAGAGGAATTCCCTAATGGAACAACTTTGACGATTGAACAAATACTAAATTATACAGTATCAGAGAGCGACAATATTGGTTGTGATATTTTGCTAAAATTAATCGGAGGAACTGATTCTGTTCAAAAATTCTTGAATGCTAATCATTTCACTGATATTTCAATCAAAGCAAACGAAGAACAAATGCACAAGGATTGGAATACCCAATATCAAAATTGGGCAACCCCAACAGCGATGAACAAACTGTTAATAGATACTTATAATAATAAGAACCAATTACTTTCTAAAAAAAGTTATGATTTTATTTGGAAAATTATGAGAGAAACAACAACAGGAAGTAACCGATTAAAAGGACAATTACCAAAGAATACAATTGTTGCTCATAAAACAGGGACTTCCGGAATAAATAATGGAATTGCAGCAGCCACTAATGATGTTGGGGTAATTACTTTACCGAATGGACAATTAATTTTTATAAGCGTATTTGTTGCAGAGTCCAAAGAAACTTCGGAAATTAATGAAAAGATTATTTCAGACATTGCAAAAATAACGTGGAATTACTATTTGAATAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002371","ARO_id":"38771","ARO_name":"VEB-2","CARD_short_name":"VEB-2","ARO_description":"VEB-2 is a beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36182":{"category_aro_accession":"3000043","category_aro_cvterm_id":"36182","category_aro_name":"VEB beta-lactamase","category_aro_description":"VEB beta-lactamases or Vietnamese extended-spectrum beta-lactamases are class A beta-lactamases that confer high-level resistance to oxyimino cephalosporins and to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1796":{"model_id":"1796","model_name":"CMY-119","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1344":{"protein_sequence":{"accession":"AIT76098.1","sequence":"MMKKSLCCALLLTASFSTFASAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGISLLHLATYTAGGLPLQIPDDVTDKAALLRFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQSEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWIQVNMDASRVQEKMLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAAEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"KM087845.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACGTTTGCCTCCGCCAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAACTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCAGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTACGGATAAAGCCGCATTACTGCGTTTTTATCAAAACTGGCAGCCGCAATGGACCCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACAGTTCCGCAAAGCGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAACCTGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGTTGGATTCAGGTCAACATGGATGCCAGCCGCGTTCAGGAGAAAATGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGTGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGCTGAGGTAAACCCGCCCGCCCCGGCAGTGAAAGCCTCATGGGTGCATAAAACGGGATCCACTGGAGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002130","ARO_id":"38530","ARO_name":"CMY-119","CARD_short_name":"CMY-119","ARO_description":"CMY-119 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1797":{"model_id":"1797","model_name":"ErmY","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"630":{"protein_sequence":{"accession":"BAB20748.1","sequence":"MNKKDIKFSQNFITSKRHINKIMSNLELNRNDNVFEIGSGKGHFTLELVQKCNYVTVIEIDSNLCIQTQNKVTNYDNFRIINKDILQFKFPNNKAYKIYGNIPYYISTDIVRKIVFESEATVSYLIVEEGFAKRLLNTNRSLALLLMTEVDISILSKIPKEYFHPKPKINSSLIILKRHPSKISYKDKKMYNNFVMKWVNQEYSKLFTKNQFNKALNYAKIKDLKNINFEQFLSVFNSYKLFNN"},"dna_sequence":{"accession":"AB014481.1","fmin":"0","fmax":"735","strand":"+","sequence":"ATGAACAAAAAAGATATAAAATTTAGTCAAAATTTTATTACTTCGAAACGACATATAAATAAAATAATGAGTAATTTAGAATTAAATAGAAATGATAATGTTTTTGAAATTGGTTCAGGAAAAGGGCATTTCACACTAGAACTGGTTCAAAAATGTAATTATGTAACAGTTATCGAGATAGATTCAAATTTATGTATTCAAACACAAAATAAAGTTACAAATTACGATAACTTTCGAATTATAAATAAGGATATATTACAGTTTAAGTTCCCAAACAACAAAGCATATAAAATCTACGGTAATATACCTTATTATATAAGTACGGATATAGTACGAAAAATTGTCTTTGAAAGTGAAGCAACAGTTAGTTACTTAATAGTTGAAGAAGGATTTGCTAAAAGGCTACTCAATACAAATCGTTCTCTAGCGTTACTTTTAATGACTGAAGTAGATATATCCATATTAAGTAAAATCCCTAAAGAATACTTTCATCCAAAGCCTAAAATTAATAGCTCTTTAATTATATTAAAAAGACACCCGTCAAAAATATCATACAAAGATAAAAAAATGTATAATAATTTTGTTATGAAATGGGTTAACCAAGAATACAGCAAACTATTTACCAAAAATCAGTTTAATAAAGCCTTAAATTATGCAAAAATAAAGGATTTAAAGAACATTAACTTCGAACAATTTTTATCAGTATTTAATAGCTATAAATTGTTTAATAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35508","NCBI_taxonomy_name":"Staphylococcus aureus","NCBI_taxonomy_id":"1280"}}}},"ARO_accession":"3002825","ARO_id":"39259","ARO_name":"ErmY","CARD_short_name":"ErmY","ARO_description":"ErmY is a plasmid-mediated methyltransferase found in Staphylococcus aureus.","ARO_category":{"36699":{"category_aro_accession":"3000560","category_aro_cvterm_id":"36699","category_aro_name":"Erm 23S ribosomal RNA methyltransferase","category_aro_description":"Erm proteins are part of the RNA methyltransferase family and methylate A2058 (E. coli nomenclature) of the 23S ribosomal RNA conferring degrees of resistance to Macrolides, Lincosamides and Streptogramin b. This is called the MLSb phenotype.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"37247":{"category_aro_accession":"3000867","category_aro_cvterm_id":"37247","category_aro_name":"oleandomycin","category_aro_description":"Oleandomycin is a 14-membered macrolide produced by Streptomyces antibioticus. It is ssimilar to erythromycin, and contains a desosamine amino sugar and an oleandrose sugar. It targets the 50S ribosomal subunit to prevent protein synthesis.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1798":{"model_id":"1798","model_name":"SHV-183","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1945":{"protein_sequence":{"accession":"CDN33427.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGASKRGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"HG934764.1","fmin":"0","fmax":"864","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTAGCAAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3001351","ARO_id":"37751","ARO_name":"SHV-183","CARD_short_name":"SHV-183","ARO_description":"SHV-183 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1799":{"model_id":"1799","model_name":"TEM-147","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1881":{"protein_sequence":{"accession":"ABB84515.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDHWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSVLPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"DQ279850.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCATTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGTCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3001014","ARO_id":"37394","ARO_name":"TEM-147","CARD_short_name":"TEM-147","ARO_description":"TEM-147 is an extended-spectrum beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1800":{"model_id":"1800","model_name":"SHV-120","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1543":{"protein_sequence":{"accession":"AEG79634.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGKRGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"JF812965.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTACTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCAAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001167","ARO_id":"37547","ARO_name":"SHV-120","CARD_short_name":"SHV-120","ARO_description":"SHV-120 is a beta-lactamase that has been found in clinical isolates.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1801":{"model_id":"1801","model_name":"AAC(6')-Ib11","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"366":{"protein_sequence":{"accession":"AAN41403.1","sequence":"MKNTIHINSNDSVTLRLMTEHDLAMLYEWLNRSHIVEWWGGEEARPTLADVQEQYLPSVLAQESVTPYIAMLNGEPIGYAQSYVALGSGDGWWEEETDPGVRGIDLSLANASQLGKGLGTKLVRALVELLFNDPEVTKIQTDPSPSNLRAIRCYEKAGFERQGTVTTPDGPAVYMVQTRQAFERTRSDA"},"dna_sequence":{"accession":"AY136758.1","fmin":"377","fmax":"947","strand":"+","sequence":"ATGAAAAACACAATACATATCAACAGCAACGATTCCGTCACACTGCGCCTCATGACTGAGCATGACCTTGCGATGCTCTATGAGTGGCTAAATCGATCTCATATCGTCGAGTGGTGGGGCGGAGAAGAAGCACGCCCGACACTTGCTGACGTACAGGAACAGTACTTGCCAAGCGTTTTAGCGCAAGAGTCCGTCACTCCATACATTGCAATGCTGAATGGAGAGCCGATTGGGTATGCCCAGTCGTACGTTGCTCTTGGAAGCGGGGACGGATGGTGGGAAGAAGAAACCGATCCAGGAGTACGCGGAATAGACCTGTCACTGGCGAATGCATCACAACTGGGCAAAGGCTTGGGAACCAAGCTGGTTCGAGCTCTGGTTGAGTTGCTGTTCAATGATCCCGAGGTCACCAAGATCCAAACGGACCCGTCGCCGAGCAACTTGCGAGCGATCCGATGCTACGAGAAAGCGGGGTTTGAGAGGCAAGGTACCGTAACCACCCCAGATGGTCCAGCCGTGTACATGGTTCAAACACGCCAGGCATTCGAGCGAACACGCAGTGATGCCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35732","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Typhimurium","NCBI_taxonomy_id":"90371"}}}},"ARO_accession":"3002582","ARO_id":"38982","ARO_name":"AAC(6')-Ib11","CARD_short_name":"AAC(6')-Ib11","ARO_description":"AAC(6')-Ib11 is an integron-encoded aminoglycoside acetyltransferase in S. enterica.","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"A category of aminoglycoside N-acetyltransferase enzymes with modification regiospecificity based at the 6'-amino group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics through acetylation of the 6-amino group of the compound.","category_aro_class_name":"AMR Gene Family"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1802":{"model_id":"1802","model_name":"OXA-168","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1452":{"protein_sequence":{"accession":"ADK35872.1","sequence":"MNKYFTCYVVASLFLSGCTVQHNLINETPSQIVQGHNQVIHQYFDEKNTSGVLVIQTDKKINLYGNALSRANTEYVPASTFKMLNALIGLENQKTDINEIFKWKGEKRSFTAWEKDMTLGEAMKLSAVPVYQELARRIGLDLMQKEVKRIGFGNAEIGQQVDNFWLVGPLKVTPIQEVEFVSQLAHTQLPFSEKVQANVKNMLLLEESNGYKIFGKTGWAMDIKPQVGWLAGWVEQPDGKIVAFALNMEMRSEMPASIRNELLMKSLKQLNII"},"dna_sequence":{"accession":"HM488989.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGAATAAATATTTTACTTGCTATGTGGTTGCTTCTCTTTTTCTTTCTGGTTGTACGGTTCAGCATAATTTAATAAATGAAACCCCGAGTCAGATTGTTCAAGGACATAATCAGGTGATTCATCAATACTTTGATGAAAAAAACACCTCAGGTGTGCTGGTTATTCAAACAGATAAAAAAATTAATCTATATGGTAATGCTCTAAGCCGCGCAAATACAGAATATGTGCCAGCCTCTACATTTAAAATGTTGAATGCCCTGATCGGATTGGAGAACCAGAAAACGGATATTAATGAAATATTTAAATGGAAGGGCGAGAAAAGGTCATTTACCGCTTGGGAAAAAGACATGACACTAGGAGAAGCCATGAAGCTTTCTGCAGTCCCAGTCTATCAGGAACTTGCGCGACGTATCGGTCTTGATCTCATGCAAAAAGAAGTAAAACGTATTGGTTTCGGTAATGCTGAAATTGGACAGCAGGTTGATAATTTCTGGTTGGTAGGACCATTAAAGGTTACGCCTATTCAAGAGGTAGAGTTTGTTTCCCAATTAGCACATACACAGCTTCCATTTAGTGAAAAAGTGCAGGCTAATGTAAAAAATATGCTTCTTTTAGAAGAGAGTAATGGCTACAAAATTTTTGGAAAGACTGGTTGGGCAATGGATATAAAACCACAAGTGGGCTGGTTGGCCGGCTGGGTTGAGCAGCCAGATGGAAAAATTGTCGCTTTTGCATTAAATATGGAAATGCGGTCAGAAATGCCGGCATCTATACGTAATGAATTATTGATGAAATCATTAAAACAGCTGAATATTATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001468","ARO_id":"37868","ARO_name":"OXA-168","CARD_short_name":"OXA-168","ARO_description":"OXA-168 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46499":{"category_aro_accession":"3007710","category_aro_cvterm_id":"46499","category_aro_name":"OXA-23-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases, specifically imipenem, derived from OXA-23, first identified in Acinetobacter baumannii.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1803":{"model_id":"1803","model_name":"QnrVC3","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"483":{"protein_sequence":{"accession":"ADI81040.1","sequence":"MEKSKQLYNQVNFSHQDLQEHIFSNCTFIHCNFKRSNLRDTQFINCTFIEQGALEGCDFSYADLRDASFKNCQLSMSHFKGANCFGIELRDCDLKGANFTQVSFVNQVSNKMYFCSAYITGCNLSYANFEQQLIEKCDLFENRWIGANLRGASFTESYLSRGDFSEDCWEQFRVQGCDLSHSELYGLDPRKIDLTGVKICSWQQEQLLEQLGVIIVPD"},"dna_sequence":{"accession":"HM015626.1","fmin":"883","fmax":"1540","strand":"+","sequence":"ATGGAAAAATCAAAGCAATTATATAATCAAGTGAACTTCTCACATCAGGACTTGCAAGAACATATCTTTAGCAATTGTACTTTTATACATTGTAATTTTAAGCGCTCAAACCTCCGAGATACACAGTTCATTAACTGTACTTTCATAGAGCAGGGGGCATTGGAAGGGTGCGATTTTTCTTATGCTGATCTTCGAGATGCTTCATTTAAAAACTGTCAGCTTTCAATGTCCCATTTTAAGGGGGCAAATTGCTTTGGTATTGAACTGAGAGATTGTGATCTTAAAGGAGCAAATTTTACTCAAGTTAGTTTTGTAAATCAGGTTTCGAATAAAATGTACTTTTGTTCTGCATACATAACAGGTTGTAACTTATCCTATGCCAATTTTGAGCAGCAGCTTATTGAAAAATGTGACCTGTTCGAAAATAGATGGATTGGTGCAAATCTTCGAGGCGCTTCATTTACAGAATCATATTTAAGCCGTGGTGATTTTTCGGAAGACTGCTGGGAACAGTTTAGAGTACAAGGCTGTGATTTAAGCCATTCAGAGCTTTATGGTTTAGATCCTCGAAAGATTGATCTTACGGGTGTAAAAATATGCTCGTGGCAACAGGAACAGTTACTGGAGCAATTAGGGGTAATCATTGTTCCTGACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36920","NCBI_taxonomy_name":"Vibrio cholerae non-O1\/non-O139","NCBI_taxonomy_id":"156539"}}}},"ARO_accession":"3002800","ARO_id":"39234","ARO_name":"QnrVC3","CARD_short_name":"QnrVC3","ARO_description":"QnrVC3 is an integron-mediated quinolone resistance protein found in Vibrio cholerae.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1804":{"model_id":"1804","model_name":"OXA-107","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1289":{"protein_sequence":{"accession":"ABV31687.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDDKAEKIKNLFNEAHTTGVLVIHQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGEKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWVVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"EF650033.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGACAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCATCAAGGTCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAATGGGATGGGGAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGGTGGTGGGTCCTCTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36939","NCBI_taxonomy_name":"Acinetobacter baumannii A424","NCBI_taxonomy_id":"1082934"}}}},"ARO_accession":"3001638","ARO_id":"38038","ARO_name":"OXA-107","CARD_short_name":"OXA-107","ARO_description":"OXA-107 is a beta-lactamase found in A. baumannii.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1805":{"model_id":"1805","model_name":"TEM-131","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1953":{"protein_sequence":{"accession":"AAR10958.1","sequence":"MSIQHFRVALIPFFAAFCFPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVKYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDSWEPELNEAIPNDERDTTTPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGTGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AY436361.1","fmin":"131","fmax":"992","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCTTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAARGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTAAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATAGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGACGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAACCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35732","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Typhimurium","NCBI_taxonomy_id":"90371"}}}},"ARO_accession":"3000995","ARO_id":"37375","ARO_name":"TEM-131","CARD_short_name":"TEM-131","ARO_description":"TEM-131 is an extended-spectrum beta-lactamase found in Salmonella enterica.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1806":{"model_id":"1806","model_name":"OXA-14","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"5856":{"protein_sequence":{"accession":"AHX74209.1","sequence":"MKTFAAYVIIACLSSTALAGSITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEDQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGIIGG"},"dna_sequence":{"accession":"KJ420612.1","fmin":"1821","fmax":"2622","strand":"+","sequence":"ATGAAAACATTTGCCGCATATGTAATTATCGCGTGTCTTTCGAGTACGGCATTAGCTGGTTCAATTACAGAAAATACGTCTTGGAACAAAGAGTTCTCTGCCGAAGCCGTCAATGGTGTCTTCGTGCTTTGTAAAAGTAGCAGTAAATCCTGCGCTACCAATGACTTAGCTCGTGCATCAAAGGAATATCTTCCAGCATCAACATTTAAGATCCCCAACGCAATTATCGGCCTAGAAACTGGTGTCATAAAGAATGAGCATCAGGTTTTCAAATGGGACGGAAAGCCAAGAGCCATGAAGCAATGGGAAAGAGACTTGACCTTAAGAGGGGCAATACAAGTTTCAGCTGTTCCCGTATTTCAACAAATCGCCAGAGAAGTTGGCGAAGTAAGAATGCAGAAATACCTTAAAAAATTTTCCTATGGCAACCAGAATATCAGTGGTGGCATTGACAAATTCTGGTTGGAAGACCAGCTTAGAATTTCCGCAGTTAATCAAGTGGAGTTTCTAGAGTCTCTATATTTAAATAAATTGTCAGCATCTAAAGAAAACCAGCTAATAGTAAAAGAGGCTTTGGTAACGGAGGCGGCACCTGAATATCTAGTGCATTCAAAAACTGGTTTTTCTGGTGTGGGAACTGAGTCAAATCCTGGTGTCGCATGGTGGGTTGGGTGGGTTGAGAAGGAGACAGAGGTTTACTTTTTCGCCTTTAACATGGATATAGACAACGAAAGTAAGTTGCCGCTAAGAAAATCCATTCCCACCAAAATCATGGAAAGTGAGGGCATCATTGGTGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3001409","ARO_id":"37809","ARO_name":"OXA-14","CARD_short_name":"OXA-14","ARO_description":"OXA-14 is a beta-lactamase found in P. aeruginosa.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46486":{"category_aro_accession":"3007697","category_aro_cvterm_id":"46486","category_aro_name":"OXA-10-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-10.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1807":{"model_id":"1807","model_name":"OXA-70","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"980":{"protein_sequence":{"accession":"AAW81341.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDKKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWNGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQHEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"AY750912.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATAAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGAACGGGCAAAAAAGGCTGTTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAACATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001618","ARO_id":"38018","ARO_name":"OXA-70","CARD_short_name":"OXA-70","ARO_description":"OXA-70 is a beta-lactamase found in A. baumannii.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1809":{"model_id":"1809","model_name":"QnrB5","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"256":{"protein_sequence":{"accession":"ABC17628.1","sequence":"MTPLLYKNTGIDMTLALVGEKIDRNRFTGEKVENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNVSALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGTQVLGATFSGSDLSGGEFSTFDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDSYQASLLMERLGIAIIG"},"dna_sequence":{"accession":"DQ303919.1","fmin":"0","fmax":"681","strand":"+","sequence":"ATGACGCCATTACTGTATAAAAACACAGGCATAGATATGACTCTGGCATTAGTTGGCGAAAAAATTGACAGAAATCGCTTCACCGGTGAGAAAGTTGAAAATAGTACATTTTTTAACTGCGATTTTTCAGGTGCCGACCTGAGCGGCACTGAATTTATCGGCTGCCAGTTCTATGATCGCGAAAGTCAGAAAGGGTGCAATTTTAGTCGCGCAATGCTGAAAGATGCCATTTTCAAAAGCTGTGATTTATCAATGGCAGATTTCCGCAACGTCAGTGCCTTGGGCATTGAAATTCGCCACTGCCGCGCACAAGGCGCAGATTTCCGCGGTGCAAGCTTTATGAATATGATCACCACGCGCACCTGGTTTTGCAGCGCATATATCACTAATACTAATCTAAGCTACGCCAATTTTTCGAAAGTCGTGTTGGAAAAGTGTGAGCTGTGGGAAAACCGCTGGATGGGGACTCAGGTACTGGGTGCGACGTTCAGTGGTTCAGATCTCTCCGGCGGCGAGTTTTCGACTTTCGACTGGCGAGCAGCAAACTTCACACATTGCGATCTGACCAATTCGGAGTTAGGTGACTTAGATATTCGGGGTGTTGATTTACAAGGCGTTAAGTTAGACAGCTACCAGGCATCGTTGCTCATGGAGCGGCTTGGCATCGCGATTATTGGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35665","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Berta","NCBI_taxonomy_id":"28142"}}}},"ARO_accession":"3002719","ARO_id":"39153","ARO_name":"QnrB5","CARD_short_name":"QnrB5","ARO_description":"QnrB5 is a plasmid-mediated quinolone resistance protein found in Salmonella enterica.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1810":{"model_id":"1810","model_name":"VIM-15","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1164":{"protein_sequence":{"accession":"ACB54702.1","sequence":"MFKLLSKLLVYLTASIMAIASPLAFSVDSSGEYPTVSEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEVEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSASVLFGGCAIYELSRTSAGNVADADLAEWPTSIERIQQHYPEAQFVIPGHGLPGGLDLLKHTTNVVKAHTNRSVVE"},"dna_sequence":{"accession":"EU419745.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGTTCAAACTTTTGAGTAAGTTATTGGTCTATTTGACCGCGTCTATCATGGCTATTGCGAGTCCGCTCGCTTTTTCCGTAGATTCTAGCGGTGAGTATCCGACAGTCAGCGAAATTCCGGTCGGGGAGGTCCGGCTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCAGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAGAAGCAAATTGGACTTCCTGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGTAGAGGGGAACGAGATTCCCACGCACTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAACTCTTCTATCCTGGTGCTGCGCATTCGACCGACAACTTAGTTGTGTACGTCCCGTCTGCGAGTGTGCTCTTTGGTGGTTGTGCGATTTATGAGTTGTCACGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCATTGAGCGGATTCAACAACACTACCCGGAAGCACAGTTCGTCATTCCGGGGCACGGCCTGCCGGGCGGTCTAGACTTGCTCAAGCACACAACGAATGTTGTAAAAGCGCACACAAATCGCTCAGTCGTTGAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002285","ARO_id":"38685","ARO_name":"VIM-15","CARD_short_name":"VIM-15","ARO_description":"VIM-15 is a beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1811":{"model_id":"1811","model_name":"CARB-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8841":{"protein_sequence":{"accession":"AAA25741.1","sequence":"MKFLLAFSLLIPSVVFASSSKFQQVEQDVKAIEVSLSARIGVSVLDTQNGEYWDYNGNQRFPLTSTFKTIACAKLLYDAEQGKVNPNSTVEIKKADLVTYSPVIEKQVGQAITLDDACFATMTTSDNTAANIILSAVGGPKGVTDFLRQIGDKETRLDRIEPDLNEGKLGDLRDTTTPKAIASTLNKFLFGSALSEMNQKKLESWMVNNQVTGNLLRSVLPAGWNIADRSGAGGFGARSITAVVWSEHQAPIIVSIYLAQTQASMAERNDAIVKIGHSIFDVYTSQSR"},"dna_sequence":{"accession":"M69058.1","fmin":"145","fmax":"1012","strand":"+","sequence":"ATGAAGTTTTTATTGGCATTTTCGCTTTTAATACCATCCGTGGTTTTTGCAAGTAGTTCAAAGTTTCAGCAAGTTGAACAAGACGTTAAGGCAATTGAAGTTTCTCTTTCTGCTCGTATAGGTGTTTCCGTTCTTGATACTCAAAATGGAGAATATTGGGATTACAATGGCAATCAGCGCTTCCCGTTAACAAGTACTTTTAAAACAATAGCTTGCGCTAAATTACTATATGATGCTGAGCAAGGAAAAGTTAATCCCAATAGTACAGTCGAGATTAAGAAAGCAGATCTTGTGACCTATTCCCCTGTAATAGAAAAGCAAGTAGGGCAGGCAATCACACTCGATGATGCGTGCTTCGCAACTATGACTACAAGTGATAATACTGCGGCAAATATCATCCTAAGTGCTGTAGGTGGCCCCAAAGGCGTTACTGATTTTTTAAGACAAATTGGGGACAAAGAGACTCGTCTAGACCGTATTGAGCCTGATTTAAATGAAGGTAAGCTCGGTGATTTGAGGGATACGACAACTCCTAAGGCAATAGCCAGTACTTTGAATAAATTTTTATTTGGTTCCGCGCTATCTGAAATGAACCAGAAAAAATTAGAGTCTTGGATGGTGAACAATCAAGTCACTGGTAATTTACTACGTTCAGTATTGCCGGCGGGATGGAACATTGCGGATCGCTCAGGTGCTGGCGGATTTGGTGCTCGGAGTATTACAGCAGTTGTGTGGAGTGAGCATCAAGCCCCAATTATTGTGAGCATCTATCTAGCTCAAACACAGGCTTCAATGGCAGAGCGAAATGATGCGATTGTTAAAATTGGTCATTCAATTTTTGACGTTTATACATCACAGTCGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002241","ARO_id":"38641","ARO_name":"CARB-2","CARD_short_name":"CARB-2","ARO_description":"CARB-2 is a beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36230":{"category_aro_accession":"3000091","category_aro_cvterm_id":"36230","category_aro_name":"CARB beta-lactamase","category_aro_description":"CARB beta-lactamases are class A lactamases that can hydrolyze carbenicillin. Many of the PSE beta-lactamases have been renamed as CARB-lactamases with the notable exception of PSE-2 which is now OXA-10.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1813":{"model_id":"1813","model_name":"MOX-4","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1199":{"protein_sequence":{"accession":"ACI89425.1","sequence":"MQQRQSILWGALATLMWAGLAHAGDTSAVDPLRPVVDASIRPLLKEHRIPGMAVAVLKDGKAHYFNYGVADRERAVGVSEQTLFEIGSVSKPLTATLGAYAVVKGAMQLDDKASRHAPWLKGSAFDSITMGELATYSAGGLPLQFPEEVDSLEKMQAYYRQWTPAYSPGSHRQYSNPSIGLFGHLAASSMKQPFAQLMEQTLLPGLGLHHTYVNVPKQAMASYAYGYSKEDKPIRVSPGMLADEAYGIKTSSADLLRFVKANISGVDDKALQQAISLTHKGHYSVGGMTQGLGWESYAYPVSEQTLLAGNSAEVILEANPTAAPRESGNLMLFNKTGSTSGFGAYVAFVPAKGIGIVMLANRNYPIPARVKAAHAILTQLAR"},"dna_sequence":{"accession":"FJ262599.1","fmin":"0","fmax":"1149","strand":"+","sequence":"ATGCAACAACGACAATCCATCCTGTGGGGCGCTTTGGCCACCCTGATGTGGGCCGGTCTGGCTCATGCCGGTGACACTTCAGCGGTCGATCCCCTGCGCCCCGTGGTGGATGCCAGCATCCGGCCGCTGCTCAAGGAGCACAGGATCCCGGGCATGGCGGTGGCCGTGCTCAAGGATGGCAAGGCCCACTATTTCAACTACGGTGTGGCCGATCGGGAGCGCGCGGTCGGTGTCAGCGAGCAGACCCTGTTCGAGATAGGCTCCGTGAGCAAGCCCCTGACCGCGACCCTAGGAGCCTATGCGGTGGTCAAGGGAGCGATGCAACTGGATGACAAGGCGAGCCGGCACGCCCCCTGGCTCAAGGGATCCGCCTTTGACAGCATCACCATGGGGGAGCTGGCTACCTACAGCGCGGGCGGCTTGCCGCTGCAATTCCCCGAGGAGGTGGATTCGCTCGAGAAGATGCAGGCCTACTACCGCCAGTGGACCCCAGCCTACTCGCCGGGTTCCCATCGCCAGTACTCTAACCCCAGCATAGGGCTGTTCGGCCACCTGGCGGCGAGCAGCATGAAGCAGCCGTTTGCCCAGTTGATGGAGCAGACGCTCCTGCCGGGGCTTGGCCTGCACCACACCTATGTCAATGTGCCGAAGCAGGCCATGGCGAGTTATGCCTATGGCTATTCGAAAGAGGACAAGCCCATCAGGGTCAGCCCCGGCATGCTGGCGGACGAGGCCTACGGCATCAAGACCAGCTCGGCGGATCTGCTGCGCTTTGTGAAGGCCAACATCAGCGGGGTTGATGACAAGGCGTTGCAGCAGGCCATCTCCCTGACCCACAAAGGGCACTACTCGGTAGGCGGGATGACCCAGGGACTGGGTTGGGAGAGTTACGCCTATCCCGTCAGCGAGCAGACATTGCTGGCGGGCAATTCGGCCGAGGTGATTCTCGAAGCCAATCCGACGGCGGCGCCCCGGGAGTCGGGGAACCTGATGCTCTTCAACAAGACCGGCTCGACCAGCGGCTTCGGCGCCTATGTGGCCTTCGTGCCGGCCAAAGGGATCGGCATCGTCATGCTGGCCAACCGCAACTATCCTATCCCGGCCAGGGTGAAAGCGGCCCACGCCATCCTGACGCAACTGGCCAGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36936","NCBI_taxonomy_name":"Aeromonas caviae","NCBI_taxonomy_id":"648"}}}},"ARO_accession":"3002184","ARO_id":"38584","ARO_name":"MOX-4","CARD_short_name":"MOX-4","ARO_description":"MOX-4 is a beta-lactamase found in Aeromonas caviae.","ARO_category":{"36222":{"category_aro_accession":"3000083","category_aro_cvterm_id":"36222","category_aro_name":"MOX beta-lactamase","category_aro_description":"MOX beta-lactamases are plasmid-mediated AmpC-type beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1699":{"model_id":"1699","model_name":"vanX gene in vanO cluster","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"200"}},"model_sequences":{"sequence":{"23":{"protein_sequence":{"accession":"AHA41501.1","sequence":"MNDDFVYVDDWVPGVRWDAKYATWDNFTGKPVDGYLANRIVGTRALCAALEQAREKAASLGFGLLLWDGYRPRRAVDSFLRWSEQPEDGQTKQRHYPNIDRPEMLEKGYVATQSGHSRGGAVDLTLYHLATGELAPMGGDHDLMDPISHHRARGIKPIESKNRELLRSIMEDCGFDRYDCEWWHYTLKREPYPDVYFDFPIT"},"dna_sequence":{"accession":"KF478993.1","fmin":"2576","fmax":"3185","strand":"+","sequence":"ATGAACGACGACTTCGTCTACGTCGACGACTGGGTGCCCGGAGTCCGCTGGGATGCCAAGTACGCCACGTGGGACAACTTCACCGGCAAACCGGTAGACGGCTACCTCGCGAATCGAATCGTCGGCACCCGGGCTTTGTGCGCGGCCCTCGAGCAAGCACGCGAGAAGGCAGCTTCCCTCGGCTTCGGATTGCTTCTCTGGGACGGCTACCGTCCTCGACGCGCCGTCGACAGCTTCCTACGCTGGTCAGAACAGCCGGAGGATGGCCAGACGAAGCAGCGACACTATCCCAATATCGACAGACCCGAGATGCTCGAAAAGGGATACGTGGCAACCCAGTCGGGCCACAGTAGGGGCGGCGCCGTTGACCTGACGCTCTATCACCTTGCGACCGGTGAACTTGCTCCTATGGGTGGCGACCACGACCTCATGGACCCGATCTCACATCATCGAGCGCGAGGAATCAAGCCAATCGAGTCCAAGAATCGTGAGCTTCTTCGTTCCATCATGGAGGACTGCGGATTTGATCGGTACGACTGCGAGTGGTGGCACTACACGCTGAAACGCGAACCATATCCAGATGTCTACTTCGACTTTCCGATCACGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36897","NCBI_taxonomy_name":"Rhodococcus hoagii","NCBI_taxonomy_id":"43767"}}}},"ARO_accession":"3002954","ARO_id":"39388","ARO_name":"vanX gene in vanO cluster","CARD_short_name":"vanX_in_vanO_cl","ARO_description":"Also known as vanXO, is a vanX variant found in the vanO gene cluster.","ARO_category":{"36020":{"category_aro_accession":"3000011","category_aro_cvterm_id":"36020","category_aro_name":"vanX","category_aro_description":"VanX is a D,D-dipeptidase that cleaves D-Ala-D-Ala but not D-Ala-D-Lac, ensuring that the latter dipeptide that has reduced binding affinity with vancomycin is used to synthesize peptidoglycan substrate.","category_aro_class_name":"AMR Gene Family"},"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1713":{"model_id":"1713","model_name":"vanY gene in vanM cluster","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"50"}},"model_sequences":{"sequence":{"479":{"protein_sequence":{"accession":"ACL82959.1","sequence":"MVFQGNLLLVNNEYPVLEESIKTDVVNLFKHDELTKGYELLNREIYLSEKVAREFSEMVDAAEKEGVRHFSINSGFRNFDEQNALYQEMGSDYALPAGYSEHNLGLALDIGSTQMEMSEAPEGKWLEDNAWEYGFILRYPMDKTAITGIQYEPWHFRYVGLPHSAIIEEKNFALEEYLDFLKEQKSISGTIHGENYEISYYPITEKTDIEMPANLHYEISGNNMDGVIVTVYR"},"dna_sequence":{"accession":"FJ349556.1","fmin":"3056","fmax":"3758","strand":"+","sequence":"ATGGTCTTTCAAGGAAACTTACTCTTGGTTAATAACGAATATCCGGTTCTCGAAGAGAGTATAAAAACAGACGTTGTAAATTTATTTAAACATGATGAATTGACAAAAGGATATGAATTGCTCAATAGGGAAATTTATTTATCGGAGAAAGTTGCCCGTGAATTTTCAGAGATGGTAGATGCGGCTGAAAAAGAAGGAGTTCGCCATTTTTCAATCAATAGTGGGTTTCGAAACTTTGATGAGCAAAATGCCCTTTATCAAGAAATGGGGTCTGACTACGCCTTGCCTGCAGGTTATAGCGAACATAATTTAGGTTTAGCACTTGATATCGGATCTACTCAAATGGAAATGAGTGAGGCACCGGAAGGAAAGTGGCTAGAAGATAATGCGTGGGAATACGGCTTTATTTTACGCTATCCAATGGACAAAACGGCCATCACAGGTATTCAGTATGAACCTTGGCATTTTCGCTATGTGGGATTACCGCACAGTGCAATTATAGAGGAAAAGAATTTTGCTTTAGAAGAATATTTGGATTTCCTAAAAGAACAAAAATCCATTTCAGGTACTATACATGGCGAAAATTATGAGATTTCTTATTATCCTATTACCGAAAAAACAGACATTGAAATGCCTGCCAATCTTCATTATGAAATATCAGGAAACAATATGGATGGTGTGATTGTGACAGTGTATCGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36779","NCBI_taxonomy_name":"Enterococcus faecium","NCBI_taxonomy_id":"1352"}}}},"ARO_accession":"3002961","ARO_id":"39395","ARO_name":"vanY gene in vanM cluster","CARD_short_name":"vanY_in_vanM_cl","ARO_description":"Also known as vanYM, is a vanY variant found in the vanM gene cluster.","ARO_category":{"36216":{"category_aro_accession":"3000077","category_aro_cvterm_id":"36216","category_aro_name":"vanY","category_aro_description":"VanY is a D,D-carboxypeptidase that cleaves removes the terminal D-Ala from peptidoglycan for the addition of D-Lactate. The D-Ala-D-Lac peptidoglycan subunits have reduced binding affinity with vancomycin compared to D-Ala-D-Ala.","category_aro_class_name":"AMR Gene Family"},"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"35948":{"category_aro_accession":"0000029","category_aro_cvterm_id":"35948","category_aro_name":"teicoplanin","category_aro_description":"Teicoplanin is a glycopeptide antibiotic used in the prophylaxis and treatment of serious infections caused by Gram-positive bacteria. Teicoplanin has a unique acyl-aliphatic chain, and binds to cell wall precursors to inhibit transglycosylation  and transpeptidation.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1692":{"model_id":"1692","model_name":"tet(M)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"6139":{"protein_sequence":{"accession":"BAB82500.1","sequence":"MKIINIGVLAHVDAGKTTLTESLLYNSGAITELGSVDKGTTRTDNTLLERQRGITIQTGITSFQWENTKVNIIDTPGHMDFLAEVYRSLSVLDGAILLISAKDGVQAQTRILFHALRKMGIPTIFFINKIDQNGIDLSTVYQDIKEKLSAEIVIKQKVELYPNMCVTNFTESEQWDTVIEGNDDLLEKYTSGKLLEALELEQEESIRFHNCSLFPVYHGSAKNNIGIDNLIEVITNKFYSSTHRGQSELCGKVFKIEYTKKRQRLAYIRLYSGVLHLRDSVRVSEKEKIKVTEMYTSINGELCKIDRAYSGEIVILQNEFLKLNSVLGDTKLLPQRKKIENPHPLLQTTVEPSKPEQREMLLDALLEISDSDPLLRYYVDSTTHEIILSFLGKVQMEVISALLQEKYHVEIELKEPTVIYMERPLKNAEYTIHIEVPPNPFWASIGLSVSPLPLGSGMQYESSVSLGYLNQSFQNAVMEGIRYGCEQGLYGWNVTDCKICFKYGLYYSPVSTPADFRMLAPIVLEQVLKKAGTELLEPYLSFKIYAPQEYLSRAYNDAPKYCANIVDTQLKNNEVILSGEIPARCIQEYRSDLTFFTNGRSVCLTELKGYHVTTGEPVCQPRRPNSRIDKVRYMFNKIT"},"dna_sequence":{"accession":"AB039845.1","fmin":"25","fmax":"1945","strand":"+","sequence":"ATGAAAATTATTAATATTGGAGTTTTAGCTCATGTTGATGCGGGAAAAACTACCTTAACAGAAAGCTTATTATATAACAGTGGAGCGATTACAGAATTAGGAAGCGTGGACAAAGGTACAACGAGGACGGATAATACGCTTTTAGAACGTCAGAGAGGAATTACAATTCAGACAGGAATAACCTCTTTTCAGTGGGAAAATACGAAGGTGAACATCATAGACACGCCAGGACATATGGATTTCTTAGCAGAAGTATATCGTTCATTATCAGTTTTAGATGGGGCAATTCTACTGATTTCTGCAAAAGATGGCGTACAAGCACAAACTCGTATATTATTTCATGCACTTAGGAAAATGGGGATTCCCACAATCTTTTTTATCAATAAGATTGACCAAAATGGAATTGATTTATCAACGGTTTATCAGGATATTAAAGAGAAACTTTCTGCCGAAATTGTAATCAAACAGAAGGTAGAACTGTATCCTAATATGTGTGTGACGAACTTTACCGAATCTGAACAATGGGATACGGTAATAGAGGGAAACGATGACCTTTTAGAGAAATATACGTCTGGGAAATTATTGGAAGCATTAGAACTCGAACAAGAGGAAAGCATAAGATTTCATAATTGTTCCCTGTTCCCTGTTTATCACGGAAGTGCAAAAAACAATATAGGGATTGATAACCTTATAGAAGTGATTACGAATAAATTTTATTCATCAACACATCGAGGTCAGTCTGAACTTTGCGGAAAAGTTTTCAAAATTGAATATACAAAAAAAAGACAACGTCTTGCATATATACGCCTTTATAGTGGAGTACTACATTTACGAGATTCGGTTAGAGTATCAGAAAAAGAAAAAATAAAAGTTACAGAAATGTATACTTCAATAAATGGTGAATTATGTAAGATTGATAGAGCTTATTCTGGAGAAATTGTTATTTTGCAAAATGAGTTTTTGAAGTTAAATAGTGTTCTTGGAGATACAAAACTATTGCCACAGAGAAAAAAGATTGAAAATCCGCACCCTCTACTACAAACAACTGTTGAACCGAGTAAACCTGAACAGAGAGAAATGTTGCTTGATGCCCTTTTGGAAATCTCAGATAGTGATCCGCTTCTACGATATTACGTGGATTCTACGACACATGAAATTATACTTTCTTTCTTAGGGAAAGTACAAATGGAAGTGATTAGTGCACTGTTGCAAGAAAAGTATCATGTGGAGATAGAACTAAAAGAGCCTACAGTCATTTATATGGAGAGACCGTTAAAAAATGCAGAATATACCATTCACATCGAAGTGCCGCCAAATCCTTTCTGGGCTTCCATTGGTTTATCTGTATCACCGCTTCCGTTGGGAAGTGGAATGCAGTATGAGAGCTCGGTTTCTCTTGGATACTTAAATCAATCATTTCAAAATGCAGTTATGGAGGGGATACGCTATGGCTGTGAACAAGGATTGTATGGTTGGAATGTGACGGACTGTAAAATCTGTTTTAAGTATGGCTTATACTATAGCCCTGTTAGTACCCCAGCAGATTTTCGGATGCTTGCTCCTATTGTATTGGAACAAGTCTTAAAAAAAGCTGGAACAGAATTGTTAGAGCCATATCTTAGTTTTAAAATTTATGCGCCACAGGAATATCTTTCACGAGCATACAACGATGCTCCTAAATATTGTGCGAACATCGTAGACACTCAATTGAAAAATAATGAGGTCATTCTTAGTGGAGAAATCCCTGCTCGGTGTATTCAAGAATATCGTAGTGATTTAACTTTCTTTACAAATGGACGTAGTGTTTGTTTAACAGAGTTAAAAGGGTACCATGTTACTACCGGTGAACCTGTTTGCCAGCCCCGTCGTCCAAATAGTCGGATAGATAAAGTACGATATATGTTCAATAAAATAACTTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43311","NCBI_taxonomy_name":"Erysipelothrix rhusiopathiae","NCBI_taxonomy_id":"1648"}}}},"ARO_accession":"3000186","ARO_id":"36325","ARO_name":"tet(M)","CARD_short_name":"tet(M)","ARO_description":"Tet(M) is a ribosomal protection protein that confers tetracycline resistance. It is found on transposable DNA elements and its horizontal transfer between bacterial species has been documented.","ARO_category":{"35921":{"category_aro_accession":"0000002","category_aro_cvterm_id":"35921","category_aro_name":"tetracycline-resistant ribosomal protection protein","category_aro_description":"A family of proteins known to bind to the 30S ribosomal subunit. This interaction prevents tetracycline and tetracycline derivatives from inhibiting ribosomal function. Thus, these proteins confer elevated resistance to tetracycline derivatives as a ribosomal protection protein.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35986":{"category_aro_accession":"0000069","category_aro_cvterm_id":"35986","category_aro_name":"doxycycline","category_aro_description":"Doxycycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36291":{"category_aro_accession":"3000152","category_aro_cvterm_id":"36291","category_aro_name":"minocycline","category_aro_description":"Minocycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36667":{"category_aro_accession":"3000528","category_aro_cvterm_id":"36667","category_aro_name":"chlortetracycline","category_aro_description":"Chlortetracycline was an early, first-generation tetracycline antibiotic developed in the 1940's. It inhibits bacterial protein synthesis by binding to the 30S subunit of bacterial ribosomes, preventing the aminoacyl-tRNA from binding to the ribosome.","category_aro_class_name":"Antibiotic"},"37011":{"category_aro_accession":"3000667","category_aro_cvterm_id":"37011","category_aro_name":"demeclocycline","category_aro_description":"Demeclocycline is a tetracycline analog with 7-chloro and 6-methyl groups. Due to its fast absorption and slow excretion, it maintains higher effective blood levels compared to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37012":{"category_aro_accession":"3000668","category_aro_cvterm_id":"37012","category_aro_name":"oxytetracycline","category_aro_description":"Oxytetracycline is a derivative of tetracycline with a 5-hydroxyl group. Its activity is similar to other tetracyclines.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1708":{"model_id":"1708","model_name":"tet(36)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"374":{"protein_sequence":{"accession":"CAD55718.1","sequence":"MRTINIGILAHIDAGKTSITENLLFASGATIVRGSVDKGNTTTDSMDIEKRRGITVRASTTSIQWNDTKINIIDTPGHMDFLAEVERTFRMLDGAILVVSAKEGIQAQTRLLFNVLQQLEIPTILFVNKIDREGVNLNQLYLEIQNSLSKDIIFMQSVEGKELTSSCTIHYISEKNRETILEKDDLLLEKYLSDTQLSNLDYWNSMVRLVQAAKLHPIYHGSAMYGIGIEDLLNSITTFIETSLPQENALSAYVYKIEHNKKEQKRAYLKIIGGTLKSRKLYSLNGSDENLKIRGLKTFYSGDEIDVDEVFTNDIAIADHADNLMVGDYLGIMPNLFDKLNIPSPALKSSIHPAKVENRSKLISAMNVLSVEDPSLAFSINADNNELEVSLYGATQREVILTLLEERFSVDAYFEEVKTIYKERLKTKSEYTIHIEVPPNPYWASIGLIIEPLPIGAGLVMESEISLGYLNRSFQNAVFDGVKKACESGLYGWEVTDLKVTFSHGIYYSPVSTPADFRSLAPYVFRLALQQADVELLEPILDFKLQIPLAVNARAITDINKMQGEISTITSDGDWTTILGNIPLDTSKEYSAEVSSYTQGLGVFVTRFSGYRPTNKKVSRSVELNEKDKLMYMFEKESIK"},"dna_sequence":{"accession":"AJ514254.1","fmin":"0","fmax":"1923","strand":"+","sequence":"ATGAGAACTATAAATATAGGTATTCTTGCACATATTGATGCAGGAAAGACCTCCATTACAGAGAACTTGCTATTTGCGAGTGGAGCAACCATAGTACGTGGAAGTGTGGACAAAGGAAACACTACAACCGATTCGATGGATATCGAAAAACGAAGAGGTATCACAGTTAGAGCGTCTACAACATCTATTCAATGGAATGATACAAAGATTAATATCATCGACACTCCTGGACACATGGACTTTCTGGCAGAGGTAGAACGCACTTTTAGGATGCTAGATGGTGCTATACTTGTGGTGTCTGCCAAAGAGGGCATTCAAGCTCAAACAAGGTTGTTGTTCAATGTCCTGCAACAACTAGAAATACCTACAATTCTATTCGTCAACAAAATAGACAGAGAGGGAGTCAATCTAAATCAGCTTTATTTAGAGATACAAAATAGCCTTTCTAAAGATATTATCTTTATGCAATCCGTTGAAGGCAAGGAATTAACATCTAGCTGTACAATACACTACATATCAGAAAAGAACAGAGAAACAATTTTAGAGAAAGATGATCTCTTGCTTGAAAAATACTTGAGTGATACACAGCTTTCTAATTTAGATTATTGGAATTCAATGGTTCGTCTTGTTCAAGCTGCTAAATTACATCCTATCTATCATGGTTCAGCAATGTATGGCATTGGTATTGAAGATTTGCTAAACTCAATCACTACTTTTATCGAAACATCTCTACCTCAAGAGAACGCTTTGTCTGCCTATGTTTATAAAATTGAGCATAATAAGAAGGAACAGAAACGAGCCTATCTAAAGATTATAGGTGGAACCCTTAAATCTCGAAAATTATATAGCCTCAATGGCTCAGATGAGAATCTGAAGATAAGAGGTTTAAAGACCTTTTACTCAGGAGACGAAATAGATGTAGACGAAGTTTTTACAAATGATATTGCAATTGCAGATCATGCTGATAACTTAATGGTAGGAGATTATCTAGGAATAATGCCAAACTTATTCGACAAATTGAATATTCCTAGTCCTGCTCTCAAATCGTCTATACATCCTGCAAAAGTAGAGAATAGGAGTAAATTGATTTCTGCTATGAATGTATTATCAGTAGAAGATCCATCTTTGGCCTTTAGCATTAATGCTGATAATAATGAATTGGAGGTTTCGCTTTATGGAGCAACTCAACGGGAGGTGATTTTGACTTTATTGGAAGAGAGATTTTCGGTAGATGCTTACTTTGAAGAGGTGAAAACTATCTATAAAGAACGTCTTAAAACAAAATCGGAATACACCATTCATATCGAAGTGCCACCTAATCCGTATTGGGCATCTATTGGCTTGATTATAGAGCCTTTGCCAATTGGGGCGGGACTTGTAATGGAGAGTGAAATATCATTGGGATATTTGAATCGATCCTTTCAGAATGCAGTATTCGATGGAGTCAAGAAAGCCTGTGAATCGGGTTTGTACGGTTGGGAAGTAACTGACCTTAAAGTCACTTTTTCTCACGGAATCTATTATAGCCCAGTGAGTACACCTGCCGACTTTAGAAGTTTAGCACCTTATGTTTTTCGATTAGCTTTGCAACAAGCTGATGTTGAGTTATTGGAGCCAATCTTAGATTTTAAATTGCAAATTCCACTAGCTGTGAATGCTAGAGCTATTACAGACATCAACAAGATGCAAGGCGAAATATCTACTATTACTTCAGATGGTGATTGGACTACTATTTTGGGTAATATTCCTTTAGATACTAGTAAAGAATACTCAGCAGAGGTCAGTTCCTACACACAAGGCTTGGGCGTTTTTGTTACTCGATTTTCGGGTTATCGACCTACCAACAAAAAGGTAAGCAGAAGTGTAGAACTGAATGAAAAAGATAAGCTGATGTATATGTTTGAGAAGGAAAGTATCAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36798","NCBI_taxonomy_name":"Bacteroides coprosuis DSM 18011","NCBI_taxonomy_id":"679937"}}}},"ARO_accession":"3000197","ARO_id":"36336","ARO_name":"tet(36)","CARD_short_name":"tet(36)","ARO_description":"Tet(36) is a tetracycline resistance gene found in Bacteroides similar to Tet(Q), and binds to the ribosome to confer antibiotic resistance as a ribosomal protection protein.","ARO_category":{"35921":{"category_aro_accession":"0000002","category_aro_cvterm_id":"35921","category_aro_name":"tetracycline-resistant ribosomal protection protein","category_aro_description":"A family of proteins known to bind to the 30S ribosomal subunit. This interaction prevents tetracycline and tetracycline derivatives from inhibiting ribosomal function. Thus, these proteins confer elevated resistance to tetracycline derivatives as a ribosomal protection protein.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35986":{"category_aro_accession":"0000069","category_aro_cvterm_id":"35986","category_aro_name":"doxycycline","category_aro_description":"Doxycycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36291":{"category_aro_accession":"3000152","category_aro_cvterm_id":"36291","category_aro_name":"minocycline","category_aro_description":"Minocycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36667":{"category_aro_accession":"3000528","category_aro_cvterm_id":"36667","category_aro_name":"chlortetracycline","category_aro_description":"Chlortetracycline was an early, first-generation tetracycline antibiotic developed in the 1940's. It inhibits bacterial protein synthesis by binding to the 30S subunit of bacterial ribosomes, preventing the aminoacyl-tRNA from binding to the ribosome.","category_aro_class_name":"Antibiotic"},"37011":{"category_aro_accession":"3000667","category_aro_cvterm_id":"37011","category_aro_name":"demeclocycline","category_aro_description":"Demeclocycline is a tetracycline analog with 7-chloro and 6-methyl groups. Due to its fast absorption and slow excretion, it maintains higher effective blood levels compared to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37012":{"category_aro_accession":"3000668","category_aro_cvterm_id":"37012","category_aro_name":"oxytetracycline","category_aro_description":"Oxytetracycline is a derivative of tetracycline with a 5-hydroxyl group. Its activity is similar to other tetracyclines.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1815":{"model_id":"1815","model_name":"CTX-M-134","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1964":{"protein_sequence":{"accession":"AFX60298.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGSYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"JX896165.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCAGCTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001992","ARO_id":"38392","ARO_name":"CTX-M-134","CARD_short_name":"CTX-M-134","ARO_description":"CTX-M-134 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1816":{"model_id":"1816","model_name":"TEM-8","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"932":{"protein_sequence":{"accession":"CAA46344.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDKLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVKYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDSWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGASERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"X65252.1","fmin":"175","fmax":"1036","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATAAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTAAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATAGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCAGTGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3000880","ARO_id":"37260","ARO_name":"TEM-8","CARD_short_name":"TEM-8","ARO_description":"TEM-8 is an extended-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1817":{"model_id":"1817","model_name":"vgaB","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1080"}},"model_sequences":{"sequence":{"8145":{"protein_sequence":{"accession":"AAB95639.1","sequence":"MLKIDMKNVKKYYADKLILNIKELKIYSGDKIGIVGKNGVGKTTLLKIIKGLIEIDEGNIIISEKTTIKYISQLEEPHSKIIDGKYASIFQVENKWNDNMSGGEKTRFKLAEGFQDQCSLMLVDEPTSNLDIEGIELITNTFKEYRDTFLVVSHDRIFLDQVCTKIFEIENGYIREFIGNYTNYIEQKEMLLRKQQEEYEKYNSKRKQLEQAIKLKENKAQGMIKPPSKTMGTSESRIWKMQHATKQKKMHRNTKSLETRIDKLNHVEKIKELPSIKMDLPNREQFHGRNVISLKNLSIKFNNQFLWRDASFVIKGGEKVAIIGNNGVGKTTLLKLILEKVESVIISPSVKIGYVSQNLDVLQSHKSILENVMSTSIQDETIARIVLARLHFYRNDVHKEINVLSGGEQIKVAFAKLFVSDCNTLILDEPTNYLDIDAVEALEELLITYEGVVLFASHDKKFIQNLAEQLLIIENNKVKKFEGTYIEYLKIKDKPKLNTNEKELKEKKMILEMQISSLLSKISMEENEEKNKELDEKYKLKLKELKSLNKNI"},"dna_sequence":{"accession":"U82085.2","fmin":"628","fmax":"2287","strand":"+","sequence":"ATGCTTAAAATCGACATGAAGAATGTAAAAAAATATTATGCAGATAAATTAATTTTAAATATAAAAGAACTAAAGATTTATAGTGGGGATAAAATAGGTATTGTAGGTAAGAATGGAGTTGGCAAAACAACACTTTTAAAAATAATAAAAGGACTAATAGAGATTGACGAAGGAAATATAATTATAAGTGAAAAAACAACTATTAAATATATCTCTCAATTAGAAGAACCACATAGTAAGATAATTGATGGAAAATATGCTTCAATATTTCAAGTTGAAAATAAGTGGAATGACAATATGAGTGGTGGTGAAAAAACTAGATTTAAACTAGCAGAGGGATTTCAAGATCAATGTTCTTTAATGCTCGTAGATGAACCTACAAGTAATTTAGATATCGAAGGAATAGAGTTGATAACAAATACTTTTAAAGAGTACCGTGATACTTTTTTGGTAGTATCTCATGATAGAATTTTTTTAGATCAAGTTTGTACAAAAATTTTTGAAATTGAAAATGGATATATTAGAGAATTCATCGGTAATTATACAAACTATATAGAGCAAAAAGAAATGCTTCTACGAAAGCAACAAGAAGAATACGAAAAGTATAATTCTAAAAGAAAGCAATTGGAGCAAGCTATAAAGCTAAAAGAGAATAAGGCGCAAGGAATGATTAAGCCCCCTTCAAAAACAATGGGAACATCTGAATCTAGAATATGGAAAATGCAACATGCTACTAAACAAAAAAAGATGCATAGAAATACGAAATCGTTGGAAACACGAATAGATAAATTAAATCATGTAGAAAAAATAAAAGAGCTTCCTTCTATTAAAATGGATTTACCTAATAGAGAGCAATTTCATGGTCGCAATGTAATTAGTTTAAAAAACTTATCTATAAAATTTAATAATCAATTTCTTTGGAGAGATGCTTCATTTGTCATTAAAGGTGGAGAAAAGGTTGCTATAATTGGTAACAATGGTGTAGGAAAAACAACATTGTTGAAGCTGATTCTAGAAAAAGTAGAATCAGTAATAATATCACCATCAGTTAAAATTGGATACGTCAGTCAAAACTTAGATGTTCTACAATCTCATAAATCTATCTTAGAAAATGTTATGTCTACCTCCATTCAAGATGAAACAATAGCAAGAATTGTTCTAGCAAGATTACATTTTTATCGCAATGATGTTCATAAAGAAATAAATGTTTTGAGTGGTGGAGAACAAATAAAGGTTGCTTTTGCCAAGCTATTTGTTAGCGATTGTAATACATTAATTCTTGATGAACCAACAAACTATTTGGATATCGATGCTGTTGAGGCATTAGAAGAATTGTTAATTACCTATGAAGGTGTTGTGTTATTTGCTTCCCATGATAAAAAATTTATACAAAACCTAGCTGAACAATTGTTAATAATAGAAAATAATAAAGTGAAAAAATTCGAAGGAACATATATAGAATATTTAAAAATTAAAGATAAACCAAAATTAAATACAAATGAAAAAGAACTCAAAGAAAAAAAGATGATACTAGAAATGCAAATTTCATCATTATTAAGTAAAATCTCAATGGAAGAAAATGAAGAAAAAAACAAAGAATTAGATGAAAAGTACAAATTGAAATTAAAAGAATTGAAAAGCCTAAATAAAAATATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35508","NCBI_taxonomy_name":"Staphylococcus aureus","NCBI_taxonomy_id":"1280"}}}},"ARO_accession":"3000118","ARO_id":"36257","ARO_name":"vgaB","CARD_short_name":"vgaB","ARO_description":"Vga(B) is an ABC-F protein expressed in staphylococci that confers resistance to streptogramin A antibiotics and related compounds. It is associated with plasmid DNA.","ARO_category":{"36252":{"category_aro_accession":"3000113","category_aro_cvterm_id":"36252","category_aro_name":"vga-type ABC-F protein","category_aro_description":"Vga-type plasmid-borne ABC-F proteins, expressed in staphylococci that confer resistance to streptogramin A antibiotics through ribosomal protection.","category_aro_class_name":"AMR Gene Family"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"virginiamycin M1","category_aro_description":"Virginiamycin M1 is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35952":{"category_aro_accession":"0000034","category_aro_cvterm_id":"35952","category_aro_name":"streptogramin A antibiotic","category_aro_description":"Streptogramin A antibiotics are cyclic polyketide peptide hybrids that bind to the ribosomal peptidyl transfer centre. Structural variation arises from substituting a proline for its desaturated derivative and by its substitution for Ala or Cys. Used alone, streptogramin A antibiotics are bacteriostatic, but is bactericidal when used with streptogramin B antibiotics.","category_aro_class_name":"Drug Class"},"37014":{"category_aro_accession":"3000670","category_aro_cvterm_id":"37014","category_aro_name":"pleuromutilin antibiotic","category_aro_description":"Pleuromutilins are natural fungal products that target bacterial protein translation by binding the the 23S rRNA, blocking the ribosome P site at the 50S subunit. They are mostly used for agriculture and veterinary purposes.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1818":{"model_id":"1818","model_name":"GES-26","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"2105":{"protein_sequence":{"accession":"AJP67510.1","sequence":"MRFIHALLLAAIAHSAYASEKLTFKTDLEKLEREKAAQIGVAIVDPQGEIVAGHRMAQRFAMCSTFKFPLAALVFERIDSGTERGDRKLSYGPDMIVEWSPATERFLASGHMTVLEAAQAAVQLSDNGATNLLLREIGGPAAMTQYFRKIGDSVSRLDRKEPEMGDNTPGDLRDTTTPIAMARTVAKVLYGGALTSTSTHTIERWLIGNQTGDATLRAGFPKDWVVGEKTGTCANGGRNDIGFFKAQERDYAVAVYTTAPKLSAVERDELVASVGQVITQLILSTDK"},"dna_sequence":{"accession":"KP096411.1","fmin":"0","fmax":"864","strand":"+","sequence":"ATGCGCTTCATTCACGCACTATTACTGGCAGCGATCGCTCACTCTGCATATGCGTCGGAAAAATTAACCTTCAAGACCGATCTTGAGAAGCTAGAGCGCGAAAAAGCAGCTCAGATCGGTGTTGCGATCGTCGATCCCCAAGGAGAGATCGTCGCGGGCCACCGAATGGCGCAGCGTTTTGCAATGTGCTCAACGTTCAAGTTTCCGCTAGCCGCGCTGGTCTTTGAAAGAATTGACTCAGGCACCGAGCGGGGGGATCGAAAACTTTCATATGGGCCGGACATGATCGTCGAATGGTCTCCTGCCACGGAGCGGTTTCTAGCATCGGGACACATGACGGTTCTCGAGGCAGCGCAAGCTGCGGTGCAGCTTAGCGACAATGGGGCTACTAACCTCTTACTGAGAGAAATTGGCGGACCTGCTGCAATGACGCAGTATTTTCGTAAAATTGGCGACTCTGTGAGTCGGCTAGACCGGAAAGAGCCGGAGATGGGCGACAACACACCTGGCGACCTCAGAGATACAACTACGCCTATTGCTATGGCACGTACTGTGGCTAAAGTCCTCTATGGCGGCGCACTGACGTCCACCTCGACCCACACCATTGAGAGGTGGCTGATCGGAAACCAAACGGGAGACGCGACACTACGAGCGGGTTTTCCTAAAGATTGGGTTGTTGGAGAGAAAACTGGTACCTGCGCCAACGGGGGCCGGAACGACATTGGTTTTTTTAAAGCCCAGGAGAGAGATTACGCTGTAGCGGTGTATACAACGGCCCCGAAACTATCGGCCGTAGAACGTGACGAATTAGTTGCCTCTGTCGGTCAAGTTATTACACAACTCATCCTGAGCACGGACAAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3003181","ARO_id":"39758","ARO_name":"GES-26","CARD_short_name":"GES-26","ARO_description":"GES-26 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36205":{"category_aro_accession":"3000066","category_aro_cvterm_id":"36205","category_aro_name":"GES beta-lactamase","category_aro_description":"GES beta-lactamases or Guiana extended-spectrum beta-lactamases are related to the other plasmid-located class A beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1819":{"model_id":"1819","model_name":"TEM-3","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4678":{"protein_sequence":{"accession":"CAA45828.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDKLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVKYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGASERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"X64523.1","fmin":"476","fmax":"1337","strand":"-","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATAAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTAAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCAGTGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3000875","ARO_id":"37255","ARO_name":"TEM-3","CARD_short_name":"TEM-3","ARO_description":"TEM-3 is an extended-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1820":{"model_id":"1820","model_name":"bacA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4677":{"protein_sequence":{"accession":"AAC76093.1","sequence":"MSDMHSLLIAAILGVVEGLTEFLPVSSTGHMIIVGHLLGFEGDTAKTFEVVIQLGSILAVVVMFWRRLFGLIGIHFGRPLQHEGESKGRLTLIHILLGMIPAVVLGLLFHDTIKSLFNPINVMYALVVGGLLLIAAECLKPKEPRAPGLDDMTYRQAFMIGCFQCLALWPGFSRSGATISGGMLMGVSRYAASEFSFLLAVPMMMGATALDLYKSWGFLTSGDIPMFAVGFITAFVVALIAIKTFLQLIKRISFIPFAIYRFIVAAAVYVVFF"},"dna_sequence":{"accession":"U00096.3","fmin":"3203309","fmax":"3204131","strand":"-","sequence":"ATGAGCGATATGCACTCGCTGCTGATAGCGGCAATATTGGGTGTGGTCGAAGGATTGACAGAATTTCTGCCGGTATCCAGCACGGGCCATATGATTATTGTCGGTCACTTGTTGGGGTTTGAGGGCGACACGGCGAAAACCTTTGAAGTTGTGATCCAGTTAGGATCAATTCTGGCGGTAGTAGTGATGTTCTGGCGGCGTCTGTTTGGCCTGATTGGCATCCACTTTGGCCGCCCGTTGCAGCACGAAGGTGAAAGCAAAGGTCGTTTAACGCTGATCCACATTTTGCTGGGGATGATTCCGGCGGTGGTATTGGGGCTGTTGTTCCACGACACGATTAAGTCATTGTTTAACCCGATAAATGTGATGTATGCGCTGGTCGTTGGCGGTTTGTTGCTGATTGCCGCCGAATGCCTGAAGCCGAAAGAGCCGCGTGCGCCGGGTCTTGATGATATGACCTATCGTCAGGCATTTATGATTGGCTGTTTCCAGTGTCTGGCGCTGTGGCCGGGTTTCTCCCGTTCCGGGGCGACCATTTCAGGTGGGATGCTGATGGGGGTGAGCCGTTACGCTGCTTCCGAGTTTTCGTTCCTGCTGGCGGTGCCGATGATGATGGGCGCAACGGCGCTCGATCTCTACAAAAGCTGGGGCTTCCTGACAAGCGGCGATATCCCGATGTTTGCCGTTGGGTTTATCACCGCTTTTGTGGTGGCGCTGATAGCGATTAAAACCTTCCTGCAATTGATTAAGCGCATTTCGTTTATCCCGTTCGCCATTTATCGCTTTATTGTGGCGGCTGCGGTGTATGTCGTGTTCTTTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36849","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. MG1655","NCBI_taxonomy_id":"511145"}}}},"ARO_accession":"3002986","ARO_id":"39420","ARO_name":"bacA","CARD_short_name":"bacA","ARO_description":"The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.","ARO_category":{"39982":{"category_aro_accession":"3003398","category_aro_cvterm_id":"39982","category_aro_name":"undecaprenyl pyrophosphate related proteins","category_aro_description":"Undecaprenyl phosphate is a universal lipid carrier of glycan biosynthetic intermediates for carbohydrate polymers that are exported to the bacterial cell envelope. Antibiotics that targets this compound or proteins associated with the production of this compound leads to cell death.","category_aro_class_name":"AMR Gene Family"},"35959":{"category_aro_accession":"0000041","category_aro_cvterm_id":"35959","category_aro_name":"bacitracin","category_aro_description":"Bacitracin is a mixture of related cyclic polypeptides produced by organisms of the licheniformis group of Bacillus subtilis var Tracy. Bacitracin interferes with the dephosphorylation of the C55-isoprenyl pyrophosphate, a molecule which carries the building blocks of the peptidoglycan bacterial cell wall outside of the inner membrane.","category_aro_class_name":"Antibiotic"},"36973":{"category_aro_accession":"3000629","category_aro_cvterm_id":"36973","category_aro_name":"bacitracin A","category_aro_description":"Bacitracin A is the primary component of bacitracin. It contains many uncommon amino acids and interferes with bacterial cell wall synthesis.","category_aro_class_name":"Antibiotic"},"36974":{"category_aro_accession":"3000630","category_aro_cvterm_id":"36974","category_aro_name":"bacitracin B","category_aro_description":"Bacitracin B is a component of bacitracin, an antibiotic mixture that interferes with bacterial cell wall synthesis. It differs from Bacitracin A with a valine instead of an isoleucine in its peptide.","category_aro_class_name":"Antibiotic"},"36975":{"category_aro_accession":"3000631","category_aro_cvterm_id":"36975","category_aro_name":"bacitracin F","category_aro_description":"Bacitracin F is a component of bacitracin, an antibiotic mixture that interferes with bacterial cell wall synthesis. It is formed when the thiazoline ring of bacitracin A is oxidatively deaminated.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1821":{"model_id":"1821","model_name":"AAC(6')-Ir","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"581":{"protein_sequence":{"accession":"AAD03490.1","sequence":"MKIMPVSEPFLADWLQLRILLWPDHEDAHLLEMRQLLEQPHTLQLLSYNDQQQAVAMLEASIRYEYVNGQQSSPVAFLEGIYVLPEYRRLGVASTLVQQVEHWAKQFACTEFASDAALDNTISHAMHRALGFQETECVVYFKKNIS"},"dna_sequence":{"accession":"AF031326.1","fmin":"0","fmax":"441","strand":"+","sequence":"ATGAAAATCATGCCTGTAAGCGAGCCGTTCTTGGCCGACTGGCTGCAATTAAGAATATTACTCTGGCCTGATCATGAAGACGCGCATTTACTGGAAATGCGGCAGTTACTCGAACAACCACATACCCTGCAATTATTAAGCTATAACGATCAGCAGCAAGCAGTTGCGATGCTGGAAGCGTCGATTCGATATGAATATGTGAATGGCCAGCAAAGCTCACCGGTGGCTTTTCTGGAAGGTATTTATGTGTTGCCAGAATATCGACGTTTAGGTGTTGCTAGCACGTTGGTACAGCAGGTAGAACACTGGGCCAAGCAGTTTGCATGTACCGAATTTGCTTCAGATGCTGCGCTGGATAATACGATCAGTCATGCCATGCATCGCGCACTGGGCTTTCAGGAAACCGAGTGTGTGGTTTATTTTAAGAAAAACATCAGTTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39512","NCBI_taxonomy_name":"Acinetobacter colistiniresistens","NCBI_taxonomy_id":"70345"}}}},"ARO_accession":"3002561","ARO_id":"38961","ARO_name":"AAC(6')-Ir","CARD_short_name":"AAC(6')-Ir","ARO_description":"AAC(6')-Ir is a chromosomal-encoded aminoglycoside acetyltransferase in Acinetobacter colistiniresistens.","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"A category of aminoglycoside N-acetyltransferase enzymes with modification regiospecificity based at the 6'-amino group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics through acetylation of the 6-amino group of the compound.","category_aro_class_name":"AMR Gene Family"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"46128":{"category_aro_accession":"3007378","category_aro_cvterm_id":"46128","category_aro_name":"2'-N-ethylnetilmicin","category_aro_description":"2'-N-ethylnetilmicin is an aminoglycoside antibiotic and a derivative of netilmicin.","category_aro_class_name":"Antibiotic"},"46129":{"category_aro_accession":"3007379","category_aro_cvterm_id":"46129","category_aro_name":"5-episisomicin","category_aro_description":"5-episosomicin is a semisynthetic aminoglycoside antibiotic similar to sisomicin.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1823":{"model_id":"1823","model_name":"OXY-1-3","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"815":{"protein_sequence":{"accession":"AAL78275.1","sequence":"MLKSSWRKTALMAAAAVPLLLASGSLWASADAIQQKLADLEKRSGGRLGVALINTADDSQTLYRGDERFAMCSTGKVMAAAAVLKQSESNPEVVNKRLEIKKSDLVVWSPITEKHLQSGMTLAELSAAALQYSDNTAMNKMISYLGGPEKVTAFAQSIGDVTFRLDRTEPALNSAIPGDKRDTTTPLAMAESLRKLTLGNALGEQQRAQLVTWLKGNTTGGQSIRAGLPASWAVGDKTGGGDYGTTNDIAVIWPENHAPLVLVTYFTQPQQDAKSRKEVLAAAAKIVTEGL"},"dna_sequence":{"accession":"AY077482.1","fmin":"161","fmax":"1037","strand":"+","sequence":"ATGTTGAAAAGTTCGTGGCGTAAAACCGCCCTGATGGCCGCCGCCGCCGTTCCGCTGCTGCTGGCGAGCGGTTCATTATGGGCCAGTGCCGATGCTATCCAGCAAAAGCTGGCTGATTTAGAAAAACGTTCCGGCGGTCGGCTGGGCGTAGCGCTGATTAACACGGCAGATGATTCGCAAACCCTCTATCGCGGCGATGAACGTTTTGCCATGTGCAGCACCGGTAAAGTGATGGCCGCCGCCGCGGTGTTAAAACAGAGCGAAAGCAATCCAGAGGTGGTGAATAAAAGGCTGGAGATTAAAAAATCGGATTTAGTGGTCTGGAGCCCGATCACCGAAAAACATCTGCAAAGCGGAATGACCCTGGCGGAACTCAGCGCGGCGGCGCTGCAGTACAGCGACAATACCGCGATGAATAAGATGATTAGCTACCTTGGCGGACCGGAAAAGGTGACCGCATTCGCCCAGAGTATCGGGGATGTCACTTTTCGTCTCGATCGTACGGAGCCGGCGCTGAACAGCGCGATTCCCGGCGATAAGCGCGATACCACCACCCCGTTGGCGATGGCCGAAAGCCTGCGCAAGCTGACGCTGGGCAATGCGCTGGGCGAACAGCAGCGCGCCCAGTTAGTGACGTGGCTAAAAGGCAATACCACCGGCGGGCAAAGCATTCGCGCAGGCCTGCCCGCAAGCTGGGCGGTCGGGGATAAAACCGGCGGCGGAGATTACGGCACCACCAACGATATCGCGGTGATCTGGCCGGAAAATCATGCCCCGCTGGTGCTGGTGACCTATTTTACCCAGCCGCAGCAGGATGCGAAAAGCCGCAAAGAGGTGTTAGCCGCGGCGGCAAAAATCGTCACCGAAGGGCTTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3002391","ARO_id":"38791","ARO_name":"OXY-1-3","CARD_short_name":"OXY-1-3","ARO_description":"OXY-1-3 is a beta-lactamase found in Klebsiella oxytoca.","ARO_category":{"38788":{"category_aro_accession":"3002388","category_aro_cvterm_id":"38788","category_aro_name":"OXY beta-lactamase","category_aro_description":"OXY beta-lactamases are chromosomal class A beta-lactamases that are found in Klebsiella oxytoca. At constitutive low levels, OXY beta-lactamases confer resistance to aminopenicillins and carboxypenicillins. At high induced levels,  OXY beta-lactamases confer resistance to penicillins, cephalosporins and aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1824":{"model_id":"1824","model_name":"oleI","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"8246":{"protein_sequence":{"accession":"ABA42118.2","sequence":"MTSEHRSASVTPRHISFFNIPGHGHVNPSLGIVQELVARGHRVSYAITDEFAAQVKAAGATPVVYDSILPKESNPEESWPEDQESAMGLFLDEAVRVLPQLEDAYADDRPDLIVYDIASWPAPVLGRKWDIPFVQLSPTFVAYEGFEEDVPAVQDPTADRGEEAAAPAGTGDAEEGAEAEDGLVRFFTRLSAFLEEHGVDTPATEFLIAPNRCIVALPRTFQIKGDTVGDNYTFVGPTYGDRSHQGTWEGPGDGRPVLLIALGSAFTDHLDFYRTCLSAVDGLDWHVVLSVGRFVDPADLGEVPPNVEVHQWVPQLDILTKASAFITHAGMGSTMEALSNAVPMVAVPQIAEQTMNAERIVELGLGRHIPRDQVTAEKLREAVLAVASDPGVAERLAAVRQEIREAGGARAAADILEGILAEAG"},"dna_sequence":{"accession":"DQ195535.2","fmin":"0","fmax":"1275","strand":"+","sequence":"ATGACGAGCGAGCACCGCTCTGCCTCCGTGACACCCCGTCACATCTCCTTCTTCAACATCCCCGGCCACGGCCACGTGAACCCGTCACTCGGCATCGTCCAGGAACTGGTCGCGCGCGGCCACCGGGTCAGCTACGCCATCACCGACGAGTTCGCCGCACAGGTCAAGGCGGCCGGCGCGACGCCCGTGGTGTACGACTCCATCCTGCCGAAGGAGTCCAACCCCGAGGAGTCGTGGCCGGAGGACCAGGAGTCCGCGATGGGCCTGTTCCTCGACGAAGCCGTCCGGGTCCTGCCGCAGCTGGAGGACGCCTACGCCGACGACCGGCCGGACCTGATCGTCTACGACATCGCCTCCTGGCCCGCCCCGGTGCTCGGCCGGAAGTGGGACATCCCCTTCGTCCAGCTCTCCCCGACCTTCGTCGCCTACGAGGGCTTCGAGGAGGACGTACCCGCGGTGCAGGACCCCACGGCCGACCGCGGCGAGGAGGCCGCCGCCCCCGCGGGGACCGGGGACGCCGAGGAGGGTGCCGAGGCCGAGGACGGCCTGGTGCGCTTCTTCACCCGGCTCTCGGCCTTCCTGGAGGAGCACGGGGTGGACACCCCGGCCACCGAGTTCCTCATCGCGCCCAACCGCTGCATCGTCGCGCTGCCGCGCACCTTCCAGATCAAGGGCGACACGGTCGGCGACAACTACACCTTCGTCGGTCCCACCTACGGCGACCGGTCCCACCAGGGCACCTGGGAAGGCCCCGGGGACGGGCGTCCGGTGCTGCTGATCGCCCTGGGCTCGGCGTTCACCGACCACCTCGACTTCTACCGCACCTGCCTGTCCGCCGTCGACGGCCTGGACTGGCACGTGGTGCTCTCCGTGGGCCGCTTCGTCGACCCCGCGGACCTCGGCGAGGTCCCGCCGAACGTCGAGGTGCACCAGTGGGTGCCGCAGCTCGACATCCTGACCAAAGCCTCCGCGTTCATCACGCACGCGGGCATGGGCAGCACCATGGAGGCCCTGTCGAACGCGGTGCCCATGGTCGCGGTGCCGCAGATCGCGGAGCAGACGATGAACGCCGAGCGGATCGTCGAGCTGGGCCTCGGCCGGCACATCCCGCGGGACCAGGTCACGGCCGAGAAGCTGCGCGAGGCCGTGCTCGCCGTCGCCTCCGACCCCGGTGTCGCCGAACGGCTCGCGGCCGTCCGGCAGGAGATCCGTGAGGCGGGCGGCGCCCGGGCGGCCGCCGACATCCTGGAGGGCATCCTCGCCGAAGCAGGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36823","NCBI_taxonomy_name":"Streptomyces antibioticus","NCBI_taxonomy_id":"1890"}}}},"ARO_accession":"3000866","ARO_id":"37246","ARO_name":"oleI","CARD_short_name":"oleI","ARO_description":"OleI is a glycosyltransferase found in Streptomyces antibioticus, specifically the oleandomycin biosynthetic cluster. OleI glycosylates oleandomycin to confer self-resistance.","ARO_category":{"36604":{"category_aro_accession":"3000465","category_aro_cvterm_id":"36604","category_aro_name":"ole glycosyltransferase","category_aro_description":"OleI and OleD are glycosyltransferases found in Streptomyces antibioticus which is a natural producer of antibiotic oleandomycin. OleI glycosylates antibiotic oleandomycin whereas OleD can glycosylate a wide variety of macrolides.","category_aro_class_name":"AMR Gene Family"},"37247":{"category_aro_accession":"3000867","category_aro_cvterm_id":"37247","category_aro_name":"oleandomycin","category_aro_description":"Oleandomycin is a 14-membered macrolide produced by Streptomyces antibioticus. It is ssimilar to erythromycin, and contains a desosamine amino sugar and an oleandrose sugar. It targets the 50S ribosomal subunit to prevent protein synthesis.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1825":{"model_id":"1825","model_name":"CTX-M-27","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1704":{"protein_sequence":{"accession":"AAO61597.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGGYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"AY156923.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGGCTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001889","ARO_id":"38289","ARO_name":"CTX-M-27","CARD_short_name":"CTX-M-27","ARO_description":"CTX-M-27 is a beta-lactamase found in Escherichia coli.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35975":{"category_aro_accession":"0000058","category_aro_cvterm_id":"35975","category_aro_name":"cefazolin","category_aro_description":"Cefazolin, also known as cefazoline or cephazolin, is a first generation cephalosporin antibiotic. It is administered parenterally, and is active against a broad spectrum of bacteria.","category_aro_class_name":"Antibiotic"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"35987":{"category_aro_accession":"0000070","category_aro_cvterm_id":"35987","category_aro_name":"ertapenem","category_aro_description":"Ertapenem is a carbapenem antibiotic and is highly resistant to beta-lactamases like other carbapenems. It inhibits bacterial cell wall synthesis.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"36990":{"category_aro_accession":"3000646","category_aro_cvterm_id":"36990","category_aro_name":"cefixime","category_aro_description":"Cefixime is a cephalosporin resistant to most beta-lactamases. It is active against many enterobacteria, but activity against staphylococci is poor.","category_aro_class_name":"Antibiotic"},"37084":{"category_aro_accession":"3000704","category_aro_cvterm_id":"37084","category_aro_name":"cefalotin","category_aro_description":"Cefalotin is a semisynthetic cephalosporin antibiotic activate against staphylococci. It is resistant to staphylococci beta-lactamases but hydrolyzed by enterobacterial beta-lactamases.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1826":{"model_id":"1826","model_name":"ykkC","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"180"}},"model_sequences":{"sequence":{"489":{"protein_sequence":{"accession":"CAB13166.1","sequence":"MKWGLVVLAAVFEVVWVIGLKHADSALTWSGTAIGIIFSFYLLMKATHSLPVGTVYAVFTGLGTAGTVLSEIVLFHEPVGWPKLLLIGVLLIGVIGLKLVTQDETEEKGGEA"},"dna_sequence":{"accession":"AL009126.1","fmin":"1376516","fmax":"1376855","strand":"+","sequence":"ATGAAATGGGGATTGGTCGTGCTTGCCGCTGTTTTCGAGGTTGTTTGGGTGATAGGCTTAAAGCACGCTGACTCAGCCTTAACATGGAGCGGCACTGCCATCGGCATCATATTCAGCTTTTACCTTCTAATGAAGGCGACTCACAGTCTGCCTGTTGGTACCGTGTATGCCGTCTTTACCGGGCTCGGCACAGCGGGAACAGTACTTAGTGAAATCGTTCTTTTTCATGAACCGGTTGGATGGCCGAAGCTATTGTTAATTGGCGTGCTCTTAATCGGTGTAATCGGGTTGAAGCTTGTGACACAGGATGAGACAGAGGAAAAAGGAGGCGAGGCATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39579","NCBI_taxonomy_name":"Bacillus subtilis subsp. subtilis str. 168","NCBI_taxonomy_id":"224308"}}}},"ARO_accession":"3003063","ARO_id":"39497","ARO_name":"ykkC","CARD_short_name":"ykkC","ARO_description":"ykkC is an SMR-type protein that is a subunit of the ykkCD efflux pump.","ARO_category":{"36004":{"category_aro_accession":"0010003","category_aro_cvterm_id":"36004","category_aro_name":"small multidrug resistance (SMR) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Small multidrug resistance (SMR) proteins are a relatively small family of transporters, restricted to prokaryotic cells. They are also the smallest multidrug transporters, with only four transmembrane alpha-helices and no significant extramembrane domain.","category_aro_class_name":"AMR Gene Family"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1827":{"model_id":"1827","model_name":"SHV-5","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1149":{"protein_sequence":{"accession":"CAA39164.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGASKRGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"X55640.1","fmin":"111","fmax":"972","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTACTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTAGCAAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001064","ARO_id":"37444","ARO_name":"SHV-5","CARD_short_name":"SHV-5","ARO_description":"SHV-5 is an extended-spectrum beta-lactamase found in Acinetobacter baumannii, Enterobacter cloacae, E. coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Salmonella enterica.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1828":{"model_id":"1828","model_name":"GES-6","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1969":{"protein_sequence":{"accession":"AAR97271.1","sequence":"MRFIHALLLAGIAHSAYASEKLTFKTDLEKLEREKAAQIGVAIVDPQGEIVAGHRMAQRFAMCSTFKFPLAALVFERIDSGTERGDRKLSYGPDMIVKWSPATERFLASGHMTVLEAAQAAVQLSDNGATNLLLREIGGPAAMTQYFRKIGDSVSRLDRKEPEMSDNTPGDLRDTTTPIAMARTVAKVLYGGALTSTSTHTIERWLIGNQTGDATLRAGFPKDWVVGEKTGTCANGGRNDIGFFKAQERDYAVAVYTTAPKLSAVERDELVASVGQVITQLILSTDK"},"dna_sequence":{"accession":"AY494718.1","fmin":"0","fmax":"864","strand":"+","sequence":"ATGCGCTTCATTCACGCACTATTACTGGCAGGGATCGCTCACTCTGCATATGCATCGGAAAAATTAACCTTCAAGACCGATCTTGAGAAGCTAGAGCGCGAAAAAGCAGCTCAGATCGGTGTTGCGATCGTCGATCCCCAAGGAGAGATCGTCGCGGGCCACCGAATGGCGCAGCGTTTTGCAATGTGCTCAACGTTCAAGTTTCCGCTAGCCGCGCTGGTCTTTGAAAGAATTGACTCAGGCACCGAGCGGGGGGATCGAAAACTTTCATATGGGCCGGACATGATCGTCAAATGGTCTCCTGCCACGGAGCGGTTTCTAGCATCGGGACACATGACGGTTCTCGAGGCAGCGCAAGCTGCGGTGCAGCTTAGCGACAATGGGGCTACTAACCTCTTACTGAGAGAAATTGGCGGACCTGCTGCAATGACGCAGTATTTTCGTAAAATTGGCGACTCTGTGAGTCGGCTAGACCGGAAAGAGCCGGAGATGAGCGACAACACACCTGGCGACCTCAGAGATACAACTACGCCTATTGCTATGGCACGTACTGTGGCTAAAGTCCTCTATGGCGGCGCACTGACGTCCACCTCGACCCACACCATTGAGAGGTGGCTGATCGGAAACCAAACGGGAGACGCGACACTACGAGCGGGTTTTCCTAAAGATTGGGTTGTTGGAGAGAAAACTGGTACCTGCGCCAACGGGGGCCGGAACGACATTGGTTTTTTTAAAGCCCAGGAGAGAGATTACGCTGTAGCGGTGTATACAACGGCCCCGAAACTATCGGCCGTAGAACGTGACGAATTAGTTGCCTCTGTCGGTCAAGTTATTACACAACTCATCCTGAGCACGGACAAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002335","ARO_id":"38735","ARO_name":"GES-6","CARD_short_name":"GES-6","ARO_description":"GES-6 is a beta-lactamase found in the Enterobacteriaceae family.","ARO_category":{"36205":{"category_aro_accession":"3000066","category_aro_cvterm_id":"36205","category_aro_name":"GES beta-lactamase","category_aro_description":"GES beta-lactamases or Guiana extended-spectrum beta-lactamases are related to the other plasmid-located class A beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1829":{"model_id":"1829","model_name":"CMY-87","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1284":{"protein_sequence":{"accession":"BAL63057.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAIIYEGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLNDPVTKYWPELTGKQWRGISLLHLATYTAGGLPLQIPDDVTDKAALLRFYQNWQPQWTPGAKRLYANSSIGLFGALAVQPSGMSYEEAMTRRVLQPLKLAHTWITVPQSEQKNYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIELAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPARVEAAWRILEKLQ"},"dna_sequence":{"accession":"AB699171.1","fmin":"0","fmax":"1143","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCGCTGCTGCTGACAGCCTCTTTCTCCACGTTTGCTGCCGCAAAAACAGAACAACAAATTGCCGATATCGTTAACCGCACCATCACACCACTGATGCAGGAGCAGGCTATTCCGGGCATGGCCGTGGCAATTATCTACGAGGGGAAACCTTATTACTTTACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGTTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGACGCTATCGCCCGCGGCGAAATTAAGCTCAACGACCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCGGGGTATCAGCCTGCTACACTTAGCCACCTATACAGCGGGTGGCCTGCCGCTGCAGATCCCCGATGACGTTACGGATAAAGCCGCATTACTGCGCTTTTATCAAAACTGGCAACCACAATGGACTCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGTGCGCTGGCGGTGCAACCTTCAGGTATGAGCTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAAAGCGAACAAAAAAATTATGCCTGGGGCTATCGCGAAGGGAAGCCTGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATCGATATGGCCCGCTGGGTTCAGGCCAACATGGACGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGAGCTTGCGCAGTCTCGCTACTGGCGTATTGGTGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCAGCACCTGCCGTGAAAGCCTCATGGGTGCATAAAACGGGATCCACAGGTGGATTTGGCAGCTACGTTGCCTTCGTTCCAGAAAAAAACCTTGGCATAGTGATGCTGGCAAACAAAAGCTATCCTAACCCGGCTCGCGTAGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAA","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002100","ARO_id":"38500","ARO_name":"CMY-87","CARD_short_name":"CMY-87","ARO_description":"CMY-87 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1830":{"model_id":"1830","model_name":"APH(3'')-Ib","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8275":{"protein_sequence":{"accession":"ABK33456.1","sequence":"MNRTNIFFGESHSDWLPVRGGESGDFVFRRGDGHAFAKIAPASRRGELAGERDRLIWLKGRGVACPEVINWQEEQEGACLVITAIPGVPAADLSGADLLKAWPSMGQQLGAVHSLLVDQCPFERRLSRMFGRAVDVVSRNAVNPDFLPDEDKSTPQLDLLARVERELPVRLDQERTDMVVCHGDPCMPNFMVDPKTLQCTGLIDLGRLGTADRYADLALMIANAEENWAAPDEAERAFAVLFNVLGIEAPDRERLAFYLRLDPLTWG"},"dna_sequence":{"accession":"AF313472.2","fmin":"15593","fmax":"16397","strand":"+","sequence":"TTGAATCGAACTAATATTTTTTTTGGTGAATCGCATTCTGACTGGTTGCCTGTCAGAGGCGGAGAATCTGGTGATTTTGTTTTTCGACGTGGTGACGGGCATGCCTTCGCGAAAATCGCACCTGCTTCCCGCCGCGGTGAGCTCGCTGGAGAGCGTGACCGCCTCATTTGGCTCAAAGGTCGAGGTGTGGCTTGCCCCGAGGTGATCAACTGGCAGGAGGAACAGGAGGGTGCATGCTTGGTGATAACGGCAATTCCGGGAGTACCGGCGGCTGATCTGTCTGGAGCGGATTTGCTCAAAGCGTGGCCGTCAATGGGGCAGCAACTTGGCGCTGTTCACAGCCTATTGGTTGATCAATGTCCGTTTGAGCGCAGGCTGTCGCGAATGTTCGGACGCGCCGTTGATGTGGTGTCCCGCAATGCCGTCAATCCCGACTTCTTACCGGACGAGGACAAGAGTACGCCGCAGCTCGATCTTTTGGCTCGTGTCGAACGAGAGCTACCGGTGCGGCTCGACCAAGAGCGCACCGATATGGTTGTTTGCCATGGTGATCCCTGCATGCCGAACTTCATGGTGGACCCTAAAACTCTTCAATGCACGGGTCTGATCGACCTTGGGCGGCTCGGAACAGCAGATCGCTATGCCGATTTGGCACTCATGATTGCTAACGCCGAAGAGAACTGGGCAGCGCCAGATGAAGCAGAGCGCGCCTTCGCTGTCCTATTCAATGTATTGGGGATCGAAGCCCCCGACCGCGAACGCCTTGCCTTCTATCTGCGATTGGACCCTCTGACTTGGGGTTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002639","ARO_id":"39039","ARO_name":"APH(3'')-Ib","CARD_short_name":"APH(3'')-Ib","ARO_description":"APH(3'')-Ib is an aminoglycoside phosphotransferase encoded by plasmids, transposons, integrative conjugative elements and chromosomes in Enterobacteriaceae and Pseudomonas spp.","ARO_category":{"36266":{"category_aro_accession":"3000127","category_aro_cvterm_id":"36266","category_aro_name":"APH(3'')","category_aro_description":"A category of aminoglycoside O-phosphotransferase enzymes with modification regiospecificity based at the 3''-hydroxyl group of the respective antibiotic. These enzymes are characterized by enzymatic antibiotic inactivation, specifically of streptomycin, by the ATP-dependent phosphorylation of the 3''-hydroxyl group of the compound.","category_aro_class_name":"AMR Gene Family"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1831":{"model_id":"1831","model_name":"AAC(6')-Iid","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"8166":{"protein_sequence":{"accession":"CAE50925.1","sequence":"MIISEFDRENIVLRDQLADLLRLTWPDEYGTEPMKEVEQLMAPERIAVSAIEGEELVGFVGAIPQYGKTGWELHPLVVASTHRKQQIGTRLVSYLEKEVASYGGLVIYLGTDDVEGQTNLVETDLFEDTFAKLQEIKNINHHPYTFYEKLGYQIIGVIPDANGWNQPDIWLAKRVAKREPTE"},"dna_sequence":{"accession":"AJ584700.2","fmin":"33","fmax":"582","strand":"+","sequence":"ATGATTATCAGTGAGTTTGATCGTGAGAATATTGTCTTGCGAGATCAGCTTGCAGATCTTTTAAGATTGACTTGGCCTGATGAGTATGGAACAGAGCCGATGAAAGAAGTCGAACAGTTGATGGCTCCAGAACGGATTGCTGTATCGGCGATTGAAGGGGAGGAATTGGTCGGTTTTGTTGGAGCGATCCCTCAATATGGCAAAACAGGGTGGGAGTTACATCCTTTGGTAGTAGCAAGCACACATCGCAAACAACAAATCGGGACACGATTGGTTTCCTACCTGGAAAAAGAAGTCGCTTCATATGGTGGCCTGGTCATCTATCTAGGGACAGATGATGTTGAAGGACAAACAAATTTAGTTGAAACGGATTTATTTGAAGATACCTTTGCAAAGTTACAAGAAATCAAAAATATCAATCATCATCCCTATACATTTTATGAGAAACTTGGCTATCAGATCATCGGTGTGATCCCAGATGCGAATGGGTGGAACCAGCCTGATATTTGGTTAGCAAAACGAGTGGCCAAACGAGAGCCAACGGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39521","NCBI_taxonomy_name":"Enterococcus hirae","NCBI_taxonomy_id":"1354"}}}},"ARO_accession":"3002589","ARO_id":"38989","ARO_name":"AAC(6')-Iid","CARD_short_name":"AAC(6')-Iid","ARO_description":"AAC(6')-Iid is a chromosomal-encoded aminoglycoside acetyltransferase in Enterococcus durans.","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"A category of aminoglycoside N-acetyltransferase enzymes with modification regiospecificity based at the 6'-amino group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics through acetylation of the 6-amino group of the compound.","category_aro_class_name":"AMR Gene Family"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"46128":{"category_aro_accession":"3007378","category_aro_cvterm_id":"46128","category_aro_name":"2'-N-ethylnetilmicin","category_aro_description":"2'-N-ethylnetilmicin is an aminoglycoside antibiotic and a derivative of netilmicin.","category_aro_class_name":"Antibiotic"},"46129":{"category_aro_accession":"3007379","category_aro_cvterm_id":"46129","category_aro_name":"5-episisomicin","category_aro_description":"5-episosomicin is a semisynthetic aminoglycoside antibiotic similar to sisomicin.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1832":{"model_id":"1832","model_name":"QnrS2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"145":{"protein_sequence":{"accession":"ABF47470.1","sequence":"METYRHTYRHHSFSHQDLSDITFTACTFIRCDFRRANLRDATFINCKFIEQGDIEGCHFDVADLRDASFQQCQLAMANFSNANCYGIELRECDLKGANFSRANFANQVSNRMYFCSAFITGCNLSYANMERVCLEKCELFENRWIGTHLAGASLKESDLSRGVFSEDVWGQFSLQGANLCHAELDGLDPRKVDTSGIKIASWQQEQLLEALGIVVFPD"},"dna_sequence":{"accession":"DQ485530.1","fmin":"0","fmax":"657","strand":"+","sequence":"ATGGAAACCTACCGTCACACATATCGACACCACAGTTTTTCACATCAAGATCTAAGTGATATTACTTTCACTGCTTGCACCTTTATCCGATGCGATTTTCGACGTGCTAACTTGCGTGATGCGACATTTATTAACTGCAAGTTCATTGAACAGGGTGATATCGAAGGTTGCCATTTTGATGTCGCAGACCTTCGCGATGCAAGTTTCCAACAATGCCAGCTTGCGATGGCAAACTTTAGTAACGCCAATTGCTACGGTATTGAGTTACGTGAGTGTGATTTAAAAGGGGCCAACTTTTCCCGAGCAAACTTTGCCAATCAAGTGAGTAATCGTATGTACTTTTGCTCAGCCTTTATTACTGGATGTAACCTGTCTTATGCCAATATGGAGCGGGTCTGTTTAGAAAAATGTGAGCTGTTTGAAAATCGCTGGATAGGGACTCACCTCGCGGGCGCATCACTGAAAGAGTCAGACTTAAGTCGAGGTGTTTTTTCTGAAGATGTCTGGGGACAGTTTAGCCTACAGGGTGCTAATTTATGTCACGCCGAACTCGACGGTTTAGATCCTCGAAAAGTCGATACATCAGGTATCAAAATTGCCAGCTGGCAACAAGAACAGCTTCTCGAAGCGTTGGGTATTGTTGTTTTTCCTGACTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35715","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Anatum","NCBI_taxonomy_id":"58712"}}}},"ARO_accession":"3002791","ARO_id":"39225","ARO_name":"QnrS2","CARD_short_name":"QnrS2","ARO_description":"QnrS2 is a plasmid-mediated quinolone resistance protein found in Salmonella enterica.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1833":{"model_id":"1833","model_name":"OXA-374","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1379":{"protein_sequence":{"accession":"AHL30274.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKTTTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPKGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"KF986255.1","fmin":"16","fmax":"841","strand":"+","sequence":"ATGAACATTAAAGCCCTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTCTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGACAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGACGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTAAAGGAAATATTGTAGCATTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001560","ARO_id":"37960","ARO_name":"OXA-374","CARD_short_name":"OXA-374","ARO_description":"OXA-374 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1834":{"model_id":"1834","model_name":"TEM-94","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"852":{"protein_sequence":{"accession":"CAC85661.1","sequence":"MSIQHFRVALIPFFAAFCFPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVKYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTTPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGASERGSRGIIAALGPDGKPSRIVVIYMTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AJ318094.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCTTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTAAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGACGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCAGTGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACATGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000961","ARO_id":"37341","ARO_name":"TEM-94","CARD_short_name":"TEM-94","ARO_description":"TEM-94 is an extended-spectrum beta-lactamase found in E. coli.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1836":{"model_id":"1836","model_name":"OXA-201","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1372":{"protein_sequence":{"accession":"ADX07746.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDVKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIQVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWVVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"HQ734812.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGTAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCAAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGGTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAACAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001666","ARO_id":"38066","ARO_name":"OXA-201","CARD_short_name":"OXA-201","ARO_description":"OXA-201 is a beta-lactamase found in A. baumannii.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1837":{"model_id":"1837","model_name":"CTX-M-59","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1781":{"protein_sequence":{"accession":"ABD73290.1","sequence":"MMTQSIRRSMLTVMATLPLLFSSATLHAQANSVQQQLEALEKSSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKQSESDKLLLNQRVEIKKSDLVNYNPIAEKHVNGTMTLAELGAAALQYSDNTAMNKLIAHLGGPDKVTAFARSLGDETFRLDRTEPTLNTAIPGDPRDTTTPLAMAQTLKNLTLGKALAETQRAQLVTWLKGNTTGSASIRAGLPKSWVVGDKTGSGDYGTTNDIAVIWPENHAPLVLVTYFTQPEQKAESRRDILAAAAKIVTHGF"},"dna_sequence":{"accession":"DQ408762.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGATGACTCAGAGCATTCGCCGCTCAATGTTAACGGTGATGGCGACGCTACCCCTGCTATTTAGCAGCGCAACGCTGCATGCGCAGGCGAACAGCGTGCAACAGCAGCTGGAAGCCCTGGAGAAAAGTTCGGGAGGTCGGCTTGGCGTTGCGCTGATTAACACCGCCGATAATTCGCAGATTCTCTACCGTGCCGATGAACGTTTTGCGATGTGCAGTACCAGTAAGGTGATGGCGGCCGCGGCGGTGCTTAAACAGAGCGAGAGCGATAAGCTCCTGCTAAATCAGCGCGTTGAAATCAAGAAGAGCGACCTGGTTAACTACAATCCCATTGCGGAGAAACACGTTAACGGCACGATGACGCTGGCTGAGCTTGGCGCAGCGGCGCTGCAGTATAGCGACAATACTGCCATGAATAAGCTGATTGCCCATCTGGGTGGTCCCGATAAAGTGACGGCGTTTGCTCGCTCGTTGGGTGATGAGACCTTCCGTCTGGACAGAACCGAGCCCACGCTCAATACCGCCATTCCAGGCGACCCGCGTGATACCACCACGCCGCTCGCGATGGCGCAGACCCTGAAAAATCTGACGCTGGGTAAAGCGCTGGCGGAAACTCAGCGGGCACAGTTGGTGACGTGGCTTAAGGGCAATACTACCGGTAGCGCGAGCATTCGGGCGGGTCTGCCGAAATCATGGGTAGTGGGCGATAAAACCGGCAGCGGAGATTATGGCACCACCAACGATATCGCGGTTATCTGGCCGGAAAACCACGCACCGCTGGTTCTGGTGACCTACTTTACCCAACCGGAGCAGAAGGCGGAAAGCCGTCGGGATATTCTGGCTGCGGCGGCGAAAATCGTAACCCACGGTTTCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001920","ARO_id":"38320","ARO_name":"CTX-M-59","CARD_short_name":"CTX-M-59","ARO_description":"CTX-M-59 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1838":{"model_id":"1838","model_name":"ACT-5","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1893":{"protein_sequence":{"accession":"ACJ05689.1","sequence":"MMKKSLCCALLLGISCSALAAPVSEKQLAEVVANTVTPLMKAQSIPGMAVAVIYQGKPHYYTFGKADIAASKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNAALLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMPFEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGMKTNVQDMANWVMANMAPENVADASLKQGISLAQSRYWRIGSMYQGLGWEMLNWPVEANTVIEGSDSKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANKSYPNPARVEAAYPILDALQ"},"dna_sequence":{"accession":"FJ237369.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCTCTTTGCTGCGCCCTGCTGCTCGGCATCTCTTGCTCTGCTCTCGCCGCGCCAGTGTCAGAAAAACAGCTGGCGGAGGTGGTCGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCGATTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGTAAACCGCACTATTACACGTTTGGCAAAGCCGATATCGCGGCCAGCAAACCCGTTACGCCTCAGACTCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGGGTTTTAGGTGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTGACGGGCAAGCAGTGGCAGGGGATTCGTATGCTGGATCTCGCAACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAATGCCGCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGTATCGGTCTTTTTGGCGCGCTGGCGGTCAAACCTTCCGGCATGCCCTTTGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTTCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGATATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGAATGCTGGATGCACAAGCCTATGGCATGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAATATGGCGCCGGAGAACGTTGCTGATGCCTCACTTAAGCAGGGCATCTCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGATCGAGGGCAGCGACAGTAAGGTGGCGCTGGCACCGCTGCCCGTGGCAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGCTCTACTGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCCTATCCTCGACGCGCTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001824","ARO_id":"38224","ARO_name":"ACT-5","CARD_short_name":"ACT-5","ARO_description":"ACT-5 is a beta-lactamase found in Escherichia coli.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1839":{"model_id":"1839","model_name":"aadA14","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"4676":{"protein_sequence":{"accession":"CAI57696.1","sequence":"MTNKPPESIAEQVSEARSILENHLETIQAIHLFGSAVDGGLKPFSDIDLLVTVGTPLNESTRAALMSDLLAVSAFPGTDSKRRALEVTVLTQEDVVPWRYPAKRQMQFGEWLRDDINARIFEPALMDHDLAILLTKVRRHSVALYGPAAHEFFDEIPVVDVQRSLLETLTLWTTEADWKGDERNIVLALVRIWYTAMTGEITSKVAAADWALQRLPREIKSVVIAARDAYLGLEAADLAAYPKERADLRNHIHSSVTAKLQ"},"dna_sequence":{"accession":"AJ884726.1","fmin":"539","fmax":"1325","strand":"-","sequence":"ATGACTAATAAGCCCCCTGAGTCGATTGCAGAACAAGTATCCGAGGCTCGATCAATTTTAGAAAATCATCTTGAAACTATTCAGGCGATTCACTTGTTTGGTTCCGCAGTAGATGGTGGATTAAAGCCATTTAGTGATATCGACCTGTTGGTTACGGTGGGCACTCCTTTAAACGAGTCAACCAGAGCTGCATTGATGTCCGATTTGTTGGCGGTATCCGCTTTCCCTGGCACCGATTCAAAACGCCGTGCACTTGAGGTGACGGTGCTGACTCAGGAAGACGTAGTGCCGTGGCGATATCCAGCGAAACGGCAAATGCAATTTGGTGAATGGTTGCGTGATGATATCAATGCGAGGATTTTCGAGCCCGCACTGATGGATCATGACCTCGCCATCTTGCTGACGAAAGTGCGGCGACATAGCGTTGCCTTGTACGGCCCAGCTGCTCACGAATTTTTCGATGAAATTCCTGTCGTCGATGTGCAGCGTTCGTTACTGGAAACATTGACACTCTGGACTACAGAGGCGGATTGGAAAGGGGATGAGAGAAACATCGTTCTCGCCTTGGTGCGTATCTGGTACACCGCAATGACCGGAGAGATTACTTCTAAAGTTGCTGCAGCAGACTGGGCGCTTCAGCGTCTGCCTCGTGAGATCAAAAGCGTTGTTATTGCCGCAAGGGATGCGTATCTGGGGCTGGAAGCCGCAGATCTGGCAGCTTATCCGAAAGAACGGGCAGACCTTCGGAACCATATCCATTCTAGCGTGACGGCGAAACTGCAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36867","NCBI_taxonomy_name":"Pasteurella multocida","NCBI_taxonomy_id":"747"}}}},"ARO_accession":"3002614","ARO_id":"39014","ARO_name":"aadA14","CARD_short_name":"aadA14","ARO_description":"aadA14 is a plasmid-encoded aminoglycoside nucleotidyltransferase gene in Pasteurella multocida.","ARO_category":{"41439":{"category_aro_accession":"3004275","category_aro_cvterm_id":"41439","category_aro_name":"ANT(3'')","category_aro_description":"A category of aminoglycoside O-nucleotidyltransferase enzymes with modification regiospecificity based at the 3''-hydroxyl group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics by transfer of an AMP group from an ATP substrate to the 3''-hydroxyl group of the compound.","category_aro_class_name":"AMR Gene Family"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1840":{"model_id":"1840","model_name":"CMY-59","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6218":{"protein_sequence":{"accession":"BAJ17544.1","sequence":"GPGHLFAFNYGTDFMMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHASPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"AB587082.1","fmin":"0","fmax":"1188","strand":"+","sequence":"GGGCCCGGACACCTTTTTGCTTTTAATTACGGAACTGATTTCATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGCTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002069","ARO_id":"38469","ARO_name":"CMY-59","CARD_short_name":"CMY-59","ARO_description":"CMY-59 is a beta-lactamase found in Shigella spp.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1841":{"model_id":"1841","model_name":"OXA-76","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1465":{"protein_sequence":{"accession":"AAX51234.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDVKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEKLGIL"},"dna_sequence":{"accession":"AY949203.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGTAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAACAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAAAAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001621","ARO_id":"38021","ARO_name":"OXA-76","CARD_short_name":"OXA-76","ARO_description":"OXA-76 is a beta-lactamase found in A. baumannii.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1842":{"model_id":"1842","model_name":"IMI-3","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1356":{"protein_sequence":{"accession":"ACX71212.1","sequence":"MSLNVKQSRIAILFISCLFSISFFSQANTKGIDEIKNLETDFNGRVGVYALDTGSGKSFSYKANERFPLCSSFKGFLAAAVLKGSQDNQLNLNQIVNYNTRSLEFHSPITTKYKDNGMSLGDMAAAALQYSDNGATNIILERYIGGPEGMTKFMRSIGDEDFRLDRWELDLNTAIPGDERDTSTPAAVAKSLKTLALGNILSEREKETYQTWLKGNTTGAARIRASVPSDWVVGDKTGSCGAYGTANDYAVVWPKNRAPLIISVYTTKNEKEAKHEDKVIAEASRIAIDNLK"},"dna_sequence":{"accession":"GU015024.1","fmin":"0","fmax":"879","strand":"+","sequence":"ATGTCACTTAATGTAAAACAAAGTAGAATAGCCATCTTGTTTATCTCTTGTTTATTTTCAATATCATTTTTCTCACAGGCCAATACAAAGGGTATCGATGAGATTAAAAACCTTGAAACAGATTTCAATGGTAGAGTTGGTGTCTACGCTTTAGACACTGGCTCAGGTAAATCATTTTCGTACAAAGCAAATGAACGATTTCCATTATGTAGTTCTTTCAAAGGCTTTTTAGCTGCTGCTGTATTAAAAGGCTCTCAAGATAATCAACTCAATCTTAATCAGATCGTGAATTACAATACAAGAAGTTTAGAGTTCCATTCACCCATCACAACTAAATATAAAGATAATGGAATGTCATTAGGTGATATGGCTGCTGCCGCTTTACAATATAGCGACAATGGTGCTACTAATATTATTCTTGAACGTTATATCGGTGGTCCTGAGGGTATGACTAAATTCATGCGGTCGATTGGAGATGAAGATTTTAGACTCGATCGTTGGGAGTTAGATCTAAACACAGCTATTCCAGGCGATGAACGTGACACATCTACACCTGCAGCAGTAGCTAAGAGCCTGAAAACTCTTGCTCTGGGTAACATACTTAGTGAGCGTGAAAAGGAAACCTATCAGACATGGTTAAAGGGTAACACAACCGGTGCAGCGCGTATTCGTGCTAGCGTACCAAGCGATTGGGTAGTTGGCGATAAAACTGGTAGTTGCGGAGCATACGGTACTGCAAATGATTATGCGGTAGTCTGGCCAAAGAACCGGGCTCCTCTTATAATTTCTGTATACACAACAAAAAACGAAAAAGAAGCCAAGCATGAGGATAAAGTAATCGCAGAAGCTTCAAGAATYGCAATTGATAACCTTAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3001860","ARO_id":"38260","ARO_name":"IMI-3","CARD_short_name":"IMI-3","ARO_description":"IMI-3 is a beta-lactamase found in Enterobacteriaceae.","ARO_category":{"36027":{"category_aro_accession":"3000018","category_aro_cvterm_id":"36027","category_aro_name":"IMI beta-lactamase","category_aro_description":"IMI beta-lactamases are a group of TEM-1-like beta-lactamase that are known to hydrolyze imipenem. IMI beta-lactamases are inhibited by clavulanic acid and tazobactam.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1843":{"model_id":"1843","model_name":"rmtD","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"4675":{"protein_sequence":{"accession":"ABY64751.1","sequence":"MSELKEKLLASKKYRDVCPDTIERIWRECSAKFKKEKDVDKAAREALHGVTGAFMTEREYKRAMEMAAARDWEALLGMHASTRERLPVESMDRVFDQLFEASGTPARILDLACGLNPVYLAHRLPNAAITGVDISGQCVNVIRAFGGAEARLGDLLCEIPEDEANAALLFKVLPLLERQRAGAAMDALMRVNAEWIVASFPTRSLGGRNVGMEKHYSEWMEAHVPENRAIAARLTGENELFYVLKRK"},"dna_sequence":{"accession":"EU269034.2","fmin":"1479","fmax":"2223","strand":"-","sequence":"ATGAGCGAACTGAAGGAAAAACTGCTCGCTTCGAAAAAATATCGCGACGTTTGCCCGGACACGATCGAGCGCATATGGCGTGAATGCAGCGCGAAATTCAAAAAGGAAAAGGACGTGGACAAGGCGGCGCGCGAAGCGCTTCACGGCGTGACCGGCGCGTTCATGACCGAGCGCGAATACAAACGCGCAATGGAAATGGCGGCGGCACGCGATTGGGAAGCGCTGCTTGGAATGCACGCGTCCACGCGCGAACGGCTGCCTGTGGAATCGATGGATCGCGTGTTCGATCAGCTGTTTGAAGCCAGCGGAACGCCGGCGCGAATCCTCGATCTCGCGTGCGGGCTGAATCCTGTCTACCTCGCGCATCGATTGCCAAATGCGGCGATTACCGGCGTGGATATCAGCGGTCAGTGCGTAAACGTAATTCGTGCGTTTGGCGGCGCGGAAGCGCGTTTGGGCGATTTGCTGTGCGAAATCCCGGAAGACGAGGCGAATGCGGCGCTGCTGTTTAAGGTGCTGCCGCTTTTGGAGCGCCAGCGTGCGGGCGCGGCGATGGATGCGCTAATGCGCGTGAATGCGGAATGGATCGTCGCATCGTTTCCGACGCGTTCGCTCGGCGGGCGCAACGTCGGCATGGAAAAGCACTATTCCGAATGGATGGAGGCGCACGTGCCGGAAAATCGCGCGATTGCCGCGCGGCTGACCGGCGAAAACGAGCTGTTTTACGTGCTGAAACGAAAATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002667","ARO_id":"39067","ARO_name":"rmtD","CARD_short_name":"rmtD","ARO_description":"RmtD is a 16S rRNA methyltransferase found in Pseudomonas aeruginosa which methylates G1405 of the 16S rRNA. It confers high level resistance to many aminoglycosides.","ARO_category":{"41435":{"category_aro_accession":"3004271","category_aro_cvterm_id":"41435","category_aro_name":"16S rRNA methyltransferase (G1405)","category_aro_description":"Methyltransferases that methylate the G1405 position of 16S rRNA, which is part of an aminoglycoside binding site.","category_aro_class_name":"AMR Gene Family"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"40942":{"category_aro_accession":"3004015","category_aro_cvterm_id":"40942","category_aro_name":"gentamicin A","category_aro_description":"Gentamicin A is part of a complex of broad spectrum aminoglycoside antibiotics. Gentamicin inhibits protein synthesis, resulting in bacterial cell death.","category_aro_class_name":"Antibiotic"},"46133":{"category_aro_accession":"3007382","category_aro_cvterm_id":"46133","category_aro_name":"gentamicin","category_aro_description":"Gentamicin is a commonly used aminoglycoside antibiotic derived from members of the Micromonospora genus of bacteria. It acts by binding the 30S ribosomal subunit, thus inhibiting protein synthesis. Gentamicin is typically used to treat Gram-negative infections of the repiratory and urinary tract, as well as infections of the bone and soft tissue. It also exhibits considerable nephrotoxicity and ototoxicity. Gentamicin is administered as a mixture of gentamicin type C (which makes about around 80% of the complex) and types A, B, and X (distributed in the remaining 20% of the complex).","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1844":{"model_id":"1844","model_name":"OXA-128","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1368":{"protein_sequence":{"accession":"ABY77907.1","sequence":"MNIKALLLITSAIFISACSPYIVSANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNVLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQEVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"EU375515.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGTCTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGTTCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACTACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTAGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAGAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001648","ARO_id":"38048","ARO_name":"OXA-128","CARD_short_name":"OXA-128","ARO_description":"OXA-128 is a beta-lactamase found in A. baumannii.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1845":{"model_id":"1845","model_name":"OXA-312","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1298":{"protein_sequence":{"accession":"AGU69250.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKTTTTEVFKWDGQKRLFPEWEKDMTLGDAMKASALPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"KF057029.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCCCTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTCTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGACAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGACGCTATGAAAGCTTCCGCTCTTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCATTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001683","ARO_id":"38083","ARO_name":"OXA-312","CARD_short_name":"OXA-312","ARO_description":"OXA-312 is a beta-lactamase found in A. baumannii.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1846":{"model_id":"1846","model_name":"CTX-M-91","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1864":{"protein_sequence":{"accession":"ACX34099.1","sequence":"MMRKSVRRAMLMTTACVSLLLASVPLCAQANDVQQKLAALEKSSGGRLGVALINTADNTQTLYRADERFAMCSTSKVMAVAAVLKQSETQKGLLSQRVEIKPSDLINYNPIAEKHVNGTMTFGELSAAALQYSDNTAMNKLIAHLGGPDKVTAFARTIGDDTFRLDRTEPTLNTAIPGDPRDTTTPLAMAQSLRNLTLGNALGDTQRAQLVMWLKGNTTGAASIQAGLPTSWVVGDKTGSGDYGTTNDIAVIWPEGRAPLVLVTYFTQSEPKAESRRDVLAAAARIVTDGY"},"dna_sequence":{"accession":"GQ870432.1","fmin":"30","fmax":"906","strand":"+","sequence":"ATGATGAGAAAAAGCGTAAGGCGGGCGATGTTAATGACGACAGCCTGTGTTTCGCTGCTGTTGGCCAGTGTGCCGCTGTGTGCCCAGGCGAACGATGTTCAACAGAAGCTCGCGGCGCTGGAGAAAAGCAGCGGGGGACGACTGGGTGTGGCGTTGATTAACACCGCCGATAACACGCAGACGCTCTACCGCGCCGACGAGCGTTTTGCCATGTGCAGCACCAGTAAAGTGATGGCGGTAGCGGCGGTGCTTAAGCAAAGTGAAACGCAAAAGGGCTTGTTGAGTCAGCGGGTTGAAATTAAGCCCTCAGACTTGATTAACTACAACCCCATTGCGGAAAAACACGTCAATGGCACGATGACATTCGGGGAGTTGAGCGCGGCGGCGCTACAGTACAGCGATAATACTGCCATGAATAAGCTGATTGCCCATCTCGGGGGGCCGGATAAAGTGACGGCATTTGCCCGTACGATTGGCGATGACACGTTCCGGCTCGATCGTACCGAGCCGACGCTCAACACCGCGATCCCCGGCGACCCGCGCGATACCACCACGCCGTTAGCGATGGCGCAGTCTCTGCGCAATCTGACGTTGGGCAATGCCCTGGGTGACACTCAGCGTGCGCAGCTGGTGATGTGGCTGAAAGGCAACACCACCGGCGCTGCCAGCATTCAGGCAGGGCTACCCACATCGTGGGTTGTCGGGGATAAAACCGGCAGCGGCGATTATGGTACGACGAATGATATCGCGGTTATTTGGCCGGAAGGTCGCGCGCCGCTCGTTCTGGTGACTTACTTCACCCAGTCGGAGCCGAAGGCAGAGAGCCGTCGTGACGTGCTCGCTGCTGCCGCCAGAATTGTCACCGACGGTTATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3001951","ARO_id":"38351","ARO_name":"CTX-M-91","CARD_short_name":"CTX-M-91","ARO_description":"CTX-M-91 is a beta-lactamase found in Escherichia coli.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1847":{"model_id":"1847","model_name":"emrB","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"900"}},"model_sequences":{"sequence":{"20":{"protein_sequence":{"accession":"AAC75733.1","sequence":"MQQQKPLEGAQLVIMTIALSLATFMQVLDSTIANVAIPTIAGNLGSSLSQGTWVITSFGVANAISIPLTGWLAKRVGEVKLFLWSTIAFAIASWACGVSSSLNMLIFFRVIQGIVAGPLIPLSQSLLLNNYPPAKRSIALALWSMTVIVAPICGPILGGYISDNYHWGWIFFINVPIGVAVVLMTLQTLRGRETRTERRRIDAVGLALLVIGIGSLQIMLDRGKELDWFSSQEIIILTVVAVVAICFLIVWELTDDNPIVDLSLFKSRNFTIGCLCISLAYMLYFGAIVLLPQLLQEVYGYTATWAGLASAPVGIIPVILSPIIGRFAHKLDMRRLVTFSFIMYAVCFYWRAYTFEPGMDFGASAWPQFIQGFAVACFFMPLTTITLSGLPPERLAAASSLSNFTRTLAGSIGTSITTTMWTNRESMHHAQLTESVNPFNPNAQAMYSQLEGLGMTQQQASGWIAQQITNQGLIISANEIFWMSAGIFLVLLGLVWFAKPPFGAGGGGGGAH"},"dna_sequence":{"accession":"U00096.1","fmin":"2812615","fmax":"2814154","strand":"+","sequence":"ATGCAACAGCAAAAACCGCTGGAAGGCGCGCAACTGGTCATTATGACGATTGCGCTGTCACTGGCGACATTCATGCAGGTGCTGGACTCCACCATTGCTAACGTGGCGATCCCCACTATCGCCGGGAATCTGGGCTCATCGCTCAGCCAGGGAACGTGGGTAATCACTTCTTTCGGGGTGGCGAATGCCATCTCGATCCCGCTTACCGGCTGGCTGGCAAAGCGCGTCGGGGAAGTGAAACTGTTCCTTTGGTCCACCATCGCCTTTGCTATTGCGTCGTGGGCGTGTGGTGTCTCCAGCAGCCTGAATATGCTGATCTTCTTCCGCGTGATTCAGGGGATTGTCGCCGGGCCGTTGATCCCGCTTTCGCAAAGTCTATTGCTGAATAACTACCCGCCAGCCAAACGCTCGATCGCGCTGGCGTTGTGGTCGATGACGGTGATTGTCGCGCCAATTTGCGGCCCGATCCTCGGCGGTTATATCAGCGATAATTACCACTGGGGCTGGATATTCTTCATCAACGTGCCGATTGGCGTGGCGGTGGTGTTGATGACACTGCAAACTCTGCGCGGACGTGAAACCCGCACCGAACGGCGGCGGATTGATGCCGTGGGGCTGGCACTGCTGGTTATTGGTATCGGCAGCCTGCAGATTATGCTCGACCGCGGTAAAGAGCTGGACTGGTTTTCATCACAGGAAATTATCATCCTTACCGTGGTGGCGGTGGTGGCTATCTGCTTCCTGATTGTCTGGGAGCTGACCGACGATAACCCGATAGTCGATCTGTCGTTGTTTAAGTCGCGCAACTTCACCATCGGCTGCTTGTGTATCAGCCTCGCGTATATGCTCTACTTCGGCGCTATTGTTCTGCTGCCGCAGTTGTTGCAGGAGGTCTACGGTTACACGGCGACCTGGGCAGGTTTGGCCTCTGCGCCGGTAGGGATTATTCCGGTGATCCTGTCGCCGATTATCGGCCGCTTCGCGCATAAACTGGATATGCGGCGGCTGGTAACCTTCAGCTTTATTATGTATGCCGTCTGCTTCTACTGGCGTGCCTATACCTTTGAACCAGGTATGGATTTTGGCGCGTCGGCCTGGCCGCAGTTTATCCAGGGGTTTGCGGTGGCCTGCTTCTTTATGCCGCTGACCACCATTACGCTGTCTGGTTTGCCACCGGAACGACTGGCGGCGGCATCGAGCCTCTCTAACTTTACGCGAACGCTGGCGGGGTCTATCGGCACGTCGATAACCACGACCATGTGGACCAACCGCGAGTCGATGCACCATGCGCAGTTGACTGAGTCGGTAAACCCGTTCAACCCGAATGCCCAGGCGATGTACAGTCAACTGGAAGGGCTTGGGATGACGCAACAGCAGGCATCAGGCTGGATTGCCCAGCAGATCACCAATCAGGGGCTGATTATTTCCGCCAATGAGATCTTCTGGATGTCAGCCGGGATATTCCTCGTCCTGCTGGGGCTGGTGTGGTTTGCTAAACCGCCATTTGGCGCAGGTGGCGGCGGAGGCGGTGCGCACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36849","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. MG1655","NCBI_taxonomy_id":"511145"}}}},"ARO_accession":"3000074","ARO_id":"36213","ARO_name":"emrB","CARD_short_name":"emrB","ARO_description":"emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP), nalidixic acid, and thioloactomycin.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1848":{"model_id":"1848","model_name":"CTX-M-75","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1743":{"protein_sequence":{"accession":"ACS32294.1","sequence":"MMTQSIRRSMLTVMATLSLLFSSATLHAQANSVQQQLEALEKSSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKQSESDKHLLNQRVEIKKSDLVNYNPIAEKHVNGTMTLAELGAAALQYSDNTAMNKLIAHLGGPDKVTAFARSLGDETFRLDRTEPTLNTAIPGDPRDTTTPLAMAQTLKNLTLGKALAETQRAQLVTWLKGNTTGSASIRAGLPKSWVVGDKTGSGDYGTTNDIAVIWPENHAPLVLVTYFTQPEQKAESRRDILAAAAKIVTHGF"},"dna_sequence":{"accession":"GQ149244.1","fmin":"0","fmax":"873","strand":"+","sequence":"ATGATGACCCAGAGCATTCGCCGCAGCATGCTGACCGTGATGGCGACCCTGAGCCTGCTGTTTAGCAGCGCGACCCTGCATGCGCAGGCGAACAGCGTGCAGCAGCAGCTGGAAGCGCTGGAAAAAAGCAGCGGCGGCCGCCTGGGCGTGGCGCTGATTAACACCGCGGATAACAGCCAGATTCTGTATCGCGCGGATGAACGCTTTGCGATGTGCAGCACCAGCAAAGTGATGGCGGCGGCGGCGGTGCTGAAACAGAGCGAAAGCGATAAACATCTGCTGAACCAGCGCGTGGAAATTAAAAAAAGCGATCTGGTGAACTATAACCCGATTGCGGAAAAACATGTGAACGGCACCATGACCCTGGCGGAACTGGGCGCGGCGGCGCTGCAGTATAGCGATAACACCGCGATGAACAAACTGATTGCGCATCTGGGCGGCCCGGATAAAGTGACCGCGTTTGCGCGCAGCCTGGGCGATGAAACCTTTCGCCTGGATCGCACCGAACCGACCCTGAACACCGCGATTCCGGGCGATCCGCGCGATACCACCACCCCGCTGGCGATGGCGCAGACCCTGAAAAACCTGACCCTGGGCAAAGCGCTGGCGGAAACCCAGCGCGCGCAGCTGGTGACCTGGCTGAAAGGCAACACCACCGGCAGCGCGAGCATTCGCGCGGGCCTGCCGAAAAGCTGGGTGGTGGGCGATAAAACCGGCAGCGGCGATTATGGCACCACCAACGATATTGCGGTGATTTGGCCGGAAAACCATGCGCCGCTGGTGCTGGTGACCTATTTTACCCAGCCGGAACAGAAAGCGGAAAGCCGCCGCGATATTCTGGCGGCGGCGGCGAAAATTGTGACCCATGGCTTT","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36946","NCBI_taxonomy_name":"Providencia stuartii","NCBI_taxonomy_id":"588"}}}},"ARO_accession":"3001936","ARO_id":"38336","ARO_name":"CTX-M-75","CARD_short_name":"CTX-M-75","ARO_description":"CTX-M-75 is a beta-lactamase found in the Enterobacteriaceae family.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1850":{"model_id":"1850","model_name":"FomB","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"653":{"protein_sequence":{"accession":"BAA32494.1","sequence":"MLENLTIRSSRVVDLNLVKVRLSTNLEDFAAYSYFSAFAEDESAPADYEVVCVDLDRDDIPAELYADRTDRTFRGKRFKGGYYLVHYFGEPAHLITVGRTFYVFGRSLEKTVWPYFVKHILTVHSADHGFLHLKAAGFELPGAGATLLVGRNGAGKTVFLAQACLNGARFLSNTHTLVRDGVAHGVPSSIRVRRDQCFGELIDKHDLTAHMESGDYVTDSSTLFESPQISTARVRNVVIVDYDPARPQGLMPISPAAAGTFMEQFSFAVTTYGLKDDLLAHHGDFDTYVDSLARMRAQLTELVEGARCYRANADMLAKEVRDSTLKQLAE"},"dna_sequence":{"accession":"AB016934.1","fmin":"7388","fmax":"8381","strand":"+","sequence":"ATGCTGGAAAACCTCACGATCCGCAGCAGCCGCGTCGTCGACCTCAACCTGGTCAAGGTCAGGCTGTCCACCAACCTCGAGGACTTCGCGGCGTACTCCTACTTCTCGGCCTTCGCCGAGGACGAGTCCGCGCCCGCCGACTACGAGGTCGTCTGCGTCGACCTGGACCGGGACGACATCCCGGCCGAGCTGTACGCCGACCGGACCGACCGGACCTTCCGCGGCAAGCGGTTCAAGGGCGGCTACTACCTCGTCCACTACTTCGGGGAGCCCGCCCACCTCATCACGGTGGGCCGCACGTTCTACGTGTTCGGCAGGTCCCTCGAGAAGACCGTCTGGCCCTACTTCGTCAAGCACATCCTGACCGTCCACTCCGCGGACCACGGCTTCCTGCACCTGAAGGCGGCGGGCTTCGAACTGCCCGGCGCCGGAGCCACCCTGCTCGTCGGGCGCAACGGCGCGGGGAAGACCGTCTTCCTGGCCCAGGCGTGCCTCAACGGCGCCCGGTTCCTCAGCAACACCCACACGCTGGTCCGGGACGGGGTCGCGCACGGCGTCCCCTCCTCGATCCGGGTGCGCCGCGACCAGTGCTTCGGTGAACTCATCGACAAGCACGACCTGACGGCGCACATGGAGTCGGGCGACTACGTCACCGACTCCTCGACTCTCTTCGAGAGTCCGCAGATCAGCACGGCACGCGTCCGGAACGTCGTCATCGTCGACTACGACCCCGCACGCCCCCAGGGCCTCATGCCGATCTCGCCGGCCGCGGCCGGCACCTTCATGGAGCAGTTCTCCTTCGCGGTCACCACCTACGGCCTCAAGGACGATCTGCTCGCCCACCACGGGGACTTCGACACCTACGTCGACTCCCTGGCCCGGATGCGGGCGCAGCTGACCGAACTGGTCGAGGGCGCGCGCTGCTACCGGGCCAACGCAGACATGCTGGCCAAGGAAGTCCGGGATTCGACGCTCAAGCAGCTTGCCGAATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39587","NCBI_taxonomy_name":"Streptomyces wedmorensis","NCBI_taxonomy_id":"43759"}}}},"ARO_accession":"3000449","ARO_id":"36588","ARO_name":"FomB","CARD_short_name":"FomB","ARO_description":"An enzyme which on its own cannot provide fosfomycin resistance, however in conjunction with FomA, it leads to the formation of fosfomycin with three phosphates total, which makes it inactive.","ARO_category":{"41410":{"category_aro_accession":"3004246","category_aro_cvterm_id":"41410","category_aro_name":"Fom phosphotransferase family","category_aro_description":"Two members of the Fom family have been identified, FomA and FomB. FomB must interact with FomA confer resistance to fosfomycin, however FomA is capable of conferring resistance alone.","category_aro_class_name":"AMR Gene Family"},"35944":{"category_aro_accession":"0000025","category_aro_cvterm_id":"35944","category_aro_name":"fosfomycin","category_aro_description":"Fosfomycin (also known as phosphomycin and phosphonomycin) is a broad-spectrum antibiotic produced by certain Streptomyces species. It is effective on gram positive and negative bacteria as it targets the cell wall, an essential feature shared by both bacteria. Its specific target is MurA (MurZ in E.coli), which attaches phosphoenolpyruvate (PEP) to UDP-N-acetylglucosamine, a step of commitment to cell wall synthesis. In the active site of MurA, the active cysteine molecule is alkylated which stops the catalytic reaction.","category_aro_class_name":"Antibiotic"},"45731":{"category_aro_accession":"3007149","category_aro_cvterm_id":"45731","category_aro_name":"phosphonic acid antibiotic","category_aro_description":"A group of antibiotics derived from phosphonic acids.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1851":{"model_id":"1851","model_name":"KPC-13","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1869":{"protein_sequence":{"accession":"AEA73284.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLGTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKYSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"HQ342889.1","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGGCACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCTATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGTACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3002323","ARO_id":"38723","ARO_name":"KPC-13","CARD_short_name":"KPC-13","ARO_description":"KPC-13 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1852":{"model_id":"1852","model_name":"rmtF","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"691":{"protein_sequence":{"accession":"AFJ11385.1","sequence":"MDERAQAALDALLSAKNLRDVCPETVRRVFMELLPRYRKPKDAEKAARTHLHQITGAFMTADAQKKARALLARWNEGDESALAAALSLHASTRERLPGADEWMRRVSPFLGADARVLDLACGLNPILLGSMGVTNALGMDIHLGCVRLVNETARARGWHTRARACDLLSEIPAEEADAALLMKLLPVLEAQKTGRAAELLASLRAPRLVVTFPTRTLGGRGVGMEKHYADWFERILPDTLSVRDRFTVSDELVYLVERT"},"dna_sequence":{"accession":"JQ808129.1","fmin":"1598","fmax":"2378","strand":"+","sequence":"ATGGATGAACGAGCGCAGGCGGCACTGGACGCGCTGCTTTCCGCGAAGAATCTGCGGGACGTATGTCCCGAGACGGTGCGGCGCGTGTTTATGGAGCTTTTGCCGCGATACAGAAAACCGAAGGACGCGGAGAAGGCGGCGCGCACGCATCTGCACCAGATCACCGGCGCGTTCATGACGGCGGACGCGCAGAAAAAGGCGCGGGCATTGCTTGCGCGCTGGAACGAGGGCGACGAATCGGCGCTCGCTGCCGCGCTGTCCCTGCACGCGTCCACGCGCGAGCGCCTGCCGGGCGCGGATGAATGGATGCGGCGCGTTTCGCCGTTTCTGGGCGCGGACGCGCGCGTGCTCGATCTGGCCTGCGGGCTGAACCCGATCCTACTGGGCTCCATGGGCGTGACGAACGCGCTGGGCATGGACATTCATCTGGGCTGCGTGCGACTTGTGAACGAAACGGCGCGGGCGCGCGGCTGGCATACGCGCGCGCGAGCCTGCGACCTGCTGAGCGAGATTCCCGCGGAGGAAGCCGACGCGGCGCTTCTGATGAAGCTCCTGCCCGTGCTGGAAGCCCAGAAAACCGGCCGCGCCGCCGAGCTGCTCGCAAGCCTCCGCGCCCCCAGGCTGGTCGTGACCTTCCCCACCCGCACCCTCGGCGGCCGCGGCGTGGGCATGGAAAAGCACTATGCCGACTGGTTCGAGCGCATCCTCCCCGATACCCTCTCCGTCCGCGACCGATTTACGGTGTCGGACGAGCTGGTGTATCTGGTGGAGCGGACGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002666","ARO_id":"39066","ARO_name":"rmtF","CARD_short_name":"rmtF","ARO_description":"RmtF is a 16S rRNA methyltransferase found in Pseudomonas aeruginosa which methylates G1405 of the 16S rRNA. It confers high level resistance to many aminoglycosides.","ARO_category":{"41435":{"category_aro_accession":"3004271","category_aro_cvterm_id":"41435","category_aro_name":"16S rRNA methyltransferase (G1405)","category_aro_description":"Methyltransferases that methylate the G1405 position of 16S rRNA, which is part of an aminoglycoside binding site.","category_aro_class_name":"AMR Gene Family"},"35922":{"category_aro_accession":"0000003","category_aro_cvterm_id":"35922","category_aro_name":"astromicin","category_aro_description":"Astromicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Astromicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"40942":{"category_aro_accession":"3004015","category_aro_cvterm_id":"40942","category_aro_name":"gentamicin A","category_aro_description":"Gentamicin A is part of a complex of broad spectrum aminoglycoside antibiotics. Gentamicin inhibits protein synthesis, resulting in bacterial cell death.","category_aro_class_name":"Antibiotic"},"46133":{"category_aro_accession":"3007382","category_aro_cvterm_id":"46133","category_aro_name":"gentamicin","category_aro_description":"Gentamicin is a commonly used aminoglycoside antibiotic derived from members of the Micromonospora genus of bacteria. It acts by binding the 30S ribosomal subunit, thus inhibiting protein synthesis. Gentamicin is typically used to treat Gram-negative infections of the repiratory and urinary tract, as well as infections of the bone and soft tissue. It also exhibits considerable nephrotoxicity and ototoxicity. Gentamicin is administered as a mixture of gentamicin type C (which makes about around 80% of the complex) and types A, B, and X (distributed in the remaining 20% of the complex).","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1853":{"model_id":"1853","model_name":"OXA-20","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"5512":{"protein_sequence":{"accession":"ACC55538.1","sequence":"MIIRFLALLFSAVVLVSLGHAQEKTHESSNWGKYFSDFNAKGTIVVVDERTNGNSTSVYNESRAQQRYSPASTFKIPHTLFALDAGAVRDEFHVFRWDGAKRSFAGHNQDQNLRSAMRNSTVWVYQLFAKEIGENKARSYLEKLNYGNADPSTKSGDYWIDGNLAISANEQISILKKLYRNELPFRVEHQRLVKDLMIVEAKRDWILRAKTGWDGQMGWWVGWVEWPTGPVFFALNIDTPNRMEDLHKREAIARAILQSVNALPPN"},"dna_sequence":{"accession":"CP000863.1","fmin":"251961","fmax":"252762","strand":"+","sequence":"TTGATAATCCGATTTCTAGCACTGCTTTTCTCAGCTGTTGTACTTGTCTCTCTTGGTCATGCACAAGAAAAAACGCATGAGAGCTCTAATTGGGGGAAATACTTTAGTGATTTCAACGCTAAAGGTACAATAGTTGTAGTAGATGAACGCACAAACGGTAATTCCACATCGGTTTATAATGAATCCCGGGCTCAGCAGCGCTATTCGCCTGCGTCCACATTCAAGATTCCGCATACCCTTTTTGCGCTGGATGCAGGGGCGGTTCGCGATGAGTTTCATGTTTTTCGATGGGACGGCGCTAAAAGAAGCTTTGCAGGTCACAATCAAGACCAAAACCTACGATCGGCAATGCGCAATTCTACCGTTTGGGTCTATCAACTATTCGCAAAAGAAATAGGCGAAAACAAAGCACGAAGCTACCTAGAAAAATTAAACTACGGCAATGCAGACCCCTCGACCAAGAGCGGTGACTACTGGATAGATGGAAATCTTGCAATTTCAGCAAATGAACAAATTTCCATCCTAAAGAAGCTTTATCGAAATGAGCTTCCTTTTAGGGTAGAGCACCAACGCTTGGTTAAAGACTTGATGATTGTCGAAGCCAAACGTGATTGGATACTACGTGCCAAAACAGGCTGGGATGGTCAAATGGGTTGGTGGGTCGGTTGGGTAGAGTGGCCTACAGGCCCAGTATTTTTTGCGTTAAATATCGACACGCCAAACAGGATGGAAGACCTTCATAAACGAGAGGCAATTGCGCGTGCTATTCTTCAATCCGTCAATGCTTTGCCACCCAACTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35523","NCBI_taxonomy_name":"Acinetobacter baumannii ACICU","NCBI_taxonomy_id":"405416"}}}},"ARO_accession":"3001415","ARO_id":"37815","ARO_name":"OXA-20","CARD_short_name":"OXA-20","ARO_description":"OXA-20 is a beta-lactamase found in P. aeruginosa.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1854":{"model_id":"1854","model_name":"rmtA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"8181":{"protein_sequence":{"accession":"BAC20579.1","sequence":"MSFDDALASILSSKKYRSLCPDTVRRILDQEWGRHKSPKLAVEATRTRLHGICGAYVTPESLKAAAAALSVGDVQKALSLHASTKERLAELDCLYDFIFSGGVPHRVLDIACGLNPLALFIRDITSVWACDIHQGLGDVITPFAHHQGLDFTFALQDVMCTPPTETGDLALVFKLLPLLEREQAGAAMALLQALATPRIAVSFPTRSLGGRGKGMEANYSAWFEGALPDEFEIEDTKTIGIELVYMIKRNK"},"dna_sequence":{"accession":"AB083212.2","fmin":"5481","fmax":"6237","strand":"+","sequence":"ATGAGCTTTGACGATGCCCTAGCGTCCATCCTTTCCTCAAAAAAATATCGTTCCCTCTGCCCGGATACCGTACGGCGGATTTTAGATCAGGAATGGGGGCGGCACAAATCGCCTAAGCTGGCAGTGGAGGCCACTCGCACCCGGCTGCACGGGATTTGCGGGGCCTATGTCACGCCGGAATCGCTCAAGGCTGCAGCAGCGGCATTATCGGTTGGCGATGTGCAAAAGGCACTGTCGCTGCACGCCTCTACCAAGGAGCGGTTGGCCGAATTGGACTGCCTCTACGATTTTATCTTTTCTGGCGGGGTGCCCCATCGTGTGTTGGATATCGCTTGCGGCCTAAACCCGCTGGCCCTCTTTATACGTGACATAACATCTGTATGGGCGTGCGACATCCATCAGGGGTTGGGCGATGTGATCACCCCCTTTGCCCATCATCAGGGATTGGACTTCACGTTCGCCCTGCAGGATGTGATGTGTACGCCGCCCACTGAGACGGGGGATTTGGCACTGGTATTTAAATTACTGCCTTTGCTGGAGCGAGAGCAAGCTGGCGCCGCCATGGCGCTACTGCAGGCACTAGCTACCCCTCGGATTGCCGTCAGCTTCCCCACCCGCAGTTTAGGCGGGCGCGGCAAGGGCATGGAAGCAAACTATTCCGCATGGTTCGAGGGGGCACTGCCTGATGAATTTGAAATTGAGGATACCAAGACCATTGGAATAGAGCTTGTGTACATGATAAAAAGGAATAAGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3000859","ARO_id":"37239","ARO_name":"rmtA","CARD_short_name":"rmtA","ARO_description":"RmtA is a 16S rRNA methyltransferase found in Pseudomonas aeruginosa which methylates G1405 of the 16S rRNA. It confers high level resistance to many aminoglycosides.","ARO_category":{"41435":{"category_aro_accession":"3004271","category_aro_cvterm_id":"41435","category_aro_name":"16S rRNA methyltransferase (G1405)","category_aro_description":"Methyltransferases that methylate the G1405 position of 16S rRNA, which is part of an aminoglycoside binding site.","category_aro_class_name":"AMR Gene Family"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36997":{"category_aro_accession":"3000653","category_aro_cvterm_id":"36997","category_aro_name":"G418","category_aro_description":"A gentamicin class aminoglycoside antibiotic often used in mammalian cell culture work as a selectable marker for the neo cassette (APH3').","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"46133":{"category_aro_accession":"3007382","category_aro_cvterm_id":"46133","category_aro_name":"gentamicin","category_aro_description":"Gentamicin is a commonly used aminoglycoside antibiotic derived from members of the Micromonospora genus of bacteria. It acts by binding the 30S ribosomal subunit, thus inhibiting protein synthesis. Gentamicin is typically used to treat Gram-negative infections of the repiratory and urinary tract, as well as infections of the bone and soft tissue. It also exhibits considerable nephrotoxicity and ototoxicity. Gentamicin is administered as a mixture of gentamicin type C (which makes about around 80% of the complex) and types A, B, and X (distributed in the remaining 20% of the complex).","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1855":{"model_id":"1855","model_name":"CTX-M-72","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1591":{"protein_sequence":{"accession":"AAV97957.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDGTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGDYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"AY847148.1","fmin":"8","fmax":"884","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACGGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGACTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001933","ARO_id":"38333","ARO_name":"CTX-M-72","CARD_short_name":"CTX-M-72","ARO_description":"CTX-M-72 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1856":{"model_id":"1856","model_name":"QnrB20","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"573":{"protein_sequence":{"accession":"BAG55487.1","sequence":"MTPLLYKKTGTNMALALVGEKINRNRFTGEKIENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNASALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGAQVLGATFSGSDLSGGEFSTFDWRAANFTHCDLTNSELGDLDIRRVDLQGVKLDNYQASLLMERLGIAVIG"},"dna_sequence":{"accession":"AB379831.1","fmin":"0","fmax":"681","strand":"+","sequence":"ATGACGCCATTACTGTATAAAAAAACAGGCACAAATATGGCTCTGGCACTCGTTGGCGAAAAAATTAACAGAAACCGCTTCACCGGTGAGAAAATTGAAAATAGTACATTTTTTAACTGTGATTTTTCAGGTGCCGACCTGAGCGGCACTGAATTTATCGGCTGTCAGTTCTATGATCGTGAAAGCCAGAAAGGGTGCAATTTTAGTCGTGCGATGCTGAAAGATGCCATTTTTAAAAGCTGTGATTTATCCATGGCGGATTTTCGCAATGCCAGTGCGCTTGGCATTGAAATTCGCCACTGTCGTGCGCAAGGCGCAGATTTTCGCGGCGCAAGTTTTATGAATATGATCACTACTCGCACCTGGTTTTGCAGTGCATATATCACTAACACAAATCTAAGCTACGCCAATTTTTCGAAAGTCGTGTTGGAAAAGTGTGAGCTGTGGGAAAACCGTTGGATGGGGGCCCAGGTACTGGGCGCGACGTTCAGTGGTTCAGATCTCTCCGGCGGCGAGTTTTCGACTTTCGACTGGCGAGCAGCAAACTTCACACATTGCGATCTGACCAATTCGGAGTTGGGTGACTTAGATATTCGGCGCGTTGATTTACAAGGCGTTAAGTTGGACAACTACCAGGCATCGTTGCTCATGGAACGTCTTGGCATCGCGGTGATTGGTTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002735","ARO_id":"39169","ARO_name":"QnrB20","CARD_short_name":"QnrB20","ARO_description":"QnrB20 is a plasmid-mediated quinolone resistance protein found in Escherichia coli.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1857":{"model_id":"1857","model_name":"VIM-9","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1166":{"protein_sequence":{"accession":"AAS13760.1","sequence":"MFKLLSKLLVYLTASIMAIASPLAFSVDSSGEYPTVSEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSIRRLAEVEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSASVLYGGCAIYELSRTSAGNVADADLAEWPTSIERIQQHYPEAQFVIPGHGLPGGLDLLKHTTNVVKAHTNRSVVE"},"dna_sequence":{"accession":"AY524988.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGTTCAAACTTTTGAGTAAGTTATTGGTCTATTTGACCGCGTCTATCATGGCTATTGCGAGTCCGCTCGCTTTTTCCGTAGATTCTAGCGGTGAGTATCCGACAGTCAGCGAAATTCCGGTCGGGGAGGTCCGGCTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCAGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAGAAGCAAATTGGACTTCCTGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGATACGCCGGCTAGCCGAGGTAGAGGGGAACGAGATTCCCACGCACTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAACTCTTCTATCCTGGTGCTGCGCATTCGACCGACAACTTAGTTGTGTACGTCCCGTCTGCGAGTGTGCTCTATGGTGGTTGTGCGATTTATGAGTTGTCACGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCATTGAGCGGATTCAACAACACTACCCGGAAGCACAGTTCGTCATTCCGGGGCACGGCCTGCCGGGCGGTCTAGACTTGCTCAAGCACACAACGAATGTTGTAAAAGCGCACACAAATCGCTCAGTCGTTGAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002279","ARO_id":"38679","ARO_name":"VIM-9","CARD_short_name":"VIM-9","ARO_description":"VIM-9 is a beta-lactamase found in Pseudomonas spp.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1858":{"model_id":"1858","model_name":"OXA-387","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1135":{"protein_sequence":{"accession":"AHK51384.1","sequence":"MNIKTLLLITSAIFISACSPYIMTANPNHSASKSDEKAEKIKNLFNEVHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"KJ173478.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAACACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAATGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGTACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTTGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001573","ARO_id":"37973","ARO_name":"OXA-387","CARD_short_name":"OXA-387","ARO_description":"OXA-387 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1859":{"model_id":"1859","model_name":"QnrVC7","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"3307":{"protein_sequence":{"accession":"AJA36815.1","sequence":"MDKTDQLYVQADFSHQDLSGQYFKNCKFFCCSFKRANLRDTQFVDCSFIERGELEGCDFSYSDLRDASFKNCSLSMSYFKGANCFGIEFRECDLKGANFAQASFMNQVSNRMYFCSAYITGCNLSYANFERQCIEKCDLFENRWIGANLSGTSFKESDLSRGVFSEGCWSQCRLQGCDLSHSELYGLDPRKVDLTGVKICSWQQEQLLEQLGLIVVPD"},"dna_sequence":{"accession":"KM555152.1","fmin":"0","fmax":"657","strand":"+","sequence":"ATGGATAAAACAGACCAGTTATATGTACAAGCTGACTTTTCACATCAAGACTTGAGTGGTCAGTATTTTAAAAATTGCAAATTTTTCTGCTGTTCCTTTAAACGGGCAAACCTCCGCGATACACAATTTGTAGATTGTTCTTTCATTGAACGAGGAGAATTAGAGGGGTGTGATTTTTCTTACTCGGATCTTAGAGACGCATCTTTTAAAAACTGCAGTCTTTCAATGTCGTATTTCAAAGGTGCAAATTGTTTTGGTATCGAGTTCAGAGAGTGCGATTTAAAGGGGGCAAATTTTGCTCAAGCTAGCTTCATGAATCAGGTATCGAACAGAATGTATTTTTGTTCAGCCTATATAACAGGTTGTAATCTGTCATACGCAAATTTTGAAAGGCAGTGTATCGAAAAGTGTGATTTGTTTGAGAATAGATGGATTGGTGCAAATTTGAGTGGGACATCATTTAAAGAGTCTGATTTAAGTCGGGGAGTATTTTCTGAAGGGTGCTGGAGCCAGTGTAGGTTGCAAGGTTGTGATTTGAGCCACTCGGAGCTGTATGGTTTAGACCCCCGGAAAGTTGACCTTACAGGTGTAAAAATCTGTTCGTGGCAACAAGAACAACTTTTAGAGCAATTAGGTTTAATAGTAGTTCCTGACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36789","NCBI_taxonomy_name":"Vibrio cholerae","NCBI_taxonomy_id":"666"}}}},"ARO_accession":"3003193","ARO_id":"39770","ARO_name":"QnrVC7","CARD_short_name":"QnrVC7","ARO_description":"QnrVC7 is a fluoroquinolone resistance gene in Lahey's list of qnr genes.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1860":{"model_id":"1860","model_name":"OXA-165","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1205":{"protein_sequence":{"accession":"ADK35869.1","sequence":"MNKYFTCYVVASLFLSGCTVQHNLINETPSQIVQGHNQVIHQYFDEKNTSGVLVIQTDKKINLYGNALSRANTEYVPASTFKMLNALIGLENQKTDINEIFKWKGEKRSFTAWEKDMTLGEAMKLSAVPVYQELARRIGLDLMQKEVKRIGFGNAEIGQQVDNFWLVGPLKVTPIQEVEFVSQLAHTQLPFSEKVQANVKNMLLLEESNGYKIFGKTGWAMDVKPQVGWLTGWVEQPDGKIVAFALNMEMRSEMPASIRNELLMKSLKQLNII"},"dna_sequence":{"accession":"HM488986.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGAATAAATATTTTACTTGCTATGTGGTTGCTTCTCTTTTTCTTTCTGGTTGTACGGTTCAGCATAATTTAATAAATGAAACCCCGAGTCAGATTGTTCAAGGACATAATCAGGTGATTCATCAATACTTTGATGAAAAAAACACCTCAGGTGTGCTGGTTATTCAAACAGATAAAAAAATTAATCTATATGGTAATGCTCTAAGCCGCGCAAATACAGAATATGTGCCAGCCTCTACATTTAAAATGTTGAATGCCCTGATCGGATTGGAGAACCAGAAAACGGATATTAATGAAATATTTAAATGGAAGGGCGAGAAAAGGTCATTTACCGCTTGGGAAAAAGACATGACACTAGGAGAAGCCATGAAGCTTTCTGCAGTCCCAGTCTATCAGGAACTTGCGCGACGTATCGGTCTTGATCTCATGCAAAAAGAAGTAAAACGTATTGGTTTCGGTAATGCTGAAATTGGACAGCAGGTTGATAATTTCTGGTTGGTAGGACCATTAAAGGTTACGCCTATTCAAGAGGTAGAGTTTGTTTCCCAATTAGCACATACACAGCTTCCATTTAGTGAAAAAGTGCAGGCTAATGTAAAAAATATGCTTCTTTTAGAAGAGAGTAATGGCTACAAAATTTTTGGAAAGACTGGTTGGGCAATGGATGTAAAACCACAAGTGGGCTGGTTGACCGGCTGGGTTGAGCAGCCAGATGGAAAAATTGTCGCTTTTGCATTAAATATGGAAATGCGGTCAGAAATGCCGGCATCTATACGTAATGAATTATTGATGAAATCATTAAAACAGCTGAATATTATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001465","ARO_id":"37865","ARO_name":"OXA-165","CARD_short_name":"OXA-165","ARO_description":"OXA-165 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46499":{"category_aro_accession":"3007710","category_aro_cvterm_id":"46499","category_aro_name":"OXA-23-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases, specifically imipenem, derived from OXA-23, first identified in Acinetobacter baumannii.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1861":{"model_id":"1861","model_name":"LEN-15","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"1268":{"protein_sequence":{"accession":"AAL50725.1","sequence":"MRYVRLCVISLLATLPLVVYAGPQPLEQIKQSESQLSGRVGMVEMDLASGRTLAAWRADERFPMVSTFKVLLCGAVLARVDAGLEQLDRRIHYRQQDLVDYSPVSEKHLVDGMTIGELCAAAITLSDNSAGNLLLATVGGPAGLTAFLRQIGDNVTRLDRWETALNEALPGDARDTTTPASMAATLRKLLTAQHLSPRSQQQLLQWMVDDRVAGPLIRAVLPAGWFIADKTGAGERGARGIVALLGPDGKPERIVVIYLRDTPASMAERNQHIAGIGQR"},"dna_sequence":{"accession":"AF452105.1","fmin":"0","fmax":"840","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGTGTTATCTCCCTGTTAGCCACCCTGCCACTGGTGGTATACGCCGGTCCACAGCCGCTTGAGCAGATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTGGGGATGGTGGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCGATGAACGCTTTCCCATGGTGAGCACCTTTAAAGTGCTGCTGTGCGGCGCGGTGCTGGCGCGGGTGGATGCCGGGCTCGAACAACTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGTCGACGGGATGACGATCGGCGAACTCTGCGCCGCCGCCATCACCCTGAGCGATAACAGCGCTGGCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCGGGATTAACTGCCTTTCTGCGCCAGATCGGTGACAACGTCACCCGTCTTGACCGCTGGGAAACGGCACTGAATGAGGCGCTTCCCGGCGACGCGCGCGACACCACCACCCCGGCCAGCATGGCCGCCACGCTGCGCAAACTACTGACCGCGCAGCATCTGAGCCCCCGTTCGCAACAGCAACTCCTGCAGTGGATGGTGGACGATCGGGTTGCCGGCCCGCTGATCCGCGCCGTGCTGCCGGCGGGCTGGTTTATCGCCGACAAGACCGGGGCTGGCGAACGGGGTGCGCGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAACCGGAGCGCATTGTGGTGATCTATCTGCGGGATACCCCGGCGAGTATGGCCGAGCGTAATCAACATATCGCCGGGATCGGCCAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002478","ARO_id":"38878","ARO_name":"LEN-15","CARD_short_name":"LEN-15","ARO_description":"LEN-15 is a beta-lactamase. From the Pasteur Institute list of LEN beta-lactamases.","ARO_category":{"36236":{"category_aro_accession":"3000097","category_aro_cvterm_id":"36236","category_aro_name":"LEN beta-lactamase","category_aro_description":"LEN beta-lactamases are chromosomal class A beta-lactamases that confer resistance to ampicillin, amoxicillin, carbenicillin, and ticarcillin but not to extended-spectrum beta-lactams.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1862":{"model_id":"1862","model_name":"OXA-109","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1449":{"protein_sequence":{"accession":"ABV31689.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDVKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIQVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"EF650035.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGTAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCAAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAACAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001640","ARO_id":"38040","ARO_name":"OXA-109","CARD_short_name":"OXA-109","ARO_description":"OXA-109 is a beta-lactamase found in A. baumannii.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1863":{"model_id":"1863","model_name":"VIM-3","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1006":{"protein_sequence":{"accession":"AAG27703.1","sequence":"MFKLLSKLLVYLTASIMAIASPLAFSVDSSGEYPTVSEIPVGEVRLYQIADGVWSHIATKSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEVEGSEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSASVLYGGCAIYELSRTSAGNVADADLAEWPTSIERIQQHYPEAQFVIPGHGLPGGLDLLKHTTNVVKAHTNRSVVE"},"dna_sequence":{"accession":"AF300454.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGTTCAAACTTTTGAGTAAGTTATTGGTCTATTTGACCGCGTCTATCATGGCTATTGCGAGTCCGCTCGCTTTTTCCGTAGATTCTAGCGGTGAGTATCCGACAGTCAGCGAAATTCCGGTCGGGGAGGTCCGGCTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGAAGTCGTTTGATGGCGCAGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAGAAGCAAATTGGACTTCCTGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGTAGAGGGGAGCGAGATTCCCACGCACTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAACTCTTCTATCCTGGTGCTGCGCATTCGACCGACAACTTAGTTGTGTACGTCCCGTCTGCGAGTGTGCTCTATGGTGGTTGTGCGATTTATGAGTTGTCACGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCATTGAGCGGATTCAACAACACTACCCGGAAGCACAGTTCGTCATTCCGGGGCACGGCCTGCCGGGCGGTCTAGACTTGCTCAAGCACACAACGAATGTTGTAAAAGCGCACACAAATCGCTCAGTCGTTGAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002273","ARO_id":"38673","ARO_name":"VIM-3","CARD_short_name":"VIM-3","ARO_description":"VIM-3 is a beta-lactamase found in Pseudomonas spp.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1864":{"model_id":"1864","model_name":"CMY-67","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"864":{"protein_sequence":{"accession":"AFK08541.1","sequence":"MMKKSICCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAIIYEGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWRGISLLHLATYTAGGLPLQIPDEVTDKAALLRFYQNWQPQWTPGAKRLYANSSIGLFGALAVQPSGMSYEEAMTRRVLQPLKLAHTWITVPQSEQKNYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIELAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPARVEVAWRILEKLQ"},"dna_sequence":{"accession":"JQ711185.1","fmin":"1027","fmax":"2173","strand":"+","sequence":"ATGATGAAAAAATCGATATGCTGCGCGCTGCTGCTGACAGCCTCTTTCTCCACGTTTGCTGCCGCAAAAACAGAACAACAAATTGCCGATATCGTTAACCGCACCATCACACCACTGATGCAGGAGCAGGCTATTCCGGGCATGGCCGTGGCAATTATCTACGAGGGGAAACCTTATTACTTTACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGTTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGACGCTATCGCCCGCGGCGAAATTAAGCTCAGCGACCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCGGGGTATCAGCCTGCTACACTTAGCCACCTATACAGCGGGTGGCCTGCCGCTGCAGATCCCCGATGAAGTTACGGATAAAGCCGCATTACTGCGCTTTTATCAAAACTGGCAACCACAATGGACTCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGTGCGCTGGCGGTGCAACCTTCAGGTATGAGCTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAAAGCGAACAAAAAAATTATGCCTGGGGCTATCGCGAAGGGAAGCCTGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATCGATATGGCCCGCTGGGTTCAGGCCAACATGGACGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGAGCTTGCGCAGTCTCGCTACTGGCGTATTGGTGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCAGCACCTGCCGTGAAAGCCTCATGGGTGCATAAAACAGGATCCACAGGCGGATTTGGCAGCTACGTTGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTAATGTTGGCAAACAAAAGCTACCCCAACCCGGCTCGCGTCGAGGTGGCCTGGCGCATTCTTGAAAAACTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002080","ARO_id":"38480","ARO_name":"CMY-67","CARD_short_name":"CMY-67","ARO_description":"CMY-67 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1865":{"model_id":"1865","model_name":"ACC-5","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"778":{"protein_sequence":{"accession":"CCK86740.1","sequence":"MQNTLKLLSVITCLAATAQGALAANIDESKIKDTVDDLIQPLMQKNNIPGMSVAVTVNGKNYIYNYGLAAKQPQQPVTENTLFEVGSLSKTFAATLASYAQLSGKLSLDQSVSHYVPELRGSSFDHVSVLNVGTHTSGLQLFMPEDIKNTTQLMAYLKAWKPADAAGTHRVYSNIGTGLLGMIAAKSLGVSYEDAIEKTLLPQLGMHHSYLKVPADQMENYAWGYNKKDEPVHVNMEILGNEAYGIKTTSSDLLRYVQANMGQLKLDANAKMQQALTATHTGYFKSGEITQDLMWEQLPYPVSLPNLLTGNDMAMTKSVATPIVPPLPPQENVWINKTGSTNGFGAYIAFVPAKKMGIVMLANKNYSIDQRVTVAYKILSSLEGNK"},"dna_sequence":{"accession":"HE819401.1","fmin":"0","fmax":"1161","strand":"+","sequence":"ATGCAGAACACATTGAAGCTGTTATCCGTGATTACCTGTCTGGCAGCAACTGCCCAAGGTGCTCTGGCTGCTAATATCGATGAGAGCAAAATTAAAGACACCGTTGATGACCTGATCCAGCCGCTGATGCAGAAGAATAATATTCCCGGTATGTCGGTCGCAGTGACCGTCAACGGTAAAAACTACATTTATAACTATGGGTTAGCGGCAAAACAGCCTCAGCAGCCGGTTACGGAAAATACGTTATTTGAAGTGGGTTCGCTGAGTAAAACGTTTGCTGCCACCTTGGCGTCCTATGCGCAGTTGAGCGGTAAGCTGTCTTTGGATCAAAGCGTTAGCCATTACGTTCCAGAGTTGCGTGGCAGCAGCTTTGACCACGTTAGCGTACTCAATGTGGGCACGCATACCTCAGGCCTACAGCTATTTATGCCGGAAGATATTAAAAATACCACACAGCTGATGGCTTATCTAAAAGCATGGAAACCTGCCGATGCGGCTGGAACCCATCGCGTTTATTCCAATATCGGTACTGGTTTGCTAGGGATGATTGCGGCGAAAAGTCTGGGTGTGAGCTATGAAGATGCGATTGAGAAAACCCTCCTTCCTCAGTTAGGCATGCATCACAGCTACTTGAAGGTTCCGGCTGACCAGATGGAAAACTATGCGTGGGGCTACAACAAGAAAGATGAGCCAGTGCACGTGAATATGGAGATTTTGGGTAACGAAGCTTATGGTATCAAAACCACCTCCAGTGACTTGTTACGCTACGTGCAAGCCAATATGGGGCAGTTAAAGCTTGATGCTAATGCCAAGATGCAACAGGCTCTGACTGCCACCCACACCGGCTATTTCAAATCGGGTGAGATTACTCAGGATCTGATGTGGGAGCAGCTGCCATATCCGGTTTCTCTGCCGAATTTGCTCACCGGTAACGATATGGCGATGACGAAAAGCGTGGCTACGCCGATTGTTCCCCCGTTACCGCCACAGGAAAATGTGTGGATTAATAAGACCGGATCAACTAACGGCTTCGGTGCCTATATTGCGTTTGTTCCTGCTAAGAAGATGGGGATCGTGATGCTGGCTAACAAAAACTACTCAATCGATCAGCGAGTGACGGTGGCGTATAAAATCCTGAGCTCATTGGAAGGGAATAAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36784","NCBI_taxonomy_name":"Hafnia alvei","NCBI_taxonomy_id":"569"}}}},"ARO_accession":"3001819","ARO_id":"38219","ARO_name":"ACC-5","CARD_short_name":"ACC-5","ARO_description":"ACC-5 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36212":{"category_aro_accession":"3000073","category_aro_cvterm_id":"36212","category_aro_name":"ACC beta-lactamase","category_aro_description":"ACC beta-lactamases or Ambler class C beta-lactamases are AmpC beta-lactamases. They possess an interesting resistance phenotype due to their low activity against cephamycins.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1866":{"model_id":"1866","model_name":"KPC-7","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1517":{"protein_sequence":{"accession":"ACE62798.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAIDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKYSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"EU729727.1","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATAGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGTACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002317","ARO_id":"38717","ARO_name":"KPC-7","CARD_short_name":"KPC-7","ARO_description":"KPC-7 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1867":{"model_id":"1867","model_name":"CTX-M-116","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"824":{"protein_sequence":{"accession":"AEI70324.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAVAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGDYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTNGL"},"dna_sequence":{"accession":"JF966749.1","fmin":"157","fmax":"1033","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGTCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGACGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGTGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGACTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCAACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3001976","ARO_id":"38376","ARO_name":"CTX-M-116","CARD_short_name":"CTX-M-116","ARO_description":"CTX-M-116 is a beta-lactamase found in Proteus mirabilis.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1868":{"model_id":"1868","model_name":"TEM-82","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1162":{"protein_sequence":{"accession":"AAL29434.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMVSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDEQNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AF427128.1","fmin":"208","fmax":"1069","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGGTGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACAAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000949","ARO_id":"37329","ARO_name":"TEM-82","CARD_short_name":"TEM-82","ARO_description":"TEM-82 is an inhibitor-resistant beta-lactamase found in E. coli.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1869":{"model_id":"1869","model_name":"OXY-2-6","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8255":{"protein_sequence":{"accession":"AAL78278.2","sequence":"MIKSSWRKIAMLAAAVPLLLASSALWASTDAIHQKLTDLEKRSGGRLGVALINTADNSQILYRGDERFAMCSTSKVMAAAAVLKQSESNKEVVNKRLEINAADLVVWSPITEKHLQSGMTLAELSAATLQYSDNTAMNLIIGYLGGPEKVTAFARSIGDATFRLDRTEPTLNTAIPGDERDTSTPLAMAESLRKLTLGDALGEQQRAQLVTWLKGNTTGGQSIRAGLPESWVVGDKTGAGDYGTTNDIAVIWPEDHAPLVLVTYFTQPQQDAKNRKEVLAAAAKIVTEGL"},"dna_sequence":{"accession":"AY077485.2","fmin":"183","fmax":"1056","strand":"+","sequence":"ATGATAAAAAGTTCGTGGCGTAAAATTGCAATGCTAGCCGCCGCCGTTCCGCTGCTGCTGGCGAGCAGCGCACTGTGGGCCAGTACCGATGCTATCCATCAGAAGCTGACAGATCTCGAGAAGCGTTCAGGCGGCAGGTTGGGCGTGGCGCTAATCAACACGGCAGATAATTCTCAAATCTTATATCGCGGCGACGAGCGTTTTGCCATGTGCAGCACCAGTAAAGTGATGGCCGCCGCCGCGGTATTAAAACAGAGCGAAAGCAATAAAGAGGTGGTAAATAAAAGGCTGGAGATTAACGCAGCCGATTTGGTGGTCTGGAGTCCGATTACCGAAAAACATCTCCAGAGCGGAATGACGCTGGCTGAGCTAAGCGCGGCGACGCTGCAATATAGCGACAATACGGCGATGAATCTGATCATCGGCTACCTTGGCGGGCCGGAAAAAGTCACCGCCTTCGCCCGCAGTATCGGCGATGCCACCTTTCGTCTCGATCGTACGGAGCCCACGCTGAATACCGCCATCCCGGGCGATGAGCGTGATACCAGCACGCCGCTGGCGATGGCTGAAAGCCTACGCAAGCTGACGCTTGGCGATGCGCTGGGCGAACAGCAACGCGCCCAGTTAGTCACCTGGCTGAAAGGCAATACCACCGGCGGGCAAAGCATTCGCGCGGGCCTGCCTGAAAGCTGGGTGGTCGGCGATAAAACCGGCGCCGGAGATTACGGCACCACCAATGATATTGCGGTTATCTGGCCGGAAGATCACGCTCCGCTGGTATTAGTCACCTACTTTACCCAGCCGCAGCAGGATGCGAAAAACCGCAAAGAGGTGTTAGCCGCAGCGGCAAAAATCGTGACCGAAGGGCTTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3002401","ARO_id":"38801","ARO_name":"OXY-2-6","CARD_short_name":"OXY-2-6","ARO_description":"OXY-2-6 is a beta-lactamase found in Klebsiella oxytoca.","ARO_category":{"38788":{"category_aro_accession":"3002388","category_aro_cvterm_id":"38788","category_aro_name":"OXY beta-lactamase","category_aro_description":"OXY beta-lactamases are chromosomal class A beta-lactamases that are found in Klebsiella oxytoca. At constitutive low levels, OXY beta-lactamases confer resistance to aminopenicillins and carboxypenicillins. At high induced levels,  OXY beta-lactamases confer resistance to penicillins, cephalosporins and aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1870":{"model_id":"1870","model_name":"OXA-66","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4337":{"protein_sequence":{"accession":"ABK34774.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDVKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"EF016356.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGTAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAACAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001615","ARO_id":"38015","ARO_name":"OXA-66","CARD_short_name":"OXA-66","ARO_description":"OXA-66 is a beta-lactamase found in A. baumannii.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1871":{"model_id":"1871","model_name":"OXA-389","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1302":{"protein_sequence":{"accession":"AHL30287.1","sequence":"MNIKTLLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEVHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPKWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDKVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"KJ135346.1","fmin":"14","fmax":"839","strand":"+","sequence":"ATGAACATTAAAACACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGTACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTCAAGTGGGACGGGCAAAAAAGGCTATTCCCAAAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATAAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTGGGTTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001575","ARO_id":"37975","ARO_name":"OXA-389","CARD_short_name":"OXA-389","ARO_description":"OXA-389 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1873":{"model_id":"1873","model_name":"linG","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4180":{"protein_sequence":{"accession":"ABG65740.1","sequence":"MLQLKMIELFKEGCHEDARIIAALMFGSFAIGEGDEFSDIEFAVFIQDDHFENFDQRSWLNAVSPVAAYFPDDFGHHTALFENGIRGEFHFMRKSDIPVISTWQGYGWFPSLEAAVLLDRSGELSRYASALVGGPPIREGAPLVEGLVLNLISLMLFGANLLNRGEYARAWALLSKAHENLLKLVRLHEGATDHWPTPSRALEKDISEDSYNRYLACTSSAEPRALCAAYHQTWTWSLELFKSVTEPLNIELPRTVIAQAKRLLNESATPHNK"},"dna_sequence":{"accession":"DQ836009.1","fmin":"1309","fmax":"2131","strand":"+","sequence":"ATGCTTCAGCTGAAAATGATCGAACTCTTCAAGGAAGGTTGTCATGAGGATGCACGAATAATCGCGGCATTGATGTTCGGCTCATTTGCTATCGGAGAGGGTGACGAGTTCTCTGATATCGAATTCGCAGTGTTCATCCAGGATGACCATTTTGAAAATTTCGATCAGCGCTCGTGGCTTAATGCCGTAAGTCCGGTTGCTGCTTACTTTCCGGACGACTTCGGCCACCACACCGCACTTTTTGAAAACGGCATTCGCGGTGAATTCCATTTCATGCGAAAATCGGACATACCGGTCATTTCCACTTGGCAAGGCTATGGGTGGTTTCCCTCGCTTGAGGCGGCTGTTTTGTTGGACCGATCAGGAGAGTTGTCAAGGTACGCAAGCGCTCTCGTGGGCGGTCCCCCGATACGTGAAGGCGCGCCGCTGGTGGAAGGGCTTGTGTTGAACCTCATCAGCCTGATGCTCTTTGGGGCCAATCTTTTAAATCGGGGAGAGTACGCTCGCGCCTGGGCTTTGCTCAGCAAAGCACATGAAAACCTACTCAAGCTGGTTCGACTCCACGAAGGGGCAACAGACCACTGGCCGACACCTTCACGCGCGCTCGAAAAGGATATCTCGGAGGACTCGTATAATCGCTATCTGGCATGCACAAGCAGTGCAGAACCAAGAGCACTATGTGCAGCCTATCATCAAACGTGGACGTGGAGTCTCGAATTGTTCAAGAGCGTGACAGAACCTCTGAATATCGAGCTTCCGAGAACTGTAATTGCGCAGGCAAAAAGGTTGCTCAATGAGTCTGCGACGCCGCACAACAAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35767","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Stanley","NCBI_taxonomy_id":"192953"}}}},"ARO_accession":"3002879","ARO_id":"39313","ARO_name":"linG","CARD_short_name":"linG","ARO_description":"linG is an integron-associated gene cassette, with aadA2, encoding a lincosomide nucleotidyltransferase found in Salmonella enterica. linG confers resistance to lincosomide antibiotics.","ARO_category":{"36360":{"category_aro_accession":"3000221","category_aro_cvterm_id":"36360","category_aro_name":"lincosamide nucleotidyltransferase (LNU)","category_aro_description":"Resistance to the lincosamide antibiotic by ATP-dependent modification of the 3' and\/or 4'-hydroxyl groups of the methylthiolincosamide sugar.","category_aro_class_name":"AMR Gene Family"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1874":{"model_id":"1874","model_name":"OXA-196","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"802":{"protein_sequence":{"accession":"AEB98922.1","sequence":"MNIQALLLITSAIFISACSPYIVTANPNHSASKSDVKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDHARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWVVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"HQ425494.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGAACATTCAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGTAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCATGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGGTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAACAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTA","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36949","NCBI_taxonomy_name":"Acinetobacter nosocomialis","NCBI_taxonomy_id":"106654"}}}},"ARO_accession":"3001481","ARO_id":"37881","ARO_name":"OXA-196","CARD_short_name":"OXA-196","ARO_description":"OXA-196 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1875":{"model_id":"1875","model_name":"MIR-11","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"1182":{"protein_sequence":{"accession":"AIT76112.1","sequence":"MMTKSLSCALLLSVTSSAFAAPMSEKQLAEVVERTVTPLMNAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEIALGDPVAKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDTASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMSYEQAMTTRVFKPLKLDHTWINVPKAEEAHYAWGYREGKAVHVSPGMLDAEAYGVKTNVKDMASWLIANMKPDSLQAPSLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVGGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILDALQ"},"dna_sequence":{"accession":"KM087859.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGACAAAATCCCTAAGCTGTGCCCTGCTGCTCAGCGTCACCAGCTCTGCATTCGCCGCACCGATGTCCGAAAAACAGCTGGCTGAGGTGGTGGAACGTACCGTTACGCCGCTGATGAACGCGCAGGCCATTCCGGGTATGGCGGTGGCGGTAATTTATCAGGGTCAGCCACACTACTTTACCTTCGGTAAAGCCGATGTTGCGGCGAACAAACCCGTCACCCCGCAAACCCTGTTTGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTACTGGGCGGCGATGCCATTGCCCGAGGTGAAATAGCGCTGGGCGATCCGGTAGCAAAATACTGGCCTGAGCTCACGGGCAAACAGTGGCAGGGCATTCGCATGCTGGATCTGGCAACCTATACCGCAGGCGGTCTGCCGTTACAGGTGCCGGATGAGGTCACGGATACCGCTTCTCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCGGGCACCACGCGTCTTTACGCTAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTTAAACCTTCCGGCATGAGCTATGAGCAGGCCATGACGACGCGGGTCTTTAAACCCCTCAAGCTGGACCATACCTGGATTAACGTCCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGATACCGTGAGGGTAAAGCGGTCCACGTTTCGCCAGGGATGCTGGACGCGGAAGCCTATGGCGTAAAAACTAACGTGAAGGATATGGCGAGCTGGCTGATAGCCAACATGAAGCCGGATTCTCTTCAGGCTCCCTCACTCAAGCAAGGCATTGCTCTGGCGCAGTCTCGCTACTGGCGCGTGGGGGCCATGTATCAGGGGTTGGGCTGGGAGATGCTCAACTGGCCGGTCGATGCCAAAACCGTCGTCGGAGGCAGTGATAACAAGGTGGCGCTGGCACCATTGCCCGTGGCAGAAGTGAATCCACCCGCGCCGCCGGTCAAGGCCTCCTGGGTCCATAAAACAGGCTCGACGGGCGGGTTTGGCAGCTACGTGGCATTTATTCCTGAAAAGCAGCTCGGCATTGTGATGCTGGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCGTATCCTCGACGCGCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3002176","ARO_id":"38576","ARO_name":"MIR-11","CARD_short_name":"MIR-11","ARO_description":"MIR-11 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36197":{"category_aro_accession":"3000058","category_aro_cvterm_id":"36197","category_aro_name":"MIR beta-lactamase","category_aro_description":"MIR beta-lactamases are plasmid-mediated beta-lactamases that confer resistance to oxyimino- and alpha-methoxy beta-lactams.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1876":{"model_id":"1876","model_name":"LEN-7","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"6134":{"protein_sequence":{"accession":"CTQ11867.1","sequence":"MRYVRLCVISLLATLPLAVDAGPQPLEQIKQSESQLSGRVGMVEMDLASGRTLAAWRADERFPMVSTFKVLLCGAVLARVDAGVEQLDRRIHYRQQDLVDYSPVSEKHLTDGMTIGELCAAAITLSDNSAGNLLLATVGGPAGLTAFLRQIGDNVTRLDRWETALNEALPGDARDTTTPASMAATLRKLLTAQHLSARSQQQLLQWMVDDRVAGPLIRAVLPPGWFIADKTGAGERGARGIVALLGPDGKPERIVVIYLRDTPASMAERNQHIAGIGAALIEHWQR"},"dna_sequence":{"accession":"CXPA01000063.1","fmin":"153489","fmax":"154350","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGTGTTATCTCCCTGTTAGCCACCCTGCCACTGGCGGTAGACGCCGGTCCACAGCCGCTTGAGCAGATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTGGGGATGGTGGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCGATGAACGCTTTCCCATGGTGAGCACCTTTAAAGTGCTGCTGTGCGGCGCGGTGCTGGCGCGGGTGGATGCAGGGGTCGAACAACTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTACCGACGGGATGACGATCGGCGAACTCTGCGCCGCCGCCATCACCCTGAGCGATAACAGCGCTGGCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCGGGATTAACTGCCTTTCTGCGCCAGATCGGTGACAACGTCACCCGTCTTGACCGCTGGGAAACGGCGCTGAATGAGGCGCTTCCCGGCGACGCGCGCGACACCACCACCCCGGCCAGCATGGCCGCCACGCTGCGCAAACTACTGACCGCGCAGCATCTGAGCGCCCGTTCGCAACAGCAACTCCTGCAGTGGATGGTGGACGATCGGGTTGCCGGCCCGCTGATCCGCGCCGTGCTGCCGCCGGGCTGGTTTATCGCCGACAAAACCGGGGCTGGCGAACGGGGTGCGCGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAACCGGAGCGCATTGTGGTGATCTATCTGCGGGATACCCCGGCGAGTATGGCCGAGCGTAATCAACATATCGCCGGGATCGGCGCAGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42612","NCBI_taxonomy_name":"Klebsiella variicola","NCBI_taxonomy_id":"244366"}}}},"ARO_accession":"3002457","ARO_id":"38857","ARO_name":"LEN-7","CARD_short_name":"LEN-7","ARO_description":"LEN-7 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36236":{"category_aro_accession":"3000097","category_aro_cvterm_id":"36236","category_aro_name":"LEN beta-lactamase","category_aro_description":"LEN beta-lactamases are chromosomal class A beta-lactamases that confer resistance to ampicillin, amoxicillin, carbenicillin, and ticarcillin but not to extended-spectrum beta-lactams.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1877":{"model_id":"1877","model_name":"CMY-12","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1421":{"protein_sequence":{"accession":"CAA76382.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYSNSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYARGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKNYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"Y16785.1","fmin":"0","fmax":"1143","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACTCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCCGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAACTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTACAA","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3002023","ARO_id":"38423","ARO_name":"CMY-12","CARD_short_name":"CMY-12","ARO_description":"CMY-12 is a beta-lactamase found in the Enterobacteriaceae family.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1878":{"model_id":"1878","model_name":"SRT-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"725"}},"model_sequences":{"sequence":{"8219":{"protein_sequence":{"accession":"AAS07017.3","sequence":"MTKMNRLAAALIAALILPTAQAAQQQDIDAVIQPLMKKYGVPGMAIAVSVDGKQQIYPYGVASKQTGKPITEETLFEVGSLSKTFTATLAVYAQQQGKLSFNDPASRYLPELRGSAFDGVSLLNLATHTSGLPLFVPDDVTNDAQLMAYYRAWQPKHPAGSYRVYSNLGIGMLGMIAAKSLDQPFIQAMEQGMLPALGMSHTYVQVPAAQMANYAQGYSKDDKPVRVNPGPLDAESYGIKSNARDLIRYLDANLQQVKVAQPWRDALAATHVGYYKAGAFTQDLMWENYPYPVKLSRLIEGNNAGMIMNGTPATAITPPQPELRAGWYNKTGSTGGFSTYAVFIPAKNIAVVMLANKWFPNDDRVEAAYHIVQALEKR"},"dna_sequence":{"accession":"AY524276.3","fmin":"0","fmax":"1137","strand":"+","sequence":"ATGACGAAAATGAACCGCCTGGCGGCCGCGCTGATCGCCGCACTGATCTTGCCGACCGCGCAGGCCGCGCAGCAGCAGGATATCGACGCCGTTATTCAGCCGCTGATGAAAAAATATGGCGTACCGGGCATGGCGATCGCCGTGTCGGTCGACGGCAAACAGCAGATTTACCCGTATGGCGTCGCCTCGAAGCAGACCGGCAAACCGATCACCGAGGAGACGCTGTTCGAAGTGGGCTCGCTGAGCAAAACCTTTACCGCGACGCTGGCGGTCTATGCGCAGCAGCAGGGCAAGCTGTCGTTCAACGATCCGGCCAGCCGCTATCTGCCCGAGCTGCGCGGCAGCGCCTTCGACGGCGTCAGCCTGCTGAATCTGGCGACGCATACCTCCGGCCTGCCGCTGTTCGTGCCGGACGACGTCACTAACGACGCCCAGCTGATGGCCTACTACCGGGCCTGGCAGCCGAAACACCCGGCGGGCAGCTACCGTGTCTATTCCAACCTCGGCATCGGCATGCTGGGCATGATCGCCGCCAAGAGCCTCGACCAGCCGTTTATCCAGGCGATGGAACAGGGGATGCTGCCGGCGCTGGGCATGAGCCACACCTACGTTCAGGTGCCGGCGGCGCAGATGGCTAACTATGCGCAGGGTTACAGCAAGGACGATAAGCCGGTGCGGGTCAACCCCGGCCCGCTGGATGCCGAGTCTTACGGCATCAAGTCCAACGCTCGCGATCTGATTCGCTATCTGGACGCCAACCTGCAGCAGGTGAAGGTGGCGCAGCCGTGGCGCGACGCGCTGGCCGCGACGCACGTCGGGTATTACAAGGCGGGCGCGTTCACGCAGGATCTGATGTGGGAGAACTACCCGTATCCGGTGAAACTGTCGCGTTTGATTGAAGGCAACAACGCCGGGATGATCATGAACGGCACGCCGGCCACCGCCATCACGCCGCCGCAGCCGGAATTGCGCGCCGGCTGGTATAACAAAACCGGCTCCACCGGCGGCTTCTCCACCTACGCGGTATTTATCCCGGCGAAAAATATCGCCGTGGTGATGCTGGCCAACAAGTGGTTCCCGAACGACGATCGCGTCGAGGCGGCTTACCACATCGTCCAGGCGCTGGAGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36783","NCBI_taxonomy_name":"Serratia marcescens","NCBI_taxonomy_id":"615"}}}},"ARO_accession":"3002494","ARO_id":"38894","ARO_name":"SRT-2","CARD_short_name":"SRT-2","ARO_description":"SRT-2, isolated from Serratia marcescens, is a chromosomal beta-lactamase that confers resistance to cefotaxime.","ARO_category":{"36234":{"category_aro_accession":"3000095","category_aro_cvterm_id":"36234","category_aro_name":"SRT beta-lactamase","category_aro_description":"SRT beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1879":{"model_id":"1879","model_name":"AAC(3)-IIIa","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"6":{"protein_sequence":{"accession":"CAA39184.1","sequence":"MTDLNIPHTHAHLVDAFQALGIRAGQALMLHASVKAVGAVMGGPNVILQALMDALTPDGTLMMYAGWQDIPDFIDSLPDALKAVYLEQHPPFDPATARAVRENSVLAEFLRTWPCVHRSANPEASMVAVGRQAALLTANHALDYGYGVESPLAKLVAIEGYVLMLGAPLDTITLLHHAEYLAKMRHKNVVRYPCPILRDGRKVWVTVEDYDTGDPHDDYSFEQIARDYVAQGGGTRGKVGDADAYLFAAQDLTRFAVQWLESRFGDSASYG"},"dna_sequence":{"accession":"X55652.1","fmin":"1123","fmax":"1939","strand":"+","sequence":"ATGACCGATTTGAATATCCCGCATACACACGCGCACCTTGTAGACGCATTTCAGGCGCTCGGCATCCGCGCGGGGCAGGCGCTCATGCTGCACGCATCCGTTAAAGCAGTGGGCGCGGTGATGGGCGGCCCCAATGTGATCTTGCAGGCGCTCATGGATGCGCTCACGCCCGACGGCACGCTGATGATGTATGCGGGATGGCAAGACATCCCCGACTTTATCGACTCGCTGCCGGACGCGCTCAAGGCCGTGTATCTTGAGCAGCACCCACCCTTTGACCCCGCCACCGCCCGCGCCGTGCGCGAAAACAGCGTGCTAGCGGAATTTTTGCGCACATGGCCGTGCGTGCATCGCAGCGCAAACCCCGAAGCCTCTATGGTGGCGGTAGGCAGGCAGGCCGCTTTGCTGACCGCTAATCACGCGCTGGATTATGGCTACGGAGTCGAGTCGCCGCTGGCTAAACTGGTGGCAATAGAAGGATACGTGCTGATGCTTGGCGCGCCGCTGGATACCATCACACTGCTGCACCACGCGGAATATCTGGCCAAGATGCGCCACAAGAACGTGGTCCGCTACCCGTGCCCGATTCTGCGGGACGGGCGCAAAGTGTGGGTGACCGTTGAGGACTATGACACCGGTGATCCGCACGACGATTATAGTTTTGAGCAAATCGCGCGCGATTATGTGGCGCAGGGCGGCGGCACACGCGGCAAAGTCGGTGATGCGGATGCTTACCTGTTCGCCGCGCAGGACCTCACACGGTTTGCGGTGCAGTGGCTTGAATCACGGTTCGGTGACTCAGCGTCATACGGATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002536","ARO_id":"38936","ARO_name":"AAC(3)-IIIa","CARD_short_name":"AAC(3)-IIIa","ARO_description":"AAC(3)-IIIa is a chromosomal-encoded aminoglycoside acetyltransferase in P. aeruginosa.","ARO_category":{"36461":{"category_aro_accession":"3000322","category_aro_cvterm_id":"36461","category_aro_name":"AAC(3)","category_aro_description":"A category of aminoglycoside N-acetyltransferase enzymes with modification regiospecificity based at the 3-amino group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics through acetylation of the 3-amino group of the compound.","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"37001":{"category_aro_accession":"3000657","category_aro_cvterm_id":"37001","category_aro_name":"paromomycin","category_aro_description":"An aminoglycoside antibiotic used for the treatment of parasitic infections. It is similar to neomycin sharing a similar spectrum of activity, but its hydroxyl group at the 6'-position instead of an amino group makes it resistant to AAC(6') modifying enzymes.","category_aro_class_name":"Antibiotic"},"37002":{"category_aro_accession":"3000658","category_aro_cvterm_id":"37002","category_aro_name":"lividomycin","category_aro_description":"Lividomycins are aminoglycosidic antibiotics produced by Streptomyces lividus. They contain 2-amino-2,3-dideoxy-D-glucose.","category_aro_class_name":"Antibiotic"},"46129":{"category_aro_accession":"3007379","category_aro_cvterm_id":"46129","category_aro_name":"5-episisomicin","category_aro_description":"5-episosomicin is a semisynthetic aminoglycoside antibiotic similar to sisomicin.","category_aro_class_name":"Antibiotic"},"46133":{"category_aro_accession":"3007382","category_aro_cvterm_id":"46133","category_aro_name":"gentamicin","category_aro_description":"Gentamicin is a commonly used aminoglycoside antibiotic derived from members of the Micromonospora genus of bacteria. It acts by binding the 30S ribosomal subunit, thus inhibiting protein synthesis. Gentamicin is typically used to treat Gram-negative infections of the repiratory and urinary tract, as well as infections of the bone and soft tissue. It also exhibits considerable nephrotoxicity and ototoxicity. Gentamicin is administered as a mixture of gentamicin type C (which makes about around 80% of the complex) and types A, B, and X (distributed in the remaining 20% of the complex).","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1880":{"model_id":"1880","model_name":"adeN","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"420"}},"model_sequences":{"sequence":{"569":{"protein_sequence":{"accession":"AGV28567.1","sequence":"MHDPVLESHHLVCEKPQTRRGIERRLALLLSATELFLEKGYDAVSLDDIVNHAGGSKTSIYKYFGNKDGLFTAICDYRREMFFKDICIAFQPEQTSLKDYLIQTLIRFYKPFIQPEHIAFLRLVIEQTQCNATLSQYLYEKCALDVQNTIAQALLISHQSGEITCTSPDHSSLMYFGILRDIEWRMIMGMPLPPNETEVIDYINYCVDIFLKGHHKV"},"dna_sequence":{"accession":"KF147862.1","fmin":"0","fmax":"654","strand":"+","sequence":"ATGCATGATCCAGTCCTTGAGTCACATCATCTCGTATGTGAAAAACCCCAAACACGCCGCGGTATAGAACGTCGTTTAGCTCTATTGCTAAGCGCAACCGAGCTGTTTTTGGAAAAAGGATATGATGCTGTCTCTCTTGACGACATCGTTAATCATGCTGGTGGTTCAAAAACCTCTATTTATAAATACTTCGGTAATAAAGATGGCTTATTTACTGCAATCTGCGATTATCGCCGTGAAATGTTTTTTAAAGATATCTGCATTGCATTTCAACCAGAGCAAACTTCTTTAAAAGATTATTTAATCCAAACTCTCATCCGTTTTTATAAGCCCTTTATTCAACCTGAACACATTGCCTTTTTACGTTTGGTTATTGAACAAACTCAATGTAATGCAACTTTGAGCCAATACTTATATGAAAAATGTGCTCTGGATGTCCAAAATACAATTGCTCAAGCCTTACTCATATCTCATCAATCAGGTGAAATTACCTGTACATCTCCTGATCATTCCTCTCTTATGTATTTTGGAATTTTACGTGATATTGAATGGCGAATGATTATGGGAATGCCTCTCCCACCCAATGAGACAGAAGTTATTGATTATATTAATTATTGTGTTGATATTTTCTTAAAGGGGCATCATAAAGTCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3000559","ARO_id":"36698","ARO_name":"adeN","CARD_short_name":"adeN","ARO_description":"AdeN is a repressor of AdeIJK, a RND-type efflux pump in Acinetobacter baumannii. Its inactivation increases expression of AdeJ.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36309":{"category_aro_accession":"3000170","category_aro_cvterm_id":"36309","category_aro_name":"imipenem","category_aro_description":"Imipenem is a broad-spectrum antibiotic and is usually taken with cilastatin, which prevents hydrolysis of imipenem by renal dehydropeptidase-I. It is resistant to hydrolysis by most other beta-lactamases. Notable exceptions are the KPC beta-lactamases and Ambler Class B enzymes.","category_aro_class_name":"Antibiotic"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"40523":{"category_aro_accession":"3003832","category_aro_cvterm_id":"40523","category_aro_name":"ticarcillin","category_aro_description":"Ticarcillin is a carboxypenicillin used for the treatment of Gram-negative bacteria, particularly P. aeruginosa. Ticarcillin's antibiotic properties arise from its ability to prevent cross-linking of peptidoglycan during cell wall synthesis, when the bacteria try to divide, causing cell death.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1881":{"model_id":"1881","model_name":"OXA-72","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8355":{"protein_sequence":{"accession":"ADB28892.1","sequence":"MKKFILPIFSISILVSLSACSSIKTKSEDNFHISSQQHEKAIKSYFDEAQTQGVIIIKEGKNLSTYGNALARANKEYVPASTFKMLNALIGLENHKATTNEIFKWDGKKRTYPMWEKDMTLGEAMALSAVPVYQELARRTGLELMQKEVKRVNFGNTNIGTQVDNFWLVGPLKITPVQEVNFADDLAHNRLPFKLETQEEVKKMLLIKEVNGSKIYAKSGWGMDVTPQVGWLTGWVEQANGKKIPFSLNLEMKEGMSGSIRNEITYKSLENLGII"},"dna_sequence":{"accession":"GU199039.2","fmin":"1205","fmax":"2033","strand":"+","sequence":"ATGAAAAAATTTATACTTCCTATATTCAGCATTTCTATTCTAGTTTCTCTCAGTGCATGTTCATCTATTAAAACTAAATCTGAAGATAATTTTCATATTTCTTCTCAGCAACATGAAAAAGCTATTAAAAGCTATTTTGATGAAGCTCAAACACAGGGTGTAATTATTATTAAAGAGGGTAAAAATCTTAGCACCTATGGTAATGCTCTTGCACGAGCAAATAAAGAATATGTCCCTGCATCAACATTTAAGATGCTAAATGCTTTAATCGGGCTAGAAAATCATAAAGCAACAACAAATGAGATTTTCAAATGGGATGGTAAAAAAAGAACTTATCCTATGTGGGAGAAAGATATGACTTTAGGTGAGGCAATGGCATTGTCAGCAGTTCCAGTATATCAAGAGCTTGCAAGACGGACTGGCCTAGAGCTAATGCAGAAAGAAGTAAAGCGGGTTAATTTTGGAAATACAAATATTGGAACACAGGTCGATAATTTTTGGTTAGTTGGCCCCCTTAAAATTACACCAGTACAAGAAGTTAATTTTGCCGATGACCTTGCACATAACCGATTACCTTTTAAATTAGAAACTCAAGAAGAAGTTAAAAAAATGCTTCTAATTAAAGAAGTAAATGGTAGTAAGATTTATGCAAAAAGTGGATGGGGAATGGATGTTACTCCACAGGTAGGTTGGTTGACTGGTTGGGTGGAGCAAGCTAATGGAAAAAAAATCCCCTTTTCGCTCAACTTAGAAATGAAAGAAGGAATGTCTGGTTCTATTCGTAATGAAATTACTTATAAGTCGCTAGAAAATCTTGGAATCATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001705","ARO_id":"38105","ARO_name":"OXA-72","CARD_short_name":"OXA-72","ARO_description":"OXA-72 is a beta-lactamase found in Acinetobacter spp.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46500":{"category_aro_accession":"3007711","category_aro_cvterm_id":"46500","category_aro_name":"OXA-24-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-24.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1882":{"model_id":"1882","model_name":"OXA-80","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1768":{"protein_sequence":{"accession":"ABV71247.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDVKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAILVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"EU019535.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGTAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCTAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAACAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001634","ARO_id":"38034","ARO_name":"OXA-80","CARD_short_name":"OXA-80","ARO_description":"OXA-80 is a beta-lactamase found in A. baumannii.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1883":{"model_id":"1883","model_name":"DHA-10","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"2110":{"protein_sequence":{"accession":"AJO16043.1","sequence":"MKKSLSATLISALLAFSAPGFSAADNVAAVVDSTIKPLMAQQDIPGMAVAVSVKGKPYYFNYGFADVQAKQPVTENTLFELGSVSKTFTGVLGAVSVAKKEMTLNDPAEKYQPELALPQWKGITLLDLATYTAGGLPLQVPDEVKSRADLLHFYQQWQPSRKPGDMRLYANSSIGLFGALTANAAGMPYEQLLTARILAPLGLSHTFITVPESAQSQYAYGYKNKKPVRVSPGQLDAESYGVKSASKDMLRWAEMNMEPSRAGNADLEMAMYLAQTRYYKTAAINQGLGWEMYDWPQQKDMIINGVTNEVALQPHPVTDNQVQPYNRASWVHKTGATTGFGAYVAFIPEKQVAIVILANKNYPNTERVKAAQAILSALE"},"dna_sequence":{"accession":"KP050490.1","fmin":"0","fmax":"1140","strand":"+","sequence":"ATGAAAAAATCGTTATCTGCAACACTGATTTCTGCCCTGCTGGCGTTTTCCGCCCCGGGGTTTTCTGCCGCTGATAATGTCGCGGCGGTGGTGGACAGCACCATTAAACCGCTGATGGCACAGCAGGATATTCCCGGGATGGCGGTTGCTGTCTCTGTAAAGGGTAAGCCCTATTATTTCAATTACGGTTTTGCCGATGTTCAGGCAAAACAGCCGGTCACTGAAAATACACTATTTGAGCTCGGATCTGTAAGTAAAACTTTCACAGGTGTGCTGGGTGCGGTTTCTGTGGCGAAAAAAGAGATGACGCTGAATGACCCGGCGGAAAAATACCAGCCGGAGCTGGCTCTGCCGCAGTGGAAAGGGATCACGCTGCTGGATCTGGCCACCTACACCGCAGGCGGGCTGCCGTTACAGGTACCGGATGAGGTGAAAAGCCGTGCGGATCTGCTGCATTTCTATCAGCAGTGGCAGCCGTCCCGGAAACCGGGCGATATGCGTCTGTATGCAAACAGCAGTATCGGCCTGTTTGGTGCTCTGACCGCCAACGCAGCGGGGATGCCGTATGAGCAGTTGCTGACCGCGCGGATCCTGGCACCGCTGGGGTTATCTCACACCTTTATTACCGTGCCGGAAAGTGCGCAAAGCCAGTATGCGTACGGTTATAAAAACAAAAAACCGGTCCGCGTGTCGCCGGGACAGCTTGATGCGGAATCTTACGGCGTGAAATCCGCCTCAAAAGATATGCTGCGCTGGGCAGAAATGAATATGGAGCCGTCACGGGCCGGTAATGCGGATCTGGAAATGGCAATGTATCTCGCCCAGACCCGCTACTATAAAACTGCCGCGATTAATCAGGGGCTGGGCTGGGAAATGTATGACTGGCCGCAGCAGAAAGATATGATCATTAACGGCGTGACCAACGAGGTCGCATTGCAGCCGCACCCGGTAACAGACAACCAGGTTCAGCCGTATAACCGCGCTTCCTGGGTGCATAAAACGGGGGCAACAACTGGTTTCGGCGCCTATGTGGCCTTTATTCCGGAAAAACAGGTGGCGATTGTGATTCTGGCGAATAAAAACTACCCGAATACCGAAAGAGTCAAAGCCGCACAGGCTATTTTGAGTGCACTGGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36917","NCBI_taxonomy_name":"Morganella morganii","NCBI_taxonomy_id":"582"}}}},"ARO_accession":"3002141","ARO_id":"38541","ARO_name":"DHA-10","CARD_short_name":"DHA-10","ARO_description":"DHA-10 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36207":{"category_aro_accession":"3000068","category_aro_cvterm_id":"36207","category_aro_name":"DHA beta-lactamase","category_aro_description":"DHA beta-lactamases are plasmid-mediated AmpC \u03b2-lactamases that confer resistance to cephamycins and oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1884":{"model_id":"1884","model_name":"CTX-M-111","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1740":{"protein_sequence":{"accession":"AEM44649.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGQGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"JF274243.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCAGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGACTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36953","NCBI_taxonomy_name":"Shigella sp. SH202","NCBI_taxonomy_id":"1074432"}}}},"ARO_accession":"3001971","ARO_id":"38371","ARO_name":"CTX-M-111","CARD_short_name":"CTX-M-111","ARO_description":"CTX-M-111 is a beta-lactamase found in Shigella spp.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1886":{"model_id":"1886","model_name":"LEN-24","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"8217":{"protein_sequence":{"accession":"CAP12352.2","sequence":"MRYVRLCVISLLANLPLAVDAGPQPLEQIKQSESQLSGRVGMVEMDLASGRTLAAWRADERFPMVSTFKVLLCGAVLARVDAGLEQLDRRIHYRQQDLVDYSPVSEKHLVDGMTIGELCAAAITLSDNSAGNLLLATVGGPAGLTAFLRQIGDNVTRLDRWETALNEALPGDARDTTTPASMAATLRKLLTAQHLSARSQQQLLQWMVDDRVAGPLIRAVLPPGWFIADKTGAGERGARGIVALLGPDGKPERIVVIYLRDTPASMAERNQHIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AM850914.2","fmin":"30","fmax":"891","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGTGTTATCTCCCTGTTAGCCAACCTGCCACTGGCGGTAGACGCCGGTCCACAGCCGCTTGAGCAGATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTGGGGATGGTGGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCGATGAACGCTTTCCCATGGTGAGCACCTTTAAAGTGCTGCTGTGCGGCGCGGTGCTGGCGCGGGTGGATGCCGGGCTCGAACAACTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGTCGACGGGATGACGATCGGCGAACTCTGCGCCGCCGCCATCACCCTGAGCGATAACAGCGCTGGCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCGGGATTAACTGCCTTTCTGCGCCAGATCGGTGACAACGTCACCCGTCTTGACCGCTGGGAAACGGCACTGAATGAGGCGCTTCCCGGCGACGCGCGCGACACCACCACCCCGGCCAGCATGGCCGCCACGCTGCGCAAACTACTGACCGCGCAGCATCTGAGCGCCCGTTCGCAACAGCAACTCCTGCAGTGGATGGTGGACGATCGGGTTGCCGGCCCGCTGATCCGCGCCGTGCTGCCGCCGGGCTGGTTTATCGCCGACAAAACCGGGGCTGGCGAACGGGGTGCGCGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAACCGGAGCGCATTGTGGTGATCTATCTGCGGGATACCCCGGCGAGTATGGCCGAGCGTAATCAACATATCGCCGGGATCGGCGCAGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002471","ARO_id":"38871","ARO_name":"LEN-24","CARD_short_name":"LEN-24","ARO_description":"LEN-24 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36236":{"category_aro_accession":"3000097","category_aro_cvterm_id":"36236","category_aro_name":"LEN beta-lactamase","category_aro_description":"LEN beta-lactamases are chromosomal class A beta-lactamases that confer resistance to ampicillin, amoxicillin, carbenicillin, and ticarcillin but not to extended-spectrum beta-lactams.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1887":{"model_id":"1887","model_name":"TEM-70","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1496":{"protein_sequence":{"accession":"AAF01046.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASQQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AF188199.1","fmin":"214","fmax":"1075","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCAGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000936","ARO_id":"37316","ARO_name":"TEM-70","CARD_short_name":"TEM-70","ARO_description":"TEM-70 is a beta-lactamase found in E. coli.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1888":{"model_id":"1888","model_name":"MIR-10","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"1102":{"protein_sequence":{"accession":"AIT76111.1","sequence":"MMTKSLSCALLLSVASSAFAAPMSEKQLAEVVERTVTPLMNAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEIALGDPVAKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDTASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMSYEQAMTTRVFKPLKLDHTWINVPKAEEAHYAWGYREGKAVHVSPGMLDAEAYGVKTNVKDMASWVIANMKPDSLQAPSLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVGGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILDALQ"},"dna_sequence":{"accession":"KM087858.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGACAAAATCCCTAAGCTGTGCCCTGCTGCTCAGCGTCGCCAGCTCTGCATTCGCCGCACCGATGTCCGAAAAACAGCTGGCTGAGGTGGTGGAACGTACCGTTACGCCGCTGATGAACGCGCAGGCCATTCCGGGTATGGCGGTGGCGGTAATTTATCAGGGTCAGCCACACTACTTTACCTTCGGTAAAGCCGATGTTGCGGCGAACAAACCCGTCACCCCGCAAACCCTGTTTGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTACTGGGCGGCGATGCCATTGCCCGGGGTGAAATAGCGCTGGGCGATCCGGTAGCAAAATACTGGCCTGAGCTCACGGGCAAGCAGTGGCAGGGCATTCGCATGCTGGATCTGGCAACCTATACCGCAGGCGGTCTGCCGTTACAGGTGCCGGATGAGGTCACGGATACCGCCTCTCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCGGGTACCACGCGTCTTTACGCTAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTCAAACCTTCCGGCATGAGCTATGAGCAGGCCATGACGACGCGGGTCTTTAAACCCCTCAAGCTGGACCATACCTGGATTAACGTCCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGATACCGTGAGGGTAAAGCGGTCCACGTTTCGCCAGGGATGCTGGACGCGGAAGCCTATGGCGTAAAAACTAACGTGAAGGATATGGCGAGCTGGGTGATAGCCAACATGAAGCCGGATTCTCTTCAGGCTCCCTCACTCAAGCAAGGCATTGCTCTGGCGCAGTCTCGCTACTGGCGCGTGGGGGCTATGTATCAGGGGTTAGGCTGGGAGATGCTCAACTGGCCGGTCGATGCCAAAACCGTCGTCGGAGGCAGTGATAACAAGGTGGCGCTGGCACCATTGCCCGTGGCAGAAGTGAATCCACCCGCGCCGCCGGTCAAGGCCTCCTGGGTCCATAAAACAGGCTCGACGGGCGGGTTTGGCAGCTACGTGGCATTTATTCCTGAAAAGCAGCTCGGCATTGTGATGCTGGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCGTATCCTCGACGCGCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36926","NCBI_taxonomy_name":"Enterobacter asburiae","NCBI_taxonomy_id":"61645"}}}},"ARO_accession":"3002175","ARO_id":"38575","ARO_name":"MIR-10","CARD_short_name":"MIR-10","ARO_description":"MIR-10 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36197":{"category_aro_accession":"3000058","category_aro_cvterm_id":"36197","category_aro_name":"MIR beta-lactamase","category_aro_description":"MIR beta-lactamases are plasmid-mediated beta-lactamases that confer resistance to oxyimino- and alpha-methoxy beta-lactams.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1889":{"model_id":"1889","model_name":"NDM-4","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"939":{"protein_sequence":{"accession":"AFB82585.1","sequence":"MELPNIMHPVAKLSTALAAALMLSGCMPGEIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGLVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR"},"dna_sequence":{"accession":"JQ348841.1","fmin":"0","fmax":"813","strand":"+","sequence":"ATGGAATTGCCCAATATTATGCACCCGGTCGCGAAGCTGAGCACCGCATTAGCCGCTGCATTGATGCTGAGCGGGTGCATGCCCGGTGAAATCCGCCCGACGATTGGCCAGCAAATGGAAACTGGCGACCAACGGTTTGGCGATCTGGTTTTCCGCCAGCTCGCACCGAATGTCTGGCAGCACACTTCCTATCTCGACATGCCGGGTTTCGGGGCAGTCGCTTCCAACGGTTTGATCGTCAGGGATGGCGGCCGCGTGCTGGTGGTCGATACCGCCTGGACCGATGACCAGACCGCCCAGATCCTCAACTGGATCAAGCAGGAGATCAACCTGCCGGTCGCGCTGGCGGTGGTGACTCACGCGCATCAGGACAAGATGGGCGGTATGGACGCGCTGCATGCGGCGGGGATTGCGACTTATGCCAATGCGTTGTCGAACCAGCTTGCCCCGCAAGAGGGGCTGGTTGCGGCGCAACACAGCCTGACTTTCGCCGCCAATGGCTGGGTCGAACCAGCAACCGCGCCCAACTTTGGCCCGCTCAAGGTATTTTACCCCGGCCCCGGCCACACCAGTGACAATATCACCGTTGGGATCGACGGCACCGACATCGCTTTTGGTGGCTGCCTGATCAAGGACAGCAAGGCCAAGTCGCTCGGCAATCTCGGTGATGCCGACACTGAGCACTACGCCGCGTCAGCGCGCGCGTTTGGTGCGGCGTTCCCCAAGGCCAGCATGATCGTGATGAGCCATTCCGCCCCCGATAGCCGCGCCGCAATCACTCATACGGCCCGCATGGCCGACAAGCTGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002355","ARO_id":"38755","ARO_name":"NDM-4","CARD_short_name":"NDM-4","ARO_description":"NDM-4 is a beta-lactamase found in Escherichia coli.","ARO_category":{"36196":{"category_aro_accession":"3000057","category_aro_cvterm_id":"36196","category_aro_name":"NDM beta-lactamase","category_aro_description":"NDM beta-lactamases or New Delhi metallo-beta-lactamases are class B beta-lactamases that confer resistance to a broad range of antibiotics including carbapenems, cephalosporins and penicillins.","category_aro_class_name":"AMR Gene Family"},"40523":{"category_aro_accession":"3003832","category_aro_cvterm_id":"40523","category_aro_name":"ticarcillin","category_aro_description":"Ticarcillin is a carboxypenicillin used for the treatment of Gram-negative bacteria, particularly P. aeruginosa. Ticarcillin's antibiotic properties arise from its ability to prevent cross-linking of peptidoglycan during cell wall synthesis, when the bacteria try to divide, causing cell death.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1890":{"model_id":"1890","model_name":"TEM-86","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1497":{"protein_sequence":{"accession":"CAC43230.1","sequence":"MSIQHFRVALIPFFAAFCFPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDSWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGTGKRGSRGIIAALGPDGKPSRIVVIYMTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AJ277415.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCTTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATAGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAACCGGTAAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACATGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3000953","ARO_id":"37333","ARO_name":"TEM-86","CARD_short_name":"TEM-86","ARO_description":"TEM-86 is an extended-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1891":{"model_id":"1891","model_name":"AAC(6')-Iih","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"8279":{"protein_sequence":{"accession":"CAE50926.1","sequence":"MIISEFDRDNLVLRDQLADLLRLTWPDEYGEQPMKEVERLLEDERIAVSAIEGDELIGFVGAIPQYGQTGWELHPLVVESMYRKQQVGTRLVSYLEKEIASQGGIVVYLGTDDVEGQTSLAIEEDLFEDTFDKLETIQNRKDHPYEFYEKLGYQIVGVIPDANGWNKPDIWMAKRIARKHGSE"},"dna_sequence":{"accession":"AJ584701.2","fmin":"10","fmax":"562","strand":"+","sequence":"ATGATTATCAGTGAGTTTGATCGTGATAATTTGGTTTTACGTGACCAATTAGCCGATCTTTTGAGATTGACTTGGCCAGATGAATACGGTGAACAGCCGATGAAAGAAGTAGAGCGACTGCTGGAAGATGAAAGGATCGCCGTCTCTGCAATCGAAGGAGATGAGCTGATTGGTTTTGTCGGTGCGATTCCACAATATGGTCAAACTGGTTGGGAACTGCATCCCTTAGTCGTCGAAAGTATGTACCGTAAGCAACAAGTTGGTACACGCCTAGTGAGTTATCTAGAAAAAGAGATTGCCTCACAAGGAGGAATCGTTGTCTATTTAGGAACTGATGATGTGGAAGGGCAAACAAGCTTGGCGATTGAAGAAGACCTGTTTGAAGATACCTTTGACAAGCTTGAAACGATTCAAAACAGGAAAGATCATCCTTATGAATTCTATGAGAAACTTGGCTATCAGATCGTTGGGGTAATTCCGGATGCGAATGGCTGGAACAAGCCAGATATTTGGATGGCCAAACGAATTGCTAGAAAACATGGAAGTGAATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39522","NCBI_taxonomy_name":"Enterococcus durans","NCBI_taxonomy_id":"53345"}}}},"ARO_accession":"3002590","ARO_id":"38990","ARO_name":"AAC(6')-Iih","CARD_short_name":"AAC(6')-Iih","ARO_description":"AAC(6')-Iih is a chromosomal-encoded aminoglycoside acetyltransferase in Enterococcus hirae.","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"A category of aminoglycoside N-acetyltransferase enzymes with modification regiospecificity based at the 6'-amino group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics through acetylation of the 6-amino group of the compound.","category_aro_class_name":"AMR Gene Family"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"46128":{"category_aro_accession":"3007378","category_aro_cvterm_id":"46128","category_aro_name":"2'-N-ethylnetilmicin","category_aro_description":"2'-N-ethylnetilmicin is an aminoglycoside antibiotic and a derivative of netilmicin.","category_aro_class_name":"Antibiotic"},"46129":{"category_aro_accession":"3007379","category_aro_cvterm_id":"46129","category_aro_name":"5-episisomicin","category_aro_description":"5-episosomicin is a semisynthetic aminoglycoside antibiotic similar to sisomicin.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1892":{"model_id":"1892","model_name":"OXA-114a","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1921":{"protein_sequence":{"accession":"ABX38721.1","sequence":"MTVRRLSCALGAALSLSALGGGPVQAAVLCTVVADAADGRILFQQGTQQACAERYTPASTFKLAIALMGADAGILQGPHEPVWNYQPAYPDWGGDAWRQPTDPARWIKYSVVWYSQLTAKALGQDRFQRYTSAFGYGNADVSGEPGKHNGTDGAWIISSLRISPLEQLAFLRKLVNRQLPVKAAAYELAENLFEAGQADGWRLYGKTGTGSPGSNGVYTAANAYGWFVGWARKDGRQLVYARLLQDERATRPNAGLRARDELVRDWPAMAGAWRP"},"dna_sequence":{"accession":"EU188842.1","fmin":"0","fmax":"828","strand":"+","sequence":"ATGACCGTTCGACGCCTTTCGTGCGCCCTTGGCGCAGCCCTTTCCCTGTCCGCGCTGGGCGGCGGCCCCGTCCAGGCCGCCGTCCTGTGCACCGTGGTGGCCGACGCCGCCGACGGCCGCATCCTGTTCCAGCAAGGCACGCAGCAGGCCTGCGCCGAGCGCTACACGCCGGCCTCGACCTTCAAGCTGGCCATCGCCCTGATGGGCGCCGACGCCGGCATCCTGCAAGGCCCGCACGAGCCGGTCTGGAACTACCAGCCCGCCTATCCCGACTGGGGCGGCGACGCCTGGCGCCAGCCCACCGATCCGGCGCGCTGGATCAAGTATTCGGTGGTCTGGTATTCACAGCTGACGGCCAAGGCGCTGGGACAGGACCGCTTCCAGCGCTACACCAGCGCGTTCGGCTACGGCAATGCGGACGTCTCGGGCGAGCCCGGCAAGCACAACGGCACCGACGGCGCGTGGATCATCTCGTCGCTGCGCATTTCGCCGCTGGAACAACTGGCTTTCCTGCGCAAGCTGGTGAATCGGCAATTGCCGGTCAAGGCCGCCGCCTATGAGCTTGCCGAAAACCTCTTCGAGGCGGGCCAGGCCGATGGCTGGCGCCTGTATGGCAAGACCGGCACCGGGTCGCCCGGCAGCAACGGCGTCTACACGGCGGCCAATGCCTACGGTTGGTTCGTCGGCTGGGCGCGCAAGGATGGCCGCCAGCTGGTGTACGCCCGCCTGCTGCAGGATGAGCGCGCCACCCGACCCAACGCCGGCCTGCGCGCCCGCGACGAGCTGGTGCGCGACTGGCCGGCCATGGCCGGCGCGTGGCGCCCGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36941","NCBI_taxonomy_name":"Achromobacter xylosoxidans","NCBI_taxonomy_id":"85698"}}}},"ARO_accession":"3001609","ARO_id":"38009","ARO_name":"OXA-114a","CARD_short_name":"OXA-114a","ARO_description":"OXA-114a is a beta-lactamase found in Achromobacter xylosoxidans.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46487":{"category_aro_accession":"3007698","category_aro_cvterm_id":"46487","category_aro_name":"OXA-114-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-114.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1893":{"model_id":"1893","model_name":"SHV-127","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"828":{"protein_sequence":{"accession":"ACV32637.1","sequence":"MRFIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNNAERMVVIYLRDTPASMAERNQ"},"dna_sequence":{"accession":"GQ390809.1","fmin":"0","fmax":"813","strand":"+","sequence":"ATGCGTTTTATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTACTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAATGCAGAGCGCATGGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAATCAG","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001174","ARO_id":"37554","ARO_name":"SHV-127","CARD_short_name":"SHV-127","ARO_description":"SHV-127 is a beta-lactamase that has been found in clinical isolates.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1895":{"model_id":"1895","model_name":"CfxA3","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"8285":{"protein_sequence":{"accession":"AAL79549.2","sequence":"MEKNRKKQIVVLSIALVCIFILVFSLFHKSATKDSANPPLTNVLTDSISQIVSACPGEIGVAVIVNNRDTVKVNNKSVYPMMSVFKVHQALALCNDFDNKGISLDTLVNINRDKLDPKTWSPMLKDYSGPVISLTVRDLLRYTLTQSDNNASNLMFKDMVNVAQTDSFIATLIPRSSFQIAYTEEEMSADHNKAYSNYTSPLGAAMLMNRLFTEGLIDDEKQSFIKNTLKECKTGVDRIAAPLLDKEGVVIAHKTGSGDVNENGVLAAHNDVAYICLPNNISYTLAVFVKDFKGNESQASQYVAHISAVVYSLLMQTSVKS"},"dna_sequence":{"accession":"AF472622.2","fmin":"52","fmax":"1018","strand":"+","sequence":"ATGGAAAAAAACAGAAAAAAACAAATCGTAGTTTTGAGTATAGCTTTAGTTTGCATTTTCATCTTGGTATTTTCATTGTTCCATAAATCAGCGACAAAAGATAGCGCAAATCCTCCTTTAACAAATGTTTTGACTGATAGCATTTCTCAAATTGTCTCAGCTTGTCCTGGCGAAATTGGTGTGGCGGTTATTGTTAATAACAGAGATACGGTTAAGGTCAATAATAAGAGTGTTTATCCTATGATGAGTGTGTTTAAGGTTCATCAGGCATTAGCTCTTTGTAATGACTTTGACAATAAAGGAATTTCACTTGATACCTTAGTAAATATAAATAGGGATAAACTTGACCCAAAGACTTGGAGTCCTATGCTGAAAGATTATTCAGGGCCAGTCATATCATTGACAGTGAGAGATTTGCTGCGTTATACTCTTACTCAGAGTGACAACAATGCAAGCAACCTTATGTTTAAGGATATGGTTAATGTCGCTCAAACAGATAGTTTTATAGCCACACTCATTCCTCGTTCAAGTTTTCAGATAGCTTATACGGAAGAGGAAATGTCGGCTGACCATAACAAGGCTTACTCTAACTATACATCTCCTCTTGGTGCTGCAATGTTGATGAATCGTTTGTTTACTGAAGGTCTTATCGATGATGAGAAACAAAGTTTCATTAAGAATACGTTAAAAGAATGCAAAACAGGTGTAGATAGGATAGCAGCTCCACTTCTTGATAAAGAAGGGGTTGTTATAGCGCATAAGACAGGTTCAGGTGATGTTAATGAAAATGGTGTTCTTGCAGCTCACAATGATGTTGCCTATATATGTCTGCCTAATAATATCAGTTATACCTTAGCGGTATTTGTTAAGGATTTCAAGGGAAATGAATCACAAGCGTCACAATATGTTGCGCATATATCAGCTGTAGTATATTCTTTATTAATGCAAACTTCAGTAAAATCTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36958","NCBI_taxonomy_name":"Capnocytophaga ochracea","NCBI_taxonomy_id":"1018"}}}},"ARO_accession":"3003003","ARO_id":"39437","ARO_name":"CfxA3","CARD_short_name":"CfxA3","ARO_description":"CfxA3 beta-lactamase is a class A beta-lactamase found in Capnocytophaga ochracea.","ARO_category":{"39434":{"category_aro_accession":"3003000","category_aro_cvterm_id":"39434","category_aro_name":"CfxA beta-lactamase","category_aro_description":"CfxA beta-lactamases are class A beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1896":{"model_id":"1896","model_name":"NDM-12","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1829":{"protein_sequence":{"accession":"BAO79439.1","sequence":"MELPNIMHPVAKLSTALAAALMLSGCMPGEIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGLVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLDDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR"},"dna_sequence":{"accession":"AB926431.1","fmin":"510","fmax":"1323","strand":"+","sequence":"ATGGAATTGCCCAATATTATGCACCCGGTCGCGAAGCTGAGCACCGCATTAGCCGCTGCATTGATGCTGAGCGGGTGCATGCCCGGTGAAATCCGCCCGACGATTGGCCAGCAAATGGAAACTGGCGACCAACGGTTTGGCGATCTGGTTTTCCGCCAGCTCGCACCGAATGTCTGGCAGCACACTTCCTATCTCGACATGCCGGGTTTCGGGGCAGTCGCTTCCAACGGTTTGATCGTCAGGGATGGCGGCCGCGTGCTGGTGGTCGATACCGCCTGGACCGATGACCAGACCGCCCAGATCCTCAACTGGATCAAGCAGGAGATCAACCTGCCGGTCGCGCTGGCGGTGGTGACTCACGCGCATCAGGACAAGATGGGCGGTATGGACGCGCTGCATGCGGCGGGGATTGCGACTTATGCCAATGCGTTGTCGAACCAGCTTGCCCCGCAAGAGGGGCTGGTTGCGGCGCAACACAGCCTGACTTTCGCCGCCAATGGCTGGGTCGAACCAGCAACCGCGCCCAACTTTGGCCCGCTCAAGGTATTTTACCCCGGCCCCGGCCACACCAGTGACAATATCACCGTTGGGATCGACGGCACCGACATCGCTTTTGGTGGCTGCCTGATCAAGGACAGCAAGGCCAAGTCGCTCGGCAATCTCGATGATGCCGACACTGAGCACTACGCCGCGTCAGCGCGCGCGTTTGGTGCGGCGTTCCCCAAGGCCAGCATGATCGTGATGAGCCATTCCGCCCCCGATAGCCGCGCCGCAATCACTCATACGGCCCGCATGGCCGACAAGCTGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002362","ARO_id":"38762","ARO_name":"NDM-12","CARD_short_name":"NDM-12","ARO_description":"NDM-12 is a beta-lactamase found in Escherichia coli.","ARO_category":{"36196":{"category_aro_accession":"3000057","category_aro_cvterm_id":"36196","category_aro_name":"NDM beta-lactamase","category_aro_description":"NDM beta-lactamases or New Delhi metallo-beta-lactamases are class B beta-lactamases that confer resistance to a broad range of antibiotics including carbapenems, cephalosporins and penicillins.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1898":{"model_id":"1898","model_name":"OXA-379","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1764":{"protein_sequence":{"accession":"AHL30279.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSTSKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWNGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRIGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWEWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"KF986260.1","fmin":"20","fmax":"845","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGTTCACCTTATATAGTGACTGCTAATCCAAATCACAGCACTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGAACGGGCAAAAAAGGCTGTTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTATTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGAATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001565","ARO_id":"37965","ARO_name":"OXA-379","CARD_short_name":"OXA-379","ARO_description":"OXA-379 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1900":{"model_id":"1900","model_name":"ACT-13","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1094":{"protein_sequence":{"accession":"CCK86741.1","sequence":"MMMTKSLCCALLLSTSCSVLAAPMSEKQLAEVVERTVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMSYEQAITTRVFKPLKLDHTWINVPKAEEAHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVKDMASWVMVNMKPDSLEESSLRKGLTLAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVEGSDNKVALAPLPAREVNPPAPPVNASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILSAL"},"dna_sequence":{"accession":"HE819402.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGATGACTAAATCCCTTTGCTGCGCCCTGCTGCTCAGCACCTCCTGCTCGGTATTGGCTGCACCGATGTCAGAAAAACAGCTGGCTGAGGTGGTGGAACGTACCGTTACGCCGCTGATGAAAGCGCAGGCCATTCCGGGTATGGCAGTGGCGGTGATTTATCAGGGTCAGCCGCACTACTTTACCTTCGGTAAAGCCGATGTTGCGGCGAACAAACCTGTCACCCCACAAACCTTATTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGCGTACTCGGCGGCGATGCCATTGCTCGGGGTGAAATATCGCTGGGCGATCCGGTGACCAAATACTGGCCTGAGCTGACAGGCAAGCAGTGGCAGGGGATCCGCATGCTGGATCTGGCAACCTATACCGCAGGAGGTCTGCCGTTACAGGTACCGGATGAGGTCACGGATAACGCCTCTCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCGGGCACCACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGCGCGCTGGCGGTCAAACCTTCCGGCATGAGCTATGAGCAGGCCATAACGACGCGGGTCTTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTTCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGATACCGCGACGGTAAGGCGGTACACGTTTCGCCAGGAATGCTGGACGCTGAAGCCTATGGCGTAAAAACCAACGTGAAGGATATGGCAAGCTGGGTGATGGTCAACATGAAGCCGGACTCGCTTGAGGAAAGTTCACTCAGGAAAGGCCTTACCCTGGCGCAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAGGGGTTGGGCTGGGAAATGCTTAACTGGCCGGTCGATGCAAAAACCGTGGTTGAAGGTAGCGACAATAAGGTGGCGCTGGCACCGCTGCCTGCGAGAGAAGTGAATCCACCGGCGCCCCCGGTCAACGCATCCTGGGTCCATAAAACCGGCTCTACCGGCGGGTTTGGCAGCTACGTGGCATTTATTCCTGAAAAGCAGCTCGGCATTGTGATGCTGGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCGTATTTTGAGCGCGCTGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36926","NCBI_taxonomy_name":"Enterobacter asburiae","NCBI_taxonomy_id":"61645"}}}},"ARO_accession":"3001835","ARO_id":"38235","ARO_name":"ACT-13","CARD_short_name":"ACT-13","ARO_description":"ACT-13 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1901":{"model_id":"1901","model_name":"CTX-M-51","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1256":{"protein_sequence":{"accession":"ABA62022.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAVAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTAGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"DQ211987.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGTCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAGCTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCACAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGCAGGTGATAAGACCGGCAGCGGCGACTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001913","ARO_id":"38313","ARO_name":"CTX-M-51","CARD_short_name":"CTX-M-51","ARO_description":"CTX-M-51 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1902":{"model_id":"1902","model_name":"OXA-246","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"886":{"protein_sequence":{"accession":"AHC31001.1","sequence":"MKTFAAYVIIACLSSTALAGSITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKNFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGIIGG"},"dna_sequence":{"accession":"KF711993.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGAAAACATTTGCCGCATATGTAATTATCGCGTGTCTTTCGAGTACGGCATTAGCTGGTTCAATTACAGAAAATACGTCTTGGAACAAAGAGTTCTCTGCCGAAGCCGTCAATGGTGTCTTCGTGCTTTGTAAAAGTAGCAGTAAATCCTGCGCTACCAATGACTTAGCTCGTGCATCAAAGGAATATCTTCCAGCATCAACATTTAAGATCCCCAACGCAATTATCGGCCTAGAAACTGGTGTCATAAAGAATGAGCATCAGGTTTTCAAATGGGACGGAAAGCCAAGAGCCATGAAGCAATGGGAAAGAGACTTGACCTTAAGAGGGGCAATACAAGTTTCAGCTGTTCCCGTATTTCAACAAATCGCCAGAGAAGTTGGCGAAGTAAGAATGCAGAAATACCTTAAAAACTTTTCCTATGGCAACCAGAATATCAGTGGTGGCATTGACAAATTCTGGTTGGAAGGCCAGCTTAGAATTTCCGCAGTTAATCAAGTGGAGTTTCTAGAGTCTCTATATTTAAATAAATTGTCAGCATCTAAAGAAAACCAGCTAATAGTAAAAGAGGCTTTGGTAACGGAGGCGGCACCTGAATATCTAGTGCATTCAAAAACTGGTTTTTCTGGTGTGGGAACTGAGTCAAATCCTGGTGTCGCATGGTGGGTTGGGTGGGTTGAGAAGGAGACAGAGGTTTACTTTTTCGCCTTTAACATGGATATAGACAACGAAAGTAAGTTGCCGCTAAGAAAATCCATTCCCACCAAAATCATGGAAAGTGAGGGCATCATTGGTGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3001807","ARO_id":"38207","ARO_name":"OXA-246","CARD_short_name":"OXA-246","ARO_description":"OXA-246 is a beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46486":{"category_aro_accession":"3007697","category_aro_cvterm_id":"46486","category_aro_name":"OXA-10-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-10.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1903":{"model_id":"1903","model_name":"mdtE","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"675"}},"model_sequences":{"sequence":{"4673":{"protein_sequence":{"accession":"BAE77781.1","sequence":"MNRRRKLLIPLLFCGAMLTACDDKSAENAAAMTPEVGVVTLSPGSVNVLSELPGRTVPYEVAEIRPQVGGIIIKRNFIEGDKVNQGDSLYQIDPAPLQAELNSAKGSLAKALSTASNARITFNRQASLLKTNYVSRQDYDTARTQLNEAEANVTVAKAAVEQATINLQYANVTSPITGVSGKSSVTVGALVTANQADSLVTVQRLDPIYVDLTQSVQDFLRMKEEVASGQIKQVQGSTPVQLNLENGKRYSQTGTLKFSDPTVDETTGSVTLRAIFPNPNGDLLPGMYVTALVDEGSRQNVLLVPQEGVTHNAQGKATALILDKDDVVQLREIEASKAIGDQWVVTSGLQAGDRVIVSGLQRIRPGIKARAISSSQENASTESKQ"},"dna_sequence":{"accession":"AP009048.1","fmin":"3980025","fmax":"3981183","strand":"-","sequence":"ATGAACAGAAGAAGAAAGCTGTTAATACCGTTGTTATTCTGCGGCGCGATGCTCACCGCCTGCGATGACAAATCGGCGGAAAACGCCGCCGCCATGACGCCTGAGGTCGGTGTCGTCACACTCTCCCCCGGTTCGGTCAATGTGTTGAGCGAATTGCCCGGTAGAACCGTTCCTTATGAAGTTGCCGAGATACGTCCCCAGGTGGGCGGTATTATCATTAAACGCAACTTTATCGAAGGCGATAAAGTGAACCAGGGCGATTCGCTGTATCAGATTGATCCTGCACCTTTACAGGCCGAGCTAAACTCCGCCAAAGGCTCGCTGGCGAAAGCGCTCTCTACCGCCAGCAATGCCCGCATCACCTTTAACCGCCAGGCATCGTTGCTGAAGACCAACTACGTTAGCCGTCAGGATTACGACACCGCGCGCACCCAGTTGAATGAAGCAGAAGCCAATGTCACCGTCGCCAAAGCGGCTGTTGAACAGGCGACGATCAATCTGCAATACGCGAATGTCACCTCGCCGATTACGGGCGTCAGCGGGAAATCGTCGGTGACCGTCGGCGCACTCGTTACCGCTAATCAGGCAGATTCGCTGGTTACCGTACAACGTCTGGACCCGATTTATGTCGATCTCACGCAGTCGGTGCAAGATTTCTTACGCATGAAAGAAGAGGTCGCCAGTGGGCAAATCAAACAGGTTCAGGGCAGTACGCCAGTACAGCTCAATCTGGAAAATGGTAAACGCTACAGCCAGACCGGCACGCTGAAATTCTCCGACCCGACAGTGGATGAAACCACGGGCTCCGTGACGTTACGGGCGATTTTCCCCAACCCAAATGGTGACTTGCTGCCTGGCATGTACGTCACGGCATTAGTGGATGAAGGTAGCCGCCAGAATGTATTACTGGTGCCGCAGGAAGGCGTCACCCACAACGCCCAGGGTAAAGCAACGGCGCTCATTCTGGATAAAGACGATGTCGTGCAGCTACGCGAAATTGAAGCCAGCAAAGCCATCGGCGACCAGTGGGTCGTCACCTCTGGCTTGCAGGCTGGCGATCGGGTGATCGTTTCCGGTTTGCAACGCATTCGTCCGGGTATCAAAGCACGAGCAATTTCCTCCAGCCAGGAAAACGCCAGCACCGAATCGAAACAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36839","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. W3110","NCBI_taxonomy_id":"316407"}}}},"ARO_accession":"3000795","ARO_id":"37175","ARO_name":"mdtE","CARD_short_name":"mdtE","ARO_description":"MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35930":{"category_aro_accession":"0000011","category_aro_cvterm_id":"35930","category_aro_name":"cloxacillin","category_aro_description":"Cloxacillin is a semisynthetic, isoxazolyl penicillin derivative in the beta-lactam class of antibiotics. It interferes with peptidogylcan synthesis and is commonly used for treating penicillin-resistant Staphylococcus aureus infections.","category_aro_class_name":"Antibiotic"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1904":{"model_id":"1904","model_name":"ACT-32","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1419":{"protein_sequence":{"accession":"AIT76088.1","sequence":"MMKKSLCCALLLGISCSALATPVSEKQLAEVVANTVTPLMKAQSVPGMAVAVIYQGKPHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMPYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPENVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVVEGSDSKVALAPLPVVEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANTSYPNPARVEAAYHILDALQ"},"dna_sequence":{"accession":"KM087835.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCTCTTTGCTGCGCCCTGCTGCTCGGCATCTCTTGCTCTGCTCTCGCCACGCCAGTGTCAGAAAAACAGCTGGCGGAGGTGGTCGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCTGTTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGAAAACCGCACTATTACACGTTTGGCAAGGCCGATATCGCGGCGAATAAACCCGTTACGCCTCAGACCCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGCGTTTTAGGTGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTGACGGGCAAGCAGTGGCAGGGTATTCGTATGCTGGATCTCGCCACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTCAAACCTTCTGGCATGCCCTATGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTGCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGTATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCGGAGAACGTTGCTGATGCCTCACTTAAGCAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGGTCGAGGGCAGCGACAGTAAGGTAGCGCTGGCGCCGTTGCCCGTGGTAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGCTCTACTGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATACAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCGACGCGCTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3001852","ARO_id":"38252","ARO_name":"ACT-32","CARD_short_name":"ACT-32","ARO_description":"ACT-32 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1905":{"model_id":"1905","model_name":"ACT-21","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1854":{"protein_sequence":{"accession":"AHA80106.1","sequence":"MMKKSLCCALLLGISCSALAAPVSEKQLAEVVANTVTPLMKAQSIPGMAVAVIYQGKPHYYTFGKADVAASKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNAALLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMPFEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGMKTNVQDMANWVMANMAPENVADASLKQGISLAQSRYWRIGSMYQGLGWEMLNWPVEANTVIEGSDSKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANKSYPNPARVEAAYPILDALQ"},"dna_sequence":{"accession":"KF526118.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCTCTTTGCTGCGCCCTGCTGCTCGGCATCTCTTGCTCTGCTCTCGCCGCGCCAGTGTCAGAAAAACAGCTGGCGGAGGTGGTCGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCGATTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGTAAACCGCACTATTACACGTTCGGTAAAGCCGATGTTGCGGCCAGCAAACCCGTTACGCCTCAGACTCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGGGTTTTAGGAGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTGACGGGCAAGCAGTGGCAGGGGATTCGTATGCTGGATCTCGCAACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAATGCCGCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGTATCGGTCTTTTTGGCGCGCTGGCGGTCAAACCTTCCGGCATGCCCTTTGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTTCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGATATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGAATGCTGGATGCACAAGCCTATGGCATGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAATATGGCGCCGGAGAACGTTGCTGATGCCTCACTTAAGCAGGGCATCTCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGATCGAGGGCAGCGACAGTAAGGTGGCGCTGGCACCGCTGCCCGTGGCAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGCTCTACTGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCCTATCCTCGACGCGCTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39098","NCBI_taxonomy_name":"Enterobacter hormaechei","NCBI_taxonomy_id":"158836"}}}},"ARO_accession":"3001842","ARO_id":"38242","ARO_name":"ACT-21","CARD_short_name":"ACT-21","ARO_description":"ACT-21 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1906":{"model_id":"1906","model_name":"CTX-M-17","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"907":{"protein_sequence":{"accession":"AAK71471.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAKGL"},"dna_sequence":{"accession":"AY033516.1","fmin":"2835","fmax":"3711","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGACTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCAAGGGGCTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001880","ARO_id":"38280","ARO_name":"CTX-M-17","CARD_short_name":"CTX-M-17","ARO_description":"CTX-M-17 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1908":{"model_id":"1908","model_name":"OKP-A-6","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"1675":{"protein_sequence":{"accession":"CAJ19603.1","sequence":"MRYVRLCLISLIAALPLAAFASPQPLEQVTRSESQLAGRVGYVEMDLASGRTLAAWRASERFPLMSTFKVLLCGAVLARVDAGDERLDRRIRYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAGNLLLKRVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDVRDTTTPASMAATLRKLLTSHALSDRSQQQLLQWMVDDQVAGPLIRAVLPAGWFIADKTGAGERGSRGIVALLGPNGKAERIVVIYLRDTPATMAERNQQIAKIGAALIEHWQR"},"dna_sequence":{"accession":"AM051144.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGCCTTATCTCCCTGATTGCCGCCCTGCCACTGGCGGCATTCGCCAGCCCTCAGCCGCTCGAGCAAGTTACACGCAGCGAAAGTCAGCTGGCGGGCCGCGTGGGCTATGTTGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCAGTGAGCGCTTTCCGCTGATGAGCACCTTTAAAGTGCTGCTCTGCGGCGCGGTGCTGGCACGGGTGGATGCCGGAGACGAACGGCTGGATCGGCGGATCCGCTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGCCGACGGGATGACCGTTGGCGAACTCTGCGCCGCCGCCATCACCATGAGCGACAACAGCGCCGGCAATCTGCTGTTGAAGCGCGTTGGCGGCCCCGCGGGATTGACCGCTTTTCTGCGCCAGATCGGTGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAGCTCAATGAAGCGCTTCCCGGCGACGTGCGCGACACCACCACCCCAGCCAGCATGGCCGCCACCCTGCGCAAGCTGCTAACCAGCCACGCGCTGAGCGACCGTTCGCAGCAGCAGCTGCTGCAGTGGATGGTGGACGACCAGGTGGCCGGTCCGCTGATCCGCGCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAAACCGGGGCCGGCGAGCGGGGCTCACGCGGCATTGTCGCCCTGCTCGGCCCGAACGGCAAAGCGGAGCGCATCGTGGTGATCTATCTGCGGGATACGCCGGCGACCATGGCCGAGCGTAACCAGCAGATCGCCAAAATAGGCGCGGCGCTGATCGAGCACTGGCAGCGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002423","ARO_id":"38823","ARO_name":"OKP-A-6","CARD_short_name":"OKP-A-6","ARO_description":"OKP-A-6 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"38817":{"category_aro_accession":"3002417","category_aro_cvterm_id":"38817","category_aro_name":"OKP beta-lactamase","category_aro_description":"OKP beta-lactamases are chromosomal class A beta-lactamase that confer resistance to penicillins and early cephalosporins in Klebsiella pneumoniae. OKP beta-lactamases can be subdivided into two groups: OKP-A and OKP-B which diverge by about 4.2%.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1909":{"model_id":"1909","model_name":"AAC(6')-Iak","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"4672":{"protein_sequence":{"accession":"BAO21229.1","sequence":"MTGSAATIRPAKAADAVAWAQLRLGLWPDADDPLETLVAALAEDAGAVFLACAAGGQAIGFAEVRLRHDYVNGTDSSPVGFLEGWYVQPQWQGRGVGRALLAAVRAWTRDAGCRELASDSRVEDVQAHAAHRACGFEETERVVYFRMPLEPSA"},"dna_sequence":{"accession":"AB894482.1","fmin":"35038","fmax":"35500","strand":"-","sequence":"GTGACCGGCAGCGCGGCCACGATCCGCCCGGCCAAGGCGGCCGATGCGGTCGCGTGGGCGCAGCTGCGTCTGGGCCTGTGGCCCGATGCCGATGATCCGCTGGAGACGCTGGTGGCGGCGCTGGCCGAGGACGCAGGTGCGGTTTTCCTGGCGTGTGCAGCGGGTGGCCAGGCGATCGGCTTCGCCGAAGTGCGCCTGCGCCATGACTACGTGAACGGCACCGATTCCTCGCCGGTGGGCTTCCTGGAGGGCTGGTACGTGCAGCCGCAGTGGCAAGGCCGCGGCGTGGGCCGCGCCCTGCTGGCGGCGGTGCGGGCATGGACGCGCGACGCGGGCTGCCGCGAACTGGCTTCGGACAGTCGCGTGGAGGACGTGCAGGCTCACGCCGCGCATCGGGCCTGCGGCTTCGAAGAGACCGAACGGGTGGTCTATTTCCGCATGCCACTGGAGCCATCGGCGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37076","NCBI_taxonomy_name":"Stenotrophomonas maltophilia","NCBI_taxonomy_id":"40324"}}}},"ARO_accession":"3003199","ARO_id":"39782","ARO_name":"AAC(6')-Iak","CARD_short_name":"AAC(6')-Iak","ARO_description":"AAC(6')-Iak is a 6'-N-aminoglycoside acetyltransferase-encoding gene isolated from a multidrug-resistant clinical isolate of Stenotrophomonas maltophilia.","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"A category of aminoglycoside N-acetyltransferase enzymes with modification regiospecificity based at the 6'-amino group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics through acetylation of the 6-amino group of the compound.","category_aro_class_name":"AMR Gene Family"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"46128":{"category_aro_accession":"3007378","category_aro_cvterm_id":"46128","category_aro_name":"2'-N-ethylnetilmicin","category_aro_description":"2'-N-ethylnetilmicin is an aminoglycoside antibiotic and a derivative of netilmicin.","category_aro_class_name":"Antibiotic"},"46129":{"category_aro_accession":"3007379","category_aro_cvterm_id":"46129","category_aro_name":"5-episisomicin","category_aro_description":"5-episosomicin is a semisynthetic aminoglycoside antibiotic similar to sisomicin.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1910":{"model_id":"1910","model_name":"CTX-M-136","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"2042":{"protein_sequence":{"accession":"AGG08693.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAVAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGDYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"KC351754.1","fmin":"157","fmax":"1033","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGTACCAGTAAAGTGATGGCCGTGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGACTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGTTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3001995","ARO_id":"38395","ARO_name":"CTX-M-136","CARD_short_name":"CTX-M-136","ARO_description":"CTX-M-136 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1911":{"model_id":"1911","model_name":"AAC(6')-Iad","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"264":{"protein_sequence":{"accession":"BAD12078.1","sequence":"MIRKATVQDPPLLARLAMNVWKESSLKELVAEFEQMTKSNDAVAFILFIEDQAVGFAQCQLRHDYVEGTNTSPVGYLEGIFVEKEFRHRGYASELLLKCEDWVKTKGCLQFASDCELDNIDSLAFHLKVGFTEANRMICFTKQL"},"dna_sequence":{"accession":"AB119105.1","fmin":"0","fmax":"435","strand":"+","sequence":"ATGATTAGAAAAGCAACTGTCCAAGATCCACCATTATTAGCTCGTCTAGCAATGAATGTATGGAAAGAAAGCAGTTTAAAAGAATTAGTAGCAGAATTCGAGCAGATGACTAAAAGTAATGATGCTGTGGCATTTATACTATTTATAGAGGATCAAGCTGTCGGGTTTGCTCAATGTCAATTGCGTCATGATTATGTTGAAGGGACGAATACGAGTCCTGTAGGCTATTTAGAAGGTATATTTGTCGAGAAAGAATTTCGTCACAGAGGATACGCGAGCGAACTATTGTTAAAATGCGAAGATTGGGTGAAAACAAAAGGCTGCCTTCAATTTGCTAGTGATTGTGAATTAGATAATATTGATAGCTTGGCTTTTCATCTCAAAGTAGGTTTTACTGAAGCAAATCGAATGATTTGTTTTACAAAGCAACTTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3002572","ARO_id":"38972","ARO_name":"AAC(6')-Iad","CARD_short_name":"AAC(6')-Iad","ARO_description":"AAC(6')-Iad is a plasmid-encoded aminoglycoside acetyltransferase in Acinetobacter genomosp. 3.","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"A category of aminoglycoside N-acetyltransferase enzymes with modification regiospecificity based at the 6'-amino group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics through acetylation of the 6-amino group of the compound.","category_aro_class_name":"AMR Gene Family"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"46128":{"category_aro_accession":"3007378","category_aro_cvterm_id":"46128","category_aro_name":"2'-N-ethylnetilmicin","category_aro_description":"2'-N-ethylnetilmicin is an aminoglycoside antibiotic and a derivative of netilmicin.","category_aro_class_name":"Antibiotic"},"46129":{"category_aro_accession":"3007379","category_aro_cvterm_id":"46129","category_aro_name":"5-episisomicin","category_aro_description":"5-episosomicin is a semisynthetic aminoglycoside antibiotic similar to sisomicin.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1912":{"model_id":"1912","model_name":"LRA-13","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1200"}},"model_sequences":{"sequence":{"4671":{"protein_sequence":{"accession":"ACH58991.1","sequence":"MNFRHIVMAALCGLAWTPAIHATEVCIAIAEAGTGAVLVQRGDCQRQVTPASTFKIAISLMGYDSGFLKDAHAPKLPFRPGYVDWRPSWREPTDPAKWMSDSVVWYSQQVTKSLGMQRFADYTRNFKYGNADVSGDAENDGLSMSWISSSLRISPLEQLAFLDKIVNRRLGVSAHAYDMTAQLTKFDQPPAGWRINGKTGAASGYGWYVGWASKGSRTFVFAHLMQRDATQPQDVSAGVLARDEFLKELPGLMIKDMVDRAVQPLMKKYDIPGMAVAVTDNGKNYFFNYGLASRETGQAVTSHTLFEIGSLSKTMAATLTSYAQVNGQLALTDTVSRHMPKLRGGGFDKISLLNLGTHTAGDFPMQVPDHIETYEQLMEYYKNWKPGVAAGGARTYSNLTVGLLGIITAQSMGMPFAEAMENRLFPQLGMHHSYINVPAAEMKNYAQGYNQANAPVRINPAVLATEAYGVKTDAADLIRFVDANMGLVKLDEKLQRAVTGTHTAYFKTGELTQDLIWEQYPAASKLDRMLAGVSEKMVFESNPATRLAPPMPPQADVLINKTGSTGGFGAYALFNPGKKTGIVMLANKSYPGAERVTAAWHILDQLDQR"},"dna_sequence":{"accession":"EU408352.1","fmin":"35394","fmax":"37224","strand":"-","sequence":"ATGAATTTTCGCCACATAGTCATGGCGGCGCTGTGCGGTCTCGCCTGGACGCCAGCCATCCACGCCACCGAAGTGTGTATCGCCATCGCCGAGGCCGGCACCGGCGCTGTGCTGGTCCAGCGCGGCGATTGCCAGCGCCAGGTGACGCCGGCGTCGACCTTCAAGATCGCCATCAGCCTGATGGGCTACGACTCGGGTTTTCTGAAGGACGCGCACGCGCCGAAACTGCCGTTCCGTCCAGGCTATGTCGATTGGCGGCCCAGCTGGCGCGAACCGACGGATCCGGCCAAGTGGATGAGCGATTCGGTCGTATGGTATTCGCAGCAGGTGACAAAATCCCTGGGCATGCAGCGTTTCGCCGACTACACGCGGAACTTCAAGTATGGCAATGCCGACGTTTCGGGGGACGCGGAAAATGACGGCCTGAGCATGTCGTGGATAAGTTCCTCGCTGCGGATCTCGCCGCTGGAACAACTCGCGTTCCTGGACAAGATCGTCAACCGTCGGCTGGGCGTGAGCGCCCATGCCTACGACATGACCGCGCAATTGACGAAATTCGATCAGCCTCCGGCGGGATGGCGCATCAACGGCAAGACCGGCGCCGCCTCCGGTTATGGCTGGTACGTGGGATGGGCGTCGAAAGGTTCGCGAACCTTCGTCTTTGCGCACCTGATGCAGAGGGACGCGACGCAGCCGCAAGACGTGTCGGCGGGCGTGCTGGCGCGTGACGAATTCCTCAAGGAACTCCCCGGCTTGATGATCAAGGATATGGTGGACCGCGCCGTCCAGCCGTTGATGAAGAAATACGATATCCCGGGGATGGCGGTGGCCGTCACCGACAACGGCAAGAACTACTTCTTCAACTACGGGCTGGCGTCGAGGGAAACCGGGCAAGCCGTTACCAGCCACACCCTGTTCGAGATCGGTTCGCTGAGCAAGACCATGGCGGCAACGCTGACTTCCTACGCGCAGGTCAACGGCCAGCTTGCGTTGACCGACACGGTCAGCCGGCATATGCCCAAGCTGCGCGGCGGCGGCTTCGACAAGATCAGCCTGCTCAATCTGGGCACCCACACGGCCGGCGATTTTCCGATGCAGGTTCCCGACCATATCGAGACCTACGAGCAGCTGATGGAGTACTACAAAAACTGGAAGCCCGGGGTTGCTGCGGGCGGCGCCAGGACCTACTCCAACCTGACCGTCGGCCTGCTGGGCATCATCACGGCGCAAAGCATGGGCATGCCGTTTGCGGAGGCGATGGAAAACAGGTTGTTCCCCCAGCTTGGCATGCATCACAGCTATATCAATGTGCCGGCGGCGGAGATGAAGAACTACGCGCAAGGCTACAACCAGGCCAACGCACCGGTCAGGATCAATCCGGCGGTGCTGGCAACCGAGGCATACGGGGTAAAGACCGATGCCGCCGACTTGATCCGGTTTGTCGACGCCAACATGGGGTTGGTCAAGCTGGACGAAAAACTGCAGCGCGCGGTCACCGGCACGCACACCGCCTACTTCAAGACGGGTGAGCTGACGCAGGATCTGATCTGGGAACAATATCCCGCCGCATCGAAACTCGATCGCATGCTGGCGGGCGTTTCCGAAAAAATGGTCTTTGAAAGCAATCCCGCGACCAGGCTGGCGCCGCCGATGCCGCCGCAAGCGGATGTGCTGATCAACAAGACCGGATCAACCGGCGGCTTTGGCGCCTATGCGCTGTTCAACCCGGGCAAGAAGACCGGCATCGTGATGCTGGCGAACAAGAGCTATCCTGGCGCAGAAAGGGTGACGGCGGCCTGGCACATACTGGATCAACTGGACCAGCGTTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39085","NCBI_taxonomy_name":"uncultured bacterium BLR13","NCBI_taxonomy_id":"506515"}}}},"ARO_accession":"3002484","ARO_id":"38884","ARO_name":"LRA-13","CARD_short_name":"LRA-13","ARO_description":"LRA-13 is a class D\/class C fusion bifunctional beta-lactamase isolated from soil samples in Alaska.","ARO_category":{"41395":{"category_aro_accession":"3004231","category_aro_cvterm_id":"41395","category_aro_name":"class C LRA beta-lactamase","category_aro_description":"Beta-lactamases that are part of the LRA gene family and are classified as Class C beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"41405":{"category_aro_accession":"3004241","category_aro_cvterm_id":"41405","category_aro_name":"class D LRA beta-lactamase","category_aro_description":"Beta-lactamases that are part of the LRA gene family and are classified as Class D beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1913":{"model_id":"1913","model_name":"dfrK","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"50":{"protein_sequence":{"accession":"CBL80435.1","sequence":"MKVSLIAAMDKNRVLGKENDIPWRIPKDWEYVKNTTKGYPIILGRKNLESIGRALPGRRNIILTRDKGFSFNGCEIVHSIEDVFEICNNEEEIFIFGGEQIYNLFLPYVEKMYITKIHYEFEGDTFFPEVNYEEWSEVSVTQGITDEKNPYTYYFHIYERKAS"},"dna_sequence":{"accession":"FN812951.1","fmin":"0","fmax":"492","strand":"+","sequence":"ATGAAAGTTTCTTTAATTGCTGCGATGGATAAGAATAGGGTATTAGGTAAAGAGAATGACATACCTTGGAGAATCCCAAAGGATTGGGAGTATGTTAAAAATACTACAAAGGGATATCCAATTATATTAGGAAGGAAGAATCTTGAATCAATCGGAAGAGCATTACCTGGAAGAAGAAATATTATTCTGACAAGAGATAAGGGTTTCAGCTTTAATGGTTGTGAAATTGTCCATTCAATAGAAGATGTTTTTGAGATATGTAATAACGAAGAGGAAATTTTCATTTTCGGGGGAGAACAAATTTATAATTTGTTTCTACCATATGTTGAGAAAATGTACATTACAAAAATTCATTACGAATTTGAAGGAGATACATTCTTTCCAGAAGTGAATTATGAAGAGTGGAGCGAAGTATCTGTTACACAAGGAATAACAGATGAAAAAAATCCTTATACATACTATTTTCATATTTATGAGCGAAAAGCTTCTTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35508","NCBI_taxonomy_name":"Staphylococcus aureus","NCBI_taxonomy_id":"1280"}}}},"ARO_accession":"3002869","ARO_id":"39303","ARO_name":"dfrK","CARD_short_name":"dfrK","ARO_description":"dfrK is a plasmid-encoded dihydrofolate reductase found in Staphylococcus aureus.","ARO_category":{"37617":{"category_aro_accession":"3001218","category_aro_cvterm_id":"37617","category_aro_name":"trimethoprim resistant dihydrofolate reductase dfr","category_aro_description":"Alternative dihydropteroate synthase dfr present on plasmids produces alternate proteins that are less sensitive to trimethoprim from inhibiting its role in folate synthesis, thus conferring trimethoprim resistance.","category_aro_class_name":"AMR Gene Family"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1914":{"model_id":"1914","model_name":"BEL-3","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1359":{"protein_sequence":{"accession":"ACT09140.1","sequence":"MKLLLYPLLLFLVIPAFAQADFEHAISDLEAHNQAKIGVALVSENGNLIQGYRANERFAMCSTFKLPLAALVLSRIDAGEENPERKLHYDSAFLEEYAPAAKRYVATGYMTVTEAIQSALQLSDNAAANLLLKEVGGPPLLTKYFRSLGDKVSRLDRIESTLNTNTPGDERDTTTPMSMAQTVSKLIFGDTLTYKSKGQLRRLLIGNQTGDKTIRAGLPDSWVTGDKTGSCANGGRNDVAFFITTAGKKYVLSVYTNAPELQGEERALLIASVAKLARQYVVH"},"dna_sequence":{"accession":"GQ202694.1","fmin":"0","fmax":"852","strand":"+","sequence":"ATGAAACTGCTGCTCTACCCGTTATTGCTGTTCCTTGTCATTCCAGCCTTTGCCCAGGCGGACTTTGAACATGCCATTTCAGATCTTGAGGCGCACAATCAAGCCAAGATCGGAGTGGCCCTAGTTAGTGAAAATGGCAACCTGATTCAAGGGTATCGTGCGAATGAAAGGTTCGCGATGTGCTCAACTTTCAAGTTGCCGTTGGCCGCTCTTGTTCTGAGTCGCATTGACGCTGGGGAAGAGAATCCTGAGCGCAAGCTTCATTACGATTCCGCGTTCCTTGAAGAGTACGCCCCAGCCGCAAAACGGTATGTGGCAACTGGATATATGACTGTAACTGAGGCAATTCAATCCGCCCTCCAACTCAGCGACAATGCCGCAGCTAACCTGCTGTTAAAAGAGGTTGGCGGCCCACCTTTATTGACAAAGTATTTCCGTAGCCTGGGTGATAAAGTAAGTCGCCTTGATCGTATTGAATCGACTTTGAACACCAATACGCCCGGCGATGAAAGAGATACAACAACGCCCATGTCCATGGCACAGACTGTGTCAAAGCTGATTTTTGGAGACACGTTGACATATAAATCCAAGGGGCAGCTAAGGCGATTACTCATCGGCAATCAGACCGGGGACAAAACCATTCGAGCTGGCTTGCCTGATTCATGGGTAACGGGTGACAAGACAGGCTCGTGTGCGAATGGCGGCCGTAACGATGTGGCGTTTTTTATAACCACTGCCGGAAAAAAATATGTTCTTTCTGTATATACCAATGCACCTGAATTGCAAGGCGAGGAAAGGGCGTTATTAATTGCTTCTGTAGCAAAGTTAGCACGTCAATATGTTGTTCACTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002387","ARO_id":"38787","ARO_name":"BEL-3","CARD_short_name":"BEL-3","ARO_description":"BEL-3 is a beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"38784":{"category_aro_accession":"3002384","category_aro_cvterm_id":"38784","category_aro_name":"BEL beta-lactamase","category_aro_description":"BEL beta-lactamases are class A expanded-spectrum beta-lactamases that are inhibited by clavulanic acid. They are chromosomally encoded and hydrolyze most cephalosporins and aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1915":{"model_id":"1915","model_name":"CMY-47","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"8248":{"protein_sequence":{"accession":"ADH82410.1","sequence":"MMKKSICCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAIIYEGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWRGISLLHLATYTAGGLPLQIPDEVTDKAELLRFYQNWQPQWTPGAKRLYANSSIGLFGALVVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQSEQKNYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIELAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPARVEAAWRILEKLQ"},"dna_sequence":{"accession":"HM046998.2","fmin":"1039","fmax":"2185","strand":"+","sequence":"ATGATGAAAAAATCGATATGCTGCGCGCTGCTGCTGACAGCCTCTTTCTCCACGTTTGCTGCCGCAAAAACAGAACAACAAATTGCCGATATCGTTAACCGCACCATCACACCACTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTGGCGATTATCTACGAGGGGAAACCTTATTACTTTACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAATTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGACGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCGAGGTATCAGCCTGCTGCACTTAGCCACCTATACAGCGGGTGGCCTGCCGCTGCAGATCCCCGATGAAGTTACGGATAAAGCCGAATTACTGCGCTTTTATCAAAACTGGCAACCACAATGGACTCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGTGCGTTGGTGGTAAAACCTTCAGGTATGAGCTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAAAGCGAACAAAAAAATTATGCCTGGGGCTATCGCGAAGGGAAGCCTGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATCGATATGGCCCGCTGGGTTCAGGCCAACATGGACGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGAGCTTGCGCAGTCTCGCTACTGGCGTATTGGTGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCAGCACCTGCCGTGAAAGCCTCATGGGTGCATAAAACGGGATCCACAGGTGGATTTGGCAGCTACGTTGCCTTCGTTCCAGAAAAAAACCTTGGCATAGTGATGCTGGCAAACAAAAGCTATCCTAACCCGGCTCGCGTAGAGGCGGCCTGGCGCATTCTTGAAAAACTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002058","ARO_id":"38458","ARO_name":"CMY-47","CARD_short_name":"CMY-47","ARO_description":"CMY-47 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1916":{"model_id":"1916","model_name":"TEM-208","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"929":{"protein_sequence":{"accession":"AGL39384.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDFVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"KC865667.1","fmin":"183","fmax":"1044","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTTGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001385","ARO_id":"37785","ARO_name":"TEM-208","CARD_short_name":"TEM-208","ARO_description":"TEM-208 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1918":{"model_id":"1918","model_name":"spd","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"758":{"protein_sequence":{"accession":"AGW81558.1","sequence":"MEEPNKQIDNVLIELKRLFSKDLLGVYLYGSYVKGGLKKDSDVDFLVIINRDMTKEEKRILISKIMPISKEIGEDTSLKYIELTVLNYHENENWSYPPIEEFIYGEWLREDYLNYFIPEKNNNIDLTILLYQAKLSSISIYGENNINNLIPDVPFIDLQKAIKESSKELIKDFYGDETNVILTLCRMIVTYETGKFYSKDLAGSMIIENLSENLSIEENNLISLAISSYKNGNSVDWELFPVKSVIKKLYAYLNYKL"},"dna_sequence":{"accession":"KC895984.1","fmin":"1081","fmax":"1855","strand":"+","sequence":"ATGGAGGAACCAAATAAGCAAATTGATAATGTTTTAATAGAATTGAAACGATTGTTTTCAAAAGATTTATTAGGAGTCTATTTATATGGTTCTTATGTTAAAGGGGGTTTAAAAAAAGATAGTGATGTTGATTTTCTAGTGATAATAAATAGAGATATGACTAAAGAAGAAAAAAGAATATTAATTTCGAAAATTATGCCTATCTCTAAAGAAATTGGTGAAGATACAAGTTTAAAATATATAGAATTAACTGTGCTTAATTATCATGAAAATGAAAATTGGTCTTATCCACCTATTGAAGAGTTTATCTATGGGGAATGGCTTAGAGAAGATTATTTAAATTATTTTATTCCAGAAAAGAATAACAACATTGATTTAACAATATTATTATATCAAGCCAAGCTTTCTTCAATATCAATTTATGGCGAAAATAATATTAATAACTTAATTCCTGATGTTCCATTTATTGATTTACAAAAAGCTATAAAGGAAAGTTCTAAAGAATTGATAAAAGATTTTTATGGTGATGAAACAAATGTTATTTTAACCCTTTGTCGTATGATCGTAACTTATGAAACAGGTAAGTTTTATTCAAAAGATTTAGCTGGCAGTATGATAATAGAAAATTTATCAGAAAATTTATCAATTGAAGAAAATAATTTAATAAGTTTAGCTATTTCTAGTTATAAAAATGGTAATAGCGTTGATTGGGAACTTTTTCCTGTTAAGAGTGTCATTAAAAAACTTTATGCTTATTTGAATTATAAATTATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35508","NCBI_taxonomy_name":"Staphylococcus aureus","NCBI_taxonomy_id":"1280"}}}},"ARO_accession":"3002631","ARO_id":"39031","ARO_name":"spd","CARD_short_name":"spd","ARO_description":"spd is a plasmid-encoded aminoglycoside nucleotidyltransferase gene in S. aureus.","ARO_category":{"36367":{"category_aro_accession":"3000228","category_aro_cvterm_id":"36367","category_aro_name":"ANT(9)","category_aro_description":"A category of aminoglycoside O-nucleotidyltransferase enzymes with modification regiospecificity based at the 9-hydroxyl group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics, specifically streptomycin, by transfer of an AMP group from an ATP substrate to the 9-hydroxyl group of the compound.","category_aro_class_name":"AMR Gene Family"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1919":{"model_id":"1919","model_name":"SHV-27","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1873":{"protein_sequence":{"accession":"AAG01039.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIDDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AF293345.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACATCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGACGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001085","ARO_id":"37465","ARO_name":"SHV-27","CARD_short_name":"SHV-27","ARO_description":"SHV-27 is an extended-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1921":{"model_id":"1921","model_name":"EreB","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"5540":{"protein_sequence":{"accession":"CAA27626.1","sequence":"MRFEEWVKDKHIPFKLNHPDDNYDDFKPLRKIIGDTRVVALGENSHFIKEFFLLRHTLLRFFIEDLGFTTFAFEFGFAEGQIINNWIHGQGTDDEIGRFLKHFYYPEELKTTFLWLREYNKAAKEKITFLGIDIPRNGGSYLPNMEIVHDFFRTADKEALHIIDDAFNIAKKIDYFSTSQAALNLHELTDSEKCRLTSQLARVKVRLEAMAPIHIEKYGIDKYETILHYANGMIYLDYNIQAMSGFISGGGMQGDMGAKDKYMADSVLWHLKNPQSEQKVIVVAHNAHIQKTPILYDGFLSCLPMGQRLKNAIGDDYMSLGITSYSGHTAALYPEVDTKYGFRVDNFQLQEPNEGSVEKAISGCGVTNSFVFFRNIPEDLQSIPNMIRFDSIYMKAELEKAFDGIFQIEKSSVSEVVYE"},"dna_sequence":{"accession":"X03988.1","fmin":"382","fmax":"1642","strand":"+","sequence":"ATGAGGTTCGAAGAATGGGTCAAAGATAAGCATATTCCTTTCAAACTGAATCACCCTGATGATAATTACGATGATTTTAAGCCATTAAGAAAAATAATTGGAGATACCCGAGTTGTAGCATTAGGTGAAAATTCTCATTTCATAAAAGAATTCTTTTTGTTACGACATACGCTTTTGCGTTTTTTTATCGAAGATCTAGGTTTTACTACGTTTGCTTTTGAATTTGGTTTTGCTGAGGGTCAAATCATCAATAACTGGATACATGGACAAGGAACTGACGATGAAATAGGCAGATTCTTAAAACACTTCTATTATCCAGAAGAGCTCAAAACCACATTTCTATGGCTAAGGGAGTACAATAAAGCAGCAAAAGAAAAAATCACATTTCTTGGCATTGATATACCCAGAAATGGAGGTTCATACTTACCAAATATGGAGATAGTGCATGACTTTTTTAGAACAGCGGATAAAGAAGCACTACACATTATCGATGATGCATTTAATATTGCAAAAAAGATTGATTACTTCTCCACATCACAGGCAGCCTTAAATTTACATGAGCTAACAGATTCTGAGAAATGCCGTTTAACTAGCCAATTAGCTCGAGTAAAAGTTCGCCTTGAAGCTATGGCTCCAATTCACATTGAAAAATATGGGATTGATAAATATGAGACAATTCTGCATTATGCCAACGGTATGATATACTTGGACTATAACATTCAAGCTATGTCGGGCTTTATTTCAGGAGGCGGAATGCAGGGCGATATGGGTGCAAAAGACAAATACATGGCAGATTCTGTGCTGTGGCATTTAAAAAACCCACAAAGTGAGCAGAAAGTGATAGTAGTAGCACATAATGCACATATTCAAAAAACACCCATTCTGTATGATGGATTTCTAAGTTGCCTACCAATGGGCCAAAGACTTAAAAATGCCATTGGTGATGATTATATGTCTTTAGGTATTACTTCTTATAGTGGGCATACTGCAGCCCTCTATCCGGAAGTTGATACAAAATATGGTTTTCGAGTTGATAACTTCCAACTGCAGGAACCAAATGAAGGTTCTGTCGAGAAAGCTATTTCTGGTTGTGGAGTTACTAATTCTTTTGTCTTTTTTAGAAATATTCCTGAAGATTTACAATCCATCCCGAACATGATTCGATTTGATTCTATTTACATGAAAGCAGAACTCGAGAAAGCTTTCGATGGAATATTTCAAATTGAAAAGTCATCTGTATCTGAGGTCGTTTATGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000363","ARO_id":"36502","ARO_name":"EreB","CARD_short_name":"EreB","ARO_description":"EreB is an erythromycin esterase-like protein that hydrolyses the drug's lactone ring.","ARO_category":{"36459":{"category_aro_accession":"3000320","category_aro_cvterm_id":"36459","category_aro_name":"macrolide esterase","category_aro_description":"Hydrolytic enzymes that cleave the macrocycle lactone ring of macrolide antibiotics.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35946":{"category_aro_accession":"0000027","category_aro_cvterm_id":"35946","category_aro_name":"roxithromycin","category_aro_description":"Roxithromycin is a semi-synthetic, 14-carbon ring macrolide antibiotic derived from erythromycin. It is used to treat respiratory tract, urinary and soft tissue infections. Roxithromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35982":{"category_aro_accession":"0000065","category_aro_cvterm_id":"35982","category_aro_name":"clarithromycin","category_aro_description":"Clarithromycin is a methyl derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome and is used to treat pharyngitis, tonsillitis, acute maxillary sinusitis, acute bacterial exacerbation of chronic bronchitis, pneumonia (especially atypical pneumonias associated with Chlamydia pneumoniae or TWAR), and skin structure infections.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1922":{"model_id":"1922","model_name":"marA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"230"}},"model_sequences":{"sequence":{"5219":{"protein_sequence":{"accession":"BAA15221.2","sequence":"MSRRNTDAITIHSILDWIEDNLESPLSLEKVSERSGYSKWHLQRMFKKETGHSLGQYIRSRKMTEIAQKLKESNEPILYLAERYGFESQQTLTRTFKNYFDVPPHKYRMTNMQGESRFLHPLNHYNS"},"dna_sequence":{"accession":"AP009048.1","fmin":"1621287","fmax":"1621671","strand":"+","sequence":"ATGTCCAGACGCAATACTGACGCTATTACCATTCATAGCATTTTGGACTGGATCGAGGACAACCTGGAATCGCCACTGTCACTGGAGAAAGTGTCAGAGCGTTCGGGTTACTCCAAATGGCACCTGCAACGGATGTTTAAAAAAGAAACCGGTCATTCATTAGGCCAATACATCCGCAGCCGTAAGATGACGGAAATCGCGCAAAAGCTGAAGGAAAGTAACGAGCCGATACTCTATCTGGCAGAACGATATGGCTTCGAGTCGCAACAAACTCTGACCCGAACCTTCAAAAATTACTTTGATGTTCCGCCGCATAAATACCGGATGACCAATATGCAGGGCGAATCGCGCTTTTTACATCCATTAAATCATTACAACAGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36839","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. W3110","NCBI_taxonomy_id":"316407"}}}},"ARO_accession":"3000263","ARO_id":"36402","ARO_name":"marA","CARD_short_name":"marA","ARO_description":"In the presence of antibiotic stress, E. coli overexpresses the global activator protein MarA, which besides inducing MDR efflux pump AcrAB, also down- regulates synthesis of the porin OmpF.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"41445":{"category_aro_accession":"3004281","category_aro_cvterm_id":"41445","category_aro_name":"General Bacterial Porin with reduced permeability to beta-lactams","category_aro_description":"These are GBPs that are associated with decreased susceptibility to beta-lactams either through mutations in the porin protein, absence of the porin protein, or expression of the porin protein.","category_aro_class_name":"AMR Gene Family"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"37084":{"category_aro_accession":"3000704","category_aro_cvterm_id":"37084","category_aro_name":"cefalotin","category_aro_description":"Cefalotin is a semisynthetic cephalosporin antibiotic activate against staphylococci. It is resistant to staphylococci beta-lactamases but hydrolyzed by enterobacterial beta-lactamases.","category_aro_class_name":"Antibiotic"},"37250":{"category_aro_accession":"3000870","category_aro_cvterm_id":"37250","category_aro_name":"triclosan","category_aro_description":"Triclosan is a common antibacterial agent added to many consumer products as a biocide.  It is an inhibitor of fatty acid biosynthesis by blocking enoyl-carrier protein reductase (FabI).","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"43746":{"category_aro_accession":"3005386","category_aro_cvterm_id":"43746","category_aro_name":"disinfecting agents and antiseptics","category_aro_description":"Disinfectants that can also interact with antimicrobial resistance mechanisms, e.g. molecule efflux, and thus are the targets of disinfectant resistance.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"},"36383":{"category_aro_accession":"3000244","category_aro_cvterm_id":"36383","category_aro_name":"reduced permeability to antibiotic","category_aro_description":"Reduction in permeability to antibiotic, generally through reduced production of porins, can provide resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1923":{"model_id":"1923","model_name":"APH(3'')-Ia","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"91":{"protein_sequence":{"accession":"CAA37605.1","sequence":"MSDHPGPGAVTPELFGVGGDWLAVTAGESGASVFRAADATRYAKCVPAADAAGLEAERDRIAWLSGQGVPGPRVLDWYAGDAGACLVTRAVPGVPADRVGADDLRTAWGAVADAVRRLHEVPVASCPFRRGLDSVVDAARDVVARGAVHPEFLPVEQRLVPPAELLARLTGELARRRDQEAADTVVCHGDLCLPNIVLHPETLEVSGFIDLGRLGAADRHADLALLLANARETWVDEERARFADAAFAERYGIAPDPERLRFYLHLDPLTWG"},"dna_sequence":{"accession":"X53527.1","fmin":"0","fmax":"819","strand":"+","sequence":"ATGAGTGATCACCCCGGGCCGGGGGCCGTCACGCCGGAGCTGTTCGGCGTGGGCGGCGACTGGCTGGCCGTCACCGCGGGCGAATCGGGCGCCTCCGTCTTTCGCGCCGCGGACGCCACCCGGTACGCCAAGTGCGTGCCCGCCGCGGACGCGGCCGGTCTTGAGGCGGAACGCGACCGGATCGCCTGGCTGAGCGGGCAGGGCGTACCGGGCCCCCGCGTCCTCGACTGGTACGCCGGTGACGCGGGCGCCTGCCTGGTCACCCGTGCCGTCCCCGGCGTACCCGCTGATCGGGTGGGCGCCGATGACCTTCGCACTGCCTGGGGGGCCGTCGCGGACGCGGTCCGTCGGCTGCACGAGGTGCCCGTGGCCTCGTGTCCGTTCCGCCGGGGGCTGGACTCCGTGGTCGACGCCGCCCGTGACGTGGTGGCCCGTGGCGCGGTGCATCCGGAGTTCCTGCCGGTGGAGCAGCGGCTCGTTCCCCCGGCGGAGCTGCTGGCCCGGCTCACCGGGGAGCTCGCCCGTCGGCGCGATCAGGAGGCCGCCGACACGGTCGTCTGCCACGGTGATCTCTGCCTGCCCAACATCGTCCTCCATCCGGAGACCCTGGAGGTGTCGGGCTTCATCGACCTGGGACGGCTCGGGGCGGCCGACCGCCACGCCGACCTGGCGCTGCTGCTGGCCAACGCGCGCGAGACCTGGGTGGACGAGGAGCGGGCGCGGTTCGCCGACGCGGCGTTCGCCGAGCGTTACGGCATCGCCCCGGACCCGGAACGGCTGCGCTTCTACCTCCATCTCGATCCGCTCACCTGGGGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36903","NCBI_taxonomy_name":"Streptomyces griseus","NCBI_taxonomy_id":"1911"}}}},"ARO_accession":"3002638","ARO_id":"39038","ARO_name":"APH(3'')-Ia","CARD_short_name":"APH(3'')-Ia","ARO_description":"APH(3'')-Ia is a chromosomal-encoded aminoglycoside phosphotransferase in S. griseus.","ARO_category":{"36266":{"category_aro_accession":"3000127","category_aro_cvterm_id":"36266","category_aro_name":"APH(3'')","category_aro_description":"A category of aminoglycoside O-phosphotransferase enzymes with modification regiospecificity based at the 3''-hydroxyl group of the respective antibiotic. These enzymes are characterized by enzymatic antibiotic inactivation, specifically of streptomycin, by the ATP-dependent phosphorylation of the 3''-hydroxyl group of the compound.","category_aro_class_name":"AMR Gene Family"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1924":{"model_id":"1924","model_name":"vanM","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"350"}},"model_sequences":{"sequence":{"651":{"protein_sequence":{"accession":"ACL82961.1","sequence":"MNRLKIAILFGGCSEEHNVSVKSAAEIANNIDIGKYEPIYIGITQSGVWKTCEKPCIDWDNEHCRSAVLSPDKKMHGLLIMQDKGYQIQRIDVVFSVLHGKSGEDGAIQGLFELSGIPYVGCDIQSSAVCMDKSLAYIIAKNAGIATPEFQVIYKDDKPAADSFTYPVFVKPARSGSSYGVNKVNSADELDSAIDLARQYDSKILIEQGVLGYEVGCAVLGNSFDLIVGEVDQIRLQHGIFRIHQEAEPEKGSENATITVPAELSAEERERIKEAAKNIYKALGCRGLSRVDMFLQDNGRIVLNEVNTMPGFTSYSRYPRMMVSAGITIPELIDHLIVLAVKE"},"dna_sequence":{"accession":"FJ349556.1","fmin":"4856","fmax":"5888","strand":"+","sequence":"ATGAATAGATTGAAAATAGCCATCCTGTTTGGGGGTTGCTCAGAAGAGCATAATGTATCGGTAAAATCAGCGGCAGAGATTGCCAACAACATTGATATAGGAAAATATGAACCAATATACATCGGAATAACCCAATCTGGCGTTTGGAAAACATGCGAAAAACCATGTATAGATTGGGATAATGAACACTGTCGCTCGGCAGTACTTTCTCCGGATAAAAAAATGCATGGGTTGCTTATTATGCAAGATAAAGGATATCAAATACAGCGTATAGATGTAGTCTTTTCAGTGTTGCACGGAAAATCGGGTGAAGACGGCGCCATACAAGGATTATTTGAATTGTCTGGTATACCTTATGTAGGCTGTGATATTCAAAGTTCGGCGGTTTGTATGGACAAATCACTGGCATATATTATTGCGAAAAACGCTGGCATAGCTACTCCTGAATTTCAGGTCATTTATAAAGACGATAAGCCAGCGGCAGATTCGTTTACCTATCCCGTTTTTGTTAAGCCAGCACGTTCAGGTTCCTCCTATGGTGTGAATAAAGTTAATAGTGCGGATGAATTGGACTCCGCAATTGACTTGGCAAGACAATATGACAGCAAAATCCTAATTGAGCAGGGTGTTTTAGGTTATGAGGTCGGTTGTGCCGTATTGGGAAACAGTTTCGACTTGATTGTTGGTGAAGTGGATCAAATCAGACTGCAACACGGTATTTTTCGTATTCATCAGGAAGCCGAGCCGGAAAAAGGTTCTGAAAACGCAACTATAACCGTTCCCGCAGAACTATCGGCAGAGGAGCGAGAACGGATAAAAGAAGCGGCAAAAAATATATATAAGGCGCTCGGGTGTAGAGGTCTTTCTCGTGTTGATATGTTTTTACAAGATAACGGCCGCATTGTACTAAATGAAGTCAATACCATGCCTGGTTTCACGTCATACAGCCGTTATCCACGTATGATGGTCTCAGCAGGTATAACAATTCCCGAACTGATTGACCATCTGATTGTATTAGCTGTAAAGGAGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36779","NCBI_taxonomy_name":"Enterococcus faecium","NCBI_taxonomy_id":"1352"}}}},"ARO_accession":"3002911","ARO_id":"39345","ARO_name":"vanM","CARD_short_name":"vanM","ARO_description":"VanM is a D-Ala-D-Ala ligase homolog that can synthesize D-Ala-D-Lac, an alternative substrate for peptidoglycan synthesis that reduces vancomycin binding affinity. It is associated with both vancomycin and teicoplanin resistance.","ARO_category":{"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"39340":{"category_aro_accession":"3002906","category_aro_cvterm_id":"39340","category_aro_name":"Van ligase","category_aro_description":"Van ligases synthesize alternative substrates for peptidoglycan synthesis that reduce vancomycin binding affinity.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"35948":{"category_aro_accession":"0000029","category_aro_cvterm_id":"35948","category_aro_name":"teicoplanin","category_aro_description":"Teicoplanin is a glycopeptide antibiotic used in the prophylaxis and treatment of serious infections caused by Gram-positive bacteria. Teicoplanin has a unique acyl-aliphatic chain, and binds to cell wall precursors to inhibit transglycosylation  and transpeptidation.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1926":{"model_id":"1926","model_name":"CMY-34","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1993":{"protein_sequence":{"accession":"ABN51006.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGISLLHLATYTAGGLPLQIPDDVTDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"EF394370.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCAGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTACGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTAGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002045","ARO_id":"38445","ARO_name":"CMY-34","CARD_short_name":"CMY-34","ARO_description":"CMY-34 is a beta-lactamase found in Escherichia coli.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1927":{"model_id":"1927","model_name":"SHV-29","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"2024":{"protein_sequence":{"accession":"AAG49894.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGSVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAAERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AF301532.1","fmin":"7","fmax":"868","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCAGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGTTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGCCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGGATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001087","ARO_id":"37467","ARO_name":"SHV-29","CARD_short_name":"SHV-29","ARO_description":"SHV-29 is an extended-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1928":{"model_id":"1928","model_name":"OXA-50","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"1935":{"protein_sequence":{"accession":"AAQ76277.1","sequence":"MRPLLFSALLLLSGHTQASEWNDSQAVDKLFGAAGVKGTFVLYDVQRQRYVGHDRERAETRFVPASTYKVANSLIGLSTGAVRSADEVLPYGGKPQRFKAWEHDMSLRDAIKASNVPVYQELARRIGLERMRANVSRLGYGNAEIGQVVDNFWLVGPLKISAMEQTRFLLRLAQGELPFPAPVQSTVRAMTLLESGPGWELHGKTGWCFDCTPELGWWVGWVKRNERLYGFALNIDMPGGEADIGKRVELGKASLKALGILP"},"dna_sequence":{"accession":"AY306130.1","fmin":"0","fmax":"789","strand":"+","sequence":"ATGCGCCCTCTCCTCTTCAGTGCCCTTCTCCTGCTTTCCGGGCATACCCAGGCCAGCGAATGGAACGACAGCCAGGCCGTGGACAAGCTATTCGGCGCGGCCGGGGTGAAAGGCACCTTCGTCCTCTACGATGTGCAGCGGCAGCGCTATGTTGGCCATGACCGGGAGCGCGCGGAAACCCGCTTCGTTCCCGCTTCCACCTACAAGGTGGCGAACAGCCTGATCGGCTTATCCACAGGGGCGGTTAGATCCGCCGACGAGGTTCTTCCCTATGGCGGCAAGCCCCAGCGCTTCAAGGCCTGGGAGCACGACATGAGCCTGCGCGACGCGATCAAGGCATCGAACGTACCGGTCTACCAGGAACTGGCGCGGCGCATCGGCCTGGAGCGGATGCGCGCCAATGTCTCGCGCCTGGGTTACGGCAACGCGGAAATCGGCCAGGTTGTGGATAACTTCTGGTTGGTGGGACCGCTGAAGATCAGCGCGATGGAACAGACCCGCTTTCTGCTCCGACTGGCGCAGGGAGAATTGCCATTCCCCGCCCCGGTGCAGTCCACCGTGCGCGCCATGACCCTGCTGGAAAGCGGCCCGGGCTGGGAGCTGCACGGCAAGACCGGCTGGTGCTTCGACTGCACGCCGGAACTCGGCTGGTGGGTGGGCTGGGTGAAGCGCAACGAGCGGCTCTACGGCTTCGCCCTGAACATCGACATGCCCGGCGGCGAGGCCGACATCGGCAAGCGCGTCGAACTGGGCAAGGCCAGTCTCAAGGCTCTCGGGATACTGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3001796","ARO_id":"38196","ARO_name":"OXA-50","CARD_short_name":"OXA-50","ARO_description":"OXA-50 is a beta-lactamase found in Pseudomonas aeruginosa. It confers decreased susceptibility to ampicillin and ticarcillin and, interestingly, to moxalactam and meropenem in P. aeruginosa but not in E. coli. Also confers resistance to piperacillin-tazobactam and cephalotin.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46513":{"category_aro_accession":"3007724","category_aro_cvterm_id":"46513","category_aro_name":"OXA-50-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-50.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"37084":{"category_aro_accession":"3000704","category_aro_cvterm_id":"37084","category_aro_name":"cefalotin","category_aro_description":"Cefalotin is a semisynthetic cephalosporin antibiotic activate against staphylococci. It is resistant to staphylococci beta-lactamases but hydrolyzed by enterobacterial beta-lactamases.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1929":{"model_id":"1929","model_name":"ACT-24","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"779":{"protein_sequence":{"accession":"AHL39336.1","sequence":"MMKKSLCCALLLGISCSALAAPVSEKQLAEVVANTITPLMKAQSIPGMAVAVIYQGKPHYYTFGKADIAASKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNAALLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMGYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPENVADASLKQGISLAQSRYWRIGSMYQGLGWEMLNWPVEANTVIDGSDSKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANKSYPNPARVEAAYHILDALQ"},"dna_sequence":{"accession":"KJ207207.1","fmin":"479","fmax":"1625","strand":"+","sequence":"ATGATGAAAAAATCTCTTTGCTGCGCCCTGCTGCTCGGCATCTCTTGCTCTGCTCTCGCCGCGCCAGTGTCAGAAAAACAGCTGGCGGAGGTGGTCGCGAATACGATTACCCCGCTGATGAAAGCCCAGTCGATTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGTAAACCGCACTATTATACGTTTGGCAAAGCCGATATCGCGGCCAGCAAACCCGTTACGCCTCAGACTCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGGGTTTTAGGAGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTGACGGGCAAGCAGTGGCAGGGGATTCGTATGCTGGATCTCGCAACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAATGCCGCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGTATCGGTCTTTTTGGCGCGCTGGCGGTCAAACCTTCCGGCATGGGCTATGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTTCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGAATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCGGAGAACGTTGCTGATGCCTCACTTAAGCAGGGCATCTCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGATCGACGGCAGCGACAGTAAGGTGGCGCTGGCACCGCTGCCCGTGGCAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGCTCTACTGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCGACGCGCTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3001844","ARO_id":"38244","ARO_name":"ACT-24","CARD_short_name":"ACT-24","ARO_description":"ACT-24 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1930":{"model_id":"1930","model_name":"CTX-M-29","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1862":{"protein_sequence":{"accession":"AAP22736.1","sequence":"MVKKSLRQFTLMATAAVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVDGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTNGL"},"dna_sequence":{"accession":"AY267213.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAGCCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGGGTGGCATTGATTAACACTGCGGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTGGTTAACTATAATCCGATTGCGGAAAAGCACGTCGATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCAACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001891","ARO_id":"38291","ARO_name":"CTX-M-29","CARD_short_name":"CTX-M-29","ARO_description":"CTX-M-29 is a beta-lactamase found in the Enterobacteriaceae family.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1931":{"model_id":"1931","model_name":"TEM-150","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"926":{"protein_sequence":{"accession":"CAJ66089.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPDTLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AM183304.1","fmin":"208","fmax":"1069","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGATACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001017","ARO_id":"37397","ARO_name":"TEM-150","CARD_short_name":"TEM-150","ARO_description":"TEM-150 is a beta-lactamase found in Enterobacter spp., E. coli, and Klebsiella pneumoniae.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1932":{"model_id":"1932","model_name":"IMP-32","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1339":{"protein_sequence":{"accession":"AFR33816.1","sequence":"MKKLFVLCVFFFCNIAVAEESLPDLKIEKLEEGVYVHTSFEEVKGWSVVTKHGLVVLVKNDAYLIDTPITAKDTEKLVNWFVERGYKIKGSISTHFHGDSTAGIEWLNSQSIPTYASELTNELLKKDNKVQAKHSFYGVSYSLIKNKIEVFYPGPGHTQDNVVVWLPEKKILFGGCFVKPDGLGYLGDANLEAWPKSAKILMSKYGKAKLVVSSHSDIGDVSLLKRTWEQAVKGLNESKKSSQPSD"},"dna_sequence":{"accession":"JQ002629.1","fmin":"113","fmax":"854","strand":"+","sequence":"ATGAAAAAATTATTTGTTTTATGTGTATTCTTCTTCTGCAACATTGCAGTTGCAGAAGAATCTTTGCCTGATTTAAAAATTGAGAAGCTTGAAGAAGGCGTTTATGTTCATACTTCGTTTGAAGAAGTTAAAGGTTGGAGTGTGGTCACTAAACACGGTTTGGTGGTTCTTGTGAAAAATGACGCCTATCTGATTGATACTCCAATTACTGCTAAAGATACTGAAAAATTAGTCAATTGGTTTGTTGAGCGGGGCTATAAAATCAAAGGCAGTATTTCCACACATTTCCATGGTGACAGTACGGCTGGAATAGAGTGGCTTAATTCTCAATCTATCCCCACATATGCTTCTGAATTAACAAATGAACTTCTTAAAAAAGACAATAAGGTACAAGCTAAACACTCTTTTTATGGGGTTAGTTATTCACTAATAAAAAACAAAATTGAAGTTTTTTATCCAGGCCCAGGGCACACTCAAGATAACGTAGTGGTTTGGTTACCTGAAAAGAAAATTTTATTCGGTGGTTGCTTTGTTAAACCGGACGGTCTTGGCTATTTGGGGGACGCAAATTTAGAAGCTTGGCCAAAGTCCGCTAAAATATTAATGTCTAAATATGGTAAAGCAAAACTAGTTGTGTCGAGTCATAGTGATATTGGAGATGTATCACTCTTGAAACGTACATGGGAGCAGGCTGTTAAAGGGCTGAATGAAAGTAAAAAATCATCACAGCCAAGCGACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002223","ARO_id":"38623","ARO_name":"IMP-32","CARD_short_name":"IMP-32","ARO_description":"IMP-32 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1933":{"model_id":"1933","model_name":"SHV-160","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1944":{"protein_sequence":{"accession":"AFQ23966.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSEGQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGASKRGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"JX121127.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAGGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTAGCAAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001199","ARO_id":"37579","ARO_name":"SHV-160","CARD_short_name":"SHV-160","ARO_description":"SHV-160 is a beta-lactamase.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1934":{"model_id":"1934","model_name":"lnuD","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"153":{"protein_sequence":{"accession":"ABR14060.1","sequence":"MVNKADAIEIILYAEENEIDIWLDGGWGVDALLGEETRSHNDIDLFVEEKNGKTFIEILKEKGFTEVIEAYTTTDHTVWKDDKDRIIDLHVFEFNEQGDLVFEGESYPSNVFSGIGKIGNKVVKCIDAENQVLFHLGYEHDENDVHDVRLLCERYNIPVPSEYK"},"dna_sequence":{"accession":"EF452177.1","fmin":"0","fmax":"495","strand":"+","sequence":"ATGGTAAATAAAGCAGATGCTATTGAGATAATTTTATATGCCGAAGAAAATGAGATTGACATTTGGCTAGATGGTGGTTGGGGGGTTGATGCTCTATTAGGAGAAGAAACAAGGTCCCACAACGATATTGATTTATTTGTAGAAGAAAAAAACGGCAAAACGTTTATTGAAATATTGAAAGAAAAAGGCTTTACCGAAGTTATTGAAGCTTATACCACTACAGATCACACGGTTTGGAAGGACGATAAAGACAGGATAATCGATCTTCATGTATTTGAATTCAACGAACAAGGAGACCTTGTTTTTGAAGGAGAATCGTATCCATCAAACGTGTTTAGTGGAATTGGGAAAATAGGTAACAAAGTTGTAAAATGTATAGATGCTGAAAATCAGGTTTTATTTCACCTGGGATATGAGCATGATGAAAATGATGTTCATGACGTAAGGTTATTATGCGAGAGATATAATATTCCTGTTCCTAGTGAATACAAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36887","NCBI_taxonomy_name":"Streptococcus uberis","NCBI_taxonomy_id":"1349"}}}},"ARO_accession":"3002838","ARO_id":"39272","ARO_name":"lnuD","CARD_short_name":"lnuD","ARO_description":"lnuD is a plasmid-mediated nucleotidyltransferase found in Streptococcus uberis.","ARO_category":{"36360":{"category_aro_accession":"3000221","category_aro_cvterm_id":"36360","category_aro_name":"lincosamide nucleotidyltransferase (LNU)","category_aro_description":"Resistance to the lincosamide antibiotic by ATP-dependent modification of the 3' and\/or 4'-hydroxyl groups of the methylthiolincosamide sugar.","category_aro_class_name":"AMR Gene Family"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1936":{"model_id":"1936","model_name":"CTX-M-43","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1820":{"protein_sequence":{"accession":"AAZ14955.1","sequence":"MMTQSIRRSMLTVMATLPLLFSSATLHAQANSVQQQLEALEKSSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKQSESDKHLLNQRVEIKKSDLVNYNPIAEKHVNGTMTLAELGAAALQYSDNTAMNKLIAHLGGPDKVTAFARSLGDETFRLDRTEPTLNTAIPGDPRDTTTPLAMAQTLKNLTLGKALAETQRAQLVTWLKGNTTGSASIRAGLPKSWVVGDKTGSGGYGTTNDIAVIWPENHAPLVLVTYFTQPEQKAERRRDILAAAAKIVTHGF"},"dna_sequence":{"accession":"DQ102702.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGATGACTCAGAGCATTCGCCGCTCAATGTTAACGGTGATGGCGACGCTACCCCTGCTATTTAGCAGCGCAACGCTGCATGCGCAGGCGAACAGCGTGCAACAGCAGCTGGAAGCCCTGGAGAAAAGTTCGGGAGGTCGGCTTGGCGTTGCGCTGATTAACACCGCCGATAATTCGCAGATTCTCTACCGTGCCGATGAACGTTTTGCGATGTGCAGTACCAGTAAGGTGATGGCGGCCGCGGCGGTGCTTAAACAGAGCGAGAGCGATAAGCACCTGCTAAATCAGCGCGTTGAAATCAAGAAGAGCGACCTGGTTAACTACAATCCCATTGCGGAGAAACACGTTAACGGCACGATGACGCTGGCTGAGCTTGGCGCAGCGGCGCTGCAGTATAGCGACAATACTGCCATGAATAAGCTGATTGCCCATCTGGGTGGTCCCGATAAAGTGACGGCGTTTGCTCGCTCGTTGGGTGATGAGACCTTCCGTCTGGACAGAACCGAGCCCACGCTCAATACCGCCATTCCAGGCGACCCGCGTGATACCACCACGCCGCTCGCGATGGCGCAGACCCTGAAAAATCTGACGCTGGGTAAAGCGCTGGCGGAAACTCAGCGGGCACAGTTGGTGACGTGGCTTAAGGGCAATACTACCGGTAGCGCGAGCATTCGGGCGGGTCTGCCGAAATCATGGGTAGTGGGCGATAAAACCGGCAGCGGAGGTTATGGCACCACCAACGATATCGCGGTTATCTGGCCGGAAAACCACGCACCGCTGGTTCTGGTGACCTACTTTACCCAACCGGAGCAGAAGGCGGAAAGGCGTCGGGATATTCTGGCTGCGGCGGCGAAAATCGTAACCCACGGTTTCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001905","ARO_id":"38305","ARO_name":"CTX-M-43","CARD_short_name":"CTX-M-43","ARO_description":"CTX-M-43 is a beta-lactamase found in Pseudomonas aeruginosa and Acinetobacter spp.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1937":{"model_id":"1937","model_name":"OXA-118","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"965":{"protein_sequence":{"accession":"AAK55330.1","sequence":"MAIRFLTILLSTFFLTSFVHAQEHVLERSDWKKFFSDLRAEGAIVISDERQAEHALLVFGQERAAKRYSPASTFKLPHTLFALDADAVRDEFQVFRWDGVKRSFAGHNQDQDLRSAMRNSAVWVYELFAKEIGKDKARHYLKQIDYGNADPSTIKGDYWIDGNLEISAHEQISFLRKLYRNQLPFQVEHQRLVKDLMITEAGRNWILRAKTGWEGRFGWWVGWVEWPTGPVFFALNIDTPNRTDDLFKREAIARAILRSIDALPPN"},"dna_sequence":{"accession":"AF371964.1","fmin":"118","fmax":"919","strand":"+","sequence":"ATGGCAATCCGATTCCTCACCATACTGCTATCTACTTTTTTTCTTACCTCATTCGTGCATGCGCAAGAACACGTGCTAGAGCGTTCTGACTGGAAGAAGTTCTTCAGCGACCTCCGGGCCGAAGGTGCAATCGTTATTTCAGACGAACGTCAAGCGGAGCATGCTTTATTGGTTTTTGGTCAAGAGCGAGCAGCAAAGCGTTACTCGCCTGCTTCAACCTTCAAGCTTCCACACACACTTTTTGCACTCGATGCAGACGCCGTTCGTGATGAGTTCCAGGTTTTTCGATGGGACGGCGTTAAACGGAGCTTTGCGGGCCATAATCAAGACCAAGACTTGCGATCAGCGATGCGAAATTCTGCGGTCTGGGTTTATGAGCTATTTGCAAAAGAGATCGGAAAGGACAAAGCAAGACACTATTTAAAGCAAATTGATTATGGCAACGCCGACCCTTCGACAATCAAGGGCGATTACTGGATAGATGGCAATCTTGAAATCTCAGCGCACGAACAGATTTCGTTTCTCAGAAAACTCTATCGAAATCAGCTGCCATTTCAGGTGGAACATCAGCGCTTGGTCAAAGATCTCATGATTACGGAAGCCGGGCGCAACTGGATACTACGCGCAAAGACCGGCTGGGAAGGCAGGTTTGGCTGGTGGGTAGGGTGGGTGGAGTGGCCAACCGGTCCCGTATTCTTCGCGCTGAATATTGATACGCCAAACAGAACGGATGATCTTTTCAAAAGAGAGGCAATCGCGCGGGCAATCCTTCGCTCTATCGACGCATTGCCGCCCAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36822","NCBI_taxonomy_name":"Burkholderia cepacia","NCBI_taxonomy_id":"292"}}}},"ARO_accession":"3001768","ARO_id":"38168","ARO_name":"OXA-118","CARD_short_name":"OXA-118","ARO_description":"OXA-118 is a beta-lactamase found in Burkholderia cepacia.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46509":{"category_aro_accession":"3007720","category_aro_cvterm_id":"46509","category_aro_name":"OXA-46-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-46.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1938":{"model_id":"1938","model_name":"mtrD","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"2130"}},"model_sequences":{"sequence":{"5285":{"protein_sequence":{"accession":"AAF42062.1","sequence":"MAKFFIDRPIFAWVISIFIIAAGIFGIKSLPVSQYPSVAAPTITLRATYPGASAQVMEDSVLSVIERNMNGVEGLDYMSTSADSSGSGSVSLTFTPDTDENLAQVEVQNKLSEVLSTLPATVQQYGVTVSKARSNFLMIVMLSSDVQSTEEMNDYAQRNIVPELQRIEGVGQVRLFGAQRAMRIWVDPKKLQNYNLSFADVGSALSAQNVQISAGSIGSLPAVRGQTVTATVTAQGQLGTAEEFGNVILRANTDGSNVYLKDVARVGLGMEDYSSSTRLNGVNTTGMAVMLSNSGNAMATAKAVKERMATLEKYFPQGMSWKTPYDTSKFVEISIEKVIHTLIEAMVLVFVVMYLFLQNIRYTLIPTIVVPISLLGGFAFISYMGMSINVLTMFAMVLVIGIVVDDAIVVVENVERIMAGEGLPPKEATKKAMGQISGAVIGITAVLISVFVPLAMFSGATGNIYKQFALTMASSIAFSAFLALTLTPALCATMLKTIPKGHHEEKKGFFGWFNKKFNSWTHGYEGRVAKVLRKTFRMMVVYIGLAVVGVFLFMRLPTSFLPTEDQGFVMVSVQLPAGATQERTNATLAQVTQLAKSIPEIENIITVSGFSFSGSGQNMAMGFAILKDWNERTAPGSDAVAIAGKLTGMMMGTLKDGFGIAVVPPPILELGNGSGLSINLQDRNNTGHTALLAKRNELIQKMRASGLFDPSTVRAGGLEDSPQLKIDINRAAAAAQGISFADIRTALASALSSSYVSDFPNQGRLQRVMVQADEDARMQPADILNLTVPNKSGVAVPLSTIATVSWENGTEQSVRFNGYPSMKLSASPATGVSTGQAMAAVQKMVDELGGGYSLEWGGQSREEAKGGSQTLILYGLAVAAVFLVLAALYESWSIPLAVILVIPLGLIGAAAGVTGRNLFEGLLGSVPSFANDIYFQVGFVTVMGLSAKNAILIIEFAKDLQAQGKSAVEAALEAARLRFRPIIMTSFAFILGVVPLYIAGGASSASQRAIGTTVFWGMLIGTLLSVFLVPLFYVVVRKFFKETAHEHEMAVKHAAEAGITGSDDSQH"},"dna_sequence":{"accession":"AE002098.2","fmin":"1791966","fmax":"1795170","strand":"-","sequence":"ATGGCTAAATTTTTTATCGACCGCCCCATTTTTGCGTGGGTTATTTCGATTTTCATTATTGCGGCGGGTATTTTCGGCATCAAAAGCCTGCCGGTTTCGCAATATCCGTCCGTCGCCGCCCCGACCATCACCCTGAGGGCCACTTATCCGGGCGCGTCCGCGCAGGTAATGGAAGACAGCGTGCTTTCCGTGATCGAGCGGAATATGAACGGCGTGGAAGGTTTGGATTATATGTCCACTTCCGCCGATTCGAGCGGCAGCGGCAGCGTGAGCCTGACCTTTACGCCCGATACCGACGAGAATCTGGCGCAGGTGGAAGTGCAGAACAAGCTTTCCGAAGTATTGAGCACGCTGCCGGCAACTGTCCAGCAATACGGCGTAACCGTATCCAAGGCGCGTTCCAATTTCCTGATGATTGTGATGCTTTCGTCGGATGTGCAGTCAACCGAAGAGATGAACGACTACGCGCAGCGTAATATCGTTCCCGAGTTGCAGCGTATCGAAGGCGTGGGGCAGGTACGCCTGTTCGGCGCGCAACGCGCGATGCGGATTTGGGTTGATCCTAAGAAACTGCAAAACTACAATTTGTCGTTTGCCGATGTTGGCAGCGCGCTGTCCGCCCAGAACGTCCAGATTTCAGCGGGTTCTATCGGTTCGCTTCCCGCCGTTCGCGGACAGACGGTTACGGCTACCGTAACGGCGCAAGGGCAGTTGGGTACGGCAGAAGAATTCGGCAACGTCATCCTCCGCGCCAATACCGACGGTTCTAATGTTTACCTGAAGGATGTGGCAAGGGTCGGACTGGGTATGGAAGACTATTCTTCCTCAACCCGTCTGAACGGTGTAAATACCACCGGTATGGCGGTGATGCTGTCCAACAGCGGCAATGCGATGGCGACGGCAAAGGCGGTTAAAGAACGCATGGCGACGTTGGAAAAATACTTTCCTCAGGGTATGAGCTGGAAAACCCCTTACGATACTTCCAAATTCGTCGAAATTTCGATTGAAAAAGTGATTCACACTTTAATCGAAGCGATGGTGCTGGTGTTTGTCGTAATGTATCTCTTCCTGCAAAACATCCGTTATACGCTGATTCCGACCATCGTCGTACCGATTTCGCTGTTGGGCGGTTTCGCCTTCATCTCTTATATGGGCATGTCGATTAACGTACTGACCATGTTTGCGATGGTTTTGGTCATCGGCATCGTGGTCGATGACGCGATTGTGGTGGTTGAAAACGTCGAGCGCATTATGGCGGGTGAAGGCTTGCCGCCCAAAGAAGCGACCAAAAAAGCGATGGGTCAGATTTCGGGCGCGGTCATCGGTATTACCGCCGTTCTGATTTCCGTGTTCGTACCGTTGGCGATGTTCAGCGGGGCGACGGGCAATATTTACAAACAGTTTGCCCTGACGATGGCGTCATCAATCGCATTCTCCGCCTTCCTTGCGCTGACCCTTACCCCTGCTTTGTGTGCCACAATGTTGAAGACAATCCCGAAAGGGCATCACGAAGAGAAAAAAGGTTTCTTCGGCTGGTTTAACAAGAAATTCAACAGTTGGACGCACGGTTACGAAGGCCGGGTTGCCAAAGTGCTGCGTAAGACTTTCCGCATGATGGTTGTCTATATCGGCTTGGCGGTTGTGGGCGTGTTCCTGTTTATGCGCCTGCCGACTTCATTCCTGCCGACCGAAGACCAAGGCTTCGTCATGGTCAGCGTGCAACTGCCTGCAGGAGCGACCCAAGAGCGCACCAATGCGACTTTGGCGCAAGTTACCCAACTGGCGAAAAGCATTCCTGAAATAGAAAACATCATTACCGTTTCCGGCTTCAGCTTTTCGGGCAGCGGTCAGAATATGGCGATGGGTTTTGCCATATTGAAAGATTGGAACGAGCGTACCGCGCCCGGCAGCGATGCCGTTGCGATTGCCGGCAAGCTGACGGGTATGATGATGGGGACGCTTAAAGACGGTTTTGGCATCGCCGTCGTCCCGCCTCCGATTCTGGAGTTGGGCAACGGTTCGGGTCTGAGCATCAACCTGCAAGACCGCAACAATACCGGCCATACCGCATTGCTGGCGAAGCGCAACGAGTTGATTCAGAAAATGCGTGCCAGCGGTTTGTTTGACCCCAGCACCGTCCGTGCTGGCGGTTTGGAAGACTCGCCGCAGTTGAAAATCGACATCAACCGTGCCGCGGCGGCGGCGCAAGGCATTTCGTTTGCCGACATCCGCACCGCATTGGCAAGCGCGCTGAGTTCGTCTTATGTCAGCGACTTCCCGAACCAAGGCCGTCTGCAACGCGTGATGGTGCAGGCCGACGAGGATGCCCGTATGCAGCCTGCCGATATTTTGAACCTGACCGTGCCGAACAAATCCGGCGTCGCCGTACCGCTTTCCACCATTGCTACTGTTTCTTGGGAAAACGGTACGGAACAGAGCGTACGCTTCAACGGTTATCCTTCGATGAAGCTGTCCGCTTCGCCTGCAACCGGCGTTTCCACCGGGCAGGCTATGGCGGCGGTTCAAAAAATGGTTGACGAATTGGGCGGCGGTTACAGCCTGGAGTGGGGCGGACAGTCGCGCGAAGAGGCAAAAGGCGGCTCGCAAACCCTGATTTTGTACGGTTTGGCGGTTGCAGCCGTATTTTTGGTACTTGCCGCGCTTTATGAAAGCTGGTCGATTCCGCTGGCGGTCATCCTTGTGATTCCGTTGGGTTTGATCGGTGCGGCTGCGGGCGTAACCGGGCGCAACCTGTTTGAAGGACTGTTGGGCAGCGTTCCCTCGTTCGCCAACGACATCTACTTTCAAGTCGGTTTCGTTACCGTGATGGGTTTGAGTGCGAAAAATGCGATTTTGATTATCGAATTTGCCAAAGACCTTCAAGCGCAAGGGAAAAGCGCGGTTGAAGCCGCTTTGGAAGCCGCCCGCCTGCGTTTCCGTCCGATTATCATGACCTCGTTCGCCTTTATTTTGGGCGTGGTTCCCCTGTATATTGCCGGCGGTGCAAGTTCTGCCAGCCAGCGCGCCATCGGTACAACCGTATTCTGGGGGATGCTCATCGGCACGCTCTTGTCCGTGTTCCTTGTTCCGCTTTTCTATGTGGTGGTGCGCAAATTCTTCAAAGAAACCGCGCACGAACACGAAATGGCAGTAAAACACGCCGCCGAAGCGGGCATCACCGGTTCGGACGACAGCCAACATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39597","NCBI_taxonomy_name":"Neisseria meningitidis MC58","NCBI_taxonomy_id":"122586"}}}},"ARO_accession":"3000811","ARO_id":"37191","ARO_name":"mtrD","CARD_short_name":"mtrD","ARO_description":"MtrD is the inner membrane multidrug transporter of the MtrCDE efflux complex.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1939":{"model_id":"1939","model_name":"AAC(6')-Ix","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"170":{"protein_sequence":{"accession":"AAD03496.1","sequence":"MNIMPISESQLSDWLALRSLLWPDHDDAHLLEMHQLLKQTDTLQLLAYTDSQQAVAMLEASIRHEYVNGTQTSPVAFLEGIYILPEYRRSGIATQLVQYVEEWAKQFACTEFASDAAIDNTISHAMHRALGFHETERVVYFKKNIG"},"dna_sequence":{"accession":"AF031332.1","fmin":"0","fmax":"441","strand":"+","sequence":"ATGAATATTATGCCGATATCTGAATCACAATTATCAGATTGGCTAGCATTAAGAAGCTTACTCTGGCCTGATCATGACGATGCGCATTTATTGGAAATGCATCAGCTACTTAAACAAACAGATACTTTACAATTATTGGCTTATACCGATAGCCAACAAGCAGTTGCAATGTTAGAAGCATCGATTCGGCATGAATATGTGAATGGTACGCAAACCTCACCTGTGGCTTTTCTGGAAGGGATTTATATCTTACCTGAATATCGACGTTCAGGCATTGCGACCCAGTTAGTTCAGTACGTAGAGGAGTGGGCGAAACAATTTGCATGTACTGAGTTCGCTTCAGATGCAGCGATTGACAATACGATTAGCCATGCAATGCATCGAGCACTGGGTTTTCATGAAACTGAACGTGTGGTGTATTTTAAGAAAAATATCGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39519","NCBI_taxonomy_name":"Acinetobacter sp. BM2722","NCBI_taxonomy_id":"70351"}}}},"ARO_accession":"3002568","ARO_id":"38968","ARO_name":"AAC(6')-Ix","CARD_short_name":"AAC(6')-Ix","ARO_description":"AAC(6')-Ix is a chromosomal-encoded aminoglycoside acetyltransferase in Acinetobacter sp.","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"A category of aminoglycoside N-acetyltransferase enzymes with modification regiospecificity based at the 6'-amino group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics through acetylation of the 6-amino group of the compound.","category_aro_class_name":"AMR Gene Family"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"46128":{"category_aro_accession":"3007378","category_aro_cvterm_id":"46128","category_aro_name":"2'-N-ethylnetilmicin","category_aro_description":"2'-N-ethylnetilmicin is an aminoglycoside antibiotic and a derivative of netilmicin.","category_aro_class_name":"Antibiotic"},"46129":{"category_aro_accession":"3007379","category_aro_cvterm_id":"46129","category_aro_name":"5-episisomicin","category_aro_description":"5-episosomicin is a semisynthetic aminoglycoside antibiotic similar to sisomicin.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1940":{"model_id":"1940","model_name":"QnrB30","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"327":{"protein_sequence":{"accession":"ADM52194.1","sequence":"MTPLLYKKTGTNMALALVGEKIDRNRFTGEKIENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSSDLSMADFRNASALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGAQVLGATFSGSDLSGGEFSTFDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDNYQASLLMERLGIAVIG"},"dna_sequence":{"accession":"HM439650.1","fmin":"0","fmax":"681","strand":"+","sequence":"ATGACGCCATTACTGTATAAAAAAACAGGTACAAATATGGCACTGGCACTCGTTGGCGAAAAAATTGACAGAAACCGCTTCACCGGTGAGAAAATTGAAAATAGTACATTTTTTAACTGTGATTTTTCAGGTGCCGACCTGAGCGGCACTGAATTTATCGGCTGTCAGTTCTATGATCGTGAAAGCCAGAAAGGGTGCAATTTTAGTCGTGCGATGCTAAAAGATGCCATTTTTAAAAGCAGTGATTTATCCATGGCGGATTTTCGCAATGCCAGTGCGCTGGGCATTGAAATTCGCCACTGCCGCGCACAAGGCGCAGATTTCCGCGGCGCAAGTTTTATGAATATGATCACTACTCGCACCTGGTTTTGTAGTGCATATATCACTAACACAAATCTAAGCTACGCCAATTTTTCGAAAGTCGTGCTGGAAAAGTGTGAGCTGTGGGAAAACCGTTGGATGGGTGCCCAGGTACTGGGCGCGACGTTCAGTGGTTCAGATCTCTCCGGCGGCGAGTTTTCGACTTTCGACTGGCGAGCAGCAAACTTCACACATTGCGATCTGACCAATTCGGAGTTGGGGGACTTAGATATTCGGGGCGTTGATTTACAAGGCGTTAAGTTGGACAACTACCAGGCATCGTTGCTCATGGAACGTCTTGGCATCGCGGTGATTGGTTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39584","NCBI_taxonomy_name":"Citrobacter braakii","NCBI_taxonomy_id":"57706"}}}},"ARO_accession":"3002745","ARO_id":"39179","ARO_name":"QnrB30","CARD_short_name":"QnrB30","ARO_description":"QnrB30 is a plasmid-mediated quinolone resistance protein found in Citrobacter braakii.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1925":{"model_id":"1925","model_name":"MexB","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1950"}},"model_sequences":{"sequence":{"113":{"protein_sequence":{"accession":"AAA74437.1","sequence":"MSKFFIDRPIFAWVIALVIMLAGGLSILSLPVNQYPAIAPPAIAVQVSYPGASAETVQDTVVQVIEQQMNGIDNLRYISSESNSDGSMTTTVTFEQGTDPDIAQVQVQNKLQLATPLLPQEVQRQGIRVTKAVKNFLMVVGVVSTDGSMTKEDLSNYIVSNIQDPLSRTKGVGDFQVFGSQYSMRIWLDPAKLNSYQLTPGDVSSAIQAQNVQISSGQLGGLPAVKGQQLNATIIGKTRLQTAEQFENILLKVNPDGSQVRLKDVADVGLGGQDYSINAQFNGSPASGIAIKLATGANALDTAKAIRQTIANLEPFMPQGMKVVYPYDTTPVVSASIHEVVKTLGEAILLVFLVMYLFLQNFRATLIPTIAVPVVLLGTFGVLAAFGFSINTLTMFGMVLAIGLLVDDAIVVVENVERVMAEEGLSPREAARKSMGQIQGALVGIAMVLSAVFLPMAFFGGSTGVIYRQFSITIVSAMALSVIVALILTPALCATMLKPIEKGDHGEHKGGFFGWFNRMFLSTTHGYERGVASILKHRAPYLLIYVVIVAGMIWMFTRIPTAFLPDEDQGVLFAQVQTPPGSSAERTQVVVDSMREYLLEKESSSVSSVFTVTGFNFAGRGQSSGMAFIMLKPWEERPGGENSVFELAKRAQMHFFSFKDAMVFAFAPPSVLELGNATGFDLFLQDQAGVGHEVLLQARNKFLMLAAQNPALQRVRPNGMSDEPQYKLEIDDEKASALGVSLADINSTVSIAWGSSYVNDFIDRGRVKRVYLQGRPDARMNPDDLSKWYVRNDKGEMVPFNAFATGKWEYGSPKLERYNGVPAMEILGEPAPGLSSGDAMAAVEEIVKQLPKGVGYSWTGLSYEERLSGSQAPALYALSLLVVFLCLAALYESWSIPFSVMLVVPLGVIGALLATSMRGLSNDVFFQVGLLTTIGLSAKNAILIVEFAKELHEQGKGIVEAAIEACRMRLRPIVMTSLAFILGVVPLAISTGAGSGSQHAIGTGVIGGMVTATVLAIFWVPLFYVAVSTLFKDEASKQQASVEKGQ"},"dna_sequence":{"accession":"L11616.1","fmin":"1569","fmax":"4710","strand":"+","sequence":"ATGTCGAAGTTTTTCATTGATAGGCCCATTTTCGCGTGGGTGATCGCCTTGGTGATCATGCTCGCGGGCGGCCTGTCGATCCTCAGTCTGCCGGTCAACCAGTACCCGGCCATCGCCCCGCCGGCCATCGCCGTGCAGGTGAGCTACCCGGGCGCCTCGGCCGAGACGGTGCAGGACACCGTGGTCCAGGTGATCGAGCAGCAGATGAACGGGATCGACAATCTGCGCTACATCTCCTCGGAGAGTAACTCCGACGGCAGCATGACCACCACCGTGACCTTCGAACAGGGCACCGACCCCGACATCGCCCAGGTCCAGGTGCAGAACAAGCTGCAACTGGCCACCCCGCTACTGCCGCAGGAAGTGCAGCGCCAGGGGATCCGGGTGACCAAGGCGGTGAAGAACTTCCTCATGGTGGTCGGTGTGGTTTCCACCGACGGCAGCATGACCAAGGAAGACCTGTCGAACTACATCGTTTCCAACATCCAGGACCCACTCTCGCGGACCAAGGGCGTCGGTGACTTCCAGGTGTTCGGCTCGCAGTACTCGATGCGCATCTGGCTCGACCCGGCCAAGCTGAACAGCTACCAGCTGACCCCCGGCGACGTGAGCAGCGCGATCCAGGCGCAGAACGTGCAGATTTCCTCCGGCCAGCTCGGCGGCTTGCCGGCGGTCAAGGGCCAGCAGCTCAACGCCACCATCATCGGCAAGACCCGCCTGCAGACCGCGGAGCAATTCGAGAACATCCTGCTCAAGGTCAATCCCGACGGTTCCCAGGTGCGCCTGAAGGACGTCGCCGATGTAGGCCTGGGCGGCCAGGACTACAGCATCAACGCGCAGTTCAACGGCAGCCCGGCGTCCGGTATCGCGATCAAGCTGGCCACCGGCGCCAACGCGCTGGATACCGCCAAGGCGATCCGCCAGACCATCGCCAACCTGGAACCGTTCATGCCGCAGGGCATGAAGGTGGTCTACCCGTACGACACCACCCCGGTGGTCTCGGCCTCGATCCATGAGGTAGTGAAGACCCTCGGCGAGGCGATCCTCCTCGTGTTCCTGGTGATGTACCTGTTCCTGCAGAACTTCCGCGCCACGCTGATCCCGACCATCGCCGTACCGGTGGTGCTGCTGGGGACCTTCGGCGTGCTCGCCGCGTTCGGCTTCTCGATCAACACCCTGACCATGTTCGGCATGGTGCTGGCCATCGGCTTGCTGGTGGACGACGCCATCGTGGTGGTGGAGAACGTCGAGCGGGTGATGGCCGAGGAAGGCCTGTCGCCAAGGGAGGCGGCGCGCAAGTCCATGGGCCAGATCCAGGGCGCGCTGGTCGGTATCGCCATGGTGCTCTCGGCGGTATTCCTGCCGATGGCGTTCTTCGGCGGCTCCACCGGGGTGATCTACCGGCAGTTCTCCATCACCATCGTGTCGGCCATGGCCCTCTCGGTGATCGTGGCGCTGATCCTCACCCCGGCGCTCTGCGCGACCATGCTCAAGCCGATCGAGAAAGGCGACCATGGCGAGCACAAGGGCGGCTTCTTCGGCTGGTTCAACCGGATGTTCCTTTCCACCACCCACGGCTACGAGCGGGGCGTGGCGTCGATCCTCAAGCATCGCGCGCCGTACCTGCTGATCTACGTGGTGATCGTGGCCGGGATGATCTGGATGTTCACCCGCATTCCCACCGCGTTCCTCCCCGACGAGGACCAGGGCGTACTGTTCGCCCAGGTACAGACCCCGCCGGGCTCCAGTGCCGAGCGTACCCAGGTGGTGGTGGACTCGATGCGCGAATACCTGCTGGAGAAGGAAAGCTCTTCGGTCAGCTCGGTGTTCACCGTGACCGGCTTCAACTTCGCCGGCCGCGGCCAGAGTTCGGGCATGGCGTTCATCATGCTCAAGCCCTGGGAAGAGCGTCCCGGTGGCGAGAACAGCGTGTTCGAACTGGCCAAGCGCGCGCAGATGCACTTCTTCAGCTTCAAGGACGCGATGGTGTTCGCCTTCGCGCCGCCGTCGGTACTGGAACTGGGTAACGCCACCGGCTTCGACCTGTTCCTCCAGGACCAGGCGGGTGTCGGCCACGAAGTCCTGCTCCAGGCGCGCAACAAGTTCCTCATGCTCGCCGCGCAGAACCCGGCGCTGCAACGCGTGCGCCCCAACGGCATGAGCGACGAACCGCAGTACAAGCTGGAGATCGACGACGAGAAGGCCAGCGCCCTCGGCGTGTCCCTTGCCGACATCAACAGCACCGTGTCCATCGCCTGGGGTTCCAGCTACGTCAACGATTTCATCGACCGTGGCCGGGTCAAGCGGGTCTACCTGCAGGGCAGGCCGGACGCGCGGATGAACCCGGACGACCTGAGCAAGTGGTACGTGCGCAACGACAAGGGCGAGATGGTGCCGTTCAACGCCTTCGCCACCGGCAAGTGGGAATACGGTTCGCCGAAGCTGGAGCGCTACAATGGCGTGCCGGCGATGGAGATCCTCGGCGAGCCGGCGCCCGGCCTGAGTTCCGGTGACGCCATGGCGGCGGTCGAGGAGATCGTCAAGCAATTGCCGAAAGGCGTTGGCTACTCCTGGACCGGCCTGTCCTACGAGGAGCGCTTGTCCGGCTCGCAGGCGCCGGCGCTGTATGCGCTGTCGCTGCTGGTGGTGTTCCTCTGCCTGGCGGCCCTGTACGAAAGCTGGTCGATTCCGTTCTCGGTGATGCTGGTGGTGCCGTTGGGCGTGATCGGTGCGCTGCTGGCGACGTCCATGCGCGGCCTGTCCAACGACGTGTTCTTCCAGGTGGGCCTGTTGACGACCATCGGCCTGTCGGCGAAGAACGCCATTCTCATCGTGGAGTTCGCCAAGGAGCTGCACGAGCAGGGCAAGGGCATCGTCGAGGCGGCCATCGAAGCCTGCCGCATGCGTCTGCGGCCGATCGTGATGACCTCCCTGGCGTTCATCCTCGGCGTGGTCCCGCTGGCGATCTCCACCGGCGCCGGCTCGGGCAGCCAGCATGCGATCGGTACCGGCGTGATCGGCGGCATGGTCACTGCGACCGTCCTGGCGATCTTCTGGGTACCGCTGTTCTACGTGGCGGTCAGCACGCTGTTCAAGGACGAGGCGTCCAAGCAGCAGGCGTCCGTCGAAAAGGGGCAATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3000378","ARO_id":"36517","ARO_name":"MexB","CARD_short_name":"MexB","ARO_description":"MexB is the inner membrane multidrug exporter of the efflux complex MexAB-OprM.","ARO_category":{"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1917":{"model_id":"1917","model_name":"tet(30)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"740"}},"model_sequences":{"sequence":{"606":{"protein_sequence":{"accession":"AAD09860.1","sequence":"MNKALIVILSTVALDAIGAGLIFPILPDILVEVTGGGDIGFLYGVMLGVFAVMQFVFSPILGALSDRFGRRPVLLLSLAGTLLDYLVMAFSPLGWVLVVGRAMAGITSANMAVASAYITDITPAEQRAQRFGTVGAVMSLGFIIGPVIGGVIGAWWLRAPFLVAALFNGLNLFVALFVLPESRKAGPGKFAFKELNPLAPLVWLWNFKPLLPLVTVSVVFGLVAAIPGTIWVLYGAERFGWDSVHMGLSLSVFGVSGALAQAFLVGPLSRRFGDLGTLMIGVGFDMLAYMLMAFANQSWMGYAVAPLFALGGVAMPALQSLVTSRVSDDQQGQLQGVLASLMSLAGIIGPVLTTAVFFSTKSIWIGTIWLVGAALYLLALPLFATVKTPKAVAA"},"dna_sequence":{"accession":"AF090987.1","fmin":"0","fmax":"1185","strand":"+","sequence":"ATGAACAAGGCCCTTATCGTTATTCTCTCAACCGTTGCCCTCGACGCCATTGGCGCAGGCCTGATCTTCCCGATCCTGCCGGACATCTTGGTCGAGGTGACTGGCGGCGGCGACATCGGGTTCCTCTATGGGGTCATGCTGGGGGTATTCGCCGTCATGCAATTTGTGTTCTCGCCGATCCTTGGTGCGCTCAGCGACCGGTTCGGTCGGCGCCCGGTCTTGTTGCTTTCTTTGGCCGGTACCCTGCTTGATTACCTTGTTATGGCATTTTCCCCGCTCGGCTGGGTGCTCGTCGTCGGGCGGGCCATGGCGGGGATCACCAGCGCAAATATGGCGGTGGCAAGCGCCTACATCACTGACATCACCCCAGCCGAGCAGCGCGCGCAGCGGTTTGGCACGGTTGGTGCCGTGATGAGCCTGGGCTTTATCATCGGTCCCGTCATTGGTGGCGTCATTGGCGCCTGGTGGCTTCGGGCACCATTTCTTGTGGCAGCCCTGTTCAATGGCCTCAACCTGTTCGTCGCGCTGTTTGTTCTGCCGGAAAGCCGAAAGGCCGGTCCGGGCAAGTTTGCGTTCAAGGAACTTAACCCGTTGGCGCCATTGGTGTGGCTTTGGAATTTCAAGCCGCTCCTGCCACTTGTAACCGTCTCTGTCGTCTTCGGTCTGGTGGCCGCCATCCCGGGAACGATCTGGGTGCTCTATGGCGCCGAGCGGTTCGGATGGGATTCGGTGCATATGGGCCTGTCGCTATCGGTTTTCGGCGTCAGTGGCGCCCTGGCGCAGGCCTTTCTCGTCGGGCCGCTCTCGCGCCGCTTTGGTGATTTGGGCACGTTGATGATCGGCGTTGGCTTTGACATGCTGGCTTATATGCTGATGGCCTTCGCCAACCAGAGCTGGATGGGCTACGCGGTAGCGCCCCTGTTTGCATTGGGCGGCGTTGCCATGCCGGCGCTGCAATCTCTGGTAACCAGCCGCGTGAGCGATGATCAGCAGGGCCAGTTGCAGGGCGTGCTCGCCAGCCTCATGAGCCTGGCGGGTATAATAGGGCCGGTGCTGACCACCGCAGTGTTCTTTTCCACCAAAAGCATCTGGATCGGGACGATCTGGCTGGTGGGTGCCGCACTTTATCTTCTCGCCTTGCCGCTGTTCGCAACGGTGAAAACCCCGAAGGCTGTGGCGGCTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36775","NCBI_taxonomy_name":"Agrobacterium fabrum str. C58","NCBI_taxonomy_id":"176299"}}}},"ARO_accession":"3000561","ARO_id":"36700","ARO_name":"tet(30)","CARD_short_name":"tet(30)","ARO_description":"Tet30 is a tetracycline efflux pump found in agrobacterium, a Gram-negative bacterium.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1835":{"model_id":"1835","model_name":"tet(38)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"850"}},"model_sequences":{"sequence":{"537":{"protein_sequence":{"accession":"AAV80464.1","sequence":"MNVEYSKIKKAVPILLFLFVFSLVIDNSFKLISVAIADDLNISVTTVSWQATLAGLVIGIGAVVYASLSDAISIRTLFIYGVILIIIGSIIGYIFQHQFPLLLVGRIIQTAGLAAAETLYVIYVAKYLSKEDQKTYLGLSTSSYSLSLVIGTLSGGFISTYLHWTNMFLIALIVVFTLPFLFKLLPKENNTNKAHLDFVGLILVATIATTVMLFITNFNWLYMIGALIAIIVFALYIKNAQRPLVNKSFFQNKRYASFLFIVFVMYAIQLGYIFTFPFIMEQIYHLQLDTTSLLLVPGYIVAVIVGALSGKIGEYLNSKQAIITAIILIALSLILPAFAVGNHISIFVISMIFFAGSFALMYAPLLNEAIKTIDLNMTGVAIGFYNLIINVAVSVGIAIAAALIDFKALNFPGNDALSSHFGIILIILGLMSIVGLVLFVILNRWTQSEK"},"dna_sequence":{"accession":"AY825285.1","fmin":"0","fmax":"1353","strand":"+","sequence":"ATGAATGTTGAATATTCTAAAATAAAGAAAGCAGTACCTATTTTATTATTCTTATTTGTATTCAGTTTGGTTATAGACAACTCATTTAAATTGATTTCTGTAGCCATTGCTGATGACTTAAACATATCTGTAACGACAGTAAGTTGGCAAGCGACATTAGCCGGTTTAGTAATTGGTATTGGCGCTGTAGTATACGCTTCATTATCTGATGCCATTAGTATACGCACACTATTTATTTATGGCGTGATATTAATCATTATCGGATCAATTATTGGTTACATTTTCCAACATCAATTCCCATTACTTTTAGTTGGACGTATTATTCAAACTGCCGGTTTAGCTGCTGCAGAGACATTATATGTGATATATGTTGCAAAGTATCTTTCTAAAGAGGACCAGAAGACTTACCTTGGCTTAAGTACGAGCAGTTATTCCTTGTCATTAGTTATCGGTACATTATCAGGTGGATTTATTTCTACGTATTTACACTGGACAAATATGTTTTTAATTGCATTAATCGTAGTATTTACGTTGCCATTCCTATTTAAATTATTACCAAAAGAAAATAATACGAATAAAGCTCATTTAGATTTTGTTGGCTTAATTCTAGTGGCAACTATTGCTACAACAGTCATGCTGTTTATTACGAACTTTAATTGGTTATATATGATTGGTGCCTTAATTGCGATTATCGTTTTTGCGCTATATATTAAAAATGCGCAACGTCCATTAGTAAATAAATCATTTTTCCAAAATAAACGTTATGCTTCATTTTTATTTATAGTATTTGTAATGTATGCTATCCAATTGGGTTATATTTTTACGTTCCCATTCATAATGGAGCAAATTTATCATCTGCAACTAGACACAACATCACTGTTATTAGTACCGGGTTATATAGTAGCAGTCATTGTTGGTGCATTAAGTGGTAAAATCGGCGAATATCTGAATTCAAAACAAGCGATTATCACAGCAATTATTTTAATAGCACTGAGCTTGATTTTACCTGCATTTGCAGTAGGTAATCACATTTCAATCTTCGTCATTTCTATGATATTCTTTGCAGGTAGCTTTGCTTTAATGTATGCACCTTTACTTAACGAAGCCATTAAAACAATAGATCTTAATATGACAGGTGTGGCTATTGGTTTTTATAATTTAATTATTAATGTGGCGGTATCTGTAGGTATTGCGATTGCTGCGGCTCTAATCGATTTTAAAGCATTAAATTTCCCAGGCAATGATGCATTAAGTTCACATTTCGGTATTATTTTAATTATTTTAGGTTTAATGAGTATTGTCGGATTAGTTTTATTCGTCATCTTAAATCGTTGGACACAATCTGAAAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35508","NCBI_taxonomy_name":"Staphylococcus aureus","NCBI_taxonomy_id":"1280"}}}},"ARO_accession":"3000565","ARO_id":"36704","ARO_name":"tet(38)","CARD_short_name":"tet(38)","ARO_description":"Tet38 is a tetracycline efflux pump found in the Gram-positive Staphylococcus aureus. It is regulated by mgrA, which also regulates NorB.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1808":{"model_id":"1808","model_name":"tet(A)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"5213":{"protein_sequence":{"accession":"AAN06707.1","sequence":"MSTNLSVIKNPRVQSDQRRLVRRPDVKPNRPLIVILSTVALDAVGIGLIMPVLPGLLRDLVHSNDVTAHYGILLALYALMQFACAPVLGALSDRFGRRPVLLVSLAGAAVDYAIMATAPFLWVLYIGRIVAGITGATGAVAGAYIADITDGDERARHFGFMSACFGFGMVAGPVLGGLMGGFSPHAPFFAAAALNGLNFLTGCFLLPESHKGERRPLRREALNPLASFRWARGMTVVAALMAVFFIMQLVGQVPAALWVIFGEDRFHWDATTIGISLAAFGILHSLAQAMITGPVAARLGERRALMLGMIADGTGYILLAFATRGWMAFPIMVLLASGGIGMPALQAMLSRQVDEERQGQLQGSLAALTSLTSIVGPLLFTAIYAASITTWNGWAWIAGAALYLLCLPALRRGLWRNSSNSRCT"},"dna_sequence":{"accession":"AF534183.1","fmin":"2970","fmax":"4245","strand":"+","sequence":"ATGTCCACCAACTTATCAGTGATAAAGAATCCGCGCGTTCAATCGGACCAGCGGAGGCTGGTCCGGAGGCCAGACGTGAAACCCAACAGACCCCTGATCGTAATTCTGAGCACTGTCGCGCTCGACGCTGTCGGCATCGGCCTGATTATGCCGGTGCTGCCGGGCCTCCTGCGCGATCTGGTTCACTCGAACGACGTCACCGCCCACTATGGCATTCTGCTGGCGCTGTATGCGTTGATGCAATTTGCCTGCGCACCTGTGCTGGGCGCGCTGTCGGATCGTTTCGGGCGGCGGCCGGTCTTGCTCGTCTCGCTGGCCGGCGCTGCTGTCGACTACGCCATCATGGCGACGGCGCCTTTCCTTTGGGTTCTCTATATCGGGCGGATCGTGGCCGGCATCACCGGGGCGACTGGGGCGGTAGCCGGCGCTTATATTGCCGATATCACTGATGGCGATGAGCGCGCGCGGCACTTCGGCTTCATGAGCGCCTGTTTCGGGTTCGGGATGGTCGCGGGACCTGTGCTCGGTGGGCTGATGGGCGGTTTCTCCCCCCACGCTCCGTTCTTCGCCGCGGCAGCCTTGAACGGCCTCAATTTCCTGACGGGCTGTTTCCTTTTGCCGGAGTCGCACAAAGGCGAACGCCGGCCGTTACGCCGGGAGGCTCTCAACCCGCTCGCTTCGTTCCGGTGGGCCCGGGGCATGACCGTCGTCGCCGCCCTGATGGCGGTCTTCTTCATCATGCAACTTGTCGGACAGGTGCCGGCCGCGCTTTGGGTCATTTTCGGCGAGGATCGCTTTCACTGGGACGCGACCACGATCGGCATTTCGCTTGCCGCATTTGGCATTCTGCATTCACTCGCCCAGGCAATGATCACCGGCCCTGTAGCCGCCCGGCTCGGCGAAAGGCGGGCACTCATGCTCGGAATGATTGCCGACGGCACAGGCTACATCCTGCTTGCCTTCGCGACACGGGGATGGATGGCGTTCCCGATCATGGTCCTGCTTGCTTCGGGTGGCATCGGAATGCCGGCGCTGCAAGCAATGTTGTCCAGGCAGGTGGATGAGGAACGTCAGGGGCAGCTGCAAGGCTCACTGGCGGCGCTCACCAGCCTGACCTCGATCGTCGGACCCCTCCTCTTCACGGCGATCTATGCGGCTTCTATAACAACGTGGAACGGGTGGGCATGGATTGCAGGCGCTGCCCTCTACTTGCTCTGCCTGCCGGCGCTGCGTCGCGGGCTTTGGAGAAATTCTTCAAATTCCCGTTGCACATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36790","NCBI_taxonomy_name":"Shigella sonnei","NCBI_taxonomy_id":"624"}}}},"ARO_accession":"3000165","ARO_id":"36304","ARO_name":"tet(A)","CARD_short_name":"tet(A)","ARO_description":"TetA is a tetracycline efflux pump found in many species of Gram-negative bacteria.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1885":{"model_id":"1885","model_name":"tet(Z)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"5588":{"protein_sequence":{"accession":"AAD25063.1","sequence":"MLITATLDAAGLGLVMPILPTLLDQVGAPDDMIPLHVGLLTALYAIMQFLCAPILGRLSDRFGRRRVLVASLAGATIDYLVLALTDTLWVFYLARAVAGITGATNAVTATVIADITPPDQRAKRYGWLGACYGGGMIAGPAIGGLFGGVSPHLPFLVAAALAGITLVLSASLLRETRPPGSNGSHAQQPGTAKRTAVPGMLILLAVFGIVQFIGQAPGSTWVLFTQQRLDWNPVEVGVSLSIFGMVQVFVQAALTGRIVSRIGETRAILVGIAADAIGLIGLALIASTWAMLPILAALGLGSITLPALQTLLSRRAPEQQQGRLQGTLASLNSLTSIIGPVTFTGIFALTRTNADGTLWICAAALYVLCALLMIRETCASRRSR"},"dna_sequence":{"accession":"AF121000.1","fmin":"11879","fmax":"13034","strand":"-","sequence":"GTGCTCATCACGGCGACCCTCGATGCTGCAGGGCTGGGCCTCGTGATGCCGATCTTGCCTACCCTTCTCGACCAGGTCGGTGCCCCCGACGACATGATCCCACTGCACGTCGGACTACTGACAGCGCTCTATGCGATCATGCAGTTTCTTTGCGCCCCGATCCTTGGCCGACTCTCTGACCGTTTCGGACGCCGCCGCGTGCTTGTCGCCTCCCTCGCAGGCGCGACGATCGACTACCTCGTGCTCGCACTGACGGACACGCTGTGGGTCTTTTACCTCGCCCGCGCGGTTGCAGGCATTACCGGCGCCACGAACGCCGTCACCGCGACGGTGATCGCCGACATTACTCCGCCGGATCAGCGCGCAAAACGCTACGGGTGGCTCGGCGCATGCTACGGCGGTGGCATGATCGCGGGTCCCGCCATTGGCGGTCTTTTCGGCGGGGTCTCACCGCATCTGCCATTCCTCGTCGCCGCCGCGCTCGCCGGAATCACCCTCGTACTCAGCGCGAGTCTTCTGCGTGAGACGCGGCCACCGGGCAGCAACGGCTCGCACGCACAGCAACCCGGTACGGCGAAGCGAACCGCAGTGCCGGGGATGCTTATCCTTCTCGCAGTCTTCGGCATCGTGCAGTTCATCGGCCAAGCACCAGGCTCCACCTGGGTGCTCTTCACGCAGCAGCGCCTCGACTGGAACCCCGTCGAAGTCGGCGTTTCGCTATCCATCTTCGGAATGGTGCAAGTATTCGTGCAGGCGGCACTGACCGGACGCATCGTGTCCCGGATCGGCGAGACCCGGGCGATCCTCGTCGGTATCGCCGCAGACGCCATTGGGCTCATCGGCCTTGCCCTCATCGCCAGCACATGGGCGATGCTACCGATCCTCGCAGCGCTCGGACTCGGCAGCATCACGTTGCCCGCACTGCAGACGCTGCTCTCGAGACGCGCGCCCGAGCAGCAGCAGGGACGCCTGCAGGGAACACTTGCAAGCCTGAACAGCCTCACCTCGATCATCGGCCCGGTCACCTTCACCGGCATTTTCGCACTCACCCGAACGAATGCAGACGGCACCCTCTGGATCTGCGCCGCAGCGCTCTACGTTCTCTGCGCCCTCCTGATGATCCGTGAGACATGCGCCTCACGGCGATCTCGATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36777","NCBI_taxonomy_name":"Corynebacterium glutamicum","NCBI_taxonomy_id":"1718"}}}},"ARO_accession":"3000183","ARO_id":"36322","ARO_name":"tet(Z)","CARD_short_name":"tet(Z)","ARO_description":"TetZ is a tetracycline efflux protein found in Gram-positive bacteria (Corynebacterium and Lactobacillus). It is associated with plasmid DNA.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1941":{"model_id":"1941","model_name":"SHV-98","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"994":{"protein_sequence":{"accession":"CAQ03503.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPAIMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AM941844.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGCATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGATCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001336","ARO_id":"37736","ARO_name":"SHV-98","CARD_short_name":"SHV-98","ARO_description":"SHV-98 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1944":{"model_id":"1944","model_name":"CTX-M-148","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1351":{"protein_sequence":{"accession":"AHX39589.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVIAVAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAERRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"KJ020574.1","fmin":"244","fmax":"1120","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATAGCGGTCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGACTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGCGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002006","ARO_id":"38406","ARO_name":"CTX-M-148","CARD_short_name":"CTX-M-148","ARO_description":"CTX-M-148 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1945":{"model_id":"1945","model_name":"SHV-50","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1236":{"protein_sequence":{"accession":"AAP41108.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMTATLRKLLTSQRLSARSQRHLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AY288915.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGACCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCATCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGCATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001107","ARO_id":"37487","ARO_name":"SHV-50","CARD_short_name":"SHV-50","ARO_description":"SHV-50 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1946":{"model_id":"1946","model_name":"CTX-M-10","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1995":{"protein_sequence":{"accession":"AAT68658.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTVDVQQKLAELEQQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGDYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"AY598759.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGTGGACGTACAGCAAAAACTTGCCGAATTAGAGCAGCAGTCGGGAGGAAGGCTGGGTGTGGCATTGATTAACACGGCGGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTCGAGATCAAAAAATCTGACCTGGTTAACTATAATCCGATTGCGGAAAAACACGTCAATGGGACGATGTCACTGGCTGAGCTCAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTTACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCTGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACGCTGCGTAATCTGACGCTGGGTAAAGCATTGGGTGACAGCCAACGGGCGCAGCTGGTGACGTGGATGAAAGGCAATACTACCGGTGCAGCGAGTATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGACTATGGTACCACCAACGATATCGCGGTGATTTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCCCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001873","ARO_id":"38273","ARO_name":"CTX-M-10","CARD_short_name":"CTX-M-10","ARO_description":"CTX-M-10 is a beta-lactamase found in Escherichia coli.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1947":{"model_id":"1947","model_name":"CTX-M-160","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6064":{"protein_sequence":{"accession":"AJO16046.1","sequence":"MMRKSVRRAMLMTTACVSLLLASVPLCAQANDVQQKLAALEKSSGGRLGVALINTADNTQTLYRADERFAMCSTSKVMAVAAVLKQSETQKGLLSQRVEIKPSDLVNYNPIAEKHVNGTMTFGELSAAALQYSDNTAMNKLIAHLGGPDKVTAFARTIGDDTFRLDRTEPTLNTAIPGDPRDTTTPLAMAQALRNLTLGNALGDTQRAQLVMWLKGNTTGAASIQAGLPTSWVVGDKTGSGGYGTTNDIAVIWPEGRAPLVLVTYFTQSEPKAESRRDVLAAAARIVTDGY"},"dna_sequence":{"accession":"KP050493.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGATGAGAAAAAGCGTAAGGCGGGCGATGTTAATGACGACAGCCTGTGTTTCGCTGCTGTTGGCCAGTGTGCCGCTGTGTGCCCAGGCGAACGATGTTCAACAAAAGCTCGCGGCGCTGGAGAAAAGCAGCGGGGGACGACTGGGTGTGGCGTTGATTAACACCGCCGATAACACGCAGACGCTCTACCGCGCCGACGAGCGTTTTGCCATGTGCAGCACCAGTAAAGTGATGGCGGTAGCGGCGGTGCTTAAGCAAAGTGAAACGCAAAAGGGCTTGTTGAGTCAGCGGGTTGAAATTAAGCCCTCAGACTTGGTTAACTACAACCCCATTGCGGAAAAACACGTCAATGGCACGATGACATTCGGGGAGTTGAGCGCGGCGGCGCTACAGTACAGCGATAATACTGCCATGAATAAGCTGATTGCCCATCTCGGGGGGCCGGATAAAGTGACGGCATTTGCCCGTACGATTGGCGATGACACGTTCCGGCTCGATCGTACCGAGCCGACGCTCAACACCGCGATCCCCGGCGACCCGCGCGATACCACCACGCCGTTAGCGATGGCGCAGGCTCTGCGCAATCTGACGTTGGGCAATGCCCTGGGTGACACTCAGCGTGCGCAGCTGGTGATGTGGCTGAAAGGCAACACCACCGGCGCTGCCAGCATTCAGGCAGGGCTACCCACATCGTGGGTTGTCGGGGATAAAACCGGCAGCGGCGGTTATGGTACGACGAATGATATCGCGGTTATTTGGCCGGAAGGTCGCGCGCCGCTCGTTCTGGTGACTTACTTCACCCAGTCGGAGCCGAAGGCAGAGAGCCGTCGTGACGTGCTCGCTGCTGCCGCCAGAATTGTCACCGACGGTTATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3003168","ARO_id":"39745","ARO_name":"CTX-M-160","CARD_short_name":"CTX-M-160","ARO_description":"CTX-M-160 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1948":{"model_id":"1948","model_name":"TEM-167","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"927":{"protein_sequence":{"accession":"ACJ04051.1","sequence":"MSIQHFRVALIPFFAAFCFPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVKYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSVLPAGWFIADKSGASERGSRGIIAALGPDGKPSRIVVIYMTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"FJ360884.1","fmin":"213","fmax":"1074","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCTTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTAAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGTCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCAGTGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACATGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001033","ARO_id":"37413","ARO_name":"TEM-167","CARD_short_name":"TEM-167","ARO_description":"TEM-167 is an extended-spectrum beta-lactamase found in E. coli.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1949":{"model_id":"1949","model_name":"cphA6","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"1579":{"protein_sequence":{"accession":"AAP69914.1","sequence":"MMKSWMKCTLAGAVVLMASFWGGSVRAAGISLKQVSGPVYVVEDNYYVKENSMVYFGAKGVTVVGATWTPDTARELHKLIKRVSSKPVLEVINTNYHTDRAGGNAYWKSIGAKVVSTRQTRDLMKSDWAEIVAFTRKGLPEYPDLPLVLPNVVHDGDFTLQEGKVRAFYAGPAHTPDGIFVYFPDEQVLYGNCILKEKLGNLSFANVKAYPQTIERLKAMKLPIKTVIGGHDSPLHGPELIDHYEELIKAAAHS"},"dna_sequence":{"accession":"AY227052.1","fmin":"0","fmax":"765","strand":"+","sequence":"ATGATGAAAAGTTGGATGAAGTGCACATTGGCCGGGGCCGTGGTGCTGATGGCGAGTTTCTGGGGCGGCAGCGTGCGGGCGGCGGGGATCTCCCTCAAGCAGGTAAGCGGCCCGGTGTATGTGGTGGAGGATAACTACTACGTAAAGGAAAACTCCATGGTCTATTTCGGGGCCAAGGGGGTGACTGTGGTGGGTGCGACCTGGACGCCGGATACCGCCCGCGAGCTGCACAAGCTGATCAAGCGGGTCAGCAGCAAGCCGGTGCTGGAGGTGATCAACACCAACTACCACACCGATCGGGCGGGTGGTAACGCCTACTGGAAGTCCATTGGCGCCAAGGTGGTCTCGACCCGCCAGACCCGGGATCTGATGAAGAGCGACTGGGCCGAGATTGTCGCCTTTACCCGCAAGGGGCTGCCGGAGTACCCAGATCTGCCGCTGGTGCTGCCCAACGTGGTGCACGATGGCGACTTCACCCTGCAAGAGGGCAAGGTGCGCGCCTTCTATGCGGGCCCGGCCCATACGCCGGACGGCATCTTTGTCTACTTCCCCGACGAGCAGGTGCTCTATGGCAACTGCATCCTCAAGGAGAAGCTGGGTAACCTGAGCTTTGCAAATGTGAAGGCCTATCCGCAGACCATCGAGCGACTCAAGGCGATGAAGCTGCCGATCAAGACGGTGATCGGCGGTCACGACTCGCCGCTGCACGGCCCCGAGTTGATTGATCACTATGAAGAGTTGATCAAGGCCGCTGCTCATTCATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39671","NCBI_taxonomy_name":"Aeromonas veronii bv. veronii","NCBI_taxonomy_id":"197701"}}}},"ARO_accession":"3003102","ARO_id":"39668","ARO_name":"cphA6","CARD_short_name":"cphA6","ARO_description":"cphA6 is an Ambler Class B MBL; subclass B2 originally isolated from Aeromonas veronii. This enzyme has specific activity against carbapenems and is active as a mono-zinc protein.","ARO_category":{"36720":{"category_aro_accession":"3000581","category_aro_cvterm_id":"36720","category_aro_name":"CphA beta-lactamase","category_aro_description":"CphA is an Ambler Class B MBL; subclass B2 originally isolated from Aeromonas hydrophilia.  This enzyme has specific activity against carbapenems and is active as a mono-zinc protein.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1950":{"model_id":"1950","model_name":"arr-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"250"}},"model_sequences":{"sequence":{"393":{"protein_sequence":{"accession":"AAC05822.1","sequence":"MVANPPKPFEVHESGAYLHGTKADLKVGDRLVPGRESNFEAGRIMKHVYITQTLDAAVWGAELAVGEGRGRIYIVEPEGEIEDDPNVTDKKLPGNPTRSYRTREPVRIVGELTDWEGHSPEQIAAMREGLEDLRRKGLAVIYD"},"dna_sequence":{"accession":"AF001493.1","fmin":"0","fmax":"432","strand":"+","sequence":"GTGGTGGCGAATCCGCCGAAACCGTTCGAAGTGCACGAGTCCGGGGCCTATCTGCACGGCACCAAGGCCGACCTCAAGGTGGGGGACCGACTGGTGCCCGGCCGCGAGTCCAACTTCGAGGCCGGGCGCATCATGAAGCACGTCTACATCACCCAGACGCTGGACGCCGCGGTGTGGGGCGCCGAGCTTGCTGTCGGTGAGGGTCGCGGGCGGATTTACATCGTCGAACCCGAGGGCGAGATCGAAGACGACCCGAACGTCACCGACAAGAAGCTCCCCGGCAACCCGACCCGCTCCTACCGCACCCGTGAGCCCGTGCGGATCGTCGGGGAGCTCACCGACTGGGAGGGGCATTCGCCGGAGCAGATCGCTGCCATGCGGGAGGGGCTCGAGGATCTACGGCGCAAGGGGCTCGCGGTCATCTATGACTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36871","NCBI_taxonomy_name":"Mycolicibacterium smegmatis","NCBI_taxonomy_id":"1772"}}}},"ARO_accession":"3002846","ARO_id":"39280","ARO_name":"arr-1","CARD_short_name":"arr-1","ARO_description":"arr-1 is a chromosome-encoded ribosyltransferase found in Mycolicibacterium smegmatis.","ARO_category":{"36529":{"category_aro_accession":"3000390","category_aro_cvterm_id":"36529","category_aro_name":"rifampin ADP-ribosyltransferase (Arr)","category_aro_description":"Enzyme responsible for the ADP-ribosylative inactivation of rifampin at the 23-OH position using NAD+.","category_aro_class_name":"AMR Gene Family"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36656":{"category_aro_accession":"3000517","category_aro_cvterm_id":"36656","category_aro_name":"rifaximin","category_aro_description":"Rifaximin is a semi-synthetic rifamycin used to treat traveller's diarrhea. Rifaximin inhibits RNA synthesis by binding to the beta subunit of bacterial RNA polymerase.","category_aro_class_name":"Antibiotic"},"36669":{"category_aro_accession":"3000530","category_aro_cvterm_id":"36669","category_aro_name":"rifabutin","category_aro_description":"Rifabutin is a semisynthetic rifamycin used in tuberculosis therapy. It inhibits DNA-dependent RNA synthesis.","category_aro_class_name":"Antibiotic"},"36673":{"category_aro_accession":"3000534","category_aro_cvterm_id":"36673","category_aro_name":"rifapentine","category_aro_description":"Rifapentine is a semisynthetic rifamycin that inhibits DNA-dependent RNA synthesis. It is often used in the treatment of tuberculosis and leprosy.","category_aro_class_name":"Antibiotic"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1951":{"model_id":"1951","model_name":"TEM-76","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1887":{"protein_sequence":{"accession":"AAF05613.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMGDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AF190694.1","fmin":"208","fmax":"1069","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGGGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000942","ARO_id":"37322","ARO_name":"TEM-76","CARD_short_name":"TEM-76","ARO_description":"TEM-76 is an inhibitor-resistant beta-lactamase found in E. coli.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1952":{"model_id":"1952","model_name":"OXA-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4668":{"protein_sequence":{"accession":"AFB82783.1","sequence":"MKNTIHINFAIFLIIANIIYSSASASTDISTVASPLFEGTEGCFLLYDASTNAEIAQFNKAKCATQMAPDSTFKIALSLMAFDAEIIDQKTIFKWDKTPKGMEIWNSNHTPKTWMQFSVVWVSQEITQKIGLNKIKNYLKDFDYGNQDFSGDKERNNGLTEAWLESSLKISPEEQIQFLRKIINHNLPVKNSAIENTIENMYLQDLDNSTKLYGKTGAGFTANRTLQNGWFEGFIISKSGHKYVFVSALTGNLGSNLTSSIKAKKNAITILNTLNL"},"dna_sequence":{"accession":"JN420336.1","fmin":"1399","fmax":"2230","strand":"-","sequence":"ATGAAAAACACAATACATATCAACTTCGCTATTTTTTTAATAATTGCAAATATTATCTACAGCAGCGCCAGTGCATCAACAGATATCTCTACTGTTGCATCTCCATTATTTGAAGGAACTGAAGGTTGTTTTTTACTTTACGATGCATCCACAAACGCTGAAATTGCTCAATTCAATAAAGCAAAGTGTGCAACGCAAATGGCACCAGATTCAACTTTCAAGATCGCATTATCACTTATGGCATTTGATGCGGAAATAATAGATCAGAAAACCATATTCAAATGGGATAAAACCCCCAAAGGAATGGAGATCTGGAACAGCAATCATACACCAAAGACGTGGATGCAATTTTCTGTTGTTTGGGTTTCGCAAGAAATAACCCAAAAAATTGGATTAAATAAAATCAAGAATTATCTCAAAGATTTTGATTATGGAAATCAAGACTTCTCTGGAGATAAAGAAAGAAACAACGGATTAACAGAAGCATGGCTCGAAAGTAGCTTAAAAATTTCACCAGAAGAACAAATTCAATTCCTGCGTAAAATTATTAATCACAATCTCCCAGTTAAAAACTCAGCCATAGAAAACACCATAGAGAACATGTATCTACAAGATCTGGATAATAGTACAAAACTGTATGGGAAAACTGGTGCAGGATTCACAGCAAATAGAACCTTACAAAACGGATGGTTTGAAGGGTTTATTATAAGCAAATCAGGACATAAATATGTTTTTGTGTCCGCACTTACAGGAAACTTGGGGTCGAATTTAACATCAAGCATAAAAGCCAAGAAAAATGCGATCACCATTCTAAACACACTAAATTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001396","ARO_id":"37796","ARO_name":"OXA-1","CARD_short_name":"OXA-1","ARO_description":"OXA-1 is a beta-lactamase found in E. coli.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46485":{"category_aro_accession":"3007696","category_aro_cvterm_id":"46485","category_aro_name":"OXA-1-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-1.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35981":{"category_aro_accession":"0000064","category_aro_cvterm_id":"35981","category_aro_name":"amoxicillin","category_aro_description":"Amoxicillin is a moderate-spectrum, bacteriolytic, beta-lactam antibiotic used to treat bacterial infections caused by susceptible microorganisms. A derivative of penicillin, it has a wider range of treatment but remains relatively ineffective against Gram-negative bacteria. It is commonly taken with clavulanic acid, a beta-lactamase inhibitor. Like other beta-lactams, amoxicillin interferes with the synthesis of peptidoglycan.","category_aro_class_name":"Antibiotic"},"35995":{"category_aro_accession":"0000078","category_aro_cvterm_id":"35995","category_aro_name":"piperacillin","category_aro_description":"Piperacillin is an acetylureidopenicillin and has an extended spectrum of targets relative to other beta-lactam antibiotics. It inhibits cell wall synthesis in bacteria, and is usually taken with the beta-lactamase inhibitor tazobactam to overcome penicillin-resistant bacteria.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"37084":{"category_aro_accession":"3000704","category_aro_cvterm_id":"37084","category_aro_name":"cefalotin","category_aro_description":"Cefalotin is a semisynthetic cephalosporin antibiotic activate against staphylococci. It is resistant to staphylococci beta-lactamases but hydrolyzed by enterobacterial beta-lactamases.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1953":{"model_id":"1953","model_name":"SHV-155","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1472":{"protein_sequence":{"accession":"AFQ23961.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQQ"},"dna_sequence":{"accession":"JX121122.1","fmin":"0","fmax":"858","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGTATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACAA","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001194","ARO_id":"37574","ARO_name":"SHV-155","CARD_short_name":"SHV-155","ARO_description":"SHV-155 is a beta-lactamase.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1954":{"model_id":"1954","model_name":"TEM-154","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1243":{"protein_sequence":{"accession":"ACO07310.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMLSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDSWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"FJ807656.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGCTGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATAGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001020","ARO_id":"37400","ARO_name":"TEM-154","CARD_short_name":"TEM-154","ARO_description":"TEM-154 is a CMT-type, inhibitor-resistant, extended-spectrum beta-lactamase.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1955":{"model_id":"1955","model_name":"OXA-29","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"973":{"protein_sequence":{"accession":"CAC35728.1","sequence":"MKKLSVLLWLTLFYCGTIWAQSTCFLVQENQTVLKHEGKDCNKRFAPESTFKIALSLMGFDSGILKDTLNPEWPYKKEYELYLNVWKYPHNPRTWIRDSCVWYSQVLTQQLGMTRFKNYVDAFHYGNQDISGDKGQNNGLTHSWLSSSLAISPSEQIQFLQKIVNKKLSVNPKAFTMTKDILYIQELAGGWKLYGKTGNGRQLTKDKSQKLSLQHGWFIGWIEKDGRVITFTKHIADSKKHVTFASFRAKNETLNQLFYLINELEK"},"dna_sequence":{"accession":"AJ400619.1","fmin":"33","fmax":"834","strand":"+","sequence":"ATGAAGAAACTAAGCGTACTTCTATGGTTGACACTATTTTATTGCGGAACTATTTGGGCCCAAAGTACTTGCTTTTTGGTACAGGAAAATCAAACTGTGCTAAAGCACGAGGGTAAAGATTGCAATAAGCGTTTTGCGCCAGAATCAACCTTTAAAATTGCTTTGAGTCTTATGGGTTTTGATTCAGGAATATTAAAAGACACACTCAATCCGGAATGGCCGTACAAAAAAGAATATGAACTTTATCTTAATGTTTGGAAATATCCTCATAATCCACGTACCTGGATAAGAGATTCCTGTGTTTGGTATTCACAAGTTCTAACACAACAATTAGGTATGACTCGATTTAAGAATTATGTTGATGCATTTCACTATGGCAATCAGGATATTTCCGGCGACAAAGGTCAGAATAATGGATTAACCCATTCCTGGCTATCAAGCTCGCTTGCCATCTCACCAAGTGAGCAAATTCAGTTTCTGCAAAAAATAGTCAATAAAAAACTATCCGTGAATCCCAAAGCTTTCACTATGACTAAAGACATTCTATATATTCAAGAATTAGCGGGTGGTTGGAAACTGTATGGAAAAACAGGGAATGGTCGACAGTTAACAAAAGACAAAAGCCAAAAACTATCACTACAACACGGATGGTTCATCGGCTGGATTGAGAAAGATGGTCGTGTGATTACCTTTACGAAACACATTGCAGATAGTAAAAAACATGTAACCTTCGCCAGTTTCAGAGCGAAAAATGAGACCCTGAATCAATTATTTTACTTAATTAATGAATTGGAAAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36922","NCBI_taxonomy_name":"Fluoribacter gormanii","NCBI_taxonomy_id":"464"}}}},"ARO_accession":"3001424","ARO_id":"37824","ARO_name":"OXA-29","CARD_short_name":"OXA-29","ARO_description":"OXA-29 is a beta-lactamase found in Legionella gormanii.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1956":{"model_id":"1956","model_name":"IMI-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1190":{"protein_sequence":{"accession":"AAA93461.1","sequence":"MSLNVKPSRIAILFSSCLVSISFFSQANTKGIDEIKDLETDFNGRIGVYALDTGSGKSFSYKANERFPLCSSFKGFLAAAVLKGSQDNQLNLNQIVNYNTRSLEFHSPITTKYKDNGMSLGDMAAAALQYSDNGATNIILERYIGGPEGMTKFMRSIGDKDFRLDRWELDLNTAIPGDERDTSTPAAVAKSLKTLALGNILNEREKETYQTWLKGNTTGAARIRASVPSDWVVGDKTGSCGAYGTANDYAVVWPKNRAPLIISVYTTKNEKEAKHEDKVIAEASRIAIDNLK"},"dna_sequence":{"accession":"U50278.1","fmin":"1263","fmax":"2142","strand":"+","sequence":"ATGTCACTTAATGTAAAACCAAGTAGAATAGCCATCTTGTTTAGCTCTTGTTTAGTTTCAATATCATTTTTCTCACAGGCCAATACAAAGGGCATCGATGAGATTAAAGACCTTGAAACAGATTTCAATGGTAGAATTGGTGTCTACGCTTTAGACACTGGCTCAGGCAAATCATTTTCATACAAAGCAAATGAACGATTTCCATTATGTAGTTCTTTCAAAGGTTTTTTAGCTGCTGCTGTATTAAAAGGCTCTCAAGATAATCAACTAAATCTTAATCAGATCGTGAATTATAATACAAGAAGTTTAGAGTTCCATTCACCCATCACAACTAAATATAAAGATAATGGAATGTCATTAGGTGATATGGCTGCTGCAGCTTTACAATATAGCGACAATGGTGCTACTAATATTATCCTTGAACGATATATCGGTGGTCCTGAGGGTATGACTAAATTCATGCGGTCGATTGGAGATAAAGATTTTAGACTCGATCGTTGGGAGTTAGATCTAAACACAGCTATTCCTGGCGATGAACGTGACACATCTACACCTGCAGCAGTAGCTAAGAGCCTGAAAACCCTTGCACTGGGTAACATACTCAATGAGCGTGAAAAGGAAACCTATCAGACATGGTTAAAGGGTAACACAACCGGTGCAGCGCGTATTCGTGCTAGCGTACCAAGCGATTGGGTAGTTGGCGATAAAACTGGTAGTTGCGGTGCATACGGTACGGCAAATGATTATGCGGTAGTCTGGCCAAAGAACCGAGCTCCTCTTATAATTTCTGTATACACTACAAAAAACGAAAAAGAAGCCAAGCATGAGGATAAAGTAATCGCAGAAGCTTCAAGAATCGCAATTGATAACCTTAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3001858","ARO_id":"38258","ARO_name":"IMI-1","CARD_short_name":"IMI-1","ARO_description":"IMI-1 is a beta-lactamase found in Enterobacter cloacae.","ARO_category":{"36027":{"category_aro_accession":"3000018","category_aro_cvterm_id":"36027","category_aro_name":"IMI beta-lactamase","category_aro_description":"IMI beta-lactamases are a group of TEM-1-like beta-lactamase that are known to hydrolyze imipenem. IMI beta-lactamases are inhibited by clavulanic acid and tazobactam.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1899":{"model_id":"1899","model_name":"vanY gene in vanF cluster","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"50"}},"model_sequences":{"sequence":{"380":{"protein_sequence":{"accession":"AAF36805.1","sequence":"MKKWGLLLVFALFLVFIFNILPISQDKVEDRIYEQNDKDTSDDKMTAENMQKIELTEEQIYQGNLLLVNNEHPVHQKSIKSDIINLFTHKELTKGYGLLDNEIKLSEEIAGKFSEMIAAAEEDGVSNFLISSGYRDLDEQSRLYEEMGSDFALPAGHSEHNLGLSLDVGSTQMKMDKAPEGKWIEKNCWEYGFILRYPLDKTDVTGIQYEPWHIRYVGLPHSAIMQEMNLALEEYLDYLKEEKSISVRVDGKKYTISYDPISQNETIEVEVPADEQYEISGNNIDGVIVTTFS"},"dna_sequence":{"accession":"AF155139.1","fmin":"3396","fmax":"4278","strand":"+","sequence":"ATGAAAAAGTGGGGACTTTTATTGGTTTTTGCATTATTTCTAGTATTTATTTTTAATATATTACCGATATCCCAAGATAAAGTAGAGGATCGAATATATGAACAAAATGACAAAGATACATCGGATGATAAAATGACAGCTGAAAATATGCAAAAGATTGAGCTTACGGAAGAGCAGATCTATCAAGGGAATCTACTCTTGGTCAACAATGAACATCCTGTTCACCAAAAGAGTATAAAATCGGATATTATAAATTTATTTACGCACAAAGAATTGACAAAGGGGTATGGGTTACTTGATAACGAAATTAAATTGTCAGAGGAAATAGCTGGGAAATTTTCAGAGATGATAGCTGCGGCTGAAGAGGATGGCGTTAGTAATTTTTTAATTAGCAGTGGTTATCGAGACTTGGATGAGCAAAGCAGACTTTATGAGGAAATGGGTTCTGATTTTGCTTTGCCAGCAGGTCATAGTGAACACAACTTGGGGTTATCGCTTGATGTAGGATCTACTCAAATGAAGATGGATAAAGCGCCTGAAGGAAAGTGGATAGAAAAAAATTGTTGGGAATACGGCTTTATATTACGCTATCCCTTGGATAAAACGGATGTTACAGGAATTCAATATGAACCTTGGCATATTCGCTATGTCGGTTTGCCTCACAGTGCGATTATGCAGGAAATGAATTTAGCTTTGGAAGAATATTTAGATTATTTAAAAGAAGAAAAGAGCATTTCTGTTCGTGTTGATGGGAAAAAATATACAATTTCATATGATCCCATTTCTCAAAACGAGACAATTGAAGTTGAAGTACCAGCGGATGAACAGTATGAAATATCTGGTAATAATATTGATGGAGTAATTGTGACCACATTTTCTTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39542","NCBI_taxonomy_name":"Paenibacillus popilliae ATCC 14706","NCBI_taxonomy_id":"1212764"}}}},"ARO_accession":"3002958","ARO_id":"39392","ARO_name":"vanY gene in vanF cluster","CARD_short_name":"vanY_in_vanF_cl","ARO_description":"Also known as vanYF, is a vanY variant found in the vanF gene cluster.","ARO_category":{"36216":{"category_aro_accession":"3000077","category_aro_cvterm_id":"36216","category_aro_name":"vanY","category_aro_description":"VanY is a D,D-carboxypeptidase that cleaves removes the terminal D-Ala from peptidoglycan for the addition of D-Lactate. The D-Ala-D-Lac peptidoglycan subunits have reduced binding affinity with vancomycin compared to D-Ala-D-Ala.","category_aro_class_name":"AMR Gene Family"},"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1907":{"model_id":"1907","model_name":"vanS gene in vanA cluster","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"3276":{"protein_sequence":{"accession":"AAA65954.1","sequence":"MVIKLKNKKNDYSKLERKLYMYIVAIVVVAIVFVLYIRSMIRGKLGDWILSILENKYDLNHLDAMKLYQYSIRNNIDIFIYVAIVISILILCRVMLSKFAKYFDEINTGIDVLIQNEDKQIELSAEMDVMEQKLNTLKRTLEKREQDAKLAEQRKNDVVMYLAHDIKTPLTSIIGYLSLLDEAPDMPVDQKAKYVHITLDKAYRLEQLIDEFFEITRYNLQTITLTKTHIDLYYMLVQMTDEFYPQLSAHGKQAVIHAPEDLTVSGDPDKLARVFNNILKNAAAYSEDNSIIDITAGLSGDVVSIEFKNTGSIPKDKLAAIFEKFYRLDNARSSDTGGAGLGLAIAKEIIVQHGGQIYAESNDNYTTFRVELPAMPDLVDKRRS"},"dna_sequence":{"accession":"M97297.1","fmin":"4648","fmax":"5803","strand":"+","sequence":"TTGGTTATAAAATTGAAAAATAAAAAAAACGACTATTCCAAACTAGAACGAAAACTTTACATGTATATCGTTGCAATTGTTGTGGTAGCAATTGTATTCGTGTTGTATATTCGTTCAATGATCCGAGGGAAACTTGGGGATTGGATCTTAAGTATTTTGGAAAACAAATATGACTTAAATCACCTGGACGCGATGAAATTATATCAATATTCCATACGGAACAATATAGATATCTTTATTTATGTGGCGATTGTCATTAGTATTCTTATTCTATGTCGCGTCATGCTTTCAAAATTCGCAAAATACTTTGACGAGATAAATACCGGCATTGATGTACTTATTCAGAACGAAGATAAACAAATTGAGCTTTCTGCGGAAATGGATGTTATGGAACAAAAGCTCAACACATTAAAACGGACTCTGGAAAAGCGAGAGCAGGATGCAAAGCTGGCCGAACAAAGAAAAAATGACGTTGTTATGTACTTGGCGCACGATATTAAAACGCCCCTTACATCCATTATCGGTTATTTGAGCCTGCTTGACGAGGCTCCAGACATGCCGGTAGATCAAAAGGCAAAGTATGTGCATATCACGTTGGACAAAGCGTATCGACTCGAACAGCTAATCGACGAGTTTTTTGAGATTACACGGTATAACCTACAAACGATAACGCTAACAAAAACGCACATAGACCTATACTATATGCTGGTGCAGATGACCGATGAATTTTATCCTCAGCTTTCCGCACATGGAAAACAGGCGGTTATTCACGCCCCCGAGGATCTGACCGTGTCCGGCGACCCTGATAAACTCGCGAGAGTCTTTAACAACATTTTGAAAAACGCCGCTGCATACAGTGAGGATAACAGCATCATTGACATTACCGCGGGCCTCTCCGGGGATGTGGTGTCAATCGAATTCAAGAACACTGGAAGCATCCCAAAAGATAAGCTAGCTGCCATATTTGAAAAGTTCTATAGGCTGGACAATGCTCGTTCTTCCGATACGGGTGGCGCGGGACTTGGATTGGCGATTGCAAAAGAAATTATTGTTCAGCATGGAGGGCAGATTTACGCGGAAAGCAATGATAACTATACGACGTTTAGGGTAGAGCTTCCAGCGATGCCAGACTTGGTTGATAAAAGGAGGTCCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36779","NCBI_taxonomy_name":"Enterococcus faecium","NCBI_taxonomy_id":"1352"}}}},"ARO_accession":"3002931","ARO_id":"39365","ARO_name":"vanS gene in vanA cluster","CARD_short_name":"vanS_in_vanA_cl","ARO_description":"Also known as vanSA, is a vanS variant found in the vanA gene cluster.","ARO_category":{"36210":{"category_aro_accession":"3000071","category_aro_cvterm_id":"36210","category_aro_name":"vanS","category_aro_description":"VanS is similar to histidine protein kinases like EnvZ and acts as a response regulator by activating VanR. VanS is required for high level transcription of other van glycopeptide resistance genes.","category_aro_class_name":"AMR Gene Family"},"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"35948":{"category_aro_accession":"0000029","category_aro_cvterm_id":"35948","category_aro_name":"teicoplanin","category_aro_description":"Teicoplanin is a glycopeptide antibiotic used in the prophylaxis and treatment of serious infections caused by Gram-positive bacteria. Teicoplanin has a unique acyl-aliphatic chain, and binds to cell wall precursors to inhibit transglycosylation  and transpeptidation.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1957":{"model_id":"1957","model_name":"VIM-18","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1407":{"protein_sequence":{"accession":"CAO83029.1","sequence":"MFKLLSKLLVYLTASIMAIASPLAFSVDSSGEYPTVSEIPVGEVRLYQIADGVWSHIATRSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLANEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSASVLYGGCAIYELSRTSAGNVADADLAEWPTSIERIQQHYPEAQFVIPGHGLPGGLDLLKHTTNVVKAHTNRSVVE"},"dna_sequence":{"accession":"AM778091.1","fmin":"26","fmax":"815","strand":"+","sequence":"ATGTTCAAACTTTTGAGTAAGTTATTGGTCTATTTGACCGCGTCTATCATGGCTATTGCGAGTCCGCTCGCTTTTTCCGTAGATTCTAGCGGTGAGTATCCGACAGTCAGCGAAATTCCGGTCGGGGAGGTCCGGCTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCGGTCGTTTGATGGCGCAGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAGAAGCAAATTGGACTTCCTGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCGAACGAGATTCCCACGCACTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAACTCTTCTATCCTGGTGCTGCGCATTCGACCGACAACTTAGTTGTGTACGTCCCGTCTGCGAGTGTGCTCTATGGTGGTTGTGCGATTTATGAGTTGTCACGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCATTGAGCGGATTCAACAACACTACCCGGAAGCACAGTTCGTCATTCCGGGGCACGGCCTGCCGGGCGGTCTAGACTTGCTCAAGCACACAACGAATGTTGTAAAAGCGCACACAAATCGCTCAGTCGTTGAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002288","ARO_id":"38688","ARO_name":"VIM-18","CARD_short_name":"VIM-18","ARO_description":"VIM-18 is a beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1958":{"model_id":"1958","model_name":"VIM-33","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1331":{"protein_sequence":{"accession":"AFP99175.1","sequence":"MLKVISSLLVYMTASVMAVASPLAHSGEPSGEYPTVNEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEAEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSANVLFGGCAVHELSSTSAGNVADADLAEWPTSVERIQKHYPEAEVVIPGHGLPGGLDLLQHTANVVKAHKNRSVAE"},"dna_sequence":{"accession":"JX258134.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGTTAAAAGTTATTAGTAGTTTATTGGTCTACATGACCGCGTCTGTCATGGCTGTCGCAAGTCCGTTAGCCCATTCCGGGGAGCCGAGTGGTGAGTATCCGACAGTCAACGAAATTCCGGTCGGAGAGGTCCGACTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCGGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAAAAGCAAATTGGACTTCCCGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGCAGAGGGGAACGAGATTCCCACGCATTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAGCTCTTCTATCCTGGTGCTGCGCATTCGACCGACAATCTGGTTGTATACGTCCCGTCAGCGAACGTGCTATTCGGTGGTTGTGCCGTTCATGAGTTGTCAAGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCGTTGAGCGGATTCAAAAACACTACCCGGAAGCAGAGGTCGTCATTCCCGGGCACGGTCTACCGGGCGGTCTAGACTTGCTCCAGCACACAGCGAACGTTGTCAAAGCACACAAAAATCGCTCAGTCGCCGAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002303","ARO_id":"38703","ARO_name":"VIM-33","CARD_short_name":"VIM-33","ARO_description":"VIM-33 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1959":{"model_id":"1959","model_name":"ACT-7","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"759":{"protein_sequence":{"accession":"ACJ05688.1","sequence":"MMRKSLCCALLLGISCSALATPVSEKQLAEVVANTVTPLMKAQSVPGMAVAVIYQGKPHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMPYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPENVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVVEGSDSKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANTSYPNPARVEAAYHILEALQ"},"dna_sequence":{"accession":"FJ237368.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAGAAAATCCCTTTGCTGCGCCCTGCTGCTCGGCATCTCTTGCTCTGCTCTCGCCACGCCAGTGTCAGAAAAACAGCTGGCGGAGGTGGTAGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCTGTTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGAAAACCGCACTATTACACGTTTGGCAAGGCCGATATCGCGGCGAATAAACCCGTTACGCCTCAGACCCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGCGTTTTAGGTGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTGACGGGCAAGCAGTGGCAGGGTATTCGTATGCTGGATCTCGCCACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTCAAACCTTCTGGCATGCCCTATGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTGCCGAAAGCGGAAGAGGCACATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGTATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCGGAGAACGTTGCTGATGCCTCACTTAAGCAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGGTCGAGGGCAGCGACAGTAAGGTAGCGCTGGCGCCGTTGCCCGTGGCAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGCTCTACTGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATACAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCGAGGCGCTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001830","ARO_id":"38230","ARO_name":"ACT-7","CARD_short_name":"ACT-7","ARO_description":"ACT-7 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1960":{"model_id":"1960","model_name":"smeB","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"2090"}},"model_sequences":{"sequence":{"521":{"protein_sequence":{"accession":"AAD51345.1","sequence":"MVRFFIDRPIFAWVIAIAVSLLGLLAILILPVDRYPQIAPPTITIRATYTGASSQTVENAVTQVIEQSQQSLDHLMYMTSTSASDGSAQVNLVFATGTNPDTAQVQVQNQLQAAMATLPQAVQQNGLTITKSSGSIFEVLSFTSEDGSMDNFDVANFMEARIDDQISRVSGVGNIQPIGQEYAMRIWLDPEKMRQYALMPWDIETALQAQNTDVSAGELGGQPALKGQQLDATVTARSRLHTPEQFAQVVLKADANGSVVRLGDVAKIGLGPESYDSISTFNGKPSASLGIELNAGANAIAVSKAIDARLQQLQKYWPHGYTAHVAFTTTPFVTISLKEVVITLIEAIILVVLVMYLFLQNWRATLIPTIAVPVVLLGTFGVLAAFGYSINTLTMFALVLAIGLLVDDAIVVVENVERVMTFEGLAPKPATLKAMGQITGALVGIVLVLTAVFLPMAFFSGVTGVIYRQFSVTIAAAMILSVLVAMTITPALCGSILHQIPKGGHPHGDHGGEPSLLGKFFIWFNHRFERTSNGLRHRVDRFLGRRTLGVLFYLVLSVATGLLLWHLPGAFLPDEDQGMLNALVKLPAGSTLEQTRAVMDRLSAVAVKDDGVLSIQATAGFSVTGSGQNVGQAFIRLKDWDDRKDDADTIAARLTRAMASVPDAQVFITSPPAILGLGDAGGFTLELQDEGGAGHAAAVAARNTLLKEAAKDPKLVNVRYASLEDAPVYAVKVDDAKAQAMGVNPQDVNDTLNAALGGDFVNNFIYKGRIKKVFIQGTAEARMQPQDIERWSVRNQAGQMVPLSSLISTHWTSAPAAVQRYNGISAMEITGQPAPGVSSGEAMAEIARLADTLPEGFSHAWSDMAYQEQLSGNQAPMLYAISLLFVFLCLAALYESWAVPFAVMLAVPVGMFGAVLMMNLRGLNNDVYFQVGLLTTIGLAAKNGILIVEFARILEQQGKSTREAILQAVYLRLRPIVMTSLAFLMGVLPLVFATGAGSAARRSLGTGVAGGTVASMVLGMFFVPLFYLLVRRLFPGRAPADATVPETSP"},"dna_sequence":{"accession":"AF173226.1","fmin":"3767","fmax":"6917","strand":"+","sequence":"ATGGTTCGTTTCTTCATCGACCGGCCGATCTTCGCCTGGGTGATCGCCATCGCGGTCAGCCTGCTCGGCCTGCTCGCGATCCTGATCCTGCCGGTGGACCGCTACCCGCAGATCGCCCCGCCCACCATCACCATCCGCGCCACCTACACCGGCGCCTCGTCGCAGACCGTGGAAAACGCGGTCACCCAGGTCATCGAGCAGTCCCAGCAAAGCCTCGATCACCTGATGTACATGACCTCGACCAGTGCCTCCGACGGCTCGGCGCAGGTCAACCTGGTGTTCGCCACCGGTACCAATCCGGATACCGCGCAGGTGCAGGTGCAGAACCAGCTGCAGGCCGCCATGGCCACGCTGCCGCAGGCGGTGCAGCAGAACGGCCTGACCATCACCAAGTCCAGTGGTTCGATCTTCGAGGTGCTGTCGTTCACCAGCGAAGACGGCAGCATGGACAACTTCGATGTCGCCAACTTCATGGAAGCGCGCATCGATGACCAGATCAGCCGCGTCAGCGGTGTCGGCAACATCCAGCCGATCGGCCAGGAATACGCCATGCGCATCTGGCTGGATCCGGAGAAGATGCGCCAGTACGCGCTGATGCCCTGGGACATCGAGACCGCATTGCAGGCACAGAACACCGATGTCTCCGCCGGTGAGCTGGGTGGCCAGCCGGCGCTGAAGGGCCAGCAGCTCGACGCCACGGTAACCGCGCGCAGCCGCCTGCACACGCCCGAGCAGTTCGCGCAGGTGGTGCTCAAGGCCGATGCCAACGGCAGCGTGGTGCGTCTGGGCGACGTGGCAAAGATCGGCCTCGGGCCGGAAAGCTACGACAGCATCAGCACCTTCAATGGCAAGCCGTCGGCGTCGCTGGGCATTGAACTCAATGCCGGTGCCAACGCGATCGCCGTCTCCAAGGCCATCGATGCACGGCTTCAGCAGCTGCAGAAGTACTGGCCGCATGGCTACACCGCCCACGTGGCCTTCACCACCACCCCATTCGTGACCATTTCGCTGAAGGAAGTGGTGATCACCCTGATCGAAGCGATCATCCTGGTGGTGCTGGTGATGTACCTGTTCCTGCAGAACTGGCGCGCCACGCTGATCCCGACCATCGCGGTGCCGGTGGTGCTGCTGGGCACGTTCGGCGTGCTGGCTGCATTCGGGTATTCGATCAACACCCTGACCATGTTCGCACTGGTGCTGGCCATCGGCCTGCTGGTGGACGATGCCATCGTGGTGGTGGAGAACGTAGAGCGGGTGATGACCTTCGAAGGGCTGGCGCCGAAGCCGGCCACGCTGAAGGCGATGGGCCAGATCACCGGCGCGCTGGTCGGCATCGTGCTGGTGCTGACCGCGGTGTTCCTGCCGATGGCGTTCTTCAGCGGTGTAACCGGGGTGATCTATCGCCAGTTCTCGGTGACGATCGCCGCCGCGATGATCCTGTCGGTGCTGGTGGCGATGACCATCACCCCGGCACTGTGTGGCAGCATCCTGCACCAGATTCCCAAGGGCGGCCATCCGCATGGCGACCACGGTGGCGAGCCGAGCCTGCTGGGCAAGTTCTTCATCTGGTTCAACCACCGCTTCGAGCGCACCTCCAACGGCCTGCGCCATCGCGTGGATCGTTTCCTCGGCCGCCGCACGCTCGGCGTGCTGTTCTACCTGGTGCTGAGCGTGGCCACCGGCCTGTTGCTGTGGCACCTGCCGGGCGCGTTCCTGCCCGATGAAGACCAGGGCATGCTCAACGCGCTGGTGAAGCTGCCGGCCGGTTCCACGCTGGAGCAGACGCGGGCGGTGATGGATCGTCTGAGTGCCGTCGCGGTGAAGGACGACGGCGTGCTCTCGATCCAGGCCACCGCCGGTTTCAGTGTTACCGGCAGCGGCCAGAACGTCGGCCAGGCCTTCATCCGGCTGAAGGACTGGGATGACCGCAAGGACGACGCCGATACCATCGCCGCACGCTTGACGCGGGCGATGGCCAGCGTGCCCGATGCGCAGGTGTTCATCACCTCGCCACCGGCCATCCTGGGCCTCGGCGATGCGGGTGGCTTCACCCTGGAACTGCAGGACGAAGGCGGTGCAGGCCATGCCGCCGCCGTGGCCGCGCGCAACACGCTGCTGAAGGAAGCCGCCAAGGACCCGAAGCTGGTCAACGTGCGCTACGCCAGCCTGGAAGACGCGCCGGTATACGCGGTGAAGGTGGACGACGCCAAGGCGCAGGCGATGGGCGTGAACCCGCAGGACGTCAATGACACCTTGAACGCGGCGTTGGGCGGCGACTTCGTCAACAACTTCATCTACAAGGGGCGCATCAAGAAGGTGTTCATCCAGGGCACCGCCGAAGCACGCATGCAGCCGCAGGACATCGAGCGCTGGAGCGTGCGCAACCAGGCCGGGCAGATGGTGCCGCTGTCGTCGTTGATCAGCACGCATTGGACCAGCGCGCCGGCCGCAGTGCAGCGCTACAACGGCATCTCGGCGATGGAAATCACCGGCCAGCCGGCACCGGGCGTCAGCTCCGGCGAGGCGATGGCCGAGATCGCGCGCCTGGCCGACACGCTGCCGGAAGGCTTCAGCCATGCCTGGTCGGACATGGCCTACCAGGAACAGCTGTCGGGCAACCAGGCGCCGATGCTGTACGCCATCTCGCTGCTGTTCGTGTTCCTGTGCCTGGCCGCGCTGTATGAAAGCTGGGCGGTGCCGTTCGCGGTGATGCTGGCGGTGCCGGTGGGCATGTTCGGCGCCGTGCTGATGATGAACCTGCGTGGCCTCAACAACGACGTGTACTTCCAGGTCGGCCTGCTGACCACGATTGGTCTGGCAGCGAAGAACGGCATCCTGATCGTCGAGTTCGCGCGCATCCTCGAACAGCAGGGCAAGAGCACCCGCGAAGCGATCCTGCAGGCGGTCTACCTGCGGCTGCGGCCGATCGTAATGACCTCGCTGGCGTTCCTGATGGGCGTACTGCCGCTGGTGTTCGCCACCGGCGCCGGTTCGGCTGCGCGCCGTTCGCTGGGTACCGGCGTGGCCGGTGGTACGGTTGCCTCGATGGTGCTGGGCATGTTCTTCGTGCCGTTGTTCTACCTGCTGGTGCGCCGCCTGTTCCCGGGCCGCGCGCCGGCCGACGCCACTGTCCCGGAGACAAGCCCATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37076","NCBI_taxonomy_name":"Stenotrophomonas maltophilia","NCBI_taxonomy_id":"40324"}}}},"ARO_accession":"3003052","ARO_id":"39486","ARO_name":"smeB","CARD_short_name":"smeB","ARO_description":"smeB is the inner membrane multidrug exporter of the efflux complex smeABC in Stenotrophomonas maltophilia.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1961":{"model_id":"1961","model_name":"TEM-105","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1071":{"protein_sequence":{"accession":"AAM61953.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCNAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AF516720.1","fmin":"214","fmax":"1075","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAATGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000968","ARO_id":"37348","ARO_name":"TEM-105","CARD_short_name":"TEM-105","ARO_description":"TEM-105 is a beta-lactamase found in E. coli.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1962":{"model_id":"1962","model_name":"OXA-47","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1614":{"protein_sequence":{"accession":"AAP69225.1","sequence":"MKNTIHINFAIFLIIANIIYSSASASTDISTVASQLFEGTEGCFLLYDASTNAEIAQFNKAKCAAQMAPDSTFKIALSLMAFDAEIIDQKTIFKWDKIPKGMEIWNSNHTPKTWMQFSVVWVSQEITQKIGLNKIKNYLKDFDYGNQDFSGDKERNNGLTEAWLESSLKISPEEQIQFLRKIINHNLPVRNSAIENTIDNMYLQDLENSTKLYGKTGAGFTANRTLQNGWFEGFIISKSGHKYVFVSALTGSLGSNLTSSIKAKKNAITILNTLNL"},"dna_sequence":{"accession":"AY237830.1","fmin":"0","fmax":"831","strand":"+","sequence":"ATGAAAAACACAATACATATCAACTTCGCTATTTTTTTAATAATTGCAAATATTATCTACAGCAGCGCCAGTGCATCAACAGATATCTCTACTGTTGCATCTCAATTATTTGAAGGAACTGAAGGTTGTTTTTTACTTTACGATGCATCCACAAACGCTGAAATTGCTCAATTCAATAAAGCAAAGTGCGCAGCGCAAATGGCACCAGATTCAACTTTCAAGATCGCATTATCACTTATGGCATTTGATGCGGAAATAATAGATCAGAAAACCATATTCAAATGGGATAAAATCCCAAAAGGAATGGAAATTTGGAACAGCAATCATACACCAAAGACGTGGATGCAATTTTCTGTTGTTTGGGTTTCGCAAGAAATAACCCAAAAAATTGGATTAAATAAAATCAAAAATTATCTCAAAGATTTTGATTATGGAAATCAAGACTTCTCTGGAGATAAAGAAAGAAACAACGGATTAACAGAAGCATGGCTCGAAAGTAGCTTAAAAATTTCACCGGAAGAACAAATTCAATTCCTGCGTAAAATTATTAATCACAATCTTCCAGTTAGAAATTCAGCCATAGAAAACACCATAGATAACATGTATCTACAAGATCTGGAGAATAGTACAAAACTGTATGGGAAAACTGGTGCAGGATTTACAGCAAATAGAACCCTACAAAACGGATGGTTTGAAGGGTTTATTATAAGCAAATCAGGACATAAATATGTTTTTGTGTCCGCACTTACAGGAAGCTTGGGGTCGAATTTAACATCAAGCATAAAAGCCAAGAAAAATGCAATCACCATTCTAAACACACTAAATTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001781","ARO_id":"38181","ARO_name":"OXA-47","CARD_short_name":"OXA-47","ARO_description":"OXA-47 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46485":{"category_aro_accession":"3007696","category_aro_cvterm_id":"46485","category_aro_name":"OXA-1-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-1.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1963":{"model_id":"1963","model_name":"TEM-190","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1000":{"protein_sequence":{"accession":"AEL88240.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMLSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRGEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERDRQIAEIGASLIKHW"},"dna_sequence":{"accession":"JN416112.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGCTGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATCGTGGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAGATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001050","ARO_id":"37430","ARO_name":"TEM-190","CARD_short_name":"TEM-190","ARO_description":"TEM-190 is a beta-lactamase.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1964":{"model_id":"1964","model_name":"IMP-45","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"953":{"protein_sequence":{"accession":"AIA58910.1","sequence":"MSKLFVFFMFLFCSITAAGESLPDLKIEKLDEGVYVHTSFEEVNGWGVIPKHGLVVLVNTDAYLIDTPFTAKDTENLVNWFVERGYRIKGSISSHFHSDSTGGIEWLNSQSIPTYASELTNELLKKDGKVQAKYSFSGVSYWLVKKKIEVFYPGPGHAPDNVVVWLPENRVLFGGCFVKPYGLGNLGDANLEAWPKSAKLLMSKYSKAKLVVPGHSDIGDSSLLKLTWEQTVKGFNESKKSTTAH"},"dna_sequence":{"accession":"KJ510410.1","fmin":"5740","fmax":"6478","strand":"+","sequence":"ATGAGCAAGTTATTTGTATTCTTTATGTTTTTGTTTTGTAGCATTACTGCCGCAGGAGAGTCTTTGCCAGATTTAAAAATTGAGAAGCTTGACGAAGGCGTTTATGTTCATACTTCGTTTGAAGAAGTTAACGGTTGGGGTGTTATTCCTAAACACGGCTTGGTGGTTCTTGTAAATACTGATGCCTATCTGATAGACACTCCATTTACTGCTAAAGATACTGAAAATTTAGTTAATTGGTTTGTTGAGCGCGGCTATAGAATAAAAGGCAGTATTTCCTCACATTTCCATAGCGACAGCACGGGTGGAATAGAGTGGCTTAATTCTCAATCTATCCCCACGTATGCATCTGAATTAACAAATGAACTTCTTAAAAAAGACGGTAAGGTACAAGCTAAATATTCATTTAGCGGAGTTAGCTATTGGCTAGTTAAGAAAAAGATTGAAGTTTTTTATCCTGGTCCAGGGCACGCTCCAGATAACGTAGTGGTTTGGCTGCCTGAAAATAGAGTTTTGTTCGGTGGTTGTTTTGTTAAACCCTACGGTCTAGGTAATTTGGGTGACGCAAATTTAGAAGCTTGGCCAAAATCCGCCAAATTATTAATGTCAAAATATAGTAAGGCAAAACTGGTTGTACCAGGTCATAGTGACATAGGAGATTCGTCGCTCTTGAAGCTTACATGGGAGCAGACGGTAAAAGGATTCAATGAAAGCAAAAAAAGTACCACTGCACATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002236","ARO_id":"38636","ARO_name":"IMP-45","CARD_short_name":"IMP-45","ARO_description":"IMP-45 is a beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1965":{"model_id":"1965","model_name":"LEN-11","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"6132":{"protein_sequence":{"accession":"SAU22663.1","sequence":"MRYVRLCVISLLATLPLAVDAGPQPLEQIKQSESQLSGRVGMVEMDLASGRTLAAWRADERFPMVSTFKVLLCGAVLARVDAGLEQLDRRIHYRQQDLVDYSPVSEKHLVDGMTIGELCAAAITLSDNSAGNLLLATVGGPAGLTAFLRQIGDNVTRLDRWETALNEALPGDARDTTTPASMAATLRKLLTAQHLSARSQQQLLQWMVDDRVAGPLIRAVLPAGWFIADKTGAGERGARGIVALLGPDGKPERIVVIYLRDTPASMAERNQHIAGIGAALIEHWQR"},"dna_sequence":{"accession":"FLES01000010.1","fmin":"120291","fmax":"121152","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGTGTTATCTCCCTGTTAGCCACCCTGCCACTGGCGGTAGACGCCGGTCCACAGCCGCTTGAGCAGATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTGGGGATGGTGGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCGATGAACGCTTTCCCATGGTGAGCACCTTTAAAGTGCTGCTGTGCGGCGCGGTGCTGGCGCGGGTGGATGCCGGGCTCGAACAACTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGTCGACGGGATGACGATCGGCGAACTCTGCGCCGCCGCCATCACCCTGAGCGATAACAGCGCTGGCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCGGGATTAACTGCCTTTCTGCGCCAGATCGGTGACAACGTCACCCGTCTTGACCGCTGGGAAACGGCACTGAATGAGGCGCTTCCCGGCGACGCGCGCGACACCACCACCCCGGCCAGCATGGCCGCCACGCTGCGCAAACTACTGACCGCGCAGCATCTGAGCGCCCGTTCGCAACAGCAACTCCTGCAGTGGATGGTGGACGATCGGGTTGCCGGCCCGCTGATCCGCGCCGTGCTGCCGGCGGGCTGGTTTATCGCCGACAAAACCGGGGCTGGCGAACGGGGTGCGCGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAACCGGAGCGCATTGTGGTGATCTATCTGCGGGATACCCCGGCGAGTATGGCCGAGCGTAATCAACATATCGCCGGGATCGGCGCAGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42612","NCBI_taxonomy_name":"Klebsiella variicola","NCBI_taxonomy_id":"244366"}}}},"ARO_accession":"3002461","ARO_id":"38861","ARO_name":"LEN-11","CARD_short_name":"LEN-11","ARO_description":"LEN-11 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36236":{"category_aro_accession":"3000097","category_aro_cvterm_id":"36236","category_aro_name":"LEN beta-lactamase","category_aro_description":"LEN beta-lactamases are chromosomal class A beta-lactamases that confer resistance to ampicillin, amoxicillin, carbenicillin, and ticarcillin but not to extended-spectrum beta-lactams.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1967":{"model_id":"1967","model_name":"OXA-116","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6248":{"protein_sequence":{"accession":"ABW95047.1","sequence":"LLITSAIFISACSPYIVSANPNHSASKSDDKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSL"},"dna_sequence":{"accession":"EU220744.1","fmin":"0","fmax":"786","strand":"+","sequence":"TTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGTCTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGACAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACTACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTGGGTTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTA","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001441","ARO_id":"37841","ARO_name":"OXA-116","CARD_short_name":"OXA-116","ARO_description":"OXA-116 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1968":{"model_id":"1968","model_name":"SHV-189","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"2125":{"protein_sequence":{"accession":"AJO16047.1","sequence":"MRYFRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGSVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGKRGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"KP050494.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATTTTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCAGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCAAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGGATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3003156","ARO_id":"39733","ARO_name":"SHV-189","CARD_short_name":"SHV-189","ARO_description":"SHV-189 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1970":{"model_id":"1970","model_name":"SHV-44","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"2025":{"protein_sequence":{"accession":"AAP82228.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQLQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"AY259119.1","fmin":"116","fmax":"977","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTACTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACTGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATCGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001102","ARO_id":"37482","ARO_name":"SHV-44","CARD_short_name":"SHV-44","ARO_description":"SHV-44 is a broad-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1971":{"model_id":"1971","model_name":"dfrB2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"150"}},"model_sequences":{"sequence":{"5108":{"protein_sequence":{"accession":"ABI20482.1","sequence":"MGQSSDEANAPVAGQFALPLSATFGLGDRVRKKSGAAWQGQVVGWYCTKLTPEGYAVESESHPGSVQIYPVAALERVA"},"dna_sequence":{"accession":"DQ839391.1","fmin":"38018","fmax":"38255","strand":"+","sequence":"ATGGGTCAAAGTAGCGATGAAGCCAACGCTCCCGTTGCAGGGCAGTTTGCGCTTCCCCTGAGTGCCACCTTTGGCTTAGGGGATCGCGTACGCAAGAAATCTGGTGCCGCTTGGCAGGGTCAAGTCGTCGGTTGGTATTGCACAAAACTCACTCCTGAAGGCTATGCGGTCGAGTCCGAATCCCACCCAGGCTCAGTGCAAATTTATCCTGTGGCTGCACTTGAACGTGTGGCCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36791","NCBI_taxonomy_name":"uncultured bacterium","NCBI_taxonomy_id":"77133"}}}},"ARO_accession":"3003021","ARO_id":"39455","ARO_name":"dfrB2","CARD_short_name":"dfrB2","ARO_description":"dfrB2 is an integron-encoded dihydrofolate reductase found in an uncultured bacterium from a wastewater treatment plant.","ARO_category":{"37617":{"category_aro_accession":"3001218","category_aro_cvterm_id":"37617","category_aro_name":"trimethoprim resistant dihydrofolate reductase dfr","category_aro_description":"Alternative dihydropteroate synthase dfr present on plasmids produces alternate proteins that are less sensitive to trimethoprim from inhibiting its role in folate synthesis, thus conferring trimethoprim resistance.","category_aro_class_name":"AMR Gene Family"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1972":{"model_id":"1972","model_name":"OXA-149","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1754":{"protein_sequence":{"accession":"ACX31141.1","sequence":"MNIKALLLITSAIFISACSPYIVSANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSNEVKHVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"GQ853680.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCCCTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGTCTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATTCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACTACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCATGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001454","ARO_id":"37854","ARO_name":"OXA-149","CARD_short_name":"OXA-149","ARO_description":"OXA-149 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1973":{"model_id":"1973","model_name":"TEM-111","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1643":{"protein_sequence":{"accession":"AAL77062.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVKYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGADERGSRGIIAALGPDGKPSRIVVIYMTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AF468003.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTAAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGATGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACATGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000974","ARO_id":"37354","ARO_name":"TEM-111","CARD_short_name":"TEM-111","ARO_description":"TEM-111 is a beta-lactamase found in E. coli and P. mirabilis.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1975":{"model_id":"1975","model_name":"blt","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"710":{"protein_sequence":{"accession":"AAC36944.1","sequence":"MKKSINEQKTIFIILLSNIFVAFLGIGLIIPVMPSFMKIMHLSGSTMGYLVAAFAISQLITSPFAGRWVDRFGRKKMIILGLLIFSLSELIFGLGTHVSIFYFSRILGGVSAAFIMPAVTAYVADITTLKERSKAMGYVSAAISTGFIIGPGAGGFIAGFGIRMPFFFASAIALIAAVTSVFILKESLSIEERHQLSSHTKESNFIKDLKRSIHPVYFIAFIIVFVMAFGLSAYETVFSLFSDHKFGFTPKDIAAIITISSIVAVVIQVLLFGKLVNKLGEKRMIQLCLITGAILAFVSTVMSGFLTVLLVTCFIFLAFDLLRPALTAHLSNMAGNQQGFVAGMNSTYTSLGNIFGPALGGILFDLNIHYPFLFAGFVMIVGLGLTMVWKEKKNDAAALN"},"dna_sequence":{"accession":"L32599.1","fmin":"1236","fmax":"2439","strand":"+","sequence":"ATGAAAAAATCAATAAATGAGCAAAAAACGATATTCATTATACTATTAAGCAACATCTTCGTAGCATTTCTTGGTATCGGTTTAATCATTCCAGTTATGCCTTCTTTTATGAAAATCATGCATTTATCCGGCAGCACAATGGGTTATCTTGTTGCGGCTTTTGCCATTTCTCAGTTAATTACTTCACCTTTTGCAGGTAGGTGGGTTGACCGTTTCGGGAGAAAAAAAATGATTATTCTCGGGTTGCTTATATTCAGTTTATCTGAGTTGATTTTCGGATTAGGGACCCATGTTTCAATATTTTATTTCTCGAGGATATTGGGTGGTGTAAGTGCGGCTTTTATCATGCCCGCGGTAACAGCATATGTAGCTGATATTACAACCCTAAAGGAAAGGTCAAAGGCTATGGGGTATGTTTCTGCTGCAATTAGCACCGGCTTTATTATTGGACCTGGTGCGGGAGGATTTATTGCCGGCTTTGGTATCCGCATGCCGTTTTTCTTCGCCTCCGCCATCGCGTTAATAGCAGCTGTCACTTCCGTTTTTATACTAAAAGAGTCATTGTCGATAGAAGAACGCCATCAACTCTCATCTCATACAAAGGAATCAAATTTCATTAAAGACTTGAAGAGATCCATTCATCCTGTCTATTTCATTGCATTTATTATCGTCTTTGTAATGGCTTTTGGTTTATCAGCTTATGAAACGGTATTCAGCTTGTTTTCTGATCATAAATTTGGCTTCACACCAAAAGATATTGCAGCCATTATTACGATTAGTTCCATTGTTGCGGTAGTTATTCAAGTTTTACTATTCGGGAAATTGGTCAACAAACTTGGAGAGAAAAGAATGATTCAGCTGTGCTTAATAACCGGTGCGATCTTGGCTTTCGTGTCTACTGTTATGTCAGGATTTTTAACTGTTTTGCTTGTAACTTGTTTTATTTTTCTGGCGTTCGATTTGCTACGTCCGGCCTTAACCGCTCATTTATCCAATATGGCCGGTAACCAGCAGGGTTTCGTAGCAGGCATGAACTCCACATACACCAGCCTGGGAAATATATTTGGACCTGCTCTAGGCGGTATACTATTTGATCTTAACATTCATTATCCTTTCCTTTTTGCAGGTTTCGTTATGATTGTCGGCCTTGGTCTTACAATGGTTTGGAAAGAAAAAAAGAATGATGCTGCAGCTTTGAATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39579","NCBI_taxonomy_name":"Bacillus subtilis subsp. subtilis str. 168","NCBI_taxonomy_id":"224308"}}}},"ARO_accession":"3003006","ARO_id":"39440","ARO_name":"blt","CARD_short_name":"blt","ARO_description":"blt is an MFS efflux pump that confers resistance to multiple drugs such as rhodamine and acridine dyes, and fluoroquinolone antibiotics.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35963":{"category_aro_accession":"0000045","category_aro_cvterm_id":"35963","category_aro_name":"acriflavine","category_aro_description":"Acriflavine is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"43746":{"category_aro_accession":"3005386","category_aro_cvterm_id":"43746","category_aro_name":"disinfecting agents and antiseptics","category_aro_description":"Disinfectants that can also interact with antimicrobial resistance mechanisms, e.g. molecule efflux, and thus are the targets of disinfectant resistance.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1977":{"model_id":"1977","model_name":"AAC(6')-Ik","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"541":{"protein_sequence":{"accession":"AAA87229.1","sequence":"MNIKPASEASLKDWLKLRIKLWNDLEESHLQEMHQLLAEKHALQLLVYSDDHAVGMLEASIRYEYVNGTETSPVAFLEGIYVLPEYRRLGVATLLVRQVEAWAKQFSCTEFASDAALDNVISHAMHRALGFQETERVVYFSKKID"},"dna_sequence":{"accession":"L29510.1","fmin":"368","fmax":"806","strand":"+","sequence":"ATGAATATTAAACCAGCATCAGAAGCTTCACTCAAAGATTGGTTAAAACTAAGAATAAAGCTTTGGAATGATCTTGAAGAATCACATTTGCAAGAGATGCATCAGTTATTGGCTGAAAAGCATGCATTACAATTATTAGTCTATTCGGATGATCACGCGGTTGGCATGCTAGAAGCATCTATTCGGTATGAATATGTAAACGGGACAGAGACTTCTCCCGTGGCATTTCTAGAAGGCATTTATGTACTTCCAGAATATCGTCGCTTAGGTGTAGCAACTTTACTTGTTCGTCAGGTTGAGGCGTGGGCAAAACAATTTTCTTGTACTGAGTTTGCATCTGATGCGGCATTGGACAATGTCATTAGTCATGCAATGCATCGTGCATTGGGTTTTCAAGAAACTGAAAGAGTTGTTTATTTTAGTAAAAAAATAGATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39511","NCBI_taxonomy_name":"Acinetobacter sp. CIP-A165","NCBI_taxonomy_id":"40373"}}}},"ARO_accession":"3002558","ARO_id":"38958","ARO_name":"AAC(6')-Ik","CARD_short_name":"AAC(6')-Ik","ARO_description":"AAC(6')-Ik is a chromosomal-encoded aminoglycoside acetyltransferase in Acinetobacter sp.","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"A category of aminoglycoside N-acetyltransferase enzymes with modification regiospecificity based at the 6'-amino group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics through acetylation of the 6-amino group of the compound.","category_aro_class_name":"AMR Gene Family"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"46128":{"category_aro_accession":"3007378","category_aro_cvterm_id":"46128","category_aro_name":"2'-N-ethylnetilmicin","category_aro_description":"2'-N-ethylnetilmicin is an aminoglycoside antibiotic and a derivative of netilmicin.","category_aro_class_name":"Antibiotic"},"46129":{"category_aro_accession":"3007379","category_aro_cvterm_id":"46129","category_aro_name":"5-episisomicin","category_aro_description":"5-episosomicin is a semisynthetic aminoglycoside antibiotic similar to sisomicin.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1978":{"model_id":"1978","model_name":"OXA-200","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1294":{"protein_sequence":{"accession":"ADX07745.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAILVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGLDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"HQ734811.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCCCTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCTAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTAGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAACAAAATATACGCAAAAAGTGGTTGGGGATTGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001665","ARO_id":"38065","ARO_name":"OXA-200","CARD_short_name":"OXA-200","ARO_description":"OXA-200 is a beta-lactamase found in A. baumannii.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1979":{"model_id":"1979","model_name":"FosA4","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"200"}},"model_sequences":{"sequence":{"1439":{"protein_sequence":{"accession":"BAP18892.1","sequence":"MLQGLNHLTLAVSDLASSLAFYQRLPGMRLHARWDSGAYLSCGALWLCLSLDAQRRKTPAQESDYTHYAFSVAEEHFAEVVAQLAHAGAEVWKDNRSEGASYYFLDPDGHKLELHVGHLAQRLAACRERPYKGMVFFD"},"dna_sequence":{"accession":"AB908992.1","fmin":"0","fmax":"417","strand":"+","sequence":"ATGCTGCAGGGATTGAATCATCTGACGCTGGCGGTCAGCGATCTGGCGTCAAGCCTGGCGTTTTATCAGCGGTTACCTGGAATGCGTCTGCACGCCCGTTGGGATAGCGGAGCATATCTTTCCTGCGGGGCGTTGTGGCTATGCTTGTCGCTGGATGCGCAGCGGCGTAAAACGCCCGCTCAGGAAAGCGACTATACCCATTATGCTTTCAGCGTGGCGGAAGAGCACTTTGCCGAGGTGGTCGCCCAGCTGGCGCACGCGGGGGCCGAAGTATGGAAAGACAACCGCAGCGAAGGGGCGTCGTACTATTTTCTCGACCCTGACGGCCATAAGCTGGAACTGCATGTGGGTCATTTGGCACAGCGGCTGGCCGCCTGTCGGGAACGCCCGTACAAGGGGATGGTCTTTTTTGACTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3003210","ARO_id":"39794","ARO_name":"FosA4","CARD_short_name":"FosA4","ARO_description":"FosA4 is an enzyme that confers resistance to fosfomycin in Escherichia coli by breaking the epoxide ring of the molecule.","ARO_category":{"36272":{"category_aro_accession":"3000133","category_aro_cvterm_id":"36272","category_aro_name":"fosfomycin thiol transferase","category_aro_description":"Catalyzes the addition of a thiol group from a nucleophilic molecule to fosfomycin.","category_aro_class_name":"AMR Gene Family"},"35944":{"category_aro_accession":"0000025","category_aro_cvterm_id":"35944","category_aro_name":"fosfomycin","category_aro_description":"Fosfomycin (also known as phosphomycin and phosphonomycin) is a broad-spectrum antibiotic produced by certain Streptomyces species. It is effective on gram positive and negative bacteria as it targets the cell wall, an essential feature shared by both bacteria. Its specific target is MurA (MurZ in E.coli), which attaches phosphoenolpyruvate (PEP) to UDP-N-acetylglucosamine, a step of commitment to cell wall synthesis. In the active site of MurA, the active cysteine molecule is alkylated which stops the catalytic reaction.","category_aro_class_name":"Antibiotic"},"45731":{"category_aro_accession":"3007149","category_aro_cvterm_id":"45731","category_aro_name":"phosphonic acid antibiotic","category_aro_description":"A group of antibiotics derived from phosphonic acids.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1980":{"model_id":"1980","model_name":"OXA-247","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"972":{"protein_sequence":{"accession":"AGC70814.1","sequence":"MRVLALSAVFLVASIIGMPAVAKEWQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGQTRDIATWNRDHNLITAMKYSVVPVYQEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISATEQISFLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGSNTKIGWWVGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP"},"dna_sequence":{"accession":"JX893517.1","fmin":"0","fmax":"786","strand":"+","sequence":"ATGCGTGTATTAGCCTTATCGGCTGTGTTTTTGGTGGCATCGATTATCGGAATGCCTGCGGTAGCAAAGGAATGGCAAGAAAACAAAAGTTGGAATGCTCACTTTACTGAACATAAATCACAGGGCGTAGTTGTGCTCTGGAATGAGAATAAGCAGCAAGGATTTACCAATAATCTTAAACGGGCGAACCAAGCATTTTTACCCGCATCTACCTTTAAAATTCCCAATAGCTTGATCGCCCTCGATTTGGGCGTGGTTAAGGATGAACACCAAGTCTTTAAGTGGGATGGACAGACGCGCGATATCGCCACTTGGAATCGCGATCATAATCTAATCACCGCGATGAAATATTCAGTTGTGCCTGTTTATCAAGAATTTGCCCGCCAAATTGGCGAGGCACGTATGAGCAAGATGCTACATGCTTTCGATTATGGTAATGAGGACATTTCGGGCAATGTAGACAGTTTCTGGCTCGACGGTGGTATTCGAATTTCGGCCACGGAGCAAATCAGCTTTTTAAGAAAGCTGTATCACAATAAGTTACACGTATCGGAGCGCAGCCAGCGTATTGTCAAACAAGCCATGCTGACCGAAGCCAATGGCGACTATATTATTCGGGCTAAAACTGGATCCAATACTAAGATTGGCTGGTGGGTCGGTTGGGTTGAACTTGATGATAATGTGTGGTTTTTTGCGATGAATATGGATATGCCCACATCGGATGGTTTAGGGCTGCGCCAAGCCATCACAAAAGAAGTGCTCAAACAGGAAAAAATTATTCCCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001791","ARO_id":"38191","ARO_name":"OXA-247","CARD_short_name":"OXA-247","ARO_description":"OXA-247 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46510":{"category_aro_accession":"3007721","category_aro_cvterm_id":"46510","category_aro_name":"OXA-48-like beta-lactamase","category_aro_description":"OXA-48-type beta-lactamases are now routinely encountered in bacterial infections caused by carbapenam-resistant Enterobacterales. OXA-48-like proteins confer resistance to penicillin (which is efficiently hydrolyzed) and carbapenam antibiotics (which is more slowly broken down). The spectrum of activity of these variants varies, with some hydrolyzing expanded-spectrum oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1981":{"model_id":"1981","model_name":"vanA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"350"}},"model_sequences":{"sequence":{"3277":{"protein_sequence":{"accession":"AAA65956.1","sequence":"MNRIKVAILFGGCSEEHDVSVKSAIEIAANINKEKYEPLYIGITKSGVWKMCEKPCAEWENDNCYSAVLSPDKKMHGLLVKKNHEYEINHVDVAFSALHGKSGEDGSIQGLFELSGIPFVGCDIQSSAICMDKSLTYIVAKNAGIATPAFWVINKDDRPVAATFTYPVFVKPARSGSSFGVKKVNSADELDYAIESARQYDSKILIEQAVSGCEVGCAVLGNSAALVVGEVDQIRLQYGIFRIHQEVEPEKGSENAVITVPADLSAEERGRIQETAKKIYKALGCRGLARVDMFLQDNGRIVLNEVNTLPGFTSYSRYPRMMAAAGIALPELIDRLIVLALKG"},"dna_sequence":{"accession":"M97297.1","fmin":"6978","fmax":"8010","strand":"+","sequence":"ATGAATAGAATAAAAGTTGCAATACTGTTTGGGGGTTGCTCAGAGGAGCATGACGTATCGGTAAAATCTGCAATAGAGATAGCCGCTAACATTAATAAAGAAAAATACGAGCCGTTATACATTGGAATTACGAAATCTGGTGTATGGAAAATGTGCGAAAAACCTTGCGCGGAATGGGAAAACGACAATTGCTATTCAGCTGTACTCTCGCCGGATAAAAAAATGCACGGATTACTTGTTAAAAAGAACCATGAATATGAAATCAACCATGTTGATGTAGCATTTTCAGCTTTGCATGGCAAGTCAGGTGAAGATGGATCCATACAAGGTCTGTTTGAATTGTCCGGTATCCCTTTTGTAGGCTGCGATATTCAAAGCTCAGCAATTTGTATGGACAAATCGTTGACATACATCGTTGCGAAAAATGCTGGGATAGCTACTCCCGCCTTTTGGGTTATTAATAAAGATGATAGGCCGGTGGCAGCTACGTTTACCTATCCTGTTTTTGTTAAGCCGGCGCGTTCAGGCTCATCCTTCGGTGTGAAAAAAGTCAATAGCGCGGACGAATTGGACTACGCAATTGAATCGGCAAGACAATATGACAGCAAAATCTTAATTGAGCAGGCTGTTTCGGGCTGTGAGGTCGGTTGTGCGGTATTGGGAAACAGTGCCGCGTTAGTTGTTGGCGAGGTGGACCAAATCAGGCTGCAGTACGGAATCTTTCGTATTCATCAGGAAGTCGAGCCGGAAAAAGGCTCTGAAAACGCAGTTATAACCGTTCCCGCAGACCTTTCAGCAGAGGAGCGAGGACGGATACAGGAAACGGCAAAAAAAATATATAAAGCGCTCGGCTGTAGAGGTCTAGCCCGTGTGGATATGTTTTTACAAGATAACGGCCGCATTGTACTGAACGAAGTCAATACTCTGCCCGGTTTCACGTCATACAGTCGTTATCCCCGTATGATGGCCGCTGCAGGTATTGCACTTCCCGAACTGATTGACCGCTTGATCGTATTAGCGTTAAAGGGGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36779","NCBI_taxonomy_name":"Enterococcus faecium","NCBI_taxonomy_id":"1352"}}}},"ARO_accession":"3000010","ARO_id":"36019","ARO_name":"vanA","CARD_short_name":"vanA","ARO_description":"VanA is a D-Ala-D-Ala ligase homolog that synthesizes D-Ala-D-Lac, an alternative substrate for peptidoglycan synthesis that reduces vancomycin binding affinity. It has been isolated from VREs. It is associated with both vancomycin and teicoplanin resistance.","ARO_category":{"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"39340":{"category_aro_accession":"3002906","category_aro_cvterm_id":"39340","category_aro_name":"Van ligase","category_aro_description":"Van ligases synthesize alternative substrates for peptidoglycan synthesis that reduce vancomycin binding affinity.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"35948":{"category_aro_accession":"0000029","category_aro_cvterm_id":"35948","category_aro_name":"teicoplanin","category_aro_description":"Teicoplanin is a glycopeptide antibiotic used in the prophylaxis and treatment of serious infections caused by Gram-positive bacteria. Teicoplanin has a unique acyl-aliphatic chain, and binds to cell wall precursors to inhibit transglycosylation  and transpeptidation.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1982":{"model_id":"1982","model_name":"IMP-9","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"8223":{"protein_sequence":{"accession":"AAK59385.1","sequence":"MSKLFVFFMFLFCSITAAGESLPDLKIEKLDEGVYVHTSFEEVNGWGVIPKHGLVVLVNTDAYLIDTPFTAKDTENLVNWFVERGYRIKGSISSHFHSDSTGGIEWLNSQSIPTYASELTNELLKKDGKVQAKYSFSGVSYWLVKKKIEVFYPGPGHAPDNVVVWLPENRVLFGGCFVKPYGLGNLGDANLEAWPKSAKLLMSKYSKAKLVVPSHSDIGDSSLLKLTWEQTVKGFNESKKSTTAH"},"dna_sequence":{"accession":"KC543497.1","fmin":"457139","fmax":"457877","strand":"-","sequence":"ATGAGCAAGTTATTTGTATTCTTTATGTTTTTGTTTTGTAGCATTACTGCCGCAGGAGAGTCTTTGCCAGATTTAAAAATTGAGAAGCTTGACGAAGGCGTTTATGTTCATACTTCGTTTGAAGAAGTTAACGGTTGGGGTGTTATTCCTAAACACGGCTTGGTGGTTCTTGTAAATACTGATGCCTATCTGATAGACACTCCATTTACTGCTAAAGATACTGAAAATTTAGTTAATTGGTTTGTTGAGCGCGGCTATAGAATAAAAGGCAGTATTTCCTCACATTTCCATAGCGACAGCACGGGTGGAATAGAGTGGCTTAATTCTCAATCTATCCCCACGTATGCATCTGAATTAACAAATGAACTTCTTAAAAAAGACGGTAAGGTACAAGCTAAATATTCATTTAGCGGAGTTAGCTATTGGCTAGTTAAGAAAAAGATTGAAGTTTTTTATCCTGGTCCAGGGCACGCTCCAGATAACGTAGTGGTTTGGCTGCCTGAAAATAGAGTTTTGTTCGGTGGTTGTTTTGTTAAACCCTACGGTCTAGGTAATTTGGGTGACGCAAATTTAGAAGCTTGGCCAAAATCCGCCAAATTATTAATGTCAAAATATAGTAAGGCAAAACTGGTTGTACCAAGTCATAGTGACATAGGAGATTCGTCGCTCTTGAAGCTTACATGGGAGCAGACGGTAAAAGGATTCAATGAAAGCAAAAAAAGTACCACTGCACATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002200","ARO_id":"38600","ARO_name":"IMP-9","CARD_short_name":"IMP-9","ARO_description":"IMP-9 is a beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1984":{"model_id":"1984","model_name":"SHV-144","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1871":{"protein_sequence":{"accession":"AFK93491.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPVGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"JQ926986.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGTAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGGATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001345","ARO_id":"37745","ARO_name":"SHV-144","CARD_short_name":"SHV-144","ARO_description":"SHV-144 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1985":{"model_id":"1985","model_name":"SHV-7","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1394":{"protein_sequence":{"accession":"AAA87176.1","sequence":"MRYFRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGSVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGASKRGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"U20270.1","fmin":"124","fmax":"985","strand":"+","sequence":"ATGCGTTATTTTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCAGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTAGCAAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001066","ARO_id":"37446","ARO_name":"SHV-7","CARD_short_name":"SHV-7","ARO_description":"SHV-7 is an extended-spectrum beta-lactamase found in E. coli.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1986":{"model_id":"1986","model_name":"OXA-309","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1131":{"protein_sequence":{"accession":"CCW28916.1","sequence":"MKTLQLALIALITTFGSACTTISPSVETAKNHQQQSAQQQIQQAFDQLQTTGVIVIKDKHGLHSYGNDLSRAQTPYVPASTFKMLNALIGLEHGKATRTEVFKWDGQKRSFPAWEKDMTLGQAMQASAVPVYQELARRIGVDLMQKEVQRIGYGNQQIGTVVDNFWLVGPLQITPVQEVLFVEKLANTQLAFKPDVQHTVQDMLLIEQKPNYKLYAKSGWGMDLEPQVGWWAGWVETSTGEKAYFALNMQMKTGISASVREQLVKQSLTALGII"},"dna_sequence":{"accession":"HF947514.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAAAACTTTACAGTTGGCTCTCATCGCCCTCATTACAACCTTCGGTTCTGCATGTACCACAATAAGCCCCTCAGTAGAAACAGCTAAAAATCACCAGCAACAAAGCGCGCAGCAGCAGATCCAACAGGCCTTCGATCAACTCCAAACCACTGGGGTGATTGTCATTAAGGATAAGCATGGCTTACACAGCTACGGCAATGACTTGAGCCGTGCTCAGACACCCTATGTACCCGCCTCTACCTTTAAAATGCTGAATGCCTTAATCGGACTAGAACATGGTAAAGCAACCAGAACCGAGGTGTTTAAATGGGATGGTCAAAAGCGCAGCTTCCCTGCCTGGGAAAAAGACATGACTTTAGGGCAAGCCATGCAAGCATCTGCCGTTCCCGTTTATCAGGAGCTTGCACGGCGTATTGGTGTAGATCTAATGCAAAAAGAAGTACAGCGCATTGGATATGGCAATCAACAGATTGGCACCGTTGTCGATAATTTTTGGTTAGTCGGTCCACTGCAAATTACGCCTGTTCAAGAAGTCCTTTTTGTAGAGAAGCTGGCCAATACGCAACTCGCTTTTAAGCCAGATGTGCAACATACCGTACAAGACATGCTACTGATTGAACAAAAACCGAATTATAAACTCTACGCCAAATCAGGCTGGGGTATGGACCTAGAACCACAAGTGGGCTGGTGGGCAGGCTGGGTCGAAACTTCAACAGGTGAAAAAGCGTATTTTGCTTTGAATATGCAGATGAAAACGGGAATTTCAGCCAGCGTGCGTGAGCAACTGGTCAAACAAAGTCTGACAGCACTGGGGATAATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39092","NCBI_taxonomy_name":"Acinetobacter johnsonii","NCBI_taxonomy_id":"40214"}}}},"ARO_accession":"3001504","ARO_id":"37904","ARO_name":"OXA-309","CARD_short_name":"OXA-309","ARO_description":"OXA-309 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46494":{"category_aro_accession":"3007705","category_aro_cvterm_id":"46494","category_aro_name":"OXA-211-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-211.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1987":{"model_id":"1987","model_name":"QnrA1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"403":{"protein_sequence":{"accession":"ABI50486.1","sequence":"MDIIDKVFQQEDFSRQDLSDSRFRRCRFYQCDFSHCQLQDASFEDCSFIESGAVEGCHFSYADLRDASFKACRLSLANFSGANCFGIEFRECDLKGANFSRARFYNQVSHKMYFCSAYISGCNLAYTNLSGQCLEKCELFENNWSNANLSGASLMGSDLSRGTFSRDCWQQVNLRGCDLTFADLDGLDPRRVNLEGVKICAWQQEQLLEPLGVIVLPD"},"dna_sequence":{"accession":"DQ831141.1","fmin":"8921","fmax":"9578","strand":"+","sequence":"ATGGATATTATTGATAAAGTTTTTCAGCAAGAGGATTTCTCACGCCAGGATTTGAGTGACAGCCGTTTTCGCCGCTGCCGCTTTTATCAGTGTGACTTCAGCCACTGTCAGCTGCAGGATGCCAGTTTCGAGGATTGCAGTTTCATTGAAAGCGGCGCCGTTGAAGGGTGTCACTTCAGCTATGCCGATCTGCGCGATGCCAGTTTCAAGGCCTGCCGTCTGTCTTTGGCCAACTTCAGCGGTGCCAACTGCTTTGGCATAGAGTTCAGGGAGTGCGATCTCAAGGGCGCCAACTTTTCCCGGGCCCGCTTCTACAATCAAGTCAGCCATAAGATGTACTTCTGCTCGGCTTATATCTCAGGTTGCAACCTGGCCTATACCAACTTGAGTGGCCAATGCCTGGAAAAATGCGAGCTGTTTGAAAACAACTGGAGCAATGCCAATCTCAGCGGCGCTTCCTTGATGGGCTCAGATCTCAGCCGCGGCACCTTCTCCCGCGACTGTTGGCAACAGGTCAATCTGCGGGGCTGTGACCTAACCTTTGCCGATCTGGATGGGCTCGACCCCAGACGGGTCAACCTCGAAGGAGTCAAGATCTGTGCCTGGCAACAGGAGCAACTGCTGGAACCCTTGGGAGTAATAGTGCTGCCGGATTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002707","ARO_id":"39141","ARO_name":"QnrA1","CARD_short_name":"QnrA1","ARO_description":"QnrA1 is a plasmid-mediated quinolone resistance protein found in Klebsiella pneumoniae.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1988":{"model_id":"1988","model_name":"CMY-7","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1100":{"protein_sequence":{"accession":"CAB36900.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGELAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"AJ011291.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGAGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002018","ARO_id":"38418","ARO_name":"CMY-7","CARD_short_name":"CMY-7","ARO_description":"CMY-7 is a beta-lactamase found in Salmonella typhimurium.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1990":{"model_id":"1990","model_name":"CMY-82","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"905":{"protein_sequence":{"accession":"AHL39324.1","sequence":"MMKKSICCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAIIYQGKPYYFTWGKADIANNRPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTHYWPELTGKQWQGISLLHLATYTAGGLPLQVPDDVTDKAALLRFYQNWQPQWAPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTKRVLRPLKLAHTWITVPQSEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMTRWVQANMDASQVQEKTLQQGIELAQSRYWRIGDMYQGLGWEMLNWPVKADSIISGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"KJ207203.1","fmin":"5","fmax":"1151","strand":"+","sequence":"ATGATGAAAAAATCGATATGCTGCGCGCTGCTGCTGACAGCTTCGTTCTCCACGTTTGCCGCCGCAAAAACAGAACAACAAATTGCCGATATCGTTAACCGCACCATCACACCGCTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCGATTATCTATCAGGGGAAACCTTATTACTTTACCTGGGGTAAAGCCGATATCGCCAATAACCGTCCAGTCACTCAACAAACGCTGTTTGAACTCGGATCGGTCAGTAAAACGTTCAACGGCGTGCTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGCATTACTGGCCTGAACTGACTGGTAAGCAGTGGCAGGGTATCAGCCTGCTGCACTTAGCCACCTACACGGCAGGCGGCCTGCCGCTTCAGGTTCCGGACGACGTTACGGATAAAGCCGCGTTACTACGCTTTTATCAAAACTGGCAGCCGCAATGGGCCCCAGGCGCTAAACGTCTTTATGCTAACTCCAGCATTGGTCTGTTTGGTGCCCTGGCGGTCAAACCCTCAGGCATGAGCTACGAAGAGGCGATGACCAAACGCGTCCTGCGCCCCTTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAGCGAACAAAAAGATTATGCCTGGGGTTATCGCGAAGGAAAGCCAGTGCATGTATCCCCTGGCCAACTTGATGCCGAAGCCTACGGGGTGAAATCGAGCGTTATCGATATGACCCGTTGGGTTCAGGCCAACATGGACGCCAGCCAGGTTCAGGAGAAAACGCTCCAGCAGGGCATCGAGCTTGCGCAGTCACGTTACTGGCGTATTGGCGATATGTACCAGGGCCTGGGCTGGGAGATGCTGAACTGGCCGGTGAAGGCCGACTCGATAATTAGCGGTAGCGACAGCAAAGTGGCACTGGCAGCGCTTCCTGCCGTTGAGGTAAACCCGCCCGCGCCTGCCGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGCGGATTCGGCAGCTACGTTGCGTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAGAGCTACCCAAACCCTGTTCGCGTCGAGGCCGCCTGGCGCATTCTTGAAAAACTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002095","ARO_id":"38495","ARO_name":"CMY-82","CARD_short_name":"CMY-82","ARO_description":"CMY-82 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1992":{"model_id":"1992","model_name":"dfrA1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"5109":{"protein_sequence":{"accession":"AAP74961.2","sequence":"MKLSLMVAISKNGVIGNGPDIPWSAKGEQLLFKAITYNQWLLVGRKTFESMGALPNRKYAVVTRSSFTSDNENVVIFPSIKDALTNLKKITDHVIVSGGGEIYKSLIDQVDTLHISTIDIEPEGDVYFPEIPSNFRPVFTQDFASNINYSYQIWQKG"},"dna_sequence":{"accession":"KJ541681.1","fmin":"19526","fmax":"20000","strand":"+","sequence":"GTGAAACTATCACTAATGGTAGCTATATCGAAGAATGGAGTTATCGGGAATGGCCCTGATATTCCATGGAGTGCCAAAGGTGAACAGCTCCTGTTTAAAGCTATTACCTATAACCAATGGCTGTTGGTTGGACGCAAGACTTTTGAATCAATGGGAGCATTACCCAACCGAAAGTATGCGGTCGTAACACGTTCAAGTTTTACATCTGACAATGAGAACGTAGTGATCTTTCCATCAATTAAAGATGCTTTAACCAACCTAAAGAAAATAACGGATCATGTCATTGTTTCAGGTGGTGGGGAGATATACAAAAGCCTGATCGATCAAGTAGATACACTACATATATCTACAATAGACATCGAGCCGGAAGGTGATGTTTACTTTCCTGAAATCCCCAGCAATTTTAGGCCAGTTTTTACCCAAGACTTCGCCTCTAACATAAATTATAGTTACCAAATCTGGCAAAAGGGTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3002854","ARO_id":"39288","ARO_name":"dfrA1","CARD_short_name":"dfrA1","ARO_description":"dfrA1 is an integron-encoded dihydrofolate reductase.","ARO_category":{"37617":{"category_aro_accession":"3001218","category_aro_cvterm_id":"37617","category_aro_name":"trimethoprim resistant dihydrofolate reductase dfr","category_aro_description":"Alternative dihydropteroate synthase dfr present on plasmids produces alternate proteins that are less sensitive to trimethoprim from inhibiting its role in folate synthesis, thus conferring trimethoprim resistance.","category_aro_class_name":"AMR Gene Family"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1993":{"model_id":"1993","model_name":"QnrB74","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"556":{"protein_sequence":{"accession":"AHX97725.1","sequence":"MALALVGEKIDRNRFTGEKIENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNSSALGIEIRHCRAQGADFRGASFMNMIITRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWIGAQVLGATFSGSDFFGGEFSTFDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDNYQASLLMERLGIAVIG"},"dna_sequence":{"accession":"KJ415247.1","fmin":"0","fmax":"645","strand":"+","sequence":"ATGGCTCTGGCACTCGTTGGCGAAAAAATTGACAGAAACCGTTTCACCGGTGAGAAAATTGAAAATAGTACATTTTTTAACTGTGATTTTTCAGGTGCCGACTTGAGCGGCACTGAATTTATCGGCTGTCAGTTCTATGATCGTGAAAGCCAGAAAGGGTGCAATTTTAGTCGTGCGATGCTGAAAGATGCCATTTTTAAAAGTTGTGATTTATCCATGGCGGATTTTCGCAATTCCAGTGCGCTGGGTATTGAAATTCGCCACTGCCGCGCACAAGGCGCAGATTTCCGCGGCGCAAGCTTTATGAATATGATTATCACGCGCACCTGGTTTTGTAGCGCATATATCACGAATACCAATCTAAGCTACGCCAATTTTTCGAAAGTCGTGTTGGAAAAGTGTGAGCTGTGGGAAAACCGTTGGATAGGTGCCCAGGTACTGGGCGCGACGTTCAGTGGTTCAGATTTCTTCGGCGGCGAGTTTTCGACTTTCGACTGGCGAGCAGCAAACTTCACACATTGCGATCTGACTAATTCGGAGTTGGGTGACTTAGATATTCGGGGCGTTGATTTACAAGGCGTTAAGTTGGACAACTACCAGGCGTCGTTGCTCATGGAGCGGCTTGGCATCGCGGTGATTGGTTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002786","ARO_id":"39220","ARO_name":"QnrB74","CARD_short_name":"QnrB74","ARO_description":"QnrB74 is a plasmid-mediated quinolone resistance protein found in Escherichia coli.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1995":{"model_id":"1995","model_name":"AAC(6')-Iz","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"205":{"protein_sequence":{"accession":"AAD52985.1","sequence":"MIASAPTIRQATPADAAAWAQLRLGLWPDADDPLEELTQSLADAEGAVFLACAADGETVGFAEVRLRHDYVNGTESSPVGFLEGWYVQPQWQGSGVGRALLAAVQAWTRDAGCRELASDSRVEDVQAHAAHRACGFEETERVVYFRMPLEPSA"},"dna_sequence":{"accession":"AF140221.1","fmin":"389","fmax":"851","strand":"+","sequence":"GTGATCGCCAGCGCGCCCACGATCCGCCAGGCCACGCCGGCCGATGCGGCTGCATGGGCGCAGTTGCGTCTCGGCCTGTGGCCTGATGCCGATGATCCGCTGGAGGAGCTGACGCAGTCGCTGGCAGATGCCGAAGGTGCTGTGTTCTTGGCCTGTGCCGCGGATGGCGAGACGGTTGGTTTCGCTGAAGTGCGCCTGCGCCATGACTACGTGAACGGTACCGAGTCTTCGCCGGTGGGGTTCCTGGAGGGCTGGTACGTGCAGCCGCAGTGGCAAGGCAGCGGCGTCGGCCGCGCCCTGCTGGCGGCGGTGCAGGCGTGGACGCGCGATGCGGGCTGCCGCGAACTGGCTTCGGACAGTCGCGTGGAAGACGTGCAGGCTCACGCCGCGCATCGGGCCTGCGGCTTCGAAGAGACCGAACGGGTCGTCTATTTCCGCATGCCGCTGGAGCCATCGGCGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37076","NCBI_taxonomy_name":"Stenotrophomonas maltophilia","NCBI_taxonomy_id":"40324"}}}},"ARO_accession":"3002570","ARO_id":"38970","ARO_name":"AAC(6')-Iz","CARD_short_name":"AAC(6')-Iz","ARO_description":"AAC(6')-Iz is a chromosomal-encoded aminoglycoside acetyltransferase in S. maltophilia.","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"A category of aminoglycoside N-acetyltransferase enzymes with modification regiospecificity based at the 6'-amino group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics through acetylation of the 6-amino group of the compound.","category_aro_class_name":"AMR Gene Family"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"46128":{"category_aro_accession":"3007378","category_aro_cvterm_id":"46128","category_aro_name":"2'-N-ethylnetilmicin","category_aro_description":"2'-N-ethylnetilmicin is an aminoglycoside antibiotic and a derivative of netilmicin.","category_aro_class_name":"Antibiotic"},"46129":{"category_aro_accession":"3007379","category_aro_cvterm_id":"46129","category_aro_name":"5-episisomicin","category_aro_description":"5-episosomicin is a semisynthetic aminoglycoside antibiotic similar to sisomicin.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1997":{"model_id":"1997","model_name":"tlrC","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1020"}},"model_sequences":{"sequence":{"158":{"protein_sequence":{"accession":"AAA26832.1","sequence":"MRTSPSSQLSLHGVTKRYDDRVVLSQVSLAISPGEKAGIIGDNGAGKSTLLRLLAGEERPDAGEVTVIAPGGVGYLPQTLGLPPRATVQDAIDLAMTELRVLEAELRRTEAALAEAATDEALQDALTAYARLTEQYEVRDGYGADARVDAALHGLGLPGLPRDRRLGTLSGGERSRLALAATLASQPELLLLDEPTNDLDDRAVHWLEEHLSGHRGTVVTVTHDRVFLDRLTATVLEVDGRGVSRHGDGYAGYLAAKAAERRRRQQQYDEWRAELDRNRRLAEANVARLDGIPRKMGKAAFGHGAFRARGRDHGAMSRVRNAKERVERLTANPVAPPADRLSLTARIATADGPGEAPAAELDGVVVGSRLRVPKLRLGAAERLLITGPNGAGKSTLLSVLAGELSPDAGAVSVPGRVGHLRQEETPWPAKLTVLEAFAHNRPGDRDEQADRRLSLGLFEPEALRLRVGELSYGQRRRIELARLVSEPVGLLLLDEPTNHLSPALVEELEEALTGYGGALVLVTHDRRMRSRFTGSHLELREGVVSGAR"},"dna_sequence":{"accession":"M57437.1","fmin":"0","fmax":"1647","strand":"+","sequence":"ATGCGTACATCACCTTCCTCCCAGCTTTCCCTGCACGGTGTCACCAAGCGCTACGACGACCGTGTCGTGCTCAGTCAGGTCTCCCTCGCCATCTCCCCGGGGGAGAAGGCCGGCATCATCGGCGACAACGGGGCCGGGAAGTCCACCCTGCTCCGTCTGCTCGCCGGTGAGGAACGGCCCGACGCGGGGGAGGTGACCGTGATCGCGCCCGGCGGTGTCGGCTACCTCCCGCAGACCCTCGGCCTGCCGCCGCGGGCCACGGTGCAGGACGCCATCGATCTGGCCATGACCGAGCTGCGCGTCCTGGAGGCCGAACTGCGCCGTACCGAGGCCGCGTTGGCCGAGGCCGCCACGGACGAGGCCCTGCAGGACGCCCTCACCGCGTACGCCCGTCTGACCGAGCAGTACGAGGTCCGTGACGGCTACGGCGCCGATGCCCGCGTGGACGCCGCGCTGCACGGTCTCGGGCTGCCCGGACTGCCACGTGACCGGCGGCTGGGCACCCTCTCCGGTGGAGAGCGATCGCGGCTGGCGCTGGCGGCCACCCTGGCGTCCCAGCCGGAACTGCTGCTGCTCGACGAGCCGACCAACGACCTGGACGACCGGGCCGTCCACTGGCTGGAGGAACATCTGAGCGGCCACCGCGGCACCGTCGTCACGGTGACCCACGACCGGGTGTTCCTGGACCGGCTCACCGCCACGGTCCTGGAGGTCGACGGCCGCGGCGTCTCCCGCCACGGCGACGGCTACGCGGGGTATCTCGCCGCCAAGGCCGCCGAGCGCCGCCGGCGGCAGCAGCAGTACGACGAGTGGCGCGCCGAACTCGACCGCAACCGCCGGCTGGCCGAGGCCAACGTCGCCCGGCTGGACGGCATCCCGCGCAAGATGGGGAAGGCCGCCTTCGGGCACGGCGCGTTCCGCGCGCGCGGGCGCGACCACGGCGCGATGAGCCGGGTCCGCAACGCCAAGGAGCGGGTCGAGCGGCTCACCGCGAATCCGGTGGCGCCACCGGCGGACCGGCTCTCCCTCACCGCGCGCATCGCCACGGCGGACGGCCCGGGGGAGGCGCCGGCCGCGGAACTCGACGGCGTGGTCGTCGGCAGCCGGCTGCGCGTGCCGAAGCTGCGCCTGGGCGCGGCCGAACGGCTGCTGATCACCGGCCCCAATGGCGCGGGCAAGAGCACCCTGCTGTCCGTGCTGGCCGGGGAACTGAGCCCGGACGCGGGCGCGGTGAGCGTCCCCGGGCGCGTGGGGCATCTGCGCCAGGAGGAGACGCCCTGGCCCGCGAAGCTGACCGTGCTGGAGGCCTTCGCCCACAACCGGCCCGGCGACCGGGACGAACAGGCCGACCGGCGGCTGTCCCTCGGCCTGTTCGAGCCGGAGGCGCTGCGGCTGCGGGTCGGGGAGCTGTCGTACGGTCAGCGCCGCCGCATCGAACTGGCCCGGCTGGTCAGCGAGCCGGTGGGTCTGCTCCTGCTGGACGAGCCCACCAACCACCTCTCACCGGCGCTGGTGGAGGAGTTGGAGGAGGCGCTGACGGGCTACGGGGGCGCGCTGGTGCTGGTCACCCACGACCGGCGGATGCGAAGCCGGTTCACCGGCTCGCATCTGGAGCTGCGCGAGGGCGTCGTCTCCGGCGCACGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36838","NCBI_taxonomy_name":"Streptomyces fradiae","NCBI_taxonomy_id":"1906"}}}},"ARO_accession":"3002827","ARO_id":"39261","ARO_name":"tlrC","CARD_short_name":"tlrC","ARO_description":"tlrC is an ABC-F subfamily protein found in Streptomyces fradiae and confers resistance to mycinamicin, tylosin and lincosamides. tlrC is found in the tylosin biosynthetic cluster and is one mechanism by which S. fradiae protects itself from self-destruction when producing this macrolide.","ARO_category":{"45630":{"category_aro_accession":"3007068","category_aro_cvterm_id":"45630","category_aro_name":"Miscellaneous ABC-F subfamily ATP-binding cassette ribosomal protection proteins","category_aro_description":"ABC-F subfamily ATP-binding cassette ribosomal protection proteins of unknown, unclear or miscellaneous classification which nevertheless confer resistance to antibiotics through ribosomal protection and not through antibiotic efflux. These proteins should be further reviewed to elucidate associated genes, their function, origin and classification.","category_aro_class_name":"AMR Gene Family"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"36284":{"category_aro_accession":"3000145","category_aro_cvterm_id":"36284","category_aro_name":"tylosin","category_aro_description":"Tylosin is a 16-membered macrolide, naturally produced by Streptomyces fradiae. It interacts with the bacterial ribosome 50S subunit to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"37623":{"category_aro_accession":"3001224","category_aro_cvterm_id":"37623","category_aro_name":"mycinamicin","category_aro_description":"Produced by Micromonospora\u00a0griseorubida.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1998":{"model_id":"1998","model_name":"CTX-M-83","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1170":{"protein_sequence":{"accession":"ACI29345.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTHVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"FJ214366.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCACGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGACTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35667","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Derby","NCBI_taxonomy_id":"28144"}}}},"ARO_accession":"3001944","ARO_id":"38344","ARO_name":"CTX-M-83","CARD_short_name":"CTX-M-83","ARO_description":"CTX-M-83 is a beta-lactamase found in Salmonella enterica.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1999":{"model_id":"1999","model_name":"TEM-215","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"2127":{"protein_sequence":{"accession":"AJO16045.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLRNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"KP050492.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCGCAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001392","ARO_id":"37792","ARO_name":"TEM-215","CARD_short_name":"TEM-215","ARO_description":"TEM-215 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2000":{"model_id":"2000","model_name":"TEM-24","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1801":{"protein_sequence":{"accession":"CAA46345.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDKLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVKYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDSWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGTGKRGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"X65253.1","fmin":"175","fmax":"1036","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATAAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTAAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATAGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAACCGGTAAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3000894","ARO_id":"37274","ARO_name":"TEM-24","CARD_short_name":"TEM-24","ARO_description":"TEM-24 is an extended-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2001":{"model_id":"2001","model_name":"OXA-250","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1297":{"protein_sequence":{"accession":"CCJ32598.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDDKAEKIKNLFNEAHTTGVLVIHQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGEKRLFPEWEKNMTLGDAMKASAILVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGLDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"HE963771.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGACAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCATCAAGGTCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAATGGGATGGGGAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCTGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTCTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATTGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001675","ARO_id":"38075","ARO_name":"OXA-250","CARD_short_name":"OXA-250","ARO_description":"OXA-250 is a beta-lactamase found in A. baumannii.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2004":{"model_id":"2004","model_name":"TEM-189","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"847":{"protein_sequence":{"accession":"AEL79515.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMLSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGKRGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"JN254627.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGCTGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTAAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001049","ARO_id":"37429","ARO_name":"TEM-189","CARD_short_name":"TEM-189","ARO_description":"TEM-189 is a beta-lactamase.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2005":{"model_id":"2005","model_name":"CTX-M-89","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1630":{"protein_sequence":{"accession":"ACR56321.1","sequence":"MMRKSVRRAMLMTTACVSLLLASVPLCAQANDVQQKLAALEKSSGGRLGVALINTADNTQTLYRADERFAMCSTSKVMAVAAVLKQSETQKGLLSQRVEIKPSDLINYNPIAEKHVNGTMTFGELSAAALQYSDNTAMNKLIAHLGGPDKVTAFARTIGDDTFRLDRTEPTLNTAIPGDPRDTTTPLAMAQALRNLTLGNALGDTQRAQLVMWLKGNTTGAASIQAGLPTSWVVGDKTGSGDYGTTNDIAVIWPEGRAPLVLVTYFTQSEPKAESRRDVLAAAARIVTDGY"},"dna_sequence":{"accession":"FJ971899.1","fmin":"30","fmax":"906","strand":"+","sequence":"ATGATGAGAAAAAGCGTAAGGCGGGCGATGTTAATGACGACAGCCTGTGTTTCGCTGCTGTTGGCCAGTGTGCCGCTGTGTGCCCAGGCGAACGATGTTCAACAAAAGCTCGCGGCGCTGGAGAAAAGCAGCGGGGGACGACTGGGTGTGGCGTTGATTAACACCGCCGATAACACGCAGACGCTCTACCGCGCCGACGAGCGTTTTGCCATGTGCAGCACCAGTAAAGTGATGGCGGTAGCGGCGGTGCTTAAGCAAAGTGAAACGCAAAAGGGCTTGTTGAGTCAGCGGGTTGAAATTAAGCCCTCAGACTTGATTAACTACAACCCCATTGCGGAAAAACACGTCAATGGCACGATGACATTCGGGGAGTTGAGCGCGGCGGCGCTACAGTACAGCGATAATACTGCCATGAATAAGCTGATTGCCCATCTCGGGGGGCCGGATAAAGTGACGGCATTTGCCCGTACGATTGGCGATGACACGTTCCGGCTCGATCGTACCGAGCCGACGCTCAACACCGCGATCCCCGGCGACCCGCGCGATACCACCACGCCGTTAGCGATGGCGCAGGCTCTGCGCAATCTGACGTTGGGCAATGCCCTGGGTGACACTCAGCGTGCGCAGCTGGTGATGTGGCTGAAAGGCAACACCACCGGCGCTGCCAGCATTCAGGCAGGGCTACCCACATCGTGGGTTGTCGGGGATAAAACCGGCAGCGGCGATTATGGTACGACGAATGATATCGCGGTTATTTGGCCGGAAGGTCGCGCGCCGCTCGTTCTGGTGACTTACTTCACCCAGTCGGAGCCGAAGGCAGAGAGCCGTCGTGACGTGCTCGCTGCTGCCGCCAGAATTGTCACCGACGGTTATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3001949","ARO_id":"38349","ARO_name":"CTX-M-89","CARD_short_name":"CTX-M-89","ARO_description":"CTX-M-89 is a beta-lactamase found in the Enterobacteriaceae family.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2006":{"model_id":"2006","model_name":"IMP-27","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"837":{"protein_sequence":{"accession":"AEH41427.1","sequence":"MKKLFVLCVFVFCSITVAGETLPNLRVEKLEEGVYVHTSYEEVKGWGVVTKHGLVVLIGADAYLIDTPFTAKDTEKLVNWFVERGYKIKGTVSSHFHSDSTGGIEWLNSQSIPTYASELTNELLKKDGKVQAKNSFDGVSYWLAKDKIEVFYPGPGHTQDNVVVWLPEKEILFGGCFVKPHGLGNLGDANLEAWPESAKILMEKYGKAKLVVSGHSETGDATHLKRTWEQAVKGLKESKKTLQPSN"},"dna_sequence":{"accession":"JF894248.1","fmin":"0","fmax":"741","strand":"+","sequence":"ATGAAAAAATTATTTGTTTTATGTGTCTTTGTCTTTTGTAGTATTACTGTCGCAGGTGAGACTTTGCCTAATTTGAGAGTTGAAAAGCTTGAAGAAGGTGTTTATGTTCATACATCGTATGAAGAAGTTAAAGGTTGGGGTGTTGTTACTAAACACGGTTTGGTGGTTCTCATAGGCGCTGACGCCTATCTGATTGATACTCCATTTACTGCTAAAGATACTGAAAAGTTAGTCAATTGGTTTGTGGAGCGCGGCTATAAAATAAAAGGCACTGTTTCCTCACATTTCCATAGCGACAGTACGGGGGGAATAGAGTGGCTTAACTCTCAGTCTATCCCCACGTATGCGTCTGAATTAACGAATGAACTTCTGAAAAAAGACGGTAAGGTTCAAGCCAAAAACTCATTTGACGGGGTTAGTTATTGGCTGGCGAAAGATAAAATAGAAGTGTTTTATCCTGGCCCTGGCCACACTCAAGACAACGTAGTAGTTTGGCTGCCTGAAAAGGAAATATTATTTGGCGGTTGCTTTGTTAAGCCTCACGGCCTTGGTAATTTGGGTGACGCAAATTTAGAGGCTTGGCCAGAGTCCGCCAAAATATTGATGGAAAAATATGGTAAAGCAAAGCTGGTTGTTTCAGGTCATAGCGAAACCGGAGACGCGACACACTTGAAGCGTACCTGGGAGCAGGCTGTTAAAGGACTTAAAGAAAGTAAAAAGACATTGCAGCCAAGCAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3002218","ARO_id":"38618","ARO_name":"IMP-27","CARD_short_name":"IMP-27","ARO_description":"IMP-27 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2007":{"model_id":"2007","model_name":"OXA-335","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1762":{"protein_sequence":{"accession":"AGW16417.1","sequence":"MKILILLPLLSCLGLTACSLPVSSLPSQSTSTQAIASLFDQAQSSGVLVIQRDQQVQVYGNDLNRANTEYVPASTFKMPNALIGLQHGKATTNEIFKWDGKKRSFTAWEKDMTLGQAMQASAVPVYQELARRIGLELMQQEVQRIQFGNQQIGQQVDNFWLVGPLKVTPKQEVQFVSALAREQLAFDPQVQQQVKAMLFLQERKAYRLYVKSGWGMDVEPQVGWLTGWVETPQAEIVAFSLNMQMQNGIDPAIRLEILQQALAELGLYPKAEG"},"dna_sequence":{"accession":"KF203109.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGAAAATTTTGATTTTGCTGCCTTTACTTAGTTGCTTGGGCCTGACAGCATGTAGCCTACCCGTTTCATCTCTCCCATCTCAAAGCACTTCGACTCAAGCGATTGCCAGCTTATTTGATCAGGCGCAAAGCTCTGGTGTTTTAGTGATTCAGCGTGATCAACAAGTACAGGTCTATGGCAATGATTTAAATCGTGCAAATACCGAATATGTTCCCGCCTCTACTTTTAAAATGCCCAATGCTCTGATTGGCCTGCAACATGGCAAAGCCACAACCAATGAAATTTTTAAATGGGATGGCAAGAAACGCAGCTTTACCGCCTGGGAAAAAGACATGACTCTCGGCCAAGCCATGCAAGCTTCTGCGGTACCGGTCTATCAAGAACTGGCGCGTCGTATTGGTCTGGAATTAATGCAACAGGAAGTACAACGCATCCAATTTGGTAATCAGCAGATTGGTCAACAGGTCGATAACTTCTGGTTGGTAGGCCCTTTGAAAGTTACTCCAAAACAGGAAGTCCAATTTGTTTCTGCGTTGGCCCGAGAGCAACTGGCCTTTGATCCTCAAGTCCAGCAACAAGTCAAAGCCATGTTATTTTTACAGGAGCGGAAAGCTTATCGACTATATGTCAAATCCGGTTGGGGCATGGATGTGGAACCGCAAGTCGGCTGGCTCACCGGCTGGGTTGAAACACCGCAGGCTGAAATCGTGGCATTTTCGCTGAATATGCAGATGCAAAATGGTATAGATCCGGCGATCCGCCTTGAAATTTTGCAGCAGGCTTTGGCCGAATTAGGGCTTTATCCAAAAGCTGAAGGATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36948","NCBI_taxonomy_name":"Acinetobacter lwoffii","NCBI_taxonomy_id":"28090"}}}},"ARO_accession":"3001523","ARO_id":"37923","ARO_name":"OXA-335","CARD_short_name":"OXA-335","ARO_description":"OXA-335 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46489":{"category_aro_accession":"3007700","category_aro_cvterm_id":"46489","category_aro_name":"OXA-134-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-134.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2008":{"model_id":"2008","model_name":"SHV-145","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1943":{"protein_sequence":{"accession":"AFN88952.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGERCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"JX013655.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACGCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGCATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001185","ARO_id":"37565","ARO_name":"SHV-145","CARD_short_name":"SHV-145","ARO_description":"SHV-145 is a beta-lactamase.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2009":{"model_id":"2009","model_name":"aadA6","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"199":{"protein_sequence":{"accession":"CAJ32504.1","sequence":"MSNAVPAEISVQLSLALNAIERHLESTLLAVHLYGSALDGGLKPYSDIDLLVTVAARLDETVRQALVVDLLEISASPGQSEALRALEVTIVVHGDVVPWRYPARRELQFGEWQRKDILAGIFEPATTDVDLAILLTKVRQHSLALAGSAAEDFFNPVPEGDLFKALSDTLKLWNSQPDWEGDERNVVLTLSRIWYSAATGKIAPKDIVANWAMERLPDQHKPVLLEARQAYLGQGEDCLASRADQLAAFVHFVKHEATKLLSAMPVMSNNSFKPTPLRGAA"},"dna_sequence":{"accession":"AM087411.1","fmin":"1611","fmax":"2457","strand":"+","sequence":"ATGAGTAACGCAGTACCCGCCGAGATTTCGGTACAGCTATCACTGGCTCTCAACGCCATCGAGCGTCATCTGGAATCAACGTTGCTGGCCGTGCATTTGTACGGCTCTGCACTGGACGGTGGCCTGAAGCCATACAGTGATATTGATTTGCTGGTTACTGTGGCTGCACGGCTCGATGAGACTGTCCGACAAGCCCTGGTCGTAGATCTCTTGGAAATTTCTGCCTCCCCTGGCCAAAGTGAAGCTCTCCGCGCCTTGGAAGTTACCATCGTCGTGCATGGTGATGTTGTCCCTTGGCGTTATCCGGCCAGACGGGAACTGCAATTCGGGGAGTGGCAGCGTAAGGACATTCTTGCGGGCATCTTCGAGCCCGCCACAACCGATGTTGATCTGGCTATTCTGCTAACTAAAGTAAGGCAGCATAGCCTTGCATTGGCAGGTTCGGCCGCAGAGGATTTCTTTAACCCAGTTCCGGAAGGCGATCTATTCAAGGCATTGAGCGACACTCTGAAACTATGGAATTCGCAGCCGGATTGGGAAGGCGATGAGCGGAATGTAGTGCTTACCTTGTCTCGCATTTGGTACAGCGCAGCAACCGGCAAGATCGCACCGAAGGATATCGTTGCCAACTGGGCAATGGAGCGTCTGCCAGATCAACATAAGCCCGTACTGCTTGAAGCCCGGCAGGCTTATCTTGGACAAGGAGAAGATTGCTTGGCCTCACGCGCGGATCAGTTGGCGGCGTTCGTTCACTTCGTGAAACATGAAGCCACTAAATTGCTTAGTGCCATGCCAGTGATGTCTAACAATTCATTCAAGCCGACGCCGCTTCGCGGCGCGGCTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002606","ARO_id":"39006","ARO_name":"aadA6","CARD_short_name":"aadA6","ARO_description":"aadA6 is an integron-encoded aminoglycoside nucleotidyltransferase gene in P. aeruginosa.","ARO_category":{"41439":{"category_aro_accession":"3004275","category_aro_cvterm_id":"41439","category_aro_name":"ANT(3'')","category_aro_description":"A category of aminoglycoside O-nucleotidyltransferase enzymes with modification regiospecificity based at the 3''-hydroxyl group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics by transfer of an AMP group from an ATP substrate to the 3''-hydroxyl group of the compound.","category_aro_class_name":"AMR Gene Family"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2010":{"model_id":"2010","model_name":"CTX-M-129","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1550":{"protein_sequence":{"accession":"AFJ59956.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLRGNTTGAASIRAGLPTSWTVGDKTGSGGYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"JX017364.1","fmin":"238","fmax":"1114","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAGAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGGCTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001988","ARO_id":"38388","ARO_name":"CTX-M-129","CARD_short_name":"CTX-M-129","ARO_description":"CTX-M-129 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2011":{"model_id":"2011","model_name":"QnrB60","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"690":{"protein_sequence":{"accession":"BAN04743.1","sequence":"MALALIGEKIDRNRFTGEKVENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAILKDAIFKSCDLSMADFRNVSALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKAVLEKCELWENRWMGTQVLGATLSGSDLSGGEFSSFDWRTANFTHCDLTNSELGDLDIRGVDLQGVKLDSYQAVLLMERLGIAVIG"},"dna_sequence":{"accession":"AB734055.1","fmin":"376","fmax":"1021","strand":"+","sequence":"ATGGCTCTGGCATTAATTGGCGAAAAAATTGACAGAAACCGCTTCACCGGTGAAAAAGTTGAAAATAGCACTTTTTTTAACTGTGATTTTTCGGGTGCCGACCTTAGCGGTACTGAATTTATCGGCTGTCAGTTCTATGATCGAGAAAGCCAGAAAGGGTGCAATTTCAGTCGCGCAATACTGAAAGATGCCATTTTTAAAAGCTGTGATTTATCCATGGCGGATTTTCGCAACGTCAGTGCGTTGGGCATAGAAATTCGCCACTGCCGCGCACAGGGTGCAGATTTTCGCGGCGCAAGTTTCATGAATATGATCACCACGCGCACCTGGTTTTGCAGCGCATATATCACTAATACCAATCTAAGCTACGCCAACTTTTCGAAGGCCGTGCTTGAAAAGTGCGAATTGTGGGAAAATCGCTGGATGGGAACTCAGGTGCTGGGTGCGACGTTGAGTGGTTCCGATCTCTCCGGTGGCGAGTTTTCGTCGTTCGACTGGCGGACGGCAAATTTCACGCACTGTGATTTGACCAATTCAGAACTGGGTGATTTAGATATTCGGGGCGTCGATTTACAAGGTGTCAAATTGGACAGCTATCAGGCCGTATTGCTCATGGAACGTCTTGGCATCGCTGTCATTGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002773","ARO_id":"39207","ARO_name":"QnrB60","CARD_short_name":"QnrB60","ARO_description":"QnrB60 is a plasmid-mediated quinolone resistance protein found in Citrobacter freundii.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2012":{"model_id":"2012","model_name":"SHV-178","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1473":{"protein_sequence":{"accession":"AHA80963.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWVVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"KF705209.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGGTGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGCATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001361","ARO_id":"37761","ARO_name":"SHV-178","CARD_short_name":"SHV-178","ARO_description":"SHV-178 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2013":{"model_id":"2013","model_name":"Erm(41)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"225"}},"model_sequences":{"sequence":{"8379":{"protein_sequence":{"accession":"ABW06859.1","sequence":"MDLGAGHGALTAHLVAAGARVLAVELHPGRARHLRSRFAEEDVRVAEADLLAFRWPRRPFRVVASPPYQVTSALIRSLLTPESRLLAADLVLQRGAVHKHAKRAPVRHWTLRAGITLPRSAFHHPPQVDSSVLVIRRR"},"dna_sequence":{"accession":"EU177504.3","fmin":"3052","fmax":"3469","strand":"+","sequence":"GTGGATCTGGGCGCAGGACACGGCGCGCTGACGGCACATCTGGTTGCCGCTGGCGCCAGGGTGCTAGCCGTCGAGCTGCATCCGGGGCGGGCTCGACACCTTCGTTCACGGTTTGCCGAGGAAGATGTCCGGGTAGCGGAAGCGGACCTACTCGCCTTCCGGTGGCCGCGACGGCCATTTCGGGTGGTGGCGAGCCCGCCCTACCAAGTCACCAGCGCACTGATCCGGAGTCTCTTGACGCCGGAATCCCGGCTGCTGGCTGCCGACCTGGTGCTGCAGCGCGGGGCTGTGCACAAACATGCGAAGCGAGCACCTGTTCGCCATTGGACGCTACGGGCCGGAATCACATTGCCGCGAAGCGCTTTCCATCATCCACCGCAGGTGGATTCGTCGGTGCTGGTGATCAGGCGGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36888","NCBI_taxonomy_name":"Mycobacteroides abscessus","NCBI_taxonomy_id":"36809"}}}},"ARO_accession":"3000603","ARO_id":"36742","ARO_name":"Erm(41)","CARD_short_name":"Erm(41)","ARO_description":"Erm41 confers MLSb phenotype.","ARO_category":{"36699":{"category_aro_accession":"3000560","category_aro_cvterm_id":"36699","category_aro_name":"Erm 23S ribosomal RNA methyltransferase","category_aro_description":"Erm proteins are part of the RNA methyltransferase family and methylate A2058 (E. coli nomenclature) of the 23S ribosomal RNA conferring degrees of resistance to Macrolides, Lincosamides and Streptogramin b. This is called the MLSb phenotype.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35946":{"category_aro_accession":"0000027","category_aro_cvterm_id":"35946","category_aro_name":"roxithromycin","category_aro_description":"Roxithromycin is a semi-synthetic, 14-carbon ring macrolide antibiotic derived from erythromycin. It is used to treat respiratory tract, urinary and soft tissue infections. Roxithromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35974":{"category_aro_accession":"0000057","category_aro_cvterm_id":"35974","category_aro_name":"telithromycin","category_aro_description":"Telithromycin is a semi-synthetic derivative of erythromycin. It is a 14-membered macrolide and is the first ketolide antibiotic to be used in clinics. Telithromycin binds the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"35982":{"category_aro_accession":"0000065","category_aro_cvterm_id":"35982","category_aro_name":"clarithromycin","category_aro_description":"Clarithromycin is a methyl derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome and is used to treat pharyngitis, tonsillitis, acute maxillary sinusitis, acute bacterial exacerbation of chronic bronchitis, pneumonia (especially atypical pneumonias associated with Chlamydia pneumoniae or TWAR), and skin structure infections.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"36284":{"category_aro_accession":"3000145","category_aro_cvterm_id":"36284","category_aro_name":"tylosin","category_aro_description":"Tylosin is a 16-membered macrolide, naturally produced by Streptomyces fradiae. It interacts with the bacterial ribosome 50S subunit to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"36295":{"category_aro_accession":"3000156","category_aro_cvterm_id":"36295","category_aro_name":"spiramycin","category_aro_description":"Spiramycin is a 16-membered macrolide and is natural product produced by Streptomyces ambofaciens. It binds to the 50S subunit of bacterial ribosomes and inhibits peptidyl transfer activity to disrupt protein synthesis.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"36315":{"category_aro_accession":"3000176","category_aro_cvterm_id":"36315","category_aro_name":"dirithromycin","category_aro_description":"Dirithromycin is an oxazine derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome to inhibit bacterial protein synthesis.","category_aro_class_name":"Antibiotic"},"36722":{"category_aro_accession":"3000583","category_aro_cvterm_id":"36722","category_aro_name":"pristinamycin IA","category_aro_description":"Pristinamycin IA is a type B streptogramin antibiotic produced by Streptomyces pristinaespiralis. It binds to the P site of the 50S subunit of the bacterial ribosome, preventing the extension of protein chains.","category_aro_class_name":"Antibiotic"},"36723":{"category_aro_accession":"3000584","category_aro_cvterm_id":"36723","category_aro_name":"quinupristin","category_aro_description":"Quinupristin is a type B streptogramin and a semisynthetic derivative of pristinamycin 1A. It is a component of the drug Synercid and interacts with the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"virginiamycin M1","category_aro_description":"Virginiamycin M1 is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37016":{"category_aro_accession":"3000672","category_aro_cvterm_id":"37016","category_aro_name":"madumycin II","category_aro_description":"Madumycin II is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37017":{"category_aro_accession":"3000673","category_aro_cvterm_id":"37017","category_aro_name":"griseoviridin","category_aro_description":"Griseoviridin is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"37019":{"category_aro_accession":"3000675","category_aro_cvterm_id":"37019","category_aro_name":"pristinamycin IB","category_aro_description":"Pristinamycin IB is a class B streptogramin similar to pristinamycin IA, the former containing a N-methyl-4-(methylamino)phenylalanine instead of a N-methyl-4-(dimethylamino)phenylalanine in its class A streptogramin counterpart (one less methyl group).","category_aro_class_name":"Antibiotic"},"37021":{"category_aro_accession":"3000677","category_aro_cvterm_id":"37021","category_aro_name":"virginiamycin S2","category_aro_description":"Virginiamycin S2 is a streptogramin B antibiotic.","category_aro_class_name":"Antibiotic"},"37022":{"category_aro_accession":"3000678","category_aro_cvterm_id":"37022","category_aro_name":"pristinamycin IC","category_aro_description":"Pristinamycin IC is a class B streptogramin derived from virginiamycin S1.","category_aro_class_name":"Antibiotic"},"37023":{"category_aro_accession":"3000679","category_aro_cvterm_id":"37023","category_aro_name":"vernamycin C","category_aro_description":"Vernamycin C is a streptogramin B antibiotic.","category_aro_class_name":"Antibiotic"},"37024":{"category_aro_accession":"3000680","category_aro_cvterm_id":"37024","category_aro_name":"patricin A","category_aro_description":"Patricin A is a streptogramin B antibiotic.","category_aro_class_name":"Antibiotic"},"37025":{"category_aro_accession":"3000681","category_aro_cvterm_id":"37025","category_aro_name":"patricin B","category_aro_description":"Patricin B is a streptogramin B antibiotic.","category_aro_class_name":"Antibiotic"},"37026":{"category_aro_accession":"3000682","category_aro_cvterm_id":"37026","category_aro_name":"ostreogrycin B3","category_aro_description":"Ostreogrycin B3 is a derivative of pristinamycin IA, with an additional 3-hydroxy group on its 4-oxopipecolic acid.","category_aro_class_name":"Antibiotic"},"37247":{"category_aro_accession":"3000867","category_aro_cvterm_id":"37247","category_aro_name":"oleandomycin","category_aro_description":"Oleandomycin is a 14-membered macrolide produced by Streptomyces antibioticus. It is ssimilar to erythromycin, and contains a desosamine amino sugar and an oleandrose sugar. It targets the 50S ribosomal subunit to prevent protein synthesis.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35952":{"category_aro_accession":"0000034","category_aro_cvterm_id":"35952","category_aro_name":"streptogramin A antibiotic","category_aro_description":"Streptogramin A antibiotics are cyclic polyketide peptide hybrids that bind to the ribosomal peptidyl transfer centre. Structural variation arises from substituting a proline for its desaturated derivative and by its substitution for Ala or Cys. Used alone, streptogramin A antibiotics are bacteriostatic, but is bactericidal when used with streptogramin B antibiotics.","category_aro_class_name":"Drug Class"},"35967":{"category_aro_accession":"0000050","category_aro_cvterm_id":"35967","category_aro_name":"streptogramin B antibiotic","category_aro_description":"Streptogramin B antibiotics are are cyclic hepta- or hexa-depsipeptides.  Type B streptogramins block the peptide exit tunnel of the 50S bacterial ribosome. The general composition of group B streptogramins is 3-hydroxypicolinic acid-L-Thr-D-aminobutyric acid (or D-Ala)-L-Pro-L-Phe (or 4-N-,N-(dimethylamino)-L-Phe)-X-L-phenylglycine. Used alone, streptogramin B antibiotics are bacteriostatic, but is bactericidal when used with streptogramin A antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2015":{"model_id":"2015","model_name":"DHA-3","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1631":{"protein_sequence":{"accession":"AAR87489.1","sequence":"MKKSLSATLISALLAFSAPGFSAADNVAAVVDSTIKPLMAQQDIPGMAVAVSVKGKPYYFNYGFADIQAKQPVTENTLFELGSVSKTFTGVLGAVSVAKKEMALNDPAAKYQPELALPQWKGITLLDLATYTAGGLPLQVPDAVKSRADLLNFYQQWQPSRKPGDMRLYANSSIGLFGALTANAAGMPYEQLLTARILAPLGLSHTFITVPDSAQSQYAYGYKNKKPVRVSPGQLDAESYGVKSASKDMLRWAEMNIEPSRAGNADLEMAMYLAQTRYYKTAAINQGLGWEMYDWPQQKDMIINGVTNEVALQPHPVTDNQVQPYNRASWVHKTGATTGFGAYVAFIPEKQVAIVILANKNYPNTERVKAAQAILSALE"},"dna_sequence":{"accession":"AY494945.1","fmin":"1309","fmax":"2449","strand":"+","sequence":"ATGAAAAAATCGTTATCTGCAACACTGATTTCCGCTCTGCTGGCGTTTTCCGCCCCGGGGTTTTCTGCCGCTGATAATGTCGCGGCGGTGGTGGACAGCACCATTAAACCGCTGATGGCACAGCAGGATATTCCCGGGATGGCGGTTGCCGTCTCCGTAAAGGGTAAGCCCTATTATTTCAATTATGGTTTTGCCGATATTCAGGCAAAACAGCCGGTCACTGAAAATACACTATTTGAGCTCGGATCTGTAAGTAAAACTTTCACAGGTGTGCTGGGTGCGGTTTCTGTGGCGAAAAAAGAGATGGCGCTGAATGATCCGGCGGCAAAATACCAGCCGGAGCTGGCTCTGCCGCAGTGGAAGGGGATCACATTGCTGGATCTGGCTACCTATACCGCAGGCGGACTGCCGTTACAGGTGCCGGATGCGGTAAAAAGCCGTGCGGATCTGCTGAATTTCTATCAGCAGTGGCAGCCGTCCCGGAAACCGGGCGATATGCGTCTGTATGCAAACAGCAGTATCGGCCTGTTTGGTGCTCTGACCGCAAACGCGGCGGGGATGCCGTATGAGCAGTTGCTGACTGCACGGATCCTGGCACCGCTGGGGTTATCTCACACCTTTATTACTGTGCCGGATAGTGCGCAAAGCCAGTATGCGTACGGTTATAAAAACAAAAAACCGGTCCGCGTGTCGCCAGGACAGCTTGATGCGGAATCTTACGGCGTGAAATCCGCCTCAAAAGATATGCTGCGCTGGGCGGAAATGAATATTGAGCCGTCACGGGCCGGTAATGCGGATCTGGAAATGGCAATGTATCTCGCCCAGACCCGCTACTATAAAACCGCCGCGATTAACCAGGGGCTGGGCTGGGAAATGTATGACTGGCCGCAGCAGAAAGATATGATCATTAACGGCGTGACCAACGAGGTCGCATTGCAGCCGCATCCGGTAACAGACAACCAGGTTCAGCCGTATAACCGTGCTTCCTGGGTGCATAAAACGGGCGCAACAACTGGTTTCGGCGCCTATGTGGCCTTTATTCCGGAAAAACAGGTGGCGATTGTGATTCTGGCGAATAAAAACTACCCGAATACCGAAAGAGTCAAAGCTGCACAGGCTATTTTGAGTGCACTGGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002134","ARO_id":"38534","ARO_name":"DHA-3","CARD_short_name":"DHA-3","ARO_description":"DHA-3 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36207":{"category_aro_accession":"3000068","category_aro_cvterm_id":"36207","category_aro_name":"DHA beta-lactamase","category_aro_description":"DHA beta-lactamases are plasmid-mediated AmpC \u03b2-lactamases that confer resistance to cephamycins and oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2016":{"model_id":"2016","model_name":"OXA-370","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1214":{"protein_sequence":{"accession":"AHF71363.1","sequence":"MRVLALSAVFLVASIIGMPAVAKEWQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGQTRDIATWNRDHNLITAMKYSVVPVYQEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISATEQISFLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYETRIEPKIGWWVGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP"},"dna_sequence":{"accession":"KF900153.1","fmin":"0","fmax":"798","strand":"+","sequence":"ATGCGTGTATTAGCCTTATCGGCTGTGTTTTTGGTGGCATCGATTATCGGAATGCCTGCGGTAGCAAAGGAATGGCAAGAAAACAAAAGTTGGAATGCTCACTTTACTGAACATAAATCACAGGGCGTAGTTGTGCTCTGGAATGAGAATAAGCAGCAAGGATTTACCAATAATCTTAAACGGGCGAACCAAGCATTTTTACCCGCATCTACCTTTAAAATTCCCAATAGCTTGATCGCCCTCGATTTGGGCGTGGTTAAGGATGAACACCAAGTCTTTAAGTGGGATGGACAGACGCGCGATATCGCCACTTGGAATCGCGATCATAATCTAATCACCGCGATGAAATATTCAGTTGTGCCTGTTTATCAAGAATTTGCCCGCCAAATTGGCGAGGCACGTATGAGCAAGATGCTACATGCTTTCGATTATGGTAATGAGGACATTTCGGGCAATGTAGACAGTTTCTGGCTCGACGGTGGTATTCGAATTTCGGCCACGGAGCAAATCAGCTTTTTAAGAAAGCTGTATCACAATAAGTTACACGTATCGGAGCGCAGCCAGCGTATTGTCAAACAAGCCATGCTGACCGAAGCCAATGGCGACTATATTATTCGGGCTAAAACTGGATACGAGACTAGAATCGAACCTAAGATTGGCTGGTGGGTCGGTTGGGTTGAACTTGATGATAATGTGTGGTTTTTTGCGATGAATATGGATATGCCCACATCGGATGGTTTAGGGCTGCGCCAAGCCATCACAAAAGAAGTGCTCAAACAGGAAAAAATTATTCCCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39099","NCBI_taxonomy_name":"Enterobacter sp. 87F-2","NCBI_taxonomy_id":"1445416"}}}},"ARO_accession":"3001774","ARO_id":"38174","ARO_name":"OXA-370","CARD_short_name":"OXA-370","ARO_description":"OXA-370 is a beta-lactamase found in Enterobacter hormaechei.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46510":{"category_aro_accession":"3007721","category_aro_cvterm_id":"46510","category_aro_name":"OXA-48-like beta-lactamase","category_aro_description":"OXA-48-type beta-lactamases are now routinely encountered in bacterial infections caused by carbapenam-resistant Enterobacterales. OXA-48-like proteins confer resistance to penicillin (which is efficiently hydrolyzed) and carbapenam antibiotics (which is more slowly broken down). The spectrum of activity of these variants varies, with some hydrolyzing expanded-spectrum oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2017":{"model_id":"2017","model_name":"CTX-M-37","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8243":{"protein_sequence":{"accession":"AAT70415.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLHAQTADVQQKLAELEQQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVDGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGDYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"AY649755.2","fmin":"1640","fmax":"2516","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGCATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCAGCAGTCGGGAGGAAGGCTGGGTGTGGCATTGATTAACACAGCGGATAATTCGCAAATACTTTATCGTGCAGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTGGTTAACTATAATCCGATTGCGGAAAAGCACGTCGATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGCACCGAGCCGACGTTAAACACAGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACGCTGCGTAATCTGACGCTGGGTAAAGCATTGGGTGACAGCCAACGGGCGCAGCTGGTGACGTGGATGAAAGGCAATACTACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGACTATGGTACCACCAACGATATCGCGGTGATTTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCCCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3001899","ARO_id":"38299","ARO_name":"CTX-M-37","CARD_short_name":"CTX-M-37","ARO_description":"CTX-M-37 is a beta-lactamase found in Salmonella enterica.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2018":{"model_id":"2018","model_name":"CMY-76","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1664":{"protein_sequence":{"accession":"AFK73437.1","sequence":"MMKKSICCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAIIYEEKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWRGISLLHLATYTAGGLPLQIPDDVTDKAALLRFYQNWQPQWTPGAKRLYANSSIGLFGALAVQPSGMSYEEAMTRRVLQPLKLAHTWITVPQSEQKNYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIELAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"JQ733573.1","fmin":"1027","fmax":"2173","strand":"+","sequence":"ATGATGAAAAAATCGATATGCTGCGCGCTGCTGCTGACAGCCTCTTTCTCCACGTTTGCTGCCGCAAAAACAGAACAACAAATTGCCGATATCGTTAACCGCACCATCACACCACTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTGGCGATTATCTACGAGGAGAAACCTTATTACTTTACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAATTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGACGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCGGGGTATCAGCCTGCTGCACTTAGCCACCTATACAGCGGGTGGCCTGCCGCTGCAGATCCCCGATGACGTTACGGATAAAGCCGCATTACTGCGCTTTTATCAAAACTGGCAACCACAATGGACTCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGTGCGCTGGCGGTGCAACCTTCAGGTATGAGCTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAAAGCGAACAAAAAAATTATGCCTGGGGCTATCGCGAAGGGAAGCCTGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATCGATATGGCCCGCTGGGTTCAGGCCAACATGGACGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGAGCTTGCGCAGTCTCGCTACTGGCGTATTGGTGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCAGCACCTGCCGTGAAAGCCTCATGGGTGCATAAAACGGGATCCACAGGTGGATTTGGCAGCTACGTTGCCTTCGTTCCAGAAAAAAACCTTGGCATAGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGCGTCGAGGCGGCCTGGCGCATTCTTGAAAAACTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002089","ARO_id":"38489","ARO_name":"CMY-76","CARD_short_name":"CMY-76","ARO_description":"CMY-76 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2019":{"model_id":"2019","model_name":"OXA-213","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1128":{"protein_sequence":{"accession":"AEV91552.1","sequence":"MYKKALIVATSILFLSACSSNMVKQHQIHSISANKNSEEIKSLFDQAQTTGVLVIKRGQTEEIYGNDFKRASTDYVPASTFKMLNALIGLEHHKATTTEVFKWNGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMSKEVKRVGFGNANIGSKVDNFWLVGPLKITPQQETQFAYQLAHKTLPFSKDVQEQVQSMVFIEEKNGSKIYAKSGWGWDVEPQVGWLTGWVVQPQGEIVAFSLNLEMKKGTPSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"JN861781.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGTACAAAAAAGCCCTTATCGTTGCAACAAGTATCCTATTTTTATCCGCCTGTTCTTCCAATATGGTAAAACAACATCAAATACACTCTATTTCTGCCAATAAAAATTCAGAAGAAATTAAATCACTGTTTGATCAAGCACAGACCACGGGAGTTTTGGTGATTAAGCGAGGGCAAACAGAAGAAATTTATGGCAATGATTTTAAAAGAGCATCAACCGACTATGTTCCCGCCTCTACCTTTAAAATGTTAAATGCTTTAATTGGACTTGAACATCATAAGGCAACTACAACTGAAGTATTTAAATGGAATGGGCAAAAACGTTTATTTCCTGATTGGGAAAAGGACATGACACTGGGCGATGCCATGAAAGCGTCTGCAATTCCAGTTTACCAAGAATTAGCCCGACGAATTGGTCTAGATCTTATGTCCAAAGAGGTGAAACGAGTTGGTTTTGGTAATGCTAACATTGGTTCAAAAGTAGATAATTTTTGGCTCGTTGGCCCTCTAAAAATTACACCTCAACAAGAAACCCAATTTGCTTATCAATTAGCCCATAAAACGCTTCCATTTAGTAAAGATGTACAAGAACAAGTTCAATCAATGGTGTTCATAGAAGAAAAAAATGGAAGTAAGATTTATGCCAAAAGTGGGTGGGGATGGGATGTTGAACCACAAGTTGGTTGGTTAACAGGCTGGGTCGTTCAACCACAAGGAGAAATTGTCGCATTCTCACTTAATTTAGAAATGAAAAAAGGAACTCCCAGCTCTATTCGCAAAGAAATTGCTTATAAAGGCTTAGAACAACTGGGTATCTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39094","NCBI_taxonomy_name":"Acinetobacter calcoaceticus","NCBI_taxonomy_id":"471"}}}},"ARO_accession":"3001712","ARO_id":"38112","ARO_name":"OXA-213","CARD_short_name":"OXA-213","ARO_description":"OXA-213 is a beta-lactamase found in Acinetobacter spp.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46495":{"category_aro_accession":"3007706","category_aro_cvterm_id":"46495","category_aro_name":"OXA-213-like beta-lactamase","category_aro_description":"OXA-213-like enzymes have been identified to be intrinsic to A. calcoaceticus and have been subsequently detected in A. pittii. Phylogenetic analysis of OXA-213-like proteins identified two distinct subgroups within the OXA family. The first group was linked to A. pittii and the second group to A. calcoaceticus. The carbapenemase activity of these OXAs may be related to the species-dependent effect.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2021":{"model_id":"2021","model_name":"SHV-165","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1065":{"protein_sequence":{"accession":"AFQ23970.1","sequence":"MRYIRLCIISLLAPLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGASKRGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"JX121131.1","fmin":"0","fmax":"858","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCCCCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTACTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTAGCAAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGC","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001203","ARO_id":"37583","ARO_name":"SHV-165","CARD_short_name":"SHV-165","ARO_description":"SHV-165 is a beta-lactamase.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2022":{"model_id":"2022","model_name":"CTX-M-104","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1104":{"protein_sequence":{"accession":"ADY02555.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAENRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"HQ833652.1","fmin":"235","fmax":"1111","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGACTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAACCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001963","ARO_id":"38363","ARO_name":"CTX-M-104","CARD_short_name":"CTX-M-104","ARO_description":"CTX-M-104 is a beta-lactamase found in Escherichia coli.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2023":{"model_id":"2023","model_name":"OXA-132","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1753":{"protein_sequence":{"accession":"ACD84990.1","sequence":"MNIKTLLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEVHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEMTYKSLEQLGIL"},"dna_sequence":{"accession":"EU547447.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAACACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGTACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATGACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001653","ARO_id":"38053","ARO_name":"OXA-132","CARD_short_name":"OXA-132","ARO_description":"OXA-132 is a beta-lactamase found in A. baumannii.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2024":{"model_id":"2024","model_name":"ACC-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1852":{"protein_sequence":{"accession":"AAF86691.1","sequence":"MRKKMQNTLKLLSVITCLAATAQGAMAANIDESKIKDTVDGLIQPLMQKNNIPGMSVAVTIRGRNYIYNYGLAAKQPQQPVTENTLFEVGSLSKTFAAILASYAQASGKLSLEQSVSHYVPELRGSSFDHVSVLNVGTHTSGLQLFMPEDIKNTTQLMTYLKAWKPADAAGTHRVYSNIGTGLLGMIAAKSLGVSYEDAIEQTILPLLGMNQTYLKVPADQMENYAWGYNKKDEPVHVNMEILGNEAYGIKTTSSDLLRYVQANMGQLKLDGNAKIQHALTATHTGYFKSGEITQDLMWEQLPYPVSLPNLLTGNDMAMTKSVATPIVPPLPPQENVWINKTGSTNGFGAYIAFVPAKKMGIVMLANKNYSIDQRVTVAYKILSSLEVNK"},"dna_sequence":{"accession":"AF180952.1","fmin":"1564","fmax":"2737","strand":"+","sequence":"ATGCGTAAAAAAATGCAGAACACCTTGAAGCTGTTATCCGTGATTACCTGTCTGGCAGCAACTGCCCAAGGTGCTATGGCTGCCAATATCGATGAGAGCAAAATTAAAGACACCGTCGATGGCCTAATCCAGCCGCTGATGCAGAAGAATAATATTCCCGGTATGTCGGTCGCAGTGACCATCAGAGGTAGGAACTATATTTATAACTACGGGTTAGCGGCAAAACAGCCTCAGCAGCCGGTGACGGAAAATACGTTATTTGAAGTGGGTTCGCTGAGTAAAACGTTTGCTGCCATCTTGGCGTCCTATGCGCAGGCGAGCGGTAAGCTGTCTTTGGAGCAAAGCGTTAGCCACTATGTTCCAGAACTACGTGGCAGCAGCTTTGACCACGTTAGCGTACTCAATGTGGGTACGCATACCTCAGGTCTACAGCTGTTTATGCCGGAAGATATCAAGAACACCACACAGCTGATGACTTATCTAAAAGCATGGAAACCTGCTGATGCGGCTGGAACCCATCGCGTTTATTCCAATATCGGTACCGGTTTGCTAGGGATGATTGCGGCGAAAAGTCTGGGTGTGAGCTATGAAGATGCGATTGAGCAAACCATCCTTCCTCTATTAGGCATGAATCAAACCTACCTGAAGGTTCCGGCTGACCAGATGGAAAACTATGCGTGGGGCTACAACAAGAAAGATGAGCCAGTGCACGTCAATATGGAGATTTTGGGTAACGAAGCTTATGGTATCAAAACCACCTCCAGCGACTTGTTACGCTACGTGCAAGCCAATATGGGGCAGTTAAAGCTTGATGGTAATGCCAAGATCCAACATGCACTGACAGCCACCCACACCGGCTATTTCAAATCGGGTGAGATTACTCAGGATCTGATGTGGGAGCAGCTGCCATATCCAGTTTCTCTGCCGAATTTGCTCACCGGTAACGATATGGCGATGACGAAAAGCGTGGCTACGCCGATTGTTCCCCCGTTACCGCCACAGGAAAATGTGTGGATTAATAAGACCGGATCAACTAACGGCTTCGGTGCCTATATTGCGTTTGTTCCTGCTAAGAAGATGGGGATCGTGATGCTGGCTAACAAAAACTACTCAATCGATCAACGAGTGACGGTGGCGTATAAAATCCTGAGCTCGTTGGAAGTGAATAAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36784","NCBI_taxonomy_name":"Hafnia alvei","NCBI_taxonomy_id":"569"}}}},"ARO_accession":"3001816","ARO_id":"38216","ARO_name":"ACC-2","CARD_short_name":"ACC-2","ARO_description":"ACC-2 is a beta-lactamase found in Hafnia alvei.","ARO_category":{"36212":{"category_aro_accession":"3000073","category_aro_cvterm_id":"36212","category_aro_name":"ACC beta-lactamase","category_aro_description":"ACC beta-lactamases or Ambler class C beta-lactamases are AmpC beta-lactamases. They possess an interesting resistance phenotype due to their low activity against cephamycins.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36989":{"category_aro_accession":"3000645","category_aro_cvterm_id":"36989","category_aro_name":"cefotaxime","category_aro_description":"Cefotaxime is a semisynthetic cephalosporin taken parenterally. It is resistant to most beta-lactamases and active against Gram-negative rods and cocci due to its aminothiazoyl and methoximino functional groups.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2025":{"model_id":"2025","model_name":"TEM-57","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"850":{"protein_sequence":{"accession":"ACJ43254.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLDRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"FJ405211.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGATCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000926","ARO_id":"37306","ARO_name":"TEM-57","CARD_short_name":"TEM-57","ARO_description":"TEM-57 is a broad-spectrum beta-lactamase found in E. coli.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2026":{"model_id":"2026","model_name":"OXA-84","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"2015":{"protein_sequence":{"accession":"ABC26006.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDVKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAISVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLAGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"DQ309276.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGTAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTTCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGCGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAACAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001624","ARO_id":"38024","ARO_name":"OXA-84","CARD_short_name":"OXA-84","ARO_description":"OXA-84 is a beta-lactamase found in A. baumannii.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2027":{"model_id":"2027","model_name":"CMY-84","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"1037":{"protein_sequence":{"accession":"AFK73455.1","sequence":"MMKKSICCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAIIYEGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPALTGKQWRGISLLHLATYTAGGLPLQIPDDITDKAALLRFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQSEQKNYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIELAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPARVEAAWRILEKLQ"},"dna_sequence":{"accession":"JQ733579.1","fmin":"1027","fmax":"2173","strand":"+","sequence":"ATGATGAAAAAATCGATATGCTGCGCACTGCTGCTGACAGCCTCTTTCTCCACGTTTGCTGCCGCAAAAACAGAACAACAAATTGCCGATATCGTTAACCGCACCATCACACCACTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTGGCGATTATCTACGAGGGGAAACCTTATTACTTTACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGACGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGCACTGACAGGCAAACAGTGGCGGGGTATCAGCCTGCTGCACTTAGCCACCTATACAGCGGGTGGCCTGCCGCTGCAGATCCCCGATGACATTACGGATAAAGCCGCATTACTGCGCTTTTATCAAAACTGGCAACCACAATGGACTCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGTGCGCTGGCGGTGAAACCTTCAGGTATGAGCTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAAAGCGAACAAAAAAACTATGCCTGGGGCTATCGCGAAGGGAAGCCTGTGCACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATCGATATGGCCCGCTGGGTTCAGGCCAACATGGACGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGAGCTTGCGCAGTCTCGCTACTGGCGTATTGGTGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCAGCACCTGCCGTGAAAGCCTCATGGGTGCATAAAACAGGATCCACAGGCGGATTTGGCAGCTACGTTGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTAATGTTGGCAAACAAAAGCTATCCCAACCCGGCTCGCGTCGAGGCGGCCTGGCGCATTCTTGAAAAACTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002097","ARO_id":"38497","ARO_name":"CMY-84","CARD_short_name":"CMY-84","ARO_description":"CMY-84 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2028":{"model_id":"2028","model_name":"QnrB43","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"5841":{"protein_sequence":{"accession":"WP_063866099.1","sequence":"MALALVGEKIDRNRFTGEKIENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNASALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGAQVLGATFSGSDLAGGEFSTFDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDNYQASLLMERLGIAVIG"},"dna_sequence":{"accession":"NG_050506.1","fmin":"36","fmax":"681","strand":"+","sequence":"ATGGCTCTGGCACTCGTTGGCGAAAAAATTGACAGAAACCGCTTCACCGGTGAGAAAATTGAAAATAGTACATTTTTTAACTGTGATTTTTCAGGTGCCGACCTGAGCGGCACTGAATTTATCGGCTGTCAGTTCTATGATCGTGAAAGCCAGAAAGGGTGCAATTTTAGTCGTGCGATGCTGAAAGATGCCATTTTTAAAAGCTGTGATTTATCCATGGCGGATTTTCGCAATGCCAGTGCGCTTGGCATTGAAATTCGCCACTGTCGTGCGCAAGGCGCAGATTTCCGCGGCGCAAGCTTTATGAATATGATCACTACTCGCACCTGGTTTTGCAGCGCATATATCACTAACACAAATCTAAGCTACGCCAATTTTTCGAAAGTCGTGTTGGAAAAATGTGAGCTGTGGGAAAACCGTTGGATGGGTGCCCAGGTACTGGGCGCGACGTTCAGTGGTTCAGATCTTGCCGGCGGCGAGTTTTCGACTTTCGACTGGCGAGCAGCAAACTTCACACATTGCGATCTGACCAATTCGGAGTTGGGTGACTTAGATATTCGGGGCGTTGATTTACAAGGCGTTAAGTTGGACAACTACCAGGCATCGCTGCTCATGGAACGTCTTGGCATCGCGGTAATTGGTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002758","ARO_id":"39192","ARO_name":"QnrB43","CARD_short_name":"QnrB43","ARO_description":"QnrB43 is a plasmid-mediated quinolone resistance protein found in Escherichia coli.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2029":{"model_id":"2029","model_name":"TEM-123","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1321":{"protein_sequence":{"accession":"AAQ93490.1","sequence":"MSIKHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVKYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGASERGSRGIIALGPDGKPSRIVVIYTTGSQATMDEANRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AY327539.1","fmin":"0","fmax":"858","strand":"+","sequence":"ATGAGTATTAAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTAAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCAGTGAGCGTGGATCTCGCGGTATCATTGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAAGCAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3000985","ARO_id":"37365","ARO_name":"TEM-123","CARD_short_name":"TEM-123","ARO_description":"TEM-123 is an extended-spectrum beta-lactamase found in Proteus mirabilis.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2030":{"model_id":"2030","model_name":"AAC(3)-IXa","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"655":{"protein_sequence":{"accession":"AAA25334.1","sequence":"MEEMSLLNHSGGPVTRSRIKHDLADLGLKDGDVVIFHTRMSAIGYVAGGTQTIIGALLDVVGARGTLMVPCGWNNAPPYDFLDWPRDWQDALRAEHPAYDPDLSEADYNNGRLPEALPRWPGAIRSRHPDASFAALGPAAAELMAEHPWDHPHGPDTPLARLIAHSGRVLLLGAPLDTMTLLHHAEALADVRSKRFVTYEQPILVNGQRVWRQFRDIDSEEGAFDYSTVRRGVEPFEAIARDMLSAGIGRQGRVGAADSYLFDAGPVFNFAINWIEAKLKR"},"dna_sequence":{"accession":"M55427.1","fmin":"273","fmax":"1119","strand":"+","sequence":"ATGGAAGAGATGAGCTTACTCAATCACTCCGGCGGTCCCGTTACCCGAAGCCGGATCAAGCATGACCTTGCTGATCTCGGTCTCAAAGACGGAGACGTGGTGATTTTCCACACCCGCATGTCTGCCATCGGGTACGTGGCTGGCGGAACGCAGACAATCATCGGCGCACTCCTCGACGTTGTGGGAGCCCGTGGAACCCTTATGGTGCCCTGTGGCTGGAACAACGCGCCTCCATATGACTTCCTCGATTGGCCACGGGACTGGCAGGACGCCCTGCGAGCAGAGCATCCCGCGTACGACCCGGACCTCAGTGAGGCGGACTACAATAATGGTCGTCTCCCAGAAGCGCTGCCGCGCTGGCCTGGCGCGATCCGAAGTCGGCACCCCGACGCCAGTTTCGCAGCCCTGGGGCCGGCTGCAGCCGAACTGATGGCAGAGCATCCGTGGGACCATCCTCACGGACCCGACACCCCGCTAGCACGGCTGATCGCCCATAGCGGCCGAGTCTTGTTACTTGGCGCTCCATTGGACACCATGACGCTGTTGCATCACGCTGAGGCGTTGGCCGACGTCCGCAGCAAACGGTTCGTGACCTACGAACAACCGATCCTCGTTAACGGCCAGCGGGTGTGGCGACAATTCCGCGATATCGACTCTGAGGAAGGAGCGTTTGACTACTCGACGGTGCGCCGAGGGGTGGAGCCGTTCGAGGCCATTGCACGGGACATGCTCTCGGCAGGAATCGGTCGTCAGGGCAGGGTCGGCGCCGCGGATAGCTACCTGTTTGACGCCGGGCCTGTCTTCAATTTTGCGATCAACTGGATCGAGGCCAAGCTGAAGAGATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39506","NCBI_taxonomy_name":"Micromonospora chalcea","NCBI_taxonomy_id":"1874"}}}},"ARO_accession":"3002543","ARO_id":"38943","ARO_name":"AAC(3)-IXa","CARD_short_name":"AAC(3)-IXa","ARO_description":"AAC(3)-IXa is a chromosomal-encoded aminoglycoside acetyltransferase in Micromonospora chalcea.","ARO_category":{"36461":{"category_aro_accession":"3000322","category_aro_cvterm_id":"36461","category_aro_name":"AAC(3)","category_aro_description":"A category of aminoglycoside N-acetyltransferase enzymes with modification regiospecificity based at the 3-amino group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics through acetylation of the 3-amino group of the compound.","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2031":{"model_id":"2031","model_name":"OXA-173","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1924":{"protein_sequence":{"accession":"ADI58617.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDVKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAVPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGLDVNLQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"HM113559.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGTAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTGTTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAACAAAATATACGCAAAAAGTGGTTGGGGATTGGATGTAAACCTACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001657","ARO_id":"38057","ARO_name":"OXA-173","CARD_short_name":"OXA-173","ARO_description":"OXA-173 is a beta-lactamase found in A. baumannii.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2032":{"model_id":"2032","model_name":"CTX-M-62","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8210":{"protein_sequence":{"accession":"ABP04245.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTESTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGDYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"EF219134.3","fmin":"2125","fmax":"3001","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGTCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGAAGACTGGGGGTGGCATTGATTAACACAGCGGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTCGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTGGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGTCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCAGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGACTATGGCACCACCAACGATATCGCGGTGATTTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001923","ARO_id":"38323","ARO_name":"CTX-M-62","CARD_short_name":"CTX-M-62","ARO_description":"CTX-M-62 is a beta-lactamase found in Escherichia coli.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2034":{"model_id":"2034","model_name":"TEM-108","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1320":{"protein_sequence":{"accession":"AAM28884.1","sequence":"MDPQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAELSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTSELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERSRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AF506748.1","fmin":"38","fmax":"899","strand":"+","sequence":"ATGGATCCTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGAATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTAGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCAGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAGTAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35732","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Typhimurium","NCBI_taxonomy_id":"90371"}}}},"ARO_accession":"3000971","ARO_id":"37351","ARO_name":"TEM-108","CARD_short_name":"TEM-108","ARO_description":"TEM-108 is a beta-lactamase that has been found in clinical isolates.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2035":{"model_id":"2035","model_name":"CTX-M-15","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1430":{"protein_sequence":{"accession":"AAL02127.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"AY044436.1","fmin":"1435","fmax":"2311","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001878","ARO_id":"38278","ARO_name":"CTX-M-15","CARD_short_name":"CTX-M-15","ARO_description":"CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35975":{"category_aro_accession":"0000058","category_aro_cvterm_id":"35975","category_aro_name":"cefazolin","category_aro_description":"Cefazolin, also known as cefazoline or cephazolin, is a first generation cephalosporin antibiotic. It is administered parenterally, and is active against a broad spectrum of bacteria.","category_aro_class_name":"Antibiotic"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"35979":{"category_aro_accession":"0000062","category_aro_cvterm_id":"35979","category_aro_name":"ceftriaxone","category_aro_description":"Ceftriaxone is a third-generation cephalosporin antibiotic. The presence of an aminothiazolyl sidechain increases ceftriazone's resistance to beta-lactamases. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"37084":{"category_aro_accession":"3000704","category_aro_cvterm_id":"37084","category_aro_name":"cefalotin","category_aro_description":"Cefalotin is a semisynthetic cephalosporin antibiotic activate against staphylococci. It is resistant to staphylococci beta-lactamases but hydrolyzed by enterobacterial beta-lactamases.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2036":{"model_id":"2036","model_name":"SHV-163","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"916":{"protein_sequence":{"accession":"AFQ23969.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGSVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGASERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQQ"},"dna_sequence":{"accession":"JX121130.1","fmin":"0","fmax":"858","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCAGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTAGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGGATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACAA","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001202","ARO_id":"37582","ARO_name":"SHV-163","CARD_short_name":"SHV-163","ARO_description":"SHV-163 is a beta-lactamase.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2038":{"model_id":"2038","model_name":"KPC-17","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"873":{"protein_sequence":{"accession":"AGJ01154.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQLVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"KC465200.1","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGCTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002327","ARO_id":"38727","ARO_name":"KPC-17","CARD_short_name":"KPC-17","ARO_description":"KPC-17 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2039":{"model_id":"2039","model_name":"CARB-18","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"942":{"protein_sequence":{"accession":"AIL92327.1","sequence":"MKKLFLLVGLMVCSTVSYASKLNEDISLIEKQTSGRIGVSVWDTQTDERWDYRGDERFPLMSTFKTLACATMLSDMDSGKLNKNATAKIDERNIVVWSPVMDKLAGQSTRIEHACEAAMLMSDNTAANLVLNEIGGPKAVTLFLRSIGDKATRLDRLEPRLNEAKPGDKRDTTTPNAMVNTLHTLMEDNALSYESRTQLKIWMQDNKVSDSLMRSVLPKGWSIADRSGAGNYGSRGISAMIWKDNYKPVYISIYVTDTDLSLQARDQLIAQISQLILEHYKES"},"dna_sequence":{"accession":"KJ934266.1","fmin":"0","fmax":"852","strand":"+","sequence":"ATGAAAAAGTTATTCCTGTTGGTTGGGCTGATGGTTTGCTCAACTGTTAGTTACGCCTCCAAATTAAACGAAGACATCTCCCTCATCGAGAAACAAACATCTGGGCGAATTGGAGTGTCAGTCTGGGATACACAAACGGACGAGCGTTGGGATTATCGCGGAGACGAACGTTTCCCATTAATGAGCACATTCAAAACGTTAGCGTGTGCCACCATGCTAAGCGACATGGACAGCGGCAAACTCAACAAAAATGCCACAGCGAAAATCGATGAACGCAATATTGTGGTTTGGTCTCCGGTGATGGATAAACTGGCTGGACAAAGCACACGYATCGAACACGCTTGTGAAGCCGCCATGTTGATGAGCGACAACACCGCCGCGAACTTAGTGCTAAATGAAATTGGTGGTCCTAAAGCGGTCACGCTGTTTTTGCGATCTATTGGCGACAAAGCAACGCGACTTGACCGATTGGAACCCCGTTTGAATGAAGCAAAACCGGGCGACAAGCGAGACACCACAACGCCTAACGCCATGGTAAACACCCTACATACCTTGATGGAAGATAACGCCCTATCTTACGAGTCACGCACACAGCTGAAAATCTGGATGCAAGACAACAAAGTATCGGATTCKCTCATGCGCTCTGTTCTGCCAAAAGGCTGGTCGATTGCAGACCGCTCTGGCGCAGGTAACTACGGTTCACGCGGCATTAGCGCGATGATCTGGAAAGACAACTACAAGCCGGTTTACATCAGTATTTACGTCACAGACACTGACCTTTCGCTTCAAGCTCGCGATCAACTGATCGCGCAAATCAGCCAACTGATTTTAGAGCACTACAAAGAAAGTTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39615","NCBI_taxonomy_name":"Vibrio parahaemolyticus","NCBI_taxonomy_id":"670"}}}},"ARO_accession":"3003174","ARO_id":"39751","ARO_name":"CARB-18","CARD_short_name":"CARB-18","ARO_description":"CARB-18 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36230":{"category_aro_accession":"3000091","category_aro_cvterm_id":"36230","category_aro_name":"CARB beta-lactamase","category_aro_description":"CARB beta-lactamases are class A lactamases that can hydrolyze carbenicillin. Many of the PSE beta-lactamases have been renamed as CARB-lactamases with the notable exception of PSE-2 which is now OXA-10.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2040":{"model_id":"2040","model_name":"TEM-60","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1079":{"protein_sequence":{"accession":"AAC05975.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDKLGARVGYIELDPNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVKYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDSWEPELNEAIPNDERDTTMPAAMRTTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRCALPAGWLIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AF047171.1","fmin":"135","fmax":"996","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATAAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCCTAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTAAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATAGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGCGAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTGCGCCCTTCCGGCTGGCTGGTTAATTGCTGATAAATCTGGAGCCGGTGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36946","NCBI_taxonomy_name":"Providencia stuartii","NCBI_taxonomy_id":"588"}}}},"ARO_accession":"3000929","ARO_id":"37309","ARO_name":"TEM-60","CARD_short_name":"TEM-60","ARO_description":"TEM-60 is an extended-spectrum beta-lactamase that has been found in clinical isolates.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2041":{"model_id":"2041","model_name":"OXA-424","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1055":{"protein_sequence":{"accession":"AJA32742.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGEKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"KM588352.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCCCTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTCTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAATGGGATGGGGAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAGGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATAGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3003147","ARO_id":"39724","ARO_name":"OXA-424","CARD_short_name":"OXA-424","ARO_description":"OXA-424 is a beta-lactamase found in clinical isolates of Acinetobacter baumannii found in China. It is carbapenem resistant.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2042":{"model_id":"2042","model_name":"IND-8","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1340":{"protein_sequence":{"accession":"ACZ65152.1","sequence":"MKKSIQFFIVSMLLSPFANSQVKDFVIEPPIKSNLYIYKTFGVFGGKEYSANAAYLKTKKGVILFDVPWEKVQYQSLMDTIKKRHNLPVIAVFATHSHDDRAGDLSFFNNKGIKTYATLKTNEFLKKDGKATSTEIIQTGKPYHIGGEEFVVDFLGEGHTADNVVVWFPKYNVLDGGCLVKSNSATDLGYIKEANVEQWPKTMNKLKTKYSKATLIIPGHDEWKGGGHVEHTLELLNKK"},"dna_sequence":{"accession":"GU186044.1","fmin":"39","fmax":"759","strand":"+","sequence":"ATGAAAAAAAGCATTCAATTTTTTATTGTTTCCATGTTGTTGAGCCCTTTTGCCAATTCACAGGTAAAAGATTTTGTAATTGAGCCACCTATTAAATCCAATCTATATATTTACAAGACTTTTGGAGTATTCGGAGGTAAAGAATATTCTGCCAATGCAGCCTATCTTAAGACTAAAAAAGGTGTAATTCTGTTTGATGTACCCTGGGAAAAAGTACAGTATCAAAGCCTGATGGATACCATCAAAAAACGTCATAACTTACCGGTAATTGCCGTATTTGCTACGCATTCCCATGATGACCGTGCAGGAGACTTAAGCTTTTTCAATAATAAAGGCATTAAGACGTATGCTACCCTGAAAACCAATGAGTTTCTGAAGAAAGATGGAAAAGCAACATCCACAGAGATCATCCAAACCGGAAAACCTTATCACATTGGCGGAGAAGAATTTGTGGTCGATTTTCTTGGTGAAGGACATACTGCTGATAATGTAGTGGTATGGTTTCCAAAATATAATGTTTTGGATGGCGGATGTCTTGTAAAAAGTAATTCTGCTACTGACTTAGGATACATTAAAGAAGCCAATGTAGAACAATGGCCCAAGACGATGAATAAATTAAAAACCAAATATTCAAAAGCCACATTAATTATTCCCGGGCATGATGAATGGAAAGGGGGTGGACATGTTGAACACACTTTAGAGCTTTTGAACAAAAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36916","NCBI_taxonomy_name":"Chryseobacterium indologenes","NCBI_taxonomy_id":"253"}}}},"ARO_accession":"3002264","ARO_id":"38664","ARO_name":"IND-8","CARD_short_name":"IND-8","ARO_description":"IND-8 is a beta-lactamase found in Escherichia coli.","ARO_category":{"36199":{"category_aro_accession":"3000060","category_aro_cvterm_id":"36199","category_aro_name":"IND beta-lactamase","category_aro_description":"IND beta-lactamases are class B carbapenem-hydrolyzing beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2043":{"model_id":"2043","model_name":"aadA8","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"558":{"protein_sequence":{"accession":"AAN41439.1","sequence":"MRVAVTIEISNQLSEVLSVIERHLESTLLAVHLYGSAVDGGLKPYSDIDLLVTVAVKLDETTRRALLNDLMEASAFPGESETLRAIEVTLVVHDDIIPWRYPAKRELQFGEWQRNDILAGIFEPAMIDIDLAILLTKAREHSVALVGPAAEEFFDPVPEQDLFEALRETLKLWNSQPDWAGDERNVVLTLSRIWYSAITGKIAPKDVAADWAMERLPAQYQPVILEARQAYLGQEEDRLASRADQLEEFVHYVKGEITKVVGK"},"dna_sequence":{"accession":"AY139603.1","fmin":"106","fmax":"898","strand":"+","sequence":"ATGAGGGTAGCGGTGACCATCGAAATTTCGAACCAACTATCAGAGGTGCTAAGCGTCATTGAGCGCCATCTGGAATCAACGTTGCTGGCCGTGCATTTGTACGGCTCCGCAGTGGATGGCGGCCTGAAGCCATACAGCGATATTGATTTGTTGGTTACTGTGGCCGTAAAGCTTGATGAAACGACGCGGCGAGCATTGCTCAATGACCTTATGGAGGCTTCGGCTTTCCCTGGCGAGAGCGAGACGCTCCGCGCTATAGAAGTCACCCTTGTCGTGCATGACGACATCATCCCGTGGCGTTATCCGGCTAAGCGCGAGCTGCAATTTGGAGAATGGCAGCGCAATGACATTCTTGCGGGTATCTTCGAGCCAGCCATGATCGACATTGATCTGGCTATCCTGCTTACAAAAGCAAGAGAACATAGCGTTGCCTTGGTAGGTCCGGCAGCGGAGGAATTCTTTGACCCGGTTCCTGAACAGGATCTATTCGAGGCGCTGAGGGAAACCTTGAAGCTATGGAACTCGCAGCCCGACTGGGCCGGCGATGAGCGAAATGTAGTGCTTACGTTGTCCCGCATTTGGTACAGCGCAATAACCGGCAAAATCGCGCCGAAGGATGTCGCTGCCGACTGGGCAATGGAGCGCCTGCCGGCCCAGTATCAGCCCGTCATACTTGAAGCTAGACAGGCTTATCTTGGACAAGAAGAAGATCGCTTGGCCTCGCGCGCAGATCAGTTGGAAGAATTTGTTCACTACGTGAAAGGCGAGATCACCAAGGTAGTCGGCAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36791","NCBI_taxonomy_name":"uncultured bacterium","NCBI_taxonomy_id":"77133"}}}},"ARO_accession":"3002608","ARO_id":"39008","ARO_name":"aadA8","CARD_short_name":"aadA8","ARO_description":"aadA8 is an aminoglycoside nucleotidyltransferase gene encoded by plasmids and integrons in V. cholerae, K. pneumoniae and Bacillus endophyticus.","ARO_category":{"41439":{"category_aro_accession":"3004275","category_aro_cvterm_id":"41439","category_aro_name":"ANT(3'')","category_aro_description":"A category of aminoglycoside O-nucleotidyltransferase enzymes with modification regiospecificity based at the 3''-hydroxyl group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics by transfer of an AMP group from an ATP substrate to the 3''-hydroxyl group of the compound.","category_aro_class_name":"AMR Gene Family"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2044":{"model_id":"2044","model_name":"QnrB31","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"8167":{"protein_sequence":{"accession":"ADQ43424.1","sequence":"MTPLLYKKTGTNMALALVGEKIDRNRFTGEKIENSTFFLCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNASALGIEISHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGAQVLGATFSGSDLSGGEFSTFDWRAANFTHCDLTNSELGDLDIRRVDLQGVKLDNYQASLLMERLGIAIIG"},"dna_sequence":{"accession":"HQ418999.2","fmin":"0","fmax":"681","strand":"+","sequence":"ATGACGCCATTACTGTATAAGAAAACAGGTACAAATATGGCTCTGGCGCTCGTGGGCGAAAAAATTGACAGAAACCGTTTCACCGGTGAGAAAATTGAAAATAGTACATTTTTTTTATGTGATTTTTCAGGAGCCGACCTGAGCGGCACTGAGTTTATCGGCTGTCAATTCTATGATCGTGAAAGCCAGAAAGGCTGCAATTTTAGTCGTGCGATGTTAAAGGATGCCATTTTTAAAAGCTGCGATTTATCCATGGCGGATTTTCGCAATGCAAGCGCCCTGGGTATTGAGATTTCTCATTGTAGGGCTCAGGGTGCAGATTTTCGCGGCGCAAGCTTTATGAACATGATTACCACGCGCACTTGGTTCTGCAGCGCGTATATCACGAATACGAATCTGTCTTATGCCAATTTTTCGAAAGTCGTGTTGGAGAAGTGTGAGTTATGGGAAAACCGTTGGATGGGTGCCCAGGTACTGGGCGCGACGTTCAGTGGTTCAGATCTCTCCGGCGGCGAGTTTTCAACTTTCGACTGGCGAGCAGCAAACTTTACACATTGCGATCTCACAAATTCGGAGTTGGGTGACTTAGATATTCGTCGGGTTGATTTACAAGGCGTTAAGTTGGACAACTACCAGGCTTCGTTGCTCATGGAGCGACTTGGCATCGCGATAATTGGTTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002746","ARO_id":"39180","ARO_name":"QnrB31","CARD_short_name":"QnrB31","ARO_description":"QnrB31 is a plasmid-mediated quinolone resistance protein found in Klebsiella pneumoniae.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2045":{"model_id":"2045","model_name":"OXY-2-3","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8260":{"protein_sequence":{"accession":"AAL78281.2","sequence":"MIKSSWRKIAMLAAVPLLLASGALWASTDAIHQKLTDLEKRSGGRLGVALINTADNSQILYRGDERFAMCSTSKVMAAAAVLKQSESNKEVVNKRLEINAADLVVWSPITEKHLQSGMTLAELSAATLQYSDNTAMNLIIGYLGGPEKVTAFARSIGDATFRLDRTEPTLNTAIPGDERDTSTPLAMAESLRKLTLGDALGEQQRAQLVTWLKGNTTGGQSIRAGLPESWVVGDKTGGGDYGTTNDIAVIWPEDHAPLVLVTYFTQPQQDAKNRKEVLAAAAKIVTEGL"},"dna_sequence":{"accession":"AY077488.2","fmin":"161","fmax":"1031","strand":"+","sequence":"ATGATAAAAAGTTCGTGGCGTAAAATTGCAATGCTAGCCGCCGTTCCGCTGCTGCTGGCGAGCGGCGCACTGTGGGCCAGTACCGATGCTATCCATCAGAAGCTGACAGATCTCGAGAAGCGTTCAGGCGGCAGGTTGGGCGTGGCGCTAATCAACACGGCAGATAATTCTCAAATCTTATATCGCGGCGACGAGCGTTTTGCCATGTGCAGCACCAGTAAAGTGATGGCCGCCGCCGCGGTATTAAAACAGAGCGAAAGCAATAAAGAGGTGGTAAATAAAAGGCTGGAGATTAACGCAGCCGATTTGGTGGTCTGGAGTCCGATTACCGAAAAACATCTCCAGAGCGGAATGACGCTGGCTGAGCTAAGCGCGGCGACGCTGCAATATAGCGACAATACGGCGATGAATCTGATCATCGGCTACCTTGGCGGGCCGGAAAAAGTCACCGCCTTCGCCCGCAGTATCGGCGATGCCACCTTTCGTCTCGATCGTACGGAGCCCACGCTGAATACCGCCATCCCGGGCGATGAGCGTGATACCAGCACGCCGCTGGCGATGGCTGAAAGCCTACGCAAGCTGACGCTTGGCGATGCGCTGGGCGAACAGCAACGCGCCCAGTTAGTCACCTGGCTGAAAGGCAATACCACCGGCGGGCAAAGCATTCGCGCGGGCCTGCCTGAAAGCTGGGTGGTCGGCGATAAAACCGGCGGCGGAGATTACGGCACCACCAATGATATTGCGGTTATCTGGCCGGAAGATCACGCTCCGCTGGTATTAGTCACCTACTTTACCCAGCCGCAGCAGGATGCGAAAAACCGCAAAGAGGTGTTAGCCGCAGCGGCAAAAATCGTGACCGAAGGGCTTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3002398","ARO_id":"38798","ARO_name":"OXY-2-3","CARD_short_name":"OXY-2-3","ARO_description":"OXY-2-3 is a beta-lactamase found in Klebsiella oxytoca.","ARO_category":{"38788":{"category_aro_accession":"3002388","category_aro_cvterm_id":"38788","category_aro_name":"OXY beta-lactamase","category_aro_description":"OXY beta-lactamases are chromosomal class A beta-lactamases that are found in Klebsiella oxytoca. At constitutive low levels, OXY beta-lactamases confer resistance to aminopenicillins and carboxypenicillins. At high induced levels,  OXY beta-lactamases confer resistance to penicillins, cephalosporins and aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2047":{"model_id":"2047","model_name":"OXA-322","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1930":{"protein_sequence":{"accession":"AGW16404.1","sequence":"MYKKVLIVATSILFLSACSSNSVKQHQIHSISANKNSEEIKSLFDQAQTTGVLVIKRGQTEEIYGNDLKRASTNYIPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMSKEVKRIGFGNANIGSKVDDFWLVGPLKITPQQETQFAYQLAHKTLPFSQDVQEQVQSMVFIEEKNGSKIYAKSGWGWDVEPQVGWLTGWVVQPQGEIVAFSLNLEMKKGTPSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"KF203096.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGTATAAAAAAGTCCTTATCGTTGCAACAAGTATTCTATTTTTATCCGCCTGTTCTTCTAACTCAGTAAAACAACATCAAATACATTCTATTTCTGCCAATAAAAATTCAGAAGAAATTAAATCACTTTTTGATCAAGCACAGACCACGGGAGTTTTGGTGATTAAGCGAGGGCAAACAGAAGAAATTTATGGCAATGATCTTAAAAGAGCATCAACCAACTATATTCCCGCCTCTACCTTTAAAATGTTAAATGCTTTAATTGGACTTGAACATCATAAGGCAACTACAACTGAAGTATTTAAATGGGATGGGCAAAAACGTTTATTTCCTGATTGGGAAAAGGACATGACACTGGGTGATGCCATGAAAGCTTCTGCAATCCCAGTTTACCAAGAATTAGCCCGACGAATTGGTCTGGATCTTATGTCTAAAGAAGTAAAGCGAATTGGTTTCGGTAATGCTAACATTGGCTCAAAAGTAGATGATTTCTGGCTTGTTGGCCCTCTAAAAATTACACCTCAACAAGAAACCCAATTTGCTTATCAATTAGCCCATAAAACGCTTCCATTTAGCCAAGATGTACAAGAACAAGTTCAATCAATGGTGTTCATAGAGGAAAAAAATGGAAGTAAAATTTATGCCAAAAGTGGTTGGGGATGGGATGTTGAACCGCAAGTTGGTTGGTTAACAGGCTGGGTCGTTCAACCACAAGGAGAAATTGTGGCATTTTCACTTAATTTAGAAATGAAAAAAGGAACTCCTAGCTCTATTCGCAAAGAAATTGCTTATAAAGGCTTAGAACAACTGGGTATTTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39094","NCBI_taxonomy_name":"Acinetobacter calcoaceticus","NCBI_taxonomy_id":"471"}}}},"ARO_accession":"3001510","ARO_id":"37910","ARO_name":"OXA-322","CARD_short_name":"OXA-322","ARO_description":"OXA-322 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46495":{"category_aro_accession":"3007706","category_aro_cvterm_id":"46495","category_aro_name":"OXA-213-like beta-lactamase","category_aro_description":"OXA-213-like enzymes have been identified to be intrinsic to A. calcoaceticus and have been subsequently detected in A. pittii. Phylogenetic analysis of OXA-213-like proteins identified two distinct subgroups within the OXA family. The first group was linked to A. pittii and the second group to A. calcoaceticus. The carbapenemase activity of these OXAs may be related to the species-dependent effect.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2048":{"model_id":"2048","model_name":"OXA-57","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1137":{"protein_sequence":{"accession":"CAF74882.1","sequence":"MKFRHALSSAFVLLGCIAASAHAKTICTAIADAGTGKLLVQDGDCGRRASPASTFKIAISLMGYDAGFLRNEHDPVLPYRDSYIAWGGEAWKQPTDPTRWLKYSVVWYSQQVAHHLGAQRFAQYAKAFGYGNADVSGDPGQNNGLDRAWIGSSLQISPLEQLEFLGKMLDRKLPVSPTAVDMTERIVESTTLADGTVVHGKTGVSYPLLADGTRDWARGSGWFVGWIVRGKQTLVFARLTQDERKQPVSAGIRTREAFLRDLPRLLAAR"},"dna_sequence":{"accession":"AJ631966.1","fmin":"0","fmax":"810","strand":"+","sequence":"ATGAAATTCCGACACGCGCTGTCGAGCGCATTCGTTTTGCTGGGTTGCATCGCCGCGTCGGCGCATGCGAAGACGATCTGCACGGCGATCGCCGATGCGGGCACGGGCAAGCTGCTGGTGCAGGACGGCGATTGCGGCCGCCGCGCATCGCCCGCGTCGACGTTCAAGATCGCGATCAGCCTGATGGGCTACGACGCAGGCTTCCTGCGCAACGAGCATGACCCGGTGCTGCCGTATCGCGACAGTTACATCGCGTGGGGTGGCGAAGCATGGAAGCAGCCGACCGATCCGACGCGCTGGCTCAAGTATTCGGTCGTGTGGTATTCGCAGCAGGTGGCGCACCATCTCGGCGCGCAGCGCTTCGCGCAGTATGCGAAGGCGTTCGGCTACGGCAATGCGGACGTGTCCGGCGATCCCGGCCAGAACAACGGCCTCGATCGCGCGTGGATCGGCTCGTCGCTGCAGATCTCGCCGCTCGAACAATTGGAATTCCTCGGCAAGATGCTCGATCGCAAGCTGCCCGTGTCGCCCACAGCCGTCGACATGACGGAGCGGATCGTCGAATCGACGACGCTTGCCGACGGAACGGTGGTGCACGGCAAGACCGGCGTGTCCTATCCGCTGCTGGCCGACGGCACACGCGACTGGGCGCGTGGATCCGGCTGGTTTGTCGGCTGGATCGTGCGTGGCAAGCAGACGCTGGTGTTCGCGCGCCTCACGCAGGACGAGCGCAAGCAGCCCGTTTCAGCCGGCATACGGACGCGCGAGGCCTTCCTGCGCGACTTGCCCCGGCTTCTCGCCGCGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36925","NCBI_taxonomy_name":"Burkholderia pseudomallei 576","NCBI_taxonomy_id":"557724"}}}},"ARO_accession":"3001771","ARO_id":"38171","ARO_name":"OXA-57","CARD_short_name":"OXA-57","ARO_description":"OXA-57 is a beta-lactamase found in Burkholderia pseudomallei.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46507":{"category_aro_accession":"3007718","category_aro_cvterm_id":"46507","category_aro_name":"OXA-42-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-42.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2049":{"model_id":"2049","model_name":"QnrB72","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"469":{"protein_sequence":{"accession":"AGN92479.1","sequence":"MTLALVCEKIDRNRFTGEKVENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNVSALGIEIRHCRAQGADFRGASFMNMITMRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGTQVLGATFSGSDLSGGEFSTFDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDNYQASLLMERLGIAVIG"},"dna_sequence":{"accession":"KC741443.1","fmin":"0","fmax":"645","strand":"+","sequence":"ATGACTCTGGCATTAGTTTGCGAAAAAATTGACAGAAATCGCTTCACCGGTGAGAAAGTTGAAAATAGTACATTTTTTAACTGCGATTTTTCAGGTGCCGACCTGAGCGGCACTGAATTTATCGGCTGCCAGTTCTATGATCGCGAAAGTCAGAAAGGATGCAATTTTAGTCGCGCAATGCTGAAAGATGCCATTTTCAAAAGCTGTGATTTATCAATGGCAGATTTCCGCAACGTCAGCGCATTGGGCATTGAAATTCGCCACTGCCGCGCACAAGGCGCAGATTTCCGCGGTGCAAGCTTTATGAATATGATCACCATGCGCACCTGGTTTTGCAGCGCATATATCACTAATACCAATCTAAGCTACGCCAATTTTTCGAAAGTCGTGTTGGAAAAGTGTGAGCTATGGGAAAACCGCTGGATGGGGACTCAGGTACTGGGTGCGACGTTTAGTGGTTCAGATCTCTCCGGTGGCGAGTTTTCGACTTTCGACTGGCGAGCAGCAAACTTCACACATTGCGATCTGACCAATTCGGAGTTAGGTGACTTAGATATTCGGGGTGTTGATTTACAAGGCGTTAAGTTAGACAACTACCAGGCATCGTTGCTCATGGAGCGGCTTGGCATCGCTGTGATTGGTTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39586","NCBI_taxonomy_name":"Citrobacter sp. TR21_24","NCBI_taxonomy_id":"1344960"}}}},"ARO_accession":"3002784","ARO_id":"39218","ARO_name":"QnrB72","CARD_short_name":"QnrB72","ARO_description":"QnrB72 is a plasmid-mediated quinolone resistance protein found in Citrobacter sp. TR21_24.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2050":{"model_id":"2050","model_name":"OXA-331","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1459":{"protein_sequence":{"accession":"AGW16413.1","sequence":"MYKKALIVATSILFLSACSSNTVKQNQIHSISANKNSEEIKSLFDQAQTTGVLVIKRGQTEEIYGNDLKRASTAYVPASTFKMLNALIGLEHHKATITEVFKWNGQKRLFPDWEKDMTLSDAMKASAIPVYQELARRIGLDLMSKEVKRIGFGNANIGSKVDDFWLVGPLKITPQQETQFAYQLAHKTLPFSKNVQEQVQSMVFIEEKNGSKIYAKSGWGWDVEPQVGWLTGWVVQPQGEIVAFSLNLEMKKGTPSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"KF203105.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGTATAAAAAAGCCCTTATCGTTGCAACAAGTATCCTATTTTTATCCGCCTGTTCTTCCAATACGGTAAAACAAAATCAAATACATTCTATTTCTGCCAATAAAAATTCAGAAGAAATTAAATCACTATTTGATCAAGCACAGACCACGGGTGTTTTGGTGATTAAGCGAGGACAAACAGAAGAAATTTATGGCAATGATCTTAAAAGAGCATCAACCGCCTATGTTCCCGCCTCTACCTTTAAAATGTTAAATGCTTTAATTGGACTTGAACATCATAAGGCAACTATAACTGAAGTGTTTAAATGGAATGGGCAAAAACGTTTATTTCCTGATTGGGAAAAGGATATGACACTGAGCGATGCCATGAAAGCTTCTGCAATTCCAGTTTACCAAGAATTAGCCCGACGGATTGGTCTGGATCTTATGTCCAAAGAGGTGAAACGAATTGGTTTCGGTAATGCTAACATTGGCTCAAAAGTAGATGATTTTTGGCTTGTTGGCCCTCTAAAAATTACACCTCAACAAGAAACCCAATTTGCTTATCAATTAGCCCATAAAACTCTTCCATTTAGCAAAAATGTACAAGAACAAGTTCAATCAATGGTGTTCATAGAGGAAAAAAATGGAAGTAAAATTTATGCCAAAAGTGGTTGGGGATGGGATGTTGAACCGCAAGTTGGTTGGTTAACAGGCTGGGTCGTTCAACCACAAGGAGAAATTGTGGCATTTTCACTTAATTTAGAAATGAAAAAAGGAACTCCTAGCTCTATTCGCAAAGAAATTGCTTATAAAGGCTTAGAACAACTGGGTATTTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39094","NCBI_taxonomy_name":"Acinetobacter calcoaceticus","NCBI_taxonomy_id":"471"}}}},"ARO_accession":"3001519","ARO_id":"37919","ARO_name":"OXA-331","CARD_short_name":"OXA-331","ARO_description":"OXA-331 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46495":{"category_aro_accession":"3007706","category_aro_cvterm_id":"46495","category_aro_name":"OXA-213-like beta-lactamase","category_aro_description":"OXA-213-like enzymes have been identified to be intrinsic to A. calcoaceticus and have been subsequently detected in A. pittii. Phylogenetic analysis of OXA-213-like proteins identified two distinct subgroups within the OXA family. The first group was linked to A. pittii and the second group to A. calcoaceticus. The carbapenemase activity of these OXAs may be related to the species-dependent effect.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2051":{"model_id":"2051","model_name":"dfrA15","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"2102":{"protein_sequence":{"accession":"AHB39758.1","sequence":"MKLSLMAAISKNGVIGNGPDIPWSAKGEQLLFKAITYNQWLLVGRKTFESMGALPNRKYAVVTRSSFTSSDENVLVFPSIDEALNHLKTITDHVIVSGGGEIYKSLIDKVDTLHISTIDIEPEGDVYFPEIPSSFRPVFSQDFVSNINYSYQIWQKG"},"dna_sequence":{"accession":"KF534911.1","fmin":"39","fmax":"513","strand":"+","sequence":"GTGAAACTATCACTAATGGCAGCAATTTCGAAGAATGGAGTTATCGGAAATGGCCCAGATATTCCATGGAGTGCCAAAGGGGAACAATTACTCTTCAAAGCGATTACCTATAATCAGTGGCTTTTGGTAGGCCGAAAGACTTTCGAGTCAATGGGGGCTTTACCCAACCGAAAATATGCCGTTGTAACTCGTTCAAGCTTCACTTCCAGTGATGAGAATGTATTGGTATTTCCATCTATCGATGAAGCGCTAAATCATCTGAAGACGATAACGGATCATGTGATTGTGTCTGGTGGTGGTGAAATATACAAAAGCCTGATCGATAAAGTTGATACTTTACATATTTCAACAATCGACATTGAGCCAGAAGGTGATGTCTATTTTCCAGAAATCCCCAGTAGTTTTAGGCCAGTTTTTAGCCAAGACTTCGTGTCTAACATAAATTATAGTTACCAAATCTGGCAAAAGGGTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3003013","ARO_id":"39447","ARO_name":"dfrA15","CARD_short_name":"dfrA15","ARO_description":"dfrA15 is an integron-encoded dihydrofolate reductase found in Vibrio cholerae.","ARO_category":{"37617":{"category_aro_accession":"3001218","category_aro_cvterm_id":"37617","category_aro_name":"trimethoprim resistant dihydrofolate reductase dfr","category_aro_description":"Alternative dihydropteroate synthase dfr present on plasmids produces alternate proteins that are less sensitive to trimethoprim from inhibiting its role in folate synthesis, thus conferring trimethoprim resistance.","category_aro_class_name":"AMR Gene Family"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2052":{"model_id":"2052","model_name":"APH(3'')-Ic","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"276":{"protein_sequence":{"accession":"ABC68330.1","sequence":"MTEWLPVTRGESGAGVFRNSDGSSYAKVVDAAAVADLAAERDRVSWAHRHGVPGPAVIDWRVTEDGGACLITSTVRGVAADRLSESALRAAWPAIVEAVRTLHALPADGCPYRRDLDDMLARARAVVGAGAVNPEFLSDEDREVPAEALLDRVEREADLRRREEAADWVVCHGDLCLPNILVDPDRHTVEGFIDLGRLGLADRHADLALLLANTADTVPGFAEEATAGLAAGYPAQVDPERLRFYLALDPLTWG"},"dna_sequence":{"accession":"DQ336355.1","fmin":"602","fmax":"1367","strand":"+","sequence":"GTGACCGAGTGGCTGCCCGTCACACGCGGTGAATCCGGTGCCGGGGTCTTCAGGAACTCCGACGGTTCGAGCTACGCGAAGGTGGTCGACGCCGCGGCGGTGGCAGACCTGGCCGCGGAGCGTGACCGGGTGTCCTGGGCCCACAGGCACGGTGTCCCCGGGCCCGCGGTCATCGACTGGCGTGTCACCGAAGACGGCGGCGCGTGCTTGATCACGAGCACTGTGCGCGGTGTCGCTGCCGATCGGCTTTCCGAATCGGCGCTGCGGGCGGCCTGGCCGGCGATTGTGGAGGCGGTCCGGACACTGCACGCCCTTCCGGCCGACGGTTGTCCCTACCGGCGCGATCTCGACGACATGCTGGCCCGGGCCCGCGCGGTCGTCGGCGCCGGTGCCGTGAACCCGGAGTTCCTGTCCGACGAGGACCGCGAGGTACCGGCGGAGGCGCTGCTGGACCGAGTCGAACGGGAAGCCGATCTACGTCGTCGGGAGGAGGCCGCCGACTGGGTGGTGTGCCACGGCGATCTGTGCCTGCCGAACATTTTGGTCGACCCCGACCGTCACACCGTCGAGGGATTCATCGATCTGGGCAGGCTGGGGCTGGCCGACCGGCACGCCGACCTGGCACTGCTGCTGGCCAATACGGCTGATACCGTTCCGGGCTTCGCCGAGGAGGCCACGGCGGGGTTGGCCGCGGGGTATCCGGCGCAGGTGGATCCGGAGCGGCTGCGGTTCTATCTCGCGCTCGATCCGCTGACCTGGGGATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36886","NCBI_taxonomy_name":"Mycolicibacterium fortuitum","NCBI_taxonomy_id":"1766"}}}},"ARO_accession":"3002640","ARO_id":"39040","ARO_name":"APH(3'')-Ic","CARD_short_name":"APH(3'')-Ic","ARO_description":"APH(3'')-Ic is a chromosomal-encoded aminoglycoside phosphotransferase in Mycolicibacterium fortuitum.","ARO_category":{"36266":{"category_aro_accession":"3000127","category_aro_cvterm_id":"36266","category_aro_name":"APH(3'')","category_aro_description":"A category of aminoglycoside O-phosphotransferase enzymes with modification regiospecificity based at the 3''-hydroxyl group of the respective antibiotic. These enzymes are characterized by enzymatic antibiotic inactivation, specifically of streptomycin, by the ATP-dependent phosphorylation of the 3''-hydroxyl group of the compound.","category_aro_class_name":"AMR Gene Family"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2053":{"model_id":"2053","model_name":"dfrA7","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"525":{"protein_sequence":{"accession":"ACS44716.1","sequence":"MKISLISATSENGVIGNGPDIPWSAKGEQLLFKALTYNQWLLVGRKTFDSMGVLPNRKYAVVSRKGISSSNENVLVFPSIEIALQELSKITDHLYVSGGGQIYNSLIEKADIIHLSTVHVEVEGDINFPKIPENFNLVFEQFFLSNINYTYQIWKKG"},"dna_sequence":{"accession":"FJ854362.1","fmin":"2338","fmax":"2812","strand":"+","sequence":"TTGAAAATTTCATTGATTTCTGCAACGTCAGAAAATGGCGTAATCGGTAATGGCCCTGATATCCCATGGTCAGCAAAAGGTGAGCAGTTACTCTTTAAAGCGCTCACATATAATCAGTGGCTCCTTGTTGGAAGGAAAACATTTGACTCTATGGGTGTTCTTCCAAATCGAAAATATGCAGTAGTGTCGAGGAAAGGAATTTCAAGCTCAAATGAAAATGTATTAGTCTTTCCTTCAATAGAAATCGCTTTGCAAGAACTATCGAAAATTACAGATCATTTATATGTCTCTGGTGGCGGTCAAATCTACAATAGTCTTATTGAAAAAGCAGATATAATTCATTTGTCTACTGTTCACGTTGAGGTTGAAGGTGATATCAATTTTCCTAAAATTCCAGAGAATTTCAATTTGGTTTTTGAGCAGTTTTTTTTGTCTAATATAAATTACACATATCAGATTTGGAAAAAAGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3002862","ARO_id":"39296","ARO_name":"dfrA7","CARD_short_name":"dfrA7","ARO_description":"dfrA7 is an integron-encoded dihydrofolate reductase found in Escherichia coli.","ARO_category":{"37617":{"category_aro_accession":"3001218","category_aro_cvterm_id":"37617","category_aro_name":"trimethoprim resistant dihydrofolate reductase dfr","category_aro_description":"Alternative dihydropteroate synthase dfr present on plasmids produces alternate proteins that are less sensitive to trimethoprim from inhibiting its role in folate synthesis, thus conferring trimethoprim resistance.","category_aro_class_name":"AMR Gene Family"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2054":{"model_id":"2054","model_name":"msrC","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"950"}},"model_sequences":{"sequence":{"363":{"protein_sequence":{"accession":"AAK01167.1","sequence":"MENLAVNITNLQVRFGNQLELSIDSLRVYQQDRIGIIGENGVGKTTLLKLIVGELIPNQGKIQTEITFNYLPQLTYLAEAKDLNLELASHFQLKLEETSERKWSGGEERKIELIRLLSSYEQGMLLDEPTTHLDRKSMDRLIEELRYYYGTLIFVSHDRYFLDELATKVWEVKDGEIREFPENYSAYLTQRELEKKTQLREAESIMKEKKRLEKSIQEKKKQAEKLEKVSSKKKKQQIRPDRLSSSKQKDSVQKAIQKNTKTLERRLQKIGETTKPQQMKQIRFPVPKSLELHNRYPIMGQNIQLERSGRTLLINSDFQFSLGKKIAIVGENGSGKTTLLEHIRKQGEGILLSPKVSFQVYQQKDYQMTSEESVIRFVMRQTEFSESLVRSLLNHLGFAQETLTKPLCTLSGGEATRLTIALLFTKPSNVLLLDEPTNFIDVATIEALEQLMQVYPGTILFTSHDSYFVERTADEVYEIKGQKIKKVLTRNF"},"dna_sequence":{"accession":"AF313494.1","fmin":"0","fmax":"1479","strand":"+","sequence":"ATGGAAAATTTAGCAGTAAATATAACAAACCTGCAAGTTCGTTTTGGTAACCAGTTAGAATTATCTATTGATTCTCTTCGTGTCTATCAGCAAGATCGGATAGGAATCATAGGGGAAAATGGAGTCGGTAAAACAACGTTGCTGAAACTGATAGTCGGTGAACTTATCCCCAATCAAGGGAAAATCCAAACAGAGATCACTTTCAACTATCTGCCTCAATTAACCTATCTTGCTGAGGCAAAGGACCTAAATTTGGAATTAGCCAGTCATTTCCAGTTGAAACTGGAAGAAACTTCGGAACGGAAATGGAGTGGAGGGGAAGAACGAAAGATCGAGTTGATACGTCTTCTTTCTTCTTATGAACAAGGGATGCTTCTAGACGAGCCGACAACCCATCTAGATAGAAAAAGTATGGATCGACTAATTGAAGAGCTTCGTTATTATTATGGCACGCTGATTTTTGTTAGTCATGACCGCTATTTTCTAGATGAGTTGGCAACGAAAGTCTGGGAAGTAAAAGACGGAGAAATCCGAGAGTTTCCGGAGAATTATAGTGCCTATCTCACTCAAAGGGAATTGGAGAAAAAGACTCAGCTACGAGAAGCAGAGTCGATCATGAAAGAGAAAAAACGATTGGAAAAATCGATCCAAGAAAAGAAAAAACAAGCGGAAAAGTTAGAAAAAGTGTCCAGTAAAAAGAAAAAGCAACAAATCAGACCGGATCGGTTGTCTTCCTCTAAACAAAAAGACAGTGTACAAAAAGCCATCCAAAAGAATACGAAAACATTAGAGAGAAGACTCCAAAAAATAGGAGAAACAACCAAACCGCAACAGATGAAACAAATCCGTTTTCCAGTACCAAAATCTCTTGAACTCCACAATCGTTATCCAATCATGGGACAAAATATCCAATTGGAAAGAAGCGGAAGAACATTACTGATAAATAGCGATTTTCAATTTTCTTTAGGTAAAAAAATCGCGATTGTCGGCGAAAATGGATCAGGTAAGACAACTTTATTGGAACATATCCGCAAACAAGGAGAAGGAATCCTTCTCTCTCCGAAAGTAAGCTTTCAAGTATATCAGCAAAAGGATTATCAAATGACATCTGAAGAATCCGTCATTCGTTTTGTCATGAGACAAACAGAGTTTTCGGAATCACTTGTCCGCAGTTTGTTGAATCATTTAGGGTTTGCTCAGGAAACTCTGACGAAACCGTTGTGTACGTTAAGTGGGGGAGAAGCGACTCGTTTGACGATTGCTTTGCTTTTTACTAAGCCAAGTAATGTGTTGCTGTTAGATGAACCGACTAATTTCATTGATGTGGCAACGATCGAAGCTTTAGAGCAGCTGATGCAAGTATATCCGGGAACGATTTTGTTTACTTCACATGATTCCTACTTTGTCGAGCGTACGGCTGATGAAGTTTATGAAATAAAAGGGCAGAAAATAAAAAAAGTACTTACGAGAAATTTTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36779","NCBI_taxonomy_name":"Enterococcus faecium","NCBI_taxonomy_id":"1352"}}}},"ARO_accession":"3002819","ARO_id":"39253","ARO_name":"msrC","CARD_short_name":"msrC","ARO_description":"msrC is a chromosomal-encoded ABC-F subfamily protein expressed in Enterococcus faecium that confers resistance to erythromycin and other macrolide and streptogramin B antibiotics.","ARO_category":{"41695":{"category_aro_accession":"3004471","category_aro_cvterm_id":"41695","category_aro_name":"msr-type ABC-F protein","category_aro_description":"msr-type ABC-F subfamily ribosomal protection proteins expression in Staphylococci species and confer resistance to erythromycin and streptogramin B antibiotics through antibiotic target protection mechanisms.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"36723":{"category_aro_accession":"3000584","category_aro_cvterm_id":"36723","category_aro_name":"quinupristin","category_aro_description":"Quinupristin is a type B streptogramin and a semisynthetic derivative of pristinamycin 1A. It is a component of the drug Synercid and interacts with the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35967":{"category_aro_accession":"0000050","category_aro_cvterm_id":"35967","category_aro_name":"streptogramin B antibiotic","category_aro_description":"Streptogramin B antibiotics are are cyclic hepta- or hexa-depsipeptides.  Type B streptogramins block the peptide exit tunnel of the 50S bacterial ribosome. The general composition of group B streptogramins is 3-hydroxypicolinic acid-L-Thr-D-aminobutyric acid (or D-Ala)-L-Pro-L-Phe (or 4-N-,N-(dimethylamino)-L-Phe)-X-L-phenylglycine. Used alone, streptogramin B antibiotics are bacteriostatic, but is bactericidal when used with streptogramin A antibiotics.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2055":{"model_id":"2055","model_name":"LRA-3","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1917":{"protein_sequence":{"accession":"ACH58987.1","sequence":"MKSKLLLAAALAALAGTSMAAQAAELQYKPPPITNKEWETPFPGFKIVGNMYYVGTYDLGCYLIDTGAGLILINSGADGSYPLIKANIEKLGFKTSDIKIITSTHGHGDHVGDLAAFQKDAPAAKTYMNFRDAPTIESGGNIDYRRPEGRGFYPYHPVKVDVRTKPGDHIKLGNTDLTLHQAYGHTPGATSFTFTVQDGGRNYNVLIVNMNGINAGVKLLGSPGYPTIVEDFASTLKEQATYTPDLWVSSHAGQFNLHQVYKPGDPYNPARFGDLAAYKLKIANATKAYEKQLAEERAAKAK"},"dna_sequence":{"accession":"EU408348.1","fmin":"1243","fmax":"2152","strand":"+","sequence":"ATGAAATCGAAACTGCTTCTTGCCGCGGCCTTGGCCGCACTCGCCGGCACGTCGATGGCCGCCCAGGCGGCCGAACTGCAATATAAGCCGCCGCCGATCACCAACAAGGAATGGGAGACCCCGTTCCCCGGCTTCAAGATCGTCGGCAACATGTATTATGTCGGCACCTACGATCTGGGCTGCTATCTGATCGACACGGGGGCCGGGCTTATTCTGATCAATTCCGGCGCCGACGGTTCGTATCCGCTGATCAAGGCCAATATCGAGAAGCTCGGTTTCAAGACCAGCGACATCAAGATCATCACCTCGACGCACGGCCACGGCGATCATGTCGGCGACCTCGCCGCGTTCCAGAAAGATGCGCCCGCCGCCAAGACCTATATGAATTTTCGCGATGCGCCGACCATCGAATCGGGCGGCAACATCGATTACCGGCGCCCTGAGGGGCGCGGGTTTTATCCCTACCATCCGGTGAAGGTTGATGTGCGCACCAAGCCGGGCGACCATATCAAGCTCGGCAACACCGATCTGACGCTGCACCAGGCTTACGGCCATACGCCGGGGGCGACGAGCTTCACCTTCACGGTCCAGGATGGTGGGCGCAATTACAACGTGCTGATCGTCAACATGAACGGCATCAATGCGGGCGTGAAATTGCTCGGCTCGCCGGGGTATCCGACCATCGTCGAGGATTTTGCCAGCACGCTGAAGGAACAGGCGACCTATACGCCCGACCTCTGGGTCTCTTCGCATGCGGGCCAGTTCAACCTGCATCAGGTCTACAAGCCGGGCGATCCGTACAACCCGGCGCGCTTCGGCGATTTGGCGGCCTACAAATTGAAGATCGCCAACGCGACGAAGGCTTACGAAAAACAATTGGCTGAAGAGCGCGCCGCGAAGGCGAAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39081","NCBI_taxonomy_name":"uncultured bacterium BLR3","NCBI_taxonomy_id":"506521"}}}},"ARO_accession":"3002510","ARO_id":"38910","ARO_name":"LRA-3","CARD_short_name":"LRA-3","ARO_description":"LRA-3 is a beta-lactamase isolated from soil samples in Alaska.","ARO_category":{"41390":{"category_aro_accession":"3004226","category_aro_cvterm_id":"41390","category_aro_name":"subclass B3 LRA beta-lactamase","category_aro_description":"Beta-lactamases that are part of the LRA gene family and are classified as B3 (metallo-) beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2056":{"model_id":"2056","model_name":"mdtO","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1300"}},"model_sequences":{"sequence":{"4664":{"protein_sequence":{"accession":"BAE78083.1","sequence":"MSALNSLPLPVVRLLAFFHEELSERRPGRVPQTVQLWVGCLLVILISMTFEIPFVALSLAVLFYGIQSNAFYTKFVAILFVVATVLEIGSLFLIYKWSYGEPLIRLIIAGPILMGCMFLMRTHRLGLVFFAVAIVAIYGQTFPAMLDYPEVVVRLTLWCIVVGLYPTLLMTLIGVLWFPSRAISQMHQALNDRLDDAISHLTDSLAPLPETRIEREALALQKLNVFCLADDANWRTQNAWWQSCVATVTYIYSTLNRYDPTSFADSQAIIEFRQKLASEINKLQHAVAEGQCWQSDWRISESEAMAARECNLENICQTLLQLGQMDPNTPPTPAAKPPSMAADAFTNPDYMRYAVKTLLACLICYTFYSGVDWEGIHTCMLTCVIVANPNVGSSYQKMVLRFGGAFCGAILALLFTLLVMPWLDNIVELLFVLAPIFLLGAWIATSSERSSYIGTQMVVTFALATLENVFGPVYDLVEIRDRALGIIIGTVVSAVIYTFVWPESEARTLPQKLAGTLGMLSKVMRIPRQQEVTALRTYLQIRIGLHAAFNACEEMCQRVALERQLDSEERALLIERSQTVIRQGRDLLHAWDATWNSAQALDNALQPDRAGQFADALEKYAAGLATALSRSPQITLEETPASQAILPTLLKQEQHVCQLFARLPDWTAPALTPATEQAQGATQ"},"dna_sequence":{"accession":"AP009048.1","fmin":"4304505","fmax":"4306557","strand":"-","sequence":"ATGAGCGCGCTCAACTCCCTGCCATTACCGGTGGTCAGGCTGCTGGCGTTCTTTCATGAAGAGTTAAGCGAGCGGCGACCAGGTCGCGTGCCGCAGACCGTGCAACTCTGGGTAGGCTGCCTGCTGGTGATTCTGATCTCGATGACCTTTGAGATCCCTTTTGTGGCGTTATCGCTGGCAGTGCTGTTTTACGGTATTCAGTCGAACGCGTTTTACACCAAATTTGTCGCGATCTTGTTTGTGGTTGCCACGGTGCTGGAGATCGGCAGCCTGTTTTTGATCTACAAATGGTCATACGGCGAACCGTTGATCCGATTGATCATCGCCGGACCGATCCTGATGGGCTGCATGTTTTTGATGCGCACCCATCGCTTGGGGCTGGTCTTTTTCGCCGTCGCCATTGTCGCTATTTACGGGCAAACCTTCCCCGCCATGCTCGACTATCCGGAAGTGGTCGTGCGCTTAACGCTGTGGTGTATCGTTGTTGGCCTCTATCCAACCTTGCTGATGACGTTAATCGGCGTGCTGTGGTTTCCCAGTCGTGCCATTTCGCAAATGCATCAGGCGCTTAATGATCGGCTTGATGATGCCATTAGTCACCTGACAGACAGCCTCGCACCGCTACCCGAAACGCGGATTGAAAGAGAGGCGCTGGCGCTACAAAAACTCAATGTCTTTTGCCTCGCGGACGATGCCAACTGGCGAACTCAAAACGCATGGTGGCAAAGCTGCGTGGCAACGGTAACCTACATTTACTCGACGCTGAATCGCTACGATCCCACCTCTTTTGCTGATTCTCAGGCAATTATTGAATTCCGACAAAAATTAGCTTCAGAAATCAACAAGCTGCAGCATGCCGTTGCTGAAGGTCAGTGCTGGCAAAGCGACTGGCGGATCAGTGAAAGTGAAGCGATGGCGGCACGGGAATGTAACCTGGAGAATATCTGCCAGACGTTGTTACAACTGGGTCAGATGGACCCGAATACGCCGCCAACGCCCGCAGCCAAACCGCCATCAATGGCCGCCGATGCTTTTACCAATCCAGACTATATGCGCTACGCGGTAAAAACGCTGCTCGCCTGTTTGATCTGTTACACCTTTTACAGCGGCGTGGACTGGGAAGGCATTCACACCTGTATGCTGACATGCGTGATCGTCGCTAACCCAAATGTCGGTTCGTCGTACCAGAAGATGGTGCTGCGTTTTGGCGGGGCCTTTTGCGGCGCGATTCTGGCGCTGTTATTCACGCTACTGGTCATGCCCTGGCTGGACAATATTGTCGAATTGCTGTTTGTGCTGGCACCGATTTTCCTGTTGGGCGCATGGATTGCCACCAGCTCTGAACGCTCTTCTTATATCGGCACACAGATGGTGGTCACCTTCGCGCTCGCCACGCTCGAAAACGTTTTTGGCCCAGTGTACGACCTGGTGGAAATTCGCGATCGCGCCCTGGGTATCATCATTGGTACCGTGGTGTCCGCGGTGATTTACACCTTTGTCTGGCCTGAAAGTGAAGCGCGCACACTGCCGCAAAAACTGGCTGGCACGCTGGGTATGTTAAGTAAAGTAATGCGGATCCCACGCCAGCAGGAAGTCACGGCTCTGCGCACTTATCTGCAAATTCGTATCGGTCTGCATGCGGCGTTTAATGCCTGTGAAGAGATGTGCCAACGCGTGGCGCTGGAGCGTCAACTGGACAGCGAAGAACGCGCATTACTGATTGAACGTTCGCAAACGGTTATTCGTCAGGGCCGCGATCTTCTTCACGCCTGGGATGCCACCTGGAACTCGGCGCAGGCGCTGGATAACGCACTACAGCCGGACAGAGCAGGTCAGTTTGCCGACGCCCTGGAGAAATACGCTGCCGGTCTGGCAACCGCACTCAGCCGTTCTCCTCAAATAACGCTTGAAGAGACACCCGCCTCTCAGGCCATCCTGCCCACCTTATTAAAACAGGAGCAACACGTCTGCCAGCTTTTCGCCCGCTTGCCAGACTGGACAGCCCCGGCATTAACGCCCGCCACGGAACAGGCACAAGGAGCCACGCAATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36839","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. W3110","NCBI_taxonomy_id":"316407"}}}},"ARO_accession":"3003549","ARO_id":"40151","ARO_name":"mdtO","CARD_short_name":"mdtO","ARO_description":"Multidrug resistance efflux pump. Could be involved in resistance to puromycin, acriflavine and tetraphenylarsonium chloride.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35963":{"category_aro_accession":"0000045","category_aro_cvterm_id":"35963","category_aro_name":"acriflavine","category_aro_description":"Acriflavine is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish.","category_aro_class_name":"Antibiotic"},"35965":{"category_aro_accession":"0000047","category_aro_cvterm_id":"35965","category_aro_name":"puromycin","category_aro_description":"Puromycin is an aminonucleoside antibiotic, derived from Streptomyces alboniger, that causes premature chain termination during ribosomal protein translation.","category_aro_class_name":"Antibiotic"},"36174":{"category_aro_accession":"3000034","category_aro_cvterm_id":"36174","category_aro_name":"nucleoside antibiotic","category_aro_description":"Nucleoside antibiotics are made of modified nucleosides and nucleotides with wide-ranging activities and means of antibacterial effects. This drug class includes aminonucleoside antibiotics, which contain an amino group.","category_aro_class_name":"Drug Class"},"43746":{"category_aro_accession":"3005386","category_aro_cvterm_id":"43746","category_aro_name":"disinfecting agents and antiseptics","category_aro_description":"Disinfectants that can also interact with antimicrobial resistance mechanisms, e.g. molecule efflux, and thus are the targets of disinfectant resistance.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2057":{"model_id":"2057","model_name":"SHV-179","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1559":{"protein_sequence":{"accession":"AHA80962.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMNTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"KF705208.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAACACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGCATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001362","ARO_id":"37762","ARO_name":"SHV-179","CARD_short_name":"SHV-179","ARO_description":"SHV-179 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2058":{"model_id":"2058","model_name":"pp-flo","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"285":{"protein_sequence":{"accession":"BAA07072.1","sequence":"MTTLHPAWAYTLPAALLLMAPFDILASLAMDIYLPVVPAMPGILNTTPAMIQLTLSLYMVMLGVGQVIFGPLSDRIGRRPILLAGATAFVIASLGAAWSSTAPAFVAFRLLQAVGASAMLVATFATVRDVYANRPEGVVIYGLFSSVLAFVPALGPIAGALIGEFLGWQAIFITLAILAMLALLNAGFRWHETRPLDQVKTRRSVLPIFASPAFWVYTVGFSAGMGTFFVFFSTAPRVLIGQAEYSEIGFSFAFATVALVMIVTTRFAKSFVARWGIAGCGRVGWRCLFAAVLLGIGELYGSLNSSPSSYRCGLSRSVLSSRCPLPRTALLAEFDDIAGSAVAFYFCVQSLIVSIVGTLAVALLNGDTAWPVIC"},"dna_sequence":{"accession":"D37826.1","fmin":"1070","fmax":"2195","strand":"+","sequence":"ATGACCACCCTACACCCCGCGTGGGCCTATACGCTGCCCGCAGCACTGCTGCTGATGGCTCCTTTCGACATCCTCGCTTCACTGGCGATGGATATTTATCTCCCTGTCGTTCCAGCGATGCCCGGCATCCTGAACACGACGCCCGCTATGATCCAACTCACGTTGAGCCTCTATATGGTGATGCTCGGCGTGGGCCAGGTGATTTTTGGTCCGCTCTCAGACAGAATCGGGCGACGGCCAATTCTACTTGCGGGCGCAACGGCTTTCGTCATTGCGTCTCTGGGAGCAGCTTGGTCTTCAACTGCACCGGCCTTTGTCGCTTTCCGTCTACTTCAAGCAGTGGGCGCGTCGGCCATGCTGGTGGCGACGTTCGCGACGGTTCGCGACGTTTATGCCAACCGTCCTGAGGGTGTCGTCATCTACGGCCTTTTCAGTTCGGTGCTGGCGTTCGTGCCTGCGCTCGGCCCTATCGCCGGAGCATTGATCGGCGAGTTCTTGGGATGGCAGGCGATATTCATTACTTTGGCTATACTGGCGATGCTCGCACTCCTAAATGCGGGTTTCAGGTGGCACGAAACCCGCCCTCTGGATCAAGTCAAGACGCGCCGATCTGTCTTGCCGATCTTCGCGAGTCCGGCTTTTTGGGTTTACACTGTCGGCTTTAGCGCCGGTATGGGCACCTTCTTCGTCTTCTTCTCGACGGCTCCCCGTGTGCTCATAGGCCAAGCGGAATATTCCGAGATCGGATTCAGCTTTGCCTTCGCCACTGTCGCGCTTGTAATGATCGTGACAACCCGTTTCGCGAAGTCCTTTGTCGCCAGATGGGGCATCGCAGGATGTGGGCGCGTGGGATGGCGTTGCTTGTTTGCGGCGGTCCTGTTGGGGATCGGCGAACTTTACGGCTCGCTCAATTCCTCACCTTCATCCTACCGATGTGGGTTGTCGCGGTCGGTATTGTCTTCACGGTGTCCGTTACCGCGAACGGCGCTTTTGGCAGAGTTCGACGACATCGCGGGATCAGCGGTCGCTTTCTACTTCTGCGTTCAAAGCCTGATAGTCAGCATTGTCGGGACATTGGCGGTGGCACTTTTAAACGGTGACACAGCGTGGCCCGTGATCTGTTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39539","NCBI_taxonomy_name":"Photobacterium damselae subsp. piscicida","NCBI_taxonomy_id":"38294"}}}},"ARO_accession":"3002812","ARO_id":"39246","ARO_name":"pp-flo","CARD_short_name":"pp-flo","ARO_description":"pp-flo is a plasmid chloramphenicol exporter that is found in Photobacterium damselae subsp. piscicida.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36600":{"category_aro_accession":"3000461","category_aro_cvterm_id":"36600","category_aro_name":"florfenicol","category_aro_description":"Florfenicol is a fluorine derivative of chloramphenicol, where the nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3) and the hydroxyl group (-OH), by a fluorine group (-F). The action mechanism is the same as chloramphenicol's, where the antibiotic binds to the 23S RNA of the 50S subunit of bacterial ribosomes to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2059":{"model_id":"2059","model_name":"OKP-A-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"8147":{"protein_sequence":{"accession":"CAG25812.2","sequence":"MRYVRLCLISLIAALPLAVFASPPPLEQITRSESQLAGRVGYVEMDLVSGRTLAAWRANERFPLMSTFKVLLCGAVLARVDAGDEQLDRRIRYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAGNLLLKSVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDVRDTTTPASMAATLRKLLTSHTLSARSQQQLLQWMVDDQVAGPLIRAVLPAGWFIAEKTGAGERGSRGIVALLGPNGKAERIVVIYLRDTPASMAERNQQIARIGAALIEHWQR"},"dna_sequence":{"accession":"AJ635401.2","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGCCTTATCTCCCTGATTGCCGCCCTGCCACTGGCGGTATTCGCCAGCCCTCCGCCGCTTGAGCAAATTACACGCAGCGAAAGTCAGCTGGCGGGCCGCGTGGGCTATGTTGAAATGGATCTGGTCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCAATGAGCGCTTTCCGCTGATGAGCACCTTTAAAGTGCTGCTCTGCGGCGCGGTGCTGGCCCGGGTGGATGCCGGAGACGAACAGCTGGATCGGCGGATCCGCTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGCCGACGGGATGACCGTTGGCGAACTCTGCGCCGCCGCCATCACCATGAGCGACAACAGCGCCGGCAATCTGCTGTTGAAGAGCGTTGGCGGCCCCGCTGGATTGACCGCTTTTCTGCGCCAGATCGGTGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAGCTCAATGAAGCGCTTCCCGGCGACGTGCGCGACACCACCACCCCAGCCAGCATGGCCGCCACCCTGCGCAAGCTGCTAACCAGCCACACTCTGAGCGCCCGTTCGCAGCAGCAGCTGCTGCAGTGGATGGTGGACGACCAGGTAGCCGGTCCGCTGATCCGCGCCGTGCTGCCGGCGGGCTGGTTTATCGCCGAAAAAACCGGGGCCGGCGAGCGGGGCTCACGCGGCATTGTCGCCCTGCTCGGCCCGAACGGCAAAGCGGAGCGCATCGTGGTGATCTATCTGCGGGATACGCCGGCGTCCATGGCCGAGCGTAACCAGCAGATCGCCAGAATAGGCGCGGCGCTGATCGAGCACTGGCAGCGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002418","ARO_id":"38818","ARO_name":"OKP-A-1","CARD_short_name":"OKP-A-1","ARO_description":"OKP-A-1 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"38817":{"category_aro_accession":"3002417","category_aro_cvterm_id":"38817","category_aro_name":"OKP beta-lactamase","category_aro_description":"OKP beta-lactamases are chromosomal class A beta-lactamase that confer resistance to penicillins and early cephalosporins in Klebsiella pneumoniae. OKP beta-lactamases can be subdivided into two groups: OKP-A and OKP-B which diverge by about 4.2%.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2060":{"model_id":"2060","model_name":"FosC2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"250"}},"model_sequences":{"sequence":{"580":{"protein_sequence":{"accession":"BAJ10053.1","sequence":"MLRGLNHITIAVSDLERSVEFYTRLLGMKAHVRWDSGAYLSLEATWICLSCDEVHPSQDYCHIAFDVSEENFEPVTKKLREAHVVEWKQNRSEGLSLYLLDPDGHKLEIHSGSLQSRLESLKSKPYQGLVWL"},"dna_sequence":{"accession":"AB522969.1","fmin":"0","fmax":"399","strand":"+","sequence":"GTGTTACGAGGATTGAATCATATTACTATTGCAGTAAGTGACCTTGAACGTTCCGTGGAGTTCTATACGCGTCTATTAGGAATGAAGGCACATGTCCGCTGGGATAGTGGGGCATATCTGAGCTTGGAGGCTACTTGGATTTGCTTGTCTTGTGACGAAGTGCATCCGAGCCAAGATTACTGTCACATCGCGTTTGATGTTTCCGAAGAGAATTTCGAACCAGTTACTAAAAAGCTTCGCGAAGCACATGTCGTTGAATGGAAACAAAATAGAAGCGAAGGACTTTCTTTATACTTGCTCGATCCTGACGGCCATAAATTGGAAATCCATAGCGGTAGCCTACAAAGTCGTTTGGAATCGTTGAAGTCTAAACCCTATCAAGGGTTAGTATGGCTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002874","ARO_id":"39308","ARO_name":"FosC2","CARD_short_name":"FosC2","ARO_description":"FosC2 is an enzyme that phosphorylates fosfomycin to confer resistance in Escherichia coli.","ARO_category":{"41409":{"category_aro_accession":"3004245","category_aro_cvterm_id":"41409","category_aro_name":"fosC phosphotransferase family","category_aro_description":"The fosC family of phosphotransferases phosphorylate fosfomycin to confer resistance and have been found in various bacterial isolates.","category_aro_class_name":"AMR Gene Family"},"35944":{"category_aro_accession":"0000025","category_aro_cvterm_id":"35944","category_aro_name":"fosfomycin","category_aro_description":"Fosfomycin (also known as phosphomycin and phosphonomycin) is a broad-spectrum antibiotic produced by certain Streptomyces species. It is effective on gram positive and negative bacteria as it targets the cell wall, an essential feature shared by both bacteria. Its specific target is MurA (MurZ in E.coli), which attaches phosphoenolpyruvate (PEP) to UDP-N-acetylglucosamine, a step of commitment to cell wall synthesis. In the active site of MurA, the active cysteine molecule is alkylated which stops the catalytic reaction.","category_aro_class_name":"Antibiotic"},"45731":{"category_aro_accession":"3007149","category_aro_cvterm_id":"45731","category_aro_name":"phosphonic acid antibiotic","category_aro_description":"A group of antibiotics derived from phosphonic acids.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2061":{"model_id":"2061","model_name":"VIM-7","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1007":{"protein_sequence":{"accession":"CAD61201.1","sequence":"MFQIRSFLVGISAFVMAVLGSAAYSAQPGGEYPTVDDIPVGEVRLYKIGDGVWSHIATQKLGDTVYSSNGLIVRDADELLLIDTAWGAKNTVALLAEIEKQIGLPVTRSISTHFHDDRVGGVDVLRAAGVATYTSPLTRQLAEAAGNEVPAHSLKALSSSGDVVRFGPVEVFYPGAAHSGDNLVVYVPAVRVLFGGCAVHEASRESAGNVADANLAEWPATIKRIQQRYPEAEVVIPGHGLPGGLELLQHTTNVVKTHKVRPVAE"},"dna_sequence":{"accession":"AJ536835.1","fmin":"149","fmax":"947","strand":"+","sequence":"ATGTTTCAAATTCGCAGCTTTCTGGTTGGTATCAGTGCATTCGTCATGGCCGTACTTGGATCAGCAGCATATTCCGCACAGCCTGGCGGTGAATATCCGACAGTAGATGACATACCGGTAGGGGAAGTTCGGCTGTACAAGATTGGCGATGGCGTTTGGTCGCATATCGCAACTCAGAAACTCGGTGACACGGTGTACTCGTCTAATGGACTTATCGTCCGCGATGCTGATGAGTTGCTTCTTATTGATACAGCGTGGGGGGCGAAGAACACGGTAGCCCTTCTCGCGGAGATTGAAAAGCAAATTGGACTTCCAGTAACGCGCTCAATTTCTACGCACTTCCATGACGATCGAGTCGGTGGAGTTGATGTCCTCCGGGCGGCTGGAGTGGCAACGTACACCTCACCCTTGACACGCCAGCTGGCCGAAGCGGCGGGAAACGAGGTGCCTGCGCACTCTCTAAAAGCGCTCTCCTCTAGTGGAGATGTGGTGCGCTTCGGTCCCGTAGAGGTTTTCTATCCTGGTGCTGCGCATTCGGGCGACAATCTTGTGGTATACGTGCCGGCCGTGCGCGTACTGTTTGGTGGCTGTGCAGTTCATGAGGCGTCACGCGAATCCGCGGGTAATGTTGCCGATGCCAATTTGGCAGAATGGCCTGCTACCATTAAACGAATTCAACAGCGGTATCCGGAAGCAGAGGTCGTCATCCCCGGCCACGGTCTACCGGGCGGTCTGGAATTGCTCCAACACACAACTAACGTTGTCAAAACGCACAAAGTACGCCCGGTGGCCGAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002277","ARO_id":"38677","ARO_name":"VIM-7","CARD_short_name":"VIM-7","ARO_description":"VIM-7 is a beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2062":{"model_id":"2062","model_name":"mphC","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"5190":{"protein_sequence":{"accession":"BAA34540.1","sequence":"MTRHNEIIKCAEKYQLHIQPQTISLNESGLDFQVAFGKDKHGVEWVLRLPRRPDVYKRTKPEKQTVDFLQKNVSFEVPKWKVHERDLIAYPKLTGKPAATIDPEIQNYVWEIEHKPLPENFINTLAETLVDLHNIPEENINVQHINIKTIQEIKNDFQRRMNKVKETYGVSDELWNRWKQWLENDELWPRHATMIHGDLHPGHIMVDNQANVTGLIDWTEATHSDPSMDFMGHHRVFDDEGLEQLITAYGKAGGEIWPRMKEHIIELNAVFPMFIAEFAMESGESAYETMALKELGMKE"},"dna_sequence":{"accession":"AB013298.1","fmin":"2295","fmax":"3195","strand":"+","sequence":"ATGACTCGACATAATGAAATTATTAAATGTGCAGAAAAATATCAATTACACATCCAACCTCAAACAATCTCATTGAATGAATCGGGACTTGATTTCCAAGTTGCATTTGGAAAAGATAAACATGGAGTAGAATGGGTTTTGAGACTGCCAAGAAGACCTGATGTTTATAAACGAACAAAACCCGAAAAACAAACGGTAGACTTCTTACAGAAGAATGTTTCATTTGAAGTACCGAAATGGAAAGTACACGAAAGAGACCTTATTGCGTATCCAAAACTTACAGGTAAACCCGCAGCCACAATAGATCCAGAAATACAAAATTATGTATGGGAAATTGAACACAAACCATTACCAGAAAACTTTATTAACACATTAGCTGAAACACTCGTAGATTTACACAACATACCAGAAGAAAACATTAACGTTCAGCATATAAATATCAAAACCATACAAGAAATAAAAAATGACTTTCAAAGAAGAATGAATAAAGTTAAAGAAACTTATGGTGTATCAGATGAATTATGGAACAGATGGAAACAATGGTTAGAAAACGACGAACTATGGCCTCGACATGCGACCATGATACATGGGGACTTACATCCAGGACATATAATGGTAGATAACCAAGCAAACGTCACAGGTCTCATAGACTGGACTGAAGCAACCCACTCCGACCCATCAATGGACTTTATGGGACACCATCGTGTATTCGACGACGAAGGATTAGAGCAACTCATAACAGCATATGGTAAAGCTGGAGGTGAAATATGGCCACGAATGAAAGAGCATATAATAGAACTCAATGCAGTATTCCCAATGTTTATCGCTGAGTTTGCTATGGAATCAGGAGAATCGGCGTATGAAACGATGGCATTGAAAGAGTTAGGTATGAAAGAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35508","NCBI_taxonomy_name":"Staphylococcus aureus","NCBI_taxonomy_id":"1280"}}}},"ARO_accession":"3000319","ARO_id":"36458","ARO_name":"mphC","CARD_short_name":"mphC","ARO_description":"The mphC gene was identified from Staphylococcus aureus.  This gene shows similarity to mphB gene from Escherchia coli.","ARO_category":{"36472":{"category_aro_accession":"3000333","category_aro_cvterm_id":"36472","category_aro_name":"macrolide phosphotransferase (MPH)","category_aro_description":"Macrolide phosphotransferases (MPH) are enzymes encoded by macrolide phosphotransferase genes (mph genes). These enzymes phosphorylate macrolides in GTP dependent manner at 2'-OH of desosamine sugar thereby inactivating them. Characterized MPH's are differentiated based on their substrate specificity.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35946":{"category_aro_accession":"0000027","category_aro_cvterm_id":"35946","category_aro_name":"roxithromycin","category_aro_description":"Roxithromycin is a semi-synthetic, 14-carbon ring macrolide antibiotic derived from erythromycin. It is used to treat respiratory tract, urinary and soft tissue infections. Roxithromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35974":{"category_aro_accession":"0000057","category_aro_cvterm_id":"35974","category_aro_name":"telithromycin","category_aro_description":"Telithromycin is a semi-synthetic derivative of erythromycin. It is a 14-membered macrolide and is the first ketolide antibiotic to be used in clinics. Telithromycin binds the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"35982":{"category_aro_accession":"0000065","category_aro_cvterm_id":"35982","category_aro_name":"clarithromycin","category_aro_description":"Clarithromycin is a methyl derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome and is used to treat pharyngitis, tonsillitis, acute maxillary sinusitis, acute bacterial exacerbation of chronic bronchitis, pneumonia (especially atypical pneumonias associated with Chlamydia pneumoniae or TWAR), and skin structure infections.","category_aro_class_name":"Antibiotic"},"36284":{"category_aro_accession":"3000145","category_aro_cvterm_id":"36284","category_aro_name":"tylosin","category_aro_description":"Tylosin is a 16-membered macrolide, naturally produced by Streptomyces fradiae. It interacts with the bacterial ribosome 50S subunit to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"36295":{"category_aro_accession":"3000156","category_aro_cvterm_id":"36295","category_aro_name":"spiramycin","category_aro_description":"Spiramycin is a 16-membered macrolide and is natural product produced by Streptomyces ambofaciens. It binds to the 50S subunit of bacterial ribosomes and inhibits peptidyl transfer activity to disrupt protein synthesis.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"36315":{"category_aro_accession":"3000176","category_aro_cvterm_id":"36315","category_aro_name":"dirithromycin","category_aro_description":"Dirithromycin is an oxazine derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome to inhibit bacterial protein synthesis.","category_aro_class_name":"Antibiotic"},"37247":{"category_aro_accession":"3000867","category_aro_cvterm_id":"37247","category_aro_name":"oleandomycin","category_aro_description":"Oleandomycin is a 14-membered macrolide produced by Streptomyces antibioticus. It is ssimilar to erythromycin, and contains a desosamine amino sugar and an oleandrose sugar. It targets the 50S ribosomal subunit to prevent protein synthesis.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2063":{"model_id":"2063","model_name":"blaR1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1150"}},"model_sequences":{"sequence":{"4663":{"protein_sequence":{"accession":"ABU39979.1","sequence":"MTLPHILLSLVLITATILVIFFVRAVFYKQLSAKWRYHLWFLLITVLTLPFIPIHLLTGLSFFDQGRQQITPSAQKRFGFADQNEQWMVDFGTSVSRFDDTFIHAVFVSIWIGGMIFFLLLTLYHYAKLQRLVKAASRIQNQKVENAFSDCMAELQITNKLTNLESPAIQTPMTFGWLKTYILLPKNIELYLSDDEIRHVLLHELHHYKSKHIKVNYIFVVYQIVYWFHPLVWKAFKEMRLDRELACDTEVLLTLGQREYKAYGQTIMRFLERNSRFLYLTNPLHSSKKAFKNTKSYNIAFFYWRVKSGAQLKKPWVVFAGLTRFCIAQFPFLTATAVSTERYQFDESQAVVEDYSTYFAGNEGSFVLYSLTSDQFEIYNKEKSVRRVSPNSSYKIYTALMALELGVIGRDDSWLEWDGVEYEDEAWNSGQDLKSAMSQSVTWYFQELDERIKQRNIQSFVNQLDYGNKDLSGGLNHYWLESSLKISPVEQVELLHSFYTNQLDFKEEHVQFVKEVMKLEENQKGTLYGKTGTGIVNGHAINGWFIGFVETETDTYFFATNIQQKIMHMEARLLKSLYPFCQAKEFID"},"dna_sequence":{"accession":"EF540343.1","fmin":"1463","fmax":"3230","strand":"-","sequence":"ATGACGTTACCGCATATTTTACTTTCTCTTGTATTAATAACGGCAACGATTCTAGTGATCTTTTTTGTAAGAGCGGTTTTTTATAAACAATTATCAGCAAAATGGCGTTATCATTTATGGTTTTTACTCATTACTGTGTTGACGCTTCCGTTTATACCGATTCATCTATTGACGGGCTTGTCTTTTTTTGACCAGGGGCGTCAACAGATTACCCCTTCAGCACAGAAGCGTTTCGGTTTTGCGGATCAAAATGAGCAATGGATGGTTGATTTTGGCACGTCTGTTAGTCGCTTTGACGATACATTCATTCATGCAGTGTTTGTTTCCATCTGGATTGGTGGAATGATTTTTTTCCTTTTATTGACTTTATACCATTATGCAAAGCTACAACGACTAGTAAAAGCGGCAAGTCGTATACAAAATCAAAAAGTCGAAAACGCGTTTAGCGATTGTATGGCAGAATTGCAAATAACGAATAAATTAACCAATTTAGAATCCCCTGCCATTCAAACGCCAATGACCTTTGGATGGTTAAAGACGTACATCTTGTTGCCCAAAAATATCGAATTGTATCTATCTGATGATGAAATCAGACATGTGTTGTTGCATGAGTTGCACCATTATAAAAGCAAACATATTAAAGTGAACTATATATTTGTCGTTTACCAAATTGTTTATTGGTTTCATCCTTTAGTATGGAAAGCCTTTAAAGAGATGCGTCTTGATCGGGAATTAGCTTGTGATACGGAGGTCTTGCTTACATTGGGACAGCGGGAGTATAAAGCGTATGGCCAGACGATCATGCGTTTTCTGGAAAGAAATTCTCGATTTTTATACTTAACGAACCCACTGCATAGTTCGAAAAAAGCTTTTAAAAATACGAAATCTTATAACATTGCTTTCTTTTACTGGCGAGTCAAAAGCGGCGCCCAATTAAAAAAGCCATGGGTGGTTTTTGCTGGTCTCACCCGTTTTTGCATTGCTCAATTTCCTTTTTTAACGGCAACCGCTGTTTCTACAGAGCGCTACCAATTTGATGAAAGCCAGGCGGTTGTTGAAGATTACAGCACTTATTTTGCAGGAAATGAGGGTAGTTTTGTATTATATAGCTTAACCAGCGACCAGTTCGAAATCTATAATAAAGAAAAAAGTGTAAGAAGAGTCTCCCCCAATTCTTCCTATAAAATTTACACCGCGCTCATGGCATTGGAACTAGGCGTGATTGGGCGAGATGATTCATGGTTAGAGTGGGATGGAGTCGAATACGAGGATGAAGCCTGGAATAGCGGGCAAGATTTGAAATCGGCGATGAGCCAGTCAGTCACTTGGTACTTTCAAGAGTTAGACGAGCGGATCAAACAAAGGAACATCCAATCTTTTGTAAACCAATTAGACTATGGGAATAAAGATCTTTCCGGTGGATTAAATCACTATTGGCTGGAATCTTCCTTGAAAATATCACCGGTAGAACAAGTGGAGCTTCTCCATTCCTTCTATACAAACCAACTGGACTTTAAAGAAGAGCATGTGCAATTCGTTAAAGAGGTTATGAAACTTGAAGAAAATCAAAAGGGAACGCTTTATGGAAAAACCGGGACTGGCATTGTGAACGGCCATGCAATAAATGGTTGGTTTATTGGATTTGTCGAAACTGAAACGGATACGTACTTTTTTGCGACAAACATTCAACAGAAGATCATGCATATGGAAGCACGGCTGCTGAAATCACTTTATCCATTCTGTCAAGCAAAGGAATTTATTGATTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36882","NCBI_taxonomy_name":"Alkalihalobacillus clausii","NCBI_taxonomy_id":"79880"}}}},"ARO_accession":"3000217","ARO_id":"36356","ARO_name":"blaR1","CARD_short_name":"blaR1","ARO_description":"blaR1 is a transmembrane spanning and signal transducing protein which in response to interaction with beta-lactam antibiotics results in upregulation of the blaZ\/blaR1\/blaI operon.","ARO_category":{"41361":{"category_aro_accession":"3004197","category_aro_cvterm_id":"41361","category_aro_name":"BlaZ beta-lactamase","category_aro_description":"BlaZ beta-lactamases are Class A beta-lactamases. These beta-lactamases are responsible for penicillin resistance in Staphylococcus aureus.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2064":{"model_id":"2064","model_name":"TEM-196","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"3690":{"protein_sequence":{"accession":"AFE48832.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKIFESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"JQ034306.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCTTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTCGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36790","NCBI_taxonomy_name":"Shigella sonnei","NCBI_taxonomy_id":"624"}}}},"ARO_accession":"3001376","ARO_id":"37776","ARO_name":"TEM-196","CARD_short_name":"TEM-196","ARO_description":"TEM-196 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2065":{"model_id":"2065","model_name":"CMY-5","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"5257":{"protein_sequence":{"accession":"CAB50867.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKFSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"Y17716.1","fmin":"2373","fmax":"3519","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGTTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACTTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3002016","ARO_id":"38416","ARO_name":"CMY-5","CARD_short_name":"CMY-5","ARO_description":"CMY-5 is a beta-lactamase found in Klebsiella oxytoca.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1966":{"model_id":"1966","model_name":"lmrA","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"2887":"Q52P"},"Curated-R":{"2887":"Q52P"},"clinical":{"2887":"Q52P"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"900"}},"model_sequences":{"sequence":{"5186":{"protein_sequence":{"accession":"CAA42550.1","sequence":"MSVFARATSLFSRAARTRAADEAARSRSRWVTLVFLAVLQLLIAVDVTVVNIALPAIRDSFHVDTRQLTWVVTGYTVVGGGLLMVGGRIADLFGRRRTLLFGAFLFGASSLAAGLAPNLELLVLARFGQGAGEALSLPAAMSLIACSSRTAPFQGVERLASVASVGLVLGFLLSGVITQLFSWRWIFLINIPLVSLVLVAVLLLVKKDETTARNPVDLPGALLFTAAPLLLIFGVNELGEDEPRLPLAVGSLLAAAVCAAAFVAVERRTAHPLVPLTFFGNRVRLVANGATVLLSAALSTSFFLLTMHLQEERDLSPIEAGLSFLPLGLSLILACVLVRGLIERIGTTGAAVLGMALAGPRHRLFALLPSDNSLLTSVFPGMILLLRMATGLVALQNAALHAVTEADAGVASGVQRCADQLGGASGIAVYVSIGFSPHLGGDWDPFTVAYSLAGIGLIAAVLAVLALSPDRRLAAPREQED"},"dna_sequence":{"accession":"X59926.1","fmin":"317","fmax":"1763","strand":"+","sequence":"ATGTCTGTCTTCGCTCGTGCCACCTCGCTCTTCTCCCGTGCCGCGCGGACCCGCGCGGCCGATGAGGCGGCCCGTTCCCGGTCTCGCTGGGTCACCCTCGTCTTCCTCGCCGTGCTCCAGCTCCTCATCGCGGTCGACGTGACCGTAGTGAACATCGCCCTGCCTGCGATCCGCGACAGCTTCCACGTCGACACCCGTCAACTCACCTGGGTAGTCACGGGTTACACCGTCGTGGGCGGCGGCCTGCTCATGGTGGGCGGGCGCATCGCCGACCTCTTCGGGCGGCGCCGGACCCTCCTTTTCGGGGCCTTCCTCTTCGGTGCGTCGTCCCTCGCCGCGGGCCTCGCCCCGAACCTGGAGCTGCTCGTGCTCGCACGGTTCGGGCAGGGCGCAGGAGAGGCCCTCTCCCTGCCGGCCGCGATGTCGCTCATCGCCTGCTCTTCCCGAACCGCGCCGTTCCAAGGCGTTGAGCGTCTGGCGTCGGTCGCCAGCGTCGGCCTCGTCCTCGGCTTCCTGCTCTCCGGGGTCATCACCCAGCTCTTCAGCTGGCGTTGGATCTTCCTGATCAACATCCCCCTCGTCAGCCTCGTGCTCGTCGCCGTACTGCTGCTGGTCAAGAAGGACGAGACGACCGCACGCAATCCCGTCGACCTCCCCGGCGCGCTCCTCTTCACGGCCGCGCCGCTGCTGCTCATCTTCGGCGTCAACGAGCTGGGCGAGGACGAGCCCCGGCTGCCGCTCGCCGTCGGGAGCCTGCTCGCGGCCGCGGTGTGCGCGGCCGCGTTCGTCGCCGTCGAGCGGCGCACGGCCCATCCCCTGGTTCCCCTGACGTTCTTCGGGAACCGCGTCCGCCTGGTCGCCAACGGCGCCACGGTCCTCCTCAGCGCCGCCCTCTCGACCTCCTTCTTCCTGCTGACCATGCACTTGCAGGAGGAGCGCGACCTGTCCCCCATCGAGGCGGGACTGTCCTTCCTGCCCCTGGGCCTCAGCCTCATCCTCGCCTGCGTCCTCGTCCGGGGCCTCATCGAGCGCATCGGCACCACCGGCGCGGCGGTGCTCGGCATGGCGCTCGCGGGCCCTCGGCATCGGCTCTTCGCGCTGCTGCCCAGCGACAACTCGCTGCTCACCAGCGTCTTCCCCGGCATGATCCTGCTCCTGCGGATGGCCACCGGCCTGGTCGCATTGCAGAACGCCGCCCTGCACGCGGTCACCGAGGCCGACGCGGGCGTGGCCTCCGGCGTGCAACGCTGCGCCGACCAGCTCGGCGGCGCGAGCGGTATCGCCGTCTACGTCAGCATCGGGTTCTCGCCCCACCTCGGCGGCGACTGGGACCCGTTCACCGTGGCGTACAGCCTCGCCGGCATCGGCCTGATCGCGGCCGTCCTCGCCGTCCTCGCCCTGTCTCCGGACCGCCGTCTCGCCGCCCCCCGGGAGCAGGAGGACTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36862","NCBI_taxonomy_name":"Streptomyces lincolnensis","NCBI_taxonomy_id":"1915"}}}},"ARO_accession":"3003028","ARO_id":"39462","ARO_name":"lmrA","CARD_short_name":"lmrA","ARO_description":"lmrA is the repressor to the lmrAB operon in Bacillus subtilis. lmrA mutations result in lincomycin resistance.","ARO_category":{"36002":{"category_aro_accession":"0010001","category_aro_cvterm_id":"36002","category_aro_name":"ATP-binding cassette (ABC) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding\/hydrolysis to transport substrates across cell membranes.","category_aro_class_name":"AMR Gene Family"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35965":{"category_aro_accession":"0000047","category_aro_cvterm_id":"35965","category_aro_name":"puromycin","category_aro_description":"Puromycin is an aminonucleoside antibiotic, derived from Streptomyces alboniger, that causes premature chain termination during ribosomal protein translation.","category_aro_class_name":"Antibiotic"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"36174":{"category_aro_accession":"3000034","category_aro_cvterm_id":"36174","category_aro_name":"nucleoside antibiotic","category_aro_description":"Nucleoside antibiotics are made of modified nucleosides and nucleotides with wide-ranging activities and means of antibacterial effects. This drug class includes aminonucleoside antibiotics, which contain an amino group.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2071":{"model_id":"2071","model_name":"AAC(6')-Ib8","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"5456":{"protein_sequence":{"accession":"AIK02012.1","sequence":"MSLKPGPKRIAESTGQPDQRQRDNKKTPGNTDKLGITKYSIVTNSTDSVTLRLMTEHDLAMLYEWLNRSHIVEWWGGEEARPTLADVQEQYLPSVLAQESVTPYIAMLNGEPIGYAQSYVALGSGDGWWEEETDPGVRGIDQSLANASQLGKGLGTKLVRALVELLFNDPEVTKIQTDPSPSNLRAIRCYEKAGFERQGTVTTPDGPAVYMVQTRQAFERTRSDA"},"dna_sequence":{"accession":"KF998105.1","fmin":"4171","fmax":"4849","strand":"+","sequence":"ATGAGCCTTAAACCCGGACCAAAAAGAATTGCCGAATCGACGGGGCAACCTGATCAACGCCAACGCGACAATAAAAAGACGCCTGGAAATACTGACAAGTTAGGCATCACAAAGTACAGCATCGTGACCAACAGCACCGATTCCGTCACACTGCGCCTCATGACTGAGCATGACCTTGCGATGCTCTATGAGTGGCTAAATCGATCTCATATCGTCGAGTGGTGGGGCGGAGAAGAAGCACGCCCGACACTTGCTGACGTACAGGAACAGTACTTGCCAAGCGTTTTAGCGCAAGAGTCCGTCACTCCATACATTGCAATGCTGAATGGAGAGCCGATTGGGTATGCCCAGTCGTACGTTGCTCTTGGAAGCGGGGACGGATGGTGGGAAGAAGAAACCGATCCAGGAGTACGCGGAATAGACCAGTCACTGGCGAATGCATCACAACTGGGCAAAGGCTTGGGAACCAAGCTGGTTCGAGCTCTGGTTGAGTTGCTGTTCAATGATCCCGAGGTCACCAAGATCCAAACGGACCCGTCGCCGAGCAACTTGCGAGCGATCCGATGCTACGAGAAAGCGGGGTTTGAGAGGCAAGGTACCGTAACCACCCCAGATGGTCCAGCCGTGTACATGGTTCAAACACGCCAGGCATTCGAGCGAACACGCAGTGATGCCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3002579","ARO_id":"38979","ARO_name":"AAC(6')-Ib8","CARD_short_name":"AAC(6')-Ib8","ARO_description":"AAC(6')-Ib8 is a plasmid-encoded aminoglycoside acetyltransferase in E. cloacae.","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"A category of aminoglycoside N-acetyltransferase enzymes with modification regiospecificity based at the 6'-amino group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics through acetylation of the 6-amino group of the compound.","category_aro_class_name":"AMR Gene Family"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2072":{"model_id":"2072","model_name":"NmcR","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"4662":{"protein_sequence":{"accession":"CAA79966.1","sequence":"MRARLPLNALRAFEASARYLNFTKAGLELHVSQAAVSQQVRTLEQMLGVALFTRVPRGLQLTDEGMHLLPSITEALQMMSSAMDKFHEGKIKEVLTIAVVGTFAIGWLLPRITAFLNENPWIDIRILTHNNVVNLAAEGIDASIRFGTGGWINTENILLFQAPHTVLCSPETSKKLYIPSDLKKVCLLRSYRKEEWNNWFKAAGIDPWTITGPIFDSTRLMIDAVKLGDYAALVPYHMFQKELNERSVAKPFEIYATLGGYWLTLQKSRVNHNSEALNVFKEWIIEHSREFVLKS"},"dna_sequence":{"accession":"Z21956.1","fmin":"191","fmax":"1079","strand":"-","sequence":"ATGCGTGCCAGATTACCTTTAAATGCATTACGAGCTTTTGAAGCCTCAGCAAGATATCTAAATTTTACTAAAGCCGGACTAGAACTTCATGTAAGCCAGGCCGCCGTAAGCCAGCAGGTCAGAACACTTGAACAAATGCTTGGTGTGGCTCTTTTTACAAGAGTACCGCGTGGGTTACAGTTGACAGACGAAGGCATGCATCTTTTGCCTTCGATTACAGAAGCTTTGCAGATGATGAGTTCTGCGATGGATAAATTCCATGAAGGTAAGATTAAAGAGGTGCTTACTATTGCTGTCGTAGGGACTTTTGCAATAGGATGGCTCCTTCCTCGGATTACTGCGTTTCTTAATGAAAATCCATGGATTGATATTAGAATTTTAACGCATAATAACGTTGTCAATCTTGCTGCAGAAGGTATTGATGCATCTATTAGATTTGGAACAGGCGGCTGGATTAATACGGAAAATATTTTACTCTTTCAGGCGCCGCATACAGTATTGTGTTCCCCGGAAACATCCAAGAAATTGTACATTCCATCAGACTTAAAAAAAGTTTGCTTACTGCGTTCCTATCGAAAGGAGGAATGGAATAATTGGTTTAAAGCTGCTGGGATCGACCCTTGGACTATTACAGGGCCTATCTTTGATTCTACCAGACTTATGATAGATGCTGTAAAGTTAGGTGATTATGCAGCACTAGTTCCTTATCATATGTTTCAAAAAGAATTAAATGAGCGATCCGTGGCAAAACCTTTTGAAATTTATGCCACGCTTGGCGGTTATTGGCTTACTTTGCAGAAATCTCGGGTTAATCATAATAGTGAAGCACTTAATGTTTTCAAGGAATGGATTATCGAGCATAGCAGAGAGTTTGTATTAAAATCCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3003665","ARO_id":"40275","ARO_name":"NmcR","CARD_short_name":"NmcR","ARO_description":"NmcR is a homolog of the LysR regulator found in Enterobacter cloacae that contribute to the regulation of NmcA beta-lactamase.","ARO_category":{"36027":{"category_aro_accession":"3000018","category_aro_cvterm_id":"36027","category_aro_name":"IMI beta-lactamase","category_aro_description":"IMI beta-lactamases are a group of TEM-1-like beta-lactamase that are known to hydrolyze imipenem. IMI beta-lactamases are inhibited by clavulanic acid and tazobactam.","category_aro_class_name":"AMR Gene Family"},"35927":{"category_aro_accession":"0000008","category_aro_cvterm_id":"35927","category_aro_name":"cefoxitin","category_aro_description":"Cefoxitin is a cephamycin antibiotic often grouped with the second generation cephalosporins. Cefoxitin is bactericidal and acts by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. Cefoxitin's 7-alpha-methoxy group and 3' leaving group make it a poor substrate for most beta-lactamases.","category_aro_class_name":"Antibiotic"},"35975":{"category_aro_accession":"0000058","category_aro_cvterm_id":"35975","category_aro_name":"cefazolin","category_aro_description":"Cefazolin, also known as cefazoline or cephazolin, is a first generation cephalosporin antibiotic. It is administered parenterally, and is active against a broad spectrum of bacteria.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2079":{"model_id":"2079","model_name":"sgm","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"3696":{"protein_sequence":{"accession":"WP_063978071.1","sequence":"MTAPAADDRIDEIERAITKSRRYQTVAPATVRRLARAALVAARGDVPDAVKRTKRGLHEIYGAFLPPSPPNYAALLRHLDSAVDAGDDEAVRAALLRAMSVHISTRERLPHLDEFYRELFRHLPRPNTLRDLACGLNPLAAPWMGLPAETVYIASDIDARLVGFVDEALTRLNVPHRTNVADLLEDRLDEPADVTLLLKTLPCLETQQRGSGWEVIDIVNSPNIVVTFPTKSLGQRSKGMFQNYSQSFESQARERSCRIQRLEIGNELIYVIQK"},"dna_sequence":{"accession":"NG_050600.1","fmin":"100","fmax":"925","strand":"+","sequence":"ATGACGGCACCTGCGGCCGACGACCGTATCGACGAGATTGAGCGGGCCATCACCAAGAGCAGGCGTTACCAGACGGTGGCGCCGGCCACCGTGCGCCGCCTGGCCCGCGCTGCTCTCGTCGCCGCGCGGGGTGACGTGCCCGACGCGGTGAAGCGCACCAAGCGGGGTCTGCACGAGATCTACGGCGCCTTCCTGCCGCCCAGCCCTCCCAACTACGCAGCGTTGCTGCGGCACCTGGACTCGGCAGTGGACGCCGGTGACGACGAGGCGGTTCGAGCGGCCCTACTTCGCGCTATGTCCGTACATATCTCCACCCGCGAGCGATTGCCGCACCTCGACGAGTTCTACCGGGAACTCTTCCGGCACCTCCCCCGACCGAACACGCTGCGTGACCTCGCCTGTGGTCTCAACCCCCTGGCCGCGCCCTGGATGGGCCTGCCCGCCGAGACCGTCTACATCGCCTCGGACATCGACGCCCGCCTGGTCGGCTTCGTGGACGAGGCCCTGACCCGACTCAATGTTCCACATCGGACGAACGTGGCCGACCTGCTCGAGGACCGTCTTGACGAGCCGGCCGACGTCACGCTATTGCTGAAGACGCTGCCCTGTCTGGAGACTCAGCAACGAGGATCGGGCTGGGAAGTGATTGACATTGTCAACTCGCCGAATATCGTGGTAACCTTCCCGACCAAGTCTCTCGGTCAGCGATCGAAGGGGATGTTTCAGAACTATTCACAGAGTTTTGAGTCCCAGGCCAGAGAGCGGTCATGCCGTATTCAGCGACTGGAGATTGGCAACGAGCTGATTTACGTCATTCAGAAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40607","NCBI_taxonomy_name":"Micromonospora zionensis","NCBI_taxonomy_id":"1879"}}}},"ARO_accession":"3000862","ARO_id":"37242","ARO_name":"sgm","CARD_short_name":"sgm","ARO_description":"Sgm, or sisomicin-gentamicin methyltransferase, methylates G1405 of 16S rRNA to confer resistance to various aminoglycosides.","ARO_category":{"41435":{"category_aro_accession":"3004271","category_aro_cvterm_id":"41435","category_aro_name":"16S rRNA methyltransferase (G1405)","category_aro_description":"Methyltransferases that methylate the G1405 position of 16S rRNA, which is part of an aminoglycoside binding site.","category_aro_class_name":"AMR Gene Family"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36997":{"category_aro_accession":"3000653","category_aro_cvterm_id":"36997","category_aro_name":"G418","category_aro_description":"A gentamicin class aminoglycoside antibiotic often used in mammalian cell culture work as a selectable marker for the neo cassette (APH3').","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"46133":{"category_aro_accession":"3007382","category_aro_cvterm_id":"46133","category_aro_name":"gentamicin","category_aro_description":"Gentamicin is a commonly used aminoglycoside antibiotic derived from members of the Micromonospora genus of bacteria. It acts by binding the 30S ribosomal subunit, thus inhibiting protein synthesis. Gentamicin is typically used to treat Gram-negative infections of the repiratory and urinary tract, as well as infections of the bone and soft tissue. It also exhibits considerable nephrotoxicity and ototoxicity. Gentamicin is administered as a mixture of gentamicin type C (which makes about around 80% of the complex) and types A, B, and X (distributed in the remaining 20% of the complex).","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2081":{"model_id":"2081","model_name":"patA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"5128":{"protein_sequence":{"accession":"AAK76137.1","sequence":"MLIQKIKTYKWQALASLLMTGLMVASSLLQPRYLQEVLGALLTGKYEAIYSIGAWLIGVAVVGLVAGGLNVVLAAYIAQGVSSDLREDAFRKIQTFSYADIEQFNAGNLVVRMTNDINQIQNVVMMTFQILFRLPLLFIGSFILAVQTLPSLWWVIVLMVVLIFGLTAVMMGMMGPRFAKFQTLLERINAIAKENLRGVRVVKSFVQEKEQFAKFTEVSDELLGQNLYIGYAFSVVEPFMMLVGYGAVFLSIWLVAGMVQSDPSVVGSIASFVNYLSQIIFTIVMVGFLGNSVSRAMISMRRIREILDAEPAMTFKDIPDEELVGSLSFENVTFTYPMDKEPMLKDVSFTIEPGQMVGVVGATGAGKSTLAQLIPRLFDPQDGAIKIGGKDIREVSEGTLRKTVSIVLQRAILFSGTIADNLRQGKGNATLFEMERAANIAQASEFIHRMEKTFESPVEERGTNFSGGQKQRMSIARGIVSNPRILIFDDSTSALDAKSERLVQEALNKDLKGTTTIIIAQKISSVVHADKILVLNQGRLIGQGTHADLVANNAVYREIYETQK"},"dna_sequence":{"accession":"AE005672.3","fmin":"1983115","fmax":"1984810","strand":"-","sequence":"ATGCTGATTCAGAAAATAAAAACCTACAAGTGGCAGGCCCTGGCTTCGCTCCTGATGACAGGCTTGATGGTTGCTAGTTCACTTCTGCAACCGCGTTATCTGCAGGAAGTCTTAGGCGCCCTCCTTACTGGGAAATATGAAGCTATTTATAGTATCGGGGCTTGGTTGATTGGTGTGGCCGTAGTCGGTCTAGTTGCTGGTGGACTCAATGTTGTCCTCGCAGCCTATATTGCCCAAGGAGTTTCATCCGACCTTCGGGAGGATGCCTTCCGTAAAATTCAAACCTTTTCTTATGCTGATATTGAACAATTTAATGCGGGAAATCTAGTCGTTCGAATGACAAATGATATCAACCAGATTCAGAACGTTGTCATGATGACCTTCCAAATTCTTTTCAGACTTCCCCTCTTGTTCATCGGTTCGTTTATCCTAGCGGTTCAAACCTTACCTTCTCTGTGGTGGGTGATTGTTCTCATGGTAGTCTTGATTTTTGGTTTGACTGCTGTCATGATGGGAATGATGGGGCCTCGTTTTGCCAAGTTTCAAACCCTTCTTGAGCGCATCAATGCCATTGCCAAGGAAAATTTACGTGGCGTTCGTGTGGTCAAGTCCTTTGTCCAAGAAAAAGAGCAATTTGCTAAGTTTACAGAGGTCTCAGACGAGCTTCTTGGTCAAAACCTTTACATTGGTTATGCCTTTTCAGTAGTGGAACCCTTTATGATGTTGGTTGGTTACGGGGCGGTCTTCCTCTCTATTTGGCTGGTCGCGGGAATGGTTCAGTCGGATCCGTCTGTTGTTGGTTCCATCGCTTCTTTTGTTAATTACCTAAGCCAGATTATCTTTACCATTGTTATGGTTGGATTTTTGGGAAATTCTGTCAGCCGTGCCATGATTTCCATGCGTCGTATTCGAGAAATTCTTGACGCAGAGCCAGCTATGACCTTCAAGGATATCCCAGATGAAGAGTTGGTTGGAAGTCTTAGCTTTGAAAATGTGACCTTTACCTATCCAATGGACAAGGAACCGATGCTGAAAGATGTGAGCTTTACTATTGAACCTGGTCAAATGGTTGGTGTAGTTGGAGCGACTGGTGCAGGAAAGTCAACCTTGGCTCAATTGATTCCACGTCTCTTTGATCCACAGGACGGGGCCATTAAAATCGGTGGCAAGGATATTCGAGAAGTGAGTGAAGGAACCCTGCGTAAAACAGTTTCCATCGTTCTCCAACGTGCCATTCTTTTTAGTGGAACGATTGCAGATAACTTGAGACAGGGGAAGGGGAATGCTACTCTATTTGAAATGGAGCGCGCAGCCAATATTGCCCAGGCTAGTGAATTCATTCATCGTATGGAGAAAACCTTTGAAAGTCCAGTTGAAGAACGGGGAACCAATTTCTCTGGTGGACAAAAACAAAGGATGTCGATTGCGCGTGGGATTGTCAGCAATCCACGTATTCTGATTTTTGATGATTCGACCTCAGCCTTGGATGCCAAATCAGAGCGCTTGGTGCAAGAAGCTTTGAATAAGGACTTGAAGGGGACGACAACCATTATTATTGCTCAAAAAATTAGCTCGGTTGTCCATGCAGACAAGATCTTGGTTCTAAATCAAGGACGATTGATTGGTCAAGGTACGCATGCAGACTTGGTTGCCAACAATGCCGTTTACCGTGAAATCTATGAAACACAGAAATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40078","NCBI_taxonomy_name":"Streptococcus pneumoniae TIGR4","NCBI_taxonomy_id":"170187"}}}},"ARO_accession":"3000024","ARO_id":"36033","ARO_name":"patA","CARD_short_name":"patA","ARO_description":"PatA is an ABC transporter of Streptococcus pneumoniae that interacts with PatB to confer fluoroquinolone resistance.","ARO_category":{"36002":{"category_aro_accession":"0010001","category_aro_cvterm_id":"36002","category_aro_name":"ATP-binding cassette (ABC) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding\/hydrolysis to transport substrates across cell membranes.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2087":{"model_id":"2087","model_name":"aadA13","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"5258":{"protein_sequence":{"accession":"ABW91178.1","sequence":"MRDSVTAEISTQLSKVLSVIEHHLEPTLLAVHLYGSAVDGGLKPYSDIDLLVTVTARLDDTTRRALFNDLLEVSAFPGESEILRAIEVTIVVHEDIMPWRYPAKRELQFGEWQRNDILAGIFEPATIDIDLAILLTKAREHSVALVGPAAEELFDPVPEQDLIKALNETLKLWNSQPDWAGDERNVVLTLSRIWYSAATGKIAPKDVAANWAMEHLPAQHQSVLLEARQAYLGQEEDRSVLRADKLEEFIHFMKSEITKVLGNDV"},"dna_sequence":{"accession":"EU746499.1","fmin":"639","fmax":"1437","strand":"+","sequence":"ATGAGGGACTCAGTGACCGCCGAAATTTCGACGCAACTATCCAAGGTGCTTAGTGTTATCGAGCACCATCTGGAACCGACGTTGCTTGCCGTACATTTGTACGGCTCCGCAGTGGATGGCGGCCTGAAGCCATACAGTGATATTGATTTGCTGGTTACTGTGACCGCAAGGCTTGATGACACAACGCGGCGAGCTTTGTTCAACGATCTTTTGGAGGTTTCGGCTTTCCCAGGCGAGAGTGAGATTCTCCGCGCTATAGAAGTCACCATTGTCGTGCACGAAGACATTATGCCGTGGCGTTATCCAGCCAAGCGCGAACTGCAATTTGGAGAATGGCAGCGCAATGACATTCTTGCGGGTATCTTCGAGCCAGCCACGATCGACATCGATCTGGCTATCTTGCTAACGAAAGCGAGAGAACATAGCGTGGCTTTGGTAGGTCCGGCGGCGGAGGAACTCTTTGATCCAGTTCCTGAACAAGATCTAATCAAGGCGCTGAATGAAACCTTGAAGCTATGGAACTCGCAGCCCGACTGGGCCGGCGATGAGCGAAATGTAGTGCTTACGTTGTCCCGCATTTGGTACAGCGCAGCAACTGGTAAAATCGCGCCGAAGGATGTCGCTGCCAACTGGGCAATGGAACATCTACCTGCCCAGCATCAGTCTGTCTTGCTTGAAGCTAGACAGGCTTATCTTGGGCAAGAGGAAGATCGCTCGGTCTTGCGCGCAGATAAGTTGGAAGAATTTATTCACTTCATGAAAAGCGAGATCACCAAGGTGCTCGGCAATGATGTCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002613","ARO_id":"39013","ARO_name":"aadA13","CARD_short_name":"aadA13","ARO_description":"aadA13 is an aminoglycoside nucleotidyltransferase gene encoded by plasmids and integrons in Pseudomonas rettgeri, P. aeruginosa, Y. enterocolitica and E. coli.","ARO_category":{"41439":{"category_aro_accession":"3004275","category_aro_cvterm_id":"41439","category_aro_name":"ANT(3'')","category_aro_description":"A category of aminoglycoside O-nucleotidyltransferase enzymes with modification regiospecificity based at the 3''-hydroxyl group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics by transfer of an AMP group from an ATP substrate to the 3''-hydroxyl group of the compound.","category_aro_class_name":"AMR Gene Family"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2103":{"model_id":"2103","model_name":"SHV-3","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"5455":{"protein_sequence":{"accession":"ANA06389.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQLQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGASERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"KX092356.1","fmin":"192","fmax":"1053","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTACTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACTGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTAGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGGATCGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001062","ARO_id":"37442","ARO_name":"SHV-3","CARD_short_name":"SHV-3","ARO_description":"SHV-3 is an extended-spectrum beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2110":{"model_id":"2110","model_name":"CARB-20","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"5458":{"protein_sequence":{"accession":"ATI44679.1","sequence":"MKKLFLLVGLMVCSTVSYASKLNEDISLIEKQTSGRIGVSVWDTQTDERWDYRGDERFPLMSTFKTLACATMLSDMDSGKLNKNATARIDERNIVVWSPVMDKLAGQSTRIEHACEAAMLMSDNTAANLVLNEIGGPKAVTLFLRSIGDKATRLDRLEPRLNEAKPGDKRDTTTPNAMVNTLHTLMEDNALSYESRTQLKIWMQDNKVSDSLMRSVLPKGWSIADRSGAGNYGSRGISAMIWKDNYKPVYISIYVTDTDLSLQARDQLIAQISQLILEHYKES"},"dna_sequence":{"accession":"CP023709.1","fmin":"697533","fmax":"698385","strand":"+","sequence":"ATGAAAAAGTTATTCCTGTTGGTTGGGCTGATGGTTTGCTCAACTGTTAGTTACGCCTCCAAATTAAACGAAGACATCTCCCTCATCGAGAAACAAACATCTGGGCGAATTGGAGTGTCAGTCTGGGATACACAAACGGACGAGCGTTGGGATTATCGCGGAGACGAACGTTTCCCATTAATGAGCACATTCAAAACGTTAGCGTGTGCCACCATGCTAAGCGACATGGACAGCGGCAAACTCAACAAAAATGCCACAGCGAGAATCGATGAACGCAATATTGTGGTTTGGTCTCCGGTGATGGATAAACTGGCTGGACAAAGCACGCGTATCGAACACGCTTGTGAAGCCGCCATGTTGATGAGCGACAACACCGCCGCAAACTTAGTGCTAAATGAAATTGGTGGTCCTAAAGCGGTCACGCTGTTTTTGCGCTCTATTGGCGACAAAGCAACGCGGCTTGACCGATTGGAGCCCCGTTTGAACGAAGCAAAACCGGGCGACAAGCGAGACACCACAACGCCTAACGCCATGGTAAACACCCTACACACCTTGATGGAAGATAACGCCCTATCTTACGAGTCACGCACACAGCTGAAAATCTGGATGCAAGACAACAAAGTATCGGATTCTCTCATGCGCTCTGTTCTGCCAAAAGGCTGGTCGATTGCAGACCGCTCTGGCGCAGGTAACTACGGTTCACGCGGCATTAGCGCGATGATTTGGAAAGACAACTACAAGCCAGTTTACATCAGTATTTACGTCACAGATACTGACCTTTCGCTTCAAGCTCGCGATCAACTGATCGCGCAAATCAGCCAACTGATTTTAGAGCACTACAAAGAAAGTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39615","NCBI_taxonomy_name":"Vibrio parahaemolyticus","NCBI_taxonomy_id":"670"}}}},"ARO_accession":"3003150","ARO_id":"39727","ARO_name":"CARB-20","CARD_short_name":"CARB-20","ARO_description":"CARB-20 is a beta-lactamase found worldwide in Vibrio parahaemolyticus.","ARO_category":{"36230":{"category_aro_accession":"3000091","category_aro_cvterm_id":"36230","category_aro_name":"CARB beta-lactamase","category_aro_description":"CARB beta-lactamases are class A lactamases that can hydrolyze carbenicillin. Many of the PSE beta-lactamases have been renamed as CARB-lactamases with the notable exception of PSE-2 which is now OXA-10.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2112":{"model_id":"2112","model_name":"patB","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"5129":{"protein_sequence":{"accession":"AAK76136.1","sequence":"MKTVQFFWHYFKVYKFSFVVVILMIVLATFAQALFPVFSGQAVTQLANLVQAYQNGNPELVWQSLSGIMVNLGLLVLVLFISSVIYMCLMTRVIAESTNEMRKGLFGKLAQLTVSFFDRRQDGDILSHFTSDLDNILQAFNESLIQVMSNIVLYIGLILVMFSRNVTLALITIASTPLAFLMLIFIVKMARKYTNLQQKEVGKLNAYMDESISGQKAVIVQGIQEDMMAGFLEQNERVRKATFKGRMFSGILFPVMNGMSLINTAIVIFAGSAVLLNDKSIETSTALGLIVMFAQFSQQYYQPIIQVAASWGSLQLAFTGAERIQEMFDAEEEIRPEKAPTFTKLQESVEISHIVFSYLPDKPILKDVSISAPKGQMTAVVGPTGSGKTTIMNLINRFYDVDAGGIYFDGKDIRGYDLDSLRSKVGIVLQDSVLFSGTIRDNIRFGVPDASQEMVEVAAKATHIHDYIESLPDKYDTLIDDDQSIFSTGQKQLISIARTLMTDPEVLILDEATSNVDTVTESKIQHAMEVVVAGRTSFVIAHRLKTILNADQIIVLKDGEVIERGNHHELLKLGGFYSELYHNQFVFE"},"dna_sequence":{"accession":"AE005672.3","fmin":"1980557","fmax":"1982324","strand":"-","sequence":"ATGAAGACAGTTCAATTTTTTTGGCATTATTTTAAGGTCTACAAGTTCTCATTTGTAGTTGTCATCCTGATGATTGTTCTGGCGACTTTTGCCCAAGCCCTCTTTCCAGTCTTTTCTGGACAAGCGGTGACGCAGCTAGCCAATTTAGTTCAAGCTTATCAAAATGGCAATCCAGAACTTGTATGGCAAAGCCTATCAGGAATCATGGTCAATCTTGGCCTGCTGGTTTTGGTTCTATTTATCTCTAGTGTAATATACATGTGTCTCATGACGCGCGTGATTGCAGAATCGACCAACGAGATGCGCAAAGGCCTCTTTGGTAAGCTTGCTCAGTTGACGGTTTCTTTCTTTGACCGTCGACAAGATGGCGATATCCTGTCTCATTTTACCAGTGATTTGGATAATATCCTCCAAGCCTTTAACGAAAGCTTGATTCAGGTCATGAGCAATATTGTTTTATACATTGGTCTGATTCTTGTCATGTTTTCGAGAAATGTGACGCTGGCTCTCATCACCATTGCCAGCACCCCATTGGCTTTCCTTATGCTGATTTTCATCGTGAAAATGGCACGCAAATACACCAACCTCCAGCAGAAAGAGGTAGGGAAGCTCAACGCCTATATGGATGAGAGCATCTCAGGCCAAAAAGCCGTGATTGTGCAAGGAATTCAAGAGGATATGATGGCAGGATTTCTTGAACAAAATGAGCGCGTGCGCAAGGCAACCTTTAAAGGAAGAATGTTCTCAGGAATTCTTTTCCCTGTCATGAATGGGATGAGCCTGATTAATACAGCCATCGTCATCTTTGCTGGTTCGGCTGTACTTTTGAATGATAAGTCTATTGAAACAAGTACAGCCCTAGGTTTGATTGTTATGTTTGCACAATTTTCACAGCAGTACTACCAGCCTATTATCCAAGTTGCAGCGAGTTGGGGAAGCCTTCAGTTGGCCTTTACTGGAGCTGAACGAATTCAGGAAATGTTTGATGCAGAGGAGGAAATCCGACCTGAAAAGGCTCCAACCTTCACTAAGTTGCAAGAAAGTGTTGAAATCAGTCATATCGTTTTTTCATACTTGCCTGATAAACCTATTTTGAAAGATGTCAGCATTTCTGCCCCTAAAGGCCAGATGACAGCAGTTGTTGGGCCGACAGGTTCAGGAAAAACGACTATTATGAACCTCATCAATCGCTTTTATGATGTTGATGCTGGTGGTATTTATTTTGATGGTAAAGACATTCGTGGCTATGACTTAGATAGTCTTAGAAGCAAGGTGGGAATTGTATTGCAAGATTCGGTCTTGTTTAGCGGAACGATTAGAGACAATATCCGATTTGGTGTGCCAGATGCTAGTCAGGAAATGGTTGAGGTAGCAGCAAAAGCAACCCACATTCACGACTATATCGAAAGTTTGCCTGATAAGTACGATACTCTTATTGATGATGACCAGAGCATCTTTTCAACAGGGCAGAAGCAATTGATTTCAATCGCTCGAACCCTGATGACAGATCCAGAAGTTCTCATTCTCGATGAAGCAACTTCAAACGTAGATACGGTGACAGAAAGCAAGATTCAGCATGCCATGGAGGTGGTTGTAGCAGGTAGAACTAGTTTCGTCATTGCCCACCGCTTGAAAACCATTCTCAATGCAGATCAGATTATTGTCCTTAAAGATGGAGAAGTCATTGAACGTGGTAACCACCATGAACTTTTGAAGCTAGGTGGCTTTTATTCAGAACTCTATCACAATCAATTTGTTTTCGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40078","NCBI_taxonomy_name":"Streptococcus pneumoniae TIGR4","NCBI_taxonomy_id":"170187"}}}},"ARO_accession":"3000025","ARO_id":"36034","ARO_name":"patB","CARD_short_name":"patB","ARO_description":"PatB is an ABC transporter of Streptococcus pneumoniae that interacts with PatA to confer fluoroquinolone resistance..","ARO_category":{"36002":{"category_aro_accession":"0010001","category_aro_cvterm_id":"36002","category_aro_name":"ATP-binding cassette (ABC) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding\/hydrolysis to transport substrates across cell membranes.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2114":{"model_id":"2114","model_name":"APH(3')-IIa","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"5416":{"protein_sequence":{"accession":"CAA23892.1","sequence":"MIEQDGLHAGSPAAWVERLFGYDWAQQTIGCSDAAVFRLSAQGRPVLFVKTDLSGALNELQDEAARLSWLATTGVPCAAVLDVVTEAGRDWLLLGEVPGQDLLSSHLAPAEKVSIMADAMRRLHTLDPATCPFDHQAKHRIERARTRMEAGLVDQDDLDEEHQGLAPAELFARLKARMPDGEDLVVTHGDACLPNIMVENGRFSGFIDCGRLGVADRYQDIALATRDIAEELGGEWADRFLVLYGIAAPDSQRIAFYRLLDEFF"},"dna_sequence":{"accession":"V00618.1","fmin":"150","fmax":"945","strand":"+","sequence":"ATGATTGAACAAGATGGATTGCACGCAGGTTCTCCGGCCGCTTGGGTGGAGAGGCTATTCGGCTATGACTGGGCACAACAGACAATCGGCTGCTCTGATGCCGCCGTGTTCCGGCTGTCAGCGCAGGGGCGCCCGGTTCTTTTTGTCAAGACCGACCTGTCCGGTGCCCTGAATGAACTGCAGGACGAGGCAGCGCGGCTATCGTGGCTGGCCACGACGGGCGTTCCTTGCGCAGCTGTGCTCGACGTTGTCACTGAAGCGGGAAGGGACTGGCTGCTATTGGGCGAAGTGCCGGGGCAGGATCTCCTGTCATCTCACCTTGCTCCTGCCGAGAAAGTATCCATCATGGCTGATGCAATGCGGCGGCTGCATACGCTTGATCCGGCTACCTGCCCATTCGACCACCAAGCGAAACATCGCATCGAGCGAGCACGTACTCGGATGGAAGCCGGTCTTGTCGATCAGGATGATCTGGACGAAGAGCATCAGGGGCTCGCGCCAGCCGAACTGTTCGCCAGGCTCAAGGCGCGCATGCCCGACGGCGAGGATCTCGTCGTGACCCATGGCGATGCCTGCTTGCCGAATATCATGGTGGAAAATGGCCGCTTTTCTGGATTCATCGACTGTGGCCGGCTGGGTGTGGCGGACCGCTATCAGGACATAGCGTTGGCTACCCGTGATATTGCTGAAGAGCTTGGCGGCGAATGGGCTGACCGCTTCCTCGTGCTTTACGGTATCGCCGCTCCCGATTCGCAGCGCATCGCCTTCTATCGCCTTCTTGACGAGTTCTTCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002644","ARO_id":"39044","ARO_name":"APH(3')-IIa","CARD_short_name":"APH(3')-IIa","ARO_description":"APH(3')-IIa is a transposon-encoded aminoglycoside phosphotransferase in E. coli.","ARO_category":{"36265":{"category_aro_accession":"3000126","category_aro_cvterm_id":"36265","category_aro_name":"APH(3')","category_aro_description":"A category of aminoglycoside O-phosphotransferase enzymes with modification regiospecificity based at the 3'-hydroxyl group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics, specifically kanamycin and neomycin, by the ATP-dependent phosphorylation of the 3'-hydroxyl group of the compound.","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35940":{"category_aro_accession":"0000021","category_aro_cvterm_id":"35940","category_aro_name":"ribostamycin","category_aro_description":"Ribostamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Ribostamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35943":{"category_aro_accession":"0000024","category_aro_cvterm_id":"35943","category_aro_name":"butirosin","category_aro_description":"Butirosin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Butirosin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"37001":{"category_aro_accession":"3000657","category_aro_cvterm_id":"37001","category_aro_name":"paromomycin","category_aro_description":"An aminoglycoside antibiotic used for the treatment of parasitic infections. It is similar to neomycin sharing a similar spectrum of activity, but its hydroxyl group at the 6'-position instead of an amino group makes it resistant to AAC(6') modifying enzymes.","category_aro_class_name":"Antibiotic"},"46133":{"category_aro_accession":"3007382","category_aro_cvterm_id":"46133","category_aro_name":"gentamicin","category_aro_description":"Gentamicin is a commonly used aminoglycoside antibiotic derived from members of the Micromonospora genus of bacteria. It acts by binding the 30S ribosomal subunit, thus inhibiting protein synthesis. Gentamicin is typically used to treat Gram-negative infections of the repiratory and urinary tract, as well as infections of the bone and soft tissue. It also exhibits considerable nephrotoxicity and ototoxicity. Gentamicin is administered as a mixture of gentamicin type C (which makes about around 80% of the complex) and types A, B, and X (distributed in the remaining 20% of the complex).","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2115":{"model_id":"2115","model_name":"TEM-4","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"5503":{"protein_sequence":{"accession":"CDR98216.1","sequence":"MSIQHFRVALIPFFAAFCFPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVKYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGASERGSRGIIAALGPDGKPSRIVVIYMTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"LK391770.1","fmin":"19707","fmax":"20568","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCTTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTAAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCAGTGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACATGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3000876","ARO_id":"37256","ARO_name":"TEM-4","CARD_short_name":"TEM-4","ARO_description":"TEM-4 is an extended-spectrum beta-lactamase that has been found in clinical isolates.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2117":{"model_id":"2117","model_name":"AAC(6')-Ib7","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"475"}},"model_sequences":{"sequence":{"5850":{"protein_sequence":{"accession":"AKN19287.1","sequence":"MRSRNWSRTLTERSGGNGAVAVFMACYDCFFVQSMPRASKQQARYAVGRCLMLWSSNDVTQQGSRPKTKLGITKYSIVTNSNDSVTLRLMTEHDLAMLYEWLNRSHIVEWWGGEEARPTLADVQEQYLPSVLAQESVTPYIAMLNGEPIGYAQSYVALGSGDGWWEEETDPGVRGIDQLLANASQLGKGLGTKLVRALVELLFNDPEVTKIQTDPSPSNLRAIRCYEKAGFERQGTVTTPDGPAVYMVQTRQAFERTRSDA"},"dna_sequence":{"accession":"KR091911.1","fmin":"74564","fmax":"75350","strand":"-","sequence":"ATGCGCTCACGCAACTGGTCCAGAACCTTGACCGAACGCAGCGGTGGTAACGGCGCAGTGGCGGTTTTCATGGCTTGTTATGACTGTTTTTTTGTACAGTCTATGCCTCGGGCATCCAAGCAGCAAGCGCGTTACGCCGTGGGTCGATGTTTGATGTTATGGAGCAGCAACGATGTTACGCAGCAGGGCAGTCGCCCTAAAACAAAGTTAGGCATCACAAAGTACAGCATCGTGACCAACAGCAACGATTCCGTCACACTGCGCCTCATGACTGAGCATGACCTTGCGATGCTCTATGAGTGGCTAAATCGATCTCATATCGTCGAGTGGTGGGGCGGAGAAGAAGCACGCCCGACACTTGCTGACGTACAGGAACAGTACTTGCCAAGCGTTTTAGCGCAAGAGTCCGTCACTCCATACATTGCAATGCTGAATGGAGAGCCGATTGGGTATGCCCAGTCGTACGTTGCTCTTGGAAGCGGGGACGGATGGTGGGAAGAAGAAACCGATCCAGGAGTACGCGGAATAGACCAGTTACTGGCGAATGCATCACAACTGGGCAAAGGCTTGGGAACCAAGCTGGTTCGAGCTCTGGTTGAGTTGCTGTTCAATGATCCCGAGGTCACCAAGATCCAAACGGACCCGTCGCCGAGCAACTTGCGAGCGATCCGATGCTACGAGAAAGCGGGGTTTGAGAGGCAAGGTACCGTAACCACCCCAGATGGTCCAGCCGTGTACATGGTTCAAACACGCCAGGCATTCGAGCGAACACGCAGTGATGCCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35906","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Corvallis","NCBI_taxonomy_id":"593905"}}}},"ARO_accession":"3002578","ARO_id":"38978","ARO_name":"AAC(6')-Ib7","CARD_short_name":"AAC(6')-Ib7","ARO_description":"AAC(6')-Ib7 is a plasmid-encoded aminoglycoside acetyltransferase in E. cloacae and C. freundii.","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"A category of aminoglycoside N-acetyltransferase enzymes with modification regiospecificity based at the 6'-amino group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics through acetylation of the 6-amino group of the compound.","category_aro_class_name":"AMR Gene Family"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2119":{"model_id":"2119","model_name":"LRA-10","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"4657":{"protein_sequence":{"accession":"ACH58999.1","sequence":"MAIAILSSCFAPLASRAADDSARIRAIVDQAIRPVMAEHDVPGMAVAVTVDGQPFVFNYGVASRESNTPVSDATLFELGSISKTFAATLASYAQVTGKLSLDDHPGKYMPQLKGSAIDKATLLNLGTYTAGGLPLQFPDDVSDQQMASYFQHWKPKAAPGVQRTYSNPSLGLFGHLTSLALKSRFTDALETNVLTQMGMKSTYVHVPQSAMANYAWGYDQANKPGRMNPGVLADGIYGIRSTAADMIRYVQANIAPGKLETPLRRAVEGTHVGYFKVGGMVQGLGWEQYPYPVSLQQLQAGNSTTMAWEANPAQKLTPPSVPSGATLFNKTGSTSRFGAYVAFVPEKKIGIVILANKNIPGPDRIKAAHAILEQL"},"dna_sequence":{"accession":"EU408357.1","fmin":"52","fmax":"1180","strand":"-","sequence":"ATGGCAATCGCCATCCTGTCTTCCTGTTTCGCGCCGCTCGCCAGCCGGGCCGCCGACGACAGCGCCAGGATCCGCGCCATCGTCGACCAGGCGATACGCCCCGTCATGGCCGAACACGACGTGCCGGGCATGGCGGTCGCCGTGACGGTCGACGGCCAACCGTTCGTCTTCAACTATGGCGTCGCCTCGCGCGAGAGCAACACGCCCGTCAGCGACGCGACGCTGTTCGAGCTCGGCTCCATCAGCAAGACTTTTGCCGCCACGCTGGCCTCGTATGCGCAGGTGACCGGCAAGCTGTCGCTGGACGACCATCCCGGCAAGTACATGCCGCAGCTGAAGGGCAGCGCGATCGACAAGGCCACCCTGCTCAATCTGGGCACCTACACGGCGGGCGGACTGCCGCTGCAATTCCCGGACGACGTCTCGGACCAGCAGATGGCCAGCTACTTCCAGCACTGGAAACCGAAGGCCGCGCCCGGCGTACAACGGACCTATTCCAATCCCAGCCTCGGGCTGTTCGGACACCTGACCAGCCTTGCGCTGAAGAGCCGTTTTACCGACGCGCTGGAAACGAATGTCCTCACGCAGATGGGCATGAAGAGCACCTATGTCCACGTGCCACAAAGCGCCATGGCCAATTACGCCTGGGGATACGATCAAGCAAACAAGCCTGGCCGCATGAACCCCGGCGTCCTCGCCGACGGAATCTATGGCATCCGGTCGACAGCCGCCGACATGATCCGCTATGTGCAAGCCAACATCGCCCCGGGCAAGCTGGAAACGCCGTTGCGGCGCGCGGTGGAAGGCACCCATGTCGGCTACTTCAAGGTGGGCGGCATGGTGCAGGGACTCGGCTGGGAGCAATACCCTTACCCGGTCTCCCTGCAGCAGCTACAGGCCGGCAACTCCACCACCATGGCATGGGAAGCCAACCCCGCGCAGAAACTCACGCCGCCGAGCGTACCGTCCGGCGCGACCCTGTTCAACAAGACCGGCTCCACCAGCCGCTTCGGCGCCTACGTGGCGTTCGTGCCGGAGAAGAAAATCGGCATCGTCATCCTCGCGAACAAGAACATCCCGGGTCCGGACCGTATCAAGGCGGCCCATGCGATCCTGGAACAACTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39682","NCBI_taxonomy_name":"uncultured bacterium BLR10","NCBI_taxonomy_id":"506513"}}}},"ARO_accession":"3002489","ARO_id":"38889","ARO_name":"LRA-10","CARD_short_name":"LRA-10","ARO_description":"LRA-10 is a beta-lactamase isolated from soil samples in Alaska.","ARO_category":{"41395":{"category_aro_accession":"3004231","category_aro_cvterm_id":"41395","category_aro_name":"class C LRA beta-lactamase","category_aro_description":"Beta-lactamases that are part of the LRA gene family and are classified as Class C beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2121":{"model_id":"2121","model_name":"LRA-7","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"3698":{"protein_sequence":{"accession":"ACH58998.1","sequence":"MRSKFLLATALVLSTAFTADAADAPKRLPVNITNQDWLKPFPGFKIVGNMYYVGTYDLGCYLIDTGAGLILVNTGIMGSYPLMKASIESLGFKTSDIKIITATHGHSDHVADMASFKKDAPSAVVYMSERDVESLESGGNFDYRRPAPEGRGGLVYDPIHVDVKTKPGDHIKLGNVDMTVLQAYGHTPGATSFQFQQTDAGKTYNVMIVNMNGINAGVKLLGSPKYPTIVEDFKNTIDMQATYKPDIWVSSHAGQFNLHQVYKPGDAYNPARFGDQAAYQQKIATAKANYEKQLAEERAAAK"},"dna_sequence":{"accession":"EU408356.1","fmin":"7570","fmax":"8479","strand":"+","sequence":"ATGCGGTCGAAATTCCTGCTTGCTACTGCGCTCGTTCTGTCGACGGCCTTCACCGCCGATGCAGCAGACGCGCCGAAGCGCCTTCCCGTCAACATCACCAACCAGGATTGGCTGAAGCCGTTTCCGGGATTCAAGATCGTCGGCAACATGTATTATGTCGGCACCTACGATCTCGGCTGCTACCTGATCGATACCGGCGCAGGGCTGATCCTCGTCAACACCGGCATCATGGGTTCCTACCCGCTGATGAAGGCGAGCATCGAATCCCTCGGCTTCAAGACCAGCGACATCAAGATTATCACCGCGACGCATGGCCATTCCGACCATGTCGCCGATATGGCGTCGTTCAAGAAGGACGCGCCGAGCGCCGTCGTCTATATGAGCGAGCGCGATGTGGAGAGCCTCGAAAGCGGCGGTAATTTCGATTACCGCCGCCCCGCACCGGAAGGCCGTGGCGGTCTCGTCTATGATCCCATCCATGTCGATGTGAAGACGAAGCCCGGCGATCACATCAAGCTCGGCAATGTCGATATGACCGTGCTGCAGGCCTATGGCCACACGCCGGGCGCGACGAGCTTCCAATTCCAGCAGACGGATGCGGGCAAGACCTACAATGTGATGATCGTGAACATGAACGGCATCAACGCCGGCGTTAAGCTGCTGGGTTCGCCGAAATATCCGACCATCGTCGAGGACTTCAAGAACACCATCGACATGCAGGCGACGTACAAGCCCGACATCTGGGTGTCGTCGCATGCGGGGCAGTTCAACCTGCATCAGGTCTATAAGCCGGGCGATGCGTACAATCCGGCCCGCTTCGGCGATCAGGCCGCCTATCAGCAGAAGATCGCGACCGCGAAGGCGAATTACGAGAAGCAGCTCGCCGAGGAACGCGCGGCGGCGAAATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39087","NCBI_taxonomy_name":"uncultured bacterium BLR7","NCBI_taxonomy_id":"506523"}}}},"ARO_accession":"3002486","ARO_id":"38886","ARO_name":"LRA-7","CARD_short_name":"LRA-7","ARO_description":"LRA-7 is a beta-lactamase isolated from soil samples in Alaska.","ARO_category":{"41390":{"category_aro_accession":"3004226","category_aro_cvterm_id":"41390","category_aro_name":"subclass B3 LRA beta-lactamase","category_aro_description":"Beta-lactamases that are part of the LRA gene family and are classified as B3 (metallo-) beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2123":{"model_id":"2123","model_name":"vgaC","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"5184":{"protein_sequence":{"accession":"CBL58195.1","sequence":"MVLLEAKNIKHYIKDRLLLKIDELKIEHNDRIGLVGVNGSGKTTLLNILAEKFIPDEGTITPYAQSEILPQLKKTDAAKSGGEITQEYIQQTLNSAPALLLADEPTTNLDTDHIEWVEKKLKRWQGAFVLVSHDREFLDALCSVIWELEDGEITEYKGNYSDYLKQKEVEKQQQQSTYEKYEKEKKQLEKAIQLKEEKAQRATKKPKNLSASERRIKGSKPYFAKKQKKLHKTAGALETRVEKLEKVEKIKDQPPIKMDLPNERNLKNRVIIRVEDLEGLVPKQLLWKKATFQIYGGDKLAIIGPNGSGKTTLVKKIITQENGVTISPSVKIGYFSQNLMTLDVNKSILENVQNSSKQEESLIRTVLARMHFFDEDVYKPVHVLSGGERVKVALTKLLVSDINTLVLDEPTNYLDTEALKALENLLNEYTGSIIFVSHDRTFTENIATRILEIRNKKIEIFDGTYQQFKNRSTKKERDFQQEEQLLLDTKISEVLSRLSMEPSQALEKEFQNLLKEKSKLKE"},"dna_sequence":{"accession":"FN806792.1","fmin":"100","fmax":"1669","strand":"+","sequence":"ATGGTTTTACTAGAGGCCAAAAATATAAAACACTACATCAAAGATCGCTTATTATTAAAGATTGATGAATTAAAAATTGAACATAATGACCGGATTGGCTTGGTAGGTGTAAATGGAAGTGGAAAAACAACTTTGTTAAATATCCTTGCTGAAAAATTTATTCCTGACGAGGGGACAATCACGCCGTATGCCCAGAGTGAGATATTGCCACAGTTAAAAAAGACCGATGCGGCAAAAAGTGGGGGCGAAATTACTCAGGAATATATTCAACAAACGTTAAATAGTGCTCCAGCTCTTTTATTAGCAGACGAACCGACGACCAATCTAGATACAGATCATATCGAATGGGTTGAAAAAAAATTGAAGCGTTGGCAGGGGGCCTTCGTTCTTGTTTCCCATGACCGAGAATTTTTAGACGCTCTGTGTTCTGTTATTTGGGAACTGGAAGATGGTGAAATAACGGAGTACAAGGGCAATTATAGTGATTATCTCAAGCAAAAAGAAGTAGAAAAGCAACAACAACAATCCACATATGAAAAATATGAAAAAGAAAAAAAACAGCTGGAGAAAGCAATCCAACTAAAAGAAGAAAAGGCCCAACGAGCAACTAAAAAGCCTAAAAATTTATCTGCTTCTGAGAGACGAATAAAGGGATCGAAGCCTTACTTCGCAAAAAAACAGAAAAAACTGCATAAAACTGCAGGTGCTCTTGAAACAAGAGTAGAGAAATTAGAAAAAGTAGAGAAAATAAAAGATCAGCCACCTATTAAAATGGATTTACCAAATGAAAGAAATCTTAAAAATCGTGTGATTATTCGGGTTGAGGATCTAGAAGGACTTGTTCCCAAGCAGTTACTTTGGAAAAAGGCAACTTTTCAAATTTATGGTGGGGACAAACTAGCTATCATAGGACCCAATGGTAGTGGAAAAACAACTTTAGTTAAAAAAATAATAACTCAAGAAAATGGTGTCACTATTTCTCCGTCTGTTAAGATCGGTTACTTTAGTCAGAATCTAATGACGCTAGATGTAAACAAATCTATTTTAGAGAACGTTCAAAATTCTTCGAAACAAGAAGAATCACTGATTCGAACGGTACTAGCTAGAATGCATTTCTTTGATGAAGATGTATACAAACCTGTGCATGTGCTAAGCGGTGGTGAAAGAGTAAAAGTTGCACTGACAAAACTATTAGTGAGCGATATCAATACACTCGTTTTAGATGAACCAACGAATTACTTGGATACGGAAGCACTCAAAGCATTAGAAAACCTCTTGAATGAATATACGGGAAGTATTATTTTTGTTTCTCATGATCGTACCTTTACCGAAAATATCGCTACTCGAATTTTAGAAATACGTAATAAAAAAATTGAGATATTTGATGGGACGTACCAACAATTCAAAAATAGATCTACTAAAAAGGAACGGGATTTTCAGCAAGAAGAGCAGTTACTACTAGATACAAAGATATCCGAAGTACTTAGCCGCTTAAGTATGGAACCTTCCCAAGCTTTGGAAAAAGAATTTCAAAACCTCCTAAAAGAAAAAAGTAAGTTAAAGGAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35508","NCBI_taxonomy_name":"Staphylococcus aureus","NCBI_taxonomy_id":"1280"}}}},"ARO_accession":"3002831","ARO_id":"39265","ARO_name":"vgaC","CARD_short_name":"vgaC","ARO_description":"vgaC is an ABC-F subfamily protein expressed in staphylococci that confers resistance to streptogramin A antibiotics and related compounds. It is associated with plasmid DNA.","ARO_category":{"36252":{"category_aro_accession":"3000113","category_aro_cvterm_id":"36252","category_aro_name":"vga-type ABC-F protein","category_aro_description":"Vga-type plasmid-borne ABC-F proteins, expressed in staphylococci that confer resistance to streptogramin A antibiotics through ribosomal protection.","category_aro_class_name":"AMR Gene Family"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"virginiamycin M1","category_aro_description":"Virginiamycin M1 is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37015":{"category_aro_accession":"3000671","category_aro_cvterm_id":"37015","category_aro_name":"tiamulin","category_aro_description":"Tiamulin is a pleuromutilin derivative currently used in veterinary medicine. It binds to the 23 rRNA of the 50S ribosomal subunit to inhibit protein translation.","category_aro_class_name":"Antibiotic"},"37714":{"category_aro_accession":"3001315","category_aro_cvterm_id":"37714","category_aro_name":"valnemulin","category_aro_description":"Two semi-synthetic pleuromutilin derivatives, tiamulin and valnemulin, have been developed as antibiotics for veterinary use.","category_aro_class_name":"Antibiotic"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35952":{"category_aro_accession":"0000034","category_aro_cvterm_id":"35952","category_aro_name":"streptogramin A antibiotic","category_aro_description":"Streptogramin A antibiotics are cyclic polyketide peptide hybrids that bind to the ribosomal peptidyl transfer centre. Structural variation arises from substituting a proline for its desaturated derivative and by its substitution for Ala or Cys. Used alone, streptogramin A antibiotics are bacteriostatic, but is bactericidal when used with streptogramin B antibiotics.","category_aro_class_name":"Drug Class"},"37014":{"category_aro_accession":"3000670","category_aro_cvterm_id":"37014","category_aro_name":"pleuromutilin antibiotic","category_aro_description":"Pleuromutilins are natural fungal products that target bacterial protein translation by binding the the 23S rRNA, blocking the ribosome P site at the 50S subunit. They are mostly used for agriculture and veterinary purposes.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2130":{"model_id":"2130","model_name":"opcM","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"980"}},"model_sequences":{"sequence":{"3687":{"protein_sequence":{"accession":"AAC43969.1","sequence":"MDNMHNTNGLMRFAKVAAASTLLATLLAACAVGPDYQRPDAVVPAAFKEAPTLAAGEQAGTWKTAEPSDGRTPRRMVKVFGDPVLDSLETQALAANQNLKAAAARVEEARAATRSARSQWFPQVGAGFGPTREGLSSASQFQPQGTGPTNATLWRAQGTVSYEADLFGRVGRNVEASRADQAQSEALFRSVQLALQADVAQNYFELRQLDSDQDLYHRTVELREQALKLVQRRFNEGDISELDVSRAKNELASAQADAVDVARRRAASEHALAILLGKAPADFAFKETPIVPVAVKIPPGLPSALLERRPDVSAAERAMAAANARIGLAKSAYFRSSISPGRSAISVDARQPVPVVEPYFLLGPFAGTALTLPLFDGGRRAAGVQQARAQYDEQGANYRQQVLVAFREVEDNLADLRLLDDQIRAQEAAVNASRRAATLSRSEYQEGEVAYLDVIDSERSVLQSQLQANQLTGAQAVSTVNLIRALGGGWGNAPAPTAVGDAASGKADVAAR"},"dna_sequence":{"accession":"U38944.1","fmin":"0","fmax":"1536","strand":"+","sequence":"ATGGACAACATGCACAACACGAACGGCCTGATGCGCTTCGCGAAGGTGGCGGCCGCGAGCACCCTGCTCGCGACGCTGCTCGCCGCGTGTGCGGTCGGCCCCGACTACCAGCGTCCCGACGCGGTGGTGCCCGCCGCGTTCAAGGAAGCGCCGACCCTCGCCGCCGGCGAGCAGGCCGGCACGTGGAAGACGGCCGAGCCGTCGGATGGCCGAACACCGCGGCGAATGGTGAAGGTGTTCGGCGACCCGGTGCTCGATTCGCTCGAGACGCAGGCGCTTGCCGCGAACCAGAACCTGAAGGCCGCGGCCGCGCGGGTCGAGGAAGCGCGGGCGGCGACGCGTTCGGCGCGCTCGCAATGGTTCCCGCAGGTCGGCGCCGGTTTCGGGCCGACGCGCGAGGGGCTGTCGTCGGCGTCGCAGTTCCAGCCGCAGGGCACCGGCCCGACCAACGCGACGCTGTGGCGCGCGCAGGGCACGGTGTCGTACGAAGCCGATCTGTTCGGCCGCGTCGGCCGCAACGTCGAGGCGTCGCGTGCCGATCAGGCGCAGAGCGAAGCGCTGTTCCGTTCGGTGCAGCTCGCGCTGCAGGCCGACGTCGCGCAGAACTACTTCGAACTGCGTCAGCTCGATTCGGACCAGGACCTGTACCACCGCACGGTCGAGTTGCGCGAGCAGGCACTGAAGCTCGTGCAGCGCCGCTTCAACGAAGGCGACATCAGCGAGCTCGACGTGTCGCGCGCGAAGAACGAACTGGCGAGCGCGCAGGCCGATGCGGTCGACGTCGCGCGCCGGCGCGCGGCGTCCGAGCATGCGCTCGCCATCCTGCTCGGCAAGGCGCCCGCGGATTTCGCGTTCAAGGAAACGCCGATCGTGCCGGTCGCGGTGAAGATTCCGCCGGGCCTGCCGTCCGCGCTGCTCGAACGCCGCCCGGACGTGTCGGCGGCCGAACGCGCGATGGCGGCCGCGAACGCGCGGATCGGGCTCGCGAAGTCGGCGTACTTCCGAAGCTCGATATCACCGGGTCGTTCGGCTATAAGCGTCGACGCTCGGCAACCTGTTCCTGTGGTCGAGCCGTACTTCCTGCTCGGGCCGTTCGCCGGTACCGCGCTGACGTTGCCGCTGTTCGACGGCGGACGGCGGGCGGCCGGCGTGCAGCAGGCGCGCGCGCAGTACGACGAGCAGGGCGCGAACTACCGGCAGCAGGTGCTCGTCGCGTTCCGCGAGGTCGAGGACAATCTCGCCGATCTGCGTTTGCTCGATGATCAGATCCGCGCGCAGGAGGCGGCCGTCAATGCGTCGCGCCGGGCGGCGACGTTGTCGCGCAGCGAATATCAGGAAGGCGAGGTCGCATATCTCGACGTGATCGACAGCGAGCGCTCGGTGCTGCAGTCGCAGTTGCAGGCGAACCAGTTGACGGGTGCGCAGGCGGTGTCGACCGTCAATCTGATCCGTGCGCTGGGCGGCGGGTGGGGGAATGCGCCGGCGCCGACGGCGGTGGGTGATGCGGCGTCTGGCAAGGCTGACGTAGCTGCGCGG","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36822","NCBI_taxonomy_name":"Burkholderia cepacia","NCBI_taxonomy_id":"292"}}}},"ARO_accession":"3003037","ARO_id":"39471","ARO_name":"opcM","CARD_short_name":"opcM","ARO_description":"OpcM is an outer membrane factor protein found in Burkholderia cepacia. It is part of the CeoAB-OpcM complex.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2134":{"model_id":"2134","model_name":"CMY-36","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"3695":{"protein_sequence":{"accession":"ABY58049.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDCIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPENEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"EU331426.1","fmin":"2374","fmax":"3520","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGACTGTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCTTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCAGAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCACAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002047","ARO_id":"38447","ARO_name":"CMY-36","CARD_short_name":"CMY-36","ARO_description":"CMY-36 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2135":{"model_id":"2135","model_name":"ACT-33","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"3684":{"protein_sequence":{"accession":"AIT76087.1","sequence":"MMKKSLCCALLLGISCSALATPVSEKQLAEVVANTVTPLMKAQSVPGMAVAVIYQGKPHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMPYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPENVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVVEGSDSKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANTSYPNPARVEAAYHILDALQ"},"dna_sequence":{"accession":"KM087834.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCTCTTTGCTGCGCCCTGCTGCTCGGCATCTCTTGCTCTGCTCTCGCCACGCCAGTGTCAGAAAAACAGCTGGCGGAGGTGGTAGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCTGTTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGAAAACCGCACTATTACACGTTTGGCAAGGCCGATATCGCGGCGAATAAACCCGTTACGCCTCAGACCCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGCGTTTTAGGTGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTGACGGGCAAGCAGTGGCAGGGTATTCGTATGCTGGATCTCGCCACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTCAAACCTTCTGGCATGCCCTATGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTGCCGAAAGCGGAAGAGGCACATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGTATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCGGAGAACGTTGCTGATGCCTCACTTAAGCAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGGTCGAGGGCAGCGACAGTAAGGTAGCGCTGGCGCCGTTGCCCGTGGCAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGCTCTACTGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATACAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCGACGCGCTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3001853","ARO_id":"38253","ARO_name":"ACT-33","CARD_short_name":"ACT-33","ARO_description":"ACT-33 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2156":{"model_id":"2156","model_name":"NDM-14","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"3685":{"protein_sequence":{"accession":"AJP18054.1","sequence":"MELPNIMHPVAKLSTALAAALMLSGCMPGEIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMGALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR"},"dna_sequence":{"accession":"KM210086.1","fmin":"9067","fmax":"9880","strand":"+","sequence":"ATGGAATTGCCCAATATTATGCACCCGGTCGCGAAGCTGAGCACCGCATTAGCCGCTGCATTGATGCTGAGCGGGTGCATGCCCGGTGAAATCCGCCCGACGATTGGCCAGCAAATGGAAACTGGCGACCAACGGTTTGGCGATCTGGTTTTCCGCCAGCTCGCACCGAATGTCTGGCAGCACACTTCCTATCTCGACATGCCGGGTTTCGGGGCAGTCGCTTCCAACGGTTTGATCGTCAGGGATGGCGGCCGCGTGCTGGTGGTCGATACCGCCTGGACCGATGACCAGACCGCCCAGATCCTCAACTGGATCAAGCAGGAGATCAACCTGCCGGTCGCGCTGGCGGTGGTGACTCACGCGCATCAGGACAAGATGGGCGGTATGGGCGCGCTGCATGCGGCGGGGATTGCGACTTATGCCAATGCGTTGTCGAACCAGCTTGCCCCGCAAGAGGGGATGGTTGCGGCGCAACACAGCCTGACTTTCGCCGCCAATGGCTGGGTCGAACCAGCAACCGCGCCCAACTTTGGCCCGCTCAAGGTATTTTACCCCGGCCCCGGCCACACCAGTGACAATATCACCGTTGGGATCGACGGCACCGACATCGCTTTTGGTGGCTGCCTGATCAAGGACAGCAAGGCCAAGTCGCTCGGCAATCTCGGTGATGCCGACACTGAGCACTACGCCGCGTCAGCGCGCGCGTTTGGTGCGGCGTTCCCCAAGGCCAGCATGATCGTGATGAGCCATTCCGCCCCCGATAGCCGCGCCGCAATCACTCATACGGCCCGCATGGCCGACAAGCTGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36948","NCBI_taxonomy_name":"Acinetobacter lwoffii","NCBI_taxonomy_id":"28090"}}}},"ARO_accession":"3003183","ARO_id":"39760","ARO_name":"NDM-14","CARD_short_name":"NDM-14","ARO_description":"NDM-14 is a beta-lactamase found in Acinetobacter lwoffii.","ARO_category":{"36196":{"category_aro_accession":"3000057","category_aro_cvterm_id":"36196","category_aro_name":"NDM beta-lactamase","category_aro_description":"NDM beta-lactamases or New Delhi metallo-beta-lactamases are class B beta-lactamases that confer resistance to a broad range of antibiotics including carbapenems, cephalosporins and penicillins.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3451":{"model_id":"3451","model_name":"OXA-287","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"520"}},"model_sequences":{"sequence":{"5647":{"protein_sequence":{"accession":"WP_032865068.1","sequence":"MSKKLKCLALFTAVFFAIPMTACQSFSQQKQQFSTQKNEQQQISSLFQSAQTSGVLMIYDGKKIQSYGNDLDRAEQRYIPASTFKMLNALIGIQHHKTTPDEVFKWDGKKRAFSSWEKDLTLAEAMQASAVPVYQELARRIGLELMTREVKRVGYGNKNIGTQVDNFWLVGPLKITPIEEVRFAYALAKQKLPFDQPTQQQVKAMLLVDQIQGTKIYAKSGWGMDVSPQVGWWTGWIEQPNGKITAFSLNMQMSQPEHADARKVIVYQALQELGLLAH"},"dna_sequence":{"accession":"NG_050609.1","fmin":"100","fmax":"937","strand":"+","sequence":"ATGTCGAAAAAATTAAAATGTCTGGCCCTTTTTACCGCTGTCTTTTTTGCAATTCCCATGACTGCTTGTCAAAGTTTTAGCCAACAAAAGCAACAGTTCTCGACACAAAAAAATGAGCAGCAACAGATCTCAAGTTTATTCCAGAGTGCCCAAACCAGTGGTGTTTTGATGATTTATGATGGCAAGAAAATTCAAAGCTATGGCAATGATCTTGATCGTGCAGAACAGCGCTATATCCCTGCTTCAACCTTTAAAATGTTAAACGCCTTGATCGGAATACAGCATCATAAGACCACACCAGATGAAGTATTTAAATGGGATGGCAAAAAGCGGGCATTTAGTAGTTGGGAAAAAGATTTAACCTTAGCTGAGGCGATGCAGGCATCAGCGGTACCTGTCTATCAAGAATTGGCAAGACGTATTGGTTTGGAACTGATGACCCGTGAAGTAAAGCGCGTGGGTTATGGTAATAAAAATATCGGGACACAAGTCGATAATTTCTGGTTAGTTGGCCCCTTAAAAATCACTCCCATAGAAGAAGTTCGTTTTGCCTATGCGCTGGCAAAACAGAAATTGCCATTTGACCAGCCGACACAGCAACAAGTCAAAGCGATGTTATTGGTGGATCAGATTCAGGGAACCAAAATCTATGCCAAAAGTGGTTGGGGTATGGATGTCAGCCCGCAAGTGGGATGGTGGACAGGCTGGATTGAACAGCCAAATGGCAAGATCACTGCCTTCTCACTGAATATGCAAATGAGTCAGCCTGAACATGCAGATGCACGTAAAGTGATTGTGTATCAAGCCTTGCAAGAGTTGGGATTGTTAGCCCATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42812","NCBI_taxonomy_name":"Acinetobacter sp. CIP 56.2","NCBI_taxonomy_id":"1144672"}}}},"ARO_accession":"3001742","ARO_id":"38142","ARO_name":"OXA-287","CARD_short_name":"OXA-287","ARO_description":"OXA-287 is a beta-lactamase found in Acinetobacter spp.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46503":{"category_aro_accession":"3007714","category_aro_cvterm_id":"46503","category_aro_name":"OXA-286-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-286.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"29":{"model_id":"29","model_name":"Escherichia coli folP with mutation conferring resistance to sulfonamides","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"2281":"P64S","2282":"P64A","2283":"P64H","2114":"P64R","2115":"P64L"},"Curated-R":{"2281":"P64S","2282":"P64A","2283":"P64H","2114":"P64R","2115":"P64L"},"experimental":{"2281":"P64S","2282":"P64A","2283":"P64H","2114":"P64R","2115":"P64L"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"5412":{"protein_sequence":{"accession":"AAC76209.2","sequence":"MKLFAQGTSLDLSHPHVMGILNVTPDSFSDGGTHNSLIDAVKHANLMINAGATIIDVGGESTRPGAAEVSVEEELQRVIPVVEAIAQRFEVWISVDTSKPEVIRESAKVGAHIINDIRSLSEPGALEAAAETGLPVCLMHMQGNPKTMQEAPKYDDVFAEVNRYFIEQIARCEQAGIAKEKLLLDPGFGFGKNLSHNYSLLARLAEFHHFNLPLLVGMSRKSMIGQLLNVGPSERLSGSLACAVIAAMQGAHIIRVHDVKETVEAMRVVEATLSAKENKRYE"},"dna_sequence":{"accession":"U00096.3","fmin":"3324062","fmax":"3324911","strand":"-","sequence":"ATGAAACTCTTTGCCCAGGGTACTTCACTGGACCTTAGCCATCCTCACGTAATGGGGATCCTCAACGTCACGCCTGATTCCTTTTCGGATGGTGGCACGCATAACTCGCTGATAGATGCGGTGAAACATGCGAATCTGATGATCAACGCTGGCGCGACGATCATTGACGTTGGTGGCGAGTCCACGCGCCCAGGGGCGGCGGAAGTTAGCGTTGAAGAAGAGTTGCAACGTGTTATTCCTGTGGTTGAGGCAATTGCTCAACGCTTCGAAGTCTGGATCTCAGTCGATACATCCAAACCAGAAGTCATCCGTGAGTCAGCGAAAGTTGGCGCTCACATTATTAATGATATCCGCTCCCTTTCCGAACCTGGCGCTCTGGAGGCGGCTGCAGAAACCGGTTTACCGGTTTGTCTGATGCATATGCAGGGAAATCCAAAAACCATGCAGGAAGCTCCGAAGTATGACGATGTCTTTGCAGAAGTGAATCGCTACTTTATTGAGCAAATAGCACGTTGCGAGCAGGCGGGTATCGCAAAAGAGAAATTGTTGCTCGACCCCGGATTCGGTTTCGGTAAAAATCTCTCCCATAACTATTCATTACTGGCGCGCCTGGCTGAATTTCACCATTTCAACCTGCCGCTGTTGGTGGGTATGTCACGAAAATCGATGATTGGGCAGCTGCTGAACGTGGGGCCGTCCGAGCGCCTGAGCGGTAGTCTGGCCTGTGCGGTCATTGCCGCAATGCAAGGCGCGCACATCATTCGTGTTCATGACGTCAAAGAAACCGTAGAAGCGATGCGGGTGGTGGAAGCCACTCTGTCTGCAAAGGAAAACAAACGCTATGAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36849","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. MG1655","NCBI_taxonomy_id":"511145"}}}},"ARO_accession":"3003386","ARO_id":"39970","ARO_name":"Escherichia coli folP with mutation conferring resistance to sulfonamides","CARD_short_name":"Ecol_folP_SLF","ARO_description":"Point mutations in Escherichia coli dihydropteroate synthase folP prevent sulfonamide antibiotics from inhibiting its role in folate synthesis, thus conferring sulfonamide resistance.","ARO_category":{"39999":{"category_aro_accession":"3003415","category_aro_cvterm_id":"39999","category_aro_name":"sulfonamide resistant dihydropteroate synthase folP","category_aro_description":"Point mutations in dihydropteroate synthase folP prevent sulfonamide antibiotics from inhibiting its role in folate synthesis, thus conferring sulfonamide resistance.","category_aro_class_name":"AMR Gene Family"},"36463":{"category_aro_accession":"3000324","category_aro_cvterm_id":"36463","category_aro_name":"sulfadiazine","category_aro_description":"Sulfadiazine is a potent inhibitor of dihydropteroate synthase, interfering with the tetrahydrofolic biosynthesis pathway. Tetrahydrofolic acid is essential for folate synthesis, a precursor to many nucleotides and amino acids.","category_aro_class_name":"Antibiotic"},"36464":{"category_aro_accession":"3000325","category_aro_cvterm_id":"36464","category_aro_name":"sulfadimidine","category_aro_description":"Sulfadimidine is an alkaline sulfonamide antibiotic that inhibits dihydropteroate synthase, and enzyme in the tetrahydrofolic acid biosynthesis pathway. This interferes with the production of folate, which is a precursor to many amino acids and nucleotides.","category_aro_class_name":"Antibiotic"},"36466":{"category_aro_accession":"3000327","category_aro_cvterm_id":"36466","category_aro_name":"sulfadoxine","category_aro_description":"Sulfadoxine is an inhibitor of dihydropteroate synthase, interfering with the tetrahydrofolic biosynthesis pathway. Tetrahydrofolic acid is essential for folate synthesis, a precursor to many nucleotides and amino acids.","category_aro_class_name":"Antibiotic"},"36468":{"category_aro_accession":"3000329","category_aro_cvterm_id":"36468","category_aro_name":"sulfamethoxazole","category_aro_description":"Sulfamethoxazole is a sulfonamide antibiotic usually taken with trimethoprim, a diaminopyrimidine antibiotic. Sulfamethoxazole inhibits dihydropteroate synthase, essential to tetrahydrofolic acid biosynthesis. This pathway generates compounds used in the synthesis of many amino acids and nucleotides.","category_aro_class_name":"Antibiotic"},"36469":{"category_aro_accession":"3000330","category_aro_cvterm_id":"36469","category_aro_name":"sulfisoxazole","category_aro_description":"Sulfisoxazole is an inhibitor of dihydropteroate synthase, interfering with the tetrahydrofolic biosynthesis pathway. Tetrahydrofolic acid is essential for folate synthesis, a precursor to many nucleotides and amino acids.","category_aro_class_name":"Antibiotic"},"37027":{"category_aro_accession":"3000683","category_aro_cvterm_id":"37027","category_aro_name":"sulfacetamide","category_aro_description":"Sulfacetamide is a very soluable sulfonamide antibiotic previously used to treat urinary tract infections. Its relatively low activity and toxicity to those with Stevens-Johnson syndrome have reduced its use and availability.","category_aro_class_name":"Antibiotic"},"37028":{"category_aro_accession":"3000684","category_aro_cvterm_id":"37028","category_aro_name":"mafenide","category_aro_description":"Mafenide is a sulfonamide used topically for treating burns.","category_aro_class_name":"Antibiotic"},"37042":{"category_aro_accession":"3000698","category_aro_cvterm_id":"37042","category_aro_name":"sulfasalazine","category_aro_description":"Sulfasalazine is a derivative of the early sulfonamide sulfapyridine (salicylazosulfapyridine). It was developed to increase water solubility and is taken orally for ulcerative colitis.","category_aro_class_name":"Antibiotic"},"37043":{"category_aro_accession":"3000699","category_aro_cvterm_id":"37043","category_aro_name":"sulfamethizole","category_aro_description":"Sulfamethizole is a short-acting sulfonamide that inhibits dihydropteroate synthetase.","category_aro_class_name":"Antibiotic"},"36421":{"category_aro_accession":"3000282","category_aro_cvterm_id":"36421","category_aro_name":"sulfonamide antibiotic","category_aro_description":"Sulfonamides are broad spectrum, synthetic antibiotics that contain the sulfonamide group. Sulfonamides inhibit dihydropteroate synthase, which catalyzes the conversion of p-aminobenzoic acid to dihydropteroic acid as part of the tetrahydrofolic acid biosynthetic pathway. Tetrahydrofolic acid is essential for folate synthesis, a precursor of many nucleotides and amino acids. Many sulfamides are taken with trimethoprim, an inhibitor of dihydrofolate reductase, also disturbing the trihydrofolic acid synthesis pathway.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1994":{"model_id":"1994","model_name":"gimA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"626":{"protein_sequence":{"accession":"CAA11707.1","sequence":"MRRGDLHETYRLDYAPHMHDPAHIAMFSIAAHGHVNPSLEVIRELVARGHRVTYAIPPLFAEKVAETGAEPKLWNSTLPGPDADPDAWGTTPLDNVEPFLDDAIQALPQLIAAYEGDEPDLVLHDITSYPARVLAHRWGVPAVSLSPNLVAWEGYEEEVGRPTWEEPLKTERGRAYDARFRGWLKENGITEDPDPFVGRPDRSLVLIPKALQPHADRVDEKTHTFVGACQGDRAAEGDWRRPEGAEKVVLVSLGSSFTKRPAFYRACVEAFGALPGWHVVLQVGRHVDPAELGDVPENVEVRSWVPQLAILKQADLFVTHAGAGGSQEGLATATPIVAVPQAVDQFGNADMLQGLGVGRHLPTEEATAEALRAAGLALVEDPEVARRLKEIQAGMAREGGTRRAADLIEAELAAART"},"dna_sequence":{"accession":"AJ223970.1","fmin":"796","fmax":"2050","strand":"+","sequence":"GTGAGAAGAGGTGATTTGCACGAGACGTATCGTCTTGATTACGCTCCGCACATGCACGATCCCGCTCATATCGCGATGTTCTCCATCGCCGCGCACGGTCACGTGAACCCCAGCCTGGAAGTGATCCGGGAACTCGTCGCGCGAGGGCACCGGGTGACCTACGCGATCCCGCCGCTCTTCGCCGAGAAGGTCGCCGAGACGGGCGCCGAACCCAAGCTGTGGAACAGCACGCTGCCCGGCCCCGACGCCGACCCGGACGCGTGGGGGACCACACCGCTGGACAACGTCGAGCCGTTCCTCGACGACGCGATCCAGGCGCTCCCGCAGCTCATCGCGGCGTACGAGGGCGACGAGCCGGACCTGGTCCTGCACGACATCACCTCCTACCCGGCCCGCGTCCTCGCCCATCGCTGGGGCGTTCCCGCCGTCTCGCTCTCGCCGAACCTGGTCGCCTGGGAGGGGTACGAGGAGGAGGTCGGCCGGCCGACGTGGGAGGAGCCGCTGAAGACCGAGCGCGGCCGGGCGTACGACGCCCGCTTCCGTGGCTGGCTGAAGGAGAACGGGATCACCGAGGACCCCGACCCCTTCGTCGGCCGTCCCGACCGGTCGCTGGTCCTCATCCCGAAGGCGCTCCAGCCGCACGCCGACCGGGTCGACGAGAAGACGCACACCTTCGTCGGTGCCTGCCAGGGCGACCGCGCCGCCGAGGGCGACTGGCGGCGTCCGGAGGGCGCGGAGAAGGTCGTCCTCGTCTCGCTCGGGTCCTCGTTCACCAAGCGGCCGGCGTTCTACCGGGCGTGCGTCGAGGCGTTCGGCGCGCTGCCCGGCTGGCACGTGGTGCTCCAGGTCGGCCGGCACGTCGACCCCGCCGAGCTGGGCGACGTACCGGAGAACGTGGAGGTCCGCTCCTGGGTGCCGCAGCTGGCGATCCTGAAGCAGGCTGACCTGTTCGTCACGCACGCGGGCGCGGGCGGCAGCCAGGAGGGCCTCGCCACCGCCACGCCGATAGTGGCGGTACCGCAGGCGGTGGACCAGTTCGGCAACGCGGACATGCTCCAGGGGCTCGGCGTGGGCCGCCACCTGCCCACCGAGGAAGCCACCGCCGAGGCGCTGCGCGCCGCCGGGCTCGCCCTGGTCGAGGACCCGGAGGTGGCCCGGCGGCTGAAGGAGATCCAGGCCGGGATGGCCCGGGAGGGCGGCACCCGGCGGGCCGCCGACCTGATCGAGGCGGAGCTGGCGGCGGCGAGGACCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36864","NCBI_taxonomy_name":"Streptomyces ambofaciens","NCBI_taxonomy_id":"1889"}}}},"ARO_accession":"3000463","ARO_id":"36602","ARO_name":"gimA","CARD_short_name":"gimA","ARO_description":"A macrolide glycosyltransferase encoded by the gimA gene in Streptomyces ambofaciens, a natural producer of the macrolide antibiotic spiramycin. Chalcomycin, methymycin, tylosin, pikromycin, rosaramicin, oleandomycin, josamycin, and carbomycin are preferred substrates of gimA glycosyltransferase, while erythromycin and spiramycin have notably low binding affinities. GimA may be able to inactivate spiramycin precursors. Described by Gourmelen et al. 1998.","ARO_category":{"41400":{"category_aro_accession":"3004236","category_aro_cvterm_id":"41400","category_aro_name":"gimA family macrolide glycosyltransferase","category_aro_description":"This family of macrolide glycosyltransferases derive from gimA, which was discovered in Streptomyces ambofaciens.","category_aro_class_name":"AMR Gene Family"},"36284":{"category_aro_accession":"3000145","category_aro_cvterm_id":"36284","category_aro_name":"tylosin","category_aro_description":"Tylosin is a 16-membered macrolide, naturally produced by Streptomyces fradiae. It interacts with the bacterial ribosome 50S subunit to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"37247":{"category_aro_accession":"3000867","category_aro_cvterm_id":"37247","category_aro_name":"oleandomycin","category_aro_description":"Oleandomycin is a 14-membered macrolide produced by Streptomyces antibioticus. It is ssimilar to erythromycin, and contains a desosamine amino sugar and an oleandrose sugar. It targets the 50S ribosomal subunit to prevent protein synthesis.","category_aro_class_name":"Antibiotic"},"37621":{"category_aro_accession":"3001222","category_aro_cvterm_id":"37621","category_aro_name":"chalcomycin","category_aro_description":"Produced by Streptomyces bikiniensis.","category_aro_class_name":"Antibiotic"},"37631":{"category_aro_accession":"3001232","category_aro_cvterm_id":"37631","category_aro_name":"methymycin","category_aro_description":"Produced by Streptomyces venezuelae ATCC 15439.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2003":{"model_id":"2003","model_name":"pmrA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"5431":{"protein_sequence":{"accession":"AAK99679.1","sequence":"MTEINWKDNLRIAWFGNFLTGASISLVVPFMPIFVENLGVGSQQVAFYAGLAISVSAISAALFSPIWGILADKYGRKPMMIRAGLAMTITMGGLAFVPNIYWLIFLRLLNGVFAGFVPNATALIASQVPKEKSGSALGTLSTGVVAGTLTGPFIGGFIAELFGIRTVFLLVGSFLFLAAILTICFIKEDFQPVAKEKAIPTKELFTSVKYPYLLLNLFLTSFVIQFSAQSIGPILALYVRDLGQTENLLFVSGLIVSSMGFSSMMSAGVMGKLGDKVGNHRLLVVAQFYSVIIYLLCANASSPLQLGLYRFLFGLGTGALIPGVNALLSKMTPKAGISRVFAFNQVFFYLGGVVGPMAGSAVAGQFGYHAVFYATSLCVAFSCLFNLIQFRTLLKVKEI"},"dna_sequence":{"accession":"AE007317.1","fmin":"866210","fmax":"867410","strand":"+","sequence":"ATGACAGAGATTAACTGGAAGGATAATCTGCGTATTGCCTGGTTTGGTAATTTTCTGACAGGAGCCAGTATTTCTTTGGTTGTACCTTTTATGCCCATCTTCGTGGAAAATCTAGGTGTAGGGAGTCAGCAAGTCGCTTTTTATGCAGGCTTAGCAATTTCTGTCTCTGCTATTTCCGCGGCGCTCTTTTCTCCTATTTGGGGTATTCTTGCTGACAAATACGGCCGAAAACCCATGATGATTCGGGCAGGTCTTGCTATGACTATCACTATGGGAGGCTTGGCCTTTGTCCCAAATATCTATTGGTTAATCTTTCTTCGTTTACTAAACGGTGTATTTGCAGGTTTTGTTCCTAATGCAACGGCACTGATAGCCAGTCAGGTTCCAAAGGAGAAATCAGGCTCTGCCTTAGGTACTTTGTCTACAGGCGTAGTTGCAGGTACTCTAACCGGTCCCTTTATTGGTGGCTTTATCGCAGAATTATTTGGCATTCGTACAGTTTTCTTACTGGTTGGTAGTTTTCTATTTTTAGCTGCTATTTTGACTATTTGCTTTATCAAGGAAGATTTTCAACCAGTAGCCAAGGAAAAGGCTATTCCAACAAAGGAATTATTTACCTCGGTTAAATATCCCTATCTTTTGCTCAATCTCTTTTTAACCAGTTTTGTCATCCAATTTTCAGCTCAATCGATCGGCCCTATTTTGGCTCTTTATGTACGCGACTTAGGGCAGACAGAGAATCTTCTTTTTGTCTCTGGTTTGATTGTGTCCAGTATGGGCTTTTCCAGTATGATGAGTGCAGGAGTCATGGGCAAGCTAGGTGACAAGGTGGGCAATCATCGTCTCTTGGTTGTCGCCCAGTTTTATTCAGTCATCATCTATCTCCTCTGTGCCAATGCCTCTAGCCCCCTTCAACTAGGACTCTATCGTTTCCTCTTTGGCTTGGGAACCGGTGCCTTGATTCCAGGGGTTAATGCCCTACTCAGCAAAATGACTCCCAAAGCCGGCATTTCGAGGGTCTTTGCCTTCAATCAGGTATTCTTTTATCTGGGAGGTGTTGTTGGTCCCATGGCAGGTTCTGCAGTAGCAGGTCAATTTGGCTACCATGCTGTCTTTTATGCGACAAGCCTTTGTGTTGCCTTTAGTTGTCTCTTTAACCTGATTCAATTTCGAACATTATTAAAAGTAAAGGAAATCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39596","NCBI_taxonomy_name":"Streptococcus pneumoniae R6","NCBI_taxonomy_id":"171101"}}}},"ARO_accession":"3000822","ARO_id":"37202","ARO_name":"pmrA","CARD_short_name":"pmrA","ARO_description":"PmrA is a MFS-type efflux pump expressed in Streptococcus pneumoniae that confers low-level resistance to norfloxacin, ciprofloxacin, and acriflavine.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2046":{"model_id":"2046","model_name":"tet(33)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"4246":{"protein_sequence":{"accession":"CAD12227.2","sequence":"MSSLTSARGSLATVLITASLDAAGMGLVMPILPALLHEAGVTADAVPLNVGVLIALYAVMQFIFAPVLGTLSDRFGRRRVLLVSLAGATVDYLVLATTSALSVFYIARAVAGITGATNAVTATVIADITPPHQRAKRFGLLSACYGGGMIAGPAMGGLFGAISPHLPFLLAALLSASNLALTFILLRETRPDSPARSASLAQHRGRPGLSAVPGITFLLIAFGLVQFIGQAPGATWVLFTEHRLDWSPVEVGISLSVFGIVQVLVQALLTGRIVEWIGEAKTVIIGCITDALGLVGLAIVTDAFSMAPILAALGIGGIGLPALQTLLSQRVDEQHQGRLQGVLASINSVTSIFGPVAFTTIFALTYINADGFLWLCAAALYVPCVILIMRGTAASPKFGSWASGDSM"},"dna_sequence":{"accession":"AJ420072.1","fmin":"22939","fmax":"24163","strand":"+","sequence":"GTGTCATCTCTCACTTCCGCTCGTGGCTCGTTGGCCACGGTCCTCATCACGGCTAGCCTCGACGCCGCCGGCATGGGCCTGGTGATGCCGATTCTTCCCGCACTGCTACACGAGGCAGGGGTCACCGCTGATGCGGTTCCGCTGAACGTCGGAGTGCTGATCGCGCTCTACGCGGTAATGCAGTTCATCTTTGCCCCCGTACTGGGAACGCTGTCGGACCGATTCGGCCGCCGCCGGGTGCTGCTTGTTTCCCTGGCCGGTGCGACCGTCGACTATCTCGTGCTCGCCACGACGTCCGCTCTGTCGGTGTTCTATATCGCCCGCGCAGTGGCTGGGATAACCGGAGCGACCAATGCGGTCACCGCCACCGTGATCGCCGACATCACGCCACCCCACCAGCGCGCCAAGCGTTTCGGTTTACTCAGTGCCTGCTATGGCGGCGGAATGATCGCGGGGCCAGCCATGGGTGGACTGTTCGGTGCCATCTCGCCACATCTGCCGTTTTTGCTCGCTGCTCTTCTCTCAGCGAGCAATCTGGCACTCACCTTTATCCTGTTACGCGAGACCCGTCCTGATTCCCCTGCGCGCTCTGCGTCGCTCGCTCAGCATCGTGGTCGCCCCGGCCTCAGCGCGGTGCCTGGGATTACCTTCCTATTAATCGCATTCGGCCTTGTTCAATTCATTGGGCAGGCTCCAGGTGCGACCTGGGTGCTGTTTACTGAACACCGCCTCGACTGGAGTCCCGTCGAAGTTGGAATCTCCCTGTCCGTTTTCGGGATCGTACAGGTTCTCGTGCAGGCCCTCCTTACTGGCCGCATCGTGGAGTGGATCGGTGAGGCAAAAACAGTCATCATCGGGTGTATTACCGACGCCTTGGGTCTCGTAGGCCTGGCGATTGTCACTGACGCATTTTCCATGGCACCTATCTTGGCGGCACTGGGGATCGGTGGCATCGGCCTCCCCGCTCTGCAAACCCTTCTCTCCCAGCGCGTCGATGAACAGCACCAAGGGCGCCTCCAGGGTGTGCTCGCCAGCATCAACAGCGTCACATCGATCTTCGGACCGGTCGCTTTCACAACGATCTTCGCGCTCACTTACATCAACGCCGACGGCTTCCTCTGGCTCTGCGCCGCAGCACTCTACGTGCCCTGCGTGATTCTCATCATGCGTGGTACAGCAGCGTCCCCGAAGTTCGGCTCTTGGGCGAGCGGCGACTCGATGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36777","NCBI_taxonomy_name":"Corynebacterium glutamicum","NCBI_taxonomy_id":"1718"}}}},"ARO_accession":"3000478","ARO_id":"36617","ARO_name":"tet(33)","CARD_short_name":"tet(33)","ARO_description":"Tet33 is a tetracycline efflux pump found in Gram-positive bacteria, including Arthrobacter and Corynebacterium.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1969":{"model_id":"1969","model_name":"tet(35)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"710"}},"model_sequences":{"sequence":{"4666":{"protein_sequence":{"accession":"AAK37619.1","sequence":"MCVIMPASSWGAYIITIIGGILVSHGITEYSALGAYVRLIPMNFYAVFALLMVFAVAWFGLDIGKMREHEIAASQGRGFDKDKENDSQEAHDLNEELDIRESEKGKVSDLILPIVTLIVATIASMLYTGGQALAADGKEFVLLGAFENTDVGTSLIYGSLLGLAVALFTVIKQGLPMVEIARTLWIGAKSMFGAILILVFAWTIGSVIGDMKTGSYLSTMAQGNINPHWLPVILFLLSGLMAFSTGTSWGTFGIMLPIAGDMAGATDVALMLPMLSAVLAGAVFGDHCSPISDTTILSSTGARCNHIDHVSTQLPYALSVAFVSCIGFITLGMTASIAFSFIAASITFVIVCAILSWLSKSKMASCQNA"},"dna_sequence":{"accession":"AF353562.1","fmin":"2212","fmax":"3322","strand":"-","sequence":"ATGTGTGTGATCATGCCAGCTTCTAGTTGGGGTGCGTACATCATTACCATCATCGGTGGTATCTTGGTGTCACACGGCATCACTGAATACTCGGCGCTTGGTGCTTACGTTCGTCTTATTCCTATGAACTTCTACGCAGTATTTGCTCTACTAATGGTATTTGCAGTGGCGTGGTTTGGTCTAGATATCGGTAAGATGCGTGAACATGAAATCGCAGCATCTCAAGGCCGTGGTTTTGATAAAGATAAAGAGAACGACTCACAAGAAGCACACGACCTAAACGAAGAGCTAGATATTCGTGAAAGCGAGAAGGGTAAGGTTTCTGACCTAATTCTTCCTATCGTAACGCTTATTGTGGCGACTATTGCTTCAATGCTTTACACCGGTGGTCAAGCGCTAGCAGCAGATGGTAAAGAATTTGTGCTGTTGGGTGCGTTTGAAAACACGGATGTTGGTACTTCTCTAATCTACGGTAGTTTACTTGGTCTAGCAGTTGCATTGTTCACTGTTATTAAGCAAGGTCTACCAATGGTTGAGATTGCACGCACGCTTTGGATTGGTGCTAAGTCAATGTTTGGTGCAATCCTTATCCTTGTTTTCGCTTGGACTATTGGTTCAGTTATCGGTGACATGAAGACGGGTTCTTACCTATCTACAATGGCGCAAGGCAACATCAACCCACACTGGCTACCAGTTATCCTGTTCTTGCTGTCTGGCCTAATGGCGTTCTCTACAGGTACGTCATGGGGTACGTTCGGTATCATGCTTCCAATCGCGGGTGACATGGCTGGCGCAACAGACGTGGCACTAATGCTACCAATGCTAAGTGCGGTTCTAGCTGGTGCAGTATTTGGTGACCACTGTTCACCAATTTCAGATACAACGATTCTGTCGTCAACAGGTGCACGCTGTAACCACATCGATCACGTATCGACGCAGCTACCTTATGCATTATCAGTGGCGTTTGTGTCATGTATTGGCTTTATCACGCTGGGTATGACTGCATCGATCGCGTTCTCTTTCATCGCAGCATCGATCACTTTCGTTATCGTTTGTGCGATTCTGTCGTGGCTGTCGAAGTCTAAAATGGCATCCTGCCAGAACGCGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36785","NCBI_taxonomy_name":"Vibrio harveyi","NCBI_taxonomy_id":"669"}}}},"ARO_accession":"3000481","ARO_id":"36620","ARO_name":"tet(35)","CARD_short_name":"tet(35)","ARO_description":"Tet35 is a tetracycline efflux pump found in the Gram-negative Vibrio and Stenotrophomonas. It is unrelated to other tet resistance genes.","ARO_category":{"36002":{"category_aro_accession":"0010001","category_aro_cvterm_id":"36002","category_aro_name":"ATP-binding cassette (ABC) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding\/hydrolysis to transport substrates across cell membranes.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2002":{"model_id":"2002","model_name":"Bacillus pumilus cat86","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"143":{"protein_sequence":{"accession":"AAA22289.1","sequence":"MFKQIDENYLRKEHFHHYMTLTRCSYSLVINLDITKLHAILKEKKLKVYPVQIYLLARAVQKIPEFRMDQVNDELGYWEILHPSYTILNKETKTFSSIWTPFDENFAQFYKSCVADIETFSKSSNLFPKPHMPENMFNISSLPWIDFTSFNLNVSTDEAYLLPIFTIGKFKVEEGKIILPVAIQVHHAVCDGYHAGQYVEYLRWLIEHCDEWLNDSLHIT"},"dna_sequence":{"accession":"K00544.1","fmin":"0","fmax":"663","strand":"+","sequence":"TTGTTTAAACAAATAGACGAAAATTATCTGCGAAAAGAGCACTTTCACCATTATATGACGTTAACCCGATGCTCATATAGCTTGGTGATCAATCTAGACATCACGAAATTGCATGCAATATTAAAAGAAAAAAAGCTGAAAGTATATCCTGTGCAAATTTATTTGTTAGCAAGAGCTGTGCAAAAAATTCCTGAGTTTCGGATGGATCAAGTGAACGATGAACTTGGTTACTGGGAGATTCTCCATCCTAGTTATACGATTCTAAATAAAGAAACAAAGACGTTTTCAAGTATTTGGACGCCTTTTGATGAAAACTTTGCTCAGTTTTATAAAAGCTGTGTAGCCGATATTGAAACATTTAGCAAAAGCAGCAACCTATTTCCGAAACCTCATATGCCAGAAAACATGTTCAATATTTCAAGTCTACCGTGGATTGATTTTACTTCTTTTAACCTTAATGTATCTACAGATGAAGCTTATTTACTGCCTATATTTACGATAGGCAAATTTAAGGTGGAAGAAGGAAAAATCATTTTGCCCGTTGCCATACAAGTACATCATGCTGTTTGTGATGGCTATCATGCCGGTCAATATGTTGAATATTTGAGGTGGCTTATTGAACATTGTGACGAGTGGTTAAATGATTCATTGCATATTACCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36821","NCBI_taxonomy_name":"Bacillus pumilus","NCBI_taxonomy_id":"1408"}}}},"ARO_accession":"3002672","ARO_id":"39106","ARO_name":"Bacillus pumilus cat86","CARD_short_name":"Bpum_cat86","ARO_description":"cat86 is a chromosome-encoded variant of the cat gene found in Bacillus pumilus.","ARO_category":{"36261":{"category_aro_accession":"3000122","category_aro_cvterm_id":"36261","category_aro_name":"chloramphenicol acetyltransferase (CAT)","category_aro_description":"Inactivates chloramphenicol by addition of an acyl group. CAT is used to describe many variants of the chloramphenicol acetyltransferase gene in a range of organisms including Acinetobacter calcoaceticus, Agrobacterium tumefaciens, Alkalihalobacillus clausii, Bacillus subtilis, Campylobacter coli, Enterococcus faecalis, Enterococcus faecium, Lactococcus lactis, Listeria monocytogenes, Listonella anguillarum, Morganella morganii, Photobacterium damselae subsp. piscicida, Proteus mirabilis, Salmonella typhi, Serratia marcescens, Shigella flexneri, Staphylococcus aureus, Staphylococcus haemolyticus, Staphylococcus intermedius, Streptococcus agalactiae, Streptococcus suis and Streptomyces acrimycini.","category_aro_class_name":"AMR Gene Family"},"36521":{"category_aro_accession":"3000382","category_aro_cvterm_id":"36521","category_aro_name":"azidamfenicol","category_aro_description":"Azidamfenicol is a water soluble derivative of chloramphenicol, sharing the same mode of action of inhibiting peptide synthesis by interacting with the 23S RNA of the 50S ribosomal subunit.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36595":{"category_aro_accession":"3000456","category_aro_cvterm_id":"36595","category_aro_name":"thiamphenicol","category_aro_description":"Derivative of Chloramphenicol. The nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3).","category_aro_class_name":"Antibiotic"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2033":{"model_id":"2033","model_name":"mtrR","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"410"},"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"8942":"G45D"},"Curated-R":{"8942":"G45D"},"clinical":{"8942":"G45D"}}},"model_sequences":{"sequence":{"4254":{"protein_sequence":{"accession":"ACF30254.1","sequence":"MRKTKTEALKTKEHLMLAALETFYRKGIARTSLNEIAQAAGVTRGALYWHFKNKEDLFDALFQRICDDIENCIAQDAADAEGGSWTVFRHTLLHFFERLQSNDIYYKFHNILFLKCEHTEQNAAVIAIARKHQAIWREKITAVLTEAVENQDLADDLDKETAVIFIKSTLDGLIWRWFSSGESFDLGKTAPRIIGIMMDNLENHPCLRRK"},"dna_sequence":{"accession":"CP001050.1","fmin":"1332866","fmax":"1333499","strand":"+","sequence":"ATGAGAAAAACCAAAACCGAAGCCTTGAAAACCAAAGAACACCTGATGCTTGCCGCCTTGGAAACCTTTTACCGCAAAGGGATTGCCCGCACCTCGCTCAACGAAATCGCCCAAGCCGCCGGCGTAACGCGCGGCGCGCTCTATTGGCATTTCAAAAATAAGGAAGACTTGTTTGACGCGTTGTTCCAACGTATCTGCGACGACATCGAAAACTGCATCGCGCAAGATGCCGCAGATGCCGAAGGAGGTTCTTGGACGGTATTCCGCCACACGCTGCTGCACTTTTTCGAGCGGCTGCAAAGCAACGACATCTACTACAAATTCCACAACATCCTGTTTTTAAAATGCGAACACACGGAGCAAAACGCCGCCGTTATCGCCATTGCCCGCAAGCATCAGGCAATCTGGCGCGAGAAAATTACCGCCGTTTTGACCGAAGCGGTGGAAAATCAGGATTTGGCTGACGATTTGGACAAGGAAACGGCGGTCATCTTCATCAAATCGACGTTGGACGGGCTGATTTGGCGTTGGTTCTCTTCCGGCGAAAGTTTCGATTTGGGCAAAACCGCCCCGCGCATCATCGGGATAATGATGGACAACTTGGAAAACCATCCCTGCCTGCGCCGGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37080","NCBI_taxonomy_name":"Neisseria gonorrhoeae NCCP11945","NCBI_taxonomy_id":"521006"}}}},"ARO_accession":"3000817","ARO_id":"37197","ARO_name":"mtrR","CARD_short_name":"mtrR","ARO_description":"MtrR is a repressor of mtrCDE expression. Mutations in mtrR increase multidrug resistance.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"40728":{"category_aro_accession":"3003957","category_aro_cvterm_id":"40728","category_aro_name":"palmitic acid","category_aro_description":"Palmitic acid is the most common saturated fatty acid found in animals, plants, and microorganisms. Palmitic acid is found to have antibacterial properties.","category_aro_class_name":"Antibiotic"},"40729":{"category_aro_accession":"3003958","category_aro_cvterm_id":"40729","category_aro_name":"oleic acid","category_aro_description":"Oleic acid is a fatty acid that occurs naturally in various animal and vegetable fats and oils. Oleic acid is found to have antibacterial activity, particularly in inhibiting the growth of several Gram-positive bacterial species.","category_aro_class_name":"Antibiotic"},"40730":{"category_aro_accession":"3003959","category_aro_cvterm_id":"40730","category_aro_name":"linoleic acid","category_aro_description":"Linoleic acid is a polyunsaturated omega-6 fatty acid. Linoleic acid has been found to have antibacterial activity, particularly in inhibiting the growth of Gram-positive bacterial species.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"40727":{"category_aro_accession":"3003956","category_aro_cvterm_id":"40727","category_aro_name":"antibacterial free fatty acids","category_aro_description":"Amongst the diverse and potent biological activities of free fatty acids (FFAs) is the ability to kill or inhibit the growth of bacteria. The antibacterial properties of FFAs are used by many organisms to defend against parasitic or pathogenic bacteria. The prime target of FFA action is the cell membrane, where FFAs disrupt the electron transport chain and oxidative phosphorylation. Besides interfering with cellular energy production, FFA action may also result from the inhibition of enzyme activity, impairment of nutrient uptake, generation of peroxidation and auto-oxidation degradation products or direct lysis of bacterial cells.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"90":{"model_id":"90","model_name":"Staphylococcus aureus rpoB mutants conferring resistance to rifampicin","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"2054":"H481N","2055":"A473T","2057":"L466S","2083":"A477T","2862":"Q468K","2056":"Q465R"},"Curated-R":{"2054":"H481N","2055":"A473T","2057":"L466S","2083":"A477T","2862":"Q468K","2056":"Q465R"},"clinical":{"2054":"H481N","2055":"A473T","2057":"L466S","2083":"A477T","2862":"Q468K","2056":"Q465R"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"2300"}},"model_sequences":{"sequence":{"5399":{"protein_sequence":{"accession":"CAG39568.1","sequence":"MAGQVVQYGRHRKRRNYARISEVLELPNLIEIQTKSYEWFLREGLIEMFRDISPIEDFTGNLSLEFVDYRLGEPKYDLEESKNRDATYAAPLRVKVRLIIKETGEVKEQEVFMGDFPLMTDTGTFVINGAERVIVSQLVRSPSVYFNEKIDKNGRENYDATIIPNRGAWLEYETDAKDVVYVRIDRTRKLPLTVLLRALGFSSDQEIVDLLGDNEYLRNTLEKDGTENTEQALLEIYERLRPGEPPTVENAKSLLYSRFFDPKRYDLASVGRYKTNKKLHLKHRLFNQKLAEPIVNTETGEIVVEEGTVLDRRKIDEIMDVLESNANSEVFELHGSVIDEPVEIQSIKVYVPNDDEGRTTTVIGNAFPDSEVKCITPADIIASMSYFFNLLSGIGYTDDIDHLGNRRLRSVGELLQNQFRIGLSRMERVVRERMSIQDTESITPQQLINIRPVIASIKEFFGSSQLSQFMDQANPLAELTHKRRLSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETPYRKVDLDTHAITDQIDYLTADEEDSYVVAQANSKLDENGRFMDDEVVCRFRGNNTVMAKEKMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPEAPFVGTGMEHVAARDSGAAITAKHRGRVEHVESNEILVRRLVEENGVEHEGELDRYPLAKFKRSNSGTCYNQRPIVAVGDVVEFNEILADGPSMELGEMALGRNVVVGFMTWDGYNYEDAVIMSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVSESALKNLDDRGIVYIGAEVKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGAGGIVLDVKVFNREEGDDTLSPGVNQLVRVYIVQKRKIHVGDKMCGRHGNKGVISKIVPEEDMPYLPDGRPIDIMLNPLGVPSRMNIGQVLELHLGMAAKNLGIHVASPVFDGANDDDVWSTIEEAGMARDGKTVLYDGRTGEPFDNRISVGVMYMLKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTYKSDDTVGRVKTYEAIVKGENISRPSVPESFRVLMKELQSLGLDVKVMDEQDNEIEMTDVDDDDVVERKVDLQQNDAPETQKEVTD"},"dna_sequence":{"accession":"BX571856.1","fmin":"590830","fmax":"594382","strand":"+","sequence":"TTGGCAGGTCAAGTTGTCCAATATGGAAGACATCGTAAACGTAGAAACTACGCGAGAATTTCAGAAGTATTAGAATTACCAAACTTAATAGAAATTCAAACTAAATCTTACGAGTGGTTCCTAAGAGAAGGTTTAATCGAAATGTTTAGAGACATTTCTCCAATTGAAGATTTTACTGGTAATTTGTCATTAGAGTTTGTGGATTACCGTTTAGGAGAACCAAAATATGATTTAGAAGAATCTAAAAACCGTGACGCTACTTATGCTGCACCTCTTCGTGTAAAAGTGCGTCTAATCATTAAAGAAACAGGAGAAGTTAAAGAACAAGAAGTCTTTATGGGTGATTTCCCATTAATGACTGATACAGGTACGTTCGTTATCAATGGTGCAGAACGTGTAATCGTATCTCAATTAGTTCGTTCACCATCCGTTTATTTCAATGAAAAAATCGACAAAAATGGTCGTGAAAACTATGATGCAACAATTATTCCAAACCGAGGTGCATGGTTAGAATATGAAACAGATGCTAAAGATGTTGTATACGTGCGTATTGATAGAACACGTAAACTACCATTAACAGTATTGTTACGTGCATTAGGTTTCTCAAGTGACCAAGAAATTGTTGACCTTTTAGGTGACAATGAATATTTACGTAATACTTTAGAGAAAGACGGCACTGAAAACACTGAACAAGCGTTATTAGAAATCTATGAACGTTTACGTCCAGGTGAACCACCAACTGTTGAAAATGCTAAAAGTCTATTGTATTCACGTTTCTTTGATCCAAAACGCTATGACTTAGCAAGCGTGGGTCGTTATAAAACAAACAAAAAATTACATTTAAAACATCGTTTATTCAATCAAAAATTAGCTGAGCCAATTGTGAATACTGAAACTGGTGAAATTGTAGTTGAAGAAGGTACAGTGCTTGATCGTCGTAAAATCGACGAAATCATGGATGTACTTGAATCAAACGCAAACAGCGAAGTGTTTGAATTGCATGGTAGCGTTATAGACGAGCCAGTAGAAATTCAATCAATTAAAGTATATGTTCCTAACGATGATGAAGGTCGTACGACAACTGTAATTGGTAATGCTTTCCCTGACTCAGAAGTTAAATGTATTACACCGGCAGATATCATCGCTTCAATGAGTTACTTCTTTAACTTATTAAGTGGTATTGGATATACAGATGATATTGACCATTTAGGTAACCGTCGTTTACGTTCTGTAGGTGAATTACTACAAAACCAATTCCGTATCGGTTTATCAAGAATGGAAAGAGTTGTACGTGAAAGAATGTCAATTCAAGATACTGAGTCTATCACACCTCAACAATTAATTAATATTCGACCTGTTATTGCATCTATTAAAGAATTCTTTGGTAGCTCTCAATTATCACAATTCATGGACCAAGCAAATCCATTAGCTGAGTTAACGCATAAACGTCGTCTATCAGCATTAGGACCTGGTGGTTTAACACGTGAACGTGCTCAAATGGAAGTGCGTGACGTTCACTACTCTCACTATGGCCGTATGTGTCCAATTGAAACGCCTGAGGGACCAAACATTGGATTGATTAACTCATTATCAAGTTATGCACGTGTAAATGAATTCGGCTTTATTGAAACACCATATCGTAAAGTTGATTTAGATACACATGCTATCACTGATCAAATTGACTATTTAACAGCTGACGAAGAAGATAGCTATGTTGTAGCACAAGCAAACTCTAAATTAGATGAAAATGGTCGTTTCATGGATGATGAAGTTGTATGTCGTTTCCGTGGTAACAATACAGTTATGGCTAAAGAAAAAATGGATTATATGGATGTATCGCCGAAGCAAGTTGTTTCAGCAGCGACAGCATGTATTCCATTCTTAGAAAATGATGACTCAAACCGTGCATTGATGGGTGCGAACATGCAACGTCAAGCAGTGCCTTTGATGAATCCAGAAGCACCATTTGTTGGTACAGGTATGGAACACGTTGCAGCACGTGATTCTGGTGCAGCTATTACAGCTAAGCACAGAGGTCGTGTTGAACATGTTGAATCTAATGAAATTCTTGTACGTCGTCTAGTTGAAGAGAACGGCGTTGAGCATGAAGGTGAATTAGATCGCTATCCATTAGCTAAATTTAAACGTTCAAACTCAGGTACATGTTACAACCAACGTCCAATCGTTGCAGTTGGAGATGTTGTTGAGTTTAACGAGATTTTAGCAGATGGACCATCTATGGAATTAGGAGAAATGGCATTAGGTAGAAACGTAGTAGTTGGTTTCATGACTTGGGACGGTTACAACTATGAGGATGCCGTTATCATGAGTGAAAGACTTGTGAAAGATGACGTGTATACTTCTATTCATATTGAAGAGTATGAATCAGAAGCACGTGATACTAAGTTAGGACCTGAAGAAATCACAAGAGATATTCCTAATGTTTCTGAAAGTGCACTTAAGAACTTAGACGATCGTGGTATCGTTTATATTGGTGCAGAAGTAAAAGATGGAGATATTTTAGTTGGTAAAGTAACGCCTAAAGGTGTAACTGAGTTAACTGCCGAAGAAAGATTGTTACATGCAATCTTTGGTGAAAAAGCACGTGAAGTTAGAGATACTTCATTACGTGTACCTCACGGCGCTGGCGGTATCGTTCTTGATGTAAAAGTATTCAATCGTGAAGAAGGCGACGACACATTATCACCTGGTGTAAACCAATTAGTACGTGTATATATCGTTCAAAAACGTAAAATTCATGTTGGTGATAAGATGTGTGGTCGACATGGTAACAAAGGTGTCATTTCTAAGATTGTTCCTGAAGAAGATATGCCTTACTTACCAGATGGACGTCCGATTGATATCATGTTAAATCCTCTTGGTGTACCATCTCGTATGAACATCGGACAAGTATTAGAGCTACACTTAGGTATGGCTGCTAAAAATCTTGGTATTCACGTTGCATCACCAGTATTTGACGGTGCAAACGATGACGATGTATGGTCAACAATTGAAGAAGCTGGTATGGCTCGTGATGGTAAAACTGTACTTTATGATGGACGTACAGGTGAACCATTCGATAACCGTATTTCAGTAGGTGTAATGTACATGTTGAAACTTGCGCACATGGTTGATGATAAATTACATGCGCGTTCAACAGGACCATATTCACTTGTTACACAACAACCACTTGGCGGTAAAGCGCAATTCGGTGGACAACGTTTCGGTGAGATGGAGGTATGGGCACTTGAAGCATATGGTGCTGCATACACATTACAAGAAATCTTAACTTACAAATCCGATGATACAGTAGGACGTGTGAAAACATACGAGGCTATTGTTAAAGGTGAAAACATCTCTAGACCAAGTGTTCCAGAATCATTCCGAGTATTGATGAAAGAATTACAAAGTTTAGGTTTAGATGTAAAAGTTATGGATGAGCAAGATAATGAAATCGAAATGACAGACGTTGATGACGATGATGTTGTAGAACGCAAAGTAGATTTACAACAAAATGATGCTCCTGAAACACAAAAAGAAGTTACTGATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35517","NCBI_taxonomy_name":"Staphylococcus aureus subsp. aureus MRSA252","NCBI_taxonomy_id":"282458"}}}},"ARO_accession":"3003285","ARO_id":"39869","ARO_name":"Staphylococcus aureus rpoB mutants conferring resistance to rifampicin","CARD_short_name":"Saur_rpoB_RIF","ARO_description":"Point mutations that occurs in Staphylococcus aureus rpoB resulting in resistance to rifampicin.","ARO_category":{"36349":{"category_aro_accession":"3000210","category_aro_cvterm_id":"36349","category_aro_name":"rifamycin-resistant beta-subunit of RNA polymerase (rpoB)","category_aro_description":"Rifampin resistant RNA polymerases include amino acids substitutions which disrupt the affinity of rifampin for its binding site. These mutations are frequently concentrated in the rif I region of the beta-subunit and most often involve amino acids which make direct interactions with rifampin. However, mutations which also confer resistance can occur outside this region and may involve amino acids which do not directly make contact with rifampin.","category_aro_class_name":"AMR Gene Family"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36656":{"category_aro_accession":"3000517","category_aro_cvterm_id":"36656","category_aro_name":"rifaximin","category_aro_description":"Rifaximin is a semi-synthetic rifamycin used to treat traveller's diarrhea. Rifaximin inhibits RNA synthesis by binding to the beta subunit of bacterial RNA polymerase.","category_aro_class_name":"Antibiotic"},"36669":{"category_aro_accession":"3000530","category_aro_cvterm_id":"36669","category_aro_name":"rifabutin","category_aro_description":"Rifabutin is a semisynthetic rifamycin used in tuberculosis therapy. It inhibits DNA-dependent RNA synthesis.","category_aro_class_name":"Antibiotic"},"36673":{"category_aro_accession":"3000534","category_aro_cvterm_id":"36673","category_aro_name":"rifapentine","category_aro_description":"Rifapentine is a semisynthetic rifamycin that inhibits DNA-dependent RNA synthesis. It is often used in the treatment of tuberculosis and leprosy.","category_aro_class_name":"Antibiotic"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"111":{"model_id":"111","model_name":"Escherichia coli gyrB conferring resistance to aminocoumarin","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"2156":"R136L","2158":"R136H","2159":"R136S","2160":"R136G","2161":"R136I","2162":"R136E","2157":"R136C"},"Curated-R":{"2156":"R136L","2158":"R136H","2159":"R136S","2160":"R136G","2161":"R136I","2162":"R136E","2157":"R136C"},"clinical":{"2156":"R136L","2158":"R136H","2159":"R136S","2160":"R136G","2161":"R136I","2162":"R136E","2157":"R136C"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1600"}},"model_sequences":{"sequence":{"2063":{"protein_sequence":{"accession":"BAE77595.1","sequence":"MSNSYDSSSIKVLKGLDAVRKRPGMYIGDTDDGTGLHHMVFEVVDNAIDEALAGHCKEIIVTIHADNSVSVQDDGRGIPTGIHPEEGVSAAEVIMTVLHAGGKFDDNSYKVSGGLHGVGVSVVNALSQKLELVIQREGKIHRQIYEHGVPQAPLAVTGETEKTGTMVRFWPSLETFTNVTEFEYEILAKRLRELSFLNSGVSIRLRDKRDGKEDHFHYEGGIKAFVEYLNKNKTPIHPNIFYFSTEKDGIGVEVALQWNDGFQENIYCFTNNIPQRDGGTHLAGFRAAMTRTLNAYMDKEGYSKKAKVSATGDDAREGLIAVVSVKVPDPKFSSQTKDKLVSSEVKSAVEQQMNELLAEYLLENPTDAKIVVGKIIDAARAREAARRAREMTRRKGALDLAGLPGKLADCQERDPALSELYLVEGDSAGGSAKQGRNRKNQAILPLKGKILNVEKARFDKMLSSQEVATLITALGCGIGRDEYNPDKLRYHSIIIMTDADVDGSHIRTLLLTFFYRQMPEIVERGHVYIAQPPLYKVKKGKQEQYIKDDEAMDQYQISIALDGATLHTNASAPALAGEALEKLVSEYNATQKMINRMERRYPKAMLKELIYQPTLTEADLSDEQTVTRWVNALVSELNDKEQHGSQWKFDVHTNAEQNLFEPIVRVRTHGVDTDYPLDHEFITGGEYRRICTLGEKLRGLLEEDAFIERGERRQPVASFEQALDWLVKESRRGLSIQRYKGLGEMNPEQLWETTMDPESRRMLRVTVKDAIAADQLFTTLMGDAVEPRRAFIEENALKAANIDI"},"dna_sequence":{"accession":"AP009048.1","fmin":"3760295","fmax":"3762710","strand":"+","sequence":"ATGTCGAATTCTTATGACTCCTCCAGTATCAAAGTCCTGAAAGGGCTGGATGCGGTGCGTAAGCGCCCGGGTATGTATATCGGCGACACGGATGACGGCACCGGTCTGCACCACATGGTATTCGAGGTGGTAGATAACGCTATCGACGAAGCGCTCGCGGGTCACTGTAAAGAAATTATCGTCACCATTCACGCCGATAACTCTGTCTCTGTACAGGATGACGGGCGCGGCATTCCGACCGGTATTCACCCGGAAGAGGGCGTATCGGCGGCGGAAGTGATCATGACCGTTCTGCACGCAGGCGGTAAATTTGACGATAACTCCTATAAAGTGTCCGGCGGTCTGCACGGCGTTGGTGTTTCGGTAGTAAACGCCCTGTCGCAAAAACTGGAGCTGGTTATCCAGCGCGAGGGTAAAATTCACCGTCAGATCTACGAACACGGTGTACCGCAGGCCCCGCTGGCGGTTACCGGCGAGACTGAAAAAACCGGCACCATGGTGCGTTTCTGGCCCAGCCTCGAAACCTTCACCAATGTGACCGAGTTCGAATATGAAATTCTGGCGAAACGTCTGCGTGAGTTGTCGTTCCTCAACTCCGGCGTTTCCATTCGTCTGCGCGACAAGCGCGACGGCAAAGAAGACCACTTCCACTATGAAGGCGGCATCAAGGCGTTCGTTGAATATCTGAACAAGAACAAAACGCCGATCCACCCGAATATCTTCTACTTCTCCACTGAAAAAGACGGTATTGGCGTCGAAGTGGCGTTGCAGTGGAACGATGGCTTCCAGGAAAACATCTACTGCTTTACCAACAACATTCCGCAGCGTGACGGCGGTACTCACCTGGCAGGCTTCCGTGCGGCGATGACCCGTACCCTGAACGCCTACATGGACAAAGAAGGCTACAGCAAAAAAGCCAAAGTCAGCGCCACCGGTGACGATGCGCGTGAAGGCCTGATTGCGGTCGTTTCCGTGAAAGTGCCGGACCCGAAATTCTCCTCCCAGACCAAAGACAAACTGGTTTCTTCTGAGGTGAAATCGGCGGTTGAACAGCAGATGAACGAACTGCTGGCAGAATACCTGCTGGAAAACCCAACCGACGCGAAAATCGTGGTTGGCAAAATTATCGATGCTGCCCGTGCCCGTGAAGCGGCGCGTCGCGCGCGTGAAATGACCCGCCGTAAAGGTGCGCTCGACTTAGCGGGCCTGCCGGGCAAACTGGCAGACTGCCAGGAACGCGATCCGGCGCTTTCCGAACTGTACCTGGTGGAAGGGGACTCCGCGGGCGGCTCTGCGAAGCAGGGGCGTAACCGCAAGAACCAGGCGATTCTGCCGCTGAAGGGTAAAATCCTCAACGTCGAGAAAGCGCGCTTCGATAAGATGCTCTCTTCTCAGGAAGTGGCGACGCTTATCACCGCGCTTGGCTGTGGTATCGGTCGTGACGAGTACAACCCGGACAAACTGCGTTATCACAGCATCATCATCATGACCGATGCGGACGTCGACGGCTCGCACATTCGTACGCTGCTGTTGACCTTCTTCTATCGTCAGATGCCGGAAATCGTTGAACGCGGTCACGTCTACATCGCTCAGCCGCCGCTGTACAAAGTGAAGAAAGGCAAGCAGGAACAGTACATTAAAGACGACGAAGCGATGGATCAGTACCAGATCTCTATCGCGCTGGACGGCGCAACGCTGCACACCAACGCCAGTGCACCGGCATTGGCTGGCGAAGCGTTAGAGAAACTGGTATCTGAGTACAACGCGACGCAGAAAATGATCAATCGTATGGAGCGTCGTTATCCGAAAGCAATGCTGAAAGAGCTTATCTATCAGCCGACGTTGACGGAAGCTGACCTTTCTGATGAGCAGACCGTTACCCGCTGGGTGAACGCGCTGGTCAGCGAACTGAACGACAAAGAACAGCACGGCAGCCAGTGGAAGTTTGATGTTCACACCAATGCTGAGCAAAACCTGTTCGAGCCGATTGTTCGCGTGCGTACCCACGGTGTGGATACTGACTATCCGCTGGATCACGAGTTTATCACCGGTGGCGAATATCGTCGTATCTGCACGCTGGGTGAGAAACTGCGTGGCTTGCTGGAAGAAGATGCGTTTATCGAACGTGGCGAGCGTCGTCAGCCGGTAGCCAGCTTCGAGCAGGCGCTGGACTGGCTGGTGAAAGAGTCCCGTCGCGGCCTCTCCATCCAGCGTTATAAAGGTCTGGGCGAGATGAACCCGGAACAGCTGTGGGAAACCACTATGGACCCGGAAAGTCGTCGTATGCTGCGCGTTACCGTTAAAGATGCGATTGCTGCCGACCAGTTGTTCACCACGCTGATGGGCGACGCCGTTGAACCGCGCCGTGCGTTTATTGAAGAGAACGCCCTGAAAGCGGCGAATATCGATATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36839","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. W3110","NCBI_taxonomy_id":"316407"}}}},"ARO_accession":"3003303","ARO_id":"39887","ARO_name":"Escherichia coli gyrB conferring resistance to aminocoumarin","CARD_short_name":"Ecol_gyrB_AMU","ARO_description":"Point mutation in Escherichia coli resulting in aminocoumarin resistance.","ARO_category":{"36618":{"category_aro_accession":"3000479","category_aro_cvterm_id":"36618","category_aro_name":"aminocoumarin resistant gyrB","category_aro_description":"Point mutations in DNA gyrase subunit B (gyrB) can result in resistance to aminocoumarins. These mutations usually involve arginine residues in organisms.","category_aro_class_name":"AMR Gene Family"},"36250":{"category_aro_accession":"3000111","category_aro_cvterm_id":"36250","category_aro_name":"novobiocin","category_aro_description":"Novobiocin is an aminocoumarin antibiotic produced by Streptomyces spheroides and Streptomyces niveus, and binds DNA gyrase subunit B inhibiting ATP-dependent DNA supercoiling.","category_aro_class_name":"Antibiotic"},"36271":{"category_aro_accession":"3000132","category_aro_cvterm_id":"36271","category_aro_name":"clorobiocin","category_aro_description":"Clorobiocin is an aminocoumarin antibiotic produced by Streptomyces roseochromogenes, and binds DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling.","category_aro_class_name":"Antibiotic"},"36289":{"category_aro_accession":"3000150","category_aro_cvterm_id":"36289","category_aro_name":"coumermycin A1","category_aro_description":"Coumermycin A1 is an antibiotic produced by Streptomyces rishiriensis, and binds DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling.","category_aro_class_name":"Antibiotic"},"36242":{"category_aro_accession":"3000103","category_aro_cvterm_id":"36242","category_aro_name":"aminocoumarin antibiotic","category_aro_description":"Aminocoumarin antibiotics bind DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"335":{"model_id":"335","model_name":"Staphylococcus aureus parE conferring resistance to fluoroquinolones","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"2827":"P587S","2829":"D434N","2828":"D434H"},"Curated-R":{"2827":"P587S","2829":"D434N","2828":"D434H"},"clinical":{"2827":"P587S","2829":"D434N","2828":"D434H"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"5400":{"protein_sequence":{"accession":"CAG40364.1","sequence":"MAMNKQNNYSDDSIQVLEGLEAVRKRPGMYIGSTDKRGLHHLVYEIVDNSVDEVLNGYGNEIDVTINKDGSISIEDNGRGMPTGIHKSGKPTVEVIFTVLHAGGKFGQGGYKTSGGLHGVGASVVNALSEWLEVEIHRDGNIYHQSFKNGGSPSSGLVKKGKTKKTGTKVTFKPDDTIFKASTSFNFDVLSERLQESAFLLKNLKITLNDLRSGKERQEHYHYEEGIKEFVSYVNEGKEVLHDVATFSGEANGIEVDVAFQYNDQYSESILSFVNNVRTKDGGTHEVGFKTAMTRVFNDYARRINELKTKDKNLDGNDIREGLTAVVSVRIPEELLQFEGQTKSKLGTSEARSAVDSVVADKLPFYLEEKGQLSKSLVKKAIKAQQAREAARKAREDARSGKKNKRKDTLLSGKLTPAQSKNTDKNELYLVEGDSAGGSAKLGRDRKFQAILPLRGKVINTEKARLEDIFKNEEINTIIHTIGAGVGTDFKIEDSNYNRVIIMTDADTDGAHIQVLLLTFFFKYMKPLVQAGRVFIALPPLYKLEKGKGKTKRVEYAWTDEELNKLQKELGKGFTLQRYKGLGEMNPEQLWETTMNPETRTLIRVQVEDEVRSSKRVTTLMGDKVQPRREWIEKHFEFGMQEDQSILDNSEVQVLENDQFDEEEI"},"dna_sequence":{"accession":"BX571856.1","fmin":"1417762","fmax":"1419760","strand":"+","sequence":"TTGGCAATGAATAAACAAAATAATTATTCAGATGATTCAATACAGGTTTTAGAGGGGTTAGAAGCAGTTCGTAAAAGACCTGGTATGTATATTGGATCAACTGATAAACGGGGATTACATCATCTAGTATATGAAATTGTCGATAACTCCGTCGATGAAGTATTGAATGGTTACGGTAACGAAATAGATGTAACAATTAATAAAGATGGTAGTATTTCTATAGAAGATAATGGACGTGGTATGCCAACAGGTATACATAAATCAGGTAAACCGACAGTCGAAGTTATCTTTACTGTTTTACATGCAGGAGGTAAATTTGGACAAGGCGGCTATAAAACTTCAGGTGGTCTTCACGGCGTTGGTGCTTCAGTTGTAAATGCATTGAGTGAATGGCTTGAAGTTGAAATCCATCGAGATGGTAATATATATCATCAAAGTTTTAAAAACGGTGGTTCGCCATCTTCTGGTTTAGTGAAAAAAGGTAAAACTAAGAAAACAGGTACCAAAGTAACATTTAAACCTGATGACACAATTTTTAAAGCATCTACATCATTTAATTTTGATGTTTTAAGTGAACGACTACAAGAGTCTGCGTTCTTATTGAAAAATTTAAAAATAACGCTTAATGATTTACGCAGTGGTAAAGAGCGTCAAGAGCATTACCATTATGAAGAAGGAATCAAAGAATTTGTTAGTTATGTCAATGAAGGAAAAGAAGTTTTGCATGACGTGGCTACATTTTCAGGTGAAGCAAATGGTATAGAGGTAGACGTAGCTTTCCAATATAATGATCAATATTCAGAAAGTATTTTAAGTTTTGTAAATAATGTACGTACTAAAGATGGTGGTACACATGAAGTTGGTTTTAAAACAGCAATGACACGTGTATTTAATGATTATGCACGTCGTATTAATGAACTTAAAACAAAAGATAAAAACTTAGACGGTAATGATATTCGTGAAGGTTTAACAGCTGTTGTGTCTGTACGTATTCCAGAAGAATTACTACAATTTGAAGGACAAACGAAATCTAAATTGGGTACTTCTGAAGCAAGAAGTGCTGTTGATTCAGTAGTTGCAGACAAATTACCATTCTATTTAGAAGAAAAAGGACAATTGTCTAAATCACTTGTAAAAAAAGCAATTAAAGCACAACAAGCAAGGGAAGCTGCACGTAAAGCTCGTGAAGATGCTCGTTCAGGTAAGAAAAACAAGCGTAAAGACACTTTGCTATCTGGTAAATTAACACCTGCACAAAGTAAAAATACAGATAAAAATGAATTGTATTTAGTCGAAGGTGATTCTGCGGGAGGTTCAGCAAAACTTGGACGAGACCGCAAATTCCAAGCGATATTACCATTACGTGGTAAGGTAATTAATACAGAGAAAGCACGTCTGGAAGATATTTTTAAAAATGAAGAAATTAATACAATTATCCACACAATCGGGGCAGGCGTTGGTACTGACTTTAAAATTGAAGATAGTAACTATAATCGTGTAATTATTATGACTGATGCTGATACTGATGGTGCGCATATTCAAGTGCTATTGTTAACATTCTTCTTCAAATATATGAAACCGCTTGTTCAAGCAGGTCGTGTATTTATTGCTTTACCTCCACTTTATAAATTGGAAAAAGGTAAAGGCAAAACAAAGCGAGTTGAATACGCTTGGACAGACGAAGAGCTTAATAAATTACAAAAAGAACTTGGTAAGGGCTTCACGTTACAACGTTACAAAGGTTTGGGTGAGATGAACCCTGAACAATTATGGGAAACGACGATGAACCCAGAAACACGAACTTTAATTCGTGTACAAGTTGAAGATGAAGTGCGTTCATCTAAACGTGTAACAACATTAATGGGTGACAAAGTACAACCTAGACGTGAATGGATTGAAAAGCATTTTGAGTTTGGTATGCAAGAGGACCAAAGTATTTTAGATAATTCTGAAGTACAAGTGCTTGAAAATGATCAATTTGATGAGGAGGAAATCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35517","NCBI_taxonomy_name":"Staphylococcus aureus subsp. aureus MRSA252","NCBI_taxonomy_id":"282458"}}}},"ARO_accession":"3003315","ARO_id":"39899","ARO_name":"Staphylococcus aureus parE conferring resistance to fluoroquinolones","CARD_short_name":"Saur_parE_FLO","ARO_description":"Point mutation in Staphylococcus aureus parE resulting in fluoroquinolones resistance.","ARO_category":{"39897":{"category_aro_accession":"3003313","category_aro_cvterm_id":"39897","category_aro_name":"fluoroquinolone resistant parE","category_aro_description":"ParE is a subunit of topoisomerase IV, necessary for cell survival. Point mutations in ParE prevent fluoroquinolones from inhibiting DNA synthesis, thus conferring resistance.","category_aro_class_name":"AMR Gene Family"},"35942":{"category_aro_accession":"0000023","category_aro_cvterm_id":"35942","category_aro_name":"enoxacin","category_aro_description":"Enoxacin belongs to a group called fluoroquinolones. Its mode of action depends upon blocking bacterial DNA replication by binding itself to DNA gyrase and causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37004":{"category_aro_accession":"3000660","category_aro_cvterm_id":"37004","category_aro_name":"lomefloxacin","category_aro_description":"Lomefloxacin is a difluoropiperazinyl quinolone, sharing similar activities with other fluoroquinolones. It is used to treat urinary tract infections. Relative to other fluoroquinolones, it has a longer half life and has higher serum concentrations.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37007":{"category_aro_accession":"3000663","category_aro_cvterm_id":"37007","category_aro_name":"ofloxacin","category_aro_description":"Ofloxacin is a 6-fluoro, 7-piperazinyl quinolone with a methyl-substituted oxazine ring. It has a broad spectrum of activity including many enterobacteria and mycoplasma but most anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"37008":{"category_aro_accession":"3000664","category_aro_cvterm_id":"37008","category_aro_name":"trovafloxacin","category_aro_description":"Trovafloxacin is a trifluoroquinalone with a broad spectrum of activity that acts by inhibiting the uncoiling of supercoiled DNA. While potent against many Gram-positive and Gram-negative bacteria, it is less active against pseudomonads and Cl. difficile. It is usually taken as the prodrug trovafloxacin mesylate or alatrofloxacin mesylate for oral or intravenous administration, respectively.","category_aro_class_name":"Antibiotic"},"37009":{"category_aro_accession":"3000665","category_aro_cvterm_id":"37009","category_aro_name":"grepafloxacin","category_aro_description":"Grepafloxacin is a broad-spectrum antibacterial quinoline. It is no longer taken due to its high toxicity.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"37142":{"category_aro_accession":"3000762","category_aro_cvterm_id":"37142","category_aro_name":"pefloxacin","category_aro_description":"Pefloxacin is structurally and functionally similar to norfloxacin. It is poorly active against mycobacteria, while anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"462":{"model_id":"462","model_name":"Staphylococcus aureus pgsA mutations conferring resistance to daptomycin","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"2214":"S177F","2215":"K66R","2229":"V59N","2213":"A64V"},"Curated-R":{"2214":"S177F","2215":"K66R","2229":"V59N","2213":"A64V"},"experimental":{"2214":"S177F","2215":"K66R","2229":"V59N","2213":"A64V"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"5359":{"protein_sequence":{"accession":"BAB95031.1","sequence":"MNIPNQITVFRVVLIPVFILFALVDFGFGNVSFLGGYEIRIELLISGFIFILASLSDFVDGYLARKWNLVTNMGKFLDPLADKLLVASALIVLVQLGLTNSVVAIIIIAREFAVTGLRLLQIEQGFVSAAGQLGKIKTAVTMVAITWLLLGDPLATLIGLSLGQILLYIGVIFTILSGIEYFYKGRDVFKQK"},"dna_sequence":{"accession":"BA000033.2","fmin":"1278585","fmax":"1279164","strand":"+","sequence":"ATGAATATTCCGAACCAGATTACGGTTTTTAGAGTAGTGTTAATACCAGTTTTTATATTGTTTGCGTTAGTTGATTTTGGATTTGGCAATGTGTCATTTCTAGGAGGATATGAAATAAGAATTGAGTTATTAATCAGTGGTTTTATTTTTATATTGGCTTCCCTTAGCGATTTTGTTGATGGTTATTTAGCTAGAAAATGGAATTTAGTTACAAATATGGGGAAATTTTTGGATCCATTAGCGGATAAATTATTAGTTGCAAGTGCTTTAATTGTACTTGTGCAACTAGGACTAACAAATTCTGTAGTAGCAATCATTATTATTGCCAGAGAATTTGCCGTAACTGGTTTACGTTTACTACAAATTGAACAAGGATTCGTAAGTGCAGCTGGTCAATTAGGTAAAATTAAAACAGCAGTTACTATGGTAGCAATTACTTGGTTGTTATTAGGTGATCCATTGGCAACATTGATTGGTTTGTCATTAGGACAAATTTTATTATACATTGGCGTTATTTTTACTATCTTATCTGGTATTGAATACTTTTATAAAGGTAGAGATGTTTTTAAACAAAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35515","NCBI_taxonomy_name":"Staphylococcus aureus subsp. aureus MW2","NCBI_taxonomy_id":"196620"}}}},"ARO_accession":"3003323","ARO_id":"39907","ARO_name":"Staphylococcus aureus pgsA mutations conferring resistance to daptomycin","CARD_short_name":"Saur_pgsA_DAP","ARO_description":"Point mutations that occur within Staphylococcus aureus pgsA gene resulting in resistance to daptomycin.","ARO_category":{"39627":{"category_aro_accession":"3003080","category_aro_cvterm_id":"39627","category_aro_name":"daptomycin resistant pgsA","category_aro_description":"pgsA or phosphatidylglycerophosphate synthetase is an integral membrane protein involved in phospholipid biosynthesis. It is a CDP-diacylglycerol-glycerol-3-phosphate 3-phosphatidyltransferase. Laboratory experiments have detected mutations conferring daptomycin resistance in Entercoccus.","category_aro_class_name":"AMR Gene Family"},"35985":{"category_aro_accession":"0000068","category_aro_cvterm_id":"35985","category_aro_name":"daptomycin","category_aro_description":"Daptomycin is a novel lipopeptide antibiotic used in the treatment of certain infections caused by Gram-positive organisms. Daptomycin interferes with the bacterial cell membrane, reducing membrane potential and inhibiting cell wall synthesis.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"489":{"model_id":"489","model_name":"Mycobacterium tuberculosis gidB mutation conferring resistance to streptomycin","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"15748":"M1Var","15756":"A200E","15824":"A134E","15854":"V105E","15897":"P84L","15922":"G73A","15925":"G73E","15933":"S70N","15942":"D67H","15967":"H48Q","9840":"L79S","9841":"E92D","2663":"W45C","2664":"R47Q","2665":"I55S","2667":"S70R","2668":"G71V","2670":"Q127P","2672":"A138E","2673":"W148R","2674":"A183E","3235":"P75S","3670":"A183T","3672":"W45S","3675":"H48Y","3676":"G30R","3679":"G117E","3681":"L79F","3682":"L49F","3683":"G164C","3688":"P84C","3689":"V188M","8863":"V124G","8864":"E92A","8865":"V139A","8866":"G37V","13201":"N51T","2675":"V188G"},"WHO-R":{"15748":"M1Var","15750":"M1Var","15751":"M1Var","15759":"M1Var","15768":"M1Var","15775":"M1Var","15779":"M1Var","15782":"M1Var","15786":"M1Var","15794":"M1Var","15802":"M1Var","15806":"M1Var","15821":"M1Var","15830":"M1Var","15831":"M1Var","15836":"M1Var","15837":"M1Var","15856":"M1Var","15857":"M1Var","15863":"M1Var","15877":"M1Var","15889":"M1Var","15907":"M1Var","15920":"M1Var","15928":"M1Var","15953":"M1Var","15958":"M1Var","15978":"M1Var","15984":"M1Var","15989":"M1Var","15999":"M1Var","16001":"M1Var","16008":"M1Var","16017":"M1Var","15756":"A200E","15824":"A134E","15854":"V105E","15897":"P84L","15922":"G73A","15925":"G73E","15933":"S70N","15942":"D67H","15967":"H48Q"},"clinical":{"15748":"M1Var","15756":"A200E","15824":"A134E","15854":"V105E","15897":"P84L","15922":"G73A","15925":"G73E","15933":"S70N","15942":"D67H","15967":"H48Q","9840":"L79S","9841":"E92D","2663":"W45C","2664":"R47Q","2665":"I55S","2666":"D67H","2667":"S70R","2668":"G71V","2670":"Q127P","2671":"A134E","2672":"A138E","2673":"W148R","2674":"A183E","2676":"A200E","3235":"P75S","3670":"A183T","3672":"W45S","3673":"P84L","3675":"H48Y","3676":"G30R","3679":"G117E","3681":"L79F","3682":"L49F","3683":"G164C","3688":"P84C","3689":"V188M","8863":"V124G","8864":"E92A","8865":"V139A","8866":"G37V","9962":"L79S","13201":"N51T","2675":"V188G"},"Curated-R":{"3677":"M1Var","2663":"W45C","2664":"R47Q","2665":"I55S","2666":"D67H","2667":"S70R","2668":"G71V","2670":"Q127P","2671":"A134E","2672":"A138E","2673":"W148R","2674":"A183E","2676":"A200E","3235":"P75S","3670":"A183T","3672":"W45S","3673":"P84L","3675":"H48Y","3676":"G30R","3679":"G117E","3681":"L79F","3682":"L49F","3683":"G164C","3688":"P84C","3689":"V188M","8863":"V124G","8864":"E92A","8865":"V139A","8866":"G37V","9962":"L79S","13201":"N51T","2675":"V188G"},"ReSeqTB-High":{"9840":"L79S","9842":"E92D"},"ReSeqTB-Minimal":{"9841":"E92D"}},"40394":{"param_type":"nonsense mutation","param_description":"A sequence change where, compared to a reference sequence, one codon is replaced by a termination codon through a nucleotide substitution. These are described as a substitution of the wildtype codon to a termination codon. Format is given as [wild type AA][position][Ter], for example Q42Ter where Q42 is a wildtype amino acid replaced by a premature termination codon.","param_type_id":"40394","param_value":{"15750":"R213Ter","15751":"R206Ter","15759":"Y195Ter","15768":"S181Ter","15775":"E173Ter","15779":"E170Ter","15782":"E165Ter","15786":"K163Ter","15794":"R158Ter","15802":"W148Ter","15806":"K144Ter","15821":"S136Ter","15830":"Q127Ter","15831":"Q125Ter","15836":"W123Ter","15837":"E121Ter","15856":"E103Ter","15857":"R102Ter","15863":"E99Ter","15877":"E92Ter","15889":"Q87Ter","15907":"L79Ter","15920":"L74Ter","15928":"G71Ter","15953":"E60Ter","15958":"C52Ter","15978":"W45Ter","15984":"E40Ter","15989":"G37Ter","3677":"C52Ter","15999":"G28Ter","16001":"L26Ter","16008":"Y22Ter","16017":"G13Ter"}},"40494":{"param_type":"frameshift mutation","param_description":"A frameshift is a sequence change between the translation initiation (start) and termination (stop) codon where, compared to a reference sequence, translation shifts to another reading frame as caused by nucleotide insertions and deletions. In ARO, these are annotated at the protein level with the first changed most N-terminal wildtype amino acid position. Format is given as [wildtype AA][position]fs, e.g. S531fs where S531 is a frameshifted coordinate beginning with codon 531. Termination may also be denoted as: Ter[position]fs.","param_type_id":"40494","param_value":{"9842":"R118fs"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"8818":{"protein_sequence":{"accession":"NP_218436.2","sequence":"MSPIEPAASAIFGPRLGLARRYAEALAGPGVERGLVGPREVGRLWDRHLLNCAVIGELLERGDRVVDIGSGAGLPGVPLAIARPDLQVVLLEPLLRRTEFLREMVTDLGVAVEIVRGRAEESWVQDQLGGSDAAVSRAVAALDKLTKWSMPLIRPNGRMLAIKGERAHDEVREHRRVMIASGAVDVRVVTCGANYLRPPATVVFARRGKQIARGSARMASGGTA"},"dna_sequence":{"accession":"NC_000962.3","fmin":"4407527","fmax":"4408202","strand":"-","sequence":"ATGTCTCCGATCGAGCCCGCGGCGTCTGCGATCTTCGGACCGCGGCTTGGCCTTGCTCGGCGGTACGCCGAAGCGTTGGCGGGACCCGGTGTGGAGCGGGGGCTGGTGGGACCCCGCGAAGTCGGTAGGCTATGGGACCGGCATCTACTGAACTGCGCCGTGATCGGTGAGCTCCTCGAACGCGGTGACCGGGTCGTGGATATCGGTAGCGGAGCCGGGTTGCCGGGCGTGCCATTGGCGATAGCGCGGCCGGACCTCCAGGTAGTTCTCCTAGAACCGCTACTGCGCCGCACCGAGTTTCTTCGAGAGATGGTGACAGATCTGGGCGTGGCCGTTGAGATCGTGCGGGGGCGCGCCGAGGAGTCCTGGGTGCAGGACCAATTGGGCGGCAGCGACGCTGCGGTGTCACGGGCGGTGGCCGCGTTGGACAAGTTGACGAAATGGAGCATGCCGTTGATACGGCCGAACGGGCGAATGCTCGCCATCAAAGGCGAGCGGGCTCACGACGAAGTACGGGAGCACCGGCGTGTGATGATCGCATCGGGCGCGGTTGATGTCAGGGTGGTGACATGTGGCGCGAACTATTTGCGTCCGCCCGCGACCGTGGTGTTCGCACGACGTGGAAAGCAGATCGCCCGAGGGTCGGCACGGATGGCGAGTGGAGGGACGGCGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3003470","ARO_id":"40063","ARO_name":"Mycobacterium tuberculosis gidB mutation conferring resistance to streptomycin","CARD_short_name":"Mtub_gidB_STR","ARO_description":"Specific mutations that occurs on Mycobacterium tuberculosis gidB causing it to be streptomycin resistant.","ARO_category":{"40059":{"category_aro_accession":"3003466","category_aro_cvterm_id":"40059","category_aro_name":"antibiotic resistant gidB","category_aro_description":"GidB is a m7G methyltransferase specific for 16S rRNA. Mutations within the gidB gene causes changes in the structure or 16s rRNA, leading to resistance to aminoglycosides.","category_aro_class_name":"AMR Gene Family"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2138":{"model_id":"2138","model_name":"NmcA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"575"}},"model_sequences":{"sequence":{"3362":{"protein_sequence":{"accession":"CAA79967.1","sequence":"MSLNVKQSRIAILFSSCLISISFFSQANTKGIDEIKNLETDFNGRIGVYALDTGSGKSFSYRANERFPLCSSFKGFLAAAVLKGSQDNRLNLNQIVNYNTRSLEFHSPITTKYKDNGMSLGDMAAAALQYSDNGATNIILERYIGGPEGMTKFMRSIGDEDFRLDRWELDLNTAIPGDERDTSTPAAVAKSLKTLALGNILSEHEKETYQTWLKGNTTGAARIRASVPSDWVVGDKTGSCGAYGTANDYAVVWPKNRAPLIISVYTTKNEKEAKHEDKVIAEASRIAIDNLK"},"dna_sequence":{"accession":"Z21956.1","fmin":"1220","fmax":"2099","strand":"+","sequence":"ATGTCACTTAATGTAAAGCAAAGTAGAATAGCCATCTTGTTTAGCTCTTGTTTAATTTCAATATCATTTTTCTCACAGGCCAATACGAAGGGCATTGATGAGATTAAAAACCTTGAAACAGATTTCAATGGCAGGATTGGTGTCTACGCTTTAGACACTGGCTCGGGTAAATCATTTTCGTACAGAGCAAATGAACGATTTCCATTATGTAGTTCTTTTAAAGGTTTTTTAGCTGCTGCTGTATTAAAAGGCTCTCAAGATAATCGACTTAATCTTAATCAGATTGTGAATTATAATACAAGAAGTTTAGAGTTCCATTCACCCATCACAACTAAATATAAAGATAATGGAATGTCATTAGGTGATATGGCTGCTGCTGCTTTACAATATAGCGACAATGGTGCTACTAATATTATTCTTGAACGTTATATCGGTGGTCCAGAGGGTATGACTAAATTCATGCGGTCGATTGGAGATGAAGATTTTAGACTCGATCGTTGGGAGTTAGATCTAAACACAGCTATTCCAGGCGATGAGCGTGACACATCTACACCTGCAGCAGTAGCCAAGAGTCTGAAAACCCTTGCTCTGGGTAACATACTTAGTGAACATGAAAAGGAAACCTATCAGACATGGTTAAAGGGTAACACAACCGGTGCAGCGCGTATTCGTGCTAGCGTACCAAGCGATTGGGTAGTTGGCGATAAAACTGGTAGTTGCGGAGCATACGGTACGGCAAATGATTATGCGGTAGTCTGGCCAAAGAACCGGGCTCCTCTTATAATTTCTGTATACACAACAAAAAACGAAAAAGAAGCCAAGCATGAGGATAAAGTAATCGCAGAAGCTTCAAGAATTGCAATTGATAACCTTAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3003589","ARO_id":"40199","ARO_name":"NmcA","CARD_short_name":"NmcA","ARO_description":"NmcA is a class A serine beta-lactamase isolated from Enterobacter cloacae.","ARO_category":{"36027":{"category_aro_accession":"3000018","category_aro_cvterm_id":"36027","category_aro_name":"IMI beta-lactamase","category_aro_description":"IMI beta-lactamases are a group of TEM-1-like beta-lactamase that are known to hydrolyze imipenem. IMI beta-lactamases are inhibited by clavulanic acid and tazobactam.","category_aro_class_name":"AMR Gene Family"},"35927":{"category_aro_accession":"0000008","category_aro_cvterm_id":"35927","category_aro_name":"cefoxitin","category_aro_description":"Cefoxitin is a cephamycin antibiotic often grouped with the second generation cephalosporins. Cefoxitin is bactericidal and acts by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. Cefoxitin's 7-alpha-methoxy group and 3' leaving group make it a poor substrate for most beta-lactamases.","category_aro_class_name":"Antibiotic"},"35975":{"category_aro_accession":"0000058","category_aro_cvterm_id":"35975","category_aro_name":"cefazolin","category_aro_description":"Cefazolin, also known as cefazoline or cephazolin, is a first generation cephalosporin antibiotic. It is administered parenterally, and is active against a broad spectrum of bacteria.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1942":{"model_id":"1942","model_name":"BJP-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"5242":{"protein_sequence":{"accession":"AND91341.1","sequence":"MRRLTAALCALTLLSTGAQAQTIKDFLAVAMKKWTAPFEPFQLIDNIYYVGTDGIAVYVIKTSQGLILMDTAMPQSTGMIKDNIAKLGFKVADIKLILNTHAHLDHTGGFAEIKKETGAQLVAGERDKPLLEGGYYPGDEKNEDLAFPAVKVDRAVKEGDRVTLGDTTLTAHATPGHSPGCTSWEMTVKDGKEDREVLFFCSGTVALNRLVGQPTYAGIVDDYRATFAKAKAMKIDVLLGPHPEVYGMQAKRAEMKDGAPNPFIKPGELVTYATSLSEDFDKQLAKQTAALEKK"},"dna_sequence":{"accession":"CP011360.1","fmin":"6169922","fmax":"6170807","strand":"+","sequence":"ATGAGAAGGCTGACGGCCGCGCTGTGTGCTCTGACCCTGCTCTCGACTGGCGCGCAGGCGCAAACCATCAAGGATTTTCTGGCAGTCGCCATGAAGAAATGGACGGCGCCGTTCGAGCCGTTCCAGCTCATCGACAACATCTACTATGTCGGAACCGACGGCATTGCCGTCTATGTCATCAAGACATCGCAGGGCCTGATCCTGATGGACACGGCGATGCCCCAGTCAACCGGCATGATCAAGGACAATATTGCGAAGCTCGGCTTCAAGGTTGCCGATATCAAGCTCATCCTCAACACGCACGCGCATCTCGACCACACCGGCGGCTTCGCCGAGATCAAGAAGGAGACCGGCGCGCAGCTCGTTGCCGGCGAGCGCGACAAGCCACTGCTCGAAGGCGGCTACTATCCGGGTGACGAGAAAAACGAGGACCTCGCCTTCCCCGCGGTGAAAGTCGATCGCGCGGTGAAGGAAGGCGACAGGGTCACGCTCGGAGACACCACGCTGACGGCACACGCAACACCCGGCCACTCGCCGGGCTGCACCAGCTGGGAGATGACCGTCAAGGACGGCAAGGAGGACCGCGAGGTGCTGTTCTTCTGTAGCGGCACGGTGGCGCTGAACCGGCTGGTCGGCCAGCCGACCTATGCCGGCATCGTCGACGACTACCGCGCGACTTTCGCCAAGGCCAAGGCGATGAAGATCGACGTGCTGCTCGGGCCGCATCCGGAAGTCTATGGCATGCAGGCCAAGCGCGCAGAGATGAAGGATGGCGCGCCGAACCCGTTCATCAAGCCGGGCGAGCTCGTGACCTACGCGACCAGCCTGTCGGAGGATTTCGACAAGCAGCTCGCCAAGCAGACCGCGGCGCTGGAGAAGAAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42583","NCBI_taxonomy_name":"Bradyrhizobium diazoefficiens USDA 110","NCBI_taxonomy_id":"224911"}}}},"ARO_accession":"3000856","ARO_id":"37236","ARO_name":"BJP-1","CARD_short_name":"BJP-1","ARO_description":"BJP-1 is a subclass B3 ortholog found in Bradyrhizobium japonicum that hydrolyzes most beta-lactams except aztreonam, ticarcillin, and temocillin.","ARO_category":{"41383":{"category_aro_accession":"3004219","category_aro_cvterm_id":"41383","category_aro_name":"BJP beta-lactamase","category_aro_description":"BJP beta-lactamases are a subclass B3 family.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2014":{"model_id":"2014","model_name":"PmrF","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"2115":{"protein_sequence":{"accession":"AAC75314.1","sequence":"MFEIHPVKKVSVVIPVYNEQESLPELIRRTTTACESLGKEYEILLIDDGSSDNSAHMLVEASQAENSHIVSILLNRNYGQHSAIMAGFSHVTGDLIITLDADLQNPPEEIPRLVAKADEGYDVVGTVRQNRQDSWFRKTASKMINRLIQRTTGKAMGDYGCMLRAYRRHIVDAMLHCHERSTFIPILANIFARRAIEIPVHHAEREFGESKYSFMRLINLMYDLVTCLTTTPLRMLSLLGSIIAIGGFSIAVLLVILRLTFGPQWAAEGVFMLFAVLFTFIGAQFIGMGLLGEYIGRIYTDVRARPRYFVQQVIRPSSKENE"},"dna_sequence":{"accession":"U00096.1","fmin":"2367070","fmax":"2368039","strand":"+","sequence":"ATGTTTGAAATCCACCCTGTTAAGAAAGTCTCGGTGGTTATTCCCGTTTATAACGAGCAGGAAAGCTTACCGGAATTAATCAGGCGCACCACCACAGCCTGTGAATCGTTGGGGAAAGAGTATGAGATCCTGCTGATTGATGACGGCAGTAGCGATAATTCCGCGCATATGCTGGTCGAAGCCTCACAAGCGGAGAACAGCCATATTGTGTCTATTTTGCTTAACCGCAATTACGGGCAACATTCAGCGATTATGGCGGGATTCAGTCACGTTACTGGCGACTTAATTATTACCCTTGATGCCGATCTCCAGAATCCGCCAGAAGAAATCCCCCGCCTGGTGGCAAAAGCCGATGAAGGTTACGACGTGGTAGGGACTGTACGCCAGAACCGCCAGGACAGCTGGTTTCGTAAAACCGCTTCGAAGATGATTAACCGGCTTATTCAGCGCACCACTGGCAAAGCGATGGGTGATTACGGTTGTATGCTGCGCGCCTATCGCCGTCATATTGTCGATGCGATGTTGCACTGCCATGAACGCAGCACCTTTATCCCGATTCTGGCGAATATCTTCGCCCGCCGTGCCATTGAAATTCCAGTACATCATGCCGAGCGTGAGTTTGGTGAATCCAAATACAGTTTTATGCGCCTGATTAATTTGATGTACGACCTGGTGACCTGCCTTACCACAACGCCGCTACGTATGCTGAGTCTGCTCGGCAGCATTATTGCGATTGGAGGTTTTAGCATTGCGGTGCTGCTGGTGATTTTACGCCTGACCTTCGGACCACAATGGGCGGCAGAAGGCGTCTTTATGCTATTTGCCGTGCTGTTTACTTTTATTGGCGCTCAGTTTATCGGCATGGGATTACTCGGTGAATATATCGGCAGGATCTACACCGATGTCCGCGCCCGCCCCCGCTATTTTGTTCAGCAAGTTATCCGTCCATCCAGCAAGGAAAATGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36849","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. MG1655","NCBI_taxonomy_id":"511145"}}}},"ARO_accession":"3003578","ARO_id":"40188","ARO_name":"PmrF","CARD_short_name":"PmrF","ARO_description":"PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A, which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.","ARO_category":{"41433":{"category_aro_accession":"3004269","category_aro_cvterm_id":"41433","category_aro_name":"pmr phosphoethanolamine transferase","category_aro_description":"This family of phosphoethanolamine transferase catalyze the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine to lipid A, which impedes the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36593":{"category_aro_accession":"3000454","category_aro_cvterm_id":"36593","category_aro_name":"polymyxin B","category_aro_description":"Polymyxin B is mixture of mostly polymyxins B1 and B2, mainly used for resistant gram-negative infections. They are polypeptides with cationic detergent action on cell membranes.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"196":{"model_id":"196","model_name":"Mycobacterium tuberculosis embB mutant conferring resistance to ethambutol","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"13302":"D328Y","13303":"D354A","13340":"G406A","13341":"G406D","13342":"G406S","13392":"M306I","13394":"M306V","13411":"Q497K","13412":"Q497R","13626":"N1033K","13680":"M306Var","15432":"M306L","15435":"Y319S","15437":"Y319C","15451":"G406C","9465":"Y334H","9466":"S347I","9469":"L402V","9474":"A454T","9477":"D1024N","9481":"S22C","9482":"N296H","9489":"F330S","2239":"D328G","2240":"F330V","2243":"L413P","2296":"S297A","2297":"D299E","2301":"M306T","2345":"D311H","2413":"L239P","2414":"D240H","2440":"E368A","2446":"P375A","2450":"E378A","2453":"S380R","2460":"P397Q","2478":"P446H","2482":"R460C","2485":"I465D","2486":"R469P","2487":"R471P","2490":"G745D","2491":"D959A","3589":"R507G","3594":"Y333C","3595":"Y319N","2464":"N399H","2492":"M1000R","3588":"E504Q"},"CRyPTIC-R":{"13302":"D328Y","13303":"D354A","13340":"G406A","13341":"G406D","13342":"G406S","13392":"M306I","13394":"M306V","13411":"Q497K","13412":"Q497R","13626":"N1033K","13680":"M306Var"},"clinical":{"13302":"D328Y","13303":"D354A","13340":"G406A","13341":"G406D","13342":"G406S","13392":"M306I","13394":"M306V","13411":"Q497K","13412":"Q497R","13626":"N1033K","13680":"M306Var","15432":"M306L","15433":"M306V","15434":"M306I","15435":"Y319S","15437":"Y319C","15438":"D328Y","15444":"D354A","15450":"G406S","15451":"G406C","15452":"G406D","15453":"G406A","15458":"Q497R","15459":"Q497K","9465":"Y334H","9466":"S347I","9467":"D354A","9469":"L402V","9470":"G406S","9471":"G406C","9472":"G406D","9473":"G406A","9474":"A454T","9475":"Q497K","9476":"Q497R","9477":"D1024N","9481":"S22C","9482":"N296H","9483":"M306L","9485":"M306I","9486":"Y319S","9487":"Y319C","9488":"D328Y","9489":"F330S","2238":"D328Y","2239":"D328G","2240":"F330V","2242":"G406A","2243":"L413P","2296":"S297A","2297":"D299E","2298":"M306L","2299":"M306V","2300":"M306I","2301":"M306T","2345":"D311H","2413":"L239P","2414":"D240H","2426":"Y334H","2440":"E368A","2446":"P375A","2450":"E378A","2453":"S380R","2460":"P397Q","2470":"G406S","2471":"G406C","2472":"G406D","2478":"P446H","2482":"R460C","2485":"I465D","2486":"R469P","2487":"R471P","2488":"Q497R","2489":"Q497K","2490":"G745D","2491":"D959A","2493":"D1024N","3589":"R507G","3593":"Y319C","3594":"Y333C","3595":"Y319N","9484":"M306V","2464":"N399H","2492":"M1000R","3588":"E504Q"},"WHO-R":{"15432":"M306L","15433":"M306V","15434":"M306I","15435":"Y319S","15437":"Y319C","15438":"D328Y","15444":"D354A","15450":"G406S","15451":"G406C","15452":"G406D","15453":"G406A","15458":"Q497R","15459":"Q497K"},"ReSeqTB-High":{"9465":"Y334H","9469":"L402V","9471":"G406C","9474":"A454T","9476":"Q497R","9481":"S22C","9482":"N296H","9486":"Y319S","9487":"Y319C","9488":"D328Y","9489":"F330S","9484":"M306V"},"ReSeqTB-Moderate":{"9466":"S347I","9467":"D354A","9470":"G406S","9473":"G406A","9485":"M306I"},"ReSeqTB-Minimal":{"9472":"G406D","9475":"Q497K","9477":"D1024N","9483":"M306L"},"Curated-R":{"2238":"D328Y","2239":"D328G","2240":"F330V","2242":"G406A","2243":"L413P","2296":"S297A","2297":"D299E","2298":"M306L","2299":"M306V","2300":"M306I","2301":"M306T","2345":"D311H","2413":"L239P","2414":"D240H","2426":"Y334H","2440":"E368A","2446":"P375A","2450":"E378A","2453":"S380R","2460":"P397Q","2470":"G406S","2471":"G406C","2472":"G406D","2478":"P446H","2482":"R460C","2485":"I465D","2486":"R469P","2487":"R471P","2488":"Q497R","2489":"Q497K","2490":"G745D","2491":"D959A","2493":"D1024N","3589":"R507G","3593":"Y319C","3594":"Y333C","3595":"Y319N","2464":"N399H","2492":"M1000R","3588":"E504Q"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"2000"}},"model_sequences":{"sequence":{"8805":{"protein_sequence":{"accession":"NP_218312.1","sequence":"MTQCASRRKSTPNRAILGAFASARGTRWVATIAGLIGFVLSVATPLLPVVQTTAMLDWPQRGQLGSVTAPLISLTPVDFTATVPCDVVRAMPPAGGVVLGTAPKQGKDANLQALFVVVSAQRVDVTDRNVVILSVPREQVTSPQCQRIEVTSTHAGTFANFVGLKDPSGAPLRSGFPDPNLRPQIVGVFTDLTGPAPPGLAVSATIDTRFSTRPTTLKLLAIIGAIVATVVALIALWRLDQLDGRGSIAQLLLRPFRPASSPGGMRRLIPASWRTFTLTDAVVIFGFLLWHVIGANSSDDGYILGMARVADHAGYMSNYFRWFGSPEDPFGWYYNLLALMTHVSDASLWMRLPDLAAGLVCWLLLSREVLPRLGPAVEASKPAYWAAAMVLLTAWMPFNNGLRPEGIIALGSLVTYVLIERSMRYSRLTPAALAVVTAAFTLGVQPTGLIAVAALVAGGRPMLRILVRRHRLVGTLPLVSPMLAAGTVILTVVFADQTLSTVLEATRVRAKIGPSQAWYTENLRYYYLILPTVDGSLSRRFGFLITALCLFTAVFIMLRRKRIPSVARGPAWRLMGVIFGTMFFLMFTPTKWVHHFGLFAAVGAAMAALTTVLVSPSVLRWSRNRMAFLAALFFLLALCWATTNGWWYVSSYGVPFNSAMPKIDGITVSTIFFALFAIAAGYAAWLHFAPRGAGEGRLIRALTTAPVPIVAGFMAAVFVASMVAGIVRQYPTYSNGWSNVRAFVGGCGLADDVLVEPDTNAGFMKPLDGDSGSWGPLGPLGGVNPVGFTPNGVPEHTVAEAIVMKPNQPGTDYDWDAPTKLTSPGINGSTVPLPYGLDPARVPLAGTYTTGAQQQSTLVSAWYLLPKPDDGHPLVVVTAAGKIAGNSVLHGYTPGQTVVLEYAMPGPGALVPAGRMVPDDLYGEQPKAWRNLRFARAKMPADAVAVRVVAEDLSLTPEDWIAVTPPRVPDLRSLQEYVGSTQPVLLDWAVGLAFPCQQPMLHANGIAEIPKFRITPDYSAKKLDTDTWEDGTNGGLLGITDLLLRAHVMATYLSRDWARDWGSLRKFDTLVDAPPAQLELGTATRSGLWSPGKIRIGP"},"dna_sequence":{"accession":"NC_000962.3","fmin":"4246513","fmax":"4249810","strand":"+","sequence":"ATGACACAGTGCGCGAGCAGACGCAAAAGCACCCCAAATCGGGCGATTTTGGGGGCTTTTGCGTCTGCTCGCGGGACGCGCTGGGTGGCCACCATCGCCGGGCTGATTGGCTTTGTGTTGTCGGTGGCGACGCCGCTGCTGCCCGTCGTGCAGACCACCGCGATGCTCGACTGGCCACAGCGGGGGCAACTGGGCAGCGTGACCGCCCCGCTGATCTCGCTGACGCCGGTCGACTTTACCGCCACCGTGCCGTGCGACGTGGTGCGCGCCATGCCACCCGCGGGCGGGGTGGTGCTGGGCACCGCACCCAAGCAAGGCAAGGACGCCAATTTGCAGGCGTTGTTCGTCGTCGTCAGCGCCCAGCGCGTGGACGTCACCGACCGCAACGTGGTGATCTTGTCCGTGCCGCGCGAGCAGGTGACGTCCCCGCAGTGTCAACGCATCGAGGTCACCTCTACCCACGCCGGCACCTTCGCCAACTTCGTCGGGCTCAAGGACCCGTCGGGCGCGCCGCTGCGCAGCGGCTTCCCCGACCCCAACCTGCGCCCGCAGATTGTCGGGGTGTTCACCGACCTGACCGGGCCCGCGCCGCCCGGGCTGGCGGTCTCGGCGACCATCGACACCCGGTTCTCCACCCGGCCGACCACGCTGAAACTGCTGGCGATCATCGGGGCGATCGTGGCCACCGTCGTCGCACTGATCGCGTTGTGGCGCCTGGACCAGTTGGACGGGCGGGGCTCAATTGCCCAGCTCCTCCTCAGGCCGTTCCGGCCTGCATCGTCGCCGGGCGGCATGCGCCGGCTGATTCCGGCAAGCTGGCGCACCTTCACCCTGACCGACGCCGTGGTGATATTCGGCTTCCTGCTCTGGCATGTCATCGGCGCGAATTCGTCGGACGACGGCTACATCCTGGGCATGGCCCGAGTCGCCGACCACGCCGGCTACATGTCCAACTATTTCCGCTGGTTCGGCAGCCCGGAGGATCCCTTCGGCTGGTATTACAACCTGCTGGCGCTGATGACCCATGTCAGCGACGCCAGTCTGTGGATGCGCCTGCCAGACCTGGCCGCCGGGCTAGTGTGCTGGCTGCTGCTGTCGCGTGAGGTGCTGCCCCGCCTCGGGCCGGCGGTGGAGGCCAGCAAACCCGCCTACTGGGCGGCGGCCATGGTCTTGCTGACCGCGTGGATGCCGTTCAACAACGGCCTGCGGCCGGAGGGCATCATCGCGCTCGGCTCGCTGGTCACCTATGTGCTGATCGAGCGGTCCATGCGGTACAGCCGGCTCACACCGGCGGCGCTGGCCGTCGTTACCGCCGCATTCACACTGGGTGTGCAGCCCACCGGCCTGATCGCGGTGGCCGCGCTGGTGGCCGGCGGCCGCCCGATGCTGCGGATCTTGGTGCGCCGTCATCGCCTGGTCGGCACGTTGCCGTTGGTGTCGCCGATGCTGGCCGCCGGCACCGTCATCCTGACCGTGGTGTTCGCCGACCAGACCCTGTCAACGGTGTTGGAAGCCACCAGGGTTCGCGCCAAAATCGGGCCGAGCCAGGCGTGGTATACCGAGAACCTGCGTTACTACTACCTCATCCTGCCCACCGTCGACGGTTCGCTGTCGCGGCGCTTCGGCTTTTTGATCACCGCGCTATGCCTGTTCACCGCGGTGTTCATCATGTTGCGGCGCAAGCGAATTCCCAGCGTGGCCCGCGGACCGGCGTGGCGGCTGATGGGCGTCATCTTCGGCACCATGTTCTTCCTGATGTTCACGCCCACCAAGTGGGTGCACCACTTCGGGCTGTTCGCCGCCGTAGGGGCGGCGATGGCCGCGCTGACGACGGTGTTGGTATCCCCATCGGTGCTGCGCTGGTCGCGCAACCGGATGGCGTTCCTGGCGGCGTTATTCTTCCTGCTGGCGTTGTGTTGGGCCACCACCAACGGCTGGTGGTATGTCTCCAGCTACGGTGTGCCGTTCAACAGCGCGATGCCGAAGATCGACGGGATCACAGTCAGCACAATCTTTTTCGCCCTGTTTGCGATCGCCGCCGGCTATGCGGCCTGGCTGCACTTCGCGCCCCGCGGCGCCGGCGAAGGGCGGCTGATCCGCGCGCTGACGACAGCCCCGGTACCGATCGTGGCCGGTTTCATGGCGGCGGTGTTCGTCGCGTCCATGGTGGCCGGGATCGTGCGACAGTACCCGACCTACTCCAACGGCTGGTCCAACGTGCGGGCGTTTGTCGGCGGCTGCGGACTGGCCGACGACGTACTCGTCGAGCCTGATACCAATGCGGGTTTCATGAAGCCGCTGGACGGCGATTCGGGTTCTTGGGGCCCCTTGGGCCCGCTGGGTGGAGTCAACCCGGTCGGCTTCACGCCCAACGGCGTACCGGAACACACGGTGGCCGAGGCGATCGTGATGAAACCCAACCAGCCCGGCACCGACTACGACTGGGATGCGCCGACCAAGCTGACGAGTCCTGGCATCAATGGTTCTACGGTGCCGCTGCCCTATGGGCTCGATCCCGCCCGGGTACCGTTGGCAGGCACCTACACCACCGGCGCACAGCAACAGAGCACACTCGTCTCGGCGTGGTATCTCCTGCCTAAGCCGGACGACGGGCATCCGCTGGTCGTGGTGACCGCCGCGGGCAAGATCGCCGGCAACAGCGTGCTGCACGGGTACACCCCCGGGCAGACTGTGGTGCTCGAATACGCCATGCCGGGACCCGGAGCGCTGGTACCCGCCGGGCGGATGGTGCCCGACGACCTATACGGAGAGCAGCCCAAGGCGTGGCGCAACCTGCGCTTCGCCCGAGCAAAGATGCCCGCCGATGCCGTCGCGGTCCGGGTGGTGGCCGAGGATCTGTCGCTGACACCGGAGGACTGGATCGCGGTGACCCCGCCGCGGGTACCGGACCTGCGCTCACTGCAGGAATATGTGGGCTCGACGCAGCCGGTGCTGCTGGACTGGGCGGTCGGTTTGGCCTTCCCGTGCCAGCAGCCGATGCTGCACGCCAATGGCATCGCCGAAATCCCGAAGTTCCGCATCACACCGGACTACTCGGCTAAGAAGCTGGACACCGACACGTGGGAAGACGGCACTAACGGCGGCCTGCTCGGGATCACCGACCTGTTGCTGCGGGCCCACGTCATGGCCACCTACCTGTCCCGCGACTGGGCCCGCGATTGGGGTTCCCTGCGCAAGTTCGACACCCTGGTCGATGCCCCTCCCGCCCAGCTCGAGTTGGGCACCGCGACCCGCAGCGGCCTGTGGTCACCGGGCAAGATCCGAATTGGTCCATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3003326","ARO_id":"39910","ARO_name":"Mycobacterium tuberculosis embB mutant conferring resistance to ethambutol","CARD_short_name":"Mtub_embB_EMB","ARO_description":"Point mutations that occur within Mycobacterium tuberculosis embB gene resulting in resistance to ethambutol.","ARO_category":{"36374":{"category_aro_accession":"3000235","category_aro_cvterm_id":"36374","category_aro_name":"ethambutol resistant embB","category_aro_description":"embB gene encodes for an arabinosyl transferase in the arabinogalactan synthesis pathway. It is inhibited by ethambutol. Mutations within the ERDR region of embB confers resistance to ethambutol.","category_aro_class_name":"AMR Gene Family"},"36636":{"category_aro_accession":"3000497","category_aro_cvterm_id":"36636","category_aro_name":"ethambutol","category_aro_description":"Ethambutol is an antimycobacterial drug prescribed to treat tuberculosis. It is usually given in combination with other tuberculosis drugs, such as isoniazid, rifampicin, and pyrazinamide. Ethambutol inhibits arabinosyl biosynthesis, disrupting mycobacterial cell wall formation.","category_aro_class_name":"Antibiotic"},"36666":{"category_aro_accession":"3000527","category_aro_cvterm_id":"36666","category_aro_name":"polyamine antibiotic","category_aro_description":"Polyamine antibiotics are organic compounds having two or more primary amino groups.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"366":{"model_id":"366","model_name":"Mycobacterium tuberculosis iniA mutant conferring resistance to ethambutol","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"3334":"G308R","3856":"P3A","3857":"R537H","3333":"S501W"},"Curated-R":{"3334":"G308R","3856":"P3A","3857":"R537H","3333":"S501W"},"experimental":{"3334":"G308R","3333":"S501W"},"clinical":{"3856":"P3A","3857":"R537H"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1240"}},"model_sequences":{"sequence":{"8829":{"protein_sequence":{"accession":"NP_214856.1","sequence":"MVPAGLCAYRDLRRKRARKWGDTVTQPDDPRRVGVIVELIDHTIAIAKLNERGDLVQRLTRARQRITDPQVRVVIAGLLKQGKSQLLNSLLNLPAARVGDDEATVVITVVSYSAQPSARLVLAAGPDGTTAAVDIPVDDISTDVRRAPHAGGREVLRVEVGAPSPLLRGGLAFIDTPGVGGLGQPHLSATLGLLPEADAVLVVSDTSQEFTEPEMWFVRQAHQICPVGAVVATKTDLYPRWREIVNANAAHLQRARVPMPIIAVSSLLRSHAVTLNDKELNEESNFPAIVKFLSEQVLSRATERVRAGVLGEIRSATEQLAVSLGSELSVVNDPNLRDRLASDLERRKREAQQAVQQTALWQQVLGDGFNDLTADVDHDLRTRFRTVTEDAERQIDSCDPTAHWAEIGNDVENAIATAVGDNFVWAYQRSEALADDVARSFADAGLDSVLSAELSPHVMGTDFGRLKALGRMESKPLRRGHKMIIGMRGSYGGVVMIGMLSSVVGLGLFNPLSVGAGLILGRMAYKEDKQNRLLRVRSEAKANVRRFVDDISFVVSKQSRDRLKMIQRLLRDHYREIAEEITRSLTESLQATIAAAQVAETERDNRIRELQRQLGILSQVNDNLAGLEPTLTPRASLGRA"},"dna_sequence":{"accession":"NC_000962.3","fmin":"410837","fmax":"412760","strand":"+","sequence":"ATGGTCCCCGCCGGTTTGTGCGCATACCGTGATCTGAGGCGTAAACGAGCGAGAAAGTGGGGCGACACGGTGACCCAGCCCGATGACCCACGTCGGGTCGGTGTGATCGTCGAACTGATCGATCACACTATCGCCATCGCCAAACTGAACGAGCGTGGTGATCTAGTACAGCGGTTGACGCGGGCTCGCCAGCGGATCACCGACCCGCAGGTCCGTGTGGTGATCGCCGGGCTGCTCAAACAGGGCAAGAGTCAATTGCTCAATTCGTTGCTCAACCTGCCCGCGGCGCGAGTAGGCGATGACGAGGCCACCGTGGTGATCACCGTCGTAAGCTACAGCGCCCAACCGTCGGCCCGGCTTGTGCTGGCCGCCGGGCCCGACGGGACAACCGCAGCGGTTGACATTCCCGTCGATGACATCAGCACCGATGTGCGTCGGGCTCCGCACGCCGGTGGCCGCGAGGTGTTGCGGGTCGAGGTCGGCGCGCCCAGCCCGCTGCTGCGGGGCGGGCTGGCGTTTATCGATACTCCGGGTGTGGGCGGCCTCGGACAGCCCCACCTGTCGGCGACGCTGGGGCTGCTACCCGAGGCCGATGCCGTCTTGGTGGTCAGCGACACCAGCCAGGAATTCACCGAACCCGAGATGTGGTTCGTGCGGCAGGCCCACCAGATCTGTCCGGTCGGGGCGGTCGTGGCCACCAAGACCGACCTGTATCCGCGCTGGCGGGAGATCGTCAATGCCAATGCAGCACATCTGCAGCGGGCCCGGGTTCCGATGCCGATCATCGCAGTCTCATCACTGTTGCGCAGCCACGCGGTCACGCTTAACGACAAAGAGCTCAACGAAGAGTCCAACTTTCCGGCGATCGTCAAGTTTCTCAGCGAGCAGGTGCTTTCCCGCGCGACGGAGCGAGTGCGTGCTGGGGTACTCGGCGAAATACGTTCGGCAACAGAGCAATTGGCGGTGTCTCTAGGTTCCGAACTATCGGTGGTCAACGACCCGAACCTCCGTGACCGACTTGCTTCGGATTTGGAGCGGCGCAAACGGGAAGCCCAGCAGGCGGTGCAACAGACAGCGCTGTGGCAGCAGGTGCTGGGCGACGGGTTCAACGACCTGACTGCTGACGTGGACCACGACCTACGAACCCGCTTCCGCACCGTCACCGAAGACGCCGAGCGCCAGATCGACTCCTGTGACCCGACTGCGCATTGGGCCGAGATTGGCAACGACGTCGAGAATGCGATCGCCACAGCGGTCGGCGACAACTTCGTGTGGGCATACCAGCGTTCCGAAGCGTTGGCCGACGACGTCGCTCGCTCCTTTGCCGACGCGGGGTTGGACTCGGTCCTGTCAGCAGAGCTGAGCCCCCACGTCATGGGCACCGACTTCGGCCGGCTCAAAGCGCTGGGCCGGATGGAATCGAAACCGCTGCGCCGGGGCCATAAAATGATTATCGGCATGCGGGGTTCCTATGGCGGCGTGGTCATGATTGGCATGCTGTCGTCGGTGGTCGGACTTGGGTTGTTCAACCCGCTATCGGTGGGGGCCGGGTTGATCCTCGGCCGGATGGCATATAAAGAGGACAAACAAAACCGGTTGCTGCGGGTGCGCAGCGAGGCCAAGGCCAATGTGCGGCGCTTCGTCGACGACATTTCGTTCGTCGTCAGCAAACAATCACGGGATCGGCTCAAGATGATCCAGCGTCTGCTGCGCGACCACTACCGCGAGATCGCCGAAGAGATCACCCGGTCGCTCACCGAGTCCCTGCAGGCGACCATCGCGGCGGCGCAGGTGGCGGAAACCGAGCGGGACAATCGAATTCGGGAACTTCAGCGGCAATTGGGTATCCTGAGCCAGGTCAACGACAACCTTGCCGGCTTGGAGCCAACCTTGACGCCCCGGGCGAGCTTGGGACGAGCGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3003448","ARO_id":"40041","ARO_name":"Mycobacterium tuberculosis iniA mutant conferring resistance to ethambutol","CARD_short_name":"Mtub_iniA_EMB","ARO_description":"Specific mutations in Mycobacterium tuberculosis iniA resulting in resistance to ethambutol.","ARO_category":{"40040":{"category_aro_accession":"3003447","category_aro_cvterm_id":"40040","category_aro_name":"ethambutol resistant iniA","category_aro_description":"Mutations that occurs on the iniA genes resulting in the resistance to ethambutol.","category_aro_class_name":"AMR Gene Family"},"36636":{"category_aro_accession":"3000497","category_aro_cvterm_id":"36636","category_aro_name":"ethambutol","category_aro_description":"Ethambutol is an antimycobacterial drug prescribed to treat tuberculosis. It is usually given in combination with other tuberculosis drugs, such as isoniazid, rifampicin, and pyrazinamide. Ethambutol inhibits arabinosyl biosynthesis, disrupting mycobacterial cell wall formation.","category_aro_class_name":"Antibiotic"},"36666":{"category_aro_accession":"3000527","category_aro_cvterm_id":"36666","category_aro_name":"polyamine antibiotic","category_aro_description":"Polyamine antibiotics are organic compounds having two or more primary amino groups.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"505":{"model_id":"505","model_name":"Mycobacterium tuberculosis iniC mutant conferring resistance to ethambutol","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"40394":{"param_type":"nonsense mutation","param_description":"A sequence change where, compared to a reference sequence, one codon is replaced by a termination codon through a nucleotide substitution. These are described as a substitution of the wildtype codon to a termination codon. Format is given as [wild type AA][position][Ter], for example Q42Ter where Q42 is a wildtype amino acid replaced by a premature termination codon.","param_type_id":"40394","param_value":{"3530":"Q351Ter"}},"snp":{"Curated-R":{"3530":"S501W","2346":"P248A","3352":"W83G","18563":"W83G","18562":"W83G"},"param_value":{"2346":"P248A","3352":"W83G"},"clinical":{"2346":"P248A"},"experimental":{"3352":"W83G"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"900"},"41344":{"param_type":"insertion mutation from peptide sequence","param_description":"A peptide sequence change between the translation initiation (start) and termination (stop) codon where, compared to the reference sequence, one or more amino acids are inserted. These represent in-frame insertions which do not result in frameshift variants and where the insertion is not a duplication of a sequence immediately N-terminal (5'), and are denoted with wildtype flanking residues. Format is given by [wildtype AA position]_[wildtype AA position]ins[AA sequence], e.g. K464_D465insE or P46_A47insYS.","param_type_id":"41344","param_value":{"18563":"T78_R79insT","18562":"R97_G98insA"}}},"model_sequences":{"sequence":{"8831":{"protein_sequence":{"accession":"NP_214857.1","sequence":"MSTSDRVRAILHATIQAYRGAPAYRQRGDVFCQLDRIGARLAEPLRIALAGTLKAGKSTLVNALVGDDIAPTDATEATRIVTWFRHGPTPRVTANHRGGRRANVPITRRGGLSFDLRRINPAELIDLEVEWPAEELIDATIVDTPGTSSLACDASERTLRLLVPADGVPRVDAVVFLLRTLNAADVALLKQIGGLVGGSVGALGIIGVASRADEIGAGRIDAMLSANDVAKRFTRELNQMGICQAVVPVSGLLALTARTLRQTEFIALRKLAGAERTELNRALLSVDRFVRRDSPLPVDAGIRAQLLERFGMFGIRMSIAVLAAGVTDSTGLAAELLERSGLVALRNVIDQQFAQRSDMLKAHTALVSLRRFVQTHPVPATPYVIADIDPLLADTHAFEELRMLSLLPSRATTLNDDEIASLRRIIGGSGTSAAARLGLDPANSREAPRAALAAAQHWRRRAAHPLNDPFTTRACRAAVRSAEAMVAEFSARR"},"dna_sequence":{"accession":"NC_000962.3","fmin":"412756","fmax":"414238","strand":"+","sequence":"GTGAGCACCAGCGACCGGGTCCGCGCGATTCTGCACGCAACCATCCAGGCCTACCGGGGTGCGCCGGCCTATCGTCAGCGTGGCGACGTTTTTTGCCAGCTGGACCGCATCGGTGCGCGCCTAGCCGAACCGCTGCGCATCGCGTTGGCTGGCACACTCAAGGCCGGAAAATCCACTCTCGTCAACGCCCTTGTCGGCGACGACATCGCTCCGACCGATGCCACCGAGGCCACCCGGATTGTGACCTGGTTCCGGCACGGTCCGACACCGCGGGTCACCGCCAACCATCGCGGCGGTCGACGCGCCAACGTGCCGATCACCCGTCGGGGCGGGCTGAGTTTCGACCTGCGCAGGATCAACCCGGCCGAGCTGATCGACCTGGAAGTCGAGTGGCCAGCCGAGGAACTCATCGACGCCACCATTGTTGACACCCCGGGAACGTCGTCGTTGGCATGCGATGCCTCCGAGCGCACGTTGCGGCTGCTGGTCCCCGCCGACGGGGTGCCTCGGGTGGATGCGGTGGTGTTCCTGTTGCGCACCCTGAACGCCGCTGACGTCGCGCTGCTCAAACAGATCGGTGGGCTGGTCGGCGGGTCGGTGGGAGCCCTGGGCATCATCGGGGTGGCGTCTCGCGCGGATGAGATCGGCGCGGGCCGCATCGACGCGATGCTCTCGGCCAACGACGTGGCCAAGCGGTTCACCCGCGAACTGAACCAGATGGGCATTTGCCAGGCGGTGGTGCCGGTATCCGGACTTCTTGCGCTGACCGCGCGCACACTGCGCCAGACCGAGTTCATCGCGCTGCGCAAGCTGGCCGGTGCCGAGCGCACCGAGCTCAATAGGGCCCTGCTGAGCGTGGACCGTTTTGTGCGCCGGGACAGTCCGCTACCGGTGGACGCGGGCATCCGTGCGCAATTGCTCGAGCGGTTCGGCATGTTCGGCATCCGGATGTCGATTGCCGTGCTGGCGGCCGGCGTGACCGATTCGACCGGGCTGGCCGCCGAACTGCTGGAGCGCAGCGGGCTGGTGGCGCTGCGCAATGTGATAGACCAGCAGTTCGCGCAGCGCTCCGACATGCTTAAGGCGCATACCGCCTTGGTCTCCTTGCGCCGATTCGTGCAGACGCATCCGGTGCCGGCGACCCCGTACGTCATTGCCGACATCGACCCGTTGCTAGCCGACACCCACGCCTTCGAAGAACTCCGAATGCTAAGCCTTTTGCCTTCGCGGGCAACGACATTGAACGACGACGAAATCGCGTCGCTGCGCCGCATCATCGGCGGGTCGGGCACCAGTGCCGCCGCTCGGCTGGGCCTGGATCCCGCGAATTCTCGCGAGGCCCCGCGCGCCGCGCTGGCCGCAGCGCAACACTGGCGTCGCCGTGCGGCGCATCCACTCAACGATCCGTTCACTACCAGGGCCTGTCGCGCGGCGGTGCGCAGCGCCGAGGCGATGGTGGCGGAGTTCTCTGCTCGCCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3003451","ARO_id":"40044","ARO_name":"Mycobacterium tuberculosis iniC mutant conferring resistance to ethambutol","CARD_short_name":"Mtub_iniC_EMB","ARO_description":"Specific mutations that occurs on Mycobacterium tuberculosis iniC causing it to be ethambutol resistant.","ARO_category":{"40043":{"category_aro_accession":"3003450","category_aro_cvterm_id":"40043","category_aro_name":"Ethambutol resistant iniC","category_aro_description":"Mutations that occurs on the iniC genes resulting in the resistance to ethambutol.","category_aro_class_name":"AMR Gene Family"},"36636":{"category_aro_accession":"3000497","category_aro_cvterm_id":"36636","category_aro_name":"ethambutol","category_aro_description":"Ethambutol is an antimycobacterial drug prescribed to treat tuberculosis. It is usually given in combination with other tuberculosis drugs, such as isoniazid, rifampicin, and pyrazinamide. Ethambutol inhibits arabinosyl biosynthesis, disrupting mycobacterial cell wall formation.","category_aro_class_name":"Antibiotic"},"36666":{"category_aro_accession":"3000527","category_aro_cvterm_id":"36666","category_aro_name":"polyamine antibiotic","category_aro_description":"Polyamine antibiotics are organic compounds having two or more primary amino groups.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"597":{"model_id":"597","model_name":"Klebsiella pneumoniae ramR mutants","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"2110":"K5E","2112":"T162I","2113":"A19V","2134":"A16D","2135":"I88N","2863":"G96D","2111":"T43M"},"Curated-R":{"2110":"K5E","2112":"T162I","2113":"A19V","2134":"A16D","2135":"I88N","2863":"G96D","2111":"T43M"},"clinical":{"2110":"K5E","2112":"T162I","2113":"A19V","2134":"A16D","2135":"I88N","2863":"G96D","2111":"T43M"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"360"}},"model_sequences":{"sequence":{"4572":{"protein_sequence":{"accession":"ABR76005.1","sequence":"MARPKSEDKKQALLEAATAAFAQSGIAASTSAIARSAGVAEGTLFRYFATKDELLNELYLAIKLRLVRTMIAGLDPDEKRPKENARNIWNSYIDWGVRNPMEHKAIRRMALSERITDETRRQVKESFPELNEMCQLSVKEIFLSEAYRAFGDALFLSLAETTIEFASHDPQRAREIIALGFEAMWHALHEADA"},"dna_sequence":{"accession":"CP000647.1","fmin":"622039","fmax":"622621","strand":"-","sequence":"GTGGCTCGTCCAAAGAGTGAAGATAAAAAGCAAGCGTTACTGGAAGCTGCCACCGCGGCTTTCGCCCAGTCCGGCATAGCCGCCTCGACGTCGGCCATCGCCCGCAGCGCCGGTGTGGCCGAGGGAACGCTGTTTCGCTATTTCGCCACCAAGGATGAGTTGCTCAACGAGCTGTACCTCGCGATTAAGCTGCGCCTGGTGCGCACAATGATCGCCGGGCTGGATCCGGACGAGAAGCGCCCGAAAGAGAACGCGCGCAATATCTGGAACAGCTATATCGACTGGGGCGTGCGCAACCCGATGGAGCACAAAGCGATCCGCCGGATGGCGCTCAGCGAGCGCATCACCGACGAAACCCGCCGCCAGGTAAAAGAGAGCTTTCCGGAGCTCAACGAAATGTGCCAGCTGTCGGTGAAAGAGATATTCCTCAGCGAGGCGTACCGCGCCTTTGGCGACGCCCTGTTTCTGTCGCTGGCGGAAACCACCATCGAATTCGCCAGCCACGATCCGCAGCGCGCCCGGGAGATTATCGCCCTCGGCTTTGAAGCCATGTGGCACGCCCTGCATGAGGCGGACGCCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37607","NCBI_taxonomy_name":"Klebsiella pneumoniae subsp. pneumoniae MGH 78578","NCBI_taxonomy_id":"272620"}}}},"ARO_accession":"3003380","ARO_id":"39964","ARO_name":"Klebsiella pneumoniae ramR mutants","CARD_short_name":"Kpne_ramR","ARO_description":"RamR is a repressor that regulates RamA expression. Mutations lead to the upregulation of AcrAB, which is positively regulated by RamA.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"37084":{"category_aro_accession":"3000704","category_aro_cvterm_id":"37084","category_aro_name":"cefalotin","category_aro_description":"Cefalotin is a semisynthetic cephalosporin antibiotic activate against staphylococci. It is resistant to staphylococci beta-lactamases but hydrolyzed by enterobacterial beta-lactamases.","category_aro_class_name":"Antibiotic"},"37250":{"category_aro_accession":"3000870","category_aro_cvterm_id":"37250","category_aro_name":"triclosan","category_aro_description":"Triclosan is a common antibacterial agent added to many consumer products as a biocide.  It is an inhibitor of fatty acid biosynthesis by blocking enoyl-carrier protein reductase (FabI).","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"43746":{"category_aro_accession":"3005386","category_aro_cvterm_id":"43746","category_aro_name":"disinfecting agents and antiseptics","category_aro_description":"Disinfectants that can also interact with antimicrobial resistance mechanisms, e.g. molecule efflux, and thus are the targets of disinfectant resistance.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"627":{"model_id":"627","model_name":"Escherichia coli rpoB mutants conferring resistance to rifampicin","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"2500"},"40494":{"param_type":"frameshift mutation","param_description":"A frameshift is a sequence change between the translation initiation (start) and termination (stop) codon where, compared to a reference sequence, translation shifts to another reading frame as caused by nucleotide insertions and deletions. In ARO, these are annotated at the protein level with the first changed most N-terminal wildtype amino acid position. Format is given as [wildtype AA][position]fs, e.g. S531fs where S531 is a frameshifted coordinate beginning with codon 531. Termination may also be denoted as: Ter[position]fs.","param_type_id":"40494","param_value":{"9917":"S531fs"}},"snp":{"Curated-R":{"9917":"T43M","2024":"Q513L","2025":"Q513P","2026":"H526Y","2027":"R529C","2028":"R529S","2029":"S531F","2030":"L533P","2031":"T563P","2032":"P564L","2033":"V146F","2034":"R687H"},"param_value":{"2024":"Q513L","2025":"Q513P","2026":"H526Y","2027":"R529C","2028":"R529S","2029":"S531F","2030":"L533P","2031":"T563P","2032":"P564L","2033":"V146F","2034":"R687H"},"clinical":{"2024":"Q513L","2025":"Q513P","2026":"H526Y","2027":"R529C","2028":"R529S","2029":"S531F","2030":"L533P","2031":"T563P","2032":"P564L","2033":"V146F","2034":"R687H"}}},"model_sequences":{"sequence":{"5493":{"protein_sequence":{"accession":"BAB38333.1","sequence":"MVYSYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQDPEGQYGLEAAFRSVFPIQSYSGNSELQYVSYRLGEPVFDVQECQIRGVTYSAPLRVKLRLVIYEREAPEGTVKDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNARIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFEKVIFEIRDNKLQMELVPERLRGETASFDIEANGKVYVEKGRRITARHIRQLEKDDVKLIEVPVEYIAGKVVAKDYIDESTGELICAANMELSLDLLAKLSQSGHKRIETLFTNDLDHGPYISETLRVDPTNDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGRMKFNRSLLREEIEGSGILSKDDIIDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVVTDEIHYLSAIEEGNYVIAQANSNLDEEGHFVEDLVTCRSKGESSLFSRDQVDYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAKRGGVVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVSLGEPVERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTIHIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEMQLKQAKKDLSEELQILEAGLFSRIRAVLVAGGVEAEKLDKLPRDRWLELGLTDEEKQNQLEQLAEQYDELKHEFEKKLEAKRRKITQGDDLAPGVLKIVKVYLAVKRRIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLGMAAKGIGDKINAMLKQQQEVAKLREFIQRAYDLGADVRQKVDLSTFSDEEVMRLAENLRKGMPIATPVFDGAKEAEIKELLKLGDLPTSGQIRLYDGRTGEQFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELEDE"},"dna_sequence":{"accession":"BA000007.3","fmin":"4990267","fmax":"4994296","strand":"+","sequence":"ATGGTTTACTCCTATACCGAGAAAAAACGTATTCGTAAGGATTTTGGTAAACGTCCACAAGTTCTGGATGTACCTTATCTCCTTTCTATCCAGCTTGACTCGTTTCAGAAATTTATCGAGCAAGATCCTGAAGGGCAGTATGGTCTGGAAGCTGCTTTCCGTTCCGTATTCCCGATTCAGAGCTACAGCGGTAATTCCGAGCTGCAATACGTCAGCTACCGCCTTGGCGAACCGGTGTTTGACGTCCAGGAATGTCAAATCCGTGGCGTGACCTATTCCGCACCGCTGCGCGTTAAACTGCGTCTGGTGATCTATGAGCGCGAAGCGCCGGAAGGCACCGTAAAAGACATTAAAGAACAAGAAGTCTACATGGGCGAAATTCCGCTCATGACAGACAACGGTACCTTTGTTATCAACGGTACTGAGCGTGTTATCGTTTCCCAGCTGCACCGTAGTCCGGGCGTCTTCTTTGACTCCGACAAAGGTAAAACCCACTCTTCGGGTAAAGTGCTGTATAACGCGCGCATCATCCCTTACCGTGGTTCCTGGCTGGACTTCGAATTCGATCCGAAGGACAACCTGTTCGTACGTATCGACCGTCGCCGTAAACTGCCTGCGACCATCATTCTGCGTGCCCTGAACTACACCACAGAGCAGATCCTCGACCTGTTCTTTGAAAAAGTTATCTTTGAAATCCGTGATAACAAGCTGCAGATGGAACTGGTGCCGGAACGCCTGCGTGGTGAAACCGCATCCTTTGACATCGAAGCTAACGGTAAAGTGTACGTAGAAAAAGGCCGCCGTATCACTGCGCGCCACATTCGCCAGCTGGAAAAAGACGACGTCAAACTGATCGAAGTCCCGGTTGAGTACATCGCAGGTAAAGTGGTTGCTAAAGACTATATTGATGAGTCTACCGGCGAGCTGATCTGCGCAGCGAACATGGAGCTGAGCCTGGATCTGCTGGCTAAGCTGAGCCAGTCTGGTCACAAGCGTATCGAAACGCTGTTCACCAATGATCTGGATCACGGCCCGTATATCTCTGAAACCTTACGTGTCGACCCAACTAACGACCGTCTGAGCGCACTGGTAGAAATCTACCGCATGATGCGCCCTGGCGAGCCGCCGACTCGTGAAGCAGCGGAAAGCCTGTTCGAGAACCTGTTCTTCTCCGAAGACCGTTATGACCTGTCTGCGGTTGGTCGTATGAAGTTCAACCGTTCTCTGCTGCGCGAAGAAATCGAAGGTTCTGGTATCCTGAGCAAAGACGACATCATTGATGTTATGAAAAAGCTCATCGATATCCGTAACGGTAAAGGCGAAGTCGATGATATCGACCACCTCGGCAACCGTCGTATCCGTTCCGTTGGCGAAATGGCGGAAAACCAGTTCCGCGTTGGCCTGGTACGTGTAGAGCGTGCGGTGAAAGAGCGTCTGTCTCTGGGCGATCTGGATACCCTGATGCCTCAGGATATGATCAACGCCAAGCCGATTTCCGCAGCAGTGAAAGAGTTCTTCGGTTCCAGCCAGCTGTCTCAGTTTATGGACCAGAACAACCCGCTGTCTGAGATTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGTTCGAGACGTACACCCGACTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGATCAACTCTCTGTCCGTGTACGCACAGACTAACGAATACGGCTTCCTTGAGACTCCGTATCGTAAAGTGACTGACGGTGTTGTAACTGACGAAATTCACTACCTGTCTGCTATCGAAGAAGGCAACTACGTTATCGCCCAGGCGAACTCCAACCTGGATGAAGAAGGCCACTTCGTAGAAGACCTGGTAACCTGCCGTAGCAAAGGCGAATCCAGCTTGTTCAGCCGTGACCAGGTTGACTACATGGACGTATCCACCCAGCAGGTGGTATCCGTCGGTGCGTCCCTGATCCCGTTCCTGGAACACGATGACGCCAACCGTGCATTGATGGGTGCGAACATGCAACGTCAGGCCGTTCCGACTCTGCGTGCTGATAAGCCGCTGGTTGGTACTGGTATGGAACGTGCTGTTGCCGTTGACTCCGGTGTAACTGCGGTTGCTAAACGTGGTGGTGTCGTTCAGTACGTGGATGCTTCCCGTATCGTTATCAAAGTTAACGAAGACGAGATGTATCCGGGTGAAGCAGGTATCGACATCTACAACCTGACCAAATACACCCGTTCTAACCAGAACACCTGTATTAACCAGATGCCGTGTGTGTCTCTGGGTGAACCGGTTGAACGTGGCGACGTGCTGGCAGACGGTCCGTCCACCGACCTCGGTGAACTGGCGCTTGGTCAGAACATGCGCGTAGCGTTCATGCCGTGGAATGGTTACAACTTCGAAGACTCCATCCTCGTATCCGAGCGTGTTGTTCAGGAAGACCGTTTCACCACCATCCACATTCAGGAACTGGCGTGTGTGTCCCGTGACACCAAGCTGGGGCCAGAAGAGATCACCGCTGACATCCCGAACGTGGGTGAAGCTGCGCTCTCCAAACTGGATGAATCCGGTATCGTTTATATTGGTGCGGAAGTGACCGGTGGCGACATTCTGGTTGGTAAGGTTACGCCGAAAGGTGAAACTCAGCTGACCCCAGAAGAAAAACTGCTGCGTGCGATCTTCGGTGAGAAAGCGTCTGACGTTAAAGACTCTTCTCTGCGCGTACCAAACGGTGTATCCGGTACGGTTATCGACGTTCAGGTCTTTACTCGCGATGGCGTAGAAAAAGACAAACGTGCGCTGGAAATCGAAGAAATGCAGCTCAAACAGGCGAAGAAAGACCTGTCTGAAGAACTGCAGATCCTCGAAGCGGGTCTGTTCAGCCGTATCCGTGCTGTGCTGGTAGCCGGTGGCGTTGAAGCTGAGAAGCTCGACAAATTGCCGCGCGATCGCTGGCTGGAGCTGGGCCTGACCGACGAAGAGAAACAAAATCAGCTGGAACAGCTGGCTGAGCAGTATGACGAACTGAAACACGAGTTCGAGAAGAAACTCGAAGCGAAACGCCGCAAAATCACCCAGGGCGACGATCTGGCACCGGGCGTGCTGAAGATTGTTAAGGTATATCTGGCGGTTAAACGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCCGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACTTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAGGAAGTCGCGAAACTGCGTGAATTCATCCAGCGTGCGTACGATCTGGGCGCTGACGTTCGTCAGAAAGTTGACCTGAGTACCTTCAGCGATGAAGAAGTTATGCGTCTGGCTGAAAACCTGCGCAAAGGTATGCCAATCGCAACGCCGGTGTTCGACGGTGCGAAAGAAGCAGAAATTAAAGAGCTGCTGAAACTTGGCGACCTGCCGACTTCTGGTCAGATCCGCCTGTACGACGGCCGCACTGGTGAACAGTTCGAACGTCCGGTAACCGTTGGTTACATGTACATGCTGAAACTGAACCACCTGGTCGACGACAAGATGCACGCGCGTTCCACCGGTTCTTACAGCCTGGTTACTCAGCAGCCGCTGGGTGGTAAGGCACAGTTCGGTGGTCAGCGTTTCGGGGAGATGGAAGTGTGGGCGCTGGAAGCATACGGCGCAGCATACACCCTGCAGGAAATGCTCACCGTTAAGTCTGATGACGTGAACGGTCGTACTAAGATGTATAAAAACATCGTGGACGGCAACCATCAGATGGAGCCGGGCATGCCAGAATCCTTCAACGTATTGTTGAAAGAGATTCGTTCGCTGGGTATCAACATCGAACTGGAAGACGAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36747","NCBI_taxonomy_name":"Escherichia coli O157:H7 str. Sakai","NCBI_taxonomy_id":"386585"}}}},"ARO_accession":"3003288","ARO_id":"39872","ARO_name":"Escherichia coli rpoB mutants conferring resistance to rifampicin","CARD_short_name":"Ecol_rpoB_RIF","ARO_description":"Point mutations that occurs in Escherichia coli rpoB resulting in resistance to rifampicin.","ARO_category":{"36349":{"category_aro_accession":"3000210","category_aro_cvterm_id":"36349","category_aro_name":"rifamycin-resistant beta-subunit of RNA polymerase (rpoB)","category_aro_description":"Rifampin resistant RNA polymerases include amino acids substitutions which disrupt the affinity of rifampin for its binding site. These mutations are frequently concentrated in the rif I region of the beta-subunit and most often involve amino acids which make direct interactions with rifampin. However, mutations which also confer resistance can occur outside this region and may involve amino acids which do not directly make contact with rifampin.","category_aro_class_name":"AMR Gene Family"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36656":{"category_aro_accession":"3000517","category_aro_cvterm_id":"36656","category_aro_name":"rifaximin","category_aro_description":"Rifaximin is a semi-synthetic rifamycin used to treat traveller's diarrhea. Rifaximin inhibits RNA synthesis by binding to the beta subunit of bacterial RNA polymerase.","category_aro_class_name":"Antibiotic"},"36669":{"category_aro_accession":"3000530","category_aro_cvterm_id":"36669","category_aro_name":"rifabutin","category_aro_description":"Rifabutin is a semisynthetic rifamycin used in tuberculosis therapy. It inhibits DNA-dependent RNA synthesis.","category_aro_class_name":"Antibiotic"},"36673":{"category_aro_accession":"3000534","category_aro_cvterm_id":"36673","category_aro_name":"rifapentine","category_aro_description":"Rifapentine is a semisynthetic rifamycin that inhibits DNA-dependent RNA synthesis. It is often used in the treatment of tuberculosis and leprosy.","category_aro_class_name":"Antibiotic"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"756":{"model_id":"756","model_name":"Enterococcus faecium liaR mutant conferring daptomycin resistance","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"22":"W73C"},"Curated-R":{"22":"W73C"},"clinical":{"22":"W73C"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"40":{"protein_sequence":{"accession":"AFK58562.1","sequence":"MIKVLLVDDHEMVRLGVSSYLSIQEDIEVIGEAENGRQGYEKAMTLRPDVILMDLVMEEMDGIESTKAILKDWPEAKIIIVTSFIDDEKVYPAIEAGAAGYLLKTSTAHEIADAIRATQRGERVLEPEVTTKMMEKMSRRNEPVLHEELTNRENEILMLISEGKSNQEIADELFITLKTVKTHVSNILAKLEVEDRTQAAIYAFKHGLVK"},"dna_sequence":{"accession":"CP003583.1","fmin":"914819","fmax":"915452","strand":"+","sequence":"ATGATAAAAGTTTTATTAGTAGATGACCATGAAATGGTGCGCTTAGGCGTCTCTTCTTATTTATCTATTCAAGAAGACATTGAAGTAATTGGAGAAGCTGAAAATGGACGACAAGGCTATGAGAAGGCGATGACACTTCGACCGGACGTCATTTTAATGGACTTAGTCATGGAAGAAATGGATGGTATCGAATCAACAAAAGCAATCTTAAAAGATTGGCCAGAAGCTAAAATCATTATCGTAACCAGTTTTATTGATGACGAAAAAGTTTATCCTGCCATTGAAGCAGGTGCAGCAGGGTATTTGTTGAAGACCTCTACCGCACATGAAATTGCTGATGCTATAAGGGCAACGCAACGTGGCGAGCGAGTATTAGAACCAGAAGTGACAACAAAAATGATGGAAAAAATGAGTCGGCGAAATGAGCCTGTATTACATGAAGAACTAACGAATCGGGAAAATGAAATTTTAATGCTGATTTCTGAAGGAAAAAGTAATCAGGAAATAGCGGACGAATTGTTTATTACACTGAAAACAGTAAAAACACATGTTTCCAATATATTGGCTAAGCTAGAAGTGGAAGACCGTACACAAGCCGCTATCTATGCATTCAAACATGGTTTGGTGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37599","NCBI_taxonomy_name":"Enterococcus faecium DO","NCBI_taxonomy_id":"333849"}}}},"ARO_accession":"3003078","ARO_id":"39625","ARO_name":"Enterococcus faecium liaR mutant conferring daptomycin resistance","CARD_short_name":"Efac_liaR_DAP","ARO_description":"liaR is a response regulator found in the liaFSR signal transduction pathway. Mutations confer daptomycin resistance.","ARO_category":{"41427":{"category_aro_accession":"3004263","category_aro_cvterm_id":"41427","category_aro_name":"daptomycin resistant liaR","category_aro_description":"Mutations to the liaR response regulator that confer resistance to daptomycin.","category_aro_class_name":"AMR Gene Family"},"35985":{"category_aro_accession":"0000068","category_aro_cvterm_id":"35985","category_aro_name":"daptomycin","category_aro_description":"Daptomycin is a novel lipopeptide antibiotic used in the treatment of certain infections caused by Gram-positive organisms. Daptomycin interferes with the bacterial cell membrane, reducing membrane potential and inhibiting cell wall synthesis.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"794":{"model_id":"794","model_name":"Staphylococcus aureus rpoC conferring resistance to daptomycin","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"2071":"Q961K","2070":"F632S"},"Curated-R":{"2071":"Q961K","2070":"F632S"},"experimental":{"2071":"Q961K","2070":"F632S"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"2400"}},"model_sequences":{"sequence":{"5406":{"protein_sequence":{"accession":"CAG39569.1","sequence":"MIDVNNFHYMKIGLASPEKIRSWSFGEVKKPETINYRTLKPEKDGLFCERIFGPTKDWECSCGKYKRVRYKGMVCDRCGVEVTKSKVRRERMGHIELAAPVSHIWYFKGIPSRMGLLLDMSPRALEEVIYFASYVVVDPGPTGLEKKTLLSEAEFRDYYDKYPGQFVAKMGAEGIKDLLEEIDLDEELKLLRDELESATGQRLTRAIKRLEVVESFRNSGNKPSWMILDVLPIIPPEIRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLDLGAPGIIVQNEKRMLQEAVDALIDNGRRGRPVTGPGNRPLKSLSHMLKGKQGRFRQNLLGKRVDYSGRSVIAVGPSLKMYQCGLPKEMALELFKPFVMKELVQREIATNIKNAKSKIERMDDEVWDVLEEVIREHPVLLNRAPTLHRLGIQAFEPTLVEGRAIRLHPLVTTAYNADFDGDQMAVHVPLSKEAQAEARMLMLAAQNILNPKDGKPVVTPSQDMVLGNYYLTLERKDAVNTGAIFNNTNEVLKAYANGFVHLHTRIGVHASSFNNPTFTEEQNKKILATSVGKIIFNEIIPDSFAYINEPTQENLERKTPNRYFIDPTTLGEGGLKEYFENEELIEPFNKKFLGNIIAEVFNRFSITDTSMMLDRMKDLGFKFSSKAGITVGVADIVVLPDKQQILDEHEKLVDRITKQFNRGLITEEERYNAVVEIWTDAKDQIQGELMQSLDKTNPIFMMSDSGARGNASNFTQLAGMRGLMAAPSGKIIELPITSSFREGLTVLEYFISTHGARKGLADTALKTADSGYLTRRLVDVAQDVIVREEDCGTDRGLLVSDIKEGTEMIEPFIERIEGRYSKETIRHPETDEVIIRPDELITPEIAKKITDAGIEQMYIRSAFTCNARHGVCEKCYGKNLATGEKVEVGEAVGTIAAQSIGEPGTQLTMRTFHTGGVAGSDITQGLPRIQEIFEARNPKGQAVITEIEGVVEDIKLAKDRQQEIVVKGANETRSYLASGTSRIIVEIGQPVQRGEVLTEGSIEPKNYLSVAGLNATESYLLKEVQKVYRMQGVEIDDKHVEVMVRQMLRKVRIIEAGDTKLLPGSLVDIHNFTDANREAFKHRKRPATAKPVLLGITKASLETESFLSAASFQETTRVLTDAAIKGKRDDLLGLKENVIIGKLIPAGTGMRRYSDVKYEKTAKPVAEVESQTEVTE"},"dna_sequence":{"accession":"BX571856.1","fmin":"594518","fmax":"598142","strand":"+","sequence":"TTGATTGATGTAAATAATTTCCATTATATGAAAATAGGATTGGCTTCACCTGAAAAAATCCGTTCTTGGTCTTTTGGTGAAGTTAAAAAACCTGAAACAATCAACTACCGTACATTAAAACCTGAAAAAGATGGTCTATTCTGTGAAAGAATTTTCGGACCTACAAAAGACTGGGAATGTAGTTGTGGTAAATACAAACGTGTTCGCTACAAAGGCATGGTCTGTGACAGATGTGGAGTTGAAGTAACTAAATCTAAAGTACGTCGTGAAAGAATGGGTCACATTGAACTTGCTGCTCCAGTTTCTCACATTTGGTATTTCAAAGGTATACCAAGTCGTATGGGATTATTACTTGACATGTCACCAAGAGCATTAGAAGAAGTTATTTACTTTGCTTCTTATGTTGTTGTAGATCCAGGTCCAACTGGTTTAGAAAAGAAAACTTTATTATCTGAAGCTGAATTCAGAGATTATTATGATAAATACCCAGGTCAATTCGTTGCAAAAATGGGTGCAGAAGGTATTAAAGATTTACTTGAAGAGATTGATCTTGACGAAGAACTTAAATTGTTACGCGATGAGTTGGAATCAGCTACTGGTCAAAGACTTACTCGTGCAATTAAACGTTTAGAAGTTGTTGAATCATTCCGTAATTCAGGTAACAAACCTTCATGGATGATTTTAGATGTACTTCCAATCATCCCACCAGAAATTCGTCCAATGGTTCAATTAGATGGTGGACGATTTGCAACAAGTGACTTAAACGACTTATACCGTCGTGTAATTAATCGAAATAATCGTTTGAAACGTTTATTAGATTTAGGTGCACCTGGTATCATCGTTCAAAACGAAAAACGTATGTTACAAGAAGCCGTTGACGCTTTAATTGATAATGGTCGTCGTGGTCGTCCAGTTACTGGCCCAGGTAACCGTCCATTAAAATCTTTATCTCATATGTTAAAAGGTAAACAAGGTCGTTTCCGTCAAAACCTACTTGGTAAACGTGTTGACTATTCAGGACGTTCAGTTATCGCGGTAGGTCCAAGCTTGAAAATGTACCAATGTGGTTTACCGAAAGAAATGGCACTTGAACTATTTAAACCATTTGTAATGAAAGAATTAGTTCAACGTGAAATTGCAACTAACATTAAAAATGCGAAGAGTAAAATCGAACGCATGGATGATGAAGTTTGGGACGTATTGGAAGAAGTAATTAGAGAACATCCTGTATTACTTAACCGTGCACCAACACTTCATAGACTTGGTATTCAAGCATTTGAACCAACTTTAGTTGAAGGTCGTGCGATTCGTCTACATCCACTTGTAACAACAGCTTATAACGCTGACTTTGATGGTGACCAAATGGCGGTTCACGTTCCTTTATCAAAAGAGGCACAAGCTGAAGCAAGAATGTTGATGTTAGCAGCACAAAACATCTTGAACCCTAAAGATGGTAAACCAGTAGTTACACCATCACAAGATATGGTACTTGGTAACTATTACCTTACTTTAGAAAGAAAAGATGCAGTAAATACAGGCGCAATCTTTAATAATACAAATGAAGTGTTAAAAGCATATGCAAATGGCTTTGTACATTTACACACAAGAATTGGTGTACATGCAAGTTCATTCAACAACCCAACATTTACTGAAGAACAAAACAAAAAGATTCTTGCTACGTCAGTAGGTAAAATTATATTCAATGAAATCATTCCGGATTCATTTGCTTATATTAATGAACCTACGCAAGAAAACTTAGAAAGAAAGACACCAAACAGATACTTCATCGATCCTACAACTTTAGGTGAAGGTGGATTAAAAGAATACTTTGAAAATGAAGAATTAATTGAACCTTTCAACAAAAAATTCTTAGGTAATATTATTGCAGAAGTATTCAACAGATTTAGCATCACTGATACATCAATGATGTTAGACCGTATGAAAGACTTAGGATTCAAATTCTCATCTAAAGCTGGTATTACAGTAGGTGTTGCTGATATCGTAGTATTACCTGATAAGCAACAAATACTTGATGAGCATGAAAAATTAGTCGACAGAATTACAAAACAATTCAATCGTGGTTTAATCACTGAAGAAGAAAGATATAATGCAGTTGTTGAAATTTGGACAGATGCAAAAGATCAAATTCAAGGTGAATTGATGCAATCACTTGATAAAACTAACCCAATCTTCATGATGAGTGATTCAGGTGCCCGTGGTAACGCATCTAACTTTACACAGTTAGCAGGTATGCGTGGATTGATGGCCGCACCATCTGGTAAGATTATCGAATTACCAATCACATCTTCATTCCGTGAAGGTTTAACAGTACTTGAATACTTCATCTCAACTCACGGTGCGCGTAAAGGTCTTGCCGATACAGCACTTAAGACAGCTGACTCAGGATATCTTACTCGTCGTCTTGTTGACGTGGCACAAGATGTTATTGTTCGTGAAGAAGACTGTGGTACAGATAGAGGTTTATTAGTTTCTGATATTAAAGAAGGTACAGAAATGATTGAACCATTTATCGAACGTATTGAAGGTCGTTATTCTAAAGAAACAATTCGTCATCCTGAAACTGATGAAGTTATCATTCGTCCTGATGAATTAATTACACCTGAAATTGCTAAGAAAATTACAGATGCTGGTATTGAACAAATGTATATTCGCTCAGCATTTACTTGTAACGCAAGACACGGTGTTTGTGAAAAATGTTACGGTAAAAACCTTGCTACTGGTGAAAAAGTTGAAGTTGGTGAAGCAGTTGGTACAATTGCAGCCCAATCTATCGGTGAACCAGGTACACAGCTTACAATGCGTACATTCCATACAGGTGGGGTAGCAGGTAGCGATATCACACAAGGTCTTCCTCGTATTCAAGAGATTTTCGAAGCACGTAACCCTAAAGGTCAAGCGGTAATTACGGAAATCGAAGGTGTCGTAGAAGATATTAAATTAGCAAAAGATAGACAACAAGAAATTGTTGTTAAAGGTGCTAATGAAACAAGATCATATCTTGCTTCAGGTACTTCAAGAATTATTGTAGAAATCGGTCAACCAGTACAACGTGGTGAAGTATTAACTGAAGGTTCTATTGAACCTAAGAATTACTTATCTGTTGCTGGATTAAACGCGACTGAAAGCTACTTATTAAAAGAAGTACAAAAAGTTTACCGTATGCAAGGGGTAGAAATCGACGATAAACACGTTGAGGTTATGGTTCGACAAATGTTACGTAAAGTTAGAATTATCGAAGCAGGTGATACGAAGTTATTACCAGGTTCATTAGTTGATATTCACAACTTTACAGATGCAAATAGAGAAGCATTTAAACACCGCAAGCGCCCTGCAACAGCTAAACCAGTATTACTTGGTATTACTAAAGCATCACTTGAAACAGAAAGTTTCTTATCTGCAGCATCATTCCAAGAAACAACAAGAGTTCTAACAGATGCAGCAATTAAAGGTAAGCGTGATGACTTATTAGGTCTTAAAGAAAACGTAATTATCGGTAAGCTAATTCCAGCTGGTACTGGTATGAGACGTTATAGCGACGTAAAATACGAAAAAACAGCTAAACCAGTTGCAGAAGTTGAATCTCAAACTGAAGTAACGGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35517","NCBI_taxonomy_name":"Staphylococcus aureus subsp. aureus MRSA252","NCBI_taxonomy_id":"282458"}}}},"ARO_accession":"3003291","ARO_id":"39875","ARO_name":"Staphylococcus aureus rpoC conferring resistance to daptomycin","CARD_short_name":"Saur_rpoC_DAP","ARO_description":"Point mutations that occurs in Staphylococcus aureus rpoC resulting in resistance to daptomycin.","ARO_category":{"39874":{"category_aro_accession":"3003290","category_aro_cvterm_id":"39874","category_aro_name":"daptomycin-resistant beta prime subunit of RNA polymerase (rpoC)","category_aro_description":"Daptomycin resistant RNA polymerases include amino acids substitutions which alter the binding affinity of daptomycin to the protein, resulting in antibiotic resistance.","category_aro_class_name":"AMR Gene Family"},"35985":{"category_aro_accession":"0000068","category_aro_cvterm_id":"35985","category_aro_name":"daptomycin","category_aro_description":"Daptomycin is a novel lipopeptide antibiotic used in the treatment of certain infections caused by Gram-positive organisms. Daptomycin interferes with the bacterial cell membrane, reducing membrane potential and inhibiting cell wall synthesis.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"851":{"model_id":"851","model_name":"Mycobacterium tuberculosis pncA mutations conferring resistance to pyrazinamide","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible 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substitution in promoter region","param_description":"A nucleotide sequence change where, compared to a reference sequence, one nucleotide is replaced by one other nucleotide in the promoter region of a gene. These substitutions are indicated as upstream of the reference sequence transcription initiation site. Format is given by [-][position][wildtype][>][mutation], e.g. -11t>c or -15g>Var where Var represents any possible substitution.","param_type_id":"41339","param_value":{"13253":"-11a>g","13855":"-7t>c","13854":"-12t>c","15398":"-7t>c","15399":"-11a>g","15401":"-11a>c","15402":"-12t>c","9701":"-11a>c","9702":"-11a>g","15400":"-11a>t"}},"48039":{"param_type":"synonymous substitution for alternative promoter","param_description":"A synonymous or silent substitution in the coding DNA sequence of one gene which influences the promoter region of another gene. These substitutions do not change the amino acid sequence of a protein but may still influence the phenotype, including decreased susceptibility to antimicrobial compounds.","param_type_id":"48039","param_value":{"13939":"F50F","13954":"G150G","13957":"G16G","14011":"N118N","14021":"P62P","14035":"Q122Q","14042":"S164S","14057":"T114T","14062":"T142T","14066":"T177T","14071":"V125V","14086":"V183V","14101":"Y41Y","14104":"A171A","14112":"A38A","13975":"H71H","14121":"A79A","14154":"D56D","14169":"E107E","14116":"A46A","13943":"F94F","14000":"L19L","14099":"Y34Y","14115":"A3A"}},"40394":{"param_type":"nonsense mutation","param_description":"A sequence change where, compared to a reference sequence, one codon is replaced by a termination codon through a nucleotide substitution. These are described as a substitution of the wildtype codon to a termination codon. Format is given as [wild type AA][position][Ter], for example Q42Ter where Q42 is a wildtype amino acid replaced by a premature termination codon.","param_type_id":"40394","param_value":{"14094":"W119Ter","14098":"W68Ter","14100":"Y41Ter","14102":"Y64Ter","14103":"Y95Ter","14126":"C138Ter","14129":"C14Ter","14132":"C72Ter","14170":"E111Ter","14171":"E127Ter","14173":"E144Ter","14174":"E15Ter","14178":"E181Ter","15097":"E181Ter","15108":"E174Ter","15109":"E173Ter","15120":"S164Ter","15143":"E144Ter","15150":"Q141Ter","15187":"Q122Ter","15192":"W119Ter","15201":"E111Ter","15204":"E107Ter","15213":"Y103Ter","15221":"G101Ter","15223":"Y99Ter","15236":"Y95Ter","15244":"E91Ter","15273":"W68Ter","15277":"S67Ter","15279":"S66Ter","15281":"Y64Ter","15345":"S18Ter","15350":"E15Ter","15352":"C14Ter","15370":"Q10Ter","13415":"S164Ter","13460":"Y103Ter","13808":"Q141Ter","13850":"Y99Ter","13932":"E37Ter","13933":"E91Ter","13944":"G101Ter","13990":"K48Ter","13992":"K96Ter","13996":"L151Ter","14004":"L4Ter","14029":"Q10Ter","14033":"Q122Ter","14052":"S66Ter","14053":"S67Ter","14054":"S88Ter","3433":"Y99Ter","3436":"Y41Ter","4160":"Q10Ter","4230":"W68Ter","4238":"W119Ter","4243":"Q141Ter","4309":"S88Ter","9933":"Q122Ter","15329":"Y41Ter","15333":"Y34Ter","9676":"Y103Ter","9677":"G108Ter","9695":"S164Ter","14175":"E173Ter","13327":"G108Ter","14045":"S18Ter","4168":"Y103Ter"}},"40494":{"param_type":"frameshift mutation","param_description":"A frameshift is a sequence change between the translation initiation (start) and termination (stop) codon where, compared to a reference sequence, translation shifts to another reading frame as caused by nucleotide insertions and deletions. In ARO, these are annotated at the protein level with the first changed most N-terminal wildtype amino acid position. Format is given as [wildtype AA][position]fs, e.g. S531fs where S531 is a frameshifted coordinate beginning with codon 531. Termination may also be denoted as: Ter[position]fs.","param_type_id":"40494","param_value":{"9678":"T114fs","9680":"L117fs","9683":"V131fs","9687":"D136fs"}},"40330":{"param_type":"multiple resistance variants","param_description":"A set of nucleotide or amino acid substitutions that are all required to confer resistance to an antibiotic drug or drug class, encoded as: [wild-type 1][position 1][mutation 1],[wild-type 2][position 2][mutation 2], etc. For example, D63Y,T142K.","param_type_id":"40330","param_value":{"4215":"Q10P,Y99D","4220":"A25E,A26G,A28D","9938":"D63Y,T142K"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"8786":{"protein_sequence":{"accession":"NP_216559.1","sequence":"MRALIIVDVQNDFCEGGSLAVTGGAALARAISDYLAEAADYHHVVATKDFHIDPGDHFSGTPDYSSSWPPHCVSGTPGADFHPSLDTSAIEAVFYKGAYTGAYSGFEGVDENGTPLLNWLRQRGVDEVDVVGIATDHCVRQTAEDAVRNGLATRVLVDLTAGVSADTTVAALEEMRTASVELVCSS"},"dna_sequence":{"accession":"NC_000962.3","fmin":"2288680","fmax":"2289241","strand":"-","sequence":"ATGCGGGCGTTGATCATCGTCGACGTGCAGAACGACTTCTGCGAGGGTGGCTCGCTGGCGGTAACCGGTGGCGCCGCGCTGGCCCGCGCCATCAGCGACTACCTGGCCGAAGCGGCGGACTACCATCACGTCGTGGCAACCAAGGACTTCCACATCGACCCGGGTGACCACTTCTCCGGCACACCGGACTATTCCTCGTCGTGGCCACCGCATTGCGTCAGCGGTACTCCCGGCGCGGACTTCCATCCCAGTCTGGACACGTCGGCAATCGAGGCGGTGTTCTACAAGGGTGCCTACACCGGAGCGTACAGCGGCTTCGAAGGAGTCGACGAGAACGGCACGCCACTGCTGAATTGGCTGCGGCAACGCGGCGTCGATGAGGTCGATGTGGTCGGTATTGCCACCGATCATTGTGTGCGCCAGACGGCCGAGGACGCGGTACGCAATGGCTTGGCCACCAGGGTGCTGGTGGACCTGACAGCGGGTGTGTCGGCCGATACCACCGTCGCCGCGCTGGAGGAGATGCGCACCGCCAGCGTCGAGTTGGTTTGCAGCTCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3003394","ARO_id":"39978","ARO_name":"Mycobacterium tuberculosis pncA mutations conferring resistance to pyrazinamide","CARD_short_name":"Mtub_pncA_PZA","ARO_description":"pncA is a pyrazinamidase\/nicotinamidase. It catalyzes the activation of pyrazinamide. Some mutation within pncA are associated with loss of enzyme activity, resulting in pyrazinamide resistance.","ARO_category":{"40002":{"category_aro_accession":"3003418","category_aro_cvterm_id":"40002","category_aro_name":"Pyrazinamide resistant pncA","category_aro_description":"pncA is a pyrazinamidase\/nicotinamidase. It catalyzes the activation of pyrazinamide to pyrazinoic acid. Mutations arise within the pncA gene that caused the loss of pyrazinamidase activity is the major mechanism of antibiotic resistance.","category_aro_class_name":"AMR Gene Family"},"39997":{"category_aro_accession":"3003413","category_aro_cvterm_id":"39997","category_aro_name":"pyrazinamide","category_aro_description":"Pyrazinamide is an antimycobacterial. It is highly specific and active only against Mycobacterium tuberculosis. This compound is a prodrug and needs to be activated inside the cell. It interferes with the bacterium's ability to synthesize new fatty acids, causing cell death.","category_aro_class_name":"Antibiotic"},"45737":{"category_aro_accession":"3007155","category_aro_cvterm_id":"45737","category_aro_name":"pyrazine antibiotic","category_aro_description":"A group of antibiotics derived from pyrazine.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"984":{"model_id":"984","model_name":"Bartonella bacilliformis gyrA conferring resistance to fluoroquinolones","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"2121":"D90G","2122":"D95N"},"Curated-R":{"2121":"D90G","2122":"D95N"},"clinical":{"2121":"D90G","2122":"D95N"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1500"}},"model_sequences":{"sequence":{"2058":{"protein_sequence":{"accession":"AAL82403.1","sequence":"MTDLTRLPEHDVSTGIEPVSIIEEMQCSYLDYAMSVIVSRALPDVRDGLKPVHRRILHAMNEMGLLFNKPYRKSAGVVGEVMGKFHPHGDASIYDALVRMAQDFSLRNPLIDGQGNFGSVDGDPPAAMRYTECRLEKVAEELLADIDKDTVDFQDNYDGREHEPIVLPARFPNLLVNGSGGIAVGMATNIPPHNLGEVIDGCVALIDNPNITIDEMLAIIPGPDFPTGGIILGHSGVRSAYETGRGSIIMRAKVEIEEIRNQRQAIIVSEIPYQVNKATMVEKMAELVRDKRIEGISDLRDESDRDGYRVVIELKREAVADVVLNQLYRYTPLQASFGCNMVALNGGKPEQMTLLDMLRAFVSFREEVVSRRTKYLLRKARERAHVLVGLAIAVANIDEIIELIRKAHDPQTARTQLMERRWPASEVAALIKLIDDPRHIIHEDNTYNLSEEQARAILELRLQRLTALGRNEIADELNAIGEDIADYLGILASRSRIMDIVKSELSALRETFATPRRTVFGFGSAEMDCEDLIVPEDMVVTVSHSGYIKRVPLNTYRAQRRGGKGRSGMATKDQDFVTRLFVANTHTPVLFFSSRGIVYKEKVWRLPVGTPQSRGRALINMLPLQQGERITTIMPLPEDEASWGKLDIMFATTRGTVRRNKLSDFIQVNRNGKIAMKLDEEGDEILSVETCTEHDDVVLITANGQCIRFPVTDIRVFSGRNSMGVRGINMVEGDKVISMTILEHVEATSVERSAYIKRAINERRVAGSDDEDILTVDEDGEETEVELTDERYAELSAHEQMLLTVSEFGYGKRSSSYDFRISGRGGKGIRATDLSKAAEIGKLVAAFPVGERDQIMLVSDGGQLIRVPVNCIRIAGRSTKGVTVFNTAKGEKVVSVERISESENDTNQLDIESEEHSGTVSMSEEKKL"},"dna_sequence":{"accession":"AF469609.1","fmin":"566","fmax":"3353","strand":"+","sequence":"GTGACCGATCTTACTCGACTACCAGAACATGATGTGTCGACCGGTATTGAACCAGTCAGTATCATTGAAGAAATGCAGTGCTCTTATCTAGATTATGCGATGAGCGTAATTGTGTCGCGCGCACTGCCTGATGTCCGTGATGGGCTTAAGCCTGTCCATCGGCGCATTCTTCATGCGATGAATGAAATGGGACTTTTGTTCAATAAGCCTTATCGTAAGTCAGCGGGTGTTGTTGGTGAAGTGATGGGAAAGTTTCATCCTCATGGTGATGCTTCAATTTATGATGCCTTGGTGCGTATGGCACAGGATTTTTCTTTACGAAATCCTCTGATTGATGGACAGGGAAATTTTGGCTCTGTTGACGGTGATCCACCCGCAGCGATGCGTTACACGGAATGTCGTTTAGAAAAAGTTGCAGAAGAACTTTTAGCTGATATTGATAAAGATACTGTTGATTTTCAAGATAATTATGATGGGCGTGAGCATGAACCTATAGTTTTGCCTGCACGTTTCCCTAACCTGTTAGTAAATGGATCGGGTGGTATTGCTGTAGGTATGGCAACCAATATTCCTCCACATAATCTAGGTGAGGTTATTGATGGATGTGTTGCTTTGATCGATAATCCTAACATAACTATAGATGAGATGTTAGCAATTATTCCGGGGCCTGATTTTCCTACAGGTGGTATTATTCTTGGCCATTCTGGTGTCCGTTCTGCTTATGAAACAGGGCGTGGTTCAATTATTATGCGTGCTAAGGTTGAGATCGAGGAAATTCGCAATCAGCGGCAGGCAATTATCGTAAGCGAAATACCTTATCAAGTTAATAAAGCAACAATGGTTGAGAAGATGGCCGAATTGGTGCGTGATAAACGTATCGAAGGAATCTCCGATTTGCGTGATGAATCTGATCGTGATGGGTATCGAGTTGTCATTGAGCTAAAAAGAGAAGCTGTTGCAGACGTTGTTTTGAATCAGCTTTATCGTTATACACCGTTGCAAGCCTCATTTGGTTGCAATATGGTTGCGTTGAATGGAGGAAAGCCTGAACAAATGACGTTGCTTGACATGCTTCGTGCATTTGTTTCCTTCCGCGAAGAAGTGGTAAGCCGGCGCACAAAATATCTTTTGCGTAAAGCACGTGAGCGTGCGCATGTTTTAGTTGGTCTTGCTATCGCTGTTGCTAATATTGATGAGATTATAGAATTAATTCGCAAAGCTCATGATCCACAGACAGCGCGTACACAGTTAATGGAACGGCGTTGGCCGGCTTCTGAGGTAGCAGCTTTGATTAAGCTTATAGATGATCCTCGTCATATTATTCATGAGGATAATACGTACAATTTGTCTGAAGAACAAGCGCGTGCTATTTTAGAATTGCGTTTGCAAAGATTAACAGCGCTTGGTCGTAATGAAATTGCTGATGAACTCAATGCAATTGGAGAAGATATTGCTGACTATCTTGGTATTTTAGCATCACGCTCACGGATCATGGACATTGTTAAAAGTGAGCTCAGCGCTTTGCGTGAAACATTTGCAACACCACGGCGTACTGTATTTGGTTTTGGTAGTGCCGAGATGGACTGCGAAGATCTGATTGTTCCAGAAGATATGGTGGTGACAGTGAGCCATAGTGGCTATATTAAGCGTGTGCCTCTAAATACATACCGTGCGCAGCGTCGTGGTGGTAAGGGACGTTCTGGTATGGCAACAAAGGATCAGGATTTTGTTACTCGCTTATTCGTGGCCAATACACATACACCAGTTCTTTTCTTTTCATCACGTGGGATTGTTTATAAAGAGAAGGTTTGGCGTTTACCTGTTGGTACGCCGCAATCACGCGGTAGAGCTTTAATTAATATGTTGCCTTTGCAACAAGGCGAGCGCATTACAACAATTATGCCATTGCCGGAGGATGAGGCAAGTTGGGGTAAACTGGATATTATGTTTGCAACAACGCGTGGAACTGTGCGCCGTAATAAATTATCAGACTTTATTCAAGTTAATCGCAATGGTAAAATAGCAATGAAACTTGATGAAGAGGGAGATGAGATCCTTTCTGTAGAGACCTGTACAGAACATGATGACGTTGTTCTTATTACAGCAAACGGGCAGTGTATTCGTTTTCCAGTTACTGATATTCGTGTATTTTCTGGTCGTAATTCGATGGGGGTACGCGGTATCAATATGGTTGAGGGTGATAAGGTCATTTCAATGACTATTTTAGAGCATGTTGAAGCGACATCAGTCGAACGTTCTGCTTATATTAAACGTGCAATCAATGAGCGTCGTGTTGCAGGTTCAGATGATGAAGATATTTTAACTGTTGATGAAGATGGAGAGGAAACTGAGGTTGAATTAACAGATGAACGTTATGCAGAACTTAGCGCTCATGAGCAAATGCTTTTAACAGTTAGTGAATTTGGTTATGGAAAACGCTCTTCTTCTTATGATTTCCGTATTTCAGGACGCGGTGGAAAAGGGATACGCGCAACTGATCTATCAAAGGCGGCTGAAATTGGTAAGTTAGTAGCAGCCTTTCCAGTAGGAGAACGAGATCAAATTATGTTAGTTTCGGATGGAGGACAGCTTATTCGTGTTCCCGTCAACTGTATTCGTATAGCGGGTCGTTCAACTAAAGGGGTCACAGTCTTTAATACAGCAAAAGGTGAAAAAGTTGTATCGGTTGAGCGTATTTCTGAATCTGAAAATGATACTAATCAGTTAGATATTGAAAGTGAGGAACATTCCGGAACAGTTAGCATGAGTGAAGAGAAAAAACTCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40073","NCBI_taxonomy_name":"Bartonella bacilliformis","NCBI_taxonomy_id":"774"}}}},"ARO_accession":"3003297","ARO_id":"39881","ARO_name":"Bartonella bacilliformis gyrA conferring resistance to fluoroquinolones","CARD_short_name":"Bbac_gyrA_FLO","ARO_description":"Point mutation of Bartonella bacilliformis gyrA resulted in the lowered affinity between fluoroquinolones and gyrA. Thus, conferring resistance.","ARO_category":{"39876":{"category_aro_accession":"3003292","category_aro_cvterm_id":"39876","category_aro_name":"fluoroquinolone resistant gyrA","category_aro_description":"DNA gyrase is responsible for DNA supercoiling and consists of two alpha and two beta subunits. GyrA point mutations confer resistance by preventing fluoroquinolone antibiotics from binding the alpha-subunit.","category_aro_class_name":"AMR Gene Family"},"35942":{"category_aro_accession":"0000023","category_aro_cvterm_id":"35942","category_aro_name":"enoxacin","category_aro_description":"Enoxacin belongs to a group called fluoroquinolones. Its mode of action depends upon blocking bacterial DNA replication by binding itself to DNA gyrase and causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37004":{"category_aro_accession":"3000660","category_aro_cvterm_id":"37004","category_aro_name":"lomefloxacin","category_aro_description":"Lomefloxacin is a difluoropiperazinyl quinolone, sharing similar activities with other fluoroquinolones. It is used to treat urinary tract infections. Relative to other fluoroquinolones, it has a longer half life and has higher serum concentrations.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37007":{"category_aro_accession":"3000663","category_aro_cvterm_id":"37007","category_aro_name":"ofloxacin","category_aro_description":"Ofloxacin is a 6-fluoro, 7-piperazinyl quinolone with a methyl-substituted oxazine ring. It has a broad spectrum of activity including many enterobacteria and mycoplasma but most anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"37008":{"category_aro_accession":"3000664","category_aro_cvterm_id":"37008","category_aro_name":"trovafloxacin","category_aro_description":"Trovafloxacin is a trifluoroquinalone with a broad spectrum of activity that acts by inhibiting the uncoiling of supercoiled DNA. While potent against many Gram-positive and Gram-negative bacteria, it is less active against pseudomonads and Cl. difficile. It is usually taken as the prodrug trovafloxacin mesylate or alatrofloxacin mesylate for oral or intravenous administration, respectively.","category_aro_class_name":"Antibiotic"},"37009":{"category_aro_accession":"3000665","category_aro_cvterm_id":"37009","category_aro_name":"grepafloxacin","category_aro_description":"Grepafloxacin is a broad-spectrum antibacterial quinoline. It is no longer taken due to its high toxicity.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"37142":{"category_aro_accession":"3000762","category_aro_cvterm_id":"37142","category_aro_name":"pefloxacin","category_aro_description":"Pefloxacin is structurally and functionally similar to norfloxacin. It is poorly active against mycobacteria, while anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1088":{"model_id":"1088","model_name":"Staphylococcus aureus rpoB mutants conferring resistance to daptomycin","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"2047":"I953S","2048":"A1085V","2049":"A621E"},"Curated-R":{"2047":"I953S","2048":"A1085V","2049":"A621E"},"clinical":{"2047":"I953S","2048":"A1085V","2049":"A621E"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"2300"}},"model_sequences":{"sequence":{"5226":{"protein_sequence":{"accession":"CAG39568.1","sequence":"MAGQVVQYGRHRKRRNYARISEVLELPNLIEIQTKSYEWFLREGLIEMFRDISPIEDFTGNLSLEFVDYRLGEPKYDLEESKNRDATYAAPLRVKVRLIIKETGEVKEQEVFMGDFPLMTDTGTFVINGAERVIVSQLVRSPSVYFNEKIDKNGRENYDATIIPNRGAWLEYETDAKDVVYVRIDRTRKLPLTVLLRALGFSSDQEIVDLLGDNEYLRNTLEKDGTENTEQALLEIYERLRPGEPPTVENAKSLLYSRFFDPKRYDLASVGRYKTNKKLHLKHRLFNQKLAEPIVNTETGEIVVEEGTVLDRRKIDEIMDVLESNANSEVFELHGSVIDEPVEIQSIKVYVPNDDEGRTTTVIGNAFPDSEVKCITPADIIASMSYFFNLLSGIGYTDDIDHLGNRRLRSVGELLQNQFRIGLSRMERVVRERMSIQDTESITPQQLINIRPVIASIKEFFGSSQLSQFMDQANPLAELTHKRRLSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETPYRKVDLDTHAITDQIDYLTADEEDSYVVAQANSKLDENGRFMDDEVVCRFRGNNTVMAKEKMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPEAPFVGTGMEHVAARDSGAAITAKHRGRVEHVESNEILVRRLVEENGVEHEGELDRYPLAKFKRSNSGTCYNQRPIVAVGDVVEFNEILADGPSMELGEMALGRNVVVGFMTWDGYNYEDAVIMSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVSESALKNLDDRGIVYIGAEVKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGAGGIVLDVKVFNREEGDDTLSPGVNQLVRVYIVQKRKIHVGDKMCGRHGNKGVISKIVPEEDMPYLPDGRPIDIMLNPLGVPSRMNIGQVLELHLGMAAKNLGIHVASPVFDGANDDDVWSTIEEAGMARDGKTVLYDGRTGEPFDNRISVGVMYMLKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTYKSDDTVGRVKTYEAIVKGENISRPSVPESFRVLMKELQSLGLDVKVMDEQDNEIEMTDVDDDDVVERKVDLQQNDAPETQKEVTD"},"dna_sequence":{"accession":"BX571856.1","fmin":"590830","fmax":"594382","strand":"+","sequence":"TTGGCAGGTCAAGTTGTCCAATATGGAAGACATCGTAAACGTAGAAACTACGCGAGAATTTCAGAAGTATTAGAATTACCAAACTTAATAGAAATTCAAACTAAATCTTACGAGTGGTTCCTAAGAGAAGGTTTAATCGAAATGTTTAGAGACATTTCTCCAATTGAAGATTTTACTGGTAATTTGTCATTAGAGTTTGTGGATTACCGTTTAGGAGAACCAAAATATGATTTAGAAGAATCTAAAAACCGTGACGCTACTTATGCTGCACCTCTTCGTGTAAAAGTGCGTCTAATCATTAAAGAAACAGGAGAAGTTAAAGAACAAGAAGTCTTTATGGGTGATTTCCCATTAATGACTGATACAGGTACGTTCGTTATCAATGGTGCAGAACGTGTAATCGTATCTCAATTAGTTCGTTCACCATCCGTTTATTTCAATGAAAAAATCGACAAAAATGGTCGTGAAAACTATGATGCAACAATTATTCCAAACCGAGGTGCATGGTTAGAATATGAAACAGATGCTAAAGATGTTGTATACGTGCGTATTGATAGAACACGTAAACTACCATTAACAGTATTGTTACGTGCATTAGGTTTCTCAAGTGACCAAGAAATTGTTGACCTTTTAGGTGACAATGAATATTTACGTAATACTTTAGAGAAAGACGGCACTGAAAACACTGAACAAGCGTTATTAGAAATCTATGAACGTTTACGTCCAGGTGAACCACCAACTGTTGAAAATGCTAAAAGTCTATTGTATTCACGTTTCTTTGATCCAAAACGCTATGACTTAGCAAGCGTGGGTCGTTATAAAACAAACAAAAAATTACATTTAAAACATCGTTTATTCAATCAAAAATTAGCTGAGCCAATTGTGAATACTGAAACTGGTGAAATTGTAGTTGAAGAAGGTACAGTGCTTGATCGTCGTAAAATCGACGAAATCATGGATGTACTTGAATCAAACGCAAACAGCGAAGTGTTTGAATTGCATGGTAGCGTTATAGACGAGCCAGTAGAAATTCAATCAATTAAAGTATATGTTCCTAACGATGATGAAGGTCGTACGACAACTGTAATTGGTAATGCTTTCCCTGACTCAGAAGTTAAATGTATTACACCGGCAGATATCATCGCTTCAATGAGTTACTTCTTTAACTTATTAAGTGGTATTGGATATACAGATGATATTGACCATTTAGGTAACCGTCGTTTACGTTCTGTAGGTGAATTACTACAAAACCAATTCCGTATCGGTTTATCAAGAATGGAAAGAGTTGTACGTGAAAGAATGTCAATTCAAGATACTGAGTCTATCACACCTCAACAATTAATTAATATTCGACCTGTTATTGCATCTATTAAAGAATTCTTTGGTAGCTCTCAATTATCACAATTCATGGACCAAGCAAATCCATTAGCTGAGTTAACGCATAAACGTCGTCTATCAGCATTAGGACCTGGTGGTTTAACACGTGAACGTGCTCAAATGGAAGTGCGTGACGTTCACTACTCTCACTATGGCCGTATGTGTCCAATTGAAACGCCTGAGGGACCAAACATTGGATTGATTAACTCATTATCAAGTTATGCACGTGTAAATGAATTCGGCTTTATTGAAACACCATATCGTAAAGTTGATTTAGATACACATGCTATCACTGATCAAATTGACTATTTAACAGCTGACGAAGAAGATAGCTATGTTGTAGCACAAGCAAACTCTAAATTAGATGAAAATGGTCGTTTCATGGATGATGAAGTTGTATGTCGTTTCCGTGGTAACAATACAGTTATGGCTAAAGAAAAAATGGATTATATGGATGTATCGCCGAAGCAAGTTGTTTCAGCAGCGACAGCATGTATTCCATTCTTAGAAAATGATGACTCAAACCGTGCATTGATGGGTGCGAACATGCAACGTCAAGCAGTGCCTTTGATGAATCCAGAAGCACCATTTGTTGGTACAGGTATGGAACACGTTGCAGCACGTGATTCTGGTGCAGCTATTACAGCTAAGCACAGAGGTCGTGTTGAACATGTTGAATCTAATGAAATTCTTGTACGTCGTCTAGTTGAAGAGAACGGCGTTGAGCATGAAGGTGAATTAGATCGCTATCCATTAGCTAAATTTAAACGTTCAAACTCAGGTACATGTTACAACCAACGTCCAATCGTTGCAGTTGGAGATGTTGTTGAGTTTAACGAGATTTTAGCAGATGGACCATCTATGGAATTAGGAGAAATGGCATTAGGTAGAAACGTAGTAGTTGGTTTCATGACTTGGGACGGTTACAACTATGAGGATGCCGTTATCATGAGTGAAAGACTTGTGAAAGATGACGTGTATACTTCTATTCATATTGAAGAGTATGAATCAGAAGCACGTGATACTAAGTTAGGACCTGAAGAAATCACAAGAGATATTCCTAATGTTTCTGAAAGTGCACTTAAGAACTTAGACGATCGTGGTATCGTTTATATTGGTGCAGAAGTAAAAGATGGAGATATTTTAGTTGGTAAAGTAACGCCTAAAGGTGTAACTGAGTTAACTGCCGAAGAAAGATTGTTACATGCAATCTTTGGTGAAAAAGCACGTGAAGTTAGAGATACTTCATTACGTGTACCTCACGGCGCTGGCGGTATCGTTCTTGATGTAAAAGTATTCAATCGTGAAGAAGGCGACGACACATTATCACCTGGTGTAAACCAATTAGTACGTGTATATATCGTTCAAAAACGTAAAATTCATGTTGGTGATAAGATGTGTGGTCGACATGGTAACAAAGGTGTCATTTCTAAGATTGTTCCTGAAGAAGATATGCCTTACTTACCAGATGGACGTCCGATTGATATCATGTTAAATCCTCTTGGTGTACCATCTCGTATGAACATCGGACAAGTATTAGAGCTACACTTAGGTATGGCTGCTAAAAATCTTGGTATTCACGTTGCATCACCAGTATTTGACGGTGCAAACGATGACGATGTATGGTCAACAATTGAAGAAGCTGGTATGGCTCGTGATGGTAAAACTGTACTTTATGATGGACGTACAGGTGAACCATTCGATAACCGTATTTCAGTAGGTGTAATGTACATGTTGAAACTTGCGCACATGGTTGATGATAAATTACATGCGCGTTCAACAGGACCATATTCACTTGTTACACAACAACCACTTGGCGGTAAAGCGCAATTCGGTGGACAACGTTTCGGTGAGATGGAGGTATGGGCACTTGAAGCATATGGTGCTGCATACACATTACAAGAAATCTTAACTTACAAATCCGATGATACAGTAGGACGTGTGAAAACATACGAGGCTATTGTTAAAGGTGAAAACATCTCTAGACCAAGTGTTCCAGAATCATTCCGAGTATTGATGAAAGAATTACAAAGTTTAGGTTTAGATGTAAAAGTTATGGATGAGCAAGATAATGAAATCGAAATGACAGACGTTGATGACGATGATGTTGTAGAACGCAAAGTAGATTTACAACAAAATGATGCTCCTGAAACACAAAAAGAAGTTACTGATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35517","NCBI_taxonomy_name":"Staphylococcus aureus subsp. aureus MRSA252","NCBI_taxonomy_id":"282458"}}}},"ARO_accession":"3003287","ARO_id":"39871","ARO_name":"Staphylococcus aureus rpoB mutants conferring resistance to daptomycin","CARD_short_name":"Saur_rpoB_DAP","ARO_description":"Point mutations that occurs in Staphylococcus aureus rpoB resulting in resistance to daptomycin.","ARO_category":{"39637":{"category_aro_accession":"3003090","category_aro_cvterm_id":"39637","category_aro_name":"daptomycin-resistant beta-subunit of RNA polymerase (rpoB)","category_aro_description":"Daptomycin-resistant RNA polymerases include amino acids substitutions which alter expression of the dlt operon, which increases the cell surface positive charge. Known from S. aureus.","category_aro_class_name":"AMR Gene Family"},"35985":{"category_aro_accession":"0000068","category_aro_cvterm_id":"35985","category_aro_name":"daptomycin","category_aro_description":"Daptomycin is a novel lipopeptide antibiotic used in the treatment of certain infections caused by Gram-positive organisms. Daptomycin interferes with the bacterial cell membrane, reducing membrane potential and inhibiting cell wall synthesis.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1108":{"model_id":"1108","model_name":"Enterococcus faecium liaS mutant conferring daptomycin resistance","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"2203":"E192G","2252":"H264Q","39":"A180T","44":"T120A"},"Curated-R":{"2203":"E192G","2252":"H264Q","39":"A180T","44":"T120A"},"clinical":{"2203":"E192G","2252":"H264Q","39":"A180T","44":"T120A"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"650"}},"model_sequences":{"sequence":{"37":{"protein_sequence":{"accession":"AFK58561.1","sequence":"MMGKISRAMLAVYSGIAAFLIILFSLFTYFYASNQSHWWGELLRARLLYVPLIFHLLAISLGVGLIVFLLLSLIQKTKYGKIEEKLRALSSGNYESKLLLLPIPSASDDLYIKDIDKEITKIKEKMIEVSSELQIVTSRPQYVDGQTKEEILELERHRLARELHDSVSQQLFAAMMMMSALTEQAEKSETPEMFRKQLKMVAEIINASQSEMRALLLHLRPVNLEEKSLKQGIEQLLKELQNKIQISLKWDVEDVKLSSSIEDHLFRIVQELLSNTLRHAKANELEVYLHKIDNNLLLRIIDDGTGFNMNETKTGSYGLNNIKERVAGIGGTVKIISFKGQGTSVEIKVPLMKEA"},"dna_sequence":{"accession":"CP003583.1","fmin":"913745","fmax":"914813","strand":"+","sequence":"ATGATGGGAAAAATATCCAGAGCGATGCTAGCTGTTTATTCGGGGATTGCGGCTTTCCTTATTATTCTATTTTCACTTTTCACTTATTTTTATGCCAGCAATCAAAGTCATTGGTGGGGAGAATTACTGCGTGCACGTTTATTATATGTTCCGCTTATCTTCCATTTGTTAGCCATTTCCTTAGGTGTAGGATTAATTGTCTTTCTATTATTATCACTTATTCAAAAGACAAAATACGGGAAAATCGAAGAAAAGCTGCGTGCACTTTCTTCTGGCAATTATGAATCCAAATTGTTGCTTCTTCCGATCCCAAGTGCATCGGACGATTTATACATCAAAGATATTGATAAGGAAATCACTAAGATAAAAGAAAAAATGATTGAAGTATCTAGTGAATTACAAATTGTAACGAGCCGTCCCCAATATGTAGATGGACAAACCAAAGAAGAAATTTTAGAATTAGAAAGACATCGATTAGCCCGTGAGCTGCATGATTCAGTTTCGCAACAATTGTTTGCAGCAATGATGATGATGTCGGCATTGACGGAGCAAGCAGAAAAAAGCGAGACACCAGAAATGTTTCGCAAGCAGTTGAAAATGGTAGCAGAGATCATCAACGCTTCCCAGTCTGAGATGCGTGCGCTGCTTCTTCATCTACGTCCAGTCAATTTAGAAGAGAAAAGTTTAAAGCAAGGTATCGAGCAGTTATTGAAGGAATTGCAAAATAAAATCCAGATTTCGCTGAAATGGGATGTAGAAGATGTAAAACTATCTAGTTCCATTGAGGATCACTTGTTCCGAATCGTTCAAGAATTGTTATCAAATACATTAAGACATGCTAAAGCCAATGAATTAGAGGTATATTTGCACAAAATAGACAATAATCTTTTGTTACGTATTATTGACGACGGAACAGGGTTTAATATGAATGAAACGAAAACGGGAAGTTATGGATTGAACAATATCAAAGAACGAGTAGCTGGTATTGGTGGAACAGTAAAAATCATTAGTTTTAAAGGTCAAGGTACAAGTGTAGAAATCAAGGTCCCTTTGATGAAGGAGGCATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37599","NCBI_taxonomy_name":"Enterococcus faecium DO","NCBI_taxonomy_id":"333849"}}}},"ARO_accession":"3003079","ARO_id":"39626","ARO_name":"Enterococcus faecium liaS mutant conferring daptomycin resistance","CARD_short_name":"Efac_liaS_DAP","ARO_description":"liaS is a histidine kinase found in the liaFSR signal transduction pathway. Mutations confer daptomycin resistance.","ARO_category":{"41428":{"category_aro_accession":"3004264","category_aro_cvterm_id":"41428","category_aro_name":"daptomycin resistant liaS","category_aro_description":"Mutations in the liaS histidine kinase that confer daptomycin resistance.","category_aro_class_name":"AMR Gene Family"},"35985":{"category_aro_accession":"0000068","category_aro_cvterm_id":"35985","category_aro_name":"daptomycin","category_aro_description":"Daptomycin is a novel lipopeptide antibiotic used in the treatment of certain infections caused by Gram-positive organisms. Daptomycin interferes with the bacterial cell membrane, reducing membrane potential and inhibiting cell wall synthesis.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1166":{"model_id":"1166","model_name":"Staphylococcus aureus gyrA conferring resistance to fluoroquinolones","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"2117":"S84L","2118":"S85P","2119":"E88K","2120":"E88A"},"Curated-R":{"2117":"S84L","2118":"S85P","2119":"E88K","2120":"E88A"},"clinical":{"2117":"S84L","2118":"S85P","2119":"E88K","2120":"E88A"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1500"}},"model_sequences":{"sequence":{"6035":{"protein_sequence":{"accession":"WP_000819088.1","sequence":"MAELPQSRINERNITSEMRESFLDYAMSVIVARALPDVRDGLKPVHRRILYGLNEQGMTPDKSYKKSARIVGDVMGKYHPHGDSSIYEAMVRMAQDFSYRYPLVDGQGNFGSMDGDGAAAMRYTEARMTKITLELLRDINKDTIDFIDNYDGNEREPSVLPARFPNLLANGASGIAVGMATNIPPHNLTELINGVLSLSKNPDISIAELMEDIEGPDFPTAGLILGKSGIRRAYETGRGSIQMRSRAVIEERGGGRQRIVVTEIPFQVNKARMIEKIAELVRDKKIDGITDLRDETSLRTGVRVVIDVRKDANASVILNNLYKQTPLQTSFGVNMIALVNGRPKLINLKEALVHYLEHQKTVVRRRTQYNLRKAKDRAHILEGLRIALDHIDEIISTIRESDTDKVAMESLQQRFKLSEKQAQAILDMRLRRLTGLERDKIEAEYNELLNYISELEAILADEEVLLQLVRDELTEIRDRFGDDRRTEIQLGGFENLEDEDLIPEEQIVITLSHNNYIKRLPVSTYRAQNRGGRGVQGMNTLEEDFVSQLVTLSTHDHVLFFTNKGRVYKLKGYEVPELSRQSKGIPVVNAIELENDEVISTMIAVKDLESEDNFLVFATKRGVVKRSALSNFSRINRNGKIAISFREDDELIAVRLTSGQEDILIGTSHASLIRFPESTLRPLGRTATGVKGITLREGDEVVGLDVAHANSVDEVLVVTENGYGKRTPVNDYRLSNRGGKGIKTATITERNGNVVCITTVTGEEDLMIVTNAGVIIRLDVADISQNGRAAQGVRLIRLGDDQFVSTVAKVKEDAEDETNEDEQSTSTVSEDGTEQQREAVVNDETPGNAIHTEVIDSEENDEDGRIEVRQDFMDRVEEDIQQSSDEE"},"dna_sequence":{"accession":"NC_009641.1","fmin":"7011","fmax":"9675","strand":"+","sequence":"ATGGCTGAATTACCTCAATCAAGAATAAATGAACGAAATATTACCAGTGAAATGCGTGAATCATTTTTAGATTATGCGATGAGTGTTATCGTTGCTCGTGCATTGCCAGATGTTCGTGACGGTTTAAAACCAGTACATCGTCGTATACTATATGGATTAAATGAACAAGGTATGACACCGGATAAATCATATAAAAAATCAGCACGTATCGTTGGTGACGTAATGGGTAAATATCACCCTCATGGTGACTCATCTATTTATGAAGCAATGGTACGTATGGCTCAAGATTTCAGTTATCGTTATCCGCTTGTTGATGGCCAAGGTAACTTTGGTTCAATGGATGGAGATGGCGCAGCAGCAATGCGTTATACTGAAGCGCGTATGACTAAAATCACACTTGAACTGTTACGTGATATTAATAAAGATACAATAGATTTTATCGATAACTATGATGGTAATGAAAGAGAGCCGTCAGTCTTACCTGCTCGATTCCCTAACTTATTAGCCAATGGTGCATCAGGTATCGCGGTAGGTATGGCAACGAATATTCCACCACATAACTTAACAGAATTAATCAATGGTGTACTTAGCTTAAGTAAGAACCCTGATATTTCAATTGCTGAGTTAATGGAGGATATTGAAGGTCCTGATTTCCCAACTGCTGGACTTATTTTAGGTAAGAGTGGTATTAGACGTGCATATGAAACAGGTCGTGGTTCAATTCAAATGCGTTCTCGTGCAGTTATTGAAGAACGTGGAGGCGGACGTCAACGTATTGTTGTCACTGAAATTCCTTTCCAAGTGAATAAGGCTCGTATGATTGAAAAAATTGCAGAGCTCGTTCGTGACAAGAAAATTGACGGTATCACTGATTTACGTGATGAAACAAGTTTACGTACTGGTGTGCGTGTCGTTATTGATGTGCGTAAGGATGCAAATGCTAGTGTCATTTTAAATAACTTATACAAACAAACACCTCTTCAAACATCATTTGGTGTGAATATGATTGCACTTGTAAATGGTAGACCGAAGCTTATTAATTTAAAAGAAGCGTTGGTACATTATTTAGAGCATCAAAAGACAGTTGTTAGAAGACGTACGCAATACAACTTACGTAAAGCTAAAGATCGTGCCCACATTTTAGAAGGATTACGTATCGCACTTGACCATATCGATGAAATTATTTCAACGATTCGTGAGTCAGATACAGATAAAGTTGCAATGGAAAGCTTGCAACAACGCTTCAAACTTTCTGAAAAACAAGCTCAAGCTATTTTAGACATGCGTTTAAGACGTCTAACAGGTTTAGAGAGAGACAAAATTGAAGCTGAATATAATGAGTTATTAAATTATATTAGTGAATTAGAAGCAATCTTAGCTGATGAAGAAGTGTTATTACAGTTAGTTAGAGATGAATTGACTGAAATTAGAGATCGTTTCGGTGATGATCGTCGTACAGAAATTCAATTAGGTGGATTTGAAAACTTAGAGGACGAAGACTTAATTCCAGAAGAACAAATAGTAATTACACTAAGCCATAATAACTACATTAAACGTTTGCCGGTATCTACATATCGTGCTCAAAACCGTGGTGGTCGTGGTGTTCAAGGTATGAATACATTGGAAGAAGATTTTGTCAGTCAATTGGTAACTTTAAGTACACATGACCATGTATTGTTCTTTACTAACAAAGGTCGTGTATACAAACTTAAAGGTTACGAAGTGCCTGAGTTATCAAGACAGTCTAAAGGTATTCCTGTAGTGAATGCTATTGAACTTGAAAATGATGAAGTCATTAGTACAATGATTGCTGTTAAAGACCTTGAAAGTGAAGACAACTTCTTAGTGTTTGCAACTAAACGTGGTGTCGTTAAACGTTCAGCATTAAGTAACTTCTCAAGAATAAATAGAAATGGTAAGATTGCGATTTCGTTCAGAGAAGATGATGAGTTAATTGCAGTTCGCTTAACAAGTGGTCAAGAAGATATCTTGATTGGTACATCACATGCATCATTAATTCGATTCCCTGAATCAACATTACGTCCTTTAGGCCGTACAGCAACGGGTGTGAAAGGTATTACACTTCGTGAAGGTGACGAAGTTGTAGGGCTTGATGTAGCTCATGCAAACAGTGTTGATGAAGTATTAGTAGTTACTGAAAATGGTTATGGTAAACGTACGCCAGTTAATGACTATCGCTTATCAAATCGTGGTGGTAAAGGTATTAAAACAGCTACGATTACTGAGCGTAATGGTAATGTTGTATGTATCACTACAGTAACTGGTGAAGAAGATTTAATGATTGTTACTAATGCAGGTGTCATTATTCGACTAGATGTTGCAGATATTTCTCAAAATGGTCGTGCAGCACAAGGTGTTCGCTTAATTCGCTTAGGTGATGATCAATTTGTTTCAACGGTTGCTAAAGTAAAAGAAGATGCAGAAGATGAAACGAATGAAGATGAGCAATCTACTTCAACTGTATCTGAAGATGGTACTGAACAACAACGTGAAGCGGTTGTAAATGATGAAACACCAGGAAATGCAATTCATACTGAAGTGATTGATTCAGAAGAAAATGATGAAGATGGACGTATTGAAGTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATCAGATGAAGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37074","NCBI_taxonomy_name":"Staphylococcus","NCBI_taxonomy_id":"1279"}}}},"ARO_accession":"3003296","ARO_id":"39880","ARO_name":"Staphylococcus aureus gyrA conferring resistance to fluoroquinolones","CARD_short_name":"Saur_gyrA_FLO","ARO_description":"Point mutation of Staphylococcus aureus gyrA resulted in the lowered affinity between fluoroquinolones and gyrA. Thus, conferring resistance.","ARO_category":{"39876":{"category_aro_accession":"3003292","category_aro_cvterm_id":"39876","category_aro_name":"fluoroquinolone resistant gyrA","category_aro_description":"DNA gyrase is responsible for DNA supercoiling and consists of two alpha and two beta subunits. GyrA point mutations confer resistance by preventing fluoroquinolone antibiotics from binding the alpha-subunit.","category_aro_class_name":"AMR Gene Family"},"35942":{"category_aro_accession":"0000023","category_aro_cvterm_id":"35942","category_aro_name":"enoxacin","category_aro_description":"Enoxacin belongs to a group called fluoroquinolones. Its mode of action depends upon blocking bacterial DNA replication by binding itself to DNA gyrase and causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37004":{"category_aro_accession":"3000660","category_aro_cvterm_id":"37004","category_aro_name":"lomefloxacin","category_aro_description":"Lomefloxacin is a difluoropiperazinyl quinolone, sharing similar activities with other fluoroquinolones. It is used to treat urinary tract infections. Relative to other fluoroquinolones, it has a longer half life and has higher serum concentrations.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37007":{"category_aro_accession":"3000663","category_aro_cvterm_id":"37007","category_aro_name":"ofloxacin","category_aro_description":"Ofloxacin is a 6-fluoro, 7-piperazinyl quinolone with a methyl-substituted oxazine ring. It has a broad spectrum of activity including many enterobacteria and mycoplasma but most anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"37008":{"category_aro_accession":"3000664","category_aro_cvterm_id":"37008","category_aro_name":"trovafloxacin","category_aro_description":"Trovafloxacin is a trifluoroquinalone with a broad spectrum of activity that acts by inhibiting the uncoiling of supercoiled DNA. While potent against many Gram-positive and Gram-negative bacteria, it is less active against pseudomonads and Cl. difficile. It is usually taken as the prodrug trovafloxacin mesylate or alatrofloxacin mesylate for oral or intravenous administration, respectively.","category_aro_class_name":"Antibiotic"},"37009":{"category_aro_accession":"3000665","category_aro_cvterm_id":"37009","category_aro_name":"grepafloxacin","category_aro_description":"Grepafloxacin is a broad-spectrum antibacterial quinoline. It is no longer taken due to its high toxicity.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"37142":{"category_aro_accession":"3000762","category_aro_cvterm_id":"37142","category_aro_name":"pefloxacin","category_aro_description":"Pefloxacin is structurally and functionally similar to norfloxacin. It is poorly active against mycobacteria, while anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1175":{"model_id":"1175","model_name":"Enterococcus faecium cls conferring resistance to daptomycin","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"2072":"H215R","2075":"K59T","3574":"N13I","3578":"N13T","3584":"A20D","3585":"R267H","3586":"D27N","12948":"G177T"},"Curated-R":{"2072":"H215R","2075":"K59T","3574":"N13I","3578":"N13T","3584":"A20D","3585":"R267H","3586":"D27N","12948":"G177T"},"clinical":{"2072":"H215R","2075":"K59T","3574":"N13I","3578":"N13T","3584":"A20D","3585":"R267H","3586":"D27N","12948":"G177T"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"900"}},"model_sequences":{"sequence":{"4733":{"protein_sequence":{"accession":"ALL09868.1","sequence":"MVSSIITALYLLNALIALVAILIKPRDVAAIWAWLLVLFALPGVGFVLYLFFGRGLTDKKKFYLRQSDLKELENFQSFRGDTIEHYDPDMGDKDKQQFVDFFSSLNRMPLTRMNSVTLLTDGQEKLDSLLQDLKKAKHSIHIEYYAFVTDNIGQQVLHVLEEKAAEGVEVRILYDAFGSHGTKAKDFNRLIKNGGHVHTFVTSQRALLRFRLNYHDHRKIVVIDGKISYTGGFNIANQYVNTTKKFGYWRDTHIRIFGAASSLLQLRFLTDWNVSVPEEKKVGYHLNYFFKKADRDESKLADTSIQLVSSGPNNEREQIKLSFIKLITSAKKRVWIQTPYLVPDESVIAALKIATASGVDVKIMIPNKPDHPFIYRATQYYARQLIKENVQILVYENGFLHAKTLIMDDEICMVGSANQDIRSYRLNFETSAVIYDPEFLEELATQFKEDETHCSSMTTETVKEMSNWLLFKQQISRLFSPIL"},"dna_sequence":{"accession":"CP013009.1","fmin":"1008840","fmax":"1010292","strand":"-","sequence":"GTGGTATCTAGTATTATAACCGCCCTTTATCTATTAAATGCACTTATTGCTTTGGTGGCTATTTTGATCAAACCCCGAGATGTAGCAGCCATTTGGGCATGGCTCTTAGTATTATTTGCCCTTCCTGGGGTGGGCTTTGTATTATATTTATTTTTCGGACGTGGATTAACGGATAAGAAAAAATTCTATCTCCGACAAAGTGACTTGAAAGAATTAGAAAACTTTCAGTCTTTTAGAGGAGATACCATTGAACATTACGATCCTGACATGGGCGATAAAGACAAACAGCAATTTGTTGACTTCTTCTCTTCATTAAATCGTATGCCGCTGACAAGAATGAATTCTGTCACTCTTCTCACAGACGGACAAGAGAAATTGGATTCACTGCTTCAAGATCTAAAAAAAGCCAAACATTCGATCCATATCGAATATTACGCATTTGTGACAGATAATATCGGCCAGCAAGTCTTACATGTTTTAGAAGAAAAAGCCGCAGAAGGCGTGGAAGTTCGAATATTATATGATGCATTTGGCTCTCATGGCACAAAAGCAAAAGATTTCAATCGTCTAATCAAAAATGGTGGACATGTCCATACATTTGTTACCTCACAAAGGGCATTACTTCGTTTCCGATTGAATTACCATGATCACCGAAAAATCGTTGTGATCGATGGAAAGATTAGTTATACCGGTGGTTTCAATATTGCCAATCAATATGTAAATACAACAAAAAAATTCGGCTATTGGCGCGATACGCATATACGGATTTTCGGTGCCGCTTCTTCTTTGCTCCAGCTTCGCTTCTTAACAGACTGGAACGTCTCGGTACCTGAAGAAAAAAAGGTCGGCTATCATTTGAATTATTTCTTTAAAAAAGCAGATCGAGATGAATCTAAGCTTGCTGATACATCCATCCAGCTTGTTTCAAGCGGACCGAATAACGAAAGGGAACAAATCAAGCTTTCATTTATCAAATTGATTACTTCTGCTAAAAAACGTGTTTGGATACAGACACCTTACCTTGTTCCTGATGAAAGTGTCATTGCTGCTTTAAAAATCGCAACTGCCTCTGGTGTAGATGTGAAAATCATGATTCCCAACAAACCGGATCATCCTTTTATTTATCGAGCAACACAATATTATGCTCGGCAGCTGATCAAGGAAAATGTACAAATCCTTGTCTATGAGAACGGCTTCCTCCATGCAAAAACATTGATAATGGATGATGAAATCTGCATGGTAGGTTCAGCAAATCAAGATATTCGTAGCTACCGATTGAATTTTGAAACAAGTGCTGTCATTTACGATCCTGAGTTTTTAGAAGAACTTGCTACTCAGTTCAAAGAAGATGAGACACATTGTTCATCCATGACAACTGAAACAGTCAAGGAAATGTCTAACTGGCTATTATTCAAGCAACAAATTTCTCGATTATTTTCTCCAATCCTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36779","NCBI_taxonomy_name":"Enterococcus faecium","NCBI_taxonomy_id":"1352"}}}},"ARO_accession":"3003092","ARO_id":"39639","ARO_name":"Enterococcus faecium cls conferring resistance to daptomycin","CARD_short_name":"Efac_cls_DAP","ARO_description":"cls or cardiolipin synthetase is an inner membrane protein that is involved in membrane synthesis. Specific mutations in Enterococcus can confer resistance to daptomycin.","ARO_category":{"39856":{"category_aro_accession":"3003272","category_aro_cvterm_id":"39856","category_aro_name":"daptomycin resistant cls","category_aro_description":"Cardiolipin synthetase catalyzes the formation of cardiolipin from two phosphatidylglycerol molecules. Cardiolipin is important in membrane translocation and permeabilization. Current known mutations on the enzyme confer resistance to daptomycin.","category_aro_class_name":"AMR Gene Family"},"35985":{"category_aro_accession":"0000068","category_aro_cvterm_id":"35985","category_aro_name":"daptomycin","category_aro_description":"Daptomycin is a novel lipopeptide antibiotic used in the treatment of certain infections caused by Gram-positive organisms. Daptomycin interferes with the bacterial cell membrane, reducing membrane potential and inhibiting cell wall synthesis.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1996":{"model_id":"1996","model_name":"vanX gene in vanM cluster","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"200"}},"model_sequences":{"sequence":{"717":{"protein_sequence":{"accession":"ACL82962.1","sequence":"MEKGFTFLDEILNDVRWDAKYATWDNFTGKPIDGYEVNRIIGTYELADALLKVQELAFNQGYGLLLWDGYRPQQAVNCFLQWAAQPEDNRTKAKYYPNIDRTEMVSKGYVASKSSHSRGSAIDLTLYRLDTDELVPMGSGFDFMDERSHHEAKGITSNEAQNRRFLRSIMENSGFEAYSFEWWHYVLINEPYPYSCFDFPVK"},"dna_sequence":{"accession":"FJ349556.1","fmin":"5893","fmax":"6502","strand":"+","sequence":"ATGGAAAAAGGATTTACCTTTTTAGATGAAATATTAAACGATGTTCGTTGGGACGCTAAATATGCTACGTGGGACAACTTCACTGGAAAACCAATTGATGGATATGAAGTAAATCGAATTATAGGAACATATGAGTTAGCCGATGCGCTATTGAAGGTTCAAGAATTAGCTTTTAACCAAGGTTATGGATTGCTTTTATGGGACGGTTACCGTCCCCAACAAGCTGTAAATTGTTTTTTGCAATGGGCGGCACAGCCGGAAGATAATCGAACAAAGGCAAAATATTATCCCAATATTGACCGAACTGAGATGGTTTCAAAAGGATACGTGGCTTCAAAATCAAGTCATAGCCGCGGAAGTGCAATTGATCTTACACTTTATCGATTAGACACGGACGAACTTGTTCCGATGGGGAGCGGATTTGATTTTATGGATGAGCGCTCTCATCATGAGGCAAAAGGAATTACGAGCAATGAAGCGCAAAACCGTAGATTTTTGCGTTCCATTATGGAAAACAGTGGGTTTGAAGCGTATAGTTTCGAATGGTGGCACTATGTATTGATAAACGAACCTTATCCCTATAGCTGCTTTGATTTTCCTGTCAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36779","NCBI_taxonomy_name":"Enterococcus faecium","NCBI_taxonomy_id":"1352"}}}},"ARO_accession":"3002953","ARO_id":"39387","ARO_name":"vanX gene in vanM cluster","CARD_short_name":"vanX_in_vanM_cl","ARO_description":"Also known as vanXM, is a vanX variant found in the vanM gene cluster.","ARO_category":{"36020":{"category_aro_accession":"3000011","category_aro_cvterm_id":"36020","category_aro_name":"vanX","category_aro_description":"VanX is a D,D-dipeptidase that cleaves D-Ala-D-Ala but not D-Ala-D-Lac, ensuring that the latter dipeptide that has reduced binding affinity with vancomycin is used to synthesize peptidoglycan substrate.","category_aro_class_name":"AMR Gene Family"},"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"35948":{"category_aro_accession":"0000029","category_aro_cvterm_id":"35948","category_aro_name":"teicoplanin","category_aro_description":"Teicoplanin is a glycopeptide antibiotic used in the prophylaxis and treatment of serious infections caused by Gram-positive bacteria. Teicoplanin has a unique acyl-aliphatic chain, and binds to cell wall precursors to inhibit transglycosylation  and transpeptidation.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1991":{"model_id":"1991","model_name":"otr(C)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"650"}},"model_sequences":{"sequence":{"421":{"protein_sequence":{"accession":"AAR96051.1","sequence":"MTRKTISNGARNAVEVRGLVKHFGEVKAVDGVDLDVREGTVLGVLGPXGAAXXRGALPAHVXGPDAGRRPWRFXTWCANRRALRRTIGXHRPVRXGRRESFSGRENLYMIGRXLDLSRKDARARADELLERFSLTEAAGRAAAKYSGGMRRRLDLAASMIGRPAVLYLDEPTTGLDPRTRNEVWDEVRSMVRDGATVLLTTQYMEEAEQLAHELTVIDRGRVIADGKVDELKTKVGGRTLQIRPAHAAELDRMVGAIAQAGLDGIAGATADHEDGVVNVPIVSDEQLSAVVGMLGERGFTISGHQHPSAQLXEVFLAITGQKTSEAADGGPQDGPQDQQGVQDKQYEEVPA"},"dna_sequence":{"accession":"AY509111.1","fmin":"0","fmax":"1056","strand":"+","sequence":"ATGACGCGAAAGACGATATCCAACGGCGCGAGGAACGCCGTCGAAGTGCGGGGACTGGTCAAGCACTTCGGCGAGGTGAAGGCCGTGGACGGGGTGGATCTCGATGTGAGGGAAGGCACCGTGCTCGGTGTGCTCGGGCCGANCGGCGCGGCAANANAACGTGGTGCGCTGCCTGCCCACGTTGNTGGTCCGGACGCCGGCAGGCGACCGTGGCGGTTTNAAACGTGGTGCGCCAACCGGCGCGCGTTGCGCCGCACGATCGGCCNTCACCGGCCAGTACGCNTCGGTCGACGAGAAAGCTTCTCCGGCCGNGAGAACCTGTACATGATCGGCCGCNTGCTGGACCTCTCCCGCAAGGACGCCCGCGCGCGGGCCGACGAGCTGCTGGAGCGGTTCTCCCTCACCGAGGCCGCCGGCCGGGCCGCCGCCAAGTACTCCGGCGGTATGCGCCGCCGCCTCGACCTGGCCGCCTCCATGATCGGCAGGCCCGCGGTGCTGTATCTGGACGAGCCGACGACGGGCCTCGACCCCCGCACCCGCAACGAGGTGTGGGACGAGGTCCGCAGCATGGTGCGCGACGGCGCCACGGTCCTGCTCACCACCCAGTACATGGAAGAGGCCGAGCAGCTGGCCCACGAGCTGACGGTCATCGACCGCGGCCGGGTCATCGCCGACGGCAAGGTGGACGAGCTGAAGACCAAGGTCGGCGGCCGTACGCTCCAGATACGCCCGGCGCACGCCGCCGAGCTGGACCGGATGGTCGGCGCCATCGCGCAGGCCGGCCTGGACGGCATCGCGGGCGCCACCGCCGACCACGAGGACGGCGTGGTCAACGTCCCGATCGTCAGCGACGAGCAGCTGTCCGCCGTGGTCGGCATGCTCGGCGAGCGGGGCTTCACGATCTCCGGGCATCAACACCCATCTGCCCAGCTGNACGAGGTGTTCCTGGCCATCACCGGCCAGAAGACCTCGGAGGCCGCCGACGGCGGCCCGCAGGACGGACCGCAGGACCAGCAGGGCGTTCAGGACAAGCAGTACGAGGAGGTTCCGGCATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36773","NCBI_taxonomy_name":"Streptomyces rimosus","NCBI_taxonomy_id":"1927"}}}},"ARO_accession":"3002894","ARO_id":"39328","ARO_name":"otr(C)","CARD_short_name":"otr(C)","ARO_description":"otr(C) is a tetracycline resistance efflux pump found in Streptomyces rimosus.","ARO_category":{"36002":{"category_aro_accession":"0010001","category_aro_cvterm_id":"36002","category_aro_name":"ATP-binding cassette (ABC) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding\/hydrolysis to transport substrates across cell membranes.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2020":{"model_id":"2020","model_name":"tet(O)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"4234":{"protein_sequence":{"accession":"AAA23033.2","sequence":"MKIINLGILAHVDAGKTTLTESLLYTSGAIAELGSVDEGTTRTDTMNLERQRGITIQTAVTSFQWEDVKVNIIDTPGHMDFLAEVYRSLSVLDGAVLLVSAKDGIQAQTRILFHALQIMKIPTIFFINKIDQEGIDLPMVYREMKAKLSSEIIVKQKVGQHPHINVTDNDDMEQWDAVIMGNDELLEKYMSGKPFKMSELEQEENRRFQNGTLFPVYHGSAKNNLGTRQLIEVIASKFYSSTPEGQSELCGQVFKIEYSEKRRRFVYVRIYSGTLHLRDVIRISEKEKIKITEMYVPTNGELYSSDTACSGDIVILPNDVLQLNSILGNEILLPQRKFIENPLPMIQTTIAVKKSEQREILLGALTEISDCDPLLKYYVDTTTHEIILSFLGNVQMEVICAILEEKYHVEAEIKEPTVIYMERPLRKAEYTIHIEVPPNPFWASVGLSIEPLPIGSGVQYESRVSLGYLNQSFQNAVMEGVLYGCEQGLYGWKVTDCKICFEYGLYYSPVSTPADFRLLSPIVLEQALKKAGTELLEPYLHFEIYAPQEYLSRAYHDAPRYCADIVSTQIKNDEVILKGEIPARCIQEYRNDLTYFTNGQGVCLTELKGYQPAIGKFICQPRRPNSRIDKVRHMFHKLA"},"dna_sequence":{"accession":"M18896.2","fmin":"206","fmax":"2126","strand":"+","sequence":"ATGAAAATAATTAACTTAGGCATTCTGGCTCACGTTGACGCAGGAAAGACAACATTAACGGAAAGTTTATTGTATACCAGTGGTGCAATTGCAGAACTAGGGAGCGTAGATGAAGGCACAACAAGGACAGATACAATGAATTTGGAGCGTCAAAGGGGAATCACTATCCAGACAGCAGTGACATCTTTTCAGTGGGAGGATGTAAAAGTCAACATTATAGATACGCCAGGCCATATGGATTTTTTGGCGGAAGTATACCGTTCTTTATCCGTATTAGACGGAGCAGTATTATTAGTTTCTGCAAAGGATGGCATACAGGCACAGACCCGTATACTGTTTCATGCACTACAGATAATGAAGATTCCGACAATTTTTTTCATCAATAAAATTGACCAAGAGGGGATTGATTTGCCAATGGTATATCGGGAAATGAAAGCAAAGCTTTCTTCGGAAATTATAGTGAAGCAAAAGGTTGGGCAGCATCCCCATATAAATGTAACGGACAATGACGATATGGAACAGTGGGATGCGGTAATTATGGGAAACGATGAACTATTAGAGAAATATATGTCAGGGAAACCGTTTAAAATGTCAGAACTGGAACAGGAAGAAAACAGGAGATTCCAAAACGGAACGTTATTTCCCGTTTATCACGGAAGCGCTAAAAACAATCTGGGGACTCGGCAGCTTATAGAAGTAATTGCCAGTAAATTTTATTCATCAACGCCTGAAGGTCAATCTGAACTATGCGGGCAGGTTTTTAAGATTGAATATTCAGAGAAAAGGCGGCGTTTTGTTTATGTGCGTATATATAGCGGAACATTGCATTTGAGGGATGTTATTAGAATATCTGAAAAAGAGAAAATAAAAATCACAGAGATGTATGTTCCGACAAACGGTGAATTATATTCATCCGATACAGCCTGCTCTGGTGATATTGTAATTTTACCAAATGATGTTTTGCAGCTAAACAGTATTTTGGGGAACGAAATACTGTTGCCGCAGAGAAAATTTATTGAAAATCCTCTCCCTATGATCCAAACAACGATTGCAGTAAAGAAATCTGAACAGCGGGAAATATTGCTTGGGGCACTTACAGAAATTTCAGATTGCGACCCTCTTTTAAAATATTATGTGGATACTACAACGCATGAGATTATACTTTCTTTTTTGGGGAATGTGCAGATGGAAGTCATTTGTGCCATCCTTGAGGAAAAATATCATGTGGAGGCAGAAATAAAAGAGCCTACTGTTATATATATGGAAAGACCGCTTAGAAAAGCAGAATATACCATCCACATAGAAGTCCCGCCAAATCCTTTCTGGGCTTCTGTCGGGTTGTCCATAGAGCCGCTCCCTATTGGAAGCGGAGTGCAGTATGAAAGCAGAGTTTCACTTGGATATTTAAATCAATCGTTCCAAAATGCGGTTATGGAGGGGGTTCTTTATGGCTGCGAGCAGGGGCTGTATGGATGGAAAGTGACAGACTGTAAAATCTGTTTTGAATATGGATTGTATTATAGTCCTGTAAGTACCCCCGCAGACTTTCGGCTGCTTTCCCCTATCGTATTGGAGCAGGCTTTAAAAAAAGCAGGGACAGAACTATTAGAGCCATATCTCCACTTTGAAATTTATGCACCGCAGGAATATCTCTCACGGGCGTATCATGATGCTCCAAGGTATTGTGCAGATATTGTAAGTACTCAGATAAAGAATGACGAGGTCATTCTGAAAGGAGAAATCCCTGCTAGATGTATTCAAGAATACAGGAACGATTTAACTTATTTCACAAATGGGCAGGGAGTCTGCTTGACAGAGTTAAAAGGATACCAGCCAGCTATTGGTAAATTTATTTGCCAACCCCGCCGCCCGAATAGCCGTATAGATAAGGTTCGGCATATGTTCCACAAGTTAGCTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36772","NCBI_taxonomy_name":"Campylobacter jejuni","NCBI_taxonomy_id":"197"}}}},"ARO_accession":"3000190","ARO_id":"36329","ARO_name":"tet(O)","CARD_short_name":"tet(O)","ARO_description":"Tet(O) is a ribosomal protection protein. It is associated with conjugative plasmids.","ARO_category":{"35921":{"category_aro_accession":"0000002","category_aro_cvterm_id":"35921","category_aro_name":"tetracycline-resistant ribosomal protection protein","category_aro_description":"A family of proteins known to bind to the 30S ribosomal subunit. This interaction prevents tetracycline and tetracycline derivatives from inhibiting ribosomal function. Thus, these proteins confer elevated resistance to tetracycline derivatives as a ribosomal protection protein.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35986":{"category_aro_accession":"0000069","category_aro_cvterm_id":"35986","category_aro_name":"doxycycline","category_aro_description":"Doxycycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36291":{"category_aro_accession":"3000152","category_aro_cvterm_id":"36291","category_aro_name":"minocycline","category_aro_description":"Minocycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36667":{"category_aro_accession":"3000528","category_aro_cvterm_id":"36667","category_aro_name":"chlortetracycline","category_aro_description":"Chlortetracycline was an early, first-generation tetracycline antibiotic developed in the 1940's. It inhibits bacterial protein synthesis by binding to the 30S subunit of bacterial ribosomes, preventing the aminoacyl-tRNA from binding to the ribosome.","category_aro_class_name":"Antibiotic"},"37011":{"category_aro_accession":"3000667","category_aro_cvterm_id":"37011","category_aro_name":"demeclocycline","category_aro_description":"Demeclocycline is a tetracycline analog with 7-chloro and 6-methyl groups. Due to its fast absorption and slow excretion, it maintains higher effective blood levels compared to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37012":{"category_aro_accession":"3000668","category_aro_cvterm_id":"37012","category_aro_name":"oxytetracycline","category_aro_description":"Oxytetracycline is a derivative of tetracycline with a 5-hydroxyl group. Its activity is similar to other tetracyclines.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2037":{"model_id":"2037","model_name":"tet(T)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1200"}},"model_sequences":{"sequence":{"520":{"protein_sequence":{"accession":"AAF01499.1","sequence":"MKIINIGILAHVDAGKTTVTEGLLYKSGAINKIGRVDNATTTTDSMELERDRGITIRASTVSFNYNDTKVNIIDTPGHMDFIAEVERTLKVLDGAILVISAKEGIQVQTKVIFNTLVKLNIPTLIFVNKIDRKGVCLDEIYTQIQEKLTSNLAIMQSVKIKDKGDFELTNVRDDKVIQSQIIEKLLDINDYLAEKYINGDVIAEKEYNDVFLDEINNCNLYPVFHGSALKNIGIDELLFAITKYLPTKSYNTEDLLSAYVYKIDRDEKSRKMTFLRVFSGNIRTRQDVYINGTEETFKIKSLESIMNGEIVKVGQVNSGDIAIISNANSLKIGDYIGKKYDGILDIKIAQPALRASIKPCDLSKRSKLIEALFELTEEDPFLDCEINGDTGEIILRLFGNIQMEVIESLLKSRYKIDARFGELKTIYKERPKRNSKAVIHIEVPPNPYWASIGLSIEPLPIGSGLLYKTEVSYGYLNNSFQNAVKDAVEKACKEGLYGWEVTDLKVTFDYGLYYSPVSTPSDFRNLTPYVFWEALRKAGTEILEPYLKYTVQVPNDFCGRVMSDLRKMRASIEDIIAKGEETTLSGKIPVDTSKSYQSELLSYSNGKGIFITEPYGYDIYNDKPIINDIGNDNNDSNKEGLRYLFQKQDEN"},"dna_sequence":{"accession":"L42544.1","fmin":"0","fmax":"1956","strand":"+","sequence":"ATGAAAATTATTAATATAGGAATATTAGCACATGTTGATGCAGGTAAAACAACTGTTACAGAAGGTTTATTATATAAAAGTGGGGCGATTAATAAAATTGGAAGAGTTGATAATGCTACAACGACAACGGATTCGATGGAACTTGAAAGAGATAGGGGAATAACTATACGGGCGTCTACAGTTTCATTTAATTACAATGATACAAAGGTAAATATCATAGATACACCTGGGCACATGGATTTCATAGCCGAAGTTGAGCGAACTCTGAAAGTGTTAGATGGAGCTATTTTAGTAATTTCAGCAAAAGAAGGAATTCAAGTCCAAACTAAAGTGATTTTTAATACTTTAGTGAAATTAAATATACCAACACTTATATTTGTGAATAAAATAGATCGAAAGGGAGTATGTTTGGATGAGATATACACTCAAATACAGGAGAAATTAACTTCTAATCTTGCAATAATGCAATCAGTTAAAATAAAAGATAAAGGTGATTTTGAATTGACAAATGTAAGGGATGATAAAGTAATTCAAAGTCAAATAATAGAGAAGTTACTGGATATAAATGATTATCTAGCAGAAAAATATATAAATGGCGATGTCATTGCAGAAAAAGAATATAATGATGTATTTTTGGATGAGATTAATAACTGCAATCTTTATCCTGTATTTCATGGTTCGGCTTTAAAAAATATTGGAATTGACGAGCTATTATTTGCCATTACTAAATATCTTCCTACCAAGAGCTATAATACTGAAGACCTTTTATCAGCGTATGTTTATAAGATTGATAGGGATGAAAAATCTAGAAAGATGACTTTCTTAAGAGTATTCAGTGGGAATATAAGGACACGTCAAGATGTTTATATAAATGGCACAGAAGAAACTTTCAAGATAAAAAGTCTGGAATCAATTATGAATGGTGAAATTGTGAAGGTAGGTCAGGTTAATAGTGGGGATATTGCTATTATTTCTAATGCTAATTCTCTGAAGATAGGTGATTATATTGGTAAGAAATATGACGGGATTTTAGATATAAAGATAGCCCAACCGGCATTGAGAGCATCAATTAAACCTTGTGATTTAAGCAAAAGAAGCAAACTGATAGAAGCACTATTTGAATTAACTGAAGAAGACCCATTTCTCGATTGTGAAATTAACGGAGATACTGGAGAAATCATATTGAGGCTATTTGGAAATATTCAAATGGAAGTAATAGAATCACTACTTAAAAGCCGATACAAAATAGATGCTAGATTTGGTGAATTGAAAACAATATATAAAGAACGACCTAAGAGAAACTCTAAAGCAGTAATCCATATAGAGGTTCCACCAAATCCTTATTGGGCATCTATTGGACTGTCAATAGAACCACTACCAATAGGGTCAGGATTATTATATAAGACAGAGGTGTCCTATGGATATTTAAATAATTCATTTCAAAATGCAGTAAAAGATGCTGTAGAGAAGGCTTGTAAAGAAGGGCTTTATGGATGGGAAGTTACAGACTTAAAGGTAACTTTTGACTACGGATTATACTATAGCCCGGTAAGTACCCCCTCTGACTTTAGGAATTTAACACCATATGTATTTTGGGAAGCTCTTCGAAAAGCAGGAACTGAAATATTAGAACCTTATTTAAAATATACAGTTCAAGTTCCAAATGATTTCTGCGGAAGGGTTATGAGTGATCTTAGAAAGATGAGGGCTTCTATTGAAGATATAATAGCCAAGGGAGAGGAGACAACTTTAAGTGGAAAGATACCTGTTGATACATCGAAGTCCTATCAGTCAGAATTACTTTCTTATTCAAATGGAAAGGGTATATTTATTACTGAGCCTTATGGGTATGATATATATAATGATAAGCCTATAATTAATGATATTGGGAACGACAATAATGATAGCAACAAGGAAGGGTTAAGATATTTATTTCAAAAACAGGATGAAAATTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36764","NCBI_taxonomy_name":"Streptococcus pyogenes","NCBI_taxonomy_id":"1314"}}}},"ARO_accession":"3000193","ARO_id":"36332","ARO_name":"tet(T)","CARD_short_name":"tet(T)","ARO_description":"Tet(T) is a ribosomal protection protein of streptococci. It is similar to Tet(Q).","ARO_category":{"35921":{"category_aro_accession":"0000002","category_aro_cvterm_id":"35921","category_aro_name":"tetracycline-resistant ribosomal protection protein","category_aro_description":"A family of proteins known to bind to the 30S ribosomal subunit. This interaction prevents tetracycline and tetracycline derivatives from inhibiting ribosomal function. Thus, these proteins confer elevated resistance to tetracycline derivatives as a ribosomal protection protein.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35986":{"category_aro_accession":"0000069","category_aro_cvterm_id":"35986","category_aro_name":"doxycycline","category_aro_description":"Doxycycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36291":{"category_aro_accession":"3000152","category_aro_cvterm_id":"36291","category_aro_name":"minocycline","category_aro_description":"Minocycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36667":{"category_aro_accession":"3000528","category_aro_cvterm_id":"36667","category_aro_name":"chlortetracycline","category_aro_description":"Chlortetracycline was an early, first-generation tetracycline antibiotic developed in the 1940's. It inhibits bacterial protein synthesis by binding to the 30S subunit of bacterial ribosomes, preventing the aminoacyl-tRNA from binding to the ribosome.","category_aro_class_name":"Antibiotic"},"37011":{"category_aro_accession":"3000667","category_aro_cvterm_id":"37011","category_aro_name":"demeclocycline","category_aro_description":"Demeclocycline is a tetracycline analog with 7-chloro and 6-methyl groups. Due to its fast absorption and slow excretion, it maintains higher effective blood levels compared to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37012":{"category_aro_accession":"3000668","category_aro_cvterm_id":"37012","category_aro_name":"oxytetracycline","category_aro_description":"Oxytetracycline is a derivative of tetracycline with a 5-hydroxyl group. Its activity is similar to other tetracyclines.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1176":{"model_id":"1176","model_name":"Mycobacterium tuberculosis katG mutations conferring resistance to isoniazid","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"13301":"D142G","13337":"G182R","13417":"S315I","13419":"S315T","13454":"W191R","13459":"W90R","13709":"A109V","13717":"A614E","13729":"G125D","13732":"G297V","13737":"L141F","13738":"L159P","13743":"L704S","13757":"R104Q","13760":"S481L","13762":"S700P","13765":"T180K","13780":"W191G","13781":"W300C","13782":"W328L","14855":"V1Var","13784":"S315Var","14966":"S315R","14969":"S315N","9552":"R463L","9554":"T667P","9560":"I317V","3236":"P131R","3238":"W91R","3241":"R128Q","3242":"P131Q","3243":"V68G","3246":"M126I","3693":"D194Y","3696":"D63E","3697":"R104L","3698":"W107R","3699":"H108E","3700":"H108Q","3701":"N138D","3702":"N138S","3703":"Y229F","3704":"W300G","3705":"T262R","3706":"T275P","3708":"Y337C","3709":"A350S","3710":"S315G","3712":"L587M","3713":"G629S","3714":"D735N","3723":"Q127E","3724":"P232S","3725":"N133T","3726":"S383P","3727":"H97R","3728":"R489S","3729":"M420T","3730":"D387H","3731":"G123E","3732":"G299S","3734":"M176T","3735":"R632C","3740":"Y64S","3741":"Y95C","3742":"P131T","3743":"A139P","3745":"A162V","3746":"G269D","3747":"T306P","3748":"R385W","3749":"D387G","3751":"Q439P","3752":"F483L","3753":"A541D","3754":"G32D","3755":"V47E","3756":"D194G","3757":"A256T","3760":"M624V","3762":"I335T","3764":"Q127P","3766":"Q352E","3767":"Y98C","3769":"G269R","3777":"S17T","3786":"A93T","3794":"A110V","3795":"A139V","3797":"H276M","3798":"Q295H","3802":"S17N","3803":"G19D","3804":"Q224E","3805":"A243S","3806":"A550D","3807":"P2S","3808":"S140N","3810":"G279D","3811":"G285D","3812":"G316D","3813":"S457I","3814":"G593D","8239":"S303L","8240":"S303C","8242":"D311N","8243":"D311S","8244":"L427I","8246":"L430V","8247":"T435R","8248":"L436G","8249":"Q471Y","8250":"Q471H","8252":"L472Q","8253":"L472I","8254":"V473D","8255":"V473I","8256":"V473K","8257":"V473R","8258":"V473M","8259":"V473S","8260":"V473F","8261":"V473W","8262":"V473Y","8263":"V473G","8264":"V473N","3715":"W107F","3716":"M255C","3717":"M255I","3718":"M255Y","3719":"T275V","3720":"W321F","3721":"W328F","3722":"R418L","10001":"A312P","10002":"N660D","10003":"L147P","10010":"N508D","10012":"G125S","10014":"Q461P","10015":"E607A","10017":"G111S","10018":"G33V","12300":"P365R","13045":"Q439H","13046":"Y413C","13047":"G169S","13048":"T677P","13049":"D189G","13050":"D419Y","13051":"R484H","13053":"F183L","13054":"W161C","13055":"A312E","13056":"R78P","13057":"D189N","13058":"D675Y","13059":"E233G","13060":"G124S","13061":"A122D","13062":"R385P","13063":"Q88P","13065":"L132R","13066":"M257V","13067":"T271I","13068":"T326P","13071":"A109T","13748":"P232R","13778":"V633A","3240":"L101P","3707":"W328G","3733":"D419H","3737":"D542H","3750":"T394M","3768":"A379T","8251":"L472K","10016":"H417Q","13052":"N655D"},"CRyPTIC-R":{"13301":"D142G","13337":"G182R","13417":"S315I","13419":"S315T","13454":"W191R","13459":"W90R","13709":"A109V","13717":"A614E","13729":"G125D","13732":"G297V","13737":"L141F","13738":"L159P","13743":"L704S","13757":"R104Q","13760":"S481L","13762":"S700P","13765":"T180K","13780":"W191G","13781":"W300C","13782":"W328L","13783":"W328L","13784":"S315Var","13418":"S315N","13748":"P232R","13778":"V633A"},"clinical":{"13301":"D142G","13337":"G182R","13417":"S315I","13419":"S315T","13454":"W191R","13459":"W90R","13709":"A109V","13717":"A614E","13729":"G125D","13732":"G297V","13737":"L141F","13738":"L159P","13743":"L704S","13757":"R104Q","13760":"S481L","13762":"S700P","13765":"T180K","13780":"W191G","13781":"W300C","13782":"W328L","14855":"V1Var","13784":"S315Var","14956":"W328L","14965":"S315T","14966":"S315R","14968":"S315I","14969":"S315N","9552":"R463L","9554":"T667P","9555":"W191R","9556":"S315N","9558":"S315R","9560":"I317V","2284":"S315T","3236":"P131R","3238":"W91R","3239":"R463L","3241":"R128Q","3242":"P131Q","3243":"V68G","3245":"S315N","3246":"M126I","3247":"S315I","3693":"D194Y","3696":"D63E","3697":"R104L","3698":"W107R","3699":"H108E","3700":"H108Q","3701":"N138D","3702":"N138S","3703":"Y229F","3704":"W300G","3705":"T262R","3706":"T275P","3708":"Y337C","3709":"A350S","3710":"S315G","3711":"S315R","3712":"L587M","3713":"G629S","3714":"D735N","3723":"Q127E","3724":"P232S","3725":"N133T","3726":"S383P","3727":"H97R","3728":"R489S","3729":"M420T","3730":"D387H","3731":"G123E","3732":"G299S","3734":"M176T","3735":"R632C","3740":"Y64S","3741":"Y95C","3742":"P131T","3743":"A139P","3744":"D142G","3745":"A162V","3746":"G269D","3747":"T306P","3748":"R385W","3749":"D387G","3751":"Q439P","3752":"F483L","3753":"A541D","3754":"G32D","3755":"V47E","3756":"D194G","3757":"A256T","3759":"T667P","3760":"M624V","3762":"I335T","3764":"Q127P","3766":"Q352E","3767":"Y98C","3769":"G269R","3777":"S17T","3786":"A93T","3794":"A110V","3795":"A139V","3797":"H276M","3798":"Q295H","3802":"S17N","3803":"G19D","3804":"Q224E","3805":"A243S","3806":"A550D","3807":"P2S","3808":"S140N","3810":"G279D","3811":"G285D","3812":"G316D","3813":"S457I","3814":"G593D","8239":"S303L","8240":"S303C","8242":"D311N","8243":"D311S","8244":"L427I","8246":"L430V","8247":"T435R","8248":"L436G","8249":"Q471Y","8250":"Q471H","8252":"L472Q","8253":"L472I","8254":"V473D","8255":"V473I","8256":"V473K","8257":"V473R","8258":"V473M","8259":"V473S","8260":"V473F","8261":"V473W","8262":"V473Y","8263":"V473G","8264":"V473N","10001":"A312P","10002":"N660D","10003":"L147P","10010":"N508D","10012":"G125S","10014":"Q461P","10015":"E607A","10017":"G111S","10018":"G33V","12300":"P365R","13045":"Q439H","13046":"Y413C","13047":"G169S","13048":"T677P","13049":"D189G","13050":"D419Y","13051":"R484H","13053":"F183L","13054":"W161C","13055":"A312E","13056":"R78P","13057":"D189N","13058":"D675Y","13059":"E233G","13060":"G124S","13061":"A122D","13062":"R385P","13063":"Q88P","13064":"G182R","13065":"L132R","13066":"M257V","13067":"T271I","13068":"T326P","13069":"W90R","13071":"A109T","13418":"S315N","13748":"P232R","13778":"V633A","9557":"S315T","3240":"L101P","3707":"W328G","3733":"D419H","3737":"D542H","3750":"T394M","3768":"A379T","8251":"L472K","10016":"H417Q","13052":"N655D"},"WHO-R":{"14855":"V1Var","14858":"S315Var","14872":"S315Var","14873":"S315Var","14874":"S315Var","14885":"S315Var","14889":"S315Var","14903":"S315Var","14914":"S315Var","14923":"S315Var","14929":"S315Var","14930":"S315Var","14934":"S315Var","14945":"S315Var","14946":"S315Var","14962":"S315Var","14977":"S315Var","15008":"S315Var","15009":"S315Var","15020":"S315Var","15023":"S315Var","15027":"S315Var","15033":"S315Var","15036":"S315Var","15062":"S315Var","15068":"S315Var","15082":"S315Var","15083":"S315Var","15086":"S315Var","15087":"S315Var","14956":"W328L","14965":"S315T","14966":"S315R","14968":"S315I","14969":"S315N"},"Curated-R":{"3763":"S315Var","8241":"S315Var","2284":"S315T","3236":"P131R","3238":"W91R","3239":"R463L","3241":"R128Q","3242":"P131Q","3243":"V68G","3245":"S315N","3246":"M126I","3247":"S315I","3693":"D194Y","3696":"D63E","3697":"R104L","3698":"W107R","3699":"H108E","3700":"H108Q","3701":"N138D","3702":"N138S","3703":"Y229F","3704":"W300G","3705":"T262R","3706":"T275P","3708":"Y337C","3709":"A350S","3710":"S315G","3711":"S315R","3712":"L587M","3713":"G629S","3714":"D735N","3723":"Q127E","3724":"P232S","3725":"N133T","3726":"S383P","3727":"H97R","3728":"R489S","3729":"M420T","3730":"D387H","3731":"G123E","3732":"G299S","3734":"M176T","3735":"R632C","3740":"Y64S","3741":"Y95C","3742":"P131T","3743":"A139P","3744":"D142G","3745":"A162V","3746":"G269D","3747":"T306P","3748":"R385W","3749":"D387G","3751":"Q439P","3752":"F483L","3753":"A541D","3754":"G32D","3755":"V47E","3756":"D194G","3757":"A256T","3759":"T667P","3760":"M624V","3762":"I335T","3764":"Q127P","3766":"Q352E","3767":"Y98C","3769":"G269R","3777":"S17T","3786":"A93T","3794":"A110V","3795":"A139V","3797":"H276M","3798":"Q295H","3802":"S17N","3803":"G19D","3804":"Q224E","3805":"A243S","3806":"A550D","3807":"P2S","3808":"S140N","3810":"G279D","3811":"G285D","3812":"G316D","3813":"S457I","3814":"G593D","8239":"S303L","8240":"S303C","8242":"D311N","8243":"D311S","8244":"L427I","8246":"L430V","8247":"T435R","8248":"L436G","8249":"Q471Y","8250":"Q471H","8252":"L472Q","8253":"L472I","8254":"V473D","8255":"V473I","8256":"V473K","8257":"V473R","8258":"V473M","8259":"V473S","8260":"V473F","8261":"V473W","8262":"V473Y","8263":"V473G","8264":"V473N","3715":"W107F","3716":"M255C","3717":"M255I","3718":"M255Y","3719":"T275V","3720":"W321F","3721":"W328F","3722":"R418L","10001":"A312P","10002":"N660D","10003":"L147P","10010":"N508D","10012":"G125S","10014":"Q461P","10015":"E607A","10017":"G111S","10018":"G33V","12300":"P365R","12838":"P365R","12874":"P365R","12875":"P365R","12876":"P365R","12877":"P365R","12878":"P365R","12879":"P365R","12880":"P365R","12881":"P365R","13045":"Q439H","13046":"Y413C","13047":"G169S","13048":"T677P","13049":"D189G","13050":"D419Y","13051":"R484H","13053":"F183L","13054":"W161C","13055":"A312E","13056":"R78P","13057":"D189N","13058":"D675Y","13059":"E233G","13060":"G124S","13061":"A122D","13062":"R385P","13063":"Q88P","13064":"G182R","13065":"L132R","13066":"M257V","13067":"T271I","13068":"T326P","13069":"W90R","13071":"A109T","3694":"V633A","10019":"V633A","3240":"L101P","3707":"W328G","3733":"D419H","3737":"D542H","3750":"T394M","3768":"A379T","8251":"L472K","10016":"H417Q","13052":"N655D"},"ReSeqTB-Minimal":{"9552":"R463L"},"ReSeqTB-High":{"9554":"T667P","9555":"W191R","9556":"S315N","9558":"S315R","9560":"I317V","9557":"S315T"},"experimental":{"3715":"W107F","3716":"M255C","3717":"M255I","3718":"M255Y","3719":"T275V","3720":"W321F","3721":"W328F","3722":"R418L"}},"40394":{"param_type":"nonsense mutation","param_description":"A sequence change where, compared to a reference sequence, one codon is replaced by a termination codon through a nucleotide substitution. These are described as a substitution of the wildtype codon to a termination codon. Format is given as [wild type AA][position][Ter], for example Q42Ter where Q42 is a wildtype amino acid replaced by a premature termination codon.","param_type_id":"40394","param_value":{"13783":"W505Ter","14858":"W728Ter","14872":"W689Ter","14873":"S671Ter","14874":"W668Ter","14885":"E607Ter","14889":"E588Ter","14903":"W505Ter","14914":"W477Ter","14923":"W438Ter","14929":"Y413Ter","14930":"W412Ter","14934":"W397Ter","14945":"Q352Ter","14946":"W351Ter","14962":"W321Ter","14977":"W300Ter","15008":"W204Ter","15009":"W198Ter","15020":"S175Ter","15023":"C171Ter","15027":"W161Ter","15033":"Y155Ter","15036":"W149Ter","15062":"Y113Ter","15068":"W107Ter","15082":"W90Ter","15083":"Q88Ter","15086":"W39Ter","15087":"Y28Ter","3763":"E506Ter","8241":"Y304Ter","3694":"E454Ter","10019":"W91Ter"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1400"},"40330":{"param_type":"multiple resistance variants","param_description":"A set of nucleotide or amino acid substitutions that are all required to confer resistance to an antibiotic drug or drug class, encoded as: [wild-type 1][position 1][mutation 1],[wild-type 2][position 2][mutation 2], etc. For example, D63Y,T142K.","param_type_id":"40330","param_value":{"12838":"N596S,Y597H","12874":"M126I,R496L","12875":"C20R,S315T","12876":"S211G,S315T","12877":"S315T,V581G","12878":"S315T,G466R","12879":"G279V,L436P","12880":"P92S,S315T","12881":"V431A,G490S"}}},"model_sequences":{"sequence":{"8833":{"protein_sequence":{"accession":"NP_216424.1","sequence":"MPEQHPPITETTTGAASNGCPVVGHMKYPVEGGGNQDWWPNRLNLKVLHQNPAVADPMGAAFDYAAEVATIDVDALTRDIEEVMTTSQPWWPADYGHYGPLFIRMAWHAAGTYRIHDGRGGAGGGMQRFAPLNSWPDNASLDKARRLLWPVKKKYGKKLSWADLIVFAGNCALESMGFKTFGFGFGRVDQWEPDEVYWGKEATWLGDERYSGKRDLENPLAAVQMGLIYVNPEGPNGNPDPMAAAVDIRETFRRMAMNDVETAALIVGGHTFGKTHGAGPADLVGPEPEAAPLEQMGLGWKSSYGTGTGKDAITSGIEVVWTNTPTKWDNSFLEILYGYEWELTKSPAGAWQYTAKDGAGAGTIPDPFGGPGRSPTMLATDLSLRVDPIYERITRRWLEHPEELADEFAKAWYKLIHRDMGPVARYLGPLVPKQTLLWQDPVPAVSHDLVGEAEIASLKSQIRASGLTVSQLVSTAWAAASSFRGSDKRGGANGGRIRLQPQVGWEVNDPDGDLRKVIRTLEEIQESFNSAAPGNIKVSFADLVVLGGCAAIEKAAKAAGHNITVPFTPGRTDASQEQTDVESFAVLEPKADGFRNYLGKGNPLPAEYMLLDKANLLTLSAPEMTVLVGGLRVLGANYKRLPLGVFTEASESLTNDFFVNLLDMGITWEPSPADDGTYQGKDGSGKVKWTGSRVDLVFGSNSELRALVEVYGADDAQPKFVQDFVAAWDKVMNLDRFDVR"},"dna_sequence":{"accession":"NC_000962.3","fmin":"2153888","fmax":"2156111","strand":"-","sequence":"GTGCCCGAGCAACACCCACCCATTACAGAAACCACCACCGGAGCCGCTAGCAACGGCTGTCCCGTCGTGGGTCATATGAAATACCCCGTCGAGGGCGGCGGAAACCAGGACTGGTGGCCCAACCGGCTCAATCTGAAGGTACTGCACCAAAACCCGGCCGTCGCTGACCCGATGGGTGCGGCGTTCGACTATGCCGCGGAGGTCGCGACCATCGACGTTGACGCCCTGACGCGGGACATCGAGGAAGTGATGACCACCTCGCAGCCGTGGTGGCCCGCCGACTACGGCCACTACGGGCCGCTGTTTATCCGGATGGCGTGGCACGCTGCCGGCACCTACCGCATCCACGACGGCCGCGGCGGCGCCGGGGGCGGCATGCAGCGGTTCGCGCCGCTTAACAGCTGGCCCGACAACGCCAGCTTGGACAAGGCGCGCCGGCTGCTGTGGCCGGTCAAGAAGAAGTACGGCAAGAAGCTCTCATGGGCGGACCTGATTGTTTTCGCCGGCAACTGCGCGCTGGAATCGATGGGCTTCAAGACGTTCGGGTTCGGCTTCGGCCGGGTCGACCAGTGGGAGCCCGATGAGGTCTATTGGGGCAAGGAAGCCACCTGGCTCGGCGATGAGCGTTACAGCGGTAAGCGGGATCTGGAGAACCCGCTGGCCGCGGTGCAGATGGGGCTGATCTACGTGAACCCGGAGGGGCCGAACGGCAACCCGGACCCCATGGCCGCGGCGGTCGACATTCGCGAGACGTTTCGGCGCATGGCCATGAACGACGTCGAAACAGCGGCGCTGATCGTCGGCGGTCACACTTTCGGTAAGACCCATGGCGCCGGCCCGGCCGATCTGGTCGGCCCCGAACCCGAGGCTGCTCCGCTGGAGCAGATGGGCTTGGGCTGGAAGAGCTCGTATGGCACCGGAACCGGTAAGGACGCGATCACCAGCGGCATCGAGGTCGTATGGACGAACACCCCGACGAAATGGGACAACAGTTTCCTCGAGATCCTGTACGGCTACGAGTGGGAGCTGACGAAGAGCCCTGCTGGCGCTTGGCAATACACCGCCAAGGACGGCGCCGGTGCCGGCACCATCCCGGACCCGTTCGGCGGGCCAGGGCGCTCCCCGACGATGCTGGCCACTGACCTCTCGCTGCGGGTGGATCCGATCTATGAGCGGATCACGCGTCGCTGGCTGGAACACCCCGAGGAATTGGCCGACGAGTTCGCCAAGGCCTGGTACAAGCTGATCCACCGAGACATGGGTCCCGTTGCGAGATACCTTGGGCCGCTGGTCCCCAAGCAGACCCTGCTGTGGCAGGATCCGGTCCCTGCGGTCAGCCACGACCTCGTCGGCGAAGCCGAGATTGCCAGCCTTAAGAGCCAGATCCGGGCATCGGGATTGACTGTCTCACAGCTAGTTTCGACCGCATGGGCGGCGGCGTCGTCGTTCCGTGGTAGCGACAAGCGCGGCGGCGCCAACGGTGGTCGCATCCGCCTGCAGCCACAAGTCGGGTGGGAGGTCAACGACCCCGACGGGGATCTGCGCAAGGTCATTCGCACCCTGGAAGAGATCCAGGAGTCATTCAACTCCGCGGCGCCGGGGAACATCAAAGTGTCCTTCGCCGACCTCGTCGTGCTCGGTGGCTGTGCCGCCATAGAGAAAGCAGCAAAGGCGGCTGGCCACAACATCACGGTGCCCTTCACCCCGGGCCGCACGGATGCGTCGCAGGAACAAACCGACGTGGAATCCTTTGCCGTGCTGGAGCCCAAGGCAGATGGCTTCCGAAACTACCTCGGAAAGGGCAACCCGTTGCCGGCCGAGTACATGCTGCTCGACAAGGCGAACCTGCTTACGCTCAGTGCCCCTGAGATGACGGTGCTGGTAGGTGGCCTGCGCGTCCTCGGCGCAAACTACAAGCGCTTACCGCTGGGCGTGTTCACCGAGGCCTCCGAGTCACTGACCAACGACTTCTTCGTGAACCTGCTCGACATGGGTATCACCTGGGAGCCCTCGCCAGCAGATGACGGGACCTACCAGGGCAAGGATGGCAGTGGCAAGGTGAAGTGGACCGGCAGCCGCGTGGACCTGGTCTTCGGGTCCAACTCGGAGTTGCGGGCGCTTGTCGAGGTCTATGGCGCCGATGACGCGCAGCCGAAGTTCGTGCAGGACTTCGTCGCTGCCTGGGACAAGGTGATGAACCTCGACAGGTTCGACGTGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3003392","ARO_id":"39976","ARO_name":"Mycobacterium tuberculosis katG mutations conferring resistance to isoniazid","CARD_short_name":"Mtub_katG_INH","ARO_description":"katG is a catalase-peroxidase that catalyzes the activation of isoniazid. Isoniazid inhibits mycolic acid synthesis, which prevents cell wall synthesis in mycobacteria. Mutations in katG results in inability to activate isoniazid. Over 280 different mutations have been documented in PubMed for katG, with mutations to Ser315 being the most prevalent.","ARO_category":{"40000":{"category_aro_accession":"3003416","category_aro_cvterm_id":"40000","category_aro_name":"isoniazid resistant katG","category_aro_description":"Bifunctional enzyme with both catalase and broad-spectrum peroxidase activity. It is a catalase-peroxidases that catalyzes the activation of isoniazid. Mutations that arises within this protein cause changes that results in the inability for katG to activate antibiotics, conferring resistance.","category_aro_class_name":"AMR Gene Family"},"36659":{"category_aro_accession":"3000520","category_aro_cvterm_id":"36659","category_aro_name":"isoniazid","category_aro_description":"Isoniazid is an organic compound that is the first-line anti tuberculosis medication in prevention and treatment. As a prodrug, it is activated by mycobacterial catalase-peroxidases such as M. tuberculosis KatG. Isoniazid inhibits mycolic acid synthesis, which prevents cell wall synthesis in mycobacteria.","category_aro_class_name":"Antibiotic"},"45734":{"category_aro_accession":"3007152","category_aro_cvterm_id":"45734","category_aro_name":"isoniazid-like antibiotic","category_aro_description":"A group of antibiotics containing isoniazid and its derivatives.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1197":{"model_id":"1197","model_name":"Mycobacterium tuberculosis rpsL mutations conferring resistance to Streptomycin","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"13370":"K43R","13371":"K88Q","13372":"K88R","14622":"K88M","2651":"T40I"},"CRyPTIC-R":{"13370":"K43R","13371":"K88Q","13372":"K88R"},"clinical":{"13370":"K43R","13371":"K88Q","13372":"K88R","14616":"K43R","14620":"K88R","14621":"K88Q","14622":"K88M","9844":"K43R","9845":"K88R","2045":"K88Q","2651":"T40I","2653":"K43R","2661":"K88R"},"WHO-R":{"14616":"K43R","14620":"K88R","14621":"K88Q","14622":"K88M"},"ReSeqTB-High":{"9844":"K43R","9845":"K88R"},"Curated-R":{"2045":"K88Q","2651":"T40I","2653":"K43R","2661":"K88R"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"200"}},"model_sequences":{"sequence":{"8803":{"protein_sequence":{"accession":"NP_215196.1","sequence":"MPTIQQLVRKGRRDKISKVKTAALKGSPQRRGVCTRVYTTTPKKPNSALRKVARVKLTSQVEVTAYIPGEGHNLQEHSMVLVRGGRVKDLPGVRYKIIRGSLDTQGVKNRKQARSRYGAKKEKG"},"dna_sequence":{"accession":"NC_000962.3","fmin":"781559","fmax":"781934","strand":"+","sequence":"ATGCCAACCATCCAGCAGCTGGTCCGCAAGGGTCGTCGGGACAAGATCAGTAAGGTCAAGACCGCGGCTCTGAAGGGCAGCCCGCAGCGTCGTGGTGTATGCACCCGCGTGTACACCACCACTCCGAAGAAGCCGAACTCGGCGCTTCGGAAGGTTGCCCGCGTGAAGTTGACGAGTCAGGTCGAGGTCACGGCGTACATTCCCGGCGAGGGCCACAACCTGCAGGAGCACTCGATGGTGCTGGTGCGCGGCGGCCGGGTGAAGGACCTGCCTGGTGTGCGCTACAAGATCATCCGCGGTTCGCTGGATACGCAGGGTGTCAAGAACCGCAAACAGGCACGCAGCCGTTACGGCGCTAAGAAGGAGAAGGGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3003395","ARO_id":"39979","ARO_name":"Mycobacterium tuberculosis rpsL mutations conferring resistance to Streptomycin","CARD_short_name":"Mtub_rpsL_STR","ARO_description":"Ribosomal protein S12 stabilizes the highly conserved pseudoknot structure formed by 16S rRNA. Amino acid substitutions in RpsL affect the higher-order structure of 16S rRNA and confer streptomycin resistance by disrupting interactions between 16S rRNA and streptomycin.","ARO_category":{"40003":{"category_aro_accession":"3003419","category_aro_cvterm_id":"40003","category_aro_name":"antibiotic-resistant rpsL","category_aro_description":"Ribosomal protein S12 stabilizes the highly conserved pseudoknot structure formed by 16S rRNA. Amino acid substitutions in RpsL affect the higher-order structure of 16S rRNA and confer antibiotic resistance.","category_aro_class_name":"AMR Gene Family"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1301":{"model_id":"1301","model_name":"Staphylococcus aureus cls conferring resistance to daptomycin","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"3440":"T33N","622":"A23V","687":"L52F","653":"F60S"},"Curated-R":{"3440":"T33N","622":"A23V","687":"L52F","653":"F60S"},"experimental":{"3440":"T33N"},"clinical":{"622":"A23V","687":"L52F","653":"F60S"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"900"}},"model_sequences":{"sequence":{"5513":{"protein_sequence":{"accession":"ABD31357.1","sequence":"MIELLSIALKHSNIILNSIFIGAFILNLLFAFTIIFMERRSANSIWAWLLVLVFLPLFGFILYLLLGRQIQRDQIFKIDKEDKKGLELIVDEQLAALKNENFSNSNYQIVKFKEMIQMLLYNNAAFLTTDNDLKIYTDGQEKFDDLIQDIRNATDYIHFQYYIIQNDELGRTILNELGKKAEQGVEVKILYDDMGSRGLRKKGLRPFRNKGGHAEAFFPSKLPLINLRMNNRNHRKIVVIDGQIGYVGGFNVGDEYLGKSKKFGYWRDTHLRIVGDAVNALQLRFILDWNSQATRDHISYDDRYFPDVNSGGTIGVQIASSGPDEEWEQIKYGYLKMISSAKKSIYIQSPYFIPDQAFLDSIKIAALGGVDVNIMIPNKPDHPFVFWATLKNAASLLDAGVKVFHYDNGFLHSKTLVIDDEIASVGTANMDHRSFTLNFEVNAFIYDQQIAKKLKQAFIDDLAVSSELTKARYAKRSLWIKFKEGISQLLSPIL"},"dna_sequence":{"accession":"CP000253.1","fmin":"2155375","fmax":"2156860","strand":"+","sequence":"ATGATAGAGTTATTATCCATTGCACTCAAGCATTCTAATATTATTTTAAATTCAATATTTATTGGTGCATTTATTTTAAACTTATTATTCGCCTTTACCATTATTTTCATGGAAAGACGTTCTGCCAATTCTATCTGGGCTTGGTTACTAGTCTTAGTTTTCTTGCCTTTATTCGGCTTCATTTTATACTTACTATTAGGACGACAAATTCAACGTGACCAAATTTTCAAAATTGATAAGGAAGATAAAAAAGGATTAGAGTTAATCGTTGATGAGCAATTAGCTGCTTTAAAAAATGAAAACTTTTCAAATTCCAATTATCAAATTGTAAAATTTAAAGAAATGATTCAAATGTTGTTATATAATAACGCAGCATTTTTAACAACAGACAACGATTTAAAAATATACACAGACGGCCAAGAAAAATTTGATGACCTAATACAAGACATCCGTAATGCTACTGATTATATTCATTTTCAGTACTATATTATTCAAAATGATGAATTAGGTCGTACCATTTTAAATGAACTTGGTAAAAAAGCGGAACAAGGTGTAGAAGTTAAAATTCTTTATGATGACATGGGTTCTCGTGGACTGCGTAAAAAAGGCTTACGCCCGTTTCGCAATAAAGGTGGACATGCTGAAGCATTTTTCCCATCAAAATTACCTTTAATTAACTTGCGTATGAACAATCGAAACCATCGAAAAATTGTTGTAATAGATGGGCAAATTGGATATGTTGGTGGTTTTAATGTTGGTGATGAGTACTTAGGTAAATCAAAAAAATTCGGCTATTGGCGAGATACGCATTTACGAATTGTCGGGGATGCAGTGAATGCATTGCAATTACGATTTATTCTAGATTGGAATTCACAAGCCACACGTGACCACATCTCCTATGATGATCGTTATTTCCCAGATGTAAATTCTGGTGGAACAATTGGCGTTCAAATAGCTTCTAGTGGTCCTGACGAAGAATGGGAACAGATTAAATACGGCTATTTGAAAATGATTTCATCTGCTAAAAAATCGATTTATATTCAATCTCCCTATTTCATACCTGATCAAGCCTTTTTAGATTCTATTAAAATTGCGGCATTAGGTGGTGTTGATGTCAATATCATGATTCCTAATAAACCTGACCATCCGTTTGTTTTTTGGGCTACTTTAAAAAATGCAGCATCCTTATTAGATGCCGGTGTTAAAGTATTTCACTACGACAATGGCTTTTTACACTCAAAAACACTTGTTATAGATGATGAAATTGCAAGTGTGGGAACAGCTAATATGGACCATCGCAGTTTCACATTGAATTTCGAAGTCAACGCTTTTATTTATGACCAACAAATTGCCAAAAAATTAAAACAAGCTTTTATAGATGATTTAGCAGTATCTTCTGAATTAACAAAAGCACGTTATGCTAAGCGAAGTCTTTGGATTAAATTTAAAGAAGGTATTTCACAATTATTGTCACCTATCTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35511","NCBI_taxonomy_name":"Staphylococcus aureus subsp. aureus NCTC 8325","NCBI_taxonomy_id":"93061"}}}},"ARO_accession":"3003074","ARO_id":"39621","ARO_name":"Staphylococcus aureus cls conferring resistance to daptomycin","CARD_short_name":"Saur_cls_DAP","ARO_description":"Cardiolipin synthetase (cls) is an inner membrane protein that is involved in membrane synthesis. Specific mutations in S. aureus can confer resistance to daptomycin.","ARO_category":{"39856":{"category_aro_accession":"3003272","category_aro_cvterm_id":"39856","category_aro_name":"daptomycin resistant cls","category_aro_description":"Cardiolipin synthetase catalyzes the formation of cardiolipin from two phosphatidylglycerol molecules. Cardiolipin is important in membrane translocation and permeabilization. Current known mutations on the enzyme confer resistance to daptomycin.","category_aro_class_name":"AMR Gene Family"},"35985":{"category_aro_accession":"0000068","category_aro_cvterm_id":"35985","category_aro_name":"daptomycin","category_aro_description":"Daptomycin is a novel lipopeptide antibiotic used in the treatment of certain infections caused by Gram-positive organisms. Daptomycin interferes with the bacterial cell membrane, reducing membrane potential and inhibiting cell wall synthesis.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1320":{"model_id":"1320","model_name":"Klebsiella mutant PhoP conferring antibiotic resistance to colistin","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"2871":"D191Y"},"Curated-R":{"2871":"D191Y"},"clinical":{"2871":"D191Y"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"4715":{"protein_sequence":{"accession":"CDO13981.1","sequence":"MRVLVVEDNALLRHHLKVQLQELGHQVDAAEDAREADYYLGEHLPDIAIVDLGLPDEDGLSLIRRWRSHDVSLPVLVLTAREGWQDKVEVLSAGADDYVTKPFHIEEVAARMQALLRRNSGLASQVISLPPFQVDLSRRELSVNDQPIKLTAFEYTIMETLIRNRGKVVSKDSLMLQLYPDAELRESHTIDVLMGRLRKKIQAEYPQDVITTVRGQGYLFELR"},"dna_sequence":{"accession":"FO834906.1","fmin":"2325636","fmax":"2326308","strand":"-","sequence":"ATGCGCGTACTCGTGGTTGAGGATAATGCCCTGCTGCGTCACCACCTCAAAGTTCAGCTGCAGGAGCTGGGCCATCAGGTCGATGCGGCGGAAGATGCCAGGGAAGCGGACTACTATCTGGGCGAACATCTCCCGGATATCGCCATCGTCGATCTCGGCCTGCCGGATGAAGACGGTTTATCACTGATCCGCCGCTGGCGCAGCCACGACGTGTCGCTGCCGGTGCTGGTGCTGACCGCCCGCGAAGGATGGCAGGATAAAGTGGAAGTGCTGAGCGCCGGGGCGGATGATTACGTCACCAAGCCTTTCCATATTGAAGAGGTTGCCGCCCGCATGCAGGCGCTGCTGCGCCGTAACAGCGGTCTGGCCTCGCAGGTGATCTCCCTGCCGCCGTTCCAGGTCGACCTCTCCCGGCGCGAGCTGTCGGTGAATGACCAGCCGATCAAGCTGACCGCCTTTGAATACACCATTATGGAAACCCTGATCCGTAACCGCGGCAAAGTGGTCAGCAAAGATTCGCTGATGCTCCAGCTTTACCCGGATGCCGAACTGCGAGAAAGCCACACCATCGACGTGCTGATGGGTCGGCTGCGCAAGAAAATTCAGGCTGAATACCCACAGGACGTCATCACCACGGTGCGCGGCCAGGGCTATCTGTTCGAATTGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3003585","ARO_id":"40195","ARO_name":"Klebsiella mutant PhoP conferring antibiotic resistance to colistin","CARD_short_name":"Kleb_PhoP_CST","ARO_description":"A mutant phoP activates pmrHFIJKLM expression responsible for L-aminoarabinose synthesis and polymyxin resistance, by way of alteration of negative charge.","ARO_category":{"36002":{"category_aro_accession":"0010001","category_aro_cvterm_id":"36002","category_aro_name":"ATP-binding cassette (ABC) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding\/hydrolysis to transport substrates across cell membranes.","category_aro_class_name":"AMR Gene Family"},"41433":{"category_aro_accession":"3004269","category_aro_cvterm_id":"41433","category_aro_name":"pmr phosphoethanolamine transferase","category_aro_description":"This family of phosphoethanolamine transferase catalyze the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine to lipid A, which impedes the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"46471":{"category_aro_accession":"3007684","category_aro_cvterm_id":"46471","category_aro_name":"transmembrane protein conferring colistin resistance","category_aro_description":"Mutations in mgrB transmembrane proteins can confer resistance to the antibiotic colistin.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"36593":{"category_aro_accession":"3000454","category_aro_cvterm_id":"36593","category_aro_name":"polymyxin B","category_aro_description":"Polymyxin B is mixture of mostly polymyxins B1 and B2, mainly used for resistant gram-negative infections. They are polypeptides with cationic detergent action on cell membranes.","category_aro_class_name":"Antibiotic"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"},"40429":{"category_aro_accession":"3003764","category_aro_cvterm_id":"40429","category_aro_name":"resistance by absence","category_aro_description":"Mechanism of antibiotic resistance conferred by deletion of gene (usually a porin).","category_aro_class_name":"Resistance Mechanism"}}},"1339":{"model_id":"1339","model_name":"Mycobacterium tuberculosis embR mutant conferring resistance to ethambutol","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"2369":"Q379R","2350":"C110Y"},"Curated-R":{"2369":"Q379R","2350":"C110Y"},"clinical":{"2369":"Q379R","2350":"C110Y"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"8809":{"protein_sequence":{"accession":"NP_215783.1","sequence":"MAGSATVEKRLDFGLLGPLQMTIDGTPVPSGTPKQRAVLAMLVINRNRPVGVDALITALWEEWPPSGARASIHSYVSNLRKLLGGAGIDPRVVLAAAPPGYRLSIPDNTCDLGRFVAEKTAGVHAAAAGRFEQASRHLSAALREWRGPVLDDLRDFQFVEPFATALVEDKVLAHTAKAEAEIACGRASAVIAELEALTFEHPYREPLWTQLITAYYLSDRQSDALGAYRRVKTTLADDLGIDPGPTLRALNERILRQQPLDAKKSAKTTAAGTVTVLDQRTMASGQQAVAYLHDIASGRGYPLQAAATRIGRLHDNDIVLDSANVSRHHAVIVDTGTNYVINDLRSSNGVHVQHERIRSAVTLNDGDHIRICDHEFTFQISAGTHGGT"},"dna_sequence":{"accession":"NC_000962.3","fmin":"1416180","fmax":"1417347","strand":"-","sequence":"ATGGCTGGTAGCGCGACAGTGGAGAAGCGGCTCGACTTCGGCCTGCTTGGACCATTGCAGATGACTATCGACGGCACCCCGGTGCCATCGGGCACCCCCAAGCAACGGGCTGTGCTAGCCATGTTGGTCATCAACCGCAACAGGCCCGTAGGAGTCGACGCCCTAATCACCGCCCTCTGGGAGGAGTGGCCACCCTCGGGCGCACGCGCGAGTATCCACTCCTACGTGTCTAATCTGCGTAAGCTCCTCGGTGGCGCCGGGATCGACCCACGGGTGGTGTTGGCCGCAGCGCCGCCGGGTTATCGGCTCAGCATCCCCGACAACACTTGCGATCTGGGGCGGTTTGTTGCCGAAAAAACCGCGGGCGTGCACGCGGCCGCCGCCGGCCGGTTCGAACAAGCCAGCCGCCACCTGTCGGCCGCATTGAGAGAATGGCGTGGGCCGGTGCTCGATGACCTGCGCGACTTCCAGTTCGTCGAACCCTTTGCCACGGCGCTGGTAGAAGACAAGGTTCTTGCCCATACCGCCAAGGCGGAGGCCGAAATCGCGTGTGGGCGGGCCAGCGCAGTGATCGCCGAGCTCGAGGCTCTGACATTCGAACACCCCTACCGGGAGCCGCTGTGGACACAGCTGATCACCGCCTACTACCTCTCCGACCGGCAATCCGATGCGCTGGGCGCCTATCGCCGGGTGAAGACAACACTGGCCGACGACCTCGGCATCGACCCCGGTCCGACGTTGCGCGCTCTCAACGAGCGGATTCTGCGTCAGCAACCGCTGGATGCCAAGAAGTCCGCCAAAACCACCGCTGCCGGCACCGTCACGGTGCTCGATCAGCGCACCATGGCGTCGGGCCAGCAGGCGGTGGCCTACCTGCACGACATCGCCTCGGGTCGCGGCTACCCACTGCAAGCCGCGGCGACCCGGATCGGGCGTCTGCATGACAACGACATCGTCCTAGACAGCGCCAACGTCAGCCGCCACCACGCCGTCATCGTCGACACGGGCACCAACTACGTCATCAACGACCTCCGATCGTCCAACGGCGTGCATGTGCAGCACGAGCGAATCCGCTCCGCGGTCACGCTGAACGACGGCGACCACATTCGCATCTGTGACCATGAATTCACGTTCCAGATCAGCGCGGGGACGCATGGCGGCACGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3003455","ARO_id":"40048","ARO_name":"Mycobacterium tuberculosis embR mutant conferring resistance to ethambutol","CARD_short_name":"Mtub_embR_EMB","ARO_description":"Point mutation in the M.tuberculosis embR results in increased resistance to ethambutol.","ARO_category":{"40047":{"category_aro_accession":"3003454","category_aro_cvterm_id":"40047","category_aro_name":"ethambutol resistant embR","category_aro_description":"Mutations that occurs on the embR genes resulting in the resistance to ethambutol.","category_aro_class_name":"AMR Gene Family"},"36636":{"category_aro_accession":"3000497","category_aro_cvterm_id":"36636","category_aro_name":"ethambutol","category_aro_description":"Ethambutol is an antimycobacterial drug prescribed to treat tuberculosis. It is usually given in combination with other tuberculosis drugs, such as isoniazid, rifampicin, and pyrazinamide. Ethambutol inhibits arabinosyl biosynthesis, disrupting mycobacterial cell wall formation.","category_aro_class_name":"Antibiotic"},"36666":{"category_aro_accession":"3000527","category_aro_cvterm_id":"36666","category_aro_name":"polyamine antibiotic","category_aro_description":"Polyamine antibiotics are organic compounds having two or more primary amino groups.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1354":{"model_id":"1354","model_name":"Mycobacterium tuberculosis embA mutant conferring resistance to ethambutol","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"41339":{"param_type":"nucleotide substitution in promoter region","param_description":"A nucleotide sequence change where, compared to a reference sequence, one nucleotide is replaced by one other nucleotide in the promoter region of a gene. These substitutions are indicated as upstream of the reference sequence transcription initiation site. Format is given by [-][position][wildtype][>][mutation], e.g. -11t>c or -15g>Var where Var represents any possible substitution.","param_type_id":"41339","param_value":{"13482":"-16c>g","13483":"-16c>t","13480":"-12c>t"}},"snp":{"CRyPTIC-R":{"13482":"C110Y","13483":"C110Y","13480":"A462V"},"param_value":{"2395":"D4N","2396":"A201T","2397":"G321S","2398":"G350D","2400":"D833A","2401":"P913S","3583":"G5S","2399":"A462V"},"Curated-R":{"2395":"D4N","2396":"A201T","2397":"G321S","2398":"G350D","2400":"D833A","2401":"P913S","3583":"G5S","2399":"A462V"},"clinical":{"2395":"D4N","2396":"A201T","2397":"G321S","2398":"G350D","2400":"D833A","2401":"P913S","3583":"G5S","2399":"A462V"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"2000"}},"model_sequences":{"sequence":{"8804":{"protein_sequence":{"accession":"NP_218311.1","sequence":"MPHDGNERSHRIARLAAVVSGIAGLLLCGIVPLLPVNQTTATIFWPQGSTADGNITQITAPLVSGAPRALDISIPCSAIATLPANGGLVLSTLPAGGVDTGKAGLFVRANQDTVVVAFRDSVAAVAARSTIAAGGCSALHIWADTGGAGADFMGIPGGAGTLPPEKKPQVGGIFTDLKVGAQPGLSARVDIDTRFITTPGALKKAVMLLGVLAVLVAMVGLAALDRLSRGRTLRDWLTRYRPRVRVGFASRLADAAVIATLLLWHVIGATSSDDGYLLTVARVAPKAGYVANYYRYFGTTEAPFDWYTSVLAQLAAVSTAGVWMRLPATLAGIACWLIVSRFVLRRLGPGPGGLASNRVAVFTAGAVFLSAWLPFNNGLRPEPLIALGVLVTWVLVERSIALGRLAPAAVAIIVATLTATLAPQGLIALAPLLTGARAIAQRIRRRRATDGLLAPLAVLAAALSLITVVVFRDQTLATVAESARIKYKVGPTIAWYQDFLRYYFLTVESNVEGSMSRRFAVLVLLFCLFGVLFVLLRRGRVAGLASGPAWRLIGTTAVGLLLLTFTPTKWAVQFGAFAGLAGVLGAVTAFTFARIGLHSRRNLTLYVTALLFVLAWATSGINGWFYVGNYGVPWYDIQPVIASHPVTSMFLTLSILTGLLAAWYHFRMDYAGHTEVKDNRRNRILASTPLLVVAVIMVAGEVGSMAKAAVFRYPLYTTAKANLTALSTGLSSCAMADDVLAEPDPNAGMLQPVPGQAFGPDGPLGGISPVGFKPEGVGEDLKSDPVVSKPGLVNSDASPNKPNAAITDSAGTAGGKGPVGINGSHAALPFGLDPARTPVMGSYGENNLAATATSAWYQLPPRSPDRPLVVVSAAGAIWSYKEDGDFIYGQSLKLQWGVTGPDGRIQPLGQVFPIDIGPQPAWRNLRFPLAWAPPEADVARIVAYDPNLSPEQWFAFTPPRVPVLESLQRLIGSATPVLMDIATAANFPCQRPFSEHLGIAELPQYRILPDHKQTAASSNLWQSSSTGGPFLFTQALLRTSTIATYLRGDWYRDWGSVEQYHRLVPADQAPDAVVEEGVITVPGWGRPGPIRALP"},"dna_sequence":{"accession":"NC_000962.3","fmin":"4243232","fmax":"4246517","strand":"+","sequence":"GTGCCCCACGACGGTAATGAGCGATCTCACCGGATCGCACGCCTAGCAGCCGTCGTCTCGGGAATCGCGGGTCTGCTGCTGTGCGGCATCGTTCCGCTGCTTCCGGTGAACCAAACCACCGCGACCATCTTCTGGCCGCAGGGCAGCACCGCCGACGGCAACATCACCCAGATCACCGCCCCTCTGGTATCCGGGGCGCCACGCGCGCTGGACATCTCGATCCCCTGCTCGGCCATCGCCACGCTGCCCGCCAACGGCGGCCTGGTGCTGTCCACACTGCCGGCCGGTGGCGTGGATACCGGTAAGGCCGGGCTGTTCGTCCGCGCCAACCAGGACACGGTCGTCGTGGCGTTCCGCGACTCGGTGGCCGCGGTGGCGGCCCGCTCCACGATCGCAGCGGGAGGCTGTAGCGCGCTGCATATCTGGGCCGATACCGGCGGCGCGGGCGCTGATTTTATGGGTATACCCGGCGGCGCCGGGACCCTGCCGCCGGAGAAGAAGCCACAGGTTGGCGGCATCTTCACCGACCTGAAGGTCGGAGCGCAGCCCGGGCTGTCGGCCCGCGTCGACATCGACACTCGGTTTATCACGACGCCCGGCGCGCTCAAGAAGGCCGTGATGCTCCTCGGCGTGCTGGCGGTCCTGGTAGCCATGGTGGGGCTGGCCGCGCTGGACCGGCTCAGCAGGGGCCGCACCCTGCGCGACTGGCTGACCCGATATCGCCCGCGGGTGCGGGTCGGATTCGCCAGCCGGCTCGCTGACGCAGCGGTGATCGCGACCTTGTTGCTCTGGCATGTCATCGGCGCCACCTCGTCCGATGACGGCTACCTTCTGACCGTCGCCCGGGTCGCCCCGAAGGCCGGCTATGTAGCCAACTACTACCGGTATTTCGGCACGACGGAGGCGCCGTTCGACTGGTATACATCGGTGCTTGCCCAGCTGGCGGCGGTGAGCACCGCCGGCGTCTGGATGCGCCTGCCCGCCACCCTGGCCGGAATCGCCTGCTGGCTGATCGTCAGCCGTTTCGTGCTGCGGCGGCTGGGACCGGGCCCGGGCGGGCTGGCGTCCAACCGGGTCGCTGTGTTCACCGCTGGTGCGGTGTTCCTGTCCGCCTGGCTGCCGTTCAACAACGGCCTGCGTCCCGAGCCGCTGATCGCGCTGGGTGTGCTGGTCACGTGGGTGTTGGTGGAACGGTCGATCGCGCTCGGACGGCTGGCCCCGGCCGCGGTAGCCATCATCGTGGCGACGCTTACCGCGACGCTGGCACCGCAGGGGTTGATCGCGCTGGCCCCGCTGCTGACTGGTGCGCGCGCCATCGCCCAGAGGATCCGGCGCCGCCGGGCGACCGATGGACTGCTGGCGCCGCTGGCGGTGCTGGCCGCGGCGTTGTCGCTGATCACCGTGGTGGTGTTTCGGGACCAGACGCTGGCCACGGTGGCCGAATCGGCACGCATCAAGTACAAGGTCGGCCCGACCATCGCCTGGTACCAGGACTTCCTGCGCTACTACTTCCTTACCGTGGAGAGCAACGTTGAGGGGTCGATGTCCCGCCGGTTCGCGGTGCTGGTGTTGCTGTTCTGCCTGTTCGGGGTGCTGTTCGTGCTGCTGCGGCGCGGCCGGGTGGCGGGGCTGGCCAGCGGCCCGGCCTGGCGACTGATCGGCACTACGGCGGTCGGCCTGCTGCTGCTCACGTTCACGCCAACCAAGTGGGCCGTGCAGTTCGGCGCATTCGCCGGGCTGGCCGGGGTGTTGGGTGCGGTCACCGCGTTCACCTTTGCCCGCATCGGTCTACATAGTCGACGCAACCTCACGCTGTACGTGACCGCGTTGCTGTTCGTGCTGGCGTGGGCAACCTCGGGCATCAACGGGTGGTTCTACGTCGGCAACTACGGGGTGCCGTGGTATGACATCCAGCCCGTCATCGCCAGCCACCCGGTGACGTCGATGTTTCTGACGCTGTCGATCCTCACCGGATTGCTGGCAGCCTGGTATCACTTCCGGATGGACTACGCCGGGCACACCGAAGTCAAAGACAACCGGCGCAACCGCATCTTGGCCTCTACGCCACTGCTGGTGGTCGCGGTGATCATGGTCGCAGGCGAAGTCGGCTCGATGGCCAAGGCCGCGGTGTTCCGTTACCCGCTTTACACCACCGCCAAGGCCAACCTGACCGCGCTCAGCACCGGGCTGTCCAGCTGTGCGATGGCCGACGACGTGCTGGCCGAGCCCGACCCCAATGCCGGCATGCTGCAACCGGTTCCGGGCCAGGCGTTCGGACCGGACGGACCGCTGGGCGGTATCAGTCCCGTCGGCTTCAAACCCGAGGGCGTGGGCGAGGACCTCAAGTCCGACCCGGTGGTCTCCAAACCCGGGCTGGTCAACTCCGATGCGTCGCCCAACAAACCCAACGCCGCCATCACCGACTCCGCGGGCACCGCCGGAGGGAAGGGCCCGGTCGGGATCAACGGGTCGCACGCGGCGCTGCCGTTCGGATTGGACCCGGCACGTACCCCGGTGATGGGCAGCTACGGGGAGAACAACCTGGCCGCCACGGCCACCTCGGCCTGGTACCAGTTACCGCCCCGCAGCCCGGACCGGCCGCTGGTGGTGGTTTCCGCGGCCGGCGCCATCTGGTCCTACAAGGAGGACGGCGATTTCATCTACGGCCAGTCCCTGAAACTGCAGTGGGGCGTCACCGGCCCGGACGGCCGCATCCAGCCACTGGGGCAGGTATTTCCGATCGACATCGGACCGCAACCCGCGTGGCGCAATCTGCGGTTTCCGCTGGCCTGGGCGCCGCCGGAGGCCGACGTGGCGCGCATTGTCGCCTATGACCCGAACCTGAGCCCTGAGCAATGGTTCGCCTTCACCCCGCCCCGGGTTCCGGTGCTGGAATCTCTGCAGCGGTTGATCGGGTCAGCGACACCGGTGTTGATGGACATCGCGACCGCAGCCAACTTCCCCTGCCAGCGACCGTTTTCCGAGCATCTCGGCATTGCCGAGCTTCCGCAGTACCGGATCCTGCCGGACCACAAGCAGACGGCGGCGTCGTCGAACCTATGGCAGTCCAGCTCGACCGGCGGTCCGTTCCTGTTCACCCAGGCGCTGCTGCGCACCTCGACGATCGCCACGTACCTGCGTGGGGACTGGTATCGCGACTGGGGATCGGTGGAGCAGTACCACCGGCTGGTGCCGGCCGATCAGGCTCCAGACGCCGTTGTCGAGGAGGGCGTGATCACTGTGCCCGGCTGGGGTCGGCCAGGACCGATCAGGGCGCTGCCATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3003453","ARO_id":"40046","ARO_name":"Mycobacterium tuberculosis embA mutant conferring resistance to ethambutol","CARD_short_name":"Mtub_embA_EMB","ARO_description":"Specific mutations that occurs on Mycobacterium tuberculosis embA leading to the lowered affinity of ethambutol to embA.","ARO_category":{"40045":{"category_aro_accession":"3003452","category_aro_cvterm_id":"40045","category_aro_name":"ethambutol resistant embA","category_aro_description":"Mutations that occurs on the embA genes resulting in the resistance to ethambutol.","category_aro_class_name":"AMR Gene Family"},"36636":{"category_aro_accession":"3000497","category_aro_cvterm_id":"36636","category_aro_name":"ethambutol","category_aro_description":"Ethambutol is an antimycobacterial drug prescribed to treat tuberculosis. It is usually given in combination with other tuberculosis drugs, such as isoniazid, rifampicin, and pyrazinamide. Ethambutol inhibits arabinosyl biosynthesis, disrupting mycobacterial cell wall formation.","category_aro_class_name":"Antibiotic"},"36666":{"category_aro_accession":"3000527","category_aro_cvterm_id":"36666","category_aro_name":"polyamine antibiotic","category_aro_description":"Polyamine antibiotics are organic compounds having two or more primary amino groups.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1360":{"model_id":"1360","model_name":"Bartonella bacilliformis gyrB conferring resistance to aminocoumarin","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"3428":"G124S","3429":"R184Q","3430":"T214A","3431":"T214I"},"Curated-R":{"3428":"G124S","3429":"R184Q","3430":"T214A","3431":"T214I"},"experimental":{"3428":"G124S","3429":"R184Q","3430":"T214A","3431":"T214I"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1500"}},"model_sequences":{"sequence":{"5357":{"protein_sequence":{"accession":"ABM44583.1","sequence":"MSDETTSPTSGDYGAASIKVLKGLDAVRKRPGMYIGDTDDGSGLHHMVYEVVDNAIDEALAGYATLVNVTLHADGSCSVCDNGRGIPTDIHPTEHVSAAEVIMTQLHAGGKFDQNSYKVSGGLHGVGVSVVNALSVWLRLRIKRDGKIHEMSFTHGVADAPLKVVGQCGTESGTEISFLPSPETFTMVKFDFETLERRLRELAFLNSGVHILLVNQHHADVRSVELYYEGGLIEFIKYIDQSKKPLIDAPIYITSEKDGISVDVALWWNDSYHEKVLCFTNNIPQRDGGTHLAGFRSALTRQINGYAESSGIAKKEKVNLTGDDCREGLTAILSVKVPDPKFSSQTKDKLVSSEVRPIVENLVNEGLSAWLEEHPNEAKILISKVVEAAAAREAARKARELTRRKGALDITSLPGKLADCQERDPTKSEIFIVEGDSAGGSAKSGRSRQNQAILPLRGKILNVERARFDRMLSSEMIGTLITALGTSIGKDEFSPDKLRYHKIIIMTDADVDGAHIRTLLLTFFFRQMPELIERGHLYIAQPPLYKVSRGKSSQYIKNEAAFEDFLIDSGLEETTLELSSGEVCAGIDLRQFVQDARLLRQLLNGLHTRYDRNIVEQAAIAGAFNFEAFATPETAQKIADTIAKRLDLIADDMERGWSGQYTSDGSLCFERVLRGVKDVITLDAGFINSADARQIGHIAKNLKDIYRDPPLLRRKDKSERIFGPTSLLESIFINGKKGITLQRYKGLGEMNADQLWETTLDPDARSLLQVKINDATDADSLFSQLMGDEVEPRRIFIQKNALNVANLDI"},"dna_sequence":{"accession":"CP000524.1","fmin":"1406995","fmax":"1409425","strand":"+","sequence":"ATGAGTGATGAAACAACCTCACCGACATCTGGTGACTATGGTGCCGCTTCTATCAAGGTTCTCAAAGGTCTTGATGCTGTCCGTAAACGTCCTGGTATGTACATCGGTGATACCGACGACGGTTCAGGCTTACACCATATGGTTTATGAAGTCGTCGACAACGCTATTGATGAAGCATTAGCTGGCTACGCAACTCTTGTAAATGTTACGCTCCATGCCGATGGATCCTGTTCTGTTTGTGATAATGGACGTGGAATTCCAACTGATATTCACCCAACAGAACATGTATCAGCTGCTGAAGTGATCATGACGCAACTTCATGCTGGTGGAAAATTTGATCAAAATTCTTATAAAGTTTCAGGGGGATTACACGGCGTTGGTGTCTCTGTTGTTAATGCACTATCGGTTTGGTTGCGCCTTCGAATCAAGCGTGATGGTAAAATCCATGAAATGTCGTTTACTCATGGAGTGGCTGATGCTCCGCTCAAAGTCGTTGGTCAATGCGGTACAGAAAGTGGCACAGAAATCAGCTTTTTACCAAGCCCCGAAACCTTCACCATGGTTAAATTTGATTTCGAAACATTAGAGCGTCGTCTTAGAGAATTAGCTTTTTTGAATTCTGGTGTACACATTCTTCTTGTTAACCAACACCATGCTGATGTTCGATCAGTAGAATTATATTACGAAGGTGGATTAATTGAATTTATCAAATATATTGACCAATCAAAAAAACCCTTAATTGATGCACCGATTTACATCACAAGCGAAAAAGATGGGATCAGTGTAGATGTTGCTTTATGGTGGAACGATTCTTATCATGAGAAAGTATTGTGTTTCACCAATAATATTCCTCAACGCGATGGAGGAACCCATTTAGCGGGATTCCGCAGCGCCTTAACACGTCAAATTAACGGTTATGCTGAATCCTCAGGCATTGCAAAAAAAGAAAAAGTTAATTTAACTGGCGATGATTGCCGTGAAGGACTCACAGCCATTCTTTCCGTTAAAGTTCCCGATCCAAAATTTTCTTCACAGACAAAGGATAAATTGGTTTCTTCTGAAGTCCGTCCAATTGTTGAAAATTTGGTAAATGAAGGACTTTCAGCATGGCTAGAAGAACACCCTAATGAAGCAAAAATTCTCATTAGCAAAGTTGTAGAAGCTGCTGCAGCGCGCGAAGCAGCACGCAAAGCGCGTGAACTTACACGGCGAAAAGGAGCTCTCGATATCACTTCTTTACCAGGTAAACTTGCTGATTGTCAGGAACGTGATCCTACAAAATCAGAAATTTTTATCGTCGAGGGGGATTCAGCTGGTGGTTCAGCTAAAAGCGGACGTTCACGCCAAAATCAAGCAATTTTGCCTTTACGCGGTAAAATTCTTAATGTCGAACGAGCACGTTTCGACCGAATGCTTTCATCCGAAATGATTGGTACGCTTATTACTGCCCTTGGAACCTCTATTGGTAAGGATGAATTTTCACCTGATAAATTGCGTTATCACAAAATCATCATTATGACAGATGCAGATGTTGATGGCGCTCATATTCGCACCTTGCTTCTCACTTTCTTTTTCAGACAAATGCCTGAATTAATTGAACGTGGTCATCTTTATATCGCGCAACCACCTCTTTATAAAGTATCACGTGGTAAATCCTCTCAGTACATTAAAAATGAAGCAGCATTTGAAGATTTCTTAATTGATAGTGGTTTGGAAGAAACAACATTAGAATTATCAAGTGGTGAGGTTTGTGCAGGCATTGATTTACGCCAATTCGTCCAAGATGCCCGTTTGTTGCGCCAACTCTTAAACGGTCTCCATACCCGCTATGACCGCAATATTGTTGAGCAAGCAGCAATCGCTGGTGCTTTCAATTTTGAGGCTTTTGCAACACCAGAAACAGCACAAAAAATAGCGGATACGATAGCAAAACGTCTTGATTTAATTGCTGATGATATGGAACGTGGTTGGAGCGGTCAATATACATCAGATGGAAGTTTATGCTTTGAACGCGTTTTGCGCGGAGTTAAAGATGTTATTACTCTTGATGCAGGGTTTATAAATTCAGCAGATGCACGCCAAATTGGTCATATTGCCAAAAATCTCAAAGACATCTATCGTGATCCTCCTCTTTTGCGTCGCAAAGATAAGTCAGAACGCATTTTTGGTCCTACGAGTTTATTGGAAAGTATTTTTATAAACGGTAAAAAAGGTATTACTTTACAGCGTTACAAAGGCCTTGGAGAAATGAATGCTGATCAGCTTTGGGAAACAACTCTTGATCCTGATGCGCGTTCTCTTTTACAAGTTAAAATCAATGACGCAACTGATGCAGATTCTCTCTTCTCCCAGTTAATGGGTGATGAAGTTGAACCACGGCGAATTTTTATTCAAAAAAATGCCCTAAACGTTGCTAATCTTGATATCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40079","NCBI_taxonomy_name":"Bartonella bacilliformis KC583","NCBI_taxonomy_id":"360095"}}}},"ARO_accession":"3003302","ARO_id":"39886","ARO_name":"Bartonella bacilliformis gyrB conferring resistance to aminocoumarin","CARD_short_name":"Bbac_gyrA_AMU","ARO_description":"Point mutation in Bartonella bacilliformis resulting in aminocoumarin resistance.","ARO_category":{"36618":{"category_aro_accession":"3000479","category_aro_cvterm_id":"36618","category_aro_name":"aminocoumarin resistant gyrB","category_aro_description":"Point mutations in DNA gyrase subunit B (gyrB) can result in resistance to aminocoumarins. These mutations usually involve arginine residues in organisms.","category_aro_class_name":"AMR Gene Family"},"36250":{"category_aro_accession":"3000111","category_aro_cvterm_id":"36250","category_aro_name":"novobiocin","category_aro_description":"Novobiocin is an aminocoumarin antibiotic produced by Streptomyces spheroides and Streptomyces niveus, and binds DNA gyrase subunit B inhibiting ATP-dependent DNA supercoiling.","category_aro_class_name":"Antibiotic"},"36271":{"category_aro_accession":"3000132","category_aro_cvterm_id":"36271","category_aro_name":"clorobiocin","category_aro_description":"Clorobiocin is an aminocoumarin antibiotic produced by Streptomyces roseochromogenes, and binds DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling.","category_aro_class_name":"Antibiotic"},"36289":{"category_aro_accession":"3000150","category_aro_cvterm_id":"36289","category_aro_name":"coumermycin A1","category_aro_description":"Coumermycin A1 is an antibiotic produced by Streptomyces rishiriensis, and binds DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling.","category_aro_class_name":"Antibiotic"},"36242":{"category_aro_accession":"3000103","category_aro_cvterm_id":"36242","category_aro_name":"aminocoumarin antibiotic","category_aro_description":"Aminocoumarin antibiotics bind DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4132":{"model_id":"4132","model_name":"ACT-41","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6507":{"protein_sequence":{"accession":"WP_045331818.1","sequence":"MMKKSLCCALLLGLSCSALAAPVSEKQLAEVVANTVTPLMKAQSVPGMAVAVIYQGKPHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMPYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPEKVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVVEGSDSKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANKSYPNPARVEAAYHILEALQ"},"dna_sequence":{"accession":"NG_050704.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCCCTTTGCTGCGCCCTGCTGCTGGGCCTCTCTTGCTCTGCTCTCGCCGCGCCAGTGTCAGAAAAACAGCTGGCGGAGGTGGTCGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCTGTTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGAAAACCGCACTATTACACGTTTGGCAAGGCCGATATCGCGGCGAATAAACCCGTTACGCCTCAGACCCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGCGTTTTAGGTGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTGACGGGCAAGCAGTGGCAGGGTATTCGTATGCTGGATCTCGCCACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTCAAACCTTCTGGCATGCCCTATGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTTCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGAATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCGGAGAAGGTTGCCGATGCCTCACTTAAGCAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGGTCGAAGGCAGCGACAGTAAGGTAGCGCTGGCGCCGTTACCCGTGGCAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGTTCTACTGGCGGATTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCGAGGCGCTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40540","NCBI_taxonomy_name":"Enterobacter cloacae complex","NCBI_taxonomy_id":"354276"}}}},"ARO_accession":"3006236","ARO_id":"44698","ARO_name":"ACT-41","CARD_short_name":"ACT-41","ARO_description":"ACT-41 is a ACT beta-lactamase.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1574":{"model_id":"1574","model_name":"Mycobacterium tuberculosis inhA mutations conferring resistance to isoniazid","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"13366":"I194T","13367":"I21T","13425":"S94A","9549":"T162S","2220":"I21V","2222":"I47T","2223":"V78A","2288":"I95P","2709":"I16T","10055":"G141E"},"CRyPTIC-R":{"13366":"I194T","13367":"I21T","13425":"S94A"},"clinical":{"13366":"I194T","13367":"I21T","13425":"S94A","14807":"S94A","9548":"S94A","9549":"T162S","9550":"I194T","2220":"I21V","2221":"I21T","2222":"I47T","2223":"V78A","2224":"S94A","2288":"I95P","2289":"I194T","2709":"I16T","10055":"G141E"},"WHO-R":{"14807":"S94A"},"ReSeqTB-Minimal":{"9548":"S94A"},"ReSeqTB-High":{"9549":"T162S","9550":"I194T"},"Curated-R":{"2220":"I21V","2221":"I21T","2222":"I47T","2223":"V78A","2224":"S94A","2288":"I95P","2289":"I194T","2709":"I16T","10055":"G141E"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8828":{"protein_sequence":{"accession":"NP_216000.1","sequence":"MTGLLDGKRILVSGIITDSSIAFHIARVAQEQGAQLVLTGFDRLRLIQRITDRLPAKAPLLELDVQNEEHLASLAGRVTEAIGAGNKLDGVVHSIGFMPQTGMGINPFFDAPYADVSKGIHISAYSYASMAKALLPIMNPGGSIVGMDFDPSRAMPAYNWMTVAKSALESVNRFVAREAGKYGVRSNLVAAGPIRTLAMSAIVGGALGEEAGAQIQLLEEGWDQRAPIGWNMKDATPVAKTVCALLSDWLPATTGDIIYADGGAHTQLL"},"dna_sequence":{"accession":"NC_000962.3","fmin":"1674201","fmax":"1675011","strand":"+","sequence":"ATGACAGGACTGCTGGACGGCAAACGGATTCTGGTTAGCGGAATCATCACCGACTCGTCGATCGCGTTTCACATCGCACGGGTAGCCCAGGAGCAGGGCGCCCAGCTGGTGCTCACCGGGTTCGACCGGCTGCGGCTGATTCAGCGCATCACCGACCGGCTGCCGGCAAAGGCCCCGCTGCTCGAACTCGACGTGCAAAACGAGGAGCACCTGGCCAGCTTGGCCGGCCGGGTGACCGAGGCGATCGGGGCGGGCAACAAGCTCGACGGGGTGGTGCATTCGATTGGGTTCATGCCGCAGACCGGGATGGGCATCAACCCGTTCTTCGACGCGCCCTACGCGGATGTGTCCAAGGGCATCCACATCTCGGCGTATTCGTATGCTTCGATGGCCAAGGCGCTGCTGCCGATCATGAACCCCGGAGGTTCCATCGTCGGCATGGACTTCGACCCGAGCCGGGCGATGCCGGCCTACAACTGGATGACGGTCGCCAAGAGCGCGTTGGAGTCGGTCAACAGGTTCGTGGCGCGCGAGGCCGGCAAGTACGGTGTGCGTTCGAATCTCGTTGCCGCAGGCCCTATCCGGACGCTGGCGATGAGTGCGATCGTCGGCGGTGCGCTCGGCGAGGAGGCCGGCGCCCAGATCCAGCTGCTCGAGGAGGGCTGGGATCAGCGCGCTCCGATCGGCTGGAACATGAAGGATGCGACGCCGGTCGCCAAGACGGTGTGCGCGCTGCTGTCTGACTGGCTGCCGGCGACCACGGGTGACATCATCTACGCCGACGGCGGCGCGCACACCCAATTGCTCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3003393","ARO_id":"39977","ARO_name":"Mycobacterium tuberculosis inhA mutations conferring resistance to isoniazid","CARD_short_name":"Mtub_inhA_INH","ARO_description":"inhA is a enoyl-acyl carrier reductase used in lipid metabolism and farry acid biosynthesis. It is inhibited by isoniazid. mutations in the promoter region or multiple copies of the inhA shows marked resistance to isoniazid mediated inhibition of mycolic acid biosynthesis.","ARO_category":{"43060":{"category_aro_accession":"3004874","category_aro_cvterm_id":"43060","category_aro_name":"isoniazid resistant inhA","category_aro_description":"Genes with mutations in inhA which confer resistance to isoniazid class antibiotics.","category_aro_class_name":"AMR Gene Family"},"36659":{"category_aro_accession":"3000520","category_aro_cvterm_id":"36659","category_aro_name":"isoniazid","category_aro_description":"Isoniazid is an organic compound that is the first-line anti tuberculosis medication in prevention and treatment. As a prodrug, it is activated by mycobacterial catalase-peroxidases such as M. tuberculosis KatG. Isoniazid inhibits mycolic acid synthesis, which prevents cell wall synthesis in mycobacteria.","category_aro_class_name":"Antibiotic"},"45734":{"category_aro_accession":"3007152","category_aro_cvterm_id":"45734","category_aro_name":"isoniazid-like antibiotic","category_aro_description":"A group of antibiotics containing isoniazid and its derivatives.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1822":{"model_id":"1822","model_name":"Staphylococcus aureus gyrB conferring resistance to aminocoumarin","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"2142":"S128L","2143":"R144S","2144":"R144I","2145":"I56S","2146":"I102S","2147":"T173A","3442":"G85S"},"Curated-R":{"2142":"S128L","2143":"R144S","2144":"R144I","2145":"I56S","2146":"I102S","2147":"T173A","3442":"G85S"},"experimental":{"2142":"S128L","2143":"R144S","2144":"R144I","2145":"I56S","2146":"I102S","2147":"T173A","3442":"G85S"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1200"}},"model_sequences":{"sequence":{"5405":{"protein_sequence":{"accession":"CAG39033.1","sequence":"MTALSDVNNTDNYGAGQIQVLEGLEAVRKRPGMYIGSTSERGLHHLVWEIVDNSIDEALAGYANQIEVVIEKDNWIKVTDNGRGIPVDIQEKMGRPAVEVILTVLHAGGKFGGGGYKVSGGLHGVGSSVVNALSQDLEVYVHRNETIYHQAYKKGVPQFDLKEVGTTDKTGTVIRFKADGEIFTETTVYNYETLQQRIRELAFLNKGIQITLRDERDEENVREDSYHYEGGIKSYVELLNENKEPIHDEPIYIHQSKDDIEVEIAIQYNSGYATNLLTYANNIHTYEGGTHEDGFKRALTRVLNSYGLSSKIMKEDKDRLSGEDTREGMTAIISIKHGDPQFEGQTKTKLGNSEVRQVVDKLFSEHFERFLYENPQVARTVVEKGIMAARARVAAKKAREVTRRKSALDVASLPGKLADCSSKSPEECEIFLVEGDSAGGSTKSGRDSRTQAILPLRGKILNVEKARLDRILNNNEIRQMITAFGTGIGGDFDLAKARYHKIVIMTDADVDGAHIRTLLLTFFYRFMRPLIEAGYVYIAQPPLYKLTQGKQKYYVYNDRELDKLKSELNPTPKWSIARYKGLGEMNADQLWETTMNPEHRALLQVKLEDAIEADQTFEMLMGDVVENRRQFIEDNAVYANLDF"},"dna_sequence":{"accession":"BX571856.1","fmin":"5036","fmax":"6968","strand":"+","sequence":"GTGACTGCATTGTCAGATGTAAACAACACGGATAATTATGGTGCTGGGCAAATACAAGTATTAGAAGGTTTAGAAGCAGTACGTAAAAGACCAGGTATGTATATAGGATCGACTTCAGAGAGAGGTTTGCACCATTTAGTGTGGGAAATTGTCGATAATAGTATCGATGAAGCATTAGCTGGTTATGCAAATCAAATTGAAGTTGTTATTGAAAAAGATAACTGGATTAAAGTAACGGATAACGGACGTGGTATCCCAGTTGATATTCAAGAAAAAATGGGACGTCCAGCTGTCGAAGTTATTTTAACTGTTTTACATGCTGGTGGTAAATTCGGCGGTGGCGGATACAAAGTATCTGGTGGTTTACATGGTGTTGGTTCATCAGTTGTAAACGCATTGTCACAAGACTTAGAAGTATATGTACACAGAAATGAGACTATATATCATCAAGCATATAAAAAAGGTGTACCTCAATTTGACTTAAAAGAAGTTGGCACAACTGATAAGACAGGTACTGTCATTCGTTTTAAAGCAGATGGAGAAATCTTCACAGAGACAACTGTATACAACTATGAAACATTACAGCAACGTATTAGAGAGCTTGCTTTCTTAAACAAAGGAATTCAAATCACATTAAGAGATGAACGTGATGAAGAAAACGTTAGAGAAGACTCCTATCACTATGAGGGCGGTATTAAATCTTATGTTGAGTTATTGAACGAAAATAAAGAACCTATTCATGATGAGCCGATTTATATTCATCAATCTAAAGATGATATTGAAGTAGAAATTGCGATTCAATATAACTCAGGATATGCCACAAATCTTTTAACTTACGCAAATAACATTCATACGTACGAAGGTGGTACGCATGAAGACGGATTCAAACGTGCATTAACGCGTGTCTTAAATAGTTATGGTTTAAGTAGCAAGATTATGAAAGAAGACAAAGATAGACTTTCTGGTGAAGATACACGTGAAGGTATGACAGCAATTATATCTATCAAACATGGTGATCCTCAATTCGAAGGTCAAACGAAGACAAAATTAGGTAATTCTGAAGTGCGTCAAGTTGTAGATAAATTATTCTCAGAGCACTTTGAACGATTTTTATATGAAAATCCACAAGTCGCACGTACAGTGGTTGAAAAAGGTATTATGGCGGCACGTGCACGTGTTGCTGCGAAAAAAGCGCGTGAAGTAACACGTCGTAAATCAGCGTTAGATGTAGCAAGTCTTCCAGGTAAATTAGCCGATTGCTCTAGTAAAAGTCCTGAAGAATGTGAGATTTTCTTAGTCGAAGGGGACTCTGCCGGGGGGTCTACAAAATCTGGTCGTGACTCTAGAACGCAGGCGATTTTACCATTACGAGGTAAGATATTAAATGTTGAAAAGGCACGATTAGATAGAATTTTGAATAACAATGAAATTCGTCAAATGATCACAGCATTTGGTACAGGAATCGGTGGCGACTTTGATCTAGCGAAAGCAAGATATCACAAAATCGTCATTATGACTGATGCCGATGTGGATGGAGCGCATATTAGAACATTGTTATTAACATTCTTCTATCGATTTATGAGACCGTTAATTGAAGCAGGCTATGTGTATATTGCACAGCCACCGTTGTATAAACTGACACAAGGTAAACAAAAGTATTATGTATACAATGATAGGGAACTTGATAAACTTAAATCTGAATTGAATCCAACACCAAAATGGTCTATTGCACGATACAAAGGTCTTGGAGAAATGAATGCAGATCAATTATGGGAAACAACAATGAACCCTGAGCACCGCGCTCTTTTACAAGTAAAACTTGAAGATGCGATTGAAGCGGACCAAACATTTGAAATGTTAATGGGTGACGTTGTAGAAAACCGTAGACAATTTATAGAAGATAATGCAGTTTATGCAAACTTAGACTTCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35517","NCBI_taxonomy_name":"Staphylococcus aureus subsp. aureus MRSA252","NCBI_taxonomy_id":"282458"}}}},"ARO_accession":"3003301","ARO_id":"39885","ARO_name":"Staphylococcus aureus gyrB conferring resistance to aminocoumarin","CARD_short_name":"Saur_gyrB_AMU","ARO_description":"Point mutation in Staphylococcus aureus resulting in aminocoumarin resistance.","ARO_category":{"36618":{"category_aro_accession":"3000479","category_aro_cvterm_id":"36618","category_aro_name":"aminocoumarin resistant gyrB","category_aro_description":"Point mutations in DNA gyrase subunit B (gyrB) can result in resistance to aminocoumarins. These mutations usually involve arginine residues in organisms.","category_aro_class_name":"AMR Gene Family"},"36250":{"category_aro_accession":"3000111","category_aro_cvterm_id":"36250","category_aro_name":"novobiocin","category_aro_description":"Novobiocin is an aminocoumarin antibiotic produced by Streptomyces spheroides and Streptomyces niveus, and binds DNA gyrase subunit B inhibiting ATP-dependent DNA supercoiling.","category_aro_class_name":"Antibiotic"},"36271":{"category_aro_accession":"3000132","category_aro_cvterm_id":"36271","category_aro_name":"clorobiocin","category_aro_description":"Clorobiocin is an aminocoumarin antibiotic produced by Streptomyces roseochromogenes, and binds DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling.","category_aro_class_name":"Antibiotic"},"36289":{"category_aro_accession":"3000150","category_aro_cvterm_id":"36289","category_aro_name":"coumermycin A1","category_aro_description":"Coumermycin A1 is an antibiotic produced by Streptomyces rishiriensis, and binds DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling.","category_aro_class_name":"Antibiotic"},"36242":{"category_aro_accession":"3000103","category_aro_cvterm_id":"36242","category_aro_name":"aminocoumarin antibiotic","category_aro_description":"Aminocoumarin antibiotics bind DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1849":{"model_id":"1849","model_name":"Mycobacterium tuberculosis tlyA mutations conferring resistance to aminoglycosides","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"40394":{"param_type":"nonsense mutation","param_description":"A sequence change where, compared to a reference sequence, one codon is replaced by a termination codon through a nucleotide substitution. These are described as a substitution of the wildtype codon to a termination codon. Format is given as [wild type AA][position][Ter], for example Q42Ter where Q42 is a wildtype amino acid replaced by a premature termination codon.","param_type_id":"40394","param_value":{"3828":"R18Ter","3829":"Q22Ter","3835":"Q184Ter","3908":"R3Ter"}},"snp":{"Curated-R":{"3828":"G85S","3829":"G85S","3835":"G85S","3908":"G85S","2189":"L150P","2188":"A91E","2257":"R14W","2259":"P183L","3831":"A67E","3832":"K69E","3833":"V128E","3836":"F185L","3840":"E238K","3401":"L118P","2235":"N236K"},"ReSeqTB-High":{"9448":"G85S"},"param_value":{"2189":"L150P","2188":"A91E","2257":"R14W","2259":"P183L","3831":"A67E","3832":"K69E","3833":"V128E","3836":"F185L","3840":"E238K","3401":"L118P","2235":"N236K"},"clinical":{"2189":"L150P","2257":"R14W","2235":"N236K"},"experimental":{"2188":"A91E","2259":"P183L","3831":"A67E","3832":"K69E","3833":"V128E","3836":"F185L","3840":"E238K","3401":"L118P"}},"40494":{"param_type":"frameshift mutation","param_description":"A frameshift is a sequence change between the translation initiation (start) and termination (stop) codon where, compared to a reference sequence, translation shifts to another reading frame as caused by nucleotide insertions and deletions. In ARO, these are annotated at the protein level with the first changed most N-terminal wildtype amino acid position. Format is given as [wildtype AA][position]fs, e.g. S531fs where S531 is a frameshifted coordinate beginning with codon 531. Termination may also be denoted as: Ter[position]fs.","param_type_id":"40494","param_value":{"9448":"K31fs"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"8794":{"protein_sequence":{"accession":"NP_216210.1","sequence":"MARRARVDAELVRRGLARSRQQAAELIGAGKVRIDGLPAVKPATAVSDTTALTVVTDSERAWVSRGAHKLVGALEAFAIAVAGRRCLDAGASTGGFTEVLLDRGAAHVVAADVGYGQLAWSLRNDPRVVVLERTNARGLTPEAIGGRVDLVVADLSFISLATVLPALVGCASRDADIVPLVKPQFEVGKGQVGPGGVVHDPQLRARSVLAVARRAQELGWHSVGVKASPLPGPSGNVEYFLWLRTQTDRALSAKGLEDAVHRAISEGP"},"dna_sequence":{"accession":"NC_000962.3","fmin":"1917939","fmax":"1918746","strand":"+","sequence":"GTGGCACGACGTGCCCGCGTTGACGCCGAGCTAGTCCGGCGGGGCCTGGCGCGATCACGTCAACAGGCCGCGGAGTTGATCGGCGCCGGCAAGGTGCGCATCGACGGGCTGCCGGCGGTCAAGCCGGCCACCGCCGTGTCCGACACCACCGCGCTGACCGTGGTGACCGACAGTGAACGCGCCTGGGTATCGCGCGGAGCGCACAAACTAGTCGGTGCGCTGGAGGCGTTCGCGATCGCGGTGGCGGGCCGGCGCTGTCTGGACGCGGGCGCATCGACCGGTGGGTTCACCGAAGTACTGCTGGACCGTGGTGCCGCCCACGTGGTGGCCGCCGATGTCGGATACGGCCAGCTGGCGTGGTCGCTGCGCAACGATCCTCGGGTGGTGGTCCTCGAGCGGACCAACGCACGTGGCCTCACACCGGAGGCGATCGGCGGTCGCGTCGACCTGGTAGTGGCCGACCTGTCGTTCATCTCGTTGGCTACCGTGTTGCCCGCGCTGGTTGGATGCGCTTCGCGCGACGCCGATATCGTTCCACTGGTGAAGCCGCAGTTTGAGGTGGGGAAAGGTCAGGTCGGCCCCGGTGGGGTGGTCCATGACCCGCAGTTGCGTGCGCGGTCGGTGCTCGCGGTCGCGCGGCGGGCACAGGAGCTGGGCTGGCACAGCGTCGGCGTCAAGGCCAGCCCGCTGCCGGGCCCATCGGGCAATGTCGAGTACTTCCTGTGGTTGCGCACGCAGACCGACCGGGCATTGTCGGCCAAGGGATTGGAGGATGCGGTGCACCGTGCGATTAGCGAGGGCCCGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3003445","ARO_id":"40038","ARO_name":"Mycobacterium tuberculosis tlyA mutations conferring resistance to aminoglycosides","CARD_short_name":"Mtub_tlyA_AMG","ARO_description":"Specific mutations that arise in Mycobacterium tuberculosis tlyA resulting in aminoglycosides resistance.","ARO_category":{"40036":{"category_aro_accession":"3003443","category_aro_cvterm_id":"40036","category_aro_name":"Antibiotic resistant tlyA","category_aro_description":"tlyA encodes for hemolysin. It Catalyzes the 2'-O-methylation at nucleotides C1409 in 16S rRNA and C1920 in 23S rRNA. Mutation that arise within this gene reduces the binding affinity of aminoglycosides to rRNA.","category_aro_class_name":"AMR Gene Family"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"40875":{"category_aro_accession":"3003993","category_aro_cvterm_id":"40875","category_aro_name":"capreomycin","category_aro_description":"Capreomycin is an aminoglycoside antibiotic, capable of treating a large number of infections but in particular used for killing bacteria causing tuberculosis.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1935":{"model_id":"1935","model_name":"Mycobacterium tuberculosis gyrA conferring resistance to fluoroquinolones","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"13275":"A90V","13318":"D94A","13319":"D94G","13320":"D94H","13321":"D94N","13322":"D94Y","13347":"G88A","13349":"G88C","13424":"S91P","14272":"D89N","2095":"D89G","2217":"D94V","2504":"A90G","3841":"A74S","3844":"T80A","3849":"P102H","4589":"D94T","2092":"D89V"},"CRyPTIC-R":{"13275":"A90V","13318":"D94A","13319":"D94G","13320":"D94H","13321":"D94N","13322":"D94Y","13347":"G88A","13349":"G88C","13424":"S91P"},"clinical":{"13275":"A90V","13318":"D94A","13319":"D94G","13320":"D94H","13321":"D94N","13322":"D94Y","13347":"G88A","13349":"G88C","13424":"S91P","14269":"G88C","14271":"G88A","14272":"D89N","14274":"A90V","14276":"S91P","14278":"D94N","14281":"D94H","14282":"D94Y","14283":"D94A","14284":"D94G","9603":"D94N","9605":"D94G","9609":"G88C","9612":"D94H","9622":"D94A","9625":"D89N","9626":"A90V","9627":"S91P","2091":"D94G","2093":"D94A","2094":"D89N","2095":"D89G","2096":"G88C","2180":"S91P","2181":"D94N","2216":"D94Y","2217":"D94V","2502":"G88A","2503":"A90V","2504":"A90G","3841":"A74S","3844":"T80A","3849":"P102H","4589":"D94T","2092":"D89V"},"WHO-R":{"14269":"G88C","14271":"G88A","14272":"D89N","14274":"A90V","14276":"S91P","14278":"D94N","14281":"D94H","14282":"D94Y","14283":"D94A","14284":"D94G"},"ReSeqTB-High":{"9603":"D94N","9605":"D94G","9609":"G88C","9612":"D94H","9622":"D94A","9625":"D89N","9626":"A90V"},"ReSeqTB-Moderate":{"9627":"S91P"},"Curated-R":{"2091":"D94G","2093":"D94A","2094":"D89N","2095":"D89G","2096":"G88C","2180":"S91P","2181":"D94N","2216":"D94Y","2217":"D94V","2502":"G88A","2503":"A90V","2504":"A90G","3611":"A90G","3841":"A74S","3843":"A74S","3844":"T80A","3849":"P102H","4589":"D94T","2092":"D89V","3842":"D89V"}},"40438":{"param_type":"co-dependent single resistance variant","param_description":"A set of nucleotide or amino acid substitutions in different genes that are all required to confer resistance to an antibiotic drug or drug class, encoded as: [cvterm_id gene 1],[SNP 1],[SNP 2],etc+[cvterm_id gene 2],[SNP 1],[SNP 2],etc. For example: 39879,A90V,M94V+40052,D472H. A nucleotide substitution resulting in a change from an amino acid codon to a stop codon is encoded as [wild type amino acid][position][Ter], for example Q42Ter.","param_type_id":"40438","param_value":{"3611":"39879,G247S+40052,D500N","3843":"39879,A90V+40052,D472H"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1500"},"40330":{"param_type":"multiple resistance variants","param_description":"A set of nucleotide or amino acid substitutions that are all required to confer resistance to an antibiotic drug or drug class, encoded as: [wild-type 1][position 1][mutation 1],[wild-type 2][position 2][mutation 2], etc. For example, D63Y,T142K.","param_type_id":"40330","param_value":{"3842":"A90V,D94G"}}},"model_sequences":{"sequence":{"8820":{"protein_sequence":{"accession":"NP_214520.1","sequence":"MTDTTLPPDDSLDRIEPVDIEQEMQRSYIDYAMSVIVGRALPEVRDGLKPVHRRVLYAMFDSGFRPDRSHAKSARSVAETMGNYHPHGDASIYDSLVRMAQPWSLRYPLVDGQGNFGSPGNDPPAAMRYTEARLTPLAMEMLREIDEETVDFIPNYDGRVQEPTVLPSRFPNLLANGSGGIAVGMATNIPPHNLRELADAVFWALENHDADEEETLAAVMGRVKGPDFPTAGLIVGSQGTADAYKTGRGSIRMRGVVEVEEDSRGRTSLVITELPYQVNHDNFITSIAEQVRDGKLAGISNIEDQSSDRVGLRIVIEIKRDAVAKVVINNLYKHTQLQTSFGANMLAIVDGVPRTLRLDQLIRYYVDHQLDVIVRRTTYRLRKANERAHILRGLVKALDALDEVIALIRASETVDIARAGLIELLDIDEIQAQAILDMQLRRLAALERQRIIDDLAKIEAEIADLEDILAKPERQRGIVRDELAEIVDRHGDDRRTRIIAADGDVSDEDLIAREDVVVTITETGYAKRTKTDLYRSQKRGGKGVQGAGLKQDDIVAHFFVCSTHDLILFFTTQGRVYRAKAYDLPEASRTARGQHVANLLAFQPEERIAQVIQIRGYTDAPYLVLATRNGLVKKSKLTDFDSNRSGGIVAVNLRDNDELVGAVLCSAGDDLLLVSANGQSIRFSATDEALRPMGRATSGVQGMRFNIDDRLLSLNVVREGTYLLVATSGGYAKRTAIEEYPVQGRGGKGVLTVMYDRRRGRLVGALIVDDDSELYAVTSGGGVIRTAARQVRKAGRQTKGVRLMNLGEGDTLLAIARNAEESGDDNAVDANGADQTGN"},"dna_sequence":{"accession":"NC_000962.3","fmin":"7301","fmax":"9818","strand":"+","sequence":"ATGACAGACACGACGTTGCCGCCTGACGACTCGCTCGACCGGATCGAACCGGTTGACATCGAGCAGGAGATGCAGCGCAGCTACATCGACTATGCGATGAGCGTGATCGTCGGCCGCGCGCTGCCGGAGGTGCGCGACGGGCTCAAGCCCGTGCATCGCCGGGTGCTCTATGCAATGTTCGATTCCGGCTTCCGCCCGGACCGCAGCCACGCCAAGTCGGCCCGGTCGGTTGCCGAGACCATGGGCAACTACCACCCGCACGGCGACGCGTCGATCTACGACAGCCTGGTGCGCATGGCCCAGCCCTGGTCGCTGCGCTACCCGCTGGTGGACGGCCAGGGCAACTTCGGCTCGCCAGGCAATGACCCACCGGCGGCGATGAGGTACACCGAAGCCCGGCTGACCCCGTTGGCGATGGAGATGCTGAGGGAAATCGACGAGGAGACAGTCGATTTCATCCCTAACTACGACGGCCGGGTGCAAGAGCCGACGGTGCTACCCAGCCGGTTCCCCAACCTGCTGGCCAACGGGTCAGGCGGCATCGCGGTCGGCATGGCAACCAATATCCCGCCGCACAACCTGCGTGAGCTGGCCGACGCGGTGTTCTGGGCGCTGGAGAATCACGACGCCGACGAAGAGGAGACCCTGGCCGCGGTCATGGGGCGGGTTAAAGGCCCGGACTTCCCGACCGCCGGACTGATCGTCGGATCCCAGGGCACCGCTGATGCCTACAAAACTGGCCGCGGCTCCATTCGAATGCGCGGAGTTGTTGAGGTAGAAGAGGATTCCCGCGGTCGTACCTCGCTGGTGATCACCGAGTTGCCGTATCAGGTCAACCACGACAACTTCATCACTTCGATCGCCGAACAGGTCCGAGACGGCAAGCTGGCCGGCATTTCCAACATTGAGGACCAGTCTAGCGATCGGGTCGGTTTACGCATCGTCATCGAGATCAAGCGCGATGCGGTGGCCAAGGTGGTGATCAATAACCTTTACAAGCACACCCAGCTGCAGACCAGCTTTGGCGCCAACATGCTAGCGATCGTCGACGGGGTGCCGCGCACGCTGCGGCTGGACCAGCTGATCCGCTATTACGTTGACCACCAACTCGACGTCATTGTGCGGCGCACCACCTACCGGCTGCGCAAGGCAAACGAGCGAGCCCACATTCTGCGCGGCCTGGTTAAAGCGCTCGACGCGCTGGACGAGGTCATTGCACTGATCCGGGCGTCGGAGACCGTCGATATCGCCCGGGCCGGACTGATCGAGCTGCTCGACATCGACGAGATCCAGGCCCAGGCAATCCTGGACATGCAGTTGCGGCGCCTGGCCGCACTGGAACGCCAGCGCATCATCGACGACCTGGCCAAAATCGAGGCCGAGATCGCCGATCTGGAAGACATCCTGGCAAAACCCGAGCGGCAGCGTGGGATCGTGCGCGACGAACTCGCCGAAATCGTGGACAGGCACGGCGACGACCGGCGTACCCGGATCATCGCGGCCGACGGAGACGTCAGCGACGAGGATTTGATCGCCCGCGAGGACGTCGTTGTCACTATCACCGAAACGGGATACGCCAAGCGCACCAAGACCGATCTGTATCGCAGCCAGAAACGCGGCGGCAAGGGCGTGCAGGGTGCGGGGTTGAAGCAGGACGACATCGTCGCGCACTTCTTCGTGTGCTCCACCCACGATTTGATCCTGTTCTTCACCACCCAGGGACGGGTTTATCGGGCCAAGGCCTACGACTTGCCCGAGGCCTCCCGGACGGCGCGCGGGCAGCACGTGGCCAACCTGTTAGCCTTCCAGCCCGAGGAACGCATCGCCCAGGTCATCCAGATTCGCGGCTACACCGACGCCCCGTACCTGGTGCTGGCCACTCGCAACGGGCTGGTGAAAAAGTCCAAGCTGACCGACTTCGACTCCAATCGCTCGGGCGGAATCGTGGCGGTCAACCTGCGCGACAACGACGAGCTGGTCGGTGCGGTGCTGTGTTCGGCCGGCGACGACCTGCTGCTGGTCTCGGCCAACGGGCAGTCCATCAGGTTCTCGGCGACCGACGAGGCGCTGCGGCCAATGGGTCGTGCCACCTCGGGTGTGCAGGGCATGCGGTTCAATATCGACGACCGGCTGCTGTCGCTGAACGTCGTGCGTGAAGGCACCTATCTGCTGGTGGCGACGTCAGGGGGCTATGCGAAACGTACCGCGATCGAGGAATACCCGGTACAGGGCCGCGGCGGTAAAGGTGTGCTGACGGTCATGTACGACCGCCGGCGCGGCAGGTTGGTTGGGGCGTTGATTGTCGACGACGACAGCGAGCTGTATGCCGTCACTTCCGGCGGTGGCGTGATCCGCACCGCGGCACGCCAGGTTCGCAAGGCGGGACGGCAGACCAAGGGTGTTCGGTTGATGAATCTGGGCGAGGGCGACACACTGTTGGCCATCGCGCGCAACGCCGAAGAAAGTGGCGACGATAATGCCGTGGACGCCAACGGCGCAGACCAGACGGGCAATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3003295","ARO_id":"39879","ARO_name":"Mycobacterium tuberculosis gyrA conferring resistance to fluoroquinolones","CARD_short_name":"Mtub_gyrA_FLO","ARO_description":"Point mutation of Mycobacterium tuberculosis gyrA resulted in the lowered affinity between fluoroquinolones and gyrA. Thus, conferring resistance.","ARO_category":{"39876":{"category_aro_accession":"3003292","category_aro_cvterm_id":"39876","category_aro_name":"fluoroquinolone resistant gyrA","category_aro_description":"DNA gyrase is responsible for DNA supercoiling and consists of two alpha and two beta subunits. GyrA point mutations confer resistance by preventing fluoroquinolone antibiotics from binding the alpha-subunit.","category_aro_class_name":"AMR Gene Family"},"35942":{"category_aro_accession":"0000023","category_aro_cvterm_id":"35942","category_aro_name":"enoxacin","category_aro_description":"Enoxacin belongs to a group called fluoroquinolones. Its mode of action depends upon blocking bacterial DNA replication by binding itself to DNA gyrase and causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37004":{"category_aro_accession":"3000660","category_aro_cvterm_id":"37004","category_aro_name":"lomefloxacin","category_aro_description":"Lomefloxacin is a difluoropiperazinyl quinolone, sharing similar activities with other fluoroquinolones. It is used to treat urinary tract infections. Relative to other fluoroquinolones, it has a longer half life and has higher serum concentrations.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37007":{"category_aro_accession":"3000663","category_aro_cvterm_id":"37007","category_aro_name":"ofloxacin","category_aro_description":"Ofloxacin is a 6-fluoro, 7-piperazinyl quinolone with a methyl-substituted oxazine ring. It has a broad spectrum of activity including many enterobacteria and mycoplasma but most anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"37008":{"category_aro_accession":"3000664","category_aro_cvterm_id":"37008","category_aro_name":"trovafloxacin","category_aro_description":"Trovafloxacin is a trifluoroquinalone with a broad spectrum of activity that acts by inhibiting the uncoiling of supercoiled DNA. While potent against many Gram-positive and Gram-negative bacteria, it is less active against pseudomonads and Cl. difficile. It is usually taken as the prodrug trovafloxacin mesylate or alatrofloxacin mesylate for oral or intravenous administration, respectively.","category_aro_class_name":"Antibiotic"},"37009":{"category_aro_accession":"3000665","category_aro_cvterm_id":"37009","category_aro_name":"grepafloxacin","category_aro_description":"Grepafloxacin is a broad-spectrum antibacterial quinoline. It is no longer taken due to its high toxicity.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"37142":{"category_aro_accession":"3000762","category_aro_cvterm_id":"37142","category_aro_name":"pefloxacin","category_aro_description":"Pefloxacin is structurally and functionally similar to norfloxacin. It is poorly active against mycobacteria, while anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1943":{"model_id":"1943","model_name":"Mycobacterium tuberculosis kasA mutant conferring resistance to isoniazid","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"2567":"R121K","2568":"G387D","2569":"F413L","3771":"G269S","3772":"G312S","3791":"D66N"},"Curated-R":{"2567":"R121K","2568":"G387D","2569":"F413L","3771":"G269S","3772":"G312S","3791":"D66N"},"clinical":{"2567":"R121K","2568":"G387D","2569":"F413L","3771":"G269S","3772":"G312S","3791":"D66N"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"8832":{"protein_sequence":{"accession":"NP_216761.1","sequence":"MSQPSTANGGFPSVVVTAVTATTSISPDIESTWKGLLAGESGIHALEDEFVTKWDLAVKIGGHLKDPVDSHMGRLDMRRMSYVQRMGKLLGGQLWESAGSPEVDPDRFAVVVGTGLGGAERIVESYDLMNAGGPRKVSPLAVQMIMPNGAAAVIGLQLGARAGVMTPVSACSSGSEAIAHAWRQIVMGDADVAVCGGVEGPIEALPIAAFSMMRAMSTRNDEPERASRPFDKDRDGFVFGEAGALMLIETEEHAKARGAKPLARLLGAGITSDAFHMVAPAADGVRAGRAMTRSLELAGLSPADIDHVNAHGTATPIGDAAEANAIRVAGCDQAAVYAPKSALGHSIGAVGALESVLTVLTLRDGVIPPTLNYETPDPEIDLDVVAGEPRYGDYRYAVNNSFGFGGHNVALAFGRY"},"dna_sequence":{"accession":"NC_000962.3","fmin":"2518114","fmax":"2519365","strand":"+","sequence":"GTGAGTCAGCCTTCCACCGCTAATGGCGGTTTCCCCAGCGTTGTGGTGACCGCCGTCACAGCGACGACGTCGATCTCGCCGGACATCGAGAGCACGTGGAAGGGTCTGTTGGCCGGCGAGAGCGGCATCCACGCACTCGAAGACGAGTTCGTCACCAAGTGGGATCTAGCGGTCAAGATCGGCGGTCACCTCAAGGATCCGGTCGACAGCCACATGGGCCGACTCGACATGCGACGCATGTCGTACGTCCAGCGGATGGGCAAGTTGCTGGGCGGACAGCTATGGGAGTCCGCCGGCAGCCCGGAGGTCGATCCAGACCGGTTCGCCGTTGTTGTCGGCACCGGTCTAGGTGGAGCCGAGAGGATTGTCGAGAGCTACGACCTGATGAATGCGGGCGGCCCCCGGAAGGTGTCCCCGCTGGCCGTTCAGATGATCATGCCCAACGGTGCCGCGGCGGTGATCGGTCTGCAGCTTGGGGCCCGCGCCGGGGTGATGACCCCGGTGTCGGCCTGTTCGTCGGGCTCGGAAGCGATCGCCCACGCGTGGCGTCAGATCGTGATGGGCGACGCCGACGTCGCCGTCTGCGGCGGTGTCGAAGGACCCATCGAGGCGCTGCCCATCGCGGCGTTCTCCATGATGCGGGCCATGTCGACCCGCAACGACGAGCCTGAGCGGGCCTCCCGGCCGTTCGACAAGGACCGCGACGGCTTTGTGTTCGGCGAGGCCGGTGCGCTGATGCTCATCGAGACGGAGGAGCACGCCAAAGCCCGTGGCGCCAAGCCGTTGGCCCGATTGCTGGGTGCCGGTATCACCTCGGACGCCTTTCATATGGTGGCGCCCGCGGCCGATGGTGTTCGTGCCGGTAGGGCGATGACTCGCTCGCTGGAGCTGGCCGGGTTGTCGCCGGCGGACATCGACCACGTCAACGCGCACGGCACGGCGACGCCTATCGGCGACGCCGCGGAGGCCAACGCCATCCGCGTCGCCGGTTGTGATCAGGCCGCGGTGTACGCGCCGAAGTCTGCGCTGGGCCACTCGATCGGCGCGGTCGGTGCGCTCGAGTCGGTGCTCACGGTGCTGACGCTGCGCGACGGCGTCATCCCGCCGACCCTGAACTACGAGACACCCGATCCCGAGATCGACCTTGACGTCGTCGCCGGCGAACCGCGCTATGGCGATTACCGCTACGCAGTCAACAACTCGTTCGGGTTCGGCGGCCACAATGTGGCGCTTGCCTTCGGGCGTTACTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3003463","ARO_id":"40056","ARO_name":"Mycobacterium tuberculosis kasA mutant conferring resistance to isoniazid","CARD_short_name":"Mtub_kasA_INH","ARO_description":"Specific mutations on the Mycobacterium tuberculosis kasA gene resulting in lowered affinity of isoniazid, resulting in resistance.","ARO_category":{"40055":{"category_aro_accession":"3003462","category_aro_cvterm_id":"40055","category_aro_name":"antibiotic resistant kasA","category_aro_description":"kasA is a  ketoacyl acyl carrier protein synthase that catalyzes the condensation reaction of fatty acid synthesis by the addition to an acyl acceptor of two carbons from malonyl-ACP. It is involved in elongation of fatty acids intermediate in the biosynthetic pathway of mycolic acids.","category_aro_class_name":"AMR Gene Family"},"36659":{"category_aro_accession":"3000520","category_aro_cvterm_id":"36659","category_aro_name":"isoniazid","category_aro_description":"Isoniazid is an organic compound that is the first-line anti tuberculosis medication in prevention and treatment. As a prodrug, it is activated by mycobacterial catalase-peroxidases such as M. tuberculosis KatG. Isoniazid inhibits mycolic acid synthesis, which prevents cell wall synthesis in mycobacteria.","category_aro_class_name":"Antibiotic"},"45734":{"category_aro_accession":"3007152","category_aro_cvterm_id":"45734","category_aro_name":"isoniazid-like antibiotic","category_aro_description":"A group of antibiotics containing isoniazid and its derivatives.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2068":{"model_id":"2068","model_name":"Escherichia coli 16S rRNA mutation conferring resistance to edeine","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"3073":"a1499g","4842":"t1506a"},"Curated-R":{"3073":"a1499g","4842":"t1506a"},"clinical":{"3073":"a1499g","4842":"t1506a"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"41093","param_value":"2700"}},"model_sequences":{"sequence":{"3234":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"U00096.1","fmin":"4166658","fmax":"4168200","strand":"+","sequence":"AAATTGAAGAGTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAACGGTAACAGGAAGAAGCTTGCTTCTTTGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCGGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGGAGTAAAGTTAATACCTTTGCTCATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACGAAGACTGACGCTCAGGTGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGTCGACTTGGAGGTTGTGCCCTTGAGGCGTGGCTTCCGGAGCTAACGCGTTAAGTCGACCGCCTGGGGAGTACGGCCGCAAGGTTAAAACTCAAATGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGATGCAACGCGAAGAACCTTACCTGGTCTTGACATCCACGGAAGTTTTCAGAGATGAGAATGTGCCTTCGGGAACCGTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGAAATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCCTTTGTTGCCAGCGGTCCGGCCGGGAACTCAAAGGAGACTGCCAGTGATAAACTGGAGGAAGGTGGGGATGACGTCAAGTCATCATGGCCCTTACGACCAGGGCTACACACGTGCTACAATGGCGCATACAAAGAGAAGCGACCTCGCGAGAGCAAGCGGACCTCATAAAGTGCGTCGTAGTCCGGATTGGAGTCTGCAACTCGACTCCATGAAGTCGGAATCGCTAGTAATCGTGGATCAGAATGCCACGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACACCATGGGAGTGGGTTGCAAAAGAAGTAGGTAGCTTAACCTTCGGGAGGGCGCTTACCACTTTGTGATTCATGACTGGGGTGAAGTCGTAACAAGGTAACCGTAGGGGAACCTGCGGTTGGATCACCTCCTTA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36905","NCBI_taxonomy_name":"Escherichia coli str. K-12","NCBI_taxonomy_id":"83333"}}}},"ARO_accession":"3003223","ARO_id":"39807","ARO_name":"Escherichia coli 16S rRNA mutation conferring resistance to edeine","CARD_short_name":"Ecol_16S_EDN","ARO_description":"Point mutations in the 3' minor domain of the 16S rRNA in Escherichia coli can confer resistance to edeine.","ARO_category":{"40278":{"category_aro_accession":"3003667","category_aro_cvterm_id":"40278","category_aro_name":"16s rRNA with mutation conferring resistance to peptide antibiotics","category_aro_description":"Point mutations in the 16S rRNA of bacteria can confer resistance to peptide antibiotics.","category_aro_class_name":"AMR Gene Family"},"36269":{"category_aro_accession":"3000130","category_aro_cvterm_id":"36269","category_aro_name":"edeine A","category_aro_description":"Edeine A is a subtype of the peptide antibiotic edeine, composed of beta-tyr, beta-ser, diaminopropionic acid, diaminohydroxyazelaic acid, glycine, and spermidine. Edeine A is a mixture of edeine A1 and its inactive isomer, edeine A2. Edeines bind to the 30S subunit to block fMet-tRNA interaction at the P site, inhibiting protein synthesis and subsequent structure\/function processes critical for life or replication.","category_aro_class_name":"Antibiotic"},"36273":{"category_aro_accession":"3000134","category_aro_cvterm_id":"36273","category_aro_name":"edeine B","category_aro_description":"Edeine B is a subtype of the peptide antibiotic edeine, composed of beta-tyr, beta-ser, diaminopropionic acid, diaminohydroxyazelaic acid, glycine, and guanylspermidine. Edeine B is a mixture of edeine B1 and its inactive isomer, edeine B2.  Edeines bind to the 30S subunit to block fMet-tRNA interaction at the P site, inhibiting protein synthesis and subsequent structure\/function processes critical for life or replication. Edeine B has also been shown to inhibit septation and cause filamentous morphology, also leading to cell death.","category_aro_class_name":"Antibiotic"},"36274":{"category_aro_accession":"3000135","category_aro_cvterm_id":"36274","category_aro_name":"edeine D","category_aro_description":"Edeine D is a subtype of edeine similar to edeine A with the beta-tyr replaced by beta-phe-beta-ala. Edeines bind to the 30S subunit to block fMet-tRNA interaction at the P site, inhibiting protein synthesis and subsequent structure\/function processes critical for life or replication.","category_aro_class_name":"Antibiotic"},"36275":{"category_aro_accession":"3000136","category_aro_cvterm_id":"36275","category_aro_name":"edeine F","category_aro_description":"Edeine F is a subtype of edeine similar to edeine B with beta-tyr replaced by beta-phe-beta-ala. Edeines bind to the 30S subunit to block fMet-tRNA interaction at the P site, inhibiting protein synthesis and subsequent structure\/function processes critical for life or replication.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2070":{"model_id":"2070","model_name":"Mycobacterium tuberculosis 16S rRNA mutation conferring resistance to amikacin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"13256":"a1401g","13331":"g1484t","14745":"c1402t","9442":"a514c"},"CRyPTIC-R":{"13256":"a1401g","13331":"g1484t"},"clinical":{"13256":"a1401g","13331":"g1484t","14741":"a1401g","14745":"c1402t","14756":"g1484t","9439":"a1401g","9440":"g1484t","9442":"a514c","12973":"a1401g"},"WHO-R":{"14741":"a1401g","14745":"c1402t","14756":"g1484t"},"ReSeqTB-High":{"9439":"a1401g","9440":"g1484t"},"ReSeqTB-Moderate":{"9442":"a514c"},"Curated-R":{"12973":"a1401g"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"41093","param_value":"2700"}},"model_sequences":{"sequence":{"8764":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"NC_000962.3","fmin":"1471845","fmax":"1473382","strand":"+","sequence":"TTTTGTTTGGAGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGGAAAGGTCTCTTCGGAGATACTCGAGTGGCGAACGGGTGAGTAACACGTGGGTGATCTGCCCTGCACTTCGGGATAAGCCTGGGAAACTGGGTCTAATACCGGATAGGACCACGGGATGCATGTCTTGTGGTGGAAAGCGCTTTAGCGGTGTGGGATGAGCCCGCGGCCTATCAGCTTGTTGGTGGGGTGACGGCCTACCAAGGCGACGACGGGTAGCCGGCCTGAGAGGGTGTCCGGCCACACTGGGACTGAGATACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCGACGCCGCGTGGGGGATGACGGCCTTCGGGTTGTAAACCTCTTTCACCATCGACGAAGGTCCGGGTTCTCTCGGATTGACGGTAGGTGGAGAAGAAGCACCGGCCAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGTGCGAGCGTTGTCCGGAATTACTGGGCGTAAAGAGCTCGTAGGTGGTTTGTCGCGTTGTTCGTGAAATCTCACGGCTTAACTGTGAGCGTGCGGGCGATACGGGCAGACTAGAGTACTGCAGGGGAGACTGGAATTCCTGGTGTAGCGGTGGAATGCGCAGATATCAGGAGGAACACCGGTGGCGAAGGCGGGTCTCTGGGCAGTAACTGACGCTGAGGAGCGAAAGCGTGGGGAGCGAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGGTGGGTACTAGGTGTGGGTTTCCTTCCTTGGGATCCGTGCCGTAGCTAACGCATTAAGTACCCCGCCTGGGGAGTACGGCCGCAAGGCTAAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGCGGAGCATGTGGATTAATTCGATGCAACGCGAAGAACCTTACCTGGGTTTGACATGCACAGGACGCGTCTAGAGATAGGCGTTCCCTTGTGGCCTGTGTGCAGGTGGTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTCTCATGTTGCCAGCACGTAATGGTGGGGACTCGTGAGAGACTGCCGGGGTCAACTCGGAGGAAGGTGGGGATGACGTCAAGTCATCATGCCCCTTATGTCCAGGGCTTCACACATGCTACAATGGCCGGTACAAAGGGCTGCGATGCCGCGAGGTTAAGCGAATCCTTAAAAGCCGGTCTCAGTTCGGATCGGGGTCTGCAACTCGACCCCGTGAAGTCGGAGTCGCTAGTAATCGCAGATCAGCAACGCTGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACGTCATGAAAGTCGGTAACACCCGAAGCCAGTGGCCTAACCCTCGGGAGGGAGCTGTCGAAGGTGGGATCGGCGATTGGGACGAAGTCGTAACAAGGTAGCCGTACCGGAAGGTGCGGCTGGATCACCTCCTTTCT","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3003481","ARO_id":"40077","ARO_name":"Mycobacterium tuberculosis 16S rRNA mutation conferring resistance to amikacin","CARD_short_name":"Mtub_16S_AMK","ARO_description":"Point mutations in the 3' domain of 16S rRNA of Mycobacterium tuberculosis can confer resistance to amikacin.","ARO_category":{"40277":{"category_aro_accession":"3003666","category_aro_cvterm_id":"40277","category_aro_name":"16s rRNA with mutation conferring resistance to aminoglycoside antibiotics","category_aro_description":"Point mutations in the 16S rRNA of bacteria can confer resistance to aminoglycosides.","category_aro_class_name":"AMR Gene Family"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2076":{"model_id":"2076","model_name":"Neisseria gonorrhoeae 16S rRNA mutation conferring resistance to spectinomycin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"41093","param_value":"2700"},"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"12974":"c1198t"},"Curated-R":{"12974":"c1198t"},"clinical":{"12974":"c1198t"}}},"model_sequences":{"sequence":{"4136":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"CP020418.1","fmin":"383737","fmax":"385288","strand":"+","sequence":"AGAGATTGAACATAAGAGTTTGATCCTGGCTCAGATTGAACGCTGGCGGCATGCTTTACACATGCAAGTCGGACGGCAGCACAGGGAAGCTTGCTTCTCGGGTGGCGAGTGGCGAACGGGTGAGTAACATATCGGAACGTACCGGGTAGCGGGGGATAACTGATCGAAAGATCAGCTAATACCGCATACGTCTTGAGAGGGAAAGCAGGGGACCTTCGGGCCTTGCGCTATCCGAGCGGCCGATATCTGATTAGCTGGTTGGCGGGGTAAAGGCCCACCAAGGCGACGATCAGTAGCGGGTCTGAGAGGATGATCCGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATTTTGGACAATGGGCGCAAGCCTGATCCAGCCATGCCGCGTGTCTGAAGAAGGCCTTCGGGTTGTAAAGGACTTTTGTCAGGGAAGAAAAGGCCGTTGCCAATATCGGCGGCCGATGACGGTACCTGAAGAATAAGCACCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGTGCGAGCGTTAATCGGAATTACTGGGCGTAAAGCGGGCGCAGACGGTTACTTAAGCAGGATGTGAAATCCCCGGGCTCAACCCGGGAACTGCGTTCTGAACTGGGTGACTCGAGTGTGTCAGAGGGAGGTGGAATTCCACGTGTAGCAGTGAAATGCGTAGAGATGTGGAGGAATACCGATGGCGAAGGCAGCCTCCTGGGATAACACTGACGTTCATGTCCGAAAGCGTGGGTAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCCTAAACGATGTCAATTAGCTGTTGGGCAACTTGATTGCTTGGTAGCGTAGCTAACGCGTGAAATTGACCGCCTGGGGAGTACGGTCGCAAGATTAAAACTCAAAGGAATTGACGGGGACCCGCACAAGCGGTGGATGATGTGGATTAATTCGATGCAACGCGAAGAACCTTACCTGGTTTTGACATGTGCGGAATCCTCCGGAGACGGAGGAGTGCCTTCGGGAGCCGTAACACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTCATTAGTTGCCATCATTCGGTTGGGCACTCTAATGAGACTGCCGGTGACAAGCCGGAGGAAGGTGGGGATGACGTCAAGTCCTCATGGCCCTTATGACCAGGGCTTCACACGTCATACAATGGTCGGTACAGAGGGTAGCCAAGCCGCGAGGCGGAGCCAATCTCACAAAACCGATCGTAGTCCGGATTGCACTCTGCAACTCGAGTGCATGAAGTCGGAATCGCTAGTAATCGCAGGTCAGCATACTGCGGTGAATACGTTCCCGGGTCTTGTACACACCGCCCGTCACACCATGGGAGTGGGGGATACCAGAAGTAGGTAGGGTAACCGCAAGGAGTCCGCTTACCACGGTATGCTTCATGACTGGGGTGAAGTCGTAACAAGGTAGCCGTAGGGGAACCTGCGGCTGGATCACCTCCTTTCTA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36806","NCBI_taxonomy_name":"Neisseria gonorrhoeae","NCBI_taxonomy_id":"485"}}}},"ARO_accession":"3003495","ARO_id":"40097","ARO_name":"Neisseria gonorrhoeae 16S rRNA mutation conferring resistance to spectinomycin","CARD_short_name":"Ngon_16S_SPT","ARO_description":"Point mutations in the helix 34 region of 16S rRNA of Neisseria gonorrhoeae can confer resistance against spectinomycin.","ARO_category":{"40277":{"category_aro_accession":"3003666","category_aro_cvterm_id":"40277","category_aro_name":"16s rRNA with mutation conferring resistance to aminoglycoside antibiotics","category_aro_description":"Point mutations in the 16S rRNA of bacteria can confer resistance to aminoglycosides.","category_aro_class_name":"AMR Gene Family"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2137":{"model_id":"2137","model_name":"Escherichia coli EF-Tu mutants conferring resistance to kirromycin","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"2947":"Q125K","3302":"G317D","3303":"Q125R","3306":"Y161D","3307":"Y161N","3308":"L121Q","3310":"A376S","3311":"Q125E","3312":"E379K","3410":"Q330H","3411":"A376T","3313":"Y161C","3305":"A376V"},"Curated-R":{"2947":"Q125K","3302":"G317D","3303":"Q125R","3306":"Y161D","3307":"Y161N","3308":"L121Q","3310":"A376S","3311":"Q125E","3312":"E379K","3410":"Q330H","3411":"A376T","3313":"Y161C","3305":"A376V"},"clinical":{"2947":"Q125K"},"experimental":{"3302":"G317D","3303":"Q125R","3306":"Y161D","3307":"Y161N","3308":"L121Q","3310":"A376S","3311":"Q125E","3312":"E379K","3410":"Q330H","3411":"A376T","3313":"Y161C","3305":"A376V"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"3531":{"protein_sequence":{"accession":"AAA50993.1","sequence":"MSKEKFERTKPHVNVGTIGHVDHGKTTLTAAITTVLAKTYGGAARAFDQIDNAPEEKARGITINTSHVEYDTPTRHYAHVDCPGHADYVKNMITGAAQMDGAILVVAATDGPMPQTREHILLGRQVGVPYIIVFLNKCDMVDDEELLELVEMEVRELLSQYDFPGDDTPIVRGSALKALEGDAEWEAKILELAGFLDSYIPEPERAIDKPFLLPIEDVFSISGRGTVVTGRVERGIIKVGEEVEIVGIKETQKSTCTGVEMFRKLLDEGRAGENVGVLLRGIKREEIERGQVLAKPGTIKPHTKFESEVYILSKDEGGRHTPFFKGYRPQFYFRTTDVTGTIELPEGVEMVMPGDNIKMVVTLIHPIAMDDGLRFAIREGGRTVGAGVVAKVLG"},"dna_sequence":{"accession":"AH002539.2","fmin":"1760","fmax":"2945","strand":"+","sequence":"GTGTCTAAAGAAAAATTTGAACGTACAAAACCGCACGTTAACGTTGGTACTATCGGCCACGTTGACCACGGTAAAACTACTCTGACCGCTGCAATCACCACCGTACTGGCTAAAACCTACGGCGGTGCTGCTCGTGCATTCGACCAGATCGATAACGCGCCGGAAGAAAAAGCTCGTGGTATCACCATCAACACTTCTCACGTTGAATACGACACCCCGACCCGTCACTACGCACACGTAGACTGCCCGGGGCACGCCGACTATGTTAAAAACATGATCACCGGTGCTGCTCAGATGGACGGCGCGATCCTGGTAGTTGCTGCGACTGACGGCCCGATGCCGCAGACTCGTGAGCACATCCTGCTGGGTCGTCAGGTAGGCGTTCCGTACATCATCGTGTTCCTGAACAAATGCGACATGGTTGATGACGAAGAGCTGCTGGAACTGGTTGAAATGGAAGTTCGTGAACTTCTGTCTCAGTACGACTTCCCGGGCGACGACACTCCGATCGTTCGTGGTTCTGCTCTGAAAGCGCTGGAAGGCGACGCAGAGTGGGAAGCGAAAATCCTGGAACTGGCTGGCTTCCTGGATTCTTATATTCCGGAACCAGAGCGTGCGATTGACAAGCCGTTCCTGCTGCCGATCGAAGACGTATTCTCCATCTCCGGTCGTGGTACCGTTGTTACCGGTCGTGTAGAACGCGGTATCATCAAAGTTGGTGAAGAAGTTGAAATCGTTGGTATCAAAGAGACTCAGAAGTCTACCTGTACTGGCGTTGAAATGTTCCGCAAACTGCTGGACGAAGGCCGTGCTGGTGAGAACGTAGGTGTTCTGCTGCGTGGTATCAAACGTGAAGAAATCGAACGTGGTCAGGTACTGGCTAAGCCGGGCACCATCAAGCCGCACACCAAGTTCGAATCTGAAGTGTACATTCTGTCCAAAGATGAAGGCGGCCGTCATACTCCGTTCTTCAAAGGCTACCGTCCGCAGTTCTACTTCCGTACTACTGACGTGACTGGTACCATCGAACTGCCGGAAGGCGTAGAGATGGTAATGCCGGGCGACAACATCAAAATGGTTGTTACCCTGATCCACCCGATCGCGATGGACGACGGTCTGCGTTTCGCAATCCGTGAAGGCGGCCGTACCGTTGGCGCGGGCGTTGTTGCTAAAGTTCTGGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3003368","ARO_id":"39952","ARO_name":"Escherichia coli EF-Tu mutants conferring resistance to kirromycin","CARD_short_name":"Ecol_EFTu_KIR","ARO_description":"Sequence variants of Escherichia coli elongation factor Tu that confer resistance to kirromycin.","ARO_category":{"37711":{"category_aro_accession":"3001312","category_aro_cvterm_id":"37711","category_aro_name":"elfamycin resistant EF-Tu","category_aro_description":"Sequence variants of elongation factor Tu that confer resistance to elfamycin antibiotics.","category_aro_class_name":"AMR Gene Family"},"37633":{"category_aro_accession":"3001234","category_aro_cvterm_id":"37633","category_aro_name":"kirromycin","category_aro_description":"Kirromycin, also known as mocimycin, is the representative molecule of its own class of elfamycins which is composed of more than 10 analogs. Kirromycin binds to the domain 1,2 interface of elongation factor Tu. This interaction maintains the EF-Tu*GTP conformation even after GTP is hydrolyzed to GDP. EF-Tu*GDP normally releases aa-tRNA and then exits the ribosome; however, kirromycin*EF-Tu*GDP*aa-tRNA forms a strong complex and remains bound to the ribosome, prohibits translocation of the peptide chain and translation is halted.","category_aro_class_name":"Antibiotic"},"37618":{"category_aro_accession":"3001219","category_aro_cvterm_id":"37618","category_aro_name":"elfamycin antibiotic","category_aro_description":"Elfamycins are molecules that inhibit bacterial elongation factor Tu (EF-Tu), a key protein which brings aminoacyl-tRNA (aa-tRNA) to the ribosome during protein synthesis. Elfamycins defined by their target (EF-Tu), rather than a conserved chemical backbone. Elfamycins follow two mechanisms to disrupt protein synthesis: 1. kirromycins and enacyloxin fix EF-Tu in the GTP bound conformation and lock EF-Tu onto the ribosome, and 2. pulvomycin and GE2270 cover the binding site of aa-tRNA disallowing EF-Tu from being charged with aa-tRNA. All elfamycins cause increased the affinity of EF-Tu for GTP.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2158":{"model_id":"2158","model_name":"Escherichia coli EF-Tu mutants conferring resistance to Pulvomycin","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"2934":"T335A","2965":"R334C","3019":"R234F","3020":"R234S","3030":"R231C","3044":"R231V"},"Curated-R":{"2934":"T335A","2965":"R334C","3019":"R234F","3020":"R234S","3030":"R231C","3044":"R231V"},"clinical":{"2934":"T335A","2965":"R334C","3019":"R234F","3020":"R234S","3030":"R231C","3044":"R231V"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"4655":{"protein_sequence":{"accession":"AAN82549.1","sequence":"MLSPEGESTIVRNIAVSKEKFERTKPHVNVGTIGHVDHGKTTLTAAITTVLAKTYGGAARAFDQIDNAPEEKARGITINTSHVEYDTPTRHYAHVDCPGHADYVKNMITGAAQMDGAILVVAATDGPMPQTREHILLGRQVGVPYIIVFLNKCDMVDDEELLELVEMEVRELLSQYDFPGDDTPIVRGSALKALEGDAEWEAKILELAGFLDSYIPEPERAIDKPFLLPIEDVFSISGRGTVVTGRVERGIIKVGEEVEIVGIKETQKSTCTGVEMFRKLLDEGRAGENVGVLLRGIKREEIERGQVLAKPGTIKPHTKFESEVYILSKDEGGRHTPFFKGYRPQFYFRTTDVTGTIELPEGVEMVMPGDNIKMVVTLIHPIAMDDGLRFAIREGGRTVGAGVVAKVLG"},"dna_sequence":{"accession":"AE014075.1","fmin":"3901532","fmax":"3902762","strand":"-","sequence":"GTGCTCTCTCCTGAAGGGGAGAGCACTATAGTAAGGAATATAGCCGTGTCTAAAGAAAAATTTGAACGTACAAAACCGCACGTTAACGTTGGTACTATCGGCCACGTTGACCACGGTAAAACTACTCTGACCGCTGCAATCACCACCGTACTGGCTAAAACCTACGGCGGTGCTGCTCGTGCATTCGACCAGATCGATAACGCGCCGGAAGAAAAAGCTCGTGGTATCACCATCAACACTTCTCACGTTGAATACGACACCCCGACCCGTCACTACGCGCACGTAGACTGCCCGGGGCACGCCGACTATGTTAAAAACATGATCACCGGTGCTGCTCAGATGGACGGCGCGATCCTGGTAGTTGCTGCGACTGACGGCCCGATGCCGCAGACTCGTGAGCACATCCTGCTGGGTCGTCAGGTAGGCGTTCCGTACATCATCGTGTTCCTGAACAAATGCGACATGGTTGATGACGAAGAGCTGCTGGAACTGGTTGAAATGGAAGTTCGTGAACTTCTGTCTCAGTACGACTTCCCGGGCGACGACACTCCGATCGTTCGTGGTTCTGCTCTGAAAGCGCTGGAAGGCGACGCAGAGTGGGAAGCGAAAATCCTGGAACTGGCTGGCTTCCTGGATTCTTACATTCCGGAACCAGAGCGTGCGATTGACAAGCCGTTCCTGCTGCCGATCGAAGACGTATTCTCCATCTCCGGTCGTGGTACCGTTGTTACCGGTCGTGTAGAACGCGGTATCATCAAAGTTGGTGAAGAAGTTGAAATCGTTGGTATCAAAGAGACTCAGAAGTCTACCTGTACTGGCGTTGAAATGTTCCGCAAACTGCTGGACGAAGGCCGTGCTGGTGAGAACGTAGGTGTTCTGCTGCGTGGTATCAAACGTGAAGAAATCGAACGTGGTCAGGTACTGGCTAAGCCGGGCACCATCAAGCCGCACACCAAGTTCGAATCTGAAGTGTACATTCTGTCCAAAGATGAAGGCGGTCGTCATACTCCGTTCTTCAAAGGCTACCGTCCGCAGTTCTACTTCCGTACTACTGACGTGACTGGTACCATCGAACTGCCGGAAGGCGTAGAGATGGTAATGCCGGGCGACAACATCAAAATGGTTGTTACCCTGATCCACCCGATCGCGATGGACGACGGTCTGCGTTTCGCAATCCGTGAAGGCGGCCGTACCGTTGGCGCGGGCGTTGTTGCTAAAGTTCTGGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36763","NCBI_taxonomy_name":"Escherichia coli CFT073","NCBI_taxonomy_id":"199310"}}}},"ARO_accession":"3003369","ARO_id":"39953","ARO_name":"Escherichia coli EF-Tu mutants conferring resistance to Pulvomycin","CARD_short_name":"Ecol_EFTu_PLV","ARO_description":"Sequence variants of Escherichia coli elongation factor Tu that confer resistance to Pulvomycin.","ARO_category":{"37711":{"category_aro_accession":"3001312","category_aro_cvterm_id":"37711","category_aro_name":"elfamycin resistant EF-Tu","category_aro_description":"Sequence variants of elongation factor Tu that confer resistance to elfamycin antibiotics.","category_aro_class_name":"AMR Gene Family"},"36725":{"category_aro_accession":"3000586","category_aro_cvterm_id":"36725","category_aro_name":"pulvomycin","category_aro_description":"Pulvomycin is a polyketide antibiotic that binds elongation factor Tu (EF-Tu) to inhibit protein biosynthesis by preventing the formation of the ternary complex (EF-Tu*GTP*aa-tRNA). Phenotypically, it was shown that pulvomycin sensitivity is dominant over resistance.","category_aro_class_name":"Antibiotic"},"37618":{"category_aro_accession":"3001219","category_aro_cvterm_id":"37618","category_aro_name":"elfamycin antibiotic","category_aro_description":"Elfamycins are molecules that inhibit bacterial elongation factor Tu (EF-Tu), a key protein which brings aminoacyl-tRNA (aa-tRNA) to the ribosome during protein synthesis. Elfamycins defined by their target (EF-Tu), rather than a conserved chemical backbone. Elfamycins follow two mechanisms to disrupt protein synthesis: 1. kirromycins and enacyloxin fix EF-Tu in the GTP bound conformation and lock EF-Tu onto the ribosome, and 2. pulvomycin and GE2270 cover the binding site of aa-tRNA disallowing EF-Tu from being charged with aa-tRNA. All elfamycins cause increased the affinity of EF-Tu for GTP.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2078":{"model_id":"2078","model_name":"Mycobacteroides chelonae 16S rRNA mutation conferring resistance to kanamycin A","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"41093","param_value":"2500"},"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"12951":"a1408g"},"Curated-R":{"12951":"a1408g"},"clinical":{"12951":"a1408g"}}},"model_sequences":{"sequence":{"3269":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"NR_114659.1","fmin":"0","fmax":"1441","strand":"+","sequence":"GACGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGGAAAGGCCCTTCGGGGTACTCGAGTGGCGAACGGGTGAGTAACACGTGGGTGATCTGCCCTGCACTCTGGGATAAGCCTGGGAAACTGGGTCTAATACCGGATAGGACCACACACTTCATGGTGAGTGGTGCAAAGCTTTTGCGGTGTGGGATGAGCCCGCGGCCTATCAGCTTGTTGGTGGGGTAATGGCCCACCAAGGCGACGACGGGTAGCCGGCCTGAGAGGGTGACCGGCCACACTGGGACTGAGATACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCGACGCCGCGTGAGGGATGACGGCCTTCGGGTTGTAAACCTCTTTCAGTAGGGACGAAGCGAAAGTGACGGTACCTACAGAAGAAGGACCGGCCAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGTCCGAGCGTTGTCCGGAATTACTGGGCGTAAAGAGCTCGTAGGTGGTTTGTCGCGTTGTTCGTGAAAACTCACAGCTTAACTGTGGGCGTGCGGGCGATACGGGCAGACTAGAGTACTGCAGGGGAGACTGGAATTCCTGGTGTAGCGGTGGAATGCGCAGATATCAGGAGGAACACCGGTGGCGAAGGCGGGTCTCTGGGCAGTAACTGACGCTGAGGAGCGAAAGCGTGGGTAGCGAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGGTGGGTACTAGGTGTGGGTTTCCTTCCTTGGGATCCGTGCCGTAGCTAACGCATTAAGTACCCCGCCTGGGGAGTACGGTCGCAAGACTAAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGCGGAGCATGTGGATTAATTCGATGCAACGCGAAGAACCTTACCTGGGTTTGACATGCGCAGGACGTATCTAGAGATAGGTATTCCCTTGTGGCCTGCGTGCAGGTGGTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTCCTATGTTGCCAGCGGGTAATGCCGGGGACTCGTAGGAGACTGCCGGGGTCAACTCGGAGGAAGGTGGGGATGACGTCAAGTCATCATGCCCCTTATGTCCAGGGCTTCACACATGCTACAATGGCCAGTACAGAGGGCTGCGAAGCCGCAAGGTGGAGCGAATCCCTTAAAGCTGGTCTCAGTTCGGATTGGGGTCTGCAACTCGACCCCATGAAGTCGGAGTCGCTAGTAATCGCAGATCAGCAACGCTGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACGTCATGAAAGTCGGTAACACCCGAAGCCAGTGGCCTAACCTTTTGGAGGGAGCTGTCGAAGGTGGGATCGGCGATTGGGACGAAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37061","NCBI_taxonomy_name":"Mycobacterium","NCBI_taxonomy_id":"1763"}}}},"ARO_accession":"3003515","ARO_id":"40117","ARO_name":"Mycobacteroides chelonae 16S rRNA mutation conferring resistance to kanamycin A","CARD_short_name":"Mche_16S_KAN","ARO_description":"Point mutations in the 16S rRNA of Mycobacteroides chelonae can cause resistance to kanamycin A.","ARO_category":{"40277":{"category_aro_accession":"3003666","category_aro_cvterm_id":"40277","category_aro_name":"16s rRNA with mutation conferring resistance to aminoglycoside antibiotics","category_aro_description":"Point mutations in the 16S rRNA of bacteria can confer resistance to aminoglycosides.","category_aro_class_name":"AMR Gene Family"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2124":{"model_id":"2124","model_name":"Clostridioides difficile EF-Tu mutants conferring resistance to elfamycin","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"3422":"G261E"},"Curated-R":{"3422":"G261E"},"clinical":{"3422":"G261E"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"5256":{"protein_sequence":{"accession":"AXU66539.1","sequence":"MAKAKYERTKPHVNIGTIGHVDHGKTTLTAAITKTLYDRYQLGEAVDFANIDKAPEERERGITISTAHVEYETPNRHYAHVDCPGHADYVKNMITGAAQMDGAILVCSATDGPMPQTREHILLSRQVGVPYIVVFLNKCDMVDDEELLELVEMEVRDLLTEYDFPGDDTPIVRGSALMALEDPKSEWGDKIVELFEQIDEYIPAPERDTDKPFLMPVEDVFSITGRGTVATGRVERGVLKVQDEVELVGLTEAPRKVVVTGVEMFRKLLDQAQAGDNIGALLRGVQRNEIERGQVLAKTGSVKAHTKFTAEVYVLKKEEGGRHTPFFDGYRPQFYFRTTDVTGACKLPEGIEMVMPGDNVTMEVDLINSIVVEEGLRFSIREGGRTVASGVVATIIE"},"dna_sequence":{"accession":"CP012325.1","fmin":"109610","fmax":"110804","strand":"+","sequence":"ATGGCTAAAGCTAAATACGAAAGAACAAAACCTCATGTTAATATAGGGACAATAGGACACGTAGACCACGGTAAAACTACATTAACAGCAGCAATAACAAAAACATTATATGACAGATATCAATTAGGAGAAGCAGTAGATTTCGCAAACATAGATAAAGCTCCAGAAGAAAGAGAAAGAGGAATCACAATATCAACAGCACACGTTGAGTATGAAACACCAAATAGACACTATGCACACGTTGACTGCCCAGGGCATGCTGACTACGTTAAGAACATGATAACAGGAGCAGCACAAATGGACGGAGCAATATTAGTTTGTTCAGCAACAGATGGACCAATGCCACAAACAAGAGAGCATATACTATTATCAAGACAAGTTGGAGTACCATATATAGTAGTATTCTTAAATAAATGTGACATGGTAGATGATGAAGAGTTATTAGAGTTAGTAGAGATGGAAGTAAGAGATTTATTAACAGAGTATGATTTCCCAGGAGATGACACTCCAATAGTAAGAGGATCAGCGTTAATGGCATTAGAAGATCCAAAGAGTGAGTGGGGAGATAAGATAGTAGAATTATTCGAGCAAATAGATGAATATATACCAGCACCAGAGAGAGATACAGATAAGCCATTCTTAATGCCAGTAGAAGACGTATTCTCAATCACAGGAAGAGGAACAGTTGCAACAGGAAGAGTGGAAAGAGGAGTATTAAAAGTACAAGACGAAGTAGAATTAGTAGGATTAACAGAAGCACCAAGAAAAGTAGTAGTAACAGGAGTAGAGATGTTCAGAAAATTATTAGACCAAGCACAAGCAGGGGATAATATAGGAGCATTATTAAGAGGAGTACAAAGAAACGAGATAGAAAGAGGACAAGTACTAGCAAAGACTGGATCAGTAAAGGCACACACAAAGTTTACAGCAGAAGTATATGTACTTAAAAAAGAAGAAGGTGGAAGACATACACCATTCTTTGATGGATATAGACCACAATTTTACTTCAGAACAACAGACGTAACAGGAGCTTGTAAGTTACCAGAAGGAATAGAGATGGTAATGCCTGGAGATAACGTAACAATGGAAGTAGACTTAATAAACTCAATAGTTGTAGAAGAGGGATTAAGATTCTCAATAAGAGAAGGTGGAAGAACAGTAGCTTCAGGAGTTGTTGCTACAATAATAGAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36807","NCBI_taxonomy_name":"Clostridioides difficile","NCBI_taxonomy_id":"1496"}}}},"ARO_accession":"3003357","ARO_id":"39941","ARO_name":"Clostridioides difficile EF-Tu mutants conferring resistance to elfamycin","CARD_short_name":"Cdif_EFTu_ELF","ARO_description":"Sequence variants of Clostridioides difficile elongation factor Tu that confer resistance to elfamycin antibiotics.","ARO_category":{"37711":{"category_aro_accession":"3001312","category_aro_cvterm_id":"37711","category_aro_name":"elfamycin resistant EF-Tu","category_aro_description":"Sequence variants of elongation factor Tu that confer resistance to elfamycin antibiotics.","category_aro_class_name":"AMR Gene Family"},"39998":{"category_aro_accession":"3003414","category_aro_cvterm_id":"39998","category_aro_name":"LFF571","category_aro_description":"LFF571 is a novel semi-synthetic thiopeptide antibiotic derived from GE2270. It has been shown to possess potent in vitro and in vivo activity against Gram-positive bacteria. It is hypothesized that it a translation inhibitor leading to cell death.","category_aro_class_name":"Antibiotic"},"37618":{"category_aro_accession":"3001219","category_aro_cvterm_id":"37618","category_aro_name":"elfamycin antibiotic","category_aro_description":"Elfamycins are molecules that inhibit bacterial elongation factor Tu (EF-Tu), a key protein which brings aminoacyl-tRNA (aa-tRNA) to the ribosome during protein synthesis. Elfamycins defined by their target (EF-Tu), rather than a conserved chemical backbone. Elfamycins follow two mechanisms to disrupt protein synthesis: 1. kirromycins and enacyloxin fix EF-Tu in the GTP bound conformation and lock EF-Tu onto the ribosome, and 2. pulvomycin and GE2270 cover the binding site of aa-tRNA disallowing EF-Tu from being charged with aa-tRNA. All elfamycins cause increased the affinity of EF-Tu for GTP.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1545":{"model_id":"1545","model_name":"Escherichia coli gyrA conferring resistance to fluoroquinolones","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"2050":"S83I","2051":"D87N","2052":"D87G","2053":"D87H","2084":"D87Y","3318":"S83W","3326":"S83L","3327":"D87V","3404":"A67S","3405":"A84P","3397":"Q106H","3398":"G81C"},"Curated-R":{"2050":"S83I","2051":"D87N","2052":"D87G","2053":"D87H","2084":"D87Y","3318":"S83W","3326":"S83L","3327":"D87V","3328":"D87V","3404":"A67S","3405":"A84P","3397":"Q106H","3398":"G81C","3329":"G81C"},"clinical":{"2050":"S83I","2051":"D87N","2052":"D87G","2053":"D87H","2084":"D87Y","3318":"S83W","3326":"S83L","3327":"D87V"},"experimental":{"3404":"A67S","3405":"A84P","3397":"Q106H","3398":"G81C"}},"40330":{"param_type":"multiple resistance variants","param_description":"A set of nucleotide or amino acid substitutions that are all required to confer resistance to an antibiotic drug or drug class, encoded as: [wild-type 1][position 1][mutation 1],[wild-type 2][position 2][mutation 2], etc. For example, D63Y,T142K.","param_type_id":"40330","param_value":{"3328":"S83L,D87Y","3329":"S83L,D87N"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1500"}},"model_sequences":{"sequence":{"4695":{"protein_sequence":{"accession":"AAC75291.1","sequence":"MSDLAREITPVNIEEELKSSYLDYAMSVIVGRALPDVRDGLKPVHRRVLYAMNVLGNDWNKAYKKSARVVGDVIGKYHPHGDSAVYDTIVRMAQPFSLRYMLVDGQGNFGSIDGDSAAAMRYTEIRLAKIAHELMADLEKETVDFVDNYDGTEKIPDVMPTKIPNLLVNGSSGIAVGMATNIPPHNLTEVINGCLAYIDDEDISIEGLMEHIPGPDFPTAAIINGRRGIEEAYRTGRGKVYIRARAEVEVDAKTGRETIIVHEIPYQVNKARLIEKIAELVKEKRVEGISALRDESDKDGMRIVIEVKRDAVGEVVLNNLYSQTQLQVSFGINMVALHHGQPKIMNLKDIIAAFVRHRREVVTRRTIFELRKARDRAHILEALAVALANIDPIIELIRHAPTPAEAKTALVANPWQLGNVAAMLERAGDDAARPEWLEPEFGVRDGLYYLTEQQAQAILDLRLQKLTGLEHEKLLDEYKELLDQIAELLRILGSADRLMEVIREELELVREQFGDKRRTEITANSADINLEDLITQEDVVVTLSHQGYVKYQPLSEYEAQRRGGKGKSAARIKEEDFIDRLLVANTHDHILCFSSRGRVYSMKVYQLPEATRGARGRPIVNLLPLEQDERITAILPVTEFEEGVKVFMATANGTVKKTVLTEFNRLRTAGKVAIKLVDGDELIGVDLTSGEDEVMLFSAEGKVVRFKESSVRAMGCNTTGVRGIRLGEGDKVVSLIVPRGDGAILTATQNGYGKRTAVAEYPTKSRATKGVISIKVTERNGLVVGAVQVDDCDQIMMITDAGTLVRTRVSEISIVGRNTQGVILIRTAEDENVVGLQRVAEPVDEEDLDTIDGSAAEGDDEIAPEVDVDDEPEEE"},"dna_sequence":{"accession":"U00096.3","fmin":"2336792","fmax":"2339420","strand":"-","sequence":"ATGAGCGACCTTGCGAGAGAAATTACACCGGTCAACATTGAGGAAGAGCTGAAGAGCTCCTATCTGGATTATGCGATGTCGGTCATTGTTGGCCGTGCGCTGCCAGATGTCCGAGATGGCCTGAAGCCGGTACACCGTCGCGTACTTTACGCCATGAACGTACTAGGCAATGACTGGAACAAAGCCTATAAAAAATCTGCCCGTGTCGTTGGTGACGTAATCGGTAAATACCATCCCCATGGTGACTCGGCGGTCTATGACACGATCGTCCGCATGGCGCAGCCATTCTCGCTGCGTTATATGCTGGTAGACGGTCAGGGTAACTTCGGTTCTATCGACGGCGACTCTGCGGCGGCAATGCGTTATACGGAAATCCGTCTGGCGAAAATTGCCCATGAACTGATGGCCGATCTCGAAAAAGAGACGGTCGATTTCGTTGATAACTATGACGGCACGGAAAAAATTCCGGACGTCATGCCAACCAAAATTCCTAACCTGCTGGTGAACGGTTCTTCCGGTATCGCCGTAGGTATGGCAACCAACATCCCGCCGCACAACCTGACGGAAGTCATCAACGGTTGTCTGGCGTATATTGATGATGAAGACATCAGCATTGAAGGGCTGATGGAACACATCCCGGGGCCGGACTTCCCGACGGCGGCAATCATTAACGGTCGTCGCGGTATTGAAGAAGCTTACCGTACCGGTCGCGGCAAGGTGTATATCCGCGCTCGCGCAGAAGTGGAAGTTGACGCCAAAACCGGTCGTGAAACCATTATCGTCCACGAAATTCCGTATCAGGTAAACAAAGCGCGCCTGATCGAGAAGATTGCGGAACTGGTAAAAGAAAAACGCGTGGAAGGCATCAGCGCGCTGCGTGACGAGTCTGACAAAGACGGTATGCGCATCGTGATTGAAGTGAAACGCGATGCGGTCGGTGAAGTTGTGCTCAACAACCTCTACTCCCAGACCCAGTTGCAGGTTTCTTTCGGTATCAACATGGTGGCATTGCACCATGGTCAGCCGAAGATCATGAACCTGAAAGACATCATCGCGGCGTTTGTTCGTCACCGCCGTGAAGTGGTGACCCGTCGTACTATTTTCGAACTGCGTAAAGCTCGCGATCGTGCTCATATCCTTGAAGCATTAGCCGTGGCGCTGGCGAACATCGACCCGATCATCGAACTGATCCGTCATGCGCCGACGCCTGCAGAAGCGAAAACTGCGCTGGTTGCTAATCCGTGGCAGCTGGGCAACGTTGCCGCGATGCTCGAACGTGCTGGCGACGATGCTGCGCGTCCGGAATGGCTGGAGCCAGAGTTCGGCGTGCGTGATGGTCTGTACTACCTGACCGAACAGCAAGCTCAGGCGATTCTGGATCTGCGTTTGCAGAAACTGACCGGTCTTGAGCACGAAAAACTGCTCGACGAATACAAAGAGCTGCTGGATCAGATCGCGGAACTGTTGCGTATTCTTGGTAGCGCCGATCGTCTGATGGAAGTGATCCGTGAAGAGCTGGAGCTGGTTCGTGAACAGTTCGGTGACAAACGTCGTACTGAAATCACCGCCAACAGCGCAGACATCAACCTGGAAGATCTGATCACCCAGGAAGATGTGGTCGTGACGCTCTCTCACCAGGGCTACGTTAAGTATCAGCCGCTTTCTGAATACGAAGCGCAGCGTCGTGGCGGGAAAGGTAAATCTGCCGCACGTATTAAAGAAGAAGACTTTATCGACCGACTGCTGGTGGCGAACACTCACGACCATATTCTGTGCTTCTCCAGCCGTGGTCGCGTCTATTCGATGAAAGTTTATCAGTTGCCGGAAGCCACTCGTGGCGCGCGCGGTCGTCCGATCGTCAACCTGCTGCCGCTGGAGCAGGACGAACGTATCACTGCGATCCTGCCAGTGACCGAGTTTGAAGAAGGCGTGAAAGTCTTCATGGCGACCGCTAACGGTACCGTGAAGAAAACTGTCCTCACCGAGTTCAACCGTCTGCGTACCGCCGGTAAAGTGGCGATCAAACTGGTTGACGGCGATGAGCTGATCGGCGTTGACCTGACCAGCGGCGAAGACGAAGTAATGCTGTTCTCCGCTGAAGGTAAAGTGGTGCGCTTTAAAGAGTCTTCTGTCCGTGCGATGGGCTGCAACACCACCGGTGTTCGCGGTATTCGCTTAGGTGAAGGCGATAAAGTCGTCTCTCTGATCGTGCCTCGTGGCGATGGCGCAATCCTCACCGCAACGCAAAACGGTTACGGTAAACGTACCGCAGTGGCGGAATACCCAACCAAGTCGCGTGCGACGAAAGGGGTTATCTCCATCAAGGTTACCGAACGTAACGGTTTAGTTGTTGGCGCGGTACAGGTAGATGACTGCGACCAGATCATGATGATCACCGATGCCGGTACGCTGGTACGTACTCGCGTTTCGGAAATCAGCATCGTGGGCCGTAACACCCAGGGCGTGATCCTCATCCGTACTGCGGAAGATGAAAACGTAGTGGGTCTGCAACGTGTTGCTGAACCGGTTGACGAGGAAGATCTGGATACCATCGACGGCAGTGCCGCGGAAGGGGACGATGAAATCGCTCCGGAAGTGGACGTTGACGACGAGCCAGAAGAAGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36849","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. MG1655","NCBI_taxonomy_id":"511145"}}}},"ARO_accession":"3003294","ARO_id":"39878","ARO_name":"Escherichia coli gyrA conferring resistance to fluoroquinolones","CARD_short_name":"Ecol_gyrA_FLO","ARO_description":"Point mutation of Escherichia coli gyrA resulted in the lowered affinity between fluoroquinolones and gyrA. Thus, conferring resistance.","ARO_category":{"39876":{"category_aro_accession":"3003292","category_aro_cvterm_id":"39876","category_aro_name":"fluoroquinolone resistant gyrA","category_aro_description":"DNA gyrase is responsible for DNA supercoiling and consists of two alpha and two beta subunits. GyrA point mutations confer resistance by preventing fluoroquinolone antibiotics from binding the alpha-subunit.","category_aro_class_name":"AMR Gene Family"},"35942":{"category_aro_accession":"0000023","category_aro_cvterm_id":"35942","category_aro_name":"enoxacin","category_aro_description":"Enoxacin belongs to a group called fluoroquinolones. Its mode of action depends upon blocking bacterial DNA replication by binding itself to DNA gyrase and causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37004":{"category_aro_accession":"3000660","category_aro_cvterm_id":"37004","category_aro_name":"lomefloxacin","category_aro_description":"Lomefloxacin is a difluoropiperazinyl quinolone, sharing similar activities with other fluoroquinolones. It is used to treat urinary tract infections. Relative to other fluoroquinolones, it has a longer half life and has higher serum concentrations.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37007":{"category_aro_accession":"3000663","category_aro_cvterm_id":"37007","category_aro_name":"ofloxacin","category_aro_description":"Ofloxacin is a 6-fluoro, 7-piperazinyl quinolone with a methyl-substituted oxazine ring. It has a broad spectrum of activity including many enterobacteria and mycoplasma but most anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"37008":{"category_aro_accession":"3000664","category_aro_cvterm_id":"37008","category_aro_name":"trovafloxacin","category_aro_description":"Trovafloxacin is a trifluoroquinalone with a broad spectrum of activity that acts by inhibiting the uncoiling of supercoiled DNA. While potent against many Gram-positive and Gram-negative bacteria, it is less active against pseudomonads and Cl. difficile. It is usually taken as the prodrug trovafloxacin mesylate or alatrofloxacin mesylate for oral or intravenous administration, respectively.","category_aro_class_name":"Antibiotic"},"37009":{"category_aro_accession":"3000665","category_aro_cvterm_id":"37009","category_aro_name":"grepafloxacin","category_aro_description":"Grepafloxacin is a broad-spectrum antibacterial quinoline. It is no longer taken due to its high toxicity.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"37142":{"category_aro_accession":"3000762","category_aro_cvterm_id":"37142","category_aro_name":"pefloxacin","category_aro_description":"Pefloxacin is structurally and functionally similar to norfloxacin. It is poorly active against mycobacteria, while anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1005":{"model_id":"1005","model_name":"Escherichia coli soxR with mutation conferring antibiotic resistance","model_type":"protein overexpression model","model_type_id":"41091","model_description":"Protein Overexpression Models (POM) are similar to Protein Variant Models (PVM) in that they include a protein reference sequence, a curated BLASTP bitscore cut-off, and mapped resistance variants. Whereas PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, reporting only those with curated mutations conferring AMR, POMs are restricted to regulatory proteins and report both wild-type sequences and\/or sequences with mutations leading to overexpression of efflux complexes. The former lead to efflux of antibiotics at basal levels, while the latter can confer clinical resistance. POMs include a protein reference sequence (often from wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Perfect RGI match is 100% identical to the wild-type reference protein sequence along its entire length, a Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value may or may not contain at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off may or may not contain at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"2230":"R20H","2233":"G121D","3895":"R90G","3896":"S31A","3897":"R71S"},"Curated-R":{"2230":"R20H","2233":"G121D","3895":"R90G","3896":"S31A","3897":"R71S","7541":"R71S","12870":"R71S","18555":"R71S"},"clinical":{"2230":"R20H","2233":"G121D","3895":"R90G","3896":"S31A","3897":"R71S"}},"40494":{"param_type":"frameshift mutation","param_description":"A frameshift is a sequence change between the translation initiation (start) and termination (stop) codon where, compared to a reference sequence, translation shifts to another reading frame as caused by nucleotide insertions and deletions. In ARO, these are annotated at the protein level with the first changed most N-terminal wildtype amino acid position. Format is given as [wildtype AA][position]fs, e.g. S531fs where S531 is a frameshifted coordinate beginning with codon 531. Termination may also be denoted as: Ter[position]fs.","param_type_id":"40494","param_value":{"7541":"L148fs"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"300"},"40330":{"param_type":"multiple resistance variants","param_description":"A set of nucleotide or amino acid substitutions that are all required to confer resistance to an antibiotic drug or drug class, encoded as: [wild-type 1][position 1][mutation 1],[wild-type 2][position 2][mutation 2], etc. For example, D63Y,T142K.","param_type_id":"40330","param_value":{"12870":"T38S,G74R"}},"41342":{"param_type":"deletion mutation from peptide sequence","param_description":"A peptide sequence change between the translation initiation (start) and termination (stop) codon where, compared to a reference sequence, one or more amino acids are deleted and therefore are not present. These represent in-frame deletions which do not result in frameshift variants and may include multiple amino acids. Format is given by [wildtype AA][position]del for a single peptide deletion or [wildtype AA][position]_[wildtype AA][position]del for a deleted peptide range, e.g. K527del or Q517_N518del.","param_type_id":"41342","param_value":{"18555":"S128del"}}},"model_sequences":{"sequence":{"2074":{"protein_sequence":{"accession":"AAC77033.1","sequence":"MEKKLPRIKALLTPGEVAKRSGVAVSALHFYESKGLITSIRNSGNQRRYKRDVLRYVAIIKIAQRIGIPLATIGEAFGVLPEGHTLSAKEWKQLSSQWREELDRRIHTLVALRDELDGCIGCGCLSRSDCPLRNPGDRLGEEGTGARLLEDEQN"},"dna_sequence":{"accession":"U00096.1","fmin":"4277468","fmax":"4277933","strand":"+","sequence":"ATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAACGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACCAGTATCCGTAACAGCGGCAATCAGCGGCGATATAAACGTGATGTGTTGCGATATGTTGCAATTATCAAAATTGCTCAGCGTATTGGCATTCCGCTGGCGACCATTGGTGAAGCGTTTGGCGTGTTGCCCGAAGGGCATACGTTAAGTGCGAAAGAGTGGAAACAGCTTTCGTCCCAATGGCGAGAAGAGTTGGATCGGCGCATTCATACCTTAGTGGCGCTGCGTGACGAACTGGACGGATGTATTGGTTGTGGCTGCCTTTCGCGCAGTGATTGCCCGTTGCGTAACCCGGGCGACCGCTTAGGAGAAGAAGGTACCGGCGCACGCTTGCTGGAAGATGAACAAAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36849","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. MG1655","NCBI_taxonomy_id":"511145"}}}},"ARO_accession":"3003381","ARO_id":"39965","ARO_name":"Escherichia coli soxR with mutation conferring antibiotic resistance","CARD_short_name":"Ecol_soxR_MULT","ARO_description":"SoxR is a sensory protein that upregulates soxS expression in the presence of redox-cycling drugs. This stress response leads to the expression many multidrug efflux pumps.","ARO_category":{"36002":{"category_aro_accession":"0010001","category_aro_cvterm_id":"36002","category_aro_name":"ATP-binding cassette (ABC) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding\/hydrolysis to transport substrates across cell membranes.","category_aro_class_name":"AMR Gene Family"},"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37084":{"category_aro_accession":"3000704","category_aro_cvterm_id":"37084","category_aro_name":"cefalotin","category_aro_description":"Cefalotin is a semisynthetic cephalosporin antibiotic activate against staphylococci. It is resistant to staphylococci beta-lactamases but hydrolyzed by enterobacterial beta-lactamases.","category_aro_class_name":"Antibiotic"},"37250":{"category_aro_accession":"3000870","category_aro_cvterm_id":"37250","category_aro_name":"triclosan","category_aro_description":"Triclosan is a common antibacterial agent added to many consumer products as a biocide.  It is an inhibitor of fatty acid biosynthesis by blocking enoyl-carrier protein reductase (FabI).","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"43746":{"category_aro_accession":"3005386","category_aro_cvterm_id":"43746","category_aro_name":"disinfecting agents and antiseptics","category_aro_description":"Disinfectants that can also interact with antimicrobial resistance mechanisms, e.g. molecule efflux, and thus are the targets of disinfectant resistance.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1055":{"model_id":"1055","model_name":"Escherichia coli parE conferring resistance to fluoroquinolones","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"2226":"D476N"},"Curated-R":{"2226":"D476N"},"clinical":{"2226":"D476N"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"5533":{"protein_sequence":{"accession":"BAE77086.1","sequence":"MTQTYNADAIEVLTGLEPVRRRPGMYTDTTRPNHLGQEVIDNSVDEALAGHAKRVDVILHADQSLEVIDDGRGMPVDIHPEEGVPAVELILCRLHAGGKFSNKNYQFSGGLHGVGISVVNALSKRVEVNVRRDGQVYNIAFENGEKVQDLQVVGTCGKRNTGTSVHFWPDETFFDSPRFSVSRLTHVLKAKAVLCPGVEITFKDEINNTEQRWCYQDGLNDYLAEAVNGLPTLPEKPFIGNFAGDTEAVDWALLWLPEGGELLTESYVNLIPTMQGGTHVNGLRQGLLDAMREFCEYRNILPRGVKLSAEDIWDRCAYVLSVKMQDPQFAGQTKERLSSRQCAAFVSGVVKDAFILWLNQNVQAAELLAEMAISSAQRRMRAAKKVVRKKLTSGPALPGKLADCTAQDLNRTELFLVEGDSAGGSAKQARDREYQAIMPLKGKILNTWEVSSDEVLASQEVHDISVAIGIDPDSDDLSQLRYGKICILADADSDGLHIATLLCALFVKHFRALVKHGHVYVALPPLYRIDLGKEVYYALTEEEKEGVLEQLKRKKGKPNVQRFKGLGEMNPMQLRETTLDPNTRRLVQLTIDDEDDQRTDAMMDMLLAKKRSEDRRNWLQEKGDMAEIEV"},"dna_sequence":{"accession":"AP009048.1","fmin":"3172159","fmax":"3174052","strand":"-","sequence":"ATGACGCAAACTTATAACGCTGATGCCATTGAGGTACTCACCGGGCTTGAGCCGGTTCGCCGCCGTCCGGGGATGTATACCGATACCACTCGCCCTAACCATTTGGGGCAAGAAGTCATTGATAACAGTGTGGATGAAGCACTGGCGGGTCACGCAAAACGCGTGGACGTTATTTTACATGCTGACCAGTCGTTAGAAGTTATTGACGATGGGCGCGGGATGCCGGTGGATATTCACCCGGAAGAGGGTGTACCGGCGGTTGAACTGATTCTTTGCCGTCTGCATGCAGGCGGTAAATTCTCTAACAAAAATTACCAGTTCTCTGGCGGCCTGCATGGCGTGGGGATTTCGGTGGTTAACGCCCTGTCGAAGCGCGTAGAAGTTAACGTGCGCCGCGATGGTCAGGTTTATAACATCGCCTTTGAAAATGGCGAAAAGGTGCAGGATTTACAGGTTGTCGGCACTTGCGGTAAACGCAATACTGGTACCAGTGTGCACTTCTGGCCGGATGAAACCTTCTTTGACAGCCCGCGATTTTCTGTTTCACGCCTGACGCATGTGCTGAAAGCCAAAGCGGTATTGTGCCCTGGCGTTGAGATCACTTTTAAAGATGAGATCAACAATACCGAACAACGCTGGTGCTATCAGGACGGTCTGAATGATTACCTGGCGGAAGCGGTAAATGGTCTGCCGACGCTGCCGGAAAAACCGTTTATCGGTAATTTCGCTGGTGATACTGAAGCTGTGGACTGGGCGCTACTGTGGCTGCCGGAAGGCGGTGAACTGCTGACCGAAAGCTACGTCAACCTTATCCCAACGATGCAGGGCGGTACCCATGTTAATGGTCTGCGTCAGGGCCTGTTGGACGCGATGCGTGAGTTCTGTGAATACCGCAATATTCTGCCGCGCGGTGTAAAGCTGTCGGCGGAAGATATCTGGGATCGCTGCGCCTATGTGCTGTCAGTAAAAATGCAGGATCCGCAGTTTGCCGGGCAGACGAAAGAGCGTCTCTCTTCGCGTCAATGCGCGGCATTCGTTTCTGGCGTGGTGAAAGATGCCTTTATCCTGTGGCTGAACCAGAACGTTCAGGCGGCTGAACTGCTGGCGGAGATGGCGATTTCCAGCGCCCAGCGCCGTATGCGTGCGGCCAAAAAAGTGGTGCGTAAAAAGCTGACCAGCGGCCCGGCGTTGCCTGGCAAACTGGCTGATTGTACCGCGCAGGACCTTAACCGTACCGAGCTGTTCCTTGTGGAAGGTGACTCCGCAGGCGGATCTGCCAAGCAGGCGCGCGATCGCGAATATCAGGCGATCATGCCACTGAAAGGTAAGATCCTTAACACCTGGGAAGTCTCTTCCGACGAAGTGCTGGCTTCGCAGGAAGTGCACGATATTTCGGTAGCGATCGGTATCGATCCTGACAGCGACGATCTGAGCCAGCTTCGTTATGGCAAAATCTGTATCCTCGCGGATGCGGACTCTGATGGTCTGCACATTGCCACGCTGCTCTGCGCTTTGTTCGTAAAACATTTCCGCGCGTTGGTGAAACACGGTCACGTTTACGTCGCACTGCCACCGCTCTACCGTATTGATCTCGGGAAAGAGGTTTATTACGCGCTGACGGAAGAAGAGAAAGAGGGCGTACTTGAGCAATTAAAACGCAAGAAAGGCAAGCCGAACGTCCAGCGTTTTAAAGGTCTGGGGGAAATGAACCCGATGCAATTGCGCGAAACCACGCTTGATCCGAACACTCGCCGTCTGGTGCAGTTGACTATCGATGATGAAGACGATCAGCGTACTGACGCGATGATGGATATGCTGCTGGCGAAGAAACGCTCGGAAGATCGCCGCAACTGGTTGCAAGAGAAAGGCGACATGGCGGAGATTGAGGTTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36839","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. W3110","NCBI_taxonomy_id":"316407"}}}},"ARO_accession":"3003316","ARO_id":"39900","ARO_name":"Escherichia coli parE conferring resistance to fluoroquinolones","CARD_short_name":"Ecol_parE_FLO","ARO_description":"Point mutation in Escherichia coli parE resulting in fluoroquinolones resistance.","ARO_category":{"39897":{"category_aro_accession":"3003313","category_aro_cvterm_id":"39897","category_aro_name":"fluoroquinolone resistant parE","category_aro_description":"ParE is a subunit of topoisomerase IV, necessary for cell survival. Point mutations in ParE prevent fluoroquinolones from inhibiting DNA synthesis, thus conferring resistance.","category_aro_class_name":"AMR Gene Family"},"35942":{"category_aro_accession":"0000023","category_aro_cvterm_id":"35942","category_aro_name":"enoxacin","category_aro_description":"Enoxacin belongs to a group called fluoroquinolones. Its mode of action depends upon blocking bacterial DNA replication by binding itself to DNA gyrase and causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37004":{"category_aro_accession":"3000660","category_aro_cvterm_id":"37004","category_aro_name":"lomefloxacin","category_aro_description":"Lomefloxacin is a difluoropiperazinyl quinolone, sharing similar activities with other fluoroquinolones. It is used to treat urinary tract infections. Relative to other fluoroquinolones, it has a longer half life and has higher serum concentrations.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37007":{"category_aro_accession":"3000663","category_aro_cvterm_id":"37007","category_aro_name":"ofloxacin","category_aro_description":"Ofloxacin is a 6-fluoro, 7-piperazinyl quinolone with a methyl-substituted oxazine ring. It has a broad spectrum of activity including many enterobacteria and mycoplasma but most anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"37008":{"category_aro_accession":"3000664","category_aro_cvterm_id":"37008","category_aro_name":"trovafloxacin","category_aro_description":"Trovafloxacin is a trifluoroquinalone with a broad spectrum of activity that acts by inhibiting the uncoiling of supercoiled DNA. While potent against many Gram-positive and Gram-negative bacteria, it is less active against pseudomonads and Cl. difficile. It is usually taken as the prodrug trovafloxacin mesylate or alatrofloxacin mesylate for oral or intravenous administration, respectively.","category_aro_class_name":"Antibiotic"},"37009":{"category_aro_accession":"3000665","category_aro_cvterm_id":"37009","category_aro_name":"grepafloxacin","category_aro_description":"Grepafloxacin is a broad-spectrum antibacterial quinoline. It is no longer taken due to its high toxicity.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"37142":{"category_aro_accession":"3000762","category_aro_cvterm_id":"37142","category_aro_name":"pefloxacin","category_aro_description":"Pefloxacin is structurally and functionally similar to norfloxacin. It is poorly active against mycobacteria, while anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2066":{"model_id":"2066","model_name":"Escherichia coli soxS with mutation conferring antibiotic resistance","model_type":"protein overexpression model","model_type_id":"41091","model_description":"Protein Overexpression Models (POM) are similar to Protein Variant Models (PVM) in that they include a protein reference sequence, a curated BLASTP bitscore cut-off, and mapped resistance variants. Whereas PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, reporting only those with curated mutations conferring AMR, POMs are restricted to regulatory proteins and report both wild-type sequences and\/or sequences with mutations leading to overexpression of efflux complexes. The former lead to efflux of antibiotics at basal levels, while the latter can confer clinical resistance. POMs include a protein reference sequence (often from wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Perfect RGI match is 100% identical to the wild-type reference protein sequence along its entire length, a Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value may or may not contain at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off may or may not contain at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"3562":"A12S"},"Curated-R":{"3562":"A12S"},"clinical":{"3562":"A12S"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"200"}},"model_sequences":{"sequence":{"5276":{"protein_sequence":{"accession":"AAC77032.1","sequence":"MSHQKIIQDLIAWIDEHIDQPLNIDVVAKKSGYSKWYLQRMFRTVTHQTLGDYIRQRRLLLAAVELRTTERPIFDIAMDLGYVSQQTFSRVFRRQFDRTPSDYRHRL"},"dna_sequence":{"accession":"U00096.3","fmin":"4277059","fmax":"4277383","strand":"-","sequence":"ATGTCCCATCAGAAAATTATTCAGGATCTTATCGCATGGATTGACGAGCATATTGACCAGCCGCTTAACATTGATGTAGTCGCAAAAAAATCAGGCTATTCAAAGTGGTACTTGCAACGAATGTTCCGCACGGTGACGCATCAGACGCTTGGCGATTACATTCGCCAACGCCGCCTGTTACTGGCCGCCGTTGAGTTGCGCACCACCGAGCGTCCGATTTTTGATATCGCAATGGACCTGGGTTATGTCTCGCAGCAGACCTTCTCCCGCGTTTTCCGTCGGCAGTTTGATCGCACTCCCAGCGATTATCGCCACCGCCTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36849","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. MG1655","NCBI_taxonomy_id":"511145"}}}},"ARO_accession":"3003511","ARO_id":"40113","ARO_name":"Escherichia coli soxS with mutation conferring antibiotic resistance","CARD_short_name":"Ecol_soxS_MULT","ARO_description":"SoxS is a global regulator that up-regulates the expression of AcrAB efflux genes. It also reduces OmpF expression to decrease cell membrane permeability.","ARO_category":{"36002":{"category_aro_accession":"0010001","category_aro_cvterm_id":"36002","category_aro_name":"ATP-binding cassette (ABC) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding\/hydrolysis to transport substrates across cell membranes.","category_aro_class_name":"AMR Gene Family"},"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"41445":{"category_aro_accession":"3004281","category_aro_cvterm_id":"41445","category_aro_name":"General Bacterial Porin with reduced permeability to beta-lactams","category_aro_description":"These are GBPs that are associated with decreased susceptibility to beta-lactams either through mutations in the porin protein, absence of the porin protein, or expression of the porin protein.","category_aro_class_name":"AMR Gene Family"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37084":{"category_aro_accession":"3000704","category_aro_cvterm_id":"37084","category_aro_name":"cefalotin","category_aro_description":"Cefalotin is a semisynthetic cephalosporin antibiotic activate against staphylococci. It is resistant to staphylococci beta-lactamases but hydrolyzed by enterobacterial beta-lactamases.","category_aro_class_name":"Antibiotic"},"37250":{"category_aro_accession":"3000870","category_aro_cvterm_id":"37250","category_aro_name":"triclosan","category_aro_description":"Triclosan is a common antibacterial agent added to many consumer products as a biocide.  It is an inhibitor of fatty acid biosynthesis by blocking enoyl-carrier protein reductase (FabI).","category_aro_class_name":"Antibiotic"},"45604":{"category_aro_accession":"3007045","category_aro_cvterm_id":"45604","category_aro_name":"enrofloxacin","category_aro_description":"Enrofloxacin is a broad-spectrum fluoroquinolone antibiotic. It is used in veterinary medicine predominately for dogs and cats but is sometimes used for other animals.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"43746":{"category_aro_accession":"3005386","category_aro_cvterm_id":"43746","category_aro_name":"disinfecting agents and antiseptics","category_aro_description":"Disinfectants that can also interact with antimicrobial resistance mechanisms, e.g. molecule efflux, and thus are the targets of disinfectant resistance.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"},"36383":{"category_aro_accession":"3000244","category_aro_cvterm_id":"36383","category_aro_name":"reduced permeability to antibiotic","category_aro_description":"Reduction in permeability to antibiotic, generally through reduced production of porins, can provide resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1989":{"model_id":"1989","model_name":"Klebsiella pneumoniae acrR with mutation conferring multidrug antibiotic resistance","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"2128":"Y114F","2185":"M109I","2867":"V165I"},"Curated-R":{"2128":"Y114F","2185":"M109I","2867":"V165I"},"clinical":{"2128":"Y114F","2185":"M109I","2867":"V165I"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"410"}},"model_sequences":{"sequence":{"2069":{"protein_sequence":{"accession":"ABR75897.1","sequence":"MARKTKQQARETRQLILDVALRLFSQQGVSSTSLATIAKAAGVTRGAIYWHFKNKSDLFNEIWELSDASISDLEIEYRAKFPNDPLSVIREILVYVLEATVTEERRRLMMEIIYHKCEFVGEMTVVQQAQRQLSLASYERIEQTLKECIAAKLLPANLLTRRAAVLMRSYLSGLMENWLFAPDSFDLHAEARDYVAILLEMYQFCPTLRGPESLSA"},"dna_sequence":{"accession":"CP000647.1","fmin":"489264","fmax":"489915","strand":"+","sequence":"ATGGCACGAAAAACCAAACAACAGGCACGTGAAACCCGGCAACTGATTCTGGATGTTGCTCTGCGTCTGTTTTCGCAGCAAGGCGTATCATCTACCTCGTTGGCAACAATTGCAAAAGCTGCGGGTGTAACGAGGGGGGCTATCTACTGGCATTTCAAGAATAAATCAGATTTATTCAACGAAATTTGGGAGCTGTCAGACGCCAGTATTAGCGATCTCGAAATTGAGTATCGGGCAAAATTCCCCAACGATCCACTCTCAGTTATCAGGGAGATTCTAGTCTATGTTCTTGAAGCGACAGTGACAGAAGAACGTCGACGATTAATGATGGAGATTATCTATCATAAGTGTGAGTTCGTCGGTGAAATGACCGTGGTGCAGCAGGCCCAGCGGCAGCTCTCCCTGGCGAGTTATGAGCGTATCGAGCAGACCTTGAAAGAGTGCATCGCGGCGAAGCTGCTGCCCGCCAATTTACTCACCCGGCGGGCGGCCGTGTTAATGCGCAGCTACCTTTCCGGGCTGATGGAAAACTGGCTGTTTGCCCCCGATTCGTTCGACCTGCATGCGGAAGCGCGGGACTACGTCGCTATTCTGCTGGAGATGTATCAATTCTGCCCGACGCTACGCGGCCCGGAGAGCTTGTCAGCTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37607","NCBI_taxonomy_name":"Klebsiella pneumoniae subsp. pneumoniae MGH 78578","NCBI_taxonomy_id":"272620"}}}},"ARO_accession":"3003373","ARO_id":"39957","ARO_name":"Klebsiella pneumoniae acrR with mutation conferring multidrug antibiotic resistance","CARD_short_name":"Kpne_acrR_MULT","ARO_description":"AcrR is a repressor of the AcrAB-TolC multidrug efflux complex. AcrR mutations result in high level antibiotic resistance.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"37084":{"category_aro_accession":"3000704","category_aro_cvterm_id":"37084","category_aro_name":"cefalotin","category_aro_description":"Cefalotin is a semisynthetic cephalosporin antibiotic activate against staphylococci. It is resistant to staphylococci beta-lactamases but hydrolyzed by enterobacterial beta-lactamases.","category_aro_class_name":"Antibiotic"},"37250":{"category_aro_accession":"3000870","category_aro_cvterm_id":"37250","category_aro_name":"triclosan","category_aro_description":"Triclosan is a common antibacterial agent added to many consumer products as a biocide.  It is an inhibitor of fatty acid biosynthesis by blocking enoyl-carrier protein reductase (FabI).","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"43746":{"category_aro_accession":"3005386","category_aro_cvterm_id":"43746","category_aro_name":"disinfecting agents and antiseptics","category_aro_description":"Disinfectants that can also interact with antimicrobial resistance mechanisms, e.g. molecule efflux, and thus are the targets of disinfectant resistance.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1721":{"model_id":"1721","model_name":"Mycobacterium leprae folP with mutation conferring resistance to dapsone","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"2140":"T53A","2175":"T53I","2200":"P55R","2201":"P55L","2202":"P55S","3292":"T53P","3293":"T53N","3294":"P55T","3295":"P55A","3296":"P55H","3407":"V48G","3408":"V48A","3409":"V48F","3406":"R54G"},"Curated-R":{"2140":"T53A","2175":"T53I","2200":"P55R","2201":"P55L","2202":"P55S","3292":"T53P","3293":"T53N","3294":"P55T","3295":"P55A","3296":"P55H","3407":"V48G","3408":"V48A","3409":"V48F","3406":"R54G"},"clinical":{"2140":"T53A","2175":"T53I","2200":"P55R","2201":"P55L","2202":"P55S"},"experimental":{"3292":"T53P","3293":"T53N","3294":"P55T","3295":"P55A","3296":"P55H","3407":"V48G","3408":"V48A","3409":"V48F","3406":"R54G"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"2070":{"protein_sequence":{"accession":"CAC29732.1","sequence":"MSLAPVQVIGVLNVTDNSFSDGGRYLDPDDAVQHGLAMVAEGAAIVDVGGESTRPGAIRTDPRVELSRIVPVVKELAAQGITVSIDTTRADVARAALQSGARIVNDVSGGRADPAMAPLVAEAGVAWVLMHWRLMSAERPYEAPNYRDVVAEVRADLLAGVDQAVAAGVDPGSLVIDPGLGFAKTGQHNWALLNALPELVATGVPILLGASRKRFLGRLLAGADGAVRPPDGRETATAVISALAALHGAWGVRVHDVRASVDALKVVGAWLHAGPQIEKVRCDG"},"dna_sequence":{"accession":"AL450380.1","fmin":"296695","fmax":"297550","strand":"+","sequence":"GTGAGTTTGGCGCCAGTGCAGGTTATTGGGGTTTTGAACGTCACTGACAATTCGTTCTCAGATGGCGGACGTTACCTTGATCCTGACGATGCTGTCCAGCACGGCCTGGCAATGGTCGCGGAAGGCGCGGCGATTGTCGACGTCGGTGGCGAATCGACCCGGCCCGGTGCCATTAGGACCGATCCTCGAGTTGAACTCTCTCGTATCGTTCCTGTCGTAAAAGAACTTGCAGCACAGGGGATTACAGTAAGTATCGATACTACGCGCGCTGATGTTGCACGGGCGGCGCTGCAAAGCGGCGCACGGATCGTCAACGATGTGTCTGGTGGGCGAGCAGATCCCGCGATGGCTCCTCTGGTGGCTGAAGCCGGTGTTGCGTGGGTGTTGATGCACTGGCGACTGATGTCGGCTGAACGGCCGTATGAGGCTCCGAATTACCGCGACGTGGTGGCTGAAGTGCGTGCCGACCTACTGGCTGGTGTCGATCAGGCTGTGGCCGCAGGTGTTGATCCTGGGAGTCTAGTGATCGATCCCGGGCTTGGATTCGCCAAGACGGGACAGCACAATTGGGCGCTGCTGAATGCGTTACCGGAGTTGGTGGCTACTGGGGTCCCGATTCTACTTGGCGCCTCGCGTAAACGGTTCCTGGGTAGGTTATTAGCTGGGGCTGATGGCGCGGTACGACCGCCGGACGGACGTGAGACGGCGACCGCGGTGATTTCCGCACTTGCTGCCCTACACGGGGCTTGGGGTGTTCGGGTGCACGATGTGCGTGCCTCGGTCGACGCACTCAAGGTCGTCGGGGCTTGGCTGCATGCTGGGCCGCAGATTGAAAAGGTTAGATGTGATGGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40083","NCBI_taxonomy_name":"Mycobacterium leprae TN","NCBI_taxonomy_id":"272631"}}}},"ARO_accession":"3003389","ARO_id":"39973","ARO_name":"Mycobacterium leprae folP with mutation conferring resistance to dapsone","CARD_short_name":"Mlep_folP_DAO","ARO_description":"Dapsone inhibits bacterial synthesis of dihydrofolic acid by competing with with para-aminobenzoate for the active site of dihydropteroate synthetase. Point mutation within the Mycobacterium leprae folP gene results in lowered affinity of dapsone for folP.","ARO_category":{"39972":{"category_aro_accession":"3003388","category_aro_cvterm_id":"39972","category_aro_name":"dapsone resistant dihydropteroate synthase folP","category_aro_description":"Dapsone inhibits bacterial synthesis of dihydrofolic acid by competing with with para-aminobenzoate for the active site of dihydropteroate synthetase. Thus acts as a competitive inhibitor of folP. Point mutation within the folP gene results in lowered affinity of dapsone for folP.","category_aro_class_name":"AMR Gene Family"},"39996":{"category_aro_accession":"3003412","category_aro_cvterm_id":"39996","category_aro_name":"dapsone","category_aro_description":"Dapsone is a sulfone in which it inhibits folic acid synthesis, such as the dihydropteroate synthase.","category_aro_class_name":"Antibiotic"},"39985":{"category_aro_accession":"3003401","category_aro_cvterm_id":"39985","category_aro_name":"sulfone antibiotic","category_aro_description":"A sulfone active against a wide range of bacteria but mainly employed for its actions against mycobacterium laprae. Its mechanism of action  involves inhibition of folic acid synthesis in susceptible organisms.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"100":{"model_id":"100","model_name":"Mycobacterium tuberculosis ethA with mutation conferring resistance to ethionamide","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"15477":"M1Var","15503":"C403Y","15516":"S390F","15526":"N379D","15544":"A341V","15611":"R207G","15617":"V202G","15673":"T88I","15696":"S57Y","15715":"L35R","9504":"T342K","9510":"H281P","2496":"I338S","2497":"G385D","2498":"T392A","2499":"G413D","2500":"R463S","4143":"G43C","4144":"P51L","4145":"D58A","4150":"A381P","4151":"T186K","8346":"Y84D","2494":"G43S","2495":"E223K"},"WHO-R":{"15477":"M1Var","15480":"M1Var","15482":"M1Var","15485":"M1Var","15489":"M1Var","15492":"M1Var","15494":"M1Var","15497":"M1Var","15499":"M1Var","15504":"M1Var","15511":"M1Var","15515":"M1Var","15517":"M1Var","15522":"M1Var","15531":"M1Var","15533":"M1Var","15534":"M1Var","15537":"M1Var","15546":"M1Var","15554":"M1Var","15557":"M1Var","15558":"M1Var","15559":"M1Var","15561":"M1Var","15565":"M1Var","15566":"M1Var","15570":"M1Var","15571":"M1Var","15579":"M1Var","15581":"M1Var","15583":"M1Var","15587":"M1Var","15589":"M1Var","15593":"M1Var","15644":"M1Var","15645":"M1Var","15646":"M1Var","15647":"M1Var","15659":"M1Var","15661":"M1Var","15663":"M1Var","15666":"M1Var","15668":"M1Var","15670":"M1Var","15672":"M1Var","15674":"M1Var","15677":"M1Var","15682":"M1Var","15683":"M1Var","15685":"M1Var","15691":"M1Var","15704":"M1Var","15718":"M1Var","15720":"M1Var","15725":"M1Var","15503":"C403Y","15516":"S390F","15526":"N379D","15544":"A341V","15611":"R207G","15617":"V202G","15673":"T88I","15696":"S57Y","15715":"L35R","15594":"L35R","15599":"L35R","15602":"L35R","15603":"L35R","15608":"L35R","15613":"L35R","15618":"L35R","15639":"L35R","15640":"L35R","15743":"L35R"},"clinical":{"15477":"M1Var","15503":"C403Y","15516":"S390F","15526":"N379D","15544":"A341V","15611":"R207G","15617":"V202G","15673":"T88I","15696":"S57Y","15715":"L35R","9504":"T342K","9505":"N379D","9510":"H281P","2496":"I338S","2497":"G385D","2498":"T392A","2499":"G413D","2500":"R463S","4143":"G43C","4144":"P51L","4145":"D58A","4149":"T342K","4150":"A381P","4151":"T186K","8346":"Y84D","2494":"G43S","2495":"E223K"},"ReSeqTB-High":{"9504":"T342K","9505":"N379D","9510":"H281P","9506":"H281P","9508":"Y84D","9507":"E223K"},"Curated-R":{"2496":"I338S","2497":"G385D","2498":"T392A","2499":"G413D","2500":"R463S","4143":"G43C","4144":"P51L","4145":"D58A","4149":"T342K","4150":"A381P","4151":"T186K","8346":"Y84D","8312":"Y84D","2494":"G43S","2495":"E223K"}},"40394":{"param_type":"nonsense mutation","param_description":"A sequence change where, compared to a reference sequence, one codon is replaced by a termination codon through a nucleotide substitution. These are described as a substitution of the wildtype codon to a termination codon. Format is given as [wild type AA][position][Ter], for example Q42Ter where Q42 is a wildtype amino acid replaced by a premature termination codon.","param_type_id":"40394","param_value":{"15480":"E476Ter","15482":"Y461Ter","15485":"W455Ter","15489":"Q449Ter","15492":"Y438Ter","15494":"E427Ter","15497":"R421Ter","15499":"Y408Ter","15504":"S399Ter","15511":"K394Ter","15515":"W391Ter","15517":"Y386Ter","15522":"Y382Ter","15531":"Y369Ter","15533":"Q360Ter","15534":"Q359Ter","15537":"Q347Ter","15546":"E332Ter","15554":"C294Ter","15557":"L293Ter","15558":"R292Ter","15559":"Q291Ter","15561":"W289Ter","15565":"R279Ter","15566":"Y276Ter","15570":"Q271Ter","15571":"Q269Ter","15579":"W256Ter","15581":"Q254Ter","15583":"C253Ter","15587":"Y250Ter","15589":"Q246Ter","15593":"K241Ter","15644":"E155Ter","15645":"Y147Ter","15646":"Y143Ter","15647":"Y140Ter","15659":"E132Ter","15661":"C131Ter","15663":"Q121Ter","15666":"W116Ter","15668":"W109Ter","15670":"K103Ter","15672":"Y92Ter","15674":"K86Ter","15677":"Y84Ter","15682":"Q73Ter","15683":"W69Ter","15685":"R65Ter","15691":"Y60Ter","15704":"W45Ter","15718":"Y32Ter","15720":"Q24Ter","15725":"W21Ter","15594":"W240Ter","15599":"W228Ter","15602":"Q215Ter","15603":"Y211Ter","15608":"S208Ter","15613":"Q206Ter","15618":"S197Ter","15639":"W167Ter","15640":"Q165Ter","9508":"Y147Ter"}},"41339":{"param_type":"nucleotide substitution in promoter region","param_description":"A nucleotide sequence change where, compared to a reference sequence, one nucleotide is replaced by one other nucleotide in the promoter region of a gene. These substitutions are indicated as upstream of the reference sequence transcription initiation site. Format is given by [-][position][wildtype][>][mutation], e.g. -11t>c or -15g>Var where Var represents any possible substitution.","param_type_id":"41339","param_value":{"15743":"-7t>c","8312":"-11t>c"}},"40494":{"param_type":"frameshift mutation","param_description":"A frameshift is a sequence change between the translation initiation (start) and termination (stop) codon where, compared to a reference sequence, translation shifts to another reading frame as caused by nucleotide insertions and deletions. In ARO, these are annotated at the protein level with the first changed most N-terminal wildtype amino acid position. Format is given as [wildtype AA][position]fs, e.g. S531fs where S531 is a frameshifted coordinate beginning with codon 531. Termination may also be denoted as: Ter[position]fs.","param_type_id":"40494","param_value":{"9506":"P422fs","9507":"G11fs"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"900"}},"model_sequences":{"sequence":{"8813":{"protein_sequence":{"accession":"NP_218371.1","sequence":"MTEHLDVVIVGAGISGVSAAWHLQDRCPTKSYAILEKRESMGGTWDLFRYPGIRSDSDMYTLGFRFRPWTGRQAIADGKPILEYVKSTAAMYGIDRHIRFHHKVISADWSTAENRWTVHIQSHGTLSALTCEFLFLCSGYYNYDEGYSPRFAGSEDFVGPIIHPQHWPEDLDYDAKNIVVIGSGATAVTLVPALADSGAKHVTMLQRSPTYIVSQPDRDGIAEKLNRWLPETMAYTAVRWKNVLRQAAVYSACQKWPRRMRKMFLSLIQRQLPEGYDVRKHFGPHYNPWDQRLCLVPNGDLFRAIRHGKVEVVTDTIERFTATGIRLNSGRELPADIIITATGLNLQLFGGATATIDGQQVDITTTMAYKGMMLSGIPNMAYTVGYTNASWTLKADLVSEFVCRLLNYMDDNGFDTVVVERPGSDVEERPFMEFTPGYVLRSLDELPKQGSRTPWRLNQNYLRDIRLIRRGKIDDEGLRFAKRPAPVGV"},"dna_sequence":{"accession":"NC_000962.3","fmin":"4326003","fmax":"4327473","strand":"-","sequence":"ATGACCGAGCACCTCGACGTTGTCATCGTGGGCGCTGGAATCTCCGGTGTCAGCGCGGCCTGGCACCTGCAGGACCGTTGCCCGACCAAGAGCTACGCCATCCTGGAAAAGCGGGAATCCATGGGCGGCACCTGGGATTTGTTCCGTTATCCCGGAATTCGCTCCGACTCCGACATGTACACGCTAGGTTTCCGATTCCGTCCCTGGACCGGACGGCAGGCGATCGCCGACGGCAAGCCCATCCTCGAGTACGTCAAGAGCACCGCGGCCATGTATGGAATCGACAGGCATATCCGGTTCCACCACAAGGTGATCAGTGCCGATTGGTCGACCGCGGAAAACCGCTGGACCGTTCACATCCAAAGCCACGGCACGCTCAGCGCCCTCACCTGCGAATTCCTCTTTCTGTGCAGCGGCTACTACAACTACGACGAGGGCTACTCGCCGAGATTCGCCGGCTCGGAGGATTTCGTCGGGCCGATCATCCATCCGCAGCACTGGCCCGAGGACCTCGACTACGACGCTAAGAACATCGTCGTGATCGGCAGTGGCGCAACGGCGGTCACGCTCGTGCCGGCGCTGGCGGACTCGGGCGCCAAGCACGTCACGATGCTGCAGCGCTCACCCACCTACATCGTGTCGCAGCCAGACCGGGACGGCATCGCCGAGAAGCTCAACCGCTGGCTGCCGGAGACCATGGCCTACACCGCGGTACGGTGGAAGAACGTGCTGCGCCAGGCGGCCGTGTACAGCGCCTGCCAGAAGTGGCCACGGCGCATGCGGAAGATGTTCCTGAGCCTGATCCAGCGCCAGCTACCCGAGGGGTACGACGTGCGAAAGCACTTCGGCCCGCACTACAACCCCTGGGACCAGCGATTGTGCTTGGTGCCCAACGGCGACCTGTTCCGGGCCATTCGTCACGGGAAGGTCGAGGTGGTGACCGACACCATTGAACGGTTCACCGCGACCGGAATCCGGCTGAACTCAGGTCGCGAACTGCCGGCTGACATCATCATTACCGCAACGGGGTTGAACCTGCAGCTTTTTGGTGGGGCGACGGCGACTATCGACGGACAACAAGTGGACATCACCACGACGATGGCCTACAAGGGCATGATGCTTTCCGGCATCCCCAACATGGCCTACACGGTTGGCTACACCAATGCCTCCTGGACGCTGAAGGCCGACCTGGTGTCGGAGTTTGTCTGTCGCTTGTTGAATTACATGGACGACAACGGTTTTGACACCGTGGTCGTCGAGCGACCGGGCTCAGATGTCGAAGAGCGGCCCTTCATGGAGTTCACCCCAGGTTACGTGCTGCGCTCGCTGGACGAGCTGCCCAAGCAGGGTTCGCGTACACCGTGGCGCCTGAATCAGAACTACCTACGTGACATCCGGCTCATCCGGCGCGGCAAGATCGACGACGAGGGTCTGCGGTTCGCCAAAAGGCCTGCCCCGGTGGGGGTTTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3003458","ARO_id":"40051","ARO_name":"Mycobacterium tuberculosis ethA with mutation conferring resistance to ethionamide","CARD_short_name":"Mtub_ethA_ETO","ARO_description":"Mycobacterium tuberculosis ethA (Rv3854c) is a mono-oxygenase enzyme which activates the antibiotic ethionamide in vivo. Mutations in ethA confer resistance to ethionamide by modulating the activation and activity of the ethionamide prodrug.","ARO_category":{"40050":{"category_aro_accession":"3003457","category_aro_cvterm_id":"40050","category_aro_name":"ethionamide resistant ethA","category_aro_description":"Mutations that occurs on the ethA genes resulting in the inability to catalyzes the oxidation of ethionamide (ETH) to the corresponding sulfoxide (the active drug).","category_aro_class_name":"AMR Gene Family"},"40067":{"category_aro_accession":"3003474","category_aro_cvterm_id":"40067","category_aro_name":"ethionamide","category_aro_description":"Ethionamide is a second-line antitubercular agent that inhibits mycolic acid synthesis.","category_aro_class_name":"Antibiotic"},"45738":{"category_aro_accession":"3007156","category_aro_cvterm_id":"45738","category_aro_name":"thioamide antibiotic","category_aro_description":"A group of antibiotics possessing the thioamide functional group.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1323":{"model_id":"1323","model_name":"Salmonella serovars parE conferring resistance to fluoroquinolones","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"2227":"V461G"},"Curated-R":{"2227":"V461G"},"experimental":{"2227":"V461G"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"5465":{"protein_sequence":{"accession":"AAL22055.1","sequence":"MTQTYNADAIEVLTGLEPVRRRPGMYTDTTRPNHLGQEVIDNSVDEALAGHAKRVDVILHADQSLEVIDDGRGMPVDIHPEEGVPAVELILCRLHAGGKFSNKNYQFSGGLHGVGISVVNALSKRVEVTVRRDGQVYNIAFENGEKVQDLQVVGTCGKRNTGTSVHFWPDESFFDSPRFSVSRLMHVLKAKAVLCPGVEITFKDEVNNSEQRWCYQDGLNDYLGEAVNGLPTLPEKPFIGNFNGETEAVDWALLWLPEGGELLTESYVNLIPTMQGGTHVNGLRQGLLDAMREFCEYRNILPRGVKLSAEDIWDRCAYVLSVKMQDPQFAGQTKERLSSRQCAAFVSGVVKDAFSLWLNQNVQAAEQLAEMAIASAQRRLRAAKKVVRKKLTSGPALPGKLADCTAQDLNRTELFLVEGDSAGGSAKQARDREYQAIMPLKGKILNTWEVSSDEVLASQEVHDISVAIGIDPDSDDLSQLRYGKICILADADSDGLHIATLLCALFVRHFRALVKNGHVYVALPPLYRIDLGKEVYYALTEEEKAGVLEQLKRKKGKPNVQRFKGLGEMNPMQLRETTLDPNTRRLVQLTISDEDDQRTNAMMDMLLAKKRSEDRRNWLQEKGDLADLDV"},"dna_sequence":{"accession":"AE006468.2","fmin":"3343968","fmax":"3345861","strand":"-","sequence":"ATGACGCAAACTTATAACGCTGATGCCATTGAGGTACTCACTGGGCTTGAGCCGGTACGCCGCCGCCCGGGGATGTACACCGATACGACCCGCCCCAACCATTTGGGTCAGGAAGTGATTGATAATAGTGTGGATGAAGCACTGGCAGGTCACGCCAAACGCGTGGATGTCATTTTACATGCCGATCAATCGCTGGAAGTGATTGACGACGGACGCGGGATGCCGGTGGATATCCATCCGGAAGAGGGGGTTCCGGCGGTAGAACTGATCCTCTGTCGGCTTCATGCCGGCGGTAAATTCTCCAATAAGAACTATCAGTTCTCTGGTGGTCTGCATGGGGTGGGGATTTCGGTAGTAAATGCCCTGTCAAAGCGCGTGGAAGTGACCGTGCGCCGCGACGGTCAGGTCTATAACATCGCGTTTGAAAACGGCGAAAAAGTGCAGGATTTGCAGGTTGTCGGCACCTGCGGTAAACGTAATACTGGAACCAGCGTCCATTTCTGGCCGGACGAAAGTTTCTTCGACAGCCCGCGTTTTTCTGTCTCTCGCTTAATGCACGTTCTGAAAGCAAAAGCGGTGCTGTGTCCCGGCGTGGAAATCACTTTTAAAGATGAAGTGAATAACAGCGAGCAGCGCTGGTGCTACCAGGATGGTCTGAACGACTATCTGGGCGAAGCGGTAAACGGCCTGCCGACGCTGCCGGAAAAGCCGTTTATCGGTAATTTTAACGGTGAAACGGAAGCGGTTGACTGGGCGCTATTGTGGCTGCCGGAAGGCGGCGAATTACTGACGGAAAGCTACGTCAACCTGATCCCGACCATGCAGGGGGGGACGCACGTCAACGGTCTGCGCCAGGGCCTGCTCGACGCGATGCGCGAATTTTGCGAATACCGCAATATTCTGCCGCGCGGCGTCAAACTGTCGGCGGAAGATATCTGGGATCGCTGCGCTTATGTGCTTTCCGTGAAAATGCAGGACCCGCAATTTGCCGGGCAGACCAAAGAGCGTCTGTCGTCGCGTCAATGTGCGGCATTTGTTTCCGGCGTGGTGAAAGATGCCTTCAGCCTGTGGCTGAACCAGAACGTGCAGGCGGCGGAACAACTGGCAGAGATGGCGATTGCCAGCGCGCAGCGGCGACTGCGCGCCGCAAAAAAAGTGGTGCGCAAAAAGCTCACCAGCGGCCCGGCGTTGCCGGGGAAACTGGCGGACTGTACCGCGCAGGATCTTAATCGGACCGAGCTGTTCCTTGTGGAAGGGGATTCGGCGGGCGGTTCCGCCAAGCAGGCGCGCGATCGCGAATATCAGGCGATCATGCCGCTCAAAGGTAAGATCCTTAACACCTGGGAGGTCTCTTCCGATGAAGTGCTGGCCTCGCAAGAAGTGCATGATATTTCCGTGGCGATCGGTATCGATCCGGACAGCGACGATCTGAGTCAGCTGCGCTACGGCAAGATCTGTATCCTGGCGGATGCGGACTCCGATGGTTTGCATATCGCTACTCTGCTTTGCGCGCTGTTTGTCAGACACTTCCGCGCGCTGGTGAAGAATGGTCATGTCTACGTCGCGCTACCGCCGCTATACCGTATCGATTTGGGTAAAGAGGTCTATTACGCGCTGACGGAAGAAGAGAAGGCGGGCGTACTGGAACAACTGAAGCGTAAGAAAGGCAAGCCGAACGTACAGCGTTTCAAAGGCCTGGGAGAAATGAACCCGATGCAGTTACGCGAAACCACGCTTGATCCGAATACTCGCCGCCTGGTGCAGCTCACCATTAGCGATGAAGACGATCAGCGTACTAATGCGATGATGGATATGCTGCTGGCGAAGAAACGTTCTGAAGATCGACGCAACTGGCTACAGGAAAAAGGCGATCTCGCGGATCTCGACGTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35734","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Typhimurium str. LT2","NCBI_taxonomy_id":"99287"}}}},"ARO_accession":"3003317","ARO_id":"39901","ARO_name":"Salmonella serovars parE conferring resistance to fluoroquinolones","CARD_short_name":"Sser_parE_FLO","ARO_description":"Point mutation in Salmonella serovars parE resulting in fluoroquinolones resistance.","ARO_category":{"39897":{"category_aro_accession":"3003313","category_aro_cvterm_id":"39897","category_aro_name":"fluoroquinolone resistant parE","category_aro_description":"ParE is a subunit of topoisomerase IV, necessary for cell survival. Point mutations in ParE prevent fluoroquinolones from inhibiting DNA synthesis, thus conferring resistance.","category_aro_class_name":"AMR Gene Family"},"35942":{"category_aro_accession":"0000023","category_aro_cvterm_id":"35942","category_aro_name":"enoxacin","category_aro_description":"Enoxacin belongs to a group called fluoroquinolones. Its mode of action depends upon blocking bacterial DNA replication by binding itself to DNA gyrase and causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37004":{"category_aro_accession":"3000660","category_aro_cvterm_id":"37004","category_aro_name":"lomefloxacin","category_aro_description":"Lomefloxacin is a difluoropiperazinyl quinolone, sharing similar activities with other fluoroquinolones. It is used to treat urinary tract infections. Relative to other fluoroquinolones, it has a longer half life and has higher serum concentrations.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37007":{"category_aro_accession":"3000663","category_aro_cvterm_id":"37007","category_aro_name":"ofloxacin","category_aro_description":"Ofloxacin is a 6-fluoro, 7-piperazinyl quinolone with a methyl-substituted oxazine ring. It has a broad spectrum of activity including many enterobacteria and mycoplasma but most anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"37008":{"category_aro_accession":"3000664","category_aro_cvterm_id":"37008","category_aro_name":"trovafloxacin","category_aro_description":"Trovafloxacin is a trifluoroquinalone with a broad spectrum of activity that acts by inhibiting the uncoiling of supercoiled DNA. While potent against many Gram-positive and Gram-negative bacteria, it is less active against pseudomonads and Cl. difficile. It is usually taken as the prodrug trovafloxacin mesylate or alatrofloxacin mesylate for oral or intravenous administration, respectively.","category_aro_class_name":"Antibiotic"},"37009":{"category_aro_accession":"3000665","category_aro_cvterm_id":"37009","category_aro_name":"grepafloxacin","category_aro_description":"Grepafloxacin is a broad-spectrum antibacterial quinoline. It is no longer taken due to its high toxicity.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"37142":{"category_aro_accession":"3000762","category_aro_cvterm_id":"37142","category_aro_name":"pefloxacin","category_aro_description":"Pefloxacin is structurally and functionally similar to norfloxacin. It is poorly active against mycobacteria, while anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1671":{"model_id":"1671","model_name":"Salmonella serovars soxS with mutation conferring antibiotic resistance","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"2234":"E52K"},"Curated-R":{"2234":"E52K"},"clinical":{"2234":"E52K"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"215"}},"model_sequences":{"sequence":{"5363":{"protein_sequence":{"accession":"AAL23089.1","sequence":"MSHQQIIQTLIEWIDEHIDQPLNIDVVAKKSGYSKWYLQRMFRTVTHQTLGEYIRQRRLLLAAVELRTTERPIFDIAMDLGYVSQQTFSRVFRREFDRTPSDYRHRL"},"dna_sequence":{"accession":"AE006468.2","fmin":"4503985","fmax":"4504309","strand":"-","sequence":"ATGTCGCATCAGCAGATAATTCAGACCCTTATCGAATGGATTGATGAACATATCGACCAACCGCTAAACATTGATGTGGTGGCAAAAAAATCGGGCTACTCCAAGTGGTATTTGCAGCGGATGTTTCGTACGGTAACGCATCAAACATTAGGCGAGTATATTCGCCAGCGCCGTCTCCTGTTGGCGGCCGTTGAGCTACGAACGACCGAGCGCCCGATTTTTGATATCGCGATGGACCTGGGCTATGTATCGCAGCAAACCTTCTCGCGTGTATTCCGCCGCGAGTTCGATCGCACTCCCAGCGATTACCGTCACCGCCTGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35734","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Typhimurium str. LT2","NCBI_taxonomy_id":"99287"}}}},"ARO_accession":"3003383","ARO_id":"39967","ARO_name":"Salmonella serovars soxS with mutation conferring antibiotic resistance","CARD_short_name":"Sent_soxS_MULT","ARO_description":"SoxS is a global regulator that up-regulates the expression of AcrAB efflux genes. It also reduces OmpF expression to decrease cell membrane permeability.","ARO_category":{"36002":{"category_aro_accession":"0010001","category_aro_cvterm_id":"36002","category_aro_name":"ATP-binding cassette (ABC) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding\/hydrolysis to transport substrates across cell membranes.","category_aro_class_name":"AMR Gene Family"},"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"41445":{"category_aro_accession":"3004281","category_aro_cvterm_id":"41445","category_aro_name":"General Bacterial Porin with reduced permeability to beta-lactams","category_aro_description":"These are GBPs that are associated with decreased susceptibility to beta-lactams either through mutations in the porin protein, absence of the porin protein, or expression of the porin protein.","category_aro_class_name":"AMR Gene Family"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37084":{"category_aro_accession":"3000704","category_aro_cvterm_id":"37084","category_aro_name":"cefalotin","category_aro_description":"Cefalotin is a semisynthetic cephalosporin antibiotic activate against staphylococci. It is resistant to staphylococci beta-lactamases but hydrolyzed by enterobacterial beta-lactamases.","category_aro_class_name":"Antibiotic"},"37250":{"category_aro_accession":"3000870","category_aro_cvterm_id":"37250","category_aro_name":"triclosan","category_aro_description":"Triclosan is a common antibacterial agent added to many consumer products as a biocide.  It is an inhibitor of fatty acid biosynthesis by blocking enoyl-carrier protein reductase (FabI).","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"43746":{"category_aro_accession":"3005386","category_aro_cvterm_id":"43746","category_aro_name":"disinfecting agents and antiseptics","category_aro_description":"Disinfectants that can also interact with antimicrobial resistance mechanisms, e.g. molecule efflux, and thus are the targets of disinfectant resistance.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"},"36383":{"category_aro_accession":"3000244","category_aro_cvterm_id":"36383","category_aro_name":"reduced permeability to antibiotic","category_aro_description":"Reduction in permeability to antibiotic, generally through reduced production of porins, can provide resistance.","category_aro_class_name":"Resistance Mechanism"}}},"953":{"model_id":"953","model_name":"Enterococcus faecalis liaF mutant conferring daptomycin resistance","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"3862":"T194I"},"Curated-R":{"3862":"T194I","18554":"T194I","18553":"T194I"},"experimental":{"3862":"T194I"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"},"41344":{"param_type":"insertion mutation from peptide sequence","param_description":"A peptide sequence change between the translation initiation (start) and termination (stop) codon where, compared to the reference sequence, one or more amino acids are inserted. These represent in-frame insertions which do not result in frameshift variants and where the insertion is not a duplication of a sequence immediately N-terminal (5'), and are denoted with wildtype flanking residues. Format is given by [wildtype AA position]_[wildtype AA position]ins[AA sequence], e.g. K464_D465insE or P46_A47insYS.","param_type_id":"41344","param_value":{"18554":"R177_T178insI"}},"41342":{"param_type":"deletion mutation from peptide sequence","param_description":"A peptide sequence change between the translation initiation (start) and termination (stop) codon where, compared to a reference sequence, one or more amino acids are deleted and therefore are not present. These represent in-frame deletions which do not result in frameshift variants and may include multiple amino acids. Format is given by [wildtype AA][position]del for a single peptide deletion or [wildtype AA][position]_[wildtype AA][position]del for a deleted peptide range, e.g. K527del or Q517_N518del.","param_type_id":"41342","param_value":{"18553":"R177del"}}},"model_sequences":{"sequence":{"8887":{"protein_sequence":{"accession":"WP_002381168.1","sequence":"MNNPWRFFIVAEALLFILALWQIVHNPGLAVLLTIGVLLVAYVSRKASKTHFNNFQFVLGVVFIVIGAMNSTAVWFMLIFGVLFIGLKGFEISGVDIAERAPWRKKQMIMVETAAKEPKNGKRFKRRWFANERIGNNIYEWDDINIDLISGDTIIDLGNTLLPKEDNIIIIRKGFGRTRILVPLGVAILLEHSTFYGTVRFEEEKYQLKNESLKIYSNDYDTNLRRLKIMTNTLVGDVEVIRV"},"dna_sequence":{"accession":"NC_004668.1","fmin":"2790820","fmax":"2791552","strand":"-","sequence":"ATGAATAACCCTTGGCGCTTTTTTATCGTCGCAGAAGCATTACTTTTTATTCTGGCGTTATGGCAAATTGTACATAATCCTGGATTAGCTGTTTTATTAACAATTGGCGTTTTACTTGTGGCCTACGTTTCCAGGAAAGCATCTAAAACACATTTTAACAACTTTCAATTCGTCCTCGGCGTTGTTTTTATTGTCATTGGTGCAATGAATAGCACGGCTGTTTGGTTTATGTTGATTTTTGGCGTACTCTTTATCGGCTTAAAAGGCTTTGAGATTTCAGGCGTGGATATAGCTGAGCGAGCACCTTGGCGAAAAAAACAAATGATTATGGTGGAGACGGCGGCAAAAGAACCTAAAAATGGCAAACGGTTTAAACGCCGCTGGTTTGCCAACGAACGCATTGGTAACAATATCTATGAATGGGACGATATCAATATTGATTTAATCTCTGGGGACACCATTATTGATTTAGGTAATACGCTACTACCGAAAGAAGACAATATTATTATTATTCGTAAAGGTTTTGGCCGCACGCGAATTCTAGTGCCGTTAGGTGTAGCTATTTTGTTAGAACATTCAACTTTTTACGGAACGGTACGTTTTGAAGAAGAAAAATATCAATTGAAAAACGAATCATTAAAAATTTACAGCAATGATTATGATACCAATCTTCGTCGTTTGAAAATTATGACGAACACTTTAGTAGGAGATGTTGAGGTGATCCGTGTATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37592","NCBI_taxonomy_name":"Enterococcus faecalis V583","NCBI_taxonomy_id":"226185"}}}},"ARO_accession":"3003077","ARO_id":"39624","ARO_name":"Enterococcus faecalis liaF mutant conferring daptomycin resistance","CARD_short_name":"Efae_liaF_DAP","ARO_description":"liaF is an accessory protein that acts as a negative regulator of liaRS signal transduction pathway. Mutations confer daptomycin resistance.","ARO_category":{"41426":{"category_aro_accession":"3004262","category_aro_cvterm_id":"41426","category_aro_name":"daptomycin resistant liaF","category_aro_description":"Mutations to the liaF accessory protein that confer resistance to daptomycin.","category_aro_class_name":"AMR Gene Family"},"35985":{"category_aro_accession":"0000068","category_aro_cvterm_id":"35985","category_aro_name":"daptomycin","category_aro_description":"Daptomycin is a novel lipopeptide antibiotic used in the treatment of certain infections caused by Gram-positive organisms. Daptomycin interferes with the bacterial cell membrane, reducing membrane potential and inhibiting cell wall synthesis.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1135":{"model_id":"1135","model_name":"Staphylococcus aureus parE conferring resistance to aminocoumarin","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1250"},"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"2193":"R136G","4410":"G78S"},"Curated-R":{"2193":"R136G","4410":"G78S"},"clinical":{"2193":"R136G","4410":"G78S"}}},"model_sequences":{"sequence":{"3681":{"protein_sequence":{"accession":"BAA11086.1","sequence":"MNKQNNYSDDSIQVLEGLEAVRKRPGMYIGSTDKRGLHHLVYEIVDNSVDEVLNGYGNEIDVTINKDGSISIEDNGRGMPTGIHKSGKPTVEVIFTVLHAGGKFGQGGYKTSGGLHGVGASVVNALSEWLEVEIHRDGNIYHQSFKNGGSPSSGLVKKGKTKKTGTKVTFKPDDTIFKASTSFNFDVLSERLQESAFLLKNLKITLNDLRSGKERQEHYHYEEGIKEFVSYVNEGKEVLHDVATFSGEANGIEVDVAFQYNDQYSESILSFVNNVRTKDGGTHEVGFKTAMTRVFNDYARRINELKTKDKNLDGNDIREGLTAVVSVRIPEELLQFEGQTKSKLGTSEARSAVDSVVADKLPFYLEEKGQLSKSLVKKAIKAQQAREAARKAREDARSGKKNKRKDTLLSGKLTPAQSKNTEKNELYLVEGDSAGGSAKLGRDRKFQAILPLRGKVINTEKARLEDIFKNEEINTIIHTIGAGVGTDFKIEDSNYNRVIIMTDADTDGAHIQVLLLTFFFKYMKPLVQAGRVFIALPPLYKLEKGKGKTKRVEYAWTDEELNKLQKELGKGFTLQRYKGLGEMNPEQLWETTMNPETRTLIRVQVEDEVRSSKRVTTLMGDKVQPRREWIEKHVEFGMQEDQSILDNSEVQVLENDQFDEEEI"},"dna_sequence":{"accession":"D67075.1","fmin":"384","fmax":"2376","strand":"+","sequence":"ATGAATAAACAAAATAATTATTCAGATGATTCAATACAGGTTTTAGAGGGGTTAGAAGCAGTTCGTAAAAGACCTGGTATGTATATTGGATCAACTGATAAACGGGGATTACATCATCTAGTATATGAAATTGTCGATAACTCCGTCGATGAAGTATTGAATGGTTACGGTAACGAAATAGATGTAACAATTAATAAAGATGGTAGTATTTCTATAGAAGATAATGGACGTGGTATGCCAACAGGTATACATAAATCAGGTAAACCGACAGTCGAAGTTATCTTTACTGTTTTACATGCAGGAGGTAAATTTGGACAAGGCGGCTATAAAACTTCAGGTGGTCTTCACGGTGTTGGTGCTTCAGTTGTAAATGCATTGAGTGAATGGCTTGAAGTTGAAATCCATCGAGATGGTAATATATATCATCAAAGTTTTAAAAACGGTGGTTCGCCATCTTCTGGTTTAGTGAAAAAAGGTAAAACTAAGAAAACAGGTACCAAAGTAACATTTAAACCTGATGACACAATTTTTAAAGCATCTACATCATTTAATTTTGATGTTTTAAGTGAACGACTACAAGAGTCTGCGTTCTTATTGAAAAATTTAAAAATAACGCTTAATGATTTACGCAGTGGTAAAGAGCGTCAAGAGCATTACCATTATGAAGAAGGAATCAAAGAGTTTGTTAGTTATGTCAATGAAGGAAAAGAAGTTTTGCATGACGTGGCTACATTTTCAGGTGAAGCAAATGGTATAGAGGTAGACGTAGCTTTCCAATATAATGATCAATATTCAGAAAGTATTTTAAGTTTTGTAAATAATGTACGTACTAAAGATGGTGGTACACATGAAGTTGGTTTTAAAACAGCAATGACACGTGTATTTAATGATTATGCACGTCGTATTAATGAACTTAAAACAAAAGATAAAAACTTAGATGGTAATGATATTCGTGAAGGTTTAACAGCTGTTGTGTCTGTTCGTATTCCAGAAGAATTATTGCAATTTGAAGGACAAACGAAATCTAAATTGGGTACTTCTGAAGCTAGAAGTGCTGTTGATTCAGTTGTTGCAGACAAATTGCCATTCTATTTAGAAGAAAAAGGACAATTGTCTAAATCACTTGTGAAAAAAGCGATTAAAGCACAACAAGCAAGGGAAGCTGCACGTAAAGCTCGTGAAGATGCTCGTTCAGGTAAGAAAAACAAGCGTAAAGACACTTTGCTATCTGGTAAATTAACACCTGCACAAAGTAAAAACACTGAAAAAAATGAATTGTATTTAGTCGAAGGTGATTCTGCGGGAGGTTCAGCAAAACTTGGACGAGACCGCAAATTCCAAGCGATATTACCATTACGTGGTAAGGTAATTAATACAGAGAAAGCACGTCTAGAAGATATTTTTAAAAATGAAGAAATTAATACAATTATCCACACAATCGGGGCAGGCGTTGGTACTGACTTTAAAATTGAAGATAGTAATTATAATCGTGTAATTATTATGACTGATGCTGATACTGATGGTGCGCATATTCAAGTGCTATTGTTAACATTCTTCTTCAAATATATGAAACCGCTTGTTCAAGCAGGTCGTGTATTTATTGCTTTACCTCCACTTTATAAATTGGAAAAAGGTAAAGGCAAAACAAAGCGAGTTGAATACGCTTGGACAGACGAAGAGCTTAATAAATTGCAAAAAGAACTTGGTAAAGGCTTCACGTTACAACGTTACAAAGGTTTGGGTGAAATGAACCCTGAGCAATTATGGGAAACGACGATGAACCCAGAAACACGAACTTTAATTCGTGTACAAGTTGAAGATGAAGTGCGTTCATCTAAACGTGTAACAACATTAATGGGTGACAAAGTACAACCTAGACGTGAATGGATTGAAAAGCATGTTGAGTTTGGTATGCAAGAGGACCAAAGTATTTTAGATAATTCTGAAGTACAAGTGCTTGAAAATGATCAATTTGATGAGGAGGAAATCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35597","NCBI_taxonomy_name":"Staphylococcus aureus subsp. aureus RN4220","NCBI_taxonomy_id":"561307"}}}},"ARO_accession":"3003314","ARO_id":"39898","ARO_name":"Staphylococcus aureus parE conferring resistance to aminocoumarin","CARD_short_name":"Saur_parE_AMU","ARO_description":"Point mutation in Staphylococcus aureus parE resulting in aminocoumarin resistance.","ARO_category":{"36596":{"category_aro_accession":"3000457","category_aro_cvterm_id":"36596","category_aro_name":"aminocoumarin resistant parE","category_aro_description":"ParE is a subunit of topoisomerase IV, which decatenates and relaxes DNA to allow access to genes for transcription or translation. Point mutations in ParE prevent anticoumarin antibiotics from inhibiting DNA synthesis, thus conferring resistance.","category_aro_class_name":"AMR Gene Family"},"36250":{"category_aro_accession":"3000111","category_aro_cvterm_id":"36250","category_aro_name":"novobiocin","category_aro_description":"Novobiocin is an aminocoumarin antibiotic produced by Streptomyces spheroides and Streptomyces niveus, and binds DNA gyrase subunit B inhibiting ATP-dependent DNA supercoiling.","category_aro_class_name":"Antibiotic"},"36271":{"category_aro_accession":"3000132","category_aro_cvterm_id":"36271","category_aro_name":"clorobiocin","category_aro_description":"Clorobiocin is an aminocoumarin antibiotic produced by Streptomyces roseochromogenes, and binds DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling.","category_aro_class_name":"Antibiotic"},"36289":{"category_aro_accession":"3000150","category_aro_cvterm_id":"36289","category_aro_name":"coumermycin A1","category_aro_description":"Coumermycin A1 is an antibiotic produced by Streptomyces rishiriensis, and binds DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling.","category_aro_class_name":"Antibiotic"},"36242":{"category_aro_accession":"3000103","category_aro_cvterm_id":"36242","category_aro_name":"aminocoumarin antibiotic","category_aro_description":"Aminocoumarin antibiotics bind DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"570":{"model_id":"570","model_name":"Streptococcus pyogenes folP with mutation conferring resistance to sulfonamides","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"2116":"F25I"},"Curated-R":{"2116":"F25I"},"clinical":{"2116":"F25I"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"2095":{"protein_sequence":{"accession":"AAL97684.1","sequence":"MKIGRFVIEGNAAIMGILNVTPDSFSDGGSYTTVQKALDHVEQMIADGAKIIDVGGESTRPGCQFVSATDEIDRVVPVIKAIKENYDILISIDTYKTETARAALEAGADILNDVWAGLYDGQMFALAAEYDAPIILMHNQDEEVYQEVTQDVCDFLGNRAQAALDAGVPKNNIWIDPGFGFAKSVQQNTELLKGLDRVCQLGYPVLFGISRKRVVDALLGGNTKAKERDGATAALSAYALGKGCQIVRVHDVKANQDIVAVLSQLM"},"dna_sequence":{"accession":"AE009949.1","fmin":"878481","fmax":"879282","strand":"+","sequence":"ATGAAAATTGGAAGGTTTGTGATTGAGGGCAATGCGGCTATCATGGGGATTTTAAATGTGACTCCAGATTCTTTTTCAGATGGGGGGTCTTACACTACTGTGCAAAAAGCATTAGATCACGTTGAGCAAATGATTGCTGATGGTGCTAAAATCATCGACGTTGGTGGAGAATCAACACGTCCAGGTTGCCAATTTGTAAGCGCTACCGATGAAATTGACAGGGTGGTTCCTGTGATCAAGGCCATCAAAGAAAACTATGATATTCTAATCAGCATTGATACCTATAAAACCGAAACAGCTAGAGCAGCTTTAGAGGCGGGTGCCGATATTCTCAATGATGTTTGGGCAGGTTTGTACGACGGTCAAATGTTTGCCTTAGCAGCCGAGTACGATGCGCCTATCATCTTGATGCATAACCAAGACGAAGAAGTTTATCAAGAGGTAACACAAGACGTTTGTGATTTTCTAGGCAATAGAGCACAAGCAGCTCTTGATGCTGGCGTGCCAAAAAACAATATTTGGATTGATCCAGGATTTGGATTTGCCAAATCTGTTCAACAGAATACGGAGTTATTAAAAGGATTGGACCGCGTCTGTCAGTTGGGCTATCCTGTCTTGTTTGGTATTTCGAGAAAGCGTGTCGTAGATGCCTTGTTAGGCGGCAATACCAAAGCTAAAGAGCGAGACGGAGCGACAGCAGCCTTGTCTGCTTATGCCCTTGGAAAAGGCTGTCAGATTGTACGCGTACACGATGTCAAGGCTAATCAAGACATTGTGGCTGTGTTGAGCCAGTTGATGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40082","NCBI_taxonomy_name":"Streptococcus pyogenes MGAS8232","NCBI_taxonomy_id":"186103"}}}},"ARO_accession":"3003387","ARO_id":"39971","ARO_name":"Streptococcus pyogenes folP with mutation conferring resistance to sulfonamides","CARD_short_name":"Spyo_folP_SLF","ARO_description":"Point mutations in Streptococcus pyogenes dihydropteroate synthase folP prevent sulfonamide antibiotics from inhibiting its role in folate synthesis, thus conferring sulfonamide resistance.","ARO_category":{"39999":{"category_aro_accession":"3003415","category_aro_cvterm_id":"39999","category_aro_name":"sulfonamide resistant dihydropteroate synthase folP","category_aro_description":"Point mutations in dihydropteroate synthase folP prevent sulfonamide antibiotics from inhibiting its role in folate synthesis, thus conferring sulfonamide resistance.","category_aro_class_name":"AMR Gene Family"},"36463":{"category_aro_accession":"3000324","category_aro_cvterm_id":"36463","category_aro_name":"sulfadiazine","category_aro_description":"Sulfadiazine is a potent inhibitor of dihydropteroate synthase, interfering with the tetrahydrofolic biosynthesis pathway. Tetrahydrofolic acid is essential for folate synthesis, a precursor to many nucleotides and amino acids.","category_aro_class_name":"Antibiotic"},"36464":{"category_aro_accession":"3000325","category_aro_cvterm_id":"36464","category_aro_name":"sulfadimidine","category_aro_description":"Sulfadimidine is an alkaline sulfonamide antibiotic that inhibits dihydropteroate synthase, and enzyme in the tetrahydrofolic acid biosynthesis pathway. This interferes with the production of folate, which is a precursor to many amino acids and nucleotides.","category_aro_class_name":"Antibiotic"},"36466":{"category_aro_accession":"3000327","category_aro_cvterm_id":"36466","category_aro_name":"sulfadoxine","category_aro_description":"Sulfadoxine is an inhibitor of dihydropteroate synthase, interfering with the tetrahydrofolic biosynthesis pathway. Tetrahydrofolic acid is essential for folate synthesis, a precursor to many nucleotides and amino acids.","category_aro_class_name":"Antibiotic"},"36468":{"category_aro_accession":"3000329","category_aro_cvterm_id":"36468","category_aro_name":"sulfamethoxazole","category_aro_description":"Sulfamethoxazole is a sulfonamide antibiotic usually taken with trimethoprim, a diaminopyrimidine antibiotic. Sulfamethoxazole inhibits dihydropteroate synthase, essential to tetrahydrofolic acid biosynthesis. This pathway generates compounds used in the synthesis of many amino acids and nucleotides.","category_aro_class_name":"Antibiotic"},"36469":{"category_aro_accession":"3000330","category_aro_cvterm_id":"36469","category_aro_name":"sulfisoxazole","category_aro_description":"Sulfisoxazole is an inhibitor of dihydropteroate synthase, interfering with the tetrahydrofolic biosynthesis pathway. Tetrahydrofolic acid is essential for folate synthesis, a precursor to many nucleotides and amino acids.","category_aro_class_name":"Antibiotic"},"37027":{"category_aro_accession":"3000683","category_aro_cvterm_id":"37027","category_aro_name":"sulfacetamide","category_aro_description":"Sulfacetamide is a very soluable sulfonamide antibiotic previously used to treat urinary tract infections. Its relatively low activity and toxicity to those with Stevens-Johnson syndrome have reduced its use and availability.","category_aro_class_name":"Antibiotic"},"37028":{"category_aro_accession":"3000684","category_aro_cvterm_id":"37028","category_aro_name":"mafenide","category_aro_description":"Mafenide is a sulfonamide used topically for treating burns.","category_aro_class_name":"Antibiotic"},"37042":{"category_aro_accession":"3000698","category_aro_cvterm_id":"37042","category_aro_name":"sulfasalazine","category_aro_description":"Sulfasalazine is a derivative of the early sulfonamide sulfapyridine (salicylazosulfapyridine). It was developed to increase water solubility and is taken orally for ulcerative colitis.","category_aro_class_name":"Antibiotic"},"37043":{"category_aro_accession":"3000699","category_aro_cvterm_id":"37043","category_aro_name":"sulfamethizole","category_aro_description":"Sulfamethizole is a short-acting sulfonamide that inhibits dihydropteroate synthetase.","category_aro_class_name":"Antibiotic"},"36421":{"category_aro_accession":"3000282","category_aro_cvterm_id":"36421","category_aro_name":"sulfonamide antibiotic","category_aro_description":"Sulfonamides are broad spectrum, synthetic antibiotics that contain the sulfonamide group. Sulfonamides inhibit dihydropteroate synthase, which catalyzes the conversion of p-aminobenzoic acid to dihydropteroic acid as part of the tetrahydrofolic acid biosynthetic pathway. Tetrahydrofolic acid is essential for folate synthesis, a precursor of many nucleotides and amino acids. Many sulfamides are taken with trimethoprim, an inhibitor of dihydrofolate reductase, also disturbing the trihydrofolic acid synthesis pathway.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2116":{"model_id":"2116","model_name":"Pasteurella multocida 16S rRNA mutation conferring resistance to spectinomycin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"41093","param_value":"2700"},"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"12981":"c1194g"},"Curated-R":{"12981":"c1194g"},"clinical":{"12981":"c1194g"}}},"model_sequences":{"sequence":{"3252":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"NC_002663.1","fmin":"341426","fmax":"342977","strand":"+","sequence":"TTGAATTGAAGAGTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCTTAACACATGCAAGTCGAACGGTAGCAGGAAGAAAGCTTGCTTTCTTTGCTGACGAGTGGCGGACGGGTGAGTAATGCTTGGGAATCTGGCTTATGGAGGGGGATAACTGTGGGAAACTGCAGCTAATACCGCGTATTCTCTGAGGAGGAAAGGGTGGGACCTTAGGGCCACCTGCCATAAGATGAGCCCAAGTGGGATTAGGTAGTTGGTGGGGTAAAGGCCTACCAAGCCTGCGATCTCTAGCTGGTCTGAAAGGATGACCAGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCGCAATGGGGGGAACCCTGACGCAGCCATGCCGCGTGAATGAAGAAGGCCTTCGGGTTGTAAAGTTCTTTCGGTAATGAGGAAGGGATGTTGTTAAATAGATAGCATCATTGACGTTAATTACAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCGAGCGTTAATCGGAATAACTGGGCGTAAAGGGCACGCAGGCGGACTTTTAAGTGAGATGTGAAATCCCCGAGCTTAACTTGGGAACTGCATTTCAGACTGGGAGTCTAGAGTACTTTAGGGAGGGGTAGAATTCCACGTGTAGCGGTGAAATGCGTAGAGATGTGGAGGAATACCGAAGGCGAAGGCAGCCCCTTGGGAATGTACTGACGCTCATGTGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCTGTAAACGCTGTCGATTTGGGGATTGGGCTATATGCTTGGTGCCCGAAGCTAACGTGATAAATCGACCGCCTGGGGAGTACGGCCGCAAGGTTAAAACTCAAATGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGATGCAACGCGAAGAACCTTACCTACTCTTGACATCCTAAGAAGAGCTCAGAGATGAGCTTGTGCCTTCGGGAACTTAGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGAAATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCCTTTGTTGCCAGCGATTCGGTCGGGAACTCAAAGGAGACTGCCAGTGACAAACTGGAGGAAGGTGGGGATGACGTCAAGTCATCATGGCCCTTACGAGTAGGGCTACACACGTGCTACAATGGTGCATACAGAGGGCAGCGAGAGTGCGAGCTTGAGCGAATCTCAGAAAGTGCATCTAAGTCCGGATTGGAGTCTGCAACTCGACTCCATGAAGTCGGAATCGCTAGTAATCGCAAATCAGAATGTTGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCCGTACACCATGGGAGTGGGTTGTACCAGAAGTAGATAGCTTAACCTTCGGGAGGGCGTTTACCACGGTATGATTCATGACTGGGGTGAAGTCGTAACAAGGTAACCGTAGGGGAACCTGCGGTTGGATCACCTCCTTACCTAAAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39783","NCBI_taxonomy_name":"Pasteurella multocida 36950","NCBI_taxonomy_id":"1075089"}}}},"ARO_accession":"3003493","ARO_id":"40095","ARO_name":"Pasteurella multocida 16S rRNA mutation conferring resistance to spectinomycin","CARD_short_name":"Pmul_16S_SPT","ARO_description":"Point mutations in the helix 34 region of 16S rRNA of Pasteurella multocida can confer resistance to spectinomycin.","ARO_category":{"40277":{"category_aro_accession":"3003666","category_aro_cvterm_id":"40277","category_aro_name":"16s rRNA with mutation conferring resistance to aminoglycoside antibiotics","category_aro_description":"Point mutations in the 16S rRNA of bacteria can confer resistance to aminoglycosides.","category_aro_class_name":"AMR Gene Family"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2147":{"model_id":"2147","model_name":"Escherichia coli EF-Tu mutants conferring resistance to Enacyloxin IIa","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"3566":"A375T","3567":"G316D","3568":"Q124K","3569":"Q329H"},"Curated-R":{"3566":"A375T","3567":"G316D","3568":"Q124K","3569":"Q329H"},"clinical":{"3566":"A375T","3567":"G316D","3568":"Q124K","3569":"Q329H"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"5280":{"protein_sequence":{"accession":"AAC76364.1","sequence":"MSKEKFERTKPHVNVGTIGHVDHGKTTLTAAITTVLAKTYGGAARAFDQIDNAPEEKARGITINTSHVEYDTPTRHYAHVDCPGHADYVKNMITGAAQMDGAILVVAATDGPMPQTREHILLGRQVGVPYIIVFLNKCDMVDDEELLELVEMEVRELLSQYDFPGDDTPIVRGSALKALEGDAEWEAKILELAGFLDSYIPEPERAIDKPFLLPIEDVFSISGRGTVVTGRVERGIIKVGEEVEIVGIKETQKSTCTGVEMFRKLLDEGRAGENVGVLLRGIKREEIERGQVLAKPGTIKPHTKFESEVYILSKDEGGRHTPFFKGYRPQFYFRTTDVTGTIELPEGVEMVMPGDNIKMVVTLIHPIAMDDGLRFAIREGGRTVGAGVVAKVLG"},"dna_sequence":{"accession":"U00096.3","fmin":"3470144","fmax":"3471329","strand":"-","sequence":"GTGTCTAAAGAAAAATTTGAACGTACAAAACCGCACGTTAACGTTGGTACTATCGGCCACGTTGACCACGGTAAAACTACTCTGACCGCTGCAATCACCACCGTACTGGCTAAAACCTACGGCGGTGCTGCTCGTGCATTCGACCAGATCGATAACGCGCCGGAAGAAAAAGCTCGTGGTATCACCATCAACACTTCTCACGTTGAATACGACACCCCGACCCGTCACTACGCACACGTAGACTGCCCGGGGCACGCCGACTATGTTAAAAACATGATCACCGGTGCTGCTCAGATGGACGGCGCGATCCTGGTAGTTGCTGCGACTGACGGCCCGATGCCGCAGACTCGTGAGCACATCCTGCTGGGTCGTCAGGTAGGCGTTCCGTACATCATCGTGTTCCTGAACAAATGCGACATGGTTGATGACGAAGAGCTGCTGGAACTGGTTGAAATGGAAGTTCGTGAACTTCTGTCTCAGTACGACTTCCCGGGCGACGACACTCCGATCGTTCGTGGTTCTGCTCTGAAAGCGCTGGAAGGCGACGCAGAGTGGGAAGCGAAAATCCTGGAACTGGCTGGCTTCCTGGATTCTTATATTCCGGAACCAGAGCGTGCGATTGACAAGCCGTTCCTGCTGCCGATCGAAGACGTATTCTCCATCTCCGGTCGTGGTACCGTTGTTACCGGTCGTGTAGAACGCGGTATCATCAAAGTTGGTGAAGAAGTTGAAATCGTTGGTATCAAAGAGACTCAGAAGTCTACCTGTACTGGCGTTGAAATGTTCCGCAAACTGCTGGACGAAGGCCGTGCTGGTGAGAACGTAGGTGTTCTGCTGCGTGGTATCAAACGTGAAGAAATCGAACGTGGTCAGGTACTGGCTAAGCCGGGCACCATCAAGCCGCACACCAAGTTCGAATCTGAAGTGTACATTCTGTCCAAAGATGAAGGCGGCCGTCATACTCCGTTCTTCAAAGGCTACCGTCCGCAGTTCTACTTCCGTACTACTGACGTGACTGGTACCATCGAACTGCCGGAAGGCGTAGAGATGGTAATGCCGGGCGACAACATCAAAATGGTTGTTACCCTGATCCACCCGATCGCGATGGACGACGGTCTGCGTTTCGCAATCCGTGAAGGCGGCCGTACCGTTGGCGCGGGCGTTGTTGCTAAAGTTCTGGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36849","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. MG1655","NCBI_taxonomy_id":"511145"}}}},"ARO_accession":"3003370","ARO_id":"39954","ARO_name":"Escherichia coli EF-Tu mutants conferring resistance to Enacyloxin IIa","CARD_short_name":"Ecol_EFTu_ENC","ARO_description":"Sequence variants of Escherichia coli elongation factor Tu that confer resistance to Enacyloxin IIa.","ARO_category":{"37711":{"category_aro_accession":"3001312","category_aro_cvterm_id":"37711","category_aro_name":"elfamycin resistant EF-Tu","category_aro_description":"Sequence variants of elongation factor Tu that confer resistance to elfamycin antibiotics.","category_aro_class_name":"AMR Gene Family"},"37641":{"category_aro_accession":"3001242","category_aro_cvterm_id":"37641","category_aro_name":"enacyloxin IIa","category_aro_description":"Enacyloxin IIa is structurally distinct but acts in a similar mechanism to kirromycin-like elfamycins. It prohibits the transfer of the amino acid at the A site to the elongating peptide chain. It is most likely that the mechanism of action is that EF-Tu*GDP is locked in the EF-Tu*GTP form, and EF-Tu*GDP*aa-tRNA is immobilized on the ribosome. It is an open question whether enacyloxin IIa actually belongs to the kirromycin-like group of elfamycins due to their high similarity.","category_aro_class_name":"Antibiotic"},"37618":{"category_aro_accession":"3001219","category_aro_cvterm_id":"37618","category_aro_name":"elfamycin antibiotic","category_aro_description":"Elfamycins are molecules that inhibit bacterial elongation factor Tu (EF-Tu), a key protein which brings aminoacyl-tRNA (aa-tRNA) to the ribosome during protein synthesis. Elfamycins defined by their target (EF-Tu), rather than a conserved chemical backbone. Elfamycins follow two mechanisms to disrupt protein synthesis: 1. kirromycins and enacyloxin fix EF-Tu in the GTP bound conformation and lock EF-Tu onto the ribosome, and 2. pulvomycin and GE2270 cover the binding site of aa-tRNA disallowing EF-Tu from being charged with aa-tRNA. All elfamycins cause increased the affinity of EF-Tu for GTP.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2131":{"model_id":"2131","model_name":"Mycobacterium tuberculosis 16S rRNA mutation conferring resistance to streptomycin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"13273":"a514c","13288":"c517t","14687":"g878a","9846":"a1401g","2949":"g427c","3054":"a906g","4802":"c513t","4804":"c492t","4805":"a514t","7820":"c516t"},"CRyPTIC-R":{"13273":"a514c","13288":"c517t"},"clinical":{"13273":"a514c","13288":"c517t","14665":"a514c","14668":"c517t","14687":"g878a","9846":"a1401g","9848":"a514c","9849":"c517t","2911":"a1401g","2949":"g427c","3052":"a514c","3054":"a906g","4801":"c517t","4802":"c513t","4804":"c492t","4805":"a514t","7820":"c516t","12595":"g878a"},"WHO-R":{"14665":"a514c","14668":"c517t","14687":"g878a"},"ReSeqTB-Moderate":{"9846":"a1401g"},"ReSeqTB-High":{"9848":"a514c","9849":"c517t"},"Curated-R":{"2911":"a1401g","2949":"g427c","3052":"a514c","3054":"a906g","4801":"c517t","4802":"c513t","4804":"c492t","4805":"a514t","7820":"c516t","12595":"g878a"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"41093","param_value":"2700"}},"model_sequences":{"sequence":{"8766":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"NC_000962.3","fmin":"1471845","fmax":"1473382","strand":"+","sequence":"TTTTGTTTGGAGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGGAAAGGTCTCTTCGGAGATACTCGAGTGGCGAACGGGTGAGTAACACGTGGGTGATCTGCCCTGCACTTCGGGATAAGCCTGGGAAACTGGGTCTAATACCGGATAGGACCACGGGATGCATGTCTTGTGGTGGAAAGCGCTTTAGCGGTGTGGGATGAGCCCGCGGCCTATCAGCTTGTTGGTGGGGTGACGGCCTACCAAGGCGACGACGGGTAGCCGGCCTGAGAGGGTGTCCGGCCACACTGGGACTGAGATACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCGACGCCGCGTGGGGGATGACGGCCTTCGGGTTGTAAACCTCTTTCACCATCGACGAAGGTCCGGGTTCTCTCGGATTGACGGTAGGTGGAGAAGAAGCACCGGCCAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGTGCGAGCGTTGTCCGGAATTACTGGGCGTAAAGAGCTCGTAGGTGGTTTGTCGCGTTGTTCGTGAAATCTCACGGCTTAACTGTGAGCGTGCGGGCGATACGGGCAGACTAGAGTACTGCAGGGGAGACTGGAATTCCTGGTGTAGCGGTGGAATGCGCAGATATCAGGAGGAACACCGGTGGCGAAGGCGGGTCTCTGGGCAGTAACTGACGCTGAGGAGCGAAAGCGTGGGGAGCGAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGGTGGGTACTAGGTGTGGGTTTCCTTCCTTGGGATCCGTGCCGTAGCTAACGCATTAAGTACCCCGCCTGGGGAGTACGGCCGCAAGGCTAAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGCGGAGCATGTGGATTAATTCGATGCAACGCGAAGAACCTTACCTGGGTTTGACATGCACAGGACGCGTCTAGAGATAGGCGTTCCCTTGTGGCCTGTGTGCAGGTGGTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTCTCATGTTGCCAGCACGTAATGGTGGGGACTCGTGAGAGACTGCCGGGGTCAACTCGGAGGAAGGTGGGGATGACGTCAAGTCATCATGCCCCTTATGTCCAGGGCTTCACACATGCTACAATGGCCGGTACAAAGGGCTGCGATGCCGCGAGGTTAAGCGAATCCTTAAAAGCCGGTCTCAGTTCGGATCGGGGTCTGCAACTCGACCCCGTGAAGTCGGAGTCGCTAGTAATCGCAGATCAGCAACGCTGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACGTCATGAAAGTCGGTAACACCCGAAGCCAGTGGCCTAACCCTCGGGAGGGAGCTGTCGAAGGTGGGATCGGCGATTGGGACGAAGTCGTAACAAGGTAGCCGTACCGGAAGGTGCGGCTGGATCACCTCCTTTCT","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3003480","ARO_id":"40076","ARO_name":"Mycobacterium tuberculosis 16S rRNA mutation conferring resistance to streptomycin","CARD_short_name":"Mtub_16S_STR","ARO_description":"Point mutations within the 530 loop of the 16S rRNA of Mycobacterium tuberculosis can result in resistance against streptomycin. These mutations do not directly inhibit the binding of streptomycin, but is hypothesized that they interfere with conformational perturbations that account for streptomycin's action on the ribosome.","ARO_category":{"40277":{"category_aro_accession":"3003666","category_aro_cvterm_id":"40277","category_aro_name":"16s rRNA with mutation conferring resistance to aminoglycoside antibiotics","category_aro_description":"Point mutations in the 16S rRNA of bacteria can confer resistance to aminoglycosides.","category_aro_class_name":"AMR Gene Family"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3301":{"model_id":"3301","model_name":"LnuP","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"5200":{"protein_sequence":{"accession":"ACS83559.1","sequence":"MIGINDACEILSWAYNNNIEIWLDGGWGVDALLGKETRQHNDIDLFVEEKNYNKFIEIIKNKGFNEIVVEYTSEVHTIWSDNKLRIIDLHMFKDNCDGTICYEGEVFQKNIFDGVGKIGNIMVSCINAKNQVLFHLGYEFGESDIHDVKLLCKEFNIPIPKEYENF"},"dna_sequence":{"accession":"FJ589781.1","fmin":"1302","fmax":"1803","strand":"+","sequence":"GTGATTGGAATAAATGATGCTTGTGAAATATTGAGTTGGGCATATAATAATAATATAGAAATATGGTTAGATGGTGGTTGGGGTGTAGATGCTTTACTTGGAAAAGAAACACGTCAGCATAATGACATTGATTTATTTGTAGAAGAAAAAAACTATAATAAATTTATTGAAATAATTAAAAATAAAGGATTTAATGAAATTGTAGTGGAGTATACAAGTGAAGTGCATACTATTTGGTCTGATAATAAATTACGAATTATTGATTTACACATGTTTAAAGATAACTGTGATGGAACCATATGTTATGAAGGCGAAGTTTTTCAAAAAAATATATTCGATGGTGTTGGAAAAATAGGAAATATTATGGTTTCTTGTATAAATGCTAAAAATCAAGTCTTATTTCACTTAGGGTATGAATTTGGAGAAAGTGATATTCATGATGTAAAATTATTATGTAAAGAATTTAACATTCCGATACCTAAAGAATATGAAAATTTTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36812","NCBI_taxonomy_name":"Clostridium perfringens","NCBI_taxonomy_id":"1502"}}}},"ARO_accession":"3004601","ARO_id":"42534","ARO_name":"LnuP","CARD_short_name":"LnuP","ARO_description":"LnuP is a lincosamide nucleotidyltransferase major efflux facilitator.","ARO_category":{"36360":{"category_aro_accession":"3000221","category_aro_cvterm_id":"36360","category_aro_name":"lincosamide nucleotidyltransferase (LNU)","category_aro_description":"Resistance to the lincosamide antibiotic by ATP-dependent modification of the 3' and\/or 4'-hydroxyl groups of the methylthiolincosamide sugar.","category_aro_class_name":"AMR Gene Family"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1558":{"model_id":"1558","model_name":"Bacillus subtilis mprF","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1650"}},"model_sequences":{"sequence":{"8183":{"protein_sequence":{"accession":"CAX52582.1","sequence":"MLIKKNALSILKIVFPIAVLLFVIYQSKKELTNLSFKRTLMVINGLERTDLFMLVLIGLLAVAAMSLYDYVLKYSLRLSITNGKVFRVSWIANSFNNVLGFGGLAGVGLRMMFYKEHTKDHKALVKGIAWLTSSMLLGLSVFSIFVAARVLPVDEVIHEKPWLWAVVIGFALILPLSLAVSKIKDRKAGDEENADKVKNPIFAYIGASVVEWLMAGTVIYFALFAMGIHADIRYVFGVFVIAAIGGMISLVPGGFGSFDLLFLLGMEQLGYHQEAIVTSIVLYRLAYSFIPFILGLFFAAGDLTENTMKRLETNPRIAPAIETTNVLLVVQRAVLVRILQGSLSLIVFVAGLIVLASVSLPIDRLTVIPHIPRPALLLFNGLSLSSALILLILPIELYKRTKRSYTMAITALVGGFVFSFLKGLNISAIFVLPMIIVLLVLLKKQFVREQASYTLGQLIFAVALFTVALFNYNLIAGFIWDRMKKVLRHEYFVHSTSHITHATIMAIIIVPLFFLIFTVVYHKRTKPIGEKADPERLAAFLNEKGGNALSHLGFLGDKRFYFSSDGNALLLFGKIARRLVVLGDPSGQRESFPLVLEEFLNEAHQKGFSVLFYQIEREDMALYHDFGYNFFKLGEEAYVDLNTFTLTGKKKAGLRAINNRFEREEYTFHVDHPPFSDAFLEELKQISDEWLGSKKEKGFSLGFFDPSYLQKAPIAYMKNAEGEIVAFANVMPMYQEGEISVDLMRYRGDAPNGIMDALFIRMFLWAKEEGCTSFNMGMAPLANVGTAFTSFWSERFAAVIFNNVRYMYSFSGLRAFKEKYKPEWRGKYLAYRKNRSLSVTMFLVTRLIGKSKKDSV"},"dna_sequence":{"accession":"AL009126.3","fmin":"916777","fmax":"919348","strand":"+","sequence":"TTGCTGATTAAAAAGAATGCTTTATCAATATTAAAAATCGTTTTTCCTATTGCTGTTTTGCTATTTGTTATTTATCAATCGAAAAAAGAACTGACAAATCTGTCATTCAAACGTACGCTCATGGTCATCAACGGACTGGAACGAACGGATTTATTCATGCTTGTGTTGATCGGCTTGCTGGCTGTTGCGGCTATGTCGCTGTATGATTACGTCCTGAAGTACTCACTGCGCCTATCGATCACAAACGGAAAAGTTTTCAGGGTTTCCTGGATCGCCAATTCATTTAATAATGTGTTGGGATTCGGCGGTTTAGCCGGAGTCGGGTTAAGAATGATGTTCTATAAGGAGCATACGAAAGACCATAAGGCACTCGTGAAAGGAATCGCCTGGCTCACATCATCTATGCTGCTCGGATTATCTGTTTTCAGCATTTTCGTTGCTGCGAGAGTGCTGCCAGTTGATGAAGTGATTCATGAGAAGCCTTGGCTGTGGGCGGTCGTTATCGGTTTTGCACTGATATTGCCGTTATCTTTAGCGGTGTCCAAAATAAAAGACCGCAAAGCTGGGGACGAAGAGAATGCGGATAAAGTGAAAAATCCGATTTTCGCATATATTGGAGCTTCAGTTGTTGAATGGCTCATGGCCGGGACCGTCATCTATTTTGCTTTGTTCGCTATGGGCATTCATGCAGATATCAGGTATGTGTTCGGGGTGTTCGTCATTGCGGCGATCGGAGGAATGATCAGCCTCGTGCCGGGCGGCTTCGGCTCGTTTGACCTTTTATTTTTGCTGGGGATGGAGCAGCTTGGCTATCATCAAGAGGCCATCGTTACTTCTATTGTGTTGTACAGGCTCGCCTACTCATTTATCCCATTTATCTTGGGACTGTTCTTTGCCGCCGGCGACCTGACGGAAAATACAATGAAGCGGCTCGAAACGAACCCGCGCATCGCACCGGCAATTGAGACGACAAACGTTCTGCTTGTTGTTCAGCGTGCGGTATTAGTGAGAATTTTGCAAGGCTCGCTTTCCCTTATTGTGTTCGTAGCAGGTCTGATTGTCTTGGCCTCAGTTTCCTTGCCGATTGACAGGCTGACGGTTATACCGCACATTCCGCGCCCGGCGCTTTTGCTGTTCAACGGCCTGTCCTTAAGCTCAGCGCTCATTCTGCTCATTTTGCCGATCGAGCTTTATAAACGGACAAAACGTTCCTACACGATGGCCATTACAGCGCTTGTCGGCGGCTTTGTGTTCAGCTTTTTAAAAGGGCTTAACATCAGCGCGATATTCGTACTGCCGATGATTATCGTATTGCTTGTGCTATTGAAAAAACAATTTGTCCGCGAACAGGCATCCTATACACTGGGACAATTGATATTCGCTGTGGCGCTGTTTACTGTGGCGCTCTTTAACTACAATCTGATCGCGGGCTTTATTTGGGACCGGATGAAGAAGGTGCTGCGTCACGAATATTTCGTCCACAGCACCTCGCATATTACACATGCAACCATCATGGCGATCATCATTGTGCCGCTGTTCTTCTTGATATTTACAGTGGTCTATCATAAGAGAACGAAACCGATCGGAGAGAAAGCTGACCCTGAGCGTCTTGCTGCGTTTCTCAATGAAAAAGGCGGCAACGCGCTGAGCCATCTTGGTTTTCTTGGAGATAAGCGGTTTTATTTTTCTAGCGATGGAAATGCACTGCTTCTGTTTGGGAAAATCGCCAGAAGGCTGGTCGTGCTCGGCGATCCATCTGGCCAAAGAGAATCATTCCCGCTCGTGCTGGAAGAATTTCTGAACGAAGCGCATCAGAAGGGATTCAGTGTTTTGTTCTATCAAATTGAACGAGAGGACATGGCGCTGTATCACGATTTTGGCTACAACTTCTTTAAATTGGGTGAGGAAGCATATGTAGATTTAAATACATTTACCTTGACTGGGAAGAAAAAAGCCGGCCTTCGGGCAATCAATAACCGCTTTGAGCGGGAGGAGTATACTTTCCATGTGGATCATCCCCCATTTTCTGATGCGTTTTTGGAGGAGCTGAAGCAAATCTCAGACGAATGGCTCGGCTCGAAAAAAGAGAAGGGATTCTCGCTCGGATTTTTTGATCCTTCCTATTTACAGAAAGCGCCGATCGCCTATATGAAAAATGCAGAAGGAGAGATCGTTGCATTCGCAAATGTCATGCCGATGTACCAGGAAGGAGAGATATCGGTCGATCTGATGCGCTATCGCGGCGACGCTCCAAATGGCATTATGGACGCATTGTTTATCCGTATGTTTTTATGGGCAAAGGAAGAGGGCTGTACGTCATTTAATATGGGGATGGCACCCTTGGCCAATGTCGGCACTGCCTTTACATCCTTCTGGTCCGAAAGGTTTGCCGCTGTCATTTTTAATAATGTCAGATACATGTACAGTTTCAGCGGCCTAAGAGCCTTTAAAGAAAAATATAAACCGGAGTGGCGAGGGAAATACTTAGCGTATCGGAAAAACAGATCTCTTTCTGTCACCATGTTCCTCGTTACACGTCTGATTGGCAAAAGCAAAAAAGACTCCGTCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39579","NCBI_taxonomy_name":"Bacillus subtilis subsp. subtilis str. 168","NCBI_taxonomy_id":"224308"}}}},"ARO_accession":"3003324","ARO_id":"39908","ARO_name":"Bacillus subtilis mprF","CARD_short_name":"Bsub_mprF","ARO_description":"MprF is a integral membrane protein that modifies the negatively-charged phosphatidylglycerol on the membrane surface. This confers resistance to cationic peptides that disrupt the cell membrane, including defensins. Additionally, large-scale mutations causing loss of function of the gene result in increased susceptibility to daptomycin.","ARO_category":{"37243":{"category_aro_accession":"3000863","category_aro_cvterm_id":"37243","category_aro_name":"defensin resistant mprF","category_aro_description":"MprF is a integral membrane protein that modifies the negatively-charged phosphatidylglycerol on the membrane surface of both Gram-positive and Gram-negative bacteria. This confers resistance to cationic peptides that disrupt the cell membrane, including defensins.","category_aro_class_name":"AMR Gene Family"},"37037":{"category_aro_accession":"3000693","category_aro_cvterm_id":"37037","category_aro_name":"defensin","category_aro_description":"Defensins are natural cationic peptides that have antibiotic properties. It is part of the innate immune system of plants and animals.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"821":{"model_id":"821","model_name":"Mycobacterium tuberculosis embB with mutation conferring resistance to rifampicin","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"2649":"Y319D","2650":"Y333H"},"Curated-R":{"2649":"Y319D","2650":"Y333H"},"clinical":{"2649":"Y319D","2650":"Y333H"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"2000"}},"model_sequences":{"sequence":{"8806":{"protein_sequence":{"accession":"NP_218312.1","sequence":"MTQCASRRKSTPNRAILGAFASARGTRWVATIAGLIGFVLSVATPLLPVVQTTAMLDWPQRGQLGSVTAPLISLTPVDFTATVPCDVVRAMPPAGGVVLGTAPKQGKDANLQALFVVVSAQRVDVTDRNVVILSVPREQVTSPQCQRIEVTSTHAGTFANFVGLKDPSGAPLRSGFPDPNLRPQIVGVFTDLTGPAPPGLAVSATIDTRFSTRPTTLKLLAIIGAIVATVVALIALWRLDQLDGRGSIAQLLLRPFRPASSPGGMRRLIPASWRTFTLTDAVVIFGFLLWHVIGANSSDDGYILGMARVADHAGYMSNYFRWFGSPEDPFGWYYNLLALMTHVSDASLWMRLPDLAAGLVCWLLLSREVLPRLGPAVEASKPAYWAAAMVLLTAWMPFNNGLRPEGIIALGSLVTYVLIERSMRYSRLTPAALAVVTAAFTLGVQPTGLIAVAALVAGGRPMLRILVRRHRLVGTLPLVSPMLAAGTVILTVVFADQTLSTVLEATRVRAKIGPSQAWYTENLRYYYLILPTVDGSLSRRFGFLITALCLFTAVFIMLRRKRIPSVARGPAWRLMGVIFGTMFFLMFTPTKWVHHFGLFAAVGAAMAALTTVLVSPSVLRWSRNRMAFLAALFFLLALCWATTNGWWYVSSYGVPFNSAMPKIDGITVSTIFFALFAIAAGYAAWLHFAPRGAGEGRLIRALTTAPVPIVAGFMAAVFVASMVAGIVRQYPTYSNGWSNVRAFVGGCGLADDVLVEPDTNAGFMKPLDGDSGSWGPLGPLGGVNPVGFTPNGVPEHTVAEAIVMKPNQPGTDYDWDAPTKLTSPGINGSTVPLPYGLDPARVPLAGTYTTGAQQQSTLVSAWYLLPKPDDGHPLVVVTAAGKIAGNSVLHGYTPGQTVVLEYAMPGPGALVPAGRMVPDDLYGEQPKAWRNLRFARAKMPADAVAVRVVAEDLSLTPEDWIAVTPPRVPDLRSLQEYVGSTQPVLLDWAVGLAFPCQQPMLHANGIAEIPKFRITPDYSAKKLDTDTWEDGTNGGLLGITDLLLRAHVMATYLSRDWARDWGSLRKFDTLVDAPPAQLELGTATRSGLWSPGKIRIGP"},"dna_sequence":{"accession":"NC_000962.3","fmin":"4246513","fmax":"4249810","strand":"+","sequence":"ATGACACAGTGCGCGAGCAGACGCAAAAGCACCCCAAATCGGGCGATTTTGGGGGCTTTTGCGTCTGCTCGCGGGACGCGCTGGGTGGCCACCATCGCCGGGCTGATTGGCTTTGTGTTGTCGGTGGCGACGCCGCTGCTGCCCGTCGTGCAGACCACCGCGATGCTCGACTGGCCACAGCGGGGGCAACTGGGCAGCGTGACCGCCCCGCTGATCTCGCTGACGCCGGTCGACTTTACCGCCACCGTGCCGTGCGACGTGGTGCGCGCCATGCCACCCGCGGGCGGGGTGGTGCTGGGCACCGCACCCAAGCAAGGCAAGGACGCCAATTTGCAGGCGTTGTTCGTCGTCGTCAGCGCCCAGCGCGTGGACGTCACCGACCGCAACGTGGTGATCTTGTCCGTGCCGCGCGAGCAGGTGACGTCCCCGCAGTGTCAACGCATCGAGGTCACCTCTACCCACGCCGGCACCTTCGCCAACTTCGTCGGGCTCAAGGACCCGTCGGGCGCGCCGCTGCGCAGCGGCTTCCCCGACCCCAACCTGCGCCCGCAGATTGTCGGGGTGTTCACCGACCTGACCGGGCCCGCGCCGCCCGGGCTGGCGGTCTCGGCGACCATCGACACCCGGTTCTCCACCCGGCCGACCACGCTGAAACTGCTGGCGATCATCGGGGCGATCGTGGCCACCGTCGTCGCACTGATCGCGTTGTGGCGCCTGGACCAGTTGGACGGGCGGGGCTCAATTGCCCAGCTCCTCCTCAGGCCGTTCCGGCCTGCATCGTCGCCGGGCGGCATGCGCCGGCTGATTCCGGCAAGCTGGCGCACCTTCACCCTGACCGACGCCGTGGTGATATTCGGCTTCCTGCTCTGGCATGTCATCGGCGCGAATTCGTCGGACGACGGCTACATCCTGGGCATGGCCCGAGTCGCCGACCACGCCGGCTACATGTCCAACTATTTCCGCTGGTTCGGCAGCCCGGAGGATCCCTTCGGCTGGTATTACAACCTGCTGGCGCTGATGACCCATGTCAGCGACGCCAGTCTGTGGATGCGCCTGCCAGACCTGGCCGCCGGGCTAGTGTGCTGGCTGCTGCTGTCGCGTGAGGTGCTGCCCCGCCTCGGGCCGGCGGTGGAGGCCAGCAAACCCGCCTACTGGGCGGCGGCCATGGTCTTGCTGACCGCGTGGATGCCGTTCAACAACGGCCTGCGGCCGGAGGGCATCATCGCGCTCGGCTCGCTGGTCACCTATGTGCTGATCGAGCGGTCCATGCGGTACAGCCGGCTCACACCGGCGGCGCTGGCCGTCGTTACCGCCGCATTCACACTGGGTGTGCAGCCCACCGGCCTGATCGCGGTGGCCGCGCTGGTGGCCGGCGGCCGCCCGATGCTGCGGATCTTGGTGCGCCGTCATCGCCTGGTCGGCACGTTGCCGTTGGTGTCGCCGATGCTGGCCGCCGGCACCGTCATCCTGACCGTGGTGTTCGCCGACCAGACCCTGTCAACGGTGTTGGAAGCCACCAGGGTTCGCGCCAAAATCGGGCCGAGCCAGGCGTGGTATACCGAGAACCTGCGTTACTACTACCTCATCCTGCCCACCGTCGACGGTTCGCTGTCGCGGCGCTTCGGCTTTTTGATCACCGCGCTATGCCTGTTCACCGCGGTGTTCATCATGTTGCGGCGCAAGCGAATTCCCAGCGTGGCCCGCGGACCGGCGTGGCGGCTGATGGGCGTCATCTTCGGCACCATGTTCTTCCTGATGTTCACGCCCACCAAGTGGGTGCACCACTTCGGGCTGTTCGCCGCCGTAGGGGCGGCGATGGCCGCGCTGACGACGGTGTTGGTATCCCCATCGGTGCTGCGCTGGTCGCGCAACCGGATGGCGTTCCTGGCGGCGTTATTCTTCCTGCTGGCGTTGTGTTGGGCCACCACCAACGGCTGGTGGTATGTCTCCAGCTACGGTGTGCCGTTCAACAGCGCGATGCCGAAGATCGACGGGATCACAGTCAGCACAATCTTTTTCGCCCTGTTTGCGATCGCCGCCGGCTATGCGGCCTGGCTGCACTTCGCGCCCCGCGGCGCCGGCGAAGGGCGGCTGATCCGCGCGCTGACGACAGCCCCGGTACCGATCGTGGCCGGTTTCATGGCGGCGGTGTTCGTCGCGTCCATGGTGGCCGGGATCGTGCGACAGTACCCGACCTACTCCAACGGCTGGTCCAACGTGCGGGCGTTTGTCGGCGGCTGCGGACTGGCCGACGACGTACTCGTCGAGCCTGATACCAATGCGGGTTTCATGAAGCCGCTGGACGGCGATTCGGGTTCTTGGGGCCCCTTGGGCCCGCTGGGTGGAGTCAACCCGGTCGGCTTCACGCCCAACGGCGTACCGGAACACACGGTGGCCGAGGCGATCGTGATGAAACCCAACCAGCCCGGCACCGACTACGACTGGGATGCGCCGACCAAGCTGACGAGTCCTGGCATCAATGGTTCTACGGTGCCGCTGCCCTATGGGCTCGATCCCGCCCGGGTACCGTTGGCAGGCACCTACACCACCGGCGCACAGCAACAGAGCACACTCGTCTCGGCGTGGTATCTCCTGCCTAAGCCGGACGACGGGCATCCGCTGGTCGTGGTGACCGCCGCGGGCAAGATCGCCGGCAACAGCGTGCTGCACGGGTACACCCCCGGGCAGACTGTGGTGCTCGAATACGCCATGCCGGGACCCGGAGCGCTGGTACCCGCCGGGCGGATGGTGCCCGACGACCTATACGGAGAGCAGCCCAAGGCGTGGCGCAACCTGCGCTTCGCCCGAGCAAAGATGCCCGCCGATGCCGTCGCGGTCCGGGTGGTGGCCGAGGATCTGTCGCTGACACCGGAGGACTGGATCGCGGTGACCCCGCCGCGGGTACCGGACCTGCGCTCACTGCAGGAATATGTGGGCTCGACGCAGCCGGTGCTGCTGGACTGGGCGGTCGGTTTGGCCTTCCCGTGCCAGCAGCCGATGCTGCACGCCAATGGCATCGCCGAAATCCCGAAGTTCCGCATCACACCGGACTACTCGGCTAAGAAGCTGGACACCGACACGTGGGAAGACGGCACTAACGGCGGCCTGCTCGGGATCACCGACCTGTTGCTGCGGGCCCACGTCATGGCCACCTACCTGTCCCGCGACTGGGCCCGCGATTGGGGTTCCCTGCGCAAGTTCGACACCCTGGTCGATGCCCCTCCCGCCCAGCTCGAGTTGGGCACCGCGACCCGCAGCGGCCTGTGGTCACCGGGCAAGATCCGAATTGGTCCATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3003465","ARO_id":"40058","ARO_name":"Mycobacterium tuberculosis embB with mutation conferring resistance to rifampicin","CARD_short_name":"Mtub_embB_RIF","ARO_description":"Specific mutations that occurs on Mycobacterium tuberculosis embB causing it to be rifampicin resistant.","ARO_category":{"40057":{"category_aro_accession":"3003464","category_aro_cvterm_id":"40057","category_aro_name":"rifamycin-resistant arabinosyltransferase","category_aro_description":"Arabinosyl transferases allow for the polymerization of arabinose to form arabinan. Arabanan is required for formation of mycobacterial cell walls and arabinosyltransferases are targets of the drug ethambutol. Mutations in these genes can confer resistance to rifampicin.","category_aro_class_name":"AMR Gene Family"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1001":{"model_id":"1001","model_name":"Staphylococcus aureus mprF with mutation conferring resistance to daptomycin","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"2206":"S295L","2207":"G61V","2208":"S337L","2210":"P314L","2211":"T345I","2212":"T345A","3609":"I420N","3613":"T345K","3614":"T472K","3615":"M347R","3616":"L341S","3617":"V351E","2209":"L826F"},"Curated-R":{"2206":"S295L","2207":"G61V","2208":"S337L","2210":"P314L","2211":"T345I","2212":"T345A","3609":"I420N","3613":"T345K","3614":"T472K","3615":"M347R","3616":"L341S","3617":"V351E","2209":"L826F"},"clinical":{"2206":"S295L","2207":"G61V","2208":"S337L","2210":"P314L","2211":"T345I","2212":"T345A","3609":"I420N","3613":"T345K","3614":"T472K","3615":"M347R","3616":"L341S","3617":"V351E","2209":"L826F"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1600"}},"model_sequences":{"sequence":{"3542":{"protein_sequence":{"accession":"ADJ67256.1","sequence":"MNQEVKNKIFSILKITFATALFIFVAITLYRELSGINFKDTLVEFSKINRMSLVLLFIGGGASLVILSMYDVILSRALKMDISLGKVLRVSYIINALNAIVGFGGFIGAGVRAMVYKNYTHDKKKLVHFISLILISMLTGLSLLSLLIVFHVFDASLILDKITWVRWVLYVVSFFLPLFIIYSMVRPPDKNNRFVGLYCTLVSCVEWLAAAVVLYFCGVIVDAHVSFMSFIAIFIIAALSGLVSFIPGGFGAFDLVVLLGFKTLGVPEEKVLLMLLLYRFAYYFVPVIIALILSSFEFGTSAKKYIEGSKYFIPAKDVTSFLMSYQKDIIAKIPSLSLAILVFFTSMINLTIVYDALYDGNHLTYYILLAIHTSACLLLLLNVVGIYKQSRRAIIFAMISILLITVATFFTYASYILITWLAIIFVLLIVAFRRARRLKRPVRMRNIVAMLLFSLFILYVNHIFIAGTLYALDIYTIEMHTSVLRYYFWLTILIIAIIIGMIAWLFDYQFSKVRISSKIEDCEEIINQYGGNYLSHLIYSGDKQFFTNENKTAFLMYRYKASSLVVLGDPLGDENAFDELLEAFYNYAEYLGYDVIFYQVTDQHMPLYHNFGNQFFKLGEEAIIDLTQFSTSGKKRRGFRATLNKFDELNISFEIIEPPFSTEFINELQHVSDLWLDNRQEMHFSVGEFNEEYLSKAPIGVMRNEENEVIAFCSLMPTYFNDAISVDLIRWLPELDLPLMDGLYLHMLLWSKEQGYTKFNMGMATLSNVGQLHYSYLRERLAGRVFEHFNGLYRFQGLRRYKSKYNPNWEPRFLVYRKDNSLWESLSKVMRVIRHK"},"dna_sequence":{"accession":"HM140977.1","fmin":"0","fmax":"2511","strand":"+","sequence":"ATGAATCAGGAAGTTAAAAACAAAATATTTTCAATCTTAAAAATTACGTTTGCTACAGCTTTATTTATTTTTGTAGCAATCACATTGTATCGGGAGTTATCTGGTATTAACTTTAAAGATACGTTGGTTGAATTTAGTAAGATTAACCGTATGTCCTTAGTGTTACTATTTATTGGTGGTGGGGCATCGCTTGTTATTCTATCAATGTATGATGTGATTTTATCTAGAGCTTTAAAAATGGATATATCCTTAGGCAAAGTTTTAAGAGTAAGTTATATCATCAATGCATTGAATGCGATTGTAGGTTTCGGTGGCTTTATTGGTGCAGGCGTTAGAGCAATGGTTTATAAAAACTATACGCATGATAAAAAGAAATTAGTTCACTTTATATCCTTAATACTTATTTCAATGTTGACAGGTTTAAGCTTATTATCATTGCTAATTGTATTCCATGTTTTCGATGCATCTTTAATCTTAGATAAGATTACATGGGTAAGATGGGTATTATATGTAGTGTCATTTTTCTTACCATTATTCATTATTTATTCAATGGTTAGACCACCCGATAAAAACAATCGTTTTGTAGGATTGTACTGCACTTTAGTGTCGTGTGTTGAATGGTTAGCAGCTGCAGTTGTATTATATTTCTGTGGTGTAATTGTTGACGCTCATGTATCATTCATGTCCTTTATTGCAATATTTATCATTGCTGCATTATCAGGTTTAGTCAGCTTTATTCCTGGTGGTTTCGGCGCTTTCGATTTAGTTGTATTACTAGGATTTAAAACTTTAGGTGTCCCTGAGGAAAAAGTATTATTAATGCTACTTCTATATCGTTTTGCGTACTATTTTGTACCGGTAATTATTGCATTAATTTTATCATCATTTGAATTTGGTACATCAGCTAAGAAGTACATTGAGGGATCTAAATACTTTATTCCTGCTAAAGATGTTACGTCATTTTTAATGTCTTATCAAAAGGATATTATTGCTAAAATTCCATCATTATCATTAGCAATTTTAGTATTCTTTACAAGTATGATCAACTTAACGATTGTTTACGATGCTTTATATGATGGAAATCACTTAACGTATTATATTCTATTGGCAATTCATACTAGTGCTTGTTTATTACTTTTACTGAATGTAGTTGGTATTTATAAGCAAAGTAGACGTGCCATTATCTTTGCTATGATTTCAATTTTATTAATCACAGTGGCGACATTCTTCACTTACGCTTCATATATTTTAATAACATGGTTAGCTATTATTTTTGTTCTGCTTATTGTAGCTTTCCGTAGAGCACGTAGGTTGAAACGCCCAGTAAGAATGAGAAATATAGTTGCAATGCTTTTATTCAGTTTATTTATTTTATATGTTAACCATATATTTATTGCTGGAACGTTATATGCATTAGATATTTATACGATTGAAATGCATACATCTGTATTGCGCTATTACTTCTGGCTTACGATTTTAATCATCGCTATCATCATAGGTATGATTGCATGGTTGTTTGATTATCAATTTAGCAAAGTACGTATTTCTTCTAAAATTGAAGATTGCGAGGAGATTATTAATCAGTACGGCGGTAATTATTTGAGTCACTTGATATATAGTGGTGACAAGCAGTTTTTCACTAATGAAAATAAAACAGCATTTTTAATGTATCGTTATAAAGCAAGTTCATTAGTGGTTCTTGGAGATCCGTTAGGTGATGAAAATGCCTTTGATGAATTGTTAGAAGCATTCTATAATTACGCTGAGTATTTAGGCTATGATGTTATATTCTATCAAGTTACAGATCAACACATGCCTTTATATCATAATTTCGGTAACCAATTTTTCAAATTAGGTGAAGAAGCAATTATTGATTTAACGCAATTTTCAACTTCAGGTAAAAAACGCCGTGGATTTAGAGCGACTTTAAATAAATTCGATGAACTTAATATTTCGTTCGAAATTATTGAACCACCGTTTTCAACTGAATTTATAAATGAACTTCAACATGTAAGTGATTTATGGCTAGATAATCGTCAGGAAATGCATTTCTCTGTTGGTGAATTTAATGAAGAATACTTATCTAAAGCGCCAATTGGTGTAATGCGAAATGAAGAAAATGAAGTAATTGCATTTTGTAGTTTAATGCCAACATACTTTAATGATGCCATTTCAGTCGATTTAATTAGATGGTTGCCAGAGTTAGATTTACCATTAATGGATGGTCTATACTTGCATATGTTACTTTGGAGTAAAGAACAAGGTTATACAAAATTTAATATGGGTATGGCAACGTTATCGAACGTTGGTCAATTGCATTATTCATATTTAAGAGAACGACTTGCAGGCCGTGTCTTTGAACATTTCAACGGTCTATATCGTTTCCAAGGATTACGTCGTTATAAATCTAAATATAATCCGAATTGGGAACCACGCTTTTTAGTTTATCGTAAAGATAATTCGCTTTGGGAATCACTTTCTAAAGTAATGCGTGTAATACGTCACAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35508","NCBI_taxonomy_name":"Staphylococcus aureus","NCBI_taxonomy_id":"1280"}}}},"ARO_accession":"3003319","ARO_id":"39903","ARO_name":"Staphylococcus aureus mprF with mutation conferring resistance to daptomycin","CARD_short_name":"Saur_mprF_DAP","ARO_description":"Point mutations that occur within Staphylococcus aureus mprF gene resulting in resistance to daptomycin.","ARO_category":{"39638":{"category_aro_accession":"3003091","category_aro_cvterm_id":"39638","category_aro_name":"daptomycin resistant mprF","category_aro_description":"MprF is a integral membrane protein that modifies the negatively-charged phosphatidylglycerol on the membrane surface of both Gram-positive and Gram-negative bacteria. This confers resistance to cationic peptides that disrupt the cell membrane, including defensins. Mutations in mprF can additionally confer resistance to daptomycin in S. aureus.","category_aro_class_name":"AMR Gene Family"},"35985":{"category_aro_accession":"0000068","category_aro_cvterm_id":"35985","category_aro_name":"daptomycin","category_aro_description":"Daptomycin is a novel lipopeptide antibiotic used in the treatment of certain infections caused by Gram-positive organisms. Daptomycin interferes with the bacterial cell membrane, reducing membrane potential and inhibiting cell wall synthesis.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1203":{"model_id":"1203","model_name":"Mycobacterium tuberculosis ndh with mutation conferring resistance to isoniazid","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"9583":"R268H","2310":"V18A","2402":"R13C","3641":"A300P","3643":"T110A","3644":"G313R","3646":"L50V","10057":"G339A"},"ReSeqTB-Minimal":{"9583":"R268H"},"clinical":{"9583":"R268H","2310":"V18A","2402":"R13C","3641":"A300P","3642":"R268H","3643":"T110A","3644":"G313R","3646":"L50V","10057":"G339A"},"Curated-R":{"2310":"V18A","2402":"R13C","3641":"A300P","3642":"R268H","3643":"T110A","3644":"G313R","3646":"L50V","10057":"G339A"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"8780":{"protein_sequence":{"accession":"NP_216370.1","sequence":"MSPQQEPTAQPPRRHRVVIIGSGFGGLNAAKKLKRADVDIKLIARTTHHLFQPLLYQVATGIISEGEIAPPTRVVLRKQRNVQVLLGNVTHIDLAGQCVVSELLGHTYQTPYDSLIVAAGAGQSYFGNDHFAEFAPGMKSIDDALELRGRILSAFEQAERSSDPERRAKLLTFTVVGAGPTGVEMAGQIAELAEHTLKGAFRHIDSTKARVILLDAAPAVLPPMGAKLGQRAAARLQKLGVEIQLGAMVTDVDRNGITVKDSDGTVRRIESACKVWSAGVSASRLGRDLAEQSRVELDRAGRVQVLPDLSIPGYPNVFVVGDMAAVEGVPGVAQGAIQGAKYVASTIKAELAGANPAEREPFQYFDKGSMATVSRFSAVAKIGPVEFSGFIAWLIWLVLHLAYLIGFKTKITTLLSWTVTFLSTRRGQLTITDQQAFARTRLEQLAELAAEAQGSAASAKVAS"},"dna_sequence":{"accession":"NC_000962.3","fmin":"2101650","fmax":"2103042","strand":"-","sequence":"ATGAGTCCCCAGCAAGAACCCACAGCGCAACCACCTCGTAGGCATCGAGTTGTGATCATCGGATCTGGGTTCGGCGGGCTAAACGCGGCAAAGAAGCTCAAGCGGGCCGACGTTGACATCAAGCTGATCGCGCGCACCACCCATCACCTGTTCCAGCCGCTGCTGTACCAAGTGGCCACCGGGATTATCTCCGAGGGAGAAATCGCTCCGCCGACCCGGGTCGTGCTGCGTAAGCAGCGCAATGTCCAGGTACTGTTGGGCAACGTCACCCACATCGACCTGGCCGGGCAGTGCGTCGTCTCGGAATTGCTCGGTCACACCTACCAAACCCCCTACGACAGCCTGATCGTCGCCGCGGGTGCTGGCCAGTCTTATTTCGGCAACGACCATTTCGCCGAATTCGCACCCGGCATGAAGTCCATCGACGACGCGTTGGAGTTGCGTGGCCGCATATTGAGCGCTTTCGAGCAAGCCGAACGGTCCAGCGATCCGGAACGGCGGGCCAAGCTACTGACATTCACCGTTGTCGGGGCTGGCCCCACCGGTGTTGAAATGGCCGGACAGATCGCCGAGCTGGCCGAGCACACGTTGAAGGGCGCATTCCGGCACATCGACTCGACCAAGGCGCGGGTGATTCTGCTTGACGCCGCCCCGGCGGTGCTGCCACCGATGGGCGCAAAGCTCGGTCAGCGGGCGGCTGCCCGGTTGCAGAAGCTGGGCGTGGAAATCCAGCTGGGTGCGATGGTCACCGACGTCGACCGCAACGGCATCACCGTCAAGGACTCCGACGGCACCGTCCGGCGCATCGAGTCGGCCTGCAAGGTCTGGTCGGCCGGGGTTTCGGCCAGTCGGTTGGGCAGGGACCTTGCCGAGCAATCACGGGTTGAGCTCGACCGGGCCGGCCGGGTCCAAGTGCTGCCCGACCTGTCCATTCCCGGGTACCCGAACGTGTTCGTGGTGGGCGATATGGCCGCTGTGGAGGGTGTGCCGGGTGTGGCGCAGGGCGCCATCCAGGGGGCGAAATACGTCGCCAGCACGATCAAGGCCGAACTGGCCGGCGCCAACCCGGCGGAGCGTGAGCCATTCCAGTACTTCGACAAGGGATCGATGGCCACGGTTTCGAGGTTTTCGGCGGTGGCCAAGATCGGTCCCGTTGAGTTCAGCGGCTTTATCGCCTGGCTGATTTGGCTGGTGCTGCACCTGGCGTACCTGATCGGGTTCAAGACCAAGATCACCACTCTGCTGTCGTGGACGGTGACTTTCCTCAGTACTCGCCGCGGCCAGCTGACCATCACCGACCAGCAGGCATTTGCGCGAACGCGGCTCGAACAGCTGGCCGAGCTGGCCGCCGAGGCGCAGGGCTCAGCGGCAAGCGCTAAGGTGGCCAGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3003461","ARO_id":"40054","ARO_name":"Mycobacterium tuberculosis ndh with mutation conferring resistance to isoniazid","CARD_short_name":"Mtub_ndh_INH","ARO_description":"Point mutations in the Mycobacterium tuberculosis ndh gene shown clinically to confer resistance to isoniazid.","ARO_category":{"40053":{"category_aro_accession":"3003460","category_aro_cvterm_id":"40053","category_aro_name":"antibiotic resistant ndh","category_aro_description":"ndh is a NADH oxidase. It participates in antibiotic resistance by diminishing NADH oxidation and consequently causes an increase in NADH concentration and depletion of NAD+. This alteration of the NADH\/NAD+ ratio prevents the peroxidation reactions required for the activation of INH, as well as the displacement of the NADH-isonicotinic acyl complex from InhA enzyme binding site.","category_aro_class_name":"AMR Gene Family"},"36659":{"category_aro_accession":"3000520","category_aro_cvterm_id":"36659","category_aro_name":"isoniazid","category_aro_description":"Isoniazid is an organic compound that is the first-line anti tuberculosis medication in prevention and treatment. As a prodrug, it is activated by mycobacterial catalase-peroxidases such as M. tuberculosis KatG. Isoniazid inhibits mycolic acid synthesis, which prevents cell wall synthesis in mycobacteria.","category_aro_class_name":"Antibiotic"},"45734":{"category_aro_accession":"3007152","category_aro_cvterm_id":"45734","category_aro_name":"isoniazid-like antibiotic","category_aro_description":"A group of antibiotics containing isoniazid and its derivatives.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1395":{"model_id":"1395","model_name":"Neisseria gonorrhoeae porin PIB (por)","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"40330":{"param_type":"multiple resistance variants","param_description":"A set of nucleotide or amino acid substitutions that are all required to confer resistance to an antibiotic drug or drug class, encoded as: [wild-type 1][position 1][mutation 1],[wild-type 2][position 2][mutation 2], etc. For example, D63Y,T142K.","param_type_id":"40330","param_value":{"3288":"G120R,A121H","3289":"G120P,A121P"}},"snp":{"Curated-R":{"3288":"G339A","3289":"G339A","60":"G120K","61":"G120D","64":"A121D"},"param_value":{"60":"G120K","61":"G120D","64":"A121D"},"clinical":{"60":"G120K","61":"G120D","64":"A121D"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"54":{"protein_sequence":{"accession":"AAB57788.1","sequence":"MKKSLIALTLAALPVAATADVTLYGAIKAGVQTYRSVEHTKGKVSKVETGSEIADFGSKIGFKGQEDLGNGLKAVWQLEQGASVAGTNTGWGNKQSFVGLKGGFGTIRAGSLNSPLKNTGANVNAWESGKFTGNVLEISGMAQREHRYLSVRYDSPEFAGFSGSVQYAPKDNSGSNGESYHVGLNYRNNGFFAQYAGLFQRYGEGTKKIEYEHQVYSIPSLFVEKLQVHRLVGGYDNNALYVSVAAQQQDAKLYGARRANSHNSQTEVAATAAYRFGNVTPRVSYAHGFKGTVDSADHDNTYDQVVVGAEYDFSKRTSALVSAGWLQEGKGADKIVSTASAVVLRHKF"},"dna_sequence":{"accession":"U75641.1","fmin":"19","fmax":"1066","strand":"+","sequence":"ATGAAAAAATCCCTGATTGCCCTGACTTTGGCAGCCCTTCCTGTTGCGGCAACGGCCGATGTCACCCTGTACGGCGCCATCAAAGCCGGCGTACAAACTTACCGTTCTGTAGAACATACAAAAGGCAAGGTAAGTAAAGTGGAAACCGGCAGCGAAATCGCCGACTTCGGTTCAAAAATCGGCTTCAAAGGCCAAGAAGACCTCGGCAACGGCCTGAAGGCCGTTTGGCAGTTGGAACAAGGTGCCTCCGTCGCCGGCACTAACACCGGCTGGGGCAACAAACAATCCTTCGTCGGCTTGAAGGGCGGCTTCGGTACCATCCGCGCCGGTAGCCTGAACAGCCCCCTGAAAAACACCGGCGCCAACGTCAATGCTTGGGAATCCGGCAAATTTACCGGCAATGTGCTGGAAATCAGCGGAATGGCCCAACGGGAACACCGCTACCTGTCCGTACGCTACGATTCTCCCGAATTTGCCGGCTTCAGCGGCAGCGTACAATACGCACCTAAAGACAATTCAGGCTCAAACGGCGAATCTTACCACGTTGGTTTGAACTACCGAAACAACGGCTTCTTCGCACAATACGCCGGCTTGTTCCAAAGATACGGCGAAGGCACTAAAAAAATCGAATACGAACATCAAGTTTATAGTATCCCCAGCCTGTTTGTTGAAAAACTGCAAGTTCACCGTTTGGTAGGCGGTTACGACAATAATGCCCTGTACGTTTCCGTAGCCGCGCAACAACAAGATGCCAAATTGTATGGAGCAAGGAGGGCTAATTCGCACAACTCTCAAACCGAAGTTGCCGCTACCGCGGCATACCGTTTCGGCAATGTAACGCCCCGCGTTTCTTACGCCCACGGCTTCAAAGGCACTGTTGATAGTGCAGACCACGACAATACTTATGACCAAGTGGTTGTCGGTGCGGAATACGACTTCTCCAAACGCACTTCTGCCTTGGTTTCTGCCGGCTGGTTGCAAGAAGGCAAAGGCGCAGACAAAATCGTATCGACTGCCAGCGCCGTCGTTCTGCGCCACAAATTCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36806","NCBI_taxonomy_name":"Neisseria gonorrhoeae","NCBI_taxonomy_id":"485"}}}},"ARO_accession":"3000464","ARO_id":"36603","ARO_name":"Neisseria gonorrhoeae porin PIB (por)","CARD_short_name":"Ngon_porin","ARO_description":"Mutant forms of the porin Por result in reduced permeability to antibiotics, particularly tetracyclines and beta-lactams.","ARO_category":{"41445":{"category_aro_accession":"3004281","category_aro_cvterm_id":"41445","category_aro_name":"General Bacterial Porin with reduced permeability to beta-lactams","category_aro_description":"These are GBPs that are associated with decreased susceptibility to beta-lactams either through mutations in the porin protein, absence of the porin protein, or expression of the porin protein.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36383":{"category_aro_accession":"3000244","category_aro_cvterm_id":"36383","category_aro_name":"reduced permeability to antibiotic","category_aro_description":"Reduction in permeability to antibiotic, generally through reduced production of porins, can provide resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1432":{"model_id":"1432","model_name":"Mycobacterium tuberculosis embC mutant conferring resistance to ethambutol","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"9492":"V987G","2261":"T270I","2263":"Q491R","2264":"L502P","2371":"A247P","2372":"L251R","2373":"A254G","2375":"H285Y","2376":"V287F","2377":"G288W","2378":"G288V","2379":"Y296H","2380":"Y296S","2381":"I297L","2382":"I297T","2383":"M300R","2385":"V303G","2386":"A307T","2387":"G308D","2388":"Y309N","2389":"M310K","2390":"G325S","2391":"W326R","2392":"Y327N","2393":"N394D","2394":"V981L","3612":"R738Q","2262":"P398S","2384":"R302G"},"ReSeqTB-Moderate":{"9492":"V987G"},"clinical":{"9492":"V987G","2261":"T270I","2263":"Q491R","2264":"L502P","2371":"A247P","2372":"L251R","2373":"A254G","2375":"H285Y","2376":"V287F","2377":"G288W","2378":"G288V","2379":"Y296H","2380":"Y296S","2381":"I297L","2382":"I297T","2383":"M300R","2385":"V303G","2386":"A307T","2387":"G308D","2388":"Y309N","2389":"M310K","2390":"G325S","2391":"W326R","2392":"Y327N","2393":"N394D","2394":"V981L","3612":"R738Q","2262":"P398S","2384":"R302G"},"Curated-R":{"2261":"T270I","2263":"Q491R","2264":"L502P","2371":"A247P","2372":"L251R","2373":"A254G","2375":"H285Y","2376":"V287F","2377":"G288W","2378":"G288V","2379":"Y296H","2380":"Y296S","2381":"I297L","2382":"I297T","2383":"M300R","2385":"V303G","2386":"A307T","2387":"G308D","2388":"Y309N","2389":"M310K","2390":"G325S","2391":"W326R","2392":"Y327N","2393":"N394D","2394":"V981L","3612":"R738Q","4128":"R738Q","4130":"R738Q","4135":"R738Q","4138":"R738Q","4139":"R738Q","2262":"P398S","2384":"R302G"}},"40330":{"param_type":"multiple resistance variants","param_description":"A set of nucleotide or amino acid substitutions that are all required to confer resistance to an antibiotic drug or drug class, encoded as: [wild-type 1][position 1][mutation 1],[wild-type 2][position 2][mutation 2], etc. For example, D63Y,T142K.","param_type_id":"40330","param_value":{"4128":"I297L,W326R","4130":"T270I,I297T","4135":"G288W,V303G","4138":"Y296S,R302G","4139":"V287F,Y309N"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"2000"}},"model_sequences":{"sequence":{"8808":{"protein_sequence":{"accession":"NP_218310.1","sequence":"MATEAAPPRIAVRLPSTSVRDAGANYRIARYVAVVAGLLGAVLAIATPLLPVNQTTAQLNWPQNGTFASVEAPLIGYVATDLNITVPCQAAAGLAGSQNTGKTVLLSTVPKQAPKAVDRGLLLQRANDDLVLVVRNVPLVTAPLSQVLGPTCQRLTFTAHADRVAAEFVGLVQGPNAEHPGAPLRGERSGYDFRPQIVGVFTDLAGPAPPGLSFSASVDTRYSSSPTPLKMAAMILGVALTGAALVALHILDTADGMRHRRFLPARWWSTGGLDTLVIAVLVWWHFVGANTSDDGYILTMARVSEHAGYMANYYRWFGTPEAPFGWYYDLLALWAHVSTASIWMRLPTLAMALTCWWVISREVIPRLGHAVKTSRAAAWTAAGMFLAVWLPLDNGLRPEPIIALGILLTWCSVERAVATSRLLPVAIACIIGALTLFSGPTGIASIGALLVAIGPLRTILHRRSRRFGVLPLVAPILAAATVTAIPIFRDQTFAGEIQANLLKRAVGPSLKWFDEHIRYERLFMASPDGSIARRFAVLALVLALAVSVAMSLRKGRIPGTAAGPSRRIIGITIISFLAMMFTPTKWTHHFGVFAGLAGSLGALAAVAVTGAAMRSRRNRTVFAAVVVFVLALSFASVNGWWYVSNFGVPWSNSFPKWRWSLTTALLELTVLVLLLAAWFHFVANGDGRRTARPTRFRARLAGIVQSPLAIATWLLVLFEVVSLTQAMISQYPAWSVGRSNLQALAGKTCGLAEDVLVELDPNAGMLAPVTAPLADALGAGLSEAFTPNGIPADVTADPVMERPGDRSFLNDDGLITGSEPGTEGGTTAAPGINGSRARLPYNLDPARTPVLGSWRAGVQVPAMLRSGWYRLPTNEQRDRAPLLVVTAAGRFDSREVRLQWATDEQAAAGHHGGSMEFADVGAAPAWRNLRAPLSAIPSTATQVRLVADDQDLAPQHWIALTPPRIPRVRTLQNVVGAADPVFLDWLVGLAFPCQRPFGHQYGVDETPKWRILPDRFGAEANSPVMDHNGGGPLGITELLMRATTVASYLKDDWFRDWGALQRLTPYYPDAQPADLNLGTVTRSGLWSPAPLRRG"},"dna_sequence":{"accession":"NC_000962.3","fmin":"4239862","fmax":"4243147","strand":"+","sequence":"ATGGCTACCGAAGCCGCCCCACCCCGTATCGCCGTCCGGCTACCATCTACCTCCGTGCGCGACGCGGGAGCAAACTACCGGATCGCCCGGTACGTCGCTGTGGTGGCGGGTCTGCTAGGCGCTGTGCTGGCCATCGCCACCCCACTGCTGCCGGTCAACCAGACCACCGCGCAATTGAACTGGCCCCAAAACGGCACGTTCGCCAGTGTCGAGGCACCGCTGATTGGCTACGTGGCCACCGACTTGAACATCACCGTCCCCTGCCAGGCCGCCGCCGGACTGGCCGGATCGCAGAACACCGGCAAGACGGTGTTGTTGTCAACGGTGCCCAAGCAGGCGCCTAAGGCCGTCGATCGCGGGCTGCTGCTGCAACGGGCCAACGACGACCTGGTGCTTGTGGTGCGTAATGTCCCGTTGGTCACCGCCCCGCTGAGTCAGGTGCTCGGCCCGACCTGTCAGCGGTTGACATTCACCGCGCACGCCGATCGGGTCGCCGCCGAATTCGTCGGACTGGTGCAGGGACCCAATGCTGAGCACCCCGGTGCACCGCTGCGCGGTGAGCGCAGCGGCTACGACTTCCGCCCGCAGATCGTCGGGGTGTTCACCGACCTGGCCGGGCCGGCGCCACCGGGTCTGAGCTTCTCGGCGAGCGTGGATACCCGCTACAGCAGCAGCCCCACGCCGCTGAAGATGGCCGCCATGATCCTCGGGGTAGCGCTCACCGGCGCCGCCCTGGTGGCGCTGCACATCCTGGACACCGCCGACGGCATGCGGCACCGGCGGTTCCTGCCCGCGCGCTGGTGGTCGACCGGCGGTCTGGACACCCTGGTTATCGCCGTGCTGGTGTGGTGGCATTTCGTCGGGGCCAACACCTCCGACGACGGCTACATCCTGACCATGGCCCGGGTGTCCGAGCATGCGGGCTATATGGCCAACTACTACCGCTGGTTCGGCACACCCGAGGCGCCTTTCGGCTGGTACTACGACCTGCTGGCGCTGTGGGCTCATGTCAGCACGGCCAGTATCTGGATGCGCCTACCCACCCTGGCGATGGCGCTCACCTGCTGGTGGGTAATCAGCCGTGAGGTCATTCCCCGGCTGGGGCACGCCGTCAAGACGAGCCGGGCAGCGGCGTGGACGGCGGCGGGCATGTTTCTGGCTGTCTGGCTGCCGCTGGACAACGGCCTTCGGCCCGAGCCGATCATCGCCCTGGGCATCCTGCTGACCTGGTGCTCGGTGGAGCGGGCGGTGGCCACCAGCCGGCTGCTGCCGGTGGCAATCGCCTGCATCATCGGTGCCTTGACCCTGTTCTCCGGGCCGACGGGCATCGCCTCGATCGGTGCGCTGCTGGTCGCGATCGGGCCGCTACGGACCATCCTGCACCGGCGTTCCAGGCGGTTCGGCGTGCTACCACTGGTGGCGCCGATCCTGGCCGCGGCCACCGTCACCGCGATCCCGATCTTTCGTGATCAGACCTTCGCGGGCGAGATCCAGGCCAACCTCCTCAAGCGTGCCGTAGGGCCCAGCCTGAAGTGGTTCGACGAACACATCCGCTACGAGCGGCTGTTCATGGCCAGCCCCGACGGCTCGATCGCCCGCCGCTTCGCCGTGCTGGCCTTGGTGCTGGCGCTCGCGGTATCGGTGGCAATGTCGTTACGTAAGGGCCGCATTCCAGGTACCGCTGCTGGACCGAGCCGCCGCATCATCGGCATCACGATCATTTCCTTCCTCGCGATGATGTTCACCCCGACAAAGTGGACCCATCACTTCGGGGTGTTCGCGGGGTTGGCCGGGTCGCTGGGGGCGCTTGCCGCGGTCGCGGTGACGGGCGCTGCGATGCGCTCGCGGCGGAACCGGACCGTGTTCGCCGCCGTGGTGGTCTTCGTGTTGGCCCTGTCGTTCGCCAGTGTCAACGGCTGGTGGTACGTGTCCAACTTCGGTGTGCCATGGTCGAACTCGTTTCCGAAGTGGCGATGGTCGCTTACCACCGCACTCCTCGAGCTGACGGTGCTGGTGCTGCTGCTAGCGGCATGGTTCCACTTCGTCGCCAACGGTGACGGGCGCCGAACAGCCAGGCCAACCCGGTTTAGGGCACGACTAGCCGGAATTGTCCAGTCCCCGTTGGCAATTGCCACGTGGTTGCTGGTGCTTTTCGAGGTGGTATCGCTGACCCAGGCGATGATTTCCCAGTACCCGGCGTGGTCGGTTGGCCGGTCTAACCTACAGGCTTTGGCCGGCAAGACCTGCGGGCTGGCCGAAGACGTGCTGGTGGAGCTGGATCCCAACGCAGGCATGCTGGCGCCGGTGACCGCGCCGTTGGCCGACGCCCTGGGAGCCGGCCTGTCTGAAGCCTTCACACCCAACGGCATTCCCGCCGACGTCACCGCCGACCCGGTGATGGAACGTCCAGGGGATCGCAGTTTCCTCAACGACGACGGGCTGATCACCGGCAGCGAACCCGGCACCGAAGGGGGCACCACGGCCGCACCGGGAATCAACGGCTCCCGCGCCCGGCTGCCCTACAACCTGGACCCGGCCCGTACACCGGTGCTGGGCAGCTGGCGAGCCGGCGTGCAGGTGCCCGCCATGCTGCGGTCGGGCTGGTACCGGCTGCCCACCAACGAGCAGCGGGACAGGGCGCCGCTGCTGGTGGTGACGGCGGCCGGGCGATTCGACTCCCGCGAGGTCCGGTTGCAGTGGGCCACCGACGAGCAAGCGGCCGCCGGACACCACGGTGGGTCGATGGAATTCGCCGACGTCGGTGCCGCGCCGGCCTGGCGCAACCTGCGCGCACCACTGTCCGCCATCCCGAGCACCGCCACCCAGGTCCGGTTGGTCGCCGACGACCAGGATCTGGCGCCGCAGCACTGGATCGCCCTCACACCACCGCGGATTCCGCGGGTGCGCACGCTGCAGAACGTGGTGGGCGCAGCGGATCCGGTGTTCCTGGACTGGCTGGTGGGGCTGGCATTCCCCTGCCAACGCCCGTTCGGCCACCAATACGGCGTCGACGAGACACCCAAGTGGCGGATCCTGCCGGACCGGTTCGGCGCCGAAGCCAACTCACCGGTGATGGATCACAATGGCGGTGGCCCGCTGGGCATCACCGAGCTGCTGATGCGCGCAACCACGGTGGCCAGCTACCTCAAAGACGACTGGTTTAGGGACTGGGGCGCGTTACAGCGGTTGACGCCTTACTACCCCGACGCCCAGCCCGCTGATCTGAACCTAGGAACGGTGACTCGCAGCGGGCTGTGGAGTCCGGCGCCGTTGCGCCGCGGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3003327","ARO_id":"39911","ARO_name":"Mycobacterium tuberculosis embC mutant conferring resistance to ethambutol","CARD_short_name":"Mtub_embC_EMB","ARO_description":"Point mutations in Mycobacterium tuberculosis embC that result in lower affinity between ethambutol and EmbC, resulting in resistance.","ARO_category":{"39140":{"category_aro_accession":"3002706","category_aro_cvterm_id":"39140","category_aro_name":"ethambutol resistant embC","category_aro_description":"Mycobacterium tuberculosis embC mutations at codon 270 confer resistance to ethambutol.","category_aro_class_name":"AMR Gene Family"},"36636":{"category_aro_accession":"3000497","category_aro_cvterm_id":"36636","category_aro_name":"ethambutol","category_aro_description":"Ethambutol is an antimycobacterial drug prescribed to treat tuberculosis. It is usually given in combination with other tuberculosis drugs, such as isoniazid, rifampicin, and pyrazinamide. Ethambutol inhibits arabinosyl biosynthesis, disrupting mycobacterial cell wall formation.","category_aro_class_name":"Antibiotic"},"36666":{"category_aro_accession":"3000527","category_aro_cvterm_id":"36666","category_aro_name":"polyamine antibiotic","category_aro_description":"Polyamine antibiotics are organic compounds having two or more primary amino groups.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1710":{"model_id":"1710","model_name":"Mycobacterium leprae gyrB conferring resistance to fluoroquinolones","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"2165":"D464N","2169":"N502D","2172":"E504V"},"Curated-R":{"2165":"D464N","2169":"N502D","2172":"E504V"},"clinical":{"2165":"D464N","2169":"N502D","2172":"E504V"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1200"}},"model_sequences":{"sequence":{"2066":{"protein_sequence":{"accession":"CAC29513.1","sequence":"MAAQRKAQDEYGAASITILEGLEAVRKRPGMYVGSTGERGLHHLIWEVVDNSVDEAMAGYATQVDVRLFDDGSVEVADNGRGIPVAVHATGVPTVDVVMTQLHAGGKFGGKDSGYNVSGGLHGVGVSVVNALSTRVEVDIKRDGYEWSQFYDKAVPGILKQGEATEATGTTIRFWADPDIFETTKYDFGTVARRIQEVAFLNKGLTINLVDERVKQDEVVDDVVSDTAEAPVAMTVEEKSTESSAPHKVRHRTFHYPGGLVDFVKHINRTKTPIQQSIIDFDGKGAGHEVEVAMQWNGGYSESVHTFANTINTHEGGTHEEGFRSALTSVVNKYAKDKKLLKDKDPNLTGDDIREGLAAVISVKVSEPQFEGQTKTKLGNTEVKSFVQRVCNEQLIHWFEANPVDAKAVVNKAISSAQARIAARKARELVRRKSATDLGGLPGKLADCRSTDPRSSELYVVEGDSAGGSAKSGRDSMFQAILPLRGKIINVEKARIDRVLKNTEVQAIITALGTGIHDEFDISRLRYHKIVLMADADVDGQHISTLLLTLLFRFMRPLIEHGYVFLAQPPLYKLKWQRMDPEFAYSDSERDGLLETGLKLGKKINKEDGIQRYKGLGEMDAKELWETTMDPSVRVLRQVTLDDAAAADELFSILMGEDVDARRSFITRNAKDVRFLDV"},"dna_sequence":{"accession":"AL450380.1","fmin":"5228","fmax":"7265","strand":"+","sequence":"GTGGCTGCCCAGAGGAAGGCCCAAGACGAATATGGCGCTGCGTCCATCACTATTCTTGAAGGGCTGGAGGCCGTTCGCAAACGTCCCGGTATGTACGTCGGGTCAACTGGTGAGCGTGGTCTCCACCATCTGATATGGGAAGTGGTGGACAACTCAGTAGATGAGGCGATGGCCGGTTATGCTACGCAAGTTGATGTGCGGTTATTCGACGACGGTAGTGTCGAGGTCGCCGATAACGGTCGTGGTATTCCGGTGGCAGTGCATGCTACGGGGGTACCGACTGTTGACGTAGTTATGACCCAATTACATGCCGGCGGTAAATTCGGTGGTAAAGATAGCGGTTATAACGTCAGTGGTGGTTTGCATGGGGTAGGTGTGTCGGTGGTTAACGCATTGTCCACCAGGGTCGAGGTCGACATCAAACGTGACGGCTATGAATGGTCACAGTTTTACGACAAGGCTGTGCCGGGCATTCTTAAGCAAGGCGAAGCTACTGAGGCGACGGGAACGACGATTAGATTTTGGGCAGATCCTGACATTTTCGAAACCACAAAGTATGACTTTGGGACGGTGGCGCGCCGAATTCAAGAAGTGGCTTTCTTGAACAAGGGTTTGACGATCAATCTTGTTGACGAACGGGTGAAGCAGGACGAAGTTGTCGACGATGTCGTCAGCGATACAGCCGAGGCTCCTGTGGCTATGACCGTTGAAGAAAAGTCAACGGAGTCGAGTGCGCCGCACAAGGTTAGACACCGTACGTTCCACTACCCCGGAGGCCTGGTGGACTTCGTCAAGCACATCAACCGGACTAAGACTCCTATTCAACAGAGCATTATCGATTTTGATGGCAAAGGTGCCGGTCACGAGGTTGAAGTTGCGATGCAGTGGAACGGCGGCTATTCGGAATCAGTGCATACCTTTGCGAACACGATTAACACCCATGAAGGCGGCACCCACGAAGAAGGTTTCCGTAGCGCTTTGACATCAGTGGTGAACAAGTACGCTAAGGATAAAAAACTACTCAAAGACAAGGATCCCAACCTAACTGGCGACGATATCCGTGAAGGTCTGGCGGCGGTTATCTCGGTTAAGGTCAGTGAACCACAGTTTGAGGGTCAGACCAAAACAAAGCTGGGGAACACCGAAGTTAAGTCATTCGTGCAGAGGGTCTGTAATGAGCAACTTATTCACTGGTTTGAAGCCAATCCAGTAGATGCGAAAGCGGTTGTGAATAAGGCGATATCGTCGGCACAAGCCCGAATAGCTGCACGTAAAGCACGAGAGTTAGTGCGTCGAAAAAGTGCCACCGATCTTGGTGGACTTCCTGGAAAACTTGCCGATTGCCGCTCTACTGATCCTCGAAGTTCTGAACTGTATGTAGTGGAAGGTGATTCGGCTGGTGGTTCAGCAAAGAGTGGCCGTGATTCGATGTTTCAGGCAATCCTTCCGTTACGTGGCAAGATCATAAATGTTGAAAAGGCACGTATTGACCGAGTGCTAAAGAACACCGAAGTTCAAGCAATTATTACGGCATTGGGTACTGGAATCCATGATGAATTCGATATCTCCAGGCTGCGTTATCACAAAATTGTTTTGATGGCCGACGCTGACGTTGACGGCCAACATATCTCGACGCTGTTGTTGACTTTGTTATTTCGGTTCATGCGACCACTCATCGAGCATGGGTACGTGTTTTTAGCGCAGCCGCCACTTTACAAATTGAAGTGGCAACGTATGGATCCGGAATTTGCTTACTCCGATAGCGAGCGCGACGGCTTATTAGAGACCGGGCTTAAGCTTGGCAAGAAAATCAACAAAGAGGATGGTATCCAACGTTATAAAGGTTTAGGTGAAATGGATGCCAAGGAGTTGTGGGAAACCACCATGGACCCGTCGGTGCGAGTTTTGCGTCAAGTAACACTGGATGACGCGGCGGCTGCTGACGAGTTATTCTCTATTCTGATGGGTGAGGACGTCGATGCACGCCGTAGCTTTATCACCCGTAATGCCAAGGATGTTCGTTTCCTGGATGTCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40083","NCBI_taxonomy_name":"Mycobacterium leprae TN","NCBI_taxonomy_id":"272631"}}}},"ARO_accession":"3003304","ARO_id":"39888","ARO_name":"Mycobacterium leprae gyrB conferring resistance to fluoroquinolones","CARD_short_name":"Mlep_gyrB_FLO","ARO_description":"Point mutation in Mycobacterium leprae gyrB resulting in fluoroquinolone resistance.","ARO_category":{"37244":{"category_aro_accession":"3000864","category_aro_cvterm_id":"37244","category_aro_name":"fluoroquinolone resistant gyrB","category_aro_description":"Point mutations in DNA gyrase subunit B (gyrB) observed in Mycobacterium tuberculosis can result in resistance to fluoroquinolones.","category_aro_class_name":"AMR Gene Family"},"35942":{"category_aro_accession":"0000023","category_aro_cvterm_id":"35942","category_aro_name":"enoxacin","category_aro_description":"Enoxacin belongs to a group called fluoroquinolones. Its mode of action depends upon blocking bacterial DNA replication by binding itself to DNA gyrase and causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37004":{"category_aro_accession":"3000660","category_aro_cvterm_id":"37004","category_aro_name":"lomefloxacin","category_aro_description":"Lomefloxacin is a difluoropiperazinyl quinolone, sharing similar activities with other fluoroquinolones. It is used to treat urinary tract infections. Relative to other fluoroquinolones, it has a longer half life and has higher serum concentrations.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37007":{"category_aro_accession":"3000663","category_aro_cvterm_id":"37007","category_aro_name":"ofloxacin","category_aro_description":"Ofloxacin is a 6-fluoro, 7-piperazinyl quinolone with a methyl-substituted oxazine ring. It has a broad spectrum of activity including many enterobacteria and mycoplasma but most anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"37008":{"category_aro_accession":"3000664","category_aro_cvterm_id":"37008","category_aro_name":"trovafloxacin","category_aro_description":"Trovafloxacin is a trifluoroquinalone with a broad spectrum of activity that acts by inhibiting the uncoiling of supercoiled DNA. While potent against many Gram-positive and Gram-negative bacteria, it is less active against pseudomonads and Cl. difficile. It is usually taken as the prodrug trovafloxacin mesylate or alatrofloxacin mesylate for oral or intravenous administration, respectively.","category_aro_class_name":"Antibiotic"},"37009":{"category_aro_accession":"3000665","category_aro_cvterm_id":"37009","category_aro_name":"grepafloxacin","category_aro_description":"Grepafloxacin is a broad-spectrum antibacterial quinoline. It is no longer taken due to its high toxicity.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"37142":{"category_aro_accession":"3000762","category_aro_cvterm_id":"37142","category_aro_name":"pefloxacin","category_aro_description":"Pefloxacin is structurally and functionally similar to norfloxacin. It is poorly active against mycobacteria, while anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2069":{"model_id":"2069","model_name":"Escherichia coli 16S rRNA (rrsB) mutation conferring resistance to neomycin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"3060":"a1408g"},"Curated-R":{"3060":"a1408g"},"clinical":{"3060":"a1408g"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"41093","param_value":"2700"}},"model_sequences":{"sequence":{"3235":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"U00096.1","fmin":"4166658","fmax":"4168200","strand":"+","sequence":"AAATTGAAGAGTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAACGGTAACAGGAAGAAGCTTGCTTCTTTGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCGGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGGAGTAAAGTTAATACCTTTGCTCATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACGAAGACTGACGCTCAGGTGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGTCGACTTGGAGGTTGTGCCCTTGAGGCGTGGCTTCCGGAGCTAACGCGTTAAGTCGACCGCCTGGGGAGTACGGCCGCAAGGTTAAAACTCAAATGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGATGCAACGCGAAGAACCTTACCTGGTCTTGACATCCACGGAAGTTTTCAGAGATGAGAATGTGCCTTCGGGAACCGTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGAAATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCCTTTGTTGCCAGCGGTCCGGCCGGGAACTCAAAGGAGACTGCCAGTGATAAACTGGAGGAAGGTGGGGATGACGTCAAGTCATCATGGCCCTTACGACCAGGGCTACACACGTGCTACAATGGCGCATACAAAGAGAAGCGACCTCGCGAGAGCAAGCGGACCTCATAAAGTGCGTCGTAGTCCGGATTGGAGTCTGCAACTCGACTCCATGAAGTCGGAATCGCTAGTAATCGTGGATCAGAATGCCACGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACACCATGGGAGTGGGTTGCAAAAGAAGTAGGTAGCTTAACCTTCGGGAGGGCGCTTACCACTTTGTGATTCATGACTGGGGTGAAGTCGTAACAAGGTAACCGTAGGGGAACCTGCGGTTGGATCACCTCCTTA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36905","NCBI_taxonomy_name":"Escherichia coli str. K-12","NCBI_taxonomy_id":"83333"}}}},"ARO_accession":"3003402","ARO_id":"39986","ARO_name":"Escherichia coli 16S rRNA (rrsB) mutation conferring resistance to neomycin","CARD_short_name":"Ecol_16rrsB_NEO","ARO_description":"Point mutations in the 3' minor domain of helix 44, in the rrsB 16S rRNA gene of Escherichia coli can confer resistance to neomycin.","ARO_category":{"40277":{"category_aro_accession":"3003666","category_aro_cvterm_id":"40277","category_aro_name":"16s rRNA with mutation conferring resistance to aminoglycoside antibiotics","category_aro_description":"Point mutations in the 16S rRNA of bacteria can confer resistance to aminoglycosides.","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2073":{"model_id":"2073","model_name":"Escherichia coli 16S rRNA (rrsB) mutation conferring resistance to G418","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"4812":"t1406a"},"Curated-R":{"4812":"t1406a"},"clinical":{"4812":"t1406a"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"41093","param_value":"2700"}},"model_sequences":{"sequence":{"3230":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"U00096.1","fmin":"4166658","fmax":"4168200","strand":"+","sequence":"AAATTGAAGAGTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAACGGTAACAGGAAGAAGCTTGCTTCTTTGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCGGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGGAGTAAAGTTAATACCTTTGCTCATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACGAAGACTGACGCTCAGGTGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGTCGACTTGGAGGTTGTGCCCTTGAGGCGTGGCTTCCGGAGCTAACGCGTTAAGTCGACCGCCTGGGGAGTACGGCCGCAAGGTTAAAACTCAAATGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGATGCAACGCGAAGAACCTTACCTGGTCTTGACATCCACGGAAGTTTTCAGAGATGAGAATGTGCCTTCGGGAACCGTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGAAATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCCTTTGTTGCCAGCGGTCCGGCCGGGAACTCAAAGGAGACTGCCAGTGATAAACTGGAGGAAGGTGGGGATGACGTCAAGTCATCATGGCCCTTACGACCAGGGCTACACACGTGCTACAATGGCGCATACAAAGAGAAGCGACCTCGCGAGAGCAAGCGGACCTCATAAAGTGCGTCGTAGTCCGGATTGGAGTCTGCAACTCGACTCCATGAAGTCGGAATCGCTAGTAATCGTGGATCAGAATGCCACGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACACCATGGGAGTGGGTTGCAAAAGAAGTAGGTAGCTTAACCTTCGGGAGGGCGCTTACCACTTTGTGATTCATGACTGGGGTGAAGTCGTAACAAGGTAACCGTAGGGGAACCTGCGGTTGGATCACCTCCTTA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36905","NCBI_taxonomy_name":"Escherichia coli str. K-12","NCBI_taxonomy_id":"83333"}}}},"ARO_accession":"3003397","ARO_id":"39981","ARO_name":"Escherichia coli 16S rRNA (rrsB) mutation conferring resistance to G418","CARD_short_name":"Ecol_16S_G418","ARO_description":"Point mutations in the 3' minor domain of helix 44, in the rrsB 16S rRNA gene of Escherichia coli can confer resistance to G418.","ARO_category":{"40277":{"category_aro_accession":"3003666","category_aro_cvterm_id":"40277","category_aro_name":"16s rRNA with mutation conferring resistance to aminoglycoside antibiotics","category_aro_description":"Point mutations in the 16S rRNA of bacteria can confer resistance to aminoglycosides.","category_aro_class_name":"AMR Gene Family"},"36997":{"category_aro_accession":"3000653","category_aro_cvterm_id":"36997","category_aro_name":"G418","category_aro_description":"A gentamicin class aminoglycoside antibiotic often used in mammalian cell culture work as a selectable marker for the neo cassette (APH3').","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2074":{"model_id":"2074","model_name":"Salmonella enterica 16S rRNA (rrsD) mutation conferring resistance to spectinomycin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"41093","param_value":"2700"},"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"12949":"c1066t","4810":"c1192t"},"Curated-R":{"12949":"c1066t","4810":"c1192t"},"clinical":{"12949":"c1066t","4810":"c1192t"}}},"model_sequences":{"sequence":{"3227":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"AE006468.1","fmin":"3570462","fmax":"3572006","strand":"+","sequence":"AGGTAAGGAGGTGATCCAACCGCAGGTTCCCCTACGGTTACCTTGTTACGACTTCACCCCAGTCATGAATCACAAAGTGGTAAGCGCCCTCCCGAAGGTTAAGCTACCTACTTCTTTTGCAACCCACTCCCATGGTGTGACGGGCGGTGTGTACAAGGCCCGGGAACGTATTCACCGTGGCATTCTGATCCACGATTACTAGCGATTCCGACTTCATGGAGTCGAGTTGCAGACTCCAATCCGGACTACGACGCACTTTATGAGGTCCGCTTGCTCTCGCGAGGTCGCTTCTCTTTGTATGCGCCATTGTAGCACGTGTGTAGCCCTGGTCGTAAGGGCCATGATGACTTGACGTCATCCCCACCTTCCTCCAGTTTATCACTGGCAGTCTCCTTTGAGTTCCCGACCTAATCGCTGGCAACAAAGGATAAGGGTTGCGCTCGTTGCGGGACTTAACCCAACATTTCACAACACGAGCTGACGACAGCCATGCAGCACCTGTCTCACAGTTCCCGAAGGCACCAATCCATCTCTGGAAAGTTCTGTGGATGTCAAGACCAGGTAAGGTTCTTCGCGTTGCATCGAATTAAACCACATGCTCCACCGCTTGTGCGGGCCCCCGTCAATTCATTTGAGTTTTAACCTTGCGGCCGTACTCCCCAGGCGGTCTACTTAACGCGTTAGCTCCGGAAGCCACGCCTCAAGGGCACAACCTCCAAGTAGACATCGTTTACGGCGTGGACTACCAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGCACCTGAGCGTCAGTCTTTGTCCAGGGGGCCGCCTTCGCCACCGGTATTCCTCCAGATCTCTACGCATTTCACCGCTACACCTGGAATTCTACCCCCCTCTACAAGACTCAAGCCTGCCAGTTTCGAATGCAGTTCCCAGGTTGAGCCCGGGGATTTCACATCCGACTTGACAGACCGCCTGCGTGCGCTTTACGCCCAGTAATTCCGATTAACGCTTGCACCCTCCGTATTACCGCGGCTGCTGGCACGGAGTTAGCCGGTGCTTCTTCTGCGGGTAACGTCAATTGCTGCGGTTATTAACCACAACACCTTCCTCCCCGCTGAAAGTACTTTACAACCCGAAGGCCTTCTTCATACACGCGGCATGGCTGCATCAGGCTTGCGCCCATTGTGCAATATTCCCCACTGCTGCCTCCCGTAGGAGTCTGGACCGTGTCTCAGTTCCAGTGTGGCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTTGGTGAGCCGTTACCTCACCAACAAGCTAATCCCATCTGGGCACATCTGATGGCAAGAGGCCCGAAGGTCCCCCTCTTTGGTCTTGCGACGTTATGCGGTATTAGCCACCGTTTCCAGTAGTTATCCCCCTCCATCAGGCAGTTTCCCAGACATTACTCACCCGTCCGCCACTCGTCAGCGAAGCAGCAAGCTGCTTCCTGTTACCGTTCGACTTGCATGTGTTAGGCCTGCCGCCAGCGTTCAATCTGAGCCATGATCAAACTCTTCAATT","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35717","NCBI_taxonomy_name":"Salmonella enterica subsp. salamae","NCBI_taxonomy_id":"59202"}}}},"ARO_accession":"3003512","ARO_id":"40114","ARO_name":"Salmonella enterica 16S rRNA (rrsD) mutation conferring resistance to spectinomycin","CARD_short_name":"Sent_16S_SPT","ARO_description":"Point mutations in the helix 34 region of the rrsD 16S rRNA gene of Salmonella enterica serovar Typhimurium can confer resistance to spectinomycin.","ARO_category":{"40277":{"category_aro_accession":"3003666","category_aro_cvterm_id":"40277","category_aro_name":"16s rRNA with mutation conferring resistance to aminoglycoside antibiotics","category_aro_description":"Point mutations in the 16S rRNA of bacteria can confer resistance to aminoglycosides.","category_aro_class_name":"AMR Gene Family"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2109":{"model_id":"2109","model_name":"Mycobacterium tuberculosis gyrB mutant conferring resistance to fluoroquinolones","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"14218":"A504V","14237":"S447F","14240":"D461H","14241":"D461N","14243":"N499D","14245":"N499T","14249":"E501V","14250":"E501D","3460":"V301L","3505":"T500P","3504":"T500N","3508":"N499K","9615":"V457L"},"CRyPTIC-R":{"14218":"A504V"},"clinical":{"14218":"A504V","14237":"S447F","14240":"D461H","14241":"D461N","14243":"N499D","14245":"N499T","14249":"E501V","14250":"E501D","14252":"A504V","9616":"E501D","9630":"N499T","3460":"V301L","3845":"N499D","9615":"V457L","3462":"N499D","3461":"D461H"},"WHO-R":{"14237":"S447F","14240":"D461H","14241":"D461N","14243":"N499D","14245":"N499T","14249":"E501V","14250":"E501D","14252":"A504V"},"ReSeqTB-High":{"9616":"E501D","9630":"N499T"},"Curated-R":{"3460":"V301L","3463":"V301L","3464":"V301L","3505":"T500P","3506":"T500P","3513":"E501V","3504":"T500N","3508":"N499K","3512":"N499K","3507":"E501D","3845":"N499D","3462":"N499D","3461":"D461H"},"experimental":{"3505":"T500P","3513":"E501V","3504":"T500N","3508":"N499K","3507":"E501D"},"ReSeqTB-Moderate":{"9615":"V457L"}},"40330":{"param_type":"multiple resistance variants","param_description":"A set of nucleotide or amino acid substitutions that are all required to confer resistance to an antibiotic drug or drug class, encoded as: [wild-type 1][position 1][mutation 1],[wild-type 2][position 2][mutation 2], etc. For example, D63Y,T142K.","param_type_id":"40330","param_value":{"3463":"N538D,T546M","3464":"R485C,T539N","3506":"N538T,T546M","3512":"R485C,T546M"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1200"}},"model_sequences":{"sequence":{"8772":{"protein_sequence":{"accession":"NP_214519.2","sequence":"MAAQKKKAQDEYGAASITILEGLEAVRKRPGMYIGSTGERGLHHLIWEVVDNAVDEAMAGYATTVNVVLLEDGGVEVADDGRGIPVATHASGIPTVDVVMTQLHAGGKFDSDAYAISGGLHGVGVSVVNALSTRLEVEIKRDGYEWSQVYEKSEPLGLKQGAPTKKTGSTVRFWADPAVFETTEYDFETVARRLQEMAFLNKGLTINLTDERVTQDEVVDEVVSDVAEAPKSASERAAESTAPHKVKSRTFHYPGGLVDFVKHINRTKNAIHSSIVDFSGKGTGHEVEIAMQWNAGYSESVHTFANTINTHEGGTHEEGFRSALTSVVNKYAKDRKLLKDKDPNLTGDDIREGLAAVISVKVSEPQFEGQTKTKLGNTEVKSFVQKVCNEQLTHWFEANPTDAKVVVNKAVSSAQARIAARKARELVRRKSATDIGGLPGKLADCRSTDPRKSELYVVEGDSAGGSAKSGRDSMFQAILPLRGKIINVEKARIDRVLKNTEVQAIITALGTGIHDEFDIGKLRYHKIVLMADADVDGQHISTLLLTLLFRFMRPLIENGHVFLAQPPLYKLKWQRSDPEFAYSDRERDGLLEAGLKAGKKINKEDGIQRYKGLGEMDAKELWETTMDPSVRVLRQVTLDDAAAADELFSILMGEDVDARRSFITRNAKDVRFLDV"},"dna_sequence":{"accession":"NC_000962.3","fmin":"5239","fmax":"7267","strand":"+","sequence":"GTGGCTGCCCAGAAAAAGAAGGCCCAAGACGAATACGGCGCTGCGTCTATCACCATTCTCGAAGGGCTGGAGGCCGTCCGCAAACGTCCCGGCATGTACATTGGCTCGACCGGTGAGCGCGGTTTACACCATCTCATTTGGGAGGTGGTCGACAACGCGGTCGACGAGGCGATGGCCGGTTATGCAACCACAGTGAACGTAGTGCTGCTTGAGGATGGCGGTGTCGAGGTCGCCGACGACGGCCGCGGCATTCCGGTCGCCACCCACGCCTCCGGCATACCGACCGTCGACGTGGTGATGACACAACTACATGCCGGCGGCAAGTTCGACTCGGACGCGTATGCGATATCTGGTGGTCTGCACGGCGTCGGCGTGTCGGTGGTTAACGCGCTATCCACCCGGCTCGAAGTCGAGATCAAGCGCGACGGGTACGAGTGGTCTCAGGTTTATGAGAAGTCGGAACCCCTGGGCCTCAAGCAAGGGGCGCCGACCAAGAAGACGGGGTCAACGGTGCGGTTCTGGGCCGACCCCGCTGTTTTCGAAACCACGGAATACGACTTCGAAACCGTCGCCCGCCGGCTGCAAGAGATGGCGTTCCTCAACAAGGGGCTGACCATCAACCTGACCGACGAGAGGGTGACCCAAGACGAGGTCGTCGACGAAGTGGTCAGCGACGTCGCCGAGGCGCCGAAGTCGGCAAGTGAACGCGCAGCCGAATCCACTGCACCGCACAAAGTTAAGAGCCGCACCTTTCACTATCCGGGTGGCCTGGTGGACTTCGTGAAACACATCAACCGCACCAAGAACGCGATTCATAGCAGCATCGTGGACTTTTCCGGCAAGGGCACCGGGCACGAGGTGGAGATCGCGATGCAATGGAACGCCGGGTATTCGGAGTCGGTGCACACCTTCGCCAACACCATCAACACCCACGAGGGCGGCACCCACGAAGAGGGCTTCCGCAGCGCGCTGACGTCGGTGGTGAACAAGTACGCCAAGGACCGCAAGCTACTGAAGGACAAGGACCCCAACCTCACCGGTGACGATATCCGGGAAGGCCTGGCCGCTGTGATCTCGGTGAAGGTCAGCGAACCGCAGTTCGAGGGCCAGACCAAGACCAAGTTGGGCAACACCGAGGTCAAATCGTTTGTGCAGAAGGTCTGTAACGAACAGCTGACCCACTGGTTTGAAGCCAACCCCACCGACGCGAAAGTCGTTGTGAACAAGGCTGTGTCCTCGGCGCAAGCCCGTATCGCGGCACGTAAGGCACGAGAGTTGGTGCGGCGTAAGAGCGCCACCGACATCGGTGGATTGCCCGGCAAGCTGGCCGATTGCCGTTCCACGGATCCGCGCAAGTCCGAACTGTATGTCGTAGAAGGTGACTCGGCCGGCGGTTCTGCAAAAAGCGGTCGCGATTCGATGTTCCAGGCGATACTTCCGCTGCGCGGCAAGATCATCAATGTGGAGAAAGCGCGCATCGACCGGGTGCTAAAGAACACCGAAGTTCAGGCGATCATCACGGCGCTGGGCACCGGGATCCACGACGAGTTCGATATCGGCAAGCTGCGCTACCACAAGATCGTGCTGATGGCCGACGCCGATGTTGACGGCCAACATATTTCCACGCTGTTGTTGACGTTGTTGTTCCGGTTCATGCGGCCGCTCATCGAGAACGGGCATGTGTTTTTGGCACAACCGCCGCTGTACAAACTCAAGTGGCAGCGCAGTGACCCGGAATTCGCATACTCCGACCGCGAGCGCGACGGTCTGCTGGAGGCGGGGCTGAAGGCCGGGAAGAAGATCAACAAGGAAGACGGCATTCAGCGGTACAAGGGTCTAGGTGAAATGGACGCTAAGGAGTTGTGGGAGACCACCATGGATCCCTCGGTTCGTGTGTTGCGTCAAGTGACGCTGGACGACGCCGCCGCCGCCGACGAGTTGTTCTCCATCCTGATGGGCGAGGACGTCGACGCGCGGCGCAGCTTTATCACCCGCAACGCCAAGGATGTTCGGTTCCTGGATGTCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3003459","ARO_id":"40052","ARO_name":"Mycobacterium tuberculosis gyrB mutant conferring resistance to fluoroquinolones","CARD_short_name":"Mtub_gyrB_FLO","ARO_description":"Point mutation in Mycobacterium tuberculosis gyrB resulting in fluoroquinolone resistance.","ARO_category":{"37244":{"category_aro_accession":"3000864","category_aro_cvterm_id":"37244","category_aro_name":"fluoroquinolone resistant gyrB","category_aro_description":"Point mutations in DNA gyrase subunit B (gyrB) observed in Mycobacterium tuberculosis can result in resistance to fluoroquinolones.","category_aro_class_name":"AMR Gene Family"},"35942":{"category_aro_accession":"0000023","category_aro_cvterm_id":"35942","category_aro_name":"enoxacin","category_aro_description":"Enoxacin belongs to a group called fluoroquinolones. Its mode of action depends upon blocking bacterial DNA replication by binding itself to DNA gyrase and causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37004":{"category_aro_accession":"3000660","category_aro_cvterm_id":"37004","category_aro_name":"lomefloxacin","category_aro_description":"Lomefloxacin is a difluoropiperazinyl quinolone, sharing similar activities with other fluoroquinolones. It is used to treat urinary tract infections. Relative to other fluoroquinolones, it has a longer half life and has higher serum concentrations.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37007":{"category_aro_accession":"3000663","category_aro_cvterm_id":"37007","category_aro_name":"ofloxacin","category_aro_description":"Ofloxacin is a 6-fluoro, 7-piperazinyl quinolone with a methyl-substituted oxazine ring. It has a broad spectrum of activity including many enterobacteria and mycoplasma but most anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"37008":{"category_aro_accession":"3000664","category_aro_cvterm_id":"37008","category_aro_name":"trovafloxacin","category_aro_description":"Trovafloxacin is a trifluoroquinalone with a broad spectrum of activity that acts by inhibiting the uncoiling of supercoiled DNA. While potent against many Gram-positive and Gram-negative bacteria, it is less active against pseudomonads and Cl. difficile. It is usually taken as the prodrug trovafloxacin mesylate or alatrofloxacin mesylate for oral or intravenous administration, respectively.","category_aro_class_name":"Antibiotic"},"37009":{"category_aro_accession":"3000665","category_aro_cvterm_id":"37009","category_aro_name":"grepafloxacin","category_aro_description":"Grepafloxacin is a broad-spectrum antibacterial quinoline. It is no longer taken due to its high toxicity.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"37142":{"category_aro_accession":"3000762","category_aro_cvterm_id":"37142","category_aro_name":"pefloxacin","category_aro_description":"Pefloxacin is structurally and functionally similar to norfloxacin. It is poorly active against mycobacteria, while anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2077":{"model_id":"2077","model_name":"Mycolicibacterium smegmatis 16S rRNA (rrsA) mutation conferring resistance to neomycin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"41093","param_value":"2700"},"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"12950":"a1389g"},"Curated-R":{"12950":"a1389g"},"clinical":{"12950":"a1389g"}}},"model_sequences":{"sequence":{"4145":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"NC_008596.1","fmin":"3823614","fmax":"3825143","strand":"-","sequence":"AGAAAGGAGGTGATCCAGCCGCACCTTCCGGTACGGCTACCTTGTTACGACTTCGTCCCAATCGCCGATCCCACCTTCGACGGCTCCCTCCACAAGGGTTAGGCCACCGGCTTCGGGTGTTACCGACTTTCATGACGTGACGGGCGGTGTGTACAAGGCCCGGGAACGTATTCACCGCAGCGTTGCTGATCTGCGATTACTAGCGACTCCGACTTCACGGGGTCGAGTTGCAGACCCCGATCCGAACTGAGACCGGCTTTGAAAGGATTCGCTCCACCTCACGGCATCGCAGCCCTTTGTACCGGCCATTGTAGCATGTGTGAAGCCCTGGACATAAGGGGCATGATGACTTGACGTCATCCCCACCTTCCTCCGAGTTGACCCCGGCAGTCTCTCACGAGTCCCCACCATAACGTGCTGGCAACATGAGACAAGGGTTGCGCTCGTTGCGGGACTTAACCCAACATCTCACGACACGAGCTGACGACAGCCATGCACCACCTGCACACAGGCCACAAGGGAACCGACATCTCTGCCGGCGTCCTGTGCATGTCAAACCCAGGTAAGGTTCTTCGCGTTGCATCGAATTAATCCACATGCTCCGCCGCTTGTGCGGGCCCCCGTCAATTCCTTTGAGTTTTAGCCTTGCGGCCGTACTCCCCAGGCGGGGTACTTAATGCGTTAGCTACGGCACGGATCCCAAGGAAGGAAACCCACACCTAGTACCCACCGTTTACGGCGTGGACTACCAGGGTATCTAATCCTGTTCGCTCCCCACGCTTTCGCTCCTCAGCGTCAGTTACTGCCCAGAGACCCGCCTTCGCCACCGGTGTTCCTCCTGATATCTGCGCATTCCACCGCTACACCAGGAATTCCAGTCTCCCCTGCAGTACTCTAGTCTGCCCGTATCGCCCGCACGCCCACAGTTAAGCTGTGAGTTTTCACGAACAACGCGACAAACCACCTACGAGCTCTTTACGCCCAGTAATTCCGGACAACGCTCGGACCCTACGTATTACCGCGGCTGCTGGCACGTAGTTGGCCGGTCCTTCTTCTGCACATACCGTCACTTGCGCTTCGTCTGTGCTGAAAGAGGTTTACAACCCGAAGGCCGTCATCCCTCACGCGGCGTCGCTGCATCAGGCTTGCGCCCATTGTGCAATATTCCCCACTGCTGCCTCCCGTAGGAGTCTGGGCCGTATCTCAGTCCCAGTGTGGCCGGTCACCCTCTCAGGCCGGCTACCCGTCGTCGCCTTGGTAGGCCATCACCCCACCAACAAGCTGATAGGCCGCGGGCCCATCCCACACCGCAAAAGCTTTCCCCTACCAGGCCATGCGACCAGCAGGGTGTATTCGGTATTAGACCCAGTTTCCCAGGCTTATCCCAAAGTGCAGGGCAGATCACCCACGTGTTACTCACCCGTTCGCCACTCGAGTACCCCCGAAAGGGCCTTTCCGTTCGACTTGCATGTGTTAAGCACGCCGCCAGCGTTCGTCCTGAGCCAGGATCAAACTCTCCAAACAAAAAC","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36769","NCBI_taxonomy_name":"Mycolicibacterium smegmatis MC2 155","NCBI_taxonomy_id":"246196"}}}},"ARO_accession":"3003544","ARO_id":"40146","ARO_name":"Mycolicibacterium smegmatis 16S rRNA (rrsA) mutation conferring resistance to neomycin","CARD_short_name":"Msme_16rrsA_NEO","ARO_description":"Point mutations in the helix 44 region of the 16S rRNA rrsA gene of Mycolicibacterium smegmatis can confer resistance to neomycin.","ARO_category":{"40277":{"category_aro_accession":"3003666","category_aro_cvterm_id":"40277","category_aro_name":"16s rRNA with mutation conferring resistance to aminoglycoside antibiotics","category_aro_description":"Point mutations in the 16S rRNA of bacteria can confer resistance to aminoglycosides.","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"212":{"model_id":"212","model_name":"Staphylococcus aureus parC conferring resistance to fluoroquinolones","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"3982":"S80F","3984":"E84G","3983":"S80Y"},"Curated-R":{"3982":"S80F","3984":"E84G","3983":"S80Y"},"clinical":{"3982":"S80F","3984":"E84G","3983":"S80Y"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1400"}},"model_sequences":{"sequence":{"6038":{"protein_sequence":{"accession":"WP_001289569.1","sequence":"MSEIIQDLSLEDVLGDRFGRYSKYIIQERALPDVRDGLKPVQRRILYAMYSSGNTHDKNFRKSAKTVGDVIGQYHPHGDSSVYEAMVRLSQDWKLRHVLIEMHGNNGSIDNDPPAAMRYTEAKLSLLAEELLRDINKETVSFIPNYDDTTLEPMVLPSRFPNLLVNGSTGISAGYATDIPPHNLAEVIQATLKYIDNPDITVNQLMKYIKGPDFPTGGIIQGIDGIKKAYESGKGRIIVRSKVEEETLRNGRKQLIITEIPYEVNKSSLVKRIDELRADKKVDGIVEVRDETDRTGLRIAIELKKDVNSESIKNYLYKNSDLQISYNFNMVAISDGRPKLMGIRQIIDSYLNHQIEVVANRTKFELDNAEKRMHIVEGLIKALSILDKVIELIRSSKNKRDAKENLIEVYEFTEEQAEAIVMLQLYRLTNTDIVALEGEHKELEALIKQLRHILDNHDALLNVIKEELNEIKKKFKSERLSLIEAEIEEIKIDKEVMVPSEEVILSMTRHGYIKRTSIRSFNASGVEDIGLKDGDSLLKHQEVNTQDTVLVFTNKGRYLFIPVHKLADIRWKELGQHVSQIVPIEEDEVVINVFNEKDFNTDAFYVFATQNGMIKKSTVPLFKTTRFNKPLIATKVKENDDLISVMRFEKDQLITVITNKGMSLTYNTSELSDTGLRAAGVKSINLKAEDFVVMTEGVSENDTILMATQRGSLKRISFKILQVAKRAQRGITLLKELKKNPHRIVAAHVVTGEHSQYTLYSKSNEEHGLINDIHKSEQYTNGSFIVDTDDFGEVIDMYIS"},"dna_sequence":{"accession":"NC_002951.2","fmin":"1397969","fmax":"1400372","strand":"+","sequence":"GTGAGTGAAATAATTCAAGATTTATCACTTGAAGATGTTTTAGGTGATCGCTTTGGAAGATATAGTAAATATATTATTCAAGAGCGTGCATTGCCAGATGTTCGTGATGGTTTAAAACCAGTACAACGTCGTATTTTATATGCAATGTATTCAAGTGGTAATACACACGATAAAAATTTCCGTAAAAGTGCGAAAACAGTCGGTGATGTTATTGGTCAATATCATCCACATGGAGACTCCTCAGTGTACGAAGCAATGGTCCGTTTAAGTCAAGACTGGAAGTTACGACATGTCTTAATAGAAATGCATGGTAATAATGGTAGTATCGATAATGATCCGCCAGCGGCAATGCGTTACACTGAAGCTAAGTTAAGCTTACTAGCTGAAGAGTTATTACGTGATATTAATAAAGAGACAGTTTCTTTCATTCCAAACTATGATGATACGACACTCGAACCAATGGTATTGCCATCAAGATTTCCTAACTTACTAGTGAATGGTTCTACAGGTATATCTGCAGGTTACGCGACAGATATACCACCACATAATTTAGCTGAAGTGATTCAAGCAACACTTAAATATATTGATAATCCGGATATTACAGTCAATCAATTAATGAAATATATTAAAGGTCCTGATTTTCCAACTGGTGGTATTATTCAAGGTATTGATGGTATTAAAAAAGCTTATGAATCAGGTAAAGGTAGAATTATAGTTCGTTCTAAAGTTGAAGAAGAAACTTTACGCAATGGACGTAAACAGTTAATTATTACTGAAATTCCATATGAAGTGAACAAAAGTAGCTTAGTAAAACGTATCGATGAATTACGTGCTGACAAAAAAGTCGATGGTATCGTTGAAGTACGTGATGAAACTGATAGAACTGGTTTACGAATAGCAATTGAATTGAAAAAAGATGTGAACAGTGAATCAATCAAAAATTATCTTTATAAAAACTCTGATTTACAGATTTCATATAATTTCAACATGGTCGCTATTAGTGATGGTCGTCCAAAATTGATGGGTATTCGTCAAATTATAGATAGTTATTTGAATCACCAAATTGAGGTTGTTGCAAATAGAACGAAGTTTGAATTAGATAATGCAGAAAAACGTATGCATATCGTTGAAGGTTTGATTAAAGCGTTGTCAATTTTAGATAAAGTAATCGAATTGATTCGTAGCTCTAAAAACAAGCGTGACGCTAAAGAAAACCTTATCGAAGTATACGAGTTCACAGAAGAACAGGCTGAAGCAATTGTAATGTTACAGTTATATCGTTTAACAAATACTGACATAGTTGCGCTTGAAGGTGAACATAAAGAACTTGAAGCATTAATCAAACAATTACGTCATATTCTTGATAACCATGATGCATTATTGAATGTCATAAAAGAAGAATTGAATGAAATTAAAAAGAAATTCAAATCTGAACGACTGTCTTTAATTGAAGCAGAAATTGAAGAAATTAAAATTGACAAAGAAGTTATGGTGCCTAGTGAAGAAGTTATTTTAAGTATGACACGTCATGGATATATTAAACGTACTTCTATTCGTAGCTTTAATGCTAGCGGTGTTGAAGATATTGGTTTAAAAGATGGTGACAGTTTACTTAAACATCAAGAAGTAAATACGCAAGATACCGTACTAGTATTTACAAATAAAGGTCGTTATCTATTTATACCGGTTCATAAATTAGCAGATATTCGTTGGAAAGAATTGGGACAACATGTATCACAAATAGTTCCTATCGAAGAAGATGAAGTGGTTATTAATGTCTTTAATGAAAAGGACTTTAATACAGATGCATTTTATGTTTTTGCGACTCAAAATGGCATGATTAAGAAAAGTACAGTGCCTCTATTTAAAACAACGCGTTTTAATAAACCTTTAATTGCTACTAAAGTTAAAGAAAATGATGATTTGATTAGTGTTATGCGCTTTGAAAAAGATCAATTAATTACCGTCATTACTAATAAAGGTATGTCATTAACGTATAATACAAGTGAACTATCAGATACCGGATTAAGGGCAGCTGGTGTTAAATCAATAAATCTTAAAGCTGAAGATTTCGTTGTTATGACAGAAGGTGTTTCTGAAAATGATACTATATTGATGGCCACACAACGCGGCTCGTTAAAACGTATTAGTTTTAAAATCTTACAAGTTGCTAAAAGAGCACAACGTGGAATAACTTTATTAAAAGAATTAAAGAAAAATCCACATCGTATTGTAGCTGCACATGTAGTGACAGGTGAACATAGTCAATATACATTATATTCAAAATCAAATGAAGAACATGGTTTAATTAATGATATTCATAAATCTGAACAATATACAAATGGCTCATTCATTGTAGATACAGATGATTTTGGTGAAGTAATAGACATGTATATTAGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37074","NCBI_taxonomy_name":"Staphylococcus","NCBI_taxonomy_id":"1279"}}}},"ARO_accession":"3003312","ARO_id":"39896","ARO_name":"Staphylococcus aureus parC conferring resistance to fluoroquinolones","CARD_short_name":"Saur_parC_FLO","ARO_description":"Point mutation in Staphylococcus aureus parC resulting in fluoroquinolone resistance.","ARO_category":{"36913":{"category_aro_accession":"3000619","category_aro_cvterm_id":"36913","category_aro_name":"fluoroquinolone resistant parC","category_aro_description":"ParC is a subunit of topoisomerase IV, which decatenates and relaxes DNA to allow access to genes for transcription or translation. Point mutations in ParC prevent fluoroquinolone antibiotics from inhibiting DNA synthesis, and confer low-level resistance. Higher-level resistance results from both gyrA and parC mutations.","category_aro_class_name":"AMR Gene Family"},"35942":{"category_aro_accession":"0000023","category_aro_cvterm_id":"35942","category_aro_name":"enoxacin","category_aro_description":"Enoxacin belongs to a group called fluoroquinolones. Its mode of action depends upon blocking bacterial DNA replication by binding itself to DNA gyrase and causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37004":{"category_aro_accession":"3000660","category_aro_cvterm_id":"37004","category_aro_name":"lomefloxacin","category_aro_description":"Lomefloxacin is a difluoropiperazinyl quinolone, sharing similar activities with other fluoroquinolones. It is used to treat urinary tract infections. Relative to other fluoroquinolones, it has a longer half life and has higher serum concentrations.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37007":{"category_aro_accession":"3000663","category_aro_cvterm_id":"37007","category_aro_name":"ofloxacin","category_aro_description":"Ofloxacin is a 6-fluoro, 7-piperazinyl quinolone with a methyl-substituted oxazine ring. It has a broad spectrum of activity including many enterobacteria and mycoplasma but most anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"37008":{"category_aro_accession":"3000664","category_aro_cvterm_id":"37008","category_aro_name":"trovafloxacin","category_aro_description":"Trovafloxacin is a trifluoroquinalone with a broad spectrum of activity that acts by inhibiting the uncoiling of supercoiled DNA. While potent against many Gram-positive and Gram-negative bacteria, it is less active against pseudomonads and Cl. difficile. It is usually taken as the prodrug trovafloxacin mesylate or alatrofloxacin mesylate for oral or intravenous administration, respectively.","category_aro_class_name":"Antibiotic"},"37009":{"category_aro_accession":"3000665","category_aro_cvterm_id":"37009","category_aro_name":"grepafloxacin","category_aro_description":"Grepafloxacin is a broad-spectrum antibacterial quinoline. It is no longer taken due to its high toxicity.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"37142":{"category_aro_accession":"3000762","category_aro_cvterm_id":"37142","category_aro_name":"pefloxacin","category_aro_description":"Pefloxacin is structurally and functionally similar to norfloxacin. It is poorly active against mycobacteria, while anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"535":{"model_id":"535","model_name":"Morganella morganii gyrB conferring resistance to fluoroquinolones","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"2164":"S464Y","3448":"S463A"},"Curated-R":{"2164":"S464Y","3448":"S463A"},"clinical":{"2164":"S464Y","3448":"S463A"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1200"}},"model_sequences":{"sequence":{"5211":{"protein_sequence":{"accession":"AGG29535.1","sequence":"MSNTYDSSSIKVLKGLDAVRKRPGMYIGDTDDGTGLHHMVFEVVDNAIDEALAGYCKDIIVTIHNDNSVSVQDDGRGIPTGIHEEEGVSAAEVIMTVLHAGGKFDDNSYKVSGGLHGVGVSVVNALSEKLELVIRRDGKVHEQIYRHGEPQDRLTVVGETDKTGTRVRFWPSMDTFKGETEFQYDILAKRLRELSFLNSGVSIRLIDKRDGKEDHFHYEGGIKAFVEYLSRAKTSIHNNVFYFSTEKDDIGVEISMQWNDSFQENVYCFTNNIPQRDGGAHLAGFRAAMTRTLNSYIEKEGLNKKSKVSTTGDDAREGLVAVISVKVPDPKFSSQTKDKLVSSEVKTAVETLMNEKLSEYLDENPNDTKIIVGKIIDAARAREAARRAREMTRRKGALDLAGLPGKLADCQERDPAFSELYLVEGDSAGGSAKQGRNRKNQAILPLKGKILNVEKARFDKMLASQEVATLITALGCGIGRDEYNPDKLRYHSIIIMTDADVDGSHIRTLLLTFFYRQMPEIIERGYVYIAQPPLYKVKKGKQEQYIKDDEAMEQYQVSIALDGAALYVNENAAPIQGEHLEKLLHEYNGAHKIIRRLERLYPLALLNSLVYQPKLEESALLNKTEVEAWAQSLTERLTRHEEHGSTYSYRIAENKERQLFEPVLTIRTHGVDTDYNLDFDFVHGSEYARISKLGELIRGLIEEGAYVVRGERRQNVSNFEQALDWLMKESRRGLAVQRYKGLGEMNPEQLWETTMNPETRRMLQVTVKDAIATDQLFTTLMGDDVEPRRAFIEENALKAANIDV"},"dna_sequence":{"accession":"CP004345.1","fmin":"545199","fmax":"547614","strand":"-","sequence":"ATGTCGAATACCTATGACTCCTCAAGTATCAAAGTATTAAAAGGGCTGGACGCGGTGCGTAAACGCCCGGGAATGTACATTGGTGATACCGATGACGGAACCGGTTTACACCACATGGTCTTCGAGGTTGTTGACAACGCTATCGACGAAGCCCTCGCCGGTTACTGTAAAGACATCATTGTGACCATTCACAATGATAATTCAGTCTCCGTACAGGATGACGGTCGCGGTATCCCGACCGGGATCCATGAAGAAGAAGGCGTCTCCGCCGCAGAAGTTATCATGACTGTTCTGCACGCCGGCGGGAAGTTCGATGATAACTCCTATAAAGTCTCAGGCGGCCTGCACGGCGTCGGGGTCTCTGTTGTTAACGCCCTGTCTGAAAAACTGGAACTGGTTATCCGCCGTGACGGCAAAGTTCACGAGCAGATTTACCGCCACGGTGAACCGCAGGATCGCCTGACTGTTGTCGGCGAAACCGATAAAACCGGGACACGCGTGCGTTTCTGGCCGAGCATGGACACCTTCAAAGGCGAGACTGAATTCCAGTACGACATTCTGGCAAAACGCCTGCGCGAACTCTCCTTCCTGAACTCCGGTGTATCGATCCGTCTGATCGATAAACGCGACGGCAAAGAAGATCACTTTCACTACGAAGGCGGTATCAAAGCATTCGTGGAATATTTAAGCCGCGCCAAAACTTCGATTCATAACAACGTTTTCTATTTCTCCACTGAGAAAGACGATATCGGCGTGGAAATCTCCATGCAGTGGAATGACTCCTTCCAGGAAAACGTATACTGCTTCACCAACAACATTCCGCAGCGCGACGGTGGTGCTCACCTCGCCGGTTTCCGCGCCGCCATGACCCGTACCCTCAACAGCTATATTGAGAAAGAAGGGCTGAATAAAAAATCCAAAGTCAGCACCACCGGGGACGATGCCCGTGAAGGACTGGTGGCGGTCATTTCCGTCAAAGTGCCGGATCCGAAATTCTCCTCCCAGACTAAAGACAAGCTGGTCTCTTCCGAAGTGAAAACGGCGGTTGAAACCCTGATGAACGAAAAGCTGTCTGAATATCTGGATGAAAACCCGAACGACACCAAAATCATTGTCGGCAAAATTATTGATGCCGCACGCGCCCGTGAAGCTGCACGCCGTGCCCGTGAAATGACCCGCCGTAAAGGCGCGCTGGATTTAGCCGGTCTGCCGGGTAAACTGGCGGATTGTCAGGAACGCGACCCGGCCTTCTCCGAACTGTACTTAGTGGAAGGGGACTCTGCGGGCGGCTCTGCAAAACAGGGGCGTAACCGTAAGAACCAGGCTATCCTGCCGCTGAAAGGTAAAATCCTGAACGTTGAGAAGGCGCGTTTTGATAAAATGCTGGCTTCTCAGGAAGTTGCCACCCTGATCACCGCACTCGGCTGCGGTATCGGCCGCGACGAATACAACCCGGACAAACTGCGCTATCACAGCATCATCATCATGACCGATGCCGACGTCGATGGTTCACACATCCGTACCCTGTTACTGACTTTCTTCTACCGTCAGATGCCGGAAATCATTGAGCGCGGTTATGTGTATATCGCACAGCCGCCGCTGTATAAAGTGAAAAAAGGCAAGCAGGAACAGTATATTAAAGATGACGAAGCGATGGAGCAGTATCAGGTCTCTATCGCACTGGATGGCGCGGCACTGTATGTAAACGAAAATGCAGCTCCGATTCAGGGCGAACATCTGGAAAAACTGCTGCACGAATACAACGGCGCACACAAAATTATCCGCCGTTTAGAGCGTCTCTATCCGCTGGCACTGTTAAACAGCCTGGTCTACCAGCCGAAACTGGAAGAATCCGCGCTGCTGAACAAAACCGAGGTGGAAGCCTGGGCACAGAGCCTGACAGAGCGCCTGACCCGTCATGAAGAGCACGGCAGCACCTACAGCTACCGTATTGCGGAAAACAAAGAGCGCCAGCTGTTTGAGCCGGTACTGACTATCCGTACCCACGGTGTGGATACTGACTACAATCTGGATTTCGATTTTGTTCACGGCAGCGAATATGCCCGTATCTCCAAACTGGGTGAGCTTATCCGTGGTCTGATTGAAGAAGGTGCTTATGTTGTCCGTGGTGAACGCCGTCAGAACGTCAGCAACTTTGAGCAGGCACTGGACTGGCTGATGAAAGAATCACGCCGTGGTCTGGCTGTACAGCGCTATAAAGGGCTGGGTGAAATGAACCCGGAACAGCTGTGGGAAACCACAATGAACCCGGAAACCCGCCGTATGTTGCAGGTCACGGTAAAAGATGCGATTGCAACGGATCAGTTATTCACCACACTGATGGGTGATGATGTTGAACCGCGCCGTGCCTTTATCGAAGAGAATGCCCTGAAAGCGGCAAACATCGACGTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40075","NCBI_taxonomy_name":"Morganella morganii subsp. morganii KT","NCBI_taxonomy_id":"1124991"}}}},"ARO_accession":"3003306","ARO_id":"39890","ARO_name":"Morganella morganii gyrB conferring resistance to fluoroquinolones","CARD_short_name":"Mmor_gyrB_FLO","ARO_description":"Point mutation in Morganella morganii resulting in fluoroquinolone resistance.","ARO_category":{"37244":{"category_aro_accession":"3000864","category_aro_cvterm_id":"37244","category_aro_name":"fluoroquinolone resistant gyrB","category_aro_description":"Point mutations in DNA gyrase subunit B (gyrB) observed in Mycobacterium tuberculosis can result in resistance to fluoroquinolones.","category_aro_class_name":"AMR Gene Family"},"35942":{"category_aro_accession":"0000023","category_aro_cvterm_id":"35942","category_aro_name":"enoxacin","category_aro_description":"Enoxacin belongs to a group called fluoroquinolones. Its mode of action depends upon blocking bacterial DNA replication by binding itself to DNA gyrase and causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37004":{"category_aro_accession":"3000660","category_aro_cvterm_id":"37004","category_aro_name":"lomefloxacin","category_aro_description":"Lomefloxacin is a difluoropiperazinyl quinolone, sharing similar activities with other fluoroquinolones. It is used to treat urinary tract infections. Relative to other fluoroquinolones, it has a longer half life and has higher serum concentrations.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37007":{"category_aro_accession":"3000663","category_aro_cvterm_id":"37007","category_aro_name":"ofloxacin","category_aro_description":"Ofloxacin is a 6-fluoro, 7-piperazinyl quinolone with a methyl-substituted oxazine ring. It has a broad spectrum of activity including many enterobacteria and mycoplasma but most anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"37008":{"category_aro_accession":"3000664","category_aro_cvterm_id":"37008","category_aro_name":"trovafloxacin","category_aro_description":"Trovafloxacin is a trifluoroquinalone with a broad spectrum of activity that acts by inhibiting the uncoiling of supercoiled DNA. While potent against many Gram-positive and Gram-negative bacteria, it is less active against pseudomonads and Cl. difficile. It is usually taken as the prodrug trovafloxacin mesylate or alatrofloxacin mesylate for oral or intravenous administration, respectively.","category_aro_class_name":"Antibiotic"},"37009":{"category_aro_accession":"3000665","category_aro_cvterm_id":"37009","category_aro_name":"grepafloxacin","category_aro_description":"Grepafloxacin is a broad-spectrum antibacterial quinoline. It is no longer taken due to its high toxicity.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"37142":{"category_aro_accession":"3000762","category_aro_cvterm_id":"37142","category_aro_name":"pefloxacin","category_aro_description":"Pefloxacin is structurally and functionally similar to norfloxacin. It is poorly active against mycobacteria, while anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"36":{"model_id":"36","model_name":"Mycobacterium leprae gyrA conferring resistance to fluoroquinolones","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"2127":"A91T"},"Curated-R":{"2127":"A91T"},"clinical":{"2127":"A91T"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1500"}},"model_sequences":{"sequence":{"2059":{"protein_sequence":{"accession":"CAC29514.1","sequence":"MTDITLPPGDGSIQRVEPVDIQQEMQRSYIDYAMSVIVGRALPEVRDGLKPVHRRVLYAMLDSGFRPDRSHAKSARSVAETMGNYHPHGDASIYDTLVRMAQPWSLRYPLVDGQGNFGSPGNDPPAAMRYCVSGNSLVRLLFGKSIRIGDIVTGAQFNSDNPIDLKVLDRHGNPVVADYLFHSGEHQTYTVRTTEGYEITGTSNHPLLCLVNVGGIPTLLWKLIGEIRSGDYVVLQRIPPVEFGPADWYSTMEALLFGAFISGGFVFQDHAGFNSLDRDYFTMVVNAYDTVVGGLRCISSRITVSGSTLLELDVYNLIEFKKTRLSGLCGQRSADKLVPDWLWHSPSTVKRAFLQALFEGEGFSSILSRNIIEISYSTLSERLAADVQQMLLEFGVVSERYCHTVNEYKVVIANRAQVEMFFTQVGFGVTKQAKLIRDVVSMSPCVGMDINCVPGLATFIRKHCDNRWVEEDSFNQHNVDCVQHWHHHSAEIVGHIADPDIRAIVTDLTDGRFYYARVASVTDTGIQPVFSLHVDTEDHSFLTNGFISHNTEARLTPLAMEMLREIDEETVDFISNYDGRVQEPMVLPSRFPNLLANGSGGIAVGMATNIPPHNLYELADAVFWCLENHDADEETMLVAVMERVKGPDFPTAGLIVGSQGIADAYKTGRGSIRIRGVVEVEEDSRGRTSLVITELPYQVNHDNFITSIAEQVRTGRLAGISNVEDQGSDRVGVRIVIEIKRDAVAKVVLNNLYKHTQLQTSFGANMLSIVDGVPRTLRLDQMICYYVEHQLDVIVRRTTYRLRKANERAHILRGLVKALDALDEVITLIRASQTVDIARVGVVELLDIDDIQAQAILDMQLRRLAALERQRIIDDLAKIEVEIADLGDILAKPERRRGIIRNELTEIAEKYGDDRRTRIIAVDGDVNDEDLIAREEVVVTITETGYAKRTKTDLYRSQKRGGKGVQGAGLKQDDIVRHFFVCSTHDWILFFTTQGRVYRAKAYELPEASRTARGQHVANLLAFQPEERIAQVIQIRSYEDAPYLVLATRAGLVKKSKLTDFDSNRSGGIVAINLRDNDELVGAVLCAADGDLLLVSANGQSIRFSATDEALRPMGRATSGVQGMRFNADDRLLSLNVVREDTYLLVATSGGYAKRTSIEEYPMQGRGGKGVLTVMYDRRRGSLVGAIVVDEDSELYAITSGGGVIRTTARQVRQAGRQTKGVRLMNLGEGDTLLAIARNAEESADGGVG"},"dna_sequence":{"accession":"AL450380.1","fmin":"7317","fmax":"11067","strand":"+","sequence":"ATGACTGATATCACGCTGCCACCAGGTGACGGTTCTATACAGCGGGTTGAGCCGGTCGACATTCAGCAGGAAATGCAGCGCAGCTATATTGATTACGCGATGAGTGTGATTGTGGGCCGGGCGTTGCCTGAAGTCCGCGATGGTCTCAAACCGGTACATCGTCGGGTCTTGTACGCGATGTTAGACTCCGGTTTCCGCCCGGACCGTAGCCACGCTAAGTCAGCACGGTCAGTCGCTGAGACGATGGGCAATTACCATCCGCACGGCGACGCATCGATTTATGACACGTTAGTGCGCATGGCGCAGCCGTGGTCGCTGCGGTATCCCTTGGTTGATGGGCAAGGCAATTTCGGTTCGCCGGGTAATGACCCACCGGCAGCGATGCGTTATTGTGTGTCAGGAAATTCCTTGGTGAGGTTGCTATTTGGGAAATCAATACGAATCGGTGATATCGTTACTGGAGCTCAGTTCAATTCGGACAATCCGATCGACTTGAAGGTTCTTGATCGGCATGGTAATCCGGTTGTAGCCGATTATTTATTCCATTCAGGAGAGCACCAAACCTATACAGTGCGCACCACTGAAGGCTATGAGATCACCGGGACGTCGAACCATCCCTTGTTGTGTTTAGTGAATGTCGGCGGTATACCCACCTTGTTGTGGAAGCTGATTGGAGAAATTCGATCAGGAGACTACGTTGTTTTACAGCGGATCCCACCAGTGGAATTTGGTCCGGCGGACTGGTATTCTACGATGGAAGCATTGTTATTCGGAGCCTTTATTAGTGGGGGCTTCGTTTTTCAGGACCATGCTGGATTTAACAGCCTTGACCGTGACTATTTCACCATGGTTGTTAATGCTTATGATACGGTTGTGGGTGGCCTGCGTTGCATATCTTCTCGAATCACCGTATCGGGGTCGACGCTACTCGAACTTGATGTTTATAACCTCATCGAGTTTAAGAAGACAAGACTTAGCGGTTTATGCGGGCAACGGTCTGCGGACAAGTTGGTACCTGACTGGTTGTGGCACTCACCTTCCACCGTCAAACGAGCATTCCTTCAGGCATTGTTTGAAGGTGAAGGATTTTCTTCGATATTGTCGCGAAATATAATTGAGATTTCCTACTCGACACTTAGTGAGCGACTGGCCGCCGACGTCCAGCAGATGCTGCTTGAATTCGGAGTCGTGTCTGAGCGCTATTGCCATACTGTCAATGAGTACAAGGTTGTCATAGCTAACCGCGCTCAAGTAGAAATGTTTTTCACCCAAGTCGGTTTCGGTGTTACTAAACAAGCTAAGCTTATCCGGGACGTGGTATCTATGTCTCCATGCGTTGGCATGGATATCAACTGCGTACCAGGTTTGGCCACTTTCATTCGTAAGCATTGTGATAACCGCTGGGTCGAGGAAGACTCATTTAATCAGCATAATGTTGATTGCGTCCAACATTGGCACCATCATAGCGCGGAAATCGTCGGCCACATCGCCGATCCCGATATTCGTGCCATCGTGACTGACCTTACTGATGGCCGGTTCTACTACGCGCGCGTCGCGTCCGTGACTGATACCGGTATTCAACCTGTGTTCAGTCTACATGTGGACACCGAGGATCATTCGTTTTTGACTAATGGATTCATCAGCCATAACACCGAGGCTCGGCTTACTCCATTGGCGATGGAAATGTTGCGCGAGATCGACGAGGAGACAGTTGATTTCATATCTAACTACGATGGCCGGGTGCAGGAACCGATGGTGTTGCCTAGCCGTTTTCCCAACCTGTTGGCTAATGGTTCTGGCGGTATCGCGGTCGGCATGGCTACCAATATCCCGCCGCACAACCTGTATGAGCTCGCCGACGCTGTGTTTTGGTGCCTAGAGAACCATGACGCTGACGAAGAGACGATGCTGGTCGCTGTTATGGAACGGGTCAAAGGTCCTGATTTCCCTACCGCCGGGTTGATTGTCGGTTCGCAAGGCATTGCCGATGCTTACAAGACTGGCCGTGGTTCCATTCGGATACGCGGAGTTGTTGAGGTTGAAGAAGATTCACGCGGAAGGACGTCATTGGTCATCACTGAGCTACCGTATCAGGTCAACCACGACAACTTCATCACTTCTATCGCTGAGCAAGTCCGCACTGGCCGGCTAGCCGGCATCTCCAATGTAGAAGACCAAGGCAGCGACCGGGTTGGTGTACGTATCGTCATCGAGATCAAGCGTGACGCGGTGGCCAAAGTGGTGCTCAATAACCTGTACAAGCATACTCAGCTGCAAACTAGTTTCGGAGCCAACATGTTGTCAATCGTTGACGGCGTGCCGCGCACTTTGCGGTTGGATCAGATGATTTGTTATTATGTCGAACATCAACTGGACGTCATTGTCCGGCGCACTACCTACCGATTGCGTAAAGCCAACGAGCGGGCTCATATTTTGCGTGGATTGGTCAAAGCGCTCGATGCGTTAGATGAGGTTATTACGTTGATTCGGGCATCGCAGACCGTGGATATTGCTCGTGTTGGGGTGGTCGAGTTACTCGATATCGACGACATTCAGGCTCAAGCTATCCTGGACATGCAGCTGCGGCGTTTGGCGGCTTTGGAGCGTCAACGCATTATTGATGATCTCGCTAAGATTGAGGTCGAGATCGCTGATCTGGGAGATATTCTGGCTAAGCCGGAGCGTCGGCGTGGTATCATTCGTAATGAACTGACTGAGATCGCAGAGAAGTACGGTGATGACCGTCGTACTCGGATAATAGCGGTTGATGGTGATGTCAACGACGAGGATTTGATTGCTCGTGAAGAGGTCGTTGTCACGATAACTGAAACTGGATATGCTAAACGTACTAAAACTGACCTGTATCGCAGCCAGAAACGCGGCGGGAAAGGTGTTCAAGGCGCCGGTTTGAAGCAGGACGACATCGTCCGGCATTTCTTCGTGTGTTCAACTCACGATTGGATCCTGTTTTTCACCACCCAAGGCCGCGTATACCGGGCCAAGGCCTATGAATTGCCAGAGGCTTCTCGAACGGCACGCGGGCAACACGTGGCCAATTTGCTTGCATTCCAGCCTGAAGAGCGCATCGCTCAGGTAATTCAGATCCGTAGCTATGAAGACGCTCCATACTTGGTCCTTGCCACGCGCGCCGGTCTGGTTAAGAAGTCAAAGTTGACCGATTTTGACTCTAATCGTTCGGGTGGGATCGTGGCAATTAATTTACGTGACAACGATGAGTTGGTCGGTGCAGTGTTGTGCGCGGCCGACGGCGACTTGCTTCTGGTATCGGCTAACGGCCAGTCTATCCGGTTCTCAGCGACTGACGAGGCCTTGCGTCCGATGGGGCGGGCTACCTCTGGTGTGCAGGGCATGCGGTTTAACGCCGATGATCGACTGTTGTCGTTGAATGTGGTTCGCGAAGATACTTACCTGCTTGTCGCAACGTCTGGGGGTTACGCTAAACGCACCTCGATTGAGGAGTACCCGATGCAGGGCCGTGGCGGAAAGGGTGTTCTAACGGTCATGTACGATCGTCGGCGCGGTAGCTTGGTTGGGGCCATCGTGGTTGATGAAGACAGCGAGTTGTACGCGATCACCTCAGGGGGTGGGGTAATTCGTACAACGGCACGCCAGGTTCGCCAGGCAGGACGCCAGACCAAGGGTGTTCGGTTGATGAACTTAGGTGAGGGCGACACGCTGTTAGCCATCGCACGTAATGCCGAAGAAAGCGCCGACGGCGGTGTCGGTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40083","NCBI_taxonomy_name":"Mycobacterium leprae TN","NCBI_taxonomy_id":"272631"}}}},"ARO_accession":"3003298","ARO_id":"39882","ARO_name":"Mycobacterium leprae gyrA conferring resistance to fluoroquinolones","CARD_short_name":"Mlep_gyrA_FLO","ARO_description":"Point mutation of Mycobacterium leprae gyrA resulted in the lowered affinity between fluoroquinolones and gyrA. Thus, conferring resistance.","ARO_category":{"39876":{"category_aro_accession":"3003292","category_aro_cvterm_id":"39876","category_aro_name":"fluoroquinolone resistant gyrA","category_aro_description":"DNA gyrase is responsible for DNA supercoiling and consists of two alpha and two beta subunits. GyrA point mutations confer resistance by preventing fluoroquinolone antibiotics from binding the alpha-subunit.","category_aro_class_name":"AMR Gene Family"},"35942":{"category_aro_accession":"0000023","category_aro_cvterm_id":"35942","category_aro_name":"enoxacin","category_aro_description":"Enoxacin belongs to a group called fluoroquinolones. Its mode of action depends upon blocking bacterial DNA replication by binding itself to DNA gyrase and causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37004":{"category_aro_accession":"3000660","category_aro_cvterm_id":"37004","category_aro_name":"lomefloxacin","category_aro_description":"Lomefloxacin is a difluoropiperazinyl quinolone, sharing similar activities with other fluoroquinolones. It is used to treat urinary tract infections. Relative to other fluoroquinolones, it has a longer half life and has higher serum concentrations.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37007":{"category_aro_accession":"3000663","category_aro_cvterm_id":"37007","category_aro_name":"ofloxacin","category_aro_description":"Ofloxacin is a 6-fluoro, 7-piperazinyl quinolone with a methyl-substituted oxazine ring. It has a broad spectrum of activity including many enterobacteria and mycoplasma but most anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"37008":{"category_aro_accession":"3000664","category_aro_cvterm_id":"37008","category_aro_name":"trovafloxacin","category_aro_description":"Trovafloxacin is a trifluoroquinalone with a broad spectrum of activity that acts by inhibiting the uncoiling of supercoiled DNA. While potent against many Gram-positive and Gram-negative bacteria, it is less active against pseudomonads and Cl. difficile. It is usually taken as the prodrug trovafloxacin mesylate or alatrofloxacin mesylate for oral or intravenous administration, respectively.","category_aro_class_name":"Antibiotic"},"37009":{"category_aro_accession":"3000665","category_aro_cvterm_id":"37009","category_aro_name":"grepafloxacin","category_aro_description":"Grepafloxacin is a broad-spectrum antibacterial quinoline. It is no longer taken due to its high toxicity.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"37142":{"category_aro_accession":"3000762","category_aro_cvterm_id":"37142","category_aro_name":"pefloxacin","category_aro_description":"Pefloxacin is structurally and functionally similar to norfloxacin. It is poorly active against mycobacteria, while anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1696":{"model_id":"1696","model_name":"Salmonella serovars gyrB conferring resistance to fluoroquinolones","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"2174":"E466D"},"Curated-R":{"2174":"E466D"},"experimental":{"2174":"E466D"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1200"}},"model_sequences":{"sequence":{"5308":{"protein_sequence":{"accession":"AAL22694.1","sequence":"MSNSYDSSSIKVLKGLDAVRKRPGMYIGDTDDGTGLHHMVFEVVDNAIDEALAGHCKDIVVTIHADNSVSVTDDGRGIPTGIHPEEGVSAAEVIMTVLHAGGKFDDNSYKVSGGLHGVGVSVVNALSQKLELVIQRDGKIHRQIYEHGVPQAPLAVTGDTDKTGTMVRFWPSHETFTNVTEFEYEILAKRLRELSFLNSGVSIRLRDKRDGKEDHFHYEGGIKAFVEYLNKNKTPIHPNIFYFSTEKDGIGVEVALQWNDGFQENIYCFTNNIPQRDGGTHLAGFRAAMTRTLNAYMDKEGYSKKAKVSATGDDAREGLIAVVSVKVPDPKFSSQTKDKLVSSEVKSAVEQQMNELLSEYLLENPSDAKIVVGKIIDAARAREAARRAREMTRRKGALDLAGLPGKLADCQERDPALSELYLVEGDSAGGSAKQGRNRKNQAILPLKGKILNVEKARFDKMLSSQEVATLITALGCGIGRDEYNPDKLRYHSIIIMTDADVDGSHIRTLLLTFFYRQMPEIVERGHVYIAQPPLYKVKKGKQEQYIKDDEAMDQYQISIALDGATLHANAHAPALSGEALEKLVSEYNATQKMIGRMERRFPKALLKELVYQPTLTEADLSDEQTVTRWVNALITELNEKEQHGSQWKFDVHTNTEQNLFEPIVRVRTHGVDTDYPLDHEFVTGAEYRRICTLGEKLRGLIEEDAFIERGERRQPVTSFEQALEWLVKESRRGLAIQRYKGLGEMNPDQLWETTMDPESRRMLRVTVKDAIAADQLFTTLMGDAVEPRRAFIEENALKAANIDI"},"dna_sequence":{"accession":"AE006468.2","fmin":"4038867","fmax":"4041282","strand":"-","sequence":"ATGTCGAATTCTTATGACTCCTCCAGTATCAAAGTCCTGAAAGGGCTGGATGCGGTGCGTAAGCGCCCGGGTATGTATATCGGCGACACGGATGACGGCACCGGTCTGCACCACATGGTATTCGAGGTGGTAGATAACGCTATCGACGAAGCGCTCGCAGGTCACTGTAAAGATATCGTCGTGACTATTCACGCCGATAACTCCGTGTCCGTAACGGATGATGGCCGTGGCATTCCGACCGGGATTCACCCGGAAGAAGGCGTCTCGGCGGCGGAAGTGATCATGACCGTTCTGCACGCGGGCGGTAAATTTGACGATAACTCCTATAAAGTCTCCGGCGGTCTGCACGGCGTGGGCGTCTCGGTAGTCAACGCTCTGTCGCAAAAACTGGAACTGGTTATCCAGCGAGATGGCAAAATTCACCGTCAGATCTACGAGCACGGCGTGCCGCAGGCACCCCTGGCCGTCACTGGCGATACCGATAAAACCGGCACGATGGTACGTTTCTGGCCGAGCCACGAAACCTTCACCAACGTCACTGAATTTGAATATGAGATCCTGGCGAAACGCCTGCGTGAACTGTCATTCCTGAACTCAGGCGTCTCCATCCGCCTGCGCGACAAGCGCGATGGCAAAGAAGATCATTTCCACTACGAAGGCGGCATCAAGGCGTTTGTTGAATATCTGAACAAGAATAAAACGCCGATCCACCCGAATATCTTCTATTTCTCCACCGAAAAAGACGGTATCGGCGTGGAAGTAGCGCTGCAGTGGAACGATGGTTTCCAGGAAAACATCTACTGCTTTACCAACAACATTCCGCAGCGCGACGGCGGTACTCACCTTGCAGGCTTCCGTGCGGCGATGACCCGTACGCTGAACGCCTACATGGACAAAGAAGGCTACAGCAAAAAAGCCAAAGTCAGCGCCACCGGCGACGATGCCCGTGAAGGTCTGATTGCGGTGGTTTCCGTAAAAGTACCGGATCCGAAATTCTCCTCACAGACCAAAGATAAGCTGGTCTCTTCCGAGGTGAAATCGGCGGTAGAACAGCAGATGAACGAACTGCTGAGCGAATACCTGCTGGAAAACCCATCTGACGCGAAAATCGTCGTCGGCAAAATTATCGACGCCGCGCGTGCGCGTGAAGCGGCGCGTCGCGCCCGTGAAATGACCCGTCGTAAAGGCGCGCTCGATTTAGCCGGTCTGCCGGGCAAACTGGCGGACTGTCAGGAACGCGACCCGGCGCTGTCCGAACTGTACCTGGTGGAAGGGGACTCCGCGGGCGGCTCTGCGAAGCAGGGGCGTAACCGCAAGAACCAGGCGATTCTGCCGCTGAAAGGTAAAATCCTTAACGTCGAGAAAGCGCGCTTCGACAAGATGCTTTCCTCCCAGGAAGTGGCGACGCTGATCACCGCGCTGGGCTGCGGTATCGGTCGCGACGAGTACAACCCGGACAAGCTGCGCTATCACAGCATCATCATCATGACCGATGCGGACGTCGACGGCTCGCACATCCGTACGCTGCTGTTGACCTTCTTCTATCGTCAGATGCCGGAAATTGTCGAGCGTGGCCACGTCTACATTGCGCAGCCGCCGCTGTACAAAGTGAAGAAAGGTAAGCAGGAACAGTACATTAAAGACGACGAAGCGATGGATCAGTACCAGATTTCCATCGCGCTTGACGGTGCGACTCTGCACGCGAACGCTCATGCGCCGGCGCTATCCGGCGAAGCGTTAGAAAAACTGGTCTCTGAATATAACGCCACGCAGAAAATGATTGGTCGTATGGAGCGTCGCTTCCCGAAAGCGCTGCTCAAAGAGCTGGTGTATCAGCCAACTCTGACCGAAGCCGATCTTTCTGATGAGCAGACTGTAACGCGCTGGGTGAATGCGCTGATTACCGAGCTGAACGAGAAAGAGCAGCACGGCAGTCAGTGGAAGTTCGATGTTCATACTAATACGGAACAGAATCTGTTCGAGCCGATCGTTCGCGTGCGTACGCATGGCGTGGATACCGATTATCCGTTGGATCACGAGTTTGTGACCGGCGCGGAATATCGTCGTATCTGCACGCTGGGCGAGAAGCTGCGTGGTCTGATTGAAGAGGACGCGTTTATCGAACGCGGCGAGCGTCGCCAGCCGGTAACCAGCTTCGAGCAGGCGCTGGAGTGGCTGGTGAAAGAATCACGTCGCGGTCTGGCTATCCAGCGTTATAAAGGTCTGGGTGAAATGAACCCGGATCAGCTGTGGGAAACCACCATGGACCCGGAAAGCCGCCGTATGCTGCGCGTGACCGTCAAAGATGCAATTGCTGCCGACCAGCTGTTCACTACGCTGATGGGTGATGCCGTTGAGCCGCGTCGTGCCTTTATCGAGGAGAACGCCCTGAAAGCAGCGAATATCGATATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35734","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Typhimurium str. LT2","NCBI_taxonomy_id":"99287"}}}},"ARO_accession":"3003307","ARO_id":"39891","ARO_name":"Salmonella serovars gyrB conferring resistance to fluoroquinolones","CARD_short_name":"Sser_gyrB_FLO","ARO_description":"Point mutation in Salmonella serovars resulting in fluoroquinolone resistance.","ARO_category":{"37244":{"category_aro_accession":"3000864","category_aro_cvterm_id":"37244","category_aro_name":"fluoroquinolone resistant gyrB","category_aro_description":"Point mutations in DNA gyrase subunit B (gyrB) observed in Mycobacterium tuberculosis can result in resistance to fluoroquinolones.","category_aro_class_name":"AMR Gene Family"},"35942":{"category_aro_accession":"0000023","category_aro_cvterm_id":"35942","category_aro_name":"enoxacin","category_aro_description":"Enoxacin belongs to a group called fluoroquinolones. Its mode of action depends upon blocking bacterial DNA replication by binding itself to DNA gyrase and causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37004":{"category_aro_accession":"3000660","category_aro_cvterm_id":"37004","category_aro_name":"lomefloxacin","category_aro_description":"Lomefloxacin is a difluoropiperazinyl quinolone, sharing similar activities with other fluoroquinolones. It is used to treat urinary tract infections. Relative to other fluoroquinolones, it has a longer half life and has higher serum concentrations.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37007":{"category_aro_accession":"3000663","category_aro_cvterm_id":"37007","category_aro_name":"ofloxacin","category_aro_description":"Ofloxacin is a 6-fluoro, 7-piperazinyl quinolone with a methyl-substituted oxazine ring. It has a broad spectrum of activity including many enterobacteria and mycoplasma but most anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"37008":{"category_aro_accession":"3000664","category_aro_cvterm_id":"37008","category_aro_name":"trovafloxacin","category_aro_description":"Trovafloxacin is a trifluoroquinalone with a broad spectrum of activity that acts by inhibiting the uncoiling of supercoiled DNA. While potent against many Gram-positive and Gram-negative bacteria, it is less active against pseudomonads and Cl. difficile. It is usually taken as the prodrug trovafloxacin mesylate or alatrofloxacin mesylate for oral or intravenous administration, respectively.","category_aro_class_name":"Antibiotic"},"37009":{"category_aro_accession":"3000665","category_aro_cvterm_id":"37009","category_aro_name":"grepafloxacin","category_aro_description":"Grepafloxacin is a broad-spectrum antibacterial quinoline. It is no longer taken due to its high toxicity.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"37142":{"category_aro_accession":"3000762","category_aro_cvterm_id":"37142","category_aro_name":"pefloxacin","category_aro_description":"Pefloxacin is structurally and functionally similar to norfloxacin. It is poorly active against mycobacteria, while anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1441":{"model_id":"1441","model_name":"Klebsiella aerogenes Omp36","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"2085":"G133D"},"Curated-R":{"2085":"G133D"},"clinical":{"2085":"G133D"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"2109":{"protein_sequence":{"accession":"AAK11270.1","sequence":"MKVKVLSLLVPALLVAGAANAAEIYNKDGNKLDLYGKIDGLHYFSSDDSVDGDQTYMRIGVKGETQINDQLTGYGQWEYNVQANNTESSSDQAWTRLAFAGLKFGDAGSFDYGRNYGVVYDVTSWTDVLPEFGGDTYGSDNFLQSRANGVATYRNSDFFGLVDGLNFALQYQGKNGSVSGEDQTNNGRDFQKQNGEGFGTSVTYDIWDGISAGFAYSSSKRTDEQNNSTFVSKTDGGRYGVLGEGDHAETYTGGLKYDANNIYLATQYTQTYNATRTGNIGFANKAQNFEVVAQYQFDFGLRPSVAYLQSKGKDMGRYGDQDILKYVDLGATYYFNKNMSTYVDYKINLLDDNKFTKDASISTDNVVALGLVYQF"},"dna_sequence":{"accession":"AF335467.1","fmin":"36","fmax":"1164","strand":"+","sequence":"ATGAAAGTTAAAGTACTGTCCCTCCTGGTACCAGCACTGCTGGTAGCGGGCGCAGCAAATGCGGCTGAAATTTATAACAAAGACGGCAACAAATTAGACCTGTACGGTAAAATCGACGGTCTGCACTACTTCTCTTCCGACGACAGCGTCGACGGCGACCAGACCTACATGCGTATCGGCGTGAAAGGCGAAACCCAGATCAACGACCAGCTGACCGGTTACGGCCAGTGGGAATACAACGTTCAGGCGAACAACACTGAAAGCTCCAGCGACCAGGCATGGACTCGTCTGGCCTTCGCGGGTCTGAAATTCGGCGACGCGGGTTCTTTCGACTACGGTCGTAACTACGGCGTTGTTTACGACGTAACTTCCTGGACCGACGTTCTGCCGGAATTCGGCGGCGACACCTACGGTTCCGACAACTTCCTGCAGTCCCGTGCTAACGGTGTTGCCACCTACCGTAACTCTGACTTCTTCGGTCTGGTTGACGGCCTGAACTTTGCTCTGCAGTACCAGGGTAAAAACGGCAGCGTGAGCGGCGAAGATCAGACCAACAACGGTCGTGACTTCCAGAAACAGAACGGCGAAGGCTTCGGCACCTCCGTAACTTATGATATCTGGGACGGCATCAGCGCTGGTTTCGCGTACTCCAGCTCTAAACGTACCGACGAGCAGAACAACTCTACCTTCGTGTCTAAGACCGATGGTGGTCGTTACGGTGTTCTGGGTGAAGGCGATCACGCTGAAACCTACACCGGTGGTCTGAAATACGACGCCAACAACATCTACCTGGCGACTCAGTACACCCAGACTTACAACGCAACCCGCACCGGTAACATCGGTTTTGCTAACAAAGCGCAGAACTTCGAAGTCGTTGCTCAGTACCAGTTCGACTTCGGTCTGCGTCCGTCCGTGGCTTACCTGCAGTCTAAAGGTAAAGACATGGGCCGTTACGGCGACCAGGACATCCTGAAATATGTTGACCTGGGTGCGACCTACTACTTCAACAAAAACATGTCCACCTACGTTGATTACAAAATCAACCTGCTGGACGACAACAAGTTCACTAAAGATGCAAGCATCTCTACTGACAACGTTGTGGCTCTGGGCCTGGTTTACCAGTTCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36770","NCBI_taxonomy_name":"Klebsiella aerogenes","NCBI_taxonomy_id":"548"}}}},"ARO_accession":"3003385","ARO_id":"39969","ARO_name":"Klebsiella aerogenes Omp36","CARD_short_name":"Kaer_Omp36","ARO_description":"Mutant forms of the porin Omp36 result in reduced permeability to antibiotics.","ARO_category":{"41445":{"category_aro_accession":"3004281","category_aro_cvterm_id":"41445","category_aro_name":"General Bacterial Porin with reduced permeability to beta-lactams","category_aro_description":"These are GBPs that are associated with decreased susceptibility to beta-lactams either through mutations in the porin protein, absence of the porin protein, or expression of the porin protein.","category_aro_class_name":"AMR Gene Family"},"35976":{"category_aro_accession":"0000059","category_aro_cvterm_id":"35976","category_aro_name":"cefepime","category_aro_description":"Cefepime (INN) is a fourth-generation cephalosporin antibiotic developed in 1994. It contains an aminothiazolyl group that decreases its affinity with beta-lactamases. Cefepime shows high binding affinity with penicillin-binding proteins and has an extended spectrum of activity against Gram-positive and Gram-negative bacteria, with greater activity against both Gram-negative and Gram-positive organisms than third-generation agents.","category_aro_class_name":"Antibiotic"},"36309":{"category_aro_accession":"3000170","category_aro_cvterm_id":"36309","category_aro_name":"imipenem","category_aro_description":"Imipenem is a broad-spectrum antibiotic and is usually taken with cilastatin, which prevents hydrolysis of imipenem by renal dehydropeptidase-I. It is resistant to hydrolysis by most other beta-lactamases. Notable exceptions are the KPC beta-lactamases and Ambler Class B enzymes.","category_aro_class_name":"Antibiotic"},"42781":{"category_aro_accession":"3004726","category_aro_cvterm_id":"42781","category_aro_name":"cefpirome","category_aro_description":"Cefpirome is a fourth generation cephalosporin with activity against methicillin-susceptible Staphylococcus aureus, coagulase-negative staphylococci and viridans group streptococci, and in vitro activity towards Streptococcus pneumoniae.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36383":{"category_aro_accession":"3000244","category_aro_cvterm_id":"36383","category_aro_name":"reduced permeability to antibiotic","category_aro_description":"Reduction in permeability to antibiotic, generally through reduced production of porins, can provide resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2085":{"model_id":"2085","model_name":"Escherichia coli 16S rRNA (rrnB) mutation conferring resistance to spectinomycin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"2925":"g1068a"},"Curated-R":{"2925":"g1068a"},"clinical":{"2925":"g1068a"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"41093","param_value":"2700"}},"model_sequences":{"sequence":{"3239":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"U00096.1","fmin":"4166658","fmax":"4168200","strand":"+","sequence":"AAATTGAAGAGTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAACGGTAACAGGAAGAAGCTTGCTTCTTTGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCGGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGGAGTAAAGTTAATACCTTTGCTCATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACGAAGACTGACGCTCAGGTGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGTCGACTTGGAGGTTGTGCCCTTGAGGCGTGGCTTCCGGAGCTAACGCGTTAAGTCGACCGCCTGGGGAGTACGGCCGCAAGGTTAAAACTCAAATGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGATGCAACGCGAAGAACCTTACCTGGTCTTGACATCCACGGAAGTTTTCAGAGATGAGAATGTGCCTTCGGGAACCGTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGAAATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCCTTTGTTGCCAGCGGTCCGGCCGGGAACTCAAAGGAGACTGCCAGTGATAAACTGGAGGAAGGTGGGGATGACGTCAAGTCATCATGGCCCTTACGACCAGGGCTACACACGTGCTACAATGGCGCATACAAAGAGAAGCGACCTCGCGAGAGCAAGCGGACCTCATAAAGTGCGTCGTAGTCCGGATTGGAGTCTGCAACTCGACTCCATGAAGTCGGAATCGCTAGTAATCGTGGATCAGAATGCCACGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACACCATGGGAGTGGGTTGCAAAAGAAGTAGGTAGCTTAACCTTCGGGAGGGCGCTTACCACTTTGTGATTCATGACTGGGGTGAAGTCGTAACAAGGTAACCGTAGGGGAACCTGCGGTTGGATCACCTCCTTA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36905","NCBI_taxonomy_name":"Escherichia coli str. K-12","NCBI_taxonomy_id":"83333"}}}},"ARO_accession":"3003377","ARO_id":"39961","ARO_name":"Escherichia coli 16S rRNA (rrnB) mutation conferring resistance to spectinomycin","CARD_short_name":"Ecol_16S_SPT","ARO_description":"Point mutations in the 3' major domain of helix 35, in the rrnB gene operon for 16S rRNA of Escherichia coli can confer resistance to spectinomycin.","ARO_category":{"40277":{"category_aro_accession":"3003666","category_aro_cvterm_id":"40277","category_aro_name":"16s rRNA with mutation conferring resistance to aminoglycoside antibiotics","category_aro_description":"Point mutations in the 16S rRNA of bacteria can confer resistance to aminoglycosides.","category_aro_class_name":"AMR Gene Family"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2097":{"model_id":"2097","model_name":"Escherichia coli 16S rRNA (rrsB) mutation conferring resistance to paromomycin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"2995":"a1408g"},"Curated-R":{"2995":"a1408g"},"clinical":{"2995":"a1408g"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"41093","param_value":"2700"}},"model_sequences":{"sequence":{"3238":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"U00096.1","fmin":"4166658","fmax":"4168200","strand":"+","sequence":"AAATTGAAGAGTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAACGGTAACAGGAAGAAGCTTGCTTCTTTGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCGGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGGAGTAAAGTTAATACCTTTGCTCATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACGAAGACTGACGCTCAGGTGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGTCGACTTGGAGGTTGTGCCCTTGAGGCGTGGCTTCCGGAGCTAACGCGTTAAGTCGACCGCCTGGGGAGTACGGCCGCAAGGTTAAAACTCAAATGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGATGCAACGCGAAGAACCTTACCTGGTCTTGACATCCACGGAAGTTTTCAGAGATGAGAATGTGCCTTCGGGAACCGTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGAAATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCCTTTGTTGCCAGCGGTCCGGCCGGGAACTCAAAGGAGACTGCCAGTGATAAACTGGAGGAAGGTGGGGATGACGTCAAGTCATCATGGCCCTTACGACCAGGGCTACACACGTGCTACAATGGCGCATACAAAGAGAAGCGACCTCGCGAGAGCAAGCGGACCTCATAAAGTGCGTCGTAGTCCGGATTGGAGTCTGCAACTCGACTCCATGAAGTCGGAATCGCTAGTAATCGTGGATCAGAATGCCACGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACACCATGGGAGTGGGTTGCAAAAGAAGTAGGTAGCTTAACCTTCGGGAGGGCGCTTACCACTTTGTGATTCATGACTGGGGTGAAGTCGTAACAAGGTAACCGTAGGGGAACCTGCGGTTGGATCACCTCCTTA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36905","NCBI_taxonomy_name":"Escherichia coli str. K-12","NCBI_taxonomy_id":"83333"}}}},"ARO_accession":"3003403","ARO_id":"39987","ARO_name":"Escherichia coli 16S rRNA (rrsB) mutation conferring resistance to paromomycin","CARD_short_name":"Ecol_16rrsB_PAR","ARO_description":"Point mutations in the 3' minor domain of helix 44, in the rrsB 16S rRNA gene of Escherichia coli can confer resistance to paromomycin.","ARO_category":{"40277":{"category_aro_accession":"3003666","category_aro_cvterm_id":"40277","category_aro_name":"16s rRNA with mutation conferring resistance to aminoglycoside antibiotics","category_aro_description":"Point mutations in the 16S rRNA of bacteria can confer resistance to aminoglycosides.","category_aro_class_name":"AMR Gene Family"},"37001":{"category_aro_accession":"3000657","category_aro_cvterm_id":"37001","category_aro_name":"paromomycin","category_aro_description":"An aminoglycoside antibiotic used for the treatment of parasitic infections. It is similar to neomycin sharing a similar spectrum of activity, but its hydroxyl group at the 6'-position instead of an amino group makes it resistant to AAC(6') modifying enzymes.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2113":{"model_id":"2113","model_name":"Escherichia coli 16S rRNA (rrsB) mutation conferring resistance to tobramycin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"4827":"t1406a"},"Curated-R":{"4827":"t1406a"},"clinical":{"4827":"t1406a"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"41093","param_value":"2700"}},"model_sequences":{"sequence":{"3241":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"U00096.1","fmin":"4166658","fmax":"4168200","strand":"+","sequence":"AAATTGAAGAGTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAACGGTAACAGGAAGAAGCTTGCTTCTTTGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCGGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGGAGTAAAGTTAATACCTTTGCTCATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACGAAGACTGACGCTCAGGTGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGTCGACTTGGAGGTTGTGCCCTTGAGGCGTGGCTTCCGGAGCTAACGCGTTAAGTCGACCGCCTGGGGAGTACGGCCGCAAGGTTAAAACTCAAATGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGATGCAACGCGAAGAACCTTACCTGGTCTTGACATCCACGGAAGTTTTCAGAGATGAGAATGTGCCTTCGGGAACCGTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGAAATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCCTTTGTTGCCAGCGGTCCGGCCGGGAACTCAAAGGAGACTGCCAGTGATAAACTGGAGGAAGGTGGGGATGACGTCAAGTCATCATGGCCCTTACGACCAGGGCTACACACGTGCTACAATGGCGCATACAAAGAGAAGCGACCTCGCGAGAGCAAGCGGACCTCATAAAGTGCGTCGTAGTCCGGATTGGAGTCTGCAACTCGACTCCATGAAGTCGGAATCGCTAGTAATCGTGGATCAGAATGCCACGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACACCATGGGAGTGGGTTGCAAAAGAAGTAGGTAGCTTAACCTTCGGGAGGGCGCTTACCACTTTGTGATTCATGACTGGGGTGAAGTCGTAACAAGGTAACCGTAGGGGAACCTGCGGTTGGATCACCTCCTTA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36905","NCBI_taxonomy_name":"Escherichia coli str. K-12","NCBI_taxonomy_id":"83333"}}}},"ARO_accession":"3003408","ARO_id":"39992","ARO_name":"Escherichia coli 16S rRNA (rrsB) mutation conferring resistance to tobramycin","CARD_short_name":"Ecol_16rrsB_TOB","ARO_description":"Point mutations in the 3' minor domain of the rrnB 16S rRNA gene of Escherichia coli can confer resistance to tobramycin.","ARO_category":{"40277":{"category_aro_accession":"3003666","category_aro_cvterm_id":"40277","category_aro_name":"16s rRNA with mutation conferring resistance to aminoglycoside antibiotics","category_aro_description":"Point mutations in the 16S rRNA of bacteria can confer resistance to aminoglycosides.","category_aro_class_name":"AMR Gene Family"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2129":{"model_id":"2129","model_name":"Escherichia coli 16S rRNA (rrsB) mutation conferring resistance to spectinomycin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"2910":"c1192a","2919":"g1064a","2959":"g1064c","3070":"c1192g","4815":"g1064t","4816":"c1192t","4817":"c1066t"},"Curated-R":{"2910":"c1192a","2919":"g1064a","2959":"g1064c","3070":"c1192g","4815":"g1064t","4816":"c1192t","4817":"c1066t"},"clinical":{"2910":"c1192a","2919":"g1064a","2959":"g1064c","3070":"c1192g","4815":"g1064t","4816":"c1192t","4817":"c1066t"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"41093","param_value":"2700"}},"model_sequences":{"sequence":{"3240":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"U00096.1","fmin":"4166658","fmax":"4168200","strand":"+","sequence":"AAATTGAAGAGTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAACGGTAACAGGAAGAAGCTTGCTTCTTTGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCGGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGGAGTAAAGTTAATACCTTTGCTCATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACGAAGACTGACGCTCAGGTGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGTCGACTTGGAGGTTGTGCCCTTGAGGCGTGGCTTCCGGAGCTAACGCGTTAAGTCGACCGCCTGGGGAGTACGGCCGCAAGGTTAAAACTCAAATGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGATGCAACGCGAAGAACCTTACCTGGTCTTGACATCCACGGAAGTTTTCAGAGATGAGAATGTGCCTTCGGGAACCGTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGAAATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCCTTTGTTGCCAGCGGTCCGGCCGGGAACTCAAAGGAGACTGCCAGTGATAAACTGGAGGAAGGTGGGGATGACGTCAAGTCATCATGGCCCTTACGACCAGGGCTACACACGTGCTACAATGGCGCATACAAAGAGAAGCGACCTCGCGAGAGCAAGCGGACCTCATAAAGTGCGTCGTAGTCCGGATTGGAGTCTGCAACTCGACTCCATGAAGTCGGAATCGCTAGTAATCGTGGATCAGAATGCCACGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACACCATGGGAGTGGGTTGCAAAAGAAGTAGGTAGCTTAACCTTCGGGAGGGCGCTTACCACTTTGTGATTCATGACTGGGGTGAAGTCGTAACAAGGTAACCGTAGGGGAACCTGCGGTTGGATCACCTCCTTA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36905","NCBI_taxonomy_name":"Escherichia coli str. K-12","NCBI_taxonomy_id":"83333"}}}},"ARO_accession":"3003376","ARO_id":"39960","ARO_name":"Escherichia coli 16S rRNA (rrsB) mutation conferring resistance to spectinomycin","CARD_short_name":"Ecol_16rrsB_SPT","ARO_description":"Point mutations in the 3' major domain of the rrsB 16S rRNA gene of Escherichia coli can confer resistance to spectinomycin.","ARO_category":{"40277":{"category_aro_accession":"3003666","category_aro_cvterm_id":"40277","category_aro_name":"16s rRNA with mutation conferring resistance to aminoglycoside antibiotics","category_aro_description":"Point mutations in the 16S rRNA of bacteria can confer resistance to aminoglycosides.","category_aro_class_name":"AMR Gene Family"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1894":{"model_id":"1894","model_name":"Salmonella enterica ramR mutants","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"2136":"R46P","2137":"M84I","2138":"Y59H","2139":"T18P","2155":"G25A","2864":"E160D","3899":"T50P"},"Curated-R":{"2136":"R46P","2137":"M84I","2138":"Y59H","2139":"T18P","2155":"G25A","2864":"E160D","3899":"T50P"},"clinical":{"2136":"R46P","2137":"M84I","2138":"Y59H","2139":"T18P","2155":"G25A","2864":"E160D","3899":"T50P"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"370"}},"model_sequences":{"sequence":{"4674":{"protein_sequence":{"accession":"ACH50230.1","sequence":"MARPKSEDKKQALLEAATQAIAQSGIAASTAVIARNAGVAEGTLFRYFATKDELINTLYLHLKQDLCQSMIMELDRSITDAKMMTRFIWNSYISWGLNHPARHRAIRQLAVSEKLTKETEQRADDMFPELRDLCHRSVLMVFMSDEYRAFGDGLFLALAETTMDFAARDPARAGEYIALGFEAMWRALTREEQ"},"dna_sequence":{"accession":"CP001138.1","fmin":"613435","fmax":"614017","strand":"-","sequence":"GTGGCTCGTCCGAAGAGTGAAGACAAAAAACAAGCATTACTGGAAGCGGCAACCCAGGCGATAGCGCAATCCGGTATCGCCGCCTCAACGGCGGTGATTGCGCGTAACGCAGGTGTTGCAGAAGGAACATTGTTTCGCTATTTCGCGACCAAAGATGAGCTGATTAACACGTTGTATTTGCATTTAAAGCAGGATCTCTGCCAGTCAATGATAATGGAGCTGGATCGATCCATTACCGATGCCAAAATGATGACCCGTTTTATCTGGAACAGTTACATCAGTTGGGGTCTGAACCATCCCGCGCGCCATCGGGCGATCCGTCAACTGGCCGTCAGCGAAAAGCTCACCAAAGAGACGGAACAACGGGCCGACGATATGTTCCCCGAATTGCGCGATTTATGTCATCGTTCCGTTTTGATGGTGTTTATGTCGGATGAGTACCGCGCCTTCGGCGACGGCCTTTTTCTGGCGCTGGCTGAAACAACAATGGATTTCGCCGCGCGCGATCCCGCTCGCGCTGGCGAATATATTGCGCTGGGATTCGAAGCCATGTGGCGCGCGCTGACTCGCGAGGAGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35834","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Agona str. SL483","NCBI_taxonomy_id":"454166"}}}},"ARO_accession":"3003379","ARO_id":"39963","ARO_name":"Salmonella enterica ramR mutants","CARD_short_name":"Sent_ramR","ARO_description":"RamR is a repressor that regulates RamA expression. Mutations lead to the upregulation of AcrAB, which is positively regulated by RamA.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"37084":{"category_aro_accession":"3000704","category_aro_cvterm_id":"37084","category_aro_name":"cefalotin","category_aro_description":"Cefalotin is a semisynthetic cephalosporin antibiotic activate against staphylococci. It is resistant to staphylococci beta-lactamases but hydrolyzed by enterobacterial beta-lactamases.","category_aro_class_name":"Antibiotic"},"37250":{"category_aro_accession":"3000870","category_aro_cvterm_id":"37250","category_aro_name":"triclosan","category_aro_description":"Triclosan is a common antibacterial agent added to many consumer products as a biocide.  It is an inhibitor of fatty acid biosynthesis by blocking enoyl-carrier protein reductase (FabI).","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"43746":{"category_aro_accession":"3005386","category_aro_cvterm_id":"43746","category_aro_name":"disinfecting agents and antiseptics","category_aro_description":"Disinfectants that can also interact with antimicrobial resistance mechanisms, e.g. molecule efflux, and thus are the targets of disinfectant resistance.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2133":{"model_id":"2133","model_name":"Mycobacterium tuberculosis 16S rRNA mutation conferring resistance to viomycin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"41093","param_value":"2700"},"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"12983":"a1401g"},"Curated-R":{"12983":"a1401g"},"clinical":{"12983":"a1401g"}}},"model_sequences":{"sequence":{"8767":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"NC_000962.3","fmin":"1471845","fmax":"1473382","strand":"+","sequence":"TTTTGTTTGGAGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGGAAAGGTCTCTTCGGAGATACTCGAGTGGCGAACGGGTGAGTAACACGTGGGTGATCTGCCCTGCACTTCGGGATAAGCCTGGGAAACTGGGTCTAATACCGGATAGGACCACGGGATGCATGTCTTGTGGTGGAAAGCGCTTTAGCGGTGTGGGATGAGCCCGCGGCCTATCAGCTTGTTGGTGGGGTGACGGCCTACCAAGGCGACGACGGGTAGCCGGCCTGAGAGGGTGTCCGGCCACACTGGGACTGAGATACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCGACGCCGCGTGGGGGATGACGGCCTTCGGGTTGTAAACCTCTTTCACCATCGACGAAGGTCCGGGTTCTCTCGGATTGACGGTAGGTGGAGAAGAAGCACCGGCCAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGTGCGAGCGTTGTCCGGAATTACTGGGCGTAAAGAGCTCGTAGGTGGTTTGTCGCGTTGTTCGTGAAATCTCACGGCTTAACTGTGAGCGTGCGGGCGATACGGGCAGACTAGAGTACTGCAGGGGAGACTGGAATTCCTGGTGTAGCGGTGGAATGCGCAGATATCAGGAGGAACACCGGTGGCGAAGGCGGGTCTCTGGGCAGTAACTGACGCTGAGGAGCGAAAGCGTGGGGAGCGAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGGTGGGTACTAGGTGTGGGTTTCCTTCCTTGGGATCCGTGCCGTAGCTAACGCATTAAGTACCCCGCCTGGGGAGTACGGCCGCAAGGCTAAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGCGGAGCATGTGGATTAATTCGATGCAACGCGAAGAACCTTACCTGGGTTTGACATGCACAGGACGCGTCTAGAGATAGGCGTTCCCTTGTGGCCTGTGTGCAGGTGGTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTCTCATGTTGCCAGCACGTAATGGTGGGGACTCGTGAGAGACTGCCGGGGTCAACTCGGAGGAAGGTGGGGATGACGTCAAGTCATCATGCCCCTTATGTCCAGGGCTTCACACATGCTACAATGGCCGGTACAAAGGGCTGCGATGCCGCGAGGTTAAGCGAATCCTTAAAAGCCGGTCTCAGTTCGGATCGGGGTCTGCAACTCGACCCCGTGAAGTCGGAGTCGCTAGTAATCGCAGATCAGCAACGCTGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACGTCATGAAAGTCGGTAACACCCGAAGCCAGTGGCCTAACCCTCGGGAGGGAGCTGTCGAAGGTGGGATCGGCGATTGGGACGAAGTCGTAACAAGGTAGCCGTACCGGAAGGTGCGGCTGGATCACCTCCTTTCT","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3003437","ARO_id":"40021","ARO_name":"Mycobacterium tuberculosis 16S rRNA mutation conferring resistance to viomycin","CARD_short_name":"Mtub_16S_VIO","ARO_description":"Peptide antibiotics inhibit protein synthesis. Resistance to viomycin can be caused by an altered RNA molecule in the 16S ribosomal subunit.","ARO_category":{"40278":{"category_aro_accession":"3003667","category_aro_cvterm_id":"40278","category_aro_name":"16s rRNA with mutation conferring resistance to peptide antibiotics","category_aro_description":"Point mutations in the 16S rRNA of bacteria can confer resistance to peptide antibiotics.","category_aro_class_name":"AMR Gene Family"},"35937":{"category_aro_accession":"0000018","category_aro_cvterm_id":"35937","category_aro_name":"viomycin","category_aro_description":"Viomycin sulfate (Viocin) is an polypeptide antibiotic used in the treatment of tuberculosis. It is produced by the actinomycete Streptomyces puniceus and binds to the bacterial ribosome, inhibiting prokaryotic protein synthesis and certain forms of RNA splicing.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2152":{"model_id":"2152","model_name":"Neisseria meningitidis 16S rRNA mutation conferring resistance to spectinomycin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"2897":"g1065c"},"Curated-R":{"2897":"g1065c"},"clinical":{"2897":"g1065c"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"41093","param_value":"2700"}},"model_sequences":{"sequence":{"4137":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"NC_003112.1","fmin":"60970","fmax":"62514","strand":"+","sequence":"TGAACATAAGAGTTTGATCCTGGCTCAGATTGAACGCTGGCGGCATGCTTTACACATGCAAGTCGGACGGCAGCACAGAGAAGCTTGCTTCTCGGGTGGCGAGTGGCGAACGGGTGAGTAACATATCGGAACGTACCGAGTAGTGGGGGATAACTGATCGAAAGATCAGCTAATACCGCATACGTCTTGAGAGAGAAAGCAGGGGACCTTCGGGCCTTGCGCTATTCGAGCGGCCGATATCTGATTAGCTAGTTGGTGGGGTAAAGGCCTACCAAGGCGACGATCAGTAGCGGGTCTGAGAGGATGATCCGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATTTTGGACAATGGGCGCAAGCCTGATCCAGCCATGCCGCGTGTCTGAAGAAGGCCTTCGGGTTGTAAAGGACTTTTGTCAGGGAAGAAAAGGCTGTTGCTAATATCAGCGGCTGATGACGGTACCTGAAGAATAAGCACCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGTGCGAGCGTTAATCGGAATTACTGGGCGTAAAGCGGGCGCAGACGGTTACTTAAGCAGGATGTGAAATCCCCGGGCTCAACCCGGGAACTGCGTTCTGAACTGGGTGACTCGAGTGTGTCAGAGGGAGGTAGAATTCCACGTGTAGCAGTGAAATGCGTAGAGATGTGGAGGAATACCGATGGCGAAGGCAGCCTCCTGGGACAACACTGACGTTCATGCCCGAAAGCGTGGGTAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCCTAAACGATGTCAATTAGCTGTTGGGCAACCTGATTGCTTGGTAGCGTAGCTAACGCGTGAAATTGACCGCCTGGGGAGTACGGTCGCAAGATTAAAACTCAAAGGAATTGACGGGGACCCGCACAAGCGGTGGATGATGTGGATTAATTCGATGCAACGCGAAGAACCTTACCTGGTCTTGACATGTACGGAATCCTCCGGAGACGGAGGAGTGCCTTCGGGAGCCGTAACACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTCATTAGTTGCCATCATTCAGTTGGGCACTCTAATGAGACTGCCGGTGACAAGCCGGAGGAAGGTGGGGATGACGTCAAGTCCTCATGGCCCTTATGACCAGGGCTTCACACGTCATACAATGGTCGGTACAGAGGGTAGCCAAGCCGCGAGGCGGAGCCAATCTCACAAAACCGATCGTAGTCCGGATTGCACTCTGCAACTCGAGTGCATGAAGTCGGAATCGCTAGTAATCGCAGGTCAGCATACTGCGGTGAATACGTTCCCGGGTCTTGTACACACCGCCCGTCACACCATGGGAGTGGGGGATACCAGAAGTAGGTAGGATAACCACAAGGAGTCCGCTTACCACGGTATGCTTCATGACTGGGGTGAAGTCGTAACAAGGTAGCCGTAGGGGAACCTGCGGCTGGATCACCTCCTTTCT","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39597","NCBI_taxonomy_name":"Neisseria meningitidis MC58","NCBI_taxonomy_id":"122586"}}}},"ARO_accession":"3003497","ARO_id":"40099","ARO_name":"Neisseria meningitidis 16S rRNA mutation conferring resistance to spectinomycin","CARD_short_name":"Nmen_16S_SPT","ARO_description":"Point mutations in the 16S rRNA of Neisseria meningitidis can confer resistance to spectinomycin.","ARO_category":{"40277":{"category_aro_accession":"3003666","category_aro_cvterm_id":"40277","category_aro_name":"16s rRNA with mutation conferring resistance to aminoglycoside antibiotics","category_aro_description":"Point mutations in the 16S rRNA of bacteria can confer resistance to aminoglycosides.","category_aro_class_name":"AMR Gene Family"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2176":{"model_id":"2176","model_name":"glycopeptide resistance gene cluster VanN","model_type":"gene cluster meta-model","model_type_id":"40298","model_description":"Gene Cluster Meta-Models (GCM) are used to curate spatial clusters of individual genes within operons, such as for glycopeptide resistance gene clusters. The individual genes will have their own individual detection models (e.g. PHM, PVM, POM, etc.) while the GCM checks to see if all the component genes of the cluster have a Strict or Perfect hit and are ordered correctly within an operon. GCMs are encoded using the gene order parameter. This model type is still under development and not currently supported by the Resistance Gene Identifier (RGI) software.","model_param":{"40297":{"param_type":"gene order","param_description":"Spatial clusters of genes are encoded using the gene order parameter: [gene type]:[cvterm_id],[gene type]:[cvterm_id], etc. The gene type designations are: R = regulatory, C = core, A = accessory.","param_type_id":"40297","param_value":{"4681":"C:39346,C:39403,C:39409,R:39363,R:39374"}},"snp":{"Curated-R":{"4681":"g1065c"}}},"ARO_accession":"3002917","ARO_id":"39351","ARO_name":"glycopeptide resistance gene cluster VanN","CARD_short_name":"vanN_cluster","ARO_description":"Homologous to vanC, contains a D-Ala-D-Ser ligase. The plasmid-located vanM gene cluster is inducible and confers low resistance to vancomycin. vanN organisms remain susceptible to teicoplanin. Gene orientation: N(XY)TRS.","ARO_category":{"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2177":{"model_id":"2177","model_name":"glycopeptide resistance gene cluster VanA","model_type":"gene cluster meta-model","model_type_id":"40298","model_description":"Gene Cluster Meta-Models (GCM) are used to curate spatial clusters of individual genes within operons, such as for glycopeptide resistance gene clusters. The individual genes will have their own individual detection models (e.g. PHM, PVM, POM, etc.) while the GCM checks to see if all the component genes of the cluster have a Strict or Perfect hit and are ordered correctly within an operon. GCMs are encoded using the gene order parameter. This model type is still under development and not currently supported by the Resistance Gene Identifier (RGI) software.","model_param":{"40297":{"param_type":"gene order","param_description":"Spatial clusters of genes are encoded using the gene order parameter: [gene type]:[cvterm_id],[gene type]:[cvterm_id], etc. The gene type designations are: R = regulatory, C = core, A = accessory.","param_type_id":"40297","param_value":{"4671":"R:39353,R:39365,C:39376,C:36019,C:39383,A:39389,A:39396"}},"snp":{"Curated-R":{"4671":"g1065c"}}},"ARO_accession":"3000236","ARO_id":"36375","ARO_name":"glycopeptide resistance gene cluster VanA","CARD_short_name":"vanA_cluster","ARO_description":"This inducible cluster confers high resistance to both vancomycin and teicoplanin by allowing restructuring of peptidoglycan precursors to end in D-Ala-D-Lac. The vanA gene cluster can be located either on plasmids or on the chromosome. Gene orientation: vanRSHAXYZ.","ARO_category":{"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"35948":{"category_aro_accession":"0000029","category_aro_cvterm_id":"35948","category_aro_name":"teicoplanin","category_aro_description":"Teicoplanin is a glycopeptide antibiotic used in the prophylaxis and treatment of serious infections caused by Gram-positive bacteria. Teicoplanin has a unique acyl-aliphatic chain, and binds to cell wall precursors to inhibit transglycosylation  and transpeptidation.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2178":{"model_id":"2178","model_name":"glycopeptide resistance gene cluster VanO","model_type":"gene cluster meta-model","model_type_id":"40298","model_description":"Gene Cluster Meta-Models (GCM) are used to curate spatial clusters of individual genes within operons, such as for glycopeptide resistance gene clusters. The individual genes will have their own individual detection models (e.g. PHM, PVM, POM, etc.) while the GCM checks to see if all the component genes of the cluster have a Strict or Perfect hit and are ordered correctly within an operon. GCMs are encoded using the gene order parameter. This model type is still under development and not currently supported by the Resistance Gene Identifier (RGI) software.","model_param":{"40297":{"param_type":"gene order","param_description":"Spatial clusters of genes are encoded using the gene order parameter: [gene type]:[cvterm_id],[gene type]:[cvterm_id], etc. The gene type designations are: R = regulatory, C = core, A = accessory.","param_type_id":"40297","param_value":{"4682":"R:39364,R:39375,C:39382,C:39347,C:39388"}},"snp":{"Curated-R":{"4682":"g1065c"}}},"ARO_accession":"3002918","ARO_id":"39352","ARO_name":"glycopeptide resistance gene cluster VanO","CARD_short_name":"vanO_cluster","ARO_description":"Homologous to vanA, contains a D-Ala-D-Lac ligase. The chromosome-located vanO gene cluster is inducible. Not much is known about the biochemistry about the vanO gene cluster. Gene orientation: orf1 RS orf2 HOX.","ARO_category":{"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2179":{"model_id":"2179","model_name":"glycopeptide resistance gene cluster VanE","model_type":"gene cluster meta-model","model_type_id":"40298","model_description":"Gene Cluster Meta-Models (GCM) are used to curate spatial clusters of individual genes within operons, such as for glycopeptide resistance gene clusters. The individual genes will have their own individual detection models (e.g. PHM, PVM, POM, etc.) while the GCM checks to see if all the component genes of the cluster have a Strict or Perfect hit and are ordered correctly within an operon. GCMs are encoded using the gene order parameter. This model type is still under development and not currently supported by the Resistance Gene Identifier (RGI) software.","model_param":{"40297":{"param_type":"gene order","param_description":"Spatial clusters of genes are encoded using the gene order parameter: [gene type]:[cvterm_id],[gene type]:[cvterm_id], etc. The gene type designations are: R = regulatory, C = core, A = accessory.","param_type_id":"40297","param_value":{"4679":"C:39341,C:39401,C:39405,R:39358,R:39369"}},"snp":{"Curated-R":{"4679":"g1065c"}}},"ARO_accession":"3000259","ARO_id":"36398","ARO_name":"glycopeptide resistance gene cluster VanE","CARD_short_name":"vanE_cluster","ARO_description":"Homologous to VanC, contains a D-Ala-D-Ser ligase. The chromosome-located vanE gene cluster is inducible and confers low resistance to vancomycin. vanE organisms remain susceptible to teicoplanin. Gene orientation: E(XY)TRS.","ARO_category":{"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2180":{"model_id":"2180","model_name":"glycopeptide resistance gene cluster VanL","model_type":"gene cluster meta-model","model_type_id":"40298","model_description":"Gene Cluster Meta-Models (GCM) are used to curate spatial clusters of individual genes within operons, such as for glycopeptide resistance gene clusters. The individual genes will have their own individual detection models (e.g. PHM, PVM, POM, etc.) while the GCM checks to see if all the component genes of the cluster have a Strict or Perfect hit and are ordered correctly within an operon. GCMs are encoded using the gene order parameter. This model type is still under development and not currently supported by the Resistance Gene Identifier (RGI) software.","model_param":{"40297":{"param_type":"gene order","param_description":"Spatial clusters of genes are encoded using the gene order parameter: [gene type]:[cvterm_id],[gene type]:[cvterm_id], etc. The gene type designations are: R = regulatory, C = core, A = accessory.","param_type_id":"40297","param_value":{"4680":"C:39344,C:39402,C:39407,C:39408,R:39361,R:39372"}},"snp":{"Curated-R":{"4680":"g1065c"}}},"ARO_accession":"3000260","ARO_id":"36399","ARO_name":"glycopeptide resistance gene cluster VanL","CARD_short_name":"vanL_cluster","ARO_description":"Homologous to VanC, contains a D-Ala-D-Ser ligase. The chromosome-located vanL gene cluster is inducible and confers low resistance to vancomycin. vanL organisms remain susceptible to teicoplanin. It is the only van gene cluster with two vanT genes. Gene orientation: vanL(XY)TmTrRS.","ARO_category":{"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2181":{"model_id":"2181","model_name":"glycopeptide resistance gene cluster VanF","model_type":"gene cluster meta-model","model_type_id":"40298","model_description":"Gene Cluster Meta-Models (GCM) are used to curate spatial clusters of individual genes within operons, such as for glycopeptide resistance gene clusters. The individual genes will have their own individual detection models (e.g. PHM, PVM, POM, etc.) while the GCM checks to see if all the component genes of the cluster have a Strict or Perfect hit and are ordered correctly within an operon. GCMs are encoded using the gene order parameter. This model type is still under development and not currently supported by the Resistance Gene Identifier (RGI) software.","model_param":{"40297":{"param_type":"gene order","param_description":"Spatial clusters of genes are encoded using the gene order parameter: [gene type]:[cvterm_id],[gene type]:[cvterm_id], etc. The gene type designations are: R = regulatory, C = core, A = accessory.","param_type_id":"40297","param_value":{"4676":"R:39359,R:39370,A:39392,A:39397,C:39379,C:39342,C:39386"}},"snp":{"Curated-R":{"4676":"g1065c"}}},"ARO_accession":"3000255","ARO_id":"36394","ARO_name":"glycopeptide resistance gene cluster VanF","CARD_short_name":"vanF_cluster","ARO_description":"Homologous to vanA, contains a D-Ala-D-Lac ligase. The vanF gene cluster is inducible and confers high resistance to vancomycin in Paenibacillus popilliae. vanF organisms remain susceptible to teicoplanin. Gene orientation: RSYZHFX.","ARO_category":{"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2182":{"model_id":"2182","model_name":"glycopeptide resistance gene cluster VanD","model_type":"gene cluster meta-model","model_type_id":"40298","model_description":"Gene Cluster Meta-Models (GCM) are used to curate spatial clusters of individual genes within operons, such as for glycopeptide resistance gene clusters. The individual genes will have their own individual detection models (e.g. PHM, PVM, POM, etc.) while the GCM checks to see if all the component genes of the cluster have a Strict or Perfect hit and are ordered correctly within an operon. GCMs are encoded using the gene order parameter. This model type is still under development and not currently supported by the Resistance Gene Identifier (RGI) software.","model_param":{"40297":{"param_type":"gene order","param_description":"Spatial clusters of genes are encoded using the gene order parameter: [gene type]:[cvterm_id],[gene type]:[cvterm_id], etc. The gene type designations are: R = regulatory, C = core, A = accessory.","param_type_id":"40297","param_value":{"4674":"R:39357,R:39368,A:39391,C:39378,C:36014,C:39600"}},"snp":{"Curated-R":{"4674":"g1065c"}}},"ARO_accession":"3000253","ARO_id":"36392","ARO_name":"glycopeptide resistance gene cluster VanD","CARD_short_name":"vanD_cluster","ARO_description":"Homologous to vanA, contains a D-Ala-D-Lac ligase.  This cluster is constitutively expressed in the chromosome due to a dysfunctional D-ala-D-ala ligase and confers moderate resistance to both vancomycin and teicoplanin. Gene orientation: vanRSYHDX.","ARO_category":{"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"35948":{"category_aro_accession":"0000029","category_aro_cvterm_id":"35948","category_aro_name":"teicoplanin","category_aro_description":"Teicoplanin is a glycopeptide antibiotic used in the prophylaxis and treatment of serious infections caused by Gram-positive bacteria. Teicoplanin has a unique acyl-aliphatic chain, and binds to cell wall precursors to inhibit transglycosylation  and transpeptidation.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2183":{"model_id":"2183","model_name":"glycopeptide resistance gene cluster VanB","model_type":"gene cluster meta-model","model_type_id":"40298","model_description":"Gene Cluster Meta-Models (GCM) are used to curate spatial clusters of individual genes within operons, such as for glycopeptide resistance gene clusters. The individual genes will have their own individual detection models (e.g. PHM, PVM, POM, etc.) while the GCM checks to see if all the component genes of the cluster have a Strict or Perfect hit and are ordered correctly within an operon. GCMs are encoded using the gene order parameter. This model type is still under development and not currently supported by the Resistance Gene Identifier (RGI) software.","model_param":{"40297":{"param_type":"gene order","param_description":"Spatial clusters of genes are encoded using the gene order parameter: [gene type]:[cvterm_id],[gene type]:[cvterm_id], etc. The gene type designations are: R = regulatory, C = core, A = accessory.","param_type_id":"40297","param_value":{"4672":"R:39355,R:39366,A:39390,A:39398,C:39377,C:36022,C:39384,A:39350"}},"snp":{"Curated-R":{"4672":"g1065c"}}},"ARO_accession":"3000238","ARO_id":"36377","ARO_name":"glycopeptide resistance gene cluster VanB","CARD_short_name":"vanB_cluster","ARO_description":"This inducible cluster confers resistance to vancomycin but organisms remain sensitive to teicoplanin by allowing restructuring of peptidoglycan precursors to end in D-Ala-D-Lac.  Sensitivity to teicoplanin is due to lack of binding to the sensor kinase VanS. The vanB gene cluster can be located either on plasmids or on the chromosome. Gene orientation: vanRSYWHBX.","ARO_category":{"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2184":{"model_id":"2184","model_name":"glycopeptide resistance gene cluster VanC","model_type":"gene cluster meta-model","model_type_id":"40298","model_description":"Gene Cluster Meta-Models (GCM) are used to curate spatial clusters of individual genes within operons, such as for glycopeptide resistance gene clusters. The individual genes will have their own individual detection models (e.g. PHM, PVM, POM, etc.) while the GCM checks to see if all the component genes of the cluster have a Strict or Perfect hit and are ordered correctly within an operon. GCMs are encoded using the gene order parameter. This model type is still under development and not currently supported by the Resistance Gene Identifier (RGI) software.","model_param":{"40297":{"param_type":"gene order","param_description":"Spatial clusters of genes are encoded using the gene order parameter: [gene type]:[cvterm_id],[gene type]:[cvterm_id], etc. The gene type designations are: R = regulatory, C = core, A = accessory.","param_type_id":"40297","param_value":{"4673":"C:36507,C:39400,C:39404,R:39356,R:39367"}},"snp":{"Curated-R":{"4673":"g1065c"}}},"ARO_accession":"3000246","ARO_id":"36385","ARO_name":"glycopeptide resistance gene cluster VanC","CARD_short_name":"vanC_cluster","ARO_description":"Confers low vancomycin resistance by engineering peptidoglycan precursors ending in D-Ala-D-Ser in an inducible or constitutive manner.  The vanC cluster is intrinsic to the Enterococcus gallinarum chromosome. vanC organisms remain susceptible to teicoplanin. Gene orientation: vanC(XY)TRS.","ARO_category":{"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2185":{"model_id":"2185","model_name":"glycopeptide resistance gene cluster VanM","model_type":"gene cluster meta-model","model_type_id":"40298","model_description":"Gene Cluster Meta-Models (GCM) are used to curate spatial clusters of individual genes within operons, such as for glycopeptide resistance gene clusters. The individual genes will have their own individual detection models (e.g. PHM, PVM, POM, etc.) while the GCM checks to see if all the component genes of the cluster have a Strict or Perfect hit and are ordered correctly within an operon. GCMs are encoded using the gene order parameter. This model type is still under development and not currently supported by the Resistance Gene Identifier (RGI) software.","model_param":{"40297":{"param_type":"gene order","param_description":"Spatial clusters of genes are encoded using the gene order parameter: [gene type]:[cvterm_id],[gene type]:[cvterm_id], etc. The gene type designations are: R = regulatory, C = core, A = accessory.","param_type_id":"40297","param_value":{"4677":"R:39362,R:39373,A:39395,C:39381,C:39345,C:39387"}},"snp":{"Curated-R":{"4677":"g1065c"}}},"ARO_accession":"3000256","ARO_id":"36395","ARO_name":"glycopeptide resistance gene cluster VanM","CARD_short_name":"vanM_cluster","ARO_description":"Homologous to vanA, contains a D-Ala-D-Lac ligase. The plasmid-located vanM gene cluster is inducible and confers high resistance to vancomycin and teicoplanin. Gene orientation: RSYHMX.","ARO_category":{"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"35948":{"category_aro_accession":"0000029","category_aro_cvterm_id":"35948","category_aro_name":"teicoplanin","category_aro_description":"Teicoplanin is a glycopeptide antibiotic used in the prophylaxis and treatment of serious infections caused by Gram-positive bacteria. Teicoplanin has a unique acyl-aliphatic chain, and binds to cell wall precursors to inhibit transglycosylation  and transpeptidation.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2186":{"model_id":"2186","model_name":"glycopeptide resistance gene cluster VanG","model_type":"gene cluster meta-model","model_type_id":"40298","model_description":"Gene Cluster Meta-Models (GCM) are used to curate spatial clusters of individual genes within operons, such as for glycopeptide resistance gene clusters. The individual genes will have their own individual detection models (e.g. PHM, PVM, POM, etc.) while the GCM checks to see if all the component genes of the cluster have a Strict or Perfect hit and are ordered correctly within an operon. GCMs are encoded using the gene order parameter. This model type is still under development and not currently supported by the Resistance Gene Identifier (RGI) software.","model_param":{"40297":{"param_type":"gene order","param_description":"Spatial clusters of genes are encoded using the gene order parameter: [gene type]:[cvterm_id],[gene type]:[cvterm_id], etc. The gene type designations are: R = regulatory, C = core, A = accessory.","param_type_id":"40297","param_value":{"4678":"R:39360,R:39371,C:39549,A:39399,C:39343,A:39393,C:39406,R:36714"}},"snp":{"Curated-R":{"4678":"g1065c"}}},"ARO_accession":"3000257","ARO_id":"36396","ARO_name":"glycopeptide resistance gene cluster VanG","CARD_short_name":"vanG_cluster","ARO_description":"Contains a D-Ala-D-Ser ligase. The vanG gene cluster is inducible and confers low resistance to vancomycin. vanG organisms remain susceptible to teicoplanin. It is the only van gene cluster that contains two vanY genes. Gene orientation: vanRSYWGYT.","ARO_category":{"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1":{"model_id":"1","model_name":"PDC-4","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"1619":{"protein_sequence":{"accession":"ACQ82809.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDEMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"FJ666067.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACGAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTATGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002501","ARO_id":"38901","ARO_name":"PDC-4","CARD_short_name":"PDC-4","ARO_description":"PDC-4 is a extended-spectrum beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2192":{"model_id":"2192","model_name":"TriA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"650"}},"model_sequences":{"sequence":{"5270":{"protein_sequence":{"accession":"AAG03546.1","sequence":"MSDARGAFHSKGRWSRMALPAILCAGLLVGCGAEPPAEEHVRVLAQTVKMAEFASATSITGDIQARVQADQSFRVGGKIVERLVDVGDHVAAGQVLARLDPQDQRSNVENAQAAVAAQQAQSKLADLNYQRQKALLPKGYTSQSEYDQALASVRSAQSSLKAAQAQLANARDLLSYTELRASDAGVITARQAEVGQVVQATVPIFTLARDGERDAVFNVYESLFSHDVDGQRITVSLLGKPEVTASGKVREITPTVDERSGTLKVKVGLDSVPAEMSLGSVVNASVAAPAEHSVVLPWSALSKVGEQPAVWLLDQQGKARLQPVRVARYASEKVVIDGGLEAGQTVVTVGGQLLHPGQVVEVAQPPQPTQSTASRDAVGGGQP"},"dna_sequence":{"accession":"AE004091.2","fmin":"177306","fmax":"178458","strand":"+","sequence":"ATGTCAGACGCCAGAGGCGCTTTTCATTCCAAAGGTCGCTGGTCGCGGATGGCGCTGCCCGCCATCCTGTGCGCCGGCCTGCTTGTCGGTTGCGGCGCCGAGCCGCCCGCCGAGGAACACGTCCGTGTGCTGGCGCAGACGGTGAAGATGGCCGAGTTCGCCTCGGCCACCTCGATCACCGGCGACATCCAGGCACGGGTACAGGCCGACCAGTCGTTCCGTGTCGGCGGCAAGATCGTCGAGCGCCTGGTCGATGTCGGCGACCACGTCGCGGCTGGCCAGGTGCTGGCGCGGCTCGACCCGCAGGACCAGCGCAGCAACGTGGAGAACGCCCAGGCGGCGGTCGCCGCGCAGCAGGCGCAGTCGAAGCTCGCCGACCTCAACTACCAGCGGCAGAAGGCGCTGCTGCCCAAGGGCTACACCAGCCAGAGCGAGTACGACCAGGCGCTGGCCTCGGTGCGCAGCGCGCAGAGTTCGCTGAAGGCCGCCCAGGCGCAGTTGGCCAACGCCCGCGACCTGCTTTCCTATACCGAGCTGCGTGCCTCCGACGCCGGGGTCATCACCGCCCGCCAGGCCGAGGTCGGCCAGGTGGTGCAGGCCACCGTGCCGATCTTCACCCTGGCCCGCGACGGCGAGCGCGACGCGGTGTTCAACGTCTACGAGTCGTTGTTCAGCCACGATGTCGACGGCCAGCGGATCACCGTCAGCCTGCTCGGCAAGCCGGAAGTCACCGCCAGCGGCAAGGTCCGCGAGATCACCCCCACGGTGGACGAGCGCAGCGGTACGCTGAAGGTCAAGGTCGGCCTCGACTCGGTGCCGGCGGAAATGAGCCTCGGCAGCGTGGTCAACGCCAGCGTCGCCGCGCCGGCCGAGCACAGCGTGGTGCTGCCCTGGTCGGCGCTGTCCAAGGTCGGCGAGCAGCCGGCGGTCTGGTTGCTCGACCAGCAAGGCAAGGCGCGTCTGCAACCGGTGCGGGTGGCACGCTACGCCAGCGAGAAGGTGGTCATCGACGGTGGCCTGGAGGCGGGCCAGACGGTGGTCACGGTGGGCGGCCAACTGCTCCATCCGGGCCAGGTGGTCGAGGTGGCCCAGCCGCCGCAGCCGACCCAGAGCACCGCCAGCCGCGACGCCGTGGGCGGAGGCCAGCCATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36804","NCBI_taxonomy_name":"Pseudomonas aeruginosa PAO1","NCBI_taxonomy_id":"208964"}}}},"ARO_accession":"3003679","ARO_id":"40314","ARO_name":"TriA","CARD_short_name":"TriA","ARO_description":"TriA is a membrane protein that is fused to TriB and both are required for the triclosan efflux pump function of TriABC-OpmH in P. aeruginosa.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"37250":{"category_aro_accession":"3000870","category_aro_cvterm_id":"37250","category_aro_name":"triclosan","category_aro_description":"Triclosan is a common antibacterial agent added to many consumer products as a biocide.  It is an inhibitor of fatty acid biosynthesis by blocking enoyl-carrier protein reductase (FabI).","category_aro_class_name":"Antibiotic"},"43746":{"category_aro_accession":"3005386","category_aro_cvterm_id":"43746","category_aro_name":"disinfecting agents and antiseptics","category_aro_description":"Disinfectants that can also interact with antimicrobial resistance mechanisms, e.g. molecule efflux, and thus are the targets of disinfectant resistance.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2193":{"model_id":"2193","model_name":"TriB","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"5384":{"protein_sequence":{"accession":"AAG03547.1","sequence":"MKPFSLAGLFGFALLLSGCGDEPPPAPPRPVLTVTVKTLKNDDLGRFAGSIQARYESVLGFRTNGRIASRLFDVGDFVGKGALLATLDPTDQQNQLRASQGDLASAEAQLIDAQANARRQEELFARSVTAQARLDDARTRLKTSQASFDQAKAAVQQARDQLSYTRLVTDFDGVITTWHAEAGQVVSAGQAVVTLARPEVREAVFDLPTEVAESLPADARFLVSAQLDPQARTTGSIRELGPQADASTRTRRVRLSLAQTPEAFRLGSTIQVQLSSAGSVRSVLPASVLLERDGKTQVWVVDGKQSSVALREVQVLSRDERQVVIGQGLADGDRVVRAGVNSLKPGQKIKLDEDAR"},"dna_sequence":{"accession":"AE004091.2","fmin":"178454","fmax":"179525","strand":"+","sequence":"ATGAAGCCGTTTTCCCTCGCCGGCCTGTTCGGCTTCGCCCTGCTCCTCTCCGGCTGCGGCGACGAGCCGCCGCCGGCACCGCCGCGGCCGGTGCTGACGGTGACCGTGAAGACCCTGAAGAACGACGACCTCGGTCGCTTCGCCGGGAGCATCCAGGCGCGCTACGAGAGCGTGCTCGGCTTCCGCACCAACGGACGGATCGCCTCGCGCCTGTTCGACGTCGGTGACTTCGTCGGCAAGGGCGCGCTGCTGGCGACCCTCGACCCCACCGACCAGCAGAACCAGTTGCGCGCCAGCCAGGGCGACCTGGCCAGCGCCGAGGCACAGTTGATCGACGCCCAGGCCAATGCCCGGCGCCAGGAAGAACTGTTCGCCCGCAGCGTCACCGCCCAGGCGCGCCTGGACGATGCGCGGACCCGCCTGAAGACCAGCCAGGCCAGCTTCGACCAGGCCAAAGCGGCGGTGCAGCAGGCCAGGGACCAGCTTTCCTACACGCGCCTGGTGACCGATTTCGACGGCGTCATCACCACCTGGCACGCCGAGGCCGGGCAAGTGGTCAGCGCCGGCCAGGCGGTGGTCACCCTGGCCCGGCCCGAAGTGCGCGAGGCAGTCTTCGACCTGCCCACCGAGGTCGCCGAGAGCCTGCCGGCCGACGCGCGCTTCCTGGTCAGCGCCCAGCTCGACCCGCAGGCCAGGACCACCGGCAGCATCCGCGAGCTGGGTCCGCAGGCCGACGCCTCGACCCGCACCCGTCGCGTGCGCCTGAGCCTGGCGCAGACGCCGGAGGCGTTTCGCCTCGGTTCGACCATCCAGGTCCAGCTGAGCAGCGCCGGTAGCGTGCGCAGCGTGCTGCCGGCCAGCGTGCTGCTGGAGCGCGACGGCAAGACCCAGGTCTGGGTCGTCGATGGGAAACAGTCCAGCGTGGCCCTGCGCGAGGTACAGGTGCTCAGCCGCGACGAACGCCAGGTGGTGATCGGACAGGGCCTGGCCGACGGCGACCGGGTGGTCCGCGCCGGAGTCAACAGCCTCAAGCCCGGCCAGAAGATCAAACTCGACGAGGATGCGCGATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36804","NCBI_taxonomy_name":"Pseudomonas aeruginosa PAO1","NCBI_taxonomy_id":"208964"}}}},"ARO_accession":"3003680","ARO_id":"40315","ARO_name":"TriB","CARD_short_name":"TriB","ARO_description":"TriB is a membrane protein that is fused to TriA and both are required for the triclosan efflux pump function of TriABC-OpmH in P. aeruginosa.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"37250":{"category_aro_accession":"3000870","category_aro_cvterm_id":"37250","category_aro_name":"triclosan","category_aro_description":"Triclosan is a common antibacterial agent added to many consumer products as a biocide.  It is an inhibitor of fatty acid biosynthesis by blocking enoyl-carrier protein reductase (FabI).","category_aro_class_name":"Antibiotic"},"43746":{"category_aro_accession":"3005386","category_aro_cvterm_id":"43746","category_aro_name":"disinfecting agents and antiseptics","category_aro_description":"Disinfectants that can also interact with antimicrobial resistance mechanisms, e.g. molecule efflux, and thus are the targets of disinfectant resistance.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2194":{"model_id":"2194","model_name":"TriC","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1900"}},"model_sequences":{"sequence":{"5383":{"protein_sequence":{"accession":"AAG03548.1","sequence":"MKGGFNLSDWALRHQSLVWYLMAVSLVMGVFSYLNLGREEDPSFAIKTMVIQTRWPGATVDDTLEQVTDRIEKKLEELDSLDYVKSYTRPGESTVFVYLKDTTKAGDIPDIWYQVRKKISDIQGEFPQGIQGPGFNDEFGDVFGSVYAFTADGLDFRQLRDYVEKVRLDIRSVKDLGKVQMIGAQNEVIYLNFSTRKLAALGLDQRQVVQSLQAQNAVTPSGVVEAGPERISVRTSGNFRSEKDLQAVNLRVNDRFYRLSDLASISRDFVDPPTSLFRYKGEPAIGLAVAMKEGGNILEFGEALNARMQEITGELPVGVGVHQVSNQAQVVKKAVGGFTRALFEAVVIVLIVSFVSLGLRAGLVVACSIPLVLAMVFVFMEYTDITMQRVSLGALIIALGLLVDDAMITVEMMITRLELGDSLHDSATYAYTSTAFPMLTGTLVTVAGFVPIGLNASSAGEYTFTLFAVIAVALLLSWIVAVLFAPVIAVHILPKTLKHKSEQKKGRIAERFDSLLHLAMRRRWTTIFLTALLFGVSLFLMKFVQHQFFPSSDRPELLVDLNLPQNSSIHETRAVMDRLEATLKDDEDIDHWSAYVGEGAIRFYLPLDQQLQNNFYGQLVIVTKDLEARERVAARLRDRLRKDYVGISTYVQPLEMGPPVGRPIQYRVSGPQIDKVREYAMGLAGVLDGNPNIGDIVYDWNEPGKMLKIDIAQDKARQLGLSSEDVAQIMNSVVTGSAVTQVRDDIYLVNVIGRAEDSERGSLETLESLQIVTPSGTSIPLKAFAKVSYELEQPLVWRRDRKPTITVKASLRGEIQPTDLVARLAPEVKRFADGLPANYRIEVGGTVEESGKAEGPIAKVVPLMLFLMATFLMIQLQSVQKLFLVASVAPLGLIGVVAALLPTGTPMGFVAILGILALIGIIIRNSVILVTQIDAFEKDGKTPWEAVLEATHHRTRPILLTAAAASLGMIPIAREVFWGPMAYAMIGGIVAATLLTLIFLPALYVAWYRIPEPGR"},"dna_sequence":{"accession":"AE004091.2","fmin":"179521","fmax":"182569","strand":"+","sequence":"ATGAAGGGCGGTTTCAACCTGTCGGACTGGGCCCTGCGCCACCAGTCCCTGGTCTGGTACCTGATGGCGGTATCGCTGGTGATGGGCGTGTTCTCCTACCTCAACCTGGGGCGCGAGGAGGATCCCTCGTTCGCCATCAAGACCATGGTCATCCAGACCCGCTGGCCGGGCGCCACGGTGGACGACACCCTGGAGCAGGTCACCGACCGCATCGAGAAGAAGCTCGAGGAGCTGGACTCGCTGGATTACGTGAAGAGCTACACGCGACCCGGCGAATCGACGGTCTTCGTCTACCTCAAGGACACCACCAAGGCCGGCGACATCCCGGATATCTGGTACCAGGTGCGCAAGAAGATATCCGACATCCAGGGCGAATTCCCCCAGGGCATCCAGGGACCGGGTTTCAACGACGAGTTCGGCGACGTGTTCGGCAGCGTCTACGCCTTCACCGCCGATGGCCTGGACTTCCGCCAGCTGCGCGACTACGTGGAGAAGGTGCGCCTGGACATCCGCTCGGTGAAAGACCTGGGCAAGGTGCAGATGATCGGTGCGCAGAACGAGGTCATCTACCTCAACTTCTCTACCCGCAAGCTGGCCGCCCTCGGTCTCGACCAGCGCCAGGTCGTGCAGAGCCTGCAGGCGCAGAACGCGGTGACCCCGTCCGGCGTGGTCGAGGCCGGCCCCGAGCGCATCTCGGTGCGCACCTCCGGCAACTTCCGTTCGGAAAAGGACCTGCAGGCGGTCAACCTGCGGGTCAACGATCGTTTCTACCGGCTGTCCGACCTGGCCAGCATCAGCCGCGATTTCGTCGACCCGCCGACCTCGCTGTTCCGCTACAAGGGCGAGCCGGCCATCGGCCTGGCGGTGGCGATGAAGGAGGGCGGCAATATCCTCGAGTTCGGCGAGGCGCTCAATGCGCGCATGCAGGAGATCACCGGCGAACTGCCGGTTGGCGTCGGCGTGCACCAGGTGTCGAACCAGGCCCAGGTGGTGAAGAAGGCGGTCGGCGGTTTCACCCGGGCGCTGTTCGAGGCGGTGGTGATCGTCCTCATCGTCAGCTTCGTCAGCCTCGGCCTGCGCGCCGGGCTGGTGGTGGCCTGCTCGATCCCGCTGGTGCTGGCGATGGTCTTCGTGTTCATGGAATACACCGACATCACCATGCAGCGGGTTTCCCTCGGCGCGCTGATCATCGCCCTCGGCCTGCTGGTGGACGATGCCATGATCACCGTGGAGATGATGATCACGCGCCTCGAACTGGGCGACTCGCTACACGACTCGGCGACCTACGCCTACACCTCGACGGCCTTCCCGATGCTCACCGGGACCCTGGTGACGGTGGCCGGCTTCGTACCCATCGGGCTCAACGCCAGCTCCGCCGGCGAGTACACCTTCACCCTGTTCGCAGTGATCGCCGTGGCGCTGCTGCTGTCGTGGATCGTCGCGGTGCTGTTCGCCCCGGTGATCGCCGTGCACATCCTGCCGAAGACTCTCAAGCACAAGTCGGAGCAGAAGAAGGGCCGCATTGCCGAGCGTTTCGACAGCCTGCTGCACCTGGCGATGCGCCGGCGCTGGACGACCATCTTCCTCACCGCGCTGCTGTTCGGCGTGTCGCTGTTCCTGATGAAGTTCGTCCAGCACCAGTTCTTCCCGTCTTCCGACCGTCCGGAACTGCTGGTCGACCTCAACCTGCCGCAGAACAGCAGCATCCACGAGACCAGGGCGGTGATGGACCGCCTGGAAGCGACGCTGAAGGACGACGAGGACATCGACCACTGGAGCGCCTACGTCGGCGAAGGCGCGATCCGCTTCTACCTGCCGCTGGACCAGCAGTTGCAGAACAACTTCTATGGCCAGCTGGTGATCGTCACCAAGGACCTGGAGGCCCGCGAGCGCGTCGCCGCACGCCTGCGCGATCGCTTGCGCAAGGACTACGTCGGCATCAGCACCTACGTGCAGCCGCTGGAGATGGGGCCGCCGGTGGGACGGCCGATCCAGTACCGGGTCAGCGGACCGCAGATCGACAAGGTCCGCGAGTACGCCATGGGCCTGGCCGGCGTGCTCGACGGCAACCCGAACATCGGCGATATCGTCTACGACTGGAACGAGCCCGGGAAGATGCTCAAGATCGACATCGCCCAGGACAAGGCGCGCCAGCTCGGGCTTTCCTCCGAGGACGTGGCGCAGATCATGAACAGCGTGGTGACCGGCAGCGCGGTGACCCAGGTGCGCGACGACATCTACCTGGTGAACGTCATCGGCCGCGCCGAGGATAGCGAGCGCGGCTCGCTGGAGACCCTGGAGAGCCTGCAGATCGTCACGCCCAGCGGCACCTCGATCCCGCTCAAGGCGTTCGCCAAGGTCAGCTACGAGCTGGAGCAGCCGCTGGTGTGGCGCCGCGACCGCAAGCCGACGATCACGGTGAAGGCGTCGCTGCGCGGCGAGATCCAGCCCACCGACCTGGTCGCCCGGCTGGCGCCGGAGGTCAAGCGCTTCGCCGACGGCCTGCCGGCGAACTACCGGATCGAAGTGGGCGGCACGGTGGAGGAGAGCGGCAAGGCCGAGGGCCCGATCGCCAAGGTGGTGCCGCTGATGCTGTTCCTCATGGCGACCTTCCTGATGATCCAGTTGCAGAGCGTGCAGAAGCTATTCCTGGTGGCCAGCGTCGCGCCGCTGGGGCTGATCGGGGTGGTCGCGGCGTTGCTGCCGACCGGCACGCCGATGGGCTTCGTGGCGATCCTCGGGATTCTCGCGCTGATCGGCATCATCATCCGCAACTCGGTGATCCTGGTGACCCAGATCGATGCCTTCGAGAAAGACGGCAAGACGCCCTGGGAAGCCGTGCTGGAAGCCACCCACCACCGCACCCGGCCGATCCTGCTGACGGCGGCGGCGGCCAGCCTGGGGATGATCCCCATCGCCCGCGAAGTGTTCTGGGGGCCGATGGCCTATGCGATGATCGGCGGCATCGTCGCCGCCACGCTGCTCACGCTGATCTTCCTGCCGGCGCTGTACGTCGCCTGGTACCGGATTCCGGAACCGGGACGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36804","NCBI_taxonomy_name":"Pseudomonas aeruginosa PAO1","NCBI_taxonomy_id":"208964"}}}},"ARO_accession":"3003681","ARO_id":"40316","ARO_name":"TriC","CARD_short_name":"TriC","ARO_description":"TriC is a resistance nodulation cell division (RND) transporter that is a part of TriABC-OpmH, a triclosan-specific efflux protein.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"37250":{"category_aro_accession":"3000870","category_aro_cvterm_id":"37250","category_aro_name":"triclosan","category_aro_description":"Triclosan is a common antibacterial agent added to many consumer products as a biocide.  It is an inhibitor of fatty acid biosynthesis by blocking enoyl-carrier protein reductase (FabI).","category_aro_class_name":"Antibiotic"},"43746":{"category_aro_accession":"3005386","category_aro_cvterm_id":"43746","category_aro_name":"disinfecting agents and antiseptics","category_aro_description":"Disinfectants that can also interact with antimicrobial resistance mechanisms, e.g. molecule efflux, and thus are the targets of disinfectant resistance.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2195":{"model_id":"2195","model_name":"OpmH","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"850"}},"model_sequences":{"sequence":{"5382":{"protein_sequence":{"accession":"AAG08359.1","sequence":"MLRRLSLAAAVAAATGVAWAAQPTPLPTKTDLISVYKEAVDNNADLAAAQADYLARKEVVPQARAGLLPQLGAGARVGDTRIAFDERPATVKRNSQVVQATLSQPLFRADRWFQWQAAKETSDQARLEFSATQQDLILRSAETYFTVLRAQDNLATSKAEEAAFKRQLDQANERFDVGLSDKTDVLEAQASYDTARANRLIAEQRVDDAFQALVTLTNRDYSAIEGMRHTLPVVPPAPNDAKAWVDTAVQQNLRLLASNYAVNAAEETLRQRKAGHLPTLDAVAQYQKGDNDALGFANSAANPLVHYGKYVDERSIGLELNIPIYSGGLTSSQVRESYQRLNQSEQSREGQRRQVVQDTRNLHRAVNTDVEQVQARRQAIISNQSSLEATEIGYQVGTRNIVDVLNAQRQLYAAVRDYNNSRYDYILDTLRLKQAAGTLSPADLEALSAYLKQDYDPDKDFLPPDLAKAAAEQLQSKPRQQY"},"dna_sequence":{"accession":"AE004091.2","fmin":"5584100","fmax":"5585549","strand":"+","sequence":"ATGCTGCGCAGACTCTCCCTGGCGGCCGCCGTGGCCGCTGCTACCGGTGTCGCCTGGGCCGCCCAGCCGACCCCGCTGCCGACCAAGACCGACCTGATCAGCGTCTACAAGGAAGCCGTCGACAACAACGCCGACCTCGCCGCCGCCCAGGCCGACTACCTGGCGCGCAAGGAAGTGGTGCCCCAGGCCCGCGCCGGCCTGCTGCCGCAACTCGGCGCCGGCGCCCGCGTCGGAGACACCCGGATCGCATTCGACGAGCGTCCGGCGACCGTCAAGCGCAACAGCCAGGTCGTCCAGGCCACCCTCAGCCAGCCGTTGTTCCGCGCCGACCGCTGGTTCCAGTGGCAGGCCGCCAAGGAAACCAGCGACCAGGCCCGGCTGGAATTCTCCGCGACCCAGCAGGACCTGATCCTGCGCAGCGCCGAGACCTACTTCACGGTGCTCCGCGCCCAGGACAACCTGGCCACCAGCAAGGCCGAGGAAGCCGCCTTCAAGCGCCAGCTGGACCAGGCCAACGAGCGCTTCGACGTGGGCCTTTCCGACAAGACCGACGTGCTCGAGGCCCAGGCCAGCTACGACACCGCCCGCGCCAACCGGTTGATCGCCGAACAGCGCGTGGACGATGCCTTCCAGGCCCTGGTGACCCTGACCAACCGCGACTACAGCGCCATCGAGGGCATGCGCCACACCCTGCCGGTGGTGCCGCCGGCGCCGAACGACGCCAAGGCCTGGGTCGACACCGCGGTGCAGCAGAACCTGCGCCTGCTGGCCAGCAACTACGCGGTCAACGCCGCCGAGGAAACCCTCCGCCAGCGCAAGGCCGGGCACCTGCCGACCCTCGATGCCGTGGCCCAGTACCAGAAGGGCGACAACGACGCCCTCGGCTTCGCCAACAGCGCCGCCAATCCGCTGGTGCACTATGGCAAGTATGTCGACGAGCGCAGCATTGGCCTGGAACTGAACATCCCGATCTACAGCGGCGGCCTGACCTCCTCCCAGGTCCGCGAGTCCTACCAGCGCCTCAACCAGAGCGAGCAATCCCGCGAAGGCCAGCGCCGCCAGGTGGTGCAGGATACCCGCAACCTGCACCGCGCGGTGAATACCGACGTCGAGCAGGTCCAGGCGCGGCGCCAGGCGATCATCTCCAACCAGAGTTCGCTGGAAGCCACCGAGATCGGCTACCAGGTCGGCACCCGCAACATCGTCGACGTGCTCAACGCCCAGCGCCAGCTGTACGCCGCCGTGCGCGACTACAACAACAGCCGCTACGACTACATCCTCGATACCCTGCGCCTGAAGCAGGCGGCCGGCACCCTCAGCCCGGCCGACCTGGAGGCGCTCAGCGCCTACCTGAAGCAGGACTACGATCCGGACAAGGACTTCCTCCCGCCGGACCTGGCCAAGGCCGCCGCCGAGCAGTTACAGAGCAAGCCGCGCCAGCAGTACTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36804","NCBI_taxonomy_name":"Pseudomonas aeruginosa PAO1","NCBI_taxonomy_id":"208964"}}}},"ARO_accession":"3003682","ARO_id":"40317","ARO_name":"OpmH","CARD_short_name":"OpmH","ARO_description":"OpmH is an outer membrane efflux protein required for triclosan-specific efflux pump function.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"37250":{"category_aro_accession":"3000870","category_aro_cvterm_id":"37250","category_aro_name":"triclosan","category_aro_description":"Triclosan is a common antibacterial agent added to many consumer products as a biocide.  It is an inhibitor of fatty acid biosynthesis by blocking enoyl-carrier protein reductase (FabI).","category_aro_class_name":"Antibiotic"},"43746":{"category_aro_accession":"3005386","category_aro_cvterm_id":"43746","category_aro_name":"disinfecting agents and antiseptics","category_aro_description":"Disinfectants that can also interact with antimicrobial resistance mechanisms, e.g. molecule efflux, and thus are the targets of disinfectant resistance.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"3542":{"model_id":"3542","model_name":"OXA-480","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"5737":{"protein_sequence":{"accession":"ALL53530.1","sequence":"MNIKALLFITSAIFISACSPYIVTANPNHSASKSDVKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"KR872296.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTATTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGTAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAACAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3003637","ARO_id":"40247","ARO_name":"OXA-480","CARD_short_name":"OXA-480","ARO_description":"OXA-480 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4133":{"model_id":"4133","model_name":"ACT-42","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6508":{"protein_sequence":{"accession":"WP_040117106.1","sequence":"MMKKSLCCALLLGISCSALATPVSEKQLAEVVANTVTPLMKAQSVPGMAVAVIYQGKPHYYTFGKADIAANKPVTPQTLFELGSISKTFTAVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMPYEQAMTTRVLKPLKLDHTRINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPENVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVVEGSDSKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANTSYPNPARVEAAYHILEALQ"},"dna_sequence":{"accession":"NG_050705.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCCCTTTGCTGCGCCCTGCTGCTCGGCATCTCTTGCTCTGCTCTCGCCACGCCAGTGTCAGAAAAACAGCTGGCGGAGGTGGTCGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCTGTTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGAAAACCGCACTATTACACGTTTGGCAAGGCCGATATCGCGGCGAATAAACCCGTTACGCCTCAGACCCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGCCGTTTTAGGTGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTGACGGGCAAGCAGTGGCAGGGTATTCGTATGCTGGATCTCGCCACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTCAAACCTTCTGGCATGCCCTATGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCAGGATTAACGTGCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGTATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCGGAGAACGTTGCTGATGCCTCACTTAAGCAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGGTCGAGGGCAGCGACAGTAAGGTAGCACTGGCGCCGTTGCCCGTGGCAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGCTCTACTGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATACAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCGAGGCGCTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40540","NCBI_taxonomy_name":"Enterobacter cloacae complex","NCBI_taxonomy_id":"354276"}}}},"ARO_accession":"3006237","ARO_id":"44699","ARO_name":"ACT-42","CARD_short_name":"ACT-42","ARO_description":"ACT-42 is a ACT beta-lactamase.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2196":{"model_id":"2196","model_name":"Pseudomonas aeruginosa gyrA conferring resistance to fluoroquinolones","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"40330":{"param_type":"multiple resistance variants","param_description":"A set of nucleotide or amino acid substitutions that are all required to confer resistance to an antibiotic drug or drug class, encoded as: [wild-type 1][position 1][mutation 1],[wild-type 2][position 2][mutation 2], etc. For example, D63Y,T142K.","param_type_id":"40330","param_value":{"3315":"T83I,D87G","3316":"T83I,D87N","3317":"T83I,D87H"}},"snp":{"Curated-R":{"3315":"g1065c","3316":"g1065c","3143":"T83I","3144":"H80R","3145":"D87N","3317":"D87N"},"param_value":{"3143":"T83I","3144":"H80R","3145":"D87N"},"clinical":{"3143":"T83I","3144":"H80R","3145":"D87N"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1500"}},"model_sequences":{"sequence":{"5277":{"protein_sequence":{"accession":"AAG06556.1","sequence":"MGELAKEILPVNIEDELKQSYLDYAMSVIVGRALPDARDGLKPVHRRVLYAMSELGNDWNKPYKKSARVVGDVIGKYHPHGDTAVYDTIVRMAQPFSLRYMLVDGQGNFGSVDGDNAAAMRYTEVRMAKLAHELLADLEKETVDWVPNYDGTEQIPAVMPTKIPNLLVNGSSGIAVGMATNIPPHNLGEVIDGCLALMDNPDLTVDELMQYIPGPDFPTAGIINGRAGIIEAYRTGRGRIYIRARAVVEEMEKGGGREQIIITELPYQLNKARLIEKIAELVKEKKIEGISELRDESDKDGMRVVIELRRGEVGEVVLNNLYAQTQLQSVFGINVVALVDGQPRTLNLKDMLEVFVRHRREVVTRRTVYELRKARERGHILEGQAVALSNIDPVIELIKSSPTPAEAKERLIATAWESSAVEAMVERAGADACRPEDLDPQYGLRDGKYYLSPEQAQAILELRLHRLTGLEHEKLLSEYQEILNLIGELIRILTNPARLMEVIREELEAVKAEFGDARRTEIVASQVDLTIADLITEEDRVVTISHGGYAKSQPLAAYQAQRRGGKGKSATGMKDEDYIEHLLVANSHATLLLFSSKGKVYWLRTFEIPEASRTARGRPLVNLLPLDEGERITAMLQIDLEALQQNGGADDDLDEAEGAVLEGEVVEAAEVEEVEGETAELVAEPTGAYIFMATAFGTVKKTPLVQFSRPRSSGLIALKLEEGDTLIAAAITDGAKEVMLFSSAGKVIRFAESVVRIMGRNARGVRGMRLGKGQQLISMLIPESGAQILTASERGFGKRTPLSKFPRRGRGGQGVIAMVTNERNGALIAAVQVQEGEEIMLISDQGTLVRTRVDEVSLSGRNTQGVTLIKLASDEVLVGLERVQEPSGGDDEDLPEGEEAAESLGESAESESEPAAEAEGNEE"},"dna_sequence":{"accession":"AE004091.2","fmin":"3556426","fmax":"3559198","strand":"-","sequence":"ATGGGCGAACTGGCCAAAGAAATTCTCCCGGTCAATATCGAAGACGAGCTGAAACAGTCCTATCTCGACTACGCGATGAGCGTGATCGTCGGGCGGGCCCTGCCGGATGCACGTGACGGCCTGAAGCCGGTGCACCGCCGTGTGCTTTATGCCATGAGCGAGCTGGGCAACGACTGGAACAAGCCCTACAAGAAATCCGCCCGTGTGGTCGGCGACGTGATCGGTAAGTACCACCCGCACGGCGACACCGCGGTCTACGACACCATCGTGCGCATGGCGCAGCCGTTCTCGCTGCGCTACATGCTGGTAGACGGCCAGGGCAACTTCGGTTCGGTGGACGGCGACAACGCCGCAGCCATGCGATACACCGAAGTGCGCATGGCCAAGCTGGCCCACGAACTGCTGGCGGACCTGGAAAAGGAAACCGTCGACTGGGTGCCCAACTACGATGGCACCGAGCAGATCCCGGCGGTCATGCCGACCAAGATTCCCAACCTGCTGGTCAACGGTTCCAGCGGTATCGCCGTGGGCATGGCGACCAACATCCCGCCGCACAACCTCGGCGAAGTGATCGACGGCTGCCTGGCGCTGATGGACAACCCCGACCTGACCGTCGATGAGCTGATGCAGTACATCCCCGGTCCGGACTTCCCCACCGCCGGCATCATCAACGGCCGCGCCGGGATCATCGAGGCCTACCGCACCGGTCGCGGGCGCATCTACATCCGTGCCCGCGCCGTCGTCGAGGAGATGGAGAAGGGCGGCGGTCGCGAGCAGATTATCATCACCGAGCTGCCGTACCAGTTGAACAAGGCGCGGTTGATCGAGAAGATCGCCGAGCTGGTGAAAGAGAAGAAGATCGAGGGTATTTCCGAGCTGCGCGACGAGTCTGACAAGGACGGCATGCGCGTGGTCATCGAGCTGCGTCGCGGCGAGGTGGGCGAGGTGGTCCTCAACAACCTCTATGCCCAGACCCAGCTGCAGAGCGTGTTCGGCATCAACGTGGTGGCCCTGGTCGACGGCCAGCCGCGCACGCTGAACCTGAAGGACATGCTCGAGGTGTTCGTCCGCCACCGCCGCGAAGTGGTGACCCGGCGTACCGTCTACGAGCTGCGCAAGGCCCGCGAGCGCGGGCACATCCTGGAAGGCCAGGCGGTCGCCCTGTCGAACATCGACCCGGTGATCGAGCTGATCAAGAGTTCGCCGACCCCGGCCGAGGCCAAGGAACGCCTGATCGCCACTGCCTGGGAGTCCAGCGCGGTGGAAGCGATGGTCGAGCGTGCCGGCGCCGACGCCTGTCGTCCGGAAGACCTGGATCCGCAGTACGGCCTGCGCGACGGCAAGTACTACCTGTCGCCGGAGCAGGCCCAGGCGATCCTCGAGCTGCGCCTGCATCGCCTGACCGGCCTGGAGCACGAGAAGCTGCTCTCCGAATACCAGGAAATCCTCAACCTGATCGGCGAGCTGATCCGCATCCTGACCAACCCGGCGCGCCTGATGGAGGTGATCCGTGAGGAACTGGAAGCGGTCAAGGCCGAATTCGGCGATGCTCGCCGCACCGAGATCGTGGCTTCCCAGGTCGACCTGACCATCGCCGACCTGATCACCGAGGAAGACCGCGTGGTGACCATCTCGCACGGCGGCTACGCCAAGTCCCAGCCGCTGGCCGCCTACCAGGCGCAGCGTCGCGGCGGCAAAGGCAAGTCCGCCACCGGGATGAAGGACGAGGACTACATCGAACACCTGCTGGTGGCCAACAGCCATGCGACCCTCCTGCTGTTCTCCAGCAAGGGCAAGGTCTACTGGCTGCGTACCTTCGAGATTCCGGAAGCCTCGCGTACCGCGCGTGGCCGGCCGCTGGTGAACCTGCTGCCGCTGGATGAGGGCGAGCGGATCACCGCGATGTTGCAGATCGACCTGGAGGCGCTGCAGCAGAACGGTGGCGCCGATGACGACCTCGACGAAGCCGAAGGCGCGGTGCTCGAGGGCGAGGTGGTCGAGGCCGCCGAGGTCGAGGAAGTCGAGGGCGAGACCGCCGAGCTGGTGGCCGAGCCGACCGGCGCCTACATCTTCATGGCCACCGCCTTCGGTACCGTGAAGAAGACCCCGCTGGTGCAGTTCAGCCGTCCGCGCAGCAGCGGCCTGATCGCGCTCAAGCTGGAAGAGGGCGACACCCTGATCGCCGCCGCGATCACCGATGGCGCCAAGGAAGTCATGCTGTTCTCCAGCGCCGGCAAGGTGATCCGCTTCGCCGAGAGCGTGGTGCGCATCATGGGCCGCAACGCCCGCGGCGTACGTGGCATGCGCCTGGGCAAGGGGCAGCAGCTGATCTCCATGCTGATTCCGGAGTCCGGGGCGCAGATCCTCACCGCCTCCGAGCGCGGCTTCGGCAAGCGTACCCCGCTGAGCAAGTTCCCGCGTCGCGGCCGCGGCGGCCAGGGGGTGATCGCCATGGTCACCAACGAGCGCAACGGCGCGCTGATCGCCGCGGTACAGGTCCAGGAAGGCGAGGAGATCATGCTGATTTCCGACCAGGGCACCCTGGTGCGGACGCGTGTCGACGAAGTCTCCCTGTCCGGCCGCAATACCCAGGGCGTAACCCTGATCAAGCTCGCCAGCGACGAGGTACTGGTCGGTCTGGAGCGTGTCCAGGAGCCGTCGGGCGGAGATGACGAGGACCTGCCCGAGGGCGAGGAAGCTGCCGAATCTCTGGGCGAGTCGGCCGAGTCCGAGTCCGAGCCCGCGGCGGAAGCGGAAGGCAACGAAGAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36804","NCBI_taxonomy_name":"Pseudomonas aeruginosa PAO1","NCBI_taxonomy_id":"208964"}}}},"ARO_accession":"3003684","ARO_id":"40319","ARO_name":"Pseudomonas aeruginosa gyrA conferring resistance to fluoroquinolones","CARD_short_name":"Paer_gyrA_FLO","ARO_description":"Point mutation of Pseudomonas aeruginosa gyrA resulted in the lowered affinity between fluoroquinolones and gyrA. Thus, conferring resistance.","ARO_category":{"39876":{"category_aro_accession":"3003292","category_aro_cvterm_id":"39876","category_aro_name":"fluoroquinolone resistant gyrA","category_aro_description":"DNA gyrase is responsible for DNA supercoiling and consists of two alpha and two beta subunits. GyrA point mutations confer resistance by preventing fluoroquinolone antibiotics from binding the alpha-subunit.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"37007":{"category_aro_accession":"3000663","category_aro_cvterm_id":"37007","category_aro_name":"ofloxacin","category_aro_description":"Ofloxacin is a 6-fluoro, 7-piperazinyl quinolone with a methyl-substituted oxazine ring. It has a broad spectrum of activity including many enterobacteria and mycoplasma but most anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"37142":{"category_aro_accession":"3000762","category_aro_cvterm_id":"37142","category_aro_name":"pefloxacin","category_aro_description":"Pefloxacin is structurally and functionally similar to norfloxacin. It is poorly active against mycobacteria, while anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"40338":{"category_aro_accession":"3003690","category_aro_cvterm_id":"40338","category_aro_name":"sitafloxacin","category_aro_description":"Sitafloxacin is a fluoroquinolone active against multi-resistant Gram-positive and negative pathogens. Sitafloxacin shows inhibitory activity against DNA gyrase and topoisomerase IV, which blocks bacterial DNA replication, thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2211":{"model_id":"2211","model_name":"mexP","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"650"}},"model_sequences":{"sequence":{"3405":{"protein_sequence":{"accession":"BAE06007.1","sequence":"MNLRHFIRITATLGVAALIAGCGESAPPGAASAPPSVPVAEVVVRPVTPYAEFTGSLTAVEQVELRPRVAGYIQDVTVPEGRLVEKGQQLFLIDPRVFKAAQDAARARLREAEAAALLARTEHERAELLYARKVVARERLDSAIASRNASKAQVDAARAALDAAQLDLGFTRVTAPIGGRVGHIQVTEGNYVTNGVTALTSIVSVDPLYVYFDVDERTYLQALAPTRGREGEQAPRVKVALLTDESYGRSSRLDFLANAADRGTGTVRVRAVVDNPDGQLTPGLFAKVRLETGKPRAQVLVADHSIGTDQGRRYVLVVDEGNKTQYRPVELGPMVDGLRVVRQGLQPGERIVVKGLVRPDMQITPRLAEIDGTPVDLSKTVGAAQ"},"dna_sequence":{"accession":"AB219524.1","fmin":"22","fmax":"1180","strand":"+","sequence":"ATGAATCTCAGACACTTCATCCGCATCACCGCGACGCTAGGTGTCGCGGCCCTTATCGCTGGCTGCGGGGAATCGGCGCCGCCGGGGGCGGCGAGCGCCCCGCCAAGCGTTCCCGTCGCCGAGGTGGTGGTTCGCCCGGTGACACCCTACGCCGAGTTCACCGGCTCGCTGACCGCTGTCGAGCAGGTAGAACTGCGGCCGCGCGTCGCCGGCTACATCCAGGACGTTACGGTGCCGGAAGGCCGCCTGGTAGAGAAGGGCCAGCAACTGTTCCTCATCGACCCGCGCGTGTTCAAGGCGGCGCAGGATGCCGCCAGGGCACGCCTGCGCGAGGCCGAGGCCGCGGCGTTGCTGGCGCGCACCGAACACGAGCGAGCCGAGCTGCTGTATGCGCGGAAGGTCGTCGCCCGGGAGCGGCTCGACAGCGCCATCGCCTCGCGCAATGCCAGCAAGGCCCAGGTCGATGCGGCCAGGGCCGCCCTCGACGCGGCGCAACTGGATCTCGGCTTCACGCGGGTGACGGCACCGATCGGCGGGCGTGTCGGGCATATCCAGGTCACCGAGGGCAACTACGTCACCAATGGCGTCACCGCGCTGACCAGCATCGTTTCGGTCGATCCGCTGTACGTGTACTTCGATGTCGACGAGCGCACCTACCTGCAGGCCCTGGCGCCGACCCGCGGCAGGGAAGGCGAGCAGGCCCCCAGGGTCAAGGTGGCGCTGCTCACCGACGAGTCCTATGGACGAAGCAGTCGCCTCGATTTCCTCGCCAACGCCGCCGACCGCGGGACCGGCACGGTCCGGGTTCGGGCGGTGGTGGACAACCCGGACGGGCAACTGACGCCGGGGCTGTTCGCCAAGGTCAGGCTGGAGACCGGCAAGCCTCGCGCGCAGGTGCTGGTCGCCGACCATTCCATCGGCACCGACCAGGGCAGGCGCTATGTGCTGGTCGTCGACGAAGGCAACAAGACCCAGTACCGGCCGGTGGAACTCGGCCCGATGGTCGACGGCCTGCGGGTCGTCCGCCAGGGCCTGCAGCCGGGCGAGCGCATCGTCGTCAAGGGCCTGGTCCGGCCGGACATGCAGATCACACCGCGCCTTGCGGAAATCGATGGCACGCCCGTCGACCTGTCGAAGACCGTGGGGGCCGCACAATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3003698","ARO_id":"40350","ARO_name":"mexP","CARD_short_name":"mexP","ARO_description":"MexP is the membrane fusion protein of the MexPQ-OpmE multidrug efflux complex.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35963":{"category_aro_accession":"0000045","category_aro_cvterm_id":"35963","category_aro_name":"acriflavine","category_aro_description":"Acriflavine is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36309":{"category_aro_accession":"3000170","category_aro_cvterm_id":"36309","category_aro_name":"imipenem","category_aro_description":"Imipenem is a broad-spectrum antibiotic and is usually taken with cilastatin, which prevents hydrolysis of imipenem by renal dehydropeptidase-I. It is resistant to hydrolysis by most other beta-lactamases. Notable exceptions are the KPC beta-lactamases and Ambler Class B enzymes.","category_aro_class_name":"Antibiotic"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36595":{"category_aro_accession":"3000456","category_aro_cvterm_id":"36595","category_aro_name":"thiamphenicol","category_aro_description":"Derivative of Chloramphenicol. The nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3).","category_aro_class_name":"Antibiotic"},"37626":{"category_aro_accession":"3001227","category_aro_cvterm_id":"37626","category_aro_name":"kitasamycin","category_aro_description":"Kitasamycin is a macrolide antibiotic and is produced by Streptoverticillium kitasatoense. The drug has antimicrobial activity against a wide spectrum of pathogens.","category_aro_class_name":"Antibiotic"},"40353":{"category_aro_accession":"3003701","category_aro_cvterm_id":"40353","category_aro_name":"rokitamycin","category_aro_description":"Rokitamycin is a macrolide antibiotic. Synthesized from strains of Streptomyces kitasatoensis.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"43746":{"category_aro_accession":"3005386","category_aro_cvterm_id":"43746","category_aro_name":"disinfecting agents and antiseptics","category_aro_description":"Disinfectants that can also interact with antimicrobial resistance mechanisms, e.g. molecule efflux, and thus are the targets of disinfectant resistance.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"4180":{"model_id":"4180","model_name":"ADC-104","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6555":{"protein_sequence":{"accession":"WP_068981611.1","sequence":"MRFKKISCLLLSPLFIFNTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKVLKNTPIDQVNLLQLATYTSSNLALQFPDEVQTDQQVLTFFKDWQPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPTDIQRAINETHQGFYQLGTMYQALGWEEFSYPATLQTLLDINSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKE"},"dna_sequence":{"accession":"NG_051443.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAATACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCATTATTAGAAAAATATGATGTACCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGTGCTAAAAAATACACCGATTGATCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTAGCAACCTCGCTTTACAATTTCCAGATGAAGTACAAACAGATCAACAAGTTTTAACTTTTTTCAAAGACTGGCAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTGGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTTGATGCCCCAGCATACGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTTAACCCACAGAAATATCCGACAGATATTCAACGGGCAATTAATGAAACACATCAAGGGTTCTATCAATTAGGAACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACATTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCAACGGTTTCGGAACATATGTGGTGTTTATTCCCAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAACGCATTAAGGCAGCGTATGCAGTTTTAAATGCAATAAAGGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006284","ARO_id":"44746","ARO_name":"ADC-104","CARD_short_name":"ADC-104","ARO_description":"ADC-104 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2212":{"model_id":"2212","model_name":"mexQ","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1900"}},"model_sequences":{"sequence":{"3406":{"protein_sequence":{"accession":"BAE06008.1","sequence":"MTFPRFFIDRPIFAIVLSVLMMIGGIVSFFQLPLSEYPAVTPPTVQVTTAYPGANPDVIAQTVATPLEQAITGVEGMLYMSSQSATDGRMILTITFDQHIDPDMAQIQVQNRVSRVLSRLPDEVQRQGVVTQKTSPDILMVVHLLSPEQRYDPLYISNYAYLQVRDELLRLPGISDVVVWGAGEYSMRLWLDPDLIAARGLTAGEVIAAVREQNVQVAAGAVGQAPDSTAAFQVTVNTLGRLSDEEQFGDIIVRTGADGQVTRLRDVARIEMGGDAYALRSLLDGEPAVALQIIQSPGANALDTAEAVRATVARLEGNFPAGLSARIAYDPTVFVRASLQTVATTLLEAILLVVVVVVLFLRSWRASLIPLMAVPVSLVGTFAVMHLMGFSLNTLSLFGLVLSIGIVVDDAIVVVENVERHIENGEPPLQAARRAMDEVTGPIMAITSVLAAVFIPTAFLSGLQGEFYRQFALTIAISTILSALNSLTLSPALAGLLLRPRPAGGAVAGRFQRLLQVLGRPLRNAPEAYGNAVRKVVRVSGLALVVYGGLLGLTWVGFQAVPPGFVPMQDKYYLIGIAQLPNGASLERTDAVVRQMSRIGLDEPGVESVVAFPGLSVNGFVNVPNAAVMFFMLDPFESRTSADLGALAIAGRLQARFASIPDGFLGVFPPPPVPGLGTIGGFKMQVEDRGGAGLEALARQTQVLMMKATESGQLGGLMTSFDINAPQLEVVVDRTKVKSQGVRLADVFEALQVYLGSLYINDFNRFGRTYKVTAQADAPHRMQAEAIGRLQVRNAAGAMLPLSSFVTVTPSSGPDRVIHYNGYPSADISGGALPGVSSGQAVALMERLAGEVLPEGMTFEWTDLTYQQKLAGNSALFIFPLCVLLAYLILAAQYNSWLLPLAVLLIVPMCLLSAIAGVWLVGGDNNVFVQIGLVVLVGLAAKNAILIVEFARTLEAEGARALEAVVEACRLRLRPILMTSLAFIAGVVPLVMASGAGAEMRQAMGVAVFAGMLGVTLFGLFLTPVFYVLVRALAARLERRAGGSLAHLEGGRP"},"dna_sequence":{"accession":"AB219524.1","fmin":"1176","fmax":"4338","strand":"+","sequence":"ATGACATTCCCACGCTTCTTCATCGATAGGCCGATCTTCGCCATCGTTCTTTCGGTGCTGATGATGATCGGAGGCATCGTTTCGTTCTTCCAGTTGCCGCTGAGCGAATACCCGGCGGTGACGCCGCCGACCGTGCAGGTGACTACCGCCTATCCCGGCGCCAACCCCGACGTGATCGCGCAGACGGTGGCGACACCGCTGGAGCAGGCGATCACCGGGGTCGAGGGGATGCTGTACATGTCCTCGCAGTCGGCCACCGACGGGCGAATGATCCTGACCATCACCTTCGACCAGCACATCGATCCCGACATGGCCCAGATCCAGGTGCAGAACCGGGTCTCGCGGGTGCTCTCGCGCCTGCCCGACGAGGTGCAGCGGCAGGGCGTGGTCACCCAGAAGACCTCGCCGGACATCCTCATGGTGGTGCACCTGCTGTCGCCGGAGCAACGCTACGACCCGCTGTACATCTCGAACTACGCCTACCTCCAGGTGCGCGACGAACTGCTGCGCCTGCCGGGGATCAGCGATGTGGTGGTGTGGGGCGCCGGCGAGTACAGCATGCGCCTGTGGCTCGACCCCGACCTGATCGCCGCGCGCGGGCTGACGGCGGGCGAAGTGATCGCCGCGGTACGCGAACAGAACGTCCAGGTGGCGGCCGGCGCCGTCGGCCAGGCGCCGGACTCCACCGCGGCCTTCCAGGTCACGGTGAATACCCTCGGGCGGCTGAGCGACGAAGAGCAGTTCGGCGACATCATCGTCCGCACCGGCGCCGACGGCCAGGTGACGCGCCTGCGCGACGTCGCGCGGATCGAGATGGGCGGCGATGCCTATGCGCTGCGCAGCCTGCTGGACGGCGAGCCGGCGGTGGCCTTGCAGATCATCCAGAGCCCCGGAGCCAACGCGCTGGATACCGCCGAAGCGGTGCGTGCCACCGTGGCGAGGCTCGAAGGCAACTTCCCGGCCGGCCTGAGCGCGCGCATCGCCTACGACCCGACGGTGTTCGTCCGCGCTTCGTTGCAGACCGTGGCCACCACCCTGCTGGAGGCGATCCTGCTGGTCGTGGTGGTGGTGGTGCTGTTCCTGCGTAGCTGGCGTGCTTCGCTGATTCCGCTGATGGCCGTGCCGGTCTCGCTGGTCGGCACCTTCGCCGTCATGCACCTGATGGGTTTCTCGCTGAATACCCTGTCGTTGTTCGGCCTGGTGTTGTCGATCGGCATCGTCGTCGATGACGCCATCGTGGTGGTGGAAAACGTCGAGCGCCACATCGAGAACGGCGAGCCGCCGCTCCAGGCCGCGCGGCGTGCGATGGACGAGGTCACCGGGCCGATCATGGCGATCACCTCGGTGCTGGCGGCGGTGTTCATCCCCACGGCCTTTCTCAGTGGCCTGCAGGGCGAGTTCTATCGTCAGTTCGCCCTGACCATCGCCATCTCCACCATCCTGTCGGCGCTCAACTCGCTGACCCTCAGCCCGGCCCTGGCGGGCCTGCTGTTGCGTCCGCGGCCGGCCGGAGGTGCGGTGGCGGGGCGCTTCCAGCGACTGCTCCAGGTCCTCGGCCGACCGTTGCGAAATGCCCCCGAGGCCTACGGCAACGCGGTGCGCAAGGTGGTGCGGGTGAGCGGCCTGGCCCTGGTGGTGTATGGGGGCCTGCTTGGCCTGACCTGGGTCGGTTTCCAGGCGGTGCCGCCGGGCTTCGTGCCGATGCAGGACAAGTACTATCTGATCGGCATCGCCCAGTTGCCGAACGGAGCGTCGCTGGAGCGTACCGATGCGGTGGTCAGGCAGATGTCCCGGATCGGCCTCGACGAGCCGGGGGTGGAGAGCGTCGTGGCCTTCCCGGGCCTGTCGGTGAACGGTTTCGTCAACGTGCCGAACGCCGCGGTCATGTTCTTCATGCTCGATCCGTTCGAATCGCGCACCTCCGCCGATCTCGGCGCGCTGGCCATCGCCGGGCGCCTGCAAGCCAGGTTCGCCAGCATTCCCGACGGCTTCCTCGGGGTCTTCCCGCCGCCGCCGGTACCGGGGCTGGGAACCATCGGCGGCTTCAAGATGCAGGTCGAGGATCGCGGCGGCGCCGGGCTGGAAGCCCTGGCCAGGCAGACCCAGGTGCTGATGATGAAGGCCACTGAGTCCGGCCAGCTCGGGGGCTTGATGACCAGCTTCGATATCAATGCCCCGCAGCTCGAGGTGGTGGTCGACCGCACCAAGGTGAAGAGCCAGGGCGTTCGCCTGGCCGATGTGTTCGAGGCATTGCAGGTCTACCTCGGCTCGCTGTACATCAACGACTTCAACCGCTTCGGTCGCACCTACAAGGTCACTGCCCAGGCCGATGCGCCGCACCGCATGCAGGCCGAAGCCATCGGGCGCCTGCAGGTACGCAATGCCGCCGGGGCGATGTTGCCGCTGTCCTCGTTCGTCACCGTGACGCCCAGCTCCGGTCCCGACCGGGTGATCCACTACAACGGCTATCCGTCGGCGGATATCAGCGGCGGCGCGCTTCCCGGCGTCAGTTCGGGACAGGCGGTGGCGTTGATGGAGCGCCTGGCCGGCGAAGTGCTGCCCGAGGGCATGACCTTCGAATGGACCGACCTGACCTACCAGCAGAAGCTGGCCGGCAACAGCGCGCTGTTCATCTTCCCGCTGTGCGTGCTGCTGGCCTACCTGATCCTCGCCGCGCAGTACAACAGCTGGCTGTTGCCGCTGGCGGTCCTGCTGATCGTGCCGATGTGCCTGCTCAGCGCGATCGCCGGGGTGTGGCTGGTGGGCGGCGACAACAACGTGTTCGTCCAGATCGGGCTGGTGGTGCTGGTAGGCCTGGCGGCGAAGAACGCGATCCTGATCGTCGAGTTCGCCCGCACGCTGGAGGCCGAGGGCGCCCGTGCGCTGGAGGCGGTGGTCGAGGCTTGCCGCCTGCGCCTGCGGCCGATCCTGATGACCTCGCTGGCGTTCATCGCCGGCGTGGTGCCGTTGGTCATGGCCAGCGGCGCCGGAGCGGAAATGCGCCAGGCGATGGGCGTCGCGGTATTCGCCGGGATGCTCGGGGTGACGCTGTTCGGCCTGTTCCTCACGCCGGTGTTCTACGTACTGGTACGGGCACTGGCGGCGCGCCTGGAGCGACGCGCCGGCGGCAGCCTGGCGCATCTGGAGGGAGGCCGTCCATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3003699","ARO_id":"40351","ARO_name":"mexQ","CARD_short_name":"mexQ","ARO_description":"MexQ is the inner membrane transporter of the multidrug efflux pump MexPQ-OpmE.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35963":{"category_aro_accession":"0000045","category_aro_cvterm_id":"35963","category_aro_name":"acriflavine","category_aro_description":"Acriflavine is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36309":{"category_aro_accession":"3000170","category_aro_cvterm_id":"36309","category_aro_name":"imipenem","category_aro_description":"Imipenem is a broad-spectrum antibiotic and is usually taken with cilastatin, which prevents hydrolysis of imipenem by renal dehydropeptidase-I. It is resistant to hydrolysis by most other beta-lactamases. Notable exceptions are the KPC beta-lactamases and Ambler Class B enzymes.","category_aro_class_name":"Antibiotic"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36595":{"category_aro_accession":"3000456","category_aro_cvterm_id":"36595","category_aro_name":"thiamphenicol","category_aro_description":"Derivative of Chloramphenicol. The nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3).","category_aro_class_name":"Antibiotic"},"37626":{"category_aro_accession":"3001227","category_aro_cvterm_id":"37626","category_aro_name":"kitasamycin","category_aro_description":"Kitasamycin is a macrolide antibiotic and is produced by Streptoverticillium kitasatoense. The drug has antimicrobial activity against a wide spectrum of pathogens.","category_aro_class_name":"Antibiotic"},"40353":{"category_aro_accession":"3003701","category_aro_cvterm_id":"40353","category_aro_name":"rokitamycin","category_aro_description":"Rokitamycin is a macrolide antibiotic. Synthesized from strains of Streptomyces kitasatoensis.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"43746":{"category_aro_accession":"3005386","category_aro_cvterm_id":"43746","category_aro_name":"disinfecting agents and antiseptics","category_aro_description":"Disinfectants that can also interact with antimicrobial resistance mechanisms, e.g. molecule efflux, and thus are the targets of disinfectant resistance.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2075":{"model_id":"2075","model_name":"Salmonella enterica soxR with mutation conferring antibiotic resistance","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"3900":"R20H","3901":"G121D"},"Curated-R":{"3900":"R20H","3901":"G121D"},"clinical":{"3900":"R20H","3901":"G121D"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"5221":{"protein_sequence":{"accession":"CAD09250.1","sequence":"MEKKSPRLKALLTPGEVAKRSGVAVSALHFYESKGLITSIRNSGNQRRYKRDVLRYVAIIKIAQRIGIPLATIGDAFGILPEGHTLSAKEWKQLSSQWREELDRRIHTLVALRDELDGCIGCGCLSRSDCPLRNPGDRLGEHGTGARLLEDD"},"dna_sequence":{"accession":"AL513382.1","fmin":"4349504","fmax":"4349963","strand":"+","sequence":"ATGGAAAAAAAATCTCCCCGTTTAAAAGCCTTACTGACGCCGGGGGAAGTTGCGAAACGTAGCGGTGTTGCTGTGTCCGCCCTGCACTTCTATGAAAGCAAAGGGCTAATTACCAGTATCCGTAATAGCGGTAACCAACGGCGATACAAGCGTGACGTGTTGCGTTATGTCGCGATTATCAAGATTGCCCAGCGTATCGGCATCCCGCTGGCAACTATCGGCGACGCGTTTGGTATCTTGCCGGAAGGGCATACGTTAAGCGCGAAAGAGTGGAAGCAGCTCTCCTCGCAGTGGCGCGAAGAGTTAGACCGACGTATTCATACGCTGGTGGCGTTGCGCGATGAGCTGGACGGTTGTATCGGCTGCGGCTGTTTATCGCGTAGCGACTGTCCGCTGCGGAATCCAGGCGACAGGCTTGGCGAACACGGGACGGGCGCCCGGCTGCTTGAAGATGATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35776","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Typhi str. CT18","NCBI_taxonomy_id":"220341"}}}},"ARO_accession":"3003382","ARO_id":"39966","ARO_name":"Salmonella enterica soxR with mutation conferring antibiotic resistance","CARD_short_name":"Sent_soxR_MULT","ARO_description":"SoxR is a sensory protein that upregulates soxS expression in the presence of redox-cycling drugs. This stress response leads to the expression of many multidrug efflux pumps.","ARO_category":{"36002":{"category_aro_accession":"0010001","category_aro_cvterm_id":"36002","category_aro_name":"ATP-binding cassette (ABC) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding\/hydrolysis to transport substrates across cell membranes.","category_aro_class_name":"AMR Gene Family"},"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37084":{"category_aro_accession":"3000704","category_aro_cvterm_id":"37084","category_aro_name":"cefalotin","category_aro_description":"Cefalotin is a semisynthetic cephalosporin antibiotic activate against staphylococci. It is resistant to staphylococci beta-lactamases but hydrolyzed by enterobacterial beta-lactamases.","category_aro_class_name":"Antibiotic"},"37250":{"category_aro_accession":"3000870","category_aro_cvterm_id":"37250","category_aro_name":"triclosan","category_aro_description":"Triclosan is a common antibacterial agent added to many consumer products as a biocide.  It is an inhibitor of fatty acid biosynthesis by blocking enoyl-carrier protein reductase (FabI).","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"43746":{"category_aro_accession":"3005386","category_aro_cvterm_id":"43746","category_aro_name":"disinfecting agents and antiseptics","category_aro_description":"Disinfectants that can also interact with antimicrobial resistance mechanisms, e.g. molecule efflux, and thus are the targets of disinfectant resistance.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2093":{"model_id":"2093","model_name":"Chlamydophila psittaci 16S rRNA mutation conferring resistance to spectinomycin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"3027":"c1193g","4808":"c1193t","2932":"g1194c","3010":"a1192g"},"Curated-R":{"3027":"c1193g","4808":"c1193t","2932":"g1194c","3010":"a1192g"},"clinical":{"3027":"c1193g","4808":"c1193t","2932":"g1194c","3010":"a1192g"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"41093","param_value":"2600"}},"model_sequences":{"sequence":{"3780":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"AB001778.1","fmin":"0","fmax":"1507","strand":"+","sequence":"AGAATTTGATCTTGGTTCAGATTGAACGCTGGCGGCGTGGATGAGGCATGCAAGTCGAACGGAATAATGACTTCGGTTGTTATTTAGTGGCGGAAGGGTTAGTAATACATAGATAATCTGTCCTCAACTTGGGAATAACGGTTGGAAACGACCGCTAATACCGAATGTGGTATGTTTAGGCATCTAAAACATATTAAAGAAGGGGATCTTCGGACCTTTCGGTTGAGGGAGAGTCTATGGGATATCAGCTTGTTGGTGGGGTAATGGCCTACCAAGGCTTTGACGTCTAGGCGGATTGAGAGATTGACCGCCAACACTGGGACTGAGACACTGCCCAGACTTCTACGGAAGGCTGCAGTCGAGAATCTTTCGCAATGGACGAAAGTCTGACGAAGCGACGCCGCGTGTGTGATGAAGGCTCTAGGGTTGTAAAGCACTTTCGCTTGGGAATAAGAGAGATTGGCTAATATCCAATCGATTTGAGCGTACCAGGTAAAGAAGCACCGGCTAACTCCGTGCCAGCAGCTGCGGTAATACGGAGGGTGCTAGCGTTAATCGGATTTATTGGGCGTAAAGGGCGTGTAGGCGGAAAGGAAAGTTAGATGTTAAATCTTGGGGCTCAACCCCAAGCCAGCATCTAATACTATCTTTCTAGAGGGTAGATGGAGAAAAGGGAATTCCACGTGTAGCGGTGAAATGCGTAGATATGTGGAAGAACACCAGTGGCGAAGGCGCTTTTCTAATTTACACCTGACGCTAAGGCGCGAAAGCAAGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCTTGCCGTAAACGATGCATACTTGATGTGGATAGTCTCAACCCTATCCGTGTCGTAGCTAACGCGTTAAGTATGCCGCCTGAGGAGTACACTCGCAAGGGTGAAACTCAAAAGAATTGACGGGGGCCCGCACAAGCAGTGGAGCATGTGGTTTAATTCGATGCAACGCGAAGAACCTTACCTGGGCTTGACATGTATTTGACCGCGGCAGAAATGTCGTTTTCCGCAAGGACAGATACACAGGTGCTGCATGGCTGTCGTCAGCTCGTGCCGTGAGGTGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCGTTAGTTGCCAACACTTAGGGTGGGAACTCTAACGAGACTGCCTGGGTTAACCAGGAGGAAGGCGAGGATGACGTCAAGTCAGCATGGCCCTTATGCCCAGGGCTACACACGTGCTACAATGGCCAGTACAGAAGGTAGCAATATCGTGAGATGGAGCAAATCCTCAAAGCTGGCCCCAGTTCGGATTGTAGTCTGCAACTCGACTACATGAAGTCGGAATTGCTAGTAATGGCGTGTCAGCTATAACGCCGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACATCATGGGAGTTGGTTTTGCCTTAAGTCGTTGACTCAACCTGCAAAGGAGAGAGGCGCCCAAGGTGAGGCTGATGACTGGGATGAAGTCGTAACAAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40343","NCBI_taxonomy_name":"Chlamydia psittaci 6BC","NCBI_taxonomy_id":"331636"}}}},"ARO_accession":"3003485","ARO_id":"40087","ARO_name":"Chlamydophila psittaci 16S rRNA mutation conferring resistance to spectinomycin","CARD_short_name":"Cpsi_16S_SPT","ARO_description":"Point mutation in the 16S rRNA helix 34 region of Chlamydophila psittaci can confer resistance against spectinomycin.","ARO_category":{"40277":{"category_aro_accession":"3003666","category_aro_cvterm_id":"40277","category_aro_name":"16s rRNA with mutation conferring resistance to aminoglycoside antibiotics","category_aro_description":"Point mutations in the 16S rRNA of bacteria can confer resistance to aminoglycosides.","category_aro_class_name":"AMR Gene Family"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2143":{"model_id":"2143","model_name":"Borreliella burgdorferi 16S rRNA mutation conferring resistance to gentamicin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"41093","param_value":"2500"},"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"12986":"a1401g"},"Curated-R":{"12986":"a1401g"},"clinical":{"12986":"a1401g"}}},"model_sequences":{"sequence":{"3268":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"NR_044732.2","fmin":"0","fmax":"1477","strand":"+","sequence":"AATAACGAAGAGTTTGATCCTGGCTTAGAACTAACGCTGGCAGTGCGTCTTAAGCATGCAAGTCAAACGGGATGTAGCAATACATTCAGTGGCGAACGGGTGAGTAACGCGTGGATGATCTACCTATGAGATGGGGATAACTATTAGAAATAGTAGCTAATACCGAATAAGGTCAGTTAATTTGTTAATTGATGAAAGGAAGCCTTTAAACGTTCGCTTGTAGATGAGTCTGCGTCTTATTAGCTAGTTGGTAGGGTAAATGCCTACCAAGGCAATGATAAGTAACCGGCCTGAGAGGGTGAACGGTCACACTGGAACTGAGATACGGTCCAGNCTCCTACGGGAGGCAGCAGCTAAGAATCTTCCGCAATGGGCGAAAGCCTGACGGAGCGACACTGCGTGAATGAAGAAGGTCGAAAGATTGTAAAATTCTTTTATAAATGAGGAATAAGCTTTGTAGGAAATGACAAAGTGATGACGTTAATTTATGAATAAGCCCCGGCTAATTACGTGCCAGNAGCCGCGGTAATACGTAAGGGNNNAGCGTTGTTCGGGATTATTGGGCGTAAAGGGTGAGTAGGCGGATATATAAGTCTATGCATAAAATACCACAGCTCAACTGTGGACCTATGTTGGAAACTATATGTCTAGAGTCTGATAGAGGAAGTTAGAATTTCTGGTGTAAGGGTGGAATCTGTTGATATCAGAAAGAATACCGGAGGCGAAGGCGAACTTCTGGGTCAAGACTGACGCTGAGTCACGAAAGCGTAGGGAGCAAACAGGATTAGATACCCTGGTAGTCTACGCTGTAAACGATGCACACTTGGTGTTAACTAAAAGTTAGTACCGAAGCTAACGTGTTAAGTGTGCAGCCTGGGGAGTATGCTCGCAAGAGNGAAACTCAAAGGNATTNANNNGNGCCNGCACAAGNNGTGGAGCATGTGGTTTNNNNNNANNNTACGCGAGGAACCTTACCAGGGCTTGACATATATAGGATATAGTTAGAGATAATTATTCCCCGTTTGGGGTCTATATACAGGTGCTGCATGGTTGTCGTCAGCTCGTGCTGTGAGGTGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTTATCTGTTACCAGCATGTAATGGTGGGGACTCAGATAAGACTGCCGGTGATAAGTCGGAGGAAGGTGAGGATGACGTCAAATCATCATGGCCCTTATGTCCTGGGCTACACACGTGCTACAATGGCCTGTACAAAGCGAAGCGAAACAGTGATGTGAAGCAAAACGCATAAAGCAGGTCTCAGTCCGGATTGAAGTCTGAAACTCGACTTCATGAAGTTGGAATCGCTAGTAATCGTATATCAGAATGATACGGTGAATACGTTCTCGGGCNTTGTACACACCGCCCGTCACACCACCCGAGTTGAGGATACCCGAAGCTATTATTCTAACCCGTAAGGGAGGAAGGTATTTAAGGTATGTTTAGCA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40345","NCBI_taxonomy_name":"Borreliella burgdorferi","NCBI_taxonomy_id":"139"}}}},"ARO_accession":"3003504","ARO_id":"40106","ARO_name":"Borreliella burgdorferi 16S rRNA mutation conferring resistance to gentamicin","CARD_short_name":"Bbur_16S_GEN","ARO_description":"Point mutations in the 3' minor domain of the 16S rRNA gene of Borreliella burgdorferi can confer resistance to gentamicin.","ARO_category":{"40277":{"category_aro_accession":"3003666","category_aro_cvterm_id":"40277","category_aro_name":"16s rRNA with mutation conferring resistance to aminoglycoside antibiotics","category_aro_description":"Point mutations in the 16S rRNA of bacteria can confer resistance to aminoglycosides.","category_aro_class_name":"AMR Gene Family"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"46133":{"category_aro_accession":"3007382","category_aro_cvterm_id":"46133","category_aro_name":"gentamicin","category_aro_description":"Gentamicin is a commonly used aminoglycoside antibiotic derived from members of the Micromonospora genus of bacteria. It acts by binding the 30S ribosomal subunit, thus inhibiting protein synthesis. Gentamicin is typically used to treat Gram-negative infections of the repiratory and urinary tract, as well as infections of the bone and soft tissue. It also exhibits considerable nephrotoxicity and ototoxicity. Gentamicin is administered as a mixture of gentamicin type C (which makes about around 80% of the complex) and types A, B, and X (distributed in the remaining 20% of the complex).","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2132":{"model_id":"2132","model_name":"Mycobacterium tuberculosis 16S rRNA mutation conferring resistance to kanamycin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"13258":"a1401g","14747":"c1402t","14758":"g1484t","9600":"a514c","9601":"c517t","2923":"c1402a"},"CRyPTIC-R":{"13258":"a1401g"},"clinical":{"13258":"a1401g","14743":"a1401g","14747":"c1402t","14758":"g1484t","9599":"a1401g","9600":"a514c","9601":"c517t","2923":"c1402a","3014":"a1401g","4800":"g1484t","4799":"c1402t"},"WHO-R":{"14743":"a1401g","14747":"c1402t","14758":"g1484t"},"ReSeqTB-High":{"9599":"a1401g"},"ReSeqTB-Minimal":{"9600":"a514c","9601":"c517t"},"Curated-R":{"2923":"c1402a","3014":"a1401g","4800":"g1484t","4799":"c1402t"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"41093","param_value":"2700"}},"model_sequences":{"sequence":{"8765":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"NC_000962.3","fmin":"1471845","fmax":"1473382","strand":"+","sequence":"TTTTGTTTGGAGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGGAAAGGTCTCTTCGGAGATACTCGAGTGGCGAACGGGTGAGTAACACGTGGGTGATCTGCCCTGCACTTCGGGATAAGCCTGGGAAACTGGGTCTAATACCGGATAGGACCACGGGATGCATGTCTTGTGGTGGAAAGCGCTTTAGCGGTGTGGGATGAGCCCGCGGCCTATCAGCTTGTTGGTGGGGTGACGGCCTACCAAGGCGACGACGGGTAGCCGGCCTGAGAGGGTGTCCGGCCACACTGGGACTGAGATACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCGACGCCGCGTGGGGGATGACGGCCTTCGGGTTGTAAACCTCTTTCACCATCGACGAAGGTCCGGGTTCTCTCGGATTGACGGTAGGTGGAGAAGAAGCACCGGCCAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGTGCGAGCGTTGTCCGGAATTACTGGGCGTAAAGAGCTCGTAGGTGGTTTGTCGCGTTGTTCGTGAAATCTCACGGCTTAACTGTGAGCGTGCGGGCGATACGGGCAGACTAGAGTACTGCAGGGGAGACTGGAATTCCTGGTGTAGCGGTGGAATGCGCAGATATCAGGAGGAACACCGGTGGCGAAGGCGGGTCTCTGGGCAGTAACTGACGCTGAGGAGCGAAAGCGTGGGGAGCGAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGGTGGGTACTAGGTGTGGGTTTCCTTCCTTGGGATCCGTGCCGTAGCTAACGCATTAAGTACCCCGCCTGGGGAGTACGGCCGCAAGGCTAAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGCGGAGCATGTGGATTAATTCGATGCAACGCGAAGAACCTTACCTGGGTTTGACATGCACAGGACGCGTCTAGAGATAGGCGTTCCCTTGTGGCCTGTGTGCAGGTGGTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTCTCATGTTGCCAGCACGTAATGGTGGGGACTCGTGAGAGACTGCCGGGGTCAACTCGGAGGAAGGTGGGGATGACGTCAAGTCATCATGCCCCTTATGTCCAGGGCTTCACACATGCTACAATGGCCGGTACAAAGGGCTGCGATGCCGCGAGGTTAAGCGAATCCTTAAAAGCCGGTCTCAGTTCGGATCGGGGTCTGCAACTCGACCCCGTGAAGTCGGAGTCGCTAGTAATCGCAGATCAGCAACGCTGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACGTCATGAAAGTCGGTAACACCCGAAGCCAGTGGCCTAACCCTCGGGAGGGAGCTGTCGAAGGTGGGATCGGCGATTGGGACGAAGTCGTAACAAGGTAGCCGTACCGGAAGGTGCGGCTGGATCACCTCCTTTCT","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3003436","ARO_id":"40020","ARO_name":"Mycobacterium tuberculosis 16S rRNA mutation conferring resistance to kanamycin","CARD_short_name":"Mtub_16S_KAN","ARO_description":"Point mutations in the 3' domain of 16S rRNA of Mycobacterium tuberculosis can confer resistance to kanamycin.","ARO_category":{"40277":{"category_aro_accession":"3003666","category_aro_cvterm_id":"40277","category_aro_name":"16s rRNA with mutation conferring resistance to aminoglycoside antibiotics","category_aro_description":"Point mutations in the 16S rRNA of bacteria can confer resistance to aminoglycosides.","category_aro_class_name":"AMR Gene Family"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2127":{"model_id":"2127","model_name":"Borreliella burgdorferi 16S rRNA mutation conferring resistance to kanamycin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"41093","param_value":"2500"},"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"13021":"a1402g"},"Curated-R":{"13021":"a1402g"},"clinical":{"13021":"a1402g"}}},"model_sequences":{"sequence":{"8691":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"NZ_ABCW02000003.1","fmin":"0","fmax":"1536","strand":"+","sequence":"TTACAAAAGGTAGAATAGTATACAGGGAGAAATAAAATTAAACCCTTTTAAAAAATTTTCAAGTGTTGTAAATATTTATTTTTTAGATCAAATCATCTTTCAAGGACACAACAAAATTCTTGTGAATCCAGCCTTGAAGTCCATAACTTGTTTCAATAAGAACAAAATCATCTTTGCTGTCAAGAATATAAACACTTGCATTTCCTTTTAAAAATCTCCAACTCCTTGAAAAATTGTCAGGAACTTTATAAAGAGAGACTAAATCACCCTTAATTATTCCTACTTCAGATTGTTGCTCATAATAAAAATAATATGTTTCAAATATAGTAAAACAAACCGCAGAAAAAAGTAAAAATATAATTATTTTTTTCAAATTTTTTGCCAAAAATCTATAAGAAATAGATACAACTAAAAAATTAATCAAAAATAAACTGATAATAAAAAAAATATTAGAAAAAATAAAACTATTGTTACGAACATTGTCTGTAACTCCATTTTTAGCTTCAATCAAATCAATAACTTTATAAGAGGTTTCATTATTCGGAGAAGCCAAAAATGCCTTATAAGCTGAATAAATAGCATCAAAATCTCTATCCATTTTACTTAAAACAAGGGCTCTATTTAACCAAAGTCCTGAATAATTTGGATATTTTTTAAGAATGTTATCTATCTTGATAAGTGCAGTATCATAATTTTTAGTATTATAGTTTTCAATCAAATCATTTACATTTTTCTCCGACAATAAACCATCATTTACAGCATTTAAACTAATGCCAACAGCCAATATTAAAATAACCAGCCCAAAACTTGATGCTGCAAAAAATTTTTTATAGTTAATTAAAATAATTAAAGATAATAAAAATCCTGGAATCAAAAGTAAATAATAGTATGAAACAAAAAATAAAAAAGTTTTATTTTTATAATTCAAAATATCGGCATAAGATAATAGTTTAAAATCATAATCTACATTATTTTGTGCTCTATTTATGCTGTTAAACTCTCCTGAATATTCGTACTTCAATTTTTTCCCTTTAAGGGTATAAACTGTATCATTATCAGGATTTAAATAATTAAAATCACCAATATTTAAAAATACACTACCTTTAGTGTCGGGCTTAACTGTATAAATTTGAGAAATACTACCCTTATATCCATTTTTAGAAGGCTTAAAGCTATAATTTTTCTTTTTATTAAGAATTTTAGAATTATAAGTTTCAATCTCTGGAAAGTAAAAATGTGGAAAATTCCCTTGACCTGTAATTTTTATTAAAATAGTAAATATATCTTGCTCAATTGTCGAATAAGTTGGAGTCTCATAATCAACTCTAAAAGTTCCTACTGCTAAAGATTTAACCTCTCCAGGAATCGGTTTAACTTTTAATAAAAGCTCAGGGGTATTCCTAACAAGGCCAGAACCAATATTAAAAGAAAAACTGGGAATCAAAACATTTTTTGAGCCCTTAAGAGGAGTTAGCACAAAGTTATAAAAAGGTACATCTAAAATCTCTTTATTATGAAAAGTTCTATATTTAATAT","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"46296","NCBI_taxonomy_name":"Borreliella burgdorferi Bol26","NCBI_taxonomy_id":"445984"}}}},"ARO_accession":"3003503","ARO_id":"40105","ARO_name":"Borreliella burgdorferi 16S rRNA mutation conferring resistance to kanamycin","CARD_short_name":"Bbur_16S_KAN","ARO_description":"Point mutations in the 3' minor domain of the 16S rRNA gene of Borreliella burgdorferi can confer resistance to kanamycin.","ARO_category":{"40277":{"category_aro_accession":"3003666","category_aro_cvterm_id":"40277","category_aro_name":"16s rRNA with mutation conferring resistance to aminoglycoside antibiotics","category_aro_description":"Point mutations in the 16S rRNA of bacteria can confer resistance to aminoglycosides.","category_aro_class_name":"AMR Gene Family"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2154":{"model_id":"2154","model_name":"Borreliella burgdorferi 16S rRNA mutation conferring resistance to spectinomycin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"2975":"a1184g","4806":"c1185t"},"Curated-R":{"2975":"a1184g","4806":"c1185t"},"clinical":{"2975":"a1184g","4806":"c1185t"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"41093","param_value":"2500"}},"model_sequences":{"sequence":{"3267":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"NR_044732.2","fmin":"0","fmax":"1477","strand":"+","sequence":"AATAACGAAGAGTTTGATCCTGGCTTAGAACTAACGCTGGCAGTGCGTCTTAAGCATGCAAGTCAAACGGGATGTAGCAATACATTCAGTGGCGAACGGGTGAGTAACGCGTGGATGATCTACCTATGAGATGGGGATAACTATTAGAAATAGTAGCTAATACCGAATAAGGTCAGTTAATTTGTTAATTGATGAAAGGAAGCCTTTAAACGTTCGCTTGTAGATGAGTCTGCGTCTTATTAGCTAGTTGGTAGGGTAAATGCCTACCAAGGCAATGATAAGTAACCGGCCTGAGAGGGTGAACGGTCACACTGGAACTGAGATACGGTCCAGNCTCCTACGGGAGGCAGCAGCTAAGAATCTTCCGCAATGGGCGAAAGCCTGACGGAGCGACACTGCGTGAATGAAGAAGGTCGAAAGATTGTAAAATTCTTTTATAAATGAGGAATAAGCTTTGTAGGAAATGACAAAGTGATGACGTTAATTTATGAATAAGCCCCGGCTAATTACGTGCCAGNAGCCGCGGTAATACGTAAGGGNNNAGCGTTGTTCGGGATTATTGGGCGTAAAGGGTGAGTAGGCGGATATATAAGTCTATGCATAAAATACCACAGCTCAACTGTGGACCTATGTTGGAAACTATATGTCTAGAGTCTGATAGAGGAAGTTAGAATTTCTGGTGTAAGGGTGGAATCTGTTGATATCAGAAAGAATACCGGAGGCGAAGGCGAACTTCTGGGTCAAGACTGACGCTGAGTCACGAAAGCGTAGGGAGCAAACAGGATTAGATACCCTGGTAGTCTACGCTGTAAACGATGCACACTTGGTGTTAACTAAAAGTTAGTACCGAAGCTAACGTGTTAAGTGTGCAGCCTGGGGAGTATGCTCGCAAGAGNGAAACTCAAAGGNATTNANNNGNGCCNGCACAAGNNGTGGAGCATGTGGTTTNNNNNNANNNTACGCGAGGAACCTTACCAGGGCTTGACATATATAGGATATAGTTAGAGATAATTATTCCCCGTTTGGGGTCTATATACAGGTGCTGCATGGTTGTCGTCAGCTCGTGCTGTGAGGTGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTTATCTGTTACCAGCATGTAATGGTGGGGACTCAGATAAGACTGCCGGTGATAAGTCGGAGGAAGGTGAGGATGACGTCAAATCATCATGGCCCTTATGTCCTGGGCTACACACGTGCTACAATGGCCTGTACAAAGCGAAGCGAAACAGTGATGTGAAGCAAAACGCATAAAGCAGGTCTCAGTCCGGATTGAAGTCTGAAACTCGACTTCATGAAGTTGGAATCGCTAGTAATCGTATATCAGAATGATACGGTGAATACGTTCTCGGGCNTTGTACACACCGCCCGTCACACCACCCGAGTTGAGGATACCCGAAGCTATTATTCTAACCCGTAAGGGAGGAAGGTATTTAAGGTATGTTTAGCA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40345","NCBI_taxonomy_name":"Borreliella burgdorferi","NCBI_taxonomy_id":"139"}}}},"ARO_accession":"3003502","ARO_id":"40104","ARO_name":"Borreliella burgdorferi 16S rRNA mutation conferring resistance to spectinomycin","CARD_short_name":"Bbur_16S_SPT","ARO_description":"Point mutations in the 3' major domain of the 16S rRNA gene of Borreliella burgdorferi can confer resistance to spectinomycin.","ARO_category":{"40277":{"category_aro_accession":"3003666","category_aro_cvterm_id":"40277","category_aro_name":"16s rRNA with mutation conferring resistance to aminoglycoside antibiotics","category_aro_description":"Point mutations in the 16S rRNA of bacteria can confer resistance to aminoglycosides.","category_aro_class_name":"AMR Gene Family"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2122":{"model_id":"2122","model_name":"Mycobacteroides chelonae 16S rRNA mutation conferring resistance to neomycin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"41093","param_value":"2500"},"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"12982":"a1355g"},"Curated-R":{"12982":"a1355g"},"clinical":{"12982":"a1355g"}}},"model_sequences":{"sequence":{"3271":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"NR_114659.1","fmin":"0","fmax":"1441","strand":"+","sequence":"GACGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGGAAAGGCCCTTCGGGGTACTCGAGTGGCGAACGGGTGAGTAACACGTGGGTGATCTGCCCTGCACTCTGGGATAAGCCTGGGAAACTGGGTCTAATACCGGATAGGACCACACACTTCATGGTGAGTGGTGCAAAGCTTTTGCGGTGTGGGATGAGCCCGCGGCCTATCAGCTTGTTGGTGGGGTAATGGCCCACCAAGGCGACGACGGGTAGCCGGCCTGAGAGGGTGACCGGCCACACTGGGACTGAGATACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCGACGCCGCGTGAGGGATGACGGCCTTCGGGTTGTAAACCTCTTTCAGTAGGGACGAAGCGAAAGTGACGGTACCTACAGAAGAAGGACCGGCCAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGTCCGAGCGTTGTCCGGAATTACTGGGCGTAAAGAGCTCGTAGGTGGTTTGTCGCGTTGTTCGTGAAAACTCACAGCTTAACTGTGGGCGTGCGGGCGATACGGGCAGACTAGAGTACTGCAGGGGAGACTGGAATTCCTGGTGTAGCGGTGGAATGCGCAGATATCAGGAGGAACACCGGTGGCGAAGGCGGGTCTCTGGGCAGTAACTGACGCTGAGGAGCGAAAGCGTGGGTAGCGAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGGTGGGTACTAGGTGTGGGTTTCCTTCCTTGGGATCCGTGCCGTAGCTAACGCATTAAGTACCCCGCCTGGGGAGTACGGTCGCAAGACTAAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGCGGAGCATGTGGATTAATTCGATGCAACGCGAAGAACCTTACCTGGGTTTGACATGCGCAGGACGTATCTAGAGATAGGTATTCCCTTGTGGCCTGCGTGCAGGTGGTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTCCTATGTTGCCAGCGGGTAATGCCGGGGACTCGTAGGAGACTGCCGGGGTCAACTCGGAGGAAGGTGGGGATGACGTCAAGTCATCATGCCCCTTATGTCCAGGGCTTCACACATGCTACAATGGCCAGTACAGAGGGCTGCGAAGCCGCAAGGTGGAGCGAATCCCTTAAAGCTGGTCTCAGTTCGGATTGGGGTCTGCAACTCGACCCCATGAAGTCGGAGTCGCTAGTAATCGCAGATCAGCAACGCTGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACGTCATGAAAGTCGGTAACACCCGAAGCCAGTGGCCTAACCTTTTGGAGGGAGCTGTCGAAGGTGGGATCGGCGATTGGGACGAAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37061","NCBI_taxonomy_name":"Mycobacterium","NCBI_taxonomy_id":"1763"}}}},"ARO_accession":"3003518","ARO_id":"40120","ARO_name":"Mycobacteroides chelonae 16S rRNA mutation conferring resistance to neomycin","CARD_short_name":"Mche_16S_NEO","ARO_description":"Point mutations in the 16S rRNA of Mycobacteroides chelonae can cause resistance to neomycin.","ARO_category":{"40277":{"category_aro_accession":"3003666","category_aro_cvterm_id":"40277","category_aro_name":"16s rRNA with mutation conferring resistance to aminoglycoside antibiotics","category_aro_description":"Point mutations in the 16S rRNA of bacteria can confer resistance to aminoglycosides.","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2128":{"model_id":"2128","model_name":"Mycobacteroides abscessus 16S rRNA mutation conferring resistance to gentamicin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"2958":"a1375g","4796":"c1376t","4797":"g1458t","4798":"t1373a"},"Curated-R":{"2958":"a1375g","4796":"c1376t","4797":"g1458t","4798":"t1373a"},"clinical":{"2958":"a1375g","4796":"c1376t","4797":"g1458t","4798":"t1373a"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"41093","param_value":"2600"}},"model_sequences":{"sequence":{"3256":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"CU458896.1","fmin":"1462397","fmax":"1463901","strand":"+","sequence":"AGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGGAAAGGCCCTTCGGGGTACTCGAGTGGCGAACGGGTGAGTAACACGTGGGTGATCTGCCCTGCACTCTGGGATAAGCCTGGGAAACTGGGTCTAATACCGGATAGGACCACACACTTCATGGTGAGTGGTGCAAAGCTTTTGCGGTGTGGGATGAGCCCGCGGCCTATCAGCTTGTTGGTGGGGTAATGGCCCACCAAGGCGACGACGGGTAGCCGGCCTGAGAGGGTGACCGGCCACACTGGGACTGAGATACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCGACGCCGCGTGAGGGATGACGGCCTTCGGGTTGTAAACCTCTTTCAGTAGGGACGAAGCGAAAGTGACGGTACCTACAGAAGAAGGACCGGCCAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGTCCGAGCGTTGTCCGGAATTACTGGGCGTAAAGAGCTCGTAGGTGGTTTGTCGCGTTGTTCGTGAAAACTCACAGCTTAACTGTGGGCGTGCGGGCGATACGGGCAGACTAGAGTACTGCAGGGGAGACTGGAATTCCTGGTGTAGCGGTGGAATGCGCAGATATCAGGAGGAACACCGGTGGCGAAGGCGGGTCTCTGGGCAGTAACTGACGCTGAGGAGCGAAAGCGTGGGTAGCGAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGGTGGGTACTAGGTGTGGGTTTCCTTCCTTGGGATCCGTGCCGTAGCTAACGCATTAAGTACCCCGCCTGGGGAGTACGGTCGCAAGACTAAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGCGGAGCATGTGGATTAATTCGATGCAACGCGAAGAACCTTACCTGGGTTTGACATGCACAGGACGTACCTAGAGATAGGTATTCCCTTGTGGCCTGTGTGCAGGTGGTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTCCTATGTTGCCAGCGGGTAATGCCGGGGACTCGTAGGAGACTGCCGGGGTCAACTCGGAGGAAGGTGGGGATGACGTCAAGTCATCATGCCCCTTATGTCCAGGGCTTCACACATGCTACAATGGCCAGTACAGAGGGCTGCGAAGCCGTAAGGTGGAGCGAATCCCTTAAAGCTGGTCTCAGTTCGGATTGGGGTCTGCAACTCGACCCCATGAAGTCGGAGTCGCTAGTAATCGCAGATCAGCAACGCTGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACGTCATGAAAGTCGGTAACACCCGAAGCCAGTGGCCTAACCTTTTGGAGGGAGCTGTCGAAGGTGGGATCGGCGATTGGGACGAAGTCGTAACAAGGTAGCCGTACCGGAAGGTGCGGCTGGATCACCT","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36888","NCBI_taxonomy_name":"Mycobacteroides abscessus","NCBI_taxonomy_id":"36809"}}}},"ARO_accession":"3003240","ARO_id":"39824","ARO_name":"Mycobacteroides abscessus 16S rRNA mutation conferring resistance to gentamicin","CARD_short_name":"Mabs_16S_GEN","ARO_description":"Point mutations in the 16S rRNA of Mycobacteroides abscessus conferring resistance to gentamicin.","ARO_category":{"40277":{"category_aro_accession":"3003666","category_aro_cvterm_id":"40277","category_aro_name":"16s rRNA with mutation conferring resistance to aminoglycoside antibiotics","category_aro_description":"Point mutations in the 16S rRNA of bacteria can confer resistance to aminoglycosides.","category_aro_class_name":"AMR Gene Family"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"46133":{"category_aro_accession":"3007382","category_aro_cvterm_id":"46133","category_aro_name":"gentamicin","category_aro_description":"Gentamicin is a commonly used aminoglycoside antibiotic derived from members of the Micromonospora genus of bacteria. It acts by binding the 30S ribosomal subunit, thus inhibiting protein synthesis. Gentamicin is typically used to treat Gram-negative infections of the repiratory and urinary tract, as well as infections of the bone and soft tissue. It also exhibits considerable nephrotoxicity and ototoxicity. Gentamicin is administered as a mixture of gentamicin type C (which makes about around 80% of the complex) and types A, B, and X (distributed in the remaining 20% of the complex).","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2111":{"model_id":"2111","model_name":"Mycobacteroides chelonae 16S rRNA mutation conferring resistance to tobramycin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"41093","param_value":"2500"},"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"12980":"a1355g"},"Curated-R":{"12980":"a1355g"},"clinical":{"12980":"a1355g"}}},"model_sequences":{"sequence":{"3270":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"NR_114659.1","fmin":"0","fmax":"1441","strand":"+","sequence":"GACGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGGAAAGGCCCTTCGGGGTACTCGAGTGGCGAACGGGTGAGTAACACGTGGGTGATCTGCCCTGCACTCTGGGATAAGCCTGGGAAACTGGGTCTAATACCGGATAGGACCACACACTTCATGGTGAGTGGTGCAAAGCTTTTGCGGTGTGGGATGAGCCCGCGGCCTATCAGCTTGTTGGTGGGGTAATGGCCCACCAAGGCGACGACGGGTAGCCGGCCTGAGAGGGTGACCGGCCACACTGGGACTGAGATACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCGACGCCGCGTGAGGGATGACGGCCTTCGGGTTGTAAACCTCTTTCAGTAGGGACGAAGCGAAAGTGACGGTACCTACAGAAGAAGGACCGGCCAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGTCCGAGCGTTGTCCGGAATTACTGGGCGTAAAGAGCTCGTAGGTGGTTTGTCGCGTTGTTCGTGAAAACTCACAGCTTAACTGTGGGCGTGCGGGCGATACGGGCAGACTAGAGTACTGCAGGGGAGACTGGAATTCCTGGTGTAGCGGTGGAATGCGCAGATATCAGGAGGAACACCGGTGGCGAAGGCGGGTCTCTGGGCAGTAACTGACGCTGAGGAGCGAAAGCGTGGGTAGCGAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGGTGGGTACTAGGTGTGGGTTTCCTTCCTTGGGATCCGTGCCGTAGCTAACGCATTAAGTACCCCGCCTGGGGAGTACGGTCGCAAGACTAAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGCGGAGCATGTGGATTAATTCGATGCAACGCGAAGAACCTTACCTGGGTTTGACATGCGCAGGACGTATCTAGAGATAGGTATTCCCTTGTGGCCTGCGTGCAGGTGGTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTCCTATGTTGCCAGCGGGTAATGCCGGGGACTCGTAGGAGACTGCCGGGGTCAACTCGGAGGAAGGTGGGGATGACGTCAAGTCATCATGCCCCTTATGTCCAGGGCTTCACACATGCTACAATGGCCAGTACAGAGGGCTGCGAAGCCGCAAGGTGGAGCGAATCCCTTAAAGCTGGTCTCAGTTCGGATTGGGGTCTGCAACTCGACCCCATGAAGTCGGAGTCGCTAGTAATCGCAGATCAGCAACGCTGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACGTCATGAAAGTCGGTAACACCCGAAGCCAGTGGCCTAACCTTTTGGAGGGAGCTGTCGAAGGTGGGATCGGCGATTGGGACGAAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37061","NCBI_taxonomy_name":"Mycobacterium","NCBI_taxonomy_id":"1763"}}}},"ARO_accession":"3003516","ARO_id":"40118","ARO_name":"Mycobacteroides chelonae 16S rRNA mutation conferring resistance to tobramycin","CARD_short_name":"Mche_16S_TOB","ARO_description":"Point mutations in the 16S rRNA of Mycobacteroides chelonae can cause resistance to tobramycin.","ARO_category":{"40277":{"category_aro_accession":"3003666","category_aro_cvterm_id":"40277","category_aro_name":"16s rRNA with mutation conferring resistance to aminoglycoside antibiotics","category_aro_description":"Point mutations in the 16S rRNA of bacteria can confer resistance to aminoglycosides.","category_aro_class_name":"AMR Gene Family"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2084":{"model_id":"2084","model_name":"Mycobacteroides abscessus 16S rRNA mutation conferring resistance to amikacin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"4795":"c1376t","3036":"a1375g","4793":"g1458t","4794":"t1373a"},"Curated-R":{"4795":"c1376t","3036":"a1375g","4793":"g1458t","4794":"t1373a"},"clinical":{"4795":"c1376t","3036":"a1375g","4793":"g1458t","4794":"t1373a"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"41093","param_value":"2600"}},"model_sequences":{"sequence":{"3254":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"CU458896.1","fmin":"1462397","fmax":"1463901","strand":"+","sequence":"AGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGGAAAGGCCCTTCGGGGTACTCGAGTGGCGAACGGGTGAGTAACACGTGGGTGATCTGCCCTGCACTCTGGGATAAGCCTGGGAAACTGGGTCTAATACCGGATAGGACCACACACTTCATGGTGAGTGGTGCAAAGCTTTTGCGGTGTGGGATGAGCCCGCGGCCTATCAGCTTGTTGGTGGGGTAATGGCCCACCAAGGCGACGACGGGTAGCCGGCCTGAGAGGGTGACCGGCCACACTGGGACTGAGATACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCGACGCCGCGTGAGGGATGACGGCCTTCGGGTTGTAAACCTCTTTCAGTAGGGACGAAGCGAAAGTGACGGTACCTACAGAAGAAGGACCGGCCAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGTCCGAGCGTTGTCCGGAATTACTGGGCGTAAAGAGCTCGTAGGTGGTTTGTCGCGTTGTTCGTGAAAACTCACAGCTTAACTGTGGGCGTGCGGGCGATACGGGCAGACTAGAGTACTGCAGGGGAGACTGGAATTCCTGGTGTAGCGGTGGAATGCGCAGATATCAGGAGGAACACCGGTGGCGAAGGCGGGTCTCTGGGCAGTAACTGACGCTGAGGAGCGAAAGCGTGGGTAGCGAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGGTGGGTACTAGGTGTGGGTTTCCTTCCTTGGGATCCGTGCCGTAGCTAACGCATTAAGTACCCCGCCTGGGGAGTACGGTCGCAAGACTAAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGCGGAGCATGTGGATTAATTCGATGCAACGCGAAGAACCTTACCTGGGTTTGACATGCACAGGACGTACCTAGAGATAGGTATTCCCTTGTGGCCTGTGTGCAGGTGGTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTCCTATGTTGCCAGCGGGTAATGCCGGGGACTCGTAGGAGACTGCCGGGGTCAACTCGGAGGAAGGTGGGGATGACGTCAAGTCATCATGCCCCTTATGTCCAGGGCTTCACACATGCTACAATGGCCAGTACAGAGGGCTGCGAAGCCGTAAGGTGGAGCGAATCCCTTAAAGCTGGTCTCAGTTCGGATTGGGGTCTGCAACTCGACCCCATGAAGTCGGAGTCGCTAGTAATCGCAGATCAGCAACGCTGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACGTCATGAAAGTCGGTAACACCCGAAGCCAGTGGCCTAACCTTTTGGAGGGAGCTGTCGAAGGTGGGATCGGCGATTGGGACGAAGTCGTAACAAGGTAGCCGTACCGGAAGGTGCGGCTGGATCACCT","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36888","NCBI_taxonomy_name":"Mycobacteroides abscessus","NCBI_taxonomy_id":"36809"}}}},"ARO_accession":"3003239","ARO_id":"39823","ARO_name":"Mycobacteroides abscessus 16S rRNA mutation conferring resistance to amikacin","CARD_short_name":"Mabs_16S_AMK","ARO_description":"Point mutations in the 16S rRNA of Mycobacteroides abscessus conferring resistance to amikacin.","ARO_category":{"40277":{"category_aro_accession":"3003666","category_aro_cvterm_id":"40277","category_aro_name":"16s rRNA with mutation conferring resistance to aminoglycoside antibiotics","category_aro_description":"Point mutations in the 16S rRNA of bacteria can confer resistance to aminoglycosides.","category_aro_class_name":"AMR Gene Family"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2105":{"model_id":"2105","model_name":"Mycobacteroides abscessus 16S rRNA mutation conferring resistance to neomycin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"41093","param_value":"2600"},"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"2896":"a1375g"},"Curated-R":{"2896":"a1375g"},"clinical":{"2896":"a1375g"}}},"model_sequences":{"sequence":{"3255":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"CU458896.1","fmin":"1462397","fmax":"1463901","strand":"+","sequence":"AGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGGAAAGGCCCTTCGGGGTACTCGAGTGGCGAACGGGTGAGTAACACGTGGGTGATCTGCCCTGCACTCTGGGATAAGCCTGGGAAACTGGGTCTAATACCGGATAGGACCACACACTTCATGGTGAGTGGTGCAAAGCTTTTGCGGTGTGGGATGAGCCCGCGGCCTATCAGCTTGTTGGTGGGGTAATGGCCCACCAAGGCGACGACGGGTAGCCGGCCTGAGAGGGTGACCGGCCACACTGGGACTGAGATACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCGACGCCGCGTGAGGGATGACGGCCTTCGGGTTGTAAACCTCTTTCAGTAGGGACGAAGCGAAAGTGACGGTACCTACAGAAGAAGGACCGGCCAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGTCCGAGCGTTGTCCGGAATTACTGGGCGTAAAGAGCTCGTAGGTGGTTTGTCGCGTTGTTCGTGAAAACTCACAGCTTAACTGTGGGCGTGCGGGCGATACGGGCAGACTAGAGTACTGCAGGGGAGACTGGAATTCCTGGTGTAGCGGTGGAATGCGCAGATATCAGGAGGAACACCGGTGGCGAAGGCGGGTCTCTGGGCAGTAACTGACGCTGAGGAGCGAAAGCGTGGGTAGCGAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGGTGGGTACTAGGTGTGGGTTTCCTTCCTTGGGATCCGTGCCGTAGCTAACGCATTAAGTACCCCGCCTGGGGAGTACGGTCGCAAGACTAAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGCGGAGCATGTGGATTAATTCGATGCAACGCGAAGAACCTTACCTGGGTTTGACATGCACAGGACGTACCTAGAGATAGGTATTCCCTTGTGGCCTGTGTGCAGGTGGTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTCCTATGTTGCCAGCGGGTAATGCCGGGGACTCGTAGGAGACTGCCGGGGTCAACTCGGAGGAAGGTGGGGATGACGTCAAGTCATCATGCCCCTTATGTCCAGGGCTTCACACATGCTACAATGGCCAGTACAGAGGGCTGCGAAGCCGTAAGGTGGAGCGAATCCCTTAAAGCTGGTCTCAGTTCGGATTGGGGTCTGCAACTCGACCCCATGAAGTCGGAGTCGCTAGTAATCGCAGATCAGCAACGCTGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACGTCATGAAAGTCGGTAACACCCGAAGCCAGTGGCCTAACCTTTTGGAGGGAGCTGTCGAAGGTGGGATCGGCGATTGGGACGAAGTCGTAACAAGGTAGCCGTACCGGAAGGTGCGGCTGGATCACCT","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36888","NCBI_taxonomy_name":"Mycobacteroides abscessus","NCBI_taxonomy_id":"36809"}}}},"ARO_accession":"3003238","ARO_id":"39822","ARO_name":"Mycobacteroides abscessus 16S rRNA mutation conferring resistance to neomycin","CARD_short_name":"Mabs_16S_NEO","ARO_description":"Point mutations in the 16S rRNA of Mycobacteroides abscessus conferring resistance to neomycin.","ARO_category":{"40277":{"category_aro_accession":"3003666","category_aro_cvterm_id":"40277","category_aro_name":"16s rRNA with mutation conferring resistance to aminoglycoside antibiotics","category_aro_description":"Point mutations in the 16S rRNA of bacteria can confer resistance to aminoglycosides.","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2155":{"model_id":"2155","model_name":"Cutibacterium acnes 16S rRNA mutation conferring resistance to tetracycline","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"2931":"g1032c"},"Curated-R":{"2931":"g1032c"},"clinical":{"2931":"g1032c"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"41093","param_value":"2600"}},"model_sequences":{"sequence":{"3259":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"NR_040847.1","fmin":"0","fmax":"1486","strand":"+","sequence":"AGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGGAAAGGCCCTGCTTTTGTGGGGTGCTCGAGTGGCGAACGGGTGAGTAACACGTGAGTAACCTGCCCTTGACTTTGGGATAACTTCAGGAAACTGGGGCTAATACCGGATAGGAGCTCCTGCTGCATGGTGGGGGTTGGAAAGTTTCGGCGGTTGGGGATGGACTCGCGGCTTATCAGCTTGTTGGTGGGGTAGTGGCTTACCAAGGCTTTGACGGGTAGCCGGCCTGAGAGGGTGACCGGCCACATTGGGACTGAGATACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGGAAGCCTGATGCAGCAACGCCGCGTGCGGGATGACGGCCTTCGGGTTGTAAACCGCTTTCGCCTGTGACGAAGCGTGAGTGACGGTAATGGGTAAAGAAGCACCGGCTAACTACGTGCCAGCAGCCGCGGTGATACGTAGGGTGCGAGCGTTGTCCGGATTTATTGGGCGTAAAGGGCTCGTAGGTGGTTGATCGCGTCGGAAGTGTAATCTTGGGGCTTAACCCTGAGCGTGCTTTCGATACGGGTTGACTTGAGGAAGGTAGGGGAGAATGGAATTCCTGGTGGAGCGGTGGAATGCGCAGATATCAGGAGGAACACCAGTGGCGAAGGCGGTTCTCTGGGCCTTTCCTGACGCTGAGGAGCGAAAGCGTGGGGAGCGAACAGGCTTAGATACCCTGGTAGTCCACGCTGTAAACGGTGGGTACTAGGTGTGGGGTCCATTCCACGGGTTCCGTGCCGTAGCTAACGCTTTAAGTACCCCGCCTGGGGAGTACGGCCGCAAGGCTAAAACTCAAAGGAATTGACGGGGCCCCGCACAAGCGGCGGAGCATGCGGATTAATTCGATGCAACGCGTAGAACCTTACCTGGGTTTGACATGGATCGGGAGTGCTCAGAGATGGGTGTGCCTCTTTTGGGGTCGGTTCACAGGTGGTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTTCACTGTTGCCAGCACGTTATGGTGGGGACTCAGTGGAGACCGCCGGGGTCAACTCGGAGGAAGGTGGGGATGACGTCAAGTCATCATGCCCCTTATGTCCAGGGCTTCACGCATGCTACAATGGCTGGTACAGAGAGTGGCGAGCCTGTGAGGGTGAGCGAATCTCGGAAAGCCGGTCTCAGTTCGGATTGGGGTCTGCAACTCGACCTCATGAAGTCGGAGTCGCTAGTAATCGCAGATCAGCAACGCTGCGGTGAATACGTTCCCGGGGCTTGTACACACCGCCCGTCAAGTCATGAAAGTTGGTAACACCCGAAGCCGGTGGCCTAACCGTTGTGGGGGAGCCGTCGAAGGTGGGACTGGTGATTAGGACTAAGTCGTAACAAGGTAACC","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40344","NCBI_taxonomy_name":"Cutibacterium acnes","NCBI_taxonomy_id":"1747"}}}},"ARO_accession":"3003499","ARO_id":"40101","ARO_name":"Cutibacterium acnes 16S rRNA mutation conferring resistance to tetracycline","CARD_short_name":"Cacn_16S_TET","ARO_description":"Tetracycline binds tightly to the helix 34 domain in 16S rRNA, where it interferes sterically with the binding of aminoacyl-tRNA to the ribosome A site to block protein synthesis. Mutations in the nucleotide sequence in this domain for Cutibacterium acnes can result in resistance against tetracycline.","ARO_category":{"40280":{"category_aro_accession":"3003669","category_aro_cvterm_id":"40280","category_aro_name":"16S rRNA with mutation conferring resistance to tetracycline derivatives","category_aro_description":"Point mutations in the bacterial 16S rRNA region shown clinically to confer resistance to tetracycline and tetracycline derivatives (polyketide antibiotics).","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2100":{"model_id":"2100","model_name":"Mycobacteroides chelonae 16S rRNA mutation conferring resistance to amikacin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"41093","param_value":"2500"},"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"2981":"a1355g"},"Curated-R":{"2981":"a1355g"},"clinical":{"2981":"a1355g"}}},"model_sequences":{"sequence":{"3272":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"NR_114659.1","fmin":"0","fmax":"1441","strand":"+","sequence":"GACGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGGAAAGGCCCTTCGGGGTACTCGAGTGGCGAACGGGTGAGTAACACGTGGGTGATCTGCCCTGCACTCTGGGATAAGCCTGGGAAACTGGGTCTAATACCGGATAGGACCACACACTTCATGGTGAGTGGTGCAAAGCTTTTGCGGTGTGGGATGAGCCCGCGGCCTATCAGCTTGTTGGTGGGGTAATGGCCCACCAAGGCGACGACGGGTAGCCGGCCTGAGAGGGTGACCGGCCACACTGGGACTGAGATACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCGACGCCGCGTGAGGGATGACGGCCTTCGGGTTGTAAACCTCTTTCAGTAGGGACGAAGCGAAAGTGACGGTACCTACAGAAGAAGGACCGGCCAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGTCCGAGCGTTGTCCGGAATTACTGGGCGTAAAGAGCTCGTAGGTGGTTTGTCGCGTTGTTCGTGAAAACTCACAGCTTAACTGTGGGCGTGCGGGCGATACGGGCAGACTAGAGTACTGCAGGGGAGACTGGAATTCCTGGTGTAGCGGTGGAATGCGCAGATATCAGGAGGAACACCGGTGGCGAAGGCGGGTCTCTGGGCAGTAACTGACGCTGAGGAGCGAAAGCGTGGGTAGCGAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGGTGGGTACTAGGTGTGGGTTTCCTTCCTTGGGATCCGTGCCGTAGCTAACGCATTAAGTACCCCGCCTGGGGAGTACGGTCGCAAGACTAAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGCGGAGCATGTGGATTAATTCGATGCAACGCGAAGAACCTTACCTGGGTTTGACATGCGCAGGACGTATCTAGAGATAGGTATTCCCTTGTGGCCTGCGTGCAGGTGGTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTCCTATGTTGCCAGCGGGTAATGCCGGGGACTCGTAGGAGACTGCCGGGGTCAACTCGGAGGAAGGTGGGGATGACGTCAAGTCATCATGCCCCTTATGTCCAGGGCTTCACACATGCTACAATGGCCAGTACAGAGGGCTGCGAAGCCGCAAGGTGGAGCGAATCCCTTAAAGCTGGTCTCAGTTCGGATTGGGGTCTGCAACTCGACCCCATGAAGTCGGAGTCGCTAGTAATCGCAGATCAGCAACGCTGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACGTCATGAAAGTCGGTAACACCCGAAGCCAGTGGCCTAACCTTTTGGAGGGAGCTGTCGAAGGTGGGATCGGCGATTGGGACGAAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37061","NCBI_taxonomy_name":"Mycobacterium","NCBI_taxonomy_id":"1763"}}}},"ARO_accession":"3003514","ARO_id":"40116","ARO_name":"Mycobacteroides chelonae 16S rRNA mutation conferring resistance to amikacin","CARD_short_name":"Mche_16S_AMK","ARO_description":"Point mutations in the 16S rRNA of Mycobacteroides chelonae can cause resistance to amikacin.","ARO_category":{"40277":{"category_aro_accession":"3003666","category_aro_cvterm_id":"40277","category_aro_name":"16s rRNA with mutation conferring resistance to aminoglycoside antibiotics","category_aro_description":"Point mutations in the 16S rRNA of bacteria can confer resistance to aminoglycosides.","category_aro_class_name":"AMR Gene Family"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2091":{"model_id":"2091","model_name":"Mycobacteroides chelonae 16S rRNA mutation conferring resistance to gentamicin C","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"3008":"a1355g"},"Curated-R":{"3008":"a1355g"},"clinical":{"3008":"a1355g"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"41093","param_value":"2500"}},"model_sequences":{"sequence":{"3273":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"NR_114659.1","fmin":"0","fmax":"1441","strand":"+","sequence":"GACGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGGAAAGGCCCTTCGGGGTACTCGAGTGGCGAACGGGTGAGTAACACGTGGGTGATCTGCCCTGCACTCTGGGATAAGCCTGGGAAACTGGGTCTAATACCGGATAGGACCACACACTTCATGGTGAGTGGTGCAAAGCTTTTGCGGTGTGGGATGAGCCCGCGGCCTATCAGCTTGTTGGTGGGGTAATGGCCCACCAAGGCGACGACGGGTAGCCGGCCTGAGAGGGTGACCGGCCACACTGGGACTGAGATACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCGACGCCGCGTGAGGGATGACGGCCTTCGGGTTGTAAACCTCTTTCAGTAGGGACGAAGCGAAAGTGACGGTACCTACAGAAGAAGGACCGGCCAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGTCCGAGCGTTGTCCGGAATTACTGGGCGTAAAGAGCTCGTAGGTGGTTTGTCGCGTTGTTCGTGAAAACTCACAGCTTAACTGTGGGCGTGCGGGCGATACGGGCAGACTAGAGTACTGCAGGGGAGACTGGAATTCCTGGTGTAGCGGTGGAATGCGCAGATATCAGGAGGAACACCGGTGGCGAAGGCGGGTCTCTGGGCAGTAACTGACGCTGAGGAGCGAAAGCGTGGGTAGCGAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGGTGGGTACTAGGTGTGGGTTTCCTTCCTTGGGATCCGTGCCGTAGCTAACGCATTAAGTACCCCGCCTGGGGAGTACGGTCGCAAGACTAAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGCGGAGCATGTGGATTAATTCGATGCAACGCGAAGAACCTTACCTGGGTTTGACATGCGCAGGACGTATCTAGAGATAGGTATTCCCTTGTGGCCTGCGTGCAGGTGGTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTCCTATGTTGCCAGCGGGTAATGCCGGGGACTCGTAGGAGACTGCCGGGGTCAACTCGGAGGAAGGTGGGGATGACGTCAAGTCATCATGCCCCTTATGTCCAGGGCTTCACACATGCTACAATGGCCAGTACAGAGGGCTGCGAAGCCGCAAGGTGGAGCGAATCCCTTAAAGCTGGTCTCAGTTCGGATTGGGGTCTGCAACTCGACCCCATGAAGTCGGAGTCGCTAGTAATCGCAGATCAGCAACGCTGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACGTCATGAAAGTCGGTAACACCCGAAGCCAGTGGCCTAACCTTTTGGAGGGAGCTGTCGAAGGTGGGATCGGCGATTGGGACGAAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37061","NCBI_taxonomy_name":"Mycobacterium","NCBI_taxonomy_id":"1763"}}}},"ARO_accession":"3003517","ARO_id":"40119","ARO_name":"Mycobacteroides chelonae 16S rRNA mutation conferring resistance to gentamicin C","CARD_short_name":"Mche_16S_GENC","ARO_description":"Point mutations in the 16S rRNA of Mycobacteroides chelonae can confer resistance to gentamicin C.","ARO_category":{"40277":{"category_aro_accession":"3003666","category_aro_cvterm_id":"40277","category_aro_name":"16s rRNA with mutation conferring resistance to aminoglycoside antibiotics","category_aro_description":"Point mutations in the 16S rRNA of bacteria can confer resistance to aminoglycosides.","category_aro_class_name":"AMR Gene Family"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"46133":{"category_aro_accession":"3007382","category_aro_cvterm_id":"46133","category_aro_name":"gentamicin","category_aro_description":"Gentamicin is a commonly used aminoglycoside antibiotic derived from members of the Micromonospora genus of bacteria. It acts by binding the 30S ribosomal subunit, thus inhibiting protein synthesis. Gentamicin is typically used to treat Gram-negative infections of the repiratory and urinary tract, as well as infections of the bone and soft tissue. It also exhibits considerable nephrotoxicity and ototoxicity. Gentamicin is administered as a mixture of gentamicin type C (which makes about around 80% of the complex) and types A, B, and X (distributed in the remaining 20% of the complex).","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2090":{"model_id":"2090","model_name":"Mycobacteroides abscessus 16S rRNA mutation conferring resistance to kanamycin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"4786":"t1373a","4787":"g1458t","4788":"c1376t","3075":"a1375g"},"Curated-R":{"4786":"t1373a","4787":"g1458t","4788":"c1376t","3075":"a1375g"},"clinical":{"4786":"t1373a","4787":"g1458t","4788":"c1376t","3075":"a1375g"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"41093","param_value":"2600"}},"model_sequences":{"sequence":{"3257":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"CU458896.1","fmin":"1462397","fmax":"1463901","strand":"+","sequence":"AGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGGAAAGGCCCTTCGGGGTACTCGAGTGGCGAACGGGTGAGTAACACGTGGGTGATCTGCCCTGCACTCTGGGATAAGCCTGGGAAACTGGGTCTAATACCGGATAGGACCACACACTTCATGGTGAGTGGTGCAAAGCTTTTGCGGTGTGGGATGAGCCCGCGGCCTATCAGCTTGTTGGTGGGGTAATGGCCCACCAAGGCGACGACGGGTAGCCGGCCTGAGAGGGTGACCGGCCACACTGGGACTGAGATACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCGACGCCGCGTGAGGGATGACGGCCTTCGGGTTGTAAACCTCTTTCAGTAGGGACGAAGCGAAAGTGACGGTACCTACAGAAGAAGGACCGGCCAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGTCCGAGCGTTGTCCGGAATTACTGGGCGTAAAGAGCTCGTAGGTGGTTTGTCGCGTTGTTCGTGAAAACTCACAGCTTAACTGTGGGCGTGCGGGCGATACGGGCAGACTAGAGTACTGCAGGGGAGACTGGAATTCCTGGTGTAGCGGTGGAATGCGCAGATATCAGGAGGAACACCGGTGGCGAAGGCGGGTCTCTGGGCAGTAACTGACGCTGAGGAGCGAAAGCGTGGGTAGCGAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGGTGGGTACTAGGTGTGGGTTTCCTTCCTTGGGATCCGTGCCGTAGCTAACGCATTAAGTACCCCGCCTGGGGAGTACGGTCGCAAGACTAAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGCGGAGCATGTGGATTAATTCGATGCAACGCGAAGAACCTTACCTGGGTTTGACATGCACAGGACGTACCTAGAGATAGGTATTCCCTTGTGGCCTGTGTGCAGGTGGTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTCCTATGTTGCCAGCGGGTAATGCCGGGGACTCGTAGGAGACTGCCGGGGTCAACTCGGAGGAAGGTGGGGATGACGTCAAGTCATCATGCCCCTTATGTCCAGGGCTTCACACATGCTACAATGGCCAGTACAGAGGGCTGCGAAGCCGTAAGGTGGAGCGAATCCCTTAAAGCTGGTCTCAGTTCGGATTGGGGTCTGCAACTCGACCCCATGAAGTCGGAGTCGCTAGTAATCGCAGATCAGCAACGCTGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACGTCATGAAAGTCGGTAACACCCGAAGCCAGTGGCCTAACCTTTTGGAGGGAGCTGTCGAAGGTGGGATCGGCGATTGGGACGAAGTCGTAACAAGGTAGCCGTACCGGAAGGTGCGGCTGGATCACCT","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36888","NCBI_taxonomy_name":"Mycobacteroides abscessus","NCBI_taxonomy_id":"36809"}}}},"ARO_accession":"3003236","ARO_id":"39820","ARO_name":"Mycobacteroides abscessus 16S rRNA mutation conferring resistance to kanamycin","CARD_short_name":"Mabs_16S_KAN","ARO_description":"Point mutations in the 16S rRNA of Mycobacteroides abscessus conferring resistance to kanamycin.","ARO_category":{"40277":{"category_aro_accession":"3003666","category_aro_cvterm_id":"40277","category_aro_name":"16s rRNA with mutation conferring resistance to aminoglycoside antibiotics","category_aro_description":"Point mutations in the 16S rRNA of bacteria can confer resistance to aminoglycosides.","category_aro_class_name":"AMR Gene Family"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2126":{"model_id":"2126","model_name":"Mycobacteroides abscessus 16S rRNA mutation conferring resistance to tobramycin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"3049":"a1375g","4790":"c1376t","4791":"g1458t","4792":"t1373a"},"Curated-R":{"3049":"a1375g","4790":"c1376t","4791":"g1458t","4792":"t1373a"},"clinical":{"3049":"a1375g","4790":"c1376t","4791":"g1458t","4792":"t1373a"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"41093","param_value":"2600"}},"model_sequences":{"sequence":{"3253":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"CU458896.1","fmin":"1462397","fmax":"1463901","strand":"+","sequence":"AGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGGAAAGGCCCTTCGGGGTACTCGAGTGGCGAACGGGTGAGTAACACGTGGGTGATCTGCCCTGCACTCTGGGATAAGCCTGGGAAACTGGGTCTAATACCGGATAGGACCACACACTTCATGGTGAGTGGTGCAAAGCTTTTGCGGTGTGGGATGAGCCCGCGGCCTATCAGCTTGTTGGTGGGGTAATGGCCCACCAAGGCGACGACGGGTAGCCGGCCTGAGAGGGTGACCGGCCACACTGGGACTGAGATACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCGACGCCGCGTGAGGGATGACGGCCTTCGGGTTGTAAACCTCTTTCAGTAGGGACGAAGCGAAAGTGACGGTACCTACAGAAGAAGGACCGGCCAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGTCCGAGCGTTGTCCGGAATTACTGGGCGTAAAGAGCTCGTAGGTGGTTTGTCGCGTTGTTCGTGAAAACTCACAGCTTAACTGTGGGCGTGCGGGCGATACGGGCAGACTAGAGTACTGCAGGGGAGACTGGAATTCCTGGTGTAGCGGTGGAATGCGCAGATATCAGGAGGAACACCGGTGGCGAAGGCGGGTCTCTGGGCAGTAACTGACGCTGAGGAGCGAAAGCGTGGGTAGCGAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGGTGGGTACTAGGTGTGGGTTTCCTTCCTTGGGATCCGTGCCGTAGCTAACGCATTAAGTACCCCGCCTGGGGAGTACGGTCGCAAGACTAAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGCGGAGCATGTGGATTAATTCGATGCAACGCGAAGAACCTTACCTGGGTTTGACATGCACAGGACGTACCTAGAGATAGGTATTCCCTTGTGGCCTGTGTGCAGGTGGTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTCCTATGTTGCCAGCGGGTAATGCCGGGGACTCGTAGGAGACTGCCGGGGTCAACTCGGAGGAAGGTGGGGATGACGTCAAGTCATCATGCCCCTTATGTCCAGGGCTTCACACATGCTACAATGGCCAGTACAGAGGGCTGCGAAGCCGTAAGGTGGAGCGAATCCCTTAAAGCTGGTCTCAGTTCGGATTGGGGTCTGCAACTCGACCCCATGAAGTCGGAGTCGCTAGTAATCGCAGATCAGCAACGCTGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACGTCATGAAAGTCGGTAACACCCGAAGCCAGTGGCCTAACCTTTTGGAGGGAGCTGTCGAAGGTGGGATCGGCGATTGGGACGAAGTCGTAACAAGGTAGCCGTACCGGAAGGTGCGGCTGGATCACCT","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36888","NCBI_taxonomy_name":"Mycobacteroides abscessus","NCBI_taxonomy_id":"36809"}}}},"ARO_accession":"3003237","ARO_id":"39821","ARO_name":"Mycobacteroides abscessus 16S rRNA mutation conferring resistance to tobramycin","CARD_short_name":"Mabs_16S_TOB","ARO_description":"Point mutations in the 16S rRNA of Mycobacteroides abscessus conferring resistance to tobramycin.","ARO_category":{"40277":{"category_aro_accession":"3003666","category_aro_cvterm_id":"40277","category_aro_name":"16s rRNA with mutation conferring resistance to aminoglycoside antibiotics","category_aro_description":"Point mutations in the 16S rRNA of bacteria can confer resistance to aminoglycosides.","category_aro_class_name":"AMR Gene Family"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2198":{"model_id":"2198","model_name":"Pseudomonas aeruginosa parE conferring resistance to fluoroquinolones","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"3149":"M437I","3150":"A473V"},"Curated-R":{"3149":"M437I","3150":"A473V"},"clinical":{"3149":"M437I","3150":"A473V"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"5275":{"protein_sequence":{"accession":"AAG08352.1","sequence":"MATYNADAIEVLSGLDPVRKRPGMYTDTTRPNHLAQEVIDNSVDEALAGHAKSVQVILHQDNSLEVIDDGRGMPVDIHPEEGVPGVELILTKLHAGGKFSNKNYQFSGGLHGVGISVVNALSTRVEVRVKRDANEYRMTFADGFKDSDLEVIGTVGKRNTGTSVHFWPDPKYFDSAKFSVSRLKHVLKAKAVLCPGLSVVFEDKNTGERVEWHFEDGLRSYLTDAVAELPRLPDEPFCGNLEGSKEAVSWALLWLPEGGESVQESYVNLIPTAQGGTHVNGLRQGLLDAMREFCEFRNLLPRGVKLAPEDVWERIAFVLSMKMQEPQFSGQTKERLSSREAAAFVSGVVKDAFSLWLNEHAEIGLQLAELAISNAGRRLKAGKKVERKKITQGPALPGKLADCAGQEPMRAELFLVEGDSAGGSAKQARDKEFQAIMPLRGKILNTWEVDGGEVLASQEVHDIAVAIGVDPGASDLAQLRYGKICILADADSDGLHIATLLCALFVRHFRPLVEAGHVYVAMPPLYRIDLGKDIYYALDEAERDGILERLAAEKKRGKPQVTRFKGLGEMNPLQLRETTMDPNTRRLVQLTLEDATGTLEIMDMLLAKKRAGDRKSWLESKGNLAEVLV"},"dna_sequence":{"accession":"AE004091.2","fmin":"5576027","fmax":"5577917","strand":"-","sequence":"ATGGCTACTTACAACGCAGACGCCATCGAAGTCCTTTCCGGCCTCGACCCGGTGCGCAAGCGCCCGGGGATGTACACCGACACCACCCGCCCCAACCATCTGGCCCAGGAAGTCATCGACAACAGCGTCGACGAAGCCCTGGCCGGCCATGCGAAGAGCGTGCAGGTGATCCTGCACCAGGACAACTCGCTGGAAGTCATCGACGATGGCCGCGGCATGCCGGTGGACATCCACCCGGAAGAGGGCGTGCCGGGCGTCGAGCTGATCCTTACCAAGCTGCATGCCGGCGGCAAGTTCTCGAACAAGAACTACCAGTTCTCCGGCGGCTTGCACGGGGTCGGCATCTCGGTGGTGAACGCGCTCTCGACCCGGGTCGAGGTACGCGTCAAGCGCGACGCCAACGAGTACCGGATGACCTTCGCCGACGGCTTCAAGGACAGCGATCTGGAAGTCATCGGCACGGTCGGCAAGCGCAATACCGGTACCAGCGTGCATTTCTGGCCGGATCCGAAGTATTTCGATTCGGCGAAGTTCTCGGTCAGCCGCCTCAAGCATGTGCTCAAGGCCAAGGCGGTGCTGTGCCCGGGCCTGAGCGTGGTGTTCGAGGACAAGAACACCGGCGAGCGCGTCGAGTGGCACTTCGAGGACGGCCTGCGCTCCTACCTGACCGACGCGGTCGCCGAGCTGCCGCGCCTGCCCGATGAACCCTTCTGCGGCAACCTCGAAGGTTCCAAGGAAGCGGTGAGCTGGGCCCTGCTGTGGCTGCCCGAGGGCGGTGAGTCGGTGCAGGAAAGCTACGTCAACCTGATTCCCACGGCCCAGGGCGGCACCCATGTGAACGGCCTGCGCCAGGGCCTGCTCGACGCCATGCGCGAGTTCTGCGAGTTCCGCAACCTGTTGCCGCGCGGCGTCAAGCTGGCGCCCGAGGACGTCTGGGAGCGGATCGCCTTCGTCCTCTCGATGAAGATGCAGGAGCCGCAGTTCTCCGGGCAGACCAAGGAGCGCCTGTCGTCCCGCGAGGCGGCGGCGTTCGTCTCGGGCGTGGTGAAGGACGCCTTCAGCCTGTGGCTCAACGAGCACGCCGAAATCGGCCTGCAACTGGCGGAACTGGCGATCAGCAACGCCGGGCGTCGCCTCAAGGCGGGCAAGAAGGTCGAGCGCAAGAAGATCACCCAGGGGCCGGCGCTGCCCGGCAAACTGGCCGACTGCGCCGGACAGGAACCGATGCGCGCGGAACTGTTCCTGGTCGAGGGCGACTCCGCCGGCGGCTCGGCGAAGCAGGCGCGGGACAAGGAATTCCAGGCGATCATGCCGCTGCGCGGAAAGATCCTGAACACCTGGGAAGTGGACGGCGGCGAGGTGCTCGCCAGCCAGGAGGTCCACGACATCGCGGTGGCCATCGGCGTCGATCCGGGTGCCAGTGACCTGGCCCAGCTGCGCTACGGCAAGATCTGTATCCTCGCGGATGCCGACTCCGACGGGCTGCACATCGCCACGCTGCTCTGCGCGCTGTTCGTCCGCCATTTCCGCCCGCTGGTGGAAGCCGGCCACGTCTACGTGGCGATGCCGCCGCTGTACCGCATCGACCTCGGCAAGGACATCTACTACGCCCTCGACGAAGCCGAGCGCGACGGCATCCTCGAGCGCCTGGCCGCAGAGAAGAAGCGCGGCAAGCCGCAGGTCACCCGCTTCAAGGGCCTTGGCGAAATGAATCCGTTGCAACTGCGCGAGACCACCATGGATCCGAATACCCGGCGGCTGGTCCAGCTCACCCTGGAGGACGCCACCGGTACCCTGGAGATCATGGACATGCTGCTGGCCAAGAAGCGCGCCGGTGACCGCAAGTCCTGGCTGGAAAGCAAGGGCAACCTGGCCGAGGTGCTGGTCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36804","NCBI_taxonomy_name":"Pseudomonas aeruginosa PAO1","NCBI_taxonomy_id":"208964"}}}},"ARO_accession":"3003685","ARO_id":"40320","ARO_name":"Pseudomonas aeruginosa parE conferring resistance to fluoroquinolones","CARD_short_name":"Paer_parE_FLO","ARO_description":"Point mutation in Pseudomonas aeruginosa parE resulting in sensitivity to fluoroquinolones (ciprofloxacin). In combination with a gyrase mutation (gyrA or gyrB), it confers a high level of resistance to ciprofloxacin.","ARO_category":{"39897":{"category_aro_accession":"3003313","category_aro_cvterm_id":"39897","category_aro_name":"fluoroquinolone resistant parE","category_aro_description":"ParE is a subunit of topoisomerase IV, necessary for cell survival. Point mutations in ParE prevent fluoroquinolones from inhibiting DNA synthesis, thus conferring resistance.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2136":{"model_id":"2136","model_name":"Escherichia coli 16S rRNA (rrsB) mutation conferring resistance to kanamycin A","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"2904":"a1408g","4813":"t1406a"},"Curated-R":{"2904":"a1408g","4813":"t1406a"},"clinical":{"2904":"a1408g","4813":"t1406a"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"41093","param_value":"2700"}},"model_sequences":{"sequence":{"3232":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"U00096.1","fmin":"4166658","fmax":"4168200","strand":"+","sequence":"AAATTGAAGAGTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAACGGTAACAGGAAGAAGCTTGCTTCTTTGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCGGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGGAGTAAAGTTAATACCTTTGCTCATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACGAAGACTGACGCTCAGGTGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGTCGACTTGGAGGTTGTGCCCTTGAGGCGTGGCTTCCGGAGCTAACGCGTTAAGTCGACCGCCTGGGGAGTACGGCCGCAAGGTTAAAACTCAAATGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGATGCAACGCGAAGAACCTTACCTGGTCTTGACATCCACGGAAGTTTTCAGAGATGAGAATGTGCCTTCGGGAACCGTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGAAATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCCTTTGTTGCCAGCGGTCCGGCCGGGAACTCAAAGGAGACTGCCAGTGATAAACTGGAGGAAGGTGGGGATGACGTCAAGTCATCATGGCCCTTACGACCAGGGCTACACACGTGCTACAATGGCGCATACAAAGAGAAGCGACCTCGCGAGAGCAAGCGGACCTCATAAAGTGCGTCGTAGTCCGGATTGGAGTCTGCAACTCGACTCCATGAAGTCGGAATCGCTAGTAATCGTGGATCAGAATGCCACGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACACCATGGGAGTGGGTTGCAAAAGAAGTAGGTAGCTTAACCTTCGGGAGGGCGCTTACCACTTTGTGATTCATGACTGGGGTGAAGTCGTAACAAGGTAACCGTAGGGGAACCTGCGGTTGGATCACCTCCTTA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36905","NCBI_taxonomy_name":"Escherichia coli str. K-12","NCBI_taxonomy_id":"83333"}}}},"ARO_accession":"3003399","ARO_id":"39983","ARO_name":"Escherichia coli 16S rRNA (rrsB) mutation conferring resistance to kanamycin A","CARD_short_name":"Ecol_16rrsB_KAN","ARO_description":"Point mutations in the 3' minor domain of helix 44, in the rrsB 16S rRNA gene of Escherichia coli can confer resistance to kanamycin A.","ARO_category":{"40277":{"category_aro_accession":"3003666","category_aro_cvterm_id":"40277","category_aro_name":"16s rRNA with mutation conferring resistance to aminoglycoside antibiotics","category_aro_description":"Point mutations in the 16S rRNA of bacteria can confer resistance to aminoglycosides.","category_aro_class_name":"AMR Gene Family"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2140":{"model_id":"2140","model_name":"Escherichia coli 16S rRNA (rrsB) mutation conferring resistance to streptomycin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"2966":"a523c"},"Curated-R":{"2966":"a523c"},"clinical":{"2966":"a523c"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"41093","param_value":"2700"}},"model_sequences":{"sequence":{"3231":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"U00096.1","fmin":"4166658","fmax":"4168200","strand":"+","sequence":"AAATTGAAGAGTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAACGGTAACAGGAAGAAGCTTGCTTCTTTGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCGGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGGAGTAAAGTTAATACCTTTGCTCATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACGAAGACTGACGCTCAGGTGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGTCGACTTGGAGGTTGTGCCCTTGAGGCGTGGCTTCCGGAGCTAACGCGTTAAGTCGACCGCCTGGGGAGTACGGCCGCAAGGTTAAAACTCAAATGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGATGCAACGCGAAGAACCTTACCTGGTCTTGACATCCACGGAAGTTTTCAGAGATGAGAATGTGCCTTCGGGAACCGTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGAAATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCCTTTGTTGCCAGCGGTCCGGCCGGGAACTCAAAGGAGACTGCCAGTGATAAACTGGAGGAAGGTGGGGATGACGTCAAGTCATCATGGCCCTTACGACCAGGGCTACACACGTGCTACAATGGCGCATACAAAGAGAAGCGACCTCGCGAGAGCAAGCGGACCTCATAAAGTGCGTCGTAGTCCGGATTGGAGTCTGCAACTCGACTCCATGAAGTCGGAATCGCTAGTAATCGTGGATCAGAATGCCACGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACACCATGGGAGTGGGTTGCAAAAGAAGTAGGTAGCTTAACCTTCGGGAGGGCGCTTACCACTTTGTGATTCATGACTGGGGTGAAGTCGTAACAAGGTAACCGTAGGGGAACCTGCGGTTGGATCACCTCCTTA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36905","NCBI_taxonomy_name":"Escherichia coli str. K-12","NCBI_taxonomy_id":"83333"}}}},"ARO_accession":"3003405","ARO_id":"39989","ARO_name":"Escherichia coli 16S rRNA (rrsB) mutation conferring resistance to streptomycin","CARD_short_name":"Ecol_16rrsB_STR","ARO_description":"Point mutations in the 5' domain of helix 18, in the rrsB 16S rRNA gene of Escherichia coli can confer resistance to streptomycin.","ARO_category":{"40277":{"category_aro_accession":"3003666","category_aro_cvterm_id":"40277","category_aro_name":"16s rRNA with mutation conferring resistance to aminoglycoside antibiotics","category_aro_description":"Point mutations in the 16S rRNA of bacteria can confer resistance to aminoglycosides.","category_aro_class_name":"AMR Gene Family"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2146":{"model_id":"2146","model_name":"Escherichia coli 16S rRNA (rrnB) mutation conferring resistance to streptomycin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"4825":"c528t","4826":"g527t"},"Curated-R":{"4825":"c528t","4826":"g527t"},"clinical":{"4825":"c528t","4826":"g527t"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"41093","param_value":"2700"}},"model_sequences":{"sequence":{"3237":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"U00096.1","fmin":"4166658","fmax":"4168200","strand":"+","sequence":"AAATTGAAGAGTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAACGGTAACAGGAAGAAGCTTGCTTCTTTGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCGGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGGAGTAAAGTTAATACCTTTGCTCATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACGAAGACTGACGCTCAGGTGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGTCGACTTGGAGGTTGTGCCCTTGAGGCGTGGCTTCCGGAGCTAACGCGTTAAGTCGACCGCCTGGGGAGTACGGCCGCAAGGTTAAAACTCAAATGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGATGCAACGCGAAGAACCTTACCTGGTCTTGACATCCACGGAAGTTTTCAGAGATGAGAATGTGCCTTCGGGAACCGTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGAAATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCCTTTGTTGCCAGCGGTCCGGCCGGGAACTCAAAGGAGACTGCCAGTGATAAACTGGAGGAAGGTGGGGATGACGTCAAGTCATCATGGCCCTTACGACCAGGGCTACACACGTGCTACAATGGCGCATACAAAGAGAAGCGACCTCGCGAGAGCAAGCGGACCTCATAAAGTGCGTCGTAGTCCGGATTGGAGTCTGCAACTCGACTCCATGAAGTCGGAATCGCTAGTAATCGTGGATCAGAATGCCACGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACACCATGGGAGTGGGTTGCAAAAGAAGTAGGTAGCTTAACCTTCGGGAGGGCGCTTACCACTTTGTGATTCATGACTGGGGTGAAGTCGTAACAAGGTAACCGTAGGGGAACCTGCGGTTGGATCACCTCCTTA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36905","NCBI_taxonomy_name":"Escherichia coli str. K-12","NCBI_taxonomy_id":"83333"}}}},"ARO_accession":"3003406","ARO_id":"39990","ARO_name":"Escherichia coli 16S rRNA (rrnB) mutation conferring resistance to streptomycin","CARD_short_name":"Ecol_16S_STR","ARO_description":"Point mutations in the 5' domain of helix 18, in the rrnB 16S rRNA gene of Escherichia coli can confer resistance to streptomycin.","ARO_category":{"40277":{"category_aro_accession":"3003666","category_aro_cvterm_id":"40277","category_aro_name":"16s rRNA with mutation conferring resistance to aminoglycoside antibiotics","category_aro_description":"Point mutations in the 16S rRNA of bacteria can confer resistance to aminoglycosides.","category_aro_class_name":"AMR Gene Family"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2157":{"model_id":"2157","model_name":"Escherichia coli 16S rRNA (rrsB) mutation conferring resistance to gentamicin C","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"3018":"a1408g"},"Curated-R":{"3018":"a1408g"},"clinical":{"3018":"a1408g"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"41093","param_value":"2700"}},"model_sequences":{"sequence":{"3233":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"U00096.1","fmin":"4166658","fmax":"4168200","strand":"+","sequence":"AAATTGAAGAGTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAACGGTAACAGGAAGAAGCTTGCTTCTTTGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCGGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGGAGTAAAGTTAATACCTTTGCTCATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACGAAGACTGACGCTCAGGTGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGTCGACTTGGAGGTTGTGCCCTTGAGGCGTGGCTTCCGGAGCTAACGCGTTAAGTCGACCGCCTGGGGAGTACGGCCGCAAGGTTAAAACTCAAATGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGATGCAACGCGAAGAACCTTACCTGGTCTTGACATCCACGGAAGTTTTCAGAGATGAGAATGTGCCTTCGGGAACCGTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGAAATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCCTTTGTTGCCAGCGGTCCGGCCGGGAACTCAAAGGAGACTGCCAGTGATAAACTGGAGGAAGGTGGGGATGACGTCAAGTCATCATGGCCCTTACGACCAGGGCTACACACGTGCTACAATGGCGCATACAAAGAGAAGCGACCTCGCGAGAGCAAGCGGACCTCATAAAGTGCGTCGTAGTCCGGATTGGAGTCTGCAACTCGACTCCATGAAGTCGGAATCGCTAGTAATCGTGGATCAGAATGCCACGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACACCATGGGAGTGGGTTGCAAAAGAAGTAGGTAGCTTAACCTTCGGGAGGGCGCTTACCACTTTGTGATTCATGACTGGGGTGAAGTCGTAACAAGGTAACCGTAGGGGAACCTGCGGTTGGATCACCTCCTTA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36905","NCBI_taxonomy_name":"Escherichia coli str. K-12","NCBI_taxonomy_id":"83333"}}}},"ARO_accession":"3003396","ARO_id":"39980","ARO_name":"Escherichia coli 16S rRNA (rrsB) mutation conferring resistance to gentamicin C","CARD_short_name":"Ecol_16S_GENC","ARO_description":"Point mutations in the 3' minor domain of helix 44, in the rrsB 16S rRNA gene of Escherichia coli can confer resistance to gentamicin C.","ARO_category":{"40277":{"category_aro_accession":"3003666","category_aro_cvterm_id":"40277","category_aro_name":"16s rRNA with mutation conferring resistance to aminoglycoside antibiotics","category_aro_description":"Point mutations in the 16S rRNA of bacteria can confer resistance to aminoglycosides.","category_aro_class_name":"AMR Gene Family"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"46133":{"category_aro_accession":"3007382","category_aro_cvterm_id":"46133","category_aro_name":"gentamicin","category_aro_description":"Gentamicin is a commonly used aminoglycoside antibiotic derived from members of the Micromonospora genus of bacteria. It acts by binding the 30S ribosomal subunit, thus inhibiting protein synthesis. Gentamicin is typically used to treat Gram-negative infections of the repiratory and urinary tract, as well as infections of the bone and soft tissue. It also exhibits considerable nephrotoxicity and ototoxicity. Gentamicin is administered as a mixture of gentamicin type C (which makes about around 80% of the complex) and types A, B, and X (distributed in the remaining 20% of the complex).","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1450":{"model_id":"1450","model_name":"Escherichia coli parC conferring resistance to fluoroquinolones","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"3972":"S80I","3973":"E84G"},"Curated-R":{"3972":"S80I","3973":"E84G"},"clinical":{"3972":"S80I","3973":"E84G"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1400"}},"model_sequences":{"sequence":{"4704":{"protein_sequence":{"accession":"AAC76055.1","sequence":"MSDMAERLALHEFTENAYLNYSMYVIMDRALPFIGDGLKPVQRRIVYAMSELGLNASAKFKKSARTVGDVLGKYHPHGDSACYEAMVLMAQPFSYRYPLVDGQGNWGAPDDPKSFAAMRYTESRLSKYSELLLSELGQGTADWVPNFDGTLQEPKMLPARLPNILLNGTTGIAVGMATDIPPHNLREVAQAAIALIDQPKTTLDQLLDIVQGPDYPTEAEIITSRAEIRKIYENGRGSVRMRAVWKKEDGAVVISALPHQVSGARVLEQIAAQMRNKKLPMVDDLRDESDHENPTRLVIVPRSNRVDMDQVMNHLFATTDLEKSYRINLNMIGLDGRPAVKNLLEILSEWLVFRRDTVRRRLNYRLEKVLKRLHILEGLLVAFLNIDEVIEIIRNEDEPKPALMSRFGLTETQAEAILELKLRHLAKLEEMKIRGEQSELEKERDQLQGILASERKMNNLLKKELQADAQAYGDDRRSPLQEREEAKAMSEHDMLPSEPVTIVLSQMGWVRSAKGHDIDAPGLNYKAGDSFKAAVKGKSNQPVVFVDSTGRSYAIDPITLPSARGQGEPLTGKLTLPPGATVDHMLMESDDQKLLMASDAGYGFVCTFNDLVARNRAGKALITLPENAHVMPPVVIEDASDMLLAITQAGRMLMFPVSDLPQLSKGKGNKIINIPSAEAARGEDGLAQLYVLPPQSTLTIHVGKRKIKLRPEELQKVTGERGRRGTLMRGLQRIDRVEIDSPRRASSGDSEE"},"dna_sequence":{"accession":"U00096.3","fmin":"3163714","fmax":"3165973","strand":"-","sequence":"ATGAGCGATATGGCAGAGCGCCTTGCGCTACATGAATTTACGGAAAACGCCTACTTAAACTACTCCATGTACGTGATCATGGACCGTGCGTTGCCGTTTATTGGTGATGGTCTGAAACCTGTTCAGCGCCGCATTGTGTATGCGATGTCTGAACTGGGCCTGAATGCCAGCGCCAAATTTAAAAAATCGGCCCGTACCGTCGGTGACGTACTGGGTAAATACCATCCGCACGGCGATAGCGCCTGTTATGAAGCGATGGTCCTGATGGCGCAACCGTTCTCTTACCGTTATCCGCTGGTTGATGGTCAGGGGAACTGGGGCGCGCCGGACGATCCGAAATCGTTCGCGGCAATGCGTTACACCGAATCCCGGTTGTCGAAATATTCCGAGCTGCTATTGAGCGAGCTGGGGCAGGGGACGGCTGACTGGGTGCCAAACTTCGACGGCACTTTGCAGGAGCCGAAAATGCTACCTGCCCGTCTGCCAAACATTTTGCTTAACGGCACCACCGGTATTGCCGTCGGCATGGCGACCGATATTCCACCGCATAACCTGCGTGAAGTGGCTCAGGCGGCAATCGCATTAATCGACCAGCCGAAAACCACGCTCGATCAGCTGCTGGATATCGTGCAGGGGCCGGATTATCCGACTGAAGCGGAAATTATCACTTCGCGCGCCGAGATCCGTAAAATCTACGAGAACGGACGTGGTTCAGTGCGTATGCGCGCGGTGTGGAAGAAAGAAGATGGCGCGGTGGTTATCAGCGCATTGCCGCATCAGGTTTCAGGTGCGCGCGTACTGGAGCAAATTGCTGCGCAAATGCGCAACAAAAAGCTGCCGATGGTTGACGATCTGCGCGATGAATCTGACCACGAGAACCCGACCCGCCTGGTGATTGTGCCGCGTTCCAACCGCGTGGATATGGATCAGGTGATGAACCACCTCTTCGCTACCACCGATCTGGAAAAGAGCTATCGTATTAACCTTAATATGATCGGTCTGGATGGTCGTCCGGCGGTGAAAAACCTGCTGGAAATCCTCTCCGAATGGCTGGTGTTCCGCCGCGATACCGTGCGCCGCCGACTGAACTATCGTCTGGAGAAAGTCCTCAAGCGCCTGCATATCCTCGAAGGTTTGCTGGTGGCGTTTCTCAATATCGACGAAGTGATTGAGATCATTCGTAATGAAGATGAACCGAAACCGGCGCTGATGTCGCGGTTTGGCCTTACGGAAACCCAGGCGGAAGCGATCCTCGAACTGAAACTGCGTCATCTTGCCAAACTGGAAGAGATGAAGATTCGCGGTGAGCAGAGTGAACTGGAAAAAGAGCGCGACCAGTTGCAGGGCATTTTGGCTTCCGAGCGTAAAATGAATAACCTGCTGAAGAAAGAACTGCAGGCAGACGCGCAAGCCTACGGTGACGATCGTCGTTCGCCGTTGCAGGAACGCGAAGAAGCGAAAGCGATGAGCGAGCACGACATGCTGCCGTCTGAACCTGTCACCATTGTGCTGTCGCAGATGGGCTGGGTACGCAGCGCTAAAGGCCATGATATCGACGCGCCGGGCCTGAATTATAAAGCGGGTGATAGCTTCAAAGCGGCGGTGAAAGGTAAGAGCAACCAACCGGTAGTGTTTGTTGATTCCACCGGTCGTAGCTATGCCATTGACCCGATTACGCTGCCGTCGGCGCGTGGTCAGGGCGAGCCGCTCACCGGCAAATTAACGTTGCCGCCTGGGGCGACCGTTGACCATATGCTGATGGAAAGCGACGATCAGAAACTGCTGATGGCTTCCGATGCGGGTTACGGTTTCGTCTGCACCTTTAACGATCTGGTGGCGCGTAACCGTGCAGGTAAGGCTTTGATCACCTTACCGGAAAATGCCCATGTTATGCCGCCGGTGGTGATTGAAGATGCTTCCGATATGCTGCTGGCAATCACTCAGGCAGGCCGTATGTTGATGTTCCCGGTAAGTGATCTGCCGCAGCTGTCGAAGGGCAAAGGCAACAAGATTATCAACATTCCATCGGCAGAAGCCGCGCGTGGAGAAGATGGTCTGGCGCAATTGTACGTTCTGCCGCCGCAAAGCACGCTGACCATTCATGTTGGGAAACGCAAAATTAAACTGCGCCCGGAAGAGTTACAGAAAGTCACTGGCGAACGTGGACGCCGCGGTACGTTGATGCGCGGTTTGCAGCGTATCGATCGTGTTGAGATCGACTCTCCTCGCCGTGCCAGCAGCGGTGATAGCGAAGAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36849","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. MG1655","NCBI_taxonomy_id":"511145"}}}},"ARO_accession":"3003308","ARO_id":"39892","ARO_name":"Escherichia coli parC conferring resistance to fluoroquinolones","CARD_short_name":"Ecol_parC_FLO","ARO_description":"Point mutation in Escherichia coli parC resulting in fluoroquinolone resistance.","ARO_category":{"36913":{"category_aro_accession":"3000619","category_aro_cvterm_id":"36913","category_aro_name":"fluoroquinolone resistant parC","category_aro_description":"ParC is a subunit of topoisomerase IV, which decatenates and relaxes DNA to allow access to genes for transcription or translation. Point mutations in ParC prevent fluoroquinolone antibiotics from inhibiting DNA synthesis, and confer low-level resistance. Higher-level resistance results from both gyrA and parC mutations.","category_aro_class_name":"AMR Gene Family"},"35942":{"category_aro_accession":"0000023","category_aro_cvterm_id":"35942","category_aro_name":"enoxacin","category_aro_description":"Enoxacin belongs to a group called fluoroquinolones. Its mode of action depends upon blocking bacterial DNA replication by binding itself to DNA gyrase and causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37004":{"category_aro_accession":"3000660","category_aro_cvterm_id":"37004","category_aro_name":"lomefloxacin","category_aro_description":"Lomefloxacin is a difluoropiperazinyl quinolone, sharing similar activities with other fluoroquinolones. It is used to treat urinary tract infections. Relative to other fluoroquinolones, it has a longer half life and has higher serum concentrations.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37007":{"category_aro_accession":"3000663","category_aro_cvterm_id":"37007","category_aro_name":"ofloxacin","category_aro_description":"Ofloxacin is a 6-fluoro, 7-piperazinyl quinolone with a methyl-substituted oxazine ring. It has a broad spectrum of activity including many enterobacteria and mycoplasma but most anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"37008":{"category_aro_accession":"3000664","category_aro_cvterm_id":"37008","category_aro_name":"trovafloxacin","category_aro_description":"Trovafloxacin is a trifluoroquinalone with a broad spectrum of activity that acts by inhibiting the uncoiling of supercoiled DNA. While potent against many Gram-positive and Gram-negative bacteria, it is less active against pseudomonads and Cl. difficile. It is usually taken as the prodrug trovafloxacin mesylate or alatrofloxacin mesylate for oral or intravenous administration, respectively.","category_aro_class_name":"Antibiotic"},"37009":{"category_aro_accession":"3000665","category_aro_cvterm_id":"37009","category_aro_name":"grepafloxacin","category_aro_description":"Grepafloxacin is a broad-spectrum antibacterial quinoline. It is no longer taken due to its high toxicity.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"37142":{"category_aro_accession":"3000762","category_aro_cvterm_id":"37142","category_aro_name":"pefloxacin","category_aro_description":"Pefloxacin is structurally and functionally similar to norfloxacin. It is poorly active against mycobacteria, while anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2083":{"model_id":"2083","model_name":"Mycoplasma hominis parC conferring resistance to fluoroquinolones","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1400"},"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"9862":"S91I","9864":"K149R"},"Curated-R":{"9862":"S91I","9864":"K149R"},"clinical":{"9862":"S91I","9864":"K149R"}}},"model_sequences":{"sequence":{"5886":{"protein_sequence":{"accession":"AKJ52802.1","sequence":"MKKDRKEEIQEVTENIIEKNMADIMSDRFGRYSKYIIQQRAIPDARDGLKPVQRRILYSMWNLHLKNSEPFKKSARIVGDVIGRYHPHGDSSIYEALVRMAQDWKSNFPLIEMHGNKGSIDDDPAAAMRYTESRLEKISELMLRDLDRKVVKMAPNFDDSEYEPIVLPALFPNLLVNGAKGIAAGFATEIPPHNLGEVIDATIALIKNPTISIEELSEIVKGPDFPTGAIINGINEIKKALSSGQGRITISSKYHYVYDKKDESKIIGIEIIEIPFGVVKSKLVADIDAIAIDKKISGIKEVLDQTDRNGISIFIQLEDGANADAIIAYLMNKTELSISYSYNMVAIDNNRPVILNLYSALIAYLSHLKEVNINGINYDLKKFKLRLEIVEGFIKVAEISDEVIHLIKESDNSKKGVILALMNKFKFSELQATAIAELRLYKLSRMDQIEFQEEKKNLEIQIENCNKLLNDKWEFNQYLIKQLLEIKNQYSKPRLTEISDQKIDKEIDHKLLTKNEDFYLYITKDGYYKKISLKVYTSNELNTFKLKEEDNVFYFDKVNSLSKILFFTNLGNYFIIDCHLFKDCNWKDLGQHISSIVALESSEKIIRVIEITSFNSYANFILMSKLGYAKKVNLRDFENKSSLKTKTCMSFKDDNDELIDAQISNDEKMLFILLNNGMYHLVSENELKVGISLKARGIRLLLNLYKHPQLQVSGFITVSKYNNIIYLTQGGYIKCWDTSKLELTTRNTPKMLFTPLKNNILGLQSLAVTLSNLKMLYTDNNGNLAEYDWKFILKDKTKESKLLKLDYSFTNPGYFITPIKINELIEADEIEQEKIRQEYQGYIDKNIELTAEHALIKKSYDQDIQHLNNEEQEELFQISTEDIELPNVSNNVNDNQKDKKNIATKESVSQKIQEIEKIDLETIMQKIKQIKKK"},"dna_sequence":{"accession":"CP011538.1","fmin":"660262","fmax":"663064","strand":"-","sequence":"ATGAAAAAAGATAGAAAAGAAGAAATACAAGAAGTTACTGAAAACATTATTGAAAAAAATATGGCCGATATAATGTCTGATAGATTCGGACGTTATTCAAAATACATTATTCAACAAAGAGCAATTCCTGATGCTCGTGATGGACTAAAACCTGTTCAACGTCGGATTTTATATTCAATGTGAAATTTACATTTAAAAAATAGCGAGCCTTTTAAAAAATCAGCTAGAATCGTTGGGGATGTTATCGGACGTTATCACCCTCATGGAGATAGTTCAATATACGAGGCATTAGTCAGAATGGCTCAAGATTGAAAAAGCAATTTCCCATTAATTGAAATGCATGGTAATAAAGGTTCAATTGATGATGACCCTGCCGCTGCAATGCGTTACACTGAATCAAGACTTGAAAAAATTAGTGAACTGATGTTGAGAGATTTAGACAGAAAAGTTGTAAAAATGGCTCCAAACTTTGATGACTCTGAATACGAACCAATTGTTTTGCCGGCCTTATTTCCTAATTTATTAGTTAACGGTGCTAAAGGAATTGCTGCTGGTTTTGCTACAGAAATCCCACCACATAATCTAGGCGAAGTTATTGATGCAACAATTGCATTAATCAAAAATCCTACAATATCAATTGAAGAATTAAGTGAAATAGTTAAAGGCCCAGATTTCCCAACAGGAGCAATTATTAATGGTATAAATGAAATAAAAAAAGCTCTTTCAAGTGGGCAAGGTAGAATTACAATTTCTTCGAAATATCATTACGTTTATGATAAAAAAGATGAATCGAAAATTATTGGTATTGAAATAATTGAAATTCCTTTTGGGGTTGTTAAATCAAAATTAGTTGCCGACATTGATGCAATTGCAATAGATAAAAAAATTTCTGGTATTAAAGAAGTTTTGGACCAAACAGATAGAAATGGAATTTCAATATTTATTCAATTAGAAGATGGTGCAAATGCTGACGCAATAATTGCATACTTAATGAATAAAACCGAACTAAGCATCTCGTATAGTTATAACATGGTTGCAATTGACAATAACCGTCCAGTAATTTTGAATCTCTATAGTGCCTTAATTGCTTATTTAAGTCATTTAAAAGAAGTTAATATAAATGGTATTAATTATGATTTAAAGAAGTTTAAATTGAGACTAGAAATAGTTGAAGGGTTCATTAAAGTAGCCGAAATTTCTGATGAAGTTATACATTTGATTAAAGAAAGCGATAACTCAAAAAAAGGTGTTATCCTTGCATTGATGAATAAATTTAAATTTAGTGAATTGCAAGCAACAGCGATTGCTGAATTAAGATTGTATAAGCTTTCAAGAATGGATCAAATCGAATTTCAAGAAGAAAAGAAAAACCTTGAAATTCAAATTGAAAATTGCAATAAATTATTAAATGATAAATGAGAATTTAATCAATATTTAATAAAGCAATTGCTTGAAATAAAAAATCAATATTCAAAGCCAAGATTAACGGAAATTTCAGATCAAAAAATCGATAAAGAAATTGATCATAAATTATTGACAAAAAATGAAGATTTTTATTTATATATAACCAAAGATGGATATTATAAAAAAATAAGTTTAAAAGTTTATACTAGCAATGAATTAAACACATTCAAATTAAAAGAAGAAGATAATGTTTTCTATTTTGATAAAGTAAACTCATTATCAAAGATATTATTCTTTACAAATTTAGGGAATTATTTTATTATTGATTGCCATTTGTTTAAAGATTGCAATTGAAAAGATCTTGGTCAACATATTTCATCAATAGTAGCTCTAGAAAGCTCAGAAAAAATTATTAGAGTTATAGAAATTACGTCATTCAATAGTTATGCAAACTTTATTTTAATGTCAAAATTAGGATATGCCAAAAAAGTTAATTTAAGAGATTTTGAAAATAAATCTTCTCTTAAAACAAAAACTTGCATGTCGTTTAAGGATGATAATGATGAATTAATAGATGCCCAAATTTCTAATGATGAAAAAATGCTATTTATTTTACTAAATAATGGTATGTATCATTTAGTTTCAGAAAACGAACTAAAGGTTGGAATTTCTTTGAAAGCAAGAGGCATTAGACTTCTTTTAAACTTATATAAACATCCTCAACTTCAAGTAAGTGGTTTTATAACAGTTTCAAAATACAACAATATAATTTATTTAACGCAAGGTGGTTATATAAAATGTTGGGATACTAGCAAATTAGAATTGACCACACGCAATACTCCAAAAATGTTGTTTACGCCACTAAAAAATAATATTTTAGGTCTTCAATCACTTGCTGTTACATTGAGCAATTTAAAAATGTTATACACTGATAATAATGGTAATTTGGCAGAATATGATTGAAAATTTATATTAAAAGATAAGACTAAGGAAAGTAAACTTCTTAAATTAGATTATTCATTTACTAACCCTGGGTATTTTATTACGCCAATAAAAATTAATGAATTAATTGAAGCTGATGAAATAGAGCAGGAAAAAATAAGACAAGAATATCAAGGATATATTGATAAAAATATTGAATTGACCGCTGAACATGCTTTGATTAAAAAATCCTATGATCAAGATATTCAACATTTAAATAATGAAGAACAAGAAGAACTATTTCAAATATCTACAGAAGATATTGAATTACCAAATGTTTCAAATAATGTTAATGACAACCAAAAAGATAAAAAAAATATAGCAACAAAAGAAAGCGTTAGTCAGAAAATACAAGAAATTGAAAAAATAGATCTTGAAACAATAATGCAAAAAATTAAACAAATTAAGAAAAAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40311","NCBI_taxonomy_name":"Mycoplasma hominis","NCBI_taxonomy_id":"2098"}}}},"ARO_accession":"3003310","ARO_id":"39894","ARO_name":"Mycoplasma hominis parC conferring resistance to fluoroquinolones","CARD_short_name":"Mhom_23S_FLO","ARO_description":"Point mutation in Mycoplasma hominis parC resulting in fluoroquinolone resistance.","ARO_category":{"36913":{"category_aro_accession":"3000619","category_aro_cvterm_id":"36913","category_aro_name":"fluoroquinolone resistant parC","category_aro_description":"ParC is a subunit of topoisomerase IV, which decatenates and relaxes DNA to allow access to genes for transcription or translation. Point mutations in ParC prevent fluoroquinolone antibiotics from inhibiting DNA synthesis, and confer low-level resistance. Higher-level resistance results from both gyrA and parC mutations.","category_aro_class_name":"AMR Gene Family"},"35942":{"category_aro_accession":"0000023","category_aro_cvterm_id":"35942","category_aro_name":"enoxacin","category_aro_description":"Enoxacin belongs to a group called fluoroquinolones. Its mode of action depends upon blocking bacterial DNA replication by binding itself to DNA gyrase and causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37004":{"category_aro_accession":"3000660","category_aro_cvterm_id":"37004","category_aro_name":"lomefloxacin","category_aro_description":"Lomefloxacin is a difluoropiperazinyl quinolone, sharing similar activities with other fluoroquinolones. It is used to treat urinary tract infections. Relative to other fluoroquinolones, it has a longer half life and has higher serum concentrations.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37007":{"category_aro_accession":"3000663","category_aro_cvterm_id":"37007","category_aro_name":"ofloxacin","category_aro_description":"Ofloxacin is a 6-fluoro, 7-piperazinyl quinolone with a methyl-substituted oxazine ring. It has a broad spectrum of activity including many enterobacteria and mycoplasma but most anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"37008":{"category_aro_accession":"3000664","category_aro_cvterm_id":"37008","category_aro_name":"trovafloxacin","category_aro_description":"Trovafloxacin is a trifluoroquinalone with a broad spectrum of activity that acts by inhibiting the uncoiling of supercoiled DNA. While potent against many Gram-positive and Gram-negative bacteria, it is less active against pseudomonads and Cl. difficile. It is usually taken as the prodrug trovafloxacin mesylate or alatrofloxacin mesylate for oral or intravenous administration, respectively.","category_aro_class_name":"Antibiotic"},"37009":{"category_aro_accession":"3000665","category_aro_cvterm_id":"37009","category_aro_name":"grepafloxacin","category_aro_description":"Grepafloxacin is a broad-spectrum antibacterial quinoline. It is no longer taken due to its high toxicity.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"37142":{"category_aro_accession":"3000762","category_aro_cvterm_id":"37142","category_aro_name":"pefloxacin","category_aro_description":"Pefloxacin is structurally and functionally similar to norfloxacin. It is poorly active against mycobacteria, while anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2096":{"model_id":"2096","model_name":"Escherichia coli 16S rRNA (rrsC) mutation conferring resistance to kasugamicin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"2941":"g926c","2951":"a1519c","2979":"a794g","2998":"a1519g","3050":"g926a","4822":"a794t","4823":"a1519t","4824":"g926t"},"Curated-R":{"2941":"g926c","2951":"a1519c","2979":"a794g","2998":"a1519g","3050":"g926a","4822":"a794t","4823":"a1519t","4824":"g926t"},"clinical":{"2941":"g926c","2951":"a1519c","2979":"a794g","2998":"a1519g","3050":"g926a","4822":"a794t","4823":"a1519t","4824":"g926t"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"41093","param_value":"2700"}},"model_sequences":{"sequence":{"3229":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"U00096.1","fmin":"3941807","fmax":"3943349","strand":"+","sequence":"AAATTGAAGAGTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAACGGTAACAGGAAACAGCTTGCTGTTTCGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGGAGTAAAGTTAATACCTTTGCTCATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACGAAGACTGACGCTCAGGTGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGTCGACTTGGAGGTTGTGCCCTTGAGGCGTGGCTTCCGGAGCTAACGCGTTAAGTCGACCGCCTGGGGAGTACGGCCGCAAGGTTAAAACTCAAATGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGATGCAACGCGAAGAACCTTACCTGGTCTTGACATCCACGGAAGTTTTCAGAGATGAGAATGTGCCTTCGGGAACCGTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGAAATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCCTTTGTTGCCAGCGGTCCGGCCGGGAACTCAAAGGAGACTGCCAGTGATAAACTGGAGGAAGGTGGGGATGACGTCAAGTCATCATGGCCCTTACGACCAGGGCTACACACGTGCTACAATGGCGCATACAAAGAGAAGCGACCTCGCGAGAGCAAGCGGACCTCATAAAGTGCGTCGTAGTCCGGATTGGAGTCTGCAACTCGACTCCATGAAGTCGGAATCGCTAGTAATCGTGGATCAGAATGCCACGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACACCATGGGAGTGGGTTGCAAAAGAAGTAGGTAGCTTAACCTTCGGGAGGGCGCTTACCACTTTGTGATTCATGACTGGGGTGAAGTCGTAACAAGGTAACCGTAGGGGAACCTGCGGTTGGATCACCTCCTTA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36905","NCBI_taxonomy_name":"Escherichia coli str. K-12","NCBI_taxonomy_id":"83333"}}}},"ARO_accession":"3003333","ARO_id":"39917","ARO_name":"Escherichia coli 16S rRNA (rrsC) mutation conferring resistance to kasugamicin","CARD_short_name":"Ecol_16rrsC_KAS","ARO_description":"Point mutations in the 3' minor, 3' major, and central domains in the rrsC 16S rRNA gene of Escherichia coli can confer resistance to kasugamicin.","ARO_category":{"40277":{"category_aro_accession":"3003666","category_aro_cvterm_id":"40277","category_aro_name":"16s rRNA with mutation conferring resistance to aminoglycoside antibiotics","category_aro_description":"Point mutations in the 16S rRNA of bacteria can confer resistance to aminoglycosides.","category_aro_class_name":"AMR Gene Family"},"37695":{"category_aro_accession":"3001296","category_aro_cvterm_id":"37695","category_aro_name":"kasugamycin","category_aro_description":"An unusual aminoglycoside because the cyclitol ring is not amino substituted; it was discovered as a fermentation product of Streptomyces kasugaensis.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2145":{"model_id":"2145","model_name":"Escherichia coli 16S rRNA (rrsB) mutation conferring resistance to tetracycline","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"41093","param_value":"2700"},"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"3061":"g1058c"},"Curated-R":{"3061":"g1058c"},"clinical":{"3061":"g1058c"}}},"model_sequences":{"sequence":{"3242":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"U00096.1","fmin":"4166658","fmax":"4168200","strand":"+","sequence":"AAATTGAAGAGTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAACGGTAACAGGAAGAAGCTTGCTTCTTTGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCGGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGGAGTAAAGTTAATACCTTTGCTCATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACGAAGACTGACGCTCAGGTGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGTCGACTTGGAGGTTGTGCCCTTGAGGCGTGGCTTCCGGAGCTAACGCGTTAAGTCGACCGCCTGGGGAGTACGGCCGCAAGGTTAAAACTCAAATGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGATGCAACGCGAAGAACCTTACCTGGTCTTGACATCCACGGAAGTTTTCAGAGATGAGAATGTGCCTTCGGGAACCGTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGAAATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCCTTTGTTGCCAGCGGTCCGGCCGGGAACTCAAAGGAGACTGCCAGTGATAAACTGGAGGAAGGTGGGGATGACGTCAAGTCATCATGGCCCTTACGACCAGGGCTACACACGTGCTACAATGGCGCATACAAAGAGAAGCGACCTCGCGAGAGCAAGCGGACCTCATAAAGTGCGTCGTAGTCCGGATTGGAGTCTGCAACTCGACTCCATGAAGTCGGAATCGCTAGTAATCGTGGATCAGAATGCCACGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACACCATGGGAGTGGGTTGCAAAAGAAGTAGGTAGCTTAACCTTCGGGAGGGCGCTTACCACTTTGTGATTCATGACTGGGGTGAAGTCGTAACAAGGTAACCGTAGGGGAACCTGCGGTTGGATCACCTCCTTA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36905","NCBI_taxonomy_name":"Escherichia coli str. K-12","NCBI_taxonomy_id":"83333"}}}},"ARO_accession":"3003410","ARO_id":"39994","ARO_name":"Escherichia coli 16S rRNA (rrsB) mutation conferring resistance to tetracycline","CARD_short_name":"Ecol_16rrsB_TET","ARO_description":"Point mutations in the 3' major domain of the rrsB 16S rRNA gene of Escherichia coli can confer resistance to tetracycline.","ARO_category":{"40280":{"category_aro_accession":"3003669","category_aro_cvterm_id":"40280","category_aro_name":"16S rRNA with mutation conferring resistance to tetracycline derivatives","category_aro_description":"Point mutations in the bacterial 16S rRNA region shown clinically to confer resistance to tetracycline and tetracycline derivatives (polyketide antibiotics).","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2102":{"model_id":"2102","model_name":"Mycolicibacterium smegmatis 16S rRNA (rrsB) mutation conferring resistance to hygromycin B","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"41093","param_value":"2700"},"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"7842":"t1348c","7843":"c1439t","7844":"t1441c"},"Curated-R":{"7842":"t1348c","7843":"c1439t","7844":"t1441c"},"clinical":{"7842":"t1348c","7843":"c1439t","7844":"t1441c"}}},"model_sequences":{"sequence":{"4148":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"X52922.1","fmin":"0","fmax":"1454","strand":"+","sequence":"GGCGGCGTGCTTAACACATGCAAGTCGAACGGAAAGGCCCTTTCGGGGGTACTCGAGTGGCGAACGGGTGAGTAACACGTGGGTGATCTGCCCTGCACTTTGGGATAAGCCTGGGAAACTGGGTCTAATACCGAATACACCCTGCTGGTCGCATGGCCTGGTAGGGGAAAGCTTTTGCGGTGTGGGATGGGCCCGCGGCCTATCAGCTTGTTGGTGGGGTGATGGCCTACCAAGGCGACGACGGGTAGCCGGCCTGAGAGGGTGACCGGCCACACTGGGACTGAGATACGGCCCAGACTNCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCGACGCCGCGTGAGGGATGACGGCCTTCGGGTTGTAAACCTCTTTCAGCACAGACGAAGCGCAAGTGACGGTATGTGCAGAAGAAGGACCGGCCAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGTCCGAGCGTTGTCCGGAATTACTGGGCGTAAAGAGCTCGTAGGTGGTTTGTCGCGTTGTTCGTGAAAACTCACAGCTTAACTGTGGGCGTGCGGGCGATACGGGCAGACTAGAGTACTGCAGGGGAGACTGGAATTCCTGGTGTAGCGGTGGAATGCGCAGATATCAGGAGGAACACCGGTGGCGAAGGCGGGTCTCTGGGCAGTAACTGACGCTGAGGAGCGAAAGCGTGGGGAGCGAACAGGATTAGATACCCTGGTAGTCCACGNCGTAAACGGTGGGTACTAGGTGTGGGTTTCCTTCCTTGGGATCCGTGCCGTAGCTAACGCATTAAGTANCCCGCCTGGGGAGTACGGNCGCAAGGCTAAAACTCAAAGGAATTGACGGGGGNCCGCACAAGCGGCGGAGCATGTGGATTAATTCGATGCAACGCGAAGAACCTTACCTGGGTTTGACATGCACAGGACGCCGGCAGAGATGTCGGTTCCCTTGTGGCCTGTGTGCAGGTGGTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTCTCATGTTGCCAGCACGTTATGGTGGGGACTCGTGAGAGACTGCCGGGGTCAACTCGGAGGAAGGTGGGGATGACGTCAAGTCATCATGCCCCTTATGTCCAGGGCTTCACACATGCTACAATGGCCGGTACAAAGGGCTGCGATGCCGTGAGGTGGAGCGAATCCTTTCAAAGCCGGTCTCAGTTCGGATCGGGGTCTGCAACTCGACCCCGTGAAGTCGGAGTCGCTAGTAATCGCAGATCAGCAACGCTGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACGTCATGAAAGTCGGTAACACCCGAAGCCGGTGGCCTAACCCTTGTGGAGGGAGCCGTCGAAGGTGGGATCGGCGATTGGGACGAAGTCGTAACAAGGTAGCCG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36871","NCBI_taxonomy_name":"Mycolicibacterium smegmatis","NCBI_taxonomy_id":"1772"}}}},"ARO_accession":"3003540","ARO_id":"40142","ARO_name":"Mycolicibacterium smegmatis 16S rRNA (rrsB) mutation conferring resistance to hygromycin B","CARD_short_name":"Msme_16rrsB_HGM","ARO_description":"Point mutations in the highly conserved helix 44 of the 16S rrsB rRNA gene of Mycolicibacterium smegmatis can confer resistance to hygromycin B. Resistance against hygromycin B is the result of conformational alterations that distorts a strong hydrogen bond leading to a change in the local geometry of the hygromycin B binding site.","ARO_category":{"40277":{"category_aro_accession":"3003666","category_aro_cvterm_id":"40277","category_aro_name":"16s rRNA with mutation conferring resistance to aminoglycoside antibiotics","category_aro_description":"Point mutations in the 16S rRNA of bacteria can confer resistance to aminoglycosides.","category_aro_class_name":"AMR Gene Family"},"36353":{"category_aro_accession":"3000214","category_aro_cvterm_id":"36353","category_aro_name":"hygromycin B","category_aro_description":"Hygromycin B is an aminoglycoside antibiotic used to treat different types of bacterial infections. Hygromycin B works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Hygromycin B has also been shown to interact with eukaryotic cells.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2149":{"model_id":"2149","model_name":"Mycolicibacterium smegmatis 16S rRNA (rrsA) mutation conferring resistance to hygromycin B","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"4831":"t1389c","4832":"c1480t","4830":"t1482c"},"Curated-R":{"4831":"t1389c","4832":"c1480t","4830":"t1482c"},"clinical":{"4831":"t1389c","4832":"c1480t","4830":"t1482c"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"41093","param_value":"2700"}},"model_sequences":{"sequence":{"4142":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"NC_008596.1","fmin":"3823614","fmax":"3825143","strand":"-","sequence":"AGAAAGGAGGTGATCCAGCCGCACCTTCCGGTACGGCTACCTTGTTACGACTTCGTCCCAATCGCCGATCCCACCTTCGACGGCTCCCTCCACAAGGGTTAGGCCACCGGCTTCGGGTGTTACCGACTTTCATGACGTGACGGGCGGTGTGTACAAGGCCCGGGAACGTATTCACCGCAGCGTTGCTGATCTGCGATTACTAGCGACTCCGACTTCACGGGGTCGAGTTGCAGACCCCGATCCGAACTGAGACCGGCTTTGAAAGGATTCGCTCCACCTCACGGCATCGCAGCCCTTTGTACCGGCCATTGTAGCATGTGTGAAGCCCTGGACATAAGGGGCATGATGACTTGACGTCATCCCCACCTTCCTCCGAGTTGACCCCGGCAGTCTCTCACGAGTCCCCACCATAACGTGCTGGCAACATGAGACAAGGGTTGCGCTCGTTGCGGGACTTAACCCAACATCTCACGACACGAGCTGACGACAGCCATGCACCACCTGCACACAGGCCACAAGGGAACCGACATCTCTGCCGGCGTCCTGTGCATGTCAAACCCAGGTAAGGTTCTTCGCGTTGCATCGAATTAATCCACATGCTCCGCCGCTTGTGCGGGCCCCCGTCAATTCCTTTGAGTTTTAGCCTTGCGGCCGTACTCCCCAGGCGGGGTACTTAATGCGTTAGCTACGGCACGGATCCCAAGGAAGGAAACCCACACCTAGTACCCACCGTTTACGGCGTGGACTACCAGGGTATCTAATCCTGTTCGCTCCCCACGCTTTCGCTCCTCAGCGTCAGTTACTGCCCAGAGACCCGCCTTCGCCACCGGTGTTCCTCCTGATATCTGCGCATTCCACCGCTACACCAGGAATTCCAGTCTCCCCTGCAGTACTCTAGTCTGCCCGTATCGCCCGCACGCCCACAGTTAAGCTGTGAGTTTTCACGAACAACGCGACAAACCACCTACGAGCTCTTTACGCCCAGTAATTCCGGACAACGCTCGGACCCTACGTATTACCGCGGCTGCTGGCACGTAGTTGGCCGGTCCTTCTTCTGCACATACCGTCACTTGCGCTTCGTCTGTGCTGAAAGAGGTTTACAACCCGAAGGCCGTCATCCCTCACGCGGCGTCGCTGCATCAGGCTTGCGCCCATTGTGCAATATTCCCCACTGCTGCCTCCCGTAGGAGTCTGGGCCGTATCTCAGTCCCAGTGTGGCCGGTCACCCTCTCAGGCCGGCTACCCGTCGTCGCCTTGGTAGGCCATCACCCCACCAACAAGCTGATAGGCCGCGGGCCCATCCCACACCGCAAAAGCTTTCCCCTACCAGGCCATGCGACCAGCAGGGTGTATTCGGTATTAGACCCAGTTTCCCAGGCTTATCCCAAAGTGCAGGGCAGATCACCCACGTGTTACTCACCCGTTCGCCACTCGAGTACCCCCGAAAGGGCCTTTCCGTTCGACTTGCATGTGTTAAGCACGCCGCCAGCGTTCGTCCTGAGCCAGGATCAAACTCTCCAAACAAAAAC","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36769","NCBI_taxonomy_name":"Mycolicibacterium smegmatis MC2 155","NCBI_taxonomy_id":"246196"}}}},"ARO_accession":"3003539","ARO_id":"40141","ARO_name":"Mycolicibacterium smegmatis 16S rRNA (rrsA) mutation conferring resistance to hygromycin B","CARD_short_name":"Msme_16rrsA_HGM","ARO_description":"Point mutations in the highly conserved helix 44 of the 16S rrsA rRNA gene of Mycolicibacterium smegmatis can confer resistance to hygromycin B. Resistance against hygromycin B is the result of conformational alterations that distorts a strong hydrogen bond leading to a change in the local geometry of the hygromycin B binding site.","ARO_category":{"40277":{"category_aro_accession":"3003666","category_aro_cvterm_id":"40277","category_aro_name":"16s rRNA with mutation conferring resistance to aminoglycoside antibiotics","category_aro_description":"Point mutations in the 16S rRNA of bacteria can confer resistance to aminoglycosides.","category_aro_class_name":"AMR Gene Family"},"36353":{"category_aro_accession":"3000214","category_aro_cvterm_id":"36353","category_aro_name":"hygromycin B","category_aro_description":"Hygromycin B is an aminoglycoside antibiotic used to treat different types of bacterial infections. Hygromycin B works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Hygromycin B has also been shown to interact with eukaryotic cells.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2106":{"model_id":"2106","model_name":"Mycolicibacterium smegmatis 16S rRNA (rrsA) mutation conferring resistance to kanamycin A","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"2929":"a1391g","4838":"t1389a"},"Curated-R":{"2929":"a1391g","4838":"t1389a"},"clinical":{"2929":"a1391g","4838":"t1389a"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"41093","param_value":"2700"}},"model_sequences":{"sequence":{"4144":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"NC_008596.1","fmin":"3823614","fmax":"3825143","strand":"-","sequence":"AGAAAGGAGGTGATCCAGCCGCACCTTCCGGTACGGCTACCTTGTTACGACTTCGTCCCAATCGCCGATCCCACCTTCGACGGCTCCCTCCACAAGGGTTAGGCCACCGGCTTCGGGTGTTACCGACTTTCATGACGTGACGGGCGGTGTGTACAAGGCCCGGGAACGTATTCACCGCAGCGTTGCTGATCTGCGATTACTAGCGACTCCGACTTCACGGGGTCGAGTTGCAGACCCCGATCCGAACTGAGACCGGCTTTGAAAGGATTCGCTCCACCTCACGGCATCGCAGCCCTTTGTACCGGCCATTGTAGCATGTGTGAAGCCCTGGACATAAGGGGCATGATGACTTGACGTCATCCCCACCTTCCTCCGAGTTGACCCCGGCAGTCTCTCACGAGTCCCCACCATAACGTGCTGGCAACATGAGACAAGGGTTGCGCTCGTTGCGGGACTTAACCCAACATCTCACGACACGAGCTGACGACAGCCATGCACCACCTGCACACAGGCCACAAGGGAACCGACATCTCTGCCGGCGTCCTGTGCATGTCAAACCCAGGTAAGGTTCTTCGCGTTGCATCGAATTAATCCACATGCTCCGCCGCTTGTGCGGGCCCCCGTCAATTCCTTTGAGTTTTAGCCTTGCGGCCGTACTCCCCAGGCGGGGTACTTAATGCGTTAGCTACGGCACGGATCCCAAGGAAGGAAACCCACACCTAGTACCCACCGTTTACGGCGTGGACTACCAGGGTATCTAATCCTGTTCGCTCCCCACGCTTTCGCTCCTCAGCGTCAGTTACTGCCCAGAGACCCGCCTTCGCCACCGGTGTTCCTCCTGATATCTGCGCATTCCACCGCTACACCAGGAATTCCAGTCTCCCCTGCAGTACTCTAGTCTGCCCGTATCGCCCGCACGCCCACAGTTAAGCTGTGAGTTTTCACGAACAACGCGACAAACCACCTACGAGCTCTTTACGCCCAGTAATTCCGGACAACGCTCGGACCCTACGTATTACCGCGGCTGCTGGCACGTAGTTGGCCGGTCCTTCTTCTGCACATACCGTCACTTGCGCTTCGTCTGTGCTGAAAGAGGTTTACAACCCGAAGGCCGTCATCCCTCACGCGGCGTCGCTGCATCAGGCTTGCGCCCATTGTGCAATATTCCCCACTGCTGCCTCCCGTAGGAGTCTGGGCCGTATCTCAGTCCCAGTGTGGCCGGTCACCCTCTCAGGCCGGCTACCCGTCGTCGCCTTGGTAGGCCATCACCCCACCAACAAGCTGATAGGCCGCGGGCCCATCCCACACCGCAAAAGCTTTCCCCTACCAGGCCATGCGACCAGCAGGGTGTATTCGGTATTAGACCCAGTTTCCCAGGCTTATCCCAAAGTGCAGGGCAGATCACCCACGTGTTACTCACCCGTTCGCCACTCGAGTACCCCCGAAAGGGCCTTTCCGTTCGACTTGCATGTGTTAAGCACGCCGCCAGCGTTCGTCCTGAGCCAGGATCAAACTCTCCAAACAAAAAC","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36769","NCBI_taxonomy_name":"Mycolicibacterium smegmatis MC2 155","NCBI_taxonomy_id":"246196"}}}},"ARO_accession":"3003543","ARO_id":"40145","ARO_name":"Mycolicibacterium smegmatis 16S rRNA (rrsA) mutation conferring resistance to kanamycin A","CARD_short_name":"Msme_16rrsA_KAN","ARO_description":"Point mutations in the helix 44 region of the 16S rRNA rrsA gene of Mycolicibacterium smegmatis can confer resistance to kanamycin A.","ARO_category":{"40277":{"category_aro_accession":"3003666","category_aro_cvterm_id":"40277","category_aro_name":"16s rRNA with mutation conferring resistance to aminoglycoside antibiotics","category_aro_description":"Point mutations in the 16S rRNA of bacteria can confer resistance to aminoglycosides.","category_aro_class_name":"AMR Gene Family"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2088":{"model_id":"2088","model_name":"Mycolicibacterium smegmatis 16S rRNA (rrsB) mutation conferring resistance to streptomycin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"2948":"a503c","3056":"g504c","4828":"c502t","4829":"c506t"},"Curated-R":{"2948":"a503c","3056":"g504c","4828":"c502t","4829":"c506t"},"clinical":{"2948":"a503c","3056":"g504c","4828":"c502t","4829":"c506t"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"41093","param_value":"2700"}},"model_sequences":{"sequence":{"3250":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"NC_008596.1","fmin":"5027947","fmax":"5029475","strand":"+","sequence":"TTTTTGTTTGGAGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGGAAAGGCCCTTTCGGGGGTACTCGAGTGGCGAACGGGTGAGTAACACGTGGGTGATCTGCCCTGCACTTTGGGATAAGCCTGGGAAACTGGGTCTAATACCGAATACACCCTGCTGGTCGCATGGCCTGGTAGGGGAAAGCTTTTGCGGTGTGGGATGGGCCCGCGGCCTATCAGCTTGTTGGTGGGGTGATGGCCTACCAAGGCGACGACGGGTAGCCGGCCTGAGAGGGTGACCGGCCACACTGGGACTGAGATACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCGACGCCGCGTGAGGGATGACGGCCTTCGGGTTGTAAACCTCTTTCAGCACAGACGAAGCGCAAGTGACGGTATGTGCAGAAGAAGGACCGGCCAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGTCCGAGCGTTGTCCGGAATTACTGGGCGTAAAGAGCTCGTAGGTGGTTTGTCGCGTTGTTCGTGAAAACTCACAGCTTAACTGTGGGCGTGCGGGCGATACGGGCAGACTAGAGTACTGCAGGGGAGACTGGAATTCCTGGTGTAGCGGTGGAATGCGCAGATATCAGGAGGAACACCGGTGGCGAAGGCGGGTCTCTGGGCAGTAACTGACGCTGAGGAGCGAAAGCGTGGGGAGCGAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGGTGGGTACTAGGTGTGGGTTTCCTTCCTTGGGATCCGTGCCGTAGCTAACGCATTAAGTACCCCGCCTGGGGAGTACGGCCGCAAGGCTAAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGCGGAGCATGTGGATTAATTCGATGCAACGCGAAGAACCTTACCTGGGTTTGACATGCACAGGACGCCGGCAGAGATGTCGGTTCCCTTGTGGCCTGTGTGCAGGTGGTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTCTCATGTTGCCAGCACGTTATGGTGGGGACTCGTGAGAGACTGCCGGGGTCAACTCGGAGGAAGGTGGGGATGACGTCAAGTCATCATGCCCCTTATGTCCAGGGCTTCACACATGCTACAATGGCCGGTACAAAGGGCTGCGATGCCGTGAGGTGGAGCGAATCCTTTCAAAGCCGGTCTCAGTTCGGATCGGGGTCTGCAACTCGACCCCGTGAAGTCGGAGTCGCTAGTAATCGCAGATCAGCAACGCTGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACGTCATGAAAGTCGGTAACACCCGAAGCCGGTGGCCTAACCCTTGTGGAGGGAGCCGTCGAAGGTGGGATCGGCGATTGGGACGAAGTCGTAACAAGGTAGCCGTACCGGAAGGTGCGGCTGGATCACCTCCTTTCT","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36769","NCBI_taxonomy_name":"Mycolicibacterium smegmatis MC2 155","NCBI_taxonomy_id":"246196"}}}},"ARO_accession":"3003541","ARO_id":"40143","ARO_name":"Mycolicibacterium smegmatis 16S rRNA (rrsB) mutation conferring resistance to streptomycin","CARD_short_name":"Msme_16rrsB_STR","ARO_description":"Point mutations in the helix 44 region of the 16S rRNA rrsB gene of Mycolicibacterium smegmatis can confer resistance to streptomycin.","ARO_category":{"40277":{"category_aro_accession":"3003666","category_aro_cvterm_id":"40277","category_aro_name":"16s rRNA with mutation conferring resistance to aminoglycoside antibiotics","category_aro_description":"Point mutations in the 16S rRNA of bacteria can confer resistance to aminoglycosides.","category_aro_class_name":"AMR Gene Family"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2141":{"model_id":"2141","model_name":"Mycolicibacterium smegmatis 16S rRNA (rrsB) mutation conferring resistance to neomycin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"4840":"t1389a"},"Curated-R":{"4840":"t1389a"},"clinical":{"4840":"t1389a"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"41093","param_value":"2700"}},"model_sequences":{"sequence":{"3249":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"NC_008596.1","fmin":"5027947","fmax":"5029475","strand":"+","sequence":"TTTTTGTTTGGAGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGGAAAGGCCCTTTCGGGGGTACTCGAGTGGCGAACGGGTGAGTAACACGTGGGTGATCTGCCCTGCACTTTGGGATAAGCCTGGGAAACTGGGTCTAATACCGAATACACCCTGCTGGTCGCATGGCCTGGTAGGGGAAAGCTTTTGCGGTGTGGGATGGGCCCGCGGCCTATCAGCTTGTTGGTGGGGTGATGGCCTACCAAGGCGACGACGGGTAGCCGGCCTGAGAGGGTGACCGGCCACACTGGGACTGAGATACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCGACGCCGCGTGAGGGATGACGGCCTTCGGGTTGTAAACCTCTTTCAGCACAGACGAAGCGCAAGTGACGGTATGTGCAGAAGAAGGACCGGCCAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGTCCGAGCGTTGTCCGGAATTACTGGGCGTAAAGAGCTCGTAGGTGGTTTGTCGCGTTGTTCGTGAAAACTCACAGCTTAACTGTGGGCGTGCGGGCGATACGGGCAGACTAGAGTACTGCAGGGGAGACTGGAATTCCTGGTGTAGCGGTGGAATGCGCAGATATCAGGAGGAACACCGGTGGCGAAGGCGGGTCTCTGGGCAGTAACTGACGCTGAGGAGCGAAAGCGTGGGGAGCGAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGGTGGGTACTAGGTGTGGGTTTCCTTCCTTGGGATCCGTGCCGTAGCTAACGCATTAAGTACCCCGCCTGGGGAGTACGGCCGCAAGGCTAAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGCGGAGCATGTGGATTAATTCGATGCAACGCGAAGAACCTTACCTGGGTTTGACATGCACAGGACGCCGGCAGAGATGTCGGTTCCCTTGTGGCCTGTGTGCAGGTGGTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTCTCATGTTGCCAGCACGTTATGGTGGGGACTCGTGAGAGACTGCCGGGGTCAACTCGGAGGAAGGTGGGGATGACGTCAAGTCATCATGCCCCTTATGTCCAGGGCTTCACACATGCTACAATGGCCGGTACAAAGGGCTGCGATGCCGTGAGGTGGAGCGAATCCTTTCAAAGCCGGTCTCAGTTCGGATCGGGGTCTGCAACTCGACCCCGTGAAGTCGGAGTCGCTAGTAATCGCAGATCAGCAACGCTGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACGTCATGAAAGTCGGTAACACCCGAAGCCGGTGGCCTAACCCTTGTGGAGGGAGCCGTCGAAGGTGGGATCGGCGATTGGGACGAAGTCGTAACAAGGTAGCCGTACCGGAAGGTGCGGCTGGATCACCTCCTTTCT","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36769","NCBI_taxonomy_name":"Mycolicibacterium smegmatis MC2 155","NCBI_taxonomy_id":"246196"}}}},"ARO_accession":"3003545","ARO_id":"40147","ARO_name":"Mycolicibacterium smegmatis 16S rRNA (rrsB) mutation conferring resistance to neomycin","CARD_short_name":"Msme_16rrsB_NEO","ARO_description":"Point mutations in the helix 44 region of the 16S rRNA rrsB gene of Mycolicibacterium smegmatis can confer resistance to neomycin.","ARO_category":{"40277":{"category_aro_accession":"3003666","category_aro_cvterm_id":"40277","category_aro_name":"16s rRNA with mutation conferring resistance to aminoglycoside antibiotics","category_aro_description":"Point mutations in the 16S rRNA of bacteria can confer resistance to aminoglycosides.","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2099":{"model_id":"2099","model_name":"Mycolicibacterium smegmatis 16S rRNA (rrsB) mutation conferring resistance to kanamycin A","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"3029":"a1391g","4837":"t1389a"},"Curated-R":{"3029":"a1391g","4837":"t1389a"},"clinical":{"3029":"a1391g","4837":"t1389a"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"41093","param_value":"2700"}},"model_sequences":{"sequence":{"3251":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"NC_008596.1","fmin":"5027947","fmax":"5029475","strand":"+","sequence":"TTTTTGTTTGGAGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGGAAAGGCCCTTTCGGGGGTACTCGAGTGGCGAACGGGTGAGTAACACGTGGGTGATCTGCCCTGCACTTTGGGATAAGCCTGGGAAACTGGGTCTAATACCGAATACACCCTGCTGGTCGCATGGCCTGGTAGGGGAAAGCTTTTGCGGTGTGGGATGGGCCCGCGGCCTATCAGCTTGTTGGTGGGGTGATGGCCTACCAAGGCGACGACGGGTAGCCGGCCTGAGAGGGTGACCGGCCACACTGGGACTGAGATACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCGACGCCGCGTGAGGGATGACGGCCTTCGGGTTGTAAACCTCTTTCAGCACAGACGAAGCGCAAGTGACGGTATGTGCAGAAGAAGGACCGGCCAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGTCCGAGCGTTGTCCGGAATTACTGGGCGTAAAGAGCTCGTAGGTGGTTTGTCGCGTTGTTCGTGAAAACTCACAGCTTAACTGTGGGCGTGCGGGCGATACGGGCAGACTAGAGTACTGCAGGGGAGACTGGAATTCCTGGTGTAGCGGTGGAATGCGCAGATATCAGGAGGAACACCGGTGGCGAAGGCGGGTCTCTGGGCAGTAACTGACGCTGAGGAGCGAAAGCGTGGGGAGCGAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGGTGGGTACTAGGTGTGGGTTTCCTTCCTTGGGATCCGTGCCGTAGCTAACGCATTAAGTACCCCGCCTGGGGAGTACGGCCGCAAGGCTAAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGCGGAGCATGTGGATTAATTCGATGCAACGCGAAGAACCTTACCTGGGTTTGACATGCACAGGACGCCGGCAGAGATGTCGGTTCCCTTGTGGCCTGTGTGCAGGTGGTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTCTCATGTTGCCAGCACGTTATGGTGGGGACTCGTGAGAGACTGCCGGGGTCAACTCGGAGGAAGGTGGGGATGACGTCAAGTCATCATGCCCCTTATGTCCAGGGCTTCACACATGCTACAATGGCCGGTACAAAGGGCTGCGATGCCGTGAGGTGGAGCGAATCCTTTCAAAGCCGGTCTCAGTTCGGATCGGGGTCTGCAACTCGACCCCGTGAAGTCGGAGTCGCTAGTAATCGCAGATCAGCAACGCTGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACGTCATGAAAGTCGGTAACACCCGAAGCCGGTGGCCTAACCCTTGTGGAGGGAGCCGTCGAAGGTGGGATCGGCGATTGGGACGAAGTCGTAACAAGGTAGCCGTACCGGAAGGTGCGGCTGGATCACCTCCTTTCT","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36769","NCBI_taxonomy_name":"Mycolicibacterium smegmatis MC2 155","NCBI_taxonomy_id":"246196"}}}},"ARO_accession":"3003542","ARO_id":"40144","ARO_name":"Mycolicibacterium smegmatis 16S rRNA (rrsB) mutation conferring resistance to kanamycin A","CARD_short_name":"Msme_16rrsB_KAN","ARO_description":"Point mutations in the helix 44 region of the 16S rRNA rrsB gene of Mycolicibacterium smegmatis can confer resistance to kanamycin A.","ARO_category":{"40277":{"category_aro_accession":"3003666","category_aro_cvterm_id":"40277","category_aro_name":"16s rRNA with mutation conferring resistance to aminoglycoside antibiotics","category_aro_description":"Point mutations in the 16S rRNA of bacteria can confer resistance to aminoglycosides.","category_aro_class_name":"AMR Gene Family"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2142":{"model_id":"2142","model_name":"Mycolicibacterium smegmatis 16S rRNA (rrsA) mutation conferring resistance to viomycin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"41093","param_value":"2700"},"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"12984":"g1475a","12985":"g1475t"},"Curated-R":{"12984":"g1475a","12985":"g1475t"},"clinical":{"12984":"g1475a","12985":"g1475t"}}},"model_sequences":{"sequence":{"4143":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"NC_008596.1","fmin":"3823614","fmax":"3825143","strand":"-","sequence":"AGAAAGGAGGTGATCCAGCCGCACCTTCCGGTACGGCTACCTTGTTACGACTTCGTCCCAATCGCCGATCCCACCTTCGACGGCTCCCTCCACAAGGGTTAGGCCACCGGCTTCGGGTGTTACCGACTTTCATGACGTGACGGGCGGTGTGTACAAGGCCCGGGAACGTATTCACCGCAGCGTTGCTGATCTGCGATTACTAGCGACTCCGACTTCACGGGGTCGAGTTGCAGACCCCGATCCGAACTGAGACCGGCTTTGAAAGGATTCGCTCCACCTCACGGCATCGCAGCCCTTTGTACCGGCCATTGTAGCATGTGTGAAGCCCTGGACATAAGGGGCATGATGACTTGACGTCATCCCCACCTTCCTCCGAGTTGACCCCGGCAGTCTCTCACGAGTCCCCACCATAACGTGCTGGCAACATGAGACAAGGGTTGCGCTCGTTGCGGGACTTAACCCAACATCTCACGACACGAGCTGACGACAGCCATGCACCACCTGCACACAGGCCACAAGGGAACCGACATCTCTGCCGGCGTCCTGTGCATGTCAAACCCAGGTAAGGTTCTTCGCGTTGCATCGAATTAATCCACATGCTCCGCCGCTTGTGCGGGCCCCCGTCAATTCCTTTGAGTTTTAGCCTTGCGGCCGTACTCCCCAGGCGGGGTACTTAATGCGTTAGCTACGGCACGGATCCCAAGGAAGGAAACCCACACCTAGTACCCACCGTTTACGGCGTGGACTACCAGGGTATCTAATCCTGTTCGCTCCCCACGCTTTCGCTCCTCAGCGTCAGTTACTGCCCAGAGACCCGCCTTCGCCACCGGTGTTCCTCCTGATATCTGCGCATTCCACCGCTACACCAGGAATTCCAGTCTCCCCTGCAGTACTCTAGTCTGCCCGTATCGCCCGCACGCCCACAGTTAAGCTGTGAGTTTTCACGAACAACGCGACAAACCACCTACGAGCTCTTTACGCCCAGTAATTCCGGACAACGCTCGGACCCTACGTATTACCGCGGCTGCTGGCACGTAGTTGGCCGGTCCTTCTTCTGCACATACCGTCACTTGCGCTTCGTCTGTGCTGAAAGAGGTTTACAACCCGAAGGCCGTCATCCCTCACGCGGCGTCGCTGCATCAGGCTTGCGCCCATTGTGCAATATTCCCCACTGCTGCCTCCCGTAGGAGTCTGGGCCGTATCTCAGTCCCAGTGTGGCCGGTCACCCTCTCAGGCCGGCTACCCGTCGTCGCCTTGGTAGGCCATCACCCCACCAACAAGCTGATAGGCCGCGGGCCCATCCCACACCGCAAAAGCTTTCCCCTACCAGGCCATGCGACCAGCAGGGTGTATTCGGTATTAGACCCAGTTTCCCAGGCTTATCCCAAAGTGCAGGGCAGATCACCCACGTGTTACTCACCCGTTCGCCACTCGAGTACCCCCGAAAGGGCCTTTCCGTTCGACTTGCATGTGTTAAGCACGCCGCCAGCGTTCGTCCTGAGCCAGGATCAAACTCTCCAAACAAAAAC","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36769","NCBI_taxonomy_name":"Mycolicibacterium smegmatis MC2 155","NCBI_taxonomy_id":"246196"}}}},"ARO_accession":"3003546","ARO_id":"40148","ARO_name":"Mycolicibacterium smegmatis 16S rRNA (rrsA) mutation conferring resistance to viomycin","CARD_short_name":"Msme_16rrsA_VIO","ARO_description":"Point mutations in the helix 44 region of the 16S rRNA rrsA gene of Mycolicibacterium smegmatis can confer resistance to viomycin.","ARO_category":{"40278":{"category_aro_accession":"3003667","category_aro_cvterm_id":"40278","category_aro_name":"16s rRNA with mutation conferring resistance to peptide antibiotics","category_aro_description":"Point mutations in the 16S rRNA of bacteria can confer resistance to peptide antibiotics.","category_aro_class_name":"AMR Gene Family"},"35937":{"category_aro_accession":"0000018","category_aro_cvterm_id":"35937","category_aro_name":"viomycin","category_aro_description":"Viomycin sulfate (Viocin) is an polypeptide antibiotic used in the treatment of tuberculosis. It is produced by the actinomycete Streptomyces puniceus and binds to the bacterial ribosome, inhibiting prokaryotic protein synthesis and certain forms of RNA splicing.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2205":{"model_id":"2205","model_name":"MexJ","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"690"}},"model_sequences":{"sequence":{"5274":{"protein_sequence":{"accession":"AAG07065.1","sequence":"MYRHIPLVALSLFSSLFLAACGNGTPPPAAARPAIVVQPQPAGEVSQAFPGEIRARHEPELAFRIGGKVIRRLVEVGERVKKDQPLAELDPQDVRLQLEAARAQVSAAEANLQTVRAEYRRYRTLLDRNLVSHSQFENIQNSYRAGEARLKQIRAEFNVADNQAGYAVLRSPQDGVIASRRVEVGQVVAAGQTVFSLAADGEREVLIGLPEHSFERFRIGQPVSVELWSQRDRRFAGHIRELSPAADPQSRTFAARVAFDDRATPAELGQSARVYVAAAEAVPLSVPLSALTAEAGQAFVWVVEPGSSTLRRQAVRTGPYAEDRVPVLEGLKAGDWVVATGVQVLREGQQVRPIDRANRTVKLAAKE"},"dna_sequence":{"accession":"AE004091.2","fmin":"4119269","fmax":"4120373","strand":"-","sequence":"ATGTACCGCCATATCCCGCTCGTCGCCCTGTCCCTGTTTTCCTCCCTGTTCCTCGCCGCCTGCGGCAACGGCACGCCGCCGCCAGCCGCGGCGCGTCCGGCGATCGTCGTCCAGCCCCAGCCGGCGGGGGAGGTGAGCCAGGCCTTTCCCGGCGAGATCCGCGCCCGCCACGAGCCGGAGCTGGCCTTCCGCATCGGCGGCAAGGTCATCCGCCGGCTGGTGGAAGTCGGCGAGCGGGTAAAGAAGGACCAGCCCCTGGCCGAACTCGATCCCCAGGACGTGCGCCTGCAACTGGAGGCGGCGCGGGCCCAGGTCAGTGCCGCCGAGGCCAACTTGCAGACCGTGCGCGCCGAGTACCGGCGCTACCGCACCTTGCTCGACCGCAACCTGGTCAGCCATTCCCAGTTCGAGAACATCCAGAACAGCTACCGCGCCGGCGAGGCGCGGCTGAAGCAGATCCGCGCCGAATTCAACGTCGCCGACAACCAGGCCGGCTACGCCGTGCTGCGCTCGCCCCAGGATGGCGTGATCGCCAGCCGGCGCGTCGAGGTGGGCCAGGTGGTGGCGGCCGGACAGACGGTCTTCAGCCTGGCCGCCGACGGCGAACGCGAGGTGCTGATCGGCCTGCCGGAACACAGCTTCGAACGTTTCCGCATCGGCCAGCCGGTGTCGGTCGAACTCTGGTCGCAACGCGACAGACGCTTCGCCGGGCATATCCGCGAGCTCTCGCCCGCGGCCGATCCGCAATCGCGTACCTTCGCCGCCCGGGTGGCCTTCGACGACCGCGCGACTCCGGCCGAACTGGGCCAGAGCGCGCGGGTCTACGTCGCCGCCGCCGAGGCGGTGCCGTTATCGGTTCCCTTGTCGGCGCTGACCGCAGAGGCCGGCCAGGCGTTCGTCTGGGTGGTCGAGCCGGGCAGCTCGACCCTGCGCCGGCAGGCGGTGCGCACCGGTCCCTATGCCGAGGACCGGGTGCCGGTGCTCGAAGGCCTGAAGGCTGGCGACTGGGTGGTGGCCACCGGGGTCCAGGTGCTTCGCGAAGGGCAGCAGGTGCGTCCGATCGACCGGGCCAACCGCACGGTGAAACTGGCGGCCAAGGAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36804","NCBI_taxonomy_name":"Pseudomonas aeruginosa PAO1","NCBI_taxonomy_id":"208964"}}}},"ARO_accession":"3003692","ARO_id":"40340","ARO_name":"MexJ","CARD_short_name":"MexJ","ARO_description":"MexJ is the membrane fusion protein of the MexJK multidrug efflux protein.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2206":{"model_id":"2206","model_name":"MexK","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1900"}},"model_sequences":{"sequence":{"4651":{"protein_sequence":{"accession":"AAG07064.1","sequence":"MSFNLSAWALQNRQIVLYLMILLGAVGALSYSKLGQSEDPPFTFKAMVVQTNWPGASAEEVARQVTERIEKKLMETGDYDRIVSFSRPGVSQVTFMAREDIHSSEIPELWYQIRKKISDIRATLPQSIQGPFFNDEFGTTYGNIYALTGKGFDYAVMKDYADRLQLQLQRIRNVGKVELIGLQDEKIWIDLSNTKLATLGLPLAAVQKALEEQNAVASSGFFETASDRVQLRVSGRFDSVEEIRDFPIRVGDRTFRIGDVAEVRRGFNDPPAPRMRFMGEDAIGLAVAMKPGGDILVLGKALETEFARLQQSLPAGLELRKVSDQPAAVRTGVGEFIRVLAEALVIVLLVSFFSLGLRTGLVVALSIPLVLAMTFAAMHYFGIGLHKISLGALVLALGLLVDDAIIAVEMMAVKMEQGYDRLKAASFAWTSTAFPMLTGTLITAAGFLPIATAQSGTGEYTRSLFQVVTIALVVSWFAAVVFVPYLGAKLLPDLARLHAQKHGGSADGYDPYATAFYQRFRRLVEWCVRYRKTVIVLTLAAFVGALLLFRLVPQQFFPPSARLELLLDIKLAEGASLRSTGEEVQRLEKMLQGHDGIDNYVAYVGTGSPRFYLPLDQQLPAASFAQVVVLAKDLESREALRKWLIERMNEDFPHLRSRISRLENGPPVGYPVQFRVSGEDIPQVRELARKVADKMRENPHVVNVHLDWEEPSKVVYLSIDQERARALGVSTASLSQFLQSALTGSHVSFFREDNELIEILLRGTEQERRDLSLLPSLAVPTENGRSVALSQIATLEYGFEEGIIWHRNRLPTVTVRADIYDDSLPATLVAQIAPTLEPIRAELPDGYLLEVGGTVEDAAKGQSSVNAGVPLFIVVVLSLLMVQLRSFSRMAMVFLTAPLGLIGVTLFLLLFRQPFGFVAMLGTIALAGMIMRNSVILVDQIEQDISHGLDRWHAIIEATVRRFRPIVLTALAAVLAMIPLSRSVFFGPMAVAIMGGLIVATVLTLLFLPALYAAWFRVKKDEARA"},"dna_sequence":{"accession":"AE004091.2","fmin":"4116187","fmax":"4119265","strand":"-","sequence":"ATGTCCTTCAACCTTTCCGCCTGGGCGTTGCAGAATCGCCAGATCGTCCTGTACCTGATGATCCTGCTTGGCGCGGTCGGCGCGCTGTCCTACAGCAAGCTGGGGCAGAGCGAAGACCCGCCGTTCACCTTCAAGGCCATGGTGGTGCAGACCAACTGGCCGGGCGCCAGCGCCGAAGAGGTGGCCCGGCAGGTCACCGAGCGTATCGAGAAGAAGCTGATGGAAACCGGCGACTACGATCGCATCGTGTCCTTCTCCCGCCCCGGCGTCTCGCAGGTGACCTTCATGGCCCGCGAGGACATCCATTCCAGCGAGATCCCCGAACTCTGGTACCAGATCCGCAAGAAGATCAGCGACATTCGCGCCACCTTGCCGCAAAGCATCCAGGGCCCGTTCTTCAACGACGAGTTCGGCACCACCTACGGCAACATCTATGCGCTCACCGGCAAGGGCTTCGACTACGCGGTGATGAAGGACTATGCCGACCGCCTGCAACTGCAATTGCAGCGGATCAGGAACGTCGGCAAGGTCGAGCTGATCGGCCTGCAGGACGAGAAGATCTGGATCGACCTGTCCAACACCAAGCTGGCCACCCTCGGCCTGCCCCTGGCGGCGGTACAGAAGGCGCTGGAGGAACAGAACGCGGTGGCCTCCTCCGGGTTCTTCGAGACCGCCAGCGACCGCGTGCAGTTGCGCGTTTCCGGGCGTTTCGATTCGGTGGAGGAGATCCGCGACTTCCCCATCCGCGTCGGCGACCGCACCTTCCGCATCGGCGACGTGGCCGAGGTTCGCCGCGGCTTCAACGATCCGCCGGCGCCGCGCATGCGCTTCATGGGCGAGGACGCCATCGGCCTGGCGGTAGCGATGAAGCCGGGCGGCGACATCCTGGTGCTGGGCAAGGCCCTGGAAACCGAGTTCGCCCGCCTGCAGCAGTCGCTGCCGGCCGGACTGGAACTGCGCAAGGTGTCCGACCAGCCGGCGGCGGTACGTACCGGGGTCGGCGAGTTCATCCGGGTGCTGGCCGAGGCGCTGGTGATCGTCCTGCTGGTGAGCTTCTTCTCCCTCGGCCTGCGCACCGGCCTGGTGGTGGCGCTGTCGATCCCGCTGGTGCTGGCGATGACCTTCGCCGCCATGCATTACTTCGGCATCGGCCTGCACAAGATCTCCCTCGGCGCCCTGGTGCTGGCGCTGGGATTACTGGTGGACGACGCGATCATCGCGGTGGAGATGATGGCGGTGAAGATGGAGCAGGGCTACGACCGCCTCAAGGCGGCCAGCTTCGCCTGGACCAGCACCGCCTTCCCGATGCTCACCGGCACCCTGATCACCGCCGCCGGCTTCCTGCCGATCGCCACCGCGCAGTCCGGCACCGGCGAATACACCCGCTCGTTGTTCCAGGTGGTGACCATCGCCCTGGTGGTCTCCTGGTTCGCCGCGGTGGTCTTCGTTCCCTACCTGGGGGCCAAGCTGCTGCCGGACCTGGCCAGGTTGCACGCGCAGAAGCACGGCGGCAGCGCCGATGGCTACGATCCCTATGCTACGGCCTTCTACCAGCGCTTCCGGCGTCTGGTGGAGTGGTGCGTGCGCTACCGCAAGACGGTGATCGTCCTGACTCTCGCGGCCTTCGTCGGCGCGCTGCTGCTGTTCCGCCTGGTGCCGCAGCAGTTCTTCCCGCCCTCGGCGCGCCTGGAGCTGCTGCTGGACATCAAGCTGGCGGAGGGTGCCTCACTGCGCTCTACCGGCGAGGAAGTCCAGCGCCTGGAAAAAATGCTGCAGGGCCATGACGGCATCGACAACTACGTGGCCTACGTCGGCACCGGCTCGCCCCGCTTCTACCTGCCGCTGGACCAGCAATTGCCGGCGGCCAGCTTCGCCCAGGTGGTGGTGCTGGCCAAGGACCTGGAGAGCCGCGAGGCGCTGCGCAAGTGGCTGATCGAGCGGATGAACGAGGACTTCCCGCACCTGCGCAGCCGCATCAGTCGCCTGGAGAACGGGCCGCCGGTGGGCTATCCGGTGCAGTTCCGGGTTTCCGGCGAGGACATCCCGCAGGTTCGCGAACTGGCGCGCAAGGTCGCCGACAAGATGCGCGAGAACCCGCACGTGGTGAATGTGCACCTGGATTGGGAAGAGCCGAGCAAGGTGGTGTACCTGAGCATCGACCAGGAGCGCGCCCGTGCCCTGGGGGTGAGCACCGCCAGCCTGTCGCAGTTCCTGCAGAGCGCGCTGACCGGCTCGCACGTGAGCTTCTTCCGCGAAGACAACGAGCTGATCGAGATCCTCCTGCGCGGCACCGAGCAGGAGCGTCGTGACCTGTCGTTGCTGCCGAGCCTGGCGGTGCCGACCGAGAATGGCCGGAGCGTGGCGCTGTCGCAGATCGCTACGCTCGAATACGGCTTCGAAGAGGGCATCATCTGGCACCGCAACCGCCTGCCGACGGTCACCGTGCGCGCCGATATCTACGACGATTCGCTGCCGGCGACCCTGGTCGCGCAGATCGCCCCGACCCTGGAACCGATCCGCGCCGAGTTGCCGGACGGCTACCTGCTGGAGGTGGGCGGCACGGTGGAGGACGCGGCGAAGGGCCAGAGTTCGGTGAACGCCGGCGTGCCGCTGTTCATCGTGGTGGTGTTGAGCCTGCTGATGGTGCAGTTGCGCAGCTTCTCGCGGATGGCGATGGTATTCCTCACCGCACCGCTGGGCCTGATCGGCGTGACCCTGTTCCTGCTGCTGTTCCGCCAGCCGTTCGGCTTCGTGGCGATGCTCGGGACCATCGCCCTGGCCGGCATGATCATGCGCAACTCGGTGATCCTGGTGGACCAGATCGAACAGGACATCAGCCATGGACTGGATCGCTGGCACGCCATCATCGAGGCTACCGTGCGGCGTTTCAGGCCCATCGTGCTGACCGCGCTGGCGGCGGTGCTGGCGATGATCCCGCTGTCGCGCAGCGTGTTCTTCGGGCCGATGGCGGTGGCGATCATGGGCGGGCTGATCGTCGCCACCGTGCTCACCCTGCTGTTCCTGCCGGCGCTCTATGCCGCCTGGTTCCGCGTGAAGAAGGACGAGGCGCGGGCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36804","NCBI_taxonomy_name":"Pseudomonas aeruginosa PAO1","NCBI_taxonomy_id":"208964"}}}},"ARO_accession":"3003693","ARO_id":"40341","ARO_name":"MexK","CARD_short_name":"MexK","ARO_description":"MexK is the inner membrane resistance-nodulation-cell division (RND) transporter in the MexJK multidrug efflux protein.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2207":{"model_id":"2207","model_name":"MexV","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"650"}},"model_sequences":{"sequence":{"3464":{"protein_sequence":{"accession":"AAG07762.1","sequence":"MLLRRMLIMLAAVIAVVAILAGYKVYSIRQQIALFSAPKPPISVTASLAEKRPWQSRLPAIGSLKAFQGVTLTAEVSGTVRDVLFLSGDQVKLDQPLIQLESDVEEATLRTAEADLGLARAEYQRGRELIGSKAISKSEFDRLAAQWAKTSATVAELKAALAKKRVLAPFAGTIGIRQVDVGDYVSPGTPIATLQDLSTLLLDFHLPEQDFPLLSRGQLVKVRVAAYPAQVFDAEIAAINPKVDNETRNLQVRAALENPDGKLLPGMFANLEVMLPGEEQRVVVPETAITFTLYGDSIYVVGQKKDEQGQVSKDDKGQPQQVVERRFVRIGERREGLAVVLEGLEGGEQVVTSGQLKLDNGAAVAIVAERDLQQEH"},"dna_sequence":{"accession":"AE004091.2","fmin":"4903465","fmax":"4904596","strand":"+","sequence":"ATGTTGCTCCGCCGCATGTTGATCATGCTCGCCGCGGTGATCGCCGTGGTGGCGATTCTCGCCGGCTACAAGGTCTACTCCATCCGTCAGCAGATCGCCCTTTTCAGCGCACCGAAACCGCCGATCAGCGTGACCGCCAGCCTGGCCGAAAAGCGTCCCTGGCAGAGCCGCCTGCCAGCCATCGGCAGCCTCAAGGCATTCCAGGGCGTGACCCTCACCGCCGAAGTCTCCGGCACGGTACGCGACGTACTGTTCCTTTCCGGCGACCAGGTGAAGCTGGACCAACCGCTGATCCAGTTGGAAAGCGACGTCGAGGAAGCCACCCTGCGCACTGCCGAGGCCGATCTCGGCCTGGCCAGGGCCGAGTACCAGCGCGGCCGCGAACTGATCGGCAGCAAGGCCATCTCGAAAAGCGAATTCGATCGTCTCGCCGCGCAGTGGGCCAAGACCAGCGCCACCGTCGCCGAGCTGAAGGCGGCGCTGGCGAAGAAGCGCGTGCTCGCGCCCTTCGCCGGGACCATCGGCATCCGCCAGGTGGACGTCGGCGACTACGTCTCGCCCGGGACGCCGATCGCCACCTTGCAGGACCTTTCCACCCTGCTCCTGGATTTCCACCTGCCCGAGCAGGACTTCCCCCTGCTCAGCCGCGGCCAACTGGTGAAGGTCCGGGTCGCCGCCTACCCCGCCCAGGTGTTCGACGCCGAGATCGCCGCCATCAACCCCAAGGTCGACAACGAGACCCGCAACCTGCAGGTCCGCGCTGCCCTGGAGAACCCGGACGGCAAGCTGCTGCCGGGCATGTTCGCCAACCTCGAGGTGATGTTGCCTGGCGAGGAACAACGCGTCGTGGTCCCGGAGACGGCGATCACCTTCACCCTCTACGGCGACTCGATCTACGTCGTCGGGCAGAAGAAGGACGAGCAGGGCCAGGTGTCGAAGGATGACAAGGGCCAGCCGCAACAGGTCGTCGAGCGCCGCTTCGTCAGGATCGGCGAACGCCGCGAAGGCCTGGCGGTGGTGCTCGAAGGCCTTGAGGGCGGCGAGCAGGTAGTGACTTCCGGGCAACTGAAGCTCGACAACGGCGCCGCGGTGGCCATCGTCGCCGAGCGGGACCTCCAGCAAGAGCACTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36804","NCBI_taxonomy_name":"Pseudomonas aeruginosa PAO1","NCBI_taxonomy_id":"208964"}}}},"ARO_accession":"3003030","ARO_id":"39464","ARO_name":"MexV","CARD_short_name":"MexV","ARO_description":"MexV is the membrane fusion protein of the MexVW-OprM multidrug efflux complex.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35963":{"category_aro_accession":"0000045","category_aro_cvterm_id":"35963","category_aro_name":"acriflavine","category_aro_description":"Acriflavine is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"43746":{"category_aro_accession":"3005386","category_aro_cvterm_id":"43746","category_aro_name":"disinfecting agents and antiseptics","category_aro_description":"Disinfectants that can also interact with antimicrobial resistance mechanisms, e.g. molecule efflux, and thus are the targets of disinfectant resistance.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2208":{"model_id":"2208","model_name":"MexW","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1900"}},"model_sequences":{"sequence":{"3462":{"protein_sequence":{"accession":"AAG07763.1","sequence":"MAFTDPFIRRPVLASVVSLLIVLLGMQAFSKLVIREYPQMENALITVTTLYAGANAETIQGYITQPLQQSLASAEGIDYMTSVSRQNYSTISIYARIGANTDRLVTELLAKSNEVKSQLPPDAEDPVLQKEAADASALMYISFYSEQMNNPQITDYLSRVIQPKLATLPGIAEAEILGNQVFAMRLWLDPVKMAAFGVTAGEINQAVQQYNFLAAAGEVKGQLVVTSVNASTDLKSPQAFAAIPVKTDGDRRVLMGDVARVELGAASYDAISSFNGIPSVYIGIKGTPSANPLDVIKEVRAKMPELEEQLPPNLKVSIAYDATRFIQASIDEVVKTLGEAVLIVIVVVFLFLGAFRSVLIPVVTIPLSMIGVLFFMQAMGYSINLLTLLAMVLAIGLVVDDAIVVVENIHRHIEEGKPPFEAALEGAREIAVPVVSMTITLAAVYAPIGFLTGLTGALFKEFAFTLAGAVIISGIVALTLSPMMCSRLLRHEENPSGLAHRLDLIFEGLKQRYQRALHGTLDTRPVVLVFAVLVLALIPVLLMFTKKELAPEEDQGIVFLMTNSPQTANLDYLNRYTAEFEGIFRSFPEYYSAFQINGYNGVQAGIGGMLLKPWDEREKSQMELLHAVQAKLNEIPGVQIFAFNLPSLPGTGEGLPFQFVLNTANDYESLLQVAQRVKQRASESGKFAFLDLDLAFDKPELVVDIDREKAAQMGVSMQDLGVALASLLGEGEINRFTIDGRSYKVIAQVERPYRDNPGWLGSYYVKSRNGQLVALSTLIETHERARPRQLNQFQQLNSAIISGFPIVSMGEAIETVQQIAREEAPRGFAVDYAGASRQYVQEGSALLVTFGLALAIIFLVLAAQFESFRDPLVIMVTVPLSICGALIPLFLGVSSLNIYTQVGLVTLIGLISKHGILIVEFANQLRHEQGLGRREAIEQAAAIRLRPVLMTTAAMVLGVIPLILATGAGAVSRFDIGIVIATGMSVGTLFTLFVLPCIYTLVARPDAPPGVTQAANAH"},"dna_sequence":{"accession":"NC_002516.2","fmin":"4904646","fmax":"4907703","strand":"+","sequence":"ATGGCTTTTACCGATCCGTTCATCCGTCGTCCGGTCCTGGCGAGCGTGGTCAGCCTGCTGATCGTCCTGCTCGGCATGCAGGCCTTCAGCAAGCTGGTGATCCGCGAGTATCCGCAAATGGAGAACGCGCTGATCACGGTGACCACGCTCTACGCCGGCGCCAACGCGGAAACCATCCAGGGCTACATCACCCAGCCGCTGCAGCAGAGCCTGGCCAGCGCCGAAGGCATCGACTACATGACCTCGGTGAGCCGGCAGAACTATTCGACCATCTCCATCTACGCGCGGATCGGCGCCAATACCGATCGCCTGGTCACCGAGCTGCTGGCCAAGTCCAACGAAGTGAAGAGCCAGCTGCCGCCGGACGCCGAGGACCCGGTGCTGCAGAAGGAGGCCGCGGACGCCTCGGCGCTGATGTACATCAGCTTCTACAGCGAGCAGATGAACAACCCGCAGATCACCGACTACCTGTCGCGGGTGATCCAGCCCAAGCTGGCGACCCTGCCCGGTATCGCCGAGGCGGAGATCCTCGGCAACCAGGTGTTCGCCATGCGCCTGTGGCTGGACCCGGTGAAGATGGCCGCGTTCGGCGTCACCGCCGGCGAGATCAACCAGGCGGTGCAGCAGTACAACTTCCTCGCCGCCGCCGGCGAGGTGAAGGGCCAGTTGGTGGTCACCAGCGTCAATGCTTCCACCGACCTCAAGTCGCCCCAGGCCTTCGCCGCCATCCCGGTGAAGACCGACGGCGACCGCCGGGTGCTGATGGGTGATGTCGCACGGGTCGAACTGGGCGCCGCCAGCTACGACGCGATCAGTTCGTTCAATGGGATTCCCTCGGTCTACATCGGCATCAAGGGCACGCCCAGCGCCAACCCGCTGGACGTGATCAAGGAAGTGCGGGCGAAGATGCCCGAACTGGAAGAGCAATTGCCGCCCAACCTCAAGGTGTCCATCGCCTACGACGCCACGCGCTTCATTCAGGCCTCCATCGATGAAGTGGTGAAGACCCTCGGCGAGGCGGTGCTGATCGTCATCGTGGTGGTGTTCCTGTTCCTCGGCGCGTTCCGTTCGGTACTGATCCCGGTGGTGACCATTCCGCTGTCGATGATCGGCGTATTGTTCTTCATGCAGGCCATGGGCTACTCGATCAACCTGCTGACCCTGCTGGCGATGGTCCTGGCCATCGGCCTGGTGGTGGACGACGCGATCGTGGTGGTGGAAAACATCCACCGCCACATCGAGGAGGGCAAGCCGCCCTTCGAGGCTGCCCTGGAGGGCGCGCGGGAGATCGCCGTACCGGTGGTCAGCATGACCATCACCCTCGCCGCGGTCTACGCGCCGATCGGCTTCCTCACCGGCCTCACCGGCGCCCTGTTCAAGGAGTTCGCCTTCACCCTGGCCGGCGCGGTGATCATTTCCGGGATCGTCGCCCTGACCCTGTCGCCGATGATGTGCTCGCGCCTGTTGCGCCACGAGGAGAATCCCTCGGGCCTGGCGCATCGCCTCGACCTGATCTTCGAGGGCCTGAAGCAACGCTACCAGCGCGCCCTCCACGGCACCCTGGACACCCGTCCGGTGGTCCTGGTGTTCGCCGTGCTGGTACTGGCGCTGATCCCGGTACTGCTGATGTTCACCAAGAAGGAGCTGGCGCCGGAAGAGGACCAGGGCATCGTGTTCCTCATGACCAACTCGCCGCAAACCGCCAACCTCGACTACCTGAATCGCTACACCGCCGAGTTCGAAGGCATCTTCCGCAGCTTCCCGGAGTATTACTCGGCGTTCCAGATCAACGGCTACAACGGCGTCCAGGCCGGCATCGGCGGCATGCTGCTCAAGCCCTGGGACGAACGCGAAAAGAGCCAGATGGAATTGCTCCATGCGGTGCAGGCGAAGCTCAACGAGATTCCCGGCGTGCAGATCTTCGCCTTCAACCTGCCGTCGCTACCGGGCACCGGCGAGGGCCTGCCATTCCAGTTCGTGCTCAACACCGCCAACGACTACGAGTCGCTGCTGCAAGTGGCGCAACGGGTGAAGCAGCGCGCCAGCGAGTCCGGCAAGTTCGCCTTCCTCGATCTCGACCTGGCGTTCGACAAACCCGAGCTGGTGGTCGACATCGACCGCGAGAAGGCCGCGCAGATGGGCGTCTCCATGCAGGACCTGGGGGTGGCGCTGGCCAGCCTGCTCGGCGAGGGCGAGATCAACCGCTTCACCATCGACGGGCGCAGCTACAAGGTCATCGCCCAGGTCGAACGCCCCTATCGCGACAATCCCGGCTGGCTCGGCAGCTACTACGTGAAGAGCCGCAACGGCCAACTGGTCGCCCTCTCGACCCTGATCGAGACCCACGAACGGGCACGGCCACGGCAACTGAACCAGTTCCAGCAGCTCAACTCGGCGATCATCTCCGGCTTCCCCATCGTCAGCATGGGCGAGGCCATCGAGACGGTTCAGCAGATCGCCCGCGAGGAAGCCCCGCGTGGCTTCGCCGTCGACTACGCCGGCGCTTCCCGGCAATACGTGCAGGAAGGCAGCGCATTGCTGGTCACCTTCGGACTGGCCCTGGCGATCATCTTCCTGGTCCTCGCCGCACAGTTCGAAAGCTTCCGCGATCCGCTGGTGATCATGGTCACCGTGCCGCTGTCGATCTGCGGTGCGCTGATACCGCTGTTCCTCGGCGTGTCGAGCCTGAACATCTATACCCAGGTCGGCCTGGTGACCCTGATCGGCCTGATCAGCAAACACGGCATCCTGATCGTCGAGTTCGCCAACCAGTTGCGCCACGAACAGGGGCTGGGGCGTCGCGAGGCCATCGAGCAGGCCGCCGCGATCCGCCTGCGGCCAGTACTGATGACCACCGCGGCGATGGTGCTCGGGGTGATCCCGCTGATCCTCGCCACCGGCGCCGGGGCGGTCAGTCGCTTCGACATCGGCATCGTGATCGCGACCGGCATGTCGGTGGGCACCCTCTTCACCCTGTTCGTCCTGCCGTGCATCTACACCCTGGTGGCCAGGCCGGATGCCCCGCCAGGCGTGACGCAAGCGGCAAACGCACACTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36804","NCBI_taxonomy_name":"Pseudomonas aeruginosa PAO1","NCBI_taxonomy_id":"208964"}}}},"ARO_accession":"3003031","ARO_id":"39465","ARO_name":"MexW","CARD_short_name":"MexW","ARO_description":"MexW is the RND-type membrane protein of the efflux complex MexVW-OprM.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35963":{"category_aro_accession":"0000045","category_aro_cvterm_id":"35963","category_aro_name":"acriflavine","category_aro_description":"Acriflavine is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"43746":{"category_aro_accession":"3005386","category_aro_cvterm_id":"43746","category_aro_name":"disinfecting agents and antiseptics","category_aro_description":"Disinfectants that can also interact with antimicrobial resistance mechanisms, e.g. molecule efflux, and thus are the targets of disinfectant resistance.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2213":{"model_id":"2213","model_name":"opmE","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"850"}},"model_sequences":{"sequence":{"3407":{"protein_sequence":{"accession":"BAE06009.1","sequence":"MKPYLRSSLSALILLGGCAAVGPDYAPPSASAPASFGAMPAGIDGSGVEIEWWRGFDEPALESLIQRALAANLDIALAGARLDEAKALLRENREEFLPRGGPAFDYQARRRGEVETPAGQQRDIETYRGALDASWEIDLFGRVRRSVEAAEAQAGSREALLRNVQASVAATVAMSWFQLQGIEAELAVVHDIAGNQRDSLEMVERLVSAGSAHEFDRLRAEALLHNVEAAVPDLERRRAATRNALAVLLAEAPQAFSPPVARASGERLTLRTLGVGDPAGLLARRADIAAAERNLAAATARIGVETAGLYPQVEVRGSIGLVAGNLDALDESGTSFNVLNPVIRWALLDRGRVWARIAASEARAQEALILYDRTVLRALQETDDAFNGYGAAADRLRLRLLEATANREAARLARERFVQGDGEYLDVLEAERSDYLSRRALSIARTEQRLAVVGIYKALGGGWEACAGARRCGVATDDTSPGVARQRDSRS"},"dna_sequence":{"accession":"AB219524.1","fmin":"4334","fmax":"5810","strand":"+","sequence":"ATGAAGCCATACCTGCGGTCTTCGTTGAGCGCGCTGATCCTGCTGGGCGGCTGTGCCGCGGTGGGGCCCGACTATGCGCCGCCGAGCGCGTCCGCACCGGCCAGCTTCGGCGCGATGCCGGCGGGTATCGATGGCAGTGGCGTGGAGATCGAGTGGTGGCGCGGGTTCGACGAGCCAGCCCTGGAGTCTCTGATCCAGCGGGCGCTCGCGGCGAACCTCGACATCGCCCTTGCCGGCGCGCGCCTGGACGAAGCGAAGGCGCTGCTGCGCGAGAACCGCGAAGAGTTCCTGCCGCGCGGCGGCCCGGCGTTCGATTACCAGGCCCGGCGGCGCGGCGAGGTGGAAACACCGGCCGGCCAGCAGCGCGACATCGAGACCTATCGCGGCGCGCTGGATGCTTCCTGGGAAATCGACCTGTTCGGCCGGGTGCGGCGCTCGGTGGAGGCCGCCGAGGCGCAGGCGGGCTCGCGCGAGGCCCTGCTGCGCAACGTGCAGGCGAGCGTCGCGGCTACGGTTGCCATGTCCTGGTTCCAGCTACAGGGCATCGAGGCCGAACTTGCGGTGGTCCATGACATCGCCGGCAACCAGCGCGACAGCCTGGAGATGGTCGAACGCCTGGTCAGCGCCGGCTCCGCCCACGAGTTCGACCGGTTGCGCGCCGAAGCGTTATTGCACAACGTCGAGGCGGCCGTGCCCGACCTCGAACGGCGCCGCGCCGCCACCCGCAATGCGCTGGCCGTTCTCCTCGCGGAAGCCCCGCAGGCCTTCAGCCCGCCGGTCGCCCGTGCCTCCGGGGAAAGGCTGACGCTCCGCACCCTCGGGGTCGGCGACCCGGCGGGACTGCTGGCGCGTCGCGCTGACATCGCCGCGGCCGAACGCAACCTGGCGGCCGCGACCGCACGTATCGGCGTCGAGACCGCGGGGCTGTATCCGCAGGTCGAGGTACGCGGCTCGATCGGCCTGGTCGCCGGCAATCTCGATGCTTTGGACGAGAGTGGTACGTCCTTCAACGTCCTGAACCCGGTGATTCGCTGGGCGTTACTCGACCGCGGTCGCGTGTGGGCGCGGATCGCCGCCAGCGAAGCCCGTGCGCAGGAGGCATTGATCCTCTACGACCGGACGGTACTGCGCGCCCTGCAGGAGACCGATGATGCCTTCAACGGCTATGGCGCTGCCGCTGACAGGCTCCGCCTGCGCCTGCTCGAGGCGACGGCCAATCGCGAGGCGGCGCGCCTGGCCCGGGAGCGCTTCGTCCAGGGGGACGGCGAGTACCTGGACGTGCTCGAGGCGGAACGCTCGGACTACCTCAGCCGGCGCGCATTGAGCATCGCGCGCACCGAGCAGCGCCTTGCCGTCGTGGGTATCTACAAGGCGCTGGGGGGTGGCTGGGAGGCCTGCGCGGGGGCGCGGCGCTGTGGCGTGGCTACCGACGATACCTCTCCAGGCGTGGCACGGCAGCGCGACAGTCGCTCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3003700","ARO_id":"40352","ARO_name":"opmE","CARD_short_name":"opmE","ARO_description":"opmE is an outer membrane factor protein that is part of the multidrug efflux pump MexPQ-OpmE.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35963":{"category_aro_accession":"0000045","category_aro_cvterm_id":"35963","category_aro_name":"acriflavine","category_aro_description":"Acriflavine is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36309":{"category_aro_accession":"3000170","category_aro_cvterm_id":"36309","category_aro_name":"imipenem","category_aro_description":"Imipenem is a broad-spectrum antibiotic and is usually taken with cilastatin, which prevents hydrolysis of imipenem by renal dehydropeptidase-I. It is resistant to hydrolysis by most other beta-lactamases. Notable exceptions are the KPC beta-lactamases and Ambler Class B enzymes.","category_aro_class_name":"Antibiotic"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36595":{"category_aro_accession":"3000456","category_aro_cvterm_id":"36595","category_aro_name":"thiamphenicol","category_aro_description":"Derivative of Chloramphenicol. The nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3).","category_aro_class_name":"Antibiotic"},"37626":{"category_aro_accession":"3001227","category_aro_cvterm_id":"37626","category_aro_name":"kitasamycin","category_aro_description":"Kitasamycin is a macrolide antibiotic and is produced by Streptoverticillium kitasatoense. The drug has antimicrobial activity against a wide spectrum of pathogens.","category_aro_class_name":"Antibiotic"},"40353":{"category_aro_accession":"3003701","category_aro_cvterm_id":"40353","category_aro_name":"rokitamycin","category_aro_description":"Rokitamycin is a macrolide antibiotic. Synthesized from strains of Streptomyces kitasatoensis.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"43746":{"category_aro_accession":"3005386","category_aro_cvterm_id":"43746","category_aro_name":"disinfecting agents and antiseptics","category_aro_description":"Disinfectants that can also interact with antimicrobial resistance mechanisms, e.g. molecule efflux, and thus are the targets of disinfectant resistance.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2216":{"model_id":"2216","model_name":"mexM","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"650"}},"model_sequences":{"sequence":{"3409":{"protein_sequence":{"accession":"BAE06005.1","sequence":"MQALRSGGGRVLVGVLAAGLVAFGGWAWLGGDAGAKAAPAPARVPVIVARVERRDVEQQVSGIGTVTSLHNVVIRTQIDGQLTRLLVSEGQMVEAGELLATIDDRAVVAALEQAQASRASNQAQLKSAEQDLQRYRSLYAERAVSRQLLDQQQATVDQLRATLKANDATINAERVRLSYTRITSPVSGKVGIRNVDVGNLVRVGDSLGLFSVTQIAPISVVFSLQQEQLLQLQALLGGEAAVRAYSRDGGSALGEGRLLTIDNQIDSSTGTIRVRASFDNRQARLWPGQFVAVSLHTGVRRDQLVLSSKAVRRGLEGNFVYRVADDRVEAVPVRVLQDIDGLSVVEGLASGDQVVVDGHSRLMPGALVDIQEPRPSLAQATERRP"},"dna_sequence":{"accession":"AB219523.1","fmin":"21","fmax":"1179","strand":"+","sequence":"ATGCAGGCGTTGCGCAGTGGTGGGGGACGGGTCCTGGTGGGCGTGCTGGCGGCGGGCCTGGTCGCCTTCGGCGGTTGGGCATGGCTCGGCGGCGACGCCGGGGCGAAGGCGGCGCCCGCGCCGGCCAGGGTCCCGGTGATCGTGGCGCGGGTGGAGCGGCGCGACGTCGAGCAACAGGTCAGCGGCATCGGCACGGTGACTTCGTTGCACAACGTGGTGATCCGCACCCAGATCGACGGCCAGTTGACCCGCCTGCTGGTGAGCGAAGGGCAGATGGTCGAGGCGGGCGAGTTACTGGCGACCATCGATGACCGCGCCGTCGTCGCCGCGCTGGAGCAGGCGCAGGCCTCCAGGGCGAGCAACCAGGCCCAGCTGAAATCCGCCGAGCAGGACCTGCAACGCTACCGCAGCCTGTATGCCGAGCGTGCGGTGTCACGCCAACTGCTGGACCAGCAGCAGGCGACGGTCGACCAGTTGCGCGCGACCCTGAAGGCCAACGATGCCACCATCAACGCCGAGCGGGTGCGCCTGTCCTACACCCGGATCACCTCGCCGGTATCCGGCAAGGTCGGTATCCGCAACGTCGATGTCGGCAACCTGGTGCGGGTCGGCGACAGTCTCGGCCTGTTCAGCGTGACCCAGATCGCACCGATCTCCGTAGTCTTCTCCCTGCAACAGGAACAGTTGCTCCAGTTGCAGGCGCTGCTCGGCGGCGAGGCGGCGGTGCGCGCCTACAGCCGCGACGGCGGGAGCGCGCTGGGCGAGGGCCGGTTGCTGACCATCGACAACCAGATCGACAGTTCCACCGGCACCATCCGCGTGCGCGCCTCCTTCGATAACCGCCAGGCCCGGCTCTGGCCCGGGCAGTTCGTCGCGGTGAGCCTGCACACCGGGGTCCGGCGCGACCAGTTGGTGCTGTCGAGCAAGGCGGTGCGCCGCGGCCTGGAGGGCAATTTCGTCTACCGGGTCGCCGACGACCGGGTCGAGGCGGTGCCGGTGCGGGTGCTCCAGGACATCGACGGCCTCAGTGTGGTGGAAGGCCTGGCCAGCGGTGACCAGGTGGTGGTGGACGGCCACTCGCGGCTGATGCCCGGCGCCCTGGTCGATATCCAGGAGCCGCGCCCGAGCCTGGCCCAGGCCACGGAGCGGCGGCCGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3003704","ARO_id":"40358","ARO_name":"mexM","CARD_short_name":"mexM","ARO_description":"mexM is the membrane fusion protein of the MexMN-OprM multidrug efflux complex.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36595":{"category_aro_accession":"3000456","category_aro_cvterm_id":"36595","category_aro_name":"thiamphenicol","category_aro_description":"Derivative of Chloramphenicol. The nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3).","category_aro_class_name":"Antibiotic"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2217":{"model_id":"2217","model_name":"mexN","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1900"}},"model_sequences":{"sequence":{"3410":{"protein_sequence":{"accession":"BAE06006.1","sequence":"MTPRAGISGWCVRHPIATALLTLASLLLGLLAFLRLGVAPLPEADFPTIQINALLPGGSPETMASSVATPLEVQFSAIPGITEMTSSSALGTTTLTLQFSLDKSIDVAAQEVQAAINAAAGRLPVDMPNLPTWRKVNPADSPIMILRVNSEMMPLIELSDYAETILARQLSQVNGVGQIFVVGQQRPAIRIQAQPEKLAAYQLTLADLRQSLQSASVNLAKGALYGEGRVSTLAANDQLFNASDYDDLVVAYRQGAPVFLKDVARIVSAPEDDYVQAWPNGVPGVALVILRQPGANIVDTADAIQAALPRLREMLPATIEVDVLNDRTRTIRSSLHEVELTLLLTIGLVVLVMGLFLRQLSATLIVATVLAVSLSASFAAMYVLGFTLNNLTLVALIIAVGFIVDDAIVVVENIHRHLEAGASKVEAALKGAAEIGFTVISISFSLIAAFIPLLFMGGIVGRLFREFAVSVTVAILISVVASLTLAPMLASRFMPALRHAEAPRKGFAEWLTGGYERGLRWALGHQRLMLVGFAFTVLVAVAGYVGIPKGFFPLQDTAFVIGTSQAAEDISYDDMVAKHRQLAEIIASDPAVQSYNHAVGVTGGSQSLANGRFWIVLKDRGERDVSVGEFIDRLRPQLAKVPGIMLYLRAAQDINLSSGPSRTQYQYALRSSDSTQLALWAQRLTERLKQVPGLMDVSNDLQVGASVTALDIDRVAAARFGLSAEDVSQTLYDAFGQRQVGEYQTEVNQYKVVLELDARQRGRAESLDWFYLRSPLSGEMVPLSAIAKVAAPRSGPLQINHNGMFPAVNLSFNLAAGVSLGEAVQAVQRAQEEIGMPSTIIGVFQGAAQAFQSSLASQPLLILAALIAVYIILGVLYESFVHPLTILSTLPSAGIGAVFLLWAWGQDFSIMALIGIVLLIGIVKKNGILMVDFAIVAQREQGMSAEQAIYQACLTRFRPIMMTTLAALLGAIPLMIGFGTGSELRQPLGIAVVGGLLVSQVLTLFSTPVVYLALERLFHRRGTTTSDGGTAGATAT"},"dna_sequence":{"accession":"AB219523.1","fmin":"1175","fmax":"4286","strand":"+","sequence":"GTGACGCCGCGCGCCGGGATTTCCGGCTGGTGCGTACGGCACCCGATCGCCACCGCGCTGCTGACCCTGGCCTCGCTGCTGCTGGGGCTGCTGGCGTTCCTCCGGCTCGGTGTGGCGCCGTTGCCGGAGGCGGACTTCCCGACCATCCAGATCAACGCCTTGCTGCCCGGCGGTAGCCCGGAGACCATGGCCTCGTCGGTGGCCACCCCCTTGGAAGTGCAGTTCAGCGCGATTCCCGGGATCACCGAGATGACTTCCAGCAGCGCCCTGGGCACCACCACCCTGACCCTGCAGTTCAGCCTCGACAAGAGCATCGACGTCGCCGCCCAGGAGGTCCAGGCGGCGATCAACGCCGCGGCCGGGCGGCTGCCGGTGGACATGCCGAACCTGCCGACCTGGCGCAAGGTCAACCCGGCGGACAGCCCGATCATGATCCTGCGGGTCAACTCGGAGATGATGCCGCTGATCGAACTCAGCGATTACGCCGAGACCATCCTCGCCCGCCAGCTCAGCCAGGTGAACGGCGTGGGGCAGATCTTCGTGGTCGGCCAGCAGCGCCCGGCGATCCGCATCCAGGCCCAGCCGGAGAAGCTCGCCGCCTACCAGCTGACCCTGGCCGACCTGCGCCAGTCGTTGCAGTCGGCCAGCGTCAACCTGGCCAAGGGCGCGCTCTACGGCGAGGGGCGGGTGTCGACCCTCGCGGCCAACGACCAGTTGTTCAACGCCAGCGACTATGACGACCTGGTGGTCGCCTACCGCCAGGGCGCGCCGGTGTTCCTCAAGGACGTGGCGCGGATCGTCTCGGCGCCCGAGGACGACTACGTGCAGGCCTGGCCGAACGGCGTGCCCGGGGTGGCGCTGGTGATCCTGCGCCAGCCTGGGGCGAACATCGTCGATACCGCCGACGCGATCCAGGCCGCGCTGCCACGCCTGCGCGAGATGCTCCCGGCGACCATCGAGGTAGACGTGCTCAACGACCGCACCCGGACCATCCGCTCGTCGTTGCACGAGGTCGAACTGACCCTGCTGCTGACCATTGGCCTGGTGGTGCTGGTGATGGGCCTGTTCCTCCGCCAGCTGTCGGCGACCCTGATCGTCGCCACGGTGCTGGCGGTGTCCCTGAGCGCCAGCTTCGCGGCGATGTACGTGCTCGGCTTCACCCTCAACAACCTGACCCTGGTGGCGCTGATCATCGCTGTCGGCTTCATCGTCGACGACGCCATCGTGGTCGTGGAGAACATCCACCGACACCTGGAAGCGGGCGCCTCGAAGGTCGAGGCGGCGCTCAAGGGCGCGGCGGAGATCGGCTTTACCGTGATTTCCATCAGCTTCTCGCTGATCGCCGCGTTCATTCCCCTGCTGTTCATGGGCGGGATCGTCGGCCGGCTGTTCCGCGAATTCGCGGTCAGCGTGACGGTGGCGATCCTGATCTCGGTGGTCGCTTCGCTGACCCTGGCGCCGATGCTGGCTTCGCGCTTCATGCCGGCATTGCGGCATGCCGAAGCGCCGAGAAAGGGCTTCGCCGAATGGCTGACCGGCGGCTACGAACGCGGCCTGCGCTGGGCGCTCGGGCACCAGCGGCTGATGCTGGTCGGCTTCGCCTTTACCGTGCTGGTGGCGGTGGCCGGCTACGTCGGGATTCCCAAGGGTTTCTTCCCCTTGCAGGACACCGCCTTCGTCATCGGCACGAGCCAGGCTGCCGAGGATATCTCCTACGACGACATGGTCGCCAAGCACCGGCAACTGGCCGAGATCATCGCCAGCGACCCGGCGGTGCAGAGCTACAACCATGCGGTGGGCGTCACCGGCGGTAGCCAGAGCCTGGCCAACGGACGTTTCTGGATCGTCCTCAAGGACCGTGGCGAGCGCGATGTCTCGGTCGGCGAGTTCATCGACCGGCTGCGCCCGCAACTGGCCAAGGTGCCGGGAATCATGCTCTACCTGCGCGCGGCGCAGGACATCAACCTCAGTTCCGGACCCTCGCGGACCCAGTACCAGTACGCCCTGCGCAGCAGCGACAGCACCCAGCTGGCGCTCTGGGCGCAACGCCTCACCGAGCGCCTGAAGCAGGTGCCGGGGCTGATGGATGTGTCCAACGACCTGCAGGTCGGCGCCAGCGTCACCGCGCTGGACATCGACCGGGTGGCCGCGGCGCGTTTCGGCCTCAGCGCCGAGGATGTCAGCCAGACCCTCTACGACGCCTTCGGCCAGCGCCAGGTCGGCGAGTACCAGACCGAGGTCAACCAGTACAAGGTGGTCCTCGAACTCGATGCGCGCCAGCGCGGCCGCGCGGAAAGCCTGGACTGGTTCTACCTGCGCTCGCCGCTGAGCGGCGAGATGGTCCCGCTGTCGGCCATCGCCAAGGTCGCGGCGCCGCGCTCCGGGCCGCTGCAGATCAACCACAACGGCATGTTCCCGGCGGTCAACCTGTCCTTCAACCTGGCTGCCGGGGTGTCCCTCGGCGAGGCGGTGCAGGCGGTGCAGCGCGCCCAGGAGGAGATCGGCATGCCCTCGACCATTATCGGCGTGTTCCAGGGCGCGGCGCAGGCCTTCCAGAGCTCGCTGGCCTCGCAACCGCTGCTGATCCTCGCCGCGCTGATCGCGGTGTACATCATCCTCGGCGTGCTCTACGAGAGTTTCGTACATCCGCTGACGATCCTCTCGACCCTGCCCTCGGCGGGGATCGGCGCGGTGTTCCTGCTCTGGGCCTGGGGCCAGGACTTCTCGATCATGGCGCTGATCGGCATCGTGCTGCTGATCGGCATCGTCAAGAAGAACGGCATCCTCATGGTCGACTTCGCCATCGTCGCCCAGCGCGAGCAGGGCATGAGCGCGGAGCAGGCGATCTACCAGGCCTGCCTGACCCGTTTCCGGCCGATCATGATGACCACCCTGGCCGCGCTGCTGGGCGCGATACCCCTGATGATCGGCTTCGGCACCGGTTCCGAGCTGCGCCAGCCTCTGGGCATCGCGGTGGTCGGCGGGCTGCTGGTGAGCCAGGTGCTGACCCTGTTCAGCACGCCGGTGGTATACCTGGCCCTGGAGCGGCTGTTCCACCGGCGCGGGACGACGACCTCGGACGGCGGAACCGCTGGGGCGACGGCGACATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3003705","ARO_id":"40359","ARO_name":"mexN","CARD_short_name":"mexN","ARO_description":"MexN is the inner membrane transporter of the MexMN-OprM multidrug efflux complex.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36595":{"category_aro_accession":"3000456","category_aro_cvterm_id":"36595","category_aro_name":"thiamphenicol","category_aro_description":"Derivative of Chloramphenicol. The nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3).","category_aro_class_name":"Antibiotic"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2191":{"model_id":"2191","model_name":"AAC(6')-Iaj","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"3379":{"protein_sequence":{"accession":"BAM46120.1","sequence":"MEYSIINIVEQNNYQIDAARILTNTFLDIGNKTWPTIQSAIDEVEECIDLPNICIGLIHNNQLIGWVGLRPMYDKTWELHPLVVRTDYQSKGIGSVLLAEVEKRAREVGIIGIILGTDDEYNKTSLSEITIDENNIFDAIQNIKNIHNHPYEFYQKNGYMIVGIIPNANGLRKPDIWMWKSLLN"},"dna_sequence":{"accession":"AB709942.1","fmin":"1194","fmax":"1749","strand":"+","sequence":"ATGGAATATTCAATTATCAATATAGTAGAGCAAAACAATTATCAGATCGATGCTGCAAGAATTCTTACAAATACTTTTCTTGATATAGGTAATAAAACTTGGCCAACTATTCAAAGCGCAATCGATGAAGTCGAAGAGTGTATTGATCTGCCCAATATATGTATAGGTTTAATTCATAACAATCAATTAATTGGATGGGTCGGATTACGTCCGATGTATGATAAAACGTGGGAATTGCACCCATTAGTTGTAAGAACTGACTATCAAAGTAAGGGGATCGGTAGTGTATTACTTGCTGAAGTTGAAAAAAGGGCAAGAGAAGTTGGAATAATTGGAATAATATTAGGAACTGATGATGAATATAACAAAACAAGTCTTTCTGAAATAACTATAGATGAAAATAATATATTCGATGCAATACAAAATATTAAGAATATACATAATCATCCATATGAGTTTTACCAAAAAAATGGATATATGATTGTTGGAATAATTCCAAATGCAAATGGACTAAGAAAACCCGATATTTGGATGTGGAAAAGTCTACTCAATTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3003677","ARO_id":"40309","ARO_name":"AAC(6')-Iaj","CARD_short_name":"AAC(6')-Iaj","ARO_description":"AAC(6')-Iaj is a functional acetyltransferase that modifies the amino groups at the 6' positions of aminoglycosides and contributes to aminoglycoside resistance of P. aeruginosa.","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"A category of aminoglycoside N-acetyltransferase enzymes with modification regiospecificity based at the 6'-amino group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics through acetylation of the 6-amino group of the compound.","category_aro_class_name":"AMR Gene Family"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"46128":{"category_aro_accession":"3007378","category_aro_cvterm_id":"46128","category_aro_name":"2'-N-ethylnetilmicin","category_aro_description":"2'-N-ethylnetilmicin is an aminoglycoside antibiotic and a derivative of netilmicin.","category_aro_class_name":"Antibiotic"},"46129":{"category_aro_accession":"3007379","category_aro_cvterm_id":"46129","category_aro_name":"5-episisomicin","category_aro_description":"5-episosomicin is a semisynthetic aminoglycoside antibiotic similar to sisomicin.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2227":{"model_id":"2227","model_name":"VCC-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"3430":{"protein_sequence":{"accession":"ALU64000.1","sequence":"MKRIAMYVALSISTSTAFADEHNKNMADIEAAFEGRVGVYAINTGSGKAYSYRANERFPLCSSFKAFLAAAVLKMDQDSPGVLLEKVNYHNRTMEPHSPITEKFQSQGMAVGELAAATLQYSDNGAANLLMEKYIKGPEGMTQFMNSIGDTKFRLDRWELDLNSAIPGDERDTSTPKAVAESLNKLISNTVLDNYHQEIFKKWMIGNTTGDNRIRAAVPDGWVVGDKTGTCGKYGTANDHAFILQGNNAAPLILSIYTTRKGEHMKHDDEVIAKAARIAIENVK"},"dna_sequence":{"accession":"KT818596.1","fmin":"10010","fmax":"10865","strand":"+","sequence":"ATGAAACGTATTGCTATGTATGTTGCATTATCAATCTCTACTTCAACAGCTTTCGCTGATGAGCACAACAAAAATATGGCTGATATTGAAGCTGCTTTTGAGGGGCGTGTCGGTGTTTACGCAATAAACACTGGCAGCGGCAAGGCATATTCATATCGAGCTAACGAACGCTTCCCCTTATGTAGTTCATTTAAAGCATTTTTGGCGGCAGCAGTTTTAAAAATGGATCAAGATAGTCCTGGAGTCCTGCTTGAAAAAGTAAATTATCATAACAGAACTATGGAACCCCATTCACCCATAACAGAGAAATTTCAGTCACAAGGAATGGCCGTAGGGGAACTGGCTGCTGCAACACTTCAGTATAGTGATAATGGTGCTGCTAACCTTCTCATGGAGAAATATATAAAAGGACCAGAGGGCATGACTCAGTTCATGAACAGTATTGGTGATACTAAGTTTAGGTTGGACCGATGGGAGTTGGACCTTAATAGTGCTATACCTGGAGATGAACGTGACACATCAACACCGAAGGCCGTGGCAGAAAGTCTGAATAAGTTAATATCAAATACCGTCTTAGACAACTACCATCAAGAGATATTCAAAAAGTGGATGATCGGTAATACTACAGGAGATAATAGAATAAGAGCTGCTGTGCCTGATGGTTGGGTTGTCGGTGATAAAACGGGAACTTGCGGAAAGTATGGCACAGCAAACGATCATGCGTTTATTTTACAAGGTAATAATGCTGCCCCTCTGATTTTATCTATATATACAACCAGAAAGGGAGAACATATGAAGCATGATGATGAGGTGATTGCTAAAGCAGCTAGGATTGCAATAGAAAATGTAAAGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36789","NCBI_taxonomy_name":"Vibrio cholerae","NCBI_taxonomy_id":"666"}}}},"ARO_accession":"3003713","ARO_id":"40367","ARO_name":"VCC-1","CARD_short_name":"VCC-1","ARO_description":"VCC-1 is a Class A carbapenemase isolated from Vibrio cholerae and exhibits resistance to penicillins, carbapenems and monobactam antibiotics.","ARO_category":{"41360":{"category_aro_accession":"3004196","category_aro_cvterm_id":"41360","category_aro_name":"VCC beta-lactamase","category_aro_description":"VCC beta-lactamases are Class A beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35987":{"category_aro_accession":"0000070","category_aro_cvterm_id":"35987","category_aro_name":"ertapenem","category_aro_description":"Ertapenem is a carbapenem antibiotic and is highly resistant to beta-lactamases like other carbapenems. It inhibits bacterial cell wall synthesis.","category_aro_class_name":"Antibiotic"},"35990":{"category_aro_accession":"0000073","category_aro_cvterm_id":"35990","category_aro_name":"meropenem","category_aro_description":"Meropenem is an ultra-broad spectrum injectable antibiotic used to treat a wide variety of infections, including meningitis and pneumonia. It is a beta-lactam and belongs to the subgroup of carbapenem, similar to imipenem and ertapenem.","category_aro_class_name":"Antibiotic"},"36309":{"category_aro_accession":"3000170","category_aro_cvterm_id":"36309","category_aro_name":"imipenem","category_aro_description":"Imipenem is a broad-spectrum antibiotic and is usually taken with cilastatin, which prevents hydrolysis of imipenem by renal dehydropeptidase-I. It is resistant to hydrolysis by most other beta-lactamases. Notable exceptions are the KPC beta-lactamases and Ambler Class B enzymes.","category_aro_class_name":"Antibiotic"},"36689":{"category_aro_accession":"3000550","category_aro_cvterm_id":"36689","category_aro_name":"aztreonam","category_aro_description":"Aztreonam was the first monobactam discovered, and is greatly effective against Gram-negative bacteria while inactive against Gram-positive bacteria. Artreonam is a poor substrate for beta-lactamases, and may even act as an inhibitor. In Gram-negative bacteria, Aztreonam interferes with filamentation, inhibiting cell division and leading to cell death.","category_aro_class_name":"Antibiotic"},"36984":{"category_aro_accession":"3000640","category_aro_cvterm_id":"36984","category_aro_name":"doripenem","category_aro_description":"Doripenem is a carbapenem with a broad range of activity against Gram-positive and Gram-negative bacteria, and along with meropenem, it is the most active beta-lactam antibiotic against Pseudomonas aeruginosa. It inhibits bacterial cell wall synthesis.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2228":{"model_id":"2228","model_name":"PEDO-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"3429":{"protein_sequence":{"accession":"AJP77059.1","sequence":"MKIKFIFCLLLFPLFVFSQNVQEPTDTPKEWSAAYAPFRIVGNVYYVGTYDLACYLITTPKGNILINTGLRSSAAQIKKNVELLGFNFKDIKILLTTQAHYDHLGAMAEIKKLTGAKMMVDEKDASVMKDGGRTDYALGNGKTTYAPIIPDRLLKDGDQIQLGNTSIVMLHHPGHTKGSCSFMLKTKDETRDYSVLIANMPSIVTEKKFSEIPAYPQIEKDYAYTLSSLKKLSFDIWLSSHASQFCLHEKHKPGDKYNPTAFIDRAGYDKVLNSLQLEFDKKIGKK"},"dna_sequence":{"accession":"KP109677.1","fmin":"4318","fmax":"5179","strand":"+","sequence":"ATGAAAATTAAATTTATTTTTTGCCTCTTGCTTTTTCCGCTCTTTGTATTTTCACAAAATGTACAAGAACCTACCGATACGCCAAAAGAGTGGTCGGCTGCTTATGCCCCATTCCGCATTGTTGGGAATGTTTATTATGTTGGCACTTACGATCTGGCCTGCTACCTTATTACCACTCCGAAAGGAAATATACTGATCAATACCGGACTGCGTTCCTCGGCTGCGCAGATCAAAAAAAACGTGGAACTTTTGGGCTTTAACTTTAAAGACATCAAAATCCTGCTGACCACACAGGCACATTACGACCATTTGGGTGCTATGGCGGAGATCAAGAAACTTACTGGTGCAAAAATGATGGTTGATGAAAAAGATGCCAGTGTGATGAAGGATGGCGGCCGTACGGATTACGCACTGGGTAACGGAAAAACAACCTACGCTCCTATTATACCAGACCGTTTATTAAAGGATGGAGATCAGATCCAGCTCGGAAATACCAGTATTGTAATGCTCCACCACCCCGGCCATACTAAAGGATCATGCAGTTTTATGCTTAAAACTAAAGATGAAACAAGAGACTATTCGGTGCTGATTGCGAATATGCCCAGTATTGTTACCGAAAAAAAGTTTTCTGAAATACCAGCTTATCCGCAAATTGAAAAAGATTACGCCTATACTTTAAGTTCGCTCAAAAAATTATCATTTGATATCTGGTTGTCGTCTCATGCAAGCCAGTTTTGTCTGCACGAGAAACATAAACCTGGCGATAAATATAATCCTACCGCTTTTATAGATCGTGCAGGATACGATAAGGTATTAAACAGCCTTCAGCTCGAATTTGATAAAAAGATTGGCAAGAAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40283","NCBI_taxonomy_name":"Pedobacter sp. SI-33","NCBI_taxonomy_id":"1620222"}}}},"ARO_accession":"3003670","ARO_id":"40288","ARO_name":"PEDO-1","CARD_short_name":"PEDO-1","ARO_description":"PEDO-1 is a subclass B3 metallo-beta lactamase isolated from Pedobacter roseus exhibiting resistance to carbapenems.","ARO_category":{"41384":{"category_aro_accession":"3004220","category_aro_cvterm_id":"41384","category_aro_name":"subclass B3 PEDO beta-lactamase","category_aro_description":"PEDO family enzymes that are classified under subclass B3 (metallo-) beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2229":{"model_id":"2229","model_name":"PEDO-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"3428":{"protein_sequence":{"accession":"AJP77071.1","sequence":"MKKIFLMVLFSCSLLGFAQTVTEPANNPKEWSQATEPFRIAGNLYYVGTYDLASYLIVTEKGNILINTGLANSLSIIKENIKALGFDYKSIKILLLTQAHFDHLGAMSEIKKETGAKLYVDEKDADALETGGKLDYELGKYGISFKPVKPDFLLKNNDKIKLGNTTLTMLHHPGHTKGSCSFIFDTKDKNSSYKILIANMPSIIVDRKFSEIASYKDIQKDYTETFKAMKKLDFDLWVASHASQFELHDKRKSGAPYNPKIFMDKSKFFKNLEDLENIFLEKIKN"},"dna_sequence":{"accession":"KP109678.1","fmin":"5817","fmax":"6675","strand":"+","sequence":"ATGAAAAAAATATTTTTAATGGTTTTATTTTCTTGCAGTCTGTTGGGTTTTGCTCAAACAGTAACAGAGCCGGCTAATAATCCAAAAGAATGGTCTCAAGCTACAGAGCCATTTAGAATTGCAGGTAATCTATATTATGTTGGCACTTATGATTTAGCTTCTTATTTAATTGTAACAGAAAAAGGAAATATATTAATAAATACAGGTTTAGCTAATTCGCTTTCAATAATAAAAGAAAATATAAAAGCTTTGGGATTTGATTATAAATCAATCAAAATTTTGCTCTTAACCCAAGCTCATTTTGATCATTTGGGTGCGATGTCTGAGATTAAAAAAGAAACCGGTGCAAAACTTTATGTAGATGAGAAAGATGCGGACGCTCTTGAAACAGGCGGAAAATTGGATTATGAGCTTGGAAAATATGGCATAAGTTTCAAGCCTGTAAAACCTGATTTCCTATTGAAGAATAACGATAAGATTAAATTAGGCAACACTACTTTAACAATGCTTCATCATCCTGGGCATACTAAAGGATCGTGTAGTTTTATATTTGATACAAAAGATAAAAATTCTAGCTACAAAATTTTGATTGCCAATATGCCATCCATAATTGTTGATAGAAAATTCTCAGAAATAGCATCATATAAAGATATCCAAAAAGATTATACCGAAACTTTTAAAGCAATGAAAAAGCTTGACTTTGATCTTTGGGTTGCCTCTCATGCAAGTCAGTTTGAGCTCCATGATAAACGTAAATCAGGAGCCCCTTATAATCCAAAAATCTTTATGGATAAAAGTAAATTTTTCAAGAATCTTGAAGATCTGGAAAATATTTTCCTCGAAAAAATAAAAAATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40284","NCBI_taxonomy_name":"Pedobacter sp. ALS-14","NCBI_taxonomy_id":"1620221"}}}},"ARO_accession":"3003714","ARO_id":"40368","ARO_name":"PEDO-2","CARD_short_name":"PEDO-2","ARO_description":"PEDO-2 is a subclass B3 metallo-beta lactamase isolated from Pedobacter borealis exhibiting carbapenem resistance.","ARO_category":{"41384":{"category_aro_accession":"3004220","category_aro_cvterm_id":"41384","category_aro_name":"subclass B3 PEDO beta-lactamase","category_aro_description":"PEDO family enzymes that are classified under subclass B3 (metallo-) beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2230":{"model_id":"2230","model_name":"PEDO-3","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"5834":{"protein_sequence":{"accession":"AJP77076.1","sequence":"MRYLLSFLLCLSAFASFAQNPKIKIKHLTGDLYVYTTYNTYKGALTDANAVYLVTNKGVVVIDAPWDATQFQPFLDSIQTKHHQKVVLAIATHSHGDRAGGLAFFKSKGIKTYTNKLTDEILKTNKEPRAAYTFTNDTTFTVGQYKINTYYAGKGHTKDNLVVWFPKDKVLFGGCLIKSIEANDLGYIGESDLAAWPKSIEKLKQKYPDTKIVITGHAAWGNRESLDHTLKLLREKK"},"dna_sequence":{"accession":"KP109679.1","fmin":"2260","fmax":"2974","strand":"-","sequence":"ATGCGTTATCTTCTTTCCTTTTTACTTTGTTTATCTGCCTTTGCCTCTTTCGCGCAAAATCCAAAAATAAAAATCAAACATTTAACTGGCGATCTTTATGTTTACACCACATACAATACCTACAAAGGCGCTTTAACAGATGCAAATGCGGTTTACCTGGTTACCAATAAAGGTGTTGTAGTAATCGATGCCCCTTGGGATGCTACGCAGTTCCAGCCCTTTTTAGACTCTATTCAGACCAAACATCACCAAAAAGTAGTGCTGGCCATTGCCACACATTCGCATGGCGACCGCGCAGGCGGTTTAGCGTTCTTTAAAAGTAAGGGCATAAAAACCTATACCAATAAATTAACCGACGAAATTCTGAAAACTAATAAAGAGCCACGCGCAGCCTACACCTTTACCAACGACACTACTTTTACAGTGGGACAATATAAAATAAACACCTACTATGCCGGCAAGGGGCATACAAAGGATAATCTGGTAGTTTGGTTTCCAAAAGACAAAGTTTTATTCGGTGGCTGCCTGATTAAAAGCATCGAAGCCAATGATTTGGGCTATATTGGAGAATCCGATTTAGCCGCATGGCCAAAAAGCATCGAAAAGTTAAAACAGAAATATCCTGATACCAAAATTGTTATTACCGGACACGCTGCCTGGGGAAACAGGGAATCTCTAGACCATACCCTAAAGCTATTGAGGGAGAAAAAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40285","NCBI_taxonomy_name":"Pedobacter sp. Stok-3","NCBI_taxonomy_id":"1620223"}}}},"ARO_accession":"3003715","ARO_id":"40369","ARO_name":"PEDO-3","CARD_short_name":"PEDO-3","ARO_description":"PEDO-3 is a class B1 metallo-beta lactamase isolated from Pedobacter kyungheensis exhibiting resistance to carbapenems.","ARO_category":{"41391":{"category_aro_accession":"3004227","category_aro_cvterm_id":"41391","category_aro_name":"subclass B1 PEDO beta-lactamase","category_aro_description":"Beta-lactamases that are part of the PEDO gene family and are classified as subclass B1 (metallo-) beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2231":{"model_id":"2231","model_name":"CPS-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"3431":{"protein_sequence":{"accession":"AJP77054.1","sequence":"MRNLTLLFLLCLSFFGTAQTVTEPKNNPAEWSKDYEPFKIVGNLYYVGTYDLASYLIVTDKGNILINTGLADSYSTIKKNIEKFGFKYKDIKILTLTQAHYDHMGAMAQIKKETGAKLYVDEKDAAELKSGGKSDYEMGKYGVTFEPVHPDFLLKNNAKIKLGNTVLTLLHHPGHTKGSCSFLFETKEGNKNYKVLIANLPSIIIDHKFSDVKKYPTIQKDYGYTFEAMKKINFDVWVASHASQFDLHKKRKEGDSYNPKLFMDKENYFKRLKDLENDYLEKVKEDSAKK"},"dna_sequence":{"accession":"KP109675.1","fmin":"1328","fmax":"2201","strand":"+","sequence":"ATGAGAAACCTGACACTTTTATTTTTACTATGCCTATCTTTTTTTGGAACTGCACAAACCGTAACAGAGCCTAAAAATAATCCGGCAGAATGGTCAAAAGACTATGAACCTTTCAAAATTGTGGGGAATTTATATTATGTAGGAACTTACGATCTTGCATCTTATCTTATCGTGACCGATAAAGGCAATATTTTGATCAACACAGGTTTGGCGGATTCTTATTCTACCATTAAAAAAAATATCGAAAAGTTTGGTTTTAAGTATAAAGATATCAAAATTCTTACCTTAACGCAGGCACATTATGATCACATGGGAGCAATGGCTCAAATAAAAAAAGAAACCGGTGCAAAACTTTATGTTGACGAAAAAGATGCTGCAGAACTTAAAAGTGGTGGAAAATCTGACTACGAAATGGGAAAATACGGCGTTACTTTCGAACCTGTGCATCCTGATTTTCTTTTGAAAAACAATGCTAAAATAAAATTGGGAAATACGGTATTAACCTTGCTTCATCATCCCGGTCATACAAAAGGATCTTGCAGTTTCTTATTTGAAACCAAAGAAGGAAACAAAAATTACAAAGTTTTGATCGCCAATTTACCTTCAATTATTATTGACCATAAATTTTCTGATGTAAAGAAATATCCTACCATTCAGAAAGATTATGGATACACTTTTGAGGCCATGAAAAAAATAAATTTCGATGTTTGGGTAGCTTCGCATGCAAGTCAGTTTGATCTTCATAAAAAGCGGAAAGAAGGAGATTCTTACAATCCGAAATTGTTTATGGATAAAGAAAATTATTTTAAAAGGCTTAAAGATCTGGAAAACGATTATCTGGAAAAAGTAAAAGAAGATTCAGCGAAAAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40281","NCBI_taxonomy_name":"Chryseobacterium sp. Stok-1","NCBI_taxonomy_id":"1620218"}}}},"ARO_accession":"3003716","ARO_id":"40370","ARO_name":"CPS-1","CARD_short_name":"CPS-1","ARO_description":"CPS-1 is a subclass B3 metallo-beta lactamase isolated from Chyseobacterium piscium exhibiting carbapenem resistance.","ARO_category":{"41385":{"category_aro_accession":"3004221","category_aro_cvterm_id":"41385","category_aro_name":"CPS beta-lactamase","category_aro_description":"CPS beta-lactamases are a subclass B3 family.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2232":{"model_id":"2232","model_name":"ESP-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"3432":{"protein_sequence":{"accession":"AJP77085.1","sequence":"MKKLTLILSLIIAFFGYAQTVTEPTNHSAEWSQPYEPFRIVGNLYYVGTYDLASYLIVTEKGNILINTGLADSYPQIKANIEKLGFKYKDTKILTLTQAHFDHMGAMADIKAETGAKLYVDEADAAELKSGGKSDYELGKYGVTFKPLTPDFLLKNNGKIKLGNTTLTLLHHPGHTKGSCSFIFETKDENRKYKVVIANMPSIIIDHKFSDVKTYPSIQKDYAYTLEAMKKLDFDVWVASHASQFDLHKKRKEGDAYNPKLFMDKENYFKRLKDLEDDYLEKVKEENKPE"},"dna_sequence":{"accession":"KP109681.1","fmin":"1642","fmax":"2515","strand":"+","sequence":"ATGAAAAAACTTACCCTAATACTTTCACTGATCATTGCCTTTTTCGGATATGCACAAACCGTAACAGAACCAACCAATCATTCTGCAGAATGGTCGCAACCTTACGAGCCATTCAGAATTGTCGGGAATTTGTATTACGTTGGAACTTATGATTTGGCTTCGTATCTCATTGTGACGGAAAAGGGAAATATCCTTATCAACACAGGTTTGGCGGATTCTTATCCTCAAATAAAAGCGAATATCGAGAAACTCGGATTCAAATACAAAGACACCAAAATCCTGACTTTGACACAAGCGCATTTTGACCATATGGGCGCAATGGCCGATATCAAAGCGGAAACCGGCGCAAAACTTTATGTAGACGAAGCAGATGCTGCGGAACTGAAATCAGGCGGAAAATCGGATTACGAACTGGGAAAATATGGTGTGACTTTCAAACCCTTAACGCCGGATTTTCTTCTGAAAAATAATGGTAAAATAAAATTAGGAAATACCACCTTGACCTTGCTTCATCATCCTGGTCACACAAAAGGTTCGTGCAGTTTTATCTTCGAAACCAAAGATGAAAATCGAAAATATAAAGTTGTGATCGCCAATATGCCATCCATCATCATCGATCATAAATTTTCTGATGTGAAAACTTATCCTTCAATTCAGAAAGATTATGCTTACACTTTGGAGGCGATGAAAAAACTGGATTTCGATGTTTGGGTAGCTTCGCACGCCAGCCAATTCGATCTTCATAAAAAAAGAAAAGAAGGCGATGCTTACAACCCGAAACTATTTATGGATAAAGAGAATTATTTTAAAAGACTGAAAGATTTGGAAGATGATTATCTGGAGAAAGTGAAAGAAGAAAATAAACCAGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40287","NCBI_taxonomy_name":"Chryseobacterium sp. Stok-2","NCBI_taxonomy_id":"1620219"}}}},"ARO_accession":"3003717","ARO_id":"40371","ARO_name":"ESP-1","CARD_short_name":"ESP-1","ARO_description":"ESP-1 is a subclass B3 metallo-beta lactamase isolated from Epilithonimonas tenax conferring resistance to carbapenems.","ARO_category":{"41386":{"category_aro_accession":"3004222","category_aro_cvterm_id":"41386","category_aro_name":"ESP beta-lactamase","category_aro_description":"ESP family beta-lactamases are subclass B3 (metallo-) beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2233":{"model_id":"2233","model_name":"MSI-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"3433":{"protein_sequence":{"accession":"AJP77057.1","sequence":"MGARSCSRAWCCSRATRSAPPGRRSGRLSCARCRRPSTGCNPSSTPPITGDIMKHIRLACVAAGLVAAASSVSAIGADWNAPQEPFALFGNSYYVGPHGVASVLITSNQGHILIDGGSDKSPPQIAARIRQLGFKPEDIRFILVSHEHIDHAGGVAELQRLSNAEVLAGAAAVPVLHSGEAGRNDPQYGGLPKMAPVARVRAVRDGEVVKLGPLAVTMHATPGHTQGGASWTWQSNEGGRTANMVYADSLTAFGSGGFRYSGDARYPSARADVERSIAKVAALPCDILVSAHPEVSELWTRYERRAAQGNAAFIDAGACKAYAVKARVKLQEQLARETAKP"},"dna_sequence":{"accession":"KP109676.1","fmin":"0","fmax":"1026","strand":"+","sequence":"ATGGGCGCACGATCGTGTTCGCGCGCATGGTGCTGCAGCCGCGCGACCCGGAGCGCGCCGCCGGGCCGGCGCTCAGGCAGGCTTTCCTGCGCGCGTTGCCGGCGACCCTCGACAGGCTGTAATCCTTCCTCTACTCCACCCATCACGGGAGACATCATGAAGCACATCCGCCTCGCCTGCGTCGCGGCCGGACTGGTCGCGGCCGCATCCTCCGTCAGCGCCATCGGCGCCGACTGGAACGCGCCGCAGGAACCGTTCGCCCTGTTCGGCAACAGCTACTACGTCGGCCCGCACGGCGTGGCCTCGGTCTTGATCACGTCGAATCAGGGTCACATCCTGATCGACGGCGGCAGCGACAAATCGCCGCCGCAGATCGCCGCGCGCATCCGCCAGCTCGGCTTCAAGCCGGAAGACATCCGCTTCATCCTGGTCTCGCACGAGCACATCGACCATGCGGGCGGTGTCGCCGAGCTGCAGCGCCTGTCGAACGCCGAGGTGCTGGCCGGCGCCGCCGCGGTGCCGGTGCTGCATAGCGGCGAGGCCGGTCGCAACGATCCGCAATACGGCGGCCTGCCGAAGATGGCGCCGGTGGCGCGGGTGCGCGCGGTGCGCGACGGCGAGGTGGTCAAACTCGGGCCGCTGGCGGTGACGATGCACGCCACGCCGGGCCATACGCAGGGTGGCGCCAGCTGGACCTGGCAATCAAACGAAGGCGGACGCACGGCCAACATGGTGTATGCCGACAGCCTGACGGCGTTCGGATCCGGGGGCTTTCGCTACAGCGGCGATGCGCGCTATCCGAGCGCGCGCGCCGACGTCGAGCGATCGATCGCGAAGGTCGCCGCGCTGCCGTGCGACATCCTGGTGTCGGCGCATCCGGAAGTGAGCGAGCTGTGGACCCGGTACGAGCGGCGCGCGGCGCAAGGCAACGCCGCGTTCATCGACGCCGGCGCCTGCAAGGCCTATGCCGTCAAGGCCCGCGTGAAGCTGCAGGAACAACTGGCCAGGGAAACGGCCAAGCCATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40282","NCBI_taxonomy_name":"Massilia sp. SB1-3","NCBI_taxonomy_id":"1620220"}}}},"ARO_accession":"3003718","ARO_id":"40372","ARO_name":"MSI-1","CARD_short_name":"MSI-1","ARO_description":"MSI-1 is a subclass B3 metallo-beta lactamase isolated from Massilia oculi conferring resistance to carbapenems.","ARO_category":{"41387":{"category_aro_accession":"3004223","category_aro_cvterm_id":"41387","category_aro_name":"MSI beta-lactamase","category_aro_description":"MSI beta-lactamases are a family of subclass B3 (metallo-) beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2234":{"model_id":"2234","model_name":"MSI-OXA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"3434":{"protein_sequence":{"accession":"AJP77058.1","sequence":"MSHTFIIDRLGASMIKQILAALLLISPLLAQAAEWKESAQVARLFKQEGVSGTFVVYDVAADSYTVHDRQRANTRFIPASTFKIPNTLIALAHGAVANVDEVVPYGGKPVARPEWARDMGLREAIRISNVPVYQEVARRVGLDRMRSELVRMKYGNMQTGTVVDRFWLDGPLKISAVEQTEFLTKLAQGTLPFTNVAMAAVREISRQDGAPELYAKTGWGSRPGEADIGWWVGWLKKDGKLYAFALNMDLPDGAQDKRVSLAKAALRELGLL"},"dna_sequence":{"accession":"KP109676.1","fmin":"1022","fmax":"1841","strand":"+","sequence":"ATGAGTCACACGTTCATCATCGACCGACTTGGAGCATCCATGATCAAGCAAATTCTCGCAGCACTGTTGTTGATCAGCCCGCTGCTGGCGCAGGCCGCCGAATGGAAGGAAAGCGCGCAGGTGGCGCGCCTGTTCAAGCAGGAAGGCGTGAGCGGCACCTTCGTCGTCTACGACGTGGCCGCCGACAGCTACACGGTGCATGACCGCCAGCGCGCCAACACGCGCTTCATTCCGGCGTCGACCTTCAAGATCCCGAACACGCTGATCGCGCTGGCGCATGGCGCGGTGGCCAACGTCGACGAAGTGGTGCCGTATGGCGGCAAGCCGGTAGCGCGGCCCGAGTGGGCGCGCGACATGGGGCTGCGCGAGGCGATCCGGATCTCGAACGTGCCGGTGTACCAGGAAGTGGCGCGGCGCGTGGGCCTGGACCGGATGCGCTCGGAGCTGGTCCGGATGAAGTACGGGAACATGCAGACCGGGACCGTGGTGGACCGGTTCTGGCTCGATGGGCCTTTGAAGATCAGCGCGGTGGAGCAGACCGAATTTTTGACCAAGCTGGCGCAGGGTACGCTGCCGTTCACCAACGTGGCGATGGCGGCGGTGCGCGAGATCAGCCGTCAGGATGGAGCGCCCGAGCTGTATGCCAAGACCGGGTGGGGCAGTCGGCCGGGCGAGGCCGATATCGGGTGGTGGGTCGGTTGGCTGAAGAAGGATGGCAAGCTGTATGCATTTGCGCTGAATATGGATCTTCCCGATGGTGCGCAGGACAAGCGGGTGTCGCTGGCGAAGGCGGCGTTGCGGGAACTGGGCCTGCTGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40282","NCBI_taxonomy_name":"Massilia sp. SB1-3","NCBI_taxonomy_id":"1620220"}}}},"ARO_accession":"3003719","ARO_id":"40373","ARO_name":"MSI-OXA","CARD_short_name":"MSI-OXA","ARO_description":"MSI-OXA is an OXA-85-like class D beta lactamase isolated from Massilia oculi.","ARO_category":{"41406":{"category_aro_accession":"3004242","category_aro_cvterm_id":"41406","category_aro_name":"MSI-OXA family beta-lactamase","category_aro_description":"Members of the MSI-OXA family are class D beta-lactamases that encompass hybrids of MSI-1 and putative OXA homologues.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2235":{"model_id":"2235","model_name":"SPG-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"5827":{"protein_sequence":{"accession":"AJP77080.1","sequence":"MRPLILLASALAMTAPSGALAQSAEQRAKWNGPREPFRITGNLYYVGTSGLSAYLIAGPRGHVLIDGALPESAPLIAANIRKLGFKLSDVKYLLSNHSHVDHAGGLAELKRLTGAQMVANVADKPDLEAGTTIGRTDIADFPAVKVDRVIGDGDRLTLGPIALVAILTPGHTKGATSWTTRIGSKNVIFTSSISVAGQNLINNINYPNAAADFRASFAKLRALKADIFLSFHAEAFALDEKRARAQAGATDAFVDPNELSRQVDLAEKAFDATLAKQQAANADRR"},"dna_sequence":{"accession":"KP109680.1","fmin":"1254","fmax":"2112","strand":"-","sequence":"ATGCGCCCCCTGATACTGCTCGCATCCGCGCTCGCCATGACAGCCCCATCCGGCGCCCTCGCCCAATCGGCCGAGCAGCGCGCGAAATGGAACGGGCCGCGCGAGCCATTCCGCATCACCGGCAATCTCTATTATGTCGGCACCAGCGGGCTTTCGGCCTATCTGATCGCCGGGCCGCGCGGCCATGTGCTGATCGACGGCGCTCTGCCGGAAAGCGCGCCGCTGATCGCCGCGAACATCCGCAAACTGGGCTTCAAACTGTCCGATGTGAAATATCTGCTCAGCAACCATTCGCATGTCGATCACGCCGGTGGACTGGCCGAACTCAAGCGGCTGACCGGCGCGCAAATGGTCGCAAACGTTGCGGACAAGCCCGATCTCGAAGCAGGTACCACCATCGGCCGCACCGATATCGCGGACTTTCCGGCAGTGAAGGTCGATCGTGTGATCGGCGACGGCGACCGGCTGACGCTCGGCCCGATCGCGCTCGTCGCCATCCTGACACCCGGCCATACAAAAGGCGCGACGAGCTGGACGACCCGCATTGGCAGCAAGAATGTGATCTTCACATCGAGTATCAGTGTCGCCGGCCAAAATCTTATCAATAATATAAATTATCCGAACGCCGCCGCCGATTTCCGTGCCAGCTTTGCGAAACTCCGCGCGTTGAAGGCAGATATCTTCCTGAGCTTCCACGCCGAGGCTTTCGCGCTCGATGAAAAACGCGCCAGGGCGCAGGCGGGTGCCACCGACGCCTTTGTCGATCCGAACGAATTGTCACGCCAGGTCGATCTGGCGGAGAAGGCTTTCGATGCGACGCTGGCGAAGCAGCAAGCGGCGAATGCGGATCGGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40286","NCBI_taxonomy_name":"Sphingomonas sp. ALS-13","NCBI_taxonomy_id":"1620224"}}}},"ARO_accession":"3003720","ARO_id":"40374","ARO_name":"SPG-1","CARD_short_name":"SPG-1","ARO_description":"SPG-1 is a subclass B3 metallo-beta lactamase isolated from Sphingomonas sp.","ARO_category":{"41388":{"category_aro_accession":"3004224","category_aro_cvterm_id":"41388","category_aro_name":"SPG beta-lactamase","category_aro_description":"SPG beta-lactamases are a family of subclass B3 (metallo-) beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3452":{"model_id":"3452","model_name":"OXA-288","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"540"}},"model_sequences":{"sequence":{"5648":{"protein_sequence":{"accession":"ENX60508.1","sequence":"MMMSKKLKCLAFFTAIFFAIPMTACQSFSQQKQQLSTQKNEQQQISSLFQSAQTSGVLVIYDGKKIQSYGNDLDRAEQRYIPASTFKMLNALIGIQHHKTTPDEMFKWDGKKRAFSSWEKDLTLAEAMQASAVPVYQELARRIGLELMTREVKRVGYGNKNIGTQVDNFWLVGPLKITPVEEVRFAYALAKQKLPFDQSTQQQVKGMLLIDEVQGTKIYAKSGWGMDVSPQVGWWTGWIEQANGKITAFSLNMEMSRPEHAEARKAIVYQALQQLDLLAN"},"dna_sequence":{"accession":"APRN01000033.1","fmin":"307089","fmax":"307932","strand":"-","sequence":"ATGATGATGTCGAAAAAATTAAAATGTCTGGCCTTTTTTACAGCCATCTTTTTTGCAATTCCCATGACTGCTTGTCAAAGTTTTAGCCAACAAAAGCAACAGCTCTCGACACAAAAAAATGAGCAGCAGCAGATCTCAAGTTTATTCCAGAGTGCCCAAACCAGTGGTGTTTTGGTGATTTATGATGGTAAGAAAATTCAAAGCTATGGCAATGATCTTGATCGTGCAGAACAGCGCTATATTCCTGCCTCAACCTTTAAAATGTTAAACGCCTTGATCGGAATACAGCATCATAAGACCACACCAGATGAAATGTTTAAATGGGATGGCAAAAAGCGAGCATTTAGCAGTTGGGAAAAAGATTTAACCTTAGCTGAGGCGATGCAGGCATCGGCGGTACCTGTCTATCAAGAATTGGCAAGACGTATTGGTCTGGAACTGATGACTCGGGAAGTTAAGCGAGTGGGCTATGGCAATAAAAATATAGGAACTCAAGTCGATAACTTTTGGTTAGTAGGCCCATTAAAAATTACGCCTGTAGAGGAAGTACGCTTTGCCTACGCATTAGCGAAGCAGAAGCTGCCATTTGATCAGTCAACTCAGCAACAAGTAAAAGGCATGTTATTGATTGATGAGGTTCAAGGCACCAAGATCTACGCTAAAAGTGGTTGGGGGATGGACGTTAGCCCACAAGTGGGATGGTGGACAGGTTGGATAGAGCAAGCAAATGGCAAGATCACCGCATTTTCATTAAATATGGAAATGAGTCGACCAGAGCATGCGGAGGCACGGAAGGCGATTGTTTATCAAGCTTTGCAGCAGCTAGATTTATTGGCGAATTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42813","NCBI_taxonomy_name":"Acinetobacter sp. CIP 70.18","NCBI_taxonomy_id":"1217700"}}}},"ARO_accession":"3001743","ARO_id":"38143","ARO_name":"OXA-288","CARD_short_name":"OXA-288","ARO_description":"OXA-288 is a beta-lactamase found in Acinetobacter spp.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46503":{"category_aro_accession":"3007714","category_aro_cvterm_id":"46503","category_aro_name":"OXA-286-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-286.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3586":{"model_id":"3586","model_name":"FONA-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"5784":{"protein_sequence":{"accession":"CAB61637.1","sequence":"MVKNTLRKTTLMVATVMPLLFSSAPLWAQTANAKANIQQQLSELEKNSGGRLGVALIDTADNSQILYRGDERFPMCSTSKVMAVSALLKQSETDKNLLAKRMEIKQSDLVNYNPIAEKHLDTGMTLAEFSAATIQYSDNTAMNKILEHLGGPAKVTEFARTIGDKTFRLDRTEPTLNTAIPGDPRDTSSPLAMAKSLQNLTLGKALGEPQRAQLVEWMKGNTTGGASIRAGLPTTWIVGDKTGSGDYGTTNDIAVIWPANHAPLVLVTYFTQPQQNAEARKDVLAAAAKIVTEGL"},"dna_sequence":{"accession":"AJ251240.1","fmin":"1053","fmax":"1941","strand":"+","sequence":"ATGGTTAAAAATACACTACGTAAAACCACCCTGATGGTCGCTACGGTTATGCCGTTGCTGTTCAGTAGCGCACCGCTATGGGCGCAAACTGCTAATGCCAAGGCGAATATTCAGCAGCAACTGTCTGAACTGGAGAAAAACTCCGGTGGCCGCCTGGGCGTGGCGCTGATCGATACCGCCGATAATTCGCAGATCCTGTATCGCGGGGATGAACGTTTTCCTATGTGCAGCACCAGCAAGGTGATGGCGGTGTCGGCGTTGTTAAAACAGAGCGAGACGGATAAAAATCTTTTGGCTAAGCGGATGGAAATCAAGCAATCCGATCTGGTCAACTACAACCCGATCGCCGAAAAACACCTGGATACCGGGATGACCCTGGCCGAGTTCAGCGCCGCCACCATCCAGTACAGTGACAACACGGCGATGAACAAGATCCTTGAGCATCTTGGCGGCCCGGCAAAAGTAACAGAATTTGCGCGTACCATCGGCGATAAAACCTTCCGTCTTGATCGTACCGAGCCCACCTTGAATACCGCCATTCCGGGTGATCCGCGTGACACGAGTTCGCCGCTGGCGATGGCAAAAAGCCTGCAAAACCTGACCTTGGGTAAGGCGCTGGGTGAACCACAGCGTGCTCAACTGGTTGAATGGATGAAGGGGAATACTACCGGCGGAGCCAGCATTCGCGCAGGTCTGCCAACCACGTGGATAGTCGGTGATAAAACCGGCAGCGGTGATTACGGTACCACTAACGATATCGCCGTGATTTGGCCAGCTAACCACGCACCGTTGGTGCTGGTCACCTATTTCACCCAGCCACAGCAGAATGCTGAAGCCCGCAAAGACGTGTTGGCTGCGGCCGCTAAAATTGTTACCGAAGGGCTTTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39675","NCBI_taxonomy_name":"Serratia fonticola","NCBI_taxonomy_id":"47917"}}}},"ARO_accession":"3004789","ARO_id":"42907","ARO_name":"FONA-2","CARD_short_name":"FONA-2","ARO_description":"FONA-2 is a class A beta-lactamase gene found in Serratia fonticola.","ARO_category":{"42905":{"category_aro_accession":"3004787","category_aro_cvterm_id":"42905","category_aro_name":"FONA beta-lactamase","category_aro_description":"FONA is a class A beta-lactamase gene family found in Serratia fonticola.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4010":{"model_id":"4010","model_name":"PDC-118","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"6374":{"protein_sequence":{"accession":"WP_094009806.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGNMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_055482.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCACGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCAACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005278","ARO_id":"43635","ARO_name":"PDC-118","CARD_short_name":"PDC-118","ARO_description":"PDC-118 is a class C beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2240":{"model_id":"2240","model_name":"vanJ","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"5377":{"protein_sequence":{"accession":"CAB45459.1","sequence":"MVLRSAARPELWKRAPVLTVSALLLGLVMMLHAEIPNRFGSVGSLVETFLPWFGLFVPVLAAGALWRRSAAAVTALVLPVTVWLSLFGGLLGDKSGAGGEFTMASHNVGAENPDPAGTARDLAASGVDVLALEEITAQDREVYEKGLAREYPYHTVQGTVGLWSKLPLSGTRPVDIATDYGPLADTKPADVTMAGNRALRTTVATERGPLVVYVAHLGSVRLNPRAGFWTDSRDRNAWALGEALAADRSERIALLGDLNGTVDDRALAGITSQLHSVQEAAGNGFGFTWPAKFPVARIDQILVRGVEPTGSWTLPATGSDHLPVAAGVSW"},"dna_sequence":{"accession":"AL939117.1","fmin":"50871","fmax":"51864","strand":"+","sequence":"GTGGTGCTCCGCAGCGCCGCCCGGCCGGAGCTCTGGAAGCGTGCGCCGGTACTCACGGTGTCGGCGCTGTTGCTGGGCCTCGTGATGATGCTGCACGCGGAGATTCCAAATCGGTTCGGGTCCGTCGGCAGCCTGGTCGAGACCTTCCTGCCGTGGTTCGGTCTGTTCGTCCCCGTGCTGGCCGCCGGAGCGCTGTGGCGCCGCTCCGCCGCCGCGGTGACCGCGCTGGTGCTGCCGGTCACGGTGTGGCTGAGCCTCTTCGGCGGGCTGCTCGGCGACAAGTCAGGCGCGGGCGGCGAATTCACCATGGCCTCCCACAACGTCGGCGCCGAGAACCCGGACCCGGCCGGCACCGCCCGCGACCTGGCTGCCTCCGGAGTGGACGTACTGGCGCTGGAGGAGATCACCGCACAGGACCGGGAGGTGTATGAGAAGGGGCTGGCCAGGGAGTATCCGTACCACACGGTGCAGGGCACGGTCGGGTTGTGGAGCAAGCTGCCGCTGTCGGGCACGCGGCCGGTCGACATCGCGACGGACTACGGGCCGCTGGCGGACACCAAACCGGCCGACGTCACGATGGCCGGCAACCGAGCGCTGCGCACCACGGTGGCCACGGAAAGGGGCCCGCTGGTGGTGTACGTGGCCCACCTGGGCTCCGTACGGCTCAATCCTCGGGCGGGGTTCTGGACGGACTCCCGCGACCGGAACGCGTGGGCGCTCGGCGAGGCCCTCGCCGCCGACCGCAGTGAGCGGATCGCGCTGCTCGGCGACCTGAACGGCACCGTGGACGACCGCGCGTTGGCGGGCATCACCTCGCAGCTGCACTCGGTCCAGGAGGCGGCCGGGAACGGGTTCGGCTTCACCTGGCCGGCGAAGTTCCCGGTGGCGCGGATCGACCAGATCCTGGTGCGCGGCGTGGAGCCGACCGGTTCGTGGACGCTGCCCGCCACCGGCAGCGACCACCTGCCTGTGGCGGCGGGGGTCAGCTGGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36881","NCBI_taxonomy_name":"Streptomyces coelicolor A3(2)","NCBI_taxonomy_id":"100226"}}}},"ARO_accession":"3002914","ARO_id":"39348","ARO_name":"vanJ","CARD_short_name":"vanJ","ARO_description":"vanJ is a novel membrane protein that confers resistance to teicoplanin and its derivatives in Streptomyces coelicolor by recycling undecaprenol pyrophosphate during cell wall biosynthesis.","ARO_category":{"41419":{"category_aro_accession":"3004255","category_aro_cvterm_id":"41419","category_aro_name":"vanJ membrane protein","category_aro_description":"vanJ and vanJ homologue proteins confer resistance to teicoplanin.","category_aro_class_name":"AMR Gene Family"},"35948":{"category_aro_accession":"0000029","category_aro_cvterm_id":"35948","category_aro_name":"teicoplanin","category_aro_description":"Teicoplanin is a glycopeptide antibiotic used in the prophylaxis and treatment of serious infections caused by Gram-positive bacteria. Teicoplanin has a unique acyl-aliphatic chain, and binds to cell wall precursors to inhibit transglycosylation  and transpeptidation.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2248":{"model_id":"2248","model_name":"fusD","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"375"}},"model_sequences":{"sequence":{"5373":{"protein_sequence":{"accession":"ASE57902.1","sequence":"MEKQLYPYQFNYIKERVAHLVNAYNSVNDPNTIASIKDVTRDEILSTFNSRNTTIRSNVEKLMNVQLTKEQAQKILTTIQMYVKPFEHPSNKQVTNLFKKVKKLKTPLISDEVLQTSTYIGWNDIASNRKFIIYYDNFGKLNGVYGDISNQTVKSFCSICNKESRVALFMRKTRTGNDGQYTKKGDYICFDSTLCNHQISDLSHFHHFLNKIQ"},"dna_sequence":{"accession":"CP022056.2","fmin":"166813","fmax":"167455","strand":"+","sequence":"ATGGAAAAACAACTTTACCCTTATCAATTTAACTATATAAAAGAACGCGTTGCACATTTAGTCAATGCTTATAATTCGGTCAACGATCCCAATACAATCGCTTCAATCAAAGATGTCACACGTGATGAAATACTTAGTACATTTAACTCAAGAAACACTACCATTCGTTCAAATGTTGAAAAGCTCATGAATGTACAACTAACTAAAGAACAAGCTCAAAAAATTTTAACGACCATACAAATGTATGTTAAGCCATTTGAACACCCGAGTAATAAACAAGTCACTAACCTTTTTAAAAAAGTTAAAAAGCTAAAAACACCACTTATCAGTGATGAAGTGCTACAAACAAGTACGTATATCGGTTGGAATGATATTGCTTCAAATAGAAAATTCATCATTTATTATGATAACTTTGGAAAATTAAACGGTGTATACGGAGACATTTCTAACCAAACTGTCAAAAGTTTCTGCTCTATTTGCAATAAAGAATCCCGTGTTGCTCTATTTATGCGAAAAACACGTACTGGCAATGATGGCCAATATACCAAAAAAGGTGACTACATTTGTTTTGATAGCACATTATGTAACCATCAAATATCCGATTTATCGCACTTCCATCATTTTTTGAATAAGATTCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40387","NCBI_taxonomy_name":"Staphylococcus saprophyticus","NCBI_taxonomy_id":"29385"}}}},"ARO_accession":"3003731","ARO_id":"40386","ARO_name":"fusD","CARD_short_name":"fusD","ARO_description":"A specific fusidic acid resistance gene conferring intrinsic resistance in the bacteria Staphylococcus saprophyticus. FusD behaves by causing dissociation of EF-G from the ribosome thus counteracting the action of Fusidic acid. It is considered a FusB-type protein.","ARO_category":{"43297":{"category_aro_accession":"3005086","category_aro_cvterm_id":"43297","category_aro_name":"Target protecting FusB-type protein conferring resistance to Fusidic acid","category_aro_description":"Fusidic acid resistance determinants through the mediation of target protection. These protein drive the dissociation of EF-G from the ribosome thus counteracting the action of Fusidic acid.","category_aro_class_name":"AMR Gene Family"},"37139":{"category_aro_accession":"3000759","category_aro_cvterm_id":"37139","category_aro_name":"fusidic acid","category_aro_description":"Fusidic acid is the only commercially available fusidane, a group of steroid-like antibiotics. It is most active against Gram-positive bacteria, and acts by inhibiting elongation factor G to  block protein synthesis.","category_aro_class_name":"Antibiotic"},"45735":{"category_aro_accession":"3007153","category_aro_cvterm_id":"45735","category_aro_name":"fusidane antibiotic","category_aro_description":"A group of antibiotics possessing steroid rings or steroid-like structures.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3323":{"model_id":"3323","model_name":"QnrS11","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"455"}},"model_sequences":{"sequence":{"5346":{"protein_sequence":{"accession":"AFM45990.1","sequence":"METYNHTYRHHNFSHKDLSGLTFTACTFIRSDFRRANLRDTTFVNCKFIEQGDIEGCHFDVADLRDASFQQCQLAMANFSNANCYGIEFRACDLKGANFSRTNFAHQVSNRMYFCSAFISGCNLSYANMERVCLEKCELFENRWIGTNLAGASLKESDLSRGVFSEDVWGQFSLQGANLCHAELDGLDPRKVDTSGIKIAAWQQELILEALGIVVYPD"},"dna_sequence":{"accession":"JQ269335.1","fmin":"33232","fmax":"33889","strand":"-","sequence":"ATGGAAACCTACAATCATACATATCGGCACCACAACTTTTCACATAAAGACTTAAGTGGTCTCACCTTCACCGCTTGCACATTCATTCGCAGCGACTTTCGACGTGCTAACTTGCGTGATACGACATTCGTCAACTGCAAGTTCATTGAACAGGGTGATATCGAAGGCTGCCACTTTGATGTCGCAGATCTTCGTGATGCAAGTTTCCAACAATGCCAACTTGCGATGGCAAACTTCAGTAATGCCAATTGCTACGGTATAGAGTTCCGTGCGTGTGATTTAAAAGGTGCCAACTTTTCCCGAACAAACTTTGCCCATCAAGTGAGTAATCGTATGTACTTTTGCTCAGCATTTATTTCTGGATGTAATCTTTCCTATGCCAATATGGAGAGGGTTTGTTTAGAAAAATGTGAGTTGTTTGAAAATCGCTGGATAGGAACGAACCTAGCGGGTGCATCACTGAAAGAGTCAGACTTAAGTCGAGGTGTTTTTTCCGAAGATGTCTGGGGGCAATTTAGCCTACAGGGTGCCAATTTATGCCACGCCGAACTCGACGGTTTAGATCCCCGCAAAGTCGATACATCAGGTATCAAAATTGCAGCCTGGCAGCAAGAACTGATTCTCGAAGCACTGGGTATTGTTGTTTATCCTGACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3004624","ARO_id":"42606","ARO_name":"QnrS11","CARD_short_name":"QnrS11","ARO_description":"QnrS11 is a plasmid-mediated quinolone resistance protein.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4181":{"model_id":"4181","model_name":"ADC-105","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6556":{"protein_sequence":{"accession":"WP_068981612.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSITIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKE"},"dna_sequence":{"accession":"NG_051444.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTACGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCATTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCTTATTTGGAAAAGTTGTTGCTTTGTCTATGAATAAACCTTTCGATCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCTGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTTAACCCACAGAAATATCCGGCTGATATTCAAAGGGCAATTAATGAAACACATCAAGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAAATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCAACGGTTTCGGAACGTATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAACGCATTAAGGCAGCGTATGCAGTTTTAAATGCAATAAAGGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006285","ARO_id":"44747","ARO_name":"ADC-105","CARD_short_name":"ADC-105","ARO_description":"ADC-105 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2249":{"model_id":"2249","model_name":"LpxA","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"3337":"Q72K","3335":"H159D","3336":"G68D"},"Curated-R":{"3337":"Q72K","3335":"H159D","3336":"G68D"},"clinical":{"3337":"Q72K","3335":"H159D","3336":"G68D"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"4645":{"protein_sequence":{"accession":"AJF82049.1","sequence":"MSNHDLIHSTAIIDPSAVIASDVQIGPYCIIGPQVTIGAGTKLHSHVVVGGFTRIGQNNEIFQFASVGEVCQDLKYKGEETWLEIGNNNLIREHCSLHRGTVQDNALTKIGSHNLLMVNTHIAHDCIVGDHNIFANNVGVAGHVHIGDHVIVGGNSGIHQFCKIDSYSMIGGASLILKDVPAYVMASGNPAHAFGINIEGMRRKGWSKNTIQGLREAYKLIFKSGLTSVQAIDQIKSEILPSVPEAQLLIDSLEQSERGIVR"},"dna_sequence":{"accession":"CP010781.1","fmin":"2255674","fmax":"2256463","strand":"-","sequence":"ATGAGCAATCACGATTTAATCCATTCTACCGCCATTATTGATCCATCTGCAGTGATTGCTTCAGATGTTCAAATAGGACCTTATTGTATTATCGGTCCTCAAGTGACTATTGGTGCTGGTACTAAATTACATTCTCATGTGGTTGTAGGTGGTTTTACCAGAATTGGCCAAAATAACGAAATCTTTCAATTTGCAAGTGTTGGCGAAGTTTGCCAAGACCTCAAATATAAAGGTGAAGAAACGTGGCTTGAAATTGGTAACAATAATCTAATTCGCGAACATTGCAGCTTACATAGAGGTACGGTGCAAGATAATGCATTAACCAAGATAGGTAGTCATAACCTATTAATGGTAAATACACATATTGCACATGATTGTATCGTAGGTGACCATAATATCTTTGCTAATAATGTAGGTGTCGCTGGACATGTACATATTGGTGATCACGTTATTGTGGGTGGTAATTCTGGAATTCATCAATTCTGTAAGATCGATTCTTATAGCATGATTGGTGGGGCTTCTTTGATCCTTAAAGATGTTCCAGCCTATGTGATGGCTTCTGGTAACCCTGCACATGCGTTTGGTATAAATATTGAAGGTATGCGAAGAAAAGGTTGGTCTAAAAATACAATTCAAGGCTTAAGAGAAGCTTATAAATTGATATTTAAATCTGGATTAACTTCTGTTCAAGCTATTGACCAAATTAAAAGTGAAATTTTACCTTCAGTTCCAGAAGCTCAACTCTTGATTGATTCTCTTGAACAATCAGAGCGTGGAATTGTGCGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3003573","ARO_id":"40183","ARO_name":"LpxA","CARD_short_name":"LpxA","ARO_description":"The LpxA gene is widely known to be involved in the biosynthesis of lipid A in Gram-negative bacteria and mutations to this gene may cause resistance to antimicrobial peptides that target the outer membrane.","ARO_category":{"40191":{"category_aro_accession":"3003581","category_aro_cvterm_id":"40191","category_aro_name":"Acinetobacter mutant Lpx gene conferring resistance to colistin","category_aro_description":"These genes are involved in the biosynthesis of lipid A in Gram-negative bacteria and mutations to this gene may cause resistance to antimicrobial peptides that target the outer membrane. Mutation by absence or insertion of ISAba11 sequence is a known cause of resistance in Acinetobacter baumannii\u25bf.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2251":{"model_id":"2251","model_name":"LpxC","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"3342":"P30L"},"Curated-R":{"3342":"P30L"},"clinical":{"3342":"P30L"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"4644":{"protein_sequence":{"accession":"AJF83452.1","sequence":"MVKQRTLNRVVKASGIGLHSGQKVMINFIPHTVDGGIVFRRIDLDPPVDIPANALLIQEAFMCSNLVTGDIKVGTIEHVMSAIAGLGIDNLIVEVSASEVPIMDGSAGPFIYLLMQGGLREQDAPKKFIKILKPVEALIDDKKAIFSPHNGFQLNFTIDFDHPAFAKEYQSATIDFSTETFVYEVSEARTFGFMKDLDYLKANNLALGASLDNAIGVDDTGVVNEEGLRFADEFVRHKILDAVGDLYLLGHQIIAKFDGYKSGHALNNQLLRNVQSDPSNYEIVTFDDEKDCPIPYVSVT"},"dna_sequence":{"accession":"CP010781.1","fmin":"3758031","fmax":"3758934","strand":"-","sequence":"ATGGTGAAACAGCGTACTCTCAATCGTGTGGTAAAAGCGAGTGGAATAGGTCTTCATAGCGGTCAAAAAGTGATGATCAATTTCATTCCACATACCGTGGATGGAGGTATTGTATTTCGCCGTATCGATTTGGATCCACCTGTCGATATTCCTGCTAATGCATTGCTGATTCAAGAAGCATTTATGTGTTCAAATCTTGTTACTGGCGATATTAAAGTCGGGACAATCGAACATGTGATGAGTGCGATTGCCGGTTTAGGAATCGATAACTTAATTGTGGAAGTGTCTGCTTCTGAAGTTCCAATTATGGATGGTAGTGCTGGTCCATTTATTTATTTGCTCATGCAAGGTGGCTTGCGTGAACAAGATGCTCCTAAGAAATTTATAAAAATATTAAAGCCAGTTGAGGCTTTAATTGATGATAAAAAAGCAATATTCAGCCCGCATAATGGCTTTCAGCTTAACTTTACGATTGATTTTGATCATCCTGCATTTGCCAAAGAATATCAGTCTGCAACTATCGATTTTTCTACTGAAACGTTTGTGTATGAGGTCAGTGAGGCACGAACTTTTGGTTTTATGAAAGACTTGGATTACCTTAAAGCAAATAATTTAGCTTTAGGAGCAAGTCTAGATAATGCAATTGGCGTAGATGATACAGGTGTTGTAAACGAAGAAGGTTTACGATTTGCCGATGAGTTTGTTCGTCACAAAATTTTAGATGCAGTTGGTGATTTGTATTTACTTGGTCATCAAATTATTGCCAAGTTTGATGGCTATAAATCAGGACATGCCTTAAATAATCAGCTATTACGCAATGTTCAAAGCGATCCGAGTAATTATGAAATTGTAACATTTGATGACGAGAAAGACTGTCCAATTCCATACGTGAGTGTGACATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3003574","ARO_id":"40184","ARO_name":"LpxC","CARD_short_name":"LpxC","ARO_description":"The LpxC gene is widely known to be involved in the biosynthesis of lipid A in Gram-negative bacteria and mutations to this gene may cause resistance to antimicrobial peptides that target the outer membrane.","ARO_category":{"40191":{"category_aro_accession":"3003581","category_aro_cvterm_id":"40191","category_aro_name":"Acinetobacter mutant Lpx gene conferring resistance to colistin","category_aro_description":"These genes are involved in the biosynthesis of lipid A in Gram-negative bacteria and mutations to this gene may cause resistance to antimicrobial peptides that target the outer membrane. Mutation by absence or insertion of ISAba11 sequence is a known cause of resistance in Acinetobacter baumannii\u25bf.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2257":{"model_id":"2257","model_name":"Planobispora rosea EF-Tu mutants conferring resistance to inhibitor GE2270A","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"3418":"G261S","3419":"V278A","3420":"G279A","3421":"V295C"},"Curated-R":{"3418":"G261S","3419":"V278A","3420":"G279A","3421":"V295C"},"clinical":{"3418":"G261S","3419":"V278A","3420":"G279A","3421":"V295C"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"3512":{"protein_sequence":{"accession":"AAB39605.1","sequence":"MAKAKFERTKPHMNIGTIGHIDHGKTTLTAAITKVLHDRYPELNKATPFDKIDKAPEEKARGITISIAHVEYQTEKRHYAHVDCPGHADYVKNMITGAAQMDGAILVVAATAGPMPQTKEHVLLARQVGVPYIVVALNKADMVDDEEILELVELEVRELLSAQEFPGDDLPVVRVSALKALEGDEKWADSIIELMNAVDENIPEPPRDTDKPFLMPIEDVFSITGRGTVVTGRIERGVVKVNEQVDIIGIKSEKTTTTVTSIEMFNKMLDEGHAGDNAALLLRGIKREQVERGQCIIKPGTTTPHTEFEAQVYILSKDEGGRHTPFFNNYRPQFYFRTTDVTGVVNLPEGTEMVMPGDNTEMTVQLIQPIAMEEGLKFAIREGGRTVGAGRVTKILK"},"dna_sequence":{"accession":"U67308.1","fmin":"476","fmax":"1670","strand":"+","sequence":"GTGGCCAAGGCCAAGTTCGAGCGGACCAAGCCGCACATGAACATCGGCACCATTGGGCATATCGACCACGGCAAGACCACTCTGACCGCGGCGATCACCAAGGTGCTCCACGACCGGTACCCCGAGCTGAACAAGGCGACCCCGTTCGACAAGATCGACAAGGCGCCCGAGGAGAAGGCTCGTGGCATCACGATCTCCATCGCGCACGTCGAGTACCAGACCGAGAAGCGCCACTACGCCCACGTGGACTGCCCCGGTCACGCCGACTACGTGAAGAACATGATCACCGGTGCTGCTCAGATGGACGGCGCCATCCTCGTGGTCGCCGCCACCGCCGGCCCGATGCCGCAGACGAAGGAGCACGTCCTCCTGGCCCGTCAGGTCGGCGTCCCCTACATCGTCGTGGCCCTGAACAAGGCCGACATGGTGGACGACGAGGAGATCCTGGAGCTCGTCGAGCTCGAGGTCCGCGAGCTGCTCTCGGCTCAGGAGTTCCCCGGCGACGACCTGCCGGTCGTGCGCGTCTCCGCTCTCAAGGCCCTCGAGGGCGACGAGAAGTGGGCCGACAGCATCATCGAGCTGATGAACGCTGTGGACGAGAACATCCCCGAGCCGCCGCGTGACACCGACAAGCCGTTCCTCATGCCGATCGAGGACGTCTTCTCGATCACCGGTCGTGGAACCGTCGTCACCGGCCGTATCGAGCGCGGTGTCGTCAAGGTCAACGAGCAGGTCGACATCATCGGCATCAAGAGCGAGAAGACCACGACCACCGTCACCAGCATCGAGATGTTCAACAAGATGCTGGACGAGGGCCACGCGGGTGACAACGCGGCCCTGCTGCTCCGCGGCATCAAGCGTGAGCAGGTCGAGCGCGGCCAGTGCATCATCAAGCCGGGCACGACCACCCCGCACACCGAGTTCGAGGCTCAGGTCTACATCCTGTCCAAGGACGAGGGCGGCCGCCACACGCCGTTCTTCAACAACTACCGTCCGCAGTTCTACTTCCGTACGACTGACGTGACCGGTGTCGTGAACCTGCCCGAGGGCACCGAGATGGTCATGCCCGGTGACAACACCGAGATGACCGTCCAGCTCATCCAGCCGATCGCGATGGAGGAAGGCCTCAAGTTCGCGATCCGTGAGGGTGGCCGGACCGTCGGCGCCGGCCGCGTCACCAAGATCCTCAAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40395","NCBI_taxonomy_name":"Planobispora rosea","NCBI_taxonomy_id":"35762"}}}},"ARO_accession":"3003361","ARO_id":"39945","ARO_name":"Planobispora rosea EF-Tu mutants conferring resistance to inhibitor GE2270A","CARD_short_name":"Pros_EFTu_GE2A","ARO_description":"Sequence variants of Planobispora rosea elongation factor Tu that confer resistance to inhibitor GE2270A.","ARO_category":{"37711":{"category_aro_accession":"3001312","category_aro_cvterm_id":"37711","category_aro_name":"elfamycin resistant EF-Tu","category_aro_description":"Sequence variants of elongation factor Tu that confer resistance to elfamycin antibiotics.","category_aro_class_name":"AMR Gene Family"},"37636":{"category_aro_accession":"3001237","category_aro_cvterm_id":"37636","category_aro_name":"GE2270A","category_aro_description":"GE2270A is the model molecule of cyclic thiazolyl peptide elfamycins. GE2270A is produced by Planobispora rosea. Biosynthesis of the molecule has been shown to originate as a ribosomally synthesized peptide that undergoes significant post-translational modification. Clinical use of cyclic thiazolyl peptides is hindered by their low water solubility and bioavailability.","category_aro_class_name":"Antibiotic"},"37618":{"category_aro_accession":"3001219","category_aro_cvterm_id":"37618","category_aro_name":"elfamycin antibiotic","category_aro_description":"Elfamycins are molecules that inhibit bacterial elongation factor Tu (EF-Tu), a key protein which brings aminoacyl-tRNA (aa-tRNA) to the ribosome during protein synthesis. Elfamycins defined by their target (EF-Tu), rather than a conserved chemical backbone. Elfamycins follow two mechanisms to disrupt protein synthesis: 1. kirromycins and enacyloxin fix EF-Tu in the GTP bound conformation and lock EF-Tu onto the ribosome, and 2. pulvomycin and GE2270 cover the binding site of aa-tRNA disallowing EF-Tu from being charged with aa-tRNA. All elfamycins cause increased the affinity of EF-Tu for GTP.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2259":{"model_id":"2259","model_name":"mphG","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"5087":{"protein_sequence":{"accession":"BAL43359.1","sequence":"MKNRDIQKLAERNGLILSDEMSFNEMGIDFKVGFATDRDGTKWLLRIPRRTTLGEQIANEKRILQLVSKYLSVQVPDWRIANEKLVAYPLLDGKPALTYDAETYEVTWNMSKENDLYIPSLAKALIELHSIPTEEVLRNNLKILTPEQVRNEISERLILVKSELGINAELELRYQKWLDNDALWPNFTKFIHGDLYAGHTLTHHNGEVCGIIDWSTAQVSDIAQDFSGHVTVFGEESLKNLIAAYEKQGGEVWDKLFEQAVERAAAAPLAYGYFALETQDEIHLSSAKLQLGVE"},"dna_sequence":{"accession":"AB571865.1","fmin":"143423","fmax":"144308","strand":"-","sequence":"ATGAAAAATAGAGATATTCAAAAATTAGCGGAAAGAAATGGGTTAATTCTTTCGGATGAAATGAGTTTTAATGAAATGGGAATTGATTTTAAGGTTGGTTTCGCTACAGATAGGGATGGCACAAAGTGGTTGTTGCGTATTCCAAGAAGAACAACCTTAGGCGAACAGATTGCGAATGAGAAACGCATTCTTCAATTGGTGTCGAAATACCTTTCGGTTCAAGTTCCTGATTGGCGTATAGCTAATGAAAAACTGGTAGCCTATCCTTTGCTCGATGGAAAACCTGCACTTACTTATGATGCGGAGACTTATGAAGTAACCTGGAATATGTCTAAAGAAAACGACCTTTATATACCATCATTAGCGAAAGCACTTATAGAACTTCATTCAATTCCTACGGAAGAAGTACTTCGTAATAATCTAAAAATTTTGACACCTGAACAGGTTAGAAATGAGATTTCTGAAAGATTGATTTTGGTGAAATCTGAATTAGGGATAAATGCCGAATTAGAACTTCGGTACCAAAAATGGCTGGATAATGATGCCTTATGGCCGAATTTTACAAAATTCATTCACGGTGATTTGTATGCAGGTCATACACTTACTCATCATAATGGAGAAGTTTGTGGAATTATTGATTGGTCAACTGCACAAGTCAGCGATATAGCACAAGATTTTTCAGGTCACGTTACTGTTTTCGGTGAAGAAAGTCTGAAAAATTTAATTGCGGCATACGAAAAACAAGGTGGAGAAGTATGGGATAAACTGTTTGAACAAGCAGTTGAACGAGCTGCTGCCGCACCTCTAGCTTATGGATATTTTGCTTTAGAAACACAAGATGAAATTCATCTTAGTTCTGCAAAATTACAGTTAGGTGTTGAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40398","NCBI_taxonomy_name":"Photobacterium damselae subsp. damselae","NCBI_taxonomy_id":"85581"}}}},"ARO_accession":"3003742","ARO_id":"40397","ARO_name":"mphG","CARD_short_name":"mphG","ARO_description":"The mphG gene encodes a macrolide 2'-phosphotransferase found in Photobacterium damselae sharing sequence similarity to mphA in E. coli.","ARO_category":{"36472":{"category_aro_accession":"3000333","category_aro_cvterm_id":"36472","category_aro_name":"macrolide phosphotransferase (MPH)","category_aro_description":"Macrolide phosphotransferases (MPH) are enzymes encoded by macrolide phosphotransferase genes (mph genes). These enzymes phosphorylate macrolides in GTP dependent manner at 2'-OH of desosamine sugar thereby inactivating them. Characterized MPH's are differentiated based on their substrate specificity.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35982":{"category_aro_accession":"0000065","category_aro_cvterm_id":"35982","category_aro_name":"clarithromycin","category_aro_description":"Clarithromycin is a methyl derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome and is used to treat pharyngitis, tonsillitis, acute maxillary sinusitis, acute bacterial exacerbation of chronic bronchitis, pneumonia (especially atypical pneumonias associated with Chlamydia pneumoniae or TWAR), and skin structure infections.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2224":{"model_id":"2224","model_name":"Pseudomonas aeruginosa oprD with mutation conferring resistance to imipenem","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"3176":"Q142X"},"Curated-R":{"3176":"Q142X"},"clinical":{"3176":"Q142X"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"5273":{"protein_sequence":{"accession":"AAG04347.1","sequence":"MKVMKWSAIALAVSAGSTQFAVADAFVSDQAEAKGFIEDSSLDLLLRNYYFNRDGKSGSGDRVDWTQGFLTTYESGFTQGTVGFGVDAFGYLGLKLDGTSDKTGTGNLPVMNDGKPRDDYSRAGGAVKVRISKTMLKWGEMQPTAPVFAAGGSRLFPQTATGFQLQSSEFEGLDLEAGHFTEGKEPTTVKSRGELYATYAGETAKSADFIGGRYAITDNLSASLYGAELEDIYRQYYLNSNYTIPLASDQSLGFDFNIYRTNDEGKAKAGDISNTTWSLAAAYTLDAHTFTLAYQKVHGDQPFDYIGFGRNGSGAGGDSIFLANSVQYSDFNGPGEKSWQARYDLNLASYGVPGLTFMVRYINGKDIDGTKMSDNNVGYKNYGYGEDGKHHETNLEAKYVVQSGPAKDLSFRIRQAWHRANADQGEGDQNEFRLIVDYPLSIL"},"dna_sequence":{"accession":"AE004091.2","fmin":"1043982","fmax":"1045314","strand":"-","sequence":"ATGAAAGTGATGAAGTGGAGCGCCATTGCACTGGCGGTTTCCGCAGGTAGCACTCAGTTCGCCGTGGCCGACGCATTCGTCAGCGATCAGGCCGAAGCGAAGGGGTTCATCGAAGACAGCAGCCTCGACCTGCTGCTCCGCAACTACTATTTCAACCGTGACGGCAAGAGCGGCAGCGGGGACCGCGTCGACTGGACCCAAGGCTTCCTCACCACCTATGAATCCGGCTTCACCCAAGGCACTGTGGGCTTCGGCGTCGATGCCTTCGGCTACCTGGGCCTGAAGCTCGACGGCACCTCCGACAAGACCGGCACCGGCAACCTGCCGGTGATGAACGACGGCAAGCCGCGCGATGACTACAGCCGCGCCGGCGGCGCCGTGAAGGTGCGCATCTCCAAGACCATGCTGAAGTGGGGCGAGATGCAACCGACCGCCCCGGTCTTCGCCGCTGGCGGCAGCCGCCTGTTCCCGCAGACCGCGACCGGCTTCCAGCTGCAGAGCAGCGAATTCGAAGGGCTCGACCTCGAGGCAGGCCACTTCACCGAGGGCAAGGAGCCGACCACCGTCAAATCGCGTGGCGAACTCTATGCCACCTACGCAGGCGAGACCGCCAAGAGCGCCGATTTCATTGGGGGCCGCTACGCAATCACCGATAACCTCAGCGCCTCCCTGTACGGCGCCGAACTCGAAGACATCTATCGCCAGTATTACCTGAACAGCAACTACACCATCCCACTGGCATCCGACCAATCGCTGGGCTTCGATTTCAACATCTACCGCACAAACGATGAAGGCAAGGCCAAGGCCGGCGACATCAGCAACACCACTTGGTCCCTGGCGGCAGCCTACACTCTGGATGCGCACACTTTCACCTTGGCCTACCAGAAGGTCCATGGCGATCAGCCGTTTGATTATATCGGCTTCGGCCGCAACGGCTCTGGCGCAGGTGGCGACTCGATTTTCCTCGCCAACTCTGTCCAGTACTCCGACTTCAACGGCCCTGGCGAGAAATCCTGGCAGGCTCGCTACGACCTGAACCTAGCCTCCTATGGCGTTCCCGGCCTGACTTTCATGGTCCGCTATATCAATGGCAAGGACATCGATGGCACCAAGATGTCTGACAACAACGTCGGCTATAAGAACTACGGCTACGGCGAGGATGGCAAGCACCACGAAACCAACCTCGAAGCCAAGTACGTGGTCCAGTCCGGTCCGGCCAAGGACCTGTCGTTCCGCATCCGCCAGGCCTGGCACCGTGCCAACGCCGACCAGGGCGAAGGCGACCAGAACGAGTTCCGCCTGATCGTCGACTATCCGCTGTCGATCCTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36804","NCBI_taxonomy_name":"Pseudomonas aeruginosa PAO1","NCBI_taxonomy_id":"208964"}}}},"ARO_accession":"3003686","ARO_id":"40321","ARO_name":"Pseudomonas aeruginosa oprD with mutation conferring resistance to imipenem","CARD_short_name":"Paer_oprD_IPM","ARO_description":"oprD is an outer membrane porin which facilitates the uptake of basic amino acids and imipenem in Pseudomonas aeruginosa.","ARO_category":{"41442":{"category_aro_accession":"3004278","category_aro_cvterm_id":"41442","category_aro_name":"Outer Membrane Porin (Opr)","category_aro_description":"The Opr family consists of porins in Pseudomonas species, and other Gram-negative bacteria, that exhibit a variety of substrate selectivities.","category_aro_class_name":"AMR Gene Family"},"36309":{"category_aro_accession":"3000170","category_aro_cvterm_id":"36309","category_aro_name":"imipenem","category_aro_description":"Imipenem is a broad-spectrum antibiotic and is usually taken with cilastatin, which prevents hydrolysis of imipenem by renal dehydropeptidase-I. It is resistant to hydrolysis by most other beta-lactamases. Notable exceptions are the KPC beta-lactamases and Ambler Class B enzymes.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36383":{"category_aro_accession":"3000244","category_aro_cvterm_id":"36383","category_aro_name":"reduced permeability to antibiotic","category_aro_description":"Reduction in permeability to antibiotic, generally through reduced production of porins, can provide resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2241":{"model_id":"2241","model_name":"vanI","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"350"}},"model_sequences":{"sequence":{"4649":{"protein_sequence":{"accession":"KTE89608.1","sequence":"MTKLKIAIIFGGCSEEHPVSVKSAGEVAKNLDPEKYEPFYIGITKDGVWQLCHYPEVNWEKGSCRPAILSPDRSVQGLLVLEQGQYQRIPLDLVFPVLHGKFGEDGAMQGLLELSGIPYVGCDIPSSALCMDKSLAYIVAGKAGIATPKFRTVTVKETIDAERLTYPVYVKPARSGSSFGVTKVCRQEELLNAVEIASQYDSKVLIEETVIGTEIGCAIFGNDLDLIAGEVDQIRLSHGFFRIHQENEPEKGSENSTLIVPAGISAEARSRVQETAKAIYRALGCRGLARVDMFLKEDGTVILNEVNTLPGMTSYSRFPRMMAAAGLPFAEVIDRLVSLALKGKTGTN"},"dna_sequence":{"accession":"LOCK01000072.1","fmin":"166343","fmax":"167390","strand":"-","sequence":"ATGACTAAGTTGAAAATTGCAATTATCTTCGGAGGCTGTTCCGAAGAACATCCCGTCTCCGTTAAATCTGCTGGGGAGGTCGCCAAAAACCTGGATCCCGAAAAGTATGAACCCTTCTATATCGGGATTACGAAAGATGGGGTTTGGCAGCTTTGCCACTACCCTGAGGTCAATTGGGAAAAGGGCAGCTGCCGTCCGGCTATCCTGTCACCGGACAGAAGCGTCCAGGGATTGCTTGTTCTGGAGCAGGGACAATACCAAAGGATACCTTTGGATCTGGTGTTTCCCGTTCTGCATGGCAAATTTGGCGAGGATGGGGCGATGCAAGGCTTGCTGGAGCTTTCCGGCATCCCCTATGTGGGCTGTGATATCCCGAGTTCGGCTCTGTGCATGGACAAATCCCTGGCTTATATCGTCGCTGGAAAGGCAGGAATTGCCACGCCAAAGTTCCGGACGGTCACGGTGAAGGAAACCATTGACGCTGAACGGCTTACTTATCCCGTTTATGTCAAGCCGGCCCGTTCGGGTTCATCCTTCGGCGTCACTAAGGTATGCCGCCAAGAAGAATTGCTGAATGCGGTGGAAATCGCCAGCCAGTATGACTCGAAGGTGCTGATTGAAGAGACTGTCATCGGCACTGAGATAGGGTGTGCGATATTTGGGAACGATCTGGATTTGATCGCCGGCGAGGTCGATCAGATTCGTCTGTCTCATGGCTTTTTCAGAATCCATCAGGAGAATGAGCCGGAAAAGGGTTCCGAAAACTCAACACTAATCGTTCCCGCCGGCATTTCGGCAGAGGCGCGCTCGCGTGTTCAGGAGACGGCAAAAGCCATCTATCGCGCTTTGGGCTGCAGGGGACTGGCGCGGGTGGATATGTTTCTGAAAGAAGATGGAACAGTAATCCTCAACGAGGTGAATACCTTGCCCGGCATGACCTCATACAGCCGTTTTCCGAGAATGATGGCGGCCGCAGGCTTGCCCTTTGCCGAAGTGATCGACCGGCTTGTCTCGTTGGCCTTGAAAGGAAAAACAGGAACCAATTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40382","NCBI_taxonomy_name":"Desulfitobacterium hafniense","NCBI_taxonomy_id":"49338"}}}},"ARO_accession":"3003723","ARO_id":"40377","ARO_name":"vanI","CARD_short_name":"vanI","ARO_description":"VanI is a D-Ala-D-Lac ligase that reduces vancomycin binding affinity, helping to confer vancomycin resistance as part of the VanI resistance gene cluster in Desulfitobacterium spp. and Desulfosporosinus spp.","ARO_category":{"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"39340":{"category_aro_accession":"3002906","category_aro_cvterm_id":"39340","category_aro_name":"Van ligase","category_aro_description":"Van ligases synthesize alternative substrates for peptidoglycan synthesis that reduce vancomycin binding affinity.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"35948":{"category_aro_accession":"0000029","category_aro_cvterm_id":"35948","category_aro_name":"teicoplanin","category_aro_description":"Teicoplanin is a glycopeptide antibiotic used in the prophylaxis and treatment of serious infections caused by Gram-positive bacteria. Teicoplanin has a unique acyl-aliphatic chain, and binds to cell wall precursors to inhibit transglycosylation  and transpeptidation.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3480":{"model_id":"3480","model_name":"OXA-346","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"5674":{"protein_sequence":{"accession":"AHN07464.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDDKAEKIKNLFNEAHTTGVLVIHQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGEKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSILFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"KF048919.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGACAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCATCAAGGTCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAATGGGATGGGGAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATACTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001534","ARO_id":"37934","ARO_name":"OXA-346","CARD_short_name":"OXA-346","ARO_description":"OXA-346 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3509":{"model_id":"3509","model_name":"OXA-439","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"5704":{"protein_sequence":{"accession":"AKR53961.1","sequence":"MRVLALSAVFLVASIIGMPAVAKEWQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGQTRDIATWNRDHNLITAMKYSVVPVHQEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISATEQISFLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYDTKIGWWVGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP"},"dna_sequence":{"accession":"KP727573.1","fmin":"0","fmax":"786","strand":"+","sequence":"ATGCGTGTATTAGCCTTATCGGCTGTGTTTTTGGTGGCATCGATTATCGGAATGCCTGCGGTAGCAAAGGAATGGCAAGAAAACAAAAGTTGGAATGCTCACTTTACTGAACATAAATCACAGGGCGTAGTTGTGCTCTGGAATGAGAATAAGCAGCAAGGATTTACCAATAATCTTAAACGGGCGAACCAAGCATTTTTACCCGCATCTACCTTTAAAATTCCCAATAGCTTGATCGCCCTCGATTTGGGCGTGGTTAAGGATGAACACCAAGTCTTTAAGTGGGATGGACAGACGCGCGATATCGCCACTTGGAATCGCGATCATAATCTAATCACCGCGATGAAATATTCAGTTGTGCCTGTTCATCAAGAATTTGCCCGCCAAATTGGCGAGGCACGTATGAGCAAGATGCTACATGCTTTCGATTATGGTAATGAGGACATTTCGGGCAATGTAGACAGTTTCTGGCTCGACGGTGGTATTCGAATTTCGGCCACGGAGCAAATCAGCTTTTTAAGAAAGCTGTATCACAATAAGTTACACGTATCGGAGCGCAGCCAGCGTATTGTCAAACAAGCCATGCTGACCGAAGCCAATGGCGACTATATTATTCGGGCTAAAACTGGATACGATACTAAGATTGGCTGGTGGGTCGGTTGGGTTGAACTTGATGATAATGTGTGGTTTTTTGCGATGAATATGGATATGCCCACATCGGATGGTTTAGGGCTGCGCCAAGCCATCACAAAAGAAGTGCTCAAACAGGAAAAAATTATTCCCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3003595","ARO_id":"40205","ARO_name":"OXA-439","CARD_short_name":"OXA-439","ARO_description":"OXA-439 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46510":{"category_aro_accession":"3007721","category_aro_cvterm_id":"46510","category_aro_name":"OXA-48-like beta-lactamase","category_aro_description":"OXA-48-type beta-lactamases are now routinely encountered in bacterial infections caused by carbapenam-resistant Enterobacterales. OXA-48-like proteins confer resistance to penicillin (which is efficiently hydrolyzed) and carbapenam antibiotics (which is more slowly broken down). The spectrum of activity of these variants varies, with some hydrolyzing expanded-spectrum oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3539":{"model_id":"3539","model_name":"OXA-477","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"520"}},"model_sequences":{"sequence":{"5734":{"protein_sequence":{"accession":"ALC79292.1","sequence":"MSKKNFILIFIFVILISCKNTEKISNETTLIDNVFTNSNAEGTLVIYNLNDDKYIIHNKERAEQRFYPASTFKIYNSLIGLNEKAVKDVDEVFYKYIGEKVFLEFWAKDSNLRYAIKNSQVPAYKELARRIGLKKMKENIEKLDFGNKNIGDSVDTFWLEGPLEISAMEQVELLTKLAQNELPYPIEIQKAVSDITILEQTYNYTLHGKTGLADSKNMTTEPIGWFVGWLEENDNIYVFALNIDNINSDDLAKRINIVKESLKALNLLK"},"dna_sequence":{"accession":"KR182170.1","fmin":"0","fmax":"810","strand":"+","sequence":"ATGTCTAAAAAAAATTTTATATTAATATTTATTTTTGTTATTTTAATATCTTGTAAAAATACAGAAAAAATATCAAATGAAACTACATTAATAGATAATGTATTTACTAATAGCAATGCTGAAGGAACATTAGTTATATATAATTTAAATGATGATAAATATATAATTCATAATAAAGAAAGAGCTGAACAAAGATTTTATCCAGCATCAACATTTAAAATATATAATAGTTTAATAGGCTTAAATGAAAAAGCAGTTAAAGATGTAGATGAAGTATTTTATAAATATATTGGCGAAAAAGTTTTTCTTGAATTTTGGGCTAAGGACTCTAATTTAAGATATGCAATTAAAAATTCGCAAGTACCGGCATATAAAGAATTAGCAAGAAGAATAGGTCTTAAAAAGATGAAAGAGAATATAGAAAAACTAGATTTTGGTAATAAAAATATAGGTGATAGTGTAGATACTTTTTGGCTTGAAGGACCTTTGGAAATAAGTGCGATGGAGCAAGTTGAATTATTAACTAAATTAGCTCAAAATGAATTACCGTATCCTATAGAAATACAAAAAGCTGTTTCTGATATTACTATACTAGAGCAAACTTACAATTATACGCTTCATGGAAAAACTGGATTAGCTGATTCTAAAAACATGACAACTGAGCCTATTGGTTGGTTCGTAGGCTGGCTTGAAGAAAATGATAATATATATGTCTTTGCTTTAAATATTGATAATATCAATTCAGATGACCTTGCAAAAAGGATAAATATAGTAAAAGAAAGTTTAAAAGCATTAAATTTATTAAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36935","NCBI_taxonomy_name":"Brachyspira pilosicoli","NCBI_taxonomy_id":"52584"}}}},"ARO_accession":"3003634","ARO_id":"40244","ARO_name":"OXA-477","CARD_short_name":"OXA-477","ARO_description":"OXA-477 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46521":{"category_aro_accession":"3007732","category_aro_cvterm_id":"46521","category_aro_name":"OXA-63-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-63.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2260":{"model_id":"2260","model_name":"vatF","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"3514":{"protein_sequence":{"accession":"AAF63432.1","sequence":"MEDKPILGPDPQCKHPMVGFSQVCFIKNTTQNPNIIIGDYTYYDDPQDSENFERNVLYHYPFIGDKLIIGKFCALAHGVKFIMNGANHKMSGLSTYPFNIFGNGWERVAPSRDELPYKGDTHVGNDVWIGYDVLIMPGVTIGNGAIISSRSVVTRDVPAYSVVGGNPATLIKNRFSAEVIGKLQTIAWWDWPIDAISRNLHLIVAGDIEALARAASEIDHT"},"dna_sequence":{"accession":"AF170730.1","fmin":"69","fmax":"735","strand":"+","sequence":"ATGGAAGATAAGCCAATATTAGGGCCAGATCCCCAGTGTAAACACCCGATGGTGGGGTTTTCTCAAGTATGCTTTATCAAAAATACCACACAGAATCCGAACATTATTATCGGTGATTATACCTACTACGACGATCCACAAGATTCTGAAAACTTTGAACGTAACGTGCTTTATCACTACCCCTTTATTGGTGATAAGCTGATTATCGGCAAATTCTGTGCATTAGCTCATGGGGTGAAGTTCATTATGAATGGTGCCAACCATAAAATGTCTGGGTTATCGACTTACCCATTCAATATTTTTGGTAACGGTTGGGAAAGAGTCGCCCCGTCCAGGGATGAGCTGCCTTATAAAGGCGATACTCATGTCGGAAATGATGTGTGGATTGGCTATGATGTGTTGATTATGCCAGGTGTCACCATTGGCAATGGGGCAATTATTTCATCACGCTCAGTGGTCACGCGCGATGTGCCCGCTTATAGTGTGGTCGGCGGTAATCCCGCAACACTGATTAAAAATCGCTTCTCAGCCGAGGTTATCGGTAAGCTACAAACCATTGCCTGGTGGGATTGGCCAATAGACGCGATCAGTCGCAATCTACACCTGATCGTTGCCGGTGATATCGAGGCATTAGCGCGAGCAGCCAGCGAGATTGATCACACCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40164","NCBI_taxonomy_name":"Yersinia enterocolitica","NCBI_taxonomy_id":"630"}}}},"ARO_accession":"3003744","ARO_id":"40399","ARO_name":"vatF","CARD_short_name":"vatF","ARO_description":"vatF is a streptogramin A acetyl transferase gene isolated from the chromosome of Yersinia enterocolitica.","ARO_category":{"36592":{"category_aro_accession":"3000453","category_aro_cvterm_id":"36592","category_aro_name":"streptogramin vat acetyltransferase","category_aro_description":"vat (Virginiamycin acetyltransferases) enzymes catalyze the transfer of an acetyl group from acetyl-CoA to the secondary alcohol of streptogramin A compounds, thus inactivating virginiamycin-like antibiotics and conferring resistance to these compounds.","category_aro_class_name":"AMR Gene Family"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"virginiamycin M1","category_aro_description":"Virginiamycin M1 is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37016":{"category_aro_accession":"3000672","category_aro_cvterm_id":"37016","category_aro_name":"madumycin II","category_aro_description":"Madumycin II is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37017":{"category_aro_accession":"3000673","category_aro_cvterm_id":"37017","category_aro_name":"griseoviridin","category_aro_description":"Griseoviridin is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35952":{"category_aro_accession":"0000034","category_aro_cvterm_id":"35952","category_aro_name":"streptogramin A antibiotic","category_aro_description":"Streptogramin A antibiotics are cyclic polyketide peptide hybrids that bind to the ribosomal peptidyl transfer centre. Structural variation arises from substituting a proline for its desaturated derivative and by its substitution for Ala or Cys. Used alone, streptogramin A antibiotics are bacteriostatic, but is bactericidal when used with streptogramin B antibiotics.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2261":{"model_id":"2261","model_name":"lnuE","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"3515":{"protein_sequence":{"accession":"AGT57825.1","sequence":"MGKNNVTEKHLFYILDLLKDLQITYWLDGGWGVDVLTGKQQREHRDIDIDFDSQHTDKLVKKLKEIGYITVVDWMPSRMELKHEEYGYLDIHPLDLKKDGTATQADPKGGFYLFEKDWFTTTNYKNRKIPCISKEAQLLFHSGYELTEKDQFDIKNLNSINQVKKEGHFSNDF"},"dna_sequence":{"accession":"KF287643.1","fmin":"0","fmax":"522","strand":"+","sequence":"TTGGGAAAAAATAATGTCACAGAAAAACATCTATTTTATATTTTAGATTTACTTAAAGACCTCCAAATAACTTATTGGTTAGACGGTGGATGGGGAGTAGATGTACTCACTGGAAAGCAACAGAGAGAACACAGAGACATAGATATCGATTTTGATTCACAACATACAGACAAATTAGTTAAAAAATTAAAAGAGATTGGATACATCACAGTTGTAGATTGGATGCCTTCCAGAATGGAATTAAAACACGAAGAATACGGATATTTAGATATACATCCCTTAGATTTAAAAAAAGATGGCACAGCAACTCAAGCCGATCCAAAAGGCGGTTTTTATCTATTCGAAAAAGATTGGTTCACAACTACAAATTACAAAAATCGAAAAATACCATGCATTTCAAAAGAAGCACAACTACTTTTTCACTCTGGATATGAATTAACAGAAAAAGACCAATTTGATATTAAAAATTTAAACTCAATAAATCAAGTTAAGAAAGAAGGTCATTTTTCAAATGACTTCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36748","NCBI_taxonomy_name":"synthetic construct","NCBI_taxonomy_id":"32630"}}}},"ARO_accession":"3003762","ARO_id":"40400","ARO_name":"lnuE","CARD_short_name":"lnuE","ARO_description":"lnuE encodes a lincosamide resistance gene isolated from Streptococcus suis that was truncated by an ISEnfa5-cfr-ISEnfa5 segment insertion. It shares the closest sequence similarity to lnuA.","ARO_category":{"36360":{"category_aro_accession":"3000221","category_aro_cvterm_id":"36360","category_aro_name":"lincosamide nucleotidyltransferase (LNU)","category_aro_description":"Resistance to the lincosamide antibiotic by ATP-dependent modification of the 3' and\/or 4'-hydroxyl groups of the methylthiolincosamide sugar.","category_aro_class_name":"AMR Gene Family"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2264":{"model_id":"2264","model_name":"oleC","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"3518":{"protein_sequence":{"accession":"AAA26793.1","sequence":"MTVRGLVKHYGETKALDGVDLDVREGTVMGVLGPNGAGKTTLVRILSTLITPDSGQATVAGYDVVRQPRQLRRVIGLTGQYASVDEKLPGWENLYLIGRLLDLSRKEARARADELLERFSLTEAARRPAGTYSGGMRRRLDLAASMIGRPAVLYLDEPTTGLDPRTRNEVWDEVKAMVGDGVTVLLTTQYMEEAEQLASELTVVDRGRVIAKGGIEELKARVGGRTLRVRPVDPLQLRPLAGMLDELGITGLASTTVDTETGALLVPILSDEQLTAVVGAVTARGITLSSITTELPSLDEVFLSLTGHRASAPQDAEPARQEVAV"},"dna_sequence":{"accession":"L06249.1","fmin":"1527","fmax":"2505","strand":"+","sequence":"GTGACCGTACGGGGGCTGGTCAAGCACTACGGCGAGACCAAGGCGCTGGACGGCGTCGACCTGGACGTGCGCGAGGGCACCGTGATGGGTGTGCTCGGGCCGAACGGCGCCGGCAAGACCACCCTCGTCCGCATCCTGTCCACCCTGATCACCCCGGACTCCGGGCAGGCCACCGTGGCCGGCTACGACGTCGTACGCCAGCCCCGGCAGCTGCGCCGGGTCATCGGGCTCACCGGCCAGTACGCGTCGGTGGACGAGAAGCTCCCGGGCTGGGAGAACCTCTACCTGATCGGCCGGCTGCTGGACCTGTCCCGCAAGGAGGCCCGGGCCCGCGCCGACGAGCTGCTGGAGCGGTTCTCGCTGACCGAGGCCGCCCGGCGCCCGGCCGGCACCTACTCCGGCGGTATGCGGCGCCGACTGGACCTGGCCGCCTCGATGATCGGCCGGCCGGCCGTGCTGTACCTGGACGAGCCGACCACCGGCCTCGACCCGCGCACCCGCAACGAGGTGTGGGACGAGGTCAAGGCGATGGTCGGCGACGGCGTCACCGTGCTGCTCACCACCCAGTACATGGAGGAGGCCGAGCAGCTCGCCTCGGAACTGACCGTGGTGGACCGCGGCCGGGTCATCGCCAAGGGCGGCATCGAGGAGCTGAAGGCCCGCGTCGGCGGGCGCACCCTGCGGGTGCGGCCGGTCGACCCGCTCCAGCTGCGCCCGCTCGCCGGCATGCTGGACGAGCTGGGCATCACCGGGCTGGCTTCCACCACCGTGGACACCGAGACCGGGGCCCTGCTGGTGCCGATCCTCAGCGACGAGCAGCTGACCGCCGTGGTCGGCGCGGTCACCGCGCGCGGCATCACGCTGTCCTCCATCACCACCGAACTGCCCAGCCTGGACGAGGTGTTCCTGTCCCTCACCGGCCACCGCGCCAGTGCCCCGCAGGACGCCGAGCCCGCCCGCCAGGAGGTCGCCGTATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36823","NCBI_taxonomy_name":"Streptomyces antibioticus","NCBI_taxonomy_id":"1890"}}}},"ARO_accession":"3003748","ARO_id":"40404","ARO_name":"oleC","CARD_short_name":"oleC","ARO_description":"oleC is an ABC transporter isolated from Streptomyces antibioticus and is involved in oleandomycin secretion.","ARO_category":{"36002":{"category_aro_accession":"0010001","category_aro_cvterm_id":"36002","category_aro_name":"ATP-binding cassette (ABC) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding\/hydrolysis to transport substrates across cell membranes.","category_aro_class_name":"AMR Gene Family"},"37247":{"category_aro_accession":"3000867","category_aro_cvterm_id":"37247","category_aro_name":"oleandomycin","category_aro_description":"Oleandomycin is a 14-membered macrolide produced by Streptomyces antibioticus. It is ssimilar to erythromycin, and contains a desosamine amino sugar and an oleandrose sugar. It targets the 50S ribosomal subunit to prevent protein synthesis.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2265":{"model_id":"2265","model_name":"salA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1100"}},"model_sequences":{"sequence":{"3519":{"protein_sequence":{"accession":"AGN74946.1","sequence":"MLFLFEEKALEVEHKVLIPELTFSIEDHEHLAIVGVNGVGKSTLLKVIHQDQSVDSAMMEQDLTPYYDWTVMDYIIESYPEIAKIRLQLNHTDMINKYIELDGYIIEGEIVTEAKKLGIKEEQLEQKISTLSGGEQTKVSFLKVKMSKASLLLIDEPTNHMDLEMKEWLTKAFKQEQRAILFVSHDRTFLNETPDAILELSLDGAKKYIGKYDKYKQQKDIEHETLKLQYEKQQKEQAAIEETIKKYKAWYQKAEQSASVRSPYQQKQLSKLAKRFKSKEQQLNRKLDQEHIPNPHKKEKTFSIQHHNFKSHYLVQFNHVSFAYDNRKIFDDVSFYIKRNQNVIVEGRNGTGKSTLIKLILGELEPTKGDITVHPELEIGYFSQDFENLNMHHTVLDEILEIPEMKEADARTILASFYFDKDRINDVVETLSMGEKCRLQFVKLYFSNPHIMILDEPTNYFDIGMQENIIQLIQSFQGSVLIVSHDNYFKSQIKDQTWTIKNHQMTHENVQVKDPINTESMKHHLKELEQYTDERNRETEF"},"dna_sequence":{"accession":"KC693025.1","fmin":"0","fmax":"1626","strand":"+","sequence":"ATGCTATTTTTATTTGAAGAAAAAGCATTAGAAGTTGAACATAAAGTATTAATACCCGAGTTGACTTTTTCAATAGAGGACCATGAACATTTAGCAATCGTTGGTGTTAATGGTGTTGGAAAATCAACATTATTAAAAGTCATTCATCAAGATCAATCAGTTGATTCAGCGATGATGGAACAAGATTTAACACCTTATTATGATTGGACTGTTATGGATTATATAATTGAATCATATCCTGAAATCGCAAAGATTAGATTGCAACTTAATCATACAGATATGATTAATAAATATATTGAATTAGATGGATACATTATAGAAGGTGAAATCGTAACAGAAGCAAAAAAGCTCGGAATAAAAGAGGAACAACTAGAACAGAAAATTTCTACTTTAAGTGGTGGAGAACAAACAAAAGTATCATTTTTAAAAGTGAAAATGTCTAAAGCATCATTACTATTAATCGATGAACCAACAAACCACATGGATTTAGAAATGAAGGAATGGTTGACGAAAGCTTTTAAACAAGAACAACGTGCTATATTATTTGTATCTCATGACCGAACATTTTTAAATGAAACGCCAGATGCTATATTAGAATTGAGTCTTGATGGGGCTAAGAAGTATATCGGTAAATACGATAAATACAAACAACAAAAAGATATAGAGCATGAAACATTAAAGCTACAGTATGAAAAACAACAAAAAGAACAAGCGGCCATTGAAGAAACGATTAAAAAATATAAAGCATGGTATCAAAAAGCAGAACAAAGTGCTTCTGTGAGAAGCCCATATCAACAAAAACAATTAAGTAAGTTAGCGAAACGGTTTAAATCAAAAGAACAACAATTAAATCGTAAACTTGATCAAGAGCATATCCCAAATCCACATAAAAAAGAGAAAACTTTCTCAATACAACATCATAATTTTAAATCACATTATTTAGTTCAATTTAATCATGTTTCGTTTGCTTATGATAACCGGAAAATATTCGATGATGTATCATTCTATATTAAGCGAAATCAAAATGTTATTGTTGAAGGCAGAAATGGTACAGGTAAATCAACTTTAATCAAATTGATACTCGGTGAACTCGAGCCAACTAAAGGTGATATAACTGTTCATCCAGAATTAGAAATTGGATATTTCTCTCAAGATTTTGAGAATTTAAATATGCATCATACTGTCTTAGATGAAATATTAGAAATTCCTGAAATGAAAGAAGCAGATGCAAGAACCATATTAGCAAGCTTTTATTTTGATAAAGATAGGATAAATGATGTTGTTGAAACACTATCGATGGGTGAAAAATGTAGGTTACAATTTGTAAAATTATATTTTTCAAATCCTCATATTATGATATTAGATGAGCCAACAAACTATTTCGATATTGGCATGCAAGAAAATATCATTCAATTAATACAATCATTTCAAGGTTCGGTCCTTATTGTATCTCATGATAATTATTTTAAATCACAAATTAAAGATCAGACTTGGACTATAAAAAATCATCAAATGACGCATGAAAATGTTCAAGTCAAAGATCCTATTAATACAGAATCTATGAAACATCATTTAAAAGAATTAGAACAATATACAGATGAAAGAAATCGTGAAACAGAGTTCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36794","NCBI_taxonomy_name":"Mammaliicoccus sciuri","NCBI_taxonomy_id":"1296"}}}},"ARO_accession":"3003749","ARO_id":"40405","ARO_name":"salA","CARD_short_name":"salA","ARO_description":"salA is an ABC-F subfamily protein gene isolated from the chromosome of Mammaliicoccus sciuri conferring resistance to lincosamides and streptogramins.","ARO_category":{"45589":{"category_aro_accession":"3007030","category_aro_cvterm_id":"45589","category_aro_name":"sal-type ABC-F protein","category_aro_description":"Sal proteins are a part of the ABC-F proteins, expressed in staphylococci that confer resistance to group A streptogramin, lincosamide, and pleuromutilin antibiotics through ribosomal protection.","category_aro_class_name":"AMR Gene Family"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"virginiamycin M1","category_aro_description":"Virginiamycin M1 is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37015":{"category_aro_accession":"3000671","category_aro_cvterm_id":"37015","category_aro_name":"tiamulin","category_aro_description":"Tiamulin is a pleuromutilin derivative currently used in veterinary medicine. It binds to the 23 rRNA of the 50S ribosomal subunit to inhibit protein translation.","category_aro_class_name":"Antibiotic"},"37713":{"category_aro_accession":"3001314","category_aro_cvterm_id":"37713","category_aro_name":"retapamulin","category_aro_description":"Retapamulin is a semi-synthetic pleuromutilin antibiotic approved for the treatment of skin infections.","category_aro_class_name":"Antibiotic"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35952":{"category_aro_accession":"0000034","category_aro_cvterm_id":"35952","category_aro_name":"streptogramin A antibiotic","category_aro_description":"Streptogramin A antibiotics are cyclic polyketide peptide hybrids that bind to the ribosomal peptidyl transfer centre. Structural variation arises from substituting a proline for its desaturated derivative and by its substitution for Ala or Cys. Used alone, streptogramin A antibiotics are bacteriostatic, but is bactericidal when used with streptogramin B antibiotics.","category_aro_class_name":"Drug Class"},"37014":{"category_aro_accession":"3000670","category_aro_cvterm_id":"37014","category_aro_name":"pleuromutilin antibiotic","category_aro_description":"Pleuromutilins are natural fungal products that target bacterial protein translation by binding the the 23S rRNA, blocking the ribosome P site at the 50S subunit. They are mostly used for agriculture and veterinary purposes.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2274":{"model_id":"2274","model_name":"RlmA(II)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"3534":{"protein_sequence":{"accession":"AJD73064.1","sequence":"MNTNLKPKLQRFASATAFACPICQENLTLLETNFKCCNRHSFDLAKFGYVNLAPQIKQSANYNKENFQNRQQILEAGFYQAILDAVSDLLASSKTTTTILDIGCGEGFYSRKLQESHSEKTFYAFDISKDSVQIAAKSEPNWAVNWFVGDLARLPIKDANMDILLDIFSPANYGEFRRVLSKDGILIKVIPTENHLKEIRQRVQDQLTNKEYSNQDIKEHFQEHFTILSSQTASLTKTITAEQLQALLSMTPLLFHVDQSKIDWSQLTEITIEAEILVGKAF"},"dna_sequence":{"accession":"CP007593.1","fmin":"2148923","fmax":"2149772","strand":"+","sequence":"ATGAATACAAATCTCAAGCCCAAACTTCAGCGTTTTGCTTCTGCGACTGCCTTTGCCTGTCCTATCTGTCAAGAAAATCTGACTCTGTTAGAGACTAATTTCAAGTGCTGCAACCGTCATTCTTTTGACTTGGCGAAATTTGGCTATGTCAATCTAGCACCTCAAATCAAGCAATCTGCTAACTATAACAAGGAAAATTTTCAAAACCGTCAACAAATCCTAGAAGCCGGCTTTTACCAAGCTATCTTAGATGCTGTATCTGACTTGCTTGCAAGCTCAAAAACTACCACAACAATTTTGGATATCGGTTGTGGTGAAGGATTCTATTCTCGCAAACTACAAGAAAGTCACTCTGAAAAAACTTTCTATGCCTTTGACATCTCCAAAGATTCAGTCCAAATCGCTGCTAAAAGTGAACCCAACTGGGCAGTCAATTGGTTTGTTGGCGACTTGGCACGACTTCCTATAAAAGACGCTAACATGGATATTCTGCTTGATATCTTCTCACCTGCCAACTATGGAGAATTTCGTCGCGTTTTATCCAAAGACGGTATCTTGATAAAGGTTATCCCAACTGAAAATCACCTCAAAGAAATCCGTCAAAGAGTACAGGACCAGCTGACAAACAAGGAGTATTCTAACCAAGATATCAAGGAGCATTTCCAGGAACACTTTACCATCCTATCTAGTCAAACTGCCTCTCTGACTAAGACTATCACAGCAGAACAACTCCAAGCCCTACTCAGTATGACTCCTCTCCTCTTTCACGTTGACCAGAGCAAGATTGACTGGAGCCAACTGACAGAGATTACCATCGAAGCAGAGATTTTGGTTGGGAAAGCATTCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35917","NCBI_taxonomy_name":"Streptococcus pneumoniae","NCBI_taxonomy_id":"1313"}}}},"ARO_accession":"3001301","ARO_id":"37700","ARO_name":"RlmA(II)","CARD_short_name":"RlmA(II)","ARO_description":"RlmA(II) is a methyltransferase found in Streptococcus pneumoniae and confers resistance to tylosin and mycinamicin. Specifically, this enzyme adds a methyl group to guanosine 748 (E. coli numbering) of 23S ribosomal RNA.","ARO_category":{"37697":{"category_aro_accession":"3001298","category_aro_cvterm_id":"37697","category_aro_name":"non-erm 23S ribosomal RNA methyltransferase (G748)","category_aro_description":"Non-erm 23S ribosomal RNA methyltransferases modify guanosine 748 (E. coli numbering) to confer resistance to some macrolides and lincosamides.","category_aro_class_name":"AMR Gene Family"},"36284":{"category_aro_accession":"3000145","category_aro_cvterm_id":"36284","category_aro_name":"tylosin","category_aro_description":"Tylosin is a 16-membered macrolide, naturally produced by Streptomyces fradiae. It interacts with the bacterial ribosome 50S subunit to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"37623":{"category_aro_accession":"3001224","category_aro_cvterm_id":"37623","category_aro_name":"mycinamicin","category_aro_description":"Produced by Micromonospora\u00a0griseorubida.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3311":{"model_id":"3311","model_name":"ACT-38","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"5243":{"protein_sequence":{"accession":"AKS43590.1","sequence":"MMTKSLCCALLLSTSCSVLAAPMSEKQLAEVVERTVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVAANNPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPELTGKQWLGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMSYEQAITMRVFKPLKLDHTWINVPKAEEAHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVKDMANWVMVNMKPDSLQDSSLKEGITLAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVEGSDNKVALAPLPAREVNPPAPPVNASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILDALQ"},"dna_sequence":{"accession":"KP836350.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGACTAAATCCCTTTGCTGCGCCCTGCTGCTCAGCACCTCCTGCTCGGTATTGGCTGCCCCGATGTCAGAAAAACAGCTGGCTGAGGTGGTGGAACGTACCGTTACGCCGCTGATGAAAGCGCAGGCCATTCCGGGTATGGCGGTGGCGGTGATTTATCAGGGTCAGCCGCACTACTTTACCTTCGGTAAAGCCGATGTTGCGGCGAACAACCCTGTCACCCCACAAACCTTATTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGCGTACTCGGCGGCGATGCCATTGCTCGCGGTGAAATATCGCTGGGCGATCCGGTGACAAAATACTGGCCTGAGCTGACAGGCAAGCAGTGGCTGGGGATCCGCATGCTGGATCTGGCAACCTATACCGCAGGTGGTTTGCCGTTACAGGTACCGGATGAGGTCACGGATAACGCCTCTCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCGGGCACCACGCGTCTTTATGCCAACGCCAGCATCGGTCTTTTTGGCGCGCTGGCGGTCAAACCTTCCGGCATGAGCTATGAGCAGGCCATAACGATGCGGGTCTTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTTCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGATACCGCGACGGTAAGGCGGTACACGTTTCGCCAGGAATGCTGGACGCTGAAGCCTATGGCGTAAAAACCAACGTGAAGGATATGGCAAACTGGGTGATGGTCAACATGAAGCCGGACTCGCTTCAGGATAGTTCACTCAAGGAAGGCATTACCCTGGCGCAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAGGGATTAGGCTGGGAAATGCTTAACTGGCCGGTCGATGCCAAAACCGTGGTTGAAGGTAGCGACAATAAGGTGGCGCTGGCACCGCTGCCTGCGAGAGAAGTGAATCCACCGGCGCCCCCGGTCAATGCGTCATGGGTCCATAAAACAGGCTCTACCGGCGGGTTTGGCAGCTACGTGGCATTTATTCCTGAAAAGCAGCTCGGCATTGTGATGCTGGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCGTATCCTCGACGCGCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3003655","ARO_id":"40265","ARO_name":"ACT-38","CARD_short_name":"ACT-38","ARO_description":"A class C beta-lactamase from Citrobacter freundii.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3320":{"model_id":"3320","model_name":"QnrS10","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"425"}},"model_sequences":{"sequence":{"5333":{"protein_sequence":{"accession":"AEU11363.1","sequence":"MEIYSHTYRHHNFSHKDLSDLTFTACTFIRSDFRRANLRDTTFVNCKFIEQGDIEGCHFDVADLRDASFQQCQLAMANFSNANCYGIEFRACDLKGANFSRTNFAHQVSNRMYFCSAFISGCNLSYANMERVCLEKCELFENRWIGTNLAGASLKESDLSRGVFSEDVWGQFSLQGANLCHAELDGLDPRKVDTSGIKIAAWQQELILEALGIVVYPD"},"dna_sequence":{"accession":"JN836269.1","fmin":"0","fmax":"657","strand":"+","sequence":"ATGGAAATCTACAGTCATACATATCGGCACCACAACTTTTCACATAAAGACTTAAGTGATCTCACCTTCACCGCTTGCACATTCATTCGCAGCGACTTTCGACGTGCTAACTTGCGTGATACGACATTCGTCAACTGCAAGTTCATTGAACAGGGTGATATCGAAGGCTGCCACTTTGATGTCGCAGATCTTCGTGATGCAAGTTTCCAACAATGCCAACTTGCGATGGCAAACTTCAGTAATGCCAATTGCTACGGTATAGAGTTCCGTGCGTGTGATTTAAAAGGTGCCAACTTTTCCCGAACAAACTTTGCCCATCAAGTGAGTAATCGTATGTACTTTTGCTCAGCATTTATTTCTGGATGTAATCTTTCCTATGCCAATATGGAGAGGGTTTGTTTAGAAAAATGTGAGTTGTTTGAAAATCGCTGGATAGGAACGAACCTAGCGGGTGCATCACTGAAAGAGTCAGACTTAAGTCGAGGTGTTTTTTCCGAAGATGTCTGGGGGCAATTTAGCCTACAGGGTGCCAATTTATGCCACGCCGAACTCGACGGTTTAGATCCCCGCAAAGTCGATACATCAGGTATCAAAATTGCAGCCTGGCAGCAAGAACTGATTCTCGAAGCACTGGGTATTGTTGTTTATCCTGACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3004622","ARO_id":"42603","ARO_name":"QnrS10","CARD_short_name":"QnrS10","ARO_description":"QnrS10 is a plasmid-mediated quinolone resistance protein.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2139":{"model_id":"2139","model_name":"vanS gene in vanD cluster","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"3440":{"protein_sequence":{"accession":"ACM47284.1","sequence":"MKNRNKTSHEDDYLLFKNRLSVKILLMMACSILIIAGVYLFILKDNFANVVVAILDSFIYHDRDEAVVVYLRTFKAYEIWLFLIAVMGVFFMIFRRYLDSISKYFKEINRGIDTLVNEDANDITLPPELASTERKINSIRHTLTKRKTDAELAEQRKNDLVMYLAHDLKTPLSSVIGYLNLLRDENQISEELREKYLSISLDKAERLEELINEFFEITRLIFQISRLCTAKSI"},"dna_sequence":{"accession":"EU999036.1","fmin":"688","fmax":"1390","strand":"+","sequence":"TTGAAAAATAGAAATAAAACCAGTCATGAAGATGACTATTTACTTTTTAAAAACAGATTGTCCGTTAAAATATTGCTTATGATGGCGTGCTCCATTCTGATTATTGCGGGTGTTTATCTGTTTATCTTAAAAGATAATTTTGCAAATGTCGTGGTAGCCATTTTAGACAGCTTTATCTATCATGATCGGGATGAGGCGGTGGTTGTTTATCTGAGAACCTTTAAGGCGTATGAGATATGGCTTTTCCTGATAGCGGTTATGGGTGTGTTTTTTATGATCTTTCGCCGCTATCTGGACAGCATTTCAAAATATTTTAAGGAGATCAACCGTGGGATCGATACTTTGGTGAATGAGGATGCCAACGATATCACATTGCCTCCGGAGTTGGCTTCGACCGAAAGGAAAATCAATTCCATACGGCATACCCTGACGAAACGGAAAACGGACGCTGAGCTTGCAGAGCAAAGGAAAAACGACCTTGTCATGTATCTGGCCCATGACCTGAAGACCCCGCTTTCATCGGTCATAGGATATTTGAACCTATTAAGGGATGAGAATCAGATCTCCGAGGAACTCAGGGAAAAATATCTGTCCATATCATTGGATAAGGCTGAGCGTCTGGAAGAGCTGATCAATGAGTTTTTTGAAATTACGAGGTTAATCTTTCAAATATCACGCTTGTGTACAGCAAAATCAATCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36779","NCBI_taxonomy_name":"Enterococcus faecium","NCBI_taxonomy_id":"1352"}}}},"ARO_accession":"3002934","ARO_id":"39368","ARO_name":"vanS gene in vanD cluster","CARD_short_name":"vanS_in_vanD_cl","ARO_description":"Also known as vanSD, is a mutated vanS variant found in the vanD gene cluster that caused constitutive expression of vanD peptidoglycan synthesis.","ARO_category":{"36210":{"category_aro_accession":"3000071","category_aro_cvterm_id":"36210","category_aro_name":"vanS","category_aro_description":"VanS is similar to histidine protein kinases like EnvZ and acts as a response regulator by activating VanR. VanS is required for high level transcription of other van glycopeptide resistance genes.","category_aro_class_name":"AMR Gene Family"},"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"35948":{"category_aro_accession":"0000029","category_aro_cvterm_id":"35948","category_aro_name":"teicoplanin","category_aro_description":"Teicoplanin is a glycopeptide antibiotic used in the prophylaxis and treatment of serious infections caused by Gram-positive bacteria. Teicoplanin has a unique acyl-aliphatic chain, and binds to cell wall precursors to inhibit transglycosylation  and transpeptidation.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2201":{"model_id":"2201","model_name":"PvrR","model_type":"protein knockout model","model_type_id":"40354","model_description":"Protein Knockout Models (PKM) reflect resistance by the absence of a gene product, most often deletion of a gene involved in antibiotic import, such as Vibrio cholerae OmpT. Like Protein Homolog Models (PHMs), PKMs include a reference sequence and a bitscore cut-off for detection using BLASTP but instead are designed to only report lack of detection under Perfect or Strict criteria. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff. This model type is still under development and not currently supported by the Resistance Gene Identifier (RGI) software.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"3389":{"protein_sequence":{"accession":"AAM15533.1","sequence":"MSWKSYRVLVVEDQPFQREYLLNLFRERGVQYLVGAGDGAEALRCLKQDRFDLILSDLMMPGMDGIQMILQLPYLKHRPKLALMSSSSQRMMLSASRVAQSLGLSVIDLLPKPTLPKAIGQLLEHLERCLRQKLEPETDETPHGRTALLDALHNEQLVTWFQAKKSLHTGRIVGAEALIRWSHPQHGLLLPSCFMSDVDATGLHEALLWRVLEQTLNAQESWRRAGYEIPVSVNLPPHLLDNQELPDRLYEYVGARGACTSSLCFELTESSVTTLSSNYYAGACRLRMKGFGLAQDDFGQGYSSFYNLVTTPFTELKIDRSLVQGCVEDNGLNAAVISCIELGHRLNLDVVAEGVETCEELNLLRRLGCDRAQGFLISKAVSAREFERQLREDGPSLLV"},"dna_sequence":{"accession":"AF482691.2","fmin":"2796","fmax":"3996","strand":"+","sequence":"ATGAGCTGGAAATCCTATCGGGTGCTGGTGGTCGAAGATCAGCCGTTTCAGCGCGAATACCTGCTCAACCTGTTTCGCGAGCGCGGCGTGCAGTACCTGGTAGGTGCCGGCGACGGCGCGGAGGCGTTGCGCTGCCTGAAGCAGGACAGGTTCGACCTGATCCTCAGCGATCTGATGATGCCGGGCATGGATGGTATCCAAATGATCCTGCAACTGCCGTATCTCAAGCATCGTCCGAAGCTGGCGCTGATGAGCTCCTCGTCGCAGCGGATGATGCTCAGTGCCAGCCGGGTCGCCCAGAGTCTCGGCTTGTCGGTAATCGACCTGTTGCCCAAGCCGACTCTGCCCAAGGCCATCGGCCAACTTCTGGAACACCTGGAAAGATGCCTCAGGCAGAAGCTGGAGCCGGAAACCGACGAGACTCCGCATGGGCGCACGGCGTTGCTGGATGCCCTGCATAACGAGCAACTGGTGACCTGGTTCCAGGCTAAGAAATCCCTCCACACCGGGCGCATAGTCGGCGCCGAGGCGTTGATACGCTGGAGCCACCCGCAGCATGGCCTGTTGCTGCCCAGCTGTTTCATGAGTGATGTCGACGCTACCGGTCTGCACGAGGCGTTGCTCTGGCGCGTGCTCGAACAGACCCTGAACGCCCAGGAATCGTGGCGCAGGGCGGGTTACGAGATTCCGGTTTCGGTGAATCTGCCGCCGCACCTGCTCGATAACCAGGAACTTCCGGATCGACTCTATGAGTACGTCGGCGCTCGCGGGGCTTGTACCAGCTCACTATGTTTCGAGTTGACCGAGAGCAGTGTCACAACTCTGTCAAGTAACTACTATGCAGGTGCCTGTCGCTTGCGCATGAAAGGGTTCGGATTGGCCCAGGACGACTTTGGCCAGGGTTACAGCTCGTTCTATAACCTGGTCACGACGCCTTTCACGGAGCTGAAGATCGACCGCTCCCTAGTCCAGGGATGCGTAGAGGATAACGGCCTCAATGCAGCTGTCATCAGTTGTATTGAGTTGGGTCACCGCCTGAATCTCGACGTGGTGGCCGAAGGCGTGGAGACCTGCGAGGAACTGAATCTTCTTCGTCGTCTTGGCTGCGACCGGGCGCAGGGTTTCCTGATTTCTAAGGCAGTGTCTGCTCGTGAGTTCGAGCGGCAGTTAAGGGAGGACGGCCCCAGCCTCCTTGTTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3003688","ARO_id":"40325","ARO_name":"PvrR","CARD_short_name":"PvrR","ARO_description":"PvrR is a response regulator that controls the conversion between antibiotic-resistant and antibiotic-susceptible forms of Pseudomonas aeruginosa biofilms through porin deletion\/gene absence.","ARO_category":{"41450":{"category_aro_accession":"3004286","category_aro_cvterm_id":"41450","category_aro_name":"phenotypic variant regulator","category_aro_description":"Phenotypic variant regulator proteins play a role in controlling the switch between antibiotic-susceptible and antibiotic-resistant forms of bacteria. The characterized member of this family is the PvrR protein in Pseudomonas aeruginosa, which when absent, confers antibiotic resistance.","category_aro_class_name":"AMR Gene Family"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35961":{"category_aro_accession":"0000043","category_aro_cvterm_id":"35961","category_aro_name":"carbenicillin","category_aro_description":"Carbenicillin is a semi-synthetic antibiotic belonging to the carboxypenicillin subgroup of the penicillins. It has gram-negative coverage which includes Pseudomonas aeruginosa but limited gram-positive coverage. The carboxypenicillins are susceptible to degradation by beta-lactamase enzymes. Carbenicillin antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"40942":{"category_aro_accession":"3004015","category_aro_cvterm_id":"40942","category_aro_name":"gentamicin A","category_aro_description":"Gentamicin A is part of a complex of broad spectrum aminoglycoside antibiotics. Gentamicin inhibits protein synthesis, resulting in bacterial cell death.","category_aro_class_name":"Antibiotic"},"46133":{"category_aro_accession":"3007382","category_aro_cvterm_id":"46133","category_aro_name":"gentamicin","category_aro_description":"Gentamicin is a commonly used aminoglycoside antibiotic derived from members of the Micromonospora genus of bacteria. It acts by binding the 30S ribosomal subunit, thus inhibiting protein synthesis. Gentamicin is typically used to treat Gram-negative infections of the repiratory and urinary tract, as well as infections of the bone and soft tissue. It also exhibits considerable nephrotoxicity and ototoxicity. Gentamicin is administered as a mixture of gentamicin type C (which makes about around 80% of the complex) and types A, B, and X (distributed in the remaining 20% of the complex).","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"40429":{"category_aro_accession":"3003764","category_aro_cvterm_id":"40429","category_aro_name":"resistance by absence","category_aro_description":"Mechanism of antibiotic resistance conferred by deletion of gene (usually a porin).","category_aro_class_name":"Resistance Mechanism"}}},"2279":{"model_id":"2279","model_name":"Listeria monocytogenes mprF","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1650"}},"model_sequences":{"sequence":{"5223":{"protein_sequence":{"accession":"CAC99773.1","sequence":"MKEKLMQAYAWFQKNSTVVKIVFITFVMAFVIFEIINIATGIDYPSLKENLTSQSPEQIFIMFIVGLIAVTPMLLYDYVIVKLLPGKFSPSHVIASGWITNTFTNIGGFGGVLGASLRASFYGKNASHKEILLAISKIALFLVSGLSIYCLVSLATLLIPGFADHFVNYWPWLLAGGLYFPILFTITKWKSKSLFVDLPIKRELTLIIASLLEWGFAFGCFAIIGTLMGEPVDIFKVFPLFVIASVIGIASMVPGGVGTFDVVMILGLSQLGVSQELALAWMLFYRIFYYIIPFVVGLLFFVQKAGKKVNDFLEGLPLLFLQKVAHRFLVIFVYGSGLLLILSSAVPNAIYHVPFLYKIMPFNFLFTSQITIVAFGFLLLGLARGIECKTKKAYIITVIVLGCAIFNTLARVFSMKQAIFLGIVLLCLFLARNEFYREKLVYTWSKVIIDSIIFIVCLAGYIVIGIYNSPNIKHSKEIPDYLRIASEHLWLVGFVGVFIAVVSLVIIYIYLSTTKEKLGSPFEAVKVREHLAKWGGNEVSHTMFLRDKLLFWAAEGEVLFSYRIIADKMVIMGEPTGNMDKMEAAIEEVMMNADRFGYRPVFYEVRGTMIPYLHDHGFDFIKLGEEGFVDVQNFTMSGKKKKGERALMNKLEREGYTFEIIEPPFNHDTWTTLRAVSDEWLDGREEKGFSLGFFDTYYLEQAPIAIAKNGEGTIVGFASMMPSYTDEMTSIDLMRYSKEAPSGIMDFLFINLFEKAKEDGFQTFNAGMAPLANVGESKYAFLGERLAGLVYRYSQGFYGFKGLRNFKSKYVTEWEQKFVAFRKRSSIAFTMLQLMILVGKKRPLANSQVVLDFPLEEETKKPDSE"},"dna_sequence":{"accession":"AL591981.1","fmin":"5693","fmax":"8291","strand":"-","sequence":"ATGAAAGAAAAATTAATGCAAGCCTATGCCTGGTTTCAAAAAAATAGTACCGTCGTAAAAATCGTTTTTATTACTTTTGTGATGGCTTTTGTTATTTTTGAAATTATTAATATTGCGACGGGGATTGACTATCCGTCGCTAAAAGAAAATTTAACTTCTCAAAGCCCGGAACAAATATTTATTATGTTTATCGTGGGCTTAATTGCTGTCACTCCAATGCTTTTGTATGATTATGTCATCGTTAAGTTGTTACCTGGAAAGTTTTCGCCAAGTCATGTGATTGCCTCTGGTTGGATTACGAATACCTTTACTAATATTGGCGGTTTTGGTGGCGTATTAGGTGCCAGTTTAAGAGCAAGTTTTTATGGGAAAAATGCATCTCATAAGGAAATTTTACTAGCTATTTCTAAGATTGCTTTATTTTTAGTATCTGGTTTATCGATTTACTGTTTAGTATCATTAGCCACTTTACTCATTCCAGGATTTGCAGATCATTTTGTTAATTACTGGCCATGGCTTCTTGCGGGTGGTCTTTACTTCCCGATTTTATTTACTATTACGAAATGGAAAAGTAAGTCACTCTTTGTTGATTTACCTATCAAAAGAGAATTAACGTTAATTATCGCTTCTCTTTTGGAGTGGGGCTTCGCTTTTGGATGTTTCGCGATTATCGGTACATTGATGGGAGAACCAGTCGATATTTTCAAAGTGTTCCCGTTATTTGTTATTGCTTCGGTAATTGGGATTGCTTCGATGGTACCTGGTGGAGTAGGGACATTTGACGTCGTGATGATTCTTGGACTTAGCCAATTAGGTGTTTCTCAAGAATTAGCGCTCGCTTGGATGCTATTTTACCGAATTTTCTACTATATTATTCCTTTTGTAGTGGGACTACTTTTCTTCGTCCAAAAAGCTGGTAAAAAAGTAAATGACTTTTTAGAAGGATTACCGTTATTATTCTTACAAAAAGTGGCCCATCGCTTCTTAGTTATTTTTGTTTACGGCTCTGGGTTATTGTTAATTTTGTCTTCCGCCGTACCAAACGCTATTTACCATGTGCCATTCTTATACAAAATTATGCCGTTTAATTTCTTATTCACTTCCCAAATTACCATTGTTGCATTTGGCTTTTTACTACTGGGGCTTGCGAGAGGGATTGAATGTAAAACAAAGAAAGCGTATATTATTACAGTAATTGTTCTAGGTTGCGCGATTTTCAACACACTTGCTCGCGTATTTTCGATGAAGCAGGCAATCTTTTTAGGAATTGTGCTGTTATGTTTATTCTTAGCTCGAAACGAATTTTACCGAGAAAAACTGGTTTATACTTGGAGTAAAGTAATTATTGATAGCATTATTTTCATCGTATGTCTGGCAGGTTACATTGTTATCGGTATTTACAACTCACCAAATATCAAACACTCCAAAGAAATCCCTGACTATTTACGCATTGCCTCAGAGCATTTATGGTTAGTCGGCTTCGTTGGCGTATTTATCGCCGTTGTTAGTTTAGTCATTATTTACATTTATTTATCCACAACAAAAGAAAAACTTGGCTCTCCATTTGAAGCAGTCAAAGTACGCGAACATTTAGCGAAATGGGGCGGAAATGAAGTCAGTCATACGATGTTCTTACGTGATAAACTGCTATTTTGGGCAGCAGAGGGGGAAGTACTTTTCTCTTACCGAATCATTGCGGACAAAATGGTCATCATGGGCGAACCAACTGGGAACATGGACAAAATGGAAGCAGCGATTGAAGAGGTAATGATGAACGCTGATAGATTTGGCTATCGACCTGTTTTCTATGAAGTCCGGGGCACGATGATTCCATATTTACATGATCACGGATTTGACTTTATCAAGCTTGGCGAGGAAGGTTTTGTCGACGTCCAAAACTTTACAATGAGTGGTAAAAAGAAAAAAGGTGAGCGAGCTCTCATGAATAAATTAGAACGAGAAGGTTATACTTTTGAAATAATAGAACCACCATTCAATCACGACACTTGGACAACTTTACGAGCAGTTTCTGATGAGTGGCTAGATGGTAGGGAAGAAAAAGGTTTCTCATTAGGATTCTTCGATACGTATTATCTCGAACAAGCTCCGATTGCTATCGCTAAAAACGGAGAAGGTACTATCGTTGGATTTGCTTCGATGATGCCGTCATATACAGACGAAATGACTTCGATTGATTTAATGCGTTACTCCAAAGAAGCGCCATCAGGTATTATGGATTTCCTTTTCATTAACCTATTCGAAAAAGCCAAAGAAGATGGCTTCCAAACATTTAATGCCGGTATGGCACCACTTGCCAATGTTGGGGAAAGTAAATATGCTTTCCTAGGTGAACGATTAGCCGGACTTGTATACCGTTATAGTCAAGGTTTTTACGGTTTCAAAGGATTACGTAATTTTAAATCCAAATATGTTACAGAATGGGAACAAAAATTTGTTGCCTTTAGAAAAAGAAGTTCCATTGCTTTCACCATGTTACAATTAATGATTCTTGTTGGTAAAAAACGACCACTTGCAAATAGCCAAGTAGTCCTTGATTTCCCACTCGAAGAAGAAACAAAAAAACCAGATTCTGAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40443","NCBI_taxonomy_name":"Listeria monocytogenes EGD-e","NCBI_taxonomy_id":"169963"}}}},"ARO_accession":"3003770","ARO_id":"40442","ARO_name":"Listeria monocytogenes mprF","CARD_short_name":"Lmon_mprF","ARO_description":"MprF is a integral membrane protein that modifies the negatively-charged phosphatidylglycerol on the membrane surface. This confers resistance to cationic peptides that disrupt the cell membrane, including defensins.","ARO_category":{"37243":{"category_aro_accession":"3000863","category_aro_cvterm_id":"37243","category_aro_name":"defensin resistant mprF","category_aro_description":"MprF is a integral membrane protein that modifies the negatively-charged phosphatidylglycerol on the membrane surface of both Gram-positive and Gram-negative bacteria. This confers resistance to cationic peptides that disrupt the cell membrane, including defensins.","category_aro_class_name":"AMR Gene Family"},"37037":{"category_aro_accession":"3000693","category_aro_cvterm_id":"37037","category_aro_name":"defensin","category_aro_description":"Defensins are natural cationic peptides that have antibiotic properties. It is part of the innate immune system of plants and animals.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2281":{"model_id":"2281","model_name":"Brucella suis mprF","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1650"}},"model_sequences":{"sequence":{"8174":{"protein_sequence":{"accession":"AAN33774.1","sequence":"MLWWDDISMSLIDDEIPSSQPQVSGRHFGWLKQYQHFLFPIAGIAIALLAIYVLENLLRHTSRTETLAALHNISWTTLALAVFFTALSYAAVALYDVVAVDTIAPNQIPRRIAAVAGAAGYAISNALGFSLLTGGALRYRIYAAEGISLADIGKIVGTSWFAIWFALIIMVGAALLIDPQDVPFLSAIDIRIDIVAGILILGGIGWLIYWLSHGERNVSIGSFSLRLPNSKGALTQIFAGVVDVGAAAATLYVLLPEGAVPSFAVFALVYVIAIVLGIASHAPGGLGAFEATIIAGLGLGGKPDAIAGLLAYRLIYTVLPLVVATAGILIWEVMRRRHMLDKQARFAKRLVEPLVPGLSASIIFLGGIILLISGATPDMRYRVKLLSDIVPEFLVEMSHLAASLVGVALLIVARGLSKRLERAWVAAMVLLLCGAVFSIAKGLDWEEASILCLFALSLWGFRDSFYRRPIAGPFELSWNWIATVGTTVLVSTWLGFFVYRHIEYSSDLWWDFAWNGNAPRFLRATVLVFAVVAAVGLHSIINRHGQRRRKVDHSIPDAVPALVARCPHTDAALAMLGDKQFLLAPDDSAFIMYAQSGGSLIALGEPIGDAEAGKELAWSFHSLADRLALRTVFYGVGPQSLPLFLDMGLIALKLGEVARVDLTDFSLEGPRRQPFRYADRKVDKDGLTFEIIPAADVPPLIPRLRAISDAWLDHKSGSEKGFSLGYFNDEYLKRFDIAVLKKDGEIVAFANIWRGADKYEITVDLMRYMPNVHKLLMDALFAKLLTFSKQEGYKWFNLGAAPLSGLSGSRLASRWNRFGSFIYRRGADLYHFDGLKAFKEKFDPVWTPHYMVCPGGLETPRALLDATTLINGSPLEFIRK"},"dna_sequence":{"accession":"AE014292.2","fmin":"568280","fmax":"570923","strand":"+","sequence":"TTGCTCTGGTGGGACGACATTTCGATGAGCCTGATTGATGATGAAATACCTTCTTCGCAACCGCAAGTGTCAGGTAGGCATTTCGGCTGGTTGAAACAATATCAGCATTTTCTGTTTCCAATCGCAGGCATCGCCATTGCGTTATTGGCTATTTATGTTCTGGAAAATCTTCTCAGGCACACCTCCCGCACCGAAACGCTTGCAGCCCTTCACAATATTTCATGGACGACGCTCGCACTGGCCGTCTTTTTCACAGCATTAAGCTATGCCGCAGTGGCGCTTTATGATGTCGTGGCGGTGGACACCATAGCGCCCAACCAGATACCGCGCCGCATCGCGGCGGTGGCGGGTGCTGCGGGCTATGCGATTTCCAACGCGCTCGGCTTCTCGCTCCTGACCGGCGGGGCGCTGCGTTATCGCATTTATGCCGCAGAAGGCATAAGCCTGGCCGATATCGGCAAGATCGTCGGCACCTCATGGTTCGCCATCTGGTTCGCCCTCATCATCATGGTGGGCGCAGCCCTGCTGATCGATCCGCAGGACGTGCCTTTTCTTTCCGCCATCGATATACGGATTGATATTGTCGCAGGCATTCTCATCCTTGGCGGCATTGGCTGGCTGATCTACTGGCTTTCGCATGGCGAACGCAATGTCAGCATCGGTTCGTTCAGCCTGCGCCTGCCCAATTCAAAAGGCGCGCTCACGCAGATTTTTGCGGGCGTGGTGGATGTGGGCGCTGCCGCGGCCACGCTCTATGTGCTGTTGCCGGAAGGGGCTGTGCCAAGCTTCGCCGTCTTTGCGCTCGTTTATGTCATCGCCATCGTGCTTGGCATTGCAAGCCACGCGCCAGGCGGCCTCGGCGCTTTTGAGGCAACAATCATCGCAGGGCTTGGCCTCGGTGGAAAACCCGATGCAATTGCGGGCCTGCTGGCCTATCGCCTCATTTACACGGTTCTTCCCCTCGTGGTTGCCACCGCCGGAATCCTCATCTGGGAGGTCATGCGCCGCCGCCATATGCTCGACAAGCAGGCCCGATTCGCCAAGCGGCTGGTGGAGCCGCTGGTTCCGGGGCTTTCAGCCAGCATCATCTTTCTCGGTGGCATCATCCTGCTTATCTCAGGCGCCACGCCCGATATGCGCTATCGTGTGAAGTTGCTGTCCGACATCGTGCCGGAATTTCTTGTGGAGATGTCGCATCTGGCGGCAAGCCTCGTCGGCGTTGCTCTTCTCATCGTCGCGCGCGGCCTTTCCAAACGGCTGGAGCGCGCCTGGGTGGCCGCGATGGTGCTTCTTCTTTGCGGCGCGGTGTTTTCGATCGCAAAAGGACTGGACTGGGAAGAGGCAAGCATTTTGTGCCTTTTTGCCCTTTCACTCTGGGGCTTTCGCGATTCCTTCTACCGTCGTCCGATTGCCGGCCCGTTTGAACTGAGCTGGAACTGGATCGCAACCGTTGGAACCACGGTTCTCGTGTCCACCTGGCTTGGTTTTTTCGTCTACCGCCATATCGAATATTCAAGCGATCTCTGGTGGGATTTCGCGTGGAACGGCAACGCCCCGCGTTTCCTGCGCGCCACCGTTCTGGTTTTCGCAGTCGTGGCGGCAGTCGGCCTTCATTCGATCATCAACCGGCATGGCCAGCGCAGGCGCAAGGTTGATCATTCCATCCCCGATGCCGTGCCCGCACTCGTCGCCCGGTGCCCGCATACAGATGCAGCCCTTGCCATGCTGGGCGACAAGCAATTTCTGCTGGCGCCCGACGACAGCGCGTTCATCATGTATGCGCAGTCGGGCGGCAGCCTGATCGCGCTTGGCGAGCCTATCGGCGATGCCGAAGCGGGCAAGGAACTTGCCTGGTCTTTCCATTCGCTTGCCGACCGTCTGGCGCTGCGCACTGTCTTCTATGGTGTCGGCCCGCAAAGCCTGCCGCTTTTCCTCGATATGGGCCTGATTGCGCTCAAGCTGGGTGAAGTCGCACGCGTTGACCTGACAGATTTTTCGCTGGAAGGCCCGCGCCGCCAGCCCTTCCGTTATGCCGACCGCAAGGTGGACAAGGATGGGCTGACCTTCGAGATTATCCCTGCTGCGGACGTGCCGCCGCTGATCCCGCGCCTGCGCGCAATTTCCGACGCTTGGCTCGACCATAAATCAGGCAGCGAAAAGGGTTTTTCGCTTGGCTATTTCAACGATGAGTATTTAAAGCGTTTCGATATTGCCGTGCTGAAGAAAGACGGCGAAATCGTTGCTTTCGCCAATATATGGCGCGGTGCCGACAAGTATGAGATCACGGTCGACCTGATGCGCTACATGCCCAATGTGCACAAGCTCCTGATGGATGCGCTGTTCGCCAAGCTGCTGACCTTTTCCAAGCAAGAAGGCTACAAATGGTTCAACCTTGGCGCGGCCCCGCTTTCCGGCCTTAGCGGCAGCAGGCTTGCCTCGCGCTGGAACCGTTTCGGCTCGTTCATCTATCGCCGTGGGGCCGATCTTTATCACTTCGACGGGCTCAAAGCCTTCAAGGAAAAATTCGATCCCGTCTGGACCCCGCATTATATGGTTTGCCCCGGCGGGCTTGAAACGCCGCGCGCCCTTCTTGATGCCACAACACTGATTAACGGCAGCCCTTTGGAGTTCATTCGCAAATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36780","NCBI_taxonomy_name":"Brucella suis 1330","NCBI_taxonomy_id":"204722"}}}},"ARO_accession":"3003772","ARO_id":"40445","ARO_name":"Brucella suis mprF","CARD_short_name":"Bsui_mprF","ARO_description":"MprF is a integral membrane protein that modifies the negatively-charged phosphatidylglycerol on the membrane surface. This confers resistance to cationic peptides that disrupt the cell membrane, including defensins.","ARO_category":{"37243":{"category_aro_accession":"3000863","category_aro_cvterm_id":"37243","category_aro_name":"defensin resistant mprF","category_aro_description":"MprF is a integral membrane protein that modifies the negatively-charged phosphatidylglycerol on the membrane surface of both Gram-positive and Gram-negative bacteria. This confers resistance to cationic peptides that disrupt the cell membrane, including defensins.","category_aro_class_name":"AMR Gene Family"},"37037":{"category_aro_accession":"3000693","category_aro_cvterm_id":"37037","category_aro_name":"defensin","category_aro_description":"Defensins are natural cationic peptides that have antibiotic properties. It is part of the innate immune system of plants and animals.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2282":{"model_id":"2282","model_name":"Clostridium perfringens mprF","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"4635":{"protein_sequence":{"accession":"ABG86067.1","sequence":"MWDSLKKSYRHLKNILGFVTDKRNYENIKKLLKNYKILSDISNIIVSVLVFLSGILLIISGIYPSIFYKIKFLDNIYSLSFLRFSHRASILIGLMLIMTSKEVFFKVKRAYYVTLTLLIVGGAFAFIKDLDYKEGIFILGVIILLILSKKSFYRKSIPIKVTKLSGILIVLSIVMIIFASFIHKFNIHFSKNYKYYIDFFHSTKGYLRIALFTYISFIIFVIIWYLTMPKIEDDERYMDADLEKVSKFFKEIDYGTIFSHLVYLKDKKVFWANEGESLIMYSKYKDKIIVLGDPIATKENLYSCIEEFQAFTNLYGYDVVFYEIEEKNFSTYHDAGYYFFKLGEEARIDLEEFNLIGSKKSAFRNTLRRVEREGYNFSIIEPPFNNEVVSQLKEISDKWLGDRKEKGFSLGWFSEDYIQRSPIAILKNEEENKIMGFVTIMDANDGGETVAIDLMRIDKDAPNASMDYLMLNLFLTFKEKGYKYFSLGEAPLSNVGFNTHSHLQEKLARLVYNSGNIFYSFDGLRRYKSKFSPIWQPRYLAYPKFMSLPEVFINLCLLIANSKERVEKK"},"dna_sequence":{"accession":"CP000312.1","fmin":"1756064","fmax":"1757774","strand":"-","sequence":"ATGTGGGATTCACTAAAAAAAAGTTATAGACATTTAAAAAATATTTTAGGATTTGTTACTGATAAAAGAAATTATGAAAATATAAAGAAGCTATTAAAAAATTACAAAATCTTAAGTGATATATCAAATATAATAGTATCAGTTTTGGTATTTCTAAGTGGTATTCTTTTAATAATTTCAGGGATTTATCCTAGTATATTTTATAAGATAAAATTTTTAGATAATATATACAGTTTATCTTTTTTAAGGTTTTCACATAGAGCTTCAATATTAATTGGATTAATGTTAATAATGACCTCTAAGGAAGTTTTCTTTAAGGTAAAAAGAGCTTATTATGTTACATTAACATTGCTTATAGTAGGAGGAGCCTTTGCCTTTATAAAAGATTTAGATTACAAAGAAGGAATTTTTATTTTAGGAGTAATAATACTTCTAATATTATCAAAAAAGAGTTTTTACAGAAAAAGTATTCCTATTAAGGTTACTAAATTAAGTGGGATATTAATAGTTCTTTCAATTGTAATGATTATCTTTGCGAGTTTTATACATAAATTTAACATACATTTTAGCAAGAACTATAAATACTATATAGACTTTTTCCATAGCACAAAGGGGTATTTAAGAATAGCATTATTCACATATATATCCTTTATAATATTTGTGATAATATGGTATTTAACAATGCCTAAAATAGAAGATGACGAAAGGTATATGGATGCTGATTTAGAAAAGGTATCAAAATTCTTTAAAGAAATAGATTATGGAACAATATTCTCCCATTTAGTTTATTTAAAGGATAAAAAGGTCTTTTGGGCTAATGAAGGAGAGTCCTTAATAATGTATAGCAAGTACAAAGATAAGATAATAGTTTTAGGAGATCCTATAGCTACTAAGGAAAACCTATATAGTTGTATAGAAGAGTTTCAAGCTTTTACAAATTTATATGGATATGATGTTGTCTTTTATGAAATAGAAGAAAAAAACTTTTCTACCTATCATGATGCAGGGTATTATTTCTTTAAGTTAGGAGAAGAGGCAAGGATAGATTTAGAAGAATTTAATTTGATTGGTTCTAAAAAGAGTGCCTTTAGAAACACCTTAAGAAGAGTTGAAAGGGAAGGATATAATTTTAGCATTATAGAGCCTCCTTTTAATAATGAGGTAGTAAGTCAATTGAAGGAAATATCTGATAAATGGTTAGGGGACAGAAAAGAAAAGGGATTTTCTTTAGGATGGTTTAGTGAGGATTATATACAAAGATCACCTATAGCTATTTTAAAGAATGAAGAAGAAAATAAGATTATGGGCTTTGTAACAATAATGGATGCTAATGATGGAGGGGAGACAGTAGCAATAGATTTAATGAGAATAGATAAAGATGCTCCAAATGCCTCTATGGATTACCTAATGCTTAATTTATTCTTAACCTTTAAAGAAAAAGGATATAAGTATTTTAGCTTAGGAGAAGCACCATTATCTAATGTAGGATTTAACACTCATTCACATTTACAAGAAAAGCTTGCAAGGTTAGTTTATAATAGTGGTAATATATTCTATAGTTTTGATGGACTAAGAAGATATAAGTCAAAGTTTTCTCCAATTTGGCAACCTAGATATTTAGCATATCCTAAGTTTATGTCCTTACCAGAGGTGTTTATTAACTTATGTTTATTAATAGCTAATTCAAAGGAAAGAGTAGAGAAAAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40448","NCBI_taxonomy_name":"Clostridium perfringens SM101","NCBI_taxonomy_id":"289380"}}}},"ARO_accession":"3003773","ARO_id":"40447","ARO_name":"Clostridium perfringens mprF","CARD_short_name":"Cper_mprF","ARO_description":"MprF is a integral membrane protein that modifies the negatively-charged phosphatidylglycerol on the membrane surface. This confers resistance to cationic peptides that disrupt the cell membrane, including defensins.","ARO_category":{"37243":{"category_aro_accession":"3000863","category_aro_cvterm_id":"37243","category_aro_name":"defensin resistant mprF","category_aro_description":"MprF is a integral membrane protein that modifies the negatively-charged phosphatidylglycerol on the membrane surface of both Gram-positive and Gram-negative bacteria. This confers resistance to cationic peptides that disrupt the cell membrane, including defensins.","category_aro_class_name":"AMR Gene Family"},"37037":{"category_aro_accession":"3000693","category_aro_cvterm_id":"37037","category_aro_name":"defensin","category_aro_description":"Defensins are natural cationic peptides that have antibiotic properties. It is part of the innate immune system of plants and animals.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2283":{"model_id":"2283","model_name":"Streptococcus agalactiae mprF","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1650"}},"model_sequences":{"sequence":{"4634":{"protein_sequence":{"accession":"AAN00989.1","sequence":"MLKKLIEKVKSLTSVIKIVFFISVLVLIIVEMIHLKRTISVEQLKSVFGQLSPMNLFLIILVGVIAVLPTTGYDFVLNGLLRTDKSKRYILQTSWCINTFNNLSGFGGLIDIGLRMAFYGKKGQEKSDLREVTRFLPYLISGLSFISVIALIMSHIFHAKASVDYYYLVLIGASMYFPVIYWISGHKGSHYFGDMPSSTRIKLGVVSFFEWGCAAAAFIIIGYLMGIHLPVYKILPLFCIGCAVGIVSLIPGGLGSFELVLFTGFAAEGLPKETVVAWLLLYRLAYYIIPFFAGIYFFIHYLGSQINQRYENVPKELVSTVLQTMVSHLMRILGAFLIFSTAFFENITYIMWLQKLGLDPLQEQMLWQFPGLLLGVCFILLARTIDQKVKNAFPIAIIWITLTLFYLNLGHISWRLSFWFILLLLGLLVIKPTLYKKQFIYSWEERIKDGIIIVSLMGVLFYIAGLLFPIRAHITGGSIERLHYIIAWEPIALATLILTLVYLCLVKILQGKSCQIGDVFNVDRYKKLLQAYGGSSDSGLAFLNDKRLYWYQKNGEDCVAFQFVIVNNKCLIMGEPAGDDTYIREAIESFIDDADKLDYDLVFYSIGQKLTLLLHEYGFDFMKVGEDALVNLETFTLKGNKYKPFRNALNRVEKDGFYFEVVQSPHSQELLNSLEEISNTWLEGRPEKGFSLGYFNKDYFQQAPIALVKNAEHEVVAFANIMPNYEKSIISIDLMRHDKQKIPNGVMDFLFLSLFSYYQEKGYHYFDLGMAPLSGVGRVETSFAKERMAYLVYHFGSHFYSFNGLHKYKKKFTPLWSERYISCSRSSWLICAICALLMEDSKIKIVK"},"dna_sequence":{"accession":"AE009948.1","fmin":"2111276","fmax":"2113820","strand":"-","sequence":"TTGTTGAAAAAGCTAATTGAAAAAGTCAAATCACTGACTTCTGTGATTAAAATTGTATTTTTTATATCTGTTTTAGTGCTTATTATTGTTGAAATGATTCATTTGAAACGAACTATTTCTGTTGAGCAACTAAAGAGTGTTTTTGGGCAATTATCTCCAATGAATCTTTTCTTAATTATCCTTGTGGGGGTTATCGCTGTCTTACCGACAACCGGATATGACTTTGTACTGAATGGACTTTTACGTACAGATAAAAGCAAAAGGTATATTTTACAGACTAGTTGGTGTATCAACACTTTTAATAACTTGTCAGGATTCGGTGGCTTAATCGATATTGGGTTGCGCATGGCTTTTTATGGTAAAAAAGGTCAAGAGAAGAGTGACCTAAGAGAAGTGACTCGTTTTTTACCCTATCTTATTTCTGGTCTGTCATTTATTAGTGTGATTGCCTTAATCATGAGCCATATTTTTCATGCCAAAGCTAGTGTTGATTACTATTATTTGGTATTAATTGGTGCTAGTATGTATTTTCCTGTTATTTATTGGATTTCTGGTCATAAAGGAAGCCATTATTTCGGAGATATGCCATCTAGTACTCGTATAAAATTAGGTGTTGTTTCTTTTTTTGAATGGGGATGTGCGGCCGCAGCATTTATAATTATCGGTTATTTAATGGGCATTCATCTACCAGTTTATAAAATTTTACCACTATTTTGTATTGGTTGTGCCGTCGGGATTGTATCCCTTATTCCCGGTGGATTAGGAAGTTTTGAATTAGTTCTATTTACAGGGTTTGCTGCCGAGGGACTACCTAAAGAAACTGTGGTTGCATGGTTATTACTTTATCGTTTAGCCTACTATATTATTCCATTCTTTGCAGGTATCTATTTCTTTATCCATTATTTAGGTAGTCAAATAAATCAACGTTATGAAAATGTCCCGAAAGAGTTAGTATCAACTGTTCTACAAACCATGGTGAGCCATTTGATGCGTATTTTAGGTGCATTCTTAATATTTTCAACAGCATTTTTTGAAAATATTACTTATATTATGTGGTTGCAGAAGCTAGGCTTGGACCCATTACAAGAACAAATGTTATGGCAGTTTCCAGGTTTATTGCTGGGGGTTTGTTTTATTCTCTTAGCTAGAACTATTGATCAAAAAGTGAAAAATGCTTTTCCAATTGCTATTATCTGGATTACTTTGACATTGTTTTATCTTAATTTAGGTCATATTAGTTGGCGACTATCTTTCTGGTTTATTTTACTATTGTTAGGCTTATTAGTCATTAAGCCAACTCTCTATAAAAAACAATTTATTTATAGCTGGGAAGAGCGTATTAAGGATGGAATCATTATCGTTAGTTTAATGGGAGTTCTATTTTATATTGCAGGACTACTATTCCCTATCAGGGCTCATATTACAGGTGGTAGTATTGAACGCCTGCATTATATCATAGCATGGGAGCCGATAGCATTGGCTACGTTGATTCTTACTCTCGTTTATTTATGTTTGGTTAAGATTTTACAAGGAAAATCTTGTCAGATTGGTGATGTGTTCAATGTGGATCGTTATAAAAAACTACTTCAAGCTTACGGTGGTTCTTCGGATAGCGGTTTAGCCTTTTTAAATGATAAAAGGCTCTACTGGTACCAAAAAAATGGAGAAGATTGCGTTGCGTTCCAATTTGTAATTGTCAATAATAAATGTCTTATTATGGGGGAACCAGCCGGTGATGACACTTATATTCGTGAAGCTATTGAATCGTTTATTGATGATGCTGATAAGCTAGACTATGACCTTGTTTTTTACAGTATTGGACAGAAGTTGACACTACTTTTACATGAGTATGGTTTTGACTTTATGAAAGTTGGTGAGGATGCTTTAGTTAATTTAGAAACGTTTACTCTTAAAGGGAATAAGTACAAACCTTTCAGAAATGCCCTAAATAGAGTTGAAAAGGATGGTTTCTATTTCGAAGTTGTACAATCGCCACATAGTCAAGAGCTACTAAATAGTTTGGAAGAGATTTCTAATACTTGGTTAGAAGGACGTCCTGAAAAAGGTTTCTCACTAGGATATTTTAATAAAGATTATTTCCAACAAGCCCCAATAGCTTTGGTAAAAAATGCTGAACACGAAGTTGTTGCTTTTGCTAATATTATGCCAAACTATGAAAAGAGTATTATCTCTATTGATTTAATGCGTCACGATAAACAGAAAATTCCGAATGGCGTTATGGATTTCCTCTTTTTATCATTATTCTCTTATTATCAAGAGAAGGGATACCACTATTTTGATTTGGGGATGGCACCTTTATCAGGAGTTGGTCGCGTTGAAACAAGTTTTGCTAAAGAGAGAATGGCGTATCTTGTCTATCATTTCGGTAGTCATTTCTACTCATTTAATGGTTTACACAAGTATAAGAAGAAGTTTACACCATTGTGGTCGGAACGTTATATTTCTTGTTCTCGTTCGTCCTGGTTAATTTGTGCTATTTGTGCCCTATTAATGGAAGATAGTAAAATTAAGATTGTTAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41042","NCBI_taxonomy_name":"Streptococcus agalactiae 2603V\/R","NCBI_taxonomy_id":"208435"}}}},"ARO_accession":"3003774","ARO_id":"40449","ARO_name":"Streptococcus agalactiae mprF","CARD_short_name":"Saga_mprF","ARO_description":"MprF is a integral membrane protein that modifies the negatively-charged phosphatidylglycerol on the membrane surface. This confers resistance to cationic peptides that disrupt the cell membrane, including defensins.","ARO_category":{"37243":{"category_aro_accession":"3000863","category_aro_cvterm_id":"37243","category_aro_name":"defensin resistant mprF","category_aro_description":"MprF is a integral membrane protein that modifies the negatively-charged phosphatidylglycerol on the membrane surface of both Gram-positive and Gram-negative bacteria. This confers resistance to cationic peptides that disrupt the cell membrane, including defensins.","category_aro_class_name":"AMR Gene Family"},"37037":{"category_aro_accession":"3000693","category_aro_cvterm_id":"37037","category_aro_name":"defensin","category_aro_description":"Defensins are natural cationic peptides that have antibiotic properties. It is part of the innate immune system of plants and animals.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2276":{"model_id":"2276","model_name":"Staphylococcus aureus ileS with mutation conferring resistance to mupirocin","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"3605":"V588F","3606":"V631F"},"Curated-R":{"3605":"V588F","3606":"V631F"},"clinical":{"3605":"V588F","3606":"V631F"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1800"}},"model_sequences":{"sequence":{"3538":{"protein_sequence":{"accession":"CAA52296.1","sequence":"MDYKETLLMPKTDFPMRGGLPNKEPQIQEKWDAEDQYHKALEKNKGNETFILHDGPPYANGNLHMGHALNKILKDFIVRYKTMQGFYAPYVPGWDTHGLPIEQALTKKGVDRKKMSTAEFREKCKEFALEQIELQKKDFRRLGVRGDFNDPYITLKPEYEAAQIRIFGEMADKGLIYKGKKPVYWSPSSESSLAEAEIEYHDKRSASIYVAFNVKDDKGVVDADAKFIIWTTTPWTIPSNVAITVHPELKYGQYNVNGEKYIIAEALSDAVAEALDWDKASIKLEKEYTGKELEYVVAQHPFLDRESLVINGDHVTTDAGTGCVHTAPGHGEDDYIVGQKYELPVISPIDDKGVFTEEGGQFEGMFYDKANKAVTDLLTEKGALLKLDFITHSYPHDWRTKKPVIFRATPQWFASISKVRQDILDAIENTNFKVNWGKTRIYNMVRDRGEWVISRQRVWGVPLPVFYAENGEIIMTKETVNHVADLFAEHGSNIWFEREAKDLLPEGFTHPGSPNGTFTKETDIMDVWFDSGSSHRGVLETRPELSFPADMYLEGSDQYRGWFNSSITTSVATRGVSPYKFLLSHGFVMDGEGKKMSKSLGNVIVPDQVVKQKGADIARLWVSSTDYLADVRISDEILKQTSDVYRKIRNTLRFMLGNINDFNPDTDSIPESELLEVDRYLLNRLREFTASTINNYENFDYLNIYQEVQNFINVELSNFYLDYGKDILYIEQRDSHIRRSMQTVLYQILVDMTKLLAPILVHTAEEVWSHTPHVKEESVHLADMPKVVEVDQALLDKWRTFMNLRDDVNRALETARNEKVIGKSLEAKVTIASNDKFNASEFLTSFDALHQLFIVSQVKVVDKLDDQATAYEHGDIVIEHADGEKCERCWNYSEDLGAVDELTHLCPRCQQVVKSLV"},"dna_sequence":{"accession":"X74219.1","fmin":"90","fmax":"2844","strand":"+","sequence":"ATGGATTACAAAGAAACGTTATTAATGCCTAAAACAGATTTCCCAATGCGAGGTGGTTTACCAAACAAGGAACCGCAAATTCAAGAAAAATGGGATGCAGAAGATCAATACCATAAAGCGTTAGAAAAAAATAAAGGTAACGAAACATTCATTTTACATGATGGCCCACCATACGCGAATGGTAACTTACATATGGGACATGCCTTGAACAAAATTTTAAAAGACTTTATTGTACGTTATAAAACTATGCAAGGGTTCTATGCACCATACGTACCAGGTTGGGATACACATGGTTTGCCAATTGAACAAGCATTAACGAAAAAAGGTGTTGACCGTAAGAAAATGTCAACAGCTGAATTCCGTGAGAAATGTAAAGAATTTGCTTTAGAACAAATTGAATTACAGAAAAAAGATTTTAGACGTTTAGGTGTTCGTGGTGACTTTAATGATCCATATATTACATTAAAACCTGAATACGAAGCTGCACAAATTCGTATTTTTGGAGAAATGGCAGATAAAGGTTTAATTTATAAAGGTAAAAAGCCAGTTTATTGGTCTCCTTCAAGTGAGTCTTCATTAGCAGAAGCAGAAATTGAATATCACGATAAACGTTCAGCATCAATTTACGTTGCATTTAACGTTAAAGATGACAAAGGTGTCGTTGATGCAGATGCTAAATTTATTATCTGGACAACAACGCCATGGACAATTCCATCAAATGTTGCGATTACCGTTCATCCAGAATTAAAATACGGTCAATACAATGTAAATGGCGAAAAATATATTATTGCAGAAGCCTTATCTGACGCCGTAGCAGAAGCACTGGATTGGGATAAAGCATCAATCAAATTAGAAAAAGAATACACAGGTAAGGAATTGGAGTATGTTGTAGCACAACATCCATTCTTAGATAGAGAATCGTTAGTGATTAATGGTGATCATGTTACTACAGATGCTGGTACAGGTTGTGTACATACAGCACCAGGTCACGGGGAAGATGACTATATTGTTGGTCAAAAATATGAATTGCCAGTAATTAGTCCAATCGATGATAAAGGTGTATTTACTGAAGAAGGCGGCCAATTTGAAGGAATGTTCTATGATAAAGCTAATAAAGCCGTTACTGATTTATTAACAGAAAAAGGTGCACTATTAAAATTAGACTTTATTACACATAGCTATCCACACGACTGGAGAACAAAAAAACCTGTAATTTTCCGTGCTACACCACAATGGTTTGCTTCAATCAGTAAAGTAAGACAAGATATTTTAGATGCAATCGAAAATACAAACTTCAAAGTAAATTGGGGTAAAACACGTATTTACAATATGGTTCGTGACCGTGGCGAATGGGTTATTTCTCGTCAACGTGTTTGGGGTGTACCGTTACCAGTATTTTATGCTGAAAATGGCGAAATTATCATGACGAAAGAAACAGTGAATCATGTTGCTGATTTATTTGCAGAACACGGTTCAAATATTTGGTTTGAAAGAGAAGCGAAAGACTTACTACCAGAAGGATTTACACATCCAGGCAGCCCTAACGGTACATTTACTAAAGAAACAGACATTATGGACGTTTGGTTTGATTCTGGTTCATCACACCGTGGCGTGTTGGAAACAAGACCGGAATTAAGTTTCCCAGCAGATATGTATTTAGAAGGTAGTGACCAATATCGTGGTTGGTTCAACTCTTCTATTACAACTTCAGTTGCTACAAGAGGAGTATCACCTTATAAATTCTTACTTTCTCATGGTTTTGTTATGGACGGTGAAGGTAAGAAAATGAGTAAATCTTTAGGTAATGTGATTGTACCTGACCAAGTGGTTAAACAAAAAGGTGCTGATATTGCGAGACTTTGGGTAAGTAGTACGGACTATTTAGCTGATGTTAGAATTTCTGATGAAATTTTAAAACAAACATCTGATGTTTATCGTAAAATCAGAAATACATTAAGATTTATGTTAGGTAATATTAATGATTTCAATCCTGATACAGATAGCATTCCTGAATCAGAGTTATTAGAAGTTGATCGTTACTTGCTAAATCGTTTACGTGAATTTACTGCAAGTACGATTAACAACTATGAAAACTTTGACTACTTAAATATTTATCAAGAAGTTCAAAACTTTATCAATGTTGAGTTAAGTAATTTCTATTTGGATTACGGTAAAGATATTTTATATATTGAACAACGTGATTCTCATATCCGTCGTAGTATGCAAACAGTGTTATATCAAATTTTAGTTGATATGACGAAGTTGTTAGCACCAATCTTAGTGCATACAGCTGAAGAAGTTTGGTCTCATACACCACATGTTAAAGAAGAAAGTGTTCACTTAGCAGACATGCCTAAAGTTGTAGAAGTAGATCAAGCTTTATTGGATAAATGGCGTACATTTATGAATTTACGTGATGATGTGAACCGTGCATTAGAAACTGCTCGTAATGAAAAAGTTATTGGTAAATCATTAGAAGCTAAAGTTACGATTGCTAGTAACGATAAATTTAATGCATCTGAATTCTTAACTTCATTTGATGCATTACATCAATTATTTATCGTGTCACAAGTTAAAGTTGTAGATAAGTTAGATGATCAGGCAACAGCTTATGAACATGGTGATATTGTCATCGAACATGCAGATGGTGAAAAATGTGAAAGATGTTGGAACTATTCAGAGGATCTTGGTGCTGTTGATGAATTGACGCATCTATGCCCACGATGCCAACAAGTTGTAAAATCACTTGTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35508","NCBI_taxonomy_name":"Staphylococcus aureus","NCBI_taxonomy_id":"1280"}}}},"ARO_accession":"3003729","ARO_id":"40418","ARO_name":"Staphylococcus aureus ileS with mutation conferring resistance to mupirocin","CARD_short_name":"Saur_ileS_MUP","ARO_description":"Point mutations to the isoleucyl-tRNA synthetase (ileS) in Staphylococcus aureus that confer resistance to mupirocin.","ARO_category":{"36585":{"category_aro_accession":"3000446","category_aro_cvterm_id":"36585","category_aro_name":"antibiotic-resistant isoleucyl-tRNA synthetase (ileS)","category_aro_description":"Mupirocin inhibits protein synthesis by interfering with isoleucyl-tRNA synthetase (ileS).  Mutations in ileS can confer low-level mupirocin resistance.","category_aro_class_name":"AMR Gene Family"},"36693":{"category_aro_accession":"3000554","category_aro_cvterm_id":"36693","category_aro_name":"mupirocin","category_aro_description":"Mupirocin, also known as pseudomonic acid, is a bacteriostatic polyketide antibiotic from Pseudomonas fluorescens used to treat S. aureus and MRSA. It inhibits Ile tRNA synthetase.","category_aro_class_name":"Antibiotic"},"45733":{"category_aro_accession":"3007151","category_aro_cvterm_id":"45733","category_aro_name":"mupirocin-like antibiotic","category_aro_description":"A group of antibiotics including mupirocin and similar mixtures (such as those including pseudomonic acid A).","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2284":{"model_id":"2284","model_name":"Escherichia coli murA with mutation conferring resistance to fosfomycin","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"3623":"D369N","3624":"L370I","3627":"C115D","3628":"C115E","3639":"C115S"},"Curated-R":{"3623":"D369N","3624":"L370I","3627":"C115D","3628":"C115E","3639":"C115S"},"clinical":{"3623":"D369N","3624":"L370I"},"experimental":{"3627":"C115D","3628":"C115E","3639":"C115S"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"3548":{"protein_sequence":{"accession":"AIL15701.1","sequence":"MDKFRVQGPTKLQGEVTISGAKNAALPILFAALLAEEPVEIQNVPKLKDVDTSMKLLSQLGAKVERNGSVHIDARDVNVFCAPYDLVKTMRASIWALGPLVARFGQGQVSLPGGCTIGARPVDLHISGLEQLGATIKLEEGYVKASVDGRLKGAHIVMDKVSVGATVTIMCAATLAEGTTIIENAAREPEIVDTANFLITLGAKISGQGTDRIVIEGVERLGGGVYRVLPDRIETGTFLVAAAISRGKIICRNAQPDTLDAVLAKLRDAGADIEVGEDWISLDMHGKRPKAVNVRTAPHPAFPTDMQAQFTLLNLVAEGTGFITETVFENRFMHVPELSRMGAHAEIESNTVICHGVEKLSGAQVMATDLRASASLVLAGCIAEGTTVVDRIYHIDRGYERIEDKLRALGANIERVKGE"},"dna_sequence":{"accession":"CP009072.1","fmin":"1414817","fmax":"1416077","strand":"+","sequence":"ATGGATAAATTTCGTGTTCAGGGGCCAACGAAGCTCCAGGGCGAAGTCACAATTTCCGGCGCTAAAAATGCTGCTCTGCCTATCCTTTTTGCCGCACTACTGGCGGAAGAACCGGTAGAGATCCAGAACGTCCCGAAACTAAAAGACGTCGATACATCAATGAAGCTGCTAAGCCAGCTGGGTGCGAAAGTAGAACGTAATGGTTCTGTGCATATTGATGCCCGCGACGTTAATGTATTCTGCGCACCTTACGATCTGGTTAAAACCATGCGTGCTTCTATCTGGGCGCTGGGGCCGCTGGTAGCGCGCTTTGGTCAGGGGCAAGTTTCACTGCCTGGCGGTTGTACGATCGGCGCACGTCCGGTTGATCTACACATTTCTGGCCTCGAACAATTAGGCGCGACCATCAAACTGGAAGAAGGTTACGTTAAAGCTTCCGTCGATGGTCGTTTGAAAGGCGCACATATCGTGATGGATAAAGTCAGCGTTGGCGCAACGGTGACCATCATGTGTGCTGCAACCCTTGCGGAAGGCACCACGATTATTGAAAACGCAGCGCGTGAACCGGAAATCGTCGATACCGCGAACTTCCTGATTACGCTGGGTGCGAAAATTAGCGGTCAGGGCACCGATCGTATCGTCATCGAAGGTGTGGAACGTTTAGGCGGCGGTGTCTATCGCGTGCTGCCGGATCGTATCGAAACCGGTACTTTCCTGGTGGCGGCGGCGATCTCTCGCGGCAAAATTATCTGCCGTAACGCGCAGCCAGATACTCTGGACGCCGTGCTGGCGAAACTGCGTGACGCTGGAGCGGACATCGAAGTCGGCGAGGACTGGATTAGCCTGGATATGCATGGCAAACGTCCGAAGGCTGTTAACGTACGTACCGCGCCGCATCCGGCATTCCCTACCGATATGCAGGCCCAGTTCACGCTGTTGAACCTGGTGGCAGAAGGGACCGGATTCATCACCGAAACGGTCTTTGAAAACCGCTTTATGCATGTGCCAGAGCTGAGCCGTATGGGCGCGCACGCCGAAATCGAAAGCAATACCGTTATTTGTCACGGTGTTGAAAAACTTTCTGGCGCACAGGTTATGGCAACCGATCTGCGTGCATCAGCAAGCCTGGTGCTGGCTGGCTGTATTGCGGAAGGGACGACGGTGGTTGATCGTATTTATCACATCGATCGTGGCTACGAACGCATTGAAGACAAACTACGCGCTTTAGGTGCAAATATTGAGCGTGTGAAAGGCGAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40452","NCBI_taxonomy_name":"Escherichia coli ATCC 25922","NCBI_taxonomy_id":"1322345"}}}},"ARO_accession":"3003775","ARO_id":"40451","ARO_name":"Escherichia coli murA with mutation conferring resistance to fosfomycin","CARD_short_name":"Ecol_murA_FOF","ARO_description":"murA or UDP-N-acetylglucosamine enolpyruvyl transferase catalyses the initial step in peptidoglycan biosynthesis and is inhibited by fosfomycin. Overexpression of murA through mutations such as Asp369Asn and Leu370Ile confers fosfomycin resistance. Extensive evidence has shown the significance of C115 mutations in conferring fosfomycin resistance since this residue represents a primary binding site for the antibiotic across many species.","ARO_category":{"39245":{"category_aro_accession":"3002811","category_aro_cvterm_id":"39245","category_aro_name":"antibiotic-resistant murA transferase","category_aro_description":"murA or UDP-N-acetylglucosamine enolpyruvyl transferase catalyses the initial step in peptidoglycan biosynthesis and is inhibited by fosfomycin. Overexpression of murA through mutations confers fosfomycin resistance.","category_aro_class_name":"AMR Gene Family"},"35944":{"category_aro_accession":"0000025","category_aro_cvterm_id":"35944","category_aro_name":"fosfomycin","category_aro_description":"Fosfomycin (also known as phosphomycin and phosphonomycin) is a broad-spectrum antibiotic produced by certain Streptomyces species. It is effective on gram positive and negative bacteria as it targets the cell wall, an essential feature shared by both bacteria. Its specific target is MurA (MurZ in E.coli), which attaches phosphoenolpyruvate (PEP) to UDP-N-acetylglucosamine, a step of commitment to cell wall synthesis. In the active site of MurA, the active cysteine molecule is alkylated which stops the catalytic reaction.","category_aro_class_name":"Antibiotic"},"45731":{"category_aro_accession":"3007149","category_aro_cvterm_id":"45731","category_aro_name":"phosphonic acid antibiotic","category_aro_description":"A group of antibiotics derived from phosphonic acids.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2290":{"model_id":"2290","model_name":"Mycobacterium tuberculosis intrinsic murA conferring resistance to fosfomycin","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"750"},"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"13249":"D117C"},"Curated-R":{"13249":"D117C"},"clinical":{"13249":"D117C"}}},"model_sequences":{"sequence":{"8840":{"protein_sequence":{"accession":"NP_215831.1","sequence":"MAERFVVTGGNRLSGEVAVGGAKNSVLKLMAATLLAEGTSTITNCPDILDVPLMAEVLRGLGATVELDGDVARITAPDEPKYDADFAAVRQFRASVCVLGPLVGRCKRARVALPGGDAIGSRPLDMHQAGLRQLGAHCNIEHGCVVARAETLRGAEIQLEFPSVGATENILMAAVVAEGVTTIHNAAREPDVVDLCTMLNQMGAQVEGAGSPTMTITGVPRLHPTEHRVIGDRIVAATWGIAAAMTRGDISVAGVDPAHLQLVLHKLHDAGATVTQTDASFRVTQYERPKAVNVATLPFPGFPTDLQPMAIALASIADGTSMITENVFEARFRFVEEMIRLGADARTDGHHAVVRGLPQLSSAPVWCSDIRAGAGLVLAGLVADGDTEVHDVFHIDRGYPLFVENLVSLGAEIERVCC"},"dna_sequence":{"accession":"NC_000962.3","fmin":"1470320","fmax":"1471577","strand":"+","sequence":"GTGGCCGAGCGTTTCGTCGTGACTGGGGGCAACCGGTTATCAGGCGAAGTGGCCGTCGGCGGCGCCAAGAACAGCGTGCTCAAGCTCATGGCTGCGACGTTGTTGGCCGAGGGCACCAGCACGATCACCAACTGTCCCGACATCCTCGATGTGCCGCTGATGGCGGAGGTACTGCGTGGTCTGGGCGCCACCGTCGAACTCGACGGTGACGTGGCCCGGATCACCGCACCTGACGAGCCGAAGTACGATGCCGACTTCGCTGCGGTGCGGCAATTCCGCGCCTCGGTCTGTGTGCTGGGACCGCTGGTCGGGCGGTGCAAACGGGCCAGGGTCGCGCTGCCGGGCGGTGACGCGATCGGGTCGCGTCCGTTGGATATGCACCAGGCGGGCCTACGGCAATTGGGTGCCCACTGCAACATCGAGCACGGCTGCGTGGTAGCCCGAGCGGAAACGTTGCGCGGTGCGGAGATTCAGTTGGAGTTCCCCTCGGTGGGAGCCACCGAGAACATCTTGATGGCCGCCGTGGTGGCCGAGGGAGTCACCACTATTCACAATGCGGCTCGAGAACCCGACGTCGTCGACTTGTGCACGATGTTGAACCAGATGGGCGCACAGGTCGAAGGTGCGGGTTCGCCGACAATGACCATCACCGGTGTCCCGCGGCTGCATCCAACCGAGCACCGGGTGATCGGAGACCGTATCGTTGCCGCCACATGGGGCATCGCTGCCGCAATGACCCGTGGTGATATATCAGTGGCGGGCGTAGACCCGGCGCATCTGCAGCTGGTGCTGCACAAATTGCACGACGCGGGCGCAACCGTCACCCAGACTGACGCCAGCTTCCGGGTGACCCAGTACGAGCGTCCGAAGGCTGTCAACGTTGCGACCTTGCCGTTCCCCGGGTTTCCCACGGATCTGCAGCCGATGGCTATCGCTTTGGCGTCGATCGCCGACGGCACATCGATGATCACGGAGAACGTGTTCGAGGCGCGGTTCCGCTTCGTTGAAGAGATGATCCGGCTCGGTGCAGACGCTCGGACCGACGGGCACCACGCCGTGGTGCGGGGCCTCCCGCAGCTGTCGAGCGCTCCGGTGTGGTGTTCGGACATCCGTGCCGGGGCCGGCTTGGTGCTGGCGGGGCTCGTTGCCGACGGCGACACCGAGGTCCACGATGTATTCCACATCGATCGCGGATATCCGTTGTTCGTGGAGAACCTGGTGAGTCTCGGTGCCGAGATCGAACGGGTATGCTGTTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3003784","ARO_id":"40467","ARO_name":"Mycobacterium tuberculosis intrinsic murA conferring resistance to fosfomycin","CARD_short_name":"Mtub_murA_FOF","ARO_description":"Mycobacterium tuberculosis murA confers intrinsic resistance to fosfomycin. The presence of an aspartic acid residue in place of the critical cysteine at position 117 that enables fosfomycin binding is believed to be responsible for this intrinsic resistance.","ARO_category":{"39245":{"category_aro_accession":"3002811","category_aro_cvterm_id":"39245","category_aro_name":"antibiotic-resistant murA transferase","category_aro_description":"murA or UDP-N-acetylglucosamine enolpyruvyl transferase catalyses the initial step in peptidoglycan biosynthesis and is inhibited by fosfomycin. Overexpression of murA through mutations confers fosfomycin resistance.","category_aro_class_name":"AMR Gene Family"},"35944":{"category_aro_accession":"0000025","category_aro_cvterm_id":"35944","category_aro_name":"fosfomycin","category_aro_description":"Fosfomycin (also known as phosphomycin and phosphonomycin) is a broad-spectrum antibiotic produced by certain Streptomyces species. It is effective on gram positive and negative bacteria as it targets the cell wall, an essential feature shared by both bacteria. Its specific target is MurA (MurZ in E.coli), which attaches phosphoenolpyruvate (PEP) to UDP-N-acetylglucosamine, a step of commitment to cell wall synthesis. In the active site of MurA, the active cysteine molecule is alkylated which stops the catalytic reaction.","category_aro_class_name":"Antibiotic"},"45731":{"category_aro_accession":"3007149","category_aro_cvterm_id":"45731","category_aro_name":"phosphonic acid antibiotic","category_aro_description":"A group of antibiotics derived from phosphonic acids.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3312":{"model_id":"3312","model_name":"Mycoplasma genitalium 23S rRNA mutations confers resistance to fluoroquinolone and macrolide antibiotics","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"8730":"a2071c","8732":"a2071t","8733":"a2072g","8731":"a2071g"},"Curated-R":{"8730":"a2071c","8732":"a2071t","8733":"a2072g","8731":"a2071g"},"clinical":{"8730":"a2071c","8732":"a2071t","8733":"a2072g","8731":"a2071g"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"41093","param_value":"4500"}},"model_sequences":{"sequence":{"5599":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"L43967.2","fmin":"171727","fmax":"174461","strand":"+","sequence":"ACAATAAGTTACTAAGGGCTTATGGTGGATGCCTTGGCACTAAAAGGCGATGAAGGACGTGTTAACCTGCGATAAGCTTCGGGGAGGTGGTAAAAACCTGAGATCCGGAGGTGTCCGAATGGAGCAATCTGGTAGCTTGCAAAAGTTACCATTAATTAATGAATTCATAGTTAATTAAAGCGATACGTGGTGAAGTGAAACATCTCAGTAACCACAGGAAAAGAAAACGAATGTGATTCCGTGTGTAGTGGCGAGCGAAAGCGGAACAGGCCAAACCTATCTGAGGATAGGGGTTGTAGGGCTTGCATTATGGAAGTTAAAAGGATAGAAGAAGCTGTTGGAAAGCAGCGCCAAAGAGGGTGATAGCCCCGTATTTGAAATCTTTTTAATACCTAGCAAGAAACCTGAGTAGCTCGAAAAACGTTATTTTGAGTGAATCTGCCCAGACCATTGGGTAAGCCTAAATACTAATTAGTGACCGATAGCGAAACAGTACCGTGAGGGAAAGGTGAAAAGAACCCAGAGATGGGAGTGAAATAGATTCTGAAACCATATGCCTACAACGTGTCAGAGCACATTAATGTGTGATGGCGTGCGTTTTGAAGTATGAGCCGGCGAGTTATGATAGCAAGCGTTAGTTAACCAGGAGATGGGGAGCTGTAGCGAAAGCGAGTTTTAAGAGAGCGTTTGTTTGTTATCATAGACCCGAAACGGGTTGAGCTAGTCATGAGCAGGTTGAAGGTTGAGTAACATTAACTGGAGGACCGAACCGACTCTCGTTGAAACGATAGCGGATGACTTGTGATTAGGGGTGAAATTCCAATCGAAATCCGTGATAGCTGGTTCTCGTCGAAATAGCTTTAAGGCTAGCGTAAGATCACAAATAAGTGGAGGTAAAGCTACTGAATGTATGATGGCGCCACCTAGGCGTACTGAATACAATTAAACTCTGAATGCCATTTATTTTATTCTTGCAGTCAGACAGTGGGGGATAAGCTTCATTGTCAAGAGGGGAAGAGCCCAGATCATTAAATAAGGTCCCCAAAATATACTAAGTGGAAAAGGATGTGAAAGTGCTAAAACAGCAAGGATGTTGGCTTAGAAGCAGCCATCGTTTAAAGAGTGCGTAACAGCTCACTTGTCGAGTGTTTTTGCGCCGAAGATGTAACGGGGCTAAGTATATTACCGAATTTATGGATAAGATATTTTTATCTTGTGGTAGACGAGCGTTGTATTGGAGTTGAAGTCAAAGCGTGAGCATTGGTGGATCCAATACAAGTGAGAATGCCGGCGTGAGTAACGCTTGGGAGTGAGAATCTCCCAAACCGATTGACTAAGGTTTCCTGGACCAGGGTCGTCCTTCCAGGGTTAGTCTGGACCTAAGCTGAGGCTGAAGAGCGTAGGCGATGGACAACAGGTTAATATTCCTGTACTTACAGTTAGACTGATGGAGTGACAAAGAAGGTTATCCACCCCCATTATTGGATTTGGGGATAAACCATAAGGTGGTACAATAGGCAAATCCGTTGTGCATAACACTGAGTGGTGATGTCGAGTGAACGAGTGATCAAGTAGCGAAGGTGGCAATTAATCATGCTTTCAAGAAAAGCTGCTAGGGCTAATTTAACTGTAACCAGTACCGAGAACGAACACACGTAGTCAAGGAGAGGATCCTAAGGTTAGCGAGTGAACTATAGCCAAGGAACTCTGCAAATTAACCCCGTAAGTTAGCGAGAAGGGGTGCTTATCTAAAAGTAAGCCGCAGTGAAGAACGAGGGGGGACTGTTTAACTAAAACACAACTCTATGCCAAACCGTAAGGTGATGTATATGGGGTGACACCTGCCCAGTGCTGGAAGGTTAAAGAAGGAGGTTAGCAATTTATTGCAAAGCTTTTAACTGAAGCCCCAGTGAACGGCGGCCGTAACTATAACGGTCCTAAGGTAGCGAAATTCCTAGTCGGGTAAATTCCGTCCCGCTTGAATGGTGTAACCATCTCTTGACTGTCTCGGCTATAGACTCGGTGAAATCCAGGTACGGGTGAAGACACCCGTTAGGCGCAACGGGACGGAAAGACCCCGTGAAGCTTTACTGTAGCTTAATATTGATCAAAACACCACCATGTAGAGAATAGGTAGGAGCAATTGATGCAAGTTCGCAAGGATTTGTTGATGTGAAATGTGGAATACTACCCTTGGTTATGTTTTGTTCTAATTGGTAACTGTGATCCAGTTTCAAGACAGTGTTAGGTGGGCAGTTTGACTGGGGCGGTCGCCTCCTAAAAGGTAACGGAGGCGCACAAAGGTACCTTCAGTACGGTTGGAAATCGTATTTAGAGTGTAATGGTATAAGGGTGCTTGACTGTGAGACTTACAGGTCGAACAGGTGAGAAATCAGGTCATAGTGATCCGGTGGTTCAGTATGGAATGGCCATCGCTCAACGGATAAAAGCTACTCCGGGGATAACAGGCTGATACTGCCCAAGAGTTCATATCGACGGCAGTGTTTGGCACCTCGATGTCGACTCATCTCATCCTCGAGCTGAAGCAGGTTCGAAGGGTTCGGCTGTTCGCCGATTAAAGAGATACGTGAGTTGGGTTCAAACCGTCGTGAGACAGGTTGGTCCCTATCTATTGTGCCCACAGGAAGATTGAAGAGCTTTGCTTCTAGTACGAGAGGACCGGAGCGAGGACACCGCTTATGCTCCAGTTGTAGCGCCAGCTGCACCGCTGGGT","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42585","NCBI_taxonomy_name":"Mycoplasma genitalium G37","NCBI_taxonomy_id":"243273"}}}},"ARO_accession":"3004616","ARO_id":"42584","ARO_name":"Mycoplasma genitalium 23S rRNA mutations confers resistance to fluoroquinolone and macrolide antibiotics","CARD_short_name":"Mgen_23S_MULT","ARO_description":"Mycoplasma genitalium strain M6320 contains mutations that lead to resistance to fluoroquinolone and macrolide antibiotics.","ARO_category":{"41251":{"category_aro_accession":"3004125","category_aro_cvterm_id":"41251","category_aro_name":"23S rRNA with mutation conferring resistance to macrolide antibiotics","category_aro_description":"Nucleotide point mutations in the 23S rRNA subunit may confer resistance to macrolide antibiotics.","category_aro_class_name":"AMR Gene Family"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2277":{"model_id":"2277","model_name":"mphM","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"5319":{"protein_sequence":{"accession":"AMR06225.1","sequence":"MNKQKAIEIARKYGLEVKEGSIIFNESGLDFLVAYAEDYKGEEWVLRFPRRDDVMPRTIVEKKALDLVNKYATFQVPVWSLYKNDLIAYKKLTGVPAGTIDPEIQNYLWEMDYENVPERFHQTLAKALASLHTIPKEEALKVGLFVQTAEEARKSMIERMEKVKAKFDVGKSLWNRWQAWIKNEELWPQKTGLIHGDVHAGHTMIDKDANVTGLIDWTEAKVTDVSNDFVFQYRAFGEASLEKLIQHYRQAGGIYWPAMKEHVIELNAAYPVAIAEFAIISGLEEYEQMAKETLQVNDR"},"dna_sequence":{"accession":"CP014284.1","fmin":"189532","fmax":"190432","strand":"-","sequence":"TTGAACAAACAAAAAGCGATAGAAATAGCAAGAAAGTATGGCTTGGAAGTTAAAGAGGGATCCATTATATTCAACGAGTCCGGTTTAGATTTTCTAGTTGCGTATGCAGAAGATTATAAAGGCGAAGAATGGGTGCTAAGGTTTCCGAGACGAGACGATGTGATGCCTAGGACTATAGTGGAGAAGAAAGCACTGGATCTTGTAAACAAATATGCCACTTTTCAGGTTCCAGTCTGGTCGCTTTATAAAAACGATCTAATAGCTTATAAAAAGTTAACCGGAGTGCCAGCAGGCACAATTGATCCAGAGATTCAAAATTATTTGTGGGAGATGGATTATGAAAATGTACCTGAACGATTTCACCAGACATTAGCCAAAGCGTTGGCTTCGCTACACACAATTCCGAAAGAAGAGGCTCTTAAAGTAGGCCTTTTTGTCCAGACAGCAGAAGAGGCCAGAAAATCGATGATTGAGCGTATGGAAAAGGTTAAGGCGAAGTTTGATGTAGGAAAATCCTTATGGAACCGCTGGCAGGCCTGGATAAAAAATGAAGAATTGTGGCCGCAGAAAACAGGCCTGATTCACGGTGATGTTCATGCTGGCCACACGATGATTGATAAAGATGCTAACGTAACCGGTTTAATCGACTGGACTGAAGCAAAAGTAACGGATGTATCAAATGACTTTGTTTTCCAGTACCGGGCATTTGGGGAAGCATCCCTGGAGAAACTGATCCAACATTACCGGCAAGCAGGCGGAATTTACTGGCCTGCCATGAAAGAGCACGTCATTGAACTTAATGCTGCATACCCTGTTGCGATAGCTGAGTTTGCGATTATCTCAGGTTTGGAAGAATATGAGCAGATGGCGAAAGAAACATTGCAAGTGAATGACCGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39644","NCBI_taxonomy_name":"Bacillus thuringiensis","NCBI_taxonomy_id":"1428"}}}},"ARO_accession":"3003767","ARO_id":"40436","ARO_name":"mphM","CARD_short_name":"mphM","ARO_description":"mphM is a chromosomally-encoded macrolide phosphotransferases that inactivate 14-, 15- and 16-membered macrolides.","ARO_category":{"36472":{"category_aro_accession":"3000333","category_aro_cvterm_id":"36472","category_aro_name":"macrolide phosphotransferase (MPH)","category_aro_description":"Macrolide phosphotransferases (MPH) are enzymes encoded by macrolide phosphotransferase genes (mph genes). These enzymes phosphorylate macrolides in GTP dependent manner at 2'-OH of desosamine sugar thereby inactivating them. Characterized MPH's are differentiated based on their substrate specificity.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3365":{"model_id":"3365","model_name":"cmlA8","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"815"}},"model_sequences":{"sequence":{"5549":{"protein_sequence":{"accession":"ABW91179.1","sequence":"MRSKNFSWRYSLAATVLLLSPFDLLASLGMDMYLPAVPFMPNALGTTTSTIQLTLTTYLVMIGAGQLLFGPLSDRLGRRPVLLGGGLAYVVASMGLALTSSAEVFLGLRILQACGASACLVSTFATVRDIYAGREESNVIYGILGSMLAMVPAIGPLLGALVDTWLGWRAIFAFLGLGMIAASAAAWRFWPETRVQRVAGLQWSQLLLPIKCLNFWLYTLCYTAGMGSFFVFFSIAPGLMMGRQGVSQLDFSLLFATVAIAMVFTARFMGRVIPKWGSPSVLRMGMGCLIAGAVLLAITEIWVSQSVLGFIAPMWLVGVGVATAVSVAPNGALRGFDHVAGTVTAVYFCLGGVLLGSIGTLIIWLLPRNTAWPVVVYCLTLATVVLGLSCVSRAKGFRGQREHDVVALQNAESTSNPNR"},"dna_sequence":{"accession":"EU182575.1","fmin":"1685","fmax":"2945","strand":"+","sequence":"GTGCGCTCAAAGAACTTTAGTTGGCGGTACTCCCTTGCCGCCACGGTGTTGTTGTTATCACCGTTCGATTTACTGGCATCACTCGGCATGGATATGTACTTGCCGGCAGTGCCCTTCATGCCAAACGCACTTGGCACGACAACGAGTACAATTCAGCTTACGCTGACAACGTACTTGGTCATGATCGGTGCCGGTCAGCTCTTGTTTGGACCACTATCGGACCGACTAGGTCGCCGCCCCGTTCTATTGGGGGGTGGCCTCGCCTACGTTGTGGCGTCAATGGGCCTCGCTCTTACGTCGTCGGCTGAAGTCTTTCTGGGGCTTCGGATTCTTCAGGCTTGTGGTGCCTCGGCGTGCCTTGTTTCCACGTTTGCAACAGTACGTGACATTTACGCAGGTCGTGAGGAAAGTAACGTCATTTACGGCATACTCGGGTCCATGCTGGCCATGGTCCCGGCGATAGGCCCATTGCTGGGAGCACTCGTCGACACGTGGCTTGGGTGGCGGGCTATCTTTGCGTTTCTAGGTTTGGGCATGATCGCTGCATCTGCAGCAGCGTGGCGATTCTGGCCTGAAACCCGGGTGCAACGAGTTGCGGGCTTGCAATGGTCGCAGCTGCTACTCCCCATTAAGTGCCTGAACTTCTGGTTGTACACGTTGTGTTACACCGCTGGAATGGGTAGCTTTTTCGTCTTTTTCTCCATTGCGCCCGGGCTAATGATGGGCAGGCAAGGTGTGTCTCAGCTTGACTTCAGCCTGCTGTTCGCCACAGTGGCAATCGCCATGGTGTTTACGGCTCGTTTTATGGGGCGAGTGATACCCAAGTGGGGAAGTCCAAGTGTCTTGCGAATGGGAATGGGATGCCTGATAGCGGGAGCAGTATTGCTTGCCATCACCGAAATATGGGTTTCGCAGTCCGTGTTGGGCTTTATTGCTCCAATGTGGCTAGTGGGTGTTGGTGTCGCCACAGCGGTATCTGTGGCGCCCAATGGCGCTCTTCGAGGATTCGACCACGTTGCCGGAACGGTCACGGCAGTCTACTTCTGCTTGGGCGGTGTACTGCTAGGAAGCATCGGAACGTTGATCATTTGGCTGTTGCCGCGCAACACGGCTTGGCCGGTTGTCGTGTACTGTTTGACCCTTGCAACAGTCGTGCTTGGTCTGTCTTGTGTTTCCCGAGCGAAGGGCTTTCGCGGCCAGAGGGAGCATGATGTGGTCGCGCTACAAAATGCGGAAAGTACGTCAAATCCCAATCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3004665","ARO_id":"42708","ARO_name":"cmlA8","CARD_short_name":"cmlA8","ARO_description":"cmlA8 is a plasmid that confers resistance to chloramphenicol.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2246":{"model_id":"2246","model_name":"vanR gene in vanI cluster","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"5264":{"protein_sequence":{"accession":"BAE85478.1","sequence":"MAANILIVDDEQAIADLVEVYLKNENYNLFKFYNGKDALDCIEKEKLDLAILDVMLPDVDGFSICRQIREKHNFPVIMLTAKEEEIDKITGLTLGADDYITKPFRPLELIARVKAQLRRFTKYNSAEPNQEEHVIAFSGLVLDMDTHECTLNEKKLSLTPTEFSILWVLCSNRGRVVSSEELFSEVWGDKYFTNSNNTVMVHIRHLREKMQDSAEHPKYIKTVWGVGYKIEK"},"dna_sequence":{"accession":"AP008230.1","fmin":"4201992","fmax":"4202691","strand":"-","sequence":"TTGGCTGCTAATATTTTGATTGTTGATGATGAACAAGCTATTGCCGATTTGGTGGAAGTTTATCTGAAAAATGAGAACTATAATCTCTTTAAATTTTATAACGGCAAGGATGCCCTTGACTGTATTGAAAAGGAAAAACTGGATCTCGCCATTTTGGATGTCATGCTCCCTGATGTAGACGGTTTTTCAATCTGCCGGCAAATCCGGGAAAAGCATAATTTTCCGGTGATCATGCTGACAGCCAAGGAAGAAGAAATCGATAAGATTACCGGGCTGACCTTAGGCGCGGACGACTATATCACCAAGCCGTTCCGTCCCTTGGAGCTGATTGCCCGCGTCAAGGCGCAGCTGCGGAGATTTACCAAGTATAATTCTGCAGAGCCAAACCAAGAGGAACACGTGATTGCCTTTTCCGGCTTGGTCTTAGACATGGATACCCATGAATGTACCTTGAATGAAAAAAAACTATCCCTCACGCCTACGGAGTTCTCCATTCTTTGGGTCCTTTGCTCCAACCGCGGCCGGGTAGTCAGTTCGGAAGAATTGTTCAGTGAGGTATGGGGAGACAAGTATTTCACCAACAGCAATAATACGGTCATGGTGCATATCCGGCATTTAAGGGAAAAAATGCAAGACAGCGCGGAACATCCTAAATATATCAAAACGGTATGGGGGGTTGGCTATAAAATTGAAAAGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42594","NCBI_taxonomy_name":"Desulfitobacterium hafniense Y51","NCBI_taxonomy_id":"138119"}}}},"ARO_accession":"3003728","ARO_id":"40385","ARO_name":"vanR gene in vanI cluster","CARD_short_name":"vanR_in_vanI_cl","ARO_description":"Also known as vanRI, is the regulatory transcriptional activator in the vanSR regulator within the vanI glycopeptide resistance gene cluster.","ARO_category":{"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"36713":{"category_aro_accession":"3000574","category_aro_cvterm_id":"36713","category_aro_name":"vanR","category_aro_description":"VanR is a OmpR-family transcriptional activator in the VanSR regulatory system. When activated by VanS, it promotes cotranscription of VanA, VanH, and VanX.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"35948":{"category_aro_accession":"0000029","category_aro_cvterm_id":"35948","category_aro_name":"teicoplanin","category_aro_description":"Teicoplanin is a glycopeptide antibiotic used in the prophylaxis and treatment of serious infections caused by Gram-positive bacteria. Teicoplanin has a unique acyl-aliphatic chain, and binds to cell wall precursors to inhibit transglycosylation  and transpeptidation.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2243":{"model_id":"2243","model_name":"vanX gene in vanI cluster","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"200"}},"model_sequences":{"sequence":{"5507":{"protein_sequence":{"accession":"ACL19707.1","sequence":"MKSDFVFVDELVSGIRWDAKYATWDNFTGKPVDGYAANRIVGTRALCAALEKARENAASLGFGLLLWDGYRPQCAVDCFLRWSKQPEDGRTKQKHYPNIDRSEIIEKGYVAAKSGHSRGSAIDLTLYHLASGTLVPMGGDFDLMDSVSHHGAHGISQAEARNRQYLCSIMEASGFVSYACEWWHYSLKHEPYPNTYFDFLIA"},"dna_sequence":{"accession":"CP001336.1","fmin":"1776504","fmax":"1777113","strand":"+","sequence":"ATGAAAAGTGATTTTGTCTTTGTGGACGAGTTGGTATCAGGAATACGTTGGGATGCTAAATACGCCACCTGGGATAATTTTACCGGCAAACCGGTGGACGGCTATGCAGCCAATCGAATTGTCGGTACGAGAGCGTTGTGCGCGGCCTTGGAAAAAGCACGGGAAAACGCCGCATCCTTGGGCTTTGGCTTGCTTCTTTGGGATGGTTACCGCCCTCAATGCGCCGTAGATTGCTTTCTGCGCTGGTCTAAACAGCCGGAAGATGGCCGGACGAAACAGAAACACTATCCGAATATTGACCGATCCGAGATCATCGAAAAAGGATATGTGGCTGCCAAGTCGGGCCACAGCCGGGGCAGCGCCATTGATTTAACCCTTTATCATTTAGCTTCCGGAACACTTGTGCCCATGGGCGGTGATTTTGATTTGATGGATTCAGTCTCACATCATGGCGCACATGGAATCAGCCAAGCCGAAGCGAGAAACCGTCAATATCTTTGTTCGATCATGGAGGCCAGCGGTTTTGTTTCCTACGCTTGCGAGTGGTGGCATTACAGCCTGAAACACGAACCTTATCCCAACACTTACTTTGATTTTCTCATCGCCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42687","NCBI_taxonomy_name":"Desulfitobacterium hafniense DCB-2","NCBI_taxonomy_id":"272564"}}}},"ARO_accession":"3003725","ARO_id":"40381","ARO_name":"vanX gene in vanI cluster","CARD_short_name":"vanX_in_vanI_cl","ARO_description":"Also known as vanXI, is a vanX variant found in the vanI glycopeptide resistance gene cluster. It is a D-Ala-D-Ala dipeptidase.","ARO_category":{"36020":{"category_aro_accession":"3000011","category_aro_cvterm_id":"36020","category_aro_name":"vanX","category_aro_description":"VanX is a D,D-dipeptidase that cleaves D-Ala-D-Ala but not D-Ala-D-Lac, ensuring that the latter dipeptide that has reduced binding affinity with vancomycin is used to synthesize peptidoglycan substrate.","category_aro_class_name":"AMR Gene Family"},"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"35948":{"category_aro_accession":"0000029","category_aro_cvterm_id":"35948","category_aro_name":"teicoplanin","category_aro_description":"Teicoplanin is a glycopeptide antibiotic used in the prophylaxis and treatment of serious infections caused by Gram-positive bacteria. Teicoplanin has a unique acyl-aliphatic chain, and binds to cell wall precursors to inhibit transglycosylation  and transpeptidation.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2250":{"model_id":"2250","model_name":"fusC","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"375"}},"model_sequences":{"sequence":{"5372":{"protein_sequence":{"accession":"CAG41812.1","sequence":"MNKIEVYKFVKVKQLVYQLIKLYRTNDMNSHKTQKDFLLNEINDIFKEKDIDISDFITSIDDVKLTKKKAEHLLNELKVYIQDFEIPSSSQLEKIFRKVKKLKRPDINLIDTKEISYLGWNDNSSNRKYIVYKNLDDKFEGIYGEISPNKVKGFCKICNQESDTSLFLNKTKHNKSSGTYTKKGDYICYDSFKCNQNLDDINNLYEFIVKIK"},"dna_sequence":{"accession":"BX571857.1","fmin":"52819","fmax":"53458","strand":"+","sequence":"ATGAATAAAATAGAAGTGTATAAGTTTGTTAAAGTAAAGCAGTTAGTATATCAATTGATTAAGTTATATCGTACAAACGATATGAATTCCCATAAAACACAAAAAGATTTTTTACTAAATGAAATTAATGATATCTTTAAAGAAAAAGATATTGATATCTCGGACTTTATTACATCGATTGACGATGTAAAATTAACTAAGAAAAAAGCAGAACATCTTTTAAATGAATTAAAAGTGTACATCCAAGATTTTGAAATACCTTCATCAAGTCAACTGGAGAAAATTTTTCGTAAAGTAAAAAAATTAAAGAGACCAGATATAAATTTAATTGATACAAAAGAAATTTCATATTTAGGATGGAATGATAATTCTTCTAACCGAAAATATATCGTTTATAAAAATTTAGATGATAAATTCGAAGGTATATATGGCGAAATTTCACCAAATAAAGTAAAAGGATTCTGTAAAATTTGTAATCAGGAATCTGATACATCACTCTTTCTCAATAAAACTAAACATAATAAGAGTAGTGGAACATATACTAAAAAAGGAGATTACATTTGTTATGACAGTTTTAAATGTAATCAGAACCTAGATGATATAAATAATCTTTACGAATTTATTGTTAAAATAAAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35518","NCBI_taxonomy_name":"Staphylococcus aureus subsp. aureus MSSA476","NCBI_taxonomy_id":"282459"}}}},"ARO_accession":"3003733","ARO_id":"40388","ARO_name":"fusC","CARD_short_name":"fusC","ARO_description":"FusC is a fusidic acid resistance gene enabling ribosomal translocase EF-G dissociation from the ribosome that has been detected in Staphylococcus aureus and Staphylococcus intermedius. Its mechanism is believed to be similar to fusB due to its high level of sequence homology. It is considered a FusB-type protein.","ARO_category":{"43297":{"category_aro_accession":"3005086","category_aro_cvterm_id":"43297","category_aro_name":"Target protecting FusB-type protein conferring resistance to Fusidic acid","category_aro_description":"Fusidic acid resistance determinants through the mediation of target protection. These protein drive the dissociation of EF-G from the ribosome thus counteracting the action of Fusidic acid.","category_aro_class_name":"AMR Gene Family"},"37139":{"category_aro_accession":"3000759","category_aro_cvterm_id":"37139","category_aro_name":"fusidic acid","category_aro_description":"Fusidic acid is the only commercially available fusidane, a group of steroid-like antibiotics. It is most active against Gram-positive bacteria, and acts by inhibiting elongation factor G to  block protein synthesis.","category_aro_class_name":"Antibiotic"},"45735":{"category_aro_accession":"3007153","category_aro_cvterm_id":"45735","category_aro_name":"fusidane antibiotic","category_aro_description":"A group of antibiotics possessing steroid rings or steroid-like structures.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"651":{"model_id":"651","model_name":"Staphylococcus aureus mprF","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1600"},"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"8269":"T345A"},"Curated-R":{"8269":"T345A"},"clinical":{"8269":"T345A"}}},"model_sequences":{"sequence":{"59":{"protein_sequence":{"accession":"ADJ67256.1","sequence":"MNQEVKNKIFSILKITFATALFIFVAITLYRELSGINFKDTLVEFSKINRMSLVLLFIGGGASLVILSMYDVILSRALKMDISLGKVLRVSYIINALNAIVGFGGFIGAGVRAMVYKNYTHDKKKLVHFISLILISMLTGLSLLSLLIVFHVFDASLILDKITWVRWVLYVVSFFLPLFIIYSMVRPPDKNNRFVGLYCTLVSCVEWLAAAVVLYFCGVIVDAHVSFMSFIAIFIIAALSGLVSFIPGGFGAFDLVVLLGFKTLGVPEEKVLLMLLLYRFAYYFVPVIIALILSSFEFGTSAKKYIEGSKYFIPAKDVTSFLMSYQKDIIAKIPSLSLAILVFFTSMINLTIVYDALYDGNHLTYYILLAIHTSACLLLLLNVVGIYKQSRRAIIFAMISILLITVATFFTYASYILITWLAIIFVLLIVAFRRARRLKRPVRMRNIVAMLLFSLFILYVNHIFIAGTLYALDIYTIEMHTSVLRYYFWLTILIIAIIIGMIAWLFDYQFSKVRISSKIEDCEEIINQYGGNYLSHLIYSGDKQFFTNENKTAFLMYRYKASSLVVLGDPLGDENAFDELLEAFYNYAEYLGYDVIFYQVTDQHMPLYHNFGNQFFKLGEEAIIDLTQFSTSGKKRRGFRATLNKFDELNISFEIIEPPFSTEFINELQHVSDLWLDNRQEMHFSVGEFNEEYLSKAPIGVMRNEENEVIAFCSLMPTYFNDAISVDLIRWLPELDLPLMDGLYLHMLLWSKEQGYTKFNMGMATLSNVGQLHYSYLRERLAGRVFEHFNGLYRFQGLRRYKSKYNPNWEPRFLVYRKDNSLWESLSKVMRVIRHK"},"dna_sequence":{"accession":"HM140977.1","fmin":"0","fmax":"2511","strand":"+","sequence":"ATGAATCAGGAAGTTAAAAACAAAATATTTTCAATCTTAAAAATTACGTTTGCTACAGCTTTATTTATTTTTGTAGCAATCACATTGTATCGGGAGTTATCTGGTATTAACTTTAAAGATACGTTGGTTGAATTTAGTAAGATTAACCGTATGTCCTTAGTGTTACTATTTATTGGTGGTGGGGCATCGCTTGTTATTCTATCAATGTATGATGTGATTTTATCTAGAGCTTTAAAAATGGATATATCCTTAGGCAAAGTTTTAAGAGTAAGTTATATCATCAATGCATTGAATGCGATTGTAGGTTTCGGTGGCTTTATTGGTGCAGGCGTTAGAGCAATGGTTTATAAAAACTATACGCATGATAAAAAGAAATTAGTTCACTTTATATCCTTAATACTTATTTCAATGTTGACAGGTTTAAGCTTATTATCATTGCTAATTGTATTCCATGTTTTCGATGCATCTTTAATCTTAGATAAGATTACATGGGTAAGATGGGTATTATATGTAGTGTCATTTTTCTTACCATTATTCATTATTTATTCAATGGTTAGACCACCCGATAAAAACAATCGTTTTGTAGGATTGTACTGCACTTTAGTGTCGTGTGTTGAATGGTTAGCAGCTGCAGTTGTATTATATTTCTGTGGTGTAATTGTTGACGCTCATGTATCATTCATGTCCTTTATTGCAATATTTATCATTGCTGCATTATCAGGTTTAGTCAGCTTTATTCCTGGTGGTTTCGGCGCTTTCGATTTAGTTGTATTACTAGGATTTAAAACTTTAGGTGTCCCTGAGGAAAAAGTATTATTAATGCTACTTCTATATCGTTTTGCGTACTATTTTGTACCGGTAATTATTGCATTAATTTTATCATCATTTGAATTTGGTACATCAGCTAAGAAGTACATTGAGGGATCTAAATACTTTATTCCTGCTAAAGATGTTACGTCATTTTTAATGTCTTATCAAAAGGATATTATTGCTAAAATTCCATCATTATCATTAGCAATTTTAGTATTCTTTACAAGTATGATCAACTTAACGATTGTTTACGATGCTTTATATGATGGAAATCACTTAACGTATTATATTCTATTGGCAATTCATACTAGTGCTTGTTTATTACTTTTACTGAATGTAGTTGGTATTTATAAGCAAAGTAGACGTGCCATTATCTTTGCTATGATTTCAATTTTATTAATCACAGTGGCGACATTCTTCACTTACGCTTCATATATTTTAATAACATGGTTAGCTATTATTTTTGTTCTGCTTATTGTAGCTTTCCGTAGAGCACGTAGGTTGAAACGCCCAGTAAGAATGAGAAATATAGTTGCAATGCTTTTATTCAGTTTATTTATTTTATATGTTAACCATATATTTATTGCTGGAACGTTATATGCATTAGATATTTATACGATTGAAATGCATACATCTGTATTGCGCTATTACTTCTGGCTTACGATTTTAATCATCGCTATCATCATAGGTATGATTGCATGGTTGTTTGATTATCAATTTAGCAAAGTACGTATTTCTTCTAAAATTGAAGATTGCGAGGAGATTATTAATCAGTACGGCGGTAATTATTTGAGTCACTTGATATATAGTGGTGACAAGCAGTTTTTCACTAATGAAAATAAAACAGCATTTTTAATGTATCGTTATAAAGCAAGTTCATTAGTGGTTCTTGGAGATCCGTTAGGTGATGAAAATGCCTTTGATGAATTGTTAGAAGCATTCTATAATTACGCTGAGTATTTAGGCTATGATGTTATATTCTATCAAGTTACAGATCAACACATGCCTTTATATCATAATTTCGGTAACCAATTTTTCAAATTAGGTGAAGAAGCAATTATTGATTTAACGCAATTTTCAACTTCAGGTAAAAAACGCCGTGGATTTAGAGCGACTTTAAATAAATTCGATGAACTTAATATTTCGTTCGAAATTATTGAACCACCGTTTTCAACTGAATTTATAAATGAACTTCAACATGTAAGTGATTTATGGCTAGATAATCGTCAGGAAATGCATTTCTCTGTTGGTGAATTTAATGAAGAATACTTATCTAAAGCGCCAATTGGTGTAATGCGAAATGAAGAAAATGAAGTAATTGCATTTTGTAGTTTAATGCCAACATACTTTAATGATGCCATTTCAGTCGATTTAATTAGATGGTTGCCAGAGTTAGATTTACCATTAATGGATGGTCTATACTTGCATATGTTACTTTGGAGTAAAGAACAAGGTTATACAAAATTTAATATGGGTATGGCAACGTTATCGAACGTTGGTCAATTGCATTATTCATATTTAAGAGAACGACTTGCAGGCCGTGTCTTTGAACATTTCAACGGTCTATATCGTTTCCAAGGATTACGTCGTTATAAATCTAAATATAATCCGAATTGGGAACCACGCTTTTTAGTTTATCGTAAAGATAATTCGCTTTGGGAATCACTTTCTAAAGTAATGCGTGTAATACGTCACAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35508","NCBI_taxonomy_name":"Staphylococcus aureus","NCBI_taxonomy_id":"1280"}}}},"ARO_accession":"3003769","ARO_id":"40441","ARO_name":"Staphylococcus aureus mprF","CARD_short_name":"Saur_mprF","ARO_description":"MprF is a integral membrane protein that modifies the negatively-charged phosphatidylglycerol on the membrane surface. A point mutation in the putative mprF synthase domain is associated with enhanced expression, increased synthesis and reduced daptomycin surface binding. This confers resistance to cationic peptides that disrupt the cell membrane, including defensins.","ARO_category":{"37243":{"category_aro_accession":"3000863","category_aro_cvterm_id":"37243","category_aro_name":"defensin resistant mprF","category_aro_description":"MprF is a integral membrane protein that modifies the negatively-charged phosphatidylglycerol on the membrane surface of both Gram-positive and Gram-negative bacteria. This confers resistance to cationic peptides that disrupt the cell membrane, including defensins.","category_aro_class_name":"AMR Gene Family"},"37037":{"category_aro_accession":"3000693","category_aro_cvterm_id":"37037","category_aro_name":"defensin","category_aro_description":"Defensins are natural cationic peptides that have antibiotic properties. It is part of the innate immune system of plants and animals.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2252":{"model_id":"2252","model_name":"LpxD","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"650"},"40494":{"param_type":"frameshift mutation","param_description":"A frameshift is a sequence change between the translation initiation (start) and termination (stop) codon where, compared to a reference sequence, translation shifts to another reading frame as caused by nucleotide insertions and deletions. In ARO, these are annotated at the protein level with the first changed most N-terminal wildtype amino acid position. Format is given as [wildtype AA][position]fs, e.g. S531fs where S531 is a frameshifted coordinate beginning with codon 531. Termination may also be denoted as: Ter[position]fs.","param_type_id":"40494","param_value":{"3906":"K137fs"}},"snp":{"Curated-R":{"3906":"T345A"}}},"model_sequences":{"sequence":{"4643":{"protein_sequence":{"accession":"AJF82051.1","sequence":"MKVQQYRLDELAHLVKGELIGEGSLQFSNLASLENAEVNHLTFVNGEKHLDQAKVSRAGAYIVTAALKEHLPEKDNFIIVDNPYLAFAILTHVFDKKISSTGIESTAQIHPSAVISETAYIGHYVVIGENCVVGDNTVIQSHTKLDDNVEVGKDCFIDSHVTITGGSKLRDRVRIHSSTVIGGEGFGFAPYQGKWHRIAQLGSVLIGNDVRIGSNCSIDRGALDNTILEDGVIIDNLVQIAHNVHIGSNTAIAAKCGIAGSTKIGKNCILAGACGVAGHLSIADNVTLTGMSMVTKNISEAGTYSSGTGLFENNHWKKTIVRLRQLADVPLTQITKRLDHIQAQIESLESTFNLRK"},"dna_sequence":{"accession":"CP010781.1","fmin":"2256951","fmax":"2258022","strand":"-","sequence":"ATGAAAGTGCAACAATATCGTTTAGATGAATTAGCTCACCTTGTTAAAGGTGAGCTAATTGGTGAAGGTAGTCTTCAATTTTCAAACTTGGCGAGTTTGGAAAATGCAGAGGTTAACCATCTTACTTTTGTGAATGGTGAGAAACATCTTGATCAAGCTAAAGTAAGTCGTGCGGGCGCTTACATTGTTACCGCAGCTTTAAAAGAACATCTTCCTGAAAAAGATAATTTTATTATTGTTGATAATCCCTATCTTGCGTTTGCAATCCTTACCCATGTATTTGATAAAAAGATTAGCTCAACAGGCATAGAAAGCACTGCCCAAATTCATCCATCTGCTGTTATTTCCGAAACTGCTTATATTGGTCACTATGTGGTTATTGGTGAGAATTGTGTAGTTGGCGATAATACCGTCATTCAGTCACATACCAAACTTGATGATAATGTAGAAGTTGGAAAAGACTGTTTTATTGATTCTCATGTCACTATTACAGGTGGTTCTAAATTACGAGATCGCGTCCGTATTCATTCAAGTACTGTCATTGGTGGAGAAGGTTTTGGTTTTGCTCCATATCAAGGAAAGTGGCATCGTATTGCTCAATTAGGTTCAGTTTTAATTGGAAATGATGTCCGAATTGGATCAAATTGTAGTATTGATAGAGGCGCACTTGATAATACAATTTTGGAAGATGGGGTTATTATTGATAACCTTGTGCAAATTGCACATAACGTCCATATTGGTTCAAATACTGCTATTGCAGCGAAGTGCGGTATTGCCGGAAGTACAAAAATTGGCAAAAACTGTATTCTAGCTGGGGCGTGTGGAGTGGCAGGACACCTTTCAATTGCTGATAATGTGACTTTGACTGGAATGTCAATGGTCACAAAAAATATTTCTGAAGCTGGAACTTACTCTTCGGGAACCGGATTATTTGAAAATAATCATTGGAAAAAGACGATTGTACGCTTGCGACAATTAGCAGATGTGCCATTGACCCAAATCACTAAACGACTTGATCATATACAAGCTCAAATAGAGTCTCTTGAATCAACTTTTAATTTGCGTAAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3003575","ARO_id":"40185","ARO_name":"LpxD","CARD_short_name":"LpxD","ARO_description":"The LpxD gene is widely known to be involved in the biosynthesis of lipid A in Gram-negative bacteria and mutations to this gene may cause resistance to antimicrobial peptides that target the outer membrane.","ARO_category":{"40191":{"category_aro_accession":"3003581","category_aro_cvterm_id":"40191","category_aro_name":"Acinetobacter mutant Lpx gene conferring resistance to colistin","category_aro_description":"These genes are involved in the biosynthesis of lipid A in Gram-negative bacteria and mutations to this gene may cause resistance to antimicrobial peptides that target the outer membrane. Mutation by absence or insertion of ISAba11 sequence is a known cause of resistance in Acinetobacter baumannii\u25bf.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2263":{"model_id":"2263","model_name":"optrA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1300"}},"model_sequences":{"sequence":{"3517":{"protein_sequence":{"accession":"AKA86814.1","sequence":"MSKATFAIASTNAKEDMKMQYKIINGAVYYDGNMVLENIGIEINDNEKIAIVGRNGCGKTTLLKAIIGEIELEEGTGESEFQVIKTGNPYISYLRQMPFEDESISMVDEVRTVFKTLIDMENKMKQLIDKMENQYDDKIINEYSDISERYMALGGLTYQKEYETMIRSMGFTEADYKKPISEFSGGQRTKIAFIKILLTKPDILLLDEPTNHLDIETIQWLESYLRSYKSTLVIISHDRMFLNRIVDKVYEIEWGETKCYKGNYSAFEEQKRENHIKQQKDYDLQQIEIERITRLIERFRYKPTKAKMVQSKIKLLQRMQILNAPDQYDTKTYMSKFQPRISSSRQVLSASELVIGYDTPLAKVNFNLERGQKLGIVGSNGIGKSTLLKTLMGGVAALSGDFKFGYNVEISYFDQQLAQISGDDTLFEIFQSEYPELNDTEVRTALGSFQFSGDDVFRPVSSLSGGEKVRLTLCKLLYKRTNVLILDEPTNHMDIIGKENLENILCSYQGTIIFVSHDRYFTNKIADRLLVFDKDGVEFVQSTYGEYEKKRMNSEKPFNNIKVEQKVEKNNTVKGDRNSIEKEKVKKEKRIEKLEVLINQYDEELERLNKIISEPNNSSDYIVLTEIQKSIDDVKRCQGNYFNEWEQLMRELEVM"},"dna_sequence":{"accession":"KP399637.1","fmin":"31476","fmax":"33444","strand":"+","sequence":"TTGTCCAAAGCCACCTTTGCAATTGCTAGTACTAACGCAAAGGAGGATATGAAAATGCAATACAAAATAATTAATGGTGCCGTTTACTATGATGGTAATATGGTGTTGGAAAACATCGGTATTGAAATCAATGATAATGAAAAGATTGCTATTGTTGGTAGAAATGGATGTGGAAAAACAACCTTGCTAAAAGCTATTATAGGCGAAATTGAATTAGAAGAAGGAACTGGTGAAAGTGAGTTTCAAGTAATAAAGACCGGTAACCCTTATATTAGCTATTTAAGACAGATGCCTTTTGAAGATGAAAGTATATCAATGGTGGATGAAGTCCGTACGGTATTTAAGACGCTTATTGATATGGAAAACAAGATGAAACAGCTGATAGATAAAATGGAGAATCAATATGATGATAAAATCATCAATGAATACTCTGATATCAGTGAAAGGTATATGGCTCTTGGAGGTCTAACCTACCAAAAAGAATATGAAACGATGATTCGTAGTATGGGTTTTACTGAAGCAGATTATAAAAAACCCATTTCTGAATTTTCAGGTGGTCAGCGAACTAAGATAGCTTTTATAAAAATACTTTTAACAAAGCCAGACATTCTATTACTTGATGAACCTACTAACCACCTTGATATAGAAACAATACAATGGTTGGAGAGTTATTTGAGAAGTTATAAATCTACATTGGTTATTATTTCCCATGATAGAATGTTTCTTAATCGAATTGTGGATAAGGTTTATGAAATCGAATGGGGAGAGACCAAATGTTATAAAGGTAATTATTCAGCCTTTGAGGAGCAAAAACGAGAAAATCATATCAAACAGCAAAAAGATTACGACTTGCAACAGATAGAAATTGAAAGGATTACACGCTTGATTGAACGTTTTCGTTATAAACCTACGAAAGCTAAAATGGTGCAATCTAAAATTAAATTATTACAGCGTATGCAAATATTAAATGCACCAGACCAATACGATACAAAAACTTATATGTCTAAATTTCAACCGAGAATCAGTAGTTCAAGGCAAGTATTAAGTGCTTCAGAACTTGTGATAGGCTATGATACTCCTCTTGCAAAGGTTAATTTCAACCTTGAAAGGGGACAGAAGCTTGGAATTGTTGGGAGTAATGGTATTGGTAAATCCACGTTGCTTAAAACACTTATGGGTGGTGTGGCAGCATTGTCTGGAGATTTTAAATTCGGATACAATGTTGAAATTAGCTATTTTGACCAACAGCTTGCTCAAATCAGTGGAGATGATACACTATTCGAAATTTTTCAAAGCGAATACCCTGAGCTAAATGACACAGAGGTCAGAACTGCTCTTGGCTCATTTCAGTTTAGTGGAGATGATGTTTTTAGACCGGTGTCCTCTTTGTCAGGTGGAGAAAAGGTTAGATTGACATTATGTAAATTATTATATAAACGTACTAATGTTTTAATCTTAGATGAACCGACAAACCACATGGATATTATTGGAAAAGAGAATTTAGAGAATATCTTATGCAGTTATCAAGGTACAATTATTTTTGTGTCACATGATAGATATTTTACTAATAAGATTGCTGACAGATTACTTGTTTTTGATAAGGATGGTGTAGAGTTTGTACAATCTACTTATGGTGAGTACGAGAAAAAAAGGATGAATTCTGAAAAGCCATTTAATAACATTAAAGTTGAGCAGAAAGTAGAGAAAAATAACACAGTAAAAGGCGATCGTAACTCCATTGAGAAGGAGAAGGTTAAGAAGGAGAAACGAATTGAAAAGCTTGAAGTGTTAATAAATCAATATGATGAAGAATTAGAAAGATTGAATAAAATCATTTCTGAACCAAACAATTCTTCTGATTATATAGTACTGACGGAAATACAAAAATCAATTGATGATGTTAAAAGGTGTCAGGGTAATTATTTTAATGAATGGGAACAGTTGATGAGAGAATTGGAAGTTATGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35918","NCBI_taxonomy_name":"Enterococcus faecalis","NCBI_taxonomy_id":"1351"}}}},"ARO_accession":"3003746","ARO_id":"40402","ARO_name":"optrA","CARD_short_name":"optrA","ARO_description":"OptrA is a member of the ABC-F protein subfamily that confers resistance to oxazolidinones. The gene encoding the protein was originally isolated from a plasmid in Enterococcus faecalis and Enterococcus faecium.","ARO_category":{"45630":{"category_aro_accession":"3007068","category_aro_cvterm_id":"45630","category_aro_name":"Miscellaneous ABC-F subfamily ATP-binding cassette ribosomal protection proteins","category_aro_description":"ABC-F subfamily ATP-binding cassette ribosomal protection proteins of unknown, unclear or miscellaneous classification which nevertheless confer resistance to antibiotics through ribosomal protection and not through antibiotic efflux. These proteins should be further reviewed to elucidate associated genes, their function, origin and classification.","category_aro_class_name":"AMR Gene Family"},"35989":{"category_aro_accession":"0000072","category_aro_cvterm_id":"35989","category_aro_name":"linezolid","category_aro_description":"Linezolid is a synthetic antibiotic used for the treatment of serious infections caused by Gram-positive bacteria that are resistant to several other antibiotics. It inhibits protein synthesis by binding to domain V of the 23S rRNA of the 50S subunit of bacterial ribosomes.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36600":{"category_aro_accession":"3000461","category_aro_cvterm_id":"36600","category_aro_name":"florfenicol","category_aro_description":"Florfenicol is a fluorine derivative of chloramphenicol, where the nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3) and the hydroxyl group (-OH), by a fluorine group (-F). The action mechanism is the same as chloramphenicol's, where the antibiotic binds to the 23S RNA of the 50S subunit of bacterial ribosomes to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"40599":{"category_aro_accession":"3003897","category_aro_cvterm_id":"40599","category_aro_name":"tedizolid","category_aro_description":"Tedizolid is a synthetic oxazolidinone antibiotic that is administered to the patient as a prodrug that is activated in vivo. It acts as an inhibitor of protein synthesis by binding the 50S subunit of the ribosome and preventing formation of the 70S initiation complex. It is active against Gram-positive pathogens.","category_aro_class_name":"Antibiotic"},"36218":{"category_aro_accession":"3000079","category_aro_cvterm_id":"36218","category_aro_name":"oxazolidinone antibiotic","category_aro_description":"Oxazolidinones are a class of synthetic antibiotics discovered the the 1980's.  They inhibit protein synthesis by binding to domain V of the 23S rRNA of the 50S subunit of bacterial ribosomes.  Linezolid is the only member of this class currently in clinical use.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2268":{"model_id":"2268","model_name":"eatAv","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"3466":"T450I"},"Curated-R":{"3466":"T450I"},"clinical":{"3466":"T450I"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"3626":{"protein_sequence":{"accession":"AGQ48857.1","sequence":"MSKIEIKNLTFGYDSQGTLLFEQANLNFDTQWKLGLIGRNGRGKTTLLNILQNKLPYQGQVIHQQEFAYFPQQTKDKERLTYYVLNDITDFEIWEIERELQLMQTDPEILWREFSTLSGGEKTKVLLALLFVDDTHFPLIDEPTNHLDISGRKQVAAYLKKKKQGFIVVSHDRGFIDEVVDHVLAIEKSQLELYQGNFSIYEEQKKLRDEFEMAQNEKLKKEVSRLKKTAAEKAEWSRSREGDKTKKQVGFIDTESRRVNKGAVGADAARTMKRSKAIVNRMETQISEKEKLLKDIEYIDSLTMNSQASHHKRLLSVEDLQLGYENLLFEPIHFTIEPHQRVAISGPNGAGKSSIIHYLLGAFNGKVIGEKYQPKHLSISYASQNYEDNRGTLAEFAEKNQVDYQAFLNNLRKLGMERDVFHNKIEQMSMGQRKKVELAKSLSQPAELYIWDEPLNYLDVFNQEQLEQLILNVKPAMLLVEHDQTFLDKVSTEIISLERI"},"dna_sequence":{"accession":"KF010779.1","fmin":"0","fmax":"1503","strand":"+","sequence":"ATGTCTAAAATCGAAATAAAAAATCTGACATTCGGCTACGACAGCCAAGGCACATTATTATTTGAACAAGCAAATCTAAATTTTGACACACAATGGAAACTAGGACTTATCGGACGAAACGGTCGAGGAAAGACAACTTTACTGAATATTCTACAAAACAAACTACCTTATCAAGGGCAAGTAATCCATCAGCAAGAATTTGCCTATTTCCCGCAACAGACAAAAGATAAAGAACGTTTAACCTATTACGTGTTAAATGATATTACGGATTTTGAGATATGGGAAATCGAAAGAGAGCTCCAATTGATGCAAACAGATCCTGAAATCTTATGGAGAGAATTCAGCACACTATCGGGGGGAGAGAAGACAAAAGTCCTACTGGCACTTTTATTTGTGGATGACACTCATTTCCCGTTAATCGATGAACCAACGAATCATTTGGATATCTCTGGTAGAAAACAAGTAGCGGCTTATTTGAAAAAGAAAAAACAAGGCTTCATCGTGGTCAGCCATGACCGGGGATTTATCGATGAAGTAGTGGACCATGTTTTAGCAATCGAAAAAAGTCAACTGGAACTTTATCAAGGGAATTTCTCTATCTATGAAGAACAGAAAAAACTTCGTGATGAATTTGAAATGGCTCAAAATGAAAAATTGAAAAAAGAAGTCAGTAGGCTAAAGAAAACAGCAGCTGAAAAAGCCGAATGGTCTCGTTCCCGAGAAGGAGATAAAACAAAGAAACAAGTCGGATTCATCGATACTGAATCTAGACGAGTGAATAAAGGAGCAGTGGGTGCTGATGCTGCACGGACGATGAAACGATCCAAAGCAATCGTGAATCGGATGGAGACCCAGATCAGCGAGAAAGAAAAACTATTAAAAGATATCGAATATATCGATTCTTTGACGATGAATAGCCAAGCGTCTCACCATAAGCGACTTTTAAGCGTAGAAGATCTTCAATTAGGGTATGAAAATCTGTTATTCGAGCCAATTCATTTTACAATCGAGCCTCATCAGCGGGTGGCGATTTCAGGTCCTAACGGTGCAGGAAAGTCATCCATTATCCATTATCTTCTGGGGGCATTCAACGGCAAGGTTATAGGAGAAAAATACCAGCCAAAACATCTGAGCATTAGTTATGCAAGCCAAAATTATGAAGACAATCGAGGAACGTTGGCGGAATTTGCAGAGAAAAACCAAGTAGACTACCAAGCATTTTTGAACAACCTCCGAAAGCTTGGGATGGAAAGAGATGTTTTTCATAACAAGATCGAGCAGATGAGTATGGGCCAACGGAAAAAAGTGGAATTGGCTAAATCTTTATCACAGCCAGCTGAACTATATATATGGGATGAACCATTGAATTATTTGGATGTCTTCAATCAAGAACAATTAGAACAACTGATCTTGAACGTGAAACCTGCCATGTTACTAGTGGAACATGATCAAACCTTCCTGGATAAAGTATCTACTGAGATTATTTCTCTTGAGAGAATCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36779","NCBI_taxonomy_name":"Enterococcus faecium","NCBI_taxonomy_id":"1352"}}}},"ARO_accession":"3003761","ARO_id":"40408","ARO_name":"eatAv","CARD_short_name":"eatAv","ARO_description":"eatAv is a mutated form of the wildtype eatA ABC-F subfamily protein isolated from Enterococcus faecium conferring resistance to lincosamides, streptogramin A's and pleuromutilins (LSaP phenotype).","ARO_category":{"45630":{"category_aro_accession":"3007068","category_aro_cvterm_id":"45630","category_aro_name":"Miscellaneous ABC-F subfamily ATP-binding cassette ribosomal protection proteins","category_aro_description":"ABC-F subfamily ATP-binding cassette ribosomal protection proteins of unknown, unclear or miscellaneous classification which nevertheless confer resistance to antibiotics through ribosomal protection and not through antibiotic efflux. These proteins should be further reviewed to elucidate associated genes, their function, origin and classification.","category_aro_class_name":"AMR Gene Family"},"37716":{"category_aro_accession":"3001317","category_aro_cvterm_id":"37716","category_aro_name":"pleuromutilin","category_aro_description":"Pleuromutilin is a natural product antibiotic produced by Clitopilus passeckerianus. Related antibiotics of clinical significance, such as tiamulin and retapamulin, are semi-synthetic derivatives of this compound.","category_aro_class_name":"Antibiotic"},"37014":{"category_aro_accession":"3000670","category_aro_cvterm_id":"37014","category_aro_name":"pleuromutilin antibiotic","category_aro_description":"Pleuromutilins are natural fungal products that target bacterial protein translation by binding the the 23S rRNA, blocking the ribosome P site at the 50S subunit. They are mostly used for agriculture and veterinary purposes.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4182":{"model_id":"4182","model_name":"ADC-106","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6557":{"protein_sequence":{"accession":"WP_068981613.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPINQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPTDIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_051445.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAGCTAAAAAATACACCGATTAACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTCCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCTTATTTGGAAAAGTTGTTGCTTTGTCTATGAATAAACCTTTCGATCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATACGGCGTCAAATCCACCTTACCGGATATGTTGAGTTTTATTCATGCCAACCTTAACCCACAGAAATATCCGACAGATATTCAACGGGCAATTAATGAAACACATCAAGGTCGCTATCAAGTAAATACCATGTATCAAGCGCTTGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAGCCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACATATGTAGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006286","ARO_id":"44748","ARO_name":"ADC-106","CARD_short_name":"ADC-106","ARO_description":"ADC-106 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2285":{"model_id":"2285","model_name":"Staphylococcus aureus murA with mutation conferring resistance to fosfomycin","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"40394":{"param_type":"nonsense mutation","param_description":"A sequence change where, compared to a reference sequence, one codon is replaced by a termination codon through a nucleotide substitution. These are described as a substitution of the wildtype codon to a termination codon. Format is given as [wild type AA][position][Ter], for example Q42Ter where Q42 is a wildtype amino acid replaced by a premature termination codon.","param_type_id":"40394","param_value":{"3638":"L42Ter"}},"snp":{"Curated-R":{"3638":"T450I","3630":"V65L","3631":"G257D","3632":"D278E","3633":"E291D","3634":"Q362R","3635":"T396N"},"param_value":{"3630":"V65L","3631":"G257D","3632":"D278E","3633":"E291D","3634":"Q362R","3635":"T396N"},"clinical":{"3630":"V65L","3631":"G257D","3632":"D278E","3633":"E291D","3634":"Q362R","3635":"T396N"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"4633":{"protein_sequence":{"accession":"CAG41169.1","sequence":"MDKIVIKGGNKLTGEVKVEGAKNAVLPILTASLLASDKPSKLVNVPALSDVETINNVLTTLNADVTYKKDENAVVVDATKTLNEEAPYEYVSKMRASILVMGPLLARLGHAIVALPGGCAIGSRPIEQHIKGFEALGAEIHLENGNIYANAKDGLKGTSIHLDFPSVGATQNIIMAASLAKGKTLIENAAKEPEIVDLANYINEMGGRITGAGTDTITINGVESLHGVEHAIIPDRIEAGTLLIAGAITRGDIFVRGAIKEHMASLVYKLEEMGVELEYQEDGIRVRAEGDLQPVDIKTLPHPGFPTDMQSQMMALLLTANGHKVVTETVFENRFMHVAEFKRMNANINVEGRSAKLEGKSQLQGAQVKATDLRAAAALILAGLVADGKTSVTELTHLDRGYVDLHGKLKQLGADIERIND"},"dna_sequence":{"accession":"BX571856.1","fmin":"2257045","fmax":"2258311","strand":"-","sequence":"ATGGATAAAATAGTAATCAAAGGTGGAAATAAATTAACGGGTGAAGTTAAAGTAGAAGGTGCTAAAAATGCAGTATTACCTATATTAACAGCATCTTTATTAGCTTCTGATAAACCGAGCAAATTAGTTAATGTTCCAGCTTTAAGTGATGTAGAAACAATAAATAATGTATTAACAACCTTAAATGCTGACGTTACATACAAAAAGGACGAAAATGCTGTTGTCGTTGATGCAACAAAGACTCTAAATGAAGAGGCACCATATGAATATGTTAGTAAAATGCGTGCAAGTATTTTAGTTATGGGACCTCTTTTAGCAAGACTAGGACATGCTATTGTTGCATTGCCTGGTGGTTGTGCAATTGGAAGTAGACCGATTGAGCAACACATTAAAGGTTTTGAAGCTTTAGGCGCAGAAATTCATCTTGAAAATGGTAATATTTATGCTAATGCTAAAGATGGATTAAAAGGTACATCAATTCATTTAGATTTTCCAAGTGTAGGAGCAACACAAAATATTATTATGGCAGCATCATTAGCTAAGGGTAAGACTTTAATTGAAAATGCAGCTAAAGAACCTGAAATTGTTGATTTAGCAAACTACATTAATGAAATGGGCGGTAGAATTACTGGTGCTGGTACAGACACAATTACAATCAATGGTGTAGAATCATTACATGGTGTAGAACATGCTATCATTCCAGATAGAATTGAAGCAGGCACATTACTGATCGCTGGTGCCATTACTCGTGGCGATATTTTTGTACGTGGTGCAATCAAAGAACATATGGCTAGTTTAGTGTATAAATTAGAAGAAATGGGCGTTGAATTGGAATATCAAGAAGATGGTATTCGTGTACGTGCTGAAGGAGATTTACAGCCTGTTGACATCAAAACATTACCGCATCCTGGTTTTCCAACCGATATGCAGTCACAAATGATGGCATTATTATTAACAGCAAACGGACATAAAGTAGTAACTGAAACTGTATTTGAAAATCGTTTTATGCATGTCGCAGAGTTCAAACGTATGAATGCTAATATCAATGTAGAAGGTCGTAGTGCTAAACTTGAAGGTAAAAGTCAATTGCAAGGTGCACAAGTTAAAGCGACTGATTTAAGAGCAGCAGCAGCCTTAATTTTAGCTGGATTAGTTGCTGATGGTAAAACAAGCGTTACTGAATTAACGCACCTAGATAGAGGCTATGTTGACTTACACGGTAAATTGAAGCAATTAGGTGCAGACATTGAACGTATTAACGATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35517","NCBI_taxonomy_name":"Staphylococcus aureus subsp. aureus MRSA252","NCBI_taxonomy_id":"282458"}}}},"ARO_accession":"3003776","ARO_id":"40453","ARO_name":"Staphylococcus aureus murA with mutation conferring resistance to fosfomycin","CARD_short_name":"Saur_murA_FOF","ARO_description":"murA or UDP-N-acetylglucosamine enolpyruvyl transferase catalyses the initial step in peptidoglycan biosynthesis and is inhibited by fosfomycin. Overexpression of murA through mutations confers fosfomycin resistance.","ARO_category":{"39245":{"category_aro_accession":"3002811","category_aro_cvterm_id":"39245","category_aro_name":"antibiotic-resistant murA transferase","category_aro_description":"murA or UDP-N-acetylglucosamine enolpyruvyl transferase catalyses the initial step in peptidoglycan biosynthesis and is inhibited by fosfomycin. Overexpression of murA through mutations confers fosfomycin resistance.","category_aro_class_name":"AMR Gene Family"},"35944":{"category_aro_accession":"0000025","category_aro_cvterm_id":"35944","category_aro_name":"fosfomycin","category_aro_description":"Fosfomycin (also known as phosphomycin and phosphonomycin) is a broad-spectrum antibiotic produced by certain Streptomyces species. It is effective on gram positive and negative bacteria as it targets the cell wall, an essential feature shared by both bacteria. Its specific target is MurA (MurZ in E.coli), which attaches phosphoenolpyruvate (PEP) to UDP-N-acetylglucosamine, a step of commitment to cell wall synthesis. In the active site of MurA, the active cysteine molecule is alkylated which stops the catalytic reaction.","category_aro_class_name":"Antibiotic"},"45731":{"category_aro_accession":"3007149","category_aro_cvterm_id":"45731","category_aro_name":"phosphonic acid antibiotic","category_aro_description":"A group of antibiotics derived from phosphonic acids.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3314":{"model_id":"3314","model_name":"ADC-10","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"5246":{"protein_sequence":{"accession":"ABI18382.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLERYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVPAYGVKSTLPDMLSFIHANLNPQEYPADIQRAINETHQGFYQANTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVTLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"DQ883640.1","fmin":"0","fmax":"1167","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAGATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAGCTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTCCCAGATGAAGTACAAACAGATCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTGTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCCCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTTAACCCACAGGAATATCCGGCAGATATTCAACGGGCAATTAATGAAACACATCAAGGGTTCTATCAAGCAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACATATGTAGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCACGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3003855","ARO_id":"40554","ARO_name":"ADC-10","CARD_short_name":"ADC-10","ARO_description":"ADC-10 is a beta-lactamase found in Acinetobacter baumannii.","ARO_category":{"40543":{"category_aro_accession":"3003846","category_aro_cvterm_id":"40543","category_aro_name":"ADC beta-lactamase without carbapenemase activity","category_aro_description":"ADC beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases with extended-spectrum resistance to cephalosporins but not to carbapenems. ADC beta-lactamases are found in Acinetobacter sp. and Oligella urethralis.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3315":{"model_id":"3315","model_name":"ADC-30","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"5247":{"protein_sequence":{"accession":"AEL30572.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVKTDQQVLTFFKDWKPKNSIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTTGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"JF265068.1","fmin":"954","fmax":"2106","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAGTATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAATTTCCAGATGAAGTAAAAACAGATCAGCAAGTTTTAACATTTTTTAAAGACTGGAAACCTAAAAACTCAATCGGTGAATATCGACAATATTCAAACCCAAGCATTGGTTTATTTGGAAAAGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTAAATCCACAAAAATATCCAGCAGATATTCAACGGGCAATTAATGAAACACATCAGGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTACCGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3004617","ARO_id":"42587","ARO_name":"ADC-30","CARD_short_name":"ADC-30","ARO_description":"An ADC beta-lactamase and cephalosporinase from Acinetobacter baumannii.","ARO_category":{"40543":{"category_aro_accession":"3003846","category_aro_cvterm_id":"40543","category_aro_name":"ADC beta-lactamase without carbapenemase activity","category_aro_description":"ADC beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases with extended-spectrum resistance to cephalosporins but not to carbapenems. ADC beta-lactamases are found in Acinetobacter sp. and Oligella urethralis.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3316":{"model_id":"3316","model_name":"ADC-58","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"5249":{"protein_sequence":{"accession":"AFG25594.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVKTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANFNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPAPLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYVVLNAIKK"},"dna_sequence":{"accession":"JQ319653.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTTTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAGTATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAATTTCCAGATGAAGTAAAAACAGATCAGCAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCTTATTTGGAAAAGTTGTTGCTTTGTCTATGAATAAACCTTTCGATCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACTTCAACCCACAGAAATATCCGGCAGATATTCAACGGGCAATTAATGAAACACATCAAGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCACCTTTACAAACTTTATTAGACAGTAATTCAGAACAAATTGTGATGAAGCCTAATAAAGTGACTGCTATTTCAAAAGAGCCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACATATGTAGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGTTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3004618","ARO_id":"42588","ARO_name":"ADC-58","CARD_short_name":"ADC-58","ARO_description":"An ADC beta-lactamase and cephalosporinase from Acinetobacter baumannii.","ARO_category":{"40543":{"category_aro_accession":"3003846","category_aro_cvterm_id":"40543","category_aro_name":"ADC beta-lactamase without carbapenemase activity","category_aro_description":"ADC beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases with extended-spectrum resistance to cephalosporins but not to carbapenems. ADC beta-lactamases are found in Acinetobacter sp. and Oligella urethralis.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3310":{"model_id":"3310","model_name":"ADC-11","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"5241":{"protein_sequence":{"accession":"ADG46039.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNRSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWQPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGFYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLDAIKK"},"dna_sequence":{"accession":"GU591983.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATCGCAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGCAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTGGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCATTTGGTTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCTGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTTAACCCACAGAAATATCCGGCTGATATTCAACGGGCAATTAATGAAACACATCAAGGGTTCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCAACGGTTTCGGAACATATGTAGTGTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGGATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35535","NCBI_taxonomy_name":"Acinetobacter baumannii AYE","NCBI_taxonomy_id":"509173"}}}},"ARO_accession":"3004615","ARO_id":"42582","ARO_name":"ADC-11","CARD_short_name":"ADC-11","ARO_description":"ADC-11 is a class C beta-lactamase found in Acinetobacter baumannii.","ARO_category":{"40543":{"category_aro_accession":"3003846","category_aro_cvterm_id":"40543","category_aro_name":"ADC beta-lactamase without carbapenemase activity","category_aro_description":"ADC beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases with extended-spectrum resistance to cephalosporins but not to carbapenems. ADC beta-lactamases are found in Acinetobacter sp. and Oligella urethralis.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2298":{"model_id":"2298","model_name":"SPM-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"3564":{"protein_sequence":{"accession":"CAD37801.1","sequence":"MNSPKSRALLGFMGAFCLLLVAGAPLSAKSSDHVDLPYNLTATKIDSDVFVVTDRDFYSSNVLVAKMLDGTVVIVSSPFENLGTQTLMDWVAKTMKPKKVVAINTHFHLDGTGGNEIYKKMGAETWSSDLTKQLRLEENKKDRIKAAEFYKNEDLKRRILSSHPVPADNVFDLKQGKVFSFSNELVEVSFPGPAHSPDNVVVYFPKKKLLFGGCMIKPKELGYLGDANVKAWPDSARRLKKFDAKIVIPGHGEWGGPEMVNKTIKVAEKAVGEMRL"},"dna_sequence":{"accession":"AJ492820.1","fmin":"404","fmax":"1235","strand":"+","sequence":"ATGAACTCACCTAAATCGAGAGCCCTGCTTGGATTCATGGGCGCGTTTTGTTTGTTGCTCGTTGCGGGAGCGCCATTGTCTGCAAAAAGTTCGGATCATGTCGACTTGCCCTACAATCTAACGGCGACCAAGATTGATTCGGACGTTTTCGTCGTCACAGACCGCGATTTCTATTCTTCGAATGTCTTAGTAGCGAAAATGCTTGATGGGACCGTTGTCATTGTCTCTTCGCCGTTTGAAAATCTGGGTACGCAAACGCTTATGGATTGGGTGGCTAAGACTATGAAGCCGAAGAAAGTAGTAGCCATCAATACGCACTTTCATTTGGACGGCACGGGTGGAAATGAAATTTACAAGAAGATGGGCGCGGAGACGTGGTCGAGCGATCTGACAAAGCAGTTGCGACTTGAGGAAAACAAGAAAGACCGGATAAAAGCAGCTGAGTTCTATAAAAACGAGGATCTGAAGCGAAGGATTCTGAGTTCCCATCCTGTTCCAGCGGATAATGTTTTTGATTTGAAACAAGGCAAGGTCTTCTCGTTTTCTAATGAGCTGGTTGAGGTTTCATTTCCAGGACCGGCTCACTCGCCCGATAATGTCGTCGTATATTTTCCCAAGAAGAAACTGCTGTTTGGCGGCTGCATGATAAAGCCGAAGGAACTTGGTTATCTGGGAGATGCCAATGTGAAGGCATGGCCCGATTCAGCTCGGCGGCTAAAAAAGTTTGATGCGAAAATTGTTATACCTGGACACGGCGAATGGGGCGGACCGGAGATGGTTAACAAGACGATCAAGGTCGCGGAAAAGGCCGTTGGCGAAATGAGACTGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3003793","ARO_id":"40478","ARO_name":"SPM-1","CARD_short_name":"SPM-1","ARO_description":"Plasmid-mediated SPM metallo-beta-lactamase conferring resistance to carbapenem. Originally isolated from Pseudomonas aeruginosa. Responsible for carbapenem-resistant Pseudomonas aeruginosa (CRPA) outbreaks in Brazil.","ARO_category":{"36719":{"category_aro_accession":"3000580","category_aro_cvterm_id":"36719","category_aro_name":"SPM beta-lactamase","category_aro_description":"Sao Paulo metallo-beta-lactamase (SPM-1) confers resistance to carbapenem in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3313":{"model_id":"3313","model_name":"ACT-8","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"5245":{"protein_sequence":{"accession":"CBI75448.1","sequence":"MMMTKSLCCALLLSTSCSVLATPMSEKQLAEVVERTVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMSYEQAITTRVFKPLKLDHTWINVPKAEESHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVQDMANWVMVNMKPDSLQDSSLRKGITLAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVEGSDNKVALAPLPAREVNPPAPPVNASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILSAL"},"dna_sequence":{"accession":"FN645445.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGATGACTAAATCCCTTTGCTGCGCCCTGCTGCTCAGCACCTCCTGCTCGGTATTGGCTACCCCGATGTCAGAAAAACAGCTGGCTGAGGTGGTGGAACGTACCGTTACGCCGCTGATGAAAGCTCAGGCCATTCCGGGTATGGCGGTGGCGGTGATTTATCAGGGTCAGCCGCACTACTTTACCTTCGGTAAAGCCGATGTTGCGGCGAATAAACCTGTCACCCCACAAACCTTATTCGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTACTGGGCGGCGATGCCATTGCTCGGGGTGAAATATCGCTGGGCGATCCGGTGACCAAATACTGGCCTGAACTGACAGGCAAGCAGTGGCAGGGGATCCGCATGCTGGATCTGGCAACCTATACCGCAGGAGGTTTGCCGTTACAGGTACCGGATGAGGTCACGGATAACGCCTCTCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCGGGCACTACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGCGCGCTGGCGGTCAAACCTTCCGGCATGAGCTATGAGCAGGCCATAACGACGCGGGTCTTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTTCCCAAAGCGGAAGAGTCGCATTACGCCTGGGGATACCGCGACGGTAAAGCGGTACACGTTTCGCCAGGCATGCTGGACGCTGAAGCCTATGGCGTAAAAACCAACGTGCAGGATATGGCAAACTGGGTGATGGTCAACATGAAGCCGGACTCGCTTCAGGATAGTTCACTCAGGAAAGGCATTACCCTGGCGCAGTCTCGCTACTGGCGCGTAGGTGCCATGTATCAGGGTTTAGGCTGGGAAATGCTTAACTGGCCGGTCGATGCCAAAACCGTGGTTGAAGGTAGCGACAATAAGGTGGCGCTGGCACCGCTGCCTGCGAGAGAAGTGAATCCACCGGCGCCCCCGGTCAATGCGTCATGGGTCCATAAAACAGGCTCTACCGGCGGGTTTGGCAGCTACGTGGCGTTTATTCCCGAAAAGCAGCTCGGTATTGTGATGCTGGCAAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCGTATTTTGAGCGCGCTGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001831","ARO_id":"38231","ARO_name":"ACT-8","CARD_short_name":"ACT-8","ARO_description":"ACT-8 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3317":{"model_id":"3317","model_name":"ADC-59","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"5251":{"protein_sequence":{"accession":"AFG25595.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVKTDQQVLTFFKDWKPKNSIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKIIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTTGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYVVLNAIKK"},"dna_sequence":{"accession":"JQ319654.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTTTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAGTATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAATTTCCAGATGAAGTAAAAACAGATCAGCAAGTTTTAACATTTTTTAAAGACTGGAAACCTAAAAACTCAATCGGTGAATATCGACAATATTCAAACCCAAGCATTGGTTTATTTGGAAAAGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAATAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTAAATCCACAAAAATATCCAGCAGATATTCAACGGGCAATTAATGAAACACATCAGGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTACCGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGTTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3004619","ARO_id":"42591","ARO_name":"ADC-59","CARD_short_name":"ADC-59","ARO_description":"An ADC beta-lactamase and cephalosporinase from Acinetobacter baumannii.","ARO_category":{"40543":{"category_aro_accession":"3003846","category_aro_cvterm_id":"40543","category_aro_name":"ADC beta-lactamase without carbapenemase activity","category_aro_description":"ADC beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases with extended-spectrum resistance to cephalosporins but not to carbapenems. ADC beta-lactamases are found in Acinetobacter sp. and Oligella urethralis.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2286":{"model_id":"2286","model_name":"Borreliella burgdorferi murA with mutation conferring resistance to fosfomycin","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"3640":"D116C"},"Curated-R":{"3640":"D116C"},"experimental":{"3640":"D116C"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"5489":{"protein_sequence":{"accession":"AAC66824.2","sequence":"MHSYIVEGGYKIGGQITASGNKNAALPCILAALLTDEEVILENIPNINDVKVVLDILNDIGADIAREGNTLKIKVLNIVKTEIDSSFTDLIRASILLLGPFVSRFGKIDMALPGGDVIGKRRLDTHFYGLCKLGAKLSTKDRRIVLKANKLVGAEMFLDEASVTATENIIMAAVLAEGNTVIMNAACEPHVQDLCNMLNSMGANILGIGSNVLEIKGVKKLSGTVFRIGADFMQVGSLISLAALTGGELEIKKADPQHFRLIRHVYSRLGINFEYDRENVYVRNKQELKVKLDFGGHIPKIDDGPWPAFPTDLMSIIVVTATQVEGTVLVFEKMFESRMFFVDKLIKMGARIVLCDPHRVVVTGKSSLKGNVLSSPDVRAGMSLLIAAFVAEGRSEIQNVYQIERGYEDVVNKLINLGAKIKKVKSQ"},"dna_sequence":{"accession":"AE000783.1","fmin":"490643","fmax":"491927","strand":"+","sequence":"ATGCATAGTTATATTGTAGAAGGCGGCTATAAGATAGGTGGTCAAATTACAGCTAGTGGGAATAAGAACGCTGCTTTACCCTGTATTTTGGCTGCTTTACTTACCGATGAAGAGGTTATTTTAGAAAATATTCCTAATATTAATGATGTAAAAGTTGTTTTAGATATTTTAAATGACATAGGAGCAGATATTGCAAGAGAGGGAAATACTTTAAAAATAAAAGTTTTAAATATTGTGAAAACAGAAATAGATTCTTCTTTTACAGATTTAATTAGGGCTTCCATACTTTTATTAGGGCCTTTTGTTTCTAGGTTTGGAAAAATAGATATGGCGCTTCCAGGAGGAGATGTGATTGGAAAGAGGAGGCTTGATACTCATTTTTACGGGCTTTGCAAGCTGGGGGCCAAGTTAAGCACAAAAGATAGAAGGATTGTTTTAAAGGCTAACAAGCTTGTTGGCGCTGAAATGTTTTTAGATGAAGCTTCTGTTACAGCCACAGAAAATATCATTATGGCTGCAGTTCTTGCTGAAGGAAATACTGTTATTATGAACGCTGCTTGTGAGCCACATGTTCAAGATTTGTGTAATATGTTAAATTCAATGGGCGCTAATATTTTAGGAATTGGTTCAAATGTTTTAGAAATAAAAGGTGTAAAAAAATTAAGTGGGACCGTATTTAGAATAGGAGCCGATTTCATGCAAGTTGGTTCTTTAATTAGCCTTGCTGCATTAACAGGGGGTGAGTTGGAAATTAAAAAAGCAGATCCCCAACATTTCAGATTAATTAGGCATGTATATTCAAGACTTGGCATTAATTTTGAATATGACAGGGAAAATGTATATGTAAGAAATAAACAAGAATTAAAAGTTAAGTTAGATTTTGGTGGGCACATTCCAAAAATTGATGATGGCCCATGGCCAGCCTTTCCAACAGACCTTATGAGTATTATTGTAGTTACTGCAACGCAAGTAGAAGGCACAGTTTTAGTTTTTGAGAAGATGTTTGAATCTAGGATGTTTTTTGTAGATAAATTAATAAAAATGGGTGCTCGAATTGTGCTTTGTGATCCACACCGCGTAGTAGTTACGGGCAAATCTTCTCTTAAAGGCAATGTTTTGTCTTCTCCGGATGTACGAGCGGGAATGTCTCTTCTTATTGCTGCTTTTGTTGCTGAAGGTCGCAGCGAGATTCAAAATGTTTATCAAATTGAAAGAGGATACGAAGATGTAGTTAACAAATTGATTAATTTGGGTGCAAAAATCAAGAAAGTTAAAAGTCAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40455","NCBI_taxonomy_name":"Borreliella burgdorferi B31","NCBI_taxonomy_id":"224326"}}}},"ARO_accession":"3003777","ARO_id":"40454","ARO_name":"Borreliella burgdorferi murA with mutation conferring resistance to fosfomycin","CARD_short_name":"Bbur_mur_FOF","ARO_description":"murA or UDP-N-acetylglucosamine enolpyruvyl transferase catalyses the initial step in peptidoglycan biosynthesis and is inhibited by fosfomycin. Mutations to the murA enzyme confers resistance to the antibiotic.","ARO_category":{"39245":{"category_aro_accession":"3002811","category_aro_cvterm_id":"39245","category_aro_name":"antibiotic-resistant murA transferase","category_aro_description":"murA or UDP-N-acetylglucosamine enolpyruvyl transferase catalyses the initial step in peptidoglycan biosynthesis and is inhibited by fosfomycin. Overexpression of murA through mutations confers fosfomycin resistance.","category_aro_class_name":"AMR Gene Family"},"35944":{"category_aro_accession":"0000025","category_aro_cvterm_id":"35944","category_aro_name":"fosfomycin","category_aro_description":"Fosfomycin (also known as phosphomycin and phosphonomycin) is a broad-spectrum antibiotic produced by certain Streptomyces species. It is effective on gram positive and negative bacteria as it targets the cell wall, an essential feature shared by both bacteria. Its specific target is MurA (MurZ in E.coli), which attaches phosphoenolpyruvate (PEP) to UDP-N-acetylglucosamine, a step of commitment to cell wall synthesis. In the active site of MurA, the active cysteine molecule is alkylated which stops the catalytic reaction.","category_aro_class_name":"Antibiotic"},"45731":{"category_aro_accession":"3007149","category_aro_cvterm_id":"45731","category_aro_name":"phosphonic acid antibiotic","category_aro_description":"A group of antibiotics derived from phosphonic acids.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3321":{"model_id":"3321","model_name":"AAC(3)-IIe","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"565"}},"model_sequences":{"sequence":{"5340":{"protein_sequence":{"accession":"ABS70978.1","sequence":"MHTRKAITEAIRKFGVQTGDLLMVHASLKAIGPVEGGAETVVAALRSAVGPTGTVMGYASWDRSPYEETLNGARLDDKARRTWPPFDPATAGTYRGFGLLNQFLVQAPGARRSAHPDASMVAVGPLAETLTEPHELGHALGEGSPVERFVRLGGKALLLGAPLNSVTALHYAEAVADIPNKRWVTYEMPMLGRNGEVAWKTASEYDSNGILDCFAIEGKPDAVETIANAYVKLGRHREGVVGFAQCYLFDAQDIVTFGVTYLEKHFGATPIVPAQKAAQRSCEPSG"},"dna_sequence":{"accession":"EU022315.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCATACGCGGAAGGCAATAACGGAGGCAATTCGAAAATTCGGAGTCCAAACCGGTGACCTGTTGATGGTGCATGCCTCACTTAAAGCGATTGGTCCGGTCGAAGGAGGAGCGGAGACGGTCGTTGCCGCGTTACGCTCCGCGGTTGGGCCGACTGGCACTGTGATGGGATACGCGTCGTGGGACCGATCACCCTACGAGGAGACTCTGAATGGCGCTCGGTTGGATGACAAAGCCCGCCGTACCTGGCCGCCGTTCGATCCCGCAACGGCCGGGACTTACCGTGGGTTCGGCCTGCTGAATCAATTTCTGGTTCAAGCCCCCGGCGCGCGGCGCAGCGCGCACCCCGATGCATCGATGGTCGCGGTTGGTCCGCTAGCTGAAACGCTGACGGAGCCTCACGAACTCGGTCACGCCTTGGGGGAAGGGTCGCCCGTCGAGCGGTTCGTCCGCCTTGGCGGGAAGGCCCTGCTGTTGGGTGCGCCGCTAAACTCCGTTACCGCATTGCACTACGCCGAGGCGGTTGCGGATATCCCCAACAAACGATGGGTGACGTATGAGATGCCGATGCTTGGAAGAAACGGTGAAGTCGCCTGGAAAACGGCATCAGAATACGATTCAAACGGCATTCTCGATTGCTTTGCTATCGAAGGAAAGCCGGATGCGGTCGAAACTATAGCAAATGCTTACGTGAAGCTCGGTCGCCATCGAGAAGGTGTCGTGGGCTTTGCTCAGTGCTACCTGTTCGACGCGCAGGACATCGTGACGTTCGGCGTCACCTATCTTGAGAAGCACTTCGGAGCCACTCCGATCGTGCCAGCACAGAAAGCCGCCCAGCGCTCTTGCGAGCCTTCAGGTTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3004621","ARO_id":"42600","ARO_name":"AAC(3)-IIe","CARD_short_name":"AAC(3)-IIe","ARO_description":"AAC(3)-IIe is a plasmid-encoded aminoglycoside acetyltransferase in E. coli.","ARO_category":{"36461":{"category_aro_accession":"3000322","category_aro_cvterm_id":"36461","category_aro_name":"AAC(3)","category_aro_description":"A category of aminoglycoside N-acetyltransferase enzymes with modification regiospecificity based at the 3-amino group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics through acetylation of the 3-amino group of the compound.","category_aro_class_name":"AMR Gene Family"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"46127":{"category_aro_accession":"3007377","category_aro_cvterm_id":"46127","category_aro_name":"6'-N-ethylnetilmicin","category_aro_description":"6'-N-ethylnetilmicin is an aminoglycoside antibiotic and a derivative of netilmicin.","category_aro_class_name":"Antibiotic"},"46128":{"category_aro_accession":"3007378","category_aro_cvterm_id":"46128","category_aro_name":"2'-N-ethylnetilmicin","category_aro_description":"2'-N-ethylnetilmicin is an aminoglycoside antibiotic and a derivative of netilmicin.","category_aro_class_name":"Antibiotic"},"46133":{"category_aro_accession":"3007382","category_aro_cvterm_id":"46133","category_aro_name":"gentamicin","category_aro_description":"Gentamicin is a commonly used aminoglycoside antibiotic derived from members of the Micromonospora genus of bacteria. It acts by binding the 30S ribosomal subunit, thus inhibiting protein synthesis. Gentamicin is typically used to treat Gram-negative infections of the repiratory and urinary tract, as well as infections of the bone and soft tissue. It also exhibits considerable nephrotoxicity and ototoxicity. Gentamicin is administered as a mixture of gentamicin type C (which makes about around 80% of the complex) and types A, B, and X (distributed in the remaining 20% of the complex).","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2288":{"model_id":"2288","model_name":"Mycobacterium tuberculosis variant bovis ndh with mutation conferring resistance to isoniazid","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"},"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"3664":"R202W","3665":"L239P","3666":"V329A","3667":"D366G"},"Curated-R":{"3664":"R202W","3665":"L239P","3666":"V329A","3667":"D366G"},"experimental":{"3664":"R202W","3665":"L239P","3666":"V329A","3667":"D366G"}}},"model_sequences":{"sequence":{"8778":{"protein_sequence":{"accession":"NP_216370.1","sequence":"MSPQQEPTAQPPRRHRVVIIGSGFGGLNAAKKLKRADVDIKLIARTTHHLFQPLLYQVATGIISEGEIAPPTRVVLRKQRNVQVLLGNVTHIDLAGQCVVSELLGHTYQTPYDSLIVAAGAGQSYFGNDHFAEFAPGMKSIDDALELRGRILSAFEQAERSSDPERRAKLLTFTVVGAGPTGVEMAGQIAELAEHTLKGAFRHIDSTKARVILLDAAPAVLPPMGAKLGQRAAARLQKLGVEIQLGAMVTDVDRNGITVKDSDGTVRRIESACKVWSAGVSASRLGRDLAEQSRVELDRAGRVQVLPDLSIPGYPNVFVVGDMAAVEGVPGVAQGAIQGAKYVASTIKAELAGANPAEREPFQYFDKGSMATVSRFSAVAKIGPVEFSGFIAWLIWLVLHLAYLIGFKTKITTLLSWTVTFLSTRRGQLTITDQQAFARTRLEQLAELAAEAQGSAASAKVAS"},"dna_sequence":{"accession":"NC_000962.3","fmin":"2101650","fmax":"2103042","strand":"-","sequence":"ATGAGTCCCCAGCAAGAACCCACAGCGCAACCACCTCGTAGGCATCGAGTTGTGATCATCGGATCTGGGTTCGGCGGGCTAAACGCGGCAAAGAAGCTCAAGCGGGCCGACGTTGACATCAAGCTGATCGCGCGCACCACCCATCACCTGTTCCAGCCGCTGCTGTACCAAGTGGCCACCGGGATTATCTCCGAGGGAGAAATCGCTCCGCCGACCCGGGTCGTGCTGCGTAAGCAGCGCAATGTCCAGGTACTGTTGGGCAACGTCACCCACATCGACCTGGCCGGGCAGTGCGTCGTCTCGGAATTGCTCGGTCACACCTACCAAACCCCCTACGACAGCCTGATCGTCGCCGCGGGTGCTGGCCAGTCTTATTTCGGCAACGACCATTTCGCCGAATTCGCACCCGGCATGAAGTCCATCGACGACGCGTTGGAGTTGCGTGGCCGCATATTGAGCGCTTTCGAGCAAGCCGAACGGTCCAGCGATCCGGAACGGCGGGCCAAGCTACTGACATTCACCGTTGTCGGGGCTGGCCCCACCGGTGTTGAAATGGCCGGACAGATCGCCGAGCTGGCCGAGCACACGTTGAAGGGCGCATTCCGGCACATCGACTCGACCAAGGCGCGGGTGATTCTGCTTGACGCCGCCCCGGCGGTGCTGCCACCGATGGGCGCAAAGCTCGGTCAGCGGGCGGCTGCCCGGTTGCAGAAGCTGGGCGTGGAAATCCAGCTGGGTGCGATGGTCACCGACGTCGACCGCAACGGCATCACCGTCAAGGACTCCGACGGCACCGTCCGGCGCATCGAGTCGGCCTGCAAGGTCTGGTCGGCCGGGGTTTCGGCCAGTCGGTTGGGCAGGGACCTTGCCGAGCAATCACGGGTTGAGCTCGACCGGGCCGGCCGGGTCCAAGTGCTGCCCGACCTGTCCATTCCCGGGTACCCGAACGTGTTCGTGGTGGGCGATATGGCCGCTGTGGAGGGTGTGCCGGGTGTGGCGCAGGGCGCCATCCAGGGGGCGAAATACGTCGCCAGCACGATCAAGGCCGAACTGGCCGGCGCCAACCCGGCGGAGCGTGAGCCATTCCAGTACTTCGACAAGGGATCGATGGCCACGGTTTCGAGGTTTTCGGCGGTGGCCAAGATCGGTCCCGTTGAGTTCAGCGGCTTTATCGCCTGGCTGATTTGGCTGGTGCTGCACCTGGCGTACCTGATCGGGTTCAAGACCAAGATCACCACTCTGCTGTCGTGGACGGTGACTTTCCTCAGTACTCGCCGCGGCCAGCTGACCATCACCGACCAGCAGGCATTTGCGCGAACGCGGCTCGAACAGCTGGCCGAGCTGGCCGCCGAGGCGCAGGGCTCAGCGGCAAGCGCTAAGGTGGCCAGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3003779","ARO_id":"40461","ARO_name":"Mycobacterium tuberculosis variant bovis ndh with mutation conferring resistance to isoniazid","CARD_short_name":"Mbov_ndh_INH","ARO_description":"Mutations in the Mycobacterium tuberculosis variant bovis ndh gene that results in increased resistance to isoniazid.","ARO_category":{"40053":{"category_aro_accession":"3003460","category_aro_cvterm_id":"40053","category_aro_name":"antibiotic resistant ndh","category_aro_description":"ndh is a NADH oxidase. It participates in antibiotic resistance by diminishing NADH oxidation and consequently causes an increase in NADH concentration and depletion of NAD+. This alteration of the NADH\/NAD+ ratio prevents the peroxidation reactions required for the activation of INH, as well as the displacement of the NADH-isonicotinic acyl complex from InhA enzyme binding site.","category_aro_class_name":"AMR Gene Family"},"36659":{"category_aro_accession":"3000520","category_aro_cvterm_id":"36659","category_aro_name":"isoniazid","category_aro_description":"Isoniazid is an organic compound that is the first-line anti tuberculosis medication in prevention and treatment. As a prodrug, it is activated by mycobacterial catalase-peroxidases such as M. tuberculosis KatG. Isoniazid inhibits mycolic acid synthesis, which prevents cell wall synthesis in mycobacteria.","category_aro_class_name":"Antibiotic"},"45734":{"category_aro_accession":"3007152","category_aro_cvterm_id":"45734","category_aro_name":"isoniazid-like antibiotic","category_aro_description":"A group of antibiotics containing isoniazid and its derivatives.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2324":{"model_id":"2324","model_name":"gadW","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"470"}},"model_sequences":{"sequence":{"4620":{"protein_sequence":{"accession":"ANK04027.1","sequence":"MAHVCSVILVRRSFDIHHEQQKISLHNESILLLDKNLADDFAFCSLDTRRLDIEELTVCHYLQNIRQLPRNLGLHSKDRLLINQSPPIQLVTAIFDSFNDPRVNSPILSKMLYLSCLSMFSHKKELIPLLFNSISTVSGKVERLISFDIAKRWYLRDIAERMYTSESLIKKKLQDENTCFSKILLASRMSMARRLLELRQIPLHTIAEKCGYSSTSYFINTFRQYYGVTPHQFSQHSPGTFS"},"dna_sequence":{"accession":"CP015085.1","fmin":"2551711","fmax":"2552440","strand":"-","sequence":"ATGGCTCATGTCTGCTCGGTGATCCTCGTTCGTCGTTCATTCGATATTCATCATGAACAGCAAAAAATATCGTTGCATAACGAGAGTATCCTGCTGCTGGATAAAAATTTGGCAGACGATTTTGCGTTTTGTTCACTGGATACGCGACGGCTGGATATCGAAGAGCTGACAGTTTGCCATTACTTACAAAATATTCGTCAGTTGCCACGCAATTTAGGATTGCATAGCAAAGACCGTTTGTTAATTAACCAGTCACCCCCCATACAGCTGGTGACGGCGATTTTTGATAGTTTCAATGACCCCCGGGTCAATTCGCCGATACTGAGCAAAATGCTCTATCTTTCCTGTTTATCAATGTTTTCTCATAAGAAAGAACTGATCCCCTTACTTTTCAATAGTATCAGTACTGTTTCAGGAAAAGTTGAACGCCTTATTAGCTTTGATATCGCTAAACGTTGGTATCTACGCGATATCGCAGAAAGAATGTACACCAGCGAGAGTCTCATCAAAAAAAAGTTGCAGGATGAAAATACCTGTTTCAGTAAAATATTACTCGCCTCCAGGATGTCGATGGCCAGACGATTACTCGAGTTACGTCAAATACCTCTGCATACTATTGCGGAAAAATGTGGCTATAGCAGTACGTCATACTTTATAAATACATTTAGACAATATTATGGTGTAACGCCACATCAGTTTTCGCAACATTCGCCGGGTACCTTTTCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40530","NCBI_taxonomy_name":"Escherichia coli O25b:H4","NCBI_taxonomy_id":"941280"}}}},"ARO_accession":"3003838","ARO_id":"40529","ARO_name":"gadW","CARD_short_name":"gadW","ARO_description":"GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and, in situations where GadX is missing, activates gadA and gadBC.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35930":{"category_aro_accession":"0000011","category_aro_cvterm_id":"35930","category_aro_name":"cloxacillin","category_aro_description":"Cloxacillin is a semisynthetic, isoxazolyl penicillin derivative in the beta-lactam class of antibiotics. It interferes with peptidogylcan synthesis and is commonly used for treating penicillin-resistant Staphylococcus aureus infections.","category_aro_class_name":"Antibiotic"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2321":{"model_id":"2321","model_name":"cdeA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"810"}},"model_sequences":{"sequence":{"4621":{"protein_sequence":{"accession":"CAE00499.1","sequence":"MENLFTRKFTTFEFLKFVSPAIISMIFISLYTIIDGIFVSTLVGSDALASINIVLPIINLVCGFGIMMATGGGAIVSIRMGENRQDEANSTFSFIVLFSLIVGILFTVISYFFIKEISILLGATDKLLPYCITYGKVMILCTPFYILKFIFEYFARTDGNSKFSLFLSVIGGVTNIILDYVFIKYFGMGLLGAAVATAIGIILTCVLGIIYFLSNKSTLKLRKPKTDFRLIRDTMINGSSEMVTELSTGITTFLFNVVALKLAGENGLAALTIVLYAHFLMTSVYLGFAAGVSPLISYNFGAENSDKLKETFKHSLKFIFISSLLVFIIALVFAPFIVRVFVNPDNTVFKLALQGLKIFAFAFLFVGINIFASGFFTAFHNGKISAIISFSRAFVFIIIGIIILPPMLNMTGLWLTVPFAEVITIFISILFIKKYKGRYKY"},"dna_sequence":{"accession":"AJ574887.1","fmin":"370","fmax":"1696","strand":"-","sequence":"ATGGAAAATTTATTTACAAGAAAATTCACTACTTTTGAATTTCTAAAATTTGTTTCTCCTGCAATTATATCCATGATATTTATATCTTTGTACACAATAATAGATGGCATCTTTGTATCGACATTAGTTGGTTCTGATGCTCTTGCTAGTATAAATATTGTACTACCTATAATTAACCTTGTTTGTGGATTTGGAATAATGATGGCAACTGGTGGAGGTGCTATCGTTTCTATACGTATGGGTGAAAATAGACAGGATGAAGCCAACTCTACATTTTCTTTTATAGTTTTGTTTTCATTGATTGTTGGGATTTTATTCACAGTAATCTCATATTTCTTTATCAAAGAAATATCTATTTTGCTTGGTGCAACAGATAAGTTATTACCATATTGTATAACTTATGGTAAAGTTATGATTTTATGTACACCATTTTATATTTTAAAATTTATATTTGAGTACTTTGCAAGAACTGATGGAAATTCTAAATTTAGTTTATTTCTATCAGTCATTGGTGGTGTAACAAATATAATATTGGATTATGTATTTATTAAATATTTTGGAATGGGTCTTTTAGGAGCTGCAGTTGCAACTGCTATAGGTATTATTTTAACTTGTGTTTTAGGTATTATTTACTTCTTATCTAATAAATCTACACTAAAATTAAGAAAACCAAAAACCGATTTTAGACTTATAAGAGATACTATGATAAACGGTTCTTCTGAAATGGTTACAGAATTATCTACAGGAATTACAACATTCTTATTTAATGTAGTAGCTTTAAAATTAGCAGGAGAAAATGGACTTGCTGCTCTTACTATAGTATTGTATGCTCATTTTTTAATGACATCAGTCTATCTAGGATTCGCTGCTGGAGTGTCTCCATTAATAAGCTATAATTTTGGTGCTGAAAACAGTGATAAATTAAAAGAAACATTTAAACATTCTCTAAAATTTATATTTATTTCTTCTCTTTTAGTGTTTATTATTGCTTTAGTATTTGCACCATTTATTGTTAGGGTCTTTGTAAATCCAGATAACACAGTATTTAAACTAGCCTTACAAGGATTAAAAATATTTGCATTTGCTTTTTTGTTTGTTGGTATAAATATATTTGCATCAGGATTTTTTACAGCATTTCACAATGGAAAAATTTCAGCTATTATATCTTTTAGTCGTGCCTTTGTTTTTATAATCATAGGAATCATAATTCTTCCTCCTATGTTAAACATGACTGGATTATGGCTTACAGTTCCATTTGCTGAGGTTATAACCATATTTATATCTATTCTATTTATAAAAAAATATAAAGGTAGATATAAGTATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36807","NCBI_taxonomy_name":"Clostridioides difficile","NCBI_taxonomy_id":"1496"}}}},"ARO_accession":"3003835","ARO_id":"40526","ARO_name":"cdeA","CARD_short_name":"cdeA","ARO_description":"Clostridioides difficile and Escherichia coli multidrug efflux transporter with antiporter function. Confers resistance to fluoroquinolones in E. coli and acriflavin in Clostridioides difficile.","ARO_category":{"36251":{"category_aro_accession":"3000112","category_aro_cvterm_id":"36251","category_aro_name":"multidrug and toxic compound extrusion (MATE) transporter","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Multidrug and toxic compound extrusion (MATE) transporters utilize the cationic gradient across the membrane as an energy source. Although there is a diverse substrate specificity, almost all MATE transporters recognize fluoroquinolones. Arciflavine, ethidium and aminoglycosides are also good substrates.","category_aro_class_name":"AMR Gene Family"},"35963":{"category_aro_accession":"0000045","category_aro_cvterm_id":"35963","category_aro_name":"acriflavine","category_aro_description":"Acriflavine is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"43746":{"category_aro_accession":"3005386","category_aro_cvterm_id":"43746","category_aro_name":"disinfecting agents and antiseptics","category_aro_description":"Disinfectants that can also interact with antimicrobial resistance mechanisms, e.g. molecule efflux, and thus are the targets of disinfectant resistance.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"3481":{"model_id":"3481","model_name":"OXA-364","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"5675":{"protein_sequence":{"accession":"AFR53898.2","sequence":"MPLRLPLRALGAALSLFALAGAPASAAVLCTVVADAADGRIVFQQGTQAACAERYTPASTFKLPIALMGADAGILQGAHAPVWNYQPGYPDWGGDAWRQPTDPARWIKYSVVWYSQLTARALGQERFQRYASAFQYGNEDVSGEPGKHNGLDGAWINSSLRISPLEQLAFLRKLVNRQLPLKPAAYDLAETLFDAGEAGGWRLYGKTGTGSPGSNGVYTPDNAYGWFVGWARKDGRQLVFARLLQDEKATRPNAGLRARDELLREWPAMADAPRQ"},"dna_sequence":{"accession":"JX306689.2","fmin":"0","fmax":"828","strand":"+","sequence":"ATGCCCCTCCGACTCCCTCTGCGCGCCCTGGGCGCGGCCCTGTCCCTGTTCGCGCTGGCCGGCGCCCCCGCCAGCGCGGCGGTTTTGTGCACCGTGGTGGCCGACGCGGCCGACGGCCGCATCGTGTTCCAGCAAGGCACGCAGGCGGCCTGCGCCGAGCGCTACACGCCCGCCTCGACCTTCAAGCTGCCGATCGCGCTGATGGGCGCGGACGCGGGCATCCTGCAAGGCGCGCACGCGCCAGTCTGGAACTACCAGCCGGGCTACCCCGACTGGGGCGGCGACGCCTGGCGCCAGCCGACGGACCCGGCGCGCTGGATCAAGTATTCGGTGGTCTGGTACTCACAACTGACCGCCCGGGCGCTGGGGCAGGAGCGCTTCCAGCGCTACGCCTCGGCCTTCCAGTACGGCAACGAGGACGTCTCGGGCGAGCCCGGCAAGCACAACGGCCTGGACGGCGCGTGGATCAACTCGTCGCTGCGCATTTCGCCGCTGGAGCAACTGGCGTTCCTGCGCAAGCTGGTCAACCGCCAATTGCCGCTCAAGCCCGCGGCCTACGATCTGGCCGAGACGCTGTTCGACGCCGGCGAGGCCGGCGGCTGGCGCCTGTATGGCAAGACCGGCACCGGCTCGCCGGGCAGCAACGGCGTCTACACGCCGGACAACGCCTACGGCTGGTTCGTCGGCTGGGCGCGCAAGGACGGCCGCCAACTGGTGTTCGCGCGCCTGCTGCAGGACGAGAAAGCCACCCGGCCCAATGCCGGCCTGCGCGCCCGCGACGAGCTGTTGCGCGAGTGGCCGGCCATGGCCGACGCGCCCCGCCAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42832","NCBI_taxonomy_name":"Achromobacter dolens","NCBI_taxonomy_id":"1287738"}}}},"ARO_accession":"3001551","ARO_id":"37951","ARO_name":"OXA-364","CARD_short_name":"OXA-364","ARO_description":"OXA-364 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46505":{"category_aro_accession":"3007716","category_aro_cvterm_id":"46505","category_aro_name":"OXA-364-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-364.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2310":{"model_id":"2310","model_name":"Streptomyces cinnamoneus EF-Tu mutants conferring resistance to elfamycin","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"},"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"8300":"A379T"},"Curated-R":{"8300":"A379T"},"clinical":{"8300":"A379T"}}},"model_sequences":{"sequence":{"3578":{"protein_sequence":{"accession":"CAA67349.1","sequence":"MAKAKFERTKPHVNIGTIGHVDHGKTTLTAAITKVLHDAIPDLNPFTPFDEIDKAPEERQRGITISIAHVEYQTESRHYAHVDCPGHADYIKNMITGAAQMDGAILVVAATDGPMPQTKEHVLLARQSGVPYIVVALNKADMVDDEEIMELVELEVRELLSEYEFDGDNCPVVQVSALKALEGDKEWGEKLLGLMKAVDENIPQPERDVDKPFLMPIEDVFTITGRGTVVTGRIERGVLKVNETVDIIGIKTEKTTTTVTGIEMFRKLLDEGQAGENVGLLLRGIKREDVERGQCIIKPGTVTPHTEFEATAYILSKDEGGRHTPFFNNYRPQFYFRTTDVTGVVTLKEGTEMVMPGDNAEMTVNLIQPVAMEEGLRFTIREGGRTVGAGQVVKINK"},"dna_sequence":{"accession":"X98831.1","fmin":"361","fmax":"1555","strand":"+","sequence":"GTGGCGAAGGCGAAGTTCGAGCGGACTAAGCCGCACGTCAACATCGGCACCATCGGTCACGTCGACCACGGTAAGACGACTCTTACCGCGGCGATCACCAAGGTGCTGCACGACGCGATCCCGGACCTGAACCCCTTCACGCCGTTCGACGAGATCGACAAGGCGCCGGAAGAGCGTCAGCGCGGTATCACGATCTCGATCGCTCACGTTGAGTACCAGACCGAGTCGCGTCACTACGCCCACGTCGACTGCCCGGGTCACGCAGACTACATCAAGAACATGATCACCGGTGCCGCCCAGATGGACGGCGCGATCCTCGTGGTCGCCGCGACCGACGGTCCGATGCCGCAGACCAAGGAGCACGTGCTCCTGGCCCGCCAGTCCGGCGTTCCGTACATTGTGGTGGCCCTGAACAAGGCCGACATGGTGGACGACGAGGAGATCATGGAGCTCGTCGAGCTCGAGGTCCGTGAGCTCCTCTCCGAGTACGAGTTCGACGGCGACAACTGCCCCGTCGTCCAGGTCTCGGCTCTCAAGGCGCTCGAGGGCGACAAGGAGTGGGGCGAGAAGCTCCTCGGCCTCATGAAGGCCGTGGACGAGAACATCCCGCAGCCCGAGCGTGACGTCGACAAGCCGTTCCTGATGCCGATCGAGGACGTCTTCACGATCACCGGTCGTGGCACCGTCGTCACCGGTCGTATCGAGCGCGGTGTCCTCAAGGTCAACGAGACCGTCGACATCATCGGCATCAAGACCGAGAAGACCACCACCACGGTCACCGGTATCGAGATGTTCCGCAAGCTGCTCGACGAGGGCCAGGCCGGTGAGAACGTCGGTCTGCTCCTCCGTGGCATCAAGCGCGAGGACGTCGAGCGCGGCCAGTGCATCATCAAGCCCGGTACGGTCACGCCGCACACCGAGTTCGAGGCCACGGCGTACATCCTGTCGAAGGACGAGGGTGGCCGTCACACCCCGTTCTTCAACAACTACCGTCCGCAGTTCTACTTCCGTACGACTGACGTGACCGGTGTTGTGACCCTCAAGGAGGGCACGGAGATGGTCATGCCCGGCGACAACGCCGAGATGACCGTCAACCTGATCCAGCCTGTCGCGATGGAGGAGGGCCTGCGCTTCACCATCCGTGAGGGTGGCCGCACCGTCGGCGCCGGCCAGGTCGTCAAGATCAACAAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40498","NCBI_taxonomy_name":"Streptomyces cinnamoneus","NCBI_taxonomy_id":"53446"}}}},"ARO_accession":"3003359","ARO_id":"39943","ARO_name":"Streptomyces cinnamoneus EF-Tu mutants conferring resistance to elfamycin","CARD_short_name":"Scin_EFTu_ELF","ARO_description":"Sequence variants of Streptomyces cinnamoneus elongation factor Tu that confer resistance to elfamycin antibiotics.","ARO_category":{"37711":{"category_aro_accession":"3001312","category_aro_cvterm_id":"37711","category_aro_name":"elfamycin resistant EF-Tu","category_aro_description":"Sequence variants of elongation factor Tu that confer resistance to elfamycin antibiotics.","category_aro_class_name":"AMR Gene Family"},"37633":{"category_aro_accession":"3001234","category_aro_cvterm_id":"37633","category_aro_name":"kirromycin","category_aro_description":"Kirromycin, also known as mocimycin, is the representative molecule of its own class of elfamycins which is composed of more than 10 analogs. Kirromycin binds to the domain 1,2 interface of elongation factor Tu. This interaction maintains the EF-Tu*GTP conformation even after GTP is hydrolyzed to GDP. EF-Tu*GDP normally releases aa-tRNA and then exits the ribosome; however, kirromycin*EF-Tu*GDP*aa-tRNA forms a strong complex and remains bound to the ribosome, prohibits translocation of the peptide chain and translation is halted.","category_aro_class_name":"Antibiotic"},"37618":{"category_aro_accession":"3001219","category_aro_cvterm_id":"37618","category_aro_name":"elfamycin antibiotic","category_aro_description":"Elfamycins are molecules that inhibit bacterial elongation factor Tu (EF-Tu), a key protein which brings aminoacyl-tRNA (aa-tRNA) to the ribosome during protein synthesis. Elfamycins defined by their target (EF-Tu), rather than a conserved chemical backbone. Elfamycins follow two mechanisms to disrupt protein synthesis: 1. kirromycins and enacyloxin fix EF-Tu in the GTP bound conformation and lock EF-Tu onto the ribosome, and 2. pulvomycin and GE2270 cover the binding site of aa-tRNA disallowing EF-Tu from being charged with aa-tRNA. All elfamycins cause increased the affinity of EF-Tu for GTP.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2294":{"model_id":"2294","model_name":"Campylobacter jejuni gyrA conferring resistance to fluoroquinolones","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"3817":"T86I"},"Curated-R":{"3817":"T86I"},"clinical":{"3817":"T86I"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1200"}},"model_sequences":{"sequence":{"5216":{"protein_sequence":{"accession":"CAL35145.1","sequence":"MENIFSKDSDIELVDIENSIKSSYLDYSMSVIIGRALPDARDGLKPVHRRILYAMQNDEAKSRTDFVKSARIVGAVIGRYHPHGDTAVYDALVRMAQDFSMRYPSITGQGNFGSIDGDSAAAMRYTEAKMSKLSHELLKDIDKDTVDFVPNYDGSESEPDVLPSRVPNLLLNGSSGIAVGMATNIPPHSLNELIDGLLYLLDNKDASLEEIMQFIKGPDFPTGGIIYGKKGIIEAYRTGRGRVKVRAKTHIEKKTNKDVIVIDELPYQTNKARLIEQIAELVKERQIEGISEVRDESNKEGIRVVIELKREAMSEIVLNNLFKSTTMESTFGVIMLAIHNKEPKIFSLLELLNLFLTHRKTVIIRRTIFELQKARARAHILEGLKIALDNIDEVIALIKNSSDNNTARDSLVAKFGLSELQANAILDMKLGRLTGLEREKIENELAELMKEIARLEEILKSETLLENLIRDELKEIRSKFDVPRITQIEDDYDDIDIEDLIPNENMVVTITHRGYIKRVPSKQYEKQKRGGKGKLAVTTYDDDFIESFFTANTHDTLMFVTDRGQLYWLKVYKIPEGSRTAKGKAVVNLINLQAEEKIMAIIPTTDFDESKSLCFFTKNGIVKRTNLSEYQNIRSVGVRAINLDENDELVTAIIVQRDEDEIFATGGEENLENQEIENLDDENLENEESVSTQGKMLFAVTKKGMCIKFPLAKVREIGRVSRGVTAIKFKEKNDELVGAVVIENDEQEILSISAKGIGKRTNAGEYRLQSRGGKGVICMKLTEKTKDLISVVIVDETMDLMALTSSGKMIRVDMQSIRKAGRNTSGVIVVNVENDEVVSIAKCPKEENDEDELSDENFGLDLQ"},"dna_sequence":{"accession":"AL111168.1","fmin":"957630","fmax":"960222","strand":"-","sequence":"ATGGAGAATATTTTTAGCAAAGATTCTGATATTGAACTTGTAGATATAGAAAATTCTATAAAAAGTAGTTATTTAGACTATTCTATGAGTGTTATTATAGGTCGTGCTTTGCCTGACGCAAGAGATGGTTTAAAGCCTGTTCATAGAAGAATTTTATATGCTATGCAAAATGATGAGGCAAAAAGTAGAACAGATTTTGTCAAATCAGCCCGTATAGTGGGTGCTGTTATAGGTCGTTATCACCCACATGGAGATACAGCAGTTTATGATGCTTTGGTTAGAATGGCTCAAGATTTTTCTATGAGATATCCAAGTATTACAGGACAAGGCAACTTTGGATCTATAGATGGTGATAGTGCCGCTGCGATGCGTTATACTGAAGCAAAAATGAGTAAACTTTCTCATGAGCTTTTAAAAGATATAGATAAAGATACGGTCGATTTTGTTCCAAATTATGATGGTTCAGAAAGCGAACCTGATGTTTTACCTTCTAGGGTTCCAAATTTATTATTAAATGGTTCAAGTGGTATAGCTGTAGGTATGGCGACAAACATCCCACCTCATAGTTTAAATGAGTTGATAGATGGACTTTTATATTTGCTTGATAATAAAGATGCAAGCCTAGAAGAGATTATGCAGTTTATCAAAGGTCCAGATTTTCCAACAGGTGGAATAATTTATGGTAAAAAAGGTATTATAGAAGCTTATCGCACAGGGCGTGGTCGCGTGAAAGTGCGAGCTAAAACTCATATTGAAAAAAAGACAAATAAAGATGTTATTGTTATCGATGAGCTTCCTTATCAAACCAATAAAGCTAGGCTTATAGAGCAGATTGCAGAGCTTGTTAAAGAAAGGCAAATTGAAGGAATATCTGAAGTAAGAGATGAGAGCAATAAAGAAGGAATCCGCGTTGTTATAGAGCTTAAACGTGAGGCTATGAGTGAAATTGTTTTAAATAATCTATTTAAATCTACCACTATGGAAAGTACTTTTGGTGTGATTATGTTGGCAATTCATAATAAAGAACCTAAAATTTTCTCTTTGTTGGAACTTTTAAATCTTTTCTTAACTCATAGAAAAACAGTTATTATTAGAAGAACGATTTTTGAACTTCAAAAGGCAAGAGCAAGAGCTCATATTTTAGAAGGTCTTAAAATTGCACTTGATAATATAGATGAAGTGATTGCTTTAATTAAAAATAGTTCTGATAATAATACCGCAAGAGATTCTTTAGTAGCTAAATTTGGTCTTAGTGAGCTTCAAGCCAATGCTATTTTAGATATGAAACTTGGTCGTTTAACAGGACTTGAAAGAGAAAAAATCGAAAATGAACTTGCAGAATTAATGAAAGAAATTGCAAGACTTGAAGAAATTTTAAAAAGTGAAACCTTGCTTGAAAATTTAATTCGCGATGAATTAAAAGAAATTAGAAGTAAATTTGATGTGCCACGTATTACTCAAATTGAAGATGATTACGATGATATTGATATTGAAGATTTGATTCCTAATGAAAATATGGTTGTAACTATCACACATCGTGGTTATATTAAGCGTGTGCCTAGTAAACAATATGAAAAACAAAAACGAGGTGGAAAAGGAAAATTAGCCGTTACGACTTATGATGATGATTTTATAGAAAGTTTCTTTACGGCAAATACACATGATACGCTTATGTTTGTAACAGATCGTGGACAGCTTTATTGGCTTAAAGTTTATAAAATTCCTGAAGGCTCAAGAACGGCTAAAGGAAAAGCAGTGGTAAATCTTATCAATTTACAAGCTGAAGAAAAAATCATGGCTATTATTCCAACCACGGATTTTGATGAGAGCAAATCTTTATGTTTCTTTACTAAAAATGGTATTGTAAAGCGTACAAATTTGAGTGAATATCAAAATATCAGAAGTGTAGGAGTTAGAGCGATCAACTTGGATGAAAATGATGAGTTGGTAACTGCTATTATTGTTCAAAGAGATGAAGATGAAATTTTTGCCACTGGTGGTGAAGAAAATTTAGAAAATCAAGAAATTGAAAATTTAGATGATGAAAATCTTGAAAATGAAGAAAGTGTAAGCACACAAGGTAAAATGCTCTTTGCAGTAACCAAAAAAGGTATGTGTATCAAATTCCCACTTGCTAAAGTGCGTGAAATCGGCCGTGTAAGTCGTGGGGTGACGGCTATTAAGTTTAAAGAGAAAAATGACGAATTAGTAGGTGCAGTTGTTATAGAAAATGATGAGCAAGAAATTTTAAGCATAAGTGCAAAAGGTATAGGAAAACGCACCAATGCTGGAGAATATAGATTGCAAAGCAGAGGTGGTAAGGGTGTAATTTGTATGAAACTTACAGAAAAAACCAAAGATCTTATTAGCGTAGTTATAGTAGATGAAACTATGGATTTAATGGCTCTTACAAGTTCAGGTAAGATGATACGTGTTGATATGCAAAGCATTAGAAAAGCAGGGCGTAATACGAGTGGTGTCATTGTAGTTAATGTGGAAAATGACGAGGTGGTTAGCATCGCTAAGTGTCCTAAAGAGGAAAATGACGAGGATGAGTTAAGCGATGAAAACTTTGGTTTAGATTTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36956","NCBI_taxonomy_name":"Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819","NCBI_taxonomy_id":"192222"}}}},"ARO_accession":"3003789","ARO_id":"40474","ARO_name":"Campylobacter jejuni gyrA conferring resistance to fluoroquinolones","CARD_short_name":"Cjej_gyrA_FLO","ARO_description":"Campylobacter jejuni is a major bacterial infectious agent associated with gastroenteritis. Quinolone resistance is reportedly conferred by a single C-257-T nucleotide substitution in the gyrA gene.","ARO_category":{"39876":{"category_aro_accession":"3003292","category_aro_cvterm_id":"39876","category_aro_name":"fluoroquinolone resistant gyrA","category_aro_description":"DNA gyrase is responsible for DNA supercoiling and consists of two alpha and two beta subunits. GyrA point mutations confer resistance by preventing fluoroquinolone antibiotics from binding the alpha-subunit.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2313":{"model_id":"2313","model_name":"Enterococcus faecalis YvlB with mutation conferring daptomycin resistance","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"40494":{"param_type":"frameshift mutation","param_description":"A frameshift is a sequence change between the translation initiation (start) and termination (stop) codon where, compared to a reference sequence, translation shifts to another reading frame as caused by nucleotide insertions and deletions. In ARO, these are annotated at the protein level with the first changed most N-terminal wildtype amino acid position. Format is given as [wildtype AA][position]fs, e.g. S531fs where S531 is a frameshifted coordinate beginning with codon 531. Termination may also be denoted as: Ter[position]fs.","param_type_id":"40494","param_value":{"3956":"V289fs"}},"snp":{"Curated-R":{"3956":"T86I"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"5209":{"protein_sequence":{"accession":"AAO81526.1","sequence":"MKERERVLELVKKGILTSEEALILLENMATEKDEKQIEKAAEKVDTQNIGTTNKEDQVADLMNALEKGESEGPTVDSFEENTQDSAEKDRENLERILDELATKANRASAELDEVNAEIAGIKEEIKEVAEEIGTLDTKEELDALTEDEQVQRKDLHVLLAQLEEKLATQSTEKTALEEELKNIRKEQWKGQWNDTKEKVSSQFSEEWKDQATDTFNQVGGKVAEVGGQVGEFLKKTFNSFSDTMNDNVEWKDIKMKVPGVATTKFEHEFNYPNPQASLIDVKVANGTVVFKTWDQEDVKVEAKIKLYGKMAGDSPMEAFLERSDIDVDDETISFQVPNKRVKADLTFYLPKRTYDHVSVKLLNGNVLVEELTAKDVYTKSTNGTITFKKIDATMLEIEGVNGEIKVLEGTILDNIIETVNGDVSISAAPESLSVSLINGDIRITAKEKTLRRVEASSANGNIKLALPNDLGVEGQVKTNLGSINSRLTDIEVVREKKDRGNQQLHFRRVLEESMAQINASTTTGSIFLKDTDK"},"dna_sequence":{"accession":"AE016830.1","fmin":"1699211","fmax":"1700813","strand":"-","sequence":"ATGAAAGAAAGAGAACGCGTATTAGAATTAGTGAAAAAAGGTATTCTAACGTCAGAAGAAGCGTTAATTTTATTAGAAAATATGGCAACTGAAAAAGATGAAAAACAAATCGAAAAAGCTGCTGAAAAAGTTGATACACAAAATATTGGAACAACAAATAAAGAAGATCAAGTCGCAGATTTAATGAATGCATTAGAAAAAGGCGAATCAGAAGGACCTACTGTTGATTCGTTTGAAGAAAATACACAGGACAGTGCAGAAAAAGATCGTGAAAACTTAGAAAGAATTCTTGATGAGTTAGCAACAAAAGCCAATCGTGCTTCGGCTGAATTGGACGAAGTCAACGCAGAAATTGCCGGCATCAAAGAAGAAATTAAAGAAGTCGCAGAAGAAATTGGAACATTAGATACAAAAGAAGAATTAGATGCATTAACAGAAGATGAACAAGTTCAACGAAAAGACTTGCACGTTTTACTTGCACAATTAGAAGAAAAATTAGCGACTCAAAGTACTGAAAAAACAGCACTGGAAGAAGAACTAAAAAACATTCGCAAAGAACAATGGAAAGGTCAATGGAATGATACAAAAGAAAAAGTTTCTTCTCAATTCTCTGAAGAGTGGAAAGATCAAGCCACAGACACCTTTAACCAAGTCGGCGGCAAAGTTGCCGAAGTTGGTGGTCAAGTGGGAGAATTCTTGAAAAAAACATTTAATTCTTTCAGTGATACCATGAATGATAATGTGGAATGGAAAGACATTAAAATGAAAGTTCCTGGTGTGGCAACAACTAAGTTTGAACATGAGTTTAACTATCCAAATCCACAAGCAAGTTTAATTGATGTCAAGGTAGCAAATGGTACCGTGGTTTTCAAAACTTGGGATCAAGAAGATGTGAAAGTCGAAGCAAAAATCAAATTATATGGTAAAATGGCAGGAGATTCACCAATGGAAGCTTTCTTAGAACGAAGTGACATTGATGTGGATGATGAAACGATTTCTTTCCAAGTGCCAAACAAACGGGTGAAAGCAGATTTAACGTTCTATTTACCAAAACGCACTTACGATCATGTATCTGTTAAATTATTAAACGGAAATGTCTTAGTAGAAGAGTTAACAGCGAAAGATGTTTACACAAAATCAACGAATGGGACGATTACGTTTAAAAAAATTGATGCAACTATGTTAGAAATTGAAGGTGTGAATGGTGAAATTAAAGTCCTAGAAGGAACGATTTTAGATAACATTATTGAAACAGTCAATGGTGATGTGTCTATTTCCGCGGCACCAGAAAGTCTAAGTGTCTCTCTGATTAATGGAGATATCCGCATTACAGCTAAAGAAAAAACGCTTCGCCGTGTTGAAGCAAGCTCTGCAAATGGGAATATCAAATTGGCCTTGCCAAATGACTTAGGTGTTGAAGGGCAAGTGAAAACTAATTTAGGTAGTATTAACAGCCGTTTAACAGATATTGAAGTTGTTCGTGAAAAGAAAGATCGCGGCAATCAACAATTACATTTTAGACGTGTACTGGAAGAATCAATGGCTCAAATTAATGCTTCTACAACAACGGGAAGTATTTTCCTAAAAGATACGGATAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37592","NCBI_taxonomy_name":"Enterococcus faecalis V583","NCBI_taxonomy_id":"226185"}}}},"ARO_accession":"3003815","ARO_id":"40504","ARO_name":"Enterococcus faecalis YvlB with mutation conferring daptomycin resistance","CARD_short_name":"Efae_YvlB_DAP","ARO_description":"YvlB is a putative target of the liaFSR signalling pathway, whose mutations confer daptomycin resistance.","ARO_category":{"40505":{"category_aro_accession":"3003816","category_aro_cvterm_id":"40505","category_aro_name":"daptomycin resistant YvlB","category_aro_description":"Mutations to the putative liaFSR target YvlB confer daptomycin resistance.","category_aro_class_name":"AMR Gene Family"},"35985":{"category_aro_accession":"0000068","category_aro_cvterm_id":"35985","category_aro_name":"daptomycin","category_aro_description":"Daptomycin is a novel lipopeptide antibiotic used in the treatment of certain infections caused by Gram-positive organisms. Daptomycin interferes with the bacterial cell membrane, reducing membrane potential and inhibiting cell wall synthesis.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2312":{"model_id":"2312","model_name":"Enterococcus faecalis drmA with mutation conferring daptomycin resistance","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"40394":{"param_type":"nonsense mutation","param_description":"A sequence change where, compared to a reference sequence, one codon is replaced by a termination codon through a nucleotide substitution. These are described as a substitution of the wildtype codon to a termination codon. Format is given as [wild type AA][position][Ter], for example Q42Ter where Q42 is a wildtype amino acid replaced by a premature termination codon.","param_type_id":"40394","param_value":{"3953":"L4Ter"}},"snp":{"Curated-R":{"3953":"T86I","3954":"T86I"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"},"40494":{"param_type":"frameshift mutation","param_description":"A frameshift is a sequence change between the translation initiation (start) and termination (stop) codon where, compared to a reference sequence, translation shifts to another reading frame as caused by nucleotide insertions and deletions. In ARO, these are annotated at the protein level with the first changed most N-terminal wildtype amino acid position. Format is given as [wildtype AA][position]fs, e.g. S531fs where S531 is a frameshifted coordinate beginning with codon 531. Termination may also be denoted as: Ter[position]fs.","param_type_id":"40494","param_value":{"3954":"N150fs"}}},"model_sequences":{"sequence":{"5210":{"protein_sequence":{"accession":"AAO81566.1","sequence":"MQFLKKYGGYFLVLGVLLDFFTPYYVGFKDQGYNQLTEVISLLGDVNSPVRENFNRLTIIAGMLMLASLPRIYAIFSRKTKKGAWLVVAMIGAYGLFDCIFSGLFSVDTSSAGTVAAALHNGGSAVGYTGFLLLSGVLTIIYSKYGSQKNKNLFGFLFILCMLAAGLYGLARIPQLQQVKPFNYLGLWQRVSSFCNYLPMLALCLQTKTNDKFD"},"dna_sequence":{"accession":"AE016830.1","fmin":"1738704","fmax":"1739349","strand":"-","sequence":"ATGCAGTTTTTAAAAAAATATGGCGGCTATTTTTTAGTTTTAGGGGTCTTACTTGATTTTTTTACACCTTATTATGTCGGATTCAAAGATCAAGGTTACAATCAATTGACAGAAGTAATTAGCTTATTAGGTGATGTGAATAGTCCAGTTAGGGAAAACTTTAATCGGTTAACTATCATTGCGGGAATGTTGATGTTAGCAAGTTTACCTAGGATATATGCTATTTTTTCCAGAAAAACGAAAAAAGGTGCTTGGTTAGTAGTGGCAATGATTGGCGCTTATGGTTTATTTGATTGTATTTTCAGTGGGCTCTTCAGCGTAGACACTTCAAGCGCTGGCACAGTTGCTGCCGCGCTTCATAACGGAGGATCAGCAGTCGGTTATACAGGCTTTTTGTTGTTATCAGGCGTCTTAACCATTATCTACAGTAAATACGGTTCGCAAAAAAATAAAAACCTTTTTGGCTTTTTGTTTATTTTATGTATGCTTGCAGCCGGCTTATATGGCTTAGCAAGGATTCCACAGTTGCAACAGGTAAAACCATTTAATTATTTAGGCTTATGGCAAAGAGTGAGTTCATTTTGTAATTATCTACCAATGCTGGCACTGTGTTTACAAACTAAAACCAATGACAAATTTGATTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37592","NCBI_taxonomy_name":"Enterococcus faecalis V583","NCBI_taxonomy_id":"226185"}}}},"ARO_accession":"3003813","ARO_id":"40502","ARO_name":"Enterococcus faecalis drmA with mutation conferring daptomycin resistance","CARD_short_name":"Efae_drmA_DAP","ARO_description":"drmA is an uncharacterized 6-pass membrane protein, with mutations to the protein causing modest resistance to daptomycin.","ARO_category":{"40503":{"category_aro_accession":"3003814","category_aro_cvterm_id":"40503","category_aro_name":"daptomycin resistant drmA","category_aro_description":"Mutations to drmA confer daptomycin resistance.","category_aro_class_name":"AMR Gene Family"},"35985":{"category_aro_accession":"0000068","category_aro_cvterm_id":"35985","category_aro_name":"daptomycin","category_aro_description":"Daptomycin is a novel lipopeptide antibiotic used in the treatment of certain infections caused by Gram-positive organisms. Daptomycin interferes with the bacterial cell membrane, reducing membrane potential and inhibiting cell wall synthesis.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2302":{"model_id":"2302","model_name":"Enterococcus faecalis gdpD with mutation conferring daptomycin resistance","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"},"41342":{"param_type":"deletion mutation from peptide sequence","param_description":"A peptide sequence change between the translation initiation (start) and termination (stop) codon where, compared to a reference sequence, one or more amino acids are deleted and therefore are not present. These represent in-frame deletions which do not result in frameshift variants and may include multiple amino acids. Format is given by [wildtype AA][position]del for a single peptide deletion or [wildtype AA][position]_[wildtype AA][position]del for a deleted peptide range, e.g. K527del or Q517_N518del.","param_type_id":"41342","param_value":{"18558":"I170del"}},"snp":{"Curated-R":{"18558":"T86I"}}},"model_sequences":{"sequence":{"5218":{"protein_sequence":{"accession":"AAO81656.1","sequence":"MFSYFKNSIVNTLDFLKGTTAYFRDVLLMHGFMLFVLLPLLTSLSKLVLKEGGIDYISYDNLGAIATQHPYVLLTFLLIGLLILLALFFEFTFLLLSVYFIKKKQPITLTQLLHGTLLQIKKVRGITFLFFLAYFFLILPLSGLTFRSYLLTRVKIPAFILDFIFANRVIIIIGFVLLELIILYLAIRLAFALPELILRDVGFRESLKRSWQITKRRFFQILGQFIIIGGTVLGIFTAGYFLIFLGQTAVETFKPEWSLPSAVIAMTLLQVMMLLNLVLSSVAIFYIIVDDMEDEGILPDTPEWFTPKSEVRVEWTTFRVVLFCLIAIIFGIGVGTYNTNYLSHTPDRKPVTISHRGVNGNNGVQNTLDSLIETNKAKPDYVEMDIQETKDHQFIVMHDFNLRALTGVNKRPNQLTLKELTNMNVTENGQTAKMVSFDDYLAKANQLKQRLLIEIKTTPQDSPDLVQRFVKQYRENIFENGHILHTLTYDTAMALKKEEPRFYVGYVIPFNIVGPPKMPVDFFTMEYSTMNRNFVNAAHHDGKKVYAWTANDEDVMTRMIFYGVDGIITDQLSLLNETMKTDLENPTYSDKLLNFAIGMG"},"dna_sequence":{"accession":"AE016830.1","fmin":"1847768","fmax":"1849571","strand":"+","sequence":"ATGTTTAGTTATTTTAAAAATAGTATTGTGAATACGCTAGATTTTCTTAAAGGGACAACGGCGTATTTTCGCGATGTGCTCTTGATGCACGGATTTATGTTATTCGTTCTATTGCCTTTATTGACAAGTTTGTCCAAATTGGTACTCAAAGAAGGTGGGATTGATTATATTTCCTACGATAACTTAGGGGCAATTGCTACGCAACATCCCTATGTCCTTTTGACTTTTCTACTAATTGGGCTGTTAATTTTACTGGCGCTCTTTTTTGAATTTACCTTTTTATTGCTTAGTGTCTATTTTATTAAGAAAAAGCAACCAATTACTCTAACGCAATTATTGCACGGCACCTTGCTTCAGATCAAAAAAGTTCGAGGAATTACCTTTCTGTTTTTCCTGGCATATTTCTTTTTGATTTTACCATTAAGTGGGTTAACCTTCCGCTCTTATTTATTAACAAGAGTTAAGATTCCAGCCTTTATCTTAGATTTTATTTTTGCAAATCGCGTCATTATTATTATTGGTTTCGTATTGTTAGAACTGATTATCTTATATTTAGCGATTCGACTTGCTTTTGCCCTTCCAGAGTTGATTTTACGTGATGTTGGTTTTCGTGAGTCTTTAAAACGTAGTTGGCAAATTACAAAGCGGCGCTTTTTCCAGATTTTAGGGCAATTTATTATCATTGGAGGAACTGTTTTAGGGATTTTTACGGCTGGCTATTTCTTGATATTTTTAGGTCAAACCGCAGTCGAAACGTTTAAACCTGAGTGGTCTTTACCTAGCGCTGTCATCGCTATGACACTCCTTCAGGTTATGATGCTCTTAAACTTGGTGTTGTCTAGTGTTGCTATTTTTTACATTATTGTTGATGATATGGAAGATGAAGGGATTTTGCCTGACACGCCAGAATGGTTCACCCCGAAATCAGAGGTTCGGGTAGAATGGACCACCTTCAGAGTCGTTCTTTTTTGTTTGATTGCAATCATCTTCGGAATTGGTGTAGGCACCTATAATACGAATTACCTAAGTCATACACCTGACCGAAAACCGGTTACCATCTCCCATCGTGGTGTTAATGGTAACAATGGCGTTCAAAACACCTTGGACTCTTTAATCGAGACCAATAAGGCAAAACCTGATTATGTTGAAATGGATATTCAAGAAACCAAAGACCATCAATTTATTGTCATGCACGATTTTAATTTACGGGCGTTAACGGGCGTTAATAAACGACCGAATCAATTAACACTTAAAGAATTAACGAATATGAATGTCACAGAAAATGGTCAAACTGCTAAAATGGTTTCTTTCGATGATTATTTAGCCAAAGCCAATCAATTAAAACAACGTTTATTAATTGAAATCAAAACCACGCCTCAAGATAGCCCTGATTTAGTACAGCGCTTTGTCAAACAATACCGTGAAAATATTTTTGAAAACGGCCATATCCTTCATACCTTAACCTATGATACGGCGATGGCCTTAAAGAAAGAAGAACCACGCTTTTATGTAGGCTACGTTATTCCTTTCAACATTGTGGGACCGCCTAAAATGCCAGTTGACTTTTTTACTATGGAATACAGTACAATGAATCGTAACTTTGTAAATGCCGCTCATCATGATGGGAAAAAGGTTTATGCTTGGACAGCAAATGATGAAGATGTTATGACACGAATGATTTTTTATGGCGTCGATGGCATCATTACCGATCAGCTCAGTCTACTGAACGAAACAATGAAAACCGATTTAGAAAACCCAACATACTCCGATAAACTGTTGAATTTCGCTATTGGAATGGGTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37592","NCBI_taxonomy_name":"Enterococcus faecalis V583","NCBI_taxonomy_id":"226185"}}}},"ARO_accession":"3003800","ARO_id":"40485","ARO_name":"Enterococcus faecalis gdpD with mutation conferring daptomycin resistance","CARD_short_name":"Efae_gdpD_DAP","ARO_description":"gdpD is a glycerolphosphodiesterase whose mutations confer resistance to daptomycin.","ARO_category":{"40487":{"category_aro_accession":"3003802","category_aro_cvterm_id":"40487","category_aro_name":"daptomycin resistant gdpD","category_aro_description":"Mutations to the gdpD glycerolphosphodiesterase confer resistance to daptomycin.","category_aro_class_name":"AMR Gene Family"},"35985":{"category_aro_accession":"0000068","category_aro_cvterm_id":"35985","category_aro_name":"daptomycin","category_aro_description":"Daptomycin is a novel lipopeptide antibiotic used in the treatment of certain infections caused by Gram-positive organisms. Daptomycin interferes with the bacterial cell membrane, reducing membrane potential and inhibiting cell wall synthesis.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2314":{"model_id":"2314","model_name":"Acinetobacter baumannii gyrA conferring resistance to fluoroquinolones","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1500"},"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"9881":"G79C","9882":"S81L"},"Curated-R":{"9881":"G79C","9882":"S81L"},"clinical":{"9881":"G79C","9882":"S81L"}}},"model_sequences":{"sequence":{"4623":{"protein_sequence":{"accession":"AJF82744.1","sequence":"MSVSEIRPIAIEDELKHSYLDYAMSVIVSRALPDVRDGLKPVHRRVLYAMHELGNDYNKAYKKSARVVGDVIGKYHPHGDSAVYETIVRMAQDFSLRYLLVDGQGNFGSIDGDSAAAMRYTEVRMTKLAHELLADLEKDTVDWEDNYDGSERIPEVLPTRVPNLLINGAAGIAVGMATNMAPHNMTEVVNACLAYADNPNISIEGLMEYITGPDFPTGGIIYGKSGIVDAYRTGKGRLHIRGKYHFEEDEKTGRTTIVFTEIPYQVNKARVIERIAELVKEKKLEGISELRDESDKEGMRIAIDLKRGENAEVVVNNLFLNTQLENSFSINMVCLDNGQPKLMNLKDIIAAFIRHRQEVVTRRTMFELRKARERGHILEGLTVALANIDEIIETIKTSANPAEARERLLAGEWAGGGVVALLEKAGAISVRPDEIEGEDPNRPFGLSDSIYRLSPTQVGAILELRLHRLTGLEQDKLHAEYTEILGQIAELTAILNDFNLLMGVIREELAQVLQQYGDARRTEIVESRVDFCREDLIPEEQVVLTVSQTGYAKTQPLSDYQAQRRGGRGKSATSMKDDDFIQHLIVASNHATVLCFTNVGKVYRLKVFEVPQASRGAKGRPIVNLLPLDATETVTAILPLTEFPENHYVFMATASGTVKRVELEQFANIRSNGLRAIELNEEDTLIGVAITDGNQQIMLFSNEGKAIRFAETDVRAMGRTAKGVRGMRVSFASSTLSEEDADVENDDSDDNDDSTDSSLVSRIVSLVVVPETGEVLCASANGYGKRTPVNDFPTKKRGGKGVIAIKTSERNGELVGAVSIDETKELLLISDGGTLVRTRAAEVAMTGRNAQGVRLIRLSEEETLVGVVSIEAVEDEEELLEGEVDTTETDSEEAVSNNEDTSEE"},"dna_sequence":{"accession":"CP010781.1","fmin":"2990040","fmax":"2992755","strand":"-","sequence":"ATGAGCGTATCGGAAATCCGACCGATTGCCATTGAGGACGAACTCAAGCATTCATATTTAGATTACGCGATGAGTGTAATTGTATCTCGTGCATTGCCGGATGTGAGAGACGGTCTTAAACCTGTTCACCGTCGTGTGCTTTATGCCATGCACGAATTGGGCAATGACTATAACAAAGCCTACAAGAAATCTGCTCGTGTCGTTGGGGACGTAATCGGTAAATATCACCCGCATGGTGACTCAGCTGTTTATGAAACCATTGTTCGTATGGCTCAAGACTTTAGCTTACGTTATTTATTGGTTGATGGTCAGGGTAACTTCGGTTCGATCGATGGTGATAGCGCTGCGGCAATGCGTTATACCGAAGTCCGTATGACTAAGCTGGCACATGAGCTTCTTGCAGATTTAGAAAAAGACACAGTTGACTGGGAAGATAACTACGACGGTTCGGAACGTATCCCTGAAGTACTTCCGACACGTGTTCCAAACTTATTAATTAACGGTGCTGCTGGTATTGCTGTAGGTATGGCAACTAACATGGCACCACACAACATGACAGAAGTTGTGAATGCTTGTTTGGCTTATGCTGACAATCCGAATATCTCGATTGAAGGATTGATGGAATACATTACTGGTCCTGACTTCCCTACAGGCGGTATTATTTACGGTAAATCAGGTATTGTTGATGCCTACCGTACCGGTAAAGGTCGTTTACACATTCGTGGTAAATACCATTTCGAAGAAGATGAAAAGACAGGTCGTACAACCATCGTCTTTACTGAAATTCCATATCAAGTAAACAAAGCAAGAGTTATTGAACGTATTGCCGAGTTAGTAAAAGAGAAAAAGCTTGAAGGTATTTCAGAACTTCGTGATGAGTCTGATAAAGAAGGTATGCGTATTGCAATTGACTTGAAACGCGGTGAAAACGCAGAAGTCGTTGTAAATAACTTATTCTTAAATACCCAGCTTGAAAACTCATTCAGCATCAACATGGTTTGTCTAGACAATGGACAACCAAAATTGATGAATCTAAAAGATATTATTGCGGCATTTATTCGTCACCGCCAAGAAGTTGTGACACGCCGTACCATGTTCGAATTACGTAAAGCACGTGAACGTGGTCATATCTTGGAAGGCTTGACAGTTGCCTTAGCCAATATTGATGAAATTATTGAAACCATCAAAACTTCTGCAAACCCTGCTGAAGCGCGTGAGCGTTTACTTGCGGGTGAGTGGGCAGGTGGTGGCGTTGTTGCACTACTTGAAAAAGCTGGTGCAATTTCTGTTCGCCCAGATGAAATTGAAGGTGAAGATCCAAATCGTCCATTTGGTTTAAGTGATTCAATTTATCGTCTGTCACCAACACAAGTAGGCGCAATTTTAGAATTACGTTTACACCGTTTAACTGGTCTTGAACAAGACAAGTTACATGCGGAATATACTGAAATTTTAGGTCAAATTGCTGAACTTACTGCAATTTTAAATGACTTTAACTTGTTAATGGGTGTTATTCGCGAAGAGTTGGCACAAGTTTTACAACAATATGGCGATGCACGTCGTACCGAAATTGTTGAATCTCGTGTGGATTTCTGCCGTGAAGATTTAATTCCTGAAGAGCAAGTGGTATTAACGGTTTCGCAAACGGGTTATGCAAAAACTCAACCTCTTTCAGACTATCAGGCACAGCGCCGTGGTGGACGTGGTAAGTCTGCAACCTCAATGAAAGATGATGACTTTATTCAACATCTGATTGTGGCATCGAACCATGCGACCGTACTTTGCTTTACCAATGTGGGTAAAGTGTACCGTCTGAAAGTATTTGAAGTTCCTCAAGCATCACGTGGGGCAAAAGGCCGTCCAATCGTGAACTTGTTACCTCTAGATGCAACAGAAACCGTAACCGCAATCTTGCCGTTAACCGAGTTCCCGGAAAACCACTATGTGTTTATGGCGACAGCTTCTGGTACGGTTAAGCGTGTTGAGTTAGAGCAATTTGCAAACATTCGTTCAAATGGTCTACGTGCTATTGAACTTAATGAAGAAGATACTTTAATTGGTGTTGCGATTACTGATGGTAATCAGCAAATCATGTTGTTCTCTAACGAAGGTAAGGCAATTCGTTTTGCTGAAACTGACGTACGTGCAATGGGTCGTACAGCGAAAGGTGTACGCGGTATGCGCGTGAGTTTTGCAAGCAGCACCTTAAGTGAAGAAGATGCAGATGTTGAAAATGATGATTCAGATGATAATGATGATTCAACAGATTCAAGTCTAGTAAGTCGCATCGTATCGCTTGTTGTTGTACCTGAGACAGGCGAAGTACTGTGTGCGAGTGCCAACGGTTATGGTAAACGTACTCCAGTAAATGACTTCCCGACCAAGAAACGTGGTGGTAAGGGTGTTATTGCGATCAAGACAAGTGAACGTAACGGTGAGCTAGTTGGTGCAGTTTCTATTGATGAAACCAAAGAGTTATTATTAATTTCTGATGGTGGTACGCTTGTTCGTACGCGTGCTGCAGAAGTTGCAATGACAGGCCGTAATGCTCAAGGTGTTCGTCTGATCCGTTTAAGCGAAGAAGAAACGCTCGTTGGCGTAGTTTCAATTGAAGCTGTAGAAGACGAAGAAGAACTTCTTGAAGGTGAAGTAGATACGACTGAAACTGATAGCGAAGAAGCTGTATCTAATAATGAAGATACTTCTGAAGAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3003817","ARO_id":"40507","ARO_name":"Acinetobacter baumannii gyrA conferring resistance to fluoroquinolones","CARD_short_name":"Abau_gyrA_FLO","ARO_description":"Mutations in the A subunit of DNA gyrase reduce its affinity for fluoroquinolones, thereby conferring resistance.","ARO_category":{"39876":{"category_aro_accession":"3003292","category_aro_cvterm_id":"39876","category_aro_name":"fluoroquinolone resistant gyrA","category_aro_description":"DNA gyrase is responsible for DNA supercoiling and consists of two alpha and two beta subunits. GyrA point mutations confer resistance by preventing fluoroquinolone antibiotics from binding the alpha-subunit.","category_aro_class_name":"AMR Gene Family"},"35942":{"category_aro_accession":"0000023","category_aro_cvterm_id":"35942","category_aro_name":"enoxacin","category_aro_description":"Enoxacin belongs to a group called fluoroquinolones. Its mode of action depends upon blocking bacterial DNA replication by binding itself to DNA gyrase and causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37004":{"category_aro_accession":"3000660","category_aro_cvterm_id":"37004","category_aro_name":"lomefloxacin","category_aro_description":"Lomefloxacin is a difluoropiperazinyl quinolone, sharing similar activities with other fluoroquinolones. It is used to treat urinary tract infections. Relative to other fluoroquinolones, it has a longer half life and has higher serum concentrations.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37007":{"category_aro_accession":"3000663","category_aro_cvterm_id":"37007","category_aro_name":"ofloxacin","category_aro_description":"Ofloxacin is a 6-fluoro, 7-piperazinyl quinolone with a methyl-substituted oxazine ring. It has a broad spectrum of activity including many enterobacteria and mycoplasma but most anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"37008":{"category_aro_accession":"3000664","category_aro_cvterm_id":"37008","category_aro_name":"trovafloxacin","category_aro_description":"Trovafloxacin is a trifluoroquinalone with a broad spectrum of activity that acts by inhibiting the uncoiling of supercoiled DNA. While potent against many Gram-positive and Gram-negative bacteria, it is less active against pseudomonads and Cl. difficile. It is usually taken as the prodrug trovafloxacin mesylate or alatrofloxacin mesylate for oral or intravenous administration, respectively.","category_aro_class_name":"Antibiotic"},"37009":{"category_aro_accession":"3000665","category_aro_cvterm_id":"37009","category_aro_name":"grepafloxacin","category_aro_description":"Grepafloxacin is a broad-spectrum antibacterial quinoline. It is no longer taken due to its high toxicity.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"37142":{"category_aro_accession":"3000762","category_aro_cvterm_id":"37142","category_aro_name":"pefloxacin","category_aro_description":"Pefloxacin is structurally and functionally similar to norfloxacin. It is poorly active against mycobacteria, while anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2305":{"model_id":"2305","model_name":"Enterococcus faecalis gshF with mutation conferring daptomycin resistance","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"3891":"E554K"},"Curated-R":{"3891":"E554K"},"experimental":{"3891":"E554K"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1500"}},"model_sequences":{"sequence":{"5214":{"protein_sequence":{"accession":"AMR95642.1","sequence":"MNYRELMQKKNVRPYVLMARFGLEKENQRSTREGLLATTDHPTVFGNRSYHPYIQTDFSETQLELITPVANSGTEMLRFLDAIHDVARRSIPEDEMLWPLSMPPQLPTKDEEIKIAKLDQYDAVLYRRYLAKEYGKRKQMVSGIHFNFEYDQALIQQLYDEQSEVTDCKQFKTKVYMKVARNFLRYRWLITYLFGASPVSEDGYFRVYDDQPQEPIRSIRNSTYGYRNHDNVKVSYASLERYLEDIHRMVENGLLSEEKEFYAPVRLRGGKQMSDLPKTGIRYIELRNLDLNPFSRLGIVEDTVDFLHYFMLYLLWTDEKEEADEWVKTGDILNEQVALGHPHETIKLIAEGDRIFSEMIDMLDALGIRKGKEVVGKYYQQLRNPQDTVSGKMWTIIQENSNSELGNIFGNQYQSMAFERPYQLAGFREMELSTQIFLFDAIQKGLEIEILDEQEQFLKLQHGEHIEYVKNANMTSKDNYVVPLIMENKTVTKKILSAAGFHVPGGEEFSSFIEAQEAHLRYANKAFVVKPKSTNYGLGITIFKEGASLEDFTEALRIAFKEDTAVLIEEFLPGTEYRFFVLDNDVKAIMLRVPANVTGDGKHTVEELVAAKNSDPLRGTNHRAPLELIQLNDLEKLMLKEQGLTIYSVPEKEQIVYLRENSNVSTGGDSIDMTDVIDDSYKQIAIEAVAALGAKICGIDLIIPDKDVKGTRDSLTYGIIEANFNPAMHMHVYPYAGQGRRLTMDVLKLLYPEVVQ"},"dna_sequence":{"accession":"CP014949.1","fmin":"1661364","fmax":"1663635","strand":"-","sequence":"ATGAATTATAGAGAATTAATGCAAAAGAAAAATGTTCGTCCTTACGTATTGATGGCTCGTTTTGGTTTAGAAAAAGAAAACCAACGTAGTACACGAGAAGGGCTTTTAGCGACAACTGATCATCCCACGGTTTTTGGTAACCGTTCTTATCATCCATATATTCAAACAGATTTTAGTGAAACACAATTAGAACTAATCACGCCTGTAGCAAATAGCGGCACAGAAATGCTTCGTTTTTTAGATGCCATTCACGATGTGGCTCGTCGTTCGATTCCAGAAGATGAAATGCTGTGGCCATTAAGTATGCCGCCACAATTACCAACAAAAGATGAAGAGATTAAAATTGCTAAATTAGATCAATATGATGCAGTGTTATATCGTCGTTATTTGGCAAAAGAGTATGGCAAACGAAAACAAATGGTCAGCGGAATTCATTTTAATTTTGAATATGACCAAGCCCTGATTCAGCAATTATATGATGAACAATCCGAAGTGACAGATTGCAAACAATTTAAAACGAAAGTGTACATGAAAGTTGCCCGTAACTTTTTACGTTATCGTTGGTTAATTACGTATCTTTTTGGGGCTTCGCCAGTTAGTGAAGACGGCTACTTTAGAGTCTATGACGACCAACCGCAAGAACCCATTCGCAGTATTCGGAATAGTACGTATGGCTACAGAAATCATGACAATGTGAAAGTATCGTATGCCTCATTGGAACGCTATTTAGAAGATATTCATCGCATGGTGGAAAATGGTTTACTTTCTGAAGAAAAAGAATTTTATGCGCCTGTGCGCTTACGTGGTGGGAAACAAATGTCTGATCTGCCTAAAACAGGTATTCGCTATATCGAGTTGCGTAATTTAGACTTAAATCCTTTTTCACGTTTAGGCATTGTGGAAGATACTGTGGATTTCTTACATTATTTCATGTTGTATTTATTGTGGACAGATGAAAAAGAAGAAGCGGATGAATGGGTAAAAACTGGCGATATTTTAAATGAACAAGTGGCTCTTGGTCATCCTCATGAAACGATTAAGTTAATTGCAGAAGGCGATCGGATTTTTTCAGAAATGATTGATATGTTAGATGCTCTAGGCATTCGTAAAGGCAAAGAAGTTGTCGGTAAGTATTATCAACAACTGCGGAATCCACAAGACACCGTTTCTGGCAAAATGTGGACGATTATTCAAGAAAACTCCAACAGTGAACTGGGAAATATTTTTGGAAACCAATATCAAAGTATGGCCTTTGAACGCCCTTATCAATTAGCTGGTTTCCGTGAGATGGAATTATCCACACAAATTTTCTTGTTTGATGCGATTCAAAAAGGTTTGGAAATCGAAATTTTAGATGAACAAGAGCAATTTTTGAAACTGCAACATGGCGAGCACATTGAATACGTCAAAAATGCCAACATGACTAGCAAAGATAACTACGTGGTACCATTGATTATGGAAAACAAAACCGTGACAAAGAAAATTTTGTCTGCAGCAGGGTTCCATGTGCCTGGCGGTGAAGAATTTTCATCTTTTATTGAGGCACAAGAAGCACATTTACGCTACGCCAATAAAGCGTTTGTCGTGAAACCAAAATCAACGAATTACGGTTTAGGAATTACCATTTTTAAAGAAGGCGCTTCGTTGGAAGACTTTACGGAAGCGTTACGGATTGCTTTTAAAGAGGACACAGCGGTTTTAATTGAAGAGTTTTTACCTGGAACAGAATATCGGTTCTTTGTGTTAGATAATGATGTAAAAGCCATCATGTTGCGCGTGCCAGCCAATGTTACCGGAGATGGCAAACACACTGTAGAAGAATTGGTGGCCGCTAAAAATAGTGATCCATTGCGGGGGACCAATCACCGTGCACCACTAGAATTAATCCAGTTAAATGATTTAGAAAAACTAATGTTGAAAGAACAAGGTTTAACTATCTATTCTGTGCCAGAAAAAGAGCAAATCGTGTACTTGCGAGAAAATTCTAATGTTAGCACGGGCGGGGATTCGATTGATATGACCGATGTCATTGATGATAGTTATAAACAAATCGCCATTGAGGCCGTAGCTGCTTTAGGAGCCAAAATTTGTGGCATTGATTTAATCATTCCTGACAAAGACGTAAAAGGCACACGTGATAGCTTAACGTACGGGATTATCGAAGCAAACTTTAATCCAGCCATGCACATGCATGTGTATCCATACGCTGGACAGGGTAGACGCTTGACAATGGACGTTTTAAAACTTTTATACCCAGAAGTGGTTCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35918","NCBI_taxonomy_name":"Enterococcus faecalis","NCBI_taxonomy_id":"1351"}}}},"ARO_accession":"3003805","ARO_id":"40490","ARO_name":"Enterococcus faecalis gshF with mutation conferring daptomycin resistance","CARD_short_name":"Efae_gshF_DAP","ARO_description":"gshF is a bifunctional glutamate-cysteine ligase\/ glutathione synthetase that when mutated, confers daptomycin resistance.","ARO_category":{"40491":{"category_aro_accession":"3003806","category_aro_cvterm_id":"40491","category_aro_name":"daptomycin resistant gshF","category_aro_description":"Mutations to the glutathione synthetase gshF confers daptomycin resistance.","category_aro_class_name":"AMR Gene Family"},"35985":{"category_aro_accession":"0000068","category_aro_cvterm_id":"35985","category_aro_name":"daptomycin","category_aro_description":"Daptomycin is a novel lipopeptide antibiotic used in the treatment of certain infections caused by Gram-positive organisms. Daptomycin interferes with the bacterial cell membrane, reducing membrane potential and inhibiting cell wall synthesis.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2301":{"model_id":"2301","model_name":"Enterococcus faecalis YybT with mutation conferring daptomycin resistance","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"3878":"I440S"},"Curated-R":{"3878":"I440S"},"experimental":{"3878":"I440S"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1250"}},"model_sequences":{"sequence":{"5217":{"protein_sequence":{"accession":"AAO79895.1","sequence":"MQKKRIQKNGFLIVVGLLLVEFLLYFLLTNKWLLLAVIIALDIFLLVVIRLLIRDVEITNVEKIQEASSIAEQSLDYVVNEVPVGIITYNGETRAVEWLNPYAASIFNKDNQLTLTASQVTSYLELAERNQDIFTIDENTYRFSVNKEQHTITFEDITKESNLYQEKVEMQTAIGIVSVDNYDDVTDTMDEKEISYLNSFITTMVSDWMDQYKVFYKRINAERYFFIAQWEDIQKMMDEKFSILDTIRKESANHEVAITLSMGIAYGGPTLDQTGTTAQTNLDTALVRGGDQVVVKEAKDEAKPLFFGGKTAVTTKRSQVRSRAMSMAIKGIIAESADIYIMGHRYPDMDALGSAFGVARLASFNNRKAWIVLDENEIIPDVKRVLEAIKEYPELEERIISPKEAMKRKKESSLLVMVDYHKPSLSISQELYERFDKVVIIDHHRRGDEFPAKPLLSYIESSASSASELVTELIEYQSNSANKLQAFEATMMLAGIVVDTKSFNTRTTARTFDVASYLRTCGADSSLVQYLLSSDLTSYLEMNNLISKSEYVTKDTVVVAGSEDKEYDSVTAAKTADTLLSMAGINAAFVITKRTDQQIGISARSNGSINVQIIMENLGGGGHFTNAAVQLSNVTVAEVKEQLLDVIRQNINEMYEQE"},"dna_sequence":{"accession":"AE016830.1","fmin":"10732","fmax":"12709","strand":"+","sequence":"ATGCAAAAGAAGAGAATTCAAAAAAACGGTTTCTTAATTGTTGTGGGTCTTCTCTTAGTAGAATTTCTCCTCTATTTCTTACTAACAAATAAATGGCTGCTATTGGCGGTAATTATCGCATTAGATATCTTTCTCTTAGTGGTTATTCGGCTGTTGATTAGAGATGTAGAAATTACGAACGTAGAAAAGATTCAAGAAGCAAGTTCCATTGCTGAACAATCGTTGGATTATGTTGTAAATGAAGTACCTGTGGGAATTATTACGTATAACGGGGAAACACGCGCGGTAGAATGGCTTAATCCTTATGCTGCTTCTATTTTTAATAAAGACAATCAGCTAACGTTAACCGCTAGCCAAGTTACGTCTTATTTAGAATTAGCAGAACGAAACCAAGATATTTTTACGATTGACGAAAATACCTATCGCTTTAGCGTCAATAAAGAACAACATACAATTACTTTTGAAGATATCACTAAAGAAAGTAATTTGTATCAAGAAAAAGTCGAAATGCAAACGGCTATTGGCATTGTGTCTGTCGATAATTATGATGATGTCACCGATACAATGGATGAGAAAGAAATTTCTTATTTGAATAGTTTCATTACGACGATGGTTTCTGATTGGATGGACCAATACAAAGTTTTTTATAAGCGAATCAACGCAGAACGTTATTTTTTCATTGCCCAATGGGAAGATATTCAAAAAATGATGGACGAAAAATTTTCTATTTTGGATACGATCCGTAAGGAATCAGCTAACCATGAAGTAGCCATTACGTTAAGTATGGGGATTGCTTATGGGGGCCCAACCTTAGATCAAACCGGGACCACGGCTCAAACAAACCTAGATACAGCTTTAGTTCGTGGTGGTGATCAAGTGGTTGTAAAAGAAGCCAAAGATGAAGCGAAGCCGTTATTTTTTGGTGGAAAAACGGCAGTAACGACGAAACGTTCCCAAGTACGTTCTCGCGCAATGAGCATGGCAATTAAGGGAATTATTGCGGAATCTGCTGACATCTATATTATGGGCCATCGTTATCCAGATATGGATGCGTTAGGTTCAGCATTTGGTGTTGCTCGTTTAGCCTCGTTTAATAATCGAAAAGCGTGGATTGTTTTAGATGAAAATGAAATCATTCCCGATGTCAAAAGAGTGTTAGAGGCGATTAAAGAGTACCCAGAATTAGAAGAGCGCATTATTAGTCCTAAAGAGGCCATGAAGCGCAAGAAAGAAAGTAGCTTATTAGTTATGGTAGATTACCATAAACCGTCTCTATCGATCTCACAAGAGCTCTATGAGCGTTTTGATAAAGTAGTAATCATTGATCACCATCGACGAGGAGACGAATTTCCAGCAAAACCCTTGCTTTCTTATATTGAATCTTCTGCCTCTTCTGCTTCAGAATTAGTCACAGAATTGATCGAATATCAAAGTAATAGCGCAAATAAACTGCAGGCCTTTGAAGCAACCATGATGTTGGCGGGAATTGTGGTTGATACGAAAAGTTTCAATACACGAACGACGGCGCGAACATTTGATGTGGCTAGTTATTTACGAACTTGTGGAGCAGACTCATCTTTAGTACAATATCTATTAAGTTCTGATCTTACAAGCTATCTGGAAATGAACAATTTAATCTCTAAAAGCGAATATGTCACAAAAGATACCGTCGTTGTTGCAGGGAGTGAAGACAAAGAATATGATAGTGTCACAGCTGCCAAAACAGCGGACACATTACTTTCTATGGCAGGGATTAATGCAGCATTTGTCATTACCAAGCGGACGGATCAACAGATTGGCATTAGTGCTCGGAGTAATGGTTCAATTAATGTCCAAATTATTATGGAAAATTTAGGTGGTGGCGGTCACTTTACTAATGCGGCAGTACAATTATCAAACGTAACAGTAGCAGAAGTAAAAGAGCAACTACTTGATGTAATTCGTCAAAATATTAATGAAATGTATGAACAGGAGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37592","NCBI_taxonomy_name":"Enterococcus faecalis V583","NCBI_taxonomy_id":"226185"}}}},"ARO_accession":"3003797","ARO_id":"40482","ARO_name":"Enterococcus faecalis YybT with mutation conferring daptomycin resistance","CARD_short_name":"Efae_YybT_DAP","ARO_description":"YybT has phosphodiesterase activity towards cyclic dinucleotides using a c-di-GMP hydrolyzing phosphodiesterase domain. Mutations to the gene confer resistance to daptomycin.","ARO_category":{"40483":{"category_aro_accession":"3003798","category_aro_cvterm_id":"40483","category_aro_name":"daptomycin resistant YybT","category_aro_description":"Mutations to the YybT gene confers daptomycin resistance.","category_aro_class_name":"AMR Gene Family"},"35985":{"category_aro_accession":"0000068","category_aro_cvterm_id":"35985","category_aro_name":"daptomycin","category_aro_description":"Daptomycin is a novel lipopeptide antibiotic used in the treatment of certain infections caused by Gram-positive organisms. Daptomycin interferes with the bacterial cell membrane, reducing membrane potential and inhibiting cell wall synthesis.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3510":{"model_id":"3510","model_name":"OXA-440","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"5705":{"protein_sequence":{"accession":"AKR53962.1","sequence":"MNKYFTCYVVASLFLSGCTVQHNLINETPSQIVQGHNQVIHQYFDEKNTSGVLVIQTDKKINLYGNALSRANTEYVPASTFKMLNALIGLENQKTDINEIFKWKGEKRSFTAWEKDMTLGEAMKLSAVPVYQELARRIGLDLMQKEVKRIGFGNAEIGQQVDNFWLVGPLKVTPIQEVEFVSQLAHTQLPFSEKVQANVKNMLLLEESNGYKIFGKTGWAMDKKPQVGWLTGWVEQPDGKIVAFALNMEMRSEMPASIRNELLMKSLKQLNII"},"dna_sequence":{"accession":"KP727574.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGAATAAATATTTTACTTGCTATGTGGTTGCTTCTCTTTTTCTTTCTGGTTGTACGGTTCAGCATAATTTAATAAATGAAACCCCGAGTCAGATTGTTCAAGGACATAATCAGGTGATTCATCAATACTTTGATGAAAAAAACACCTCAGGTGTGCTGGTTATTCAAACAGATAAAAAAATTAATCTATATGGTAATGCTCTAAGCCGCGCAAATACAGAATATGTGCCAGCCTCTACATTTAAAATGTTGAATGCCCTGATCGGATTGGAGAACCAGAAAACGGATATTAATGAAATATTTAAATGGAAGGGCGAGAAAAGGTCATTTACCGCTTGGGAAAAAGACATGACACTAGGAGAAGCCATGAAGCTTTCTGCAGTCCCAGTCTATCAGGAACTTGCGCGACGTATCGGTCTTGATCTCATGCAAAAAGAAGTAAAACGTATTGGTTTCGGTAATGCTGAAATTGGACAGCAGGTTGATAATTTCTGGTTGGTAGGACCATTAAAGGTTACGCCTATTCAAGAGGTAGAGTTTGTTTCCCAATTAGCACATACACAGCTTCCATTTAGTGAAAAAGTGCAGGCTAATGTAAAAAATATGCTTCTTTTAGAAGAGAGTAATGGCTACAAAATTTTTGGAAAGACTGGTTGGGCAATGGATAAAAAACCACAAGTGGGCTGGTTGACCGGCTGGGTTGAGCAGCCAGATGGAAAAATTGTCGCTTTTGCATTAAATATGGAAATGCGGTCAGAAATGCCGGCATCTATACGTAATGAATTATTGATGAAATCATTAAAACAGCTGAATATTATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3003596","ARO_id":"40206","ARO_name":"OXA-440","CARD_short_name":"OXA-440","ARO_description":"OXA-440 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46499":{"category_aro_accession":"3007710","category_aro_cvterm_id":"46499","category_aro_name":"OXA-23-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases, specifically imipenem, derived from OXA-23, first identified in Acinetobacter baumannii.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2295":{"model_id":"2295","model_name":"Enterococcus faecium liaF mutant conferring daptomycin resistance","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"3859":"I144T","3860":"L39F"},"Curated-R":{"3859":"I144T","3860":"L39F"},"clinical":{"3859":"I144T","3860":"L39F"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"4630":{"protein_sequence":{"accession":"CUX99269.1","sequence":"MNSSWRFFVVVEALLLLFAVWQIVNNTGLLLLVIFGIFNIYLAMRKYPRTKFQNFQLILGSLVIFFSLVNSPALWMMVVLAVLFIGLKGVEISGIDLTKNAFWRKKQIMMVQTEQLKTHNNERKRQQLFGNQRIGNDVYEWDDINIAIISGDTIIDLGNTLLPKDDNIVIVRKGIGRTRILVPLGVAIRLEHATLVGNVLFEEEQFSLKNEQIKICSSDYDENPRRLKIITNTLVGDVEVIRI"},"dna_sequence":{"accession":"LN999844.1","fmin":"1854250","fmax":"1854982","strand":"-","sequence":"ATGAATAGTTCTTGGCGTTTTTTTGTGGTAGTCGAAGCACTGCTGCTGTTATTTGCTGTTTGGCAAATCGTAAACAATACTGGACTTTTGCTTTTAGTAATATTCGGTATTTTCAATATATATCTAGCTATGCGCAAATATCCTCGTACTAAATTTCAAAATTTTCAATTGATCTTAGGGAGCTTGGTCATTTTTTTTAGCTTAGTCAACAGTCCTGCTTTATGGATGATGGTTGTATTGGCCGTTTTATTTATCGGCCTGAAAGGTGTAGAGATTTCAGGAATAGATTTGACAAAAAATGCTTTTTGGCGAAAAAAACAGATCATGATGGTCCAAACAGAGCAATTAAAAACACATAATAATGAGCGTAAAAGACAGCAATTATTTGGTAACCAACGTATTGGAAACGACGTCTATGAATGGGATGATATCAACATTGCCATCATTTCTGGTGATACTATCATCGATTTGGGCAATACACTTTTGCCAAAAGATGATAATATTGTGATTGTAAGAAAAGGGATAGGCAGAACACGGATCTTAGTACCCCTGGGAGTGGCTATTCGATTAGAGCATGCGACATTAGTAGGAAATGTCTTGTTTGAAGAAGAGCAGTTTTCCTTAAAAAATGAACAGATCAAAATCTGCAGCAGTGATTATGATGAAAATCCTCGCAGATTGAAGATCATTACCAATACCTTGGTTGGAGATGTCGAGGTGATACGAATATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36779","NCBI_taxonomy_name":"Enterococcus faecium","NCBI_taxonomy_id":"1352"}}}},"ARO_accession":"3003790","ARO_id":"40475","ARO_name":"Enterococcus faecium liaF mutant conferring daptomycin resistance","CARD_short_name":"Efac_liaF_DAP","ARO_description":"liaF is an accessory protein that acts as a negative regulator of liaRS signal transduction pathway. Mutations confer daptomycin resistance.","ARO_category":{"41426":{"category_aro_accession":"3004262","category_aro_cvterm_id":"41426","category_aro_name":"daptomycin resistant liaF","category_aro_description":"Mutations to the liaF accessory protein that confer resistance to daptomycin.","category_aro_class_name":"AMR Gene Family"},"35985":{"category_aro_accession":"0000068","category_aro_cvterm_id":"35985","category_aro_name":"daptomycin","category_aro_description":"Daptomycin is a novel lipopeptide antibiotic used in the treatment of certain infections caused by Gram-positive organisms. Daptomycin interferes with the bacterial cell membrane, reducing membrane potential and inhibiting cell wall synthesis.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2296":{"model_id":"2296","model_name":"Enterococcus faecalis liaS mutant conferring daptomycin resistance","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"3865":"A180T"},"Curated-R":{"3865":"A180T"},"clinical":{"3865":"A180T"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"650"}},"model_sequences":{"sequence":{"4629":{"protein_sequence":{"accession":"AAO82600.1","sequence":"MTDRISRRMISLYASLSTFIVILITLFSYFHSIKQNRWLLELLQRKVFYLPLIVHIVLISLLIGLLTFLLISLVQKGQYGRIEEKLRLLANGNYESPVLNKPTTSENQDHYLTEVEQDIWSIKNKLLEMSKELQLLNSRPQLMDGQTKEEILENERHRLARELHDSVSQQLFAAMMMLSALNEQAQRTETPEPYRKQLAMVAEIINASQSEMRALLLHLRPISLEGKSLRKGIEQLLKELQTKIKIELIWDVEDVHLNSSIEDHLFRIVQELLSNTLRHAKAKELEVYLHQVDKNVLLRIVDDGVGFDMKEQSNKAGSYGLNNIRERVVGMGGTVKIISFKGQGTSVEIKVPVIKEETASDQSNVSG"},"dna_sequence":{"accession":"AE016830.1","fmin":"2789720","fmax":"2790824","strand":"-","sequence":"ATGACCGATCGGATTTCAAGACGCATGATTTCATTATATGCGTCCCTTAGCACCTTTATTGTTATCTTAATTACATTGTTTTCATATTTTCATTCGATTAAACAAAACCGGTGGTTATTAGAGCTTCTTCAGAGAAAAGTCTTTTATTTACCACTAATTGTGCACATTGTTCTCATATCCTTACTAATAGGCTTATTGACCTTTTTACTGATTTCATTGGTTCAAAAAGGGCAATATGGACGGATTGAAGAAAAACTTCGGTTATTGGCCAACGGTAATTATGAAAGTCCAGTCTTAAACAAACCAACGACCAGTGAAAATCAAGACCATTATCTAACCGAAGTCGAACAAGATATTTGGTCGATTAAAAATAAATTATTAGAGATGTCTAAAGAATTGCAATTATTAAACAGTCGACCGCAATTAATGGATGGGCAAACAAAAGAAGAAATTTTAGAGAACGAGCGGCATCGTTTGGCGCGGGAGTTGCATGATTCAGTCAGTCAACAACTTTTTGCAGCCATGATGATGTTGTCTGCATTAAATGAACAAGCACAACGAACAGAAACCCCGGAACCATATCGTAAACAACTAGCCATGGTGGCAGAAATCATTAATGCCTCCCAATCGGAAATGCGCGCGCTACTATTGCACTTGCGTCCTATCAGTCTAGAAGGAAAAAGTTTGCGTAAAGGTATTGAACAATTACTGAAAGAACTACAAACAAAAATTAAAATTGAATTGATTTGGGATGTTGAAGATGTTCATTTAAATAGCAGCATTGAGGATCATCTTTTCCGAATTGTGCAGGAGTTACTTTCAAATACCTTAAGACATGCCAAAGCAAAGGAATTAGAGGTATACTTACACCAAGTCGATAAAAACGTGTTATTGCGTATTGTTGATGATGGTGTCGGCTTTGATATGAAGGAACAAAGTAATAAAGCCGGTAGTTATGGCTTAAATAATATTCGAGAACGTGTTGTCGGCATGGGCGGTACAGTTAAAATTATTAGTTTTAAAGGGCAGGGAACCAGCGTTGAAATTAAAGTTCCTGTCATAAAGGAGGAAACTGCAAGTGATCAAAGTAATGTTAGTGGATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37592","NCBI_taxonomy_name":"Enterococcus faecalis V583","NCBI_taxonomy_id":"226185"}}}},"ARO_accession":"3003791","ARO_id":"40476","ARO_name":"Enterococcus faecalis liaS mutant conferring daptomycin resistance","CARD_short_name":"Efae_liaS_DAP","ARO_description":"liaS is a histidine kinase found in the liaFSR signal transduction pathway. Mutations confer daptomycin resistance.","ARO_category":{"41428":{"category_aro_accession":"3004264","category_aro_cvterm_id":"41428","category_aro_name":"daptomycin resistant liaS","category_aro_description":"Mutations in the liaS histidine kinase that confer daptomycin resistance.","category_aro_class_name":"AMR Gene Family"},"35985":{"category_aro_accession":"0000068","category_aro_cvterm_id":"35985","category_aro_name":"daptomycin","category_aro_description":"Daptomycin is a novel lipopeptide antibiotic used in the treatment of certain infections caused by Gram-positive organisms. Daptomycin interferes with the bacterial cell membrane, reducing membrane potential and inhibiting cell wall synthesis.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2297":{"model_id":"2297","model_name":"Enterococcus faecalis liaR mutant conferring daptomycin resistance","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"3870":"D191N"},"Curated-R":{"3870":"D191N"},"experimental":{"3870":"D191N"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"350"}},"model_sequences":{"sequence":{"5215":{"protein_sequence":{"accession":"AAO82599.1","sequence":"MIKVMLVDDHEMVRLGVSSYLSIQEDIEVVGEAENGKIGYEKALELRPDVILMDLVMEEMDGIDSTKAILKDWPEAKIIIVTSFIDDEKVYPAIEAGAAGYLLKTSTAHEIADAIRATYRGERVLEPEVTHKMMERLTKKQEPVLHEDLTNREHEILMLIAQGKSNQEIADELFITLKTVKTHVSNILAKLDVDDRTQAAIYAFQHGLAK"},"dna_sequence":{"accession":"AE016830.1","fmin":"2789113","fmax":"2789746","strand":"-","sequence":"GTGATCAAAGTAATGTTAGTGGATGACCATGAAATGGTCCGTTTAGGCGTTTCATCATATTTATCTATTCAAGAGGATATAGAAGTCGTAGGCGAAGCAGAAAACGGTAAGATTGGCTATGAAAAAGCATTGGAACTACGTCCAGATGTTATTTTGATGGATTTGGTAATGGAAGAAATGGACGGCATTGATTCAACAAAAGCGATCTTGAAAGATTGGCCAGAAGCCAAGATTATTATTGTGACGAGTTTTATTGATGATGAAAAAGTGTATCCGGCGATTGAAGCTGGTGCAGCGGGCTACCTATTAAAGACATCAACAGCACATGAGATTGCTGATGCAATTCGGGCGACTTATCGCGGAGAGCGTGTGTTGGAACCTGAAGTGACGCATAAGATGATGGAACGGTTAACAAAAAAACAAGAGCCGGTGTTGCACGAAGATTTGACAAACCGGGAACACGAAATTTTAATGTTGATTGCACAAGGTAAAAGTAATCAGGAAATAGCTGATGAACTCTTTATCACTTTGAAAACAGTTAAAACACATGTTTCAAACATTTTAGCAAAACTAGATGTGGATGATCGGACCCAAGCGGCGATTTATGCTTTTCAACATGGTTTAGCCAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37592","NCBI_taxonomy_name":"Enterococcus faecalis V583","NCBI_taxonomy_id":"226185"}}}},"ARO_accession":"3003792","ARO_id":"40477","ARO_name":"Enterococcus faecalis liaR mutant conferring daptomycin resistance","CARD_short_name":"Efae_liaR_DAP","ARO_description":"liaR is a response regulator found in the liaFSR signal transduction pathway. Mutations confer daptomycin resistance.","ARO_category":{"41427":{"category_aro_accession":"3004263","category_aro_cvterm_id":"41427","category_aro_name":"daptomycin resistant liaR","category_aro_description":"Mutations to the liaR response regulator that confer resistance to daptomycin.","category_aro_class_name":"AMR Gene Family"},"35985":{"category_aro_accession":"0000068","category_aro_cvterm_id":"35985","category_aro_name":"daptomycin","category_aro_description":"Daptomycin is a novel lipopeptide antibiotic used in the treatment of certain infections caused by Gram-positive organisms. Daptomycin interferes with the bacterial cell membrane, reducing membrane potential and inhibiting cell wall synthesis.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"3540":{"model_id":"3540","model_name":"OXA-478","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"520"}},"model_sequences":{"sequence":{"5735":{"protein_sequence":{"accession":"ALC79293.1","sequence":"MSKKNFILIFIFVILISCKNTEKISNETTLIDNIFTNSNAEGTLVIYNLNDDKYIIHNKERAELRFYPASTFKIYNSLIGLNEKAVKDVDEVFYKYNGEKVFLESWAKDSNSRYAIKNSQVPAYKELARRIGLKKMKENIEKLDFGNKSIGDSVDTFGIEGPLEISAMEQVKLLTKLAQNELPYPIEIQKAVSDITILEQTYNYTLHGKTGLVDSKNMTTEPIGWFVGWLEENDNIYVFALNIDNINSDDLAKRINIVKESLKALNLLK"},"dna_sequence":{"accession":"KR182171.1","fmin":"0","fmax":"810","strand":"+","sequence":"ATGTCTAAAAAAAATTTTATATTAATATTTATTTTTGTTATTTTAATATCTTGTAAAAATACAGAAAAAATATCAAATGAAACTACATTAATAGATAATATATTTACTAATAGCAATGCTGAAGGAACATTAGTTATATATAATTTAAATGATGATAAATATATAATTCATAATAAAGAAAGAGCTGAACTAAGATTTTATCCAGCATCAACATTTAAAATATATAATAGTTTAATAGGCTTAAATGAAAAAGCAGTTAAAGATGTAGATGAAGTATTTTATAAATATAATGGCGAAAAAGTTTTTCTTGAATCTTGGGCTAAGGACTCTAATTCAAGATATGCAATTAAAAATTCGCAAGTACCGGCATATAAAGAATTAGCAAGAAGAATAGGTCTTAAAAAGATGAAAGAGAATATAGAAAAACTAGATTTTGGTAATAAAAGTATAGGTGATAGTGTAGATACTTTTGGAATTGAAGGACCTTTGGAAATAAGTGCGATGGAGCAAGTTAAATTATTAACTAAATTAGCTCAAAATGAATTACCGTATCCTATAGAAATACAAAAAGCTGTTTCTGATATTACTATACTAGAGCAAACTTACAATTATACGCTTCATGGAAAAACTGGATTAGTTGATTCTAAAAACATGACAACTGAGCCTATTGGTTGGTTCGTAGGCTGGCTTGAAGAAAATGATAATATATATGTCTTTGCTTTAAATATTGATAATATCAATTCAGATGACCTTGCAAAAAGGATAAATATAGTAAAAGAAAGTTTAAAAGCATTAAATTTATTAAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36935","NCBI_taxonomy_name":"Brachyspira pilosicoli","NCBI_taxonomy_id":"52584"}}}},"ARO_accession":"3003635","ARO_id":"40245","ARO_name":"OXA-478","CARD_short_name":"OXA-478","ARO_description":"OXA-478 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46521":{"category_aro_accession":"3007732","category_aro_cvterm_id":"46521","category_aro_name":"OXA-63-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-63.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3583":{"model_id":"3583","model_name":"FAR-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"5781":{"protein_sequence":{"accession":"AAB81957.1","sequence":"MAAAAAIALLGGCGADAGSEPATTAASTTAPSTATDAATAEFAALEQRSGARLGVYAVDTTSGAEVAYRADERFGMASTFKGLACGALLREHPLSSGYFDQVVRYSREEVVSYSPVTETRVDTGMTVAELCHATITVSDNTAGNQILKLLGGPAGFTAFLRSLGDEVSRLDRWETELNEVPPGEERDTTTPAAVAANYRALVLGDVLAEPERAQLRDWLVANTTGDQRIRAGVPAGWTVGDKTGGGSHGGNNDVAVAWTETGDPIVIALLSHRTDPAAKADNALLAEATRAVVTALR"},"dna_sequence":{"accession":"AF024601.1","fmin":"302","fmax":"1196","strand":"+","sequence":"ATGGCGGCCGCCGCGGCGATCGCGCTACTGGGCGGCTGCGGCGCGGACGCGGGTTCCGAGCCCGCCACCACCGCGGCGAGCACGACCGCGCCGAGCACGGCCACCGACGCGGCGACCGCCGAGTTCGCCGCACTGGAACAGCGATCCGGCGCGCGGCTGGGCGTCTACGCGGTCGACACGACCAGCGGCGCCGAGGTCGCCTACCGGGCGGACGAGCGGTTCGGCATGGCCTCCACCTTCAAGGGCCTGGCCTGCGGCGCGCTGCTGCGCGAGCACCCGCTGTCGTCCGGCTATTTCGACCAGGTCGTCCGCTACTCCCGCGAGGAGGTGGTGTCCTATTCGCCGGTCACCGAGACCCGCGTGGACACCGGGATGACCGTCGCCGAACTGTGCCACGCCACGATCACCGTCAGCGACAACACCGCGGGCAACCAGATCCTGAAACTGCTCGGCGGCCCCGCCGGTTTCACCGCCTTCCTGCGCTCGCTCGGCGACGAGGTGAGCCGGCTGGACCGCTGGGAGACCGAACTCAACGAGGTGCCGCCCGGCGAGGAACGCGACACCACCACCCCCGCCGCCGTGGCGGCGAACTACCGCGCGCTGGTGCTCGGTGACGTGCTCGCCGAGCCCGAGCGCGCCCAGTTGCGGGACTGGCTGGTCGCCAACACCACCGGCGACCAGCGCATCCGTGCGGGCGTGCCCGCGGGCTGGACGGTCGGCGACAAGACCGGCGGCGGCAGCCACGGCGGCAACAACGACGTGGCCGTGGCCTGGACCGAGACCGGCGACCCGATCGTCATCGCCCTGCTCTCGCACCGCACCGACCCCGCCGCCAAGGCCGACAACGCCCTGCTCGCCGAGGCGACCCGGGCGGTGGTCACCGCCCTGCGATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42902","NCBI_taxonomy_name":"Nocardia farcinica","NCBI_taxonomy_id":"37329"}}}},"ARO_accession":"3004784","ARO_id":"42901","ARO_name":"FAR-1","CARD_short_name":"FAR-1","ARO_description":"FAR-1 is a class A beta-lactamase gene found in Nocardia farcinica.","ARO_category":{"42900":{"category_aro_accession":"3004783","category_aro_cvterm_id":"42900","category_aro_name":"FAR beta-lactamase","category_aro_description":"FAR is a class A extended spectrum beta-lactamase gene family found in Nocardia farcinica.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3640":{"model_id":"3640","model_name":"LEN-41","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"5911":{"protein_sequence":{"accession":"AZA07958.1","sequence":"MRYVRLCVISLLATLPLAVDAGPQPLEQIKQSESQLSGRVGMVEMDLASGRTLAAWRADERFPMVSTFKVLLCGAVLARVDAGVEQLDRRIHYRQQDLVDYSPVSEKHLVDGMTIGELCAAAITMSDNSAGNLLLATVGGPAGLTAFLRQIGDNVTRLDRWETALNEALPGDARDTTTPASMAATLRKLLTAQHLSARSQQQLLQWMVDDRVAGPLIRAVLPAGWFIADKTGAGERGARGIVALLGPDGNAERIVVIYLRDTPASMAERNQHIAGIGAALIEHWQR"},"dna_sequence":{"accession":"MK161461.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGTGTTATCTCCCTGTTAGCCACCCTGCCACTGGCGGTAGACGCCGGTCCACAGCCGCTTGAGCAGATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTGGGGATGGTGGAAATGGATCTGGCCAGCGGCCGCACGCTGGCGGCCTGGCGCGCCGATGAACGCTTTCCCATGGTGAGCACCTTTAAAGTGCTGCTGTGCGGCGCGGTGCTGGCGCGGGTGGATGCCGGGGTCGAACAACTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGTCGACGGGATGACGATCGGCGAACTCTGCGCCGCCGCCATCACCATGAGCGATAACAGCGCCGGCAATCTGCTGCTGGCCACCGTCGGTGGCCCCGCGGGATTGACCGCCTTTCTGCGCCAGATCGGTGACAACGTCACCCGCCTTGACCGCTGGGAAACGGCACTGAATGAGGCGCTTCCCGGCGACGCGCGCGATACCACTACCCCGGCCAGCATGGCCGCCACGCTGCGCAAACTACTGACCGCGCAGCATCTGAGCGCCCGTTCGCAACAGCAGCTCCTGCAGTGGATGGTGGACGATCGGGTTGCCGGCCCGCTGATCCGCGCCGTGCTGCCGGCGGGCTGGTTTATCGCCGACAAAACCGGGGCTGGCGAACGGGGTGCGCGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAACGCGGAGCGCATTGTGGTGATCTATCTGCGGGATACCCCGGCGAGTATGGCCGAGCGTAATCAACATATCGCCGGGATCGGCGCAGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42976","NCBI_taxonomy_name":"Klebsiella variicola subsp. tropica","NCBI_taxonomy_id":"2489014"}}}},"ARO_accession":"3004844","ARO_id":"42979","ARO_name":"LEN-41","CARD_short_name":"LEN-41","ARO_description":"A class-A broad-spectrum beta-lactamase identified from Klebsiella.","ARO_category":{"36236":{"category_aro_accession":"3000097","category_aro_cvterm_id":"36236","category_aro_name":"LEN beta-lactamase","category_aro_description":"LEN beta-lactamases are chromosomal class A beta-lactamases that confer resistance to ampicillin, amoxicillin, carbenicillin, and ticarcillin but not to extended-spectrum beta-lactams.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2326":{"model_id":"2326","model_name":"TLA-3","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"5278":{"protein_sequence":{"accession":"BAQ22139.1","sequence":"MKKHLIVIAFCALFASAFAAKGTDSLKNSAKGTDSLKNSIEKYLKDKKAKVGVAVLGIEDNFKLNVNEKHHYPMQSTYKFHLALAVLDKLDKENISVDKKLFVKKSDLQPNTWSPLKDKYPNGNLELSFSEIIKSTVSHSDNNGCDILFRFVGGTNKVHNFISKLGVKNISIKATEEEMHKAWNVQYTNWTTPDATVQLLKKFYKNEILSKNSYDFLLNTMIETTTGPKRLKGLLPDGTVVAHKTGSSDTNNKGITAATNDIGIITLPNGKHFAIAVYVSDSSEKSDVNEKIIAEICKSVWDYLVKDGK"},"dna_sequence":{"accession":"AP014611.1","fmin":"149223","fmax":"150153","strand":"-","sequence":"ATGAAAAAACATCTTATTGTAATTGCATTTTGTGCGCTTTTTGCTTCTGCCTTTGCGGCTAAAGGTACGGATTCGCTTAAAAACAGTGCTAAAGGTACGGATTCGCTTAAAAACAGTATTGAAAAATATCTTAAAGATAAAAAAGCAAAAGTCGGTGTTGCCGTTTTGGGAATTGAAGATAATTTTAAATTGAACGTTAACGAAAAGCATCACTATCCTATGCAAAGTACTTATAAATTCCATTTAGCGTTGGCAGTGCTTGATAAACTTGATAAAGAGAATATTTCCGTTGACAAGAAGCTTTTTGTAAAGAAATCCGACCTTCAACCGAATACTTGGAGCCCGCTAAAAGATAAATATCCTAACGGAAATTTGGAATTGTCATTTAGTGAAATTATTAAGTCTACAGTTTCTCACAGCGATAACAACGGCTGCGATATTCTTTTCAGATTTGTCGGCGGAACAAATAAAGTCCACAATTTTATTAGCAAGCTTGGCGTTAAGAATATTTCTATCAAAGCTACAGAAGAAGAAATGCACAAGGCATGGAATGTACAATATACCAATTGGACAACTCCCGATGCTACCGTTCAGCTCTTAAAGAAGTTCTACAAAAATGAAATACTCTCAAAAAATAGTTACGACTTTTTGCTTAATACCATGATTGAAACTACTACCGGACCTAAACGACTCAAAGGACTTTTGCCGGATGGAACTGTTGTTGCGCATAAAACCGGAAGCTCAGATACTAACAATAAAGGAATTACTGCTGCCACAAATGATATCGGTATTATTACTTTGCCGAACGGCAAGCACTTTGCCATTGCTGTTTATGTGTCGGATTCAAGCGAAAAGAGCGATGTTAACGAAAAAATTATTGCCGAAATTTGCAAAAGCGTTTGGGATTATCTAGTTAAGGATGGGAAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36783","NCBI_taxonomy_name":"Serratia marcescens","NCBI_taxonomy_id":"615"}}}},"ARO_accession":"3003204","ARO_id":"39788","ARO_name":"TLA-3","CARD_short_name":"TLA-3","ARO_description":"TLA-3 is a beta-lactamase found in a transferable plasmid of Serratia marcescens clinical isolate. It confers resistance to ceftazidime, cefotaxime and cefepime, but not to cefmetazole and meropenem.","ARO_category":{"39785":{"category_aro_accession":"3003201","category_aro_cvterm_id":"39785","category_aro_name":"TLA beta-lactamase","category_aro_description":"The TLA beta-lactamases are resistant to expanded-spectrum cephalosporins, and aztreonam but was susceptible to amikacin, cefotetan, and imipenem.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3318":{"model_id":"3318","model_name":"ADC-60","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"5253":{"protein_sequence":{"accession":"AFH53180.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVKTDQQVLTFFKDWKPKNSIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRANPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTTGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYVVLNAIKK"},"dna_sequence":{"accession":"JQ692087.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTTTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAGTATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAATTTCCAGATGAAGTAAAAACAGATCAGCAAGTTTTAACATTTTTTAAAGACTGGAAACCTAAAAACTCAATCGGTGAATATCGACAATATTCAAACCCAAGCATTGGTTTATTTGGAAAAGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGCTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTAAATCCACAAAAATATCCAGCAGATATTCAACGGGCAATTAATGAAACACATCAGGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTACCGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGTTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3004620","ARO_id":"42592","ARO_name":"ADC-60","CARD_short_name":"ADC-60","ARO_description":"An ADC beta-lactamase and cephalosporinase from Acinetobacter baumannii.","ARO_category":{"40543":{"category_aro_accession":"3003846","category_aro_cvterm_id":"40543","category_aro_name":"ADC beta-lactamase without carbapenemase activity","category_aro_description":"ADC beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases with extended-spectrum resistance to cephalosporins but not to carbapenems. ADC beta-lactamases are found in Acinetobacter sp. and Oligella urethralis.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2329":{"model_id":"2329","model_name":"MOX-9","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"5282":{"protein_sequence":{"accession":"AIG22447.1","sequence":"MQQQVRMTLLMASTLLWAGLAQATADTQADPLRPLVDASIRPVLKEHRIPGMAVAVLKDGKAHYFNYGVANRESGARVSEQTLFEIGSVSKTLTATLGAYAVVKGALKLDDKVSQHGPWLKGSAFDGITMAELATYSAGGLPLQFPDEVDSIDKMRAYYRQWTPAYRAGSHRQYSNPSIGLFGHLAAQSLGQPFEQLMSQTLLPGLGLEHTYLKVPAEAMANYAYGYSKEDKPIRVNPGVLADEAYGIKTSSADLLKFVGANMTGTGDEAMQQAIALTHKGVYSVGAMTQGLGWESYAYPVTEETLLAGNSGKVILEANPTAPASNETGSQVLFNKTGSTGGFGAYVAFVPAKGIGIVMLANRNYPIQARVETAHAILSKLAE"},"dna_sequence":{"accession":"KJ746495.1","fmin":"1420","fmax":"2572","strand":"+","sequence":"ATGCAACAACAGGTGCGGATGACATTGCTGATGGCGAGCACGCTGCTCTGGGCCGGTCTGGCCCAGGCCACGGCGGACACCCAGGCCGATCCCCTGCGCCCCCTGGTGGATGCCAGTATCCGGCCCGTGCTCAAGGAGCACCGGATCCCCGGCATGGCGGTGGCGGTGCTGAAAGATGGCAAGGCCCACTACTTCAACTACGGGGTGGCCAACCGGGAGAGCGGGGCCCGTGTCAGCGAGCAGACCCTGTTCGAGATTGGATCGGTCAGCAAGACTCTTACGGCAACGCTTGGGGCTTATGCCGTGGTGAAGGGGGCGCTCAAGCTCGATGACAAGGTGAGTCAGCATGGGCCCTGGCTGAAAGGATCGGCTTTTGACGGTATCACCATGGCCGAGCTCGCCACCTACAGCGCCGGGGGCTTGCCGCTGCAATTCCCCGACGAGGTGGATTCCATCGACAAGATGCGTGCCTACTATCGCCAGTGGACGCCTGCCTATCGGGCGGGCAGCCATCGCCAGTACTCCAACCCCAGCATCGGCCTGTTCGGCCATCTCGCGGCCCAGAGCCTGGGCCAACCCTTTGAACAGTTGATGAGCCAGACCCTGCTGCCCGGGCTTGGTCTCGAGCACACCTATCTCAAGGTCCCTGCCGAGGCCATGGCGAACTACGCCTATGGCTACTCGAAAGAGGACAAGCCTATCAGGGTCAACCCGGGGGTCCTGGCGGACGAGGCCTATGGCATCAAGACCAGCTCGGCGGATCTGCTGAAGTTTGTCGGCGCCAACATGACAGGCACCGGGGACGAGGCGATGCAGCAGGCGATTGCCCTGACCCACAAGGGGGTTTACTCGGTGGGTGCCATGACTCAGGGGCTCGGCTGGGAGAGTTATGCCTATCCCGTGACCGAAGAGACCTTGCTTGCAGGCAACTCGGGCAAGGTGATCCTCGAGGCCAACCCGACGGCGCCCGCCTCCAACGAGACGGGTAGCCAGGTGCTCTTCAACAAGACCGGCTCCACCGGCGGCTTTGGTGCCTATGTGGCCTTTGTGCCAGCCAAGGGGATTGGCATCGTCATGCTGGCCAATCGCAACTATCCCATCCAGGCCAGGGTAGAGACGGCCCACGCCATCCTGAGCAAGCTGGCCGAGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002191","ARO_id":"38591","ARO_name":"MOX-9","CARD_short_name":"MOX-9","ARO_description":"MOX-9 is a beta-lactamase found in Citrobacter freundii.","ARO_category":{"36222":{"category_aro_accession":"3000083","category_aro_cvterm_id":"36222","category_aro_name":"MOX beta-lactamase","category_aro_description":"MOX beta-lactamases are plasmid-mediated AmpC-type beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3319":{"model_id":"3319","model_name":"AAC(6')-Ian","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"330"}},"model_sequences":{"sequence":{"5297":{"protein_sequence":{"accession":"BAQ22025.1","sequence":"MLVQQGRLAIRALQKSDAPVMLRWLQDERVLEFYEGRDKHFDLQTVIEVFIEDQGETTPCLVLLDDKPLGYVQFYPLDSEDKQALELPVEDVIYGLDQFIGEPDFWGLGLGTELVSLVRDYLITDKAAQRLVLDPQSRNSRAIACYEKCGFEKLRLLPAHEMHEGQLQDCWLMQYYPARSSLMASSRPKI"},"dna_sequence":{"accession":"AP014611.1","fmin":"26117","fmax":"26690","strand":"-","sequence":"ATGCTGGTGCAGCAAGGCAGATTGGCAATACGTGCATTACAGAAAAGCGATGCGCCGGTGATGCTGCGCTGGCTGCAGGATGAGCGGGTGCTGGAATTTTACGAAGGGCGTGACAAACACTTCGATCTGCAAACGGTCATTGAAGTTTTTATCGAGGATCAGGGGGAAACCACACCGTGTCTGGTGTTACTGGATGATAAACCGCTTGGTTATGTGCAGTTCTACCCGCTGGATAGCGAAGATAAACAGGCGCTGGAACTACCGGTTGAGGATGTGATCTACGGGCTGGATCAGTTTATCGGCGAACCGGATTTCTGGGGGCTGGGACTTGGTACTGAGCTTGTCTCGCTGGTGCGCGATTATCTCATAACAGACAAGGCCGCACAGCGCCTTGTTCTCGACCCGCAAAGCCGCAACTCACGCGCAATTGCCTGCTATGAAAAATGCGGCTTTGAAAAACTCCGCTTGCTGCCCGCCCATGAAATGCATGAAGGGCAGCTGCAAGATTGCTGGCTGATGCAGTATTATCCCGCGCGCAGCAGTCTGATGGCTTCGTCACGCCCGAAAATATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36783","NCBI_taxonomy_name":"Serratia marcescens","NCBI_taxonomy_id":"615"}}}},"ARO_accession":"3003200","ARO_id":"39784","ARO_name":"AAC(6')-Ian","CARD_short_name":"AAC(6')-Ian","ARO_description":"AAC(6')-Ian is an amikacin acetyltransferase gene found on a transferable plasmid of the Serratia marcescens strain NUBL-11663. It catalyzes the transfer of an acetyl group from acetyl coenzyme A onto an amine at the 6'-position of various aminoglycosides.","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"A category of aminoglycoside N-acetyltransferase enzymes with modification regiospecificity based at the 6'-amino group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics through acetylation of the 6-amino group of the compound.","category_aro_class_name":"AMR Gene Family"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"46128":{"category_aro_accession":"3007378","category_aro_cvterm_id":"46128","category_aro_name":"2'-N-ethylnetilmicin","category_aro_description":"2'-N-ethylnetilmicin is an aminoglycoside antibiotic and a derivative of netilmicin.","category_aro_class_name":"Antibiotic"},"46129":{"category_aro_accession":"3007379","category_aro_cvterm_id":"46129","category_aro_name":"5-episisomicin","category_aro_description":"5-episosomicin is a semisynthetic aminoglycoside antibiotic similar to sisomicin.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3592":{"model_id":"3592","model_name":"FRI-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"575"}},"model_sequences":{"sequence":{"5790":{"protein_sequence":{"accession":"ALE30770.1","sequence":"MFFFKKGASTFIFLLCLPLNSFASQVINSVEEMRELETSFGGRIGVYILNPKNGKEFAYRQDERFPLCSSFKAFLAASVLKRTQEKSVSLDDMVEYSGRVMEKHSPVSEKYRKTGASVQTLAKAAIQYSDNGASNLLMERYIGGPEGLTAFMRSTGDTDFRLDRWELELNTAIPGDERDTSTPKAVAMSLKNIAFGSVLDAKNKSLLQEWLKGNTTGNARIRAAVPDKWVVGDKTGTCGFYGTANDVAILWTDANSPAVMAVYTTRPNQNDKHDEAVIKNAAKIAIKAVYGSYK"},"dna_sequence":{"accession":"KT192551.1","fmin":"3491","fmax":"4376","strand":"-","sequence":"ATGTTTTTTTTTAAAAAAGGTGCAAGTACATTTATTTTTTTGCTCTGTCTTCCATTGAACTCATTCGCCTCTCAGGTAATTAATAGTGTTGAGGAAATGAGGGAATTGGAAACTTCTTTTGGGGGGCGGATAGGTGTTTATATTTTAAACCCAAAAAATGGGAAAGAATTTGCCTACAGACAAGATGAGAGATTTCCTTTATGTAGTTCATTTAAGGCGTTCCTCGCTGCATCCGTATTAAAAAGAACTCAGGAGAAATCTGTTTCTCTTGATGATATGGTGGAATATTCTGGACGTGTTATGGAAAAGCATTCTCCTGTGTCAGAAAAATACCGTAAAACAGGAGCAAGCGTGCAGACTTTGGCCAAGGCAGCAATTCAGTATAGTGACAATGGAGCTTCTAATCTATTAATGGAAAGATACATAGGAGGTCCTGAGGGTTTGACTGCATTTATGCGGTCAACGGGAGACACTGACTTCAGGCTTGATCGTTGGGAATTAGAATTAAACACAGCTATTCCAGGCGATGAACGAGATACTTCAACTCCAAAAGCAGTGGCAATGAGCCTTAAAAATATTGCTTTTGGTTCAGTACTCGATGCTAAAAATAAATCATTGCTGCAGGAATGGCTTAAAGGCAACACTACTGGTAATGCGCGAATTAGAGCTGCGGTTCCAGATAAGTGGGTTGTTGGCGATAAAACAGGCACCTGTGGTTTTTATGGTACAGCCAATGATGTTGCTATTTTATGGACAGACGCCAATTCACCTGCAGTTATGGCTGTCTACACAACACGTCCTAATCAAAACGACAAACATGACGAAGCAGTAATTAAAAATGCTGCAAAAATAGCTATAAAGGCAGTTTATGGAAGTTATAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3004797","ARO_id":"42916","ARO_name":"FRI-1","CARD_short_name":"FRI-1","ARO_description":"FRI-1 is a carbapenem-hydrolyzing Class A beta-lactamase found in Enterobacter cloacae.","ARO_category":{"42915":{"category_aro_accession":"3004796","category_aro_cvterm_id":"42915","category_aro_name":"FRI beta-lactamase","category_aro_description":"FRI is a carbapenem-Hydrolyzing Class A beta-Lactamase from Enterobacter cloacae.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2331":{"model_id":"2331","model_name":"kdpE","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"5205":{"protein_sequence":{"accession":"AAC73788.1","sequence":"MTNVLIVEDEQAIRRFLRTALEGDGMRVFEAETLQRGLLEAATRKPDLIILDLGLPDGDGIEFIRDLRQWSAVPVIVLSARSEESDKIAALDAGADDYLSKPFGIGELQARLRVALRRHSATTAPDPLVKFSDVTVDLAARVIHRGEEEVHLTPIEFRLLAVLLNNAGKVLTQRQLLNQVWGPNAVEHSHYLRIYMGHLRQKLEQDPARPRHFITETGIGYRFML"},"dna_sequence":{"accession":"U00096.3","fmin":"721055","fmax":"721733","strand":"-","sequence":"GTGACAAACGTTCTGATTGTTGAAGATGAACAGGCTATTCGTCGCTTTCTGCGCACGGCGCTGGAGGGCGACGGGATGCGCGTCTTTGAGGCCGAAACGCTGCAACGCGGCTTGCTGGAAGCGGCAACCCGTAAGCCAGATTTGATTATTCTCGATCTCGGCCTGCCCGATGGTGATGGGATTGAGTTTATCCGCGACCTGCGCCAGTGGAGCGCGGTGCCGGTGATTGTGCTTTCCGCACGCAGCGAAGAGAGCGACAAAATCGCCGCGCTGGATGCCGGAGCGGATGATTATCTGAGTAAGCCGTTTGGCATTGGCGAATTGCAGGCCCGTCTGCGCGTCGCATTACGCCGCCACTCTGCCACCACCGCGCCCGATCCGCTGGTAAAATTTTCCGATGTTACCGTCGATTTAGCCGCCCGCGTGATTCACCGGGGTGAGGAAGAGGTGCATCTCACACCAATTGAGTTCCGCCTGCTGGCGGTGCTGCTCAACAATGCCGGAAAAGTACTCACCCAGCGCCAGCTCCTTAACCAGGTGTGGGGGCCAAACGCGGTCGAACACAGTCACTATTTGCGTATTTATATGGGACATCTGCGACAAAAACTGGAACAGGATCCCGCCCGCCCACGCCATTTCATTACTGAAACCGGTATTGGCTATCGGTTTATGCTTTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36849","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. MG1655","NCBI_taxonomy_id":"511145"}}}},"ARO_accession":"3003841","ARO_id":"40534","ARO_name":"kdpE","CARD_short_name":"kdpE","ARO_description":"kdpE is a transcriptional activator that is part of the two-component system KdpD\/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.","ARO_category":{"41098":{"category_aro_accession":"3004046","category_aro_cvterm_id":"41098","category_aro_name":"kdpDE","category_aro_description":"kdpDE is a two-component regulatory system in Escherichia coli, well studied for its role in potassium transport and homeostasis. kdpE is also implicated in virulence loci regulation and overexpression of kdpE is shown to confer resistance to aminoglycoside antibiotics.","category_aro_class_name":"AMR Gene Family"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2333":{"model_id":"2333","model_name":"LEN-26","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"5283":{"protein_sequence":{"accession":"AGB34168.1","sequence":"MRYVRLCVISLLANLPLAVYAGPQPLEQIKQSESQLSGRVGMVEMDLASGRTLAAWRADERFPMVSTFKVLLCGAVLARVDAGVEQLDRRIHYRQQDLVDYSPVSEKHLTDGMTIGELCAAAITMSDNSAGNLLLATVGGPAGLTAFLRQIGDNVTRLDRWETALNEALPGDMRDTTTPASMAATLRKLLTAQHLSARSQQQLLQWMVDDRVAGPLIRAVLPAGWFIADKTGAGERGARGIVALLGPDGKAERIVVIYMRDTPATIAERNQQIAAIGAALIEHWQR"},"dna_sequence":{"accession":"JX124390.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGTGTTATCTCCCTGTTAGCCAACCTGCCACTAGCGGTATACGCCGGTCCACAGCCGCTTGAGCAGATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTGGGGATGGTGGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCGATGAACGCTTTCCCATGGTGAGCACCTTTAAAGTGCTGCTGTGCGGCGCGGTGCTGGCGCGGGTGGATGCCGGGGTCGAACAACTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTACCGACGGGATGACGATCGGCGAACTCTGCGCCGCCGCCATCACCATGAGCGATAACAGCGCTGGCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCGGGATTGACCGCCTTTCTGCGCCAGATCGGTGACAACGTCACCCGTCTTGACCGCTGGGAAACGGCACTGAATGAGGCGCTTCCCGGCGACATGCGCGACACCACTACCCCGGCCAGCATGGCCGCCACGCTGCGTAAACTACTGACTGCGCAGCATCTGAGCGCCCGTTCACAGCAGCAGCTCCTGCAGTGGATGGTGGACGATCGGGTTGCCGGCCCGCTGATCCGCGCCGTGCTGCCGGCGGGCTGGTTTATCGCCGACAAGACCGGGGCTGGCGAACGGGGTGCGCGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAAGCGGAGCGCATTGTGGTGATTTATATGCGGGATACGCCGGCGACCATCGCCGAGCGTAACCAGCAGATCGCCGCTATCGGCGCGGCGCTGATCGAGCACTGGCAGCGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002474","ARO_id":"38874","ARO_name":"LEN-26","CARD_short_name":"LEN-26","ARO_description":"LEN-26 is a beta-lactamase found in Escherichia coli and Klebsiella pneumoniae.","ARO_category":{"36236":{"category_aro_accession":"3000097","category_aro_cvterm_id":"36236","category_aro_name":"LEN beta-lactamase","category_aro_description":"LEN beta-lactamases are chromosomal class A beta-lactamases that confer resistance to ampicillin, amoxicillin, carbenicillin, and ticarcillin but not to extended-spectrum beta-lactams.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2335":{"model_id":"2335","model_name":"ADC-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"5288":{"protein_sequence":{"accession":"AAO43172.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFINANLNPQKYPTDIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"AY177427.1","fmin":"1141","fmax":"2293","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCTCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAGTATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATACGGCGTCAAATCCACCTTACCGGATATGTTGAGTTTTATTAATGCCAACCTTAACCCACAAAAATATCCGACAGATATTCAACGGGCAATTAATGAAACACATCAAGGTCGCTATCAAGTAAATACCATGTATCAAGCGCTTGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAGCCTAATAAAGTGACTGCTATTTCAAAAGAGCCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACATATGTAGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36930","NCBI_taxonomy_name":"Oligella urethralis","NCBI_taxonomy_id":"90245"}}}},"ARO_accession":"3003848","ARO_id":"40545","ARO_name":"ADC-2","CARD_short_name":"ADC-2","ARO_description":"ADC-2 is a beta-lactamase found in Oligella urethralis.","ARO_category":{"40543":{"category_aro_accession":"3003846","category_aro_cvterm_id":"40543","category_aro_name":"ADC beta-lactamase without carbapenemase activity","category_aro_description":"ADC beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases with extended-spectrum resistance to cephalosporins but not to carbapenems. ADC beta-lactamases are found in Acinetobacter sp. and Oligella urethralis.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3322":{"model_id":"3322","model_name":"AAC(3)-IId","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"570"}},"model_sequences":{"sequence":{"5344":{"protein_sequence":{"accession":"ABS70977.1","sequence":"MHTRKAITEALQKLGVQTGDLLMVHASLKAIGPVEGGAETVVAALRSAVGPTGTVMGYASWDRSPYEETLNGARLDDEARRTWLPFDPATAGTYRGFGLLNQFLVQAPGARRSAHPDASMVAVGPLAETLTEPHELGHALGEGSPVERFVRLGGKALLLGAPLNSVTALHYAEAVADIPNKRWVTYEMPMLGRDGEVAWKTASDYDSNGILDCFAIEGKPDAVETIANAYVKLGRHREGVVGFAQCYLFDAQDIVTFGVTYLEKHFGTTPIVPPHEAVERSCEPSG"},"dna_sequence":{"accession":"EU022314.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCATACGCGGAAGGCAATAACGGAGGCGCTTCAAAAACTCGGAGTCCAAACCGGTGACCTCTTGATGGTGCATGCCTCACTTAAAGCGATTGGTCCGGTCGAAGGAGGAGCGGAGACGGTCGTTGCCGCGTTACGCTCCGCGGTTGGGCCGACTGGCACTGTGATGGGATACGCGTCGTGGGACCGATCACCCTACGAGGAGACTCTGAATGGCGCTCGGCTGGATGACGAAGCCCGCCGTACCTGGCTGCCGTTCGATCCCGCAACAGCCGGGACTTACCGTGGGTTCGGCCTGCTGAATCAATTTCTGGTTCAAGCCCCCGGCGCGCGGCGCAGCGCGCACCCCGATGCATCGATGGTCGCGGTTGGTCCGCTGGCTGAAACGCTGACGGAGCCTCACGAACTCGGTCACGCCTTGGGGGAAGGATCGCCCGTCGAGCGGTTCGTTCGCCTTGGCGGGAAGGCCCTGCTGTTGGGTGCGCCGCTAAACTCCGTTACCGCATTGCACTACGCCGAGGCGGTTGCCGATATCCCCAACAAACGGTGGGTGACGTATGAGATGCCGATGCTTGGAAGAGACGGTGAAGTCGCCTGGAAAACGGCATCGGATTACGATTCAAACGGCATTCTCGATTGCTTTGCTATCGAAGGAAAGCCGGATGCGGTTGAAACTATAGCAAATGCTTACGTGAAGCTCGGTCGCCATCGAGAAGGTGTCGTGGGCTTTGCTCAGTGCTACCTGTTCGACGCGCAGGACATCGTGACGTTCGGCGTCACCTATCTTGAGAAGCATTTCGGAACCACTCCGATCGTGCCTCCGCACGAGGCCGTCGAGCGCTCTTGCGAGCCTTCCGGTTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3004623","ARO_id":"42605","ARO_name":"AAC(3)-IId","CARD_short_name":"AAC(3)-IId","ARO_description":"AAC(3)-IId is a plasmid-encoded aminoglycoside acetyltransferase in E. coli.","ARO_category":{"36461":{"category_aro_accession":"3000322","category_aro_cvterm_id":"36461","category_aro_name":"AAC(3)","category_aro_description":"A category of aminoglycoside N-acetyltransferase enzymes with modification regiospecificity based at the 3-amino group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics through acetylation of the 3-amino group of the compound.","category_aro_class_name":"AMR Gene Family"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"46127":{"category_aro_accession":"3007377","category_aro_cvterm_id":"46127","category_aro_name":"6'-N-ethylnetilmicin","category_aro_description":"6'-N-ethylnetilmicin is an aminoglycoside antibiotic and a derivative of netilmicin.","category_aro_class_name":"Antibiotic"},"46128":{"category_aro_accession":"3007378","category_aro_cvterm_id":"46128","category_aro_name":"2'-N-ethylnetilmicin","category_aro_description":"2'-N-ethylnetilmicin is an aminoglycoside antibiotic and a derivative of netilmicin.","category_aro_class_name":"Antibiotic"},"46133":{"category_aro_accession":"3007382","category_aro_cvterm_id":"46133","category_aro_name":"gentamicin","category_aro_description":"Gentamicin is a commonly used aminoglycoside antibiotic derived from members of the Micromonospora genus of bacteria. It acts by binding the 30S ribosomal subunit, thus inhibiting protein synthesis. Gentamicin is typically used to treat Gram-negative infections of the repiratory and urinary tract, as well as infections of the bone and soft tissue. It also exhibits considerable nephrotoxicity and ototoxicity. Gentamicin is administered as a mixture of gentamicin type C (which makes about around 80% of the complex) and types A, B, and X (distributed in the remaining 20% of the complex).","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3324":{"model_id":"3324","model_name":"Erm(49)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"5349":{"protein_sequence":{"accession":"OPG86592.1","sequence":"MRNIKDTQNFLHSKELVRHLIGICNIKLDDVVIEIGPGKGIITNELAHKARKVVAIEFDEELYEKLKNKFQSNNKVDIIYGDILNYTPRIPSYCVFSNIPFNITSEILNKFLSDKKNEKMFLIMQYEPFIKYAGNPYGAETLRSMLYKPFFDMDLKYRFDPSDFKPAPQARIVLASFERKQFPDVKKEEEKLYKDFLAYIYTNKGETFFAKIKTLFSSNQIKRVWGQIKIDKTTKISEVPYESILKVFKLFFLYGTDANKQLVVNSFNNMNKQNNKLQKNHRNNSKAKSWNSNRKRKPYHRNNV"},"dna_sequence":{"accession":"MWVR01000009.1","fmin":"34384","fmax":"35299","strand":"-","sequence":"ATGAGAAATATTAAGGACACTCAAAATTTTTTACATAGCAAGGAGCTAGTTAGGCACTTAATAGGAATCTGTAATATAAAGTTGGACGATGTGGTTATAGAAATTGGTCCTGGAAAAGGAATAATTACTAACGAATTAGCTCATAAAGCAAGAAAGGTTGTTGCCATTGAATTTGATGAAGAACTATACGAAAAGCTAAAAAACAAATTTCAAAGCAACAATAAAGTTGACATAATTTATGGGGATATTTTAAACTATACTCCTAGAATTCCTAGTTATTGCGTTTTTTCAAACATTCCATTTAACATTACCTCTGAAATACTAAATAAGTTTTTGAGCGACAAAAAGAATGAGAAAATGTTTTTAATAATGCAATATGAGCCATTTATAAAATACGCAGGTAATCCATACGGAGCTGAAACATTAAGATCAATGCTTTATAAACCATTTTTTGATATGGATTTAAAATATAGATTCGATCCGTCTGATTTTAAGCCAGCACCACAAGCAAGAATCGTTTTGGCTTCCTTTGAAAGAAAGCAATTTCCTGATGTTAAAAAGGAAGAGGAAAAACTATATAAAGATTTTCTTGCATATATTTATACTAACAAGGGTGAAACATTCTTTGCAAAGATTAAAACATTGTTTTCAAGCAATCAAATTAAACGAGTTTGGGGTCAGATTAAGATAGACAAGACAACAAAAATAAGCGAAGTACCATATGAATCAATTTTAAAGGTTTTTAAGCTTTTTTTCTTGTACGGAACAGATGCTAATAAACAGTTAGTTGTAAATTCATTTAACAATATGAACAAGCAAAATAACAAGCTTCAAAAAAATCACAGAAACAATAGCAAGGCAAAAAGTTGGAATTCAAATCGTAAAAGAAAGCCTTATCATAGAAATAATGTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42610","NCBI_taxonomy_name":"Bifidobacterium breve","NCBI_taxonomy_id":"1685"}}}},"ARO_accession":"3004626","ARO_id":"42608","ARO_name":"Erm(49)","CARD_short_name":"Erm(49)","ARO_description":"Erm(49) is an rRNA methylase gene.","ARO_category":{"36699":{"category_aro_accession":"3000560","category_aro_cvterm_id":"36699","category_aro_name":"Erm 23S ribosomal RNA methyltransferase","category_aro_description":"Erm proteins are part of the RNA methyltransferase family and methylate A2058 (E. coli nomenclature) of the 23S ribosomal RNA conferring degrees of resistance to Macrolides, Lincosamides and Streptogramin b. This is called the MLSb phenotype.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4253":{"model_id":"4253","model_name":"ADC-188","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6628":{"protein_sequence":{"accession":"WP_136512057.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVKTDQQVLTFFKDWKPKNSIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGSLDAPAYSVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTTGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_064711.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAGTATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAATTTCCAGATGAAGTAAAAACAGATCAGCAAGTTTTAACATTTTTTAAAGACTGGAAACCTAAAAACTCAATCGGTGAATATCGACAATATTCAAACCCAAGCATTGGTTTATTTGGAAAAGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCTCACTCGATGCCCCAGCATATAGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTAAATCCACAAAAATATCCAGCAGATATTCAACGGGCAATTAATGAAACACATCAGGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTACCGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006357","ARO_id":"44819","ARO_name":"ADC-188","CARD_short_name":"ADC-188","ARO_description":"ADC-188 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2307":{"model_id":"2307","model_name":"carO","model_type":"protein knockout model","model_type_id":"40354","model_description":"Protein Knockout Models (PKM) reflect resistance by the absence of a gene product, most often deletion of a gene involved in antibiotic import, such as Vibrio cholerae OmpT. Like Protein Homolog Models (PHMs), PKMs include a reference sequence and a bitscore cut-off for detection using BLASTP but instead are designed to only report lack of detection under Perfect or Strict criteria. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff. This model type is still under development and not currently supported by the Resistance Gene Identifier (RGI) software.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"425"}},"model_sequences":{"sequence":{"3576":{"protein_sequence":{"accession":"AKL79742.1","sequence":"MKVLRVLVTTTALLAAGAAMADEAVVHDSYAFDKNQLIPVGARAEVGTTGYGGALLWQANPYVGLALGYNGGDISWRDDLSINGTKYDVDMDNNNVYLNAEIRPWGASTNRWAQGLYVAAGAAYLDNDYDLTKRSQDGTIKVNGNNYNFNGSVDGKLSYKNDIAPYLGFGFAPKINKNWGVFGEVGAYYTGNPTVNLKSNGTFVNVNGADFDKDLRAEENKIRNDDKYQWLPVGKVGVNFFW"},"dna_sequence":{"accession":"KP658477.1","fmin":"0","fmax":"729","strand":"+","sequence":"ATGAAAGTATTACGTGTTTTAGTGACAACTACAGCTTTACTTGCTGCTGGTGCTGCAATGGCGGATGAAGCTGTTGTTCATGACAGCTATGCATTCGATAAAAACCAATTAATTCCAGTAGGCGCTCGTGCTGAAGTAGGTACTACAGGTTACGGTGGTGCTTTGTTATGGCAAGCAAACCCATATGTAGGTTTAGCATTGGGTTATAACGGCGGTGACATTTCTTGGCGAGATGACTTATCAATTAATGGTACTAAATATGACGTTGATATGGATAATAACAACGTATATTTAAATGCCGAAATTCGCCCATGGGGTGCAAGTACTAACCGTTGGGCTCAAGGCTTATATGTAGCTGCAGGTGCGGCGTATTTAGATAACGATTATGACCTAACTAAACGTTCACAAGATGGGACTATTAAAGTAAATGGTAATAATTATAACTTTAATGGGTCAGTGGATGGTAAATTAAGTTATAAAAATGATATCGCTCCTTATTTAGGTTTTGGTTTTGCACCTAAAATCAATAAAAACTGGGGCGTATTCGGTGAAGTAGGTGCTTACTATACTGGTAACCCAACAGTAAATCTTAAATCAAATGGTACTTTTGTTAATGTTAACGGTGCTGACTTTGATAAAGATTTACGTGCTGAAGAAAATAAAATCCGTAACGACGATAAATATCAATGGTTGCCAGTTGGTAAAGTTGGTGTGAACTTCTTCTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3003808","ARO_id":"40493","ARO_name":"carO","CARD_short_name":"carO","ARO_description":"carO is a transmembrane beta-barrel involved in the influx of carbapenem antibiotics in Acinetobacter baumannii. Disruption of the carO gene by distinct insertion elements results in a loss of carO expression causing resistance to carbapenem antibiotics. Homologs of carO have been identified in genera Acinetobacter, Moraxella and Psychrobacter.","ARO_category":{"41447":{"category_aro_accession":"3004283","category_aro_cvterm_id":"41447","category_aro_name":"CarO porin","category_aro_description":"The imipenum resistance-associated CarO porin family is composed of the CarO porin originally identified in Acinetobacter baumannii. The loss of these porins is associated with imipenem and meropenem multi-drug resistance. The channels formed by CarO porins show slight cation selectivity.","category_aro_class_name":"AMR Gene Family"},"35990":{"category_aro_accession":"0000073","category_aro_cvterm_id":"35990","category_aro_name":"meropenem","category_aro_description":"Meropenem is an ultra-broad spectrum injectable antibiotic used to treat a wide variety of infections, including meningitis and pneumonia. It is a beta-lactam and belongs to the subgroup of carbapenem, similar to imipenem and ertapenem.","category_aro_class_name":"Antibiotic"},"36309":{"category_aro_accession":"3000170","category_aro_cvterm_id":"36309","category_aro_name":"imipenem","category_aro_description":"Imipenem is a broad-spectrum antibiotic and is usually taken with cilastatin, which prevents hydrolysis of imipenem by renal dehydropeptidase-I. It is resistant to hydrolysis by most other beta-lactamases. Notable exceptions are the KPC beta-lactamases and Ambler Class B enzymes.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36383":{"category_aro_accession":"3000244","category_aro_cvterm_id":"36383","category_aro_name":"reduced permeability to antibiotic","category_aro_description":"Reduction in permeability to antibiotic, generally through reduced production of porins, can provide resistance.","category_aro_class_name":"Resistance Mechanism"},"40429":{"category_aro_accession":"3003764","category_aro_cvterm_id":"40429","category_aro_name":"resistance by absence","category_aro_description":"Mechanism of antibiotic resistance conferred by deletion of gene (usually a porin).","category_aro_class_name":"Resistance Mechanism"}}},"2293":{"model_id":"2293","model_name":"Bacillus subtilis pgsA with mutation conferring resistance to daptomycin","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"3815":"A64V"},"Curated-R":{"3815":"A64V"},"experimental":{"3815":"A64V"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6284":{"protein_sequence":{"accession":"BAB95031.1","sequence":"MNIPNQITVFRVVLIPVFILFALVDFGFGNVSFLGGYEIRIELLISGFIFILASLSDFVDGYLARKWNLVTNMGKFLDPLADKLLVASALIVLVQLGLTNSVVAIIIIAREFAVTGLRLLQIEQGFVSAAGQLGKIKTAVTMVAITWLLLGDPLATLIGLSLGQILLYIGVIFTILSGIEYFYKGRDVFKQK"},"dna_sequence":{"accession":"BA000033.2","fmin":"1278585","fmax":"1279164","strand":"+","sequence":"ATGAATATTCCGAACCAGATTACGGTTTTTAGAGTAGTGTTAATACCAGTTTTTATATTGTTTGCGTTAGTTGATTTTGGATTTGGCAATGTGTCATTTCTAGGAGGATATGAAATAAGAATTGAGTTATTAATCAGTGGTTTTATTTTTATATTGGCTTCCCTTAGCGATTTTGTTGATGGTTATTTAGCTAGAAAATGGAATTTAGTTACAAATATGGGGAAATTTTTGGATCCATTAGCGGATAAATTATTAGTTGCAAGTGCTTTAATTGTACTTGTGCAACTAGGACTAACAAATTCTGTAGTAGCAATCATTATTATTGCCAGAGAATTTGCCGTAACTGGTTTACGTTTACTACAAATTGAACAAGGATTCGTAAGTGCAGCTGGTCAATTAGGTAAAATTAAAACAGCAGTTACTATGGTAGCAATTACTTGGTTGTTATTAGGTGATCCATTGGCAACATTGATTGGTTTGTCATTAGGACAAATTTTATTATACATTGGCGTTATTTTTACTATCTTATCTGGTATTGAATACTTTTATAAAGGTAGAGATGTTTTTAAACAAAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35515","NCBI_taxonomy_name":"Staphylococcus aureus subsp. aureus MW2","NCBI_taxonomy_id":"196620"}}}},"ARO_accession":"3003788","ARO_id":"40473","ARO_name":"Bacillus subtilis pgsA with mutation conferring resistance to daptomycin","CARD_short_name":"Bsub_pgsA_DAP","ARO_description":"Point mutations that occur within the Bacillus subtilis pgsA gene resulting in resistance to daptomycin.","ARO_category":{"39627":{"category_aro_accession":"3003080","category_aro_cvterm_id":"39627","category_aro_name":"daptomycin resistant pgsA","category_aro_description":"pgsA or phosphatidylglycerophosphate synthetase is an integral membrane protein involved in phospholipid biosynthesis. It is a CDP-diacylglycerol-glycerol-3-phosphate 3-phosphatidyltransferase. Laboratory experiments have detected mutations conferring daptomycin resistance in Entercoccus.","category_aro_class_name":"AMR Gene Family"},"35985":{"category_aro_accession":"0000068","category_aro_cvterm_id":"35985","category_aro_name":"daptomycin","category_aro_description":"Daptomycin is a novel lipopeptide antibiotic used in the treatment of certain infections caused by Gram-positive organisms. Daptomycin interferes with the bacterial cell membrane, reducing membrane potential and inhibiting cell wall synthesis.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2299":{"model_id":"2299","model_name":"Staphylococcus aureus walK with mutation conferring resistance to daptomycin","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"3875":"L10F","3887":"S221P","3888":"R263C"},"Curated-R":{"3875":"L10F","3887":"S221P","3888":"R263C"},"experimental":{"3875":"L10F","3887":"S221P","3888":"R263C"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1150"}},"model_sequences":{"sequence":{"3565":{"protein_sequence":{"accession":"CAG39047.1","sequence":"MKWLKQLQSLHTKLVIVYVLLIIIGMQIIGLYFTNNLEKELLDNFKKNITQYAKQLEISIEKVYDEKGSVNAQKDIQNLLSEYANRQEIGEIRFIDKDQIIIATTKQSNRSLINQKANDSSVQKALSLGQSNDHLILKDYGGGKDRVWVYNIPVKVDKKVIGNIYIESKINDVYNQLNNINQIFIVGTAISLLITVILGFFIARTITKPITDMRNQTVEMSRGNYTQRVKIYGNDEIGELALAFNNLSKRVQEAQANTESEKRRLDSVITHMSDGIIATDRRGRIRIVNDMALKMLGMAKEDIIGYYMLSVLSLEDEFKLEEIQENNDSFLLDLNEEEGLIARVNFSTIVQETGFVTGYIAVLHDVTEQQQVERERREFVANVSHELRTPLTSMNSYIEALEEGAWKDEELAPQFLSVTREETERMIRLVNDLLQLSKMDNESDQINKEIIDFNMFINKIINRHEMSTKDTTFIRDIPKKTIFTEFDPDKMTQVFDNVITNAMKYSRGDKRVEFHVKQNPLYNRMTIRIKDNGIGIPINKVDKIFDRFYRVDKARTRKMGGTGLGLAISKEIVEAHNGRIWANSVEGQGTSIFITLPCEVIEDGDWDE"},"dna_sequence":{"accession":"BX571856.1","fmin":"25616","fmax":"27443","strand":"+","sequence":"ATGAAGTGGCTAAAACAACTACAATCCCTTCATACTAAACTTGTAATTGTTTATGTATTACTGATTATCATTGGTATGCAAATTATCGGGCTGTATTTTACAAATAACCTTGAAAAAGAGCTGCTTGATAATTTTAAGAAGAATATTACGCAGTACGCTAAGCAATTAGAAATTAGTATTGAAAAAGTATATGACGAAAAGGGCTCCGTAAATGCACAAAAAGATATTCAAAATTTATTAAGTGAGTATGCCAACCGTCAAGAAATTGGAGAAATTCGTTTTATAGATAAAGACCAAATTATTATTGCGACGACGAAGCAGTCTAACCGTAGTCTAATCAATCAAAAAGCGAATGATAGTTCTGTCCAAAAAGCACTATCACTAGGACAATCAAACGATCATTTAATTTTAAAAGATTATGGCGGTGGTAAGGACCGTGTCTGGGTATATAATATCCCCGTTAAAGTCGATAAAAAGGTAATTGGTAATATTTATATCGAATCAAAAATTAATGACGTTTATAACCAATTAAATAATATAAATCAAATATTCATTGTTGGTACAGCTATTTCATTATTAATCACAGTCATCCTAGGATTCTTTATAGCGCGAACGATTACCAAACCAATCACCGATATGCGTAACCAGACGGTTGAAATGTCCAGAGGTAACTATACGCAACGTGTGAAGATTTATGGTAATGATGAAATTGGCGAATTAGCTTTAGCATTTAATAACTTGTCTAAACGTGTACAAGAAGCGCAGGCTAATACTGAAAGTGAGAAACGTAGACTGGACTCAGTTATCACCCATATGAGTGATGGTATTATTGCAACAGACCGTCGTGGACGTATTCGTATTGTCAATGATATGGCACTTAAGATGCTTGGTATGGCGAAAGAAGACATCATCGGATATTACATGTTAAGTGTATTAAGTCTTGAAGATGAATTTAAACTTGAAGAAATTCAAGAGAATAATGATAGTTTCTTATTAGATTTAAATGAAGAAGAAGGTCTAATCGCACGTGTTAACTTTAGTACGATTGTGCAGGAAACAGGATTTGTAACGGGTTATATCGCTGTGTTACATGACGTGACTGAACAACAACAAGTTGAACGTGAGCGTCGTGAATTTGTTGCCAATGTATCACATGAGTTACGTACACCTTTAACTTCTATGAATAGTTACATTGAAGCACTTGAAGAAGGTGCATGGAAAGATGAGGAACTTGCGCCACAATTTTTATCTGTTACCCGTGAAGAAACAGAACGAATGATTCGACTGGTCAATGACTTGCTACAGTTATCTAAAATGGATAATGAGTCTGATCAAATCAATAAAGAAATTATCGACTTTAACATGTTCATTAATAAAATTATTAATCGACATGAAATGTCTACGAAAGATACAACATTTATTCGAGATATTCCGAAAAAGACGATTTTCACAGAATTTGATCCTGATAAAATGACGCAAGTATTTGATAATGTCATTACAAATGCGATGAAATATTCTAGAGGCGATAAACGTGTCGAGTTCCACGTGAAACAAAATCCACTTTATAATCGAATGACGATTCGTATTAAAGATAATGGCATCGGTATTCCTATCAATAAAGTCGATAAGATATTCGACCGATTCTATCGTGTAGATAAGGCACGTACGCGTAAAATGGGTGGTACTGGATTAGGACTAGCCATTTCGAAAGAGATCGTGGAAGCTCACAATGGTCGTATTTGGGCAAACAGTGTAGAAGGTCAAGGCACATCTATCTTTATCACACTTCCATGTGAAGTCATTGAAGACGGTGATTGGGATGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35517","NCBI_taxonomy_name":"Staphylococcus aureus subsp. aureus MRSA252","NCBI_taxonomy_id":"282458"}}}},"ARO_accession":"3003794","ARO_id":"40479","ARO_name":"Staphylococcus aureus walK with mutation conferring resistance to daptomycin","CARD_short_name":"Saur_walK_DAP","ARO_description":"walK is the histidine kinase sensor of a two-component regulatory system controlling peptidoglycan metabolism through regulation of the expression of most of the peptidoglycan hydrolase genes. Mutations in the gene have been found that confer daptomycin resistance.","ARO_category":{"40480":{"category_aro_accession":"3003795","category_aro_cvterm_id":"40480","category_aro_name":"daptomycin resistant walK","category_aro_description":"Mutations to the walK gene, part of a cell wall metabolism 2-component regulatory system, confers resistance to antibiotics, specifically daptomycin.","category_aro_class_name":"AMR Gene Family"},"35985":{"category_aro_accession":"0000068","category_aro_cvterm_id":"35985","category_aro_name":"daptomycin","category_aro_description":"Daptomycin is a novel lipopeptide antibiotic used in the treatment of certain infections caused by Gram-positive organisms. Daptomycin interferes with the bacterial cell membrane, reducing membrane potential and inhibiting cell wall synthesis.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2315":{"model_id":"2315","model_name":"Acinetobacter baumannii parC conferring resistance to fluoroquinolones","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1400"},"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"9872":"S84L","9873":"V104I","9874":"D105E"},"Curated-R":{"9872":"S84L","9873":"V104I","9874":"D105E"},"clinical":{"9872":"S84L","9873":"V104I","9874":"D105E"}}},"model_sequences":{"sequence":{"6039":{"protein_sequence":{"accession":"WP_000202252.1","sequence":"MTSLAHHATENRSVAEFTEQAYLNYAMYVIMDRALPHISDGLKPVQRRIVYAMSELGLKSSGKPKKSARTVGDVLGKYHPHGDLACYEAMVLMAQPFSYRYPLIEGQGNWGSPDDPKSFAAMRYTEAKLSAYSELLLSELGQGTSEWQDNFDGSLKEPITLPARVPNILLNGTTGIAVGMATDIPPHNLREVVKGTIALIRNPQTSDEKLAEYIPAPDLPTKAEIITPPEELLKIQTTGRGSYRMRAVYTIEKNEIVITELPYQVSGSKVITQIADQMQAKKLPLVVDVRDESDHENPTRLVIVLRSNRIDAEAVMSHLFATTDLESSYRVNLNMIGEDGRPQVKSIRRILLEWIEIRKKTVTRRLQYHLNRIEKRLHILAGLLIAYLDIDTVIRIIREEDQPKPVLMEHFNIDEIQAEAILELKLRHLAKLEEMEIRHEQDELSAKAAIIREQLENPESLKNLIIGELKEDAKKFGDERRSPIVARAEAVQIKEQDLMPAETVTVVLSEAGWVRAAKGADVDAENLNYRAGDQYLSHAVGKTNQRVYFLDETGRSYALPISNLPSARGLGDPLSSKLSPASGVSFIQVYLDDDESELIAASSAGYGFKTQTKQLDTNAKAGKTFLTVPDKAKALPLISAQNMTHLAVLSSAGRLLILDLAELPNLNKGKGNKLIQLEGKEQILSMTTLNLDEIIQVVAGQQHLKLKGDDLQKYMGKRASKGQLLPRGYQKANKLLIQR"},"dna_sequence":{"accession":"NZ_CP009257.1","fmin":"3045126","fmax":"3047346","strand":"+","sequence":"ATGACCAGCCTTGCGCATCATGCGACAGAAAACCGCTCTGTAGCCGAATTTACTGAACAGGCTTACTTGAATTATGCCATGTACGTCATTATGGACCGTGCATTGCCGCATATCAGTGATGGCTTAAAGCCCGTACAGCGCCGTATTGTCTATGCTATGAGCGAGCTAGGCTTAAAAAGCAGTGGCAAGCCAAAAAAATCAGCGCGTACAGTGGGTGATGTACTTGGTAAATACCACCCACATGGTGACTTGGCATGTTATGAAGCCATGGTACTCATGGCTCAGCCATTTAGTTACCGCTATCCTTTAATCGAAGGTCAGGGGAACTGGGGTTCACCAGATGATCCTAAATCTTTTGCTGCGATGCGTTATACCGAAGCCAAACTCTCGGCTTATAGTGAATTATTGCTGAGCGAATTAGGTCAGGGCACTAGCGAATGGCAAGATAACTTTGATGGTTCTTTAAAAGAACCGATCACTTTACCTGCACGTGTACCTAATATTCTTCTTAATGGTACGACAGGTATTGCTGTCGGGATGGCAACTGATATCCCGCCACATAATTTGCGTGAAGTTGTAAAAGGCACAATTGCTTTAATCCGTAATCCGCAAACCTCGGACGAAAAATTAGCTGAATATATTCCGGCTCCGGATTTACCAACCAAAGCTGAAATTATTACCCCGCCAGAAGAATTACTCAAAATCCAGACCACTGGTCGTGGTAGTTACCGTATGCGAGCGGTATATACCATTGAGAAAAATGAAATCGTAATTACTGAGCTGCCATATCAAGTCTCTGGTTCTAAGGTAATTACTCAAATTGCTGACCAGATGCAGGCTAAAAAGCTGCCATTAGTCGTTGATGTGCGTGATGAATCGGATCATGAAAACCCGACACGACTCGTGATTGTACTGCGCTCTAACCGTATTGATGCGGAAGCAGTAATGAGTCACTTATTTGCGACCACCGATTTAGAATCAAGCTATCGTGTCAATTTAAACATGATTGGCGAAGATGGCCGTCCTCAGGTGAAATCAATTCGTCGTATTTTGCTTGAATGGATCGAGATCCGTAAAAAAACGGTAACTCGTCGTTTGCAGTACCATTTAAACCGTATTGAAAAGCGCCTGCATATTTTGGCAGGTCTTTTAATTGCTTATCTCGATATTGATACAGTCATTCGTATTATTCGTGAAGAAGACCAGCCTAAGCCAGTCTTGATGGAACACTTTAATATTGATGAGATACAGGCCGAGGCGATTTTAGAGCTTAAATTACGTCATTTGGCAAAGCTTGAAGAGATGGAAATTCGTCATGAACAAGATGAGCTTTCCGCGAAAGCTGCCATTATTCGTGAACAACTCGAAAATCCTGAATCTTTAAAAAATTTGATTATTGGCGAATTAAAAGAAGATGCGAAAAAGTTCGGTGATGAGCGCCGTTCTCCAATTGTTGCACGTGCTGAAGCGGTTCAAATTAAAGAACAGGATTTAATGCCAGCTGAAACGGTAACAGTCGTGTTGTCTGAAGCAGGCTGGGTTCGTGCGGCAAAAGGTGCGGATGTGGATGCTGAAAATCTGAACTACCGTGCTGGGGACCAATATTTAAGTCATGCTGTCGGGAAAACCAATCAGCGAGTTTACTTCCTTGATGAAACAGGGCGCAGCTATGCCTTGCCAATTAGTAACTTACCTTCAGCGAGAGGCTTGGGGGATCCATTAAGTTCTAAATTATCACCAGCAAGTGGCGTATCGTTTATTCAGGTTTATTTAGATGATGATGAGTCTGAGTTGATTGCTGCAAGTTCGGCAGGTTATGGTTTTAAAACGCAAACCAAGCAATTAGATACCAATGCGAAAGCCGGTAAGACATTCTTAACGGTTCCGGATAAGGCAAAGGCTTTACCACTTATTTCTGCCCAAAACATGACGCATTTGGCTGTACTGAGCTCAGCAGGGCGTTTGTTAATTTTAGATTTGGCAGAACTACCAAATTTAAATAAAGGTAAAGGTAATAAGTTGATACAACTTGAAGGCAAAGAGCAAATTTTATCCATGACAACCCTGAACTTAGATGAAATAATTCAGGTGGTTGCAGGTCAACAACATCTCAAATTAAAAGGTGATGATCTACAAAAATACATGGGTAAACGTGCTTCGAAAGGTCAGCTCTTACCACGTGGATATCAAAAAGCAAATAAACTGTTGATTCAGAGATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37046","NCBI_taxonomy_name":"Acinetobacter","NCBI_taxonomy_id":"469"}}}},"ARO_accession":"3003818","ARO_id":"40508","ARO_name":"Acinetobacter baumannii parC conferring resistance to fluoroquinolones","CARD_short_name":"Abau_parC_FLO","ARO_description":"Mutations in Acinetobacter baumannii parC that result in resistance to fluoroquinolones.","ARO_category":{"36913":{"category_aro_accession":"3000619","category_aro_cvterm_id":"36913","category_aro_name":"fluoroquinolone resistant parC","category_aro_description":"ParC is a subunit of topoisomerase IV, which decatenates and relaxes DNA to allow access to genes for transcription or translation. Point mutations in ParC prevent fluoroquinolone antibiotics from inhibiting DNA synthesis, and confer low-level resistance. Higher-level resistance results from both gyrA and parC mutations.","category_aro_class_name":"AMR Gene Family"},"35942":{"category_aro_accession":"0000023","category_aro_cvterm_id":"35942","category_aro_name":"enoxacin","category_aro_description":"Enoxacin belongs to a group called fluoroquinolones. Its mode of action depends upon blocking bacterial DNA replication by binding itself to DNA gyrase and causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37004":{"category_aro_accession":"3000660","category_aro_cvterm_id":"37004","category_aro_name":"lomefloxacin","category_aro_description":"Lomefloxacin is a difluoropiperazinyl quinolone, sharing similar activities with other fluoroquinolones. It is used to treat urinary tract infections. Relative to other fluoroquinolones, it has a longer half life and has higher serum concentrations.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37007":{"category_aro_accession":"3000663","category_aro_cvterm_id":"37007","category_aro_name":"ofloxacin","category_aro_description":"Ofloxacin is a 6-fluoro, 7-piperazinyl quinolone with a methyl-substituted oxazine ring. It has a broad spectrum of activity including many enterobacteria and mycoplasma but most anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"37008":{"category_aro_accession":"3000664","category_aro_cvterm_id":"37008","category_aro_name":"trovafloxacin","category_aro_description":"Trovafloxacin is a trifluoroquinalone with a broad spectrum of activity that acts by inhibiting the uncoiling of supercoiled DNA. While potent against many Gram-positive and Gram-negative bacteria, it is less active against pseudomonads and Cl. difficile. It is usually taken as the prodrug trovafloxacin mesylate or alatrofloxacin mesylate for oral or intravenous administration, respectively.","category_aro_class_name":"Antibiotic"},"37009":{"category_aro_accession":"3000665","category_aro_cvterm_id":"37009","category_aro_name":"grepafloxacin","category_aro_description":"Grepafloxacin is a broad-spectrum antibacterial quinoline. It is no longer taken due to its high toxicity.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"37142":{"category_aro_accession":"3000762","category_aro_cvterm_id":"37142","category_aro_name":"pefloxacin","category_aro_description":"Pefloxacin is structurally and functionally similar to norfloxacin. It is poorly active against mycobacteria, while anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2308":{"model_id":"2308","model_name":"Acinetobacter baumannii OprD conferring resistance to imipenem","model_type":"protein knockout model","model_type_id":"40354","model_description":"Protein Knockout Models (PKM) reflect resistance by the absence of a gene product, most often deletion of a gene involved in antibiotic import, such as Vibrio cholerae OmpT. Like Protein Homolog Models (PHMs), PKMs include a reference sequence and a bitscore cut-off for detection using BLASTP but instead are designed to only report lack of detection under Perfect or Strict criteria. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff. This model type is still under development and not currently supported by the Resistance Gene Identifier (RGI) software.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"4419":{"protein_sequence":{"accession":"AHB92962.1","sequence":"MLKAQKLTLAVLISAAIISSAQASEQSEAKGFVEDANGSILFRTGYISRDKKNGVDDTSSFAQTAIVNIESGFTPGIVGFGVGVVGDGSFKIGANKNAGNNMIPRETGFNDEGVLTKGAGDSYDHWARGGGSVKARFSNTTVRYGTQVLDLPVLASNTARLVPEYFTGTLLTSHEIKDLEVIAGKFTKDQYSDQVNTDGRHLDRAIVWGAKYKFDDNLNASYYGLDSKDKLERHYLNVNYKQPLANDSSLTYDFSGYHTKFDEGASTYSQTTDDLSNRKNNIWAISTAYNTGPHNIMVAYQQNSGNVGYDYGENADGGQSIYLPNSYLSDFIGNDEKSAQIQYSLDFGKLGVLPGLNWTTAFVYGWDIKVKGLTDDAEEREFFNQVKYTVQSGFAKDASLRIRNSYYRASNAYQTNAYIGDTNEWRIFLDIPVKLF"},"dna_sequence":{"accession":"CP006768.1","fmin":"3513469","fmax":"3514780","strand":"+","sequence":"ATGCTAAAAGCACAAAAACTTACATTAGCAGTTCTCATTTCTGCGGCAATAATTTCCTCAGCTCAGGCAAGCGAGCAAAGTGAGGCAAAAGGATTTGTTGAAGATGCGAACGGTTCTATTCTCTTCCGTACAGGTTACATCAGCCGTGACAAAAAAAATGGCGTAGATGACACCAGTTCATTTGCTCAAACAGCAATCGTAAATATTGAATCTGGCTTTACTCCTGGTATTGTTGGTTTCGGTGTGGGCGTTGTTGGTGACGGTTCATTTAAAATCGGCGCAAATAAAAACGCTGGCAATAACATGATTCCACGTGAAACTGGTTTCAATGACGAAGGCGTGCTAACAAAAGGTGCTGGTGATTCTTACGATCACTGGGCTCGTGGTGGCGGTAGCGTAAAAGCACGTTTCTCAAATACAACTGTACGTTACGGTACTCAAGTACTTGACCTGCCAGTTCTTGCAAGTAATACAGCACGTTTAGTGCCTGAATACTTCACAGGTACTTTATTAACCAGCCATGAAATTAAAGATTTAGAAGTGATTGCTGGTAAATTCACTAAAGATCAATATTCTGACCAAGTGAACACCGATGGCCGTCATCTTGACCGTGCAATTGTGTGGGGTGCTAAATACAAGTTTGATGATAATTTAAATGCATCTTACTATGGTTTAGATAGTAAAGATAAACTTGAACGTCATTACCTCAATGTAAACTATAAACAACCATTGGCGAATGACAGCTCATTAACTTACGATTTCAGTGGTTATCACACTAAGTTTGATGAAGGTGCTTCTACTTATTCACAAACTACTGATGACCTATCTAACCGTAAAAACAATATTTGGGCAATTTCTACAGCCTATAATACTGGTCCACATAACATCATGGTGGCTTACCAACAAAACAGTGGTAATGTCGGTTATGACTATGGTGAAAATGCTGACGGCGGTCAAAGTATTTATCTGCCAAATTCTTATTTGTCTGATTTCATCGGTAATGATGAAAAATCAGCACAAATCCAATATAGCCTCGATTTCGGTAAGTTAGGCGTATTACCTGGCTTAAACTGGACCACTGCATTTGTATACGGTTGGGACATCAAAGTTAAAGGTTTAACTGATGATGCTGAAGAACGCGAATTCTTTAACCAAGTGAAATACACAGTTCAAAGTGGTTTCGCTAAAGATGCAAGCCTTCGTATTCGTAACTCATACTACCGTGCAAGCAATGCTTATCAAACGAATGCCTACATCGGTGATACCAATGAATGGCGTATTTTCTTAGATATTCCTGTGAAATTATTCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40496","NCBI_taxonomy_name":"Acinetobacter baumannii ZW85-1","NCBI_taxonomy_id":"1400867"}}}},"ARO_accession":"3003809","ARO_id":"40495","ARO_name":"Acinetobacter baumannii OprD conferring resistance to imipenem","CARD_short_name":"Abau_OprD_IPM","ARO_description":"An outer member protein (OMP) found in Acinetobacter baumannii involved in the uptake of imipenem and basic amino acids. This porin is homologous to Pseudomonas aeruginosa OprD, which performs an identical function.","ARO_category":{"41442":{"category_aro_accession":"3004278","category_aro_cvterm_id":"41442","category_aro_name":"Outer Membrane Porin (Opr)","category_aro_description":"The Opr family consists of porins in Pseudomonas species, and other Gram-negative bacteria, that exhibit a variety of substrate selectivities.","category_aro_class_name":"AMR Gene Family"},"36309":{"category_aro_accession":"3000170","category_aro_cvterm_id":"36309","category_aro_name":"imipenem","category_aro_description":"Imipenem is a broad-spectrum antibiotic and is usually taken with cilastatin, which prevents hydrolysis of imipenem by renal dehydropeptidase-I. It is resistant to hydrolysis by most other beta-lactamases. Notable exceptions are the KPC beta-lactamases and Ambler Class B enzymes.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36383":{"category_aro_accession":"3000244","category_aro_cvterm_id":"36383","category_aro_name":"reduced permeability to antibiotic","category_aro_description":"Reduction in permeability to antibiotic, generally through reduced production of porins, can provide resistance.","category_aro_class_name":"Resistance Mechanism"},"40429":{"category_aro_accession":"3003764","category_aro_cvterm_id":"40429","category_aro_name":"resistance by absence","category_aro_description":"Mechanism of antibiotic resistance conferred by deletion of gene (usually a porin).","category_aro_class_name":"Resistance Mechanism"}}},"2328":{"model_id":"2328","model_name":"MUS-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"5281":{"protein_sequence":{"accession":"AKN19901.1","sequence":"MHRILSVITMLICTTLVHAQSDKLKIKQLNDNMYIYTTYQEFQGVTYSSNSMYVLTDEGAILIDTPWDKDQYEPLLEYIRSNHNKEVKWVITTHFHEDRSGGLGYFNSIGAQTYTYALTNEILKERNEPQAQYSFNKEKQFTFGNEKLAVYFLGEGHSLDNTVVWFPKEEVLYGGCLIKSAEATTIGNIADGNVIAWPKTIEAVKQKFKNAKVIIPGHDEWDMIGHIENTERILSAYNQQHSTKND"},"dna_sequence":{"accession":"KP658209.1","fmin":"0","fmax":"741","strand":"+","sequence":"ATGCACAGAATACTTAGTGTCATAACGATGTTAATCTGTACTACATTAGTACACGCTCAATCTGACAAGCTAAAAATCAAACAACTCAATGATAATATGTATATATACACTACTTATCAAGAGTTTCAAGGAGTAACATACTCTTCTAATTCGATGTACGTACTGACAGATGAAGGTGCTATTCTAATAGACACACCTTGGGATAAAGATCAGTACGAACCTCTATTAGAGTACATCAGATCGAATCATAACAAAGAGGTTAAATGGGTCATCACTACCCACTTCCACGAAGATCGTTCTGGTGGATTAGGTTACTTTAACAGTATAGGAGCACAGACGTATACCTATGCATTGACCAATGAAATATTAAAAGAACGCAATGAACCACAAGCTCAATATTCTTTTAATAAAGAAAAACAGTTTACCTTTGGCAATGAGAAGTTGGCTGTATACTTTTTAGGAGAAGGACATTCACTAGATAATACCGTAGTCTGGTTTCCAAAAGAAGAAGTACTATACGGAGGGTGCCTGATTAAGAGTGCCGAAGCTACCACTATAGGTAATATAGCCGATGGTAACGTGATAGCTTGGCCTAAGACTATCGAAGCCGTAAAACAAAAATTTAAGAATGCTAAAGTCATTATACCAGGACATGATGAATGGGATATGATAGGGCATATCGAGAATACTGAGCGTATATTATCAGCATACAATCAACAACATTCAACTAAAAACGATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39072","NCBI_taxonomy_name":"Myroides odoratimimus","NCBI_taxonomy_id":"76832"}}}},"ARO_accession":"3003842","ARO_id":"40535","ARO_name":"MUS-2","CARD_short_name":"MUS-2","ARO_description":"MUS-2 is a chromosome-encoded beta-lactamase from Myroides odoratimimus.","ARO_category":{"41143":{"category_aro_accession":"3004067","category_aro_cvterm_id":"41143","category_aro_name":"MUS beta-lactamase","category_aro_description":"Subclass B1 (metallo-) beta-lactamases found in Myroides spp., which confer resistance to carbapenam class beta-lactamase antibiotics.","category_aro_class_name":"AMR Gene Family"},"35981":{"category_aro_accession":"0000064","category_aro_cvterm_id":"35981","category_aro_name":"amoxicillin","category_aro_description":"Amoxicillin is a moderate-spectrum, bacteriolytic, beta-lactam antibiotic used to treat bacterial infections caused by susceptible microorganisms. A derivative of penicillin, it has a wider range of treatment but remains relatively ineffective against Gram-negative bacteria. It is commonly taken with clavulanic acid, a beta-lactamase inhibitor. Like other beta-lactams, amoxicillin interferes with the synthesis of peptidoglycan.","category_aro_class_name":"Antibiotic"},"35995":{"category_aro_accession":"0000078","category_aro_cvterm_id":"35995","category_aro_name":"piperacillin","category_aro_description":"Piperacillin is an acetylureidopenicillin and has an extended spectrum of targets relative to other beta-lactam antibiotics. It inhibits cell wall synthesis in bacteria, and is usually taken with the beta-lactamase inhibitor tazobactam to overcome penicillin-resistant bacteria.","category_aro_class_name":"Antibiotic"},"40523":{"category_aro_accession":"3003832","category_aro_cvterm_id":"40523","category_aro_name":"ticarcillin","category_aro_description":"Ticarcillin is a carboxypenicillin used for the treatment of Gram-negative bacteria, particularly P. aeruginosa. Ticarcillin's antibiotic properties arise from its ability to prevent cross-linking of peptidoglycan during cell wall synthesis, when the bacteria try to divide, causing cell death.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3328":{"model_id":"3328","model_name":"AAC(6')-Im","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"5375":{"protein_sequence":{"accession":"AAK63041.1","sequence":"MLEKKRVSFRPMNEDDLVLMLKWLTDDRVLEFYDGRDKKHTQKTIREHYTEQWADEIYRVIIEYDTIPIGYAQIYRIQGELFDEYNYHETEEKIYAMDQFIGEPEYWNMGIGAEYCRVVCQYLRTEMDADAVILDPRKNNLRAVRAYQKAGFKIIKELPEHELHEGKKEDCVLMEWRV"},"dna_sequence":{"accession":"AF337947.1","fmin":"1214","fmax":"1751","strand":"+","sequence":"ATGTTGGAAAAAAAGCGAGTTTCCTTTCGCCCGATGAATGAGGATGATTTAGTTCTAATGTTAAAATGGCTGACAGATGACCGTGTTCTTGAATTCTACGACGGTAGAGATAAAAAACATACACAGAAAACGATTCGTGAGCATTATACAGAGCAATGGGCGGATGAGATTTATCGAGTCATCATTGAATATGATACAATTCCTATCGGTTACGCACAAATATATAGAATTCAGGGGGAACTTTTCGACGAATATAATTACCATGAGACGGAAGAAAAGATTTATGCGATGGACCAATTTATCGGTGAGCCGGAATATTGGAATATGGGAATCGGTGCAGAATATTGCAGAGTAGTATGCCAATATCTACGAACGGAAATGGATGCCGATGCGGTGATTCTTGACCCACGAAAAAATAATCTACGAGCAGTACGAGCATATCAGAAGGCAGGATTTAAAATAATTAAGGAACTTCCCGAACATGAGCTACACGAGGGGAAAAAGGAAGATTGTGTGCTGATGGAATGGAGAGTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3004629","ARO_id":"42615","ARO_name":"AAC(6')-Im","CARD_short_name":"AAC(6')-Im","ARO_description":"AAC(6')-Im is an aminoglycoside acetyltransferase encoded by plasmids in E. coli, and E. faecium.","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"A category of aminoglycoside N-acetyltransferase enzymes with modification regiospecificity based at the 6'-amino group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics through acetylation of the 6-amino group of the compound.","category_aro_class_name":"AMR Gene Family"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"46128":{"category_aro_accession":"3007378","category_aro_cvterm_id":"46128","category_aro_name":"2'-N-ethylnetilmicin","category_aro_description":"2'-N-ethylnetilmicin is an aminoglycoside antibiotic and a derivative of netilmicin.","category_aro_class_name":"Antibiotic"},"46129":{"category_aro_accession":"3007379","category_aro_cvterm_id":"46129","category_aro_name":"5-episisomicin","category_aro_description":"5-episosomicin is a semisynthetic aminoglycoside antibiotic similar to sisomicin.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3332":{"model_id":"3332","model_name":"ADC-67","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"5403":{"protein_sequence":{"accession":"AFP89364.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVKTDQQVLTFFKDWKPKNSIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTTGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYVVLNAIKK"},"dna_sequence":{"accession":"JX169789.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAGTATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAATTTCCAGATGAAGTAAAAACAGATCAGCAAGTTTTAACATTTTTTAAAGACTGGAAACCTAAAAACTCAATCGGTGAATATCGACAATATTCAAACCCAAGCATTGGTTTATTTGGAAAAGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTAAATCCACAAAAATATCCAGCAGATATTCAACGGGCAATTAATGAAACACATCAGGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTACCGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGTTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3004633","ARO_id":"42622","ARO_name":"ADC-67","CARD_short_name":"ADC-67","ARO_description":"A class C beta-lactamase and cephalosporinase from Acinetobacter baumannii.","ARO_category":{"40543":{"category_aro_accession":"3003846","category_aro_cvterm_id":"40543","category_aro_name":"ADC beta-lactamase without carbapenemase activity","category_aro_description":"ADC beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases with extended-spectrum resistance to cephalosporins but not to carbapenems. ADC beta-lactamases are found in Acinetobacter sp. and Oligella urethralis.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3333":{"model_id":"3333","model_name":"ADC-73","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"680"}},"model_sequences":{"sequence":{"5411":{"protein_sequence":{"accession":"ALA14808.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVKTDQQVLTFFKDWKPKNSIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYSVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTTGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"KP881233.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAGTATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAATTTCCAGATGAAGTAAAAACAGATCAGCAAGTTTTAACATTTTTTAAAGACTGGAAACCTAAAAACTCAATCGGTGAATATCGACAATATTCAAACCCAAGCATTGGTTTATTTGGAAAAGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATAGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTAAATCCACAAAAATATCCAGCAGATATTCAACGGGCAATTAATGAAACACATCAGGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTACCGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3004634","ARO_id":"42623","ARO_name":"ADC-73","CARD_short_name":"ADC-73","ARO_description":"A class C ADC beta-lactamase and cephalosporinase found in Acinetobacter baumannii.","ARO_category":{"40543":{"category_aro_accession":"3003846","category_aro_cvterm_id":"40543","category_aro_name":"ADC beta-lactamase without carbapenemase activity","category_aro_description":"ADC beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases with extended-spectrum resistance to cephalosporins but not to carbapenems. ADC beta-lactamases are found in Acinetobacter sp. and Oligella urethralis.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3334":{"model_id":"3334","model_name":"AAC(6')-Il","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"8368":{"protein_sequence":{"accession":"AAA90937.1","sequence":"MDSSPLVRPVETTDSASWLSMRCELWPDGTCQEHQSEIAEFLSGKVARPAAVLIAVAPDGEALGFAELSIRPYAEECYSGNVAFLEGWYVVPSARRQGVGVALVKAAEHWARGRGCTEFASDTQLTNSASTSAHLAAGFTEVAQVRCFRKPL"},"dna_sequence":{"accession":"U13880.2","fmin":"308","fmax":"767","strand":"+","sequence":"ATGGATAGTTCGCCGCTCGTCAGGCCTGTTGAAACTACCGATTCGGCCAGTTGGCTAAGCATGCGCTGTGAGCTGTGGCCAGATGGCACATGTCAAGAGCACCAGTCAGAGATCGCAGAATTTCTGTCCGGAAAAGTCGCCCGGCCTGCTGCTGTCCTCATTGCTGTAGCACCCGACGGAGAAGCACTAGGGTTTGCCGAGCTTTCGATCCGCCCGTATGCGGAGGAGTGCTACTCCGGCAACGTTGCGTTCTTGGAGGGTTGGTACGTTGTGCCAAGTGCGCGGCGTCAGGGCGTAGGTGTAGCTCTGGTAAAAGCCGCCGAGCATTGGGCTCGTGGTCGCGGATGCACCGAATTCGCCTCCGACACTCAACTTACCAACAGCGCAAGCACCTCGGCGCACCTGGCGGCTGGATTCACGGAGGTTGCTCAAGTACGCTGCTTCCGGAAACCGTTGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36770","NCBI_taxonomy_name":"Klebsiella aerogenes","NCBI_taxonomy_id":"548"}}}},"ARO_accession":"3004635","ARO_id":"42624","ARO_name":"AAC(6')-Il","CARD_short_name":"AAC(6')-Il","ARO_description":"AAC(6')-Il is an aminoglycoside acetyltransferase encoded by plasmids and integrons in Enterobacter cloaecae and Klebsiella aerogenes.","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"A category of aminoglycoside N-acetyltransferase enzymes with modification regiospecificity based at the 6'-amino group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics through acetylation of the 6-amino group of the compound.","category_aro_class_name":"AMR Gene Family"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"46128":{"category_aro_accession":"3007378","category_aro_cvterm_id":"46128","category_aro_name":"2'-N-ethylnetilmicin","category_aro_description":"2'-N-ethylnetilmicin is an aminoglycoside antibiotic and a derivative of netilmicin.","category_aro_class_name":"Antibiotic"},"46129":{"category_aro_accession":"3007379","category_aro_cvterm_id":"46129","category_aro_name":"5-episisomicin","category_aro_description":"5-episosomicin is a semisynthetic aminoglycoside antibiotic similar to sisomicin.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3335":{"model_id":"3335","model_name":"qnrE1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"5434":{"protein_sequence":{"accession":"APC93960.1","sequence":"MALIFEGEKIGRNRFTGEKIENAIFRNCDFSGTDLTSSEFIGCQFYDRESQQGGNFNRAQLKDAIFKSCDLSMADFRHSNALGIEIRECRAQGADFRGASFMNMITTRTWFCCAYITKSNLSYANFSKVVLEKCELWENRWNGAQILGATFSGSDLSGGEFSSFDWRAANFTHCDLTNSELGDLDVRGIDLQGVKLDSYQVSQLMERLGIAVLG"},"dna_sequence":{"accession":"KY073238.1","fmin":"1678","fmax":"2323","strand":"+","sequence":"ATGGCATTGATTTTTGAAGGCGAAAAAATAGGTCGTAACCGTTTTACCGGAGAGAAAATAGAGAATGCAATCTTTCGTAACTGCGACTTTTCCGGTACGGATTTAACCAGCTCGGAGTTTATCGGCTGTCAGTTCTATGACCGGGAAAGCCAGCAGGGCGGTAACTTTAATCGGGCGCAACTTAAAGATGCTATTTTCAAAAGCTGCGATTTATCGATGGCGGATTTCAGGCATTCAAATGCATTAGGCATCGAAATCCGTGAATGCAGGGCGCAAGGGGCCGATTTCCGCGGGGCCAGTTTTATGAACATGATCACCACCCGTACCTGGTTTTGCTGTGCTTACATCACAAAAAGCAACCTGAGCTATGCCAATTTTTCGAAGGTGGTTCTGGAAAAATGCGAGCTGTGGGAAAACCGCTGGAACGGCGCGCAGATACTTGGCGCCACCTTTAGCGGCTCGGATCTGTCTGGGGGCGAGTTCTCATCCTTTGACTGGCGAGCGGCCAATTTTACCCACTGCGATCTGACCAATTCAGAACTGGGTGATCTGGACGTGCGGGGTATTGATTTGCAGGGCGTCAAACTGGACAGCTATCAGGTTTCCCAGTTGATGGAGCGACTTGGCATCGCTGTTTTAGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3004636","ARO_id":"42625","ARO_name":"qnrE1","CARD_short_name":"qnrE1","ARO_description":"qnrE1 is a member of the qnrE family of plasmid-borne (fluoro)quinolone-resistance genes, with chromosomal origins from Enterobacter spp.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3336":{"model_id":"3336","model_name":"qnrE2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"5440":{"protein_sequence":{"accession":"AQV34023.1","sequence":"MALIFEGEKIGRNRFTGEKIENAIFRNCDFSGTDLTSSEFIGCQFYDRASQQGGNFNRAQLKDAIFKSCDLSMADFRHSNALGIEIRECRAQGADFRGASFMNMITTRTWFCCAYITKSNLSYANFSKVVLEKCELWENRWNGAQILGATFSGSDLSGGEFSSFDWRAANFTHCDLTNSELGDLDVRGIDLQGVKLDSYQVSQLMERLGIVVLG"},"dna_sequence":{"accession":"CP018961.1","fmin":"163458","fmax":"164103","strand":"-","sequence":"ATGGCATTGATTTTTGAAGGCGAAAAAATAGGTCGTAACCGTTTTACCGGCGAGAAAATTGAGAATGCAATCTTTCGTAACTGCGACTTTTCCGGTACGGATTTAACGAGCTCGGAGTTTATCGGCTGTCAGTTCTATGACCGGGCAAGCCAGCAGGGCGGTAACTTTAATCGGGCGCAACTTAAAGATGCTATTTTCAAAAGCTGCGATTTATCGATGGCGGATTTCAGGCATTCAAATGCATTAGGCATCGAAATCCGTGAATGCAGGGCACAAGGGGCCGATTTCCGCGGGGCCAGTTTTATGAACATGATCACCACCCGTACCTGGTTTTGCTGTGCTTACATCACAAAAAGCAACCTGAGCTATGCCAATTTTTCGAAGGTGGTTCTGGAAAAATGCGAGCTGTGGGAAAACCGCTGGAACGGCGCGCAGATACTTGGCGCTACCTTTAGCGGCTCGGATCTGTCTGGGGGCGAGTTCTCATCCTTTGACTGGCGAGCGGCCAATTTTACCCACTGCGATCTGACCAATTCAGAACTGGGTGATCTGGACGTGAGGGGTATTGATTTGCAGGGCGTCAAACTGGACAGCTATCAGGTTTCCCAGTTGATGGAGCGACTTGGCATCGTTGTTTTAGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3004637","ARO_id":"42627","ARO_name":"qnrE2","CARD_short_name":"qnrE2","ARO_description":"qnrE2 is a qnrE-member of plasmid-borne (fluoro)quinolone-resistance genes.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3337":{"model_id":"3337","model_name":"Corynebacterium striatum tetA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"900"}},"model_sequences":{"sequence":{"5448":{"protein_sequence":{"accession":"NP_862226.1","sequence":"MKTYSWFVPPAPPADDPARLHPARWSSGNRVVRDMVGAYPGVLVLHILSYLIGSGISAFVPVVVGMIVDGLVGEEKFNAWWLFAVLVGIFIIQFIGEATGDGLATASVRRVTHNAQQHLSSGVLRRGAGAMSPGTVLNTIDADANTVGRYRELLSFPLMAIGYAVCAMVAMWSVSPWISLAIPASALIIALFAAWTAGPVTRVSLKRRAAEADVAGLATDASQGIRTVKGLGAGATVATRFHAETAKANGLMLTHLRVEVWLGFARFCVAWLCNLGIVGLSAWMTLRGEITPGQLTSVALLVQPALTMAGLAFGDLASGWGRAVASGQRIEQLHHAGDDAAGPEPTDTPVPGAGLWILEPAERSYATAAAWAQRADVLFPPHTVNVFEGTIADNVNPRGDVPEDVVKQALAAAHCQDILRRLGGINEAGELPDAPLGEAGLNLSGGQRQRVALARALAADPEVLILDDPTTGLDSVTQADVVAAVAALRADKTTVVITGNAAWQHAGTELEVA"},"dna_sequence":{"accession":"NC_004939.1","fmin":"4565","fmax":"6107","strand":"+","sequence":"ATGAAGACGTACAGCTGGTTCGTCCCGCCCGCGCCGCCAGCGGACGATCCGGCGCGGCTCCACCCAGCACGCTGGAGCAGCGGGAACCGTGTGGTCAGGGACATGGTAGGCGCATACCCGGGCGTGCTAGTGCTGCACATTCTGAGCTACCTCATCGGCTCCGGCATCTCCGCGTTTGTGCCGGTGGTGGTGGGCATGATCGTGGACGGCCTGGTGGGGGAAGAAAAGTTCAACGCATGGTGGCTCTTCGCAGTATTGGTCGGCATCTTCATCATCCAGTTCATCGGCGAGGCCACCGGCGACGGCCTGGCCACAGCCTCGGTGCGCCGCGTGACCCACAACGCGCAGCAGCACCTGTCCTCGGGCGTGCTGCGCCGCGGGGCGGGAGCGATGAGCCCCGGCACCGTACTCAACACCATCGACGCGGACGCGAACACCGTCGGCCGCTACCGCGAGCTGCTGTCGTTTCCGCTCATGGCCATCGGCTACGCGGTCTGCGCGATGGTGGCGATGTGGTCGGTCTCCCCGTGGATCTCACTGGCCATCCCGGCCAGCGCGCTGATCATCGCTCTGTTCGCCGCGTGGACCGCGGGGCCGGTGACGCGGGTGTCGTTGAAGCGTCGCGCCGCGGAGGCGGATGTCGCTGGCTTGGCCACGGATGCGTCGCAAGGCATTCGCACCGTCAAAGGCCTAGGCGCGGGTGCAACCGTGGCAACACGTTTTCACGCCGAAACGGCGAAGGCGAACGGCTTGATGCTCACGCACCTGCGTGTGGAGGTGTGGCTCGGTTTCGCCAGGTTTTGCGTGGCGTGGCTGTGCAACCTTGGCATCGTGGGCTTGAGCGCGTGGATGACGCTGCGCGGGGAGATCACCCCGGGGCAGCTGACATCCGTGGCACTGTTGGTGCAGCCTGCGTTGACCATGGCGGGCTTAGCGTTCGGCGACCTGGCCAGCGGGTGGGGCAGGGCCGTCGCGAGTGGCCAGCGCATCGAGCAGCTGCACCACGCGGGCGATGACGCGGCGGGGCCTGAGCCGACAGACACCCCGGTCCCAGGCGCGGGGCTGTGGATTCTCGAGCCGGCGGAGCGTTCCTACGCCACCGCCGCCGCGTGGGCGCAGCGCGCAGACGTGCTGTTCCCGCCGCACACCGTCAACGTGTTTGAGGGCACCATCGCAGACAACGTGAACCCGCGCGGGGATGTGCCGGAGGACGTCGTCAAGCAGGCGCTCGCCGCCGCCCACTGCCAAGACATCCTCCGCAGGCTCGGCGGTATCAACGAAGCAGGCGAGTTGCCGGACGCGCCGCTGGGGGAGGCCGGCCTGAACCTTTCCGGCGGGCAGCGCCAGCGCGTCGCGCTTGCCAGGGCGCTCGCCGCCGACCCGGAGGTGCTCATCCTGGACGACCCGACCACGGGGCTCGATTCCGTGACACAGGCGGACGTCGTGGCAGCCGTCGCCGCGCTCAGAGCAGACAAAACCACCGTGGTCATCACCGGAAACGCCGCGTGGCAGCACGCTGGAACCGAATTGGAGGTGGCGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39554","NCBI_taxonomy_name":"Corynebacterium striatum","NCBI_taxonomy_id":"43770"}}}},"ARO_accession":"3004639","ARO_id":"42633","ARO_name":"Corynebacterium striatum tetA","CARD_short_name":"Cstr_tetA","ARO_description":"The tetAB genes of the Corynebacterium striatum R-plasmid encode an ABC transporter and confer tetracycline, oxytetracycline, and oxalic resistance.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"37012":{"category_aro_accession":"3000668","category_aro_cvterm_id":"37012","category_aro_name":"oxytetracycline","category_aro_description":"Oxytetracycline is a derivative of tetracycline with a 5-hydroxyl group. Its activity is similar to other tetracyclines.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"3339":{"model_id":"3339","model_name":"dfrA15b","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"5459":{"protein_sequence":{"accession":"CAI29521.1","sequence":"MKLSLMAAISKNGVIGNGPDIPWSAKGEQLLFKAITYNQWLLVGRKTFESMGALPNRKYAVVTRSSFTSSDENVLVFPSIDEALNHLKTITDHVIVSGGGEIYKSLIDKADTLHISTIDIEPEGDVYFPEIPGSFRPVFSKDFVSNINYSYQIWQKG"},"dna_sequence":{"accession":"AJ867237.1","fmin":"176","fmax":"650","strand":"+","sequence":"GTGAAACTATCACTAATGGCAGCAATTTCGAAGAATGGAGTTATCGGAAATGGCCCAGATATTCCATGGAGTGCCAAAGGGGAACAATTACTCTTCAAAGCGATTACCTATAATCAGTGGCTTTTGGTAGGCCGAAAGACTTTCGAGTCAATGGGGGCTTTACCCAACCGAAAATATGCCGTTGTAACTCGTTCAAGCTTCACTTCCAGTGATGAGAATGTATTGGTATTTCCATCTATCGATGAAGCGCTAAATCATCTGAAGACGATAACGGATCATGTGATTGTGTCTGGTGGTGGTGAAATATACAAAAGCCTGATCGATAAAGCTGATACTTTACATATTTCAACAATCGACATTGAGCCAGAAGGTGATGTCTATTTTCCAGAAATCCCCGGTAGTTTTAGGCCAGTTTTTAGCAAAGACTTCGTGTCCAACATAAATTATAGTTACCAAATCTGGCAAAAGGGTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35716","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica","NCBI_taxonomy_id":"59201"}}}},"ARO_accession":"3004640","ARO_id":"42648","ARO_name":"dfrA15b","CARD_short_name":"dfrA15b","ARO_description":"A dihydrofolate reductase found in Salmonella Enterica.","ARO_category":{"37617":{"category_aro_accession":"3001218","category_aro_cvterm_id":"37617","category_aro_name":"trimethoprim resistant dihydrofolate reductase dfr","category_aro_description":"Alternative dihydropteroate synthase dfr present on plasmids produces alternate proteins that are less sensitive to trimethoprim from inhibiting its role in folate synthesis, thus conferring trimethoprim resistance.","category_aro_class_name":"AMR Gene Family"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3341":{"model_id":"3341","model_name":"Erm(K)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"5470":{"protein_sequence":{"accession":"WP_010896559.1","sequence":"MTKKKHKYSNKKLSRGEPPNFSGQHLMHNKKLLQEIVDQAKVSKKDTVLELGAGKGALTTFLSERAKRVLAVEYDQTFIQVLNRKMAHAANTTIIHEDIMRIHLPKGEFVVVSNIPYSITTPIMKKLLSNPVSGFQRGVIVMEKGAAKRFTSPFIKNAYVLAWRMWFDLEYVKGISRECFSPPPKVDSAMVFISRKPDPIVPYKDRSAFFGLAEYALREPKAPADSLLRGIFTATQLKHVKRNAGIKHDVSIGALSERQWGVIFETMTQYVRRPLWPRPRKTTL"},"dna_sequence":{"accession":"NG_047831.1","fmin":"100","fmax":"955","strand":"+","sequence":"ATGACGAAAAAGAAGCATAAATACAGCAATAAAAAACTTAGTCGCGGAGAGCCCCCCAATTTCTCCGGTCAGCATTTAATGCATAATAAAAAGCTACTGCAAGAAATTGTGGATCAGGCAAAGGTTAGTAAAAAAGATACCGTATTAGAGCTCGGCGCTGGCAAAGGGGCGTTGACGACGTTTCTTAGTGAACGAGCGAAAAGAGTGCTCGCAGTGGAATATGACCAAACGTTTATTCAAGTGTTAAACCGGAAAATGGCGCACGCCGCCAATACGACGATCATACACGAGGACATTATGCGCATTCATTTACCTAAGGGGGAATTTGTCGTCGTTTCCAATATCCCATATTCGATTACGACGCCAATTATGAAAAAGCTTCTTTCCAATCCGGTAAGTGGTTTTCAACGAGGTGTGATCGTGATGGAAAAAGGAGCAGCGAAACGGTTCACGTCGCCTTTCATCAAAAATGCATATGTGCTCGCATGGCGGATGTGGTTTGACTTGGAGTACGTCAAAGGGATTTCGAGAGAGTGTTTTTCACCTCCTCCAAAGGTGGATTCGGCGATGGTATTCATTTCTCGCAAGCCGGACCCAATTGTACCGTATAAGGATCGCTCCGCCTTTTTCGGTCTAGCAGAATATGCGCTCCGCGAGCCTAAGGCGCCAGCTGATTCACTGCTACGAGGGATTTTTACAGCTACACAATTAAAACATGTGAAGCGCAATGCTGGGATTAAGCACGATGTCTCAATTGGTGCATTATCGGAAAGGCAATGGGGCGTCATCTTTGAAACCATGACTCAATATGTAAGACGGCCGCTGTGGCCACGACCGAGAAAGACAACATTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42658","NCBI_taxonomy_name":"Alkalihalobacillus halodurans","NCBI_taxonomy_id":"86665"}}}},"ARO_accession":"3004643","ARO_id":"42655","ARO_name":"Erm(K)","CARD_short_name":"Erm(K)","ARO_description":"A 23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(K) [Alkalihalobacillus halodurans].","ARO_category":{"36699":{"category_aro_accession":"3000560","category_aro_cvterm_id":"36699","category_aro_name":"Erm 23S ribosomal RNA methyltransferase","category_aro_description":"Erm proteins are part of the RNA methyltransferase family and methylate A2058 (E. coli nomenclature) of the 23S ribosomal RNA conferring degrees of resistance to Macrolides, Lincosamides and Streptogramin b. This is called the MLSb phenotype.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3343":{"model_id":"3343","model_name":"dfrA6 from Proteus mirabilis","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"5471":{"protein_sequence":{"accession":"CAB06660.1","sequence":"MKISLMAAVSENGVIGSGLDIPWHVQGEQLLFKAMTYNQWLLVGRKTFDSMGKLPNRKYAVVTRSKIISNDPDVVYFASVESALAYLNNATAHIFVSGGGEIYKALIDQADVIHLSVIHKHISGDVFFPPVPQGFKQTFEQSFSSNIDYTYQIWAKG"},"dna_sequence":{"accession":"Z86002.1","fmin":"335","fmax":"809","strand":"+","sequence":"ATGAAAATATCTCTTATGGCAGCTGTTTCCGAGAATGGAGTAATTGGCTCTGGATTGGATATACCTTGGCATGTACAAGGCGAGCAGCTCCTATTCAAAGCCATGACTTACAATCAATGGCTTCTAGTTGGTCGTAAAACCTTCGACTCAATGGGTAAACTTCCGAATAGAAAATATGCAGTGGTTACTCGTTCTAAAATTATCTCGAATGACCCTGATGTTGTGTATTTCGCAAGTGTTGAATCGGCATTAGCTTACCTAAACAATGCGACAGCACATATCTTTGTTTCTGGTGGTGGTGAAATATATAAAGCTTTAATCGATCAAGCAGATGTTATCCATCTTTCAGTGATTCACAAGCATATCTCTGGCGATGTGTTTTTTCCTCCAGTTCCACAGGGCTTCAAGCAAACATTTGAGCAAAGTTTCAGTTCAAATATTGATTACACGTACCAAATTTGGGCAAAGGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3004644","ARO_id":"42657","ARO_name":"dfrA6 from Proteus mirabilis","CARD_short_name":"Pmir_dfrA6","ARO_description":"dfrA6 is a dihydrofolate reductase that confers resistance to trimethoprim. Found in Proteus mirabilis.","ARO_category":{"37617":{"category_aro_accession":"3001218","category_aro_cvterm_id":"37617","category_aro_name":"trimethoprim resistant dihydrofolate reductase dfr","category_aro_description":"Alternative dihydropteroate synthase dfr present on plasmids produces alternate proteins that are less sensitive to trimethoprim from inhibiting its role in folate synthesis, thus conferring trimethoprim resistance.","category_aro_class_name":"AMR Gene Family"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3344":{"model_id":"3344","model_name":"dfrI","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"350"}},"model_sequences":{"sequence":{"5472":{"protein_sequence":{"accession":"ABO40886.1","sequence":"MNQNRDDHNRAADREKTAEKRGENQCIISLILAMADNGTIGDKNALPWHLPNDLQFLKKSTMGKPIVMGRKTYQSIGRPLPGRTNVVISRSLEKEALPGCLIYSDLSVAIAALKKEPEVEEIMIMGGAQIYRAALPMMDRLYLTHVHANIEGDTQMPPFDFSHATLIFEEKHFKDEKNRYDYTFEIWDFKK"},"dna_sequence":{"accession":"CP000602.1","fmin":"93826","fmax":"94402","strand":"-","sequence":"ATGAATCAAAACAGAGACGACCATAATCGTGCAGCAGATAGAGAAAAAACAGCAGAGAAAAGAGGAGAAAACCAGTGCATCATCTCCCTTATTTTAGCAATGGCAGATAATGGCACAATTGGTGATAAAAATGCCCTACCATGGCATCTTCCTAATGATCTGCAATTTTTAAAAAAGAGCACTATGGGAAAGCCGATTGTTATGGGCCGAAAAACTTACCAATCGATTGGCCGGCCACTTCCCGGCAGAACCAATGTAGTAATCTCACGCTCTTTAGAGAAGGAGGCTCTCCCCGGATGCTTAATCTATTCCGATCTCTCAGTTGCGATAGCGGCACTTAAAAAAGAGCCCGAGGTTGAAGAGATTATGATTATGGGGGGCGCGCAGATCTATAGAGCAGCTCTTCCTATGATGGATCGACTCTATCTTACCCATGTACATGCCAATATCGAAGGGGATACCCAGATGCCCCCCTTTGATTTTAGCCATGCAACCCTCATCTTTGAAGAGAAGCATTTTAAAGATGAGAAGAATCGATATGATTACACCTTTGAGATTTGGGACTTCAAAAAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42660","NCBI_taxonomy_name":"Yersinia ruckeri","NCBI_taxonomy_id":"29486"}}}},"ARO_accession":"3004645","ARO_id":"42659","ARO_name":"dfrI","CARD_short_name":"dfrI","ARO_description":"dfrI is a dihydrofolate reductase that is resistant to trimethoprim.","ARO_category":{"37617":{"category_aro_accession":"3001218","category_aro_cvterm_id":"37617","category_aro_name":"trimethoprim resistant dihydrofolate reductase dfr","category_aro_description":"Alternative dihydropteroate synthase dfr present on plasmids produces alternate proteins that are less sensitive to trimethoprim from inhibiting its role in folate synthesis, thus conferring trimethoprim resistance.","category_aro_class_name":"AMR Gene Family"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3346":{"model_id":"3346","model_name":"AQU-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"5474":{"protein_sequence":{"accession":"AHF82023.1","sequence":"MKQTSPLSLLALSALLLSPLTQAAPADPLVGVVDDVIRPLVKEHRIPGMAVAVFKEGQPHYFNYGVAELATGKKVSEQTLFEIGSVSKTLTATLGAYAVVKGSIGLDDKVSRHAPWLKGSAFDGITMAELATYSAGGLPLQFPDEVESLEQMQAYYRQWTPAYQPGSHRQYSNPSIGLFGYLAASSLQQPFAQLMEQTLLPGLGLHHTYINVPKQAMANYAYGYSKEDKPIRVNPGMLADEAYGIKTSSADLLAFVQANINGVDDKGLQQAIALTHQGHYSVGGMTQGLGWESYPYPVSEQTLLAGNSAQVIMKANPTTAAPXEMGSQRLFNKTGSTNGFGAYVAFVPAKGVGIVMLANRNYPIQERVKAAHAILSKLAP"},"dna_sequence":{"accession":"KF730243.1","fmin":"0","fmax":"1143","strand":"+","sequence":"ATGAAGCAAACCTCACCCTTGTCGTTGCTGGCGCTGAGCGCCCTGCTGCTGTCGCCCCTCACCCAGGCCGCTCCCGCCGATCCGCTGGTCGGGGTAGTGGATGACGTCATTCGTCCGCTGGTGAAAGAGCACAGGATCCCGGGCATGGCGGTAGCCGTGTTCAAAGAGGGGCAACCCCACTACTTCAACTACGGGGTTGCCGAGCTGGCGACGGGGAAGAAGGTCAGCGAGCAGACCCTGTTCGAGATTGGCTCGGTCAGCAAGACCCTGACCGCGACCCTGGGGGCCTACGCCGTGGTCAAGGGGAGCATTGGGCTGGATGACAAGGTGAGCCGGCACGCTCCCTGGCTCAAGGGCTCCGCCTTTGATGGCATTACCATGGCCGAGCTTGCCACTTACAGTGCCGGGGGTCTGCCGCTGCAATTCCCCGACGAGGTGGAATCGCTCGAGCAGATGCAGGCTTACTATCGCCAGTGGACGCCGGCCTATCAACCAGGCAGCCATCGCCAGTACTCCAACCCCAGTATCGGCCTGTTCGGCTATCTGGCGGCGAGCAGTCTGCAGCAGCCGTTTGCCCAGTTGATGGAGCAGACCCTGCTGCCCGGGCTCGGCCTGCATCACACCTATATCAATGTGCCGAAGCAGGCCATGGCGAACTACGCCTATGGCTATTCGAAAGAGGACAAGCCCATCAGGGTCAATCCCGGCATGCTGGCCGACGAGGCCTACGGCATCAAGACTAGCTCGGCGGATCTGCTCGCCTTCGTGCAGGCCAACATCAACGGGGTGGATGACAAGGGGTTGCAGCAGGCCATCGCTTTGACCCACCAGGGGCACTACTCGGTAGGCGGGATGACTCAGGGGCTGGGCTGGGAGAGTTACCCCTATCCGGTCAGCGAGCAGACGCTGCTGGCGGGCAACTCGGCCCAGGTGATCATGAARGCCAATCCGACGACGGCCGCGCCGAAKGAGATGGGGAGCCAGCGGCTCTTCAACAAGACTGGCTCGACCAACGGCTTTGGCGCCTATGTGGCCTTCGTGCCGGCCAAGGGAGTGGGCATCGTCATGCTGGCCAACCGCAACTACCCCATCCAGGAGAGGGTAAAGGCGGCCCACGCCATCCTGAGCAAGCTGGCTCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36810","NCBI_taxonomy_name":"Aeromonas hydrophila","NCBI_taxonomy_id":"644"}}}},"ARO_accession":"3004647","ARO_id":"42664","ARO_name":"AQU-2","CARD_short_name":"AQU-2","ARO_description":"AQU-2 is a chromosomally-encoded AQU class C beta-lactamase and cephalosporinase from Aeromonas.","ARO_category":{"39426":{"category_aro_accession":"3002992","category_aro_cvterm_id":"39426","category_aro_name":"AQU beta-lactamase","category_aro_description":"AQU beta-lactamases are chromosomal class C beta-lactamases that confer resistance to cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3348":{"model_id":"3348","model_name":"cfr(B)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"5492":{"protein_sequence":{"accession":"CDF47262.1","sequence":"MQQKNKYIRIQEFLKQNKFPNYRMKQITNAIFPGRINNFNEITVLPKSLRDMLIEEFGESILNIVPLKAQQSTQVSKVLFGISGDEKIETVNMKYKAGWESFCISSQCGCNFGCKFCATGDIGLKRNLTSDEITDQILYFHLQGHSIDSISFMGMGEALANVQVFDALNVLTDPALFALSPRRLSISTIGIIPNIKKLTQNYPQVNLTFSLHSPFNEQRSELMPINERYPLSDVMDTLDEHIRVTSRKVYIAYIMLHGVNDSIEHAKEVVNLLRGRYRSGNLYHVNIIRYNPTVSSRMRFEEANEKCLVNFYKELKSAGIKVTIRSQFGIDIDAACGQLYGNYQKTNSQ"},"dna_sequence":{"accession":"HG002396.1","fmin":"5272","fmax":"6322","strand":"+","sequence":"ATGCAACAAAAAAATAAGTATATAAGAATTCAAGAGTTCTTGAAGCAGAATAAATTTCCTAATTATAGAATGAAACAAATTACAAATGCTATATTCCCAGGGAGAATAAATAATTTCAACGAAATAACGGTTCTTCCTAAATCACTAAGAGATATGTTAATTGAGGAGTTTGGAGAATCGATTTTAAATATTGTTCCTTTAAAAGCACAACAATCTACACAAGTTTCAAAAGTCTTATTTGGAATTTCAGGAGACGAAAAAATAGAAACGGTAAATATGAAATATAAAGCTGGTTGGGAGTCATTTTGTATATCATCGCAGTGCGGTTGTAATTTTGGTTGTAAATTTTGTGCAACTGGAGATATAGGTTTAAAACGTAACTTAACTTCAGATGAAATTACTGACCAGATTTTGTACTTTCACTTACAAGGGCATTCAATTGACAGTATTTCTTTTATGGGAATGGGAGAAGCATTAGCGAATGTACAAGTTTTTGATGCTTTAAATGTACTTACAGATCCTGCGTTGTTTGCTTTAAGTCCGCGTAGGTTATCTATATCCACTATAGGAATTATTCCAAACATTAAAAAATTGACTCAAAACTATCCGCAGGTCAACCTGACATTTTCATTACATTCTCCTTTTAATGAACAGCGAAGTGAGTTAATGCCAATTAATGAACGCTACCCATTATCAGATGTGATGGATACATTAGATGAGCATATACGAGTAACCTCAAGAAAAGTTTATATTGCTTATATTATGTTGCACGGAGTTAATGATTCTATTGAACATGCGAAAGAAGTCGTAAACCTTTTAAGAGGTAGATATAGGAGTGGGAACTTGTATCATGTGAACATCATTAGATATAACCCGACTGTTAGTTCACGGATGCGGTTTGAAGAAGCAAATGAGAAATGTCTTGTCAACTTTTATAAAGAATTAAAGTCAGCAGGAATTAAAGTTACCATTAGAAGTCAATTTGGCATTGATATAGACGCTGCTTGCGGTCAATTGTATGGAAACTATCAAAAAACCAATAGCCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36807","NCBI_taxonomy_name":"Clostridioides difficile","NCBI_taxonomy_id":"1496"}}}},"ARO_accession":"3004649","ARO_id":"42670","ARO_name":"cfr(B)","CARD_short_name":"cfr(B)","ARO_description":"cfr(B) has been observed in mobile genetic elements in E. faecium and Clostridioides difficile and confers resistance to linezolid, clindamycin, erythromycin, chloramphenicol, and retapamulin.","ARO_category":{"36341":{"category_aro_accession":"3000202","category_aro_cvterm_id":"36341","category_aro_name":"Cfr 23S ribosomal RNA methyltransferase","category_aro_description":"Cfr genes produce enzymes which catalyze the methylation of the 23S rRNA subunit at position 8 of adenine-2503. Methylation of 23S rRNA at this site confers resistance to some classes of antibiotics, including streptogramins, chloramphenicols, florfenicols, linezolids and clindamycin.","category_aro_class_name":"AMR Gene Family"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"35989":{"category_aro_accession":"0000072","category_aro_cvterm_id":"35989","category_aro_name":"linezolid","category_aro_description":"Linezolid is a synthetic antibiotic used for the treatment of serious infections caused by Gram-positive bacteria that are resistant to several other antibiotics. It inhibits protein synthesis by binding to domain V of the 23S rRNA of the 50S subunit of bacterial ribosomes.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"36218":{"category_aro_accession":"3000079","category_aro_cvterm_id":"36218","category_aro_name":"oxazolidinone antibiotic","category_aro_description":"Oxazolidinones are a class of synthetic antibiotics discovered the the 1980's.  They inhibit protein synthesis by binding to domain V of the 23S rRNA of the 50S subunit of bacterial ribosomes.  Linezolid is the only member of this class currently in clinical use.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1670":{"model_id":"1670","model_name":"nalC","model_type":"protein overexpression model","model_type_id":"41091","model_description":"Protein Overexpression Models (POM) are similar to Protein Variant Models (PVM) in that they include a protein reference sequence, a curated BLASTP bitscore cut-off, and mapped resistance variants. Whereas PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, reporting only those with curated mutations conferring AMR, POMs are restricted to regulatory proteins and report both wild-type sequences and\/or sequences with mutations leading to overexpression of efflux complexes. The former lead to efflux of antibiotics at basal levels, while the latter can confer clinical resistance. POMs include a protein reference sequence (often from wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Perfect RGI match is 100% identical to the wild-type reference protein sequence along its entire length, a Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value may or may not contain at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off may or may not contain at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"4363":"S209R","4364":"R97G","4366":"A186T","7533":"G71E"},"Curated-R":{"4363":"S209R","4364":"R97G","4366":"A186T","7533":"G71E"},"clinical":{"4363":"S209R","4364":"R97G","4366":"A186T","7533":"G71E"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"5506":{"protein_sequence":{"accession":"AAG07108.1","sequence":"MNDASPRLTERGRQRRRAMLDAATQAFLEHGFEGTTLDMVIERAGGSRGTLYSSFGGKEGLFAAVIAHMIGEIFDDSADQPRPAATLSATLEHFGRRFLTSLLDPRCQSLYRLVVAESPRFPAIGKSFYEQGPQQSYLLLSERLAAVAPHMDEETLYAVACQFLEMLKADLFLKALSVADFQPTMALLETRLKLSVDIIACYLEHLSQSPAQG"},"dna_sequence":{"accession":"AE004091.2","fmin":"4166517","fmax":"4167159","strand":"+","sequence":"ATGAACGATGCTTCTCCCCGTCTGACCGAACGCGGCAGGCAACGCCGCCGCGCCATGCTCGACGCCGCTACCCAGGCCTTTCTCGAACACGGTTTCGAAGGCACCACCCTGGACATGGTGATAGAACGGGCCGGTGGTTCACGGGGGACCCTGTACAGCTCCTTCGGCGGCAAGGAGGGCCTGTTCGCCGCGGTGATCGCCCACATGATCGGGGAAATCTTCGACGACAGCGCCGATCAGCCGCGCCCCGCCGCCACGCTGAGCGCCACCCTCGAGCATTTCGGCCGGCGCTTTCTCACCAGCCTGCTCGATCCCCGCTGCCAGAGCCTCTATCGCCTGGTGGTGGCGGAATCCCCGCGGTTTCCGGCGATCGGCAAGTCCTTCTACGAGCAGGGGCCGCAGCAGAGCTATCTGCTGCTCAGCGAGCGACTGGCCGCGGTCGCTCCTCACATGGACGAGGAAACGCTCTACGCGGTGGCCTGCCAGTTTCTCGAGATGCTCAAGGCCGACCTGTTCCTCAAGGCCCTCAGCGTGGCCGACTTCCAGCCGACCATGGCGCTGCTGGAAACCCGCCTCAAGCTGTCGGTGGACATCATCGCCTGCTACCTGGAACACCTGTCGCAGAGCCCCGCGCAGGGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36804","NCBI_taxonomy_name":"Pseudomonas aeruginosa PAO1","NCBI_taxonomy_id":"208964"}}}},"ARO_accession":"3000818","ARO_id":"37198","ARO_name":"nalC","CARD_short_name":"nalC","ARO_description":"NalC is a repressor of PA3720-PA3719, which are positive regulators of MexAB-OprM. Thus, nalC mutants confer multidrug resistance.","ARO_category":{"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2373":{"model_id":"2373","model_name":"Escherichia coli UhpT with mutation conferring resistance to fosfomycin","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"4358":"E350Q"},"Curated-R":{"4358":"E350Q"},"clinical":{"4358":"E350Q"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"850"}},"model_sequences":{"sequence":{"3667":{"protein_sequence":{"accession":"CDJ73208.1","sequence":"MLAFLNQVRKPTLDLPLEVRRKMWFKPFMQSYLVVFIGYLTMYLIRKNFNIAQNDMISTYGLSMTQLGMIGLGFSITYGVGKTLVSYYADGKNTKQFLPFMLILSAICMLGFSASMGSGSVSLFLMIAFYALSGFFQSTGGSCSYSTITKWTPRRKRGTFLGFWNISHNLGGAGAAGVALFGANYLFDGHVIGMFIFPSIIALIVGFIGLRYGSDSPESYGLGKAEELFGEEISEEDKETESTDMTKWQIFVEYVLKNKVIWLLCFANIFLYVVRIGIDQWSTVYAFQELKLSKAVAIQGFTLFEAGALVGTLLWGWLSDLANGRRGLVACIALALIIATLGVYQHASNEYIYLASLFALGFLVFGPQLLIGVAAVGFVPKKAIGAADGIKGTFAYLIGDSFAKLGLGMIADGTPVFGLTGWAGTFAALDIAAIGCICLMAIVAVMEERKIRREKKIQQLTVA"},"dna_sequence":{"accession":"HG738867.1","fmin":"2934266","fmax":"2935658","strand":"+","sequence":"ATGCTGGCTTTCTTAAACCAGGTTCGCAAGCCGACCCTGGACCTTCCGCTCGAAGTGCGGCGCAAAATGTGGTTCAAACCGTTCATGCAATCCTACCTGGTGGTCTTTATCGGCTACCTGACGATGTACCTGATTCGCAAGAACTTTAACATCGCGCAGAACGATATGATTTCGACCTACGGGTTGAGCATGACGCAGCTGGGGATGATCGGCCTGGGTTTCTCCATCACTTATGGCGTGGGTAAAACGCTGGTTTCCTACTACGCCGACGGCAAAAACACCAAACAATTCCTGCCGTTCATGCTGATCCTCTCTGCTATTTGTATGCTGGGCTTCAGTGCCAGTATGGGCAGCGGCTCGGTTAGCCTGTTCCTGATGATTGCCTTCTACGCCTTAAGCGGCTTTTTCCAGAGTACCGGCGGTTCGTGCAGTTACTCCACCATCACCAAATGGACGCCGCGTCGTAAACGCGGGACATTCCTCGGTTTCTGGAATATTTCTCACAACCTTGGCGGTGCAGGCGCAGCAGGTGTGGCGCTGTTCGGGGCAAATTACCTGTTCGATGGCCATGTCATCGGCATGTTTATCTTCCCGTCGATTATCGCGCTGATTGTCGGTTTTATCGGCCTGCGTTACGGCAGCGACTCCCCGGAATCTTATGGCCTCGGCAAAGCTGAAGAACTGTTCGGCGAGGAGATCAGCGAAGAGGACAAAGAGACAGAATCTACCGATATGACCAAGTGGCAGATCTTTGTTGAGTATGTGCTGAAAAACAAAGTGATCTGGCTGCTGTGCTTCGCCAACATTTTCCTCTATGTGGTACGTATTGGTATCGACCAGTGGTCAACCGTATACGCGTTCCAGGAACTGAAACTCTCTAAAGCGGTGGCGATTCAGGGCTTTACGCTGTTTGAAGCTGGTGCGCTGGTCGGTACGCTGCTGTGGGGCTGGCTCTCTGACCTGGCGAACGGTCGCCGTGGCCTGGTGGCCTGCATCGCGCTGGCGCTGATTATCGCCACGCTCGGTGTGTATCAACATGCCAGTAACGAATATATCTATCTGGCTTCTCTCTTTGCGTTGGGTTTCCTGGTCTTTGGCCCGCAATTGTTGATTGGTGTGGCTGCTGTTGGCTTTGTACCTAAAAAAGCGATTGGCGCTGCCGATGGTATTAAAGGCACCTTTGCTTACCTGATTGGTGACAGCTTTGCCAAGTTAGGTCTGGGAATGATTGCCGATGGGACGCCGGTATTCGGCCTTACCGGCTGGGCAGGCACCTTCGCCGCGCTGGATATCGCCGCGATTGGTTGTATCTGCCTGATGGCGATAGTGGCGGTAATGGAAGAACGCAAAATCCGCCGCGAGAAAAAAATTCAGCAGTTGACAGTGGCATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40589","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. MC4100","NCBI_taxonomy_id":"1403831"}}}},"ARO_accession":"3003890","ARO_id":"40592","ARO_name":"Escherichia coli UhpT with mutation conferring resistance to fosfomycin","CARD_short_name":"Ecol_UhpT_FOF","ARO_description":"Mutations to the active importer UhpT, which is involved with the uptake of many phosphorylated sugars, confer resistance to fosfomycin by reducing import of the drug into the bacteria.","ARO_category":{"41412":{"category_aro_accession":"3004248","category_aro_cvterm_id":"41412","category_aro_name":"antibiotic-resistant UhpT","category_aro_description":"UhpT encodes a transporter that can import fosfomycin-type drugs into bacterial cells. Mutations to UhpT confer resistance.","category_aro_class_name":"AMR Gene Family"},"35944":{"category_aro_accession":"0000025","category_aro_cvterm_id":"35944","category_aro_name":"fosfomycin","category_aro_description":"Fosfomycin (also known as phosphomycin and phosphonomycin) is a broad-spectrum antibiotic produced by certain Streptomyces species. It is effective on gram positive and negative bacteria as it targets the cell wall, an essential feature shared by both bacteria. Its specific target is MurA (MurZ in E.coli), which attaches phosphoenolpyruvate (PEP) to UDP-N-acetylglucosamine, a step of commitment to cell wall synthesis. In the active site of MurA, the active cysteine molecule is alkylated which stops the catalytic reaction.","category_aro_class_name":"Antibiotic"},"45731":{"category_aro_accession":"3007149","category_aro_cvterm_id":"45731","category_aro_name":"phosphonic acid antibiotic","category_aro_description":"A group of antibiotics derived from phosphonic acids.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"383":{"model_id":"383","model_name":"Pseudomonas mutant PhoQ conferring resistance to colistin","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"4370":"K123Q","4371":"V260G"},"Curated-R":{"4370":"K123Q","4371":"V260G"},"experimental":{"4370":"K123Q","4371":"V260G"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"860"}},"model_sequences":{"sequence":{"5426":{"protein_sequence":{"accession":"AAG04569.1","sequence":"MIRSLRIRLMLGAAALAVLFMLALLPALQRAFGIALENTIEQRLAADVATLVSAARVEKGRLVMPEHLPVEEFNLPEAKVLGYIYDQNGDLLWRSTSAADESINYTPRYDGRGNEFHTTRDAKGEEFFVFDVEIDLLRGKQAAYSIVTMQSVSEFESLLKGFREQLYLWLGGALLVLLGLLWLGLTWGFRAMRGLSSELDQIESGERESLSEEHPRELLRLTHSLNRLLRSEHKQRERYRHSLGDLAHSLKTPLAVLQGVGDQLAEEPGNREQVRVLQGQIERMSQQIGYQLQRASLRKSGLVRHREQLAPLVETLCDALDKVYRDKRVSLQRDFSPSFSVPVERGALLELLGNLLENAYRLCLGRVRVGARLGPGYSELWVEDDGPGVPAEQRARIIRRGERADTQHPGQGIGLAVALDIIESYDGELSLDDSELGGACFRIRFATV"},"dna_sequence":{"accession":"AE004091.2","fmin":"1278361","fmax":"1279708","strand":"+","sequence":"GTGATCCGTTCCCTGCGCATCCGTCTGATGCTCGGCGCCGCCGCCCTGGCGGTGCTGTTCATGCTGGCGCTGCTGCCGGCCCTGCAGCGGGCCTTCGGCATCGCCCTGGAGAACACCATCGAGCAGCGCCTGGCCGCCGACGTGGCGACCCTGGTCTCGGCGGCGCGGGTGGAGAAGGGCCGCCTGGTGATGCCCGAGCACCTGCCGGTGGAGGAGTTCAACCTGCCGGAGGCCAAGGTCCTCGGCTATATCTACGACCAGAATGGCGATCTGCTCTGGCGCTCCACCTCGGCGGCCGACGAGTCGATCAACTACACGCCGCGCTACGACGGCCGCGGCAACGAATTCCACACCACCCGCGATGCGAAGGGCGAGGAGTTCTTCGTGTTCGACGTCGAGATCGACCTGCTGCGCGGCAAGCAGGCGGCCTACAGCATCGTCACCATGCAATCGGTCAGCGAGTTCGAGAGCCTGCTCAAGGGGTTCCGCGAGCAGCTCTACCTGTGGCTCGGCGGCGCCCTGCTGGTCTTGCTCGGGCTGCTCTGGCTGGGTCTGACCTGGGGCTTCCGGGCGATGCGCGGGTTGAGTTCCGAGCTGGACCAGATCGAATCCGGCGAGCGCGAGAGCCTGAGCGAGGAGCATCCGCGCGAGCTGCTGCGCCTGACCCACTCGCTTAACCGCCTGTTGCGCAGCGAGCACAAACAGCGCGAGCGCTACCGCCACTCCCTCGGCGACCTGGCGCACAGTCTGAAGACGCCGCTGGCGGTCTTGCAGGGGGTCGGCGACCAGCTCGCCGAGGAGCCCGGCAACCGCGAGCAGGTGCGGGTGCTACAGGGCCAGATCGAGCGCATGAGCCAGCAGATAGGCTATCAGTTGCAGCGCGCCAGCCTGCGCAAGAGCGGCCTGGTACGCCATCGCGAGCAACTGGCGCCGCTGGTGGAGACCCTGTGCGACGCGCTGGACAAGGTCTATCGCGACAAGCGGGTAAGCCTGCAGCGGGACTTCTCGCCGTCCTTCAGCGTGCCGGTGGAGCGCGGCGCGCTGCTGGAACTGCTCGGCAACCTGCTGGAGAACGCCTATCGCCTGTGCCTGGGCCGGGTCCGCGTGGGCGCCCGGCTGGGGCCGGGTTACTCGGAGCTGTGGGTCGAGGACGACGGTCCCGGAGTGCCTGCCGAACAGCGCGCACGAATCATCCGCCGCGGCGAGCGCGCCGATACCCAGCACCCGGGGCAGGGCATCGGCCTGGCCGTGGCGCTGGACATCATCGAGAGCTACGACGGCGAACTGAGCCTGGACGATTCCGAGCTGGGCGGCGCCTGCTTCCGCATACGTTTCGCTACAGTCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36804","NCBI_taxonomy_name":"Pseudomonas aeruginosa PAO1","NCBI_taxonomy_id":"208964"}}}},"ARO_accession":"3003896","ARO_id":"40598","ARO_name":"Pseudomonas mutant PhoQ conferring resistance to colistin","CARD_short_name":"Paer_PhoQ_CST","ARO_description":"Mutations in Pseudomonas aeruginosa PhoQ of the two-component PhoPQ regulatory system. Presence of mutation confers resistance to colistin.","ARO_category":{"36002":{"category_aro_accession":"0010001","category_aro_cvterm_id":"36002","category_aro_name":"ATP-binding cassette (ABC) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding\/hydrolysis to transport substrates across cell membranes.","category_aro_class_name":"AMR Gene Family"},"41433":{"category_aro_accession":"3004269","category_aro_cvterm_id":"41433","category_aro_name":"pmr phosphoethanolamine transferase","category_aro_description":"This family of phosphoethanolamine transferase catalyze the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine to lipid A, which impedes the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"46471":{"category_aro_accession":"3007684","category_aro_cvterm_id":"46471","category_aro_name":"transmembrane protein conferring colistin resistance","category_aro_description":"Mutations in mgrB transmembrane proteins can confer resistance to the antibiotic colistin.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"36593":{"category_aro_accession":"3000454","category_aro_cvterm_id":"36593","category_aro_name":"polymyxin B","category_aro_description":"Polymyxin B is mixture of mostly polymyxins B1 and B2, mainly used for resistant gram-negative infections. They are polypeptides with cationic detergent action on cell membranes.","category_aro_class_name":"Antibiotic"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"},"40429":{"category_aro_accession":"3003764","category_aro_cvterm_id":"40429","category_aro_name":"resistance by absence","category_aro_description":"Mechanism of antibiotic resistance conferred by deletion of gene (usually a porin).","category_aro_class_name":"Resistance Mechanism"}}},"2334":{"model_id":"2334","model_name":"ADC-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"5287":{"protein_sequence":{"accession":"CAB77444.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVKTDQQVLTFFKDWKPKNSIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLGAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNRFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"AJ009979.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAGTATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAATTTCCAGATGAAGTAAAAACAGATCAGCAAGTTTTAACATTTTTTAAAGACTGGAAACCTAAAAACTCAATCGGTGAATATCGACAATATTCAAACCCAAGCATTGGTTTATTTGGAAAAGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGGTGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTAAATCCACAAAAATATCCAGCAGATATTCAACGGGCAATTAATGAAACACATCAGGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACCGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3003847","ARO_id":"40544","ARO_name":"ADC-1","CARD_short_name":"ADC-1","ARO_description":"ADC-1 is a beta-lactamase found in Acinetobacter baumannii.","ARO_category":{"40543":{"category_aro_accession":"3003846","category_aro_cvterm_id":"40543","category_aro_name":"ADC beta-lactamase without carbapenemase activity","category_aro_description":"ADC beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases with extended-spectrum resistance to cephalosporins but not to carbapenems. ADC beta-lactamases are found in Acinetobacter sp. and Oligella urethralis.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2336":{"model_id":"2336","model_name":"ADC-3","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"5289":{"protein_sequence":{"accession":"AAO59456.1","sequence":"MRFKKISCLLLSPLFFFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIYANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLSAIKK"},"dna_sequence":{"accession":"AY178995.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTTTTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCGGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACTGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTCCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTAGCTTTGTCTATGAATAAACCCTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCTGGCCCACTCGATGCCCCAGCATACGGCGTCAAATCCACCTTACCGGATATGTTGAGTTTTATTTATGCCAACCTTAACCCACAGAAATATCCGGCTGATATTCAAAGGGCAATTAATGAAACACATCAAGGTCGCTATCAAGTAAATACCATGTATCAAGCGCTTGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAGCCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCAACGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAGTGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3003849","ARO_id":"40547","ARO_name":"ADC-3","CARD_short_name":"ADC-3","ARO_description":"ADC-3 is a beta-lactamase found in Acinetobacter baumannii.","ARO_category":{"40543":{"category_aro_accession":"3003846","category_aro_cvterm_id":"40543","category_aro_name":"ADC beta-lactamase without carbapenemase activity","category_aro_description":"ADC beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases with extended-spectrum resistance to cephalosporins but not to carbapenems. ADC beta-lactamases are found in Acinetobacter sp. and Oligella urethralis.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2337":{"model_id":"2337","model_name":"ADC-4","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"5290":{"protein_sequence":{"accession":"AAO59457.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIYANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNRFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"AY178996.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCGGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACTGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTCCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCTGGCCCACTCGATGCCCCAGCATACGGCGTCAAATCCACCCTTCCGGATATGTTGAGTTTTATTTATGCCAACCTTAACCCACAGAAATATCCGGCTGATATTCAAAGGGCAATTAATGAAACACATCAAGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACCGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3003850","ARO_id":"40548","ARO_name":"ADC-4","CARD_short_name":"ADC-4","ARO_description":"ADC-4 is a beta-lactamase found in Acinetobacter baumannii.","ARO_category":{"40543":{"category_aro_accession":"3003846","category_aro_cvterm_id":"40543","category_aro_name":"ADC beta-lactamase without carbapenemase activity","category_aro_description":"ADC beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases with extended-spectrum resistance to cephalosporins but not to carbapenems. ADC beta-lactamases are found in Acinetobacter sp. and Oligella urethralis.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2339":{"model_id":"2339","model_name":"ADC-6","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"5293":{"protein_sequence":{"accession":"AUD40659.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTLFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPAMLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"MG601730.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAGCTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTCCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTGTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCAACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTAAATCCACAAAAATATCCGGCAGATATTCAACGTGCAATTAATGAAACACATCAGGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAATGTTACAAACTTTACTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCAACGGTTTCGGAACGTATGTGGTGTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCGTATGCAGTTTTAAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3003852","ARO_id":"40551","ARO_name":"ADC-6","CARD_short_name":"ADC-6","ARO_description":"ADC-6 is a beta-lactamase found in Acinetobacter baumannii.","ARO_category":{"40543":{"category_aro_accession":"3003846","category_aro_cvterm_id":"40543","category_aro_name":"ADC beta-lactamase without carbapenemase activity","category_aro_description":"ADC beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases with extended-spectrum resistance to cephalosporins but not to carbapenems. ADC beta-lactamases are found in Acinetobacter sp. and Oligella urethralis.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2340":{"model_id":"2340","model_name":"ADC-7","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"5295":{"protein_sequence":{"accession":"AAT70411.1","sequence":"MRFKKISCLLLSPLFIFSTSIYADNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSNTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPTDIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTSGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYVVLNAIKK"},"dna_sequence":{"accession":"AY648950.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTTTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGACAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCTGTAAATAGCAATACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAGTATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCTGGCCCACTCGATGCCCCAGCATACGGCGTCAAATCCACCTTACCGGATATGTTGAGTTTTATTCATGCCAACCTTAACCCACAGAAATATCCGACAGATATTCAACGGGCAATTAATGAAACACATCAAGGTCGCTATCAAGTAAATACCATGTATCAAGCGCTTGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCAGCGGTTTCGGAACATATGTAGTGTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGTTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3003853","ARO_id":"40552","ARO_name":"ADC-7","CARD_short_name":"ADC-7","ARO_description":"ADC-7 is a beta-lactamase that is found in Acinetobacter baumannii.","ARO_category":{"40543":{"category_aro_accession":"3003846","category_aro_cvterm_id":"40543","category_aro_name":"ADC beta-lactamase without carbapenemase activity","category_aro_description":"ADC beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases with extended-spectrum resistance to cephalosporins but not to carbapenems. ADC beta-lactamases are found in Acinetobacter sp. and Oligella urethralis.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2341":{"model_id":"2341","model_name":"ADC-8","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"4033":{"protein_sequence":{"accession":"CAL25116.3","sequence":"MMKDILGNLDNVPFKIMTGCIAGLLSCGTVAQSTVQQSIQQSVDRHFKPLMAQYQISGMAIAVSINGQHYYQNYGVASKQTEQNVSEHTLFELGSVSKLFNATLTGYAQAQGQLKLSDHPAQYFPELKNTAVNQATLLNLGTYTAGGFPLQFPEQIKTTQDMTQYFQHWQPKAAPRRIREYSNPSIGLMGYVTALAMKNSYSNLIENTLFPALGMHHSYINVPAAQMSNYAWGYQADQAIRVSPGMFDAEAYGIKSNTADMLKFLDAQINPQNLKPTLRKAIQTTQMGYFRVGQMRQGLGWEQYTYPVSLTTLLAGNSAKMALQPQPVTGISKPITAPQQALLNKTGATNGFSAYVVVIPSQKIGLVMLANRNFPNDARVKAAYATLQQILNADIQK"},"dna_sequence":{"accession":"AM293332.3","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGATGAAAGACATATTAGGTAACTTAGATAACGTGCCATTTAAGATCATGACAGGCTGTATTGCAGGACTATTGTCCTGTGGTACGGTCGCTCAATCGACAGTCCAACAATCAATTCAACAAAGTGTAGATCGACATTTTAAGCCCCTTATGGCTCAGTATCAAATTTCAGGAATGGCGATTGCGGTCAGCATAAATGGGCAACATTACTATCAGAATTATGGCGTAGCATCTAAACAGACCGAGCAAAATGTCTCTGAACATACTCTATTTGAGTTGGGTTCGGTGAGTAAGCTCTTTAATGCAACGCTGACGGGATATGCTCAAGCACAAGGTCAACTTAAGTTGAGTGATCATCCTGCCCAATATTTTCCAGAATTAAAAAATACAGCAGTGAATCAGGCGACTCTCCTGAATCTGGGGACCTATACCGCAGGTGGTTTTCCGCTACAGTTTCCTGAGCAGATCAAGACAACACAAGACATGACTCAGTATTTTCAGCACTGGCAGCCTAAAGCGGCTCCAAGACGTATTCGAGAATATTCAAATCCAAGCATTGGCTTGATGGGCTATGTCACCGCACTTGCGATGAAAAATAGCTATTCAAATCTAATTGAAAATACGTTATTCCCTGCGTTGGGGATGCATCATAGCTATATCAACGTTCCAGCAGCGCAGATGTCAAATTATGCATGGGGATATCAGGCAGATCAGGCGATACGTGTCTCACCAGGTATGTTTGATGCAGAGGCGTATGGCATCAAAAGTAACACTGCCGATATGCTTAAATTTCTAGATGCTCAAATAAATCCCCAAAATCTAAAACCCACGCTCCGAAAGGCCATACAAACCACTCAGATGGGTTATTTTCGGGTGGGACAGATGCGACAGGGCTTGGGTTGGGAGCAATATACTTATCCAGTATCCTTAACAACCTTGCTGGCGGGAAATTCCGCTAAAATGGCTCTACAGCCTCAACCTGTTACAGGCATTTCAAAACCTATCACTGCTCCGCAGCAGGCCCTTTTGAATAAAACTGGTGCAACCAATGGTTTTTCGGCTTATGTGGTGGTTATTCCGAGCCAAAAGATTGGACTGGTGATGCTTGCCAATCGTAATTTTCCCAATGATGCACGGGTGAAAGCAGCTTATGCCACACTACAGCAAATCCTCAATGCAGATATTCAGAAATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41144","NCBI_taxonomy_name":"Acinetobacter baylyi ADP1","NCBI_taxonomy_id":"62977"}}}},"ARO_accession":"3003854","ARO_id":"40553","ARO_name":"ADC-8","CARD_short_name":"ADC-8","ARO_description":"ADC-8 is a beta-lactamase found in Acinetobacter sp.","ARO_category":{"40543":{"category_aro_accession":"3003846","category_aro_cvterm_id":"40543","category_aro_name":"ADC beta-lactamase without carbapenemase activity","category_aro_description":"ADC beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases with extended-spectrum resistance to cephalosporins but not to carbapenems. ADC beta-lactamases are found in Acinetobacter sp. and Oligella urethralis.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2338":{"model_id":"2338","model_name":"ADC-5","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"5291":{"protein_sequence":{"accession":"CAE00827.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWQPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLTPQKYPTDIQRAINETHQGFYQVGTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"AJ575184.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCATTATTAGAAAAATATGATGTACCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAGCTAAAAAATACACCGATTGATCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGCAACCTCGCTTTACAATTTCCAGATGAAGTACAAACAGATCAACAAGTTTTAACTTTTTTCAAAGACTGGCAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTGGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTTGATGCCCCAGCATACGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTTACCCCACAGAAATATCCGACAGATATTCAACGGGCAATTAATGAAACACATCAAGGGTTCTATCAAGTCGGCACCATGTATCAGGCACTTGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCAACGGTTTCGGAACATATGTGGTCTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3003851","ARO_id":"40549","ARO_name":"ADC-5","CARD_short_name":"ADC-5","ARO_description":"ADC-5 is a beta-lactamase found in Acinetobacter pittii.","ARO_category":{"40543":{"category_aro_accession":"3003846","category_aro_cvterm_id":"40543","category_aro_name":"ADC beta-lactamase without carbapenemase activity","category_aro_description":"ADC beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases with extended-spectrum resistance to cephalosporins but not to carbapenems. ADC beta-lactamases are found in Acinetobacter sp. and Oligella urethralis.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2342":{"model_id":"2342","model_name":"ADC-12","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"5302":{"protein_sequence":{"accession":"CAK95249.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDREIKKLVDQNFKPLLDKYDVPGMAVGVIQNNKKYETYYGLQSVQDKKSVSSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKEWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPGLGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLKFINANLNPQKYPKDTQRAINETHQGFYQVGTMYQALGWEEFSYPAPLQTLLDSNSEQIVMKPNKVTAISKEPSVKMFHKTGSTNGFGSYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"AM283529.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCGAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCTTTATTAGATAAATATGATGTGCCGGGTATGGCCGTGGGCGTTATTCAGAATAATAAAAAATATGAAACGTATTATGGTCTTCAATCTGTTCAAGATAAAAAATCCGTAAGTAGCAGTACCATTTTTGAACTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCAACGTATACAAGTGGTAACCTTGCCTTGCAGTTCCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGAATGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAAGTTGTTGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGGCCTTGGCTTAAAACATAGCTATGTAAATGTACCGAAGACCCAGATGCAAAACTATGCTTTTGGCTATAATCAAGAAAATCAGCCAATTCGTGTTAACCCCGGTCCGCTAGATGCTCCAGCATATGGGGTTAAATCGACGCTACCCGATATGCTTAAGTTTATTAATGCCAACCTCAACCCACAGAAATATCCGAAAGATACTCAACGTGCAATTAATGAAACACATCAAGGTTTCTACCAAGTCGGCACGATGTATCAGGCACTTGGTTGGGAAGAATTTTCTTATCCAGCGCCTTTACAAACTTTATTAGACAGTAATTCAGAGCAAATCGTGATGAAGCCTAATAAAGTGACTGCCATTTCCAAAGAACCTTCAGTTAAGATGTTCCACAAAACTGGCTCAACAAATGGCTTTGGATCTTATGTGGTGTTTATTCCAAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAACGCATTAAGGCAGCGTATGCAGTATTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3003856","ARO_id":"40555","ARO_name":"ADC-12","CARD_short_name":"ADC-12","ARO_description":"ADC-12 is a beta-lactamase found in Acinetobacter pittii.","ARO_category":{"40543":{"category_aro_accession":"3003846","category_aro_cvterm_id":"40543","category_aro_name":"ADC beta-lactamase without carbapenemase activity","category_aro_description":"ADC beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases with extended-spectrum resistance to cephalosporins but not to carbapenems. ADC beta-lactamases are found in Acinetobacter sp. and Oligella urethralis.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4226":{"model_id":"4226","model_name":"ADC-156","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6601":{"protein_sequence":{"accession":"WP_024436624.1","sequence":"MRFKKISCLLLPPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWQPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQALEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIYANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLSAIKK"},"dna_sequence":{"accession":"NG_055286.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGCTTACTTTTACCTCCTCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGATCAACAAGTTTTAACTTTTTTCAAAGACTGGCAACCTAAAAACCCAATCGGTGAATATAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGCCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAGGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCCACCTTACCGGATATGTTGAGTTTTATTTATGCCAACCTTAACCCACAGAAATATCCGGCAGATATTCAACGTGCAATTAATGAAACACATCAGGGTCGCTATCAAGTAAATACCATGTATCAAGCGCTTGGTTGGGAAGAGTTTTCTTATCCAGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACGTATGTGGTCTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAACAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAGTGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006330","ARO_id":"44792","ARO_name":"ADC-156","CARD_short_name":"ADC-156","ARO_description":"ADC-156 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3325":{"model_id":"3325","model_name":"QnrS12","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"430"}},"model_sequences":{"sequence":{"5351":{"protein_sequence":{"accession":"OIZ71829.1","sequence":"METYNHTYRHHNFSHKDLSDLTFAACTFIRSDFRRANLRDTTFVNCKFIEQGDIEGCHFDVTDLRDASFQQCQLAMANFSNANCYGIEFRACDLKGANFSRTNFAHQVSNRMYFCSAFISGCNLSYANMERVCLEKCELFENRWIGTNLAGASLKESDLSRGVFSEDVWGQFSLQGANLCHAELDGLDPRKVDTSGIKIAAWQQELILEALGIVVYPD"},"dna_sequence":{"accession":"MKQI01000097.1","fmin":"776","fmax":"1433","strand":"+","sequence":"ATGGAAACCTACAATCATACATATCGGCACCACAACTTTTCACATAAAGACTTAAGTGATCTCACCTTCGCCGCTTGCACATTCATTCGCAGCGACTTTCGACGTGCTAACTTGCGTGATACGACATTCGTCAACTGCAAGTTCATTGAACAGGGTGATATCGAAGGCTGCCACTTTGATGTCACAGATCTTCGTGATGCAAGTTTCCAACAATGCCAACTTGCGATGGCAAACTTCAGTAATGCCAATTGCTACGGTATAGAGTTCCGTGCGTGTGATTTAAAAGGTGCCAACTTTTCCCGAACAAACTTTGCCCATCAAGTGAGTAATCGTATGTACTTTTGCTCAGCATTTATTTCTGGATGTAATCTTTCCTATGCCAATATGGAGAGGGTTTGTTTAGAAAAATGTGAGTTGTTTGAAAATCGCTGGATAGGAACGAACCTAGCGGGTGCATCACTGAAAGAGTCAGACTTAAGTCGAGGTGTTTTTTCCGAAGATGTCTGGGGGCAATTTAGCCTACAGGGTGCCAATTTATGCCACGCCGAACTCGACGGTTTAGATCCCCGCAAAGTCGATACATCAGGTATCAAAATTGCAGCCTGGCAGCAAGAACTGATTCTCGAAGCACTGGGTATTGTTGTTTATCCTGACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3004625","ARO_id":"42607","ARO_name":"QnrS12","CARD_short_name":"QnrS12","ARO_description":"QnrS12 is a plasmid-mediated quinolone resistance protein.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2383":{"model_id":"2383","model_name":"ANT(4')-Ib","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"8651":{"protein_sequence":{"accession":"AAO83986.1","sequence":"MNMNGPASMAQKERLQTCQEIAKRLHEVYGNDVLAIGVYGSVSRGTDGPFSDIEMFCVLRDSAETVDKSYEWSAGPWKAEVNVCSASILLKDAATVEDRWPLTHGPYFSPLRLYDPEGFFQRLRLAAESPTKEDFRQAIHEILVGEMYEYVGKLRNVNRNGPSTYLPSLALRFAHYGAMLIGLHNQTLFSTGAMVLPEALKLPHRPKGFDHVAELAMSGDLAQPAKIVSACEDFWKGLVAWAAEHDYVIHSKRIPF"},"dna_sequence":{"accession":"EF540343.1","fmin":"214","fmax":"985","strand":"+","sequence":"ATGAATATGAATGGACCTGCATCAATGGCGCAAAAAGAAAGACTTCAAACTTGCCAAGAAATTGCCAAGAGATTACACGAGGTTTATGGCAACGACGTTCTCGCCATTGGCGTCTACGGTTCTGTGTCCAGAGGCACAGATGGCCCTTTCTCAGATATTGAGATGTTTTGCGTACTCCGTGACTCGGCTGAAACGGTAGATAAAAGTTATGAATGGTCAGCTGGACCGTGGAAAGCGGAAGTTAACGTTTGCAGTGCGAGTATACTGTTAAAAGACGCTGCAACCGTTGAAGACCGATGGCCGCTGACACATGGGCCTTACTTCTCTCCGCTTCGTCTCTATGATCCTGAAGGCTTCTTTCAACGCTTGCGGCTCGCAGCGGAATCGCCGACAAAAGAAGATTTCCGCCAAGCTATTCATGAAATTCTTGTAGGGGAAATGTATGAATATGTTGGCAAGCTTCGAAATGTAAATCGAAATGGCCCTTCTACCTACTTGCCATCCTTGGCATTGCGCTTTGCCCACTATGGCGCAATGTTGATCGGCCTCCACAATCAGACACTCTTTTCTACGGGCGCTATGGTTTTGCCTGAAGCGCTGAAACTGCCGCATCGGCCAAAAGGGTTCGACCATGTTGCTGAGTTAGCGATGTCTGGAGACTTAGCACAACCAGCGAAGATCGTGTCAGCGTGCGAAGATTTCTGGAAAGGCCTAGTCGCGTGGGCAGCGGAGCATGATTACGTCATTCACTCAAAACGAATCCCGTTTTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36882","NCBI_taxonomy_name":"Alkalihalobacillus clausii","NCBI_taxonomy_id":"79880"}}}},"ARO_accession":"3003905","ARO_id":"40608","ARO_name":"ANT(4')-Ib","CARD_short_name":"ANT(4')-Ib","ARO_description":"Aminoglycoside nucleotidyltransferase sequence from Staphylococcus aureus plasmid.","ARO_category":{"36368":{"category_aro_accession":"3000229","category_aro_cvterm_id":"36368","category_aro_name":"ANT(4')","category_aro_description":"A category of aminoglycoside O-nucleotidyltransferase enzymes with modification regiospecificity based at the 4'-hydroxyl group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics by transfer of an AMP group from an ATP substrate to the 4-hydroxyl group of the compound.","category_aro_class_name":"AMR Gene Family"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3331":{"model_id":"3331","model_name":"ADC-62","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"5401":{"protein_sequence":{"accession":"AFK24475.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVKTDQQVLTFFKDWKPKNSIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRINSGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTTGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYVVLNAIKK"},"dna_sequence":{"accession":"JQ867374.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAGTATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAATTTCCAGATGAAGTAAAAACAGATCAGCAAGTTTTAACATTTTTTAAAGACTGGAAACCTAAAAACTCAATCGGTGAATATCGACAATATTCAAACCCAAGCATTGGTTTATTTGGAAAAGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAATTAACTCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTAAATCCACAAAAATATCCAGCAGATATTCAACGGGCAATTAATGAAACACATCAGGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTACCGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGTTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3004632","ARO_id":"42621","ARO_name":"ADC-62","CARD_short_name":"ADC-62","ARO_description":"A class ADC beta-lactamase and cephalosporinase from Acinetobacter baumannii.","ARO_category":{"40543":{"category_aro_accession":"3003846","category_aro_cvterm_id":"40543","category_aro_name":"ADC beta-lactamase without carbapenemase activity","category_aro_description":"ADC beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases with extended-spectrum resistance to cephalosporins but not to carbapenems. ADC beta-lactamases are found in Acinetobacter sp. and Oligella urethralis.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2387":{"model_id":"2387","model_name":"Erm(47)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"3705":{"protein_sequence":{"accession":"ANZ79476.1","sequence":"MNRKSVRFGQNFVTSINDINKICKKIDVNSNDVYFEIGPGKGHFTQYFVERAKEVIAIEIDSELIPILNNKFSDLDNIKIINHDFMSYELPSTFKYKVFGNIPFNLSTSIIRKLSLEKYADEIYLIVELGFAKRLEDLNRKMGLMLAPFYEISILYNIPKRYFHPIPSVEVVLIKLKRTSYNMSMKEYIKYEDFIEKWVKKDYNVLFTKNQLKQAIRYGNIDNLRILKVDQILSIFESYKLFNGLK"},"dna_sequence":{"accession":"KU612222.1","fmin":"80337","fmax":"81078","strand":"+","sequence":"ATGAACAGAAAAAGTGTTAGATTTGGACAAAATTTTGTAACTTCTATTAATGATATAAACAAAATATGTAAGAAGATAGACGTGAATTCTAATGATGTTTATTTTGAAATTGGTCCAGGTAAAGGGCATTTTACTCAATACTTTGTGGAAAGGGCTAAAGAGGTAATTGCTATTGAAATAGACAGTGAATTAATTCCTATATTAAACAACAAATTTTCAGATCTAGATAATATAAAAATTATTAATCATGACTTTATGTCTTATGAATTACCATCTACATTTAAGTATAAAGTTTTTGGAAATATTCCATTTAATTTGAGTACTTCTATTATTCGTAAACTTAGTTTAGAAAAATATGCAGATGAGATTTACTTAATAGTGGAATTAGGGTTTGCAAAAAGATTAGAAGACTTAAACCGTAAAATGGGACTAATGTTAGCTCCATTTTATGAAATTTCAATTTTATACAATATTCCAAAAAGATATTTTCATCCCATACCCAGTGTTGAGGTAGTGCTGATAAAACTAAAAAGAACTTCCTATAATATGTCCATGAAAGAATATATAAAGTATGAAGACTTTATAGAAAAATGGGTAAAAAAGGATTATAATGTTTTATTTACAAAAAATCAGCTAAAACAAGCAATCAGATATGGAAATATTGATAATTTAAGAATCCTAAAAGTTGATCAAATTCTATCCATATTTGAAAGTTACAAATTATTTAATGGGTTAAAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40615","NCBI_taxonomy_name":"Helcococcus kunzii","NCBI_taxonomy_id":"40091"}}}},"ARO_accession":"3003908","ARO_id":"40614","ARO_name":"Erm(47)","CARD_short_name":"Erm(47)","ARO_description":"Chromosome-encoded gene conferring MLSB resistance. Identified from Helcococcus kunzii.","ARO_category":{"36699":{"category_aro_accession":"3000560","category_aro_cvterm_id":"36699","category_aro_name":"Erm 23S ribosomal RNA methyltransferase","category_aro_description":"Erm proteins are part of the RNA methyltransferase family and methylate A2058 (E. coli nomenclature) of the 23S ribosomal RNA conferring degrees of resistance to Macrolides, Lincosamides and Streptogramin b. This is called the MLSb phenotype.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"36295":{"category_aro_accession":"3000156","category_aro_cvterm_id":"36295","category_aro_name":"spiramycin","category_aro_description":"Spiramycin is a 16-membered macrolide and is natural product produced by Streptomyces ambofaciens. It binds to the 50S subunit of bacterial ribosomes and inhibits peptidyl transfer activity to disrupt protein synthesis.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"36723":{"category_aro_accession":"3000584","category_aro_cvterm_id":"36723","category_aro_name":"quinupristin","category_aro_description":"Quinupristin is a type B streptogramin and a semisynthetic derivative of pristinamycin 1A. It is a component of the drug Synercid and interacts with the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35967":{"category_aro_accession":"0000050","category_aro_cvterm_id":"35967","category_aro_name":"streptogramin B antibiotic","category_aro_description":"Streptogramin B antibiotics are are cyclic hepta- or hexa-depsipeptides.  Type B streptogramins block the peptide exit tunnel of the 50S bacterial ribosome. The general composition of group B streptogramins is 3-hydroxypicolinic acid-L-Thr-D-aminobutyric acid (or D-Ala)-L-Pro-L-Phe (or 4-N-,N-(dimethylamino)-L-Phe)-X-L-phenylglycine. Used alone, streptogramin B antibiotics are bacteriostatic, but is bactericidal when used with streptogramin A antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3342":{"model_id":"3342","model_name":"dfrA3b","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"280"}},"model_sequences":{"sequence":{"8345":{"protein_sequence":{"accession":"AAN85115.1","sequence":"MTKQAIFAVAENLAFGLGGGLPWDTLKDDLQFFKRLTEGTDLVMGASTYRTLPLLPTNNRQFIVVSNTEEPSLNVHVVSPEHFKAFLSKTSRNLTIIGGSSLLTVDILSKMDKIIMTTVYGSFDADVYLPTEVVSYVTGKASNATLFNNSDAKMAVYYG"},"dna_sequence":{"accession":"AY162283.2","fmin":"5615","fmax":"6095","strand":"+","sequence":"ATGACTAAACAAGCAATATTTGCCGTAGCCGAGAACCTAGCCTTCGGGCTAGGTGGGGGTCTCCCTTGGGATACGCTGAAAGACGACTTACAATTCTTTAAGAGGCTAACTGAAGGGACTGACTTAGTAATGGGAGCCTCCACGTACAGAACGCTGCCATTGTTACCAACCAATAACAGACAGTTTATTGTGGTAAGCAATACTGAGGAGCCTAGCCTTAATGTTCATGTGGTATCTCCAGAACACTTCAAGGCTTTCCTTAGCAAAACTTCCAGAAACCTTACTATTATCGGGGGCAGCTCGTTACTAACGGTAGATATATTATCAAAAATGGATAAGATAATTATGACTACGGTGTATGGAAGTTTTGATGCAGATGTATACTTACCTACTGAAGTAGTAAGTTATGTTACTGGCAAAGCTTCAAACGCCACATTATTTAATAACTCGGACGCAAAGATGGCAGTTTATTATGGATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3004642","ARO_id":"42653","ARO_name":"dfrA3b","CARD_short_name":"dfrA3b","ARO_description":"A dihydrofolate reductase that confers resistance to trimethoprim.","ARO_category":{"37617":{"category_aro_accession":"3001218","category_aro_cvterm_id":"37617","category_aro_name":"trimethoprim resistant dihydrofolate reductase dfr","category_aro_description":"Alternative dihydropteroate synthase dfr present on plasmids produces alternate proteins that are less sensitive to trimethoprim from inhibiting its role in folate synthesis, thus conferring trimethoprim resistance.","category_aro_class_name":"AMR Gene Family"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3347":{"model_id":"3347","model_name":"AQU-3","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"5475":{"protein_sequence":{"accession":"AHF82024.1","sequence":"MKQTSPLSLLALSALLLSPLTQAAPADPLVGVVDDVIRPLVKEHRIPGMAVAVLKGGQAHYFNYGVAELATGKKVSEQTLFEIGSVSKTLTATLGAYAVVKGSIGLDDKVSRHAPWLKGSAFDGITMAELATYSAGGLPLQFPDEVESLEQMQAYYRQWTPAYQPGSHRQYSNPSIGLFGYLAASSLQQPFAQLMEQTLLPGLGLHHTYINVPKQAMANYAYGYSKEDKPIRVTPGVLADEAYGIKTSSADLLAFVKANINGVDDKGLQQAIALTHQGHYSVGGMTQGLGWESYPYPVSEQTLQVGNSREVSFKGNPVKGFKAPVTFGEARLYNKTGSTNGFGAYVAFVXAKGVGIVMLANRNYPIQERVKAAHAILSKLAP"},"dna_sequence":{"accession":"KF730244.1","fmin":"0","fmax":"1149","strand":"+","sequence":"ATGAAGCAAACCTCACCCTTGTCGTTGCTGGCGCTGAGCGCCCTGCTGCTGTCGCCCCTCACCCAGGCCGCTCCCGCCGATCCGCTGGTCGGGGTAGTGGATGACGTCATTCGTCCGCTGGTGAAAGAGCACAGGATCCCGGGCATGGCGGTCGCCGTGCTGAAGGGGGGGCAGGCCCACTACTTCAACTACGGGGTTGCCGAGCTGGCAACGGGGAAGAAGGTCAGCGAGCAGACCCTGTTCGAGATTGGCTCGGTCAGCAAGACCCTGACCGCGACCCTGGGGGCCTACGCCGTGGTCAAGGGGAGCATTGGGCTGGATGACAAGGTGAGCCGGCACGCTCCCTGGCTCAAGGGCTCCGCCTTTGATGGCATTACCATGGCCGAGCTTGCCACTTACAGTGCCGGGGGCCTGCCGCTGCAATTCCCCGACGAGGTGGAATCGCTCGAGCAGATGCAGGCTTACTATCGCCAGTGGACGCCGGCCTATCAACCAGGCAGCCATCGCCAGTACTCCAACCCCAGTATCGGCCTGTTCGGCTATCTGGCGGCGAGCAGTCTGCAGCAGCCGTTTGCCCAGTTGATGGAGCAGACCCTGCTGCCAGGGCTCGGCCTGCATCACACCTATATCAATGTGCCTAAGCAGGCGATGGCGAACTACGCCTATGGCTATTCGAAAGAGGACAAGCCCATCAGGGTCACGCCAGGGGTGCTGGCGGACGAGGCCTACGGCATCAAGACCAGCTCGGCGGATCTGCTCGCCTTCGTGAAGGCCAACATCAACGGGGTGGATGACAAGGGGTTGCAGCAGGCCATCGCTTTGACCCACCAGGGGCACTACTCGGTAGGCGGGATGACTCAGGGGCTGGGCTGGGAGAGCTACCCCTATCCAGTCAGTGAGCAGACGCTGCAGGTTGGGAACTCCCGCGAGGTGAGTTTCAAGGGCAATCCTGTCAAAGGATTCAAGGCGCCGGTTACATTTGGTGAGGCGCGGCTCTACAACAAGACCGGCTCGACCAACGGCTTTGGCGCCTATGTGGCCTTCGTGCMGGCCAAGGGAGTGGGCATCGTCATGCTGGCCAACCGCAACTACCCCATCCAGGAGAGGGTAAAGGCGGCCCACGCCATCCTGAGCAAGCTGGCTCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39651","NCBI_taxonomy_name":"Aeromonas dhakensis","NCBI_taxonomy_id":"196024"}}}},"ARO_accession":"3004648","ARO_id":"42665","ARO_name":"AQU-3","CARD_short_name":"AQU-3","ARO_description":"AQU-3 is a chromosomally-encoded AQU class C beta-lactamase and cephalosporinase from.","ARO_category":{"39426":{"category_aro_accession":"3002992","category_aro_cvterm_id":"39426","category_aro_name":"AQU beta-lactamase","category_aro_description":"AQU beta-lactamases are chromosomal class C beta-lactamases that confer resistance to cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3622":{"model_id":"3622","model_name":"LEN-17","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"576"}},"model_sequences":{"sequence":{"5820":{"protein_sequence":{"accession":"AAZ79401.1","sequence":"MRYVRLCVISLLATLPLAVDAGPQPLEQIKQSESQLSGRVGMVEMDLASGRTLAAWRADERFPMVSTFKVLLCGAVLARVDAGVEQLDRRIHYRQQDLVDYSPVSEKHLTDGMTVGELCAAAITLSDNSAGNLLLATVGGPAGLTAFLRQIGDNVTRLDRWETALNEALPGDARDTTTPASMAATLRKLLTAQHLSARSQQQLLQWMVDDRVAGPLIRAVLPPGWFIADKTGAGERGARGIVALLGPDGKPERIVVIYLRDTPASMAERNQHIAGIGAALIEHWQR"},"dna_sequence":{"accession":"DQ149134.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGTGTTATCTCCCTGTTAGCCACCCTGCCACTGGCGGTAGACGCCGGTCCACAGCCGCTTGAGCAGATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTGGGGATGGTGGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCGATGAACGCTTTCCCATGGTGAGCACCTTTAAAGTGCTGCTGTGCGGCGCGGTGCTGGCGCGGGTGGATGCAGGGGTCGAACAACTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTACCGACGGGATGACGGTCGGCGAACTCTGCGCCGCCGCCATCACCCTGAGCGATAACAGTGCTGGCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCGGGATTAACTGCCTTTCTGCGCCAGATCGGTGACAACGTCACCCGTCTTGACCGCTGGGAAACGGCACTGAATGAGGCGCTTCCCGGCGACGCACGCGACACCACCACCCCGGCCAGCATGGCCGCCACGCTGCGCAAACTACTGACCGCGCAGCATCTGAGCGCCCGTTCGCAACAGCAACTCCTGCAGTGGATGGTGGACGATCGGGTTGCCGGCCCGCTGATCCGCGCCGTGCTGCCGCCGGGCTGGTTTATCGCCGACAAGACCGGGGCTGGCGAACGGGGTGCGCGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAACCGGAGCGCATTGTGGTGATCTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGTAATCAACATATCGCCGGGATCGGCGCAGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002473","ARO_id":"38873","ARO_name":"LEN-17","CARD_short_name":"LEN-17","ARO_description":"LEN-17 is a beta-lactamase found in Escherichia coli.","ARO_category":{"36236":{"category_aro_accession":"3000097","category_aro_cvterm_id":"36236","category_aro_name":"LEN beta-lactamase","category_aro_description":"LEN beta-lactamases are chromosomal class A beta-lactamases that confer resistance to ampicillin, amoxicillin, carbenicillin, and ticarcillin but not to extended-spectrum beta-lactams.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2374":{"model_id":"2374","model_name":"Escherichia coli uhpA with mutation conferring resistance to fosfomycin","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"4362":"G97D"},"Curated-R":{"4362":"G97D"},"clinical":{"4362":"G97D"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"3668":{"protein_sequence":{"accession":"CDJ73205.1","sequence":"MITVALIDDHLIVRSGFAQLLGLEPDLQVVAEFGSGREALAGLPGRGVQVCICDISMPDISGLELLSQLPKGMATIMLSVHDSPALVEQALNAGARGFLSKRCSPDELIAAVHTVATGGCYLTPDIAIKLASGRQDPLTKRERQVAEKLAQGMAVKEIAAELGLSPKTVHVHRANLMEKLGVSNDVELARRMFDGW"},"dna_sequence":{"accession":"HG738867.1","fmin":"2930707","fmax":"2931298","strand":"+","sequence":"ATGATCACCGTTGCCCTTATAGACGATCACCTCATCGTCCGCTCCGGCTTTGCGCAGCTGCTGGGGCTGGAACCTGATTTGCAGGTAGTTGCCGAGTTTGGTTCGGGGCGCGAGGCGCTGGCGGGGCTGCCGGGGCGCGGTGTGCAGGTGTGTATTTGCGATATCTCCATGCCCGATATCTCCGGTCTGGAGCTGCTAAGCCAGCTGCCGAAAGGTATGGCGACGATTATGCTCTCCGTTCACGACAGTCCTGCGCTGGTTGAGCAGGCGCTTAACGCGGGGGCACGCGGCTTTCTTTCCAAACGCTGTAGCCCGGATGAACTCATTGCTGCGGTGCATACGGTTGCCACGGGCGGCTGTTATCTGACGCCGGATATTGCCATTAAACTGGCATCCGGTCGTCAGGACCCGCTAACCAAACGTGAACGCCAGGTGGCGGAAAAACTGGCGCAAGGAATGGCGGTGAAAGAGATTGCCGCCGAACTGGGCTTGTCACCGAAAACGGTACACGTCCATCGCGCCAATCTGATGGAAAAACTGGGCGTCAGTAACGACGTAGAGCTGGCGCGCCGCATGTTTGATGGCTGGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40589","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. MC4100","NCBI_taxonomy_id":"1403831"}}}},"ARO_accession":"3003893","ARO_id":"40595","ARO_name":"Escherichia coli uhpA with mutation conferring resistance to fosfomycin","CARD_short_name":"Ecol_uhpA_FOF","ARO_description":"uhpA is a positive activator of the fosfomycin importer uhpT, thus mutations to uhpA confer fosfomycin resistance by reducing uhpT expression. Both knockout and amino acid substitution mutations have been found that confer resistance, with the Protein Knockout model describing the large, knockout mutations causing loss of function of the gene, and the Protein Variant model describing the amino acid substitutions.","ARO_category":{"41412":{"category_aro_accession":"3004248","category_aro_cvterm_id":"41412","category_aro_name":"antibiotic-resistant UhpT","category_aro_description":"UhpT encodes a transporter that can import fosfomycin-type drugs into bacterial cells. Mutations to UhpT confer resistance.","category_aro_class_name":"AMR Gene Family"},"35944":{"category_aro_accession":"0000025","category_aro_cvterm_id":"35944","category_aro_name":"fosfomycin","category_aro_description":"Fosfomycin (also known as phosphomycin and phosphonomycin) is a broad-spectrum antibiotic produced by certain Streptomyces species. It is effective on gram positive and negative bacteria as it targets the cell wall, an essential feature shared by both bacteria. Its specific target is MurA (MurZ in E.coli), which attaches phosphoenolpyruvate (PEP) to UDP-N-acetylglucosamine, a step of commitment to cell wall synthesis. In the active site of MurA, the active cysteine molecule is alkylated which stops the catalytic reaction.","category_aro_class_name":"Antibiotic"},"45731":{"category_aro_accession":"3007149","category_aro_cvterm_id":"45731","category_aro_name":"phosphonic acid antibiotic","category_aro_description":"A group of antibiotics derived from phosphonic acids.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2379":{"model_id":"2379","model_name":"Escherichia coli cyaA with mutation conferring resistance to fosfomycin","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"4382":"S352T"},"Curated-R":{"4382":"S352T"},"clinical":{"4382":"S352T"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1650"}},"model_sequences":{"sequence":{"4616":{"protein_sequence":{"accession":"CDJ73082.1","sequence":"MYLYIETLKQRLDAINQLRVDRALAAMGPAFQQVYSLLPTLLHYHHPLMPGYLDGNVPKGICLYTPDETQRHYLNELELYRGMSVQDPPKGELPITGVYTMGSTSSVGQSCSSDLDIWVCHQSWLDSEERQLLQRKCSLLENWAASLGVEVSFFLIDENRFRHNESGSLGGEDCGSTQHILLLDEFYRTAVRLAGKRILWNMVPCDEEEHYDDYVMTLYAQGVLTPNEWLDLGGLSSLSAEEYFGASLWQLYKSIDSPYKAVLKTLLLEAYSWEYPNPRLLAKDIKQRLHDGEIVSFGLDPYCMMLERVTEYLTAIEDFTRLDLVRRCFYLKVCEKLSRERACVGWRRAVLSQLVSEWGWDEARLAMLDNRANWKIDQVREAHNELLDAMMQSYRNLIRFARRNNLSVSASPQDIGVLTRKLYAAFEALPGKVTLVNPQISPDLSEPNLTFIYVPPGRANRSGWYLYNRAPNIESIISHQPLEYNRYLNKLVAWAWFNGLLTSRTRLYIKGNGIVDLPKLQEMVADVSHHFPLRLPAPTPKALYSPCEIRHLAIIVNLEYDPTAAFRNQVVHFDFRKLDVFSFGENQNCLVGSVDLLYRNSWNEVRTLHFNGEQSMIEALKTILGKMHQDAAPPDSVEVFCYSQHLRGLIRTRVQQLVSECIELRLSSTRQETGRFKALRVSGQTWGLFFERLNVSVQKLENAIEFYGAISHNKLHGLSVQVETNHVKLPAVVDGFASEGIIQFFFEETQDENGFNIYILDESNRVEVYHHCEGSKEELVRDVSRFYSSSHDRFTYGSSFINFNLPQFYQIVKVDGREQVIPFRTKSIGNMPPANQDHDTPLLQQYFS"},"dna_sequence":{"accession":"HG738867.1","fmin":"2786398","fmax":"2788945","strand":"-","sequence":"TTGTACCTCTATATTGAGACTCTGAAACAGAGACTGGATGCCATAAATCAATTGCGTGTGGATCGCGCGCTTGCTGCTATGGGGCCTGCATTCCAACAGGTCTACAGTCTACTGCCGACATTGTTGCACTATCACCATCCGCTAATGCCGGGTTACCTTGATGGTAACGTTCCCAAAGGCATTTGCCTTTACACGCCTGATGAAACTCAACGCCACTACCTGAACGAGCTTGAACTGTATCGTGGAATGTCAGTACAGGATCCGCCGAAAGGTGAGCTTCCAATTACTGGTGTATACACCATGGGCAGCACCTCGTCCGTAGGGCAAAGTTGTTCCTCTGACCTGGATATCTGGGTCTGTCATCAATCCTGGCTCGATAGCGAAGAGCGCCAATTGCTACAACGTAAATGTAGCCTGCTGGAAAACTGGGCCGCCTCGCTGGGTGTGGAAGTCAGCTTCTTCCTGATTGATGAAAACCGCTTCCGTCATAATGAAAGCGGCAGCCTGGGGGGCGAAGATTGTGGCTCCACCCAGCATATACTGCTGCTTGACGAATTTTATCGTACCGCCGTGCGTCTCGCCGGTAAGCGTATTCTGTGGAATATGGTGCCGTGCGACGAAGAAGAGCATTACGACGACTATGTGATGACGCTTTACGCGCAGGGCGTGCTGACGCCAAATGAATGGCTGGATCTCGGTGGCTTAAGCTCGCTTTCTGCTGAAGAGTACTTTGGTGCCAGCCTTTGGCAGCTCTACAAGAGTATCGATTCCCCATACAAAGCGGTACTGAAAACACTGCTGCTGGAAGCCTATTCCTGGGAATACCCGAACCCACGTCTGCTGGCGAAAGATATCAAACAGCGTTTGCACGACGGCGAGATTGTATCGTTTGGTCTCGATCCATACTGCATGATGCTGGAGCGTGTTACTGAATACCTGACGGCGATTGAAGATTTTACCCGTCTGGATTTAGTACGTCGCTGCTTCTATTTAAAAGTGTGCGAAAAGCTCAGCCGTGAACGCGCCTGCGTAGGCTGGCGTCGCGCAGTGTTGAGCCAGTTAGTGAGCGAGTGGGGTTGGGACGAAGCTCGTCTGGCAATGCTCGATAACCGCGCTAACTGGAAGATTGATCAGGTGCGTGAGGCGCACAACGAGTTGCTCGACGCGATGATGCAGAGCTACCGTAATCTGATCCGCTTTGCGCGTCGCAATAACCTTAGCGTCTCCGCCAGTCCGCAGGATATCGGCGTGCTGACGCGTAAGCTGTATGCCGCGTTTGAAGCATTACCAGGTAAAGTGACGCTGGTAAACCCGCAGATTTCACCCGATCTCTCGGAACCGAATCTGACCTTTATTTATGTGCCGCCGGGCCGGGCTAACCGTTCAGGTTGGTATCTGTATAACCGCGCGCCAAATATTGAGTCGATCATCAGCCATCAGCCGCTGGAATATAACCGTTACCTGAATAAACTGGTGGCGTGGGCATGGTTTAACGGCCTGCTGACCTCGCGCACCCGTTTGTATATTAAAGGTAACGGCATTGTCGATTTGCCTAAGTTGCAGGAGATGGTCGCCGACGTGTCGCACCATTTCCCGCTGCGCTTACCTGCACCGACACCGAAGGCGCTCTACAGCCCGTGTGAGATCCGCCATCTGGCGATTATCGTTAACCTGGAATATGACCCGACAGCGGCGTTCCGCAATCAGGTGGTGCATTTCGATTTCCGTAAGCTGGATGTCTTCAGCTTTGGCGAGAATCAAAATTGCCTGGTAGGTAGCGTTGACCTGCTGTACCGCAACTCGTGGAACGAAGTGCGTACGCTGCACTTCAACGGCGAGCAATCGATGATCGAAGCCCTGAAAACTATTCTCGGCAAAATGCATCAGGACGCCGCACCGCCAGATAGCGTGGAAGTCTTCTGTTATAGCCAGCATCTGCGCGGCTTAATTCGTACTCGCGTGCAGCAACTGGTTTCTGAGTGTATTGAATTGCGTCTTTCCAGCACCCGCCAGGAAACCGGGCGTTTCAAGGCGCTGCGCGTTTCTGGTCAAACCTGGGGGTTGTTCTTCGAACGCCTGAATGTATCGGTACAGAAACTGGAAAACGCCATCGAGTTTTATGGCGCGATTTCGCATAACAAACTGCACGGCCTGTCAGTGCAGGTTGAAACCAATCACGTCAAATTACCGGCGGTGGTGGACGGCTTTGCCAGCGAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCTTTAATATCTACATTCTCGACGAAAGCAACCGGGTTGAGGTATATCACCACTGCGAAGGCAGCAAAGAGGAGCTGGTACGTGACGTCAGTCGCTTCTACTCGTCATCGCATGACCGCTTTACCTACGGCTCAAGCTTCATCAACTTCAACCTGCCGCAGTTCTATCAGATTGTGAAGGTTGATGGTCGTGAACAGGTGATTCCGTTCCGCACAAAATCTATCGGTAACATGCCGCCTGCCAATCAGGATCACGATACGCCGCTATTACAGCAATATTTTTCGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40589","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. MC4100","NCBI_taxonomy_id":"1403831"}}}},"ARO_accession":"3003900","ARO_id":"40602","ARO_name":"Escherichia coli cyaA with mutation conferring resistance to fosfomycin","CARD_short_name":"Ecol_cyaA_FOF","ARO_description":"CyaA (adenylate cyclase) is involved with the synthesis of cyclic AMP which regulates the fosfomycin transporter glpT. As a result, mutations to cyaA confer resistance to fosfomycin.","ARO_category":{"41415":{"category_aro_accession":"3004251","category_aro_cvterm_id":"41415","category_aro_name":"antibiotic-resistant cya adenylate cyclase","category_aro_description":"Adenylate cyclases encoded by cya genes, which are involved in the synthesis cyclic AMP which regulates the fosfomycin transporter glpT. Mutations in cya genes can confer resistance to fosfomycin.","category_aro_class_name":"AMR Gene Family"},"35944":{"category_aro_accession":"0000025","category_aro_cvterm_id":"35944","category_aro_name":"fosfomycin","category_aro_description":"Fosfomycin (also known as phosphomycin and phosphonomycin) is a broad-spectrum antibiotic produced by certain Streptomyces species. It is effective on gram positive and negative bacteria as it targets the cell wall, an essential feature shared by both bacteria. Its specific target is MurA (MurZ in E.coli), which attaches phosphoenolpyruvate (PEP) to UDP-N-acetylglucosamine, a step of commitment to cell wall synthesis. In the active site of MurA, the active cysteine molecule is alkylated which stops the catalytic reaction.","category_aro_class_name":"Antibiotic"},"45731":{"category_aro_accession":"3007149","category_aro_cvterm_id":"45731","category_aro_name":"phosphonic acid antibiotic","category_aro_description":"A group of antibiotics derived from phosphonic acids.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2396":{"model_id":"2396","model_name":"OXA-368","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"5851":{"protein_sequence":{"accession":"AMB19637.1","sequence":"MKTFAAYVIIACLSSTALAGSITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPVSTFKIPSAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGDIDKFWLEGQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGIIGG"},"dna_sequence":{"accession":"KT736121.1","fmin":"1176","fmax":"1977","strand":"+","sequence":"ATGAAAACATTTGCCGCATATGTAATTATCGCGTGTCTTTCGAGTACGGCATTAGCTGGTTCAATTACAGAAAATACGTCTTGGAACAAAGAGTTCTCTGCCGAAGCCGTCAATGGTGTCTTCGTGCTTTGTAAAAGTAGCAGTAAATCCTGCGCTACCAATGACTTAGCTCGTGCATCAAAGGAATATCTTCCAGTATCAACATTTAAGATCCCCAGCGCAATTATCGGCCTAGAAACTGGTGTCATAAAGAATGAGCATCAGGTTTTCAAATGGGACGGAAAGCCAAGAGCCATGAAGCAATGGGAAAGAGACTTGACCTTAAGAGGGGCAATACAAGTTTCAGCTGTTCCCGTATTTCAACAAATCGCCAGAGAAGTTGGCGAAGTAAGAATGCAGAAATACCTTAAAAAATTTTCCTATGGCAACCAGAATATCAGTGGTGACATTGACAAATTCTGGTTGGAAGGCCAGCTTAGAATTTCCGCAGTTAATCAAGTGGAGTTTCTAGAGTCTCTATATTTAAATAAATTGTCAGCATCTAAAGAAAACCAGCTAATAGTAAAAGAGGCTTTGGTAACGGAGGCGGCACCTGAATATCTAGTGCATTCAAAAACTGGTTTTTCTGGTGTGGGAACTGAGTCAAATCCTGGTGTCGCATGGTGGGTTGGGTGGGTTGAGAAGGAGACAGAGGTTTACTTTTTCGCCTTTAACATGGATATAGACAACGAAAGTAAGTTGCCGCTAAGAAAATCCATTCCCACCAAAATCATGGAAAGTGAGGGCATCATTGGTGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36957","NCBI_taxonomy_name":"Aeromonas sobria","NCBI_taxonomy_id":"646"}}}},"ARO_accession":"3001555","ARO_id":"37955","ARO_name":"OXA-368","CARD_short_name":"OXA-368","ARO_description":"OXA-368 is a beta-lactamase found in Aeromonas sobria. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46486":{"category_aro_accession":"3007697","category_aro_cvterm_id":"46486","category_aro_name":"OXA-10-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-10.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2398":{"model_id":"2398","model_name":"TEM-220","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"3723":{"protein_sequence":{"accession":"AIW68620.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTTPATMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"KM998962.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGACGCCTGCAACAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36806","NCBI_taxonomy_name":"Neisseria gonorrhoeae","NCBI_taxonomy_id":"485"}}}},"ARO_accession":"3003158","ARO_id":"39735","ARO_name":"TEM-220","CARD_short_name":"TEM-220","ARO_description":"TEM-220 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2399":{"model_id":"2399","model_name":"oqxA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"670"}},"model_sequences":{"sequence":{"5460":{"protein_sequence":{"accession":"AAP43109.1","sequence":"MSLQKTWGNIHLTALGAMMLSFLLVGCDDSVAQNAAPPAPTVSAAKVLVKSISQWDSFNGRIEAVESVQLRPRVSGYIDKVNYTDGQEVKKGQVLFTIDDRTYRAALEQAQAALARAKTQASLAQSEANRTDKLVHTNLVSREEWEQRRSAAVQAQADIRAAQAAVDAAQLNLDFTKVTAPIDGRASRALITSGNLVTAGDTASVLTTLVSQKTVYVYFDVDESTYLHYQNLARRGQGASSDNQALPVEIGLVGEEGYPHQGKVDFLDNQLTPSTGTIRMRALLDNSQRLFTPGLFARVRLPGSAEFKATLIDDKAVLTDQDRKYVYIVDKDGKAQRRDITPGRLADGLRIVQKGLNPGDSVIVDGLQKVFMPGMPVNAKTVAMTSSATLN"},"dna_sequence":{"accession":"EU370913.1","fmin":"46651","fmax":"47827","strand":"+","sequence":"ATGAGCCTGCAAAAAACCTGGGGAAACATTCACCTGACCGCGCTCGGCGCGATGATGCTCTCCTTTCTGCTCGTCGGCTGCGACGACAGCGTCGCACAGAATGCTGCGCCTCCCGCCCCGACGGTCAGCGCCGCTAAGGTGCTGGTGAAGTCGATCAGTCAGTGGGATAGTTTTAACGGTCGCATTGAAGCGGTGGAGAGCGTTCAGCTTCGCCCTCGCGTCTCGGGATACATTGATAAAGTGAATTACACTGACGGCCAGGAGGTGAAAAAGGGCCAGGTGCTGTTCACGATAGATGACAGAACCTATCGCGCCGCGCTGGAGCAGGCGCAGGCGGCGTTGGCAAGAGCCAAAACGCAGGCCAGCCTCGCGCAAAGCGAGGCGAACCGCACCGATAAATTAGTCCATACCAACCTCGTCTCCCGTGAAGAGTGGGAGCAGCGCCGGTCAGCCGCGGTTCAGGCGCAGGCCGACATTCGCGCCGCGCAGGCGGCGGTGGATGCCGCGCAGCTTAACCTCGACTTCACCAAAGTGACCGCCCCTATTGACGGCCGCGCCAGCCGGGCGCTGATCACCAGCGGTAACCTGGTCACCGCGGGCGACACCGCCAGCGTGCTCACCACCCTGGTCTCGCAAAAGACGGTGTACGTCTACTTTGACGTCGACGAGTCAACCTACCTCCACTATCAAAACCTCGCCCGCCGCGGGCAAGGCGCGTCCAGCGATAATCAGGCGCTCCCGGTGGAGATTGGCCTGGTGGGCGAGGAGGGTTACCCCCACCAGGGCAAAGTGGATTTTCTCGATAATCAGTTAACGCCGAGTACCGGCACCATCCGCATGCGTGCGCTGCTGGATAACTCGCAGCGTCTGTTCACGCCGGGGCTGTTTGCCCGCGTGCGTCTGCCGGGCAGCGCAGAGTTCAAAGCCACGCTGATCGACGACAAAGCGGTACTGACCGATCAGGATCGTAAATACGTCTATATCGTTGATAAAGATGGTAAAGCACAGCGCCGCGACATTACCCCAGGGCGGCTGGCAGACGGTTTACGCATCGTTCAGAAGGGGTTGAATCCTGGGGATAGCGTCATCGTCGACGGCTTACAAAAAGTGTTTATGCCGGGTATGCCGGTTAACGCCAAAACCGTTGCCATGACCTCCAGCGCCACCCTTAACTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3003922","ARO_id":"40631","ARO_name":"oqxA","CARD_short_name":"oqxA","ARO_description":"RND efflux pump conferring resistance to fluoroquinolone.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35992":{"category_aro_accession":"0000075","category_aro_cvterm_id":"35992","category_aro_name":"nitrofurantoin","category_aro_description":"Nitrofurantoin is an antibiotic used to treat urinary tract infections. It inhibits enzyme synthesis by inhibiting essential enzymes involved in the citric acid cycle, as well as those involved in DNA, RNA, and protein synthesis. It is marketed under the following brand names: Furadantin, Macrobid, Macrodantin, Nitro Macro and Urantoin.","category_aro_class_name":"Antibiotic"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"41240":{"category_aro_accession":"3004116","category_aro_cvterm_id":"41240","category_aro_name":"nitrofuran antibiotic","category_aro_description":"Nitrofurans are chemotherapeutic agents with antibacterial and antiprotozoal activity.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2400":{"model_id":"2400","model_name":"oqxB","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"2000"}},"model_sequences":{"sequence":{"5462":{"protein_sequence":{"accession":"AAP43110.2","sequence":"MDFSRFFIDRPIFAAVLSILIFITGLIAIPLLPVSEYPDVVPPSVQVRAEYPGANPKVIAETVATPLEEAINGVENMMYMKSVAGSDGVLVTTVTFRPGTDPDQAQVQVQNRVAQAEARLPEDVRRLGITTQKQSPTLTLVVHLFSPGGKYDSLYMRNYATLKVKDELARLPGVGQIQIFGSGEYAMRVWLDPNKVAARGLTASDVVTAMQEQNVQVSAGQLGAEPLPQESDFLISINAQGRLHTEEEFGNIILKTAQDGSLVRLRDVARIEMGSGSYALRSQLNNKDAVGIGIFQSPGANAIDLSNAVRAKMAELATRFPEDMQWAAPYDPTVFVRDSIRAVVQTLLEAVVLVVLVVILFLQTWRASIIPLIAVPVSVVGTFSILYLLGFSLNTLSLFGLVLAIGIVVDDAIVVVENVERNIEEGLAPLAAAHQAMREVSGPIIAIALVLCAVFVPMAFLSGVTGQFYKQFAVTIAISTVISAINSLTLSPALAALLLKPHGAKKDLPTRLIDRLFGWIFRPFNRFFLRSSNGYQGLVGKTLGRRGAVFAVYLLLLCAAGVMFKVVPGGFIPTQDKLYLIGGVKMPEGSSLARTDAVIRKMSEIGMNTEGVDYAVAFPGLNALQFTNTPNTGTVFFGLKPFDQRKHTAAEINAEINAKIAQIQQGFGFSILPPPILGLGQGSGYSLYIQDRGGLGYGALQSAVNAMSGAIMQTPGMHFPISTYQANVPQLDVQVDRDKAKAQGVSLTDLFGTLQTYLGSSYVNDFNQFGRTWRVMAQADGPYRESVEDIANLRTRNNQGEMVPIGSMVNISTTYGPDPVIRYNGYPAADLIGDADPRVLSSSQAMTHLEELSKQILPNGMNIEWTDLSFQQATQGNTALIVFPVAVLLAFLVLAALYESWTLPLAVILIVPMTMLSALFGVWLTGGDNNVFVQVGLVVLMGLACKNAILIVEFARELEIQGKGIMEAALEACRLRLRPIVMTSIAFIAGTIPLILGHGAGAEVRGVTGITVFSGMLGVTLFGLFLTPVFYVTLRKLVTRRKPVQEDLPA"},"dna_sequence":{"accession":"EU370913.1","fmin":"47850","fmax":"51003","strand":"+","sequence":"ATGGACTTTTCCCGCTTTTTTATCGACAGGCCGATTTTCGCCGCGGTGCTGTCGATTTTAATTTTTATCACCGGGTTAATCGCTATCCCACTGCTGCCGGTGAGCGAATATCCGGATGTCGTCCCGCCGAGCGTCCAGGTGCGCGCGGAGTATCCCGGCGCCAACCCGAAAGTGATTGCCGAGACCGTGGCGACGCCGCTGGAGGAAGCGATCAACGGCGTTGAAAACATGATGTACATGAAATCGGTCGCCGGCTCCGACGGCGTGCTGGTCACCACCGTCACCTTCCGCCCGGGTACCGACCCGGATCAGGCGCAGGTTCAGGTGCAGAACCGCGTCGCGCAGGCCGAAGCGCGTCTGCCGGAGGATGTACGCCGTCTGGGGATCACCACCCAGAAGCAGTCTCCGACGCTGACCCTGGTGGTGCATCTGTTCTCCCCCGGCGGGAAGTACGACTCGCTGTATATGCGCAACTACGCCACGCTGAAAGTGAAGGATGAGCTGGCGCGCCTGCCCGGCGTCGGCCAGATCCAGATTTTTGGCTCCGGTGAATATGCGATGCGCGTCTGGCTGGATCCCAATAAGGTCGCTGCCCGCGGTCTGACGGCCTCGGATGTGGTGACGGCGATGCAGGAGCAAAACGTCCAGGTGTCTGCCGGACAGCTTGGCGCCGAGCCGCTGCCGCAGGAGAGCGATTTCCTGATCTCCATTAACGCCCAGGGCCGTCTGCATACCGAAGAAGAGTTTGGCAATATCATTCTGAAAACGGCGCAGGATGGCTCGCTGGTCCGCCTGCGCGACGTGGCGCGCATCGAGATGGGTTCCGGTAGCTATGCGCTGCGCTCCCAGCTCAACAATAAGGATGCGGTCGGGATCGGTATCTTCCAGTCACCCGGCGCTAACGCCATCGATCTGTCGAACGCGGTACGCGCCAAAATGGCCGAGCTGGCCACCCGCTTCCCGGAAGATATGCAATGGGCGGCGCCGTACGACCCGACGGTTTTCGTCCGCGACTCCATCCGCGCGGTGGTGCAGACGCTGCTGGAGGCGGTAGTGCTGGTGGTGCTGGTAGTGATCCTGTTCCTGCAGACCTGGCGCGCGTCGATTATCCCGTTGATCGCTGTGCCGGTATCGGTGGTGGGTACCTTCAGCATTCTCTATCTGCTGGGCTTCTCGCTGAATACCCTGAGCCTGTTCGGGCTGGTACTGGCTATCGGTATCGTGGTGGACGACGCCATCGTGGTGGTGGAGAACGTCGAGCGTAATATCGAAGAGGGGCTTGCGCCGCTTGCCGCGGCGCATCAGGCGATGCGTGAGGTCTCCGGGCCGATTATCGCCATTGCGCTGGTGCTGTGTGCGGTGTTCGTGCCGATGGCGTTTCTCTCCGGGGTCACCGGCCAGTTCTACAAACAGTTCGCGGTGACCATCGCCATCTCGACGGTGATCTCGGCCATCAACTCGCTGACGCTCTCCCCGGCGCTGGCGGCCCTGCTGTTAAAGCCGCACGGCGCGAAGAAAGACCTCCCTACCCGGCTGATCGATCGCCTGTTTGGCTGGATTTTCCGTCCGTTTAACCGCTTTTTCCTGCGCAGCTCGAACGGCTATCAGGGACTGGTAGGCAAAACGCTTGGACGCCGTGGCGCAGTGTTTGCGGTGTACCTGCTGCTGCTCTGCGCCGCTGGGGTGATGTTTAAAGTCGTCCCCGGCGGGTTTATTCCCACCCAGGATAAGCTGTATCTCATTGGCGGCGTGAAGATGCCGGAAGGGTCGTCGCTGGCGCGCACCGACGCGGTGATCCGCAAAATGAGCGAGATCGGGATGAATACCGAAGGGGTCGACTATGCGGTCGCTTTCCCGGGGCTTAACGCGCTGCAGTTCACCAACACGCCGAATACCGGGACGGTCTTTTTTGGCCTGAAACCGTTCGACCAGCGCAAACACACGGCGGCGGAAATTAACGCGGAGATCAACGCCAAAATCGCGCAAATCCAGCAGGGCTTTGGCTTTTCCATCCTGCCGCCGCCGATTTTAGGTCTGGGTCAGGGTTCCGGCTACTCCCTGTACATCCAGGATCGCGGAGGGCTGGGCTATGGCGCGCTGCAAAGCGCGGTGAATGCGATGTCCGGGGCGATTATGCAGACGCCGGGGATGCACTTCCCGATCTCGACTTACCAGGCTAACGTGCCGCAGCTGGACGTGCAGGTCGATCGCGATAAGGCGAAAGCGCAGGGGGTATCGCTAACCGATCTGTTCGGTACGCTGCAGACCTATCTCGGCTCGTCTTATGTCAATGACTTTAACCAGTTCGGGCGTACCTGGCGCGTGATGGCCCAGGCTGACGGACCATACCGCGAGAGCGTGGAAGATATCGCCAATCTGCGCACCCGCAATAATCAGGGCGAAATGGTACCGATCGGCAGTATGGTGAATATCAGTACCACCTACGGGCCGGATCCGGTGATCCGCTACAACGGTTATCCGGCGGCGGACCTGATTGGCGATGCCGATCCGCGGGTCCTCTCTTCTTCGCAGGCGATGACGCATCTGGAAGAGCTGTCGAAGCAGATCCTGCCGAATGGGATGAATATTGAGTGGACGGATCTCAGCTTCCAGCAGGCCACCCAGGGCAACACGGCGCTGATCGTCTTCCCGGTGGCGGTGCTGCTGGCATTCCTCGTACTGGCCGCGCTGTATGAAAGCTGGACCCTGCCGCTGGCGGTGATCCTTATCGTACCGATGACGATGCTCTCCGCGCTGTTTGGCGTCTGGCTGACCGGGGGCGATAACAACGTCTTCGTGCAGGTGGGTCTGGTGGTCCTGATGGGCCTGGCCTGTAAAAACGCCATTCTGATCGTCGAGTTTGCCCGCGAGCTGGAGATCCAGGGGAAAGGCATCATGGAAGCGGCGCTGGAGGCATGCCGCCTGCGTCTGCGCCCGATCGTGATGACCTCCATCGCCTTTATCGCCGGGACCATTCCGCTGATCCTCGGCCACGGCGCGGGGGCGGAAGTCCGCGGCGTCACCGGGATCACGGTGTTCTCCGGGATGCTGGGCGTGACGCTCTTCGGTCTGTTCCTGACGCCGGTGTTTTACGTGACGCTACGGAAACTGGTGACCCGCAGGAAGCCGGTCCAGGAGGATCTGCCCGCCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3003923","ARO_id":"40632","ARO_name":"oqxB","CARD_short_name":"oqxB","ARO_description":"RND efflux pump conferring resistance to fluoroquinolone.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35992":{"category_aro_accession":"0000075","category_aro_cvterm_id":"35992","category_aro_name":"nitrofurantoin","category_aro_description":"Nitrofurantoin is an antibiotic used to treat urinary tract infections. It inhibits enzyme synthesis by inhibiting essential enzymes involved in the citric acid cycle, as well as those involved in DNA, RNA, and protein synthesis. It is marketed under the following brand names: Furadantin, Macrobid, Macrodantin, Nitro Macro and Urantoin.","category_aro_class_name":"Antibiotic"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"41240":{"category_aro_accession":"3004116","category_aro_cvterm_id":"41240","category_aro_name":"nitrofuran antibiotic","category_aro_description":"Nitrofurans are chemotherapeutic agents with antibacterial and antiprotozoal activity.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"3398":{"model_id":"3398","model_name":"aadA10","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"535"}},"model_sequences":{"sequence":{"5586":{"protein_sequence":{"accession":"AAL36430.1","sequence":"MRNTVPAEISVQLSQALNVIEHHLGSTLLAMHLYGSALDGGLKPYSDIDLLVTVTARLDESVRQALFVDLLGVSVFPGQSRVLRALEVTIVVHSDIVPWRYPARRELQFGEWQRKDILAGIFEPATTDVDLAILLTKARQHSLALAGSAAEDFFNPVPESDLFKALADTLKLWNSQPDWIGDERNVVLTLSRIWYSAATGKIAPKDVAANWVMERLPVQHQPVLLEARQAYLGQGEDCLASLTDQLEAFVHFVKHEATKLLGATPMMSKTKLDALST"},"dna_sequence":{"accession":"U37105.2","fmin":"2806","fmax":"3640","strand":"+","sequence":"ATGAGAAACACAGTGCCCGCCGAGATTTCGGTACAGTTATCACAGGCACTCAACGTCATCGAGCATCATCTGGGATCGACGTTGCTGGCCATGCATTTGTATGGCTCTGCACTCGACGGTGGCCTGAAGCCATACAGTGACATTGATTTGCTGGTTACTGTGACCGCACGGCTCGATGAGAGTGTGCGGCAAGCTCTGTTCGTCGATCTCTTGGGGGTTTCCGTTTTCCCTGGTCAAAGCAGAGTTCTCCGCGCCTTGGAAGTTACCATTGTCGTGCACAGTGACATCGTTCCTTGGCGCTATCCGGCCAGACGGGAACTGCAATTCGGGGAGTGGCAGCGCAAAGACATTCTTGCGGGCATCTTCGAGCCTGCGACAACCGATGTTGATCTAGCCATTCTGCTAACAAAAGCAAGGCAACATAGCCTTGCCTTGGCCGGTTCGGCTGCGGAAGATTTCTTCAACCCAGTCCCGGAAAGCGATCTGTTCAAGGCACTGGCCGACACCCTGAAACTATGGAACTCACAGCCGGATTGGATAGGTGACGAGCGGAATGTAGTGCTTACTTTGTCTCGTATTTGGTACAGCGCAGCAACCGGCAAGATCGCGCCGAAGGATGTTGCCGCCAACTGGGTAATGGAGCGTTTGCCAGTTCAACATCAGCCCGTGCTGCTTGAAGCCCGGCAGGCTTATCTTGGACAAGGAGAAGATTGCTTGGCTTCGCTCACGGATCAGTTAGAGGCGTTTGTTCACTTCGTGAAGCATGAAGCCACTAAACTGCTTGGTGCCACGCCAATGATGTCTAAAACAAAGTTAGATGCACTAAGCACATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3004692","ARO_id":"42744","ARO_name":"aadA10","CARD_short_name":"aadA10","ARO_description":"aadA10 is a aminoglycoside nucleotidyltransferase gene encoded by plasmids in P. aeruginosa.","ARO_category":{"41439":{"category_aro_accession":"3004275","category_aro_cvterm_id":"41439","category_aro_name":"ANT(3'')","category_aro_description":"A category of aminoglycoside O-nucleotidyltransferase enzymes with modification regiospecificity based at the 3''-hydroxyl group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics by transfer of an AMP group from an ATP substrate to the 3''-hydroxyl group of the compound.","category_aro_class_name":"AMR Gene Family"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"660":{"model_id":"660","model_name":"Streptococcus pneumoniae parC conferring resistance to fluoroquinolones","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1400"},"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"9866":"S82F","9867":"D86H","9865":"S82Y"},"Curated-R":{"9866":"S82F","9867":"D86H","9865":"S82Y"},"clinical":{"9866":"S82F","9867":"D86H","9865":"S82Y"}}},"model_sequences":{"sequence":{"6037":{"protein_sequence":{"accession":"NP_358351.1","sequence":"MYLMSNIQNMSLEDIMGERFGRYSKYIIQDRALPDIRDGLKPVQRRILYSMNKDSNTFDKSYRKSAKSVGNIMGNFHPHGDSSIYDAMVRMSQNWKNREILVEMHGNNGSMDGDPPAAMRYTEARLSEIAGYLLQDIEKKTVPFAWNFDDTEKEPTVLPAAFPNLLVNGSTGISAGYATDIPPHNLAEVIDAAVYMIDHPTAKIDKLMEFLPGPDFPTGAIIQGRDEIKKAYETGKGRVVVRSKTEIEKLKGGKEQIVITEIPYEINKANLVKKIDDVRVNNKVAGIAEVRDESDRDGLRIAIELKKDANTELVLNYLFKYTDLQINYNFNMVAIDNFTPRQVGIVPILSSYIAHRREVILARSRFDKEKAEKRLRIVEGLIRVISILDEVIALIRASENKADAKENLKVSYDFTEEQAEAIVTLQLYRLTNTDVVVLQEEEAELREKIAMLAAIIGDERTMYNLMKKELREVKKNFATPRLSSLEDTAKAIEIDTASLIAEEDTYVSVTKAGYIKRTSPRSFAASTLEEIGKRDDDRLIFVQSAKTTQHLLMFTSLGNVIYRPIHELADIRWKDIGEHLSQTITNFETNEAILYVEVLDQFDDATTYFAATRLGQIKRVERKEFTPWRTYRSKSVKYAKLKDDTDQIVAVAPIKLDDVVLVSQNGYALRFNIEEVPVVGAKAAGVKAMNLKEDDVLQSGFICNTSSFYLLTQRGSLKRVSIEEILATSRAKRGLQVLRELKNKPHRVFLAGAVAEQGFVGDFFSTEVDVNDQTLLVQSNKGTIYESRLQDLNLSERTSNGSFISDTISDEEVFDAYLQEVVTEDK"},"dna_sequence":{"accession":"NC_003098.1","fmin":"752240","fmax":"754721","strand":"+","sequence":"TTGTATCTTATGTCTAACATTCAAAACATGTCCCTGGAGGACATCATGGGAGAGCGCTTTGGTCGCTACTCCAAGTACATTATTCAAGACCGGGCTTTGCCAGATATTCGTGATGGGTTGAAGCCGGTTCAACGCCGTATTCTTTATTCTATGAATAAGGATAGCAATACTTTTGACAAGAGCTACCGTAAGTCGGCCAAGTCAGTCGGGAACATCATGGGGAATTTCCACCCACACGGGGATTCTTCTATCTATGATGCCATGGTTCGTATGTCACAGAACTGGAAAAATCGTGAGATTCTAGTTGAAATGCACGGTAATAACGGTTCTATGGACGGAGATCCTCCTGCGGCTATGCGTTATACTGAGGCACGTTTGTCTGAAATTGCAGGCTACCTTCTTCAGGATATCGAGAAAAAGACAGTTCCTTTTGCATGGAACTTTGACGATACGGAGAAAGAACCAACGGTCTTGCCAGCAGCCTTTCCAAACCTCTTGGTCAATGGTTCGACTGGGATTTCGGCTGGTTATGCCACAGACATTCCTCCCCATAATTTAGCTGAGGTCATAGATGCTGCAGTTTACATGATTGACCACCCAACTGCAAAGATTGATAAACTCATGGAATTCTTACCTGGACCAGACTTCCCTACAGGGGCTATTATTCAGGGTCGTGATGAAATCAAGAAAGCCTATGAGACTGGGAAAGGGCGCGTGGTTGTTCGTTCCAAGACTGAAATTGAAAAGCTAAAAGGTGGTAAGGAACAAATCGTTATTACTGAGATTCCTTATGAAATCAATAAGGCCAATCTAGTCAAGAAAATCGATGATGTTCGTGTTAATAACAAGGTAGCTGGGATTGCTGAGGTTCGTGATGAGTCTGACCGTGATGGTCTTCGTATCGCTATTGAACTTAAGAAAGACGCTAATACTGAGCTTGTTCTCAACTACTTATTTAAGTACACCGACCTACAAATCAACTACAACTTTAATATGGTGGCGATTGACAATTTCACACCTCGTCAGGTTGGGATTGTTCCAATCCTGTCTAGCTACATCGCTCACCGTCGAGAAGTGATTTTGGCGCGTTCACGCTTTGACAAAGAAAAGGCTGAGAAACGTCTCCGTATCGTCGAAGGTTTGATTCGTGTGATTTCGATTTTGGATGAAGTCATTGCTCTTATCCGTGCTTCTGAGAATAAGGCGGACGCCAAGGAAAACCTCAAAGTTAGCTATGATTTTACGGAAGAACAGGCTGAGGCTATCGTAACTTTGCAACTGTACCGTTTGACCAATACCGATGTGGTTGTCTTGCAGGAAGAAGAAGCAGAGCTTCGTGAGAAGATTGCTATGCTGGCGGCTATTATCGGTGATGAAAGGACTATGTACAATCTCATGAAGAAAGAACTTCGTGAGGTCAAGAAGAACTTTGCAACTCCTCGTTTGAGTTCTTTAGAAGACACTGCGAAAGCAATTGAGATTGATACAGCTAGTCTTATCGCTGAGGAAGATACCTACGTCAGCGTGACCAAGGCAGGTTACATCAAGCGTACCAGTCCACGTTCCTTTGCGGCTTCCACCTTGGAAGAAATTGGCAAGCGTGATGATGACCGTTTGATTTTTGTTCAATCTGCCAAGACAACCCAGCACCTCTTGATGTTCACAAGTCTTGGAAATGTCATCTACAGACCAATCCATGAGTTGGCAGATATTCGTTGGAAGGACATCGGAGAGCATCTGAGCCAAACCATCACAAACTTTGAAACGAATGAAGCAATCCTTTATGTGGAAGTACTGGATCAGTTTGACGATGCGACAACCTACTTTGCAGCGACTCGCCTTGGTCAAATCAAACGGGTAGAGCGAAAAGAATTCACTCCATGGCGGACCTATAGATCTAAGTCTGTCAAGTATGCTAAGCTCAAAGACGATACAGATCAGATTGTAGCAGTGGCTCCGATTAAACTAGATGATGTTGTCTTGGTTAGTCAAAATGGTTATGCCCTGCGTTTCAATATCGAAGAGGTTCCGGTTGTCGGTGCTAAGGCAGCAGGTGTCAAGGCTATGAATTTGAAAGAAGATGATGTCCTCCAATCTGGCTTTATCTGTAATACTTCGTCCTTCTACCTCTTGACCCAGCGTGGAAGCTTGAAACGTGTTTCCATTGAGGAAATTCTAGCAACCAGCCGTGCCAAACGAGGATTACAAGTCTTGCGTGAGTTGAAAAACAAACCGCATCGTGTCTTCTTGGCAGGAGCAGTTGCAGAGCAAGGATTTGTTGGCGATTTCTTCAGTACGGAAGTGGATGTGAACGACCAAACTCTGCTTGTCCAATCCAATAAAGGAACAATCTATGAAAGCCGATTGCAAGACTTGAACTTGTCAGAACGCACTAGCAATGGAAGCTTCATTTCTGACACGATTTCAGATGAAGAAGTTTTTGACGCTTATCTTCAGGAAGTAGTTACTGAAGATAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39596","NCBI_taxonomy_name":"Streptococcus pneumoniae R6","NCBI_taxonomy_id":"171101"}}}},"ARO_accession":"3003311","ARO_id":"39895","ARO_name":"Streptococcus pneumoniae parC conferring resistance to fluoroquinolones","CARD_short_name":"Spne_parC_FLO","ARO_description":"Point mutation in Streptococcus pneumoniae parC resulting in fluoroquinolone resistance.","ARO_category":{"36913":{"category_aro_accession":"3000619","category_aro_cvterm_id":"36913","category_aro_name":"fluoroquinolone resistant parC","category_aro_description":"ParC is a subunit of topoisomerase IV, which decatenates and relaxes DNA to allow access to genes for transcription or translation. Point mutations in ParC prevent fluoroquinolone antibiotics from inhibiting DNA synthesis, and confer low-level resistance. Higher-level resistance results from both gyrA and parC mutations.","category_aro_class_name":"AMR Gene Family"},"35942":{"category_aro_accession":"0000023","category_aro_cvterm_id":"35942","category_aro_name":"enoxacin","category_aro_description":"Enoxacin belongs to a group called fluoroquinolones. Its mode of action depends upon blocking bacterial DNA replication by binding itself to DNA gyrase and causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37004":{"category_aro_accession":"3000660","category_aro_cvterm_id":"37004","category_aro_name":"lomefloxacin","category_aro_description":"Lomefloxacin is a difluoropiperazinyl quinolone, sharing similar activities with other fluoroquinolones. It is used to treat urinary tract infections. Relative to other fluoroquinolones, it has a longer half life and has higher serum concentrations.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37007":{"category_aro_accession":"3000663","category_aro_cvterm_id":"37007","category_aro_name":"ofloxacin","category_aro_description":"Ofloxacin is a 6-fluoro, 7-piperazinyl quinolone with a methyl-substituted oxazine ring. It has a broad spectrum of activity including many enterobacteria and mycoplasma but most anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"37008":{"category_aro_accession":"3000664","category_aro_cvterm_id":"37008","category_aro_name":"trovafloxacin","category_aro_description":"Trovafloxacin is a trifluoroquinalone with a broad spectrum of activity that acts by inhibiting the uncoiling of supercoiled DNA. While potent against many Gram-positive and Gram-negative bacteria, it is less active against pseudomonads and Cl. difficile. It is usually taken as the prodrug trovafloxacin mesylate or alatrofloxacin mesylate for oral or intravenous administration, respectively.","category_aro_class_name":"Antibiotic"},"37009":{"category_aro_accession":"3000665","category_aro_cvterm_id":"37009","category_aro_name":"grepafloxacin","category_aro_description":"Grepafloxacin is a broad-spectrum antibacterial quinoline. It is no longer taken due to its high toxicity.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"37142":{"category_aro_accession":"3000762","category_aro_cvterm_id":"37142","category_aro_name":"pefloxacin","category_aro_description":"Pefloxacin is structurally and functionally similar to norfloxacin. It is poorly active against mycobacteria, while anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2104":{"model_id":"2104","model_name":"Ureaplasma urealyticum parC conferring resistance to fluoroquinolones","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"3974":"S83L","3975":"S83W","3976":"S84P","4636":"E87Q"},"Curated-R":{"3974":"S83L","3975":"S83W","3976":"S84P","4636":"E87Q"},"clinical":{"3974":"S83L","3975":"S83W","3976":"S84P","4636":"E87Q"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1400"}},"model_sequences":{"sequence":{"5888":{"protein_sequence":{"accession":"WP_010891786.1","sequence":"MSVNHQKIINTPLDNIVGESYAKYAKYIIQDRALPDIRDGLKPVQRRILYAMSELGIFYDKPYKKSARTVGEVIGKYHPHGDSSIYEAMVRMSQDWKNNLCLLDMHGNKGSIDGDNAAAMRYTEARLSKIASVMLANLKKDVVKFSPNFDDSEKEPSILPSLFPNLLINGATGIASGYATNIPPHNPNEVFDALIYRIDHPDCSVEKLIEICPAPDFPTGGEIHDLNGCANAHKTGEGKFIIRACIDFKINDNKINQIIISSIPYETNKALIIKEIEDIIYNKEVAGLIEVRDESDAKGISIIIDTKKDINLENVKNYLYKKTNLEISYNTKFIAIVHRTPTLVNLSTYLDAQINHSLDVINKVDLYDLNKILLRIEIVEGLIKCVDLIDEIIKIIRASESRQDAKNTLIQVFNFTNNQAEAIIMMRLHNLTRTDIFDLKNEWQTLQDEAKTLQERINSLQVRKNYLKQKMIEFKKTFGFERKTKLFDELVKVEINEDQMIEKQNLNLVISRDGYIKTVSKKSFESSKYDELGLKTNDILFYHNIINSHDKILIITSKAKLINLVAHKITSMRWKDVGEHLNNYVKFDANEKVIAVYIWNEQFKIDEYQLVLASRLNLIKRIELSELDINKNSKQISIMKLNDNDNLISANLIKKGHNQFIIAISKLGLALLFLVHEINCLNRLAKGIKIMKLKPNDEVSAILITPNNGYNVQLFLERGSKCFNISELKLSKRAATPTNLYPITKKVQNVLAAFLVAHENVFYLLDQQQKINPYYLSNPKPTKLDTKISIYENDQMITDVVKDCFLSDEAISDFKKINMYANEFDNEMLKINKNHDDSQLELIDEEEEKK"},"dna_sequence":{"accession":"NC_002162.1","fmin":"531446","fmax":"533999","strand":"+","sequence":"ATGAGTGTAAATCATCAAAAAATTATTAATACACCTTTAGACAACATTGTTGGTGAAAGTTATGCAAAATATGCAAAATACATTATTCAAGATCGTGCTTTACCTGATATTCGTGATGGTTTAAAACCTGTTCAACGACGAATTTTATACGCAATGAGTGAATTAGGAATCTTTTATGATAAACCTTATAAAAAATCTGCACGTACAGTAGGAGAAGTAATTGGTAAATATCATCCACATGGAGATTCATCAATTTATGAAGCAATGGTGAGAATGAGTCAAGATTGAAAAAATAATCTATGTTTATTAGATATGCATGGTAATAAAGGTTCAATTGATGGTGATAATGCTGCTGCAATGCGTTATACAGAAGCTCGATTATCAAAAATTGCTAGTGTAATGTTAGCCAACTTAAAAAAAGATGTTGTTAAATTTAGTCCAAACTTTGATGATAGTGAAAAAGAGCCATCAATTTTACCATCTCTTTTTCCTAATTTGTTAATCAATGGAGCAACAGGAATTGCTTCTGGTTATGCAACAAATATTCCTCCTCATAACCCTAATGAAGTTTTTGATGCTTTAATTTATCGTATTGATCATCCAGATTGTAGTGTAGAAAAACTAATTGAAATCTGTCCTGCGCCAGATTTTCCCACAGGTGGGGAAATCCACGATTTAAATGGATGTGCTAATGCTCACAAAACTGGTGAAGGTAAATTTATAATTCGTGCTTGCATTGATTTTAAAATCAATGATAATAAGATTAATCAAATTATTATTAGTTCAATCCCTTATGAAACAAACAAGGCTTTAATCATTAAAGAAATTGAAGATATTATTTATAATAAAGAAGTTGCTGGATTAATCGAAGTTCGTGATGAATCTGATGCTAAGGGAATTAGTATAATTATTGATACTAAAAAAGATATTAATTTAGAAAATGTTAAAAACTATTTATATAAAAAAACCAACTTGGAAATCAGCTATAATACAAAATTTATTGCAATTGTTCACCGAACTCCTACACTTGTAAATCTATCTACATATTTAGATGCTCAAATTAATCATAGTTTAGATGTAATTAATAAAGTCGATTTATATGATCTAAACAAAATTTTGTTACGTATTGAAATTGTTGAAGGCTTAATTAAATGCGTTGATTTAATTGATGAAATTATTAAAATTATTCGTGCTAGTGAATCGCGTCAAGATGCAAAAAATACTTTAATTCAAGTTTTTAATTTTACAAATAATCAAGCTGAAGCGATTATTATGATGCGTTTACATAATTTGACACGTACTGATATATTTGATTTAAAAAATGAATGACAAACGCTACAAGACGAAGCTAAAACGCTACAAGAACGAATAAATTCACTTCAAGTTCGCAAAAATTATTTAAAACAAAAAATGATTGAATTTAAAAAAACTTTTGGTTTTGAACGCAAAACAAAATTATTTGATGAATTAGTAAAAGTTGAAATAAACGAAGATCAAATGATCGAAAAACAAAATTTGAATTTAGTAATAAGTCGTGATGGATACATTAAAACTGTTTCTAAAAAGTCATTTGAGTCATCTAAATATGATGAATTAGGATTAAAAACTAATGATATTCTTTTTTATCATAATATCATTAATTCTCATGATAAAATCCTAATCATTACATCAAAAGCTAAATTAATTAATTTAGTTGCTCATAAAATCACTTCTATGCGGTGAAAAGATGTTGGTGAACACTTAAATAATTATGTGAAATTTGATGCTAATGAAAAAGTTATAGCTGTTTATATATGGAACGAACAATTTAAAATTGATGAATATCAATTAGTTTTGGCTTCTAGATTAAATCTAATTAAAAGAATTGAATTAAGCGAGTTGGATATAAATAAAAATAGTAAACAAATTAGCATTATGAAATTAAATGATAATGATAATTTAATCAGTGCTAATTTAATCAAAAAAGGTCATAATCAATTTATTATTGCAATTTCTAAATTAGGATTAGCCCTGCTATTTTTAGTTCATGAAATTAATTGCTTAAATCGTTTAGCTAAAGGAATTAAAATTATGAAATTAAAACCAAATGATGAGGTTAGTGCTATTTTAATTACTCCTAATAATGGTTATAATGTTCAACTTTTTTTAGAACGGGGAAGTAAGTGTTTTAATATTAGTGAATTAAAATTATCAAAACGTGCGGCCACACCAACAAATTTATATCCAATAACAAAAAAAGTGCAAAATGTTTTAGCAGCTTTTTTAGTTGCTCATGAAAATGTTTTTTATCTTTTAGATCAACAACAAAAAATAAATCCATATTACTTATCAAACCCCAAACCAACAAAACTAGATACTAAAATTAGTATCTATGAAAACGATCAAATGATCACTGATGTAGTTAAAGATTGCTTTTTAAGTGATGAAGCAATTAGTGATTTTAAAAAAATTAATATGTACGCAAATGAATTTGATAATGAAATGCTAAAAATTAATAAAAATCACGATGATTCACAATTAGAATTAATTGATGAAGAGGAAGAAAAAAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40416","NCBI_taxonomy_name":"Ureaplasma parvum","NCBI_taxonomy_id":"134821"}}}},"ARO_accession":"3003309","ARO_id":"39893","ARO_name":"Ureaplasma urealyticum parC conferring resistance to fluoroquinolones","CARD_short_name":"Uure_parC_FLO","ARO_description":"Point mutation in Ureaplasma urealyticum parC resulting in fluoroquinolone resistance.","ARO_category":{"36913":{"category_aro_accession":"3000619","category_aro_cvterm_id":"36913","category_aro_name":"fluoroquinolone resistant parC","category_aro_description":"ParC is a subunit of topoisomerase IV, which decatenates and relaxes DNA to allow access to genes for transcription or translation. Point mutations in ParC prevent fluoroquinolone antibiotics from inhibiting DNA synthesis, and confer low-level resistance. Higher-level resistance results from both gyrA and parC mutations.","category_aro_class_name":"AMR Gene Family"},"35942":{"category_aro_accession":"0000023","category_aro_cvterm_id":"35942","category_aro_name":"enoxacin","category_aro_description":"Enoxacin belongs to a group called fluoroquinolones. Its mode of action depends upon blocking bacterial DNA replication by binding itself to DNA gyrase and causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37004":{"category_aro_accession":"3000660","category_aro_cvterm_id":"37004","category_aro_name":"lomefloxacin","category_aro_description":"Lomefloxacin is a difluoropiperazinyl quinolone, sharing similar activities with other fluoroquinolones. It is used to treat urinary tract infections. Relative to other fluoroquinolones, it has a longer half life and has higher serum concentrations.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37007":{"category_aro_accession":"3000663","category_aro_cvterm_id":"37007","category_aro_name":"ofloxacin","category_aro_description":"Ofloxacin is a 6-fluoro, 7-piperazinyl quinolone with a methyl-substituted oxazine ring. It has a broad spectrum of activity including many enterobacteria and mycoplasma but most anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"37008":{"category_aro_accession":"3000664","category_aro_cvterm_id":"37008","category_aro_name":"trovafloxacin","category_aro_description":"Trovafloxacin is a trifluoroquinalone with a broad spectrum of activity that acts by inhibiting the uncoiling of supercoiled DNA. While potent against many Gram-positive and Gram-negative bacteria, it is less active against pseudomonads and Cl. difficile. It is usually taken as the prodrug trovafloxacin mesylate or alatrofloxacin mesylate for oral or intravenous administration, respectively.","category_aro_class_name":"Antibiotic"},"37009":{"category_aro_accession":"3000665","category_aro_cvterm_id":"37009","category_aro_name":"grepafloxacin","category_aro_description":"Grepafloxacin is a broad-spectrum antibacterial quinoline. It is no longer taken due to its high toxicity.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"37142":{"category_aro_accession":"3000762","category_aro_cvterm_id":"37142","category_aro_name":"pefloxacin","category_aro_description":"Pefloxacin is structurally and functionally similar to norfloxacin. It is poorly active against mycobacteria, while anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2401":{"model_id":"2401","model_name":"Haemophilus parainfluenzae gyrA conferring resistance to fluoroquinolones","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"4438":"S84Y"},"Curated-R":{"4438":"S84Y"},"clinical":{"4438":"S84Y"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1500"}},"model_sequences":{"sequence":{"5463":{"protein_sequence":{"accession":"CBW16027.1","sequence":"MTDSIHSSITPVNIEEELKSSYLDYAMSVIVGRALPDVRDGLKPVHRRVLFSMDQSGITAGKKYVKSARVVGDVIGKYHPHGDSAVYDTIVRMAQPFSLRYMLVDGQGNFGSIDGDAPAAMRYTEVRMQKITQALLTDLDKETVNFSPNYDGELMIPDVLPTRIPALLANGSSGIAVGMATNIPPHNLNEVLDGCLAYIDNENITIDELMQYIPGPDFPTAALINGRKGIEEAYRTGRGKVYVRARASVETTDKGKEQIIVTELPYQVNKAKLVEKIAELIKDKKIEGISNIIDLSNKEGIRIEIDIKRDAVGEVVLNHLYALTQMQVTFGINMVALDHGQPRLFNLKQIIEAFVMHRREVVIRRSLFELRKARERTHILEGLAVATSNIDEIIDIIRQSKERKEAAEKLISRPWKLNNEILGLLDAAARPAELAAEFGIKGSDYYLSPEQVDAILELRLHRLTGLATEEVINEYKELLVKIAELLHIINSPERLMEVIREELEQVRAQFADERRTEITAASGDIDLEDLIAQEDVVVTLSHEGYVKYQPLTDYEAQRRGGKGKSATKMKDEDFIEKLLVANTHDTILCFSSRGRLYWLKVYQLPQASRGARGRPIVNILPLQENERITAILPISAYEEDKFVIMATAGGIVKKIALTEFSRPRSSGIIALNLRDEDELIGVDITDGSNEIMLFSSQGRVVRFAESAVRAMGRLATGVRGIKLALTNDIADDESAVEIEEVSDDNAEETLDLNIDKVVSLVVPKNDGAILTATQNGYGKRTQLSEYPTKSRNTKGVISIKVSERNGKVVAATQVEETDQIMLITDAGTLVRTRVSEVSIVGRNTQGVRLIRTAEDEHVVSLERVCDVDDEDEGTEDVTSEE"},"dna_sequence":{"accession":"FQ312002.1","fmin":"1996520","fmax":"1999166","strand":"+","sequence":"ATGACGGATTCAATCCATTCCTCTATTACCCCAGTCAATATTGAAGAAGAACTAAAATCTTCTTACCTTGACTACGCCATGTCGGTGATTGTTGGGCGTGCTTTGCCTGATGTGCGTGACGGTTTAAAACCGGTGCATCGACGTGTGCTTTTCTCCATGGATCAATCTGGCATCACTGCCGGCAAAAAATACGTAAAATCTGCCCGTGTGGTAGGTGATGTAATCGGTAAATATCACCCGCACGGTGATTCTGCAGTGTACGACACCATTGTGCGTATGGCACAGCCGTTCTCATTGCGCTACATGTTGGTAGATGGGCAAGGTAACTTCGGTTCAATCGACGGTGATGCGCCAGCGGCAATGCGTTATACCGAAGTCCGTATGCAAAAAATCACCCAAGCGTTATTAACTGACTTGGATAAAGAAACCGTAAATTTCTCGCCAAACTATGATGGCGAATTAATGATTCCGGATGTATTACCAACTCGTATTCCTGCACTTTTAGCAAACGGTTCTTCCGGTATTGCGGTGGGGATGGCAACCAACATTCCACCACACAACTTAAATGAAGTTTTAGATGGATGCTTGGCTTATATTGATAACGAAAACATCACCATTGATGAGTTAATGCAATATATCCCGGGCCCAGACTTCCCAACAGCGGCATTAATTAATGGCCGTAAAGGGATTGAAGAAGCTTATCGCACTGGTCGCGGCAAAGTGTATGTTCGCGCTCGCGCTAGCGTAGAAACCACAGATAAAGGCAAAGAGCAAATTATTGTGACCGAATTGCCTTATCAAGTGAACAAAGCCAAATTAGTGGAAAAAATTGCTGAGCTTATCAAAGATAAAAAAATCGAAGGCATCAGCAATATTATCGACCTTTCGAACAAAGAAGGGATTCGCATTGAAATTGACATCAAACGTGATGCCGTAGGCGAAGTAGTATTAAATCACCTCTATGCGCTTACCCAAATGCAGGTAACCTTCGGGATTAACATGGTGGCCTTGGATCACGGTCAACCACGTTTATTCAACTTAAAACAAATCATTGAAGCCTTTGTGATGCACCGTCGCGAAGTGGTGATTCGCCGTTCTTTATTTGAATTGCGTAAAGCCCGCGAGCGTACCCATATTTTAGAAGGTTTAGCGGTTGCAACATCAAATATCGATGAAATCATCGATATCATCCGTCAATCGAAAGAGCGTAAAGAAGCGGCAGAAAAATTAATCTCTCGCCCTTGGAAATTGAATAACGAAATTTTAGGTTTACTTGATGCAGCGGCACGTCCAGCTGAGTTAGCGGCTGAATTTGGTATTAAAGGTTCGGATTACTATCTTTCTCCAGAACAAGTTGATGCAATCTTAGAACTTCGCTTGCATCGTTTAACCGGTCTTGCTACCGAAGAAGTAATCAATGAATACAAAGAGTTATTGGTTAAAATTGCAGAACTTCTCCACATCATCAACAGCCCTGAGCGTTTGATGGAAGTGATTCGTGAAGAGCTTGAACAAGTACGCGCACAATTCGCGGATGAACGTCGTACCGAAATTACTGCGGCTTCTGGTGATATTGATTTAGAAGATTTAATTGCTCAAGAAGATGTGGTAGTGACCCTTTCTCACGAAGGTTATGTGAAATATCAACCGCTTACCGACTACGAAGCACAACGTCGTGGTGGTAAAGGTAAATCCGCAACGAAGATGAAAGATGAAGACTTCATTGAAAAACTCTTAGTAGCGAATACTCACGATACGATTCTCTGTTTCTCTAGCCGCGGTCGCTTATATTGGTTGAAAGTCTATCAATTACCACAAGCAAGCCGTGGTGCGCGTGGTCGTCCGATTGTGAATATTCTACCGTTGCAAGAAAACGAGCGTATCACCGCAATCTTGCCAATCTCTGCTTATGAAGAAGATAAATTCGTCATCATGGCAACGGCTGGTGGTATTGTGAAGAAAATTGCGCTAACCGAATTCAGCCGTCCACGTTCAAGCGGTATCATCGCCTTGAACTTACGTGATGAAGATGAATTAATCGGCGTGGATATCACCGATGGTTCTAACGAAATCATGTTGTTCTCTTCGCAAGGTCGCGTAGTACGTTTCGCTGAAAGTGCAGTGCGTGCAATGGGTCGTTTAGCAACAGGTGTACGCGGTATTAAACTCGCCCTAACCAACGACATCGCTGACGATGAAAGTGCGGTCGAAATTGAAGAGGTTTCCGATGATAATGCAGAAGAAACCCTCGATCTCAATATCGATAAAGTGGTTTCCTTAGTTGTGCCGAAAAATGACGGCGCAATCCTTACGGCGACGCAAAACGGTTACGGTAAACGCACACAATTAAGCGAATACCCAACCAAATCCCGTAATACCAAAGGGGTGATTTCGATTAAAGTGAGCGAACGTAACGGTAAAGTCGTTGCGGCGACACAAGTGGAAGAAACCGACCAAATTATGCTTATCACTGATGCGGGTACCTTAGTGCGTACTCGTGTAAGTGAAGTGAGCATCGTTGGCCGTAACACCCAAGGGGTTCGTTTAATTCGTACCGCAGAAGATGAGCACGTAGTCAGTCTTGAACGTGTTTGTGATGTGGATGATGAAGACGAAGGCACTGAAGATGTGACTTCTGAAGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42651","NCBI_taxonomy_name":"Haemophilus parainfluenzae T3T1","NCBI_taxonomy_id":"862965"}}}},"ARO_accession":"3003924","ARO_id":"40633","ARO_name":"Haemophilus parainfluenzae gyrA conferring resistance to fluoroquinolones","CARD_short_name":"Hpin_gyrA_FLO","ARO_description":"Point mutation of Haemophilus parainfluenzae gyrA resulted in the lowered affinity between fluoroquinolones and GyrA. Thus, conferring resistance. Both Ser and Tyr are hydrophilic amino acids, however Tyr has an additional bulky hydrophobic group which could affect the interaction between the DNA gyrase with quinolones.","ARO_category":{"39876":{"category_aro_accession":"3003292","category_aro_cvterm_id":"39876","category_aro_name":"fluoroquinolone resistant gyrA","category_aro_description":"DNA gyrase is responsible for DNA supercoiling and consists of two alpha and two beta subunits. GyrA point mutations confer resistance by preventing fluoroquinolone antibiotics from binding the alpha-subunit.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2402":{"model_id":"2402","model_name":"Haemophilus parainfluenzae parC conferring resistance to fluoroquinolones","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"4440":"S84F"},"Curated-R":{"4440":"S84F"},"clinical":{"4440":"S84F"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1400"}},"model_sequences":{"sequence":{"3728":{"protein_sequence":{"accession":"WP_041918279.1","sequence":"MSNINYEGIEQMPLRTFTEKAYLNYSMYVIMDRALPFIGDGLKPVQRRIVYAMSELGLNAAAKFKKSARTVGDVLGKFHPHGDSACYEAMVLMAQPFSYRYPLVDGQGNWGAPDDPKSFAAMRYTESRLSKISEILLSELGQGTVDFQPNFDGTLEEPQYLPARLPHILLNGTTGIAVGMATDIPPHNINEVADAAVMLLDNPKAGLDDVLNIIQGPDFPTEAEIISPKDDIRKMYETGRGSIKMRATWHKEDGEIIISALPHQSSPSKIIAQIAEQMTAKKLPMVEDIRDEADYENPVRIVLVPRSNRVDTDALMAHLFATTDLEKSYRVNMNMIGLDHKPAVKGLLQVLIEWLTFRRTTVTRRLQHRLDKVLARLHILDGLMIAFLNIDEVIEIIRTEDEPKQVLMARFNLSDEQAEAILNLRLRHLAKLEEHQLQAEKDKLEEERSNLELILGSERRLNTLIKKEIQEDAKKYASPRMSQLVEREEAKAISESEMTPAEPVTVILSEMGWVRCAKGHDIDPEGLSYKAGDKYLAHACGKSNQPVIFIDSTGRSYALDPLSLPSARSQGEPLTGKLTLPAGATIEQVIMEPEKQELLMASDAGYGFICKFEDLIARNKAGKALISLPENAKVLKPETLSESTSLLVSLTSAGRMLIFPVRDLPALSKGKGNKIISIPAANAKARSELLVKLFLISEQASLEFHSGKRKITLKPEDLQKFRAERGRKGSQLPRGLHSNVDIVVVEPEHNS"},"dna_sequence":{"accession":"NC_015964.1","fmin":"1905162","fmax":"1907418","strand":"+","sequence":"ATGAGCAATATTAATTACGAAGGCATCGAGCAGATGCCACTTCGCACCTTTACAGAAAAGGCTTACCTTAATTATTCAATGTACGTCATCATGGATCGTGCATTGCCTTTTATTGGCGATGGCTTAAAGCCTGTTCAACGTCGTATTGTCTATGCGATGTCTGAACTGGGTTTAAATGCCGCGGCAAAATTTAAAAAGTCCGCGCGTACCGTCGGTGATGTGTTAGGTAAATTCCATCCACATGGTGACTCTGCTTGTTATGAAGCCATGGTATTAATGGCTCAGCCTTTTTCTTATCGTTATCCTTTGGTAGATGGGCAAGGAAACTGGGGGGCGCCAGATGATCCTAAATCATTTGCGGCAATGCGTTATACAGAATCTCGCCTGTCCAAAATCTCTGAAATTTTATTATCTGAATTAGGCCAAGGCACTGTTGATTTCCAACCGAACTTTGATGGTACCTTAGAAGAACCTCAATATTTGCCTGCACGTTTGCCTCATATTCTGTTAAACGGCACCACCGGGATTGCCGTCGGGATGGCAACCGATATTCCACCACATAATATTAATGAAGTGGCGGATGCCGCTGTTATGCTATTAGATAATCCAAAAGCAGGATTAGATGATGTACTCAATATCATTCAAGGCCCGGATTTCCCAACTGAAGCGGAAATTATTTCACCAAAAGATGATATTCGCAAAATGTATGAAACCGGTCGTGGTTCTATCAAAATGCGTGCAACATGGCATAAAGAAGACGGTGAAATCATCATTAGTGCACTTCCTCATCAATCTTCACCATCAAAAATCATTGCGCAAATTGCTGAACAAATGACAGCAAAAAAATTGCCAATGGTGGAAGATATTCGTGATGAAGCAGATTATGAAAACCCTGTACGTATCGTGCTTGTGCCACGTTCAAATCGTGTTGATACGGATGCCTTAATGGCGCATTTATTTGCGACGACTGATCTCGAAAAAAGCTATCGTGTAAATATGAATATGATCGGACTTGATCATAAACCAGCCGTAAAAGGCCTACTTCAAGTTCTTATCGAATGGCTGACATTCCGTCGTACTACCGTGACACGTCGTTTACAACATCGTTTAGATAAAGTACTCGCTCGTTTGCACATTTTAGATGGTTTGATGATTGCCTTCCTCAATATTGACGAAGTGATTGAGATTATTCGTACTGAAGATGAACCAAAACAAGTTTTAATGGCTCGCTTTAACTTAAGTGATGAACAGGCAGAAGCCATTTTAAACTTACGTTTACGCCATTTGGCCAAATTAGAAGAACATCAATTACAAGCTGAAAAAGATAAACTCGAAGAAGAGCGGTCAAATTTAGAGTTAATTTTAGGATCTGAACGTCGCTTAAATACCTTGATCAAAAAAGAAATTCAAGAAGATGCGAAAAAATACGCCAGCCCTAGAATGTCTCAATTAGTTGAACGTGAAGAAGCGAAAGCCATTTCTGAAAGTGAAATGACTCCGGCTGAACCCGTTACCGTTATCTTATCTGAAATGGGCTGGGTACGCTGTGCAAAAGGTCATGACATTGATCCGGAAGGATTAAGCTATAAAGCAGGCGATAAATATCTGGCTCACGCTTGCGGTAAAAGTAATCAGCCTGTAATCTTTATTGACAGCACGGGGCGTAGCTATGCTTTAGATCCATTAAGCTTGCCTTCTGCGCGTTCACAAGGTGAACCACTCACCGGTAAACTGACATTACCGGCCGGTGCGACCATTGAACAGGTTATTATGGAACCTGAAAAACAAGAATTATTGATGGCATCAGATGCAGGATATGGTTTTATTTGCAAATTTGAAGATTTAATTGCGCGTAATAAAGCAGGAAAAGCCTTGATTTCTTTGCCAGAAAATGCGAAAGTCTTGAAACCTGAGACACTTTCCGAGTCGACCTCACTTCTTGTGTCCCTCACTTCAGCGGGTCGAATGCTGATTTTTCCGGTACGGGATTTACCGGCATTATCAAAAGGGAAAGGCAACAAAATCATCAGTATTCCAGCAGCGAATGCAAAAGCGCGGTCAGAATTATTAGTGAAATTGTTCTTAATTTCAGAGCAAGCTAGCCTTGAGTTCCATTCCGGTAAACGAAAAATCACATTAAAACCGGAAGATCTGCAAAAATTCCGAGCGGAACGCGGCAGAAAAGGCTCCCAATTACCACGTGGATTACATAGCAATGTTGATATTGTGGTAGTTGAACCCGAACACAACTCATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36927","NCBI_taxonomy_name":"Haemophilus parainfluenzae","NCBI_taxonomy_id":"729"}}}},"ARO_accession":"3003925","ARO_id":"40634","ARO_name":"Haemophilus parainfluenzae parC conferring resistance to fluoroquinolones","CARD_short_name":"Hpin_parC_FLO","ARO_description":"Point mutation of Haemophilus parainfluenzae parC resulted in the lowered affinity between fluoroquinolones and ParC. Thus, conferring resistance.","ARO_category":{"36913":{"category_aro_accession":"3000619","category_aro_cvterm_id":"36913","category_aro_name":"fluoroquinolone resistant parC","category_aro_description":"ParC is a subunit of topoisomerase IV, which decatenates and relaxes DNA to allow access to genes for transcription or translation. Point mutations in ParC prevent fluoroquinolone antibiotics from inhibiting DNA synthesis, and confer low-level resistance. Higher-level resistance results from both gyrA and parC mutations.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2403":{"model_id":"2403","model_name":"Salmonella enterica gyrA conferring resistance to fluoroquinolones","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"4443":"S97P","4444":"S83F","4445":"D87N","4446":"D87Y"},"Curated-R":{"4443":"S97P","4444":"S83F","4445":"D87N","4446":"D87Y"},"clinical":{"4443":"S97P","4444":"S83F","4445":"D87N","4446":"D87Y"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1500"}},"model_sequences":{"sequence":{"5271":{"protein_sequence":{"accession":"AAL21173.1","sequence":"MSDLAREITPVNIEEELKSSYLDYAMSVIVGRALPDVRDGLKPVHRRVLYAMNVLGNDWNKAYKKSARVVGDVIGKYHPHGDSAVYDTIVRMAQPFSLRYMLVDGQGNFGSIDGDSAAAMRYTEIRLAKIAHELMADLEKETVDFVDNYDGTEKIPDVMPTKIPNLLVNGSSGIAVGMATNIPPHNLTEVINGCLAYIDNEDISIEGLMEHIPGPDFPTAAIINGRRGIEEAYRTGRGKVYIRARAEVEADAKTGRETIIVHEIPYQVNKARLIEKIAELVKDKRVEGISALRDESDKDGMRIVIEVKRDAVGEVVLNNLYSQTQLQVSFGINMVALHHGQPKIMNLKDIISAFVRHRREVVTRRTIFELRKARDRAHILEALAIALANIDPIIELIRRAPTPAEAKAALISRPWDLGNVAAMLERAGDDAARPEWLEPEFGVRDGQYYLTEQQAQAILDLRLQKLTGLEHEKLLDEYKELLEQIAELLHILGSADRLMEVIREEMELIRDQFGDERRTEITANSADINIEDLISQEDVVVTLSHQGYVKYQPLTDYEAQRRGGKGKSAARIKEEDFIDRLLVANTHDTILCFSSRGRLYWMKVYQLPEASRGARGRPIVNLLPLEANERITAILPVREYEEGVNVFMATASGTVKKTALTEFSRPRSAGIIAVNLNDGDELIGVDLTSGSDEVMLFSAAGKVVRFKEDAVRAMGRTATGVRGIKLAGDDKVVSLIIPRGEGAILTVTQNGYGKRTAADEYPTKSRATQGVISIKVTERNGSVVGAVQVDDCDQIMMITDAGTLVRTRVSEISVVGRNTQGVILIRTAEDENVVGLQRVAEPVDDEELDAIDGSVAEGDEDIAPEAESDDDVADDADE"},"dna_sequence":{"accession":"AE006468.2","fmin":"2373709","fmax":"2376346","strand":"-","sequence":"ATGAGCGACCTTGCGAGAGAAATTACACCGGTCAACATTGAGGAGGAGCTGAAGAGCTCCTATCTGGATTATGCGATGTCGGTCATTGTTGGCCGTGCGCTGCCGGATGTCCGAGATGGCCTGAAGCCGGTACACCGTCGCGTACTTTACGCCATGAACGTATTGGGCAATGACTGGAACAAAGCCTATAAAAAATCTGCCCGTGTCGTTGGTGACGTAATCGGTAAATACCATCCCCACGGCGATTCCGCAGTGTATGACACCATCGTTCGTATGGCGCAGCCATTCTCGCTGCGTTACATGCTGGTGGATGGTCAGGGTAACTTCGGTTCTATTGACGGCGACTCCGCGGCGGCAATGCGTTATACGGAGATCCGTCTGGCGAAAATCGCCCACGAACTGATGGCCGATCTCGAAAAAGAGACGGTGGATTTCGTGGATAACTATGACGGTACGGAAAAAATTCCGGACGTCATGCCGACCAAAATTCCGAATCTGCTGGTGAACGGTTCTTCCGGTATCGCAGTAGGTATGGCGACGAATATCCCGCCGCACAACCTGACGGAAGTGATTAACGGCTGCCTGGCGTATATCGACAACGAAGACATCAGCATTGAAGGGCTGATGGAACATATTCCGGGGCCGGACTTCCCGACCGCCGCGATCATCAACGGTCGTCGTGGTATCGAAGAAGCCTACCGCACCGGTCGTGGCAAAGTGTACATTCGCGCCCGCGCGGAAGTTGAAGCTGACGCCAAAACGGGCCGTGAAACCATCATCGTCCATGAAATTCCCTATCAGGTGAACAAAGCGCGCCTGATCGAGAAAATCGCCGAGCTGGTGAAAGATAAACGCGTGGAAGGCATCAGCGCGCTGCGTGACGAATCCGACAAAGACGGGATGCGCATCGTGATTGAAGTGAAACGCGATGCGGTGGGCGAGGTGGTGCTTAATAATCTCTACTCCCAGACCCAGCTACAGGTTTCCTTCGGTATTAACATGGTGGCGCTGCATCACGGCCAGCCGAAGATCATGAACCTGAAAGATATCATTTCAGCGTTCGTGCGCCACCGCCGTGAAGTGGTGACGCGTCGGACTATTTTTGAACTGCGTAAAGCCCGTGACCGTGCGCATATCCTTGAAGCTCTGGCGATTGCGCTGGCCAACATCGACCCGATTATCGAACTGATTCGCCGCGCGCCAACGCCGGCGGAAGCAAAAGCGGCGCTGATTTCGCGTCCGTGGGATCTGGGCAACGTTGCTGCGATGCTGGAGCGCGCTGGTGATGACGCCGCGCGTCCGGAATGGCTGGAGCCAGAATTTGGCGTGCGTGACGGTCAGTACTACCTGACTGAACAGCAGGCGCAGGCGATTCTGGATCTGCGTTTGCAGAAACTGACCGGCCTGGAGCATGAAAAACTGCTCGACGAATACAAAGAGCTGCTGGAGCAGATTGCTGAATTGCTGCACATTCTGGGCAGCGCCGATCGCCTGATGGAAGTGATCCGCGAAGAGATGGAGTTAATTCGCGATCAGTTCGGCGATGAGCGTCGTACCGAAATCACCGCCAACAGCGCCGATATTAATATCGAAGATCTGATTAGCCAGGAAGATGTTGTCGTGACGCTGTCTCACCAGGGTTACGTCAAATATCAACCGCTGACAGATTACGAAGCGCAACGTCGTGGTGGGAAAGGTAAATCTGCCGCGCGTATTAAAGAAGAAGACTTTATCGACCGCCTGCTGGTGGCTAACACCCATGACACCATCCTCTGCTTCTCCAGCCGGGGCCGTCTGTACTGGATGAAGGTCTATCAGCTGCCGGAAGCCAGCCGCGGCGCGCGCGGTCGTCCGATCGTCAACCTGCTGCCGCTGGAAGCCAACGAACGTATCACCGCGATTCTGCCGGTTCGTGAGTATGAAGAAGGCGTCAACGTCTTTATGGCGACCGCCAGCGGTACCGTGAAGAAAACGGCGCTGACCGAATTCAGCCGTCCGCGTTCCGCCGGTATTATCGCGGTGAACCTCAACGACGGCGACGAGCTGATTGGCGTTGACCTGACTTCTGGTTCTGACGAAGTCATGCTGTTCTCGGCCGCGGGTAAAGTGGTGCGCTTCAAAGAAGACGCCGTCCGTGCGATGGGGCGTACCGCGACCGGTGTGCGCGGTATTAAGCTGGCGGGAGACGATAAAGTCGTCTCTCTGATCATCCCACGCGGCGAAGGCGCTATTCTGACCGTAACGCAAAACGGCTACGGGAAGCGTACCGCAGCGGACGAGTACCCGACCAAGTCTCGTGCGACGCAGGGCGTTATCTCTATCAAAGTGACCGAGCGCAACGGTTCCGTTGTCGGTGCGGTACAGGTAGACGATTGCGACCAGATCATGATGATCACGGATGCCGGTACTCTGGTGCGTACCCGTGTGTCCGAGATCAGCGTAGTGGGACGTAATACCCAGGGCGTTATCCTTATCCGCACGGCGGAAGATGAAAACGTGGTGGGTCTGCAACGCGTTGCTGAACCGGTAGATGACGAAGAACTCGACGCTATCGACGGCAGCGTGGCGGAAGGGGATGAGGATATCGCCCCGGAAGCGGAAAGCGATGACGACGTTGCGGATGACGCTGACGAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35734","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Typhimurium str. LT2","NCBI_taxonomy_id":"99287"}}}},"ARO_accession":"3003926","ARO_id":"40635","ARO_name":"Salmonella enterica gyrA conferring resistance to fluoroquinolones","CARD_short_name":"Sent_gyrA_FLO","ARO_description":"Point mutations in Salmonella gyrA that confer resistance to Nalidixic acid, a fluoroquinolone antibiotic. These mutations have also been shown to reduce susceptibility to ciprofloxacin.","ARO_category":{"39876":{"category_aro_accession":"3003292","category_aro_cvterm_id":"39876","category_aro_name":"fluoroquinolone resistant gyrA","category_aro_description":"DNA gyrase is responsible for DNA supercoiling and consists of two alpha and two beta subunits. GyrA point mutations confer resistance by preventing fluoroquinolone antibiotics from binding the alpha-subunit.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2406":{"model_id":"2406","model_name":"rpsJ","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"4458":"V57L","4457":"V57M"},"Curated-R":{"4458":"V57L","4457":"V57M"},"clinical":{"4458":"V57L","4457":"V57M"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"200"}},"model_sequences":{"sequence":{"5267":{"protein_sequence":{"accession":"AAW90462.1","sequence":"MANQKIRIRLKAYDYALIDRSAQEIVETAKRTGAVVKGPIPLPTKIERFNILRSPHVNKTSREQLEIRTHLRLMDIVDWTDKTTDALMKLDLPAGVDVEIKVQ"},"dna_sequence":{"accession":"AE004969.1","fmin":"1807358","fmax":"1807670","strand":"-","sequence":"ATGGCAAACCAAAAAATCCGTATCCGCCTGAAAGCTTATGATTACGCCCTGATTGACCGTTCTGCACAAGAAATCGTTGAAACTGCAAAACGTACCGGTGCTGTTGTAAAAGGCCCGATTCCTTTGCCGACCAAAATCGAGCGTTTCAACATTTTGCGTTCTCCGCACGTGAACAAAACTTCCCGTGAACAATTGGAAATCCGCACCCATTTGCGCCTGATGGACATCGTGGATTGGACCGATAAAACTACCGATGCGCTGATGAAGCTGGATTTGCCGGCCGGTGTTGATGTAGAAATTAAAGTCCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40638","NCBI_taxonomy_name":"Neisseria gonorrhoeae FA 1090","NCBI_taxonomy_id":"242231"}}}},"ARO_accession":"3003930","ARO_id":"40640","ARO_name":"rpsJ","CARD_short_name":"rpsJ","ARO_description":"rpsJ is a tetracycline resistance protein identified in Neisseria gonorrhoeae. Tetracycline resistance is conferred by binding to the ribosome as a 30S ribosomal protection protein.","ARO_category":{"35921":{"category_aro_accession":"0000002","category_aro_cvterm_id":"35921","category_aro_name":"tetracycline-resistant ribosomal protection protein","category_aro_description":"A family of proteins known to bind to the 30S ribosomal subunit. This interaction prevents tetracycline and tetracycline derivatives from inhibiting ribosomal function. Thus, these proteins confer elevated resistance to tetracycline derivatives as a ribosomal protection protein.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2407":{"model_id":"2407","model_name":"Capnocytophaga gingivalis gyrA conferring resistance to fluoroquinolones","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"4461":"G80N"},"Curated-R":{"4461":"G80N"},"clinical":{"4461":"G80N"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1500"}},"model_sequences":{"sequence":{"3733":{"protein_sequence":{"accession":"EEK14408.1","sequence":"MVEGEKLIPINIEDQMKTAYIDYSMSVIVSRALPDVRDGLKPVHRRVLFGMHELGVRSNTAHKKSARIVGEVLGKYHPHGDSSVYDTMVRMAQWWNMRYMLVDGQGNFGSIDGDSPAAMRYTEARMRKMAEDMLIDIDKETVDHSLNFDDTLLEPTVLPTRIPNLLVNGSSGIAVGMATNMPPHNLAEVVDGIIAYLGNQDITIDELMEYIKAPDFPTGGIIYGYDGVREAFKTGRGRVVIRAKAHFEEVNGRDCIVVTEVPYQVNPETMREQTSNLVKEGKLEGLADIVDQTGKGGMRIVYELKKDAIPNVVLNNLFKHTALQSSFSVNNIALVNGRPQQLNLKDLIYHFVEHRHDVVYRRTEYELKKAKERIHILEGFMKVMATEDTMGKAIEIIRFHDKPKEDLMTEFELTEIQAEAILALQLRRINKLLILQTKEEYEQLLAQIIDLEDILARKERRTEIIKEELLEIKSKYGDERRSVIEYAGGDISIEDIIPDDQVVITISNAGYIKRTSVNEYKTQARGGVGQKASATRDKDFIEHLFIGTNHQYMLFFTEKGKCFWLRVYEIPEGGKNTKGRAIQNLINIEPDDLVKAVICTHDLKEKDYTNSHYVIMATKKGIIKKTSLEQYSRPRQNGIVAITIKEDDELLEARLTSGNSQIMLAVKSGKAIRFPEDKVRAVGRSGSGVRGISLDSDKDEVIGMIAIENPLEETVLVVSENGYGKRTFIDEPETGEAVYRITNRGGKGVKTISITEKTGNLVAIKSVLEEDDLMIINKSGMAIRLPVSGLRVMGRATQGVRLINIKGNDSIAAVAKVMKEDEDENTTEEIENPTEE"},"dna_sequence":{"accession":"ACLQ01000019.1","fmin":"24238","fmax":"26749","strand":"+","sequence":"ATGGTTGAAGGAGAAAAACTCATTCCTATTAACATAGAAGACCAGATGAAGACAGCCTACATTGACTATTCAATGTCAGTGATTGTCTCAAGAGCTTTGCCCGATGTACGCGATGGGCTGAAGCCTGTACATCGTCGTGTACTCTTTGGAATGCACGAGCTTGGCGTACGTAGCAACACCGCTCATAAGAAATCAGCCCGTATCGTAGGGGAAGTACTCGGTAAGTACCATCCACACGGCGATTCTTCCGTATATGACACAATGGTACGTATGGCACAATGGTGGAACATGCGCTATATGCTTGTAGATGGGCAAGGTAACTTTGGTTCTATCGATGGAGACTCTCCTGCAGCTATGCGTTATACCGAGGCGAGAATGAGAAAAATGGCCGAGGATATGCTGATAGATATCGACAAAGAAACAGTAGATCACAGCCTGAACTTTGACGATACCCTACTCGAACCTACTGTATTGCCTACCCGCATCCCTAACCTACTGGTGAATGGGTCTTCGGGTATTGCTGTAGGTATGGCTACCAATATGCCACCTCATAATCTTGCTGAAGTAGTTGATGGTATAATTGCTTATCTTGGCAATCAAGATATTACCATCGATGAACTTATGGAATATATCAAGGCTCCTGACTTCCCTACAGGTGGAATCATCTATGGCTATGATGGAGTAAGAGAAGCCTTCAAGACTGGACGTGGACGTGTAGTAATCCGCGCCAAGGCTCATTTTGAAGAAGTTAATGGTCGTGACTGTATTGTCGTAACTGAAGTTCCCTATCAAGTGAACCCAGAGACGATGCGTGAACAGACTTCGAACCTTGTCAAAGAAGGCAAACTCGAAGGCCTAGCCGATATCGTAGATCAAACAGGTAAAGGAGGAATGCGCATCGTATATGAACTCAAAAAAGATGCTATTCCCAACGTAGTGCTGAATAACCTCTTCAAACACACAGCATTACAATCCTCCTTCAGTGTCAATAATATTGCCTTGGTCAATGGACGCCCTCAGCAACTGAACCTCAAGGACTTAATATATCACTTTGTAGAACATCGCCACGATGTAGTATACAGACGTACTGAGTATGAGCTCAAAAAAGCCAAAGAACGTATCCATATCTTGGAAGGGTTCATGAAGGTGATGGCCACAGAAGACACTATGGGGAAAGCTATTGAAATCATCCGTTTTCATGACAAGCCCAAAGAGGATTTGATGACCGAGTTCGAGCTTACCGAAATACAAGCTGAAGCTATCTTAGCCTTACAGCTACGTCGTATCAATAAGCTATTAATCCTTCAAACCAAAGAAGAATATGAGCAATTATTAGCACAAATTATTGATTTGGAAGATATCCTTGCTCGCAAAGAACGCCGTACCGAGATTATCAAAGAAGAACTCTTGGAAATAAAATCCAAATATGGAGACGAACGTCGTTCTGTCATAGAATATGCAGGGGGTGATATCTCCATTGAGGATATTATCCCTGATGATCAAGTGGTTATTACCATTTCCAACGCAGGTTACATAAAGCGTACTTCTGTCAATGAATACAAAACCCAAGCACGTGGTGGTGTAGGACAAAAAGCCTCTGCTACTCGTGATAAGGACTTCATAGAGCATCTGTTCATAGGTACCAACCACCAGTATATGCTGTTCTTTACAGAGAAAGGTAAGTGTTTTTGGCTCAGGGTGTATGAGATTCCTGAAGGAGGTAAAAATACCAAAGGACGCGCCATACAGAACCTTATCAATATCGAACCCGATGACCTTGTTAAGGCAGTCATCTGTACCCATGACCTCAAGGAAAAAGACTATACCAATAGTCACTATGTCATCATGGCTACTAAAAAAGGGATTATTAAGAAAACCAGCTTAGAACAATATTCACGTCCACGCCAGAATGGTATCGTTGCCATCACTATCAAAGAAGATGATGAGCTATTAGAAGCACGTCTTACCTCTGGCAACAGCCAAATCATGCTAGCTGTCAAGTCTGGAAAGGCTATTCGCTTCCCAGAGGACAAGGTGAGAGCTGTAGGGCGTAGTGGCTCTGGAGTACGAGGTATCTCTTTGGATAGTGACAAAGATGAGGTAATCGGAATGATTGCCATAGAAAATCCTCTGGAAGAAACCGTATTGGTAGTTTCCGAGAATGGTTATGGTAAGCGTACCTTTATCGATGAACCAGAGACAGGAGAAGCAGTATATCGTATTACCAACCGTGGAGGAAAAGGAGTCAAGACTATTTCTATCACAGAGAAAACAGGTAATCTGGTAGCAATCAAGTCAGTTTTGGAAGAAGACGATCTGATGATTATCAATAAGTCGGGTATGGCTATTCGCCTCCCTGTAAGTGGACTCCGTGTGATGGGACGTGCTACCCAAGGAGTACGCCTTATCAATATCAAAGGAAATGACTCTATTGCCGCAGTAGCAAAGGTTATGAAAGAAGATGAGGATGAAAATACTACCGAAGAGATAGAAAACCCAACAGAAGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40642","NCBI_taxonomy_name":"Capnocytophaga gingivalis ATCC 33624","NCBI_taxonomy_id":"553178"}}}},"ARO_accession":"3003931","ARO_id":"40641","ARO_name":"Capnocytophaga gingivalis gyrA conferring resistance to fluoroquinolones","CARD_short_name":"Cgin_gyrA_FLO","ARO_description":"Point mutation in Capnocytophaga gingivalis that decreases binding affinity of fluoroquinolone antibiotics to gyrA, thereby conferring resistance.","ARO_category":{"39876":{"category_aro_accession":"3003292","category_aro_cvterm_id":"39876","category_aro_name":"fluoroquinolone resistant gyrA","category_aro_description":"DNA gyrase is responsible for DNA supercoiling and consists of two alpha and two beta subunits. GyrA point mutations confer resistance by preventing fluoroquinolone antibiotics from binding the alpha-subunit.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3454":{"model_id":"3454","model_name":"OXA-291","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"530"}},"model_sequences":{"sequence":{"5649":{"protein_sequence":{"accession":"ENW94121.1","sequence":"MSKKLKMLTLSISMMLGLPLMACQSFSQQKQQIMTQEREQQQITSLFQNAQTSGVLVIYDGKKIQKFGNDVHRADQRYIPASTFKMLNALIGIQHHKTTPKEVFKWDGQKRAFSSWEKDLTLAEAMQASAVPVYQELARRIGLELMTREVKRVGYGNKNIGTQVDNFWLVGPLKITPVEEVRFAYALAKQKLPFDQSTQQQVKGMLLVDEVHGTKIYAKSGWGMDVSPQVGWWTGWIEQANGKITAFSLNMEMSRPEHTEARKAIVYQALQQLDLLAN"},"dna_sequence":{"accession":"APRL01000010.1","fmin":"279443","fmax":"280280","strand":"-","sequence":"ATGTCAAAAAAACTAAAAATGCTCACTTTATCTATTTCAATGATGCTGGGCTTACCCTTGATGGCTTGCCAGAGCTTTAGTCAACAAAAGCAGCAAATAATGACACAGGAACGTGAACAACAGCAGATTACGAGTTTATTCCAAAATGCTCAAACCAGCGGTGTTTTGGTTATTTATGATGGAAAGAAAATTCAAAAATTTGGCAATGACGTACATCGTGCAGATCAGCGCTATATCCCAGCCTCGACCTTTAAAATGCTGAATGCGTTAATTGGTATACAGCATCATAAAACTACGCCAAAAGAAGTCTTTAAATGGGATGGACAGAAACGCGCATTCAGTAGTTGGGAAAAAGATCTCACATTAGCTGAGGCAATGCAGGCATCGGCTGTGCCTGTGTATCAAGAGCTGGCACGACGTATTGGTCTGGAGCTGATGACTCGTGAAGTTAAGCGAGTGGGCTATGGAAATAAGAATATTGGGACACAAGTCGATAACTTTTGGTTGGTTGGTCCATTAAAAATTACGCCTGTGGAGGAAGTACGTTTTGCCTACGCATTGGCGAAGCAAAAGCTGCCATTTGATCAGTCAACTCAGCAACAAGTAAAAGGCATGTTATTGGTGGATGAGGTTCATGGCACCAAAATATACGCCAAAAGTGGCTGGGGTATGGATGTTAGCCCGCAAGTGGGATGGTGGACAGGTTGGATAGAGCAAGCAAATGGCAAGATCACCGCATTTTCATTAAATATGGAAATGAGTCGACCTGAGCATACTGAGGCACGGAAGGCGATTGTTTATCAAGCTTTGCAGCAGCTAGATTTATTGGCGAATTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42814","NCBI_taxonomy_name":"Acinetobacter sp. ANC 4105","NCBI_taxonomy_id":"1217703"}}}},"ARO_accession":"3001746","ARO_id":"38146","ARO_name":"OXA-291","CARD_short_name":"OXA-291","ARO_description":"OXA-291 is a beta-lactamase found in Acinetobacter spp.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46503":{"category_aro_accession":"3007714","category_aro_cvterm_id":"46503","category_aro_name":"OXA-286-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-286.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2410":{"model_id":"2410","model_name":"Salmonella enterica parC conferring resistance to fluoroquinolones","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"4487":"W106G"},"Curated-R":{"4487":"W106G"},"clinical":{"4487":"W106G"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1400"}},"model_sequences":{"sequence":{"5266":{"protein_sequence":{"accession":"AAL22048.1","sequence":"MSDMAERLALHEFTENAYLNYSMYVIMDRALPFIGDGLKPVQRRIVYAMSELGLNATAKFKKSARTVGDVLGKYHPHGDSACYEAMVLMAQPFSYRYPLVDGQGNWGAPDDPKSFAAMRYTESRLSKYAELLLSELGQGTADWVPNFDGTMQEPKMLPARLPNILLNGTTGIAVGMATDIPPHNLREVAKAAITLIEQPKTTLDQLLDIVQGPDYPTEAEIITPRAEIRKIYENGRGSVRMRAVWTKEDGAVVISALPHQVSGAKVLEQIAAQMRNKKLPMVDDLRDESDHENPTRLVIVPRSNRVDMEQVMNHLFATTDLEKSYRINLNMIGLDGRPAVKNLLEILTEWLAFRRDTVRRRLNYRLEKVLKRLHILEGLLVAFLNIDEVIEIIRSEDEPKPALMSRFGISETQAEAILELKLRHLAKLEEMKIRGEQDELEKERDQLQGILASERKMNTLLKKELQADADAYGDDRRSPLREREEAKAMSEHDMLPSEPVTIVLSQMGWVRSAKGHDIDAPGLNYKAGDSFKAAVKGKSNQPVVFIDTTGRSYAIDPITLPSARGQGEPLTGKLTLPPGATVEHMLMEGDDQKLLMASDAGYGFVCTFNDLVARNRAGKTLITLPENAHVMPPLVIEDEHDMLLAITQAGRMLMFPVDSLPQLSKGKGNKIINIPSAEAAKGDDGLAHLYVLPPQSTLTIHVGKRKIKLRPEELQKVVGERGRRGTLMRGLQRIDRIEIDSPHRVSHGDSEE"},"dna_sequence":{"accession":"AE006468.2","fmin":"3336953","fmax":"3339212","strand":"-","sequence":"ATGAGCGATATGGCAGAGCGCCTTGCGCTACATGAATTTACGGAAAACGCCTACTTAAACTACTCCATGTACGTGATCATGGATCGTGCGTTGCCGTTTATTGGCGACGGCCTGAAGCCGGTACAGCGCCGCATCGTCTATGCGATGTCAGAGCTGGGGCTGAACGCCACCGCTAAATTTAAAAAATCCGCCCGTACCGTTGGTGACGTACTGGGTAAGTATCACCCGCATGGCGACAGCGCCTGCTATGAAGCCATGGTGCTGATGGCGCAGCCGTTCTCTTACCGTTACCCGCTGGTCGATGGCCAGGGGAACTGGGGCGCGCCGGATGATCCGAAGTCATTCGCGGCGATGCGTTATACCGAATCCCGCCTGTCCAAATACGCCGAGCTGCTGTTAAGCGAACTCGGTCAGGGGACGGCGGACTGGGTGCCAAACTTCGACGGCACCATGCAGGAACCGAAAATGTTACCGGCGCGTCTGCCGAACATCCTGCTGAACGGCACCACCGGTATTGCGGTGGGCATGGCAACAGATATCCCGCCGCACAACCTGCGCGAAGTGGCGAAAGCGGCGATTACGCTGATTGAGCAGCCGAAAACGACGCTGGATCAGTTGCTGGATATCGTTCAGGGGCCGGATTACCCGACCGAAGCGGAGATCATTACCCCACGTGCGGAAATTCGTAAAATTTACGAAAACGGGCGGGGCTCCGTGCGTATGCGCGCGGTATGGACCAAAGAAGACGGCGCTGTGGTAATTTCCGCGCTGCCGCATCAGGTCTCTGGCGCGAAAGTGCTGGAGCAGATTGCTGCGCAGATGCGTAATAAAAAACTGCCGATGGTGGACGATCTGCGCGATGAATCGGATCACGAAAACCCGACGCGTTTAGTGATTGTGCCACGCTCCAACCGTGTGGATATGGAACAGGTGATGAACCATCTGTTCGCCACCACCGATCTGGAAAAAAGCTACCGTATTAACCTGAACATGATCGGTCTGGATGGTCGTCCGGCGGTGAAAAACCTGCTGGAGATCCTCACCGAGTGGCTGGCGTTCCGCCGCGACACGGTGCGCCGTCGTCTGAACTATCGTCTGGAGAAAGTGCTTAAGCGCCTGCATATCCTCGAAGGTTTGCTGGTGGCGTTTCTCAACATCGACGAAGTGATTGAGATTATCCGTAGCGAAGACGAGCCAAAACCCGCGCTGATGTCGCGTTTCGGCATCAGCGAAACCCAGGCGGAAGCGATTCTCGAACTGAAACTGCGCCATCTCGCCAAACTGGAAGAGATGAAAATTCGCGGCGAGCAGGACGAGCTGGAAAAAGAGAGGGACCAGTTGCAGGGCATTCTCGCGTCCGAACGCAAAATGAATACCTTGCTGAAAAAAGAACTACAGGCGGACGCCGATGCCTATGGCGACGATCGCCGTTCTCCGCTGCGTGAGCGCGAAGAAGCTAAAGCGATGAGCGAACACGATATGCTGCCGTCCGAACCGGTGACTATCGTGCTGTCGCAGATGGGCTGGGTGCGCAGCGCCAAAGGTCATGATATTGATGCGCCGGGGCTTAACTATAAAGCGGGCGACAGCTTTAAAGCCGCGGTGAAAGGTAAGAGCAATCAACCGGTGGTGTTTATTGATACCACCGGGCGCAGCTATGCTATTGATCCCATTACGCTTCCGTCGGCGCGTGGGCAGGGCGAGCCGCTGACCGGCAAACTCACGCTGCCGCCGGGGGCGACCGTAGAGCATATGCTGATGGAAGGCGATGACCAGAAACTGCTGATGGCGTCGGATGCGGGCTACGGCTTCGTTTGTACGTTTAACGATCTGGTTGCCCGTAACCGTGCCGGTAAGACATTGATTACACTGCCGGAAAATGCGCACGTCATGCCGCCGCTGGTGATTGAAGACGAGCACGATATGCTGCTGGCGATTACCCAGGCCGGACGGATGTTGATGTTCCCGGTAGACTCTCTGCCGCAGCTGTCGAAAGGCAAAGGGAATAAGATCATTAATATCCCCTCTGCAGAAGCGGCGAAAGGCGATGATGGACTGGCGCACCTGTACGTGCTGCCGCCACAAAGCACTCTGACTATCCATGTCGGGAAGCGCAAAATCAAACTGCGCCCTGAAGAGTTACAAAAGGTGGTCGGTGAACGCGGACGCCGTGGCACATTAATGCGCGGCCTGCAGCGTATCGATCGCATTGAGATTGATTCGCCGCATCGCGTAAGTCATGGCGACAGCGAAGAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35734","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Typhimurium str. LT2","NCBI_taxonomy_id":"99287"}}}},"ARO_accession":"3003939","ARO_id":"40662","ARO_name":"Salmonella enterica parC conferring resistance to fluoroquinolones","CARD_short_name":"Sent_parC_FLO","ARO_description":"Point mutations in Salmonella parC gene implicated in decreased susceptibility to fluoroquinolone antibiotics, primarily ciprofloxacin and nalidixic acid.","ARO_category":{"36913":{"category_aro_accession":"3000619","category_aro_cvterm_id":"36913","category_aro_name":"fluoroquinolone resistant parC","category_aro_description":"ParC is a subunit of topoisomerase IV, which decatenates and relaxes DNA to allow access to genes for transcription or translation. Point mutations in ParC prevent fluoroquinolone antibiotics from inhibiting DNA synthesis, and confer low-level resistance. Higher-level resistance results from both gyrA and parC mutations.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2395":{"model_id":"2395","model_name":"apmA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"3717":{"protein_sequence":{"accession":"CBL58181.1","sequence":"MKTRLEQVLERYLNGREVAVWGVPTRRLLRALKPFKFHTADRVDPQYHYVVAVTDDDLTDFLSDEQSKSFQYANDYLTFDDEGGELPFERMCFNVPVGRQTYFGDGVVGACENGYIKSIGQFTSINGTAEIHANHQLNMTFVSDDIQNFFNEESMAVFQEKLRKDPKHPYAYSKEPMTIGSDVYIGAHAFINASTVTSIGDGAIIGSGAVVLENVPPFAVVVGVPARIKRYRFSKEMIETLLRVKWWDWSIEEINENVDALISPELFMKKYGSL"},"dna_sequence":{"accession":"FN806789.3","fmin":"2693","fmax":"3518","strand":"+","sequence":"ATGAAAACCAGACTTGAACAAGTTTTAGAACGTTATCTCAACGGACGCGAGGTAGCTGTATGGGGTGTTCCGACACGCCGTTTGCTTCGTGCATTAAAACCTTTTAAATTTCATACTGCCGATCGTGTTGATCCTCAATATCATTATGTTGTTGCTGTAACCGATGACGACTTAACCGACTTTTTATCCGATGAACAGAGCAAGTCGTTTCAATACGCGAATGACTACCTTACGTTTGACGACGAGGGAGGCGAACTTCCGTTTGAACGAATGTGCTTCAATGTCCCCGTTGGCAGGCAAACGTATTTTGGAGACGGTGTCGTAGGAGCTTGCGAAAACGGGTATATCAAGAGCATCGGCCAATTTACATCGATTAACGGCACGGCAGAGATCCATGCGAACCATCAGTTAAACATGACCTTTGTAAGCGACGATATTCAAAACTTCTTCAACGAAGAAAGCATGGCTGTATTCCAAGAAAAGCTGCGAAAAGACCCGAAACACCCTTATGCTTATAGCAAAGAACCTATGACCATAGGTAGCGATGTTTATATCGGCGCACATGCATTCATCAATGCTTCCACTGTGACAAGCATCGGTGACGGTGCAATAATTGGCTCAGGGGCAGTAGTTCTGGAAAATGTTCCTCCTTTTGCTGTCGTCGTTGGTGTCCCTGCGAGAATCAAGCGTTACCGCTTCTCAAAGGAGATGATTGAAACCCTCCTTCGTGTCAAATGGTGGGACTGGAGTATAGAGGAAATTAACGAAAATGTTGATGCGCTTATATCACCTGAACTATTTATGAAAAAGTACGGGAGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35508","NCBI_taxonomy_name":"Staphylococcus aureus","NCBI_taxonomy_id":"1280"}}}},"ARO_accession":"3003918","ARO_id":"40626","ARO_name":"apmA","CARD_short_name":"apmA","ARO_description":"Plasmid-borne apramycin-resistant aminocyclitol acetyltransferase gene identified from bovine MRSA.","ARO_category":{"36480":{"category_aro_accession":"3000341","category_aro_cvterm_id":"36480","category_aro_name":"AAC(2')","category_aro_description":"A category of aminoglycoside N-acetyltransferase enzymes with modification regiospecificity based at the 2'-amino group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics through acetylation of the 2-amino group of the compound.","category_aro_class_name":"AMR Gene Family"},"35955":{"category_aro_accession":"0000037","category_aro_cvterm_id":"35955","category_aro_name":"apramycin","category_aro_description":"Apramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections in animals. Apramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2411":{"model_id":"2411","model_name":"Shigella flexneri gyrA conferring resistance to fluoroquinolones","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"4489":"N57K","4490":"H80P"},"Curated-R":{"4489":"N57K","4490":"H80P"},"clinical":{"4489":"N57K","4490":"H80P"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1500"}},"model_sequences":{"sequence":{"5265":{"protein_sequence":{"accession":"AAN43827.1","sequence":"MSDLAREITPVNIEEELKSSYLDYAMSVIVGRALPDVRDGLKPVHRRVLYAMNVLGNDWNKAYKKSARVVGDVIGKYHPHGDSAVYDTIVRMAQPFSLRYMLVDGQGNFGSIDGDSAAAMRYTEIRLAKIAHELMADLEKETVDFVDNYDGTEKIPDVMPTKIPNLLVNGSSGIAVGMATNIPPHNLTEVINGCLAYIDDEDISIEGLMEHIPGPDFPTAAIINGRRGIEEAYRTGRGKVYIRARAEVEVDAKTGRETIIVHEIPYQVNKARLIEKIAELVKEKRVEGISALRDESDKDGMRIVIEVKRDAVGEVVLNNLYSQTQLQVSFGINMVALHHGQPKIMNLKDIIAAFVRHRREVVTRRTIFELRKARDRAHILEALAVALANIDPIIELIRHAPTPAEAKTALVANPWQLGNVAAMLERAGDDAARPEWLEPEFGVRDGLYYLTEQQAQAILDLRLQKLTGLEHEKLLDEYKELLDQIAELLRILGSADRLMEVIREELELVREQFGDKRRTEITANSADINLEDLITQEDVVVTLSHQGYVKYQPLSEYEAQRRGGKGKSAARIKEEDFIDRLLVANTHDHILCFSSRGRVYSMKVYQLPEATRGARGRPIVNLLPLEQDERITAILPVTEFEEGVKVFMATANGTVKKTVLTEFNRLRTAGKVAIKLVDGDELIGVDLTSGEDEVMLFSAEGKVVRFKESSVRAMGCNTTGVRGIRLGEGDKVVSLIVPRGDGAILTATQNGYGKRTAVAEYPTKSRATKGVISIKVTERNGLVVGAVQVDDCDQIMMITDAGTLVRTRVSEISIVGRNTQGVILIRTAEDENVVGLQRVAEPVDEEDLDTIDGSAAEGDDEIAPEVDVDDEPEEE"},"dna_sequence":{"accession":"AE005674.2","fmin":"2352231","fmax":"2354859","strand":"-","sequence":"ATGAGCGACCTTGCGAGAGAAATTACACCGGTCAACATTGAGGAAGAGCTAAAGAGCTCCTATCTGGATTATGCGATGTCGGTCATTGTTGGCCGTGCGCTGCCAGATGTCCGAGATGGCCTGAAGCCGGTACACCGTCGCGTACTTTACGCCATGAACGTACTAGGCAATGACTGGAACAAAGCCTATAAAAAATCTGCCCGTGTCGTTGGTGACGTAATCGGTAAATACCATCCCCATGGTGACTCGGCGGTTTATGACACGATCGTCCGTATGGCGCAGCCATTCTCGCTGCGTTACATGCTGGTAGACGGTCAGGGTAACTTCGGTTCCATCGACGGCGACTCTGCGGCGGCAATGCGTTATACGGAAATCCGTCTGGCGAAAATTGCCCATGAACTGATGGCCGATCTCGAAAAAGAGACGGTCGATTTCGTTGATAACTATGACGGCACGGAAAAAATTCCCGACGTCATGCCAACCAAAATTCCTAACCTGCTGGTGAACGGTTCTTCCGGTATCGCCGTAGGTATGGCAACCAACATCCCGCCGCACAACCTGACGGAAGTCATCAACGGTTGTCTGGCGTATATCGATGATGAAGACATCAGCATTGAAGGGCTGATGGAACACATCCCGGGGCCGGACTTCCCGACGGCGGCAATCATTAACGGTCGTCGCGGTATTGAAGAAGCTTACCGTACCGGTCGCGGCAAGGTATATATCCGCGCCCGTGCTGAAGTGGAAGTTGACGCCAAAACCGGACGTGAAACCATTATCGTCCACGAAATTCCGTATCAGGTAAACAAAGCGCGCCTGATCGAGAAGATTGCGGAACTGGTAAAAGAAAAACGCGTGGAAGGCATCAGCGCGCTGCGTGACGAGTCTGACAAAGACGGTATGCGCATCGTGATTGAAGTGAAACGCGATGCGGTCGGTGAAGTTGTGCTCAACAACCTCTACTCCCAGACCCAGTTGCAGGTTTCTTTCGGTATCAACATGGTGGCATTGCACCATGGTCAGCCGAAGATCATGAACCTGAAAGACATCATCGCGGCGTTTGTTCGTCACCGCCGTGAAGTGGTGACCCGTCGTACTATTTTCGAACTGCGTAAAGCTCGCGATCGTGCTCATATCCTTGAAGCATTAGCCGTGGCGCTGGCGAACATTGACCCGATCATCGAACTGATCCGTCATGCGCCGACGCCTGCAGAAGCGAAAACTGCGCTGGTTGCTAATCCGTGGCAGCTGGGCAACGTTGCCGCCATGTTGGAACGTGCTGGCGACGATGCTGCGCGTCCGGAATGGCTGGAGCCAGAGTTCGGCGTGCGTGATGGTCTGTACTACCTGACCGAACAGCAAGCTCAGGCGATTCTGGATCTGCGTTTGCAGAAACTGACCGGCCTTGAGCACGAAAAACTGCTCGACGAATACAAAGAGCTGCTGGATCAGATCGCGGAACTGTTGCGTATTCTTGGTAGCGCCGATCGTCTGATGGAAGTGATCCGCGAAGAGCTGGAGCTGGTTCGTGAACAGTTCGGTGACAAACGTCGTACTGAAATCACCGCCAACAGCGCAGACATCAACCTGGAAGATCTGATCACCCAGGAAGATGTGGTCGTGACGCTCTCTCACCAGGGCTACGTTAAATATCAGCCGCTTTCTGAATACGAAGCGCAGCGTCGTGGCGGGAAAGGTAAATCTGCCGCACGTATTAAAGAAGAAGACTTTATCGACCGACTGCTGGTGGCGAACACGCACGACCATATTCTGTGCTTCTCCAGCCGTGGTCGCGTCTATTCGATGAAAGTTTACCAGTTGCCGGAAGCCACTCGTGGCGCGCGCGGTCGTCCGATCGTCAACCTGCTACCGCTGGAACAGGACGAACGTATCACCGCGATCCTGCCGGTGACCGAGTTTGAAGAAGGCGTGAAAGTCTTCATGGCGACCGCTAACGGTACTGTGAAGAAAACCGTCCTCACCGAATTCAACCGTCTGCGTACCGCCGGTAAAGTGGCGATCAAACTGGTTGACGGCGATGAGCTGATCGGCGTTGATCTGACCAGTGGCGAAGATGAAGTAATGCTGTTCTCCGCCGAAGGTAAAGTGGTGCGCTTTAAAGAGTCTTCTGTCCGTGCGATGGGCTGCAATACCACTGGTGTGCGCGGTATTCGCTTAGGTGAAGGCGATAAAGTCGTCTCTCTGATCGTGCCTCGTGGCGATGGCGCAATCCTCACCGCAACGCAAAACGGTTACGGTAAACGTACTGCAGTGGCGGAATACCCAACCAAGTCGCGTGCGACGAAAGGGGTTATCTCCATCAAGGTTACCGAACGTAACGGTTTAGTGGTTGGCGCGGTGCAGGTAGATGACTGCGACCAGATCATGATGATCACCGATGCCGGTACGCTGGTACGTACTCGCGTTTCAGAAATCAGCATCGTGGGCCGTAACACCCAGGGCGTGATCCTCATCCGTACTGCGGAAGATGAAAACGTAGTGGGTCTGCAGCGTGTTGCTGAACCGGTTGACGAGGAAGATCTGGATACCATCGACGGCAGTGCCGCGGAAGGGGATGATGAAATTGCTCCGGAAGTGGACGTTGACGACGAGCCAGAAGAAGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40665","NCBI_taxonomy_name":"Shigella flexneri 2a str. 301","NCBI_taxonomy_id":"198214"}}}},"ARO_accession":"3003940","ARO_id":"40664","ARO_name":"Shigella flexneri gyrA conferring resistance to fluoroquinolones","CARD_short_name":"Sfle_gyrA_FLO","ARO_description":"Point mutations in Shigella flexneri gyrA observed to confer resistance to fluoroquinolone antibiotics.","ARO_category":{"39876":{"category_aro_accession":"3003292","category_aro_cvterm_id":"39876","category_aro_name":"fluoroquinolone resistant gyrA","category_aro_description":"DNA gyrase is responsible for DNA supercoiling and consists of two alpha and two beta subunits. GyrA point mutations confer resistance by preventing fluoroquinolone antibiotics from binding the alpha-subunit.","category_aro_class_name":"AMR Gene Family"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2412":{"model_id":"2412","model_name":"Shigella flexneri parC conferring resistance to fluoroquinolones","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"4492":"A85T","4493":"D111H","4494":"S129P"},"Curated-R":{"4492":"A85T","4493":"D111H","4494":"S129P"},"clinical":{"4492":"A85T","4493":"D111H","4494":"S129P"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1400"}},"model_sequences":{"sequence":{"5263":{"protein_sequence":{"accession":"AAN44541.1","sequence":"MSDMAERLALHEFTENAYLNYSMYVIMDRALPFIGDGLKPVQRRIVYAMSELGLNASAKFKKSARTVGDVLGKYHPHGDSACYEAMVLMAQPFSYRYPLVDGQGNWGAPDDPKSFAAMRYTESRLSKYSELLLSELGQGTADWVPNFDGTLQEPKMLPARLPNILLNGTTGIAVGMATDIPPHNLREVAQAAIALIDQPKTTLDQLLDIVQGPDYPTEAEIITSRAEIRKIYENGRGSVRMRAVWKKEDGAVVISALPHQVSGARVLEQIAAQMRNKKLPMVDDLRDESDHENPTRLVIVPRSNRVDMDQVMNHLFATTDLEKSYRINLNMIGLDGRPAVKNLLEILSEWLVFRRDTVRRRLNYRLEKVLKRLHILEGLLVAFLNIDEVIEIIRNEDEPKPALMSRFGLTETQAEAILELKLRHLAKLEEMKIRGEQSELEKERDQLQGILASERKMNNLLKKELQADAQAYGDDRRSPLQEREEAKAMSEHDMLPSEPVTIVLSQMGWVRSAKGHDIDAPGLNYKAGDSFKAAVKGKSNQPVVFVDSTGRSYAIDPITLPSARGQGEPLTGKLTLPPGATVDHMLMESDDQKLLMASDAGYGFVCTFNDLVARNRAGKALITLPENAHVMPPVVIEDASDMLLAITQAGRMLMFPVSDLPQLSKGKGNKIINIPSAEAARGEDGLAQLYVLPPQSTLTIHVGKRKIKLRPEELQKVTGERGRRGTLMRGLQRIDRVEIDSPRRASSGDSEE"},"dna_sequence":{"accession":"AE005674.2","fmin":"3159154","fmax":"3161413","strand":"-","sequence":"ATGAGCGATATGGCAGAGCGCCTTGCGCTACATGAATTTACGGAAAACGCCTACTTAAACTACTCCATGTACGTGATCATGGACCGTGCGTTGCCGTTTATTGGTGATGGTCTGAAACCTGTTCAGCGCCGCATTGTGTATGCGATGTCTGAACTGGGCCTGAATGCCAGCGCCAAATTTAAAAAATCGGCCCGTACCGTCGGTGACGTACTGGGTAAATACCATCCGCACGGCGATAGCGCCTGTTATGAAGCGATGGTCCTGATGGCGCAGCCGTTCTCTTACCGTTATCCGCTGGTTGATGGTCAGGGGAACTGGGGCGCGCCGGACGATCCGAAATCGTTCGCGGCAATGCGTTACACCGAATCCCGGTTGTCGAAATATTCCGAGCTGCTATTGAGCGAGCTGGGGCAGGGGACGGCTGACTGGGTGCCAAACTTCGACGGCACTTTGCAGGAGCCGAAAATGCTACCTGCCCGTCTGCCAAACATTTTGCTTAACGGCACCACCGGTATTGCCGTCGGCATGGCGACCGATATTCCACCGCATAACCTGCGTGAAGTAGCTCAGGCGGCAATCGCATTAATCGACCAGCCGAAAACTACGCTCGATCAGCTGCTGGATATCGTGCAGGGGCCGGATTATCCGACTGAAGCGGAAATTATCACTTCGCGCGCCGAGATTCGTAAAATCTACGAGAACGGACGTGGTTCAGTGCGTATGCGCGCGGTGTGGAAGAAAGAAGATGGCGCGGTGGTTATCAGCGCATTACCGCATCAGGTTTCAGGTGCGCGCGTACTGGAGCAAATTGCTGCGCAAATGCGCAACAAAAAGCTGCCGATGGTTGACGATCTGCGCGATGAATCTGACCACGAGAACCCGACCCGTCTGGTGATTGTGCCGCGTTCCAACCGCGTGGATATGGATCAGGTGATGAACCACCTCTTCGCTACCACCGATCTGGAAAAGAGCTATCGCATTAACCTCAATATGATCGGTCTGGATGGTCGTCCGGCGGTGAAAAACCTGCTGGAAATCCTCTCCGAATGGCTGGTGTTCCGTCGCGATACCGTGCGCCGCCGACTGAACTATCGTCTGGAGAAAGTCCTCAAGCGCCTGCATATCCTGGAAGGTTTGCTGGTGGCGTTTCTCAACATCGACGAAGTGATTGAGATCATTCGTAACGAAGATGAACCGAAACCGGCGCTGATGTCGCGGTTTGGCCTTACGGAAACCCAGGCGGAAGCGATCCTCGAACTGAAACTGCGTCATCTTGCCAAACTGGAAGAGATGAAGATTCGCGGTGAGCAGAGTGAGCTGGAAAAAGAGCGCGACCAGTTGCAGGGCATTTTGGCTTCCGAGCGTAAAATGAATAACCTGCTGAAGAAAGAACTGCAGGCAGACGCGCAAGCCTACGGTGACGATCGTCGTTCGCCGTTGCAGGAACGCGAAGAAGCGAAAGCGATGAGCGAGCACGACATGCTGCCGTCTGAACCTGTCACCATTGTGCTGTCGCAGATGGGCTGGGTACGCAGCGCTAAAGGCCATGATATCGACGCGCCGGGCCTGAATTATAAAGCGGGTGATAGCTTCAAAGCGGCGGTGAAAGGTAAGAGTAACCAACCGGTAGTGTTTGTTGATTCCACCGGTCGTAGCTATGCCATCGACCCGATTACGCTGCCGTCGGCGCGTGGTCAGGGCGAACCACTCACCGGCAAATTAACGTTGCCGCCTGGGGCGACCGTTGACCATATGCTGATGGAAAGCGACGATCAGAAACTGCTGATGGCTTCCGATGCGGGTTACGGTTTCGTCTGCACCTTTAACGATCTGGTAGCGCGTAACCGTGCGGGTAAGGCTTTGATCACCTTACCGGAAAATGCCCATGTTATGCCGCCGGTGGTGATTGAAGATGCTTCCGATATGCTGCTGGCAATCACTCAGGCAGGCCGTATGTTGATGTTCCCGGTAAGCGATCTGCCGCAGCTGTCGAAGGGCAAAGGCAACAAGATTATCAACATTCCATCGGCAGAAGCCGCGCGTGGCGAGGATGGTCTGGCGCAACTGTACGTTCTGCCGCCGCAAAGCACGCTGACCATTCATGTTGGGAAACGCAAAATTAAACTGCGTCCGGAAGAGCTACAGAAAGTCACTGGCGAACGTGGACGCCGCGGTACGTTGATGCGCGGTTTGCAGCGTATCGATCGTGTTGAGATCGACTCTCCTCGCCGTGCCAGCAGCGGTGATAGCGAAGAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40665","NCBI_taxonomy_name":"Shigella flexneri 2a str. 301","NCBI_taxonomy_id":"198214"}}}},"ARO_accession":"3003941","ARO_id":"40666","ARO_name":"Shigella flexneri parC conferring resistance to fluoroquinolones","CARD_short_name":"Sfle_parC_FLO","ARO_description":"Point mutation in parC conferring resistance to fluoroquinolone antibiotics in Shigella flexneri,.","ARO_category":{"36913":{"category_aro_accession":"3000619","category_aro_cvterm_id":"36913","category_aro_name":"fluoroquinolone resistant parC","category_aro_description":"ParC is a subunit of topoisomerase IV, which decatenates and relaxes DNA to allow access to genes for transcription or translation. Point mutations in ParC prevent fluoroquinolone antibiotics from inhibiting DNA synthesis, and confer low-level resistance. Higher-level resistance results from both gyrA and parC mutations.","category_aro_class_name":"AMR Gene Family"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2409":{"model_id":"2409","model_name":"Neisseria meningititis PBP2 conferring resistance to beta-lactam","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"4464":"G482S","4466":"F504L","4467":"A510V","4468":"I312M","4469":"V316T","4470":"N512Y","4471":"G545S","4472":"A501P"},"Curated-R":{"4464":"G482S","4466":"F504L","4467":"A510V","4468":"I312M","4469":"V316T","4470":"N512Y","4471":"G545S","4472":"A501P"},"experimental":{"4464":"G482S","4466":"F504L","4467":"A510V","4468":"I312M","4469":"V316T","4470":"N512Y","4471":"G545S","4472":"A501P"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"5467":{"protein_sequence":{"accession":"AAF40852.1","sequence":"MLIKSEYKPRMLPKEEQVKKPMTSNGRISFVLMAIAVLFAGLIARGLYLQTVTYNFLKEQGDNRIVRTQTLPATRGTVSDRNGAVLALSAPTESLFAVPKEMKEMPSAAQLERLSELVDVPVDVLRNKLEQKGKSFIWIKRQLDPKVAEEVKALGLENFVFEKELKRHYPMGNLFAHVIGFTDIDGKGQEGLELSLEDSLHGEDGAEVVLRDRQGNIVDSLDSPRNKAPKNGKDIILSLDQRIQTLAYEELNKAVEYHQAKAGTVVVLDARTGEILALANTPAYDPNRPGRADSEQRRNRAVTDMIEPGSAIKPFVIAKALDAGKTDLNERLNTQPYKIGPSPVRDTHVYPSLDVRGIMQKSSNVGTSKLSARFGAEEMYDFYHELGIGVRMHSGFPGETAGLLRNWRRWRPIEQATMSFGYGLQLSLLQLARAYTALTHDGVLLPVSFEKQAVAPQGKRIFKESTAREVRNLMVSVTEPGGTGTAGAVDGFDVGAKTGTARKFVNGRYADNKHIATFIGFAPAKNPRVIVAVTIDEPTAHGYYGGVVAGPPFKKIMGGSLNILGISPTKPLTAAAVKTPS"},"dna_sequence":{"accession":"AE002098.2","fmin":"419828","fmax":"421574","strand":"+","sequence":"ATGTTGATTAAGAGCGAATATAAGCCTCGGATGCTGCCCAAAGAAGAGCAGGTCAAAAAGCCGATGACCAGTAACGGACGGATCAGCTTCGTCCTGATGGCAATAGCGGTCTTGTTTGCCGGTCTGATTGCTCGCGGACTGTATCTGCAGACGGTAACGTATAACTTTTTGAAAGAACAGGGCGACAACCGGATTGTGCGGACTCAAACATTGCCGGCTACACGCGGTACGGTTTCGGACCGGAACGGTGCGGTTTTGGCGTTGAGTGCGCCGACGGAGTCCCTGTTTGCCGTGCCTAAAGAGATGAAGGAAATGCCGTCTGCCGCACAATTGGAACGCCTGTCCGAGCTTGTCGATGTGCCGGTTGATGTTTTGAGGAACAAGCTCGAACAGAAAGGCAAGTCGTTTATCTGGATTAAGCGGCAGCTCGATCCCAAGGTTGCCGAAGAGGTCAAAGCCTTGGGTTTGGAAAACTTTGTATTTGAAAAAGAATTAAAACGCCATTACCCGATGGGCAACCTGTTTGCACACGTCATCGGATTTACCGATATTGACGGCAAAGGTCAGGAAGGTTTGGAACTTTCGCTTGAAGACAGCCTGCATGGCGAAGACGGCGCGGAAGTCGTTTTGCGGGACCGGCAGGGCAATATTGTGGACAGCTTGGACTCCCCGCGCAATAAAGCCCCGAAAAACGGCAAAGACATCATCCTTTCCCTCGATCAGAGGATTCAGACCTTGGCCTATGAAGAGTTGAACAAGGCGGTCGAATACCATCAGGCAAAAGCCGGAACGGTGGTGGTTTTGGATGCCCGCACGGGGGAAATCCTCGCCTTGGCCAATACGCCCGCCTACGATCCCAACAGGCCCGGCCGGGCAGACAGCGAACAGCGGCGCAACCGTGCCGTAACCGATATGATCGAACCCGGTTCGGCAATCAAACCGTTTGTGATTGCGAAGGCATTGGATGCGGGCAAAACCGATTTGAACGAACGGCTGAATACGCAGCCTTATAAAATCGGACCGTCTCCCGTGCGCGATACCCATGTTTACCCCTCTTTGGATGTGCGCGGCATCATGCAGAAATCGTCCAACGTCGGCACAAGCAAACTGTCTGCGCGTTTCGGTGCCGAAGAAATGTATGACTTCTATCATGAGTTGGGCATCGGTGTGCGTATGCACTCGGGCTTTCCGGGCGAAACTGCAGGTTTGTTGAGAAATTGGCGCAGGTGGCGGCCTATCGAACAGGCGACGATGTCTTTCGGTTACGGCCTGCAATTGAGCCTGCTGCAATTGGCGCGCGCCTATACCGCACTGACGCACGACGGCGTTTTACTGCCGGTCAGCTTTGAAAAACAGGCGGTTGCGCCGCAAGGCAAACGCATATTCAAAGAATCGACCGCGCGCGAGGTACGCAATCTGATGGTTTCCGTAACCGAGCCGGGCGGCACCGGTACGGCGGGTGCGGTGGACGGTTTCGATGTCGGCGCGAAAACCGGCACGGCGCGCAAGTTCGTCAACGGGCGTTATGCCGACAACAAACACATCGCTACCTTTATCGGTTTTGCCCCCGCCAAAAATCCCCGTGTGATTGTGGCGGTAACCATTGACGAACCGACTGCCCACGGTTATTACGGCGGCGTAGTGGCAGGGCCGCCCTTCAAAAAAATTATGGGCGGCAGCCTGAACATCTTGGGCATTTCCCCGACCAAGCCACTGACCGCCGCAGCCGTCAAAACACCGTCTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39597","NCBI_taxonomy_name":"Neisseria meningitidis MC58","NCBI_taxonomy_id":"122586"}}}},"ARO_accession":"3003937","ARO_id":"40660","ARO_name":"Neisseria meningititis PBP2 conferring resistance to beta-lactam","CARD_short_name":"Nmen_PBP2_BLA","ARO_description":"Point mutation in Neisseria meningititis PBP2 (penA) decreases affinity between beta-lactam antibiotic molecule and PBP2, thereby conferring resistance to beta-lactam.","ARO_category":{"40661":{"category_aro_accession":"3003938","category_aro_cvterm_id":"40661","category_aro_name":"Penicillin-binding protein mutations conferring resistance to beta-lactam antibiotics","category_aro_description":"Mutations in PBP transpeptidases that change the affinity for penicillin thereby conferring resistance to penicillin antibiotics.","category_aro_class_name":"AMR Gene Family"},"35979":{"category_aro_accession":"0000062","category_aro_cvterm_id":"35979","category_aro_name":"ceftriaxone","category_aro_description":"Ceftriaxone is a third-generation cephalosporin antibiotic. The presence of an aminothiazolyl sidechain increases ceftriazone's resistance to beta-lactamases. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36990":{"category_aro_accession":"3000646","category_aro_cvterm_id":"36990","category_aro_name":"cefixime","category_aro_description":"Cefixime is a cephalosporin resistant to most beta-lactamases. It is active against many enterobacteria, but activity against staphylococci is poor.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2416":{"model_id":"2416","model_name":"abcA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"3000"}},"model_sequences":{"sequence":{"4691":{"protein_sequence":{"accession":"XP_753111.1","sequence":"MNESHEAGKNSSTNVEEREEEVLRLARQFTEQSSYSTAGQTPFAAEAGSALDPNGERFNARAWCKAMLQMHIGDKEAHPLRTLGVAFSNLNVHGFGSDTDYQKSVGNVWLKTLSLARIAFGQKQRKVDILQNLEGLVEAGEMLVVLGPPGSGCSTFLKTIAGETYGFHVDKNSNINFQGIAKQMAHEFRGEAIYTAEVDVHFPKLTVGDTLYFAARARTPRHIPGGVNATQYAGHMRDVIMAMFGISHTKNTIVGNDFIRGVSGGERKRVSIAEACLSNAPLQCWDNSTRGLDSANAIEFCKTLRMQADINGTTACVSLYQAPQAAYDYFDKVLVLYEGREIYFGPTSMAKHYFLQMGFVCPDRQTDADFLTSMTSHLERVVQPGYEDRVPRTPDEFAARWKASPQRAQLMQHIKSYNAKFALDGEYLDKFKQSRRAQQAKAQRVSSPYTLSYVQQVKLCLWRGYQRLKADPSVTISSLFGNTIISLVIASIFYNLKADTSTFFQRGALLFFAVLMNALGCGLEMLTLYAQRGIIEKHSRYALYHPSAEAFSSMIMDLPYKILNAITSNIVLYFMTNLRREPGAFFFFVFTSFILTLTMSMFFRSMASLSRSLVQVLPFSAVLLLGLSMYTGFAIPTGYMLGWARWIAYINPISYGFESLMINEFHNRDFPCMDYVPSGPGYTDVGLNNRVCSTVRSVPGQAFVNGNAYIESAYSYTASHKWRNIGVIFAYMFLLGAVYLVATDFITEKKPKGEILVFPRGHKALKKGKSDEDLEGGGGRSATVEKIGSDGLAMIERQTAIFQWKDVCFDIKIGKENCRILDHVDGWVKPGILTALMGVSGAGKTTLLDVLATRTTMGIISGEMLVDGQPRDESFQRKTGYAQQQDLHLSTATVREALEFSALLRQSAHVPRQEKIDYVTEVIKLLDMTEYADAVIGVPGEGLNVEQRKRLTIGVELAARPQLLLFLDEPTSGLDSQTSWAILDLLDKLKKNGQAILCTIHQPSAMLFQRFDRLLFLQAGGRTVYFGEIGQNSQILIDYFVRNGAPPCPPDANPAEWMLDVIGAAPGSHTSINWFETWRRSPEYARVQEHLAELKHERRHQTNLFRTTSGQKREDKDSYREFAAPFWAQLYQVQVRVFQQIWRSPTYIYSKTALCVLSALFVGFSLFHTPNTIQGLQNQMFGIFMLLTLFGQLIQQIMPHFVAQRALYEVRDRPAKTYSWKAFLIANIVVELPWNSLMSVLMFLCWYYPIGLYRNAEPTDAVHLRGTQMWLMIWTFLLFSSTFAHFMIAAFDAAENAGNLGNLLFLLCLLFCGVLATPDQLPRFWIFMYRVSPFTYLVSGMLSVGISNTNVTCADNEYLRFDPVNGTCGEYMGSYMSNLGGYLADEMATANCSFCPIKETNVFLGRVSSSYSDIWRNFGLMWVFIVFNIFAACSLYWWVRVPRDKKPVAKAE"},"dna_sequence":{"accession":"XM_748018.1","fmin":"0","fmax":"4359","strand":"+","sequence":"ATGAATGAAAGTCATGAAGCTGGAAAAAATTCCTCTACCAATGTGGAGGAGAGGGAAGAGGAGGTTCTTCGGCTAGCCAGACAGTTCACAGAGCAGAGCAGCTATTCCACGGCGGGACAAACCCCCTTTGCTGCGGAGGCCGGATCGGCCCTGGACCCCAATGGTGAACGCTTCAACGCTCGGGCATGGTGCAAGGCCATGCTGCAGATGCACATTGGGGACAAGGAGGCACACCCACTGCGAACCTTGGGGGTCGCCTTCAGCAATCTCAATGTGCATGGTTTCGGTTCCGACACTGATTACCAGAAAAGCGTCGGCAATGTCTGGTTAAAGACGCTCAGCCTGGCAAGAATAGCATTTGGTCAAAAGCAGCGCAAAGTCGACATTTTGCAGAACTTGGAAGGATTGGTGGAGGCTGGAGAGATGCTCGTCGTACTTGGACCCCCTGGATCTGGATGCTCCACTTTTTTGAAGACCATTGCTGGAGAGACTTACGGCTTTCATGTGGACAAAAACTCAAACATCAATTTCCAAGGCATCGCAAAGCAGATGGCCCACGAGTTCAGGGGTGAAGCCATCTATACCGCAGAGGTTGATGTCCACTTCCCCAAGCTCACGGTTGGAGATACCCTTTATTTCGCGGCTCGTGCCCGAACACCACGACACATTCCTGGGGGGGTGAATGCGACCCAGTATGCCGGCCACATGCGAGACGTGATCATGGCCATGTTTGGTATCAGCCATACGAAGAACACAATTGTCGGAAACGACTTCATCCGCGGTGTATCTGGTGGAGAGCGCAAGCGGGTTAGCATTGCGGAAGCTTGTCTCAGCAATGCACCGCTGCAATGTTGGGACAATTCGACTCGTGGTCTTGATAGTGCGAATGCCATTGAGTTCTGCAAAACCTTACGCATGCAGGCAGATATCAATGGCACCACAGCCTGTGTCTCTCTATATCAAGCTCCCCAGGCTGCGTACGACTATTTCGATAAGGTCCTGGTCCTATACGAAGGTCGCGAGATCTACTTTGGTCCCACATCCATGGCGAAGCACTACTTCCTTCAGATGGGCTTCGTATGCCCTGACCGGCAAACCGATGCCGACTTTCTCACATCTATGACTAGCCATCTTGAGCGTGTTGTTCAGCCTGGTTATGAAGATCGCGTACCTCGAACACCTGATGAGTTCGCTGCACGATGGAAGGCCTCACCACAGCGAGCACAGCTGATGCAACACATCAAGAGTTATAATGCAAAGTTCGCACTGGATGGGGAATACCTGGATAAGTTTAAGCAATCTCGGCGAGCCCAGCAAGCCAAGGCTCAGCGGGTATCATCACCCTACACTCTTTCCTATGTCCAACAGGTGAAACTGTGCCTGTGGCGCGGGTATCAACGATTGAAGGCTGACCCCAGTGTCACAATCTCTTCATTATTCGGAAATACTATCATATCCCTAGTTATCGCCAGTATCTTCTACAACCTCAAGGCTGACACCAGCACCTTTTTTCAGCGTGGTGCTCTTCTCTTCTTTGCTGTTCTTATGAACGCTCTTGGCTGCGGCCTTGAAATGCTGACTCTATACGCGCAACGAGGGATCATCGAGAAGCACTCCCGATACGCTCTCTACCATCCATCTGCTGAAGCTTTTTCATCAATGATAATGGATTTGCCCTATAAGATTCTCAACGCCATTACGTCCAATATAGTTCTGTACTTCATGACCAACTTGAGGAGAGAACCCGGGGCTTTCTTCTTCTTTGTCTTCACTTCGTTCATCCTGACTCTGACCATGTCCATGTTCTTCCGGTCTATGGCATCGCTATCCAGATCCCTTGTCCAAGTTCTGCCCTTCTCCGCCGTGCTACTTCTCGGTCTCAGCATGTACACTGGGTTCGCTATCCCGACTGGATATATGCTGGGCTGGGCTCGCTGGATTGCGTACATCAATCCCATCAGCTATGGCTTTGAGTCACTGATGATCAATGAGTTCCACAACCGCGATTTCCCGTGCATGGACTATGTCCCATCGGGTCCTGGCTATACGGATGTCGGGCTCAACAACCGTGTTTGCTCCACCGTCAGATCAGTGCCTGGACAAGCCTTTGTCAATGGCAATGCTTACATTGAGTCAGCATATAGCTATACCGCTTCTCACAAATGGAGAAACATCGGTGTCATATTCGCTTACATGTTCCTGCTTGGGGCGGTCTATCTCGTTGCTACTGACTTCATCACCGAGAAGAAGCCGAAGGGCGAGATCCTGGTATTTCCTCGCGGACACAAGGCTCTGAAGAAAGGCAAGTCAGATGAGGATCTTGAAGGGGGTGGTGGCCGCAGCGCCACAGTCGAGAAGATCGGCTCAGATGGCCTTGCCATGATTGAACGCCAAACCGCAATCTTCCAGTGGAAGGATGTCTGCTTCGATATCAAGATTGGAAAGGAGAATTGCAGGATTCTTGACCATGTTGACGGATGGGTCAAACCGGGAATCTTGACGGCGCTTATGGGTGTTTCGGGTGCTGGAAAGACCACGCTCTTGGATGTCCTTGCTACGCGCACCACGATGGGGATTATCAGTGGAGAAATGCTCGTCGATGGTCAACCGCGTGATGAGTCCTTTCAACGTAAGACCGGCTATGCTCAGCAACAAGATCTGCATTTGAGTACTGCTACCGTGCGCGAGGCACTTGAGTTCTCTGCTCTTCTACGTCAATCTGCTCACGTTCCTCGTCAAGAGAAGATTGACTACGTGACAGAAGTGATCAAGCTTCTTGACATGACGGAGTATGCTGATGCCGTTATTGGGGTGCCTGGTGAAGGCCTGAACGTTGAGCAACGTAAACGTCTCACAATCGGGGTAGAGCTTGCAGCCAGACCCCAACTCCTCCTTTTCCTAGACGAACCGACCTCAGGACTTGATTCTCAGACATCCTGGGCTATTCTTGATCTCCTCGATAAACTGAAGAAGAACGGCCAGGCTATTTTGTGTACCATCCATCAACCATCTGCCATGCTGTTTCAGCGCTTTGATCGTCTCCTCTTCCTTCAAGCTGGGGGTCGTACTGTCTACTTTGGAGAAATCGGTCAGAACTCGCAAATACTGATTGACTACTTCGTCCGCAACGGTGCCCCTCCATGTCCTCCGGATGCGAATCCTGCCGAATGGATGCTGGATGTGATCGGTGCCGCTCCCGGATCACACACCAGCATCAACTGGTTCGAGACCTGGCGTCGATCCCCCGAATATGCACGAGTCCAAGAGCACCTTGCTGAACTGAAACACGAACGTCGCCACCAAACAAACCTGTTCCGCACTACATCCGGCCAAAAGCGCGAAGACAAAGACAGCTACCGCGAGTTCGCTGCTCCTTTCTGGGCCCAGCTCTACCAAGTCCAAGTACGAGTCTTCCAGCAAATCTGGCGGTCACCCACCTACATCTACTCCAAGACCGCTCTCTGCGTGTTATCCGCTCTCTTCGTCGGCTTCTCCCTTTTCCATACACCCAACACCATCCAAGGCCTCCAGAATCAAATGTTCGGCATCTTCATGCTACTTACCCTGTTCGGCCAGCTTATCCAACAAATCATGCCGCATTTCGTCGCCCAGCGCGCGCTGTATGAAGTCCGCGACCGACCTGCAAAAACCTACTCTTGGAAAGCCTTCCTCATCGCCAACATCGTTGTTGAACTCCCCTGGAACTCGCTCATGTCCGTCCTTATGTTCCTGTGCTGGTACTACCCGATTGGTCTTTACCGCAATGCCGAACCAACTGATGCGGTGCACTTGCGGGGCACGCAAATGTGGCTGATGATCTGGACCTTCCTTCTCTTCTCGTCCACCTTTGCCCATTTTATGATCGCAGCGTTTGACGCCGCCGAGAACGCGGGAAACCTCGGAAACCTGCTTTTCCTGCTTTGTCTGCTTTTCTGCGGCGTGCTAGCGACACCGGATCAGCTCCCACGGTTCTGGATCTTCATGTATCGCGTTTCGCCGTTTACATATCTGGTGAGCGGGATGTTGTCTGTGGGTATATCGAATACGAATGTCACCTGCGCGGACAATGAGTATCTGCGCTTTGACCCCGTCAATGGGACTTGCGGCGAGTACATGGGCTCATACATGTCGAATCTGGGCGGGTACCTTGCAGACGAGATGGCGACTGCGAACTGCAGCTTCTGCCCGATCAAGGAGACGAATGTGTTCCTCGGTAGAGTTTCGTCGAGTTACTCGGATATCTGGAGGAACTTTGGGCTCATGTGGGTATTTATTGTTTTCAATATCTTTGCAGCTTGTTCGCTGTACTGGTGGGTTCGTGTTCCACGAGACAAGAAGCCAGTTGCAAAGGCCGAGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40696","NCBI_taxonomy_name":"Aspergillus fumigatus Af293","NCBI_taxonomy_id":"330879"}}}},"ARO_accession":"3003942","ARO_id":"40695","ARO_name":"abcA","CARD_short_name":"abcA","ARO_description":"AbcA is a multidrug resistant ABC transporter that confers resistance to methicillin, daptomycin, cefotaxime, and moenomycin.","ARO_category":{"36002":{"category_aro_accession":"0010001","category_aro_cvterm_id":"36002","category_aro_name":"ATP-binding cassette (ABC) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding\/hydrolysis to transport substrates across cell membranes.","category_aro_class_name":"AMR Gene Family"},"35934":{"category_aro_accession":"0000015","category_aro_cvterm_id":"35934","category_aro_name":"methicillin","category_aro_description":"Derived from penicillin to combat penicillin-resistance, methicillin is insensitive to beta-lactamases (also known as penicillinases) secreted by many penicillin-resistant bacteria. Methicillin is bactericidal, and acts by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Antibiotic"},"35985":{"category_aro_accession":"0000068","category_aro_cvterm_id":"35985","category_aro_name":"daptomycin","category_aro_description":"Daptomycin is a novel lipopeptide antibiotic used in the treatment of certain infections caused by Gram-positive organisms. Daptomycin interferes with the bacterial cell membrane, reducing membrane potential and inhibiting cell wall synthesis.","category_aro_class_name":"Antibiotic"},"36989":{"category_aro_accession":"3000645","category_aro_cvterm_id":"36989","category_aro_name":"cefotaxime","category_aro_description":"Cefotaxime is a semisynthetic cephalosporin taken parenterally. It is resistant to most beta-lactamases and active against Gram-negative rods and cocci due to its aminothiazoyl and methoximino functional groups.","category_aro_class_name":"Antibiotic"},"37041":{"category_aro_accession":"3000697","category_aro_cvterm_id":"37041","category_aro_name":"moenomycin A1","category_aro_description":"Moenomycin A1 is a major component of moenomycin mixtures. It is produced by Streptomyces ghanaensis, S. bambergiensis, S. ederensis, and S. geysiriensis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"37031":{"category_aro_accession":"3000687","category_aro_cvterm_id":"37031","category_aro_name":"moenomycin antibiotic","category_aro_description":"Moemomycin antibiotics are phosphoglycolipids that contain a 3-phosphoglyceric acid, often used as a mixture. They inhibit petidoglycan glycosyltransferases to prevent bacterial cell wall biosynthesis.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"3482":{"model_id":"3482","model_name":"OXA-372","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"480"}},"model_sequences":{"sequence":{"5676":{"protein_sequence":{"accession":"AIG22448.1","sequence":"MMHIFLVFLILCSNFALAEDKAISAIFSTEGVDGTIILKSLRGDKTITHNDARASRRFASASTFKIFNTLIAVQENVVSLSGTAFRWDGKTHDIPDWNRDQTLESAFKVSCVWCYQEIAKQVGEETYRRYLTLARYGVLTNVADTTTFWLDGSFTVSAVEQIALLEKIYLRELPFRDEAYDALKQVMLAEQTDSYKLYAKTGWAARMNPQIGWYVGYVETSDDVWFFAINLTLRSELDLGLRQKITKAALRAERIIP"},"dna_sequence":{"accession":"KJ746496.1","fmin":"0","fmax":"774","strand":"+","sequence":"ATGATGCATATTTTTTTGGTCTTTCTGATTCTTTGCTCAAATTTTGCTCTCGCTGAGGACAAAGCTATTTCGGCTATTTTTTCCACAGAAGGTGTTGATGGGACCATCATTTTGAAGTCGTTGCGAGGAGATAAGACAATCACGCACAATGATGCACGCGCTTCTCGCCGATTCGCGTCAGCCTCGACTTTCAAGATATTCAACACGCTGATTGCAGTTCAAGAAAACGTGGTGAGTTTGTCGGGTACTGCATTCCGATGGGATGGAAAAACGCATGACATCCCCGACTGGAACCGTGACCAAACACTTGAAAGCGCATTCAAAGTTTCTTGTGTGTGGTGCTATCAGGAAATCGCCAAGCAAGTGGGGGAAGAAACCTATCGCCGCTACCTTACGCTTGCGAGGTATGGTGTTCTGACCAACGTAGCCGACACTACAACCTTTTGGCTTGATGGCAGCTTTACGGTCAGCGCCGTCGAGCAGATTGCTCTGTTGGAAAAGATCTATCTGCGAGAACTTCCGTTCCGTGATGAAGCCTACGACGCTTTAAAGCAGGTAATGCTGGCAGAGCAGACCGACAGCTACAAACTTTACGCAAAGACTGGCTGGGCAGCAAGGATGAACCCCCAAATTGGGTGGTACGTTGGATATGTTGAAACATCCGATGACGTATGGTTTTTTGCCATCAATTTGACCTTGAGGTCGGAACTTGACTTAGGTTTGCGCCAGAAAATAACAAAGGCTGCGCTTAGGGCTGAACGCATTATTCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3001558","ARO_id":"37958","ARO_name":"OXA-372","CARD_short_name":"OXA-372","ARO_description":"OXA-372 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46506":{"category_aro_accession":"3007717","category_aro_cvterm_id":"46506","category_aro_name":"OXA-372-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-372.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1035":{"model_id":"1035","model_name":"Streptococcus pneumoniae PBP2b conferring resistance to amoxicillin","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"4481":"E475G","4482":"T488A","4480":"T445A"},"Curated-R":{"4481":"E475G","4482":"T488A","4480":"T445A"},"clinical":{"4481":"E475G","4482":"T488A","4480":"T445A"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1300"}},"model_sequences":{"sequence":{"5531":{"protein_sequence":{"accession":"AAL00321.1","sequence":"MRLICMRKFNSHSIPIRLNLLFSIVILLFMTIIGRLLYMQVLNKDFYEKKLASASQTKITSSSARGEIYDASGKPLVENTLKQVVSFTRSNKMTATDLKETAKKLLTYVSISSPNLTERQLADYYLADPEIYKKIVEALPSEKRLDSDGNRLSESELYNNAVDSVQTSQLNYTEDEKKEIYLFSQLNAVGNFATGTIATDPLNDSQVAVIASISKEMPGISISTSWDRKVLETSLSSIVGSVSSEKAGLPAEEAEAYLKKGYSLNDRVGTSYLEKQYEETLQGKRSVKEIHLDKYGNMESVDTIEEGSKGNNIKLTIDLAFQDSVDALLKSYFNSELENGGAKYSEGVYAVALNPKTGAVLSMSGIKHDLKTGELTPDSLGTVTNVFVPGSVVKAATISSGWENGVLSGNQTLTDQSIVFQGSAPINSWYTQAYGSFPITAVQALEYSSNTYMVQTALGLMGQTYQPNMFVGTSNLESAMEKLRSTFGEYGLGTATGIDLPDESTGFVPKEYSFANYITNAFGQFDNYTPMQLAQYVATIANNGVRVAPRIVEGIYGNNDKGGLGDLIQQLQPTEMNKVNISDSDMSILHQGFYQVAHGTSGLTTGRAFSNGALVSISGKTGTAESYVADGQQATNTNAVAYAPSDNPQIAVAVVFPHNTNLTNGVGPSIARDIINLYQKYHPMN"},"dna_sequence":{"accession":"AE007317.1","fmin":"1494215","fmax":"1496273","strand":"-","sequence":"ATGAGACTGATTTGTATGAGAAAATTTAACAGCCATTCGATTCCGATTCGGCTTAATTTATTGTTTTCAATCGTCATTTTACTCTTTATGACCATTATTGGTCGTTTGTTGTATATGCAGGTTTTGAACAAGGATTTTTACGAAAAAAAGCTAGCCTCAGCTAGTCAGACCAAGATTACAAGCAGTTCAGCCCGTGGGGAAATTTATGATGCTAGTGGAAAACCTTTGGTAGAAAATACGTTAAAGCAGGTTGTTTCCTTTACGCGTAGCAATAAAATGACGGCTACAGACTTAAAAGAAACAGCTAAAAAGTTACTGACTTATGTGAGCATCAGTTCTCCAAATTTGACAGAACGCCAGCTGGCGGATTACTATTTGGCTGATCCTGAAATCTATAAAAAAATAGTGGAAGCTCTCCCAAGCGAGAAACGCTTGGATTCAGATGGCAATCGTCTATCCGAATCAGAACTGTATAACAATGCGGTCGATAGTGTACAAACGAGTCAACTAAACTATACAGAGGATGAAAAGAAAGAAATCTATCTTTTTAGTCAGTTAAATGCTGTTGGAAACTTTGCGACAGGAACCATTGCTACAGATCCTCTAAATGATTCTCAGGTGGCTGTTATTGCCTCTATTTCAAAGGAGATGCCTGGCATTAGTATTTCTACTTCTTGGGATAGAAAGGTTTTGGAAACTTCCCTTTCTTCTATAGTTGGGAGTGTATCCAGTGAAAAAGCTGGTCTCCCAGCGGAAGAAGCAGAAGCCTATCTTAAAAAAGGCTATTCTCTAAATGACCGTGTAGGAACCTCCTATTTGGAAAAGCAATATGAAGAGACCTTACAAGGAAAACGCTCGGTAAAAGAAATCCATCTGGATAAATATGGCAATATGGAAAGCGTGGATACAATTGAGGAAGGTAGTAAGGGAAACAATATCAAACTGACCATTGATTTGGCTTTCCAAGATAGCGTGGATGCTTTACTGAAAAGTTATTTCAATTCTGAGCTAGAAAATGGTGGAGCCAAGTATTCTGAAGGTGTCTATGCAGTCGCCCTTAACCCAAAAACAGGTGCGGTTTTGTCTATGTCAGGGATTAAACATGACTTGAAAACGGGAGAGTTGACGCCTGATTCCTTGGGAACGGTAACCAATGTCTTTGTTCCAGGTTCGGTTGTCAAGGCGGCGACCATCAGCTCAGGTTGGGAAAATGGAGTCTTGTCAGGAAACCAGACCTTGACAGACCAGTCCATTGTCTTCCAAGGTTCAGCTCCCATCAATTCTTGGTATACTCAGGCTTACGGTTCATTCCCTATCACAGCGGTCCAAGCTCTGGAGTATTCATCAAATACCTATATGGTCCAAACAGCCTTAGGTCTTATGGGGCAAACCTATCAACCCAATATGTTTGTCGGCACCAGCAATCTAGAGTCTGCTATGGAGAAACTGCGTTCAACCTTTGGCGAATATGGCTTGGGTACTGCGACAGGAATTGACCTACCAGATGAATCTACTGGATTTGTTCCCAAAGAGTATAGCTTTGCTAATTACATTACTAATGCCTTTGGGCAGTTTGATAACTATACGCCGATGCAGTTGGCTCAGTATGTAGCAACTATTGCAAATAATGGTGTTCGTGTGGCTCCTCGTATTGTTGAAGGCATTTATGGTAATAATGATAAGGGAGGACTGGGTGACTTGATTCAGCAACTGCAACCGACAGAGATGAATAAGGTCAATATATCCGACTCCGATATGAGCATCTTGCACCAAGGTTTTTATCAGGTTGCCCATGGTACTAGTGGATTGACAACTGGACGTGCCTTTTCAAATGGTGCCTTGGTATCCATTAGCGGAAAAACAGGTACAGCCGAAAGCTATGTGGCAGATGGTCAGCAAGCAACCAATACCAATGCGGTGGCCTATGCCCCATCTGATAATCCCCAAATCGCTGTCGCAGTGGTCTTTCCTCATAATACCAATCTAACAAATGGTGTAGGACCTTCCATTGCGCGTGACATTATCAATCTGTATCAAAAATACCATCCAATGAATTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39596","NCBI_taxonomy_name":"Streptococcus pneumoniae R6","NCBI_taxonomy_id":"171101"}}}},"ARO_accession":"3003042","ARO_id":"39476","ARO_name":"Streptococcus pneumoniae PBP2b conferring resistance to amoxicillin","CARD_short_name":"Spne_PBP2b_AMX","ARO_description":"PBP2b is a penicillin-binding protein found in Streptococcus pneumoniae.","ARO_category":{"40661":{"category_aro_accession":"3003938","category_aro_cvterm_id":"40661","category_aro_name":"Penicillin-binding protein mutations conferring resistance to beta-lactam antibiotics","category_aro_description":"Mutations in PBP transpeptidases that change the affinity for penicillin thereby conferring resistance to penicillin antibiotics.","category_aro_class_name":"AMR Gene Family"},"35981":{"category_aro_accession":"0000064","category_aro_cvterm_id":"35981","category_aro_name":"amoxicillin","category_aro_description":"Amoxicillin is a moderate-spectrum, bacteriolytic, beta-lactam antibiotic used to treat bacterial infections caused by susceptible microorganisms. A derivative of penicillin, it has a wider range of treatment but remains relatively ineffective against Gram-negative bacteria. It is commonly taken with clavulanic acid, a beta-lactamase inhibitor. Like other beta-lactams, amoxicillin interferes with the synthesis of peptidoglycan.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2386":{"model_id":"2386","model_name":"cipA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"5212":{"protein_sequence":{"accession":"ACX65640.1","sequence":"MKYLSKYEKIRKILSALNQPNYRYSQITEAIFKNKIGNFEAMNNLPKPVRNELIKELGNNVLSITPKMEQKSNQVSKILFAIPGDEYIESVRLSYQTGWESYCISSQCGCGFGCTFCATGTLGLKRNLTTDEITDQLLYFTLNNHPLDSVSFMGMGEALANPYVFDALHLLTDPKLFGLGHRRITVSTIGLLPGVKKLTKEFPQINLTFSLHSPFHDQRSELMPINNHFPLEEVMTVLDEHIQQTKRKVYIAYILLRGINDSTKHAKAVADLLRERGSWEHLYHVNLIPYNSTDATSQSFVESDQNSINMFLRILKSKGIHVTVRTQFGSDINAACGQLYGSNGNI"},"dna_sequence":{"accession":"CP001793.1","fmin":"3931126","fmax":"3932167","strand":"-","sequence":"ATGAAGTATTTATCTAAGTATGAAAAAATACGTAAGATCTTATCGGCTCTAAATCAACCGAATTATAGATATTCGCAAATAACAGAGGCAATCTTCAAGAACAAGATCGGAAATTTCGAAGCAATGAACAACTTGCCTAAGCCTGTAAGAAATGAATTAATCAAAGAGCTTGGAAACAATGTGTTAAGCATCACACCGAAAATGGAGCAGAAATCCAACCAAGTTAGCAAAATTCTGTTTGCTATCCCAGGCGATGAATACATTGAATCCGTAAGGTTAAGTTATCAAACGGGCTGGGAATCCTATTGTATCTCTTCGCAGTGCGGTTGCGGATTTGGTTGTACATTTTGCGCTACGGGAACACTCGGTTTGAAGAGGAATCTTACAACGGATGAAATAACGGATCAACTGCTTTATTTTACTTTGAATAACCATCCCTTGGACAGTGTGTCTTTTATGGGAATGGGAGAGGCACTTGCAAATCCATATGTATTTGATGCTTTGCATTTGCTGACGGATCCTAAACTTTTCGGTTTAGGACATCGAAGGATTACGGTTTCTACCATAGGTTTATTACCTGGAGTAAAAAAGTTGACGAAGGAATTTCCACAGATTAATTTAACGTTCTCGCTTCATTCACCATTTCATGATCAGAGAAGCGAGTTAATGCCCATTAACAATCATTTTCCATTAGAAGAAGTTATGACCGTGTTGGACGAGCATATTCAGCAAACAAAGCGAAAGGTTTACATTGCTTATATCCTGCTAAGGGGTATCAACGATTCAACTAAACATGCTAAAGCCGTTGCTGATTTGTTGCGTGAAAGAGGGTCGTGGGAACATTTATATCACGTCAATCTAATTCCATACAATTCCACTGATGCCACATCACAAAGTTTTGTAGAGTCGGATCAGAACAGCATCAATATGTTCCTTAGAATCTTGAAGTCAAAGGGAATCCATGTCACCGTGAGGACCCAATTCGGATCAGACATCAACGCAGCATGCGGTCAACTATATGGATCAAACGGTAACATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40613","NCBI_taxonomy_name":"Paenibacillus sp. Y412MC10","NCBI_taxonomy_id":"481743"}}}},"ARO_accession":"3003907","ARO_id":"40612","ARO_name":"cipA","CARD_short_name":"cipA","ARO_description":"Cfr-like methyltransferase enzyme conferring resistance to multiple clinically relevant antibiotic classes.","ARO_category":{"36341":{"category_aro_accession":"3000202","category_aro_cvterm_id":"36341","category_aro_name":"Cfr 23S ribosomal RNA methyltransferase","category_aro_description":"Cfr genes produce enzymes which catalyze the methylation of the 23S rRNA subunit at position 8 of adenine-2503. Methylation of 23S rRNA at this site confers resistance to some classes of antibiotics, including streptogramins, chloramphenicols, florfenicols, linezolids and clindamycin.","category_aro_class_name":"AMR Gene Family"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"36521":{"category_aro_accession":"3000382","category_aro_cvterm_id":"36521","category_aro_name":"azidamfenicol","category_aro_description":"Azidamfenicol is a water soluble derivative of chloramphenicol, sharing the same mode of action of inhibiting peptide synthesis by interacting with the 23S RNA of the 50S ribosomal subunit.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36595":{"category_aro_accession":"3000456","category_aro_cvterm_id":"36595","category_aro_name":"thiamphenicol","category_aro_description":"Derivative of Chloramphenicol. The nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3).","category_aro_class_name":"Antibiotic"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"virginiamycin M1","category_aro_description":"Virginiamycin M1 is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37015":{"category_aro_accession":"3000671","category_aro_cvterm_id":"37015","category_aro_name":"tiamulin","category_aro_description":"Tiamulin is a pleuromutilin derivative currently used in veterinary medicine. It binds to the 23 rRNA of the 50S ribosomal subunit to inhibit protein translation.","category_aro_class_name":"Antibiotic"},"37016":{"category_aro_accession":"3000672","category_aro_cvterm_id":"37016","category_aro_name":"madumycin II","category_aro_description":"Madumycin II is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37017":{"category_aro_accession":"3000673","category_aro_cvterm_id":"37017","category_aro_name":"griseoviridin","category_aro_description":"Griseoviridin is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35952":{"category_aro_accession":"0000034","category_aro_cvterm_id":"35952","category_aro_name":"streptogramin A antibiotic","category_aro_description":"Streptogramin A antibiotics are cyclic polyketide peptide hybrids that bind to the ribosomal peptidyl transfer centre. Structural variation arises from substituting a proline for its desaturated derivative and by its substitution for Ala or Cys. Used alone, streptogramin A antibiotics are bacteriostatic, but is bactericidal when used with streptogramin B antibiotics.","category_aro_class_name":"Drug Class"},"36218":{"category_aro_accession":"3000079","category_aro_cvterm_id":"36218","category_aro_name":"oxazolidinone antibiotic","category_aro_description":"Oxazolidinones are a class of synthetic antibiotics discovered the the 1980's.  They inhibit protein synthesis by binding to domain V of the 23S rRNA of the 50S subunit of bacterial ribosomes.  Linezolid is the only member of this class currently in clinical use.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"37014":{"category_aro_accession":"3000670","category_aro_cvterm_id":"37014","category_aro_name":"pleuromutilin antibiotic","category_aro_description":"Pleuromutilins are natural fungal products that target bacterial protein translation by binding the the 23S rRNA, blocking the ribosome P site at the 50S subunit. They are mostly used for agriculture and veterinary purposes.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3511":{"model_id":"3511","model_name":"OXA-441","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"540"}},"model_sequences":{"sequence":{"5706":{"protein_sequence":{"accession":"AFZ84684.1","sequence":"MNIKALLLITSAIFISACSPYIVSANPNHSASKSDENAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTAVFKWDGQKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"JX865394.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGTCTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGAAAATGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACTACAGCAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTAGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3003597","ARO_id":"40207","ARO_name":"OXA-441","CARD_short_name":"OXA-441","ARO_description":"OXA-441 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3541":{"model_id":"3541","model_name":"OXA-479","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"520"}},"model_sequences":{"sequence":{"5736":{"protein_sequence":{"accession":"ALC79294.1","sequence":"MSKKNFILIFIFVILISCKNTEKISNETTLIDNIFTNSNAEGTLVIYNLNDDKYIIHNKERAEQRFYPASTFKIYNSLIGLNEKAVKDVDEVFYKYNGEKVFLESWAKDSNLRYAIKNSQVPAYKELARRIGLKKMKENIEKLDFGNKSIGDSVDTFWLEGPLEISAMEQIKLLTKLAQNELPYPIEIQKAVSDITILEQTYNYTLHGKTGLADSKNMTTEPIGWFVGWLEENDNIYVFALNIDNINSDDLAKRINIVKESLKALNLLK"},"dna_sequence":{"accession":"KR182172.1","fmin":"0","fmax":"810","strand":"+","sequence":"ATGTCTAAAAAAAATTTTATATTAATATTTATTTTTGTTATTTTAATATCTTGTAAAAATACAGAAAAAATATCAAATGAAACTACATTAATAGATAATATATTTACTAATAGCAATGCTGAAGGAACATTAGTTATATATAATTTAAATGATGATAAATATATAATTCATAATAAAGAAAGAGCTGAACAAAGATTTTATCCAGCATCAACATTTAAAATATATAATAGTTTAATAGGCTTAAATGAAAAAGCAGTTAAAGATGTAGATGAAGTATTTTATAAATATAATGGCGAAAAAGTTTTTCTTGAATCTTGGGCTAAGGACTCTAATTTAAGATATGCAATTAAAAATTCGCAAGTACCGGCATATAAAGAATTAGCAAGAAGAATAGGTCTTAAAAAGATGAAAGAGAATATAGAAAAACTAGATTTTGGTAATAAAAGTATAGGTGATAGTGTAGATACTTTTTGGCTTGAAGGACCTTTGGAAATAAGTGCGATGGAGCAAATTAAATTATTAACTAAATTAGCTCAAAATGAATTACCGTATCCTATAGAAATACAAAAAGCTGTTTCTGATATTACTATACTAGAGCAAACTTACAATTATACGCTTCATGGAAAAACTGGATTAGCTGATTCTAAAAACATGACAACTGAGCCTATTGGTTGGTTCGTAGGCTGGCTTGAAGAAAATGATAATATATATGTCTTTGCTTTAAATATTGATAATATAAATTCAGATGACCTTGCAAAAAGGATAAATATAGTAAAAGAAAGTTTAAAAGCATTAAATTTATTAAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36935","NCBI_taxonomy_name":"Brachyspira pilosicoli","NCBI_taxonomy_id":"52584"}}}},"ARO_accession":"3003636","ARO_id":"40246","ARO_name":"OXA-479","CARD_short_name":"OXA-479","ARO_description":"OXA-479 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46521":{"category_aro_accession":"3007732","category_aro_cvterm_id":"46521","category_aro_name":"OXA-63-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-63.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3584":{"model_id":"3584","model_name":"FIM-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8351":{"protein_sequence":{"accession":"AFV91534.1","sequence":"MRPLPHSYLKSLVICLLTAFAALTPVVNSGVQAAQPKDVPVTFTAITQGVWMHTSMKHMENWGHVPSNGLIVEKGDFSILVDTAWDDPQTAQIIEWSKDTLKKPIRWAVFTHAHDDKMGGVAALRQQGIVTYAAADSNRMAPQNGLTPAEHDLIFDSEHSTSVLHPLVIFDPGPGHTRDNIVVGLPEQGIVFGGCLIRPSGSTSLGNTADADLAHWKTAVLAVAQRFAEAQQIIPSHGPMAGRELFELTAQLAEKASIPSTP"},"dna_sequence":{"accession":"JX570731.1","fmin":"1936","fmax":"2725","strand":"+","sequence":"ATGCGCCCCTTACCCCATTCATACCTAAAGAGTCTTGTCATTTGCCTGCTGACGGCCTTCGCCGCCTTAACACCCGTCGTGAACTCTGGCGTACAAGCGGCTCAACCCAAAGACGTGCCGGTAACGTTTACCGCTATTACGCAGGGGGTGTGGATGCACACCAGCATGAAGCACATGGAAAACTGGGGGCATGTACCCAGTAACGGGCTAATCGTTGAAAAAGGAGACTTTAGTATTTTGGTGGATACGGCTTGGGACGATCCACAAACGGCACAGATTATTGAGTGGTCCAAAGATACGCTAAAAAAACCCATTCGTTGGGCGGTGTTTACCCATGCCCACGACGACAAAATGGGCGGGGTGGCTGCCTTACGACAGCAGGGCATTGTGACCTATGCGGCGGCCGACTCTAATCGAATGGCCCCACAGAATGGCTTAACCCCTGCAGAGCATGACCTCATCTTTGATAGCGAGCACAGCACAAGCGTTCTGCATCCGCTGGTCATTTTCGATCCCGGCCCAGGGCATACCCGCGACAATATTGTGGTGGGCCTGCCCGAGCAAGGGATTGTTTTTGGAGGCTGTCTCATTCGCCCATCGGGCAGCACGTCTCTGGGAAACACCGCTGACGCCGATCTCGCTCACTGGAAAACAGCGGTATTGGCCGTTGCGCAGCGCTTTGCGGAGGCCCAACAGATTATACCCAGCCACGGACCCATGGCCGGACGAGAGCTTTTTGAACTGACGGCTCAGCTGGCAGAAAAGGCCAGCATACCGTCCACACCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3004786","ARO_id":"42904","ARO_name":"FIM-1","CARD_short_name":"FIM-1","ARO_description":"FIM-1 is a metallo-beta-lactamase gene found in Pseudomonas aeruginosa from isolates in Italy.","ARO_category":{"42903":{"category_aro_accession":"3004785","category_aro_cvterm_id":"42903","category_aro_name":"FIM beta-lactamase","category_aro_description":"FIM is a metallo-beta-lactamase gene family found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3585":{"model_id":"3585","model_name":"FONA-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"5783":{"protein_sequence":{"accession":"CAB61635.1","sequence":"MIKNTLRKTTLMVATVMPLLFGSAPLWAQTANAKANIQQQLSELEKSSGGRLGVALIDTADNSQILYRGDERFPMCSTSKVMAVSALLKQSETDKNLLAKRMEIKQSDLVNYNPIAEKHLDTGMTLAEFSAATIQYSDNTAMNKILEHLGGPAKVTEFARTIGDKTFRLDRTEPTLNTAIPGDERDTSSPLAMAKSLQNLTLGKALGEPQRAQLVEWMKGNTTGGASIRAGLPTTWIVGDKTGSGDYGTTNDIAVIWPANHAPLVLVTYFTQPQQNAEARKDVLAAAAKIVTEGL"},"dna_sequence":{"accession":"AJ251239.1","fmin":"1053","fmax":"1941","strand":"+","sequence":"ATGATTAAAAATACACTACGTAAAACCACCCTGATGGTGGCTACGGTTATGCCGTTGCTGTTCGGTAGCGCACCGCTATGGGCGCAAACTGCTAATGCCAAGGCGAATATTCAGCAGCAACTGTCTGAGCTGGAGAAAAGCTCCGGTGGCCGCCTGGGCGTGGCGCTGATCGATACCGCCGATAATTCGCAGATCCTGTATCGCGGGGATGAACGTTTTCCTATGTGCAGCACCAGCAAGGTGATGGCGGTGTCGGCGTTGTTAAAACAGAGCGAGACGGATAAAAATCTTTTGGCTAAGCGGATGGAAATCAAGCAATCCGATCTGGTCAACTACAACCCGATCGCCGAAAAACACCTGGATACCGGGATGACCCTGGCCGAGTTCAGCGCCGCCACCATCCAGTACAGTGACAACACGGCGATGAACAAAATCCTTGAGCATCTTGGCGGCCCGGCAAAAGTAACAGAATTTGCGCGTACCATCGGCGATAAAACCTTCCGTCTTGATCGTACCGAGCCCACCTTGAATACCGCCATTCCGGGTGATGAACGTGACACGAGTTCGCCGCTGGCGATGGCAAAAAGCCTGCAAAACCTGACCTTGGGCAAGGCGCTGGGTGAACCACAGCGTGCTCAACTGGTTGAATGGATGAAGGGGAATACTACCGGCGGAGCCAGCATTCGCGCAGGTCTGCCAACCACGTGGATAGTCGGTGATAAAACCGGCAGCGGTGATTACGGTACCACTAACGATATCGCCGTGATTTGGCCAGCTAACCACGCACCGTTGGTGTTGGTGACCTATTTCACGCAGCCACAGCAGAATGCCGAAGCCCGCAAAGACGTGTTGGCTGCGGCTGCTAAAATTGTTACCGAAGGGCTTTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39675","NCBI_taxonomy_name":"Serratia fonticola","NCBI_taxonomy_id":"47917"}}}},"ARO_accession":"3004788","ARO_id":"42906","ARO_name":"FONA-1","CARD_short_name":"FONA-1","ARO_description":"FONA-1 is a class A beta-lactamase gene found in Serratia fonticola.","ARO_category":{"42905":{"category_aro_accession":"3004787","category_aro_cvterm_id":"42905","category_aro_name":"FONA beta-lactamase","category_aro_description":"FONA is a class A beta-lactamase gene family found in Serratia fonticola.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3591":{"model_id":"3591","model_name":"FPH-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"540"}},"model_sequences":{"sequence":{"5789":{"protein_sequence":{"accession":"AJI75632.1","sequence":"MKRLLFTSLYLIPTFLLANTTLDDSFKNLEDEYHGKLGIYTLNTDDKTNISYNENYHFPICSVFKFLLVGAVLEYDMQHKGFLDKKILITQDDIGTLGYAPVTGKNIGKTLTISQLNYAAILSDNPAANILVREIGGLEKLNKLVAKLGDKDTIIKNDEPKINHTKPDSNINKTTPKAITQDIYNLAFGNILDKKHREIFIGYLQKNNTGANRIAYSMPKNWTIGDKTGTCGEYAATNDVAIIWPQNKPPFALSILYTNPSDVKAPSNEKIIQQASKLVSESIAKKDS"},"dna_sequence":{"accession":"CP010019.1","fmin":"78318","fmax":"79185","strand":"-","sequence":"ATGAAACGTTTATTATTTACATCTTTATACTTAATTCCAACATTTTTACTAGCAAACACTACTCTAGATGACTCTTTTAAGAATCTGGAAGATGAATATCATGGTAAACTCGGTATATACACCCTCAATACAGATGATAAAACTAATATCAGCTACAATGAAAATTATCACTTCCCAATTTGTAGTGTTTTTAAATTTTTATTAGTTGGTGCAGTTCTAGAATATGATATGCAACACAAAGGTTTTTTAGATAAAAAAATTCTAATAACTCAAGACGATATTGGTACTCTAGGTTATGCTCCAGTAACAGGCAAAAATATTGGTAAAACTTTGACAATATCACAGCTCAATTACGCAGCTATTCTAAGTGATAATCCTGCTGCTAATATCCTTGTTAGAGAGATTGGGGGCTTGGAAAAGCTTAATAAATTAGTAGCAAAACTAGGAGATAAAGATACTATTATCAAAAATGATGAACCTAAAATCAATCATACAAAGCCAGATAGTAATATCAACAAAACAACGCCCAAAGCTATAACTCAAGATATCTATAATCTAGCATTTGGTAATATTTTGGATAAAAAACATCGTGAAATCTTCATAGGATATTTACAAAAAAACAATACTGGTGCAAATAGAATAGCGTATAGTATGCCTAAAAATTGGACAATTGGTGATAAGACAGGAACTTGTGGAGAGTATGCGGCTACTAATGATGTAGCTATAATTTGGCCACAGAATAAACCGCCTTTTGCTCTAAGTATTCTATATACAAACCCTAGTGATGTAAAAGCTCCAAGTAATGAAAAAATTATTCAGCAAGCATCTAAGTTAGTTTCAGAAAGTATAGCTAAGAAAGATTCTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42914","NCBI_taxonomy_name":"Francisella philomiragia subsp. philomiragia ATCC 25015","NCBI_taxonomy_id":"539329"}}}},"ARO_accession":"3004795","ARO_id":"42913","ARO_name":"FPH-1","CARD_short_name":"FPH-1","ARO_description":"FPH-1 is a carbapenem-hydrolyzing class A beta-lactamase gene found in Francisella philomiragia.","ARO_category":{"42912":{"category_aro_accession":"3004794","category_aro_cvterm_id":"42912","category_aro_name":"FPH beta-lactamase","category_aro_description":"FPH is a carbapenem-hydrolyzing class A beta-lactamase found in Francisella philomiragia.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2394":{"model_id":"2394","model_name":"Staphylococcus aureus menA with mutation conferring resistance to lysocin","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"4430":"G33D"},"Curated-R":{"4430":"G33D"},"experimental":{"4430":"G33D"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"5198":{"protein_sequence":{"accession":"ABD30105.1","sequence":"MSNQYQQYSTVKKYWHLMRPHTLTASVVPVLVGTAASKIYFLGSEDHIKISLFIAMLLACLLIQAATNMFNEYYDYKKGLDDHESVGIGGAIVRNGMSPELVLRLAIAFYILAAILGLFLAANSSFWLLPVGLVCMAVGYLYTGGPFPISWTPFGELFSGVFMGMFIIVIAFFIQTGNIQSYVIWLSVPIVITIGLINMANNIRDRVKDKASGRKTLPILLGKNASLTFMAIMYFIAYAFIVLTIIIKPGGSLFYLLALLSFPMPVKVIRRFKKNDTPPTMMPAMAAAGKTNTFFGLLYALGIYISALFAGI"},"dna_sequence":{"accession":"CP000253.1","fmin":"951801","fmax":"952740","strand":"-","sequence":"ATGAGTAATCAATATCAGCAATATTCTACAGTTAAGAAATATTGGCATTTAATGCGTCCTCATACATTAACTGCTTCCGTAGTACCCGTTTTAGTTGGTACAGCAGCATCTAAAATATATTTTCTTGGTAGCGAAGATCATATTAAAATCAGCCTATTCATTGCCATGTTACTAGCATGCTTACTTATTCAAGCAGCAACTAATATGTTTAATGAATACTATGATTATAAAAAAGGCCTCGATGATCATGAATCTGTAGGCATTGGTGGTGCCATTGTTCGCAACGGTATGAGCCCAGAGCTTGTGCTACGATTAGCCATTGCATTTTACATCTTAGCAGCAATATTAGGTTTGTTTTTAGCTGCTAACTCTTCATTTTGGTTATTACCAGTTGGATTAGTATGTATGGCTGTTGGTTACCTATATACAGGTGGCCCTTTCCCTATTTCATGGACGCCTTTCGGTGAATTATTCTCAGGCGTATTTATGGGTATGTTTATTATCGTTATTGCATTCTTTATTCAAACTGGCAATATTCAAAGTTATGTAATTTGGTTAAGTGTACCTATAGTAATCACTATCGGTTTAATTAATATGGCTAACAATATTCGCGACCGTGTCAAAGATAAAGCAAGTGGTCGCAAAACTTTACCCATTCTATTAGGTAAAAATGCTTCTTTAACATTTATGGCAATCATGTACTTTATCGCTTATGCCTTTATTGTACTTACGATCATTATTAAACCTGGTGGCTCATTATTTTACTTACTTGCGTTGTTATCATTCCCAATGCCTGTTAAAGTTATCAGACGTTTCAAGAAGAATGATACACCGCCTACAATGATGCCAGCAATGGCTGCTGCTGGTAAAACAAATACATTTTTCGGTTTATTATATGCATTAGGTATTTATATTAGTGCATTATTTGCAGGCATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35511","NCBI_taxonomy_name":"Staphylococcus aureus subsp. aureus NCTC 8325","NCBI_taxonomy_id":"93061"}}}},"ARO_accession":"3003917","ARO_id":"40625","ARO_name":"Staphylococcus aureus menA with mutation conferring resistance to lysocin","CARD_short_name":"Saur_menA_LYS","ARO_description":"menA encodes a 1,4-dihydroxy-2-naphthoate octaprenyltransferase, with mutations to the protein conferring resistance to lysocin E.","ARO_category":{"41429":{"category_aro_accession":"3004265","category_aro_cvterm_id":"41429","category_aro_name":"lysocin resistant menA","category_aro_description":"Mutations to demA confer lycosin resistance.","category_aro_class_name":"AMR Gene Family"},"40623":{"category_aro_accession":"3003915","category_aro_cvterm_id":"40623","category_aro_name":"Lysocin E","category_aro_description":"A drug which binds to menaquinone in the bacterial cell membrane. Binding of Lysocin to menaquinone facilitates lysis of the cell.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2380":{"model_id":"2380","model_name":"Staphylococcus aureus GlpT with mutation conferring resistance to fosfomycin","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"40394":{"param_type":"nonsense mutation","param_description":"A sequence change where, compared to a reference sequence, one codon is replaced by a termination codon through a nucleotide substitution. These are described as a substitution of the wildtype codon to a termination codon. Format is given as [wild type AA][position][Ter], for example Q42Ter where Q42 is a wildtype amino acid replaced by a premature termination codon.","param_type_id":"40394","param_value":{"4391":"W355Ter"}},"snp":{"Curated-R":{"4391":"G33D","4385":"W137R","4386":"F3I","4387":"L27F","4388":"A100V","4389":"V213I","4390":"G352D"},"param_value":{"4385":"W137R","4386":"F3I","4387":"L27F","4388":"A100V","4389":"V213I","4390":"G352D"},"clinical":{"4385":"W137R","4386":"F3I","4387":"L27F","4388":"A100V","4389":"V213I","4390":"G352D"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"5195":{"protein_sequence":{"accession":"CAG39357.1","sequence":"MNFLKPAKHIKPLPENQIDDTYKRLRLQVFLGIFIGYAGYYLLRKNFSLAMPALQEQGFTKAELGFALSAVSIAYGFSKFFMGTVSDRSNARIFLVLGLVLTAIVNLLMGFVPFFTSGIGIMFVLLFLNGWFQGMGWPPSGRVLVHWFSVSERGSKTALWNVAHNVGGGIMAPIAAWGITTTAFINFGYLKGFEGVFIYPALLALIIAAISYILIRDTPQSQGLPPIEIYKNDFATSDKKTLETELTTKEILFKYVLNNKWVWAIAFANIFVYFVRYGVLDWAPVYLSEEKHFDLKASGWAYFLYEWAGIPGTLLCGYISDKLFKGRRGPAGFFFMLGVTVFVLIYWLNPPGNAWLDNVSLIAIGFLIYGPVMLIGLQALDYVPKKAAGTAAGLTGLFGYLFGAVMANIVLGAVVDKFGWDVGFILLTAISVFAMLSFILTWNKVGQETVHH"},"dna_sequence":{"accession":"BX571856.1","fmin":"378555","fmax":"379914","strand":"-","sequence":"ATGAATTTTCTTAAACCTGCAAAGCATATTAAGCCTTTGCCAGAAAATCAGATAGATGATACCTATAAACGATTACGTCTCCAAGTATTTCTTGGTATTTTCATCGGTTACGCTGGGTACTATTTATTACGTAAAAACTTTTCATTAGCGATGCCGGCATTGCAAGAGCAAGGTTTTACAAAAGCAGAACTAGGTTTTGCGCTTTCTGCTGTTTCCATCGCATATGGATTTAGTAAGTTCTTTATGGGTACTGTAAGTGATCGGAGCAATGCACGGATATTCTTAGTTCTTGGATTAGTACTCACTGCTATCGTCAATTTGTTAATGGGATTTGTACCGTTCTTTACATCAGGTATCGGTATTATGTTTGTCCTATTATTCTTAAATGGATGGTTTCAAGGTATGGGCTGGCCACCTTCAGGCCGTGTTCTCGTTCACTGGTTTAGTGTAAGTGAACGCGGAAGTAAGACTGCTCTTTGGAACGTTGCGCATAATGTTGGTGGAGGTATTATGGCACCTATTGCTGCTTGGGGTATTACAACAACAGCATTTATCAACTTTGGTTATTTAAAAGGTTTTGAAGGTGTATTCATTTACCCTGCACTCTTAGCACTTATCATTGCCGCAATTTCATATATATTGATTAGAGACACACCTCAATCTCAAGGTTTACCTCCAATCGAAATTTATAAAAATGACTTTGCTACAAGCGATAAGAAAACATTAGAAACAGAATTAACTACAAAAGAAATTTTATTTAAATATGTACTGAACAATAAATGGGTATGGGCAATTGCCTTTGCAAATATATTTGTTTATTTCGTGCGTTATGGTGTACTTGATTGGGCGCCAGTCTACTTAAGTGAAGAAAAACATTTCGACTTAAAAGCATCAGGTTGGGCATACTTCTTATACGAATGGGCTGGAATTCCTGGTACATTATTATGTGGTTACATTTCTGATAAATTATTCAAAGGTCGCCGTGGACCTGCTGGTTTCTTCTTTATGTTAGGTGTCACAGTATTTGTATTAATTTATTGGTTAAATCCTCCAGGCAATGCTTGGTTAGACAATGTCTCATTAATTGCCATTGGTTTCTTAATATATGGACCAGTTATGTTAATTGGTTTACAAGCATTAGATTATGTACCTAAAAAAGCAGCTGGCACAGCAGCTGGATTAACTGGATTATTTGGTTATCTGTTTGGTGCTGTAATGGCCAACATCGTCTTAGGTGCTGTAGTTGATAAATTCGGATGGGATGTCGGTTTTATTTTATTAACAGCAATCAGTGTGTTTGCAATGTTGAGCTTTATCCTCACTTGGAATAAAGTAGGACAAGAAACTGTTCATCATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35517","NCBI_taxonomy_name":"Staphylococcus aureus subsp. aureus MRSA252","NCBI_taxonomy_id":"282458"}}}},"ARO_accession":"3003901","ARO_id":"40603","ARO_name":"Staphylococcus aureus GlpT with mutation conferring resistance to fosfomycin","CARD_short_name":"Saur_GlpT_FOF","ARO_description":"Mutations to the active importer GlpT, which is involved with the uptake of many phosphorylated sugars, confer resistance to fosfomycin by reducing import of the drug into the bacteria.","ARO_category":{"41411":{"category_aro_accession":"3004247","category_aro_cvterm_id":"41411","category_aro_name":"antibiotic-resistant GlpT","category_aro_description":"Fosfomycin is transported bacterial cells through transporters, one of them being glycerol-3-phosphate, which is encoded by the GlpT gene. Mutations in the GlpT gene can confer resistance to fosfomycin.","category_aro_class_name":"AMR Gene Family"},"35944":{"category_aro_accession":"0000025","category_aro_cvterm_id":"35944","category_aro_name":"fosfomycin","category_aro_description":"Fosfomycin (also known as phosphomycin and phosphonomycin) is a broad-spectrum antibiotic produced by certain Streptomyces species. It is effective on gram positive and negative bacteria as it targets the cell wall, an essential feature shared by both bacteria. Its specific target is MurA (MurZ in E.coli), which attaches phosphoenolpyruvate (PEP) to UDP-N-acetylglucosamine, a step of commitment to cell wall synthesis. In the active site of MurA, the active cysteine molecule is alkylated which stops the catalytic reaction.","category_aro_class_name":"Antibiotic"},"45731":{"category_aro_accession":"3007149","category_aro_cvterm_id":"45731","category_aro_name":"phosphonic acid antibiotic","category_aro_description":"A group of antibiotics derived from phosphonic acids.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2462":{"model_id":"2462","model_name":"Cutibacterium acnes gyrA conferring resistance to fluoroquinolones","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"4555":"S101L","4556":"D105G"},"Curated-R":{"4555":"S101L","4556":"D105G"},"clinical":{"4555":"S101L","4556":"D105G"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1500"}},"model_sequences":{"sequence":{"4442":{"protein_sequence":{"accession":"AER05434.1","sequence":"MADDEKPDEQNQADRQGLVTGRHVGIQPVEIRDEIQNAYLDYAMSVIVGRALPDVRDGLKPVHRRVIYAMYDGGYRPDRGWNKCSRVVGDVMGKYHPHGDSAIYDTLVRLAQPWAMRYKLVQGQGNFGSQGNDGAAAMRYTECKMAPLAMEMVRDIDQDTVDFQPNYDNKETEPVVLPSRFPNLLVNGSSGIAVGMATNIPTHNLREVNEAVQWSLAHPNASHEELLEACMERIKGPDFPGGALIVGRQGIEDAYRTGRGSVTMRAVIDMEEDKKGRQCLVVTELPYMCNPDNLATKIADLVNSGRINGIADIRDDSSARTGQRLVIVLKRDAQPRVVMNNLYKHTALQDTFGCNMLALVDNVPRTLRLDQFISYWIDHQMEVIRRRTEYRLAQAEKDAHIQRALVKALDMLDEVIALIRRSPNTEAASTGLQELLDIDEIQARAILDMQLRRLAALERQKIIDRLEELERLIADYKAILASEDRQREIISTELAEIVDKYGDERRTRIIAADGDFSEEDFIPDDDVVVTITRGGYAKRTRTDLYRVQKRGGKGVRGASLRTDDEVAQLFTTTNHQWILFFTNMGRVYRTKVWQLPEAGRDARGGHVAGLLSFLPDEKIAQVMTLRSYDDAEYLLLATRKGMVKKTALKAYDSSRQAGVIAVNFRTEDDELIGAEQCSAADDVLLISRKGQAIRFSAGDDQLRPMGRATSGVTGMKFRGDDELLSMSIIHSDMPEDDRFVFTATGGGYAKRTAVSEYRQQRRGGVGIKAMALSEERGSLVGGLVVSEADEIIAIKTSGQITRSAVSEVPAKGRSTMGVKFVSVRGDDAVSIIAVNPEHTVEEEVADESVETVEGDATKAQSGDVVRRSDTVDDDRAVDTAGNDMKPEDNGE"},"dna_sequence":{"accession":"CP003084.1","fmin":"1004589","fmax":"1007265","strand":"+","sequence":"ATGGCTGACGACGAGAAGCCCGACGAGCAGAACCAGGCCGACCGTCAAGGATTGGTGACCGGCCGTCACGTCGGAATCCAGCCGGTCGAGATTCGTGACGAGATCCAGAACGCGTACCTCGACTACGCGATGAGCGTCATCGTCGGGCGTGCCCTGCCCGATGTGCGCGACGGCCTCAAACCGGTACACCGTCGGGTCATCTACGCGATGTACGACGGCGGTTACCGCCCCGACCGTGGCTGGAATAAGTGTTCCCGCGTCGTCGGTGACGTCATGGGTAAGTACCACCCTCACGGCGACTCGGCCATTTACGACACCTTGGTGCGTCTGGCTCAGCCATGGGCTATGCGATACAAGCTTGTCCAGGGTCAGGGTAACTTCGGGTCCCAGGGCAACGATGGTGCGGCTGCCATGCGATATACCGAGTGCAAGATGGCGCCGCTGGCCATGGAGATGGTGCGCGACATCGACCAGGACACTGTCGATTTCCAGCCCAATTATGACAACAAGGAGACCGAACCGGTCGTCTTGCCGTCGAGGTTCCCCAACCTGCTTGTCAATGGTTCTTCAGGTATCGCGGTGGGCATGGCCACCAACATCCCGACCCATAATCTGCGCGAGGTCAACGAGGCCGTGCAGTGGTCTTTGGCTCATCCCAATGCTTCCCACGAGGAACTGCTCGAGGCGTGCATGGAGCGCATTAAGGGTCCGGATTTCCCCGGCGGCGCCCTCATCGTGGGTCGGCAGGGCATCGAGGACGCCTACCGCACCGGCCGCGGTTCGGTGACGATGCGTGCCGTCATCGACATGGAAGAGGACAAGAAGGGACGCCAGTGCCTGGTCGTCACCGAGTTGCCTTATATGTGCAACCCGGACAACCTCGCCACCAAGATCGCCGACCTGGTGAACTCCGGTCGCATCAACGGTATCGCCGACATCCGTGACGACTCCTCAGCCCGTACTGGTCAGCGTTTAGTCATCGTCCTCAAGCGTGACGCTCAGCCGCGTGTCGTCATGAACAACCTGTACAAGCACACGGCTTTGCAGGACACCTTCGGCTGCAACATGCTGGCTCTGGTGGACAACGTGCCGCGCACTTTGCGTCTGGACCAATTCATCAGCTACTGGATTGACCACCAGATGGAGGTCATCCGCAGGCGTACCGAGTACCGCCTGGCTCAGGCCGAAAAAGACGCCCATATCCAGCGGGCTCTCGTTAAAGCCCTCGATATGCTCGACGAGGTCATCGCGCTCATCCGTCGCTCCCCGAACACTGAGGCCGCCAGCACCGGCCTACAGGAACTGCTCGATATCGACGAGATTCAGGCTCGCGCCATCCTCGATATGCAGTTGCGTCGTCTGGCTGCCCTGGAGCGTCAAAAGATCATCGACCGACTTGAGGAACTCGAGCGCCTCATCGCTGATTACAAAGCAATTCTGGCTAGCGAGGACCGCCAGCGCGAGATCATCTCTACCGAGCTTGCCGAGATCGTCGATAAGTACGGTGACGAGCGTCGCACCCGCATTATCGCCGCCGATGGGGACTTTTCTGAGGAAGACTTCATCCCCGACGATGACGTCGTCGTCACCATTACCCGGGGCGGCTACGCCAAGCGCACCCGCACTGACCTGTACCGGGTCCAGAAACGCGGTGGCAAGGGTGTTCGCGGCGCCAGCCTGCGCACTGACGATGAGGTGGCACAGCTATTCACTACCACGAACCACCAGTGGATCCTCTTCTTCACGAATATGGGTCGGGTCTATCGCACCAAGGTATGGCAGCTGCCGGAGGCTGGTCGTGACGCCAGGGGGGGTCACGTCGCTGGGTTGCTGAGCTTCCTGCCTGACGAGAAGATCGCCCAAGTCATGACCCTACGGTCCTACGACGACGCCGAGTACCTCCTCCTGGCCACTCGCAAGGGTATGGTCAAGAAGACGGCGCTCAAGGCTTATGACTCGTCTCGTCAGGCCGGCGTTATTGCCGTTAATTTCCGTACCGAGGACGATGAGCTTATCGGCGCCGAGCAGTGCTCCGCCGCTGACGACGTGCTGCTTATCAGCCGTAAGGGGCAGGCGATCCGGTTCTCTGCCGGCGACGACCAGTTGCGCCCGATGGGGCGTGCGACTTCGGGCGTTACCGGCATGAAGTTCCGTGGTGATGACGAGTTGCTGTCAATGTCGATTATTCACTCCGACATGCCTGAGGATGATCGGTTCGTTTTCACAGCAACCGGTGGCGGCTACGCCAAGCGCACTGCTGTGTCGGAGTACCGTCAGCAGAGGCGTGGGGGAGTCGGCATCAAAGCGATGGCCCTCAGTGAGGAGCGCGGCTCCCTGGTTGGTGGCCTGGTGGTCAGCGAGGCTGACGAAATCATCGCGATTAAGACGTCAGGTCAGATCACCCGATCGGCCGTGTCTGAGGTGCCCGCCAAGGGACGCTCCACGATGGGGGTGAAGTTCGTCTCCGTACGCGGTGACGACGCTGTCTCAATCATCGCTGTCAACCCCGAACATACCGTCGAGGAGGAAGTCGCTGACGAATCGGTGGAAACTGTTGAAGGCGATGCCACGAAGGCCCAATCGGGAGATGTGGTTCGGCGAAGCGATACTGTGGATGACGACCGTGCCGTCGATACGGCGGGAAACGACATGAAGCCGGAGGACAACGGTGAGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41684","NCBI_taxonomy_name":"Cutibacterium acnes subsp. defendens ATCC 11828","NCBI_taxonomy_id":"1091045"}}}},"ARO_accession":"3003974","ARO_id":"40779","ARO_name":"Cutibacterium acnes gyrA conferring resistance to fluoroquinolones","CARD_short_name":"Cacn_gyrA_FLO","ARO_description":"Point mutations in Cutibacterium acnes gyrA protein known to confer resistance to fluoroquinolone antibiotics.","ARO_category":{"39876":{"category_aro_accession":"3003292","category_aro_cvterm_id":"39876","category_aro_name":"fluoroquinolone resistant gyrA","category_aro_description":"DNA gyrase is responsible for DNA supercoiling and consists of two alpha and two beta subunits. GyrA point mutations confer resistance by preventing fluoroquinolone antibiotics from binding the alpha-subunit.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2381":{"model_id":"2381","model_name":"Staphylococcus aureus UhpT with mutation conferring resistance to fosfomycin","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"40394":{"param_type":"nonsense mutation","param_description":"A sequence change where, compared to a reference sequence, one codon is replaced by a termination codon through a nucleotide substitution. These are described as a substitution of the wildtype codon to a termination codon. Format is given as [wild type AA][position][Ter], for example Q42Ter where Q42 is a wildtype amino acid replaced by a premature termination codon.","param_type_id":"40394","param_value":{"4399":"Y314Ter","4400":"W228Ter"}},"snp":{"Curated-R":{"4399":"D105G","4400":"D105G","4396":"G358V","4397":"G112E","4398":"W425R"},"param_value":{"4396":"G358V","4397":"G112E","4398":"W425R"},"clinical":{"4396":"G358V","4397":"G112E","4398":"W425R"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"850"}},"model_sequences":{"sequence":{"5196":{"protein_sequence":{"accession":"CAG39240.1","sequence":"MNFFDIHKIPNKGIPLSVQRKLWLRNFMQAFFVVFFVYMAMYLIRNNFKAAQPFLKEEIGLSTLELGYIGLAFSITYGLGKTLLGYFVDGRNTKRIISFLLILSAITVLIMGFVLSYFGSVMGLLIVLWGLNGVFQSVGGPASYSTISRWAPRTKRGRYLGFWNTSHNIGGAIAGGVALWGANVFFHGNVIGMFIFPSVIALLIGIATLFIGKDDPEELGWNRAEEIWEEPVDKENIDSQGMTKWEIFKKYILGNPVIWILCVSNVFVYIVRIGIDNWAPLYVSEHLHFSKGDAVNTIFYFEIGALVASLLWGYVSDLLKGRRAIVAIGCMFMITFVVLFYTNATSVMMVNISLFALGALIFGPQLLIGVSLTGFVPKNAISVANGMTGSFAYLFGDSMAKVGLAAIADPTRNGLNIFGYTLSGWTDVFIVFYVALFLGMILLGIVAFYEEKKIRSLKI"},"dna_sequence":{"accession":"BX571856.1","fmin":"246977","fmax":"248357","strand":"+","sequence":"ATGAACTTTTTTGATATCCATAAGATTCCGAACAAAGGCATTCCATTATCGGTACAACGTAAATTATGGCTTAGAAACTTCATGCAAGCTTTCTTCGTAGTGTTCTTTGTTTATATGGCTATGTATTTAATTCGAAACAACTTTAAGGCGGCACAACCGTTTTTAAAAGAGGAAATTGGATTATCTACATTAGAACTTGGTTATATCGGATTAGCATTTAGTATCACGTACGGTTTAGGGAAAACATTACTTGGATATTTTGTCGATGGACGTAACACAAAACGTATTATCTCATTCTTACTTATCTTATCTGCGATTACAGTTTTAATTATGGGATTTGTTTTAAGTTACTTTGGTTCAGTAATGGGATTATTAATTGTACTTTGGGGACTTAACGGGGTGTTCCAATCAGTTGGTGGACCTGCAAGTTATTCAACGATTTCAAGATGGGCGCCAAGAACGAAACGTGGCCGATACTTAGGGTTTTGGAATACATCACATAATATCGGTGGTGCCATTGCAGGTGGTGTTGCACTTTGGGGTGCTAATGTATTCTTCCATGGAAATGTTATAGGGATGTTCATTTTCCCATCGGTGATTGCATTACTTATTGGTATCGCAACATTATTTATCGGAAAAGATGATCCAGAAGAATTAGGATGGAATCGTGCTGAAGAAATTTGGGAAGAGCCGGTTGATAAAGAAAATATTGATTCTCAAGGTATGACAAAATGGGAGATCTTTAAAAAATATATCCTGGGAAATCCTGTTATATGGATTCTATGTGTTTCAAACGTCTTTGTATACATTGTACGAATCGGTATTGATAACTGGGCACCGTTATATGTGTCAGAGCATTTACACTTTAGTAAAGGCGATGCAGTTAATACGATATTCTACTTTGAAATTGGTGCTTTAGTTGCAAGTTTATTATGGGGCTACGTATCAGACTTATTAAAAGGTCGTCGTGCAATTGTAGCTATTGGCTGTATGTTTATGATTACATTTGTTGTCTTATTCTACACAAATGCTACAAGTGTAATGATGGTTAACATTTCATTGTTTGCATTAGGTGCGTTAATCTTTGGTCCGCAATTATTAATTGGTGTATCATTGACTGGTTTTGTTCCTAAAAATGCCATCAGTGTAGCAAACGGAATGACAGGTTCATTCGCGTATCTATTCGGTGACTCAATGGCAAAAGTTGGTTTGGCGGCTATTGCTGATCCAACACGTAACGGTTTAAACATCTTTGGATATACATTAAGTGGATGGACAGATGTTTTCATCGTCTTCTATGTTGCATTATTCCTAGGCATGATTCTATTAGGAATCGTTGCTTTCTATGAAGAAAAGAAAATTAGAAGTTTAAAAATCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35517","NCBI_taxonomy_name":"Staphylococcus aureus subsp. aureus MRSA252","NCBI_taxonomy_id":"282458"}}}},"ARO_accession":"3003902","ARO_id":"40604","ARO_name":"Staphylococcus aureus UhpT with mutation conferring resistance to fosfomycin","CARD_short_name":"Saur_UhpT_FOF","ARO_description":"Mutations to the active importer UhpT, which is involved with the uptake of many phosphorylated sugars, confer resistance to fosfomycin by reducing import of the drug into the bacteria.","ARO_category":{"41412":{"category_aro_accession":"3004248","category_aro_cvterm_id":"41412","category_aro_name":"antibiotic-resistant UhpT","category_aro_description":"UhpT encodes a transporter that can import fosfomycin-type drugs into bacterial cells. Mutations to UhpT confer resistance.","category_aro_class_name":"AMR Gene Family"},"35944":{"category_aro_accession":"0000025","category_aro_cvterm_id":"35944","category_aro_name":"fosfomycin","category_aro_description":"Fosfomycin (also known as phosphomycin and phosphonomycin) is a broad-spectrum antibiotic produced by certain Streptomyces species. It is effective on gram positive and negative bacteria as it targets the cell wall, an essential feature shared by both bacteria. Its specific target is MurA (MurZ in E.coli), which attaches phosphoenolpyruvate (PEP) to UDP-N-acetylglucosamine, a step of commitment to cell wall synthesis. In the active site of MurA, the active cysteine molecule is alkylated which stops the catalytic reaction.","category_aro_class_name":"Antibiotic"},"45731":{"category_aro_accession":"3007149","category_aro_cvterm_id":"45731","category_aro_name":"phosphonic acid antibiotic","category_aro_description":"A group of antibiotics derived from phosphonic acids.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3326":{"model_id":"3326","model_name":"QnrS15","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"5355":{"protein_sequence":{"accession":"AZP56652.1","sequence":"METYNHTYRHHNFSHKDLSDLTFTACTFIRSDFRRANLRDTTFVNCKFIEQGDIEGCRFDVADLRDASFQQCQLAMANFSNANCYGIEFRACDLKGANFSRTNFAHQVSNRMYFCSAFISGCNLSYANMERVCLEKCELFENRWIGTNLAGASLKESDLSRGVFSEDVWGQFSLQGANLCHAELDGLDPRKVDTSGIKIAAWQQELILEALGIVVYPD"},"dna_sequence":{"accession":"MK303617.1","fmin":"0","fmax":"657","strand":"+","sequence":"ATGGAAACCTACAATCATACATATCGGCACCACAACTTTTCACATAAAGACTTAAGTGATCTCACCTTCACCGCTTGCACATTCATTCGCAGCGACTTTCGACGTGCTAACTTGCGTGATACGACATTCGTCAACTGCAAGTTCATTGAACAGGGTGATATCGAAGGCTGCCGCTTTGATGTCGCAGATCTTCGTGATGCAAGTTTCCAACAATGCCAACTTGCGATGGCAAACTTCAGTAATGCCAATTGCTACGGTATAGAGTTCCGTGCGTGTGATTTAAAAGGTGCCAACTTTTCCCGAACAAACTTTGCCCATCAAGTGAGTAATCGTATGTACTTTTGCTCAGCATTTATTTCTGGATGTAATCTTTCCTATGCCAATATGGAGAGGGTTTGTTTAGAAAAATGTGAGTTGTTTGAAAATCGCTGGATAGGAACGAACCTAGCGGGTGCATCACTGAAAGAGTCAGACTTAAGTCGAGGTGTTTTTTCCGAAGATGTCTGGGGGCAATTTAGCCTACAGGGTGCCAATTTATGCCACGCCGAACTCGACGGTTTAGATCCCCGCAAAGTCGATACATCAGGTATCAAAATTGCAGCCTGGCAGCAAGAACTGATTCTCGAAGCACTGGGTATTGTTGTTTATCCTGACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3004627","ARO_id":"42611","ARO_name":"QnrS15","CARD_short_name":"QnrS15","ARO_description":"QnrS15 is a plasmid-mediated quinolone resistance protein.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3351":{"model_id":"3351","model_name":"Erm(O)-lrm","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"5497":{"protein_sequence":{"accession":"AAA26779.1","sequence":"MARPTQRARTLSQNFLADRATAERVARLAVPDRGRPPLLLEVGAGNGALTEPLARRSRELHAYEIDPRLVPGLRARFARSPHVHVVAGDFLTARPPRTPFAVAGNVPFSRTADIVDWCLTAPGLTDATLLTQLEYARKRTGDYGRWTLLTVLTWPRHEWRLVGRVGRSRFCPAPRVDAGILRIERRPTALLTGAAARRDWADLVELGFSGVGGSLHASLRRAHSRRRVDAAFRAARLDPGVLVGEVAPDRWLRLHEELTA"},"dna_sequence":{"accession":"M74717.1","fmin":"39","fmax":"822","strand":"+","sequence":"ATGGCCCGCCCCACCCAGCGTGCCCGCACGCTCTCGCAGAACTTCCTCGCCGACCGCGCCACCGCCGAACGTGTGGCGCGCCTCGCCGTCCCCGACCGGGGGCGCCCGCCCCTCCTGCTCGAAGTGGGCGCGGGCAACGGCGCCCTCACCGAGCCGCTCGCCCGCCGCAGCCGCGAACTGCACGCCTACGAGATCGACCCCCGGCTCGTCCCCGGGCTCCGCGCCCGTTTCGCGCGCAGCCCCCACGTCCACGTCGTCGCCGGTGACTTCCTCACCGCCCGGCCCCCGCGCACCCCGTTCGCCGTCGCCGGGAACGTGCCCTTCTCGCGCACCGCCGACATCGTCGACTGGTGCCTGACCGCGCCCGGCCTCACCGACGCCACCCTCCTCACCCAGCTCGAGTACGCCCGCAAACGCACCGGCGACTACGGCCGCTGGACCCTGCTCACGGTCCTGACCTGGCCGCGCCACGAGTGGCGGCTGGTGGGCCGGGTGGGCCGCAGCCGCTTCTGCCCGGCGCCGCGCGTCGACGCCGGCATCCTCCGGATCGAACGCCGCCCCACTGCGCTGCTCACCGGCGCCGCCGCCCGCCGCGACTGGGCGGACCTGGTCGAGCTGGGCTTCTCCGGCGTCGGCGGCTCGCTGCACGCGTCCCTGCGCCGCGCCCACTCCCGGCGCCGGGTGGACGCGGCGTTCCGCGCCGCGCGGCTCGATCCCGGTGTCCTCGTCGGCGAGGTCGCCCCCGACCGGTGGCTGCGGCTGCACGAGGAGTTGACGGCATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39569","NCBI_taxonomy_name":"Streptomyces lividans","NCBI_taxonomy_id":"1916"}}}},"ARO_accession":"3004652","ARO_id":"42681","ARO_name":"Erm(O)-lrm","CARD_short_name":"Erm(O)-lrm","ARO_description":"ErmO (gene lrm) lincomycin resistance methylase [Streptomyces lividans].","ARO_category":{"36699":{"category_aro_accession":"3000560","category_aro_cvterm_id":"36699","category_aro_name":"Erm 23S ribosomal RNA methyltransferase","category_aro_description":"Erm proteins are part of the RNA methyltransferase family and methylate A2058 (E. coli nomenclature) of the 23S ribosomal RNA conferring degrees of resistance to Macrolides, Lincosamides and Streptogramin b. This is called the MLSb phenotype.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"36284":{"category_aro_accession":"3000145","category_aro_cvterm_id":"36284","category_aro_name":"tylosin","category_aro_description":"Tylosin is a 16-membered macrolide, naturally produced by Streptomyces fradiae. It interacts with the bacterial ribosome 50S subunit to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2421":{"model_id":"2421","model_name":"efrA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"960"}},"model_sequences":{"sequence":{"5893":{"protein_sequence":{"accession":"WP_104671188.1","sequence":"MKLMWRYTMRYKKLLFADFICVFGFILIELGLPTILARMIDKGIIPKDMDYVYQQGIWMVVITIIGVAMNILLGYFGARITTNIVRDIRDDLFEKIQTFSHSEYESIGVSSLITRTTNDAYQIMLFMGNILRLGFMTPVMFIASLYMVMRTSPSLGMYVLGALPFLLLAVVGIARLSEPLSKKQQKNLDGINGILRENLSGLRVIRAFVNEKFEESRFNKVNETYTKSSKSLFRLMAAAQPGFFFLFNIVMVLIIWSGTVQISHGDLEVGNLIAFIEYIFHALFSFMLFASVFMMYPRAAVSASRIQEALDMEPAIREEEGVTETATKGYLEFKNVTFAYPGHAESPVIRNVSFKASPGETVAFIGSTGSGKSTLIQLIPRFYDVSEGEILIDGVNVKEYKLSALRNKIGYIPQKALLFTGTIADNLRYGKEDATLEEMERAIDIAQATEFVSQKPQGYDEPLSEGGTNFSGGQKQRLAIARAIIRNPEIYIFDDSFSALDYQTDANLRARLKKETTESTVLIVAQRVGTIMHADRIVVLNEGDVVGIGTHRELLETCPIYYDIAASQLSEEELA"},"dna_sequence":{"accession":"NZ_PTWF01000025.1","fmin":"35858","fmax":"37586","strand":"+","sequence":"TTGAAGTTAATGTGGCGTTACACAATGCGTTATAAGAAATTACTTTTCGCTGATTTTATTTGTGTGTTTGGTTTTATTTTGATTGAATTAGGCTTGCCGACCATTTTAGCACGAATGATTGACAAAGGAATTATTCCTAAAGATATGGACTATGTTTATCAGCAAGGGATTTGGATGGTTGTAATTACGATTATTGGTGTCGCAATGAATATTTTGCTAGGGTACTTTGGTGCCAGAATTACAACAAACATTGTTCGTGATATTCGTGATGATTTATTTGAAAAGATTCAAACTTTCTCACACAGTGAATATGAAAGTATTGGGGTTTCTTCCTTAATTACGCGAACTACCAATGATGCATACCAAATTATGCTCTTCATGGGAAATATTTTACGTCTTGGCTTTATGACGCCAGTGATGTTTATTGCCAGTCTTTACATGGTGATGCGGACGAGTCCGTCGTTAGGAATGTACGTTTTAGGTGCCTTGCCTTTTCTACTGCTAGCAGTTGTCGGAATTGCTCGTTTGTCAGAACCGTTATCTAAAAAGCAACAAAAGAACTTAGATGGAATCAATGGGATTTTAAGAGAAAATCTTTCTGGATTGCGGGTAATACGCGCATTTGTTAATGAAAAATTTGAAGAATCTCGTTTTAATAAAGTCAATGAAACTTACACTAAAAGTTCAAAAAGCCTGTTTCGTTTAATGGCAGCAGCCCAACCAGGGTTCTTTTTCTTATTTAATATTGTAATGGTCTTAATCATTTGGAGCGGGACTGTTCAAATCAGCCATGGGGATTTAGAAGTTGGGAATTTAATAGCTTTTATTGAATATATTTTCCATGCGCTGTTCTCGTTTATGTTATTTGCCAGTGTCTTTATGATGTATCCGCGGGCTGCGGTTTCGGCTTCGCGGATTCAAGAAGCCTTAGACATGGAACCAGCTATTCGTGAAGAAGAAGGCGTAACAGAAACAGCTACTAAAGGCTATCTAGAGTTTAAAAATGTAACCTTTGCCTATCCTGGACATGCGGAAAGCCCAGTCATCCGCAATGTAAGTTTTAAGGCGTCACCTGGTGAAACAGTGGCCTTTATTGGGAGCACAGGTAGTGGGAAATCAACATTAATTCAATTGATTCCACGGTTTTATGATGTATCAGAAGGTGAAATTTTAATCGATGGAGTGAACGTAAAAGAGTACAAACTTAGTGCATTACGCAATAAGATTGGCTATATTCCACAAAAAGCGTTACTTTTTACTGGTACAATTGCTGATAACCTTCGCTACGGTAAGGAAGATGCGACGTTAGAAGAAATGGAACGAGCAATTGACATTGCTCAAGCTACAGAATTTGTTTCACAAAAACCGCAAGGCTATGATGAACCTCTTTCAGAAGGTGGCACGAACTTTTCTGGTGGTCAAAAACAACGTTTAGCTATCGCACGGGCGATTATTCGCAATCCGGAAATTTATATATTTGATGATAGTTTTTCTGCGTTAGATTATCAAACAGATGCAAATTTACGAGCGCGTCTGAAAAAAGAAACAACAGAATCCACTGTTTTAATTGTGGCACAACGTGTTGGAACAATTATGCATGCGGACCGCATTGTTGTTTTAAACGAAGGCGACGTGGTCGGAATTGGCACACATCGTGAATTACTTGAGACTTGTCCAATTTACTATGATATTGCGGCTTCTCAATTGTCAGAGGAGGAATTAGCATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35918","NCBI_taxonomy_name":"Enterococcus faecalis","NCBI_taxonomy_id":"1351"}}}},"ARO_accession":"3003948","ARO_id":"40703","ARO_name":"efrA","CARD_short_name":"efrA","ARO_description":"efrA is a part of the EfrAB efflux pump, and both efrA and efrB are necessary to confer drug resistance.","ARO_category":{"36002":{"category_aro_accession":"0010001","category_aro_cvterm_id":"36002","category_aro_name":"ATP-binding cassette (ABC) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding\/hydrolysis to transport substrates across cell membranes.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2422":{"model_id":"2422","model_name":"efrB","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"710"}},"model_sequences":{"sequence":{"6247":{"protein_sequence":{"accession":"CDO61516.1","sequence":"LDTCRIFRRNAKSPVNIAKHAKFIRRLKWLCSENMTGFSVLKLYVRKKKPLKGFKQVNHRFKWFGFKASFISGLMLPLVQMTAYGTYIGVAVLGSYYVVAGVIVVGQLQAFIQYIWQISQPMGNITQLSAALQSASASTMRIFEILDEPEEELNEQDVPLPEPILGSVEFENVSFSYDPEKPLIRNLNFKVDAGQMVAIVGPTGAGKTTLINLLMRFYDVTEGAIKIDGIDTKKMNRSDVRSVFGMVLQDAWLYKGTIADNIRFGKLDATDYEVVDAAKTANVDHFIRTMPDGYEMEINSEGDNVSLGQKQLLTIARAVISDPKILILDEATSSVDTRLEALIQKAMDRVMEGRTSFVIAHR"},"dna_sequence":{"accession":"HG970103.1","fmin":"0","fmax":"1086","strand":"+","sequence":"TTAGATACGTGTCGCATATTCAGGAGGAATGCTAAATCACCAGTAAATATTGCAAAGCATGCAAAATTCATTAGGAGACTTAAATGGTTATGTTCAGAAAATATGACTGGGTTCAGTGTCTTAAAACTATATGTTCGGAAAAAGAAACCCTTGAAAGGCTTTAAACAAGTCAATCATCGTTTTAAATGGTTTGGCTTCAAAGCATCCTTTATCTCAGGATTAATGTTGCCATTGGTTCAAATGACCGCTTATGGGACCTATATCGGGGTAGCTGTCCTTGGTAGTTACTATGTGGTTGCTGGTGTGATCGTAGTGGGGCAGTTACAAGCGTTTATTCAATATATTTGGCAAATTAGCCAACCAATGGGGAATATTACGCAGTTGTCTGCAGCTTTACAAAGCGCTTCAGCTTCGACCATGCGGATTTTTGAAATCCTAGATGAACCAGAAGAAGAACTTAACGAACAAGATGTTCCTTTGCCAGAACCTATTTTAGGCTCTGTTGAATTTGAAAATGTCAGCTTTAGTTATGACCCAGAAAAACCGTTAATTCGTAATTTGAACTTTAAAGTTGATGCGGGCCAAATGGTTGCGATTGTGGGACCAACTGGCGCTGGGAAAACAACCTTAATCAACTTACTGATGCGTTTTTATGATGTAACAGAAGGCGCCATTAAAATTGATGGTATTGACACAAAAAAAATGAACCGTAGTGATGTCCGATCTGTATTTGGAATGGTATTGCAAGATGCTTGGTTGTATAAAGGTACCATTGCAGATAACATTCGTTTTGGGAAGTTGGATGCCACGGATTATGAAGTTGTCGATGCAGCGAAAACGGCCAATGTGGATCACTTCATTCGGACAATGCCAGATGGGTATGAAATGGAAATCAATTCTGAGGGAGATAACGTTTCCCTTGGTCAAAAACAATTGTTGACCATTGCCCGAGCGGTAATTTCTGATCCGAAAATTTTGATTTTAGATGAGGCGACTAGTTCAGTCGATACACGCTTGGAAGCCTTAATTCAAAAAGCAATGGATCGTGTTATGGAAGGACGAACGAGTTTCGTTATTGCCCACCGT","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36779","NCBI_taxonomy_name":"Enterococcus faecium","NCBI_taxonomy_id":"1352"}}}},"ARO_accession":"3003949","ARO_id":"40704","ARO_name":"efrB","CARD_short_name":"efrB","ARO_description":"efrB is a part of the EfrAB efflux pump, and both efrA and efrB are necessary to confer multidrug resistance.","ARO_category":{"36002":{"category_aro_accession":"0010001","category_aro_cvterm_id":"36002","category_aro_name":"ATP-binding cassette (ABC) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding\/hydrolysis to transport substrates across cell membranes.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"4011":{"model_id":"4011","model_name":"PDC-384","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"6381":{"protein_sequence":{"accession":"WP_150823491.1","sequence":"MRDTRFPCLCGIAASTLLFAATPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASKHWPALQGSRFDDISLLDLATYTAGGLPLQFPDSVQKDRAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMAPQPHRIARLPAPQALEGQRLLNKTGSTSGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_066540.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCGCCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCAAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGACATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCGGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCCGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCCGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAGCGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005283","ARO_id":"43640","ARO_name":"PDC-384","CARD_short_name":"PDC-384","ARO_description":"PDC-384 is a class C beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2423":{"model_id":"2423","model_name":"msbA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"5468":{"protein_sequence":{"accession":"AAC74000.1","sequence":"MHNDKDLSTWQTFRRLWPTIAPFKAGLIVAGVALILNAASDTFMLSLLKPLLDDGFGKTDRSVLVWMPLVVIGLMILRGITSYVSSYCISWVSGKVVMTMRRRLFGHMMGMPVSFFDKQSTGTLLSRITYDSEQVASSSSGALITVVREGASIIGLFIMMFYYSWQLSIILIVLAPIVSIAIRVVSKRFRNISKNMQNTMGQVTTSAEQMLKGHKEVLIFGGQEVETKRFDKVSNRMRLQGMKMVSASSISDPIIQLIASLALAFVLYAASFPSVMDSLTAGTITVVFSSMIALMRPLKSLTNVNAQFQRGMAACQTLFTILDSEQEKDEGKRVIERATGDVEFRNVTFTYPGRDVPALRNINLKIPAGKTVALVGRSGSGKSTIASLITRFYDIDEGEILMDGHDLREYTLASLRNQVALVSQNVHLFNDTVANNIAYARTEQYSREQIEEAARMAYAMDFINKMDNGLDTVIGENGVLLSGGQRQRIAIARALLRDSPILILDEATSALDTESERAIQAALDELQKNRTSLVIAHRLSTIEKADEIVVVEDGVIVERGTHNDLLEHRGVYAQLHKMQFGQ"},"dna_sequence":{"accession":"U00096.3","fmin":"966620","fmax":"968369","strand":"+","sequence":"ATGCATAACGACAAAGATCTCTCTACGTGGCAGACATTCCGCCGACTGTGGCCAACCATTGCGCCTTTCAAAGCGGGTCTGATCGTGGCGGGCGTAGCGTTAATCCTCAACGCAGCCAGCGATACCTTCATGTTATCGCTCCTTAAGCCACTTCTTGATGATGGCTTTGGTAAAACAGATCGCTCCGTGCTGGTGTGGATGCCGCTGGTGGTGATCGGGCTGATGATTTTACGTGGTATCACCAGCTATGTCTCCAGCTACTGTATCTCCTGGGTATCAGGAAAGGTGGTAATGACCATGCGTCGCCGCCTGTTTGGTCACATGATGGGAATGCCAGTTTCATTCTTTGACAAACAGTCAACGGGTACGCTGTTGTCACGTATTACCTACGATTCCGAACAGGTTGCTTCTTCTTCTTCCGGCGCACTGATTACTGTTGTGCGTGAAGGTGCGTCGATCATCGGCCTGTTCATCATGATGTTCTATTACAGTTGGCAACTGTCGATCATTTTGATTGTGCTGGCACCGATTGTTTCGATTGCGATTCGCGTTGTATCGAAGCGTTTTCGCAACATCAGTAAAAACATGCAGAACACCATGGGGCAGGTGACCACCAGCGCAGAACAAATGCTGAAGGGCCACAAAGAAGTATTGATTTTCGGTGGTCAGGAAGTGGAAACGAAACGCTTTGATAAAGTCAGCAACCGAATGCGTCTTCAGGGGATGAAAATGGTTTCAGCCTCTTCCATCTCTGATCCGATCATTCAGCTGATCGCCTCTTTGGCGCTGGCGTTTGTTCTGTATGCGGCGAGCTTCCCAAGTGTCATGGATAGCCTGACTGCCGGTACGATTACCGTTGTTTTCTCTTCAATGATTGCACTGATGCGTCCGCTGAAATCGCTGACCAACGTTAACGCCCAGTTCCAGCGCGGTATGGCGGCTTGTCAGACGCTGTTTACCATTCTGGACAGTGAGCAGGAGAAAGATGAAGGTAAGCGCGTGATCGAGCGTGCGACTGGCGACGTGGAATTCCGCAATGTCACCTTTACTTATCCGGGACGTGACGTACCTGCATTGCGTAACATCAACCTGAAAATTCCGGCAGGGAAGACGGTTGCTCTGGTTGGACGCTCTGGTTCGGGTAAATCAACCATCGCCAGCCTGATCACGCGTTTTTACGATATTGATGAAGGCGAAATCCTGATGGATGGTCACGATCTGCGCGAGTATACCCTGGCGTCGTTACGTAACCAGGTTGCTCTGGTGTCGCAGAATGTCCATCTGTTTAACGATACGGTTGCTAACAACATTGCTTACGCACGGACTGAACAGTACAGCCGTGAGCAAATTGAAGAAGCGGCGCGTATGGCCTACGCCATGGACTTCATCAATAAGATGGATAACGGTCTCGATACAGTGATTGGTGAAAACGGCGTGCTGCTCTCTGGCGGTCAGCGTCAGCGTATTGCTATCGCTCGAGCCTTGTTGCGTGATAGCCCGATTCTGATTCTGGACGAAGCTACCTCGGCTCTGGATACCGAATCCGAACGTGCGATTCAGGCGGCACTGGATGAGTTGCAGAAAAACCGTACCTCTCTGGTGATTGCCCACCGCTTGTCTACCATTGAAAAGGCAGACGAAATCGTGGTCGTCGAGGATGGTGTCATTGTGGAACGCGGTACGCATAACGATTTGCTTGAGCACCGCGGCGTTTACGCGCAACTTCACAAAATGCAGTTTGGCCAATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36849","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. MG1655","NCBI_taxonomy_id":"511145"}}}},"ARO_accession":"3003950","ARO_id":"40720","ARO_name":"msbA","CARD_short_name":"msbA","ARO_description":"MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A, a major component of the bacterial outer cell membrane, and is the only bacterial ABC transporter that is essential for cell viability.","ARO_category":{"36002":{"category_aro_accession":"0010001","category_aro_cvterm_id":"36002","category_aro_name":"ATP-binding cassette (ABC) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding\/hydrolysis to transport substrates across cell membranes.","category_aro_class_name":"AMR Gene Family"},"37033":{"category_aro_accession":"3000689","category_aro_cvterm_id":"37033","category_aro_name":"metronidazole","category_aro_description":"Metronidazole is a nitroimidazole that is active against anaerobic bacteria and protozoa. It is not effective against aerobic bacteria. Nitroimidazoles act by oxidizing DNA causing strand breaks and cell death.","category_aro_class_name":"Antibiotic"},"41239":{"category_aro_accession":"3004115","category_aro_cvterm_id":"41239","category_aro_name":"nitroimidazole antibiotic","category_aro_description":"Nitroimidazoles are a group of drugs that have both antiprotozoal and antibacterial activity, classified with respect to the location of the nitro functional group.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2425":{"model_id":"2425","model_name":"hmrM","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"900"}},"model_sequences":{"sequence":{"5260":{"protein_sequence":{"accession":"ADO96486.1","sequence":"MNFRLLSQYHTDIKKLIKISLPILLAQIAQNSMGLADTIMAGRVSSTDMAAISIGASIWMPLMFFGQGLLLALPPTISYLNGSGQHHRIAHQVRQGIWLVLGVSIPLGLLIYFCEIPLQYMQMESKMSDLARNYLHAMLWGLPAYLMLINFRCLNDGIEKTKPAMVITFLGLLINIPLNYIFIYGKFGMPAFGAVGCGIATAIVNWAMCLMMIFYSYTNTQERSLKVFSQLIEMPNPKTLKKLLRLGLPIAIAICCEVALYALTSLMLSPLGATIVASHQITLNTSSFIFMFPMSIGMATTILVGQALGAGSPQNAKKIGYAALLLGLTVTIVTALITIFFRYEIASIFVTDEIVIAMAANLLLFAALYQFSDTIQMVVGGILRGYKDTKVILYITLFSYWVIGVPLGYTLGRTDWLVPHIDAKGFWIAFVVSLTFAAFLLSLRMKKMQAMNDNAILQRLEKLK"},"dna_sequence":{"accession":"CP002276.1","fmin":"1144673","fmax":"1146068","strand":"-","sequence":"ATGAATTTTCGTCTTTTATCTCAATACCACACTGATATTAAAAAGTTGATTAAAATTTCCTTGCCTATTTTATTAGCGCAAATTGCACAAAACTCAATGGGATTAGCGGATACCATTATGGCGGGGCGAGTGAGTTCCACTGATATGGCAGCCATTTCTATTGGTGCTTCAATTTGGATGCCATTGATGTTTTTTGGGCAAGGTTTATTGTTGGCATTGCCGCCTACAATTTCTTATTTGAATGGTTCAGGCCAACACCATCGCATTGCACATCAAGTTCGCCAAGGCATTTGGCTTGTGTTAGGCGTGAGTATTCCTTTAGGTTTACTGATTTATTTCTGTGAAATTCCGCTGCAATATATGCAAATGGAAAGCAAAATGTCAGATTTAGCACGCAATTATTTACACGCGATGTTGTGGGGATTGCCAGCTTATTTGATGCTGATTAATTTTCGTTGTTTAAATGATGGGATTGAGAAAACCAAGCCTGCGATGGTCATTACCTTTTTAGGTTTATTGATTAATATTCCGCTTAATTACATTTTTATTTATGGAAAATTTGGTATGCCTGCTTTTGGTGCGGTGGGCTGTGGTATTGCGACAGCTATTGTGAACTGGGCAATGTGCTTAATGATGATTTTCTATTCCTACACGAATACTCAAGAACGTTCACTAAAAGTATTTAGTCAATTAATTGAAATGCCAAATCCGAAAACACTTAAAAAATTACTGCGTTTAGGATTACCCATTGCCATTGCAATTTGTTGCGAAGTGGCGTTATATGCACTTACGTCCTTAATGCTTTCTCCGCTGGGTGCAACTATTGTGGCAAGCCATCAAATTACGCTGAATACTAGTTCTTTTATTTTTATGTTCCCTATGTCGATTGGTATGGCAACGACGATTTTAGTTGGACAAGCATTGGGTGCAGGTTCTCCACAAAATGCGAAGAAAATTGGCTATGCCGCATTATTATTAGGGCTAACTGTGACAATTGTTACTGCATTAATTACGATTTTTTTCCGTTATGAAATTGCATCGATCTTCGTGACAGATGAAATTGTCATCGCCATGGCAGCAAATCTATTATTATTTGCCGCACTTTATCAATTTTCAGATACCATTCAAATGGTGGTTGGTGGTATTTTACGTGGTTATAAAGATACTAAAGTCATTTTATACATTACCCTTTTCTCTTATTGGGTAATTGGTGTGCCACTTGGTTATACGCTAGGTCGTACAGATTGGCTTGTGCCACACATTGATGCGAAAGGTTTCTGGATTGCCTTTGTGGTCTCGCTCACTTTTGCGGCATTCTTACTTTCTTTGAGAATGAAAAAAATGCAAGCTATGAACGACAACGCTATTTTACAACGTTTAGAAAAACTTAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42593","NCBI_taxonomy_name":"Haemophilus influenzae R2846","NCBI_taxonomy_id":"262727"}}}},"ARO_accession":"3003953","ARO_id":"40723","ARO_name":"hmrM","CARD_short_name":"hmrM","ARO_description":"hmrM is a multidrug efflux pump belonging to the MATE family and functions as a  Na+\/drug antiporter.","ARO_category":{"36251":{"category_aro_accession":"3000112","category_aro_cvterm_id":"36251","category_aro_name":"multidrug and toxic compound extrusion (MATE) transporter","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Multidrug and toxic compound extrusion (MATE) transporters utilize the cationic gradient across the membrane as an energy source. Although there is a diverse substrate specificity, almost all MATE transporters recognize fluoroquinolones. Arciflavine, ethidium and aminoglycosides are also good substrates.","category_aro_class_name":"AMR Gene Family"},"35963":{"category_aro_accession":"0000045","category_aro_cvterm_id":"35963","category_aro_name":"acriflavine","category_aro_description":"Acriflavine is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"43746":{"category_aro_accession":"3005386","category_aro_cvterm_id":"43746","category_aro_name":"disinfecting agents and antiseptics","category_aro_description":"Disinfectants that can also interact with antimicrobial resistance mechanisms, e.g. molecule efflux, and thus are the targets of disinfectant resistance.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"3353":{"model_id":"3353","model_name":"Clostridioides difficile 23S rRNA with mutation conferring resistance to erythromycin and clindamycin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"8802":"c656t"},"Curated-R":{"8802":"c656t"},"clinical":{"8802":"c656t"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"41093","param_value":"5000"}},"model_sequences":{"sequence":{"5518":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"NR_076234.1","fmin":"0","fmax":"2900","strand":"+","sequence":"TGGTCAAGTTATTAAGGGTGCAGGGCGGATGCCTTGGCACTAGGAGCCGATGAAGGACGTGATAAGCTGCGATAAGCTTCGGGGAGTTGCACGTAAACTTTGATCCGAAGATTTCCGAATGAGGAAACTCACTTAGAGTAATGTCTAAGTATCATTAAGTGAATACATAGCTTAATGAGGGGAACTCAGGGAACTGAAACATCTAAGTACCTGAAGGAAGAGAAAGAAATTCGATTCCGTAAGTAGCGGCGAGCGAACGCGGATTAGCCCAAACCAATAAAGTTTTCTTTATTGGGGTTGAGGACATACCACATATAAGAGGTCATTATAGACGAAGAAGTTTGGAAAAACTCATCATAGAAGGTAATAATCCTGTAGTCAAAATAATAATTCTTTAGGTATGATCCAGAGTACCACGGGACACGTGAAACCCTGTGGGAAGCAGGAGGGACCACCCTCCAAGGCTAAATACTACCTAGTGACCGATAGCGTATAGTACCGTGAGGGAAAGGTGAAAAGAACCCCGGGAGGGGAGTGAAATAGAACCTGAAACCCTGCACTTACAAGCTGTGGAAGCACATTTCTTGTGTGACCGCGTACTTTTTGTAGAACGGGCCAACGAGTTACGTTAAGTAGCAAGGTTAAGCACTTAAGGTGCGGAGCCGTAGCGAAAGCGAGTTTTAACTGAGCGTTCAGTTACTTGACGTAGACCCGAAACCGGGCGACCTACCCATGAGCAGGATGAAGCGAAAGTAAAATTTCGTGGAGGTCCGAACCCACGAGCGTTGAAAAGCTCGGGGATGACTTGTGGGTAGCGGTGAAATTCCAATCGAGCCCGGAGATAGCTGGTTCTCCCCGAAATAGCTTTAGGGCTAGCCTCAAGGTGAGAGATACGGAGGTAGAGCACTGAATGTCCTAGGGGGTATTGCACCTACCGAAGACTATCAAACTCCGAATGCCGTCATCTTATACTTGGGAGTCAGACTGTGGGTGATAAGATTCATAGTCGAAAGGGCAACAGCCCAGATCGTCAGCTAAGGTCCCTAAATGTAAGTTAAGTGGTAAAGGATGTGGGATTGCACAGACAACCAGGATGTTGGCTTAGAAGCAGCCACTCATTCAAAGAGTGCGTAATAGCTCACTGGTCGAGTGATCCTGCGCCGAAGATTTCCGGGGCTAAAACTTACTACCGAAGCTACGGCATCAGTAATGATGGGTAGGGGAGCTTCCCATACGGGTTGAAGCATGACCGTAAGGACATGTGGACAGTATGGGAGTGAGAATGTTGGCATGAGTAGCGAGATGTGGGTGAGAATCCCACAGGCCGTAAACCCAAGGTTTCCAGGGGAAGGTTCGTCCGCCCTGGGTTAGTCGGGACCTAAGCTGAGGCCGAAAGGCGTAGGTGATGGACAACAGGTTGATATTCCTGTACTACCGATAACCGTTTGAGAGAAGGGATGACACAGTAGGATAAGCTAAGCACACTGTTGGTTATGTGTGCCCAAGCATTGAGGCAGTCAAAGTAGGCAAATCCGCTTTGATAATGCTGGGATGTGATGGGGAGCGAAATTTAGTAGCGAAGTAGCTGATTTCACACTGTCAAGAAAAGTCTCTATCGAGGTTAAAGGTACCCGTACCGCAAACCGACACAGGTGGGTGAGGAGAGTATCCTAAGGCCAGCGAGAGAACTGTTGTTAAGGAACTCGGCAAAATGACCCCGTAACTTAGGGATAAGGGGTGCCACCATCAGGTGGCCGCAGAGAATAGGCCCAAGCGACTGTTTACCAAAAACATAGGTTTCTGCTAAGTCGCAAGACGATGTATAGGAGCTGACGCCTGCCCGGTGCTGGAAGGTTAAGGGGATCTGTTAGAGCAATCGAAGCAGTGAACTTAAGCCCCAGTAAACGGCGGCCGTAACTATAACGGTCCTAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCCGCACGAAAGGCGTAACGATTTGGGCACTGTCTCAACAACAGACTCGGTGAAATTGTAATTCCGGTGAAGATGCCGGATACCTGCGACAGGACGGAAAGACCCCATGGAGCTTTACTGTAGCTTGACATTGGGTCTTGGTACTACATGTACAGGATAGGTGGGAGGCTTTGAAACCAGGACGCCAGTTTTGGCGGAGCCATCCTTGGGATACCACCCTTGTAGTACTGGGACTCTAACCATAGGCCATGAATCTGGTCTTGGGACACTGTCAGGTGGGCAGTTTGACTGGGGCGGTCGCCTCCCAAAAGGTAACGGAGGCGCTCAAAGGTTCTCTCAGTACGGTCGGAAATCGTACGTAGAGTGTAAAGGCAAAAGAGAGCTTGATTGCAAGACATACAGGTCGAGCAAGGATGAAAATCGGACTTAGTGATCCGGTGGTTCTGCGTGGAAGGGCCATCGCTCAACGGATAAAAGCTACCCTGGGGATAACAGGCTTATCTCCCCCAAGAGTCCACATCGACGGGGAGGTTTGGCACCTCGATGTCGGCTCATCACATCCTGGGGCTGTAGTAGGTCCCAAGGGTTGGGCTGTTCGCCCATTAAAGTGGTACGCGAGCTGGGTTCAGAACGTCGTGAGACAGTTCGGTCCCTATCCGTCGCAGGCGTAGGAAATTTGAGAAGACCTGTCCTTAGTACGAGAGGACCGGGATGGACGTACCTCTGGTGTACCAGTTGTCCTGCCAAGGGCATGGCTGGGTAGCTATGTACGGAATGGATAAGCGCTGAAAGCATCTAAGCGCGAAGCCAACTTCAAGATAAGATTTCCCACCGCAAGGGTAAGACCCCAGAAAGACTATCTGGTTGATAGGTCGAAGGTGTAAGTGCAGCAATGTATTTAGCTTATCGATACTAATAGGTCGAGGACTTGACCAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36807","NCBI_taxonomy_name":"Clostridioides difficile","NCBI_taxonomy_id":"1496"}}}},"ARO_accession":"3004654","ARO_id":"42686","ARO_name":"Clostridioides difficile 23S rRNA with mutation conferring resistance to erythromycin and clindamycin","CARD_short_name":"Cdif_23S_MULT","ARO_description":"SNP causing high-level ERY resistance and low-level CLI resistance.","ARO_category":{"41251":{"category_aro_accession":"3004125","category_aro_cvterm_id":"41251","category_aro_name":"23S rRNA with mutation conferring resistance to macrolide antibiotics","category_aro_description":"Nucleotide point mutations in the 23S rRNA subunit may confer resistance to macrolide antibiotics.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2426":{"model_id":"2426","model_name":"efmA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"3757":{"protein_sequence":{"accession":"BAG75524.1","sequence":"MENEQSVVLTNWKRNYLFFLSGQFLSGITSMVVQYAIIWYLTRETGSATILSFATLLGMIPMVLLSPFVGPLVDRWDKKALLIVTDIIVAIFALILAVVGTISESFPIWLVFVSLFMRSVAQTFQMPTIQSIMPTIVPSSHITRTNGQLGMVQSANFIIAPALGAALFSVVPVNYLILLDVLGAVFGVGLLIFVKIPKVSPEILEVPLTIFKDAKFGLQQLMDNKGLWYITINGAFVMLLFMPAISLYPLMTLDYFGGSVGQAGAVEVVYAVGMLLGGALISFIGTWKDRMKPIIIAYIIMGLTIGASGLVPNDSQGFLYFLILNAGAGCATPYFNTLLMAMIQQSYESNVLGRVLGNFNSLMNLAGPIGLLFAGPLADRLGVEKMFLFSGIGILLCGIVLFLTSAARNYDKELQKKLVKEHHEQKDE"},"dna_sequence":{"accession":"AB467372.1","fmin":"284","fmax":"1571","strand":"+","sequence":"ATGGAAAATGAACAGTCGGTCGTTTTAACGAATTGGAAGAGAAATTATTTGTTCTTTTTATCGGGACAGTTTTTGTCAGGAATCACTAGTATGGTCGTCCAATATGCGATCATCTGGTATTTGACAAGAGAAACCGGTTCGGCGACAATTTTGAGTTTTGCTACTTTACTAGGAATGATTCCCATGGTTTTACTAAGCCCATTTGTAGGACCGCTAGTGGATCGCTGGGATAAAAAAGCTCTTTTGATTGTCACGGATATTATTGTAGCGATTTTCGCGCTTATTTTAGCAGTAGTCGGAACGATTTCAGAATCCTTCCCGATTTGGCTAGTTTTTGTGTCTTTGTTTATGCGTTCGGTCGCACAAACATTCCAAATGCCAACGATCCAGTCGATTATGCCGACAATCGTTCCATCTTCTCACATAACAAGGACGAATGGACAGTTAGGAATGGTCCAATCAGCGAATTTCATCATTGCGCCAGCTCTAGGTGCGGCTTTGTTTTCAGTCGTTCCTGTCAATTACCTTATTTTATTAGATGTATTGGGGGCAGTTTTTGGTGTCGGCTTATTGATTTTTGTGAAGATCCCAAAAGTTTCTCCTGAAATATTGGAAGTTCCGCTTACTATTTTTAAAGATGCAAAATTTGGGCTGCAGCAATTGATGGATAATAAAGGGTTATGGTACATAACGATCAATGGTGCATTTGTGATGCTGTTGTTCATGCCAGCAATCAGTCTGTATCCATTGATGACGCTAGATTACTTTGGTGGTTCCGTTGGACAGGCGGGAGCAGTGGAAGTAGTCTACGCAGTCGGAATGCTCTTAGGCGGTGCACTGATCAGTTTTATAGGAACATGGAAAGACCGAATGAAACCTATTATTATAGCCTACATCATTATGGGCCTGACGATCGGTGCAAGCGGATTGGTTCCAAACGATAGTCAAGGGTTCTTGTACTTTCTTATCTTGAATGCAGGAGCAGGTTGTGCAACGCCATATTTCAATACACTGCTGATGGCAATGATCCAGCAGAGTTATGAATCGAATGTTTTAGGTCGTGTCTTAGGGAACTTCAACTCTTTGATGAACCTGGCAGGTCCAATTGGATTATTATTTGCAGGACCATTAGCTGATCGTTTAGGGGTAGAAAAAATGTTCTTGTTTTCCGGAATCGGGATTTTATTATGCGGAATCGTTTTATTTTTAACGTCAGCTGCCCGAAATTATGATAAAGAATTACAGAAAAAACTGGTAAAAGAACACCATGAGCAAAAAGACGAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36779","NCBI_taxonomy_name":"Enterococcus faecium","NCBI_taxonomy_id":"1352"}}}},"ARO_accession":"3003954","ARO_id":"40724","ARO_name":"efmA","CARD_short_name":"efmA","ARO_description":"efmA is an MFS transporter permease in  E. faecium.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2427":{"model_id":"2427","model_name":"efpA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"5259":{"protein_sequence":{"accession":"CCP45647.1","sequence":"MTALNDTERAVRNWTAGRPHRPAPMRPPRSEETASERPSRYYPTWLPSRSFIAAVIAIGGMQLLATMDSTVAIVALPKIQNELSLSDAGRSWVITAYVLTFGGLMLLGGRLGDTIGRKRTFIVGVALFTISSVLCAVAWDEATLVIARLSQGVGSAIASPTGLALVATTFPKGPARNAATAVFAAMTAIGSVMGLVVGGALTEVSWRWAFLVNVPIGLVMIYLARTALRETNKERMKLDATGAILATLACTAAVFAFSIGPEKGWMSGITIGSGLVALAAAVAFVIVERTAENPVVPFHLFRDRNRLVTFSAILLAGGVMFSLTVCIGLYVQDILGYSALRAGVGFIPFVIAMGIGLGVSSQLVSRFSPRVLTIGGGYLLFGAMLYGSFFMHRGVPYFPNLVMPIVVGGIGIGMAVVPLTLSAIAGVGFDQIGPVSAIALMLQSLGGPLVLAVIQAVITSRTLYLGGTTGPVKFMNDVQLAALDHAYTYGLLWVAGAAIIVGGMALFIGYTPQQVAHAQEVKEAIDAGEL"},"dna_sequence":{"accession":"AL123456.3","fmin":"3153038","fmax":"3154631","strand":"-","sequence":"ATGACGGCTCTCAACGACACAGAGCGGGCGGTCCGTAACTGGACAGCCGGACGCCCACACCGTCCGGCCCCGATGCGCCCGCCGCGCTCGGAGGAGACCGCTTCAGAGCGCCCCAGCAGGTACTACCCGACTTGGCTGCCCTCGCGCAGCTTTATCGCTGCGGTTATTGCTATCGGCGGGATGCAGCTGCTGGCGACCATGGACAGCACCGTCGCCATCGTCGCGCTACCTAAGATTCAAAACGAGCTGAGCTTGTCTGATGCCGGCCGCAGCTGGGTGATCACCGCCTACGTGCTGACCTTCGGCGGGCTGATGCTGCTCGGCGGCCGGCTTGGCGACACCATCGGGCGCAAACGCACCTTCATTGTTGGCGTTGCGCTATTCACCATCTCGTCGGTGCTGTGCGCGGTCGCCTGGGACGAGGCGACGTTGGTGATCGCCCGGTTGTCCCAGGGTGTGGGGTCGGCCATCGCATCTCCGACCGGTCTGGCGCTGGTGGCGACCACGTTCCCCAAGGGACCTGCCCGCAACGCCGCGACGGCGGTGTTCGCCGCGATGACCGCGATCGGGTCGGTGATGGGGCTGGTGGTCGGCGGAGCACTGACCGAGGTGTCATGGCGGTGGGCGTTCCTGGTGAACGTGCCGATCGGGCTGGTGATGATCTACCTGGCCCGCACCGCCCTACGGGAAACCAACAAAGAACGGATGAAGCTCGACGCCACCGGGGCCATACTGGCCACGCTGGCATGCACCGCGGCGGTTTTCGCCTTCTCGATCGGTCCTGAAAAGGGCTGGATGTCAGGCATTACCATCGGTTCGGGCCTGGTGGCCTTGGCGGCCGCTGTCGCGTTTGTCATCGTGGAGCGCACTGCCGAGAACCCCGTCGTGCCGTTCCACTTGTTCCGCGACCGCAACCGGTTGGTCACGTTCAGCGCGATCCTGTTGGCCGGCGGCGTCATGTTCAGCCTGACCGTCTGCATCGGCCTGTACGTGCAGGACATCTTGGGCTACAGCGCGCTACGCGCGGGCGTAGGTTTCATCCCGTTCGTCATCGCGATGGGAATCGGCCTAGGTGTGTCCTCGCAGCTGGTGTCCCGGTTTTCGCCACGGGTGTTGACCATCGGCGGCGGATATCTGCTATTCGGCGCCATGCTGTACGGCTCATTTTTCATGCACCGTGGTGTGCCCTACTTCCCCAACCTGGTCATGCCGATCGTCGTCGGCGGGATTGGCATCGGCATGGCCGTCGTCCCGCTGACTCTGTCGGCGATCGCTGGCGTCGGCTTCGACCAGATCGGTCCGGTATCGGCAATTGCGCTGATGCTGCAGAGCCTGGGCGGTCCGCTGGTGCTCGCCGTCATCCAGGCTGTGATCACGTCGCGCACGCTGTACCTGGGCGGTACCACCGGTCCGGTGAAGTTCATGAACGACGTGCAGTTGGCCGCGCTTGACCACGCCTACACCTACGGCCTGCTGTGGGTGGCCGGAGCGGCCATCATCGTCGGCGGTATGGCGCTGTTTATCGGGTATACGCCGCAGCAGGTTGCCCATGCGCAGGAGGTCAAGGAAGCGATCGACGCCGGCGAGCTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3003955","ARO_id":"40726","ARO_name":"efpA","CARD_short_name":"efpA","ARO_description":"efpA is an MFS transporter found in Mycobacterium tuberculosis.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36659":{"category_aro_accession":"3000520","category_aro_cvterm_id":"36659","category_aro_name":"isoniazid","category_aro_description":"Isoniazid is an organic compound that is the first-line anti tuberculosis medication in prevention and treatment. As a prodrug, it is activated by mycobacterial catalase-peroxidases such as M. tuberculosis KatG. Isoniazid inhibits mycolic acid synthesis, which prevents cell wall synthesis in mycobacteria.","category_aro_class_name":"Antibiotic"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"45734":{"category_aro_accession":"3007152","category_aro_cvterm_id":"45734","category_aro_name":"isoniazid-like antibiotic","category_aro_description":"A group of antibiotics containing isoniazid and its derivatives.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2428":{"model_id":"2428","model_name":"farA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"730"}},"model_sequences":{"sequence":{"5478":{"protein_sequence":{"accession":"AAF40763.1","sequence":"MDTHTDETKLQNTQAKRKRRLTALTLLFALAAAAAGSAFFLWWQHEEETEDAYVAGRVVQVTPQKGGTVRKVLHDDTDAVKKGDVLAVLDDDNDVLAYERAKNELVQAVRQNRRQNAATSQAGAQVALRRADLARAQDDLRRRSALAESGAVSAEELAHARAAVSQAQAAVKAALAEESSARAALGGQVSLREQPAVQTAIGRLKDAWLNLQRTQIRAPADGQVAKRSVQVGQQVAAGAPLMAVVPLSDVWVDANFKETQLRHMKIGQPAELVSDLYGKQIVYRGRVAGFSAGTGSAFSLIPAQNATGNWIKVVQRVPVRIVLNREDVDRHPLRIGLSMTVKVDTSAAGAPVSKTPGAALPEMESTDWSEVDRTVDEILGQSAP"},"dna_sequence":{"accession":"AE002098.2","fmin":"329612","fmax":"330767","strand":"+","sequence":"ATGGATACGCACACGGACGAAACAAAACTTCAAAACACGCAAGCCAAACGCAAACGCCGCCTGACGGCATTGACGCTGCTGTTCGCGCTTGCCGCCGCAGCCGCCGGGTCGGCGTTTTTTTTATGGTGGCAGCACGAAGAGGAAACGGAAGACGCTTATGTTGCCGGACGCGTGGTTCAGGTTACGCCGCAAAAGGGCGGTACGGTGCGGAAGGTTTTGCACGACGATACGGATGCCGTGAAAAAAGGCGACGTGCTGGCGGTATTGGACGACGATAATGATGTGCTGGCTTACGAGCGGGCAAAAAACGAGCTGGTTCAGGCGGTGCGGCAAAACCGCCGGCAAAATGCCGCCACTTCGCAGGCGGGGGCGCAGGTTGCCTTGCGCCGGGCGGATTTGGCACGCGCACAGGATGATTTGCGCCGCCGGTCTGCTTTGGCGGAATCGGGCGCGGTGTCCGCCGAAGAGCTGGCACACGCCCGTGCGGCAGTGTCTCAGGCGCAGGCGGCGGTCAAAGCGGCTTTGGCGGAAGAATCTTCGGCACGTGCGGCTTTGGGCGGTCAGGTTTCTTTGCGCGAACAGCCGGCGGTTCAGACGGCAATCGGCAGGTTGAAAGATGCGTGGTTGAACCTTCAGCGGACGCAAATCCGCGCGCCGGCGGACGGTCAGGTGGCGAAGCGTTCGGTGCAGGTCGGGCAGCAGGTGGCGGCAGGCGCGCCGCTGATGGCGGTGGTGCCGCTGTCGGATGTGTGGGTGGATGCTAATTTTAAAGAGACGCAGTTGCGGCATATGAAAATCGGACAGCCTGCCGAGCTGGTGTCCGATTTGTACGGCAAACAAATTGTTTATCGCGGCAGGGTGGCAGGTTTTTCGGCAGGTACGGGCAGCGCGTTTTCGCTGATTCCGGCGCAAAACGCAACGGGCAACTGGATTAAAGTGGTGCAGCGCGTCCCCGTCCGTATCGTGCTGAACCGCGAAGATGTGGACAGGCATCCGTTGCGTATCGGTTTGTCGATGACGGTTAAAGTGGATACTTCCGCCGCAGGCGCGCCTGTTTCAAAAACGCCGGGTGCGGCATTGCCGGAAATGGAAAGTACCGACTGGTCGGAAGTCGATCGGACGGTCGATGAAATCCTCGGGCAATCCGCGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39597","NCBI_taxonomy_name":"Neisseria meningitidis MC58","NCBI_taxonomy_id":"122586"}}}},"ARO_accession":"3003961","ARO_id":"40732","ARO_name":"farA","CARD_short_name":"farA","ARO_description":"farA is the membrane fusion protein that is part of the farAB efflux pump.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"40728":{"category_aro_accession":"3003957","category_aro_cvterm_id":"40728","category_aro_name":"palmitic acid","category_aro_description":"Palmitic acid is the most common saturated fatty acid found in animals, plants, and microorganisms. Palmitic acid is found to have antibacterial properties.","category_aro_class_name":"Antibiotic"},"40729":{"category_aro_accession":"3003958","category_aro_cvterm_id":"40729","category_aro_name":"oleic acid","category_aro_description":"Oleic acid is a fatty acid that occurs naturally in various animal and vegetable fats and oils. Oleic acid is found to have antibacterial activity, particularly in inhibiting the growth of several Gram-positive bacterial species.","category_aro_class_name":"Antibiotic"},"40730":{"category_aro_accession":"3003959","category_aro_cvterm_id":"40730","category_aro_name":"linoleic acid","category_aro_description":"Linoleic acid is a polyunsaturated omega-6 fatty acid. Linoleic acid has been found to have antibacterial activity, particularly in inhibiting the growth of Gram-positive bacterial species.","category_aro_class_name":"Antibiotic"},"40727":{"category_aro_accession":"3003956","category_aro_cvterm_id":"40727","category_aro_name":"antibacterial free fatty acids","category_aro_description":"Amongst the diverse and potent biological activities of free fatty acids (FFAs) is the ability to kill or inhibit the growth of bacteria. The antibacterial properties of FFAs are used by many organisms to defend against parasitic or pathogenic bacteria. The prime target of FFA action is the cell membrane, where FFAs disrupt the electron transport chain and oxidative phosphorylation. Besides interfering with cellular energy production, FFA action may also result from the inhibition of enzyme activity, impairment of nutrient uptake, generation of peroxidation and auto-oxidation degradation products or direct lysis of bacterial cells.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2429":{"model_id":"2429","model_name":"farB","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"990"}},"model_sequences":{"sequence":{"5479":{"protein_sequence":{"accession":"AAF40764.1","sequence":"MDYPPLKGAALAWVTLSLGLAVFMEVLDTTIANVAVPVIAGNLGAATTQGTWVITSFSVANAVSVPLTGFLAKRIGEVKLFTAAAVGFVITSWLCGIAPNLQSLVVFRILQGFIAGPLIPLSQSLLMASYPPAKRTLALALWAMTVVVAPVLGPILGGWISGNWHWGWIFFINIPIGIISAWITWKHLKYRETETVKMPTDYVGLTLMVVGIGALQMMLDRGKELDWFASGEIITLGVVALVCLSYFIVWELGEKYPIVDLSLFKDRNFTVGVIATSLGFMVYMGTLTLLPLVLQTNLGYTSTWAGLAAAPVGILPVFLSPLIGRFGNKIDMRLFVTASFLTFAFTFYWRTDFYADMDIGNVIWPQFWQGVGVAMFFLPLTTITLSHMKGGQIAAAGSLSNFLRVLMGGVGVSVVSTLWERREALHHTRFAEHITPYSATLHETAAHLSQHGVSDIQTLGIINNTITQQGFIIGSNEIFMAGSLLFIIMIPVIWLAKPPFHNGGGGGH"},"dna_sequence":{"accession":"AE002098.2","fmin":"330790","fmax":"332317","strand":"+","sequence":"ATGGATTATCCACCGCTTAAGGGTGCGGCATTGGCGTGGGTTACGCTGTCTTTGGGGCTTGCCGTATTTATGGAAGTTTTAGATACGACTATCGCCAATGTCGCCGTTCCCGTCATCGCCGGCAACCTCGGTGCGGCAACCACTCAGGGGACGTGGGTCATCACTTCCTTTTCTGTGGCAAACGCCGTTTCCGTGCCGCTGACGGGCTTTTTGGCAAAACGCATCGGCGAGGTCAAATTGTTTACCGCCGCCGCTGTCGGTTTCGTCATCACATCGTGGCTGTGCGGTATTGCCCCCAACCTTCAGTCGCTGGTTGTTTTCCGCATCTTGCAGGGCTTTATCGCCGGGCCGCTGATTCCCTTGTCGCAAAGCCTGTTAATGGCATCCTATCCGCCCGCAAAACGGACGCTGGCACTGGCATTGTGGGCAATGACCGTCGTTGTCGCCCCTGTTCTCGGGCCGATACTCGGCGGCTGGATTTCCGGAAACTGGCATTGGGGTTGGATTTTCTTCATTAATATCCCTATCGGTATCATATCGGCATGGATTACATGGAAACATTTGAAATATCGGGAAACGGAAACCGTTAAAATGCCGACCGACTATGTCGGGCTTACATTGATGGTAGTCGGTATCGGCGCGTTACAGATGATGCTGGACAGGGGTAAGGAACTCGACTGGTTCGCCTCTGGAGAAATCATTACCTTGGGCGTAGTCGCACTGGTGTGCTTGTCGTATTTTATTGTTTGGGAATTGGGAGAAAAATATCCGATTGTCGATTTATCGCTGTTTAAAGATCGGAATTTTACCGTCGGCGTCATTGCCACGTCATTGGGTTTTATGGTGTATATGGGGACGCTGACCCTGCTGCCGTTAGTGTTGCAGACCAACCTGGGCTATACCTCCACGTGGGCAGGGCTTGCCGCCGCACCTGTCGGCATCCTGCCTGTTTTCCTGTCTCCGTTAATCGGCAGGTTCGGCAATAAAATCGATATGCGCCTGTTCGTAACTGCCAGCTTCCTGACCTTTGCCTTTACTTTCTATTGGCGTACGGATTTTTATGCCGATATGGATATTGGCAACGTCATCTGGCCGCAGTTTTGGCAGGGTGTCGGTGTCGCCATGTTTTTTCTGCCGCTGACCACCATCACACTGTCGCATATGAAGGGCGGGCAGATTGCCGCCGCAGGCAGCCTGTCGAATTTCTTGCGCGTGCTGATGGGCGGTGTCGGCGTATCCGTCGTCAGCACCCTGTGGGAACGGCGCGAAGCGTTGCACCACACACGCTTTGCCGAACACATCACGCCCTATTCCGCAACATTGCACGAAACGGCCGCTCATTTGTCCCAGCACGGCGTTTCCGACATTCAAACCCTAGGCATCATCAACAATACCATTACCCAGCAGGGTTTTATTATCGGCTCGAACGAAATCTTTATGGCGGGCAGCTTGTTATTCATTATCATGATACCCGTCATATGGCTGGCAAAACCGCCGTTCCACAACGGCGGCGGCGGTGGACATTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39597","NCBI_taxonomy_name":"Neisseria meningitidis MC58","NCBI_taxonomy_id":"122586"}}}},"ARO_accession":"3003962","ARO_id":"40733","ARO_name":"farB","CARD_short_name":"farB","ARO_description":"farB is the cytoplasmic transporter protein that is part of the farAB efflux pump. farB corresponds to 3 loci in Pseudomonas aeruginosa PAO1 and 3 loci in Pseudomonas aeruginosa LESB58.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"40728":{"category_aro_accession":"3003957","category_aro_cvterm_id":"40728","category_aro_name":"palmitic acid","category_aro_description":"Palmitic acid is the most common saturated fatty acid found in animals, plants, and microorganisms. Palmitic acid is found to have antibacterial properties.","category_aro_class_name":"Antibiotic"},"40729":{"category_aro_accession":"3003958","category_aro_cvterm_id":"40729","category_aro_name":"oleic acid","category_aro_description":"Oleic acid is a fatty acid that occurs naturally in various animal and vegetable fats and oils. Oleic acid is found to have antibacterial activity, particularly in inhibiting the growth of several Gram-positive bacterial species.","category_aro_class_name":"Antibiotic"},"40730":{"category_aro_accession":"3003959","category_aro_cvterm_id":"40730","category_aro_name":"linoleic acid","category_aro_description":"Linoleic acid is a polyunsaturated omega-6 fatty acid. Linoleic acid has been found to have antibacterial activity, particularly in inhibiting the growth of Gram-positive bacterial species.","category_aro_class_name":"Antibiotic"},"40727":{"category_aro_accession":"3003956","category_aro_cvterm_id":"40727","category_aro_name":"antibacterial free fatty acids","category_aro_description":"Amongst the diverse and potent biological activities of free fatty acids (FFAs) is the ability to kill or inhibit the growth of bacteria. The antibacterial properties of FFAs are used by many organisms to defend against parasitic or pathogenic bacteria. The prime target of FFA action is the cell membrane, where FFAs disrupt the electron transport chain and oxidative phosphorylation. Besides interfering with cellular energy production, FFA action may also result from the inhibition of enzyme activity, impairment of nutrient uptake, generation of peroxidation and auto-oxidation degradation products or direct lysis of bacterial cells.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"3661":{"model_id":"3661","model_name":"NDM-20","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"5933":{"protein_sequence":{"accession":"AQY45923.1","sequence":"MELPNIMHPVAKLSTALAAALMLSGCMPGEIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLLVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGLVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLH"},"dna_sequence":{"accession":"KY654092.1","fmin":"0","fmax":"813","strand":"+","sequence":"ATGGAATTGCCCAATATTATGCACCCGGTCGCGAAGCTGAGCACCGCATTAGCCGCTGCATTGATGCTGAGCGGGTGCATGCCCGGTGAAATCCGCCCGACGATTGGCCAGCAAATGGAAACTGGCGACCAACGGTTTGGCGATCTGGTTTTCCGCCAGCTCGCACCGAATGTCTGGCAGCACACTTCCTATCTCGACATGCCGGGTTTCGGGGCAGTCGCTTCCAACGGTTTGATCGTCAGGGATGGCGGCCGCGTGCTGTTGGTCGATACCGCCTGGACCGATGACCAGACCGCCCAGATCCTCAACTGGATCAAGCAGGAGATCAACCTGCCGGTCGCGCTGGCGGTGGTGACTCACGCGCATCAGGACAAGATGGGCGGTATGGACGCGCTGCATGCGGCGGGGATTGCGACTTATGCCAATGCGTTGTCGAACCAGCTTGCCCCGCAAGAGGGGCTGGTTGCGGCGCAACACAGCCTGACTTTCGCCGCCAATGGCTGGGTCGAACCAGCAACCGCGCCCAACTTTGGCCCGCTCAAGGTATTTTACCCCGGCCCCGGCCACACCAGTGACAATATCACCGTTGGGATCGACGGCACCGACATCGCTTTTGGTGGCTGCCTGATCAAGGACAGCAAGGCCAAGTCGCTCGGCAATCTCGGTGATGCCGACACTGAGCACTACGCCGCGTCAGCGCGCGCGTTTGGTGCGGCGTTCCCCAAGGCCAGCATGATCGTGATGAGCCATTCCGCCCCCGATAGCCGCGCCGCAATCACTCATACGGCCCGCATGGCCGACAAGCTGCACTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3004863","ARO_id":"43001","ARO_name":"NDM-20","CARD_short_name":"NDM-20","ARO_description":"A class B New Delhi metallo-beta-lactamase.","ARO_category":{"36196":{"category_aro_accession":"3000057","category_aro_cvterm_id":"36196","category_aro_name":"NDM beta-lactamase","category_aro_description":"NDM beta-lactamases or New Delhi metallo-beta-lactamases are class B beta-lactamases that confer resistance to a broad range of antibiotics including carbapenems, cephalosporins and penicillins.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2430":{"model_id":"2430","model_name":"hp1181","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"850"}},"model_sequences":{"sequence":{"5480":{"protein_sequence":{"accession":"AAD08227.1","sequence":"MFKKIFPLALVSSLRFLGLFIVLPVISLYADSFHSSSPLLVGLAVGGAYLTQIVFQTPMGILSDKIGRKVVVMVCLLLFLAGSLVCFIANDIVWLVIGRFIQGMGALGGVISAMVADEVKEEERTKAMAIMGAFIFISFTISMAIGPGVVAFLGGAKWLFLLTAILTLLSLLMLLKVKDAPKISYQIKNIKAYQPNSKALYLLYLSSFFEKAFMTLIFVLIPLALVNEFHKDESFLILVYVPGALLGVLSMGIASVMAEKYNKPKGVMLSGVLLFIVSYLCLFLADSSFLGKYLWLFIVGVAFFFIGFATLEPIMQSLASKFAKVHEKGKVLGQFTTFGYLGSFVGGVSGGLSYHHLGVSNTSLIVVALGLIWGLSLFLLNNPSKQKNVYFPLDAYNEEQFETLEDKIIEWYVNISEEIIIVKYNSDHISEEEIIHLAQNFRK"},"dna_sequence":{"accession":"AE000511.1","fmin":"1249487","fmax":"1250819","strand":"+","sequence":"ATGTTTAAGAAAATTTTTCCATTAGCGTTAGTGTCATCGTTGCGGTTTTTGGGGCTTTTTATTGTTTTGCCGGTCATTAGTTTGTATGCGGATAGTTTCCATTCAAGCAGTCCCTTACTCGTGGGGTTGGCTGTGGGCGGAGCGTATCTTACGCAAATTGTTTTTCAAACCCCCATGGGCATTCTTAGCGATAAGATAGGCCGTAAAGTGGTGGTTATGGTGTGCTTGCTGTTGTTTTTAGCCGGCTCGTTAGTGTGCTTTATAGCGAATGATATTGTTTGGCTCGTTATAGGGCGCTTCATTCAAGGCATGGGGGCTTTAGGGGGGGTTATTAGTGCGATGGTGGCGGATGAAGTGAAAGAAGAAGAGCGCACCAAAGCCATGGCCATCATGGGAGCGTTTATTTTCATTAGCTTCACTATAAGCATGGCGATTGGCCCTGGGGTTGTAGCGTTTTTGGGGGGGGCAAAATGGCTCTTTTTACTCACGGCGATCTTAACTTTATTGAGTTTATTGATGCTTTTAAAAGTCAAAGACGCCCCTAAAATTTCTTACCAGATCAAAAACATAAAAGCTTACCAACCCAACTCTAAAGCCTTGTATCTTTTGTATCTAAGCTCTTTTTTTGAAAAAGCGTTCATGACGCTTATTTTTGTGCTGATCCCTTTAGCCTTAGTGAATGAATTTCATAAAGATGAAAGCTTTTTAATCTTGGTGTATGTGCCTGGAGCCTTATTAGGGGTCTTAAGCATGGGAATAGCGAGCGTTATGGCTGAAAAATACAACAAGCCTAAAGGAGTGATGCTTTCTGGCGTATTATTGTTTATTGTGAGTTATTTGTGCTTGTTTTTAGCCGACTCTAGCTTTTTAGGGAAATATTTATGGCTTTTTATTGTTGGGGTGGCGTTTTTCTTTATTGGTTTTGCCACCTTAGAGCCTATCATGCAATCTTTAGCGTCTAAATTCGCCAAAGTGCATGAAAAAGGCAAGGTTTTAGGGCAATTCACTACTTTTGGCTATTTAGGGAGCTTTGTTGGGGGCGTGAGCGGGGGGTTGAGCTACCATCATTTAGGCGTTTCTAACACAAGCTTGATCGTTGTAGCTTTAGGGCTTATTTGGGGGCTATCGCTCTTTTTACTCAACAACCCTTCCAAGCAAAAAAATGTCTATTTCCCCTTAGACGCTTACAATGAGGAACAATTTGAAACTTTAGAGGATAAAATCATTGAATGGTATGTTAATATTAGCGAAGAAATCATTATTGTGAAATATAATTCCGATCACATTAGCGAAGAAGAAATCATTCACTTAGCGCAAAACTTTAGAAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36758","NCBI_taxonomy_name":"Helicobacter pylori 26695","NCBI_taxonomy_id":"85962"}}}},"ARO_accession":"3003964","ARO_id":"40735","ARO_name":"hp1181","CARD_short_name":"hp1181","ARO_description":"hp1181 is a translocase that is part of the MFS efflux pump family. It is found in H. pylori and has role in the active efflux of antibiotics.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"37033":{"category_aro_accession":"3000689","category_aro_cvterm_id":"37033","category_aro_name":"metronidazole","category_aro_description":"Metronidazole is a nitroimidazole that is active against anaerobic bacteria and protozoa. It is not effective against aerobic bacteria. Nitroimidazoles act by oxidizing DNA causing strand breaks and cell death.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"41239":{"category_aro_accession":"3004115","category_aro_cvterm_id":"41239","category_aro_name":"nitroimidazole antibiotic","category_aro_description":"Nitroimidazoles are a group of drugs that have both antiprotozoal and antibacterial activity, classified with respect to the location of the nitro functional group.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2435":{"model_id":"2435","model_name":"lmrP","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"4602":{"protein_sequence":{"accession":"ABF33001.1","sequence":"MQEFLNLPKQIQLRQLVRFVTITLGSSIFPFMAMYYTTYFGTFWTGLLMMITSLMGFVGTLYGGHLSDALGRKKVIMIGSVGTTLGWFLTILANLPNAAIPWLTFAGILLVEIASSFYGPAYEAMLIDLTDESNRRFVYTINYWFINIAVMFGAGLSGLFYDHHFLALLVALLLVNVLCFGVAYYYFDETRPETHAFDHGKGLLASFQNYRQVFQDRAFVLFTLGAIFSGSIWMQMDNYVPVHLKLYFQPTAVLGFQVTSSKMLSLMVLTNTLLIVLFMTVVNKLTEKWKLLPQLVVGSLLFTLGMLLAFTFTQFYAIWLSVVLLTFGEMINVPASQVLRADMMDHSQIGSYTGFVSMAQPLGAILASLLVSVSHFTGPLGVQCLFVVIALLGIYFTVVSAKMKKV"},"dna_sequence":{"accession":"CP000259.1","fmin":"1769089","fmax":"1770310","strand":"-","sequence":"ATGCAAGAGTTTTTAAACCTTCCTAAGCAGATTCAGCTGAGGCAACTGGTACGCTTTGTGACCATTACCTTAGGCAGTAGTATCTTTCCCTTTATGGCCATGTATTATACGACTTACTTTGGTACGTTTTGGACAGGCCTCTTAATGATGATTACCAGTTTGATGGGATTTGTTGGAACTTTATACGGTGGGCATCTGTCAGATGCTCTTGGTCGTAAAAAAGTCATTATGATTGGGTCAGTAGGAACAACGCTAGGCTGGTTTCTGACTATTTTAGCTAATTTGCCTAATGCAGCTATTCCTTGGTTAACCTTTGCGGGTATTTTATTGGTAGAGATTGCTTCTAGTTTTTATGGTCCTGCCTATGAAGCTATGTTGATTGATTTGACTGATGAGAGTAATCGTCGATTTGTTTACACCATCAATTATTGGTTTATCAATATTGCCGTCATGTTTGGTGCAGGGCTATCTGGGCTTTTTTATGACCATCATTTTTTAGCCTTGTTAGTAGCCTTATTACTCGTTAATGTACTTTGTTTTGGCGTTGCTTACTACTATTTTGATGAGACTAGACCAGAAACACACGCTTTTGATCATGGTAAAGGATTACTGGCGAGTTTTCAGAACTACCGTCAGGTGTTTCAGGATCGTGCCTTTGTCTTGTTTACCTTAGGTGCCATCTTTTCTGGTAGTATCTGGATGCAGATGGATAACTATGTGCCAGTCCATTTGAAACTGTATTTTCAGCCAACGGCTGTGTTAGGTTTCCAAGTAACTAGTTCTAAAATGTTATCATTAATGGTTTTAACTAATACATTGCTGATTGTCCTTTTCATGACAGTAGTAAATAAATTAACGGAAAAATGGAAACTATTACCTCAGCTTGTGGTTGGTTCTTTACTATTTACTCTAGGGATGCTCTTGGCATTTACCTTTACGCAGTTCTATGCTATTTGGCTATCAGTTGTTTTGTTAACTTTTGGGGAAATGATAAATGTTCCTGCTAGTCAAGTCCTACGTGCTGATATGATGGATCATTCCCAAATAGGATCTTATACAGGTTTTGTGTCAATGGCACAACCCCTAGGTGCTATTTTGGCTAGTCTACTAGTATCTGTCAGCCATTTTACAGGTCCTTTAGGTGTGCAATGCTTATTTGTAGTCATTGCTTTGCTAGGGATTTATTTTACGGTTGTTTCTGCAAAAATGAAAAAGGTGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40741","NCBI_taxonomy_name":"Streptococcus pyogenes MGAS9429","NCBI_taxonomy_id":"370551"}}}},"ARO_accession":"3003969","ARO_id":"40740","ARO_name":"lmrP","CARD_short_name":"lmrP","ARO_description":"lmrP is a proton motive force-dependent drug transporter that is part of the MFS efflux pump family.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35946":{"category_aro_accession":"0000027","category_aro_cvterm_id":"35946","category_aro_name":"roxithromycin","category_aro_description":"Roxithromycin is a semi-synthetic, 14-carbon ring macrolide antibiotic derived from erythromycin. It is used to treat respiratory tract, urinary and soft tissue infections. Roxithromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35982":{"category_aro_accession":"0000065","category_aro_cvterm_id":"35982","category_aro_name":"clarithromycin","category_aro_description":"Clarithromycin is a methyl derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome and is used to treat pharyngitis, tonsillitis, acute maxillary sinusitis, acute bacterial exacerbation of chronic bronchitis, pneumonia (especially atypical pneumonias associated with Chlamydia pneumoniae or TWAR), and skin structure infections.","category_aro_class_name":"Antibiotic"},"36291":{"category_aro_accession":"3000152","category_aro_cvterm_id":"36291","category_aro_name":"minocycline","category_aro_description":"Minocycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"36667":{"category_aro_accession":"3000528","category_aro_cvterm_id":"36667","category_aro_name":"chlortetracycline","category_aro_description":"Chlortetracycline was an early, first-generation tetracycline antibiotic developed in the 1940's. It inhibits bacterial protein synthesis by binding to the 30S subunit of bacterial ribosomes, preventing the aminoacyl-tRNA from binding to the ribosome.","category_aro_class_name":"Antibiotic"},"37011":{"category_aro_accession":"3000667","category_aro_cvterm_id":"37011","category_aro_name":"demeclocycline","category_aro_description":"Demeclocycline is a tetracycline analog with 7-chloro and 6-methyl groups. Due to its fast absorption and slow excretion, it maintains higher effective blood levels compared to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37012":{"category_aro_accession":"3000668","category_aro_cvterm_id":"37012","category_aro_name":"oxytetracycline","category_aro_description":"Oxytetracycline is a derivative of tetracycline with a 5-hydroxyl group. Its activity is similar to other tetracyclines.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35952":{"category_aro_accession":"0000034","category_aro_cvterm_id":"35952","category_aro_name":"streptogramin A antibiotic","category_aro_description":"Streptogramin A antibiotics are cyclic polyketide peptide hybrids that bind to the ribosomal peptidyl transfer centre. Structural variation arises from substituting a proline for its desaturated derivative and by its substitution for Ala or Cys. Used alone, streptogramin A antibiotics are bacteriostatic, but is bactericidal when used with streptogramin B antibiotics.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1600":{"model_id":"1600","model_name":"Pseudomonas mutant PhoP conferring resistance to colistin","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"4367":"R117L","4368":"A110V"},"Curated-R":{"4367":"R117L","4368":"A110V"},"experimental":{"4367":"R117L","4368":"A110V"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"5367":{"protein_sequence":{"accession":"AAG04568.1","sequence":"MKLLVVEDEALLRHHLYTRLGEQGHVVDAVPDAEEALYRVSEYHHDLAVIDLGLPGMSGLDLIRELRSQGKSFPILILTARGNWQDKVEGLAAGADDYVVKPFQFEELEARLNALLRRSSGFVQSTIEAGPLVLDLNRKQALVEEQPVALTAYEYRILEYLMRHHQQVVAKERLMEQLYPDDEERDANVIEVLVGRLRRKLEACGGFKPIDTVRGQGYLFTERCR"},"dna_sequence":{"accession":"AE004091.2","fmin":"1277687","fmax":"1278365","strand":"+","sequence":"ATGAAACTGCTGGTAGTGGAAGACGAGGCGCTGTTGCGCCACCACCTCTATACCCGCCTGGGTGAACAGGGGCACGTGGTGGACGCGGTACCGGATGCCGAGGAAGCCCTCTACCGGGTCAGCGAATACCACCACGACCTGGCGGTGATCGACCTCGGCCTGCCGGGCATGAGCGGCCTGGACCTGATCCGCGAGCTGCGTTCGCAGGGCAAGTCCTTCCCGATCCTGATCCTCACCGCCCGCGGCAACTGGCAGGACAAGGTCGAAGGCCTGGCCGCCGGGGCCGACGACTACGTGGTCAAGCCGTTCCAGTTCGAGGAACTGGAAGCGCGCCTGAACGCGTTGCTGCGACGCTCCTCGGGGTTCGTCCAGTCGACCATCGAGGCCGGCCCCCTGGTCCTCGACCTGAACCGCAAGCAGGCGCTGGTCGAGGAGCAACCGGTGGCGCTGACCGCCTACGAATACCGCATCCTCGAATACCTCATGCGGCATCACCAGCAGGTGGTGGCCAAGGAACGCCTGATGGAACAGCTCTATCCCGACGACGAGGAGCGCGACGCCAACGTCATCGAGGTGCTGGTCGGCCGCCTGCGGCGCAAGCTGGAGGCCTGCGGCGGCTTCAAGCCGATCGATACGGTGCGCGGCCAGGGCTACCTGTTCACCGAGCGCTGCCGGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36804","NCBI_taxonomy_name":"Pseudomonas aeruginosa PAO1","NCBI_taxonomy_id":"208964"}}}},"ARO_accession":"3003895","ARO_id":"40597","ARO_name":"Pseudomonas mutant PhoP conferring resistance to colistin","CARD_short_name":"Paer_PhoP_CST","ARO_description":"Mutations in Pseudomonas aeruginosa PhoP of the two-component PhoPQ regulatory system. Presence of mutation confers resistance to colistin.","ARO_category":{"36002":{"category_aro_accession":"0010001","category_aro_cvterm_id":"36002","category_aro_name":"ATP-binding cassette (ABC) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding\/hydrolysis to transport substrates across cell membranes.","category_aro_class_name":"AMR Gene Family"},"41433":{"category_aro_accession":"3004269","category_aro_cvterm_id":"41433","category_aro_name":"pmr phosphoethanolamine transferase","category_aro_description":"This family of phosphoethanolamine transferase catalyze the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine to lipid A, which impedes the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"46471":{"category_aro_accession":"3007684","category_aro_cvterm_id":"46471","category_aro_name":"transmembrane protein conferring colistin resistance","category_aro_description":"Mutations in mgrB transmembrane proteins can confer resistance to the antibiotic colistin.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"36593":{"category_aro_accession":"3000454","category_aro_cvterm_id":"36593","category_aro_name":"polymyxin B","category_aro_description":"Polymyxin B is mixture of mostly polymyxins B1 and B2, mainly used for resistant gram-negative infections. They are polypeptides with cationic detergent action on cell membranes.","category_aro_class_name":"Antibiotic"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"},"40429":{"category_aro_accession":"3003764","category_aro_cvterm_id":"40429","category_aro_name":"resistance by absence","category_aro_description":"Mechanism of antibiotic resistance conferred by deletion of gene (usually a porin).","category_aro_class_name":"Resistance Mechanism"}}},"4254":{"model_id":"4254","model_name":"ADC-189","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6629":{"protein_sequence":{"accession":"WP_136512058.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNRSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWQPKNPIGEYRQYSNPSIGLFRKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGFYQVNTMYQALGWEEFSYPATLQTLLDSSSEQIVMKPNKVTAISKEPSVKMYHKTGSTKGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLDAIKK"},"dna_sequence":{"accession":"NG_064712.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATCGCAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGCAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTAGAAAGGTTGTGGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCATTTGGTTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCTGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTTAACCCACAGAAATATCCGGCTGATATTCAACGGGCAATTAATGAAACACATCAAGGGTTCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAGTTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCAAAGGTTTCGGAACATATGTAGTGTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGGATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006358","ARO_id":"44820","ARO_name":"ADC-189","CARD_short_name":"ADC-189","ARO_description":"ADC-189 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2433":{"model_id":"2433","model_name":"lfrA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"910"}},"model_sequences":{"sequence":{"3766":{"protein_sequence":{"accession":"AAC43550.1","sequence":"MSTCIEGTPSTTRTPTRAWVALAVLALPVLLIAIDNTVLAFALPLIAEDFRPSATTQLWIVDVYSLVLAALLVAMGSLGDRLGRRRVLLIGGAGFAVVSALAAFAPSTELLVGARALLGVFGAMLMPSTLSLIRNIFTDASARRLAIAIWASCFTAGSALGPIVGGALLEHFHWGAVFLVAVPILLPLLVLGPRLVPESRDPNPGPFDPVSIVLSFTTMLPIVWAVKTAAHDGLSAAAAAAFAVGIVSGALFVRRQNRSATPMLDIGLFKVMPFTSSILANFLSIIGLIGFIFFISQHLQLVLGLSPLTAGLVTLPGAVVSMIAGLAVVKAAKRFAPDTLMVTGLVFVAVGFLMILLFRHNLTVAAIIASFVVLELGVGVSQTVSNDTIVASVPAAKSGAASAVSETAYELGAVVGTATLGTIFTAFYRSNVDVPAGLTPEQTGAAAESIGGAAAVAADLPAATATQLLDSARAAFDSGIAPTAVIAAMLVLAAAAVVGVAFRR"},"dna_sequence":{"accession":"U40487.1","fmin":"170","fmax":"1685","strand":"+","sequence":"ATGTCCACCTGCATCGAGGGCACGCCGTCGACGACCAGGACGCCCACGCGCGCCTGGGTGGCGCTGGCCGTCCTCGCACTTCCGGTGCTGCTCATCGCGATCGACAACACCGTGCTGGCGTTCGCGTTGCCGCTGATCGCCGAGGACTTCCGCCCGTCGGCCACCACGCAGCTGTGGATCGTCGACGTGTACTCACTGGTGCTGGCCGCGCTGCTGGTCGCCATGGGCAGCCTCGGCGACCGACTGGGCCGCCGCAGGGTGCTGCTCATCGGCGGGGCCGGGTTCGCGGTGGTCTCGGCGCTGGCGGCCTTCGCCCCGAGCACCGAGTTGCTGGTGGGAGCGCGCGCACTTCTCGGTGTGTTCGGCGCGATGCTGATGCCTTCGACGCTGTCGTTGATCCGCAACATCTTCACCGACGCGTCGGCGCGGCGGTTGGCCATCGCGATCTGGGCGTCGTGTTTCACCGCGGGTTCCGCGCTGGGCCCGATCGTCGGCGGCGCGCTGCTGGAGCATTTCCACTGGGGCGCAGTGTTCCTGGTGGCGGTGCCGATCCTGTTGCCGCTGCTGGTCCTCGGCCCGCGTCTGGTGCCCGAATCGCGTGATCCCAATCCGGGCCCGTTCGATCCCGTGAGCATCGTGCTGTCGTTCACGACCATGCTGCCCATCGTGTGGGCGGTCAAAACCGCGGCGCACGACGGTCTGTCGGCGGCGGCCGCGGCCGCGTTCGCCGTGGGCATCGTCTCGGGTGCGTTGTTCGTGCGACGGCAGAACCGCAGTGCCACACCGATGCTCGACATCGGCCTGTTCAAGGTCATGCCGTTCACGTCGTCGATCCTGGCGAACTTCCTGTCGATCATCGGCCTGATCGGGTTCATCTTCTTCATCTCGCAGCACCTTCAGTTGGTGCTGGGCCTGTCCCCGCTCACCGCCGGCCTGGTGACGCTGCCGGGTGCCGTGGTGTCGATGATCGCGGGCCTGGCCGTGGTGAAGGCCGCCAAGCGCTTCGCACCCGACACCCTGATGGTCACGGGCCTGGTGTTCGTGGCGGTCGGGTTCCTGATGATCCTGTTGTTCCGCCACAACCTCACGGTGGCCGCGATCATCGCGTCGTTCGTGGTGCTCGAGCTCGGCGTCGGCGTCTCGCAGACCGTGTCCAACGACACCATCGTGGCGTCGGTTCCCGCCGCGAAATCCGGTGCGGCGTCCGCGGTTTCCGAGACGGCCTACGAGCTGGGCGCCGTGGTGGGGACAGCGACGCTGGGCACGATCTTCACGGCGTTCTACCGCAGCAACGTCGACGTGCCCGCGGGGCTGACGCCCGAGCAGACCGGTGCGGCGGCCGAGAGCATCGGCGGTGCGGCCGCGGTGGCAGCGGATCTGCCTGCCGCCACCGCCACGCAGCTTCTCGATTCGGCCCGTGCGGCGTTCGATTCGGGTATCGCCCCGACCGCGGTGATCGCCGCGATGCTGGTGCTGGCCGCCGCCGCGGTGGTGGGTGTGGCGTTCAGGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36769","NCBI_taxonomy_name":"Mycolicibacterium smegmatis MC2 155","NCBI_taxonomy_id":"246196"}}}},"ARO_accession":"3003967","ARO_id":"40738","ARO_name":"lfrA","CARD_short_name":"lfrA","ARO_description":"lfrA is involved in the active efflux of quinolones and is found in Mycobacteroides abscessus.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2436":{"model_id":"2436","model_name":"D-Ala-D-Ala ligase","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"4524":"E13G","4525":"G99R","4526":"V241D","4527":"D295G","4528":"P313L"},"Curated-R":{"4524":"E13G","4525":"G99R","4526":"V241D","4527":"D295G","4528":"P313L","18559":"P313L"},"clinical":{"4524":"E13G","4525":"G99R","4526":"V241D","4527":"D295G","4528":"P313L"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"650"},"41342":{"param_type":"deletion mutation from peptide sequence","param_description":"A peptide sequence change between the translation initiation (start) and termination (stop) codon where, compared to a reference sequence, one or more amino acids are deleted and therefore are not present. These represent in-frame deletions which do not result in frameshift variants and may include multiple amino acids. Format is given by [wildtype AA][position]del for a single peptide deletion or [wildtype AA][position]_[wildtype AA][position]del for a deleted peptide range, e.g. K527del or Q517_N518del.","param_type_id":"41342","param_value":{"18559":"D244_V245del"}}},"model_sequences":{"sequence":{"11357":{"protein_sequence":{"accession":"AAB17902.2","sequence":"MKITLLYGGRSAEHEVSILSAFSVLNAIYYNYYQVQLVFITKEGQWVKGPLLTEKPASKDVLHLSWDPSGQTEEGFTGKVINPGEIKEEGAIVFPVLHGPNGEDGTIQGFLETLNMPYVGAGVLTSACAMDKIMTKYILQAAGVPQVPYVPVLKNQWKENPKKVFDQCEGSLLYPMFVKPANMGSSVGITKAENREELQNALATAYQYDSRAIVEQGIEAREIEVAVLGNEDVRTTLPGEVVKDVAFYDYEAKYINNKIEMQIPAEVPEEVYQKAQEYAKLAYTMLGGSGLSRCDFFLTNKNELFLNELNSMPGFTEFSMYPLLWENMGLKYGDLIEELIQLGMNRYHQRQSFFEKNE"},"dna_sequence":{"accession":"U39790.2","fmin":"42","fmax":"1119","strand":"+","sequence":"TTGAAGATTACTTTACTATATGGCGGACGCAGCGCAGAGCATGAAGTTTCCATTCTTTCCGCATTTTCAGTTTTAAATGCCATTTATTATAATTATTACCAAGTTCAACTCGTATTTATTACAAAAGAAGGACAATGGGTCAAAGGTCCATTACTAACAGAAAAACCTGCTAGCAAAGATGTCTTGCATCTTTCATGGGACCCAAGTGGACAGACAGAGGAAGGCTTTACAGGAAAAGTGATCAATCCGGGAGAAATCAAAGAAGAAGGAGCCATCGTTTTTCCAGTTTTACACGGGCCAAACGGGGAAGATGGAACGATCCAAGGCTTCTTAGAGACATTGAATATGCCTTATGTCGGCGCAGGCGTATTGACCAGTGCATGTGCCATGGATAAAATCATGACCAAGTATATTTTACAAGCTGCTGGTGTGCCGCAAGTTCCTTATGTACCAGTACTTAAGAATCAATGGAAAGAAAATCCTAAAAAAGTATTTGATCAATGTGAAGGTTCTTTGCTTTATCCGATGTTTGTCAAACCTGCGAATATGGGTTCTAGTGTCGGCATTACAAAGGCAGAAAACCGAGAAGAGCTGCAAAATGCTTTAGCAACAGCCTATCAGTATGATTCTCGAGCAATCGTTGAACAAGGAATTGAAGCGCGCGAAATCGAAGTTGCTGTATTAGGAAATGAAGATGTTCGGACGACTTTGCCTGGCGAAGTCGTAAAAGACGTAGCATTCTATGATTATGAAGCCAAATATATCAATAATAAAATCGAAATGCAGATTCCAGCCGAAGTGCCGGAAGAAGTTTATCAAAAAGCGCAAGAGTACGCGAAGTTAGCTTACACGATGTTAGGTGGAAGCGGATTGAGCCGGTGCGATTTCTTTTTGACAAATAAAAATGAATTATTCCTGAATGAATTAAACTCTATGCCAGGATTTACGGAGTTCAGTATGTACCCACTCTTATGGGAAAATATGGGCTTGAAATACGGTGATTTGATTGAAGAACTGATTCAATTAGGAATGAATCGATACCATCAGCGTCAATCTTTTTTTGAAAAAAATGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36779","NCBI_taxonomy_name":"Enterococcus faecium","NCBI_taxonomy_id":"1352"}}}},"ARO_accession":"3003970","ARO_id":"40743","ARO_name":"D-Ala-D-Ala ligase","CARD_short_name":"ddl","ARO_description":"Non-van ligases that synthesize D-Ala-D-Ala, the default cell wall precursor that makes a cell vulnerable to glycopeptide antibiotics. Mutations in the ddl gene can cause the production of nonfunctional\/inactivated D-Ala-D-Ala ligases, which can render bacteria glycopeptide dependent depending on the presence of vancomycin resistance clusters.","ARO_category":{"39340":{"category_aro_accession":"3002906","category_aro_cvterm_id":"39340","category_aro_name":"Van ligase","category_aro_description":"Van ligases synthesize alternative substrates for peptidoglycan synthesis that reduce vancomycin binding affinity.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3355":{"model_id":"3355","model_name":"catII from Escherichia coli K-12","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"420"}},"model_sequences":{"sequence":{"5535":{"protein_sequence":{"accession":"CAA37805.1","sequence":"MNFTRIDLNTWNRREHFALYRQQIKCGFSLTTKLDITALRTALAETGYKFYPLMIYLISRAVNQFPEFRMALKDNELIYWDQSDPVFTVFHKETETFSALSCRYFPDLSEFMAGYNAVTAEYQHDTRLFPQGNLPENHLNISSLPWVSFDGFNLNITGNDDYFAPVFTMAKFQQEGDRVLLPVSVQVHHAVCDGFHAARFINTLQLMCDNILK"},"dna_sequence":{"accession":"X53796.1","fmin":"186","fmax":"828","strand":"+","sequence":"ATGAATTTTACCCGGATTGACCTGAATACCTGGAATCGCAGGGAACACTTTGCCCTTTATCGTCAGCAGATTAAATGCGGATTCAGCCTGACCACCAAACTCGATATTACCGCTTTGCGTACCGCACTGGCGGAGACAGGTTATAAGTTTTATCCGCTGATGATTTACCTGATCTCCCGGGCTGTTAATCAGTTTCCGGAGTTCCGGATGGCACTGAAAGACAATGAACTTATTTACTGGGACCAGTCAGACCCGGTCTTTACTGTCTTTCATAAAGAAACCGAAACATTCTCTGCACTGTCCTGCCGTTATTTTCCGGATCTCAGTGAGTTTATGGCAGGTTATAATGCGGTAACGGCAGAATATCAGCATGATACCAGATTGTTTCCGCAGGGAAATTTACCGGAGAATCACCTGAATATATCATCATTACCGTGGGTGAGTTTTGACGGATTTAACCTGAACATCACCGGAAATGATGATTATTTTGCCCCGGTTTTTACGATGGCAAAGTTTCAGCAGGAAGGTGACCGCGTATTATTACCTGTTTCTGTACAGGTTCATCATGCAGTATGTGATGGCTTTCATGCAGCACGGTTTATTAATACACTTCAGCTGATGTGTGATAACATACTGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36905","NCBI_taxonomy_name":"Escherichia coli str. K-12","NCBI_taxonomy_id":"83333"}}}},"ARO_accession":"3004656","ARO_id":"42694","ARO_name":"catII from Escherichia coli K-12","CARD_short_name":"Ecol_catII","ARO_description":"catII is a chloramphenicol acetyltransferase. This particular catII is found in E.coli K-12. Confers resistance to chloramphenicol.","ARO_category":{"36261":{"category_aro_accession":"3000122","category_aro_cvterm_id":"36261","category_aro_name":"chloramphenicol acetyltransferase (CAT)","category_aro_description":"Inactivates chloramphenicol by addition of an acyl group. CAT is used to describe many variants of the chloramphenicol acetyltransferase gene in a range of organisms including Acinetobacter calcoaceticus, Agrobacterium tumefaciens, Alkalihalobacillus clausii, Bacillus subtilis, Campylobacter coli, Enterococcus faecalis, Enterococcus faecium, Lactococcus lactis, Listeria monocytogenes, Listonella anguillarum, Morganella morganii, Photobacterium damselae subsp. piscicida, Proteus mirabilis, Salmonella typhi, Serratia marcescens, Shigella flexneri, Staphylococcus aureus, Staphylococcus haemolyticus, Staphylococcus intermedius, Streptococcus agalactiae, Streptococcus suis and Streptomyces acrimycini.","category_aro_class_name":"AMR Gene Family"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3357":{"model_id":"3357","model_name":"catA4","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"5537":{"protein_sequence":{"accession":"AAA25655.1","sequence":"MDTKRVGILVVDLSQWGRKEHFEAFQSFAQCTFSQTVQLDITSLLKTVKQNGYKFYPTFIYIISLLVNKHAEFRMAMKDGELVIWDSVNPGYNIFHEQTETFSSLWSYYHKDINRFLKTYSEDIAQYGDDLAYFPKEFIENMFFVSANPWVSFTSFNLNMANINNFFAPVFTIGKYYTQGDKVLMPLAIQVHHAVCDGFHVGRLLNEIQQYCDEGCK"},"dna_sequence":{"accession":"M11587.1","fmin":"879","fmax":"1533","strand":"+","sequence":"ATGGACACAAAGCGCGTGGGTATATTGGTTGTTGATCTATCCCAATGGGGACGAAAAGAACACTTTGAAGCATTTCAGTCTTTTGCTCAATGCACCTTTAGCCAGACCGTTCAACTGGATATTACTTCATTATTAAAAACCGTAAAGCAAAATGGGTACAAATTCTATCCGACATTTATATACATCATTAGCCTATTGGTAAATAAACATGCAGAATTCCGCATGGCAATGAAAGACGGGGAATTGGTGATATGGGATAGTGTTAACCCTGGGTACAATATCTTTCATGAACAGACCGAAACATTTTCATCTTTATGGAGTTACTACCACAAAGATATCAATCGTTTTTTGAAAACTTATTCAGAAGATATAGCACAATACGGCGACGATCTAGCCTATTTTCCAAAAGAATTTATCGAAAATATGTTTTTTGTGTCAGCAAATCCTTGGGTAAGTTTCACCAGTTTTAACTTGAATATGGCGAATATAAACAATTTCTTTGCCCCTGTATTTACAATAGGTAAATATTATACGCAAGGAGATAAAGTTCTGATGCCACTAGCAATTCAAGTGCATCATGCCGTATGTGATGGCTTCCATGTAGGCAGATTACTCAATGAAATACAGCAATACTGCGATGAGGGATGTAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3004657","ARO_id":"42696","ARO_name":"catA4","CARD_short_name":"catA4","ARO_description":"catA4 is a chloramphenicol acetyltransferase that confers resistance to chloramphenicol.","ARO_category":{"36261":{"category_aro_accession":"3000122","category_aro_cvterm_id":"36261","category_aro_name":"chloramphenicol acetyltransferase (CAT)","category_aro_description":"Inactivates chloramphenicol by addition of an acyl group. CAT is used to describe many variants of the chloramphenicol acetyltransferase gene in a range of organisms including Acinetobacter calcoaceticus, Agrobacterium tumefaciens, Alkalihalobacillus clausii, Bacillus subtilis, Campylobacter coli, Enterococcus faecalis, Enterococcus faecium, Lactococcus lactis, Listeria monocytogenes, Listonella anguillarum, Morganella morganii, Photobacterium damselae subsp. piscicida, Proteus mirabilis, Salmonella typhi, Serratia marcescens, Shigella flexneri, Staphylococcus aureus, Staphylococcus haemolyticus, Staphylococcus intermedius, Streptococcus agalactiae, Streptococcus suis and Streptomyces acrimycini.","category_aro_class_name":"AMR Gene Family"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3358":{"model_id":"3358","model_name":"catA8","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"5543":{"protein_sequence":{"accession":"AFN69318.1","sequence":"MTFNIINLETWDRKEYFNHYFNQQTTYSVTKEFDITLLKSMIKNKGYELYPALIYTIVNIINQNKVFRTGINSEGNLGYWEKLNPLYTVFNKETEKFSNIWTESNVSFNSFYNSYKSDLLEYKDKNEMFPKKPIPENTVPISMIPWIDFSSFNLNIGNNSRFLLPIITIGKFYSKNNKIYLPVSLQVHHAVCDGYHVSLFMSEFQNIVDSVNEWI"},"dna_sequence":{"accession":"JQ922409.1","fmin":"92","fmax":"740","strand":"+","sequence":"ATGACTTTTAATATTATTAATTTGGAAACTTGGGATAGAAAAGAATATTTTAATCATTATTTCAATCAACAAACAACTTACAGTGTTACTAAAGAATTTGATATCACTTTACTTAAAAGTATGATAAAAAATAAAGGATATGAACTGTATCCTGCTTTGATTTATACAATTGTAAATATTATAAATCAAAATAAAGTATTTAGAACAGGAATTAATAGTGAGGGAAATTTGGGTTATTGGGAAAAATTAAACCCTTTATATACAGTCTTTAATAAAGAAACTGAAAAATTTTCTAACATTTGGACAGAATCAAATGTTAGTTTTAATTCTTTTTATAATAGTTATAAGAGTGACTTACTTGAATATAAAGATAAAAATGAAATGTTTCCTAAAAAACCAATACCTGAAAACACAGTTCCTATTTCGATGATTCCTTGGATTGATTTTAGTTCATTTAATTTAAATATTGGTAATAATAGTAGATTCCTATTGCCAATTATTACAATAGGTAAATTTTATAGTAAGAATAATAAGATCTATTTACCAGTCTCATTGCAAGTTCATCATGCGGTATGTGATGGTTACCATGTTTCATTATTTATGAGTGAATTTCAAAATATAGTTGATAGTGTAAATGAATGGATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36757","NCBI_taxonomy_name":"Listeria monocytogenes","NCBI_taxonomy_id":"1639"}}}},"ARO_accession":"3004658","ARO_id":"42697","ARO_name":"catA8","CARD_short_name":"catA8","ARO_description":"catA8 is a chloramphenicol acetyltransferase that confers resistance to chloramphenicol.","ARO_category":{"36261":{"category_aro_accession":"3000122","category_aro_cvterm_id":"36261","category_aro_name":"chloramphenicol acetyltransferase (CAT)","category_aro_description":"Inactivates chloramphenicol by addition of an acyl group. CAT is used to describe many variants of the chloramphenicol acetyltransferase gene in a range of organisms including Acinetobacter calcoaceticus, Agrobacterium tumefaciens, Alkalihalobacillus clausii, Bacillus subtilis, Campylobacter coli, Enterococcus faecalis, Enterococcus faecium, Lactococcus lactis, Listeria monocytogenes, Listonella anguillarum, Morganella morganii, Photobacterium damselae subsp. piscicida, Proteus mirabilis, Salmonella typhi, Serratia marcescens, Shigella flexneri, Staphylococcus aureus, Staphylococcus haemolyticus, Staphylococcus intermedius, Streptococcus agalactiae, Streptococcus suis and Streptomyces acrimycini.","category_aro_class_name":"AMR Gene Family"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3359":{"model_id":"3359","model_name":"Mef(En2)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"5539":{"protein_sequence":{"accession":"AAF74725.1","sequence":"MNHWKSTLAVIGIGQLISILTSTIVGFSIIFWISNEFKSPTALSLAILAGFLPQFVLGLFAGVYVDRWNRKKTMFYSDLFIAFCTLCLFIVITKGYKDLSFFYLLTACRSIGSTFHAPALQASIPLLVPKHHLVRVSGLYHSIQSFSEVIAPVVGASLVVWLPIQYILLIDVIGAVAACLTLLCVQIPSLQKTKVLPDFKKELTEWLHTLRRTMGILPLFVCFTLVTFVLMPVFTLFPFMTLLHFNGNILQMGVVEMGWGSGALLGGLVLACKALKSKQTLVMHTAYVILGLYLISASYLPSSAFIGFVCLTFTGGIAYSIYHALFIAIIQQNLASDMLGRTFSLIFSLSTFPSMLGIVASGYWVEAWGITSVFMISGWVIFLIGVGANFISSIKQLDNYA"},"dna_sequence":{"accession":"AF251288.1","fmin":"794","fmax":"2000","strand":"-","sequence":"ATGAATCATTGGAAATCAACTTTGGCCGTGATAGGAATAGGCCAACTCATATCTATTTTAACAAGTACGATTGTTGGCTTCTCCATTATTTTTTGGATTAGCAACGAATTTAAATCCCCGACAGCTTTATCTCTGGCTATTTTAGCTGGATTTTTACCACAATTTGTATTAGGCTTGTTTGCCGGGGTCTATGTTGACAGATGGAATCGAAAGAAAACGATGTTTTATTCGGACTTGTTCATCGCGTTCTGTACCCTATGTCTTTTTATTGTGATAACCAAGGGTTATAAAGACCTTTCTTTTTTTTATCTATTGACTGCTTGTCGTTCAATAGGCAGTACGTTTCATGCACCTGCTTTACAGGCAAGCATCCCTCTACTGGTTCCCAAGCACCATCTTGTCAGGGTATCAGGTTTGTACCATTCCATTCAATCCTTCAGTGAGGTGATAGCTCCCGTTGTAGGGGCAAGCCTCGTTGTTTGGCTTCCCATACAGTATATTCTGCTCATAGATGTGATCGGAGCTGTTGCTGCTTGTCTGACCTTACTTTGTGTCCAGATTCCTTCTCTTCAAAAAACGAAAGTTCTTCCAGATTTCAAAAAAGAACTGACGGAATGGTTGCATACCTTGCGGCGTACAATGGGCATTTTGCCTTTATTCGTATGCTTTACGCTGGTGACTTTTGTCCTTATGCCTGTTTTTACGTTATTTCCTTTTATGACGCTTCTGCATTTCAACGGAAACATTTTGCAAATGGGAGTTGTGGAAATGGGTTGGGGCTCAGGGGCATTGTTGGGCGGTTTAGTACTTGCCTGTAAGGCTTTGAAAAGCAAGCAAACATTAGTGATGCATACGGCTTATGTGATATTGGGATTGTATCTGATTAGCGCCAGTTATTTACCATCAAGCGCATTTATAGGTTTTGTTTGCCTAACATTTACAGGAGGCATAGCCTATTCCATTTACCATGCGCTTTTCATCGCTATTATTCAGCAGAACTTGGCTTCGGACATGCTTGGACGGACTTTTTCTCTCATCTTTAGTTTGAGTACCTTTCCATCAATGCTGGGTATCGTAGCTTCAGGATATTGGGTGGAAGCATGGGGTATCACATCCGTCTTTATGATCAGCGGATGGGTTATCTTTCTGATTGGAGTGGGTGCAAATTTTATTTCTTCAATCAAGCAGTTGGATAATTACGCATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35916","NCBI_taxonomy_name":"Bacteroides fragilis","NCBI_taxonomy_id":"817"}}}},"ARO_accession":"3004659","ARO_id":"42698","ARO_name":"Mef(En2)","CARD_short_name":"Mef(En2)","ARO_description":"NBU2-encoded resistance gene. An MefE homolog in Bacteroides species. Macrolide efflux MFS transporter.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"3360":{"model_id":"3360","model_name":"catB11","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"350"}},"model_sequences":{"sequence":{"5541":{"protein_sequence":{"accession":"AID93387.1","sequence":"MKNYFESPFKGKPLVEQVKNPNIKVGRYSYYSGYYHGHSFDDCARYLLPDRDDVDKLIIGSFCSIGTGASFIMAGNQGHRYDWVTSFPFFYMNEEPAFSESVDAFQAAGNTVIGSDVWIGSEAMIMPGVKVGHGAVIGSRALVTKDIEPYTIVGGNPAKEIKKRFSEQEISMLLDMKWWDWPLEQIKEAMPLLCSSDIAGLYHFWQRSSA"},"dna_sequence":{"accession":"CP008790.1","fmin":"144510","fmax":"145143","strand":"+","sequence":"ATGAAGAACTATTTTGAGAGCCCGTTTAAGGGAAAACCTCTCGTCGAACAGGTAAAGAACCCAAATATCAAGGTGGGCCGTTATAGCTATTATTCAGGCTATTACCACGGGCATTCATTTGATGATTGCGCTCGCTACCTCCTGCCTGATCGTGATGACGTTGATAAATTGATAATTGGAAGCTTTTGCTCCATAGGGACGGGTGCATCTTTTATCATGGCTGGAAATCAAGGTCACCGATATGATTGGGTTACATCATTCCCTTTTTTCTATATGAATGAGGAACCGGCATTTTCGGAATCAGTTGATGCTTTCCAGGCGGCAGGTAATACCGTCATAGGAAGCGACGTGTGGATTGGCTCTGAAGCAATGATTATGCCTGGAGTAAAGGTTGGCCATGGAGCGGTAATTGGCAGCCGGGCTTTGGTTACCAAAGATATAGAGCCATACACAATTGTTGGTGGCAACCCTGCAAAAGAGATAAAGAAGCGCTTTTCAGAACAGGAAATTTCAATGTTGCTAGATATGAAGTGGTGGGATTGGCCGTTGGAGCAAATTAAAGAAGCAATGCCTCTTTTGTGCTCGTCTGATATTGCAGGCTTGTACCATTTTTGGCAGCGTTCAAGTGCCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42700","NCBI_taxonomy_name":"Klebsiella oxytoca KONIH1","NCBI_taxonomy_id":"1333852"}}}},"ARO_accession":"3004660","ARO_id":"42699","ARO_name":"catB11","CARD_short_name":"catB11","ARO_description":"catB11 is a chloramphenicol acetyltransferase that confers resistance to chloramphenicol.","ARO_category":{"36261":{"category_aro_accession":"3000122","category_aro_cvterm_id":"36261","category_aro_name":"chloramphenicol acetyltransferase (CAT)","category_aro_description":"Inactivates chloramphenicol by addition of an acyl group. CAT is used to describe many variants of the chloramphenicol acetyltransferase gene in a range of organisms including Acinetobacter calcoaceticus, Agrobacterium tumefaciens, Alkalihalobacillus clausii, Bacillus subtilis, Campylobacter coli, Enterococcus faecalis, Enterococcus faecium, Lactococcus lactis, Listeria monocytogenes, Listonella anguillarum, Morganella morganii, Photobacterium damselae subsp. piscicida, Proteus mirabilis, Salmonella typhi, Serratia marcescens, Shigella flexneri, Staphylococcus aureus, Staphylococcus haemolyticus, Staphylococcus intermedius, Streptococcus agalactiae, Streptococcus suis and Streptomyces acrimycini.","category_aro_class_name":"AMR Gene Family"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3361":{"model_id":"3361","model_name":"lin","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"900"}},"model_sequences":{"sequence":{"5544":{"protein_sequence":{"accession":"AEO25219.1","sequence":"MSTIEINQLKIEVADRVLVEIPHLLVSKKARIGIIGQNGLGKTTLMEVIAGAKEATSGTVTTQGKLAYIKQLSTDTSTKSGGEKTRKATQHAMRQNPSVLLADEPTSNLDVESVKHLERQWSDFHGALIIISHDRAFLDALCTEIWEIKNQKIHVYKGNYHAYLEQKQQQENQAELAYKEFKNKKKQLQASQTHHEIEAGRIVKPGKRLNNKEASAFKAGKGTQQKKQHSTIKALEKRIERLGNVEKPHTTKPIKIITPDNRVIKKGNTILSAKETAYEIAGRKLFETKAFSIKAGDKVALIGENASGKTTFLKEIIQENPNLLCNPQAKIAYFDQELNGLNQTKSLLENISEISVQTKQVNREVLGSMHFKESDLHKEVRMLSGGERVKLLLSMLLLSDANFLILDEPTNYLDIYAMEALETLIKQFAGTVLFVSHDRTFVNHVAEQLLVIENNEMNFHRMTFAEYEESKAPSRITEEDKLILEMRMSEIAAKLMQPNLKPTEKAILEQDYQEIITKRQQFS"},"dna_sequence":{"accession":"CP002003.1","fmin":"954744","fmax":"956316","strand":"+","sequence":"ATGTCTACAATCGAAATAAATCAATTAAAAATAGAAGTAGCAGATAGAGTTTTAGTAGAAATTCCTCATCTGCTAGTTAGTAAAAAAGCAAGAATCGGCATCATCGGTCAAAATGGTCTAGGAAAAACAACACTAATGGAAGTGATTGCTGGCGCTAAAGAAGCGACATCTGGCACGGTGACTACACAAGGAAAACTTGCTTACATCAAACAACTTTCCACGGATACAAGTACGAAAAGCGGTGGTGAAAAAACAAGAAAAGCTACTCAACACGCGATGCGCCAAAATCCAAGTGTTCTCCTAGCAGACGAACCAACAAGCAATCTTGATGTCGAAAGCGTCAAACATTTAGAACGTCAGTGGAGCGATTTCCACGGTGCGCTCATAATTATCTCGCATGACCGCGCTTTTTTAGATGCACTTTGTACAGAAATATGGGAAATCAAAAACCAAAAAATTCACGTGTACAAAGGAAACTACCACGCGTATTTAGAACAAAAACAACAACAAGAAAACCAAGCAGAACTTGCATACAAAGAATTTAAAAACAAAAAGAAACAATTGCAAGCATCTCAAACACATCACGAAATCGAAGCAGGTCGTATCGTTAAACCCGGGAAACGCTTAAACAACAAAGAAGCCAGCGCATTTAAAGCTGGAAAAGGAACACAACAAAAGAAACAACATAGTACAATCAAAGCTTTAGAAAAACGAATTGAACGGCTTGGTAATGTCGAAAAACCACATACAACTAAACCAATCAAAATTATCACCCCAGACAATCGCGTTATAAAAAAAGGCAACACGATACTAAGTGCCAAAGAAACAGCTTACGAAATTGCCGGACGAAAACTATTTGAAACAAAAGCTTTTTCTATTAAAGCAGGGGATAAAGTGGCGCTGATCGGTGAAAATGCAAGTGGGAAAACTACATTTTTAAAAGAAATAATCCAAGAAAATCCTAATCTCTTATGTAATCCCCAAGCGAAAATTGCTTATTTCGACCAAGAATTGAATGGATTAAACCAAACGAAATCCCTATTAGAAAACATCTCGGAAATTAGCGTTCAAACCAAGCAAGTAAACAGAGAAGTACTAGGTAGTATGCATTTTAAAGAAAGCGATTTGCATAAGGAAGTGCGCATGCTCTCTGGCGGGGAACGAGTGAAGTTGCTGCTCAGTATGCTCCTTCTTAGTGACGCCAATTTCTTGATTCTTGATGAACCAACCAACTATTTGGATATCTACGCAATGGAAGCGCTGGAAACGTTAATCAAACAATTTGCGGGGACGGTACTCTTCGTTTCTCATGATAGAACTTTTGTTAATCATGTGGCAGAACAGTTACTTGTTATCGAAAATAATGAAATGAATTTCCACCGGATGACTTTTGCAGAATATGAAGAAAGTAAAGCACCAAGCCGGATTACAGAAGAAGATAAGTTGATTTTAGAAATGCGTATGTCAGAAATTGCGGCAAAACTCATGCAACCCAATTTAAAGCCCACAGAAAAAGCCATACTCGAACAAGATTATCAAGAAATTATCACAAAAAGACAGCAATTTAGTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42702","NCBI_taxonomy_name":"Listeria monocytogenes FSL R2-561","NCBI_taxonomy_id":"393126"}}}},"ARO_accession":"3004651","ARO_id":"42676","ARO_name":"lin","CARD_short_name":"lin","ARO_description":"Listeria monocytogenes EGD-e lin gene for lincomycin resistance ABC-F type ribosomal protection protein, complete CDS.","ARO_category":{"36360":{"category_aro_accession":"3000221","category_aro_cvterm_id":"36360","category_aro_name":"lincosamide nucleotidyltransferase (LNU)","category_aro_description":"Resistance to the lincosamide antibiotic by ATP-dependent modification of the 3' and\/or 4'-hydroxyl groups of the methylthiolincosamide sugar.","category_aro_class_name":"AMR Gene Family"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3362":{"model_id":"3362","model_name":"Staphylococcus aureus FosB","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"260"}},"model_sequences":{"sequence":{"5545":{"protein_sequence":{"accession":"EHS19134.1","sequence":"MLKSINHICFSVRNLNDSIHFYRDILLGKLLLTGKKTAYFELAGLWIALNEEKDIPRNEIHFSYTHIAFTIDDSEFKYWHQRLKDNNVNILEGRVRDIRDRQSIYFTDPDGHKLELHTGTLENRLNYYKEAKPHMTFYK"},"dna_sequence":{"accession":"AHLO01000073.1","fmin":"63138","fmax":"63558","strand":"+","sequence":"ATGTTAAAATCTATTAATCATATATGCTTTTCAGTCAGAAATTTAAACGATTCAATACATTTTTATAGAGATATTTTACTTGGGAAATTGCTATTGACTGGTAAAAAAACTGCTTATTTTGAGCTTGCAGGCCTATGGATTGCTTTAAATGAAGAAAAAGATATACCACGTAATGAAATTCACTTTTCATATACACATATAGCTTTCACTATAGATGACAGCGAATTTAAATATTGGCATCAGAGGTTAAAAGATAATAACGTGAATATTTTAGAAGGAAGAGTTAGAGATATTAGAGATAGACAATCAATTTACTTTACCGACCCTGATGGTCATAAGCTAGAATTACATACTGGCACACTTGAGAACAGATTAAATTATTATAAAGAGGCTAAACCACATATGACATTTTACAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42704","NCBI_taxonomy_name":"Staphylococcus aureus subsp. aureus IS-88","NCBI_taxonomy_id":"904778"}}}},"ARO_accession":"3004661","ARO_id":"42703","ARO_name":"Staphylococcus aureus FosB","CARD_short_name":"Saur_FosB","ARO_description":"The Bacillus subtilis fosB gene encodes a fosfomycin resistance protein.","ARO_category":{"36272":{"category_aro_accession":"3000133","category_aro_cvterm_id":"36272","category_aro_name":"fosfomycin thiol transferase","category_aro_description":"Catalyzes the addition of a thiol group from a nucleophilic molecule to fosfomycin.","category_aro_class_name":"AMR Gene Family"},"35944":{"category_aro_accession":"0000025","category_aro_cvterm_id":"35944","category_aro_name":"fosfomycin","category_aro_description":"Fosfomycin (also known as phosphomycin and phosphonomycin) is a broad-spectrum antibiotic produced by certain Streptomyces species. It is effective on gram positive and negative bacteria as it targets the cell wall, an essential feature shared by both bacteria. Its specific target is MurA (MurZ in E.coli), which attaches phosphoenolpyruvate (PEP) to UDP-N-acetylglucosamine, a step of commitment to cell wall synthesis. In the active site of MurA, the active cysteine molecule is alkylated which stops the catalytic reaction.","category_aro_class_name":"Antibiotic"},"45731":{"category_aro_accession":"3007149","category_aro_cvterm_id":"45731","category_aro_name":"phosphonic acid antibiotic","category_aro_description":"A group of antibiotics derived from phosphonic acids.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3363":{"model_id":"3363","model_name":"MCR-3.3","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1010"}},"model_sequences":{"sequence":{"5546":{"protein_sequence":{"accession":"ASU10319.1","sequence":"MPSLIKIKIVPLMFFLALYFAFMLNWRGVLHFYEILYKLEDFKFGFAISLPILLVAALNFVFVPFSIRYLIKPFFALLIALSAIVSYTMMKYRVLFDQNMIQNIFETNQNEALAYLSLPIIGWVTIAGFIPAILLFFVEIEYEEKWFKGILTRALSMFASLIVIAVIAALYYQDYVSVGRNNSNLQREIVPANFVNSTVKYVYNRYLAEPIPFTTLGDDAKRDTNQSKPTLMFLVVGETARGKNFSMNGYEKDTNPFTSKSGGVISFNDVRSCGTATAVSVPCMFSNMGRKEFDDNLARNSEGLLDVLQKTGVSIFWKENDGGCKGVCDRVPNIEIKPKDYPKFCDKNTCYDEVVLQELDSEIAQMKGDKLVGFHLIGSHGPTYYKRYPDAHRQFTPDCPRSDIENCTDEELTNTYDNTIRYTDFVIAEMIAKLKTYEDKYNTALLYVSDHGESLGALGLYLHGTPYKFAPDDQTRVPMQVWMSPGFIKEKGMNMECLQKNAAANRYSHDNIFSSVLGIWDVKTAIYEQELDIFKQCRNN"},"dna_sequence":{"accession":"MF495680.1","fmin":"240178","fmax":"241801","strand":"-","sequence":"ATGCCTTCCCTTATAAAAATAAAAATTGTTCCGCTTATGTTCTTTTTGGCACTGTATTTTGCATTTATGCTGAACTGGCGTGGAGTTCTCCATTTTTACGAAATCCTTTACAAATTAGAAGATTTTAAGTTTGGTTTCGCCATTTCATTACCAATATTGCTTGTTGCAGCGCTTAACTTTGTATTTGTTCCATTTTCGATACGGTATTTAATAAAGCCTTTTTTTGCACTTCTTATCGCACTTAGTGCAATCGTTAGTTACACAATGATGAAGTATAGAGTCTTGTTTGATCAAAACATGATTCAGAATATTTTTGAAACCAATCAAAATGAGGCGTTAGCATATTTAAGCTTACCAATTATAGGATGGGTTACTATTGCTGGTTTTATCCCTGCCATTTTACTTTTCTTTGTTGAAATTGAATATGAGGAAAAATGGTTCAAAGGGATTCTAACTCGTGCCCTATCGATGTTTGCATCACTTATAGTGATTGCGGTTATTGCAGCACTATACTATCAAGATTATGTGTCAGTGGGGCGCAACAATTCAAACCTCCAGCGTGAGATTGTTCCAGCCAATTTCGTTAATAGTACCGTTAAATACGTTTACAATCGTTATCTTGCTGAACCAATCCCATTTACAACTTTAGGTGATGATGCAAAACGGGATACTAATCAAAGTAAGCCCACGTTGATGTTTCTGGTCGTTGGTGAAACCGCTCGTGGTAAAAATTTCTCGATGAATGGCTATGAGAAAGACACCAATCCATTTACCAGTAAATCTGGTGGCGTGATCTCCTTTAATGATGTTCGTTCGTGTGGGACTGCAACCGCTGTATCTGTCCCCTGCATGTTTTCCAATATGGGGAGAAAGGAGTTTGATGATAATCTCGCTCGTAATAGCGAGGGTTTGTTAGATGTGTTGCAGAAAACGGGGGTCTCCATTTTTTGGAAGGAGAACGATGGCGGCTGCAAAGGCGTCTGCGACCGAGTTCCTAACATCGAGATCAAACCGAAGGATTACCCAAAGTTCTGCGATAAAAACACATGCTATGACGAGGTTGTCCTTCAAGAGCTCGACAGTGAAATTGCTCAAATGAAAGGGGATAAGCTGGTTGGCTTCCACCTGATAGGTAGCCATGGCCCAACCTACTACAAACGCTACCCTGATGCTCATCGTCAGTTCACTCCTGACTGTCCACGCAGTGATATTGAAAACTGCACAGATGAAGAGCTCACCAACACCTATGACAACACCATCCGCTACACCGATTTCGTGATTGCAGAGATGATTGCCAAGTTGAAAACCTACGAAGATAAGTACAACACCGCGTTGCTCTACGTCTCCGATCATGGTGAATCACTGGGAGCATTAGGGCTTTACCTGCACGGTACACCGTACAAGTTTGCACCGGATGATCAGACCCGTGTTCCTATGCAGGTGTGGATGTCACCTGGTTTCATCAAAGAAAAAGGCATGAATATGGAATGTTTGCAGAAAAATGCCGCAGCCAATCGCTATTCTCATGACAACATATTTTCTTCTGTCCTGGGAATATGGGATGTGAAGACGGCTATCTACGAACAAGAATTAGATATCTTTAAGCAATGTCGGAATAATTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39677","NCBI_taxonomy_name":"Aeromonas veronii","NCBI_taxonomy_id":"654"}}}},"ARO_accession":"3004662","ARO_id":"42705","ARO_name":"MCR-3.3","CARD_short_name":"MCR-3.3","ARO_description":"MCR-3.3 is a colistin resistance gene variant in the chromosome of an Aeromonas veronii. Conferred polymyxin resistance in both E. Coli and Aeromonas salmonicida.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3364":{"model_id":"3364","model_name":"FusF","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"5547":{"protein_sequence":{"accession":"AVL76727.1","sequence":"MEKQIYPYQFNYIKERIAHLLNAYKSVNDLNTIASIKETTKIDIYQQFHQIDDTLTEAIEKLMNIRITKVQVDKILETLQTYVIPFEHPSKKQVEKTFRKIKKLKSPLISDEILLESTYIGWNDIASNRKFIIYYNEQGTLTGFYGDIANQTVKGYCAICNKESNVALFMRKTRTSGDGQYTKKGDYICFDSIKCNQQLSDITQFYQFVDKIHS"},"dna_sequence":{"accession":"CP027422.1","fmin":"410229","fmax":"410874","strand":"+","sequence":"TTGGAAAAACAAATTTATCCATATCAATTTAACTATATTAAAGAACGAATCGCACATTTACTTAATGCTTATAAATCAGTAAATGACTTAAATACAATTGCTTCTATAAAAGAAACAACTAAAATAGACATTTATCAGCAGTTTCATCAAATAGATGATACGTTGACTGAAGCGATTGAAAAATTAATGAACATACGTATTACTAAAGTACAAGTAGATAAAATATTAGAAACTTTACAGACATACGTTATACCCTTTGAACACCCTTCAAAAAAACAAGTCGAAAAAACTTTTCGTAAAATTAAAAAGCTTAAATCACCGCTTATTAGTGATGAAATCCTTTTGGAAAGTACTTATATCGGATGGAACGATATCGCTTCAAACAGAAAATTTATCATCTATTATAACGAGCAAGGAACTTTAACAGGTTTTTATGGCGACATTGCTAACCAAACCGTTAAGGGCTATTGCGCAATTTGTAATAAAGAATCTAATGTCGCTCTATTTATGCGTAAAACACGTACTTCTGGTGATGGACAATATACCAAAAAAGGTGACTATATTTGTTTTGACAGTATCAAATGTAATCAACAATTGTCGGATATTACACAATTTTATCAATTTGTCGATAAAATCCACTCATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36766","NCBI_taxonomy_name":"Staphylococcus cohnii","NCBI_taxonomy_id":"29382"}}}},"ARO_accession":"3004663","ARO_id":"42706","ARO_name":"FusF","CARD_short_name":"FusF","ARO_description":"A fusidic acid resistance determinant in Staphylococcus cohnii. This protein behaves akin to FusB as it is a FusB-type protein. It mediates dissociation of EF-G from the ribosome thus counteracting the action of Fusidic acid.","ARO_category":{"43297":{"category_aro_accession":"3005086","category_aro_cvterm_id":"43297","category_aro_name":"Target protecting FusB-type protein conferring resistance to Fusidic acid","category_aro_description":"Fusidic acid resistance determinants through the mediation of target protection. These protein drive the dissociation of EF-G from the ribosome thus counteracting the action of Fusidic acid.","category_aro_class_name":"AMR Gene Family"},"37139":{"category_aro_accession":"3000759","category_aro_cvterm_id":"37139","category_aro_name":"fusidic acid","category_aro_description":"Fusidic acid is the only commercially available fusidane, a group of steroid-like antibiotics. It is most active against Gram-positive bacteria, and acts by inhibiting elongation factor G to  block protein synthesis.","category_aro_class_name":"Antibiotic"},"45735":{"category_aro_accession":"3007153","category_aro_cvterm_id":"45735","category_aro_name":"fusidane antibiotic","category_aro_description":"A group of antibiotics possessing steroid rings or steroid-like structures.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3367":{"model_id":"3367","model_name":"Staphylococcus aureus norA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"5552":{"protein_sequence":{"accession":"BAA14147.1","sequence":"MNKQIFVLYFNIFLIFLGIGLVIPVLPVYLKDLGLTGSDLGLLVAAFALSQMIISPFGGTLADKLGKKLIICIGLILFSVSEFMFAVGHNFSVLMLSRVIGGMSAGMVMPGVTGLIADISPSHQKAKNFGYMSAIINSGFILGPGIGGFMAEVSHRMPFYFAGALGILAFIMSIVLIHDPKKSTTSGFQKLEPQLLTKINWKVFITPVILTLVLSFGLSAFETLYSLYTADKVNYSPKDISIAITGGGIFGALFQIYFFDKFMKYFSELTFIAWSLLYSVVVLILLVFANGYWSIMLISFVVFIGFDMIRPAITNYFSNIAGERQGFAGGLNSTFTSMGNFIGPLIAGALFDVHIEAPIYMAIGVSLAGVVIVLIEKQHRAKLKEQNM"},"dna_sequence":{"accession":"D90119.1","fmin":"477","fmax":"1644","strand":"+","sequence":"ATGAATAAACAGATTTTTGTCTTATATTTTAATATTTTCTTGATTTTTTTAGGTATCGGTTTAGTAATACCAGTCTTGCCTGTTTATTTAAAAGATTTGGGATTAACTGGTAGTGATTTAGGATTACTAGTTGCTGCTTTTGCGTTATCTCAAATGATTATATCGCCGTTTGGTGGTACGCTAGCTGACAAATTAGGGAAGAAATTAATTATATGTATAGGATTAATTTTGTTTTCAGTGTCAGAATTTATGTTTGCAGTTGGCCACAATTTTTCGGTATTGATGTTATCGAGAGTGATTGGTGGTATGAGTGCTGGTATGGTAATGCCTGGTGTGACAGGTTTAATAGCTGACATTTCACCAAGCCATCAAAAAGCAAAAAACTTTGGCTACATGTCAGCGATTATCAATTCTGGATTCATTTTAGGACCAGGGATTGGTGGATTTATGGCAGAAGTTTCACATCGTATGCCATTTTACTTTGCAGGAGCATTAGGTATTCTAGCATTTATAATGTCAATTGTATTGATTCACGATCCGAAAAAGTCTACGACAAGTGGTTTCCAAAAGTTAGAGCCACAATTGCTAACGAAAATTAACTGGAAAGTGTTTATTACACCAGTTATTTTAACACTTGTATTATCGTTTGGTTTATCTGCATTTGAAACATTGTATTCACTATACACAGCTGACAAGGTAAATTATTCACCTAAAGATATTTCGATTGCTATTACGGGTGGCGGTATATTTGGGGCACTTTTCCAAATCTATTTCTTCGATAAATTTATGAAGTATTTCTCAGAGTTAACATTTATAGCTTGGTCATTATTATATTCAGTTGTTGTCTTAATATTATTAGTTTTTGCTAATGGCTATTGGTCAATAATGTTAATCAGTTTTGTTGTCTTCATAGGTTTTGATATGATACGACCAGCCATTACAAATTATTTTTCTAATATTGCTGGAGAAAGGCAAGGCTTTGCAGGCGGATTGAACTCGACATTCACTAGTATGGGTAATTTCATAGGTCCTTTAATCGCAGGTGCGTTATTTGATGTACACATTGAAGCACCAATTTATATGGCTATAGGTGTTTCATTAGCAGGTGTTGTTATTGTTTTAATTGAAAAGCAACATAGAGCAAAATTGAAAGAACAAAATATGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35508","NCBI_taxonomy_name":"Staphylococcus aureus","NCBI_taxonomy_id":"1280"}}}},"ARO_accession":"3004667","ARO_id":"42714","ARO_name":"Staphylococcus aureus norA","CARD_short_name":"Saur_norA","ARO_description":"NorA gene cloned from Staphylococcus aureus conferred relatively high resistance to hydrophilic quinolones such as norfloxacin, enoxacin, ofloxacin, and ciprofloxacin in S. aureus and Escherichia coli. Had low or no resistance at all to hydrophobic ones such as nalidixic acid, oxolinic acid, and sparfloxacin in S. aureus and Escherichia coli.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35942":{"category_aro_accession":"0000023","category_aro_cvterm_id":"35942","category_aro_name":"enoxacin","category_aro_description":"Enoxacin belongs to a group called fluoroquinolones. Its mode of action depends upon blocking bacterial DNA replication by binding itself to DNA gyrase and causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37007":{"category_aro_accession":"3000663","category_aro_cvterm_id":"37007","category_aro_name":"ofloxacin","category_aro_description":"Ofloxacin is a 6-fluoro, 7-piperazinyl quinolone with a methyl-substituted oxazine ring. It has a broad spectrum of activity including many enterobacteria and mycoplasma but most anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2432":{"model_id":"2432","model_name":"Klebsiella pneumoniae OmpK35","model_type":"protein knockout model","model_type_id":"40354","model_description":"Protein Knockout Models (PKM) reflect resistance by the absence of a gene product, most often deletion of a gene involved in antibiotic import, such as Vibrio cholerae OmpT. Like Protein Homolog Models (PHMs), PKMs include a reference sequence and a bitscore cut-off for detection using BLASTP but instead are designed to only report lack of detection under Perfect or Strict criteria. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff. This model type is still under development and not currently supported by the Resistance Gene Identifier (RGI) software.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"5852":{"protein_sequence":{"accession":"YP_005226137.1","sequence":"MGGDGWNYTDNYMTGRTNGVATYRNSDFFGLVDGLSFALQYQGKNDHDRAIRKQNGDGFSTAATYAFDNGIALSAGYSSSNRSVDQKADGNGDKAEAWATSAKYDANNIYAAVMYSQTYNMTPEEDNHFAGKTQNFEAVVQYQFDFGLRPSIGYVQTKGKDLQSRAGFSGGDADLVKYIEVGTWYYFNKNMNVYAAYKFNQLDDNDYTKAAGVATDDQAAVGIVYQF"},"dna_sequence":{"accession":"NC_016845.1","fmin":"1904307","fmax":"1904991","strand":"-","sequence":"ATGGGCGGTGACGGCTGGAACTATACCGACAACTACATGACCGGTCGTACCAACGGCGTCGCAACCTACCGTAACTCCGACTTCTTCGGTCTGGTTGACGGTCTGAGCTTCGCGCTGCAGTACCAGGGTAAAAACGACCATGACCGTGCGATTCGCAAGCAGAATGGCGACGGCTTCAGCACCGCAGCCACCTACGCGTTCGACAACGGTATCGCACTGTCTGCAGGCTACTCCAGCTCTAACCGTAGCGTCGATCAGAAAGCTGACGGCAATGGCGACAAAGCCGAAGCCTGGGCGACCTCTGCAAAATATGACGCTAACAACATCTATGCGGCCGTCATGTACTCCCAGACTTACAACATGACTCCGGAAGAAGATAACCACTTCGCTGGTAAAACTCAGAACTTTGAAGCAGTTGTACAGTATCAGTTTGACTTCGGCCTGCGTCCGTCCATCGGCTACGTACAGACCAAAGGCAAGGACCTGCAGTCGCGTGCTGGCTTCTCCGGCGGCGATGCGGATCTGGTTAAATACATCGAAGTGGGTACCTGGTACTACTTTAACAAGAACATGAACGTCTACGCTGCGTATAAATTCAACCAGCTGGACGACAACGATTACACCAAAGCGGCTGGTGTCGCCACTGACGACCAGGCGGCCGTGGGTATCGTTTACCAGTTCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40663","NCBI_taxonomy_name":"Klebsiella pneumoniae subsp. pneumoniae HS11286","NCBI_taxonomy_id":"1125630"}}}},"ARO_accession":"3003966","ARO_id":"40737","ARO_name":"Klebsiella pneumoniae OmpK35","CARD_short_name":"Kpne_OmpK35","ARO_description":"Klebsiella pneumoniae outer membrane porin protein. In beta-lactam-resistant Klebsiella, this porin is often deleted, limiting diffusion of the antibiotic into the cell. Klebsiella strains expressing OmpK35 are often beta-lactam sensitive even in the presence of beta-lactamases because of an inefficient mechanism.","ARO_category":{"41445":{"category_aro_accession":"3004281","category_aro_cvterm_id":"41445","category_aro_name":"General Bacterial Porin with reduced permeability to beta-lactams","category_aro_description":"These are GBPs that are associated with decreased susceptibility to beta-lactams either through mutations in the porin protein, absence of the porin protein, or expression of the porin protein.","category_aro_class_name":"AMR Gene Family"},"35927":{"category_aro_accession":"0000008","category_aro_cvterm_id":"35927","category_aro_name":"cefoxitin","category_aro_description":"Cefoxitin is a cephamycin antibiotic often grouped with the second generation cephalosporins. Cefoxitin is bactericidal and acts by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. Cefoxitin's 7-alpha-methoxy group and 3' leaving group make it a poor substrate for most beta-lactamases.","category_aro_class_name":"Antibiotic"},"35976":{"category_aro_accession":"0000059","category_aro_cvterm_id":"35976","category_aro_name":"cefepime","category_aro_description":"Cefepime (INN) is a fourth-generation cephalosporin antibiotic developed in 1994. It contains an aminothiazolyl group that decreases its affinity with beta-lactamases. Cefepime shows high binding affinity with penicillin-binding proteins and has an extended spectrum of activity against Gram-positive and Gram-negative bacteria, with greater activity against both Gram-negative and Gram-positive organisms than third-generation agents.","category_aro_class_name":"Antibiotic"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"35979":{"category_aro_accession":"0000062","category_aro_cvterm_id":"35979","category_aro_name":"ceftriaxone","category_aro_description":"Ceftriaxone is a third-generation cephalosporin antibiotic. The presence of an aminothiazolyl sidechain increases ceftriazone's resistance to beta-lactamases. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"35987":{"category_aro_accession":"0000070","category_aro_cvterm_id":"35987","category_aro_name":"ertapenem","category_aro_description":"Ertapenem is a carbapenem antibiotic and is highly resistant to beta-lactamases like other carbapenems. It inhibits bacterial cell wall synthesis.","category_aro_class_name":"Antibiotic"},"36309":{"category_aro_accession":"3000170","category_aro_cvterm_id":"36309","category_aro_name":"imipenem","category_aro_description":"Imipenem is a broad-spectrum antibiotic and is usually taken with cilastatin, which prevents hydrolysis of imipenem by renal dehydropeptidase-I. It is resistant to hydrolysis by most other beta-lactamases. Notable exceptions are the KPC beta-lactamases and Ambler Class B enzymes.","category_aro_class_name":"Antibiotic"},"36976":{"category_aro_accession":"3000632","category_aro_cvterm_id":"36976","category_aro_name":"benzylpenicillin","category_aro_description":"Benzylpenicillin, commonly referred to as penicillin G, is effective against both Gram-positive and Gram-negative bacteria. It is unstable in acid.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"37084":{"category_aro_accession":"3000704","category_aro_cvterm_id":"37084","category_aro_name":"cefalotin","category_aro_description":"Cefalotin is a semisynthetic cephalosporin antibiotic activate against staphylococci. It is resistant to staphylococci beta-lactamases but hydrolyzed by enterobacterial beta-lactamases.","category_aro_class_name":"Antibiotic"},"40926":{"category_aro_accession":"3003999","category_aro_cvterm_id":"40926","category_aro_name":"cefamandole","category_aro_description":"Cefamandole is a second-generation cephalosporin-class beta-lactam antibiotic.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36383":{"category_aro_accession":"3000244","category_aro_cvterm_id":"36383","category_aro_name":"reduced permeability to antibiotic","category_aro_description":"Reduction in permeability to antibiotic, generally through reduced production of porins, can provide resistance.","category_aro_class_name":"Resistance Mechanism"},"40429":{"category_aro_accession":"3003764","category_aro_cvterm_id":"40429","category_aro_name":"resistance by absence","category_aro_description":"Mechanism of antibiotic resistance conferred by deletion of gene (usually a porin).","category_aro_class_name":"Resistance Mechanism"}}},"2434":{"model_id":"2434","model_name":"Klebsiella pneumoniae OmpK36","model_type":"protein knockout model","model_type_id":"40354","model_description":"Protein Knockout Models (PKM) reflect resistance by the absence of a gene product, most often deletion of a gene involved in antibiotic import, such as Vibrio cholerae OmpT. Like Protein Homolog Models (PHMs), PKMs include a reference sequence and a bitscore cut-off for detection using BLASTP but instead are designed to only report lack of detection under Perfect or Strict criteria. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff. This model type is still under development and not currently supported by the Resistance Gene Identifier (RGI) software.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"650"}},"model_sequences":{"sequence":{"5853":{"protein_sequence":{"accession":"YP_005228001.1","sequence":"MKVKVLSLLVPALLVAGAANAAEIYNKDGNKLDLYGKIDGLHYFSDDKSVDGDQTYMRVGVKGETQINDQLTGYGQWEYNVQANNTESSSDQAWTRLAFAGLKFGDAGSFDYGRNYGVVYDVTSWTDVLPEFGGDTYGSDNFLQSRANGVATYRNSDFFGLVDGLNFALQYQGKNGSVSGEGALSPTNNGRTALKQNGDGYGTSLTYDIYDGISAGFAYSNSKRLGDQNSKLALGRGDNAETYTGGLKYDANNIYLATQYTQTYNATRAGSLGFANKAQNFEVVAQYQFDFGLRPSVAYLQSKGKDLEGYGDQDILKYVDVGATYYFNKNMSTYVDYKINLLDDNSFTHNAGISTDDVVALGLVYQF"},"dna_sequence":{"accession":"NC_016845.1","fmin":"3727881","fmax":"3728985","strand":"-","sequence":"ATGAAAGTTAAAGTACTGTCCCTCCTGGTACCGGCTCTGCTGGTAGCAGGCGCAGCAAATGCGGCTGAAATTTATAACAAAGACGGCAACAAATTAGACCTGTACGGTAAAATTGACGGTCTGCACTACTTCTCTGACGACAAGAGCGTCGACGGCGACCAGACCTACATGCGTGTAGGCGTGAAAGGCGAAACCCAGATCAACGACCAGCTGACCGGTTACGGCCAGTGGGAATACAACGTTCAGGCGAACAACACTGAAAGCTCCAGCGATCAGGCATGGACTCGTCTGGCATTCGCAGGCCTGAAATTTGGCGACGCGGGCTCTTTCGACTACGGTCGTAACTACGGCGTAGTATACGACGTAACGTCCTGGACCGACGTTCTGCCGGAATTCGGCGGCGACACCTACGGTTCTGACAACTTCCTGCAGTCCCGTGCTAACGGCGTTGCAACCTACCGTAACTCTGATTTCTTCGGTCTGGTTGACGGCCTGAACTTTGCTCTGCAGTATCAGGGTAAAAACGGCAGCGTCAGCGGCGAAGGCGCTCTGTCTCCTACCAACAACGGTCGTACCGCCTTGAAACAGAACGGCGACGGTTACGGTACTTCTCTGACCTATGACATCTATGATGGCATCAGCGCTGGTTTCGCATACTCTAACTCCAAACGTCTTGGCGACCAGAACAGCAAGCTGGCACTGGGTCGTGGCGACAACGCTGAAACCTACACCGGCGGTCTGAAATACGACGCGAACAACATCTACCTGGCCACTCAGTACACCCAGACCTACAACGCGACCCGCGCCGGTTCCCTGGGCTTTGCTAACAAAGCGCAGAACTTCGAAGTGGTTGCTCAGTACCAGTTCGACTTCGGTCTGCGTCCGTCCGTGGCTTACCTGCAGTCTAAAGGTAAGGATCTGGAAGGCTACGGCGACCAGGACATCCTGAAATATGTTGACGTTGGCGCGACCTACTACTTCAACAAAAACATGTCCACCTATGTTGACTACAAAATCAACCTGCTGGACGACAATAGCTTCACCCACAACGCCGGTATCTCTACCGACGACGTGGTTGCACTGGGCCTGGTTTACCAGTTCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40663","NCBI_taxonomy_name":"Klebsiella pneumoniae subsp. pneumoniae HS11286","NCBI_taxonomy_id":"1125630"}}}},"ARO_accession":"3003968","ARO_id":"40739","ARO_name":"Klebsiella pneumoniae OmpK36","CARD_short_name":"Kpne_OmpK36","ARO_description":"Klebsiella pneumoniae outer membrane porin protein. In beta-lactam-resistant Klebsiella, this porin is often deleted, limiting diffusion of the antibiotic into the cell. Klebsiella strains expressing OmpK36 are often beta-lactam sensitive even in the presence of beta-lactamases because of an inefficient mechanism.","ARO_category":{"41445":{"category_aro_accession":"3004281","category_aro_cvterm_id":"41445","category_aro_name":"General Bacterial Porin with reduced permeability to beta-lactams","category_aro_description":"These are GBPs that are associated with decreased susceptibility to beta-lactams either through mutations in the porin protein, absence of the porin protein, or expression of the porin protein.","category_aro_class_name":"AMR Gene Family"},"35979":{"category_aro_accession":"0000062","category_aro_cvterm_id":"35979","category_aro_name":"ceftriaxone","category_aro_description":"Ceftriaxone is a third-generation cephalosporin antibiotic. The presence of an aminothiazolyl sidechain increases ceftriazone's resistance to beta-lactamases. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"37084":{"category_aro_accession":"3000704","category_aro_cvterm_id":"37084","category_aro_name":"cefalotin","category_aro_description":"Cefalotin is a semisynthetic cephalosporin antibiotic activate against staphylococci. It is resistant to staphylococci beta-lactamases but hydrolyzed by enterobacterial beta-lactamases.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36383":{"category_aro_accession":"3000244","category_aro_cvterm_id":"36383","category_aro_name":"reduced permeability to antibiotic","category_aro_description":"Reduction in permeability to antibiotic, generally through reduced production of porins, can provide resistance.","category_aro_class_name":"Resistance Mechanism"},"40429":{"category_aro_accession":"3003764","category_aro_cvterm_id":"40429","category_aro_name":"resistance by absence","category_aro_description":"Mechanism of antibiotic resistance conferred by deletion of gene (usually a porin).","category_aro_class_name":"Resistance Mechanism"}}},"3369":{"model_id":"3369","model_name":"FosB1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"281"}},"model_sequences":{"sequence":{"5554":{"protein_sequence":{"accession":"BAE05988.1","sequence":"MIKGINHITYSVSNIAKSIEFYRDILGADILVESETSAYFNLGGIWLALNEEKNIPRSEIKYSYTHIAFTISDNDFEDWYNWLKENEVNILEGRDRDIRDKKSIYFTDLDGHKLELHTGSLEDRLSYYKEAKPHMNFYI"},"dna_sequence":{"accession":"AP006717.1","fmin":"121","fmax":"541","strand":"+","sequence":"ATGATTAAAGGAATAAATCATATTACTTATTCGGTTTCTAATATAGCTAAATCAATTGAATTTTACAGAGATATTTTAGGGGCTGACATTTTAGTTGAAAGTGAGACCTCGGCCTATTTTAATTTAGGTGGTATATGGTTAGCTTTGAACGAAGAAAAAAATATTCCTAGAAGCGAAATTAAATATTCGTATACTCATATAGCATTTACAATTTCAGATAACGATTTTGAAGATTGGTATAACTGGTTGAAAGAAAATGAAGTAAATATTCTTGAAGGTAGAGATAGAGATATTAGAGATAAAAAATCAATATATTTCACTGATTTAGATGGTCATAAATTAGAATTGCATACAGGAAGTTTAGAAGATAGATTGAGTTATTATAAAGAGGCTAAACCTCATATGAATTTTTATATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42718","NCBI_taxonomy_name":"Staphylococcus haemolyticus JCSC1435","NCBI_taxonomy_id":"279808"}}}},"ARO_accession":"3004670","ARO_id":"42717","ARO_name":"FosB1","CARD_short_name":"FosB1","ARO_description":"Subtype of FosB, fosfomycin resistant. S.aureus SA1129 carried a FosB1 identical to S. haemolyticus.","ARO_category":{"36272":{"category_aro_accession":"3000133","category_aro_cvterm_id":"36272","category_aro_name":"fosfomycin thiol transferase","category_aro_description":"Catalyzes the addition of a thiol group from a nucleophilic molecule to fosfomycin.","category_aro_class_name":"AMR Gene Family"},"35944":{"category_aro_accession":"0000025","category_aro_cvterm_id":"35944","category_aro_name":"fosfomycin","category_aro_description":"Fosfomycin (also known as phosphomycin and phosphonomycin) is a broad-spectrum antibiotic produced by certain Streptomyces species. It is effective on gram positive and negative bacteria as it targets the cell wall, an essential feature shared by both bacteria. Its specific target is MurA (MurZ in E.coli), which attaches phosphoenolpyruvate (PEP) to UDP-N-acetylglucosamine, a step of commitment to cell wall synthesis. In the active site of MurA, the active cysteine molecule is alkylated which stops the catalytic reaction.","category_aro_class_name":"Antibiotic"},"45731":{"category_aro_accession":"3007149","category_aro_cvterm_id":"45731","category_aro_name":"phosphonic acid antibiotic","category_aro_description":"A group of antibiotics derived from phosphonic acids.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3370":{"model_id":"3370","model_name":"FosB4","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"270"}},"model_sequences":{"sequence":{"5555":{"protein_sequence":{"accession":"ALM24139.1","sequence":"MIKGINHITYSVSNIAKSIEFYRDILGADILVESETSAYFNLGGIWLALNEEKNIPRSEIKYSYTHIAFTISDNDFEDWYIWLKENEVNILEGRDRDIRDKKSIYFTDLDGHKLELHTGSLEDRLSYYKEAKPHMNFYI"},"dna_sequence":{"accession":"KR870311.1","fmin":"98","fmax":"518","strand":"+","sequence":"ATGATTAAAGGAATAAATCATATTACTTATTCGGTTTCTAATATAGCTAAATCAATTGAATTTTACAGAGATATTTTAGGGGCTGACATTTTAGTTGAAAGTGAGACCTCGGCCTATTTTAATTTAGGTGGTATATGGTTAGCTTTGAACGAAGAAAAAAATATTCCTAGAAGCGAAATTAAATATTCGTATACTCATATAGCATTTACAATTTCAGATAACGATTTTGAAGATTGGTATATCTGGTTGAAAGAAAATGAAGTAAATATTCTTGAAGGTAGAGATAGAGATATTAGAGATAAAAAATCAATATATTTCACTGATTTAGATGGCCATAAATTAGAATTGCATACAGGAAGTTTAGAAGATAGATTGAGTTATTATAAAGAGGCTAAACCTCATATGAATTTTTATATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35508","NCBI_taxonomy_name":"Staphylococcus aureus","NCBI_taxonomy_id":"1280"}}}},"ARO_accession":"3004671","ARO_id":"42719","ARO_name":"FosB4","CARD_short_name":"FosB4","ARO_description":"Fosfomycin resistance gene. Shares a high homology with FosB1 and FosB3.","ARO_category":{"36272":{"category_aro_accession":"3000133","category_aro_cvterm_id":"36272","category_aro_name":"fosfomycin thiol transferase","category_aro_description":"Catalyzes the addition of a thiol group from a nucleophilic molecule to fosfomycin.","category_aro_class_name":"AMR Gene Family"},"35944":{"category_aro_accession":"0000025","category_aro_cvterm_id":"35944","category_aro_name":"fosfomycin","category_aro_description":"Fosfomycin (also known as phosphomycin and phosphonomycin) is a broad-spectrum antibiotic produced by certain Streptomyces species. It is effective on gram positive and negative bacteria as it targets the cell wall, an essential feature shared by both bacteria. Its specific target is MurA (MurZ in E.coli), which attaches phosphoenolpyruvate (PEP) to UDP-N-acetylglucosamine, a step of commitment to cell wall synthesis. In the active site of MurA, the active cysteine molecule is alkylated which stops the catalytic reaction.","category_aro_class_name":"Antibiotic"},"45731":{"category_aro_accession":"3007149","category_aro_cvterm_id":"45731","category_aro_name":"phosphonic acid antibiotic","category_aro_description":"A group of antibiotics derived from phosphonic acids.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3327":{"model_id":"3327","model_name":"AAC(2')-IIa","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"5361":{"protein_sequence":{"accession":"BAM16262.1","sequence":"MKDRSHDDSMAEVCRNTSENHWLKTDYRTLFRLCPDGRIERENDPDCSPGPRFWLAGCSEGNVFGVRADVPDDIALKLEELASVEPPFTPPAIPKHLERYLSLLGSDGPVTHDLGLIYELPHAQQYPSKARLIGSGSEEGESLMQSWAEDRVPEALFELGFREVADFWTPWCAAVVDGEVASIAFAARLADAGAELGLVTAKAFRGQGFAAAATAGWSRLSALRSRTLFYSTDRDNISSQRVAARLGLRLRGASLRISRA"},"dna_sequence":{"accession":"AB669090.1","fmin":"12438","fmax":"13221","strand":"+","sequence":"ATGAAAGACAGATCCCATGACGACTCAATGGCCGAGGTCTGTCGGAACACCTCTGAGAACCACTGGCTGAAGACCGATTATCGGACGTTGTTTCGGCTGTGCCCCGACGGTCGGATCGAGCGCGAGAATGATCCGGACTGCTCGCCGGGGCCGCGTTTCTGGTTGGCTGGCTGTTCGGAAGGCAACGTGTTCGGCGTACGTGCCGATGTGCCCGATGACATAGCACTAAAGCTCGAAGAACTCGCCAGCGTCGAGCCTCCGTTCACACCCCCGGCGATACCGAAGCATCTTGAACGTTATCTTTCACTGCTCGGCAGTGATGGCCCTGTTACCCACGATCTTGGTCTGATTTACGAGTTGCCGCACGCGCAGCAGTACCCGAGCAAGGCCCGGCTCATCGGCAGCGGTTCCGAGGAGGGCGAGAGTCTGATGCAGTCTTGGGCGGAGGACAGAGTACCGGAAGCTTTGTTTGAGCTTGGCTTCCGTGAGGTGGCGGACTTCTGGACGCCTTGGTGCGCGGCAGTTGTCGATGGTGAAGTCGCTTCAATCGCCTTTGCAGCGCGTCTCGCGGATGCCGGTGCCGAACTCGGGTTGGTAACGGCGAAGGCATTCAGAGGACAGGGGTTCGCCGCCGCTGCGACGGCTGGTTGGTCCCGGCTCTCCGCTCTTCGTTCCCGCACGCTGTTCTACAGCACGGACCGAGACAACATTTCATCGCAGCGCGTTGCCGCCCGCCTTGGTCTCCGGCTTCGTGGAGCCAGCTTGCGAATATCACGCGCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42614","NCBI_taxonomy_name":"Burkholderia glumae","NCBI_taxonomy_id":"337"}}}},"ARO_accession":"3004628","ARO_id":"42613","ARO_name":"AAC(2')-IIa","CARD_short_name":"AAC(2')-IIa","ARO_description":"AAC(2')-IIa is a kasugamycin 2' N-acetyltransferase protein found in Burkholderia glumae and Acidovorax avenae isolates.","ARO_category":{"36480":{"category_aro_accession":"3000341","category_aro_cvterm_id":"36480","category_aro_name":"AAC(2')","category_aro_description":"A category of aminoglycoside N-acetyltransferase enzymes with modification regiospecificity based at the 2'-amino group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics through acetylation of the 2-amino group of the compound.","category_aro_class_name":"AMR Gene Family"},"37695":{"category_aro_accession":"3001296","category_aro_cvterm_id":"37695","category_aro_name":"kasugamycin","category_aro_description":"An unusual aminoglycoside because the cyclitol ring is not amino substituted; it was discovered as a fermentation product of Streptomyces kasugaensis.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3356":{"model_id":"3356","model_name":"OXA-296","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"460"}},"model_sequences":{"sequence":{"5536":{"protein_sequence":{"accession":"ENU21024.1","sequence":"MQQRLFYFGCLLLLTQLSACHMNRAQTSNQSVQKAVLQAPSERPEEIKQLFNSAHTSAVFITYDGRQFNRYGNALARAQNAYIPASTFKILNALIGLQHHKVSTSEVFKWKGEKRSFPAWEKDMNLAQAMQLSAVPVYQQLARRIGLELMQKEISRLGFGNQKIGQQVDNFWLVGPLKITPEQEAQFVYQLATEQLPFDVKVQKQVKEMLYIERRGDTKLYAKSGWGMDVKPQVGWYTGWVEQANGQITAFVLNLEMHDGDDVGERKQLTLDALDKLGLFFYLH"},"dna_sequence":{"accession":"APOH01000009.1","fmin":"220588","fmax":"221443","strand":"-","sequence":"ATGCAACAGCGGTTATTTTACTTTGGCTGTTTATTGCTCTTAACGCAATTAAGTGCTTGCCACATGAACAGGGCGCAGACGTCTAATCAATCCGTGCAAAAAGCTGTTTTGCAGGCACCCTCTGAACGCCCAGAAGAGATTAAGCAATTGTTTAATTCTGCACACACATCAGCCGTTTTTATCACCTATGACGGTCGGCAGTTTAATCGTTATGGTAATGCTTTGGCTCGTGCCCAAAATGCCTATATTCCAGCTTCAACGTTTAAAATATTAAATGCATTGATTGGTCTTCAGCATCATAAAGTCAGTACGTCTGAAGTGTTTAAATGGAAGGGTGAAAAGCGTTCATTTCCTGCGTGGGAAAAAGATATGAACTTGGCGCAAGCCATGCAGCTTTCAGCCGTTCCAGTGTATCAGCAGCTTGCTCGACGTATAGGCTTAGAACTCATGCAGAAAGAAATTTCTCGGCTTGGTTTTGGCAATCAAAAGATTGGTCAACAGGTGGATAATTTTTGGTTGGTTGGCCCTTTAAAAATAACCCCAGAACAAGAAGCACAATTTGTCTATCAACTGGCAACAGAGCAATTACCTTTTGATGTAAAAGTACAAAAACAGGTCAAAGAGATGCTTTATATTGAGCGTCGTGGTGATACAAAATTATATGCAAAAAGTGGTTGGGGAATGGATGTTAAGCCTCAAGTGGGGTGGTATACAGGGTGGGTTGAACAAGCAAATGGACAGATCACCGCTTTTGTTTTAAATTTGGAAATGCATGATGGCGATGATGTGGGCGAACGTAAGCAGCTCACTTTGGATGCATTGGATAAGCTGGGATTATTCTTTTATTTACACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42695","NCBI_taxonomy_name":"Acinetobacter bohemicus ANC 3994","NCBI_taxonomy_id":"1217715"}}}},"ARO_accession":"3001751","ARO_id":"38151","ARO_name":"OXA-296","CARD_short_name":"OXA-296","ARO_description":"OXA-296 is a beta-lactamase found in Acinetobacter spp.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3269":{"model_id":"3269","model_name":"Clostridioides difficile rpoB with mutation conferring resistance to rifampicin","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"2500"},"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"8677":"R505K","8678":"H502N","8679":"S488P","8680":"S498T","8827":"H502L","8828":"H502Y","8830":"D492N","8831":"D492V","8832":"S550F","8833":"S550Y","8840":"Q1073R","8842":"P496S","8848":"S488T"},"Curated-R":{"8677":"R505K","8678":"H502N","8679":"S488P","8680":"S498T","8827":"H502L","8828":"H502Y","8829":"H502Y","8830":"D492N","8831":"D492V","8832":"S550F","8833":"S550Y","8840":"Q1073R","8842":"P496S","8848":"S488T","8826":"S488T"},"clinical":{"8677":"R505K","8678":"H502N","8679":"S488P","8680":"S498T","8827":"H502L","8828":"H502Y","8830":"D492N","8831":"D492V","8832":"S550F","8833":"S550Y","8840":"Q1073R","8842":"P496S","8848":"S488T"}},"40330":{"param_type":"multiple resistance variants","param_description":"A set of nucleotide or amino acid substitutions that are all required to confer resistance to an antibiotic drug or drug class, encoded as: [wild-type 1][position 1][mutation 1],[wild-type 2][position 2][mutation 2], etc. For example, D63Y,T142K.","param_type_id":"40330","param_value":{"8829":"L487F,H502Y","8826":"I548M,R505K"}}},"model_sequences":{"sequence":{"5315":{"protein_sequence":{"accession":"ADK17136.1","sequence":"MVHPVQVGKRTRMSFSRLKEIGHMPNLIEVQLDSYNWFLKEGLQEVFDDINPIQDYTANLNLEFVGYKLDMDNIKYSVEECKERDATYAAPLKVKVRLINKETGEVKEQEVFMGDFPLMTEQGTFIINGAERVIVSQLVRSPGVYYDLSVDKTGKNLFSSTVIPNRGAWLEYETDSNNVIYVRIDKTRKLPITILIRAMGYGTDAEITNFFGEDERLKATIEKDNTKTHEEALLEIYKRLRPGEPPTVDSAQSLIESLFFDAKRYDLSRVGRYKFNKKLSLHLRIANQIAAQDVVNPDTGEILIQKGEKINREKAVEIQQCGINVVDIQIEDIVLRVIGNNFVDIRSFIDFDIDDLNIKESVHYPTLKKILDNYSDEESIKEQIRKNIHELIPKHIVRDDMYATISYELGLAYGVGHTDDIDHLGNRRLRSVGELLQNQFRIGLSRMERVVKERMTIQDQEVITPQALINIRPVAASIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLSRERAGFEVRDVHHSHYGRMCPIETPEGPNIGLINSLATYARVNQYGFIETPYRKVDKENKRVTNEIVYMTADEEDEYLIGRANEPIDENGNFIDNKITVRDKEDVIVVPGQDVDYMDVSSRQLVSVATAMIPFLENDDASRALMGSNMQRQAVPLLKPQAPIVGTGIEYKAAVDSGVLPKARNAGVVSYVCANEVRVKRDSDGGTDIYRLLKFQRSNQCTCINQRPIVEKGEVVKKGTVLADGPSTDLGEIALGKNIRMGFTTWEGYNYEDAMLISEELVKKDVFTSIHLEEYESEARDTKLGPEEITRDIPNVGEDALKDIDERGIIRIGAEVRAGDILVGKVTPKGETELTAEERLLRAIFGEKAREVRDTSLRVPHGEAGIIVDVKVFTRENGDELSPGVNKLVRCYIAQKRKISVGDKMAGRHGNKGVISRVLPEEDMPFLPDGRPLQICLNPLGVPSRMNIGQVLEVHLGWAASKLGWHVATPVFDGATEEDILECLKKAGYREDGKTILYDGRTGEEFNRPVTVGYMYILKLAHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAHTLQEILTVKSDDVVGRVKTYEAIVKGENIPEPGIPESFKVLIKELQALCLDVKVLNDNKEEIKLKESVDEEMEKLDVNIEGKEDSTDLPQEQNDDYNTEQEENNDSENDSDEDLDLDYEDLTLDDLQSDLEIDDFNDEH"},"dna_sequence":{"accession":"CP001666.1","fmin":"4454798","fmax":"4458527","strand":"-","sequence":"ATGGTACATCCTGTCCAGGTTGGTAAAAGAACAAGAATGAGCTTTTCCAGACTTAAAGAAATAGGCCACATGCCTAATTTAATTGAGGTTCAGCTAGATTCCTACAATTGGTTTTTGAAAGAAGGATTACAAGAGGTATTTGATGATATTAATCCTATTCAAGATTATACTGCTAACCTTAATTTGGAATTTGTAGGATATAAGTTAGATATGGATAATATCAAATATTCTGTAGAGGAATGTAAAGAAAGAGATGCAACTTACGCAGCACCTTTAAAAGTAAAAGTAAGGCTAATTAACAAAGAAACTGGTGAAGTTAAAGAGCAAGAAGTTTTTATGGGAGATTTCCCTCTTATGACGGAGCAAGGAACCTTTATAATTAATGGTGCAGAGAGAGTTATAGTTAGCCAACTTGTAAGATCACCAGGTGTATATTATGATCTTTCAGTTGATAAAACAGGAAAAAATCTTTTTTCTTCAACTGTAATACCTAATAGAGGAGCTTGGCTAGAATATGAAACTGACTCTAACAATGTAATATACGTTAGAATAGATAAAACTAGAAAGTTACCCATAACTATTCTTATTAGAGCCATGGGTTATGGTACAGACGCAGAAATTACTAATTTCTTTGGAGAGGATGAAAGGCTAAAAGCCACAATTGAAAAAGATAATACAAAGACTCATGAAGAGGCTTTGCTTGAAATATATAAAAGGTTACGACCGGGAGAACCTCCTACAGTGGATAGTGCCCAATCACTAATTGAATCTTTATTTTTTGATGCGAAAAGATATGATCTTTCAAGAGTTGGAAGATACAAATTCAATAAGAAGTTATCATTACACCTAAGAATTGCTAATCAGATAGCAGCACAGGATGTAGTTAATCCAGATACAGGAGAAATTCTTATCCAAAAAGGTGAAAAGATAAATAGAGAAAAGGCAGTAGAAATCCAACAGTGTGGAATAAATGTAGTAGATATCCAAATTGAAGATATAGTTTTAAGAGTTATAGGTAATAACTTTGTAGACATACGTAGTTTTATTGACTTTGATATAGATGATTTAAATATAAAAGAAAGTGTTCATTATCCCACTTTAAAGAAAATTTTAGATAATTATAGTGATGAGGAAAGTATTAAGGAACAAATAAGAAAGAACATCCATGAATTAATTCCAAAACATATAGTTAGAGATGATATGTATGCTACCATTAGCTATGAGTTGGGATTAGCATATGGAGTAGGTCATACTGATGACATAGACCATCTTGGAAATAGAAGACTTAGATCTGTTGGTGAATTACTTCAAAATCAATTTAGAATAGGTCTCTCAAGAATGGAGAGAGTGGTTAAGGAAAGAATGACCATACAGGATCAGGAAGTTATAACACCTCAAGCTCTTATAAATATAAGACCAGTAGCTGCGTCTATAAAAGAGTTTTTTGGAAGTTCTCAACTTTCTCAATTCATGGATCAAACTAATCCATTGTCAGAGCTTACCCATAAGAGGAGACTATCTGCTTTAGGACCAGGCGGACTTTCAAGAGAAAGAGCTGGATTTGAAGTCAGGGATGTTCATCACTCACATTATGGAAGAATGTGTCCAATAGAGACGCCAGAAGGACCTAACATAGGACTTATTAACTCTCTAGCTACATATGCAAGAGTTAATCAATATGGCTTTATAGAAACGCCTTATAGAAAAGTAGATAAAGAAAATAAGAGAGTTACAAATGAAATTGTATATATGACAGCAGACGAGGAAGATGAATATTTAATAGGTAGGGCAAACGAGCCTATTGATGAAAATGGTAATTTTATAGATAATAAAATTACAGTTAGAGATAAAGAAGATGTTATTGTAGTACCTGGTCAAGACGTTGATTATATGGATGTGTCTTCAAGGCAATTAGTTTCTGTAGCTACAGCTATGATACCATTCCTTGAAAATGATGATGCCAGCCGTGCACTTATGGGATCAAATATGCAAAGGCAGGCAGTTCCACTTTTGAAACCACAAGCACCTATTGTAGGAACAGGTATTGAATACAAGGCTGCAGTAGATTCAGGAGTACTTCCTAAAGCTAGAAATGCAGGCGTTGTCTCTTATGTATGTGCTAACGAAGTAAGGGTTAAGAGAGACTCAGATGGAGGAACAGATATTTATAGACTTCTTAAGTTCCAGAGATCTAACCAATGCACATGCATCAATCAAAGACCTATAGTTGAAAAAGGGGAAGTAGTTAAAAAGGGAACAGTTTTAGCAGATGGACCTTCTACAGATCTTGGAGAAATAGCACTTGGAAAAAATATTAGAATGGGATTTACAACTTGGGAAGGATATAATTATGAAGACGCAATGCTTATATCTGAAGAGTTAGTAAAAAAAGATGTATTTACATCAATACATCTAGAGGAATACGAATCTGAGGCTAGAGATACAAAATTAGGACCAGAGGAAATTACAAGAGATATACCAAATGTAGGAGAAGATGCATTAAAGGATATAGATGAAAGAGGAATTATAAGAATAGGTGCAGAAGTTAGAGCAGGAGATATATTAGTAGGTAAAGTAACACCTAAGGGGGAAACTGAACTTACAGCAGAAGAAAGGCTTTTAAGAGCAATATTTGGCGAAAAGGCCAGAGAAGTTAGAGATACGTCCCTTAGAGTACCACATGGTGAAGCGGGCATAATTGTAGATGTAAAAGTATTTACAAGAGAAAATGGAGATGAGCTTTCACCAGGAGTTAACAAATTAGTTAGATGTTATATAGCTCAGAAGAGAAAGATATCTGTAGGAGATAAAATGGCAGGAAGACACGGAAATAAAGGTGTTATTTCTAGAGTACTACCAGAGGAAGATATGCCTTTCCTACCAGATGGAAGACCTCTTCAGATATGCTTAAATCCACTTGGTGTACCTTCACGTATGAATATAGGTCAGGTATTAGAAGTTCATTTAGGATGGGCTGCCAGTAAATTAGGATGGCATGTAGCGACTCCAGTATTTGATGGAGCCACAGAAGAAGATATATTGGAATGCTTGAAAAAAGCAGGGTATAGAGAAGACGGAAAAACAATACTATATGATGGTAGAACAGGAGAAGAATTTAATAGGCCTGTAACTGTAGGATATATGTATATCTTAAAATTAGCACATTTGGTTGACGATAAGATCCATGCAAGATCTACAGGACCATATTCGTTAGTAACTCAACAGCCATTGGGTGGTAAAGCTCAATTTGGTGGCCAAAGATTTGGTGAAATGGAAGTTTGGGCATTAGAGGCATATGGAGCAGCTCATACACTTCAGGAAATATTGACAGTTAAGTCAGACGATGTAGTTGGAAGAGTTAAAACTTATGAAGCTATTGTAAAAGGTGAAAATATACCAGAACCGGGAATTCCAGAATCATTTAAGGTTCTGATAAAGGAACTTCAAGCTTTATGCTTGGATGTAAAAGTATTAAATGATAATAAAGAGGAAATCAAACTTAAAGAGTCTGTGGACGAAGAGATGGAAAAACTAGATGTAAATATTGAAGGAAAAGAAGATTCTACTGATTTACCTCAAGAACAAAATGATGACTATAATACTGAGCAAGAAGAAAACAATGATAGTGAAAATGACAGCGATGAAGATCTTGATTTAGATTATGAAGATCTTACTTTAGATGATTTGCAGAGTGATTTAGAAATAGATGATTTTAATGATGAACATTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42599","NCBI_taxonomy_name":"Clostridium ljungdahlii DSM 13528","NCBI_taxonomy_id":"748727"}}}},"ARO_accession":"3004563","ARO_id":"42470","ARO_name":"Clostridioides difficile rpoB with mutation conferring resistance to rifampicin","CARD_short_name":"Cdif_rpoB_RIF","ARO_description":"Point mutations in the rpoB region of Clostridioides difficile which confer resistance to rifampin and rifampicin antibiotics.","ARO_category":{"36349":{"category_aro_accession":"3000210","category_aro_cvterm_id":"36349","category_aro_name":"rifamycin-resistant beta-subunit of RNA polymerase (rpoB)","category_aro_description":"Rifampin resistant RNA polymerases include amino acids substitutions which disrupt the affinity of rifampin for its binding site. These mutations are frequently concentrated in the rif I region of the beta-subunit and most often involve amino acids which make direct interactions with rifampin. However, mutations which also confer resistance can occur outside this region and may involve amino acids which do not directly make contact with rifampin.","category_aro_class_name":"AMR Gene Family"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36656":{"category_aro_accession":"3000517","category_aro_cvterm_id":"36656","category_aro_name":"rifaximin","category_aro_description":"Rifaximin is a semi-synthetic rifamycin used to treat traveller's diarrhea. Rifaximin inhibits RNA synthesis by binding to the beta subunit of bacterial RNA polymerase.","category_aro_class_name":"Antibiotic"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3368":{"model_id":"3368","model_name":"emtA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"8348":{"protein_sequence":{"accession":"AAL02176.1","sequence":"MTLYFASVLSGLEYVLSNEINNKVSDSEIIQINRGKVFFTTAESFTCLSSLRSADHLFQVIDQFQIGPHKKHLSQVSERISQLDLEFIDHKDLFWVNASRKGKQTYSRFELAKKAMEGINKRYPDWNIGTSQNHQIEFRLDIEHHNVIFSLRLTDATFRFRNQTRRFSRASLLPSVAHAMVWLSDPESKDVFVDFCCGSGTILSERATYPANQIIGGDISEAVTKIAKSNLDDSKVQVNVWDARKLPFSTGCVDKIVTNLPFGRQISPDEDLELFNHHIMIEVCRVLKPNGRAVILSESVNQLFWEAKRLGLFCLESYPLSLKGVNPTLFVFEKQDGLRRK"},"dna_sequence":{"accession":"AF403298.1","fmin":"659","fmax":"1685","strand":"+","sequence":"ATGACTCTTTATTTTGCGAGCGTATTGTCTGGATTAGAATACGTTTTATCAAATGAAATTAACAACAAGGTGAGTGATTCTGAAATAATTCAAATAAATAGAGGGAAGGTTTTCTTTACCACAGCTGAGTCTTTTACATGCTTAAGTTCTTTAAGGTCAGCAGATCACTTGTTTCAAGTTATTGATCAATTTCAAATCGGTCCACATAAAAAGCACTTATCTCAGGTAAGCGAGCGAATATCCCAGTTGGATTTAGAATTTATTGATCATAAAGATTTATTTTGGGTAAATGCAAGCCGTAAAGGAAAACAAACCTATAGTCGCTTTGAATTAGCAAAAAAAGCAATGGAGGGTATTAATAAGCGTTACCCTGATTGGAACATTGGAACGTCTCAAAATCATCAGATAGAATTCAGACTCGACATTGAACATCATAATGTGATTTTTTCACTTCGGCTTACAGATGCGACGTTTCGTTTTCGAAATCAGACACGACGGTTCTCTCGTGCATCATTACTTCCTTCTGTGGCTCATGCGATGGTGTGGTTGTCAGATCCTGAATCGAAAGATGTTTTCGTAGACTTTTGTTGTGGTTCAGGCACAATTTTGTCTGAACGAGCCACATACCCTGCAAATCAGATAATTGGTGGAGATATATCTGAAGCAGTCACAAAGATAGCCAAAAGTAATCTCGATGATTCGAAGGTGCAAGTTAATGTTTGGGATGCACGGAAATTGCCTTTTTCTACTGGCTGTGTCGATAAAATTGTTACTAATCTTCCATTTGGAAGACAAATTTCCCCTGACGAGGACTTAGAATTGTTCAATCACCATATTATGATTGAAGTATGTAGAGTCTTGAAGCCAAATGGGAGAGCCGTTATTTTGTCTGAGAGTGTCAATCAATTGTTTTGGGAAGCAAAACGATTAGGCCTTTTTTGTCTGGAATCTTATCCTTTGAGTTTGAAGGGCGTGAATCCTACCTTGTTTGTGTTTGAAAAACAAGATGGACTTAGAAGGAAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36779","NCBI_taxonomy_name":"Enterococcus faecium","NCBI_taxonomy_id":"1352"}}}},"ARO_accession":"3004669","ARO_id":"42716","ARO_name":"emtA","CARD_short_name":"emtA","ARO_description":"A rRNA methyltransferase conferring high-level evernimicin resistance.","ARO_category":{"37697":{"category_aro_accession":"3001298","category_aro_cvterm_id":"37697","category_aro_name":"non-erm 23S ribosomal RNA methyltransferase (G748)","category_aro_description":"Non-erm 23S ribosomal RNA methyltransferases modify guanosine 748 (E. coli numbering) to confer resistance to some macrolides and lincosamides.","category_aro_class_name":"AMR Gene Family"},"45749":{"category_aro_accession":"3007167","category_aro_cvterm_id":"45749","category_aro_name":"evernimicin","category_aro_description":"Evernimicin is a veterinary oligosaccharide antibiotic of the orthosomycin group of orthoester antibiotics. Along with avilamycin, it exhibits activity against a variety of Gram-positive and -negative bacteria and is primarily used in livestock feed.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"45748":{"category_aro_accession":"3007166","category_aro_cvterm_id":"45748","category_aro_name":"orthosomycin antibiotic","category_aro_description":"Orthosomycins are a group of experimental\/veterinary orthoester and oligosaccharide antibiotics that target the 70s ribosomal subunit. They are generally no longer considered potential clinical antibiotics, but continue to be used in livestock feed and for experimental purposes.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3371":{"model_id":"3371","model_name":"FosB5","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"265"}},"model_sequences":{"sequence":{"5556":{"protein_sequence":{"accession":"ALN12426.1","sequence":"MIKGINHITYSVSNIAKSIEFYRDILEADILVESETSAYFNLGGIWLALNEEKNIPRSEIKYSYTHIAFTISDNDFEDWYNWLKENEVNILEGRDRDIRDKKSIYFTDLDGHKLELHTGSLEDRLSYYKEAKPHMNFYI"},"dna_sequence":{"accession":"KT032253.1","fmin":"2339","fmax":"2759","strand":"+","sequence":"ATGATTAAAGGAATAAATCATATTACTTATTCGGTTTCTAATATAGCTAAATCAATTGAATTTTACAGAGATATTTTAGAGGCTGACATTTTAGTTGAAAGTGAGACCTCGGCCTATTTTAATTTAGGTGGTATATGGTTAGCTTTGAACGAAGAAAAAAATATTCCTAGAAGCGAAATTAAATATTCGTATACTCATATAGCATTTACAATTTCAGATAACGATTTTGAAGATTGGTATAACTGGTTGAAAGAAAATGAAGTAAATATTCTTGAAGGTAGAGATAGAGATATTAGAGATAAAAAATCAATATATTTCACTGATTTAGATGGTCATAAATTAGAATTGCATACAGGAAGTTTAGAAGATAGATTGAGTTATTATAAAGAGGCTAAACCTCATATGAATTTTTATATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35508","NCBI_taxonomy_name":"Staphylococcus aureus","NCBI_taxonomy_id":"1280"}}}},"ARO_accession":"3004672","ARO_id":"42720","ARO_name":"FosB5","CARD_short_name":"FosB5","ARO_description":"Fosfomycin resistance gene. High homology with FosB1 and FosB3.","ARO_category":{"36272":{"category_aro_accession":"3000133","category_aro_cvterm_id":"36272","category_aro_name":"fosfomycin thiol transferase","category_aro_description":"Catalyzes the addition of a thiol group from a nucleophilic molecule to fosfomycin.","category_aro_class_name":"AMR Gene Family"},"35944":{"category_aro_accession":"0000025","category_aro_cvterm_id":"35944","category_aro_name":"fosfomycin","category_aro_description":"Fosfomycin (also known as phosphomycin and phosphonomycin) is a broad-spectrum antibiotic produced by certain Streptomyces species. It is effective on gram positive and negative bacteria as it targets the cell wall, an essential feature shared by both bacteria. Its specific target is MurA (MurZ in E.coli), which attaches phosphoenolpyruvate (PEP) to UDP-N-acetylglucosamine, a step of commitment to cell wall synthesis. In the active site of MurA, the active cysteine molecule is alkylated which stops the catalytic reaction.","category_aro_class_name":"Antibiotic"},"45731":{"category_aro_accession":"3007149","category_aro_cvterm_id":"45731","category_aro_name":"phosphonic acid antibiotic","category_aro_description":"A group of antibiotics derived from phosphonic acids.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3374":{"model_id":"3374","model_name":"aphA15","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"5559":{"protein_sequence":{"accession":"CAD91341.1","sequence":"MTVALDEVSELKNLLSPLLDECTFEEVEYGQSDARVIRVLFPDRNTAYLKYASGSSAQEILQEHQRTRWLRTRALVPEVISYVSTSTVTILLTKALIGHNAADAADADPVIVVAEMARALRDLHSISPDDCPFDERLHLRLKLASGRLEAGLVDEEDFDHARQGMLARDVYEQLFIQMPGAEQLVVTHGDACPENFIFQGNAFVGFIDCGRVGLADKYQDLALASRNIDAVFGPELTNQFFIEYGEPNPNIAKIEYYRILDEFF"},"dna_sequence":{"accession":"Y18050.2","fmin":"4757","fmax":"5552","strand":"+","sequence":"ATGACAGTCGCCCTCGACGAAGTATCTGAACTAAAGAATTTGCTTTCACCCTTGTTGGATGAATGCACTTTTGAAGAAGTTGAGTATGGTCAGTCAGATGCTCGAGTGATTCGAGTTCTATTTCCTGATCGCAATACCGCGTATCTAAAGTACGCCTCCGGATCTTCTGCTCAAGAAATTCTTCAAGAGCATCAGCGCACTAGATGGCTCAGAACACGAGCTCTCGTACCGGAAGTGATCTCATATGTCTCGACTTCAACTGTCACCATCCTGTTGACAAAAGCATTGATTGGCCACAATGCCGCTGACGCCGCAGATGCAGATCCAGTTATTGTTGTTGCAGAGATGGCACGAGCGTTACGCGACCTCCATTCGATCTCGCCTGACGATTGCCCATTCGACGAAAGGCTCCACCTGCGACTGAAGCTGGCTTCGGGCCGTTTGGAAGCCGGGTTAGTTGATGAGGAGGACTTTGATCACGCAAGGCAAGGCATGCTGGCGCGGGATGTTTACGAGCAACTTTTTATACAAATGCCTGGAGCGGAGCAGCTGGTAGTCACACATGGCGACGCCTGTCCCGAGAACTTCATCTTCCAAGGTAATGCCTTCGTCGGCTTCATAGACTGCGGTCGGGTCGGGCTTGCCGATAAGTATCAAGACCTGGCGCTTGCATCGAGAAACATTGACGCGGTATTTGGACCAGAACTCACTAACCAGTTCTTCATCGAGTATGGAGAGCCAAATCCGAACATAGCTAAGATTGAGTACTACCGGATCTTGGATGAGTTCTTCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3004675","ARO_id":"42723","ARO_name":"aphA15","CARD_short_name":"aphA15","ARO_description":"Expression of cloned aphA15 gene in Escherichia coli reduced the susceptibility to kanamycin and neomycin, as well as to amikacin, netilmicin, and streptomycin.","ARO_category":{"36265":{"category_aro_accession":"3000126","category_aro_cvterm_id":"36265","category_aro_name":"APH(3')","category_aro_description":"A category of aminoglycoside O-phosphotransferase enzymes with modification regiospecificity based at the 3'-hydroxyl group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics, specifically kanamycin and neomycin, by the ATP-dependent phosphorylation of the 3'-hydroxyl group of the compound.","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3455":{"model_id":"3455","model_name":"OXA-292","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"530"}},"model_sequences":{"sequence":{"5650":{"protein_sequence":{"accession":"ENX53612.1","sequence":"MSKKLKMLTLSISMMLGLPLMACQSFSQQKQQIMTQESEQQQIASLFQNAQTSGVLVIYDGKKIQKFGNDVHRADQRYIPASTFKMLNALIGIQHHKTTPKEVFKWDGQKRAFSSWEKDLTLAEAMQASAVPVYQELARRIGLELMTREVKRVGYGNKNIGTQVDNFWLVGPLKITPVEEVRFAYALAKQKLPFDQSTQQQVKGMLLIDEVQGTKIYAKSGWGMDVSPQVGWWTGWIEQANGKVTAFSLNMEMSRPEHAEARKAIVYQALQQLDLLAN"},"dna_sequence":{"accession":"APRO01000007.1","fmin":"299938","fmax":"300775","strand":"-","sequence":"ATGTCGAAAAAACTAAAAATGCTCACTTTATCTATTTCAATGATGCTGGGCTTACCCTTGATGGCTTGCCAGAGCTTTAGTCAACAAAAGCAGCAAATAATGACACAGGAAAGTGAACAACAGCAGATTGCGAGTTTATTCCAAAATGCTCAAACCAGCGGTGTTTTGGTCATTTATGATGGAAAGAAAATTCAAAAATTTGGCAATGATGTACATCGTGCAGATCAGCGCTATATCCCAGCTTCGACCTTTAAAATGCTGAATGCGTTAATTGGCATACAGCATCATAAAACTACGCCAAAAGAAGTCTTTAAATGGGATGGACAGAAACGCGCATTCAGTAGTTGGGAAAAAGATCTCACATTAGCTGAGGCAATGCAGGCATCGGCTGTGCCTGTGTATCAAGAGCTGGCACGACGTATTGGTCTGGAACTGATGACTCGGGAAGTGAAGCGAGTGGGCTATGGCAATAAGAATATAGGGACACAAGTCGATAATTTTTGGTTAGTAGGCCCATTAAAAATTACGCCTGTAGAGGAAGTACGCTTTGCCTACGCATTGGCGAAGCAAAAGCTGCCATTTGATCAGTCAACTCAGCAACAAGTAAAAGGCATGTTATTGATTGATGAGGTTCAAGGCACCAAGATCTACGCTAAAAGTGGTTGGGGTATGGATGTTAGCCCGCAAGTGGGATGGTGGACAGGTTGGATAGAGCAAGCAAATGGCAAGGTCACCGCATTTTCATTAAATATGGAAATGAGTCGACCTGAGCATGCGGAGGCACGGAAGGCGATTGTTTATCAAGCTTTGCAGCAACTGGATTTATTGGCGAATTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42815","NCBI_taxonomy_name":"Acinetobacter sp. NIPH 1867","NCBI_taxonomy_id":"1217702"}}}},"ARO_accession":"3001747","ARO_id":"38147","ARO_name":"OXA-292","CARD_short_name":"OXA-292","ARO_description":"OXA-292 is a beta-lactamase found in Acinetobacter spp.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46503":{"category_aro_accession":"3007714","category_aro_cvterm_id":"46503","category_aro_name":"OXA-286-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-286.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3483":{"model_id":"3483","model_name":"OXA-373","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"5677":{"protein_sequence":{"accession":"CDM87362.1","sequence":"MKTLQLALIALITTFGSACTTISPSVETAKNHQQQSAQQQIQQAFDQLQTTGVIVIKDKHGLRSYGNDLSRAQTAYVPASTFKMLNALIGLEHGKATSTEVFKWDGQKRSFPAWEKDMTLGQAMQASAVPVYQELARRIGLDLMQKEVQRIGYGNQQIGTVVDNFWLVGPLQITPVQEVLFVEKLANTQLAFKPDVQHTVQDMLLIEQKPNYKLYAKSGWGMDLEPQVGWWTGWVETATGEKVYFALNMHMKTGISASVREQLVKQSLTALGII"},"dna_sequence":{"accession":"HG931732.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAAAACTTTACAGTTGGCTCTCATCGCCCTCATTACAACCTTCGGTTCTGCATGTACCACAATAAGCCCCTCAGTAGAAACAGCTAAAAATCACCAGCAACAAAGCGCGCAGCAGCAGATCCAACAGGCCTTCGATCAACTCCAAACCACTGGGGTGATTGTCATTAAGGATAAGCATGGCTTACGCAGCTACGGCAATGACTTGAGCCGTGCTCAGACAGCCTATGTACCCGCCTCTACCTTTAAAATGCTGAATGCCTTAATCGGACTAGAACATGGTAAAGCAACCAGCACTGAGGTGTTTAAATGGGATGGTCAAAAGCGTAGTTTCCCTGCCTGGGAAAAAGACATGACTTTAGGGCAAGCCATGCAAGCATCTGCTGTTCCCGTTTATCAGGAGCTTGCACGGCGCATTGGTCTAGACCTGATGCAAAAAGAAGTACAGCGCATTGGATATGGCAATCAACAGATTGGCACCGTTGTCGATAATTTTTGGTTAGTCGGTCCACTGCAAATTACGCCTGTGCAAGAAGTCCTTTTTGTAGAGAAGCTGGCCAATACGCAACTCGCTTTTAAGCCAGATGTGCAACATACCGTACAAGACATGCTGCTGATTGAACAAAAACCGAATTATAAACTCTACGCCAAATCTGGTTGGGGCATGGACCTAGAACCGCAAGTGGGCTGGTGGACAGGCTGGGTCGAAACAGCAACAGGTGAAAAAGTGTATTTTGCTTTGAATATGCATATGAAAACAGGAATTTCAGCCAGCGTGCGTGAGCAACTGGTCAAACAAAGTCTGACAGCACTGGGGATAATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39092","NCBI_taxonomy_name":"Acinetobacter johnsonii","NCBI_taxonomy_id":"40214"}}}},"ARO_accession":"3001559","ARO_id":"37959","ARO_name":"OXA-373","CARD_short_name":"OXA-373","ARO_description":"OXA-373 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46494":{"category_aro_accession":"3007705","category_aro_cvterm_id":"46494","category_aro_name":"OXA-211-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-211.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3512":{"model_id":"3512","model_name":"OXA-442","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"5707":{"protein_sequence":{"accession":"AKU37610.1","sequence":"MNIKALLLITSAIFISACSPYIVSANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQEVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLVMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"KP844571.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGTCTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACTACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTAGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAGAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGTAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3003598","ARO_id":"40208","ARO_name":"OXA-442","CARD_short_name":"OXA-442","ARO_description":"OXA-442 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4134":{"model_id":"4134","model_name":"ACT-43","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6509":{"protein_sequence":{"accession":"WP_015572455.1","sequence":"MMKKSLCCALLLGISCSALATPVSEKQLAEVVANTVTPLMKAQSVPGMAVAVIYQGKPHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALVVKPSGMPYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPENVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVVEGSDSKVALAPLPVVEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANTSYPNPARVEAAYHILEALQ"},"dna_sequence":{"accession":"NG_050706.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCCCTTTGCTGCGCCCTGCTGCTCGGCATCTCTTGCTCTGCTCTCGCCACGCCAGTGTCAGAAAAACAGCTGGCGGAGGTGGTCGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCTGTTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGAAAACCGCACTATTACACGTTTGGCAAGGCCGATATCGCGGCGAATAAACCCGTTACGCCTCAGACCCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGCGTTTTAGGTGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTGACGGGCAAGCAGTGGCAGGGTATTCGTATGCTGGATCTCGCCACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGTGCGCTGGTGGTCAAACCTTCTGGCATGCCCTATGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTGCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGTATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCGGAGAACGTTGCTGATGCCTCACTTAAGCAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGGTCGAGGGCAGCGACAGTAAGGTAGCGCTGGCGCCGTTGCCCGTGGTAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGCTCTACTGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATACAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCGAGGCGCTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40540","NCBI_taxonomy_name":"Enterobacter cloacae complex","NCBI_taxonomy_id":"354276"}}}},"ARO_accession":"3006238","ARO_id":"44700","ARO_name":"ACT-43","CARD_short_name":"ACT-43","ARO_description":"ACT-43 is a ACT beta-lactamase.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3391":{"model_id":"3391","model_name":"MCR-3.12","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"5578":{"protein_sequence":{"accession":"AVZ47168.1","sequence":"MPSLIKIKIVPLIFFLALYFAFMLNWRGVLHFYEILYKLEDFKFGFAISLPILLVAALNFAFVPFSIRYLVKPFFALLIALSAIVSYTMMKYRVLFDQNMIQNIFETNQNEALAYLSLPIIGWVTIAGFIPAILLFFVEIEYEEKWFKGILTRVLSMFASLIVIAVIAALYYQDYVSVGRNNSNLQREIVPANFVNSTVKYVYNRYLAEPIPFTTLGDDAKRDTNKSKPTLMFLVVGETARGKNFSMNGYEKDTNPFTSKSGGVISFNDVRSCGTATAVSVPCMFSNMGRKEFDDNLARNSEGLLDVLQKTGVSIFWKENDGGCKGVCDRVPNIEVKPKDYPKFCDKNTCYDEVVLQDLDSEIAQMKGDKLVGFHLIGSHGPTYYKRYPDAHRQFTPDCPRSDIENCTDEELTNTYDNTIRYTDFVIAEMIAKLKTYEDKYNTALLYVSDHGESLGAMGLYLHGTPYKFAPDDQTRVPMQVWMSPGFTKEKGMNMECLQQKAADTRYSHDNIFSSVLGIWDVKTSVYEKGLDIFSQCRNVQ"},"dna_sequence":{"accession":"MG564491.1","fmin":"0","fmax":"1626","strand":"+","sequence":"ATGCCTTCCCTTATAAAAATAAAAATTGTGCCGCTCATATTTTTTTTGGCACTGTATTTTGCATTTATGCTGAACTGGCGTGGAGTTCTCCATTTTTACGAAATTCTTTATAAATTAGAAGATTTTAAATTTGGTTTCGCCATTTCATTACCAATATTGCTTGTTGCAGCGCTTAATTTTGCATTTGTTCCATTTTCGATACGGTATTTAGTAAAGCCTTTTTTTGCACTTCTTATCGCACTTAGCGCAATCGTTAGTTACACAATGATGAAGTATAGAGTCTTGTTTGATCAAAACATGATTCAGAATATTTTTGAAACCAATCAAAATGAGGCATTAGCATATTTAAGTTTGCCAATTATAGGATGGGTTACTATTGCTGGATTTATCCCTGCCATTTTACTTTTCTTTGTTGAAATTGAATATGAGGAAAAATGGTTTAAAGGGATTCTAACTCGCGTCCTATCGATGTTTGCATCCCTTATAGTGATTGCGGTTATTGCAGCACTATACTATCAAGATTATGTTTCAGTGGGGCGCAACAATTCAAACCTCCAGCGTGAAATTGTTCCGGCCAATTTTGTTAATAGTACCGTTAAATATGTTTATAATCGTTATCTTGCAGAACCAATCCCATTTACTACTTTAGGTGATGATGCAAAACGGGATACTAATAAAAGTAAGCCCACGTTGATGTTCCTGGTCGTTGGTGAAACTGCTCGTGGTAAAAATTTCTCGATGAATGGCTACGAGAAAGATACCAACCCATTTACCAGTAAATCTGGTGGTGTGATCTCCTTTAATGATGTTCGTTCGTGTGGGACAGCAACCGCTGTATCTGTCCCCTGCATGTTCTCCAATATGGGGAGAAAGGAGTTTGATGATAATCTCGCTCGTAATAGCGAGGGTTTGTTAGATGTGTTGCAGAAAACGGGGGTCTCCATTTTTTGGAAGGAGAACGATGGCGGCTGCAAAGGCGTCTGCGACCGAGTACCTAACATCGAGGTCAAACCGAAGGATTACCCAAAGTTCTGCGATAAAAATACATGCTATGACGAGGTTGTCCTTCAAGACCTCGATAGTGAAATTGCTCAAATGAAAGGGGATAAGCTGGTTGGCTTCCACCTGATAGGTAGCCATGGCCCAACCTACTACAAACGCTACCCTGATGCTCATCGTCAGTTCACCCCTGATTGTCCACGCAGTGATATCGAAAACTGCACGGATGAAGAGCTCACCAACACCTATGACAACACCATCCGCTACACCGATTTCGTGATTGCAGAGATGATTGCCAAGTTGAAAACCTACGAAGATAAGTACAACACCGCATTGCTCTACGTCTCCGATCACGGTGAATCACTGGGAGCTATGGGGCTTTACCTGCACGGTACACCGTACAAGTTTGCACCGGATGATCAGACCCGCGTACCTATGCAGGTGTGGATGTCACCTGGATTTACCAAAGAGAAAGGCATGAATATGGAATGTTTGCAGCAGAAAGCCGCTGATACTCGTTACTCACACGATAATATTTTCTCATCTGTATTGGGTATCTGGGACGTCAAAACATCAGTTTACGAAAAGGGTCTAGATATTTTCAGTCAATGTCGTAATGTTCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3004693","ARO_id":"42745","ARO_name":"MCR-3.12","CARD_short_name":"MCR-3.12","ARO_description":"A plasmid-mediated phosphoethanolamine transferase and MCR-3 variant conferring resistance to colistin antibiotics.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3397":{"model_id":"3397","model_name":"sta","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"340"}},"model_sequences":{"sequence":{"5585":{"protein_sequence":{"accession":"AAA88560.1","sequence":"MTTTHGSTYEFRSARPGDAEAIEGLDGSFTTSTVFEVDVTGDGFALREVPADPPLVKVFPDDGGSDGEDGAEGEDADSRTFVAVGADGDLAGFAAVSYSAWNQRLTIEDIEVAPGHRGKGIGRVLMRHAADFARERGAGHLWLEVTNVNAPAIHAYRRMGFAFCGLDSALYQGTASEGEHALYMSMPCP"},"dna_sequence":{"accession":"M16183.1","fmin":"529","fmax":"1099","strand":"+","sequence":"ATGACCACGACCCATGGCAGCACGTACGAATTCCGCAGCGCACGACCCGGGGACGCCGAGGCCATCGAGGGCCTCGACGGCTCCTTCACCACCAGTACCGTCTTCGAAGTGGACGTCACCGGAGACGGGTTCGCCCTGCGCGAGGTCCCGGCGGACCCGCCGCTGGTGAAGGTCTTCCCCGACGACGGCGGAAGCGACGGGGAGGACGGCGCGGAGGGCGAGGACGCCGACAGCCGTACGTTCGTGGCCGTCGGCGCCGACGGCGACCTCGCCGGCTTCGCCGCAGTGTCCTACTCGGCGTGGAACCAGCGGCTGACCATCGAGGACATCGAGGTCGCCCCCGGTCACCGCGGCAAGGGCATCGGCCGTGTGCTGATGCGTCACGCGGCGGACTTCGCCCGTGAACGCGGCGCCGGGCACCTGTGGCTGGAGGTGACGAACGTCAACGCCCCGGCCATCCACGCCTACCGTCGGATGGGCTTCGCCTTCTGCGGCCTGGACAGCGCCCTGTACCAGGGCACCGCGTCCGAAGGCGAGCACGCGCTCTACATGAGCATGCCCTGCCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42752","NCBI_taxonomy_name":"Streptomyces lavendulae","NCBI_taxonomy_id":"1914"}}}},"ARO_accession":"3004699","ARO_id":"42751","ARO_name":"sta","CARD_short_name":"sta","ARO_description":"Streptothricin acetyltransferase gene (STAT gene) that confers streptothricin resistance on Escherichia coli and Bacillus subtilis.","ARO_category":{"37249":{"category_aro_accession":"3000869","category_aro_cvterm_id":"37249","category_aro_name":"streptothricin acetyltransferase (SAT)","category_aro_description":"AcetylCoA dependent acetyltransferase that acetylate streptothricins such as nourseothricin at position 16 (beta position of beta-lysine).","category_aro_class_name":"AMR Gene Family"},"35931":{"category_aro_accession":"0000012","category_aro_cvterm_id":"35931","category_aro_name":"streptothricin","category_aro_description":"Streptothricins are a group of N-glycoside antibiotics that include a carbamoylated D-glucosamine to which are attached a series of L-beta-lysine residues at position 2 and a streptolidine at position 1.  Streptothricins vary by the number of beta-lysine residues (from 1 (nourseothricin) to 7) and target protein synthesis in bacteria and eukaryotes.","category_aro_class_name":"Antibiotic"},"36174":{"category_aro_accession":"3000034","category_aro_cvterm_id":"36174","category_aro_name":"nucleoside antibiotic","category_aro_description":"Nucleoside antibiotics are made of modified nucleosides and nucleotides with wide-ranging activities and means of antibacterial effects. This drug class includes aminonucleoside antibiotics, which contain an amino group.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2144":{"model_id":"2144","model_name":"Mycobacterium tuberculosis variant bovis embB with mutation conferring resistance to ethambutol","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"2950":"T610K","2969":"Q998R","2917":"F1012S"},"Curated-R":{"2950":"T610K","2969":"Q998R","2917":"F1012S"},"clinical":{"2950":"T610K","2969":"Q998R","2917":"F1012S"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"2000"}},"model_sequences":{"sequence":{"8807":{"protein_sequence":{"accession":"NP_218312.1","sequence":"MTQCASRRKSTPNRAILGAFASARGTRWVATIAGLIGFVLSVATPLLPVVQTTAMLDWPQRGQLGSVTAPLISLTPVDFTATVPCDVVRAMPPAGGVVLGTAPKQGKDANLQALFVVVSAQRVDVTDRNVVILSVPREQVTSPQCQRIEVTSTHAGTFANFVGLKDPSGAPLRSGFPDPNLRPQIVGVFTDLTGPAPPGLAVSATIDTRFSTRPTTLKLLAIIGAIVATVVALIALWRLDQLDGRGSIAQLLLRPFRPASSPGGMRRLIPASWRTFTLTDAVVIFGFLLWHVIGANSSDDGYILGMARVADHAGYMSNYFRWFGSPEDPFGWYYNLLALMTHVSDASLWMRLPDLAAGLVCWLLLSREVLPRLGPAVEASKPAYWAAAMVLLTAWMPFNNGLRPEGIIALGSLVTYVLIERSMRYSRLTPAALAVVTAAFTLGVQPTGLIAVAALVAGGRPMLRILVRRHRLVGTLPLVSPMLAAGTVILTVVFADQTLSTVLEATRVRAKIGPSQAWYTENLRYYYLILPTVDGSLSRRFGFLITALCLFTAVFIMLRRKRIPSVARGPAWRLMGVIFGTMFFLMFTPTKWVHHFGLFAAVGAAMAALTTVLVSPSVLRWSRNRMAFLAALFFLLALCWATTNGWWYVSSYGVPFNSAMPKIDGITVSTIFFALFAIAAGYAAWLHFAPRGAGEGRLIRALTTAPVPIVAGFMAAVFVASMVAGIVRQYPTYSNGWSNVRAFVGGCGLADDVLVEPDTNAGFMKPLDGDSGSWGPLGPLGGVNPVGFTPNGVPEHTVAEAIVMKPNQPGTDYDWDAPTKLTSPGINGSTVPLPYGLDPARVPLAGTYTTGAQQQSTLVSAWYLLPKPDDGHPLVVVTAAGKIAGNSVLHGYTPGQTVVLEYAMPGPGALVPAGRMVPDDLYGEQPKAWRNLRFARAKMPADAVAVRVVAEDLSLTPEDWIAVTPPRVPDLRSLQEYVGSTQPVLLDWAVGLAFPCQQPMLHANGIAEIPKFRITPDYSAKKLDTDTWEDGTNGGLLGITDLLLRAHVMATYLSRDWARDWGSLRKFDTLVDAPPAQLELGTATRSGLWSPGKIRIGP"},"dna_sequence":{"accession":"NC_000962.3","fmin":"4246513","fmax":"4249810","strand":"+","sequence":"ATGACACAGTGCGCGAGCAGACGCAAAAGCACCCCAAATCGGGCGATTTTGGGGGCTTTTGCGTCTGCTCGCGGGACGCGCTGGGTGGCCACCATCGCCGGGCTGATTGGCTTTGTGTTGTCGGTGGCGACGCCGCTGCTGCCCGTCGTGCAGACCACCGCGATGCTCGACTGGCCACAGCGGGGGCAACTGGGCAGCGTGACCGCCCCGCTGATCTCGCTGACGCCGGTCGACTTTACCGCCACCGTGCCGTGCGACGTGGTGCGCGCCATGCCACCCGCGGGCGGGGTGGTGCTGGGCACCGCACCCAAGCAAGGCAAGGACGCCAATTTGCAGGCGTTGTTCGTCGTCGTCAGCGCCCAGCGCGTGGACGTCACCGACCGCAACGTGGTGATCTTGTCCGTGCCGCGCGAGCAGGTGACGTCCCCGCAGTGTCAACGCATCGAGGTCACCTCTACCCACGCCGGCACCTTCGCCAACTTCGTCGGGCTCAAGGACCCGTCGGGCGCGCCGCTGCGCAGCGGCTTCCCCGACCCCAACCTGCGCCCGCAGATTGTCGGGGTGTTCACCGACCTGACCGGGCCCGCGCCGCCCGGGCTGGCGGTCTCGGCGACCATCGACACCCGGTTCTCCACCCGGCCGACCACGCTGAAACTGCTGGCGATCATCGGGGCGATCGTGGCCACCGTCGTCGCACTGATCGCGTTGTGGCGCCTGGACCAGTTGGACGGGCGGGGCTCAATTGCCCAGCTCCTCCTCAGGCCGTTCCGGCCTGCATCGTCGCCGGGCGGCATGCGCCGGCTGATTCCGGCAAGCTGGCGCACCTTCACCCTGACCGACGCCGTGGTGATATTCGGCTTCCTGCTCTGGCATGTCATCGGCGCGAATTCGTCGGACGACGGCTACATCCTGGGCATGGCCCGAGTCGCCGACCACGCCGGCTACATGTCCAACTATTTCCGCTGGTTCGGCAGCCCGGAGGATCCCTTCGGCTGGTATTACAACCTGCTGGCGCTGATGACCCATGTCAGCGACGCCAGTCTGTGGATGCGCCTGCCAGACCTGGCCGCCGGGCTAGTGTGCTGGCTGCTGCTGTCGCGTGAGGTGCTGCCCCGCCTCGGGCCGGCGGTGGAGGCCAGCAAACCCGCCTACTGGGCGGCGGCCATGGTCTTGCTGACCGCGTGGATGCCGTTCAACAACGGCCTGCGGCCGGAGGGCATCATCGCGCTCGGCTCGCTGGTCACCTATGTGCTGATCGAGCGGTCCATGCGGTACAGCCGGCTCACACCGGCGGCGCTGGCCGTCGTTACCGCCGCATTCACACTGGGTGTGCAGCCCACCGGCCTGATCGCGGTGGCCGCGCTGGTGGCCGGCGGCCGCCCGATGCTGCGGATCTTGGTGCGCCGTCATCGCCTGGTCGGCACGTTGCCGTTGGTGTCGCCGATGCTGGCCGCCGGCACCGTCATCCTGACCGTGGTGTTCGCCGACCAGACCCTGTCAACGGTGTTGGAAGCCACCAGGGTTCGCGCCAAAATCGGGCCGAGCCAGGCGTGGTATACCGAGAACCTGCGTTACTACTACCTCATCCTGCCCACCGTCGACGGTTCGCTGTCGCGGCGCTTCGGCTTTTTGATCACCGCGCTATGCCTGTTCACCGCGGTGTTCATCATGTTGCGGCGCAAGCGAATTCCCAGCGTGGCCCGCGGACCGGCGTGGCGGCTGATGGGCGTCATCTTCGGCACCATGTTCTTCCTGATGTTCACGCCCACCAAGTGGGTGCACCACTTCGGGCTGTTCGCCGCCGTAGGGGCGGCGATGGCCGCGCTGACGACGGTGTTGGTATCCCCATCGGTGCTGCGCTGGTCGCGCAACCGGATGGCGTTCCTGGCGGCGTTATTCTTCCTGCTGGCGTTGTGTTGGGCCACCACCAACGGCTGGTGGTATGTCTCCAGCTACGGTGTGCCGTTCAACAGCGCGATGCCGAAGATCGACGGGATCACAGTCAGCACAATCTTTTTCGCCCTGTTTGCGATCGCCGCCGGCTATGCGGCCTGGCTGCACTTCGCGCCCCGCGGCGCCGGCGAAGGGCGGCTGATCCGCGCGCTGACGACAGCCCCGGTACCGATCGTGGCCGGTTTCATGGCGGCGGTGTTCGTCGCGTCCATGGTGGCCGGGATCGTGCGACAGTACCCGACCTACTCCAACGGCTGGTCCAACGTGCGGGCGTTTGTCGGCGGCTGCGGACTGGCCGACGACGTACTCGTCGAGCCTGATACCAATGCGGGTTTCATGAAGCCGCTGGACGGCGATTCGGGTTCTTGGGGCCCCTTGGGCCCGCTGGGTGGAGTCAACCCGGTCGGCTTCACGCCCAACGGCGTACCGGAACACACGGTGGCCGAGGCGATCGTGATGAAACCCAACCAGCCCGGCACCGACTACGACTGGGATGCGCCGACCAAGCTGACGAGTCCTGGCATCAATGGTTCTACGGTGCCGCTGCCCTATGGGCTCGATCCCGCCCGGGTACCGTTGGCAGGCACCTACACCACCGGCGCACAGCAACAGAGCACACTCGTCTCGGCGTGGTATCTCCTGCCTAAGCCGGACGACGGGCATCCGCTGGTCGTGGTGACCGCCGCGGGCAAGATCGCCGGCAACAGCGTGCTGCACGGGTACACCCCCGGGCAGACTGTGGTGCTCGAATACGCCATGCCGGGACCCGGAGCGCTGGTACCCGCCGGGCGGATGGTGCCCGACGACCTATACGGAGAGCAGCCCAAGGCGTGGCGCAACCTGCGCTTCGCCCGAGCAAAGATGCCCGCCGATGCCGTCGCGGTCCGGGTGGTGGCCGAGGATCTGTCGCTGACACCGGAGGACTGGATCGCGGTGACCCCGCCGCGGGTACCGGACCTGCGCTCACTGCAGGAATATGTGGGCTCGACGCAGCCGGTGCTGCTGGACTGGGCGGTCGGTTTGGCCTTCCCGTGCCAGCAGCCGATGCTGCACGCCAATGGCATCGCCGAAATCCCGAAGTTCCGCATCACACCGGACTACTCGGCTAAGAAGCTGGACACCGACACGTGGGAAGACGGCACTAACGGCGGCCTGCTCGGGATCACCGACCTGTTGCTGCGGGCCCACGTCATGGCCACCTACCTGTCCCGCGACTGGGCCCGCGATTGGGGTTCCCTGCGCAAGTTCGACACCCTGGTCGATGCCCCTCCCGCCCAGCTCGAGTTGGGCACCGCGACCCGCAGCGGCCTGTGGTCACCGGGCAAGATCCGAATTGGTCCATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3003325","ARO_id":"39909","ARO_name":"Mycobacterium tuberculosis variant bovis embB with mutation conferring resistance to ethambutol","CARD_short_name":"Mbov_embB_EMB","ARO_description":"Point mutations that occur within Mycobacterium tuberculosis variant bovis embB gene resulting in resistance to ethambutol.","ARO_category":{"36374":{"category_aro_accession":"3000235","category_aro_cvterm_id":"36374","category_aro_name":"ethambutol resistant embB","category_aro_description":"embB gene encodes for an arabinosyl transferase in the arabinogalactan synthesis pathway. It is inhibited by ethambutol. Mutations within the ERDR region of embB confers resistance to ethambutol.","category_aro_class_name":"AMR Gene Family"},"36636":{"category_aro_accession":"3000497","category_aro_cvterm_id":"36636","category_aro_name":"ethambutol","category_aro_description":"Ethambutol is an antimycobacterial drug prescribed to treat tuberculosis. It is usually given in combination with other tuberculosis drugs, such as isoniazid, rifampicin, and pyrazinamide. Ethambutol inhibits arabinosyl biosynthesis, disrupting mycobacterial cell wall formation.","category_aro_class_name":"Antibiotic"},"36666":{"category_aro_accession":"3000527","category_aro_cvterm_id":"36666","category_aro_name":"polyamine antibiotic","category_aro_description":"Polyamine antibiotics are organic compounds having two or more primary amino groups.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2476":{"model_id":"2476","model_name":"Halobacterium salinarum 16S rRNA mutation conferring resistance to pactamycin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"41093","param_value":"2600"},"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"7809":"a633g","7811":"c735t","7810":"c734t"},"Curated-R":{"7809":"a633g","7811":"c735t","7810":"c734t"},"clinical":{"7809":"a633g","7811":"c735t","7810":"c734t"}}},"model_sequences":{"sequence":{"3807":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"KY084523.1","fmin":"0","fmax":"1473","strand":"+","sequence":"ATTCCGGTTGATCCTGCCGGAGGCCATTGCTATCGGAGTCCGATTTAGCCATGCTAGTTGTGCGGGTTTAGACCCGCAGCGGAAAGCTCAGTAACACGTGGCCAAGCTACCCTGTGGACGGGAATACTCTCGGGAAACTGAGGCTAATCCCCGATAACGCTTTGCTCCTGGAAGGGGCAAAGCCGGAAACGCTCCGGCGCCACAGGATGCGGCTGCGGTCGCCTAGGTAGACGGTGGGGTAACGGCCCACCGTGCCCATAATCGGTACGGGCCGTGAGCCCAAGAGCCCGGAGACGGAATCTGAGACAAGATTCCGGGCCCTACGGGGCGCAGCAGGCGCGAAACCTTTACACTGTACGAAAGTGCGATAAGGGGACTCCGAGTGTGAAGGCATAGAGCCTTCACTTTTGTACACCGTAAGGTGGTGCACGAATAAGGACTGGGCAAGACCGGTGCCAGCCGCCGCGGTAATACCGGCAGTCCGAGTGATGGCCGATCTTATTGGGCCTAAAGCGTCCGTAGCTGGCTGAACAAGTCCGTTGGGAAATCTGTCCGCTTAACGGGCAGGCGTCCAGCGGCCACTGTTCAGCTTGGGACCCCCCGACCTGAGGGGTACGTCTGGGGTAGGAGTGAAATCCTGTAATCCTGGACGGACCGCCGGTGGCGAAAGCGCCTCAGGAGAACGGATCCGACAGTGAGGGACGAAAGCTAGGGTCTCGAACCGGATTAGATACCCGGGTAGTCCTAGCTGTAAACGATGTCCGCTAGGTGTGGCGCAGGCTACGAGCCTGCGCTGTGCCGTAGGGAAGCCGAGAAGCGGACCGCCTGGGAAGTACGTCTGCAAGGATGAAACTTAAAGGAATTGGCGGGGGAGCACTACAACCGGAGGAGCCTGCGGTTTAATTGGACTCAACGCCGGACATCTCACCAGCCCCGACAGTAGTAATGACGGTCAGGTTGATGACCTTACCCGAGGCTACTGAGAGGAGGTGCATGGCCGCCGTCAGCTCGTACCGTGAGGCGTCCTGTTAAGTCAGGCAACGAGCGAGACCCGCACTCCTACCTGCCAGCAGTACCCTTTGGGTAGCTGGGTACATTAGGTGGACTGCCGCTGCCAAAGCGGAGGAAGGAACGGGCAACGGTAGGTCAGTATGCCCCGAATGGGCTGGGCAACACGCGGGCTACAATGGTCGAGACAATGGGAAGCCACTCCGAGAGGAGGCGCTAATCTCCTAAACTCGATCGTAGTTCGGATTGAGGGCTGAAACTCGCCCTCATGAAGCTGGATTCGGTAGTAATCGCGTGTCAGCAGCGCGCGGTGAATACGTCCCTGCTCCTTGCACACACCGCCCGTCAAATCACCCGAGTGGGGTTCGGATGAGGCCGGCATGCGCTGGTCAAATCTGGGCTCCGCAAGGGGGATTAAGTCGTAACAAGGTAGCCGTAGGGGAATCTGCGGCTGGATCACCTCCT","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40807","NCBI_taxonomy_name":"Halobacterium salinarum","NCBI_taxonomy_id":"2242"}}}},"ARO_accession":"3003977","ARO_id":"40806","ARO_name":"Halobacterium salinarum 16S rRNA mutation conferring resistance to pactamycin","CARD_short_name":"Hsal_16S_PAC","ARO_description":"Point mutations in Halobacterium 16S rRNA that confer resistance to pactamycin antibiotic.","ARO_category":{"40805":{"category_aro_accession":"3003976","category_aro_cvterm_id":"40805","category_aro_name":"16S rRNA with mutation conferring resistance to pactamycin","category_aro_description":"Point mutations in bacterial 16S rRNA that confer resistance to antibiotic pactamycin.","category_aro_class_name":"AMR Gene Family"},"40804":{"category_aro_accession":"3003975","category_aro_cvterm_id":"40804","category_aro_name":"pactamycin","category_aro_description":"Antibiotic produced by Streptomyces pactum, considered a universal translation inhibitor.","category_aro_class_name":"Antibiotic"},"45740":{"category_aro_accession":"3007158","category_aro_cvterm_id":"45740","category_aro_name":"pactamycin-like antibiotic","category_aro_description":"A group of antibiotics including pactamycin and its derivatives.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2478":{"model_id":"2478","model_name":"Helicobacter pylori 16S rRNA mutation conferring resistance to tetracycline","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"4758":"a965g","4759":"a967c","12459":"a926g","12458":"a928c"},"Curated-R":{"4758":"a965g","4759":"a967c","4761":"a967c","12459":"a926g","12458":"a928c","4760":"a928c"},"clinical":{"4758":"a965g","4759":"a967c","12459":"a926g","12458":"a928c"}},"40330":{"param_type":"multiple resistance variants","param_description":"A set of nucleotide or amino acid substitutions that are all required to confer resistance to an antibiotic drug or drug class, encoded as: [wild-type 1][position 1][mutation 1],[wild-type 2][position 2][mutation 2], etc. For example, D63Y,T142K.","param_type_id":"40330","param_value":{"4761":"a965g,a967c","4760":"a965g,g966t"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"41093","param_value":"2700"}},"model_sequences":{"sequence":{"4114":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"CP003904.1","fmin":"1511156","fmax":"1512657","strand":"-","sequence":"AGGAGGTGATCCAACCGCAGGTTCACTACGGTTACCTTGTTACGACTTCACCCCAGTCGCTGTGTGTGCCGTGGGCAGTAGCCAATTTAGCATCCTGACTTAAGGCAAACACAACTCCCATGGTGTGACGGGCGGTGAGTACAAGACCCGGGAACGTATTCACCGCAACATGGCTGATTTGCGATTACTAGCGATTCCAGCTTCATGCAGGCGAGTTGCAGCCTACAATCCGAACTGAGAGGTGTTTTGAAGATTGGCTCCATTCGCAGTATTGCTTCTCTTTGTGCACCCCATTGTAGCACGTGTGTAGCCCTAGGCGTAAGGGCCATGATGACTTGACGTCGTCCCCACCTTCCTNCCCTTACGGAGGCAGTATCCTTAGAGTTCTCAGCATAACCTGTTAGCAACTAAGAAAAGGGGTTGCGCTCGTTGCGGGACTTAACCCAACATCTCACGACACGAGCTGACGACAGCCGTGCAGCACCTGTTTTCAAGGTCTGGCAAGCCAGACACTCCACTATTTCTAGCGGATTCTCTCAATGTCAAGCCTAGGTAAGGTTCTTCGTGTATCTTCGAATTAAACCACATGCTCCACCGCTTGTGCGGGTCCCCGTCTATTCCTTTGAGTTTTAATCTTGCGACCGTACTCCCCAGGCGGGATGCTTAATGCGTTAGCTGCATTACTGGAGAGACTAAGCCCTCCAACAACTAGCATCCATCGTTTAGGGCGTGGACTACCAGGGTATCTAATCCTGTTTGCTCCCCAACMGCTTTCGCGCAATCAGCGTCAGTAATGTTCCAGCAGGTCGCCTTCGCAATGAGTATTCCTCTTGATCTCTACGGATTTTACCCCTACACCAAGAATTCCACCTACCTCTCCCACACTCTAGAATAGTAGTTTCAAATGCAGTTCTATGGTTAAGCCATAGGATTTCACACCTGACTGACTATCCCGCCTACGCGCTCTTTACGCCCAGTGATTCCGAGTAACGCTTGCACCCTCCGTATTACCGCGGCTGCTGGCACGGAGTTAGCCGGTGCTTATTCGTTAGATACCGTCATTATCTTCTCTAACAAAAGGAGTTTACAATCCTAAAACCTTCATCCTCCACGCGGCGTTGCTGCTTCAGGGTTTCCCCCATTGAGCAATATTCCCTACTGCTGCCTCCCGTAGGAGTCTGGACCGTGTCTCAGTTCCAGTGTGTCCGTTCACCCTCTCAGGCCGGATACCCGTCATAGCCTTGGTAAGCCATTACCTTACCAACAAGCTGATAGGACATAGGCTGATCTCTTAGCGATAAATCTTTCCCCCGTAGGAGTATCTGGTATTAATCATCGTTTCCAATGGCTATCCCAAACTAAGAGGCACATAACCTATGCGTTACTCACCCGTGCGCCACTAATCAGCACTCTAGCAAGCTAGAAGCTTCATCGTTCGACTTGCATGTATTAGGCACGCCGCCAGCGTTCACTCTGAGCCAGGATCAAACTCTCCATAAAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36758","NCBI_taxonomy_name":"Helicobacter pylori 26695","NCBI_taxonomy_id":"85962"}}}},"ARO_accession":"3003510","ARO_id":"40112","ARO_name":"Helicobacter pylori 16S rRNA mutation conferring resistance to tetracycline","CARD_short_name":"Hpyl_16S_TET","ARO_description":"Tetracycline binds tightly to the helix 34 domain in 16S rRNA, where it interferes sterically with the binding of aminoacyl-tRNA to the ribosome A site to block protein synthesis. Mutations in the nucleotide sequence in this domain of Helicobacter pylori can result in resistance against tetracycline.","ARO_category":{"40280":{"category_aro_accession":"3003669","category_aro_cvterm_id":"40280","category_aro_name":"16S rRNA with mutation conferring resistance to tetracycline derivatives","category_aro_description":"Point mutations in the bacterial 16S rRNA region shown clinically to confer resistance to tetracycline and tetracycline derivatives (polyketide antibiotics).","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3641":{"model_id":"3641","model_name":"LEN-42","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"5912":{"protein_sequence":{"accession":"AZA07959.1","sequence":"MRYVRLCVISLLATLPLAVYAGPQPLEQIKQSESQLSGRVGMVEMDLASGRTLAAWRADERFPMVSTFKVLLCGAVLARVDAGVEQLDRRIHYRQQDLVDYSPVSEKHLVDGMTIGELCAAAITMSDNSAGNLLLATVGGPAGLTAFLRQIGDNVTRLDRWETALNEALPGDMRDTTTPASMAATLRKLLTAQHLSARSQQQLLQWMVDDRVAGPLIRAVLPAGWFIADKTGAGERGARGIVALLGPDGKAERIVVIYLRDTPASMAERNQHIAGIGAALIEHWQR"},"dna_sequence":{"accession":"MK161462.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGTGTTATCTCCCTGTTAGCCACCCTGCCACTGGCGGTATACGCCGGTCCACAGCCGCTAGAGCAGATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTGGGGATGGTGGAAATGGATCTGGCCAGCGGCCGCACGCTGGCTGCCTGGCGCGCCGATGAACGCTTTCCCATGGTGAGCACCTTTAAAGTGCTGCTGTGCGGCGCGGTGCTGGCGCGGGTGGATGCCGGGGTCGAACAACTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGTCGACGGGATGACGATCGGCGAACTCTGCGCCGCCGCCATCACCATGAGCGATAACAGCGCCGGAAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCGGGATTGACCGCCTTTCTGCGTCAGATCGGTGACAACGTCACCCGTCTTGACCGCTGGGAAACGGCACTGAATGAGGCGCTTCCCGGCGACATGCGCGACACCACTACCCCGGCCAGCATGGCCGCCACGCTGCGTAAACTACTGACCGCGCAGCATCTGAGCGCCCGTTCACAGCAGCAGCTCCTGCAGTGGATGGTGGACGATCGGGTTGCCGGCCCGCTGATCCGCGCCGTGCTGCCGGCGGGCTGGTTTATCGCCGACAAGACCGGGGCTGGCGAACGGGGTGCGCGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAAGCGGAGCGCATCGTGGTGATCTACCTGCGGGATACCCCGGCGAGTATGGCCGAGCGTAATCAACATATCGCCGGGATCGGCGCAGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42976","NCBI_taxonomy_name":"Klebsiella variicola subsp. tropica","NCBI_taxonomy_id":"2489014"}}}},"ARO_accession":"3004845","ARO_id":"42980","ARO_name":"LEN-42","CARD_short_name":"LEN-42","ARO_description":"A class-A broad-spectrum beta-lactamase from Klebsiella.","ARO_category":{"36236":{"category_aro_accession":"3000097","category_aro_cvterm_id":"36236","category_aro_name":"LEN beta-lactamase","category_aro_description":"LEN beta-lactamases are chromosomal class A beta-lactamases that confer resistance to ampicillin, amoxicillin, carbenicillin, and ticarcillin but not to extended-spectrum beta-lactams.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3456":{"model_id":"3456","model_name":"OXA-293","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"540"}},"model_sequences":{"sequence":{"5651":{"protein_sequence":{"accession":"WP_032877719.1","sequence":"MSAKLKILTLSISLVLGLPLMACQSFSQQKQQIMTQKSEQQQIASLFQNAQTSGVLVIYDGKKIQKYGNDTSRAEHRYIPASTFKMLNALIGIQHHKTTPNEIFKWDGRKRAFSSWEKDLTLAEAMQASAVPVYQELARRIGLELMTQEIKRVGYGNNNVGTQVDNFWLVGPLKITPVEEVRFAYALAKQKLPFDQSTQQQVKGMLLLDEVQGAKIYAKSGWGMDVSPQVGWWTGWIEQANGKITAFSLNMEMSQPEHAETRKAIVYQALQQLDLLVN"},"dna_sequence":{"accession":"NG_050610.1","fmin":"100","fmax":"937","strand":"+","sequence":"ATGTCGGCGAAACTAAAAATTCTCACTTTATCCATTTCATTGGTGCTGGGATTACCCTTGATGGCTTGCCAGAGCTTTAGTCAACAAAAGCAGCAAATAATGACACAGAAAAGTGAACAGCAGCAGATTGCGAGCTTATTCCAAAATGCTCAAACTAGCGGTGTTTTGGTCATTTATGATGGAAAGAAAATTCAAAAATATGGCAATGACACCAGTCGCGCAGAGCATCGTTATATCCCAGCCTCAACTTTTAAAATGCTGAATGCGTTAATTGGCATACAGCATCATAAAACCACGCCAAATGAAATCTTTAAATGGGATGGACGGAAACGCGCATTCAGTAGTTGGGAAAAAGACCTCACACTAGCGGAGGCGATGCAGGCATCAGCTGTGCCTGTGTATCAAGAGCTGGCACGACGTATTGGCCTAGAACTGATGACCCAAGAAATTAAGCGAGTGGGTTATGGCAATAACAATGTTGGGACACAGGTCGATAATTTCTGGTTAGTTGGCCCATTAAAAATTACTCCTGTGGAAGAAGTACGCTTTGCCTACGCATTGGCGAAGCAAAAGCTGCCATTTGATCAGTCAACTCAGCAACAAGTGAAAGGCATGTTATTGCTTGATGAAGTTCAGGGGGCCAAGATATACGCTAAAAGTGGTTGGGGTATGGATGTTAGTCCGCAAGTTGGATGGTGGACGGGTTGGATAGAACAAGCAAATGGCAAGATCACCGCATTTTCATTAAATATGGAAATGAGTCAACCTGAGCATGCAGAGACACGTAAGGCGATTGTTTATCAAGCTTTGCAGCAACTTGATTTATTGGTGAATTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42816","NCBI_taxonomy_name":"Acinetobacter sp. ANC 3929","NCBI_taxonomy_id":"1217707"}}}},"ARO_accession":"3001748","ARO_id":"38148","ARO_name":"OXA-293","CARD_short_name":"OXA-293","ARO_description":"OXA-293 is a beta-lactamase found in Acinetobacter spp.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46503":{"category_aro_accession":"3007714","category_aro_cvterm_id":"46503","category_aro_name":"OXA-286-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-286.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3716":{"model_id":"3716","model_name":"Mycobacterium tuberculosis Rv0191 mutations confer resistance to pyrazinamide","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"9723":"V179A","9724":"A213T"},"ReSeqTB-High":{"9723":"V179A"},"clinical":{"9723":"V179A","9724":"A213T"},"ReSeqTB-Minimal":{"9724":"A213T"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"710"}},"model_sequences":{"sequence":{"8775":{"protein_sequence":{"accession":"NP_214705.1","sequence":"MTAPTGTSATTTRPWTPRIATQLSVLACAAFIYVTAEILPVGALSAIARNLRVSVVLVGTLLSWYALVAAVTTVPLVRWTAHWPRRRALVVSLVCLTVSQLVSALAPNFAVLAAGRVLCAVTHGLLWAVIAPIATRLVPPSHAGRATTSIYIGTSLALVVGSPLTAAMSLMWGWRLAAVCVTGAAAAVALAARLALPEMVLRADQLEHVGRRARHHRNPRLVKVSVLTMIAVTGHFVSYTYIVVIIRDVVGVRGPNLAWLLAAYGVAGLVSVPLVARPLDRWPKGAVIVGMTGLTAAFTLLTALAFGERHTAATALLGTGAIVLWGALATAVSPMLQSAAMRSGGDDPDGASGLYVTAFQIGIMAGALLGGLLYERSLAMMLTASAGLMGVALFGMTVSQHLFENPTLSPGDG"},"dna_sequence":{"accession":"NC_000962.3","fmin":"222288","fmax":"223530","strand":"+","sequence":"ATGACTGCCCCAACCGGAACCTCCGCCACTACGACGCGACCGTGGACGCCACGGATCGCCACGCAACTGTCCGTGCTGGCTTGCGCGGCCTTTATCTATGTCACCGCCGAAATCCTGCCAGTGGGCGCGCTGTCGGCGATAGCGCGGAACTTGCGCGTCAGCGTGGTCCTAGTTGGGACCTTGCTGTCCTGGTATGCCCTTGTCGCGGCCGTGACAACGGTTCCGCTGGTGCGTTGGACCGCACACTGGCCGCGCCGCCGGGCCCTGGTGGTCAGCCTGGTCTGCCTGACCGTCTCGCAACTCGTCTCGGCGCTGGCGCCCAACTTCGCGGTGCTGGCCGCCGGGCGGGTGCTCTGCGCGGTCACCCATGGCCTGCTGTGGGCGGTCATCGCGCCGATCGCCACCCGGCTGGTGCCGCCCAGTCACGCCGGGCGCGCCACGACGTCGATCTACATCGGAACCAGTCTGGCGCTGGTCGTCGGTAGCCCACTCACGGCTGCCATGAGCCTGATGTGGGGTTGGCGGCTGGCGGCGGTGTGCGTGACCGGCGCGGCGGCCGCGGTCGCCCTGGCCGCCCGGCTGGCGTTGCCGGAGATGGTGCTGCGCGCCGACCAGCTCGAGCACGTTGGCCGACGGGCTCGTCACCACCGTAATCCTCGCCTGGTCAAGGTCAGTGTGCTCACGATGATCGCGGTAACCGGCCATTTCGTGTCCTACACCTACATCGTGGTGATCATCCGCGACGTCGTCGGTGTACGTGGGCCGAATCTGGCCTGGCTGCTCGCCGCCTATGGGGTCGCCGGCCTGGTGTCCGTGCCCCTGGTGGCGCGGCCGTTGGACCGTTGGCCCAAGGGCGCCGTCATCGTCGGTATGACCGGACTGACGGCGGCGTTCACCTTGCTGACCGCGCTGGCATTCGGTGAACGCCACACCGCGGCGACGGCACTGCTGGGCACCGGTGCGATTGTGCTGTGGGGAGCCTTGGCCACTGCCGTGTCACCGATGCTGCAATCGGCGGCGATGCGTAGCGGCGGCGACGACCCCGACGGGGCCTCAGGTTTGTATGTGACGGCGTTTCAGATCGGCATCATGGCCGGCGCTCTGCTGGGTGGGCTGCTCTACGAGCGCAGCTTGGCGATGATGCTGACCGCGTCGGCGGGTTTGATGGGTGTTGCGTTGTTCGGGATGACGGTTAGCCAGCACTTGTTCGAGAATCCGACTCTGAGTCCCGGCGACGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3004981","ARO_id":"43168","ARO_name":"Mycobacterium tuberculosis Rv0191 mutations confer resistance to pyrazinamide","CARD_short_name":"Mtub_Rv0191_PZA","ARO_description":"Mutations in the Rv0191 gene contribute to or confer resistance to pyrazinamide.","ARO_category":{"43167":{"category_aro_accession":"3004980","category_aro_cvterm_id":"43167","category_aro_name":"pyrazinamide resistant Rv0191","category_aro_description":"A probable conserved integral membrane protein that acts as an active efflux pump. Overexpression causes pyrazinamide resistance.","category_aro_class_name":"AMR Gene Family"},"39997":{"category_aro_accession":"3003413","category_aro_cvterm_id":"39997","category_aro_name":"pyrazinamide","category_aro_description":"Pyrazinamide is an antimycobacterial. It is highly specific and active only against Mycobacterium tuberculosis. This compound is a prodrug and needs to be activated inside the cell. It interferes with the bacterium's ability to synthesize new fatty acids, causing cell death.","category_aro_class_name":"Antibiotic"},"45737":{"category_aro_accession":"3007155","category_aro_cvterm_id":"45737","category_aro_name":"pyrazine antibiotic","category_aro_description":"A group of antibiotics derived from pyrazine.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3726":{"model_id":"3726","model_name":"Mycobacterium tuberculosis inbR mutations conferring resistance to isoniazid","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"12576":"R9H","12578":"L17Q"},"ReSeqTB-Moderate":{"12576":"R9H"},"clinical":{"12576":"R9H","12578":"L17Q"},"ReSeqTB-Minimal":{"12578":"L17Q"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"8773":{"protein_sequence":{"accession":"YP_177706.1","sequence":"MTRSDRPYRGVEAAERLATRRRQSLSAGLDLLGSDQHDIAELTIRTICRRAGLSVRYFYESFTDKDEFVGRVFDWVVAELVATTQAAVTAVPAREQTRAGMANIVRTITADARVGRLLFSTQLANAVITRKRAESSALFAMLSGQHAVDTLHAPANDHVKAVAHFAVGGVGQTISAWLAGDVRLDPDQLVDQLAALLDELTDPNLSRPRVAATAAKSGANDPQPPEVAGQPPSSARPARRS"},"dna_sequence":{"accession":"NC_000962.3","fmin":"330932","fmax":"331658","strand":"-","sequence":"ATGACGCGCAGTGATCGACCCTACCGCGGCGTCGAGGCCGCCGAGCGACTGGCGACGCGCCGTCGCCAGTCGCTCTCTGCCGGCCTGGACCTGTTGGGGTCCGACCAGCACGACATCGCCGAGCTAACCATCCGCACCATTTGCCGGCGGGCCGGCCTGTCGGTGCGCTACTTCTACGAAAGCTTCACCGACAAGGACGAATTCGTCGGCCGCGTGTTCGACTGGGTGGTGGCCGAGCTGGTCGCCACCACTCAGGCCGCGGTCACGGCGGTACCGGCGCGGGAGCAGACTCGCGCGGGCATGGCCAACATCGTGCGGACCATCACCGCAGACGCCCGCGTCGGACGCCTGCTGTTCAGCACACAGCTGGCCAACGCAGTGATCACCCGCAAGCGTGCGGAATCCAGCGCCCTGTTCGCCATGCTGTCCGGCCAACATGCCGTCGACACCCTGCACGCACCGGCAAATGACCACGTCAAGGCGGTCGCACACTTCGCCGTCGGCGGCGTCGGGCAGACCATCAGCGCCTGGCTGGCCGGTGACGTGCGACTCGATCCCGACCAGCTGGTCGATCAGCTAGCTGCGCTGCTCGATGAACTCACCGACCCAAACTTGTCCCGTCCCCGGGTAGCGGCAACAGCTGCCAAATCCGGGGCTAACGATCCGCAGCCACCGGAGGTCGCCGGTCAGCCGCCGTCTTCGGCACGGCCTGCGCGTCGCTCGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3004924","ARO_id":"43110","ARO_name":"Mycobacterium tuberculosis inbR mutations conferring resistance to isoniazid","CARD_short_name":"Mtub_inbR_INH","ARO_description":"Mutations that occur in inbR that result in or contribute to antibiotic resistance to isoniazid.","ARO_category":{"43085":{"category_aro_accession":"3004899","category_aro_cvterm_id":"43085","category_aro_name":"isoniazid resistant inbR","category_aro_description":"inbR is part of the transcriptional factor family TetR. It acts as a repressor to regulate efflux pumps involved in antibiotic resistance.","category_aro_class_name":"AMR Gene Family"},"36659":{"category_aro_accession":"3000520","category_aro_cvterm_id":"36659","category_aro_name":"isoniazid","category_aro_description":"Isoniazid is an organic compound that is the first-line anti tuberculosis medication in prevention and treatment. As a prodrug, it is activated by mycobacterial catalase-peroxidases such as M. tuberculosis KatG. Isoniazid inhibits mycolic acid synthesis, which prevents cell wall synthesis in mycobacteria.","category_aro_class_name":"Antibiotic"},"45734":{"category_aro_accession":"3007152","category_aro_cvterm_id":"45734","category_aro_name":"isoniazid-like antibiotic","category_aro_description":"A group of antibiotics containing isoniazid and its derivatives.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2812":{"model_id":"2812","model_name":"Mycobacteroides chelonae 23S rRNA with mutation conferring resistance to clarithromycin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"7916":"a2272c","7917":"a2272g","7918":"a2273c","7919":"a2273g"},"Curated-R":{"7916":"a2272c","7917":"a2272g","7918":"a2273c","7919":"a2273g"},"clinical":{"7916":"a2272c","7917":"a2272g","7918":"a2273c","7919":"a2273g"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"41093","param_value":"5700"}},"model_sequences":{"sequence":{"4158":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"GU143889.1","fmin":"0","fmax":"3113","strand":"+","sequence":"CTAAGTTCTTAAGGGCACATGGTGAATGCCTTGGCACTAGAAGCCGAAGAAGGACGTAGGAGGCTGCGATAAGCCTCGGGGAGCTGCCAACCGAGCTTTGATCCGAGGATGTCCGAATGGGGAAACCCAGCACGAGTGATGTCGTGTTACCCACTGCTGAATATATAGGCTTTGGGAGGAAACGCGGGGAAGTGAAACATCTCAGTACCCGTAGGAAGAGAAAACAACCGTGATTCCGTGAGTAGTGGCGAGCGAAAGCGGAAGATGGCTAAACCGCATGCATGTGATACCTGGTAGGGGTTGTGTGTGCGGGGTTGTGGGAGTTGTACTTGCCGGTTCTACCAGGCCGGCGGACAGTAAAAAAGTGTCGTGATTAGCGGAAGTGGTCTGGGACGGCCCGCCGCAGACGGTGAGAGTCCGGTACGCGAAAATCCGACACCTGTCTCGTACTTCATCCCGAGTAGCAGCGGGCTCGTGGAATCTGCTGTGAATCTGCCGGGACCACCCGGTAAGCCTAAATACTCTCTAGTGACCGATAGCGGATTAGTACCGTGAGGGAATGGTGAAAAGTACCCCGGGAGGGGAGTGAAATAGTACCTGAAACCATGTGCCTACAATCCGTCAAAGCCTCCTTGTGGGGTGATGGCGTGCCTTTTGAAGAATGAGCCTGCGAGTCAGGGACACGTCGCGAGGTTAACCCGTGAGGGGTAGCCGTAGCGAAAGCGAGTCTGAATAGGGCGCCCATAGTGGCGTGTTCTGGACCCGAAGCGGAGTGATCTACCCATGGCCAGGGTGAAGCGGCGGTAAGACGCCGTGGAGGCCCGAACCCACTTAGGTTGAAGACTGAGGGGATGAGCTGTGGGTAGGGGTGAAAGGCCAATCAAACTCCGTGATAGCTGGTTCTCCCCGAAATGCATTTAGGTGCAGCGTCGCGTGTTTCTTATTGGAGGTAGAGCTACTGGATGGCCGATGGGCCCTACTAGGTTACTGACGTCAGCCAAACTCCGAATGCCAATAAGTTAGAGCGCGGCAGTGAGACGGCGGGGGAGAAGCTCCGTACGTCGAGAGGGAAACAGCCCAGATCGCCGGCTAAGGCCCCTAAGCGTGTACTAAGTGGAAAAGGATGTGCAGTCGCAAAGACAACCAGGAGGTTGGCTTAGAAGCAGCCACCCTTGAAAGAGTGCGTAATAGCTCACTGGTCAAGTGATTGTGCGCCGACAATGTAGCGGGGCTCAAGTACACCGCCGAAGCCGCGGCATTCATGCAATACATTCCCTTCGGGGCAGTGGCATGGATGGGTAGGGGAGCGTCCTGCACCCAGCGAAGCTGCGGAGTAATCCAGCAGTGGAGGGTGCGGGAGTGAGAATGCAGGCATGAGTAGCGACAGGCAAGTGAGAAACTTGCCCGCCGAATGACCAAGGGTTCCTGGGCCAGGCTAGTCCTCCCAGGGTAAGTCGGGACCTAAGGCGAGGCCGACAGGCGTAGTCGATGGACAACGGGTTGATATTCCCGTACCCGTGTGTGCGCGCCCATGATGAATCATCGGTACTAACCACCCAAAAGGTTCTAGATCAATCTCTTCGGAGTGCGACGTGAACCCGCTGCGTGGGACCTTCGGTGGTAGTAGTCAAGCGATGGGGTGACGCAGGAAGGTAGCTGTACCGGTTAGTGGTTATACCGGAGCAAGCCCGTAGGGCGACGTCTAGGTAAATCCGGATGTCATTAAGCCTGAGAGGTGACGCATAGCCGATTGAGGCGAATTCAGTGATCCTATGCTGCCAAGAAAAGCCTCTAGTGAGTTCACACACGGCCCGTACCCCAAACCAACACAGGTGGTCAGGTAGAGAATACTAAGGCGTACGAGATAACTATGGTTAAGGAACTCGGCAAAATACCCCCGTAACTTCGGGAGAAGGGGGACCTCGCTTGGTGACCGGACTTGCTCCGTGAGCTGAACGAGGTCGCAGAGACCAGTGAGAAGCGACTGTTTACTAAAAACACAGGTCCGTGCGAAGTCGCAAGACGATGTATACGGACTGACGCCTGCCCGGTGCTGGAAGGTTAAGAGGACCCGTTAACCCTTGGGTGAAGCGGAGAATTTAAGCCCCAGTAAACGGCGGTGGTAACTATAACCATCCTAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCTGCACGAATGGCGTAACGACTTCTCAACTGTCTCAACCATAGACTCGGCGAAATTGCACTACGAGTAAAGATGCTCGTTACGCGCGGCAGGACGAAAAGACCCCGGGACCTTCACTATAGCTTGGTATTGGCGTTTGGTTCGGTTTGTGTAGGATAGGTGGGAGACTGTGAAGCAGGCACGCCAGTGTTTGTGGAGTCATCGTTGAAATACCACTCTGATCGTATTGAACCTCTAACCTCGGACCGTATATCCGGTCCAGGGACAGTGCCTGGTGGGTAGTTTAACTGGGGCGGTTGCCTCCCAAAATGTAACGGAGGCGCCCAAAGGTTCCCTCAACCTGGACGGCAATCAGGTGTTGAGTGCAAGTGCACAAGGGAGCTTGACTGCGAGACTTACAAGTCGAGCAGGGACGAAAGTCGGGACTAGTGATCCGGCATCTCTGAGTGGAAGGGATGTCGCTCAACGGATAAAAGGTACCCCGGGGATAACAGGCTGATCTTCCCCAAGAGTCCATATCGACGGGATGGTTTGGCACCTCGATGTCGGCTCGTCGCATCCTGGGGCTGGAGCAGGTCCCAAGGGTTGGGCTGTTCGCCCATTAAAGCGGCACGCGAGCTGGGTTTAGAACGTCGTGAGACAGTTCGGTCTCTATCCGCCGCGCGCGTCAGAAACTTGAGGAAACCTGTCCCTAGTACGAGAGGACCGGGACGGACGAACCTCTGGTGTACCAGTTGTTCCACCAGGAGCACGGCTGGATAGCTACGTTCGGACAGGATAACCGCTGAAAGCATCTAAGCGGGAAACCTATTCCAAGACCAGGTTTCTTACCCTTTTAGAGGGATAAGGTCACCCACAGACTATGGGTTCAATAGGCCAGACCTGTAAGCGTAGTAATACGTTCAGGGAACTGGCACTAATCGACCGAAAACTTACTAAT","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41314","NCBI_taxonomy_name":"Mycobacteroides chelonae","NCBI_taxonomy_id":"1774"}}}},"ARO_accession":"3004165","ARO_id":"41313","ARO_name":"Mycobacteroides chelonae 23S rRNA with mutation conferring resistance to clarithromycin","CARD_short_name":"Mche_23S_CLR","ARO_description":"Point mutation in the 23S rRNA of Mycobacteroides chelonae shown to confer resistance to clarithromycin, a macrolide type antibiotic.","ARO_category":{"41251":{"category_aro_accession":"3004125","category_aro_cvterm_id":"41251","category_aro_name":"23S rRNA with mutation conferring resistance to macrolide antibiotics","category_aro_description":"Nucleotide point mutations in the 23S rRNA subunit may confer resistance to macrolide antibiotics.","category_aro_class_name":"AMR Gene Family"},"35982":{"category_aro_accession":"0000065","category_aro_cvterm_id":"35982","category_aro_name":"clarithromycin","category_aro_description":"Clarithromycin is a methyl derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome and is used to treat pharyngitis, tonsillitis, acute maxillary sinusitis, acute bacterial exacerbation of chronic bronchitis, pneumonia (especially atypical pneumonias associated with Chlamydia pneumoniae or TWAR), and skin structure infections.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3366":{"model_id":"3366","model_name":"pexA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"5551":{"protein_sequence":{"accession":"ADI87853.1","sequence":"MKKFVLFCERNGIALIPIVLILLGCGLWPEMELLVPSLPDMQRAFNIQDAQIQQLLTANFVGFLIGVLFAGPLCDSAGRRTVMMIGTIGYLVSSVLCPFCNDFVLLMIARFFQGLFMTGPVIAGGVLLMEATEGVKQIFWMSIGNAAITFCMAAGPIVGSWINTGFGYVGNLWSILILGLIGCLPALFLVPESLPVEKRAAFHPKLLFKGYFALLKDFRFMCLAIPMCALAAAYWIYVGVSALYMVNQLGIAQEMFGRYQGPIVGCFSIISLGSSKLLQRFGLMKCLRAGIVSMFTGMLLLLGMSILSLDHAVATTVFMMFFVGGMAPICSMLFPYALGHLPVDLKGNAQAMVQAIRLFFASIGTSLVGVFYKSAFLPVALIMFAILLFSCYFLWKGRRYLKEGLGADHILSVGH"},"dna_sequence":{"accession":"HM537013.1","fmin":"24054","fmax":"25302","strand":"-","sequence":"ATGAAAAAGTTTGTACTTTTTTGCGAGCGTAATGGAATCGCTTTGATTCCGATCGTTTTGATCCTTTTGGGTTGTGGTCTTTGGCCAGAGATGGAACTTTTGGTTCCGAGTTTGCCTGACATGCAGCGTGCCTTTAACATCCAAGATGCGCAGATTCAACAGTTGCTGACTGCAAATTTTGTCGGATTTCTTATCGGTGTTCTCTTTGCGGGTCCCCTTTGTGACAGTGCAGGTCGAAGAACCGTAATGATGATAGGGACGATAGGTTACCTTGTTTCGTCCGTGCTTTGTCCGTTTTGTAACGACTTTGTGCTTTTAATGATTGCCCGATTTTTCCAAGGCTTGTTCATGACGGGGCCGGTCATTGCCGGTGGTGTCCTCTTGATGGAAGCCACGGAAGGGGTGAAACAAATCTTTTGGATGTCGATTGGTAATGCAGCTATTACGTTTTGCATGGCTGCAGGACCTATTGTTGGATCTTGGATCAATACAGGTTTTGGCTATGTTGGAAATCTGTGGAGCATTCTCATCCTTGGTTTGATTGGCTGCCTTCCTGCGTTATTTTTAGTGCCGGAAAGTCTTCCAGTTGAGAAGCGAGCAGCTTTCCATCCCAAACTACTTTTCAAAGGGTATTTTGCGCTATTGAAAGATTTTAGGTTTATGTGTCTTGCGATTCCCATGTGCGCACTAGCGGCAGCCTATTGGATCTACGTCGGTGTAAGTGCCTTATACATGGTGAATCAGTTGGGAATTGCGCAAGAGATGTTCGGTCGTTATCAAGGACCTATCGTTGGTTGCTTCTCGATAATCTCTCTTGGCTCTTCGAAACTTCTTCAGCGCTTTGGTTTGATGAAATGCCTACGTGCAGGAATTGTTTCCATGTTCACGGGTATGCTTCTTCTTTTAGGCATGAGCATTCTTTCTTTGGATCATGCAGTAGCGACAACGGTGTTTATGATGTTCTTCGTTGGAGGAATGGCACCGATTTGCAGCATGCTTTTCCCATATGCTTTGGGACATTTGCCTGTCGATCTAAAAGGGAATGCACAAGCCATGGTACAAGCGATTAGACTCTTTTTCGCATCAATTGGTACTTCCTTGGTTGGTGTCTTCTACAAAAGTGCTTTTTTGCCAGTAGCCCTGATTATGTTCGCCATTCTTCTCTTCAGTTGCTACTTCCTTTGGAAGGGAAGACGTTACTTGAAAGAAGGTCTTGGTGCGGATCATATTTTGAGCGTTGGTCACTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42710","NCBI_taxonomy_name":"uncultured bacterium Ak20-3","NCBI_taxonomy_id":"798570"}}}},"ARO_accession":"3004666","ARO_id":"42709","ARO_name":"pexA","CARD_short_name":"pexA","ARO_description":"pexA is a florfenicol and chloramphenicol resistance gene discovered in Alaskan soil.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36600":{"category_aro_accession":"3000461","category_aro_cvterm_id":"36600","category_aro_name":"florfenicol","category_aro_description":"Florfenicol is a fluorine derivative of chloramphenicol, where the nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3) and the hydroxyl group (-OH), by a fluorine group (-F). The action mechanism is the same as chloramphenicol's, where the antibiotic binds to the 23S RNA of the 50S subunit of bacterial ribosomes to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"3372":{"model_id":"3372","model_name":"FosB6","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"250"}},"model_sequences":{"sequence":{"5557":{"protein_sequence":{"accession":"ALM24145.1","sequence":"MIKGINHITYSVSNIAKSIEFYRDILGADILVESETSAYFNLGDIWLALNEEKNIPRSEIKYSYTHIAFTISDNDFEDWYIWLKENEVNILEGRDRDIRDKKSIYFTDLDGHKLELHTGSLEDRLNYYKEAKPHMNFYI"},"dna_sequence":{"accession":"KR870314.1","fmin":"0","fmax":"420","strand":"+","sequence":"ATGATTAAAGGAATAAATCATATTACTTATTCGGTTTCTAATATAGCTAAATCAATTGAATTTTACAGAGATATTTTAGGGGCTGACATTTTAGTTGAAAGTGAGACCTCGGCCTATTTTAATTTAGGTGATATATGGTTAGCTTTGAACGAAGAAAAAAATATTCCTAGAAGCGAAATTAAATATTCGTATACTCATATAGCATTTACAATTTCAGATAACGATTTTGAAGATTGGTATATCTGGTTGAAAGAAAATGAAGTAAATATTCTTGAAGGTAGAGATAGAGATATTAGAGATAAAAAATCAATATATTTCACTGATTTAGATGGTCATAAATTAGAATTGCATACAGGAAGTTTAGAAGATAGATTGAATTATTATAAAGAGGCTAAACCTCATATGAATTTTTATATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35508","NCBI_taxonomy_name":"Staphylococcus aureus","NCBI_taxonomy_id":"1280"}}}},"ARO_accession":"3004673","ARO_id":"42721","ARO_name":"FosB6","CARD_short_name":"FosB6","ARO_description":"Fosfomycin resistance gene. High homology with FosB1 and FosB3.","ARO_category":{"36272":{"category_aro_accession":"3000133","category_aro_cvterm_id":"36272","category_aro_name":"fosfomycin thiol transferase","category_aro_description":"Catalyzes the addition of a thiol group from a nucleophilic molecule to fosfomycin.","category_aro_class_name":"AMR Gene Family"},"35944":{"category_aro_accession":"0000025","category_aro_cvterm_id":"35944","category_aro_name":"fosfomycin","category_aro_description":"Fosfomycin (also known as phosphomycin and phosphonomycin) is a broad-spectrum antibiotic produced by certain Streptomyces species. It is effective on gram positive and negative bacteria as it targets the cell wall, an essential feature shared by both bacteria. Its specific target is MurA (MurZ in E.coli), which attaches phosphoenolpyruvate (PEP) to UDP-N-acetylglucosamine, a step of commitment to cell wall synthesis. In the active site of MurA, the active cysteine molecule is alkylated which stops the catalytic reaction.","category_aro_class_name":"Antibiotic"},"45731":{"category_aro_accession":"3007149","category_aro_cvterm_id":"45731","category_aro_name":"phosphonic acid antibiotic","category_aro_description":"A group of antibiotics derived from phosphonic acids.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3376":{"model_id":"3376","model_name":"rmtD2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8349":{"protein_sequence":{"accession":"ADW66527.1","sequence":"MSELKEKLLASKKYRDVCPDTIERIWRECSAKFKKEKDADKAAREALHGVTGAFMTEREYKRAMELAATRDWEALLGMHASTRERLPVESMDRVFDQLFEAIGTPARILDLACGLNPVYLAHRLPNAAIAGVDISGQCVNVIRAFGGAEARLGDLLCEIPEDEADAALMFKVLPLLERQRTGAAMEALMRVNAEWIVASFPTRSLGGRNVGMEKHYSEWMEAHVPENRAIAARLTGENELFYVLKRK"},"dna_sequence":{"accession":"HQ401565.1","fmin":"14138","fmax":"14882","strand":"-","sequence":"ATGAGCGAACTGAAGGAAAAACTGCTCGCTTCGAAAAAATATCGCGACGTTTGCCCGGACACGATCGAGCGCATATGGCGTGAATGCAGCGCGAAATTCAAAAAGGAAAAGGACGCGGACAAGGCGGCGCGCGAAGCGCTTCACGGTGTGACCGGCGCGTTCATGACCGAGCGCGAATACAAACGCGCGATGGAACTGGCGGCGACACGCGATTGGGAAGCGCTGCTTGGAATGCACGCGTCCACGCGCGAACGGCTGCCGGTGGAATCGATGGATCGCGTGTTCGATCAGCTGTTTGAAGCCATCGGAACGCCGGCGCGAATTCTCGATCTCGCGTGCGGGCTGAATCCGGTCTACCTCGCGCATCGATTGCCAAATGCGGCGATTGCCGGCGTGGATATCAGCGGTCAGTGCGTAAACGTAATTCGCGCGTTTGGCGGCGCGGAAGCGCGTTTGGGCGATTTGCTGTGCGAAATTCCGGAAGACGAAGCGGATGCGGCGCTGATGTTTAAGGTGCTGCCGCTTTTGGAGCGCCAGCGCACGGGCGCGGCGATGGAAGCGCTAATGCGTGTGAATGCGGAATGGATCGTCGCATCGTTTCCGACGCGTTCACTCGGCGGGCGCAACGTCGGCATGGAAAAGCACTATTCCGAATGGATGGAGGCGCACGTGCCGGAAAATCGCGCGATTGCCGCGCGGCTGACCGGCGAAAACGAGCTGTTTTACGTGCTGAAACGAAAATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36770","NCBI_taxonomy_name":"Klebsiella aerogenes","NCBI_taxonomy_id":"548"}}}},"ARO_accession":"3004677","ARO_id":"42726","ARO_name":"rmtD2","CARD_short_name":"rmtD2","ARO_description":"The first allele of a 16S rRNA methyltransferase gene, rmtD2, confers a high resistance to all clinically available aminoglycosides.","ARO_category":{"41435":{"category_aro_accession":"3004271","category_aro_cvterm_id":"41435","category_aro_name":"16S rRNA methyltransferase (G1405)","category_aro_description":"Methyltransferases that methylate the G1405 position of 16S rRNA, which is part of an aminoglycoside binding site.","category_aro_class_name":"AMR Gene Family"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"40942":{"category_aro_accession":"3004015","category_aro_cvterm_id":"40942","category_aro_name":"gentamicin A","category_aro_description":"Gentamicin A is part of a complex of broad spectrum aminoglycoside antibiotics. Gentamicin inhibits protein synthesis, resulting in bacterial cell death.","category_aro_class_name":"Antibiotic"},"46133":{"category_aro_accession":"3007382","category_aro_cvterm_id":"46133","category_aro_name":"gentamicin","category_aro_description":"Gentamicin is a commonly used aminoglycoside antibiotic derived from members of the Micromonospora genus of bacteria. It acts by binding the 30S ribosomal subunit, thus inhibiting protein synthesis. Gentamicin is typically used to treat Gram-negative infections of the repiratory and urinary tract, as well as infections of the bone and soft tissue. It also exhibits considerable nephrotoxicity and ototoxicity. Gentamicin is administered as a mixture of gentamicin type C (which makes about around 80% of the complex) and types A, B, and X (distributed in the remaining 20% of the complex).","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3379":{"model_id":"3379","model_name":"APH(3')-VIIIa","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"350"}},"model_sequences":{"sequence":{"5564":{"protein_sequence":{"accession":"AAG11411.2","sequence":"MDDALRALRGRYPGCEWVVVEDGASGAGVYRLRGGGRELFVKVAALGAGVGLLGEAERLVWLAEVGIPVPRVVEGGGDERVAWLVTEAVPGRPASARWPREQRLDVAVALAGLARSLHALDWERCPFDRSLAVTVPQAARAVAEGSVDLEDLDEERKGWSGERLLAELERTRPADEDLAVCHGDLCPDNVLLDPRTCEVTGLIDVGRVGRADRHSDLALVLRELAHEEDPWFGPECSAAFLREYGRGWDGAVSEEKLAFYRLLDEFF"},"dna_sequence":{"accession":"AF182845.2","fmin":"0","fmax":"804","strand":"+","sequence":"ATGGACGATGCGTTGCGTGCACTGCGGGGTCGGTATCCCGGTTGTGAGTGGGTTGTTGTGGAGGATGGGGCCTCGGGGGCTGGTGTTTATCGGCTTCGGGGTGGTGGGCGGGAGTTGTTTGTCAAGGTGGCAGCTCTGGGGGCCGGGGTGGGCTTGTTGGGTGAGGCTGAGCGGCTGGTGTGGTTGGCGGAGGTGGGGATTCCCGTACCTCGTGTTGTGGAGGGTGGTGGGGACGAGAGGGTCGCCTGGTTGGTCACCGAAGCGGTTCCGGGGCGTCCGGCCAGTGCGCGGTGGCCGCGGGAGCAGCGGCTGGACGTGGCGGTGGCGCTCGCGGGGCTCGCTCGTTCGCTGCACGCGCTGGACTGGGAGCGGTGTCCGTTCGATCGCAGTCTCGCGGTGACGGTGCCGCAGGCGGCCCGTGCTGTCGCTGAAGGGAGCGTCGACTTGGAGGATCTGGACGAGGAGCGGAAGGGGTGGTCGGGGGAGCGGCTTCTCGCCGAGCTGGAGCGGACTCGGCCTGCGGACGAGGATCTGGCGGTTTGCCACGGTGACCTGTGCCCGGACAACGTGCTGCTCGACCCTCGTACCTGCGAGGTGACCGGGCTGATCGACGTGGGGCGGGTCGGCCGTGCGGACCGGCACTCCGATCTCGCGCTGGTGCTGCGCGAGCTGGCCCACGAGGAGGACCCGTGGTTCGGGCCGGAGTGTTCCGCGGCGTTCCTGCGGGAGTACGGGCGCGGGTGGGATGGGGCGGTATCGGAGGAAAAGCTGGCGTTTTACCGGCTGTTGGACGAGTTCTTCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36773","NCBI_taxonomy_name":"Streptomyces rimosus","NCBI_taxonomy_id":"1927"}}}},"ARO_accession":"3004680","ARO_id":"42729","ARO_name":"APH(3')-VIIIa","CARD_short_name":"APH(3')-VIIIa","ARO_description":"APH(3')-VIIIa is an aminoglycoside phosphoryltransferase that acts on the 3-OH target of aminoglycosides found in Streptomyces rimosus.","ARO_category":{"36265":{"category_aro_accession":"3000126","category_aro_cvterm_id":"36265","category_aro_name":"APH(3')","category_aro_description":"A category of aminoglycoside O-phosphotransferase enzymes with modification regiospecificity based at the 3'-hydroxyl group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics, specifically kanamycin and neomycin, by the ATP-dependent phosphorylation of the 3'-hydroxyl group of the compound.","category_aro_class_name":"AMR Gene Family"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2519":{"model_id":"2519","model_name":"LlmA 23S ribosomal RNA methyltransferase","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"3855":{"protein_sequence":{"accession":"APB03216.1","sequence":"MYVAQDWQDYEVIDTGGGEKLERWGDVILRRPDPQIIWPIEREDGQWRSVHGHYHRSSSGGGQWDMKKQLPDRWTISYDQLKFHIRPTNFKHTGLFPEQAANWRWMMDKIASAGRPVSVLNLFAYTGGATVAAASAGAQVVHVDAAKGMVQWAKENAALSGLADRPIRYITDDVFKFVQREQRRGNKYDAIIMDPPSYGRGPSGETWKLEQSLYPFLESCMSIVSDNPLFMLINSYTTGISPTVLNNMLTMTMKPKYGGTISAGEIGLPITRSGMNLPCGILGRWES"},"dna_sequence":{"accession":"KX531046.1","fmin":"0","fmax":"864","strand":"+","sequence":"ATGTATGTAGCTCAGGATTGGCAAGATTACGAGGTCATCGATACCGGAGGCGGAGAAAAGCTGGAACGCTGGGGCGACGTGATTCTCAGACGTCCGGATCCGCAGATCATATGGCCGATTGAACGTGAAGATGGACAGTGGCGCAGTGTGCACGGACACTATCATCGCAGCTCGTCGGGCGGCGGACAATGGGACATGAAAAAGCAGCTTCCGGACCGGTGGACCATCTCATACGACCAATTGAAATTTCATATTCGACCAACCAATTTTAAACATACCGGTTTGTTTCCGGAGCAGGCAGCCAACTGGCGCTGGATGATGGATAAGATCGCTTCTGCCGGACGTCCGGTCAGCGTGCTGAACCTGTTCGCCTATACCGGCGGAGCAACCGTGGCGGCCGCTTCGGCCGGAGCTCAGGTTGTTCATGTGGATGCTGCGAAGGGAATGGTTCAATGGGCCAAGGAAAACGCGGCATTGTCCGGACTTGCCGACCGTCCTATCCGTTATATCACGGATGATGTGTTTAAATTCGTACAACGGGAGCAGCGTCGGGGGAACAAATACGATGCGATCATTATGGACCCTCCATCTTATGGCCGCGGACCAAGTGGAGAAACGTGGAAGCTTGAGCAAAGCTTGTATCCCTTCCTCGAAAGCTGCATGAGCATCGTATCGGATAATCCGCTGTTCATGCTGATTAACTCCTATACAACCGGGATCTCCCCTACCGTTCTGAATAACATGCTGACCATGACCATGAAGCCGAAATACGGCGGTACCATCAGTGCGGGAGAGATCGGATTGCCGATTACCCGCTCCGGCATGAACCTGCCGTGCGGCATCCTAGGTCGATGGGAGTCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40862","NCBI_taxonomy_name":"Paenibacillus sp. LC231","NCBI_taxonomy_id":"1120679"}}}},"ARO_accession":"3003982","ARO_id":"40864","ARO_name":"LlmA 23S ribosomal RNA methyltransferase","CARD_short_name":"LlmA_23S_CLI","ARO_description":"Lincosamide (Clindamycin) resistant (putative) ribosomal methyltransferase related to the RlmK 23S rRNA methyltransferase COG family. Detected in Paenibacillus sp. LC231, an isolated strain of Paenibacillus found in Lechuguilla Cave, NM, USA. Described by Pawlowski et al. 2016.","ARO_category":{"41437":{"category_aro_accession":"3004273","category_aro_cvterm_id":"41437","category_aro_name":"Llm 23S ribosomal RNA methyltransferase","category_aro_description":"A family of lincosamide resistant 23S rRNA methyltransferases. The only member of the family discovered so far was isolated from Paenibacillus sp. LC231, a strain found in Lechuguilla Cave, NM, USA.","category_aro_class_name":"AMR Gene Family"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2520":{"model_id":"2520","model_name":"CatU","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"3856":{"protein_sequence":{"accession":"APB03217.1","sequence":"MKFHIINVEEWTRKPYYEHYLRSNKCTFSITVDIDITRLLYSLKANGFKLYPAFIYMVTRVVNDRVEFKTSFSPEGELGYWDRMTPSYTFFHNDDHTFSCLWTAFSNDFYRFHDHYEQDMEQYRDTKGLFVKENPPPNTFPISMIPWTSFSGFNLNIVNEADYLLPIITGGKYTEQGGRVLLPVSLQVHHAVCDGYHASMFFKELQSLADSFEDWLT"},"dna_sequence":{"accession":"KX531047.1","fmin":"0","fmax":"654","strand":"+","sequence":"ATGAAGTTTCACATTATTAATGTTGAAGAGTGGACGAGAAAGCCTTATTATGAGCATTATCTTCGATCGAATAAATGCACCTTCAGCATCACCGTGGATATCGACATTACTCGCTTGTTGTATTCGTTAAAAGCTAATGGATTCAAGCTTTATCCAGCTTTTATTTATATGGTTACAAGAGTTGTCAATGACCGGGTTGAATTCAAAACTTCCTTTAGTCCCGAAGGGGAATTGGGTTACTGGGATCGGATGACGCCGAGTTATACCTTTTTCCATAACGATGACCATACCTTCTCCTGTTTATGGACAGCATTTTCGAATGATTTCTATCGATTTCATGATCATTACGAGCAGGACATGGAGCAATATCGGGATACAAAAGGGCTGTTTGTTAAAGAGAATCCACCGCCGAACACGTTTCCCATATCCATGATACCCTGGACAAGCTTTAGCGGATTTAATCTAAACATTGTCAATGAAGCAGACTATCTTCTTCCCATCATAACCGGCGGAAAATATACCGAGCAGGGTGGCCGTGTTCTGCTTCCAGTCTCATTGCAGGTGCACCATGCTGTGTGTGATGGTTATCATGCCAGCATGTTCTTTAAGGAGTTGCAGAGCTTGGCGGATTCTTTTGAAGATTGGTTAACTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40862","NCBI_taxonomy_name":"Paenibacillus sp. LC231","NCBI_taxonomy_id":"1120679"}}}},"ARO_accession":"3003983","ARO_id":"40865","ARO_name":"CatU","CARD_short_name":"CatU","ARO_description":"Chloramphenicol acetyltransferase conferring resistance to phenicol antibiotics detected in Paenibacillus sp. LC231, an isolated strain of Paenibacillus from Lechuguilla Cave, NM, USA. Described by Pawlowski et al. 2016.","ARO_category":{"36261":{"category_aro_accession":"3000122","category_aro_cvterm_id":"36261","category_aro_name":"chloramphenicol acetyltransferase (CAT)","category_aro_description":"Inactivates chloramphenicol by addition of an acyl group. CAT is used to describe many variants of the chloramphenicol acetyltransferase gene in a range of organisms including Acinetobacter calcoaceticus, Agrobacterium tumefaciens, Alkalihalobacillus clausii, Bacillus subtilis, Campylobacter coli, Enterococcus faecalis, Enterococcus faecium, Lactococcus lactis, Listeria monocytogenes, Listonella anguillarum, Morganella morganii, Photobacterium damselae subsp. piscicida, Proteus mirabilis, Salmonella typhi, Serratia marcescens, Shigella flexneri, Staphylococcus aureus, Staphylococcus haemolyticus, Staphylococcus intermedius, Streptococcus agalactiae, Streptococcus suis and Streptomyces acrimycini.","category_aro_class_name":"AMR Gene Family"},"36521":{"category_aro_accession":"3000382","category_aro_cvterm_id":"36521","category_aro_name":"azidamfenicol","category_aro_description":"Azidamfenicol is a water soluble derivative of chloramphenicol, sharing the same mode of action of inhibiting peptide synthesis by interacting with the 23S RNA of the 50S ribosomal subunit.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36595":{"category_aro_accession":"3000456","category_aro_cvterm_id":"36595","category_aro_name":"thiamphenicol","category_aro_description":"Derivative of Chloramphenicol. The nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3).","category_aro_class_name":"Antibiotic"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2521":{"model_id":"2521","model_name":"BahA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1450"}},"model_sequences":{"sequence":{"3857":{"protein_sequence":{"accession":"APB03218.1","sequence":"MEIHKEKEKEKGVTFFRRIMANRKRRGPLSPGWKGASLGLGATGFILILIQANYLLTGHGVGKFIVGTFLFLFAAALISGLASMLLHGVKKLPSRYIWMLLYSLIMFLFCFIVQPGVSAVFIVSLAIVLSLFGALAYKFAAGSYKQVSKTRKIGAMACLSLITIAIGAGSFWLIRAGDDAAPDITLKQLKTSTRYEDSTMNNPAEQGTYPVQSLLYGSPDNYRTEFNQSGSLTTQTVDASRFVEKWSSLRTKSLGFGPEAMPLNGRVWYPEGEGTFPLVLIVHGNHLMNDYSDPGYEYLGRLLASKGYIFVSVDENFLNFSPYEDLFLISPLLSENPARGLLLLEHLQTWKDWNSDPDNPFYQKVDMERIALIGHSRGGEAVAIAAAYNKLGRHPDHGDIKFDYNFSIRSLISIAGTDGQYKPQGKPLPLQDVNYLSLHGAHDMDVNSLDGAKQYHRIRYTKGTNYMKSLVYIYGANHGQFNGGWGRGDGAGLGNQLFNLRQIMPRDEQETIAKVFISSFLDATLKDQRQYREVFKDLGYAKEWIPDNLYVGNYYDSQTTLIADFHEDIDLQSTTLPGGSLRGENLQQWKEEKVKTKWGEADYSAVRLGWNSNGSSEPASYTVTLPDNGVETGRDSSIVFSLADARKTEESGDPKELINFTITVEDRKGHQASLPLSHISKLPPVIEGKLLKWPFSNAGNTSEPVFQSYDFQLDDYYKMNPDFNPQQLSKIRIEFNLTKRGSILLRDVGIRS"},"dna_sequence":{"accession":"KX531048.1","fmin":"0","fmax":"2259","strand":"+","sequence":"TTGGAAATACACAAAGAGAAAGAAAAAGAAAAAGGCGTTACGTTTTTTCGAAGAATCATGGCAAACCGGAAGCGTAGGGGGCCGCTATCCCCTGGATGGAAGGGTGCGTCGCTTGGGCTCGGCGCCACCGGCTTTATTCTAATTCTGATACAGGCCAATTATCTATTGACGGGGCATGGTGTCGGTAAATTCATCGTGGGCACATTCCTGTTTCTCTTTGCGGCTGCCCTTATAAGCGGCCTAGCATCAATGTTGCTGCACGGGGTCAAGAAACTACCAAGCCGTTATATTTGGATGCTGCTGTATTCCCTGATCATGTTTTTATTCTGTTTTATTGTGCAGCCGGGCGTATCGGCAGTCTTCATCGTCTCTTTGGCCATTGTTTTATCTTTATTTGGTGCATTGGCTTATAAATTTGCAGCGGGAAGCTACAAGCAAGTGTCTAAAACCAGGAAAATCGGCGCGATGGCTTGTTTGTCCTTGATCACCATCGCGATCGGCGCTGGCAGCTTCTGGCTGATTCGGGCCGGAGATGATGCCGCTCCGGACATCACATTGAAACAGCTGAAAACCTCAACCCGATATGAAGACTCGACGATGAACAATCCGGCCGAACAAGGCACATATCCCGTCCAAAGCCTGTTATACGGAAGTCCTGACAACTATCGGACAGAATTTAATCAAAGCGGTTCCCTAACCACCCAAACGGTGGATGCGTCCAGGTTTGTTGAGAAGTGGTCGTCTTTGCGCACGAAGTCGCTTGGATTCGGACCCGAGGCCATGCCGTTAAACGGAAGAGTGTGGTATCCCGAAGGGGAAGGCACCTTTCCGCTTGTTTTGATTGTACATGGTAATCACTTGATGAATGATTATTCCGATCCGGGTTATGAATATCTCGGCAGGCTGCTCGCGAGCAAAGGGTATATATTTGTCTCCGTGGATGAAAATTTCCTCAATTTCTCCCCATATGAGGATCTATTCCTGATCAGCCCGCTGCTAAGTGAAAATCCGGCAAGGGGTCTGCTGCTGCTGGAGCATTTGCAAACCTGGAAGGACTGGAACAGCGATCCGGACAACCCGTTTTACCAAAAGGTCGATATGGAACGAATCGCCCTCATCGGTCATTCCCGGGGCGGCGAAGCGGTCGCGATCGCGGCAGCGTATAACAAGCTTGGCCGTCATCCGGACCATGGGGATATCAAGTTTGATTATAACTTTTCGATCCGCTCGCTCATTTCCATTGCGGGAACGGACGGGCAATATAAGCCCCAAGGCAAACCTCTGCCGCTGCAAGACGTAAATTATCTGTCTTTGCATGGAGCTCATGATATGGATGTCAACAGCCTGGACGGTGCGAAGCAATATCACCGGATTCGTTATACCAAGGGCACAAATTACATGAAATCGCTGGTCTATATTTATGGAGCCAACCACGGCCAGTTTAACGGAGGCTGGGGCAGAGGGGATGGGGCAGGGTTGGGGAACCAACTGTTTAACCTACGTCAAATTATGCCACGGGATGAGCAGGAAACCATCGCAAAAGTGTTCATATCTTCGTTCCTGGATGCCACGCTGAAGGACCAACGGCAATACAGGGAGGTGTTCAAGGATTTGGGTTACGCCAAGGAATGGATTCCCGACAATCTGTATGTGGGCAATTATTACGATTCGCAGACGACCTTGATCGCCGATTTTCATGAAGACATCGATCTGCAGAGCACCACGCTTCCTGGCGGCAGCCTGCGGGGCGAGAACCTGCAGCAATGGAAGGAAGAAAAGGTTAAGACAAAATGGGGCGAAGCGGATTACAGCGCGGTTCGCTTAGGCTGGAATTCGAACGGTTCGTCCGAGCCTGCCTCCTATACGGTTACTTTGCCGGATAACGGGGTGGAAACAGGAAGGGATAGCTCGATCGTATTTTCGCTGGCAGATGCACGCAAAACAGAAGAAAGCGGCGACCCGAAAGAGCTTATCAATTTTACGATTACGGTTGAAGATAGGAAGGGCCATCAGGCAAGTCTTCCCCTCAGCCACATATCCAAGTTGCCGCCTGTTATTGAAGGTAAACTTCTCAAATGGCCATTTTCGAATGCAGGCAATACTTCAGAACCCGTATTTCAAAGCTACGATTTCCAATTAGACGATTATTACAAAATGAATCCGGACTTCAACCCGCAGCAGTTGAGCAAGATTCGCATCGAGTTCAATCTAACCAAGCGGGGAAGCATTCTGCTTCGTGATGTTGGCATTCGATCTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40862","NCBI_taxonomy_name":"Paenibacillus sp. LC231","NCBI_taxonomy_id":"1120679"}}}},"ARO_accession":"3003984","ARO_id":"40866","ARO_name":"BahA","CARD_short_name":"BahA","ARO_description":"Bacitracin amidohydrolase found in Paenibacillus sp. LC231, an isolated strain of Paenibacillus from Lechuguilla Cave, NM, USA. Confers resistance by bacitracin inactivation through amidohydrolysis. Described by Pawlowski et al. 2016.","ARO_category":{"41424":{"category_aro_accession":"3004260","category_aro_cvterm_id":"41424","category_aro_name":"Bah amidohydrolase","category_aro_description":"Bah amidohydrolases are membrane proteins that inactivate bacitracin.","category_aro_class_name":"AMR Gene Family"},"35959":{"category_aro_accession":"0000041","category_aro_cvterm_id":"35959","category_aro_name":"bacitracin","category_aro_description":"Bacitracin is a mixture of related cyclic polypeptides produced by organisms of the licheniformis group of Bacillus subtilis var Tracy. Bacitracin interferes with the dephosphorylation of the C55-isoprenyl pyrophosphate, a molecule which carries the building blocks of the peptidoglycan bacterial cell wall outside of the inner membrane.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2522":{"model_id":"2522","model_name":"TaeA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1200"}},"model_sequences":{"sequence":{"3858":{"protein_sequence":{"accession":"APB03219.1","sequence":"MNILTVEQVTKSYGDKILFQDASFGMEDQDKIGIIGVNGTGKSTFLRVIAGLEPPDSGKISMGNRIRVRYLAQNPEFDPDKTVLQQVFEGDLPEMKAVREYTETMELLELHPSHEELQQKLLKLNQTLETLQAWQLESDAKTILSKLGIRNYEAKMGTLSGGQRKRVALAAALIQPSDLLILDEPTNHIDNESVAWLEQYLQKRRGALLMITHDRYFLDRVANVMLELDHGRLFRYEANYSRFLELKAEREEREAASEQKRQNLLRSELAWIRRGAKARTTKQKARIERFEKLKDQEMVHSSGELDVSVASTRLGRKILEIEGLRMKIDDKTLIQDLSYIAVPEDRIGIVGPNGSGKSTLLNLIAGRIQPGGGEVVLGPTVKLGYFTQEHQEMDGSQRVIEYIKDEAEVVRTADGSAITAAQMLERFLFPPALQWTPIAKLSGGEKRRLYLLRVLMSAPNVLLLDEPTNDLDIQTLSVLEQYLDEFPGVCIVVSHDRFFLDRTVDKIMAFEGDGQIRVHVGSYSEYAEWMQRHGGEASGSKAEASIAKSASGSSDGTDSDSAKEAPRERLKFSYKEQREFDQIDGLIEDTESKLASIQSEMETAGSDAARLQELMKAQEETERELEHLMERWTYLNELAEKIEQSKKS"},"dna_sequence":{"accession":"KX531049.1","fmin":"0","fmax":"1947","strand":"+","sequence":"ATGAATATTTTGACCGTCGAACAGGTAACAAAAAGCTATGGAGACAAAATTCTGTTTCAAGATGCATCCTTCGGAATGGAGGATCAGGATAAAATCGGCATTATCGGCGTGAATGGCACGGGGAAATCCACATTTCTGCGGGTCATCGCGGGGCTCGAGCCGCCCGACTCCGGTAAAATATCGATGGGCAATCGCATCCGGGTTCGTTACCTCGCGCAAAATCCGGAGTTTGATCCGGACAAAACCGTCCTGCAGCAGGTGTTTGAGGGCGATCTTCCGGAGATGAAGGCCGTGCGGGAATACACCGAAACGATGGAACTGCTGGAGCTGCATCCAAGTCATGAGGAGCTCCAGCAGAAACTGCTGAAGCTCAATCAGACGCTGGAAACGCTGCAGGCATGGCAGCTTGAAAGCGATGCGAAAACCATCCTGTCCAAGCTGGGGATTCGGAATTATGAAGCGAAGATGGGAACGCTGTCGGGCGGCCAGCGTAAGCGGGTGGCATTAGCCGCCGCCTTGATTCAGCCTTCCGACTTGCTTATTTTGGACGAGCCGACCAACCACATTGACAATGAATCCGTTGCCTGGCTGGAGCAGTATTTGCAGAAGCGCCGCGGCGCGCTGCTCATGATTACGCATGACCGGTATTTTCTGGACCGGGTAGCCAATGTTATGCTGGAGCTGGATCACGGACGGCTGTTTCGATATGAGGCGAACTACAGCCGTTTTCTGGAGCTGAAGGCAGAACGCGAGGAGCGTGAAGCCGCTTCCGAGCAAAAGCGCCAAAATTTGCTGCGGAGCGAGCTTGCCTGGATCCGCAGAGGGGCCAAGGCCCGCACGACCAAGCAGAAGGCGAGGATTGAACGCTTCGAGAAACTCAAGGATCAGGAGATGGTGCACAGCTCCGGTGAACTGGACGTTTCGGTCGCTTCCACCCGCTTGGGACGCAAAATTCTGGAGATTGAAGGTCTCCGGATGAAGATCGACGACAAAACGTTAATTCAGGACCTTTCCTATATCGCCGTTCCCGAGGATCGGATAGGTATCGTAGGCCCGAACGGCAGCGGCAAATCCACGCTGCTCAATCTGATTGCCGGGCGGATTCAGCCGGGTGGCGGGGAAGTCGTGCTCGGACCGACGGTCAAGCTCGGTTATTTCACGCAGGAGCATCAGGAGATGGACGGCAGTCAGCGCGTGATTGAGTATATCAAGGATGAGGCCGAGGTTGTCCGCACGGCGGACGGTTCGGCGATTACCGCAGCCCAGATGCTGGAACGCTTTCTGTTCCCGCCCGCGCTGCAGTGGACGCCGATTGCGAAGCTGTCCGGAGGCGAGAAGCGCCGCTTGTATCTGCTGCGGGTGCTGATGAGCGCACCGAATGTGCTGCTGCTTGATGAACCGACCAATGATTTGGATATCCAGACATTGTCCGTCCTGGAGCAGTATTTGGATGAGTTCCCGGGCGTCTGTATCGTGGTATCCCATGATCGCTTTTTCCTGGATCGAACCGTGGACAAGATTATGGCTTTTGAGGGCGACGGTCAGATTCGTGTCCATGTCGGCTCTTACAGCGAATATGCGGAATGGATGCAGCGTCACGGCGGTGAAGCTTCCGGGAGCAAGGCGGAGGCATCCATAGCCAAATCTGCTTCGGGGAGCAGCGATGGCACGGACAGTGATTCAGCTAAAGAAGCGCCGCGTGAGCGCTTGAAATTCAGTTACAAAGAACAACGGGAGTTTGATCAGATTGACGGGCTCATCGAGGATACCGAGAGCAAGCTCGCTTCGATTCAATCCGAGATGGAGACCGCCGGCAGCGACGCAGCCAGGCTTCAGGAGCTGATGAAGGCTCAGGAGGAAACGGAACGTGAGCTGGAGCATCTGATGGAACGCTGGACCTATCTGAACGAGCTCGCGGAGAAGATTGAACAGAGCAAGAAATCGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40862","NCBI_taxonomy_name":"Paenibacillus sp. LC231","NCBI_taxonomy_id":"1120679"}}}},"ARO_accession":"3003986","ARO_id":"40868","ARO_name":"TaeA","CARD_short_name":"TaeA","ARO_description":"Pleuromutilin (Tiamulin) ABC efflux pump found in Paenibacillus sp. LC231, a strain of Paenibacillus isolated from Lechuguilla Cave, NM, USA. Confers resistance to pleuromutilin antibiotics. Described by Pawlowski et al. 2016.","ARO_category":{"36002":{"category_aro_accession":"0010001","category_aro_cvterm_id":"36002","category_aro_name":"ATP-binding cassette (ABC) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding\/hydrolysis to transport substrates across cell membranes.","category_aro_class_name":"AMR Gene Family"},"37716":{"category_aro_accession":"3001317","category_aro_cvterm_id":"37716","category_aro_name":"pleuromutilin","category_aro_description":"Pleuromutilin is a natural product antibiotic produced by Clitopilus passeckerianus. Related antibiotics of clinical significance, such as tiamulin and retapamulin, are semi-synthetic derivatives of this compound.","category_aro_class_name":"Antibiotic"},"37014":{"category_aro_accession":"3000670","category_aro_cvterm_id":"37014","category_aro_name":"pleuromutilin antibiotic","category_aro_description":"Pleuromutilins are natural fungal products that target bacterial protein translation by binding the the 23S rRNA, blocking the ribosome P site at the 50S subunit. They are mostly used for agriculture and veterinary purposes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2523":{"model_id":"2523","model_name":"VatI","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"3859":{"protein_sequence":{"accession":"APB03220.1","sequence":"MTGPNPNERYPIPGDNNLQFIKNTITKPNIIAGDYSYYYALNGESFEDQVLYHYEFIGTKLMIGKFCSIASEVRFMMDGGNHRMDGSTFPFNIFGNGWEKFTPSLDQLPIKGDTIIGNDVWIGRRATIMSGVRIGDGAIIAAEAVVVKDVEPYTIVGGNPAKDIRKRYSTEVIQELLDIKWWDCDIEVINQYIGAIVSGDMDLLRKMRQN"},"dna_sequence":{"accession":"KX531050.1","fmin":"0","fmax":"633","strand":"+","sequence":"ATGACAGGACCGAATCCAAATGAGAGATATCCTATACCCGGAGATAACAATCTTCAGTTTATCAAGAACACGATTACAAAACCTAATATTATCGCAGGGGATTATTCATACTACTATGCCTTAAACGGAGAATCATTTGAGGATCAAGTATTGTATCATTATGAATTCATTGGAACTAAATTAATGATCGGCAAGTTTTGTTCCATTGCTTCCGAGGTCAGATTTATGATGGATGGAGGGAACCATCGGATGGACGGTTCAACCTTTCCATTTAATATCTTTGGAAACGGCTGGGAGAAATTCACTCCATCTTTGGATCAATTGCCGATCAAGGGAGATACGATCATTGGAAATGACGTGTGGATCGGAAGGCGTGCAACGATCATGTCGGGTGTAAGGATTGGCGATGGAGCTATCATTGCCGCTGAAGCTGTCGTTGTAAAGGATGTGGAGCCTTATACGATCGTTGGAGGCAATCCAGCGAAGGATATCCGCAAGCGATATTCCACCGAAGTCATTCAAGAGTTATTGGATATTAAATGGTGGGATTGCGATATCGAAGTCATCAATCAATATATTGGCGCAATTGTAAGCGGAGATATGGACTTGCTTAGAAAAATGAGACAAAATTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40862","NCBI_taxonomy_name":"Paenibacillus sp. LC231","NCBI_taxonomy_id":"1120679"}}}},"ARO_accession":"3003987","ARO_id":"40869","ARO_name":"VatI","CARD_short_name":"VatI","ARO_description":"Streptogramin A acetyltransferase found in Paenibacillus sp. LC231, isolated from Lechuguilla Cave, NM, USA. Confers resistance to streptogramin A antibiotics. Described by Pawlowski et al. 2016.","ARO_category":{"36592":{"category_aro_accession":"3000453","category_aro_cvterm_id":"36592","category_aro_name":"streptogramin vat acetyltransferase","category_aro_description":"vat (Virginiamycin acetyltransferases) enzymes catalyze the transfer of an acetyl group from acetyl-CoA to the secondary alcohol of streptogramin A compounds, thus inactivating virginiamycin-like antibiotics and conferring resistance to these compounds.","category_aro_class_name":"AMR Gene Family"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"virginiamycin M1","category_aro_description":"Virginiamycin M1 is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37016":{"category_aro_accession":"3000672","category_aro_cvterm_id":"37016","category_aro_name":"madumycin II","category_aro_description":"Madumycin II is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37017":{"category_aro_accession":"3000673","category_aro_cvterm_id":"37017","category_aro_name":"griseoviridin","category_aro_description":"Griseoviridin is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35952":{"category_aro_accession":"0000034","category_aro_cvterm_id":"35952","category_aro_name":"streptogramin A antibiotic","category_aro_description":"Streptogramin A antibiotics are cyclic polyketide peptide hybrids that bind to the ribosomal peptidyl transfer centre. Structural variation arises from substituting a proline for its desaturated derivative and by its substitution for Ala or Cys. Used alone, streptogramin A antibiotics are bacteriostatic, but is bactericidal when used with streptogramin B antibiotics.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2524":{"model_id":"2524","model_name":"AAC(2')-IIb","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"3860":{"protein_sequence":{"accession":"APB03221.1","sequence":"MNHRKGNEPTAAALMELHVLAMFTHDGNMQIRTINEPWPGEELAPRFFMGRTIDGSSICRFRHDVPEGIAGQLRALVEDEPIVTEEVLTRPKHFAAYMNLLRAEHYTSGPCYRIPDQTTQAKQTVRITPGNIREYSLTGFEWLTTEIDYDQPCVALIHENRVVSVCRSVRITERAHEAGLETSEEFRGRGYAAAVVAGWAIEVQKMGALALYSTLWGNSSSRRVANKLGLSYYGVNFTIS"},"dna_sequence":{"accession":"KX531051.1","fmin":"0","fmax":"723","strand":"+","sequence":"ATGAACCATAGGAAAGGTAACGAGCCAACCGCTGCGGCACTGATGGAATTGCATGTTCTGGCGATGTTTACGCATGACGGGAATATGCAAATTCGCACCATCAACGAGCCTTGGCCGGGAGAGGAGCTTGCCCCGAGGTTTTTCATGGGTCGAACGATAGACGGCTCTTCGATCTGCAGGTTTCGTCATGATGTTCCCGAAGGAATTGCCGGGCAATTGAGGGCTTTGGTTGAAGATGAGCCTATCGTTACTGAAGAGGTTCTGACGAGGCCTAAACATTTTGCAGCTTATATGAACCTCCTTCGCGCTGAGCACTATACGAGCGGACCTTGTTATCGGATACCTGATCAAACAACGCAGGCCAAACAGACGGTAAGGATCACACCGGGAAATATTCGCGAATATTCGCTCACCGGTTTTGAATGGCTGACCACGGAAATTGATTATGACCAGCCTTGTGTTGCGCTCATTCATGAGAATAGGGTGGTGTCGGTTTGCCGCAGCGTCCGGATTACTGAACGAGCTCACGAAGCTGGGCTTGAAACGTCAGAGGAATTTCGTGGAAGAGGTTATGCGGCTGCTGTTGTTGCCGGATGGGCCATAGAGGTGCAAAAAATGGGCGCGCTGGCGTTGTACAGTACTTTATGGGGAAATAGCTCTTCCCGGAGAGTAGCAAATAAATTAGGGTTGTCCTATTACGGAGTTAACTTCACGATCAGTTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40862","NCBI_taxonomy_name":"Paenibacillus sp. LC231","NCBI_taxonomy_id":"1120679"}}}},"ARO_accession":"3003988","ARO_id":"40870","ARO_name":"AAC(2')-IIb","CARD_short_name":"AAC(2')-IIb","ARO_description":"AAC(2')-IIb is an intrinsic Kasugamycin 2' acetyltransferase protein found in Paenibacillus sp. LC231, a strain of Paenibacillus isolated from Lechuguilla Cave, NM, USA. Confers resistance to aminoglycoside antibiotics, including kasugamycin. Described by Pawlowski et al. 2016.","ARO_category":{"36480":{"category_aro_accession":"3000341","category_aro_cvterm_id":"36480","category_aro_name":"AAC(2')","category_aro_description":"A category of aminoglycoside N-acetyltransferase enzymes with modification regiospecificity based at the 2'-amino group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics through acetylation of the 2-amino group of the compound.","category_aro_class_name":"AMR Gene Family"},"37695":{"category_aro_accession":"3001296","category_aro_cvterm_id":"37695","category_aro_name":"kasugamycin","category_aro_description":"An unusual aminoglycoside because the cyclitol ring is not amino substituted; it was discovered as a fermentation product of Streptomyces kasugaensis.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2525":{"model_id":"2525","model_name":"AAC(6')-34","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"3861":{"protein_sequence":{"accession":"APB03223.1","sequence":"MRIGDLIREDGGIAMLVYEAGPITVRELEEKDEISLASWLSNPDVLQYYEGRDNPHDVERVREHFYVDDDETRCIIKYEGKPIGYIQFYLLDEETLGEYGYNESDADCRTFATDQFIGEPDYWNRGIGTKLMTSMVEYLVFQRQADRIVMDPQAWNERAIACYEKCGFRKVRLLEKHEQHEGELRDCWIMEYRAERK"},"dna_sequence":{"accession":"KX531053.1","fmin":"0","fmax":"594","strand":"+","sequence":"ATGAGAATTGGGGATCTAATAAGGGAAGATGGGGGGATCGCGATGCTGGTGTACGAGGCTGGACCGATTACGGTTCGCGAGCTGGAGGAGAAGGATGAAATATCCTTAGCTTCTTGGCTGTCCAATCCGGATGTGCTGCAGTATTATGAGGGACGGGACAATCCTCACGACGTGGAGCGGGTGCGGGAGCATTTTTACGTGGATGATGATGAGACTCGCTGCATCATTAAATATGAGGGGAAACCGATCGGATATATTCAGTTTTATCTTCTGGATGAAGAGACGTTAGGCGAGTATGGATATAACGAGAGTGATGCAGACTGCAGAACCTTCGCCACGGATCAATTCATCGGGGAGCCGGATTATTGGAATCGAGGCATCGGTACGAAGCTCATGACTTCCATGGTGGAGTATCTCGTGTTTCAGAGGCAGGCTGATCGGATCGTAATGGACCCGCAGGCATGGAATGAACGGGCGATTGCTTGTTACGAAAAGTGCGGCTTCCGGAAGGTCAGACTGCTGGAGAAGCATGAACAGCATGAAGGTGAACTGCGGGACTGCTGGATTATGGAGTATCGGGCAGAGCGAAAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40862","NCBI_taxonomy_name":"Paenibacillus sp. LC231","NCBI_taxonomy_id":"1120679"}}}},"ARO_accession":"3003989","ARO_id":"40871","ARO_name":"AAC(6')-34","CARD_short_name":"AAC(6')-34","ARO_description":"AAC(6')-34 is an aminoglycoside 6'-phosphotransferase found in Paenibacillus sp. LC231, a strain of Paenibacillus from Lechuguilla Cave, NM, USA. Confers resistance to aminoglycoside antibiotics. Described by Pawlowski et al. 2016.","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"A category of aminoglycoside N-acetyltransferase enzymes with modification regiospecificity based at the 6'-amino group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics through acetylation of the 6-amino group of the compound.","category_aro_class_name":"AMR Gene Family"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2527":{"model_id":"2527","model_name":"mphI","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"3863":{"protein_sequence":{"accession":"APB03226.1","sequence":"MTIAKPNDDYTQVIQEMLEIAGKHGVNLIPEGIEMNESGMDFLVGFAEEAGTGARWILRKPRRPDVLDRADNEARVLKLIQSHLSVDVPDWRIYTPELIAYPLLSGQPAASVSMEGYAWNMDHENPGDGFIRSLAEALVALHGVDHDAARAAGLRVKSPQEVRDETARNMEDIKSRLGVSDALWERWQKWLEEDSYWPTHSALIHGDLHPPHILIDERVQVTGLLDWTESEVASPAKDFVLYYAIYGEHNLRVLLDRYEQAGGKVWPRMFDHIVEQHAAYPVLIAQFALLTGQEEYMTMARNALGLTE"},"dna_sequence":{"accession":"KX531056.1","fmin":"0","fmax":"927","strand":"+","sequence":"ATGACAATAGCAAAACCAAATGATGATTATACACAAGTGATCCAAGAGATGCTGGAGATTGCCGGAAAACACGGGGTGAATTTGATTCCGGAGGGAATAGAGATGAATGAATCCGGCATGGATTTCCTTGTTGGATTCGCAGAGGAGGCAGGGACTGGAGCACGGTGGATTCTGCGGAAACCGAGACGACCGGATGTGCTGGATAGAGCAGATAACGAAGCTAGGGTCCTGAAGCTGATTCAATCCCATCTTTCGGTTGATGTACCGGATTGGCGGATTTACACGCCGGAGCTCATCGCCTATCCGCTGCTTAGCGGGCAGCCTGCCGCTTCCGTCAGCATGGAAGGATATGCATGGAATATGGATCATGAGAATCCGGGCGACGGGTTTATCCGCTCACTGGCTGAAGCGCTGGTTGCCTTGCATGGCGTCGATCATGATGCAGCCCGAGCAGCAGGTCTGCGGGTAAAGAGTCCCCAAGAGGTTCGTGATGAGACGGCGCGAAATATGGAAGACATCAAGAGCCGTCTGGGCGTTTCCGATGCGCTGTGGGAGAGATGGCAAAAATGGCTGGAGGAGGATTCCTATTGGCCGACGCATTCTGCCCTCATCCATGGCGATCTTCATCCCCCGCATATCCTGATTGATGAGCGCGTGCAGGTGACCGGACTTTTGGATTGGACGGAGTCCGAGGTAGCAAGTCCCGCCAAAGACTTCGTGTTATACTACGCTATTTATGGCGAGCATAATCTCCGTGTCCTGTTGGACCGGTATGAACAAGCCGGAGGGAAGGTATGGCCGCGCATGTTCGATCATATTGTCGAACAGCATGCCGCGTATCCCGTGCTGATCGCCCAGTTCGCTCTCCTGACAGGCCAGGAAGAGTATATGACGATGGCGCGGAATGCTCTGGGTTTGACGGAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40862","NCBI_taxonomy_name":"Paenibacillus sp. LC231","NCBI_taxonomy_id":"1120679"}}}},"ARO_accession":"3003991","ARO_id":"40873","ARO_name":"mphI","CARD_short_name":"mphI","ARO_description":"mphI is a macrolide phosphotransferase protein found in Paenibacillus sp. LC231, a strain of Paenibacillus isolated from Lechuguilla Cave, NM, USA. Confers resistance to macrolide antibiotics. Described by Pawlowski et al. 2016.","ARO_category":{"36472":{"category_aro_accession":"3000333","category_aro_cvterm_id":"36472","category_aro_name":"macrolide phosphotransferase (MPH)","category_aro_description":"Macrolide phosphotransferases (MPH) are enzymes encoded by macrolide phosphotransferase genes (mph genes). These enzymes phosphorylate macrolides in GTP dependent manner at 2'-OH of desosamine sugar thereby inactivating them. Characterized MPH's are differentiated based on their substrate specificity.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35974":{"category_aro_accession":"0000057","category_aro_cvterm_id":"35974","category_aro_name":"telithromycin","category_aro_description":"Telithromycin is a semi-synthetic derivative of erythromycin. It is a 14-membered macrolide and is the first ketolide antibiotic to be used in clinics. Telithromycin binds the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"36284":{"category_aro_accession":"3000145","category_aro_cvterm_id":"36284","category_aro_name":"tylosin","category_aro_description":"Tylosin is a 16-membered macrolide, naturally produced by Streptomyces fradiae. It interacts with the bacterial ribosome 50S subunit to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2528":{"model_id":"2528","model_name":"rphB","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1500"}},"model_sequences":{"sequence":{"3864":{"protein_sequence":{"accession":"APB03222.1","sequence":"MRSLVLDFQEMDKKQLGLVGGKGLHLGELSKIEGIRVPEGFCVTTIGYQRAIEQNETYQAMLNRLTMLSAEDRDQMVEISRKIRQTIMEVEIPSDVVTAVTRYLSRFGEEQAYAVRSSATAEDLPHASFAGQQDTYLNIIGVDAILQHISKCWASLFTDRAVIYRMQNGFDHRQVYLSVVVQRMVFPEASGILFTADPMTSNRKLLSIDAGFGLGEALVSGLVSADGYKVREGEIIEKRIAAKTLAIYGRKEGGTETKQIDPDQQKSQTLTDEQILQLARIGRQIEAHFGQPQDIEWCLAQDTFYIVQSRPITTLYPIPEANDQENHVYVSVGHQQMMTDPMKPLGLSFFLLTTPAPMRTAGGRLFVDTTAMLASPVSRENVLNTLGQSDPLIKDALMTILERGDFIKSLPIAENEQTPGKNNISSAGYQTPIDHDPTIVSDLMERTQSSIEVLKQNIQTKSGSDLFDFILEDIQELKKNLFDPQSSAVIMAAMNASTWINEKMNEWLGEKNAADTLSQSVPGNVTSEMGLALLDVADVIRPYPEIIDYLEQAKDDHFLDKLLTFDGGQQAQDAILDFLDKYGMRCAGEIDLTRTRWSEKPIALVPLILGNIKNFEPNASHRKFEQGRQEALKKEQELLDRLKQLPDGEGKAQETKRMIDLIRNFMGYREYPKYGMVNRYFIYKQALLKEAERLVQAGVIHHKEDIYYLTFEELDEVVRTNKLDNPGSMVEQQAKLAIRQMISKRKEEYNVFEKLTPPRVITSDGEIIAGEYKRENIPAEAIVGLPVSSGTVEGRARVILNMKDADLEEGDILVTAFTDPSWTPLFVSIKGLVTEVGGLMTHGAVIAREYGLPAVVGVENATKRIKDGQRIRVHGSEGYIEILS"},"dna_sequence":{"accession":"KX531052.1","fmin":"0","fmax":"2655","strand":"+","sequence":"ATGCGTTCGTTGGTTCTCGATTTTCAGGAAATGGACAAAAAGCAGCTTGGGCTCGTTGGTGGAAAAGGGCTCCATTTAGGGGAATTATCAAAAATTGAGGGAATACGAGTTCCCGAAGGATTTTGCGTGACAACCATAGGATATCAAAGAGCCATCGAACAAAACGAAACGTATCAAGCTATGCTCAATCGACTAACCATGCTATCAGCAGAGGATCGAGATCAAATGGTTGAAATCAGCAGGAAGATCAGACAAACCATTATGGAGGTAGAAATTCCATCCGATGTAGTGACAGCAGTAACTCGCTATCTCTCCCGGTTTGGCGAGGAACAGGCTTATGCCGTACGATCCAGTGCAACTGCTGAAGATTTACCGCATGCCTCTTTTGCGGGTCAACAAGACACCTATCTAAACATCATCGGCGTCGATGCCATCTTGCAGCATATCAGCAAATGCTGGGCTTCCTTGTTTACAGATCGCGCGGTGATCTATCGCATGCAAAATGGATTTGACCATCGTCAAGTTTATTTATCCGTAGTCGTTCAAAGGATGGTTTTCCCCGAGGCTTCAGGGATATTATTCACCGCTGATCCGATGACTTCTAATCGAAAGCTGCTATCCATCGATGCCGGTTTCGGACTTGGAGAAGCACTGGTCTCTGGCTTGGTATCTGCCGATGGTTACAAAGTACGGGAAGGAGAAATCATCGAGAAGCGGATAGCAGCCAAAACATTGGCGATCTACGGACGAAAAGAAGGCGGAACAGAAACAAAGCAAATCGATCCCGATCAGCAAAAGTCACAAACACTTACGGATGAGCAAATTTTACAACTGGCACGCATCGGGAGACAGATTGAGGCTCATTTTGGCCAACCCCAAGATATCGAGTGGTGTTTGGCCCAGGATACCTTTTATATTGTCCAGAGTCGGCCAATCACGACGCTATACCCGATACCTGAAGCGAATGATCAAGAAAATCACGTATACGTATCTGTCGGTCATCAACAAATGATGACGGATCCCATGAAACCGCTGGGATTGTCTTTTTTCCTGCTAACGACTCCTGCACCCATGCGTACAGCTGGCGGAAGGTTGTTTGTTGATACTACGGCTATGCTGGCTTCACCGGTTAGCAGAGAAAATGTATTAAATACCCTGGGACAATCCGATCCACTCATCAAAGACGCTCTTATGACCATCTTAGAGCGAGGAGATTTTATAAAATCGCTACCCATCGCTGAAAATGAACAGACTCCCGGAAAAAACAATATATCGTCTGCGGGTTATCAAACGCCAATCGACCACGATCCGACAATCGTTTCTGATTTAATGGAACGTACTCAATCATCGATCGAAGTGTTGAAACAAAACATCCAAACGAAATCCGGATCCGATTTATTTGATTTTATATTGGAAGATATCCAGGAACTGAAGAAGAATTTATTTGACCCACAAAGCTCGGCTGTCATCATGGCTGCAATGAATGCTTCAACCTGGATCAACGAAAAAATGAATGAATGGTTAGGCGAAAAAAACGCAGCCGACACGCTTTCTCAATCCGTACCGGGCAATGTTACTTCGGAAATGGGTCTGGCGCTGCTGGATGTTGCAGACGTCATTCGTCCTTATCCGGAAATCATTGATTATTTGGAGCAAGCAAAAGATGATCACTTTTTGGATAAGCTGCTTACATTTGATGGCGGGCAGCAAGCTCAAGACGCGATCCTAGATTTTCTTGACAAATATGGCATGCGATGTGCTGGAGAAATCGATTTAACAAGAACTCGTTGGAGTGAAAAACCAATTGCGCTTGTTCCGTTGATTCTGGGTAACATCAAAAACTTCGAGCCTAATGCCAGCCATCGGAAATTCGAGCAAGGGCGGCAGGAAGCTTTGAAAAAAGAACAAGAGCTATTAGATCGATTGAAACAATTGCCGGACGGTGAAGGAAAAGCCCAAGAAACCAAACGAATGATTGACCTCATTCGGAATTTCATGGGTTATCGGGAATACCCGAAATACGGTATGGTGAATCGTTACTTTATTTATAAGCAGGCTTTACTGAAAGAGGCTGAACGACTCGTACAAGCGGGCGTTATTCATCATAAGGAAGATATATATTATCTCACTTTTGAAGAGCTTGACGAGGTCGTACGCACAAATAAACTGGATAACCCGGGTTCCATGGTCGAGCAGCAAGCAAAGCTTGCGATCAGACAGATGATCAGCAAACGAAAAGAGGAGTACAACGTATTTGAAAAACTAACTCCTCCGCGCGTGATCACGTCGGATGGTGAAATCATCGCAGGGGAGTACAAACGAGAAAATATCCCAGCCGAAGCTATTGTCGGCCTGCCTGTTTCTTCCGGAACGGTCGAAGGACGAGCGCGTGTCATCTTAAACATGAAAGACGCCGATCTCGAGGAAGGAGATATATTAGTCACCGCTTTTACCGACCCTAGCTGGACGCCTCTGTTTGTATCCATTAAGGGCTTGGTCACCGAAGTGGGCGGACTGATGACCCATGGAGCCGTTATCGCGCGTGAATATGGCTTACCGGCCGTTGTCGGCGTTGAGAATGCTACCAAACGGATAAAGGACGGGCAGCGCATTCGCGTACATGGGTCCGAAGGCTATATTGAAATATTGTCATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40862","NCBI_taxonomy_name":"Paenibacillus sp. LC231","NCBI_taxonomy_id":"1120679"}}}},"ARO_accession":"3003992","ARO_id":"40874","ARO_name":"rphB","CARD_short_name":"rphB","ARO_description":"rphB is a rifampin phosphotransferase protein found in Paenibacillus sp. LC231, a strain of Paenibacillus isolated from Lechuguilla Cave, NM, USA. Confers resistance to rifamycin antibiotics, specifically rifampin, through rifampin inactivation. Described by Pawlowski et al. 2016.","ARO_category":{"41087":{"category_aro_accession":"3004040","category_aro_cvterm_id":"41087","category_aro_name":"rifampin phosphotransferase","category_aro_description":"Enzymes, protein or other gene products that inactivate rifampin (rifamycin) antibiotics through phosphorylation of the antibiotic at the 21-OH position.","category_aro_class_name":"AMR Gene Family"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36656":{"category_aro_accession":"3000517","category_aro_cvterm_id":"36656","category_aro_name":"rifaximin","category_aro_description":"Rifaximin is a semi-synthetic rifamycin used to treat traveller's diarrhea. Rifaximin inhibits RNA synthesis by binding to the beta subunit of bacterial RNA polymerase.","category_aro_class_name":"Antibiotic"},"36669":{"category_aro_accession":"3000530","category_aro_cvterm_id":"36669","category_aro_name":"rifabutin","category_aro_description":"Rifabutin is a semisynthetic rifamycin used in tuberculosis therapy. It inhibits DNA-dependent RNA synthesis.","category_aro_class_name":"Antibiotic"},"36673":{"category_aro_accession":"3000534","category_aro_cvterm_id":"36673","category_aro_name":"rifapentine","category_aro_description":"Rifapentine is a semisynthetic rifamycin that inhibits DNA-dependent RNA synthesis. It is often used in the treatment of tuberculosis and leprosy.","category_aro_class_name":"Antibiotic"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2529":{"model_id":"2529","model_name":"cpaA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"3865":{"protein_sequence":{"accession":"APB03224.1","sequence":"MPLRITAMTETYADQIMQWSYEPPYDFYNSEPDEEFRKELLECSYYAILDKEGQLFGFCCTGSSAQIPIAIPLGAYDEDLLDFGLGMKPESTGQCRGKEFLSFVLASIAEFHKRQSFRLTVAKFNERAIRLYTQLGFSEVATFDYGGTTFITMIKKPGSGL"},"dna_sequence":{"accession":"KX531054.1","fmin":"0","fmax":"486","strand":"+","sequence":"ATGCCTCTTCGTATCACGGCCATGACCGAAACGTATGCCGATCAAATTATGCAATGGAGCTATGAACCTCCCTATGATTTCTACAACAGCGAACCGGATGAGGAGTTTCGGAAAGAACTTCTGGAGTGCTCGTATTACGCCATACTGGACAAGGAAGGGCAGCTCTTCGGCTTTTGCTGTACAGGCTCATCAGCCCAAATTCCGATCGCAATCCCGTTAGGTGCATATGACGAGGATCTGCTGGATTTCGGACTTGGGATGAAACCGGAATCGACCGGACAATGCCGGGGAAAAGAGTTTCTCTCGTTCGTGCTGGCATCCATCGCTGAATTTCACAAGCGCCAATCGTTTCGGCTGACCGTTGCCAAATTCAATGAACGAGCCATTCGCTTGTATACCCAGCTGGGCTTCTCGGAAGTTGCAACGTTTGATTATGGCGGCACTACGTTCATAACGATGATCAAGAAGCCGGGCTCCGGATTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40862","NCBI_taxonomy_name":"Paenibacillus sp. LC231","NCBI_taxonomy_id":"1120679"}}}},"ARO_accession":"3003994","ARO_id":"40876","ARO_name":"cpaA","CARD_short_name":"cpaA","ARO_description":"cpaA is a capreomycin acetyltransferase protein found in Paenibacillus sp. LC231, an isolated strain of Paenibacillus in Lechuguilla Cave, NM, USA. Confers resistance to capreomycin, an aminoglycoside antibiotic. Described by Pawlowski et al. 2016.","ARO_category":{"41421":{"category_aro_accession":"3004257","category_aro_cvterm_id":"41421","category_aro_name":"cpa acetyltransferase","category_aro_description":"Acetyltransferases of the cpa family confer resistance to capreomycin, an aminoglycoside antibiotic.","category_aro_class_name":"AMR Gene Family"},"40875":{"category_aro_accession":"3003993","category_aro_cvterm_id":"40875","category_aro_name":"capreomycin","category_aro_description":"Capreomycin is an aminoglycoside antibiotic, capable of treating a large number of infections but in particular used for killing bacteria causing tuberculosis.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3382":{"model_id":"3382","model_name":"aadS","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"5568":{"protein_sequence":{"accession":"AAA27459.1","sequence":"MKVREEKLRTIIEWSEKNEDVRVLLLTSSLVNPLALVDEFSDLDIEFVFEDNTNYISDKSWTLKFGNPIAMIEEDESCFNHKHAMKMLLYEDGVKVDFKLYSKSKFIKETQEKELPEDWDIGYKILIDKDGITKQMLKPTYQISIIKKPSEKEFQNLINDFWWDTTYVAKCLVRDEIFYAKFMSETVIRTEYLIPLIEWHIASEHNWNITTNKYGRLFKKYLNQEMWAKTEQTFSGSDIKENWTALFSMTDLVSEIGTELSKKLEYKYPDKLENDIRKYLAGLKPKT"},"dna_sequence":{"accession":"M72415.1","fmin":"1120","fmax":"1984","strand":"+","sequence":"ATGAAAGTCAGAGAAGAAAAGTTAAGAACAATTATAGAATGGTCGGAGAAAAACGAAGATGTAAGAGTTCTTCTTCTGACAAGTTCACTTGTAAATCCTTTAGCACTTGTTGACGAATTTAGTGATTTAGACATTGAATTTGTTTTTGAGGATAATACAAATTACATTTCAGACAAAAGCTGGACGCTTAAATTCGGAAATCCAATTGCTATGATTGAAGAAGACGAAAGTTGTTTTAACCATAAACACGCAATGAAAATGCTACTTTATGAAGACGGTGTGAAAGTAGATTTTAAACTTTACAGCAAATCAAAATTTATAAAGGAAACGCAAGAGAAAGAATTACCAGAAGATTGGGATATTGGCTATAAAATTTTAATTGATAAAGATGGTATTACAAAGCAAATGCTGAAACCAACTTATCAAATTTCCATTATCAAAAAACCGTCTGAAAAAGAGTTTCAAAATCTAATAAACGATTTTTGGTGGGACACAACTTACGTGGCAAAGTGTCTTGTGAGAGATGAAATATTCTATGCGAAATTTATGTCGGAAACCGTTATTCGCACAGAATATTTAATTCCTTTAATTGAATGGCACATTGCAAGTGAACACAATTGGAACATAACGACCAATAAATATGGACGGCTTTTCAAAAAGTATCTTAACCAGGAAATGTGGGCTAAAACAGAACAAACATTTTCAGGGAGCGATATAAAGGAAAATTGGACTGCTCTATTTTCAATGACTGATTTAGTTTCAGAAATAGGAACTGAATTGTCAAAAAAATTAGAGTACAAATACCCGGATAAATTAGAAAATGACATACGAAAATATTTAGCTGGACTAAAACCCAAAACATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42733","NCBI_taxonomy_name":"Transposon Tn4551","NCBI_taxonomy_id":"2405"}}}},"ARO_accession":"3004683","ARO_id":"42732","ARO_name":"aadS","CARD_short_name":"aadS","ARO_description":"A novel Tn4551 streptomycin-resistance gene that was phenotypically silent in wild-type Bacteroides; expression could be activated by a trans-acting chromosomal mutation.","ARO_category":{"36364":{"category_aro_accession":"3000225","category_aro_cvterm_id":"36364","category_aro_name":"ANT(6)","category_aro_description":"A category of aminoglycoside O-nucleotidyltransferase enzymes with modification regiospecificity based at the 6-hydroxyl group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics, specifically streptomycin, by transfer of an AMP group from an ATP substrate to the 6-hydroxyl group of the compound.","category_aro_class_name":"AMR Gene Family"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3384":{"model_id":"3384","model_name":"MCR-1.5","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"5570":{"protein_sequence":{"accession":"APM84488.1","sequence":"MMQHTSVWYRRSVSPFVLVASVAVFLTATANLTFFDKISQTYPIADNLGFVLTIAVVLFGAMLLITTLLSSYRYVLKPVLILLLIMGAVTSYFTDTYGTVYDTTMLQNALQTDQAETKDLLNAAFIMRIIGLGVLPSLLVAFVKVDYPTWGKGLMRRLGLIVASLALILLPVVAFSSHYASFFRVHKPLRSYVNPIMPIYSVGKLASIEYKKASAPKDTIYHAKDAVQATKPDMRKPRLVVFVVGETARADHVSFNGYERDTFPQLAKIDGVTNFSNVTSCGTSTAYSVPCMFSYLGADEYDVDTAKYQENVLDTLDRLGVSILWRDNNSDSKGVMDKLPKAQFADYKSATNNAICNTNPYNECRDVGMLVGLDDFVAANNGKDMLIMLHQMGNHGPAYFKRYDEKFAKFTPVCEGNELAKCEHQSLINAYDNALLATDDFIAQSIQWLQTYSNAYDVSMLYVSDHGESLGENGVYLHGMPNAFAPKEQRSVPAFFWTDKQTGITPMATDTVLTHDAITPTLLKLFDVTADKVKDRTAFIR"},"dna_sequence":{"accession":"KY283125.1","fmin":"0","fmax":"1626","strand":"+","sequence":"ATGATGCAGCATACTTCTGTGTGGTACCGACGCTCGGTCAGTCCGTTTGTTCTTGTGGCGAGTGTTGCCGTTTTCTTGACCGCGACCGCCAATCTTACCTTTTTTGATAAAATCAGCCAAACCTATCCCATCGCGGACAATCTCGGCTTTGTGCTGACGATCGCTGTCGTGCTCTTTGGCGCGATGCTACTGATCACCACGCTGTTATCATCGTATCGCTATGTGCTAAAGCCTGTGTTGATTTTGCTATTAATCATGGGCGCGGTGACCAGTTATTTTACTGACACTTATGGCACGGTCTATGATACGACCATGCTCCAAAATGCCCTACAGACCGACCAAGCCGAGACCAAGGATCTATTAAACGCAGCGTTTATCATGCGTATCATTGGTTTGGGTGTGCTACCAAGTTTGCTTGTGGCTTTTGTTAAGGTGGATTATCCGACTTGGGGCAAGGGTTTGATGCGCCGATTGGGCTTGATCGTGGCAAGTCTTGCGCTGATTTTACTGCCTGTGGTGGCGTTCAGCAGTCATTATGCCAGTTTCTTTCGCGTGCATAAGCCGCTGCGTAGCTATGTCAATCCGATCATGCCAATCTACTCGGTGGGTAAGCTTGCCAGTATTGAGTATAAAAAAGCCAGTGCGCCAAAAGATACCATTTATCACGCCAAAGACGCGGTACAAGCAACCAAGCCTGATATGCGTAAGCCACGCCTAGTGGTGTTCGTCGTCGGTGAGACGGCACGCGCCGATCATGTCAGCTTCAATGGCTATGAGCGCGATACTTTCCCACAGCTTGCCAAGATCGATGGCGTGACCAATTTTAGCAATGTCACATCGTGCGGCACATCGACGGCGTATTCTGTGCCGTGTATGTTCAGCTATCTGGGCGCGGATGAGTATGATGTCGATACCGCCAAATACCAAGAAAATGTGCTGGATACGCTGGATCGCTTGGGCGTAAGTATCTTGTGGCGTGATAATAATTCGGACTCAAAAGGCGTGATGGATAAGCTGCCAAAAGCGCAATTTGCCGATTATAAATCCGCGACCAACAACGCCATCTGCAACACCAATCCTTATAACGAATGCCGCGATGTCGGTATGCTCGTTGGCTTAGATGACTTTGTCGCTGCCAATAACGGCAAAGATATGCTGATCATGCTGCACCAAATGGGCAATCACGGGCCTGCGTATTTTAAGCGATATGATGAAAAGTTTGCCAAATTCACGCCAGTGTGTGAAGGTAATGAGCTTGCCAAGTGCGAACATCAGTCCTTGATCAATGCTTATGACAATGCCTTGCTTGCCACCGATGATTTCATCGCTCAAAGTATCCAGTGGCTGCAGACGTACAGCAATGCCTATGATGTCTCAATGCTGTATGTCAGCGATCATGGCGAAAGTCTGGGTGAGAACGGTGTCTATCTACATGGTATGCCAAATGCCTTTGCACCAAAAGAACAGCGCAGTGTGCCTGCATTTTTCTGGACGGATAAGCAAACTGGCATCACGCCAATGGCAACCGATACCGTCCTGACCCATGACGCGATCACGCCGACATTATTAAAGCTGTTTGATGTCACCGCGGACAAAGTCAAAGACCGCACCGCATTCATCCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3004685","ARO_id":"42737","ARO_name":"MCR-1.5","CARD_short_name":"MCR-1.5","ARO_description":"A plasmid-mediated MCR-1 variant identified from polyclonal clinical Escherichia coli.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3387":{"model_id":"3387","model_name":"MCR-1.11","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"5573":{"protein_sequence":{"accession":"ATM29809.1","sequence":"MMQHTSVVWYRRSVSPFVLVASVAVFLTATANLTFFDKISQTYPIADNLGFVLTIAVVLFGAMLLITTLLSSYRYVLKPVLILLLIMGAVTSYFTDTYGTVYDTTMLQNALQTDQAETKDLLNAAFIMRIIGLGVLPSLLVAFVKVDYPTWGKGLMRRLGLIVASLALILLPVVAFSSHYASFFRVHKPLRSYVNPIMPIYSVGKLASIEYKKASAPKDTIYHAKDAVQATKPDMRKPRLVVFVVGETARADHVSFNGYERDTFPQLAKIDGVTNFSNVTSCGTSTAYSVPCMFSYLGADEYDVDTAKYQENVLDTLDRLGVSILWRDNNSDSKGVMDKLPKAQFADYKSATNNAICNTNPYNECRDVGMLVGLDDFVAANNGKDMLIMLHQMGNHGPAYFKRYDEKFAKFTPVCEGNELAKCEHQSLINAYDNALLATDDFIAQSIQWLQTHSNAYDVSMLYVSDHGESLGENGVYLHGMPNAFAPKEQRSVPAFFWTDKQTGITPMATDTVLTHDAITPTLLKLFDVTADKVKDRTAFIR"},"dna_sequence":{"accession":"KY853650.2","fmin":"51583","fmax":"53212","strand":"+","sequence":"ATGATGCAGCATACTTCTGTGGTGTGGTACCGACGCTCGGTCAGTCCGTTTGTTCTTGTGGCGAGTGTTGCCGTTTTCTTGACCGCGACCGCCAATCTTACCTTTTTTGATAAAATCAGCCAAACCTATCCCATCGCGGACAATCTCGGCTTTGTGCTGACGATCGCTGTCGTGCTCTTTGGCGCGATGCTACTGATCACCACGCTGTTATCATCGTATCGCTATGTGCTAAAGCCTGTGTTGATTTTGCTATTAATCATGGGCGCGGTGACCAGTTATTTTACTGACACTTATGGCACGGTCTATGATACGACCATGCTCCAAAATGCCCTACAGACCGACCAAGCCGAGACCAAGGATCTATTAAACGCAGCGTTTATCATGCGTATCATTGGTTTGGGTGTGCTACCAAGTTTGCTTGTGGCTTTTGTTAAGGTGGATTATCCGACTTGGGGCAAGGGTTTGATGCGCCGATTGGGCTTGATCGTGGCAAGTCTTGCGCTGATTTTACTGCCTGTGGTGGCGTTCAGCAGTCATTATGCCAGTTTCTTTCGCGTGCATAAGCCGCTGCGTAGCTATGTCAATCCGATCATGCCAATCTACTCGGTGGGTAAGCTTGCCAGTATTGAGTATAAAAAAGCCAGTGCGCCAAAAGATACCATTTATCACGCCAAAGACGCGGTACAAGCAACCAAGCCTGATATGCGTAAGCCACGCCTAGTGGTGTTCGTCGTCGGTGAGACGGCACGCGCCGATCATGTCAGCTTCAATGGCTATGAGCGCGATACTTTCCCACAGCTTGCCAAGATCGATGGCGTGACCAATTTTAGCAATGTCACATCGTGCGGCACATCGACGGCGTATTCTGTGCCGTGTATGTTCAGCTATCTGGGCGCGGATGAGTATGATGTCGATACCGCCAAATACCAAGAAAATGTGCTGGATACGCTGGATCGCTTGGGCGTAAGTATCTTGTGGCGTGATAATAATTCGGACTCAAAAGGCGTGATGGATAAGCTGCCAAAAGCGCAATTTGCCGATTATAAATCCGCGACCAACAACGCCATCTGCAACACCAATCCTTATAACGAATGCCGCGATGTCGGTATGCTCGTTGGCTTAGATGACTTTGTCGCTGCCAATAACGGCAAAGATATGCTGATCATGCTGCACCAAATGGGCAATCACGGGCCTGCGTATTTTAAGCGATATGATGAAAAGTTTGCCAAATTCACGCCAGTGTGTGAAGGTAATGAGCTTGCCAAGTGCGAACATCAGTCCTTGATCAATGCTTATGACAATGCCTTGCTTGCCACCGATGATTTCATCGCTCAAAGTATCCAGTGGCTGCAGACGCACAGCAATGCCTATGATGTCTCAATGCTGTATGTCAGCGATCATGGCGAAAGTCTGGGTGAGAACGGTGTCTATCTACATGGTATGCCAAATGCCTTTGCACCAAAAGAACAGCGCAGTGTGCCTGCATTTTTCTGGACGGATAAGCAAACTGGCATCACGCCAATGGCAACCGATACCGTCCTGACCCATGACGCGATCACGCCGACATTATTAAAGCTGTTTGATGTCACCGCGGACAAAGTCAAAGACCGCACCGCATTCATCCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3004688","ARO_id":"42740","ARO_name":"MCR-1.11","CARD_short_name":"MCR-1.11","ARO_description":"A plasmid-mediated phosphoethanolamine transferase and MCR-1 variant identified from Escherichia coli as conferring resistance to colistin antibiotics.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3380":{"model_id":"3380","model_name":"Clostridioides difficile rpoC with mutation conferring resistance to vancomycin","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"2000"},"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"8841":"D244Y"},"Curated-R":{"8841":"D244Y"},"clinical":{"8841":"D244Y"}}},"model_sequences":{"sequence":{"5565":{"protein_sequence":{"accession":"AJP09758.1","sequence":"MFELNNFESIKIALASPEKIRQWSRGEVKKPETINYRTLKPEKDGLFCERIFGPQKDWECHCGKYRRVRYKGVVCDRCGVEVTKSKVRRERMGHIELAAPMSHIWYFKGIPSRMGLLLDMSPRSLEKILYFASYVVVDPGETGLNEKQLLTEKEYRTALEKYGYTFTVGMGAEAVKTLLQNIDLEQQSKDLRAELKDSTGQKKVRTIRRLEVVEAFKKSGNKPEWMILDAIPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLELGAPDIIVRNEKRMLQEAVDALIDNGRRGRPVTGPGNRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKFYQCGLPKKMALELFKPFVMDKLVKEGYAHNIKSAKSIVEKVKPEVWDVLEDVIKSHPVLLNRAPTLHRLGIQAFEPILVEGKAIKLHPLVCTAYNADFDGDQMAVHVPLSVEAQAEARFLMLSVNNILAPKDGSPITTPSQDMVLGCYYLTIEAQDGAKGTGMVFKDFNELLLAYYNKSVHLHALVKLKVTLEDGRSSLVESTVGRFIFNENIPQDLGFVDRKENPFALEVDFLADKKSLGKIIDKCFRKHGNTETAELLDYIKALGFKYSTLGGITVAVDDMSVPEEKKVFIAEAEAKVDKYEKAYRRGLISDEERYEKVIETWTETTDKVTDALMGGLDRLNNIYIMAHSGARGSKNQIRQLAGMRGLMANASGKTVEIPVKSNFREGLSVLEYFTSSHGARKGLADTAIRTAESGYLTRRLVDVSQDVIVREIDCGTEDTTEIYAIKEGNEVIEEIYDRIVGRYTIDPILNPETGEVIVEADSMIQEDEAETIVALGIEKIRIRTVLNCKTNHGVCSKCYGRNLATGKEVNIGEAVGIIAAQSIGEPGTQLTMRTFHTGGVAGADITQGLPRVEELFEARKPKGLAVITEVSGRVEIDETGKRKEVNVIPEEGETQTYVIPYGSRLKVKQGQMLEAGDPLTQGFINPHDIVRVNGVKGVQEYIVKEVQRVYRLQGVDVNDKHIEVIVRQMLSKVKVEDPGDTDLLPGGYEDVLTFNECNKDAIDKGLRPAVAKRVLLGITKASLATDSFLSAASFQETTRVLTEAAIKGKEDHLIGLKENVILGKLIPAGTGMKKYRNIAVEKIED"},"dna_sequence":{"accession":"CP010905.2","fmin":"99212","fmax":"102698","strand":"+","sequence":"TTGTTTGAATTAAACAATTTCGAGTCGATAAAAATAGCATTGGCTTCTCCAGAAAAAATAAGACAATGGTCTAGGGGAGAAGTTAAAAAGCCAGAAACTATAAATTACCGTACTTTAAAACCAGAAAAAGATGGTCTTTTCTGTGAAAGAATATTTGGACCACAAAAAGACTGGGAGTGCCACTGTGGTAAATATAGAAGAGTTAGATATAAAGGTGTAGTTTGTGATAGATGTGGAGTAGAAGTAACTAAATCAAAAGTAAGAAGAGAGAGAATGGGACATATAGAGCTAGCTGCTCCTATGTCTCACATCTGGTACTTCAAAGGTATACCAAGTAGAATGGGACTTTTACTTGATATGTCACCAAGATCGTTAGAAAAAATATTATACTTTGCCTCATATGTGGTAGTTGATCCAGGAGAGACTGGATTAAACGAAAAACAATTGCTTACAGAAAAAGAATACAGAACTGCTCTTGAAAAGTATGGATATACTTTTACTGTAGGAATGGGTGCTGAAGCTGTAAAGACATTACTACAAAATATAGATTTAGAGCAACAAAGTAAAGACCTAAGAGCGGAGTTAAAAGATAGTACAGGGCAAAAGAAAGTTAGAACAATAAGAAGATTAGAAGTTGTAGAGGCATTTAAAAAGTCTGGAAATAAACCAGAATGGATGATTTTAGATGCAATACCAGTAATACCACCAGATTTAAGACCAATGGTACAACTTGATGGTGGAAGATTTGCGACTTCAGACCTAAATGATTTATATAGAAGAGTTATAAATAGAAACAATAGACTTAAAAGATTATTAGAGCTTGGAGCTCCAGATATAATTGTAAGAAATGAAAAAAGAATGCTTCAAGAAGCTGTTGATGCATTGATAGATAATGGTAGAAGAGGTAGACCTGTAACAGGACCTGGAAATAGACCACTTAAATCTTTATCAGATATGTTAAAAGGTAAGCAAGGTCGTTTCCGTCAAAACTTACTTGGTAAGCGTGTTGACTACTCAGGACGTTCTGTTATAGTTGTTGGACCAGAACTTAAATTTTATCAATGTGGACTTCCAAAGAAGATGGCATTAGAATTATTCAAGCCATTTGTTATGGATAAATTAGTTAAAGAAGGTTATGCACATAATATAAAAAGTGCGAAATCTATAGTAGAAAAAGTTAAGCCAGAAGTTTGGGATGTTTTAGAAGATGTTATAAAAAGTCATCCAGTTCTTCTTAACCGTGCACCGACTCTACATAGATTAGGTATACAAGCATTTGAACCAATCTTAGTTGAAGGTAAGGCTATAAAACTACATCCTCTTGTATGTACAGCTTATAATGCAGACTTTGATGGTGACCAAATGGCAGTCCATGTACCTTTATCAGTAGAAGCACAAGCAGAAGCAAGATTCTTAATGCTTTCTGTAAATAATATACTTGCTCCTAAAGATGGTTCACCTATAACTACTCCATCTCAGGATATGGTTTTAGGTTGCTATTATCTAACAATAGAAGCCCAAGATGGAGCTAAAGGAACAGGTATGGTATTTAAAGACTTTAATGAACTATTACTTGCTTATTACAATAAATCAGTTCATCTACATGCATTAGTGAAACTGAAGGTAACACTTGAAGATGGAAGAAGTTCATTGGTTGAAAGTACTGTTGGTAGATTTATATTTAATGAAAATATACCTCAAGACTTAGGTTTTGTAGATAGAAAAGAAAATCCATTTGCACTTGAAGTTGATTTCTTAGCAGATAAAAAATCTCTTGGTAAAATAATAGATAAATGCTTTAGAAAACACGGAAATACAGAAACAGCTGAATTACTAGATTATATAAAAGCTCTAGGATTTAAATATTCTACATTAGGTGGTATAACAGTTGCTGTTGATGATATGAGTGTCCCAGAAGAAAAGAAAGTATTTATAGCTGAGGCAGAAGCTAAAGTTGATAAGTATGAAAAAGCATACAGAAGAGGTCTAATCTCTGATGAAGAAAGATATGAAAAAGTTATAGAGACATGGACAGAAACAACTGATAAAGTTACTGATGCTCTTATGGGTGGACTAGATAGATTAAATAATATATATATAATGGCACATTCAGGAGCCAGAGGTTCTAAAAACCAAATTAGACAGCTGGCAGGTATGCGTGGTCTTATGGCAAATGCATCTGGTAAAACAGTTGAGATACCAGTTAAATCTAATTTCCGTGAAGGTTTATCAGTACTAGAATACTTTACATCTTCACATGGAGCCAGAAAAGGTCTTGCCGATACAGCTATACGTACAGCTGAATCTGGATATTTAACAAGAAGACTTGTTGATGTAAGTCAAGATGTTATTGTAAGGGAAATAGATTGTGGAACAGAAGATACTACAGAGATTTATGCTATAAAAGAAGGAAATGAAGTTATAGAAGAGATATATGATAGAATTGTAGGAAGATATACTATAGACCCTATATTAAATCCTGAAACTGGAGAAGTTATAGTTGAGGCTGATTCAATGATACAAGAAGATGAAGCAGAAACTATAGTAGCTTTAGGAATTGAAAAAATTAGGATAAGAACAGTTCTTAACTGTAAAACTAATCATGGAGTTTGTTCTAAGTGTTATGGTAGAAACTTGGCAACAGGAAAAGAAGTTAATATAGGTGAAGCAGTTGGTATAATAGCAGCTCAATCTATCGGTGAGCCGGGTACTCAGCTTACAATGCGTACATTCCATACTGGAGGAGTTGCAGGAGCTGATATAACTCAAGGTCTACCAAGGGTTGAAGAATTATTTGAAGCTAGAAAACCAAAAGGATTAGCTGTAATAACTGAAGTATCTGGTAGAGTTGAAATTGATGAAACAGGAAAGAGAAAAGAAGTAAATGTAATACCAGAAGAAGGCGAGACTCAAACATATGTAATTCCATATGGTTCTAGATTAAAAGTTAAGCAAGGTCAAATGCTAGAGGCTGGAGACCCTCTAACACAAGGATTTATAAATCCTCATGATATAGTAAGAGTAAATGGTGTTAAGGGAGTTCAAGAATATATAGTTAAAGAAGTTCAAAGAGTGTATAGACTTCAAGGGGTTGACGTTAATGATAAGCATATAGAAGTTATAGTAAGACAAATGCTATCTAAAGTAAAAGTTGAAGACCCAGGAGATACAGATTTATTGCCAGGTGGATATGAAGATGTATTAACATTCAATGAATGTAATAAAGATGCTATAGATAAAGGTCTAAGACCAGCAGTTGCTAAAAGAGTTTTACTTGGTATAACTAAAGCATCTCTTGCAACTGATTCATTCTTATCAGCAGCTTCTTTCCAAGAAACAACAAGAGTATTAACAGAGGCAGCAATAAAAGGTAAAGAAGACCACTTAATAGGACTTAAAGAAAATGTTATATTAGGTAAGTTAATACCAGCAGGAACAGGAATGAAGAAATATAGAAATATAGCTGTTGAAAAAATTGAAGATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37603","NCBI_taxonomy_name":"Clostridioides difficile 630","NCBI_taxonomy_id":"272563"}}}},"ARO_accession":"3004681","ARO_id":"42730","ARO_name":"Clostridioides difficile rpoC with mutation conferring resistance to vancomycin","CARD_short_name":"Cdif_rpoC_VAN","ARO_description":"Point mutations in the rpoC region of Clostridioides difficile which confer resistance to vancomycin.","ARO_category":{"42780":{"category_aro_accession":"3004725","category_aro_cvterm_id":"42780","category_aro_name":"vancomycin-resistant beta prime subunit of RNA polymerase (rpoC)","category_aro_description":"Point mutations in rpoC, an RNA polymerase subunit, which confer resistance to vancomycin.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3381":{"model_id":"3381","model_name":"aadA27","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"5567":{"protein_sequence":{"accession":"CTQ57092.1","sequence":"MSETLQLEQLTESLQQLLGESLFAIYLYGSAVDGGLGPESDLDVLVVVNQALTLHQRQQLAETLLKISYPIGAAQRALEVTIVLKEQILSGSYPLSYELQFGEWLREELNQGALLRAHTDPDLSILLKKAQMHHRSLLGPSLTQWSTAIPEQHLWQAMADTYPSIVAHWDEDADERNQILALCRIYFSLITNEIVPKDQAAHWVIAQLPSLHQPILQRMIQEYKGEIRKQNWQQQHQALGPVVDFLSSKIDEQFNKKSSLIK"},"dna_sequence":{"accession":"LN873256.1","fmin":"3238","fmax":"4027","strand":"-","sequence":"ATGTCCGAAACCTTGCAACTTGAACAGTTAACAGAATCTTTACAGCAGCTTTTGGGTGAATCCCTCTTTGCCATTTATCTGTATGGTTCAGCTGTTGATGGCGGGCTAGGTCCAGAAAGTGATCTGGATGTTTTGGTTGTGGTGAATCAAGCACTGACACTCCATCAAAGACAGCAACTGGCAGAAACCTTATTAAAAATTTCGTATCCAATTGGGGCTGCACAGCGTGCACTTGAAGTCACCATCGTACTTAAAGAGCAAATTCTCTCAGGCAGTTATCCACTCAGCTACGAACTACAATTTGGGGAGTGGTTACGGGAGGAGTTAAACCAAGGTGCTTTGCTCCGCGCACATACAGACCCTGATCTGAGTATTTTGCTGAAGAAAGCACAAATGCATCATCGTAGTTTGTTGGGGCCAAGTTTGACACAGTGGTCAACGGCAATTCCTGAACAGCACCTCTGGCAGGCAATGGCAGACACCTATCCCTCTATTGTGGCACATTGGGATGAGGATGCCGATGAACGTAATCAGATTTTGGCCTTATGCCGTATTTATTTTAGCTTGATAACGAATGAGATTGTGCCTAAAGACCAAGCCGCACACTGGGTGATAGCTCAGTTACCGTCGCTGCATCAACCCATTTTGCAGCGCATGATCCAAGAATATAAAGGTGAGATACGCAAACAAAACTGGCAACAACAGCATCAGGCTTTAGGCCCTGTTGTTGACTTCCTTAGTTCAAAAATTGATGAACAATTTAATAAGAAGAGTAGCCTAATCAAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36948","NCBI_taxonomy_name":"Acinetobacter lwoffii","NCBI_taxonomy_id":"28090"}}}},"ARO_accession":"3004682","ARO_id":"42731","ARO_name":"aadA27","CARD_short_name":"aadA27","ARO_description":"Small mobilizable plasmid pALWED1.8 containing a novel variant of the streptomycin\/spectinomycin resistance gene.","ARO_category":{"41439":{"category_aro_accession":"3004275","category_aro_cvterm_id":"41439","category_aro_name":"ANT(3'')","category_aro_description":"A category of aminoglycoside O-nucleotidyltransferase enzymes with modification regiospecificity based at the 3''-hydroxyl group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics by transfer of an AMP group from an ATP substrate to the 3''-hydroxyl group of the compound.","category_aro_class_name":"AMR Gene Family"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2717":{"model_id":"2717","model_name":"MuxA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"5206":{"protein_sequence":{"accession":"AAG05916.1","sequence":"MTPTTGKSKFRTLRPWLITALAFAAVIGLVMWLAAPASAPSSDGRPGRGGKPGAALPKANALTVGVARVEQGDLALHFNALGTVTAFNTVNVKPRVNGELVKVLFQEGQEVKAGDLLAVVDPRTYKAALAQAEGTLMQNQAQLKNAEIDLQRYKGLYAEDSIAKQTLDTQEAQVRQLQGTIRTNQGQVDDARLNLTFTEVRAPISGRLGLRQVDIGNLVTSGDTTPLVVITQVKPISVVFSLPQQQIGTVVEQMNGPGKLTVTALDRNQDKVLAEGTLTTLDNQIDTTTGTVKLKARFENADGKLFPNQFVNVRLLAQTLKGVLTIPANAVQRGTNGIYVYVVGADNKVSQRSVAIGTSENERVVVESGLKAGEQVVVEGTDRLRDGMEVRVAEASPQVLEGEPQKPQTGRPSGLQGDSVGSGSAE"},"dna_sequence":{"accession":"AE004091.2","fmin":"2854010","fmax":"2855291","strand":"-","sequence":"ATGACTCCAACGACCGGTAAATCCAAGTTCCGTACCCTGCGCCCGTGGCTGATCACCGCCCTGGCCTTCGCCGCCGTGATCGGCCTGGTGATGTGGCTGGCGGCGCCCGCCTCGGCACCGTCCTCCGACGGGCGACCCGGTCGCGGCGGCAAGCCGGGCGCCGCGCTGCCCAAGGCCAACGCGCTCACCGTCGGCGTGGCCAGGGTGGAGCAGGGCGACCTGGCGCTGCATTTCAACGCGCTTGGCACCGTCACCGCCTTCAACACGGTGAACGTCAAGCCGCGGGTCAACGGCGAGCTGGTCAAGGTGCTGTTCCAGGAGGGGCAGGAGGTCAAGGCCGGCGACCTGCTGGCGGTGGTCGACCCGCGCACCTACAAGGCGGCGCTGGCCCAGGCCGAGGGCACGCTGATGCAGAACCAGGCGCAACTGAAGAACGCCGAGATCGACCTGCAGCGCTACAAGGGGCTGTATGCCGAGGACTCGATAGCCAAGCAGACCCTGGATACCCAGGAAGCCCAGGTCCGCCAGTTGCAGGGCACCATCCGTACCAACCAGGGCCAGGTCGACGACGCCCGCCTCAACCTGACCTTCACCGAGGTCCGCGCACCGATTTCCGGGCGCCTCGGCCTGCGCCAGGTGGACATCGGCAACCTGGTCACCAGCGGCGATACCACGCCGCTGGTGGTGATCACCCAGGTCAAGCCGATCTCGGTGGTGTTCAGCCTGCCGCAGCAGCAGATCGGCACCGTCGTCGAGCAGATGAACGGCCCCGGCAAGCTGACGGTCACCGCGCTGGACCGCAACCAGGACAAGGTTCTCGCCGAAGGCACCCTGACCACCCTGGACAACCAGATCGACACCACCACCGGCACGGTCAAGCTCAAGGCGCGCTTCGAGAACGCCGACGGCAAGCTGTTCCCCAACCAGTTCGTCAACGTGCGCCTGCTGGCGCAGACCCTCAAAGGCGTGCTGACCATTCCGGCCAACGCCGTGCAGCGCGGCACCAACGGTATCTATGTCTACGTGGTCGGCGCCGACAACAAGGTCAGCCAGCGCAGCGTCGCCATCGGCACCAGCGAGAACGAGCGGGTGGTGGTGGAAAGCGGCCTGAAGGCCGGCGAGCAGGTGGTGGTGGAAGGCACCGACCGCCTGCGCGACGGTATGGAAGTGCGTGTCGCCGAGGCCTCCCCGCAGGTCCTCGAGGGCGAGCCGCAGAAACCGCAGACTGGCCGCCCCAGCGGCCTCCAGGGCGACTCGGTGGGTAGCGGGAGCGCTGAATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36804","NCBI_taxonomy_name":"Pseudomonas aeruginosa PAO1","NCBI_taxonomy_id":"208964"}}}},"ARO_accession":"3004073","ARO_id":"41155","ARO_name":"MuxA","CARD_short_name":"MuxA","ARO_description":"MuxA is a membrane fusion protein component of the efflux pump system MuxABC-OpmB in Pseudomonas aeruginosa.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36250":{"category_aro_accession":"3000111","category_aro_cvterm_id":"36250","category_aro_name":"novobiocin","category_aro_description":"Novobiocin is an aminocoumarin antibiotic produced by Streptomyces spheroides and Streptomyces niveus, and binds DNA gyrase subunit B inhibiting ATP-dependent DNA supercoiling.","category_aro_class_name":"Antibiotic"},"36689":{"category_aro_accession":"3000550","category_aro_cvterm_id":"36689","category_aro_name":"aztreonam","category_aro_description":"Aztreonam was the first monobactam discovered, and is greatly effective against Gram-negative bacteria while inactive against Gram-positive bacteria. Artreonam is a poor substrate for beta-lactamases, and may even act as an inhibitor. In Gram-negative bacteria, Aztreonam interferes with filamentation, inhibiting cell division and leading to cell death.","category_aro_class_name":"Antibiotic"},"37626":{"category_aro_accession":"3001227","category_aro_cvterm_id":"37626","category_aro_name":"kitasamycin","category_aro_description":"Kitasamycin is a macrolide antibiotic and is produced by Streptoverticillium kitasatoense. The drug has antimicrobial activity against a wide spectrum of pathogens.","category_aro_class_name":"Antibiotic"},"40353":{"category_aro_accession":"3003701","category_aro_cvterm_id":"40353","category_aro_name":"rokitamycin","category_aro_description":"Rokitamycin is a macrolide antibiotic. Synthesized from strains of Streptomyces kitasatoensis.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36242":{"category_aro_accession":"3000103","category_aro_cvterm_id":"36242","category_aro_name":"aminocoumarin antibiotic","category_aro_description":"Aminocoumarin antibiotics bind DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2517":{"model_id":"2517","model_name":"tetA(58)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"650"}},"model_sequences":{"sequence":{"3853":{"protein_sequence":{"accession":"APB03214.1","sequence":"MEHAYKKKIEPKPGDLAVEAYGLIKTFGDNRAVDGVDLNVRTGTIYGVLGPNGAGKTTTIRMLATLLRPDAGSARIFGHDVQAESQIVRQLIGVTGQYASVDESLSATENLIIFSRLLGLGRKEARRKAEELLEEFGLSEAAKRPLKNFSGGMRRRLDLAASLIAQPPLIFLDEPTTGLDPRTRSQMWDTIRRLVNTGSTVLLTTQYLEEADQLADRIAVIDYGRVVAEGTADELKMSVGTSSLHLTVEDSVDMDRACHTVEQVLGVHANVSPEAGKITAPMANAGLVTDLLIELRTAGIGLSEMSVQKPTLDEVFLTITGHGVKEDAAQESYESNDREVARV"},"dna_sequence":{"accession":"KX531044.1","fmin":"0","fmax":"1032","strand":"+","sequence":"ATGGAGCATGCATACAAAAAGAAAATAGAACCAAAACCTGGCGACTTGGCCGTTGAGGCTTACGGACTGATCAAAACATTCGGAGATAACCGCGCCGTGGATGGGGTGGATCTGAACGTACGTACCGGAACGATCTACGGTGTACTTGGCCCGAATGGGGCAGGCAAGACGACCACCATCCGAATGCTGGCGACCTTGCTAAGACCGGATGCGGGTTCGGCCCGAATCTTCGGACATGATGTGCAGGCGGAATCGCAGATTGTCCGTCAGTTGATCGGGGTAACCGGCCAATACGCGTCGGTGGACGAATCGCTCAGCGCTACGGAGAATCTGATTATATTCTCACGTTTGCTTGGTTTGGGGCGTAAGGAGGCAAGGCGCAAGGCGGAAGAGCTGCTCGAGGAATTCGGTTTGTCGGAAGCCGCGAAGCGGCCGCTAAAAAATTTCTCGGGCGGCATGCGGAGAAGGCTGGATCTGGCGGCAAGCCTGATTGCCCAGCCGCCGCTTATCTTCCTGGATGAACCGACGACGGGGCTGGATCCAAGGACGCGTTCCCAGATGTGGGATACGATCCGCCGATTGGTGAATACCGGTTCAACGGTATTGCTGACCACGCAGTATCTCGAGGAGGCCGACCAGCTGGCAGACCGCATCGCCGTTATCGATTACGGCCGGGTTGTGGCCGAGGGGACGGCCGATGAACTGAAGATGTCGGTGGGCACTTCCTCGCTGCATTTGACTGTCGAGGATTCGGTTGACATGGATCGCGCCTGCCATACCGTGGAACAAGTGTTAGGCGTCCATGCCAATGTATCGCCGGAAGCCGGAAAGATAACGGCGCCGATGGCTAATGCGGGTCTTGTTACAGACCTGCTGATCGAGCTGCGAACAGCAGGAATCGGCTTGTCCGAGATGAGCGTGCAGAAGCCGACCCTGGATGAGGTGTTCCTAACGATCACCGGCCACGGCGTGAAGGAAGACGCTGCCCAAGAGTCTTATGAATCCAATGATCGGGAGGTGGCACGGGTATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40862","NCBI_taxonomy_name":"Paenibacillus sp. LC231","NCBI_taxonomy_id":"1120679"}}}},"ARO_accession":"3003980","ARO_id":"40861","ARO_name":"tetA(58)","CARD_short_name":"tetA(58)","ARO_description":"TetA(58) is a Tetracycline efflux pump described in Paenibacillus sp. LC231, a strain of Paenibacillus isolated from Lechuguilla Cave, NM, USA. Described by Pawlowski et al. 2016.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2526":{"model_id":"2526","model_name":"vgbC","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"3862":{"protein_sequence":{"accession":"APB03225.1","sequence":"MQIAAQEYKTANRESGPYGITARQDRTIWFTEQKGNRIGRLTKDGDMRTFEVPTPDAGVMSILSAHTGDLWFTEYKANKIGRMTMEGTFAEFELPEANSSPYGLAEGPDGAIWFTELSGNRIGRITPAGIITEYDLPCEGSYPSYITAGPDGALWFTENQNNCIGRITVDGEITEYRIPTEQSGPVGITTGADGALWFVQINGNQIGRITTAGEITEFKLPSGNARPHAITAGVSGDLWFTEWGANQIGRITCTGDITEYPIPTPSAEPHGITVDSGGEVWFAEECDQIGRFTIQY"},"dna_sequence":{"accession":"KX531055.1","fmin":"0","fmax":"891","strand":"+","sequence":"ATGCAGATCGCCGCACAGGAGTACAAGACAGCGAATCGGGAATCGGGACCTTATGGTATTACGGCAAGACAAGATCGGACCATATGGTTCACGGAACAAAAAGGAAACCGGATCGGACGGCTCACCAAGGATGGGGATATGCGCACGTTCGAAGTGCCGACTCCAGATGCCGGGGTCATGTCTATCCTCTCTGCCCATACCGGTGACCTCTGGTTTACGGAGTACAAAGCAAATAAAATCGGAAGGATGACAATGGAAGGAACATTTGCGGAATTCGAGCTGCCTGAAGCCAATTCGTCTCCCTACGGCTTGGCTGAGGGTCCGGATGGAGCCATATGGTTCACCGAGCTAAGCGGCAACCGAATCGGAAGGATAACGCCGGCAGGCATTATCACGGAATATGACTTACCATGCGAAGGATCGTACCCTTCCTATATTACAGCCGGTCCGGACGGCGCGTTGTGGTTTACGGAAAACCAGAACAACTGCATCGGCCGAATTACGGTGGACGGGGAGATTACCGAGTACCGGATTCCAACAGAGCAATCCGGGCCGGTCGGCATCACGACAGGTGCCGATGGCGCTCTATGGTTTGTTCAAATCAACGGCAATCAAATCGGCCGGATCACAACGGCCGGGGAAATTACGGAATTCAAGCTCCCGTCCGGGAATGCCAGACCCCATGCCATCACGGCGGGCGTTTCCGGGGATCTATGGTTTACCGAATGGGGAGCCAATCAAATCGGACGAATTACCTGCACCGGGGACATTACCGAGTATCCAATCCCTACCCCCTCCGCAGAACCTCATGGCATAACCGTGGATTCGGGCGGCGAGGTCTGGTTCGCCGAGGAATGCGATCAGATCGGCCGGTTTACGATTCAGTATTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40862","NCBI_taxonomy_name":"Paenibacillus sp. LC231","NCBI_taxonomy_id":"1120679"}}}},"ARO_accession":"3003990","ARO_id":"40872","ARO_name":"vgbC","CARD_short_name":"vgbC","ARO_description":"VgbC is a streptogramin B-type lyase found in Paenibacillus sp. LC231, a strain of Paenibacillus isolated from Lechuguilla Cave, NM, USA. Confers resistance to streptogramin B-type antibiotics by linearization of the lactone ring on an ester bond, resulting in antibiotic inactivation. Described by Pawlowski et al. 2016.","ARO_category":{"36515":{"category_aro_accession":"3000376","category_aro_cvterm_id":"36515","category_aro_name":"streptogramin vgb lyase","category_aro_description":"vgb (Virginiamycin B) lyase inactivates type B streptogramin antibiotics by linearizing the streptogramin lactone ring at the ester linkage through an elimination mechanism, thus conferring resistance to these compounds.","category_aro_class_name":"AMR Gene Family"},"36722":{"category_aro_accession":"3000583","category_aro_cvterm_id":"36722","category_aro_name":"pristinamycin IA","category_aro_description":"Pristinamycin IA is a type B streptogramin antibiotic produced by Streptomyces pristinaespiralis. It binds to the P site of the 50S subunit of the bacterial ribosome, preventing the extension of protein chains.","category_aro_class_name":"Antibiotic"},"36723":{"category_aro_accession":"3000584","category_aro_cvterm_id":"36723","category_aro_name":"quinupristin","category_aro_description":"Quinupristin is a type B streptogramin and a semisynthetic derivative of pristinamycin 1A. It is a component of the drug Synercid and interacts with the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"37019":{"category_aro_accession":"3000675","category_aro_cvterm_id":"37019","category_aro_name":"pristinamycin IB","category_aro_description":"Pristinamycin IB is a class B streptogramin similar to pristinamycin IA, the former containing a N-methyl-4-(methylamino)phenylalanine instead of a N-methyl-4-(dimethylamino)phenylalanine in its class A streptogramin counterpart (one less methyl group).","category_aro_class_name":"Antibiotic"},"37021":{"category_aro_accession":"3000677","category_aro_cvterm_id":"37021","category_aro_name":"virginiamycin S2","category_aro_description":"Virginiamycin S2 is a streptogramin B antibiotic.","category_aro_class_name":"Antibiotic"},"37022":{"category_aro_accession":"3000678","category_aro_cvterm_id":"37022","category_aro_name":"pristinamycin IC","category_aro_description":"Pristinamycin IC is a class B streptogramin derived from virginiamycin S1.","category_aro_class_name":"Antibiotic"},"37023":{"category_aro_accession":"3000679","category_aro_cvterm_id":"37023","category_aro_name":"vernamycin C","category_aro_description":"Vernamycin C is a streptogramin B antibiotic.","category_aro_class_name":"Antibiotic"},"37024":{"category_aro_accession":"3000680","category_aro_cvterm_id":"37024","category_aro_name":"patricin A","category_aro_description":"Patricin A is a streptogramin B antibiotic.","category_aro_class_name":"Antibiotic"},"37025":{"category_aro_accession":"3000681","category_aro_cvterm_id":"37025","category_aro_name":"patricin B","category_aro_description":"Patricin B is a streptogramin B antibiotic.","category_aro_class_name":"Antibiotic"},"37026":{"category_aro_accession":"3000682","category_aro_cvterm_id":"37026","category_aro_name":"ostreogrycin B3","category_aro_description":"Ostreogrycin B3 is a derivative of pristinamycin IA, with an additional 3-hydroxy group on its 4-oxopipecolic acid.","category_aro_class_name":"Antibiotic"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35967":{"category_aro_accession":"0000050","category_aro_cvterm_id":"35967","category_aro_name":"streptogramin B antibiotic","category_aro_description":"Streptogramin B antibiotics are are cyclic hepta- or hexa-depsipeptides.  Type B streptogramins block the peptide exit tunnel of the 50S bacterial ribosome. The general composition of group B streptogramins is 3-hydroxypicolinic acid-L-Thr-D-aminobutyric acid (or D-Ala)-L-Pro-L-Phe (or 4-N-,N-(dimethylamino)-L-Phe)-X-L-phenylglycine. Used alone, streptogramin B antibiotics are bacteriostatic, but is bactericidal when used with streptogramin A antibiotics.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3383":{"model_id":"3383","model_name":"MCR-9.1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"5569":{"protein_sequence":{"accession":"WP_001572373.1","sequence":"MPVLFRVKVIPLVLLLAMIFAFLLNWPILLHFYEILSHLEHVKIGFVISIPFVLVAALNVVFMPFSVRFLLKPFFALLFITGSLVSYSTLKYKVMFDQTMIQNIIETNPQEAHSYLNGSIIIWFVFTGILPAILLFSIKIQYPEKWYKGIAYRLLSVLASLSLIAGVAALYYQDYASVGRNNSTLNKEIIPANYAYSTFQYVKDTYFTTKVPFQTLGNDAKRVVAHEKPTLMFLVIGETARSQNFSMNGYSRDTNAFTSKSGGVISFKNMHSCGTATAISVPCMFSNMNRTEYDSKKASNSENFLDIVQKTGVSLLWKENDGGCKGVCSRIPTVEIKPSDNPKLCDGKTCHDEVMLENLDDEIAKMPGDKLVAFHIIGSHGPTYYLRYPAEHRHFMPECARSDIENCTQEQLVNTYDNTLRYTDYVLAEMIEKLKNYSDQYNTVLLYVSDHGESLGESGLYLHGTPYKLAPDQQTHIPMQVWMSPGFIAGKHINMSCLENNAAKKSYSHDNLFSSILGLWDVSTSVYNPDRDLFRECRG"},"dna_sequence":{"accession":"NC_021819.1","fmin":"16013","fmax":"17633","strand":"+","sequence":"ATGCCTGTACTTTTCAGGGTGAAAGTTATTCCGCTGGTTTTACTTCTGGCAATGATCTTTGCGTTTTTACTTAACTGGCCAATATTGCTGCATTTTTACGAGATTTTGTCGCATTTAGAGCATGTCAAAATTGGTTTTGTCATTTCTATTCCCTTTGTTCTGGTTGCGGCGCTTAACGTTGTTTTTATGCCTTTCTCAGTTCGTTTTCTGCTGAAACCTTTCTTTGCTTTACTGTTTATCACTGGCTCACTGGTCAGTTATTCGACACTAAAATATAAAGTAATGTTTGATCAAACGATGATTCAAAACATTATTGAAACTAACCCCCAGGAAGCGCATTCCTATCTTAATGGCTCAATTATTATATGGTTCGTCTTTACCGGTATCCTTCCTGCCATCCTCCTTTTTTCAATAAAAATTCAATATCCTGAAAAATGGTATAAAGGCATTGCTTACCGTTTGCTCTCCGTGCTGGCATCGTTGAGTTTGATTGCAGGTGTTGCCGCACTTTATTATCAGGATTATGCCTCTGTCGGCCGCAATAACTCGACATTGAATAAAGAGATCATCCCGGCGAACTACGCTTACAGCACTTTCCAGTATGTTAAGGATACGTACTTTACGACTAAAGTGCCTTTCCAGACGCTGGGGAATGATGCTAAACGCGTCGTCGCTCACGAAAAACCCACGCTGATGTTCCTGGTGATTGGCGAAACGGCACGCAGCCAGAATTTCTCGATGAACGGTTATTCGCGTGATACCAATGCCTTTACCAGCAAATCCGGCGGCGTTATTTCGTTTAAAAATATGCATTCCTGCGGTACCGCTACCGCAATATCCGTTCCGTGCATGTTCTCGAATATGAATCGCACCGAGTACGACAGTAAAAAAGCATCTAACAGTGAAAATTTCCTCGACATCGTGCAGAAAACCGGTGTCTCGCTGTTATGGAAAGAGAACGATGGCGGTTGTAAAGGCGTATGTAGCCGCATCCCGACTGTCGAAATTAAGCCTAGTGATAACCCGAAACTGTGCGATGGCAAAACGTGCCATGACGAGGTGATGCTGGAAAACCTTGATGATGAAATCGCCAAAATGCCAGGTGATAAGCTTGTCGCCTTCCATATCATTGGCAGCCATGGACCGACTTATTACCTGCGTTATCCGGCTGAGCATCGCCACTTCATGCCCGAATGTGCACGTAGCGATATCGAAAACTGTACTCAGGAACAATTGGTCAACACCTACGACAACACCCTTCGTTATACAGACTATGTATTAGCTGAGATGATTGAAAAGCTAAAAAATTACAGCGATCAGTACAACACCGTGCTGCTTTATGTGTCCGATCATGGTGAATCATTGGGCGAAAGCGGGCTATATCTGCACGGCACGCCGTACAAACTGGCACCGGATCAGCAGACGCATATTCCGATGCAGGTCTGGATGTCACCGGGCTTTATCGCCGGGAAACACATCAACATGTCTTGCCTTGAAAATAATGCGGCGAAAAAATCATATTCCCACGACAACCTGTTCTCATCGATTTTGGGGCTGTGGGACGTAAGCACCAGCGTCTATAATCCTGACCGCGATTTGTTCCGCGAATGCCGTGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"45689","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Cubana str. CFSAN002050","NCBI_taxonomy_id":"1271863"}}}},"ARO_accession":"3004684","ARO_id":"42734","ARO_name":"MCR-9.1","CARD_short_name":"MCR-9.1","ARO_description":"A mobilized and plasmid-mediated colistin resistance gene and phosphoethanolamine transferase identified from a Salmonella enterica isolate.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3399":{"model_id":"3399","model_name":"aadA8b","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"5587":{"protein_sequence":{"accession":"CAJ13568.1","sequence":"MREAVTIEISNQLSEVLSVIERHLESTLLAVHLYGSAVDGGLKPYSDIDLLVTVAVKLDETTRRALLNDLMEASAFPGESETLRAIEVTLVVHDDIIPWRYPAKRELQFGEWQRNDILAGIFEPAMIDIDLAILLTKAREHSVALVGPAAEEFFDPVPEQDLFEALRETLKLWNSQPDWAGDERNVVLTLSRIWYSAITGKIAPKDVAADWAMERLPAQYQPVILEARQAYLGQEEDRLASRADQLEEFVHYVKGEITKVVGK"},"dna_sequence":{"accession":"AM040708.1","fmin":"1173","fmax":"1965","strand":"+","sequence":"ATGAGGGAAGCGGTGACCATCGAAATTTCGAACCAACTATCAGAGGTGCTAAGCGTCATTGAGCGCCATCTGGAATCAACGTTGCTGGCCGTGCATTTGTACGGCTCCGCAGTGGATGGCGGCCTGAAGCCATACAGCGATATTGATTTGTTGGTTACTGTGGCCGTAAAGCTTGATGAAACGACGCGGCGAGCATTGCTCAATGATCTTATGGAGGCTTCGGCTTTCCCTGGCGAGAGCGAGACGCTCCGCGCTATAGAAGTCACCCTTGTCGTGCATGACGACATCATCCCGTGGCGTTATCCGGCTAAGCGCGAGCTGCAATTTGGAGAATGGCAGCGCAATGACATTCTTGCGGGTATCTTCGAGCCAGCCATGATCGACATTGATCTAGCTATCCTGCTTACAAAAGCAAGAGAACATAGCGTTGCCTTGGTAGGTCCGGCAGCGGAGGAATTCTTTGACCCGGTTCCTGAACAGGATCTATTCGAGGCGCTGAGGGAAACCTTGAAGCTATGGAACTCGCAGCCCGACTGGGCCGGCGATGAGCGAAATGTAGTGCTTACGTTGTCCCGCATTTGGTACAGCGCAATAACCGGCAAAATCGCGCCGAAGGATGTCGCTGCCGACTGGGCAATGGAGCGCCTGCCGGCCCAGTATCAGCCCGTCATACTTGAAGCTAGACAGGCTTATCTTGGACAAGAAGAAGATCGCTTGGCCTCGCGCGCAGATCAGTTGGAAGAATTTGTCCACTACGTGAAAGGCGAGATCACCAAGGTAGTCGGCAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3004704","ARO_id":"42757","ARO_name":"aadA8b","CARD_short_name":"aadA8b","ARO_description":"aadA8b is an aminoglycoside nucleotidyltransferase gene encoded by plasmids in E. coli; can be created by a recombination event  between aadA1 and aadA2.","ARO_category":{"41439":{"category_aro_accession":"3004275","category_aro_cvterm_id":"41439","category_aro_name":"ANT(3'')","category_aro_description":"A category of aminoglycoside O-nucleotidyltransferase enzymes with modification regiospecificity based at the 3''-hydroxyl group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics by transfer of an AMP group from an ATP substrate to the 3''-hydroxyl group of the compound.","category_aro_class_name":"AMR Gene Family"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3400":{"model_id":"3400","model_name":"vga(E) Staphylococcus cohnii","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"5595":{"protein_sequence":{"accession":"AHB37625.1","sequence":"MLLFEGTSIKKQLHDRVLFDIDLIQVHDNQRIGLVGRNGTGKTSLLKIITGEELPDEGNISPFTSVKLVPQFKESRLEKSGGEITQQYLQNAFNGNPGLLLLDEPTTHLDTERIAWLEKKIRNYQGAAVVVSHDRTFLNNVCTDIWEIEKNTLKIFKGNYDEYAKQKEILKKQKQTEFEKYEREKQKLERAIRQKEERAQRATKKPKNLSSSEARIVGAKTHYANIQKKLRSSAKALETRLEQLDKVDKVKELPEIKMDMLNEENLTNQSVLRAENIKGEIEERKLWEPFSLYLYGGDKVAIIGKNGSGKTTLLKKIVKQDEGVTIPEKVKIGYFSQHLTILNDEKSIIENVQSTSSQNETLIRTVLARMHFWDEDVYKKVGILSGGEKVKLALAKLFLSEVNMLVLDEPTNFLDIAALEALETLMKSYHGTILFVTHDRMLVKNIATKIIDIKDGKITVFDGSYEAYEEWLENKTKSNNDDQLLLIETKISDVLGRLSLEPSQELEDEFQRLLKEKKELTRGE"},"dna_sequence":{"accession":"KF540226.1","fmin":"3569","fmax":"5144","strand":"-","sequence":"ATGCTATTATTTGAAGGAACATCAATCAAAAAACAATTACATGACAGAGTGCTATTTGATATTGATTTAATACAAGTGCATGATAATCAACGTATAGGCTTAGTAGGTAGGAATGGAACAGGAAAAACAAGCCTATTAAAAATTATTACAGGTGAAGAATTACCTGATGAAGGTAATATCTCTCCTTTTACCTCTGTGAAATTAGTGCCACAATTTAAAGAATCAAGATTGGAGAAAAGTGGTGGCGAAATAACACAGCAATATTTACAGAACGCATTCAATGGGAATCCAGGCTTACTGCTTTTAGATGAACCGACAACACACTTAGATACGGAAAGAATTGCTTGGCTAGAAAAAAAGATAAGAAACTATCAAGGAGCAGCTGTCGTAGTATCTCATGATCGGACATTTTTAAATAATGTATGTACTGACATATGGGAAATTGAAAAAAATACGTTAAAAATATTTAAAGGAAATTATGATGAATATGCAAAGCAAAAAGAAATACTTAAAAAACAAAAACAAACTGAATTTGAAAAGTATGAACGTGAGAAACAAAAATTAGAAAGAGCAATACGTCAAAAAGAAGAAAGAGCTCAACGAGCAACAAAAAAACCTAAGAATCTAAGTTCATCTGAAGCGAGAATAGTGGGTGCTAAAACCCACTACGCCAACATACAGAAAAAGCTGAGAAGTTCGGCAAAAGCTTTAGAAACAAGACTGGAACAATTGGATAAGGTTGACAAGGTGAAAGAGCTGCCTGAAATTAAGATGGATATGTTAAATGAAGAAAACTTAACAAACCAATCTGTATTACGTGCTGAAAATATTAAGGGAGAGATTGAAGAACGTAAGCTCTGGGAACCCTTTAGCTTATATTTATATGGAGGAGATAAAGTTGCTATCATTGGAAAAAATGGCTCAGGTAAAACAACGTTGCTTAAAAAAATAGTGAAGCAAGATGAAGGAGTGACAATTCCAGAAAAAGTAAAGATAGGTTACTTCTCTCAACACTTAACCATCCTAAATGATGAGAAATCAATCATAGAAAATGTACAATCGACCTCTAGTCAAAATGAGACATTAATAAGAACAGTTTTAGCAAGAATGCATTTTTGGGATGAAGATGTCTATAAAAAGGTAGGCATATTAAGTGGTGGTGAAAAAGTAAAGCTAGCTTTAGCTAAACTATTTTTAAGTGAGGTGAATATGCTCGTTTTAGATGAGCCGACTAACTTTTTAGACATTGCAGCTTTAGAAGCGCTAGAAACATTAATGAAAAGTTATCATGGAACGATTCTATTTGTTACTCACGACCGAATGTTAGTAAAAAATATAGCTACAAAAATAATTGATATAAAAGATGGTAAGATAACAGTATTCGATGGATCGTACGAAGCATATGAAGAGTGGCTGGAGAATAAAACAAAGTCTAACAATGATGACCAACTTTTATTAATTGAAACTAAAATATCTGATGTTCTGGGTAGGTTGAGCTTGGAACCTTCGCAAGAGTTAGAAGATGAATTTCAAAGATTATTGAAAGAAAAGAAAGAACTGACTAGAGGGGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36766","NCBI_taxonomy_name":"Staphylococcus cohnii","NCBI_taxonomy_id":"29382"}}}},"ARO_accession":"3004715","ARO_id":"42770","ARO_name":"vga(E) Staphylococcus cohnii","CARD_short_name":"Scoh_vga(E)","ARO_description":"vga(E) gene variant that confers resistance to pleuromutilins, lincosamides and streptogramin A antibiotics in staphylococci.","ARO_category":{"36252":{"category_aro_accession":"3000113","category_aro_cvterm_id":"36252","category_aro_name":"vga-type ABC-F protein","category_aro_description":"Vga-type plasmid-borne ABC-F proteins, expressed in staphylococci that confer resistance to streptogramin A antibiotics through ribosomal protection.","category_aro_class_name":"AMR Gene Family"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"virginiamycin M1","category_aro_description":"Virginiamycin M1 is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37015":{"category_aro_accession":"3000671","category_aro_cvterm_id":"37015","category_aro_name":"tiamulin","category_aro_description":"Tiamulin is a pleuromutilin derivative currently used in veterinary medicine. It binds to the 23 rRNA of the 50S ribosomal subunit to inhibit protein translation.","category_aro_class_name":"Antibiotic"},"37713":{"category_aro_accession":"3001314","category_aro_cvterm_id":"37713","category_aro_name":"retapamulin","category_aro_description":"Retapamulin is a semi-synthetic pleuromutilin antibiotic approved for the treatment of skin infections.","category_aro_class_name":"Antibiotic"},"37714":{"category_aro_accession":"3001315","category_aro_cvterm_id":"37714","category_aro_name":"valnemulin","category_aro_description":"Two semi-synthetic pleuromutilin derivatives, tiamulin and valnemulin, have been developed as antibiotics for veterinary use.","category_aro_class_name":"Antibiotic"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35952":{"category_aro_accession":"0000034","category_aro_cvterm_id":"35952","category_aro_name":"streptogramin A antibiotic","category_aro_description":"Streptogramin A antibiotics are cyclic polyketide peptide hybrids that bind to the ribosomal peptidyl transfer centre. Structural variation arises from substituting a proline for its desaturated derivative and by its substitution for Ala or Cys. Used alone, streptogramin A antibiotics are bacteriostatic, but is bactericidal when used with streptogramin B antibiotics.","category_aro_class_name":"Drug Class"},"37014":{"category_aro_accession":"3000670","category_aro_cvterm_id":"37014","category_aro_name":"pleuromutilin antibiotic","category_aro_description":"Pleuromutilins are natural fungal products that target bacterial protein translation by binding the the 23S rRNA, blocking the ribosome P site at the 50S subunit. They are mostly used for agriculture and veterinary purposes.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3485":{"model_id":"3485","model_name":"OXA-392","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"520"}},"model_sequences":{"sequence":{"5680":{"protein_sequence":{"accession":"AAN41430.1","sequence":"MKNTIHINFAIFLIIANIIYSSASASTDISTVASQLFEGTEGCFLLYDASTNAEIAQFNKAKCAAQMAPDSTFKIALSLMAFDAEIIDQKTIFKWDKIPKGMEIWNSNHTPKTWMQFSVVWVSQEITQKIGLNKIKNYLKDFDYGNQDFSGDKERNNGLTEAWLESSLKISPEEQIQFLRKIINHNLPVRNSAIENTIDNMYLQDLENSTKLYGKTGAGFTANRTLQNGWFEGFIISKSGHKYVFVSALTGNLGSNLTSSIKAKKNAITILNTLNL"},"dna_sequence":{"accession":"AY139600.1","fmin":"167","fmax":"998","strand":"+","sequence":"ATGAAAAACACAATACATATCAACTTCGCTATTTTTTTAATAATTGCAAATATTATCTACAGCAGCGCCAGTGCATCAACAGATATCTCTACTGTTGCATCTCAATTATTTGAAGGAACTGAAGGTTGTTTTTTACTTTACGATGCATCCACAAACGCTGAAATTGCTCAATTCAATAAAGCAAAGTGCGCAGCGCAAATGGCACCAGATTCAACTTTCAAGATCGCATTATCACTTATGGCATTTGATGCGGAAATAATAGATCAGAAAACCATATTCAAATGGGATAAAATCCCAAAAGGAATGGAAATTTGGAACAGCAATCATACACCAAAGACGTGGATGCAATTTTCTGTTGTTTGGGTTTCGCAAGAAATAACCCAAAAAATTGGATTAAATAAAATCAAAAATTATCTCAAAGATTTTGATTATGGAAATCAAGACTTCTCTGGAGATAAAGAAAGAAACAACGGATTAACAGAAGCATGGCTCGAAAGTAGCTTAAAAATTTCACCGGAAGAACAAATTCAATTCCTGCGTAAAATTATTAATCACAATCTTCCAGTTAGAAATTCAGCCATAGAAAACACCATAGATAACATGTATCTACAAGATCTGGAGAATAGTACAAAACTGTATGGGAAAACTGGTGCAGGATTTACAGCAAATAGAACCCTACAAAACGGATGGTTTGAAGGGTTTATTATAAGCAAATCAGGACATAAATATGTTTTTGTGTCCGCACTTACAGGAAACTTGGGGTCGAATTTAACATCAAGCATAAAAGCCAAGAAAAATGCAATCACCATTCTAAACACACTAAATTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36791","NCBI_taxonomy_name":"uncultured bacterium","NCBI_taxonomy_id":"77133"}}}},"ARO_accession":"3001578","ARO_id":"37978","ARO_name":"OXA-392","CARD_short_name":"OXA-392","ARO_description":"OXA-392 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46485":{"category_aro_accession":"3007696","category_aro_cvterm_id":"46485","category_aro_name":"OXA-1-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-1.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2550":{"model_id":"2550","model_name":"Clostridioides difficile gyrA conferring resistance to fluoroquinolones","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"4650":"A384D","8663":"C245T","8664":"D71V","8665":"T82I","8666":"T82V","8667":"A118T","8689":"T83I","8808":"D71G","8809":"T82A","8810":"D81N","8811":"R90K","8812":"D103N","8839":"L345I","8843":"A118S","8844":"A92E","8847":"P116A","8813":"Q123K"},"Curated-R":{"4650":"A384D","8663":"C245T","8664":"D71V","8665":"T82I","8666":"T82V","8667":"A118T","8689":"T83I","8808":"D71G","8809":"T82A","8810":"D81N","8811":"R90K","8812":"D103N","8839":"L345I","8843":"A118S","8844":"A92E","8845":"A92E","8847":"P116A","8813":"Q123K"},"clinical":{"4650":"A384D","8663":"C245T","8664":"D71V","8665":"T82I","8666":"T82V","8667":"A118T","8689":"T83I","8808":"D71G","8809":"T82A","8810":"D81N","8811":"R90K","8812":"D103N","8839":"L345I","8843":"A118S","8844":"A92E","8847":"P116A","8813":"Q123K"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1500"},"40330":{"param_type":"multiple resistance variants","param_description":"A set of nucleotide or amino acid substitutions that are all required to confer resistance to an antibiotic drug or drug class, encoded as: [wild-type 1][position 1][mutation 1],[wild-type 2][position 2][mutation 2], etc. For example, D63Y,T142K.","param_type_id":"40330","param_value":{"8845":"A118S,T82A"}}},"model_sequences":{"sequence":{"5529":{"protein_sequence":{"accession":"CAJ66820.1","sequence":"MEENNKILPIEIAEEMKKSYIDYSMSVIAGRALPDVRDGLKPVHRRILYSMSELNLTPDKPYRKSARIVGDVLGKYHPHGDTAVYYAMVRMAQDFSTRALLVDGHGNFGSVDGDSPAAMRYTEAKMSKLSLELLRDIEKETVDFKPNFDESLKEPSVLPARYPNLLVNGSNGIAVGMATSIPPHNLAEVIDATVYLIDNPECSVDDLIKFVQGPDFPTAAIIMGKESIAEAYRTGRGKVKVRSRAFIEELPKGKQQIIVTEIPYQVNKAKLVERIAELVKEKRIEGISDLRDESNRNGMRIVIELKRDANANIVLNNLYKHSQMEDTFSIIMLALVDGQPRVLNLKQILYHYIKHQEDVVTRRTKFELNKAEARAHILEGLKIALDNIDAVISLIRASKTGQEAKLGLIEKFKLTEIQAQAILDMRLQRLTGLERDKIEAEYEDLIKKINRLKEILADERLLLNVIKDEITIIKENYSDERRTEIRHAEGEIDMRDLISDEEIAITLTHFGYIKRLPSDTYKSQKRGGRGISALTTREEDFVRHLVTTTTHSRLLFFTNKGRVFKLNAYEIPEGKRQAKGTAIVNLLQLSADEKIATLIPIDGNDENEYLLLATKKGIVKKTKREEFKNINKSGLIAIGLRDDDELIGVELTDGKQEVLLVTKEGMSIRFDENDIRYMGRTAMGVKGITLSKEDFVVSMNLCSKGTDVLVVSKNGFGKRTNIEEYRSQIRAGKGIKTYNISEKTGTIVGADMVNEDDEIMIINSDGVLIRIRVNEISLFGRVTSGVKLMKTNDEVNVVSIAKINIEEE"},"dna_sequence":{"accession":"AM180355.1","fmin":"6065","fmax":"8492","strand":"+","sequence":"ATGGAAGAAAATAACAAAATACTCCCTATTGAAATAGCGGAAGAAATGAAAAAATCGTATATTGATTATTCAATGAGTGTTATAGCTGGACGTGCTCTTCCTGATGTTAGAGATGGTTTAAAGCCAGTTCATAGAAGAATATTATATTCAATGAGTGAGTTAAATTTAACTCCAGATAAACCATACAGGAAGTCAGCTCGTATTGTTGGGGACGTTTTAGGTAAGTACCATCCTCATGGAGATACTGCTGTTTATTATGCTATGGTAAGAATGGCACAAGATTTTTCAACTAGAGCACTTTTAGTAGATGGTCATGGTAACTTTGGTTCTGTTGATGGGGATTCACCAGCTGCTATGCGTTATACAGAAGCTAAAATGAGTAAATTATCATTAGAACTACTGAGAGATATTGAAAAGGAAACTGTAGACTTTAAACCAAACTTTGATGAGTCGTTAAAAGAGCCTTCAGTATTGCCAGCTAGATATCCTAATTTATTAGTAAATGGCTCAAATGGTATAGCTGTTGGTATGGCAACTTCAATACCTCCACATAATTTAGCAGAAGTAATTGATGCAACTGTATATTTGATAGATAATCCAGAGTGTAGTGTAGATGATTTAATAAAATTTGTTCAAGGACCAGATTTCCCTACAGCTGCAATTATAATGGGAAAAGAAAGTATAGCAGAAGCATACAGAACTGGAAGAGGAAAAGTTAAAGTTAGGTCTAGAGCTTTTATAGAAGAGCTACCAAAAGGAAAACAGCAAATAATAGTTACAGAAATACCTTATCAAGTAAATAAGGCTAAACTGGTTGAAAGAATAGCAGAGTTAGTTAAAGAAAAGAGAATAGAAGGTATATCAGACCTAAGAGACGAAAGTAATAGAAATGGTATGAGAATTGTTATAGAATTAAAGAGGGATGCTAATGCTAATATAGTATTAAATAATTTGTATAAACATTCTCAAATGGAAGATACTTTTAGTATAATAATGCTTGCACTTGTAGATGGTCAGCCAAGAGTTTTAAATCTTAAACAAATATTATATCATTATATTAAACATCAAGAAGATGTTGTTACAAGAAGAACTAAATTTGAACTAAATAAAGCTGAAGCAAGAGCACATATTTTAGAAGGATTAAAGATTGCTTTAGATAATATAGATGCTGTTATAAGCTTGATAAGAGCTTCAAAGACTGGGCAAGAAGCTAAGCTAGGTTTAATAGAAAAATTCAAATTAACTGAAATCCAAGCACAAGCTATATTAGATATGAGACTTCAAAGACTTACAGGTTTAGAAAGAGATAAGATAGAAGCTGAATATGAAGATTTAATCAAGAAGATAAATAGATTAAAAGAGATTTTAGCTGATGAAAGATTACTTTTAAATGTAATAAAGGATGAAATTACAATAATAAAAGAAAATTACTCTGATGAGAGAAGAACAGAAATAAGACATGCTGAAGGCGAAATAGATATGAGAGATCTTATAAGTGATGAAGAAATAGCAATAACTCTTACTCACTTTGGATATATAAAAAGGCTTCCATCTGATACTTATAAGAGTCAAAAAAGGGGTGGAAGAGGTATTTCAGCACTTACAACTAGAGAAGAAGATTTTGTAAGGCACTTGGTAACTACAACTACTCATAGTAGACTATTATTCTTTACAAATAAAGGTAGAGTATTTAAATTAAATGCATATGAAATACCAGAAGGTAAGAGACAGGCTAAAGGTACTGCTATAGTGAATTTACTTCAATTGTCAGCAGATGAGAAAATTGCTACTCTAATACCTATTGATGGTAATGATGAAAATGAATATTTATTACTTGCAACGAAAAAAGGTATTGTTAAAAAGACTAAGAGAGAAGAGTTCAAAAATATAAATAAATCTGGTCTTATTGCAATAGGTTTAAGAGATGATGATGAGCTTATTGGAGTAGAACTTACAGATGGAAAACAAGAAGTACTTTTAGTAACTAAAGAAGGTATGTCTATAAGATTTGATGAAAATGATATAAGATATATGGGTAGAACAGCAATGGGTGTAAAAGGTATAACTTTAAGTAAAGAAGATTTTGTTGTGTCTATGAACCTTTGTAGTAAAGGTACAGATGTGTTAGTTGTAAGTAAGAATGGTTTTGGAAAGAGAACAAATATAGAAGAGTATAGAAGTCAAATAAGAGCTGGTAAAGGAATTAAAACTTATAATATATCTGAAAAAACTGGTACAATTGTAGGTGCAGATATGGTCAACGAAGATGATGAGATAATGATTATAAATTCTGATGGAGTTCTTATTAGAATAAGAGTCAATGAAATATCACTGTTTGGAAGAGTTACAAGTGGTGTTAAATTAATGAAGACGAATGATGAAGTCAATGTAGTTTCGATTGCCAAAATAAATATTGAAGAAGAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37603","NCBI_taxonomy_name":"Clostridioides difficile 630","NCBI_taxonomy_id":"272563"}}}},"ARO_accession":"3003995","ARO_id":"40901","ARO_name":"Clostridioides difficile gyrA conferring resistance to fluoroquinolones","CARD_short_name":"Cdif_gyrA_FLO","ARO_description":"Amino acid substitutions in Clostridioides difficile gyrase subunit A which when present confer functional resistance to fluoroquinolone antibiotics.","ARO_category":{"39876":{"category_aro_accession":"3003292","category_aro_cvterm_id":"39876","category_aro_name":"fluoroquinolone resistant gyrA","category_aro_description":"DNA gyrase is responsible for DNA supercoiling and consists of two alpha and two beta subunits. GyrA point mutations confer resistance by preventing fluoroquinolone antibiotics from binding the alpha-subunit.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37007":{"category_aro_accession":"3000663","category_aro_cvterm_id":"37007","category_aro_name":"ofloxacin","category_aro_description":"Ofloxacin is a 6-fluoro, 7-piperazinyl quinolone with a methyl-substituted oxazine ring. It has a broad spectrum of activity including many enterobacteria and mycoplasma but most anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3373":{"model_id":"3373","model_name":"FosD","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"260"}},"model_sequences":{"sequence":{"5558":{"protein_sequence":{"accession":"BAG12271.1","sequence":"MIQSINHICYSVSDLKNSIRFYKNILCGELLVSGKTTAYFNIGGLWVALNEEKDIPRNEVQYSYTHVAFTIDESEFNDWYQWFKENDVNILEGRTRDVRDKQSIYFTDPDGHKLELHTGTLENRLNYYKETKPHMVFYK"},"dna_sequence":{"accession":"AB304512.1","fmin":"17042","fmax":"17462","strand":"+","sequence":"ATGATACAATCTATCAATCATATATGTTATTCCGTTAGTGATTTAAAAAATTCGATACGCTTTTATAAAAATATTTTATGTGGCGAATTATTAGTAAGTGGAAAAACAACTGCATATTTCAATATTGGTGGCTTATGGGTTGCGTTAAACGAAGAAAAAGACATTCCTCGAAATGAAGTTCAATATTCGTACACACATGTAGCGTTTACTATAGATGAAAGTGAATTTAATGATTGGTATCAATGGTTCAAGGAAAATGACGTGAATATATTAGAAGGGCGTACTAGAGATGTAAGAGATAAGCAATCAATTTATTTTACTGATCCTGACGGACACAAGTTAGAGTTACATACTGGCACACTAGAAAATAGATTGAATTATTATAAAGAAACAAAACCGCATATGGTATTTTACAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35508","NCBI_taxonomy_name":"Staphylococcus aureus","NCBI_taxonomy_id":"1280"}}}},"ARO_accession":"3004674","ARO_id":"42722","ARO_name":"FosD","CARD_short_name":"FosD","ARO_description":"A fosfomycin resistance gene.","ARO_category":{"36272":{"category_aro_accession":"3000133","category_aro_cvterm_id":"36272","category_aro_name":"fosfomycin thiol transferase","category_aro_description":"Catalyzes the addition of a thiol group from a nucleophilic molecule to fosfomycin.","category_aro_class_name":"AMR Gene Family"},"35944":{"category_aro_accession":"0000025","category_aro_cvterm_id":"35944","category_aro_name":"fosfomycin","category_aro_description":"Fosfomycin (also known as phosphomycin and phosphonomycin) is a broad-spectrum antibiotic produced by certain Streptomyces species. It is effective on gram positive and negative bacteria as it targets the cell wall, an essential feature shared by both bacteria. Its specific target is MurA (MurZ in E.coli), which attaches phosphoenolpyruvate (PEP) to UDP-N-acetylglucosamine, a step of commitment to cell wall synthesis. In the active site of MurA, the active cysteine molecule is alkylated which stops the catalytic reaction.","category_aro_class_name":"Antibiotic"},"45731":{"category_aro_accession":"3007149","category_aro_cvterm_id":"45731","category_aro_name":"phosphonic acid antibiotic","category_aro_description":"A group of antibiotics derived from phosphonic acids.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3377":{"model_id":"3377","model_name":"rmtE","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"540"}},"model_sequences":{"sequence":{"5562":{"protein_sequence":{"accession":"ADA63498.1","sequence":"MNIDEMVAEVLSSKKYTSVDPAVVRRVCMETAPKYPKKKEAIKAVKNELHIIHEVFLQNECYKNALSFLSQLSLDFNNAQLIDITMQIMQSHTSTKERLGDIEAVCSFLSTHISKEGSVMDIGCGFNPFALPLLHEFPATYYAYDICSEGINILNKYFSILKKGEYRAELLDAVSVTPKEKVDVALLFKLLPLLQQQKKGRGFSILEELDFDKAIVSFPIKSLGGKQKGMETFYSNLFEENLPSSLEIIEKQTFSNEMFYVIQNKTKNGGNQS"},"dna_sequence":{"accession":"GU201947.1","fmin":"54","fmax":"876","strand":"+","sequence":"ATGAATATTGATGAAATGGTTGCAGAGGTTCTGTCGAGCAAAAAATATACAAGCGTTGACCCTGCTGTTGTTAGGCGTGTTTGTATGGAAACAGCACCTAAATATCCGAAGAAAAAAGAAGCAATAAAAGCGGTAAAAAATGAACTGCATATCATCCATGAGGTTTTTTTGCAAAACGAATGTTACAAAAATGCGCTTTCATTTTTATCACAGCTATCCTTAGATTTTAATAATGCGCAATTGATCGATATTACTATGCAAATCATGCAATCACATACATCAACCAAAGAGAGATTAGGCGACATTGAAGCGGTTTGTTCATTCTTAAGCACCCATATATCCAAAGAGGGTTCCGTGATGGACATCGGTTGTGGCTTCAATCCATTTGCGTTGCCATTACTGCACGAGTTCCCGGCAACGTATTATGCTTATGATATATGTTCAGAAGGAATTAACATCCTAAACAAATATTTCTCCATCCTAAAAAAAGGAGAATATAGAGCGGAGCTACTTGATGCCGTGTCTGTTACGCCGAAAGAAAAGGTGGATGTTGCCCTCCTATTCAAGCTATTACCTTTGTTGCAGCAACAGAAAAAAGGTCGAGGTTTCAGCATTTTAGAAGAACTGGACTTTGACAAAGCAATTGTATCTTTTCCAATAAAAAGCTTGGGAGGAAAGCAAAAAGGAATGGAAACCTTTTATTCGAATTTGTTTGAAGAAAACCTGCCTTCCTCATTGGAAATCATTGAGAAGCAGACTTTTTCAAATGAGATGTTCTATGTGATACAAAACAAAACCAAAAACGGAGGAAATCAATCATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3004678","ARO_id":"42727","ARO_name":"rmtE","CARD_short_name":"rmtE","ARO_description":"Aminoglycoside-resistance gene.","ARO_category":{"41435":{"category_aro_accession":"3004271","category_aro_cvterm_id":"41435","category_aro_name":"16S rRNA methyltransferase (G1405)","category_aro_description":"Methyltransferases that methylate the G1405 position of 16S rRNA, which is part of an aminoglycoside binding site.","category_aro_class_name":"AMR Gene Family"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"40942":{"category_aro_accession":"3004015","category_aro_cvterm_id":"40942","category_aro_name":"gentamicin A","category_aro_description":"Gentamicin A is part of a complex of broad spectrum aminoglycoside antibiotics. Gentamicin inhibits protein synthesis, resulting in bacterial cell death.","category_aro_class_name":"Antibiotic"},"46133":{"category_aro_accession":"3007382","category_aro_cvterm_id":"46133","category_aro_name":"gentamicin","category_aro_description":"Gentamicin is a commonly used aminoglycoside antibiotic derived from members of the Micromonospora genus of bacteria. It acts by binding the 30S ribosomal subunit, thus inhibiting protein synthesis. Gentamicin is typically used to treat Gram-negative infections of the repiratory and urinary tract, as well as infections of the bone and soft tissue. It also exhibits considerable nephrotoxicity and ototoxicity. Gentamicin is administered as a mixture of gentamicin type C (which makes about around 80% of the complex) and types A, B, and X (distributed in the remaining 20% of the complex).","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3385":{"model_id":"3385","model_name":"MCR-1.7","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"5571":{"protein_sequence":{"accession":"AQQ11622.1","sequence":"MMQHTSVWYRRSVSPFVLVASVAVFLTATANLTFFDKISQTYPIADNLGFVLTIAVVLFGAMLLITTLLSSYRYVLKPVLILLLIMGAVTSYFTDTYGTVYDTTMLQNALQTDQAETKDLLNAAFIMRIIGLGVLPSLLVAFVKVDYPTWGKGLMRRLGLIVASLALILLPVVAFSSHYASFFRVHKPLRSYVNPIMPIYSVGKLASIEYKKASTPKDTIYHAKDAVQATKPDMRKPRLVVFVVGETARADHVSFNGYERDTFPQLAKIDGVTNFSNVTSCGTSTAYSVPCMFSYLGADEYDVDTAKYQENVLDTLDRLGVSILWRDNNSDSKGVMDKLPKAQFADYKSATNNAICNTNPYNECRDVGMLVGLDDFVAANNGKDMLIMLHQMGNHGPAYFKRYDEKFAKFTPVCEGNELAKCEHQSLINAYDNALLATDDFIAQSIQWLQTHSNAYDVSMLYVSDHGESLGENGVYLHGMPNAFAPKEQRSVPAFFWTDKQTGITPMATDTVLTHDAITPTLLKLFDVTADKVKDRTAFIR"},"dna_sequence":{"accession":"KY488488.1","fmin":"0","fmax":"1626","strand":"+","sequence":"ATGATGCAGCATACTTCTGTGTGGTACCGACGCTCGGTCAGTCCGTTTGTTCTTGTGGCGAGTGTTGCCGTTTTCTTGACCGCGACCGCCAATCTTACCTTTTTTGATAAAATCAGCCAAACCTATCCCATCGCGGACAATCTCGGCTTTGTGCTGACGATCGCTGTCGTGCTCTTTGGCGCGATGCTACTGATCACCACGCTGTTATCATCGTATCGCTATGTGCTAAAGCCTGTGTTGATTTTGCTATTAATCATGGGCGCGGTGACCAGTTATTTTACTGACACTTATGGCACGGTCTATGATACGACCATGCTCCAAAATGCCCTACAGACCGACCAAGCCGAGACCAAGGATCTATTAAACGCAGCGTTTATCATGCGTATCATTGGTTTGGGTGTGCTACCAAGTTTGCTTGTGGCTTTTGTTAAGGTGGATTATCCGACTTGGGGCAAGGGTTTGATGCGCCGATTGGGCTTGATCGTGGCAAGTCTTGCGCTGATTTTACTGCCTGTGGTGGCGTTCAGCAGTCATTATGCCAGTTTCTTTCGCGTGCATAAGCCGCTGCGTAGCTATGTCAATCCGATCATGCCAATCTACTCGGTGGGTAAGCTTGCCAGTATTGAGTATAAAAAAGCCAGTACGCCAAAAGATACCATTTATCACGCCAAAGACGCGGTACAAGCAACCAAGCCTGATATGCGTAAGCCACGCCTAGTGGTGTTCGTCGTCGGTGAGACGGCACGCGCCGATCATGTCAGCTTCAATGGCTATGAGCGCGATACTTTCCCACAGCTTGCCAAGATCGATGGCGTGACCAATTTTAGCAATGTCACATCGTGCGGCACATCGACGGCGTATTCTGTGCCGTGTATGTTCAGCTATCTGGGCGCGGATGAGTATGATGTCGATACCGCCAAATACCAAGAAAATGTGCTGGATACGCTGGATCGCTTGGGCGTAAGTATCTTGTGGCGTGATAATAATTCGGACTCAAAAGGCGTGATGGATAAGCTGCCAAAAGCGCAATTTGCCGATTATAAATCCGCGACCAACAACGCCATCTGCAACACCAATCCTTATAACGAATGCCGCGATGTCGGTATGCTCGTTGGCTTAGATGACTTTGTCGCTGCCAATAACGGCAAAGATATGCTGATCATGCTGCACCAAATGGGCAATCACGGGCCTGCGTATTTTAAGCGATATGATGAAAAGTTTGCCAAATTCACGCCAGTGTGTGAAGGTAATGAGCTTGCCAAGTGCGAACATCAGTCCTTGATCAATGCTTATGACAATGCCTTGCTTGCCACCGATGATTTCATCGCTCAAAGTATCCAGTGGCTGCAGACGCACAGCAATGCCTATGATGTCTCAATGCTGTATGTCAGCGATCATGGCGAAAGTCTGGGTGAGAACGGTGTCTATCTACATGGTATGCCAAATGCCTTTGCACCAAAAGAACAGCGCAGTGTGCCTGCATTTTTCTGGACGGATAAGCAAACTGGCATCACGCCAATGGCAACCGATACCGTCCTGACCCATGACGCGATCACGCCGACATTATTAAAGCTGTTTGATGTCACCGCGGACAAAGTCAAAGACCGCACCGCATTCATCCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3004686","ARO_id":"42738","ARO_name":"MCR-1.7","CARD_short_name":"MCR-1.7","ARO_description":"A plasmid-mediated MCR-1 variant identified from Escherichia coli.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3388":{"model_id":"3388","model_name":"MCR-1.12","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"5574":{"protein_sequence":{"accession":"BBB21811.1","sequence":"MMHHTSVWYRRSVSPFVLVASVAVFLTATANLTFFDKISQTYPIADNLGFVLTIAVVLFGAMLLITTLLSSYRYVLKPVLILLLIMGAVTSYFTDTYGTVYDTTMLQNALQTDQAETKDLLNAAFIMRIIGLGVLPSLLVAFVKVDYPTWGKGLMRRLGLIVASLALILLPVVAFSSHYASFFRVHKPLRSYVNPIMPIYSVGKLASIEYKKASAPKDTIYHAKDAVQATKPDMRKPRLVVFVVGETARADHVSFNGYERDTFPQLAKIDGVTNFSNVTSCGTSTAYSVPCMFSYLGADEYDVDTAKYQENVLDTLDRLGVSILWRDNNSDSKGVMDKLPKAQFADYKSATNNAICNTNPYNECRDVGMLVGLDDFVAANNGKDMLIMLHQMGNHGPAYFKRYDEKFAKFTPVCEGNELAKCEHQSLINAYDNALLATDDFIAQSIQWLQTHSNAYDVSMLYVSDHGESLGENGVYLHGMPNAFAPKEQRSVPAFFWTDKQTGITPMATDTVLTHDAITPTLLKLFDVTADKVKDRTAFIR"},"dna_sequence":{"accession":"LC337668.1","fmin":"0","fmax":"1626","strand":"+","sequence":"ATGATGCACCATACTTCTGTGTGGTACCGACGCTCGGTCAGTCCGTTTGTTCTTGTGGCGAGTGTTGCCGTTTTCTTGACCGCGACCGCCAATCTTACCTTTTTTGATAAAATCAGCCAAACCTATCCCATCGCGGACAATCTCGGCTTTGTGCTGACGATCGCTGTCGTGCTCTTTGGCGCGATGCTACTGATCACCACGCTGTTATCATCGTATCGCTATGTGCTAAAGCCTGTGTTGATTTTGCTATTAATCATGGGCGCGGTGACCAGTTATTTTACTGACACTTATGGCACGGTCTATGATACGACCATGCTCCAAAATGCCCTACAGACCGACCAAGCCGAGACCAAGGATCTATTAAACGCAGCGTTTATCATGCGTATCATTGGTTTGGGTGTGCTACCAAGTTTGCTTGTGGCTTTTGTTAAGGTGGATTATCCGACTTGGGGCAAGGGTTTGATGCGCCGATTGGGCTTGATCGTGGCAAGTCTTGCGCTGATTTTACTGCCTGTGGTGGCGTTCAGCAGTCATTATGCCAGTTTCTTTCGCGTGCATAAGCCGCTGCGTAGCTATGTCAATCCGATCATGCCAATCTACTCGGTGGGTAAGCTTGCCAGTATTGAGTATAAAAAAGCCAGTGCGCCAAAAGATACCATTTATCACGCCAAAGACGCGGTACAAGCAACCAAGCCTGATATGCGTAAGCCACGCCTAGTGGTGTTCGTCGTCGGTGAGACGGCACGCGCCGATCATGTCAGCTTCAATGGCTATGAGCGCGATACTTTCCCACAGCTTGCCAAGATCGATGGCGTGACCAATTTTAGCAATGTCACATCGTGCGGCACATCGACGGCGTATTCTGTGCCGTGTATGTTCAGCTATCTGGGCGCGGATGAGTATGATGTCGATACCGCCAAATACCAAGAAAATGTGCTGGATACGCTGGATCGCTTGGGCGTAAGTATCTTGTGGCGTGATAATAATTCGGACTCAAAAGGCGTGATGGATAAGCTGCCAAAAGCGCAATTTGCCGATTATAAATCCGCGACCAACAACGCCATCTGCAACACCAATCCTTATAACGAATGCCGCGATGTCGGTATGCTCGTTGGCTTAGATGACTTTGTCGCTGCCAATAACGGCAAAGATATGCTGATCATGCTGCACCAAATGGGCAATCACGGGCCTGCGTATTTTAAGCGATATGATGAAAAGTTTGCCAAATTCACGCCAGTGTGTGAAGGTAATGAGCTTGCCAAGTGCGAACATCAGTCCTTGATCAATGCTTATGACAATGCCTTGCTTGCCACCGATGATTTCATCGCTCAAAGTATCCAGTGGCTGCAGACGCACAGCAATGCCTATGATGTCTCAATGCTGTATGTCAGCGATCATGGCGAAAGTCTGGGTGAGAACGGTGTCTATCTACATGGTATGCCAAATGCCTTTGCACCAAAAGAACAGCGCAGTGTGCCTGCATTTTTCTGGACGGATAAGCAAACTGGCATCACGCCAATGGCAACCGATACCGTCCTGACCCATGACGCGATCACGCCGACATTATTAAAGCTGTTTGATGTCACCGCGGACAAAGTCAAAGACCGCACCGCATTCATCCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3004689","ARO_id":"42741","ARO_name":"MCR-1.12","CARD_short_name":"MCR-1.12","ARO_description":"A plasmid-mediated phosphoethanolamine transferase and MCR-1 variant identified from Escherichia coli and conferring resistance to colistin antibiotics.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3392":{"model_id":"3392","model_name":"MCR-4.2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"5579":{"protein_sequence":{"accession":"AVK94777.1","sequence":"MISRFKTLSVNQFTFITALFYVAIFNLPLFGIVRKGIEKQPEVDPLFIASMPLFLTFALSFLFSIFTVKYLLKPFFIVLTLLSSSVFFAAYQYNVVFDYGMIENTFQTHPAEALMYVNLASITNLLLTGLLPSYLIYKADIHYQPFFKELLHKLAFMLLMFVGIGIVAFFYYQDYAAFVRNNSELRRYIVPTYFVSSASKYLNEHYLQTPMEYQQLGLDAKNASRNPNTKPNLLVVVVGETARSMSYQYYGYNKPTNAHTQNQGLIAFNDTSSCGTATAVSLPCMFSRMGRADYDPRRANAQDTVIDVLSHSGIKVQWFDNDSGCKGVCDRVENLTIDLKSDPKLCSGQYCFDQVLLNKLDKILAVAPSQDTVIFLHIIGSHGPTYYLRYPPEHRKFIPDCPRSDIQNCSQEELINTYDNTILYTDFILSEVVNKLKGKQDMFDTAMLYLSDHGESLGEKGMYLHGAPYSIAPKEQTSVPMLAWVSNDFSQDNQLNMTCVAQRAEQGGFSHDNLFDSLLGLMNVKTTVYQSQLDIFAPCRY"},"dna_sequence":{"accession":"MG822663.1","fmin":"0","fmax":"1626","strand":"+","sequence":"GTGATTTCTAGATTTAAGACGTTATCGGTTAACCAATTCACTTTCATCACTGCGTTGTTTTATGTTGCCATTTTCAATCTACCGCTCTTTGGTATAGTGCGAAAAGGAATTGAAAAACAACCAGAAGTTGATCCCCTTTTCATCGCATCTATGCCGCTATTTTTAACATTTGCGCTGAGTTTTTTGTTTTCAATTTTTACCGTCAAATACCTGCTGAAGCCCTTTTTTATCGTATTGACGTTACTTTCCTCAAGTGTATTTTTTGCAGCCTATCAATACAATGTCGTGTTTGACTACGGCATGATAGAAAACACGTTTCAAACACATCCTGCTGAAGCATTGATGTATGTAAATCTTGCATCAATTACCAATCTACTGCTGACTGGGCTATTACCGTCATATCTTATTTATAAGGCCGATATTCATTATCAGCCCTTTTTTAAGGAGTTATTGCATAAATTAGCCTTTATGCTGCTAATGTTCGTTGGCATTGGGATAGTCGCCTTTTTTTACTATCAAGATTATGCTGCATTTGTTCGAAACAACAGTGAGTTAAGGCGTTACATTGTCCCTACCTATTTTGTCAGTAGTGCATCTAAATATCTCAATGAGCACTATTTGCAGACGCCCATGGAATACCAACAACTTGGCCTAGATGCGAAGAATGCCAGTCGTAACCCGAACACTAAACCTAACTTATTAGTGGTTGTTGTGGGTGAAACTGCGCGCTCAATGAGCTATCAATATTATGGATATAACAAGCCAACCAATGCTCATACCCAAAATCAGGGGCTGATTGCGTTTAACGATACTAGCTCATGCGGCACGGCCACGGCGGTGTCTCTACCCTGTATGTTTTCACGAATGGGGCGGGCAGACTATGATCCTCGCCGTGCTAATGCTCAAGACACAGTGATTGATGTGTTAAGTCATAGTGGTATAAAAGTACAGTGGTTTGATAATGATTCTGGCTGTAAAGGTGTGTGTGATCGGGTTGAAAATCTCACGATAGATTTGAAGAGTGATCCGAAGCTGTGTTCTGGCCAATATTGTTTTGACCAAGTATTGCTCAACAAATTAGATAAAATTCTGGCAGTAGCACCAAGTCAAGATACAGTAATTTTTTTGCATATCATTGGTAGTCATGGACCAACTTATTATCTTAGATACCCGCCAGAGCATCGTAAATTTATACCGGATTGTCCGCGCAGTGATATTCAAAATTGCAGTCAAGAAGAACTGATTAACACCTACGACAACACTATTCTATATACGGATTTTATTCTCAGTGAAGTGGTGAATAAATTAAAAGGTAAGCAGGATATGTTCGATACTGCAATGCTGTATCTCTCTGACCATGGTGAGTCTTTGGGTGAAAAGGGCATGTATTTACATGGTGCGCCCTATAGTATTGCACCGAAAGAACAAACTAGCGTACCAATGCTGGCTTGGGTATCTAATGACTTTAGCCAAGATAATCAGTTGAACATGACTTGTGTTGCACAGCGAGCAGAACAGGGCGGCTTTTCCCACGACAATTTGTTCGACAGTTTGCTAGGACTTATGAATGTAAAAACCACCGTCTATCAGAGCCAACTCGATATTTTTGCACCTTGCAGGTATTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3004694","ARO_id":"42746","ARO_name":"MCR-4.2","CARD_short_name":"MCR-4.2","ARO_description":"A plasmid-mediated MCR-4 variant which confers resistance to colistin antibiotics.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3457":{"model_id":"3457","model_name":"OXA-294","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"560"}},"model_sequences":{"sequence":{"5652":{"protein_sequence":{"accession":"ENU93232.1","sequence":"MSKKLKLLALCATVISAATLVGCQNIQSQAQPLVLKKQAQDQIATAFENIQTTGVLVTYDGKNFQRYGNDLSRADQRYIPASTFKMLNALIGIQHHKTSPNEVFKWDGQKRAFRSWEQDLTLAEAMQASAVPVYQELARRIGLELMASEVKRVGYGNQNIGTQFDNFWLVGPLEITPVEEVKFAYALAKQQLPFAPSTQQQVRDMLLIENVQGTRIYAKSGWGMDVNPQVGWWTGWVEQPNGQITAFSLNMEMKKAEHADARKAIVYQALQQLGLLPQ"},"dna_sequence":{"accession":"APPC01000015.1","fmin":"269861","fmax":"270698","strand":"-","sequence":"ATGTCTAAAAAATTAAAATTACTCGCGCTATGTGCAACTGTAATCTCAGCTGCAACACTGGTCGGTTGTCAAAATATTCAGTCCCAAGCTCAACCTCTAGTCTTAAAGAAACAGGCTCAGGATCAGATTGCAACTGCATTCGAAAATATCCAGACAACTGGTGTATTGGTCACCTATGACGGCAAAAATTTTCAAAGATATGGCAATGATCTCAGCCGTGCAGATCAGCGTTACATTCCTGCTTCAACTTTTAAAATGCTCAATGCCTTGATTGGTATACAGCACCATAAAACCTCACCCAATGAAGTGTTTAAATGGGATGGACAGAAACGGGCTTTTCGTAGCTGGGAGCAGGACTTAACGCTTGCTGAGGCAATGCAGGCTTCGGCTGTACCTGTCTATCAGGAGCTGGCGCGCCGTATCGGTCTAGAATTAATGGCAAGTGAAGTAAAGCGGGTTGGCTACGGCAATCAAAATATAGGGACACAATTTGATAATTTCTGGTTGGTGGGGCCTTTAGAAATTACGCCAGTTGAGGAAGTGAAATTTGCTTATGCCTTAGCCAAACAGCAACTTCCATTTGCTCCCTCAACACAGCAGCAAGTCAGAGATATGTTGTTGATCGAAAATGTTCAGGGAACCAGAATCTATGCCAAAAGTGGTTGGGGAATGGATGTAAATCCTCAAGTCGGATGGTGGACAGGTTGGGTTGAACAACCAAATGGTCAAATCACTGCATTTTCGCTGAATATGGAAATGAAAAAAGCAGAACATGCGGATGCGCGTAAAGCCATTGTTTATCAAGCTTTACAACAGTTAGGTTTATTACCTCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41199","NCBI_taxonomy_name":"Acinetobacter sp. NIPH 758","NCBI_taxonomy_id":"1217712"}}}},"ARO_accession":"3001749","ARO_id":"38149","ARO_name":"OXA-294","CARD_short_name":"OXA-294","ARO_description":"OXA-294 is a beta-lactamase found in Acinetobacter spp.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46504":{"category_aro_accession":"3007715","category_aro_cvterm_id":"46504","category_aro_name":"OXA-294-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-294.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3484":{"model_id":"3484","model_name":"tva(A)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"5679":{"protein_sequence":{"accession":"SOX29786.1","sequence":"MFIKFNKVSFSYDSSDNILNDVSFHIDNSCTAIVGENGCGKTTLAKLITGILKPNSGSIEYSNKNIITAYCDQECINLPDNAENLFYDDSSYSGYLTSIFKIDYNYLYRFDTLSFGERKRLQIASALYSNPDILVLDEPTNHIDIECKDILINVIKRLDCIVIIISHDIDFLDELVEKCIFIRNGNCKIRIGNYTQCRGYEKDEEDYNFSLYEESRKKAKILENRYKKLQNESDAKKSKCGSKRHIDKKDHDAKGKIDAARLAGKDSRLATKAKQAKSLYNNTVMEMESLYTKKREVMDMEFIGERYKGKFLFYLEAGETKINSIVLRHPELIVKKDSRIGIEGVNGAGKTSLLNYIIETMYDNSIDKEKIIYIPQDIDRESWNNTFNNIKALDHESLGFLMSFVNRLGSNAKSVINSLNHSPGEMRKIMLGMAVIKKPYIIMLDEPTNHLDIDSIERLEEALISFNCALIIVSHNRNFIKNAVNTLWSIKIEYNYSILDIKNTI"},"dna_sequence":{"accession":"LT970863.1","fmin":"0","fmax":"1518","strand":"+","sequence":"ATGTTTATAAAATTCAATAAAGTTTCTTTTTCTTATGATAGTTCTGATAATATATTAAATGATGTTTCTTTTCATATAGATAATTCATGCACTGCAATAGTAGGTGAAAATGGATGCGGTAAAACCACGCTAGCTAAACTTATAACAGGTATATTAAAGCCTAATTCAGGAAGCATAGAATATTCAAATAAAAATATTATAACTGCTTACTGCGATCAGGAATGTATCAACTTACCTGATAATGCTGAAAATTTATTTTATGATGATAGTTCATACTCAGGATATTTAACTTCTATATTTAAAATAGATTATAATTATTTATATAGATTTGATACTCTTAGTTTCGGAGAGAGAAAAAGACTACAAATAGCTTCTGCTTTATACTCTAATCCTGATATATTGGTATTAGATGAGCCTACGAATCATATTGATATAGAATGCAAAGATATACTTATTAATGTAATAAAAAGACTCGATTGTATAGTTATAATTATAAGCCATGATATTGATTTTCTTGATGAGTTAGTAGAAAAATGTATATTTATAAGAAATGGAAATTGCAAGATAAGAATAGGTAATTACACTCAATGCAGAGGATATGAAAAAGACGAAGAAGATTATAATTTTAGTTTATATGAGGAAAGCAGGAAGAAAGCTAAAATATTAGAAAATAGATACAAAAAACTACAAAATGAATCGGATGCTAAAAAAAGCAAATGCGGAAGTAAAAGACATATAGATAAAAAAGATCATGATGCTAAGGGAAAAATAGACGCAGCAAGACTTGCAGGTAAAGATTCAAGACTTGCAACTAAGGCTAAGCAGGCCAAAAGTTTATACAATAATACAGTAATGGAAATGGAATCTCTTTATACTAAGAAAAGAGAAGTTATGGATATGGAGTTTATTGGAGAAAGGTATAAAGGAAAATTTTTATTTTATCTTGAGGCAGGAGAAACAAAAATAAATAGTATAGTTCTAAGACATCCCGAACTTATAGTGAAAAAAGACAGCAGAATAGGTATTGAAGGTGTAAACGGGGCAGGTAAAACCAGTTTATTAAATTATATAATTGAAACAATGTATGATAATTCTATAGATAAAGAAAAGATAATATATATTCCTCAGGATATAGATAGAGAAAGTTGGAATAATACTTTTAATAATATAAAGGCATTGGATCATGAATCATTAGGTTTTTTAATGAGTTTTGTAAATAGACTAGGAAGCAATGCTAAATCTGTGATTAATTCATTGAATCATAGTCCGGGTGAGATGCGTAAAATAATGCTTGGAATGGCGGTTATAAAAAAGCCTTATATTATAATGTTAGATGAGCCTACGAATCATCTGGATATAGACTCAATAGAGCGTTTAGAGGAGGCTTTAATTTCTTTTAATTGTGCTTTGATTATAGTAAGTCATAATAGAAATTTTATTAAAAATGCAGTAAATACTTTATGGAGTATAAAAATAGAATATAATTACAGTATTTTAGATATTAAAAACACTATATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42835","NCBI_taxonomy_name":"Brachyspira hyodysenteriae","NCBI_taxonomy_id":"159"}}}},"ARO_accession":"3004730","ARO_id":"42834","ARO_name":"tva(A)","CARD_short_name":"tva(A)","ARO_description":"A pleuromutilin resistance gene encoding a predicted ABC-F transporter. The presence of inhibitory or sub-inhibitory concentrations of tiamulin showed that tva(A) confers reduced pleuromutilin susceptibility that does not lead to clinical resistance but facilitates the development of higher-level resistance via mutations in genes encoding ribosome-associated functions.","ARO_category":{"45630":{"category_aro_accession":"3007068","category_aro_cvterm_id":"45630","category_aro_name":"Miscellaneous ABC-F subfamily ATP-binding cassette ribosomal protection proteins","category_aro_description":"ABC-F subfamily ATP-binding cassette ribosomal protection proteins of unknown, unclear or miscellaneous classification which nevertheless confer resistance to antibiotics through ribosomal protection and not through antibiotic efflux. These proteins should be further reviewed to elucidate associated genes, their function, origin and classification.","category_aro_class_name":"AMR Gene Family"},"37716":{"category_aro_accession":"3001317","category_aro_cvterm_id":"37716","category_aro_name":"pleuromutilin","category_aro_description":"Pleuromutilin is a natural product antibiotic produced by Clitopilus passeckerianus. Related antibiotics of clinical significance, such as tiamulin and retapamulin, are semi-synthetic derivatives of this compound.","category_aro_class_name":"Antibiotic"},"37014":{"category_aro_accession":"3000670","category_aro_cvterm_id":"37014","category_aro_name":"pleuromutilin antibiotic","category_aro_description":"Pleuromutilins are natural fungal products that target bacterial protein translation by binding the the 23S rRNA, blocking the ribosome P site at the 50S subunit. They are mostly used for agriculture and veterinary purposes.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3486":{"model_id":"3486","model_name":"OXA-400","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"560"}},"model_sequences":{"sequence":{"5681":{"protein_sequence":{"accession":"AIS39036.1","sequence":"MNIKTLLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEVHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNTDIGTQVDNFWLMGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"KJ780078.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAACACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGTTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGTACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATACAGATATCGGTACCCAAGTCGATAATTTTTGGCTGATGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001586","ARO_id":"37986","ARO_name":"OXA-400","CARD_short_name":"OXA-400","ARO_description":"OXA-400 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2551":{"model_id":"2551","model_name":"glycopeptide resistance gene cluster VanI","model_type":"gene cluster meta-model","model_type_id":"40298","model_description":"Gene Cluster Meta-Models (GCM) are used to curate spatial clusters of individual genes within operons, such as for glycopeptide resistance gene clusters. The individual genes will have their own individual detection models (e.g. PHM, PVM, POM, etc.) while the GCM checks to see if all the component genes of the cluster have a Strict or Perfect hit and are ordered correctly within an operon. GCMs are encoded using the gene order parameter. This model type is still under development and not currently supported by the Resistance Gene Identifier (RGI) software.","model_param":{"40297":{"param_type":"gene order","param_description":"Spatial clusters of genes are encoded using the gene order parameter: [gene type]:[cvterm_id],[gene type]:[cvterm_id], etc. The gene type designations are: R = regulatory, C = core, A = accessory.","param_type_id":"40297","param_value":{"4683":"R:40383,R:40385,C:40377,A:40380,C:40384,C:40381"}},"snp":{"Curated-R":{"4683":"Q123K"}}},"ARO_accession":"3003722","ARO_id":"40376","ARO_name":"glycopeptide resistance gene cluster VanI","CARD_short_name":"vanI_cluster","ARO_description":"This inducible cluster confers high resistance to vancomycin and intermediate resistance to teicoplanin. It achieves this through peptidoglycan restructuring with its VanA ligase homologue, VanI, causing the precursurs to end in D-Ala-D-Lac. The cluster uniquely contains murF, the final enzyme in the synthesis of UDP-N-acetylmuramoyl-pentapeptide, the precursor of murein. The VanI gene cluster has been found in chromosomal DNA. Gene orientation: vanSRIWK-murFvanX.","ARO_category":{"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"35948":{"category_aro_accession":"0000029","category_aro_cvterm_id":"35948","category_aro_name":"teicoplanin","category_aro_description":"Teicoplanin is a glycopeptide antibiotic used in the prophylaxis and treatment of serious infections caused by Gram-positive bacteria. Teicoplanin has a unique acyl-aliphatic chain, and binds to cell wall precursors to inhibit transglycosylation  and transpeptidation.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3513":{"model_id":"3513","model_name":"OXA-443","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"545"}},"model_sequences":{"sequence":{"5708":{"protein_sequence":{"accession":"PLT17746.1","sequence":"MTKLRHATTGAFLAALATFAHAEHPVCTLVADAATGKVVLQEGKCNERVTPASTFKLALAVMGYDAGFLKDPHTPVEHFRRGDPDWGGRPWRQPVDPTLWLKYSVVWYSQRITHAMGAQMFASYVRKLDYGNMDVSGDPGKNNGLDRSWITSSLKISPEEQVGFLRRLVNRQLPVSAQTYEMVDRTVQTWQVPGGWAVQGKTGTAGPAPGNTSADGTWDQAHAYGWFVGWAKKGGRTYVFANLIQDDKIEPTSGGIRSRDAMLARLPQVLAAAKP"},"dna_sequence":{"accession":"CM009147.1","fmin":"669855","fmax":"670683","strand":"+","sequence":"ATGACGAAACTCCGCCACGCCACCACCGGCGCCTTCCTTGCCGCCCTGGCCACCTTCGCCCATGCCGAACACCCTGTCTGCACGCTCGTTGCCGACGCCGCCACGGGCAAGGTCGTCCTGCAGGAGGGCAAGTGCAACGAGCGCGTGACGCCGGCGTCCACCTTCAAGCTGGCGCTGGCCGTCATGGGCTACGACGCCGGCTTCCTGAAAGACCCGCACACGCCGGTCGAACACTTCAGGCGCGGCGACCCCGACTGGGGCGGCCGGCCGTGGCGCCAGCCTGTCGACCCGACGCTGTGGCTCAAGTATTCGGTGGTCTGGTATTCCCAGCGCATCACCCACGCGATGGGCGCGCAGATGTTCGCCTCGTACGTGCGCAAGCTCGACTACGGCAACATGGATGTGAGCGGCGACCCGGGCAAGAACAACGGCCTGGATCGCTCGTGGATCACCTCGTCGCTGAAGATCTCGCCCGAGGAGCAGGTCGGCTTTCTGCGCCGGCTCGTCAACCGGCAGTTGCCCGTGTCGGCGCAGACGTACGAGATGGTCGACCGCACCGTGCAGACGTGGCAGGTGCCCGGCGGCTGGGCCGTGCAGGGCAAGACGGGCACGGCGGGCCCGGCGCCGGGCAATACCTCGGCCGACGGCACGTGGGATCAGGCCCACGCTTATGGCTGGTTTGTCGGCTGGGCGAAGAAAGGAGGCCGGACCTACGTGTTTGCGAACCTGATCCAGGACGACAAGATCGAGCCCACCTCGGGCGGCATCCGCTCGCGCGACGCGATGCTGGCGCGCCTGCCGCAGGTGCTGGCTGCCGCCAAGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42837","NCBI_taxonomy_name":"Ralstonia mannitolilytica","NCBI_taxonomy_id":"105219"}}}},"ARO_accession":"3003599","ARO_id":"40209","ARO_name":"OXA-443","CARD_short_name":"OXA-443","ARO_description":"OXA-443 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46497":{"category_aro_accession":"3007708","category_aro_cvterm_id":"46497","category_aro_name":"OXA-22-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-22.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3543":{"model_id":"3543","model_name":"OXA-482","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"545"}},"model_sequences":{"sequence":{"5738":{"protein_sequence":{"accession":"AKF41839.1","sequence":"MNKYFTCYVVASLFLSGCTVQHNLINETPSQIVQGHNQVINQYFDEKNTSGVLVIQTDKKINLYGNALSRANTEYVPASTFKMLNALIGLENQKTDINEIFKWKGEKRSFTAWEKDMTLGEAMKLSAVPVYQELARRIGLDLMQKEVKRIGFGNAEIGQQVDNFWLVGPLKVTPIQEVEFVSQLAHTQLPFSEKVQANVKNMLLLEESNGYKIFGKTGWAMDIKPQVGWLTGWVEQPDGKIVAFALNMEMRSEMPASIRNELLMKSLKQLNII"},"dna_sequence":{"accession":"KP264124.1","fmin":"76","fmax":"898","strand":"+","sequence":"ATGAATAAATATTTTACTTGCTATGTGGTTGCTTCTCTTTTTCTTTCTGGTTGTACGGTTCAGCATAATTTAATAAATGAAACCCCGAGTCAGATTGTTCAAGGACATAATCAGGTGATTAATCAATACTTTGATGAAAAAAACACCTCAGGTGTGCTGGTTATTCAAACAGATAAAAAAATTAATCTATATGGTAATGCTCTAAGCCGCGCAAATACAGAATATGTGCCAGCCTCTACATTTAAAATGTTGAATGCCCTGATCGGATTGGAGAACCAGAAAACGGATATTAATGAAATATTTAAATGGAAGGGCGAGAAAAGGTCATTTACCGCTTGGGAAAAAGACATGACACTAGGAGAAGCCATGAAGCTTTCTGCAGTCCCAGTCTATCAGGAACTTGCGCGACGTATCGGTCTTGATCTCATGCAAAAAGAAGTAAAACGTATTGGTTTCGGTAATGCTGAAATTGGACAGCAGGTTGATAATTTCTGGTTGGTAGGACCATTAAAGGTTACGCCTATTCAAGAGGTAGAGTTTGTTTCCCAATTAGCACATACACAGCTTCCATTTAGTGAAAAAGTGCAGGCTAATGTAAAAAATATGCTTCTTTTAGAAGAGAGTAATGGCTACAAAATTTTTGGAAAGACTGGTTGGGCAATGGATATAAAACCACAAGTGGGCTGGTTGACCGGCTGGGTTGAGCAGCCAGATGGAAAAATTGTCGCTTTTGCATTAAATATGGAAATGCGGTCAGAAATGCCGGCATCTATACGTAATGAATTATTGATGAAATCATTAAAACAGCTGAATATTATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3003639","ARO_id":"40249","ARO_name":"OXA-482","CARD_short_name":"OXA-482","ARO_description":"OXA-482 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46499":{"category_aro_accession":"3007710","category_aro_cvterm_id":"46499","category_aro_name":"OXA-23-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases, specifically imipenem, derived from OXA-23, first identified in Acinetobacter baumannii.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3587":{"model_id":"3587","model_name":"FONA-3","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"585"}},"model_sequences":{"sequence":{"5785":{"protein_sequence":{"accession":"CAB61639.1","sequence":"MVKNILRKTTLMVTTVMPLLFGSAPLWAQTANAKANIQQQLSELEKNSGGRLGVALIDTADNSQILYRGDERFPMCSTSKVMAVSALLKQSETDKNLLAKRMEIKQSDLVNYNPIAEKHLDTGMTLAEFSAATIQYSDNTAMNKILEHLGGPAKVTEFARTIGDKTFRLDRTEPTLNTAIPGDKRDTTSPLAMAKSLQNLTLGKALGEPQRAQLVEWMKGNTTGGASIRAGLPTTWVVGDKTGSGDYGTTNDIAVIWPANHAPLVLVTYFTQPQQNAEARKDVLAAAAKIVTEGL"},"dna_sequence":{"accession":"AJ251241.1","fmin":"1053","fmax":"1941","strand":"+","sequence":"ATGGTTAAAAATATACTACGTAAAACCACCCTGATGGTCACTACGGTTATGCCGTTGCTGTTCGGTAGCGCACCGCTATGGGCGCAAACTGCTAATGCCAAGGCGAATATTCAGCAGCAACTGTCTGAACTGGAGAAAAACTCCGGTGGCCGCTTGGGCGTGGCGCTGATCGATACCGCCGATAATTCGCAGATCCTGTATCGCGGGGATGAACGTTTTCCTATGTGCAGCACCAGCAAGGTGATGGCGGTGTCGGCGTTGTTAAAACAGAGCGAGACGGATAAAAATCTTTTGGCTAAGCGGATGGAAATCAAGCAATCCGATCTGGTCAACTACAACCCGATCGCCGAAAAACACCTGGATACCGGGATGACCCTGGCCGAGTTCAGCGCCGCCACCATCCAGTACAGTGACAACACGGCGATGAACAAGATCCTTGAGCATCTTGGCGGCCCGGCAAAAGTGACAGAATTTGCGCGTACTATTGGCGATAAAACCTTCCGCCTCGATCGTACCGAACCCACTTTAAATACCGCCATTCCAGGTGATAAGCGTGATACCACCTCACCGCTGGCGATGGCAAAAAGCCTGCAAAACCTGACCTTGGGCAAAGCGCTGGGTGAACCACAGCGTGCTCAACTGGTTGAATGGATGAAGGGGAATACTACCGGCGGAGCCAGCATTCGCGCAGGTCTGCCAACTACATGGGTGGTTGGGGATAAAACCGGCAGCGGTGATTATGGTACCACTAACGATATCGCCGTTATTTGGCCAGCGAACCACGCGCCGTTGGTGTTAGTAACCTATTTCACGCAGCCACAGCAGAATGCCGAAGCTCGTAAAGACGTGTTGGCTGCGGCTGCTAAAATTGTTACCGAAGGGCTTTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39675","NCBI_taxonomy_name":"Serratia fonticola","NCBI_taxonomy_id":"47917"}}}},"ARO_accession":"3004790","ARO_id":"42908","ARO_name":"FONA-3","CARD_short_name":"FONA-3","ARO_description":"FONA-3 is a class A beta-lactamase gene found in Serratia fonticola.","ARO_category":{"42905":{"category_aro_accession":"3004787","category_aro_cvterm_id":"42905","category_aro_name":"FONA beta-lactamase","category_aro_description":"FONA is a class A beta-lactamase gene family found in Serratia fonticola.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3593":{"model_id":"3593","model_name":"FRI-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"590"}},"model_sequences":{"sequence":{"6129":{"protein_sequence":{"accession":"ANZ90381.1","sequence":"MFFFKKSASTFIFFLCLPLNSFASQESNSIEQMRELEASFGGRIGVYILNTKNGKEFSYRQDERFPLCSSFKAFLAASVLKKTQDKSVSLDDMMEYSGRVMEKHSPVSEKYRKTGASVRTLAKAAIQYSDNGASNLLMERYIGGPEGLTAFMRSTGDTDFRLDRWELELNSAIPGDERDTSTPKAVAMSLKNIAFGSVLDAKNKSLLQEWLKGNTTGNARIRAAVPDKWDVGDKTGTCGFYGTANDVAILWPDANSPAVMAVYTTRPNQNDKHDEAVIKDSAKIAINAVYGSYK"},"dna_sequence":{"accession":"KX620467.1","fmin":"0","fmax":"885","strand":"+","sequence":"ATGTTTTTTTTTAAAAAAAGCGCAAGTACATTTATTTTTTTTCTCTGTCTTCCATTGAACTCATTCGCCTCTCAGGAAAGTAATAGTATTGAGCAAATGAGGGAATTGGAAGCTTCTTTTGGGGGGCGGATAGGTGTTTATATTTTAAACACAAAAAATGGGAAAGAATTTTCCTACAGACAAGATGAGAGATTTCCTTTATGTAGTTCATTTAAGGCATTCCTCGCTGCATCCGTATTAAAAAAAACTCAGGATAAATCTGTTTCTCTTGATGATATGATGGAATATTCTGGACGTGTTATGGAAAAGCATTCTCCTGTGTCAGAAAAATACCGCAAAACAGGAGCAAGCGTGCGGACTTTGGCGAAGGCAGCAATTCAGTACAGTGACAATGGAGCTTCTAATCTATTAATGGAAAGATACATAGGAGGTCCTGAGGGTTTGACTGCATTTATGCGGTCAACGGGAGACACTGACTTCAGGCTTGATCGTTGGGAATTAGAATTAAACTCAGCTATTCCAGGCGATGAACGAGATACTTCAACTCCAAAAGCAGTGGCAATGAGCCTTAAAAATATTGCTTTTGGTTCAGTACTCGATGCTAAAAATAAATCATTGCTGCAGGAATGGCTTAAAGGCAACACTACTGGTAATGCGCGAATTAGAGCTGCGGTTCCAGATAAGTGGGATGTCGGCGATAAAACAGGCACCTGTGGTTTTTATGGTACAGCCAATGATGTTGCTATTTTATGGCCAGACGCTAATTCACCTGCAGTTATGGCTGTCTACACAACACGTCCTAATCAAAACGACAAACATGACGAAGCAGTAATTAAAGATTCTGCAAAAATAGCTATAAATGCAGTGTATGGAAGTTATAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36926","NCBI_taxonomy_name":"Enterobacter asburiae","NCBI_taxonomy_id":"61645"}}}},"ARO_accession":"3004798","ARO_id":"42917","ARO_name":"FRI-2","CARD_short_name":"FRI-2","ARO_description":"FRI-2 is a carbapenem-hydrolyzing Class A beta-lactamase gene found in Enterobacter asburiae.","ARO_category":{"42915":{"category_aro_accession":"3004796","category_aro_cvterm_id":"42915","category_aro_name":"FRI beta-lactamase","category_aro_description":"FRI is a carbapenem-Hydrolyzing Class A beta-Lactamase from Enterobacter cloacae.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3642":{"model_id":"3642","model_name":"LEN-43","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"5913":{"protein_sequence":{"accession":"AZA07957.1","sequence":"MRYVRLCVISLLANLPLAVYAGPQPLEQIKQSESQLSGRVGMVEMDLASGRTLAAWRADERFPMVSTFKVLLCGAVLARVDAGVEQLDRRIHYRQQDLVDYSPVSEKHLVDGMTIGELCAAAITMSDNSAGNLLLATVGGPAGLTAFLRQIGDNVTRLDRWETALNEALPGDMRDTTTPASMAATLRKLLTAQHLSARSQQQLLQWMVDDRVAGPLIRAVLPAGWFIADKTGAGERGARGIVALLGPDGKAERIVVIYLRDTPASMAERNQHIAGIGAALIEHWQR"},"dna_sequence":{"accession":"MK161460.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGTGTTATCTCCCTGTTAGCCAACCTGCCACTAGCGGTATACGCCGGTCCACAGCCGCTTGAGCAGATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTGGGGATGGTGGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCGATGAACGCTTTCCCATGGTGAGCACCTTTAAAGTGCTGCTGTGCGGCGCGGTGCTGGCGCGGGTGGATGCCGGGGTCGAACAACTGGATCGGCGGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGTCGACGGGATGACGATCGGCGAACTCTGCGCCGCCGCCATCACCATGAGCGATAACAGCGCTGGCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCGGGATTGACCGCCTTTCTGCGCCAGATCGGTGACAACGTCACCCGTCTTGACCGCTGGGAAACGGCACTGAATGAGGCGCTTCCCGGCGACATGCGCGACACCACTACCCCGGCCAGCATGGCCGCCACGCTGCGTAAACTACTGACTGCGCAGCATCTGAGCGCCCGTTCACAGCAGCAGCTCCTGCAGTGGATGGTGGACGATCGGGTTGCCGGCCCGCTGATCCGCGCCGTGCTGCCGGCGGGCTGGTTTATCGCCGACAAGACCGGGGCTGGCGAACGGGGTGCGCGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAAGCGGAGCGCATTGTGGTGATCTATCTGCGGGATACCCCGGCGAGTATGGCCGAGCGTAATCAACATATCGCCGGGATCGGCGCAGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42976","NCBI_taxonomy_name":"Klebsiella variicola subsp. tropica","NCBI_taxonomy_id":"2489014"}}}},"ARO_accession":"3004846","ARO_id":"42981","ARO_name":"LEN-43","CARD_short_name":"LEN-43","ARO_description":"A class-A broad-spectrum beta-lactamase from Klebsiella.","ARO_category":{"36236":{"category_aro_accession":"3000097","category_aro_cvterm_id":"36236","category_aro_name":"LEN beta-lactamase","category_aro_description":"LEN beta-lactamases are chromosomal class A beta-lactamases that confer resistance to ampicillin, amoxicillin, carbenicillin, and ticarcillin but not to extended-spectrum beta-lactams.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3668":{"model_id":"3668","model_name":"NDM-27","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"5940":{"protein_sequence":{"accession":"AYP70146.1","sequence":"MELPNIMHPVAKLSTALAAALMLSGCMPGEIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTNDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASVRAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR"},"dna_sequence":{"accession":"MK105832.1","fmin":"0","fmax":"813","strand":"+","sequence":"ATGGAATTGCCCAATATTATGCACCCGGTCGCGAAGCTGAGCACCGCATTAGCCGCTGCATTGATGCTGAGCGGGTGCATGCCCGGTGAAATCCGCCCGACGATTGGCCAGCAAATGGAAACTGGCGACCAACGGTTTGGCGATCTGGTTTTCCGCCAGCTCGCACCGAATGTCTGGCAGCACACTTCCTATCTCGACATGCCGGGTTTCGGGGCAGTCGCTTCCAACGGTTTGATCGTCAGGGATGGCGGCCGCGTGCTGGTGGTCGATACCGCCTGGACCAATGACCAGACCGCCCAGATCCTCAACTGGATCAAGCAGGAGATCAACCTGCCGGTCGCGCTGGCGGTGGTGACTCACGCGCATCAGGACAAGATGGGCGGTATGGACGCGCTGCATGCGGCGGGGATTGCGACTTATGCCAATGCGTTGTCGAACCAGCTTGCCCCGCAAGAGGGGATGGTTGCGGCGCAACACAGCCTGACTTTCGCCGCCAATGGCTGGGTCGAACCAGCAACCGCGCCCAACTTTGGCCCGCTCAAGGTATTTTACCCCGGCCCCGGCCACACCAGTGACAATATCACCGTTGGGATCGACGGCACCGACATCGCTTTTGGTGGCTGCCTGATCAAGGACAGCAAGGCCAAGTCGCTCGGCAATCTCGGTGATGCCGACACTGAGCACTACGCCGCGTCAGTGCGCGCGTTTGGTGCGGCGTTCCCCAAGGCCAGCATGATCGTGATGAGCCATTCCGCCCCCGATAGCCGCGCCGCAATCACTCATACGGCCCGCATGGCCGACAAGCTGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3004870","ARO_id":"43008","ARO_name":"NDM-27","CARD_short_name":"NDM-27","ARO_description":"A class B New Delhi metallo-beta-lactamase and NDM-1 variant.","ARO_category":{"36196":{"category_aro_accession":"3000057","category_aro_cvterm_id":"36196","category_aro_name":"NDM beta-lactamase","category_aro_description":"NDM beta-lactamases or New Delhi metallo-beta-lactamases are class B beta-lactamases that confer resistance to a broad range of antibiotics including carbapenems, cephalosporins and penicillins.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3717":{"model_id":"3717","model_name":"Mycobacterium tuberculosis Rv1667 mutations confer resistance to pyrazinamide","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"41339":{"param_type":"nucleotide substitution in promoter region","param_description":"A nucleotide sequence change where, compared to a reference sequence, one nucleotide is replaced by one other nucleotide in the promoter region of a gene. These substitutions are indicated as upstream of the reference sequence transcription initiation site. Format is given by [-][position][wildtype][>][mutation], e.g. -11t>c or -15g>Var where Var represents any possible substitution.","param_type_id":"41339","param_value":{"13187":"-944g>a"}},"snp":{"ReSeqTB-Minimal":{"13187":"Q123K"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"8779":{"protein_sequence":{"accession":"NP_216185.1","sequence":"MSRRPGYSNGRAGASRQAARGGSAGASSVAFSSQPNCGLTESVLGHQVTGICLGTIHLDAMQWPWSSAYRLEPAVATTLIGISAWWANGSVKQYAGDLTDRVATMTVCRRTPAPRVHYRQ"},"dna_sequence":{"accession":"NC_000962.3","fmin":"1895724","fmax":"1896087","strand":"+","sequence":"ATGTCACGGCGACCGGGATACTCGAATGGACGTGCCGGGGCCAGCCGGCAAGCTGCTCGTGGCGGCTCGGCAGGGGCGTCGTCGGTAGCTTTCTCCAGCCAGCCCAACTGCGGACTGACTGAATCAGTCTTGGGCCACCAAGTCACTGGAATATGCTTGGGCACAATACATCTTGATGCCATGCAGTGGCCATGGTCGTCGGCGTACCGATTGGAGCCGGCCGTTGCTACCACATTAATCGGCATCAGTGCCTGGTGGGCGAATGGCAGCGTGAAGCAATACGCCGGTGATCTGACTGATCGTGTCGCCACGATGACAGTTTGCCGGCGCACGCCGGCTCCGCGAGTGCATTATCGACAGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3004984","ARO_id":"43171","ARO_name":"Mycobacterium tuberculosis Rv1667 mutations confer resistance to pyrazinamide","CARD_short_name":"Mtub_Rv1667_PZA","ARO_description":"Mutations in the Rv1667 gene that can contribute to or confer resistance to pyrazinamide. Resistance may be due to an antibiotic export mechanism.","ARO_category":{"43170":{"category_aro_accession":"3004983","category_aro_cvterm_id":"43170","category_aro_name":"pyrazinamide resistant Rv1667","category_aro_description":"A probable transport protein thought to be involved in the active transport of macrolide across the membrane in mycobacterium.","category_aro_class_name":"AMR Gene Family"},"39997":{"category_aro_accession":"3003413","category_aro_cvterm_id":"39997","category_aro_name":"pyrazinamide","category_aro_description":"Pyrazinamide is an antimycobacterial. It is highly specific and active only against Mycobacterium tuberculosis. This compound is a prodrug and needs to be activated inside the cell. It interferes with the bacterium's ability to synthesize new fatty acids, causing cell death.","category_aro_class_name":"Antibiotic"},"45737":{"category_aro_accession":"3007155","category_aro_cvterm_id":"45737","category_aro_name":"pyrazine antibiotic","category_aro_description":"A group of antibiotics derived from pyrazine.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3727":{"model_id":"3727","model_name":"Mycobacterium tuberculosis mshA mutations conferring resistance to isoniazid","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"9563":"A187V","10059":"F355S"},"ReSeqTB-Minimal":{"9563":"A187V"},"clinical":{"9563":"A187V","10059":"F355S"},"Curated-R":{"10059":"F355S"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"875"}},"model_sequences":{"sequence":{"8837":{"protein_sequence":{"accession":"NP_215000.1","sequence":"MAGVRHDDGSGLIAQRRPVRGEGATRSRGPSGPSNRNVSAADDPRRVALLAVHTSPLAQPGTGDAGGMNVYMLQSALHLARRGIEVEIFTRATASADPPVVRVAPGVLVRNVVAGPFEGLDKYDLPTQLCAFAAGVLRAEAVHEPGYYDIVHSHYWLSGQVGWLARDRWAVPLVHTAHTLAAVKNAALADGDGPEPPLRTVGEQQVVDEADRLIVNTDDEARQVISLHGADPARIDVVHPGVDLDVFRPGDRRAARAALGLPVDERVVAFVGRIQPLKAPDIVLRAAAKLPGVRIIVAGGPSGSGLASPDGLVRLADELGISARVTFLPPQSHTDLATLFRAADLVAVPSYSESFGLVAVEAQACGTPVVAAAVGGLPVAVRDGITGTLVSGHEVGQWADAIDHLLRLCAGPRGRVMSRAAARHAATFSWENTTDALLASYRRAIGEYNAERQRRGGEVISDLVAVGKPRHWTPRRGVGA"},"dna_sequence":{"accession":"NC_000962.3","fmin":"575347","fmax":"576790","strand":"+","sequence":"ATGGCAGGTGTGCGGCACGATGACGGTTCAGGGTTGATCGCCCAGCGCCGTCCGGTCCGCGGCGAGGGTGCCACCCGCTCGCGCGGCCCATCCGGGCCATCCAATCGGAATGTTTCGGCAGCAGACGACCCGCGCCGGGTTGCGCTGCTGGCGGTGCACACCTCACCGCTGGCACAGCCGGGCACCGGTGACGCCGGCGGCATGAACGTCTACATGCTGCAAAGTGCGCTGCACCTGGCCCGTCGGGGCATCGAGGTGGAGATCTTCACCCGGGCCACCGCATCGGCAGATCCACCGGTGGTGCGGGTGGCACCCGGGGTGCTGGTGCGCAACGTGGTGGCGGGGCCCTTCGAGGGTTTGGACAAGTACGACCTGCCCACCCAGCTTTGTGCGTTCGCCGCCGGGGTGCTGCGCGCCGAGGCGGTCCACGAACCGGGTTACTACGACATCGTGCACTCGCACTACTGGCTGTCGGGTCAGGTCGGCTGGCTGGCGCGCGACCGCTGGGCGGTGCCGTTGGTGCACACCGCACACACGCTGGCCGCCGTGAAGAACGCGGCACTGGCCGACGGCGACGGACCCGAGCCGCCGCTGCGTACGGTCGGGGAGCAGCAGGTCGTCGACGAGGCGGATCGGTTGATCGTCAACACCGACGATGAAGCCAGGCAAGTGATTTCGCTTCATGGTGCCGATCCGGCACGAATCGACGTGGTCCATCCCGGTGTCGATCTGGACGTGTTCCGCCCGGGTGATCGGCGCGCGGCCCGGGCCGCGCTAGGACTACCAGTTGACGAGCGCGTGGTGGCCTTCGTCGGACGCATCCAGCCGCTGAAGGCACCCGACATTGTGCTGCGTGCGGCCGCCAAGTTGCCCGGGGTGCGCATCATCGTGGCCGGCGGACCGTCGGGCAGCGGTCTGGCTTCACCGGACGGACTGGTCCGGCTCGCCGACGAACTGGGCATCTCTGCACGGGTGACGTTTCTGCCGCCGCAGTCCCACACGGATCTGGCCACCTTGTTTCGGGCGGCGGACCTGGTTGCGGTGCCGAGCTACTCCGAGTCGTTCGGCCTGGTTGCTGTGGAGGCCCAAGCGTGCGGCACACCGGTGGTGGCCGCGGCGGTGGGCGGGCTGCCCGTCGCGGTGCGCGACGGGATCACCGGCACCCTGGTGTCCGGGCACGAGGTCGGTCAGTGGGCCGACGCCATCGATCACCTGCTGCGGTTGTGTGCCGGGCCACGGGGACGGGTGATGAGCCGGGCGGCGGCACGGCACGCCGCCACGTTCTCGTGGGAGAACACCACCGACGCGCTGTTGGCCAGTTATCGGCGTGCGATCGGCGAGTACAACGCCGAGCGCCAGCGCCGGGGCGGCGAGGTGATATCGGACCTGGTAGCGGTGGGCAAGCCCCGCCACTGGACGCCGCGTCGCGGGGTGGGCGCGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3004925","ARO_id":"43111","ARO_name":"Mycobacterium tuberculosis mshA mutations conferring resistance to isoniazid","CARD_short_name":"Mtub_mshA_INH","ARO_description":"Mutations that occur in Mycobacterium tuberculosis mshA that result in or contribute to antibiotic resistance to isoniazid.","ARO_category":{"43087":{"category_aro_accession":"3004901","category_aro_cvterm_id":"43087","category_aro_name":"isoniazid resistant mshA","category_aro_description":"mshA is a glycosyltransferase and is involved in the first step of mycothiol biosynthesis. This is a step that is required for growth in mycobacterium tuberculosis. Resistance has been shown in the gene to isoniazid.","category_aro_class_name":"AMR Gene Family"},"36659":{"category_aro_accession":"3000520","category_aro_cvterm_id":"36659","category_aro_name":"isoniazid","category_aro_description":"Isoniazid is an organic compound that is the first-line anti tuberculosis medication in prevention and treatment. As a prodrug, it is activated by mycobacterial catalase-peroxidases such as M. tuberculosis KatG. Isoniazid inhibits mycolic acid synthesis, which prevents cell wall synthesis in mycobacteria.","category_aro_class_name":"Antibiotic"},"45734":{"category_aro_accession":"3007152","category_aro_cvterm_id":"45734","category_aro_name":"isoniazid-like antibiotic","category_aro_description":"A group of antibiotics containing isoniazid and its derivatives.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2355":{"model_id":"2355","model_name":"ADC-31","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"5444":{"protein_sequence":{"accession":"ADX04315.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVKTDQQVLTFFKDWKPKNSIGEYRQYSNPSIGLFGKVVALSMNKPLDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTSGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"CP001921.1","fmin":"2803996","fmax":"2805148","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAGTATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAATTTCCAGATGAAGTAAAAACAGATCAGCAAGTTTTAACATTTTTTAAAGACTGGAAACCTAAAAACTCAATCGGTGAATATCGACAATATTCAAACCCAAGCATTGGTTTATTTGGAAAAGTTGTAGCTTTGTCTATGAATAAACCTTTAGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTAAATCCACAAAAATATCCAGCAGATATTCAACGGGCAATTAATGAAACACATCAGGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAGCGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35649","NCBI_taxonomy_name":"Acinetobacter baumannii 1656-2","NCBI_taxonomy_id":"696749"}}}},"ARO_accession":"3003870","ARO_id":"40569","ARO_name":"ADC-31","CARD_short_name":"ADC-31","ARO_description":"ADC-31 is a beta-lactamase found in Acinetobacter baumannii.","ARO_category":{"40543":{"category_aro_accession":"3003846","category_aro_cvterm_id":"40543","category_aro_name":"ADC beta-lactamase without carbapenemase activity","category_aro_description":"ADC beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases with extended-spectrum resistance to cephalosporins but not to carbapenems. ADC beta-lactamases are found in Acinetobacter sp. and Oligella urethralis.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2356":{"model_id":"2356","model_name":"ADC-39","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"5445":{"protein_sequence":{"accession":"ACC95874.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNRSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWQPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGFYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTTGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"EU652244.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATCGCAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGCAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTGGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCATTTGGTTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCTGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTTAACCCACAGAAATATCCGGCTGATATTCAACGGGCAATTAATGAAACACATCAAGGGTTCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCACCGGTTTCGGAACATATGTAGTGTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3003871","ARO_id":"40570","ARO_name":"ADC-39","CARD_short_name":"ADC-39","ARO_description":"ADC-39 is a beta-lactamase found in Acinetobacter baumannii.","ARO_category":{"40543":{"category_aro_accession":"3003846","category_aro_cvterm_id":"40543","category_aro_name":"ADC beta-lactamase without carbapenemase activity","category_aro_description":"ADC beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases with extended-spectrum resistance to cephalosporins but not to carbapenems. ADC beta-lactamases are found in Acinetobacter sp. and Oligella urethralis.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3378":{"model_id":"3378","model_name":"rmtE2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8350":{"protein_sequence":{"accession":"ALD03565.1","sequence":"MNIDEMAAEVLSSKKYTSVDPAVVRRVCMETAPKYPKKKEAIKAVKNELHIIHEVFLQNECYKNALSFLSQLSLDFNNAQLIDITMQIMQSHTSTKERLGDIEAVCSFLSTHISKEGSVMDIGCGFNPFALPLLHEFPATYYAYDICSEGINILNKYFSILKKGEYRAELLDAVSVTPKEKVDVALLFKLLPLLQQQKKGRGFSILEELDFDKAIVSFPIKSLGGKQKGMETFYSNLFEENLPSSLEIIEKQTFSNEMFYVIQNKTKNGGNQS"},"dna_sequence":{"accession":"KT428293.1","fmin":"1846","fmax":"2668","strand":"+","sequence":"ATGAATATTGATGAAATGGCTGCAGAGGTTCTGTCGAGCAAAAAATATACAAGCGTTGACCCTGCTGTTGTTAGGCGTGTTTGTATGGAAACAGCACCTAAATATCCGAAGAAAAAAGAAGCAATAAAAGCGGTAAAAAATGAACTGCATATCATCCATGAGGTTTTTTTGCAAAACGAATGTTACAAAAATGCGCTTTCATTTTTATCACAGCTATCCTTAGATTTTAATAATGCGCAATTGATCGATATTACTATGCAAATCATGCAATCACATACATCAACCAAAGAGAGATTAGGCGACATTGAAGCGGTTTGTTCATTCTTAAGCACCCATATATCCAAAGAGGGTTCCGTGATGGACATCGGTTGTGGCTTCAATCCATTTGCGTTGCCATTACTGCACGAGTTCCCGGCAACGTATTATGCTTATGATATATGTTCAGAAGGAATTAACATCCTAAACAAATATTTCTCCATCCTAAAAAAAGGAGAATATAGAGCGGAGCTACTTGATGCCGTGTCTGTTACGCCGAAAGAAAAGGTGGATGTTGCCCTCCTATTCAAGCTATTACCTTTGTTGCAGCAACAGAAAAAAGGTCGAGGTTTCAGCATTTTAGAAGAACTGGACTTTGACAAAGCAATTGTATCTTTTCCAATAAAAAGCTTGGGAGGAAAGCAAAAAGGAATGGAAACCTTTTATTCGAATTTGTTTGAAGAAAACCTGCCTTCCTCATTGGAAATCATTGAGAAGCAGACTTTTTCAAATGAGATGTTCTATGTGATACAAAACAAAACCAAAAACGGAGGAAATCAATCATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3004679","ARO_id":"42728","ARO_name":"rmtE2","CARD_short_name":"rmtE2","ARO_description":"A 16S rRNA mathyltransferase gene with a single nucleotide mutation compared to rmtE.","ARO_category":{"41435":{"category_aro_accession":"3004271","category_aro_cvterm_id":"41435","category_aro_name":"16S rRNA methyltransferase (G1405)","category_aro_description":"Methyltransferases that methylate the G1405 position of 16S rRNA, which is part of an aminoglycoside binding site.","category_aro_class_name":"AMR Gene Family"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"40942":{"category_aro_accession":"3004015","category_aro_cvterm_id":"40942","category_aro_name":"gentamicin A","category_aro_description":"Gentamicin A is part of a complex of broad spectrum aminoglycoside antibiotics. Gentamicin inhibits protein synthesis, resulting in bacterial cell death.","category_aro_class_name":"Antibiotic"},"46133":{"category_aro_accession":"3007382","category_aro_cvterm_id":"46133","category_aro_name":"gentamicin","category_aro_description":"Gentamicin is a commonly used aminoglycoside antibiotic derived from members of the Micromonospora genus of bacteria. It acts by binding the 30S ribosomal subunit, thus inhibiting protein synthesis. Gentamicin is typically used to treat Gram-negative infections of the repiratory and urinary tract, as well as infections of the bone and soft tissue. It also exhibits considerable nephrotoxicity and ototoxicity. Gentamicin is administered as a mixture of gentamicin type C (which makes about around 80% of the complex) and types A, B, and X (distributed in the remaining 20% of the complex).","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3386":{"model_id":"3386","model_name":"MCR-1.8","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"5572":{"protein_sequence":{"accession":"AQY61516.1","sequence":"MMRHTSVWYRRSVSPFVLVASVAVFLTATANLTFFDKISQTYPIADNLGFVLTIAVVLFGAMLLITTLLSSYRYVLKPVLILLLIMGAVTSYFTDTYGTVYDTTMLQNALQTDQAETKDLLNAAFIMRIIGLGVLPSLLVAFVKVDYPTWGKGLMRRLGLIVASLALILLPVVAFSSHYASFFRVHKPLRSYVNPIMPIYSVGKLASIEYKKASAPKDTIYHAKDAVQATKPDMRKPRLVVFVVGETARADHVSFNGYERDTFPQLAKIDGVTNFSNVTSCGTSTAYSVPCMFSYLGADEYDVDTAKYQENVLDTLDRLGVSILWRDNNSDSKGVMDKLPKAQFADYKSATNNAICNTNPYNECRDVGMLVGLDDFVAANNGKDMLIMLHQMGNHGPAYFKRYDEKFAKFTPVCEGNELAKCEHQSLINAYDNALLATDDFIAQSIQWLQTHSNAYDVSMLYVSDHGESLGENGVYLHGMPNAFAPKEQRSVPAFFWTDKQTGITPMATDTVLTHDAITPTLLKLFDVTADKVKDRTAFIR"},"dna_sequence":{"accession":"KY683842.1","fmin":"0","fmax":"1626","strand":"+","sequence":"ATGATGCGGCATACTTCTGTGTGGTACCGACGCTCGGTCAGTCCGTTTGTTCTTGTGGCGAGTGTTGCCGTTTTCTTGACCGCGACCGCCAATCTTACCTTTTTTGATAAAATCAGCCAAACCTATCCCATCGCGGACAATCTCGGCTTTGTGCTGACGATCGCTGTCGTGCTCTTTGGCGCGATGCTACTGATCACCACGCTGTTATCATCGTATCGCTATGTGCTAAAGCCTGTGTTGATTTTGCTATTAATCATGGGCGCGGTGACCAGTTATTTTACTGACACTTATGGCACGGTCTATGATACGACCATGCTCCAAAATGCCCTACAGACCGACCAAGCCGAGACCAAGGATCTATTAAACGCAGCGTTTATCATGCGTATCATTGGTTTGGGTGTGCTACCAAGTTTGCTTGTGGCTTTTGTTAAGGTGGATTATCCGACTTGGGGCAAGGGTTTGATGCGCCGATTGGGCTTGATCGTGGCAAGTCTTGCGCTGATTTTACTGCCTGTGGTGGCGTTCAGCAGTCATTATGCCAGTTTCTTTCGCGTGCATAAGCCGCTGCGTAGCTATGTCAATCCGATCATGCCAATCTACTCGGTGGGTAAGCTTGCCAGTATTGAGTATAAAAAAGCCAGTGCGCCAAAAGATACCATTTATCACGCCAAAGACGCGGTACAAGCAACCAAGCCTGATATGCGTAAGCCACGCCTAGTGGTGTTCGTCGTCGGTGAGACGGCACGCGCCGATCATGTCAGCTTCAATGGCTATGAGCGCGATACTTTCCCACAGCTTGCCAAGATCGATGGCGTGACCAATTTTAGCAATGTCACATCGTGCGGCACATCGACGGCGTATTCTGTGCCGTGTATGTTCAGCTATCTGGGCGCGGATGAGTATGATGTCGATACCGCCAAATACCAAGAAAATGTGCTGGATACGCTGGATCGCTTGGGCGTAAGTATCTTGTGGCGTGATAATAATTCGGACTCAAAAGGCGTGATGGATAAGCTGCCAAAAGCGCAATTTGCCGATTATAAATCCGCGACCAACAACGCCATCTGCAACACCAATCCTTATAACGAATGCCGCGATGTCGGTATGCTCGTTGGCTTAGATGACTTTGTCGCTGCCAATAACGGCAAAGATATGCTGATCATGCTGCACCAAATGGGCAATCACGGGCCTGCGTATTTTAAGCGATATGATGAAAAGTTTGCCAAATTCACGCCAGTGTGTGAAGGTAATGAGCTTGCCAAGTGCGAACATCAGTCCTTGATCAATGCTTATGACAATGCCTTGCTTGCCACCGATGATTTCATCGCTCAAAGTATCCAGTGGCTGCAGACGCACAGCAATGCCTATGATGTCTCAATGCTGTATGTCAGCGATCATGGCGAAAGTCTGGGTGAGAACGGTGTCTATCTACATGGTATGCCAAATGCCTTTGCACCAAAAGAACAGCGCAGTGTGCCTGCATTTTTCTGGACGGATAAGCAAACTGGCATCACGCCAATGGCAACCGATACCGTCCTGACCCATGACGCGATCACGCCGACATTATTAAAGCTGTTTGATGTCACCGCGGACAAAGTCAAAGACCGCACCGCATTCATCCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3004687","ARO_id":"42739","ARO_name":"MCR-1.8","CARD_short_name":"MCR-1.8","ARO_description":"An unpublished MCR-1 variant.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3389":{"model_id":"3389","model_name":"MCR-1.13","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"5575":{"protein_sequence":{"accession":"AVM85874.1","sequence":"MMQHTSVWYRRSVSPFVLVASVAVFLTATANLTFFDKISQTYPIADNLGFVLTIAVVLFGAMLLITTLLSSYRYVLKPVLILLLIMGAVTSYFTDTYGTVYDTTMLQNALQTDQAETKDLLNAAFIMRIIGLGVLPSLLVAFVKVDYPTWGKGLIRRLGLIVASLALILLPVVAFSSHYASFFRVHKPLRSYVNPIMPIYSVGKLASIEYKKASAPKDTIYHAKDAVQATKPDMRKPRLVVFVVGETARADHVSFNGYERDTFPQLAKIDGVTNFSNVTSCGTSTAYSVPCMFSYLGADEYDVDTAKYQENVLDTLDRLGVSILWRDNNSDSKGVMDKLPKAQFADYKSATNNAICNTNPYNECRDVGMLVGLDDFVAANNGKDMLIMLHQMGNHGPAYFKRYDEKFAKFTPVCEGNELAKCEHQSLINAYDNALLATDDFIAQSIQWLQTHSNAYDVSMLYVSDHGESLGENGVYLHGMPNAFAPKEQRSVPAFFWTDKQTGITPMATDTVLTHDAITPTLLKLFDVTADKVKDRTAFIR"},"dna_sequence":{"accession":"MG384739.1","fmin":"0","fmax":"1626","strand":"+","sequence":"ATGATGCAGCATACTTCTGTGTGGTACCGACGCTCGGTCAGTCCGTTTGTTCTTGTGGCGAGTGTTGCCGTTTTCTTGACCGCGACCGCCAATCTTACCTTTTTTGATAAAATCAGCCAAACCTATCCCATCGCGGACAATCTCGGCTTTGTGCTGACGATCGCTGTCGTGCTCTTTGGCGCGATGCTACTGATCACCACGCTGTTATCATCGTATCGCTATGTGCTAAAGCCTGTGTTGATTTTGCTATTAATCATGGGCGCGGTGACCAGTTATTTTACTGACACTTATGGCACGGTCTATGATACGACCATGCTCCAAAATGCCCTACAGACCGACCAAGCCGAGACCAAGGATCTATTAAACGCAGCGTTTATCATGCGTATCATTGGTTTGGGTGTGCTACCAAGTTTGCTTGTGGCTTTTGTTAAGGTGGATTATCCGACTTGGGGCAAGGGTTTGATACGCCGATTGGGCTTGATCGTGGCAAGTCTTGCGCTGATTTTACTGCCTGTGGTGGCGTTCAGCAGTCATTATGCCAGTTTCTTTCGCGTGCATAAGCCGCTGCGTAGCTATGTCAATCCGATCATGCCAATCTACTCGGTGGGTAAGCTTGCCAGTATTGAGTATAAAAAAGCCAGTGCGCCAAAAGATACCATTTATCACGCCAAAGACGCGGTACAAGCAACCAAGCCTGATATGCGTAAGCCACGCCTAGTGGTGTTCGTCGTCGGTGAGACGGCACGCGCCGATCATGTCAGCTTCAATGGCTATGAGCGCGATACTTTCCCACAGCTTGCCAAGATCGATGGCGTGACCAATTTTAGCAATGTCACATCGTGCGGCACATCGACGGCGTATTCTGTGCCGTGTATGTTCAGCTATCTGGGCGCGGATGAGTATGATGTCGATACCGCCAAATACCAAGAAAATGTGCTGGATACGCTGGATCGCTTGGGCGTAAGTATCTTGTGGCGTGATAATAATTCGGACTCAAAAGGCGTGATGGATAAGCTGCCAAAAGCGCAATTTGCCGATTATAAATCCGCGACCAACAACGCCATCTGCAACACCAATCCTTATAACGAATGCCGCGATGTCGGTATGCTCGTTGGCTTAGATGACTTTGTCGCTGCCAATAACGGCAAAGATATGCTGATCATGCTGCACCAAATGGGCAATCACGGGCCTGCGTATTTTAAGCGATATGATGAAAAGTTTGCCAAATTCACGCCAGTGTGTGAAGGTAATGAGCTTGCCAAGTGCGAACATCAGTCCTTGATCAATGCTTATGACAATGCCTTGCTTGCCACCGATGATTTCATCGCTCAAAGTATCCAGTGGCTGCAGACGCACAGCAATGCCTATGATGTCTCAATGCTGTATGTCAGCGATCATGGCGAAAGTCTGGGTGAGAACGGTGTCTATCTACATGGTATGCCAAATGCCTTTGCACCAAAAGAACAGCGCAGTGTGCCTGCATTTTTCTGGACGGATAAGCAAACTGGCATCACGCCAATGGCAACCGATACCGTCCTGACCCATGACGCGATCACGCCGACATTATTAAAGCTGTTTGATGTCACCGCGGACAAAGTCAAAGACCGCACCGCATTCATCCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3004690","ARO_id":"42742","ARO_name":"MCR-1.13","CARD_short_name":"MCR-1.13","ARO_description":"A plasmid-mediated phosphoethanolamine transferase and MCR-1 variant identified from Escherichia coli.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3393":{"model_id":"3393","model_name":"MCR-4.3","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"5580":{"protein_sequence":{"accession":"AUI38915.1","sequence":"MISRFKTLSVNQFTFITALFYVAIFNLPLFGIVRKGIEKQPEVDPLFIASMPLFLTFALSFLFSIFTVKYLLKPFFIVLTLLSSSVFFAAYQYNVVFDYGMIENTFQTHPAEALMYVNLASITNLLLTGLLPSYLIYKADIHYQPFFKELLHKLAFMLLMFVGIGIVAFFYYQDYAAFGRNNSELRRYIVPTYFVSSASKYLNEHYLQTPMEYQQLGLDAKNASRNPNTKPNLLVFVVGETARSMSYQYYGYNKPTNAHTQNQGLIAFNDTSSCGTATAVSLPCMFSRMGRADYDPRRANAQDTVIDVLSHSGIKVQWFDNDSGCKGVCDQVENLTIDLKSDPKLCSGQYCFDQVLLNKLDKILAVAPSQDTVIFLHIIGSHGPTYYLRYPPEHRKFIPDCPRSDIQNCSQEELINTYDNTILYTDFILSEVVNKLKGKQDMFDTAMLYLSDHGESLGEKGMYLHGAPYSIAPKEQTSVPMLAWVSNDFSQDNQLNMTCVAQRAEQGGFSHDNLFDSLLGLMNVKTTVYQSQLDIFAPCRY"},"dna_sequence":{"accession":"MG026621.1","fmin":"0","fmax":"1626","strand":"+","sequence":"GTGATTTCTAGATTTAAGACGTTATCGGTTAACCAATTCACTTTCATCACTGCGTTGTTTTATGTTGCCATTTTCAATCTACCGCTCTTTGGTATAGTGCGAAAAGGAATTGAAAAACAACCAGAAGTTGATCCCCTTTTCATCGCATCTATGCCGCTATTTTTAACATTTGCGCTGAGTTTTTTGTTTTCAATTTTTACCGTCAAATACCTGCTGAAGCCCTTTTTTATCGTATTGACGTTACTTTCCTCAAGTGTATTTTTTGCAGCCTATCAATACAATGTCGTGTTTGACTACGGCATGATAGAAAACACGTTTCAAACACATCCTGCTGAAGCATTGATGTATGTAAATCTTGCATCAATTACCAATCTACTGCTGACTGGGCTATTACCGTCATATCTTATTTATAAGGCCGATATTCATTATCAGCCCTTTTTTAAGGAGTTATTGCATAAATTAGCCTTTATGCTGCTAATGTTCGTTGGCATTGGGATAGTCGCCTTTTTTTACTATCAAGATTATGCTGCATTTGGTCGAAACAACAGTGAGTTAAGGCGTTACATTGTCCCTACCTATTTTGTCAGTAGTGCATCTAAATATCTCAATGAGCACTATTTGCAGACGCCCATGGAATACCAACAACTTGGCCTAGATGCGAAGAATGCCAGTCGTAACCCGAACACTAAACCTAACTTATTAGTGTTTGTTGTGGGTGAAACTGCGCGCTCAATGAGCTATCAATATTATGGATATAACAAGCCAACCAATGCTCATACCCAAAATCAGGGGCTGATTGCGTTTAACGATACTAGCTCATGCGGCACGGCCACGGCGGTGTCTCTACCCTGTATGTTTTCACGAATGGGGCGGGCAGACTATGATCCTCGCCGTGCTAATGCTCAAGACACAGTGATTGATGTGTTAAGTCATAGTGGTATAAAAGTACAGTGGTTTGATAATGATTCTGGCTGTAAAGGTGTGTGTGATCAGGTTGAAAATCTCACGATAGATTTGAAGAGTGATCCGAAGCTGTGTTCTGGCCAATATTGTTTTGACCAAGTATTGCTCAACAAATTAGATAAAATTCTGGCAGTAGCACCAAGTCAAGATACAGTAATTTTTTTGCATATCATTGGTAGTCATGGACCAACTTATTATCTTAGATACCCGCCAGAGCATCGTAAATTTATACCGGATTGTCCGCGCAGTGATATTCAAAATTGCAGTCAAGAAGAACTGATTAACACCTACGACAACACTATTCTATATACGGATTTTATTCTCAGTGAAGTGGTGAATAAATTAAAAGGTAAGCAGGATATGTTCGATACTGCAATGCTGTATCTCTCTGACCATGGTGAGTCTTTGGGTGAAAAGGGCATGTATTTACATGGTGCGCCCTATAGTATTGCACCGAAAGAACAAACTAGCGTACCAATGCTGGCTTGGGTATCTAATGACTTTAGCCAAGATAATCAGTTGAACATGACTTGTGTTGCACAGCGAGCAGAACAGGGCGGCTTTTCCCACGACAATTTGTTCGACAGTTTGCTAGGACTTATGAATGTAAAAACCACCGTCTATCAGAGCCAACTCGATATTTTTGCACCTTGCAGGTATTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3004695","ARO_id":"42747","ARO_name":"MCR-4.3","CARD_short_name":"MCR-4.3","ARO_description":"A plasmid-mediated MCR-4 variant and colistin resistance gene from clinical Enterobacteriaceae.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3405":{"model_id":"3405","model_name":"OXA-402","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"555"}},"model_sequences":{"sequence":{"5600":{"protein_sequence":{"accession":"AIS39035.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDKKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWNGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQHEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVRPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"KJ780077.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATAAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGAACGGGCAAAAAAGGCTGTTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAACATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCGGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001588","ARO_id":"37988","ARO_name":"OXA-402","CARD_short_name":"OXA-402","ARO_description":"OXA-402 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3428":{"model_id":"3428","model_name":"OXA-261","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"555"}},"model_sequences":{"sequence":{"5624":{"protein_sequence":{"accession":"ENW35072.1","sequence":"MNIKALLFITSAIFISACSPYIVTANPNHNASKSDDKAEKIKNLFNEAHTTGVLVIHQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWNGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"APQV01000009.1","fmin":"266252","fmax":"267077","strand":"+","sequence":"ATGAACATTAAAGCACTCTTATTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAATGCTTCAAAATCTGATGACAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCATCAAGGTCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGAACGGGCAAAAAAGGCTGTTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42792","NCBI_taxonomy_name":"Acinetobacter baumannii NIPH 201","NCBI_taxonomy_id":"1217630"}}}},"ARO_accession":"3001717","ARO_id":"38117","ARO_name":"OXA-261","CARD_short_name":"OXA-261","ARO_description":"OXA-261 is a beta-lactamase found in Acinetobacter spp.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3458":{"model_id":"3458","model_name":"OXA-295","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"5653":{"protein_sequence":{"accession":"ENX19403.1","sequence":"MSKKLKLLALCATVISAATLVGCQNIQSQAQPLVLKKQTQDQIATAFENIQTTGVLVTYDGKNFQKYGNDLSRADQRYIPASTFKMLNALIGIQHHKTSPNEVFKWDGQKRAFRSWEKDLTLAEGMQASAVPVYQELARRIGLELMASEVKRVGYGNQNIGAQVDNFWLVGPLEITPVEEVKFAYALAKQQLPFDPSTQQQVRDMLLIENVQGTRIYAKSGWGMDVNPQVGWWTGWIEQTNGQITAFSLNMEMKKAEHADARKAIVYQALQQLGLLPQ"},"dna_sequence":{"accession":"APRW01000016.1","fmin":"273958","fmax":"274795","strand":"-","sequence":"ATGTCTAAAAAATTAAAATTACTCGCGCTATGTGCAACTGTAATCTCAGCTGCAACACTGGTCGGTTGTCAAAATATTCAGTCCCAAGCTCAACCTCTAGTCTTAAAGAAACAGACGCAGGATCAGATCGCAACTGCATTCGAAAATATCCAGACAACTGGTGTATTAGTCACCTATGATGGCAAAAATTTTCAAAAATATGGCAATGATCTCAGCCGTGCAGATCAGCGTTACATTCCGGCCTCAACTTTTAAAATGCTCAATGCCTTGATTGGTATACAGCACCATAAAACCTCACCTAATGAAGTGTTTAAATGGGATGGACAGAAACGGGCTTTCCGTAGCTGGGAGAAGGACTTAACGCTTGCTGAGGGAATGCAGGCTTCGGCTGTACCTGTCTATCAGGAGCTGGCGCGCCGTATCGGTCTAGAATTAATGGCAAGTGAAGTAAAGCGGGTTGGCTACGGTAATCAAAATATAGGGGCGCAAGTTGATAATTTTTGGTTAGTGGGGCCTTTGGAGATTACGCCAGTTGAGGAAGTAAAATTTGCTTATGCCTTAGCCAAACAGCAACTTCCATTTGATCCCTCAACACAGCAGCAAGTCAGAGATATGTTGTTGATCGAAAATGTTCAGGGAACCAGAATCTATGCCAAGAGTGGTTGGGGAATGGATGTAAATCCTCAAGTTGGATGGTGGACGGGTTGGATTGAACAAACGAATGGTCAAATCACAGCATTTTCGCTGAATATGGAAATGAAAAAAGCAGAACATGCGGATGCGCGTAAAGCGATTGTTTATCAAGCTTTACAACAGTTAGGTTTATTACCTCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42817","NCBI_taxonomy_name":"Acinetobacter sp. NIPH 2168","NCBI_taxonomy_id":"1217706"}}}},"ARO_accession":"3001750","ARO_id":"38150","ARO_name":"OXA-295","CARD_short_name":"OXA-295","ARO_description":"OXA-295 is a beta-lactamase found in Acinetobacter spp.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46504":{"category_aro_accession":"3007715","category_aro_cvterm_id":"46504","category_aro_name":"OXA-294-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-294.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3487":{"model_id":"3487","model_name":"OXA-401","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"540"}},"model_sequences":{"sequence":{"5682":{"protein_sequence":{"accession":"AIS39034.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALISLEHHKATATEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKRIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"KJ780076.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCCCTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTCTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCAGCCTTGAGCACCATAAGGCAACCGCCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGACGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGCCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAAGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001587","ARO_id":"37987","ARO_name":"OXA-401","CARD_short_name":"OXA-401","ARO_description":"OXA-401 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4227":{"model_id":"4227","model_name":"ADC-157","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6602":{"protein_sequence":{"accession":"WP_088245227.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDKPGKYWKELKNTPIDQINLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFGQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMFHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKE"},"dna_sequence":{"accession":"NG_055287.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCTTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATAAGCCTGGTAAATATTGGAAAGAACTAAAAAATACACCGATTGACCAAATTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCTTATTTGGAAAAGTTGTTGCTTTGTCTATGAATAAACCTTTCGGCCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACTCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTTAACCCACAGAAATATCCGGCTGATATTCAAAGGGCAATTAATGAAACACATCAAGGTCGCTATCAAGTAAATACCATGTATCAAGCGCTTGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAGACTTTATTAGACAGTAATTCAGAACAAATTGTGATGAAGCCTAATAAAGTGACCGCTATTTCAAAAGAACCTTCAGTTAAGATGTTCCACAAAACTGGCTCAACCAATGGTTTTGGAACTTATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAACGCATTAAGGCAGCGTATGCAGTTTTAAATGCAATAAAGGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006331","ARO_id":"44793","ARO_name":"ADC-157","CARD_short_name":"ADC-157","ARO_description":"ADC-157 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3402":{"model_id":"3402","model_name":"tet(X4)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"5831":{"protein_sequence":{"accession":"QBQ69719.1","sequence":"MSNKEKQMNLLSDKNVAIIGGGPVGLTMAKLLQQNGIDVSVYERDNDREARIFGGTLDLHKGSGQEAMKKAGLLQTYYDLALPMGVNIADEKGNILSTKNVKPENRFDNPEINRNDLRAILLNSLENDTVIWDRKLVMLEPGKKKWTLTFENKPSETADLVIIANGGMSKVRKFVTDTEVEETGTFNIQADIHHPEVNCPGFFQLCNGNRLMAAHQGNLLFANPNNNGALHFGISFKTPDEWKNQTQVDFQNRNSVVDFLLKEFSDWDERYKELIRVTSSFVGLATRIFPLGKSWKSKRPLPITMIGDAAHLMPPFAGQGVNSGLMDALILSDNLTNGKFNSIEEAIENYEQQMFIYGKEAQEESTQNEIEMFKPDFTFQQLLNV"},"dna_sequence":{"accession":"MK134376.1","fmin":"324","fmax":"1482","strand":"-","sequence":"ATGAGCAATAAAGAAAAACAAATGAATTTACTTAGTGATAAGAACGTTGCAATAATTGGTGGTGGACCCGTTGGACTGACTATGGCAAAATTATTACAGCAAAACGGCATAGACGTTTCAGTTTACGAAAGAGACAACGACCGAGAGGCAAGAATTTTTGGTGGAACCCTTGACCTACACAAAGGTTCAGGTCAGGAAGCAATGAAAAAAGCGGGATTGTTACAAACTTATTATGACTTAGCCTTACCAATGGGTGTAAATATTGCTGATGAAAAAGGCAATATTTTATCCACAAAAAATGTAAAGCCCGAAAATCGATTTGACAATCCTGAAATAAACAGAAATGACTTAAGGGCTATCTTGTTGAATAGTTTAGAAAACGACACGGTTATTTGGGATAGAAAACTTGTTATGCTTGAACCTGGTAAGAAGAAGTGGACACTAACTTTTGAGAATAAACCGAGTGAAACAGCAGATCTGGTTATTATTGCCAATGGTGGAATGTCTAAAGTAAGAAAATTTGTTACCGACACGGAAGTTGAAGAAACAGGTACTTTCAATATACAAGCCGATATTCATCATCCAGAGGTGAACTGTCCTGGATTTTTTCAGCTATGCAATGGAAACCGGCTAATGGCTGCTCATCAAGGTAATTTATTATTTGCGAATCCTAATAATAATGGTGCATTGCATTTTGGAATAAGTTTTAAAACACCTGATGAATGGAAAAACCAAACGCAGGTAGATTTTCAAAACAGAAATAGTGTCGTTGATTTTCTTCTGAAAGAATTTTCCGATTGGGACGAACGCTACAAAGAACTGATTCGTGTGACATCATCTTTTGTAGGGTTAGCGACACGAATATTTCCCTTAGGTAAGTCTTGGAAAAGTAAGCGTCCATTACCCATAACGATGATTGGAGATGCTGCTCATTTGATGCCTCCTTTTGCAGGACAAGGCGTAAACAGCGGGTTGATGGATGCCTTGATATTGTCGGATAATCTGACCAATGGGAAATTTAACAGCATTGAAGAGGCTATTGAAAATTATGAACAGCAAATGTTTATCTATGGCAAAGAAGCACAAGAAGAATCAACTCAAAACGAAATTGAAATGTTTAAACCCGACTTTACGTTTCAGCAATTGTTAAATGTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3004720","ARO_id":"42775","ARO_name":"tet(X4)","CARD_short_name":"tet(X4)","ARO_description":"A tetracyline resistance gene located on an approximately 180-kb plasmid, designated p47EC. It inactivates all tetracyclines, including tigecycline, eravacycline, and omadacycline.Adjacent to insertion sequence ISVsa3 on the conjugative plasmid.","ARO_category":{"36176":{"category_aro_accession":"3000036","category_aro_cvterm_id":"36176","category_aro_name":"tetracycline inactivation enzyme","category_aro_description":"Enzymes or other gene products which hydroxylate tetracycline and other tetracycline derivatives. Hydroxylation inactivates tetracycline-like antibiotics, thus conferring resistance to these compounds.","category_aro_class_name":"AMR Gene Family"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3514":{"model_id":"3514","model_name":"OXA-444","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"5709":{"protein_sequence":{"accession":"BAQ55594.1","sequence":"MFSRWSKPLVLAATVCAMAMSAATAHAELIVRNDLKRVFDEAGVSGTFVLMDISADRTYVVDPARAARRIHPASTFKIPNSLIAFDTGAVRDDHEVLPYGGKPQPYKQWEHDMALPEAIRLSAVPIYQEVARRVGLERMQAYVDAFDYGNRQLGSVIDQFWLRGPLEISALEEARFTSRMALKQLPVKPRTWDMVHRMLLIEQQGDAALYAKTGVATEYQPEIGWWVGWVERAGRVYAFALNIDMPREGDMAKRIPLGKQLMQALDVWPVL"},"dna_sequence":{"accession":"LC030179.1","fmin":"0","fmax":"816","strand":"+","sequence":"ATGTTCTCTCGTTGGTCGAAACCTCTCGTGCTTGCCGCCACGGTGTGCGCCATGGCGATGAGCGCCGCCACCGCCCACGCCGAACTCATCGTGCGCAACGATCTCAAGCGCGTGTTCGACGAGGCCGGCGTCTCCGGTACCTTCGTCCTGATGGATATCAGCGCCGACCGCACCTACGTCGTTGACCCGGCCCGCGCCGCGCGGCGCATTCATCCGGCCTCAACTTTCAAGATCCCGAACAGCCTCATCGCCTTCGACACGGGCGCGGTGCGTGACGATCATGAAGTGCTGCCATACGGCGGCAAGCCGCAGCCCTACAAGCAGTGGGAGCACGACATGGCGCTGCCCGAGGCGATCCGCCTGTCGGCCGTGCCGATCTACCAGGAAGTGGCGCGCCGCGTCGGCTTGGAGCGCATGCAGGCGTATGTCGATGCGTTCGACTATGGCAATCGCCAGCTTGGCAGCGTGATCGACCAGTTCTGGCTGCGCGGTCCGCTCGAAATCTCGGCGCTTGAAGAGGCGCGCTTCACCAGCCGCATGGCGCTCAAGCAGTTGCCGGTGAAGCCGCGCACGTGGGACATGGTTCACCGCATGCTGCTGATCGAGCAGCAAGGGGATGCCGCGCTGTACGCCAAGACCGGCGTCGCCACGGAATACCAGCCGGAGATCGGCTGGTGGGTCGGCTGGGTCGAGCGTGCCGGACGCGTCTATGCCTTTGCGCTGAACATCGACATGCCGCGCGAGGGCGACATGGCCAAGCGCATTCCGCTGGGCAAGCAGTTGATGCAGGCGCTGGACGTGTGGCCGGTACTCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42837","NCBI_taxonomy_name":"Ralstonia mannitolilytica","NCBI_taxonomy_id":"105219"}}}},"ARO_accession":"3003600","ARO_id":"40210","ARO_name":"OXA-444","CARD_short_name":"OXA-444","ARO_description":"OXA-444 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46518":{"category_aro_accession":"3007729","category_aro_cvterm_id":"46518","category_aro_name":"OXA-60-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-60.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3544":{"model_id":"3544","model_name":"OXA-483","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"545"}},"model_sequences":{"sequence":{"5739":{"protein_sequence":{"accession":"AKF41840.1","sequence":"MNKYFTCYVVASLFLSGCTVQHNLINETPSQIVQGHNQVIHQYFDEKNTSGVLVIQTDKKINLYGNALSRANTEYVPASTFKMLNALIGLENQKTDINEIFKWKGEKRSFTAWEKDMTLGEAMKLSAVPVYQELARRIGLDLMQKEVKRIGFGNAEIGQQVDNFWLVGPLKVTPIQEVEFVSQLAHTQLPFSEKVQANVKNMLLLEESNGYKIFGKTGWAMDIKPQVGWLTGWVEQPDGKIVAVALNMEMRSEMPASIRNELLMKSLKQLNII"},"dna_sequence":{"accession":"KP264125.1","fmin":"83","fmax":"905","strand":"+","sequence":"ATGAATAAATATTTTACTTGCTATGTGGTTGCTTCTCTTTTTCTTTCTGGTTGTACGGTTCAGCATAATTTAATAAATGAAACCCCGAGTCAGATTGTTCAAGGACATAATCAGGTGATTCATCAATACTTTGATGAAAAAAACACCTCAGGTGTGCTGGTTATTCAAACAGATAAAAAAATTAATCTATATGGTAATGCTCTAAGCCGCGCAAATACAGAATATGTGCCAGCCTCTACATTTAAAATGTTGAATGCCCTGATCGGATTGGAGAACCAGAAAACGGATATTAATGAAATATTTAAATGGAAGGGCGAGAAAAGGTCATTTACCGCTTGGGAAAAAGACATGACACTAGGAGAAGCCATGAAGCTTTCTGCAGTCCCAGTCTATCAGGAACTTGCGCGACGTATCGGTCTTGATCTCATGCAAAAAGAAGTAAAACGTATTGGTTTCGGTAATGCTGAAATTGGACAGCAGGTTGATAATTTCTGGTTGGTAGGACCATTAAAGGTTACGCCTATTCAAGAGGTAGAGTTTGTTTCCCAATTAGCACATACACAGCTTCCATTTAGTGAAAAAGTGCAGGCTAATGTAAAAAATATGCTTCTTTTAGAAGAGAGTAATGGCTACAAAATTTTTGGAAAGACTGGTTGGGCAATGGATATAAAACCACAAGTGGGCTGGTTGACCGGCTGGGTTGAGCAGCCAGATGGAAAAATTGTCGCTGTTGCATTAAATATGGAAATGCGGTCAGAAATGCCGGCATCTATACGTAATGAATTATTGATGAAATCATTAAAACAGCTGAATATTATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3003640","ARO_id":"40250","ARO_name":"OXA-483","CARD_short_name":"OXA-483","ARO_description":"OXA-483 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46499":{"category_aro_accession":"3007710","category_aro_cvterm_id":"46499","category_aro_name":"OXA-23-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases, specifically imipenem, derived from OXA-23, first identified in Acinetobacter baumannii.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3588":{"model_id":"3588","model_name":"FONA-4","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"585"}},"model_sequences":{"sequence":{"5786":{"protein_sequence":{"accession":"CAB61641.1","sequence":"MVKNTLRKTTLMVATVMPLLFGSAPLWAQTANAKANIQQQLSELEKSSGGRLGVALIDTADNSQILYRGDERFPMCSTSKVMAVSALLKQSETDKNLLAKRMEIKQSDLVNYNPIAEKHLDTGMTLAEFSAATIQYSDNTAMNKILEHLGGPAKVTEFARTIGDKTFRLDRTEPTLNTAIPGDERDTSSPLAMAKSLQNLTLGKALGEPQRAQLVEWMKGNTTGGASIRAGLPTTWIVGDKTGSGDYGTTNDIAVIWPANHAPLVLVTYFTQPQQNAEARKDVLAAAAKIVTEGL"},"dna_sequence":{"accession":"AJ251242.1","fmin":"1053","fmax":"1941","strand":"+","sequence":"ATGGTTAAAAATACACTACGTAAAACCACCCTGATGGTCGCTACGGTTATGCCGTTGTTGTTCGGTAGCGCACCGCTATGGGCGCAAACTGCTAATGCCAAGGCGAATATTCAGCAGCAACTGTCTGAACTGGAGAAAAGCTCCGGTGGCCGCCTGGGCGTGGCGCTGATCGATACCGCCGATAATTCGCAGATCCTGTATCGCGGGGATGAACGTTTTCCTATGTGCAGCACCAGCAAGGTGATGGCGGTGTCGGCGTTGTTAAAACAGAGCGAGACGGATAAAAATCTTTTGGCTAAGCGGATGGAAATCAAGCAATCCGATCTGGTCAACTACAACCCGATCGCCGAAAAACACCTGGATACCGGGATGACCCTGGCCGAGTTCAGCGCCGCCACCATCCAGTACAGTGACAACACGGCGATGAACAAGATCCTTGAGCATCTTGGCGGCCCGGCAAAAGTAACAGAATTTGCGCGTACCATCGGCGATAAAACCTTCCGTCTCGATCGTACCGAACCCACCTTGAATACCGCCATTCCGGGTGATGAACGTGACACGAGTTCGCCGCTGGCGATGGCAAAAAGCCTGCAAAACCTGACCTTGGGCAAGGCGCTGGGTGAACCACAGCGTGCTCAACTGGTTGAATGGATGAAGGGGAATACTACCGGAGGAGCCAGCATTCGCGCAGGTCTGCCAACCACGTGGATAGTCGGTGATAAAACCGGCAGCGGTGATTACGGTACCACTAACGATATCGCCGTGATTTGGCCAGCTAACCACGCACCGTTGGTGTTGGTGACCTATTTCACCCAGCCACAGCAGAATGCCGAAGCCCGCAAAGACGTGTTGGCTGCGGCCGCTAAAATTGTTACCGAAGGGCTTTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39675","NCBI_taxonomy_name":"Serratia fonticola","NCBI_taxonomy_id":"47917"}}}},"ARO_accession":"3004791","ARO_id":"42909","ARO_name":"FONA-4","CARD_short_name":"FONA-4","ARO_description":"FONA-4 is a class A beta-lactamase gene found in Serratia fonticola.","ARO_category":{"42905":{"category_aro_accession":"3004787","category_aro_cvterm_id":"42905","category_aro_name":"FONA beta-lactamase","category_aro_description":"FONA is a class A beta-lactamase gene family found in Serratia fonticola.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3594":{"model_id":"3594","model_name":"FRI-3","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"5792":{"protein_sequence":{"accession":"AQS23610.1","sequence":"MFFLKKAQVHLFFFLCLPLNSFASQESNSIEQMRELEAAFGGRIGVYILNTKNGKEFSYRQDERFPLCSSFKAFLAASVLKKTQDKSVSLDDMMEYSGRVMEKHSPVSEKYRKTGASVRTLAKAAIQYSDNGASNLLMERYIGGPEGLTAFMRSTGDTDFRLDRWELELNSAIPGDERDTSTPKAVAMSLKNIAFGSVLDAKNKSLLQEWLKGNTTGNARIRAAVPDKWDVGDKTGTCGFYGTANDVAILWPDANSPAVMAVYTTRPNQNDKHDEAVIKNSAKIAINAVYGSYK"},"dna_sequence":{"accession":"KY524440.1","fmin":"0","fmax":"885","strand":"+","sequence":"ATGTTTTTTTTAAAAAAAGCGCAAGTACATTTATTTTTTTTTCTCTGTCTTCCATTGAACTCATTCGCCTCTCAGGAAAGTAATAGTATTGAGCAAATGAGGGAATTGGAAGCTGCTTTTGGGGGGCGGATAGGTGTTTATATTTTAAACACAAAGAATGGGAAAGAATTTTCCTACAGACAAGATGAGAGATTTCCTTTATGTAGTTCATTTAAGGCATTCCTCGCTGCATCCGTATTAAAAAAAACTCAGGATAAATCTGTTTCTCTTGATGATATGATGGAATATTCTGGACGTGTTATGGAAAAGCATTCTCCTGTGTCAGAAAAATACCGCAAAACAGGAGCAAGCGTGCGGACTTTGGCGAAGGCAGCAATTCAGTACAGTGACAATGGAGCTTCTAATCTATTAATGGAAAGATACATAGGAGGTCCTGAGGGTTTGACTGCATTTATGCGGTCAACGGGAGACACTGACTTCAGGCTTGATCGTTGGGAATTAGAATTAAACTCAGCTATTCCAGGCGATGAACGAGATACTTCAACTCCAAAAGCAGTGGCAATGAGCCTTAAAAATATTGCTTTTGGTTCAGTACTCGATGCTAAAAATAAATCATTGCTGCAGGAATGGCTTAAAGGCAACACTACTGGTAATGCGCGAATTAGAGCTGCGGTTCCAGATAAGTGGGATGTTGGCGATAAAACAGGCACCTGTGGTTTTTATGGTACAGCCAATGATGTTGCTATTTTATGGCCAGACGCTAATTCACCTGCAGTTATGGCTGTCTACACAACACGTCCTAATCAAAACGACAAACATGACGAAGCAGTAATTAAAAATTCTGCAAAAATAGCTATAAATGCAGTGTATGGAAGTTATAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3004799","ARO_id":"42918","ARO_name":"FRI-3","CARD_short_name":"FRI-3","ARO_description":"FRI-3 is a carbapenem-hydrolyzing Class A beta-lactamase gene found in Enterobacter cloacae.","ARO_category":{"42915":{"category_aro_accession":"3004796","category_aro_cvterm_id":"42915","category_aro_name":"FRI beta-lactamase","category_aro_description":"FRI is a carbapenem-Hydrolyzing Class A beta-Lactamase from Enterobacter cloacae.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3595":{"model_id":"3595","model_name":"FTU-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"5793":{"protein_sequence":{"accession":"ADA78299.1","sequence":"MRLLVTTLSLIPSIILAAPQLDDSFKNLENKYDGKIGIYTLNTDDKTNIKYNESYHFPICSVFKFLLVGAILDYDMHNQGFLDKKIPINQDDIGKLGYAPITAKNVGKTLTISQLNYAAILSDSPASNILVRELGGLQNLNKFIKKLGDNDTIITADEPEINYTQPHSNINKTTPKAITKDIYKLAFGNILDKKHKDIFIKYLQDNNTGANRIAFSMPKDWIIGDKTGTCGQYAATNDVAIIWPKNQQPIALGILYTNPNDKNAPSNEEIIQQAAKLIANDLTNTYK"},"dna_sequence":{"accession":"CP001633.1","fmin":"630303","fmax":"631167","strand":"-","sequence":"ATGCGTCTATTAGTTACAACTTTATCATTAATCCCGAGTATCATACTAGCTGCTCCTCAATTAGATGATTCTTTTAAAAATCTGGAAAACAAATATGATGGAAAAATTGGCATCTACACTCTCAACACTGATGATAAAACTAACATCAAATATAACGAAAGCTATCACTTCCCTATTTGTAGTGTTTTCAAGTTTTTATTAGTTGGTGCAATTTTAGATTATGATATGCATAATCAAGGCTTCTTAGATAAAAAAATTCCAATAAATCAAGATGATATTGGTAAACTCGGATATGCTCCTATTACTGCTAAAAACGTTGGTAAAACTCTAACAATATCACAACTTAACTACGCTGCTATCCTAAGTGATAGTCCTGCCAGTAACATATTAGTTAGAGAACTTGGAGGTTTACAAAACTTAAATAAATTTATAAAAAAATTAGGTGATAACGATACTATAATTACTGCTGATGAACCAGAAATTAATTATACTCAGCCACATAGTAATATAAATAAAACAACTCCAAAGGCTATTACTAAAGATATTTATAAATTAGCATTTGGCAATATTCTAGATAAAAAACATAAAGATATTTTTATAAAGTATCTACAAGATAATAATACTGGTGCAAATAGAATAGCTTTTAGCATGCCTAAAGATTGGATAATTGGCGATAAAACTGGAACTTGTGGTCAATATGCAGCAACTAATGATGTAGCTATTATATGGCCTAAAAATCAGCAACCTATTGCGTTAGGAATTTTATATACTAACCCTAATGATAAAAATGCACCAAGTAATGAAGAAATTATTCAACAAGCAGCTAAATTAATAGCTAATGATCTGACTAACACTTATAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42921","NCBI_taxonomy_name":"Francisella tularensis subsp. tularensis NE061598","NCBI_taxonomy_id":"510831"}}}},"ARO_accession":"3004801","ARO_id":"42920","ARO_name":"FTU-1","CARD_short_name":"FTU-1","ARO_description":"FTU-1 is a class A beta-lactamase gene found in Francisella tularensis. It causes Tularemia.","ARO_category":{"42919":{"category_aro_accession":"3004800","category_aro_cvterm_id":"42919","category_aro_name":"FTU beta-lactamase","category_aro_description":"FTU is a class A beta-lactamase gene family found in Francisella tularensis.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3596":{"model_id":"3596","model_name":"GOB-10","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"5794":{"protein_sequence":{"accession":"AAT68577.1","sequence":"MRNFVILFFMFICLGLNAQVVKEPENMPKEWNQTYEPFRIAGNLYYVGTYDLASYLIVTDKGNILINTGTAESLPIIKANIQKLGFNYKDIKILLLTQAHYDHTGALQDLKTETGAKFYADKEDADVLRTGGKSDYEMGKYGVTFKPVTPDKTLKDQDKITLGNTILTLLHHPGHTKGSCSFIFETKDEKRKYRVLIANMPSVIVDKKFSEVTAYPNIQSDYAYTFKAMKNLDFDIWVASHASQFDLHEKRKEGDPYNPQLFMDKQSYFQNLNDLEKSYLDKIKKDSQDK"},"dna_sequence":{"accession":"AY647247.1","fmin":"0","fmax":"873","strand":"+","sequence":"ATGAGAAATTTTGTTATACTGTTTTTCATGTTCATTTGCTTGGGCTTGAATGCTCAGGTAGTAAAAGAACCTGAAAATATGCCCAAAGAATGGAACCAGACTTATGAACCCTTCAGAATTGCAGGTAATTTATATTACGTAGGAACCTATGATTTGGCTTCTTACCTTATTGTGACAGACAAAGGCAATATTCTCATTAATACAGGAACGGCAGAATCGCTTCCAATAATAAAAGCAAATATCCAAAAGCTCGGGTTTAATTATAAAGACATTAAGATCTTGCTGCTTACTCAGGCTCACTACGACCATACAGGTGCATTACAAGATCTTAAAACAGAAACCGGTGCAAAATTCTATGCCGATAAAGAAGATGCTGATGTCCTGAGAACAGGGGGGAAGTCCGATTATGAAATGGGAAAATATGGGGTGACATTTAAACCTGTTACTCCGGATAAAACATTGAAAGATCAGGATAAAATAACACTGGGAAATACAATCCTGACTTTGCTTCATCATCCCGGACATACAAAAGGTTCCTGTAGTTTTATTTTTGAAACAAAAGACGAGAAGAGAAAATATAGAGTTTTGATAGCTAATATGCCCTCCGTTATTGTTGATAAGAAATTTTCTGAAGTTACCGCATATCCAAATATTCAGTCCGATTATGCATATACTTTCAAAGCAATGAAGAATCTGGATTTTGATATTTGGGTGGCCTCCCATGCAAGTCAGTTCGATCTCCATGAAAAACGTAAAGAAGGAGATCCGTACAATCCGCAATTGTTTATGGATAAGCAAAGCTATTTCCAAAACCTTAATGATTTGGAAAAAAGCTATCTCGACAAAATAAAAAAAGATTCCCAAGATAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36960","NCBI_taxonomy_name":"Elizabethkingia meningoseptica","NCBI_taxonomy_id":"238"}}}},"ARO_accession":"3004802","ARO_id":"42922","ARO_name":"GOB-10","CARD_short_name":"GOB-10","ARO_description":"GOB-10 is a class B beta-lactamase gene found in Chryseobacterium meningosepticum.","ARO_category":{"41376":{"category_aro_accession":"3004212","category_aro_cvterm_id":"41376","category_aro_name":"GOB beta-lactamase","category_aro_description":"The GOB family of beta-lactamases have been discovered in the Elizabethkingia meningoseptica and are classified as subclass B3 beta-lactamase. They confer resistance to cephalosporins, penicillins, and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3643":{"model_id":"3643","model_name":"LEN-51","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"5915":{"protein_sequence":{"accession":"AYW19907.1","sequence":"MRYVRLCVISLLATLPLVVYAGPQPLEQIKQSESQLSGRVGMVEMDLASGRTLAAWRADERFPMVSTFKVLLCGAVLARVDAGLEQLDRRIHYRQQDLVDYSPVSEKHLVDGMTIGELCAAAITLSDNSAGNLLLATVGGPAGLTAFLRQIGDNVTRLDRWETALNEALPGDARDTTTPASMAATLRKLLTAQHLSARSQQQLLQWMVDDRVAGPLIRAVLPPGWFIADKTGAGERGARGIVALLGPDGKPERIVVLYLRDTPASMAERNQHIAGIGAALIEHWQR"},"dna_sequence":{"accession":"CP033631.1","fmin":"3042328","fmax":"3043189","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGTGTTATCTCCCTGTTAGCCACCCTGCCACTGGTGGTATACGCCGGTCCACAGCCGCTTGAGCAGATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTGGGGATGGTGGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCGATGAACGCTTTCCCATGGTGAGCACCTTTAAAGTGCTGCTGTGCGGCGCGGTGCTGGCGCGGGTGGATGCCGGGCTCGAACAACTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGTCGACGGGATGACGATCGGCGAACTCTGCGCCGCCGCCATCACCCTGAGCGATAACAGCGCTGGCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCGGGATTAACTGCCTTTCTGCGCCAGATCGGTGACAACGTCACCCGTCTTGACCGCTGGGAAACGGCACTGAATGAGGCGCTTCCCGGCGACGCGCGCGACACCACCACCCCGGCCAGCATGGCCGCCACGCTGCGCAAACTACTGACCGCGCAGCATCTGAGCGCCCGTTCGCAACAGCAACTCCTGCAGTGGATGGTGGACGATCGGGTTGCCGGCCCGCTGATCCGCGCCGTGCTGCCGCCGGGCTGGTTTATCGCCGACAAAACCGGGGCTGGCGAACGGGGTGCGCGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAACCGGAGCGCATTGTGGTGCTCTATCTGCGGGATACCCCGGCGAGTATGGCCGAGCGTAATCAACATATCGCCGGGATCGGCGCAGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42983","NCBI_taxonomy_name":"Klebsiella sp. P1CD1","NCBI_taxonomy_id":"2267618"}}}},"ARO_accession":"3004847","ARO_id":"42982","ARO_name":"LEN-51","CARD_short_name":"LEN-51","ARO_description":"A class-A broad-spectrum beta-lactamase from Klebsiella.","ARO_category":{"36236":{"category_aro_accession":"3000097","category_aro_cvterm_id":"36236","category_aro_name":"LEN beta-lactamase","category_aro_description":"LEN beta-lactamases are chromosomal class A beta-lactamases that confer resistance to ampicillin, amoxicillin, carbenicillin, and ticarcillin but not to extended-spectrum beta-lactams.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3669":{"model_id":"3669","model_name":"NDM-28","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"5941":{"protein_sequence":{"accession":"QAT97614.1","sequence":"MELPNIMHPVAKLSTALAAALMLSGCMPGEIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMVDKLR"},"dna_sequence":{"accession":"MK425035.1","fmin":"0","fmax":"813","strand":"+","sequence":"ATGGAATTGCCCAATATTATGCACCCGGTCGCGAAGCTGAGCACCGCATTAGCCGCTGCATTGATGCTGAGCGGGTGCATGCCCGGTGAAATCCGCCCGACGATTGGCCAGCAAATGGAAACTGGCGACCAACGGTTTGGCGATCTGGTTTTCCGCCAGCTCGCACCGAATGTCTGGCAGCACACTTCCTATCTCGACATGCCGGGTTTCGGGGCAGTCGCTTCCAACGGTTTGATCGTCAGGGATGGCGGCCGCGTGCTGGTGGTCGATACCGCCTGGACCGATGACCAGACCGCCCAGATCCTCAACTGGATCAAGCAGGAGATCAACCTGCCGGTCGCGCTGGCGGTGGTGACTCACGCGCATCAGGACAAGATGGGCGGTATGGACGCGCTGCATGCGGCGGGGATTGCGACTTATGCCAATGCGTTGTCGAACCAGCTTGCCCCGCAAGAGGGGATGGTTGCGGCGCAACACAGCCTGACTTTCGCCGCCAATGGCTGGGTCGAACCAGCAACCGCGCCCAACTTTGGCCCGCTCAAGGTATTTTACCCCGGCCCCGGCCACACCAGTGACAATATCACCGTTGGGATCGACGGCACCGACATCGCTTTTGGTGGCTGCCTGATCAAGGACAGCAAGGCCAAGTCGCTCGGCAATCTCGGTGATGCCGACACTGAGCACTACGCCGCGTCAGCGCGCGCGTTTGGTGCGGCGTTCCCCAAGGCCAGCATGATCGTGATGAGCCATTCCGCCCCCGATAGCCGCGCCGCAATCACTCATACGGCCCGCATGGTCGACAAGCTGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3004871","ARO_id":"43009","ARO_name":"NDM-28","CARD_short_name":"NDM-28","ARO_description":"A class B New Delhi metallo-beta-lactamase and NDM-1 variant.","ARO_category":{"36196":{"category_aro_accession":"3000057","category_aro_cvterm_id":"36196","category_aro_name":"NDM beta-lactamase","category_aro_description":"NDM beta-lactamases or New Delhi metallo-beta-lactamases are class B beta-lactamases that confer resistance to a broad range of antibiotics including carbapenems, cephalosporins and penicillins.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4255":{"model_id":"4255","model_name":"ADC-190","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6630":{"protein_sequence":{"accession":"WP_136512059.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNRSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWQPKNPIGEYRQYSNPSIGLFRKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGFYQVNTMYQALGWEEFSYPATLQTLLDSTSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLDAIKK"},"dna_sequence":{"accession":"NG_064713.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATCGCAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGCAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTAGAAAGGTTGTGGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCATTTGGTTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCTGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTTAACCCACAGAAATATCCGGCTGATATTCAACGGGCAATTAATGAAACACATCAAGGGTTCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTACTTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCAACGGTTTCGGAACATATGTAGTGTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGGATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006359","ARO_id":"44821","ARO_name":"ADC-190","CARD_short_name":"ADC-190","ARO_description":"ADC-190 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2098":{"model_id":"2098","model_name":"Mycolicibacterium smegmatis 16S rRNA (rrsB) mutation conferring resistance to viomycin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"2985":"g1475a","4844":"g1475t"},"Curated-R":{"2985":"g1475a","4844":"g1475t"},"clinical":{"2985":"g1475a","4844":"g1475t"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"41093","param_value":"2700"}},"model_sequences":{"sequence":{"3248":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"NC_008596.1","fmin":"5027947","fmax":"5029475","strand":"+","sequence":"TTTTTGTTTGGAGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGGAAAGGCCCTTTCGGGGGTACTCGAGTGGCGAACGGGTGAGTAACACGTGGGTGATCTGCCCTGCACTTTGGGATAAGCCTGGGAAACTGGGTCTAATACCGAATACACCCTGCTGGTCGCATGGCCTGGTAGGGGAAAGCTTTTGCGGTGTGGGATGGGCCCGCGGCCTATCAGCTTGTTGGTGGGGTGATGGCCTACCAAGGCGACGACGGGTAGCCGGCCTGAGAGGGTGACCGGCCACACTGGGACTGAGATACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCGACGCCGCGTGAGGGATGACGGCCTTCGGGTTGTAAACCTCTTTCAGCACAGACGAAGCGCAAGTGACGGTATGTGCAGAAGAAGGACCGGCCAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGTCCGAGCGTTGTCCGGAATTACTGGGCGTAAAGAGCTCGTAGGTGGTTTGTCGCGTTGTTCGTGAAAACTCACAGCTTAACTGTGGGCGTGCGGGCGATACGGGCAGACTAGAGTACTGCAGGGGAGACTGGAATTCCTGGTGTAGCGGTGGAATGCGCAGATATCAGGAGGAACACCGGTGGCGAAGGCGGGTCTCTGGGCAGTAACTGACGCTGAGGAGCGAAAGCGTGGGGAGCGAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGGTGGGTACTAGGTGTGGGTTTCCTTCCTTGGGATCCGTGCCGTAGCTAACGCATTAAGTACCCCGCCTGGGGAGTACGGCCGCAAGGCTAAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGCGGAGCATGTGGATTAATTCGATGCAACGCGAAGAACCTTACCTGGGTTTGACATGCACAGGACGCCGGCAGAGATGTCGGTTCCCTTGTGGCCTGTGTGCAGGTGGTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTCTCATGTTGCCAGCACGTTATGGTGGGGACTCGTGAGAGACTGCCGGGGTCAACTCGGAGGAAGGTGGGGATGACGTCAAGTCATCATGCCCCTTATGTCCAGGGCTTCACACATGCTACAATGGCCGGTACAAAGGGCTGCGATGCCGTGAGGTGGAGCGAATCCTTTCAAAGCCGGTCTCAGTTCGGATCGGGGTCTGCAACTCGACCCCGTGAAGTCGGAGTCGCTAGTAATCGCAGATCAGCAACGCTGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACGTCATGAAAGTCGGTAACACCCGAAGCCGGTGGCCTAACCCTTGTGGAGGGAGCCGTCGAAGGTGGGATCGGCGATTGGGACGAAGTCGTAACAAGGTAGCCGTACCGGAAGGTGCGGCTGGATCACCTCCTTTCT","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36769","NCBI_taxonomy_name":"Mycolicibacterium smegmatis MC2 155","NCBI_taxonomy_id":"246196"}}}},"ARO_accession":"3003547","ARO_id":"40149","ARO_name":"Mycolicibacterium smegmatis 16S rRNA (rrsB) mutation conferring resistance to viomycin","CARD_short_name":"Msme_16rrsB_VIO","ARO_description":"Point mutations in the helix 44 region of the 16S rRNA rrsB gene of Mycolicibacterium smegmatis can confer resistance to viomycin.","ARO_category":{"40278":{"category_aro_accession":"3003667","category_aro_cvterm_id":"40278","category_aro_name":"16s rRNA with mutation conferring resistance to peptide antibiotics","category_aro_description":"Point mutations in the 16S rRNA of bacteria can confer resistance to peptide antibiotics.","category_aro_class_name":"AMR Gene Family"},"35937":{"category_aro_accession":"0000018","category_aro_cvterm_id":"35937","category_aro_name":"viomycin","category_aro_description":"Viomycin sulfate (Viocin) is an polypeptide antibiotic used in the treatment of tuberculosis. It is produced by the actinomycete Streptomyces puniceus and binds to the bacterial ribosome, inhibiting prokaryotic protein synthesis and certain forms of RNA splicing.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3718":{"model_id":"3718","model_name":"Mycobacterium tuberculosis Rv2731 mutations confer resistance to pyrazinamide","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"9731":"P82T","9732":"F89L"},"ReSeqTB-Moderate":{"9731":"P82T"},"clinical":{"9731":"P82T","9732":"F89L"},"ReSeqTB-High":{"9732":"F89L"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"8781":{"protein_sequence":{"accession":"NP_217247.1","sequence":"MTADEPRSDDSSGSAPQPAATPVPRPGPRPGPRPVPRPTSYPVGAHPPSDPHRFGRIDDDGTVWLVSASGERIVGSWQAGDPEAAFAHFGRRFDDLSTEIMLMDERLASGTGDARKIKAHAIALAETLPTACVLGDVDALADRLTSIRDRAEVIAAADRSRREEHRAAQTARKEALAAEAEELAANATQWKVAGDRLRAILDEWKTISGVDRKVDDALWKRYSTARDTFNRRRGSHFAELDRERSGVRQSKERLCERAEELSESTDWTATSAEFRKLLADWKAAGRASKDVDDALWRRFKAAQDSFFTARNAATAEKEAELRANADAKEALLAEAERLDTTNHEAARAALRSIAEKWDAIGKVSRERAAELERRLRAVEKKVREAGEADWSDPQARARAEQFRARAEQFEHQAEKAAAAGRTKEADEAKANAEQWRQWAEAAADALTRRP"},"dna_sequence":{"accession":"NC_000962.3","fmin":"3043025","fmax":"3044378","strand":"+","sequence":"ATGACGGCCGACGAGCCCCGCAGCGACGATTCGTCCGGGTCGGCCCCCCAACCGGCTGCCACGCCGGTGCCCCGCCCGGGACCGCGTCCCGGCCCCCGGCCGGTGCCGCGACCCACCTCCTACCCGGTGGGTGCGCACCCTCCCAGCGACCCGCACCGTTTCGGCCGTATCGACGACGACGGCACGGTGTGGCTGGTCAGTGCGAGCGGCGAGCGTATCGTCGGCTCCTGGCAGGCCGGCGATCCCGAAGCCGCGTTTGCCCATTTCGGCAGGCGATTCGATGACCTGAGCACCGAAATCATGCTGATGGACGAGCGGTTGGCGTCCGGCACCGGCGACGCACGCAAGATCAAAGCCCATGCGATCGCGCTGGCCGAAACGTTGCCGACGGCATGCGTGCTGGGCGATGTCGACGCGCTGGCAGACCGGTTGACAAGCATTCGTGATCGCGCGGAGGTCATCGCTGCCGCCGACCGCTCCAGACGCGAGGAACATCGAGCCGCCCAGACCGCCCGTAAAGAGGCGCTGGCCGCCGAAGCCGAGGAGCTGGCCGCCAACGCGACACAATGGAAGGTCGCCGGTGACCGGCTGCGGGCAATCCTCGATGAATGGAAGACGATTAGCGGTGTGGACCGCAAGGTCGATGACGCGCTGTGGAAGCGCTACTCGACGGCCCGCGATACGTTCAACCGGCGGCGAGGGTCCCACTTCGCCGAATTGGACCGTGAGCGATCCGGCGTCCGGCAAAGCAAGGAACGGCTTTGTGAACGGGCCGAGGAGTTGTCCGAGTCGACGGACTGGACCGCCACCAGCGCGGAGTTCCGCAAGCTGCTCGCCGACTGGAAAGCGGCGGGACGCGCGAGCAAGGATGTGGACGACGCCCTGTGGCGTCGCTTCAAGGCCGCGCAGGACTCCTTCTTCACGGCTCGCAATGCCGCCACCGCCGAGAAGGAGGCCGAGTTGCGAGCCAATGCCGACGCCAAGGAGGCGCTGCTGGCCGAAGCGGAGCGGCTCGACACGACAAACCACGAGGCCGCTCGAGCAGCGCTGCGGTCGATCGCCGAGAAGTGGGACGCGATCGGCAAGGTGTCGCGGGAGCGGGCCGCGGAGCTGGAGCGGCGACTACGCGCGGTCGAGAAAAAGGTGCGAGAAGCCGGCGAAGCGGATTGGTCCGACCCGCAGGCGCGGGCCCGCGCCGAGCAGTTCCGCGCCCGGGCCGAGCAGTTTGAACACCAGGCCGAGAAGGCAGCAGCGGCCGGTCGCACCAAGGAAGCCGACGAGGCGAAGGCGAACGCCGAACAATGGCGGCAGTGGGCCGAGGCAGCCGCCGACGCGTTGACCCGACGCCCCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3004987","ARO_id":"43174","ARO_name":"Mycobacterium tuberculosis Rv2731 mutations confer resistance to pyrazinamide","CARD_short_name":"Mtub_Rv2731_PZA","ARO_description":"Mutations in the Rv2731 gene that contribute to or confer resistance to pyrazinamide.","ARO_category":{"43173":{"category_aro_accession":"3004986","category_aro_cvterm_id":"43173","category_aro_name":"pyrazinamide resistant Rv2731","category_aro_description":"A conserved alanine and arginine-rich protein with an unknown function. The protein has shown to contribute to or confer resistance to pyrazinamide.","category_aro_class_name":"AMR Gene Family"},"39997":{"category_aro_accession":"3003413","category_aro_cvterm_id":"39997","category_aro_name":"pyrazinamide","category_aro_description":"Pyrazinamide is an antimycobacterial. It is highly specific and active only against Mycobacterium tuberculosis. This compound is a prodrug and needs to be activated inside the cell. It interferes with the bacterium's ability to synthesize new fatty acids, causing cell death.","category_aro_class_name":"Antibiotic"},"45737":{"category_aro_accession":"3007155","category_aro_cvterm_id":"45737","category_aro_name":"pyrazine antibiotic","category_aro_description":"A group of antibiotics derived from pyrazine.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3390":{"model_id":"3390","model_name":"MCR-3.4","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"5576":{"protein_sequence":{"accession":"SBZ31568.1","sequence":"MPSLIKIKIVPLMFFLALYFAFMLNWRGVLHFYEILYKLEDFKFGFAISLPILLVAALNFVFVPFSIRYLIKPFFALLIALSAIVSYTMMKYRVLFDQNMIQNIFETNQNEALAYLSLPIIVWVTIAGFIPAILLFFVEIEYEEKWFKGILTRALSMFASLIVIAVIAALYYQDYVSVGRNNSNLQREIVPANFVNSTVKYVYNRYLAEPIPFTTLGDDAKRDTNQSKPTLMFLVVGETARGKNFSMNGYEKDTNPFTSKSGGVISFNDVRSCGTATAVSVPCMFSNMGRKEFDDNRARNSEGLLDVLQKTGISIFWKENDGGCKGVCDRVPNIEIEPKDHPKFCDKNTCYDEVVLQDLDSEIAQMKGDKLVVFHLIGSHGPTYYKRYPDAHRQFTPDCPRSDIENCTDEELTNTYDNTIRYTDFVIGEMIAKLKTYEDKYNTALLYVSDHGESLGALGLYLHGTPYQFAPDDQTRVPMQVWMSPGFTKEKGVDMACLQQKAADTRYSHDNIFSSVLGIWDVKTSVYEKGLDIFSQCRNVQ"},"dna_sequence":{"accession":"FLXA01000011.1","fmin":"1587","fmax":"3213","strand":"+","sequence":"ATGCCTTCCCTTATAAAAATAAAAATTGTTCCGCTTATGTTCTTTTTGGCACTGTATTTTGCATTTATGCTGAACTGGCGTGGAGTTCTCCATTTTTACGAAATCCTTTACAAATTAGAAGATTTTAAGTTTGGTTTCGCCATTTCATTACCAATATTGCTTGTTGCAGCGCTTAACTTTGTATTTGTTCCATTTTCGATACGGTATTTAATAAAGCCTTTTTTTGCACTTCTTATCGCACTTAGTGCAATCGTTAGTTACACAATGATGAAGTATAGAGTCTTGTTTGATCAAAACATGATTCAGAATATTTTTGAAACCAATCAAAATGAGGCGTTAGCATATTTAAGCTTACCAATTATAGTATGGGTTACTATTGCTGGTTTTATCCCTGCCATTTTACTTTTCTTTGTTGAAATTGAATATGAGGAAAAATGGTTCAAAGGGATTCTAACTCGTGCCCTATCGATGTTTGCATCACTTATAGTGATTGCGGTTATTGCAGCACTATACTATCAAGATTATGTGTCAGTGGGGCGCAACAATTCAAACCTCCAGCGTGAGATTGTTCCAGCCAATTTCGTTAATAGTACCGTTAAATACGTTTACAATCGTTATCTTGCTGAACCAATCCCATTTACAACTTTAGGTGATGATGCAAAACGGGATACTAATCAAAGTAAGCCCACGTTGATGTTTCTGGTCGTTGGTGAAACCGCTCGTGGTAAAAATTTCTCGATGAATGGCTATGAGAAAGACACCAATCCATTTACCAGTAAATCTGGTGGCGTGATCTCCTTTAATGATGTTCGTTCGTGTGGGACTGCAACCGCTGTATCCGTCCCCTGCATGTTCTCCAATATGGGGAGAAAGGAGTTTGATGATAATCGCGCTCGCAATAGCGAGGGCCTGCTAGATGTGTTGCAAAAAACGGGGATCTCCATTTTTTGGAAGGAGAACGATGGAGGCTGCAAAGGCGTCTGCGACCGAGTACCTAACATCGAAATCGAACCAAAGGATCACCCTAAGTTCTGCGATAAAAACACATGCTATGACGAGGTTGTCCTTCAAGACCTCGATAGTGAAATTGCTCAAATGAAAGGGGATAAGCTGGTTGTCTTCCACCTGATAGGTAGCCATGGCCCAACCTACTACAAGCGCTACCCTGATGCTCATCGTCAGTTCACCCCTGACTGTCCACGCAGTGATATTGAAAACTGCACAGATGAAGAGCTCACCAACACCTATGACAACACCATCCGCTACACCGATTTCGTGATTGGAGAGATGATTGCCAAGTTGAAAACCTACGAAGATAAGTACAACACCGCGTTGCTCTACGTCTCCGATCATGGTGAATCACTGGGAGCATTAGGGCTTTACCTACACGGTACACCGTACCAGTTTGCACCGGATGATCAGACCCGTGTTCCTATGCAGGTGTGGATGTCACCTGGATTTACCAAAGAGAAAGGCGTTGATATGGCGTGTTTGCAGCAGAAAGCCGCTGATACTCGTTACTCACACGATAATATTTTCTCATCTGTATTGGGTATCTGGGACGTCAAAACATCAGTTTACGAAAAGGGTCTAGATATTTTCAGTCAATGTCGTAATGTTCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3004691","ARO_id":"42743","ARO_name":"MCR-3.4","CARD_short_name":"MCR-3.4","ARO_description":"A plasmid-mediated MCR-3.1 variant.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3394":{"model_id":"3394","model_name":"MCR-4.4","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"5581":{"protein_sequence":{"accession":"AVK94779.1","sequence":"MISRFKTLSVNQFTFITALFYVAIFNLPLFGIVRKGIEKQPEVDPLFIASMPLFLTFALSFLFSIFTVKYLLKPFFIVLTLLSSSVFFAAYQYNVVFDYGMIENTFQTHPAEALMYVNLASITNLLLTGLLPSYLIYKADIHYQPFFKELLHKLAFMLLMFVGIGIVAFFYYQDYAAFVRNNSELRRYIVPTYFVSSASKYLNENYLQTPMEYQQLGLDAKNASRNPNTKPNLLVVVVGETARSMSYQYYGYNKPTNAHTQNQGLIAFNDTSSCGTATAVSLPCMFSRMGRADYDPRRANAQDTVIDVLSHSGIKVQWFDNDSGCKGVCDRVENLTIDLKSDPKLCSGQYCFDQVLLNKLDKILAVAPSQDTVIFLHIIGSHGPTYYLRYPPEHRKFIPDCPRSDIQNCSQEELINTYDNTILYTDFILSEVVNKLKGKQDMFDTAMLYLSDHGESLGEKGMYLHGAPYSIAPKEQTSVPMLAWVSNDFSQDNQLNMTCVAQRAEQGGFSHDNLFDSLLGLMNVKTTVYQSQLDIFAPCRY"},"dna_sequence":{"accession":"MG822665.1","fmin":"0","fmax":"1626","strand":"+","sequence":"GTGATTTCTAGATTTAAGACGTTATCGGTTAACCAATTCACTTTCATCACTGCGTTGTTTTATGTTGCCATTTTCAATCTACCGCTCTTTGGTATAGTGCGAAAAGGAATTGAAAAACAACCAGAAGTTGATCCCCTTTTCATCGCATCTATGCCGCTATTTTTAACATTTGCGCTGAGTTTTTTGTTTTCAATTTTTACCGTCAAATACCTGCTGAAGCCCTTTTTTATCGTATTGACGTTACTTTCCTCAAGTGTATTTTTTGCAGCCTATCAATACAATGTCGTGTTTGACTACGGCATGATAGAAAACACGTTTCAAACACATCCTGCTGAAGCATTGATGTATGTAAATCTTGCATCAATTACCAATCTACTGCTGACTGGGCTATTACCGTCATATCTTATTTATAAGGCCGATATTCATTATCAGCCCTTTTTTAAGGAGTTATTGCATAAATTAGCCTTTATGCTGCTAATGTTCGTTGGCATTGGGATAGTCGCCTTTTTTTACTATCAAGATTATGCTGCATTTGTTCGAAACAACAGTGAGTTAAGGCGTTACATTGTCCCTACCTATTTTGTCAGTAGTGCATCTAAATATCTCAATGAGAACTATTTGCAGACGCCCATGGAATACCAACAACTTGGCCTAGATGCGAAGAATGCCAGTCGTAACCCGAACACTAAACCTAACTTATTAGTGGTTGTTGTGGGTGAAACTGCGCGCTCAATGAGCTATCAATATTATGGATATAACAAGCCAACCAATGCTCATACCCAAAATCAGGGGCTGATTGCGTTTAACGATACTAGCTCATGCGGCACGGCCACGGCGGTGTCTCTACCCTGTATGTTTTCACGAATGGGGCGGGCAGACTATGATCCTCGCCGTGCTAATGCTCAAGACACAGTGATTGATGTGTTAAGTCATAGTGGTATAAAAGTACAGTGGTTTGATAATGATTCTGGCTGTAAAGGTGTGTGTGATCGGGTTGAAAATCTCACGATAGATTTGAAGAGTGATCCGAAGCTGTGTTCTGGCCAATATTGTTTTGACCAAGTATTGCTCAACAAATTAGATAAAATTCTGGCAGTAGCACCAAGTCAAGATACAGTAATTTTTTTGCATATCATTGGTAGTCATGGACCAACTTATTATCTTAGATACCCGCCAGAGCATCGTAAATTTATACCGGATTGTCCGCGCAGTGATATTCAAAATTGCAGTCAAGAAGAACTGATTAACACCTACGACAACACTATTCTATATACGGATTTTATTCTCAGTGAAGTGGTGAATAAATTAAAAGGTAAGCAGGATATGTTCGATACTGCAATGCTGTATCTCTCTGACCATGGTGAGTCTTTGGGTGAAAAGGGCATGTATTTACATGGTGCGCCCTATAGTATTGCACCGAAAGAACAAACTAGCGTACCAATGCTGGCTTGGGTATCTAATGACTTTAGCCAAGATAATCAGTTGAACATGACTTGTGTTGCACAGCGAGCAGAACAGGGCGGCTTTTCCCACGACAATTTGTTCGACAGTTTGCTAGGACTTATGAATGTAAAAACCACCGTCTATCAGAGCCAACTCGATATTTTTGCACCTTGCAGGTATTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3004696","ARO_id":"42748","ARO_name":"MCR-4.4","CARD_short_name":"MCR-4.4","ARO_description":"A plasmid-mediated MCR-4 variant and colistin resistance gene.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3406":{"model_id":"3406","model_name":"OXA-140","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"420"}},"model_sequences":{"sequence":{"8421":{"protein_sequence":{"accession":"ALL27283.1","sequence":"FAIFLIIANIIYSSASASTDISTVASPLFEGTEGCFLLYDASTNAEIAQFNKAKCATQMAPDSTFKIALSLMAFDAEIIDQKTIFKWDKTPKGMEIWNSNHTPKTWMQFSVVWVSQEITQKIGLNKIKNYLKDFDYGNQDFSGDKERNNGLTEAWLESSLKISPEEQIQFLRKIINHNLPVKNSAIENTIENMYLQDLDNSTKLYGKTGAGFTANRTLQNGWFEGFIISKSGHKY"},"dna_sequence":{"accession":"KR780479.1","fmin":"1","fmax":"706","strand":"-","sequence":"TTCGCTATTTTTTTAATAATTGCAAATATTATCTACAGCAGCGCCAGTGCATCAACAGATATCTCTACTGTTGCATCTCCATTATTTGAAGGAACTGAAGGTTGTTTTTTACTTTACGATGCATCCACAAACGCTGAAATTGCTCAATTCAATAAAGCAAAGTGTGCAACGCAAATGGCACCAGATTCAACTTTCAAGATCGCATTATCACTTATGGCATTTGATGCGGAAATAATAGATCAGAAAACCATATTCAAATGGGATAAAACCCCCAAAGGAATGGAGATCTGGAACAGCAATCATACACCAAAGACGTGGATGCAATTTTCTGTTGTTTGGGTTTCGCAAGAAATAACCCAAAAAATTGGATTAAATAAAATCAAGAATTATCTCAAAGATTTTGATTATGGAAATCAAGACTTCTCTGGAGATAAAGAAAGAAACAACGGATTAACAGAAGCATGGCTCGAAAGTAGCTTAAAAATTTCACCAGAAGAACAAATTCAATTCCTGCGTAAAATTATTAATCACAATCTCCCAGTTAAAAACTCAGCCATAGAAAACACCATAGAGAACATGTATCTACAAGATCTGGATAATAGTACAAAACTGTATGGGAAAACTGGTGCAGGATTCACAGCAAATAGAACCTTACAAAACGGATGGTTTGAAGGGTTTATTATAAGCAAATCAGGACATAAATAT","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39097","NCBI_taxonomy_name":"Klebsiella pneumoniae subsp. pneumoniae","NCBI_taxonomy_id":"72407"}}}},"ARO_accession":"3001452","ARO_id":"37852","ARO_name":"OXA-140","CARD_short_name":"OXA-140","ARO_description":"OXA-140 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3429":{"model_id":"3429","model_name":"OXA-262","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"5625":{"protein_sequence":{"accession":"ENW50687.1","sequence":"MNIKTLLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEVHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAISVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGSLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"APRA01000005.1","fmin":"465153","fmax":"465978","strand":"+","sequence":"ATGAACATTAAAACACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGTACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTTCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTTCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42793","NCBI_taxonomy_name":"Acinetobacter baumannii NIPH 67","NCBI_taxonomy_id":"1217627"}}}},"ARO_accession":"3001718","ARO_id":"38118","ARO_name":"OXA-262","CARD_short_name":"OXA-262","ARO_description":"OXA-262 is a beta-lactamase found in Acinetobacter spp.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3459":{"model_id":"3459","model_name":"OXA-297","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"520"}},"model_sequences":{"sequence":{"5654":{"protein_sequence":{"accession":"ENX09209.1","sequence":"MLFNFIVMPKKLKLLVLSVVVMPSIILLGCQNIQPHVQTLVTQKQTEDQIATAFENIQTSGVLVTYDGKAIQKYGNALNRANQRYIPASTFKMLNALIGIQHHKTSPNEVFKWDGQKRVFTSWEKDLTLAEAMQASAVPVYQELARRIGLELMASEVKRVGYGNQSIGTQVDNFWLVGPLEITPVEEVKFAYALAKKQLAFDSSTQQQVKDMLLIEDIQGTKIYAKSGWGMDVKPQVGWWTGWVEQPNGQVTAFSLNMEMKKAAHAEARKAIVYQALQQLGLLPQ"},"dna_sequence":{"accession":"APRR01000006.1","fmin":"288118","fmax":"288976","strand":"-","sequence":"GTGTTGTTCAATTTTATAGTCATGCCGAAAAAATTAAAATTACTCGTTCTATCTGTAGTTGTGATGCCCTCAATAATATTGTTGGGCTGCCAAAATATTCAGCCACACGTTCAAACTTTAGTCACGCAGAAACAGACTGAAGATCAGATCGCAACTGCATTTGAAAATATCCAGACCTCCGGTGTACTGGTCACCTATGATGGCAAAGCTATTCAAAAATATGGCAATGCGCTTAACCGGGCCAATCAGCGCTATATTCCGGCTTCCACCTTTAAAATGCTGAATGCCTTGATTGGTATCCAGCATCACAAGACTTCACCGAATGAAGTATTTAAATGGGATGGACAGAAGCGGGTATTTACCAGCTGGGAAAAAGATTTAACCCTGGCAGAAGCCATGCAGGCTTCGGCTGTACCTGTGTATCAGGAACTGGCACGCCGTATCGGTCTGGAATTAATGGCCAGTGAAGTAAAACGGGTCGGGTATGGCAATCAGTCAATTGGAACGCAAGTGGATAATTTCTGGTTAGTGGGGCCTTTAGAAATTACCCCTGTGGAGGAAGTAAAATTTGCCTATGCCTTGGCGAAAAAACAACTTGCATTTGACTCATCAACCCAGCAACAAGTTAAAGATATGTTGCTGATTGAAGATATTCAGGGCACCAAAATCTATGCCAAAAGTGGATGGGGCATGGATGTAAAACCTCAGGTGGGATGGTGGACAGGTTGGGTAGAACAACCCAATGGTCAGGTCACTGCATTTTCACTGAATATGGAAATGAAAAAGGCAGCACATGCAGAAGCACGTAAAGCTATTGTGTATCAGGCTTTACAACAACTGGGTCTATTGCCCCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42818","NCBI_taxonomy_name":"Acinetobacter sp. NIPH 1847","NCBI_taxonomy_id":"1217697"}}}},"ARO_accession":"3001752","ARO_id":"38152","ARO_name":"OXA-297","CARD_short_name":"OXA-297","ARO_description":"OXA-297 is a beta-lactamase found in Acinetobacter spp.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46504":{"category_aro_accession":"3007715","category_aro_cvterm_id":"46504","category_aro_name":"OXA-294-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-294.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3488":{"model_id":"3488","model_name":"OXA-403","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"5683":{"protein_sequence":{"accession":"AIM47095.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPHHSASKSDDKAEKIKNLFNEAHTTGVLVIHQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGEKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"KJ920337.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCACATCACAGTGCTTCAAAATCTGATGACAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCATCAAGGTCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAATGGGATGGGGAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTCTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001589","ARO_id":"37989","ARO_name":"OXA-403","CARD_short_name":"OXA-403","ARO_description":"OXA-403 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"515":{"model_id":"515","model_name":"mgtA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"8170":{"protein_sequence":{"accession":"ABA28305.2","sequence":"MKRKELHETSRLAYGRRMTTRPAHIAMFSIALHGHVNPSLEVIRELVARGHRVTYAIPPLLADKVAEAGAEPKLWNSTLPGPDADPEAWGSTLLDNVEPFLADAIQSLPQLAQAYEGDEPDLVLHDIASYTARVLGRRWEVPVISLSPCMVAWEGYEQEVGEPMWEEPRKTERGQAYYARFHAWLEENGITDHPDPFIGRPDRSLVLIPKALQPHADRVDETTYTFVGACQGDRTAEGDWARPEGAEKVVLVSLGSAFTKQPAFYRECVRAFGELPGWHTVLQVGRHVDPAELGDVPDNVEVRTWVPQLAILQQADLFVTHAGAGGSQEGLATATPMIAVPQAADQFGNADMLQGLGVARTLPTEEATAKALRTAALALVDDPEVAARLKEIQARMAQEGGTRRAADLIEAELAAARG"},"dna_sequence":{"accession":"DQ185434.2","fmin":"0","fmax":"1257","strand":"+","sequence":"ATGAAGCGAAAAGAGTTGCACGAGACGTCTCGTCTCGCATACGGTCGTCGCATGACCACTCGCCCCGCGCACATCGCCATGTTCTCCATCGCCCTGCACGGCCACGTGAACCCCAGCCTGGAGGTCATCCGCGAGCTCGTCGCGCGGGGGCACCGGGTGACGTACGCGATCCCGCCGCTCCTCGCGGACAAGGTCGCCGAGGCGGGCGCCGAACCCAAGCTCTGGAACAGCACACTGCCCGGCCCCGACGCCGACCCGGAGGCCTGGGGGAGCACCCTCCTGGACAACGTGGAGCCCTTCCTCGCCGACGCGATCCAGTCGCTCCCGCAGCTCGCCCAGGCGTACGAGGGGGACGAGCCGGACCTGGTCCTGCACGACATCGCCTCCTACACCGCCCGCGTCCTGGGCCGCCGCTGGGAGGTGCCCGTGATCTCCCTGTCGCCCTGCATGGTCGCCTGGGAGGGGTACGAGCAGGAGGTCGGCGAGCCGATGTGGGAGGAGCCGCGGAAGACCGAGCGCGGGCAGGCGTACTACGCCCGCTTCCACGCCTGGCTGGAGGAGAACGGGATCACCGACCACCCCGACCCGTTCATCGGCCGCCCCGACCGCTCCCTGGTGCTGATCCCCAAGGCGCTCCAGCCCCACGCCGACCGGGTGGACGAGACGACGTACACCTTCGTCGGCGCCTGCCAGGGGGACCGCACCGCCGAGGGCGACTGGGCCCGTCCCGAGGGCGCGGAGAAGGTCGTCCTGGTCTCGCTCGGTTCGGCCTTCACCAAGCAGCCCGCGTTCTACCGGGAGTGCGTCCGGGCCTTCGGTGAGCTGCCCGGCTGGCACACCGTGCTCCAGGTCGGCCGGCACGTAGACCCGGCCGAGCTGGGCGACGTACCGGACAACGTGGAAGTCCGCACGTGGGTACCGCAGTTGGCGATCCTCCAGCAGGCCGACCTGTTCGTCACCCACGCGGGCGCGGGCGGCAGCCAGGAGGGTCTGGCCACCGCCACGCCGATGATCGCCGTACCGCAGGCCGCGGACCAGTTCGGCAACGCCGACATGCTCCAGGGCCTCGGCGTCGCCCGCACCCTCCCGACCGAGGAGGCCACCGCGAAGGCGCTGCGCACCGCCGCCCTCGCCCTGGTCGACGACCCGGAGGTGGCGGCGCGCCTGAAGGAGATCCAGGCGCGGATGGCCCAGGAGGGCGGCACCCGCCGGGCCGCCGACCTCATCGAGGCCGAACTGGCCGCCGCGCGCGGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39569","NCBI_taxonomy_name":"Streptomyces lividans","NCBI_taxonomy_id":"1916"}}}},"ARO_accession":"3000462","ARO_id":"36601","ARO_name":"mgtA","CARD_short_name":"mgtA","ARO_description":"A macrolide glycosyltransferase encoded by the mgtA gene in Streptomyces lividans. This enzyme inactivates macrolides using UDP-glucose as a cofactor. Its optimal substrates are lankamycin, calcomycin, rosaramicin, methymycin, and pikromycin, while interactions with erythomycin, oldeandomycin, azithromycin, and tylosin were weaker. It is inactive against spiramycin and carbomycin. Mechanism first described by Cundliffe, 1992.","ARO_category":{"41401":{"category_aro_accession":"3004237","category_aro_cvterm_id":"41401","category_aro_name":"mgt macrolide glycotransferase","category_aro_description":"The mgt family encompasses macrolide glycotransferases of the Streptomyces genus.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"36284":{"category_aro_accession":"3000145","category_aro_cvterm_id":"36284","category_aro_name":"tylosin","category_aro_description":"Tylosin is a 16-membered macrolide, naturally produced by Streptomyces fradiae. It interacts with the bacterial ribosome 50S subunit to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"37631":{"category_aro_accession":"3001232","category_aro_cvterm_id":"37631","category_aro_name":"methymycin","category_aro_description":"Produced by Streptomyces venezuelae ATCC 15439.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4228":{"model_id":"4228","model_name":"ADC-158","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6603":{"protein_sequence":{"accession":"WP_001211227.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPTDIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_055786.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAGTATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATACGGCGTCAAATCCACCTTACCGGATATGTTGAGTTTTATTCATGCCAACCTTAACCCACAGAAATATCCGACAGATATTCAACGGGCAATTAATGAAACACATCAAGGTCGCTATCAAGTAAATACCATGTATCAAGCGCTTGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAGCCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACATATGTAGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006332","ARO_id":"44794","ARO_name":"ADC-158","CARD_short_name":"ADC-158","ARO_description":"ADC-158 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4229":{"model_id":"4229","model_name":"ADC-160","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6604":{"protein_sequence":{"accession":"WP_032037870.1","sequence":"MRFKKISCLLFSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIYANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLSAIKK"},"dna_sequence":{"accession":"NG_055788.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTCTCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCGGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACTGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTCCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCTGGCCCACTCGATGCCCCAGCATACGGCGTCAAATCCACCTTACCGGATATGTTGAGTTTTATTTATGCCAACCTTAACCCACAGAAATATCCGGCTGATATTCAAAGGGCAATTAATGAAACACATCAAGGTCGCTATCAAGTAAATACCATGTATCAAGCGCTTGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAGCCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCAACGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAGTGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006333","ARO_id":"44795","ARO_name":"ADC-160","CARD_short_name":"ADC-160","ARO_description":"ADC-160 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3395":{"model_id":"3395","model_name":"MCR-4.5","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"5582":{"protein_sequence":{"accession":"AVK94778.1","sequence":"MISRFKTLSVNQFTFITALFYVAIFNLPLFGIVRKGIEKQPEVDPLFIASMPLFLTFALSFLFSIFTVKYLLKPFFIVLTLLSSSVFFAAYQYNVVFDYGMIENTFQTHLAEALMYVNLASITNLLLTGLLPSYLIYKADIHYQPFFKELLHKLAFMLLMFVGIGIVAFFYYQDYAAFVRNNSELRRYIVPTYFVSSASKYLNEHYLQTPMEYQQLGLDAKNASRNPNTKPNLLVVVVGETARSMSYQYYGYNKPTNAHTQNQGLIAFNDTSSCGTATAVSLPCMFSRMGRADYDPRRANAQDTVIDVLSHSGIKVQWFDNDSGCKGVCDRVENLTIDLKSDPKLCSGQYCFDQVLLNKLDKILAVAPSQDTVIFLHIIGSHGPTYYLRYPPEHRKFIPDCPRSDIQNCSQEELINTYDNTILYTDFILSEVVNKLKGKQDMFDTAMLYLSDHGESLGEKGMYLHGAPYSIAPKEQTSVPMLAWVSNDFSQDNQLNMTCVAQRAEQGGFSHDNLFDSLLGLMNVKTTVYQSQLDIFAPCRY"},"dna_sequence":{"accession":"MG822664.1","fmin":"0","fmax":"1626","strand":"+","sequence":"GTGATTTCTAGATTTAAGACGTTATCGGTTAACCAATTCACTTTCATCACTGCGTTGTTTTATGTTGCCATTTTCAATCTACCGCTCTTTGGTATAGTGCGAAAAGGAATTGAAAAACAACCAGAAGTTGATCCCCTTTTCATCGCATCTATGCCGCTATTTTTAACATTTGCGCTGAGTTTTTTGTTTTCAATTTTTACCGTCAAATACCTGCTGAAGCCCTTTTTTATCGTATTGACGTTACTTTCCTCAAGTGTATTTTTTGCAGCCTATCAATACAATGTCGTGTTTGACTACGGCATGATAGAAAACACGTTTCAAACACATCTTGCTGAAGCATTGATGTATGTAAATCTTGCATCAATTACCAATCTACTGCTGACTGGGCTATTACCGTCATATCTTATTTATAAGGCCGATATTCATTATCAGCCCTTTTTTAAGGAGTTATTGCATAAATTAGCCTTTATGCTGCTAATGTTCGTTGGCATTGGGATAGTCGCCTTTTTTTACTATCAAGATTATGCTGCATTTGTTCGAAACAACAGTGAGTTAAGGCGTTACATTGTCCCTACCTATTTTGTCAGTAGTGCATCTAAATATCTCAATGAGCACTATTTGCAGACGCCCATGGAATACCAACAACTTGGCCTAGATGCGAAGAATGCCAGTCGTAACCCGAACACTAAACCTAACTTATTAGTGGTTGTTGTGGGTGAAACTGCGCGCTCAATGAGCTATCAATATTATGGATATAACAAGCCAACCAATGCTCATACCCAAAATCAGGGGCTGATTGCGTTTAACGATACTAGCTCATGCGGCACGGCCACGGCGGTGTCTCTACCCTGTATGTTTTCACGAATGGGGCGGGCAGACTATGATCCTCGCCGTGCTAATGCTCAAGACACAGTGATTGATGTGTTAAGTCATAGTGGTATAAAAGTACAGTGGTTTGATAATGATTCTGGCTGTAAAGGTGTGTGTGATCGGGTTGAAAATCTCACGATAGATTTGAAGAGTGATCCGAAGCTGTGTTCTGGCCAATATTGTTTTGACCAAGTATTGCTCAACAAATTAGATAAAATTCTGGCAGTAGCACCAAGTCAAGATACAGTAATTTTTTTGCATATCATTGGTAGTCATGGACCAACTTATTATCTTAGATACCCGCCAGAGCATCGTAAATTTATACCGGATTGTCCGCGCAGTGATATTCAAAATTGCAGTCAAGAAGAACTGATTAACACCTACGACAACACTATTCTATATACGGATTTTATTCTCAGTGAAGTGGTGAATAAATTAAAAGGTAAGCAGGATATGTTCGATACTGCAATGCTGTATCTCTCTGACCATGGTGAGTCTTTGGGTGAAAAGGGCATGTATTTACATGGTGCGCCCTATAGTATTGCACCGAAAGAACAAACTAGCGTACCAATGCTGGCTTGGGTATCTAATGACTTTAGCCAAGATAATCAGTTGAACATGACTTGTGTTGCACAGCGAGCAGAACAGGGCGGCTTTTCCCACGACAATTTGTTCGACAGTTTGCTAGGACTTATGAATGTAAAAACCACCGTCTATCAGAGCCAACTCGATATTTTTGCACCTTGCAGGTATTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3004697","ARO_id":"42749","ARO_name":"MCR-4.5","CARD_short_name":"MCR-4.5","ARO_description":"A plasmid-mediated MCR-4 variant and colistin resistance gene.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3407":{"model_id":"3407","model_name":"OXA-103","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"5602":{"protein_sequence":{"accession":"ENV88740.1","sequence":"MNKYFTCYVVASLFLSGCTVQHNLINETPSQIVQGHNQVIHQYFDEKNTSGVLVIQTDKKINLYGNALSRANTEYVPASTFKMLNALIGLENQKTDINEIFKWKGEKRSFTAWEKDMTLGEAMKLSAVPVYQELARRIGLDLMQKEVERIDFGNAEIGQQVDNFWLIGPLKVTPIQEVEFVSQLAHTQLPFSEKVQANVKNMLLLEESNGYKIFGKTGWAMDIKPQVGWLTGWVEQPDGKIVAFALNMEMRSEMPASIRNELLMKSLKQLNII"},"dna_sequence":{"accession":"APQF01000011.1","fmin":"291557","fmax":"292379","strand":"+","sequence":"ATGAATAAATATTTTACTTGCTATGTGGTTGCTTCTCTTTTTCTTTCTGGTTGTACGGTTCAGCATAATTTAATAAATGAAACCCCGAGTCAGATTGTTCAAGGACATAATCAGGTGATTCATCAATACTTTGATGAAAAAAACACCTCAGGTGTGCTGGTTATTCAAACAGATAAAAAAATTAATCTATATGGTAATGCTCTAAGCCGCGCAAATACAGAATATGTGCCAGCCTCTACATTTAAAATGTTGAATGCCCTGATCGGATTGGAGAACCAGAAAACGGATATTAATGAAATATTTAAATGGAAGGGCGAGAAAAGGTCATTTACCGCTTGGGAAAAAGACATGACACTAGGAGAAGCCATGAAGCTTTCTGCAGTCCCAGTCTATCAGGAACTTGCAAGACGTATCGGTCTTGATCTCATGCAAAAAGAAGTAGAACGTATTGATTTCGGTAATGCTGAAATTGGACAGCAGGTTGACAATTTCTGGTTGATAGGCCCATTAAAGGTCACGCCTATTCAAGAGGTAGAGTTTGTTTCTCAATTGGCACATACACAGCTTCCATTTAGTGAAAAAGTGCAGGCTAATGTAAAAAATATGCTACTTCTAGAAGAGAGTAATGGCTACAAGATTTTTGGAAAGACTGGTTGGGCAATGGATATAAAACCACAAGTGGGCTGGTTGACCGGCTGGGTTGAGCAGCCAGATGGAAAAATTGTCGCTTTTGCATTAAATATGGAAATGCGGTCAGAAATGCCTGCATCTATACGTAATGAATTATTGATGAAATCATTAAAACAGCTGAATATTATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42784","NCBI_taxonomy_name":"Acinetobacter radioresistens DSM 6976 = NBRC 102413 = CIP 103788","NCBI_taxonomy_id":"981334"}}}},"ARO_accession":"3001707","ARO_id":"38107","ARO_name":"OXA-103","CARD_short_name":"OXA-103","ARO_description":"OXA-103 is a beta-lactamase found in Acinetobacter spp.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46499":{"category_aro_accession":"3007710","category_aro_cvterm_id":"46499","category_aro_name":"OXA-23-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases, specifically imipenem, derived from OXA-23, first identified in Acinetobacter baumannii.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3430":{"model_id":"3430","model_name":"OXA-263","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"5626":{"protein_sequence":{"accession":"ENW43915.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNYSASKSDEKAEKIKNLFNEAQTRGVLVIQQGQIQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKTTTTEVFKWNGQKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"APQY01000006.1","fmin":"416598","fmax":"417423","strand":"+","sequence":"ATGAATATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGTTCACCTTATATAGTGACCGCTAATCCAAATTACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACAAACTAGGGGTGTTTTAGTTATCCAACAAGGTCAAATTCAACAAAGTTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTTAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGACAACCACCACAGAAGTATTTAAGTGGAACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAAAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGCGTTGGTTATGGCAATGCAGATATAGGCACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTCGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42794","NCBI_taxonomy_name":"Acinetobacter baumannii NIPH 329","NCBI_taxonomy_id":"1217632"}}}},"ARO_accession":"3001719","ARO_id":"38119","ARO_name":"OXA-263","CARD_short_name":"OXA-263","ARO_description":"OXA-263 is a beta-lactamase found in Acinetobacter spp.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3460":{"model_id":"3460","model_name":"OXA-298","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"5655":{"protein_sequence":{"accession":"ENX40034.1","sequence":"MLFNFIVMPKKLKLLALSVVVMPSIILLGCQNIQPHVQALVTQKQTEDQIATAFENIQTSGVLVTYDGKAIQKYGNALNRADQRYIPASTFKMLNALIGIQHHKTSPNEVFKWDGQKRAFTSWEKDLTLAEAMQASAVPVYQELARRIGLELMASEVKRVGYGNQSIGTQVDNFWLVGPLEITPVEEVKFAYALAKKQLAFDSSTQQQVKDMLLIEDIQGTKIYAKSGWGMDVKPQVGWWTGWVEQPNGQVTAFSLNMEMKKAAHAEARKAIVYQALQQLGLLPQ"},"dna_sequence":{"accession":"APSA01000003.1","fmin":"159905","fmax":"160763","strand":"+","sequence":"GTGTTGTTCAATTTTATAGTCATGCCGAAAAAATTAAAATTACTCGCTCTATCTGTAGTTGTGATGCCCTCAATAATATTATTGGGCTGCCAAAATATTCAGCCACACGTTCAAGCTTTAGTCACACAGAAACAGACTGAAGATCAGATCGCAACTGCATTTGAAAATATCCAGACCTCCGGTGTACTGGTCACCTATGATGGCAAAGCTATTCAAAAATATGGCAATGCGCTTAACCGGGCCGATCAGCGTTATATTCCGGCTTCCACCTTTAAAATGCTGAATGCCTTGATTGGTATCCAGCATCATAAGACTTCACCAAATGAAGTATTTAAATGGGATGGACAGAAGCGGGCATTTACCAGCTGGGAAAAAGATTTAACCCTGGCAGAAGCCATGCAGGCTTCGGCTGTACCTGTGTATCAGGAACTGGCACGCCGTATTGGTCTGGAATTAATGGCCAGTGAAGTAAAACGGGTCGGGTATGGCAATCAGTCGATTGGAACGCAAGTGGATAATTTCTGGTTAGTGGGGCCTTTAGAAATTACCCCTGTGGAGGAAGTAAAATTTGCCTATGCCTTGGCGAAAAAACAACTTGCATTTGACTCATCAACCCAGCAACAAGTTAAAGATATGTTGCTGATTGAAGATATTCAGGGCACCAAAATCTATGCCAAAAGTGGATGGGGCATGGATGTAAAACCTCAGGTGGGATGGTGGACAGGTTGGGTAGAACAACCCAATGGTCAGGTCACTGCATTTTCACTGAATATGGAAATGAAAAAGGCAGCACATGCAGAAGCACGTAAAGCTATTGTGTATCAGGCTTTACAACAACTGGGTCTATTGCCCCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42819","NCBI_taxonomy_name":"Acinetobacter sp. NIPH 3623","NCBI_taxonomy_id":"1217698"}}}},"ARO_accession":"3001753","ARO_id":"38153","ARO_name":"OXA-298","CARD_short_name":"OXA-298","ARO_description":"OXA-298 is a beta-lactamase found in Acinetobacter spp.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46504":{"category_aro_accession":"3007715","category_aro_cvterm_id":"46504","category_aro_name":"OXA-294-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-294.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2685":{"model_id":"2685","model_name":"Pseudomonas aeruginosa CpxR","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"4526":{"protein_sequence":{"accession":"SIP52035.1","sequence":"MSELLLIDDDRELCELLGTWLVQEGFSVRASHDGAQARRALAEQTPDAVVLDVMLPDGSGLELLKQLRGDHPDLPVLMLSARGEPLDRILGLELGADDYLAKPCDPRELTARLRAVLRRTHPAQPSAQMQLGDLSLNLTRGVAQIDGQEISLTLSESRILEALLRQPGEPLDKQALAQLALGRKLTLYDRSLDMHVSNLRKKLGSHPDGSPRILALRGRGYYYSH"},"dna_sequence":{"accession":"LT673656.1","fmin":"1884344","fmax":"1885022","strand":"-","sequence":"ATGAGCGAACTGCTGTTGATCGACGATGACCGGGAGCTCTGCGAGCTGCTCGGTACCTGGCTGGTCCAGGAAGGTTTCTCCGTGCGTGCCAGCCACGACGGCGCCCAGGCCCGTCGCGCCCTCGCCGAGCAGACACCGGATGCCGTGGTGCTCGACGTGATGCTGCCGGACGGTAGCGGCCTGGAACTGCTCAAGCAACTGCGCGGCGACCATCCCGACCTGCCGGTGCTGATGCTGTCCGCCCGCGGCGAGCCGCTGGACCGCATCCTCGGTCTGGAACTGGGCGCCGACGACTACCTGGCCAAGCCCTGCGACCCGCGCGAACTCACCGCACGGCTGCGCGCCGTGCTGCGGCGAACCCACCCGGCGCAACCCAGCGCGCAGATGCAACTGGGCGACCTGTCGCTGAACCTGACGCGCGGCGTGGCGCAGATCGACGGCCAGGAGATCAGCCTGACCCTTTCCGAAAGCCGCATCCTCGAAGCGCTCCTGCGCCAGCCCGGCGAGCCGCTGGACAAGCAGGCCCTGGCGCAACTGGCGCTGGGCCGCAAGCTGACCCTCTACGACCGCAGCCTGGACATGCACGTCAGCAACCTGCGCAAGAAGCTCGGCAGCCACCCCGACGGCAGCCCGCGCATCCTCGCCCTGCGCGGCCGCGGCTACTACTACAGCCACTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3004054","ARO_id":"41119","ARO_name":"Pseudomonas aeruginosa CpxR","CARD_short_name":"Paer_CpxR","ARO_description":"CpxR is directly involved in activation of expression of RND efflux pump MexAB-OprM in P. aeruginosa. CpxR is required to enhance mexAB-oprM expression and drug resistance, in the absence of repressor MexR.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"35979":{"category_aro_accession":"0000062","category_aro_cvterm_id":"35979","category_aro_name":"ceftriaxone","category_aro_description":"Ceftriaxone is a third-generation cephalosporin antibiotic. The presence of an aminothiazolyl sidechain increases ceftriazone's resistance to beta-lactamases. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"35990":{"category_aro_accession":"0000073","category_aro_cvterm_id":"35990","category_aro_name":"meropenem","category_aro_description":"Meropenem is an ultra-broad spectrum injectable antibiotic used to treat a wide variety of infections, including meningitis and pneumonia. It is a beta-lactam and belongs to the subgroup of carbapenem, similar to imipenem and ertapenem.","category_aro_class_name":"Antibiotic"},"36250":{"category_aro_accession":"3000111","category_aro_cvterm_id":"36250","category_aro_name":"novobiocin","category_aro_description":"Novobiocin is an aminocoumarin antibiotic produced by Streptomyces spheroides and Streptomyces niveus, and binds DNA gyrase subunit B inhibiting ATP-dependent DNA supercoiling.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36468":{"category_aro_accession":"3000329","category_aro_cvterm_id":"36468","category_aro_name":"sulfamethoxazole","category_aro_description":"Sulfamethoxazole is a sulfonamide antibiotic usually taken with trimethoprim, a diaminopyrimidine antibiotic. Sulfamethoxazole inhibits dihydropteroate synthase, essential to tetrahydrofolic acid biosynthesis. This pathway generates compounds used in the synthesis of many amino acids and nucleotides.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36689":{"category_aro_accession":"3000550","category_aro_cvterm_id":"36689","category_aro_name":"aztreonam","category_aro_description":"Aztreonam was the first monobactam discovered, and is greatly effective against Gram-negative bacteria while inactive against Gram-positive bacteria. Artreonam is a poor substrate for beta-lactamases, and may even act as an inhibitor. In Gram-negative bacteria, Aztreonam interferes with filamentation, inhibiting cell division and leading to cell death.","category_aro_class_name":"Antibiotic"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"40362":{"category_aro_accession":"3003708","category_aro_cvterm_id":"40362","category_aro_name":"panipenem","category_aro_description":"Panipenem is a carbapenem antibacterial agent with a broad spectrum of in vitro activity covering a wide range of Gram-negative and Gram-positive aerobic and anaerobic bacterial.  It is used in combination with betamipron to inhibit panipenem uptake into the renal tubule and prevent nephrotoxicity.","category_aro_class_name":"Antibiotic"},"40957":{"category_aro_accession":"3004024","category_aro_cvterm_id":"40957","category_aro_name":"trimethoprim-sulfamethoxazole","category_aro_description":"An antibiotic cocktail containing the diaminopyrimidine antibiotic Trimethoprim and the sulfonamide antibiotic sulfamethoxazole (1 TMP:5 SMX).","category_aro_class_name":"Antibiotic"},"46133":{"category_aro_accession":"3007382","category_aro_cvterm_id":"46133","category_aro_name":"gentamicin","category_aro_description":"Gentamicin is a commonly used aminoglycoside antibiotic derived from members of the Micromonospora genus of bacteria. It acts by binding the 30S ribosomal subunit, thus inhibiting protein synthesis. Gentamicin is typically used to treat Gram-negative infections of the repiratory and urinary tract, as well as infections of the bone and soft tissue. It also exhibits considerable nephrotoxicity and ototoxicity. Gentamicin is administered as a mixture of gentamicin type C (which makes about around 80% of the complex) and types A, B, and X (distributed in the remaining 20% of the complex).","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36242":{"category_aro_accession":"3000103","category_aro_cvterm_id":"36242","category_aro_name":"aminocoumarin antibiotic","category_aro_description":"Aminocoumarin antibiotics bind DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling.","category_aro_class_name":"Drug Class"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"36421":{"category_aro_accession":"3000282","category_aro_cvterm_id":"36421","category_aro_name":"sulfonamide antibiotic","category_aro_description":"Sulfonamides are broad spectrum, synthetic antibiotics that contain the sulfonamide group. Sulfonamides inhibit dihydropteroate synthase, which catalyzes the conversion of p-aminobenzoic acid to dihydropteroic acid as part of the tetrahydrofolic acid biosynthetic pathway. Tetrahydrofolic acid is essential for folate synthesis, a precursor of many nucleotides and amino acids. Many sulfamides are taken with trimethoprim, an inhibitor of dihydrofolate reductase, also disturbing the trihydrofolic acid synthesis pathway.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"3489":{"model_id":"3489","model_name":"OXA-404","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"5684":{"protein_sequence":{"accession":"AIM47096.1","sequence":"MNIKTLLLITSAILISACSPYIVTANPPHSASKSDEKAEKIKNLFNEVHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"KJ920338.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAACACTCTTACTTATAACAAGCGCTATTCTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCACCTCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGTACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001595","ARO_id":"37995","ARO_name":"OXA-404","CARD_short_name":"OXA-404","ARO_description":"OXA-404 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3515":{"model_id":"3515","model_name":"OXA-446","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"5710":{"protein_sequence":{"accession":"AKI29907.1","sequence":"MRNFIVFILFLNIAIGEDKILGNFFKDCNTSGTFIVFDGKNYASNDFQRAKQAFSPASTFKIFNALIALDNGVVRDTKEIFYHYKGEKVFLPSWKQDASLSSAIKRSQVPAFKELARKIGLKTMQEGLNKLSYGNTKISKIDTFWLDNSLQISAKNQADLLFKLSQNSLPFSKKSQEEVKEIILFKEDKIQKIYAKTGFNDNINLAWIVGFVKTENKILSFALNIDIKDIKNIKIREELLEKYLAIITN"},"dna_sequence":{"accession":"KR061495.1","fmin":"0","fmax":"750","strand":"+","sequence":"ATGAGAAATTTTATTGTATTTATATTGTTTTTGAATATAGCCATTGGAGAGGATAAAATACTTGGTAATTTTTTTAAAGATTGTAATACAAGTGGGACTTTTATAGTCTTTGATGGAAAAAATTATGCAAGTAATGATTTTCAAAGAGCTAAACAAGCCTTTTCTCCTGCTTCAACTTTTAAAATTTTTAATGCTTTAATTGCACTTGATAATGGTGTAGTTAGAGATACAAAGGAAATTTTCTATCATTATAAGGGTGAAAAAGTATTTTTGCCCTCTTGGAAACAAGATGCTAGTTTAAGCTCAGCCATAAAACGCTCTCAAGTGCCTGCTTTTAAAGAATTGGCAAGAAAAATAGGACTTAAAACCATGCAAGAAGGCTTAAATAAACTTTCTTATGGAAATACAAAAATTTCAAAAATCGATACCTTTTGGCTCGATAATTCTTTACAAATTTCTGCAAAAAATCAAGCTGATTTGCTTTTTAAACTTTCGCAAAATTCTTTACCTTTTTCCAAAAAAAGTCAAGAAGAAGTTAAAGAAATTATTCTTTTTAAGGAAGATAAAATCCAAAAAATTTATGCTAAAACAGGTTTTAATGATAATATCAATTTAGCTTGGATTGTTGGATTTGTAAAGACTGAAAACAAAATTTTATCTTTTGCTTTAAATATTGATATAAAGGACATTAAAAATATTAAAATAAGGGAAGAATTGCTAGAAAAATATCTAGCAATCATAACAAATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36772","NCBI_taxonomy_name":"Campylobacter jejuni","NCBI_taxonomy_id":"197"}}}},"ARO_accession":"3003602","ARO_id":"40212","ARO_name":"OXA-446","CARD_short_name":"OXA-446","ARO_description":"OXA-446 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46491":{"category_aro_accession":"3007702","category_aro_cvterm_id":"46491","category_aro_name":"OXA-184-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-184.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3545":{"model_id":"3545","model_name":"OXA-484","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"5740":{"protein_sequence":{"accession":"ALI16502.1","sequence":"MRVLALSAVFLVASIIGMPAVAKEWQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGQTRDIAAWNRDHDLITAMKYSVVPVYQEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISATQQIAFLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYSTGIEPKIGWWVGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP"},"dna_sequence":{"accession":"KR401105.1","fmin":"0","fmax":"798","strand":"+","sequence":"ATGCGTGTATTAGCCTTATCGGCTGTGTTTTTGGTGGCATCGATTATCGGAATGCCAGCGGTAGCAAAGGAATGGCAAGAAAACAAAAGTTGGAATGCTCACTTTACTGAACATAAATCACAGGGCGTAGTTGTGCTCTGGAATGAGAATAAGCAGCAAGGATTTACCAATAATCTTAAACGGGCGAACCAAGCATTTTTACCCGCATCTACCTTTAAAATTCCCAATAGCTTGATCGCCCTCGATTTGGGCGTGGTTAAGGATGAACACCAAGTCTTTAAGTGGGATGGACAGACGCGTGATATCGCCGCTTGGAATCGTGACCATGACTTAATTACCGCGATGAAGTACTCAGTTGTGCCTGTTTATCAAGAATTTGCCCGCCAAATTGGTGAGGCACGTATGAGTAAAATGCTGCACGCCTTCGATTATGGCAATGAGGATATCTCGGGCAATGTAGACAGTTTTTGGCTCGATGGTGGTATTCGCATTTCGGCTACCCAGCAAATCGCTTTTTTACGCAAGCTGTATCACAACAAGCTGCACGTTTCTGAGCGTAGTCAGCGCATCGTGAAACAAGCCATGCTGACCGAAGCCAATGGCGACTATATTATTCGGGCTAAAACGGGATACTCGACTGGAATCGAACCTAAGATTGGCTGGTGGGTTGGTTGGGTTGAACTTGATGATAATGTGTGGTTTTTTGCGATGAATATGGATATGCCCACATCGGATGGTTTAGGGCTGCGCCAAGCCATCACAAAAGAAGTGCTCAAACAGGAGAAAATTATTCCCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3003641","ARO_id":"40251","ARO_name":"OXA-484","CARD_short_name":"OXA-484","ARO_description":"OXA-484 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46510":{"category_aro_accession":"3007721","category_aro_cvterm_id":"46510","category_aro_name":"OXA-48-like beta-lactamase","category_aro_description":"OXA-48-type beta-lactamases are now routinely encountered in bacterial infections caused by carbapenam-resistant Enterobacterales. OXA-48-like proteins confer resistance to penicillin (which is efficiently hydrolyzed) and carbapenam antibiotics (which is more slowly broken down). The spectrum of activity of these variants varies, with some hydrolyzing expanded-spectrum oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3589":{"model_id":"3589","model_name":"FONA-5","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"5787":{"protein_sequence":{"accession":"CAB61643.1","sequence":"MVRNTLRQTTLMVATVMPLLFGSAPLWAQPANAKANIQQQLSELEKNSGGRLGVALIDTADNSQILYRGDERFPMCSTSKVMAVSALLKQSETDKNLLAKRMEIKQSDLVNYNPIAEKHLDTGMTLAEFSAATIQYSDNTAMNKILEHLGGPAKVTEFARTIGDKTFRLDRTEPTLNTAIPGDKRDTTSPQAMAISLQNLTLGKALAEPQRAQLVEWMKGNTTGGASIRAGLPTTWVVGDKTGSGDYGTTNDIAVIWPANHAPLVLVTYFTQPQQNAEARKDVLAAAAKIVTEGL"},"dna_sequence":{"accession":"AJ251243.1","fmin":"1053","fmax":"1941","strand":"+","sequence":"ATGGTTAGAAATACATTACGTCAAACCACCCTGATGGTCGCTACGGTTATGCCGTTGCTGTTCGGTAGCGCACCGTTATGGGCGCAACCCGCTAATGCCAAGGCCAATATTCAGCAGCAACTGTCTGAACTGGAGAAAAACTCCGGTGGCCGCCTGGGCGTGGCGCTGATCGATACCGCCGATAATTCGCAGATCCTGTATCGTGGGGATGAACGTTTTCCCATGTGCAGCACCAGCAAGGTGATGGCAGTGTCGGCGTTGTTAAAACAGAGCGAGACGGATAAAAATCTTTTGGCTAAGCGGATGGAGATCAAACAATCCGATCTGGTCAACTACAACCCGATCGCCGAAAAACACCTGGATACCGGGATGACCCTGGCCGAGTTCAGCGCCGCCACTATCCAGTACAGTGACAACACGGCGATGAACAAGATCCTTGAGCATCTTGGCGGCCCGGCAAAAGTGACAGAATTTGCGCGTACTATCGGCGATAAAACCTTCCGTCTCGATCGTACCGAACCCACTTTAAATACCGCCATCCCGGGTGATAAGCGTGACACCACCTCGCCGCAGGCGATGGCAATAAGCCTGCAAAACCTGACCTTGGGCAAAGCGCTTGCTGAACCACAGCGTGCTCAACTGGTTGAATGGATGAAGGGGAATACTACCGGCGGAGCCAGCATTCGCGCAGGTCTGCCAACCACGTGGGTGGTCGGTGATAAAACCGGCAGCGGTGATTACGGTACCACTAACGATATCGCCGTGATTTGGCCAGCTAACCACGCACCGTTGGTGTTGGTGACCTATTTCACGCAGCCACAGCAGAATGCCGAAGCCCGCAAAGACGTGTTGGCTGCGGCTGCTAAAATTGTCACCGAAGGGCTTTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39675","NCBI_taxonomy_name":"Serratia fonticola","NCBI_taxonomy_id":"47917"}}}},"ARO_accession":"3004792","ARO_id":"42910","ARO_name":"FONA-5","CARD_short_name":"FONA-5","ARO_description":"FONA-5 is a class A beta-lactamase gene found in Serratia fonticola.","ARO_category":{"42905":{"category_aro_accession":"3004787","category_aro_cvterm_id":"42905","category_aro_name":"FONA beta-lactamase","category_aro_description":"FONA is a class A beta-lactamase gene family found in Serratia fonticola.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3597":{"model_id":"3597","model_name":"GOB-11","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"5795":{"protein_sequence":{"accession":"AAT68578.1","sequence":"MRNFATLFFLSACLSLSLNAQVVKEPENMPKEWNQTYEPFRIAGNLYYVGTYDLASYLIVTDKGNILINTGTAESLTIIKGNIQKLGFNYKDIKVLLLTQAHYDHTGALEDFKTETGAKFYADKADADVLKTGGKSDYELGKYGVTFKPITPDRTLKDQDKITLGNTTLTLLHHPGHTKGSCSFIFETKDEKRKYRVLIANMPSIIVDKKFSEVAAYPNIQSDYAYTFGAMKKLDFDLWVASHASQFDLHEKRKEGDPYNPQLFMDKQSYFQNLNDLEKSYLDKIKKDSQDK"},"dna_sequence":{"accession":"AY647248.1","fmin":"0","fmax":"879","strand":"+","sequence":"ATGAGAAATTTTGCTACACTGTTTTTTTTATCAGCTTGTTTGAGTTTAAGTTTGAATGCTCAGGTAGTAAAAGAACCTGAGAATATGCCTAAAGAATGGAATCAGACTTATGAACCATTCAGAATTGCAGGGAACCTATATTACGTAGGAACCTATGATTTGGCTTCTTACCTTATTGTGACAGACAAAGGCAATATTCTTATTAATACAGGAACAGCAGAATCGCTTACAATAATAAAAGGCAATATTCAAAAGCTGGGGTTTAATTATAAAGACATTAAGGTCTTGCTGCTTACCCAGGCTCATTATGACCATACAGGTGCGTTAGAGGATTTTAAAACAGAAACCGGTGCAAAATTCTATGCAGATAAAGCAGATGCTGATGTCCTGAAAACAGGGGGGAAGTCCGATTATGAATTGGGAAAATATGGTGTGACATTTAAACCTATTACTCCGGATAGAACGTTAAAAGATCAGGATAAAATAACACTGGGAAATACAACCCTGACTTTGCTTCATCACCCGGGACATACAAAAGGTTCCTGCAGTTTTATTTTTGAAACAAAAGACGAGAAGAGAAAGTATAGAGTTCTGATAGCTAATATGCCCTCTATTATTGTTGATAAGAAATTTTCTGAAGTTGCAGCATATCCGAATATTCAGTCCGATTATGCTTATACCTTTGGTGCAATGAAAAAGCTTGATTTTGACCTTTGGGTGGCATCGCATGCAAGTCAGTTCGATCTGCATGAAAAACGTAAAGAAGGAGATCCATACAATCCACAATTGTTTATGGATAAGCAAAGCTATTTCCAAAACCTTAATGATTTGGAGAAAAGCTATCTCGACAAAATAAAAAAAGATTCCCAAGATAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36960","NCBI_taxonomy_name":"Elizabethkingia meningoseptica","NCBI_taxonomy_id":"238"}}}},"ARO_accession":"3004803","ARO_id":"42923","ARO_name":"GOB-11","CARD_short_name":"GOB-11","ARO_description":"GOB-11 is a class B beta-lactamase gene found in Chryseobacterium meningosepticum.","ARO_category":{"41376":{"category_aro_accession":"3004212","category_aro_cvterm_id":"41376","category_aro_name":"GOB beta-lactamase","category_aro_description":"The GOB family of beta-lactamases have been discovered in the Elizabethkingia meningoseptica and are classified as subclass B3 beta-lactamase. They confer resistance to cephalosporins, penicillins, and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3644":{"model_id":"3644","model_name":"LEN-55","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"5916":{"protein_sequence":{"accession":"OZM21578.1","sequence":"MRYVRLCVISLLATLPLAVDAGPQPLEQIKQSESQLSGRVGMVEMDLASGRTLAAWRADERFPMVSTFKVLLCGAVLARVDAGLEQLDRRIHYRQQDLVDYSPVSEKHLVDGMTIGELCAAAITLSDNSAGNLLLATVGGPAGLTAFLRQIGDNVTRLDRWETALNEALPGDARDTTTPASMAATLRKLLTAQHLSARSQQQLLQWMVDDRVAGPLIRAVLPPGWFIADKTGAGERGARGIVALLGPDGKPERIVVIYLRDTPASMAERNQHIAGIGAALIEHWQR"},"dna_sequence":{"accession":"NLDD01000006.1","fmin":"119723","fmax":"120584","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGTGTTATCTCCCTGTTAGCCACCCTGCCACTGGCGGTAGACGCCGGTCCACAGCCGCTTGAGCAGATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTGGGGATGGTGGAAATGGATCTGGCCAGCGGCCGCACGCTGGCGGCCTGGCGCGCCGATGAACGCTTTCCCATGGTGAGCACCTTTAAAGTGCTGCTGTGCGGCGCGGTGCTGGCGCGGGTGGATGCCGGGCTCGAACAACTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGTCGACGGGATGACGATCGGCGAACTCTGCGCCGCCGCCATCACCCTGAGCGATAACAGCGCTGGCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCGGGATTAACTGCCTTTCTGCGCCAGATCGGTGACAACGTCACCCGTCTTGACCGCTGGGAAACGGCACTGAATGAGGCGCTTCCCGGCGACGCGCGCGACACCACCACCCCGGCCAGCATGGCCGCCACGCTGCGCAAACTACTGACCGCGCAGCATCTGAGCGCCCGTTCGCAACAGCAACTCCTGCAGTGGATGGTGGACGATCGGGTTGCCGGCCCGCTGATCCGCGCCGTGCTGCCGCCGGGCTGGTTTATCGCCGACAAAACCGGGGCTGGCGAACGGGGTGCGCGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAACCGGAGCGCATTGTGGTGATCTATCTGCGGGATACCCCGGCGAGTATGGCCGAGCGTAATCAACATATCGCCGGGATCGGCGCAGCGCTGATAGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42612","NCBI_taxonomy_name":"Klebsiella variicola","NCBI_taxonomy_id":"244366"}}}},"ARO_accession":"3004848","ARO_id":"42984","ARO_name":"LEN-55","CARD_short_name":"LEN-55","ARO_description":"A class-A broad-spectrum beta-lactamase from Klebsiella.","ARO_category":{"36236":{"category_aro_accession":"3000097","category_aro_cvterm_id":"36236","category_aro_name":"LEN beta-lactamase","category_aro_description":"LEN beta-lactamases are chromosomal class A beta-lactamases that confer resistance to ampicillin, amoxicillin, carbenicillin, and ticarcillin but not to extended-spectrum beta-lactams.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3729":{"model_id":"3729","model_name":"Mycobacterium tuberculosis mshC mutations conferring resistance to isoniazid","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"9566":"A403G"},"ReSeqTB-High":{"9566":"A403G"},"clinical":{"9566":"A403G"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"775"}},"model_sequences":{"sequence":{"8839":{"protein_sequence":{"accession":"NP_216646.1","sequence":"MQSWYCPPVPVLPGRGPQLRLYDSADRQVRPVAPGSKATMYVCGITPYDATHLGHAATYVTFDLIHRLWLDLGHELHYVQNITDIDDPLFERADRDGVDWRDLAQAEVALFCEDMAALRVLPPQDYVGATEAIAEMVELIEKMLACGAAYVIDREMGEYQDIYFRADATLQFGYESGYDRDTMLRLCEERGGDPRRPGKSDELDALLWRAARPGEPSWPSPFGPGRPGWHVECAAIALSRIGSGLDIQGGGSDLIFPHHEFTAAHAECVSGERRFARHYVHAGMIGWDGHKMSKSRGNLVLVSALRAQDVEPSAVRLGLLAGHYRADRFWSQQVLDEATARLHRWRTATALPAGPAAVDVVARVRRYLADDLDTPKAIAALDGWVTDAVEYGGHDAGAPKLVATAIDALLGVDL"},"dna_sequence":{"accession":"NC_000962.3","fmin":"2391214","fmax":"2392459","strand":"-","sequence":"ATGCAGTCGTGGTATTGCCCACCGGTTCCGGTGTTGCCGGGACGAGGCCCGCAGCTACGGCTGTACGACAGCGCCGACCGGCAGGTCCGTCCGGTGGCGCCCGGATCTAAGGCCACCATGTACGTCTGCGGGATCACGCCCTACGACGCCACGCATCTGGGCCATGCTGCCACCTATGTGACGTTCGACCTGATCCATCGGCTGTGGCTGGATCTCGGTCATGAATTGCACTATGTCCAGAACATCACCGACATCGACGATCCACTATTTGAGCGCGCGGATCGCGACGGTGTCGACTGGCGTGACCTTGCCCAAGCCGAGGTCGCCCTGTTCTGTGAGGACATGGCGGCGCTGCGGGTGCTACCACCGCAAGACTACGTGGGGGCCACCGAAGCGATTGCTGAAATGGTCGAGCTCATCGAAAAAATGCTGGCGTGCGGGGCGGCCTATGTCATAGACCGGGAAATGGGAGAGTACCAGGACATCTACTTCCGCGCTGACGCCACCCTGCAGTTCGGCTACGAGTCAGGGTATGACCGTGACACCATGCTGCGGCTGTGCGAGGAACGTGGCGGCGATCCGCGGCGCCCCGGCAAGAGCGACGAACTCGACGCGTTGTTGTGGCGGGCCGCGCGGCCCGGTGAGCCCAGCTGGCCGTCCCCGTTCGGGCCTGGCCGGCCAGGCTGGCATGTCGAGTGCGCAGCCATCGCGCTCAGTCGTATCGGAAGCGGCCTCGACATCCAGGGCGGTGGTAGCGATCTGATCTTTCCGCACCACGAGTTCACCGCTGCGCACGCCGAATGTGTCAGCGGCGAACGGCGATTCGCGCGGCACTACGTGCATGCCGGGATGATCGGCTGGGACGGGCACAAGATGTCAAAGAGCCGCGGCAACCTCGTGCTGGTGTCGGCGCTGCGTGCGCAGGACGTTGAGCCATCGGCGGTTCGGCTGGGTTTGCTCGCCGGACACTACCGAGCCGATCGGTTCTGGAGCCAGCAGGTGCTTGACGAGGCGACCGCCCGGCTGCACCGTTGGCGCACCGCAACCGCACTTCCCGCCGGTCCGGCCGCAGTTGACGTTGTCGCTCGGGTGCGCCGCTACCTGGCCGACGATCTCGATACGCCCAAAGCGATTGCCGCACTGGATGGTTGGGTCACCGATGCGGTGGAGTACGGCGGCCACGATGCCGGGGCGCCGAAGTTGGTGGCGACGGCGATCGATGCCCTGCTCGGGGTGGACCTGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3004927","ARO_id":"43113","ARO_name":"Mycobacterium tuberculosis mshC mutations conferring resistance to isoniazid","CARD_short_name":"Mtub_mshC_INH","ARO_description":"Mutations that occur in mshC that result in or contribute to antibiotic resistance to isoniazid.","ARO_category":{"43090":{"category_aro_accession":"3004904","category_aro_cvterm_id":"43090","category_aro_name":"isoniazid resistant mshC","category_aro_description":"Mutations that occur on the mshC gene resulting in the inability for isoniazid to function. It catalyzes the ATP-dependent condensation of GlcN-Ins and L-cysteine to form L-Cys-GlcN-Ins.","category_aro_class_name":"AMR Gene Family"},"36659":{"category_aro_accession":"3000520","category_aro_cvterm_id":"36659","category_aro_name":"isoniazid","category_aro_description":"Isoniazid is an organic compound that is the first-line anti tuberculosis medication in prevention and treatment. As a prodrug, it is activated by mycobacterial catalase-peroxidases such as M. tuberculosis KatG. Isoniazid inhibits mycolic acid synthesis, which prevents cell wall synthesis in mycobacteria.","category_aro_class_name":"Antibiotic"},"45734":{"category_aro_accession":"3007152","category_aro_cvterm_id":"45734","category_aro_name":"isoniazid-like antibiotic","category_aro_description":"A group of antibiotics containing isoniazid and its derivatives.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2646":{"model_id":"2646","model_name":"tetB(60)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1100"}},"model_sequences":{"sequence":{"3979":{"protein_sequence":{"accession":"ANZ79241.1","sequence":"MRTMKRLLSYLRYEKKGVLIGLFCLLLSTGATLTGPLVAKHIIDNVITPMGQAHDFKAGGLLLWVGIYVTVNLVGVAGAYLNRVYMKTLSNRIAKRIRDEVFEHVQTLPVSYFDHLPAGKVVSRITSDTESVRANFYVSGISTLFSTIVMLVGVYITIFLLNATLGLVLLFLVPVMILWQRTVATKQKKYYSENRELYSQLSGQLNESIQGAGIVQAFQQEEKIVAEYDATATSWVEVGRKELILESYFSWSLVGMLRNITHFGVIYYFSMQFIGGTLGISAGLLYAFIDYINRIYEPIQTFMNVVSGFQQSMAAGDRVFELMDTPSEESGEELFTFDEGCIEFKDVSFEYTAGVPVLKHLNFTVEPGQTVAFVGHTGSGKSSIMNLLFRFYDPTSGAIFIDGKNTRDFNRRSVRSEMGIVLQDPYLFTGTIASNVGLNNESIEPETIKEAIIKVGGGHLLTKSDKGLDYEVKEKGMDFSSGERQLISFARAIVFDPKILILDEATSHIDTETEEIIQNAINVVKEGRTTFMIAHRLSTIAHADQIFVLDKGEIVERGTHDELLQLQGQYAEMVALQKG"},"dna_sequence":{"accession":"KX000273.1","fmin":"0","fmax":"1740","strand":"+","sequence":"ATGAGAACGATGAAGCGATTATTAAGCTACCTCCGTTATGAGAAAAAAGGAGTTCTGATTGGACTCTTCTGCCTGTTACTCTCAACAGGAGCAACCTTAACAGGGCCACTCGTTGCGAAACACATTATCGATAATGTGATTACTCCGATGGGGCAGGCGCATGATTTCAAAGCAGGTGGCCTACTTTTATGGGTTGGTATTTACGTGACAGTGAACTTAGTGGGAGTTGCTGGGGCCTATTTAAACCGTGTATATATGAAGACTCTCTCAAACCGTATTGCAAAACGCATTCGTGACGAAGTGTTCGAGCATGTACAAACCTTGCCGGTATCGTACTTCGACCATTTACCAGCTGGGAAAGTGGTTTCTAGAATTACAAGTGATACAGAATCAGTGCGTGCAAACTTCTACGTGAGTGGGATTTCGACGCTTTTCAGTACGATTGTGATGTTGGTAGGTGTTTATATAACCATTTTCTTATTAAACGCAACGCTAGGACTCGTATTATTATTCCTAGTTCCTGTGATGATTCTATGGCAGAGAACCGTTGCTACGAAGCAGAAAAAATACTATTCCGAAAATCGTGAACTCTATAGTCAGTTGAGTGGACAATTAAACGAAAGCATTCAAGGAGCAGGCATCGTTCAAGCCTTCCAGCAAGAAGAAAAAATTGTTGCAGAATATGATGCCACGGCAACTTCTTGGGTAGAAGTTGGTCGTAAGGAATTAATTCTTGAGTCGTACTTCTCGTGGAGTCTTGTCGGCATGCTTCGAAACATTACTCATTTTGGAGTTATCTATTATTTCAGTATGCAGTTTATCGGTGGAACACTCGGGATTTCAGCAGGTCTTTTATATGCATTTATTGACTACATTAATCGTATATATGAGCCGATTCAAACTTTTATGAATGTCGTGTCTGGCTTCCAGCAATCAATGGCTGCTGGTGACCGTGTGTTTGAACTAATGGATACACCGAGCGAGGAATCGGGAGAAGAGCTCTTCACGTTTGATGAAGGATGTATCGAATTTAAAGATGTGAGTTTTGAGTACACAGCGGGAGTTCCTGTGTTGAAACACTTGAATTTCACGGTAGAACCAGGACAGACGGTTGCTTTTGTCGGACATACTGGTTCAGGGAAATCATCCATTATGAACTTACTGTTTCGCTTCTACGACCCAACGAGTGGTGCTATCTTCATCGATGGCAAAAACACACGCGACTTTAACAGACGTAGTGTTCGAAGCGAGATGGGAATCGTTCTTCAAGATCCGTACCTCTTTACAGGAACGATTGCTTCAAACGTAGGGCTCAACAATGAATCGATTGAGCCTGAGACGATAAAAGAGGCGATTATTAAAGTGGGTGGAGGACATCTACTTACGAAGAGTGACAAGGGCTTGGACTACGAGGTGAAAGAAAAAGGAATGGATTTCTCTTCAGGAGAACGCCAACTGATTTCATTTGCTCGTGCGATCGTCTTTGACCCGAAAATCTTAATTTTAGACGAGGCAACTTCGCATATCGATACCGAGACAGAAGAGATTATTCAGAATGCAATTAATGTCGTCAAAGAAGGGCGTACAACCTTTATGATTGCTCACCGACTTTCCACAATTGCTCATGCTGACCAAATTTTTGTGTTGGATAAAGGAGAAATTGTAGAACGTGGAACGCATGATGAATTGCTTCAACTGCAAGGTCAATATGCCGAAATGGTCGCCCTACAAAAAGGATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36791","NCBI_taxonomy_name":"uncultured bacterium","NCBI_taxonomy_id":"77133"}}}},"ARO_accession":"3004036","ARO_id":"41069","ARO_name":"tetB(60)","CARD_short_name":"tetB(60)","ARO_description":"tetB(60) is a subunit of tetAB(60), an ABC transporter that confers resistance to tetracycline and tigercycline identified by screening a human saliva metagenomic library in Escherichia coli, which is required for resistance.","ARO_category":{"36002":{"category_aro_accession":"0010001","category_aro_cvterm_id":"36002","category_aro_name":"ATP-binding cassette (ABC) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding\/hydrolysis to transport substrates across cell membranes.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2643":{"model_id":"2643","model_name":"tetA(46)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1100"}},"model_sequences":{"sequence":{"3976":{"protein_sequence":{"accession":"AET10444.1","sequence":"MIRAIWEYIRERKWRYVKIAMVLILYDYTLLIPTQVIQRLVDHLSQQTLTQSNFVWDMVLLVGSAILNYLTAFYWQLRLFQSSVHFKATLQGQAFRKLVAMRRPFFEKFRSGDLLTRFTTDVDGMADMAGYGMMVLLFGGGLFAFIIPTMFFISWQLTLISFIPMIFLVVSTYFLSRKQEEYVEQNREAVAQLNDEVLESIEGIRVMRAYSRRDQQVKQFQKKTASLSKTGDKIASIQYSFGPLALLFIGFSTVLLLLFGGQSLASGQLSLGKLLALQLYLVFLIEPMWMMTDLILVYQTGQMSYKKLKEVIDETDDLEPDGTHYLEQIDSVEFKDYSFSYPGAERKSLSGIDWTIQRGQTVGIVGRTGAGKTTLVRQFLRQYPVGEGEFLVNQQPIVDYNRHSIEEKIGYVSQEHILFSKSIRENIALGKKGASQEDLMEAVAQAAFADDLERMSHGMDTLIGEKGVSVSGGQKQRISLARAFLRDADLLLLDDSLSAVDAKTEQAIIDTIQKERKDKTTIIVSHRLSAVHQADWIIVLDQGQIVEEGRASDLLAQEGWYYEQYQRQQKQEGE"},"dna_sequence":{"accession":"HQ652506.1","fmin":"373","fmax":"2098","strand":"+","sequence":"ATGATCAGAGCTATTTGGGAGTATATCAGGGAGCGCAAGTGGCGATATGTGAAGATCGCTATGGTACTGATTCTTTATGATTACACTTTATTGATCCCGACGCAAGTCATTCAGCGCTTAGTGGATCATTTGAGTCAGCAGACGCTGACGCAATCGAACTTTGTATGGGATATGGTCCTCTTGGTGGGATCAGCCATCCTCAATTACCTGACGGCTTTTTATTGGCAGTTGCGACTCTTTCAGTCGTCAGTCCATTTCAAGGCGACCCTTCAGGGACAAGCTTTTCGTAAGCTAGTAGCTATGCGGCGTCCCTTTTTTGAGAAATTTCGCTCAGGGGACCTCTTGACGCGCTTTACGACGGATGTGGATGGCATGGCCGATATGGCTGGTTACGGGATGATGGTGCTCCTGTTTGGCGGTGGCTTGTTTGCCTTTATTATTCCGACCATGTTTTTCATTTCTTGGCAATTAACCTTGATTTCCTTTATTCCCATGATCTTCCTTGTCGTCTCTACCTATTTTTTGAGTAGAAAGCAGGAGGAGTATGTTGAGCAAAACCGGGAAGCGGTTGCTCAGTTGAACGATGAAGTCTTGGAGTCCATCGAAGGGATCCGGGTCATGCGGGCCTATAGTAGACGGGATCAGCAGGTCAAACAGTTTCAGAAGAAAACGGCTAGTCTATCCAAAACAGGGGACAAAATTGCTTCTATCCAATATTCTTTTGGCCCCTTAGCCCTGTTGTTTATTGGATTCTCGACAGTCTTGCTCCTGCTATTTGGAGGACAGTCCCTAGCAAGTGGGCAGTTGAGCCTTGGCAAGCTATTGGCCTTGCAACTGTATTTGGTCTTTTTAATTGAGCCTATGTGGATGATGACGGACCTGATCTTGGTCTATCAGACAGGGCAAATGTCCTATAAAAAACTAAAAGAAGTGATTGATGAGACAGATGATCTTGAGCCAGATGGTACACACTATTTAGAGCAGATCGATTCGGTAGAGTTTAAGGATTATTCCTTCAGTTATCCTGGTGCTGAGCGAAAGAGCCTATCAGGCATTGATTGGACTATCCAGCGAGGACAGACGGTTGGAATTGTTGGTCGTACCGGTGCAGGAAAGACTACCCTGGTTCGACAATTCTTGCGGCAATACCCAGTTGGTGAGGGAGAATTCTTGGTCAACCAGCAACCGATCGTGGACTACAACCGACACTCGATTGAAGAAAAAATTGGTTATGTTTCCCAAGAACATATTTTATTTTCTAAGTCTATCCGTGAGAATATAGCGCTTGGTAAAAAAGGAGCCAGCCAAGAAGACTTGATGGAAGCAGTAGCCCAAGCTGCTTTTGCGGATGATCTCGAGCGGATGTCTCATGGAATGGACACCCTGATCGGTGAGAAAGGGGTCTCTGTATCAGGAGGTCAAAAACAGCGGATCTCTTTGGCGCGTGCCTTCTTAAGAGATGCAGATCTCTTGTTGTTAGATGATTCCCTTTCGGCAGTGGATGCGAAGACCGAACAGGCCATTATTGACACCATTCAAAAAGAACGAAAAGACAAGACGACCATCATTGTTTCTCATCGCTTGTCGGCTGTCCATCAGGCTGATTGGATCATCGTCTTGGATCAAGGACAGATTGTTGAAGAAGGCAGGGCTAGTGATTTATTAGCTCAAGAGGGCTGGTATTATGAACAATACCAACGGCAACAAAAACAGGAAGGAGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41065","NCBI_taxonomy_name":"Streptococcus australis","NCBI_taxonomy_id":"113107"}}}},"ARO_accession":"3004032","ARO_id":"41064","ARO_name":"tetA(46)","CARD_short_name":"tetA(46)","ARO_description":"tetA(46) is a subunit of tetAB(46), a heterodimeric ABC transporter, that is required for conferring tetracycline resistance in Streptococcus australis isolated from the oral cavity.","ARO_category":{"36002":{"category_aro_accession":"0010001","category_aro_cvterm_id":"36002","category_aro_name":"ATP-binding cassette (ABC) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding\/hydrolysis to transport substrates across cell membranes.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2644":{"model_id":"2644","model_name":"tetB(46)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1150"}},"model_sequences":{"sequence":{"3977":{"protein_sequence":{"accession":"AET10445.1","sequence":"MKVLKRLLSRITLYPTVFLAGFICLLLATIFSELSPFLLQKMIDGPLTALTHGGGQGDLLQMGGFYLLVLSLGQLISYMGNRILLHGSNQVTASLRDQAFQVMQGLPISYFDDKPAGKIATRIVNDTETLRTQFYNSCMILVIYLVRFLFILGILFYLSPMMGLLLCLVFPIFYGIQYLYKVMTDQPMKDFFDARSEVNTQVNELLHGASMIQLYHQEPGVVEEFEATTQKMLGANDRILLADSIASWTLTELLKFLVIAGILTIAGISFLQGNIGVTAGFLFININYVINLFDLMANLSRQFPNIRRSLETGSRVLAFLDQPLEADGALELKIEKAEVVFDDVQFAYEEGKPVLKDISIQAHPGQTLALVGHTGSGKSSIMNLLYRFYDPQEGEIRIDGQNIRHFSRESLRSHMGIVLQDPYLFTGTIASNVAMSQEHIDRNAVKDALKKVGAWPFVERLEKGIDHPVVEKGSAFSSGERQLISFARTLYMNPQILILDEATSHIDTETEEIIQKAMAVLQKGRTTFIIAHRLSTIQDADQILVLSEGRIVERGQHADLVAHGGIYAQMQAIQQTVE"},"dna_sequence":{"accession":"HQ652506.1","fmin":"2099","fmax":"3836","strand":"+","sequence":"ATGAAAGTATTGAAACGATTATTATCTAGGATCACGCTTTATCCAACTGTCTTTCTTGCTGGCTTCATTTGCCTCTTACTAGCCACCATTTTTTCTGAATTGTCTCCCTTTCTTCTCCAAAAGATGATCGATGGGCCTTTGACTGCATTGACCCACGGTGGAGGACAAGGGGACTTGCTTCAGATGGGAGGATTCTATCTCTTGGTCTTGAGCCTGGGGCAGCTGATTAGCTACATGGGCAATCGGATCTTGCTACATGGAAGTAATCAAGTAACCGCTAGTCTGAGAGACCAAGCCTTTCAAGTCATGCAAGGGCTGCCTATTTCTTATTTTGATGATAAGCCGGCTGGGAAGATCGCGACAAGAATTGTCAATGATACGGAGACCTTGAGGACCCAGTTTTATAACTCTTGTATGATTTTAGTCATCTATTTGGTACGCTTTCTCTTTATCCTAGGGATTCTCTTTTACCTGAGTCCTATGATGGGCCTTCTCTTGTGTTTGGTCTTTCCGATTTTCTATGGGATCCAGTATCTCTACAAGGTCATGACGGACCAGCCTATGAAGGATTTCTTTGATGCGCGAAGCGAGGTCAATACCCAGGTCAATGAACTCTTGCACGGTGCTAGTATGATTCAGCTCTATCATCAAGAGCCTGGTGTGGTGGAGGAGTTTGAAGCCACTACCCAGAAGATGTTAGGAGCAAATGATCGAATCCTCTTAGCCGATTCTATCGCTTCTTGGACCTTGACGGAATTGCTCAAGTTTTTAGTGATTGCAGGCATTTTGACTATCGCTGGGATTTCTTTCCTACAGGGTAATATCGGTGTGACGGCTGGTTTCTTATTTATCAATATTAACTATGTGATTAATCTATTTGATCTCATGGCCAATCTTAGTCGTCAATTCCCAAATATTCGGCGATCCTTAGAAACGGGGAGCCGCGTCCTTGCCTTCTTAGACCAACCGTTAGAGGCCGATGGTGCATTGGAACTGAAGATAGAAAAGGCAGAGGTCGTGTTTGACGACGTTCAATTTGCCTATGAAGAAGGTAAGCCAGTTCTGAAGGATATTTCCATCCAAGCCCATCCAGGTCAAACCCTTGCCTTGGTTGGCCATACTGGTTCGGGTAAATCCTCCATTATGAACTTGCTCTATCGTTTCTATGATCCGCAGGAGGGAGAAATTCGGATCGACGGCCAGAATATTCGCCATTTCTCTAGAGAGAGTCTTCGCTCCCACATGGGCATTGTTCTACAAGATCCTTATCTATTTACAGGAACCATTGCTAGTAATGTGGCCATGAGTCAGGAACACATTGATCGGAATGCGGTCAAAGATGCCTTGAAAAAAGTCGGAGCATGGCCCTTTGTAGAGCGTCTTGAAAAGGGAATCGACCATCCAGTTGTAGAAAAAGGATCGGCCTTTTCAAGTGGCGAACGCCAGTTGATTTCCTTTGCGAGGACGCTCTATATGAATCCGCAAATTCTGATTTTGGATGAGGCAACCTCTCACATCGATACGGAAACAGAAGAAATCATCCAGAAAGCTATGGCTGTCCTGCAAAAGGGCCGGACCACCTTTATCATTGCCCATCGCTTGTCGACTATCCAAGATGCGGATCAGATCTTGGTTCTATCAGAAGGGCGCATTGTCGAACGTGGGCAACATGCAGACTTAGTTGCCCATGGTGGCATCTACGCCCAGATGCAAGCTATCCAACAGACGGTTGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41065","NCBI_taxonomy_name":"Streptococcus australis","NCBI_taxonomy_id":"113107"}}}},"ARO_accession":"3004033","ARO_id":"41066","ARO_name":"tetB(46)","CARD_short_name":"tetB(46)","ARO_description":"tetB(46) is a subunit of tetAB(46), a heterodimeric ABC transporter, that is required for conferring tetracycline resistance in Streptococcus australis isolated from the oral cavity.","ARO_category":{"36002":{"category_aro_accession":"0010001","category_aro_cvterm_id":"36002","category_aro_name":"ATP-binding cassette (ABC) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding\/hydrolysis to transport substrates across cell membranes.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2645":{"model_id":"2645","model_name":"tetA(60)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1100"}},"model_sequences":{"sequence":{"3978":{"protein_sequence":{"accession":"ANZ79240.1","sequence":"MNDLLKVIINFIKKHPMRYLVSFILMIGSSIAAVYPARIIGQVVDKIVASELNAEWLGTQLVILVGIILVAYITESIWTYFIFIGYYEIQKELRVKLLRNNLRKKIPFYAHFRTGEIITRSSEDVTTIGDMMGFGMFALMNSTLLMSVSIYMMVTTISLPLTIAAILPLPILSYLVYKWGFDLEEEYNKAQNAVSQLNNEVLEMIDGTYVIRAYGQEDAMMDEFRAKTKKAMKQNIIVTEIESRFIPLAQLFMMISFTIALFYGGYLVSTGAILVGDVIAFQVYMGAIMWPMFMIGDIITNYKRGKVATERINEVLKHDDEIERGGTKTLETIESIEFKDFHFMYPGEEAPLLKEINLTLRKGETLGIVGKTGSGKTTLLMQLLHQFPYRGEKLLINGEPLIDYDTQSVAGHLAYVPQEHTLFSRTIRENMLFGKEDATDDEIWEALTLASFEGDVKRMPDELDTMVGEKGVSLSGGQKQRLSIARAFLRNRECLILDDALSAVDAKTEREIISHLQQERGGCMNIISAHRLSAIRHADEIIVMNEGRISERGTHEELLEQRGWYYEQYLTQEMEEEIE"},"dna_sequence":{"accession":"KX000272.1","fmin":"0","fmax":"1740","strand":"+","sequence":"ATGAACGATTTATTAAAAGTCATTATTAATTTTATAAAGAAACATCCGATGCGCTACCTTGTTAGTTTTATTTTGATGATCGGAAGTAGTATTGCGGCGGTGTACCCAGCGCGTATTATCGGACAAGTTGTTGATAAAATCGTAGCGAGCGAACTGAATGCCGAGTGGCTTGGGACACAACTCGTGATTTTAGTCGGGATTATTCTTGTGGCGTATATTACGGAGAGTATTTGGACATATTTTATTTTTATTGGGTATTATGAAATTCAAAAAGAATTACGTGTGAAGTTACTACGTAATAATTTACGGAAGAAAATTCCGTTTTATGCGCATTTTAGAACGGGCGAAATTATTACGCGTAGCAGTGAAGACGTTACAACGATTGGCGATATGATGGGGTTTGGGATGTTTGCATTGATGAACTCTACATTGCTGATGAGCGTATCGATTTATATGATGGTCACAACGATTTCATTGCCACTGACCATCGCAGCGATTTTGCCACTGCCAATCCTTTCGTATCTTGTATATAAATGGGGATTCGATTTAGAAGAAGAGTACAACAAGGCGCAAAATGCAGTTTCACAATTAAATAATGAAGTGCTTGAGATGATTGACGGGACGTATGTGATTCGTGCTTACGGGCAAGAAGATGCGATGATGGATGAGTTCAGGGCGAAAACGAAAAAGGCCATGAAACAAAATATTATCGTGACTGAAATTGAATCGCGCTTTATTCCACTGGCGCAATTATTTATGATGATTAGCTTTACCATTGCCCTTTTCTACGGTGGGTATCTAGTATCGACTGGGGCTATTCTAGTCGGGGATGTCATTGCCTTCCAAGTCTATATGGGGGCGATTATGTGGCCGATGTTTATGATTGGCGATATTATTACGAACTATAAACGCGGAAAAGTGGCGACGGAGCGTATTAATGAAGTGTTGAAACATGACGATGAAATTGAACGCGGCGGTACAAAAACGCTCGAGACGATTGAATCCATTGAGTTTAAGGACTTCCATTTTATGTATCCAGGCGAAGAGGCACCATTATTAAAAGAGATTAACCTTACGTTACGTAAAGGCGAGACGCTTGGAATCGTTGGAAAAACGGGTTCTGGGAAGACGACGCTCTTGATGCAATTATTACATCAATTTCCGTACCGAGGAGAGAAGCTGCTCATTAACGGAGAGCCATTGATTGATTACGACACTCAATCGGTGGCAGGGCATCTAGCCTATGTGCCACAAGAACACACCCTTTTCTCACGCACGATTCGCGAGAATATGTTATTCGGAAAAGAGGATGCAACGGATGATGAAATTTGGGAAGCGTTGACGCTAGCCTCTTTTGAAGGAGACGTGAAACGAATGCCAGACGAGCTCGATACGATGGTCGGAGAAAAAGGGGTATCGCTCAGTGGAGGTCAAAAACAACGCTTATCGATTGCTCGTGCTTTCTTACGCAACCGTGAATGCTTAATTTTGGATGATGCGTTATCTGCAGTTGATGCGAAAACGGAAAGGGAAATTATCTCGCACTTGCAACAAGAACGCGGAGGTTGTATGAATATCATTTCTGCGCACAGACTTTCTGCAATTCGTCATGCGGATGAAATTATTGTGATGAATGAAGGACGTATTAGTGAGAGGGGTACCCACGAGGAGCTGCTCGAACAACGAGGATGGTACTATGAACAGTATCTCACACAAGAAATGGAGGAGGAAATCGAATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36791","NCBI_taxonomy_name":"uncultured bacterium","NCBI_taxonomy_id":"77133"}}}},"ARO_accession":"3004035","ARO_id":"41068","ARO_name":"tetA(60)","CARD_short_name":"tetA(60)","ARO_description":"tetA(60) is a subunit of tetAB(60), an ABC transporter that confers resistance to tetracycline and tigercycline identified by screening a human saliva metagenomic library in Escherichia coli, which is required for resistance.","ARO_category":{"36002":{"category_aro_accession":"0010001","category_aro_cvterm_id":"36002","category_aro_name":"ATP-binding cassette (ABC) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding\/hydrolysis to transport substrates across cell membranes.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"522":{"model_id":"522","model_name":"floR","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"8160":{"protein_sequence":{"accession":"AAG16656.1","sequence":"MTTTRPAWAYTLPAALLLMAPFDILASLAMDIYLPVVPAMPGILNTTPAMIQLTLSLYMVMLGVGQVIFGPLSDRIGRRPILLAGATAFVIASLGAAWSSTAPAFVAFRLLQAVGASAMLVATFATVRDVYANRPEGVVIYGLFSSVLAFVPALGPIAGALIGEFLGWQAIFITLAILAMLALLNAGFRWHETRPLDQVKTRRSVLPIFASPAFWVYTVGFSAGMGTFFVFFSTAPRVLIGQAEYSEIGFSFAFATVALVMIVTTRFAKSFVARWGIAGCVARGMALLVCGAVLLGIGELYGSPSFLTFILPMWVVAVGIVFTVSVTANGALAEFDDIAGSAVAFYFCVQSLIVSIVGTLAVALLNGDTAWPVICYATAMAVLVSLGLVLLRLRGAATEKSPVV"},"dna_sequence":{"accession":"AF231986.2","fmin":"3307","fmax":"4522","strand":"+","sequence":"ATGACCACCACACGCCCCGCGTGGGCCTATACGCTGCCGGCAGCACTGCTGCTGATGGCTCCTTTCGACATCCTCGCTTCACTGGCGATGGATATTTATCTCCCTGTCGTTCCAGCGATGCCCGGCATCCTGAACACGACGCCCGCTATGATCCAACTCACGTTGAGCCTCTATATGGTGATGCTCGGCGTGGGCCAGGTGATTTTTGGTCCGCTCTCAGACAGAATCGGGCGACGGCCAATTCTACTTGCGGGCGCAACGGCTTTCGTCATTGCGTCTCTGGGAGCAGCTTGGTCTTCAACTGCACCGGCCTTTGTCGCTTTCCGTCTACTTCAAGCAGTGGGCGCGTCGGCCATGCTGGTGGCGACGTTCGCGACGGTTCGCGACGTTTATGCCAACCGTCCTGAGGGTGTCGTCATCTACGGCCTTTTCAGTTCGGTGCTGGCGTTCGTGCCTGCGCTCGGCCCTATCGCCGGAGCATTGATCGGCGAGTTCTTGGGATGGCAGGCGATATTCATTACTTTGGCTATACTGGCGATGCTCGCACTCCTAAATGCGGGTTTCAGGTGGCACGAAACCCGCCCTCTGGATCAAGTCAAGACGCGCCGATCTGTCTTGCCGATCTTCGCGAGTCCGGCTTTTTGGGTTTACACTGTCGGCTTTAGCGCCGGTATGGGCACCTTCTTCGTCTTCTTCTCGACGGCTCCCCGTGTGCTCATAGGCCAAGCGGAATATTCCGAGATCGGATTCAGCTTTGCCTTCGCCACTGTCGCGCTTGTAATGATCGTGACAACCCGTTTCGCGAAGTCCTTTGTCGCCAGATGGGGCATCGCAGGATGCGTGGCGCGTGGGATGGCGTTGCTTGTTTGCGGAGCGGTCCTGTTGGGGATCGGCGAACTTTACGGCTCGCCGTCATTCCTCACCTTCATCCTACCGATGTGGGTTGTCGCGGTCGGTATTGTCTTCACGGTGTCCGTTACCGCGAACGGCGCTTTGGCAGAGTTCGACGACATCGCGGGATCAGCGGTCGCGTTCTACTTCTGCGTTCAAAGCCTGATAGTCAGCATTGTCGGGACATTGGCGGTGGCACTTTTAAACGGTGACACAGCGTGGCCCGTGATCTGTTACGCCACGGCGATGGCGGTACTGGTTTCGTTGGGGCTGGTGCTCCTTCGGCTCCGTGGGGCTGCCACCGAGAAGTCGCCAGTCGTCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002705","ARO_id":"39139","ARO_name":"floR","CARD_short_name":"floR","ARO_description":"floR is a plasmid or chromosome-encoded chloramphenicol exporter that is found in Bordetella bronchiseptica, Escherichia coli, Klebsiella pneumoniae, Salmonella enterica subsp. enterica serovar Typhimurium str. DT104 and Vibrio cholerae.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36600":{"category_aro_accession":"3000461","category_aro_cvterm_id":"36600","category_aro_name":"florfenicol","category_aro_description":"Florfenicol is a fluorine derivative of chloramphenicol, where the nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3) and the hydroxyl group (-OH), by a fluorine group (-F). The action mechanism is the same as chloramphenicol's, where the antibiotic binds to the 23S RNA of the 50S subunit of bacterial ribosomes to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2716":{"model_id":"2716","model_name":"OpmB","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"850"}},"model_sequences":{"sequence":{"5207":{"protein_sequence":{"accession":"AAG05913.1","sequence":"MKHTPSLLALALVAALGGCAIGPDYQRPDLAVPAEFKEAEGWRRAEPRDVFQRGAWWELYGDQTLNDLQMHLERSNQTLAQSVAQFRQAEALVRGARAAFFPSITGNVGKTRSGQGGGDSTVLLPGGSTVSSGGSGAISTSYSTNLSVSWEVDLWGKLRRQLEANQASLHASAADLAAVRLSQQSQLAQNYLQLRVMDEQIRLLNDTVTAYERSLKVAENKYRAGIVTRADVAQARTQLKSTQAQAIDLKYQRAQLEHAIAVLVGLPPAQFNLPPVASVPKLPDLPAVVPSQLLERRPDIASAERKVISANAQIGVAKAAYFPDLTLSAAGGYRSGSLSNWISTPNRFWSIGPQFAMTLFDGGLIGSQVDQAEATYDQTVATYRQTVLDGFREVEDYLVQLSVLDEESGVQREALESAREALRLAENQYKAGTVDYTDVVTNQATALSNERTVLTLLGSRLTASVQLIAAMGGGWDSADIERTDERLGRVEEGLPPSP"},"dna_sequence":{"accession":"AE004091.2","fmin":"2846282","fmax":"2847779","strand":"-","sequence":"ATGAAACACACCCCCTCGTTGCTCGCCCTGGCCCTGGTCGCCGCCCTCGGCGGCTGCGCCATCGGCCCCGACTACCAGCGACCGGACCTGGCGGTGCCCGCCGAATTCAAGGAAGCCGAAGGCTGGCGCCGCGCCGAGCCGCGCGACGTGTTCCAGCGCGGCGCCTGGTGGGAGCTGTACGGCGACCAGACCCTGAACGACCTGCAGATGCACCTGGAACGTTCCAACCAGACCCTGGCCCAGTCGGTGGCGCAGTTCCGCCAGGCCGAGGCGCTGGTGCGCGGCGCGCGGGCGGCGTTCTTCCCGTCGATCACCGGCAACGTGGGCAAGACCCGCAGCGGCCAGGGCGGCGGCGACAGCACCGTGTTGCTGCCGGGAGGCTCGACGGTGAGCAGCGGCGGCTCTGGCGCGATCAGCACCAGCTACTCGACCAACCTCAGTGTCAGCTGGGAGGTCGACCTCTGGGGCAAGCTGCGCCGGCAACTGGAGGCCAACCAGGCGAGCCTGCATGCCAGCGCCGCCGACCTCGCCGCGGTGCGCCTCAGCCAGCAGTCGCAACTGGCGCAGAACTACCTGCAACTGCGGGTGATGGACGAACAGATCCGCCTGCTCAACGACACGGTGACGGCCTACGAGCGTTCGCTGAAGGTGGCCGAGAACAAATACCGCGCCGGCATCGTCACCAGGGCCGACGTGGCCCAGGCCCGCACCCAGTTGAAAAGCACCCAGGCCCAGGCCATCGACCTGAAGTACCAGCGTGCCCAGCTGGAGCACGCCATCGCCGTGCTGGTCGGCCTGCCGCCGGCGCAATTCAACCTGCCGCCGGTGGCGAGCGTGCCGAAGCTGCCGGACCTGCCGGCAGTGGTGCCGTCGCAATTGCTCGAACGACGGCCGGACATCGCCTCGGCGGAACGCAAGGTGATTTCCGCCAACGCCCAGATCGGCGTGGCCAAGGCCGCCTATTTCCCCGACCTCACCCTGAGCGCCGCCGGCGGCTACCGCAGCGGCAGCCTGAGCAACTGGATCAGCACGCCGAACCGCTTCTGGTCGATCGGCCCGCAGTTCGCCATGACCCTGTTTGACGGCGGCCTGATCGGCTCCCAGGTGGACCAGGCCGAGGCTACCTACGACCAGACCGTGGCGACCTACCGGCAGACCGTGCTCGACGGTTTCCGCGAGGTGGAGGACTACCTGGTGCAATTGAGCGTCCTCGACGAGGAGAGCGGGGTGCAGCGCGAAGCCCTGGAGTCGGCCCGCGAGGCACTGCGCCTGGCCGAGAACCAGTACAAGGCCGGCACCGTCGACTACACCGACGTGGTCACCAACCAGGCCACCGCGCTGAGCAACGAACGCACCGTGCTGACCCTGCTCGGCAGCCGCCTGACCGCCAGCGTCCAGTTGATCGCGGCAATGGGCGGCGGCTGGGACAGCGCCGACATCGAGCGGACCGACGAGCGGCTCGGCCGGGTCGAAGAGGGCCTGCCGCCTTCGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36804","NCBI_taxonomy_name":"Pseudomonas aeruginosa PAO1","NCBI_taxonomy_id":"208964"}}}},"ARO_accession":"3004072","ARO_id":"41154","ARO_name":"OpmB","CARD_short_name":"OpmB","ARO_description":"OpmB is an outer membrane efflux protein in Pseudomonas aeruginosa that shows functional cooperation with MuxABC, to form the efflux pump system MuxABC-OpmB.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36250":{"category_aro_accession":"3000111","category_aro_cvterm_id":"36250","category_aro_name":"novobiocin","category_aro_description":"Novobiocin is an aminocoumarin antibiotic produced by Streptomyces spheroides and Streptomyces niveus, and binds DNA gyrase subunit B inhibiting ATP-dependent DNA supercoiling.","category_aro_class_name":"Antibiotic"},"36689":{"category_aro_accession":"3000550","category_aro_cvterm_id":"36689","category_aro_name":"aztreonam","category_aro_description":"Aztreonam was the first monobactam discovered, and is greatly effective against Gram-negative bacteria while inactive against Gram-positive bacteria. Artreonam is a poor substrate for beta-lactamases, and may even act as an inhibitor. In Gram-negative bacteria, Aztreonam interferes with filamentation, inhibiting cell division and leading to cell death.","category_aro_class_name":"Antibiotic"},"37626":{"category_aro_accession":"3001227","category_aro_cvterm_id":"37626","category_aro_name":"kitasamycin","category_aro_description":"Kitasamycin is a macrolide antibiotic and is produced by Streptoverticillium kitasatoense. The drug has antimicrobial activity against a wide spectrum of pathogens.","category_aro_class_name":"Antibiotic"},"40353":{"category_aro_accession":"3003701","category_aro_cvterm_id":"40353","category_aro_name":"rokitamycin","category_aro_description":"Rokitamycin is a macrolide antibiotic. Synthesized from strains of Streptomyces kitasatoensis.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36242":{"category_aro_accession":"3000103","category_aro_cvterm_id":"36242","category_aro_name":"aminocoumarin antibiotic","category_aro_description":"Aminocoumarin antibiotics bind DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"3396":{"model_id":"3396","model_name":"MCR-5.2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"5584":{"protein_sequence":{"accession":"AVM85875.1","sequence":"MRLSAFITFLKMRPQVRTEFLTLFISLVFTLLCNGVFWNALLAGRDSLTSGTWLMLLCTGLLITGLQWLLLLLVATRWSVKPLLILLAVMTPAAVYFMRNYGVYLDKAMLRNLMETDVREASELLQWRMLPYLLVAAVSVWWIARVRVLRTGWKQAVMMRSACLAGALAMISMGLWPVMDVLIPTLRENKPLRYLITPANYVISGIRVLTEQASSSADEAREVVAADAHRGPQQGRRPRALVLVVGETVRAANWGLSGYERQTTPELAARDVINFSDVTSCGTDTATSLPCMFSLNGRRDYDERQIRRRESVLHVLNRSDVNILWRDNQSGCKGVCDGLPFENLSSAGHPTLCHGERCLDEILLEGLAEKITTSRSDMLIVLHMLGNHGPAYFQRYPASYRRWSPTCDTTDLASCSHEALVNTYDNAVLYTDHVLARTIDLLSGIRSHDTALLYVSDHGESLGEKGLYLHGIPYVIAPDEQIKVPMIWWQSSQVYADQACMQTHASRAPVSHDHLFHTLLGMFDVKTAAYTPELDLLATCRKGQPQ"},"dna_sequence":{"accession":"MG384740.1","fmin":"0","fmax":"1641","strand":"+","sequence":"ATGCGGTTGTCTGCATTTATCACTTTCTTGAAAATGCGCCCGCAAGTGCGCACTGAATTTTTGACTCTGTTCATCAGCCTTGTGTTCACCCTGCTGTGCAATGGCGTGTTTTGGAATGCCCTTCTTGCTGGACGCGACTCCCTAACTTCTGGAACATGGCTAATGCTCCTTTGCACTGGGTTGCTGATCACCGGGCTGCAATGGTTGTTGCTCCTTCTGGTGGCCACGCGCTGGAGTGTCAAGCCACTACTGATTCTGCTTGCTGTCATGACGCCCGCCGCCGTTTATTTCATGCGCAACTACGGGGTTTATCTCGACAAGGCCATGCTGCGGAATCTGATGGAGACGGACGTCAGGGAAGCCAGTGAGCTGTTGCAATGGAGAATGCTGCCCTACTTGTTGGTTGCAGCCGTATCCGTGTGGTGGATTGCGAGAGTCAGGGTTTTACGAACGGGCTGGAAACAAGCGGTAATGATGCGCAGCGCTTGTCTGGCTGGCGCTCTCGCCATGATTTCCATGGGTCTGTGGCCAGTCATGGATGTGCTGATACCCACGCTTCGTGAAAACAAGCCGCTTCGCTATTTGATCACTCCTGCAAACTACGTCATCTCGGGCATTCGGGTTTTGACTGAACAGGCGTCATCGTCAGCAGACGAAGCAAGGGAAGTCGTTGCAGCCGATGCGCATCGAGGGCCTCAACAAGGCCGCCGTCCTCGTGCTCTCGTACTGGTTGTCGGGGAAACCGTCAGGGCGGCTAATTGGGGGTTGAGCGGCTATGAACGACAAACCACCCCTGAGTTGGCCGCACGCGACGTGATCAATTTTTCCGATGTCACCAGTTGCGGGACGGATACGGCTACATCCCTTCCCTGCATGTTTTCCCTCAATGGTCGGCGCGACTACGACGAACGCCAGATTCGTCGGCGCGAGTCCGTGCTGCACGTTTTAAACCGTAGTGACGTCAACATTCTCTGGCGCGATAACCAGTCGGGCTGTAAAGGCGTCTGTGATGGACTGCCCTTTGAAAACCTGTCTTCGGCAGGCCATCCCACACTGTGCCATGGCGAGCGCTGCCTGGATGAAATTCTGCTCGAAGGGTTGGCCGAGAAGATAACAACAAGCCGCAGCGATATGCTGATCGTTCTGCATATGCTGGGCAATCACGGCCCAGCGTATTTCCAGCGCTATCCCGCAAGCTACCGACGCTGGTCGCCAACCTGCGACACCACCGATCTGGCCAGCTGTTCGCATGAAGCCTTGGTGAACACCTACGACAACGCCGTGCTTTACACCGATCATGTGCTTGCCCGTACCATTGACCTGCTGTCCGGCATCCGCTCACACGACACGGCGCTGCTGTACGTTTCCGATCATGGGGAATCGCTCGGCGAGAAAGGCCTGTATCTCCATGGCATACCTTACGTCATCGCGCCGGATGAGCAGATCAAGGTGCCGATGATCTGGTGGCAGTCGAGTCAGGTTTATGCCGACCAAGCCTGTATGCAAACTCATGCCTCTCGGGCACCGGTAAGTCACGATCACCTGTTTCACACCTTGCTCGGGATGTTCGACGTGAAAACCGCTGCCTACACGCCAGAGTTGGACCTTCTGGCAACATGCAGAAAAGGACAACCACAATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3004698","ARO_id":"42750","ARO_name":"MCR-5.2","CARD_short_name":"MCR-5.2","ARO_description":"A plasmid-mediated MCR-5 variant from Escheichia coli which confers resistance to colistin antibiotics.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"347":{"model_id":"347","model_name":"SFH-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1878":{"protein_sequence":{"accession":"AAF09244.1","sequence":"MASEKNLTLTHFKGPLYIVEDKEYVQENSMVYIGTDGITIIGATWTPETAETLYKEIRKVSPLPINEVINTNYHTDRAGGNAYWKTLGAKIVATQMTYDLQKSQWGSIVNFTRQGNNKYPNLEKSLPDTVFPGDFNLQNGSIRAMYLGEAHTKDGIFVYFPAERVLYGNCILKENLGNMSFANRTEYPKTLEKLKGLIEQGELKVDSIIAGHDTPIHDVGLIDHYLTLLEKAPK"},"dna_sequence":{"accession":"AF197943.1","fmin":"0","fmax":"705","strand":"+","sequence":"ATGGCTTCTGAAAAAAACTTAACGCTTACCCATTTCAAAGGTCCGCTCTATATTGTAGAAGATAAGGAGTATGTACAGGAAAACTCAATGGTTTACATCGGCACCGATGGTATAACCATCATTGGTGCGACATGGACTCCTGAGACTGCTGAAACTCTTTATAAAGAAATACGGAAGGTCAGCCCCCTCCCCATAAACGAAGTCATTAATACCAATTACCATACTGATCGAGCTGGTGGAAATGCTTATTGGAAAACGCTTGGGGCAAAGATCGTGGCCACACAGATGACCTACGACCTGCAGAAAAGCCAGTGGGGAAGTATTGTAAACTTCACTCGACAAGGTAATAATAAATACCCAAATCTGGAGAAAAGTCTGCCGGATACTGTTTTTCCTGGAGACTTTAACTTGCAAAATGGCAGCATCCGCGCCATGTATTTAGGCGAAGCACATACTAAGGATGGTATCTTTGTGTACTTCCCAGCAGAGCGCGTTTTGTATGGGAACTGCATTCTCAAAGAAAATCTGGGTAATATGAGTTTTGCCAACAGAACTGAGTACCCAAAAACCTTGGAAAAACTTAAAGGACTTATCGAGCAGGGGGAGCTTAAAGTCGACTCGATCATTGCAGGGCATGATACTCCGATACATGACGTAGGCCTGATCGATCACTACCTTACACTGCTTGAGAAGGCGCCTAAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39675","NCBI_taxonomy_name":"Serratia fonticola","NCBI_taxonomy_id":"47917"}}}},"ARO_accession":"3000849","ARO_id":"37229","ARO_name":"SFH-1","CARD_short_name":"SFH-1","ARO_description":"SFH-1 confers resistance to carbapenems in Serratia fonticola.","ARO_category":{"41374":{"category_aro_accession":"3004210","category_aro_cvterm_id":"41374","category_aro_name":"SFH beta-lactamase","category_aro_description":"This type of Subclass B2 beta-lactamases was first identified from a Serratia fonticola environmental isolate.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2654":{"model_id":"2654","model_name":"adeL","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"650"}},"model_sequences":{"sequence":{"4541":{"protein_sequence":{"accession":"ALH22601.1","sequence":"MRVFNKVVETNSFSLAADSLGLPRASVTTTIQALEKHLQVRLLNRTTRKISLTPDGAVYYDRTARILADVADIESSFHDAERGPRGQLRIDVPVSIGRLILIPRLRDFHARYPDIDLVIGLNDRPVDLVGEAVDCAIRVGELKDSSLIARRIGTFQCATAASPIYLEKYGEPTSIEDLQKNHKAIHFFSSRTGRNFDWDFVVDDLIKSVSVRGRVSVNDGDAYIDLALQGFGIIQGPRYMLTNHLESGLLKEVLPQWTPAPMPISAVYLQNRHLSLKVKVFVDWVAELFAGCPLLGGTALPFDQKCEFACDKETGHEYTIRTLVEQHNIAEAYTLKT"},"dna_sequence":{"accession":"KR297239.1","fmin":"414","fmax":"1428","strand":"-","sequence":"ATGAGAGTATTCAACAAAGTTGTTGAAACAAATAGTTTCAGTTTAGCAGCTGATAGTTTGGGTTTACCGCGTGCTTCTGTGACTACAACCATTCAGGCTTTAGAGAAGCATTTACAAGTTCGATTGCTTAATCGGACAACACGAAAAATTAGTCTCACACCGGATGGCGCCGTATATTATGATCGGACAGCCCGTATTTTAGCGGATGTTGCCGATATTGAATCTTCTTTTCATGATGCAGAGCGGGGGCCAAGAGGTCAGCTTCGTATTGATGTGCCTGTATCGATTGGACGTTTAATTTTAATTCCAAGGCTCCGTGATTTTCATGCACGCTATCCTGATATTGATTTAGTGATTGGTCTGAACGACCGACCTGTAGACTTGGTTGGAGAAGCGGTTGATTGTGCAATTCGGGTGGGTGAATTAAAAGATTCAAGCTTAATTGCGCGTCGTATCGGAACTTTCCAGTGTGCAACAGCTGCTTCACCGATTTATTTAGAAAAATATGGCGAACCTACCTCAATTGAAGATTTGCAAAAAAATCATAAAGCGATTCACTTCTTTTCAAGCCGTACCGGACGCAACTTCGATTGGGACTTTGTGGTTGATGATTTAATTAAAAGTGTGTCAGTACGTGGACGTGTTTCGGTAAATGACGGTGATGCTTATATCGACTTGGCTTTGCAAGGTTTTGGTATAATTCAAGGCCCACGTTATATGCTCACCAACCATTTAGAATCAGGTTTGTTAAAAGAGGTATTGCCTCAGTGGACGCCAGCACCGATGCCGATTTCAGCAGTTTATCTTCAAAATCGTCATTTATCGCTTAAAGTAAAAGTGTTTGTAGATTGGGTCGCTGAACTTTTTGCAGGCTGTCCATTACTTGGCGGTACAGCTTTACCTTTCGACCAGAAATGTGAATTTGCCTGTGATAAAGAAACTGGTCATGAATATACAATTCGTACTTTGGTCGAGCAGCATAATATTGCTGAAGCTTATACGCTCAAAACTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3000620","ARO_id":"36962","ARO_name":"adeL","CARD_short_name":"adeL","ARO_description":"AdeL is a regulator of AdeFGH in Acinetobacter baumannii. AdeL mutations are associated with AdeFGH overexpression and multidrug resistance.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2655":{"model_id":"2655","model_name":"Pseudomonas aeruginosa emrE","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"170"}},"model_sequences":{"sequence":{"5488":{"protein_sequence":{"accession":"AAG08375.1","sequence":"MTNYLYLAIAIAAEVVATTSLKAVAGFSKPLPLLLVVGGYVLAFSMLVLVMRTLPVGVVYAIWSGLGIVLVSLVAMFVYGQRLDPAALLGIGLIIAGVLVIQLFSRASGH"},"dna_sequence":{"accession":"AE004091.2","fmin":"5606102","fmax":"5606435","strand":"+","sequence":"ATGACCAACTATCTCTACCTCGCCATCGCCATCGCCGCCGAAGTGGTCGCCACCACCTCGCTGAAAGCCGTCGCCGGATTCAGCAAGCCACTGCCGCTGCTGCTGGTGGTGGGCGGCTACGTGCTCGCCTTCAGCATGCTCGTGCTGGTCATGCGCACCCTGCCGGTCGGCGTGGTCTACGCCATCTGGTCCGGACTCGGCATCGTCCTGGTCAGCCTGGTGGCGATGTTCGTCTACGGCCAGCGCCTGGACCCCGCCGCCCTCCTCGGCATCGGCCTGATCATCGCCGGCGTGCTGGTGATCCAGTTGTTCTCCCGCGCTTCGGGGCACTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36804","NCBI_taxonomy_name":"Pseudomonas aeruginosa PAO1","NCBI_taxonomy_id":"208964"}}}},"ARO_accession":"3004038","ARO_id":"41082","ARO_name":"Pseudomonas aeruginosa emrE","CARD_short_name":"Paer_emrE","ARO_description":"EmrE is a small multidrug transporter that functions as a homodimer and that couples the efflux of small polyaromatic cations from the cell with the import of protons down an electrochemical gradient. Confers resistance to tetraphenylphosphonium, methyl viologen, gentamicin, kanamycin, and neomycin.","ARO_category":{"36004":{"category_aro_accession":"0010003","category_aro_cvterm_id":"36004","category_aro_name":"small multidrug resistance (SMR) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Small multidrug resistance (SMR) proteins are a relatively small family of transporters, restricted to prokaryotic cells. They are also the smallest multidrug transporters, with only four transmembrane alpha-helices and no significant extramembrane domain.","category_aro_class_name":"AMR Gene Family"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"46133":{"category_aro_accession":"3007382","category_aro_cvterm_id":"46133","category_aro_name":"gentamicin","category_aro_description":"Gentamicin is a commonly used aminoglycoside antibiotic derived from members of the Micromonospora genus of bacteria. It acts by binding the 30S ribosomal subunit, thus inhibiting protein synthesis. Gentamicin is typically used to treat Gram-negative infections of the repiratory and urinary tract, as well as infections of the bone and soft tissue. It also exhibits considerable nephrotoxicity and ototoxicity. Gentamicin is administered as a mixture of gentamicin type C (which makes about around 80% of the complex) and types A, B, and X (distributed in the remaining 20% of the complex).","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2656":{"model_id":"2656","model_name":"Escherichia coli emrE","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"190"}},"model_sequences":{"sequence":{"4413":{"protein_sequence":{"accession":"CAA77936.1","sequence":"MNPYIYLGGAILAEVIGTTLMKFSEGFTRLWPSVGTIICYCASFWLLAQTLAYIPTGIAYAIWSGVGIVLISLLSWGFFGQRLDLPAIIGMMLICAGVLIINLLSRSTPH"},"dna_sequence":{"accession":"Z11877.1","fmin":"485","fmax":"818","strand":"+","sequence":"ATGAACCCTTATATTTATCTTGGTGGTGCAATACTTGCAGAGGTCATTGGTACAACCTTAATGAAGTTTTCAGAAGGTTTTACACGGTTATGGCCATCTGTTGGTACAATTATTTGTTATTGTGCATCATTCTGGTTATTAGCTCAGACGCTGGCTTATATTCCTACAGGGATTGCTTATGCTATCTGGTCAGGAGTCGGTATTGTCCTGATTAGCTTACTGTCATGGGGATTTTTCGGCCAACGGCTGGACCTGCCAGCCATTATAGGCATGATGTTGATTTGTGCCGGTGTGTTGATTATTAATTTATTGTCACGAAGCACACCACATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3004039","ARO_id":"41083","ARO_name":"Escherichia coli emrE","CARD_short_name":"Ecol_emrE","ARO_description":"Member of the small MDR (multidrug resistance) family of transporters; in Escherichia coli this protein provides resistance against a number of positively charged compounds including ethidium bromide and erythromycin; proton-dependent secondary transporter which exchanges protons for compound translocation.","ARO_category":{"36004":{"category_aro_accession":"0010003","category_aro_cvterm_id":"36004","category_aro_name":"small multidrug resistance (SMR) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Small multidrug resistance (SMR) proteins are a relatively small family of transporters, restricted to prokaryotic cells. They are also the smallest multidrug transporters, with only four transmembrane alpha-helices and no significant extramembrane domain.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"3408":{"model_id":"3408","model_name":"OXA-122","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"5603":{"protein_sequence":{"accession":"ABX45061.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEVHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEIAYKSLEQLGIL"},"dna_sequence":{"accession":"EU255291.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGTACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTGCTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001444","ARO_id":"37844","ARO_name":"OXA-122","CARD_short_name":"OXA-122","ARO_description":"OXA-122 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2659":{"model_id":"2659","model_name":"Klebsiella pneumoniae acrA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"770"}},"model_sequences":{"sequence":{"3994":{"protein_sequence":{"accession":"CAC41008.1","sequence":"MNKNRGLTPLAVVLMLSGSLALTGCDDKPAQQGAQHMPEVGIVTLKSAPLQITTELPGRTSAYRIAEVRPQVSGIILKRNFVEGSDIQAGVFLYQIDPATYQGSYDSAKGDLAKAQAAANMDQLTVKRYQKLLGTQYISQQDYDPAVATAQQNNAAVVAAKTAVETARINLAYTQKSPLRSAAGSGKSPVTEGALVQNGQTTALATVQQVDPIYVDVTQSSNDFLRLKQELADARLKQENGKAKVELVTNDGLKYPQSGTLEFSDVTVDQTTGSITLRAIFPNPDHTLLPGMFVRARLEEGINPDALLVPQQGVTRTPRGDASVMVVGEGDKVEVRQVTASQAIGDKWLVTDGLKSGDRVIVTGLQKIKPGVQVKAQEVASDDKQQAAGNAPSEQTKS"},"dna_sequence":{"accession":"AJ318073.1","fmin":"793","fmax":"1990","strand":"+","sequence":"ATGAACAAAAACAGAGGGTTAACGCCTCTGGCGGTCGTTCTGATGCTCTCAGGCAGCTTAGCGCTAACAGGATGTGACGATAAACCGGCTCAACAGGGAGCCCAGCACATGCCGGAAGTCGGTATTGTGACGCTCAAATCCGCACCTCTACAAATAACCACCGAACTGCCAGGCCGCACCAGCGCCTATCGCATTGCGGAAGTCCGTCCTCAGGTCAGTGGCATTATTTTAAAACGTAACTTCGTGGAAGGTAGCGATATCCAGGCCGGCGTCTTCCTGTATCAGATCGATCCAGCCACCTATCAAGGCAGCTATGACAGCGCCAAAGGCGACCTGGCAAAAGCCCAGGCGGCGGCAAACATGGATCAACTGACGGTCAAGCGTTATCAGAAACTGTTGGGCACCCAATATATTAGTCAACAAGACTACGATCCCGCCGTTGCGACGGCGCAACAAAACAATGCCGCCGTGGTCGCGGCGAAAACTGCCGTTGAAACCGCGCGCATCAATTTGGCCTACACCCAAAAGTCACCTCTCCGATCAGCGGCCGGATCGGGTAAATCCCCCGTGACCGAAGGGGCGTTGGTACAGAATGGTCAAACGACCGCCTTGGCAACCGTTCAGCAAGTGGATCCGATCTATGTTGACGTCACCCAGTCGAGCAATGATTTCCTGCGCCTGAAGCAGGAGCTAGCCGACGCCCGCCTGAAACAGGAAAACGGCAAAGCGAAAGTGGAGCTGGTGACTAATGACGGGCTTAAGTATCCGCAGTCCGGCACGCTGGAATTCTCGGATGTCACCGTCGATCAGACCACCGGCTCAATCACGCTACGCGCTATTTTCCCGAACCCGGATCACACCCTGCTTCCGGGGATGTTCGTCCGTGCCCGTCTGGAAGAAGGGATTAACCCTGACGCCCTGCTGGTACCGCAACAGGGTGTTACCCGTACGCCGCGCGGCGACGCCAGCGTCATGGTAGTGGGTGAAGGCGATAAAGTCGAAGTCCGCCAGGTCACTGCTTCTCAGGCGATCGGCGATAAATGGCTGGTCACTGACGGTCTGAAATCCGGCGATCGCGTTATCGTCACCGGCCTGCAAAAAATCAAACCAGGTGTGCAGGTAAAAGCGCAGGAAGTAGCTTCTGATGATAAACAGCAAGCCGCAGGCAACGCGCCATCAGAACAAACCAAGTCTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3004041","ARO_id":"41088","ARO_name":"Klebsiella pneumoniae acrA","CARD_short_name":"Kpne_acrA","ARO_description":"AcrA is a subunit of the AcrAB multidrug efflux system that is found in K. pneumoniae, which is encoded by the acrRAB operon.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"37084":{"category_aro_accession":"3000704","category_aro_cvterm_id":"37084","category_aro_name":"cefalotin","category_aro_description":"Cefalotin is a semisynthetic cephalosporin antibiotic activate against staphylococci. It is resistant to staphylococci beta-lactamases but hydrolyzed by enterobacterial beta-lactamases.","category_aro_class_name":"Antibiotic"},"37250":{"category_aro_accession":"3000870","category_aro_cvterm_id":"37250","category_aro_name":"triclosan","category_aro_description":"Triclosan is a common antibacterial agent added to many consumer products as a biocide.  It is an inhibitor of fatty acid biosynthesis by blocking enoyl-carrier protein reductase (FabI).","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"43746":{"category_aro_accession":"3005386","category_aro_cvterm_id":"43746","category_aro_name":"disinfecting agents and antiseptics","category_aro_description":"Disinfectants that can also interact with antimicrobial resistance mechanisms, e.g. molecule efflux, and thus are the targets of disinfectant resistance.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2660":{"model_id":"2660","model_name":"Enterobacter cloacae acrA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"760"}},"model_sequences":{"sequence":{"3995":{"protein_sequence":{"accession":"ABG77965.1","sequence":"MNKNRGLTPLAVVLMLSGSLALTGCDDKPAQQGAQQAPEVGVVTLKSEPLQITTELPGRTNAYRIAEVRPQVSGIILKRNFTEGGDVQAGESLYQIDPATYQASYESAKGDLAKAQAAAKIAQLTLNRYQKLLGTKYISQQDYDTALADAQQANAAVVAAKAAVETARINLAYTKVTSPISGRIGKSSVTEGALVQNGQTTALATVQQLDPIYVDVTQSSNDFLRLKQELANGTLKQENGKAKVELITNDGIKFPQEGTLEFSDVTVDQTTGSITLRAIFPNPDKNLLPGMFVRARLEEGTNPTALLVPQQGVTRTPRGDASALVVGADNKVEMRNITATQAIGDKWLVTEGLKDGDRVIVTGLQKVRPGAQVKAQEVKSDDKQQASAAGQSEQTKS"},"dna_sequence":{"accession":"DQ679966.1","fmin":"299","fmax":"1493","strand":"+","sequence":"ATGAACAAAAACAGAGGGTTAACGCCTCTGGCGGTCGTTCTGATGCTTTCAGGCAGCTTAGCGCTAACAGGATGTGACGACAAACCGGCTCAACAAGGAGCTCAGCAGGCGCCAGAAGTAGGCGTTGTGACGCTCAAATCTGAACCTCTACAAATCACCACCGAATTACCCGGCCGTACAAATGCTTACCGCATTGCGGAAGTGCGTCCTCAGGTTAGCGGCATTATCCTGAAACGCAACTTCACCGAAGGCGGTGATGTGCAGGCCGGTGAGTCTCTGTATCAGATTGATCCCGCAACCTATCAGGCGTCTTATGAAAGCGCGAAAGGCGATCTGGCTAAAGCGCAGGCCGCGGCTAAAATTGCCCAGCTGACGCTGAACCGCTATCAAAAACTGCTCGGTACCAAGTACATCAGTCAGCAGGATTACGATACCGCCCTGGCGGATGCCCAGCAGGCTAACGCCGCCGTGGTGGCAGCCAAAGCGGCCGTCGAAACCGCGCGCATTAACCTGGCCTATACCAAAGTGACCTCCCCTATCAGCGGTCGTATTGGTAAATCTTCCGTCACGGAAGGGGCTCTGGTGCAAAACGGTCAGACCACTGCGCTGGCGACCGTGCAGCAGCTCGATCCGATCTATGTTGACGTCACGCAGTCCAGCAATGATTTCCTGCGCCTGAAACAGGAGTTGGCTAACGGCACCCTGAAACAGGAAAACGGCAAAGCCAAAGTGGAGCTGATTACCAACGACGGTATCAAGTTCCCGCAGGAAGGGACGCTGGAATTCTCTGACGTGACGGTCGACCAGACCACCGGTTCCATCACCTTACGTGCGATTTTCCCGAACCCTGACAAAAATCTGCTGCCAGGTATGTTCGTTCGCGCACGTCTGGAAGAAGGAACGAATCCAACCGCCCTTCTGGTTCCACAGCAGGGTGTGACCCGTACGCCACGCGGCGATGCGAGCGCACTGGTTGTTGGGGCTGATAACAAAGTCGAAATGCGCAACATCACCGCCACCCAGGCGATTGGGGATAAATGGCTGGTGACGGAAGGTCTGAAAGATGGCGATCGCGTGATTGTTACTGGTTTGCAAAAAGTTCGTCCTGGCGCGCAGGTTAAAGCACAGGAAGTGAAATCTGACGATAAACAACAAGCTTCGGCCGCTGGCCAGTCAGAACAAACCAAGTCTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3004042","ARO_id":"41089","ARO_name":"Enterobacter cloacae acrA","CARD_short_name":"Eclo_acrA","ARO_description":"AcrA is a subunit of the AcrAB-TolC multidrug efflux system in E. cloacae.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"37084":{"category_aro_accession":"3000704","category_aro_cvterm_id":"37084","category_aro_name":"cefalotin","category_aro_description":"Cefalotin is a semisynthetic cephalosporin antibiotic activate against staphylococci. It is resistant to staphylococci beta-lactamases but hydrolyzed by enterobacterial beta-lactamases.","category_aro_class_name":"Antibiotic"},"37250":{"category_aro_accession":"3000870","category_aro_cvterm_id":"37250","category_aro_name":"triclosan","category_aro_description":"Triclosan is a common antibacterial agent added to many consumer products as a biocide.  It is an inhibitor of fatty acid biosynthesis by blocking enoyl-carrier protein reductase (FabI).","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"43746":{"category_aro_accession":"3005386","category_aro_cvterm_id":"43746","category_aro_name":"disinfecting agents and antiseptics","category_aro_description":"Disinfectants that can also interact with antimicrobial resistance mechanisms, e.g. molecule efflux, and thus are the targets of disinfectant resistance.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2661":{"model_id":"2661","model_name":"Escherichia coli acrA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"670"}},"model_sequences":{"sequence":{"5262":{"protein_sequence":{"accession":"AAC73565.1","sequence":"MNKNRGFTPLAVVLMLSGSLALTGCDDKQAQQGGQQMPAVGVVTVKTEPLQITTELPGRTSAYRIAEVRPQVSGIILKRNFKEGSDIEAGVSLYQIDPATYQATYDSAKGDLAKAQAAANIAQLTVNRYQKLLGTQYISKQEYDQALADAQQANAAVTAAKAAVETARINLAYTKVTSPISGRIGKSNVTEGALVQNGQATALATVQQLDPIYVDVTQSSNDFLRLKQELANGTLKQENGKAKVSLITSDGIKFPQDGTLEFSDVTVDQTTGSITLRAIFPNPDHTLLPGMFVRARLEEGLNPNAILVPQQGVTRTPRGDATVLVVGADDKVETRPIVASQAIGDKWLVTEGLKAGDRVVISGLQKVRPGVQVKAQEVTADNNQQAASGAQPEQSKS"},"dna_sequence":{"accession":"U00096.3","fmin":"484425","fmax":"485619","strand":"-","sequence":"ATGAACAAAAACAGAGGGTTTACGCCTCTGGCGGTCGTTCTGATGCTCTCAGGCAGCTTAGCCCTAACAGGATGTGACGACAAACAGGCCCAACAAGGTGGCCAGCAGATGCCCGCCGTTGGCGTAGTAACAGTCAAAACTGAACCTCTGCAGATCACAACCGAGCTTCCGGGTCGCACCAGTGCCTACCGGATCGCAGAAGTTCGTCCTCAAGTTAGCGGGATTATCCTGAAGCGTAATTTCAAAGAAGGTAGCGACATCGAAGCAGGTGTCTCTCTCTATCAGATTGATCCTGCGACCTATCAGGCGACATACGACAGTGCGAAAGGTGATCTGGCGAAAGCCCAGGCTGCAGCCAATATCGCGCAATTGACGGTGAATCGTTATCAGAAACTGCTCGGTACTCAGTACATCAGTAAGCAAGAGTACGATCAGGCTCTGGCTGATGCGCAACAGGCGAATGCTGCGGTAACTGCGGCGAAAGCTGCCGTTGAAACTGCGCGGATCAATCTGGCTTACACCAAAGTCACCTCTCCGATTAGCGGTCGCATTGGTAAGTCGAACGTGACGGAAGGCGCATTGGTACAGAACGGTCAGGCGACTGCGCTGGCAACCGTGCAGCAACTTGATCCGATCTACGTTGATGTGACCCAGTCCAGCAACGACTTCCTGCGCCTGAAACAGGAACTGGCGAATGGCACGCTGAAACAAGAGAACGGCAAAGCCAAAGTGTCACTGATCACCAGTGACGGCATTAAGTTCCCGCAGGACGGTACGCTGGAATTCTCTGACGTTACCGTTGATCAGACCACTGGGTCTATCACCCTACGCGCTATCTTCCCGAACCCGGATCACACTCTGCTGCCGGGTATGTTCGTGCGCGCACGTCTGGAAGAAGGGCTTAATCCAAACGCTATTTTAGTCCCGCAACAGGGCGTAACCCGTACGCCGCGTGGCGATGCCACCGTACTGGTAGTTGGCGCGGATGACAAAGTGGAAACCCGTCCGATCGTTGCAAGCCAGGCTATTGGCGATAAGTGGCTGGTGACAGAAGGTCTGAAAGCAGGCGATCGCGTAGTAATAAGTGGGCTGCAGAAAGTGCGTCCTGGTGTCCAGGTAAAAGCACAAGAAGTTACCGCTGATAATAACCAGCAAGCCGCAAGCGGTGCTCAGCCTGAACAGTCCAAGTCTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36849","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. MG1655","NCBI_taxonomy_id":"511145"}}}},"ARO_accession":"3004043","ARO_id":"41090","ARO_name":"Escherichia coli acrA","CARD_short_name":"Ecol_acrA","ARO_description":"AcrA is a subunit of the AcrAB-TolC multidrug efflux system found in E. coli.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"37084":{"category_aro_accession":"3000704","category_aro_cvterm_id":"37084","category_aro_name":"cefalotin","category_aro_description":"Cefalotin is a semisynthetic cephalosporin antibiotic activate against staphylococci. It is resistant to staphylococci beta-lactamases but hydrolyzed by enterobacterial beta-lactamases.","category_aro_class_name":"Antibiotic"},"37250":{"category_aro_accession":"3000870","category_aro_cvterm_id":"37250","category_aro_name":"triclosan","category_aro_description":"Triclosan is a common antibacterial agent added to many consumer products as a biocide.  It is an inhibitor of fatty acid biosynthesis by blocking enoyl-carrier protein reductase (FabI).","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"43746":{"category_aro_accession":"3005386","category_aro_cvterm_id":"43746","category_aro_name":"disinfecting agents and antiseptics","category_aro_description":"Disinfectants that can also interact with antimicrobial resistance mechanisms, e.g. molecule efflux, and thus are the targets of disinfectant resistance.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"3431":{"model_id":"3431","model_name":"OXA-264","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"5627":{"protein_sequence":{"accession":"ENW20318.1","sequence":"MKLSKLYTLTVLIGFGLSGVACQHIHTPVLFNQIENDQTKQIASLFENVQTTGVLITFDGQAYKAYGNDLNRAKTAYIPASTFKILNALIGIEHDKTSPNEVFKWDGQKRAFESWEKDLTLAEAMQASAVPVYQALAQRIGLDLMAKEVKRVGFGNTRIGTQVDNFWLIGPLKITPIEEAQFAYRLAKQELPFTPKTQQQVIDMLLVDEIRGTKVYAKSGWGMDITPQVGWWTGWIEDPNGKVIAFSLNMEMNQPAHAAARKEIVYQALTQLKLL"},"dna_sequence":{"accession":"APQQ01000012.1","fmin":"286900","fmax":"287728","strand":"-","sequence":"ATGAAGCTATCAAAATTATACACCCTCACTGTGCTCATAGGATTTGGATTAAGCGGTGTCGCCTGCCAGCATATCCATACTCCAGTCTTGTTCAATCAAATTGAAAACGATCAAACAAAGCAGATCGCTTCCTTGTTTGAGAATGTTCAAACAACAGGTGTTCTAATTACCTTTGATGGACAGGCGTATAAAGCATACGGTAATGATCTGAATCGTGCCAAAACTGCGTATATCCCAGCATCTACTTTCAAAATATTAAATGCTTTGATTGGTATTGAACATGATAAAACTTCACCAAATGAAGTATTTAAGTGGGATGGTCAGAAACGTGCTTTTGAAAGTTGGGAAAAAGATCTGACTTTAGCTGAAGCCATGCAAGCTTCTGCTGTACCTGTTTATCAAGCGCTTGCCCAGAGAATCGGATTGGATTTGATGGCAAAGGAAGTCAAAAGAGTCGGCTTCGGTAATACACGCATCGGAACACAAGTTGATAACTTCTGGCTCATTGGACCTTTAAAGATCACGCCAATCGAAGAAGCTCAATTTGCTTACAGGCTTGCGAAACAGGAGTTACCATTTACCCCAAAAACACAACAGCAAGTGATTGATATGCTGCTGGTGGATGAAATACGGGGAACTAAAGTTTACGCCAAAAGTGGTTGGGGAATGGATATTACTCCGCAAGTAGGATGGTGGACTGGATGGATTGAAGATCCGAACGGAAAAGTGATCGCTTTTTCTCTCAATATGGAAATGAATCAACCTGCGCATGCAGCTGCACGTAAAGAAATTGTTTATCAGGCACTTACGCAATTGAAATTATTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42795","NCBI_taxonomy_name":"Acinetobacter haemolyticus CIP 64.3 = MTCC 9819","NCBI_taxonomy_id":"1217659"}}}},"ARO_accession":"3001720","ARO_id":"38120","ARO_name":"OXA-264","CARD_short_name":"OXA-264","ARO_description":"OXA-264 is a beta-lactamase found in Acinetobacter spp.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46496":{"category_aro_accession":"3007707","category_aro_cvterm_id":"46496","category_aro_name":"OXA-214-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-214.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3461":{"model_id":"3461","model_name":"OXA-299","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"5656":{"protein_sequence":{"accession":"ENV82218.1","sequence":"MNPFTKYCAILCPIIFLGACTISPFSHDQAHSAHASQLTDAATIRNLFNQANVQGVILIKSGNDLQAYGNAIQRADQPFIPASTFKMLNALIGIEHNKTSPDEVFKWNGEKRSFPAWEKDLTLAQAMTASAVPVYQELAHRIGLELMQNEVKRVQFGNGDIGAQVDNFWLMGPLKITPRQEVQFADQLSHLQLPFRKSTQQQVIQMLFIEQIGSKALYAKSGWGMDVEPQVGWYTGWVEDAQGKTTAFSLNLEMDQSTPASLRKELVISSLKQLKIL"},"dna_sequence":{"accession":"APQD01000016.1","fmin":"31095","fmax":"31929","strand":"+","sequence":"ATGAATCCCTTCACAAAATACTGTGCAATTTTATGCCCCATAATTTTTCTGGGCGCCTGCACAATATCCCCTTTTTCACACGATCAAGCGCATTCTGCCCATGCCAGCCAATTAACAGATGCAGCCACTATCCGCAATTTGTTTAATCAAGCCAATGTTCAGGGCGTGATTCTCATTAAAAGCGGCAATGATCTTCAAGCATATGGCAATGCGATACAGCGCGCAGATCAGCCATTTATACCGGCCTCCACGTTTAAAATGCTGAATGCCCTGATTGGCATTGAACACAACAAAACTTCCCCAGACGAAGTATTCAAATGGAATGGGGAAAAACGCAGCTTTCCAGCTTGGGAAAAAGATTTAACCTTAGCGCAGGCCATGACCGCCTCTGCCGTACCGGTATATCAAGAATTGGCGCACAGAATTGGCTTAGAGCTGATGCAAAATGAAGTGAAGCGGGTTCAATTTGGCAATGGCGATATTGGCGCTCAAGTCGATAATTTCTGGCTGATGGGCCCGCTTAAAATTACACCAAGGCAGGAAGTGCAATTTGCCGATCAGCTGTCCCACTTGCAATTGCCCTTTCGCAAAAGCACACAGCAACAAGTGATTCAAATGCTGTTTATTGAACAGATCGGCAGTAAAGCGCTCTATGCCAAAAGCGGCTGGGGCATGGATGTTGAGCCTCAAGTCGGCTGGTATACCGGCTGGGTTGAAGATGCTCAAGGCAAAACCACAGCCTTTTCACTCAACCTAGAAATGGATCAATCCACACCGGCATCTCTGCGTAAAGAGCTGGTGATCAGCAGCTTAAAGCAGCTCAAAATCCTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42820","NCBI_taxonomy_name":"Acinetobacter bouvetii DSM 14964 = CIP 107468","NCBI_taxonomy_id":"1120925"}}}},"ARO_accession":"3001754","ARO_id":"38154","ARO_name":"OXA-299","CARD_short_name":"OXA-299","ARO_description":"OXA-299 is a beta-lactamase found in Acinetobacter spp.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3490":{"model_id":"3490","model_name":"OXA-405","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"5685":{"protein_sequence":{"accession":"AJA30430.1","sequence":"MRVLALSAVFLVASIIGMPAVAKEWQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGQTRDIATWNRDHNLITAMKYSVVPVYQEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISATEQISFLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYSPKIGWWVGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP"},"dna_sequence":{"accession":"KM589641.1","fmin":"0","fmax":"786","strand":"+","sequence":"ATGCGTGTATTAGCCTTATCGGCTGTGTTTTTGGTGGCATCGATTATCGGAATGCCTGCGGTAGCAAAGGAATGGCAAGAAAACAAAAGTTGGAATGCTCACTTTACTGAACATAAATCACAGGGCGTAGTTGTGCTCTGGAATGAGAATAAGCAGCAAGGATTTACCAATAATCTTAAACGGGCGAACCAAGCATTTTTACCCGCATCTACCTTTAAAATTCCCAATAGCTTGATCGCCCTCGATTTGGGCGTGGTTAAGGATGAACACCAAGTCTTTAAGTGGGATGGACAGACGCGCGATATCGCCACTTGGAATCGCGATCATAATCTAATCACCGCGATGAAATATTCAGTTGTGCCTGTTTATCAAGAATTTGCCCGCCAAATTGGCGAGGCACGTATGAGCAAGATGCTACATGCTTTCGATTATGGTAATGAGGACATTTCGGGCAATGTAGACAGTTTCTGGCTCGACGGTGGTATTCGAATTTCGGCCACGGAGCAAATCAGCTTTTTAAGAAAGCTGTATCACAATAAGTTACACGTATCGGAGCGCAGCCAGCGTATTGTCAAACAAGCCATGCTGACCGAAGCCAATGGTGACTATATTATTCGGGCTAAAACTGGATACTCACCTAAGATTGGCTGGTGGGTCGGTTGGGTTGAACTTGATGATAATGTGTGGTTTTTTGCGATGAATATGGATATGCCCACATCGGATGGTTTAGGGCTGCGCCAAGCCATCACAAAAGAAGTGCTCAAACAGGAAAAAATTATTCCCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36783","NCBI_taxonomy_name":"Serratia marcescens","NCBI_taxonomy_id":"615"}}}},"ARO_accession":"3001596","ARO_id":"37996","ARO_name":"OXA-405","CARD_short_name":"OXA-405","ARO_description":"OXA-405 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46510":{"category_aro_accession":"3007721","category_aro_cvterm_id":"46510","category_aro_name":"OXA-48-like beta-lactamase","category_aro_description":"OXA-48-type beta-lactamases are now routinely encountered in bacterial infections caused by carbapenam-resistant Enterobacterales. OXA-48-like proteins confer resistance to penicillin (which is efficiently hydrolyzed) and carbapenam antibiotics (which is more slowly broken down). The spectrum of activity of these variants varies, with some hydrolyzing expanded-spectrum oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3516":{"model_id":"3516","model_name":"OXA-447","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"5711":{"protein_sequence":{"accession":"AKI29908.1","sequence":"MRNFIVFILFLNIAIGEDKILGNFFKDCNTSGTFIVFDGKNYASNDFKRAKQAFSPASTFKIFNALIALDNGVVRDTKEIFYHYKGEKVFLPSWKQDASLSSAIKRSQVPAFKELARKIGLKTMQESLNKLSYGNAKISKIDTFWLDNSLQISAKNQADLLFKLSQNSLPFSKKIQEEVKEIILFKEDKIQKIYAKTGFNDNINLAWIVGFVKTENKILSFALNVDIKDIKNIKIREELLNKYLANFFNNNRIKSFY"},"dna_sequence":{"accession":"KR061496.1","fmin":"0","fmax":"774","strand":"+","sequence":"ATGAGAAATTTTATTGTATTTATATTGTTTTTGAATATAGCCATTGGAGAGGATAAAATACTTGGTAATTTTTTTAAAGATTGTAATACAAGTGGGACTTTTATAGTCTTTGATGGAAAAAATTATGCAAGTAATGATTTTAAAAGAGCTAAACAAGCCTTTTCTCCTGCTTCAACTTTTAAAATTTTTAATGCTTTAATTGCACTTGATAATGGTGTAGTTAGAGATACAAAGGAAATTTTTTATCATTATAAGGGCGAAAAAGTATTTTTGCCCTCTTGGAAACAAGATGCTAGTTTAAGCTCAGCTATAAAACGCTCTCAAGTGCCTGCTTTTAAAGAATTGGCAAGAAAAATAGGACTTAAAACCATGCAAGAAAGCTTAAATAAACTTTCTTATGGAAATGCAAAAATTTCAAAAATCGATACCTTTTGGCTCGATAATTCTTTACAAATTTCTGCAAAAAATCAAGCTGATTTACTTTTTAAACTTTCGCAAAATTCTTTACCTTTTTCTAAAAAAATTCAAGAAGAAGTTAAAGAAATTATTCTTTTTAAGGAAGATAAAATCCAAAAAATTTATGCTAAAACAGGTTTTAATGATAATATCAATTTAGCTTGGATTGTTGGATTTGTAAAGACTGAAAACAAAATTTTATCTTTTGCTTTAAATGTTGATATAAAGGACATTAAAAATATTAAAATAAGGGAAGAATTATTAAATAAGTATTTAGCTAATTTTTTCAACAATAATAGGATTAAAAGCTTTTACTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36772","NCBI_taxonomy_name":"Campylobacter jejuni","NCBI_taxonomy_id":"197"}}}},"ARO_accession":"3003603","ARO_id":"40213","ARO_name":"OXA-447","CARD_short_name":"OXA-447","ARO_description":"OXA-447 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46491":{"category_aro_accession":"3007702","category_aro_cvterm_id":"46491","category_aro_name":"OXA-184-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-184.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3546":{"model_id":"3546","model_name":"OXA-485","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"5741":{"protein_sequence":{"accession":"KSG40284.1","sequence":"MRPLLFSALLLLSGRAQASEWNDSQAVDKLFGAAGVKGTFVLYDVQRQRYVGHDRERAETRFVPASTYKVANSLIGLSTGAVRSADEVLPYGGKPQRFKAWEHDMSLRDAIKASNVPVYQELARRIGLERMRANVSHLGYGNAEIGQVVDNFWLVGPLKISAMEQTRFLLRLAQGELPFPAPVQSTVRAMTLLESGPGWELHGKTGWCFDCTPELGWWVGWVKRNERLYGFALNIDMPGGEADIGKRVELGKASLKALGILP"},"dna_sequence":{"accession":"LLNM01000004.1","fmin":"97677","fmax":"98466","strand":"-","sequence":"ATGCGCCCTCTCCTCTTCAGCGCCCTTCTCCTGCTCTCCGGGCGTGCCCAGGCCAGCGAATGGAACGACAGCCAGGCCGTGGACAAGCTATTCGGAGCGGCCGGTGTGAAAGGCACCTTCGTCCTTTACGATGTGCAGCGGCAGCGCTATGTCGGCCATGACCGGGAGCGCGCGGAAACCCGCTTCGTTCCCGCTTCCACCTACAAGGTGGCGAACAGCCTGATCGGCTTATCCACAGGGGCGGTTAGATCCGCCGACGAGGTTCTTCCCTATGGCGGCAAGCCCCAGCGCTTCAAGGCCTGGGAGCACGACATGAGCCTGCGCGACGCGATCAAGGCATCGAACGTACCGGTCTACCAGGAACTGGCGCGGCGCATCGGCCTGGAGCGGATGCGCGCCAATGTCTCGCACCTGGGTTATGGCAACGCGGAAATCGGCCAGGTTGTGGATAACTTCTGGTTGGTGGGACCGCTGAAGATCAGCGCGATGGAACAGACCCGCTTTCTGCTCCGACTGGCGCAGGGAGAATTGCCATTCCCCGCCCCGGTGCAGTCCACCGTGCGCGCCATGACCCTGCTGGAAAGCGGCCCGGGCTGGGAGCTGCACGGCAAGACCGGCTGGTGCTTCGACTGCACGCCGGAACTCGGCTGGTGGGTGGGCTGGGTGAAGCGCAACGAGCGGCTCTACGGCTTCGCCCTGAACATCGACATGCCCGGCGGCGAGGCCGACATCGGCAAGCGCGTCGAACTGGGCAAGGCCAGTCTCAAGGCTCTCGGGATACTGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3003642","ARO_id":"40252","ARO_name":"OXA-485","CARD_short_name":"OXA-485","ARO_description":"OXA-485 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46513":{"category_aro_accession":"3007724","category_aro_cvterm_id":"46513","category_aro_name":"OXA-50-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-50.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3590":{"model_id":"3590","model_name":"FONA-6","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"5788":{"protein_sequence":{"accession":"CAB61645.1","sequence":"MVKNTLRQTTLMVATVMPLLFGSAPLWAQTANAKANIQQQLSELEKSSGGRLGVALIDTADNSQILYRADERFPMCSTSKVMAVSALLKQSETDKNLLAKRMEIKQSDLVNYNPIAEKHLDTGMTLAEFSAATIQYSDNTAMNKILEHLGGPAKVTEFARTIGDKTFRLDRTEPTLNTAIPGDKRDTTSPLAMAKSLQNLTLGKALGEPQRAQLVEWMKGNTTGGASIRAGLPTTWVVGDKTGSGDYGTTNDIAVIWPANHAPLVLVTYFTQPQQNAEARKDVLAAAAKIVTEGL"},"dna_sequence":{"accession":"AJ251244.1","fmin":"1053","fmax":"1941","strand":"+","sequence":"ATGGTTAAAAATACATTACGTCAAACCACCCTGATGGTGGCTACGGTTATGCCGTTGCTGTTCGGTAGCGCACCGCTATGGGCGCAAACTGCTAATGCCAAGGCGAATATTCAGCAGCAACTGTCTGAACTGGAGAAAAGCTCCGGTGGCCGCCTGGGCGTGGCGCTGATCGATACCGCCGATAATTCGCAGATCCTGTATCGCGCGGATGAACGTTTTCCTATGTGCAGCACCAGCAAGGTGATGGCAGTGTCGGCGTTGTTAAAACAGAGCGAGACGGATAAAAATCTTTTGGCTAAGCGGATGGAGATCAAGCAATCCGATCTGGTCAACTACAACCCGATCGCCGAAAAACACCTGGATACCGGGATGACCCTGGCCGAGTTCAGCGCCGCCACCATCCAGTACAGTGACAACACGGCGATGAACAAGATCCTTGAGCATCTTGGCGGCCCGGCAAAAGTGACAGAATTTGCGCGTACTATTGGCGATAAAACCTTCCGCCTCGATCGTACCGAACCCACTTTAAATACCGCCATTCCAGGTGATAAGCGTGATACCACCTCACCGCTGGCGATGGCAAAAAGCCTGCAAAACCTGACCTTGGGCAAAGCGCTGGGTGAACCACAGCGTGCTCAACTGGTTGAATGGATGAAGGGGAATACTACCGGCGGAGCAAGCATTCGCGCAGGTCTGCCAACTACATGGGTGGTTGGGGATAAAACCGGCAGCGGTGATTACGGTACCACTAACGATATCGCCGTAATTTGGCCAGCGAACCACGCACCGTTGGTGTTGGTGACCTATTTCACGCAGCCACAGCAGAATGCCGAAGCTCGCAAAGACGTGTTGGCTGCGGCTGCTAAAATTGTTACCGAAGGGCTTTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39675","NCBI_taxonomy_name":"Serratia fonticola","NCBI_taxonomy_id":"47917"}}}},"ARO_accession":"3004793","ARO_id":"42911","ARO_name":"FONA-6","CARD_short_name":"FONA-6","ARO_description":"FONA-6 is a class A beta-lactamase gene found in Serratia fonticola.","ARO_category":{"42905":{"category_aro_accession":"3004787","category_aro_cvterm_id":"42905","category_aro_name":"FONA beta-lactamase","category_aro_description":"FONA is a class A beta-lactamase gene family found in Serratia fonticola.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3598":{"model_id":"3598","model_name":"GOB-12","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"5796":{"protein_sequence":{"accession":"AAT68579.1","sequence":"MRNFATLFFMFVCLGLNAQVVKEPENMPKEWNQTYEPFRIAGNLYYVGTYDLASYLIVTDKGNILINTGTAESLPIIKANIQKLGFNYKDIKILLLTQAHYDHTGALQDLKTETAAKFYADKADADVLRTGGKSDYEMGKYGVTFKPITPDRTLKDQDKITLGNTTLTLLHHPGHTKGSCSFIFETKDEKRKYRVLIANMPSIIVDKKFSEVTAYPNIQSDYAYTFGAMKKLDFDLWVASHASQFDLHEKRKEGDPYNPQLFMDKQSYFQNLNDLEKSYLDKIKKDSQDK"},"dna_sequence":{"accession":"AY647249.1","fmin":"0","fmax":"873","strand":"+","sequence":"ATGAGAAATTTTGCTACACTGTTTTTCATGTTCGTTTGCTTGGGCTTGAATGCTCAGGTAGTAAAAGAACCTGAAAATATGCCCAAAGAATGGAACCAGACTTATGAACCATTCAGAATTGCAGGGAACCTATATTACGTAGGAACCTATGATTTGGCTTCTTACCTTATTGTGACAGACAAAGGCAATATTCTCATTAATACAGGAACGGCAGAATCGCTTCCAATAATAAAAGCAAATATCCAAAAGCTCGGGTTTAATTATAAAGACATTAAGATCTTGCTGCTTACTCAGGCTCACTACGACCATACAGGTGCATTACAAGATCTTAAAACAGAAACCGCTGCAAAATTCTATGCCGATAAAGCAGATGCTGATGTCCTGAGAACAGGGGGGAAGTCCGATTATGAAATGGGAAAATATGGGGTGACATTTAAACCTATTACTCCGGATAGAACGTTAAAAGATCAGGATAAAATAACACTGGGAAATACAACCCTGACTTTGCTTCATCACCCGGGACATACAAAAGGTTCCTGCAGTTTTATTTTTGAAACAAAAGACGAGAAGAGAAAGTATAGAGTTCTGATAGCTAATATGCCCTCTATTATTGTTGATAAGAAATTTTCTGAAGTTACAGCATATCCGAATATTCAGTCCGATTATGCTTATACCTTTGGTGCTATGAAAAAGCTTGATTTTGATCTTTGGGTAGCATCGCATGCAAGTCAGTTCGATCTGCATGAAAAACGTAAAGAAGGGGATCCGTACAATCCACAATTGTTTATGGATAAGCAAAGCTATTTCCAAAACCTTAATGATTTGGAGAAAAGCTATCTCGACAAAATAAAAAAAGATTCCCAAGATAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36960","NCBI_taxonomy_name":"Elizabethkingia meningoseptica","NCBI_taxonomy_id":"238"}}}},"ARO_accession":"3004804","ARO_id":"42924","ARO_name":"GOB-12","CARD_short_name":"GOB-12","ARO_description":"GOB-12 is a class B beta-lactamase gene found in Elizabethkingia meningoseptica.","ARO_category":{"41376":{"category_aro_accession":"3004212","category_aro_cvterm_id":"41376","category_aro_name":"GOB beta-lactamase","category_aro_description":"The GOB family of beta-lactamases have been discovered in the Elizabethkingia meningoseptica and are classified as subclass B3 beta-lactamase. They confer resistance to cephalosporins, penicillins, and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3645":{"model_id":"3645","model_name":"LEN-58","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"5917":{"protein_sequence":{"accession":"SXE97430.1","sequence":"MRYVRLCVISLLATLPLAVDAGPQPLEQIKQSESQLSGRVGMVEMDLASGRTLAAWRADERFPMVSTFKVLLCGAVLARVDAGVEQLDRRIHYRQQDLVDYSPVSEKHLFDGMTIGELCAAAITLSDNSAGNLLLATVGGPAGLTAFLRQIGDNVTRLDRWETALNEALPGDARDTTTPASMAATLRKLLTAQHLSARSQQQLLQWMVDDRVAGPLIRAVLPPGWFIADKTGAGERGARGIVALLGPDGKPERIVVIYLRDTPASMAERNQHIAGIGAALIEHWQR"},"dna_sequence":{"accession":"UKAA01000001.1","fmin":"322202","fmax":"323063","strand":"-","sequence":"ATGCGTTATGTTCGCCTGTGTGTTATCTCCCTGTTAGCCACCCTGCCACTGGCGGTAGACGCCGGTCCACAGCCGCTTGAGCAGATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTGGGGATGGTGGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCGATGAACGCTTTCCCATGGTGAGCACCTTTAAAGTGCTGCTGTGCGGCGCGGTGCTGGCGCGGGTGGATGCAGGGGTCGAACAACTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTTTCGACGGGATGACGATCGGCGAACTCTGCGCCGCCGCCATCACCCTGAGCGATAACAGCGCTGGCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCGGGATTAACTGCCTTTCTGCGCCAGATCGGTGACAACGTCACCCGTCTTGACCGCTGGGAAACGGCACTGAATGAGGCGCTTCCCGGCGACGCGCGCGACACCACCACCCCGGCCAGCATGGCCGCCACGCTGCGCAAACTACTGACCGCGCAGCATCTGAGCGCCCGTTCGCAACAGCAACTCCTGCAGTGGATGGTGGACGATCGGGTTGCCGGCCCGCTGATCCGCGCCGTGCTGCCGCCGGGCTGGTTTATCGCCGACAAAACCGGGGCTGGCGAACGGGGTGCGCGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAACCGGAGCGCATTGTGGTGATCTATCTGCGGGATACCCCGGCGAGTATGGCCGAGCGTAATCAACATATCGCCGGGATCGGCGCAGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42612","NCBI_taxonomy_name":"Klebsiella variicola","NCBI_taxonomy_id":"244366"}}}},"ARO_accession":"3004849","ARO_id":"42985","ARO_name":"LEN-58","CARD_short_name":"LEN-58","ARO_description":"A class-A broad-spectrum beta-lactamase from Klebsiella.","ARO_category":{"36236":{"category_aro_accession":"3000097","category_aro_cvterm_id":"36236","category_aro_name":"LEN beta-lactamase","category_aro_description":"LEN beta-lactamases are chromosomal class A beta-lactamases that confer resistance to ampicillin, amoxicillin, carbenicillin, and ticarcillin but not to extended-spectrum beta-lactams.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"320":{"model_id":"320","model_name":"Streptococcus pneumoniae PBP2x conferring resistance to amoxicillin","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"4473":"I371T","4474":"R384G","4475":"N514H","4477":"N605T","4478":"M400T","4479":"M339F","4476":"L546V"},"Curated-R":{"4473":"I371T","4474":"R384G","4475":"N514H","4477":"N605T","4478":"M400T","4479":"M339F","4476":"L546V"},"clinical":{"4473":"I371T","4474":"R384G","4475":"N514H","4477":"N605T","4478":"M400T","4479":"M339F","4476":"L546V"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1450"}},"model_sequences":{"sequence":{"331":{"protein_sequence":{"accession":"AFC91898.1","sequence":"MKWTKRVIRYATKNRKSPAENRRRVGKSLSLLSVFVFAIFLVNFAVIIGTGTRFGTDLAKEAKKVHQTTRTVPAKRGTIYDRNGVPIAEDATSYNVYAVIDENYKSATGKILYVEKTQFNKVAEVFHKYLDMEESYVREQLSQPNLKQVSFGAKGNGITYANMMSIKKELETAEVKGIDFTTSPNRSYPNGQFASSFIGLAQLHENEDGSKSLLGTSGMESSLNSILAGKDGIITYEKDRLGNVVPGTEQVSQQTVDGKDVYTTISSTLQSFMETQMNAFQEKVKGKYMTATLVSAKTGEILATTQRPTFDADTKEGLTKDFVWRDILYQSNYEPGSPMKVMTLAASIDNNTFPGGEYFNSSELKIADVTIRDWDVNESLTGGGMMTFSQGFAHSSNVGMTLLEQKMGDATWLDYLNRFKFGVPTRFGLTDEYAGQLPADNIVNIAQSSFGQGISVTQTQMIRAFTAIANDGVMLEPKFISAIYDPNDQTARKSQKEVVGNPVSKDAASLTRTNMILVGTDPVYGTMYNHSTGKPTVTVPGQNVALKSGTAQIADEKNGGYLVGLTNYIFSAVSMNPAENPDFILYVTVQQPEHYSGIQLGEFANPILERASAMKDSLNLQTTAKALEQVSQQSPYPMPSVKDISPGDLAEELRRNLVQPIVVGTGTKIKESSVEEGTNLAPNQQVILLSDKVEEIPDMYGWKKETAEAFAKWLDIELEFEGSGSVVQKQDVRTNTAIKNIKKITLTLGD"},"dna_sequence":{"accession":"JN645706.1","fmin":"0","fmax":"2253","strand":"+","sequence":"ATGAAGTGGACAAAAAGAGTAATCCGTTATGCGACCAAAAATCGGAAATCGCCGGCTGAAAACAGACGCAGAGTTGGAAAAAGTCTGAGTTTATTATCTGTCTTTGTTTTTGCCATTTTTTTAGTCAATTTTGCGGTCATTATTGGGACAGGCACTCGCTTTGGAACAGATTTAGCGAAGGAAGCTAAGAAGGTTCATCAAACCACCCGTACAGTTCCTGCCAAACGTGGGACTATTTATGACCGAAATGGAGTCCCGATTGCTGAGGATGCAACCTCCTATAATGTCTATGCGGTCATTGATGAGAACTATAAGTCAGCAACGGGTAAGATTCTTTACGTAGAAAAAACACAATTTAACAAGGTTGCAGAGGTCTTTCATAAGTATCTGGACATGGAAGAATCCTATGTAAGAGAGCAACTCTCGCAACCTAATCTCAAGCAAGTTTCCTTTGGAGCAAAGGGCAATGGGATTACCTATGCCAATATGATGTCTATCAAAAAAGAGTTGGAAACTGCAGAGGTCAAGGGGATTGATTTTACAACCAGTCCTAATCGTAGTTACCCAAACGGACAATTTGCTTCTAGTTTTATCGGACTAGCTCAGCTCCATGAAAATGAAGATGGGAGCAAGAGTTTGCTGGGAACTTCTGGGATGGAGAGTTCCTTGAACAGTATTCTCGCAGGGAAAGATGGCATTATTACTTATGAAAAGGATCGTCTAGGTAATGTTGTACCCGGAACAGAACAAGTTTCCCAACAAACGGTAGATGGCAAGGATGTTTATACAACGATTTCCAGCACCCTTCAGTCCTTCATGGAGACCCAGATGAATGCCTTTCAAGAAAAAGTAAAAGGTAAGTATATGACGGCGACCTTGGTCAGTGCTAAAACAGGGGAAATTCTTGCAACAACGCAGAGACCAACCTTTGATGCCGATACTAAGGAAGGACTTACCAAGGACTTTGTTTGGCGTGATATCCTCTATCAAAGTAACTATGAGCCGGGGTCACCCATGAAGGTCATGACGCTAGCAGCTTCTATTGATAACAATACCTTCCCAGGTGGAGAATACTTCAATAGCAGTGAATTAAAAATAGCGGATGTGACAATTCGAGATTGGGACGTTAATGAAAGTTTGACCGGTGGTGGTATGATGACATTTTCTCAAGGATTTGCTCACTCAAGTAACGTTGGGATGACCCTCCTTGAGCAAAAGATGGGAGATGCTACCTGGCTTGATTATCTTAATCGTTTTAAATTTGGTGTTCCGACCCGTTTCGGTTTGACGGATGAGTATGCTGGTCAGCTTCCTGCGGATAATATCGTTAACATTGCGCAAAGCTCATTTGGGCAAGGGATTTCAGTGACCCAGACGCAAATGATTCGTGCCTTTACAGCTATTGCTAATGACGGTGTCATGCTGGAACCTAAATTTATTAGTGCCATTTATGATCCAAATGATCAAACTGCTCGGAAATCTCAAAAAGAAGTTGTGGGAAATCCTGTTTCCAAAGATGCAGCTAGTCTAACTCGGACTAACATGATTTTGGTAGGGACGGATCCGGTTTATGGAACCATGTATAACCACAGCACAGGCAAGCCAACTGTAACTGTTCCTGGGCAAAATGTAGCCCTCAAGTCTGGTACGGCTCAGATTGCTGACGAGAAAAATGGTGGTTATCTAGTCGGGTTAACCAACTATATTTTCTCGGCTGTATCAATGAACCCTGCTGAAAATCCTGATTTTATCTTGTATGTGACGGTCCAACAACCTGAACATTATTCAGGTATTCAGTTGGGAGAATTTGCCAATCCTATCTTGGAGCGGGCTTCAGCTATGAAAGACTCTCTCAATCTTCAAACAACAGCTAAAGCTTTGGAGCAAGTAAGTCAACAAAGTCCTTATCCTATGCCTAGTGTCAAGGATATTTCACCTGGTGATTTAGCAGAAGAATTGCGTCGCAATCTTGTACAACCCATCGTTGTGGGAACAGGAACAAAGATTAAAGAATCATCTGTAGAAGAAGGGACCAATCTTGCACCAAACCAACAAGTTATCCTTTTATCGGATAAGGTAGAAGAAATTCCAGACATGTATGGCTGGAAAAAAGAGACTGCTGAGGCCTTTGCTAAATGGTTGGATATCGAGCTGGAATTTGAAGGTTCAGGTTCCGTCGTTCAGAAGCAGGATGTTCGGACTAATACAGCTATCAAAAACATTAAAAAAATTACATTAACTTTAGGAGACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35917","NCBI_taxonomy_name":"Streptococcus pneumoniae","NCBI_taxonomy_id":"1313"}}}},"ARO_accession":"3003043","ARO_id":"39477","ARO_name":"Streptococcus pneumoniae PBP2x conferring resistance to amoxicillin","CARD_short_name":"Spne_PBP2x_AMX","ARO_description":"PBP2x is a penicillin-binding protein found in Streptococcus pneumoniae.","ARO_category":{"40661":{"category_aro_accession":"3003938","category_aro_cvterm_id":"40661","category_aro_name":"Penicillin-binding protein mutations conferring resistance to beta-lactam antibiotics","category_aro_description":"Mutations in PBP transpeptidases that change the affinity for penicillin thereby conferring resistance to penicillin antibiotics.","category_aro_class_name":"AMR Gene Family"},"35981":{"category_aro_accession":"0000064","category_aro_cvterm_id":"35981","category_aro_name":"amoxicillin","category_aro_description":"Amoxicillin is a moderate-spectrum, bacteriolytic, beta-lactam antibiotic used to treat bacterial infections caused by susceptible microorganisms. A derivative of penicillin, it has a wider range of treatment but remains relatively ineffective against Gram-negative bacteria. It is commonly taken with clavulanic acid, a beta-lactamase inhibitor. Like other beta-lactams, amoxicillin interferes with the synthesis of peptidoglycan.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4256":{"model_id":"4256","model_name":"ADC-191","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6631":{"protein_sequence":{"accession":"WP_003112187.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKVLKNTPIDQVNLLQLATYTSGNLALKFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGFYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTTGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLDAIKK"},"dna_sequence":{"accession":"NG_064714.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACCCCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCATTATTAGAAAAATATGATGTGCCGGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGTGCTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGAAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGTCCACTCGATGCCCCAGCATACGGCGTCAAATCCACCTTACCGGATATGTTGAGTTTTATTCATGCCAACCTCAACCCACAGAAATATCCGGCAGATATTCAACGGGCAATTAATGAAACACATCAAGGGTTCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCACCGGTTTCGGAACATATGTGGTCTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGGATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006360","ARO_id":"44822","ARO_name":"ADC-191","CARD_short_name":"ADC-191","ARO_description":"ADC-191 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3720":{"model_id":"3720","model_name":"Mycobacterium tuberculosis Rv3169 mutations confer resistance to pyrazinamide","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"40394":{"param_type":"nonsense mutation","param_description":"A sequence change where, compared to a reference sequence, one codon is replaced by a termination codon through a nucleotide substitution. These are described as a substitution of the wildtype codon to a termination codon. Format is given as [wild type AA][position][Ter], for example Q42Ter where Q42 is a wildtype amino acid replaced by a premature termination codon.","param_type_id":"40394","param_value":{"9733":"Y53Ter"}},"snp":{"ReSeqTB-Minimal":{"9733":"L546V","9734":"N56S","9737":"A194P","9736":"A190G"},"param_value":{"9734":"N56S","9735":"W171R","9737":"A194P","9736":"A190G"},"clinical":{"9734":"N56S","9735":"W171R","9737":"A194P","9736":"A190G"},"ReSeqTB-High":{"9735":"W171R"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"680"}},"model_sequences":{"sequence":{"8783":{"protein_sequence":{"accession":"NP_217685.1","sequence":"MPQMLGPLDEYPLHQLPQPIAWPGSSDRNFYDRSYFNAHDRTGNIFLITGIGYYPNLGVKDAFVLIRRADIQTAVHLSDAIDSDRLHQHVNGYRVEVVEPLRKLRIVLDETEGVAADLTWEGLFDVVQEQPHVLRSGNRVTLDAQRFAQLGTWSGRIVVDGERIAVDPATWLGSRDRSWGIRPVGEPEPAGRPADPPFEGMWWLYVPLAFDDFAVVLIIQEEPDGFRSLNDCTRIWRDGHVEQLGWPRVRIHYRSGTRIPTGATIEASTPDGAPVHFDVESKLAVPTHVGGGYGGDSDWSHGMWKGEKFVERRTYDMTDPTIIARAGFGVIDHVGRALCRDGDGNPVQGWGLFEHGALGRHDPSGFADWSTLAP"},"dna_sequence":{"accession":"NC_000962.3","fmin":"3537237","fmax":"3538362","strand":"+","sequence":"ATGCCGCAAATGCTAGGCCCACTCGACGAGTACCCGCTACATCAGCTTCCCCAGCCGATCGCCTGGCCGGGCTCCTCCGACCGCAACTTCTACGACCGCTCCTACTTCAACGCCCACGACCGCACCGGGAACATCTTTCTGATCACCGGTATCGGCTACTACCCTAACCTGGGCGTGAAAGACGCGTTCGTGCTGATCAGGCGTGCGGACATACAGACCGCGGTGCATCTTTCGGATGCCATCGACTCCGACCGGCTACACCAGCACGTCAACGGTTACCGGGTGGAGGTCGTCGAGCCGCTGCGAAAACTGCGTATCGTGCTCGACGAAACCGAAGGTGTGGCGGCCGATCTCACCTGGGAGGGCCTGTTCGACGTCGTCCAGGAACAGCCGCACGTCTTGCGCTCCGGCAACCGGGTGACCCTGGATGCGCAGCGCTTCGCGCAGCTGGGCACCTGGAGCGGCCGCATCGTCGTCGACGGCGAACGGATCGCCGTCGATCCGGCGACCTGGCTCGGCAGCCGGGACCGGTCCTGGGGCATCCGGCCGGTGGGGGAACCAGAACCGGCGGGCCGGCCCGCCGACCCACCCTTCGAGGGCATGTGGTGGCTGTATGTGCCGTTGGCCTTCGACGACTTCGCCGTCGTGCTGATCATCCAGGAAGAACCCGACGGGTTCCGCTCGCTCAACGACTGCACCCGGATCTGGCGTGACGGCCACGTCGAGCAGCTGGGCTGGCCGCGGGTGCGGATCCACTACCGCTCCGGCACCCGCATCCCGACCGGGGCGACGATCGAGGCAAGCACCCCCGACGGCGCGCCGGTGCACTTCGACGTGGAGTCCAAACTGGCGGTGCCGACCCATGTCGGTGGCGGCTACGGGGGTGACTCGGACTGGTCACATGGCATGTGGAAGGGCGAGAAGTTCGTCGAGCGAAGAACCTACGACATGACCGATCCGACGATCATCGCGCGGGCCGGCTTCGGCGTCATCGACCACGTCGGTCGCGCGCTATGCCGCGACGGCGACGGGAATCCAGTGCAGGGCTGGGGTCTGTTTGAACACGGGGCGCTGGGCCGCCACGACCCATCGGGGTTCGCCGACTGGTCTACGCTGGCGCCCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3004993","ARO_id":"43180","ARO_name":"Mycobacterium tuberculosis Rv3169 mutations confer resistance to pyrazinamide","CARD_short_name":"Mtub_Rv3169_PZA","ARO_description":"Mutations in the Rv3169 gene that can contribute to or confer resistance to pyrazinamide resistance.","ARO_category":{"43179":{"category_aro_accession":"3004992","category_aro_cvterm_id":"43179","category_aro_name":"pyrazinamide resistant Rv3169","category_aro_description":"A conserved protein with an unknown function determined through proteomics study. May contribute or confer resistance to pyrazinamide resistance.","category_aro_class_name":"AMR Gene Family"},"39997":{"category_aro_accession":"3003413","category_aro_cvterm_id":"39997","category_aro_name":"pyrazinamide","category_aro_description":"Pyrazinamide is an antimycobacterial. It is highly specific and active only against Mycobacterium tuberculosis. This compound is a prodrug and needs to be activated inside the cell. It interferes with the bacterium's ability to synthesize new fatty acids, causing cell death.","category_aro_class_name":"Antibiotic"},"45737":{"category_aro_accession":"3007155","category_aro_cvterm_id":"45737","category_aro_name":"pyrazine antibiotic","category_aro_description":"A group of antibiotics derived from pyrazine.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2303":{"model_id":"2303","model_name":"bcr-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4627":{"protein_sequence":{"accession":"ALV80601.1","sequence":"MPASASRIQVGSGERRLLLLLSALVAFGPLSIDMYLPSLPAIAADLGASDAQVQRSISGFLVGFCVGMLFYGPLSDRFGRRPVLLAGIALYLFSSLACALADSAGQLVLLRVLQALGGGAASVLARAMVRDLYPLGEAARMLALMHMVTMLAPLAAPLLGGYLMLWAGWRALFVVLALFAGLCLLAVWRVAESHPPERRGGSLAQAFLAYGRLLGDRRALGYVLCMGLAFAGMFAYISAAPFVFIEHFGVRAERFGWFFGLNILGVMLATWCSARLVRRHGPRPLLRAGSLLACVSGLFLLGYAALGERGGLWALVPGLLCFVSVTGLLGANCIASLLALYPGQAGAASAVAVSGQFGLGCLASLAVGWLALPGVLPMALVMAVCGVGSLLALGLALHGGNR"},"dna_sequence":{"accession":"CP012901.1","fmin":"5979156","fmax":"5980365","strand":"-","sequence":"GTGCCTGCGAGTGCATCGAGGATTCAGGTCGGAAGCGGCGAACGACGCCTGTTGCTGCTGTTGTCGGCGCTGGTGGCGTTCGGCCCGCTGTCGATCGACATGTACCTGCCGAGCCTGCCGGCGATCGCCGCCGATCTCGGCGCCAGCGATGCCCAGGTGCAGCGGAGCATCAGCGGCTTCCTGGTCGGCTTCTGCGTCGGCATGCTGTTCTACGGCCCCTTGTCCGACCGTTTCGGCCGGCGCCCGGTGCTGCTGGCCGGTATCGCCTTGTACCTGTTCAGCAGCCTGGCCTGCGCGCTGGCCGACAGCGCGGGGCAACTGGTCCTGCTGAGGGTGCTCCAGGCCCTCGGCGGCGGCGCCGCGTCGGTGCTGGCGCGGGCCATGGTGCGCGACCTCTATCCGTTGGGCGAGGCCGCCCGGATGCTGGCATTGATGCACATGGTGACCATGCTGGCACCGCTGGCCGCGCCGCTGCTCGGCGGCTACCTGATGCTCTGGGCCGGCTGGCGCGCGTTGTTCGTGGTCCTGGCGCTGTTCGCCGGGCTCTGCCTGCTGGCGGTCTGGCGGGTCGCCGAAAGCCACCCGCCGGAGCGCCGCGGCGGCAGCCTGGCCCAGGCCTTTCTCGCCTATGGGCGGCTGCTCGGCGACCGTCGCGCGCTGGGCTACGTGCTGTGCATGGGGCTGGCGTTCGCCGGGATGTTCGCCTACATCAGCGCCGCGCCCTTCGTGTTCATCGAGCATTTCGGCGTGCGCGCGGAGCGCTTCGGCTGGTTCTTCGGCCTGAACATCCTCGGCGTGATGCTCGCCACCTGGTGCAGCGCGCGCCTGGTGCGCCGCCACGGTCCGCGGCCGCTGCTGCGGGCCGGCAGCCTGCTGGCCTGCGTGTCCGGGCTGTTCCTCCTCGGCTATGCGGCGCTCGGCGAGCGGGGCGGGTTGTGGGCGCTGGTGCCCGGCCTGCTGTGCTTCGTCAGCGTCACCGGCCTGCTCGGCGCCAACTGCATCGCCAGCCTGCTGGCGTTGTATCCCGGACAGGCCGGGGCGGCTTCGGCGGTGGCGGTGTCCGGGCAGTTCGGCCTCGGCTGCCTGGCCAGCCTGGCGGTCGGCTGGCTGGCGCTGCCCGGCGTGCTGCCGATGGCGCTGGTGATGGCCGTCTGCGGCGTCGGCAGCCTGCTCGCGCTGGGCTTGGCCCTGCACGGCGGAAACCGTTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3003801","ARO_id":"40486","ARO_name":"bcr-1","CARD_short_name":"bcr-1","ARO_description":"Transmembrane protein which expels bicyclomycin from the cell, leading to bicyclomycin resistance. Identified in Pseudomonas aeruginosa strains responsible for outbreaks in Brazil, often appearing with blaSPM-1, another bicyclomycin resistance gene.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35972":{"category_aro_accession":"0000055","category_aro_cvterm_id":"35972","category_aro_name":"bicyclomycin","category_aro_description":"Bicyclomycin represents a unique class of antibiotics, discovered in 1972. It is obtained by the fermentation of Streptomyces sapporonensis. In the crystalline form bicyclomycin is observed to be rhombic or monoclinic, depending on the solvent used. This antibiotic kills bacteria by inhibiting the Rho transcription terminator factor, halting ribonucleic acid (RNA) synthesis.","category_aro_class_name":"Antibiotic"},"45732":{"category_aro_accession":"3007150","category_aro_cvterm_id":"45732","category_aro_name":"bicyclomycin-like antibiotic","category_aro_description":"A group of antibiotics including bicyclomycin and its analogues.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2705":{"model_id":"2705","model_name":"MexEF-OprN with MexS mutations conferring resistance to chloramphenicol, ciprofloxacin, and trimethoprim","model_type":"efflux pump system meta-model","model_type_id":"41112","model_description":"Efflux Pump System Meta-Models (EPS) are dedicated to efflux complexes and their regulators, such as AcrAB-TolC. Using the efflux pump components parameter, this model type simply includes a list of detection models for each component of the complex. This model type is still under development and not currently supported by the Resistance Gene Identifier (RGI) software.","model_param":{"41141":{"param_type":"efflux pump components","param_description":"Association of proteins within efflux protein complexes or regulatory networks are encoded by the efflux pump components parameter: model_id,model_id,model_id, etc.","param_type_id":"41141","param_value":{"7584":"1041,1608,1067,1300,172"}},"snp":{"Curated-R":{"7584":"A190G"}}},"ARO_accession":"3004068","ARO_id":"41145","ARO_name":"MexEF-OprN with MexS mutations conferring resistance to chloramphenicol, ciprofloxacin, and trimethoprim","CARD_short_name":"Paer_MexS_MULT","ARO_description":"The MexEF\u2013OprN efflux pump with MexS mutations conferring resistance to chloramphenicol and ciprofloxacin. The model includes the MexT regulator, as MexS is suggested to inactivate MexT.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2348":{"model_id":"2348","model_name":"ADC-18","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"5421":{"protein_sequence":{"accession":"CAK95243.1","sequence":"MRFKKISCLLLPPLFIFSTSIYAGNTPKEQEVKKLVDQNFKPLLDKYDVPGMAVGVIQNNKKYEIYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKAKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKTKNAIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPPLHLKNSYVNVPKTQMQNYAYGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLTFINANLNPQKYPKDIQRAISETHQGFYQVGTMYQALGWEEFSYPAPLQTLLDSNSEQIVMKPNKVTAISKEPSVKMFHKTGSTNGFGSYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"AM283523.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGCTTACTTTTACCGCCTCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGAACAAGAAGTTAAAAAACTGGTAGATCAAAATTTTAAGCCTTTATTAGATAAATATGATGTGCCTGGTATGGCCGTGGGGGTCATTCAAAATAATAAAAAATATGAAATATATTATGGCCTACAATCCGTTCAGGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAACTAGGTTCGGTCAGTAAATTATTTACCGCTACAGCTGGTGGATATGCAAAAGCAAAAGGAAAAATCTCTTTTGATGACACACCCGGAAAATATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAATCTTCTTCAACTTGCGACGTATACAAGTGGCAATCTCGCCTTACAATTTCCAGATGAAGTTCAAACAGACCAACAAGTTTTAACTTTTTTCAAAGATTGGAAAACTAAAAACGCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCTTATTTGGAAAAGTTGTGGCTTTGTCTATGAATAAACCTTTTGACCAAGTCTTAGAAAAAACAATTTTTCCACCTCTCCATTTAAAAAATAGCTATGTAAATGTACCCAAAACTCAAATGCAAAATTATGCATATGGCTATAACCAAGAAAATCAGCCGATCCGAGTTAACCCTGGCCCGCTAGATGCTCCAGCATACGGCGTTAAATCGACACTACCAGATATGCTGACTTTTATTAATGCCAACCTCAACCCACAGAAATATCCGAAAGATATTCAACGTGCAATTAGTGAAACACATCAAGGTTTCTATCAAGTCGGTACGATGTATCAAGCATTGGGTTGGGAAGAATTTTCTTATCCAGCACCTTTACAAACTTTATTAGACAGTAATTCAGAGCAAATCGTGATGAAGCCTAATAAAGTGACTGCCATTTCCAAAGAACCTTCAGTTAAGATGTTCCACAAAACTGGCTCAACAAATGGCTTTGGATCTTATGTGGTGTTTATTCCAAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAACGCATTAAGGCAGCGTATGCAGTATTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3003862","ARO_id":"40561","ARO_name":"ADC-18","CARD_short_name":"ADC-18","ARO_description":"ADC-18 is a beta-lactamase found in Acinetobacter pittii.","ARO_category":{"40543":{"category_aro_accession":"3003846","category_aro_cvterm_id":"40543","category_aro_name":"ADC beta-lactamase without carbapenemase activity","category_aro_description":"ADC beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases with extended-spectrum resistance to cephalosporins but not to carbapenems. ADC beta-lactamases are found in Acinetobacter sp. and Oligella urethralis.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1213":{"model_id":"1213","model_name":"nalD","model_type":"protein overexpression model","model_type_id":"41091","model_description":"Protein Overexpression Models (POM) are similar to Protein Variant Models (PVM) in that they include a protein reference sequence, a curated BLASTP bitscore cut-off, and mapped resistance variants. Whereas PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, reporting only those with curated mutations conferring AMR, POMs are restricted to regulatory proteins and report both wild-type sequences and\/or sequences with mutations leading to overexpression of efflux complexes. The former lead to efflux of antibiotics at basal levels, while the latter can confer clinical resistance. POMs include a protein reference sequence (often from wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Perfect RGI match is 100% identical to the wild-type reference protein sequence along its entire length, a Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value may or may not contain at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off may or may not contain at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"6750":"S32N"},"Curated-R":{"6750":"S32N"},"clinical":{"6750":"S32N"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"375"}},"model_sequences":{"sequence":{"5527":{"protein_sequence":{"accession":"AAG06962.1","sequence":"MRRTKEDSEKTRTAILLAAEELFLEKGVSHTSLEQIARAAGVTRGAVYWHFQNKAHLFNEMLNQVRLPPEQLTERLSGCDGSDPLRSLYDLCLEAVQSLLTQEKKRRILTILMQRCEFTEELREAQERNNAFVQMFIELCEQLFARDECRVRLHPGMTPRIASRALHALILGLFNDWLRDPRLFDPDTDAEHLLEPMFRGLVRDWGQASSAP"},"dna_sequence":{"accession":"AE004091.2","fmin":"4006509","fmax":"4007148","strand":"+","sequence":"ATGCGACGCACAAAGGAAGATTCTGAAAAAACCCGTACGGCCATCCTCCTGGCCGCCGAGGAACTGTTCCTGGAAAAGGGCGTGTCCCATACCAGCCTGGAACAGATCGCCAGGGCCGCCGGGGTGACCCGTGGCGCCGTCTACTGGCACTTCCAGAACAAGGCCCACCTGTTCAACGAGATGCTCAACCAGGTACGCCTGCCGCCGGAGCAACTCACCGAGCGCCTGTCCGGCTGCGATGGCAGCGACCCGCTGCGCTCGCTCTACGACCTCTGCCTGGAGGCCGTGCAATCGTTGCTGACGCAGGAGAAGAAGCGCCGCATCCTGACCATCCTGATGCAACGTTGCGAATTCACCGAGGAACTGCGCGAGGCGCAGGAACGCAACAACGCCTTCGTGCAGATGTTCATCGAACTCTGCGAGCAGTTGTTCGCCCGCGACGAATGCCGTGTGCGGCTGCATCCGGGCATGACCCCGAGGATCGCCTCGCGCGCCTTGCACGCGCTGATCCTGGGCCTGTTCAACGACTGGTTGCGCGACCCGCGCCTGTTCGATCCGGATACGGACGCGGAACACCTGCTGGAGCCGATGTTCCGTGGCCTGGTGCGCGACTGGGGTCAGGCCAGCTCGGCGCCGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36804","NCBI_taxonomy_name":"Pseudomonas aeruginosa PAO1","NCBI_taxonomy_id":"208964"}}}},"ARO_accession":"3000819","ARO_id":"37199","ARO_name":"nalD","CARD_short_name":"nalD","ARO_description":"NalD is a repressor of MexAB-OprM. Mutations lead to multidrug resistance and MexAB-OprM overexpression.","ARO_category":{"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1474":{"model_id":"1474","model_name":"MexR","model_type":"protein overexpression model","model_type_id":"41091","model_description":"Protein Overexpression Models (POM) are similar to Protein Variant Models (PVM) in that they include a protein reference sequence, a curated BLASTP bitscore cut-off, and mapped resistance variants. Whereas PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, reporting only those with curated mutations conferring AMR, POMs are restricted to regulatory proteins and report both wild-type sequences and\/or sequences with mutations leading to overexpression of efflux complexes. The former lead to efflux of antibiotics at basal levels, while the latter can confer clinical resistance. POMs include a protein reference sequence (often from wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Perfect RGI match is 100% identical to the wild-type reference protein sequence along its entire length, a Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value may or may not contain at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off may or may not contain at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"2760":"I72N","2761":"L75P","2762":"L75R","2763":"R83C","2825":"R91C","2826":"R91H","2888":"L45P","2889":"I46N","2890":"L57R","6704":"L57P","7614":"N53D","7615":"H107P","2891":"T69I"},"Curated-R":{"2760":"I72N","2761":"L75P","2762":"L75R","2763":"R83C","2825":"R91C","2826":"R91H","2888":"L45P","2889":"I46N","2890":"L57R","6704":"L57P","7614":"N53D","7615":"H107P","2891":"T69I"},"clinical":{"2760":"I72N","2761":"L75P","2762":"L75R","2763":"R83C","2825":"R91C","2826":"R91H","2888":"L45P","2889":"I46N","2890":"L57R","6704":"L57P","7614":"N53D","7615":"H107P","2891":"T69I"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"270"}},"model_sequences":{"sequence":{"5452":{"protein_sequence":{"accession":"AAG03813.1","sequence":"MNYPVNPDLMPALMAVFQHVRTRIQSELDCQRLDLTPPDVHVLKLIDEQRGLNLQDLGRQMCRDKALITRKIRELEGRNLVRRERNPSDQRSFQLFLTDEGLAIHQHAEAIMSRVHDELFAPLTPVEQATLVHLLDQCLAAQPLEDI"},"dna_sequence":{"accession":"AE004091.2","fmin":"471305","fmax":"471749","strand":"-","sequence":"ATGAACTACCCCGTGAATCCCGACCTGATGCCCGCGCTGATGGCGGTCTTCCAGCATGTGCGGACGCGCATCCAGAGCGAGCTCGATTGCCAGCGACTCGACCTGACCCCGCCCGACGTCCATGTATTGAAGCTTATCGACGAACAACGCGGGCTGAACCTGCAGGACCTGGGACGCCAGATGTGCCGCGACAAGGCACTGATCACCCGGAAGATCCGCGAGCTGGAGGGAAGAAACCTGGTCCGCCGCGAGCGCAACCCCAGCGACCAGCGCAGCTTCCAGCTCTTCCTCACCGACGAGGGGCTGGCCATCCACCAGCATGCGGAGGCCATCATGTCACGCGTGCATGACGAGTTGTTTGCCCCGCTCACCCCGGTGGAACAGGCCACCCTGGTGCATCTCCTCGACCAGTGCCTGGCCGCGCAACCGCTTGAGGATATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36804","NCBI_taxonomy_name":"Pseudomonas aeruginosa PAO1","NCBI_taxonomy_id":"208964"}}}},"ARO_accession":"3000506","ARO_id":"36645","ARO_name":"MexR","CARD_short_name":"MexR","ARO_description":"MexR is the repressor of the MexRAB-OprM operon. Mutant forms of mexR result in up-regulation of efflux pump system MexAB-OprM.","ARO_category":{"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"3409":{"model_id":"3409","model_name":"OXA-123","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"5604":{"protein_sequence":{"accession":"ABX45062.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDKKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWNGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"EU255292.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATAAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGAACGGGCAAAAAAGGCTGTTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001445","ARO_id":"37845","ARO_name":"OXA-123","CARD_short_name":"OXA-123","ARO_description":"OXA-123 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1240":{"model_id":"1240","model_name":"mphL","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4721":{"protein_sequence":{"accession":"EEL41021.1","sequence":"MEEIKMNTLKIKQLATKEGLNILEDSIKINESGVDFQVAHAKEQNGDKWILRIPRRPESMRHVLQEKKALEIIKNHAGFQVPDWSIFTEDLIAYKQLSGVPAATIDIEQQGYIWSFNEKNAPSEYHISLGKVLANLHSLPQQEFNNIGIEILTANELRASMEQRMNRVKEQYYVNQKLWDRWQAWLTEDSFWPSHVGVTHGDIHPGHILIDKKNNVTGLIDWTEVGIADVSIDFTSHYLLFGKDGLTKLISSYDNAGGKTWSRMDEHIIELLTTSSITVAEYAQVSGLKEMHEAAVHMLATES"},"dna_sequence":{"accession":"ACMJ01000036.1","fmin":"72074","fmax":"72986","strand":"-","sequence":"TTGGAGGAAATAAAAATGAACACACTTAAAATTAAACAATTAGCAACTAAGGAAGGCCTAAATATCTTAGAAGATTCAATAAAAATCAATGAATCTGGTGTTGACTTTCAAGTAGCACACGCTAAAGAACAAAACGGAGATAAATGGATACTAAGAATTCCTCGTAGACCAGAATCTATGAGACATGTCCTACAAGAAAAAAAGGCATTGGAAATCATAAAAAACCATGCAGGATTCCAAGTTCCTGATTGGTCTATATTCACTGAAGACTTAATTGCCTATAAGCAACTAAGTGGCGTTCCTGCCGCCACTATTGATATAGAACAACAAGGATATATATGGAGCTTTAATGAAAAAAACGCACCATCTGAATACCATATTTCATTAGGAAAAGTTCTAGCGAATTTACACTCATTACCTCAACAAGAATTTAATAATATCGGTATTGAAATTCTTACTGCTAATGAATTAAGAGCTTCTATGGAACAAAGGATGAATCGAGTGAAGGAACAATACTATGTCAATCAAAAATTATGGGATCGTTGGCAAGCATGGCTAACTGAAGATTCTTTTTGGCCATCTCATGTAGGAGTAACGCATGGGGATATACATCCAGGTCATATCCTGATTGATAAGAAAAATAATGTAACTGGCTTAATCGATTGGACAGAAGTAGGGATAGCTGATGTTTCTATAGATTTCACATCACATTATCTGCTCTTTGGGAAAGATGGACTAACAAAGTTAATTAGCTCTTATGACAATGCTGGTGGTAAAACTTGGTCAAGAATGGATGAACATATTATCGAACTTCTAACAACAAGTAGTATCACTGTTGCTGAATATGCTCAAGTGTCAGGTTTGAAAGAGATGCATGAAGCAGCTGTACACATGCTAGCAACTGAAAGTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39617","NCBI_taxonomy_name":"Bacillus cereus Rock3-29","NCBI_taxonomy_id":"526984"}}}},"ARO_accession":"3003072","ARO_id":"39614","ARO_name":"mphL","CARD_short_name":"mphL","ARO_description":"mphL is a chromosomally-encoded macrolide phosphotransferases that inactivate 14- and 15-membered macrolides such as erythromycin, clarithromycin, azithromycin.","ARO_category":{"36472":{"category_aro_accession":"3000333","category_aro_cvterm_id":"36472","category_aro_name":"macrolide phosphotransferase (MPH)","category_aro_description":"Macrolide phosphotransferases (MPH) are enzymes encoded by macrolide phosphotransferase genes (mph genes). These enzymes phosphorylate macrolides in GTP dependent manner at 2'-OH of desosamine sugar thereby inactivating them. Characterized MPH's are differentiated based on their substrate specificity.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35982":{"category_aro_accession":"0000065","category_aro_cvterm_id":"35982","category_aro_name":"clarithromycin","category_aro_description":"Clarithromycin is a methyl derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome and is used to treat pharyngitis, tonsillitis, acute maxillary sinusitis, acute bacterial exacerbation of chronic bronchitis, pneumonia (especially atypical pneumonias associated with Chlamydia pneumoniae or TWAR), and skin structure infections.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2688":{"model_id":"2688","model_name":"ArmR","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"100"}},"model_sequences":{"sequence":{"5228":{"protein_sequence":{"accession":"AAG07106.1","sequence":"MSLNTPRNKPSRTETEAVAASSGRSAVGRRDYTEQLRRAARRNAWDLYGEHFY"},"dna_sequence":{"accession":"AE004091.2","fmin":"4165718","fmax":"4165880","strand":"-","sequence":"ATGTCCCTGAACACTCCGCGCAACAAACCGTCCCGCACCGAGACCGAAGCTGTCGCTGCCAGCTCGGGACGATCCGCCGTCGGCCGGCGGGATTACACCGAGCAGCTGCGCCGGGCAGCCCGGCGCAATGCCTGGGACCTCTACGGCGAGCACTTCTACTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36804","NCBI_taxonomy_name":"Pseudomonas aeruginosa PAO1","NCBI_taxonomy_id":"208964"}}}},"ARO_accession":"3004056","ARO_id":"41121","ARO_name":"ArmR","CARD_short_name":"ArmR","ARO_description":"ArmR, a 53-amino-acid antirepressor, allosterically inhibits MexR dimer-DNA binding by occupying a hydrophobic binding cavity within the center of the MexR dimer. ArmR up-regulation and MexR-ArmR complex formation have previously been shown to upregulate MexAB-OprM.","ARO_category":{"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"3432":{"model_id":"3432","model_name":"OXA-265","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"5628":{"protein_sequence":{"accession":"RFX69805.1","sequence":"MKLSKLYTLTVLIGFGLSGVACQHIHTPVSFNQIENDQTKQIASLFENVQTTGVLITFDGQAYKAYGNDLNRAKAAYIPASTFKILNALIGIEHDKTSPNEVFKWDGQKRAFESWEKDLTLAEAMQASAVPVYQALAQRIGLDLMAKEVKRVGFGNTRIGTQVDNFWLIGPLKITPIEEAQFAYRLAKQELPFTPKTQQQVIDMLLVDEIRGTKVYAKSGWGMDITPQVGWWTGWIEDPNGKVIAFSLNMEMNQPAHAAARKEIVYQALTQLKLL"},"dna_sequence":{"accession":"PXZD01000001.1","fmin":"1356634","fmax":"1357462","strand":"-","sequence":"ATGAAGCTATCAAAATTATACACCCTCACTGTGCTCATAGGATTTGGATTAAGCGGTGTCGCCTGCCAGCATATCCATACTCCAGTCTCGTTCAATCAAATTGAAAACGATCAAACAAAGCAGATCGCTTCCTTGTTTGAGAATGTTCAAACAACAGGTGTTCTAATTACCTTTGATGGACAGGCGTATAAAGCATACGGTAATGATCTGAATCGTGCCAAAGCTGCGTATATCCCAGCATCTACTTTCAAAATATTAAATGCTTTGATTGGCATTGAACATGATAAAACTTCACCAAATGAAGTATTTAAGTGGGATGGTCAGAAGCGTGCTTTTGAAAGTTGGGAAAAAGATCTGACTTTAGCTGAAGCCATGCAAGCTTCTGCTGTACCTGTTTATCAAGCGCTTGCCCAGAGAATCGGATTGGATTTGATGGCAAAGGAAGTCAAAAGAGTCGGCTTCGGTAATACACGCATCGGAACACAAGTTGATAACTTCTGGCTCATTGGACCTTTAAAGATCACGCCAATCGAAGAAGCTCAATTTGCTTACAGGCTTGCAAAACAGGAGTTACCGTTTACCCCAAAAACACAACAGCAAGTGATTGATATGCTGCTGGTGGATGAAATACGGGGAACTAAAGTTTACGCCAAAAGTGGTTGGGGAATGGATATTACCCCGCAAGTAGGATGGTGGACTGGATGGATTGAAGATCCGAACGGAAAAGTGATCGCTTTTTCTCTCAATATGGAAATGAATCAACCTGCGCATGCAGCTGCACGTAAAGAAATTGTTTATCAGGCACTTACGCAATTGAAATTATTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36938","NCBI_taxonomy_name":"Acinetobacter haemolyticus","NCBI_taxonomy_id":"29430"}}}},"ARO_accession":"3001721","ARO_id":"38121","ARO_name":"OXA-265","CARD_short_name":"OXA-265","ARO_description":"OXA-265 is a beta-lactamase found in Acinetobacter spp.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46496":{"category_aro_accession":"3007707","category_aro_cvterm_id":"46496","category_aro_name":"OXA-214-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-214.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2689":{"model_id":"2689","model_name":"Staphylococcus aureus 23S rRNA with mutation conferring resistance to linezolid","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"41093","param_value":"5000"},"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"7941":"g2604t","7940":"c2579t"},"Curated-R":{"7941":"g2604t","7940":"c2579t"},"clinical":{"7941":"g2604t","7940":"c2579t"}}},"model_sequences":{"sequence":{"4128":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"NZ_CP009828.1","fmin":"497113","fmax":"500039","strand":"+","sequence":"AGATTAAGTTATTAAGGGCGCACGGTGGATGCCTTGGCACTAGAAGCCGATGAAGGACGTTACTAACGACGATATGCTTTGGGGAGCTGTAAGTAAGCTTTGATCCAGAGATTTCCGAATGGGGAAACCCAGCATGAGTTATGTCATGTTATCGATATGTGAATACATAGCATATCAGAAGGCACACCCGGAGAACTGAAACATCTTAGTACCCGGAGGAAGAGAAAGAAAATTCGATTCCCTTAGTAGCGGCGAGCGAAACGGGAAGAGCCCAAACCAACAAGCTTGCTTGTTGGGGTTGTAGGACACTCTATACGGAGTTACAAAGGACGACATTAGACGAATCATCTGGAAAGATGAATCAAAGAAGGTAATAATCCTGTAGTCGAAAATGTTGTCTCTCTTGAGTGGATCCTGAGTACGACGGAGCACGTGAAATTCCGTCGGAATCTGGGAGGACCATCTCCTAAGGCTAAATACTCTCTAGTGACCGATAGTGAACCAGTACCGTGAGGGAAAGGTGAAAAGCACCCCGGAAGGGGAGTGAAATAGAACCTGAAACCGTGTGCTTACAAGTAGTCAGAGCCCGTTAATGGGTGATGGCGTGCCTTTTGTAGAATGAACCGGCGAGTTACGATTTGATGCAAGGTTAAGCAGTAAATGTGGAGCCGTAGCGAAAGCGAGTCTGAATAGGGCGTTTAGTATTTGGTCGTAGACCCGAAACCAGGTGATCTACCCTTGGTCAGGTTGAAGTTCAGGTAACACTGAATGGAGGACCGAACCGACTTACGTTGAAAAGTGAGCGGATGAACTGAGGGTAGCGGAGAAATTCCAATCGAACCTGGAGATAGCTGGTTCTCTCCGAAATAGCTTTAGGGCTAGCCTCAAGTGATGATTATTGGAGGTAGAGCACTGTTTGGACGAGGGGCCCCTCTCGGGTTACCGAATTCAGACAAACTCCGAATGCCAATTAATTTAACTTGGGAGTCAGAACATGGGTGATAAGGTCCGTGTTCGAAAGGGAAACAGCCCAGACCACCAGCTAAGGTCCCAAAATATATGTTAAGTGGAAAAGGATGTGGCGTTGCCCAGACAACTAGGATGTTGGCTTAGAAGCAGCCATCATTTAAAGAGTGCGTAATAGCTCACTAGTCGAGTGACACTGCGCCGAAAATGTACCGGGGCTAAACATATTACCGAAGCTGTGGATTGTCCTTTGGACAATGGTAGGAGAGCGTTCTAAGGGCGTTGAAGCATGATCGTAAGGACATGTGGAGCGCTTAGAAGTGAGAATGCCGGTGTGAGTAGCGAAAGACGGGTGAGAATCCCGTCCACCGATTGACTAAGGTTTCCAGAGGAAGGCTCGTCCGCTCTGGGTTAGTCGGGTCCTAAGCTGAGGCCGACAGGCGTAGGCGATGGATAACAGGTTGATATTCCTGTACCACCTATAATCGTTTTAATCGATGGGGGGACGCAGTAGGATAGGCGAAGCGTGCGATTGGATTGCACGTCTAAGCAGTAAGGCTGAGTATTAGGCAAATCCGGTACTCGTTAAGGCTGAGCTGTGATGGGGAGAAGACATTGTGTCTTCGAGTCGTTGATTTCACACTGCCGAGAAAAGCCTCTAGATAGAAAATAGGTGCCCGTACCGCAAACCGACACAGGTAGTCAAGATGAGAATTCTAAGGTGAGCGAGCGAACTCTCGTTAAGGAACTCGGCAAAATGACCCCGTAACTTCGGGAGAAGGGGTGCTCTTTAGGGTTAACGCCCAGAAGAGCCGCAGTGAATAGGCCCAAGCGACTGTTTATCAAAAACACAGGTCTCTGCTAAACCGTAAGGTGATGTATAGGGGCTGACGCCTGCCCGGTGCTGGAAGGTTAAGAGGAGTGGTTAGCTTCTGCGAAGCTACGAATCGAAGCCCCAGTAAACGGCGGCCGTAACTATAACGGTCCTAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCCGCACGAAAGGCGTAACGATTTGGGCACTGTCTCAACGAGAGACTCGGTGAAATCATAGTACCTGTGAAGATGCAGGTTACCCGCGACAGGACGGAAAGACCCCGTGGAGCTTTACTGTAGCCTGATATTGAAATTCGGCACAGCTTGTACAGGATAGGTAGGAGCCTTTGAAACGTGAGCGCTAGCTTACGTGGAGGCGCTGGTGGGATACTACCCTAGCTGTGTTGGCTTTCTAACCCGCACCACTTATCGTGGTGGGAGACAGTGTCAGGCGGGCAGTTTGACTGGGGCGGTCGCCTCCTAAAAGGTAACGGAGGCGCTCAAAGGTTCCCTCAGAATGGTTGGAAATCATTCATAGAGTGTAAAGGCATAAGGGAGCTTGACTGCGAGACCTACAAGTCGAGCAGGGTCGAAAGACGGACTTAGTGATCCGGTGGTTCCGCATGGAAGGGCCATCGCTCAACGGATAAAAGCTACCCCGGGGATAACAGGCTTATCTCCCCCAAGAGTTCACATCGACGGGGAGGTTTGGCACCTCGATGTCGGCTCATCGCATCCTGGGGCTGTAGTCGGTCCCAAGGGTTGGGCTGTTCGCCCATTAAAGCGGTACGCGAGCTGGGTTCAGAACGTCGTGAGACAGTTCGGTCCCTATCCGTCGTGGGCGTAGGAAATTTGAGAGGAGCTGTCCTTAGTACGAGAGGACCGGGATGGACATACCTCTGGTGTACCAGTTGTCGTGCCAACGGCATAGCTGGGTAGCTATGTGTGGACGGGATAAGTGCTGAAAGCATCTAAGCATGAAGCCCCCCTCAAGATGAGATTTCCCAACTTCGGTTATAAGATCCCTCAAAGATGATGAGGTTAATAGGTTCGAGGTGGAAGCATGGTGACATGTGGAGCTGACGAATACTAATCGATCGAAGACTTAATCAAAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35508","NCBI_taxonomy_name":"Staphylococcus aureus","NCBI_taxonomy_id":"1280"}}}},"ARO_accession":"3004058","ARO_id":"41124","ARO_name":"Staphylococcus aureus 23S rRNA with mutation conferring resistance to linezolid","CARD_short_name":"Saur_23S_LZD","ARO_description":"Point mutations in the 23S rRNA subunit of the large ribosomal bacterial subunit in Staphylococcus aureus, which confer resistance to linezolid by disrupting antibiotic target binding.","ARO_category":{"41123":{"category_aro_accession":"3004057","category_aro_cvterm_id":"41123","category_aro_name":"23S rRNA with mutation conferring resistance to linezolid antibiotics","category_aro_description":"Point mutations in the 23S rRNA subunit may confer resistance to linezolid and other oxazolidinone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35989":{"category_aro_accession":"0000072","category_aro_cvterm_id":"35989","category_aro_name":"linezolid","category_aro_description":"Linezolid is a synthetic antibiotic used for the treatment of serious infections caused by Gram-positive bacteria that are resistant to several other antibiotics. It inhibits protein synthesis by binding to domain V of the 23S rRNA of the 50S subunit of bacterial ribosomes.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"36218":{"category_aro_accession":"3000079","category_aro_cvterm_id":"36218","category_aro_name":"oxazolidinone antibiotic","category_aro_description":"Oxazolidinones are a class of synthetic antibiotics discovered the the 1980's.  They inhibit protein synthesis by binding to domain V of the 23S rRNA of the 50S subunit of bacterial ribosomes.  Linezolid is the only member of this class currently in clinical use.","category_aro_class_name":"Drug Class"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"37014":{"category_aro_accession":"3000670","category_aro_cvterm_id":"37014","category_aro_name":"pleuromutilin antibiotic","category_aro_description":"Pleuromutilins are natural fungal products that target bacterial protein translation by binding the the 23S rRNA, blocking the ribosome P site at the 50S subunit. They are mostly used for agriculture and veterinary purposes.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2691":{"model_id":"2691","model_name":"Type A NfxB","model_type":"protein overexpression model","model_type_id":"41091","model_description":"Protein Overexpression Models (POM) are similar to Protein Variant Models (PVM) in that they include a protein reference sequence, a curated BLASTP bitscore cut-off, and mapped resistance variants. Whereas PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, reporting only those with curated mutations conferring AMR, POMs are restricted to regulatory proteins and report both wild-type sequences and\/or sequences with mutations leading to overexpression of efflux complexes. The former lead to efflux of antibiotics at basal levels, while the latter can confer clinical resistance. POMs include a protein reference sequence (often from wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Perfect RGI match is 100% identical to the wild-type reference protein sequence along its entire length, a Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value may or may not contain at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off may or may not contain at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"7548":"R42G"},"Curated-R":{"7548":"R42G"},"clinical":{"7548":"R42G"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"310"}},"model_sequences":{"sequence":{"5520":{"protein_sequence":{"accession":"AAG07988.1","sequence":"MTLISHDERLIKALAVAIVDRPRATLKELAEAAGVSKATLHRFCGTRDNLVQMLEDHGETVLNQIIQACDLEHAEPLEALQRLIKEHLTHRELLVFLVFQYRPDFLDPHGEGARWQSYLEALDAFFLRGQQKGVFRIDITAAVFTELFITLVYGMVDAERRGRAASSNSAHTLEQMFLHGASNPARS"},"dna_sequence":{"accession":"AE004091.2","fmin":"5155560","fmax":"5156124","strand":"+","sequence":"ATGACCCTGATTTCCCATGACGAGCGACTCATCAAGGCGCTGGCAGTCGCTATCGTCGACCGCCCGCGAGCGACGCTGAAGGAACTGGCCGAGGCGGCCGGCGTAAGCAAGGCCACCCTGCACCGCTTCTGCGGCACGCGGGACAACCTGGTGCAGATGCTCGAGGACCACGGAGAGACCGTACTGAACCAGATCATCCAGGCCTGCGACCTGGAGCATGCCGAGCCTCTGGAGGCGTTGCAGCGCCTGATCAAGGAACACCTCACCCACCGCGAGCTGCTGGTATTCCTGGTATTCCAGTACCGCCCGGACTTCCTCGACCCGCACGGCGAAGGCGCACGCTGGCAGTCCTACCTGGAAGCGCTGGACGCCTTCTTCCTGCGCGGACAGCAGAAAGGCGTGTTTCGCATCGACATCACGGCGGCCGTGTTCACCGAACTGTTCATCACCCTGGTCTACGGCATGGTCGATGCGGAACGTCGCGGACGGGCGGCCAGCTCCAATTCCGCGCATACCCTGGAGCAGATGTTCCTCCATGGCGCCTCCAATCCGGCTCGCTCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36804","NCBI_taxonomy_name":"Pseudomonas aeruginosa PAO1","NCBI_taxonomy_id":"208964"}}}},"ARO_accession":"3004059","ARO_id":"41125","ARO_name":"Type A NfxB","CARD_short_name":"Type_A_NfxB","ARO_description":"Type A NfxB mutants are four to eight times more resistant to ofloxacin, erythromycin, and new zwitterionic cephems, i.e., cefpirome, cefclidin, cefozopran, and cefoselis, than the parent strain, PAO1. nfxB corresponds to 2 loci in Pseudomonas aeruginosa PAO1 (gene name: esrC\/nfxB) and 2 loci in Pseudomonas aeruginosa LESB58 (gene name: nfxB).","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36250":{"category_aro_accession":"3000111","category_aro_cvterm_id":"36250","category_aro_name":"novobiocin","category_aro_description":"Novobiocin is an aminocoumarin antibiotic produced by Streptomyces spheroides and Streptomyces niveus, and binds DNA gyrase subunit B inhibiting ATP-dependent DNA supercoiling.","category_aro_class_name":"Antibiotic"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"37007":{"category_aro_accession":"3000663","category_aro_cvterm_id":"37007","category_aro_name":"ofloxacin","category_aro_description":"Ofloxacin is a 6-fluoro, 7-piperazinyl quinolone with a methyl-substituted oxazine ring. It has a broad spectrum of activity including many enterobacteria and mycoplasma but most anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36242":{"category_aro_accession":"3000103","category_aro_cvterm_id":"36242","category_aro_name":"aminocoumarin antibiotic","category_aro_description":"Aminocoumarin antibiotics bind DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling.","category_aro_class_name":"Drug Class"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"3462":{"model_id":"3462","model_name":"OXA-300","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"5657":{"protein_sequence":{"accession":"ENV20093.1","sequence":"MKFKMKGLFCVILSSLAFSGCVYDSKLQRPVISERETEIPLLFNQAQTQAVFVTYDGIHLKSYGNDLSRAKTEYIPASTFKMLNALIGLQNGKATNTEVFQWNGEKRAFSAWEKDMTLAEAMQASAVPVYQELARRIGLKLMREEVKRVGFGNAEIGQQVDNFWLVGPLKISPEQEVQFAYQLAMKQLPFDRNVQQQVKDMLYIESRGDSKLYAKSGWGMDVEPQVGWYTGWVEQPNGKVTAFALNMNMQAGDDPAERKQLTLSILDKLGLFFYLR"},"dna_sequence":{"accession":"APPK01000054.1","fmin":"255915","fmax":"256746","strand":"-","sequence":"ATGAAGTTTAAAATGAAAGGTTTATTTTGTGTCATCCTCAGTAGTTTGGCATTTTCAGGTTGTGTTTATGATTCAAAACTACAACGCCCAGTCATATCAGAGCGAGAAACTGAGATTCCTTTATTATTTAATCAAGCACAGACTCAAGCTGTGTTTGTTACTTATGATGGGATTCATCTAAAAAGTTATGGTAATGATCTAAGCCGAGCAAAGACTGAATATATTCCTGCATCTACATTTAAGATGTTGAATGCTTTAATTGGCTTGCAAAATGGAAAAGCAACCAATACTGAAGTATTTCAGTGGAATGGTGAAAAGCGTGCTTTTTCAGCATGGGAAAAAGATATGACTTTGGCAGAAGCGATGCAGGCTTCAGCTGTTCCCGTATATCAAGAGCTTGCTCGACGTATTGGCTTGAAATTGATGCGTGAAGAAGTGAAGCGTGTAGGTTTTGGTAATGCGGAGATTGGTCAGCAAGTCGATAATTTTTGGTTAGTGGGTCCTTTAAAAATCTCCCCTGAACAAGAAGTTCAATTTGCTTATCAACTGGCGATGAAGCAATTACCTTTTGATCGAAATGTACAGCAACAAGTCAAAGATATGCTTTATATAGAAAGTCGTGGTGACAGCAAACTGTATGCTAAAAGTGGTTGGGGAATGGATGTTGAACCTCAAGTGGGTTGGTATACGGGATGGGTTGAACAACCCAATGGCAAGGTGACTGCATTTGCGTTAAATATGAACATGCAAGCAGGTGATGATCCAGCTGAACGTAAACAATTAACCTTAAGTATTTTGGACAAATTGGGTCTATTTTTTTATTTAAGATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42821","NCBI_taxonomy_name":"Acinetobacter bereziniae NIPH 3","NCBI_taxonomy_id":"1217651"}}}},"ARO_accession":"3001755","ARO_id":"38155","ARO_name":"OXA-300","CARD_short_name":"OXA-300","ARO_description":"OXA-300 is a beta-lactamase found in Acinetobacter spp.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46498":{"category_aro_accession":"3007709","category_aro_cvterm_id":"46498","category_aro_name":"OXA-229-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-229.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2693":{"model_id":"2693","model_name":"Type B NfxB","model_type":"protein overexpression model","model_type_id":"41091","model_description":"Protein Overexpression Models (POM) are similar to Protein Variant Models (PVM) in that they include a protein reference sequence, a curated BLASTP bitscore cut-off, and mapped resistance variants. Whereas PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, reporting only those with curated mutations conferring AMR, POMs are restricted to regulatory proteins and report both wild-type sequences and\/or sequences with mutations leading to overexpression of efflux complexes. The former lead to efflux of antibiotics at basal levels, while the latter can confer clinical resistance. POMs include a protein reference sequence (often from wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Perfect RGI match is 100% identical to the wild-type reference protein sequence along its entire length, a Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value may or may not contain at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off may or may not contain at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"7549":"H87R"},"Curated-R":{"7549":"H87R"},"clinical":{"7549":"H87R"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"310"}},"model_sequences":{"sequence":{"5519":{"protein_sequence":{"accession":"AAG07988.1","sequence":"MTLISHDERLIKALAVAIVDRPRATLKELAEAAGVSKATLHRFCGTRDNLVQMLEDHGETVLNQIIQACDLEHAEPLEALQRLIKEHLTHRELLVFLVFQYRPDFLDPHGEGARWQSYLEALDAFFLRGQQKGVFRIDITAAVFTELFITLVYGMVDAERRGRAASSNSAHTLEQMFLHGASNPARS"},"dna_sequence":{"accession":"AE004091.2","fmin":"5155560","fmax":"5156124","strand":"+","sequence":"ATGACCCTGATTTCCCATGACGAGCGACTCATCAAGGCGCTGGCAGTCGCTATCGTCGACCGCCCGCGAGCGACGCTGAAGGAACTGGCCGAGGCGGCCGGCGTAAGCAAGGCCACCCTGCACCGCTTCTGCGGCACGCGGGACAACCTGGTGCAGATGCTCGAGGACCACGGAGAGACCGTACTGAACCAGATCATCCAGGCCTGCGACCTGGAGCATGCCGAGCCTCTGGAGGCGTTGCAGCGCCTGATCAAGGAACACCTCACCCACCGCGAGCTGCTGGTATTCCTGGTATTCCAGTACCGCCCGGACTTCCTCGACCCGCACGGCGAAGGCGCACGCTGGCAGTCCTACCTGGAAGCGCTGGACGCCTTCTTCCTGCGCGGACAGCAGAAAGGCGTGTTTCGCATCGACATCACGGCGGCCGTGTTCACCGAACTGTTCATCACCCTGGTCTACGGCATGGTCGATGCGGAACGTCGCGGACGGGCGGCCAGCTCCAATTCCGCGCATACCCTGGAGCAGATGTTCCTCCATGGCGCCTCCAATCCGGCTCGCTCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36804","NCBI_taxonomy_name":"Pseudomonas aeruginosa PAO1","NCBI_taxonomy_id":"208964"}}}},"ARO_accession":"3004060","ARO_id":"41127","ARO_name":"Type B NfxB","CARD_short_name":"Type_B_NfxB","ARO_description":"Type B NfxB mutants are more resistant to tetracycline and chloramphenicol, as well as ofloxacin, erythromycin, and the new zwitterionic cephems, than was PAO1, and they are four to eight times more susceptible to carbenicillin, sulbenicillin, imipenem, panipenem, biapenem, moxalactam, aztreonam, gentamicin, and kanamycin than PAO1. The mutation at the 46th amino acid position is sufficient for overproduction of OprJ and the multidrug resistance. nfxB corresponds to 2 loci in Pseudomonas aeruginosa PAO1 (gene name: esrC\/nfxB) and 2 loci in Pseudomonas aeruginosa LESB58 (gene name: nfxB).","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36250":{"category_aro_accession":"3000111","category_aro_cvterm_id":"36250","category_aro_name":"novobiocin","category_aro_description":"Novobiocin is an aminocoumarin antibiotic produced by Streptomyces spheroides and Streptomyces niveus, and binds DNA gyrase subunit B inhibiting ATP-dependent DNA supercoiling.","category_aro_class_name":"Antibiotic"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"37007":{"category_aro_accession":"3000663","category_aro_cvterm_id":"37007","category_aro_name":"ofloxacin","category_aro_description":"Ofloxacin is a 6-fluoro, 7-piperazinyl quinolone with a methyl-substituted oxazine ring. It has a broad spectrum of activity including many enterobacteria and mycoplasma but most anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"46133":{"category_aro_accession":"3007382","category_aro_cvterm_id":"46133","category_aro_name":"gentamicin","category_aro_description":"Gentamicin is a commonly used aminoglycoside antibiotic derived from members of the Micromonospora genus of bacteria. It acts by binding the 30S ribosomal subunit, thus inhibiting protein synthesis. Gentamicin is typically used to treat Gram-negative infections of the repiratory and urinary tract, as well as infections of the bone and soft tissue. It also exhibits considerable nephrotoxicity and ototoxicity. Gentamicin is administered as a mixture of gentamicin type C (which makes about around 80% of the complex) and types A, B, and X (distributed in the remaining 20% of the complex).","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36242":{"category_aro_accession":"3000103","category_aro_cvterm_id":"36242","category_aro_name":"aminocoumarin antibiotic","category_aro_description":"Aminocoumarin antibiotics bind DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling.","category_aro_class_name":"Drug Class"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"3491":{"model_id":"3491","model_name":"OXA-406","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"5686":{"protein_sequence":{"accession":"AJD07402.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDKKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWNGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"KJ584915.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATAAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGAACGGGCAAAAAAGGCTGTTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATAGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTGGGTTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGTATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001597","ARO_id":"37997","ARO_name":"OXA-406","CARD_short_name":"OXA-406","ARO_description":"OXA-406 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2697":{"model_id":"2697","model_name":"EdeQ","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"250"}},"model_sequences":{"sequence":{"4026":{"protein_sequence":{"accession":"AHH86051.1","sequence":"MSVTLREVTLENWEECIELEPTPEQSEFVAPNLYSIAESKFQTTFVPLAIYHDDTMVGFVMYGLDPDDGNYWIYRLLIDAKYQRLGYGRTAISQVIEILKAKEDCQKIVIGYAPANVAAENLYASLGFQKNGMVLFGETIAELNF"},"dna_sequence":{"accession":"KC771276.1","fmin":"44894","fmax":"45332","strand":"+","sequence":"ATGTCTGTGACACTTCGTGAAGTAACTTTGGAAAACTGGGAAGAGTGTATTGAACTGGAACCTACTCCCGAACAGAGCGAGTTTGTTGCCCCAAACCTTTACTCCATCGCTGAATCAAAGTTTCAAACTACATTTGTTCCTTTGGCCATATACCATGATGACACGATGGTTGGCTTTGTCATGTATGGGCTTGACCCTGACGATGGGAATTACTGGATTTACAGACTCTTAATTGATGCGAAGTACCAACGACTAGGCTATGGACGTACTGCCATTTCACAAGTCATTGAGATCCTGAAAGCAAAGGAAGATTGTCAAAAAATTGTCATTGGCTATGCCCCAGCCAATGTCGCAGCCGAAAACCTTTACGCTTCGCTCGGATTTCAAAAGAATGGAATGGTTTTGTTCGGCGAGACGATTGCAGAATTGAACTTTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41133","NCBI_taxonomy_name":"Brevibacillus brevis","NCBI_taxonomy_id":"1393"}}}},"ARO_accession":"3004063","ARO_id":"41130","ARO_name":"EdeQ","CARD_short_name":"EdeQ","ARO_description":"EdeQ is an N-acetyltransferase enzyme that confers high-level self-resistance to edeine in Brevibacillus brevis, a natural edeine producer. EdeQ converts active edeine to N-acetyledeine, which is ineffective in vivo.","ARO_category":{"41131":{"category_aro_accession":"3004064","category_aro_cvterm_id":"41131","category_aro_name":"Edeine acetyltransferase","category_aro_description":"Edeine acetyltransferase enzymes catalyze the transfer of an acetyl group to active edeine, converting it to an inactive form in vivo. This mechanism is used for high-level self-resistance in edeine-producing Brevibacillus spp.","category_aro_class_name":"AMR Gene Family"},"36269":{"category_aro_accession":"3000130","category_aro_cvterm_id":"36269","category_aro_name":"edeine A","category_aro_description":"Edeine A is a subtype of the peptide antibiotic edeine, composed of beta-tyr, beta-ser, diaminopropionic acid, diaminohydroxyazelaic acid, glycine, and spermidine. Edeine A is a mixture of edeine A1 and its inactive isomer, edeine A2. Edeines bind to the 30S subunit to block fMet-tRNA interaction at the P site, inhibiting protein synthesis and subsequent structure\/function processes critical for life or replication.","category_aro_class_name":"Antibiotic"},"36273":{"category_aro_accession":"3000134","category_aro_cvterm_id":"36273","category_aro_name":"edeine B","category_aro_description":"Edeine B is a subtype of the peptide antibiotic edeine, composed of beta-tyr, beta-ser, diaminopropionic acid, diaminohydroxyazelaic acid, glycine, and guanylspermidine. Edeine B is a mixture of edeine B1 and its inactive isomer, edeine B2.  Edeines bind to the 30S subunit to block fMet-tRNA interaction at the P site, inhibiting protein synthesis and subsequent structure\/function processes critical for life or replication. Edeine B has also been shown to inhibit septation and cause filamentous morphology, also leading to cell death.","category_aro_class_name":"Antibiotic"},"36274":{"category_aro_accession":"3000135","category_aro_cvterm_id":"36274","category_aro_name":"edeine D","category_aro_description":"Edeine D is a subtype of edeine similar to edeine A with the beta-tyr replaced by beta-phe-beta-ala. Edeines bind to the 30S subunit to block fMet-tRNA interaction at the P site, inhibiting protein synthesis and subsequent structure\/function processes critical for life or replication.","category_aro_class_name":"Antibiotic"},"36275":{"category_aro_accession":"3000136","category_aro_cvterm_id":"36275","category_aro_name":"edeine F","category_aro_description":"Edeine F is a subtype of edeine similar to edeine B with beta-tyr replaced by beta-phe-beta-ala. Edeines bind to the 30S subunit to block fMet-tRNA interaction at the P site, inhibiting protein synthesis and subsequent structure\/function processes critical for life or replication.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36666":{"category_aro_accession":"3000527","category_aro_cvterm_id":"36666","category_aro_name":"polyamine antibiotic","category_aro_description":"Polyamine antibiotics are organic compounds having two or more primary amino groups.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3517":{"model_id":"3517","model_name":"OXA-448","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"5712":{"protein_sequence":{"accession":"AKI29909.1","sequence":"MKKIILFLWILNFAFGQDKILEDFFKDYNTSGTFIIFDGKNYASNDFQRAKQTFSPASTFKIFNALIALDNGVVKDTKEIFYHYKGEKVFLPSWKQDASLSSAIKRSQVPAFKELARKIGLKTMQESLNKLSYGNAKISKIDTFWLDNSLQISAKNQADLLFKLSQNSLPFSNKSQEEVKKLLLFKENKIQKIYAKTGFNDNINLAWIVGFVKTKNKILSFALNVDIKDIKNIKIREELLEKYIYSLN"},"dna_sequence":{"accession":"KR061497.1","fmin":"0","fmax":"747","strand":"+","sequence":"ATGAAAAAAATCATCTTGTTTTTATGGATTTTAAATTTTGCCTTTGGACAAGATAAAATATTAGAAGATTTTTTTAAAGATTATAATACAAGTGGGACTTTTATAATCTTTGATGGAAAAAATTATGCAAGTAATGATTTTCAAAGAGCAAAACAAACCTTTTCTCCTGCTTCAACTTTTAAAATTTTTAATGCTTTAATTGCGCTTGATAATGGTGTAGTTAAAGATACAAAGGAAATTTTTTATCATTATAAGGGCGAAAAAGTATTTTTGCCCTCTTGGAAACAAGATGCTAGTTTAAGCTCAGCCATAAAACGCTCTCAAGTGCCTGCTTTTAAAGAATTGGCAAGAAAAATAGGACTTAAAACCATGCAAGAAAGCTTAAATAAACTTTCTTATGGAAATGCAAAAATTTCAAAAATCGATACTTTTTGGCTGGATAATTCTTTGCAAATTTCTGCAAAAAATCAAGCTGATTTACTTTTTAAACTTTCACAAAATTCTTTACCCTTTTCCAATAAAAGTCAAGAAGAAGTTAAAAAACTTCTTCTTTTTAAAGAAAATAAAATACAAAAAATTTATGCTAAAACAGGTTTTAATGATAATATAAATTTAGCTTGGATTGTTGGATTCGTAAAGACTAAAAACAAAATTTTATCTTTTGCTTTAAATGTTGATATAAAGGACATTAAAAATATTAAAATAAGAGAAGAATTGCTAGAAAAATATATTTATTCTTTAAATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36772","NCBI_taxonomy_name":"Campylobacter jejuni","NCBI_taxonomy_id":"197"}}}},"ARO_accession":"3003604","ARO_id":"40214","ARO_name":"OXA-448","CARD_short_name":"OXA-448","ARO_description":"OXA-448 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46491":{"category_aro_accession":"3007702","category_aro_cvterm_id":"46491","category_aro_name":"OXA-184-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-184.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3547":{"model_id":"3547","model_name":"OXA-486","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"5742":{"protein_sequence":{"accession":"QBY97442.1","sequence":"MRPLLFSALLLLSGHTQASEWNDSQAVDKLFGAAGVKGTFVLYDVQRQCYVGHDRERAETRFVPASTYKVANSLIGLSTGAVRSADEVLPYGGKPQRFKAWEHDMSLREAIKASNVPVYQELARRIGLERMRANVSRLGYGNAEIGQVVDNFWLVGPLKISAMEQTRFLLRLAQGELPFPAPVQSTVRAMTLLESGPGWELHGKTGWCFDCTPELGWWVGWVKRNERLYGFALNIDMPGGEADIGKRVELGKASLKALGILP"},"dna_sequence":{"accession":"CP038661.1","fmin":"6223618","fmax":"6224407","strand":"+","sequence":"ATGCGCCCTCTCCTCTTCAGTGCCCTTCTCCTGCTTTCCGGGCATACCCAGGCCAGCGAATGGAACGACAGCCAGGCCGTGGACAAGCTATTCGGCGCGGCCGGGGTGAAAGGCACCTTCGTCCTCTACGATGTGCAGCGGCAGTGCTATGTCGGCCATGACCGGGAGCGCGCGGAAACCCGCTTCGTTCCCGCTTCCACCTACAAGGTGGCGAACAGCCTGATCGGCTTATCCACAGGGGCGGTTAGATCCGCCGACGAGGTTCTTCCCTATGGCGGCAAGCCCCAGCGCTTCAAGGCCTGGGAGCACGACATGAGCCTGCGCGAGGCGATCAAGGCATCGAACGTACCGGTCTACCAGGAACTGGCGCGGCGCATCGGCCTGGAGCGGATGCGCGCCAATGTCTCGCGCCTGGGTTACGGCAACGCGGAAATCGGCCAGGTTGTGGATAACTTCTGGTTGGTGGGACCGCTGAAGATCAGCGCGATGGAACAGACCCGCTTTCTGCTCCGACTGGCGCAGGGAGAATTGCCATTCCCCGCCCCGGTGCAGTCCACCGTGCGCGCCATGACCCTGCTGGAAAGCGGCCCGGGCTGGGAGCTGCACGGCAAGACCGGCTGGTGCTTCGACTGCACGCCGGAACTCGGCTGGTGGGTGGGCTGGGTGAAGCGCAACGAGCGGCTCTACGGCTTCGCCCTGAACATCGACATGCCCGGCGGCGAGGCCGACATCGGCAAGCGCGTCGAACTGGGCAAGGCCAGTCTCAAGGCTCTCGGGATACTGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3003643","ARO_id":"40253","ARO_name":"OXA-486","CARD_short_name":"OXA-486","ARO_description":"OXA-486 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46513":{"category_aro_accession":"3007724","category_aro_cvterm_id":"46513","category_aro_name":"OXA-50-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-50.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3599":{"model_id":"3599","model_name":"GOB-13","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"575"}},"model_sequences":{"sequence":{"5797":{"protein_sequence":{"accession":"AAT68580.1","sequence":"MRNFATLFFLSVCLNLNLNAQVVKEPENMPKEWNQTYEPFRIAGNLYYVGTYDLASYLIVTDKGNILINTGTAESLPIIKGNIQKLGFNYKDIKILLLTQAHYDHTGALQDFKTETGAKFYTDKADADVLKTGGKSDYELGKYGVTFKPITPDRTLKDQDKITLGNTTLTLLHHPGHTKGSCSFIFDTKDEKRKYRVLIANMPSIIVDKKFSEVTAYPNIQSDYAYTFGAMKKLDFDLWVASHASQFDLHEKRKEGDPYNPQLFMDKQNYFQSLNNLEKSYLDKIKKDSQDK"},"dna_sequence":{"accession":"AY647250.1","fmin":"0","fmax":"879","strand":"+","sequence":"ATGAGAAATTTTGCTACACTGTTTTTTCTGTCAGTTTGTTTGAATTTGAATTTGAACGCTCAGGTAGTAAAAGAACCTGAGAATATGCCTAAAGAATGGAATCAGACTTATGAACCATTCAGAATTGCAGGTAACTTATATTACGTAGGAACCTATGATTTGGCTTCTTACCTTATTGTGACGGACAAAGGCAATATTCTCATTAATACAGGAACGGCAGAATCGCTTCCAATAATAAAAGGCAATATTCAAAAGCTGGGGTTTAATTATAAAGACATTAAGATCTTGCTGCTTACCCAGGCTCATTATGACCATACAGGTGCGTTACAGGATTTCAAAACAGAAACCGGTGCAAAATTCTATACCGATAAAGCAGATGCTGATGTCCTGAAAACAGGGGGTAAGTCCGATTATGAATTGGGAAAATATGGTGTGACATTTAAACCTATTACTCCGGATAGAACGTTAAAAGATCAGGATAAAATAACACTGGGAAATACAACCCTGACTTTGCTTCATCACCCGGGACATACAAAAGGTTCCTGCAGTTTTATTTTTGACACAAAAGACGAGAAGAGAAAGTATAGAGTTCTGATAGCTAATATGCCCTCTATTATTGTTGATAAGAAATTTTCTGAAGTTACAGCATATCCGAATATTCAGTCCGATTATGCTTATACCTTTGGTGCAATGAAAAAGCTTGATTTTGATCTTTGGGTAGCATCGCATGCAAGTCAGTTCGATCTGCATGAAAAACGTAAAGAAGGAGATCCGTACAACCCACAATTGTTTATGGATAAGCAAAACTATTTCCAAAGTCTTAATAATCTGGAGAAAAGCTATCTTGATAAAATTAAAAAAGATTCCCAAGATAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36960","NCBI_taxonomy_name":"Elizabethkingia meningoseptica","NCBI_taxonomy_id":"238"}}}},"ARO_accession":"3004805","ARO_id":"42925","ARO_name":"GOB-13","CARD_short_name":"GOB-13","ARO_description":"GOB-13 is a class B beta-lactamase gene found in Elizabethkingia meningoseptica.","ARO_category":{"41376":{"category_aro_accession":"3004212","category_aro_cvterm_id":"41376","category_aro_name":"GOB beta-lactamase","category_aro_description":"The GOB family of beta-lactamases have been discovered in the Elizabethkingia meningoseptica and are classified as subclass B3 beta-lactamase. They confer resistance to cephalosporins, penicillins, and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2706":{"model_id":"2706","model_name":"MvaT","model_type":"protein knockout model","model_type_id":"40354","model_description":"Protein Knockout Models (PKM) reflect resistance by the absence of a gene product, most often deletion of a gene involved in antibiotic import, such as Vibrio cholerae OmpT. Like Protein Homolog Models (PHMs), PKMs include a reference sequence and a bitscore cut-off for detection using BLASTP but instead are designed to only report lack of detection under Perfect or Strict criteria. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff. This model type is still under development and not currently supported by the Resistance Gene Identifier (RGI) software.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"200"}},"model_sequences":{"sequence":{"4034":{"protein_sequence":{"accession":"NP_253005.1","sequence":"MSLINEYRATEEAIKELQERLKSLEQDDKLKKELEFEEKLRTLMGTYQKSLRDVISLLDPDAKIGKSTRTAKAPAGKRARKVKQYKNPHTGEVIETKGGNHKTLKEWKAKWGPEAVESWATLLG"},"dna_sequence":{"accession":"NC_002516.2","fmin":"4843811","fmax":"4844186","strand":"+","sequence":"ATGTCCCTGATCAACGAATATCGCGCCACGGAAGAAGCCATCAAGGAACTTCAGGAGCGCCTGAAGTCCCTGGAACAAGACGACAAACTGAAAAAAGAACTGGAATTCGAAGAGAAGCTGCGCACGCTGATGGGCACTTACCAGAAGTCCCTGCGTGACGTGATTTCCCTGCTCGATCCGGACGCCAAGATCGGCAAGAGCACCCGCACCGCCAAGGCACCTGCCGGCAAGCGCGCGCGCAAGGTCAAGCAGTACAAGAACCCGCACACCGGCGAAGTCATCGAGACCAAGGGCGGCAACCACAAGACTTTGAAAGAGTGGAAAGCCAAGTGGGGCCCCGAGGCCGTCGAGAGCTGGGCCACCCTGCTCGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36804","NCBI_taxonomy_name":"Pseudomonas aeruginosa PAO1","NCBI_taxonomy_id":"208964"}}}},"ARO_accession":"3004069","ARO_id":"41146","ARO_name":"MvaT","CARD_short_name":"MvaT","ARO_description":"MvaT, a global regulator of virulence genes in P. aeruginosa, has also shown to be able to repress the expression of the MexEF-OprN pump.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2707":{"model_id":"2707","model_name":"MexEF-OprN with MvaT deletion conferring resistance to chloramphenicol and norfloxacin","model_type":"efflux pump system meta-model","model_type_id":"41112","model_description":"Efflux Pump System Meta-Models (EPS) are dedicated to efflux complexes and their regulators, such as AcrAB-TolC. Using the efflux pump components parameter, this model type simply includes a list of detection models for each component of the complex. This model type is still under development and not currently supported by the Resistance Gene Identifier (RGI) software.","model_param":{"41141":{"param_type":"efflux pump components","param_description":"Association of proteins within efflux protein complexes or regulatory networks are encoded by the efflux pump components parameter: model_id,model_id,model_id, etc.","param_type_id":"41141","param_value":{"7585":"2706,1067,1300,172"}},"snp":{"Curated-R":{"7585":"H87R"}}},"ARO_accession":"3004070","ARO_id":"41147","ARO_name":"MexEF-OprN with MvaT deletion conferring resistance to chloramphenicol and norfloxacin","CARD_short_name":"Paer_MvaT_MULT","ARO_description":"A deletion of MvaT results in the overexpression of MexEF-OprN conferring resistance to chloramphenicol and norfloxacin.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2267":{"model_id":"2267","model_name":"Escherichia coli nfsA mutations conferring resistance to nitrofurantoin","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"40394":{"param_type":"nonsense mutation","param_description":"A sequence change where, compared to a reference sequence, one codon is replaced by a termination codon through a nucleotide substitution. These are described as a substitution of the wildtype codon to a termination codon. Format is given as [wild type AA][position][Ter], for example Q42Ter where Q42 is a wildtype amino acid replaced by a premature termination codon.","param_type_id":"40394","param_value":{"8193":"K141Ter","8194":"E233Ter","8192":"Q44Ter"}},"snp":{"Curated-R":{"8193":"H87R","8194":"H87R","3467":"R15C","3469":"R203L","3470":"R203C","3471":"G131D","3472":"S33R","8195":"R133S","8192":"R133S"},"param_value":{"3467":"R15C","3469":"R203L","3470":"R203C","3471":"G131D","3472":"S33R","8195":"R133S"},"clinical":{"3467":"R15C","3469":"R203L","3470":"R203C","3471":"G131D","3472":"S33R","8195":"R133S"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"425"}},"model_sequences":{"sequence":{"5371":{"protein_sequence":{"accession":"AAC73938.1","sequence":"MTPTIELICGHRSIRHFTDEPISEAQREAIINSARATSSSSFLQCSSIIRITDKALREELVTLTGGQKHVAQAAEFWVFCADFNRHLQICPDAQLGLAEQLLLGVVDTAMMAQNALIAAESLGLGGVYIGGLRNNIEAVTKLLKLPQHVLPLFGLCLGWPADNPDLKPRLPASILVHENSYQPLDKGALAQYDEQLAEYYLTRGSNNRRDTWSDHIRRTIIKESRPFILDYLHKQGWATR"},"dna_sequence":{"accession":"U00096.3","fmin":"891183","fmax":"891906","strand":"+","sequence":"ATGACGCCAACCATTGAACTTATTTGTGGCCATCGCTCCATTCGCCATTTCACTGATGAACCCATTTCCGAAGCGCAGCGTGAGGCGATTATTAACAGCGCCCGTGCGACGTCCAGTTCCAGTTTTTTGCAGTGCAGTAGCATTATTCGCATTACCGACAAAGCGTTACGTGAAGAACTGGTGACGCTGACCGGCGGGCAAAAACACGTAGCGCAAGCGGCGGAGTTCTGGGTGTTCTGTGCCGACTTTAACCGCCATTTACAGATCTGTCCGGATGCTCAGCTCGGCCTGGCGGAACAACTGTTGCTCGGTGTCGTTGATACGGCAATGATGGCGCAGAATGCATTAATCGCAGCGGAATCGCTGGGATTGGGCGGGGTATATATCGGCGGCCTGCGCAATAATATTGAAGCGGTGACGAAACTGCTTAAATTACCGCAGCATGTTCTGCCGCTGTTTGGGCTGTGCCTTGGCTGGCCTGCGGATAATCCGGATCTTAAGCCGCGTTTACCGGCCTCCATTTTGGTGCATGAAAACAGCTATCAACCGCTGGATAAAGGCGCACTGGCGCAGTATGACGAGCAACTGGCGGAATATTACCTCACCCGTGGCAGCAATAATCGCCGGGATACCTGGAGCGATCATATCCGCCGAACAATCATTAAAGAAAGCCGCCCATTTATTCTGGATTATTTGCACAAACAGGGTTGGGCGACGCGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36849","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. MG1655","NCBI_taxonomy_id":"511145"}}}},"ARO_accession":"3003751","ARO_id":"40407","ARO_name":"Escherichia coli nfsA mutations conferring resistance to nitrofurantoin","CARD_short_name":"Ecol_nfsA_NIT","ARO_description":"nfsA encodes the major oxygen-insesitive nitroreductase in E. coli. The first step of resistance to nitrofurazone is mutation of nfsA.","ARO_category":{"40411":{"category_aro_accession":"3003754","category_aro_cvterm_id":"40411","category_aro_name":"antibiotic resistant nfsA","category_aro_description":"The nfsA-encoded nitroreductase is the major oxygen-insensitive nitroreductase present in E. coli. NfsA uses only NADPH and has broad electron acceptor specificity. Mutations in nfsA cause resistance to nitrofurazone and furazolidone. Resistance to nitrofurantoin via mutation of nfsA reduces the fitness of clinical isolates of E. coli.","category_aro_class_name":"AMR Gene Family"},"35992":{"category_aro_accession":"0000075","category_aro_cvterm_id":"35992","category_aro_name":"nitrofurantoin","category_aro_description":"Nitrofurantoin is an antibiotic used to treat urinary tract infections. It inhibits enzyme synthesis by inhibiting essential enzymes involved in the citric acid cycle, as well as those involved in DNA, RNA, and protein synthesis. It is marketed under the following brand names: Furadantin, Macrobid, Macrodantin, Nitro Macro and Urantoin.","category_aro_class_name":"Antibiotic"},"41240":{"category_aro_accession":"3004116","category_aro_cvterm_id":"41240","category_aro_name":"nitrofuran antibiotic","category_aro_description":"Nitrofurans are chemotherapeutic agents with antibacterial and antiprotozoal activity.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1897":{"model_id":"1897","model_name":"tet(L)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"880"}},"model_sequences":{"sequence":{"518":{"protein_sequence":{"accession":"AAA22851.1","sequence":"MNTSYSQSNLRHNQILIWLCILSFFSVLNEMVLNVSLPDIANDFNKPPASTNWVNTAFMLTFSIGTAVYGKLSDQLGIKRLLLFGIIINCFGSVIGFVGHSFFSLLIMARFIQGAGAAAFPALVMVVVARYIPKENRGKAFGLIGSIVAMGEGVGPAIGGMIAHYIHWSYLLLIPMITIITVPFLMKLLKKEVRIKGHFDIKGIILMSVGIVFFMLFTTSYSISFLIVSVLSFLIFVKHIRKVTDPFVDPGLGKNIPFMIGVLCGGIIFGTVAGFVSMVPYMMKDVHQLSTAEIGSVIIFPGTMSVIIFGYIGGILVDRRGPLYVLNIGVTFLSVSFLTASFLLETTSWFMTIIIVFVLGGLLFTKTVISTIVSSSLKQQEAGAGMSLLNFTSFLSEGTGIAIVGGLLSIPLLDQRLLPMEVDQSTYLYSNLLLLFSGIIVISWLVTLNVYKHSQRDF"},"dna_sequence":{"accession":"M11036.1","fmin":"0","fmax":"1377","strand":"+","sequence":"GTGAATACATCCTATTCACAATCGAATTTACGACACAACCAAATTTTAATTTGGCTTTGCATTTTATCTTTTTTTAGCGTATTAAATGAAATGGTTTTGAACGTCTCATTACCTGATATTGCAAATGATTTTAATAAACCACCTGCGAGTACAAACTGGGTGAACACAGCCTTTATGTTAACCTTTTCCATTGGAACAGCTGTATATGGAAAGCTATCTGATCAATTAGGCATCAAAAGGTTACTCCTATTTGGAATTATAATAAATTGTTTCGGGTCGGTAATTGGGTTTGTTGGCCATTCTTTCTTTTCCTTACTTATTATGGCTCGTTTTATTCAAGGGGCTGGTGCAGCTGCATTTCCAGCACTCGTAATGGTTGTAGTTGCGCGCTATATTCCAAAGGAAAATAGGGGTAAAGCATTTGGTCTTATTGGATCGATAGTAGCCATGGGAGAAGGAGTCGGTCCAGCGATTGGTGGAATGATAGCCCATTATATTCATTGGTCCTATCTTCTACTCATTCCTATGATAACAATTATCACTGTTCCGTTTCTTATGAAATTATTAAAGAAAGAAGTAAGGATAAAAGGTCATTTTGATATCAAAGGAATTATACTAATGTCTGTAGGCATTGTATTTTTTATGTTGTTTACAACATCATATAGCATTTCTTTTCTTATCGTTAGCGTGCTGTCATTCCTGATATTTGTAAAACATATCAGGAAAGTAACAGATCCTTTTGTTGATCCCGGATTAGGGAAAAATATACCTTTTATGATTGGAGTTCTTTGTGGGGGAATTATATTTGGAACAGTAGCAGGGTTTGTCTCTATGGTTCCTTATATGATGAAAGATGTTCACCAGCTAAGTACTGCCGAAATCGGAAGTGTAATTATTTTCCCTGGAACAATGAGTGTCATTATTTTCGGCTACATTGGTGGGATACTTGTTGATAGAAGAGGTCCTTTATACGTGTTAAACATCGGAGTTACATTTCTTTCTGTTAGCTTTTTAACTGCTTCCTTTCTTTTAGAAACAACATCATGGTTCATGACAATTATAATCGTATTTGTTTTAGGTGGGCTTCTGTTCACCAAAACAGTTATATCAACAATTGTTTCAAGTAGCTTGAAACAGCAGGAAGCTGGTGCTGGAATGAGTTTGCTTAACTTTACCAGCTTTTTATCAGAGGGAACAGGTATTGCAATTGTAGGTGGTTTATTATCCATACCCTTACTTGATCAAAGGTTATTACCTATGGAAGTTGATCAGTCAACTTATCTGTATAGTAATTTGTTATTACTTTTTTCAGGAATCATTGTCATTAGTTGGCTGGTTACCTTGAATGTATATAAACATTCTCAAAGGGATTTCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36826","NCBI_taxonomy_name":"Geobacillus stearothermophilus","NCBI_taxonomy_id":"1422"}}}},"ARO_accession":"3000179","ARO_id":"36318","ARO_name":"tet(L)","CARD_short_name":"tet(L)","ARO_description":"TetL is a tetracycline efflux protein found in many species of Gram-negative and Gram-positive bacteria.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"249":{"model_id":"249","model_name":"basS","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"900"}},"model_sequences":{"sequence":{"3375":{"protein_sequence":{"accession":"AEX49906.1","sequence":"MSRAAVPSVRRRLLVNLLVGFVLCWLSVAALTYHLSLKQVNRLFDDDMVDFGEAALRLLDLATEDQAGEDGSITEIIERSREAIQGLPLLRRESALGYALWRDGQPLLSSLNLPPEITAQGPGFSTVEAQGTHWRVLQLNIDGFQIWISENLIYRQHTMNLLLFYSLFPLLLALPLLGGLVWFGVARGLAPLREVQAEVQQRSARHLQPIAVEAVPLEIRGLIDELNLLLERLRTALEAERRLTSDAAHEIRTPLASLRTHAQVALRSEDPKAHARGLLQVSRSVERISTLMEQILLLARLDGDALLEQFHPVNLATLAEDVLSELARQAIDKDIELSLHQETVHVMGIDLWLKAMVGNLVGNALRYTPAGGQVEIRVENRAQHAVLRVRDNGPGVALEEQQAIFTRFYRSPATSSGEGSGLGLPIVKRIVELHFGSIGLGKGLEGKGLEVQVFLPKTQPDATRPPARGPDSGRSHI"},"dna_sequence":{"accession":"JQ340365.1","fmin":"0","fmax":"1434","strand":"+","sequence":"ATGTCCCGTGCCGCCGTCCCCTCCGTCCGCCGGCGCCTGCTGGTCAACCTGCTGGTCGGCTTCGTGCTGTGCTGGCTGAGCGTGGCGGCGCTGACCTACCACCTCTCGCTGAAGCAGGTGAACCGCCTGTTCGACGACGACATGGTGGACTTCGGCGAAGCCGCCCTGCGCCTGCTCGACCTTGCCACCGAAGACCAGGCCGGCGAGGACGGCTCCATCACCGAGATCATCGAACGCAGCCGCGAAGCGATCCAGGGTCTGCCCCTGCTGCGCCGCGAAAGCGCCCTCGGCTACGCCCTGTGGCGCGACGGCCAGCCGCTGCTGTCGAGCCTCAACCTGCCGCCGGAGATCACGGCCCAGGGCCCCGGCTTCAGCACCGTGGAAGCCCAGGGCACCCACTGGCGGGTGCTCCAGCTGAACATCGACGGCTTCCAGATCTGGATCAGCGAAAACCTGATCTACCGCCAGCACACCATGAACCTGCTGCTGTTCTACTCGCTGTTCCCACTGCTGCTGGCGCTGCCGTTGCTCGGCGGCCTGGTCTGGTTCGGCGTTGCCCGCGGCCTGGCGCCGCTACGCGAAGTGCAGGCCGAGGTCCAGCAGCGCTCCGCGCGACACCTGCAGCCGATCGCGGTGGAAGCGGTGCCGCTGGAGATCCGCGGCCTCATCGACGAACTCAACCTCCTGCTGGAGCGTCTGCGCACCGCCCTCGAGGCCGAACGCCGACTGACCAGCGACGCCGCCCATGAAATCCGCACGCCACTGGCCAGCCTGCGCACCCATGCCCAGGTCGCGCTGCGTTCGGAAGACCCCAAGGCCCACGCCCGCGGCCTGCTGCAAGTCAGTCGCAGCGTCGAGCGGATCAGCACCTTGATGGAGCAGATCCTGCTCCTCGCCCGCCTCGACGGCGACGCCCTGCTGGAGCAATTCCACCCGGTCAACCTCGCCACCCTGGCCGAAGACGTACTCTCCGAACTGGCGCGCCAGGCCATCGACAAGGACATCGAGCTGTCGTTGCACCAGGAGACCGTGCACGTGATGGGCATCGACCTGTGGCTGAAGGCGATGGTCGGCAACCTGGTGGGCAACGCCCTGCGCTACACACCGGCCGGGGGCCAGGTCGAGATCCGCGTCGAGAATCGCGCCCAGCACGCCGTGCTGCGGGTGCGCGACAACGGCCCCGGGGTCGCCCTGGAAGAGCAGCAGGCGATCTTCACCCGCTTCTACCGCAGCCCCGCCACCAGCAGCGGCGAGGGCAGCGGCCTGGGCCTGCCGATCGTCAAGCGCATCGTCGAACTGCACTTCGGCAGTATCGGCCTGGGCAAGGGACTGGAGGGCAAAGGGCTGGAAGTGCAGGTGTTCCTGCCGAAGACCCAGCCGGACGCGACGCGGCCGCCGGCCAGAGGTCCGGACAGCGGGCGGTCACATATCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3003583","ARO_id":"40193","ARO_name":"basS","CARD_short_name":"basS","ARO_description":"Histidine protein kinase sensor Lipid A modification gene; part of a two-component system involved in polymyxin resistance that senses high extracellular Fe(2+).","ARO_category":{"41433":{"category_aro_accession":"3004269","category_aro_cvterm_id":"41433","category_aro_name":"pmr phosphoethanolamine transferase","category_aro_description":"This family of phosphoethanolamine transferase catalyze the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine to lipid A, which impedes the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36593":{"category_aro_accession":"3000454","category_aro_cvterm_id":"36593","category_aro_name":"polymyxin B","category_aro_description":"Polymyxin B is mixture of mostly polymyxins B1 and B2, mainly used for resistant gram-negative infections. They are polypeptides with cationic detergent action on cell membranes.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2291":{"model_id":"2291","model_name":"Chlamydia trachomatis intrinsic murA conferring resistance to fosfomycin","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"3556":{"protein_sequence":{"accession":"AAN28945.1","sequence":"MPGIKVFGETVLRGSVRVSGAKNATTKLLVASLLSDQRTILKNVPNIEDVRQTVDLCRVLGAIVEWDQQAQVIEIHTPRILLSKVPPQFSCVNRIPILLLGALLRRCPYGIFVPILGGDAIGPRTLHFHLEGWKKLGAEIVISDEGYWASAPNGLVGAHITLPYPSVGATENLILASVGAQGRTIIKNAALEVEIIDLIVFLQKAGVEITTDNDKTIEIFGCQDFYSVEHFIIPDKIEAASFGMAAVVSQGRIFVEQARHEHMIPFLKVLRSIGGGFSVHENGIEFFYDKPLKGGVLLETDVHPGFITDWQQPFAVLLSQSEGCSVIHETVHENRLGYLKGLVKMGAHCDLFHECLSAKSCRYSTGNHPHSAVIHGPTPLQATDLVIPDLRAGFAYVMAALIAEGGASWIENTEMLDRGYTDWRGKLERLGAKVLARDAVSVYV"},"dna_sequence":{"accession":"AY152390.1","fmin":"0","fmax":"1335","strand":"+","sequence":"ATGCCTGGTATCAAGGTTTTTGGAGAAACGGTCTTAAGAGGATCTGTGCGCGTGTCAGGAGCTAAAAATGCTACAACTAAATTACTTGTAGCCTCCTTACTTTCGGATCAGCGAACGATTTTAAAGAACGTCCCTAATATTGAAGATGTTCGGCAAACGGTAGATCTTTGTCGGGTTTTAGGGGCGATTGTAGAGTGGGATCAGCAAGCGCAAGTGATTGAAATTCACACTCCGCGCATTTTATTGTCCAAGGTTCCTCCGCAATTTTCTTGTGTTAATCGGATTCCTATTTTGCTGTTAGGAGCGTTGTTACGTCGTTGTCCTTATGGGATTTTTGTTCCTATTTTGGGAGGGGATGCTATAGGACCTCGTACGCTACATTTCCATTTAGAAGGATGGAAGAAGCTTGGAGCAGAGATAGTAATTAGTGATGAAGGCTATTGGGCTTCAGCTCCAAATGGTCTTGTTGGAGCACACATCACGTTACCCTACCCTTCTGTGGGAGCCACAGAAAACCTCATCCTTGCTTCTGTAGGGGCTCAAGGACGAACGATTATTAAGAATGCTGCTCTTGAAGTGGAAATCATTGATTTGATTGTCTTTTTACAGAAAGCAGGCGTGGAGATTACAACAGATAATGATAAGACCATCGAAATTTTTGGATGTCAGGATTTCTATTCTGTTGAGCACTTCATTATTCCAGATAAAATCGAGGCTGCTTCTTTCGGTATGGCTGCGGTAGTTTCTCAGGGAAGGATCTTCGTAGAACAAGCGCGCCATGAGCATATGATCCCTTTTTTAAAGGTATTAAGATCGATAGGAGGGGGATTCTCTGTACATGAGAATGGGATCGAATTTTTCTACGATAAGCCTTTGAAAGGGGGTGTTCTTCTAGAAACGGATGTGCATCCAGGGTTTATTACAGATTGGCAACAACCTTTTGCCGTATTGCTCTCTCAGTCAGAAGGTTGTTCGGTGATCCATGAGACAGTGCATGAGAATCGTCTTGGGTATTTGAAAGGTTTGGTAAAAATGGGAGCGCATTGTGATTTATTTCACGAGTGTTTGAGTGCTAAGTCGTGTCGCTATTCTACAGGGAATCATCCTCATAGCGCAGTCATTCATGGTCCGACTCCTTTGCAGGCAACAGACTTAGTGATTCCTGATTTGCGCGCAGGATTTGCTTATGTCATGGCCGCACTCATTGCAGAAGGCGGAGCCTCATGGATTGAGAATACCGAGATGCTGGATCGAGGGTACACTGATTGGCGAGGGAAATTAGAAAGATTAGGAGCTAAGGTTTTAGCGCGAGACGCAGTATCTGTGTATGTTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40470","NCBI_taxonomy_name":"Chlamydia trachomatis","NCBI_taxonomy_id":"813"}}}},"ARO_accession":"3003785","ARO_id":"40469","ARO_name":"Chlamydia trachomatis intrinsic murA conferring resistance to fosfomycin","CARD_short_name":"Ctra_murA_FOF","ARO_description":"Chlamydia murA confers intrinsic resistance to fosfomycin. The presence of an aspartic acid residue in place of the critical cysteine at position 119 that enables fosfomycin binding is believed to be responsible for this intrinsic resistance.","ARO_category":{"39245":{"category_aro_accession":"3002811","category_aro_cvterm_id":"39245","category_aro_name":"antibiotic-resistant murA transferase","category_aro_description":"murA or UDP-N-acetylglucosamine enolpyruvyl transferase catalyses the initial step in peptidoglycan biosynthesis and is inhibited by fosfomycin. Overexpression of murA through mutations confers fosfomycin resistance.","category_aro_class_name":"AMR Gene Family"},"35944":{"category_aro_accession":"0000025","category_aro_cvterm_id":"35944","category_aro_name":"fosfomycin","category_aro_description":"Fosfomycin (also known as phosphomycin and phosphonomycin) is a broad-spectrum antibiotic produced by certain Streptomyces species. It is effective on gram positive and negative bacteria as it targets the cell wall, an essential feature shared by both bacteria. Its specific target is MurA (MurZ in E.coli), which attaches phosphoenolpyruvate (PEP) to UDP-N-acetylglucosamine, a step of commitment to cell wall synthesis. In the active site of MurA, the active cysteine molecule is alkylated which stops the catalytic reaction.","category_aro_class_name":"Antibiotic"},"45731":{"category_aro_accession":"3007149","category_aro_cvterm_id":"45731","category_aro_name":"phosphonic acid antibiotic","category_aro_description":"A group of antibiotics derived from phosphonic acids.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2108":{"model_id":"2108","model_name":"Enterococcus faecium EF-Tu mutants conferring resistance to GE2270A","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"3055":"G258A","4119":"G275A"},"Curated-R":{"3055":"G258A","4119":"G275A"},"clinical":{"3055":"G258A","4119":"G275A"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"5307":{"protein_sequence":{"accession":"AFK57679.1","sequence":"MGMWCTLCTSYTYQTNKKYIVFLGGHFKMAKEKFDRSKPHVNIGTIGHVDHGKTTLTAAITTVLSKKNGGQAMAYDQIDGAPEERERGITISTAHVEYETDTRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSAADGPMPQTREHILLSRQVGVPYIVVFLNKVDMVDDEELLELVEMEVRDLLTEYEFPGDDVPVVAGSALKALEGDASYEEKILELMAAVDEYIPTPERDNDKPFMMPVEDVFSITGRGTVATGRVERGQVRVGDEVEVVGIAEETSKTTVTGVEMFRKLLDYAEAGDNIGALLRGVAREDIQRGQVLAKPGTITPHTKFSAEVYVLTKEEGGRHTPFFTNYRPQFYFRTTDVTGVVELPEGTEMVMPGDNVTMEVELIHPIAIENGTKFSIREGGRTVGAGVVTEIKA"},"dna_sequence":{"accession":"CP003583.1","fmin":"60337","fmax":"61609","strand":"+","sequence":"ATGGGCATGTGGTGTACCTTGTGTACATCATATACCTATCAGACAAATAAAAAATATATTGTATTTTTAGGAGGACATTTTAAAATGGCAAAAGAAAAATTTGACCGTTCTAAACCACACGTTAACATTGGTACTATCGGACACGTTGACCATGGTAAAACTACATTAACAGCTGCAATCACAACTGTACTATCTAAGAAAAACGGCGGCCAAGCTATGGCTTACGATCAAATCGATGGTGCTCCAGAAGAACGCGAACGCGGAATCACAATCTCAACAGCTCACGTTGAGTATGAAACAGATACACGCCACTACGCTCACGTTGACTGCCCAGGACACGCGGATTACGTTAAAAACATGATCACTGGTGCTGCTCAAATGGACGGAGCTATCTTGGTAGTTTCTGCTGCTGACGGCCCAATGCCTCAAACTCGTGAACACATCCTATTGTCTCGTCAAGTTGGTGTTCCTTACATCGTTGTATTCTTGAACAAAGTAGACATGGTTGATGACGAAGAATTACTAGAATTAGTTGAAATGGAAGTTCGTGACCTATTAACAGAATACGAATTCCCTGGTGACGATGTTCCTGTAGTTGCTGGATCAGCTTTGAAAGCTCTAGAAGGCGACGCTTCATACGAAGAAAAAATTCTTGAATTAATGGCTGCAGTTGACGAATACATCCCAACTCCAGAACGTGACAACGACAAACCATTCATGATGCCAGTTGAAGACGTGTTCTCAATTACTGGACGTGGTACTGTTGCTACAGGTCGTGTTGAACGTGGACAAGTTCGCGTTGGTGACGAAGTTGAAGTTGTTGGTATTGCTGAAGAAACTTCAAAAACAACAGTTACTGGTGTTGAAATGTTCCGTAAATTGTTAGACTACGCTGAAGCTGGAGACAACATTGGTGCTTTACTACGTGGTGTTGCACGTGAAGACATCCAACGTGGACAAGTTTTAGCTAAACCAGGTACAATCACACCTCATACAAAATTCTCTGCAGAAGTATACGTGTTGACAAAAGAAGAAGGTGGACGTCATACTCCATTCTTCACTAACTACCGTCCACAATTCTACTTCCGTACAACTGACGTAACAGGTGTTGTTGAATTACCAGAAGGAACTGAAATGGTTATGCCTGGCGACAACGTAACAATGGAAGTTGAATTAATCCACCCAATCGCTATCGAAAACGGTACTAAATTCTCAATCCGTGAAGGCGGACGTACAGTTGGTGCCGGTGTCGTTACAGAAATCAAAGCTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37599","NCBI_taxonomy_name":"Enterococcus faecium DO","NCBI_taxonomy_id":"333849"}}}},"ARO_accession":"3003438","ARO_id":"40022","ARO_name":"Enterococcus faecium EF-Tu mutants conferring resistance to GE2270A","CARD_short_name":"Efac_EFTu_GE2A","ARO_description":"Sequence variants of Enterococcus faecium elongation factor Tu that confer resistance to GE2270A.","ARO_category":{"37711":{"category_aro_accession":"3001312","category_aro_cvterm_id":"37711","category_aro_name":"elfamycin resistant EF-Tu","category_aro_description":"Sequence variants of elongation factor Tu that confer resistance to elfamycin antibiotics.","category_aro_class_name":"AMR Gene Family"},"37636":{"category_aro_accession":"3001237","category_aro_cvterm_id":"37636","category_aro_name":"GE2270A","category_aro_description":"GE2270A is the model molecule of cyclic thiazolyl peptide elfamycins. GE2270A is produced by Planobispora rosea. Biosynthesis of the molecule has been shown to originate as a ribosomally synthesized peptide that undergoes significant post-translational modification. Clinical use of cyclic thiazolyl peptides is hindered by their low water solubility and bioavailability.","category_aro_class_name":"Antibiotic"},"37618":{"category_aro_accession":"3001219","category_aro_cvterm_id":"37618","category_aro_name":"elfamycin antibiotic","category_aro_description":"Elfamycins are molecules that inhibit bacterial elongation factor Tu (EF-Tu), a key protein which brings aminoacyl-tRNA (aa-tRNA) to the ribosome during protein synthesis. Elfamycins defined by their target (EF-Tu), rather than a conserved chemical backbone. Elfamycins follow two mechanisms to disrupt protein synthesis: 1. kirromycins and enacyloxin fix EF-Tu in the GTP bound conformation and lock EF-Tu onto the ribosome, and 2. pulvomycin and GE2270 cover the binding site of aa-tRNA disallowing EF-Tu from being charged with aa-tRNA. All elfamycins cause increased the affinity of EF-Tu for GTP.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1300":{"model_id":"1300","model_name":"MexF","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"2110"}},"model_sequences":{"sequence":{"5530":{"protein_sequence":{"accession":"AAG05882.1","sequence":"MNFSQFFIQRPIFAAVLSLLILIGGAISLFQLPISEYPEVVPPTVVVRANFPGANPKVIGETVASPLEQAITGVENMLYMSSQSTSDGKLTLTITFALGTDLDNAQVQVQNRVTRTEPKLPEEVTRLGITVDKASPDLTMVVHLTSPDNRYDMLYLSNYAVLNVKDELARLDGVGDVQLFGLGDYSLRVWLDPNKVASRNLTATDVVNAIREQNRQVAAGTLGAPPAPSDTSFQLSINTQGRLVTEEEFENIIIRAGANGEITRLRDIARVELGSNQYALRSLLNNKPAVAIPIFQRPGSNAIEISNLVREKMAELKHSFPQGMDYSIVYDPTIFVRGSIEAVVHTLFEALVLVVLVVILFLQTWRASIIPLAAVPVSLIGTFAVMHMLGFSLNALSLFGLVLAIGIVVDDAIVVVENVERNIGLGLKPVEATKRAMREVTGPIIATALVLCAVFIPTAFISGLTGQFYRQFALTIAISTVISAFNSLTLSPALAAVLLKGHHEPKDRFSVFLDKLLGSWLFRPFNRFFDRASHGYVGTVNRVLRGSSIALLVYGGLMVLTYFGFSSTPTGFVPQQDKQYLVAFAQLPDAASLDRTEAVIKQMSEIALAQPGVADSVAFPGLSINGFTNSPNSGIVFTPLKPFDERKDPSQSAGAIAAALNAKYADIQDAYIAIFPPPPVQGLGTIGGFRLQIEDRGNQGYEELFKQTQNIITKARALPELEPSSVFSSYQVNVPQIDADIDREKAKTHGVAISDIFDTLQVYLGSLYANDFNRFGRTYQVNVQAEQQFRLEPEQIGQLKVRNNLGEMVPLASFIKVSDTSGPDRVMHYNGFITAELNGAPAAGYSSGQAQAAIEKLLKEELPNGMTYEWTELTYQQILAGNTALFVFPLCVLLAFLVLAAQYESWSLPLAVILIVPMTLLSAITGVILAGSDNNIFTQIGLIVLVGLACKNAILIVEFAKDKQEEGMDRVAAVLEACRLRLRPILMTSIAFIMGVVPLVISTGAGAEMRHAMGVAVFSGMIGVTFFGLLLTPVFYVLIRRFVENREARRAANDKGLPEVHA"},"dna_sequence":{"accession":"AE004091.2","fmin":"2810008","fmax":"2813197","strand":"+","sequence":"ATGAATTTCTCCCAATTCTTCATCCAGCGGCCGATCTTCGCCGCGGTGCTGTCGCTGCTGATCCTGATTGGCGGCGCCATCTCCCTGTTCCAGCTACCCATCAGCGAATACCCGGAAGTGGTGCCGCCGACCGTCGTGGTCCGCGCCAACTTCCCCGGCGCCAACCCGAAAGTCATCGGCGAGACCGTCGCCTCTCCCCTTGAACAGGCGATCACCGGGGTGGAGAACATGCTCTACATGTCCTCCCAGTCGACCTCCGACGGCAAGCTGACCCTGACCATCACCTTCGCCCTCGGCACCGACCTGGACAACGCCCAGGTGCAGGTGCAGAACCGCGTCACCCGGACCGAGCCGAAGCTCCCGGAAGAAGTGACCCGGCTCGGCATCACCGTCGACAAGGCCTCGCCCGACCTGACCATGGTCGTGCACCTGACCTCGCCGGATAACCGCTACGACATGCTCTACCTGTCGAACTACGCGGTGCTCAACGTGAAGGACGAACTGGCCCGCCTCGACGGCGTCGGCGACGTCCAGTTGTTCGGCCTCGGCGACTATTCGCTGCGCGTCTGGCTGGACCCGAACAAGGTCGCCTCGCGCAACCTCACCGCCACCGACGTGGTCAACGCCATCCGCGAGCAGAACCGCCAGGTCGCCGCCGGCACCCTGGGCGCGCCGCCGGCGCCGAGCGATACCAGCTTCCAGTTGTCGATCAACACCCAGGGTCGCCTGGTCACCGAGGAAGAGTTCGAGAACATCATCATCCGCGCCGGCGCCAACGGCGAGATCACCCGTCTGCGCGACATCGCCCGGGTCGAGCTGGGCTCCAACCAGTACGCCCTGCGTTCGCTGCTGAACAACAAGCCGGCGGTGGCGATCCCGATCTTCCAGCGTCCCGGCTCGAACGCCATCGAGATCTCCAACCTGGTGCGGGAGAAGATGGCCGAGCTGAAGCACAGCTTCCCGCAAGGCATGGACTACTCCATCGTCTACGACCCGACCATCTTCGTCCGCGGCTCCATCGAGGCGGTGGTGCACACCCTGTTCGAAGCCCTGGTGCTGGTGGTGCTGGTGGTGATCCTGTTCCTGCAGACCTGGCGCGCCTCGATCATCCCGCTGGCCGCGGTGCCGGTGTCGCTGATCGGCACCTTCGCGGTGATGCACATGCTCGGCTTCTCGCTCAACGCGCTGTCGCTGTTCGGCCTGGTGCTGGCCATCGGCATCGTGGTGGACGACGCCATCGTGGTGGTGGAGAACGTCGAGCGCAACATCGGCCTCGGCCTCAAGCCGGTGGAAGCCACCAAGCGTGCCATGCGCGAGGTGACCGGGCCGATCATCGCCACGGCGCTGGTGCTCTGCGCGGTGTTCATCCCGACCGCGTTCATCTCCGGCCTCACCGGGCAGTTCTACCGCCAGTTCGCCCTGACCATCGCGATCTCCACGGTGATCTCGGCGTTCAACTCGCTGACCCTGTCGCCAGCGCTGGCGGCGGTCCTGCTCAAGGGCCACCACGAGCCGAAGGACCGCTTCTCGGTGTTCCTCGACAAGCTCCTCGGCAGTTGGCTGTTCCGTCCGTTCAACCGTTTCTTCGACCGCGCCAGCCATGGCTACGTCGGCACGGTGAACCGGGTCCTGCGCGGCAGCTCGATCGCCCTGCTGGTCTACGGCGGACTGATGGTGCTGACCTACTTCGGCTTCTCCAGCACGCCGACCGGTTTCGTCCCGCAGCAGGACAAGCAGTACCTGGTGGCCTTCGCCCAGTTGCCCGACGCGGCCAGCCTGGACCGTACCGAGGCGGTGATCAAGCAGATGTCCGAGATCGCCCTGGCGCAGCCCGGCGTGGCGGACTCGGTGGCCTTCCCCGGCCTGTCGATCAACGGCTTCACCAACAGCCCGAACAGCGGCATCGTGTTCACCCCGCTGAAGCCGTTCGACGAGCGCAAGGACCCGAGCCAGTCGGCCGGGGCCATCGCCGCCGCGCTGAACGCCAAGTACGCCGACATTCAGGACGCCTACATCGCGATCTTCCCGCCGCCGCCGGTACAGGGGCTGGGGACCATCGGCGGCTTCCGCCTGCAGATCGAGGACCGTGGCAACCAGGGCTACGAGGAGCTGTTCAAGCAGACCCAGAACATCATCACCAAGGCCCGTGCGCTGCCTGAGCTGGAACCCAGCTCGGTGTTCTCCAGCTACCAGGTCAACGTGCCGCAGATCGACGCCGACATCGACCGCGAGAAGGCCAAGACCCACGGCGTGGCGATCAGCGACATCTTCGACACCCTGCAGGTCTACCTCGGCTCGCTGTACGCGAACGACTTCAACCGCTTCGGCCGTACCTATCAGGTCAACGTCCAGGCCGAGCAGCAGTTCCGCCTCGAACCCGAGCAGATCGGCCAGCTGAAGGTGCGCAACAACCTCGGCGAGATGGTCCCGCTGGCGTCCTTCATCAAGGTCAGCGACACCTCCGGTCCGGACCGTGTGATGCACTACAACGGCTTCATCACCGCCGAACTCAACGGCGCCCCGGCCGCGGGCTACAGCTCCGGCCAGGCGCAGGCGGCGATCGAGAAGCTGCTGAAGGAGGAACTGCCCAACGGCATGACCTACGAGTGGACCGAGCTGACCTACCAGCAGATCCTCGCCGGCAATACCGCGCTGTTCGTCTTCCCGCTCTGCGTGCTGCTGGCCTTCCTCGTGCTGGCCGCCCAGTACGAGAGCTGGAGCCTACCGCTGGCGGTGATCCTGATCGTGCCGATGACCCTGCTGTCGGCGATCACCGGGGTGATCCTGGCCGGCAGCGACAACAACATCTTTACCCAGATCGGCCTGATCGTTCTGGTGGGGCTGGCGTGCAAGAACGCGATCCTGATCGTCGAGTTCGCCAAGGACAAGCAGGAGGAAGGCATGGACCGCGTCGCCGCGGTGCTGGAAGCCTGCCGCCTGCGCCTGCGGCCGATCCTGATGACGTCCATCGCCTTCATCATGGGTGTGGTGCCGCTGGTGATCTCCACCGGCGCCGGCGCCGAGATGCGCCATGCGATGGGCGTGGCGGTGTTCTCCGGGATGATCGGGGTGACCTTCTTCGGCCTGCTGCTGACGCCGGTGTTCTACGTCCTCATCCGCCGCTTCGTGGAGAACCGCGAAGCGCGCCGCGCCGCCAACGACAAAGGCCTGCCAGAGGTGCATGCATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36804","NCBI_taxonomy_name":"Pseudomonas aeruginosa PAO1","NCBI_taxonomy_id":"208964"}}}},"ARO_accession":"3000804","ARO_id":"37184","ARO_name":"MexF","CARD_short_name":"MexF","ARO_description":"MexF is the multidrug inner membrane transporter of the MexEF-OprN complex. mexF corresponds to 2 loci in Pseudomonas aeruginosa PAO1 (gene name: mexF\/mexB) and 4 loci in Pseudomonas aeruginosa LESB58 (gene name: mexD\/mexB).","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"624":{"model_id":"624","model_name":"Mycobacterium leprae rpoB mutations conferring resistance to rifampicin","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"2300"},"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"2040":"V472I","2041":"S456L"},"Curated-R":{"2040":"V472I","2041":"S456L"},"clinical":{"2040":"V472I","2041":"S456L"}}},"model_sequences":{"sequence":{"4581":{"protein_sequence":{"accession":"CAC30845.1","sequence":"MLEGCILPDFGQSKTDVSPSQSRPQSSPNNSVPGAPNRISFAKLREPLEVPGLLDVQTDSFEWLIGSPCWRAAAASRGDLKPVGGLEEVLYELSPIEDFSGSMSLSFSDPRFDEVKAPVEECKDKDMTYAAPLFVTAEFINNNTGEIKSQTVFMGDFPMMTEKGTFIINGTERVVVSQLVRSPGVYFDETIDKSTEKTLHSVKVIPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTSEQITERFGFSEIMRSTLEKDNTVGTDEALLDIYRKLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYKVNKKLGLHAGELITSSTLTEEDVVATIEYLVRLHEGQSTMTVPGGVEVPVETDDIDHFGNRRLRTVGELIQNQIRVGMSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIKEFFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGLEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSVYARVNPFGFIETPYRKVVDGVVSDEIEYLTADEEDRHVVAQANSPIDEAGRFLEPRVLVRRKAGEVEYVASSEVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAPLVGTGMELRAAIDAGHVVVAEKSGVIEEVSADYITVMADDGTRRTYRMRKFARSNHGTCANQSPIVDAGDRVEAGQVIADGPCTENGEMALGKNLLVAIMPWEGHNYEDAIILSNRLVEEDVLTSIHIEEHEIDARDTKLGAEEITRDIPNVSDEVLADLDERGIVRIGAEVRDGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSHEDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPAEDMPFLPDGTPVDIILNTHGVPRRMNVGQILETHLGWVAKSGWKIDVAGGIPDWAVNLPEELLHAAPNQIVSTPVFDGAKEEELQGLLSSTLPNRDGDVMVGGDGKAVLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMECWAMQAYGAAYTLQELLTIKSDDTVGRVKVYEAIVKGENIPEPGIPESFKVLLKELQSLCLNVEVLSSDGAAIELREGEDEDLERAAANLGINLSRNESASIEDLA"},"dna_sequence":{"accession":"AL450380.1","fmin":"2273268","fmax":"2276805","strand":"-","sequence":"GTGCTGGAAGGATGCATCTTGCCAGATTTCGGCCAGAGCAAGACAGACGTTAGTCCTAGCCAGAGTCGCCCCCAAAGTTCGCCCAACAACTCCGTGCCCGGCGCGCCCAACCGAATTTCATTTGCCAAGCTCCGCGAACCGCTTGAGGTTCCGGGGCTACTTGATGTGCAGACTGATTCATTTGAGTGGTTGATCGGATCGCCGTGCTGGCGTGCAGCGGCCGCAAGCCGCGGCGATCTCAAGCCGGTGGGTGGTCTCGAAGAGGTGCTCTACGAGCTGTCGCCGATCGAGGATTTCTCCGGCTCAATGTCATTGTCTTTCTCCGATCCCCGTTTTGACGAAGTCAAGGCGCCCGTCGAAGAGTGCAAAGACAAGGACATGACGTACGCGGCCCCGCTGTTCGTCACGGCCGAGTTCATCAACAACAACACCGGGGAGATCAAGAGCCAGACGGTGTTTATGGGCGACTTCCCTATGATGACTGAGAAGGGAACCTTCATCATCAACGGGACCGAGCGTGTCGTCGTTAGCCAGCTGGTGCGCTCCCCTGGAGTATACTTCGACGAGACGATCGACAAGTCCACAGAAAAGACGCTGCATAGTGTCAAGGTGATTCCCAGCCGCGGTGCCTGGTTGGAATTCGATGTCGATAAACGCGACACCGTCGGTGTCCGCATTGACCGGAAGCGCCGGCAACCCGTCACGGTGCTTCTCAAAGCGCTAGGTTGGACCAGTGAGCAGATCACCGAGCGTTTCGGTTTCTCCGAGATCATGCGCTCGACGCTGGAGAAGGACAACACAGTTGGCACCGACGAGGCGCTGCTAGACATCTATCGTAAGTTGCGCCCAGGTGAGCCGCCGACTAAGGAGTCCGCGCAGACGCTGTTGGAGAACCTGTTCTTCAAGGAGAAACGCTACGACCTGGCCAGGGTTGGTCGTTACAAGGTCAACAAGAAGCTCGGGTTGCACGCCGGTGAGTTGATCACGTCGTCCACGCTGACCGAAGAGGATGTCGTCGCCACCATAGAGTACCTGGTTCGTCTGCATGAGGGTCAGTCGACAATGACTGTCCCAGGTGGGGTAGAAGTGCCAGTGGAAACTGACGATATCGACCACTTCGGCAACCGCCGGCTGCGCACGGTCGGCGAATTGATCCAGAACCAGATCCGGGTCGGTATGTCGCGGATGGAGCGGGTGGTCCGGGAGCGGATGACCACCCAGGACGTCGAGGCGATCACGCCGCAGACGCTGATCAATATCCGTCCGGTGGTCGCCGCTATCAAGGAATTCTTCGGCACCAGCCAGCTGTCGCAGTTCATGGATCAGAACAACCCTCTGTCGGGCCTGACCCACAAGCGCCGGCTGTCGGCGCTGGGCCCGGGTGGTTTGTCGCGTGAGCGTGCCGGGCTAGAGGTCCGTGACGTGCACCCTTCGCACTACGGCCGGATGTGCCCGATCGAGACTCCGGAGGGCCCGAACATAGGTCTGATCGGTTCATTGTCGGTGTACGCGCGGGTCAACCCCTTCGGGTTCATCGAAACACCGTACCGCAAAGTGGTTGACGGTGTGGTCAGCGACGAGATCGAATACTTGACCGCTGACGAGGAAGACCGCCATGTCGTGGCGCAGGCCAACTCGCCGATCGACGAGGCCGGCCGCTTCCTCGAGCCGCGCGTGTTGGTGCGCCGCAAGGCGGGCGAGGTGGAGTACGTGGCCTCGTCCGAGGTGGATTACATGGATGTCTCGCCACGCCAGATGGTGTCGGTGGCCACAGCGATGATTCCGTTCCTTGAGCACGACGACGCCAACCGTGCCCTGATGGGCGCTAACATGCAGCGCCAAGCGGTTCCGTTGGTGCGCAGCGAAGCACCGTTGGTGGGTACCGGTATGGAGTTGCGCGCGGCCATCGACGCTGGCCACGTCGTCGTTGCGGAGAAGTCCGGGGTGATCGAGGAGGTTTCCGCCGACTACATCACCGTGATGGCCGATGACGGCACCCGGCGGACTTATCGGATGCGTAAGTTCGCGCGCTCCAACCACGGCACCTGCGCCAACCAGTCCCCGATCGTGGATGCGGGGGATCGGGTCGAGGCCGGCCAAGTGATTGCTGACGGTCCGTGCACTGAGAACGGCGAGATGGCGTTGGGCAAGAACTTGCTGGTGGCGATCATGCCGTGGGAGGGTCACAACTACGAGGATGCGATCATCCTGTCTAACCGACTGGTCGAAGAGGACGTGCTTACTTCGATTCACATTGAGGAGCATGAGATCGACGCCCGTGACACCAAGCTGGGTGCTGAGGAGATCACCCGGGACATTCCCAACGTCTCCGATGAGGTGCTAGCCGACTTGGACGAGCGGGGCATCGTGCGGATTGGCGCGGAGGTTCGTGACGGTGATATCCTGGTTGGCAAGGTCACCCCGAAGGGGGAAACTGAGCTGACACCGGAAGAGCGGTTGCTGCGGGCGATCTTCGGCGAAAAGGCCCGCGAGGTCCGTGACACGTCGCTGAAGGTGCCACACGGCGAATCCGGCAAGGTGATCGGCATTCGGGTGTTCTCCCATGAGGATGACGACGAGCTGCCCGCCGGCGTCAACGAGCTGGTCCGTGTCTACGTAGCCCAGAAGCGCAAGATCTCTGACGGTGACAAGCTGGCTGGGCGGCACGGCAACAAGGGCGTGATCGGCAAGATCCTGCCTGCCGAGGATATGCCGTTTCTGCCAGACGGCACCCCGGTGGACATCATCCTCAACACTCACGGGGTGCCGCGGCGGATGAACGTCGGTCAGATCTTGGAAACCCACCTTGGGTGGGTAGCCAAGTCCGGCTGGAAGATCGACGTGGCCGGCGGTATACCGGATTGGGCGGTCAACTTGCCTGAGGAGTTGTTGCACGCTGCGCCCAACCAGATCGTGTCGACCCCGGTGTTCGACGGCGCCAAGGAAGAGGAACTACAGGGCCTGTTGTCCTCCACGTTGCCCAACCGCGACGGCGATGTGATGGTGGGCGGCGACGGCAAGGCGGTGCTCTTCGATGGGCGCAGCGGTGAGCCGTTCCCTTATCCGGTGACGGTTGGCTACATGTACATCATGAAGCTGCACCACTTGGTGGACGACAAGATCCACGCCCGCTCCACCGGCCCGTACTCGATGATTACCCAGCAGCCGTTGGGTGGTAAGGCACAGTTCGGTGGCCAGCGATTCGGTGAGATGGAGTGCTGGGCCATGCAGGCCTACGGTGCGGCCTACACGCTGCAGGAGCTGTTGACCATCAAGTCCGACGACACCGTCGGTCGGGTCAAGGTTTACGAGGCTATCGTTAAGGGTGAGAACATCCCCGAGCCGGGCATCCCCGAGTCGTTCAAGGTGCTGCTCAAGGAGTTACAGTCGCTGTGTCTCAACGTCGAGGTGCTGTCGTCCGACGGTGCGGCGATCGAGTTGCGCGAAGGTGAGGATGAGGACCTCGAGCGGGCTGCGGCCAACCTCGGTATCAACTTGTCCCGCAACGAATCGGCGTCCATAGAAGATCTGGCTTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40074","NCBI_taxonomy_name":"Mycobacterium leprae","NCBI_taxonomy_id":"1769"}}}},"ARO_accession":"3003284","ARO_id":"39868","ARO_name":"Mycobacterium leprae rpoB mutations conferring resistance to rifampicin","CARD_short_name":"Mlep_rpoB_RIF","ARO_description":"Point mutations that occurs in Mycobacterium leprae rpoB resulting in resistance to rifampicin.","ARO_category":{"36349":{"category_aro_accession":"3000210","category_aro_cvterm_id":"36349","category_aro_name":"rifamycin-resistant beta-subunit of RNA polymerase (rpoB)","category_aro_description":"Rifampin resistant RNA polymerases include amino acids substitutions which disrupt the affinity of rifampin for its binding site. These mutations are frequently concentrated in the rif I region of the beta-subunit and most often involve amino acids which make direct interactions with rifampin. However, mutations which also confer resistance can occur outside this region and may involve amino acids which do not directly make contact with rifampin.","category_aro_class_name":"AMR Gene Family"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36656":{"category_aro_accession":"3000517","category_aro_cvterm_id":"36656","category_aro_name":"rifaximin","category_aro_description":"Rifaximin is a semi-synthetic rifamycin used to treat traveller's diarrhea. Rifaximin inhibits RNA synthesis by binding to the beta subunit of bacterial RNA polymerase.","category_aro_class_name":"Antibiotic"},"36669":{"category_aro_accession":"3000530","category_aro_cvterm_id":"36669","category_aro_name":"rifabutin","category_aro_description":"Rifabutin is a semisynthetic rifamycin used in tuberculosis therapy. It inhibits DNA-dependent RNA synthesis.","category_aro_class_name":"Antibiotic"},"36673":{"category_aro_accession":"3000534","category_aro_cvterm_id":"36673","category_aro_name":"rifapentine","category_aro_description":"Rifapentine is a semisynthetic rifamycin that inhibits DNA-dependent RNA synthesis. It is often used in the treatment of tuberculosis and leprosy.","category_aro_class_name":"Antibiotic"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1305":{"model_id":"1305","model_name":"OprM","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"850"}},"model_sequences":{"sequence":{"5378":{"protein_sequence":{"accession":"AAG03816.1","sequence":"MKRSFLSLAVAAVVLSGCSLIPDYQRPEAPVAAAYPQGQAYGQNTGAAAVPAADIGWREFFRDPQLQQLIGVALENNRDLRVAALNVEAFRAQYRIQRADLFPRIGVDGSGTRQRLPGDLSTTGSPAISSQYGVTLGTTAWELDLFGRLRSLRDQALEQYLATEQAQRSAQTTLVASVATAYLTLKADQAQLQLTKDTLGTYQKSFDLTQRSYDVGVASALDLRQAQTAVEGARATLAQYTRLVAQDQNALVLLLGSGIPANLPQGLGLDQTLLTEVPAGLPSDLLQRRPDILEAEHQLMAANASIGAARAAFFPSISLTANAGTMSRQLSGLFDAGSGSWLFQPSINLPIFTAGSLRASLDYAKIQKDINVAQYEKAIQTAFQEVADGLAARGTFTEQLQAQRDLVKASDEYYQLADKRYRTGVDNYLTLLDAQRSLFTAQQQLITDRLNQLTSEVNLYKALGGGWNQQTVTQQQTAKKEDPQA"},"dna_sequence":{"accession":"AE004091.2","fmin":"476332","fmax":"477790","strand":"+","sequence":"ATGAAACGGTCCTTCCTTTCCCTGGCGGTAGCCGCTGTCGTTCTGTCCGGCTGCTCGCTGATCCCCGACTACCAGCGCCCCGAGGCGCCGGTAGCCGCGGCCTACCCGCAAGGGCAGGCCTACGGGCAGAACACCGGCGCGGCGGCCGTTCCGGCCGCCGACATCGGCTGGCGCGAGTTCTTCCGCGACCCGCAGTTGCAGCAACTGATCGGCGTGGCGCTGGAAAACAACCGCGACCTGCGGGTCGCCGCGCTGAACGTCGAGGCCTTCCGGGCGCAGTACCGCATCCAGCGGGCCGACCTGTTCCCGCGGATCGGCGTGGACGGTAGCGGCACCCGCCAGCGTTTGCCGGGCGACCTGTCGACCACCGGCAGTCCGGCGATTTCCAGCCAGTACGGGGTGACCCTGGGCACTACCGCCTGGGAACTCGATCTCTTCGGCCGCCTGCGCAGCCTGCGCGACCAGGCCCTGGAGCAGTACCTGGCGACCGAACAGGCGCAGCGCAGCGCGCAGACCACCCTGGTGGCCAGCGTGGCGACCGCCTACCTGACGCTGAAGGCCGACCAGGCGCAGTTGCAGCTGACCAAGGACACCCTGGGCACCTACCAGAAGAGTTTCGACCTGACCCAGCGCAGCTACGACGTCGGCGTCGCCTCCGCGCTCGACCTGCGCCAGGCGCAGACCGCCGTGGAAGGCGCCCGCGCGACCCTGGCGCAGTACACCCGCCTGGTAGCCCAGGACCAGAATGCGCTGGTCCTGCTGCTGGGCTCCGGGATCCCGGCGAACCTGCCGCAAGGCCTGGGCCTGGACCAGACCCTGCTGACCGAAGTGCCGGCGGGTCTGCCGTCGGACCTGCTGCAACGGCGCCCGGACATCCTCGAGGCCGAGCACCAGCTCATGGCTGCCAACGCCAGCATCGGCGCCGCGCGCGCGGCGTTCTTCCCGAGCATCAGCCTGACCGCCAACGCCGGCACCATGAGCCGCCAACTGTCCGGCCTGTTCGACGCCGGTTCGGGTTCCTGGTTGTTCCAGCCGTCGATCAACCTGCCGATCTTCACCGCCGGCAGCCTGCGTGCCAGCCTGGACTACGCGAAGATCCAGAAGGACATCAACGTCGCGCAGTACGAGAAGGCGATCCAGACGGCGTTCCAGGAAGTCGCCGACGGCCTGGCCGCGCGCGGTACCTTCACCGAGCAGTTGCAGGCGCAGCGCGATCTGGTCAAGGCCAGCGACGAGTACTACCAGCTCGCCGACAAGCGCTATCGCACGGGGGTGGACAACTACCTGACCCTGCTCGACGCGCAACGCTCGCTGTTCACCGCGCAGCAGCAACTGATCACCGACCGCCTCAATCAGCTGACCAGCGAGGTCAACCTGTACAAGGCCCTCGGCGGCGGCTGGAACCAGCAGACCGTGACCCAGCAGCAGACCGCGAAGAAGGAAGATCCCCAGGCTTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36804","NCBI_taxonomy_name":"Pseudomonas aeruginosa PAO1","NCBI_taxonomy_id":"208964"}}}},"ARO_accession":"3000379","ARO_id":"36518","ARO_name":"OprM","CARD_short_name":"OprM","ARO_description":"OprM is an outer membrane factor protein found in Pseudomonas aeruginosa and Burkholderia vietnamiensis. It is part of the MexAB-OprM, MexVW-OprM, MexXY-OprM and the AmrAB-OprM complex.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35963":{"category_aro_accession":"0000045","category_aro_cvterm_id":"35963","category_aro_name":"acriflavine","category_aro_description":"Acriflavine is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35990":{"category_aro_accession":"0000073","category_aro_cvterm_id":"35990","category_aro_name":"meropenem","category_aro_description":"Meropenem is an ultra-broad spectrum injectable antibiotic used to treat a wide variety of infections, including meningitis and pneumonia. It is a beta-lactam and belongs to the subgroup of carbapenem, similar to imipenem and ertapenem.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36595":{"category_aro_accession":"3000456","category_aro_cvterm_id":"36595","category_aro_name":"thiamphenicol","category_aro_description":"Derivative of Chloramphenicol. The nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3).","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37007":{"category_aro_accession":"3000663","category_aro_cvterm_id":"37007","category_aro_name":"ofloxacin","category_aro_description":"Ofloxacin is a 6-fluoro, 7-piperazinyl quinolone with a methyl-substituted oxazine ring. It has a broad spectrum of activity including many enterobacteria and mycoplasma but most anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"46133":{"category_aro_accession":"3007382","category_aro_cvterm_id":"46133","category_aro_name":"gentamicin","category_aro_description":"Gentamicin is a commonly used aminoglycoside antibiotic derived from members of the Micromonospora genus of bacteria. It acts by binding the 30S ribosomal subunit, thus inhibiting protein synthesis. Gentamicin is typically used to treat Gram-negative infections of the repiratory and urinary tract, as well as infections of the bone and soft tissue. It also exhibits considerable nephrotoxicity and ototoxicity. Gentamicin is administered as a mixture of gentamicin type C (which makes about around 80% of the complex) and types A, B, and X (distributed in the remaining 20% of the complex).","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"43746":{"category_aro_accession":"3005386","category_aro_cvterm_id":"43746","category_aro_name":"disinfecting agents and antiseptics","category_aro_description":"Disinfectants that can also interact with antimicrobial resistance mechanisms, e.g. molecule efflux, and thus are the targets of disinfectant resistance.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2695":{"model_id":"2695","model_name":"MexCD-OprJ with type B NfxB mutation","model_type":"efflux pump system meta-model","model_type_id":"41112","model_description":"Efflux Pump System Meta-Models (EPS) are dedicated to efflux complexes and their regulators, such as AcrAB-TolC. Using the efflux pump components parameter, this model type simply includes a list of detection models for each component of the complex. This model type is still under development and not currently supported by the Resistance Gene Identifier (RGI) software.","model_param":{"41141":{"param_type":"efflux pump components","param_description":"Association of proteins within efflux protein complexes or regulatory networks are encoded by the efflux pump components parameter: model_id,model_id,model_id, etc.","param_type_id":"41141","param_value":{"7552":"2693,805,1523,704"}},"snp":{"Curated-R":{"7552":"S456L"}}},"ARO_accession":"3004062","ARO_id":"41129","ARO_name":"MexCD-OprJ with type B NfxB mutation","CARD_short_name":"Paer_NfxBb_MULT","ARO_description":"MexCD-OprJ with Type B NfxB mutions are more resistant to tetracycline and chloramphenicol, as well as ofloxacin, erythromycin, and the new zwitterionic cephems, than was PAO1, and they are four to eight times more susceptible to carbenicillin, sulbenicillin, imipenem, panipenem, biapenem, moxalactam, aztreonam, gentamicin, and kanamycin than PAO1.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36250":{"category_aro_accession":"3000111","category_aro_cvterm_id":"36250","category_aro_name":"novobiocin","category_aro_description":"Novobiocin is an aminocoumarin antibiotic produced by Streptomyces spheroides and Streptomyces niveus, and binds DNA gyrase subunit B inhibiting ATP-dependent DNA supercoiling.","category_aro_class_name":"Antibiotic"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"37007":{"category_aro_accession":"3000663","category_aro_cvterm_id":"37007","category_aro_name":"ofloxacin","category_aro_description":"Ofloxacin is a 6-fluoro, 7-piperazinyl quinolone with a methyl-substituted oxazine ring. It has a broad spectrum of activity including many enterobacteria and mycoplasma but most anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"46133":{"category_aro_accession":"3007382","category_aro_cvterm_id":"46133","category_aro_name":"gentamicin","category_aro_description":"Gentamicin is a commonly used aminoglycoside antibiotic derived from members of the Micromonospora genus of bacteria. It acts by binding the 30S ribosomal subunit, thus inhibiting protein synthesis. Gentamicin is typically used to treat Gram-negative infections of the repiratory and urinary tract, as well as infections of the bone and soft tissue. It also exhibits considerable nephrotoxicity and ototoxicity. Gentamicin is administered as a mixture of gentamicin type C (which makes about around 80% of the complex) and types A, B, and X (distributed in the remaining 20% of the complex).","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36242":{"category_aro_accession":"3000103","category_aro_cvterm_id":"36242","category_aro_name":"aminocoumarin antibiotic","category_aro_description":"Aminocoumarin antibiotics bind DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling.","category_aro_class_name":"Drug Class"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"255":{"model_id":"255","model_name":"BRP(MBL)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"200"}},"model_sequences":{"sequence":{"5446":{"protein_sequence":{"accession":"AGH88989.1","sequence":"MADHVTPNLPSRDFDVTEAFYAKLGFATSWKDRGWMILQRGGLQLEFFPYPDLDPATSSFGCCLRLDDLDAMVALVNAAGAEEKSTGWPRFKAPQLEASGLRIGYLIDPDCTLVRLIQNPD"},"dna_sequence":{"accession":"KC503911.1","fmin":"9883","fmax":"10249","strand":"+","sequence":"ATGGCTGACCACGTCACCCCCAATCTGCCATCGCGCGATTTCGATGTGACAGAGGCGTTTTATGCGAAGCTGGGCTTTGCGACGAGTTGGAAGGATCGCGGCTGGATGATCCTGCAGCGCGGCGGTTTGCAGCTCGAATTCTTCCCCTATCCTGACCTCGACCCAGCTACGAGCTCGTTCGGCTGTTGCCTGCGGTTGGATGATCTCGATGCCATGGTGGCATTGGTGAACGCGGCGGGAGCCGAGGAAAAAAGCACCGGCTGGCCGCGCTTCAAAGCTCCGCAACTGGAGGCGAGCGGCCTGAGGATCGGCTACCTGATCGATCCCGACTGCACGCTGGTGCGGCTGATCCAGAACCCCGACTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001205","ARO_id":"37586","ARO_name":"BRP(MBL)","CARD_short_name":"BRP(MBL)","ARO_description":"A novel bleomycin resistance protein encoded by a metallo-beta-lactamase-associated ble gene. Expression of BRP(MBL) confers resistance to bleomycin and bleomycin-like antibiotics in Enterobacteriaceae and Acinetobacter, where it is co-expressed with an MBL and controlled by the same promoter region.","ARO_category":{"41420":{"category_aro_accession":"3004256","category_aro_cvterm_id":"41420","category_aro_name":"Bleomycin resistant protein","category_aro_description":"Bleomycin resistant proteins (BRP) confer resistance to bleomycin and to bleomycin-like molecules.","category_aro_class_name":"AMR Gene Family"},"35970":{"category_aro_accession":"0000053","category_aro_cvterm_id":"35970","category_aro_name":"bleomycin","category_aro_description":"Bleomycin is a family of glycopeptide antibiotics produced by the bacterium Streptomyces verticillus. Bleomycins, taken as a mixture, act by the induction of DNA and RNA strand breaks. In addition to its antibacterial activity, bleomycin is also used as an anticancer agent.","category_aro_class_name":"Antibiotic"},"37034":{"category_aro_accession":"3000690","category_aro_cvterm_id":"37034","category_aro_name":"bleomycinic acid","category_aro_description":"Bleomycinic acid is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37035":{"category_aro_accession":"3000691","category_aro_cvterm_id":"37035","category_aro_name":"bleomycin A2","category_aro_description":"Bleomycin A2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"37036":{"category_aro_accession":"3000692","category_aro_cvterm_id":"37036","category_aro_name":"bleomycin B2","category_aro_description":"Bleomycin B2 is a glycopeptide antibiotic produced by Streptomyces verticillus taken as a mixture of bleomycins. It induces stand breaks in bacterial nucleic acids.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2755":{"model_id":"2755","model_name":"ANT(3'')-IIc","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"8749":{"protein_sequence":{"accession":"ESK39014.1","sequence":"MSETLQLEQLTGSLQQLLGESLFAIYLYGSAVDGGLGPESDLDVLVVVSQALTLQQRQQLAETLLKISYPIGAAQRALEVTIVLKAQILSGSYPLSYELQFGEWLREELNQGALLRTHTDPDLSILLKKAQVHHRSLLGPSLTQWSTAIPEQHLWQAMADTYPSIVEHWDEDADERNQILALCRIYFSLVTSEIVPKDQAAHWVIAQLPSQHQPILQRMIQEYKGEIGKQSWQQQHQALGAVVDFLSSKIDEQFKKKSSLIK"},"dna_sequence":{"accession":"AYEQ01000163.1","fmin":"124018","fmax":"124807","strand":"-","sequence":"ATGTCCGAAACCTTGCAACTCGAACAGTTAACAGGATCTTTACAGCAGCTTTTGGGTGAATCCCTATTTGCCATTTATCTGTATGGTTCAGCTGTTGATGGCGGGCTAGGTCCAGAAAGTGATCTGGATGTTTTGGTTGTGGTGAGTCAAGCTCTGACACTCCAGCAACGACAGCAACTGGCAGAAACCTTATTAAAAATTTCGTATCCAATTGGGGCAGCACAGCGTGCACTTGAAGTCACCATCGTACTTAAAGCGCAAATTCTTTCAGGCAGTTATCCACTCAGCTACGAACTACAATTTGGAGAATGGTTACGGGAGGAGTTAAACCAAGGTGCTTTGCTCCGCACACATACAGACCCTGATCTGAGTATTTTGCTGAAGAAAGCACAAGTGCATCATCGTAGTTTGTTGGGGCCAAGTTTGACACAGTGGTCAACGGCAATTCCTGAACAGCACCTCTGGCAGGCAATGGCAGACACCTATCCCTCGATTGTGGAACATTGGGATGAGGATGCCGATGAGCGTAATCAAATTTTGGCCTTATGCCGTATTTATTTTAGTTTGGTGACGAGTGAGATTGTGCCTAAAGACCAGGCCGCACACTGGGTGATAGCTCAGTTACCGTCGCAGCATCAACCCATTTTGCAGCGCATGATCCAAGAATATAAAGGTGAGATAGGCAAGCAAAGCTGGCAACAACAGCATCAGGCTTTAGGAGCTGTTGTTGACTTCCTGAGTTCAAAAATTGATGAACAATTTAAGAAGAAGAGTAGCCTGATCAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"46540","NCBI_taxonomy_name":"Acinetobacter gyllenbergii NIPH 230","NCBI_taxonomy_id":"1217658"}}}},"ARO_accession":"3004091","ARO_id":"41197","ARO_name":"ANT(3'')-IIc","CARD_short_name":"ANT(3'')-IIc","ARO_description":"ANT(3'')-IIc is a aminoglycoside nucleotidyltransferase identified in Acinetobacter spp. via horizontal gene transfer mechanisms.","ARO_category":{"41439":{"category_aro_accession":"3004275","category_aro_cvterm_id":"41439","category_aro_name":"ANT(3'')","category_aro_description":"A category of aminoglycoside O-nucleotidyltransferase enzymes with modification regiospecificity based at the 3''-hydroxyl group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics by transfer of an AMP group from an ATP substrate to the 3''-hydroxyl group of the compound.","category_aro_class_name":"AMR Gene Family"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2712":{"model_id":"2712","model_name":"MexXY-OprA","model_type":"efflux pump system meta-model","model_type_id":"41112","model_description":"Efflux Pump System Meta-Models (EPS) are dedicated to efflux complexes and their regulators, such as AcrAB-TolC. Using the efflux pump components parameter, this model type simply includes a list of detection models for each component of the complex. This model type is still under development and not currently supported by the Resistance Gene Identifier (RGI) software.","model_param":{"41141":{"param_type":"efflux pump components","param_description":"Association of proteins within efflux protein complexes or regulatory networks are encoded by the efflux pump components parameter: model_id,model_id,model_id, etc.","param_type_id":"41141","param_value":{"7589":"2223,334,1786,1570"}},"snp":{"Curated-R":{"7589":"S456L"}}},"ARO_accession":"3003038","ARO_id":"39472","ARO_name":"MexXY-OprA","CARD_short_name":"MexXY-OprA","ARO_description":"MexXY-OprA is a multidrug efflux protein expressed in Pseudomonas aeruginosa. MexY is the membrane fusion protein; MexX is the RND-type membrane protein; and OprA is the outer membrane channel. MexXY-OprA is associated with resistance to aminoglycosides.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35990":{"category_aro_accession":"0000073","category_aro_cvterm_id":"35990","category_aro_name":"meropenem","category_aro_description":"Meropenem is an ultra-broad spectrum injectable antibiotic used to treat a wide variety of infections, including meningitis and pneumonia. It is a beta-lactam and belongs to the subgroup of carbapenem, similar to imipenem and ertapenem.","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37007":{"category_aro_accession":"3000663","category_aro_cvterm_id":"37007","category_aro_name":"ofloxacin","category_aro_description":"Ofloxacin is a 6-fluoro, 7-piperazinyl quinolone with a methyl-substituted oxazine ring. It has a broad spectrum of activity including many enterobacteria and mycoplasma but most anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"46133":{"category_aro_accession":"3007382","category_aro_cvterm_id":"46133","category_aro_name":"gentamicin","category_aro_description":"Gentamicin is a commonly used aminoglycoside antibiotic derived from members of the Micromonospora genus of bacteria. It acts by binding the 30S ribosomal subunit, thus inhibiting protein synthesis. Gentamicin is typically used to treat Gram-negative infections of the repiratory and urinary tract, as well as infections of the bone and soft tissue. It also exhibits considerable nephrotoxicity and ototoxicity. Gentamicin is administered as a mixture of gentamicin type C (which makes about around 80% of the complex) and types A, B, and X (distributed in the remaining 20% of the complex).","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2349":{"model_id":"2349","model_name":"ADC-19","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"5424":{"protein_sequence":{"accession":"CAK95242.1","sequence":"MRFKKISCLLLSPLFIFNTSIYAGNTSKEQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKKLKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNSIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPDLGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLKFINANLNPQKYPKDIQRAINETHQGFYQVGTMYQALGWEEFSYPALLQTLLDSNSEQIVMKPNKVTAISKEPSVKMFHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"AM283522.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGCTTACTTTTATCTCCTCTTTTTATTTTTAATACATCAATTTATGCGGGCAATACATCAAAAGAACAAGAAATTAAAAAACTGGTAGATCAGAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCTGTAAATAGCAGTACCATTTTTGAGCTAGGTTCAGTTAGTAAATTATTTACCGCAACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAAAACTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCAACGTATACAAGTGGTAACCTTGCCTTGCAGTTCCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACTCAATCGGTGAATATAGACAATATTCAAATCCAAGCATTGGTTTATTTGGAAAAGTTGTGGCATTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCAGATCTTGGCTTAAAACATAGCTATGTAAATGTTCCTAAAACTCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCAATTCGTGTTAACCCTGGTCCACTAGATGCTCCAGCATATGGGGTTAAATCGACGCTACCCGATATGCTTAAGTTTATTAATGCCAACCTCAACCCACAGAAATATCCGAAAGATATTCAACGTGCAATTAATGAAACACATCAAGGTTTCTACCAAGTCGGCACGATGTATCAGGCACTTGGTTGGGAAGAATTTTCTTATCCAGCGCTTTTACAAACTTTATTAGACAGTAATTCAGAACAAATTGTGATGAAGCCTAATAAAGTGACTGCCATTTCAAAAGAACCTTCAGTTAAGATGTTCCACAAAACTGGTTCAACCAATGGTTTCGGAACTTATGTCGTGTTCATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAACGCATTAAGGCAGCGTATGCAGTATTAAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3003863","ARO_id":"40562","ARO_name":"ADC-19","CARD_short_name":"ADC-19","ARO_description":"ADC-19 is a beta-lactamase found in Acinetobacter pittii.","ARO_category":{"40543":{"category_aro_accession":"3003846","category_aro_cvterm_id":"40543","category_aro_name":"ADC beta-lactamase without carbapenemase activity","category_aro_description":"ADC beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases with extended-spectrum resistance to cephalosporins but not to carbapenems. ADC beta-lactamases are found in Acinetobacter sp. and Oligella urethralis.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2350":{"model_id":"2350","model_name":"ADC-20","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"5427":{"protein_sequence":{"accession":"CAK95241.1","sequence":"MRFKKISCLLLSPLFIFSTSIYADNTPKDQEIKKLVDQNFKPLLDKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKTVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTSGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPGLGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLKFINANLNPQKYPKDIQRAINETHQGFYQVGTMYQALGWEEFSYPAPLQTLLDSNSEQIVMKPNKVTAISKEPSVKMFHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"AM283521.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGACAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCTTTATTAGATAAATATGATGTGCCGGGTATGGCCGTGGGTGTTATTCAGAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAACCGTAAATAGCAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGTCTGGTAAATATTGGAAAGAACTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCAACGTATACAAGTGGTAACCTTGCCTTGCAATTCCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGCATTGGTTTATTTGGAAAAGTTGTTGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGGCCTTGGCTTAAAACATAGCTATGTAAATGTTCCTAAAACTCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCAATTCGTGTTAACCCTGGTCCGCTAGATGCTCCAGCATATGGGGTTAAATCGACGCTACCCGATATGCTTAAGTTTATTAATGCCAACCTCAACCCACAGAAATATCCGAAAGATATTCAACGTGCAATTAATGAAACACATCAGGGTTTCTATCAAGTCGGCACCATGTATCAGGCACTTGGTTGGGAAGAATTTTCTTATCCAGCGCCTTTACAAACTTTATTAGACAGTAATTCAGAACAAATTGTGATGAAGCCTAATAAAGTGACTGCCATTTCAAAAGAACCTTCAGTTAAGATGTTCCACAAAACTGGTTCAACCAATGGTTTCGGAACTTATGTCGTGTTCATTCCTAAAGAAAATATTGGCCTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAACGCATTAAAGCAGCGTATGCCGTGTTAAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3003864","ARO_id":"40563","ARO_name":"ADC-20","CARD_short_name":"ADC-20","ARO_description":"ADC-20 is a beta-lactamase found in Acinetobacter pittii.","ARO_category":{"40543":{"category_aro_accession":"3003846","category_aro_cvterm_id":"40543","category_aro_name":"ADC beta-lactamase without carbapenemase activity","category_aro_description":"ADC beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases with extended-spectrum resistance to cephalosporins but not to carbapenems. ADC beta-lactamases are found in Acinetobacter sp. and Oligella urethralis.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4135":{"model_id":"4135","model_name":"ACT-44","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6510":{"protein_sequence":{"accession":"WP_045340466.1","sequence":"MMKKSLCCALLLGISCSALATPVSEKQLAEVVANTVTPLMKAQSVPGMAVAVIYQGKPHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMPYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPENVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVVEGSDSKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANTNYPNPARVEAAYHILEALQ"},"dna_sequence":{"accession":"NG_050707.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCCCTTTGCTGCGCCCTGCTGCTCGGCATCTCTTGCTCTGCTCTCGCCACGCCAGTGTCAGAAAAACAGCTGGCGGAGGTGGTAGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCTGTTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGAAAACCGCACTATTACACGTTTGGCAAGGCCGATATCGCGGCGAATAAACCCGTTACGCCTCAGACCCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGCGTTTTAGGTGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTGACGGGCAAGCAGTGGCAGGGTATTCGTATGCTGGATCTCGCCACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTCAAACCTTCTGGCATGCCCTATGAGCAAGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTGCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGTATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCGGAGAACGTTGCTGATGCCTCACTTAAGCAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGGTCGAGGGCAGCGACAGTAAGGTGGCGCTGGCGCCGTTGCCCGTGGCAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGCTCTACTGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATACAAACTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCGAGGCGCTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40540","NCBI_taxonomy_name":"Enterobacter cloacae complex","NCBI_taxonomy_id":"354276"}}}},"ARO_accession":"3006239","ARO_id":"44701","ARO_name":"ACT-44","CARD_short_name":"ACT-44","ARO_description":"ACT-44 is a ACT beta-lactamase.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2351":{"model_id":"2351","model_name":"ADC-21","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"5432":{"protein_sequence":{"accession":"CAK95240.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLDKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVSSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKLKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPDLGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFINANINPQKYPADIQRAINETHQGFYQVGTMYQALGWEEFSYPAPLQTLLDSNSEQIVMKPNKVTAISKEPSIKMFHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"AM283520.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCTTTATTAGATAAATATGATGTGCCGGGTATGGCCGTGGGTGTTATTCAGAATAATAAAAAGTATGAAATGTATTATGGTCTACAATCTGTTCAAGATAAAAAAGCCGTAAGTAGCAGTACCATTTTTGAACTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCAACGTATACAAGTGGTAACCTTGCCTTGCAGTTCCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACTTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAAGTTGTTGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCAGATCTGGGATTAAAACATAGTTATGTAAATGTGCCTAAAACTCAGATGCAAAACTATGCTTTTGGCTATAATCAAGAAAATCAGCCAATTCGTGTTAACCCCGGTCCGCTAGATGCTCCAGCATACGGCGTTAAATCGACCCTACCTGATATGCTGAGTTTCATTAATGCCAATATAAATCCACAAAAATATCCAGCAGATATTCAACGTGCAATTAATGAAACACATCAAGGTTTCTATCAAGTCGGCACCATGTATCAGGCACTTGGTTGGGAAGAATTTTCTTATCCAGCGCCTTTACAAACTTTATTAGACAGTAATTCAGAACAAATTGTGATGAAGCCTAATAAAGTGACTGCCATTTCCAAAGAACCTTCAATTAAGATGTTCCACAAAACTGGTTCGACTAACGGTTTTGGAACATATGTCGTGTTCATTCCTAAAGAAAATATTGGCTTAGTCATGTTGACCAATAAACGTATTCCGAATGAAGAACGCATTAAAGCAGCTTATGCTGTGTTAAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3003865","ARO_id":"40564","ARO_name":"ADC-21","CARD_short_name":"ADC-21","ARO_description":"ADC-21 is a beta-lactamase found in Acinetobacter pittii.","ARO_category":{"40543":{"category_aro_accession":"3003846","category_aro_cvterm_id":"40543","category_aro_name":"ADC beta-lactamase without carbapenemase activity","category_aro_description":"ADC beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases with extended-spectrum resistance to cephalosporins but not to carbapenems. ADC beta-lactamases are found in Acinetobacter sp. and Oligella urethralis.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2352":{"model_id":"2352","model_name":"ADC-22","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"5878":{"protein_sequence":{"accession":"CAK95239.1","sequence":"MRFKKISCLLLPPLFIFSTSIYAGNTPKDREIKKLVDQNFKPLLDKYDVPGMAVGVIQNNKKYETYYGLQSVQDKKAVSSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNSIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPDLGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLKFINANLNTQKYPKDIQRAINETHQGFYQVGTMYQALGWEEFSYPAPLQTLLDSNSEQIVMKPNKVTAISKEPSVKMFHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"AM283519.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGCTTACTTTTACCTCCTCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCGAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCTTTATTAGATAAATATGATGTGCCGGGTATGGCCGTGGGCGTTATTCAGAATAATAAAAAATATGAAACGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAGTAGCAGCACCATTTTTGAACTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATTTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCAACGTATACAAGTGGTAACCTTGCCTTGCAGTTCCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACTCAATCGGTGAATATAGACAATATTCAAATCCAAGCATTGGTTTATTTGGAAAAGTTGTGGCATTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCAGATCTTGGCTTAAAACATAGCTATGTAAATGTTCCTAAAACTCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCAATTCGTGTTAACCCTGGTCCGCTAGATGCTCCAGCATATGGGGTTAAATCGACGCTACCCGATATGCTTAAGTTTATTAATGCCAACCTCAACACACAGAAATATCCGAAAGATATTCAACGTGCAATTAATGAAACACATCAGGGTTTCTATCAAGTCGGCACCATGTATCAGGCACTTGGTTGGGAAGAATTTTCTTATCCAGCGCCTTTACAAACTTTATTAGACAGTAATTCAGAACAAATTGTGATGAAGCCTAATAAAGTGACTGCCATTTCAAAAGAACCTTCAGTTAAGATGTTCCACAAAACTGGTTCAACCAATGGTTTCGGAACTTATGTCGTGTTCATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAACGCATTAAGGCAGCGTATGCCGTGTTAAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3003866","ARO_id":"40565","ARO_name":"ADC-22","CARD_short_name":"ADC-22","ARO_description":"ADC-22 is a beta-lactamase found in Acinetobacter pittii.","ARO_category":{"40543":{"category_aro_accession":"3003846","category_aro_cvterm_id":"40543","category_aro_name":"ADC beta-lactamase without carbapenemase activity","category_aro_description":"ADC beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases with extended-spectrum resistance to cephalosporins but not to carbapenems. ADC beta-lactamases are found in Acinetobacter sp. and Oligella urethralis.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2353":{"model_id":"2353","model_name":"ADC-23","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"5438":{"protein_sequence":{"accession":"CAK95238.1","sequence":"MRFKKISCLLLPPLFIFSTSIYAGNTPKEQEVKKLVDQNFKPLLDKYDVPGMAVGVIQNNKKYEIYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKAKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKTKNAIGEYRQYSNPSIGLFGKIVALSMNKPFDQVLEKTIFPPLHLKNSYVNVPKTQMQNYAYGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLTFINANLNPQKYPKDIQRAINETHQGFYQVGTMYQALGWEEFSYPASLQTLLDSNSEQIVMKPNKVTAISKEPSVKMFHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"AM283518.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGCTTACTTTTACCGCCTCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGAACAAGAAGTTAAAAAACTGGTAGATCAAAATTTTAAGCCTTTATTAGATAAATATGATGTGCCTGGTATGGCCGTGGGGGTCATTCAAAATAATAAAAAATATGAAATATATTATGGCCTACAATCCGTTCAGGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAACTAGGTTCGGTCAGTAAATTATTTACCGCTACAGCTGGTGGATATGCAAAAGCAAAAGGAAAAATCTCTTTTGATGACACACCCGGAAAATATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAATCTTCTTCAACTTGCGACGTATACAAGTGGCAATCTCGCCTTACAATTTCCAGATGAAGTTCAAACAGACCAACAAGTTTTAACTTTTTTCAAAGATTGGAAAACTAAAAACGCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCTTATTTGGAAAAATTGTGGCTTTGTCTATGAATAAACCTTTTGACCAAGTCTTAGAAAAAACAATTTTTCCACCTCTCCATTTAAAAAATAGCTATGTAAATGTACCTAAAACTCAAATGCAAAATTATGCATATGGCTATAACCAAGAAAATCAGCCGATCCGAGTTAACCCTGGTCCGCTAGATGCCCCTGCGTACGGCGTTAAATCGACACTACCAGATATGCTGACTTTTATTAATGCCAACCTCAACCCACAGAAATATCCGAAAGATATTCAACGTGCAATTAATGAAACACATCAAGGTTTCTATCAAGTCGGTACGATGTATCAAGCATTGGGTTGGGAAGAATTTTCTTATCCAGCGTCTTTACAAACTTTATTAGACAGTAATTCAGAGCAAATCGTGATGAAGCCTAATAAAGTGACTGCCATTTCAAAAGAACCTTCAGTTAAGATGTTCCACAAAACTGGCTCAACAAATGGCTTTGGAACTTATGTGGTGTTTATTCCAAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAACGCATTAAGGCAGCGTATGCAGTATTAAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3003867","ARO_id":"40566","ARO_name":"ADC-23","CARD_short_name":"ADC-23","ARO_description":"ADC-23 is a beta-lactamase found in Acinetobacter pittii.","ARO_category":{"40543":{"category_aro_accession":"3003846","category_aro_cvterm_id":"40543","category_aro_name":"ADC beta-lactamase without carbapenemase activity","category_aro_description":"ADC beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases with extended-spectrum resistance to cephalosporins but not to carbapenems. ADC beta-lactamases are found in Acinetobacter sp. and Oligella urethralis.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2718":{"model_id":"2718","model_name":"MuxB","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1900"}},"model_sequences":{"sequence":{"5204":{"protein_sequence":{"accession":"AAG05915.1","sequence":"MNPSRPFILRPVATTLLMVAILLSGLIAYRFLPISALPEVDYPTIQVVTLYPGASPEIMTSSITAPLENQLGQIPGLNEMSSSSSGGASVITLQFSLQSNLDVAEQEVQAAINAAQSLLPNDLPNQPVFSKVNPADAPILTLAVMSDGMPLPQIQDLVDTRLAQKISQISGVGLVSISGGQRPAVRVRANPTALAAAGLSLEDLRSTVTSNNLNGPKGSFDGPTRASTLDANDQLRSADAYRDLIIAYKNGSPLRIRDVASVEDDAENVRLAAWANNLPAVVLNIQRQPGANVIEVVDRIKALLPQLQSTLPGNLDVQVLTDRTTTIRASVKDVQFELALAVALVVMVTFLFLRNVYATLIPSFAVPLSLIGTFGVMYLSGFSINNLTLMALTIATGFVVDDAIVMVENIARYLEQGDSPLEAALKGSKQIGFTIISLTFSLIAVLIPLLFMGDVAGRLFREFAITLAVAILISGFVSLTLTPMLSAKLLRHIDEDQQGRFARAAGRVIDGLIAQYAKALRVVLRHQPLTLLVAIATLALTALLYLAMPKGFFPVQDTGVIQGVAEAPQSISFQAMSERQRALAEVVLKDPAVASLSSYIGVDGSNPTLNTGRLLINLKPHSERDVTASEVIQRLQPELDHLPGIKLYMQPVQDLTIEDRVARTQYQFTLQDADPDVLAEWVPKLVARLQELPQLADVASDWQDKGLQAYLNIDRDTASRLGVKLSDIDSVLYNAFGQRLISTIFTQATQYRVVLEVAPQFQLGPQALEQLYVPSSDGTQVRLSSLAKVEERHTLLAINHIAQFPSATLSFNLAKGYSLGEAVEAIRGVEASLELPLSMQGSFRGAALAFEASLSNTLLLILASVVTMYIVLGILYESFIHPVTILSTLPSAGVGALLALMLAGQEIGIVAIIGIILLIGIVKKNAIMMIDFALDAERNEGKPPHEAIYQACLLRFRPILMTTMAALLGALPLMLAGGAGAELRQPLGITMVGGLLLSQVLTLFTTPVIYLYFDRLARRWAAWRKQRGLDLNTEAGFDGDAGR"},"dna_sequence":{"accession":"AE004091.2","fmin":"2850882","fmax":"2854014","strand":"-","sequence":"ATGAACCCGTCCCGCCCGTTCATCCTGCGGCCGGTCGCGACCACCCTGCTGATGGTGGCGATCCTGCTCTCGGGCCTGATCGCCTACCGCTTCCTGCCGATCTCGGCGTTGCCGGAAGTGGACTACCCGACCATCCAGGTGGTCACCCTGTACCCCGGCGCCAGCCCGGAGATCATGACCTCGTCGATCACCGCGCCGCTGGAGAACCAGCTCGGGCAGATTCCGGGGCTCAACGAGATGTCTTCCAGCAGTTCCGGCGGCGCCTCGGTGATCACCCTGCAATTCAGCCTGCAGAGCAACCTCGATGTCGCCGAGCAGGAAGTCCAGGCGGCGATCAACGCCGCGCAGAGCCTGCTGCCCAACGACCTGCCGAACCAGCCGGTGTTCAGCAAGGTGAATCCGGCGGACGCACCGATCCTGACCCTGGCGGTGATGTCCGACGGCATGCCGCTGCCGCAGATCCAGGACCTGGTGGATACCCGCCTGGCACAGAAGATCTCGCAGATCTCCGGGGTCGGCCTGGTCAGCATCAGCGGCGGCCAGCGCCCGGCGGTGCGGGTGCGCGCCAACCCGACGGCGCTGGCGGCGGCGGGGCTGAGCCTGGAGGACCTGCGCAGCACGGTGACCAGCAACAACCTCAACGGCCCCAAGGGCAGCTTCGACGGCCCGACCCGTGCCTCGACCCTGGACGCCAACGACCAGTTGCGCTCGGCCGACGCCTACCGCGACCTGATCATCGCCTACAAGAACGGCTCGCCGCTGCGCATCCGCGACGTCGCCAGCGTCGAGGACGACGCCGAGAACGTGCGCCTGGCCGCCTGGGCCAACAACCTGCCGGCGGTGGTGCTGAACATCCAGCGCCAGCCGGGGGCCAACGTGATCGAGGTGGTCGACCGGATCAAGGCGCTGCTGCCGCAGCTGCAATCGACCCTGCCGGGCAATCTCGACGTGCAGGTGCTGACCGACCGCACCACCACCATCCGCGCCTCGGTCAAGGACGTGCAGTTCGAGCTGGCGCTGGCGGTGGCGCTGGTGGTGATGGTCACCTTCCTGTTCCTGCGCAACGTCTACGCCACCCTGATTCCCAGCTTCGCCGTGCCGCTGTCGCTGATCGGTACCTTCGGCGTGATGTACCTGTCCGGCTTCTCGATCAACAACCTGACCCTGATGGCGCTGACCATCGCCACCGGCTTCGTGGTCGACGACGCGATCGTCATGGTGGAGAACATCGCCCGCTACCTGGAGCAGGGCGACTCGCCGCTGGAAGCGGCGCTCAAGGGCTCGAAGCAGATCGGCTTCACCATCATCTCGCTGACTTTCTCGCTGATCGCCGTGCTGATCCCGCTGCTGTTCATGGGCGACGTCGCCGGGCGGCTGTTCCGCGAGTTCGCCATCACCCTGGCGGTGGCGATCCTGATTTCCGGCTTCGTCTCCCTGACCCTTACGCCGATGCTCAGCGCCAAGCTGCTGCGCCACATCGACGAGGACCAGCAGGGCCGCTTCGCGCGCGCCGCGGGGCGGGTCATCGATGGCCTGATCGCACAGTACGCCAAGGCCCTGCGGGTGGTCCTGCGGCACCAGCCGCTGACCCTGCTGGTGGCCATCGCCACCCTGGCGCTGACCGCGCTACTCTACCTGGCCATGCCCAAGGGCTTCTTCCCGGTGCAGGACACCGGGGTGATCCAGGGCGTCGCCGAAGCGCCGCAGTCGATCTCCTTCCAGGCCATGTCCGAGCGCCAGCGCGCCCTTGCCGAGGTGGTGCTGAAGGACCCGGCGGTGGCCAGCCTGTCCTCCTACATCGGCGTCGACGGCAGCAACCCGACCCTCAACACCGGCCGCCTGCTGATCAACCTCAAGCCGCACAGCGAGCGCGACGTCACCGCCAGCGAAGTGATCCAGCGCCTGCAGCCCGAACTCGACCACCTGCCCGGGATCAAGCTGTACATGCAGCCGGTGCAGGACCTGACCATCGAGGACCGGGTCGCCCGCACCCAGTACCAGTTCACCTTGCAGGACGCCGACCCGGACGTGCTCGCCGAGTGGGTGCCGAAGCTGGTGGCGCGGCTGCAGGAGTTGCCGCAGCTCGCCGACGTCGCCAGCGACTGGCAGGACAAGGGCTTGCAGGCCTACCTGAACATCGACCGCGACACCGCCTCGCGCCTCGGCGTGAAGCTCTCCGACATCGACAGCGTGCTCTACAACGCCTTCGGCCAGCGGCTGATCTCGACCATCTTCACCCAGGCCACCCAGTACCGCGTGGTGCTGGAGGTGGCGCCGCAGTTCCAGCTCGGCCCGCAGGCCCTGGAGCAGCTCTACGTGCCGTCCAGCGACGGCACCCAGGTGCGCCTGTCGAGCCTGGCGAAGGTGGAGGAGCGGCATACCCTGCTGGCGATCAACCATATCGCCCAGTTCCCCTCGGCGACCCTGTCGTTCAACCTGGCCAAGGGTTACTCCCTGGGCGAGGCGGTCGAGGCGATCCGTGGCGTCGAGGCCAGCCTGGAGCTGCCGCTGAGCATGCAGGGCAGCTTCCGCGGCGCGGCGCTGGCCTTCGAGGCCTCGCTGTCGAACACGCTGCTGCTGATCCTCGCCTCGGTGGTGACCATGTACATCGTCCTGGGCATCCTCTACGAGAGCTTCATCCATCCGGTGACCATCCTCTCGACCCTGCCCTCGGCCGGGGTCGGCGCGCTGCTGGCGCTGATGCTGGCGGGGCAGGAGATCGGCATCGTGGCGATCATCGGCATCATCCTGCTGATCGGCATCGTCAAGAAGAACGCGATCATGATGATCGATTTCGCCCTCGACGCCGAGCGCAACGAAGGCAAGCCGCCCCATGAGGCGATCTACCAGGCCTGCCTGCTGCGCTTCCGGCCGATCCTGATGACCACCATGGCCGCGCTGCTCGGCGCGCTGCCGCTGATGCTCGCCGGCGGCGCCGGCGCCGAGCTGCGCCAGCCGCTGGGCATCACCATGGTCGGTGGCCTGCTGCTGAGCCAGGTCCTGACCCTGTTCACCACCCCGGTGATCTATCTCTACTTCGACCGCCTGGCCCGTCGCTGGGCGGCCTGGCGCAAGCAGCGCGGGCTGGACCTGAACACCGAGGCCGGGTTCGACGGGGACGCCGGGCGATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36804","NCBI_taxonomy_name":"Pseudomonas aeruginosa PAO1","NCBI_taxonomy_id":"208964"}}}},"ARO_accession":"3004074","ARO_id":"41156","ARO_name":"MuxB","CARD_short_name":"MuxB","ARO_description":"MuxB is one of the two necessary RND components in the Pseudomonas aeruginosa efflux pump system MuxABC-OpmB.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36250":{"category_aro_accession":"3000111","category_aro_cvterm_id":"36250","category_aro_name":"novobiocin","category_aro_description":"Novobiocin is an aminocoumarin antibiotic produced by Streptomyces spheroides and Streptomyces niveus, and binds DNA gyrase subunit B inhibiting ATP-dependent DNA supercoiling.","category_aro_class_name":"Antibiotic"},"36689":{"category_aro_accession":"3000550","category_aro_cvterm_id":"36689","category_aro_name":"aztreonam","category_aro_description":"Aztreonam was the first monobactam discovered, and is greatly effective against Gram-negative bacteria while inactive against Gram-positive bacteria. Artreonam is a poor substrate for beta-lactamases, and may even act as an inhibitor. In Gram-negative bacteria, Aztreonam interferes with filamentation, inhibiting cell division and leading to cell death.","category_aro_class_name":"Antibiotic"},"37626":{"category_aro_accession":"3001227","category_aro_cvterm_id":"37626","category_aro_name":"kitasamycin","category_aro_description":"Kitasamycin is a macrolide antibiotic and is produced by Streptoverticillium kitasatoense. The drug has antimicrobial activity against a wide spectrum of pathogens.","category_aro_class_name":"Antibiotic"},"40353":{"category_aro_accession":"3003701","category_aro_cvterm_id":"40353","category_aro_name":"rokitamycin","category_aro_description":"Rokitamycin is a macrolide antibiotic. Synthesized from strains of Streptomyces kitasatoensis.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36242":{"category_aro_accession":"3000103","category_aro_cvterm_id":"36242","category_aro_name":"aminocoumarin antibiotic","category_aro_description":"Aminocoumarin antibiotics bind DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"3410":{"model_id":"3410","model_name":"OXA-124","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"5605":{"protein_sequence":{"accession":"ABX45063.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDDKAEKIKNLFNEAHTTGVLVIHQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWNGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNAHIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"EU255293.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGACAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCATCAAGGTCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGAACGGGCAAAAAAGGCTGTTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCACATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001446","ARO_id":"37846","ARO_name":"OXA-124","CARD_short_name":"OXA-124","ARO_description":"OXA-124 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3433":{"model_id":"3433","model_name":"OXA-266","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"5629":{"protein_sequence":{"accession":"ENV38192.1","sequence":"MRKKFKVALLCSSLCLSLGLVACHSLNSELQIAEQQKQQQKISKLFVNAKTEGVFVTYDGQKIHEYGNALNRAQTSYIPASTFKMLNALIGIQHHKTTPNEVFKWNGEKRRFKSWEKDLTLTEAIQASAVPIYQELARRIGLDLMASEVKRIGFGNSDIGNQVDNFWLVGPLKITPIQEVRFTYALANEQLAFDIPVQQQVKQMLLVDQMNGTKVYAKSGWGMDVEPQVGWWTGWVEQPNGKVTAFSLNMEMNKTEHVEARKTIVYEALQQLGLI"},"dna_sequence":{"accession":"APPO01000008.1","fmin":"267572","fmax":"268400","strand":"-","sequence":"ATGCGAAAAAAGTTCAAAGTTGCTCTGCTATGTAGTTCGTTATGCTTAAGTTTAGGCTTGGTTGCTTGTCACAGCTTAAATTCAGAGCTGCAGATTGCAGAACAGCAAAAGCAACAACAAAAAATTTCTAAGCTATTTGTGAATGCCAAAACAGAAGGCGTATTTGTCACTTATGACGGTCAAAAGATACATGAATATGGGAATGCCTTAAATCGAGCTCAAACGTCGTATATCCCTGCATCTACTTTTAAAATGCTCAATGCTTTGATTGGCATCCAACATCATAAAACGACACCCAATGAAGTTTTTAAATGGAATGGAGAAAAGCGCAGATTTAAGAGCTGGGAAAAAGATTTGACCTTAACTGAGGCGATTCAAGCATCCGCTGTTCCTATTTATCAAGAATTAGCCAGACGAATAGGTTTAGATTTGATGGCATCTGAAGTTAAAAGAATAGGTTTTGGAAATTCAGATATAGGCAATCAGGTCGATAATTTTTGGTTGGTTGGCCCATTAAAAATCACACCGATTCAAGAAGTCAGATTTACCTACGCGTTGGCAAATGAGCAATTGGCGTTTGACATTCCTGTTCAGCAGCAAGTTAAGCAAATGTTATTGGTGGATCAGATGAATGGGACAAAAGTTTATGCGAAAAGTGGTTGGGGAATGGATGTTGAGCCACAAGTGGGATGGTGGACAGGATGGGTAGAGCAGCCTAATGGTAAAGTAACTGCATTTTCTCTAAATATGGAGATGAATAAAACTGAACATGTGGAGGCTCGGAAAACGATTGTTTATGAGGCATTGCAGCAGTTAGGTTTAATTTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42796","NCBI_taxonomy_name":"Acinetobacter venetianus RAG-1 = CIP 110063","NCBI_taxonomy_id":"1191460"}}}},"ARO_accession":"3001722","ARO_id":"38122","ARO_name":"OXA-266","CARD_short_name":"OXA-266","ARO_description":"OXA-266 is a beta-lactamase found in Acinetobacter spp.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46501":{"category_aro_accession":"3007712","category_aro_cvterm_id":"46501","category_aro_name":"OXA-266-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-266.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2720":{"model_id":"2720","model_name":"MuxC","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1900"}},"model_sequences":{"sequence":{"5199":{"protein_sequence":{"accession":"AAG05914.1","sequence":"MSLSTPFIRRPVATTLLTLALLLAGTLSFGLLPVAPLPNVDFPAIVVSASLPGASPETMASSVATPLERSLGRIAGISEMTSSSSLGSTTVVLVFDLEKDIDGAAREVQAAINGAMSLLPSGMPNNPSYRKANPSDMPIMVLTLTSETQSRGEMYDLASTVLAPKLSQVQGVGQVSIGGSSLPAVRVDLNPDAMSQYGLSLDSVRTAIAAANSNGPKGAVEKDDKHWQVDANDQLRKAREYEPLVIHYNADNGAAVRLGDVAKVSDSVEDVRNAGFSDDLPAVLLIVTRQPGANIIEATDAIHAQLPVLQELLGPQVKLNVMDDRSPSIRASLEEAELTLLISVALVILVVFLFLRNGRATLIPSLAVPVSLIGTFAVMYLCDFSLNNLSLMALIIATGFVVDDAIVVVENIARRIEEGDPPIQAAITGARQVGFTVLSMTLSLVAVFIPLLLMGGLTGRLFREFAVTLSAAILVSLVVSLTLTPMLCARLLRPLKRPEGASLARRSDRFFAAFMLRYRASLGWALEHSRLMVVIMLACIAMNLWLFVVVPKGFLPQQDSGRLRGYAVADQSISFQSLSAKMGEYRKILSSDPAVENVVGFIGGGRWQSSNTGSFFVTLKPIGERDPVEKVLTRLRERIAKVPGAALYLNAGQDVRLGGRDSNAQYEFTLRSDDLTLLREWAPKVEAAMRKLPQLVDVNSDSQDKGVQTRLVIDRDRAATLGINVEMVDAVLNDSFGQRQVSTIFNPLNQYRVVMEVDQQYQQSPEILRQVQVIGNDGQRVPLSAFSHYEPSRAPLEVNHQGQFAATTLSFNLAPGAQIGPTREAIMQALEPLHIPVDVQTSFEGNAGAVQDTQNQMPWLILLALLAVYIVLGILYESYVHPLTILSTLPSAGVGALLALILCRSELSLIALIGIILLIGIVKKNAIMMIDFALEAERNHGLSPREAILEACMMRFRPIMMTTLAALLGALPLIFGIGGDAALRRPLGITIVGGLIGSQLLTLYTTPVVYLYLDRLRHWVNQKRGVRTDGALETPL"},"dna_sequence":{"accession":"AE004091.2","fmin":"2847775","fmax":"2850886","strand":"-","sequence":"ATGAGTCTGTCCACGCCCTTCATCCGCCGCCCGGTCGCCACCACGCTGCTGACCCTGGCGTTGCTGCTGGCCGGCACCCTGTCGTTCGGCCTGCTGCCGGTGGCGCCGCTGCCCAACGTCGATTTTCCGGCCATCGTGGTCAGCGCCAGCCTGCCGGGCGCCAGCCCGGAAACCATGGCCTCGTCGGTGGCCACGCCGCTGGAGCGCTCGCTGGGACGGATCGCCGGGATCAGCGAGATGACCTCCAGCAGTTCGCTGGGCTCGACCACCGTGGTGCTCGTGTTCGACCTGGAGAAGGACATCGACGGCGCCGCCCGCGAGGTGCAGGCGGCGATCAACGGCGCGATGAGCCTGCTGCCCAGCGGTATGCCGAACAATCCCAGCTACCGCAAGGCCAACCCCTCGGACATGCCGATCATGGTCCTCACCCTGACCTCGGAGACCCAGAGTCGCGGCGAGATGTACGACCTCGCCTCGACCGTGCTGGCGCCCAAGCTGTCGCAGGTGCAGGGGGTAGGGCAGGTGAGCATCGGCGGCAGCTCGCTGCCGGCGGTGCGGGTCGACCTCAACCCGGATGCCATGAGCCAGTACGGGCTGTCCCTGGACAGCGTGCGCACGGCCATCGCCGCGGCCAACAGCAACGGCCCCAAGGGCGCCGTCGAGAAGGACGACAAGCACTGGCAGGTGGACGCCAACGACCAGTTGCGCAAGGCCCGCGAGTACGAGCCGCTGGTGATCCACTACAACGCCGACAACGGCGCCGCGGTGCGCCTCGGCGACGTGGCCAAGGTCAGCGACTCGGTGGAGGACGTGCGCAACGCCGGCTTTTCCGACGACCTGCCGGCTGTGCTGCTAATCGTCACCCGCCAGCCCGGCGCCAACATCATCGAGGCCACCGACGCCATCCACGCGCAACTGCCGGTGTTGCAGGAACTGCTCGGGCCGCAGGTCAAGCTGAACGTGATGGACGATCGCAGCCCGTCGATCCGTGCGTCGCTGGAAGAGGCCGAGCTGACCCTGCTGATCTCGGTGGCGCTGGTGATCCTGGTGGTCTTCCTGTTCCTGCGCAACGGCCGCGCCACGCTGATCCCCAGCCTGGCGGTGCCGGTCTCGCTGATCGGCACCTTCGCGGTCATGTACCTGTGCGACTTCAGCCTGAACAACCTGTCGCTGATGGCGCTGATCATCGCCACCGGCTTCGTGGTGGATGACGCCATAGTGGTGGTGGAGAACATCGCCCGACGCATCGAGGAGGGCGATCCGCCGATCCAGGCGGCGATCACCGGCGCCCGCCAGGTCGGTTTCACCGTGCTGTCGATGACGCTCTCGCTGGTCGCGGTGTTCATCCCGCTGCTGCTCATGGGTGGCCTCACCGGACGGCTGTTCCGCGAGTTCGCGGTGACTCTCTCGGCGGCGATCCTGGTGTCCCTGGTGGTATCCCTGACCCTCACGCCGATGCTCTGCGCGCGTCTGCTGCGTCCGCTGAAACGGCCCGAAGGCGCTTCCCTGGCGCGGCGCAGCGATCGCTTCTTCGCCGCCTTCATGCTGCGCTACCGCGCCAGCCTGGGCTGGGCGCTGGAGCACTCGCGGCTGATGGTGGTGATCATGCTGGCCTGCATCGCCATGAACCTCTGGTTGTTCGTGGTGGTGCCCAAGGGCTTCCTCCCGCAGCAGGACTCCGGGCGCCTGCGCGGCTACGCGGTGGCCGACCAGAGCATCTCGTTCCAGTCCCTGAGCGCGAAGATGGGCGAGTACCGCAAGATCCTCTCTTCCGATCCGGCGGTGGAAAACGTGGTCGGCTTCATCGGTGGCGGCCGTTGGCAGTCGAGCAACACCGGTTCGTTCTTCGTCACTCTCAAGCCGATCGGCGAGCGCGACCCGGTGGAGAAGGTCCTCACCCGGCTGCGCGAGCGGATCGCCAAGGTGCCCGGCGCGGCGCTCTATCTCAACGCCGGCCAGGACGTGCGCCTGGGCGGCCGCGACAGCAACGCGCAGTACGAATTCACCCTGCGCAGCGACGACCTGACCCTGCTCCGCGAATGGGCGCCGAAGGTCGAGGCGGCGATGCGCAAGCTGCCGCAGCTGGTGGACGTCAACAGCGACTCCCAGGACAAGGGCGTGCAGACCCGCCTGGTGATCGACCGCGACCGCGCGGCGACCCTGGGGATCAACGTGGAAATGGTCGACGCGGTGCTCAACGACTCTTTCGGCCAGCGCCAGGTGTCGACCATCTTCAACCCGCTGAACCAGTACCGGGTGGTGATGGAGGTCGACCAGCAGTACCAGCAGAGCCCGGAGATCCTCCGCCAGGTCCAGGTGATCGGCAACGACGGCCAGCGCGTGCCGCTGTCCGCGTTCAGCCACTACGAACCGAGCCGGGCACCGCTGGAGGTCAACCACCAGGGCCAGTTCGCCGCCACCACGCTGTCCTTCAACCTGGCACCGGGCGCGCAGATCGGCCCGACCCGCGAGGCCATCATGCAGGCCCTGGAGCCGCTGCACATCCCGGTGGACGTGCAGACCAGCTTCGAGGGCAACGCCGGCGCGGTGCAGGACACGCAGAACCAGATGCCCTGGCTGATCCTCCTGGCGCTGCTGGCGGTGTACATCGTCCTCGGCATCCTCTACGAGAGCTACGTGCACCCGCTGACCATCCTCTCGACCCTGCCTTCGGCCGGGGTCGGCGCGCTGCTCGCGCTGATCCTCTGCCGCAGCGAGCTGAGCCTGATCGCGCTGATCGGCATCATCCTGCTGATCGGCATCGTCAAGAAGAACGCGATCATGATGATCGACTTCGCCCTGGAGGCCGAGCGCAACCACGGCCTGAGCCCGCGCGAGGCGATCCTCGAGGCCTGCATGATGCGCTTCCGGCCGATCATGATGACCACCCTGGCCGCCTTGCTCGGCGCCTTGCCGCTGATCTTCGGCATCGGCGGCGACGCCGCGCTGCGCCGGCCGCTGGGCATCACCATCGTCGGCGGGCTGATCGGCAGCCAGTTGCTGACCCTGTACACCACCCCGGTGGTCTACCTCTATCTCGACCGCCTGCGCCACTGGGTCAACCAGAAACGCGGCGTACGCACGGACGGTGCGCTGGAGACACCCCTATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36804","NCBI_taxonomy_name":"Pseudomonas aeruginosa PAO1","NCBI_taxonomy_id":"208964"}}}},"ARO_accession":"3004075","ARO_id":"41158","ARO_name":"MuxC","CARD_short_name":"MuxC","ARO_description":"MuxC is one of the two necessary RND components of the MuxABC-OpmB efflux pumps system in Pseudomonas aeruginosa.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36250":{"category_aro_accession":"3000111","category_aro_cvterm_id":"36250","category_aro_name":"novobiocin","category_aro_description":"Novobiocin is an aminocoumarin antibiotic produced by Streptomyces spheroides and Streptomyces niveus, and binds DNA gyrase subunit B inhibiting ATP-dependent DNA supercoiling.","category_aro_class_name":"Antibiotic"},"36689":{"category_aro_accession":"3000550","category_aro_cvterm_id":"36689","category_aro_name":"aztreonam","category_aro_description":"Aztreonam was the first monobactam discovered, and is greatly effective against Gram-negative bacteria while inactive against Gram-positive bacteria. Artreonam is a poor substrate for beta-lactamases, and may even act as an inhibitor. In Gram-negative bacteria, Aztreonam interferes with filamentation, inhibiting cell division and leading to cell death.","category_aro_class_name":"Antibiotic"},"37626":{"category_aro_accession":"3001227","category_aro_cvterm_id":"37626","category_aro_name":"kitasamycin","category_aro_description":"Kitasamycin is a macrolide antibiotic and is produced by Streptoverticillium kitasatoense. The drug has antimicrobial activity against a wide spectrum of pathogens.","category_aro_class_name":"Antibiotic"},"40353":{"category_aro_accession":"3003701","category_aro_cvterm_id":"40353","category_aro_name":"rokitamycin","category_aro_description":"Rokitamycin is a macrolide antibiotic. Synthesized from strains of Streptomyces kitasatoensis.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36242":{"category_aro_accession":"3000103","category_aro_cvterm_id":"36242","category_aro_name":"aminocoumarin antibiotic","category_aro_description":"Aminocoumarin antibiotics bind DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"3463":{"model_id":"3463","model_name":"OXA-301","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"5658":{"protein_sequence":{"accession":"ENV90372.1","sequence":"MKFKMKGLFCVILSSLAFSGCVYDSKLQRPVISERETEIPLLFNQAQTQAVFVTYDGIHLKSYGNDLSRAKTEYIPASTFKMLNALIGLQNAKATNTEVFHWNGEKRAFSAWEKDMTLAEAMQASAVPVYQELARRIGLELMREEVKRVGFGNAEIGQQVDNFWLVGPLKISPEQEVQFAYQLAMKQLPFDSNVQQQVKDMLYIERRGDSKLYAKSGWGMDVEPQVGWYTGWVEQPNGKVTAFALNMNMQAGNDPAERKQLTLSILDKLGLFFYLR"},"dna_sequence":{"accession":"APQG01000050.1","fmin":"21327","fmax":"22158","strand":"-","sequence":"ATGAAGTTTAAAATGAAAGGTTTATTTTGTGTCATCCTCAGTAGTTTGGCATTTTCAGGTTGTGTTTATGATTCAAAACTACAACGCCCAGTCATATCAGAGCGAGAAACTGAGATTCCTTTATTATTTAATCAAGCACAGACTCAAGCTGTGTTTGTTACTTATGATGGGATTCATCTAAAAAGTTATGGTAATGATCTAAGCCGAGCAAAGACTGAATATATTCCTGCATCTACATTTAAGATGTTGAATGCTTTAATTGGCTTGCAAAATGCAAAAGCAACCAATACTGAAGTATTTCATTGGAATGGTGAAAAGCGCGCTTTTTCAGCATGGGAAAAAGATATGACTTTGGCAGAAGCGATGCAGGCTTCAGCTGTTCCTGTATATCAAGAGCTTGCTCGACGTATTGGCTTGGAATTGATGCGTGAAGAAGTGAAGCGTGTAGGTTTTGGCAATGCGGAGATTGGTCAGCAAGTCGATAATTTTTGGTTGGTGGGTCCTTTAAAAATCTCCCCTGAACAAGAAGTTCAATTTGCCTATCAACTGGCAATGAAGCAATTGCCTTTTGATTCAAATGTACAGCAACAAGTCAAAGATATGCTTTATATCGAGAGACGTGGTGACAGTAAACTGTATGCTAAAAGTGGTTGGGGAATGGATGTTGAACCTCAAGTGGGTTGGTATACGGGATGGGTTGAACAACCCAATGGCAAGGTGACTGCATTTGCGTTAAATATGAACATGCAAGCAGGTAATGATCCAGCTGAACGTAAACAATTAACCTTAAGTATTTTGGACAAATTGGGTCTATTTTTTTATTTAAGATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42822","NCBI_taxonomy_name":"Acinetobacter bereziniae LMG 1003 = CIP 70.12","NCBI_taxonomy_id":"981324"}}}},"ARO_accession":"3001756","ARO_id":"38156","ARO_name":"OXA-301","CARD_short_name":"OXA-301","ARO_description":"OXA-301 is a beta-lactamase found in Acinetobacter spp.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46498":{"category_aro_accession":"3007709","category_aro_cvterm_id":"46498","category_aro_name":"OXA-229-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-229.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3492":{"model_id":"3492","model_name":"OXA-407","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"5687":{"protein_sequence":{"accession":"AJD07403.1","sequence":"MNIKTLLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEVHTTGVLVIHQGQTQQSYGNDLTRASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSEEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFTLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"KJ584916.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAACACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGTACACACTACGGGTGTTTTAGTTATCCATCAAGGTCAAACTCAACAAAGCTATGGTAATGATCTTACTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTGAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCACCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001598","ARO_id":"37998","ARO_name":"OXA-407","CARD_short_name":"OXA-407","ARO_description":"OXA-407 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3518":{"model_id":"3518","model_name":"OXA-449","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"5713":{"protein_sequence":{"accession":"AKI29910.1","sequence":"MKKIILFLWILNFAFGQDKILEDFFKDYNTSGIFIIFDGKNYASNDFQRAKQTFSPASTFKIFNALIALDNGVVKDTKEIFYHYKGEKVFLPSWKQDASLSSAIKRSQVPAFKELARKIGLKTMQESLNKLSYGNAKISKIDTFWLDNSLQISAKNQADLLFKLSQNSLPFSKKSQEEVKKLLLFKENKIQKIYAKTGFNDNINLAWIVGFVKTKNKILSFALNVDIKHIKNIKIREELLEKYLAIITN"},"dna_sequence":{"accession":"KR061498.1","fmin":"0","fmax":"750","strand":"+","sequence":"ATGAAAAAAATCATCTTGTTTTTATGGATTTTAAATTTTGCCTTTGGACAAGATAAAATATTAGAAGATTTTTTTAAAGATTATAATACAAGTGGGATTTTTATAATCTTTGATGGAAAAAATTATGCAAGTAATGATTTTCAAAGAGCAAAACAAACCTTTTCTCCTGCTTCAACTTTTAAAATTTTTAATGCTTTAATTGCGCTTGATAATGGTGTAGTTAAAGATACAAAGGAAATTTTTTATCATTATAAGGGCGAAAAAGTATTTTTGCCCTCTTGGAAACAAGATGCTAGTTTAAGCTCAGCCATAAAACGCTCTCAAGTGCCTGCTTTTAAAGAATTGGCAAGAAAAATAGGACTTAAAACCATGCAAGAAAGCTTAAATAAACTTTCTTATGGAAATGCAAAAATTTCAAAAATCGATACCTTTTGGCTGGATAATTCTTTGCAAATTTCTGCAAAAAATCAAGCTGATTTACTTTTTAAACTTTCACAAAATTCTTTACCTTTTTCCAAGAAAAGTCAAGAAGAAGTTAAAAAACTTCTTCTTTTTAAAGAAAATAAAATACAAAAAATTTATGCCAAAACAGGTTTTAATGATAATATAAATTTAGCTTGGATTGTTGGATTCGTAAAGACTAAAAACAAAATTTTATCTTTTGCTTTAAATGTTGATATAAAGCACATTAAAAATATTAAAATAAGAGAAGAATTGCTAGAAAAATATCTAGCAATCATAACAAATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36772","NCBI_taxonomy_name":"Campylobacter jejuni","NCBI_taxonomy_id":"197"}}}},"ARO_accession":"3003605","ARO_id":"40215","ARO_name":"OXA-449","CARD_short_name":"OXA-449","ARO_description":"OXA-449 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46491":{"category_aro_accession":"3007702","category_aro_cvterm_id":"46491","category_aro_name":"OXA-184-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-184.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3522":{"model_id":"3522","model_name":"OXA-453","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"5717":{"protein_sequence":{"accession":"AKI29919.1","sequence":"MKKITLFLLFLNLVFGQDKILNNWFKEYNTSGTFVFYDGKTWASNDFSRAMETFSPASTFKIFNALIALDSGVIKTKKEIFYHYRGGKVFLSSWAQDMNLSSAIKYSNVLAFKEVARRIGIKTMQEYLNKLHYGNAKISKIDTFWLDNSLKISAKEQAILLFRLSQNSLPFSQEAMNSVKEMIYLKNMENLELFGKTGFNDEQKIAWIVGFVYLKDENKYKAFALNLDIDKFEDLYKREKILEKYLDELVKKVKNDG"},"dna_sequence":{"accession":"KR061507.1","fmin":"0","fmax":"774","strand":"+","sequence":"ATGAAAAAAATAACTTTATTTTTACTTTTCTTAAATTTAGTGTTTGGGCAAGATAAGATATTAAATAATTGGTTTAAAGAGTATAATACAAGCGGCACTTTTGTTTTTTATGATGGAAAAACTTGGGCGAGTAACGACTTTTCAAGGGCTATGGAGACTTTCTCTCCCGCTTCCACTTTTAAAATTTTTAATGCTCTAATTGCACTTGATAGTGGTGTGATAAAAACTAAAAAAGAAATTTTTTATCACTATAGAGGTGGAAAAGTATTTTTATCTTCTTGGGCGCAAGATATGAATTTAAGTTCAGCTATAAAATATTCTAATGTTCTTGCTTTTAAAGAAGTGGCAAGAAGAATTGGTATCAAAACTATGCAAGAATATTTAAACAAGCTTCATTATGGTAATGCTAAAATTTCCAAGATCGATACTTTTTGGCTTGACAACTCACTAAAAATAAGCGCTAAAGAACAAGCAATTTTGCTTTTTAGACTTTCACAAAATAGCTTACCTTTTTCTCAAGAAGCAATGAATAGTGTTAAGGAAATGATTTATTTAAAAAATATGGAAAATTTAGAGCTTTTTGGAAAAACAGGTTTTAATGATGAGCAAAAAATTGCTTGGATTGTAGGTTTTGTGTATTTAAAAGATGAAAATAAATATAAGGCTTTCGCGCTAAATTTAGATATTGATAAATTTGAAGATTTATATAAAAGAGAAAAAATTTTAGAAAAATATTTAGATGAACTTGTAAAAAAAGTTAAAAATGATGGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36772","NCBI_taxonomy_name":"Campylobacter jejuni","NCBI_taxonomy_id":"197"}}}},"ARO_accession":"3003609","ARO_id":"40219","ARO_name":"OXA-453","CARD_short_name":"OXA-453","ARO_description":"OXA-453 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46519":{"category_aro_accession":"3007730","category_aro_cvterm_id":"46519","category_aro_name":"OXA-61-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-61.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3548":{"model_id":"3548","model_name":"OXA-488","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"5743":{"protein_sequence":{"accession":"TKV86805.1","sequence":"MRPLLFSALLLLSGHAQASEWNDSRAVDKLFGAAGVKGTFVLYDVQRQRYVGHDRERAETRFVPASTYKVANSLIGLSTGAVRSADEVLPYGGKPQRFKAWEHDMSLRDAIKASNVPVYQELARRIGLERMRANVSRLGYGNAEIGQVVDNFWLVGPLKISAMEQTRFLLRLAQGELPFPAPVQSTVRAMTLLESGPGWELHGKTGWCFDCTPELGWWVGWVKRNERLYGFALNIDMPGGEADIGKRVELGKASLKALGILP"},"dna_sequence":{"accession":"SMRY02000082.1","fmin":"17219","fmax":"18008","strand":"-","sequence":"ATGCGCCCTCTCCTCTTCAGCGCCCTTCTCCTGCTCTCCGGGCATGCCCAGGCCAGCGAATGGAACGACAGCCGGGCCGTGGACAAGCTATTCGGAGCGGCCGGTGTGAAAGGCACCTTCGTCCTTTACGATGTGCAGCGGCAGCGCTATGTCGGCCATGACCGGGAGCGCGCGGAAACCCGCTTCGTTCCCGCTTCCACCTACAAGGTGGCGAACAGCCTGATCGGCTTATCCACAGGGGCGGTTAGATCCGCCGACGAGGTTCTTCCCTATGGCGGCAAACCCCAGCGCTTCAAGGCCTGGGAGCACGACATGAGCCTGCGCGACGCGATCAAGGCATCGAACGTACCGGTCTACCAGGAACTGGCGCGGCGCATCGGCCTGGAGCGGATGCGCGCCAATGTCTCGCGCCTGGGTTACGGCAACGCGGAAATCGGCCAGGTTGTGGATAACTTCTGGTTGGTGGGACCGCTGAAGATCAGCGCGATGGAACAGACCCGCTTTCTGCTCCGACTGGCGCAGGGAGAATTGCCATTCCCCGCCCCGGTGCAGTCCACCGTGCGCGCCATGACCCTGCTGGAAAGCGGCCCGGGCTGGGAGCTGCACGGCAAGACCGGCTGGTGCTTCGACTGCACGCCGGAACTCGGCTGGTGGGTGGGCTGGGTGAAGCGCAACGAGCGGCTCTACGGCTTCGCCCTGAACATCGACATGCCCGGCGGCGAGGCCGACATCGGCAAGCGCGTCGAACTGGGCAAGGCCAGTCTCAAGGCTCTCGGGATACTGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3003645","ARO_id":"40255","ARO_name":"OXA-488","CARD_short_name":"OXA-488","ARO_description":"OXA-488 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46513":{"category_aro_accession":"3007724","category_aro_cvterm_id":"46513","category_aro_name":"OXA-50-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-50.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3549":{"model_id":"3549","model_name":"ARL-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"5744":{"protein_sequence":{"accession":"APY23733.1","sequence":"MKKFFTIFVLLCVCFAYTTATASAQGLTKLEHKNDATVGVYGINTATGQTYSHNADTRFAYASTFKAITSGLLLQQNSPEALNKTVTIKESDIVAYSPVTEQYVGKTMTLRQLISAAMLQSDNTASNIIMEQLGGLDQLSSRLQALGDTTTNPQRYEPELNNYDPQSTADTSTPRATAHNLQKLLTTDAVAPQQRKFLQNLMFNNKTGESLIKKGVPNSYKVGDKSGQGTTYGTRNDVAVIYPKHQTKPIILVVFTKHQQQDAQPQDELVAQAARHAIHQLD"},"dna_sequence":{"accession":"KY363215.1","fmin":"79488","fmax":"80337","strand":"+","sequence":"ATGAAAAAGTTTTTTACTATCTTTGTCTTACTCTGTGTTTGCTTCGCTTACACAACTGCTACTGCTTCAGCGCAAGGTTTAACTAAATTAGAACATAAAAATGATGCCACAGTAGGTGTTTATGGCATTAATACTGCTACTGGACAAACTTATTCGCACAACGCTGATACCCGTTTTGCTTATGCATCAACTTTTAAAGCCATTACGAGTGGGTTATTATTACAGCAAAATTCTCCTGAAGCATTAAACAAAACTGTAACGATAAAAGAATCAGATATCGTGGCGTATTCACCTGTTACCGAACAATATGTCGGAAAAACCATGACCCTACGCCAATTAATTTCCGCTGCTATGTTACAGAGTGACAATACTGCTAGCAATATCATAATGGAACAACTCGGTGGTCTAGATCAGCTTTCGTCTCGCTTACAAGCACTCGGTGACACAACAACAAACCCACAACGTTATGAACCCGAATTAAATAACTATGATCCACAAAGTACGGCAGATACATCAACACCTCGTGCTACTGCCCATAATTTGCAAAAACTATTAACAACAGATGCCGTTGCACCACAACAGCGTAAGTTTTTACAAAATTTAATGTTCAACAATAAAACAGGTGAGAGTTTAATCAAAAAAGGTGTCCCTAACAGTTATAAAGTAGGTGACAAAAGTGGCCAAGGTACAACTTATGGCACGCGTAATGATGTTGCCGTCATCTATCCAAAACATCAAACAAAACCAATTATTTTAGTCGTCTTTACGAAACATCAGCAACAAGACGCACAACCACAAGATGAGTTAGTTGCACAAGCAGCACGTCATGCAATACATCAGCTCGATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42844","NCBI_taxonomy_name":"Staphylococcus arlettae","NCBI_taxonomy_id":"29378"}}}},"ARO_accession":"3004734","ARO_id":"42843","ARO_name":"ARL-1","CARD_short_name":"ARL-1","ARO_description":"ARL-1 is a beta-lactamase gene found in Staphylococcus Arlettae.","ARO_category":{"42853":{"category_aro_accession":"3004742","category_aro_cvterm_id":"42853","category_aro_name":"ARL Beta-lactamase","category_aro_description":"ARL beta-lactamase is an AMR Gene Family associated with Staphylococcus arlettae.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2724":{"model_id":"2724","model_name":"MuxABC-OpmB","model_type":"efflux pump system meta-model","model_type_id":"41112","model_description":"Efflux Pump System Meta-Models (EPS) are dedicated to efflux complexes and their regulators, such as AcrAB-TolC. Using the efflux pump components parameter, this model type simply includes a list of detection models for each component of the complex. This model type is still under development and not currently supported by the Resistance Gene Identifier (RGI) software.","model_param":{"41141":{"param_type":"efflux pump components","param_description":"Association of proteins within efflux protein complexes or regulatory networks are encoded by the efflux pump components parameter: model_id,model_id,model_id, etc.","param_type_id":"41141","param_value":{"7597":"2717,2718,2720,2716"}},"snp":{"Curated-R":{"7597":"S456L"}}},"ARO_accession":"3004076","ARO_id":"41159","ARO_name":"MuxABC-OpmB","CARD_short_name":"MuxABC-OpmB","ARO_description":"MuxABC-OpmB is an RND-type multidrug efflux pump in Pseudomonas aeruginosa. This efflux pump confers resistance to aztreonam, novobiocin, tetracycline, erythromycin, kitasamycin and rokitamycin.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36250":{"category_aro_accession":"3000111","category_aro_cvterm_id":"36250","category_aro_name":"novobiocin","category_aro_description":"Novobiocin is an aminocoumarin antibiotic produced by Streptomyces spheroides and Streptomyces niveus, and binds DNA gyrase subunit B inhibiting ATP-dependent DNA supercoiling.","category_aro_class_name":"Antibiotic"},"36689":{"category_aro_accession":"3000550","category_aro_cvterm_id":"36689","category_aro_name":"aztreonam","category_aro_description":"Aztreonam was the first monobactam discovered, and is greatly effective against Gram-negative bacteria while inactive against Gram-positive bacteria. Artreonam is a poor substrate for beta-lactamases, and may even act as an inhibitor. In Gram-negative bacteria, Aztreonam interferes with filamentation, inhibiting cell division and leading to cell death.","category_aro_class_name":"Antibiotic"},"37626":{"category_aro_accession":"3001227","category_aro_cvterm_id":"37626","category_aro_name":"kitasamycin","category_aro_description":"Kitasamycin is a macrolide antibiotic and is produced by Streptoverticillium kitasatoense. The drug has antimicrobial activity against a wide spectrum of pathogens.","category_aro_class_name":"Antibiotic"},"40353":{"category_aro_accession":"3003701","category_aro_cvterm_id":"40353","category_aro_name":"rokitamycin","category_aro_description":"Rokitamycin is a macrolide antibiotic. Synthesized from strains of Streptomyces kitasatoensis.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36242":{"category_aro_accession":"3000103","category_aro_cvterm_id":"36242","category_aro_name":"aminocoumarin antibiotic","category_aro_description":"Aminocoumarin antibiotics bind DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"3559":{"model_id":"3559","model_name":"BCL-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"5754":{"protein_sequence":{"accession":"ABU39980.1","sequence":"MKRSFFMLKTKITSSILVGACLLIGCSNGNEQPVSNEPEPEESVETGEAVFKALEEEYAARLGVFALDTGTGQTVSYRSDERFTYASAHKPLAVAVLLQQKSIEELEQLITYSADDLVNYNPITENHVETGMTLRELSDASIRYSDNTAANFIFDEIGGPEGFKEGLRAIGDTVTEPERIEPELNHVEPGEIQDTSTPEALAKSLQEFALGEALPADKQELLIDWLIGNTTGDALIRAGVPEGWEVGDKTGAGSYGTRNDIAILWPPEKEPIILAVLSSKDEKDAEYDDELIAKATEEVINLLAQTE"},"dna_sequence":{"accession":"EF540343.1","fmin":"3312","fmax":"4236","strand":"+","sequence":"ATGAAAAGGAGTTTTTTTATGCTGAAAACAAAAATCACGTCGTCTATCCTTGTAGGTGCCTGTTTACTGATTGGTTGTTCGAATGGCAATGAGCAACCGGTTTCCAACGAACCTGAACCTGAAGAGTCTGTCGAGACGGGAGAGGCGGTTTTTAAAGCGTTAGAAGAAGAGTACGCTGCCCGCCTTGGCGTATTTGCTTTAGACACCGGGACAGGACAAACCGTTTCCTACCGCTCCGATGAACGCTTCACCTATGCGTCTGCCCATAAACCACTTGCCGTTGCCGTTCTGCTTCAACAAAAATCAATCGAAGAGTTGGAACAATTGATTACGTACTCGGCCGATGATTTAGTAAACTACAATCCAATTACCGAAAACCACGTTGAGACAGGCATGACACTAAGAGAGTTAAGCGATGCTTCGATTCGTTATAGCGATAACACGGCTGCAAACTTCATTTTCGATGAAATTGGAGGGCCAGAGGGCTTTAAAGAAGGACTTCGAGCGATTGGAGACACGGTAACCGAACCTGAACGAATCGAACCTGAGCTCAATCATGTTGAACCTGGAGAGATCCAAGATACGAGTACACCAGAGGCGTTGGCCAAAAGCTTGCAAGAATTTGCTTTAGGAGAGGCGCTGCCAGCTGACAAACAGGAACTGTTAATCGATTGGCTAATAGGAAACACGACTGGAGATGCTTTAATACGTGCTGGGGTGCCGGAAGGTTGGGAAGTTGGCGACAAAACAGGCGCAGGTTCCTATGGGACTCGAAATGATATTGCCATTCTTTGGCCACCTGAAAAAGAGCCCATTATTTTAGCCGTCCTATCGAGCAAAGACGAAAAGGATGCCGAATATGATGATGAACTGATCGCGAAAGCGACAGAGGAAGTGATCAATCTCCTCGCCCAAACAGAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36882","NCBI_taxonomy_name":"Alkalihalobacillus clausii","NCBI_taxonomy_id":"79880"}}}},"ARO_accession":"3004749","ARO_id":"42861","ARO_name":"BCL-1","CARD_short_name":"BCL-1","ARO_description":"BCL-1 is a class A beta-lactamase found in Alkalihalobacillus clausii.","ARO_category":{"42860":{"category_aro_accession":"3004748","category_aro_cvterm_id":"42860","category_aro_name":"BCL Beta-lactamase","category_aro_description":"BCL beta-lactamase is a class A beta-lactamase.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3565":{"model_id":"3565","model_name":"BRO-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"5904":{"protein_sequence":{"accession":"AAA92126.1","sequence":"MQRRHFLQKTLLALPIIFSGNLLTGCKTNLSDDYLPDDKITNNPNLLQNKLKEILPIWENKFNAKIGMTIIADNGELSSHRGNEYFPVNSTIKAFIASHILLLVDKEKLDLNEKIIIKESDLIEYSPVCKKYFDENKPISISELCEATITLSDNGSANILLDKIGGLTAFNQFLKEIGADMVLANNEPLLNRSHYGETSDTAKPIPYTKSLKALIVGNILSNQSKEQLITWLINDKVADNLLRKYLPKNWRIGDKTGTGSESKNIIAVIWNENNKPYFISLFITQPHDGKSLDFKNQKDEIMAQIGKEIYPFL"},"dna_sequence":{"accession":"U49269.2","fmin":"1975","fmax":"2917","strand":"+","sequence":"ATGCAACGCCGGCATTTTTTACAAAAAACCTTATTGGCACTACCTATTATTTTTTCTGGCAATTTATTAACTGGATGTAAAACGAATTTATCTGATGATTATTTGCCCGATGATAAGATAACAAACAATCCAAATTTATTACAAAATAAATTAAAAGAGATATTGCCAATTTGGGAAAATAAATTTAATGCCAAAATTGGTATGACGATTATTGCTGACAATGGTGAACTATCCAGTCATCGTGGTAATGAATATTTTCCTGTTAATAGTACCATTAAAGCCTTTATTGCAAGTCATATATTATTACTTGTAGATAAAGAAAAATTGGATTTAAACGAAAAAATCATCATTAAAGAAAGCGATTTGATAGAATATTCTCCTGTCTGTAAAAAATACTTTGATGAGAATAAACCAATTTCTATTAGTGAATTGTGCGAAGCTACCATAACACTGAGTGATAATGGTTCTGCTAATATCTTGTTGGATAAAATTGGGGGTTTGACTGCATTCAATCAATTTTTGAAAGAGATTGGGGCGGATATGGTGCTGGCAAATAATGAGCCTTTATTAAATCGCTCACATTATGGTGAAACCAGTGATACCGCAAAACCAATTCCTTACACAAAAAGCCTAAAAGCACTGATTGTAGGCAATATCCTATCCAATCAAAGCAAAGAACAGTTGATAACTTGGCTTATCAATGATAAAGTTGCTGATAATTTATTGAGAAAATATTTACCAAAAAATTGGCGAATTGGCGACAAAACAGGCACAGGTAGTGAATCAAAAAATATCATTGCTGTGATTTGGAATGAAAATAATAAACCTTATTTTATCAGCCTATTTATCACCCAGCCCCATGATGGTAAATCCCTTGATTTTAAAAATCAAAAAGATGAAATAATGGCACAAATTGGTAAAGAAATTTATCCATTTTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41250","NCBI_taxonomy_name":"Moraxella catarrhalis","NCBI_taxonomy_id":"480"}}}},"ARO_accession":"3004761","ARO_id":"42874","ARO_name":"BRO-1","CARD_short_name":"BRO-1","ARO_description":"BRO-1 is a class A beta-lactamase found in M.catarrhalis.","ARO_category":{"42873":{"category_aro_accession":"3004760","category_aro_cvterm_id":"42873","category_aro_name":"BRO Beta-lactamase","category_aro_description":"BRO is a class A beta-lactamase that is found in M.catarrhalis.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3600":{"model_id":"3600","model_name":"GOB-14","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"575"}},"model_sequences":{"sequence":{"5798":{"protein_sequence":{"accession":"AAT68582.1","sequence":"MRNFATLFFLSVCLDLNLNAQVVKEPENMPKEWNQTYEPFRIAGNLYYVGTYDLASYLIVTDKGNILINTGTAESLPIIKGNIQKLGFNYKDIKILLLTQAHYDHTGALQDFKTETGAKFYTDKADADVLKTGGKSDYELGKYGVTFKPITPDRTLKDQDKITLGNTTLTLLHHPGHTKGSCSFIFDTKDEKRKYRVLIANMPSIIVDKKFSEVTAYPNIQSDYAYTFGAMKKLDFDLWVASHASQFDLHEKRKEGDPYNPQLFMDKQNYFQSLNNLEKSYLDKIKKDSQDK"},"dna_sequence":{"accession":"AY647252.1","fmin":"0","fmax":"879","strand":"+","sequence":"ATGAGAAATTTTGCTACACTGTTTTTTCTGTCAGTTTGTTTGGATTTGAATTTGAACGCTCAGGTAGTAAAAGAACCTGAGAATATGCCTAAAGAATGGAATCAGACTTATGAACCATTCAGAATTGCAGGTAACTTATATTACGTAGGAACCTATGATTTGGCTTCTTACCTTATTGTGACGGACAAAGGCAATATTCTCATTAATACAGGAACGGCAGAATCGCTTCCAATAATAAAAGGCAATATTCAAAAGCTGGGGTTTAATTATAAAGACATTAAGATCTTGCTGCTTACCCAGGCTCATTATGACCATACAGGTGCGTTACAGGATTTCAAAACAGAAACCGGTGCAAAATTCTATACCGATAAAGCAGATGCTGATGTCCTGAAAACAGGGGGTAAGTCCGATTATGAATTGGGAAAATATGGTGTGACATTTAAACCTATTACTCCGGATAGAACGTTAAAAGATCAGGATAAAATAACACTGGGAAATACAACCCTGACTTTGCTTCATCACCCGGGACATACAAAAGGTTCCTGCAGTTTTATTTTTGACACAAAAGACGAGAAGAGAAAGTATAGAGTTCTGATAGCTAATATGCCCTCTATTATTGTTGATAAGAAATTTTCTGAAGTTACAGCATATCCGAATATTCAGTCCGATTATGCTTATACCTTTGGTGCAATGAAAAAGCTTGATTTTGATCTTTGGGTAGCATCGCATGCAAGTCAGTTCGATCTGCATGAAAAACGTAAAGAAGGAGATCCGTACAACCCACAATTGTTTATGGATAAGCAAAACTATTTCCAAAGTCTTAATAATCTGGAGAAAAGCTATCTTGATAAAATTAAAAAAGATTCCCAAGATAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36960","NCBI_taxonomy_name":"Elizabethkingia meningoseptica","NCBI_taxonomy_id":"238"}}}},"ARO_accession":"3004806","ARO_id":"42926","ARO_name":"GOB-14","CARD_short_name":"GOB-14","ARO_description":"GOB-14 is a class B beta-lactamase gene found in Elizabethkingia meningoseptica.","ARO_category":{"41376":{"category_aro_accession":"3004212","category_aro_cvterm_id":"41376","category_aro_name":"GOB beta-lactamase","category_aro_description":"The GOB family of beta-lactamases have been discovered in the Elizabethkingia meningoseptica and are classified as subclass B3 beta-lactamase. They confer resistance to cephalosporins, penicillins, and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3557":{"model_id":"3557","model_name":"MIR-23","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"5752":{"protein_sequence":{"accession":"AIG20028.1","sequence":"MMTKSLSCALLLSVASSAFAAPMSEKQLAEVVERTVTPLMNAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEIALGDPVAKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDTASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMSYEQAMTTRVFKPLKLDHTWINVPKAEEAHYAWGYREGKAVHVSPGMLDAEAYGVKTNVKDMASWLIANMKPDSLQASSLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVGGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILDALQ"},"dna_sequence":{"accession":"KJ949106.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGACAAAATCCCTAAGCTGTGCCCTGCTGCTCAGCGTCGCCAGTTCTGCATTCGCCGCACCGATGTCCGAAAAACAGCTGGCTGAGGTGGTGGAACGTACCGTTACGCCGCTGATGAACGCGCAGGCCATTCCGGGTATGGCGGTGGCGGTAATTTATCAGGGTCAGCCACACTACTTTACCTTCGGTAAAGCCGATGTTGCGGCGAACAAACCCGTCACCCCGCAAACCCTGTTTGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTACTGGGCGGCGATGCCATTGCCCGGGGTGAAATAGCGCTGGGCGATCCGGTAGCAAAATACTGGCCTGAGCTCACGGGCAAGCAGTGGCAGGGCATTCGCATGCTGGATCTGGCAACCTATACCGCAGGCGGTCTGCCGTTACAGGTGCCGGATGAGGTCACGGATACCGCCTCTCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCGGGTACCACGCGTCTTTACGCTAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTCAAACCTTCCGGCATGAGCTATGAGCAGGCCATGACGACGCGGGTCTTTAAACCCCTCAAGCTGGACCATACCTGGATTAACGTCCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGATACCGTGAGGGTAAAGCGGTCCACGTTTCGCCAGGGATGCTGGACGCGGAAGCCTATGGCGTAAAAACTAACGTGAAGGATATGGCGAGCTGGCTGATAGCCAACATGAAGCCGGATTCTCTTCAGGCTTCCTCACTCAAGCAAGGCATTGCTCTGGCGCAGTCTCGCTACTGGCGCGTGGGGGCCATGTATCAGGGGTTGGGCTGGGAGATGCTCAACTGGCCGGTCGATGCCAAAACCGTCGTCGGAGGCAGTGATAACAAGGTGGCGCTGGCACCATTGCCCGTGGCAGAAGTGAATCCACCCGCGCCGCCGGTTAAGGCCTCCTGGGTCCATAAAACAGGCTCGACGGGTGGGTTTGGCAGCTACGTGGCATTTATTCCTGAAAAGCAGCTCGGCATTGTGATGCTGGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCGTATCCTCGACGCGCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3004745","ARO_id":"42856","ARO_name":"MIR-23","CARD_short_name":"MIR-23","ARO_description":"MIR-23, originally described as AZECL-25, is a class C beta-lactamase that is found in Enterobacter cloacae.","ARO_category":{"36197":{"category_aro_accession":"3000058","category_aro_cvterm_id":"36197","category_aro_name":"MIR beta-lactamase","category_aro_description":"MIR beta-lactamases are plasmid-mediated beta-lactamases that confer resistance to oxyimino- and alpha-methoxy beta-lactams.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3731":{"model_id":"3731","model_name":"Mycobacterium tuberculosis mymA mutations conferring resistance to isoniazid","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"40394":{"param_type":"nonsense mutation","param_description":"A sequence change where, compared to a reference sequence, one codon is replaced by a termination codon through a nucleotide substitution. These are described as a substitution of the wildtype codon to a termination codon. Format is given as [wild type AA][position][Ter], for example Q42Ter where Q42 is a wildtype amino acid replaced by a premature termination codon.","param_type_id":"40394","param_value":{"9575":"W271Ter"}},"snp":{"ReSeqTB-High":{"9575":"S456L","9569":"M371I","9574":"A205T"},"param_value":{"9569":"M371I","9574":"A205T"},"clinical":{"9569":"M371I","9574":"A205T"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"980"}},"model_sequences":{"sequence":{"6033":{"protein_sequence":{"accession":"NP_217599.1","sequence":"MNQHFDVLIIGAGLSGIGTACHVTAEFPDKTIALLERRERLGGTWDLFRYPGVRSDSDMFTFGYKFRPWRDVKVLADGASIRQYIADTATEFGVDEKIHYGLKVNTAEWSSRQCRWTVAGVHEATGETRTYTCDYLISCTGYYNYDAGYLPDFPGVHRFGGRCVHPQHWPEDLDYSGKKVVVIGSGATAVTLVPAMAGSNPGSAAHVTMLQRSPSYIFSLPAVDKISEVLGRFLPDRWVYEFGRRRNIAIQRKLYQACRRWPKLMRRLLLWEVRRRLGRSVDMSNFTPNYLPWDERLCAVPNGDLFKTLASGAASVVTDQIETFTEKGILCKSGREIEADIIVTATGLNIQMLGGMRLIVDGAEYQLPEKMTYKGVLLENAPNLAWIIGYTNASWTLKSDIAGAYLCRLLRHMADNGYTVATPRDAQDCALDVGMFDQLNSGYVKRGQDIMPRQGSKHPWRVLMHYEKDAKILLEDPIDDGVLHFAAAAQDHAAA"},"dna_sequence":{"accession":"NC_000962.3","fmin":"3448503","fmax":"3449991","strand":"+","sequence":"ATGAACCAGCATTTCGACGTCCTGATCATCGGCGCCGGCCTATCCGGCATCGGGACGGCCTGTCACGTGACGGCCGAGTTCCCCGACAAGACAATCGCCCTCCTGGAACGACGGGAGCGCCTGGGCGGCACCTGGGACTTGTTCCGCTACCCGGGAGTTCGTTCGGACTCCGACATGTTCACCTTCGGCTACAAGTTCCGCCCGTGGCGCGACGTGAAGGTGCTCGCCGACGGCGCGTCGATCCGGCAGTACATCGCCGACACCGCCACGGAGTTCGGCGTCGACGAGAAGATTCACTACGGCCTGAAGGTCAACACCGCCGAGTGGTCGAGCCGGCAGTGCCGTTGGACCGTCGCGGGCGTGCACGAGGCGACCGGCGAAACCCGGACCTACACCTGCGATTACCTCATCAGCTGCACCGGCTACTACAACTACGACGCGGGTTATCTGCCGGACTTCCCCGGCGTGCACCGGTTCGGCGGCCGGTGCGTGCACCCGCAGCACTGGCCCGAAGACCTCGATTATTCCGGCAAGAAGGTCGTCGTCATCGGCAGCGGCGCAACGGCGGTCACTTTGGTTCCGGCGATGGCCGGCTCCAACCCCGGCAGTGCCGCGCACGTGACGATGCTGCAGCGATCCCCGTCGTACATCTTCTCGCTGCCGGCGGTCGACAAGATCTCCGAAGTCCTGGGCCGCTTCCTGCCGGATCGCTGGGTCTACGAGTTTGGCCGCAGGCGCAACATCGCCATCCAGCGAAAGCTCTACCAGGCCTGCCGGCGCTGGCCCAAGCTGATGCGGCGATTGCTGCTGTGGGAGGTACGACGCCGCCTCGGCCGCTCCGTGGACATGAGCAACTTCACCCCGAACTACCTGCCGTGGGACGAGCGGTTGTGCGCCGTGCCCAACGGCGATCTGTTTAAGACGCTGGCCTCGGGCGCGGCGTCGGTGGTGACCGATCAGATCGAGACCTTCACCGAGAAGGGCATCCTGTGCAAGTCCGGCCGGGAGATCGAGGCCGACATCATCGTCACCGCGACCGGTCTGAACATCCAGATGCTGGGCGGGATGCGACTCATCGTGGACGGCGCCGAATACCAGCTGCCGGAGAAGATGACCTATAAGGGTGTGCTGCTGGAAAACGCCCCCAATCTGGCCTGGATCATCGGCTACACCAACGCGTCATGGACCCTGAAGTCCGACATCGCCGGCGCCTACCTGTGCCGGCTGCTGCGGCACATGGCCGACAACGGCTACACGGTGGCAACGCCGCGCGATGCGCAGGACTGCGCGCTGGACGTTGGCATGTTCGACCAGCTGAACTCCGGCTATGTGAAGCGCGGCCAGGACATCATGCCGCGCCAGGGCTCCAAGCATCCGTGGAGGGTGCTCATGCACTACGAGAAGGACGCCAAGATCCTGCTCGAAGACCCCATCGATGACGGCGTGCTGCACTTCGCCGCAGCGGCCCAAGACCACGCGGCGGCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3004928","ARO_id":"43114","ARO_name":"Mycobacterium tuberculosis mymA mutations conferring resistance to isoniazid","CARD_short_name":"Mtub_mymA_INH","ARO_description":"Mutations that occur in the mymA operon that result in or contribute to antibiotic resistance to isoniazid.","ARO_category":{"43092":{"category_aro_accession":"3004906","category_aro_cvterm_id":"43092","category_aro_name":"isoniazid resistant mymA","category_aro_description":"mymA is an operon that begins at Rv3083 and ends at Rv3089 and is required for maintaining the appropriate mycolic acid composition and permeability of the envelope on its exposure to acidic pH. It has shown to be resistant to isoniazid.","category_aro_class_name":"AMR Gene Family"},"36659":{"category_aro_accession":"3000520","category_aro_cvterm_id":"36659","category_aro_name":"isoniazid","category_aro_description":"Isoniazid is an organic compound that is the first-line anti tuberculosis medication in prevention and treatment. As a prodrug, it is activated by mycobacterial catalase-peroxidases such as M. tuberculosis KatG. Isoniazid inhibits mycolic acid synthesis, which prevents cell wall synthesis in mycobacteria.","category_aro_class_name":"Antibiotic"},"45734":{"category_aro_accession":"3007152","category_aro_cvterm_id":"45734","category_aro_name":"isoniazid-like antibiotic","category_aro_description":"A group of antibiotics containing isoniazid and its derivatives.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2729":{"model_id":"2729","model_name":"MexJK-OprM","model_type":"efflux pump system meta-model","model_type_id":"41112","model_description":"Efflux Pump System Meta-Models (EPS) are dedicated to efflux complexes and their regulators, such as AcrAB-TolC. Using the efflux pump components parameter, this model type simply includes a list of detection models for each component of the complex. This model type is still under development and not currently supported by the Resistance Gene Identifier (RGI) software.","model_param":{"41141":{"param_type":"efflux pump components","param_description":"Association of proteins within efflux protein complexes or regulatory networks are encoded by the efflux pump components parameter: model_id,model_id,model_id, etc.","param_type_id":"41141","param_value":{"7606":"2205,2206,2219,1305"}},"snp":{"Curated-R":{"7606":"A205T"}}},"ARO_accession":"3003694","ARO_id":"40346","ARO_name":"MexJK-OprM","CARD_short_name":"MexJK-OprM","ARO_description":"MexJK-OprM is a multidrug efflux protein expressed in the Gram-negative Pseudomonas aeruginosa. MexJ is the membrane fusion protein, MexK is the inner membrane resistance-nodulation-cell division (RND) transporter, and OprM is the outer membrane factor protein.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2731":{"model_id":"2731","model_name":"MexJK-OpmH","model_type":"efflux pump system meta-model","model_type_id":"41112","model_description":"Efflux Pump System Meta-Models (EPS) are dedicated to efflux complexes and their regulators, such as AcrAB-TolC. Using the efflux pump components parameter, this model type simply includes a list of detection models for each component of the complex. This model type is still under development and not currently supported by the Resistance Gene Identifier (RGI) software.","model_param":{"41141":{"param_type":"efflux pump components","param_description":"Association of proteins within efflux protein complexes or regulatory networks are encoded by the efflux pump components parameter: model_id,model_id,model_id, etc.","param_type_id":"41141","param_value":{"7607":"2205,2206,2219,2195"}},"snp":{"Curated-R":{"7607":"A205T"}}},"ARO_accession":"3003691","ARO_id":"40339","ARO_name":"MexJK-OpmH","CARD_short_name":"MexJK-OpmH","ARO_description":"MexJK-OpmH is a triclosan efflux protein expressed in the Gram-negative Pseudomonas aeruginosa. MexJ is the membrane fusion protein, MexK is the inner membrane resistance-nodulation-cell division (RND) transporter, and OpmH is the outer membrane efflux protein. MexJK is constitutively expressed in mexL mutants.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"37250":{"category_aro_accession":"3000870","category_aro_cvterm_id":"37250","category_aro_name":"triclosan","category_aro_description":"Triclosan is a common antibacterial agent added to many consumer products as a biocide.  It is an inhibitor of fatty acid biosynthesis by blocking enoyl-carrier protein reductase (FabI).","category_aro_class_name":"Antibiotic"},"43746":{"category_aro_accession":"3005386","category_aro_cvterm_id":"43746","category_aro_name":"disinfecting agents and antiseptics","category_aro_description":"Disinfectants that can also interact with antimicrobial resistance mechanisms, e.g. molecule efflux, and thus are the targets of disinfectant resistance.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2732":{"model_id":"2732","model_name":"MexVW-OprM","model_type":"efflux pump system meta-model","model_type_id":"41112","model_description":"Efflux Pump System Meta-Models (EPS) are dedicated to efflux complexes and their regulators, such as AcrAB-TolC. Using the efflux pump components parameter, this model type simply includes a list of detection models for each component of the complex. This model type is still under development and not currently supported by the Resistance Gene Identifier (RGI) software.","model_param":{"41141":{"param_type":"efflux pump components","param_description":"Association of proteins within efflux protein complexes or regulatory networks are encoded by the efflux pump components parameter: model_id,model_id,model_id, etc.","param_type_id":"41141","param_value":{"7705":"2207,2208,1305"}},"snp":{"Curated-R":{"7705":"A205T"}}},"ARO_accession":"3003029","ARO_id":"39463","ARO_name":"MexVW-OprM","CARD_short_name":"MexVW-OprM","ARO_description":"MexVW-OprM is a multidrug efflux protein expressed in Pseudomonas aeruginosa. MexV is the membrane fusion protein; MexW is the RND-type membrane protein; and OprM is the outer membrane channel. MexVW-OprM is associated with resistance to fluoroquinolones, tetracycline, chloramphenicol, erythromycin and acriflavine.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35963":{"category_aro_accession":"0000045","category_aro_cvterm_id":"35963","category_aro_name":"acriflavine","category_aro_description":"Acriflavine is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"43746":{"category_aro_accession":"3005386","category_aro_cvterm_id":"43746","category_aro_name":"disinfecting agents and antiseptics","category_aro_description":"Disinfectants that can also interact with antimicrobial resistance mechanisms, e.g. molecule efflux, and thus are the targets of disinfectant resistance.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2733":{"model_id":"2733","model_name":"TriABC-OpmH","model_type":"efflux pump system meta-model","model_type_id":"41112","model_description":"Efflux Pump System Meta-Models (EPS) are dedicated to efflux complexes and their regulators, such as AcrAB-TolC. Using the efflux pump components parameter, this model type simply includes a list of detection models for each component of the complex. This model type is still under development and not currently supported by the Resistance Gene Identifier (RGI) software.","model_param":{"41141":{"param_type":"efflux pump components","param_description":"Association of proteins within efflux protein complexes or regulatory networks are encoded by the efflux pump components parameter: model_id,model_id,model_id, etc.","param_type_id":"41141","param_value":{"7609":"2192,2193,2194,2195"}},"snp":{"Curated-R":{"7609":"A205T"}}},"ARO_accession":"3003678","ARO_id":"40313","ARO_name":"TriABC-OpmH","CARD_short_name":"TriABC-OpmH","ARO_description":"TriABC-OpmH is a triclosan-specific efflux pump expressed in the Gram-negative Pseudomonas aeruginosa. TriABC is the only P. aeruginosa resistance nodulation cell division (RND) pump which contains two membrane fusion proteins, TriA and TriB, and both are required for efflux pump function. TriABC associated with OpmH assemble a functional triclosan efflux pump.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"37250":{"category_aro_accession":"3000870","category_aro_cvterm_id":"37250","category_aro_name":"triclosan","category_aro_description":"Triclosan is a common antibacterial agent added to many consumer products as a biocide.  It is an inhibitor of fatty acid biosynthesis by blocking enoyl-carrier protein reductase (FabI).","category_aro_class_name":"Antibiotic"},"43746":{"category_aro_accession":"3005386","category_aro_cvterm_id":"43746","category_aro_name":"disinfecting agents and antiseptics","category_aro_description":"Disinfectants that can also interact with antimicrobial resistance mechanisms, e.g. molecule efflux, and thus are the targets of disinfectant resistance.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2734":{"model_id":"2734","model_name":"PmpM","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"900"}},"model_sequences":{"sequence":{"5376":{"protein_sequence":{"accession":"AAG04750.1","sequence":"MNSPALPLSRGLRIRAELKELLTLAAPIMIAQLATTAMGFVDAVMAGRASPHDLAAVALGNSIWIPMFLLMTGTLLATTAKVAQRHGAGDQPGTGPLVRQALWLALLIGPLSGAVLWWLSEPILGLMKVRPELIGPSLLYLKGIALGFPAAALYHVLRCYTNGLGRTRPSMVLGIGGLLLNIPINYALIYGHFGMPKMGGPGCGWATGSVMWFMFLGMLFWVNKASIYRASQLFSRWEWPDRATIGPLVAVGLPIGIAVFAESSIFSVIALLIGGLDENVVAGHQIALNFSALVFMIPYSLGMAVTVRVGHNLGAGLPRDARFAAGVGMAAALGYACVSASLMLLLREQIAAMYSPDPAVIAIAASLIVFSALFQFSDALQVTAAGALRGYQDTRVTMIMTLFAYWGIGLPVGYSLGLTDWFQEPTGPRGLWQGLVVGLTGAAIMLCIRLARSARRFIRQHERLQREDAEAASVLGR"},"dna_sequence":{"accession":"AE004091.2","fmin":"1472546","fmax":"1473980","strand":"-","sequence":"GTGAACAGCCCCGCCCTGCCCCTTTCCCGTGGCTTGCGCATCCGCGCCGAACTCAAGGAACTGCTGACCCTCGCCGCGCCGATCATGATCGCGCAACTGGCGACCACCGCCATGGGCTTCGTCGATGCGGTGATGGCCGGGCGCGCCAGTCCGCACGACCTGGCAGCGGTGGCGCTGGGCAACTCCATCTGGATCCCGATGTTCCTGCTGATGACCGGCACCCTGCTCGCCACCACGGCCAAGGTCGCCCAGCGCCATGGCGCCGGCGACCAGCCCGGCACCGGGCCGCTGGTGCGCCAGGCGCTGTGGCTGGCGCTGCTGATCGGACCGCTGTCGGGGGCGGTGCTGTGGTGGTTGTCGGAGCCGATCCTCGGCTTGATGAAAGTGCGCCCGGAACTGATCGGGCCGAGCCTGCTGTACCTCAAGGGCATCGCCCTGGGCTTCCCGGCGGCGGCGCTGTACCACGTACTGCGCTGCTACACCAACGGCCTGGGACGGACCCGGCCGAGCATGGTGCTGGGGATCGGCGGGCTGCTGCTGAACATCCCGATCAACTACGCGCTGATCTACGGCCACTTCGGCATGCCGAAGATGGGTGGCCCCGGCTGCGGCTGGGCCACCGGCTCGGTGATGTGGTTCATGTTCCTCGGCATGCTGTTCTGGGTGAACAAGGCCTCGATCTACCGCGCCAGCCAGTTGTTCTCGCGCTGGGAGTGGCCGGATCGCGCGACCATCGGCCCGCTGGTGGCGGTCGGCCTGCCGATCGGCATCGCGGTGTTCGCCGAGTCGAGCATCTTCTCGGTGATCGCCCTGCTGATCGGCGGGCTCGACGAGAACGTGGTGGCCGGCCACCAGATCGCCCTGAACTTCAGCGCGCTGGTGTTCATGATTCCCTATTCGCTGGGGATGGCGGTGACCGTGCGGGTCGGCCACAACCTCGGCGCCGGCCTGCCGCGCGACGCGCGCTTCGCCGCCGGCGTGGGGATGGCCGCGGCGCTGGGCTACGCCTGCGTCTCGGCGAGCCTGATGTTGTTGCTGCGCGAGCAGATCGCCGCGATGTATTCGCCGGACCCGGCGGTGATCGCCATCGCCGCCTCGCTGATCGTGTTCTCCGCGCTGTTCCAGTTCTCCGACGCCCTGCAGGTCACCGCCGCCGGGGCCCTGCGCGGCTACCAGGACACCCGGGTGACGATGATCATGACCCTGTTCGCCTACTGGGGCATCGGCCTGCCGGTGGGCTACAGCCTCGGCCTCACCGACTGGTTCCAGGAACCCACCGGACCGCGCGGTCTGTGGCAAGGCCTGGTGGTGGGCCTGACCGGCGCGGCGATCATGCTCTGCATCCGCCTGGCGCGCAGCGCGCGGCGCTTCATCCGCCAGCACGAGCGCCTGCAGCGGGAGGACGCGGAGGCCGCCTCAGTCCTTGGCCGGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36804","NCBI_taxonomy_name":"Pseudomonas aeruginosa PAO1","NCBI_taxonomy_id":"208964"}}}},"ARO_accession":"3004077","ARO_id":"41170","ARO_name":"PmpM","CARD_short_name":"PmpM","ARO_description":"PmpM is a multidrug efflux pump belonging to the MATE family of Pseudomonas aeruginosa. PmpM is an H+ drug antiporter and is the first reported case of an H+ coupled efflux pump in the MATE family. PmpM confers resistance to fluoroquinolones, fradiomycin, benzalkonium chloride, chlorhexidine gluconate, ethidium bromide, tetraphenylphosphonium chloride (TPPCl), and rhodamine 6G.","ARO_category":{"36251":{"category_aro_accession":"3000112","category_aro_cvterm_id":"36251","category_aro_name":"multidrug and toxic compound extrusion (MATE) transporter","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Multidrug and toxic compound extrusion (MATE) transporters utilize the cationic gradient across the membrane as an energy source. Although there is a diverse substrate specificity, almost all MATE transporters recognize fluoroquinolones. Arciflavine, ethidium and aminoglycosides are also good substrates.","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"40514":{"category_aro_accession":"3003823","category_aro_cvterm_id":"40514","category_aro_name":"benzalkonium chloride","category_aro_description":"Benzalkonium chloride is a type of cationic surfactant. It is an organic salt called a quaternary ammonium compound. It has three main categories of use: as a biocide, a cationic surfactant, and as a phase transfer agent.","category_aro_class_name":"Antibiotic"},"45598":{"category_aro_accession":"3007039","category_aro_cvterm_id":"45598","category_aro_name":"chlorhexidine","category_aro_description":"Chlorhexidine is a disinfectant and antiseptic that is used for skin disinfection, including mouthwashes (chlorhexidine gluconate).","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"43746":{"category_aro_accession":"3005386","category_aro_cvterm_id":"43746","category_aro_name":"disinfecting agents and antiseptics","category_aro_description":"Disinfectants that can also interact with antimicrobial resistance mechanisms, e.g. molecule efflux, and thus are the targets of disinfectant resistance.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2745":{"model_id":"2745","model_name":"AcrAB-TolC","model_type":"efflux pump system meta-model","model_type_id":"41112","model_description":"Efflux Pump System Meta-Models (EPS) are dedicated to efflux complexes and their regulators, such as AcrAB-TolC. Using the efflux pump components parameter, this model type simply includes a list of detection models for each component of the complex. This model type is still under development and not currently supported by the Resistance Gene Identifier (RGI) software.","model_param":{"41141":{"param_type":"efflux pump components","param_description":"Association of proteins within efflux protein complexes or regulatory networks are encoded by the efflux pump components parameter: model_id,model_id,model_id, etc.","param_type_id":"41141","param_value":{"7768":"2661,1104,826,2306,431,1922,2776,228,2066,520"}},"snp":{"Curated-R":{"7768":"A205T"}}},"ARO_accession":"3000384","ARO_id":"36523","ARO_name":"AcrAB-TolC","CARD_short_name":"AcrAB-TolC","ARO_description":"AcrAB-TolC is a tripartite RND efflux system that confers resistance to tetracycline, chloramphenicol, ampicillin, nalidixic acid, and rifampin  in Gram-negative bacteria. The system spans the cell membrane (AcrB) and the outer-membrane (TolC), and is linked together in the periplasm by AcrA.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"37084":{"category_aro_accession":"3000704","category_aro_cvterm_id":"37084","category_aro_name":"cefalotin","category_aro_description":"Cefalotin is a semisynthetic cephalosporin antibiotic activate against staphylococci. It is resistant to staphylococci beta-lactamases but hydrolyzed by enterobacterial beta-lactamases.","category_aro_class_name":"Antibiotic"},"37250":{"category_aro_accession":"3000870","category_aro_cvterm_id":"37250","category_aro_name":"triclosan","category_aro_description":"Triclosan is a common antibacterial agent added to many consumer products as a biocide.  It is an inhibitor of fatty acid biosynthesis by blocking enoyl-carrier protein reductase (FabI).","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"43746":{"category_aro_accession":"3005386","category_aro_cvterm_id":"43746","category_aro_name":"disinfecting agents and antiseptics","category_aro_description":"Disinfectants that can also interact with antimicrobial resistance mechanisms, e.g. molecule efflux, and thus are the targets of disinfectant resistance.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2750":{"model_id":"2750","model_name":"APH(3')-VIIIb","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"350"}},"model_sequences":{"sequence":{"4499":{"protein_sequence":{"accession":"EPF73263.1","sequence":"MKLPQKIRNFIGNNRLIVNKVGQSPSDVYCFERNRETFFLKVSSVQYATTTYSVAREAQMMLWLADKINVPELVFSEIDQNFEYMLSKSIDAQPISDLSLAQSELIMLYQDVLSQLRSVPVQNCPFNSDINSRLQESQYFMEIGLLNQVDDENIDIELWGEHQSYLELWTELNNHRVKENLVFTHGDITDSNIFVDQSNKIYFLDLGRAGLADEFVDIAFVERCLREDGSEESAQKFLKQLSFDDLSKRQYFLKLDELN"},"dna_sequence":{"accession":"ATGI01000028.1","fmin":"7477","fmax":"8257","strand":"-","sequence":"ATGAAACTACCTCAGAAAATTAGAAATTTTATTGGAAATAATCGATTAATCGTTAACAAAGTTGGTCAATCACCTTCTGATGTATATTGCTTTGAACGAAATCGGGAAACGTTCTTCTTAAAAGTGTCTAGTGTGCAATATGCAACAACAACTTATAGTGTTGCGCGTGAAGCACAGATGATGCTTTGGTTAGCTGATAAGATTAACGTACCTGAGTTAGTATTCAGTGAAATAGATCAAAATTTTGAGTATATGTTAAGCAAGTCTATTGATGCTCAACCTATATCAGATTTGTCCTTAGCTCAATCCGAATTAATCATGCTTTATCAAGATGTATTAAGCCAGTTACGATCAGTACCTGTACAAAATTGTCCATTTAATTCAGATATCAATAGCCGTTTACAAGAATCCCAATACTTTATGGAGATTGGGTTGTTAAATCAGGTTGATGATGAAAATATTGATATAGAGCTATGGGGTGAGCATCAGAGTTATCTAGAACTGTGGACAGAGTTAAACAATCATCGTGTGAAAGAAAATTTAGTGTTTACACATGGAGATATTACTGACAGTAATATTTTCGTTGATCAGTCAAATAAGATTTATTTTTTGGACTTAGGACGCGCTGGCTTGGCAGATGAGTTTGTAGATATTGCCTTTGTTGAACGTTGTCTTCGTGAAGATGGTTCTGAAGAGAGTGCTCAGAAGTTTCTCAAACAATTAAGTTTTGATGACCTATCCAAACGTCAATATTTTCTAAAACTTGATGAGTTAAATTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41191","NCBI_taxonomy_name":"Acinetobacter rudis CIP 110305","NCBI_taxonomy_id":"421052"}}}},"ARO_accession":"3004086","ARO_id":"41190","ARO_name":"APH(3')-VIIIb","CARD_short_name":"APH(3')-VIIIb","ARO_description":"APH(3')-VIIIb is an aminoglycoside phosphoryltransferase that acts on the 3-OH target of aminoglycosides found in Acinetobacter rudis.","ARO_category":{"36265":{"category_aro_accession":"3000126","category_aro_cvterm_id":"36265","category_aro_name":"APH(3')","category_aro_description":"A category of aminoglycoside O-phosphotransferase enzymes with modification regiospecificity based at the 3'-hydroxyl group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics, specifically kanamycin and neomycin, by the ATP-dependent phosphorylation of the 3'-hydroxyl group of the compound.","category_aro_class_name":"AMR Gene Family"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2748":{"model_id":"2748","model_name":"oqxAB","model_type":"efflux pump system meta-model","model_type_id":"41112","model_description":"Efflux Pump System Meta-Models (EPS) are dedicated to efflux complexes and their regulators, such as AcrAB-TolC. Using the efflux pump components parameter, this model type simply includes a list of detection models for each component of the complex. This model type is still under development and not currently supported by the Resistance Gene Identifier (RGI) software.","model_param":{"41141":{"param_type":"efflux pump components","param_description":"Association of proteins within efflux protein complexes or regulatory networks are encoded by the efflux pump components parameter: model_id,model_id,model_id, etc.","param_type_id":"41141","param_value":{"7704":"2399,2400"}},"snp":{"Curated-R":{"7704":"A205T"}}},"ARO_accession":"3003921","ARO_id":"40630","ARO_name":"oqxAB","CARD_short_name":"oqxAB","ARO_description":"oqxAB encodes for OqxAB, a plasmid-encoded efflux pump, which confer resistance to multiple agents including fluoroquinolones.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35992":{"category_aro_accession":"0000075","category_aro_cvterm_id":"35992","category_aro_name":"nitrofurantoin","category_aro_description":"Nitrofurantoin is an antibiotic used to treat urinary tract infections. It inhibits enzyme synthesis by inhibiting essential enzymes involved in the citric acid cycle, as well as those involved in DNA, RNA, and protein synthesis. It is marketed under the following brand names: Furadantin, Macrobid, Macrodantin, Nitro Macro and Urantoin.","category_aro_class_name":"Antibiotic"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"41240":{"category_aro_accession":"3004116","category_aro_cvterm_id":"41240","category_aro_name":"nitrofuran antibiotic","category_aro_description":"Nitrofurans are chemotherapeutic agents with antibacterial and antiprotozoal activity.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2749":{"model_id":"2749","model_name":"lnuG","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"4181":{"protein_sequence":{"accession":"APU52409.1","sequence":"MLKQKELMARVKELVQSDERISACMMYGSFTKGEGDQYSDIEYYVFLKDDTISTFDSAKWLNEVASYTLLYQNEYGTEVVIFENLIRGEFHFLSENEMNIIPSFKESGYIPDTKAMFIYDETGQLELYLSELEGPGPNRLTEENVNFLLNNFSNLWLMGINVLKRGENARSLELLSQLQKNILQLIRIAEENADNWFNMTKNLEKEISPENYEKFKKTTARLNELELYEAYKNSLLLVMELRNLVEKQYQLTISDDFLGKLFNYMNE"},"dna_sequence":{"accession":"KX470419.1","fmin":"3811","fmax":"4615","strand":"+","sequence":"TTGTTAAAACAAAAGGAACTAATGGCAAGGGTTAAGGAACTTGTCCAGTCAGATGAACGAATATCTGCTTGTATGATGTATGGCTCTTTTACAAAAGGAGAGGGAGATCAATACTCTGATATAGAATATTACGTTTTTCTAAAAGATGATACAATTTCCACCTTTGATTCAGCAAAATGGCTAAATGAAGTCGCTTCCTACACTTTACTCTATCAAAATGAGTACGGTACGGAAGTAGTAATTTTTGAAAATCTAATACGTGGTGAATTTCATTTCCTTTCCGAAAACGAAATGAATATTATTCCTTCATTCAAAGAATCAGGCTACATTCCTGACACAAAAGCAATGTTTATTTATGATGAAACAGGACAACTAGAATTGTATTTATCAGAGTTGGAAGGTCCGGGACCAAATAGACTTACAGAAGAAAACGTAAATTTTTTATTGAATAATTTTTCCAACCTATGGTTAATGGGGATTAATGTTCTTAAAAGAGGGGAAAATGCACGTTCACTGGAACTTTTATCTCAATTACAAAAAAATATACTACAACTCATTCGAATTGCGGAAGAAAATGCCGATAATTGGTTTAATATGACAAAGAATCTTGAAAAAGAAATTAGTCCTGAAAACTATGAAAAGTTTAAAAAGACTACTGCCCGATTAAATGAATTAGAACTATATGAAGCCTATAAGAACTCTTTGCTTCTCGTTATGGAACTTCGAAATCTCGTTGAAAAACAGTATCAATTAACCATTAGCGATGATTTTTTAGGCAAACTGTTTAATTATATGAACGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35918","NCBI_taxonomy_name":"Enterococcus faecalis","NCBI_taxonomy_id":"1351"}}}},"ARO_accession":"3004085","ARO_id":"41189","ARO_name":"lnuG","CARD_short_name":"lnuG","ARO_description":"lnuG is a transposon-mediated lincosamide nucleotidyltransferase found in Enterococcus faecalis on Tn6260.","ARO_category":{"36360":{"category_aro_accession":"3000221","category_aro_cvterm_id":"36360","category_aro_name":"lincosamide nucleotidyltransferase (LNU)","category_aro_description":"Resistance to the lincosamide antibiotic by ATP-dependent modification of the 3' and\/or 4'-hydroxyl groups of the methylthiolincosamide sugar.","category_aro_class_name":"AMR Gene Family"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2752":{"model_id":"2752","model_name":"ANT(3'')-IIa","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"8748":{"protein_sequence":{"accession":"EEX02086.1","sequence":"MPDFIQLEYLQEKLQQLLAESLFAIYLYGSAVDGGLGPESDLDVLVVVTQPLTSALREQLAQELLKISQPVGELQRPLEVTILLKDEIQAGNYPLSYEMQFGEWLREELKEGGTLSSQKDPDISILLRKARFHHTVLFGPALDQWAPEISDQELWQAMSDTYPEIVAHWDEDADERNQILALCRIYFSLVMKDIASKDNAARWVMPQLPPEQKFVLQRLIQEYRGEIGKQNWQEEHYALQPIVNFLSSKIEEQFEQKRNLIT"},"dna_sequence":{"accession":"GG704579.1","fmin":"34580","fmax":"35369","strand":"-","sequence":"ATGCCTGATTTCATTCAGTTAGAATATCTACAAGAAAAATTACAGCAACTTTTAGCGGAATCATTATTTGCAATCTATCTTTATGGTTCAGCTGTTGATGGTGGCTTAGGGCCAGAAAGTGACCTTGATGTTCTGGTCGTGGTTACTCAACCATTAACATCTGCTTTACGCGAGCAGCTTGCACAAGAATTACTAAAAATTTCACAGCCTGTTGGGGAATTACAAAGACCATTAGAAGTTACTATTTTATTAAAAGATGAGATTCAGGCTGGAAATTATCCTTTAAGTTATGAAATGCAGTTTGGTGAATGGCTACGTGAAGAACTTAAAGAAGGTGGAACATTAAGTTCGCAGAAAGACCCAGATATTAGTATATTGCTTAGAAAAGCGAGATTTCATCATACAGTTTTATTTGGTCCAGCTTTGGACCAATGGGCACCTGAAATTTCTGATCAAGAACTATGGCAAGCAATGTCTGATACTTATCCCGAAATTGTAGCTCATTGGGATGAGGATGCAGATGAAAGAAACCAGATTTTAGCTTTATGCCGGATCTATTTTAGTTTAGTCATGAAGGATATTGCTTCAAAAGACAATGCAGCTCGATGGGTTATGCCTCAGCTTCCTCCTGAGCAGAAATTCGTATTGCAGCGGCTTATACAGGAATATAGAGGGGAAATAGGCAAACAAAATTGGCAAGAGGAACATTATGCTTTGCAGCCTATTGTTAATTTTCTGAGTTCAAAAATTGAAGAGCAGTTTGAGCAGAAAAGAAATTTGATCACATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35598","NCBI_taxonomy_name":"Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841","NCBI_taxonomy_id":"575584"}}}},"ARO_accession":"3004089","ARO_id":"41195","ARO_name":"ANT(3'')-IIa","CARD_short_name":"ANT(3'')-IIa","ARO_description":"ANT(3'')-IIa is a aminoglycoside nucleotidyltransferase identified in Acinetobacter spp. via horizontal gene transfer mechanisms.","ARO_category":{"41439":{"category_aro_accession":"3004275","category_aro_cvterm_id":"41439","category_aro_name":"ANT(3'')","category_aro_description":"A category of aminoglycoside O-nucleotidyltransferase enzymes with modification regiospecificity based at the 3''-hydroxyl group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics by transfer of an AMP group from an ATP substrate to the 3''-hydroxyl group of the compound.","category_aro_class_name":"AMR Gene Family"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2754":{"model_id":"2754","model_name":"ANT(3'')-IIb","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"200"}},"model_sequences":{"sequence":{"4496":{"protein_sequence":{"accession":"ENU91137.1","sequence":"MSEQFQLQQLQEYLHALFAESLFAIYLYGSAVDGGLGPESDLDLLVVVTQPLTHVQRQQLAQALLTLSHPIGGLQRALEVTILLKEEVISGRYPLNYELQFGEWLREELVDGGELSAQNDPDISILLKKAHMHHRTLFGPDLTSWLDEIPDQQLWQAMADLYPSIVAHWDEDGDERNQILALCRIYFSLSLGEIVSKSHAAQWVIAQLEEKDQPVLQRMVQEYKGEMTKQDWPSQHQVLQPIVNFLSQHIETFFDKKGLKIKQ"},"dna_sequence":{"accession":"APPC01000022.1","fmin":"55968","fmax":"56760","strand":"-","sequence":"ATGTCAGAACAATTTCAGCTTCAGCAGTTACAAGAATATTTACATGCTTTATTTGCAGAATCATTATTTGCGATTTACTTGTATGGTTCTGCTGTGGATGGCGGTTTAGGCCCGGAAAGTGATCTGGATCTTCTGGTCGTTGTGACTCAACCTCTAACACACGTTCAGCGACAGCAGCTTGCACAAGCCTTATTAACGCTTTCACATCCAATTGGTGGATTGCAACGAGCACTTGAAGTAACTATCTTGCTCAAAGAAGAAGTGATTTCAGGCAGATATCCTTTAAATTATGAATTACAGTTTGGGGAATGGTTGCGTGAGGAACTCGTCGATGGAGGGGAGCTGTCAGCACAAAATGATCCAGACATCAGTATCTTGTTAAAGAAAGCGCACATGCATCACCGAACATTGTTTGGGCCAGATTTAACAAGTTGGTTAGATGAGATTCCAGATCAGCAACTTTGGCAAGCGATGGCAGACCTTTATCCATCAATAGTGGCACATTGGGATGAAGATGGTGATGAACGTAATCAGATTTTAGCGTTATGCCGAATCTATTTTAGTTTGAGTCTAGGTGAGATTGTTTCTAAGTCGCATGCTGCCCAATGGGTGATCGCTCAACTTGAGGAAAAAGATCAGCCTGTTTTACAACGAATGGTGCAAGAGTATAAAGGCGAGATGACAAAACAGGACTGGCCAAGTCAGCATCAGGTTTTACAGCCTATCGTTAATTTTCTGAGTCAGCACATAGAGACTTTTTTTGATAAAAAGGGCCTGAAAATAAAACAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41199","NCBI_taxonomy_name":"Acinetobacter sp. NIPH 758","NCBI_taxonomy_id":"1217712"}}}},"ARO_accession":"3004090","ARO_id":"41196","ARO_name":"ANT(3'')-IIb","CARD_short_name":"ANT(3'')-IIb","ARO_description":"ANT(3'')-IIb is a aminoglycoside nucleotidyltransferase identified in Acinetobacter spp. via horizontal gene transfer mechanisms.","ARO_category":{"41439":{"category_aro_accession":"3004275","category_aro_cvterm_id":"41439","category_aro_name":"ANT(3'')","category_aro_description":"A category of aminoglycoside O-nucleotidyltransferase enzymes with modification regiospecificity based at the 3''-hydroxyl group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics by transfer of an AMP group from an ATP substrate to the 3''-hydroxyl group of the compound.","category_aro_class_name":"AMR Gene Family"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2756":{"model_id":"2756","model_name":"NDM-17","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4073":{"protein_sequence":{"accession":"AOT73359.1","sequence":"MELPNIMHPVAKLSTALAAALMLSGCMPGEIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLLVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGLVAAQHSLTFAANGWVKPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR"},"dna_sequence":{"accession":"KX812714.1","fmin":"0","fmax":"813","strand":"+","sequence":"ATGGAATTGCCCAATATTATGCACCCGGTCGCGAAGCTGAGCACCGCATTAGCCGCTGCATTGATGCTGAGCGGGTGCATGCCCGGTGAAATCCGCCCGACGATTGGCCAGCAAATGGAAACTGGCGACCAACGGTTTGGCGATCTGGTTTTCCGCCAGCTCGCACCGAATGTCTGGCAGCACACTTCCTATCTCGACATGCCGGGTTTCGGGGCAGTCGCTTCCAACGGTTTGATCGTCAGGGATGGCGGCCGCGTGCTGTTGGTCGATACCGCCTGGACCGATGACCAGACCGCCCAGATCCTCAACTGGATCAAGCAGGAGATCAACCTGCCGGTCGCGCTGGCGGTGGTGACTCACGCGCATCAGGACAAGATGGGCGGTATGGACGCGCTGCATGCGGCGGGGATTGCGACTTATGCCAATGCGTTGTCGAACCAGCTTGCCCCGCAAGAGGGGCTGGTTGCGGCGCAACACAGCCTGACTTTCGCCGCCAATGGCTGGGTCAAACCAGCAACCGCGCCCAACTTTGGCCCGCTCAAGGTATTTTACCCCGGCCCCGGCCACACCAGTGACAATATCACCGTTGGGATCGACGGCACCGACATCGCTTTTGGTGGCTGCCTGATCAAGGACAGCAAGGCCAAGTCGCTCGGCAATCTCGGTGATGCCGACACTGAGCACTACGCCGCGTCAGCGCGCGCGTTTGGTGCGGCGTTCCCCAAGGCCAGCATGATCGTGATGAGCCATTCCGCCCCCGATAGCCGCGCCGCAATCACTCATACGGCCCGCATGGCCGACAAGCTGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3004093","ARO_id":"41201","ARO_name":"NDM-17","CARD_short_name":"NDM-17","ARO_description":"NDM-17 is a metallo-beta-lactamase isolated from Escherichia coli with enhanced carbapenemase activity compared to NDM-1.","ARO_category":{"36196":{"category_aro_accession":"3000057","category_aro_cvterm_id":"36196","category_aro_name":"NDM beta-lactamase","category_aro_description":"NDM beta-lactamases or New Delhi metallo-beta-lactamases are class B beta-lactamases that confer resistance to a broad range of antibiotics including carbapenems, cephalosporins and penicillins.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2354":{"model_id":"2354","model_name":"ADC-25","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"5443":{"protein_sequence":{"accession":"ABK34773.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVKTDQQVLTFFKDWKPKNSIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"EF016355.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAGTATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAATTTCCAGATGAAGTAAAAACAGATCAGCAAGTTTTAACATTTTTTAAAGACTGGAAACCTAAAAACTCAATCGGTGAATATCGACAATATTCAAACCCAAGCATTGGTTTATTTGGAAAAGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTAAATCCACAAAAATATCCAGCAGATATTCAACGGGCAATTAATGAAACACATCAGGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3003868","ARO_id":"40567","ARO_name":"ADC-25","CARD_short_name":"ADC-25","ARO_description":"ADC-25 is a beta-lactamase found in Acinetobacter baumannii.","ARO_category":{"40543":{"category_aro_accession":"3003846","category_aro_cvterm_id":"40543","category_aro_name":"ADC beta-lactamase without carbapenemase activity","category_aro_description":"ADC beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases with extended-spectrum resistance to cephalosporins but not to carbapenems. ADC beta-lactamases are found in Acinetobacter sp. and Oligella urethralis.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3411":{"model_id":"3411","model_name":"OXA-125","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"567"}},"model_sequences":{"sequence":{"5606":{"protein_sequence":{"accession":"ABX45064.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDKKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWNGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQHEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVRPQGNIVAFSLNLEMKKGIASSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"EU255294.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATAAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGAACGGGCAAAAAAGGCTGTTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAACATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCGGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATAGCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001447","ARO_id":"37847","ARO_name":"OXA-125","CARD_short_name":"OXA-125","ARO_description":"OXA-125 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2758":{"model_id":"2758","model_name":"LpeA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"680"}},"model_sequences":{"sequence":{"4077":{"protein_sequence":{"accession":"CAH14032.1","sequence":"MLGIQFNRGQWRSNYYWQIPVLIIAVISILFFISKKLFYSKVTPESIPNKLVEVEPIKSHNLQQTIHLLGTIHPKHATTLIAKESGMLDTLIPTGQKVTKGTLIAKINNPDLEKNLQLSLSAVELAKAQYERITPLIKSGYVSTKEVEEKKQAWIDAQKELSKTRIELDNLRFYAPFDGIIGAYKKREGAQVNAGESVVSIYDPSALVVDFDIPCSNLATLNEGQPVYVLGKRYSLSHLQKMLDEDTHMCPADVDIQCDDCLIGATTSVELLVAEKNNTIVIPFQAIFLRNSKPFVYLVKKGKIVLASVKTGLQQEDKIEIVEGLKAGQQLVTKGQERLYPEMTVDIYHPATSSS"},"dna_sequence":{"accession":"CR628336.1","fmin":"3280793","fmax":"3281861","strand":"+","sequence":"GTGTTAGGAATTCAATTCAATAGAGGTCAATGGCGGTCAAACTATTATTGGCAAATACCTGTGCTGATAATAGCTGTTATTAGCATTCTGTTTTTCATCAGTAAAAAATTATTCTACTCAAAAGTTACGCCAGAAAGCATACCTAATAAACTGGTGGAAGTTGAGCCCATTAAAAGCCACAACTTACAACAAACAATCCATTTATTAGGTACCATTCATCCAAAACACGCAACGACATTAATTGCTAAAGAATCAGGTATGTTGGACACCCTTATCCCAACTGGTCAAAAAGTCACAAAAGGGACACTTATTGCAAAAATCAACAACCCTGATCTTGAAAAAAATCTACAGCTTTCATTAAGTGCGGTAGAATTGGCAAAAGCACAATATGAACGTATCACCCCTTTAATTAAATCAGGATATGTCAGTACAAAGGAAGTCGAAGAAAAAAAACAAGCCTGGATTGATGCCCAAAAAGAATTATCAAAAACAAGGATTGAATTAGATAACCTCCGCTTTTACGCTCCTTTCGACGGAATAATTGGAGCATACAAAAAGAGAGAAGGAGCACAAGTCAATGCAGGTGAATCTGTTGTAAGTATTTACGACCCTTCTGCTTTAGTTGTCGATTTTGATATTCCTTGCAGTAATTTGGCAACTCTTAATGAAGGTCAGCCGGTTTATGTGCTGGGTAAACGGTATTCATTAAGTCATTTACAAAAAATGCTCGACGAAGACACCCACATGTGCCCTGCTGATGTTGATATTCAATGTGATGATTGTCTTATTGGTGCGACCACAAGTGTTGAGCTCCTTGTTGCGGAAAAAAATAACACTATTGTCATCCCCTTCCAGGCAATATTTTTGAGAAATAGTAAACCTTTTGTATATCTTGTAAAAAAGGGAAAGATTGTGCTTGCTTCAGTGAAAACTGGGTTGCAACAAGAGGATAAAATTGAAATTGTCGAGGGATTAAAAGCTGGGCAACAACTGGTTACAAAAGGCCAGGAACGCTTATATCCTGAAATGACCGTTGATATTTATCATCCAGCGACAAGTAGCAGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41208","NCBI_taxonomy_name":"Legionella pneumophila str. Paris","NCBI_taxonomy_id":"297246"}}}},"ARO_accession":"3004099","ARO_id":"41207","ARO_name":"LpeA","CARD_short_name":"LpeA","ARO_description":"LpeA is a subunit of the LpeAB efflux pump in Legionella pneumophila, which is homologous to AcrA in E. coli.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"36295":{"category_aro_accession":"3000156","category_aro_cvterm_id":"36295","category_aro_name":"spiramycin","category_aro_description":"Spiramycin is a 16-membered macrolide and is natural product produced by Streptomyces ambofaciens. It binds to the 50S subunit of bacterial ribosomes and inhibits peptidyl transfer activity to disrupt protein synthesis.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2759":{"model_id":"2759","model_name":"LpeB","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1700"}},"model_sequences":{"sequence":{"4076":{"protein_sequence":{"accession":"CAH14033.1","sequence":"MKLTSYFIKHPVITIILNAMIVVLGLLCLYNLSVREYPDINFPTITVSASYPNASPDLVETAITNVLEDRLAGIEGLETITSQSSAGYAQITLMFRSGTSMDRALSTTQDAVGVAKALLPPEVRSPTVERQRKSNGLPFIGISLESTSKDFGELTHYANLNLKNVFRSVQGVASVEVWGQPYTYNITLQPEKLFSFGVNVDEIVNALAKNRISLPAGNYRNKIPSTLNSELKTREDYENLLIKANSKHPILLKSLANVALETDNSQMRVRVNGHAGVVLSINKANEANPIEVSKEIRKVIKGLQQGLPKDLKINTIIDQSDFINASIKNIRSAIGEAIFLVLIIVFLFLRNIKATIIPLITIPISLLGSLLFLKLFGFSINLMTLLAMVLAIGLVVDDAIIVLENIWRHIESGLSPLDAALKGAREIGFAIIAMTFTLSSVYLPIAFIQGMLGQLFVEFAVALAGSVFISGIVALTLSPLMCANLLSASSKNWWPQFDNALEKLTKHYSNILQFILKHQKITLLTALISVVACFGFYNLISHETAPKEDRGLIGIYIPPVAGEDIGMLDNKTGKLEKKLDAIPEANNRLTFIGDWGGSIVLPLKPHAQRHRSANQIVEKLRPSFNHFPSMDPHVWSWDTGLPGVDDAGSGSELTLVISTPDHFRQLFDETEKLKSVLDKSKLFAAVNYDLRLDTMGYNIDLDYNQLAKLGLTANQVAKTIEVFFSGDKSQTFEKDGVVYNISIKGDSSPWTLNELYLTTNEGKSVSLGAITKMQPKAQPATLDHYQQMRSTTLHVQLHKGDSMAKAIEKLWGTTKEVMPQHYKLTWIGAAKAFHESSNSMLFLFFLSLAFIYAILCTQFENFTDPFIILFTVPLACSGALLFTYLFGQSLNIYTQVGLITLIGLISKHGILIVEFANKLHKDGASLPEAIQKSAALRLRPILMTTGAMVFGAIPLVLSHDAGSESRHAIGTVLISGLGLGTLFTLFVLPAVYNIIKSKLIDMQKTGGKKRCSKE"},"dna_sequence":{"accession":"CR628336.1","fmin":"3281865","fmax":"3284910","strand":"+","sequence":"ATGAAACTCACCAGCTATTTCATCAAACATCCTGTAATCACCATCATCTTAAACGCCATGATTGTTGTTCTGGGGTTATTATGTCTCTATAATTTATCCGTTAGGGAATATCCTGATATCAATTTTCCTACAATAACTGTTTCAGCAAGCTACCCCAACGCCAGTCCCGATTTAGTTGAAACCGCAATAACCAATGTTCTGGAGGACCGTCTTGCAGGTATAGAAGGGTTAGAAACAATTACGTCGCAATCAAGTGCAGGCTATGCGCAAATCACCTTGATGTTTCGTTCCGGAACATCCATGGATAGAGCACTGAGTACCACTCAAGACGCCGTAGGAGTAGCCAAAGCACTTCTGCCACCGGAGGTAAGATCGCCAACAGTTGAACGCCAACGCAAATCCAATGGCCTTCCTTTTATTGGGATTTCATTGGAATCAACATCCAAAGACTTTGGTGAGCTGACTCATTACGCTAATCTTAATTTAAAAAATGTCTTTCGCAGTGTGCAAGGTGTTGCTTCCGTTGAAGTATGGGGGCAACCCTATACATACAACATTACCCTTCAACCTGAAAAATTATTTTCTTTTGGAGTTAATGTTGATGAAATAGTGAATGCGCTCGCAAAAAATCGTATTTCGTTGCCCGCAGGTAATTATAGAAATAAAATTCCCAGTACTCTTAATTCTGAGCTGAAAACCCGGGAAGATTATGAGAATCTTTTAATCAAGGCAAATTCCAAACATCCCATTTTACTCAAATCACTGGCTAATGTCGCATTGGAAACCGATAACTCACAAATGCGAGTTCGCGTTAATGGGCACGCTGGTGTTGTGCTTTCTATCAATAAAGCGAATGAAGCCAATCCTATTGAAGTCTCTAAAGAAATTAGAAAAGTGATTAAAGGATTACAACAAGGGTTGCCCAAGGATCTGAAAATAAACACTATTATTGATCAATCGGATTTTATTAATGCCTCCATTAAAAACATTAGATCCGCGATTGGTGAAGCCATTTTTTTAGTCTTAATCATAGTCTTCCTTTTTTTACGTAATATTAAAGCCACCATCATCCCTCTAATTACCATTCCAATTTCATTATTGGGGTCCTTGCTTTTCCTTAAATTGTTTGGTTTTTCAATCAATTTAATGACCTTACTGGCTATGGTATTGGCAATCGGTTTGGTTGTAGACGATGCGATTATTGTCTTGGAAAACATTTGGCGTCATATTGAAAGCGGATTATCTCCTTTGGATGCTGCGCTTAAAGGAGCACGTGAAATTGGCTTCGCCATTATAGCGATGACATTTACCCTTAGCAGTGTTTATTTGCCTATAGCCTTTATCCAGGGGATGCTGGGACAGCTCTTCGTTGAATTTGCTGTTGCTCTGGCAGGCAGTGTTTTCATTTCGGGGATTGTTGCCCTGACACTTTCACCATTGATGTGTGCCAACCTTTTGAGTGCATCTTCTAAAAACTGGTGGCCACAATTCGATAATGCTCTTGAAAAGTTAACTAAACATTACTCCAATATTTTACAATTCATTCTGAAACACCAAAAGATTACTTTGCTAACAGCTCTAATTTCTGTCGTTGCTTGCTTTGGATTTTATAATTTAATTAGCCATGAAACCGCTCCTAAAGAAGATCGAGGTTTAATAGGTATTTATATCCCTCCTGTAGCAGGAGAAGACATAGGGATGTTGGACAACAAAACAGGAAAACTTGAAAAAAAACTAGATGCCATCCCCGAGGCAAATAATCGCCTGACTTTTATTGGTGACTGGGGCGGGTCAATAGTACTGCCATTAAAACCTCATGCTCAACGTCATCGAAGTGCGAACCAGATTGTTGAGAAATTAAGACCTTCTTTTAACCACTTCCCCTCCATGGATCCTCATGTATGGAGTTGGGATACAGGCTTACCAGGAGTTGATGATGCCGGGAGTGGATCTGAATTGACTCTGGTTATTTCTACCCCAGACCATTTCAGGCAATTATTTGATGAAACTGAAAAATTAAAAAGTGTTCTAGACAAGAGCAAATTATTTGCAGCAGTGAACTATGACCTTCGCCTTGATACCATGGGATACAATATAGACCTTGATTATAACCAACTGGCGAAACTTGGACTGACAGCAAATCAGGTGGCAAAGACGATTGAGGTATTTTTCAGTGGCGACAAGTCACAAACCTTTGAAAAAGATGGGGTCGTTTATAATATATCGATTAAAGGAGATTCCTCCCCCTGGACTTTGAATGAACTTTATTTAACTACAAATGAAGGGAAGTCTGTTTCATTGGGAGCTATTACCAAAATGCAGCCCAAGGCTCAACCGGCAACTCTTGATCATTATCAGCAAATGCGTTCGACCACTCTCCATGTCCAATTACATAAGGGAGACTCTATGGCAAAGGCTATTGAAAAATTATGGGGCACTACCAAAGAAGTGATGCCTCAACACTATAAACTGACCTGGATTGGTGCGGCCAAAGCATTCCATGAATCTTCCAATTCCATGTTATTTTTGTTTTTCTTATCTTTGGCTTTCATCTATGCCATTTTATGCACACAATTCGAGAATTTTACTGACCCCTTCATTATTCTATTCACTGTACCACTAGCCTGCTCGGGCGCCTTATTATTCACTTATTTATTTGGACAATCCTTAAACATTTATACTCAGGTAGGTTTGATTACTTTAATCGGGCTCATTAGCAAACACGGTATTTTAATAGTGGAATTTGCTAATAAACTTCATAAAGATGGTGCTTCGTTGCCAGAAGCTATACAGAAATCAGCTGCATTGCGTTTACGGCCTATATTAATGACAACTGGCGCCATGGTTTTTGGCGCCATCCCTTTGGTATTATCGCATGATGCGGGTTCTGAATCCCGGCATGCCATAGGAACTGTATTGATTAGCGGGCTCGGTCTTGGAACACTATTTACCCTATTTGTTTTGCCTGCGGTTTACAACATCATCAAATCCAAACTAATTGATATGCAAAAAACAGGGGGCAAAAAACGGTGCAGCAAAGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41208","NCBI_taxonomy_name":"Legionella pneumophila str. Paris","NCBI_taxonomy_id":"297246"}}}},"ARO_accession":"3004100","ARO_id":"41209","ARO_name":"LpeB","CARD_short_name":"LpeB","ARO_description":"LpeB is a subunit of the LpeAB efflux pump in Legionella pneumophila, which is homologous to AcrB in E. coli.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"36295":{"category_aro_accession":"3000156","category_aro_cvterm_id":"36295","category_aro_name":"spiramycin","category_aro_description":"Spiramycin is a 16-membered macrolide and is natural product produced by Streptomyces ambofaciens. It binds to the 50S subunit of bacterial ribosomes and inhibits peptidyl transfer activity to disrupt protein synthesis.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2760":{"model_id":"2760","model_name":"MexGHI-OpmD","model_type":"efflux pump system meta-model","model_type_id":"41112","model_description":"Efflux Pump System Meta-Models (EPS) are dedicated to efflux complexes and their regulators, such as AcrAB-TolC. Using the efflux pump components parameter, this model type simply includes a list of detection models for each component of the complex. This model type is still under development and not currently supported by the Resistance Gene Identifier (RGI) software.","model_param":{"41141":{"param_type":"efflux pump components","param_description":"Association of proteins within efflux protein complexes or regulatory networks are encoded by the efflux pump components parameter: model_id,model_id,model_id, etc.","param_type_id":"41141","param_value":{"7742":"995,1344,1647,442"}},"snp":{"Curated-R":{"7742":"A205T"}}},"ARO_accession":"3000799","ARO_id":"37179","ARO_name":"MexGHI-OpmD","CARD_short_name":"MexGHI-OpmD","ARO_description":"MexGHI-OpmD is an efflux complex expressed in Pseudomonas aeruginosa. MexG is a membrane protein required for drug export; MexH is the membrane fusion protein; MexI is the inner membrane transporter; and MexJ is the outer membrane channel protein. MexGHI-OpmD confers resistance to vanadium, norfloxacin, and acriflavin.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35963":{"category_aro_accession":"0000045","category_aro_cvterm_id":"35963","category_aro_name":"acriflavine","category_aro_description":"Acriflavine is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"43746":{"category_aro_accession":"3005386","category_aro_cvterm_id":"43746","category_aro_name":"disinfecting agents and antiseptics","category_aro_description":"Disinfectants that can also interact with antimicrobial resistance mechanisms, e.g. molecule efflux, and thus are the targets of disinfectant resistance.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2761":{"model_id":"2761","model_name":"MexPQ-OpmE","model_type":"efflux pump system meta-model","model_type_id":"41112","model_description":"Efflux Pump System Meta-Models (EPS) are dedicated to efflux complexes and their regulators, such as AcrAB-TolC. Using the efflux pump components parameter, this model type simply includes a list of detection models for each component of the complex. This model type is still under development and not currently supported by the Resistance Gene Identifier (RGI) software.","model_param":{"41141":{"param_type":"efflux pump components","param_description":"Association of proteins within efflux protein complexes or regulatory networks are encoded by the efflux pump components parameter: model_id,model_id,model_id, etc.","param_type_id":"41141","param_value":{"7743":"2211,2212,2213"}},"snp":{"Curated-R":{"7743":"A205T"}}},"ARO_accession":"3003697","ARO_id":"40349","ARO_name":"MexPQ-OpmE","CARD_short_name":"MexPQ-OpmE","ARO_description":"MexPQ-OpmE multidrug efflux pump expressed in Pseudomonas aeruginosa. MexP is the membrane fusion protein; MexQ is the inner membrane transporter; and OpmE is the outer membrane channel.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35963":{"category_aro_accession":"0000045","category_aro_cvterm_id":"35963","category_aro_name":"acriflavine","category_aro_description":"Acriflavine is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36309":{"category_aro_accession":"3000170","category_aro_cvterm_id":"36309","category_aro_name":"imipenem","category_aro_description":"Imipenem is a broad-spectrum antibiotic and is usually taken with cilastatin, which prevents hydrolysis of imipenem by renal dehydropeptidase-I. It is resistant to hydrolysis by most other beta-lactamases. Notable exceptions are the KPC beta-lactamases and Ambler Class B enzymes.","category_aro_class_name":"Antibiotic"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36595":{"category_aro_accession":"3000456","category_aro_cvterm_id":"36595","category_aro_name":"thiamphenicol","category_aro_description":"Derivative of Chloramphenicol. The nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3).","category_aro_class_name":"Antibiotic"},"37626":{"category_aro_accession":"3001227","category_aro_cvterm_id":"37626","category_aro_name":"kitasamycin","category_aro_description":"Kitasamycin is a macrolide antibiotic and is produced by Streptoverticillium kitasatoense. The drug has antimicrobial activity against a wide spectrum of pathogens.","category_aro_class_name":"Antibiotic"},"40353":{"category_aro_accession":"3003701","category_aro_cvterm_id":"40353","category_aro_name":"rokitamycin","category_aro_description":"Rokitamycin is a macrolide antibiotic. Synthesized from strains of Streptomyces kitasatoensis.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"43746":{"category_aro_accession":"3005386","category_aro_cvterm_id":"43746","category_aro_name":"disinfecting agents and antiseptics","category_aro_description":"Disinfectants that can also interact with antimicrobial resistance mechanisms, e.g. molecule efflux, and thus are the targets of disinfectant resistance.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2901":{"model_id":"2901","model_name":"CFE-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"4464":{"protein_sequence":{"accession":"AWX35642.1","sequence":"MMKKSICCALLVTASLSTFAADKTEQQIADIVNRTITPLMQEQAIPGMRFAIIYQGKPYYFTWGKADIANDRPVTRQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTQYWPKLTGKQWLGISLLHLATYTAGGLPLQVPDDVTDKAALLRFYQNWQPQWAPGAKRLYANPSIGLFGALAVKPSGMGYEEAMTKRVLQPLKLAHTWITVPQSEQKDYALGYREGRPVHVSPGQLDAEAYGVKSSLVDMTRWIQANMDASQVQEKTLRQGIEIAQARYWHIGDMYQGLGWEMVNWPVNADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGTSGGFGTYVALVPEKNLVGMMLANKSYPKPARVEAAWRILEKLQ"},"dna_sequence":{"accession":"MF543129.1","fmin":"2483","fmax":"3629","strand":"-","sequence":"ATGATGAAAAAATCGATTTGCTGCGCGTTGCTGGTCACAGCCTCTCTGTCAACGTTTGCCGCCGACAAAACAGAACAACAGATTGCCGATATCGTAAACCGTACCATCACACCGCTGATGCAAGAACAGGCTATTCCGGGTATGCGCTTCGCAATTATCTACCAGGGAAAACCCTATTACTTTACCTGGGGGAAAGCCGATATCGCCAATGACCGCCCCGTCACCCGGCAAACGCTGTTTGAGCTTGGATCGGTAAGTAAGACGTTTAACGGTGTGCTGGGCGGCGATGCTATCGCCCGTGGTGAAATTAAGCTCAGCGATCCGGTCACCCAATACTGGCCCAAATTAACTGGCAAACAATGGCTGGGTATCAGCCTGCTGCATCTGGCCACCTATACGGCGGGTGGCCTGCCGCTTCAGGTACCTGACGACGTTACAGATAAAGCGGCATTACTGCGCTTTTATCAAAACTGGCAGCCGCAATGGGCCCCGGGCGCTAAACGCCTGTATGCTAACCCAAGTATTGGTCTGTTTGGCGCACTGGCGGTGAAACCTTCAGGAATGGGCTATGAAGAGGCGATGACCAAACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCACAGAGCGAACAAAAGGATTATGCCTTGGGTTATCGCGAAGGAAGGCCCGTGCACGTATCTCCGGGCCAGCTTGATGCCGAAGCCTACGGGGTGAAATCCAGCCTTGTCGATATGACTCGCTGGATTCAGGCCAACATGGACGCCAGCCAGGTGCAGGAGAAAACGCTCCGACAGGGAATTGAAATTGCGCAGGCTCGTTACTGGCATATTGGCGATATGTACCAGGGATTAGGTTGGGAGATGGTCAACTGGCCGGTGAATGCCGACTCGATAATCAACGGTAGCGACAGTAAAGTCGCGTTAGCGGCGCTTCCCGCCGTTGAGGTCAATCCGCCCGCCCCTGCAGTGAAAGCCTCATGGGTGCACAAAACCGGCACTTCCGGCGGATTTGGCACGTACGTTGCGTTGGTTCCGGAAAAAAATCTCGTCGGCATGATGCTGGCAAACAAAAGCTACCCAAAGCCTGCTCGCGTCGAGGCCGCCTGGCGCATTCTTGAAAAATTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3004464","ARO_id":"41680","ARO_name":"CFE-2","CARD_short_name":"CFE-2","ARO_description":"CFE-2 is a plasmid-encoded AmpC beta-lactamase first described from Citrobacter freundii by Chen et al. 2018.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2762":{"model_id":"2762","model_name":"MexMN-OprM","model_type":"efflux pump system meta-model","model_type_id":"41112","model_description":"Efflux Pump System Meta-Models (EPS) are dedicated to efflux complexes and their regulators, such as AcrAB-TolC. Using the efflux pump components parameter, this model type simply includes a list of detection models for each component of the complex. This model type is still under development and not currently supported by the Resistance Gene Identifier (RGI) software.","model_param":{"41141":{"param_type":"efflux pump components","param_description":"Association of proteins within efflux protein complexes or regulatory networks are encoded by the efflux pump components parameter: model_id,model_id,model_id, etc.","param_type_id":"41141","param_value":{"7744":"2216,2217,1305"}},"snp":{"Curated-R":{"7744":"A205T"}}},"ARO_accession":"3003703","ARO_id":"40357","ARO_name":"MexMN-OprM","CARD_short_name":"MexMN-OprM","ARO_description":"MexMN-OprM is a multidrug efflux pump expressed in Pseudomonas aeruginosa. MexM is the membrane fusion protein; MexN is the inner membrane transporter; and OprM is the outer membrane channel.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36595":{"category_aro_accession":"3000456","category_aro_cvterm_id":"36595","category_aro_name":"thiamphenicol","category_aro_description":"Derivative of Chloramphenicol. The nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3).","category_aro_class_name":"Antibiotic"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2763":{"model_id":"2763","model_name":"MdtABC-TolC","model_type":"efflux pump system meta-model","model_type_id":"41112","model_description":"Efflux Pump System Meta-Models (EPS) are dedicated to efflux complexes and their regulators, such as AcrAB-TolC. Using the efflux pump components parameter, this model type simply includes a list of detection models for each component of the complex. This model type is still under development and not currently supported by the Resistance Gene Identifier (RGI) software.","model_param":{"41141":{"param_type":"efflux pump components","param_description":"Association of proteins within efflux protein complexes or regulatory networks are encoded by the efflux pump components parameter: model_id,model_id,model_id, etc.","param_type_id":"41141","param_value":{"7745":"387,820,1315,826,986,1337,152,2764"}},"snp":{"Curated-R":{"7745":"A205T"}}},"ARO_accession":"3000787","ARO_id":"37167","ARO_name":"MdtABC-TolC","CARD_short_name":"MdtABC-TolC","ARO_description":"MdtABC-TolC is a multidrug efflux system in Gram-negative bacteria, including E. coli and Salmonella. MdtA is a membrane fusion protein; TolC is the outer membrane channel; MdtBC form a drug transporter. In the absence of MdtB, the MdtAC-TolC has narrower drug specificity, leading to the loss of novobiocin resistance, for example.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"36250":{"category_aro_accession":"3000111","category_aro_cvterm_id":"36250","category_aro_name":"novobiocin","category_aro_description":"Novobiocin is an aminocoumarin antibiotic produced by Streptomyces spheroides and Streptomyces niveus, and binds DNA gyrase subunit B inhibiting ATP-dependent DNA supercoiling.","category_aro_class_name":"Antibiotic"},"36242":{"category_aro_accession":"3000103","category_aro_cvterm_id":"36242","category_aro_name":"aminocoumarin antibiotic","category_aro_description":"Aminocoumarin antibiotics bind DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2765":{"model_id":"2765","model_name":"EmrAB-TolC","model_type":"efflux pump system meta-model","model_type_id":"41112","model_description":"Efflux Pump System Meta-Models (EPS) are dedicated to efflux complexes and their regulators, such as AcrAB-TolC. Using the efflux pump components parameter, this model type simply includes a list of detection models for each component of the complex. This model type is still under development and not currently supported by the Resistance Gene Identifier (RGI) software.","model_param":{"41141":{"param_type":"efflux pump components","param_description":"Association of proteins within efflux protein complexes or regulatory networks are encoded by the efflux pump components parameter: model_id,model_id,model_id, etc.","param_type_id":"41141","param_value":{"7747":"1757,1847,826,1330"}},"snp":{"Curated-R":{"7747":"A205T"}}},"ARO_accession":"3000344","ARO_id":"36483","ARO_name":"EmrAB-TolC","CARD_short_name":"EmrAB-TolC","ARO_description":"EmrAB-TolC is a multidrug efflux system found in E. coli. EmrB is the electrochemical-gradient powered transporter; EmrA is the linker; and TolC is the outer membrane channel. It confers resistance to nalidixic acid and thiolactomycin.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2766":{"model_id":"2766","model_name":"EmrKY-TolC","model_type":"efflux pump system meta-model","model_type_id":"41112","model_description":"Efflux Pump System Meta-Models (EPS) are dedicated to efflux complexes and their regulators, such as AcrAB-TolC. Using the efflux pump components parameter, this model type simply includes a list of detection models for each component of the complex. This model type is still under development and not currently supported by the Resistance Gene Identifier (RGI) software.","model_param":{"41141":{"param_type":"efflux pump components","param_description":"Association of proteins within efflux protein complexes or regulatory networks are encoded by the efflux pump components parameter: model_id,model_id,model_id, etc.","param_type_id":"41141","param_value":{"7748":"609,540,826,1318,1015,1248"}},"snp":{"Curated-R":{"7748":"A205T"}}},"ARO_accession":"3000373","ARO_id":"36512","ARO_name":"EmrKY-TolC","CARD_short_name":"EmrKY-TolC","ARO_description":"EmrKY is a homolog of EmrAB found in E. coli. Together with TolC, it is a tripartite multidrug transporter.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"3434":{"model_id":"3434","model_name":"OXA-267","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"560"}},"model_sequences":{"sequence":{"5630":{"protein_sequence":{"accession":"ENV93423.1","sequence":"MYKKALIAATSILFLSACSSNTVKQHQIHSISANKNSEEIKSLFDQAQTMGVLVIKRGQTEEIYGNDLKRASTAYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMSKEVKRIGFGNANIGSKVDDFWLVGPLKITPQQETLFAYQLAHKTLPFSQDVQEQVQSMVFIEEKNGSKIYAKSGWGWDVEPQVGWLTGWVVQSQGEIVAFSLNLEMKKGTPSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"APQH01000006.1","fmin":"1454173","fmax":"1454995","strand":"+","sequence":"ATGTATAAAAAAGCCCTTATCGCTGCAACAAGTATCCTATTTTTATCCGCCTGTTCTTCCAATACGGTAAAACAACATCAAATACACTCTATTTCTGCCAATAAAAATTCAGAAGAAATTAAATCACTGTTTGATCAGGCACAGACCATGGGTGTTTTGGTGATTAAGCGAGGGCAAACAGAAGAAATTTATGGCAATGATCTTAAAAGAGCATCAACCGCCTATGTTCCCGCTTCTACCTTTAAAATGTTAAATGCTTTAATTGGACTTGAACATCATAAGGCAACTACAACTGAAGTATTTAAATGGGATGGGCAAAAACGTTTATTTCCTGATTGGGAAAAGGACATGACACTGGGTGATGCCATGAAAGCTTCTGCAATTCCAGTTTACCAAGAATTAGCCCGACGAATTGGACTTGACCTTATGTCCAAAGAGGTGAAACGAATTGGTTTCGGTAATGCTAACATTGGCTCAAAAGTAGATGATTTCTGGCTTGTTGGCCCTCTAAAAATTACACCTCAACAAGAAACCCTATTTGCTTATCAATTAGCTCATAAAACGCTTCCATTTAGCCAAGATGTACAAGAACAAGTTCAATCAATGGTGTTCATAGAGGAAAAAAATGGAAGTAAAATTTATGCCAAAAGTGGTTGGGGATGGGATGTTGAACCACAAGTTGGTTGGTTAACAGGCTGGGTCGTTCAATCACAAGGAGAAATTGTCGCATTCTCACTTAATTTAGAAATGAAAAAAGGAACTCCTAGCTCTATTCGCAAAGAAATTGCTTATAAAGGCTTAGAACAACTGGGTATCTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42797","NCBI_taxonomy_name":"Acinetobacter calcoaceticus ANC 3680","NCBI_taxonomy_id":"1217653"}}}},"ARO_accession":"3001723","ARO_id":"38123","ARO_name":"OXA-267","CARD_short_name":"OXA-267","ARO_description":"OXA-267 is a beta-lactamase found in Acinetobacter spp.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46495":{"category_aro_accession":"3007706","category_aro_cvterm_id":"46495","category_aro_name":"OXA-213-like beta-lactamase","category_aro_description":"OXA-213-like enzymes have been identified to be intrinsic to A. calcoaceticus and have been subsequently detected in A. pittii. Phylogenetic analysis of OXA-213-like proteins identified two distinct subgroups within the OXA family. The first group was linked to A. pittii and the second group to A. calcoaceticus. The carbapenemase activity of these OXAs may be related to the species-dependent effect.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2768":{"model_id":"2768","model_name":"MdtEF-TolC","model_type":"efflux pump system meta-model","model_type_id":"41112","model_description":"Efflux Pump System Meta-Models (EPS) are dedicated to efflux complexes and their regulators, such as AcrAB-TolC. Using the efflux pump components parameter, this model type simply includes a list of detection models for each component of the complex. This model type is still under development and not currently supported by the Resistance Gene Identifier (RGI) software.","model_param":{"41141":{"param_type":"efflux pump components","param_description":"Association of proteins within efflux protein complexes or regulatory networks are encoded by the efflux pump components parameter: model_id,model_id,model_id, etc.","param_type_id":"41141","param_value":{"7750":"1903,121,826,869,1015,1318,91,1248,2324"}},"snp":{"Curated-R":{"7750":"A205T"}}},"ARO_accession":"3000788","ARO_id":"37168","ARO_name":"MdtEF-TolC","CARD_short_name":"MdtEF-TolC","ARO_description":"MdtEF-TolC is a multidrug efflux complex in Gram-negative bacteria, including E. coli. MdtE is the membrane fusion protein, MdtF is the inner membrane transporter, while TolC is the outer membrane channel.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35930":{"category_aro_accession":"0000011","category_aro_cvterm_id":"35930","category_aro_name":"cloxacillin","category_aro_description":"Cloxacillin is a semisynthetic, isoxazolyl penicillin derivative in the beta-lactam class of antibiotics. It interferes with peptidogylcan synthesis and is commonly used for treating penicillin-resistant Staphylococcus aureus infections.","category_aro_class_name":"Antibiotic"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2858":{"model_id":"2858","model_name":"PDC-79","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6230":{"protein_sequence":{"accession":"AKR18019.1","sequence":"GEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALTQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAKGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"KR057748.1","fmin":"0","fmax":"1116","strand":"+","sequence":"GGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGACCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTTCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCAAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3004342","ARO_id":"41510","ARO_name":"PDC-79","CARD_short_name":"PDC-79","ARO_description":"An AmpC-like beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2859":{"model_id":"2859","model_name":"PDC-80","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6137":{"protein_sequence":{"accession":"ANJ78206.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALTQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAGGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"KX354370.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGACCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGGAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCACTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3004343","ARO_id":"41511","ARO_name":"PDC-80","CARD_short_name":"PDC-80","ARO_description":"An AmpC-like beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2769":{"model_id":"2769","model_name":"MdtNOP","model_type":"efflux pump system meta-model","model_type_id":"41112","model_description":"Efflux Pump System Meta-Models (EPS) are dedicated to efflux complexes and their regulators, such as AcrAB-TolC. Using the efflux pump components parameter, this model type simply includes a list of detection models for each component of the complex. This model type is still under development and not currently supported by the Resistance Gene Identifier (RGI) software.","model_param":{"41141":{"param_type":"efflux pump components","param_description":"Association of proteins within efflux protein complexes or regulatory networks are encoded by the efflux pump components parameter: model_id,model_id,model_id, etc.","param_type_id":"41141","param_value":{"7752":"1442,2056,45,2330"}},"snp":{"Curated-R":{"7752":"A205T"}}},"ARO_accession":"3004101","ARO_id":"41212","ARO_name":"MdtNOP","CARD_short_name":"MdtNOP","ARO_description":"MdtNOP is a MFS efflux pump protein found in E. coli. The deletion of mdtP from strain W3110 resulted in increased susceptibility to acriflavin, puromycin, and tetraphenylarsonium chloride. An E. coli mdtN null mutant is more sensitive to sulfur drugs than wild type.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35963":{"category_aro_accession":"0000045","category_aro_cvterm_id":"35963","category_aro_name":"acriflavine","category_aro_description":"Acriflavine is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish.","category_aro_class_name":"Antibiotic"},"35965":{"category_aro_accession":"0000047","category_aro_cvterm_id":"35965","category_aro_name":"puromycin","category_aro_description":"Puromycin is an aminonucleoside antibiotic, derived from Streptomyces alboniger, that causes premature chain termination during ribosomal protein translation.","category_aro_class_name":"Antibiotic"},"36174":{"category_aro_accession":"3000034","category_aro_cvterm_id":"36174","category_aro_name":"nucleoside antibiotic","category_aro_description":"Nucleoside antibiotics are made of modified nucleosides and nucleotides with wide-ranging activities and means of antibacterial effects. This drug class includes aminonucleoside antibiotics, which contain an amino group.","category_aro_class_name":"Drug Class"},"43746":{"category_aro_accession":"3005386","category_aro_cvterm_id":"43746","category_aro_name":"disinfecting agents and antiseptics","category_aro_description":"Disinfectants that can also interact with antimicrobial resistance mechanisms, e.g. molecule efflux, and thus are the targets of disinfectant resistance.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2770":{"model_id":"2770","model_name":"kamB","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"4082":{"protein_sequence":{"accession":"WP_063964000.1","sequence":"MRRVVGKRVQEFSDAEFEQLRSQYDDVVLDVGTGDGKHPYKVARQNPSRLVVALDADKSRMEKISAKAAAKPAKGGLPNLLYLWATAERLPPLSGVGELHVLMPWGSLLRGVLGSSPEMLRGMAAVCRPGASFLVALNLHAWRPSVPEVGEHPEPTPDSADEWLAPRYAEAGWKLADCRYLEPEEVAGLETSWTRRLHSSRDRFDVLALTGTISP"},"dna_sequence":{"accession":"NG_050561.1","fmin":"100","fmax":"748","strand":"+","sequence":"ATGCGCCGCGTGGTGGGCAAGCGGGTCCAGGAGTTCTCCGACGCCGAGTTCGAGCAGCTACGGAGTCAGTACGACGACGTGGTGCTCGACGTCGGCACCGGCGACGGGAAGCATCCGTACAAGGTCGCCCGCCAGAACCCCTCCCGGCTGGTGGTGGCGCTCGACGCCGACAAGAGCCGGATGGAGAAGATCTCGGCGAAGGCGGCGGCCAAGCCCGCGAAGGGCGGCCTGCCCAACCTGCTGTACCTGTGGGCCACCGCCGAGCGGCTCCCCCCGTTGTCGGGGGTGGGCGAGCTGCACGTCCTCATGCCGTGGGGCAGCCTGCTGCGCGGGGTCCTCGGCTCCTCGCCGGAGATGCTGCGCGGGATGGCGGCGGTGTGCCGGCCGGGCGCGTCCTTCCTGGTCGCGCTGAACCTGCACGCCTGGCGGCCCTCGGTGCCGGAGGTGGGCGAGCACCCCGAGCCCACCCCGGACTCCGCCGACGAGTGGCTGGCGCCCCGCTACGCCGAGGCCGGGTGGAAGCTCGCCGACTGCCGCTACCTGGAGCCGGAGGAGGTGGCGGGTCTGGAGACCTCCTGGACCCGCCGTCTGCACTCCTCCCGCGACCGGTTCGACGTGCTCGCGCTCACCGGCACGATCAGTCCGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41214","NCBI_taxonomy_name":"Streptoalloteichus tenebrarius","NCBI_taxonomy_id":"1933"}}}},"ARO_accession":"3004102","ARO_id":"41213","ARO_name":"kamB","CARD_short_name":"kamB","ARO_description":"Methyltransferase enzyme first described in Streptoalloteichus tenebrarius. Confers resistance to aminoglycoside antibiotics (esp. apramycin) through methylation of the 16S rRNA at A1408, thereby modifying the antibiotic target.","ARO_category":{"41436":{"category_aro_accession":"3004272","category_aro_cvterm_id":"41436","category_aro_name":"16S rRNA methyltransferase (A1408)","category_aro_description":"Methyltransferases that methylate the A1408 position of 16S rRNA, which is part of an aminoglycoside binding site.","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35955":{"category_aro_accession":"0000037","category_aro_cvterm_id":"35955","category_aro_name":"apramycin","category_aro_description":"Apramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections in animals. Apramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2771":{"model_id":"2771","model_name":"QepA2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"850"}},"model_sequences":{"sequence":{"8346":{"protein_sequence":{"accession":"ACF70723.1","sequence":"MSATLHDTAADRRKATRREWIGLAVVALPCLVYAMDLTVLNLALPVLSRELQPSSAQLLWILDIYGFFVAGFLITMGTLGDRIGRRRLLLIGAAFFAFGSVLAALADTAALLIAARALLGLAGATIAPSTMALIRNMFHDPRQRQFAIGVWIAAFSLGSAIGPLVGGVLLEFFHWGAVFWLNVPVMLLTLALGPRFLPEYRDPDAGHLDLASVLLSLAAVLLTIYGLKQLAEHGAGLASMAALLAGLAVGALFLRRQGHIAYPLLDLRLFAHAPFRAALAAYALAALAMFGVYIFMTQYLQLVLGLSPLQAGLATLPWSLCFVIGSLLSPQLAARWPAARILVVGLSAAAFGFAVLGLGQGLWWLVPATIVMGLGLAPVFTIGNEIIITSAPSERAGAASALSETVSEFSGALGIALFGSVGLVVYRQALTSAALPGLPADALQAAGASLGGAVHLADTLPAWQGAALLAAARAGFTDALQATAWAGAVLVLVAAGLVARLLRKRPALASG"},"dna_sequence":{"accession":"EU847537.1","fmin":"1671","fmax":"3207","strand":"+","sequence":"ATGTCCGCCACGCTCCACGACACCGCAGCGGATCGTCGGAAGGCCACCCGCCGCGAATGGATCGGCCTGGCCGTGGTCGCCCTGCCGTGCCTGGTCTACGCCATGGACCTCACGGTGCTGAACCTGGCGCTGCCGGTGCTCAGCCGTGAACTGCAGCCCTCCAGCGCCCAGCTTCTCTGGATCCTGGACATCTACGGCTTCTTCGTCGCCGGCTTCCTGATCACCATGGGCACGCTGGGCGACCGCATCGGCCGGCGCCGGCTGTTGTTGATCGGCGCGGCGTTCTTCGCATTCGGCTCGGTGCTCGCGGCGCTGGCCGATACCGCCGCGCTGTTGATCGCGGCGCGCGCCTTGCTCGGCCTGGCCGGCGCCACCATCGCGCCGTCCACCATGGCGCTGATCCGCAACATGTTCCACGACCCGCGCCAGCGCCAGTTCGCCATCGGCGTGTGGATCGCCGCGTTTTCGCTGGGCAGCGCGATCGGTCCGCTGGTCGGCGGCGTGTTGCTGGAGTTCTTCCACTGGGGCGCCGTGTTCTGGCTCAACGTGCCGGTGATGCTGCTGACGCTGGCGCTCGGCCCTCGCTTCCTGCCCGAGTATCGTGATCCGGACGCGGGGCACCTGGACCTGGCCAGCGTGCTGCTGTCGCTGGCGGCGGTGCTGCTGACGATCTACGGGCTCAAGCAGTTGGCCGAGCATGGAGCGGGCCTCGCCTCGATGGCTGCGCTGCTGGCCGGGCTGGCGGTCGGGGCGCTGTTCCTGCGCCGCCAGGGCCACATCGCCTACCCGCTGCTGGACCTGCGGCTGTTCGCGCACGCGCCGTTCCGCGCGGCGCTGGCGGCGTATGCGCTGGCCGCGCTGGCCATGTTCGGCGTCTACATCTTCATGACGCAGTACCTGCAGCTCGTGCTGGGGCTGTCGCCGCTGCAGGCCGGGCTGGCCACGCTGCCCTGGTCCCTGTGCTTCGTCATCGGTTCGCTGTTGTCGCCGCAGCTCGCGGCGCGCTGGCCGGCGGCGCGCATCCTCGTCGTGGGCCTGTCGGCAGCGGCGTTCGGCTTCGCCGTGCTGGGGCTGGGGCAGGGCCTGTGGTGGCTGGTGCCGGCCACGATCGTCATGGGCCTGGGCCTGGCGCCGGTGTTCACCATCGGCAACGAGATCATCATCACCAGCGCGCCGTCCGAGCGCGCGGGCGCGGCCTCGGCCTTGTCGGAGACGGTGTCCGAATTCAGCGGCGCGCTGGGCATCGCGCTGTTCGGCAGCGTCGGCCTGGTGGTCTACCGGCAGGCGCTGACCAGCGCGGCGCTGCCCGGCCTGCCGGCCGATGCGCTGCAGGCGGCCGGTGCCTCGCTCGGGGGCGCCGTGCACCTGGCCGACACCCTGCCGGCGTGGCAGGGCGCGGCCTTGCTGGCGGCCGCACGCGCGGGCTTCACCGATGCGCTGCAGGCCACGGCCTGGGCCGGCGCGGTGCTGGTGCTGGTGGCCGCTGGGCTGGTGGCGCGCCTGCTGCGCAAGCGCCCAGCGCTCGCATCTGGTTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3004103","ARO_id":"41215","ARO_name":"QepA2","CARD_short_name":"QepA2","ARO_description":"QepA2 is a plasmid-mediated quinolone resistance pump found in an Escherichia coli isolate from France.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"3464":{"model_id":"3464","model_name":"OXA-302","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"560"}},"model_sequences":{"sequence":{"5659":{"protein_sequence":{"accession":"ENX18112.1","sequence":"MMMSKKLKCLALLTPCILILQLTACQSVSQQKQQLSTQTNEQQQISSLFQSAQTKGVLVIYDGKKIQSYGNDLNRAEQRYIPASTFKILNALIGIQYHKTTPNEVFKWDGKKRTFSSWEKDLSLAEAMQASAVPVYQELARRIGLELMTREVKRVGYGNKNIGTQVDNFWLVGPLQITPVEEVRFVYALAKQKLPFDQSTQQQVKGMLLADERQGTKIYAKSGWGMDVSPQVGWWTGWIEQPNGKTIAFSLNMQMSQPEHANARKVIVYQALQELGLLAN"},"dna_sequence":{"accession":"APRT01000004.1","fmin":"76527","fmax":"77370","strand":"+","sequence":"ATGATGATGTCGAAAAAATTAAAATGTCTAGCGCTTCTTACACCCTGCATATTGATTCTTCAATTGACTGCTTGTCAAAGTGTTAGCCAGCAAAAGCAACAGCTTTCGACACAAACAAATGAACAGCAACAGATTTCAAGCTTATTTCAAAGTGCCCAAACCAAGGGAGTTTTGGTGATTTATGATGGCAAGAAAATTCAAAGTTATGGCAATGATCTTAATCGTGCAGAGCAACGTTATATTCCTGCTTCGACCTTTAAAATCTTAAACGCCTTGATTGGCATACAGTATCATAAGACCACACCAAATGAAGTGTTTAAATGGGATGGTAAAAAGCGGACTTTCAGCAGCTGGGAAAAAGATTTAAGCCTAGCTGAAGCCATGCAGGCATCGGCTGTACCTGTCTATCAGGAGCTAGCACGACGGATTGGTCTAGAACTTATGACCCGTGAGGTGAAGCGTGTGGGCTATGGCAATAAAAATATTGGCACCCAAGTCGATAATTTTTGGTTGGTCGGGCCTTTGCAAATTACACCTGTAGAAGAAGTTCGATTCGTTTATGCATTAGCAAAGCAAAAACTACCATTTGACCAGTCAACTCAACAACAAGTGAAAGGTATGTTATTGGCAGATGAGCGTCAGGGGACCAAGATTTATGCCAAGAGCGGTTGGGGCATGGACGTTAGCCCACAGGTTGGATGGTGGACCGGCTGGATTGAACAGCCAAATGGCAAAACCATTGCATTTTCACTGAATATGCAAATGAGTCAGCCTGAGCATGCAAATGCGCGTAAAGTGATTGTTTATCAAGCATTGCAAGAATTGGGATTGTTAGCGAATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42823","NCBI_taxonomy_name":"Acinetobacter sp. CIP 64.2","NCBI_taxonomy_id":"1217694"}}}},"ARO_accession":"3001757","ARO_id":"38157","ARO_name":"OXA-302","CARD_short_name":"OXA-302","ARO_description":"OXA-302 is a beta-lactamase found in Acinetobacter spp.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46503":{"category_aro_accession":"3007714","category_aro_cvterm_id":"46503","category_aro_name":"OXA-286-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-286.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2773":{"model_id":"2773","model_name":"TMB-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"350"}},"model_sequences":{"sequence":{"5515":{"protein_sequence":{"accession":"CBY88906.1","sequence":"MRPFLFLIIFISHFAFANEEIPGLEVEEIDNGVFLHKSYSRVEGWGLVSSNGLVVISGGKAFIIDTPWSESDTEKLVDWIRSKKYELAGSISTHSHEDKTAGIKWLNGKSITTYASALTNEILKREGKEQARSSFKGNEFSLMDGFLEVYYPGGGHTIDNLVVWIPSSKILYGGCFIRSLESSGLGYTGEAKIDQWPQSARNTISKYPEAKIVVPGHGKIGDFELLKHTKVLAEKASNKANHGDR"},"dna_sequence":{"accession":"FR771847.1","fmin":"15","fmax":"753","strand":"+","sequence":"ATGCGACCATTTTTATTTTTAATAATTTTTATCAGTCATTTCGCTTTTGCCAACGAAGAAATACCCGGATTGGAAGTTGAGGAAATTGACAACGGCGTTTTTTTGCACAAGTCATACAGCCGGGTGGAAGGCTGGGGCCTGGTAAGTTCAAACGGACTTGTTGTCATCAGCGGCGGAAAAGCATTCATTATTGACACTCCATGGTCGGAATCAGATACAGAAAAGCTTGTAGATTGGATACGATCAAAAAAGTATGAGCTGGCGGGAAGCATTTCTACACATTCACACGAAGACAAGACTGCCGGTATAAAATGGCTAAACGGCAAATCCATTACTACATATGCCTCAGCGCTGACTAATGAAATTCTAAAAAGAGAGGGTAAGGAGCAGGCAAGGAGCTCATTCAAAGGTAATGAATTTTCGCTGATGGACGGTTTTCTAGAAGTCTATTATCCCGGAGGCGGCCATACTATTGATAACTTAGTGGTATGGATCCCTAGTTCAAAAATATTGTATGGCGGCTGTTTCATACGTAGCTTGGAATCCAGTGGGCTAGGTTACACTGGTGAAGCTAAAATTGATCAGTGGCCACAATCCGCTAGAAATACAATTTCGAAGTATCCTGAAGCTAAGATTGTGGTGCCTGGTCATGGAAAAATTGGCGATTTCGAGTTGTTAAAACATACCAAGGTCCTTGCAGAAAAGGCCTCTAACAAGGCCAATCACGGCGACCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42688","NCBI_taxonomy_name":"Achromobacter sp. sallbros1","NCBI_taxonomy_id":"944673"}}}},"ARO_accession":"3004105","ARO_id":"41217","ARO_name":"TMB-1","CARD_short_name":"TMB-1","ARO_description":"TMB-1 is a TMB metallo-beta-lactamase found in Achromobacter sp.","ARO_category":{"41216":{"category_aro_accession":"3004104","category_aro_cvterm_id":"41216","category_aro_name":"TMB beta-lactamase","category_aro_description":"TMB-1, the first known member of the Tripoli metallo-beta-lactamase family (TMB) was isolated from Achromobacter xylosoxidans in a Tripoli central hospital. TMB-1 was located on a class 1 integron and is a chromosomally-encoded beta-lactamase capable of hydrolyzing multiple antibiotics.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2774":{"model_id":"2774","model_name":"TMB-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"350"}},"model_sequences":{"sequence":{"4086":{"protein_sequence":{"accession":"BAM73613.1","sequence":"MRPFLFLIIFISHFAFANEEIPGLEVEEIDNGVFLHKSYSRVEGWGLVSSNGLVVISGGKAFIIDTPWSESDTEKLVDWIRSKKYELAGSISTHSHEDKTAGIKWLNGKSITTYASALTNEILKREGKEQARSSFKGNEFSLMDGFLEVYYPGGGHTIDNLVVWIPSSKILYGGCFIRSLEPSGLGYTGEAKIDQWPQSARNTISKYPEAKIVVPGHGKIGDFELLKHTKVLAEKASNKANHGDR"},"dna_sequence":{"accession":"AB758278.1","fmin":"98","fmax":"836","strand":"+","sequence":"ATGCGACCATTTTTATTTTTAATAATTTTTATCAGTCATTTCGCTTTTGCCAACGAAGAAATACCCGGATTGGAAGTTGAGGAAATTGACAACGGCGTTTTTTTGCACAAGTCATACAGCCGGGTGGAAGGCTGGGGCCTGGTAAGTTCAAACGGACTTGTTGTCATCAGCGGCGGAAAAGCATTCATTATTGACACTCCATGGTCGGAATCAGATACAGAAAAGCTTGTAGATTGGATACGATCAAAAAAGTATGAGCTGGCGGGAAGCATTTCTACACATTCACACGAAGACAAGACTGCCGGTATAAAATGGCTAAACGGCAAATCCATTACTACATATGCCTCAGCGCTGACTAATGAAATTCTAAAAAGAGAGGGTAAGGAGCAGGCAAGGAGCTCATTCAAAGGTAATGAATTTTCGCTGATGGACGGTTTTCTAGAAGTCTATTATCCCGGAGGCGGCCATACTATTGATAACTTAGTGGTATGGATCCCTAGTTCAAAAATATTGTATGGCGGCTGTTTCATACGTAGCTTGGAACCCAGTGGGCTAGGTTACACTGGTGAAGCTAAAATTGATCAGTGGCCACAATCCGCTAGAAATACAATTTCGAAGTATCCTGAAGCTAAGATTGTGGTGCCTGGTCATGGAAAAATTGGCGATTTCGAGTTGTTAAAACATACCAAGGTCCTTGCAGAAAAGGCCTCTAACAAGGCCAATCACGGCGACCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41219","NCBI_taxonomy_name":"Acinetobacter courvalinii","NCBI_taxonomy_id":"280147"}}}},"ARO_accession":"3004106","ARO_id":"41218","ARO_name":"TMB-2","CARD_short_name":"TMB-2","ARO_description":"TMB-2 is a TMB metallo-beta-lactamase found in Acinetobacter sp.","ARO_category":{"41216":{"category_aro_accession":"3004104","category_aro_cvterm_id":"41216","category_aro_name":"TMB beta-lactamase","category_aro_description":"TMB-1, the first known member of the Tripoli metallo-beta-lactamase family (TMB) was isolated from Achromobacter xylosoxidans in a Tripoli central hospital. TMB-1 was located on a class 1 integron and is a chromosomally-encoded beta-lactamase capable of hydrolyzing multiple antibiotics.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2775":{"model_id":"2775","model_name":"Pseudomonas aeruginosa soxR","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"200"}},"model_sequences":{"sequence":{"5395":{"protein_sequence":{"accession":"AAG05661.1","sequence":"MKNSCASRELSVGELARRAGVAVSALHFYETKGLISSQRNAGNQRRFSRETLRRVVVIKVAQRVGIPLAEIARALQTLPAGRSPSAADWARLSAQWKEDLTERIDKLLLLRDQLDGCIGCGCLSLQACPLRNPGDQLSAEGPGAHWLDAEGREHDG"},"dna_sequence":{"accession":"AE004091.2","fmin":"2503424","fmax":"2503895","strand":"-","sequence":"ATGAAGAATTCCTGCGCATCTCGTGAACTGAGCGTCGGCGAACTGGCCAGGCGTGCCGGCGTGGCGGTCTCCGCCCTGCATTTCTACGAAACCAAGGGGCTGATCAGCAGCCAGCGCAACGCCGGCAACCAGCGGCGCTTCAGTCGCGAGACGCTACGCCGGGTGGTGGTGATCAAGGTCGCCCAGCGGGTCGGCATTCCCCTCGCGGAGATCGCTCGCGCCCTGCAGACCCTGCCGGCGGGGCGCAGCCCTAGCGCGGCGGACTGGGCGCGCCTGTCGGCGCAGTGGAAGGAGGATCTCACCGAGCGCATCGACAAGCTGCTGCTGTTGCGCGACCAACTGGACGGCTGCATCGGTTGCGGCTGCCTGTCGCTCCAGGCCTGCCCGTTGCGCAACCCCGGCGACCAGCTTTCCGCCGAGGGGCCGGGAGCGCACTGGCTGGACGCCGAGGGCCGCGAGCACGACGGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36804","NCBI_taxonomy_name":"Pseudomonas aeruginosa PAO1","NCBI_taxonomy_id":"208964"}}}},"ARO_accession":"3004107","ARO_id":"41228","ARO_name":"Pseudomonas aeruginosa soxR","CARD_short_name":"Paer_soxR","ARO_description":"SoxR is a redox-sensitive transcriptional activator that induces expression of a small regulon that includes the RND efflux pump-encoding operon mexGHI-opmD. SoxR was shown to be activated by pyocyanin.","ARO_category":{"36002":{"category_aro_accession":"0010001","category_aro_cvterm_id":"36002","category_aro_name":"ATP-binding cassette (ABC) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding\/hydrolysis to transport substrates across cell membranes.","category_aro_class_name":"AMR Gene Family"},"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37084":{"category_aro_accession":"3000704","category_aro_cvterm_id":"37084","category_aro_name":"cefalotin","category_aro_description":"Cefalotin is a semisynthetic cephalosporin antibiotic activate against staphylococci. It is resistant to staphylococci beta-lactamases but hydrolyzed by enterobacterial beta-lactamases.","category_aro_class_name":"Antibiotic"},"37250":{"category_aro_accession":"3000870","category_aro_cvterm_id":"37250","category_aro_name":"triclosan","category_aro_description":"Triclosan is a common antibacterial agent added to many consumer products as a biocide.  It is an inhibitor of fatty acid biosynthesis by blocking enoyl-carrier protein reductase (FabI).","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"43746":{"category_aro_accession":"3005386","category_aro_cvterm_id":"43746","category_aro_name":"disinfecting agents and antiseptics","category_aro_description":"Disinfectants that can also interact with antimicrobial resistance mechanisms, e.g. molecule efflux, and thus are the targets of disinfectant resistance.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"3493":{"model_id":"3493","model_name":"OXA-408","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"566"}},"model_sequences":{"sequence":{"5688":{"protein_sequence":{"accession":"AJD07404.1","sequence":"MNIQALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRIGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGISSSVRKEITYRSLEQLGIL"},"dna_sequence":{"accession":"KJ584917.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTCAAGCCCTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATAGGCCTTGAGCACCATAAGGCAACCACTACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTATTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAACAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATATCTAGCTCTGTTCGAAAAGAGATTACTTATAGAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001599","ARO_id":"37999","ARO_name":"OXA-408","CARD_short_name":"OXA-408","ARO_description":"OXA-408 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2779":{"model_id":"2779","model_name":"FosA6","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"280"}},"model_sequences":{"sequence":{"4755":{"protein_sequence":{"accession":"AMQ12811.1","sequence":"MLSGLNHLTLAVSQLAPSVAFYQQLLGMTLHARWDSGAYLSCGDLWLCLSLDPQRRVTPPEESDYTHYAFSISEADFASFAARLEAAGVAIWKLNRSEGASHYFLDPDGHKLELHVGSLAQRLAACREQQYKGMVFFDQ"},"dna_sequence":{"accession":"KU254579.1","fmin":"59421","fmax":"59841","strand":"+","sequence":"ATGCTGAGTGGACTGAATCACCTGACCCTGGCAGTCAGCCAGCTGGCGCCGAGCGTGGCGTTTTATCAGCAGCTGCTGGGCATGACGCTGCATGCCCGCTGGGACAGCGGGGCTTATCTCTCCTGCGGCGATTTGTGGCTGTGCCTGTCGCTGGATCCGCAGCGGCGCGTTACTCCGCCGGAAGAGAGCGACTACACCCATTATGCGTTTAGTATTAGCGAAGCCGATTTTGCTAGCTTCGCCGCCCGCCTTGAGGCTGCCGGCGTGGCGATCTGGAAGCTGAACCGTAGCGAAGGTGCCTCGCACTATTTCCTCGATCCCGATGGCCATAAGCTGGAGCTGCACGTCGGCAGTCTCGCCCAGCGTCTGGCCGCCTGCCGCGAACAGCAGTATAAGGGGATGGTGTTTTTTGATCAGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3004111","ARO_id":"41232","ARO_name":"FosA6","CARD_short_name":"FosA6","ARO_description":"FosA6 is a plasmid-encoded enzyme that confers resistance to fosfomycin in Escherichia coli by breaking the epoxide ring of the molecule.","ARO_category":{"36272":{"category_aro_accession":"3000133","category_aro_cvterm_id":"36272","category_aro_name":"fosfomycin thiol transferase","category_aro_description":"Catalyzes the addition of a thiol group from a nucleophilic molecule to fosfomycin.","category_aro_class_name":"AMR Gene Family"},"35944":{"category_aro_accession":"0000025","category_aro_cvterm_id":"35944","category_aro_name":"fosfomycin","category_aro_description":"Fosfomycin (also known as phosphomycin and phosphonomycin) is a broad-spectrum antibiotic produced by certain Streptomyces species. It is effective on gram positive and negative bacteria as it targets the cell wall, an essential feature shared by both bacteria. Its specific target is MurA (MurZ in E.coli), which attaches phosphoenolpyruvate (PEP) to UDP-N-acetylglucosamine, a step of commitment to cell wall synthesis. In the active site of MurA, the active cysteine molecule is alkylated which stops the catalytic reaction.","category_aro_class_name":"Antibiotic"},"45731":{"category_aro_accession":"3007149","category_aro_cvterm_id":"45731","category_aro_name":"phosphonic acid antibiotic","category_aro_description":"A group of antibiotics derived from phosphonic acids.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2780":{"model_id":"2780","model_name":"FosA7","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"250"}},"model_sequences":{"sequence":{"4093":{"protein_sequence":{"accession":"KKE03230.1","sequence":"MLQSLNHLTLAVSNLQTSLTFWRDLLGLQLHAEWDTGAYLTCGDLWVCLSYDVSCNYVAPQECDYTHYAFSIAPEDFEPFSYKLKQAGVTVWKDNKSEGQSFYFLDPDGHKLELHVGDLASRLAQCREKPYSGMRFGPGK"},"dna_sequence":{"accession":"LAPJ01000014.1","fmin":"36822","fmax":"37245","strand":"+","sequence":"ATGCTTCAATCTCTGAACCACTTAACGCTTGCTGTCAGTAATTTGCAAACTAGCCTGACCTTCTGGCGCGATTTGCTGGGGTTGCAGCTACATGCTGAGTGGGATACTGGCGCTTACCTTACCTGTGGCGACCTTTGGGTCTGTCTTTCTTACGACGTATCCTGTAACTACGTGGCCCCGCAGGAATGTGACTATACCCACTACGCATTCAGCATCGCGCCAGAAGATTTTGAACCGTTCTCGTATAAGCTGAAACAGGCGGGAGTGACGGTCTGGAAAGACAATAAAAGCGAAGGGCAATCTTTCTATTTTCTTGACCCCGATGGCCACAAGCTGGAACTGCATGTGGGAGATTTAGCATCTCGACTGGCGCAGTGCCGGGAGAAGCCTTACTCTGGAATGCGTTTCGGGCCTGGAAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35663","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Heidelberg","NCBI_taxonomy_id":"611"}}}},"ARO_accession":"3004113","ARO_id":"41234","ARO_name":"FosA7","CARD_short_name":"FosA7","ARO_description":"FosA7 is an enzyme that confers resistance to fosfomycin in Escherichia coli by breaking the epoxide ring of the molecule.","ARO_category":{"36272":{"category_aro_accession":"3000133","category_aro_cvterm_id":"36272","category_aro_name":"fosfomycin thiol transferase","category_aro_description":"Catalyzes the addition of a thiol group from a nucleophilic molecule to fosfomycin.","category_aro_class_name":"AMR Gene Family"},"35944":{"category_aro_accession":"0000025","category_aro_cvterm_id":"35944","category_aro_name":"fosfomycin","category_aro_description":"Fosfomycin (also known as phosphomycin and phosphonomycin) is a broad-spectrum antibiotic produced by certain Streptomyces species. It is effective on gram positive and negative bacteria as it targets the cell wall, an essential feature shared by both bacteria. Its specific target is MurA (MurZ in E.coli), which attaches phosphoenolpyruvate (PEP) to UDP-N-acetylglucosamine, a step of commitment to cell wall synthesis. In the active site of MurA, the active cysteine molecule is alkylated which stops the catalytic reaction.","category_aro_class_name":"Antibiotic"},"45731":{"category_aro_accession":"3007149","category_aro_cvterm_id":"45731","category_aro_name":"phosphonic acid antibiotic","category_aro_description":"A group of antibiotics derived from phosphonic acids.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2787":{"model_id":"2787","model_name":"Moraxella catarrhalis M35","model_type":"protein knockout model","model_type_id":"40354","model_description":"Protein Knockout Models (PKM) reflect resistance by the absence of a gene product, most often deletion of a gene involved in antibiotic import, such as Vibrio cholerae OmpT. Like Protein Homolog Models (PHMs), PKMs include a reference sequence and a bitscore cut-off for detection using BLASTP but instead are designed to only report lack of detection under Perfect or Strict criteria. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff. This model type is still under development and not currently supported by the Resistance Gene Identifier (RGI) software.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"650"}},"model_sequences":{"sequence":{"4101":{"protein_sequence":{"accession":"AAX99225.1","sequence":"MKKLALATAVAALSVSAAQATPTVYGKAFLTVDANNTDTTYNSGLVQLSEDTNESGLNSNTSRIGFKGSEALNANTDVVYQLEYKIDIDADRGDNFKSRDTYLGLAHKQYGTLLAGRLTTIDDSVDFASMLEDNNVADIGPTFNAPRANNAFAYVSPEYNGTQFLAMYAFDSDTDKGGLAKDDQFGVGATYSTGPINAGATYIHYGDDSHIRLSGNYAVSPALTVGALYQISEFGVAAKNQKASPLSEGKVGDKKENTLIVSGEMKTATPWTAYGQATLIKNVAGNDGDESVGVGIGGKYAFNKATTGHVYTGYVNSERKNVKYEGSNETHKNAHKDTKFDGYKNSGFGIGAGLEYKF"},"dna_sequence":{"accession":"AY905613.1","fmin":"0","fmax":"1077","strand":"+","sequence":"ATGAAAAAACTTGCTCTAGCAACCGCTGTCGCTGCTTTATCTGTATCTGCTGCACAAGCAACACCGACTGTTTACGGTAAAGCGTTTTTAACTGTTGATGCCAACAATACTGATACAACTTATAATTCAGGTCTTGTACAATTATCTGAAGATACCAATGAAAGCGGGCTTAACTCAAATACCTCACGCATTGGTTTTAAAGGTTCTGAAGCTTTAAATGCTAATACTGATGTTGTGTATCAACTTGAATATAAGATTGACATTGATGCTGATCGTGGCGATAACTTTAAATCTCGTGATACTTACCTAGGTCTTGCTCATAAACAATACGGCACATTGTTGGCTGGTCGCTTAACGACTATTGATGACAGTGTTGATTTTGCCAGCATGTTGGAAGATAATAATGTCGCTGACATCGGTCCTACTTTTAATGCCCCTCGTGCCAACAATGCCTTTGCTTATGTATCACCTGAGTATAATGGTACTCAGTTCTTAGCTATGTATGCATTTGACTCAGATACTGACAAGGGCGGTCTTGCCAAAGATGACCAGTTTGGTGTGGGTGCAACTTATAGCACAGGCCCTATCAATGCAGGTGCGACTTATATTCACTACGGTGATGACAGTCACATTCGCCTATCTGGCAACTATGCGGTTTCTCCAGCATTGACTGTAGGTGCTTTATATCAAATCTCAGAATTTGGTGTCGCTGCCAAAAATCAAAAAGCCAGTCCTTTGTCTGAGGGCAAGGTAGGCGATAAAAAAGAAAACACCCTTATCGTGAGTGGCGAGATGAAAACTGCCACGCCATGGACAGCCTATGGTCAGGCAACTTTGATTAAAAATGTTGCTGGTAATGATGGCGATGAGTCAGTGGGTGTTGGTATTGGTGGTAAATATGCCTTTAATAAAGCCACCACAGGTCATGTCTACACTGGCTATGTCAACAGCGAGCGTAAAAATGTCAAGTATGAGGGCAGTAATGAAACACATAAAAATGCACACAAAGATACAAAGTTTGATGGTTATAAGAACAGTGGCTTTGGTATCGGCGCAGGTTTAGAATATAAATTCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41250","NCBI_taxonomy_name":"Moraxella catarrhalis","NCBI_taxonomy_id":"480"}}}},"ARO_accession":"3004124","ARO_id":"41249","ARO_name":"Moraxella catarrhalis M35","CARD_short_name":"Mcat_M35_AMX","ARO_description":"The outer membrane protein M35 of Moraxella catarrhalis is an antigenically conserved porin. Down-regulation of M35 significantly increases the MICs of aminopenicillins, specifically amoxicillin.","ARO_category":{"41445":{"category_aro_accession":"3004281","category_aro_cvterm_id":"41445","category_aro_name":"General Bacterial Porin with reduced permeability to beta-lactams","category_aro_description":"These are GBPs that are associated with decreased susceptibility to beta-lactams either through mutations in the porin protein, absence of the porin protein, or expression of the porin protein.","category_aro_class_name":"AMR Gene Family"},"35981":{"category_aro_accession":"0000064","category_aro_cvterm_id":"35981","category_aro_name":"amoxicillin","category_aro_description":"Amoxicillin is a moderate-spectrum, bacteriolytic, beta-lactam antibiotic used to treat bacterial infections caused by susceptible microorganisms. A derivative of penicillin, it has a wider range of treatment but remains relatively ineffective against Gram-negative bacteria. It is commonly taken with clavulanic acid, a beta-lactamase inhibitor. Like other beta-lactams, amoxicillin interferes with the synthesis of peptidoglycan.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36383":{"category_aro_accession":"3000244","category_aro_cvterm_id":"36383","category_aro_name":"reduced permeability to antibiotic","category_aro_description":"Reduction in permeability to antibiotic, generally through reduced production of porins, can provide resistance.","category_aro_class_name":"Resistance Mechanism"},"40429":{"category_aro_accession":"3003764","category_aro_cvterm_id":"40429","category_aro_name":"resistance by absence","category_aro_description":"Mechanism of antibiotic resistance conferred by deletion of gene (usually a porin).","category_aro_class_name":"Resistance Mechanism"}}},"2781":{"model_id":"2781","model_name":"porin OmpC","model_type":"protein knockout model","model_type_id":"40354","model_description":"Protein Knockout Models (PKM) reflect resistance by the absence of a gene product, most often deletion of a gene involved in antibiotic import, such as Vibrio cholerae OmpT. Like Protein Homolog Models (PHMs), PKMs include a reference sequence and a bitscore cut-off for detection using BLASTP but instead are designed to only report lack of detection under Perfect or Strict criteria. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff. This model type is still under development and not currently supported by the Resistance Gene Identifier (RGI) software.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"675"}},"model_sequences":{"sequence":{"4096":{"protein_sequence":{"accession":"APB87301.1","sequence":"MKVKVLSLLVPALLVAGAANAAEVYNKDGNKLDLYGKVDGLHYFSDNKDVDGDQTYMRLGFKGETQVTDQLTGYGQWEYQIQGNSAENENNSWTRVAFAGLKFQDVGSFDYGRNYGVVYDVTSWTDVLPEFGGDTYGSDNFMQQRGNGFATYRNTDFFGLVDGLNFAVQYQGKNGSVSGEGMTNNGRDALRQNGDGVGGSITYDYEGFGIGAAVSSSKRTDAQNTAAYIGNGDRAETYTGGLKYDANNIYLAAQYTQTYNATRVGSLGWANKAQNFEAVAQYQFDFGLRPSVAYLQSKGKNLGVINGRNYDDEDILKYVDVGATYYFNKNMSTYVDYKINLLDDNQFTRDAGINTDNIVALGLVYQF"},"dna_sequence":{"accession":"KY086517.1","fmin":"0","fmax":"1104","strand":"+","sequence":"ATGAAAGTTAAAGTACTGTCCCTCCTGGTCCCAGCTCTGCTGGTAGCAGGCGCAGCAAACGCTGCTGAAGTTTACAACAAAGACGGCAACAAATTAGATCTGTACGGTAAAGTAGACGGCCTGCACTATTTCTCTGACAACAAAGATGTAGATGGCGACCAGACCTACATGCGTCTTGGCTTCAAAGGTGAAACTCAGGTTACTGACCAGCTGACCGGTTACGGCCAGTGGGAATATCAGATCCAGGGCAACAGCGCTGAAAACGAAAACAACTCCTGGACCCGTGTGGCATTCGCAGGTCTGAAATTCCAGGATGTGGGTTCTTTCGACTACGGTCGTAACTACGGCGTTGTTTACGACGTAACTTCCTGGACCGACGTACTGCCAGAATTCGGTGGCGACACCTACGGTTCTGACAACTTCATGCAGCAGCGTGGTAACGGCTTTGCGACCTACCGTAACACTGACTTCTTCGGTCTGGTTGACGGCCTGAACTTTGCTGTTCAGTACCAGGGCAAAAACGGTAGCGTAAGCGGCGAAGGCATGACCAACAATGGTCGCGATGCTCTGCGTCAGAACGGCGACGGCGTTGGCGGTTCTATCACTTATGATTACGAAGGCTTCGGTATCGGTGCTGCAGTTTCCAGCTCCAAACGTACTGATGCTCAGAACACCGCTGCTTACATCGGTAACGGCGACCGTGCTGAAACCTACACCGGTGGTCTGAAATACGACGCTAACAACATCTACCTGGCTGCTCAGTACACCCAGACCTACAACGCAACTCGCGTAGGTTCCCTGGGTTGGGCGAACAAAGCACAGAACTTCGAAGCTGTTGCTCAGTACCAGTTCGACTTCGGTCTGCGTCCGTCTGTAGCATACCTGCAGTCTAAAGGTAAAAACCTGGGTGTCATCAATGGTCGTAACTACGACGACGAAGATATCCTGAAATATGTTGATGTTGGCGCGACCTACTACTTCAACAAAAACATGTCCACCTACGTTGACTACAAAATCAACCTGCTGGACGACAACCAGTTCACTCGTGACGCTGGCATCAACACTGATAACATCGTAGCTCTGGGTCTGGTTTACCAGTTCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3004114","ARO_id":"41238","ARO_name":"porin OmpC","CARD_short_name":"porin_OmpC","ARO_description":"In the presence of antibiotic stress, there is a coupled down-regulation of the porin OmpC with the OmpF.  Mutants both lacking both OmpC and OmpF proteins are resistant to cephaloridine and cefazolin. Analyses of genes involved in the increased resistance to tetracycline suggest that the up-regulation of efflux pump genes is accompanied by a decrease of OmpF and OmpC synthesis. Homologs of OmpC have been identified in Escherichia coli, Salmonella enterica, Klebsiella aerogenes and Serratia marcescens.","ARO_category":{"41445":{"category_aro_accession":"3004281","category_aro_cvterm_id":"41445","category_aro_name":"General Bacterial Porin with reduced permeability to beta-lactams","category_aro_description":"These are GBPs that are associated with decreased susceptibility to beta-lactams either through mutations in the porin protein, absence of the porin protein, or expression of the porin protein.","category_aro_class_name":"AMR Gene Family"},"35975":{"category_aro_accession":"0000058","category_aro_cvterm_id":"35975","category_aro_name":"cefazolin","category_aro_description":"Cefazolin, also known as cefazoline or cephazolin, is a first generation cephalosporin antibiotic. It is administered parenterally, and is active against a broad spectrum of bacteria.","category_aro_class_name":"Antibiotic"},"41256":{"category_aro_accession":"3004129","category_aro_cvterm_id":"41256","category_aro_name":"cephaloridine","category_aro_description":"Cephaloridine is a semisynthetic, broad-spectrum, first-generation cephalosporin with antibacterial activity. Cephaloridine binds to and inactivates penicillin-binding proteins (PBPs) located on the inner membrane of the bacterial cell wall. PBPs are enzymes involved in the terminal stages of assembling the bacterial cell wall and in reshaping the cell wall during growth and division. Inactivation of PBPs interferes with the cross-linkage of peptidoglycan chains necessary for bacterial cell wall strength and rigidity. This results in the weakening of the bacterial cell wall and causes cell lysis.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36383":{"category_aro_accession":"3000244","category_aro_cvterm_id":"36383","category_aro_name":"reduced permeability to antibiotic","category_aro_description":"Reduction in permeability to antibiotic, generally through reduced production of porins, can provide resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2782":{"model_id":"2782","model_name":"Vibrio cholerae OmpU","model_type":"protein knockout model","model_type_id":"40354","model_description":"Protein Knockout Models (PKM) reflect resistance by the absence of a gene product, most often deletion of a gene involved in antibiotic import, such as Vibrio cholerae OmpT. Like Protein Homolog Models (PHMs), PKMs include a reference sequence and a bitscore cut-off for detection using BLASTP but instead are designed to only report lack of detection under Perfect or Strict criteria. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff. This model type is still under development and not currently supported by the Resistance Gene Identifier (RGI) software.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"4097":{"protein_sequence":{"accession":"AID70696.1","sequence":"MNKTLIALAVSAAAVATGAYADGINQSGDKAGSTVYSAKGTSLEIGGRAEARLSLKDGKAEDKSRVRLNFLGKAEINDSLYGIGFYEGEFTTADNADGSELDNRYTYAGIGGTYGEVTYGKNDGALGVITDFTDIMSYHGNSAADKIAVADRTDNMLAYKGQFGDLGVKASYRFADRDTSTGEFTDNKKEDGYSLSAIYAFGDTGFNIGAGYADQNDNNEYMLAASYRMENVYFGALFTDGEKNFNSKSNGNNSVVKGKFTGVQDYTGYELAAGYKLGQAAFTTTYNNAETANDTSANNVAIDATYYFKPNFRTYISYNFNLLDSGDKLGNSSVSKIDAEDELAIGLRYDF"},"dna_sequence":{"accession":"KJ699300.1","fmin":"0","fmax":"1056","strand":"+","sequence":"ATGAACAAGACTCTGATTGCTCTTGCTGTATCAGCTGCTGCAGTGGCTACTGGCGCTTACGCTGACGGAATCAACCAAAGCGGTGACAAAGCAGGTTCAACCGTTTACAGCGCGAAAGGTACTTCTCTAGAAATCGGTGGCCGTGCTGAAGCGCGCCTATCTCTGAAAGATGGCAAAGCTGAAGATAAATCTCGCGTACGCCTGAATTTCCTAGGTAAAGCAGAAATCAATGACAGCCTATACGGCATCGGTTTCTACGAAGGTGAATTCACTACTGCAGATAACGCTGACGGCTCAGAATTAGATAACCGTTACACCTACGCTGGTATCGGTGGCACTTACGGTGAAGTGACTTATGGTAAAAACGATGGTGCATTGGGCGTAATCACTGACTTCACCGATATCATGTCTTACCACGGTAACTCAGCCGCAGACAAAATCGCTGTAGCTGACCGTACAGACAACATGTTGGCTTACAAAGGCCAATTTGGTGACCTGGGCGTAAAAGCAAGCTACCGTTTTGCAGATCGTGATACTTCAACGGGTGAATTCACTGACAATAAAAAAGAAGACGGTTACTCACTATCTGCTATCTACGCCTTTGGTGACACTGGTTTCAACATCGGTGCAGGCTATGCAGATCAAAACGATAACAACGAGTACATGCTAGCCGCTTCTTACCGTATGGAAAATGTGTACTTCGGTGCTCTATTTACTGACGGTGAAAAGAATTTCAATAGTAAAAGCAACGGTAATAACTCTGTTGTGAAGGGCAAATTTACAGGTGTCCAAGATTATACTGGTTACGAATTAGCTGCTGGTTACAAGCTAGGTCAAGCTGCATTTACGACTACGTACAACAACGCAGAGACTGCAAACGATACATCAGCAAACAACGTAGCTATTGATGCTACTTACTACTTTAAGCCAAACTTCCGCACTTATATCTCTTACAACTTCAACCTACTTGACTCTGGTGACAAGCTAGGTAACAGCTCTGTATCTAAGATCGACGCTGAAGACGAACTGGCTATCGGTCTACGTTACGACTTCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36789","NCBI_taxonomy_name":"Vibrio cholerae","NCBI_taxonomy_id":"666"}}}},"ARO_accession":"3004117","ARO_id":"41241","ARO_name":"Vibrio cholerae OmpU","CARD_short_name":"Vcho_OmpU","ARO_description":"A ToxR-Regulated outer membrane porin. In Vibrio cholerae, ToxR controls resistance to P2 (a BPI-derived antimicrobial peptide) by regulating the production of OmpU. OmpU also confers resistance to polymyxin B sulfate.","ARO_category":{"41446":{"category_aro_accession":"3004282","category_aro_cvterm_id":"41446","category_aro_name":"General Bacterial Porin with reduced permeability to peptide antibiotics","category_aro_description":"These are GBPs that are associated with decreased susceptibility to peptide antibiotics either through mutations in the porin protein, absence of the porin protein, or expression of the porin protein.","category_aro_class_name":"AMR Gene Family"},"41245":{"category_aro_accession":"3004121","category_aro_cvterm_id":"41245","category_aro_name":"BPI","category_aro_description":"Bactericidal\/permeability-increasing (BPI) protein is a member of a new generation of proteins known as super-antibiotics that are implicated as endotoxin neutralising agents. The potent (nM) cytotoxicity of BPI is limited to gram-negative bacteria (GNB), reflecting the high affinity (<10 nM) of BPI for bacterial lipopolysaccharides (LPS). Binding of BPI to live bacteria via LPS causes immediate growth arrest, actual killing coincides with later damage to the inner membrane.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36383":{"category_aro_accession":"3000244","category_aro_cvterm_id":"36383","category_aro_name":"reduced permeability to antibiotic","category_aro_description":"Reduction in permeability to antibiotic, generally through reduced production of porins, can provide resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3519":{"model_id":"3519","model_name":"OXA-450","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"514"}},"model_sequences":{"sequence":{"5714":{"protein_sequence":{"accession":"AKI29914.1","sequence":"MKKITLFLLFLNLVFGQDKILNNWFKEYNTSGTFVFYDGKTWASNDFSRTMETFSPASTFKIFNALIALDSGVIKTKKEIFYHYRGEKVFLSSWAQDMNLSSAIKYSNVLAFKEVARRIGIKTMQEYLNKLHYGNAKISKIDTFWLDNSLKISAKEQAILLFRLSQNSLPFSQEAMNSVKEMIYLKNMENLELFGKTGFNDEQKIAWIVGFVYLKDENKYKAFALNLDIDKFEDLYKREKILEKYLDELVKKVKNDG"},"dna_sequence":{"accession":"KR061502.1","fmin":"0","fmax":"774","strand":"+","sequence":"ATGAAAAAAATAACTTTATTTTTACTTTTCTTAAATTTAGTGTTTGGGCAAGATAAGATATTAAATAATTGGTTTAAAGAGTATAATACAAGCGGCACTTTTGTTTTTTATGATGGAAAAACTTGGGCGAGTAACGACTTTTCAAGGACTATGGAGACTTTCTCTCCCGCTTCCACTTTTAAAATTTTTAATGCTCTAATTGCACTTGATAGTGGTGTGATAAAAACTAAAAAAGAAATTTTTTATCACTATAGAGGTGAAAAAGTATTTTTATCTTCTTGGGCGCAAGATATGAATTTAAGTTCAGCTATAAAATATTCTAATGTTCTTGCTTTTAAAGAAGTGGCAAGAAGAATTGGTATCAAAACTATGCAAGAATATTTAAACAAGCTTCATTATGGTAATGCTAAAATTTCCAAGATCGATACTTTTTGGCTTGACAACTCACTAAAAATAAGCGCTAAAGAACAAGCAATTTTGCTTTTTAGACTTTCACAAAATAGCTTACCTTTTTCTCAAGAAGCAATGAATAGTGTTAAGGAAATGATTTATTTAAAAAATATGGAAAATTTAGAGCTTTTTGGAAAAACAGGTTTTAATGATGAGCAAAAAATTGCTTGGATTGTAGGTTTTGTGTATTTAAAAGATGAAAATAAATATAAGGCTTTCGCGCTAAATTTAGATATTGATAAATTTGAAGATTTATATAAAAGAGAAAAAATTTTAGAAAAATATTTAGATGAACTTGTAAAAAAAGTTAAAAATGATGGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36835","NCBI_taxonomy_name":"Campylobacter coli","NCBI_taxonomy_id":"195"}}}},"ARO_accession":"3003606","ARO_id":"40216","ARO_name":"OXA-450","CARD_short_name":"OXA-450","ARO_description":"OXA-450 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46519":{"category_aro_accession":"3007730","category_aro_cvterm_id":"46519","category_aro_name":"OXA-61-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-61.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3523":{"model_id":"3523","model_name":"OXA-455","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"5718":{"protein_sequence":{"accession":"ALC76097.1","sequence":"MTVRRFSCALGAALSLSALAGAPARAAVLCTVVADAADGRIVFQQGTQAACAERYTPASTFKLPIALMGADAGILQGPHAPVWNYQPGYPDWGGDAWRQPTDPARWIKYSVVWYSQLTARALGQERFQRYASAFQYGNEDVSGEPGKHNGLDGAWINSSLRISPLEQLAFLRKLVNRQLPLKPAAYDLAETLFDAGEAGGWRLYGKTGTGSPGGNGVYTPDNAYGWFVGWARKDGRQLVFARLLQDEKATRPNAGLRARDDLMRDWPAMADAPRQ"},"dna_sequence":{"accession":"KP903885.1","fmin":"0","fmax":"828","strand":"+","sequence":"ATGACCGTTCGACGTTTTTCGTGCGCCCTGGGCGCAGCCCTTTCCCTGTCCGCGCTGGCGGGCGCCCCCGCCCGCGCCGCGGTTTTGTGCACCGTGGTGGCCGACGCCGCCGACGGCCGCATCGTGTTCCAGCAAGGCACGCAGGCGGCCTGCGCCGAGCGCTACACGCCGGCCTCGACCTTCAAGCTGCCGATCGCGCTGATGGGCGCGGACGCGGGCATCCTGCAAGGCCCGCACGCGCCGGTCTGGAACTACCAGCCGGGCTACCCCGACTGGGGCGGCGACGCCTGGCGCCAGCCGACGGATCCGGCGCGCTGGATCAAGTATTCGGTGGTCTGGTATTCGCAGCTGACCGCCAGGGCGCTGGGGCAGGAGCGCTTCCAGCGCTACGCCTCGGCCTTCCAGTACGGCAACGAGGACGTCTCGGGCGAGCCCGGCAAGCACAACGGCCTGGATGGCGCGTGGATCAACTCGTCGCTGCGCATTTCGCCGCTGGAGCAACTGGCGTTCCTGCGCAAGCTGGTCAACCGGCAATTGCCGCTCAAGCCCGCGGCCTACGATCTGGCCGAGACGCTGTTCGACGCCGGCGAGGCCGGCGGCTGGCGCCTGTATGGCAAGACCGGCACCGGCTCGCCCGGCGGCAACGGCGTCTACACACCGGACAACGCCTACGGCTGGTTCGTCGGCTGGGCGCGCAAGGACGGCCGCCAGCTGGTGTTCGCCCGCCTGCTGCAGGACGAGAAGGCCACCAGGCCCAACGCCGGCCTGCGCGCCCGCGATGACCTGATGCGCGACTGGCCGGCCATGGCCGACGCGCCCCGCCAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42556","NCBI_taxonomy_name":"Achromobacter insuavis","NCBI_taxonomy_id":"1287735"}}}},"ARO_accession":"3003611","ARO_id":"40221","ARO_name":"OXA-455","CARD_short_name":"OXA-455","ARO_description":"OXA-455 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46505":{"category_aro_accession":"3007716","category_aro_cvterm_id":"46505","category_aro_name":"OXA-364-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-364.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2788":{"model_id":"2788","model_name":"Escherichia coli LamB","model_type":"protein knockout model","model_type_id":"40354","model_description":"Protein Knockout Models (PKM) reflect resistance by the absence of a gene product, most often deletion of a gene involved in antibiotic import, such as Vibrio cholerae OmpT. Like Protein Homolog Models (PHMs), PKMs include a reference sequence and a bitscore cut-off for detection using BLASTP but instead are designed to only report lack of detection under Perfect or Strict criteria. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff. This model type is still under development and not currently supported by the Resistance Gene Identifier (RGI) software.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"850"}},"model_sequences":{"sequence":{"8289":{"protein_sequence":{"accession":"BAB38442.1","sequence":"MMITLRKLPLAVAVAAGVMSAQAMAVDFHGYARSGIGWTGSGGEQQCFQTTGAQSKYRLGNECETYAELKLGQEVWKEGDKSFYFDTNVAYSVAQQNDWEATDPAFREANVQGKNLIEWLPGSTIWAGKRFYQRHDVHMIDFYYWDISGPGAGLENIDVGFGKLSLAATRSSEAGGSSSFASNNIYDYTNETANDVFDVRLAQMEVNPGGTLELGVDYGRANLRDNYRLVDGASKDGWLFTAEHTQSVLKGFNKFVVQYATDSMTSQGKGLSQGSGVAFDNEKFAYNINNNGHMLRILDHGAISMGDNWDMMYVGMYQDINWDNDNGTKWWTVGIRPMYKWTPIMSTVMEIGYDNVESQRTGDKNNQYKITLAQQWQAGDSIWSRPAIRVFATYAKWDEKWGYDYNGDSKVNPNYGKAVPADFNGGSFGRGDSDEWTFGAQMEIWW"},"dna_sequence":{"accession":"BA000007.3","fmin":"5101371","fmax":"5102712","strand":"+","sequence":"ATGATGATTACTCTGCGCAAACTTCCTCTGGCGGTTGCCGTCGCAGCGGGCGTAATGTCTGCTCAGGCAATGGCTGTTGATTTCCACGGCTATGCACGTTCCGGTATTGGCTGGACAGGTAGCGGCGGTGAACAACAGTGTTTCCAGACTACCGGTGCTCAAAGTAAATACCGTCTTGGCAACGAATGTGAAACTTATGCTGAATTAAAATTGGGTCAGGAAGTGTGGAAAGAGGGCGATAAGAGCTTCTATTTCGACACTAACGTGGCCTATTCCGTCGCGCAACAGAATGACTGGGAAGCTACCGACCCGGCCTTCCGTGAAGCAAACGTGCAGGGTAAAAACCTGATCGAATGGCTGCCAGGCTCCACCATCTGGGCAGGTAAGCGCTTCTACCAACGTCATGACGTTCATATGATCGACTTCTACTACTGGGATATTTCTGGTCCTGGTGCCGGTCTGGAAAACATCGATGTTGGCTTCGGTAAACTCTCTCTGGCAGCAACCCGCTCCTCTGAAGCAGGTGGTTCTTCCTCTTTCGCCAGCAACAATATTTATGACTATACCAACGAAACCGCGAACGACGTTTTCGATGTGCGTTTAGCGCAGATGGAAGTCAACCCGGGCGGCACATTAGAACTGGGTGTCGACTACGGTCGTGCCAACCTGCGTGATAACTATCGTCTGGTTGATGGCGCATCGAAAGACGGCTGGTTATTCACTGCTGAACATACTCAGAGTGTCCTGAAGGGCTTTAACAAGTTTGTTGTTCAGTACGCTACTGACTCGATGACCTCGCAGGGTAAAGGTCTGTCGCAGGGTTCTGGCGTTGCATTTGATAACGAAAAATTTGCCTACAATATCAACAACAACGGTCACATGCTGCGTATCCTCGACCACGGTGCGATCTCCATGGGCGACAACTGGGACATGATGTACGTGGGTATGTACCAGGATATCAACTGGGATAACGACAACGGCACCAAGTGGTGGACCGTCGGTATTCGCCCGATGTACAAGTGGACGCCAATCATGAGCACCGTGATGGAAATCGGCTACGACAACGTCGAATCCCAGCGCACCGGCGACAAGAACAATCAGTACAAAATTACCCTCGCACAACAATGGCAGGCTGGCGACAGCATCTGGTCACGCCCGGCTATTCGTGTCTTCGCAACCTACGCCAAGTGGGATGAGAAATGGGGTTACGACTACAACGGCGATAGCAAGGTTAACCCGAACTACGGCAAAGCCGTTCCTGCTGATTTCAACGGCGGCAGCTTCGGTCGTGGCGACAGCGACGAGTGGACCTTCGGTGCCCAGATGGAAATCTGGTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36747","NCBI_taxonomy_name":"Escherichia coli O157:H7 str. Sakai","NCBI_taxonomy_id":"386585"}}}},"ARO_accession":"3004126","ARO_id":"41252","ARO_name":"Escherichia coli LamB","CARD_short_name":"Ecol_LamB","ARO_description":"LamB is a negative regulator for antibiotic resistance, it serves as a porin to influx antibiotic. When down-regulated, it increases resistance to chlortetracycline, ciprofloxacin, balofloxacin and nalidixic acid. It also interacts with Odp1, an energy metabolic enzyme, creating a complex that decreases in antibiotic-resistant strains.","ARO_category":{"41443":{"category_aro_accession":"3004279","category_aro_cvterm_id":"41443","category_aro_name":"Sugar Porin (SP)","category_aro_description":"Members of the Sugar Porin family tend to facilitate the transport of maltodextrins and other sugars across the outer membrane of Gram-negative bacteria. These porins form a homotrimeric structure.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"36667":{"category_aro_accession":"3000528","category_aro_cvterm_id":"36667","category_aro_name":"chlortetracycline","category_aro_description":"Chlortetracycline was an early, first-generation tetracycline antibiotic developed in the 1940's. It inhibits bacterial protein synthesis by binding to the 30S subunit of bacterial ribosomes, preventing the aminoacyl-tRNA from binding to the ribosome.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"41257":{"category_aro_accession":"3004130","category_aro_cvterm_id":"41257","category_aro_name":"balofloxacin","category_aro_description":"Balofloxacin is an 8-methoxy fluoroquinolone antibiotic. It shows potent bactericidal activity and inhibits the supercoiling activity of DNA gyrase of S. aureus, E. coli, and P. aeruginosa.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36383":{"category_aro_accession":"3000244","category_aro_cvterm_id":"36383","category_aro_name":"reduced permeability to antibiotic","category_aro_description":"Reduction in permeability to antibiotic, generally through reduced production of porins, can provide resistance.","category_aro_class_name":"Resistance Mechanism"},"40429":{"category_aro_accession":"3003764","category_aro_cvterm_id":"40429","category_aro_name":"resistance by absence","category_aro_description":"Mechanism of antibiotic resistance conferred by deletion of gene (usually a porin).","category_aro_class_name":"Resistance Mechanism"}}},"4257":{"model_id":"4257","model_name":"ADC-192","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6632":{"protein_sequence":{"accession":"WP_136512060.1","sequence":"MQFKKISCLLLSPLFIFSTSIYADNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGFYQLETMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_064715.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCAATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGACAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTAGGTTCTGTTAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAGCTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGCTGAGTTTTATTCATGCCAACCTCAACCCACAGAAATATCCGGCAGATATTCAACGGGCAATTAATGAAACACATCAAGGGTTCTATCAATTAGAAACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGATAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCAACGGTTTCGGAACATATGTAGTGTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006361","ARO_id":"44823","ARO_name":"ADC-192","CARD_short_name":"ADC-192","ARO_description":"ADC-192 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2747":{"model_id":"2747","model_name":"AcrEF-TolC confers resistance to ciprofloxacin","model_type":"efflux pump system meta-model","model_type_id":"41112","model_description":"Efflux Pump System Meta-Models (EPS) are dedicated to efflux complexes and their regulators, such as AcrAB-TolC. Using the efflux pump components parameter, this model type simply includes a list of detection models for each component of the complex. This model type is still under development and not currently supported by the Resistance Gene Identifier (RGI) software.","model_param":{"41141":{"param_type":"efflux pump components","param_description":"Association of proteins within efflux protein complexes or regulatory networks are encoded by the efflux pump components parameter: model_id,model_id,model_id, etc.","param_type_id":"41141","param_value":{"7771":"520,1445,1437,826,1248"}},"snp":{"Curated-R":{"7771":"A205T"}}},"ARO_accession":"3004083","ARO_id":"41185","ARO_name":"AcrEF-TolC confers resistance to ciprofloxacin","CARD_short_name":"AcrEF_TolC_CIP","ARO_description":"AcrEF-TolC efflux pump system of E. coli confers resistance to fluoroquinolones (ciprofloxacin).","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2786":{"model_id":"2786","model_name":"Burkholderia pseudomallei Omp38","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"4100":{"protein_sequence":{"accession":"AAP82271.1","sequence":"MNKTLIVAAVAASFATVAHAQSSVTLYGVLDAGITYQSNVATPSGSGKSLWSVGAGVDQSRFGLRGSEDLGGGLKAIFTLESGFNIGNGRFNNGGGMFNRQAFVGLSSNYGTVTLGRQYDATQDYLSPLSATGTWGGTYFAHPLNNDRLNTNGDVAVNNTVKFTSANYAGLQFGGTYSFSNNSQFANNRAYSAGASYQFQGLKVGAAYSQANNAGANTTGATDPLTGFNIGGTNAASIQGRSRVYGAGASYAYGPLQGGLLWTQSRLDNLANGAPTIRADNYEANVKYNLTPALGLGVAYTYTNAKANGESTHWNQVGVQADYALSKRTDVYAQAVYQRSSKNANASIYNGDLSTPFSTSINQTAATVGLRHRF"},"dna_sequence":{"accession":"AY312416.1","fmin":"0","fmax":"1122","strand":"+","sequence":"ATGAACAAGACTCTGATTGTTGCAGCAGTTGCTGCATCGTTCGCAACCGTCGCTCACGCGCAAAGCAGCGTCACGCTGTACGGTGTGCTCGACGCGGGCATCACGTACCAAAGCAACGTCGCGACGCCGTCGGGCTCGGGCAAGTCGCTGTGGTCGGTCGGCGCCGGCGTCGACCAAAGCCGTTTCGGTCTGCGCGGCTCGGAAGACCTGGGTGGCGGCCTGAAGGCGATCTTCACGTTGGAAAGCGGCTTCAACATCGGTAACGGCCGCTTCAACAACGGTGGCGGCATGTTCAACCGTCAAGCGTTCGTCGGTCTGTCGAGCAACTACGGCACCGTCACGCTGGGCCGTCAGTACGACGCAACCCAAGACTACCTGTCGCCGCTGTCGGCAACGGGCACCTGGGGCGGCACGTACTTCGCGCACCCGCTCAACAACGACCGCCTGAACACGAACGGCGACGTCGCGGTGAACAATACGGTCAAGTTCACGAGCGCGAACTACGCCGGCCTGCAATTCGGCGGCACGTACTCGTTCTCGAACAACTCGCAATTCGCGAACAACCGTGCATACAGCGCGGGCGCTTCGTACCAGTTCCAAGGCCTGAAGGTCGGTGCGGCGTACTCGCAAGCTAACAACGCTGGCGCGAATACCACGGGCGCAACGGATCCGCTGACCGGCTTCAACATCGGCGGCACGAACGCAGCAAGCATCCAAGGCCGTTCGCGCGTGTACGGCGCCGGCGCAAGCTACGCTTACGGCCCGCTGCAAGGCGGCCTGCTCTGGACGCAATCGCGTCTCGACAACCTGGCAAACGGCGCGCCGACCATCCGTGCCGACAACTACGAAGCAAACGTGAAGTACAACCTGACGCCGGCTCTGGGTCTGGGTGTTGCTTACACGTACACGAACGCGAAGGCGAACGGCGAAAGCACTCACTGGAACCAAGTTGGCGTCCAGGCCGACTACGCGCTGTCGAAGCGCACCGACGTGTACGCACAAGCCGTGTACCAGCGTTCGTCGAAGAACGCGAATGCGTCGATCTACAACGGCGACCTCAGCACGCCGTTCAGCACGTCGATCAACCAAACCGCAGCGACGGTTGGTCTGCGTCACCGCTTC","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36923","NCBI_taxonomy_name":"Burkholderia pseudomallei","NCBI_taxonomy_id":"28450"}}}},"ARO_accession":"3004123","ARO_id":"41248","ARO_name":"Burkholderia pseudomallei Omp38","CARD_short_name":"Bpse_Omp38","ARO_description":"Heterologous expression of Burkholderia pseudomallei Omp38 (BpsOmp38) in Omp-deficient E. coli host cells lowers their permeability and in consequence, their antimicrobial susceptibility to penicillin G, cefoxitin, ceftazidime and imipenem.","ARO_category":{"41445":{"category_aro_accession":"3004281","category_aro_cvterm_id":"41445","category_aro_name":"General Bacterial Porin with reduced permeability to beta-lactams","category_aro_description":"These are GBPs that are associated with decreased susceptibility to beta-lactams either through mutations in the porin protein, absence of the porin protein, or expression of the porin protein.","category_aro_class_name":"AMR Gene Family"},"35927":{"category_aro_accession":"0000008","category_aro_cvterm_id":"35927","category_aro_name":"cefoxitin","category_aro_description":"Cefoxitin is a cephamycin antibiotic often grouped with the second generation cephalosporins. Cefoxitin is bactericidal and acts by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. Cefoxitin's 7-alpha-methoxy group and 3' leaving group make it a poor substrate for most beta-lactamases.","category_aro_class_name":"Antibiotic"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36309":{"category_aro_accession":"3000170","category_aro_cvterm_id":"36309","category_aro_name":"imipenem","category_aro_description":"Imipenem is a broad-spectrum antibiotic and is usually taken with cilastatin, which prevents hydrolysis of imipenem by renal dehydropeptidase-I. It is resistant to hydrolysis by most other beta-lactamases. Notable exceptions are the KPC beta-lactamases and Ambler Class B enzymes.","category_aro_class_name":"Antibiotic"},"36976":{"category_aro_accession":"3000632","category_aro_cvterm_id":"36976","category_aro_name":"benzylpenicillin","category_aro_description":"Benzylpenicillin, commonly referred to as penicillin G, is effective against both Gram-positive and Gram-negative bacteria. It is unstable in acid.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36383":{"category_aro_accession":"3000244","category_aro_cvterm_id":"36383","category_aro_name":"reduced permeability to antibiotic","category_aro_description":"Reduction in permeability to antibiotic, generally through reduced production of porins, can provide resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2783":{"model_id":"2783","model_name":"Vibrio cholerae OmpT","model_type":"protein knockout model","model_type_id":"40354","model_description":"Protein Knockout Models (PKM) reflect resistance by the absence of a gene product, most often deletion of a gene involved in antibiotic import, such as Vibrio cholerae OmpT. Like Protein Homolog Models (PHMs), PKMs include a reference sequence and a bitscore cut-off for detection using BLASTP but instead are designed to only report lack of detection under Perfect or Strict criteria. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff. This model type is still under development and not currently supported by the Resistance Gene Identifier (RGI) software.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"8288":{"protein_sequence":{"accession":"AAC28105.1","sequence":"MKKTLLALAVLAAAGSVNAAEILKSDAGTVDFYGQLRTELKFLEDKDPTIGSGSSRAGVDANYTVNDSLALQGKVEFALKDSGDMYVRNHILGVKTNFGKFSFGKQWTTSDDVYGADYSYFFGGTGLRYGTLSDALHDSQVKYVYEADSFWVKAGYGFPEDNAKQELAELYVGATFGDLAVHAGGGQNRDKAFKVGSNTVGTTTTDIKADVTNSYFEVTGEYTIGDALIGVTYYNAELDVENNPLVIDEDAISVAGTYKVADKTKLYAGYEYVMQEANTGADEDGTLVYLGVEYKFASWARVYAEYGYGDGTTLGYTNKGSDAEVKATKVDSANNFGIGARIYW"},"dna_sequence":{"accession":"AF079766.2","fmin":"786","fmax":"1821","strand":"+","sequence":"ATGAAAAAAACTCTATTAGCACTCGCAGTGCTTGCAGCCGCAGGCTCTGTAAACGCAGCTGAAATTCTAAAATCAGATGCTGGCACTGTTGATTTTTACGGTCAGCTACGTACAGAATTGAAATTCTTAGAAGATAAAGATCCAACAATTGGTTCTGGTTCTTCGCGCGCTGGTGTTGATGCAAACTACACCGTTAACGATAGCTTAGCGTTACAAGGTAAAGTGGAATTCGCACTAAAAGACAGTGGCGATATGTATGTTCGTAACCACATTCTTGGTGTAAAAACTAATTTTGGTAAGTTTAGCTTTGGTAAACAATGGACTACATCTGACGATGTATACGGTGCTGACTACTCTTATTTCTTTGGTGGTACAGGTCTTCGTTACGGCACACTGTCTGATGCACTACACGATTCTCAAGTCAAGTATGTTTACGAAGCTGACAGCTTCTGGGTTAAAGCTGGTTACGGTTTTCCAGAAGATAATGCAAAGCAAGAGCTAGCAGAACTGTATGTAGGTGCAACATTTGGTGATTTGGCTGTGCACGCTGGTGGTGGTCAAAACCGTGATAAAGCATTCAAAGTTGGTAGTAATACGGTTGGCACAACAACCACAGATATTAAAGCTGACGTAACAAATAGTTACTTTGAAGTGACAGGTGAGTACACTATTGGTGATGCACTGATTGGTGTTACTTACTACAACGCAGAACTAGATGTAGAAAATAACCCACTAGTGATCGATGAAGACGCTATTTCTGTTGCTGGTACATACAAAGTTGCTGACAAGACAAAATTGTATGCTGGCTATGAGTATGTAATGCAAGAAGCGAACACTGGCGCAGATGAAGATGGTACTCTTGTTTACCTAGGTGTTGAATACAAATTTGCAAGCTGGGCTCGTGTATATGCTGAGTATGGCTACGGCGATGGTACAACTCTGGGTTACACCAACAAGGGTTCTGACGCAGAAGTTAAAGCAACGAAAGTCGACAGCGCTAATAACTTTGGTATCGGCGCTCGTATCTACTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36789","NCBI_taxonomy_name":"Vibrio cholerae","NCBI_taxonomy_id":"666"}}}},"ARO_accession":"3004118","ARO_id":"41242","ARO_name":"Vibrio cholerae OmpT","CARD_short_name":"Vcho_OmpT","ARO_description":"A ToxR negatively regulated outer membrane porin. In Vibrio cholerae, ToxR controls resistance to P2 (a BPI-derived antimicrobial peptide) by regulating the production of OmpT, especially in the absence of OmpU.","ARO_category":{"41446":{"category_aro_accession":"3004282","category_aro_cvterm_id":"41446","category_aro_name":"General Bacterial Porin with reduced permeability to peptide antibiotics","category_aro_description":"These are GBPs that are associated with decreased susceptibility to peptide antibiotics either through mutations in the porin protein, absence of the porin protein, or expression of the porin protein.","category_aro_class_name":"AMR Gene Family"},"41245":{"category_aro_accession":"3004121","category_aro_cvterm_id":"41245","category_aro_name":"BPI","category_aro_description":"Bactericidal\/permeability-increasing (BPI) protein is a member of a new generation of proteins known as super-antibiotics that are implicated as endotoxin neutralising agents. The potent (nM) cytotoxicity of BPI is limited to gram-negative bacteria (GNB), reflecting the high affinity (<10 nM) of BPI for bacterial lipopolysaccharides (LPS). Binding of BPI to live bacteria via LPS causes immediate growth arrest, actual killing coincides with later damage to the inner membrane.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36383":{"category_aro_accession":"3000244","category_aro_cvterm_id":"36383","category_aro_name":"reduced permeability to antibiotic","category_aro_description":"Reduction in permeability to antibiotic, generally through reduced production of porins, can provide resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3550":{"model_id":"3550","model_name":"ARL-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"580"}},"model_sequences":{"sequence":{"5745":{"protein_sequence":{"accession":"APY23841.1","sequence":"MKKFFTIFVLLCVCFAYTTATASAQGLTKLEHKNDATVGVYGINTATGQTYSHNADTRFAYASTFKAITSGLLLQQNSPEALNKTVTIKESDIVAYSPVTEQYVGKTMTLRQLISAAMLQSDNTASNIIMEQLGGLDQISSRLQALGDTTTNPQRYEPELNNYDPQSTADTSTPRATAHSLQQLLTTDAVAPQQRKFLQNLMFNNETGDSLIKKGVPDSYKVGDKSGQGTTYGTRNDVALIYPKHQTKPIVLVVFTKHQQQDAQPQDELVAQAARHAIHQLD"},"dna_sequence":{"accession":"KY363207.1","fmin":"2236","fmax":"3085","strand":"+","sequence":"ATGAAAAAGTTTTTTACTATCTTTGTCTTACTCTGTGTTTGCTTCGCTTACACAACTGCTACTGCTTCAGCGCAAGGTTTAACTAAATTAGAACATAAAAATGATGCCACAGTAGGTGTTTATGGCATTAATACTGCTACTGGACAAACTTATTCGCACAACGCTGATACCCGTTTTGCTTATGCATCAACTTTTAAAGCCATTACGAGTGGGTTATTATTACAGCAAAATTCTCCTGAAGCATTAAACAAAACTGTAACAATAAAAGAATCAGATATCGTGGCATATTCACCTGTTACTGAACAATATGTTGGAAAAACAATGACCCTACGTCAACTCATTTCCGCTGCTATGTTACAGAGTGACAATACTGCTAGCAATATCATAATGGAGCAACTCGGTGGTCTGGATCAAATTTCGTCTCGTTTACAAGCACTCGGAGATACAACAACAAACCCACAACGTTACGAACCTGAGTTAAACAACTATGACCCTCAAAGTACAGCAGATACATCAACACCTCGTGCTACTGCCCATAGTTTACAACAGCTGTTAACAACTGATGCAGTTGCACCACAACAACGCAAGTTCTTACAAAATTTAATGTTTAATAATGAAACAGGCGATAGTTTAATCAAAAAAGGTGTTCCAGACAGTTATAAAGTAGGCGACAAAAGTGGTCAGGGTACAACTTATGGTACACGTAATGATGTTGCCCTCATATATCCAAAACATCAAACTAAGCCAATTGTTTTAGTCGTCTTTACGAAACATCAGCAACAAGACGCACAACCACAAGATGAGTTAGTTGCACAAGCAGCACGTCATGCAATACATCAGCTCGATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42844","NCBI_taxonomy_name":"Staphylococcus arlettae","NCBI_taxonomy_id":"29378"}}}},"ARO_accession":"3004735","ARO_id":"42845","ARO_name":"ARL-2","CARD_short_name":"ARL-2","ARO_description":"ARL-2 is a beta-lactamase gene found in Staphylococcus Arlettae.","ARO_category":{"42853":{"category_aro_accession":"3004742","category_aro_cvterm_id":"42853","category_aro_name":"ARL Beta-lactamase","category_aro_description":"ARL beta-lactamase is an AMR Gene Family associated with Staphylococcus arlettae.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3558":{"model_id":"3558","model_name":"BAT-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"5753":{"protein_sequence":{"accession":"EIM09515.1","sequence":"MKKRKMPAVFLALIGAAGLLFTTSVQPISEASAAEKNLNIKKLDVDEFFADHNGTFILRDMNKGKTFIYNHERANQRFAPQSTFKVPNALIGLQVGAVEDEYSIKYWDGVKREIDIWNQDHTLGSGMRHSVVWYYQAMARDIGESRMKEWIEKISYGNQDISGGIDQFWLSSTLKISPIEQADFMERLYKENLPFDKDVMKTVKRMMIQEEEDHSTLYGKTGSGTGIGWFFGFVKIDNRAYSFVTNIDGTGAEAKNITMDILKKYKLY"},"dna_sequence":{"accession":"AJRJ01000061.1","fmin":"17603","fmax":"18410","strand":"+","sequence":"ATGAAAAAACGCAAGATGCCAGCAGTTTTCTTAGCATTGATCGGTGCAGCCGGTCTATTATTTACTACAAGTGTACAGCCAATAAGCGAAGCTAGTGCTGCCGAAAAGAATCTGAATATCAAAAAGCTCGATGTCGATGAATTTTTTGCCGATCATAACGGAACGTTTATATTACGTGATATGAATAAAGGCAAAACATTTATCTATAATCATGAACGCGCCAACCAAAGATTTGCACCGCAATCGACTTTTAAAGTTCCTAATGCACTCATTGGCTTACAAGTAGGAGCTGTAGAAGATGAATATTCCATTAAATATTGGGATGGCGTGAAGCGGGAAATTGACATCTGGAATCAAGATCACACGCTTGGGTCTGGGATGAGGCATTCAGTTGTTTGGTATTATCAAGCGATGGCCCGTGACATTGGAGAAAGTCGAATGAAGGAATGGATCGAAAAAATTTCCTATGGCAACCAAGATATAAGCGGTGGAATTGACCAGTTTTGGTTAAGCAGCACACTCAAAATTTCTCCGATAGAACAAGCAGACTTTATGGAAAGATTGTATAAAGAGAACCTGCCTTTTGATAAGGATGTCATGAAAACAGTAAAACGGATGATGATTCAGGAGGAAGAAGATCACTCTACTCTTTACGGAAAAACAGGTTCAGGGACAGGCATAGGGTGGTTTTTCGGTTTTGTGAAAATAGACAATCGAGCGTATAGTTTTGTTACGAATATTGATGGAACAGGTGCAGAAGCTAAAAACATCACAATGGATATTTTAAAGAAATATAAGTTATATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42859","NCBI_taxonomy_name":"Bacillus atrophaeus C89","NCBI_taxonomy_id":"334727"}}}},"ARO_accession":"3004747","ARO_id":"42858","ARO_name":"BAT-1","CARD_short_name":"BAT-1","ARO_description":"BAT-1 is a class D beta-lactamase found in Bacillus atrophaeus.","ARO_category":{"42857":{"category_aro_accession":"3004746","category_aro_cvterm_id":"42857","category_aro_name":"BAT Beta-lactamase","category_aro_description":"BAT is a class D beta-lactamase.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3560":{"model_id":"3560","model_name":"BES-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"590"}},"model_sequences":{"sequence":{"5755":{"protein_sequence":{"accession":"AAF61147.1","sequence":"MWQWLGKVRWLLVVIALLGGKVMAASELDSALARLEQQHHGRLGLAYIDSGSGESYSYRGEERFAFCSTFKAVLAGAVLQRSVSQPGLLDKRVHYAATDLLAYAPITKTHLDKGMRIGELAAAAVQYSDNTAANLLLQEIGGVQALNRFVQGLGDPAFRLDRIEPHLNSAEPGDVRDTTTPLAMAHTLQAMTLGKGLPQAQQAQLVSWLKGNTTGAQRIQAGVPAGWQVGDKTGTGGYGTTNDIAILWPEQGAPKVLAIYFTQPAADAEANRAILAEATRLVLQDKSINKIK"},"dna_sequence":{"accession":"AF234999.1","fmin":"189","fmax":"1068","strand":"+","sequence":"ATGTGGCAGTGGCTTGGAAAAGTGCGGTGGTTGCTGGTGGTGATAGCGCTGCTGGGTGGCAAGGTCATGGCGGCGTCTGAACTGGATAGCGCGCTGGCCAGACTCGAGCAGCAGCATCATGGGCGTCTGGGGCTGGCCTATATCGATAGTGGCAGCGGCGAGAGTTACAGCTATCGCGGTGAGGAGCGTTTTGCCTTTTGCAGCACCTTCAAGGCGGTGCTGGCGGGGGCGGTGCTGCAGCGAAGCGTCAGTCAGCCCGGTTTGCTCGATAAGCGGGTGCATTATGCGGCCACGGATCTGCTCGCCTATGCCCCCATCACCAAGACGCATCTGGATAAAGGGATGCGCATCGGTGAACTGGCCGCAGCGGCGGTGCAATATAGTGACAACACGGCGGCCAACCTGCTGCTGCAAGAAATTGGCGGCGTCCAGGCGCTGAACCGGTTTGTGCAGGGGTTGGGAGATCCGGCATTCCGTCTGGATAGGATAGAGCCTCACCTTAATAGTGCCGAGCCAGGAGATGTGCGCGATACCACCACGCCGCTGGCCATGGCCCACACCCTGCAGGCCATGACTCTGGGCAAGGGGTTACCACAGGCCCAGCAGGCGCAACTGGTGAGCTGGCTTAAAGGCAATACCACGGGGGCACAGCGTATTCAAGCTGGCGTACCGGCAGGCTGGCAGGTAGGCGACAAGACTGGCACAGGTGGTTACGGCACCACCAACGATATCGCCATCCTCTGGCCGGAGCAGGGTGCTCCCAAGGTGCTGGCCATCTACTTTACCCAGCCCGCAGCCGATGCCGAGGCCAACCGCGCCATACTGGCCGAAGCCACCCGACTGGTACTGCAAGATAAAAGTATCAATAAAATCAAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36783","NCBI_taxonomy_name":"Serratia marcescens","NCBI_taxonomy_id":"615"}}}},"ARO_accession":"3004751","ARO_id":"42863","ARO_name":"BES-1","CARD_short_name":"BES-1","ARO_description":"BES-1 is a class A beta-lactamase that is found in Serratia marcescens.","ARO_category":{"42862":{"category_aro_accession":"3004750","category_aro_cvterm_id":"42862","category_aro_name":"BES Beta-lactamase","category_aro_description":"BES beta-lactamase is a class A beta-lactamase family.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3566":{"model_id":"3566","model_name":"BRO-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"634"}},"model_sequences":{"sequence":{"5761":{"protein_sequence":{"accession":"CAA90891.1","sequence":"MMQRRHFLQKTLLALPIIFSGNLLTGCKTNLSDDYLPDDKITNNPNLLQNKLKEILPIWENKFNAKIGMTIIADNGELSSHRGNEYFPVNSTIKAFIASHILLLVDKEKLDLNEKIIIKESDLIEYSPVCKKYFDENKPISISELCEATITLSDNGSANILLDKIGGLTAFNQFLKEIGADMVLANNEPLLNRSHYGETSDTAKPIPYTKSLKALIVGNILSNQSKEQLITWLINDKVADNLLRKYLPKNWRIGDKTGTGSESKNIIAVIWNENNKPYFISLFITQPHDGKSLGFKNQKDEIMAQIGKEIYPFL"},"dna_sequence":{"accession":"Z54181.1","fmin":"62","fmax":"1007","strand":"+","sequence":"ATGATGCAACGCCGTCATTTTTTACAAAAAACCTTATTGGCACTACCTATTATTTTTTCTGGCAATTTATTAACTGGATGTAAAACGAATTTGTCTGATGATTATTTGCCCGATGACAAGATAACAAACAATCCAAATTTATTACAAAATAAATTAAAAGAGATATTGCCAATTTGGGAAAATAAATTTAATGCCAAAATTGGTATGACGATTATTGCTGACAATGGTGAACTATCCAGTCATCGTGGTAATGAATATTTTCCTGTTAATAGTACCATTAAAGCCTTTATTGCAAGTCATATATTATTACTTGTAGATAAAGAAAAATTGGATTTAAACGAAAAAATCATCATTAAAGAAAGCGATTTGATAGAATATTCTCCTGTCTGTAAAAAATACTTTGATGAGAATAAACCAATTTCTATTAGTGAATTGTGCGAAGCTACCATAACACTGAGTGATAATGGTTCTGCTAATATCTTGTTGGATAAAATTGGGGGTTTGACTGCATTCAATCAATTTTTGAAAGAGATTGGGGCGGATATGGTGCTGGCAAATAATGAACCTTTATTAAATCGCTCACATTATGGTGAAACCAGTGATACCGCAAAACCAATTCCTTACACAAAAAGCCTAAAAGCACTGATTGTAGGCAATATCCTATCCAATCAAAGCAAAGAACAGTTGATAACTTGGCTTATCAACGATAAAGTTGCTGATAATTTATTGAGAAAATATTTACCAAAAAATTGGCGAATTGGCGACAAAACAGGCACAGGTAGTGAATCAAAAAATATCATTGCTGTGATTTGGAATGAAAATAATAAACCTTATTTTATCAGCCTATTTATCACCCAGCCCCATGATGGTAAATCCCTTGGTTTTAAAAATCAAAAAGATGAAATAATGGCACAAATTGGTAAAGAAATTTATCCATTTTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42876","NCBI_taxonomy_name":"Moraxella catarrhalis ATCC 43617","NCBI_taxonomy_id":"857580"}}}},"ARO_accession":"3004762","ARO_id":"42875","ARO_name":"BRO-2","CARD_short_name":"BRO-2","ARO_description":"BRO-2 is a class A beta-lactamase found in M.catarrhalis.","ARO_category":{"42873":{"category_aro_accession":"3004760","category_aro_cvterm_id":"42873","category_aro_name":"BRO Beta-lactamase","category_aro_description":"BRO is a class A beta-lactamase that is found in M.catarrhalis.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2790":{"model_id":"2790","model_name":"Serratia marcescens Omp1","model_type":"protein knockout model","model_type_id":"40354","model_description":"Protein Knockout Models (PKM) reflect resistance by the absence of a gene product, most often deletion of a gene involved in antibiotic import, such as Vibrio cholerae OmpT. Like Protein Homolog Models (PHMs), PKMs include a reference sequence and a bitscore cut-off for detection using BLASTP but instead are designed to only report lack of detection under Perfect or Strict criteria. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff. This model type is still under development and not currently supported by the Resistance Gene Identifier (RGI) software.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"5857":{"protein_sequence":{"accession":"AIA49384.1","sequence":"MKRNILAVVIPALLAAGAANAAEIYNKDGNKLDLYGKVDGLHYFSDDKGNDGDQTYVRFGFKGETQITDQLTGYGQWEYNVQANHSESQGTEGTKTRLGFAGLKFADYGSFDYGRNYGVLYDVEGWTDMLPEFGGDTYTYTDNFMTGRTNGVATYRNNNFFGLVDGLNFAVQYQGKNQNDGRNVKKQNGDGWGISSTYDIGEGVSFGAAYASSNRTDDQKLRSNERGDKADAWTVGAKYDANNVYLAAMYAETRNMTPFGGGNFGAGCAATDDKCGGFASKTQNFEVTAQYQFDFGLRPEVSYLQSKGKNLNVPGVGSDQDLVKYVSVGTTYYFNKNMSTYVDYKINLLDDNEFTKATGTATDDIVAVGLVYQF"},"dna_sequence":{"accession":"CP005927.1","fmin":"4318934","fmax":"4320059","strand":"+","sequence":"ATGAAGCGCAACATTCTTGCAGTGGTTATCCCGGCTCTGTTGGCTGCTGGTGCAGCAAACGCAGCTGAAATCTACAACAAAGACGGCAACAAGCTGGATCTGTACGGCAAAGTTGACGGTCTGCACTACTTCTCCGACGACAAAGGTAATGACGGCGATCAGACCTATGTTCGTTTCGGCTTCAAAGGTGAAACTCAGATTACTGACCAACTGACCGGTTACGGCCAGTGGGAATACAACGTCCAGGCTAACCACTCCGAATCTCAGGGCACCGAAGGCACCAAAACCCGTCTGGGCTTCGCGGGTCTGAAATTCGCTGACTACGGCTCCTTCGACTACGGCCGTAACTACGGCGTACTGTACGACGTGGAAGGCTGGACCGATATGCTGCCAGAGTTCGGTGGCGATACTTACACCTACACCGACAACTTCATGACCGGCCGTACCAACGGCGTTGCGACCTATCGTAACAACAACTTCTTCGGTCTGGTTGACGGTCTGAACTTCGCCGTTCAGTACCAGGGCAAAAACCAGAACGACGGCCGTAACGTCAAGAAACAAAACGGCGACGGCTGGGGCATCTCCTCTACTTATGACATCGGCGAAGGCGTAAGCTTCGGCGCTGCATACGCATCTTCTAACCGTACCGACGACCAAAAACTGCGTTCCAACGAGCGTGGCGACAAGGCTGACGCATGGACCGTGGGCGCGAAATACGACGCCAACAACGTTTACCTGGCGGCGATGTACGCAGAAACCCGTAACATGACTCCGTTCGGCGGCGGTAACTTCGGTGCTGGCTGTGCAGCTACCGATGACAAGTGCGGCGGCTTCGCGAGCAAAACTCAGAACTTCGAAGTGACTGCTCAGTACCAGTTCGACTTCGGTCTGCGTCCAGAAGTGTCTTACCTGCAGTCTAAAGGTAAAAACCTGAACGTCCCAGGCGTGGGTTCTGACCAGGATCTGGTTAAATATGTTTCTGTTGGTACCACCTATTACTTCAACAAGAACATGTCCACCTACGTTGATTACAAAATCAACCTGCTGGATGACAACGAGTTCACCAAAGCAACCGGCACCGCTACCGACGATATCGTAGCTGTTGGTCTGGTATACCAGTTCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41255","NCBI_taxonomy_name":"Serratia sp. FS14","NCBI_taxonomy_id":"1327989"}}}},"ARO_accession":"3004128","ARO_id":"41254","ARO_name":"Serratia marcescens Omp1","CARD_short_name":"Smar_Omp1","ARO_description":"Omp1 is an outer membrane porin that confers resistance by absence in S. marcescens.  Knockout, deletion or other inhibition of the omp1 gene confers resistance to certain beta-lactamase antibiotics - including Cefoxitin, Ceftriaxone, Cefotaxime, and Moxalactam - as well as Ciprofloxacin, Tetracycline, and Chloramphenicol, by preventing passage of the antibiotic into the cell.","ARO_category":{"41445":{"category_aro_accession":"3004281","category_aro_cvterm_id":"41445","category_aro_name":"General Bacterial Porin with reduced permeability to beta-lactams","category_aro_description":"These are GBPs that are associated with decreased susceptibility to beta-lactams either through mutations in the porin protein, absence of the porin protein, or expression of the porin protein.","category_aro_class_name":"AMR Gene Family"},"35927":{"category_aro_accession":"0000008","category_aro_cvterm_id":"35927","category_aro_name":"cefoxitin","category_aro_description":"Cefoxitin is a cephamycin antibiotic often grouped with the second generation cephalosporins. Cefoxitin is bactericidal and acts by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. Cefoxitin's 7-alpha-methoxy group and 3' leaving group make it a poor substrate for most beta-lactamases.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35979":{"category_aro_accession":"0000062","category_aro_cvterm_id":"35979","category_aro_name":"ceftriaxone","category_aro_description":"Ceftriaxone is a third-generation cephalosporin antibiotic. The presence of an aminothiazolyl sidechain increases ceftriazone's resistance to beta-lactamases. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36989":{"category_aro_accession":"3000645","category_aro_cvterm_id":"36989","category_aro_name":"cefotaxime","category_aro_description":"Cefotaxime is a semisynthetic cephalosporin taken parenterally. It is resistant to most beta-lactamases and active against Gram-negative rods and cocci due to its aminothiazoyl and methoximino functional groups.","category_aro_class_name":"Antibiotic"},"40944":{"category_aro_accession":"3004017","category_aro_cvterm_id":"40944","category_aro_name":"moxalactam","category_aro_description":"Moxalactam (Latamoxef) is a broad spectrum cephalosporin (oxacephem) and beta-lactam antibiotic. Moxalactam binding to PBPs inhibits peptidoglycan cross-linkage in the cell wall, resulting in cell death. Moxalactam is proposed to be effective against meningitides as it passes the blood-brain barrier.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36383":{"category_aro_accession":"3000244","category_aro_cvterm_id":"36383","category_aro_name":"reduced permeability to antibiotic","category_aro_description":"Reduction in permeability to antibiotic, generally through reduced production of porins, can provide resistance.","category_aro_class_name":"Resistance Mechanism"},"40429":{"category_aro_accession":"3003764","category_aro_cvterm_id":"40429","category_aro_name":"resistance by absence","category_aro_description":"Mechanism of antibiotic resistance conferred by deletion of gene (usually a porin).","category_aro_class_name":"Resistance Mechanism"}}},"2805":{"model_id":"2805","model_name":"Mycoplasma gallisepticum 23S rRNA mutation conferring resistance to pleuromutilin antibiotics","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"7889":"a2072g","7890":"a2073g","7892":"g2461a","7891":"g2075t","7895":"g2461t","7897":"a2586t","7896":"t2518g","7894":"c2069a","7893":"a2517t"},"Curated-R":{"7889":"a2072g","7890":"a2073g","7892":"g2461a","7891":"g2075t","7895":"g2461t","7897":"a2586t","7896":"t2518g","7894":"c2069a","7893":"a2517t"},"clinical":{"7889":"a2072g","7890":"a2073g","7892":"g2461a","7891":"g2075t","7895":"g2461t","7897":"a2586t","7896":"t2518g","7894":"c2069a","7893":"a2517t"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"41093","param_value":"5000"}},"model_sequences":{"sequence":{"4152":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"NC_004829.2","fmin":"80510","fmax":"83423","strand":"+","sequence":"ATACATAAGTTACTAAGGGCTTATGGTGGATGCCTTGGCACTAGAAGGCGATGAAGGACGTGCAAACCTGCGAAATGCTACGGGGAGCTGGTTGGAAGCGATAATCCGTAGATGTCCGAATGGGGGAACCTGATTAATAGTGATATTAATTATTTAGATCTGAATACATAGGGTCTAAAAGCAATACGTTGTGAAGTGAAACATCTCAGTAGCAACAGGAAAAGAAATCGAAAGAGATTCCGTGTGTAGTGGCGAGCGAAAGCGGAACAGGCCAAACCAAGATTTATCTTGGGGTTATAGGACTGCAATGTGGACTTTGAACTGATAGGAGAAGTAGTTGAAAAGCTACGCGATAAAGGGTTATAGCCCCGTATCTTAAATTGGTTTAATACCTAGCAGGATCCTGAGTACATCGAGAAACGTTATCTTGATGGAAGTCGCCCAGACCATTGGGCAAGCCTAAATACTAACTAGTGACCGATAGCGTATAGTACCGTGAGGGAAAGGTGAAAAGAACCCAGGGATGGGAGTGAAATAGATTCTGAAGCCATATGCCTACAACGTGTCAGAGCACATTAATGTGTGATGGCGTGCGTTTTGAAGTATGAGCCGGCGAGTTATGATAGCAAGCAGGTTAACCTTTAGAAGGGAAGCCGAAGCGAAAGCGAGTTTGAATAGAGCGAATTAAAGTGTTTGTTATTATAGACCCGAAACGGGTTGAGCTAGTCATGGGCAGGTTGAAGTTAGAGTAACATCTAATGGAGGACCGAACCGACTTTCGTTGAAACGACAGCGGATGACCTGTGACTAGGGGTGAAATTCCAATCGAAATCCGTGATAGCTGGTTCTCGTCGAAATAGTTTTAAGACTAGCGTAAGATCATGATCAACTGGAGGTAGAGCTACTGAATGTATGATGGCGCCGCCTTGGTGTACTGAATACAATTAAACTCCGAATGCCAATTGATTTATTCTTGCAGTCAGACAGTGGGGGATAAGCTTCATTGTCACAAGGGGAAGAGCCCAGATCATTAAATAAGGTCCCTAAAATATGCTAAGTGGAAAAGGTTGTTAAAATACTTAAACAGCAAGGATGTTGGCTTAGAAGCAGCCATCGTTTAAAGAGTGCGTAACAGCTCACTTGTCGAGTGTTTTTGCGCCGAAGATGTAACGGGGCTAAGCATATTACCGAATTTATGGATTATTATTCGTAAGAATGATAGTGGTAGACGAGCGTTGTATATGGGATGAAGTCAAACCGTGAGGATTGGTGGACTGTATACAAGTGAGAATGCCGGTGTAAGTAACGCTTGAGAGTGAGAATCTCTCAAACCGATTGACTAAGGTTTCCTGGACGAGGGTCGTCCTTCCAGGGTTAGTCTGGACCTAAGGCGAGGCAGAAATACGTAGTCGATGGAAGAACAGGTTAATATTCCTGTACAAACAAATAGCTGATGGAGTGACGGAGAAGGTTAATGCATCCCCATTATCGGATTTGGGGTTAAATAAGAAGTCTTAAGGGTTGGCAAATCCGCCTTTTTTAAGGACAACTTATGAATACGAGTGAACGCTTTGCAAGTAGCGAAGATGCATACATCACGCTTCCAAGAAAAGCTTCTAGGGTTAACTATTTGTTTCCAGTACCGAGAACGAACACACGTGGTCAAGGAGAAGATCCTAAGGTTAGCGAGTGAACTATAGCTAAGGAACTCTGCAAATTCATCCCGTAAGTTCGCAAGAAGGGATGCTCAATGTAACAGTTGAGCCGCAGTGAAGAACGAGGGGGGACTGTTTAACTAAAACACAGCTCTATGCTAAATCGCAAGATGATGTATATGGGGTGACACCTGCCCAGTGCTGGAAGGTTAAAGAAGGGTGTTAGAGCAATCAAAGCTCCCGACTGAAGCCCCAGTGAACGGCGGCCGTAACTATAACGGTCCTAAGGTAGCGAAATTCCTTGTCGGGTAAATTCCGTCCCGCTTGAATGGTGTAACCATCTCTTGACTGTCTCGGCTATAGACTCGGTGAAATCCAGGTACGGGTGAAGACACCCGTTAGGCGCAACGGGACGGAAAGACCCCATGAAGCTTTACTGTAACTTAATATTGGGCAGAGTTTAGACATATAGAGAATAGGTGGGAGACTTTGAAGCAACTTCGCTAGGAGTTGTGGAGTCACCAGTGGAATACCACCTTTGTTTAAATTCTTCTCTAACTAGTTGCTGTTATCCAGCAATAGGACAGTGTTAGGCGGGCAGTTTGACTGGGGCGGTCGCCTCCCAAAAGGTAACGGAGGCGTGCAAAGGTACCCTCAGCACGGTTGGAAATCGTGTTAAGAGTGTAATGGTATAAGGGTGCTTGACTGTGAGACTAACAGGTCGAACAGGTAAGAAATTAGGTCATAGTGATCCGGTGGTTCAGTATGGAATGGCCATCGCTCAACGGATAAAAGCTACTCTGGGGATAACAGGCTGATACTGCCCAAGAGTTCACATCGACGGCAGTGTTTGGCACCTCGATGTCGACTCATCTCATCCTCGAGCTGAAGCAGGTTCGAAGGGTTCGGCTGTTCGCCGATTAAAGAGATACGTGAGTTGGGTTCAAACCGTCGCGAGACAGGTTGGTCCCTATCTATTGTGCCCGCAGGAAGATTGAAAAGATTTACTCTTAGTACGAGAGGACCGGAGTGAAGACACCTCTTGTGCTCCAGTTGTAGTGCCAACTGCACCGCTGGGTAGCAACGTGTCGAACGGATAAACGCTGAAAGCATCTAAGTGTGAAACCGACTTTAAGAATAATCTTCCCTTCCAGCAATGGAGTAAGAATCGTTGTAGACTACGACGTTGATAGGCTAAAGGTGTAAGTGCCGCGAGGTATTTAGCTGATTAGTACTAATAATTCGAGGACTTAGATTT","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41282","NCBI_taxonomy_name":"Mycoplasma gallisepticum str. R(low)","NCBI_taxonomy_id":"710127"}}}},"ARO_accession":"3004159","ARO_id":"41306","ARO_name":"Mycoplasma gallisepticum 23S rRNA mutation conferring resistance to pleuromutilin antibiotics","CARD_short_name":"Mgal_23S_PLM","ARO_description":"Point mutations in the 23S rRNA (domain V) of Mycoplasma gallisepticum can confer resistance to pleuromutilin antibiotics (tiamulin and valnemulin). The mutants also show cross-resistance to lincomycin, chloramphenicol and florfenicol.","ARO_category":{"41330":{"category_aro_accession":"3004178","category_aro_cvterm_id":"41330","category_aro_name":"23S rRNA with mutation conferring resistance to pleuromutilin antibiotics","category_aro_description":"Point mutations in the 23S rRNA subunit may confer resistance to pleuromutilin antibiotics.","category_aro_class_name":"AMR Gene Family"},"37716":{"category_aro_accession":"3001317","category_aro_cvterm_id":"37716","category_aro_name":"pleuromutilin","category_aro_description":"Pleuromutilin is a natural product antibiotic produced by Clitopilus passeckerianus. Related antibiotics of clinical significance, such as tiamulin and retapamulin, are semi-synthetic derivatives of this compound.","category_aro_class_name":"Antibiotic"},"37014":{"category_aro_accession":"3000670","category_aro_cvterm_id":"37014","category_aro_name":"pleuromutilin antibiotic","category_aro_description":"Pleuromutilins are natural fungal products that target bacterial protein translation by binding the the 23S rRNA, blocking the ribosome P site at the 50S subunit. They are mostly used for agriculture and veterinary purposes.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2791":{"model_id":"2791","model_name":"Streptococcus mitis CdsA with mutation conferring daptomycin resistance","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"7791":"D222N"},"Curated-R":{"7791":"D222N"},"clinical":{"7791":"D222N"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"475"}},"model_sequences":{"sequence":{"4106":{"protein_sequence":{"accession":"AQA08261.1","sequence":"MTKDLQKRTLFAVLALAIFLPVLFAGGLLLQIGIGLLAMLGVHELLHMKGLKTMTIEGALTLFATFALTVPLENYLTFLPVDGNVVAYSVLITIMLGTTVFSKNYTIEDAAFPIAVSFYVGFGFNALLDARVAGFDKVLLALFIVWATDSAAYLTGMNFGKHKLAPRVSPNKSIEGFVGGILGAVLITVIFMLVDSTVALPYGIYRMSLFAAFFSVAGQFGDLIESAMKRHFGVKDSGKFIPGHGGVLDRFDSMLIVFPMMHLFGLF"},"dna_sequence":{"accession":"CP019562.1","fmin":"220125","fmax":"220929","strand":"+","sequence":"ATGACCAAGGATTTACAAAAGAGAACATTGTTTGCGGTATTGGCCCTGGCGATTTTCCTTCCAGTCTTGTTTGCGGGAGGGCTCTTGTTGCAGATAGGGATTGGCTTGTTAGCGATGCTAGGCGTCCATGAACTCTTGCATATGAAGGGACTAAAGACTATGACCATTGAGGGTGCTTTGACTCTTTTTGCGACCTTCGCTCTCACAGTTCCTTTAGAAAATTACCTAACTTTTTTGCCTGTTGATGGAAATGTGGTTGCCTATAGTGTTCTGATTACCATAATGCTAGGGACGACCGTTTTCAGTAAAAACTATACGATTGAAGATGCCGCTTTTCCAATTGCTGTGAGTTTTTATGTTGGTTTTGGCTTCAATGCCTTACTAGATGCTCGGGTGGCAGGTTTTGACAAGGTACTTTTGGCCCTTTTTATCGTTTGGGCGACAGATAGCGCAGCCTACCTGACAGGGATGAATTTTGGTAAACATAAGTTGGCTCCGAGAGTTTCTCCTAATAAGAGTATTGAGGGCTTTGTCGGTGGTATTCTAGGTGCGGTACTGATAACAGTGATTTTCATGTTAGTGGACAGCACAGTTGCTCTTCCTTATGGGATTTATAGAATGAGTCTCTTTGCTGCCTTCTTCAGTGTGGCCGGTCAGTTTGGTGACTTGATTGAAAGTGCCATGAAACGCCATTTCGGTGTCAAGGATTCTGGCAAATTTATCCCTGGACATGGCGGTGTGTTGGATCGCTTTGACAGCATGCTGATTGTGTTTCCAATGATGCACTTATTTGGCCTGTTTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39527","NCBI_taxonomy_name":"Streptococcus oralis","NCBI_taxonomy_id":"1303"}}}},"ARO_accession":"3004097","ARO_id":"41205","ARO_name":"Streptococcus mitis CdsA with mutation conferring daptomycin resistance","CARD_short_name":"Smit_CdsA_DAP","ARO_description":"CdsA is a phosphatidate cytidylyltransferase which plays a role in the production of membrane phosphatidylglycerol and cardiolipin.","ARO_category":{"41204":{"category_aro_accession":"3004096","category_aro_cvterm_id":"41204","category_aro_name":"daptomycin resistant CdsA","category_aro_description":"Mutations to the CdsA phosphatidate cytidylyltransferase conferring resistance to daptomycin.","category_aro_class_name":"AMR Gene Family"},"35985":{"category_aro_accession":"0000068","category_aro_cvterm_id":"35985","category_aro_name":"daptomycin","category_aro_description":"Daptomycin is a novel lipopeptide antibiotic used in the treatment of certain infections caused by Gram-positive organisms. Daptomycin interferes with the bacterial cell membrane, reducing membrane potential and inhibiting cell wall synthesis.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2833":{"model_id":"2833","model_name":"Brachyspira hyodysenteriae 23S rRNA with mutation conferring resistance to tylosin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"8198":"a2058g","8199":"a2058t"},"Curated-R":{"8198":"a2058g","8199":"a2058t"},"clinical":{"8198":"a2058g","8199":"a2058t"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"41093","param_value":"2000"}},"model_sequences":{"sequence":{"4183":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"NZ_CP015910.2","fmin":"2512812","fmax":"2515808","strand":"-","sequence":"ATATGGTCAAGTCATTGGTCTGATTAGTGCTGCTCAGCTGAACAGGTATTTCTTCCCTGCTTACACTTGCAGTCTATCAACGTCGTAGTCTCCAACGAAACTCATAGGGAAAGTTAATCTTGAAGGAGGCTTCCCACTTAGATGCTTTCAGCGGTTATCCCGTCCGCACATAGCTACTCTGCGATGCTCTTGGCAGAACAACAGATACACCAGCGGTGCGTTCATTCCGGTCCTCTCGTACTAAGAATGACTCTTCTCAACTTTCCAACGCCCACAACGGATAGGGACCAAACTGTCTCACGACGTTCTGAACCCAGCTCGCGTACCGCTTTAATTGGCGAACAGCCAAACCCTTGGGACCTGCTCCAGCCCCAGGATGCGATGAGCCGACATCGAGGTGCCAAACCTCCCCGTCGATATGAACTCTTGGGGGAGATAAGCCTGTTATCCCCGGAGTACCTTTTGTCCGTTTAGCGATGGCCCTTCCACTCGGGACCACCGGATCACTAAAACCTACTTTCGTACCTGCTCGAGATGTCTCTCTCGCAGTCAAGCCACCTTATGCCTTTATACTCTACTACCGATTTCTATTCGGTTTGAGGTGACCTTTGCACGCCTCCGTTACTCTTTAGGAGGCGACCGCCCCAGTCAAACTACCCGCCTGACAATGTCCGACTGCCGGATAACGGCTAATCGTTAGAATCCCATTTTGCGAAGGATGGTATTTCAACGATGGCTCCATGAAAGCTGGCGCTCCCACTTCAAAGCCTCCCATCTATCCTACACATCACAAAACAAAACTCAATGTCAAGTTATAGTAAAGGTTCACGGGGTCTTTCCGTCCTGTTGCGGGTAATCAGCATCTTCACTGATAATTCAATTTCACCGAGTTCTTCCCCGAGACAGTGCCCGGATCGTTACACCATTCGTGCAGGTCGGAACTTACCCGACAAGGAATTTCGCTACCTTAGGACCGTCATAGTTACGGCCGCCGTTTACTGGGGCTTCAATTCGAAGCTTCGCTTACGCTAACCTCTCCTTTTAACCTTCCAGCACTGGGCAGGTGTCAATCCCTATACATCCATTTACATGTTTGCAGAGATCTGTGTTTTTGTTAAACAGTCGGCCAGGCCTTTTCACTGCGACTCTCCTCTCAATATTGCTACCAAGATTCAAGCGTCTCTTTTTCCGAAGTTACAAGACTAATTTGCAGAGTTCCTTAGGGAAGATTATCTCGAGCGCCTTAGAATACTCATCTCACCCACCTGTGTCGGTTTGCGGTACGATTATGACATGCCTAACCTTAGAAATTATTTCTCGACAGCCTAGCTCATGCAACTTCCTGAACCCGAAAGCCCAGTCACTATCCAGCCTCAACCTTAAAGAAGCAAGCATTTGACTCACCTCAAGTCTAAACTGTTTGACGTTATCTACCAATCTAACGCGTACATAAACAATCTGTGTCATTCCATCGAAACATATCATAGTACAGGAATATTTACCTGTTTCCCATCGACTACGCTTTTCAGCCTCATCTTAGGGGTCGACTAACCCTAGGCAGATTAGCTTTACCTAGGAAACCTTGGGTTTGCGGCGAACGGGTTTCTCACCCGTTTTCTCGTTACTCATGCCTGCATCCTCACTTCTTATACCTCCAGCCCACCTCACGATGAACCTTCGACGGCTTAAAGAACGCTCTCCTACCAATTATAGATTAACTCTATAATTCCCTAGCTTCGGTACTATGTTTGAGCCCCGTTACATTTTCGGCGCAAGAACACTCGACCAGTGAGCTGTTACGCACTCTTTAAAGGAATGGCTGCTTCTAAGCCAACCTCCTGGCTGTTTAAGTATTCTCACATCCTTTCCCACTTAACATAGATTTTGGGACCTTAGCTGAGGATCTGGGCTGTTTCCCTTTTGACAATGACGCTTATCCGCCGCTGTCTAACTGCCATGTTCTTAACTTACGGTATTCGGAGTTTAGTTGGGTTTGGTACTCGGTTAGGAGCCCTAGTCCATTTAGTGCTCTACCCCCGCAAGTAAACACATAACGCTGCCCCTAAAGACATTTCGGAGAGAACCAGCTATCTCCAAGTTTGATTAGCCTTTCACTCCTACCCACAAGTCATCCAAAGCCTTTTCACGGCCACTGGTTCGCACCTCCATTCGATGTTACTCGAGTTTCGCGCTGCTCATAGGTAGATCACTTGGCTTCGGGTCGTATAGCATGCAACTAATTTCGCCCTATTAAGGCTCGCTTTCACTACGACTACAAGGCTATTACCTCTTAATCTTGCTACATACTATAAGTCGCAGGCTCATTCTACAAAAGGCACGCCATCAGGCCATCTACTATTGCTAGCAGGGTACCCTCTGACTACTTGTAAGCTTAAGGTTTCAGGTTCTATTTAATAACCCTCAACGGGAGACTTTTCACCTTTCCCTCACGGTACTCTACACTATTGGTCACTGGTTAGTATTTTGCCTTGGATAGTGGTCTACCCAGATTCAAACAGGGTTTCACGTGCCCCGCCCTACTCAGGAACGATAAAACCTTGTCTATATGATTTCGTGTACAGGACTATCACCCACTATGGTCTGCTTTTCCAAAACAGTTCCACTATCATATAAAGCAAAGTCGATGCATGCAAGTACATCGCTTACCGCCCTACAACACCATAATAACAACGCCTTGCAGCTTGACATTATTAAGGTTTAGGCTCTTCCCCTTTCGCTCGCCACTACTTAGGGAATCTCAATTTTGATTACTCTTCCTCCAGGTACTTAGATGTTTCAGTTCCCTGGGTGTCGCCTCATACACCTATGGATTCAGTGTATGATATAGAAGGTTTACTTCTATAGGTTTTCCCATTCGGTGATCTACGGATCATAGAATATTTGCTTCTCCCCGTAGCTTATCGCAGCTTGTCACGACCTTCATCGCCTTCCAGTGCCTAGGCATCCACCTTAAGCCCTTACTTACTTGACCATAT","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41351","NCBI_taxonomy_name":"Brachyspira hyodysenteriae ATCC 27164","NCBI_taxonomy_id":"1266923"}}}},"ARO_accession":"3004133","ARO_id":"41260","ARO_name":"Brachyspira hyodysenteriae 23S rRNA with mutation conferring resistance to tylosin","CARD_short_name":"Bhyo_23S_TYL","ARO_description":"Point mutation in B. hyodysenteriae 23S rRNA shown to confer resistance to tylosin and erythromycin.","ARO_category":{"41251":{"category_aro_accession":"3004125","category_aro_cvterm_id":"41251","category_aro_name":"23S rRNA with mutation conferring resistance to macrolide antibiotics","category_aro_description":"Nucleotide point mutations in the 23S rRNA subunit may confer resistance to macrolide antibiotics.","category_aro_class_name":"AMR Gene Family"},"36284":{"category_aro_accession":"3000145","category_aro_cvterm_id":"36284","category_aro_name":"tylosin","category_aro_description":"Tylosin is a 16-membered macrolide, naturally produced by Streptomyces fradiae. It interacts with the bacterial ribosome 50S subunit to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2792":{"model_id":"2792","model_name":"Moraxella catarrhalis 23S rRNA with mutation conferring resistance to macrolide antibiotics","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"41093","param_value":"5000"},"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"7794":"a2330t"},"Curated-R":{"7794":"a2330t"},"clinical":{"7794":"a2330t"}}},"model_sequences":{"sequence":{"5678":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"CP002005.1","fmin":"317713","fmax":"320869","strand":"-","sequence":"ATGGTCAAGCCAAACGAGCAATTAGTATTGGTTAGCTACATGTATCACTACACTTCCACACCCAACCTATCAACGTCGTCGTCTACAACGGCTCTTTAGGGAAATCTTATCTTGAGGTGGGCTTCCCGCTTAGATGCTTTCAGCGGTTATCCCATCCGAACATAGCTACTCGGCAATGCCACTGGCGTGACAACCGAAACACCAGAGGTTCGTCCACTCTGGTCCTCTCGTACTAGGAGCAGATCCTCTCAAATTTCCAACGCCCACGGTAGATAGGGACCGAACTGTCTCACGACGTTCTAAACCCAGCTCGCGTACCTCTTTAAATGGCGAACAGCCATACCCTTGGGACCTGCTTCAGCCCCAGGATGAGATGAGCCGACATCGAGGTGCCAAACACCGCCGTCGATATGAACTCTTGGGCGGTATCAGCCTGTTATCCCCAGAGTACCTTTTATCCGTTGAGCGATGGCCCTTCCATACAGAACCACCGGATCACTAAGACCTACTTTCGTACCTGCTCGACTTGTGGGTCTCGCAGTTAAGCGCGCTTTTGCCTTTATACTCTTTGAACGATTTCCGACCGTTCTGAGCGCACCTTCGTACTCCTCCGTTACTCTTTAGGAGGAGACCGCCCCAGTCAAACTACCCACCATACATTGTCCTTGGATTTGTTGATCCTAAGTTAGAACCCCAACATAACCAGGGTGGTATTTCAAGGTTGGCTCCACAAATACTGGCGTATCTGCTTCAAAGCCTCCCACCTATCCTACACAAGTTAGGTCAAAGTTCAATGTAAAGCTGTAGTAAAGGTTCACGGGGTCTTTCCGTCTAGCCGCGGGTACACAGCATCTTCACTGCGATTTCGATTTCACTGAGTCTCTGCTGGAGACAGCGCTGCCATCATTATGCCATTCGTGCAGGTCGGAACTTACCCGACAAGGAATTTCGCTACCTTAGGACCGTTATAGTTACGGCCGCCGTTTACTGGGGCTTCGATCAAGAGCTTCGCTTACGCTAACCCCATCAATTAACCTTCCAGCACCGGGCAGGCATCACACCCTATACGTCCACTTTCGTGTTTGCAGAGTGCTGTGTTTTTAATAAACAGTTGCAGCAGCCTGGTATCTGCGACTGCCAACAGCTCAAAGAGCAAGTCTTATCACCATCGGCAGCGTACCTTCTCCCGAAGTTACGGTACCATTTTGCCTAGTTCCTTCAGCAGAGTTCTCTCAAGCGCCTTGGTATTCTCTACCTGACCACCTGTGTCGGTTTCGGGTACGATTCGTTTATGACTATCGCTTAGAAGCTTTTCCTGGAAGCAGGGTATTTGCCACTTTGCCAGTAAACTGGCTTGCTATCAGATCTCATTAATAACCGAGCGGATTTGCCTACTCAGTCTAACTACATCCTTCCACCTGGACAACCATCGCCAGGCTGGCATAACCTTCTCCGTCCCTCCATCGCATCATAAACAAGTATCGGAATATTAACCGATTTCCCATCGACTACGCCTTTCGGCCTCGCCTTAGGGGTCGACTCACCCAGCCCCGATTAACGTTGGACTGGAACCCTTGGTCTTCCGGCGAACGGGCTTTTCACCCGTTTTGTCGTTACTCACGTCAGCATTCGCTCTTGTGATACCTCCAGCACACCTTACAGTGCACCTTCACAGGCTTACACAACGCTCCCCTACCACTTAATTGAAACAATTAAATCCGCAGCTTCGGCTCCTAGTTTGAGCCCCGTTACATCTTCCGCGCAGGCCGACTCGACTAGTGAGCTATTACGCTTTCTTTAAAGGGTGGCTGCTTCTAAGCCAACCTCCTAGCTGTCTGTGCCTTCCCACATCGTTTCCCACTTAACTAGGAATTTGGGGCCTTAGCTGGCGGTCTGGGTTGTTTCCCTCTTGACGACGGACGTTAGCACCCGCCGTCTGTCTCCCGGATATTACTCATCGGTATTCGGAGTTTGCATCGGTTTGGTAAGTCGGTGTGACCCCCTAGCCGAAACAGTGCTCTACCCCCAATGGTATTCGTCCGAGGCGCTACCTAAATAGCTTTCGGGGAGAACCAGCTATCACCGAGTTTGATTAGCCTTTCACCCCTATCCACAAGTCATCCCCTGGCTTTTCAACGACAGTGGGTTCGGTCCTCCGGTGCCTGTTACGGCACTTTCAACCTGCTCATGGATAGATCACTCGGTTTCGGGTCTATACCCTGCAACTCATTCGCCCTATTAAGACTCGGTTTCCCTACGGCTCCCCTATTCGGTTAACCTTGCTACAGAATATAAGTCGCTGACCCATTATACAAAAGGTACGCCGTCACCCGACCACTTAATCGTTCTGATTGTCAAATTGTGATTTGACACGATTCATCAAGAAAGTTCTCATACGACCATTATTTTTTATGGTTCGCTCTCGTTTTCTTGCCACTTGTTCATTAATGTAGGCTTCACAATAAACAATACGCCATGTTCTTGCTCTGGTTGAGTAAGTTGTGCCATTATTATGGTCATCAATTCTTTGTTTTAAACTGGTGGTAAAACCAACATAAAACTCATCATGATTATCCACGTTTTGTATGACATAGACGTAGTAAAAATTCATTGTTATCCTCAAAACGATTAAGTGGTCGGGCTCCGACTGCTTGTATGCACACGGTTTCAGGTTCTATTTCACTCCCCTAACAGGGGTTCTTTTCGCCTTTCCCTCACGGTACTGGTTCACTATCGGTCAGTCAGGAGTATTTAGCCTTGGAGGATGGTCCCCCCATCTTCAGACAGAATTTCTCGTGTTCCGCCCTACTTAATATGTCGCTTAAACAGTTTCGCATACAGGACTATCACCTACTATGGTTGGCTTTCCCACGCCATTTTGCTACTGTAAAATTGATCGGCTCCTCCGTGTTCGCTCGCCGCTACTTACGGAATCTCATTTGATGTCTTTTCCTCGGGGTACTGAGATGTTTCACTTCTCCCGGTTTGCCTTACACAGTAAACTGTGTAATAACCAACTTATGTTGGTTGGGTTTCCCCATTCAGAAATCGCCGGGTCACAGGATATTGCCACCTCACCGACGCTTATCGCAGGCTATCACGTCTTTCATCGCCTCTGACTGCCAAGGCATCCACCATGTGCACTTCATTACTTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42626","NCBI_taxonomy_name":"Moraxella catarrhalis BBH18","NCBI_taxonomy_id":"1236608"}}}},"ARO_accession":"3004138","ARO_id":"41265","ARO_name":"Moraxella catarrhalis 23S rRNA with mutation conferring resistance to macrolide antibiotics","CARD_short_name":"Mcat_23S_MAC","ARO_description":"Point mutations in the 23S ribosomal RNA subunit of M. catarrhalis shown clinically to confer resistance to macrolide class antibiotics.","ARO_category":{"41251":{"category_aro_accession":"3004125","category_aro_cvterm_id":"41251","category_aro_name":"23S rRNA with mutation conferring resistance to macrolide antibiotics","category_aro_description":"Nucleotide point mutations in the 23S rRNA subunit may confer resistance to macrolide antibiotics.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2794":{"model_id":"2794","model_name":"Helicobacter pylori 23S rRNA with mutation conferring resistance to clarithromycin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"41093","param_value":"2000"},"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"7905":"a2146c","7908":"a2147g","7909":"a2147c","7907":"a2146t","12515":"a1410g","12516":"a2167g","12517":"c1707t","12518":"c2922t","12597":"a2144g","13112":"a2142g","7906":"a2146g","12514":"a2143g"},"Curated-R":{"7905":"a2146c","7908":"a2147g","7909":"a2147c","7907":"a2146t","12515":"a1410g","12516":"a2167g","12517":"c1707t","12518":"c2922t","12519":"c2922t","12597":"a2144g","13112":"a2142g","7906":"a2146g","12514":"a2143g"},"clinical":{"7905":"a2146c","7908":"a2147g","7909":"a2147c","7907":"a2146t","12515":"a1410g","12516":"a2167g","12517":"c1707t","12518":"c2922t","12597":"a2144g","13112":"a2142g","7906":"a2146g","12514":"a2143g"}},"40330":{"param_type":"multiple resistance variants","param_description":"A set of nucleotide or amino acid substitutions that are all required to confer resistance to an antibiotic drug or drug class, encoded as: [wild-type 1][position 1][mutation 1],[wild-type 2][position 2][mutation 2], etc. For example, D63Y,T142K.","param_type_id":"40330","param_value":{"12519":"c2248t,g2287a"}}},"model_sequences":{"sequence":{"4113":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"AB162858.1","fmin":"0","fmax":"2975","strand":"+","sequence":"AAGGCAGTGGTAGCGCTGAAGAATATTCGTGCAATTGTCGTTATTCATTATAAAAGGGCAGGTTTTAAAGGATATTTTAAAATTTAAAACAAGCTTTTAAGAGCAGATGGCGGATGCCTTGCCAAAGAGAGGCGATGAAGGACGTACTAGACTGCGATAAGCTATGCGGAGCTGTCAAGGAGCTTTGATGCGTAGATGTCCGAATGGGGCAACCCAACTAATAGAGATATTAGTTACTCTAATTTAGAGAGCGAACCTAGTGAAGTGAAACATCTCAGTAACTAGAGGAAAAGAAATCAACGAGATTCCCTAAGTAGTGGCGAGCGAACGGGGAAAAGGGCAAACCGAGTGCTTGCATTCGGGGTTGAGGACTGCAACATCCAAGAGAACGCTTTAGCAGAGTTACCTGGAAAGGTAAGCCATAGAAAGTGATAGCCTTGTATGCGACAAGGCGTTCTTAGGTAGCAGGATCCAGAGTAGGCCAGGACACGAGAAATCCAGGTTGAAGCTGGGGAGACCACTCTCCAACCCTAAATACTACTCTTTGAGCGATAGCGAACAAGTACCGTGAGGGAAAGGTGAAAAGAACCGCAGTGAGCGGAGTGAAATAGAACCTGAAACCATCTGCTTACAATCATTCAGAGCCCTATGATTTATCAGGGTGATGGACTGCCTTTTGCATAATGATCCTGCGAGTTGTGGTATCTGGCAAGGTTAAGCGGATGCGAAGCCGTAGCGAAAGCGAGTCTTAATAGGGCGGTTTAAGTCAGATGCTGCAGACCCGAAGCTAAGTGATCTATCCATGGCCAAGTTGAAACGCGTGTAATAGCGCGTGGAGGACTGAACTCGTACCCATTGAAACGGGTTGGGATGAGCTGTGGATAGGGGTGAAAGGTCAAACAAACTTAGTGATAGCTGGTTCTCTTCGAAATATATTTAGGTATAGCCTCAAGTGATAATAAAAGGGGGTAGAGCTCTGATTGGGCTAGGGCTGCTCGCCGCGGTACCAAACCCTATCAAACTTCGAATACCTTTTATCGTATCTTGGGAGTCAGGCGGTGGGTGATAAAATCAATCGTCAAAAGGGGAACAACCCAGACTACCAAATAAGGTCCCTAAGTTCTATTCTGAGTGGAAAAAGATGTGTGGCTACTCAAACAACCAGGAGGTTGGCTTAGAAGCAGCCATCCTTTAAAGAAAGCGTAACAGCTCACTGGTCTAGTGGTCATGCGCTGAAAATATAACGGGGCTAAGATAGACACCGAATTTGTAGATTGTGTTAAACACAGTGGTAGAAGAGCGTTCATACCAGCGTTGAAGGTATACCGGTAAGGAGTGCTGGAGCGGTATGAAGTGAGCATGCAGGAATGAGTAACGATAAGATATATGAGAATTGTATCCGCCGTAAATCTAAGGTTTCCTACGCGATGGTCGTCATCGTAGGGTTAGTCGGGTCCTAAGCCGAGTCCGAAAGGGGTAGGTGATGGCAAATTGGTTAATATTCCAATACCGACTCATGGAGCGTGATGGGGGGACGCATAGGGTTAAGCGAGCTAGCTGATGGAAGTGCTAGTCTAAGGGCGTAGATTGGAGGGAAGGCAAATCCACCTCTGTATTTGAAACCCAAACAGGCTCTTTGAGTCCTTTCAGGACAAAGGGAGAATCGCTGATACCGTCGTGCCAAGAAAAGCCTCTAAGCATATCCATAGTCGTCCGTACCGCAAACCGACACAGGTAGATGAGATGAGTATTCTAAGGCGCGTGAAAGAACTCTGGTTAAGGAACTCTGCAAACTAGCACCGTAAGTTCGCGATAAGGTGTGCCGCAGCAATGCGGTCTCAGCAAAGAGTCCCTCCCGACTGTTTACCAAAAACACAGCACTTTGCCAACTCGTAAGAGGAAGTATAAGGTGTGACGCCTGCCCGGTGCTCGAAGGTTAAGAGGATGCGTCAGTCGCAAGATGAAGCGTTGAATTGAAGCCCGAGTAAACGGCGGCCGTAACTATAACGGTCCTAAGGTAGCGAAATTCCTTGTCGGTTAAATACCGACCTGCATGAATGGCGTAACGAGATGGGAGCTGTCTCAACCAGAGATTCAGTGAAATTGTAGTGGAGGTGAAAATTCCTCCTACCCGCGGCAAGACGGAAAGACCCCGTGGACCTTTACTACAACTTAGCACTGCTAACGGGAATATCATGTGCAGGATAGGTGGGAGGCTTTGAAGTAAGGGCTTTGGCTCTTATGGAGCCATCCTTGAGATACCACCCTTGATGTTTCTGTTAGCTAACTGGCCTGTGTTATCCACAGGCAGGACAATGCTTGGTGGGTAGTTTGACTGGGGCGGTCGCCTCCTAAAAAGTAACGGAGGCTTGCAAAGGTTGGCTCATTGCGGTTGGAAATCGCAAGTTGAGTGTAATGGCACAAGCCAGCCTGACTGTAAGACATACAAGTCAAGCAGAGACGAAAGTCGGTCATAGTGATCCGGTGGTTCTGTGTGGAAGGGCCATCGCTCAAAGGATAAAAGGTACCCCGGGGATAACAGGCTGATCTCCCCCAAGAGCTCACATCGACGGGGAGGTTTGGCACCTCGATGTCGGCTCATCGCATCCTGGGGCTGGAGCAGGTCCCAAGGGTATGGCTGTTCGCCATTTAAAGCGGTACGCGAGCTGGGTTCAGAACGTCGTGAGACAGTTCGGTCCCTATCTGCCGTGGGCGTAGGAAAGTTGAGGAGAGCTGTCCCTAGTACGAGAGGACCGGGATGGACGTGTCACTGGTGCACCAGTTGTTCTGCCAAGAGCATCGCTGGGTAGCTACACACGGATGTGATAACTGCTGAAAGCATCTAAGCAGGAAGCCAACTCCAAGATAAACTTTCCCTGAAGCTCGCACAAAGACTATGTGCTTGATAGGGTAGATGTGTAAGCGCAGTAATGCGTTTAGCTGACTACTACTAATAGAGCGTTTGGCTTGTTTTT","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36906","NCBI_taxonomy_name":"Helicobacter pylori","NCBI_taxonomy_id":"210"}}}},"ARO_accession":"3004134","ARO_id":"41261","ARO_name":"Helicobacter pylori 23S rRNA with mutation conferring resistance to clarithromycin","CARD_short_name":"Hpyl_23S_CLR","ARO_description":"Point mutations in Helicobacter pylori shown to confer resistance to clarithromycin, a macrolide antibiotic.","ARO_category":{"41251":{"category_aro_accession":"3004125","category_aro_cvterm_id":"41251","category_aro_name":"23S rRNA with mutation conferring resistance to macrolide antibiotics","category_aro_description":"Nucleotide point mutations in the 23S rRNA subunit may confer resistance to macrolide antibiotics.","category_aro_class_name":"AMR Gene Family"},"35982":{"category_aro_accession":"0000065","category_aro_cvterm_id":"35982","category_aro_name":"clarithromycin","category_aro_description":"Clarithromycin is a methyl derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome and is used to treat pharyngitis, tonsillitis, acute maxillary sinusitis, acute bacterial exacerbation of chronic bronchitis, pneumonia (especially atypical pneumonias associated with Chlamydia pneumoniae or TWAR), and skin structure infections.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2796":{"model_id":"2796","model_name":"OprZ","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"8185":{"protein_sequence":{"accession":"EGP45230.2","sequence":"MKPVAMTLLALALSGCSLAPTHERPAAPVPAQYDTPAQPGQAAAPQDWRAYFNDPALQAWIAAALANNRDLRVAALRIEEARALYGVQQSERLPAIDASGEFSRGRATEPGQPRTPVSNRYRAAVGITAFELDFFGRVRSLSDAALARYLASEEAHRAATLALVAETATAYFNQRSLAEQLRLTDDTLALRETTLKLTQRRYDAGLETAIGLRTAQMLVESSRATRAELTREASLARHALGLLAGDFALPLGVDPTPLESQSLTPLAAGLPSELLTRRPDLRQAEQALRAANADIGAARAAFFPSVQLTTDIGTTADRFSDLFSGGTGGWSFAPRLTLPIFNAGRNRANLSLAETRKHIAVAQYEGSIQAAFRDVADALSARDALRDQIEAQRKVRDADRERQRLAERRYARGVANYLEMLEAQRSLFESEQEFIRLQQRRLVNAVDLYKALGGWDDGSSPAS"},"dna_sequence":{"accession":"AFRQ01000061.1","fmin":"22598","fmax":"23990","strand":"-","sequence":"ATGAAACCCGTGGCAATGACCCTGCTGGCGCTGGCATTGTCCGGCTGCTCGCTGGCGCCCACCCATGAGCGCCCCGCGGCGCCGGTGCCGGCGCAGTACGACACGCCGGCGCAGCCCGGCCAGGCCGCCGCGCCGCAGGACTGGCGCGCCTATTTCAACGATCCGGCGCTGCAGGCCTGGATCGCGGCCGCGCTGGCCAACAACCGCGACCTGCGCGTGGCGGCGCTGCGCATCGAGGAAGCGCGCGCGCTGTACGGCGTGCAGCAATCCGAACGCCTGCCGGCCATCGACGCCAGCGGCGAATTCAGCCGCGGCCGCGCGACCGAGCCGGGCCAGCCGCGCACGCCGGTGTCCAACCGCTACCGCGCGGCCGTCGGCATCACCGCGTTCGAGCTGGACTTCTTCGGCCGGGTGCGGAGCCTGTCGGACGCCGCGCTGGCGCGCTACCTGGCCAGCGAGGAAGCGCACCGCGCCGCCACGCTGGCGCTGGTGGCGGAGACGGCGACGGCCTACTTCAACCAGCGTTCGCTGGCCGAGCAACTGCGCCTGACCGACGACACGCTGGCGCTGCGCGAGACCACGCTCAAGCTGACCCAGCGCCGCTACGACGCCGGGCTGGAAACCGCCATCGGCCTGCGCACCGCGCAGATGCTGGTGGAAAGCTCGCGCGCCACGCGCGCCGAGCTGACCCGCGAGGCCAGCCTGGCGCGGCACGCGCTGGGCCTGCTGGCCGGCGATTTCGCGCTGCCGCTCGGCGTCGACCCTACGCCGCTGGAAAGCCAGAGCCTGACGCCGCTGGCGGCGGGGCTGCCGTCCGAACTGCTGACGCGCCGCCCCGACCTGCGCCAGGCAGAGCAGGCGCTGCGCGCGGCCAACGCCGACATCGGCGCGGCGCGCGCGGCGTTCTTCCCGTCGGTGCAGCTGACCACGGACATCGGCACCACCGCCGACCGCTTCTCGGATCTGTTCAGCGGCGGCACCGGCGGCTGGAGCTTCGCGCCGCGCCTGACGCTGCCGATCTTCAACGCCGGCCGCAACCGCGCCAACCTGTCGCTGGCCGAGACCCGCAAGCACATCGCGGTGGCCCAGTACGAAGGCAGCATCCAGGCCGCGTTCCGCGACGTGGCCGACGCGCTGTCGGCGCGCGACGCGCTGCGCGACCAGATCGAGGCCCAGCGCAAGGTGCGCGACGCCGACCGCGAACGCCAGCGGCTGGCCGAGCGGCGTTATGCGCGCGGGGTGGCGAACTACCTGGAGATGCTGGAGGCCCAGCGCAGCCTGTTCGAGTCGGAACAGGAATTCATCCGGCTGCAGCAGCGCCGGCTGGTCAACGCGGTGGATCTGTACAAGGCGCTGGGCGGCTGGGACGACGGCTCATCGCCGGCGTCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41271","NCBI_taxonomy_name":"Achromobacter insuavis AXX-A","NCBI_taxonomy_id":"1003200"}}}},"ARO_accession":"3004142","ARO_id":"41270","ARO_name":"OprZ","CARD_short_name":"OprZ","ARO_description":"OprZ is the outer membrane component of the AxyXY-OprZ efflux pump system in Achromobacter spp.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35976":{"category_aro_accession":"0000059","category_aro_cvterm_id":"35976","category_aro_name":"cefepime","category_aro_description":"Cefepime (INN) is a fourth-generation cephalosporin antibiotic developed in 1994. It contains an aminothiazolyl group that decreases its affinity with beta-lactamases. Cefepime shows high binding affinity with penicillin-binding proteins and has an extended spectrum of activity against Gram-positive and Gram-negative bacteria, with greater activity against both Gram-negative and Gram-positive organisms than third-generation agents.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2797":{"model_id":"2797","model_name":"AxyX","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4485":{"protein_sequence":{"accession":"EGP45232.2","sequence":"MTHRVPFRTLAFASVLVLVSACSKQEAPEAAKAPAEVGVIVARATPTAVASELPGRLEPYREAEVRARVAGIVTRRLYEEGQEVTRGTPLFQIDPAPLQAAYDSEAAALARAQANLSAAADKLRRYADLVSDRAISERDHAESVAQERQARAEVALAKANLQSARLRLEYARVTSPIDGRARRALVTEGALVGEGQATPLTVVQQLDPIYVNFSQPAAEVMQLQKQIRAGALQGVAPDKMRVRLLLPDGSEYGQGGTLSFADLAVDPGTDNVTMRALFANPGRELLPGMYVRVRLEQAVNRDTFLVPRNALLRNADGAHVLVAGDDGELRSVAVTAHRLLGPNWVVTEGLAGGERVVVENAAQLAPGQKIKPVERTAPSAPVATAGNNEKR"},"dna_sequence":{"accession":"AFRQ01000061.1","fmin":"27130","fmax":"28306","strand":"-","sequence":"ATGACGCACCGAGTTCCCTTCAGAACGCTCGCATTCGCATCCGTACTGGTTCTCGTTTCCGCATGCTCGAAGCAGGAAGCCCCCGAAGCCGCCAAGGCCCCCGCCGAAGTCGGCGTCATCGTGGCCAGGGCCACGCCCACCGCCGTCGCCAGCGAGCTGCCCGGCCGGCTGGAGCCCTATCGCGAGGCCGAGGTCCGCGCCCGCGTGGCCGGCATCGTCACCCGCCGCCTGTATGAAGAAGGCCAGGAAGTGACGCGCGGCACGCCGCTGTTCCAGATCGATCCGGCGCCGCTGCAGGCGGCCTACGATTCCGAGGCGGCCGCGTTGGCGCGTGCCCAGGCCAACCTGTCGGCCGCCGCCGACAAGCTGCGCCGCTACGCCGACCTGGTGTCGGACCGCGCCATCAGCGAACGCGACCACGCCGAGAGCGTGGCCCAGGAACGCCAGGCCCGCGCCGAAGTGGCGTTGGCCAAGGCCAACCTGCAGAGCGCCAGGCTGCGGCTGGAATACGCCCGCGTCACCTCGCCGATCGACGGCCGCGCGCGCCGCGCGCTGGTCACCGAGGGCGCGCTGGTGGGCGAAGGCCAGGCCACGCCGCTGACGGTGGTGCAGCAACTCGACCCGATCTACGTCAACTTCTCGCAACCCGCGGCCGAGGTCATGCAGTTGCAGAAGCAGATCCGCGCCGGCGCCCTGCAAGGCGTCGCGCCCGACAAGATGCGGGTGCGCCTGCTGCTGCCGGACGGCTCCGAGTATGGCCAGGGCGGCACGCTGTCGTTCGCCGACCTGGCGGTCGACCCCGGCACCGACAACGTGACCATGCGCGCGCTGTTCGCCAACCCGGGCCGCGAACTGTTGCCGGGCATGTACGTGCGGGTGCGGCTGGAGCAGGCGGTCAACCGCGACACCTTCCTGGTGCCGCGCAACGCCCTGCTGCGCAACGCCGACGGCGCGCACGTGCTGGTGGCCGGCGACGACGGCGAGCTGCGCAGCGTGGCGGTGACCGCGCACCGGCTGCTGGGCCCGAACTGGGTCGTCACCGAGGGCCTGGCGGGCGGCGAACGCGTGGTGGTGGAAAACGCCGCGCAGCTGGCCCCCGGCCAGAAAATCAAACCGGTCGAGCGGACCGCGCCGAGCGCGCCCGTGGCGACCGCGGGAAATAACGAAAAAAGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41271","NCBI_taxonomy_name":"Achromobacter insuavis AXX-A","NCBI_taxonomy_id":"1003200"}}}},"ARO_accession":"3004143","ARO_id":"41272","ARO_name":"AxyX","CARD_short_name":"AxyX","ARO_description":"AxyX is the inner membrane transporter of the AxyXY-OprZ efflux pump system in Achromobacter spp.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35976":{"category_aro_accession":"0000059","category_aro_cvterm_id":"35976","category_aro_name":"cefepime","category_aro_description":"Cefepime (INN) is a fourth-generation cephalosporin antibiotic developed in 1994. It contains an aminothiazolyl group that decreases its affinity with beta-lactamases. Cefepime shows high binding affinity with penicillin-binding proteins and has an extended spectrum of activity against Gram-positive and Gram-negative bacteria, with greater activity against both Gram-negative and Gram-positive organisms than third-generation agents.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2798":{"model_id":"2798","model_name":"AxyZ","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"7819":"V29G"},"Curated-R":{"7819":"V29G"},"clinical":{"7819":"V29G"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"4134":{"protein_sequence":{"accession":"EGP45233.1","sequence":"MARKTKEESQRTRDRILDAAEHVFLSKGVASTTMSDIADFAGVSRGAVYGHYKNKIDVCIAMCDRALGEAVSLTRVSTDGEALEALYASMRQYVQIYAEEGSVQRVLEILYLKCERSDENAPLLRRRDLWERHALRTSEKLLRAAVSREDLPPALDVRLSNVYLHSLVEGVFGTICWSDRLKGDIWPRVERMLRAAIDTLRLSPQLRLPQAA"},"dna_sequence":{"accession":"AFRQ01000061.1","fmin":"28538","fmax":"29177","strand":"+","sequence":"ATGGCCCGCAAGACGAAAGAAGAATCCCAACGCACCCGCGACCGCATCCTGGACGCCGCCGAACACGTGTTCCTGTCCAAGGGCGTGGCCAGCACCACCATGAGCGATATCGCTGATTTCGCGGGCGTGTCCCGGGGCGCCGTCTACGGCCATTACAAGAACAAGATCGATGTCTGCATCGCCATGTGCGACCGGGCCCTGGGGGAAGCGGTGTCGCTGACCCGCGTGTCGACCGACGGCGAGGCGCTGGAAGCGCTCTACGCGTCGATGCGCCAGTACGTGCAGATCTACGCCGAGGAAGGCTCGGTGCAGCGTGTGCTGGAAATCCTCTACCTGAAATGCGAGCGCAGCGACGAGAACGCGCCGCTCCTGCGCCGCCGCGACCTGTGGGAGCGCCACGCCCTGCGCACTTCCGAAAAGTTGCTGCGCGCCGCCGTCAGCCGCGAGGACCTGCCGCCCGCGCTGGACGTGCGTCTGTCCAATGTCTACCTGCACTCCCTGGTCGAGGGCGTGTTTGGCACCATCTGCTGGTCCGATCGCCTCAAGGGCGATATCTGGCCGCGCGTCGAGCGCATGCTCCGCGCCGCCATCGACACGCTGCGCCTGTCGCCGCAACTGCGGTTGCCACAGGCCGCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41271","NCBI_taxonomy_name":"Achromobacter insuavis AXX-A","NCBI_taxonomy_id":"1003200"}}}},"ARO_accession":"3004145","ARO_id":"41274","ARO_name":"AxyZ","CARD_short_name":"AxyZ","ARO_description":"AxyZ is a transcriptional regulator of the AxyXY-OprZ efflux pump system.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35976":{"category_aro_accession":"0000059","category_aro_cvterm_id":"35976","category_aro_name":"cefepime","category_aro_description":"Cefepime (INN) is a fourth-generation cephalosporin antibiotic developed in 1994. It contains an aminothiazolyl group that decreases its affinity with beta-lactamases. Cefepime shows high binding affinity with penicillin-binding proteins and has an extended spectrum of activity against Gram-positive and Gram-negative bacteria, with greater activity against both Gram-negative and Gram-positive organisms than third-generation agents.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2799":{"model_id":"2799","model_name":"AxyY","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1700"}},"model_sequences":{"sequence":{"4484":{"protein_sequence":{"accession":"EGP45231.1","sequence":"MARFFIDRPVFAWVISLLIALVGLLSIRALPVAQYPDIAPPVVNIGASYPGASAKVVEEAVTAIIEREMNGAPGLMYTSSSSDSTGWASINLTFKQGTNPDIAAVEVQNRLKAVEPRLPESVRRDGVRVEKAADNIQLVVSLKSDGSLDDMQLGELAASNVLQALRRVEGVGKVQSFGAEAAMRIWPDPAKLTALSLTPGDIVSALRSHNARVTIGELGNQAVPKDAPLNASIVAGESLHTPEQFANIPLRALPDGATLRLKDVARVELGGTDYMYLSRVNGLTGTGLGIKLAPGSNAVETTRRIRETMRELAQYFPPGVTWDIPYETSTFVEISIKKVLMTLLEAVALVFCVMYLFMQNLRATLIPTLVVPVALLGTLGVMLGLGYSINVLTMFGMVLAIGILVDDAIVVVENVERIMAEEGLSPHDATVKAMGQISGAIVGITVVLVSVFVPMAFFDGAVGNIYRQFAVTLAVSIAFSAFLALSLTPALCASLLKPVPAGHHEKRGFFGWFNRAFARLTTRYTARVAGVLARPVRFGLAYALVIGVAALLFARLPSSFLPDEDQGSFMAMVILPQGSPQAETMAVVKDVERYMMEHEPVQYVYSVNGFSQYGSGPNSAMFFVTLKDWKERRDASQHVDAVVKRINKAFADRKNLMVFALNSPPLPDLGSTSGFDFRLQDRGGLGYEALTQARQKLLAKAAEHPALTDVVFAGQEEAPQLQLRVDRDKAQAMGVPIDEINTALAVMYGSDYIGDFMLNGQVRRVMVQADGKRRVDVDDISRLHVRNLQGQMVPLSAFATLTWSMGPPQLNRYNGFPSFTINGSAARGHSSGEAMRAMETLAAELPRGIGFDWSGQSYEERLSGNQAPVLFALSVLIVFLALAALYESWSIPLAVILVVPLGVIGALLGVTVRGMPNDIYFKVGLIATIGLSAKNAILIVEVAKDLVRDGQGILSATLEAARLRLRPIVMTSLAFGVGVLPLALATGAASGAQAAIGTGVLGGIITATVLAVFLVPLFFLIVGRMVGMRARPARPDGREPLETTP"},"dna_sequence":{"accession":"AFRQ01000061.1","fmin":"23986","fmax":"27124","strand":"-","sequence":"ATGGCGCGTTTCTTTATCGATCGCCCCGTTTTCGCGTGGGTGATCTCGCTGCTCATCGCGCTGGTCGGCCTGTTGTCGATCCGCGCGCTGCCGGTGGCGCAGTATCCGGACATCGCTCCGCCCGTCGTCAACATCGGCGCCAGCTATCCCGGCGCCTCGGCCAAGGTGGTCGAGGAAGCCGTCACCGCCATCATCGAACGCGAGATGAACGGCGCCCCGGGCCTGATGTACACCTCGTCCAGCAGCGATTCGACCGGCTGGGCCAGCATCAACCTGACCTTCAAGCAGGGCACCAACCCCGACATCGCGGCGGTGGAAGTGCAGAACCGCCTGAAGGCGGTCGAGCCTCGCCTGCCCGAATCGGTGCGGCGCGATGGCGTGCGCGTGGAAAAGGCGGCCGACAACATCCAGCTGGTGGTGTCGTTGAAGTCGGACGGCAGCCTGGACGACATGCAACTGGGCGAGCTGGCCGCCTCCAATGTGCTGCAGGCGCTGCGGCGGGTCGAAGGCGTGGGCAAGGTGCAGTCGTTCGGCGCGGAAGCGGCGATGCGCATCTGGCCGGACCCGGCCAAGCTCACCGCCCTGTCGCTGACGCCGGGCGACATCGTCTCGGCGCTGCGCAGCCACAACGCGCGCGTCACCATCGGCGAACTGGGCAACCAGGCCGTGCCCAAGGACGCGCCGCTGAACGCCAGCATCGTGGCGGGCGAATCGCTGCACACGCCGGAACAGTTCGCCAACATCCCGCTGCGGGCGCTGCCGGACGGCGCCACGCTGCGCCTGAAGGACGTGGCGCGGGTGGAGCTGGGCGGCACCGACTACATGTACCTGTCGCGCGTCAACGGCCTGACCGGCACCGGCCTGGGCATCAAGCTGGCGCCCGGCTCCAACGCCGTCGAAACCACCCGCCGCATCCGCGAGACCATGCGCGAGCTGGCGCAATACTTCCCGCCGGGCGTGACCTGGGACATTCCGTACGAGACCTCCACCTTCGTCGAGATCTCGATCAAGAAGGTCCTGATGACGCTGCTGGAGGCGGTGGCGCTGGTGTTCTGCGTGATGTACCTGTTCATGCAGAACCTGCGCGCCACGCTGATCCCGACCCTGGTGGTGCCGGTGGCGCTGCTGGGCACGCTGGGGGTGATGCTGGGGCTGGGCTATTCGATCAACGTGCTGACGATGTTCGGCATGGTGCTGGCCATCGGCATCCTGGTGGACGACGCCATCGTGGTGGTCGAGAACGTCGAGCGCATCATGGCCGAGGAAGGCCTGTCGCCGCATGACGCCACGGTCAAGGCCATGGGCCAGATCAGCGGCGCCATCGTCGGCATCACCGTGGTGCTGGTGTCGGTGTTCGTGCCGATGGCGTTCTTCGACGGCGCGGTGGGCAACATCTACCGCCAGTTCGCCGTGACGCTGGCGGTGTCGATCGCCTTCTCGGCCTTCCTGGCGCTGTCGCTGACGCCGGCGCTGTGCGCCAGCCTGCTCAAACCCGTCCCGGCCGGCCACCACGAGAAGCGCGGCTTCTTCGGCTGGTTCAACCGCGCCTTCGCGCGCCTGACCACGCGCTATACGGCGCGGGTGGCCGGCGTGCTGGCGCGGCCGGTACGCTTCGGCCTGGCCTATGCGCTGGTGATCGGCGTGGCGGCGTTGCTGTTCGCGCGGCTGCCATCGTCGTTCCTGCCGGACGAGGACCAGGGCAGCTTCATGGCCATGGTGATCCTGCCGCAGGGCTCGCCGCAGGCCGAGACCATGGCGGTGGTCAAGGACGTCGAACGCTACATGATGGAGCACGAGCCGGTGCAGTACGTGTATTCGGTCAACGGCTTCAGCCAGTACGGCAGCGGCCCGAACTCCGCCATGTTCTTCGTCACGCTGAAGGACTGGAAGGAACGCCGCGATGCCTCGCAACACGTGGACGCGGTGGTCAAGCGCATCAACAAGGCGTTCGCGGATCGCAAGAACCTGATGGTGTTCGCGCTGAACTCGCCGCCGCTGCCTGACCTGGGCTCGACCTCGGGCTTCGACTTCCGGCTGCAGGATCGCGGCGGCCTCGGCTACGAAGCCCTGACGCAGGCGCGCCAGAAGCTGCTGGCCAAGGCGGCCGAGCATCCCGCGCTGACGGACGTGGTGTTCGCCGGCCAGGAAGAGGCGCCGCAGCTGCAACTGCGCGTCGACCGCGACAAGGCGCAGGCCATGGGCGTGCCGATCGACGAGATCAACACCGCGCTGGCTGTGATGTACGGCTCGGACTACATCGGCGACTTCATGCTCAACGGCCAGGTTCGGCGCGTGATGGTGCAGGCCGACGGCAAGCGCCGCGTGGACGTGGACGACATCTCGCGCCTGCACGTGCGCAACCTGCAGGGCCAGATGGTGCCGCTGTCGGCGTTCGCCACGCTGACGTGGTCGATGGGGCCGCCGCAGCTGAACCGCTACAACGGCTTCCCGTCGTTCACCATCAACGGCTCGGCGGCGCGCGGCCACAGCAGCGGCGAGGCCATGCGCGCCATGGAGACGCTGGCGGCCGAGCTGCCGCGCGGCATCGGCTTCGACTGGTCGGGCCAATCGTACGAAGAGCGGCTGTCCGGCAACCAGGCGCCGGTGCTGTTCGCGCTGTCGGTGCTGATCGTGTTCCTGGCGCTGGCGGCGCTGTATGAAAGCTGGTCGATTCCGCTGGCGGTGATCCTGGTGGTGCCGCTGGGCGTGATCGGCGCGCTGCTGGGGGTGACCGTGCGCGGCATGCCCAACGACATCTACTTCAAGGTCGGCCTGATCGCCACCATCGGCCTGTCCGCCAAGAACGCGATCCTGATCGTGGAAGTGGCCAAGGACCTGGTGCGCGACGGCCAGGGCATCCTGTCCGCCACGCTGGAAGCGGCGCGGCTGCGGCTGCGGCCGATCGTGATGACCTCGCTGGCCTTTGGCGTGGGCGTGCTGCCGCTGGCGCTGGCCACTGGCGCCGCCTCGGGCGCGCAGGCCGCCATCGGCACCGGCGTGCTGGGCGGGATCATCACGGCGACCGTGCTGGCGGTGTTCCTGGTGCCGCTGTTCTTTCTCATCGTGGGACGCATGGTCGGCATGCGCGCCCGCCCCGCGCGCCCCGACGGCCGCGAACCGCTGGAGACGACGCCATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41271","NCBI_taxonomy_name":"Achromobacter insuavis AXX-A","NCBI_taxonomy_id":"1003200"}}}},"ARO_accession":"3004144","ARO_id":"41273","ARO_name":"AxyY","CARD_short_name":"AxyY","ARO_description":"AxyY is the periplasmic adaptor protein of the AxyXY-OprZ efflux pump system in Achromobacter spp.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35976":{"category_aro_accession":"0000059","category_aro_cvterm_id":"35976","category_aro_name":"cefepime","category_aro_description":"Cefepime (INN) is a fourth-generation cephalosporin antibiotic developed in 1994. It contains an aminothiazolyl group that decreases its affinity with beta-lactamases. Cefepime shows high binding affinity with penicillin-binding proteins and has an extended spectrum of activity against Gram-positive and Gram-negative bacteria, with greater activity against both Gram-negative and Gram-positive organisms than third-generation agents.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2800":{"model_id":"2800","model_name":"cfrC","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"5389":{"protein_sequence":{"accession":"CAL84423.1","sequence":"MKQTKTKYGKMKQIASNLKLPDYRYEQLTKAIFHQRIDNFHDMHILPKALRIALVNEFGKNVSSVTPIFSQDSKQAQKLLFELTDGERIEAVGLKYKQGWESFCISSQCGCSFGCRFCATGSAGFKRNLTADEITDQLLYFYFNDHRLNSISFMGMGEAFANPELFDAVKILTDQNLFGLSQRRITISTIGIIPGIQRLTKEFPQVNLAFSLHSPFESQRSDLMPINKRFPLNEVMKTLDEHIIHTGRRVFIAYIMLEGINDSKEHAEAIIGLLRNRGSWEHLYHIDLIPYNSTDKTTFKFQSSSAIKQFCSTLKKASISATVRTQFGSEISAACGQLCYENEL"},"dna_sequence":{"accession":"AM412317.1","fmin":"3035492","fmax":"3036527","strand":"-","sequence":"ATGAAACAGACAAAAACGAAATATGGAAAAATGAAACAAATAGCATCGAATTTAAAATTACCTGATTATAGATACGAACAGCTTACAAAAGCTATTTTTCATCAAAGAATAGATAATTTTCATGATATGCATATACTACCAAAAGCGTTAAGGATAGCTTTAGTAAATGAGTTTGGAAAGAATGTATCTAGTGTAACACCTATTTTTTCACAAGATTCTAAACAAGCTCAAAAGTTGTTATTTGAATTGACTGATGGAGAAAGAATAGAAGCCGTTGGACTAAAGTATAAACAGGGGTGGGAATCGTTTTGTATTTCTTCCCAATGTGGTTGTAGTTTTGGATGTCGTTTTTGTGCAACGGGAAGTGCTGGATTTAAACGCAATCTTACTGCTGATGAGATAACTGACCAATTACTTTATTTCTATTTTAATGACCATAGATTGAATAGTATTTCATTTATGGGAATGGGTGAGGCTTTTGCAAATCCAGAGTTATTTGATGCAGTAAAAATTTTAACTGATCAAAATTTATTTGGGTTAAGTCAACGAAGAATTACTATTTCAACAATTGGCATTATACCAGGAATTCAAAGACTGACTAAAGAATTTCCACAAGTGAATCTGGCTTTTTCACTTCATTCACCATTTGAAAGTCAACGAAGCGATTTAATGCCTATAAATAAAAGATTTCCATTGAATGAGGTAATGAAGACATTAGATGAACATATCATTCATACGGGACGACGAGTGTTTATTGCTTATATTATGCTTGAAGGAATTAATGATTCGAAAGAACATGCAGAGGCAATTATAGGTTTATTGAGAAATCGTGGTTCATGGGAGCATTTATATCACATTGATTTGATACCTTATAATTCTACGGACAAAACAACTTTTAAATTTCAATCTTCAAGTGCTATCAAGCAATTTTGCAGTACACTAAAGAAAGCTAGTATTAGTGCAACTGTTAGAACACAATTTGGTTCTGAAATTAGTGCTGCTTGCGGACAATTGTGTTATGAAAATGAATTATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41276","NCBI_taxonomy_name":"Clostridium botulinum A str. ATCC 3502","NCBI_taxonomy_id":"413999"}}}},"ARO_accession":"3004146","ARO_id":"41275","ARO_name":"cfrC","CARD_short_name":"cfrC","ARO_description":"A cfr-like 23S rRNA methyltransferase shown to confer resistance to linezolid and phenicol antibiotics, including florfenicol and chloramphenicol, in Clostridium.","ARO_category":{"36341":{"category_aro_accession":"3000202","category_aro_cvterm_id":"36341","category_aro_name":"Cfr 23S ribosomal RNA methyltransferase","category_aro_description":"Cfr genes produce enzymes which catalyze the methylation of the 23S rRNA subunit at position 8 of adenine-2503. Methylation of 23S rRNA at this site confers resistance to some classes of antibiotics, including streptogramins, chloramphenicols, florfenicols, linezolids and clindamycin.","category_aro_class_name":"AMR Gene Family"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36600":{"category_aro_accession":"3000461","category_aro_cvterm_id":"36600","category_aro_name":"florfenicol","category_aro_description":"Florfenicol is a fluorine derivative of chloramphenicol, where the nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3) and the hydroxyl group (-OH), by a fluorine group (-F). The action mechanism is the same as chloramphenicol's, where the antibiotic binds to the 23S RNA of the 50S subunit of bacterial ribosomes to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"36218":{"category_aro_accession":"3000079","category_aro_cvterm_id":"36218","category_aro_name":"oxazolidinone antibiotic","category_aro_description":"Oxazolidinones are a class of synthetic antibiotics discovered the the 1980's.  They inhibit protein synthesis by binding to domain V of the 23S rRNA of the 50S subunit of bacterial ribosomes.  Linezolid is the only member of this class currently in clinical use.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2860":{"model_id":"2860","model_name":"PDC-81","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6231":{"protein_sequence":{"accession":"AKR18021.1","sequence":"GEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNLSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"KR057750.1","fmin":"0","fmax":"1116","strand":"+","sequence":"GGCGAGGCCCCGGCGGATCGCCTGAAGGCATTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCTGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCTAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTATGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3004344","ARO_id":"41512","ARO_name":"PDC-81","CARD_short_name":"PDC-81","ARO_description":"An AmpC-like beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4183":{"model_id":"4183","model_name":"ADC-107","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6558":{"protein_sequence":{"accession":"WP_068981614.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDKPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLKFIHANLNPQKYPADIQRAINETHQGFYQLETMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_051446.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATAAGCCTGGTAAATATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCTTATTTGGAAAAGTTGTTGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACTCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGCTTAAGTTTATTCATGCCAATCTGAACCCACAGAAATATCCGGCTGATATTCAACGGGCAATTAATGAAACACATCAAGGGTTCTATCAATTAGAAACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCGTATGCAGTTTTAAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006287","ARO_id":"44749","ARO_name":"ADC-107","CARD_short_name":"ADC-107","ARO_description":"ADC-107 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4184":{"model_id":"4184","model_name":"ADC-109","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6559":{"protein_sequence":{"accession":"WP_136512052.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKRYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVKTDQQVLTFFKDWKPKNSIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLGAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNRFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_064669.1","fmin":"100","fmax":"1252","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAGGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAGTATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAATTTCCAGATGAAGTAAAAACAGATCAGCAAGTTTTAACATTTTTTAAAGACTGGAAACCTAAAAACTCAATCGGTGAATATCGACAATATTCAAACCCAAGCATTGGTTTATTTGGAAAAGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGGTGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTAAATCCACAAAAATATCCAGCAGATATTCAACGGGCAATTAATGAAACACATCAGGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACCGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006288","ARO_id":"44750","ARO_name":"ADC-109","CARD_short_name":"ADC-109","ARO_description":"ADC-109 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2806":{"model_id":"2806","model_name":"Escherichia coli 23S rRNA with mutation conferring resistance to clindamycin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"7898":"g2032a"},"Curated-R":{"7898":"g2032a"},"clinical":{"7898":"g2032a"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"41093","param_value":"5000"}},"model_sequences":{"sequence":{"4153":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"AE014075.1","fmin":"237159","fmax":"240063","strand":"+","sequence":"GGTTAAGCGACTAAGCGTACACGGTGGATGCCCTGGCAGTCAGAGGCGATGAAGGACGTGCTAATCTGCGATAAGCGTCGGTAAGGTGATATGAACCGTTATAACCGGCGATTTCCGAATGGGGAAACCCAGTGTGTTTCGACACACTATCATTAACTGAATCCATAGGTTAATGAGGCGAACCGGGGGAACTGAAACATCTAAGTACCCCGAGGAAAAGAAATCAACCGAGATTCCCCCAGTAGCGGCGAGCGAACGGGGAGGAGCCCAGAGCCTGAATCAGTGTGTGTGTTAGTGGAAGCGTCTGGAAAGGCGCGCGATACAGGGTGACAGCCCCGTACACAAAAATGCACATGCTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGGGGGACCATCCTCCAAGGCTAAATACTCCTGACTGACCGATAGTGAACCAGTACCGTGAGGGAAAGGCGAAAAGAACCCCGGCGAGGGGAGTGAAAAAGAACCTGAAACCGTGTACGTACAAGCAGTGGGAGCATGCTTAGGCGTGTGACTGCGTACCTTTTGTATAATGGGTCAGCGACTTATATTCTGTAGCAAGGTTAACCGAATAGGGGAGCCGAAGGGAAACCGAGTCTTAACTGGGCGTTAAGTTGCAGGGTATAGACCCGAAACCCGGTGATCTAGCCATGGGCAGGTTGAAGGTTGGGTAACACTAACTGGAGGACCGAACCGACTAATGTTGAAAAATTAGCGGATGACTTGTGGCTGGGGGTGAAAGGCCAATCAAACCGGGAGATAGCTGGTTCTCCCCGAAAGCTATTTAGGTAGCGCCTCGTGAACTCATCTCCGGGGGTAGAGCACTGTTTCGGCAAGGGGGTCATCCCGACTTACCAACCCGATGCAAACTGCGAATACCGGAGAATGTTATCACGGGAGACACACGGCGGGTGCTAACGTCCGTCGNGAAGAGGGAAACAACCCAGACCGCCAGCTAAGGTCCCAAAGTCATGGTTAAGTGGGAAACGATGTGGGAAGGCCCAGACAGCCAGGATGTTGGCTTAGAAGCAGCCATCATTTAAAGAAAGCGTAATAGCTCACTGGTCGAGTCGGCCTGCGCGGAAGATGTAACGGGGCTAAACCATGCACCGAAGCTGCGGCAGCGACGCTTATGCGTTGTTGGGTAGGGGAGCGTTCTGTAAGCCTGTGAAGGTGTACTGTGAGGTATGCTGGAGGTATCAGAAGTGCGAATGCTGACATAAGTAACGATAAAGCGGGTGAAAAGCCCGCTCGCCGGAAGACCAAGGGTTCCTGTCCAACGTTAATCGGGGCAGGGTGAGTCGACCCCTAAGGCGAGGCCGAAAGGCGTAGTCGATGGGAAACAGGTTAATATTCCTGTACTTGGTGTTACTGCGAAGGGGGGACGGAGAAGGCTATGTTGGCCGGGCGACGGTTGTCCCGGTTTAAGCGTGTAGGCTGGTTTTCCAGGCAAATCCGGAAAATCAAGGCTGAGGCGTGATGACGAGGCACTACGGTGCTGAAGCAACAAATGCCCTGCTTCCAGGAAAAGCCTCTAAGCATCAGGTAACATCAAATCGTACCCCAAACCGACACAGGTGGTCAGGTAGAGAATACCAAGGCGCTTGAGAGAACTCGGGTGAAGGAACTAGGCAAAATGGTGCCGTAACTTCGGGAGAAGGCACGCTGATATGTAGGTGAAGCGACTTGCTCGTGGAGCTGAAATCAGTCGAAGATACCAGCTGGCTGCAACTGTTTATTAAAAACACAGCACTGTGCAAACACGAAAGTGGACGTATACGGTGTGACGCCTGCCCGGTGCCGGAAGGTTAATTGATGGGGTTAGCGCAAGCGAAGCTCTTGATCGAAGCCCCGGTAAACGGCGGCCGTAACTATAACGGTCCTAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCTGCACGAATGGCGTAATGATGGCCAGGCTGTCTCCACCCGAGACTCAGTGAAATTGAACTCGCTGTGAAGATGCAGTGTACCCGCGGCAAGACGGAAAGACCCCGTGAACCTTTACTATAGCTTGACACTGAACATTGAGCCTTGATGTGTAGGATAGGTGGGAGGCTTTGAAGTGTGGACGCCAGTCTGCATGGAGCCGACCTTGAAATACCACCCTTTAATGTTTGATGTTCTAACGTTGACCCGTAATCCGGGTTGCGGACAGTGTCTGGTGGGTAGTTTGACTGGGGCGGTCTCCTCCTAAAGAGTAACGGAGGAGCACGAAGGTTGGCTAATCCTGGTCGGACATCAGGAGGTTAGTGCAATGGCATAAGCCAGCTTGACTGCGAGCGTGACGGCGCGAGCAGGTGCGAAAGCAGGTCATAGTGATCCGGTGGTTCTGAATGGAAGGGCCATCGCTCAACGGATAAAAGGTACTCCGGGGATAACAGGCTGATACCGCCCAAGAGTTCATATCGACGGCGGTGTTTGGCACCTCGATGTCGGCTCATCACATCCTGGGGCTGAAGTAGGTCCCAAGGGTATGGCTGTTCGCCATTTAAAGTGGTACGCGAGCTGGGTTTAGAACGTCGTGAGACAGTTCGGTCCCTATCTGCCGTGGGCGCTGGAGAACTGAGGGGGGCTGCTCCTAGTACGAGAGGACCGGAGTGGACGCATCACTGGTGTTCGGGTTGTCATGCCAATGGCACTGCCCGGTAGCTAAATGCGGAAGAGATAAGTGCTGAAAGCATCTAAGCACGAAACTTGCCCCGAGATGAGTTCTCCCTGACTCCTTGAGGGTCCTGAAGGAACGTTGAAGACGACGACGTTGATAGGCCGGGTGTGTAAGCGCAGCGATGCGTTGAGCTAACCGGTACTAATGAACCGTGAGGCTTAACCTT","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36763","NCBI_taxonomy_name":"Escherichia coli CFT073","NCBI_taxonomy_id":"199310"}}}},"ARO_accession":"3004149","ARO_id":"41296","ARO_name":"Escherichia coli 23S rRNA with mutation conferring resistance to clindamycin","CARD_short_name":"Ecol_23S_CLI","ARO_description":"Point mutation in the 23S rRNA of Escherichia coli shown clinically to confer resistance to clindamycin, a lincosamide antibiotic.","ARO_category":{"41349":{"category_aro_accession":"3004187","category_aro_cvterm_id":"41349","category_aro_name":"23S rRNA with mutation conferring resistance to lincosamide antibiotics","category_aro_description":"Point mutations in the 23S rRNA subunit may confer resistance to lincosamide antibiotics by reducing antibiotic binding-site affinity.","category_aro_class_name":"AMR Gene Family"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2807":{"model_id":"2807","model_name":"Escherichia coli 23S rRNA with mutation conferring resistance to clarithromycin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"7899":"g2032t"},"Curated-R":{"7899":"g2032t"},"clinical":{"7899":"g2032t"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"41093","param_value":"5000"}},"model_sequences":{"sequence":{"4154":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"AE014075.1","fmin":"237159","fmax":"240063","strand":"+","sequence":"GGTTAAGCGACTAAGCGTACACGGTGGATGCCCTGGCAGTCAGAGGCGATGAAGGACGTGCTAATCTGCGATAAGCGTCGGTAAGGTGATATGAACCGTTATAACCGGCGATTTCCGAATGGGGAAACCCAGTGTGTTTCGACACACTATCATTAACTGAATCCATAGGTTAATGAGGCGAACCGGGGGAACTGAAACATCTAAGTACCCCGAGGAAAAGAAATCAACCGAGATTCCCCCAGTAGCGGCGAGCGAACGGGGAGGAGCCCAGAGCCTGAATCAGTGTGTGTGTTAGTGGAAGCGTCTGGAAAGGCGCGCGATACAGGGTGACAGCCCCGTACACAAAAATGCACATGCTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGGGGGACCATCCTCCAAGGCTAAATACTCCTGACTGACCGATAGTGAACCAGTACCGTGAGGGAAAGGCGAAAAGAACCCCGGCGAGGGGAGTGAAAAAGAACCTGAAACCGTGTACGTACAAGCAGTGGGAGCATGCTTAGGCGTGTGACTGCGTACCTTTTGTATAATGGGTCAGCGACTTATATTCTGTAGCAAGGTTAACCGAATAGGGGAGCCGAAGGGAAACCGAGTCTTAACTGGGCGTTAAGTTGCAGGGTATAGACCCGAAACCCGGTGATCTAGCCATGGGCAGGTTGAAGGTTGGGTAACACTAACTGGAGGACCGAACCGACTAATGTTGAAAAATTAGCGGATGACTTGTGGCTGGGGGTGAAAGGCCAATCAAACCGGGAGATAGCTGGTTCTCCCCGAAAGCTATTTAGGTAGCGCCTCGTGAACTCATCTCCGGGGGTAGAGCACTGTTTCGGCAAGGGGGTCATCCCGACTTACCAACCCGATGCAAACTGCGAATACCGGAGAATGTTATCACGGGAGACACACGGCGGGTGCTAACGTCCGTCGNGAAGAGGGAAACAACCCAGACCGCCAGCTAAGGTCCCAAAGTCATGGTTAAGTGGGAAACGATGTGGGAAGGCCCAGACAGCCAGGATGTTGGCTTAGAAGCAGCCATCATTTAAAGAAAGCGTAATAGCTCACTGGTCGAGTCGGCCTGCGCGGAAGATGTAACGGGGCTAAACCATGCACCGAAGCTGCGGCAGCGACGCTTATGCGTTGTTGGGTAGGGGAGCGTTCTGTAAGCCTGTGAAGGTGTACTGTGAGGTATGCTGGAGGTATCAGAAGTGCGAATGCTGACATAAGTAACGATAAAGCGGGTGAAAAGCCCGCTCGCCGGAAGACCAAGGGTTCCTGTCCAACGTTAATCGGGGCAGGGTGAGTCGACCCCTAAGGCGAGGCCGAAAGGCGTAGTCGATGGGAAACAGGTTAATATTCCTGTACTTGGTGTTACTGCGAAGGGGGGACGGAGAAGGCTATGTTGGCCGGGCGACGGTTGTCCCGGTTTAAGCGTGTAGGCTGGTTTTCCAGGCAAATCCGGAAAATCAAGGCTGAGGCGTGATGACGAGGCACTACGGTGCTGAAGCAACAAATGCCCTGCTTCCAGGAAAAGCCTCTAAGCATCAGGTAACATCAAATCGTACCCCAAACCGACACAGGTGGTCAGGTAGAGAATACCAAGGCGCTTGAGAGAACTCGGGTGAAGGAACTAGGCAAAATGGTGCCGTAACTTCGGGAGAAGGCACGCTGATATGTAGGTGAAGCGACTTGCTCGTGGAGCTGAAATCAGTCGAAGATACCAGCTGGCTGCAACTGTTTATTAAAAACACAGCACTGTGCAAACACGAAAGTGGACGTATACGGTGTGACGCCTGCCCGGTGCCGGAAGGTTAATTGATGGGGTTAGCGCAAGCGAAGCTCTTGATCGAAGCCCCGGTAAACGGCGGCCGTAACTATAACGGTCCTAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCTGCACGAATGGCGTAATGATGGCCAGGCTGTCTCCACCCGAGACTCAGTGAAATTGAACTCGCTGTGAAGATGCAGTGTACCCGCGGCAAGACGGAAAGACCCCGTGAACCTTTACTATAGCTTGACACTGAACATTGAGCCTTGATGTGTAGGATAGGTGGGAGGCTTTGAAGTGTGGACGCCAGTCTGCATGGAGCCGACCTTGAAATACCACCCTTTAATGTTTGATGTTCTAACGTTGACCCGTAATCCGGGTTGCGGACAGTGTCTGGTGGGTAGTTTGACTGGGGCGGTCTCCTCCTAAAGAGTAACGGAGGAGCACGAAGGTTGGCTAATCCTGGTCGGACATCAGGAGGTTAGTGCAATGGCATAAGCCAGCTTGACTGCGAGCGTGACGGCGCGAGCAGGTGCGAAAGCAGGTCATAGTGATCCGGTGGTTCTGAATGGAAGGGCCATCGCTCAACGGATAAAAGGTACTCCGGGGATAACAGGCTGATACCGCCCAAGAGTTCATATCGACGGCGGTGTTTGGCACCTCGATGTCGGCTCATCACATCCTGGGGCTGAAGTAGGTCCCAAGGGTATGGCTGTTCGCCATTTAAAGTGGTACGCGAGCTGGGTTTAGAACGTCGTGAGACAGTTCGGTCCCTATCTGCCGTGGGCGCTGGAGAACTGAGGGGGGCTGCTCCTAGTACGAGAGGACCGGAGTGGACGCATCACTGGTGTTCGGGTTGTCATGCCAATGGCACTGCCCGGTAGCTAAATGCGGAAGAGATAAGTGCTGAAAGCATCTAAGCACGAAACTTGCCCCGAGATGAGTTCTCCCTGACTCCTTGAGGGTCCTGAAGGAACGTTGAAGACGACGACGTTGATAGGCCGGGTGTGTAAGCGCAGCGATGCGTTGAGCTAACCGGTACTAATGAACCGTGAGGCTTAACCTT","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36763","NCBI_taxonomy_name":"Escherichia coli CFT073","NCBI_taxonomy_id":"199310"}}}},"ARO_accession":"3004160","ARO_id":"41307","ARO_name":"Escherichia coli 23S rRNA with mutation conferring resistance to clarithromycin","CARD_short_name":"Ecol_23S_CLR","ARO_description":"Point mutation in the 23S rRNA of Escherichia coli shown clinically to confer resistance to clarithromycin, a macrolide antibiotic.","ARO_category":{"41251":{"category_aro_accession":"3004125","category_aro_cvterm_id":"41251","category_aro_name":"23S rRNA with mutation conferring resistance to macrolide antibiotics","category_aro_description":"Nucleotide point mutations in the 23S rRNA subunit may confer resistance to macrolide antibiotics.","category_aro_class_name":"AMR Gene Family"},"35982":{"category_aro_accession":"0000065","category_aro_cvterm_id":"35982","category_aro_name":"clarithromycin","category_aro_description":"Clarithromycin is a methyl derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome and is used to treat pharyngitis, tonsillitis, acute maxillary sinusitis, acute bacterial exacerbation of chronic bronchitis, pneumonia (especially atypical pneumonias associated with Chlamydia pneumoniae or TWAR), and skin structure infections.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2808":{"model_id":"2808","model_name":"Propionibacteria 23S rRNA with mutation conferring resistance to macrolide antibiotics","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"7900":"g2281a","7901":"g2294a","7902":"g2295a"},"Curated-R":{"7900":"g2281a","7901":"g2294a","7902":"g2295a"},"clinical":{"7900":"g2281a","7901":"g2294a","7902":"g2295a"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"41093","param_value":"5000"}},"model_sequences":{"sequence":{"4155":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"Y10819.1","fmin":"1849","fmax":"4984","strand":"+","sequence":"GTGACAAGCTACTAAGTGCGATCGGTGGATGCCTAGGCACCAAGAGCCGATGAAGGACGTTGTAACCTGCGATAAGCCCTGGGGAGCTGGTAAACGAGCTTTGATCCGGGGATGTCCGAATGGGGAAACCTCGAAGGTGACCAGTTTAGCTACTGGCGACCGCCGCCTGAATGTATAGGGCGGTTGGAGGGAACGTGGGGAAGTGAAACATCTTAGTACCCACAGGAAGAGRAAACAACCGTGAWTCCGTGAATATTGGCGAGCGAAAGCGGAAGAGGCCAAACCGGAGTGTGTGATAGCCGGCAGGTGTTGCATGTGCGGGGTTGTGGGAAGCGTTTTGACTGAACTGCCGTGAGGTCGGAGAGTGATAAAGGATTGATGAAGCAGAAGCGTCTGGGAAGGCGCGGCATAGATGGTGATACCCCTGTATGCGTAAGTTGATCTCTCTCTTAATGTTTTCCCAAGTAGTACGGAACCCCTGAAATYCCGTACGAATCTGGCGGACCACCCGTTAAGCCTAAATACBCCTTGGTGACCGATMGCGGACAAGTACCCGTGAGGGAAAGGGTGAAAATGTACCCCCGGGAGGGGAGTGAAATAGTMCCTGAAACCGATCGCATACAATCCGTCGGAGCCTGCCCTTGTGGTGGGTGACGGCGTGCCTTTTGRAAGAATGAGCCTGCGAGTTAGTGGTGTGTGGCGAGGTTAACCCGTGTGGGGAAGCCGTAGCGAAAGCGAGTCCGAATAGGGCGTTTGAGTCGCATGCTCTAGACCCGAAGCGGTGTGATCTATCCATGGCCAGGGTGAAGCGACGGTAAGACGTCGTGGAGGCCCGAACCCACCAGGGTTGCAAACCTGGGGGATGAGCTGTGGATAGGGGTGAAAGGCCAATCAAACACCGTGATAGCTGGTTCTCCCCGAAATGCATTTAGGTGCAGCGTCATGTGTTTCTTGTCGGAGGTAGAGCACTGGATGGTCTAGGGGGCTTACCAGCTTACCGAAATCAGCCAAACTCCGAATGCCGACAAGTGAGAGCATGGCAGTGAGACGGCGGGGGATAAGCTTCGTCGTCGAGAGGGAAACAGCCCAGATCATCAGCTAAGGCCCCTAAGTGGTGACTAAGTGGAAAAGGACGTGGAGTTGCGGAGACAACCAGGAGGTTGGCTTGGAAGCAGCCATCCTTGAAAGAGTGCGTAATAGCTCACTGGTCAAGTGATTCTGCACCGACAATTTAGCGGGGCTCAAGTCATCCGCCGAAGCTGTGGCATCTACGCGTGTATCCGGCATCCTTTGGGGTGTCCAGGTGCGTGGATGGGTAGGGGAGCGTTGTGTGTGCGTTGAAGCGGCGGGGTGACCCGGTCGTGGAGTGCACGCAAGTGAGAATGCAGGCATGAGTAGCGTATGACGGGTGAGAAACCCGTCCGCCGAATATCCAAGGGTTCCAGGGTCAAGCTAATCTGCCCTGGGTGAGTCGGGTCCTAAGGCGAGGCCGACAGGCGTAGTCGATGGACAACGGGTTGATATTCCCGTACCGGCGCGAGAACGATCCTGCCGAGGTGAGTGATGCTAAGCATGCAAGGCGGTCGTGGGGGCTTCGGTTCCCTGATCGTTGAGTCTGTAACCCGATCTTGTAGTAGGCAAGCTGCGGAGGGACGCAGGAAGGTAGTCTGGCACCGTATTGGTTTGCGGTGTTAAGCCTGTAGGGTGTCTGGCCAGGTAAATCCGGTCGGACGTGTGCCTGAGAGGTGATGAGTGGTGCCACTTTTGTGGTACGTATCCGGATGATCCTATGCTGCCTAGAAAATCTTCGTGAGCGAGTTCTCGAGCTGCCCGTACCCCAAACCGACACTGGTGGATAGGTAGAGAATACCAAGGCGATCGAGATAATCATGGTGAAGGAACTCGGCAAAATCCTCCCGTAACTTCGGAATAAGGGAGACTGGAGGCGTGACGGCAGTTTACTTGTCGGTGCGTCGATAGTCGCAGAGAATAGGCCCAAGCGACTGCTTACTAAAAGCACAGGTCCGTGCTAAGTCGAAAGACGATGTATACGGACTGACTCCTGCCCGGTGCTCKGAAGGTTAAGGGGACGTGTTAGCACTTTTGTGCGAGGCACTGAACTTAAGCCCCAGTAAACGGCGGTGGTAACTATAACCATCCTAAGGKAGCGAAATTCCTTGTCGGGKAAGTTCCGRCCTGSACGAATGGAGTAACGACTTGGGCGCTGTCTCCACCATGAACTCGGCGAAATTGCATTACGAGTAAAGATGCTCGTTACGCGCACAGGGACGGAAAGVNCCCGGGACCTTTACTATAGTTTGGTATTGGTGATCGGTACGACTTGTGTAGGATAGGTGGGAGACTTTGAAGCGGTCACGCTAGTGATTGTGGAGTCATTGTTGAAATACCACTCTGGTCGTTCTGGTTATCTAACCTAGGTCCGTGATCCGGATCAGGGACAGTGCCTGATGGGTAGTTTGACTGGGGCGGTCGCCTCCMAAAAGGTAACGGAGGCGCCCAAAGGTTCCCTCAGCCTGGTTGGTAATCAGGTGTTGAGTGTAAGTGCACAAGGGAGCTTGACTGTGAGACAGACATGTCGAGCAGGGACGAAAGTCGGGACTAGTGATCYTCTGGTGGATTGTGGAATCGCCAGAACTCAACGGATAAAAGGTACCCCGGGGATAACAGGCTGATCTTTCCCGAGCGCTCACAGCGACGGAATGGNTTGGCACCTCGATGTCGGCTCGTCGCATCCTGGGGCTGGAGTCGGTCCCAAGGGTTGGGCTGTTCGCCCATTAAAGCGGCACGCGARGCTGGGGKTAAGAACGTCGTGAGACAGTTCCGGKCCCTATACCGCTGCSCGTMGKATCTTGAGAGGGCTGTCCTTAGTACGCAAGGACCGGGACGGACCAACCTCTGGTGTGCCAGTTGTTCCACCAGGAGCATGGCTGGTTGGCTACGTTGGGGAGTGATAACCGCTGAAAGCATCTAAGTGGGAAGCACGCTTCAAGATGAGGGTTCCTGCACAGTTAATGTGGTAAGGCCCCCGGTAGACCACCGGGTGATAGGTCGGATGTGGAAGCATGGTGACATGTGGAGCTGACCGATACTAAGTGGCCGAGGGCTTGTCCCACA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41309","NCBI_taxonomy_name":"Propionibacterium freudenreichii","NCBI_taxonomy_id":"1744"}}}},"ARO_accession":"3004161","ARO_id":"41308","ARO_name":"Propionibacteria 23S rRNA with mutation conferring resistance to macrolide antibiotics","CARD_short_name":"Prop_23S_MAC","ARO_description":"Point mutation in the 23S rRNA of Propionibacteria shown clinically to confer resistance to macrolides.","ARO_category":{"41251":{"category_aro_accession":"3004125","category_aro_cvterm_id":"41251","category_aro_name":"23S rRNA with mutation conferring resistance to macrolide antibiotics","category_aro_description":"Nucleotide point mutations in the 23S rRNA subunit may confer resistance to macrolide antibiotics.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2803":{"model_id":"2803","model_name":"Mycobacterium tuberculosis thyA with mutation conferring resistance to para-aminosalicylic acid","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"40394":{"param_type":"nonsense mutation","param_description":"A sequence change where, compared to a reference sequence, one codon is replaced by a termination codon through a nucleotide substitution. These are described as a substitution of the wildtype codon to a termination codon. Format is given as [wild type AA][position][Ter], for example Q42Ter where Q42 is a wildtype amino acid replaced by a premature termination codon.","param_type_id":"40394","param_value":{"7856":"G76Ter","7859":"W83Ter","7861":"W98Ter"}},"snp":{"Curated-R":{"7856":"g2295a","7859":"g2295a","7861":"g2295a","7851":"W101R","7852":"H75N","7853":"T22A","7854":"T202A","7855":"Y36C","7857":"V77F","7858":"W83C","7860":"G91R","7862":"S105P","7863":"R126Q","7864":"F152V","7865":"C161T","7866":"H207R","7868":"P224L","7869":"R235P"},"param_value":{"7851":"W101R","7852":"H75N","7853":"T22A","7854":"T202A","7855":"Y36C","7857":"V77F","7858":"W83C","7860":"G91R","7862":"S105P","7863":"R126Q","7864":"F152V","7865":"C161T","7866":"H207R","7868":"P224L","7869":"R235P"},"clinical":{"7851":"W101R","7852":"H75N","7853":"T22A","7854":"T202A","7855":"Y36C","7857":"V77F","7858":"W83C","7860":"G91R","7862":"S105P","7863":"R126Q","7864":"F152V","7865":"C161T","7866":"H207R","7868":"P224L","7869":"R235P"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8792":{"protein_sequence":{"accession":"NP_217280.1","sequence":"MTPYEDLLRFVLETGTPKSDRTGTGTRSLFGQQMRYDLSAGFPLLTTKKVHFKSVAYELLWFLRGDSNIGWLHEHGVTIWDEWASDTGELGPIYGVQWRSWPAPSGEHIDQISAALDLLRTDPDSRRIIVSAWNVGEIERMALPPCHAFFQFYVADGRLSCQLYQRSADLFLGVPFNIASYALLTHMMAAQAGLSVGEFIWTGGDCHIYDNHVEQVRLQLSREPRPYPKLLLADRDSIFEYTYEDIVVKNYDPHPAIKAPVAV"},"dna_sequence":{"accession":"NC_000962.3","fmin":"3073679","fmax":"3074471","strand":"-","sequence":"GTGACGCCATACGAGGACCTGCTGCGCTTCGTGCTCGAAACGGGTACGCCCAAATCCGACCGCACCGGCACCGGAACCCGCAGCCTGTTCGGCCAGCAGATGCGCTATGATTTGTCGGCCGGTTTCCCGCTGCTCACTACCAAGAAAGTCCATTTCAAATCGGTAGCCTACGAGCTGCTGTGGTTTTTGCGCGGCGATTCCAATATCGGTTGGCTGCACGAGCACGGAGTCACCATCTGGGACGAATGGGCAAGTGATACAGGCGAACTCGGGCCGATCTACGGTGTACAATGGCGATCGTGGCCGGCTCCATCCGGTGAGCACATCGACCAGATCAGCGCGGCGCTGGATTTGCTGCGCACCGATCCCGATTCCCGGCGCATCATCGTGTCGGCCTGGAACGTCGGCGAAATCGAGCGGATGGCGCTGCCGCCCTGTCATGCGTTCTTCCAGTTCTACGTCGCCGATGGCCGGCTGAGCTGTCAGCTCTACCAACGCAGCGCCGACCTGTTTCTGGGTGTGCCGTTCAACATCGCCAGCTATGCGTTGCTCACCCACATGATGGCCGCCCAGGCCGGCTTGTCGGTCGGCGAGTTCATCTGGACCGGTGGCGACTGCCACATCTACGACAATCACGTCGAGCAAGTACGGCTGCAGCTCAGCCGCGAGCCGCGGCCATATCCGAAACTACTTCTAGCCGACCGGGATTCAATCTTCGAGTACACCTATGAAGACATCGTTGTGAAGAACTACGATCCGCATCCGGCGATCAAAGCTCCAGTCGCGGTATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3004153","ARO_id":"41300","ARO_name":"Mycobacterium tuberculosis thyA with mutation conferring resistance to para-aminosalicylic acid","CARD_short_name":"Mtub_thyA_PAS","ARO_description":"Point mutations in the thymidylate synthetase thyA gene shown clinically to confer resistance to para-aminosalicylic acid. Loss-of-function mutations in thyA disrupt the catalytic activity and substrate-binding affinity, thus conferring resistance.","ARO_category":{"41299":{"category_aro_accession":"3004152","category_aro_cvterm_id":"41299","category_aro_name":"aminosalicylate resistant thymidylate synthase","category_aro_description":"Antibiotic resistant form of thymidylate synthase (synthetase), an enzyme that catalyzes the conversion of dUMP to dTMP in nucleotide biosynthesis. Loss-of-function mutations in thymidylate synthase confer resistance to p-aminosalicylic acid by disrupting the substrate-binding affinity and catalytic activity.","category_aro_class_name":"AMR Gene Family"},"40948":{"category_aro_accession":"3004019","category_aro_cvterm_id":"40948","category_aro_name":"para-aminosalicylic acid","category_aro_description":"Para-aminosalicylic acid (PAS) is an anti-tubercular antibiotic agent, often used in conjunction with Isoniazid for treatment of M. tuberculosis infections. PAS diminishes bacterial cell growth by limiting folic acid production.","category_aro_class_name":"Antibiotic"},"45741":{"category_aro_accession":"3007159","category_aro_cvterm_id":"45741","category_aro_name":"salicylic acid antibiotic","category_aro_description":"A group of antibiotics derived from salicylic acid.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2804":{"model_id":"2804","model_name":"Mycobacterium tuberculosis folC with mutation conferring resistance to para-aminosalicylic acid","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"7874":"E40Q","7875":"E40G","7873":"T20P","7876":"I43T","7877":"I43S","7878":"I43A","7879":"R49P","7880":"R49W","7881":"L56V","7882":"R91W","7883":"S150G","7884":"S150C","7885":"E153A","7886":"E153G","7887":"A420V"},"Curated-R":{"7874":"E40Q","7875":"E40G","7873":"T20P","7876":"I43T","7877":"I43S","7878":"I43A","7879":"R49P","7880":"R49W","7881":"L56V","7882":"R91W","7883":"S150G","7884":"S150C","7885":"E153A","7886":"E153G","7887":"A420V"},"clinical":{"7874":"E40Q","7875":"E40G","7873":"T20P","7876":"I43T","7877":"I43S","7878":"I43A","7879":"R49P","7880":"R49W","7881":"L56V","7882":"R91W","7883":"S150G","7884":"S150C","7885":"E153A","7886":"E153G","7887":"A420V"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8816":{"protein_sequence":{"accession":"NP_216963.1","sequence":"MNSTNSGPPDSGSATGVVPTPDEIASLLQVEHLLDQRWPETRIDPSLTRISALMDLLGSPQRSYPSIHIAGTNGKTSVARMVDALVTALHRRTGRTTSPHLQSPVERISIDGKPISPAQYVATYREIEPLVALIDQQSQASAGKGGPAMSKFEVLTAMAFAAFADAPVDVAVVEVGMGGRWDATNVINAPVAVITPISIDHVDYLGADIAGIAGEKAGIITRAPDGSPDTVAVIGRQVPKVMEVLLAESVRADASVAREDSEFAVLRRQIAVGGQVLQLQGLGGVYSDIYLPLHGEHQAHNAVLALASVEAFFGAGAQRQLDGDAVRAGFAAVTSPGRLERMRSAPTVFIDAAHNPAGASALAQTLAHEFDFRFLVGVLSVLGDKDVDGILAALEPVFDSVVVTHNGSPRALDVEALALAAGERFGPDRVRTAENLRDAIDVATSLVDDAAADPDVAGDAFSRTGIVITGSVVTAGAARTLFGRDPQ"},"dna_sequence":{"accession":"NC_000962.3","fmin":"2746134","fmax":"2747598","strand":"-","sequence":"ATGAATTCGACGAATTCCGGCCCGCCTGACTCGGGATCGGCCACCGGCGTCGTGCCCACTCCGGACGAGATCGCGTCCCTGCTGCAGGTTGAGCATCTACTCGACCAACGCTGGCCGGAGACCCGCATCGATCCGAGCCTGACCCGGATCAGCGCGTTGATGGACCTGCTGGGCTCGCCCCAACGCAGCTATCCGTCGATCCATATCGCGGGCACCAACGGCAAGACCTCGGTGGCGCGCATGGTCGACGCGCTGGTCACCGCGCTGCACCGGCGCACCGGCCGAACCACCAGCCCACACCTGCAGTCACCGGTGGAACGCATTTCGATCGACGGCAAGCCGATCAGCCCGGCGCAGTATGTGGCGACCTACCGGGAGATCGAGCCGTTGGTGGCGCTGATCGACCAGCAGTCGCAGGCTTCTGCGGGTAAGGGTGGCCCGGCGATGAGCAAGTTCGAGGTGCTCACCGCGATGGCGTTCGCGGCCTTTGCGGACGCGCCCGTCGACGTGGCAGTGGTCGAGGTGGGCATGGGCGGACGTTGGGACGCCACCAACGTGATCAACGCACCGGTCGCCGTCATCACCCCGATCAGCATTGATCACGTCGACTATCTCGGTGCCGATATCGCCGGGATCGCCGGGGAGAAGGCGGGCATCATCACTCGGGCCCCCGACGGTTCGCCGGACACCGTCGCGGTCATCGGGCGTCAGGTCCCGAAGGTCATGGAGGTGCTGCTGGCCGAATCGGTGCGCGCCGACGCGTCGGTGGCCCGGGAGGATTCCGAATTCGCGGTGCTACGGCGACAGATCGCGGTCGGCGGTCAGGTACTGCAACTGCAGGGCCTCGGCGGGGTTTACTCCGACATCTACTTGCCGCTGCACGGTGAACACCAGGCGCACAACGCGGTGCTCGCCCTCGCTTCCGTCGAGGCCTTTTTCGGTGCCGGTGCGCAGCGTCAGCTCGACGGCGACGCCGTCCGGGCCGGCTTTGCCGCCGTCACCAGTCCCGGCCGGTTGGAGCGCATGCGCAGCGCACCCACGGTGTTCATCGACGCCGCGCACAATCCGGCCGGGGCGAGTGCTCTGGCACAAACGCTGGCGCATGAGTTCGACTTCCGATTTCTGGTCGGGGTGCTCAGCGTGCTGGGCGACAAGGACGTGGACGGCATCCTGGCCGCACTGGAGCCGGTGTTCGATTCCGTCGTCGTGACCCACAACGGGTCGCCGCGGGCGCTGGATGTCGAGGCCCTGGCGCTGGCGGCCGGCGAGCGGTTCGGACCCGACCGGGTGCGCACCGCCGAGAACCTGCGCGATGCTATCGACGTTGCCACCTCACTGGTCGACGACGCCGCCGCCGACCCGGATGTGGCCGGGGACGCATTCTCGAGAACCGGGATCGTCATCACCGGCTCGGTTGTCACCGCAGGGGCGGCTCGGACCTTGTTCGGTCGTGATCCGCAATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3004157","ARO_id":"41304","ARO_name":"Mycobacterium tuberculosis folC with mutation conferring resistance to para-aminosalicylic acid","CARD_short_name":"Mtub_folC_PAS","ARO_description":"Point mutations in the dihydrofolate synthetase folC gene shown clinically to confer resistance to p-aminosalicylic acid or other aminosalicylates. Mutations in folC inhibit bioactivation of PAS and thus confer resistance.","ARO_category":{"41302":{"category_aro_accession":"3004155","category_aro_cvterm_id":"41302","category_aro_name":"aminosalicylate resistant dihydrofolate synthase","category_aro_description":"Dihydrofolate synthase (synthetase) enzymes resistant to aminosalicylates (inc. para-aminosalicylic acid) caused by mutation. Dihydrofolate synthase is required for bioactivation of p-aminosalicylic acid, and mutation in dihydrofolate synthase inhibits production of the dihydrofolate analog hydroxyl-dihydrofolate, thus preventing activation and conferring resistance.","category_aro_class_name":"AMR Gene Family"},"40948":{"category_aro_accession":"3004019","category_aro_cvterm_id":"40948","category_aro_name":"para-aminosalicylic acid","category_aro_description":"Para-aminosalicylic acid (PAS) is an anti-tubercular antibiotic agent, often used in conjunction with Isoniazid for treatment of M. tuberculosis infections. PAS diminishes bacterial cell growth by limiting folic acid production.","category_aro_class_name":"Antibiotic"},"45741":{"category_aro_accession":"3007159","category_aro_cvterm_id":"45741","category_aro_name":"salicylic acid antibiotic","category_aro_description":"A group of antibiotics derived from salicylic acid.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2816":{"model_id":"2816","model_name":"Mycolicibacterium smegmatis 23S rRNA with mutation conferring resistance to clarithromycin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"7925":"a2266g","7926":"a2267g"},"Curated-R":{"7925":"a2266g","7926":"a2267g"},"clinical":{"7925":"a2266g","7926":"a2267g"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"41093","param_value":"5000"}},"model_sequences":{"sequence":{"4161":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"AB011184.1","fmin":"0","fmax":"3162","strand":"+","sequence":"TTGTAAGTGTTTAAGGGCGCATGGTGGATGCCTTGGCACTGGGAGCCGATGAAGGACGTAGGAGGCTGCGATAAGCCTCGGGGAGCTGTCAACCGAGCGTTGATCCGAGGATGTCCGAATGGGGAAACCCGGCACGAGTGATGTCGTGTCACCAGGCGCTGAATATATAGGCGTCTGGGGGGAACGCGGGGAAGTGAAACATCTCAGTACCCGTAGGAAGAGAAAACAAAATGTGATTCCGTGAGTAGTGGCGAGCGAAAGCGGAGGATGGCTAAACCGTATGCATGTGATACCGGGTAGGGGTTGTGTGTGCGGGGTTGTGGGACCTATCTTTCCGGCTCTACCTGGCTGGAGGGCAGTGAGAAAATGTTGTGGTTAGCGGAAATGGCTTGGGATGGCCTGCCGTAGACGGTGAGAGCCCGGTACGTGAAAACCCGACGTCTGTCTTGATGGTGTTCCCGAGTAGCAGCGGGCCCGTGGAATCTGCTGTGAATCTGCCGGGACCACCCGGTAAGCCTGAATACTTCCCAGTGACCGATAGCGGATTAGTACCGTGAGGGAATGGTGAAAAGTACCCCGGGAGGGGAGTGAAAGAGTACCTGAAACCGTGCGCTTACAATCCGTCAGAGCCCTCGACGTGTCGTGGGGTGATGGCGTGCCTTTTGAAGAATGAGCCTGCGAGTCAGGGACATGTCGCGAGGTTAACCCGGGTGGGGTAGCCGCAGCGAAAGCGAGTCTGAATAGGGCGTATCCACGCAACAGTGTGTGGTGTAGTGGTGTGTTCTGGACCCGAAGCGGAGTGATCTACCCATGGCCAGGGTGAAGCGCGGGTAAGACCGCGTGGAGGCCCGAACCCACTTAGGTTGAAGACTGAGGGGATGAGCTGTGGGTAGGGGTGAAAGGCCAATCAAACTCCGTGATAGCTGGTTCTCCCCGAAATGCATTTAGGTGCAGCGTTGCGTGTTTCTTGCCGGAGGTAGAGCTACTGGATGGCCGATGGGCCCCACAGGGTTACTGACGTCAGCCAAACTCCGAATGCCGGTAAGTCCAAGAGTGCGGCAGTGAGACGGCGGGGGATAAGCTCCGTGCGTCGAGAGGGAAACAGCCCAGATCGCCGGCTAAGGCCCCTAAGCGTGTGCTAAGTGGAAAAGGATGTGCAGTCGCGAAGACAACCAGGAGGTTGGCTTAGAAGCAGCCACCCTTGAAAGAGTGCGTAATAGCTCACTGGTCAAGTGATTGTGCGCCGATAATGTAGCGGGGCTCAAGCACACCGCCGAAGCCGCGGCAACGACCTTGTGTCGTTGGGTAGGGGAGCGTCCTGCATCCGGTGAAGCCGCCGAGTGATCGAGTGGTGGAGGGTGTGGGAGTGAGAATGCAGGCATGAGTAGCGATTAGGCAAGTGAGAACCTTGCCCGCCGAAAGACCAAGGGTTCCTGGGCCAGGCCAGTCCGCCCAGGGTGAGTCGGGACCTAAGGCGAGGCCGACAGGCGTAGTCGATGGACAACGGGTTGATATTCCCGTACCCGTGTATGTGCGTCCATGATGAATCAGCGGTACTAACCATCCAAAACCACCGTGACTGCACCTTTCGGGGTGTGGCGTTGGTGGGGCTGCATGGGACCTTCGTTGGTAGTAGTCAAGCGATGGGGTGACGCAGGAAGGTAGCCGTACCGGTCAGTGGTAATACCGGGGTAAGCCTGTAGGGAGTCAGATAGGTAAATCCGTCTGGCATATATCCTGAGAGGTGATGCATAGCCGAGTGAGGCGAATTCGGTGATCCTATGCTGCCGAGAAAAGCCTCTAGCGAGGACATACACGGCCCGTACCCCAAACCAACACAGGTGGTCAGGTAGAGAATACTAAGGCGTACGAGTGAACTATGGTTAAGGAACTCGGCAAAATGCCCCCGTAACTTCGGGAGAAGGGGGACCCACATGGCGTGTAAGCCTTTACGGCCCAAGCGTGAGTGGGTGGCACAAACCAGTGAGAAGCGACTGTTTACTAAAAACACAGGTCCGTGCGAAGTCGCAAGACGATGTATACGGACTGACGCCTGCCCGGTGCTGGAAGGTTAAGAGGACCCGTTAACCCTTCGGGGTGAAGCGGAGAATTTAAGCCCCAGTAAACGGCGGTGGTAACTATAACCATCCTAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCTGCACGAATGGCGTAACGACTTCTCAACTGTCTCAACCATAGACTCGGCGAAATTGCACTACGAGTAAAGATGCTCGTTACGCGCGGCAGGACGAAAAGACCCCGGGACCTTCACTACAACTTGGTATTGGTGCTCGATACGGTTTGTGTAGGATAGGTGGGAGACTGTGAAGCTCACACGCCAGTGTGGGTGGAGTCGTTGTTGAAATACCACTCTGATCGTATTGGGCCTCTAACCTCGGACCGTATATCCGGTTCAGGGACAGTGCCTGGTGGGTAGTTTAACTGGGGCGGTTGCCTCCTAAAATGTAACGGAGGCGCCCAAAGGTTCCCTCAACCTGGACGGCAATCAGGTGTTGAGTGTAAGTGCACAAGGGAGCTTGACTGCGAGACGGACATGTCGAGCAGGGACGAAAGTCGGGACTAGTGATCCGGCACCTCTGAGTGGAAGGGGTGTCGCTCAACGGATAAAAGGTACCCCGGGGATAACAGGCTGATCTTCCCCAAGAGTCCATATCGACGGGATGGTTTGGCACCTCGATGTCGGCTCGTCGCATCCTGGGGCTGGAGCAGGTCCCAAGGGTTGGGCTGTTCGCCCATTAAAGCGGCACGCGAGCTGGGTTTAGAACGTCGTGAGACAGTTCGGTCTCTATCCGCCGCGCGCGTCAGAAGCTTGAGGAAACCTGTCCCTAGTACGAGAGGACCGGGACGGACGAACCTCTGGTATACCAGTTGTCCCACCAGGGGCACGGCTGGATAGCCACGTTCGGACAGGATAACCGCTGAAAGCATCTAAGCGGGAAACCTCTTCCAAGACCAGGCTTCTCACCCTCTAGGAGGGATAAGGCCCCCCGCAGACCACGGGATTGATAGACCAGACCTGGAAGCCTAGTAATAGGTGCAGGGAACTGGCACTAACCGGCCGAAAACTTACAACACCCCATAATCGTTGTAAGAAGAAAACATTGACGCACC","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36871","NCBI_taxonomy_name":"Mycolicibacterium smegmatis","NCBI_taxonomy_id":"1772"}}}},"ARO_accession":"3004169","ARO_id":"41319","ARO_name":"Mycolicibacterium smegmatis 23S rRNA with mutation conferring resistance to clarithromycin","CARD_short_name":"Msme_23S_CLR","ARO_description":"Point mutation in the 23S rRNA of Mycolicibacterium smegmatis shown to confer resistance to clarithromycin, a macrolide type antibiotic.","ARO_category":{"41251":{"category_aro_accession":"3004125","category_aro_cvterm_id":"41251","category_aro_name":"23S rRNA with mutation conferring resistance to macrolide antibiotics","category_aro_description":"Nucleotide point mutations in the 23S rRNA subunit may confer resistance to macrolide antibiotics.","category_aro_class_name":"AMR Gene Family"},"35982":{"category_aro_accession":"0000065","category_aro_cvterm_id":"35982","category_aro_name":"clarithromycin","category_aro_description":"Clarithromycin is a methyl derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome and is used to treat pharyngitis, tonsillitis, acute maxillary sinusitis, acute bacterial exacerbation of chronic bronchitis, pneumonia (especially atypical pneumonias associated with Chlamydia pneumoniae or TWAR), and skin structure infections.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2811":{"model_id":"2811","model_name":"Mycobacterium avium 23S rRNA with mutation conferring resistance to clarithromycin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"7914":"a2274g","7915":"a2274t","7913":"a2272c"},"Curated-R":{"7914":"a2274g","7915":"a2274t","7913":"a2272c"},"clinical":{"7914":"a2274g","7915":"a2274t","7913":"a2272c"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"41093","param_value":"5700"}},"model_sequences":{"sequence":{"4157":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"NG_041979.1","fmin":"0","fmax":"3112","strand":"+","sequence":"TGTGTGTAAGTAAGTGTTTAAGGGCGCATGGTGGATGCCTTGGCATCGAGAGCCGATGAAGGACGTGGGAGGCTGCGATATGCCTCGGGGAGCTGTCAACCGAGCATTGATCCGAGGATTTCCGAATGGGGAAACCCAGCACGAGTGATGTCGTGTTACCCGTATCTGAATATATAGGGTGCGGGAGGTAACGCGGGGAAGTGAAACATCTCAGTACCCGTAGGAGAAGAAAACAATTGTGATTCCGTCAGTAGTGGCGAGCGAACGCGGAACAGGCTAAACCGCATGCATGGACAACCGGGTAGGGGTTGTGTGTGCGGGGTTGTGGGATTGATATGTCTCAGCTCTACCTGGCTGAGGGGTAGTCAGAAAGTGTCGTGGTTAGCGGAAGTGGCCTGGGACGGCCCGCCGTAGACGGTGAGAGCCCGGTACGCGAAAACCCGGCACCTGCCTTATATCAACACCCGAGTAGCAGCGGGCCCGTGGAATCTGCTGTGAATCTGCCGGGACCACCCGGTAAGCCTAAATACTTCTCGATGACCGATAGCGGATTAGTACCGTGAGGGAATGGTGAAAAGTACCCCGGGAGGGGAGTGAAATAGTACCTGAAACCGTGTGCCTACAATCCGTCAGAGCCTCCTCGTGGGGTGATGGCGTGCCTTTTGAAGAATGAGCCTGCGAGTCAGGGACACGTCGCGAGGTTAACCCGTGCGGGGTAGCCGCAGCGAAAGCGAGTCTGAATAGGGCGCATCCCCTTTGGGGTGTAGTGGCGTGTTCTGGACCCGAAGCGGAGTGATCTACCCATGGCCAGGGTGAAGCGCGGGTAAGACCGCGTGGAGGCCCGAACCCACTTAGGTTGAAGACTGAGGGGATGAGCTGTGGGTAGGGGTGAAAGGCCAATCAAACTCCGTGATAGCTGGTTCTCCCCGAAATGCATTTAGGTGCAGCGTTGCGTGGTTCACCACGGAGGTAGAGCTACTGGATGGCCGATGGGCCCTACTAGGTTACTGACGTCAGCCAAACTCCGAATGCCGTGGTGTAAAGCGTGGCAGTGAGACGGCGGGGGATAAGCTCCGTACGTCGAAAGGGAAACAGCCCAGATCGCCGGCTAAGGCCCCTAAGCGTGTGCTAAGTGGAAAAGGATGTGTAGTCGCAGAGACAACCAGGAGGTTGGCTTAGAAGCAGCCACCCTTGAAAGAGTGCGTAATAGCTCACTGGTCAAGTGATTATGCGCCGATAATGTAGCGGGGCTCAAGCACACCGCCGAAGCCGCGGCACATTCATCTTTACGGTGGATGTGGGTAGGGGAGCGTCCCCCATTCAGCGAAGCCTCCGGGTGACCGGTGGTGGAGGGTGGGGGAGTGAGAATGCAGGCATGAGTAGCGATAAGGCAAGTGAGAACCTTGCCCGCCGTAAGACCAAGGGTTCCTGGGCCAGGCCAGTCCGCCCAGGGTGAGTCGGGACCTAAGGCGAGGCCGACAGGCGTAGTCGATGGACAACGGGTTGATATTCCCGTACCCGTGTATGGGCGTCCCTGATGAATCAGCGGTACTAACCACCCAAAACCGGATCGACCATTCCCCTTCGGGGGCGTGGCGATTCGGGGCTGCGTGGGACCTTCGCTGGTAGTAGTCAAGCAATGGGGTGACGCAGGAAGGCAGCCGTACCAGTCAGTGGTAATACTGGGGCAAGCCCGTAGGGAGAGCGATAGGCAAATCCGTCGCTCACTAATCCTGAGAGGTGATGCATAGCCGGTTGAGGCGAATTCGGTGATCCTCTGCTGCCAAGAAAAGCCTCTAGCGAGCACATACACGGCCCGTACCCCAAACCAACACAGGTGGTCAGGTAGAGAATACCAAGGCGTACGAGATAACTATGGTTAAGGAACTCGGCAAAATGCCCCCGTAACTTCGGGAGAAGGGGGGCCGGAATACCGTGAACACCCTTGCGGTGGGAGCGGGATTCGGCCGCAGAAACCAGTGGGTAGCGACTGTTTACTAAAAACACAGGTCCGTGCGAAGTCGCAAGACGATGTATACGGACTGACGCCTGCCCGGTGCTGGAAGGTTAAGAGGACCCGTTAACCCGTAAGGGTGAAGCGGAGAATTTAAGCCCCAGTAAACGGCGGTGGTAACTATAACCATCCTAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCTGCACGAATGGCGTAACGACTTCCCAACTGTCTCAACCATAGACTCGGCGAAATTGCACTACGAGTAAAGATGCTCGTTACGCGCGGCAGGACGAAAAGACCCCGGGACCTTCACTACAACTTGGTATTGGTGTTCGGTACGGTTTGTGTAGGATAGGTGGGAGACTTTGAAGCACAGACGCCAGTTTGTGTGGAGTCGTTGTTGAAATACCACTCTGATCGTATTGGACACCTAACGTCGAACCCTTATCGGGTTCACGGACAGTGCCTGGCGGGTAGTTTAACTGGGGCGGTTGCCTCCTAAAATGTAACGGAGGCGCCCAAAGGTTCCCTCAACCTGGACGGCAATCAGGTGGCGAGTGTAAGTGCACAAGGGAGCTTGACTGCGAGACTTACAAGTCAAGCAGGGACGAAAGTCGGGACTAGTGATCCGGCACCCCCGAGTGGAAGGGGTGTCGCTCAACGGATAAAAGGTACCCCGGGGATAACAGGCTGATCTTCCCCAAGAGTCCATATCGACGGGATGGTTTGGCACCTCGATGTCGGCTCGTCGCATCCTGGGGCTGGAGCAGGTCCCAAGGGTTGGGCTGTTCGCCCATTAAAGCGGCACGCGAGCTGGGTTTAGAACGTCGTGAGACAGTTCGGTCTCTATCCGCCGCGCGCGTCAGAAACTTGAGGAAACCTGTCCCTAGTACGAGAGGACCGGGACGGACGAACCTCTGGTATACCAGTTGTCCCACCAGGGGCACGGCTGGATAGCCACGTTCGGACAGGATAACCGCTGAAAGCATCTAAGCGGGAAACCTTCTCCAAGATCAGGTTTCTCACCCTTTTAGAGGGATAAGGCCCCCCGCAGACCACGGGATTGATAGGCCAGACCTGGAAGCTCAGTAATGAGTGCAGGGAACTGGCACTAACCGGCCGAAAAC","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39582","NCBI_taxonomy_name":"Mycobacterium avium","NCBI_taxonomy_id":"1764"}}}},"ARO_accession":"3004164","ARO_id":"41312","ARO_name":"Mycobacterium avium 23S rRNA with mutation conferring resistance to clarithromycin","CARD_short_name":"Mavi_23S_CLR","ARO_description":"Point mutation in the 23S rRNA of Mycobacterium avium shown to confer resistance to clarithromycin, a macrolide type antibiotic.","ARO_category":{"41251":{"category_aro_accession":"3004125","category_aro_cvterm_id":"41251","category_aro_name":"23S rRNA with mutation conferring resistance to macrolide antibiotics","category_aro_description":"Nucleotide point mutations in the 23S rRNA subunit may confer resistance to macrolide antibiotics.","category_aro_class_name":"AMR Gene Family"},"35982":{"category_aro_accession":"0000065","category_aro_cvterm_id":"35982","category_aro_name":"clarithromycin","category_aro_description":"Clarithromycin is a methyl derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome and is used to treat pharyngitis, tonsillitis, acute maxillary sinusitis, acute bacterial exacerbation of chronic bronchitis, pneumonia (especially atypical pneumonias associated with Chlamydia pneumoniae or TWAR), and skin structure infections.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2813":{"model_id":"2813","model_name":"Mycobacterium intracellulare 23S rRNA with mutation conferring resistance to clarithromycin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"8173":"a2266c","8174":"a2266g","8172":"a2266t"},"Curated-R":{"8173":"a2266c","8174":"a2266g","8172":"a2266t"},"clinical":{"8173":"a2266c","8174":"a2266g","8172":"a2266t"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"41093","param_value":"5700"}},"model_sequences":{"sequence":{"4177":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"NR_076151.1","fmin":"0","fmax":"3103","strand":"+","sequence":"TAAGTGTTTAAGGGCGCATGGTGGATGCCTTGGCATCGAGAGCCGATGAAGGACGTGGGAGGCTGCGATATGCCTCGGGGAGCTGTCAACCGAGCATTGATCCGAGGATTTCCGAATGGGGAAACCCAGCACGAGTGATGTCGTGTTACCCGCATCTGAATATATAGGGTGCGGGAGGGAACGCGGGGAAGTGAAACATCTCAGTACCCGTAGGAGAAGAAAACAATTGTGATTCCGTAAGTAGTGGCGAGCGAACGCGGAACAGGCTAAACCGCACGCATGTGATACCGGGTAGGGGTTGTGTGTGCGGGGTTGTGGGAGGATACATCTCAGCTCTACCTGGCTGAGGGGTAGTCAGAAAGTGTCGTGGTTAGCGGAAGTGGCCTGGGATGGTCTGCCGTAGACGGTGAGAGCCCGGTACGCGAAAACCCGTCACCTACCTTGTATCAATTCCCGAGTAGCAGCGGGCCCGTGGAATCTGCTGTGAATCTGCCGGGACCACCCGGTAAGCCTAAATACTTCTCGATGACCGATAGCGGATTAGTACCGTGAGGGAATGGTGAAAAGTACCCCGGGAGGGGAGTGAAATAGTACCTGAAACCGTGTGCCTACAATCCGTCAGAGCCTCCTTGTGGGGTGATGGCGTGCCTTTTGAAGAATGAGCCTGCGAGTCAGGGACACGTCGCGAGGTTAACCCGTGCGGGGTAGCCGCAGCGAAAGCGAGTCTGAATAGGGCGCATCCCCTTTGGGGTGTAGTGGCGTGTTCTGGACCCGAAGCGGAGTGATCTACCCATGGCCAGGGTGAAGCGCGGGTAAGACCGCGTGGAGGCCCGAACCCACTTAGGTTGAAGACTGAGGGGATGAGCTGTGGGTAGGGGTGAAAGGCCAATCAAACTCCGTGATAGCTGGTTCTCCCCGAAATGCATTTAGGTGCAGCGTTGCGTGGTTCACCACGGAGGTAGAGCTACTGGATGGCCGATGGGCCCTACTAGGTTACTGACGTCAGCCAAACTCCGAATGCCGTGGTGTAAAGCGTGGCAGTGAGACGGCGGGGGATAAGCTCCGTACGTCGAAAGGGAAACAGCCCAGATCGCCGGCTAAGGCCCCTAAGCGTGTGCTAAGTGGAAAAGGATGTGTAGTCGCAGAGACAACCAGGAGGTTGGCTTAGAAGCAGCCACCCTTGAAAGAGTGCGTAATAGCTCACTGGTCAAGTGATTATGCGCCGATAATGTAGCGGGGCTCAAGCACACCGCCGAAGCCGCGGCACATTCACGTTTACGTGGATGTGGGTAGGGGGAGCGTCCCTCATTCAGCGAAGCCTCCGGGTGACCGGTGGTGGAGGGTGGGGGAGTGAGAATGCAGGCATGAGTAGCGATAAGGCAAGTGAGAACCTTGCCCGCCGTAAGACCAAGGGTTCCTGGGCCAGGCCAGTCCGCCCAGGGTGAGTCGGGACCTAAGGCGAGGCCGACAGGCGTAGTCGATGGACAACGGGTTGATATTCCCGTACCCGTGTATGGGCGTCCCTGATGAATCAGCGGTACTAACCACCCAAAACCGGATCGACCATTCCCCTTCGGGGGCATGGAGTTTCGGGGCTGCGTGGGACCTTCGCTGGTAGTAGTCAAGCAATGGGGTGACGCAGGAAGGTAGCCGTACCAGTCAGTGGTAATACTGGGGCAAGCCTGTAGGGAGAGCGATAGGCAAATCCGTCGCTCATTAATCCTGAGAGGTGATGCATAGCCGATTGAGGTGAATTCGGTGATCCTCTGCTGCCAAGAAAAGCCTCTAGCGAGCACATACACGGCCCGTACCCCAAACCAACACAGGTGGTCAGGTAGAGAATACCAAGGCGTACGAGATAACTATGGTTAAGGAACTCGGCAAAATGCCCCCGTAACTTCGGGAGAAGGGGGGCCGGAATACCGTGAACACCCTTGCGGTGGGAGCGGGATCCGGCCGCAGAAACCAGTGGGTAGCGACTGTTTACTAAAAACACAGGTCCGTGCGAAGTCGCAAGACGATGTATACGGACTGACGCCTGCCCGGTGCTGGAAGGTTAAGAGGACCCGTTAACCGTAAGGTGAAGCGGAGAATTTAAGCCCCAGTAAACGGCGGTGGTAACTATAACCATCCTAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCTGCACGAATGGCGTAACGACTTCCCAACTGTCTCAACCATAGACTCGGCGAAATTGCACTACGAGTAAAGATGCTCGTTACGCGCGGCAGGACGAAAAGACCCCGGGACCTTCACTACAACTTGGTATTGGTGTTCGGTACGGTTTGTGTAGGATAGGTGGGAGACTGTGAAATACAGACGCCAGTTTGTATGGAGTCGTTGTTGAAATACCACTCTGATCGTATTGGACACCTAACGTCGAACCCTTATCGGGTTCACGGACAGTGCCTGGCGGGTAGTTTAACTGGGGCGGTTGCCTCCTAAAATGTAACGGAGGCGCCCAAAGGTTCCCTCAACCTGGACGGCAATCAGGTGACGAGTGTAAGTGCACAAGGGAGCTTGACTGCGAGACTTACAAGTCAAGCAGGGACGAAAGTCGGGACTAGTGATCCGGCACCCCCGAGTGGAAGGGGTGTCGCTCAACGGATAAAAGGTACCCCGGGGATAACAGGCTGATCTTCCCCAAGAGTCCATATCGACGGGATGGTTTGGCACCTCGATGTCGGCTCGTCGCATCCTGGGGCTGGAGCAGGTCCCAAGGGTTGGGCTGTTCGCCCATTAAAGCGGCACGCGAGCTGGGTTTAGAACGTCGTGAGACAGTTCGGTCTCTATCCGCCGCGCGCGTCAGAAACTTGAGGAAACCTGTCCCTAGTACGAGAGGACCGGGACGGACGAACCTCTGGTATACCAGTTGTTCCACCAGGAGCACGGCTGGATAGCCACGTTCGGACAGGATAACCGCTGAAAGCATCTAAGCGGGAAACCTTCTCCAAGATCAGGTTTCTCACCCTTTTAGAGGGATAAGGCCCCCCGCAGACCACGGGTTCGATAGGCTAGACCTGGAAGCTCAGCAATGAGTGCAGGGAACTGGCACTAACCGGCCGAAAACTTAC","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41317","NCBI_taxonomy_name":"Mycobacterium intracellulare","NCBI_taxonomy_id":"1767"}}}},"ARO_accession":"3004166","ARO_id":"41315","ARO_name":"Mycobacterium intracellulare 23S rRNA with mutation conferring resistance to clarithromycin","CARD_short_name":"Mint_23S_CLR","ARO_description":"Point mutation in the 23S rRNA of Mycobacterium intracellulare shown to confer resistance to clarithromycin, a macrolide type antibiotic.","ARO_category":{"41251":{"category_aro_accession":"3004125","category_aro_cvterm_id":"41251","category_aro_name":"23S rRNA with mutation conferring resistance to macrolide antibiotics","category_aro_description":"Nucleotide point mutations in the 23S rRNA subunit may confer resistance to macrolide antibiotics.","category_aro_class_name":"AMR Gene Family"},"35982":{"category_aro_accession":"0000065","category_aro_cvterm_id":"35982","category_aro_name":"clarithromycin","category_aro_description":"Clarithromycin is a methyl derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome and is used to treat pharyngitis, tonsillitis, acute maxillary sinusitis, acute bacterial exacerbation of chronic bronchitis, pneumonia (especially atypical pneumonias associated with Chlamydia pneumoniae or TWAR), and skin structure infections.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2814":{"model_id":"2814","model_name":"Mycobacterium intracellulare 23S rRNA with mutation conferring resistance to azithromycin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"7923":"a2268c"},"Curated-R":{"7923":"a2268c"},"clinical":{"7923":"a2268c"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"41093","param_value":"5700"}},"model_sequences":{"sequence":{"4159":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"NR_076151.1","fmin":"0","fmax":"3103","strand":"+","sequence":"TAAGTGTTTAAGGGCGCATGGTGGATGCCTTGGCATCGAGAGCCGATGAAGGACGTGGGAGGCTGCGATATGCCTCGGGGAGCTGTCAACCGAGCATTGATCCGAGGATTTCCGAATGGGGAAACCCAGCACGAGTGATGTCGTGTTACCCGCATCTGAATATATAGGGTGCGGGAGGGAACGCGGGGAAGTGAAACATCTCAGTACCCGTAGGAGAAGAAAACAATTGTGATTCCGTAAGTAGTGGCGAGCGAACGCGGAACAGGCTAAACCGCACGCATGTGATACCGGGTAGGGGTTGTGTGTGCGGGGTTGTGGGAGGATACATCTCAGCTCTACCTGGCTGAGGGGTAGTCAGAAAGTGTCGTGGTTAGCGGAAGTGGCCTGGGATGGTCTGCCGTAGACGGTGAGAGCCCGGTACGCGAAAACCCGTCACCTACCTTGTATCAATTCCCGAGTAGCAGCGGGCCCGTGGAATCTGCTGTGAATCTGCCGGGACCACCCGGTAAGCCTAAATACTTCTCGATGACCGATAGCGGATTAGTACCGTGAGGGAATGGTGAAAAGTACCCCGGGAGGGGAGTGAAATAGTACCTGAAACCGTGTGCCTACAATCCGTCAGAGCCTCCTTGTGGGGTGATGGCGTGCCTTTTGAAGAATGAGCCTGCGAGTCAGGGACACGTCGCGAGGTTAACCCGTGCGGGGTAGCCGCAGCGAAAGCGAGTCTGAATAGGGCGCATCCCCTTTGGGGTGTAGTGGCGTGTTCTGGACCCGAAGCGGAGTGATCTACCCATGGCCAGGGTGAAGCGCGGGTAAGACCGCGTGGAGGCCCGAACCCACTTAGGTTGAAGACTGAGGGGATGAGCTGTGGGTAGGGGTGAAAGGCCAATCAAACTCCGTGATAGCTGGTTCTCCCCGAAATGCATTTAGGTGCAGCGTTGCGTGGTTCACCACGGAGGTAGAGCTACTGGATGGCCGATGGGCCCTACTAGGTTACTGACGTCAGCCAAACTCCGAATGCCGTGGTGTAAAGCGTGGCAGTGAGACGGCGGGGGATAAGCTCCGTACGTCGAAAGGGAAACAGCCCAGATCGCCGGCTAAGGCCCCTAAGCGTGTGCTAAGTGGAAAAGGATGTGTAGTCGCAGAGACAACCAGGAGGTTGGCTTAGAAGCAGCCACCCTTGAAAGAGTGCGTAATAGCTCACTGGTCAAGTGATTATGCGCCGATAATGTAGCGGGGCTCAAGCACACCGCCGAAGCCGCGGCACATTCACGTTTACGTGGATGTGGGTAGGGGGAGCGTCCCTCATTCAGCGAAGCCTCCGGGTGACCGGTGGTGGAGGGTGGGGGAGTGAGAATGCAGGCATGAGTAGCGATAAGGCAAGTGAGAACCTTGCCCGCCGTAAGACCAAGGGTTCCTGGGCCAGGCCAGTCCGCCCAGGGTGAGTCGGGACCTAAGGCGAGGCCGACAGGCGTAGTCGATGGACAACGGGTTGATATTCCCGTACCCGTGTATGGGCGTCCCTGATGAATCAGCGGTACTAACCACCCAAAACCGGATCGACCATTCCCCTTCGGGGGCATGGAGTTTCGGGGCTGCGTGGGACCTTCGCTGGTAGTAGTCAAGCAATGGGGTGACGCAGGAAGGTAGCCGTACCAGTCAGTGGTAATACTGGGGCAAGCCTGTAGGGAGAGCGATAGGCAAATCCGTCGCTCATTAATCCTGAGAGGTGATGCATAGCCGATTGAGGTGAATTCGGTGATCCTCTGCTGCCAAGAAAAGCCTCTAGCGAGCACATACACGGCCCGTACCCCAAACCAACACAGGTGGTCAGGTAGAGAATACCAAGGCGTACGAGATAACTATGGTTAAGGAACTCGGCAAAATGCCCCCGTAACTTCGGGAGAAGGGGGGCCGGAATACCGTGAACACCCTTGCGGTGGGAGCGGGATCCGGCCGCAGAAACCAGTGGGTAGCGACTGTTTACTAAAAACACAGGTCCGTGCGAAGTCGCAAGACGATGTATACGGACTGACGCCTGCCCGGTGCTGGAAGGTTAAGAGGACCCGTTAACCGTAAGGTGAAGCGGAGAATTTAAGCCCCAGTAAACGGCGGTGGTAACTATAACCATCCTAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCTGCACGAATGGCGTAACGACTTCCCAACTGTCTCAACCATAGACTCGGCGAAATTGCACTACGAGTAAAGATGCTCGTTACGCGCGGCAGGACGAAAAGACCCCGGGACCTTCACTACAACTTGGTATTGGTGTTCGGTACGGTTTGTGTAGGATAGGTGGGAGACTGTGAAATACAGACGCCAGTTTGTATGGAGTCGTTGTTGAAATACCACTCTGATCGTATTGGACACCTAACGTCGAACCCTTATCGGGTTCACGGACAGTGCCTGGCGGGTAGTTTAACTGGGGCGGTTGCCTCCTAAAATGTAACGGAGGCGCCCAAAGGTTCCCTCAACCTGGACGGCAATCAGGTGACGAGTGTAAGTGCACAAGGGAGCTTGACTGCGAGACTTACAAGTCAAGCAGGGACGAAAGTCGGGACTAGTGATCCGGCACCCCCGAGTGGAAGGGGTGTCGCTCAACGGATAAAAGGTACCCCGGGGATAACAGGCTGATCTTCCCCAAGAGTCCATATCGACGGGATGGTTTGGCACCTCGATGTCGGCTCGTCGCATCCTGGGGCTGGAGCAGGTCCCAAGGGTTGGGCTGTTCGCCCATTAAAGCGGCACGCGAGCTGGGTTTAGAACGTCGTGAGACAGTTCGGTCTCTATCCGCCGCGCGCGTCAGAAACTTGAGGAAACCTGTCCCTAGTACGAGAGGACCGGGACGGACGAACCTCTGGTATACCAGTTGTTCCACCAGGAGCACGGCTGGATAGCCACGTTCGGACAGGATAACCGCTGAAAGCATCTAAGCGGGAAACCTTCTCCAAGATCAGGTTTCTCACCCTTTTAGAGGGATAAGGCCCCCCGCAGACCACGGGTTCGATAGGCTAGACCTGGAAGCTCAGCAATGAGTGCAGGGAACTGGCACTAACCGGCCGAAAACTTAC","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41317","NCBI_taxonomy_name":"Mycobacterium intracellulare","NCBI_taxonomy_id":"1767"}}}},"ARO_accession":"3004167","ARO_id":"41316","ARO_name":"Mycobacterium intracellulare 23S rRNA with mutation conferring resistance to azithromycin","CARD_short_name":"Mint_23S_AZM","ARO_description":"Point mutation in the 23S rRNA of Mycobaccterium avium shown to confer resistance to azithromycin, a macrolide type antibiotic.","ARO_category":{"41251":{"category_aro_accession":"3004125","category_aro_cvterm_id":"41251","category_aro_name":"23S rRNA with mutation conferring resistance to macrolide antibiotics","category_aro_description":"Nucleotide point mutations in the 23S rRNA subunit may confer resistance to macrolide antibiotics.","category_aro_class_name":"AMR Gene Family"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2815":{"model_id":"2815","model_name":"Mycobacterium kansasii 23S rRNA with mutation conferring resistance to clarithromycin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"41093","param_value":"5700"},"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"8171":"a2265t"},"Curated-R":{"8171":"a2265t"},"clinical":{"8171":"a2265t"}}},"model_sequences":{"sequence":{"4178":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"NZ_CP019883.1","fmin":"5018387","fmax":"5021505","strand":"+","sequence":"TTGTAAGTGTCTAAGGGCGCATGGTGGATGCCTTGGCATCGAGAGCCGATGAAGGACGTGGGAGGCTGCGATAAGCCTCGGGGAGCTGTCAACCGAGCGTGGATCCGAGGATTTCCGAATGGGGAAACCCAGCACGAGTGATGTCGTGTTACCCGCATCTGAATATATAGGGTGCGGGAGGGAACGCGGGGAAGTGAAACATCTCAGTACCCGTAGGAGAAGAAAACAAAAGTGATTCCGTAAGTAGTGGCGAGCGAACGCGGAACATGGCTAAACCGCACGCATGGGTAACCGGGTAGGGGTTGTGTGTGCGGGGTTGTGGGATCGATACGTCTCAGCTCTACCCGGCTGAGGGGCAGTCAGAAAGTGTCGTGGTTAACGGAAGTGGCCTGGGATGGTCTGCCGTAGACGGTGAGAGCCCGGTACGTGAAAACCCGGCACCTGCCTTGTATCAATTCCCGAGTAGCAGCGGGCCCGTGGAATCTGCTGTGAATCTGCCGGGACCACCCGGTAAGCCTAAATACTCCTCGATGACCGATAGCGGAATAGTACCGTGAGGGAATGGTGAAAAGTACCCCGGGAGGGGAGTGAAAGAGTACCTGAAACCGTGTGCCTACAATCCGTCAGAGCCCTTTCGTGGGGTGATGGCGTGCCTTTTGAAGAATGAGCCTGCGAGTCAGGGACATGTCGCGAGGTTAACCCGTGCGGGGTAGCCGCAGCGAAAGCGAGTCTGAATAGGGCGTATCGCGCGCGAGCGTGTGTAGTGGCGTGTTCTGGACCCGAAGCGGAGTGATCTACCCATGGCCAGGGTGAAGCGCGGGTAAGACCGCGTGGAGGCCCGAACCCACTTAGGTTGAAGACTGAGGGGATGAGCTGTGGGTAGGGGTGAAAGGCCAATCAAACTCCGTGATAGCTGGTTCTCCCCGAAATGCATTTAGGTGCAGCGTTGCGTGTTTCACCACGGAGGTAGAGCTACTGGATGGCCGATGGGCCCCACTAGGTTACTGACGTCAGCCAAACTCCGAATGCCGTGGTGTATAGCGTGGCAGTGAGACGGCGGGGGATAAGCTCCGTACGTCGAAAGGGAAACAGCCCAGATCGCCGGCTAAGGCCCCAAAGCGTGTGCTAAGTGGGAAAGGATGTGCAGTCGCAGAGACAACCAGGAGGTTGGCTTAGAAGCAGCCACCCTTGAAAGAGTGCGTAATAGCTCACTGGTCAAGTGATTGTGCGCCGATAATGTAGCGGGGCTCAAGCACACCGCCGAAGCCGCGACAACCGCAAGGTTGGGTAGGGGAGCGTCCCTCATTCAGCGAAGCTGCCGGGTGACCGGTGGTGGAGGATGGGGGAGTGAGAATGCAGGCATGAGTAGCGATAAGGCAAGTGAGAACCTTGCCCGCCGAAAGACCAAGGGTTCCTGGGCCAGGCCAGTCCGCCCAGGGTGAGTCGGGACCTAAGGCGAGGCCGACAGGCGTAGTCGATGGACAACGGGTTGATATTCCCGTACCCGTGTGTGGGCGCCCGTGATGAATCAGCGGTACTAACCACCCAAAACCGGATCGATCACTCCCCTTCGGGGGCGTGGAGGTCTGGGGCTGCGTGGAGCCTTCGCTGGTAGTAGTCAAGCGATGGGGTGACGCAGGAAGGCAGCCGTACCAGTCAGTGGTAATACTGGGGCAAGCCAGTAGGGAGAGCGATAGGCAAATCCGTCGCTCACAAATCCTGAGAGGTGACGCATAGCCGATTGAGGCGAATTCGGTGATCCTCTGCTGCCAAGAAAAGCCTCTAGCGAGCACACACACGGCCCGTACCCCAAACCGACACAGGTGGTCAGGTAGAGAATACCAAGGCGTACGAGATAACTATGGTTAAGGAACTCGGCAAAATGCCCCCGTAACTTCGGGAGAAGGGGGACCGGAATACCGTGAACACCCTTGCGGTGGGAGCGGGATTCGGTCGCAGAAACCAGTGAGAAGCGACTGTTTACTAAAAACACAGGTCCGTGCGAAGTCGCAAGACGATGTATACGGACTGACGCCTGCCCGGTGCTGGAAGGTTAAGAGGACCCGTTAACCCGCAAGGGTGAAGCGGAGAATTTAAGCCCCAGTAAACGGCGGTGGTAACTATAACCATCCTAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCTGCACGAATGGCGTAACGACTTCTCAACTGTCTCAACCATAGACTCGGCGAAATTGCACTACGAGTAAAGATGCTCGTTACGCGCGGCAGGACGAAAAGACCCCGGGACCTTCACTACAACTTGGTATTGGTGTTCGGTACGGTTTGTGTAGGATAGGTGGGAGACTGTGAAACCTCAACGCCAGTTGGGGTGGAGTCGTTGTTGAAATACCACTCTGATCGTATTGGACACCTAACGTCGAACCCTGAATCGGGTTCACGGACAGTGCCTGGCGGGTAGTTTAACTGGGGCGGTTGCCTCCTAAAATGTAACGGAGGCGCCCAAAGGTTCCCTCAACCTGGACGGCAATCAGGTGGCGAGTGTAAGTGCACAAGGGAGCTTGACTGCGAGACCTACAAGTCAAGCAGGGACGAAAGTCGGGACTAGTGATCCGGCACCTCTGAGTGGAAGGGGTGTCGCTCAACGGATAAAAGGTACCCCGGGGATAACAGGCTGATCTTCCCCAAGAGTCCATATCGACGGGATGGTTTGGCACCTCGATGTCGGCTCGTCGCATCCTGGGGCTGGAGCAGGTCCCAAGGGTTGGGCTGTTCGCCCATTAAAGCGGCACGCGAGCTGGGTTTAGAACGTCGTGAGACAGTTCGGTCTCTATCCGCCGCGCGCGTCAGAAGCTTGAGGAAACCTGTCCCTAGTACGAGAGGACCGGGACGGACGAACCTCTAGTGCACCAGTTGTCCCACCAGGGGCACCGCTGGATAGCTACGTTCGGACAGGATAACCGCTGAAAGCATCTAAGCGGGAAACCTTCTCCAAGATCAGGCTTCTCACCCACTTGGTGGGATAAGGCCCCCCGCAGAACACGGGTTCGATAGGCCAGACCTGGAAGCTCAGTAATGAGTGAAGGGAACTGGCACTAACCGGCCGAAAACTTACCAACACAAATAATCG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41347","NCBI_taxonomy_name":"Mycobacterium kansasii","NCBI_taxonomy_id":"1768"}}}},"ARO_accession":"3004168","ARO_id":"41318","ARO_name":"Mycobacterium kansasii 23S rRNA with mutation conferring resistance to clarithromycin","CARD_short_name":"Mkan_23S_CLR","ARO_description":"Point mutation in the 23S rRNA of Mycobacterium kansasii shown to confer resistance to clarithromycin, a macrolide type antibiotic.","ARO_category":{"41251":{"category_aro_accession":"3004125","category_aro_cvterm_id":"41251","category_aro_name":"23S rRNA with mutation conferring resistance to macrolide antibiotics","category_aro_description":"Nucleotide point mutations in the 23S rRNA subunit may confer resistance to macrolide antibiotics.","category_aro_class_name":"AMR Gene Family"},"35982":{"category_aro_accession":"0000065","category_aro_cvterm_id":"35982","category_aro_name":"clarithromycin","category_aro_description":"Clarithromycin is a methyl derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome and is used to treat pharyngitis, tonsillitis, acute maxillary sinusitis, acute bacterial exacerbation of chronic bronchitis, pneumonia (especially atypical pneumonias associated with Chlamydia pneumoniae or TWAR), and skin structure infections.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4258":{"model_id":"4258","model_name":"ADC-193","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6633":{"protein_sequence":{"accession":"WP_013197184.1","sequence":"MRFNKISCLLLSPLFIFNTSIYAGNTPKEQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYETYYGLQSVQDKKVVNSSTIFELGSVSKLFTATAGGYAKTKGTISFKDTPGKYWKELKNTPIDQVNLLQLATYTSGNLGLQFPDEVKTDQQVLTFFKDWKPKNSIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPDLGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFVNANLNPQKYPADIQRAINETHKGFYQVGTMYQALGWEEFSYPAPLQTLLDSNSEQIVMKPNKVTAISKEPSVKMFHKTGSTNGFGTCVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_064716.1","fmin":"100","fmax":"1252","strand":"+","sequence":"ATGCGATTTAACAAAATTTCTTGCTTACTTTTATCCCCTCTTTTTATTTTTAATACCTCAATTTATGCAGGGAATACACCAAAAGAGCAAGAAATTAAGAAACTGGTTGATCAAAATTTTAAACCGTTATTAGAAAAATATGATGTACCCGGTATGGCGGTTGGCGTCATCCAAAATAATAAAAAGTATGAAACATATTATGGTCTACAATCCGTTCAAGATAAAAAAGTCGTAAATAGCAGTACCATTTTTGAGCTCGGTTCAGTCAGTAAATTATTTACCGCTACAGCAGGTGGATATGCCAAAACAAAAGGAACAATTTCTTTTAAAGACACACCCGGAAAATATTGGAAAGAATTAAAAAACACACCGATTGACCAAGTTAATTTACTTCAACTTGCGACCTATACAAGTGGCAACCTTGGCTTACAGTTTCCAGATGAAGTCAAAACAGATCAGCAAGTTTTAACTTTTTTCAAAGACTGGAAGCCTAAAAACTCAATCGGTGAATATCGACAATATTCAAATCCAAGCATTGGTTTATTTGGAAAAGTTGTTGCTTTGTCTATGAATAAACCTTTTGACCAAGTCTTAGAAAAAACCATTTTTCCAGATCTTGGCTTAAAACATAGCTATGTAAATGTGCCTAAAACTCAAATGCAAAACTATGCATTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCGCTAGATGCACCTGCATACGGCGTTAAATCGACCTTACCGGATATGCTGAGTTTCGTTAATGCCAATCTAAATCCACAGAAATATCCGGCAGATATTCAACGCGCAATTAATGAAACACATAAAGGTTTCTACCAAGTAGGCACGATGTATCAAGCATTAGGTTGGGAAGAGTTCTCTTATCCAGCACCGTTACAGACTTTATTAGACAGTAATTCAGAACAAATCGTGATGAAGCCTAATAAAGTGACTGCTATTTCAAAAGAACCTTCAGTTAAGATGTTCCACAAAACTGGTTCAACCAACGGTTTTGGAACCTGTGTTGTGTTTATTCCAAAAGAAAATATTGGTTTAGTTATGTTAACCAATAAACGTATTCCGAATGAAGAACGCATTAAAGCAGCGTATGCAGTATTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3006362","ARO_id":"44824","ARO_name":"ADC-193","CARD_short_name":"ADC-193","ARO_description":"ADC-193 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2793":{"model_id":"2793","model_name":"Chlamydomonas reinhardtii 23S rRNA with mutation conferring resistance to erythromycin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"41093","param_value":"2000"},"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"7818":"g1627a"},"Curated-R":{"7818":"g1627a","7817":"g1627a"},"clinical":{"7818":"g1627a"}},"48039":{"param_type":"synonymous substitution for alternative promoter","param_description":"A synonymous or silent substitution in the coding DNA sequence of one gene which influences the promoter region of another gene. These substitutions do not change the amino acid sequence of a protein but may still influence the phenotype, including decreased susceptibility to antimicrobial compounds.","param_type_id":"48039","param_value":{"7817":"g1628g"}}},"model_sequences":{"sequence":{"4139":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"NC_005353.1","fmin":"148590","fmax":"151993","strand":"-","sequence":"AAGGTCAAAATCAAACGGCCTTTAGTATATCTCGGCTAAAGCCATTGCTGACTGTACACCTGATACCTATATAACGGCTTGTCTAGCCGCGGCCTTAGAGAGCACTCATCTTGAGTTTAGCTTCCTACTTAGATGCTTTCAGCAGTTATCTATCCATGCGTAGCTACCCAGCGTTTCCCATTGGAATGAGAACTGGTACACAATTGGCATGTCCTTTCAGGTCCTCTCGTACTATGAAAGGCTACTCTCAATGCTCTAACGCCTACACCGGATATGGACCAAACTGTCTCACGCATGAAATTTTAAAGCCGAATAAAACTTGCGGTCTTTAAAACTAACCCCTTTACTTTCGTAAAGGCATGGACTATGTCTTCATCCTGCTACTGTTAATGGCAGGAGTCGGCGTATTATACTTTCCCACTCTCGAGAAAATATCCTATAAATCGAGCAACAATAAATAAATTGTATGTAAACATTCTTTTAGAGATTGGCTAAATTTATAAAGTCTCTACGGGGACGATTTCTTTTTTTCACTTAAACTGTCTAGCACAGCACGAACGGTTTCAGAAGTTGTTTTACGCGTCTTCGAATCATTCAGAGCTGCAATTTGATCCACCCATGTACAAACTTCTAAGAATTTGTCCGGGGATTCTTTTGCTGACGGAAGCCGCCAAATAATTTTTAAAACTAAATTTGCTTGTTTTTGTTTTAGTTTTAGAAAAGGTTGTAGTTGTGTTAAAAAATTATGCAAAGGCTTGATTTCGCTTAGAATATAATCCGAAACGCTACCCCTATCTCTTACATAACCAACCCCAATTTCATCCACTAATTTGTCTAAAAACCAACGTCTCTGTGTCTTTTGCGTGACTTGGAACGCGAGTGATAGCTGATGCTTAAATTTATAAGACTGATTAGGCTTAATTTGAGCGATTATGCTACCGTCACCGTCTACAAACCCTGCTAAGTAGAGTAAGAACTCTTTATTATATTTTGTATTCATAAGATGTTTTATTTAATTTATTGAATTATTAAACCAAAAAGAAATGGTCTTCCCTCGGCGTTGCCATCTATTGCCCACGAATGTGGTTTATGCGACAGTTTGTACTTAAAACAATAGGAAGGTTTCACCGATATAAGCCGATACTTTGCTTACATTACTGCAAGCACACGCAGTGTTATTTACGTTTTGAACCCAGCTCACGTACCACTTTAATGGGCGAACAGCCCAACCCTTCGGACCTACTACAGACCGAGGATGTGATGAGCCGACATCGAGGTGCCAAACCTTCCCGTCGATGTGAACTCTTGGGGAAGATCAGCCTGTTATCCCTAGAGTAACTTTTATCCGTTGAGCGACGGCCCTTCCACGCGGCACCGTCGGATCACTAAGGCCGGCTTTCGCCCCTGCTCGACTTGTAGGTCTTGCAGTCAAGCTCCCTTTTGCCTTTACACTCAATGTCTGATTTCCGTCCAGACTGAGGGAACCTTTGCACGCCTCCGTTACCTTTTAGGAGGCATTCGCCCCAAATAAACTGCCCACCTGAAACTGTCAAGGGTCCTGATTCAAGGATCCCCATTAGGATTCTAGCTCTTCCAGAGTGGTCTCTCAATGACGGCTCTAATTACCCCGGAAGGTAATCTTCATAGCCTCCCACCTAGGCTGCGCAAGAAAAGCCCAAACCCAATTCCAAGATACAGTCAAGCTTCATAGGGTCTTTCTGTCCAGGTGTAGGTAGTCCGCATCTTCACGGGACAAGTCTATTTCACCGAGCCTCTCTCCGAGACAGCGCCCAGATCGTTACGCCTTTCGTGCAGGTCGAAACTTACTCGACAATGAATTTCGCTACCTTAGGATCGTTATAGTTACGACCGCCGTTCACCGGGGCTTCGGTCGTCAGCTTTTTTCTTACGAAATAACCAACTTCCTTAACCTTCCGGCACTGGGCAGGCGTCAGCCCCCATATATTGTCTTACGACTTTGCGGAGACCTGTGTTTTTGGTAAACAGTCGCCTGGGCCTGGTCACTGCGACCCACCTTGTTACGGATGGGTGCCCCTTCTTCCGAAGTTACGGGGCCAGTTTGCCGAGTTCCTTAGAGAGAGTTCTCTCGCGCCCCTTGGTATTCTCTACCAACCTACCTGTGTCGGTTTCAGGTACAGGTCATTAAATTATAAAGATGTATGAGCTTTTCTTGGAAGTATGACATCACTAGCTACTCGACGGCGAACCATCAAATAGGGATCACGTCTCCACTCAAGATAGCTTTTTTTCTATCTCTCAACGTCTAAACGCTTCCACTGCAATCCAAAAACAGTTCTAGCTTAGCCTCCTTCGTCCCTCAGATCATAATTTAACTCGTACAGGAATATTAACCTGTTTTCCATCGACGACGCCGTTTGGCCTAGTCTTAGGTCCTGACTAACCCCCCATGGACGAACCTAGTGGAGGAACCCTTAGGTTTTCGGGGCATTGGATTCTCACCAATGTTTTCGTTACTCAAGCCGACATTCTCACTTCCGCTTCGTCCATCCCCACTTACGTGAAAACTTCACCCGAGAGCGGAACGCTCCCCTACCTATAATTTATATAATAAATTATATCACAGCTTCGGCAGGTCACTTAGTCCCGGCCATTATCGGCGCAAGAACGCTTTACCAGTGAGCTATTACGCACTCTTTGAAGGGTGGCTGCTTCTAAGCAAACCTCCTGGTTGTTTCAGCATTCTCACATCCTTTTCCACTTAGTGACCATTTAGGGGCCTTAGCTGGTGATCTGGGCTGTTTCCCTCTTGACAATGAAGCTTATCCCCCACTGTCTCACTGGTTTACGGAAGACATGTCTTGTATTCTGAGTTTGCCACGACTTGGTACCGCTTTCGCAGCCCGCATCGAAACAGTAGCTTTACCCCAAGACAGTTCATCGTTACCGCTGCGCCTCAACGCATTTCGGGGAGATCCAGCTAGCTCCGAGTTCGATTGGAATTTCTCCCCTATTCACAGCTCATCCGCCGATTTTTCAACATCGGTCGGTTCGGACCTCCACTTGGTGTTACCCAAGCTTCATCCTGGCCATGAATAGATCACCCGGGTTCGGGTCCATAAGAAGTGACCATTTGCGCCCTATTCAGACTCGCTTTCGCTTGGGCTCCGGATTTTACTCCTTAACCCAGCCACTCCCTATAAGTCGCCGGCTCATTCTTCAACAGGCACGCGGTCACAAGCATTCTTGCTCCCACTGCTTGTCAGCATACGGTTTCATGTTCTATTTCACTCCCCAACAGGGGTTCTTTTCACCTTTCCCTCGTGGTACTATTTCGCTATCGGTCACTCAGGAGTATTTAGCCTTACGAGGTGGTCCTCGCTGATTCACACGGGATTTCACGTGCCCCATGCTACTCGGGATT","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40815","NCBI_taxonomy_name":"Chlamydomonas reinhardtii","NCBI_taxonomy_id":"3055"}}}},"ARO_accession":"3004132","ARO_id":"41259","ARO_name":"Chlamydomonas reinhardtii 23S rRNA with mutation conferring resistance to erythromycin","CARD_short_name":"Crei_23S_ERY","ARO_description":"Point mutation in 23S rRNA of C. reinhardtii chloroplast shown clinically to confer resistance to Erythromycin, a macrolide antibiotic.","ARO_category":{"41251":{"category_aro_accession":"3004125","category_aro_cvterm_id":"41251","category_aro_name":"23S rRNA with mutation conferring resistance to macrolide antibiotics","category_aro_description":"Nucleotide point mutations in the 23S rRNA subunit may confer resistance to macrolide antibiotics.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2802":{"model_id":"2802","model_name":"Escherichia coli 23S rRNA with mutation conferring resistance to erythromycin and telithromycin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"7848":"a2058g","7845":"t754a","7850":"c2611t","7847":"g2057a","7849":"a2058t"},"Curated-R":{"7848":"a2058g","7845":"t754a","7850":"c2611t","7847":"g2057a","7849":"a2058t"},"clinical":{"7848":"a2058g","7845":"t754a","7850":"c2611t","7847":"g2057a","7849":"a2058t"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"41093","param_value":"5000"}},"model_sequences":{"sequence":{"4149":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"AE014075.1","fmin":"237159","fmax":"240063","strand":"+","sequence":"GGTTAAGCGACTAAGCGTACACGGTGGATGCCCTGGCAGTCAGAGGCGATGAAGGACGTGCTAATCTGCGATAAGCGTCGGTAAGGTGATATGAACCGTTATAACCGGCGATTTCCGAATGGGGAAACCCAGTGTGTTTCGACACACTATCATTAACTGAATCCATAGGTTAATGAGGCGAACCGGGGGAACTGAAACATCTAAGTACCCCGAGGAAAAGAAATCAACCGAGATTCCCCCAGTAGCGGCGAGCGAACGGGGAGGAGCCCAGAGCCTGAATCAGTGTGTGTGTTAGTGGAAGCGTCTGGAAAGGCGCGCGATACAGGGTGACAGCCCCGTACACAAAAATGCACATGCTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGGGGGACCATCCTCCAAGGCTAAATACTCCTGACTGACCGATAGTGAACCAGTACCGTGAGGGAAAGGCGAAAAGAACCCCGGCGAGGGGAGTGAAAAAGAACCTGAAACCGTGTACGTACAAGCAGTGGGAGCATGCTTAGGCGTGTGACTGCGTACCTTTTGTATAATGGGTCAGCGACTTATATTCTGTAGCAAGGTTAACCGAATAGGGGAGCCGAAGGGAAACCGAGTCTTAACTGGGCGTTAAGTTGCAGGGTATAGACCCGAAACCCGGTGATCTAGCCATGGGCAGGTTGAAGGTTGGGTAACACTAACTGGAGGACCGAACCGACTAATGTTGAAAAATTAGCGGATGACTTGTGGCTGGGGGTGAAAGGCCAATCAAACCGGGAGATAGCTGGTTCTCCCCGAAAGCTATTTAGGTAGCGCCTCGTGAACTCATCTCCGGGGGTAGAGCACTGTTTCGGCAAGGGGGTCATCCCGACTTACCAACCCGATGCAAACTGCGAATACCGGAGAATGTTATCACGGGAGACACACGGCGGGTGCTAACGTCCGTCGNGAAGAGGGAAACAACCCAGACCGCCAGCTAAGGTCCCAAAGTCATGGTTAAGTGGGAAACGATGTGGGAAGGCCCAGACAGCCAGGATGTTGGCTTAGAAGCAGCCATCATTTAAAGAAAGCGTAATAGCTCACTGGTCGAGTCGGCCTGCGCGGAAGATGTAACGGGGCTAAACCATGCACCGAAGCTGCGGCAGCGACGCTTATGCGTTGTTGGGTAGGGGAGCGTTCTGTAAGCCTGTGAAGGTGTACTGTGAGGTATGCTGGAGGTATCAGAAGTGCGAATGCTGACATAAGTAACGATAAAGCGGGTGAAAAGCCCGCTCGCCGGAAGACCAAGGGTTCCTGTCCAACGTTAATCGGGGCAGGGTGAGTCGACCCCTAAGGCGAGGCCGAAAGGCGTAGTCGATGGGAAACAGGTTAATATTCCTGTACTTGGTGTTACTGCGAAGGGGGGACGGAGAAGGCTATGTTGGCCGGGCGACGGTTGTCCCGGTTTAAGCGTGTAGGCTGGTTTTCCAGGCAAATCCGGAAAATCAAGGCTGAGGCGTGATGACGAGGCACTACGGTGCTGAAGCAACAAATGCCCTGCTTCCAGGAAAAGCCTCTAAGCATCAGGTAACATCAAATCGTACCCCAAACCGACACAGGTGGTCAGGTAGAGAATACCAAGGCGCTTGAGAGAACTCGGGTGAAGGAACTAGGCAAAATGGTGCCGTAACTTCGGGAGAAGGCACGCTGATATGTAGGTGAAGCGACTTGCTCGTGGAGCTGAAATCAGTCGAAGATACCAGCTGGCTGCAACTGTTTATTAAAAACACAGCACTGTGCAAACACGAAAGTGGACGTATACGGTGTGACGCCTGCCCGGTGCCGGAAGGTTAATTGATGGGGTTAGCGCAAGCGAAGCTCTTGATCGAAGCCCCGGTAAACGGCGGCCGTAACTATAACGGTCCTAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCTGCACGAATGGCGTAATGATGGCCAGGCTGTCTCCACCCGAGACTCAGTGAAATTGAACTCGCTGTGAAGATGCAGTGTACCCGCGGCAAGACGGAAAGACCCCGTGAACCTTTACTATAGCTTGACACTGAACATTGAGCCTTGATGTGTAGGATAGGTGGGAGGCTTTGAAGTGTGGACGCCAGTCTGCATGGAGCCGACCTTGAAATACCACCCTTTAATGTTTGATGTTCTAACGTTGACCCGTAATCCGGGTTGCGGACAGTGTCTGGTGGGTAGTTTGACTGGGGCGGTCTCCTCCTAAAGAGTAACGGAGGAGCACGAAGGTTGGCTAATCCTGGTCGGACATCAGGAGGTTAGTGCAATGGCATAAGCCAGCTTGACTGCGAGCGTGACGGCGCGAGCAGGTGCGAAAGCAGGTCATAGTGATCCGGTGGTTCTGAATGGAAGGGCCATCGCTCAACGGATAAAAGGTACTCCGGGGATAACAGGCTGATACCGCCCAAGAGTTCATATCGACGGCGGTGTTTGGCACCTCGATGTCGGCTCATCACATCCTGGGGCTGAAGTAGGTCCCAAGGGTATGGCTGTTCGCCATTTAAAGTGGTACGCGAGCTGGGTTTAGAACGTCGTGAGACAGTTCGGTCCCTATCTGCCGTGGGCGCTGGAGAACTGAGGGGGGCTGCTCCTAGTACGAGAGGACCGGAGTGGACGCATCACTGGTGTTCGGGTTGTCATGCCAATGGCACTGCCCGGTAGCTAAATGCGGAAGAGATAAGTGCTGAAAGCATCTAAGCACGAAACTTGCCCCGAGATGAGTTCTCCCTGACTCCTTGAGGGTCCTGAAGGAACGTTGAAGACGACGACGTTGATAGGCCGGGTGTGTAAGCGCAGCGATGCGTTGAGCTAACCGGTACTAATGAACCGTGAGGCTTAACCTT","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36763","NCBI_taxonomy_name":"Escherichia coli CFT073","NCBI_taxonomy_id":"199310"}}}},"ARO_accession":"3004131","ARO_id":"41258","ARO_name":"Escherichia coli 23S rRNA with mutation conferring resistance to erythromycin and telithromycin","CARD_short_name":"Ecol_23S_MULT","ARO_description":"Point mutation in the 23S rRNA of Escherichia coli shown clinically to confer resistance to the macrolide-class antibiotics erythromycin and telithromycin.","ARO_category":{"41251":{"category_aro_accession":"3004125","category_aro_cvterm_id":"41251","category_aro_name":"23S rRNA with mutation conferring resistance to macrolide antibiotics","category_aro_description":"Nucleotide point mutations in the 23S rRNA subunit may confer resistance to macrolide antibiotics.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35974":{"category_aro_accession":"0000057","category_aro_cvterm_id":"35974","category_aro_name":"telithromycin","category_aro_description":"Telithromycin is a semi-synthetic derivative of erythromycin. It is a 14-membered macrolide and is the first ketolide antibiotic to be used in clinics. Telithromycin binds the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2810":{"model_id":"2810","model_name":"Mycobacteroides abscessus 23S rRNA with mutation conferring resistance to clarithromycin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"7910":"a2271g","7911":"a2272g","7912":"a2272c","8349":"a2058c","8350":"a2058g","8351":"a2058t","8353":"a2059g","8352":"a2059c"},"Curated-R":{"7910":"a2271g","7911":"a2272g","7912":"a2272c","8349":"a2058c","8350":"a2058g","8351":"a2058t","8353":"a2059g","8352":"a2059c"},"clinical":{"7910":"a2271g","7911":"a2272g","7912":"a2272c","8349":"a2058c","8350":"a2058g","8351":"a2058t","8353":"a2059g","8352":"a2059c"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"41093","param_value":"5700"}},"model_sequences":{"sequence":{"4156":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"NC_010397.1","fmin":"1464207","fmax":"1467319","strand":"+","sequence":"CTAAGTTCTTAAGGGCGCATGGTGAATGCCTTGGCACTAGAAGCCGAAGAAGGACGTAGGAGGCTGCGATAAGCCTCGGGGAGCTGCCAACCGAGCTTTGATCCGAGGATCTCCGAATGGGGAAACCCAGCACGAGTGATGTCGTGTTACCCACTGCTGAATATATAGGCTTTGGGAGGAAACGCGGGGAAGTGAAACATCTCAGTACCCGTAGGAAGAGAAAACAACCGTGATTCCGTGAGTAGTGGCGAGCGAAAGCGGAAGATGGCTAAACCGCATGCATGTGATACCTGGTAGGGGTTGTGTGTGCGGGGTTGTGGGAGTTGTACTTGCCGGTTCTACCAGGCCGGCGGACAGTAAAAAAGTGTCGTGATTAGCGGAAGTGGTCTGGGACGGCCCGCCGCAGACGGTGAGAGTCCGGTACGCGAAAATCCGACACCTGTCTCGTACTTCATCCCGAGTAGCAGCGGGCTCGTGGAATCTGCTGTGAATCTGCCGGGACCACCCGGTAAGCCTAAATACTCTCTAGTGACCGATAGCGGATTAGTACCGTGAGGGAATGGTGAAAAGTACCCCGGGAGGGGAGTGAAATAGTACCTGAAACCATGTGCCTACAATCCGTCAAAGCCTCCTCGTGGGGTGATGGCGTGCCTTTTGAAGAATGAGCCTGCGAGTCAGGGACACGTCGCGAGGTTAACCCGTGTGGGGTAGCCGTAGCGAAAGCGAGTCTGAATAGGGCGCCCATAGTGGCGTGTTCTGGACCCGAAGCGGAGTGATCTACCCATGGCCAGGGTGAAGCGGCGGTAAGACGCCGTGGAGGCCCGAACCCACTTAGGTTGAAGACTGAGGGGATGAGCTGTGGGTAGGGGTGAAAGGCCAATCAAACTCCGTGATAGCTGGTTCTCCCCGAAATGCATTTAGGTGCAGCGTCGCGTGTTTCTTGTTGGAGGTAGAGCTACTGGATGGCCGATGGGCCCTACTAGGTTACTGACGTCAGCCAAACTCCGAATGCCAATAAGTTAGAGCGCGGCAGTGAGACGGCGGGGGAGAAGCTCCGTACGTCGAGAGGGAAACAGCCCAGATCGCCGGCTAAGGCCCCTAAGCGTGTACTAAGTGGAAAAGGATGTGCAGTCGCGAAGACAACCAGGAGGTTGGCTTAGAAGCAGCCACCCTTGAAAGAGTGCGTAATAGCTCACTGGTCAAGTGATTGTGCGCCGACAATGTAGCGGGGCTCAAGTACACCGCCGAAGCCGCGGCATTCATGCAATACATTCCCTTCGGGGCAGTGGCATGGATGGGTAGGGGAGCGTCCTGCACCCAGCGAAGCTGCGAAGTAATTCAGCAGTGGAGGGTGCGGGAGTGAGAATGCAGGCATGAGTAGCGACAGGCAAGTGAGAAACTTGCCCGCCGAATGACCAAGGGTTCCTGGGCCAGGCTAGTCCTCCCAGGGTAAGTCGGGACCTAAGGCGAGGCCGACAGGCGTAGTCGATGGACAACGGGTTGATATTCCCGTACCCGTGTGTGCGCGCCCATGATGAATCATCGGTACTAACCACCCAAAAGGTTCTAGATCAATCTCTTCGGAGTGCGACGTGAACCCGCTGCGTGGGACCTTCGGTGGTAGTAGTCAAGCGATGGGGTGACGCAGGAAGGTAGCTGTACCGGTTAGTGGTTATACCGGAGCAAGCCCGTAGGACGACATCTAGGCAAATCCGGATGTCATACGTCTGAGAGGTGACGCATAGCCGATTGAGGCGAATTCAGTGATCCTATGCTGCCAAGAAAAGCCTCTAGTGAGTTCACACACGGCCCGTACCCCAAACCAACACAGGTGGTCAGGTAGAGAATACTAAGGCGTACGAGATAACTATGGTTAAGGAACTCGGCAAAATACCCCCGTAACTTCGGGAGAAGGGGGACCTCGCTTGGTGACCGGACTTGCTCCGTGAGCTGAACGAGGTCGCAGAGACCAGTGAGAAGCGACTGTTTACTAAAAACACAGGTCCGTGCGAAGTCGCAAGACGATGTATACGGACTGACGCCTGCCCGGTGCTGGAAGGTTAAGAGGACCCGTTAACCCTTGGGTGAAGCGGAGAATTTAAGCCCCAGTAAACGGCGGTGGTAACTATAACCATCCTAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCTGCACGAATGGCGTAACGACTTCTCAACTGTCTCAACCATAGACTCGGCGAAATTGCACTACGAGTAAAGATGCTCGTTACGCGCGGCAGGACGAAAAGACCCCGGGACCTTCACTATAGCTTGGTATTGGCGTTTGGTTCGGTTTGTGTAGGATAGGTGGGAGACTGTGAAGCAGGCACGCCAGTGTTTGTGGAGTCATCGTTGAAATACCACTCTGATCGTATTGAACCTCTAACCTCGGACCGTATATCCGGTCCAGGGACAGTGCCTGGTGGGTAGTTTAACTGGGGCGGTTGCCTCCCAAAATGTAACGGAGGCGCCCAAAGGTTCCCTCAACCTGGACGGCAATCAGGTGTTGAGTGCAAGTGCACAAGGGAGCTTGACTGCGAGACCTACAAGTCAAGCAGGGACGAAAGTCGGGACTAGTGATCCGGCACCTCTGAGTGGAAGGGGTGTCGCTCAACGGATAAAAGGTACCCCGGGGATAACAGGCTGATCTTCCCCAAGAGTCCATATCGACGGGATGGTTTGGCACCTCGATGTCGGCTCGTCGCATCCTGGGGCTGGAGCAGGTCCCAAGGGTTGGGCTGTTCGCCCATTAAAGCGGCACGCGAGCTGGGTTTAGAACGTCGTGAGACAGTTCGGTCTCTATCCGCCGCGCGCGTCAGAAACTTGAGGAAACCTGTCCCTAGTACGAGAGGACCGGGACGGACGAACCTCTGGTGTACCAGTTGTTCCACCAGGAGCACGGCTGGATAGCTACGTTCGGACAGGATAACCGCTGAAAGCATCTAAGCGGGAAACCTATTCCAAGACCAGGTTTCTTACCCTTTTAGAGGGATAAGGTCACCCACAGACTATGGGTTCAATAGGCCAGACCTGCAAGCGTAGTAATACGTTCAGGGAACTGGCACTAATCGACCGAAAACTTACTAAT","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36888","NCBI_taxonomy_name":"Mycobacteroides abscessus","NCBI_taxonomy_id":"36809"}}}},"ARO_accession":"3004163","ARO_id":"41311","ARO_name":"Mycobacteroides abscessus 23S rRNA with mutation conferring resistance to clarithromycin","CARD_short_name":"Mabs_23S_CLR","ARO_description":"Point mutation in the 23S rRNA of Mycobacteroides abscessus shown to confer resistance to clarithromycin, a macrolide type antibiotic.","ARO_category":{"41251":{"category_aro_accession":"3004125","category_aro_cvterm_id":"41251","category_aro_name":"23S rRNA with mutation conferring resistance to macrolide antibiotics","category_aro_description":"Nucleotide point mutations in the 23S rRNA subunit may confer resistance to macrolide antibiotics.","category_aro_class_name":"AMR Gene Family"},"35982":{"category_aro_accession":"0000065","category_aro_cvterm_id":"35982","category_aro_name":"clarithromycin","category_aro_description":"Clarithromycin is a methyl derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome and is used to treat pharyngitis, tonsillitis, acute maxillary sinusitis, acute bacterial exacerbation of chronic bronchitis, pneumonia (especially atypical pneumonias associated with Chlamydia pneumoniae or TWAR), and skin structure infections.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2817":{"model_id":"2817","model_name":"Streptococcus pneumoniae 23S rRNA with mutation conferring resistance to macrolide antibiotics","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"8175":"a2125g","8177":"c2641a","8178":"c2641g","8176":"a2126g"},"Curated-R":{"8175":"a2125g","8177":"c2641a","8178":"c2641g","8176":"a2126g"},"clinical":{"8175":"a2125g","8177":"c2641a","8178":"c2641g","8176":"a2126g"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"41093","param_value":"5000"}},"model_sequences":{"sequence":{"5408":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"NZ_CP018138.1","fmin":"1692408","fmax":"1695312","strand":"-","sequence":"AGGTTAAGTTAATAAGGGCGCACGGTGGATGCCTTGGCACTAGGAGCCGACGAAGGACGTGACAAACGACGATATACCTTGGGTAGCTGTAAGTAAGCGATGATCCAGGGATTTCCGAATGGGGGAACCCAACAGGTAATACCTGTTACCCACATCTGTTAAGGATGTGAGGAGGAAGACGCAGTGAACTGAAACATCTAAGTAGCTGCAGGAAGAGAAAGCAAAAGCGATTGCCTTAGTAGCGGCGAGCGAAACGGCAGAAGGGCAAACCGAAGAGTTTACTCTTCGGGGTTGTAGGACTGCAATGTGGACTCAAAGATTATAGAAGAATGATTTGGGAAGATCAGCCAAAGAGAGTAATAGCCTCGTATTTAAAATAGTCTTTGTACCTAGCAGTATCCTGAGTACGGCGGGACACGTGAAATCCCGTCGGAATCTGGGAGGACCATCTCCCAACCCTAAATACTCCCTAGTGACCGATAGTGAACCAGTACCGTGAGGGAAAGGTGAAAAGCACCCCGGGAGGGGAGTGAAATAGAACCTGAAACCGTGTGCCTACAACAAGTTCGAGCCCGTTAATGGGTGAGAGCGTGCCTTTTGTAGAATGAACCGGCGAGTTACGTTATGATGCGAGGTTAAGTTGAAGAGACGGAGCCGTAGGGAAACCGAGTCTGAACAGGGCGAATTAGTATCATGACGTAGACCCGAAACCATGTGACCTACCCATGAGCAGGTTGAAGGTGCGGTAAGACGCACTGGAGGACCGAACCAGGGCACGTTGAAAAGTGCTTGGATGACTTGTGGGTAGCGGAGAAATTCCAAACGAACTTGGAGATAGCTGGTTCTCTCCGAAATAGCTTTAGGGCTAGCGTCGACATTAGAGATTCTTGGAGGTAGAGCACTGTTTGGGTGAGGGGTCCATCCCGGATTACCAATCTCAGATAAACTCCGAATGCCAATGAATTATGGTCGGCAGTCAGACTGCGAGTGCTAAGATCCGTAGTCGAAAGGGAAACAGCCCAGACCACCAGCTAAGGTCCCAAAATAATTGTTAAGTGGAAAAGGATGTGGGGTTGCACAGACAACTAGGATGTTAGCTTAGAAGCAGCTATTCATTCAAAGAGTGCGTAATAGCTCACTAGTCGAGTGACCCTGCGCCGAAAATGTACCGGGGCTAAAACAATTTACCGAAGCTGTGGATACCTTTATAGGTATGGTAGGAGAGCGTTCTATGTGTGATGAAGGTATACCGTGAGGAGTGCTGGAACGCATAGAAGTGAGAATGCCGGTATGAGTAGCGAAAGACAGGTGAGAATCCTGTCCACCGTAAGACTAAGGTTTCCAGGGGAAGGCTCGTCCGCCCTGGGTTAGTCGGGACCTAAGGAGAGACCGAAAGGTGTATCCGATGGACAACAGGTTGATATTCCTGTACTAGAGTATGTAGTGATGGAGGGACGCAGTAGGCTAACTAAAGCAGACGATTGGAAGAGTCTGTCTAAGCAGTGAGGTGTGAATTGAGTCAAATGCTTAATTCTATAACATTGAGCTGTGATGGGGAGCGAAGTTTAGTAGCGAAGTTAGTGACGTCACACTGCCAAGAAAAGCTTCTAGCGTTTAAACATACTCTACCCGTACCGCAAACCGACACAGGTAGTCGAGGCGAGTAGCCTCAGGTGAGCGAGAGAACTCTCGTTAAGGAACTCGGCAAAATGACCCCGTAACTTCGGGAGAAGGGGTGCTGACTTTAGGTCAGCCGCAGTGAATAGGCCCAAGCAACTGTTTATCAAAAACACAGCTCTCTGCTAAATCGTAAGATGATGTATAGGGGGTGACGCCTGCCCGGTGCTGGAAGGTTAAGAGGAGTGCTTAGCGTAAGCGAAGGTATGAATTGAAGCCCCAGTAAACGGCGGCCGTAACTATAACGGTCCTAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCCGCACGAAAGGCGTAATGATTTGGGCACTGTCTCAACGAGAGACTCGGTGAAATTTTAGTACCTGTGAAGATGCAGGTTACCCGCGACAGGACGGAAAGACCCCATGGAGCTTTACTGCAGTTTGATATTGAGTGTCTGTACCACATGTACAGGATAGGTAGGAGTCTAAGAGATCGGGACGCCAGTTTCGAAGGAGACGCTGTTGGGATACTACCCTTGTGTTATGGCCACTCTAACCCAGATAGGTGATCCCTATCGGAGACAGTGTCTGACGGGCAGTTTGACTGGGGCGGTCGCCTCCTAAAAGGTAACGGAGGCGCCCAAAGGTTCCCTCAGAATGGTTGGAAATCATTCGCAGAGTATAAAGGTATAAGGGAGCTTGACTGCGAGAGCTACAACTCGAGCAGGGACGAAAGTCGGGCTTAGTGATCCGGTGGTTCCGTATGGAAGGGCCATCGCTCAACGGATAAAAGCTACCCTGGGGATAACAGGCTTATCTCCCCCAAGAGTTCACATCGACGGGGAGGTTTGGCACCTCGATGTCGGCTCGTCGCATCCTGGGGCTGTAGTCGGTCCCAAGGGTTGGGCTGTTCGCCCATTAAAGCGGCACGCGAGCTGGGTTCAGAACGTCGTGAGACAGTTCGGTCCCTATCCGTCGCGGGCGTAGGAAATTTGAGAGGATCTGCTCCTAGTACGAGAGGACCAGAGTGGACTTACCGCTGGTGTACCAGTTGTCTTGCCAAAGGCATCGCTGGGTAGCTATGTAGGGAAGGGATAAACGCTGAAAGCATCTAAGTGTGAAACCCACCTCAAGATGAGATTTCCCATGATTATATATCAGTAAGAGCCCTGAGAGATGATCAGGTAGATAGGTTAGAAGTGGAAGTGTGGCGACACATGTAGCGGACTAATACTAATAGCTCGAGGACTTATCCAAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35917","NCBI_taxonomy_name":"Streptococcus pneumoniae","NCBI_taxonomy_id":"1313"}}}},"ARO_accession":"3004170","ARO_id":"41320","ARO_name":"Streptococcus pneumoniae 23S rRNA with mutation conferring resistance to macrolide antibiotics","CARD_short_name":"Spne_23S_MAC","ARO_description":"Point mutation in the 23S rRNA of Streptococcus pneumoniae shown to confer resistance to macrolide type antibiotics.","ARO_category":{"41251":{"category_aro_accession":"3004125","category_aro_cvterm_id":"41251","category_aro_name":"23S rRNA with mutation conferring resistance to macrolide antibiotics","category_aro_description":"Nucleotide point mutations in the 23S rRNA subunit may confer resistance to macrolide antibiotics.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"36295":{"category_aro_accession":"3000156","category_aro_cvterm_id":"36295","category_aro_name":"spiramycin","category_aro_description":"Spiramycin is a 16-membered macrolide and is natural product produced by Streptomyces ambofaciens. It binds to the 50S subunit of bacterial ribosomes and inhibits peptidyl transfer activity to disrupt protein synthesis.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2819":{"model_id":"2819","model_name":"Escherichia coli 23S rRNA with mutation conferring resistance to oxazolidinone antibiotics","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"7932":"g2032a","7934":"g2032c","7935":"g2447t","7933":"g2032t"},"Curated-R":{"7932":"g2032a","7934":"g2032c","7935":"g2447t","7933":"g2032t"},"clinical":{"7932":"g2032a","7934":"g2032c","7935":"g2447t","7933":"g2032t"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"41093","param_value":"5000"}},"model_sequences":{"sequence":{"4164":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"AE014075.1","fmin":"237159","fmax":"240063","strand":"+","sequence":"GGTTAAGCGACTAAGCGTACACGGTGGATGCCCTGGCAGTCAGAGGCGATGAAGGACGTGCTAATCTGCGATAAGCGTCGGTAAGGTGATATGAACCGTTATAACCGGCGATTTCCGAATGGGGAAACCCAGTGTGTTTCGACACACTATCATTAACTGAATCCATAGGTTAATGAGGCGAACCGGGGGAACTGAAACATCTAAGTACCCCGAGGAAAAGAAATCAACCGAGATTCCCCCAGTAGCGGCGAGCGAACGGGGAGGAGCCCAGAGCCTGAATCAGTGTGTGTGTTAGTGGAAGCGTCTGGAAAGGCGCGCGATACAGGGTGACAGCCCCGTACACAAAAATGCACATGCTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGGGGGACCATCCTCCAAGGCTAAATACTCCTGACTGACCGATAGTGAACCAGTACCGTGAGGGAAAGGCGAAAAGAACCCCGGCGAGGGGAGTGAAAAAGAACCTGAAACCGTGTACGTACAAGCAGTGGGAGCATGCTTAGGCGTGTGACTGCGTACCTTTTGTATAATGGGTCAGCGACTTATATTCTGTAGCAAGGTTAACCGAATAGGGGAGCCGAAGGGAAACCGAGTCTTAACTGGGCGTTAAGTTGCAGGGTATAGACCCGAAACCCGGTGATCTAGCCATGGGCAGGTTGAAGGTTGGGTAACACTAACTGGAGGACCGAACCGACTAATGTTGAAAAATTAGCGGATGACTTGTGGCTGGGGGTGAAAGGCCAATCAAACCGGGAGATAGCTGGTTCTCCCCGAAAGCTATTTAGGTAGCGCCTCGTGAACTCATCTCCGGGGGTAGAGCACTGTTTCGGCAAGGGGGTCATCCCGACTTACCAACCCGATGCAAACTGCGAATACCGGAGAATGTTATCACGGGAGACACACGGCGGGTGCTAACGTCCGTCGNGAAGAGGGAAACAACCCAGACCGCCAGCTAAGGTCCCAAAGTCATGGTTAAGTGGGAAACGATGTGGGAAGGCCCAGACAGCCAGGATGTTGGCTTAGAAGCAGCCATCATTTAAAGAAAGCGTAATAGCTCACTGGTCGAGTCGGCCTGCGCGGAAGATGTAACGGGGCTAAACCATGCACCGAAGCTGCGGCAGCGACGCTTATGCGTTGTTGGGTAGGGGAGCGTTCTGTAAGCCTGTGAAGGTGTACTGTGAGGTATGCTGGAGGTATCAGAAGTGCGAATGCTGACATAAGTAACGATAAAGCGGGTGAAAAGCCCGCTCGCCGGAAGACCAAGGGTTCCTGTCCAACGTTAATCGGGGCAGGGTGAGTCGACCCCTAAGGCGAGGCCGAAAGGCGTAGTCGATGGGAAACAGGTTAATATTCCTGTACTTGGTGTTACTGCGAAGGGGGGACGGAGAAGGCTATGTTGGCCGGGCGACGGTTGTCCCGGTTTAAGCGTGTAGGCTGGTTTTCCAGGCAAATCCGGAAAATCAAGGCTGAGGCGTGATGACGAGGCACTACGGTGCTGAAGCAACAAATGCCCTGCTTCCAGGAAAAGCCTCTAAGCATCAGGTAACATCAAATCGTACCCCAAACCGACACAGGTGGTCAGGTAGAGAATACCAAGGCGCTTGAGAGAACTCGGGTGAAGGAACTAGGCAAAATGGTGCCGTAACTTCGGGAGAAGGCACGCTGATATGTAGGTGAAGCGACTTGCTCGTGGAGCTGAAATCAGTCGAAGATACCAGCTGGCTGCAACTGTTTATTAAAAACACAGCACTGTGCAAACACGAAAGTGGACGTATACGGTGTGACGCCTGCCCGGTGCCGGAAGGTTAATTGATGGGGTTAGCGCAAGCGAAGCTCTTGATCGAAGCCCCGGTAAACGGCGGCCGTAACTATAACGGTCCTAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCTGCACGAATGGCGTAATGATGGCCAGGCTGTCTCCACCCGAGACTCAGTGAAATTGAACTCGCTGTGAAGATGCAGTGTACCCGCGGCAAGACGGAAAGACCCCGTGAACCTTTACTATAGCTTGACACTGAACATTGAGCCTTGATGTGTAGGATAGGTGGGAGGCTTTGAAGTGTGGACGCCAGTCTGCATGGAGCCGACCTTGAAATACCACCCTTTAATGTTTGATGTTCTAACGTTGACCCGTAATCCGGGTTGCGGACAGTGTCTGGTGGGTAGTTTGACTGGGGCGGTCTCCTCCTAAAGAGTAACGGAGGAGCACGAAGGTTGGCTAATCCTGGTCGGACATCAGGAGGTTAGTGCAATGGCATAAGCCAGCTTGACTGCGAGCGTGACGGCGCGAGCAGGTGCGAAAGCAGGTCATAGTGATCCGGTGGTTCTGAATGGAAGGGCCATCGCTCAACGGATAAAAGGTACTCCGGGGATAACAGGCTGATACCGCCCAAGAGTTCATATCGACGGCGGTGTTTGGCACCTCGATGTCGGCTCATCACATCCTGGGGCTGAAGTAGGTCCCAAGGGTATGGCTGTTCGCCATTTAAAGTGGTACGCGAGCTGGGTTTAGAACGTCGTGAGACAGTTCGGTCCCTATCTGCCGTGGGCGCTGGAGAACTGAGGGGGGCTGCTCCTAGTACGAGAGGACCGGAGTGGACGCATCACTGGTGTTCGGGTTGTCATGCCAATGGCACTGCCCGGTAGCTAAATGCGGAAGAGATAAGTGCTGAAAGCATCTAAGCACGAAACTTGCCCCGAGATGAGTTCTCCCTGACTCCTTGAGGGTCCTGAAGGAACGTTGAAGACGACGACGTTGATAGGCCGGGTGTGTAAGCGCAGCGATGCGTTGAGCTAACCGGTACTAATGAACCGTGAGGCTTAACCTT","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36763","NCBI_taxonomy_name":"Escherichia coli CFT073","NCBI_taxonomy_id":"199310"}}}},"ARO_accession":"3004173","ARO_id":"41324","ARO_name":"Escherichia coli 23S rRNA with mutation conferring resistance to oxazolidinone antibiotics","CARD_short_name":"Ecol_23S_OXZ","ARO_description":"Point mutation in the 23S rRNA of Escherichia coli shown to confer resistance to oxazolidinone type antibiotics.","ARO_category":{"41323":{"category_aro_accession":"3004172","category_aro_cvterm_id":"41323","category_aro_name":"23S rRNA with mutation conferring resistance to oxazolidinone antibiotics","category_aro_description":"Point mutations in the 23S rRNA subunit may confer resistance to oxazolidinone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35989":{"category_aro_accession":"0000072","category_aro_cvterm_id":"35989","category_aro_name":"linezolid","category_aro_description":"Linezolid is a synthetic antibiotic used for the treatment of serious infections caused by Gram-positive bacteria that are resistant to several other antibiotics. It inhibits protein synthesis by binding to domain V of the 23S rRNA of the 50S subunit of bacterial ribosomes.","category_aro_class_name":"Antibiotic"},"36218":{"category_aro_accession":"3000079","category_aro_cvterm_id":"36218","category_aro_name":"oxazolidinone antibiotic","category_aro_description":"Oxazolidinones are a class of synthetic antibiotics discovered the the 1980's.  They inhibit protein synthesis by binding to domain V of the 23S rRNA of the 50S subunit of bacterial ribosomes.  Linezolid is the only member of this class currently in clinical use.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2820":{"model_id":"2820","model_name":"Chlamydia trachomatis 23S rRNA with mutation conferring resistance to macrolide antibiotics","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"8725":"c196a","9884":"a2107c","9885":"a2107g","9886":"a2109g","9887":"t2663c","7939":"a2663c"},"Curated-R":{"8725":"c196a","9884":"a2107c","9885":"a2107g","9886":"a2109g","9887":"t2663c","7939":"a2663c"},"clinical":{"8725":"c196a","9884":"a2107c","9885":"a2107g","9886":"a2109g","9887":"t2663c","7939":"a2663c"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"41093","param_value":"5000"}},"model_sequences":{"sequence":{"4165":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"NR_076160.1","fmin":"0","fmax":"2940","strand":"+","sequence":"CAGACCAAGTTAATAAGAGCTATTGGTGGATGCCTTGGCATTGACAGGCGAAGAAGGACGCGAATACCTGCGAAAAGCTCCGGCGAGCTGGTGATAAGCAAAGACCCGGAGGTATCCGAATGGGGAAACCCGGTAGAGTAATAGACTACCATTGCATGCTGAATACATAGGTATGCAAAGCGACACCTGCCGAACTGAAACATCTTAGTAAGCAGAGGAAAAGAAATCGAAGAGATTCCCTGTGTAGCGGCGAGCGAAAGGGGAATAGCCTAAACCGAGCTGATAAGGCTCGGGGTTGTAGGATTGAGGATAAAGGATCAGGACTCCTAGTTGAACACATCTGGAAAGATGGATGATACAGGGTGATAGTCCCGTAGACGAAAGGAGAGAAAGACCGACCTCAACACCTGAGTAGGACTAGACACGTGAAACCTAGTCTGAATCTGGGGAGACCACTCTCCAAGGCTAAATACTAGTCAATGACCGATAGTGAACCAGTACTGTGAAGGAAAGGCGAAAAGAACCCTTGTTAAGGGAGTGAAATAGAACCTGAAACCAGTAGCTTACAAGCGGTCGGAGACCAATGGCCCGTAAGGGTCAAGGTTGACGGCGTGCCTTTTGCATGATGAGCCAGGGAGTTAAGCTAAACGGCGAGGTTAAGGGATATACATTCCGGAGCCGGAGCGAAAGCGAGTTTTAAAAGAGCGAAGAGTCGTTTGGTTTAGACACGAAACCAAGTGAGCTATTTATGACCAGGTTGAAGCATGGGTAAAACTATGTGGAGGACCGAACTAGTACCTGTTGAAAAAGGTTTGGATGAGTTGTGAATAGGGGTGAAAGGCCAATCAAACTTGGAGATATCTTGTTCTCTCCGAAATAACTTTAGGGTTAGCCTCGGATAATAAGCTTTTGGGGGTAGAGCACTGAATTCTAGCGGGGGCCTACCGGCTTACCAACGGAAATCAAACTCCGAATACCAGAAGCGAGTCCGGGAGATAGACAGCGGGGGCTAAGCTTCGTTGTCGAGAGGGGAACAGCCCAGACCGCCGATTAAGGTCCCTAATTTTATGCTAAGTGGGTAAGGAAGTGATGATTCGAAGACAGTTGGAATGTTGGCTTAGAGGCAGCAATCATTTAAAGAGTGCGTAACAGCTCACCAATCGAGAATCATTGCGCCGATAATAAACGGGACTAAGCATAAAACCGACATCGCGGGTGTGTCGATAAGACACGCGGTAGGAGAGCGTAGTATTCAGCAGAGAAGGTGTACCGGAAGGAGCGCTGGAGCGGATACTAGTGAAGATCCATGGCATAAGTAACGATAAAGGGAGTGAAAATCTCCCTCGCCGTAAGCCCAAGGTTTCCAGGGTCAAGCTCGTCTTCCCTGGGTTAGTCGGCCCCTAAGTTGAGGCGTAACTGCGTAGACGATGGAGCAGCAGGTTAAATATTCCTGCACCACCTAAAACTATAGCGAAGGAATGACGGAGTAAGTTAAGCACGCGGACGATTGGAAGAGTCCGTAGAGCGATGAGAACGGTTAGTAGGCAAATCCGCTAACATAAGATCAGGTCGCGATCAAGGGGAATCTTCGGGGGAACCGATGGTGTGGAGCGAGGCTTTCAAGAAATAATTTCTAGCTGTTGATGGTGACCGTACCAAAACCGACACAGGTGGGCGAGATGAATATTCTAAGGCGCGCGAGATAACTTTCGTTAAGGAACTCGGCAAATTATCCCCGTAACTTCGGAATAAGGGGAGCCTTTTAGGGTGACTATGGAACGATAGGAGCCCCGGGGGGCCGCAGAGAAATGGCCCAGGCGACTGTTTAGCAAAAACACAGCACTATGCAAACCTCTAAGGGGAAGTATATGGTGTGACGCCTGCCCAATGCCAAAAGGTTAAAGGGATATGTCAGCTGCAAAGCGAAGCATTGAACCTAAGCCCTGGTGAATGGCCGCCGTAACTATAACGGTGCTAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCTGCACGAATGGTGTAACGATCTGGGCACTGTCTCAACGAAAGACTCGGTGAAATTGTAGTAGCAGTGAAGATGCTGTTTACCCGCGAAAGGACGAAAAGACCCCGTGAACCTTTACTGTACTTTGGTATTGATTTTTGGTTTGTTATGTGTAGGATAGCCAGGAGACTAAGAACACTCTTCTTCAGGAGAGTGGGAGTCAACGTTGAAATACTGGTCTTAACAAGCTGGGAATCTAACATTATTCCATGAATCTGGAAGATGGACATTGCCAGACGGGCAGTTTTACTGGGGCGGTATCCTCCTAAAAAGTAACGGAGGAGCCCAAAGCTTATTTCATCGTGGTTGGCAATCACGAGTAGAGCGTAAAGGTATAAGATAGGTTGACTGCAAGACCAACAAGTCGAGCAGAGACGAAAGTCGGGCTTAGTGATCCGGCGGTGGAAAGTGGAATCGCCGTCGCTTAACGGATAAAAGGTACTCCGGGGATAACAGGCTGATCGCCACCAAGAGTTCATATCGACGTGGCGGTTTGGCACCTCGATGTCGGCTCATCGCATCCTGGGGCTGGAGAAGGTCCCAAGGGTTTGGCTGTTCGCCAATTAAAGCGGTACGCGAGCTGGGTTCAAAACGTCGTGAGACAGTTTGGTCTCTATCCTTCGTGGGCGCAGGATACTTGAGAGGAGCTGTTCCTAGTACGAGAGGACCGGAATGGACGAACCAATGGTGTGTCGGTTGTTTTGCCAAGGGCATAGCCGGGTGGCTCACGTTCGGAAAGGATAAGCATTGAAAGCATCTAAATGCCAAGCCTCCCTCAAGATAAGGTATCCCAATGAGACTCCATGTAGACTACGTGGTTGATAGGTTGGAGGTGTAAGCACAGTAATGTGTTCAGCTAACCAATACTAATAAGTCCAAAGACTTGGTCTT","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40470","NCBI_taxonomy_name":"Chlamydia trachomatis","NCBI_taxonomy_id":"813"}}}},"ARO_accession":"3004174","ARO_id":"41325","ARO_name":"Chlamydia trachomatis 23S rRNA with mutation conferring resistance to macrolide antibiotics","CARD_short_name":"Ctra_23S_MAC","ARO_description":"Point mutation in the 23S rRNA of Chlamydia trachomatis shown to confer resistance to macrolide type antibiotics.","ARO_category":{"41251":{"category_aro_accession":"3004125","category_aro_cvterm_id":"41251","category_aro_name":"23S rRNA with mutation conferring resistance to macrolide antibiotics","category_aro_description":"Nucleotide point mutations in the 23S rRNA subunit may confer resistance to macrolide antibiotics.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"37620":{"category_aro_accession":"3001221","category_aro_cvterm_id":"37620","category_aro_name":"josamycin","category_aro_description":"A macrolide antibiotic from Streptomyces narbonensis\u00a0subsp.\u00a0josamyceticus. The drug has antimicrobial activity against a wide spectrum of pathogens.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3412":{"model_id":"3412","model_name":"OXA-126","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"566"}},"model_sequences":{"sequence":{"5607":{"protein_sequence":{"accession":"ABX45065.1","sequence":"MNIKALLLITSAIFISACSPYIVTTNPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNTDIGTQVDNFWLMGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"EU255295.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTACTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATACAGATATCGGTACCCAAGTCGATAATTTTTGGCTGATGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001448","ARO_id":"37848","ARO_name":"OXA-126","CARD_short_name":"OXA-126","ARO_description":"OXA-126 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2824":{"model_id":"2824","model_name":"Mycoplasma pneumoniae 23S rRNA mutation conferring resistance to erythromycin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"7945":"a2063g","7946":"a2064g"},"Curated-R":{"7945":"a2063g","7946":"a2064g"},"clinical":{"7945":"a2063g","7946":"a2064g"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"41093","param_value":"5000"}},"model_sequences":{"sequence":{"4169":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"NR_077056.1","fmin":"0","fmax":"2905","strand":"+","sequence":"CAATAAGTTACTAAGGGCTTATGGTGGATGCCTTGGCACTAATAGGCGATGAAGGACGTGTTAACCTGCGATAAGCTTCGGGTAGGTGGTAAGAACCTCAGATCCGGAGATTTCCGAATGGAGCAATCCGGTAGTTGGAAACAGCTATCATTAATTGATGAATAAATAGTCAATTAAAGCAATACGTGGTGAAGTGAAACATCTCAGTAGCCACAGGAAAAGAAAACGAATGTGATTCCGTGTGTAGTGGCGAGCGAAAGCGGAACAGGCCAAACTTATCATTAGATAGGGGTTGTAGGGCTTGCAATGTGGACTTGAAAACGATAGAAGAAGCTGTTGGAAAGCAGCGCGCAAAAGGGTGATAGCCCCGTATTTGAAATTGTTTTCATACCTAGCGAGATCCCTGAGTAGCTCGGAAAACGTTATTTTGAGTGAATCTGCCCAGACCATTGGGTAAGCCTAAATACTAATTAGTGACCGATAGCGAAACAGTACCGTGAGGGAAAGGTGAAAAGAACCCAGAGATGGGAGTGAAATAGATTCTGAAACCATATGCCTACAACGTGTCAGAGCACATTAATGTGTGATGGCGTGCGTTTTGAAGTATGAGCCGGCGAGTTATGATAGCAAGCGTTAGTTAACCAGGAGATGGGGAGCTGTAGCGAAAGCGAGTTTTAAAAGAGCGTTTGTTTGTTATTATAGACCCGAAACGGGTTGAGCTAGTCATGAGCAGGTTGAAGGTTGAGTAACATCAACTGGAGGACCGAACCGACTCTCGTTGAAACGATAGCGGATGACTTGTGATTAGGGGTGAAATTCCAATCGAAATCCGTGATAGCTGGTTCTCGTCGAAATAGCTTTAAGGCTAGCGTGAGATCACAAATAAGTGGAGGTAAAGCTACTGAATGTATGATGGCGCCACCTAGGCGTACTGAATACAATTAAACTCTGAATGCCATTTATTTTATTCTCGCAGTCAGACAGTGGGGGATAAGCTTCATTGTCAAGAGGGGAAGAGCCCAGATCATTAAATAAGGTCCCCAAAATATACTAAGTGGAAAAGGATGTGAAAGTGCTAAAACAGCAAGGATGTTGGCTTAGAAGCAGCCATCGTTTAAAGAGTGCGTAACAGCTCACTTGTCGAGTGTTTTTGCGCCGAAGATGTAACGGGGCTAAGTATATTACCGAATTTATGGATAAGATTTATATCTTGTGGTAGACGAGCGTTGTATTGGAGTTGAAGTCAAAGCGTGAGCATTGGTGGATCCAATACAAGTGAGAATGCCGGCATGAGTAACGCTTGGGAGTGAGAATCTCCCAAACCGATTGACTAAGGTTTCCTGGACCAGGGTCGTCCTTCCAGGGTTAGTCTGGACCTAAGCTGAGGCTGAAAAGCGTAGGCGATGGACAACAGGTTAATATTCCTGTACTTACAGTTAGACTGATGGAGTGACAAAGAAGGTTTTCCACCCCCATAATTGGATTTGGGGATAAATCATAAGGTGGTACAATAGGCAAATCCGTTGTGCATAACATTGAGTGATGATGTCGAGTGAATGAGTGATCAAGTAGCGAAGGTGGTATTAATCATGCTTTCAAGAAAAGCTTCTAGGGTTAATCTAGCTGTAACCAGTACCGAGAACGAACACACGTAGTCAAGGAGAGGATCCTAAGGTTAGCGAGTGAACTATAGCCAAGGAACTCTGCAAATTAACCCCGTAAGTTAGCGAGAAGGGGTGCTTATGTAAAAGTAAGCCGCAGTGAAGAACGAGGGGGGACTGTTTAACTAAAACACAACTCTATGCCAAACCGTAAGGTGATGTATATGGGGTGACACCTGCCCAGTGCTGGAAGGTTAAAGAAGGAGGTTAGCGCAAGCGAAGCTTTTAACTGAAGCCCCAGTGAACGGCGGCCGTAACTATAACGGTCCTAAGGTAGCGAAATTCCTAGTCGGGTAAATTCCGTCCCGCTTGAATGGTGTAACCATCTCTTGACTGTCTCGGCTATAGACTCGGTGAAATCCAGGTACGGGTGAAGACACCCGTTAGGCGCAACGGGACGGAAAGACCCCGTGAAGCTTTACTGTAGCTTAATATTGATCAGGACATTATCATGTAGAGAATAGGTAGGAGCAATCGATGCAAGTTCGCTAGGACTTGTTGATGCGAAAGGTGGAATACTACCCTTGGTTGTGTGCTGTTCTAATTGGTAACTGTTATCCAGTTTCAAGACAGTGTTAGGTGGGCAGTTTGACTGGGGCGGTCGCCTCCTAAAAGGTAACGGAGGCGTACAAAGGTACCTTCAGTACGGTTGGAAATCGTATGTAGAGTGTAATGGTGTAAGGGTGCTTGACTGTGAGACATACAGGTCGAACAGGTGAGAAATCAGGTCATAGTGATCCGGTGGTCCAGTATGGAATGGCCATCGCTCAACGGATAAAAGCTACTCCGGGGATAACAGGCTGATACTGCCCAAGAGTTCATATCGACGGCAGTGTTTGGCACCTCGATGTCGACTCATCTCATCCTCGAGCTGAAGCAGGTTCGAAGGGTTCGGCTGTTCGCCGATTAAAGAGATACGTGAGTTGGGTTCAAACCGTCGTGAGACAGGTTGGTCCCTATCTATTGTGCCCGTAGGAAGATTGAAGAGTGTTGCTTCTAGTACGAGAGGACCGAAGCGAGGACACCTCTTATGCTCCAGTTGTAGCGCCAGCTGCACCGCTGGGTAGTAACGTGTCTATTAGATAAACGCTGAAAGCATCTAAGTGTGAAACTATCTCAAAGATTAATCTTCCCATTTCGCAAGAAAGTAAGAGCCGTCAAAGACGATGACGTTGATAGGTTACAGGTGTAAGCATAGTGATATGTTGAGCTGAGTAATACTAATTGCTCGAGGACTTATTGGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41332","NCBI_taxonomy_name":"Mycoplasma pneumoniae","NCBI_taxonomy_id":"2104"}}}},"ARO_accession":"3004179","ARO_id":"41331","ARO_name":"Mycoplasma pneumoniae 23S rRNA mutation conferring resistance to erythromycin","CARD_short_name":"Mpne_23S_ERY","ARO_description":"Point mutation in the 23S rRNA of Mycoplasma pneumoniae shown to confer resistance to erythromycin.","ARO_category":{"41251":{"category_aro_accession":"3004125","category_aro_cvterm_id":"41251","category_aro_name":"23S rRNA with mutation conferring resistance to macrolide antibiotics","category_aro_description":"Nucleotide point mutations in the 23S rRNA subunit may confer resistance to macrolide antibiotics.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2825":{"model_id":"2825","model_name":"Halobacterium halobium 23S rRNA mutation conferring resistance to chloramphenicol","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"7947":"a2088c","7948":"c2471t"},"Curated-R":{"7947":"a2088c","7948":"c2471t"},"clinical":{"7947":"a2088c","7948":"c2471t"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"41093","param_value":"5300"}},"model_sequences":{"sequence":{"4170":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"X03407.1","fmin":"2910","fmax":"5815","strand":"+","sequence":"GTGGCTACTGTGCCACCTGGTGGATAGCTCGGCTCGGATGCCGACGAAGGACGTGCCAAGCTGCGATAAGCCTGAGGGAGCCGCACGGAGGCTAAGAACTCAGGATCTCCTAATGGGAATCCCTATAACAATTGCCTTGCGCAATGGGGAACGGCCGGAATTGAAGCATCTCAGTACGGCCAGGAAGAGAAATCGAATGAGACGCCGTTAGTAATGGCGAATGAACGCGGCACAGTCCAAACCGAAGCCTTCGGGCAATGTGGTGTTCGGACTGACTTTCATCGTTTGACCGTTCGTGTGAAGTCTCCTGAAACGGAGCGCGATACAGGGTGACAGCCCCGTATCACGGACCAGTACGACGTGCGTCAGCTCCAGAGTAGCGGGGGTTGGAAATCCCTCGTGAATTGTGGCAGGCATCGACTGCCAAGACTAAGTACTCTCCGAGACCGATAGTGAACAAGTAGTGTGAACGAACGCTGAAAAGCACCCCACAAAGGGGGGTGAAATAGGGCTTGAAATCAGGTGGCGATGGAGCGACGGGGCATAAAAGGCCTCTCTGGGAACGACTTGAGTGCAAACTCATGGTAGGACCTGAGAGGAGCCGATGTTCCGTCGTACGTTTTGAAAAACGAGCTAGGGAGTGTGCCTGTTTGACGAGTCTAACCGGAGTATCCGGGAAGGCGTAGGGAAACCAATATGGCCGCGGCATTGCGAGGGCCACCGTGTTCAAGCGCGGGGAGTCAAACGGGCACGACCCGAAACCCGGTGATCTACGCGTGGGCAAGGTGAAGCATGGCGAAAGCCATGTGGAGGCCTGTTAGGGTTGGTGTCTTTCAACACCCTCCCGTGACCTACGTGTAGGGGTGAAAGGCCCATCGAACCGGGCAACAGCTGGTTCCAACCGAAACATGTCGAAGCATGACCTCTGCCGAGGTAGTTCGTGGGGTAGAGCGACCGATTGGGGAGTTCAACTCCGAGAGGAGTTGTCTCCCCTGTCAAACTCCAAACCTACGGACGCCGTCGACGCAGGGAATCCGGTGTGCGGGGTAAGCCTGTGCACCGTGAGGGAGACAACCCAGAGTTAGGTTAAGGTCCCAAAGTGCGAGCTAAGTGCGATTGAAGGTGGTCTCGAGCCCTAGACAGCCGGGAGGTGAGCTTAGAAGCAGCTACCCTCTAAGAAAAGCGTAACAGCTTACCGGCCGAGGTTCGAGGCGCCCAAAATGATCGGGGCTTAAGTTCGCCACCGAGACCTAACGGCACGGGTAACACCGTGATCCAGTAGGTTGGCATTCTGTTCGGGTGGAAGCTCGGGTGAGAACTCGAGTGGACCGAGTGGAAAAGAAAATCCTGGCCATAGTAGCAGCGTTAGTCGGGTAAGAATCCCGATGGCCGAAAGAGCAAGGGTTCCTCGGCAATGCTTATCAGCCGAGGGTTAGCCGATCCTAAGGCCCGTCGTAATTCGAGCGGGTCAAAAGGGAAACTGGTTAATATTCCAGTGCCACCGTACATTGAAAGTCGACGCCTCGGAGCAGCTTGAGCCGGGCATTCGCCCGGTCGAACCGTCGAAGTTCGTGGAAGCCGTAATGGCAGGAAGCGAACGAACGTCGGAACAGGGAAACTCAAGTCAATCTGGGGCCCGTGAAAAGGCGAGTACGGTGTTCGTACCGAGATCCGACACAGGTGCTCTGGCAGAGGAAGCCAAGGCCTGTCGGGAATAACCGACGTTAGGGAATTCGGCAAGTTAGTCCCGTAAGTTCGCGATAAGGGATGCCTGCCACGCAATGAGGCAGGTCGCAGTGACTCGGAGGCTCCGACTGTCTAATAACAACATAGGTGACCGCAAATCCGCAAGGACGCGTACGGTCACTGAATCCTGCCCAGTGCGGGTATCTGAACACCCAGTACAATGGGGCGAAGGACCCGTTAACGGCGGGGGTAACTATGACCCTCTTAAGGTAGCGTAGTACCTTGCCGCTTCAGTAGCGGCTTGCATGAATGGATCAACGAGAGCCTCACTGTCCCAACGTTGGGCCCGGTGAACTGTACGTTCCAGTGCGGAGTCTGGAGACCCCCAAGGGGAAGCGAAGACCCTATAGAGCTTTACTGCAGGCTGTCGCTGGGACACGGTCGCTGATGTGCAGAGTAGGTAGGAGACGTTACACAGGTACGTGCGCTAGCACGCCACCGAGTCACACATGAAACACTACCCGTCAGTGACTGTGACCCTCACTCCGGGAGGAGGACACCGGTAGCCGGGCAGTTTGACTGGGGCGGTACGCGCTTGAAAAGATATCGAGCGCGCCCTAAGCCTATCTCAGCCGAGTCAGAGACTCGGCGAAGAGTGCAAGAGCATAAGATAGGCTGACAGTGTCCTACACAACGAGGGACGCTGACGCGAAAGCTGGTCTAGCGAACCAATTAGGCTGCTTGATGCGGCCAATTGCTGACAGAAAAGCTACCTTAGGGATAACAGAGTCGTCACTCGCAAGAGCACATATCGACCGAGTGGCTGCTACCTCGATGTCGGTTCCCTCCATCCTGCCCGTGCAGAAGCGGGCAAGGGTGAGGTTGTTCGCCTATTAAAGGAGGTCGTGAGCTGGGTTTAGACCGTCGTGAGACAGGTCGGCTGCTATCTATTGGGGGTGTTTTGGTGCTTGACAGGAACGTTCGTATAGTACGAGAGGAACTACGAACGGGTGCCACTGGTGTATCGGTTGTCCGAGAGGGCATGTGCCGAGCAGCTACGCACCACGGGGTAAGAGCTGAATGCATCTAAGCTCGAAACCCACCTGGAAAAGAAGCACCACTGAGACCGCTCGTAGAAGACGAGTTCGATAGACTTGGGGTGTACGCGTCGAGGCAACGAGACGTTTAGCCCGCGAGTACTAACAGGTCAATGCCACAC","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40807","NCBI_taxonomy_name":"Halobacterium salinarum","NCBI_taxonomy_id":"2242"}}}},"ARO_accession":"3004180","ARO_id":"41333","ARO_name":"Halobacterium halobium 23S rRNA mutation conferring resistance to chloramphenicol","CARD_short_name":"Hhal_23S_CHL","ARO_description":"Point mutation in the 23S rRNA of Halobacterium halobium shown to confer resistance to chloramphenicol.","ARO_category":{"41350":{"category_aro_accession":"3004188","category_aro_cvterm_id":"41350","category_aro_name":"23S rRNA with mutation conferring resistance to phenicol antibiotics","category_aro_description":"Point mutations in the 23S rRNA subunit shown clinically to confer resistance to phenicol class antibiotics, including chloramphenicol and florfenicol, by disrupting antibiotic binding-site affinity.","category_aro_class_name":"AMR Gene Family"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2826":{"model_id":"2826","model_name":"Streptococcus pneumoniae 23S rRNA mutation conferring resistance to macrolides and streptogramins antibiotics","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"7949":"a2129c"},"Curated-R":{"7949":"a2129c"},"clinical":{"7949":"a2129c"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"41093","param_value":"5000"}},"model_sequences":{"sequence":{"4171":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"NZ_CP018138.1","fmin":"1692408","fmax":"1695312","strand":"-","sequence":"TTTGGATAAGTCCTCGAGCTATTAGTATTAGTCCGCTACATGTGTCGCCACACTTCCACTTCTAACCTATCTACCTGATCATCTCTCAGGGCTCTTACTGATATATAATCATGGGAAATCTCATCTTGAGGTGGGTTTCACACTTAGATGCTTTCAGCGTTTATCCCTTCCCTACATAGCTACCCAGCGATGCCTTTGGCAAGACAACTGGTACACCAGCGGTAAGTCCACTCTGGTCCTCTCGTACTAGGAGCAGATCCTCTCAAATTTCCTACGCCCGCGACGGATAGGGACCGAACTGTCTCACGACGTTCTGAACCCAGCTCGCGTGCCGCTTTAATGGGCGAACAGCCCAACCCTTGGGACCGACTACAGCCCCAGGATGCGACGAGCCGACATCGAGGTGCCAAACCTCCCCGTCGATGTGAACTCTTGGGGGAGATAAGCCTGTTATCCCCAGGGTAGCTTTTATCCGTTGAGCGATGGCCCTTCCATACGGAACCACCGGATCACTAAGCCCGACTTTCGTCCCTGCTCGAGTTGTAGCTCTCGCAGTCAAGCTCCCTTATACCTTTATACTCTGCGAATGATTTCCAACCATTCTGAGGGAACCTTTGGGCGCCTCCGTTACCTTTTAGGAGGCGACCGCCCCAGTCAAACTGCCCGTCAGACACTGTCTCCGATAGGGATCACCTATCTGGGTTAGAGTGGCCATAACACAAGGGTAGTATCCCAACAGCGTCTCCTTCGAAACTGGCGTCCCGATCTCTTAGACTCCTACCTATCCTGTACATGTGGTACAGACACTCAATATCAAACTGCAGTAAAGCTCCATGGGGTCTTTCCGTCCTGTCGCGGGTAACCTGCATCTTCACAGGTACTAAAATTTCACCGAGTCTCTCGTTGAGACAGTGCCCAAATCATTACGCCTTTCGTGCGGGTCGGAACTTACCCGACAAGGAATTTCGCTACCTTAGGACCGTTATAGTTACGGCCGCCGTTTACTGGGGCTTCAATTCATACCTTCGCTTACGCTAAGCACTCCTCTTAACCTTCCAGCACCGGGCAGGCGTCACCCCCTATACATCATCTTACGATTTAGCAGAGAGCTGTGTTTTTGATAAACAGTTGCTTGGGCCTATTCACTGCGGCTGACCTAAAGTCAGCACCCCTTCTCCCGAAGTTACGGGGTCATTTTGCCGAGTTCCTTAACGAGAGTTCTCTCGCTCACCTGAGGCTACTCGCCTCGACTACCTGTGTCGGTTTGCGGTACGGGTAGAGTATGTTTAAACGCTAGAAGCTTTTCTTGGCAGTGTGACGTCACTAACTTCGCTACTAAACTTCGCTCCCCATCACAGCTCAATGTTATAGAATTAAGCATTTGACTCAATTCACACCTCACTGCTTAGACAGACTCTTCCAATCGTCTGCTTTAGTTAGCCTACTGCGTCCCTCCATCACTACATACTCTAGTACAGGAATATCAACCTGTTGTCCATCGGATACACCTTTCGGTCTCTCCTTAGGTCCCGACTAACCCAGGGCGGACGAGCCTTCCCCTGGAAACCTTAGTCTTACGGTGGACAGGATTCTCACCTGTCTTTCGCTACTCATACCGGCATTCTCACTTCTATGCGTTCCAGCACTCCTCACGGTATACCTTCATCACACATAGAACGCTCTCCTACCATACCTATAAAGGTATCCACAGCTTCGGTAAATTGTTTTAGCCCCGGTACATTTTCGGCGCAGGGTCACTCGACTAGTGAGCTATTACGCACTCTTTGAATGAATAGCTGCTTCTAAGCTAACATCCTAGTTGTCTGTGCAACCCCACATCCTTTTCCACTTAACAATTATTTTGGGACCTTAGCTGGTGGTCTGGGCTGTTTCCCTTTCGACTACGGATCTTAGCACTCGCAGTCTGACTGCCGACCATAATTCATTGGCATTCGGAGTTTATCTGAGATTGGTAATCCGGGATGGACCCCTCACCCAAACAGTGCTCTACCTCCAAGAATCTCTAATGTCGACGCTAGCCCTAAAGCTATTTCGGAGAGAACCAGCTATCTCCAAGTTCGTTTGGAATTTCTCCGCTACCCACAAGTCATCCAAGCACTTTTCAACGTGCCCTGGTTCGGTCCTCCAGTGCGTCTTACCGCACCTTCAACCTGCTCATGGGTAGGTCACATGGTTTCGGGTCTACGTCATGATACTAATTCGCCCTGTTCAGACTCGGTTTCCCTACGGCTCCGTCTCTTCAACTTAACCTCGCATCATAACGTAACTCGCCGGTTCATTCTACAAAAGGCACGCTCTCACCCATTAACGGGCTCGAACTTGTTGTAGGCACACGGTTTCAGGTTCTATTTCACTCCCCTCCCGGGGTGCTTTTCACCTTTCCCTCACGGTACTGGTTCACTATCGGTCACTAGGGAGTATTTAGGGTTGGGAGATGGTCCTCCCAGATTCCGACGGGATTTCACGTGTCCCGCCGTACTCAGGATACTGCTAGGTACAAAGACTATTTTAAATACGAGGCTATTACTCTCTTTGGCTGATCTTCCCAAATCATTCTTCTATAATCTTTGAGTCCACATTGCAGTCCTACAACCCCGAAGAGTAAACTCTTCGGTTTGCCCTTCTGCCGTTTCGCTCGCCGCTACTAAGGCAATCGCTTTTGCTTTCTCTTCCTGCAGCTACTTAGATGTTTCAGTTCACTGCGTCTTCCTCCTCACATCCTTAACAGATGTGGGTAACAGGTATTACCTGTTGGGTTCCCCCATTCGGAAATCCCTGGATCATCGCTTACTTACAGCTACCCAAGGTATATCGTCGTTTGTCACGTCCTTCGTCGGCTCCTAGTGCCAAGGCATCCACCGTGCGCCCTTATTAACTTAACCT","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35917","NCBI_taxonomy_name":"Streptococcus pneumoniae","NCBI_taxonomy_id":"1313"}}}},"ARO_accession":"3004181","ARO_id":"41334","ARO_name":"Streptococcus pneumoniae 23S rRNA mutation conferring resistance to macrolides and streptogramins antibiotics","CARD_short_name":"Spne_23S_MULT","ARO_description":"Point mutation in the 23S rRNA of Streptococcus pneumoniae shown to confer resistance to macrolides and streptogramins types of antibiotics.","ARO_category":{"41251":{"category_aro_accession":"3004125","category_aro_cvterm_id":"41251","category_aro_name":"23S rRNA with mutation conferring resistance to macrolide antibiotics","category_aro_description":"Nucleotide point mutations in the 23S rRNA subunit may confer resistance to macrolide antibiotics.","category_aro_class_name":"AMR Gene Family"},"41335":{"category_aro_accession":"3004182","category_aro_cvterm_id":"41335","category_aro_name":"23S rRNA with mutation conferring resistance to streptogramins antibiotics","category_aro_description":"Nucleotide point mutations in the 23S rRNA subunit may confer resistance to streptogramins antibiotics.","category_aro_class_name":"AMR Gene Family"},"36284":{"category_aro_accession":"3000145","category_aro_cvterm_id":"36284","category_aro_name":"tylosin","category_aro_description":"Tylosin is a 16-membered macrolide, naturally produced by Streptomyces fradiae. It interacts with the bacterial ribosome 50S subunit to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"36722":{"category_aro_accession":"3000583","category_aro_cvterm_id":"36722","category_aro_name":"pristinamycin IA","category_aro_description":"Pristinamycin IA is a type B streptogramin antibiotic produced by Streptomyces pristinaespiralis. It binds to the P site of the 50S subunit of the bacterial ribosome, preventing the extension of protein chains.","category_aro_class_name":"Antibiotic"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"virginiamycin M1","category_aro_description":"Virginiamycin M1 is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37620":{"category_aro_accession":"3001221","category_aro_cvterm_id":"37620","category_aro_name":"josamycin","category_aro_description":"A macrolide antibiotic from Streptomyces narbonensis\u00a0subsp.\u00a0josamyceticus. The drug has antimicrobial activity against a wide spectrum of pathogens.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35952":{"category_aro_accession":"0000034","category_aro_cvterm_id":"35952","category_aro_name":"streptogramin A antibiotic","category_aro_description":"Streptogramin A antibiotics are cyclic polyketide peptide hybrids that bind to the ribosomal peptidyl transfer centre. Structural variation arises from substituting a proline for its desaturated derivative and by its substitution for Ala or Cys. Used alone, streptogramin A antibiotics are bacteriostatic, but is bactericidal when used with streptogramin B antibiotics.","category_aro_class_name":"Drug Class"},"35967":{"category_aro_accession":"0000050","category_aro_cvterm_id":"35967","category_aro_name":"streptogramin B antibiotic","category_aro_description":"Streptogramin B antibiotics are are cyclic hepta- or hexa-depsipeptides.  Type B streptogramins block the peptide exit tunnel of the 50S bacterial ribosome. The general composition of group B streptogramins is 3-hydroxypicolinic acid-L-Thr-D-aminobutyric acid (or D-Ala)-L-Pro-L-Phe (or 4-N-,N-(dimethylamino)-L-Phe)-X-L-phenylglycine. Used alone, streptogramin B antibiotics are bacteriostatic, but is bactericidal when used with streptogramin A antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2827":{"model_id":"2827","model_name":"Mycobacterium tuberculosis ribD with mutation conferring resistance to para-aminosalicylic acid","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"41339":{"param_type":"nucleotide substitution in promoter region","param_description":"A nucleotide sequence change where, compared to a reference sequence, one nucleotide is replaced by one other nucleotide in the promoter region of a gene. These substitutions are indicated as upstream of the reference sequence transcription initiation site. Format is given by [-][position][wildtype][>][mutation], e.g. -11t>c or -15g>Var where Var represents any possible substitution.","param_type_id":"41339","param_value":{"8013":"-11g>a"}},"snp":{"Curated-R":{"8013":"a2129c","7951":"G8R"},"param_value":{"7951":"G8R"},"clinical":{"7951":"G8R"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"8796":{"protein_sequence":{"accession":"NP_217187.1","sequence":"MPDSGQLGAADTPLRLLSSVHYLTDGELPQLYDYPDDGTWLRANFISSLDGGATVDGTSGAMAGPGDRFVFNLLRELADVIVVGVGTVRIEGYSGVRMGVVQRQHRQARGQSEVPQLAIVTRSGRLDRDMAVFTRTEMAPLVLTTTAVADDTRQRLAGLAEVIACSGDDPGTVDEAVLVSQLAARGLRRILTEGGPTLLGTFVERDVLDELCLTIAPYVVGGLARRIVTGPGQVLTRMRCAHVLTDDSGYLYTRYVKT"},"dna_sequence":{"accession":"NC_000962.3","fmin":"2986838","fmax":"2987615","strand":"+","sequence":"ATGCCCGACTCTGGTCAGCTCGGAGCCGCTGACACCCCGCTAAGGCTGCTCAGCTCGGTGCATTACCTCACCGACGGCGAACTCCCCCAGCTTTACGACTATCCGGATGACGGCACCTGGTTGCGGGCGAACTTCATCAGCAGCTTGGACGGCGGCGCTACCGTCGATGGCACCAGCGGGGCGATGGCCGGGCCCGGCGACCGATTCGTCTTCAACCTGTTGCGTGAACTTGCCGACGTCATCGTGGTCGGCGTGGGCACCGTGCGCATTGAGGGCTACTCCGGCGTCCGGATGGGTGTCGTCCAGCGCCAGCACCGGCAGGCCCGAGGCCAAAGCGAAGTTCCGCAACTGGCAATCGTCACCAGGTCCGGTCGCCTTGACCGTGACATGGCGGTATTCACCCGGACCGAGATGGCACCGTTGGTGCTCACCACCACGGCGGTCGCCGATGACACGCGCCAGCGGCTCGCGGGCCTCGCCGAGGTGATCGCGTGCTCCGGCGACGATCCGGGCACGGTCGATGAGGCAGTGCTCGTGTCCCAGCTCGCGGCTCGCGGTCTGCGCCGGATCCTTACCGAAGGCGGGCCGACGTTGCTCGGGACATTCGTCGAGCGTGACGTGCTCGACGAGCTGTGTCTGACGATCGCCCCCTACGTCGTCGGCGGCCTGGCGCGCCGCATAGTGACGGGACCCGGGCAGGTGCTGACCCGGATGCGCTGTGCCCATGTCCTCACCGACGACTCCGGCTACCTGTACACCCGCTACGTCAAGACCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3004184","ARO_id":"41337","ARO_name":"Mycobacterium tuberculosis ribD with mutation conferring resistance to para-aminosalicylic acid","CARD_short_name":"Mtub_ribD_PAS","ARO_description":"ribD is a Mycobacterium tuberculosis riboflavin biosynthesis enzyme. Point mutations in ribD cause enzyme overexpression, which allows the C-terminal reductase domain to act as an alternative dihydrofolate reductase. Thus, mutations in ribD confer resistance to DHFR inhibitors such as para-aminosalicylic acid.","ARO_category":{"41336":{"category_aro_accession":"3004183","category_aro_cvterm_id":"41336","category_aro_name":"aminosalicylate resistant dihydrofolate reductase","category_aro_description":"Antibiotic target replacement dihydrofolate reductase enzymes or domains with catalytic activity that confer resistance to aminosalicylates, esp. p-aminosalicylic acid.","category_aro_class_name":"AMR Gene Family"},"40948":{"category_aro_accession":"3004019","category_aro_cvterm_id":"40948","category_aro_name":"para-aminosalicylic acid","category_aro_description":"Para-aminosalicylic acid (PAS) is an anti-tubercular antibiotic agent, often used in conjunction with Isoniazid for treatment of M. tuberculosis infections. PAS diminishes bacterial cell growth by limiting folic acid production.","category_aro_class_name":"Antibiotic"},"45741":{"category_aro_accession":"3007159","category_aro_cvterm_id":"45741","category_aro_name":"salicylic acid antibiotic","category_aro_description":"A group of antibiotics derived from salicylic acid.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2828":{"model_id":"2828","model_name":"mecD","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"4173":{"protein_sequence":{"accession":"AQX82857.1","sequence":"MKNIKVKILIVCSLCLISFFLYNLLKENEIDKIFSSIENRNVDEINENITFLSRNTFSKKQRYDRMNHIDNSLGIKKVNITDIKLLEEIVDTRKYSANMHYDSKFGKFTKKGYFEFEKNGESKRWELNWTPEVIIPGLTATNEVRVEELKSSRGEIVDRNGIPLAIDGEHYQVGIDPKNYNKKDSKQIAKLLNINESTLKNKLKQSWVKDGVFVPIKSYVELSDEIKNKIPEYGLSVNKIKGRTYPLKEASAHLLGYIGEINADELNDPKFKGYDSHSIVGKTGIEYMYDKELQNRDGLIVYITDDDGLTDSKEILVHKKPKNGKKIVLSIDSRVQNSIYNHLKDDNGSGTAMNPKTGELLALVSYPSFNPYDFMFGISNKKYQALLNDKKAPLLNKFQELTSPGSTQKLLTSIIGLNNGVINESKSYEINGKGWRKDGSWGGYKVTRFEVVNGRIDLEKAIAHSDNIFFARTTLEMGGKKFVRGMKDLGVGEETPSDYPVRTGQIANKINLERNLNNDILLADSGYGQGEILVNPIHILSIYSSLVNEGNMMAPKLNMEHKSKVWKKHITSQKNIDILTSSMRKVVTGTHKLDTERNYANFAGKTGTAELKMTQNEGLGTQIGWFVGYDQQNPNMMLAINVKNVEDKGMSSYNAQKFAQVMDDLYEHGARTYEPDSE"},"dna_sequence":{"accession":"KY013611.1","fmin":"15437","fmax":"17474","strand":"+","sequence":"ATGAAGAATATAAAAGTTAAAATATTAATAGTTTGTAGCCTATGTCTTATATCATTTTTCTTATATAATTTATTGAAAGAAAATGAAATTGATAAAATATTTTCTTCAATTGAAAATCGAAATGTAGATGAAATAAATGAGAATATTACTTTTTTATCAAGAAATACTTTTAGTAAAAAACAAAGATACGATAGAATGAATCATATTGATAATTCTCTAGGCATAAAAAAAGTAAATATAACTGATATAAAGTTATTAGAAGAAATTGTAGACACTCGAAAATATAGTGCTAATATGCACTATGATTCTAAATTCGGTAAATTCACAAAAAAAGGTTATTTTGAGTTTGAAAAAAATGGTGAGAGTAAACGTTGGGAATTGAACTGGACACCAGAGGTTATAATTCCAGGACTTACAGCAACTAATGAAGTACGAGTAGAAGAATTGAAATCAAGTAGAGGTGAAATTGTAGATAGAAATGGAATTCCTTTAGCGATAGATGGTGAACATTATCAGGTAGGAATTGATCCTAAAAATTATAATAAGAAGGATAGTAAACAAATAGCTAAGTTATTAAATATAAATGAGAGTACTTTAAAGAACAAATTAAAACAATCATGGGTTAAAGATGGAGTATTTGTTCCAATCAAATCATATGTAGAATTAAGTGATGAAATTAAAAATAAAATACCTGAATACGGATTATCTGTGAATAAAATAAAAGGTAGAACTTACCCATTAAAAGAAGCAAGTGCTCATTTGTTAGGTTATATTGGTGAAATAAATGCAGATGAGCTTAATGATCCAAAATTTAAAGGATATGATTCTCATTCAATTGTTGGTAAAACTGGTATTGAATATATGTACGATAAAGAATTACAAAACAGAGATGGTTTAATAGTATATATTACTGATGATGATGGTTTAACAGATTCAAAAGAAATATTAGTTCATAAGAAACCTAAAAATGGAAAAAAGATAGTTTTATCGATAGATAGTAGAGTTCAAAATAGTATTTACAATCATTTAAAAGATGATAATGGATCTGGTACTGCTATGAATCCCAAAACAGGAGAATTATTAGCTTTAGTAAGCTATCCATCATTTAATCCTTATGATTTTATGTTTGGTATTTCAAATAAAAAATATCAGGCCTTATTAAATGATAAAAAGGCTCCGCTTTTAAATAAATTTCAAGAATTAACTTCTCCAGGTTCTACTCAAAAATTGCTAACTTCTATAATAGGTTTAAATAATGGGGTTATAAATGAAAGCAAAAGTTATGAAATAAATGGTAAAGGATGGAGAAAAGATGGGAGCTGGGGAGGATATAAAGTAACAAGATTTGAAGTTGTCAATGGACGAATTGATTTAGAGAAAGCTATAGCACATTCAGACAATATCTTTTTTGCTAGAACAACCCTAGAAATGGGTGGGAAAAAATTTGTAAGGGGAATGAAGGATTTAGGTGTAGGAGAGGAAACGCCTTCTGATTACCCTGTTCGGACTGGCCAAATAGCGAATAAAATTAATCTAGAAAGAAATTTGAATAATGATATATTGTTAGCAGACTCAGGTTATGGACAAGGTGAAATATTGGTGAATCCAATTCATATTTTATCTATATATAGTTCATTAGTAAATGAAGGGAATATGATGGCACCTAAATTAAATATGGAACATAAAAGCAAAGTATGGAAAAAACATATTACATCACAAAAAAATATTGATATATTAACAAGTAGTATGAGAAAAGTTGTTACAGGCACTCATAAATTAGATACCGAAAGAAATTATGCTAACTTTGCTGGAAAAACTGGTACAGCAGAATTAAAAATGACTCAGAATGAAGGATTAGGTACACAAATTGGATGGTTTGTGGGTTATGATCAACAAAATCCAAATATGATGTTAGCTATAAATGTTAAAAATGTTGAAGACAAAGGTATGTCTAGCTATAATGCACAAAAATTTGCGCAAGTAATGGATGATTTATATGAACATGGAGCTAGGACTTATGAACCAGACTCAGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40025","NCBI_taxonomy_name":"Macrococcus caseolyticus","NCBI_taxonomy_id":"69966"}}}},"ARO_accession":"3004185","ARO_id":"41338","ARO_name":"mecD","CARD_short_name":"mecD","ARO_description":"mecD is a PBP2a variant identified on a genomic resistance island in Macrococcus caseolyticus. MecD confers resistance to methicillin and other beta-lactam antibiotics through the production of an alternative low-affinity PBP. First described by Schwendener et al. 2017 and identified from canine and bovine sources.","ARO_category":{"37589":{"category_aro_accession":"3001208","category_aro_cvterm_id":"37589","category_aro_name":"methicillin resistant PBP2","category_aro_description":"In methicillin sensitive S. aureus (MSSA), beta-lactams bind to native penicillin-binding proteins (PBPs) and disrupt synthesis of the cell membrane's peptidoglycan layer. In methicillin resistant S. aureus (MRSA), foreign PBP2a acquired by lateral gene transfer is able to perform peptidoglycan synthesis in the presence of beta-lactams.","category_aro_class_name":"AMR Gene Family"},"35934":{"category_aro_accession":"0000015","category_aro_cvterm_id":"35934","category_aro_name":"methicillin","category_aro_description":"Derived from penicillin to combat penicillin-resistance, methicillin is insensitive to beta-lactamases (also known as penicillinases) secreted by many penicillin-resistant bacteria. Methicillin is bactericidal, and acts by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"37":{"model_id":"37","model_name":"Escherichia coli mdfA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"561":{"protein_sequence":{"accession":"AFH35853.1","sequence":"MQNKLASGARLGRQALLFPLCLVLYEFSTYIGNDMRQPGMLENVEQYQAGIEWVPTSMNAYLAGGMFIQWLLGPLSDRIGRRPVMLAGVVWFIVTCLAILLAQNIEQFTLLRFLHGISLCFIGAVGYDAIQESFEEAVCIKITALMANVALIAPLLGPLVGASWIHVLPWEGMFVLFAALAAISFFGLQRAMPETATRIGEKLSLKELGRDYKLVLKNGRFVAGALALGFLSLPLLAWIAQSPIIIITGEQLSSYEYGLLQVPIFGALIAGNLLLARLTSRRTVRSLIIMGGWPIMIGLLVAAAATVISSHAYLWMTAGLSIYAFGIGLANAGLVRLTLFASVMSKGTVSAAMGMLQMLIFTVGIEISKHAWLNGGNGLFNLFNLVNGILLLSLMVIFLKDKQMGNSHEG"},"dna_sequence":{"accession":"JQ394987.1","fmin":"0","fmax":"1233","strand":"+","sequence":"ATGCAAAATAAATTAGCTTCCGGTGCCAGGCTTGGACGTCAGGCGTTACTTTTTCCTCTCTGTCTGGTGCTTTACGAATTTTCAACCTATATCGGCAACGATATGAGGCAACCCGGTATGTTGGAAAATGTGGAACAATATCAGGCGGGCATTGAGTGGGTTCCTACTTCGATGAACGCGTATCTGGCGGGCGGGATGTTTATACAATGGCTGCTGGGGCCGCTGTCGGATCGTATTGGTCGTCGTCCGGTGATGCTGGCGGGAGTGGTGTGGTTTATCGTCACATGTCTGGCAATATTGCTGGCGCAAAACATTGAACAATTCACCCTGTTGCGCTTCTTGCACGGCATAAGCCTCTGTTTCATTGGCGCTGTGGGATACGACGCAATTCAGGAATCCTTCGAAGAGGCGGTTTGTATCAAGATCACCGCGCTGATGGCGAACGTGGCGCTGATTGCTCCGCTACTTGGTCCGCTGGTGGGCGCGTCGTGGATCCATGTGCTGCCCTGGGAGGGGATGTTTGTTTTGTTTGCCGCATTGGCAGCGATCTCCTTTTTCGGTCTGCAACGGGCCATGCCTGAAACCGCCACGCGTATAGGCGAGAAACTGTCACTGAAAGAACTCGGTCGTGACTATAAGCTGGTGCTGAAGAACGGCCGCTTTGTGGCGGGGGCGCTGGCGCTGGGATTCCTTAGTCTGCCGTTGCTGGCGTGGATCGCCCAGTCGCCGATTATCATCATTACCGGCGAGCAGTTGAGCAGCTATGAATATGGCTTGCTGCAAGTGCCTATTTTCGGGGCGTTAATTGCGGGTAACTTGCTGTTAGCGCGTCTGACCTCGCGCCGCACCGTACGTTCGCTGATTATTATGGGCGGCTGGCCGATTATGATTGGTCTATTGGTCGCTGCTGCGGCAACGGTTATCTCATCGCACGCGTATTTATGGATGACTGCCGGGTTAAGTATTTATGCTTTCGGTATTGGTCTGGCGAATGCGGGACTGGTGCGATTAACCCTGTTTGCCAGCGTTATGAGTAAAGGTACGGTTTCTGCCGCGATGGGAATGCTGCAAATGCTGATCTTTACCGTTGGTATTGAAATCAGCAAACATGCCTGGCTGAACGGGGGCAACGGACTGTTTAATCTCTTCAACCTTGTCAACGGAATTTTGTTGCTGTCGCTGATGGTTATCTTTTTAAAAGATAAACAGATGGGAAATTCTCACGAAGGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001328","ARO_id":"37727","ARO_name":"Escherichia coli mdfA","CARD_short_name":"Ecol_mdfA","ARO_description":"Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr\/CmlA chloramphenicol exporter.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36595":{"category_aro_accession":"3000456","category_aro_cvterm_id":"36595","category_aro_name":"thiamphenicol","category_aro_description":"Derivative of Chloramphenicol. The nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3).","category_aro_class_name":"Antibiotic"},"40514":{"category_aro_accession":"3003823","category_aro_cvterm_id":"40514","category_aro_name":"benzalkonium chloride","category_aro_description":"Benzalkonium chloride is a type of cationic surfactant. It is an organic salt called a quaternary ammonium compound. It has three main categories of use: as a biocide, a cationic surfactant, and as a phase transfer agent.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"43746":{"category_aro_accession":"3005386","category_aro_cvterm_id":"43746","category_aro_name":"disinfecting agents and antiseptics","category_aro_description":"Disinfectants that can also interact with antimicrobial resistance mechanisms, e.g. molecule efflux, and thus are the targets of disinfectant resistance.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"328":{"model_id":"328","model_name":"Salmonella enterica cmlA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"8282":{"protein_sequence":{"accession":"CAD31707.1","sequence":"MDMYLPAVPFMPNALGTTASTIQLTLTTYLVMIGAGQLLFGPLSDRLGRRPVLLGGGLANVVASMGLALTSSAEVFLGLRILQACGASACLVSTFATVRDIYAGREESNVIYGILGSMLAMVPAVGPLLGALVDMWLGWRAIFAFLGLGMIAASAAAWRFWPETRVQRVAGLQWSQLLLPVKCLNFWLYTLCYAAGMGSFFVFFSIAPGLMMGRQGVSQLGFSLLFATVAIAMVFTARFMGRVIPKWGSPSVLRMGMGCLIAGAVLLAITEIWALQSVLGFIAPMWLVGIGVATAVSVAPNGALRGFDHVAGTVTAVYFCLGGVLLGSIGTLIISLLPRNTAWPVVVYCLTLATVVLGLSCVSRVKGSRGQGEHDVVALQSAGSTSNPNR"},"dna_sequence":{"accession":"AJ487033.2","fmin":"1685","fmax":"2858","strand":"+","sequence":"ATGGACATGTACTTGCCAGCAGTGCCGTTTATGCCAAACGCGCTTGGTACGACAGCGAGCACAATTCAGCTTACGCTGACAACGTACTTGGTCATGATTGGTGCCGGTCAGCTCTTGTTTGGACCGCTATCGGACCGACTGGGGCGCCGCCCCGTTCTACTGGGAGGTGGCCTCGCAAACGTTGTGGCGTCAATGGGCCTCGCTCTTACGTCATCGGCTGAAGTCTTTCTGGGGCTTCGGATTCTTCAGGCTTGTGGTGCCTCGGCGTGCCTTGTTTCCACATTTGCAACAGTACGTGACATTTACGCAGGTCGCGAGGAAAGTAATGTCATTTACGGCATACTCGGATCCATGCTGGCCATGGTCCCGGCGGTAGGCCCATTGCTCGGAGCGCTCGTCGACATGTGGCTTGGGTGGCGGGCTATCTTTGCGTTTCTAGGTTTGGGCATGATCGCTGCATCTGCAGCAGCGTGGCGATTCTGGCCTGAAACCCGGGTGCAACGAGTTGCGGGCTTGCAATGGTCGCAGCTGCTACTCCCCGTTAAGTGCCTGAACTTCTGGTTGTACACGTTGTGTTACGCCGCTGGAATGGGTAGCTTCTTCGTCTTTTTCTCCATTGCGCCCGGACTAATGATGGGCAGGCAAGGTGTGTCTCAGCTTGGCTTCAGCCTGCTGTTCGCCACAGTGGCAATTGCCATGGTGTTTACGGCTCGTTTTATGGGGCGTGTGATACCCAAGTGGGGCAGCCCAAGTGTCTTGCGAATGGGAATGGGATGCCTGATAGCTGGAGCAGTATTGCTTGCCATCACCGAAATATGGGCTTTGCAGTCCGTGTTAGGCTTTATTGCTCCAATGTGGCTAGTGGGTATTGGTGTCGCCACAGCGGTATCTGTGGCGCCCAATGGCGCTCTTCGAGGATTCGACCATGTTGCTGGAACGGTCACGGCAGTCTACTTCTGCTTGGGCGGTGTACTGCTAGGAAGCATCGGAACGTTGATCATTTCGCTGTTGCCGCGCAACACGGCTTGGCCGGTTGTCGTGTACTGTTTGACCCTTGCAACAGTCGTGCTCGGTCTGTCTTGTGTTTCCCGAGTGAAGGGCTCTCGCGGCCAGGGGGAGCATGATGTGGTCGCGCTACAAAGTGCGGGAAGTACATCAAATCCCAATCGTTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35732","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Typhimurium","NCBI_taxonomy_id":"90371"}}}},"ARO_accession":"3002691","ARO_id":"39125","ARO_name":"Salmonella enterica cmlA","CARD_short_name":"Sent_cmlA","ARO_description":"cmlA is a plasmid-encoded chloramphenicol exporter that is found in Salmonella typhimurium.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2704":{"model_id":"2704","model_name":"MexEF-OprN with MexT mutation conferring resistance to chloramphenicol, ciprofloxacin, and trimethoprim","model_type":"efflux pump system meta-model","model_type_id":"41112","model_description":"Efflux Pump System Meta-Models (EPS) are dedicated to efflux complexes and their regulators, such as AcrAB-TolC. Using the efflux pump components parameter, this model type simply includes a list of detection models for each component of the complex. This model type is still under development and not currently supported by the Resistance Gene Identifier (RGI) software.","model_param":{"41141":{"param_type":"efflux pump components","param_description":"Association of proteins within efflux protein complexes or regulatory networks are encoded by the efflux pump components parameter: model_id,model_id,model_id, etc.","param_type_id":"41141","param_value":{"7572":"1608,1067,1300,172"}},"snp":{"Curated-R":{"7572":"G8R"}}},"ARO_accession":"3004066","ARO_id":"41142","ARO_name":"MexEF-OprN with MexT mutation conferring resistance to chloramphenicol, ciprofloxacin, and trimethoprim","CARD_short_name":"Paer_MexT_MULT","ARO_description":"The MexEF\u2013OprN efflux pump in P. aeruginosa is overexpressed with MexT mutation conferring resistance to chloramphenicol and ciprofloxacin.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2832":{"model_id":"2832","model_name":"AAC(2')-Ie","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"350"}},"model_sequences":{"sequence":{"5510":{"protein_sequence":{"accession":"CAC32082.1","sequence":"MDTHHVHTARLVHTADLDGETLRRLQQMVTDAFAGDFDETDWEHALGGMHALIWRHGTIIAHAAVVQRRLFYHGNALRCGYLEGVAVRKDCRGRGLVHALLDAIEQVIRGAYQFGALSSSDRARRVYMSRGWLPWLGPTSVLAPTGVIRTPDDDGSVFVLPVGINPDTSSGLMCDWRAGNVW"},"dna_sequence":{"accession":"AL583926.1","fmin":"40191","fmax":"40740","strand":"+","sequence":"ATGGATACCCACCACGTACATACCGCCCGCCTGGTTCATACCGCCGATCTCGACGGCGAGACTCTCCGGCGCCTCCAGCAGATGGTCACCGACGCTTTCGCCGGAGACTTCGACGAGACCGACTGGGAACACGCATTGGGCGGGATGCACGCCCTGATCTGGCGGCACGGCACAATCATTGCGCACGCCGCGGTCGTTCAGCGGCGACTATTCTACCACGGCAACGCGTTGCGTTGCGGTTACCTCGAAGGTGTCGCGGTACGGAAGGACTGCCGGGGCCGCGGACTTGTACATGCGCTGCTGGACGCTATCGAGCAAGTGATACGCGGCGCCTATCAATTCGGTGCCTTGAGTTCCTCGGACCGAGCCCGTCGGGTGTATATGTCGCGCGGGTGGTTACCATGGCTCGGCCCGACGTCAGTGCTGGCTCCTACCGGTGTGATCCGTACGCCCGATGATGACGGCTCGGTGTTTGTCCTTCCGGTCGGCATCAACCCGGACACCTCCTCGGGGTTGATGTGCGATTGGCGCGCAGGCAACGTGTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40074","NCBI_taxonomy_name":"Mycobacterium leprae","NCBI_taxonomy_id":"1769"}}}},"ARO_accession":"3002527","ARO_id":"38927","ARO_name":"AAC(2')-Ie","CARD_short_name":"AAC(2')-Ie","ARO_description":"AAC(2')-Ie is a chromosomal-encoded aminoglycoside acetyltransferase in M. leprae.","ARO_category":{"36480":{"category_aro_accession":"3000341","category_aro_cvterm_id":"36480","category_aro_name":"AAC(2')","category_aro_description":"A category of aminoglycoside N-acetyltransferase enzymes with modification regiospecificity based at the 2'-amino group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics through acetylation of the 2-amino group of the compound.","category_aro_class_name":"AMR Gene Family"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"46127":{"category_aro_accession":"3007377","category_aro_cvterm_id":"46127","category_aro_name":"6'-N-ethylnetilmicin","category_aro_description":"6'-N-ethylnetilmicin is an aminoglycoside antibiotic and a derivative of netilmicin.","category_aro_class_name":"Antibiotic"},"46133":{"category_aro_accession":"3007382","category_aro_cvterm_id":"46133","category_aro_name":"gentamicin","category_aro_description":"Gentamicin is a commonly used aminoglycoside antibiotic derived from members of the Micromonospora genus of bacteria. It acts by binding the 30S ribosomal subunit, thus inhibiting protein synthesis. Gentamicin is typically used to treat Gram-negative infections of the repiratory and urinary tract, as well as infections of the bone and soft tissue. It also exhibits considerable nephrotoxicity and ototoxicity. Gentamicin is administered as a mixture of gentamicin type C (which makes about around 80% of the complex) and types A, B, and X (distributed in the remaining 20% of the complex).","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2834":{"model_id":"2834","model_name":"Mycobacterium tuberculosis iniB with mutation conferring resistance to ethambutol","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"41339":{"param_type":"nucleotide substitution in promoter region","param_description":"A nucleotide sequence change where, compared to a reference sequence, one nucleotide is replaced by one other nucleotide in the promoter region of a gene. These substitutions are indicated as upstream of the reference sequence transcription initiation site. Format is given by [-][position][wildtype][>][mutation], e.g. -11t>c or -15g>Var where Var represents any possible substitution.","param_type_id":"41339","param_value":{"8201":"-89c>t"}},"snp":{"Curated-R":{"8201":"G8R","8200":"A47T"},"param_value":{"8200":"A47T"},"clinical":{"8200":"A47T"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"8830":{"protein_sequence":{"accession":"NP_214855.1","sequence":"MTSLIDYILSLFRSEDAARSFVAAPGRAMTSAGLIDIAPHQISSVAANVVPGLNLGAGDPMSGLRQAVAARHGFAQDVANVGFAGDAGAGVASVITTDVGAGLASGLGAGFLGQGGLALAASSGGFGGQVGLAAQVGLGFTAVIEAEVGAQVGAGLGIGTGLGAQAGMGFGGGVGLGLGGQAGGVIGGSAAGAIGAGVGGRLGGNGQIGVAGQGAVGAGVGAGVGGQAGIASQIGVSAGGGLGGVGNVSGLTGVSSNAVLASNASGQAGLIASEGAALNGAAMPHLSGPLAGVGVGGQAGAAGGAGLGFGAVGHPTPQPAALGAAGVVAKTEAAAGVVGGVGGATAAGVGGAHGDILGHEGAALGSVDTVNAGVTPVEHGLVLPSGPLIHGGTGGYGGMNPPVTDAPAPQVPARAQPMTTAAEHTPAVTQPQHTPVEPPVHDKPPSHSVFDVGHEPPVTHTPPAPIELPSYGLFGLPGF"},"dna_sequence":{"accession":"NC_000962.3","fmin":"409361","fmax":"410801","strand":"+","sequence":"ATGACCTCGCTTATCGATTACATCCTGAGCCTGTTCCGCAGCGAAGACGCCGCCCGGTCGTTCGTTGCCGCTCCGGGACGGGCCATGACCAGTGCCGGGCTGATCGATATCGCGCCGCACCAAATCTCATCGGTGGCGGCCAATGTGGTGCCGGGTCTGAATCTGGGTGCCGGCGACCCCATGAGCGGATTGCGGCAGGCCGTCGCCGCTCGGCATGGCTTTGCGCAGGACGTCGCCAATGTCGGCTTCGCCGGTGACGCGGGCGCGGGGGTGGCAAGCGTCATCACGACCGATGTCGGTGCGGGCCTGGCTAGCGGACTGGGTGCTGGGTTCCTGGGTCAGGGTGGCCTGGCTCTCGCCGCGTCAAGCGGTGGTTTCGGCGGTCAGGTCGGCTTGGCTGCCCAGGTCGGTCTGGGTTTTACTGCCGTGATTGAGGCCGAGGTCGGCGCTCAGGTTGGTGCTGGGTTAGGTATTGGGACGGGTCTGGGTGCTCAGGCCGGTATGGGCTTTGGCGGCGGGGTTGGCCTGGGTCTGGGTGGTCAGGCCGGCGGTGTGATCGGTGGGAGCGCGGCCGGGGCTATCGGTGCCGGCGTCGGCGGTCGCCTAGGCGGCAATGGCCAGATCGGAGTTGCCGGCCAGGGTGCCGTTGGCGCTGGTGTCGGCGCTGGTGTCGGCGGCCAGGCGGGCATCGCTAGCCAGATCGGTGTCTCAGCCGGTGGTGGGCTCGGCGGCGTCGGCAATGTCAGCGGCCTGACCGGGGTCAGCAGCAACGCAGTGTTGGCTTCCAACGCAAGCGGCCAGGCGGGGTTGATCGCCAGTGAAGGCGCTGCCTTGAACGGCGCTGCTATGCCTCATCTGTCGGGCCCGTTAGCCGGTGTCGGTGTGGGTGGTCAGGCCGGCGCCGCTGGCGGCGCCGGGTTGGGCTTCGGAGCGGTCGGGCACCCGACTCCTCAGCCGGCGGCCCTGGGCGCGGCTGGCGTGGTGGCCAAGACCGAGGCGGCTGCTGGAGTGGTTGGCGGGGTCGGCGGGGCAACCGCGGCCGGGGTCGGCGGGGCACACGGCGACATCCTGGGCCACGAGGGAGCCGCACTGGGCAGTGTCGACACGGTCAACGCCGGTGTCACGCCCGTCGAGCATGGCTTGGTCCTGCCCAGTGGCCCCCTGATCCACGGCGGTACCGGCGGCTATGGCGGCATGAACCCGCCAGTGACCGATGCGCCGGCACCGCAAGTTCCGGCGCGGGCCCAGCCGATGACCACGGCGGCCGAGCACACGCCGGCGGTTACCCAACCGCAGCACACGCCGGTCGAGCCGCCGGTCCACGATAAGCCGCCGAGCCATTCGGTGTTTGACGTCGGTCACGAGCCGCCGGTGACGCACACGCCGCCGGCGCCCATCGAACTGCCGTCGTACGGCCTTTTCGGACTACCCGGGTTCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3004135","ARO_id":"41262","ARO_name":"Mycobacterium tuberculosis iniB with mutation conferring resistance to ethambutol","CARD_short_name":"Mtub_iniB_EMB","ARO_description":"Point mutations in M. tuberculosis iniB shown to confer resistance to ethambutol.","ARO_category":{"41263":{"category_aro_accession":"3004136","category_aro_cvterm_id":"41263","category_aro_name":"Ethambutol resistant iniB","category_aro_description":"Point mutations occurring in the iniB region of the iniBAC operon shown to confer resistance to ethambutol.","category_aro_class_name":"AMR Gene Family"},"36636":{"category_aro_accession":"3000497","category_aro_cvterm_id":"36636","category_aro_name":"ethambutol","category_aro_description":"Ethambutol is an antimycobacterial drug prescribed to treat tuberculosis. It is usually given in combination with other tuberculosis drugs, such as isoniazid, rifampicin, and pyrazinamide. Ethambutol inhibits arabinosyl biosynthesis, disrupting mycobacterial cell wall formation.","category_aro_class_name":"Antibiotic"},"36666":{"category_aro_accession":"3000527","category_aro_cvterm_id":"36666","category_aro_name":"polyamine antibiotic","category_aro_description":"Polyamine antibiotics are organic compounds having two or more primary amino groups.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2835":{"model_id":"2835","model_name":"PatA-PatB","model_type":"efflux pump system meta-model","model_type_id":"41112","model_description":"Efflux Pump System Meta-Models (EPS) are dedicated to efflux complexes and their regulators, such as AcrAB-TolC. Using the efflux pump components parameter, this model type simply includes a list of detection models for each component of the complex. This model type is still under development and not currently supported by the Resistance Gene Identifier (RGI) software.","model_param":{"41141":{"param_type":"efflux pump components","param_description":"Association of proteins within efflux protein complexes or regulatory networks are encoded by the efflux pump components parameter: model_id,model_id,model_id, etc.","param_type_id":"41141","param_value":{"8203":"2081,2112"}},"snp":{"Curated-R":{"8203":"A47T"}}},"ARO_accession":"3000769","ARO_id":"37149","ARO_name":"PatA-PatB","CARD_short_name":"PatA-PatB","ARO_description":"PatA-PatB is an efflux protein complex that is associated with fluoroquinolone resistance in Streptococcus pneumoniae. Experiments indicate that PatA and PatB form a heterodimeric transporter.","ARO_category":{"36002":{"category_aro_accession":"0010001","category_aro_cvterm_id":"36002","category_aro_name":"ATP-binding cassette (ABC) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding\/hydrolysis to transport substrates across cell membranes.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2836":{"model_id":"2836","model_name":"Bla2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"475"}},"model_sequences":{"sequence":{"4187":{"protein_sequence":{"accession":"AAR20596.1","sequence":"MKNTLLKLGVCVSLLGITPFVSTISSVQAERKVEHKVIKNETGTISISQLNKNVWVHTELGCFNGEAVPSNGLILNTSKGLVLVDSSWDDKLTKELIEMAEKKFKKSVTDVIITHAHADRIGGIKTLKERGIKAHSTTLTAELAKKNGYEEPLGDLQAITKLKFGNMKVETFYPGKGHTEDNIVVWLPQYNMLVGGCLVKSASAKDLGNITDAYVNEWSTSIENVLKRYENINFVVPGHGEVGDKGLLLHTLDLLK"},"dna_sequence":{"accession":"AY453162.1","fmin":"500","fmax":"1271","strand":"+","sequence":"ATGAAAAATACATTATTAAAATTAGGGGTATGTGTTAGTTTACTAGGAATAACTCCATTTGTTAGTACAATTTCTTCTGTACAAGCAGAACGAAAGGTAGAGCATAAAGTAATAAAAAATGAGACAGGAACTATTTCAATTTCTCAGTTAAACAAAAATGTTTGGGTTCATACGGAGTTAGGTTGTTTTAACGGAGAAGCAGTTCCTTCGAACGGTTTAATCCTTAATACTTCTAAAGGATTAGTACTTGTCGATTCTTCTTGGGATGATAAGTTAACGAAGGAATTAATAGAGATGGCAGAAAAGAAATTTAAGAAGAGTGTAACGGATGTTATTATTACACATGCACACGCTGATCGGATTGGTGGAATAAAAACGTTGAAAGAAAGAGGCATTAAAGCGCATAGTACAACGTTAACTGCGGAACTAGCAAAGAAAAATGGATATGAAGAACCACTTGGAGACTTACAAGCAATTACGAAATTGAAGTTTGGAAATATGAAAGTAGAAACGTTTTATCCAGGGAAAGGACATACAGAAGATAATATCGTCGTATGGTTACCACAATACAACATGTTAGTTGGAGGCTGTTTAGTGAAGTCTGCGTCCGCGAAAGATTTAGGAAATATTACTGATGCTTATGTAAATGAATGGTCTACATCGATTGAGAATGTGCTGAAGCGATATGAAAATATAAATTTTGTAGTACCTGGTCATGGAGAAGTAGGGGACAAAGGATTACTTTTACATACATTGGATTTGTTAAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36786","NCBI_taxonomy_name":"Bacillus anthracis","NCBI_taxonomy_id":"1392"}}}},"ARO_accession":"3004189","ARO_id":"41353","ARO_name":"Bla2","CARD_short_name":"Bla2","ARO_description":"Bla2 is a chromosomal-encoded beta-lactamase, found in Bacillus anthracis, which has penicillin, cephalosporin, and carbapenem-hydrolizing abilities.","ARO_category":{"41394":{"category_aro_accession":"3004230","category_aro_cvterm_id":"41394","category_aro_name":"subclass B1 Bacillus anthracis Bla beta-lactamase","category_aro_description":"Beta-lactamases belonging to the Bla genes from Bacillus anthracis that are classified as subclass B1 beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2861":{"model_id":"2861","model_name":"PDC-82","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6232":{"protein_sequence":{"accession":"AKR18022.1","sequence":"GEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQLPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLLEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"KR057751.1","fmin":"0","fmax":"1116","strand":"+","sequence":"GGCGAGGCCCCGGCGGATCGCCTGAAGGCATTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGCTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCCTGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCTAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTATGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3004345","ARO_id":"41513","ARO_name":"PDC-82","CARD_short_name":"PDC-82","ARO_description":"An AmpC-like beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4185":{"model_id":"4185","model_name":"ADC-110","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6560":{"protein_sequence":{"accession":"WP_136512053.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVKTDQQVLTFFKDWKPKNSIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLGAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTTDFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_064670.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTTTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAGTATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAATTTCCAGATGAAGTAAAAACAGATCAGCAAGTTTTAACATTTTTTAAAGACTGGAAACCTAAAAACTCAATCGGTGAATATCGACAATATTCAAACCCAAGCATTGGTTTATTTGGAAAAGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGGTGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTAAATCCACAAAAATATCCAGCAGATATTCAACGGGCAATTAATGAAACACATCAGGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTACCGATTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006289","ARO_id":"44751","ARO_name":"ADC-110","CARD_short_name":"ADC-110","ARO_description":"ADC-110 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2837":{"model_id":"2837","model_name":"APH(2'')-If","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4188":{"protein_sequence":{"accession":"AAW34150.1","sequence":"MDIKKIIEEKCNIVVDSIKLIGEGYDSKAYIVNNEYVFKIKFSANKKKGYEKEKAIYDFLNKKLNTNIKIPNIEYSYISEELSILGYKEIKGTFLTPEIYFALSKEKQELLKQDIAMFLRQMHDLDYSEISSYTIDNKQNVLEEYQLLKETIYDSLTDIEKQYVEEFMQRLNSTTIFDGKKCLCHNDFSCNHLLLDDENRLCGVIDFGDSGIIDEYCDFIYLLEDSEEEIGVSFGEDILRLYGNIDISKAKEYQDVVEQYYPIETIVYGIKNNRPDFIEKGRKEIYIRTRKDEKLRK"},"dna_sequence":{"accession":"AY701528.1","fmin":"9695","fmax":"10589","strand":"+","sequence":"ATGGATATAAAAAAGATAATAGAAGAAAAATGCAATATAGTTGTTGATAGTATAAAGTTGATTGGTGAGGGTTATGACAGCAAAGCATACATTGTAAATAATGAATATGTTTTCAAAATCAAATTTAGTGCTAATAAGAAAAAAGGGTATGAAAAAGAAAAAGCAATATATGATTTTCTAAACAAAAAATTAAATACAAATATTAAAATACCAAATATAGAATATTCATATATAAGTGAAGAATTATCTATTTTAGGATATAAAGAAATTAAAGGAACTTTTTTAACACCAGAAATATATTTTGCCTTATCAAAAGAAAAGCAAGAATTATTAAAGCAAGATATTGCTATGTTTTTAAGACAAATGCACGATTTAGATTATAGTGAAATAAGTTCATATACGATAGACAATAAACAAAATGTTTTAGAAGAATATCAATTACTTAAAGAAACAATATATGATAGTCTTACTGATATTGAAAAACAATATGTAGAAGAATTTATGCAAAGATTAAATAGTACAACTATATTTGATGGTAAAAAATGCTTATGCCATAATGATTTTAGTTGTAATCATTTATTACTTGATGATGAAAATAGATTATGTGGTGTAATAGATTTTGGAGATTCTGGAATTATAGATGAATACTGTGATTTCATATATTTGCTAGAAGATAGTGAAGAAGAAATTGGCGTGTCTTTTGGAGAAGATATATTAAGATTATACGGAAATATTGATATTTCAAAAGCAAAGGAATATCAAGATGTTGTAGAACAATATTATCCAATAGAAACTATTGTATATGGTATTAAAAATAATAGACCTGATTTTATAGAAAAAGGTAGAAAAGAGATTTATATAAGAACTCGCAAAGATGAAAAATTAAGGAAGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36772","NCBI_taxonomy_name":"Campylobacter jejuni","NCBI_taxonomy_id":"197"}}}},"ARO_accession":"3004191","ARO_id":"41355","ARO_name":"APH(2'')-If","CARD_short_name":"APH(2'')-If","ARO_description":"Aminoglycoside 2''-phosphotransferase identified from the gram-negative pathogen Campylobacter jejuni. APH(2'')-If was shown to confer resistance to 4,6-disubstituted antibiotics kanamycin, tobramycin, dibekacin, gentamicin and sisomicin through antibiotic phosphorylation. Described by Toth et al. 2013.","ARO_category":{"36267":{"category_aro_accession":"3000128","category_aro_cvterm_id":"36267","category_aro_name":"APH(2'')","category_aro_description":"A category of aminoglycoside O-phosphotransferase enzymes with modification regiospecificity based at the 2''-hydroxyl group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics, specifically kanamycin, tobramycin and amikacin, by the ATP-dependent phosphorylation of the 3'-hydroxyl group of the compound.","category_aro_class_name":"AMR Gene Family"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"40942":{"category_aro_accession":"3004015","category_aro_cvterm_id":"40942","category_aro_name":"gentamicin A","category_aro_description":"Gentamicin A is part of a complex of broad spectrum aminoglycoside antibiotics. Gentamicin inhibits protein synthesis, resulting in bacterial cell death.","category_aro_class_name":"Antibiotic"},"46133":{"category_aro_accession":"3007382","category_aro_cvterm_id":"46133","category_aro_name":"gentamicin","category_aro_description":"Gentamicin is a commonly used aminoglycoside antibiotic derived from members of the Micromonospora genus of bacteria. It acts by binding the 30S ribosomal subunit, thus inhibiting protein synthesis. Gentamicin is typically used to treat Gram-negative infections of the repiratory and urinary tract, as well as infections of the bone and soft tissue. It also exhibits considerable nephrotoxicity and ototoxicity. Gentamicin is administered as a mixture of gentamicin type C (which makes about around 80% of the complex) and types A, B, and X (distributed in the remaining 20% of the complex).","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2838":{"model_id":"2838","model_name":"MCR-1.2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"4479":{"protein_sequence":{"accession":"ANR95875.1","sequence":"MMLHTSVWYRRSVSPFVLVASVAVFLTATANLTFFDKISQTYPIADNLGFVLTIAVVLFGAMLLITTLLSSYRYVLKPVLILLLIMGAVTSYFTDTYGTVYDTTMLQNALQTDQAETKDLLNAAFIMRIIGLGVLPSLLVAFVKVDYPTWGKGLMRRLGLIVASLALILLPVVAFSSHYASFFRVHKPLRSYVNPIMPIYSVGKLASIEYKKASAPKDTIYHAKDAVQATKPDMRKPRLVVFVVGETARADHVSFNGYERDTFPQLAKIDGVTNFSNVTSCGTSTAYSVPCMFSYLGADEYDVDTAKYQENVLDTLDRLGVSILWRDNNSDSKGVMDKLPKAQFADYKSATNNAICNTNPYNECRDVGMLVGLDDFVAANNGKDMLIMLHQMGNHGPAYFKRYDEKFAKFTPVCEGNELAKCEHQSLINAYDNALLATDDFIAQSIQWLQTHSNAYDVSMLYVSDHGESLGENGVYLHGMPNAFAPKEQRSVPAFFWTDKQTGITPMATDTVLTHDAITPTLLKLFDVTADKVKDRTAFIR"},"dna_sequence":{"accession":"KX236309.1","fmin":"3136","fmax":"4762","strand":"-","sequence":"ATGATGCTGCATACTTCTGTGTGGTACCGACGCTCGGTCAGTCCGTTTGTTCTTGTGGCGAGTGTTGCCGTTTTCTTGACCGCGACCGCCAATCTTACCTTTTTTGATAAAATCAGCCAAACCTATCCCATCGCGGACAATCTCGGCTTTGTGCTGACGATCGCTGTCGTGCTCTTTGGCGCGATGCTACTGATCACCACGCTGTTATCATCGTATCGCTATGTGCTAAAGCCTGTGTTGATTTTGCTATTAATCATGGGCGCGGTGACCAGTTATTTTACTGACACTTATGGCACGGTCTATGATACGACCATGCTCCAAAATGCCCTACAGACCGACCAAGCCGAGACCAAGGATCTATTAAACGCAGCGTTTATCATGCGTATCATTGGTTTGGGTGTGCTACCAAGTTTGCTTGTGGCTTTTGTTAAGGTGGATTATCCGACTTGGGGCAAGGGTTTGATGCGCCGATTGGGCTTGATCGTGGCAAGTCTTGCGCTGATTTTACTGCCTGTGGTGGCGTTCAGCAGTCATTATGCCAGTTTCTTTCGCGTGCATAAGCCGCTGCGTAGCTATGTCAATCCGATCATGCCAATCTACTCGGTGGGTAAGCTTGCCAGTATTGAGTATAAAAAAGCCAGTGCGCCAAAAGATACCATTTATCACGCCAAAGACGCGGTACAAGCAACCAAGCCTGATATGCGTAAGCCACGCCTAGTGGTGTTCGTCGTCGGTGAGACGGCACGCGCCGATCATGTCAGCTTCAATGGCTATGAGCGCGATACTTTCCCACAGCTTGCCAAGATCGATGGCGTGACCAATTTTAGCAATGTCACATCGTGCGGCACATCGACGGCGTATTCTGTGCCGTGTATGTTCAGCTATCTGGGCGCGGATGAGTATGATGTCGATACCGCCAAATACCAAGAAAATGTGCTGGATACGCTGGATCGCTTGGGCGTAAGTATCTTGTGGCGTGATAATAATTCGGACTCAAAAGGCGTGATGGATAAGCTGCCAAAAGCGCAATTTGCCGATTATAAATCCGCGACCAACAACGCCATCTGCAACACCAATCCTTATAACGAATGCCGCGATGTCGGTATGCTCGTTGGCTTAGATGACTTTGTCGCTGCCAATAACGGCAAAGATATGCTGATCATGCTGCACCAAATGGGCAATCACGGGCCTGCGTATTTTAAGCGATATGATGAAAAGTTTGCCAAATTCACGCCAGTGTGTGAAGGTAATGAGCTTGCCAAGTGCGAACATCAGTCCTTGATCAATGCTTATGACAATGCCTTGCTTGCCACCGATGATTTCATCGCTCAAAGTATCCAGTGGCTGCAGACGCACAGCAATGCCTATGATGTCTCAATGCTGTATGTCAGCGATCATGGCGAAAGTCTGGGTGAGAACGGTGTCTATCTACATGGTATGCCAAATGCCTTTGCACCAAAAGAACAGCGCAGTGTGCCTGCATTTTTCTGGACGGATAAGCAAACTGGCATCACGCCAATGGCAACCGATACCGTCCTGACCCATGACGCGATCACGCCGACATTATTAAAGCTGTTTGATGTCACCGCGGACAAAGTCAAAGACCGCACCGCATTCATCCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3004194","ARO_id":"41358","ARO_name":"MCR-1.2","CARD_short_name":"MCR-1.2","ARO_description":"A plasmid-borne novel MCR-1 functional variant detected in a Klebsiella pneumoniae isolate collected from a rectal swab in Italy. MCR-1.2 differs from MCR-1 by a single amino acid substitution from Glutamine to Leucine at position 3 in the N-terminal region. Described by DiPilato et al. 2016.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2839":{"model_id":"2839","model_name":"GOB-18","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4756":{"protein_sequence":{"accession":"AAY53478.1","sequence":"MRNFATLFFMFICLGLSAQVVKEPENMPKEWNQAYEPFRIAGNLYYVGTYDLASYLIVTDKGNILINTGTAESFPIIKANIQKLGFNYKDIKILLLTQAHYDHTGALQDFKTETAAKFYVDKADVDVLRTGGKSDYEMGKYGVTFKPVTPDKTLKDQDKIKLGNITLTLLHHPGHTKGSCSFIFETKDEKRKYRVLIANMPSVIVDKKFSEVTAYPNIQSDYAYTFGVMKKLDFDIWVASHASQFDLHEKRKEGDPYNPQLFMDKQSYFQNLNDLEKSYLNKIKKDSQDK"},"dna_sequence":{"accession":"DQ004496.1","fmin":"0","fmax":"873","strand":"+","sequence":"ATGAGAAATTTTGCTACACTGTTTTTCATGTTCATTTGCTTGGGCTTGAGTGCTCAGGTAGTAAAAGAACCTGAAAATATGCCCAAAGAATGGAATCAGGCTTATGAACCATTCAGAATTGCAGGTAATTTATATTACGTAGGAACCTATGATTTGGCTTCTTACCTTATTGTGACAGACAAAGGCAATATTCTCATTAATACAGGAACGGCAGAATCGTTTCCAATAATAAAAGCAAATATCCAAAAGCTCGGGTTTAATTATAAAGACATTAAGATCTTGCTGCTTACTCAGGCTCACTACGACCATACAGGTGCATTACAGGATTTTAAAACAGAAACCGCTGCAAAATTCTATGTCGATAAAGCAGATGTTGATGTCCTGAGAACAGGGGGGAAGTCCGATTATGAAATGGGAAAATATGGTGTGACATTTAAACCTGTTACTCCGGATAAAACATTGAAAGATCAGGATAAAATAAAACTGGGAAATATAACCCTGACTTTGCTTCATCATCCGGGACATACAAAAGGTTCCTGTAGTTTTATTTTTGAAACAAAAGACGAGAAGAGAAAATATAGAGTTTTGATAGCTAATATGCCCTCCGTTATTGTTGATAAGAAATTTTCTGAAGTTACCGCATATCCAAATATTCAGTCCGATTATGCTTATACCTTTGGTGTTATGAAAAAGCTGGATTTTGATATTTGGGTGGCCTCCCATGCAAGTCAGTTCGATCTCCATGAAAAACGTAAAGAAGGAGATCCGTACAATCCGCAATTGTTTATGGATAAGCAAAGCTATTTCCAAAACCTTAATGATTTGGAAAAAAGCTATCTCAACAAAATAAAAAAAGATTCCCAAGATAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36960","NCBI_taxonomy_name":"Elizabethkingia meningoseptica","NCBI_taxonomy_id":"238"}}}},"ARO_accession":"3004213","ARO_id":"41377","ARO_name":"GOB-18","CARD_short_name":"GOB-18","ARO_description":"GOB-18 is a member of subclass B3 GOB family of beta-lactamases isolated from Elizabethkingia meningoseptica. GOB-18 is unlike other subclass B3 beta-lactamases as it is fully active against a broad range of beta-lactam substrates using a single Zn(II) ion in its active site.","ARO_category":{"41376":{"category_aro_accession":"3004212","category_aro_cvterm_id":"41376","category_aro_name":"GOB beta-lactamase","category_aro_description":"The GOB family of beta-lactamases have been discovered in the Elizabethkingia meningoseptica and are classified as subclass B3 beta-lactamase. They confer resistance to cephalosporins, penicillins, and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2840":{"model_id":"2840","model_name":"NPS-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"4191":{"protein_sequence":{"accession":"AAK14791.1","sequence":"MLKSTLLAFGLFIALSARAENQAIAQLFQRAGVDGTIVIESLTTRQRLVHNDPRAQQRYPAASTFKVLNTLIALEEGAISGENQIFHWNGTQYSIANWNQDQTLDSAFKVSCVWCYQQIALRVGALKYPAYIQQTNYGHLLEPFNGTEFWLDGSLTISAEEQVAFLRRVVERKLPFKASSYDSLKKVMFADENAQYRLYAKTGWATRITPSVGWYVGYVEAQDDVWLFALNLATRDANDLPLRTQIAKDALKAIGAFHAK"},"dna_sequence":{"accession":"AY027589.1","fmin":"45","fmax":"828","strand":"+","sequence":"ATGCTGAAGAGCACCCTTCTGGCCTTTGGTCTCTTTATCGCACTCTCAGCGCGTGCAGAGAACCAGGCAATCGCCCAGCTTTTCCAGAGGGCAGGAGTCGATGGGACCATCGTCATCGAGTCTCTAACCACCAGACAGCGCTTGGTTCACAACGATCCTCGTGCGCAACAACGATACCCGGCAGCTTCCACGTTCAAGGTACTCAATACCTTGATTGCTCTCGAAGAGGGCGCCATTTCAGGTGAGAACCAGATCTTTCACTGGAACGGTACCCAGTATTCGATTGCGAATTGGAACCAGGACCAGACTCTAGACAGTGCGTTTAAAGTGAGTTGTGTCTGGTGCTACCAGCAGATTGCCCTTCGAGTGGGGGCACTCAAGTACCCAGCCTATATTCAACAGACAAACTATGGTCATTTACTGGAACCCTTCAATGGAACGGAGTTTTGGCTGGATGGCTCTTTGACGATCAGCGCGGAAGAACAGGTTGCCTTTCTCCGACGGGTTGTTGAGCGAAAACTACCGTTCAAAGCGAGCAGCTATGATTCCCTGAAGAAAGTCATGTTCGCCGATGAGAATGCCCAGTATCGCCTTTATGCAAAAACGGGTTGGGCGACCCGCATCACTCCCTCGGTGGGTTGGTATGTTGGCTATGTTGAAGCACAGGACGATGTTTGGCTGTTTGCCCTGAATCTTGCTACCCGCGACGCAAATGACCTGCCCCTACGAACGCAGATAGCCAAAGACGCGCTGAAGGCGATAGGTGCGTTTCATGCGAAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3004239","ARO_id":"41403","ARO_name":"NPS-1","CARD_short_name":"NPS-1","ARO_description":"NPS-1 is a plasmid-encoded class D beta-lactamases identified from two Pseudomonas aeruginosa isolates in 1986.","ARO_category":{"41404":{"category_aro_accession":"3004240","category_aro_cvterm_id":"41404","category_aro_name":"NPS beta-lactamase","category_aro_description":"NPS beta-lactamases are class D beta-lactamases that have partial hydrolyzing abilities against penicillins and cephalosporin.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2841":{"model_id":"2841","model_name":"Escherichia coli 23S rRNA with mutation conferring resistance to chloramphenicol","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"41093","param_value":"5000"},"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"8226":"g2057a"},"Curated-R":{"8226":"g2057a"},"clinical":{"8226":"g2057a"}}},"model_sequences":{"sequence":{"4193":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"AE014075.1","fmin":"237159","fmax":"240063","strand":"+","sequence":"GGTTAAGCGACTAAGCGTACACGGTGGATGCCCTGGCAGTCAGAGGCGATGAAGGACGTGCTAATCTGCGATAAGCGTCGGTAAGGTGATATGAACCGTTATAACCGGCGATTTCCGAATGGGGAAACCCAGTGTGTTTCGACACACTATCATTAACTGAATCCATAGGTTAATGAGGCGAACCGGGGGAACTGAAACATCTAAGTACCCCGAGGAAAAGAAATCAACCGAGATTCCCCCAGTAGCGGCGAGCGAACGGGGAGGAGCCCAGAGCCTGAATCAGTGTGTGTGTTAGTGGAAGCGTCTGGAAAGGCGCGCGATACAGGGTGACAGCCCCGTACACAAAAATGCACATGCTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGGGGGACCATCCTCCAAGGCTAAATACTCCTGACTGACCGATAGTGAACCAGTACCGTGAGGGAAAGGCGAAAAGAACCCCGGCGAGGGGAGTGAAAAAGAACCTGAAACCGTGTACGTACAAGCAGTGGGAGCATGCTTAGGCGTGTGACTGCGTACCTTTTGTATAATGGGTCAGCGACTTATATTCTGTAGCAAGGTTAACCGAATAGGGGAGCCGAAGGGAAACCGAGTCTTAACTGGGCGTTAAGTTGCAGGGTATAGACCCGAAACCCGGTGATCTAGCCATGGGCAGGTTGAAGGTTGGGTAACACTAACTGGAGGACCGAACCGACTAATGTTGAAAAATTAGCGGATGACTTGTGGCTGGGGGTGAAAGGCCAATCAAACCGGGAGATAGCTGGTTCTCCCCGAAAGCTATTTAGGTAGCGCCTCGTGAACTCATCTCCGGGGGTAGAGCACTGTTTCGGCAAGGGGGTCATCCCGACTTACCAACCCGATGCAAACTGCGAATACCGGAGAATGTTATCACGGGAGACACACGGCGGGTGCTAACGTCCGTCGNGAAGAGGGAAACAACCCAGACCGCCAGCTAAGGTCCCAAAGTCATGGTTAAGTGGGAAACGATGTGGGAAGGCCCAGACAGCCAGGATGTTGGCTTAGAAGCAGCCATCATTTAAAGAAAGCGTAATAGCTCACTGGTCGAGTCGGCCTGCGCGGAAGATGTAACGGGGCTAAACCATGCACCGAAGCTGCGGCAGCGACGCTTATGCGTTGTTGGGTAGGGGAGCGTTCTGTAAGCCTGTGAAGGTGTACTGTGAGGTATGCTGGAGGTATCAGAAGTGCGAATGCTGACATAAGTAACGATAAAGCGGGTGAAAAGCCCGCTCGCCGGAAGACCAAGGGTTCCTGTCCAACGTTAATCGGGGCAGGGTGAGTCGACCCCTAAGGCGAGGCCGAAAGGCGTAGTCGATGGGAAACAGGTTAATATTCCTGTACTTGGTGTTACTGCGAAGGGGGGACGGAGAAGGCTATGTTGGCCGGGCGACGGTTGTCCCGGTTTAAGCGTGTAGGCTGGTTTTCCAGGCAAATCCGGAAAATCAAGGCTGAGGCGTGATGACGAGGCACTACGGTGCTGAAGCAACAAATGCCCTGCTTCCAGGAAAAGCCTCTAAGCATCAGGTAACATCAAATCGTACCCCAAACCGACACAGGTGGTCAGGTAGAGAATACCAAGGCGCTTGAGAGAACTCGGGTGAAGGAACTAGGCAAAATGGTGCCGTAACTTCGGGAGAAGGCACGCTGATATGTAGGTGAAGCGACTTGCTCGTGGAGCTGAAATCAGTCGAAGATACCAGCTGGCTGCAACTGTTTATTAAAAACACAGCACTGTGCAAACACGAAAGTGGACGTATACGGTGTGACGCCTGCCCGGTGCCGGAAGGTTAATTGATGGGGTTAGCGCAAGCGAAGCTCTTGATCGAAGCCCCGGTAAACGGCGGCCGTAACTATAACGGTCCTAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCTGCACGAATGGCGTAATGATGGCCAGGCTGTCTCCACCCGAGACTCAGTGAAATTGAACTCGCTGTGAAGATGCAGTGTACCCGCGGCAAGACGGAAAGACCCCGTGAACCTTTACTATAGCTTGACACTGAACATTGAGCCTTGATGTGTAGGATAGGTGGGAGGCTTTGAAGTGTGGACGCCAGTCTGCATGGAGCCGACCTTGAAATACCACCCTTTAATGTTTGATGTTCTAACGTTGACCCGTAATCCGGGTTGCGGACAGTGTCTGGTGGGTAGTTTGACTGGGGCGGTCTCCTCCTAAAGAGTAACGGAGGAGCACGAAGGTTGGCTAATCCTGGTCGGACATCAGGAGGTTAGTGCAATGGCATAAGCCAGCTTGACTGCGAGCGTGACGGCGCGAGCAGGTGCGAAAGCAGGTCATAGTGATCCGGTGGTTCTGAATGGAAGGGCCATCGCTCAACGGATAAAAGGTACTCCGGGGATAACAGGCTGATACCGCCCAAGAGTTCATATCGACGGCGGTGTTTGGCACCTCGATGTCGGCTCATCACATCCTGGGGCTGAAGTAGGTCCCAAGGGTATGGCTGTTCGCCATTTAAAGTGGTACGCGAGCTGGGTTTAGAACGTCGTGAGACAGTTCGGTCCCTATCTGCCGTGGGCGCTGGAGAACTGAGGGGGGCTGCTCCTAGTACGAGAGGACCGGAGTGGACGCATCACTGGTGTTCGGGTTGTCATGCCAATGGCACTGCCCGGTAGCTAAATGCGGAAGAGATAAGTGCTGAAAGCATCTAAGCACGAAACTTGCCCCGAGATGAGTTCTCCCTGACTCCTTGAGGGTCCTGAAGGAACGTTGAAGACGACGACGTTGATAGGCCGGGTGTGTAAGCGCAGCGATGCGTTGAGCTAACCGGTACTAATGAACCGTGAGGCTTAACCTT","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36763","NCBI_taxonomy_name":"Escherichia coli CFT073","NCBI_taxonomy_id":"199310"}}}},"ARO_accession":"3004150","ARO_id":"41297","ARO_name":"Escherichia coli 23S rRNA with mutation conferring resistance to chloramphenicol","CARD_short_name":"Ecol_23S_CHL","ARO_description":"Point mutation in the 23S rRNA of Escherichia coli shown clinically to confer resistance to chloramphenicol.","ARO_category":{"41350":{"category_aro_accession":"3004188","category_aro_cvterm_id":"41350","category_aro_name":"23S rRNA with mutation conferring resistance to phenicol antibiotics","category_aro_description":"Point mutations in the 23S rRNA subunit shown clinically to confer resistance to phenicol class antibiotics, including chloramphenicol and florfenicol, by disrupting antibiotic binding-site affinity.","category_aro_class_name":"AMR Gene Family"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2842":{"model_id":"2842","model_name":"Vibrio cholerae varG","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4194":{"protein_sequence":{"accession":"AAF94716.1","sequence":"MFVSHLSFPHLIEERKMKLSTLALAPITAALLTFNASAKGHDHDNQRAIFFPGETVQDTVKVEVEPSATQSLKLGQKINNLYERQFDNSQATVQKLGKNTYWIGVNYYNATVVVNEDSVLLIDPLGDGRIDALFKGVQSITNKPITTIMYSHYHLDHLGGGNQLVDLIKKNYPKVDKIRVIASQTVADKINQHAEVGENGVKTPKVPAPNDIYDLTKPQTVQFGSMKIKMMAPKGSGHTPDNTMILIPSDRVLHFADMINPDQLPFYNFAGAEHFHGYEEDLQSLLSKPLSKQWDFINGGHGNIGSKQDVKDLLEYIADIRTEVGKQLEVAPYTPVLSDGNHFVWFKRWQDEITNNVHTALANKYGHMYGFDSGVVETHAAMILADMIDH"},"dna_sequence":{"accession":"AE003852.1","fmin":"1674272","fmax":"1675445","strand":"+","sequence":"ATGTTTGTTTCTCATTTATCTTTTCCCCACCTGATTGAGGAGAGAAAAATGAAACTATCCACCTTAGCTTTAGCCCCTATTACTGCAGCACTACTTACTTTTAATGCAAGTGCTAAAGGCCATGACCACGACAATCAACGCGCGATTTTTTTCCCTGGTGAAACTGTTCAAGACACTGTGAAAGTCGAAGTTGAGCCTTCTGCGACTCAGTCTCTGAAACTGGGACAAAAAATTAATAATCTGTATGAGCGCCAGTTTGATAACAGCCAAGCCACCGTTCAAAAATTGGGCAAGAATACCTACTGGATAGGGGTCAATTATTACAACGCTACCGTTGTGGTTAACGAAGACTCTGTCTTGCTGATTGACCCACTAGGCGATGGTCGTATTGATGCGCTTTTTAAAGGGGTGCAATCCATCACGAATAAACCGATCACTACGATTATGTATTCTCACTACCACTTAGATCATTTAGGTGGTGGCAACCAACTGGTTGACTTAATTAAGAAAAATTATCCAAAAGTAGATAAAATCCGCGTTATTGCTAGCCAAACCGTTGCGGACAAGATCAACCAACACGCCGAAGTAGGCGAAAACGGTGTGAAAACCCCGAAAGTTCCAGCGCCGAATGACATATACGACCTGACGAAGCCTCAAACGGTTCAATTTGGCTCAATGAAAATCAAGATGATGGCACCAAAAGGCTCTGGCCATACACCTGATAACACCATGATTCTGATCCCAAGCGATCGCGTGTTGCATTTCGCGGACATGATTAATCCCGATCAACTACCGTTTTACAATTTCGCGGGAGCAGAACATTTCCACGGTTACGAAGAAGATCTACAAAGCCTTCTGAGCAAACCGCTGAGCAAACAGTGGGACTTTATTAACGGTGGCCATGGCAATATAGGTTCGAAACAGGATGTAAAAGATCTGCTTGAGTATATTGCGGACATCAGAACTGAAGTGGGCAAGCAGCTAGAAGTCGCCCCCTACACTCCAGTGTTGAGTGACGGTAACCACTTTGTTTGGTTCAAACGCTGGCAAGATGAGATCACTAACAATGTACATACCGCACTGGCAAACAAGTATGGCCACATGTACGGTTTCGATTCAGGCGTGGTTGAAACACACGCGGCAATGATTCTCGCAGATATGATTGATCACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39595","NCBI_taxonomy_name":"Vibrio cholerae O1 biovar El Tor str. N16961","NCBI_taxonomy_id":"243277"}}}},"ARO_accession":"3004289","ARO_id":"41453","ARO_name":"Vibrio cholerae varG","CARD_short_name":"Vcho_varG","ARO_description":"varG is an Ambler class B metallo-beta-lactamase found on the antibiotic resistance var regulon in Vibrio cholerae, along with an antibiotic efflux pump varABCDEF. These genes are organized as a regulon under the control of VarR transcriptional activator. VarG was shown to have beta-lactamase activity against penicillins, carbapenems and cephalosporins in-vitro. Described by Lin HV et al. 2017.","ARO_category":{"41452":{"category_aro_accession":"3004288","category_aro_cvterm_id":"41452","category_aro_name":"Subclass B1 Vibrio cholerae varG beta-lactamase","category_aro_description":"varG is an Ambler class B metallo-beta-lactamase found on the antibiotic resistance var regulon in Vibrio cholerae, along with an antibiotic efflux pump varABCDEF. These genes are organized as a regulon under the control of VarR transcriptional activator. VarG was shown to have beta-lactamase activity against penicillins, carbapenems and cephalosporins in-vitro.","category_aro_class_name":"AMR Gene Family"},"35990":{"category_aro_accession":"0000073","category_aro_cvterm_id":"35990","category_aro_name":"meropenem","category_aro_description":"Meropenem is an ultra-broad spectrum injectable antibiotic used to treat a wide variety of infections, including meningitis and pneumonia. It is a beta-lactam and belongs to the subgroup of carbapenem, similar to imipenem and ertapenem.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3621":{"model_id":"3621","model_name":"LAP-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"585"}},"model_sequences":{"sequence":{"5819":{"protein_sequence":{"accession":"ABV89601.1","sequence":"MKKIRLIIISLLAGMCTPALSTPVNVTDTIQSTEDHIKGRVGFTEIDFLSGKVLSSHRREERFPMMSTFKVLLCGAILVRVDKGLEQLERRITYNKHDLDDYSPLTSQHIADGMTVSELCNAAITTSDNTAANLLLSTIGGPEGLTHFLRSTGDSYTRLDRHEPSLNEAKPGDERDTTTPAAMAQTLQKLLNESVLTEKSRKKLISWMQEDKVGGPLFRSVLPAGWMIADKTGAGDHGSRGIVALLGPGGKPSRIVVLYITNTHSSMNELNEHIAGIGDSVIKNW"},"dna_sequence":{"accession":"EU159120.1","fmin":"0","fmax":"858","strand":"+","sequence":"ATGAAAAAGATCCGCCTTATTATAATCTCTTTACTGGCTGGAATGTGTACTCCAGCATTATCTACACCAGTCAATGTTACTGATACAATACAAAGCACAGAAGACCATATCAAAGGTCGGGTTGGTTTTACTGAAATAGACTTTTTATCCGGGAAGGTTCTGAGTAGTCATCGCCGTGAAGAACGTTTTCCTATGATGAGCACATTCAAAGTTTTGTTATGTGGAGCAATATTAGTACGTGTTGATAAAGGGCTTGAACAACTTGAACGCCGAATTACCTATAATAAGCATGACCTGGACGACTATTCTCCACTAACCAGTCAGCACATTGCAGATGGAATGACGGTTTCTGAGTTATGCAATGCTGCCATTACCACCAGTGATAACACTGCTGCAAATTTATTGCTATCAACTATTGGCGGGCCGGAGGGATTAACTCATTTTCTGCGTAGCACTGGTGATAGTTATACAAGGCTTGATCGACACGAACCCAGCCTTAATGAGGCGAAGCCTGGCGATGAGCGTGATACCACCACTCCGGCAGCGATGGCTCAAACGCTACAAAAATTGTTAAACGAAAGTGTACTTACAGAAAAATCTCGAAAAAAATTAATAAGCTGGATGCAGGAAGATAAAGTCGGCGGGCCTCTGTTCCGCTCTGTACTGCCAGCTGGCTGGATGATAGCGGATAAAACAGGAGCAGGTGATCACGGATCTCGGGGCATCGTTGCACTGTTGGGCCCCGGAGGCAAGCCATCTCGTATAGTAGTCCTGTATATTACAAATACTCATTCATCTATGAATGAACTCAACGAGCATATTGCAGGGATCGGAGATTCAGTAATTAAGAACTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3004826","ARO_id":"42956","ARO_name":"LAP-2","CARD_short_name":"LAP-2","ARO_description":"LAP-2 is an Ambler Class A beta-lactamase gene.","ARO_category":{"42954":{"category_aro_accession":"3004824","category_aro_cvterm_id":"42954","category_aro_name":"LAP beta-lactamase","category_aro_description":"LAP is a Ambler Class A beta-lactamase gene family that confers resistance to beta-lactams.","category_aro_class_name":"AMR Gene Family"},"35976":{"category_aro_accession":"0000059","category_aro_cvterm_id":"35976","category_aro_name":"cefepime","category_aro_description":"Cefepime (INN) is a fourth-generation cephalosporin antibiotic developed in 1994. It contains an aminothiazolyl group that decreases its affinity with beta-lactamases. Cefepime shows high binding affinity with penicillin-binding proteins and has an extended spectrum of activity against Gram-positive and Gram-negative bacteria, with greater activity against both Gram-negative and Gram-positive organisms than third-generation agents.","category_aro_class_name":"Antibiotic"},"35980":{"category_aro_accession":"0000063","category_aro_cvterm_id":"35980","category_aro_name":"cefuroxime","category_aro_description":"Cefuroxime is a second-generation cephalosporin antibiotic with increased stability with beta-lactamases than first-generation cephalosporins. Cefuroxime is active against Gram-positive organisms but less active against methicillin-resistant strains.","category_aro_class_name":"Antibiotic"},"35981":{"category_aro_accession":"0000064","category_aro_cvterm_id":"35981","category_aro_name":"amoxicillin","category_aro_description":"Amoxicillin is a moderate-spectrum, bacteriolytic, beta-lactam antibiotic used to treat bacterial infections caused by susceptible microorganisms. A derivative of penicillin, it has a wider range of treatment but remains relatively ineffective against Gram-negative bacteria. It is commonly taken with clavulanic acid, a beta-lactamase inhibitor. Like other beta-lactams, amoxicillin interferes with the synthesis of peptidoglycan.","category_aro_class_name":"Antibiotic"},"35995":{"category_aro_accession":"0000078","category_aro_cvterm_id":"35995","category_aro_name":"piperacillin","category_aro_description":"Piperacillin is an acetylureidopenicillin and has an extended spectrum of targets relative to other beta-lactam antibiotics. It inhibits cell wall synthesis in bacteria, and is usually taken with the beta-lactamase inhibitor tazobactam to overcome penicillin-resistant bacteria.","category_aro_class_name":"Antibiotic"},"36976":{"category_aro_accession":"3000632","category_aro_cvterm_id":"36976","category_aro_name":"benzylpenicillin","category_aro_description":"Benzylpenicillin, commonly referred to as penicillin G, is effective against both Gram-positive and Gram-negative bacteria. It is unstable in acid.","category_aro_class_name":"Antibiotic"},"37084":{"category_aro_accession":"3000704","category_aro_cvterm_id":"37084","category_aro_name":"cefalotin","category_aro_description":"Cefalotin is a semisynthetic cephalosporin antibiotic activate against staphylococci. It is resistant to staphylococci beta-lactamases but hydrolyzed by enterobacterial beta-lactamases.","category_aro_class_name":"Antibiotic"},"40523":{"category_aro_accession":"3003832","category_aro_cvterm_id":"40523","category_aro_name":"ticarcillin","category_aro_description":"Ticarcillin is a carboxypenicillin used for the treatment of Gram-negative bacteria, particularly P. aeruginosa. Ticarcillin's antibiotic properties arise from its ability to prevent cross-linking of peptidoglycan during cell wall synthesis, when the bacteria try to divide, causing cell death.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2844":{"model_id":"2844","model_name":"Rhodobacter sphaeroides ampC beta-lactamase","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"5508":{"protein_sequence":{"accession":"ABA81355.1","sequence":"MKHLSPLSILLMVGALTPALAQDTTPSFESAAAAAFESVIEEHDIPGLVVGVTHGGRHSFYQTGLASREDQQPVTPDTLFELGSISKIFNVTLAALAEERGALSLDAPVADYLPSLRGSPAGELTLIDLATHHTGGLPLQVPDEVADVDRLVDWLRSWRPPEPGTRSYSNISIGLLGHITAGVLGMSYADASQTVIFPALGLKSTWIDVPTDAMGRYAFGYDRKTDAPTRVTPGVLDDEAYGVKSSARDMLTLLDLELGTGTASPEVQTAVATTQEGRFQTRLYTQAMIWEAYPWPVDPERLVEGNGYDFILQPQPVDEVDTTPDRRVILNKTGSTNGFGGYIAIVPSEDLGVVVLANRNYPNEARVRATYDLITHILAE"},"dna_sequence":{"accession":"CP000144.2","fmin":"874560","fmax":"875703","strand":"+","sequence":"ATGAAGCACCTTTCCCCCCTCTCCATCCTGCTCATGGTGGGCGCGCTGACGCCCGCGCTTGCGCAAGACACCACGCCGTCGTTCGAGAGCGCCGCCGCCGCGGCCTTCGAGAGCGTCATCGAGGAGCATGACATTCCCGGTCTGGTGGTGGGCGTGACCCACGGCGGACGGCACAGTTTCTATCAGACAGGCTTGGCCTCACGGGAAGATCAGCAGCCGGTAACCCCTGACACGCTTTTTGAGCTCGGTTCGATCAGCAAGATCTTCAACGTGACGCTGGCGGCCTTGGCAGAGGAGCGGGGCGCGCTGTCGCTCGATGCGCCGGTCGCCGACTATCTTCCCTCCCTGCGAGGTTCTCCTGCAGGAGAGCTGACGCTGATCGATCTGGCGACGCACCATACCGGCGGCCTCCCGTTGCAGGTGCCGGACGAAGTTGCAGATGTAGATCGCCTGGTCGACTGGCTACGGAGTTGGCGACCGCCCGAGCCCGGTACGCGCAGCTATTCCAACATCAGCATCGGCCTATTGGGGCACATCACCGCGGGCGTGCTGGGCATGAGCTATGCTGATGCGTCCCAGACGGTTATCTTCCCGGCGCTCGGATTGAAGAGCACGTGGATCGACGTCCCCACCGATGCGATGGGACGCTACGCCTTCGGCTATGACCGCAAGACAGACGCGCCAACCCGGGTTACGCCCGGCGTGCTGGACGATGAAGCGTACGGGGTAAAATCCTCCGCTCGCGACATGCTGACGCTGCTCGACCTCGAGCTTGGAACCGGCACTGCCTCGCCCGAAGTTCAAACGGCGGTGGCCACCACGCAGGAGGGCCGGTTCCAGACCCGCCTGTACACGCAGGCCATGATATGGGAGGCCTATCCTTGGCCTGTCGACCCAGAGCGTCTGGTGGAGGGGAACGGGTATGACTTCATCCTCCAGCCTCAGCCTGTGGACGAGGTGGACACGACACCCGATCGGAGGGTCATCCTGAACAAGACAGGTTCCACGAACGGCTTCGGTGGGTACATCGCGATCGTGCCAAGCGAGGATCTGGGCGTCGTCGTCCTTGCCAACCGCAACTACCCCAACGAGGCGCGGGTTCGAGCCACTTACGACCTGATCACTCACATCTTGGCCGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41456","NCBI_taxonomy_name":"Cereibacter sphaeroides 2.4.1","NCBI_taxonomy_id":"272943"}}}},"ARO_accession":"3004291","ARO_id":"41455","ARO_name":"Rhodobacter sphaeroides ampC beta-lactamase","CARD_short_name":"Rsph_ampC_BLA","ARO_description":"A periplasmic cephalosporinase described in Rhodobacter sphaeroides shown to contribute to resistance of beta-lactam antibiotics.","ARO_category":{"41396":{"category_aro_accession":"3004232","category_aro_cvterm_id":"41396","category_aro_name":"ampC-type beta-lactamase","category_aro_description":"AmpC beta-lactamases are clinically important class C beta-lactamase enzymes which confer resistance to cephalosporins and penicillin-like antibiotics. AmpC beta-lactamases are typically found in Enterobacteriaceae, and were described in Escherichia coli in 1940 as the first reported enzymatic deactivation of penicillin. The name AmpC connects these enzymes functionally across many species, however these enzymes are generally unnamed and not phylogenetically related.","category_aro_class_name":"AMR Gene Family"},"36976":{"category_aro_accession":"3000632","category_aro_cvterm_id":"36976","category_aro_name":"benzylpenicillin","category_aro_description":"Benzylpenicillin, commonly referred to as penicillin G, is effective against both Gram-positive and Gram-negative bacteria. It is unstable in acid.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2822":{"model_id":"2822","model_name":"Mycoplasma hominis 23S rRNA with mutation conferring resistance to macrolide antibiotics","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"7942":"g2087a","7943":"a2578t"},"Curated-R":{"7942":"g2087a","7943":"a2578t"},"clinical":{"7942":"g2087a","7943":"a2578t"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"41093","param_value":"5000"}},"model_sequences":{"sequence":{"4166":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"CP011538.1","fmin":"333282","fmax":"336166","strand":"-","sequence":"ACCAATAAATTTATTAGTACTGGTCAGCTGAATGCATTGCTGCACTTACACCTCCAGCCTATCAACCTCATAGTCTATAAGGAATTTTAAAGGGAATACTAATCTTTGAGGGGGCTTCCCGCTTAGATGCTTTCAGCGGTTATCCCTGCCGCACTTGGCTACCCAGCTATGCTTCTGGCGAAACAACTGGCACACCATCGGTGCGTCCACTCCGGTCCTCTCGTACTAAGAGTAGCTCTCATCAATATTCCAACGCCCACATCAGATAGGAACCAAACTGTCTCACGACGTTTTGAACCCAGCTCGCGTACCGCTTTAATGGGCGAACAGCCCAACCCTTGGAACCGACTCCAGCTCCAGGATGCGATGAGCCGACATCGAGGTGCCAAACCTTCCCGTCGATGTGATCTCTTGGGAAAGATAAGCCTGTTATCCCCGGGGTAGCTTTTATCCGTTGAGCGACGGCCTTTCCACGAAGAACCGCCGGATCACTAAGTCCTGCTTTCGCACCTGCTCGACTTGTAGGTCTCACAGTCAATCACACTTCTACCTTTATGCTCTTAGATACGGTTTCTGACCGTATTGAGTGTAACTTTGAACGCCTCCGTTACCCTTTAGGAGGCGACCGCCCCAGTCAAACTACCCACCACACACTGTCCTCTTCCCGGATAACGGGAACAAGTTAGAAGTTCAATGTAACAAGGGTGGTATTTCAACGGCGACTACTCTTAAACTAGCGTTCAAGCATCAACGTCTCCCACCTATCCTACACATGTTAAATCAAACTCCAATATGAAGTTATAGTAAAGCTCCACGGGGTCTTTTCGTCTAGATGCGGGTCTCCGGCGTCTTCGCCGGAACCATAATTTCACCGAGTCTATTGTCGAGACAGTTAAGAGATAATTACTCCTTTCGTGCAGGTCAGTATTTAGCCGACAAGGAATTTCGCTACCTTAGGACCGTTATAGTTACGGCCGCCGTTCACCCGGGCTTCACATTAATGCTTCGCTAATGCTAACACCTCTGCTTAACCTTCGGGCACTGGGCAGGAGTCACCCCATATACATCATCTTACGACTTAGCATAGAGCTGTGTTTTTGATAAACAGTTCCCCCTTACTATTCACTGCGGCCCACATTTTATTGTGGGCATCCCTTCTTGCGAACTTACGGGATGAATTTGCAGAGTTCCTTGACAATAGTTTTCTCGCTCGCCTTAGAATACTCATCTTGGGGACGTGTGTCCGTTCTCGGTACGGGTTTCCTAACACTTAATGTTAGAAGCTTTTTTAAGAGGCATGAAATCATCTAATTCGCTACTCAGTTGCCCTTTTGCTATGCGTCGTAACTCCCAGTTAAGTTATGCGGATTTGCCTACATAACCCAGTTGTTACTTACCCCACAATCCAATTAGTGGTAAAATTATCCTTCCCCGTCACTCCATCACATGTTAAGAAAGTACAGGAATATTAACCTGTTGTCCATCGGCTACGCCTTTCGGCCTCGTCTTAGGACCCGACTAACCCTGGGTGGACGAACCTTGCCCAGGAAACCTTCCCCAATAGGCGTCAGAGATTCTCACTCTGAATCGTTACTCATACCGGCATTCTCACTTGTAAGCGCTCCACCAGTCCTCACGGTCTGGCTTCTAAGCCCTTACAACGCTCTCCTAACGCATTTCTGCCCGTAGCTTCGGTATTGTGTTTTAGTCCCGTTGAATTATCGGCACAAAGTCTCTCGACTAGTGAGCTATTACGCACTCTTTAAACGGTGGCTGCTTCTAAGCCAACATCCTAGCTGTTTAAGAAACTTCACAACCTTTCTCACTTAACACAATTTTGGGACCTTAGCTGACGATCTGGGTTGTTCCCCTCGCGTGCATCGACGTTATCACCGATGTACCGACTGCATAGTAATACATGATAGTATTCGGAGTTTGATTATAGTCAGTACGGCTAGGCGCCGCCATTCCATATTCAGTGCTCTACCCCCATCATTTAACACTACACGCTAGCCCTAAAGCTATTTCGGAGAGAACCAGCTATCTCCAAGTTCGATTGGAATTTCACCCCTACCCACAAGTCATCCGGGCACTTTTTAGCGTACTGCGGTTCGGTCCTCCACTTAGTGTTACCTAAGTTTCAACCTGCTCATGGGTAGATCACCTGGTTTCGGGTCTATATCAACATACTAAATCGCCCTATTCAGACTCGATTTCTCTACGGCTTCGCTTTATTCTACTTAACCTCGCATGTTGACATAACTCGCCGGTCCATTCTGCAAGATGTACGCCATCACCCATTAACGGGCTCTGACTAACTGTAAGTAATTGGTTTCAGAATCTATTTCACTCCCCTCCCGGGGTTCTTTTCACCTTTCCCTCACGGTACTAGTTCACTATCGGTGTCTGGTTAGTATTTAGCCTTACCGGGTGGTCCCGGCAAATTCAGACAGGGTTTCACGTGCCCCGCCCTACTCAGGATACTGCTAGGAGATTTATACATTTCGCTTACGGGAATTTCACCCTCTATGTTTAAGCGTTCCAACTTATTCTGCTATGTACAAATTCATTAATCCATGTCGCAGTCCTACAACCCCAACAACATGTGTTGGTTTGGGCTCTTCCCCGTTCGCTCGCCACTACTTAGGGAATCATTCTTTATTTTCTCTTCCTGCTGCTACTGAGATGTTTCAATTCACAGCGTGTCTCTTCATTCGACTATGAATTCATCGATATGATAATTGAGGATTAGCTCAATTAGGTTTCCCCATTCGGAAATCCCCGGATAACAGCTTATTTCCAGCTAACCGAGGCTTATCGCAGGTAATCACGTCCTTCATCGACTTCCAGACCCAAGGCATCCACCAAAAACTCTTGCTTGTTT","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40311","NCBI_taxonomy_name":"Mycoplasma hominis","NCBI_taxonomy_id":"2098"}}}},"ARO_accession":"3004176","ARO_id":"41327","ARO_name":"Mycoplasma hominis 23S rRNA with mutation conferring resistance to macrolide antibiotics","CARD_short_name":"Mhom_23S_MAC","ARO_description":"Point mutation in the 23S rRNA of Mycoplasma hominis shown to confer resistance to macrolide type antibiotics.","ARO_category":{"41251":{"category_aro_accession":"3004125","category_aro_cvterm_id":"41251","category_aro_name":"23S rRNA with mutation conferring resistance to macrolide antibiotics","category_aro_description":"Nucleotide point mutations in the 23S rRNA subunit may confer resistance to macrolide antibiotics.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35974":{"category_aro_accession":"0000057","category_aro_cvterm_id":"35974","category_aro_name":"telithromycin","category_aro_description":"Telithromycin is a semi-synthetic derivative of erythromycin. It is a 14-membered macrolide and is the first ketolide antibiotic to be used in clinics. Telithromycin binds the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"35982":{"category_aro_accession":"0000065","category_aro_cvterm_id":"35982","category_aro_name":"clarithromycin","category_aro_description":"Clarithromycin is a methyl derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome and is used to treat pharyngitis, tonsillitis, acute maxillary sinusitis, acute bacterial exacerbation of chronic bronchitis, pneumonia (especially atypical pneumonias associated with Chlamydia pneumoniae or TWAR), and skin structure infections.","category_aro_class_name":"Antibiotic"},"36284":{"category_aro_accession":"3000145","category_aro_cvterm_id":"36284","category_aro_name":"tylosin","category_aro_description":"Tylosin is a 16-membered macrolide, naturally produced by Streptomyces fradiae. It interacts with the bacterial ribosome 50S subunit to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"36295":{"category_aro_accession":"3000156","category_aro_cvterm_id":"36295","category_aro_name":"spiramycin","category_aro_description":"Spiramycin is a 16-membered macrolide and is natural product produced by Streptomyces ambofaciens. It binds to the 50S subunit of bacterial ribosomes and inhibits peptidyl transfer activity to disrupt protein synthesis.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2831":{"model_id":"2831","model_name":"rpoB2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"2200"}},"model_sequences":{"sequence":{"4176":{"protein_sequence":{"accession":"BAD59497.1","sequence":"MLEGRIVTVSSRTESPLAAPGVPGAPRRLSFARIREPLAVPGLLDIQTESFGWLIGAPDWCARAAARGTEPVAGLAEVLAEISPIEDFAGTMSLTLSDPRFEEVKASVEECKDKDLTYAAPWFVTAEFVNNNTGEIKSQTVFMGDFPMMTAHGTFVVNGTERVVVSQLVRSPGVYFDHAIDKGSEKDVHSARVIPSRGAWLEFDVDKRDTLGVRIDRKRRQPVTVLLKALGWSAERIAERFGFAPLIMASLAKDNVAGTDDALLEIHRKLRPGEPPTKESAQNLLANLFFTEKRYDLARVGRYKIDKKLGLRAPGAPRVLTEDDIAATIEYLVRLHAGERTMIAPGGVEVPVEVDDIDHFGNRRVRTVGELIQNQIRVGLSRMERVVRERMTTQDVEAITPQSLMNIRPVVAAMKEFFGTSQLSQFMDQRNPLASLTNKRRLSALGPGGLSRERAGLEVRDVHYSHYGRMCPIETPEGPNIGLMGYLSVYARVNPFGFVETPYRRVVDGRVTDEVDYLTADEEDRHVVAQANEPLDAEGRFLAARIPVRRKNSEVELVDSAAVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGANMQRQAVPLIRSEAPIVGTGMELRAAVDAGDVVVNEKAGVVEEVSADYVTVMADDGTRKSYRMRKFNRSNQGTCSNQRPIVDEGQRVEAGQVLADGPCTENGEMALGKNLLVAIMPWEGHNYEDAIILSQRLVEQDVLTSIHIEEHEIDARDTKLGAEEITRDIPNVSDEVLADLDERGIVRIGAEVRDGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDDDLPPGVNELVRVYVAQKRKIQDGDKLAGRHGNKGVIGKILPTEDMPFLPDGTPVDIILNTHGVPRRMNIGQILETHLGWIGKAGWKVEGNPEWAKDLPEEMWEAPADSNIATPVFDGAREEELTGLLGSTLPNRDGERMVDDNGKAVLFDGRSGEPFPYPVAVGYMYILKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMECWAMQAYGAAYTLQELLTIKSDDVVGRVKVYEAIVKGDNIPEPGVPESFKVLLKELQALCLNVEVLSAGAAVELAHGVDDDHERTAANLGINLSRAESITETELSG"},"dna_sequence":{"accession":"AP006618.1","fmin":"4835199","fmax":"4838688","strand":"+","sequence":"GTGCTGGAAGGACGCATCGTGACAGTCTCGAGTCGGACCGAGTCCCCGCTCGCCGCGCCCGGAGTCCCGGGTGCGCCCCGGCGGCTCTCGTTCGCCAGAATCCGCGAGCCCCTGGCGGTTCCGGGCCTGCTGGACATTCAGACCGAATCGTTCGGGTGGCTGATCGGCGCACCCGACTGGTGCGCCCGCGCGGCAGCCCGCGGGACGGAACCGGTCGCCGGGCTGGCCGAGGTGCTCGCCGAGATCAGCCCCATCGAGGACTTCGCGGGCACGATGTCGCTGACGTTGTCCGATCCGCGGTTCGAGGAGGTCAAGGCCTCCGTCGAGGAGTGCAAGGACAAGGATCTGACCTATGCCGCGCCGTGGTTCGTCACGGCGGAATTCGTGAACAACAACACCGGCGAGATCAAGAGCCAGACCGTTTTCATGGGTGATTTCCCCATGATGACCGCGCACGGGACATTCGTCGTCAACGGCACCGAACGGGTGGTCGTGTCGCAACTGGTGCGCTCGCCGGGCGTGTACTTCGACCACGCGATCGACAAGGGTTCGGAGAAGGACGTGCACAGCGCGCGGGTGATCCCGTCGCGCGGTGCCTGGCTGGAGTTCGACGTCGACAAGCGCGACACCCTGGGCGTGCGCATCGACCGCAAGCGCCGTCAGCCGGTAACGGTGCTGCTCAAGGCGCTGGGCTGGAGTGCGGAGCGAATCGCCGAGCGATTCGGGTTCGCCCCGCTGATCATGGCCTCGCTGGCCAAGGACAACGTGGCGGGCACCGACGACGCTTTGCTCGAGATCCATCGCAAGCTGCGTCCGGGCGAGCCGCCGACCAAGGAGTCGGCACAGAACCTGCTGGCAAATCTGTTCTTCACCGAGAAGCGCTACGACCTGGCGCGGGTGGGCCGTTACAAGATCGACAAGAAGCTCGGGCTGCGCGCTCCGGGGGCACCGCGGGTGCTCACCGAGGACGACATCGCGGCCACCATCGAGTACCTGGTGCGCCTGCACGCCGGGGAGAGGACGATGATCGCGCCCGGCGGGGTCGAGGTGCCGGTGGAGGTCGACGACATCGACCATTTCGGTAACCGCCGGGTGCGCACCGTGGGTGAGCTGATCCAGAACCAGATCCGCGTGGGTCTGTCCCGGATGGAACGGGTGGTGCGGGAGCGCATGACCACCCAGGACGTCGAGGCGATCACGCCGCAGTCGCTGATGAACATCCGCCCGGTGGTCGCGGCGATGAAGGAGTTCTTCGGCACCTCGCAGCTGTCGCAGTTCATGGACCAGCGCAACCCGCTGGCGAGCCTGACCAACAAGCGGCGGCTGTCCGCGCTCGGGCCGGGCGGGCTCTCGCGCGAACGGGCCGGCTTGGAGGTCCGCGACGTGCACTACAGCCACTACGGCCGGATGTGCCCGATCGAGACGCCGGAGGGGCCGAACATCGGCCTGATGGGGTACCTGTCGGTGTACGCGCGGGTCAACCCGTTCGGTTTCGTCGAGACCCCCTACCGGCGGGTGGTGGACGGCCGGGTCACCGACGAGGTCGATTACCTCACCGCCGACGAGGAGGACCGGCACGTGGTGGCCCAGGCGAACGAACCGCTGGACGCCGAGGGCCGCTTCCTGGCCGCGCGAATCCCGGTGCGCCGGAAGAACTCCGAGGTGGAACTCGTCGATTCCGCCGCGGTGGATTACATGGATGTGTCGCCGCGGCAGATGGTGTCGGTGGCGACGGCGATGATTCCGTTCCTCGAGCATGATGATGCCAACCGTGCGCTGATGGGTGCGAATATGCAGCGTCAGGCGGTGCCGTTGATTCGGTCGGAGGCGCCGATCGTGGGTACCGGTATGGAGCTGCGTGCGGCGGTGGATGCCGGTGATGTGGTGGTGAACGAGAAGGCCGGTGTGGTCGAGGAGGTTTCGGCCGATTACGTCACGGTGATGGCCGATGACGGGACTCGTAAGTCGTATCGGATGCGGAAGTTCAACCGGTCGAATCAGGGGACGTGTTCGAATCAGCGGCCGATCGTGGACGAGGGTCAGCGGGTCGAGGCCGGGCAGGTGTTGGCTGATGGGCCGTGCACCGAGAACGGTGAGATGGCGCTGGGTAAGAACCTGTTGGTGGCGATCATGCCGTGGGAGGGGCACAACTACGAGGACGCGATCATCCTGTCGCAGCGGTTGGTGGAGCAGGATGTGTTGACCTCGATCCATATCGAGGAGCACGAGATCGATGCTCGTGACACCAAGCTCGGTGCCGAGGAGATCACTCGCGACATTCCGAATGTCTCCGATGAGGTGTTGGCGGATCTGGACGAGCGTGGCATCGTGCGGATCGGTGCGGAGGTGCGTGATGGTGACATCCTGGTCGGTAAGGTCACGCCCAAGGGTGAGACCGAGCTGACGCCGGAGGAGCGGTTGCTGCGGGCGATCTTCGGGGAGAAGGCGCGTGAGGTGCGTGATACCTCGTTGAAGGTGCCCCACGGTGAGTCGGGCAAGGTCATCGGGATCCGGGTGTTCTCTCGGGAGGACGATGACGATCTGCCGCCCGGTGTCAACGAGTTGGTGCGGGTGTATGTGGCGCAGAAGCGCAAGATCCAAGACGGTGACAAGCTGGCCGGTCGGCACGGGAACAAGGGTGTGATCGGCAAGATCCTGCCCACCGAGGACATGCCGTTCCTGCCCGATGGCACCCCGGTCGACATCATCCTCAACACCCACGGTGTGCCGCGGCGTATGAACATCGGCCAGATCCTGGAAACCCACCTCGGCTGGATCGGCAAAGCCGGCTGGAAGGTCGAGGGCAACCCCGAGTGGGCCAAGGATCTGCCGGAGGAGATGTGGGAGGCCCCCGCGGACTCCAACATCGCGACTCCGGTGTTCGACGGTGCCCGCGAGGAGGAGCTGACGGGTCTGCTGGGCTCGACGCTGCCCAACCGTGACGGTGAGCGGATGGTCGACGACAACGGCAAGGCCGTGCTGTTCGACGGTCGTTCCGGTGAGCCGTTCCCGTACCCGGTGGCGGTGGGCTACATGTACATCCTGAAGCTGCACCACCTGGTCGACGACAAGATCCACGCTCGCTCCACCGGCCCGTACTCGATGATCACCCAGCAGCCGCTCGGTGGTAAGGCCCAGTTCGGTGGCCAGCGCTTCGGTGAGATGGAGTGCTGGGCGATGCAGGCCTACGGCGCGGCCTACACCCTGCAGGAACTGCTCACGATCAAGTCCGACGACGTCGTCGGCCGCGTGAAGGTCTACGAGGCGATCGTCAAGGGCGACAACATCCCGGAACCCGGTGTGCCGGAATCGTTCAAGGTGTTGTTGAAGGAACTCCAGGCACTGTGCCTCAACGTCGAGGTGCTGTCCGCCGGTGCCGCGGTCGAACTGGCGCACGGGGTCGACGACGATCACGAGCGGACGGCCGCGAACCTCGGCATCAACCTGTCCCGCGCCGAATCCATCACGGAGACCGAGCTGTCCGGGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41346","NCBI_taxonomy_name":"Nocardia farcinica IFM 10152","NCBI_taxonomy_id":"247156"}}}},"ARO_accession":"3000501","ARO_id":"36640","ARO_name":"rpoB2","CARD_short_name":"rpoB2","ARO_description":"Due to gene duplication, the genomes of Nocardia species include both rifampin-sensitive beta-subunit of RNA polymerase (rpoB) and rifampin-resistant beta-subunit of RNA polymerase (rpoB2) genes, with ~88% similarity between the two gene products. Expression of the rpoB2 variant results in replacement of rifampin sensitivity with rifampin resistance.","ARO_category":{"36349":{"category_aro_accession":"3000210","category_aro_cvterm_id":"36349","category_aro_name":"rifamycin-resistant beta-subunit of RNA polymerase (rpoB)","category_aro_description":"Rifampin resistant RNA polymerases include amino acids substitutions which disrupt the affinity of rifampin for its binding site. These mutations are frequently concentrated in the rif I region of the beta-subunit and most often involve amino acids which make direct interactions with rifampin. However, mutations which also confer resistance can occur outside this region and may involve amino acids which do not directly make contact with rifampin.","category_aro_class_name":"AMR Gene Family"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36656":{"category_aro_accession":"3000517","category_aro_cvterm_id":"36656","category_aro_name":"rifaximin","category_aro_description":"Rifaximin is a semi-synthetic rifamycin used to treat traveller's diarrhea. Rifaximin inhibits RNA synthesis by binding to the beta subunit of bacterial RNA polymerase.","category_aro_class_name":"Antibiotic"},"36669":{"category_aro_accession":"3000530","category_aro_cvterm_id":"36669","category_aro_name":"rifabutin","category_aro_description":"Rifabutin is a semisynthetic rifamycin used in tuberculosis therapy. It inhibits DNA-dependent RNA synthesis.","category_aro_class_name":"Antibiotic"},"36673":{"category_aro_accession":"3000534","category_aro_cvterm_id":"36673","category_aro_name":"rifapentine","category_aro_description":"Rifapentine is a semisynthetic rifamycin that inhibits DNA-dependent RNA synthesis. It is often used in the treatment of tuberculosis and leprosy.","category_aro_class_name":"Antibiotic"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2843":{"model_id":"2843","model_name":"Escherichia coli ampC beta-lactamase","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"5393":{"protein_sequence":{"accession":"AAC77110.1","sequence":"MFKTTLCALLITASCSTFAAPQQINDIVHRTITPLIEQQKIPGMAVAVIYQGKPYYFTWGYADIAKKQPVTQQTLFELGSVSKTFTGVLGGDAIARGEIKLSDPTTKYWPELTAKQWNGITLLHLATYTAGGLPLQVPDEVKSSSDLLRFYQNWQPAWAPGTQRLYANSSIGLFGALAVKPSGLSFEQAMQTRVFQPLKLNHTWINVPPAEEKNYAWGYREGKAVHVSPGALDAEAYGVKSTIEDMARWVQSNLKPLDINEKTLQQGIQLAQSRYWQTGDMYQGLGWEMLDWPVNPDSIINGSDNKIALAARPVKAITPPTPAVRASWVHKTGATGGFGSYVAFIPEKELGIVMLANKNYPNPARVDAAWQILNALQ"},"dna_sequence":{"accession":"U00096.3","fmin":"4377810","fmax":"4378944","strand":"-","sequence":"ATGTTCAAAACGACGCTCTGCGCCTTATTAATTACCGCCTCTTGCTCCACATTTGCTGCCCCTCAACAAATCAACGATATTGTGCATCGCACAATTACCCCGCTTATAGAGCAACAAAAGATCCCGGGTATGGCGGTGGCGGTAATTTATCAGGGTAAACCTTATTACTTTACCTGGGGCTATGCGGACATCGCCAAAAAGCAGCCCGTCACACAGCAAACGTTGTTTGAGTTAGGTTCGGTCAGCAAAACATTTACTGGCGTGCTTGGTGGCGACGCTATTGCTCGAGGGGAAATCAAGTTAAGCGATCCCACAACAAAATACTGGCCTGAACTTACCGCTAAACAGTGGAATGGGATCACACTATTACATCTCGCAACCTACACTGCTGGCGGCCTGCCATTGCAGGTGCCGGATGAGGTGAAATCCTCAAGCGACTTGCTGCGCTTCTATCAAAACTGGCAGCCTGCATGGGCTCCAGGAACACAACGTCTGTATGCCAACTCCAGTATCGGTTTGTTCGGCGCACTGGCTGTGAAGCCGTCTGGTTTGAGTTTTGAGCAGGCGATGCAAACTCGTGTCTTCCAGCCACTCAAACTCAACCATACGTGGATTAATGTACCGCCCGCAGAAGAAAAGAATTACGCCTGGGGATATCGCGAAGGTAAGGCAGTGCATGTTTCGCCTGGGGCGTTAGATGCTGAAGCTTATGGTGTGAAGTCGACCATTGAAGATATGGCCCGCTGGGTGCAAAGCAATTTAAAACCCCTTGATATCAATGAGAAAACGCTTCAACAAGGGATACAACTGGCACAATCTCGCTACTGGCAAACCGGCGATATGTATCAGGGCCTGGGCTGGGAAATGCTGGACTGGCCGGTAAATCCTGACAGCATCATTAACGGCAGTGACAATAAAATTGCACTGGCAGCACGCCCCGTAAAAGCGATTACGCCCCCAACTCCTGCAGTACGCGCATCATGGGTACATAAAACAGGGGCGACCGGCGGATTTGGTAGCTATGTCGCGTTTATTCCAGAAAAAGAGCTGGGTATCGTGATGCTGGCAAACAAAAACTATCCCAATCCAGCGAGAGTCGACGCCGCCTGGCAGATTCTTAACGCTCTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36849","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. MG1655","NCBI_taxonomy_id":"511145"}}}},"ARO_accession":"3004290","ARO_id":"41454","ARO_name":"Escherichia coli ampC beta-lactamase","CARD_short_name":"Ecol_ampC_BLA","ARO_description":"A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics.","ARO_category":{"41396":{"category_aro_accession":"3004232","category_aro_cvterm_id":"41396","category_aro_name":"ampC-type beta-lactamase","category_aro_description":"AmpC beta-lactamases are clinically important class C beta-lactamase enzymes which confer resistance to cephalosporins and penicillin-like antibiotics. AmpC beta-lactamases are typically found in Enterobacteriaceae, and were described in Escherichia coli in 1940 as the first reported enzymatic deactivation of penicillin. The name AmpC connects these enzymes functionally across many species, however these enzymes are generally unnamed and not phylogenetically related.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2846":{"model_id":"2846","model_name":"BUT-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4198":{"protein_sequence":{"accession":"AAN17791.1","sequence":"MCRTLCHVTYGRFSMMKKTLCCALVLSASFSAFAAQKTLSDKQLEEAVNQTLKPMITAQAIPGMAVAVIYQGKPHYFTYGVADIAKNQPVTTQTIFELGSVSKTFTGVLGGDIVARGEVKLSDPAMKYWPELTGKQWQGITLLDLATYTAGGLPLQVPDEVDNQAALLKFYQNWQPDWAPGTRRQYANSSIGLFGALAVKPSGMTFNDAMRQRVLQPLNLKHTWLTVPASEENHYAWGYRDGKAMHVGPGMLDTEAYGVKSTIEDMASWVQYNMNPQQVKQPTLQKGLEIAQSRYWRSGSMYQGLGWEMLNWPVAAATVINGSDNKVALAASPVTAIEPPVAPVKASLVHKTGSTNGFGAYVAFIPEKQIGIVMLANKMYPNTERVKAANTLLNTLQ"},"dna_sequence":{"accession":"AF440406.1","fmin":"959","fmax":"2153","strand":"+","sequence":"ATGTGCCGGACCCTCTGTCATGTTACTTATGGAAGATTTTCAATGATGAAAAAAACACTCTGCTGCGCGCTGGTTCTGAGCGCCTCTTTCTCCGCCTTTGCTGCACAAAAAACATTGAGTGACAAACAGTTAGAAGAGGCTGTCAATCAAACGCTTAAACCGATGATTACAGCCCAGGCCATTCCCGGCATGGCGGTGGCGGTGATTTATCAGGGCAAGCCGCACTACTTTACCTACGGCGTGGCCGACATCGCGAAAAATCAGCCGGTGACGACACAGACGATTTTTGAGCTGGGCTCCGTGAGTAAAACTTTCACCGGCGTGCTGGGCGGCGATATCGTGGCGCGCGGGGAAGTGAAGCTGAGTGACCCGGCGATGAAATACTGGCCAGAACTGACGGGCAAGCAGTGGCAGGGCATCACGTTGCTGGATCTGGCGACCTACACCGCCGGCGGCTTGCCGTTGCAGGTGCCGGATGAGGTCGATAATCAGGCCGCGCTGCTGAAGTTTTACCAGAACTGGCAGCCGGACTGGGCGCCGGGAACCCGTCGTCAGTACGCCAACTCGAGCATTGGCCTGTTTGGTGCGTTGGCAGTGAAACCGTCCGGGATGACGTTTAACGATGCGATGCGCCAGCGCGTTCTGCAACCGCTGAACCTGAAACATACCTGGCTCACCGTTCCGGCCAGTGAAGAAAATCATTACGCCTGGGGCTATCGTGACGGCAAAGCCATGCACGTCGGGCCGGGCATGCTGGATACCGAAGCCTACGGTGTCAAATCCACCATCGAAGATATGGCGAGCTGGGTGCAATACAACATGAACCCGCAGCAGGTGAAACAGCCGACGCTGCAAAAAGGGCTGGAGATTGCGCAGTCGCGCTACTGGCGCAGCGGCAGTATGTATCAGGGCTTAGGCTGGGAAATGCTGAACTGGCCGGTTGCGGCGGCGACCGTCATTAACGGCAGCGATAACAAAGTGGCGCTGGCGGCTTCGCCCGTGACGGCCATTGAACCGCCGGTTGCGCCGGTGAAAGCTTCTCTGGTGCATAAAACCGGGTCGACCAACGGCTTCGGCGCGTACGTGGCGTTCATTCCTGAAAAACAAATCGGCATCGTGATGCTGGCTAACAAAATGTATCCGAATACCGAGCGGGTTAAAGCGGCAAATACTCTTCTCAACACGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41461","NCBI_taxonomy_name":"Buttiauxella agrestis","NCBI_taxonomy_id":"82977"}}}},"ARO_accession":"3004294","ARO_id":"41460","ARO_name":"BUT-1","CARD_short_name":"BUT-1","ARO_description":"A chromosome-encoded  class C cephalosporinase and penicillinase from Buttiauxella spp. shown clinically to confer resistance to beta-lactam antibiotics. Described by Fihman et al. 2002.","ARO_category":{"41459":{"category_aro_accession":"3004293","category_aro_cvterm_id":"41459","category_aro_name":"BUT beta-lactamase","category_aro_description":"A class C beta-lactamase family of chromosome-encoded antibiotic resistance genes originally described from Buttiauxella spp.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2343":{"model_id":"2343","model_name":"ADC-13","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"5304":{"protein_sequence":{"accession":"CAK95248.2","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEIYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKTKGTISFKDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPGLSLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLKFINANLNPQKYPADIQRAINETHQGFYQVGTMYQALGWEEFSYPAPLQTLLDSNSEQIVMKPNKVTAISKEPSVKMFHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"AM283528.2","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTTGTAGATCAAAATTTTAAACCGTTATTAGAAAAATATGATGTGCCGGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATTTATTATGGTCTACAATCCGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTAGGTTCAGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAACAAAAGGAACAATCTCTTTTAAAGACACACCCGGAAAATATTGGAAAGAGCTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTTGCTACCTATACAAGTGGGAACCTTGCTTTGCAATTTCCAGATGAAGTACAAACAGATCAACAAGTTTTAACTTTTTTCAAAGATTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAAGTTGTTGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGGCCTTAGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAATCAAGAAAATCAGCCAATTCGTGTTAACCCTGGTCCGCTAGATGCTCCAGCATACGGCGTTAAATCGACACTACCAGACATGCTTAAGTTTATTAATGCCAACCTAAATCCACAAAAATATCCAGCAGATATTCAACGTGCAATTAATGAAACACATCAAGGTTTCTATCAAGTCGGCACCATGTATCAAGCATTAGGTTGGGAAGAATTTTCTTATCCAGCGCCTTTACAAACTTTATTAGACAGTAATTCAGAACAAATTGTGATGAAGCCTAATAAAGTGACTGCTATTTCAAAAGAACCTTCAGTTAAGATGTTCCACAAAACTGGCTCAACCAATGGTTTCGGAACATATGTCGTGTTCATTCCTAAAGAAAATATTGGCTTAGTCATGTTGACCAATAAACGTATTCCAAATGAAGAACGCATTAAGGCAGCGTATGCAGTGTTAAACGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3003857","ARO_id":"40556","ARO_name":"ADC-13","CARD_short_name":"ADC-13","ARO_description":"ADC-13 is a beta-lactamase found in Acinetobacter pittii.","ARO_category":{"40543":{"category_aro_accession":"3003846","category_aro_cvterm_id":"40543","category_aro_name":"ADC beta-lactamase without carbapenemase activity","category_aro_description":"ADC beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases with extended-spectrum resistance to cephalosporins but not to carbapenems. ADC beta-lactamases are found in Acinetobacter sp. and Oligella urethralis.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2344":{"model_id":"2344","model_name":"ADC-14","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"5306":{"protein_sequence":{"accession":"CAK95247.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEIYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKTKGTISFKDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPGLSLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLKFINANLNPQKYPADIQRAINETHQGFYQVGTMYQALGWEEFSYPAPLQTLLDSNSEQIVMKPNKVTAISKEPSVKMFHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERFKAAYAVLNAIKK"},"dna_sequence":{"accession":"AM283527.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTTGTAGATCAAAATTTTAAACCGTTATTAGAAAAATATGATGTGCCGGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATTTATTATGGTCTACAATCCGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTAGGTTCAGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAACAAAAGGAACAATCTCTTTTAAAGACACACCCGGAAAATATTGGAAAGAGCTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAGCTTGCTACCTATACAAGTGGGAACCTTGCTTTGCAATTTCCAGATGAAGTACAAACAGATCAACAAGTTTTAACTTTTTTCAAAGATTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAAGTTGTTGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGGCCTTAGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAATCAAGAAAATCAGCCAATTCGTGTTAACCCTGGTCCGCTAGATGCTCCAGCATACGGCGTTAAATCGACACTACCAGACATGCTTAAGTTTATTAATGCCAACCTAAATCCACAAAAATATCCAGCAGATATTCAACGTGCAATTAATGAAACACATCAAGGTTTCTATCAAGTCGGCACCATGTATCAAGCATTAGGTTGGGAAGAATTTTCTTATCCAGCGCCTTTACAAACTTTATTAGACAGTAATTCAGAACAAATTGTGATGAAGCCTAATAAAGTGACCGCTATTTCAAAAGAACCTTCAGTTAAGATGTTCCACAAAACTGGCTCAACCAATGGTTTCGGAACATATGTCGTGTTCATTCCTAAAGAAAATATTGGCTTAGTCATGTTGACCAATAAACGTATTCCAAATGAAGAACGCTTTAAGGCAGCGTATGCAGTGTTAAACGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3003858","ARO_id":"40557","ARO_name":"ADC-14","CARD_short_name":"ADC-14","ARO_description":"ADC-14 is a beta-lactamase found in Acinetobacter pittii.","ARO_category":{"40543":{"category_aro_accession":"3003846","category_aro_cvterm_id":"40543","category_aro_name":"ADC beta-lactamase without carbapenemase activity","category_aro_description":"ADC beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases with extended-spectrum resistance to cephalosporins but not to carbapenems. ADC beta-lactamases are found in Acinetobacter sp. and Oligella urethralis.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2345":{"model_id":"2345","model_name":"ADC-15","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"5360":{"protein_sequence":{"accession":"CAK95246.1","sequence":"MRFKKISCLLLSPLFIFNTSIYAGNTPKDQEIKKLVDQNFKPLLDKYDVPGMAVGVIQNNKKYETYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKTKGTISFKDTTGKYWKELKNTPIDQVNLFQLATYTSGNLGLQFPDEVQTDQQVLTFFKDWKPKNSIGEYRQYSNPSIGLFGKVVALSMNKPFDQLLEKTIFPDLGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLKFINANLNPQKYPKDIQRAINETHQGFYQVGTMYQALGWEEFSYPAPLQTLLDSNSEQIVMKPNKVTAISKEPSVKIFHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"AM283526.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAATACCTCAATTTATGCAGGGAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCTTTATTAGATAAATATGATGTGCCGGGTATGGCCGTGGGCGTTATTCAGAATAATAAAAAATATGAAACGTATTACGGCCTACAATCCGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTCGGTTCAGTTAGTAAATTATTTACCGCTACAGCAGGTGGATATGCCAAAACAAAAGGAACAATTTCTTTTAAAGACACAACCGGAAAATATTGGAAAGAATTAAAAAACACACCAATTGACCAAGTTAACTTATTTCAACTTGCTACTTATACGAGTGGCAACCTTGGCTTACAGTTTCCAGATGAAGTCCAAACAGATCAGCAAGTTTTAACTTTTTTCAAAGACTGGAAGCCTAAAAACTCAATCGGTGAATATCGACAATATTCAAATCCAAGCATTGGTTTATTTGGAAAAGTTGTTGCATTGTCTATGAATAAACCTTTCGACCAACTCTTAGAAAAAACAATTTTTCCAGATCTTGGCTTAAAACATAGCTATGTAAATGTACCGAAGACCCAGATGCAAAACTATGCTTTTGGCTATAATCAAGAAAATCAGCCAATTCGTGTTAACCCTGGTCCGTTAGATGCACCTGCGTACGGCGTCAAATCGACACTACCCGATATGCTTAAGTTTATTAATGCCAACCTCAACCCACAGAAATATCCGAAAGATATTCAACGTGCAATTAATGAAACACATCAGGGTTTCTATCAAGTCGGCACCATGTATCAGGCACTTGGTTGGGAAGAATTTTCTTATCCAGCGCCTTTACAAACTTTATTAGACAGTAATTCAGAACAAATTGTGATGAAGCCTAATAAAGTGACTGCCATTTCAAAAGAACCTTCAGTTAAGATATTCCACAAAACTGGTTCAACCAATGGTTTCGGAACTTATGTCGTGTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTGACCAATAAACGTATTCCAAATGAAGAACGCATTAAGGCAGCGTATGCGGTGTTAAATGCAATAAAAAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3003859","ARO_id":"40558","ARO_name":"ADC-15","CARD_short_name":"ADC-15","ARO_description":"ADC-15 is a beta-lactamase found in Acinetobacter pittii.","ARO_category":{"40543":{"category_aro_accession":"3003846","category_aro_cvterm_id":"40543","category_aro_name":"ADC beta-lactamase without carbapenemase activity","category_aro_description":"ADC beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases with extended-spectrum resistance to cephalosporins but not to carbapenems. ADC beta-lactamases are found in Acinetobacter sp. and Oligella urethralis.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2347":{"model_id":"2347","model_name":"ADC-17","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"5419":{"protein_sequence":{"accession":"CAK95244.1","sequence":"MRFKKISCLLLPPLFIFSTSIYAGNTPKDREIKKLVDQNFKPLLDKYDVPGMAVGVIQNNKKYETYYGLQSVQDKKAVSSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDRQVLTFFKDWKPKNSIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPDLGLKHSYVNVPKTQMQNYAFGYNRENQPIRVNPGPLDAPAYGVKSTLPDMLKFINANLNTQKYPKDIQRAINETHQGFYQVGTMYQALGWEEFSYPAPLQTLLDSNSEQIVMKPNKVTAISKEPSVKMFHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"AM283524.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGCTTACTTTTACCTCCTCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCGAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCTTTGTTAGATAAATATGATGTGCCGGGTATGGCCGTGGGCGTTATTCAGAATAATAAAAAATATGAAACGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAGTAGCAGTACCATTTTTGAACTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATTTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAACACGCCGATTGACCAAGTTAACTTACTTCAACTCGCAACGTATACAAGTGGTAACCTTGCCTTGCAGTTCCCAGATGAAGTACAAACAGACCGACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACTCAATCGGTGAATATAGACAATATTCAAATCCAAGCATTGGTTTATTTGGAAAAGTTGTGGCATTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCAGATCTTGGCCTAAAACATAGCTATGTAAATGTTCCTAAAACTCAGATGCAAAACTATGCTTTTGGCTATAACCGAGAAAATCAGCCAATTCGTGTTAACCCTGGTCCGCTAGATGCTCCAGCATATGGGGTTAAATCGACGCTACCCGATATGCTTAAGTTTATTAATGCCAACCTCAACACACAGAAATATCCGAAAGATATTCAACGTGCAATTAATGAAACACATCAGGGTTTCTATCAAGTCGGCACCATGTATCAGGCACTTGGTTGGGAAGAATTTTCTTATCCAGCGCCTTTACAAACTTTATTAGACAGTAATTCAGAACAAATTGTGATGAAGCCTAATAAAGTGACTGCCATTTCAAAAGAACCTTCAGTTAAGATGTTCCACAAAACTGGTTCAACCAATGGTTTCGGAACTTATGTCGTGTTCATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAACGCATTAAGGCAGCGTATGCCGTGTTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3003861","ARO_id":"40560","ARO_name":"ADC-17","CARD_short_name":"ADC-17","ARO_description":"ADC-17 is a beta-lactamase found in Acinetobacter pittii.","ARO_category":{"40543":{"category_aro_accession":"3003846","category_aro_cvterm_id":"40543","category_aro_name":"ADC beta-lactamase without carbapenemase activity","category_aro_description":"ADC beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases with extended-spectrum resistance to cephalosporins but not to carbapenems. ADC beta-lactamases are found in Acinetobacter sp. and Oligella urethralis.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2346":{"model_id":"2346","model_name":"ADC-16","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"5364":{"protein_sequence":{"accession":"CAK95245.1","sequence":"MRFKKISCLLLPPLFIFSSSIYAGNTPKEQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSNTIFELGSVSKLFTATAGGYAKTKGTISFNDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVKTDQQVLTFFKEWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPDLGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFINANLNPQKYPANIQRAINETHQGFYQVGTMYQALGWEEFSYPALLQTLLDSNSEQIVMKPNKVTAISKEPSVKMFHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"AM283525.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGCTTACTTTTACCGCCTCTTTTTATTTTTAGTAGCTCAATTTATGCGGGTAATACACCAAAAGAGCAAGAGATCAAAAAACTGGTTGATCAAAATTTTAAGCCTTTATTAGAAAAATATGATGTGCCCGGTATGGCTGTGGGCGTTATTCAAAATAACAAAAAGTATGAAATGTATTATGGTCTACAATCCGTTCAAGATAAAAAAGCCGTTAATAGCAATACCATTTTTGAGCTAGGCTCGGTCAGTAAATTATTTACCGCTACAGCAGGCGGATATGCCAAAACAAAAGGAACAATCTCTTTTAATGACACGCCTGGAAAATATTGGAAAGAACTAAAAAATACACCGATTGATCAAGTGAATTTACTTCAACTTGCGACATATACCAGTGGCAACCTTGCCTTGCAATTTCCAGATGAAGTAAAAACAGATCAGCAAGTTTTAACGTTTTTCAAAGAATGGAAACCTAAAAACCCAATCGGTGAATATCGACAATATTCAAACCCAAGCATTGGTTTATTTGGAAAAGTTGTTGCTTTGTCTATGAATAAACCTTTTGACCAAGTCTTGGAAAAAACCATTTTTCCAGATCTTGGCTTAAAACATAGCTATGTAAATGTGCCTAAAACTCAAATGCAAAACTATGCATTTGGCTATAACCAAGAAAATCAGCCGATTCGCGTCAATCCTGGTCCACTCGATGCACCAGCATACGGCGTTAAATCTACCCTACCGGATATGCTGAGTTTTATTAATGCAAACCTAAATCCACAAAAATATCCAGCAAATATTCAACGTGCAATTAATGAAACACATCAAGGTTTCTACCAAGTCGGCACCATGTATCAAGCACTAGGTTGGGAAGAGTTCTCTTATCCAGCACTTTTACAAACTTTATTAGACAGTAATTCAGAACAAATCGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAACCTTCCGTTAAGATGTTCCACAAAACTGGATCGACTAACGGTTTTGGAACATATGTCGTGTTCATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACTAATAAACGTATTCCCAATGAAGAACGCATTAAAGCAGCTTATGCTGTGTTAAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3003860","ARO_id":"40559","ARO_name":"ADC-16","CARD_short_name":"ADC-16","ARO_description":"ADC-16 is a beta-lactamase found in Acinetobacter pittii.","ARO_category":{"40543":{"category_aro_accession":"3003846","category_aro_cvterm_id":"40543","category_aro_name":"ADC beta-lactamase without carbapenemase activity","category_aro_description":"ADC beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases with extended-spectrum resistance to cephalosporins but not to carbapenems. ADC beta-lactamases are found in Acinetobacter sp. and Oligella urethralis.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2357":{"model_id":"2357","model_name":"ADC-41","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"5292":{"protein_sequence":{"accession":"ACN62070.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLDKYDVPGMAVGVIQNNKKYETYYGLQSVQDKKAVSSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPGLGLKHSYVNVPKNQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLKFINANLNPQKYPADIQRAINETHQGFYQVGIMYQALGWEEFSYPAPLQTLLDSNSEQIVMKPNKVTAISKEPSVKMFHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"FJ744160.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCTTTATTAGATAAATATGATGTGCCGGGTATGGCCGTGGGCGTTATTCAGAATAATAAAAAATATGAAACGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAGTAGCAGTACCATTTTTGAACTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCAACGTATACAAGTGGTAACCTTGCCTTGCAGTTCCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAAGTTGTTGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGGCCTTGGCTTAAAACATAGCTATGTAAATGTACCGAAGAACCAGATGCAAAACTATGCTTTTGGCTATAATCAAGAAAATCAGCCAATTCGTGTTAACCCTGGTCCGCTAGATGCTCCAGCATACGGCGTCAAATCGACACTACCCGATATGCTTAAGTTTATTAATGCCAACCTAAATCCACAAAAATATCCAGCAGATATTCAACGTGCAATTAATGAAACACATCAAGGTTTCTATCAAGTCGGCATCATGTATCAAGCATTAGGTTGGGAAGAATTTTCTTATCCAGCGCCTTTACAAACTTTATTAGACAGTAATTCAGAACAAATTGTGATGAAGCCTAATAAAGTGACTGCCATTTCAAAAGAACCTTCAGTTAAGATGTTCCACAAAACTGGTTCAACCAATGGTTTCGGAACTTATGTCGTGTTCATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAACGCATTAAGGCAGCGTATGCCGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3003872","ARO_id":"40571","ARO_name":"ADC-41","CARD_short_name":"ADC-41","ARO_description":"ADC-41 is a beta-lactamase found in Acinetobacter pittii.","ARO_category":{"40543":{"category_aro_accession":"3003846","category_aro_cvterm_id":"40543","category_aro_name":"ADC beta-lactamase without carbapenemase activity","category_aro_description":"ADC beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases with extended-spectrum resistance to cephalosporins but not to carbapenems. ADC beta-lactamases are found in Acinetobacter sp. and Oligella urethralis.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2358":{"model_id":"2358","model_name":"ADC-42","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"5294":{"protein_sequence":{"accession":"ACN62071.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDREIKKLVDQNFKPLLDKYDVPGMAVGVIQNNKKYETYYGLQSVQDKKSVSSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTSGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKEWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPGLGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFINANINPQKYPKDTQRAINETHQGFYQVGTMYQALGWEEFSYPAPLQTLLDSNSEQIVMKPNKVTAISKEPSVKMFHKTGSTNGFGSYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"FJ744161.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCGAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCTTTATTAGATAAATATGATGTGCCGGGTATGGCCGTGGGCGTTATTCAGAATAATAAAAAATATGAAACGTATTATGGTCTTCAATCTGTTCAAGATAAAAAATCCGTAAGTAGCAGTACCATTTTTGAACTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGTCTGGTAAATATTGGAAAGAACTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCAACGTATACAAGTGGTAACCTTGCCTTGCAGTTCCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGAATGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAAGTTGTTGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGGCCTTGGCTTAAAACATAGCTATGTAAATGTACCGAAGACCCAGATGCAAAACTATGCTTTTGGCTATAATCAAGAAAATCAGCCAATTCGTGTTAACCCCGGTCCGCTAGATGCTCCAGCATACGGTGTTAAATCGACCTTACCTGATATGCTGAGTTTCATTAATGCCAATATAAATCCACAAAAATATCCGAAAGATACTCAACGTGCAATTAATGAAACACATCAAGGTTTCTACCAAGTCGGCACGATGTATCAGGCACTTGGTTGGGAAGAATTTTCTTATCCAGCGCCTTTACAAACTTTATTAGACAGTAATTCAGAGCAAATCGTGATGAAGCCTAATAAAGTGACTGCCATTTCCAAAGAACCTTCAGTTAAGATGTTCCACAAAACTGGCTCAACAAATGGCTTTGGATCTTATGTGGTGTTTATTCCAAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAACGCATTAAGGCAGCGTATGCAGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3003873","ARO_id":"40572","ARO_name":"ADC-42","CARD_short_name":"ADC-42","ARO_description":"ADC-42 is a beta-lactamase found in Acinetobacter pittii.","ARO_category":{"40543":{"category_aro_accession":"3003846","category_aro_cvterm_id":"40543","category_aro_name":"ADC beta-lactamase without carbapenemase activity","category_aro_description":"ADC beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases with extended-spectrum resistance to cephalosporins but not to carbapenems. ADC beta-lactamases are found in Acinetobacter sp. and Oligella urethralis.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2359":{"model_id":"2359","model_name":"ADC-43","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"5300":{"protein_sequence":{"accession":"ACN62072.1","sequence":"MRFKKISCLLLPPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLDKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPGLGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFINANLNPLKYPKDIQRAINETHKGFYQVGTMYQALGWEEFSYPAPLQTLLDSNSEQIVMKPNKVTAISKEPSVKMFHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"FJ744162.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGCTTACTTTTACCCCCTCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCTTTATTAGATAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTCGGTTCAGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAATTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCAACGTATACAAGTGGTAACCTTGCCTTGCAATTCCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAAGTTGTTGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGGCCTTGGCTTAAAACATAGCTATGTAAATGTTCCTAAAACTCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCAATTCGTGTTAACCCTGGTCCGCTAGATGCTCCTGCATACGGCGTTAAATCGACACTACCAGACATGCTGAGTTTTATTAATGCCAACCTCAACCCACTGAAATATCCGAAAGATATTCAACGTGCAATTAATGAAACACATAAAGGTTTCTATCAAGTCGGCACCATGTATCAAGCCTTGGGTTGGGAAGAATTTTCTTATCCAGCGCCTTTACAAACTTTATTAGACAGTAATTCAGAGCAAATCGTGATGAAGCCTAATAAAGTGACTGCCATTTCCAAAGAACCTTCAGTTAAGATGTTCCACAAAACTGGCTCAACAAATGGCTTTGGAACTTATGTGGTGTTTATTCCAAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAACGCATTAAGGCAGCGTATGCAGTATTGAATGCTATAAAAAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3003874","ARO_id":"40573","ARO_name":"ADC-43","CARD_short_name":"ADC-43","ARO_description":"ADC-43 is a beta-lactamase found in Acinetobacter pittii.","ARO_category":{"40543":{"category_aro_accession":"3003846","category_aro_cvterm_id":"40543","category_aro_name":"ADC beta-lactamase without carbapenemase activity","category_aro_description":"ADC beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases with extended-spectrum resistance to cephalosporins but not to carbapenems. ADC beta-lactamases are found in Acinetobacter sp. and Oligella urethralis.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2360":{"model_id":"2360","model_name":"ADC-44","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"5301":{"protein_sequence":{"accession":"ACN62073.1","sequence":"MRFKKISCLLLPPLFIFSTSIYAGNTSKEQEIKKLVDQNFKPLLDKYNVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKTKGTISFKDTPGKYWKELKNTPIDQVNLLQLATYTSGNLGLQFPDEVQTDQQVLTFFKDWKPKNSIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPGLSLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLKFINANLNPQKYPKDIQRAINETHQGFYQVGTMYQALGWEEFSYPAPLQTLLDSNSEQIVMKPNKVTAISKEPSIKMFHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"FJ744163.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGCTTACTTTTACCCCCTCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACATCAAAAGAACAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCTTTATTAGATAAATATAATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTAGGTTCAGTTAGTAAATTATTTACCGCGACAGCAGGTGGATATGCCAAAACAAAAGGAACAATCTCTTTTAAAGACACACCCGGAAAATATTGGAAAGAGCTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTTGCTACCTATACAAGTGGCAACCTTGGCTTACAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAGCCTAAAAACTCAATCGGTGAATATCGACAATATTCAAATCCAAGCATTGGTTTATTTGGAAAAGTTGTTGCATTGTCTATGAATAAACCTTTCGATCAAGTCTTAGAAAAAACAATTTTTCCGGGCCTTAGCTTAAAACATAGCTATGTAAATGTTCCTAAAACTCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCAATTCGTGTTAACCCTGGTCCGTTAGATGCACCTGCGTACGGCGTCAAATCGACACTACCCGATATGCTTAAGTTTATTAATGCCAACCTCAACCCACAGAAATATCCGAAAGATATTCAACGTGCAATTAATGAAACACATCAGGGTTTCTACCAAGTCGGCACGATGTATCAGGCACTTGGTTGGGAAGAATTTTCTTATCCAGCGCCTTTACAAACTTTATTAGACAGTAATTCAGAGCAAATCGTGATGAAGCCTAATAAAGTGACTGCCATTTCAAAAGAACCTTCAATTAAGATGTTCCACAAAACTGGCTCAACAAATGGCTTTGGAACTTATGTGGTGTTTATTCCAAAAGAAAATATTGGCTTAGTCATGTTGACCAATAAACGTATTCCAAATGAAGAACGCATTAAGGCAGCATATGCGGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3003876","ARO_id":"40575","ARO_name":"ADC-44","CARD_short_name":"ADC-44","ARO_description":"ADC-44 is a beta-lactamase found in Acinetobacter pittii.","ARO_category":{"40543":{"category_aro_accession":"3003846","category_aro_cvterm_id":"40543","category_aro_name":"ADC beta-lactamase without carbapenemase activity","category_aro_description":"ADC beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases with extended-spectrum resistance to cephalosporins but not to carbapenems. ADC beta-lactamases are found in Acinetobacter sp. and Oligella urethralis.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2361":{"model_id":"2361","model_name":"ADC-56","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"5303":{"protein_sequence":{"accession":"AEG47700.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVKTDQQVLTFFKDWKPKNSIGEYQQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTTGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"HQ662682.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAGTATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAATTTCCAGATGAAGTAAAAACAGATCAGCAAGTTTTAACATTTTTTAAAGACTGGAAACCTAAAAACTCAATCGGTGAATATCAACAATATTCAAACCCAAGCATTGGTTTATTTGGAAAAGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTAAATCCACAAAAATATCCAGCAGATATTCAACGGGCAATTAATGAAACACATCAGGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTACCGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3003878","ARO_id":"40577","ARO_name":"ADC-56","CARD_short_name":"ADC-56","ARO_description":"ADC-56 is a beta-lactamase found in Acinetobacter baumannii.","ARO_category":{"40543":{"category_aro_accession":"3003846","category_aro_cvterm_id":"40543","category_aro_name":"ADC beta-lactamase without carbapenemase activity","category_aro_description":"ADC beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases with extended-spectrum resistance to cephalosporins but not to carbapenems. ADC beta-lactamases are found in Acinetobacter sp. and Oligella urethralis.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2362":{"model_id":"2362","model_name":"ADC-61","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"5305":{"protein_sequence":{"accession":"AFI56570.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVKTDQQVLTFFKDWKPKNSIGEYRQYSNPSIGLFGKVVALSMNKPLDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTTGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"JQ753702.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAGTATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAATTTCCAGATGAAGTAAAAACAGATCAGCAAGTTTTAACATTTTTTAAAGACTGGAAACCTAAAAACTCAATCGGTGAATATCGACAATATTCAAACCCAAGCATTGGTTTATTTGGAAAAGTTGTAGCTTTGTCTATGAATAAACCTCTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTAAATCCACAAAAATATCCAGCAGATATTCAACGGGCAATTAATGAAACACATCAGGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTACCGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3003879","ARO_id":"40578","ARO_name":"ADC-61","CARD_short_name":"ADC-61","ARO_description":"ADC-61 is a beta-lactamase found in Acinetobacter baumannii.","ARO_category":{"40543":{"category_aro_accession":"3003846","category_aro_cvterm_id":"40543","category_aro_name":"ADC beta-lactamase without carbapenemase activity","category_aro_description":"ADC beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases with extended-spectrum resistance to cephalosporins but not to carbapenems. ADC beta-lactamases are found in Acinetobacter sp. and Oligella urethralis.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2363":{"model_id":"2363","model_name":"ADC-74","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"5362":{"protein_sequence":{"accession":"ALA14809.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNRSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWQPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRANPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGFYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTTGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLDAIKK"},"dna_sequence":{"accession":"KP881234.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATCGCAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGCAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTGGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCATTTGGTTATAACCAAGAAAATCAGCCGATTCGAGCTAACCCCGGCCCACTCGATGCCCCTGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTTAACCCACAGAAATATCCGGCTGATATTCAACGGGCAATTAATGAAACACATCAAGGGTTCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCACCGGTTTCGGAACATATGTAGTGTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGGATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3003880","ARO_id":"40579","ARO_name":"ADC-74","CARD_short_name":"ADC-74","ARO_description":"ADC-74 is a beta-lactamase found in Acinetobacter baumannii.","ARO_category":{"40543":{"category_aro_accession":"3003846","category_aro_cvterm_id":"40543","category_aro_name":"ADC beta-lactamase without carbapenemase activity","category_aro_description":"ADC beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases with extended-spectrum resistance to cephalosporins but not to carbapenems. ADC beta-lactamases are found in Acinetobacter sp. and Oligella urethralis.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2364":{"model_id":"2364","model_name":"ADC-75","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"5365":{"protein_sequence":{"accession":"ALA14810.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVKTDQQVLTFFKDWKPKNSIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGFYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTTGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"KP881235.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAGTATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAATTTCCAGATGAAGTAAAAACAGATCAGCAAGTTTTAACATTTTTTAAAGACTGGAAACCTAAAAACTCAATCGGTGAATATCGACAATATTCAAACCCAAGCATTGGTTTATTTGGAAAAGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTAAATCCACAAAAATATCCAGCAGATATTCAACGGGCAATTAATGAAACACATCAAGGGTTCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTACCGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3003881","ARO_id":"40580","ARO_name":"ADC-75","CARD_short_name":"ADC-75","ARO_description":"ADC-75 is a beta-lactamase found in Acinetobacter baumannii.","ARO_category":{"40543":{"category_aro_accession":"3003846","category_aro_cvterm_id":"40543","category_aro_name":"ADC beta-lactamase without carbapenemase activity","category_aro_description":"ADC beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases with extended-spectrum resistance to cephalosporins but not to carbapenems. ADC beta-lactamases are found in Acinetobacter sp. and Oligella urethralis.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2365":{"model_id":"2365","model_name":"ADC-76","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"5420":{"protein_sequence":{"accession":"ALA14811.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKVLKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGESRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPTDIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"KP881236.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACCCCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCGTTATTAGAAAAATATGATGTGCCGGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGTGCTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATCCAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATACGGTGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTTAACCCACAGAAATATCCGACAGATATTCAACGGGCAATTAATGAAACACATCAAGGTCGCTATCAAGTAAATACCATGTATCAAGCGCTTGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGTATTAAGGCAGCGTATGCAGTTTTAAATGCAATAAAAAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3003882","ARO_id":"40581","ARO_name":"ADC-76","CARD_short_name":"ADC-76","ARO_description":"ADC-76 is a beta-lactamase found in Acinetobacter baumannii.","ARO_category":{"40543":{"category_aro_accession":"3003846","category_aro_cvterm_id":"40543","category_aro_name":"ADC beta-lactamase without carbapenemase activity","category_aro_description":"ADC beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases with extended-spectrum resistance to cephalosporins but not to carbapenems. ADC beta-lactamases are found in Acinetobacter sp. and Oligella urethralis.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2366":{"model_id":"2366","model_name":"ADC-77","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"5423":{"protein_sequence":{"accession":"ALA14812.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFINANLNPQKYPTDIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTTGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"KP881237.1","fmin":"53","fmax":"1205","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCTCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAGTATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATACGGCGTCAAATCCACCTTACCGGATATGTTGAGTTTTATTAATGCCAACCTTAACCCACAAAAATATCCGACAGATATTCAACGGGCAATTAATGAAACACATCAAGGTCGCTATCAAGTAAATACCATGTATCAAGCGCTTGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAGCCTAATAAAGTGACTGCTATTTCAAAAGAGCCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTACCGGTTTCGGAACATATGTAGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3003883","ARO_id":"40582","ARO_name":"ADC-77","CARD_short_name":"ADC-77","ARO_description":"ADC-77 is a beta-lactamase found in Acinetobacter baumannii.","ARO_category":{"40543":{"category_aro_accession":"3003846","category_aro_cvterm_id":"40543","category_aro_name":"ADC beta-lactamase without carbapenemase activity","category_aro_description":"ADC beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases with extended-spectrum resistance to cephalosporins but not to carbapenems. ADC beta-lactamases are found in Acinetobacter sp. and Oligella urethralis.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2367":{"model_id":"2367","model_name":"ADC-78","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"5425":{"protein_sequence":{"accession":"ALA14813.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVKTDQQVLTFFKDWKPKNSIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTTGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLDAIKK"},"dna_sequence":{"accession":"KP881238.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAGTATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAATTTCCAGATGAAGTAAAAACAGATCAGCAAGTTTTAACATTTTTTAAAGACTGGAAACCTAAAAACTCAATCGGTGAATATCGACAATATTCAAACCCAAGCATTGGTTTATTTGGAAAAGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTAAATCCACAAAAATATCCAGCAGATATTCAACGGGCAATTAATGAAACACATCAGGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTACCGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGGATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3003884","ARO_id":"40583","ARO_name":"ADC-78","CARD_short_name":"ADC-78","ARO_description":"ADC-78 is a beta-lactamase found in Acinetobacter baumannii.","ARO_category":{"40543":{"category_aro_accession":"3003846","category_aro_cvterm_id":"40543","category_aro_name":"ADC beta-lactamase without carbapenemase activity","category_aro_description":"ADC beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases with extended-spectrum resistance to cephalosporins but not to carbapenems. ADC beta-lactamases are found in Acinetobacter sp. and Oligella urethralis.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2368":{"model_id":"2368","model_name":"ADC-79","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"5428":{"protein_sequence":{"accession":"ALA14814.1","sequence":"MQFKKISCLLLSPLFIFSTSIYADNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGFYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"KP881239.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCAATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGACAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCATTATTAGAAAAATATGATGTGCCGGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAGCTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTCCCAGATGAAGTACAAACAGATCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTGTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTTAACCCACAGAAATATCCGGCAGATATTCAACGGGCAATTAATGAAACACATCAAGGGTTCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACATATGTAGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3003885","ARO_id":"40584","ARO_name":"ADC-79","CARD_short_name":"ADC-79","ARO_description":"ADC-79 is a beta-lactamase found in Acinetobacter baumannii.","ARO_category":{"40543":{"category_aro_accession":"3003846","category_aro_cvterm_id":"40543","category_aro_name":"ADC beta-lactamase without carbapenemase activity","category_aro_description":"ADC beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases with extended-spectrum resistance to cephalosporins but not to carbapenems. ADC beta-lactamases are found in Acinetobacter sp. and Oligella urethralis.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2370":{"model_id":"2370","model_name":"ADC-81","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"5437":{"protein_sequence":{"accession":"ALA14816.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNRSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWQPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGFYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLDAIKK"},"dna_sequence":{"accession":"KP881241.1","fmin":"0","fmax":"1167","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATCGCAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGCAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTGGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCATTTGGTTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCTGCATATGGCGCCCCTGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTTAACCCACAGAAATATCCGGCTGATATTCAACGGGCAATTAATGAAACACATCAAGGGTTCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCAACGGTTTCGGAACATATGTAGTGTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGGATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3003887","ARO_id":"40586","ARO_name":"ADC-81","CARD_short_name":"ADC-81","ARO_description":"ADC-81 is a beta-lactamase found in Acinetobacter baumannii.","ARO_category":{"40543":{"category_aro_accession":"3003846","category_aro_cvterm_id":"40543","category_aro_name":"ADC beta-lactamase without carbapenemase activity","category_aro_description":"ADC beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases with extended-spectrum resistance to cephalosporins but not to carbapenems. ADC beta-lactamases are found in Acinetobacter sp. and Oligella urethralis.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4230":{"model_id":"4230","model_name":"ADC-162","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6605":{"protein_sequence":{"accession":"WP_031980335.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVKTDQQVLTFFKDWKPKNSIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPEYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTTGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_056060.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAGTATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAATTTCCAGATGAAGTAAAAACAGATCAGCAAGTTTTAACATTTTTTAAAGACTGGAAACCTAAAAACTCAATCGGTGAATATCGACAATATTCAAACCCAAGCATTGGTTTATTTGGAAAAGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGAATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTAAATCCACAAAAATATCCAGCAGATATTCAACGGGCAATTAATGAAACACATCAGGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTACCGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006334","ARO_id":"44796","ARO_name":"ADC-162","CARD_short_name":"ADC-162","ARO_description":"ADC-162 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2371":{"model_id":"2371","model_name":"ADC-82","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"5441":{"protein_sequence":{"accession":"EXE65374.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVKTDQQVLTFFKDWKPKNSIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDALAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTTGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"JEXY01000001.1","fmin":"379","fmax":"1531","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAGTATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAATTTCCAGATGAAGTAAAAACAGATCAGCAAGTTTTAACATTTTTTAAAGACTGGAAACCTAAAAACTCAATCGGTGAATATCGACAATATTCAAACCCAAGCATTGGTTTATTTGGAAAAGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCTAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTAAATCCACAAAAATATCCAGCAGATATTCAACGGGCAATTAATGAAACACATCAGGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTACCGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42628","NCBI_taxonomy_name":"Acinetobacter baumannii 1552865","NCBI_taxonomy_id":"1310679"}}}},"ARO_accession":"3003888","ARO_id":"40587","ARO_name":"ADC-82","CARD_short_name":"ADC-82","ARO_description":"ADC-82 is a beta-lactamase found in Acinetobacter baumannii.","ARO_category":{"40543":{"category_aro_accession":"3003846","category_aro_cvterm_id":"40543","category_aro_name":"ADC beta-lactamase without carbapenemase activity","category_aro_description":"ADC beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases with extended-spectrum resistance to cephalosporins but not to carbapenems. ADC beta-lactamases are found in Acinetobacter sp. and Oligella urethralis.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2377":{"model_id":"2377","model_name":"Escherichia coli PtsI with mutation conferring resistance to fosfomycin","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"4379":"V25I"},"Curated-R":{"4379":"V25I"},"clinical":{"4379":"V25I"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1100"}},"model_sequences":{"sequence":{"3675":{"protein_sequence":{"accession":"CDJ72759.1","sequence":"MISGILASPGIAFGKALLLKEDEIVIDRKKISADQVDQEVERFLSGRAKASAQLETIKTKAGETFGEEKEAIFEGHIMLLEDEELEQEIIALIKDKHMTADAAAHEVIEGQASALEELDDEYLKERAADVRDIGKRLLRNILGLKIIDLSAIQDEVILVAADLTPSETAQLNLKKVLGFITDAGGRTSHTSIMARSLELPAIVGTGSVTSQVKNDDYLILDAVNNQVYVNPTNEVIDKMRAVQEQVASEKAELAKLKDLPAITLDGHQVEVCANIGTVRDVEGAERNGAEGVGLYRTEFLFMDRDALPTEEEQFAAYKAVAEACGSQAVIVRTMDIGGDKELPYMNFPKEENPFLGWRAIRIAMDRREILRDQLRAILRASAFGKLRIMFPMIISVEEVRALRKEIEIYKQELRDEGKAFDESIEIGVMVETPAAATIARHLAKEVDFFSIGTNDLTQYTLAVDRGNDMISHLYQPMSPSVLNLIKQVIDASHAEGKWTGMCGELAGDERATLLLLGMGLDEFSMSAISIPRIKKIIRNTNFEDAKVLAEQALAQPTTDELMTLVNKFIEEKTIC"},"dna_sequence":{"accession":"HG738867.1","fmin":"2416338","fmax":"2418066","strand":"+","sequence":"ATGATTTCAGGCATTTTAGCATCCCCGGGTATCGCTTTCGGTAAAGCTCTGCTTCTGAAAGAAGACGAAATTGTCATTGACCGGAAAAAAATTTCTGCCGACCAGGTTGATCAGGAAGTTGAACGTTTTCTGAGCGGTCGTGCCAAGGCATCAGCCCAGCTGGAAACGATCAAAACGAAAGCTGGTGAAACGTTCGGTGAAGAAAAAGAAGCCATCTTTGAAGGGCATATTATGCTGCTCGAAGATGAGGAGCTGGAGCAGGAAATCATAGCCCTGATTAAAGATAAGCACATGACAGCTGACGCAGCTGCTCATGAAGTTATCGAAGGTCAGGCTTCTGCCCTGGAAGAGCTGGATGATGAATACCTGAAAGAACGTGCGGCTGACGTACGTGATATCGGTAAGCGCCTGCTGCGCAACATCCTGGGCCTGAAGATTATCGACCTGAGCGCCATTCAGGATGAAGTCATTCTGGTTGCCGCTGACCTGACGCCGTCCGAAACCGCACAGCTGAACCTGAAGAAGGTGCTGGGTTTCATCACCGACGCGGGTGGCCGTACTTCCCACACCTCTATCATGGCGCGTTCTCTGGAACTACCTGCTATCGTGGGTACCGGTAGCGTCACCTCTCAGGTGAAAAATGACGACTATCTGATTCTGGATGCCGTAAATAATCAGGTTTACGTCAATCCAACCAACGAAGTTATTGATAAAATGCGCGCTGTTCAGGAGCAAGTGGCTTCTGAAAAAGCAGAGCTTGCTAAACTGAAAGATCTGCCAGCTATTACGCTGGACGGTCACCAGGTAGAAGTATGCGCTAACATTGGTACGGTTCGTGACGTTGAAGGTGCAGAGCGTAACGGCGCTGAAGGCGTTGGTCTGTATCGTACTGAGTTCCTGTTCATGGACCGCGACGCACTGCCCACTGAAGAAGAACAGTTTGCTGCTTACAAAGCAGTGGCTGAAGCGTGTGGCTCGCAAGCGGTTATCGTTCGTACCATGGACATCGGCGGCGACAAAGAGCTGCCATACATGAACTTCCCGAAAGAAGAGAACCCGTTCCTCGGCTGGCGCGCTATCCGTATCGCGATGGATCGTAGAGAGATCCTGCGCGATCAGCTCCGCGCTATCCTGCGTGCCTCGGCTTTCGGTAAATTGCGCATTATGTTCCCGATGATCATCTCTGTTGAAGAAGTGCGTGCACTGCGCAAAGAGATCGAAATCTACAAACAGGAACTGCGCGACGAAGGTAAAGCGTTTGACGAGTCAATTGAAATCGGCGTAATGGTGGAAACACCGGCTGCCGCAACAATTGCACGTCATTTAGCCAAAGAAGTTGATTTCTTTAGTATCGGCACCAATGATTTAACGCAGTACACTCTGGCAGTTGACCGTGGTAATGATATGATTTCACACCTTTACCAGCCAATGTCACCGTCCGTGCTGAACTTGATCAAGCAAGTTATTGATGCTTCTCATGCTGAAGGCAAATGGACTGGCATGTGTGGTGAGCTTGCTGGCGATGAACGTGCTACACTTCTGTTGCTGGGGATGGGTCTGGACGAATTCTCTATGAGCGCCATTTCTATCCCGCGCATTAAGAAGATTATCCGTAACACGAACTTCGAAGATGCGAAGGTGTTAGCAGAGCAGGCTCTTGCTCAACCGACAACGGACGAGTTAATGACGCTGGTTAACAAGTTCATTGAAGAAAAAACAATCTGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40589","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. MC4100","NCBI_taxonomy_id":"1403831"}}}},"ARO_accession":"3003899","ARO_id":"40601","ARO_name":"Escherichia coli PtsI with mutation conferring resistance to fosfomycin","CARD_short_name":"Ecol_PtsI_FOF","ARO_description":"PtsI (phosphoenolpyruvate-protein phosphotransferase) is involved in cyclic AMP synthesis, which regulates glpT expression. As a result, mutations to ptsI confer resistance to fosfomycin by affecting the regulation of fosfomycin import.","ARO_category":{"41414":{"category_aro_accession":"3004250","category_aro_cvterm_id":"41414","category_aro_name":"antibiotic-resistant ptsI phosphotransferase","category_aro_description":"PtsI family phosphotransferases are involved in cyclic AMP synthesis, which regulates glpT expression. Mutations in PtsI family genes can negatively affect expression of UhpT, which is needed for fosfomycin import.","category_aro_class_name":"AMR Gene Family"},"35944":{"category_aro_accession":"0000025","category_aro_cvterm_id":"35944","category_aro_name":"fosfomycin","category_aro_description":"Fosfomycin (also known as phosphomycin and phosphonomycin) is a broad-spectrum antibiotic produced by certain Streptomyces species. It is effective on gram positive and negative bacteria as it targets the cell wall, an essential feature shared by both bacteria. Its specific target is MurA (MurZ in E.coli), which attaches phosphoenolpyruvate (PEP) to UDP-N-acetylglucosamine, a step of commitment to cell wall synthesis. In the active site of MurA, the active cysteine molecule is alkylated which stops the catalytic reaction.","category_aro_class_name":"Antibiotic"},"45731":{"category_aro_accession":"3007149","category_aro_cvterm_id":"45731","category_aro_name":"phosphonic acid antibiotic","category_aro_description":"A group of antibiotics derived from phosphonic acids.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2850":{"model_id":"2850","model_name":"Salmonella enterica gyrA with mutation conferring resistance to triclosan","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1500"},"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"8272":"S83F","8273":"D87G"},"Curated-R":{"8272":"S83F","8273":"D87G"},"clinical":{"8272":"S83F","8273":"D87G"}}},"model_sequences":{"sequence":{"5394":{"protein_sequence":{"accession":"AAL21173.1","sequence":"MSDLAREITPVNIEEELKSSYLDYAMSVIVGRALPDVRDGLKPVHRRVLYAMNVLGNDWNKAYKKSARVVGDVIGKYHPHGDSAVYDTIVRMAQPFSLRYMLVDGQGNFGSIDGDSAAAMRYTEIRLAKIAHELMADLEKETVDFVDNYDGTEKIPDVMPTKIPNLLVNGSSGIAVGMATNIPPHNLTEVINGCLAYIDNEDISIEGLMEHIPGPDFPTAAIINGRRGIEEAYRTGRGKVYIRARAEVEADAKTGRETIIVHEIPYQVNKARLIEKIAELVKDKRVEGISALRDESDKDGMRIVIEVKRDAVGEVVLNNLYSQTQLQVSFGINMVALHHGQPKIMNLKDIISAFVRHRREVVTRRTIFELRKARDRAHILEALAIALANIDPIIELIRRAPTPAEAKAALISRPWDLGNVAAMLERAGDDAARPEWLEPEFGVRDGQYYLTEQQAQAILDLRLQKLTGLEHEKLLDEYKELLEQIAELLHILGSADRLMEVIREEMELIRDQFGDERRTEITANSADINIEDLISQEDVVVTLSHQGYVKYQPLTDYEAQRRGGKGKSAARIKEEDFIDRLLVANTHDTILCFSSRGRLYWMKVYQLPEASRGARGRPIVNLLPLEANERITAILPVREYEEGVNVFMATASGTVKKTALTEFSRPRSAGIIAVNLNDGDELIGVDLTSGSDEVMLFSAAGKVVRFKEDAVRAMGRTATGVRGIKLAGDDKVVSLIIPRGEGAILTVTQNGYGKRTAADEYPTKSRATQGVISIKVTERNGSVVGAVQVDDCDQIMMITDAGTLVRTRVSEISVVGRNTQGVILIRTAEDENVVGLQRVAEPVDDEELDAIDGSVAEGDEDIAPEAESDDDVADDADE"},"dna_sequence":{"accession":"AE006468.2","fmin":"2373709","fmax":"2376346","strand":"-","sequence":"ATGAGCGACCTTGCGAGAGAAATTACACCGGTCAACATTGAGGAGGAGCTGAAGAGCTCCTATCTGGATTATGCGATGTCGGTCATTGTTGGCCGTGCGCTGCCGGATGTCCGAGATGGCCTGAAGCCGGTACACCGTCGCGTACTTTACGCCATGAACGTATTGGGCAATGACTGGAACAAAGCCTATAAAAAATCTGCCCGTGTCGTTGGTGACGTAATCGGTAAATACCATCCCCACGGCGATTCCGCAGTGTATGACACCATCGTTCGTATGGCGCAGCCATTCTCGCTGCGTTACATGCTGGTGGATGGTCAGGGTAACTTCGGTTCTATTGACGGCGACTCCGCGGCGGCAATGCGTTATACGGAGATCCGTCTGGCGAAAATCGCCCACGAACTGATGGCCGATCTCGAAAAAGAGACGGTGGATTTCGTGGATAACTATGACGGTACGGAAAAAATTCCGGACGTCATGCCGACCAAAATTCCGAATCTGCTGGTGAACGGTTCTTCCGGTATCGCAGTAGGTATGGCGACGAATATCCCGCCGCACAACCTGACGGAAGTGATTAACGGCTGCCTGGCGTATATCGACAACGAAGACATCAGCATTGAAGGGCTGATGGAACATATTCCGGGGCCGGACTTCCCGACCGCCGCGATCATCAACGGTCGTCGTGGTATCGAAGAAGCCTACCGCACCGGTCGTGGCAAAGTGTACATTCGCGCCCGCGCGGAAGTTGAAGCTGACGCCAAAACGGGCCGTGAAACCATCATCGTCCATGAAATTCCCTATCAGGTGAACAAAGCGCGCCTGATCGAGAAAATCGCCGAGCTGGTGAAAGATAAACGCGTGGAAGGCATCAGCGCGCTGCGTGACGAATCCGACAAAGACGGGATGCGCATCGTGATTGAAGTGAAACGCGATGCGGTGGGCGAGGTGGTGCTTAATAATCTCTACTCCCAGACCCAGCTACAGGTTTCCTTCGGTATTAACATGGTGGCGCTGCATCACGGCCAGCCGAAGATCATGAACCTGAAAGATATCATTTCAGCGTTCGTGCGCCACCGCCGTGAAGTGGTGACGCGTCGGACTATTTTTGAACTGCGTAAAGCCCGTGACCGTGCGCATATCCTTGAAGCTCTGGCGATTGCGCTGGCCAACATCGACCCGATTATCGAACTGATTCGCCGCGCGCCAACGCCGGCGGAAGCAAAAGCGGCGCTGATTTCGCGTCCGTGGGATCTGGGCAACGTTGCTGCGATGCTGGAGCGCGCTGGTGATGACGCCGCGCGTCCGGAATGGCTGGAGCCAGAATTTGGCGTGCGTGACGGTCAGTACTACCTGACTGAACAGCAGGCGCAGGCGATTCTGGATCTGCGTTTGCAGAAACTGACCGGCCTGGAGCATGAAAAACTGCTCGACGAATACAAAGAGCTGCTGGAGCAGATTGCTGAATTGCTGCACATTCTGGGCAGCGCCGATCGCCTGATGGAAGTGATCCGCGAAGAGATGGAGTTAATTCGCGATCAGTTCGGCGATGAGCGTCGTACCGAAATCACCGCCAACAGCGCCGATATTAATATCGAAGATCTGATTAGCCAGGAAGATGTTGTCGTGACGCTGTCTCACCAGGGTTACGTCAAATATCAACCGCTGACAGATTACGAAGCGCAACGTCGTGGTGGGAAAGGTAAATCTGCCGCGCGTATTAAAGAAGAAGACTTTATCGACCGCCTGCTGGTGGCTAACACCCATGACACCATCCTCTGCTTCTCCAGCCGGGGCCGTCTGTACTGGATGAAGGTCTATCAGCTGCCGGAAGCCAGCCGCGGCGCGCGCGGTCGTCCGATCGTCAACCTGCTGCCGCTGGAAGCCAACGAACGTATCACCGCGATTCTGCCGGTTCGTGAGTATGAAGAAGGCGTCAACGTCTTTATGGCGACCGCCAGCGGTACCGTGAAGAAAACGGCGCTGACCGAATTCAGCCGTCCGCGTTCCGCCGGTATTATCGCGGTGAACCTCAACGACGGCGACGAGCTGATTGGCGTTGACCTGACTTCTGGTTCTGACGAAGTCATGCTGTTCTCGGCCGCGGGTAAAGTGGTGCGCTTCAAAGAAGACGCCGTCCGTGCGATGGGGCGTACCGCGACCGGTGTGCGCGGTATTAAGCTGGCGGGAGACGATAAAGTCGTCTCTCTGATCATCCCACGCGGCGAAGGCGCTATTCTGACCGTAACGCAAAACGGCTACGGGAAGCGTACCGCAGCGGACGAGTACCCGACCAAGTCTCGTGCGACGCAGGGCGTTATCTCTATCAAAGTGACCGAGCGCAACGGTTCCGTTGTCGGTGCGGTACAGGTAGACGATTGCGACCAGATCATGATGATCACGGATGCCGGTACTCTGGTGCGTACCCGTGTGTCCGAGATCAGCGTAGTGGGACGTAATACCCAGGGCGTTATCCTTATCCGCACGGCGGAAGATGAAAACGTGGTGGGTCTGCAACGCGTTGCTGAACCGGTAGATGACGAAGAACTCGACGCTATCGACGGCAGCGTGGCGGAAGGGGATGAGGATATCGCCCCGGAAGCGGAAAGCGATGACGACGTTGCGGATGACGCTGACGAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35734","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Typhimurium str. LT2","NCBI_taxonomy_id":"99287"}}}},"ARO_accession":"3004334","ARO_id":"41502","ARO_name":"Salmonella enterica gyrA with mutation conferring resistance to triclosan","CARD_short_name":"Sent_gyrA_TRC","ARO_description":"Point mutations in Salmonella enterica serovar Typhimurium which have been shown to increase the minimum inhibitory concentration of the antibiotic triclosan. It is hypothesized that decreased susceptibility to triclosan in Salmonella gyrA mutants occurs indirectly due to alterations in the stress response pathways.","ARO_category":{"41501":{"category_aro_accession":"3004333","category_aro_cvterm_id":"41501","category_aro_name":"triclosan resistant gyrA","category_aro_description":"DNA gyrase is responsible for DNA supercoiling and consists of two alpha and two beta subunits. Point mutations in gyrA have been shown to decrease susceptibility to the antibiotic triclosan. Although the mechanism is unclear, it is hypothesized that changes in supercoiling activity of mutant DNA gyrase proteins alters expression of stress response pathways thereby indirectly decreasing triclosan susceptibility. It has been shown that triclosan does not interact directly with gyrA.","category_aro_class_name":"AMR Gene Family"},"37250":{"category_aro_accession":"3000870","category_aro_cvterm_id":"37250","category_aro_name":"triclosan","category_aro_description":"Triclosan is a common antibacterial agent added to many consumer products as a biocide.  It is an inhibitor of fatty acid biosynthesis by blocking enoyl-carrier protein reductase (FabI).","category_aro_class_name":"Antibiotic"},"43746":{"category_aro_accession":"3005386","category_aro_cvterm_id":"43746","category_aro_name":"disinfecting agents and antiseptics","category_aro_description":"Disinfectants that can also interact with antimicrobial resistance mechanisms, e.g. molecule efflux, and thus are the targets of disinfectant resistance.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2900":{"model_id":"2900","model_name":"EBR-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"4438":{"protein_sequence":{"accession":"ALG03771.1","sequence":"MKKIFSLIALIGSFAFGQIKPIQIDPINNNLFVYQTFNSFNDVEYNANGMYLVTNKGIVLFDVPWQKSQYQELNDILQEKYNLPVIAVFATHSHDDRAGDLSFYNELNIPTYATSLTNSKLKKEGKATSKFEIELGKTYKFGNEKFVVEYFGEGHTSDNVVVWFPKYKVLNGGCLIKGADAVNLGYTGEANVVEWPKTVHKLVAKHPTIKQVIPGHDNWKATGHIENTFKLLEKK"},"dna_sequence":{"accession":"KR131616.1","fmin":"0","fmax":"708","strand":"+","sequence":"ATGAAAAAAATATTTTCACTTATTGCATTGATAGGAAGTTTTGCATTTGGTCAAATAAAACCAATTCAAATTGATCCAATTAATAATAATCTATTTGTTTATCAAACATTTAATTCGTTTAATGATGTTGAATATAATGCAAATGGAATGTATTTGGTAACGAATAAAGGAATCGTTTTGTTTGATGTTCCTTGGCAGAAATCGCAGTATCAAGAGTTAAATGATATATTGCAAGAAAAGTATAATTTGCCAGTTATCGCTGTCTTTGCAACACATTCGCATGATGATAGAGCAGGAGATTTGAGTTTTTATAATGAGTTGAATATTCCTACTTATGCAACTTCTTTAACCAATTCTAAATTAAAAAAAGAAGGAAAAGCAACTTCTAAATTTGAGATTGAATTAGGTAAAACATACAAGTTTGGTAATGAAAAGTTTGTTGTTGAATATTTTGGAGAAGGACATACTTCTGATAATGTTGTGGTTTGGTTTCCGAAATATAAAGTGTTGAATGGAGGTTGTTTGATAAAGGGTGCTGATGCTGTAAATTTAGGTTACACAGGCGAAGCTAATGTTGTTGAATGGCCAAAAACAGTACACAAACTAGTTGCAAAACATCCAACGATTAAACAAGTTATTCCAGGTCATGATAATTGGAAAGCTACTGGACACATCGAAAATACGTTTAAACTTTTAGAAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41679","NCBI_taxonomy_name":"Empedobacter falsenii","NCBI_taxonomy_id":"343874"}}}},"ARO_accession":"3004463","ARO_id":"41678","ARO_name":"EBR-2","CARD_short_name":"EBR-2","ARO_description":"EBR-2 is a novel EBR-like class B beta-lactamase isolated from an extensively drug-resistant strain of Empedobacter falsenii.","ARO_category":{"41368":{"category_aro_accession":"3004204","category_aro_cvterm_id":"41368","category_aro_name":"EBR beta-lactamase","category_aro_description":"EBR beta-lactamases are Class B beta-lactamases first isolated from Empedobacter brevis and are able to hydrolyze penicillins, cephalosporins, and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4012":{"model_id":"4012","model_name":"PDC-324","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"6376":{"protein_sequence":{"accession":"WP_150823482.1","sequence":"MRDTRFSCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPSPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_066531.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCTCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCAGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCCGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACTCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATTCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005279","ARO_id":"43636","ARO_name":"PDC-324","CARD_short_name":"PDC-324","ARO_description":"PDC-324 is a class C beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2851":{"model_id":"2851","model_name":"Escherichia coli gyrA with mutation conferring resistance to triclosan","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1500"},"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"8275":"S83F","8276":"D87G"},"Curated-R":{"8275":"S83F","8276":"D87G"},"clinical":{"8275":"S83F","8276":"D87G"}}},"model_sequences":{"sequence":{"4469":{"protein_sequence":{"accession":"AAC75291.1","sequence":"MSDLAREITPVNIEEELKSSYLDYAMSVIVGRALPDVRDGLKPVHRRVLYAMNVLGNDWNKAYKKSARVVGDVIGKYHPHGDSAVYDTIVRMAQPFSLRYMLVDGQGNFGSIDGDSAAAMRYTEIRLAKIAHELMADLEKETVDFVDNYDGTEKIPDVMPTKIPNLLVNGSSGIAVGMATNIPPHNLTEVINGCLAYIDDEDISIEGLMEHIPGPDFPTAAIINGRRGIEEAYRTGRGKVYIRARAEVEVDAKTGRETIIVHEIPYQVNKARLIEKIAELVKEKRVEGISALRDESDKDGMRIVIEVKRDAVGEVVLNNLYSQTQLQVSFGINMVALHHGQPKIMNLKDIIAAFVRHRREVVTRRTIFELRKARDRAHILEALAVALANIDPIIELIRHAPTPAEAKTALVANPWQLGNVAAMLERAGDDAARPEWLEPEFGVRDGLYYLTEQQAQAILDLRLQKLTGLEHEKLLDEYKELLDQIAELLRILGSADRLMEVIREELELVREQFGDKRRTEITANSADINLEDLITQEDVVVTLSHQGYVKYQPLSEYEAQRRGGKGKSAARIKEEDFIDRLLVANTHDHILCFSSRGRVYSMKVYQLPEATRGARGRPIVNLLPLEQDERITAILPVTEFEEGVKVFMATANGTVKKTVLTEFNRLRTAGKVAIKLVDGDELIGVDLTSGEDEVMLFSAEGKVVRFKESSVRAMGCNTTGVRGIRLGEGDKVVSLIVPRGDGAILTATQNGYGKRTAVAEYPTKSRATKGVISIKVTERNGLVVGAVQVDDCDQIMMITDAGTLVRTRVSEISIVGRNTQGVILIRTAEDENVVGLQRVAEPVDEEDLDTIDGSAAEGDDEIAPEVDVDDEPEEE"},"dna_sequence":{"accession":"U00096.3","fmin":"2336792","fmax":"2339420","strand":"-","sequence":"ATGAGCGACCTTGCGAGAGAAATTACACCGGTCAACATTGAGGAAGAGCTGAAGAGCTCCTATCTGGATTATGCGATGTCGGTCATTGTTGGCCGTGCGCTGCCAGATGTCCGAGATGGCCTGAAGCCGGTACACCGTCGCGTACTTTACGCCATGAACGTACTAGGCAATGACTGGAACAAAGCCTATAAAAAATCTGCCCGTGTCGTTGGTGACGTAATCGGTAAATACCATCCCCATGGTGACTCGGCGGTCTATGACACGATCGTCCGCATGGCGCAGCCATTCTCGCTGCGTTATATGCTGGTAGACGGTCAGGGTAACTTCGGTTCTATCGACGGCGACTCTGCGGCGGCAATGCGTTATACGGAAATCCGTCTGGCGAAAATTGCCCATGAACTGATGGCCGATCTCGAAAAAGAGACGGTCGATTTCGTTGATAACTATGACGGCACGGAAAAAATTCCGGACGTCATGCCAACCAAAATTCCTAACCTGCTGGTGAACGGTTCTTCCGGTATCGCCGTAGGTATGGCAACCAACATCCCGCCGCACAACCTGACGGAAGTCATCAACGGTTGTCTGGCGTATATTGATGATGAAGACATCAGCATTGAAGGGCTGATGGAACACATCCCGGGGCCGGACTTCCCGACGGCGGCAATCATTAACGGTCGTCGCGGTATTGAAGAAGCTTACCGTACCGGTCGCGGCAAGGTGTATATCCGCGCTCGCGCAGAAGTGGAAGTTGACGCCAAAACCGGTCGTGAAACCATTATCGTCCACGAAATTCCGTATCAGGTAAACAAAGCGCGCCTGATCGAGAAGATTGCGGAACTGGTAAAAGAAAAACGCGTGGAAGGCATCAGCGCGCTGCGTGACGAGTCTGACAAAGACGGTATGCGCATCGTGATTGAAGTGAAACGCGATGCGGTCGGTGAAGTTGTGCTCAACAACCTCTACTCCCAGACCCAGTTGCAGGTTTCTTTCGGTATCAACATGGTGGCATTGCACCATGGTCAGCCGAAGATCATGAACCTGAAAGACATCATCGCGGCGTTTGTTCGTCACCGCCGTGAAGTGGTGACCCGTCGTACTATTTTCGAACTGCGTAAAGCTCGCGATCGTGCTCATATCCTTGAAGCATTAGCCGTGGCGCTGGCGAACATCGACCCGATCATCGAACTGATCCGTCATGCGCCGACGCCTGCAGAAGCGAAAACTGCGCTGGTTGCTAATCCGTGGCAGCTGGGCAACGTTGCCGCGATGCTCGAACGTGCTGGCGACGATGCTGCGCGTCCGGAATGGCTGGAGCCAGAGTTCGGCGTGCGTGATGGTCTGTACTACCTGACCGAACAGCAAGCTCAGGCGATTCTGGATCTGCGTTTGCAGAAACTGACCGGTCTTGAGCACGAAAAACTGCTCGACGAATACAAAGAGCTGCTGGATCAGATCGCGGAACTGTTGCGTATTCTTGGTAGCGCCGATCGTCTGATGGAAGTGATCCGTGAAGAGCTGGAGCTGGTTCGTGAACAGTTCGGTGACAAACGTCGTACTGAAATCACCGCCAACAGCGCAGACATCAACCTGGAAGATCTGATCACCCAGGAAGATGTGGTCGTGACGCTCTCTCACCAGGGCTACGTTAAGTATCAGCCGCTTTCTGAATACGAAGCGCAGCGTCGTGGCGGGAAAGGTAAATCTGCCGCACGTATTAAAGAAGAAGACTTTATCGACCGACTGCTGGTGGCGAACACTCACGACCATATTCTGTGCTTCTCCAGCCGTGGTCGCGTCTATTCGATGAAAGTTTATCAGTTGCCGGAAGCCACTCGTGGCGCGCGCGGTCGTCCGATCGTCAACCTGCTGCCGCTGGAGCAGGACGAACGTATCACTGCGATCCTGCCAGTGACCGAGTTTGAAGAAGGCGTGAAAGTCTTCATGGCGACCGCTAACGGTACCGTGAAGAAAACTGTCCTCACCGAGTTCAACCGTCTGCGTACCGCCGGTAAAGTGGCGATCAAACTGGTTGACGGCGATGAGCTGATCGGCGTTGACCTGACCAGCGGCGAAGACGAAGTAATGCTGTTCTCCGCTGAAGGTAAAGTGGTGCGCTTTAAAGAGTCTTCTGTCCGTGCGATGGGCTGCAACACCACCGGTGTTCGCGGTATTCGCTTAGGTGAAGGCGATAAAGTCGTCTCTCTGATCGTGCCTCGTGGCGATGGCGCAATCCTCACCGCAACGCAAAACGGTTACGGTAAACGTACCGCAGTGGCGGAATACCCAACCAAGTCGCGTGCGACGAAAGGGGTTATCTCCATCAAGGTTACCGAACGTAACGGTTTAGTTGTTGGCGCGGTACAGGTAGATGACTGCGACCAGATCATGATGATCACCGATGCCGGTACGCTGGTACGTACTCGCGTTTCGGAAATCAGCATCGTGGGCCGTAACACCCAGGGCGTGATCCTCATCCGTACTGCGGAAGATGAAAACGTAGTGGGTCTGCAACGTGTTGCTGAACCGGTTGACGAGGAAGATCTGGATACCATCGACGGCAGTGCCGCGGAAGGGGACGATGAAATCGCTCCGGAAGTGGACGTTGACGACGAGCCAGAAGAAGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36849","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. MG1655","NCBI_taxonomy_id":"511145"}}}},"ARO_accession":"3004335","ARO_id":"41503","ARO_name":"Escherichia coli gyrA with mutation conferring resistance to triclosan","CARD_short_name":"Ecol_gyrA_TRC","ARO_description":"Point mutations in Escherichia coli which have been shown to increase the minimum inhibitory concentration of the antibiotic triclosan. It is hypothesized that decreased susceptibility to triclosan in E. coli gyrA mutants occurs indirectly due to alterations in the stress response pathways.","ARO_category":{"41501":{"category_aro_accession":"3004333","category_aro_cvterm_id":"41501","category_aro_name":"triclosan resistant gyrA","category_aro_description":"DNA gyrase is responsible for DNA supercoiling and consists of two alpha and two beta subunits. Point mutations in gyrA have been shown to decrease susceptibility to the antibiotic triclosan. Although the mechanism is unclear, it is hypothesized that changes in supercoiling activity of mutant DNA gyrase proteins alters expression of stress response pathways thereby indirectly decreasing triclosan susceptibility. It has been shown that triclosan does not interact directly with gyrA.","category_aro_class_name":"AMR Gene Family"},"37250":{"category_aro_accession":"3000870","category_aro_cvterm_id":"37250","category_aro_name":"triclosan","category_aro_description":"Triclosan is a common antibacterial agent added to many consumer products as a biocide.  It is an inhibitor of fatty acid biosynthesis by blocking enoyl-carrier protein reductase (FabI).","category_aro_class_name":"Antibiotic"},"43746":{"category_aro_accession":"3005386","category_aro_cvterm_id":"43746","category_aro_name":"disinfecting agents and antiseptics","category_aro_description":"Disinfectants that can also interact with antimicrobial resistance mechanisms, e.g. molecule efflux, and thus are the targets of disinfectant resistance.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2852":{"model_id":"2852","model_name":"PDC-73","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6225":{"protein_sequence":{"accession":"AKR18013.1","sequence":"GEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNLSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"KR057742.1","fmin":"0","fmax":"1116","strand":"+","sequence":"GGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCTGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3004336","ARO_id":"41504","ARO_name":"PDC-73","CARD_short_name":"PDC-73","ARO_description":"An AmpC-like beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2853":{"model_id":"2853","model_name":"PDC-74","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6136":{"protein_sequence":{"accession":"WP_040184286.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPRPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_051744.1","fmin":"100","fmax":"1294","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGTCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCCGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3004337","ARO_id":"41505","ARO_name":"PDC-74","CARD_short_name":"PDC-74","ARO_description":"An AmpC-like beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2854":{"model_id":"2854","model_name":"PDC-75","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6226":{"protein_sequence":{"accession":"AKR18015.1","sequence":"GEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPRPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"KR057744.1","fmin":"0","fmax":"1116","strand":"+","sequence":"GGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCCCTACGGGTCGGTCCCCGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCATGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3004338","ARO_id":"41506","ARO_name":"PDC-75","CARD_short_name":"PDC-75","ARO_description":"An AmpC-like beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2855":{"model_id":"2855","model_name":"PDC-76","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6227":{"protein_sequence":{"accession":"AKR18016.1","sequence":"GEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPIAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"KR057745.1","fmin":"0","fmax":"1116","strand":"+","sequence":"GGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGTCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCCCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCATTGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3004339","ARO_id":"41507","ARO_name":"PDC-76","CARD_short_name":"PDC-76","ARO_description":"An AmpC-like beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2856":{"model_id":"2856","model_name":"PDC-77","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"6228":{"protein_sequence":{"accession":"AKR18017.1","sequence":"GEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALTQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPRPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"KR057746.1","fmin":"0","fmax":"1116","strand":"+","sequence":"GGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGACCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTTCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCCGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3004340","ARO_id":"41508","ARO_name":"PDC-77","CARD_short_name":"PDC-77","ARO_description":"An AmpC-like beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2857":{"model_id":"2857","model_name":"PDC-78","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"6229":{"protein_sequence":{"accession":"AKR18018.1","sequence":"GEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALTQDKMRLDDRASQHWPALQGSHFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPRPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"KR057747.1","fmin":"0","fmax":"1116","strand":"+","sequence":"GGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGACCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCACTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTTCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCCGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3004341","ARO_id":"41509","ARO_name":"PDC-78","CARD_short_name":"PDC-78","ARO_description":"An AmpC-like beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4186":{"model_id":"4186","model_name":"ADC-112","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6561":{"protein_sequence":{"accession":"WP_136512054.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVKTDQQVLTFFKDWKPKNSIGEYRQYSNPSIGLFGKVVALSTNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_064671.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAGTATTGGAAAGAACTAAAAAATACACCGATTGACCAGGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAATTTCCAGATGAAGTAAAAACAGATCAGCAAGTTTTAACATTTTTTAAAGACTGGAAACCTAAAAACTCAATCGGTGAATATCGACAATATTCAAACCCAAGCATTGGTTTATTTGGAAAAGTTGTAGCTTTGTCTACGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTAAATCCACAAAAATATCCAGCAGATATTCAACGGGCAATTAATGAAACACATCAGGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006290","ARO_id":"44752","ARO_name":"ADC-112","CARD_short_name":"ADC-112","ARO_description":"ADC-112 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2862":{"model_id":"2862","model_name":"PDC-83","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6233":{"protein_sequence":{"accession":"AKR18023.1","sequence":"GEAPADRLKALVDAAVQPAMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRAGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"KR057752.1","fmin":"0","fmax":"1116","strand":"+","sequence":"GGCGAGGCCCCGGCGGATCGCCTGAAGGCATTGGTCGACGCCGCCGTACAACCGGCGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGCCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCTAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTATGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3004346","ARO_id":"41514","ARO_name":"PDC-83","CARD_short_name":"PDC-83","ARO_description":"An AmpC-like beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2863":{"model_id":"2863","model_name":"PDC-84","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6234":{"protein_sequence":{"accession":"AKR18024.1","sequence":"GEAPADRLKALVDAAVQPAMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRAGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPIAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"KR057753.1","fmin":"0","fmax":"1116","strand":"+","sequence":"GGCGAGGCCCCGGCGGATCGCCTGAAGGCATTGGTCGACGCCGCCGTACAACCGGCGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGCCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCTAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCATTGCCGAGCGGGTGAAGATCGCCTATGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3004347","ARO_id":"41515","ARO_name":"PDC-84","CARD_short_name":"PDC-84","ARO_description":"An AmpC-like beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2864":{"model_id":"2864","model_name":"PDC-85","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"6235":{"protein_sequence":{"accession":"AKR18025.1","sequence":"GEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGHGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"KR057754.1","fmin":"0","fmax":"1116","strand":"+","sequence":"GGCGAGGCCCCGGCGGATCGCCTGAAGGCATTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCCATGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCTAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTATGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3004348","ARO_id":"41516","ARO_name":"PDC-85","CARD_short_name":"PDC-85","ARO_description":"An AmpC-like beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2865":{"model_id":"2865","model_name":"PDC-86","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6138":{"protein_sequence":{"accession":"KSN86152.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAKGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"LLSH01000109.1","fmin":"88827","fmax":"90021","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCTTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCAAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATTCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3004349","ARO_id":"41517","ARO_name":"PDC-86","CARD_short_name":"PDC-86","ARO_description":"An AmpC-like beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2866":{"model_id":"2866","model_name":"PDC-87","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6236":{"protein_sequence":{"accession":"AKR18027.1","sequence":"DEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPIAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"KR057756.1","fmin":"0","fmax":"1116","strand":"+","sequence":"GATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCTTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATTCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCATTGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3004350","ARO_id":"41518","ARO_name":"PDC-87","CARD_short_name":"PDC-87","ARO_description":"An AmpC-like beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2867":{"model_id":"2867","model_name":"PDC-88","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6237":{"protein_sequence":{"accession":"AKR18028.1","sequence":"DEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"KR057757.1","fmin":"0","fmax":"1110","strand":"+","sequence":"GATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCTTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATTCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3004351","ARO_id":"41519","ARO_name":"PDC-88","CARD_short_name":"PDC-88","ARO_description":"An AmpC-like beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2868":{"model_id":"2868","model_name":"PDC-89","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6238":{"protein_sequence":{"accession":"AKR18029.1","sequence":"DEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"KR057758.1","fmin":"0","fmax":"1107","strand":"+","sequence":"GATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGTCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCAATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGGCGCTGCAGCCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3004352","ARO_id":"41520","ARO_name":"PDC-89","CARD_short_name":"PDC-89","ARO_description":"An AmpC-like beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2869":{"model_id":"2869","model_name":"PDC-90","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6239":{"protein_sequence":{"accession":"AKR18030.1","sequence":"DEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"KR057759.1","fmin":"0","fmax":"1107","strand":"+","sequence":"GATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCCGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACTCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATTCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3004353","ARO_id":"41521","ARO_name":"PDC-90","CARD_short_name":"PDC-90","ARO_description":"An AmpC-like beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2870":{"model_id":"2870","model_name":"PDC-91","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6240":{"protein_sequence":{"accession":"AKR18031.1","sequence":"DEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSLQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"KR057760.1","fmin":"0","fmax":"1104","strand":"+","sequence":"GATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCTTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATTCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3004354","ARO_id":"41522","ARO_name":"PDC-91","CARD_short_name":"PDC-91","ARO_description":"An AmpC-like beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2871":{"model_id":"2871","model_name":"PDC-92","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6241":{"protein_sequence":{"accession":"AKR18032.1","sequence":"DEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMAPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"KR057761.1","fmin":"0","fmax":"1110","strand":"+","sequence":"GATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAACTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3004355","ARO_id":"41523","ARO_name":"PDC-92","CARD_short_name":"PDC-92","ARO_description":"An AmpC-like beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2872":{"model_id":"2872","model_name":"PDC-93","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6242":{"protein_sequence":{"accession":"AKR18033.1","sequence":"DEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMAPQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"KR057762.1","fmin":"0","fmax":"1116","strand":"+","sequence":"GATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAACTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCCGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3004356","ARO_id":"41524","ARO_name":"PDC-93","CARD_short_name":"PDC-93","ARO_description":"An AmpC-like beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2873":{"model_id":"2873","model_name":"catV","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"4232":{"protein_sequence":{"accession":"ATL63235.1","sequence":"MKFQRIDLDNWSRRSYFEHYLNRVNCTFSMTANIDITELLPALRQKEMKLYPAFLYMVTNAVNAHREFRTSFHADGELGYWESMIPSYTFFHQDDQTFSTMWTEFADEFPVFYQNYVADMKKYGDNKGLVAKELEPPYTFPVSCIPWVSFSGFNLNISGDGRYLLPIITSGKYFGQEGKTLLPVSLQVHHAVCDGYHASLFIHDLQKWATNYKEWLGVE"},"dna_sequence":{"accession":"KY753886.1","fmin":"0","fmax":"660","strand":"+","sequence":"ATGAAATTTCAGCGAATCGATCTAGATAATTGGAGCAGAAGGTCTTATTTCGAGCATTATCTGAACCGAGTGAATTGCACCTTCAGTATGACTGCCAACATAGATATAACGGAATTGCTGCCCGCTCTACGGCAAAAGGAGATGAAGCTGTACCCGGCTTTTCTGTATATGGTGACAAACGCTGTCAATGCGCATCGTGAATTTCGGACTTCCTTCCATGCGGATGGCGAGTTGGGCTATTGGGAGAGCATGATACCCAGCTATACTTTTTTTCACCAGGATGATCAAACTTTTTCTACGATGTGGACGGAATTCGCTGACGAGTTCCCTGTGTTTTATCAAAATTACGTAGCGGATATGAAAAAGTATGGGGACAACAAAGGTCTTGTGGCAAAAGAGTTGGAACCGCCTTACACTTTCCCTGTCTCGTGTATTCCCTGGGTGAGCTTCAGTGGGTTTAATCTGAATATTTCGGGAGATGGGCGATATTTGCTGCCAATCATTACGAGCGGAAAGTATTTCGGGCAAGAAGGCAAAACGTTATTGCCTGTTTCTTTGCAGGTCCATCATGCGGTTTGTGATGGCTATCACGCGAGCCTGTTCATCCATGATCTGCAAAAATGGGCAACAAACTATAAGGAATGGTTAGGTGTCGAGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41526","NCBI_taxonomy_name":"Brevibacillus brevis Vm4","NCBI_taxonomy_id":"1289602"}}}},"ARO_accession":"3004357","ARO_id":"41525","ARO_name":"catV","CARD_short_name":"catV","ARO_description":"A chloramphenicol acetyltransferase identified in Brevibacillus brevis and shown to confer resistance to chloramphenicol antibiotics. Described by Pawlowski et al. 2017.","ARO_category":{"36261":{"category_aro_accession":"3000122","category_aro_cvterm_id":"36261","category_aro_name":"chloramphenicol acetyltransferase (CAT)","category_aro_description":"Inactivates chloramphenicol by addition of an acyl group. CAT is used to describe many variants of the chloramphenicol acetyltransferase gene in a range of organisms including Acinetobacter calcoaceticus, Agrobacterium tumefaciens, Alkalihalobacillus clausii, Bacillus subtilis, Campylobacter coli, Enterococcus faecalis, Enterococcus faecium, Lactococcus lactis, Listeria monocytogenes, Listonella anguillarum, Morganella morganii, Photobacterium damselae subsp. piscicida, Proteus mirabilis, Salmonella typhi, Serratia marcescens, Shigella flexneri, Staphylococcus aureus, Staphylococcus haemolyticus, Staphylococcus intermedius, Streptococcus agalactiae, Streptococcus suis and Streptomyces acrimycini.","category_aro_class_name":"AMR Gene Family"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2874":{"model_id":"2874","model_name":"ACI-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"4259":{"protein_sequence":{"accession":"CAB51471.1","sequence":"MKKFCFLFLIICGLMVFCLQDCQARQKLNLADLENKYNAVIGVYAVDMENGKKICYKPDTRFSYCSTHKVFTAAELLRQKNTSDLNEIRKFSAEDILSYAPITKDHVADGMTLAEICSASLRWSDNTAANLILQEIGGVENFKVALKNIGDKTTKPARNEPELNLFNPKDNRDTSTPRQMVKNLQVYIFGDILSDDKKKLLIDWMSDNSITDTLIKAETPQGWKVIDKSGSGDYGARNDIAVIYPPNRKPIVMAIMSRRTEKNAKSDDAMIAEAAKRIFDNLVF"},"dna_sequence":{"accession":"AJ007350.1","fmin":"239","fmax":"1094","strand":"+","sequence":"ATGAAGAAATTTTGTTTTTTGTTTTTGATAATCTGTGGCTTGATGGTTTTCTGCCTTCAGGATTGTCAAGCGCGGCAGAAATTAAATCTTGCTGATCTGGAAAATAAATATAACGCCGTGATTGGTGTTTACGCCGTTGACATGGAGAATGGAAAAAAAATTTGCTACAAACCTGATACGCGTTTTTCCTACTGCTCGACACACAAAGTTTTTACGGCTGCAGAATTGCTAAGACAAAAAAATACCTCCGATTTGAATGAAATTCGTAAGTTTTCGGCGGAAGATATTTTGTCCTACGCGCCAATCACCAAAGACCATGTTGCTGATGGCATGACGCTGGCGGAAATTTGTTCGGCATCGCTCAGGTGGAGTGACAACACGGCGGCAAATTTAATTTTGCAGGAGATCGGCGGCGTGGAAAATTTCAAGGTGGCACTTAAAAATATTGGCGACAAAACTACCAAACCTGCGCGAAATGAACCTGAACTTAATCTTTTCAATCCAAAAGATAATCGTGATACTAGCACGCCGAGACAGATGGTAAAAAATTTGCAAGTCTATATATTCGGCGATATTTTGAGCGACGACAAGAAAAAACTGCTGATTGATTGGATGAGCGACAATTCCATAACCGACACGCTTATCAAGGCAGAAACTCCGCAAGGTTGGAAAGTTATCGACAAGAGCGGTTCAGGCGATTATGGGGCGCGGAATGATATTGCCGTGATTTATCCGCCCAATCGCAAACCCATTGTCATGGCGATAATGTCGCGCCGCACGGAAAAAAATGCAAAATCTGACGACGCTATGATTGCGGAGGCGGCAAAACGAATTTTTGATAATTTAGTATTTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41532","NCBI_taxonomy_name":"Acidaminococcus fermentans","NCBI_taxonomy_id":"905"}}}},"ARO_accession":"3004359","ARO_id":"41531","ARO_name":"ACI-1","CARD_short_name":"ACI-1","ARO_description":"A class A beta-lactamase described in Acidaminococcus fermentans. ACI-1 was the first description of a beta-lactamase enzyme in a gram-negative anaerobic cocci. Described by Galan et al 2000.","ARO_category":{"41530":{"category_aro_accession":"3004358","category_aro_cvterm_id":"41530","category_aro_name":"ACI beta-lactamase","category_aro_description":"A family of class A beta-lactamase enzymes described in the gram-negative cocci Acidaminococcus fermentans.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"35981":{"category_aro_accession":"0000064","category_aro_cvterm_id":"35981","category_aro_name":"amoxicillin","category_aro_description":"Amoxicillin is a moderate-spectrum, bacteriolytic, beta-lactam antibiotic used to treat bacterial infections caused by susceptible microorganisms. A derivative of penicillin, it has a wider range of treatment but remains relatively ineffective against Gram-negative bacteria. It is commonly taken with clavulanic acid, a beta-lactamase inhibitor. Like other beta-lactams, amoxicillin interferes with the synthesis of peptidoglycan.","category_aro_class_name":"Antibiotic"},"36989":{"category_aro_accession":"3000645","category_aro_cvterm_id":"36989","category_aro_name":"cefotaxime","category_aro_description":"Cefotaxime is a semisynthetic cephalosporin taken parenterally. It is resistant to most beta-lactamases and active against Gram-negative rods and cocci due to its aminothiazoyl and methoximino functional groups.","category_aro_class_name":"Antibiotic"},"40523":{"category_aro_accession":"3003832","category_aro_cvterm_id":"40523","category_aro_name":"ticarcillin","category_aro_description":"Ticarcillin is a carboxypenicillin used for the treatment of Gram-negative bacteria, particularly P. aeruginosa. Ticarcillin's antibiotic properties arise from its ability to prevent cross-linking of peptidoglycan during cell wall synthesis, when the bacteria try to divide, causing cell death.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2875":{"model_id":"2875","model_name":"sul4","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"5844":{"protein_sequence":{"accession":"WP_102607457.1","sequence":"MSTTLTSFKWGERTYIMGILNVTPDSFSGDGVMVEEDVIAKAVAQAKQFVADGADIIDIGGESTRPGSSPISAEEELARVLPVVQAVRQAVDVVISIDSYRASVAEAALAAGASWLNDVWGLRMDPDMAGLAAQAGCPIVLMHNRSKPKNIAQEKKLGGRFIGVKYDDLITDVKRELQESIDIALKAGVKESQIILDPGIGFGKTVEQSLQLLDQINQFKTMGFPILIGPSRKSFIGYTLDLPPDQRIEGTAATVAIGIDRGADVVRVHDVKAIVRVARMTDAIVRR"},"dna_sequence":{"accession":"NG_056174.1","fmin":"100","fmax":"964","strand":"+","sequence":"ATGTCAACCACACTAACCAGCTTCAAATGGGGTGAACGCACCTACATCATGGGCATCCTCAACGTCACTCCAGACAGCTTTTCTGGAGATGGCGTTATGGTTGAAGAAGATGTCATCGCCAAAGCGGTAGCCCAGGCCAAACAATTTGTAGCCGACGGCGCAGACATCATCGACATTGGCGGCGAGAGTACCCGCCCTGGCAGCTCACCTATAAGCGCAGAGGAAGAACTGGCGCGGGTGCTGCCGGTGGTGCAGGCCGTACGCCAGGCTGTGGACGTCGTTATTTCCATCGACAGCTACCGCGCTTCCGTGGCCGAAGCGGCCCTGGCGGCAGGCGCCAGCTGGCTCAACGACGTCTGGGGGCTGCGCATGGACCCGGACATGGCCGGCCTGGCAGCACAAGCCGGCTGCCCCATCGTCCTTATGCACAACCGCAGCAAACCAAAGAACATAGCGCAAGAAAAAAAGCTGGGCGGGCGCTTCATCGGGGTAAAATACGACGACCTCATCACCGACGTTAAACGTGAATTACAAGAAAGCATCGACATCGCCTTAAAAGCCGGCGTAAAAGAGTCCCAAATTATCCTGGATCCCGGCATCGGCTTCGGTAAAACCGTCGAGCAAAGTTTGCAACTGCTCGACCAGATTAATCAGTTCAAAACAATGGGATTTCCCATCTTAATAGGTCCGTCGCGCAAATCATTTATTGGCTATACGCTCGATTTGCCGCCAGACCAGCGCATAGAAGGAACGGCGGCCACCGTCGCCATTGGCATTGACCGAGGAGCCGACGTTGTGCGCGTCCATGACGTCAAAGCAATCGTTCGGGTCGCCCGTATGACAGATGCAATCGTGAGACGTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36791","NCBI_taxonomy_name":"uncultured bacterium","NCBI_taxonomy_id":"77133"}}}},"ARO_accession":"3004361","ARO_id":"41534","ARO_name":"sul4","CARD_short_name":"sul4","ARO_description":"sul4 is a dihydropteroate synthase gene and mobile sulfonamide resistance gene shown to confer resistance when expressed in E. coli.","ARO_category":{"41402":{"category_aro_accession":"3004238","category_aro_cvterm_id":"41402","category_aro_name":"sulfonamide resistant sul","category_aro_description":"The sul genes encode forms of dihydropteroate synthase that confer resistance to sulfonamide.","category_aro_class_name":"AMR Gene Family"},"36468":{"category_aro_accession":"3000329","category_aro_cvterm_id":"36468","category_aro_name":"sulfamethoxazole","category_aro_description":"Sulfamethoxazole is a sulfonamide antibiotic usually taken with trimethoprim, a diaminopyrimidine antibiotic. Sulfamethoxazole inhibits dihydropteroate synthase, essential to tetrahydrofolic acid biosynthesis. This pathway generates compounds used in the synthesis of many amino acids and nucleotides.","category_aro_class_name":"Antibiotic"},"36421":{"category_aro_accession":"3000282","category_aro_cvterm_id":"36421","category_aro_name":"sulfonamide antibiotic","category_aro_description":"Sulfonamides are broad spectrum, synthetic antibiotics that contain the sulfonamide group. Sulfonamides inhibit dihydropteroate synthase, which catalyzes the conversion of p-aminobenzoic acid to dihydropteroic acid as part of the tetrahydrofolic acid biosynthetic pathway. Tetrahydrofolic acid is essential for folate synthesis, a precursor of many nucleotides and amino acids. Many sulfamides are taken with trimethoprim, an inhibitor of dihydrofolate reductase, also disturbing the trihydrofolic acid synthesis pathway.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4259":{"model_id":"4259","model_name":"ADC-194","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6634":{"protein_sequence":{"accession":"WP_133972424.1","sequence":"MRFKKISCLLLPPLFIFNTSIYAGNTPKEQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSIQDKKVVNGSTIFELGSVSKLFTATAGGYAKTKGKISFEDTPGKYWKELKNTPIDQVNLLQLATYTSGNLGLQFPDEVQTDQQVLTFFKEWKPKNQIGEYRQYSNPSIGLFGKIVGLSMNQPFSQVLEKTIFPSLHLKNSYVNVPKIQMQNYAFGYNQENQPIRVTPGPLDAPAYGVKSTLPDMLSFIDANLNPQKYPADIRRAIDETHKGFYQIGTMYQALGWEEFSYPAPLQTLLDSNSEQIVMKSNKVTAISKEPSIKIFHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_066693.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCCTGCTTACTTTTACCGCCTCTTTTCATTTTTAATACCTCAATTTATGCGGGCAATACACCAAAAGAGCAAGAAATTAAAAAACTGGTTGATCAAAACTTTAAACCATTATTAGAAAAATATGACGTGCCCGGTATGGCGGTTGGTGTCATCCAAAATAATAAAAAGTATGAAATGTATTATGGCCTACAATCGATTCAAGATAAAAAAGTTGTAAATGGTAGTACTATTTTTGAGCTAGGTTCAGTCAGTAAATTATTTACTGCGACGGCAGGCGGCTATGCAAAAACAAAAGGAAAAATCTCTTTTGAAGACACCCCAGGAAAATACTGGAAAGAACTAAAAAACACGCCTATTGATCAGGTCAATCTACTTCAACTTGCTACATATACGAGTGGCAACCTTGGCTTACAATTCCCAGATGAAGTACAAACAGACCAGCAAGTTTTAACTTTTTTCAAAGAATGGAAACCTAAAAATCAAATCGGTGAATATCGGCAATATTCAAACCCAAGTATTGGCTTATTTGGAAAAATTGTAGGCTTATCGATGAATCAGCCTTTTAGTCAGGTTTTAGAAAAGACAATTTTTCCGTCTCTTCACTTAAAAAATAGCTATGTAAATGTGCCTAAAATTCAGATGCAAAACTATGCATTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTACCCCAGGCCCACTCGATGCCCCTGCCTACGGGGTTAAATCTACATTACCAGACATGCTTAGCTTTATTGATGCCAATCTAAATCCACAAAAATATCCAGCAGATATTCGACGCGCAATTGATGAGACTCATAAAGGTTTTTATCAAATCGGCACCATGTATCAAGCATTAGGTTGGGAAGAATTTTCTTATCCAGCCCCTTTACAAACTTTATTAGACAGTAACTCTGAACAAATTGTGATGAAATCTAATAAAGTGACTGCCATTTCCAAAGAACCTTCAATCAAAATATTCCATAAAACGGGTTCAACTAACGGATTTGGAACTTATGTCGTGTTTATTCCCAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGCATTCCAAATGAAGAACGTATTAAAGCGGCTTACGCTGTATTGAATGCGATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39094","NCBI_taxonomy_name":"Acinetobacter calcoaceticus","NCBI_taxonomy_id":"471"}}}},"ARO_accession":"3006363","ARO_id":"44825","ARO_name":"ADC-194","CARD_short_name":"ADC-194","ARO_description":"ADC-194 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2876":{"model_id":"2876","model_name":"OXA-436","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4261":{"protein_sequence":{"accession":"ARX76025.1","sequence":"MRALALSAVLMVTTMIGMPAVAKEWQENKSWNAHFSEHKTQGVVVLWNENTQQGFTNDLKRANQAFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGQTRDIAAWNRDHDLITAMKYSVVPVYQEFARQIGEARMSKMLHAFDYGNEDISGNLDSFWLDGGIRISATQQIAFLRKLYHNKLHVSERSQRIVKQAMLTEANADYIIRAKTGYSVRIEPKIGWWVGWIELDDNVWFFATNMDMPTAEGLGLRQTITKAVLKQEKIIP"},"dna_sequence":{"accession":"KY863418.1","fmin":"140925","fmax":"141723","strand":"+","sequence":"ATGCGTGCGTTAGCCTTATCGGCTGTGTTGATGGTGACAACGATGATTGGCATGCCTGCGGTGGCAAAGGAGTGGCAAGAGAACAAGAGTTGGAATGCTCACTTTAGCGAACATAAAACCCAAGGCGTGGTTGTGCTCTGGAACGAGAATACACAGCAGGGTTTTACCAACGATCTTAAACGGGCAAACCAAGCATTTTTACCTGCATCGACCTTTAAGATCCCAAACAGTTTAATTGCCTTGGACTTAGGTGTGGTTAAGGATGAGCATCAAGTCTTTAAATGGGATGGACAGACGCGAGATATCGCCGCGTGGAATCGCGACCATGACTTAATCACCGCGATGAAGTATTCGGTTGTGCCTGTTTATCAAGAATTTGCCCGCCAAATTGGCGAGGCCCGTATGAGTAAAATGTTGCACGCCTTCGATTATGGTAATGAGGATATCTCGGGCAATTTGGACAGTTTTTGGCTCGATGGTGGTATTCGCATTTCGGCTACCCAGCAAATCGCTTTTTTACGCAAGCTGTACCACAACAAGTTGCACGTTTCTGAGCGTAGTCAGCGCATCGTTAAACAAGCCATGCTGACCGAGGCAAATGCCGACTATATCATCCGGGCGAAAACTGGCTATTCGGTCAGAATTGAACCGAAAATCGGTTGGTGGGTTGGCTGGATCGAACTGGATGACAATGTGTGGTTCTTCGCGACAAATATGGATATGCCCACCGCTGAGGGCTTAGGGTTGCGTCAAACCATTACGAAAGCAGTGCTGAAACAGGAAAAAATTATTCCTTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36926","NCBI_taxonomy_name":"Enterobacter asburiae","NCBI_taxonomy_id":"61645"}}}},"ARO_accession":"3003128","ARO_id":"39705","ARO_name":"OXA-436","CARD_short_name":"OXA-436","ARO_description":"An OXA-48-like plasmid-encoded beta-lactamase shown to confer resistance to carbapenems through hydrolysis. Identified in multiple Enterobacteriaceae isolates from several patients in Denmark. Beta-lactamase activity against carbapenems and penicillins but little to no activity against cephalosporin antibiotics. Described by Samuelsen et al. 2017.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46510":{"category_aro_accession":"3007721","category_aro_cvterm_id":"46510","category_aro_name":"OXA-48-like beta-lactamase","category_aro_description":"OXA-48-type beta-lactamases are now routinely encountered in bacterial infections caused by carbapenam-resistant Enterobacterales. OXA-48-like proteins confer resistance to penicillin (which is efficiently hydrolyzed) and carbapenam antibiotics (which is more slowly broken down). The spectrum of activity of these variants varies, with some hydrolyzing expanded-spectrum oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2877":{"model_id":"2877","model_name":"OXA-535","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4262":{"protein_sequence":{"accession":"AOQ26572.1","sequence":"MRALALSAVLMVTTMIGMPAVAKEWQENKSWNAHFSEHKTQGVVVLWNENTQQGFTNDLKRANQAFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGQTRDIAAWNRDHDLITAMKYSVVPVYQGFARQIGEARMSKMLHAFDYGNEDISGNLDSFWLDGGIRISATQQIAFLRKLYHNKLHVSERSQRIVKQAMLTEANADYIIRAKTGYSVRIEPKIGWWVGWVELDDNVWFFATNMDMPTAEGLGLRQSITKAVLKQEKIIP"},"dna_sequence":{"accession":"KX828709.1","fmin":"0","fmax":"798","strand":"+","sequence":"ATGCGTGCGTTAGCCTTATCGGCTGTGTTGATGGTGACAACGATGATTGGCATGCCTGCGGTAGCGAAGGAGTGGCAAGAGAACAAGAGCTGGAATGCTCACTTTAGCGAACATAAAACCCAAGGCGTGGTTGTGCTCTGGAACGAGAATACACAGCAGGGTTTTACTAACGATCTTAAACGGGCAAACCAAGCATTTTTACCAGCATCGACCTTTAAGATCCCAAACAGTTTAATTGCCTTGGACTTAGGCGTGGTTAAGGATGAACATCAAGTCTTTAAATGGGATGGACAGACGCGTGATATCGCCGCGTGGAATCGTGACCATGATTTAATCACCGCGATGAAGTATTCGGTTGTGCCTGTTTATCAAGGATTTGCCCGCCAAATTGGCGAGGCACGTATGAGTAAAATGCTGCATGCCTTCGATTATGGCAATGAGGATATCTCGGGCAATTTAGACAGCTTTTGGCTCGATGGTGGTATTCGCATTTCGGCTACCCAGCAAATCGCTTTTTTACGCAAGCTCTACCACAACAAGCTGCACGTTTCTGAGCGTAGTCAGCGCATTGTCAAACAAGCCATGCTGACCGAGGCAAATGCTGACTATATCATCCGGGCGAAAACTGGCTATTCGGTCAGAATTGAACCGAAAATTGGTTGGTGGGTTGGCTGGGTCGAACTCGATGACAATGTGTGGTTCTTCGCGACTAATATGGATATGCCCACCGCTGAGGGCTTAGGGTTGCGTCAAAGCATTACGAAAGCAGTGCTGAAACAGGAAAAAATTATTCCTTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41536","NCBI_taxonomy_name":"Shewanella sp.","NCBI_taxonomy_id":"50422"}}}},"ARO_accession":"3004362","ARO_id":"41535","ARO_name":"OXA-535","CARD_short_name":"OXA-535","ARO_description":"A chromosome-carried OXA-48-like beta-lactamase, OXA-535, identified in Shewanella spp. JAB-1. Likely the progenitor to the plasmid-carried OXA-436. Expression of OXA-535 in E. coli demonstrated carbapenem-hydrolyzing activity. Described by Jousset et al. 2017.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46510":{"category_aro_accession":"3007721","category_aro_cvterm_id":"46510","category_aro_name":"OXA-48-like beta-lactamase","category_aro_description":"OXA-48-type beta-lactamases are now routinely encountered in bacterial infections caused by carbapenam-resistant Enterobacterales. OXA-48-like proteins confer resistance to penicillin (which is efficiently hydrolyzed) and carbapenam antibiotics (which is more slowly broken down). The spectrum of activity of these variants varies, with some hydrolyzing expanded-spectrum oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2878":{"model_id":"2878","model_name":"almG","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"5309":{"protein_sequence":{"accession":"AAF94731.1","sequence":"MRIFWLKALTSGLFYLPLSIKNGLCRLVAKPISRKKMAAALTQLNYALPDLGDVKKQAIVEQSTRLSLKNLLGFCHLKRYQYQVEQPDLVQEILDNQGGGIIVCPHMGVYDGVTWWLNQQGKKAVTIFGAGSSGDRPDENAMISQAAKLAGVPYLLRKQNLMLELAQRIKQGEWVVLHTDMRTEGVPVRWFGQATQLSATPFFLAHKLACPIYFHYALSEGMTQRLHFSRFALHQTDDLSRNIAQDAQQLADMMQQAITAHPEQWIWLYRRFK"},"dna_sequence":{"accession":"AE003852.1","fmin":"1687437","fmax":"1688259","strand":"-","sequence":"GTGCGTATTTTTTGGTTAAAAGCGTTAACCTCAGGTTTATTTTATTTACCACTGTCGATAAAAAATGGTTTATGCCGCCTCGTGGCTAAGCCGATAAGTCGGAAAAAAATGGCAGCGGCTTTAACGCAACTTAATTACGCGTTACCTGATTTGGGTGACGTAAAAAAGCAGGCGATTGTTGAGCAATCCACGCGCTTATCATTGAAGAATTTACTCGGGTTTTGCCATCTTAAGCGTTACCAATATCAAGTTGAACAGCCTGACTTGGTTCAAGAGATCCTAGATAACCAAGGCGGCGGTATTATCGTTTGTCCTCATATGGGCGTTTACGATGGGGTGACTTGGTGGCTTAACCAGCAAGGTAAAAAAGCCGTCACCATTTTTGGTGCGGGCAGTTCAGGCGATCGTCCAGATGAAAATGCCATGATCTCCCAAGCCGCGAAATTAGCCGGAGTTCCCTATCTGCTACGCAAGCAAAACTTGATGTTGGAGTTAGCACAGCGGATCAAACAAGGTGAATGGGTGGTGTTACATACGGATATGCGAACGGAAGGTGTGCCTGTTCGTTGGTTTGGGCAAGCCACACAATTATCGGCAACGCCTTTTTTCCTTGCGCATAAACTCGCATGCCCGATCTATTTTCATTATGCGCTCAGTGAGGGGATGACGCAGAGACTGCATTTCTCGCGCTTTGCCTTGCACCAAACCGATGACTTAAGTCGCAATATTGCGCAGGATGCGCAGCAGTTAGCCGACATGATGCAGCAAGCGATCACCGCGCATCCCGAGCAGTGGATCTGGCTTTATCGGCGTTTTAAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39595","NCBI_taxonomy_name":"Vibrio cholerae O1 biovar El Tor str. N16961","NCBI_taxonomy_id":"243277"}}}},"ARO_accession":"3004364","ARO_id":"41538","ARO_name":"almG","CARD_short_name":"almG","ARO_description":"A member of the AlmEFG operon, responsible for polymyxin resistance in Vibrio cholerae. AlmG is a glycyltransferase closely related to lipid A acyltransferases. Described by Henderson JC et al. 2017.","ARO_category":{"41537":{"category_aro_accession":"3004363","category_aro_cvterm_id":"41537","category_aro_name":"lipid A acyltransferase","category_aro_description":"Lipid A acyltransferase genes confer resistance to certain types of peptide antibiotics such as polymyxins through the aminoacylation of lipopolysaccharide, thereby decreasing the negative charge of the outer membrane surface.","category_aro_class_name":"AMR Gene Family"},"46184":{"category_aro_accession":"3007428","category_aro_cvterm_id":"46184","category_aro_name":"polymyxin resistance operon","category_aro_description":"Operon or gene clusters confering resistance to polymyxin antibiotics.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3413":{"model_id":"3413","model_name":"OXA-127","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"565"}},"model_sequences":{"sequence":{"5608":{"protein_sequence":{"accession":"ABX45066.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDVKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWQVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"EU255296.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGTAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCAGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAACAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001449","ARO_id":"37849","ARO_name":"OXA-127","CARD_short_name":"OXA-127","ARO_description":"OXA-127 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3435":{"model_id":"3435","model_name":"OXA-268","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"560"}},"model_sequences":{"sequence":{"5631":{"protein_sequence":{"accession":"ENU09033.1","sequence":"MYKKALIVTTSILFLSACSSNSVKQHQIHSMSANKNSEEIKSLFDQAQTTGVLVIKRGKTEEIYGNDLKRASTAYIPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPDWEKDMTLGNAMKASAIPVYQELARRIGLDLMSKEVKRIGFGNANIGSKVDNFWLVGPLKITPQQETQFAYQLAHKTLPFSKDVQEQVQSMVFIEEKNGSKIYAKSGWGWDVEPQVGWLTGWVVQPQGEIVAFSLNLEMKKGTPSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"APOE01000008.1","fmin":"972088","fmax":"972910","strand":"-","sequence":"ATGTATAAAAAAGCGCTTATCGTTACAACAAGTATCCTATTTTTATCCGCCTGTTCTTCTAATTCAGTAAAACAACATCAAATACACTCTATGTCTGCCAATAAAAATTCAGAAGAAATTAAATCACTGTTTGATCAAGCACAAACCACGGGTGTTTTGGTAATTAAGCGAGGGAAAACAGAAGAAATTTATGGCAATGATCTTAAAAGAGCATCAACCGCCTATATTCCCGCCTCTACCTTTAAAATGTTAAATGCTTTAATTGGACTTGAACATCATAAGGCAACTACAACTGAAGTATTTAAATGGGATGGCCAAAAACGTTTATTTCCTGATTGGGAAAAGGACATGACACTGGGTAATGCGATGAAAGCTTCTGCAATTCCAGTTTACCAAGAATTAGCCCGACGAATTGGACTTGACCTTATGTCTAAAGAGGTAAAAAGAATTGGTTTCGGTAATGCTAACATTGGTTCAAAAGTAGATAATTTTTGGCTTGTTGGCCCTCTAAAAATTACGCCTCAACAAGAAACCCAATTTGCTTATCAATTAGCCCATAAAACGCTTCCATTTAGCAAAGATGTACAAGAACAAGTTCAATCAATGGTGTTCATAGAGGAAAAAAATGGAAGTAAGATTTATGCCAAAAGTGGTTGGGGATGGGATGTTGAACCACAAGTTGGTTGGTTAACAGGCTGGGTCGTTCAACCACAAGGAGAAATTGTCGCATTCTCACTTAATTTAGAAATGAAAAAAGGAACTCCTAGCTCTATTCGCAAAGAAATTGCTTATAAAGGCTTAGAACAACTGGGTATATTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42798","NCBI_taxonomy_name":"Acinetobacter calcoaceticus NIPH 13","NCBI_taxonomy_id":"1217654"}}}},"ARO_accession":"3001724","ARO_id":"38124","ARO_name":"OXA-268","CARD_short_name":"OXA-268","ARO_description":"OXA-268 is a beta-lactamase found in Acinetobacter spp.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46495":{"category_aro_accession":"3007706","category_aro_cvterm_id":"46495","category_aro_name":"OXA-213-like beta-lactamase","category_aro_description":"OXA-213-like enzymes have been identified to be intrinsic to A. calcoaceticus and have been subsequently detected in A. pittii. Phylogenetic analysis of OXA-213-like proteins identified two distinct subgroups within the OXA family. The first group was linked to A. pittii and the second group to A. calcoaceticus. The carbapenemase activity of these OXAs may be related to the species-dependent effect.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2880":{"model_id":"2880","model_name":"QepA4","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"900"}},"model_sequences":{"sequence":{"4268":{"protein_sequence":{"accession":"AQX36338.1","sequence":"MSATLHDTAADRRKATRREWIGLAVVALPCLVYAMDLTVLNLALPVLSRELQPSSAQLLWILDIYGFFVAGFLITMGTLGDRIGRRRLLLIGAALFAFASVLAALADTAALLIAARALLGLAGATIAPSTMALIRNMFHDPRQRQFAIGVWIAAFSLGSAIGPLVGGVLLEFFHWGAVFWLNVPVMLLTLALGPRFLPEYRDPDAGHLDLASVLLSLAAVLLTIYGLKQLAEHGAGLASMAALLAGLAVGALFLRRQGHIAYPLLDLRLFAHAPFRAALAAYALAALAMFGVYIFMTQYLQLVLGLSPLQAGLATLPWSLCFVIGSLLSPQLAARWPAARILVVGLSAAAFGFAVLGLGQGLWWLVPATIVMGLGLAPVFTIGNEIIITSAPSERAGAASALSETVSEFSGALGIALFGSVGLVVYRQALTSAALPGLPADALQAAGASLGGAVHLADTLPAWQGAALLAAARAGFTDALQATAWAGAVLVLVAAGLVARLLRKRPALASG"},"dna_sequence":{"accession":"KX686116.1","fmin":"0","fmax":"1536","strand":"+","sequence":"ATGTCCGCCACGCTCCACGACACCGCAGCGGATCGTCGGAAGGCCACCCGCCGCGAATGGATCGGCCTGGCCGTGGTCGCCCTGCCGTGCCTGGTCTACGCCATGGACCTCACGGTGCTGAACCTGGCGCTGCCGGTGCTCAGCCGTGAACTGCAGCCCTCCAGCGCCCAGCTTCTCTGGATCCTGGACATCTACGGCTTCTTCGTCGCCGGCTTCCTGATCACCATGGGCACGCTGGGCGACCGCATCGGCCGGCGCCGGCTGTTGTTGATCGGCGCGGCGTTATTCGCATTCGCCTCGGTGCTCGCGGCGCTGGCCGATACCGCCGCGCTGTTGATCGCGGCGCGCGCCTTGCTCGGCCTGGCCGGCGCCACCATCGCGCCGTCCACCATGGCGCTGATCCGCAACATGTTCCACGACCCGCGCCAGCGCCAGTTCGCCATCGGCGTGTGGATCGCCGCGTTTTCGCTGGGCAGCGCGATCGGTCCGCTGGTCGGCGGCGTGTTGCTGGAGTTCTTCCACTGGGGCGCCGTGTTCTGGCTCAACGTGCCGGTGATGCTGCTGACGCTGGCGCTCGGCCCTCGCTTCCTGCCCGAGTATCGTGATCCGGACGCGGGGCACCTGGACCTGGCCAGCGTGCTGCTGTCGCTGGCGGCGGTGCTGCTGACGATCTACGGGCTCAAGCAGTTGGCCGAGCATGGAGCGGGCCTCGCCTCGATGGCTGCGCTGCTGGCCGGGCTGGCGGTCGGGGCGCTGTTCCTGCGCCGCCAGGGCCACATCGCCTACCCGCTGCTGGACCTGCGGCTGTTCGCGCACGCGCCGTTCCGCGCGGCGCTGGCGGCGTATGCGCTGGCCGCGCTGGCCATGTTCGGCGTCTACATCTTCATGACGCAGTACCTGCAGCTCGTGCTGGGGCTGTCGCCGCTGCAGGCCGGGCTGGCCACGCTGCCCTGGTCCCTGTGCTTCGTCATCGGTTCGCTGTTGTCGCCGCAGCTCGCGGCGCGCTGGCCGGCGGCGCGCATCCTCGTCGTGGGCCTGTCGGCAGCGGCGTTCGGCTTCGCCGTGCTGGGGCTGGGGCAGGGCCTGTGGTGGCTGGTGCCGGCCACGATCGTCATGGGCCTGGGCCTGGCGCCGGTGTTCACCATCGGCAACGAGATCATCATCACCAGCGCGCCGTCCGAGCGCGCGGGCGCGGCCTCGGCCTTGTCGGAGACGGTGTCCGAATTCAGCGGCGCGCTGGGCATCGCGCTGTTCGGCAGCGTCGGCCTGGTGGTCTACCGGCAGGCGCTGACCAGCGCGGCGCTGCCCGGCCTGCCGGCCGATGCGCTGCAGGCGGCCGGTGCCTCGCTCGGGGGCGCCGTGCACCTGGCCGACACCCTGCCGGCGTGGCAGGGCGCGGCCTTGCTGGCGGCCGCACGCGCGGGCTTCACCGATGCGCTGCAGGCCACGGCCTGGGCCGGCGCGGTGCTGGTGCTGGTGGCCGCTGGGCTGGTGGCGCGCCTGCTGCGCAAGCGCCCAGCGCTCGCATCTGGTTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3004379","ARO_id":"41553","ARO_name":"QepA4","CARD_short_name":"QepA4","ARO_description":"A plasmid-mediated quinolone efflux pump variant described in Escherichia coli. QepA4 confers resistance to quinolone and fluoroquinolone antibiotics by expulsion from the cell. Described by Manageiro et al. 2017.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2881":{"model_id":"2881","model_name":"tet(59)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4269":{"protein_sequence":{"accession":"AMP42492.1","sequence":"MNKFAITALTITALDAMGIGLIMPVLPTLLREYVSAENLANHYGILLALYAIMQVFFAPLLGKWSDKFGRRPILLLSLAGAAVDYTLLALSSSLWMLYVGRLISGVTGATGAVAASVIADNTASQERTKWFGRLGAAFGIGLIAGPAIGGFTGQFSAHLPFIIAAILNALSFLVIMLIFKDNKIKNTEKNTTETAENSRPFLQVIKPVILLLFIFFMTQMIGQIPATTWVLFTEHRFQWGSMEVGLSLAGLGIMHALFQAFVAGAIAKKFNEKVTIIVGFVVDGAAFIILSLLTKGWMIYPTLILLAGGSIALPALQGLMSAQVNQTNQGKLQGVLVSLTNTTGVIGPLLFSFIFGQTLASWDGWIWMIGAIMYVLLIVFILSFYRSTKKIVKIAKLPAS"},"dna_sequence":{"accession":"KU736879.1","fmin":"22312","fmax":"23515","strand":"+","sequence":"ATGAATAAATTTGCGATCACCGCTTTAACGATCACCGCCCTAGATGCTATGGGGATCGGCTTGATCATGCCTGTATTGCCTACATTGTTACGTGAATACGTGTCGGCTGAAAATTTAGCAAATCATTACGGTATCCTGCTGGCACTGTATGCCATCATGCAGGTTTTTTTTGCTCCTCTACTTGGCAAATGGTCTGATAAATTCGGGCGCCGACCAATATTACTACTATCTCTTGCAGGCGCTGCTGTGGATTACACTTTGCTTGCATTATCTAGCTCACTTTGGATGCTATACGTTGGGCGATTAATTTCTGGAGTTACTGGCGCAACAGGTGCGGTCGCCGCTTCTGTTATTGCTGACAATACTGCTTCACAAGAGCGTACTAAGTGGTTTGGACGCTTAGGGGCGGCTTTTGGTATCGGGTTAATCGCTGGCCCTGCAATTGGCGGCTTTACAGGGCAATTCTCAGCTCACCTTCCTTTTATTATTGCTGCCATTTTAAATGCGCTCTCTTTTTTAGTTATTATGTTGATATTTAAAGATAATAAAATCAAAAATACTGAAAAAAACACCACAGAAACAGCAGAAAATTCGCGACCTTTCCTGCAAGTGATCAAGCCAGTCATACTATTGTTATTTATCTTTTTTATGACTCAAATGATAGGGCAAATTCCAGCAACGACATGGGTGTTATTTACGGAACATCGTTTTCAATGGGGCAGTATGGAGGTCGGCCTATCTTTAGCGGGGTTAGGCATCATGCATGCCTTGTTCCAAGCATTTGTAGCGGGCGCAATCGCCAAGAAATTCAATGAAAAAGTGACGATTATTGTGGGCTTTGTTGTTGATGGAGCAGCATTCATTATTTTGTCATTATTGACAAAGGGTTGGATGATTTACCCTACATTAATCTTACTCGCCGGCGGCAGTATTGCGCTACCAGCCTTACAGGGGTTAATGTCAGCTCAAGTCAATCAAACTAACCAAGGTAAGCTACAAGGCGTTCTAGTCAGCTTAACCAATACGACGGGGGTGATCGGCCCATTATTATTTAGCTTTATTTTTGGTCAAACACTGGCAAGTTGGGATGGCTGGATATGGATGATTGGTGCGATAATGTATGTTTTATTGATTGTATTTATTTTATCTTTTTATAGAAGCACCAAAAAGATAGTTAAAATAGCGAAGCTACCAGCGAGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41633","NCBI_taxonomy_name":"uncultured bacterium IN-14","NCBI_taxonomy_id":"1805592"}}}},"ARO_accession":"3004441","ARO_id":"41632","ARO_name":"tet(59)","CARD_short_name":"tet(59)","ARO_description":"Tet(59) is a chromosome-encoded tetracycline efflux pump described from a Chinese pig manure sample.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36667":{"category_aro_accession":"3000528","category_aro_cvterm_id":"36667","category_aro_name":"chlortetracycline","category_aro_description":"Chlortetracycline was an early, first-generation tetracycline antibiotic developed in the 1940's. It inhibits bacterial protein synthesis by binding to the 30S subunit of bacterial ribosomes, preventing the aminoacyl-tRNA from binding to the ribosome.","category_aro_class_name":"Antibiotic"},"37012":{"category_aro_accession":"3000668","category_aro_cvterm_id":"37012","category_aro_name":"oxytetracycline","category_aro_description":"Oxytetracycline is a derivative of tetracycline with a 5-hydroxyl group. Its activity is similar to other tetracyclines.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2882":{"model_id":"2882","model_name":"tet(W\/N\/W)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"4270":{"protein_sequence":{"accession":"AMP42147.1","sequence":"MKIINIGILAHVDAGKTTLTESLLYASGAISEPGSVEKGTTRTDTMFLERQRGITIQAAVTSFQWHRCKVNIVDTPGHMDFLAEVYRSLAVLDGAILVISAKDGVQAQTRILFHALRKMNIPTVIFINKIDQAGVDLQSVYQSVRDKLSADIIIKQTVSLSPEIVLEENTDIEAWDAVIENNDELLEKYIAGEPISREKLAREEQQRVQDASLFPVYHGSAKNGLGIQPLMDAVTGLFQPIGEQGGAALCGSVFKVEYTDCGQRLVYLRLYSGTLRLRDTVALAGREKLKITEMRIPSKGEIVRTDTAHKGEIVILPSDSLRLNDILGDKTQLPREMWSDVPFPMLRTTITPKTAEQRDRLLDALTQIADTDPLLHYEVDSITHEIILSFLGRVQLEVVSALLSEKYKLETVVKEPTVIYMERPLKAASHTIHIEVPPNPFWASIGLSVTPLPLGSGVQYESRVSLGYLNQSFQNAVRDGIRYGLEQGLFGWNVTDCKICFEYGLYYSPVSTPADFRSLAPIVLEQALKESGTQLLEPYLSFTLYAPREYLSRAYHDAPKYCATIETVQVKKDEVVFTGEIPARCIQAYRTDLAFYTNGRSVCLTELKGYQATVGEPIIQPRRPNSRLDKVRHMFSKIP"},"dna_sequence":{"accession":"KU736867.1","fmin":"19653","fmax":"21573","strand":"+","sequence":"ATGAAAATAATCAATATTGGAATTCTTGCCCATGTAGACGCTGGAAAGACGACCTTGACGGAGAGCCTGCTATATGCCAGCGGAGCCATTTCAGAACCGGGGAGCGTCGAAAAAGGGACAACGAGGACGGACACCATGTTTTTGGAGCGGCAGCGTGGGATTACCATTCAAGCGGCAGTCACTTCCTTCCAGTGGCACAGATGTAAAGTTAACATTGTGGATACGCCCGGCCACATGGATTTTTTGGCGGAGGTGTACCGCTCTTTGGCTGTTTTAGATGGGGCCATCTTGGTGATCTCCGCTAAAGATGGCGTGCAGGCCCAGACCCGTATTCTGTTCCATGCCCTGCGGAAAATGAACATTCCCACCGTTATCTTTATCAACAAGATCGACCAGGCTGGCGTTGATTTGCAGAGCGTATATCAGTCTGTTCGGGATAAGCTCTCCGCCGATATTATCATCAAGCAGACGGTGTCGCTGTCCCCGGAAATAGTCCTGGAGGAAAATACCGACATAGAAGCATGGGATGCGGTCATCGAAAATAACGATGAATTATTGGAAAAGTATATCGCAGGAGAACCAATCAGCCGGGAAAAACTTGCGCGGGAGGAACAGCAGCGGGTTCAAGACGCCTCCCTGTTCCCAGTCTATCATGGCAGCGCCAAAAATGGCCTTGGCATTCAACCGTTGATGGATGCGGTGACAGGGCTGTTCCAACCGATTGGGGAACAGGGGGGCGCCGCCCTATGCGGCAGCGTTTTCAAGGTGGAGTATACAGATTGCGGCCAGAGGCTTGTCTATCTGCGGCTATACAGCGGAACGCTGCGTCTGCGGGATACGGTGGCCCTAGCCGGGAGAGAAAAGCTGAAAATCACAGAGATGCGTATTCCATCCAAAGGGGAGATTGTTCGGACAGATACCGCCCATAAGGGCGAAATTGTCATCCTTCCCAGCGACAGCTTGAGATTAAACGATATATTGGGGGACAAAACCCAACTTCCTCGTGAAATGTGGAGTGATGTTCCCTTCCCTATGCTGCGGACGACGATTACGCCAAAAACGGCAGAGCAAAGAGACCGGTTGCTGGACGCTCTTACGCAAATTGCGGATACTGACCCGCTTTTGCACTACGAGGTGGATTCCATCACCCATGAGATCATTCTTTCTTTTTTGGGCCGGGTGCAGTTGGAGGTTGTTTCCGCTTTGCTGTCGGAAAAATACAAGCTTGAAACAGTGGTAAAGGAACCCACCGTCATTTATATGGAGCGGCCGCTCAAAGCAGCCAGCCACACCATCCATATCGAGGTGCCGCCCAACCCGTTTTGGGCATCCATCGGACTGTCTGTTACACCACTCCCGCTTGGCTCCGGTGTACAATACGAGAGCCGGGTTTCGCTGGGATACTTGAACCAGAGTTTTCAAAACGCTGTCAGGGATGGTATCCGTTACGGGCTGGAGCAGGGCTTGTTCGGCTGGAACGTAACGGACTGTAAGATTTGCTTTGAATACGGGCTTTATTACAGTCCGGTCAGCACGCCGGCGGACTTCCGCTCATTGGCCCCGATTGTATTGGAACAGGCATTGAAGGAATCAGGGACGCAACTGCTGGAACCTTATCTCTCCTTCACCCTCTATGCGCCCCGGGAATATCTTTCCAGGGCTTATCATGATGCACCGAAATACTGTGCCACCATCGAAACGGTCCAGGTAAAAAAGGATGAAGTTGTCTTTACTGGCGAGATTCCCGCCCGTTGCATACAGGCATACCGTACTGATTTGGCCTTTTACACCAACGGGCGGAGTGTGTGCCTGACGGAACTGAAAGGGTATCAGGCCACTGTCGGCGAGCCAATCATCCAGCCCCGTCGTCCAAACAGCCGTTTGGATAAGGTGCGCCATATGTTCAGTAAGATTCCTTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41635","NCBI_taxonomy_name":"uncultured bacterium IN-02","NCBI_taxonomy_id":"1805580"}}}},"ARO_accession":"3004442","ARO_id":"41634","ARO_name":"tet(W\/N\/W)","CARD_short_name":"tet(W\/N\/W)","ARO_description":"tet(W\/N\/W) is a mosaic tetracycline resistance gene and ribosomal protection protein.","ARO_category":{"35921":{"category_aro_accession":"0000002","category_aro_cvterm_id":"35921","category_aro_name":"tetracycline-resistant ribosomal protection protein","category_aro_description":"A family of proteins known to bind to the 30S ribosomal subunit. This interaction prevents tetracycline and tetracycline derivatives from inhibiting ribosomal function. Thus, these proteins confer elevated resistance to tetracycline derivatives as a ribosomal protection protein.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36291":{"category_aro_accession":"3000152","category_aro_cvterm_id":"36291","category_aro_name":"minocycline","category_aro_description":"Minocycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36667":{"category_aro_accession":"3000528","category_aro_cvterm_id":"36667","category_aro_name":"chlortetracycline","category_aro_description":"Chlortetracycline was an early, first-generation tetracycline antibiotic developed in the 1940's. It inhibits bacterial protein synthesis by binding to the 30S subunit of bacterial ribosomes, preventing the aminoacyl-tRNA from binding to the ribosome.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2886":{"model_id":"2886","model_name":"Haemophilus influenzae PBP3 conferring resistance to beta-lactam antibiotics","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"},"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"8321":"D350N","8322":"S357N","8323":"S385T","8324":"L389F","8325":"V562L"},"Curated-R":{"8321":"D350N","8322":"S357N","8323":"S385T","8324":"L389F","8325":"V562L"},"clinical":{"8321":"D350N","8322":"S357N","8323":"S385T","8324":"L389F","8325":"V562L"}}},"model_sequences":{"sequence":{"5502":{"protein_sequence":{"accession":"AAC22787.1","sequence":"MVKFNSSRKSGKSKKTIRKLTAPETVKQNKPQKVFEKCFMRGRYMLSTVLILLGLCALVARAAYVQSINADTLSNEADKRSLRKDEVLSVRGSILDRNGQLLSVSVPMSAIVADPKTMLKENSLADKERIAALAEELGMTENDLVKKIEKNSKSGYLYLARQVELSKANYIRRLKIKGIILETEHRRFYPRVEEAAHVVGYTDIDGNGIEGIEKSFNSLLVGKDGSRTVRKDKRGNIVAHISDEKKYDAQDVTLSIDEKLQSMVYREIKKAVSENNAESGTAVLVDVRTGEVLAMATAPSYNPNNRVGVKSELMRNRAITDTFEPGSTVKPFVVLTALQRGVVKRDEIIDTTSFKLSGKEIVDVAPRAQQTLDEILMNSSNRGVSRLALRMPPSALMETYQNAGLSKPTDLGLIGEQVGILNANRKRWADIERATVAYGYGITATPLQIARAYATLGSFGVYRPLSITKVDPPVIGKRVFSEKITKDIVGILEKVAIKNKRAMVEGYRVGVKTGTARKIENGHYVNKYVAFTAGIAPISDPRYALVVLINDPKAGEYYGGAVSAPVFSNIMGYALRANAIPQDAEAAENTTTKSAKRIVYIGEHKNQKVN"},"dna_sequence":{"accession":"L42023.1","fmin":"1197839","fmax":"1199672","strand":"+","sequence":"ATGGTGAAATTTAATTCCTCGCGTAAATCAGGTAAGTCAAAAAAAACAATTAGAAAATTGACCGCACCTGAAACTGTAAAGCAAAACAAGCCTCAAAAGGTGTTTGAAAAATGCTTTATGCGTGGACGTTATATGCTTTCTACGGTTCTTATTTTACTTGGCCTGTGTGCTTTAGTCGCACGAGCAGCTTATGTTCAATCTATTAATGCCGATACGTTATCGAATGAAGCGGATAAGCGTTCTTTGCGTAAAGATGAAGTATTATCGGTGCGTGGTTCTATTTTAGATCGTAATGGTCAGCTTTTATCTGTAAGCGTGCCGATGAGCGCGATTGTGGCAGATCCAAAAACGATGTTGAAGGAAAATTCGCTTGCGGATAAAGAACGAATTGCAGCTTTAGCCGAAGAATTAGGTATGACTGAAAATGATTTAGTGAAAAAAATTGAGAAAAATTCTAAATCTGGTTATTTGTATTTAGCACGTCAAGTTGAATTAAGTAAAGCTAACTATATTCGTAGATTAAAAATTAAGGGTATTATTTTAGAAACAGAGCATCGCCGTTTTTATCCTCGTGTAGAAGAAGCTGCACACGTGGTGGGTTATACGGATATTGATGGAAATGGTATTGAAGGCATTGAGAAAAGTTTTAATTCCCTGCTTGTTGGTAAAGACGGTTCACGTACTGTTCGTAAAGATAAACGTGGGAATATTGTTGCACATATCTCCGATGAGAAAAAATATGATGCACAAGATGTTACCTTAAGTATCGATGAAAAATTGCAATCTATGGTGTATCGTGAGATTAAAAAGGCGGTGTCTGAGAATAATGCTGAGTCTGGTACTGCGGTGTTAGTTGATGTTCGAACAGGGGAAGTGTTAGCTATGGCGACTGCGCCCTCTTATAATCCAAACAACCGTGTCGGCGTGAAATCAGAGTTAATGCGTAACCGTGCAATTACCGATACTTTTGAGCCAGGTTCTACGGTAAAACCTTTCGTTGTTTTAACCGCACTTCAACGAGGTGTAGTTAAACGAGATGAAATTATTGATACTACGTCCTTTAAATTAAGCGGTAAAGAAATTGTGGACGTTGCACCACGTGCTCAGCAAACTTTAGACGAGATTTTAATGAACTCTAGTAACCGTGGTGTAAGTCGTCTTGCATTACGTATGCCACCTAGTGCATTAATGGAAACTTATCAAAATGCAGGTTTAAGTAAACCGACAGATTTAGGCTTGATCGGAGAGCAAGTTGGGATTTTGAATGCAAATCGTAAACGCTGGGCAGATATTGAGCGTGCAACAGTCGCTTATGGTTATGGTATTACTGCGACACCTTTACAAATTGCTCGTGCCTATGCAACCCTTGGTAGTTTCGGTGTTTATCGTCCGCTTTCTATCACTAAAGTTGATCCGCCAGTTATTGGGAAACGGGTTTTCTCTGAAAAAATAACTAAAGATATTGTGGGAATTTTAGAGAAAGTAGCAATTAAAAATAAACGCGCAATGGTGGAAGGCTACCGTGTCGGCGTAAAAACAGGTACGGCACGTAAGATTGAAAATGGACATTATGTAAATAAGTATGTGGCATTTACTGCGGGTATTGCACCAATTAGTGATCCTCGTTATGCATTAGTGGTTTTGATCAATGATCCAAAAGCAGGAGAATATTATGGTGGTGCGGTTTCTGCCCCTGTATTCTCTAACATTATGGGCTATGCGTTACGTGCAAATGCTATTCCGCAAGATGCTGAAGCAGCTGAAAACACAACAACGAAAAGTGCAAAACGTATTGTTTATATTGGCGAACACAAGAATCAAAAAGTGAATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41640","NCBI_taxonomy_name":"Haemophilus influenzae Rd KW20","NCBI_taxonomy_id":"71421"}}}},"ARO_accession":"3004446","ARO_id":"41639","ARO_name":"Haemophilus influenzae PBP3 conferring resistance to beta-lactam antibiotics","CARD_short_name":"Hinf_PBP3_BLA","ARO_description":"PBP3 is a penicillin-binding protein and beta-lactam resistance enzyme encoded by the ftsI gene in Haemophilus influenzae. Mutations in ftsI confer resistance to beta-lactam antibiotics.","ARO_category":{"40661":{"category_aro_accession":"3003938","category_aro_cvterm_id":"40661","category_aro_name":"Penicillin-binding protein mutations conferring resistance to beta-lactam antibiotics","category_aro_description":"Mutations in PBP transpeptidases that change the affinity for penicillin thereby conferring resistance to penicillin antibiotics.","category_aro_class_name":"AMR Gene Family"},"35979":{"category_aro_accession":"0000062","category_aro_cvterm_id":"35979","category_aro_name":"ceftriaxone","category_aro_description":"Ceftriaxone is a third-generation cephalosporin antibiotic. The presence of an aminothiazolyl sidechain increases ceftriazone's resistance to beta-lactamases. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"36988":{"category_aro_accession":"3000644","category_aro_cvterm_id":"36988","category_aro_name":"cefaclor","category_aro_description":"Cefaclor is a semisynthetic cephalosporin derived from cephalexin. It has broad-spectrum antibiotic activity.","category_aro_class_name":"Antibiotic"},"36989":{"category_aro_accession":"3000645","category_aro_cvterm_id":"36989","category_aro_name":"cefotaxime","category_aro_description":"Cefotaxime is a semisynthetic cephalosporin taken parenterally. It is resistant to most beta-lactamases and active against Gram-negative rods and cocci due to its aminothiazoyl and methoximino functional groups.","category_aro_class_name":"Antibiotic"},"36993":{"category_aro_accession":"3000649","category_aro_cvterm_id":"36993","category_aro_name":"cefditoren","category_aro_description":"Cefditoren is a semisynthetic cephalosporin active against staphylococci, streptococci, and and most enterobacteria. It is resistant to staphylococcal and most enterobacterial beta-lactamases, and is usually taken as the prodrug cefditoren pivoxil.","category_aro_class_name":"Antibiotic"},"36994":{"category_aro_accession":"3000650","category_aro_cvterm_id":"36994","category_aro_name":"cefdinir","category_aro_description":"Cefdinir is similar to cefixime with a modified side-chain at its 7-amino position. It also shares similar activity with cefixime but is more active against staphylococci. It has also be shown to enhance phagocytosis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3436":{"model_id":"3436","model_name":"OXA-269","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"560"}},"model_sequences":{"sequence":{"5632":{"protein_sequence":{"accession":"EOQ63861.1","sequence":"MYKKVLIVATTTLFLSACSSKTVKQHQIHSISANQNSEEIKSLFDQAQTTGVLVIKRGQTEEIYGNDLKRSSTEYVPASTFKILNALIGLEHHKVTTTEVFKWDGQKRLFPDWEKDMTLGDAMQASAIPVYQKLARRIGLDLMSKEVKRVGFGNADIGSRVDNFWLVGPLKITPLQEAEFAYELAHKTLPFSKNVQEQVQSLVFIEEKNGRKIYAKSGWALDIDPQVGWLTGWVVQPQGEIVAFSLNLEMKKGTPSIIRKEITYKGLEQLGIL"},"dna_sequence":{"accession":"APQJ01000007.1","fmin":"349333","fmax":"350155","strand":"+","sequence":"ATGTATAAAAAAGTCCTTATCGTGGCAACAACTACTCTATTTTTATCTGCCTGCTCTTCTAAGACGGTAAAACAACATCAAATACACTCTATTTCTGCCAATCAAAATTCAGAAGAAATTAAATCACTGTTTGATCAGGCGCAGACTACGGGGGTTTTGGTGATTAAGCGTGGGCAAACAGAAGAAATTTATGGTAATGATTTGAAAAGATCATCAACCGAATATGTTCCCGCCTCTACCTTTAAAATATTGAATGCTTTAATTGGACTTGAACATCATAAGGTAACAACAACTGAAGTGTTTAAATGGGATGGGCAAAAGCGTTTATTTCCTGATTGGGAAAAGGACATGACACTGGGCGATGCCATGCAAGCTTCTGCTATTCCAGTTTATCAAAAATTAGCCCGAAGAATTGGCCTGGATCTTATGTCTAAAGAGGTGAAACGAGTTGGTTTCGGTAATGCGGACATTGGTTCACGAGTAGATAATTTTTGGCTTGTTGGTCCACTCAAAATTACACCTCTGCAAGAAGCCGAATTTGCTTATGAATTAGCTCATAAAACTCTTCCATTTAGCAAAAATGTACAAGAACAAGTTCAGTCACTGGTGTTCATAGAAGAAAAAAATGGACGTAAAATTTACGCAAAAAGTGGTTGGGCATTGGATATTGATCCACAAGTTGGTTGGTTAACAGGCTGGGTCGTTCAACCACAAGGAGAAATTGTGGCATTCTCACTTAATTTAGAAATGAAAAAAGGAACTCCTAGCATTATTCGTAAAGAAATTACTTATAAAGGATTAGAACAACTGGGTATCTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42799","NCBI_taxonomy_name":"Acinetobacter calcoaceticus ANC 3811","NCBI_taxonomy_id":"1217690"}}}},"ARO_accession":"3001725","ARO_id":"38125","ARO_name":"OXA-269","CARD_short_name":"OXA-269","ARO_description":"OXA-269 is a beta-lactamase found in Acinetobacter spp.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46495":{"category_aro_accession":"3007706","category_aro_cvterm_id":"46495","category_aro_name":"OXA-213-like beta-lactamase","category_aro_description":"OXA-213-like enzymes have been identified to be intrinsic to A. calcoaceticus and have been subsequently detected in A. pittii. Phylogenetic analysis of OXA-213-like proteins identified two distinct subgroups within the OXA family. The first group was linked to A. pittii and the second group to A. calcoaceticus. The carbapenemase activity of these OXAs may be related to the species-dependent effect.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2889":{"model_id":"2889","model_name":"TRU-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"5501":{"protein_sequence":{"accession":"ABW05394.1","sequence":"MKQRIALSLLALGPLLLVPRVYAAADEPMANIVEKAVQPLLEEYRIPGMAVAVLKEGKPHYFNYGVANRESGRRISERTLFEIGSVSKTFTATLGTYAVVKGGFRLDDKVSQHAPWLQNSAFDRVTMAQLATYSAGGLPLQFPDAVDSNERMRQYYRQWSPLYAAGTHREYSNPSIGLFGHLAASTLGQPFRQLMSQTLLPKLDLQHTYLEVPDAAMVDYAYGYSKEDKPVRVNPGVLADEAYGIKTSAADLIKFVGANMTGSGDKAVQQALAMTRTGFYSVGEMTQGLGWESYAYPVTEQALLAGNSPAVSFKANPVKPFVAPRVMGNERLYNKTGSTNGFGAYVVFVPARGVGIVMLANRNYPIEARVKAAYAIMRHLAP"},"dna_sequence":{"accession":"EU046614.1","fmin":"0","fmax":"1149","strand":"+","sequence":"ATGAAACAACGAATCGCGCTATCACTGCTGGCATTGGGGCCCCTGTTGCTCGTCCCACGCGTTTATGCCGCGGCAGATGAGCCCATGGCGAACATAGTGGAAAAGGCTGTCCAGCCGCTGCTGGAGGAGTACCGGATCCCGGGCATGGCGGTCGCCGTGCTGAAGGAGGGCAAGCCTCACTACTTCAATTATGGCGTCGCCAATCGGGAGAGCGGCCGGCGCATCAGCGAGCGGACCCTGTTCGAGATTGGTTCGGTCAGCAAGACCTTTACTGCGACCTTGGGCACCTACGCGGTCGTCAAAGGGGGCTTTCGGCTGGATGACAAGGTGAGCCAGCACGCGCCTTGGTTGCAGAATTCGGCGTTTGATCGCGTCACCATGGCCCAGCTGGCGACCTACAGCGCAGGGGGCTTGCCGTTGCAGTTTCCCGATGCGGTCGACTCAAACGAGAGAATGCGCCAGTACTACCGGCAGTGGTCACCGCTTTATGCGGCAGGCACTCATCGCGAGTACTCCAACCCCAGCATAGGTCTGTTCGGCCATCTGGCGGCGAGCACCCTGGGCCAACCATTCAGACAACTGATGAGCCAGACTCTGCTGCCCAAGCTCGATTTGCAGCACACCTATCTCGAGGTGCCAGACGCAGCCATGGTTGACTACGCCTATGGCTATTCGAAGGAAGACAAACCCGTCAGGGTCAATCCCGGAGTGCTGGCGGACGAAGCCTATGGCATCAAGACCAGCGCGGCGGATCTCATCAAGTTTGTGGGCGCCAACATGACAGGCAGTGGCGACAAGGCGGTGCAGCAAGCGCTGGCCATGACCCGTACCGGTTTCTACTCGGTGGGAGAGATGACCCAGGGGCTGGGGTGGGAGAGCTACGCCTATCCCGTGACCGAACAGGCGCTGCTGGCGGGCAATTCACCGGCGGTGAGCTTCAAGGCCAATCCGGTCAAACCCTTTGTGGCTCCCAGAGTGATGGGGAACGAGCGACTCTACAACAAGACAGGCTCGACCAACGGCTTTGGTGCCTATGTGGTGTTTGTCCCGGCCAGAGGCGTGGGCATCGTCATGCTGGCCAATCGCAACTACCCCATCGAGGCCAGGGTCAAGGCTGCCTATGCCATCATGCGCCATCTGGCACCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41646","NCBI_taxonomy_name":"Aeromonas enteropelogenes","NCBI_taxonomy_id":"29489"}}}},"ARO_accession":"3004450","ARO_id":"41645","ARO_name":"TRU-1","CARD_short_name":"TRU-1","ARO_description":"A class C beta-lactamase enzyme identified from Aeromonas enteropelogenes. TRU-1 confers resistance to penicillin and cephalosporin antibiotics.","ARO_category":{"41644":{"category_aro_accession":"3004449","category_aro_cvterm_id":"41644","category_aro_name":"TRU beta-lactamase","category_aro_description":"A class C beta-lactamase endogenous to Aeromonas enteropelogenes (tructi).","category_aro_class_name":"AMR Gene Family"},"37084":{"category_aro_accession":"3000704","category_aro_cvterm_id":"37084","category_aro_name":"cefalotin","category_aro_description":"Cefalotin is a semisynthetic cephalosporin antibiotic activate against staphylococci. It is resistant to staphylococci beta-lactamases but hydrolyzed by enterobacterial beta-lactamases.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"237":{"model_id":"237","model_name":"Chryseobacterium meningosepticum BlaB","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"5396":{"protein_sequence":{"accession":"AIL46641.1","sequence":"MLKKIKISLILALGLTSLKAFGQENPDVKIEKLKDNLYVYTTYNTFNGTKYAANAVYLVTDKGVVVIDCPWGEDKFKSFTDEIYKKHGKKVIMNIATHSHDDRAGGLEYFGKIGAKTYSTKMTDSILAKENKPRAQYTFDNNKSFKVGKSEFQVYYPGKGHTADNVVVWFPKEKVLVGGCIIKSADSKDLGYIGEAYVNDWTQSVHNIQQKFSGAQYVVAGHDDWKDQRSIQHTLDLINEYQQKQKASN"},"dna_sequence":{"accession":"CP007547.1","fmin":"3053571","fmax":"3054321","strand":"-","sequence":"ATGTTGAAAAAAATAAAAATAAGCTTGATTCTTGCTCTTGGGCTTACCAGTTTGAAGGCATTTGGACAGGAGAATCCTGATGTCAAAATTGAAAAGCTAAAAGATAATCTGTATGTATACACAACCTACAATACATTTAACGGGACTAAATATGCCGCAAATGCAGTATATCTGGTAACTGATAAGGGTGTTGTGGTTATAGACTGTCCGTGGGGAGAAGACAAATTTAAAAGCTTTACGGACGAGATTTATAAAAAACACGGAAAGAAAGTTATTATGAATATTGCAACACATTCTCATGATGATCGTGCCGGAGGTCTTGAATATTTTGGTAAAATAGGTGCAAAAACTTATTCTACTAAAATGACAGATTCTATTTTAGCAAAAGAGAATAAGCCAAGAGCACAATATACTTTTGACAATAATAAATCTTTCAAAGTAGGAAAATCCGAGTTTCAGGTTTACTATCCCGGAAAAGGGCACACAGCAGATAATGTGGTGGTATGGTTTCCAAAAGAAAAAGTATTGGTTGGAGGTTGTATTATAAAAAGTGCTGATTCAAAGGACCTGGGGTATATTGGAGAAGCATATGTAAACGACTGGACGCAGTCTGTACACAATATTCAACAAAAGTTTTCCGGTGCTCAGTACGTTGTTGCAGGGCATGATGATTGGAAAGATCAAAGATCAATACAACATACACTAGACTTAATCAATGAATATCAACAAAAACAAAAGGCTTCAAATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42619","NCBI_taxonomy_name":"Elizabethkingia anophelis NUHP1","NCBI_taxonomy_id":"1338011"}}}},"ARO_accession":"3000579","ARO_id":"36718","ARO_name":"Chryseobacterium meningosepticum BlaB","CARD_short_name":"Cmen_BlaB","ARO_description":"This BlaB specific to Chryseobacterium meningosepticum mediates resistance against many beta-lactam antibiotics, notably penams and carbapenems.","ARO_category":{"41365":{"category_aro_accession":"3004201","category_aro_cvterm_id":"41365","category_aro_name":"BlaB beta-lactamase","category_aro_description":"BlaB beta-lactamases are class B beta-lactamases that are found in a variety of species and have the ability to hydrolyze penams and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2890":{"model_id":"2890","model_name":"Agrobacterium fabrum chloramphenicol acetyltransferase","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"4423":{"protein_sequence":{"accession":"AAA22081.1","sequence":"MENYFESPFRGITLDKQVKSPNLVVGKYSYYSGYYHGHSFEDCARYLLPDEGADRLVIGSFCSIGSGAAFIMAGNQGHRNEWISTFPFFFMPEVPEFENAANGYLPAGDTVIGNDVWIGSEAIIMPGITVGDGAVIGTRALVTKDVEPYAIVGGNPAKTIRKRFDDDSIALLLEMKWWGWPAERLKAAMPLMTSGNVAALYRFWRSDSL"},"dna_sequence":{"accession":"M58472.1","fmin":"147","fmax":"777","strand":"+","sequence":"ATGGAAAACTATTTCGAAAGCCCATTCCGGGGCATTACACTCGACAAGCAGGTGAAGAGCCCGAACCTGGTGGTCGGAAAATACAGCTATTATTCCGGCTATTACCACGGCCACAGTTTCGAGGATTGCGCCCGGTACCTGCTGCCCGATGAGGGCGCGGACAGGCTGGTGATCGGAAGCTTCTGCTCGATCGGTTCGGGCGCCGCCTTCATCATGGCGGGCAATCAGGGGCACCGCAACGAATGGATCAGTACCTTCCCGTTCTTCTTCATGCCGGAGGTGCCGGAATTCGAGAATGCCGCCAACGGTTATCTGCCGGCGGGCGACACCGTCATCGGCAACGATGTCTGGATCGGTTCGGAAGCGATCATCATGCCCGGCATCACCGTCGGTGATGGCGCGGTGATCGGAACGCGGGCGCTGGTGACGAAGGACGTCGAGCCCTACGCCATCGTCGGCGGCAACCCCGCAAAAACGATCCGCAAGCGGTTTGACGACGATAGCATCGCCCTGCTGCTCGAGATGAAATGGTGGGGCTGGCCGGCGGAGCGGCTGAAAGCTGCAATGCCGCTGATGACCAGCGGCAATGTCGCGGCGCTCTATCGTTTCTGGCGGTCCGATAGCCTCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36775","NCBI_taxonomy_name":"Agrobacterium fabrum str. C58","NCBI_taxonomy_id":"176299"}}}},"ARO_accession":"3004451","ARO_id":"41662","ARO_name":"Agrobacterium fabrum chloramphenicol acetyltransferase","CARD_short_name":"Afab_ACT_CHL","ARO_description":"A chloramphenicol resistance determinant described in the Gram-negative bacterium Agrobacterium fabrum.","ARO_category":{"36261":{"category_aro_accession":"3000122","category_aro_cvterm_id":"36261","category_aro_name":"chloramphenicol acetyltransferase (CAT)","category_aro_description":"Inactivates chloramphenicol by addition of an acyl group. CAT is used to describe many variants of the chloramphenicol acetyltransferase gene in a range of organisms including Acinetobacter calcoaceticus, Agrobacterium tumefaciens, Alkalihalobacillus clausii, Bacillus subtilis, Campylobacter coli, Enterococcus faecalis, Enterococcus faecium, Lactococcus lactis, Listeria monocytogenes, Listonella anguillarum, Morganella morganii, Photobacterium damselae subsp. piscicida, Proteus mirabilis, Salmonella typhi, Serratia marcescens, Shigella flexneri, Staphylococcus aureus, Staphylococcus haemolyticus, Staphylococcus intermedius, Streptococcus agalactiae, Streptococcus suis and Streptomyces acrimycini.","category_aro_class_name":"AMR Gene Family"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2893":{"model_id":"2893","model_name":"Campylobacter coli chloramphenicol acetyltransferase","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"350"}},"model_sequences":{"sequence":{"4426":{"protein_sequence":{"accession":"AAA23018.1","sequence":"MQFTKIDINNWTRKEYFDHYFGNTPCTYSMTVKLDISKLKKDGKKLYPTLLYGVTTIINRHEEFRTALDENGQVGVFSEMLPCYTVFHKETETFSSIWTEFTADYTEFLQNYQKDIDAFGERMGMSAKPNPPENTFPVSMIPWTSFEGFNLNLKKGYDYLLPIFTFGKYYEEGGKYYIPLSIQVHHAVCDGFHVCRFLDELQDLLNK"},"dna_sequence":{"accession":"M35190.1","fmin":"308","fmax":"932","strand":"+","sequence":"ATGCAATTCACAAAGATTGATATAAATAATTGGACACGAAAAGAGTATTTCGACCACTATTTTGGCAATACGCCCTGCACATATAGTATGACGGTAAAACTCGATATTTCTAAGTTGAAAAAGGATGGAAAAAAGTTATACCCAACTCTTTTATATGGAGTTACAACGATCATCAATCGACATGAAGAGTTCAGGACCGCATTAGATGAAAACGGACAGGTAGGCGTTTTTTCAGAAATGCTGCCTTGCTACACAGTTTTTCATAAGGAAACTGAAACCTTTTCGAGTATTTGGACTGAGTTTACAGCAGACTATACTGAGTTTCTTCAGAACTATCAAAAGGATATAGACGCTTTTGGTGAACGAATGGGAATGTCCGCAAAGCCTAATCCTCCGGAAAACACTTTCCCTGTTTCTATGATACCGTGGACAAGCTTTGAAGGCTTTAACTTAAATCTAAAAAAAGGATATGACTATCTACTGCCGATATTTACGTTTGGGAAGTATTATGAGGAGGGCGGAAAATACTATATTCCCTTATCGATTCAAGTGCATCATGCCGTTTGTGACGGCTTTCATGTTTGCCGTTTTTTGGATGAATTACAAGACTTGCTGAATAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36835","NCBI_taxonomy_name":"Campylobacter coli","NCBI_taxonomy_id":"195"}}}},"ARO_accession":"3004454","ARO_id":"41665","ARO_name":"Campylobacter coli chloramphenicol acetyltransferase","CARD_short_name":"Ccol_ACT_CHL","ARO_description":"A chloramphenicol resistance determinant described in Campylobacter coli.","ARO_category":{"36261":{"category_aro_accession":"3000122","category_aro_cvterm_id":"36261","category_aro_name":"chloramphenicol acetyltransferase (CAT)","category_aro_description":"Inactivates chloramphenicol by addition of an acyl group. CAT is used to describe many variants of the chloramphenicol acetyltransferase gene in a range of organisms including Acinetobacter calcoaceticus, Agrobacterium tumefaciens, Alkalihalobacillus clausii, Bacillus subtilis, Campylobacter coli, Enterococcus faecalis, Enterococcus faecium, Lactococcus lactis, Listeria monocytogenes, Listonella anguillarum, Morganella morganii, Photobacterium damselae subsp. piscicida, Proteus mirabilis, Salmonella typhi, Serratia marcescens, Shigella flexneri, Staphylococcus aureus, Staphylococcus haemolyticus, Staphylococcus intermedius, Streptococcus agalactiae, Streptococcus suis and Streptomyces acrimycini.","category_aro_class_name":"AMR Gene Family"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2894":{"model_id":"2894","model_name":"Streptococcus suis chloramphenicol acetyltransferase","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"350"}},"model_sequences":{"sequence":{"4427":{"protein_sequence":{"accession":"BAC11901.1","sequence":"MNFNKIDLDNWKRKEIFNHYLNQQTTFSITTEIDISVLYRNIKQKRYKFYPAFVFLVTRVINSNTAFRTGYNSEGELGYWDKLDPLYTIFDSVSKTFSGIWTPARNDFKEFYDLYLSDVEKYNGSGKLFPKTPIPENAFSISIIPWTSFTGFNLNINNNSNYLLPIITAGKFINKGNSIYLPLSLQVHHSVCDGYHAGLFMNSIQELADRPNDWLF"},"dna_sequence":{"accession":"AB080798.1","fmin":"2658","fmax":"3309","strand":"+","sequence":"ATGAACTTTAATAAAATTGATTTAGACAATTGGAAGAGAAAAGAGATATTTAATCATTATTTGAACCAACAAACGACTTTTAGTATAACCACAGAAATTGATATTAGTGTTTTATACCGAAACATAAAACAAAAAAGATATAAATTTTATCCTGCATTTGTTTTCTTAGTGACAAGGGTGATAAACTCAAATACAGCTTTTAGAACTGGTTACAATAGCGAGGGAGAGTTAGGCTATTGGGATAAGTTAGACCCACTATACACAATTTTTGATAGTGTATCTAAAACATTCTCTGGTATTTGGACTCCTGCAAGGAATGACTTCAAAGAGTTTTATGATTTATACCTTTCTGATGTAGAGAAATATAATGGTTCGGGGAAATTGTTTCCCAAAACACCTATACCCGAAAATGCTTTTTCTATTTCTATTATTCCATGGACTTCATTTACTGGGTTTAACTTAAATATCAATAATAATAGTAATTATCTTCTACCCATTATTACAGCAGGAAAATTCATTAATAAAGGTAATTCAATATATTTACCGCTATCTTTACAGGTACATCATTCTGTTTGTGATGGTTATCATGCAGGATTGTTTATGAACTCTATTCAGGAATTGGCAGATAGGCCTAATGACTGGCTTTTTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39534","NCBI_taxonomy_name":"Streptococcus suis","NCBI_taxonomy_id":"1307"}}}},"ARO_accession":"3004455","ARO_id":"41666","ARO_name":"Streptococcus suis chloramphenicol acetyltransferase","CARD_short_name":"Ssui_ACT_CHL","ARO_description":"A chloramphenicol resistance determinant described in Streptococcus suis.","ARO_category":{"36261":{"category_aro_accession":"3000122","category_aro_cvterm_id":"36261","category_aro_name":"chloramphenicol acetyltransferase (CAT)","category_aro_description":"Inactivates chloramphenicol by addition of an acyl group. CAT is used to describe many variants of the chloramphenicol acetyltransferase gene in a range of organisms including Acinetobacter calcoaceticus, Agrobacterium tumefaciens, Alkalihalobacillus clausii, Bacillus subtilis, Campylobacter coli, Enterococcus faecalis, Enterococcus faecium, Lactococcus lactis, Listeria monocytogenes, Listonella anguillarum, Morganella morganii, Photobacterium damselae subsp. piscicida, Proteus mirabilis, Salmonella typhi, Serratia marcescens, Shigella flexneri, Staphylococcus aureus, Staphylococcus haemolyticus, Staphylococcus intermedius, Streptococcus agalactiae, Streptococcus suis and Streptomyces acrimycini.","category_aro_class_name":"AMR Gene Family"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2895":{"model_id":"2895","model_name":"Enterococcus faecium chloramphenicol acetyltransferase","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"350"}},"model_sequences":{"sequence":{"5487":{"protein_sequence":{"accession":"AAO52851.1","sequence":"MTFNIINLETWDRKEYFNHYFNQQTTYSVTKELDITLLKSMIKDKGYELYPALIHAIVSVINRNKVFRTGINSEGNLGYWDKLEPLYTVFNKETEKFSNIWTESNASFNSFYNSYKNDLFKYKDKNEMFPKKPIPENTVPISMIPWIDFSSFNLNIGNNSRFLLPIITIGKFYSKDDKIYLPFSLQVHHAVCDGYHVSLFMNEFQNIIDNVNEWI"},"dna_sequence":{"accession":"AF507977.1","fmin":"17463","fmax":"18111","strand":"+","sequence":"ATGACTTTTAATATTATTAATTTAGAAACTTGGGATAGAAAAGAATATTTCAATCATTATTTTAATCAACAAACAACTTATAGTGTTACTAAAGAATTAGATATTACCTTGTTAAAAAGTATGATAAAAGATAAAGGATATGAACTGTATCCTGCTTTGATTCATGCAATTGTAAGTGTTATAAATCGAAATAAAGTATTTAGAACAGGGATTAATAGTGAGGGGAATTTGGGTTATTGGGATAAATTAGAACCTTTATATACAGTCTTTAATAAAGAAACTGAAAAATTTTCTAATATTTGGACAGAATCAAATGCTAGTTTTAACTCTTTTTATAATAGTTATAAGAATGATTTATTTAAATATAAAGATAAAAATGAAATGTTTCCTAAAAAGCCGATACCTGAAAACACAGTTCCTATCTCGATGATTCCTTGGATTGATTTTAGTTCATTTAATTTAAATATTGGTAATAATAGTAGATTTTTATTGCCAATTATTACAATAGGTAAATTTTATAGTAAGGATGATAAGATCTATTTACCATTTTCATTGCAAGTTCATCATGCAGTATGTGATGGTTACCATGTTTCATTATTTATGAATGAATTTCAAAATATAATTGATAATGTAAATGAATGGATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36779","NCBI_taxonomy_name":"Enterococcus faecium","NCBI_taxonomy_id":"1352"}}}},"ARO_accession":"3004456","ARO_id":"41667","ARO_name":"Enterococcus faecium chloramphenicol acetyltransferase","CARD_short_name":"Efac_ACT_CHL","ARO_description":"A chloramphenicol resistance determinant described in an Enterococcus faecium plasmid.","ARO_category":{"36261":{"category_aro_accession":"3000122","category_aro_cvterm_id":"36261","category_aro_name":"chloramphenicol acetyltransferase (CAT)","category_aro_description":"Inactivates chloramphenicol by addition of an acyl group. CAT is used to describe many variants of the chloramphenicol acetyltransferase gene in a range of organisms including Acinetobacter calcoaceticus, Agrobacterium tumefaciens, Alkalihalobacillus clausii, Bacillus subtilis, Campylobacter coli, Enterococcus faecalis, Enterococcus faecium, Lactococcus lactis, Listeria monocytogenes, Listonella anguillarum, Morganella morganii, Photobacterium damselae subsp. piscicida, Proteus mirabilis, Salmonella typhi, Serratia marcescens, Shigella flexneri, Staphylococcus aureus, Staphylococcus haemolyticus, Staphylococcus intermedius, Streptococcus agalactiae, Streptococcus suis and Streptomyces acrimycini.","category_aro_class_name":"AMR Gene Family"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2896":{"model_id":"2896","model_name":"Staphylococcus intermedius chloramphenicol acetyltransferase","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"350"}},"model_sequences":{"sequence":{"4429":{"protein_sequence":{"accession":"AAA26615.1","sequence":"MTFNIIKLENWDRKEYFEHYFNQQTTYSITKEIDITLFKDMIKKKGYEIYPSLIYAIMEVVNKNKVFRTGINSENKLGYWDKLNPLYTVFNKQTEKFTNIWTESDNNFTSFYNNYKNDLFEYKDKEEMFPKKPIPENTIPISMIPWIDFSSFNLNIGNNSSFLLPIITIGKFYSENNKIYIPVALQLHHAVCDGYHASLFINEFQDIIKKVDDWI"},"dna_sequence":{"accession":"M64281.1","fmin":"207","fmax":"855","strand":"+","sequence":"ATGACTTTTAATATTATCAAATTAGAAAATTGGGATAGAAAAGAATATTTTGAACACTATTTTAACCAGCAAACTACGTATAGCATTACTAAAGAAATTGATATTACTTTGTTTAAAGATATGATAAAAAAGAAAGGATATGAAATTTATCCTTCTTTGATTTATGCAATTATGGAAGTTGTAAATAAAAATAAAGTGTTTAGAACAGGAATTAATAGTGAGAATAAATTAGGCTATTGGGATAAGTTAAATCCTTTGTATACAGTTTTTAATAAGCAAACTGAAAAATTTACTAACATTTGGACTGAATCTGATAACAACTTCACTTCTTTTTATAATAATTATAAAAATGACTTGTTTGAATATAAAGATAAAGAAGAAATGTTTCCTAAAAAACCGATACCTGAAAACACCATACCGATTTCAATGATTCCTTGGATTGATTTTAGTTCATTTAATTTAAACATTGGTAACAATAGCAGCTTTTTATTGCCTATTATTACGATAGGTAAATTTTATAGTGAGAATAATAAAATTTATATACCAGTTGCCTTACAGCTTCATCATGCTGTATGTGATGGTTACCATGCTTCATTATTTATAAATGAATTTCAAGATATAATTAAGAAGGTAGATGATTGGATTTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36842","NCBI_taxonomy_name":"Staphylococcus intermedius","NCBI_taxonomy_id":"1285"}}}},"ARO_accession":"3004457","ARO_id":"41668","ARO_name":"Staphylococcus intermedius chloramphenicol acetyltransferase","CARD_short_name":"Sint_ACT_CHL","ARO_description":"A chloramphenicol resistance determinant described in Staphylococcus intermedius.","ARO_category":{"36261":{"category_aro_accession":"3000122","category_aro_cvterm_id":"36261","category_aro_name":"chloramphenicol acetyltransferase (CAT)","category_aro_description":"Inactivates chloramphenicol by addition of an acyl group. CAT is used to describe many variants of the chloramphenicol acetyltransferase gene in a range of organisms including Acinetobacter calcoaceticus, Agrobacterium tumefaciens, Alkalihalobacillus clausii, Bacillus subtilis, Campylobacter coli, Enterococcus faecalis, Enterococcus faecium, Lactococcus lactis, Listeria monocytogenes, Listonella anguillarum, Morganella morganii, Photobacterium damselae subsp. piscicida, Proteus mirabilis, Salmonella typhi, Serratia marcescens, Shigella flexneri, Staphylococcus aureus, Staphylococcus haemolyticus, Staphylococcus intermedius, Streptococcus agalactiae, Streptococcus suis and Streptomyces acrimycini.","category_aro_class_name":"AMR Gene Family"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2897":{"model_id":"2897","model_name":"Enterococcus faecalis chloramphenicol acetyltransferase","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"350"}},"model_sequences":{"sequence":{"4467":{"protein_sequence":{"accession":"CAA63498.2","sequence":"MTFNIIELENWDRKEYFEHYFNQQTTYSITKEIDITLFKDMIKKKGYEIYPSLIYAIMEVVNKNKVFRTGINSENKLGYWDKLNPLYTVFNKQTEKFTNIWTESDKNFISFYNNYKNDLLEYKDKEEMFPKKPIPENTIPISMIPWIDFSSFNLNIGNNSSFLLPIITIGKFYSENNKIYIPVALQLHHSVCDGYHASLFMNEFQDIIHRVDDWI"},"dna_sequence":{"accession":"X92945.2","fmin":"8934","fmax":"9582","strand":"-","sequence":"ATGACTTTTAATATTATTGAATTAGAAAATTGGGATAGAAAAGAATATTTTGAACACTATTTTAATCAGCAAACTACTTATAGCATTACTAAAGAAATTGATATTACTTTGTTTAAAGATATGATAAAAAAGAAAGGATATGAAATTTATCCCTCTTTAATTTATGCAATTATGGAAGTTGTAAATAAAAATAAAGTGTTTAGAACAGGAATTAATAGTGAGAATAAATTAGGTTATTGGGATAAGTTAAATCCTTTGTATACAGTTTTTAATAAGCAAACTGAAAAATTTACTAACATTTGGACTGAATCTGATAAAAACTTCATTTCTTTTTATAATAATTATAAAAATGACTTGCTTGAATATAAAGATAAAGAAGAAATGTTTCCTAAAAAACCGATACCTGAAAACACCATACCGATTTCAATGATTCCTTGGATTGATTTTAGTTCATTTAATTTAAATATTGGTAACAATAGCAGCTTTTTATTGCCTATTATTACGATAGGTAAATTTTATAGTGAGAATAATAAAATTTATATACCAGTTGCTCTGCAACTTCATCATTCTGTATGTGATGGTTACCATGCTTCACTATTTATGAATGAATTTCAAGATATAATTCATAGGGTAGATGATTGGATTTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35918","NCBI_taxonomy_name":"Enterococcus faecalis","NCBI_taxonomy_id":"1351"}}}},"ARO_accession":"3004458","ARO_id":"41669","ARO_name":"Enterococcus faecalis chloramphenicol acetyltransferase","CARD_short_name":"Efae_ACT_CHL","ARO_description":"A chloramphenicol acetyltransferase and resistance determinant described in Enterococcus faecalis.","ARO_category":{"36261":{"category_aro_accession":"3000122","category_aro_cvterm_id":"36261","category_aro_name":"chloramphenicol acetyltransferase (CAT)","category_aro_description":"Inactivates chloramphenicol by addition of an acyl group. CAT is used to describe many variants of the chloramphenicol acetyltransferase gene in a range of organisms including Acinetobacter calcoaceticus, Agrobacterium tumefaciens, Alkalihalobacillus clausii, Bacillus subtilis, Campylobacter coli, Enterococcus faecalis, Enterococcus faecium, Lactococcus lactis, Listeria monocytogenes, Listonella anguillarum, Morganella morganii, Photobacterium damselae subsp. piscicida, Proteus mirabilis, Salmonella typhi, Serratia marcescens, Shigella flexneri, Staphylococcus aureus, Staphylococcus haemolyticus, Staphylococcus intermedius, Streptococcus agalactiae, Streptococcus suis and Streptomyces acrimycini.","category_aro_class_name":"AMR Gene Family"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2899":{"model_id":"2899","model_name":"Vibrio anguillarum chloramphenicol acetyltransferase","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"350"}},"model_sequences":{"sequence":{"4432":{"protein_sequence":{"accession":"AAB23649.1","sequence":"MEFRLVDLKTWKRKEYFTHYFESVPCTYSMTVKLDITTIKTGKAKLYPALLYAVSTVVNRHEEFRMTVDDEGQIGIFSEMMPCYTIFQKDTEMFSNIWTEYIGDYTEFCKQYEKDMQQYGENKGMMAKPNPPVNTFPVSMIPWTTFEGFNLNLQKGYGYLLPIFTFGRYYEENGKYWIPLSIQVHHAVCDGFHTCRFINELQDVIQSLQNHGGDEE"},"dna_sequence":{"accession":"S48276.1","fmin":"478","fmax":"1129","strand":"+","sequence":"ATGGAGTTTCGTTTGGTTGATCTGAAAACATGGAAAAGAAAAGAGTACTTTACGCATTATTTTGAATCTGTGCCTTGCACATATAGCATGACCGTAAAGCTGGATATTACTACGATAAAAACCGGTAAAGCGAAATTGTATCCCGCCCTTTTGTATGCCGTTTCAACAGTAGTTAACCGGCATGAAGAATTCCGTATGACTGTGGACGATGAAGGTCAAATCGGGATATTTAGTGAAATGATGCCGTGCTATACAATTTTCCAAAAGGACACGGAGATGTTTTCAAATATCTGGACCGAGTATATCGGTGATTATACGGAGTTCTGCAAACAGTATGAAAAAGATATGCAGCAATACGGTGAAAACAAGGGCATGATGGCAAAGCCAAATCCGCCTGTGAATACTTTCCCAGTCTCTATGATTCCATGGACAACCTTTGAAGGATTTAATTTAAATTTGCAAAAGGGATATGGGTATCTGCTTCCCATTTTTACGTTTGGACGATATTATGAAGAAAACGGGAAATATTGGATTCCGTTATCTATTCAGGTACATCATGCGGTATGCGATGGATTTCATACCTGCCGTTTTATCAATGAATTACAGGATGTAATCCAAAGTTTACAAAACCATGGAGGTGACGAAGAATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39536","NCBI_taxonomy_name":"Vibrio anguillarum","NCBI_taxonomy_id":"55601"}}}},"ARO_accession":"3004460","ARO_id":"41671","ARO_name":"Vibrio anguillarum chloramphenicol acetyltransferase","CARD_short_name":"Vang_ACT_CHL","ARO_description":"A chloramphenicol resistance determinant described in a Vibrio anguillarum plasmid sequence.","ARO_category":{"36261":{"category_aro_accession":"3000122","category_aro_cvterm_id":"36261","category_aro_name":"chloramphenicol acetyltransferase (CAT)","category_aro_description":"Inactivates chloramphenicol by addition of an acyl group. CAT is used to describe many variants of the chloramphenicol acetyltransferase gene in a range of organisms including Acinetobacter calcoaceticus, Agrobacterium tumefaciens, Alkalihalobacillus clausii, Bacillus subtilis, Campylobacter coli, Enterococcus faecalis, Enterococcus faecium, Lactococcus lactis, Listeria monocytogenes, Listonella anguillarum, Morganella morganii, Photobacterium damselae subsp. piscicida, Proteus mirabilis, Salmonella typhi, Serratia marcescens, Shigella flexneri, Staphylococcus aureus, Staphylococcus haemolyticus, Staphylococcus intermedius, Streptococcus agalactiae, Streptococcus suis and Streptomyces acrimycini.","category_aro_class_name":"AMR Gene Family"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1042":{"model_id":"1042","model_name":"Pseudomonas aeruginosa catB7","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"4740":{"protein_sequence":{"accession":"NP_249397.1","sequence":"MGNYFESPFRGKLLSEQVSNPNIRVGRYSYYSGYYHGHSFDDCARYLMPDRDDVDKLVIGSFCSIGSGAAFIMAGNQGHRAEWASTFPFHFMHEEPVFAGAVNGYQPAGDTLIGHDVWIGTEAMFMPGVRVGHGAIIGSRALVTGDVEPYAIVGGNPARTIRKRFSDGDIQNLLEMAWWDWPLADIEAAMPLLCTGDIPALYRHWKQRQATA"},"dna_sequence":{"accession":"NC_002516.2","fmin":"779462","fmax":"780101","strand":"-","sequence":"ATGGGCAACTATTTCGAGAGCCCCTTCAGGGGCAAGCTGCTCTCGGAACAGGTCAGCAACCCGAACATACGGGTGGGGCGCTACAGCTACTACTCCGGCTACTATCACGGGCATTCCTTCGACGACTGCGCCCGCTACCTGATGCCGGACCGCGACGACGTGGACAAGCTGGTCATCGGCAGTTTCTGCTCGATCGGCAGTGGCGCCGCCTTCATCATGGCCGGCAACCAGGGACACCGCGCCGAATGGGCGTCGACCTTCCCCTTCCACTTCATGCACGAAGAGCCTGTCTTCGCCGGCGCCGTGAACGGCTATCAGCCAGCCGGCGACACGCTGATCGGCCATGACGTCTGGATCGGTACCGAGGCGATGTTCATGCCCGGCGTACGGGTCGGCCACGGAGCCATCATCGGCAGCCGCGCGCTGGTGACCGGCGATGTCGAGCCCTATGCCATCGTCGGCGGTAACCCGGCCCGGACCATTCGTAAGCGCTTTTCCGATGGCGATATCCAGAACCTGCTGGAAATGGCCTGGTGGGACTGGCCACTGGCCGATATCGAGGCAGCCATGCCACTGCTGTGTACTGGGGATATCCCCGCCTTGTACCGGCACTGGAAACAGCGCCAGGCCACGGCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36804","NCBI_taxonomy_name":"Pseudomonas aeruginosa PAO1","NCBI_taxonomy_id":"208964"}}}},"ARO_accession":"3002679","ARO_id":"39113","ARO_name":"Pseudomonas aeruginosa catB7","CARD_short_name":"Paer_catB7","ARO_description":"catB7 is a chromosome-encoded variant of the cat gene found in Pseudomonas aeruginosa.","ARO_category":{"36261":{"category_aro_accession":"3000122","category_aro_cvterm_id":"36261","category_aro_name":"chloramphenicol acetyltransferase (CAT)","category_aro_description":"Inactivates chloramphenicol by addition of an acyl group. CAT is used to describe many variants of the chloramphenicol acetyltransferase gene in a range of organisms including Acinetobacter calcoaceticus, Agrobacterium tumefaciens, Alkalihalobacillus clausii, Bacillus subtilis, Campylobacter coli, Enterococcus faecalis, Enterococcus faecium, Lactococcus lactis, Listeria monocytogenes, Listonella anguillarum, Morganella morganii, Photobacterium damselae subsp. piscicida, Proteus mirabilis, Salmonella typhi, Serratia marcescens, Shigella flexneri, Staphylococcus aureus, Staphylococcus haemolyticus, Staphylococcus intermedius, Streptococcus agalactiae, Streptococcus suis and Streptomyces acrimycini.","category_aro_class_name":"AMR Gene Family"},"36521":{"category_aro_accession":"3000382","category_aro_cvterm_id":"36521","category_aro_name":"azidamfenicol","category_aro_description":"Azidamfenicol is a water soluble derivative of chloramphenicol, sharing the same mode of action of inhibiting peptide synthesis by interacting with the 23S RNA of the 50S ribosomal subunit.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36595":{"category_aro_accession":"3000456","category_aro_cvterm_id":"36595","category_aro_name":"thiamphenicol","category_aro_description":"Derivative of Chloramphenicol. The nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3).","category_aro_class_name":"Antibiotic"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4013":{"model_id":"4013","model_name":"PDC-323","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"6377":{"protein_sequence":{"accession":"WP_150823481.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPRDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_066530.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGTCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCGGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCAATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAGCCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005280","ARO_id":"43637","ARO_name":"PDC-323","CARD_short_name":"PDC-323","ARO_description":"PDC-323 is a class C beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2902":{"model_id":"2902","model_name":"ICR-Mc","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"4463":{"protein_sequence":{"accession":"EGE18576.1","sequence":"MSLKHNQTHNTTFTKFLKSNSFWSKGFWSNRHHRTKDLKGLDAYLFMAIVAIFLTTTANVTFFQQVMSVYPLANYAPFIASLAVVLTGVLLLLLVLLGYRHTLKTVAICFILIAAFAGHFTDTYGTVYDTTMLQNALQTDTAETKDLLSMKLLIRVVLLAGLPICWIIGQPLSFGTLKASLMKRLVTYLVALALVGLPILAFSSQYASFFREHKPLRFFTNPVTVMYSAGKLANMSYKNATKPTETIMHANDAIQKTTASTRKPRLVVMVVGETARADHASFNGYQRATFPHMDKLIGLGQVHNFGNVTSCGTSTAYSVPCMFSYLGAEKYDVDTADYHENVIDTLDRLGVAILWRDNNSDSKGVMNRLPAKQYQDYKNSPLQGGNNTICHTNPYDECRDVGMLVDLDDHVKAHANQDILIVLHQMGNHGPAYYKRYDDEFAQFLPVCTSSELAECERQTVINAYDNALLATDDFLKQTIDWLAAQTHADTAMLYLSDHGESLGEKGVYLHGMPKAFAPKEQLSIPALLWLGADTPFAVANSPTAGFSHDAITPTLLNLFDVSTQATADKTAFVNPLD"},"dna_sequence":{"accession":"AERH01000018.1","fmin":"16203","fmax":"17940","strand":"-","sequence":"ATGTCCCTTAAACACAACCAAACCCACAACACCACTTTTACCAAATTTTTAAAGTCCAACAGCTTTTGGTCTAAGGGCTTTTGGTCTAACCGCCATCACCGCACCAAAGATTTAAAAGGGTTAGATGCTTATCTGTTTATGGCAATTGTGGCGATATTTTTGACCACAACTGCCAATGTGACATTTTTTCAACAAGTCATGTCAGTATACCCATTGGCAAATTACGCACCTTTTATCGCTTCATTGGCGGTGGTCTTAACAGGCGTTTTGTTGCTCTTATTGGTGTTGCTTGGCTATCGGCATACCTTAAAGACGGTGGCAATTTGTTTTATTTTAATCGCTGCTTTTGCTGGTCATTTTACCGACACCTATGGCACTGTCTACGACACCACCATGCTACAAAATGCCTTACAAACTGACACGGCAGAAACCAAAGATTTATTAAGCATGAAGCTTTTAATCCGTGTTGTGTTGTTGGCTGGTTTGCCCATCTGTTGGATTATTGGGCAGCCATTGTCATTTGGCACACTCAAAGCAAGTTTAATGAAGCGGCTGGTTACCTATCTTGTGGCTTTGGCATTGGTTGGCTTGCCCATTTTGGCATTTAGCAGTCAATACGCCAGTTTTTTTAGGGAACATAAACCGTTGCGATTTTTTACCAATCCTGTAACGGTGATGTATTCAGCAGGCAAACTTGCCAATATGAGTTATAAAAACGCCACCAAACCCACCGAAACCATCATGCACGCCAATGATGCCATACAAAAAACCACCGCTTCCACTCGCAAGCCCAGATTGGTGGTGATGGTGGTGGGTGAGACGGCCCGTGCTGACCATGCGTCTTTTAATGGTTATCAGCGAGCCACTTTCCCTCATATGGACAAACTCATTGGCTTAGGGCAAGTGCATAATTTTGGTAATGTCACTTCTTGTGGCACATCAACGGCATATTCTGTCCCATGTATGTTCAGTTATTTGGGAGCAGAAAAATACGATGTTGATACCGCCGATTACCATGAAAATGTCATTGACACCTTAGACCGCTTGGGTGTGGCGATATTGTGGCGAGATAATAACTCTGATTCAAAAGGCGTGATGAATCGCCTGCCTGCCAAACAGTATCAAGACTACAAAAACAGCCCCCTTCAAGGTGGCAATAACACCATTTGCCACACCAACCCTTATGATGAATGCCGTGATGTGGGCATGTTGGTGGATTTAGATGACCATGTCAAGGCTCATGCCAATCAAGACATATTAATAGTGTTGCATCAAATGGGCAACCATGGCCCTGCTTATTATAAACGCTATGACGATGAATTTGCTCAGTTTTTGCCTGTTTGTACAAGTAGCGAGTTGGCAGAATGTGAGCGACAAACGGTCATTAATGCTTATGACAATGCGTTATTGGCGACTGATGACTTTTTAAAACAAACCATCGATTGGTTGGCAGCACAAACACACGCTGACACCGCCATGTTATATTTAAGCGACCATGGTGAAAGCTTAGGAGAAAAAGGCGTTTATTTACATGGCATGCCTAAGGCGTTTGCCCCAAAAGAACAACTGAGCATTCCTGCGTTACTTTGGTTGGGAGCAGACACTCCATTTGCAGTGGCAAATTCGCCAACGGCTGGCTTTAGCCACGATGCCATCACCCCGACACTGCTCAACTTATTTGATGTCAGCACACAAGCCACGGCAGATAAAACAGCATTTGTTAATCCTTTGGATTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41683","NCBI_taxonomy_name":"Moraxella catarrhalis BC1","NCBI_taxonomy_id":"857576"}}}},"ARO_accession":"3004466","ARO_id":"41682","ARO_name":"ICR-Mc","CARD_short_name":"ICR-Mc","ARO_description":"A chromosomally-encoded colistin resistance phosphoethanolamine (PEtN) transferase of Moraxella catarrhalis. ICR-Mc is the protein that represents the closest known ortholog to the colistin resistance MCR-1 and MCR-2 PEtN transferases.","ARO_category":{"41681":{"category_aro_accession":"3004465","category_aro_cvterm_id":"41681","category_aro_name":"intrinsic colistin resistant phosphoethanolamine transferase","category_aro_description":"Chromosomally-encoded phosphoethanolamine (PEtN) transferases shown to confer resistance to polymyxin antibiotics, including colistin.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2904":{"model_id":"2904","model_name":"poxtA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"4458":{"protein_sequence":{"accession":"AVI44920.1","sequence":"MKGKNMNLAFGLEEIYEDAEFQIGDLDKVGIVGVNGAGKTTLFRLLLGELELDNGSLTSGNARIGYLPQEIVLEDEDITVWDFLFEGRPIKKYEQELEEIYKKLETAVNAEQEALLARMGTLQERLEYFDFYEAETILLEFADKMSIDAELYHRPMRELSGGQKSKMAFARLLYSKPEILLLDEPTNHLDVSTKDFVIKYLKNYRGSVLIISHDIDFLNRIINKIMYINKATHKISVYDGDYYIYKKKYAEEQRIREMAIVQQEKEIKELSDFVQKAKQASQTNHHLKRMGQERALRLDKKRGELQKRNRLYKRVKMDIRPKREGAQVPLEVENITFHYSGYPTLYQNLSFQINGRERFLVVGENGVGKSTLLKLMMGILSPDEGCIRFNQKTDIAYYAQELEQLDENKTVIDNVESEGYTPWQIRAVLSNFLFYDDDVNKKVSVLSPGEKARVALCKILLQKANLLILDEPTNHLDPETQKIIGGNFNLFEGTIIAVSHNPSFVEQIGISRMLILPSGRIEPYSRELLEYYYEINGSVAKF"},"dna_sequence":{"accession":"MF095097.1","fmin":"1855","fmax":"3484","strand":"-","sequence":"ATGAAAGGTAAAAATATGAATTTAGCCTTTGGGTTGGAAGAAATTTATGAGGATGCTGAGTTTCAAATCGGAGATTTGGATAAGGTCGGTATTGTCGGCGTGAACGGAGCCGGAAAGACCACCTTGTTCCGCCTGCTGTTGGGAGAACTTGAACTTGATAATGGTTCACTGACCAGTGGAAATGCCCGTATTGGTTATCTCCCACAGGAAATTGTCTTGGAAGATGAGGATATTACCGTTTGGGATTTCCTTTTTGAGGGACGTCCGATTAAAAAGTATGAGCAGGAATTGGAAGAAATCTATAAAAAGCTTGAAACCGCAGTCAATGCAGAGCAGGAAGCACTGCTTGCCCGAATGGGAACATTGCAAGAACGCTTGGAGTATTTCGACTTCTATGAGGCAGAAACAATTCTGTTGGAGTTTGCAGATAAAATGAGCATTGATGCAGAATTATATCATCGTCCGATGAGAGAGCTTTCAGGCGGACAAAAATCCAAAATGGCATTTGCCAGACTACTATATTCAAAACCGGAAATTCTATTGTTGGATGAGCCTACCAACCATTTAGATGTCAGCACAAAGGATTTTGTTATAAAATACTTAAAGAATTATAGGGGTTCGGTACTGATTATCAGCCATGATATTGATTTTCTAAATCGGATTATCAACAAAATTATGTACATCAACAAAGCTACCCATAAAATATCTGTTTATGATGGAGACTACTACATCTACAAGAAAAAGTATGCAGAGGAACAGCGGATTCGTGAAATGGCGATTGTACAGCAGGAAAAAGAAATAAAGGAGCTTTCCGATTTTGTACAAAAAGCAAAACAAGCCAGTCAGACCAATCATCACCTCAAACGAATGGGTCAAGAGCGAGCCTTGCGGCTTGATAAAAAGCGTGGAGAGCTGCAAAAGAGAAATCGACTGTACAAGCGTGTGAAGATGGATATTCGCCCCAAGCGTGAAGGGGCACAAGTTCCCTTAGAGGTGGAAAATATCACCTTCCACTATTCGGGGTATCCCACCCTTTATCAGAACCTTTCCTTTCAGATTAACGGAAGAGAACGATTTCTTGTGGTGGGTGAAAACGGTGTCGGTAAATCCACCTTATTGAAATTGATGATGGGTATTCTCAGTCCAGATGAAGGATGCATTCGCTTTAACCAGAAAACTGATATTGCATATTATGCACAGGAACTCGAACAGCTTGATGAAAACAAAACGGTCATTGACAATGTGGAGTCTGAAGGATATACACCGTGGCAAATCAGAGCCGTACTGAGCAACTTCCTGTTTTATGATGACGATGTAAACAAGAAAGTATCTGTGCTGTCCCCTGGAGAAAAAGCAAGGGTTGCCCTTTGCAAAATCCTATTACAGAAAGCCAATCTTTTGATACTGGACGAGCCGACCAACCACCTTGACCCAGAAACGCAGAAAATCATTGGCGGCAACTTCAATTTGTTTGAGGGAACCATTATTGCCGTTAGCCATAACCCATCCTTTGTGGAACAAATCGGAATTAGCCGTATGCTTATTTTGCCCAGCGGTCGAATTGAACCCTATTCCCGTGAGCTGCTTGAGTATTATTATGAAATCAACGGTTCTGTTGCAAAGTTTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35508","NCBI_taxonomy_name":"Staphylococcus aureus","NCBI_taxonomy_id":"1280"}}}},"ARO_accession":"3004470","ARO_id":"41688","ARO_name":"poxtA","CARD_short_name":"poxtA","ARO_description":"PoxtA is an ABC-F subfamily ATP-binding cassette protein that confers resistance to tetracycline, -phenicol, and oxazolidinone via modification of the bacterial ribosome. The encoding gene was isolated from a methicillin-resistant Staphylococcus aureus strain.","ARO_category":{"45630":{"category_aro_accession":"3007068","category_aro_cvterm_id":"45630","category_aro_name":"Miscellaneous ABC-F subfamily ATP-binding cassette ribosomal protection proteins","category_aro_description":"ABC-F subfamily ATP-binding cassette ribosomal protection proteins of unknown, unclear or miscellaneous classification which nevertheless confer resistance to antibiotics through ribosomal protection and not through antibiotic efflux. These proteins should be further reviewed to elucidate associated genes, their function, origin and classification.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35986":{"category_aro_accession":"0000069","category_aro_cvterm_id":"35986","category_aro_name":"doxycycline","category_aro_description":"Doxycycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"35989":{"category_aro_accession":"0000072","category_aro_cvterm_id":"35989","category_aro_name":"linezolid","category_aro_description":"Linezolid is a synthetic antibiotic used for the treatment of serious infections caused by Gram-positive bacteria that are resistant to several other antibiotics. It inhibits protein synthesis by binding to domain V of the 23S rRNA of the 50S subunit of bacterial ribosomes.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36600":{"category_aro_accession":"3000461","category_aro_cvterm_id":"36600","category_aro_name":"florfenicol","category_aro_description":"Florfenicol is a fluorine derivative of chloramphenicol, where the nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3) and the hydroxyl group (-OH), by a fluorine group (-F). The action mechanism is the same as chloramphenicol's, where the antibiotic binds to the 23S RNA of the 50S subunit of bacterial ribosomes to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36218":{"category_aro_accession":"3000079","category_aro_cvterm_id":"36218","category_aro_name":"oxazolidinone antibiotic","category_aro_description":"Oxazolidinones are a class of synthetic antibiotics discovered the the 1980's.  They inhibit protein synthesis by binding to domain V of the 23S rRNA of the 50S subunit of bacterial ribosomes.  Linezolid is the only member of this class currently in clinical use.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3465":{"model_id":"3465","model_name":"OXA-303","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"570"}},"model_sequences":{"sequence":{"5660":{"protein_sequence":{"accession":"ENX56371.1","sequence":"MMMSKKLKCLAFFTAIFFAIPMTACQSFSQQKQQLSTQKNEQQQISSLFQSAQTNGVLVIYDGKKIQKFGNDLDRAEQRYIPASTFKMLNALIGIQHHKTTPDEVFKWDGKKRAFSSWEKDLTLAEAMQASAVPVYQELARRIGLELMTREVKRVGYGNKNIGTQVDNFWLVGPLKITPIEEVRFAYALAKQKLPFDQPTQQQVKAMLLVDQIQGTKIYAKSGWGMDVSPQVGWWTGWIEQPNGKITAFSLNMQMSQPEHADARKVIVYQALQELGLLAH"},"dna_sequence":{"accession":"APSD01000035.1","fmin":"194492","fmax":"195335","strand":"+","sequence":"ATGATGATGTCGAAAAAATTAAAATGTCTGGCCTTTTTTACAGCCATCTTTTTTGCAATTCCCATGACTGCTTGTCAAAGTTTTAGCCAACAAAAGCAACAGCTCTCGACACAAAAAAATGAGCAGCAGCAGATCTCAAGTTTATTCCAGAGTGCCCAAACCAATGGTGTTTTGGTGATTTATGATGGCAAGAAAATTCAAAAATTTGGCAATGATCTTGATCGTGCAGAACAGCGCTATATTCCTGCCTCAACCTTTAAAATGTTAAACGCCTTGATCGGAATACAGCATCATAAGACCACACCAGATGAAGTATTTAAATGGGATGGTAAAAAGCGGGCATTCAGCAGTTGGGAAAAAGACCTCACATTAGCTGAGGCGATGCAGGCATCGGCGGTACCCGTGTATCAAGAATTGGCAAGACGTATTGGTTTGGAACTGATGACCCGTGAAGTAAAGCGTGTGGGTTATGGTAATAAAAATATCGGGACACAAGTCGATAATTTCTGGTTAGTTGGCCCCTTAAAAATCACTCCCATAGAAGAAGTTCGCTTTGCCTATGCGCTGGCAAAACAGAAATTGCCCTTTGACCAGCCGACACAGCAACAAGTCAAAGCGATGTTATTGGTGGATCAGATTCAGGGAACCAAAATCTATGCCAAAAGTGGTTGGGGTATGGATGTCAGCCCGCAAGTGGGATGGTGGACAGGCTGGATTGAACAGCCAAATGGCAAGATCACAGCCTTCTCACTGAATATGCAAATGAGTCAGCCTGAACATGCAGATGCACGCAAAGTGATTGTGTATCAAGCCTTGCAAGAGTTGGGATTGTTAGCCCATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42824","NCBI_taxonomy_name":"Acinetobacter sp. ANC 3880","NCBI_taxonomy_id":"1217701"}}}},"ARO_accession":"3001758","ARO_id":"38158","ARO_name":"OXA-303","CARD_short_name":"OXA-303","ARO_description":"OXA-303 is a beta-lactamase found in Acinetobacter spp.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46503":{"category_aro_accession":"3007714","category_aro_cvterm_id":"46503","category_aro_name":"OXA-286-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-286.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3494":{"model_id":"3494","model_name":"OXA-409","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"565"}},"model_sequences":{"sequence":{"5689":{"protein_sequence":{"accession":"AJD07405.1","sequence":"MNIKALLLITSAIFISACCSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWNGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEKKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"KJ584918.1","fmin":"0","fmax":"828","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGAACGGGCAAAAAAGGCTGTTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAAAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001600","ARO_id":"38000","ARO_name":"OXA-409","CARD_short_name":"OXA-409","ARO_description":"OXA-409 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3520":{"model_id":"3520","model_name":"OXA-451","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"514"}},"model_sequences":{"sequence":{"5715":{"protein_sequence":{"accession":"AKI29916.1","sequence":"MKKITLFLLFLNLVFGQDKILNNWFKEYNTSGTFVFYDGKTWASNDFSRAMETFSPASTFKIFNALIVLDSGVIKTKKEIFYHYRGEKVFLSSWAQDMNLSSAIKYSNVLAFKEVARRIGIKTMQEYLNKLHYGNAKISKIDTFWLDNSLKISAKEQAILLFRLSQNSLPFSQEAMNSVKEMIYLKNMENLELFGKTGFNDEQKIAWIVGFVYLKDENKYKAFALNLDIDKFEDLYKREKILEKYLDELVKKVKNDG"},"dna_sequence":{"accession":"KR061504.1","fmin":"0","fmax":"774","strand":"+","sequence":"ATGAAAAAAATAACTTTATTTTTACTTTTCTTAAATTTAGTGTTTGGGCAAGATAAGATATTAAATAATTGGTTTAAAGAGTATAATACAAGCGGCACTTTTGTTTTTTATGATGGAAAAACTTGGGCGAGTAACGACTTTTCAAGGGCTATGGAGACTTTCTCTCCCGCTTCCACTTTTAAAATTTTTAATGCTCTAATTGTACTTGATAGTGGTGTGATAAAAACTAAAAAAGAAATTTTTTATCACTATAGAGGTGAAAAAGTATTTTTATCTTCTTGGGCGCAAGATATGAATTTAAGTTCAGCTATAAAATATTCTAATGTTCTTGCTTTTAAAGAAGTGGCAAGAAGAATTGGTATCAAAACTATGCAAGAATATTTAAACAAGCTTCATTATGGTAATGCTAAAATTTCCAAGATCGATACTTTTTGGCTTGACAACTCACTAAAAATAAGCGCTAAAGAACAAGCAATTTTGCTTTTTAGACTTTCACAAAATAGCTTACCTTTTTCTCAAGAAGCAATGAATAGTGTTAAGGAAATGATTTATTTAAAAAATATGGAAAATTTAGAGCTTTTTGGAAAAACAGGTTTTAATGATGAGCAAAAAATTGCTTGGATTGTAGGTTTTGTGTATTTAAAAGATGAAAATAAATATAAGGCTTTCGCGCTAAATTTAGATATTGATAAATTTGAAGATTTATATAAAAGAGAAAAAATTTTAGAAAAATATTTAGATGAACTTGTAAAAAAAGTTAAAAATGATGGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36772","NCBI_taxonomy_name":"Campylobacter jejuni","NCBI_taxonomy_id":"197"}}}},"ARO_accession":"3003607","ARO_id":"40217","ARO_name":"OXA-451","CARD_short_name":"OXA-451","ARO_description":"OXA-451 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46519":{"category_aro_accession":"3007730","category_aro_cvterm_id":"46519","category_aro_name":"OXA-61-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-61.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3524":{"model_id":"3524","model_name":"OXA-457","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"555"}},"model_sequences":{"sequence":{"5719":{"protein_sequence":{"accession":"ALC76098.1","sequence":"MTVRLFSTALGAALSLSALAGAPAQAAILCTVVADAADGRIVYQQGTQQACAARYTPASTFKLPIALMGADAGILTGPHAPVWNYQPGYPDWGGDAWRQPTDPARWIKYSVVWYSQLTARALGQERFQRYASAFHYGNEDVSGEPGKHNGLDGAWINSSLRISPLEQLAFLRKLVNRQLPVKAAAYDLAENLFEVGEASGWHLYGKTGTGSPGSNGVYTAANAYGWFVGWARKDGRQLVFARLVQDEQATKPNAGLRARDDLMRDWPAMADAPRK"},"dna_sequence":{"accession":"KP903886.1","fmin":"0","fmax":"828","strand":"+","sequence":"ATGACCGTTCGCCTCTTTTCGACCGCTCTCGGCGCGGCCCTTTCCCTGTCCGCGCTGGCCGGCGCCCCCGCCCAGGCGGCCATCCTGTGCACCGTGGTGGCCGACGCCGCCGACGGCCGCATCGTGTACCAGCAGGGCACGCAGCAGGCGTGCGCCGCGCGCTACACGCCGGCCTCGACCTTCAAGCTGCCCATCGCCCTGATGGGCGCGGACGCCGGCATCCTGACGGGCCCGCACGCGCCGGTCTGGAACTACCAGCCCGGCTACCCCGACTGGGGCGGCGACGCCTGGCGCCAGCCCACGGATCCGGCGCGCTGGATCAAGTATTCGGTGGTCTGGTATTCGCAGCTGACCGCCCGGGCGCTGGGGCAGGAGCGCTTCCAGCGCTATGCCTCGGCCTTCCATTACGGCAACGAGGACGTCTCGGGCGAACCCGGCAAGCACAACGGCCTGGACGGCGCATGGATCAACTCGTCGCTGCGGATTTCTCCGTTGGAACAACTGGCGTTCTTGCGCAAGCTGGTCAACCGGCAATTGCCGGTCAAGGCGGCGGCCTACGACCTGGCCGAGAACCTGTTCGAGGTCGGCGAAGCCAGCGGCTGGCACCTGTATGGCAAGACCGGCACCGGCTCGCCTGGCAGCAACGGCGTCTACACGGCGGCCAACGCCTACGGCTGGTTCGTCGGCTGGGCCCGCAAGGACGGCCGCCAGCTGGTGTTCGCCCGCCTGGTGCAGGACGAGCAGGCCACCAAGCCCAACGCCGGCCTGCGCGCCCGCGACGACCTGATGCGCGACTGGCCCGCCATGGCCGACGCGCCGCGCAAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42840","NCBI_taxonomy_name":"Achromobacter sp. 2015clin2ach","NCBI_taxonomy_id":"1707589"}}}},"ARO_accession":"3003613","ARO_id":"40223","ARO_name":"OXA-457","CARD_short_name":"OXA-457","ARO_description":"OXA-457 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3551":{"model_id":"3551","model_name":"ARL-3","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"580"}},"model_sequences":{"sequence":{"5746":{"protein_sequence":{"accession":"APY23844.1","sequence":"MKKFFTIFVLLCVCFAYTTATASAQGLTKLEHKNDATVGVYGINTATGQTYSHNADTRFAYASTFKAITSGLLLQQSSPEALNKTVTIKESDIVAYSPVTEQYVGKTMTLRQLISAAMLQSDNTASNIIMEQLGGLDQISSRLQALGDTTTNPQRYEPELNNYDPQSTADTSTPRATAHSLQQLLTTDAVAPQQRKFLQNLMFNNETGDSLIKKGVPDSYKVGDKSGQGTTYGTRNDVALIYPKHQTKPIVLVVFTKHQQQDAQPQDELVAQAARHAIHQLD"},"dna_sequence":{"accession":"KY363208.1","fmin":"2236","fmax":"3085","strand":"+","sequence":"ATGAAAAAGTTTTTTACTATCTTTGTCTTACTCTGTGTTTGCTTCGCTTACACAACTGCTACTGCTTCAGCGCAAGGTTTAACTAAATTAGAACATAAAAATGATGCCACAGTAGGTGTTTATGGCATTAATACTGCTACTGGACAAACTTATTCGCACAACGCTGATACCCGTTTTGCTTATGCATCAACATTTAAAGCCATTACAAGTGGGTTATTATTACAACAAAGTTCTCCTGAAGCATTAAACAAGACTGTCACTATAAAAGAGTCAGATATCGTGGCATATTCACCTGTTACTGAACAATATGTTGGAAAAACAATGACCCTACGTCAACTCATTTCCGCTGCTATGTTACAGAGTGACAATACTGCTAGCAATATCATAATGGAGCAACTCGGTGGTCTGGATCAAATTTCGTCTCGTTTACAAGCACTCGGAGATACAACAACAAACCCACAACGTTACGAACCTGAGTTAAACAACTATGACCCTCAAAGTACAGCAGATACATCAACACCTCGTGCTACTGCCCATAGTTTACAACAGCTGTTAACAACTGATGCAGTTGCACCACAACAACGCAAGTTCTTACAAAATTTAATGTTTAATAATGAAACAGGCGATAGTTTAATCAAAAAAGGTGTTCCAGACAGTTATAAAGTAGGCGACAAAAGTGGTCAGGGTACAACTTATGGTACACGTAATGATGTTGCCCTCATATATCCAAAACATCAAACTAAGCCAATTGTTTTAGTCGTCTTTACGAAACATCAGCAACAAGACGCACAACCACAAGATGAGTTAGTTGCACAAGCAGCACGTCATGCAATACATCAGCTCGATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42844","NCBI_taxonomy_name":"Staphylococcus arlettae","NCBI_taxonomy_id":"29378"}}}},"ARO_accession":"3004736","ARO_id":"42846","ARO_name":"ARL-3","CARD_short_name":"ARL-3","ARO_description":"ARL-3 is a beta-lactamase gene found in Staphylococcus arlettae.","ARO_category":{"42853":{"category_aro_accession":"3004742","category_aro_cvterm_id":"42853","category_aro_name":"ARL Beta-lactamase","category_aro_description":"ARL beta-lactamase is an AMR Gene Family associated with Staphylococcus arlettae.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4187":{"model_id":"4187","model_name":"ADC-113","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6562":{"protein_sequence":{"accession":"WP_136512055.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVSGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVKTDQQVLTFFKDWKPKNSIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_064672.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGTCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAGTATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAATTTCCAGATGAAGTAAAAACAGATCAGCAAGTTTTAACATTTTTTAAAGACTGGAAACCTAAAAACTCAATCGGTGAATATCGACAATATTCAAACCCAAGCATTGGTTTATTTGGAAAAGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTAAATCCACAAAAATATCCAGCAGATATTCAACGGGCAATTAATGAAACACATCAGGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006291","ARO_id":"44753","ARO_name":"ADC-113","CARD_short_name":"ADC-113","ARO_description":"ADC-113 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3561":{"model_id":"3561","model_name":"BIC-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"5756":{"protein_sequence":{"accession":"ADB56658.1","sequence":"MARPSKLALSFSLLLPFLPFTSFAETWPQGDIARQKIVKLEKDFGGRIGVSAIDTGANRTFDFRADERFPLCSSFKGFLAGAVLSHSQQQEGLLEKRIDYKNRVMEPHSPISAQHSSTGMTVAQLAAAALQYSDNGATNLLLENVLGGPAGMTTFMRTLGDTTFRLDRWELELNSAIPGDDRDTSTPHAIARSLQKIALGEALQTAPRQQLVDWLIGNTTGGARIRAGVPVEWVVGDKTGTCGVYGTANDYAVIWPKTSAPIVLAIYTAKPNKEDKHSDAVIAEVTRAVLESFE"},"dna_sequence":{"accession":"GQ260093.1","fmin":"0","fmax":"885","strand":"+","sequence":"ATGGCACGTCCTTCTAAACTAGCTTTATCATTTTCTCTTCTGTTGCCTTTTTTACCCTTCACCAGCTTCGCTGAAACCTGGCCACAGGGCGATATCGCCCGACAAAAAATCGTAAAGCTGGAAAAGGATTTTGGTGGGCGGATTGGAGTATCTGCCATCGATACGGGCGCCAATCGAACTTTTGACTTTCGAGCGGACGAACGTTTCCCTTTATGCAGCTCCTTTAAGGGCTTTCTGGCTGGCGCCGTGCTCTCCCACAGCCAACAGCAGGAAGGCTTACTGGAGAAACGTATCGACTATAAGAATCGGGTGATGGAACCTCACTCTCCCATCAGCGCACAACATAGTTCGACGGGTATGACCGTGGCGCAATTAGCGGCAGCGGCGCTGCAGTACAGCGACAACGGTGCGACAAATTTGCTTCTGGAAAACGTTCTGGGCGGGCCCGCCGGGATGACGACCTTCATGAGGACCTTAGGCGATACAACGTTTCGCTTAGATCGATGGGAACTCGAACTCAATAGCGCCATTCCGGGCGACGATCGAGATACCTCGACCCCCCACGCCATAGCCCGCAGCTTGCAAAAAATAGCGTTGGGTGAGGCGTTGCAAACCGCACCGCGTCAGCAGCTGGTTGATTGGCTCATCGGAAATACGACAGGTGGAGCGCGGATCCGGGCAGGCGTTCCTGTCGAGTGGGTTGTAGGGGATAAAACGGGCACGTGCGGTGTGTACGGCACCGCCAATGATTATGCCGTCATATGGCCAAAAACATCCGCCCCGATTGTCTTGGCGATTTACACCGCGAAACCGAACAAGGAGGACAAACATAGCGATGCCGTTATTGCCGAAGTGACCCGTGCCGTTCTGGAAAGCTTTGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36937","NCBI_taxonomy_name":"Pseudomonas fluorescens","NCBI_taxonomy_id":"294"}}}},"ARO_accession":"3004753","ARO_id":"42865","ARO_name":"BIC-1","CARD_short_name":"BIC-1","ARO_description":"BIC-1 is a beta-lactamase conferring resistance to carbapenems that is found in Pseudomonas fluorescens.","ARO_category":{"42864":{"category_aro_accession":"3004752","category_aro_cvterm_id":"42864","category_aro_name":"BIC Beta-lactamase","category_aro_description":"BIC is a class A beta-lactamase conferring resistance to carbapenem.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3567":{"model_id":"3567","model_name":"CBP-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"5764":{"protein_sequence":{"accession":"ALF06101.1","sequence":"MKKIVNSKLKVNKFKMCIFISILIFSLTGCGNVENKTSENTKPEIQYNSAFSKIESDYGVKLGVYAFDTETNKEVTYNADKRFAYCSTFKSLISGAILQKYSSDQLKQVIKYSPKDVLSYAPVTKNHVDKGMTIEELCDAAVRFSDNTAANLLINLIGGPNGFKSALNQLGDTVTEPARIEPELNVATPGDNRDTSTPRQLSIDLKEYTTGNILSDDKKKILINWMSGNATGDKLIRAGAPKDWMVSDKSGTGSYGTRNDIAIVIPPNKKPIFIAILSSKNDKDAKYDDKTISEASKIVFDYFINTRK"},"dna_sequence":{"accession":"KP718480.1","fmin":"0","fmax":"927","strand":"+","sequence":"ATGAAAAAAATAGTAAACTCAAAATTAAAGGTAAATAAATTTAAAATGTGTATATTTATATCAATTCTTATATTTTCTCTTACTGGATGTGGAAATGTAGAAAATAAAACTTCTGAAAATACAAAACCTGAGATACAATATAATTCAGCATTTTCAAAAATTGAAAGTGATTATGGTGTTAAACTTGGTGTATATGCTTTTGATACAGAAACAAATAAAGAAGTTACATATAATGCTGATAAGAGATTCGCTTACTGTTCTACCTTTAAATCTTTAATATCCGGTGCGATTTTACAAAAATATTCATCAGACCAACTTAAACAAGTAATTAAATATAGCCCAAAAGATGTACTGTCTTATGCACCAGTTACAAAAAATCATGTTGATAAAGGTATGACTATTGAAGAACTTTGCGATGCGGCAGTACGCTTTAGTGATAATACAGCTGCAAATCTTTTGATTAATCTTATAGGTGGACCTAATGGTTTTAAATCAGCACTTAATCAATTAGGTGACACAGTTACAGAACCTGCACGTATCGAACCAGAACTAAATGTTGCTACACCTGGAGATAATAGGGATACTAGTACTCCAAGACAATTATCAATTGATTTAAAAGAATACACAACTGGAAATATATTATCAGATGATAAGAAAAAAATTCTTATTAATTGGATGTCAGGAAATGCAACAGGTGATAAGCTAATTCGTGCAGGAGCACCAAAAGACTGGATGGTTTCTGATAAAAGTGGAACTGGTTCTTACGGAACAAGAAATGATATTGCAATAGTAATACCACCAAATAAAAAGCCTATATTTATTGCAATATTATCAAGTAAAAACGATAAAGATGCTAAATATGATGACAAAACAATTTCTGAGGCTTCTAAAATTGTATTTGATTATTTTATTAACACCAGGAAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41649","NCBI_taxonomy_name":"Clostridium botulinum","NCBI_taxonomy_id":"1491"}}}},"ARO_accession":"3004764","ARO_id":"42878","ARO_name":"CBP-1","CARD_short_name":"CBP-1","ARO_description":"CBP-1 is a class A beta-lactamase gene found in C. botulinum.","ARO_category":{"42877":{"category_aro_accession":"3004763","category_aro_cvterm_id":"42877","category_aro_name":"CBP beta-lactamase","category_aro_description":"CBP is a class A beta-lactamase family found in C. botulinum.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3601":{"model_id":"3601","model_name":"GOB-15","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"555"}},"model_sequences":{"sequence":{"5799":{"protein_sequence":{"accession":"AAV65595.1","sequence":"MRNFATLFFLSVCLNLNLNAQVVKEPENMPKEWNQTYEPFRIAGNLYYVGTYDLASYLIVTDKGNILINTGTAEPLPIIKGNIQKLGFNYKDIKILLLTQAHYDHTGALQDFKTETGAKFYTDKADADVLKTGGKSDYELGKYGVTFKPITPDRTLKDQDKITLGNTTLTLLHHPGHTKGSCSFIFDTKDEKRKYRVLIANMPSIIVDKKFSEVTAYPNIQSDYAYTFGAMKKLDFDLWVASHASQFDLHEKRKEGDPYNPQLFMDKQNYFQSLNNLEKSYLDKIKKDSQDK"},"dna_sequence":{"accession":"AY775547.1","fmin":"0","fmax":"879","strand":"+","sequence":"ATGAGAAATTTTGCTACACTGTTTTTTCTGTCAGTTTGTTTGAATTTGAATTTGAACGCTCAGGTAGTAAAAGAACCTGAGAATATGCCTAAAGAATGGAATCAGACTTATGAACCATTCAGAATTGCAGGTAACTTATATTACGTAGGAACCTATGATTTGGCTTCTTACCTTATTGTGACGGACAAAGGCAATATTCTCATTAATACAGGAACGGCAGAACCGCTTCCAATAATAAAAGGCAATATTCAAAAGCTGGGGTTTAATTATAAAGACATTAAGATCTTGCTGCTTACCCAGGCTCATTATGACCATACAGGTGCGTTACAGGATTTCAAAACAGAAACCGGTGCAAAATTCTATACCGATAAAGCAGATGCTGATGTCCTGAAAACAGGGGGTAAGTCCGATTATGAATTGGGAAAATATGGTGTGACATTTAAACCTATTACTCCGGATAGAACGTTAAAAGATCAGGATAAAATAACACTGGGAAATACAACCCTGACTTTGCTTCATCACCCGGGACATACAAAAGGTTCCTGCAGTTTTATTTTTGACACAAAAGACGAGAAGAGAAAGTATAGAGTTCTGATAGCTAATATGCCCTCTATTATTGTTGATAAGAAATTTTCTGAAGTTACAGCATATCCGAATATTCAGTCCGATTATGCTTATACCTTTGGTGCAATGAAAAAGCTTGATTTTGATCTTTGGGTAGCATCGCATGCAAGTCAGTTCGATCTGCATGAAAAACGTAAAGAAGGAGATCCGTACAACCCACAATTGTTTATGGATAAGCAAAACTATTTCCAAAGTCTTAATAATCTGGAGAAAAGCTATCTTGATAAAATTAAAAAAGATTCCCAAGATAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36960","NCBI_taxonomy_name":"Elizabethkingia meningoseptica","NCBI_taxonomy_id":"238"}}}},"ARO_accession":"3004807","ARO_id":"42927","ARO_name":"GOB-15","CARD_short_name":"GOB-15","ARO_description":"GOB-15 is a class B beta-lactamase gene found in Elizabethkingia meningoseptica.","ARO_category":{"41376":{"category_aro_accession":"3004212","category_aro_cvterm_id":"41376","category_aro_name":"GOB beta-lactamase","category_aro_description":"The GOB family of beta-lactamases have been discovered in the Elizabethkingia meningoseptica and are classified as subclass B3 beta-lactamase. They confer resistance to cephalosporins, penicillins, and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3707":{"model_id":"3707","model_name":"Mycobacterium tuberculosis eis mutations confer resistance to kanamycin","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"41339":{"param_type":"nucleotide substitution in promoter region","param_description":"A nucleotide sequence change where, compared to a reference sequence, one nucleotide is replaced by one other nucleotide in the promoter region of a gene. These substitutions are indicated as upstream of the reference sequence transcription initiation site. Format is given by [-][position][wildtype][>][mutation], e.g. -11t>c or -15g>Var where Var represents any possible substitution.","param_type_id":"41339","param_value":{"13328":"-10g>a","13284":"-14c>t","15412":"-10g>a","15413":"-12c>t","15414":"-14c>t","15415":"-37g>t"}},"snp":{"CRyPTIC-R":{"13328":"V562L","13284":"V562L"},"WHO-R":{"15412":"V562L","15413":"V562L","15414":"V562L","15415":"V562L"},"param_value":{"9594":"V163I"},"ReSeqTB-High":{"9594":"V163I"},"clinical":{"9594":"V163I"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"725"}},"model_sequences":{"sequence":{"8827":{"protein_sequence":{"accession":"NP_216932.2","sequence":"MTVTLCSPTEDDWPGMFLLAAASFTDFIGPESATAWRTLVPTDGAVVVRDGAGPGSEVVGMALYMDLRLTVPGEVVLPTAGLSFVAVAPTHRRRGLLRAMCAELHRRIADSGYPVAALHASEGGIYGRFGYGPATTLHELTVDRRFARFHADAPGGGLGGSSVRLVRPTEHRGEFEAIYERWRQQVPGGLLRPQVLWDELLAECKAAPGGDRESFALLHPDGYALYRVDRTDLKLARVSELRAVTADAHCALWRALIGLDSMERISIITHPQDPLPHLLTDTRLARTTWRQDGLWLRIMNVPAALEARGYAHEVGEFSTVLEVSDGGRFALKIGDGRARCTPTDAAAEIEMDRDVLGSLYLGAHRASTLAAANRLRTKDSQLLRRLDAAFASDVPVQTAFEF"},"dna_sequence":{"accession":"NC_000962.3","fmin":"2714123","fmax":"2715332","strand":"-","sequence":"GTGACTGTGACCCTGTGTAGCCCGACCGAGGACGACTGGCCGGGGATGTTCCTACTGGCCGCGGCCAGTTTCACCGATTTCATCGGCCCTGAATCAGCGACCGCCTGGCGGACCCTGGTGCCCACCGACGGAGCGGTGGTGGTCCGCGATGGTGCCGGCCCGGGTTCTGAGGTGGTCGGGATGGCGCTGTACATGGATCTGCGGTTGACGGTGCCTGGTGAAGTGGTGCTCCCGACCGCCGGTCTCAGTTTCGTCGCGGTGGCGCCGACGCATCGCCGGCGCGGCTTGCTGCGCGCGATGTGCGCCGAACTGCACCGCCGCATAGCCGATTCCGGCTATCCGGTCGCGGCACTGCATGCTAGCGAGGGCGGCATCTACGGCCGGTTCGGCTACGGGCCCGCTACCACCTTGCATGAGCTGACGGTCGACCGACGCTTCGCGCGCTTTCACGCCGACGCACCGGGCGGCGGCCTAGGTGGCAGCAGCGTCCGGTTGGTCAGACCCACCGAGCATCGCGGCGAGTTTGAGGCGATCTACGAGCGATGGCGCCAGCAGGTGCCGGGCGGGCTGCTACGCCCGCAGGTGCTCTGGGACGAGCTGCTGGCAGAATGCAAAGCCGCGCCCGGTGGAGACCGTGAATCGTTCGCGTTACTGCATCCCGACGGGTACGCGCTGTACCGGGTGGATCGCACCGATCTCAAGCTAGCGCGCGTCAGCGAACTCAGGGCGGTAACCGCAGATGCGCATTGTGCGTTGTGGCGGGCCCTGATTGGCCTCGACTCCATGGAGCGAATCAGCATCATCACCCATCCACAGGACCCGTTACCCCACCTGCTCACCGATACCCGACTGGCCCGCACTACCTGGCGCCAGGACGGCCTGTGGTTGCGCATCATGAACGTACCGGCCGCACTCGAGGCGCGTGGTTACGCTCACGAAGTTGGCGAGTTTTCCACGGTCCTCGAGGTATCCGATGGCGGCCGGTTCGCGCTCAAGATCGGTGACGGCCGTGCGCGGTGTACCCCGACCGATGCGGCAGCCGAGATCGAAATGGATCGGGACGTACTGGGCAGCCTTTACCTTGGAGCGCACCGCGCTTCGACGTTAGCCGCCGCTAACCGGTTGCGCACCAAAGATTCCCAGCTGCTTCGTCGACTCGACGCGGCGTTTGCCAGTGATGTTCCCGTCCAGACCGCGTTCGAGTTCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3004963","ARO_id":"43149","ARO_name":"Mycobacterium tuberculosis eis mutations confer resistance to kanamycin","CARD_short_name":"Mtub_eis_KAN","ARO_description":"Mutations in eis that contribute to or confer resistance to kanamycin.","ARO_category":{"43148":{"category_aro_accession":"3004962","category_aro_cvterm_id":"43148","category_aro_name":"kanamycin resistant eis","category_aro_description":"Involved in acetylation and intracellular survival. Associated with the cell surface and secretion proteins.","category_aro_class_name":"AMR Gene Family"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3701":{"model_id":"3701","model_name":"Neisseria gonorrhoeae folP with mutation conferring resistance to sulfonamides","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"200"},"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"9878":"R228S"},"Curated-R":{"9878":"R228S"},"clinical":{"9878":"R228S"}}},"model_sequences":{"sequence":{"5974":{"protein_sequence":{"accession":"KAE9504908.1","sequence":"MARHVWRAGRFEIGLDKPKIMGIVNLTPDSFSDGGAYSQNAQTALAHAERLLKEGADILDIGGESTRPGADFVPPEEEEWARVEPVLAEAAGWGVPVSLDTRRTVVMEKALALGGIDIINDVAALTDEGAVELLARQADTGICLMHMRGLPETMQDNPKYQDVVGEVARYLKTRSETCVAAGIAPQRITLDPGFGFGKNLQHNIALMRHLPELMAETGLPLLIGVSRKRMIGELTGEADAAARVHGSVAAALASVARGAQIVRVHDVKATADALKVWEALGVNR"},"dna_sequence":{"accession":"WHPL01000002.1","fmin":"1956330","fmax":"1957185","strand":"+","sequence":"ATGGCACGACACGTTTGGCGGGCAGGACGGTTTGAAATCGGTTTGGACAAACCGAAAATCATGGGCATCGTGAATCTCACGCCCGATTCTTTTTCCGACGGCGGCGCGTATTCGCAAAACGCCCAAACAGCTTTGGCGCATGCCGAACGGCTTTTGAAAGAGGGTGCGGACATTCTCGACATCGGCGGCGAATCGACGCGGCCGGGTGCGGATTTCGTTCCGCCCGAAGAAGAAGAATGGGCGCGGGTTGAGCCTGTATTGGCGGAAGCGGCGGGGTGGGGCGTTCCCGTCAGTTTGGACACGCGCCGCACGGTGGTTATGGAAAAGGCGTTGGCACTCGGCGGCATCGATATTATCAATGATGTGGCGGCGTTGACCGACGAAGGTGCGGTCGAATTGCTGGCGCGCCAGGCGGACACGGGCATTTGCCTGATGCATATGCGGGGCTTGCCCGAAACCATGCAGGACAATCCGAAATATCAGGATGTGGTCGGCGAAGTGGCACGTTATCTGAAAACACGGTCAGAAACCTGTGTCGCGGCAGGCATCGCGCCGCAACGGATTACGCTCGACCCGGGTTTCGGCTTCGGCAAGAACCTGCAACACAATATCGCACTGATGCGGCATTTGCCCGAATTGATGGCGGAAACCGGTTTGCCGCTGCTGATCGGTGTGTCGCGCAAACGCATGATAGGTGAGCTGACCGGTGAGGCGGACGCGGCGGCGCGCGTACACGGCAGCGTGGCAGCGGCTTTGGCTTCCGTGGCACGCGGAGCGCAAATCGTGCGCGTGCACGATGTGAAGGCGACGGCGGACGCGTTGAAGGTGTGGGAAGCGTTGGGCGTGAACCGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36806","NCBI_taxonomy_name":"Neisseria gonorrhoeae","NCBI_taxonomy_id":"485"}}}},"ARO_accession":"3004873","ARO_id":"43059","ARO_name":"Neisseria gonorrhoeae folP with mutation conferring resistance to sulfonamides","CARD_short_name":"Ngon_folP_SLF","ARO_description":"Point mutations in Neisseria gonorrhoeae dihydropteroate synthase folP prevent sulfonamide antibiotics from inhibiting its role in folate synthesis, thus conferring sulfonamide resistance.","ARO_category":{"39999":{"category_aro_accession":"3003415","category_aro_cvterm_id":"39999","category_aro_name":"sulfonamide resistant dihydropteroate synthase folP","category_aro_description":"Point mutations in dihydropteroate synthase folP prevent sulfonamide antibiotics from inhibiting its role in folate synthesis, thus conferring sulfonamide resistance.","category_aro_class_name":"AMR Gene Family"},"36469":{"category_aro_accession":"3000330","category_aro_cvterm_id":"36469","category_aro_name":"sulfisoxazole","category_aro_description":"Sulfisoxazole is an inhibitor of dihydropteroate synthase, interfering with the tetrahydrofolic biosynthesis pathway. Tetrahydrofolic acid is essential for folate synthesis, a precursor to many nucleotides and amino acids.","category_aro_class_name":"Antibiotic"},"36421":{"category_aro_accession":"3000282","category_aro_cvterm_id":"36421","category_aro_name":"sulfonamide antibiotic","category_aro_description":"Sulfonamides are broad spectrum, synthetic antibiotics that contain the sulfonamide group. Sulfonamides inhibit dihydropteroate synthase, which catalyzes the conversion of p-aminobenzoic acid to dihydropteroic acid as part of the tetrahydrofolic acid biosynthetic pathway. Tetrahydrofolic acid is essential for folate synthesis, a precursor of many nucleotides and amino acids. Many sulfamides are taken with trimethoprim, an inhibitor of dihydrofolate reductase, also disturbing the trihydrofolic acid synthesis pathway.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3702":{"model_id":"3702","model_name":"Mycobacterium tuberculosis inhA mutations conferring resistance to ethionamide","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"14806":"S94A","9515":"I194T","9517":"I21T","9516":"I21V"},"WHO-R":{"14806":"S94A"},"clinical":{"14806":"S94A","9515":"I194T","9517":"I21T","9516":"I21V"},"ReSeqTB-Moderate":{"9515":"I194T"},"ReSeqTB-High":{"9517":"I21T","9516":"I21V"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8774":{"protein_sequence":{"accession":"NP_216000.1","sequence":"MTGLLDGKRILVSGIITDSSIAFHIARVAQEQGAQLVLTGFDRLRLIQRITDRLPAKAPLLELDVQNEEHLASLAGRVTEAIGAGNKLDGVVHSIGFMPQTGMGINPFFDAPYADVSKGIHISAYSYASMAKALLPIMNPGGSIVGMDFDPSRAMPAYNWMTVAKSALESVNRFVAREAGKYGVRSNLVAAGPIRTLAMSAIVGGALGEEAGAQIQLLEEGWDQRAPIGWNMKDATPVAKTVCALLSDWLPATTGDIIYADGGAHTQLL"},"dna_sequence":{"accession":"NC_000962.3","fmin":"1674201","fmax":"1675011","strand":"+","sequence":"ATGACAGGACTGCTGGACGGCAAACGGATTCTGGTTAGCGGAATCATCACCGACTCGTCGATCGCGTTTCACATCGCACGGGTAGCCCAGGAGCAGGGCGCCCAGCTGGTGCTCACCGGGTTCGACCGGCTGCGGCTGATTCAGCGCATCACCGACCGGCTGCCGGCAAAGGCCCCGCTGCTCGAACTCGACGTGCAAAACGAGGAGCACCTGGCCAGCTTGGCCGGCCGGGTGACCGAGGCGATCGGGGCGGGCAACAAGCTCGACGGGGTGGTGCATTCGATTGGGTTCATGCCGCAGACCGGGATGGGCATCAACCCGTTCTTCGACGCGCCCTACGCGGATGTGTCCAAGGGCATCCACATCTCGGCGTATTCGTATGCTTCGATGGCCAAGGCGCTGCTGCCGATCATGAACCCCGGAGGTTCCATCGTCGGCATGGACTTCGACCCGAGCCGGGCGATGCCGGCCTACAACTGGATGACGGTCGCCAAGAGCGCGTTGGAGTCGGTCAACAGGTTCGTGGCGCGCGAGGCCGGCAAGTACGGTGTGCGTTCGAATCTCGTTGCCGCAGGCCCTATCCGGACGCTGGCGATGAGTGCGATCGTCGGCGGTGCGCTCGGCGAGGAGGCCGGCGCCCAGATCCAGCTGCTCGAGGAGGGCTGGGATCAGCGCGCTCCGATCGGCTGGAACATGAAGGATGCGACGCCGGTCGCCAAGACGGTGTGCGCGCTGCTGTCTGACTGGCTGCCGGCGACCACGGGTGACATCATCTACGCCGACGGCGGCGCGCACACCCAATTGCTCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3004876","ARO_id":"43062","ARO_name":"Mycobacterium tuberculosis inhA mutations conferring resistance to ethionamide","CARD_short_name":"Mtub_inhA_ETO","ARO_description":"inhA is a enoyl-acyl carrier reductase used in lipid metabolism and farry acid biosynthesis. It is inhibited by ethionamide. Mutations in the promoter region or multiple copies of the inhA show marked resistance to ethionamide mediated inhibition of mycolic acid biosynthesis.","ARO_category":{"43061":{"category_aro_accession":"3004875","category_aro_cvterm_id":"43061","category_aro_name":"inhA with mutations with conferring resistance to ethionamide","category_aro_description":"Genes with mutations in inhA which confer resistance to ethionamide class antibiotics.","category_aro_class_name":"AMR Gene Family"},"40067":{"category_aro_accession":"3003474","category_aro_cvterm_id":"40067","category_aro_name":"ethionamide","category_aro_description":"Ethionamide is a second-line antitubercular agent that inhibits mycolic acid synthesis.","category_aro_class_name":"Antibiotic"},"45738":{"category_aro_accession":"3007156","category_aro_cvterm_id":"45738","category_aro_name":"thioamide antibiotic","category_aro_description":"A group of antibiotics possessing the thioamide functional group.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3703":{"model_id":"3703","model_name":"Mycobacterium tuberculosis nudC mutations conferring resistance to isoniazid","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"9587":"S287N","9590":"P239R"},"ReSeqTB-High":{"9587":"S287N","9588":"P239R"},"clinical":{"9587":"S287N","9590":"P239R"},"ReSeqTB-Minimal":{"9590":"P239R"}},"40494":{"param_type":"frameshift mutation","param_description":"A frameshift is a sequence change between the translation initiation (start) and termination (stop) codon where, compared to a reference sequence, translation shifts to another reading frame as caused by nucleotide insertions and deletions. In ARO, these are annotated at the protein level with the first changed most N-terminal wildtype amino acid position. Format is given as [wildtype AA][position]fs, e.g. S531fs where S531 is a frameshifted coordinate beginning with codon 531. Termination may also be denoted as: Ter[position]fs.","param_type_id":"40494","param_value":{"9588":"A216fs"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"8784":{"protein_sequence":{"accession":"NP_217715.1","sequence":"MTNVSGVDFQLRSVPLLSRVGADRADRLRTDMEAAAAGWPGAALLRVDSRNRVLVANGRVLLGAAIELADKPPPEAVFLGRVEGGRHVWAVRAALQPIADPDIPAEAVDLRGLGRIMDDTSSQLVSSASALLNWHDNARFSALDGAPTKPARAGWSRVNPITGHEEFPRIDPAVICLVHDGADRAVLARQAAWPERMFSLLAGFVEAGESFEVCVAREIREEIGLTVRDVRYLGSQQWPFPRSLMVGFHALGDPDEEFSFSDGEIAEAAWFTRDEVRAALAAGDWSSASESKLLLPGSISIARVIIESWAACE"},"dna_sequence":{"accession":"NC_000962.3","fmin":"3571601","fmax":"3572543","strand":"-","sequence":"GTGACGAACGTAAGCGGCGTGGATTTTCAGCTGAGAAGCGTTCCGTTGCTTTCGCGCGTCGGCGCCGACCGGGCCGACCGGCTGAGGACCGACATGGAGGCGGCCGCCGCGGGATGGCCAGGCGCGGCATTGCTGCGGGTGGATTCCCGCAATCGCGTGCTGGTCGCCAACGGCCGGGTGTTGCTTGGCGCGGCCATCGAGCTGGCCGACAAGCCACCGCCAGAGGCGGTATTCCTGGGTCGCGTCGAGGGCGGCCGCCACGTCTGGGCGGTGCGGGCAGCGCTGCAGCCGATCGCTGATCCCGACATACCAGCCGAGGCGGTGGACCTTCGTGGGCTCGGCCGAATCATGGACGACACCAGCAGCCAACTGGTGTCGTCGGCATCGGCGCTGTTGAACTGGCATGACAACGCACGATTCAGCGCCCTAGACGGCGCGCCGACGAAACCGGCCAGGGCCGGCTGGTCACGGGTCAACCCGATCACCGGTCATGAGGAGTTCCCCCGTATCGACCCGGCGGTGATCTGCCTGGTTCACGACGGCGCTGATCGTGCCGTGTTGGCTCGCCAGGCGGCGTGGCCGGAACGGATGTTCTCGCTGTTGGCTGGCTTTGTCGAGGCCGGAGAGTCGTTCGAAGTCTGCGTCGCCCGGGAGATCCGCGAGGAAATCGGCCTGACCGTTCGCGATGTGCGCTATCTGGGCAGCCAGCAGTGGCCGTTCCCGCGGTCGTTAATGGTTGGCTTTCATGCCTTGGGTGACCCGGATGAGGAGTTCTCGTTCAGCGACGGCGAAATCGCCGAAGCCGCGTGGTTCACCCGCGATGAGGTGCGCGCAGCGCTTGCCGCCGGCGATTGGTCCAGTGCGTCGGAGTCGAAACTGCTACTGCCCGGGTCGATCTCGATCGCCCGCGTGATCATCGAATCGTGGGCAGCGTGCGAATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3004931","ARO_id":"43117","ARO_name":"Mycobacterium tuberculosis nudC mutations conferring resistance to isoniazid","CARD_short_name":"Mtub_nudC_INH","ARO_description":"Mutations that occur in nudC which through overexpression of the enzyme can result in or contribute to antibiotic resistance to isoniazid.","ARO_category":{"43097":{"category_aro_accession":"3004911","category_aro_cvterm_id":"43097","category_aro_name":"isoniazid resistant nudC","category_aro_description":"nudC is a NADH pyrophosphatase that is involved in nicotinate and nicotinamide metabolism. Mutations that occur on the nudC gene resulting in the inability for isoniazid to function.","category_aro_class_name":"AMR Gene Family"},"36659":{"category_aro_accession":"3000520","category_aro_cvterm_id":"36659","category_aro_name":"isoniazid","category_aro_description":"Isoniazid is an organic compound that is the first-line anti tuberculosis medication in prevention and treatment. As a prodrug, it is activated by mycobacterial catalase-peroxidases such as M. tuberculosis KatG. Isoniazid inhibits mycolic acid synthesis, which prevents cell wall synthesis in mycobacteria.","category_aro_class_name":"Antibiotic"},"45734":{"category_aro_accession":"3007152","category_aro_cvterm_id":"45734","category_aro_name":"isoniazid-like antibiotic","category_aro_description":"A group of antibiotics containing isoniazid and its derivatives.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3415":{"model_id":"3415","model_name":"OXA-151","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"570"}},"model_sequences":{"sequence":{"5825":{"protein_sequence":{"accession":"SUA76968.1","sequence":"MNTIISRRWRAGLWRRLVGAVVLPATLAATPAAYAADVPKAAPGRITERADWGKLFTAEGVKGTIVVLDARTQTYQAYDAARAEKRMSPASTYKIFNSLLALDSGALDNERAIIPWDGKPRRIKNWNAAMDLRTAFRVSCLPCYQVVSHKIGRRYAQAKLNEVGYGNRTIGGAPDAYWVDDSLQISAREQVDFLQRLARGTLPFSARSQDIVRQMSIVEATPDYVLHGKTGWFVDKKPDIGWWVGWIERDGNIASVAINIDMLSEADAPKRARIVKSVLKDLKLI"},"dna_sequence":{"accession":"UGSG01000001.1","fmin":"1909222","fmax":"1910080","strand":"-","sequence":"ATGAATACGATAATTTCTCGCCGGTGGCGTGCCGGCCTGTGGCGGCGGCTGGTCGGCGCGGTCGTCTTGCCCGCAACGCTCGCCGCCACCCCTGCGGCCTATGCGGCCGACGTGCCGAAAGCCGCGCCGGGGCGCATCACCGAGCGCGCCGACTGGGGCAAGCTGTTCACCGCGGAGGGCGTGAAGGGCACGATCGTGGTGCTCGACGCACGCACGCAAACCTATCAGGCCTACGACGCCGCACGTGCCGAGAAGCGCATGTCGCCGGCGTCGACTTACAAGATATTCAACAGCCTGCTGGCGCTCGACTCCGGGGCGCTGGACAACGAACGCGCGATCATTCCCTGGGATGGCAAGCCGCGACGCATCAAGAACTGGAACGCGGCGATGGACCTGAGGACCGCGTTTCGCGTGTCATGCCTGCCCTGCTATCAGGTCGTCTCGCACAAGATCGGGCGCCGGTACGCGCAGGCGAAGCTGAACGAGGTCGGGTATGGCAACCGCACCATTGGCGGCGCGCCGGACGCCTATTGGGTCGACGACAGTCTGCAGATTTCGGCGCGTGAGCAGGTGGACTTCCTGCAGCGTCTCGCGCGTGGCACGTTGCCGTTCTCTGCGCGCTCGCAGGACATCGTGCGCCAGATGTCGATCGTCGAAGCCACGCCGGACTATGTGCTTCACGGCAAGACGGGCTGGTTCGTCGACAAGAAGCCCGATATCGGCTGGTGGGTAGGGTGGATCGAGCGCGACGGCAACATCGCCAGCGTCGCGATCAACATCGACATGCTGTCGGAGGCGGACGCCCCGAAACGGGCACGCATCGTGAAGTCGGTGCTGAAGGACCTGAAGCTGATCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36932","NCBI_taxonomy_name":"Pandoraea pnomenusa","NCBI_taxonomy_id":"93220"}}}},"ARO_accession":"3001456","ARO_id":"37856","ARO_name":"OXA-151","CARD_short_name":"OXA-151","ARO_description":"OXA-151 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46520":{"category_aro_accession":"3007731","category_aro_cvterm_id":"46520","category_aro_name":"OXA-62-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-62.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3437":{"model_id":"3437","model_name":"OXA-270","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"560"}},"model_sequences":{"sequence":{"5633":{"protein_sequence":{"accession":"EOQ69512.1","sequence":"MTKKALFFAISTIFLSACSFNTVQHHQIHAISTHKNSEEIKSLFDQAQTTGVLVIKRGNTEEIYGNDLKRASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMSKEVKRIGFGNADIGSKVDNFWLIGPLKITPQQEAQFAYELAHKTLPFSKNVQEQVQSMVFVEEKNGRKIYAKSGWGWDVEPQVGWLTGWVVQPQGEIVAFSLNLEMKKGTPSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"APQM01000006.1","fmin":"256342","fmax":"257164","strand":"+","sequence":"ATGACTAAAAAAGCTCTTTTCTTTGCCATTAGTACCATATTTTTGTCAGCATGTTCTTTCAATACAGTACAACATCACCAAATACACGCTATTTCTACTCATAAAAATTCAGAAGAAATAAAATCACTGTTTGATCAAGCACAGACCACAGGTGTTTTGGTTATTAAGCGCGGAAATACAGAGGAAATTTATGGCAATGATCTAAAAAGGGCATCAACTGAATATGTCCCTGCATCTACCTTTAAAATGTTAAATGCTCTAATTGGTCTTGAACATCATAAAGCAACAACCACTGAAGTGTTCAAATGGGATGGACAAAAGCGTTTATTTCCTGATTGGGAAAAGGATATGACTCTAGGTGATGCCATGAAAGCTTCTGCTATTCCTGTGTATCAAGAACTAGCTCGACGAATTGGCCTTGATCTTATGTCCAAAGAGGTCAAGCGTATTGGTTTCGGTAATGCTGATATTGGTTCAAAAGTAGATAATTTTTGGCTTATCGGTCCACTCAAAATTACGCCTCAACAGGAAGCACAGTTTGCTTATGAATTAGCACATAAAACTCTTCCCTTTAGCAAAAATGTACAAGAACAAGTTCAATCTATGGTGTTCGTAGAAGAAAAAAACGGACGTAAAATTTACGCTAAAAGCGGTTGGGGATGGGATGTGGAGCCTCAAGTGGGCTGGTTAACAGGCTGGGTCGTTCAACCACAAGGAGAAATTGTAGCGTTCTCACTCAATTTAGAAATGAAAAAAGGAACACCTAGTTCTATTCGAAAAGAAATTGCTTATAAAGGATTAGAACAGCTAGGTATTTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42800","NCBI_taxonomy_name":"Acinetobacter pittii ANC 4050","NCBI_taxonomy_id":"1217691"}}}},"ARO_accession":"3001726","ARO_id":"38126","ARO_name":"OXA-270","CARD_short_name":"OXA-270","ARO_description":"OXA-270 is a beta-lactamase found in Acinetobacter spp.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46495":{"category_aro_accession":"3007706","category_aro_cvterm_id":"46495","category_aro_name":"OXA-213-like beta-lactamase","category_aro_description":"OXA-213-like enzymes have been identified to be intrinsic to A. calcoaceticus and have been subsequently detected in A. pittii. Phylogenetic analysis of OXA-213-like proteins identified two distinct subgroups within the OXA family. The first group was linked to A. pittii and the second group to A. calcoaceticus. The carbapenemase activity of these OXAs may be related to the species-dependent effect.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3466":{"model_id":"3466","model_name":"OXA-304","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"560"}},"model_sequences":{"sequence":{"5661":{"protein_sequence":{"accession":"ENX45276.1","sequence":"MYKKVLVVAIATLFLSACSSNTVKQHQIHSISANKNSEEIKSLFDQAQTTGVLVIKRGQTEEIYGNDIKRASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMSKEVKRIGFGNADIGSKVDNFWLVGPLKITPEQETQFAYELANKTLPFSKNVQEQVQSMVFIEEKNGRKIYAKSGWGWDVEPQVGWLTGWVVQPQGEIVAFSLNLEMKKGIPSSIRKEIAYKGLEQLGVL"},"dna_sequence":{"accession":"APSC01000007.1","fmin":"142138","fmax":"142960","strand":"-","sequence":"ATGTATAAAAAAGTCCTTGTCGTTGCAATAGCTACTCTTTTTTTATCTGCCTGCTCTTCTAACACGGTAAAACAACATCAAATACATTCTATTTCTGCCAATAAAAATTCAGAAGAAATTAAATCTCTGTTTGATCAGGCACAGACCACGGGAGTTTTAGTGATTAAGCGTGGGCAGACCGAAGAAATTTATGGCAATGATATTAAAAGAGCATCAACAGAATATGTTCCCGCCTCTACCTTTAAAATGCTAAATGCTTTAATTGGACTTGAACATCATAAAGCAACGACAACTGAAGTATTTAAATGGGACGGGCAAAAGCGTTTATTTCCTGATTGGGAAAAGGACATGACTTTAGGCGATGCAATGAAAGCTTCTGCTATTCCAGTTTATCAAGAACTAGCGCGAAGAATTGGACTTGATCTTATGTCTAAAGAGGTAAAACGTATTGGTTTCGGTAATGCAGACATTGGTTCAAAAGTAGATAATTTTTGGCTTGTCGGCCCACTTAAAATTACTCCTGAGCAAGAAACCCAATTTGCTTATGAATTAGCTAATAAAACTCTTCCATTTAGTAAAAATGTACAAGAACAAGTCCAATCAATGGTGTTCATAGAAGAAAAAAATGGACGTAAAATTTATGCTAAAAGTGGTTGGGGATGGGATGTTGAACCACAAGTTGGCTGGTTAACTGGCTGGGTCGTTCAACCGCAAGGAGAAATTGTGGCATTCTCACTCAATTTAGAAATGAAAAAAGGAATTCCTAGTTCTATTCGAAAAGAAATTGCTTATAAAGGATTAGAACAACTCGGTGTTTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42825","NCBI_taxonomy_name":"Acinetobacter sp. NIPH 542","NCBI_taxonomy_id":"1217688"}}}},"ARO_accession":"3001759","ARO_id":"38159","ARO_name":"OXA-304","CARD_short_name":"OXA-304","ARO_description":"OXA-304 is a beta-lactamase found in Acinetobacter spp.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46495":{"category_aro_accession":"3007706","category_aro_cvterm_id":"46495","category_aro_name":"OXA-213-like beta-lactamase","category_aro_description":"OXA-213-like enzymes have been identified to be intrinsic to A. calcoaceticus and have been subsequently detected in A. pittii. Phylogenetic analysis of OXA-213-like proteins identified two distinct subgroups within the OXA family. The first group was linked to A. pittii and the second group to A. calcoaceticus. The carbapenemase activity of these OXAs may be related to the species-dependent effect.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3495":{"model_id":"3495","model_name":"OXA-411","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"566"}},"model_sequences":{"sequence":{"5690":{"protein_sequence":{"accession":"AJD07406.1","sequence":"MNIKTLLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEVHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKTTTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"KJ584920.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAACACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGTACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGACAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001602","ARO_id":"38002","ARO_name":"OXA-411","CARD_short_name":"OXA-411","ARO_description":"OXA-411 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3521":{"model_id":"3521","model_name":"OXA-452","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"513"}},"model_sequences":{"sequence":{"5716":{"protein_sequence":{"accession":"AKI29917.1","sequence":"MKKITLFLLFLNLVFGQDKILNNWFKEYNISGTFVFYDGKTWASNDFSRAMETFSPASTFKIFNALIALDSGVIKTKKEIFYHYRGEKVFLSSWAQDMNLSSAIKYSNVLAFKEVARRIGIKTMQEYLNKLHYGNAKISKIDTFWLDNSLKISAKEQAILLFRLSQNSLPFSQEAMNSVKEMIYLKNMENLELFGKTGFNDEQKIAWIVGFVYLKDENKYKAFALNLDIDKFEDLYKREKILEKYLDELVKKVKNDG"},"dna_sequence":{"accession":"KR061505.1","fmin":"0","fmax":"774","strand":"+","sequence":"ATGAAAAAAATAACTTTATTTTTACTTTTCTTAAATTTAGTGTTTGGGCAAGATAAGATATTAAATAATTGGTTTAAAGAGTATAATATAAGCGGCACTTTTGTTTTTTATGATGGAAAAACTTGGGCGAGTAACGACTTTTCAAGGGCTATGGAGACTTTCTCTCCCGCTTCCACTTTTAAAATTTTTAATGCTCTAATTGCACTTGATAGTGGTGTGATAAAAACTAAAAAAGAAATTTTTTATCACTATAGAGGTGAAAAAGTATTTTTATCTTCTTGGGCGCAAGATATGAATTTAAGTTCAGCTATAAAATATTCTAATGTTCTTGCTTTTAAAGAAGTGGCAAGAAGAATTGGTATCAAAACTATGCAAGAATATTTAAACAAGCTTCATTATGGTAATGCTAAAATTTCCAAGATCGATACTTTTTGGCTTGACAACTCACTAAAAATAAGCGCTAAAGAACAAGCAATTTTGCTTTTTAGACTTTCACAAAATAGCTTACCTTTTTCTCAAGAAGCAATGAATAGTGTTAAGGAAATGATTTATTTAAAAAATATGGAAAATTTAGAGCTTTTTGGAAAAACAGGTTTTAATGATGAGCAAAAAATTGCTTGGATTGTAGGTTTTGTGTATTTAAAAGATGAAAATAAATATAAGGCTTTCGCGCTAAATTTAGATATTGATAAATTTGAAGATTTATATAAAAGAGAAAAAATTTTAGAAAAATATTTAGATGAACTTGTAAAAAAAGTTAAAAATGATGGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36772","NCBI_taxonomy_name":"Campylobacter jejuni","NCBI_taxonomy_id":"197"}}}},"ARO_accession":"3003608","ARO_id":"40218","ARO_name":"OXA-452","CARD_short_name":"OXA-452","ARO_description":"OXA-452 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46519":{"category_aro_accession":"3007730","category_aro_cvterm_id":"46519","category_aro_name":"OXA-61-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-61.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3525":{"model_id":"3525","model_name":"OXA-458","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"555"}},"model_sequences":{"sequence":{"5720":{"protein_sequence":{"accession":"ALC76100.1","sequence":"MTVRLSSTALGAALSLSALAGAPAQAAVLCTVVADAADGRIVYQQGTQQACAARYTPASTFKLPIALMGADAGILTGPHAPVWNYQPGYPDWGGDAWRQPTDPARWIKYSVVWYSQLTARALGQERFQRYASAFHYGNEDVSGEPGKHNGLDGAWINSSLRISPLEQLAFLRKLVNRQLPLKAAAYDLAENLFEVGEAGGWRMHGKTGTGSPGSNGVYTAANAYGWFVGWARKDGRQLVFARLVQDEQATKPNAGLRARDDLMRDWPAMADAPRK"},"dna_sequence":{"accession":"KP903888.1","fmin":"0","fmax":"828","strand":"+","sequence":"ATGACCGTTCGCCTCTCTTCGACCGCTCTCGGCGCGGCCCTTTCCCTGTCCGCGCTGGCCGGCGCCCCCGCCCAGGCGGCCGTCCTGTGCACCGTGGTGGCCGACGCCGCCGACGGCCGCATCGTGTACCAGCAGGGTACGCAGCAGGCCTGCGCCGCGCGCTACACGCCGGCCTCGACCTTCAAGCTGCCCATCGCCCTGATGGGCGCGGACGCCGGCATCCTGACGGGCCCGCACGCGCCGGTCTGGAACTACCAGCCCGGCTACCCCGACTGGGGCGGCGACGCCTGGCGCCAGCCCACGGATCCGGCGCGCTGGATCAAGTATTCGGTGGTCTGGTATTCGCAGCTGACCGCCCGGGCGCTGGGGCAGGAGCGCTTCCAGCGCTATGCCTCGGCCTTCCATTACGGCAACGAGGACGTCTCGGGCGAACCCGGCAAACACAACGGCCTGGACGGCGCATGGATCAACTCGTCGCTGCGGATTTCTCCGTTGGAACAACTGGCGTTCTTGCGCAAGCTGGTCAACCGGCAATTGCCGCTCAAGGCGGCGGCCTACGACCTGGCCGAGAACCTGTTCGAGGTCGGCGAAGCCGGCGGCTGGCGTATGCACGGCAAGACCGGCACCGGCTCGCCTGGCAGCAACGGCGTCTACACGGCGGCCAACGCCTACGGCTGGTTCGTCGGCTGGGCACGCAAGGACGGCCGCCAGCTGGTGTTCGCCCGCTTGGTGCAGGACGAGCAAGCCACCAAGCCCAACGCCGGCCTGCGCGCCCGCGACGACCTGATGCGCGACTGGCCCGCCATGGCCGACGCACCGCGCAAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42841","NCBI_taxonomy_name":"Achromobacter sp. 2015clin4ach","NCBI_taxonomy_id":"1707590"}}}},"ARO_accession":"3003614","ARO_id":"40224","ARO_name":"OXA-458","CARD_short_name":"OXA-458","ARO_description":"OXA-458 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3552":{"model_id":"3552","model_name":"ARL-4","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"581"}},"model_sequences":{"sequence":{"5747":{"protein_sequence":{"accession":"APY23838.1","sequence":"MKKFFTIFVLLCVCFAYTTATASAQGLTKLEHKNDATVGVYGINTATGKTYSHNADTRFAYASTFKAITSGLLLQQSSPEALNKTVTIKESDIVAYSPVTEQYVGKTMTLRQLISAAMLQSDNTASNIIMEQLGGLDQISSRLQALGDTTTNPQRYEPELNNYDPQSTADTSTPRATAHSLQQLLTTDAVAPQQRKFLQNLMFNNETGDSLIKKGVPDSYKVGDKSGQGTTYGTRNDVALIYPKHQTKPIVLVVFTKHQQQDAQPQDELVAQAARHAIHQLD"},"dna_sequence":{"accession":"KY363206.1","fmin":"2236","fmax":"3085","strand":"+","sequence":"ATGAAAAAGTTTTTTACTATCTTTGTCTTACTCTGTGTTTGCTTCGCTTACACAACTGCTACTGCTTCAGCGCAAGGTTTAACTAAATTAGAACATAAAAATGATGCCACAGTAGGTGTTTATGGTATTAATACTGCTACCGGAAAAACTTACTCACACAATGCTGACACACGTTTTGCTTATGCATCAACATTTAAAGCCATTACAAGTGGTTTATTATTACAACAAAGTTCTCCTGAAGCATTAAACAAGACTGTCACTATAAAAGAGTCAGATATCGTGGCATATTCACCTGTTACTGAACAATATGTTGGAAAAACAATGACCCTACGTCAACTCATTTCCGCTGCTATGTTACAGAGTGACAATACTGCTAGCAATATCATAATGGAGCAACTCGGTGGTCTGGATCAAATTTCGTCTCGTTTACAAGCACTCGGAGATACAACAACAAACCCACAACGTTACGAACCTGAGTTAAACAACTATGACCCTCAAAGTACAGCAGATACATCAACACCTCGTGCTACTGCCCATAGTTTACAACAGCTGTTAACAACTGATGCAGTTGCACCACAACAACGCAAGTTCTTACAAAATTTAATGTTTAATAATGAAACAGGCGATAGTTTAATCAAAAAAGGTGTTCCAGACAGTTATAAAGTAGGCGACAAAAGTGGTCAGGGTACAACTTATGGTACACGTAATGATGTTGCCCTCATATATCCAAAACATCAAACTAAGCCAATTGTTTTAGTCGTCTTTACGAAACATCAGCAACAAGACGCACAACCACAAGATGAGTTAGTTGCACAAGCAGCACGTCATGCAATACATCAGCTCGATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42844","NCBI_taxonomy_name":"Staphylococcus arlettae","NCBI_taxonomy_id":"29378"}}}},"ARO_accession":"3004737","ARO_id":"42847","ARO_name":"ARL-4","CARD_short_name":"ARL-4","ARO_description":"ARL-4 is a beta-lactamase gene found in Staphylococcus arlettae.","ARO_category":{"42853":{"category_aro_accession":"3004742","category_aro_cvterm_id":"42853","category_aro_name":"ARL Beta-lactamase","category_aro_description":"ARL beta-lactamase is an AMR Gene Family associated with Staphylococcus arlettae.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3562":{"model_id":"3562","model_name":"BIL-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"780"}},"model_sequences":{"sequence":{"5757":{"protein_sequence":{"accession":"CAA52618.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGRDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWAYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDTKVALAAVPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVIVANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"X74512.1","fmin":"126","fmax":"1272","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCCGCGATGCTATCGCGCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGCGTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACACGAAAGTGGCATTGGCAGCCGTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATCGTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3004755","ARO_id":"42867","ARO_name":"BIL-1","CARD_short_name":"BIL-1","ARO_description":"BIL-1 is a plasmid-borne beta-lactamase that is also a class C beta-lactamase.","ARO_category":{"42866":{"category_aro_accession":"3004754","category_aro_cvterm_id":"42866","category_aro_name":"BIL Beta-lactamase","category_aro_description":"BIL beta-lactamase is plasmid-borne and is a class C beta-lactamase.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3568":{"model_id":"3568","model_name":"CGA-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"590"}},"model_sequences":{"sequence":{"5765":{"protein_sequence":{"accession":"AAL55262.1","sequence":"MKKTTLLFLLISAFSLAQTSLLEQKINSIIKNKKATVGVSVLGFENGFKYDKNGDKKLPMQSVFKFHIAAAVLNAVDQGKLSLDQKIMLNQSNLLENTWSPLRDKYPAGNIEIPLSEVIEYTVAKSDNNGCDILLRLLGGTQVVQKFMDSKGVKGFQIKYNEEDMHKDWNVQYENYSTTKSAADVLKKLYDGKLLSKKSTDYLMKVMLSTSTGLNKMVEQLPKNTPVARKTGASGKNNAGLTGAENEIGIVTLPNGKHYALAVFVSNSMETDAVNCRMISDISKEVWEYFNK"},"dna_sequence":{"accession":"AF339733.1","fmin":"436","fmax":"1315","strand":"+","sequence":"ATGAAAAAAACAACACTTCTTTTTCTTCTGATTTCAGCATTTTCATTGGCTCAGACTTCTTTATTGGAACAAAAAATTAATTCAATCATTAAGAACAAAAAAGCTACAGTCGGTGTTTCTGTTCTTGGGTTTGAAAATGGCTTTAAGTACGATAAAAACGGAGATAAAAAACTCCCGATGCAAAGTGTGTTTAAATTTCACATTGCAGCAGCAGTCCTGAATGCTGTAGATCAGGGAAAACTTTCTCTGGATCAGAAAATTATGCTAAACCAATCGAATTTACTGGAAAATACATGGTCGCCGCTTCGTGATAAGTATCCGGCAGGAAATATTGAAATTCCGTTAAGCGAAGTGATTGAATATACAGTTGCCAAAAGTGACAATAATGGCTGTGATATTCTTCTGAGGCTGCTGGGAGGAACCCAGGTTGTCCAGAAGTTTATGGATTCTAAAGGAGTAAAAGGTTTTCAGATCAAATACAATGAAGAGGATATGCATAAAGACTGGAATGTTCAGTATGAAAATTATAGTACTACAAAATCCGCTGCTGATGTCCTGAAAAAGTTGTATGACGGAAAATTATTATCCAAAAAATCCACAGACTATCTGATGAAAGTAATGCTTTCTACTTCAACCGGATTGAATAAAATGGTGGAACAGCTTCCCAAAAACACACCTGTCGCAAGAAAAACGGGAGCTTCCGGGAAGAATAATGCCGGTTTAACAGGCGCAGAAAATGAAATCGGAATTGTTACTTTACCCAACGGGAAACATTATGCATTAGCTGTATTTGTCAGTAATTCAATGGAAACGGATGCAGTGAACTGCAGGATGATTTCAGATATTTCGAAGGAGGTTTGGGAATATTTTAATAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39078","NCBI_taxonomy_name":"Chryseobacterium gleum","NCBI_taxonomy_id":"250"}}}},"ARO_accession":"3004766","ARO_id":"42880","ARO_name":"CGA-1","CARD_short_name":"CGA-1","ARO_description":"CGA-1 is a class A beta-lactamase gene found in Chryseobacterium gleum.","ARO_category":{"42879":{"category_aro_accession":"3004765","category_aro_cvterm_id":"42879","category_aro_name":"CGA beta-lactamase","category_aro_description":"CGA is a class A beta-lactamase family that is found in Chryseobacterium gleum.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3602":{"model_id":"3602","model_name":"GOB-16","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"490"}},"model_sequences":{"sequence":{"11351":{"protein_sequence":{"accession":"AAW82618.1","sequence":"MRNFAILFFLLITFSWKAQVVKEPENTNEEWSRSYEPFRIAGNLYYVGTYDLASYLIVTDKGNILINTGLAGSLPMIKENIKKLGFNYKDIKILLLTQAHYDHTGALKDLQTETGAKFYADSADADVLKTGGKSDYEMGKYGATFKAIKPDILLKDQDKIKLGNTTLTLLHHPGHTKGSCSFIFETKDENRNYKVLIANMPSVIVDRKFSEIKDYPNIQADYAYTFKAMKKLDFDLWVASHASQFDLHTKHKEGDPYNPQVFMDKANYFAFLNSLETDYLEKIKNDSQKK"},"dna_sequence":{"accession":"AY899331.1","fmin":"0","fmax":"873","strand":"+","sequence":"ATGAGAAACTTTGCAATTTTATTTTTTTTACTGATCACTTTCAGCTGGAAAGCACAGGTTGTTAAAGAACCGGAAAATACAAATGAAGAATGGTCCCGATCATATGAGCCATTCAGAATTGCGGGTAACTTATACTATGTAGGAACTTACGATCTGGCTTCTTATTTAATAGTTACCGATAAAGGAAATATTCTCATTAATACAGGATTGGCTGGTTCTCTTCCTATGATAAAAGAGAATATTAAAAAACTGGGATTCAATTATAAAGACATTAAAATTCTGCTTTTAACCCAGGCGCATTATGATCATACAGGTGCATTAAAAGATTTGCAAACAGAAACAGGTGCGAAATTTTATGCAGACAGTGCTGATGCTGATGTATTGAAAACGGGCGGTAAATCCGATTATGAAATGGGGAAATACGGGGCAACCTTTAAGGCGATTAAGCCTGATATCCTGTTGAAAGATCAGGATAAAATAAAACTGGGGAATACAACCTTAACTTTACTTCATCATCCGGGGCACACAAAAGGTTCATGCAGTTTTATATTTGAAACAAAGGATGAAAACAGAAATTATAAAGTGCTGATAGCCAATATGCCATCGGTTATAGTTGACCGTAAGTTTTCCGAAATAAAAGATTACCCTAATATTCAGGCCGATTATGCTTATACATTTAAAGCCATGAAAAAACTGGATTTTGATCTTTGGGTCGCTTCACATGCAAGTCAGTTTGATTTACATACAAAACATAAAGAGGGAGACCCTTATAACCCACAGGTATTTATGGATAAGGCCAATTATTTTGCATTCCTCAATAGCCTGGAAACAGATTATCTGGAAAAAATTAAAAACGACTCACAAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36960","NCBI_taxonomy_name":"Elizabethkingia meningoseptica","NCBI_taxonomy_id":"238"}}}},"ARO_accession":"3004808","ARO_id":"42928","ARO_name":"GOB-16","CARD_short_name":"GOB-16","ARO_description":"GOB-16 is a class B beta-lactamase gene found in Elizabethkingia meningoseptica.","ARO_category":{"41376":{"category_aro_accession":"3004212","category_aro_cvterm_id":"41376","category_aro_name":"GOB beta-lactamase","category_aro_description":"The GOB family of beta-lactamases have been discovered in the Elizabethkingia meningoseptica and are classified as subclass B3 beta-lactamase. They confer resistance to cephalosporins, penicillins, and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3416":{"model_id":"3416","model_name":"OXA-152","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"570"}},"model_sequences":{"sequence":{"5611":{"protein_sequence":{"accession":"ALA99186.1","sequence":"MNTIISRRWRAGLWRRLVGAVVLPATLAATPAAYAADVPKAAPGRITERADWGKLFAAEGVKGTIVVLDARTQTYQAYDAARAGKRMSPASTYKIFNSLLALDSGALDNERAIIPWDGKPRRIKNWNAAMDLRTAFRVSCLPCYQVVSHKIGRQYAQAKLNEVGYGNRTIGGAPDAYWVDDSLQISAREQVDFVQRLARGTLPFSARSQDIVRQMSIVEATPDYVLHGKTGWFVDKKPDIGWWVGWIERDGNITSVAINIDMLSEADAPKRARIVKAVLKDLKLI"},"dna_sequence":{"accession":"KP771980.1","fmin":"3","fmax":"861","strand":"+","sequence":"ATGAATACGATAATCTCTCGCCGGTGGCGTGCCGGCCTGTGGCGGCGGCTGGTCGGCGCGGTCGTCTTGCCCGCAACGCTCGCCGCCACCCCTGCGGCCTATGCGGCCGACGTGCCGAAAGCCGCGCCGGGGCGCATCACCGAGCGCGCCGACTGGGGCAAGCTGTTCGCCGCGGAGGGCGTGAAGGGCACGATCGTGGTGCTCGACGCACGCACGCAAACCTATCAGGCCTACGACGCCGCACGTGCCGGGAAGCGCATGTCGCCGGCGTCGACTTACAAGATATTCAACAGCCTGCTGGCGCTCGACTCCGGGGCGCTGGACAACGAACGTGCGATCATTCCCTGGGATGGCAAGCCGCGACGCATCAAGAACTGGAACGCGGCGATGGACCTGAGGACCGCGTTTCGCGTGTCATGCCTGCCCTGCTATCAGGTCGTCTCGCACAAGATCGGGCGCCAGTACGCGCAGGCGAAGCTGAACGAGGTCGGGTATGGCAACCGCACCATTGGCGGCGCGCCGGACGCCTATTGGGTCGACGACAGTCTGCAGATTTCGGCGCGTGAGCAGGTGGACTTCGTGCAGCGTCTCGCGCGTGGCACGTTGCCGTTCTCTGCGCGCTCGCAGGACATCGTGCGCCAGATGTCGATCGTCGAAGCCACGCCGGACTATGTGCTTCACGGCAAGACGGGCTGGTTCGTCGACAAGAAGCCCGATATCGGCTGGTGGGTAGGGTGGATCGAGCGCGACGGCAACATCACCAGCGTCGCGATCAACATCGACATGCTGTCGGAGGCGGACGCCCCGAAACGGGCACGCATCGTGAAGGCGGTGCTGAAGGACCTGAAGCTGATCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36932","NCBI_taxonomy_name":"Pandoraea pnomenusa","NCBI_taxonomy_id":"93220"}}}},"ARO_accession":"3001457","ARO_id":"37857","ARO_name":"OXA-152","CARD_short_name":"OXA-152","ARO_description":"OXA-152 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46520":{"category_aro_accession":"3007731","category_aro_cvterm_id":"46520","category_aro_name":"OXA-62-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-62.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3438":{"model_id":"3438","model_name":"OXA-271","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"560"}},"model_sequences":{"sequence":{"5634":{"protein_sequence":{"accession":"EOQ72432.1","sequence":"MTKKALFLAISTIFLSACSFNTVQQHQIHALSTHKNSEEIQSLFDQAQTTGVLVIKRGKKEEIYGNDLKRASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMSKEIKRVDFGNADIGSKVDNFWLVGPLKITPQQEAQFAYELAHKTLPFSKNVQEQVQSMVFVEEKNGRKIYAKSGWGWDVEPQVGWLTGWVVQQQGEIVAFSLNLEMKKGIPSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"APQO01000006.1","fmin":"134980","fmax":"135802","strand":"-","sequence":"ATGACTAAAAAAGCTCTTTTCCTTGCTATTAGTACTATATTTTTGTCAGCATGTTCTTTCAATACAGTACAACAGCACCAAATACACGCTCTTTCTACCCATAAAAATTCAGAAGAAATTCAATCACTGTTTGATCAAGCGCAGACCACCGGTGTTTTGGTTATTAAGCGTGGAAAAAAAGAGGAAATTTATGGCAATGATCTAAAAAGAGCATCAACTGAATATGTTCCCGCCTCTACCTTTAAAATGTTAAATGCTCTAATTGGTCTTGAACATCATAAAGCAACAACAACTGAAGTGTTCAAATGGGACGGGCAAAAGCGTTTGTTTCCTGATTGGGAAAAAGATATGACCTTAGGCGATGCCATGAAAGCTTCTGCTATTCCTGTGTATCAAGAACTAGCTCGACGAATTGGCCTTGATCTTATGTCCAAAGAGATCAAGCGTGTGGATTTCGGTAATGCTGATATTGGTTCAAAAGTAGATAATTTTTGGCTTGTCGGTCCACTCAAAATTACGCCTCAACAGGAAGCACAGTTTGCTTATGAATTAGCCCATAAAACTCTTCCCTTTAGCAAAAATGTACAAGAACAAGTTCAATCTATGGTGTTCGTAGAAGAAAAAAACGGACGTAAAATTTACGCTAAAAGCGGTTGGGGATGGGATGTGGAGCCTCAAGTGGGCTGGTTAACAGGCTGGGTTGTTCAACAACAAGGAGAAATTGTAGCTTTCTCACTCAATTTAGAAATGAAAAAAGGAATACCTAGTTCTATTCGAAAAGAAATTGCTTATAAAGGATTAGAACAGCTAGGTATTTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42801","NCBI_taxonomy_name":"Acinetobacter lactucae","NCBI_taxonomy_id":"1785128"}}}},"ARO_accession":"3001727","ARO_id":"38127","ARO_name":"OXA-271","CARD_short_name":"OXA-271","ARO_description":"OXA-271 is a beta-lactamase found in Acinetobacter spp.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46495":{"category_aro_accession":"3007706","category_aro_cvterm_id":"46495","category_aro_name":"OXA-213-like beta-lactamase","category_aro_description":"OXA-213-like enzymes have been identified to be intrinsic to A. calcoaceticus and have been subsequently detected in A. pittii. Phylogenetic analysis of OXA-213-like proteins identified two distinct subgroups within the OXA family. The first group was linked to A. pittii and the second group to A. calcoaceticus. The carbapenemase activity of these OXAs may be related to the species-dependent effect.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3467":{"model_id":"3467","model_name":"OXA-305","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"560"}},"model_sequences":{"sequence":{"5662":{"protein_sequence":{"accession":"ENV02983.1","sequence":"MYKKVLVVATATLFLSACSSNTVKQHQIHSISANKNSEEIKSLFDQAQTTGVLVVKRGQTEEIYGNDLKRASTEYVPASTFKMLNALIGLEHHKATTTEIFKWDGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIRLDLMTKEVKRIGFGNADIGSKVDNFWLVGPLKITPEQETQFAYKLANKTLPFSKNVQEQVQSMVFIEEKNGRKIYAKSGWGWDVEPQVGWLTGWVVQPQGEIVAFSLNLEMKKGIPSSIRKEIAYKGLEQLGVL"},"dna_sequence":{"accession":"APPF01000021.1","fmin":"348832","fmax":"349654","strand":"+","sequence":"ATGTATAAAAAAGTCCTTGTCGTTGCAACAGCTACTCTATTTTTATCTGCCTGCTCTTCTAACACGGTAAAACAACATCAAATACATTCTATTTCCGCCAATAAAAATTCAGAAGAAATTAAATCTCTGTTTGATCAGGCACAGACCACAGGAGTTTTAGTGGTTAAGCGTGGGCAAACCGAAGAAATTTATGGCAATGATCTTAAAAGAGCATCAACCGAATATGTTCCCGCCTCTACCTTTAAAATGCTAAATGCTTTAATTGGACTTGAACATCATAAAGCAACGACAACTGAAATATTTAAATGGGATGGGCAAAAGCGTTTATTTCCTGATTGGGAAAAGGACATGACTCTAGGCGATGCTATGAAAGCTTCTGCTATTCCAGTTTATCAAGAACTAGCTCGTCGTATTAGACTTGATCTTATGACTAAAGAGGTAAAACGTATTGGTTTCGGTAATGCTGATATTGGTTCAAAAGTAGATAATTTTTGGCTTGTCGGTCCACTTAAAATTACACCTGAGCAAGAAACCCAATTTGCTTATAAATTAGCTAATAAAACTCTTCCATTTAGTAAAAATGTACAAGAGCAAGTCCAATCAATGGTGTTTATAGAAGAAAAAAATGGACGTAAAATTTATGCTAAAAGTGGTTGGGGATGGGATGTTGAACCACAAGTTGGCTGGTTAACCGGCTGGGTCGTTCAACCGCAAGGAGAAATTGTGGCATTCTCGCTCAATTTAGAAATGAAAAAAGGAATCCCTAGTTCTATCCGAAAAGAGATTGCTTATAAGGGATTAGAACAACTCGGCGTTTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42826","NCBI_taxonomy_name":"Acinetobacter sp. NIPH 817","NCBI_taxonomy_id":"520708"}}}},"ARO_accession":"3001760","ARO_id":"38160","ARO_name":"OXA-305","CARD_short_name":"OXA-305","ARO_description":"OXA-305 is a beta-lactamase found in Acinetobacter spp.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46495":{"category_aro_accession":"3007706","category_aro_cvterm_id":"46495","category_aro_name":"OXA-213-like beta-lactamase","category_aro_description":"OXA-213-like enzymes have been identified to be intrinsic to A. calcoaceticus and have been subsequently detected in A. pittii. Phylogenetic analysis of OXA-213-like proteins identified two distinct subgroups within the OXA family. The first group was linked to A. pittii and the second group to A. calcoaceticus. The carbapenemase activity of these OXAs may be related to the species-dependent effect.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3496":{"model_id":"3496","model_name":"OXA-412","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"566"}},"model_sequences":{"sequence":{"5691":{"protein_sequence":{"accession":"AJD07407.1","sequence":"MNVKALLLITSAIFISACSPYIVTANPNHSASKSDKKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWNGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"KJ584921.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACGTTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATAAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGAACGGGCAAAAAAGGCTGTTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACGCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001603","ARO_id":"38003","ARO_name":"OXA-412","CARD_short_name":"OXA-412","ARO_description":"OXA-412 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3526":{"model_id":"3526","model_name":"OXA-459","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"560"}},"model_sequences":{"sequence":{"5721":{"protein_sequence":{"accession":"ALC76101.1","sequence":"MTVRLSSCALGAALSLSALAGAPAQAAVLCTVVADAADGRIVYQQGTQQACAARYTPASTFKLPIALMGADAGILTGPHAPVWNYQPDYPDWGGDAWRQPTDPARWIKYSVVWYSQLTARALGQERFQRYASAFHYGNEDVSGEPGKHNGTDGAWIISSLRISPLEQLAFLRKVVNRQLPVKAAAYDLAENLFEVGEAGGWRLHGKTGTGSPGSNGVYTAANAYGWFVGWARKDGRQLVFARLVQDEQATKPNAGLRARDDLMRDWPAMADAPRK"},"dna_sequence":{"accession":"KP903889.1","fmin":"0","fmax":"828","strand":"+","sequence":"ATGACCGTTCGACTCTCTTCGTGCGCCCTCGGCGCAGCCCTTTCCCTGTCCGCGCTGGCCGGCGCCCCCGCCCAGGCGGCCGTCCTGTGCACCGTGGTGGCCGACGCCGCCGACGGCCGCATCGTGTACCAGCAGGGCACGCAGCAGGCCTGCGCCGCGCGCTACACGCCGGCCTCGACCTTCAAGCTGCCCATCGCCCTGATGGGCGCGGACGCCGGCATCCTGACGGGCCCGCACGCGCCGGTCTGGAACTACCAGCCCGACTACCCCGACTGGGGCGGCGACGCTTGGCGCCAGCCCACGGATCCTGCACGCTGGATCAAGTATTCGGTGGTCTGGTATTCGCAGCTGACCGCGCGGGCGCTGGGCCAGGAACGCTTCCAGCGCTATGCCTCGGCCTTCCATTACGGCAACGAGGATGTCTCGGGCGAACCCGGCAAGCACAACGGCACCGACGGCGCCTGGATCATCTCGTCGCTGCGCATCTCGCCGCTGGAACAGCTGGCCTTCCTGCGCAAGGTGGTCAACCGGCAGTTGCCGGTCAAGGCGGCGGCCTACGACCTGGCCGAGAACCTGTTCGAGGTCGGCGAAGCCGGCGGCTGGCGCCTGCATGGCAAGACCGGCACCGGCTCGCCGGGCAGCAACGGCGTCTACACGGCGGCCAACGCCTACGGCTGGTTCGTCGGCTGGGCGCGCAAGGACGGCCGCCAGCTGGTGTTCGCCCGCTTGGTGCAGGACGAACAGGCCACCAAGCCCAACGCCGGCCTGCGCGCCCGCGACGACCTGATGCGCGACTGGCCCGCCATGGCCGACGCGCCCCGCAAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42556","NCBI_taxonomy_name":"Achromobacter insuavis","NCBI_taxonomy_id":"1287735"}}}},"ARO_accession":"3003615","ARO_id":"40225","ARO_name":"OXA-459","CARD_short_name":"OXA-459","ARO_description":"OXA-459 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3553":{"model_id":"3553","model_name":"ARL-5","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"570"}},"model_sequences":{"sequence":{"5748":{"protein_sequence":{"accession":"APY23862.1","sequence":"MKKFFTIFVLLCVCFAYTTASASAQDLTKLEHKNDATVGVYGINTATGKTYSHNADTRFAYASTFKAITSGLLLQQSSPEALNKTVTIKESDIVAYSPVTEQYVGKTMTLRQLISAAMLQSDNTASNVIMEQLGGLDQISSRLQALGDTTTNPQRYEPELNNYDPQSTADTSTPRATAHSLQQLLTTDAVAPQQRKFLQNLMFNNETGDSLIKKGVPDSYKVGDKSGQGTTYGTRNDVALIYPKHQTKPIVLVVFTKHKQQDAKPQDALVAQAARQAIQQLD"},"dna_sequence":{"accession":"KY363214.1","fmin":"2237","fmax":"3086","strand":"+","sequence":"ATGAAAAAATTTTTTACTATCTTTGTCTTACTCTGTGTTTGCTTTGCTTACACAACTGCTAGTGCTTCAGCGCAAGATTTAACAAAATTGGAACATAAGAATGATGCCACAGTTGGTGTTTATGGTATTAATACTGCTACCGGAAAAACTTACTCACACAATGCTGACACACGTTTTGCTTATGCATCAACATTTAAAGCCATTACAAGTGGTTTATTATTACAACAAAGTTCTCCTGAAGCATTAAACAAGACTGTCACTATAAAAGAGTCAGATATCGTGGCATATTCACCTGTTACTGAACAATATGTTGGAAAAACAATGACCCTACGTCAACTCATTTCCGCTGCTATGTTACAGAGTGACAATACTGCTAGCAATGTCATAATGGAGCAACTCGGTGGTCTGGATCAAATTTCGTCTCGTTTACAAGCACTCGGAGATACAACAACAAACCCACAACGTTACGAACCTGAGTTAAACAACTATGACCCTCAAAGTACAGCAGATACATCAACACCTCGTGCAACTGCCCATAGTTTACAACAGCTGTTAACAACTGATGCAGTTGCACCACAACAACGCAAGTTCTTACAAAATTTAATGTTTAATAATGAAACAGGCGATAGTTTAATCAAAAAAGGTGTTCCAGACAGTTATAAAGTAGGCGACAAAAGTGGTCAGGGTACAACTTATGGTACACGTAATGATGTTGCCCTCATATATCCAAAACATCAAACTAAGCCAATTGTTTTAGTTGTCTTTACCAAACACAAGCAACAAGACGCAAAGCCACAAGATGCGCTTGTAGCACAAGCAGCACGTCAGGCTATACAGCAGCTCGATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42844","NCBI_taxonomy_name":"Staphylococcus arlettae","NCBI_taxonomy_id":"29378"}}}},"ARO_accession":"3004738","ARO_id":"42848","ARO_name":"ARL-5","CARD_short_name":"ARL-5","ARO_description":"ARL-5 is a beta-lactamase gene found in Staphylococcus arlettae.","ARO_category":{"42853":{"category_aro_accession":"3004742","category_aro_cvterm_id":"42853","category_aro_name":"ARL Beta-lactamase","category_aro_description":"ARL beta-lactamase is an AMR Gene Family associated with Staphylococcus arlettae.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3563":{"model_id":"3563","model_name":"BKC-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"5758":{"protein_sequence":{"accession":"AKD43328.1","sequence":"MTITFSRRQAIAGALLAVPAVSTLAASAGALLAVPAVSTLAASAGAATGGPLEKRLAELEGRHKGRIGVAIHNLATGARIGHRADERFLMCSTFKALLAAHILARVDRKEETLDRRIVVGKSDLVDWSPVVETRVGGEGISIAELCEAAITLSDNAAANLLLSASGGPKAVTQFLRGFGDDVTRLDRTEPTLNYRETPDDERDTTTPAAMAETLRKLIIGDVLARGSKAQLAAWLVMNKTGDTRLRAGFPVDWTTGDKTGTNGDRHGNANDVAIAWSPDRGAVVVTAFCEIPGISGDERNAVIAEIGRIAAEA"},"dna_sequence":{"accession":"KP689347.1","fmin":"8602","fmax":"9544","strand":"-","sequence":"ATGACGATCACATTTTCGCGCCGGCAGGCGATTGCCGGCGCTCTCCTTGCCGTTCCCGCCGTGTCCACGCTGGCCGCCAGCGCCGGCGCTCTCCTTGCCGTTCCCGCCGTGTCCACGCTGGCCGCCAGCGCCGGGGCGGCCACGGGCGGCCCGCTGGAAAAGAGGCTGGCCGAGCTGGAAGGGCGTCACAAGGGCCGCATCGGCGTTGCCATACATAATCTCGCAACGGGCGCCCGCATCGGCCACCGGGCGGACGAGCGCTTCCTGATGTGCAGCACCTTCAAGGCGTTGCTGGCGGCCCATATCCTCGCCCGCGTCGACAGGAAGGAAGAAACGCTCGACCGGCGGATCGTCGTCGGGAAATCCGATCTTGTGGACTGGTCGCCGGTGGTGGAAACCCGTGTCGGCGGCGAGGGCATCTCGATTGCCGAGCTTTGCGAGGCGGCGATCACGCTCAGCGACAACGCCGCGGCCAATCTCCTGCTGTCCGCCTCGGGCGGGCCGAAGGCCGTCACGCAGTTCCTGCGCGGTTTCGGCGACGACGTGACGCGCCTCGACCGCACCGAACCGACGCTCAACTATCGCGAGACGCCGGACGACGAGCGCGACACGACCACGCCCGCCGCCATGGCCGAGACGCTGCGCAAGCTGATCATCGGCGATGTCCTCGCGCGCGGCTCGAAGGCGCAGCTTGCCGCCTGGCTGGTGATGAACAAGACCGGCGACACGCGATTGCGCGCCGGCTTCCCGGTCGACTGGACGACCGGCGACAAGACCGGCACGAACGGCGACAGGCACGGCAACGCCAACGATGTCGCCATCGCCTGGTCGCCGGATCGCGGCGCGGTGGTCGTCACCGCTTTCTGCGAGATTCCCGGCATTTCCGGGGATGAGCGCAACGCCGTCATCGCCGAGATTGGTCGCATTGCCGCCGAGGCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3004757","ARO_id":"42869","ARO_name":"BKC-1","CARD_short_name":"BKC-1","ARO_description":"BKC-1 is a beta-lactamase conferring resistance to carbapenem and is found in Brazilian Klebsiella.","ARO_category":{"42868":{"category_aro_accession":"3004756","category_aro_cvterm_id":"42868","category_aro_name":"BKC Beta-lactamase","category_aro_description":"BKC beta-lactamase is a class A beta-lactamase.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3603":{"model_id":"3603","model_name":"GOB-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"519"}},"model_sequences":{"sequence":{"5801":{"protein_sequence":{"accession":"AAF89152.1","sequence":"KEPENMPNEWNQAYEPFRIAGNLYYLGTYDLASYLIVTDKGNILINTGTAESLPIIKANIQKLGFNYKDIKILLLTQAHYDHTGALQDFKTETAAKFYADKADVDVLRTGGKSDYEMGKYGVTFKPVTPDKTLKDQDKIKLGNITLTLLHHPGHTKGSCSFIFETKDEKRKYRVLIANMPSVIVDKKFSEVTAYPNIQSDYAYTFGVMKKLDFDIWVASHASQFDLHEKRKEGDPYNPQLFMDKQSYFQNLN"},"dna_sequence":{"accession":"AF189296.1","fmin":"0","fmax":"756","strand":"+","sequence":"AAAGAACCTGAAAATATGCCCAATGAATGGAACCAGGCTTATGAACCATTCAGAATTGCAGGTAATTTATATTACCTAGGAACCTATGATTTGGCTTCTTACCTTATTGTGACAGACAAAGGCAATATTCTCATTAATACAGGAACGGCAGAATCGCTTCCAATAATAAAAGCAAATATCCAAAAGCTCGGGTTTAATTATAAAGACATTAAGATCTTGCTGCTTACTCAGGCTCACTACGACCATACAGGTGCATTACAGGATTTTAAAACAGAAACCGCTGCAAAATTCTATGCCGATAAAGCAGATGTTGATGTCCTGAGAACAGGGGGGAAGTCCGATTATGAAATGGGAAAATATGGTGTGACATTTAAACCTGTTACTCCGGATAAAACATTGAAAGATCAGGATAAAATAAAACTGGGAAATATAACCCTGACTTTGCTTCATCATCCGGGACATACAAAAGGTTCCTGTAGTTTTATTTTTGAAACAAAAGACGAGAAGAGAAAATATAGAGTTTTGATAGCTAATATGCCCTCCGTTATTGTTGATAAGAAATTTTCTGAAGTTACCGCATATCCAAATATTCAGTCCGATTATGCTTATACCTTTGGTGTTATGAAAAAGCTGGATTTTGATATTTGGGTGGCCTCCCATGCAAGTCAGTTCGATCTCCATGAAAAACGTAAAGAAGGAGATCCGTACAATCCGCAATTGTTTATGGATAAGCAAAGCTATTTCCAAAACCTTAAT","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36960","NCBI_taxonomy_name":"Elizabethkingia meningoseptica","NCBI_taxonomy_id":"238"}}}},"ARO_accession":"3004809","ARO_id":"42929","ARO_name":"GOB-2","CARD_short_name":"GOB-2","ARO_description":"GOB-2 is class B beta-lactamase gene found in Elizabethkingia meningoseptica.","ARO_category":{"41376":{"category_aro_accession":"3004212","category_aro_cvterm_id":"41376","category_aro_name":"GOB beta-lactamase","category_aro_description":"The GOB family of beta-lactamases have been discovered in the Elizabethkingia meningoseptica and are classified as subclass B3 beta-lactamase. They confer resistance to cephalosporins, penicillins, and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3620":{"model_id":"3620","model_name":"LAP-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"585"}},"model_sequences":{"sequence":{"5818":{"protein_sequence":{"accession":"ABK58097.1","sequence":"MKKIRLIIISLLAGMCTPALSTPVNVTDTIQSTEDHIKGRVGFTEIDFLSGKVLSSHRREERFPMMSTFKVLLCGAILVRVDKGLEQLERRITYNKHDLDDYSPLTSQHIADGMTVSELCNAAITTSDNTAANLLLSTIGGPEGLTHFLRSTGDSYTRLDRHEPSLNEAKPGDERDTTTPAAMAQTLQKLLNGSVLTEKSRKKLISWMQEDKVGGPLFRSVLPAGWMIADKTGAGDHGSRGIVALLGPGGKPSRIVVLYITNTHSSMNELNEHIAGIGDSVIKNW"},"dna_sequence":{"accession":"EF026092.1","fmin":"0","fmax":"858","strand":"+","sequence":"ATGAAAAAGATCCGCCTTATTATAATCTCTTTACTGGCTGGAATGTGTACTCCAGCATTATCTACACCAGTCAATGTTACTGATACAATACAAAGCACAGAAGACCATATCAAAGGTCGGGTTGGTTTTACTGAAATAGACTTTTTATCCGGGAAGGTTCTGAGTAGTCATCGCCGTGAAGAACGTTTTCCTATGATGAGCACATTCAAAGTTTTGTTATGTGGAGCAATATTAGTACGTGTTGATAAAGGGCTTGAACAACTTGAACGCCGAATTACCTATAATAAGCATGACCTGGACGACTATTCTCCACTAACCAGTCAGCACATTGCAGATGGAATGACGGTTTCTGAGTTATGCAATGCTGCCATTACCACCAGTGATAACACTGCTGCAAATTTATTGCTATCAACTATTGGCGGGCCGGAGGGATTAACTCATTTTCTGCGTAGCACTGGTGATAGTTATACAAGGCTTGATCGACACGAACCCAGCCTTAATGAGGCGAAGCCTGGCGATGAGCGTGATACCACCACTCCGGCAGCGATGGCTCAAACGCTACAAAAATTGTTAAACGGAAGTGTACTTACAGAAAAATCTCGAAAAAAATTAATAAGCTGGATGCAGGAAGATAAAGTCGGCGGGCCTCTGTTCCGCTCTGTACTGCCAGCTGGCTGGATGATAGCGGATAAAACAGGAGCAGGTGATCACGGATCTCGGGGCATCGTTGCACTGTTGGGCCCCGGAGGCAAGCCATCTCGTATAGTAGTCCTGTATATTACAAATACTCATTCATCTATGAATGAACTCAACGAGCATATTGCAGGGATCGGAGATTCAGTAATTAAGAACTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3004825","ARO_id":"42955","ARO_name":"LAP-1","CARD_short_name":"LAP-1","ARO_description":"LAP-1 is an Ambler Class A beta-lactamase gene.","ARO_category":{"42954":{"category_aro_accession":"3004824","category_aro_cvterm_id":"42954","category_aro_name":"LAP beta-lactamase","category_aro_description":"LAP is a Ambler Class A beta-lactamase gene family that confers resistance to beta-lactams.","category_aro_class_name":"AMR Gene Family"},"35976":{"category_aro_accession":"0000059","category_aro_cvterm_id":"35976","category_aro_name":"cefepime","category_aro_description":"Cefepime (INN) is a fourth-generation cephalosporin antibiotic developed in 1994. It contains an aminothiazolyl group that decreases its affinity with beta-lactamases. Cefepime shows high binding affinity with penicillin-binding proteins and has an extended spectrum of activity against Gram-positive and Gram-negative bacteria, with greater activity against both Gram-negative and Gram-positive organisms than third-generation agents.","category_aro_class_name":"Antibiotic"},"35980":{"category_aro_accession":"0000063","category_aro_cvterm_id":"35980","category_aro_name":"cefuroxime","category_aro_description":"Cefuroxime is a second-generation cephalosporin antibiotic with increased stability with beta-lactamases than first-generation cephalosporins. Cefuroxime is active against Gram-positive organisms but less active against methicillin-resistant strains.","category_aro_class_name":"Antibiotic"},"35981":{"category_aro_accession":"0000064","category_aro_cvterm_id":"35981","category_aro_name":"amoxicillin","category_aro_description":"Amoxicillin is a moderate-spectrum, bacteriolytic, beta-lactam antibiotic used to treat bacterial infections caused by susceptible microorganisms. A derivative of penicillin, it has a wider range of treatment but remains relatively ineffective against Gram-negative bacteria. It is commonly taken with clavulanic acid, a beta-lactamase inhibitor. Like other beta-lactams, amoxicillin interferes with the synthesis of peptidoglycan.","category_aro_class_name":"Antibiotic"},"35995":{"category_aro_accession":"0000078","category_aro_cvterm_id":"35995","category_aro_name":"piperacillin","category_aro_description":"Piperacillin is an acetylureidopenicillin and has an extended spectrum of targets relative to other beta-lactam antibiotics. It inhibits cell wall synthesis in bacteria, and is usually taken with the beta-lactamase inhibitor tazobactam to overcome penicillin-resistant bacteria.","category_aro_class_name":"Antibiotic"},"36976":{"category_aro_accession":"3000632","category_aro_cvterm_id":"36976","category_aro_name":"benzylpenicillin","category_aro_description":"Benzylpenicillin, commonly referred to as penicillin G, is effective against both Gram-positive and Gram-negative bacteria. It is unstable in acid.","category_aro_class_name":"Antibiotic"},"37084":{"category_aro_accession":"3000704","category_aro_cvterm_id":"37084","category_aro_name":"cefalotin","category_aro_description":"Cefalotin is a semisynthetic cephalosporin antibiotic activate against staphylococci. It is resistant to staphylococci beta-lactamases but hydrolyzed by enterobacterial beta-lactamases.","category_aro_class_name":"Antibiotic"},"40523":{"category_aro_accession":"3003832","category_aro_cvterm_id":"40523","category_aro_name":"ticarcillin","category_aro_description":"Ticarcillin is a carboxypenicillin used for the treatment of Gram-negative bacteria, particularly P. aeruginosa. Ticarcillin's antibiotic properties arise from its ability to prevent cross-linking of peptidoglycan during cell wall synthesis, when the bacteria try to divide, causing cell death.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3417":{"model_id":"3417","model_name":"OXA-153","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"5829":{"protein_sequence":{"accession":"CFB60580.1","sequence":"MKKIISRWRRGVFGLRVALAVVSPMVFAVPAHATEAAGGAAGTKAAAVHMKERADWGKFFDAEGVKGTIVVLDGRTQTYQAFDTARAERRMSPASTYKIFNSLLALESGALDNEREIIPWDGKPRRGKYWNAAMDLRTAFRVSCLPCYQVVSHKIARQFAQSKLNEAGYGNHTIGRAADAYWVDDSLQISAREQVDFLQRLARGTLPFSARSQDIVRQISIVEANPDYVLHGKTGWFVDKKPDIGWWVGWIERDGNITSVALNIDLKDDADAPKRARIVRAVLSSLQLI"},"dna_sequence":{"accession":"CEWL01000009.1","fmin":"23801","fmax":"24671","strand":"-","sequence":"ATGAAAAAGATAATTTCTCGCTGGCGGCGTGGTGTCTTCGGGCTGCGGGTTGCGCTCGCGGTCGTGTCTCCCATGGTGTTCGCCGTTCCGGCGCATGCGACGGAAGCGGCGGGCGGGGCCGCGGGGACTAAGGCCGCTGCGGTGCACATGAAGGAGCGTGCCGATTGGGGCAAGTTCTTCGATGCGGAAGGTGTTAAGGGAACGATCGTGGTGCTCGACGGACGCACGCAAACGTATCAGGCGTTCGACACGGCGCGCGCCGAGCGGCGGATGTCGCCTGCATCGACGTACAAGATCTTCAACAGCCTGCTGGCGCTCGAGTCGGGCGCCCTCGATAACGAACGCGAGATCATTCCCTGGGACGGCAAGCCGCGACGCGGGAAGTACTGGAACGCGGCGATGGATCTGCGCACGGCGTTTCGCGTGTCGTGTTTGCCGTGCTATCAGGTGGTCTCGCACAAGATTGCGCGTCAGTTTGCACAGAGCAAACTCAATGAGGCCGGGTATGGGAACCACACTATCGGTCGTGCCGCAGACGCCTACTGGGTCGACGACAGCTTGCAGATCTCGGCACGCGAGCAGGTCGATTTCCTGCAACGTCTCGCGCGAGGGACGTTACCGTTCTCTGCACGCTCGCAAGACATCGTGCGTCAGATTTCGATTGTCGAGGCCAATCCTGATTACGTGTTGCATGGCAAGACGGGCTGGTTCGTCGACAAGAAGCCGGACATCGGCTGGTGGGTGGGCTGGATTGAGCGCGACGGCAACATCACGAGCGTAGCGTTGAACATCGATCTGAAGGACGATGCCGATGCGCCCAAGCGCGCCCGTATCGTTCGTGCCGTGCTCAGTAGTTTGCAGTTGATCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42785","NCBI_taxonomy_name":"Pandoraea apista","NCBI_taxonomy_id":"93218"}}}},"ARO_accession":"3001458","ARO_id":"37858","ARO_name":"OXA-153","CARD_short_name":"OXA-153","ARO_description":"OXA-153 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46520":{"category_aro_accession":"3007731","category_aro_cvterm_id":"46520","category_aro_name":"OXA-62-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-62.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3439":{"model_id":"3439","model_name":"OXA-272","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"5635":{"protein_sequence":{"accession":"ENW16915.1","sequence":"MTKKALFFAIGTMFLSACSFNTVQQHQIQSISTNKNSEKIKSLFDQAQTEGVLVIKRGQTEEIYGNDLKRSSTEYVPASTFKMLNALIGLEHHKATPTEVFKWYGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMSKEVKRIGFGNADIGSKVDDFWLVGPLKITPQQEVRFAYKLANKTLPFSKNVQEQVQSMVFIEEKNGRKIYAKSGWGWDVDPQVGWFTGWVVQPQGEIIAFSLNLEMKKGIPSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"APQP01000003.1","fmin":"306251","fmax":"307073","strand":"+","sequence":"ATGACTAAAAAAGCTCTTTTCTTTGCCATTGGTACGATGTTTTTGTCGGCATGTTCTTTTAATACCGTACAACAACATCAAATACAGTCAATTTCTACCAATAAAAACTCAGAGAAAATTAAATCATTGTTTGATCAAGCACAAACTGAAGGTGTTTTAGTTATAAAACGTGGGCAAACAGAGGAAATCTATGGTAATGATCTTAAAAGATCATCAACCGAATATGTTCCCGCCTCTACCTTTAAAATGTTAAATGCTTTGATAGGACTTGAGCATCATAAAGCAACACCAACTGAAGTGTTTAAATGGTATGGGCAAAAGCGTTTATTTCCCGATTGGGAAAAAGACATGACCTTAGGTGATGCTATGAAAGCTTCTGCTATTCCAGTTTATCAGGAACTAGCTCGACGAATTGGCCTTGATCTTATGTCTAAAGAGGTAAAACGCATTGGTTTCGGTAATGCTGATATTGGTTCAAAAGTAGATGATTTTTGGCTTGTTGGTCCACTTAAAATTACACCTCAACAAGAAGTACGGTTTGCTTACAAATTAGCCAACAAAACTCTTCCCTTTAGTAAAAATGTACAAGAACAAGTTCAATCTATGGTGTTCATTGAAGAAAAAAATGGACGAAAAATTTATGCCAAAAGTGGTTGGGGATGGGATGTTGACCCTCAAGTGGGTTGGTTTACAGGCTGGGTAGTTCAACCTCAGGGAGAAATTATAGCTTTCTCACTTAATTTAGAAATGAAGAAAGGCATACCTAGTTCTATTCGAAAAGAAATTGCTTATAAAGGATTAGAGCAGCTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42802","NCBI_taxonomy_name":"Acinetobacter pittii ATCC 19004 = CIP 70.29","NCBI_taxonomy_id":"1311774"}}}},"ARO_accession":"3001728","ARO_id":"38128","ARO_name":"OXA-272","CARD_short_name":"OXA-272","ARO_description":"OXA-272 is a beta-lactamase found in Acinetobacter spp.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46495":{"category_aro_accession":"3007706","category_aro_cvterm_id":"46495","category_aro_name":"OXA-213-like beta-lactamase","category_aro_description":"OXA-213-like enzymes have been identified to be intrinsic to A. calcoaceticus and have been subsequently detected in A. pittii. Phylogenetic analysis of OXA-213-like proteins identified two distinct subgroups within the OXA family. The first group was linked to A. pittii and the second group to A. calcoaceticus. The carbapenemase activity of these OXAs may be related to the species-dependent effect.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3468":{"model_id":"3468","model_name":"OXA-306","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"5663":{"protein_sequence":{"accession":"ENX38336.1","sequence":"MSKRLKTLALSASFTFALPLVACQSFGDQTQHIMAQKSEQQNIATLFQQAQTSGVLVIYDGKKIQKYGNDTSRAEQRYIPASTFKMLNALIGIQHHKTTPNEVFKWDGQKRAFSSWEKDLTLAEAMQASAVPVYQELARRIGLELMTREVKRVGYGNKNIGTQVDNFWLVGPLKITPVEEVRFAYALAKQKLPFDQSTQQQVKGMLLIDEVQGTKIYAKSGWGMDVNPQVGWWTGWIEQANGKVTAFSLNMEMNRPEHADARKAIVYQALQQLDLLAN"},"dna_sequence":{"accession":"APSB01000022.1","fmin":"299955","fmax":"300792","strand":"-","sequence":"ATGTCAAAAAGATTAAAAACTCTCGCGTTGAGTGCATCATTTACTTTTGCTTTACCCTTGGTCGCTTGCCAGAGCTTTGGCGATCAAACACAGCACATCATGGCGCAGAAAAGTGAACAACAAAATATTGCCACCCTTTTCCAACAGGCTCAAACAAGTGGTGTATTGGTGATCTATGATGGAAAGAAAATTCAAAAATATGGCAATGACACCAGTCGCGCAGAGCAACGTTATATCCCTGCTTCAACATTTAAAATGCTGAATGCGTTAATTGGCATACAACATCATAAAACCACGCCAAATGAAGTCTTTAAATGGGATGGCCAAAAACGCGCATTCAGTAGCTGGGAAAAAGATCTCACATTAGCTGAGGCAATGCAGGCATCGGCTGTGCCTGTATATCAAGAGCTGGCACGACGGATTGGTCTGGAACTGATGACCCGTGAAGTGAAGCGAGTGGGTTATGGGAATAAGAATATTGGCACACAAGTCGATAATTTTTGGTTAGTCGGCCCATTAAAAATCACCCCTGTAGAAGAAGTACGCTTTGCCTATGCATTGGCGAAGCAAAAGCTGCCATTTGATCAATCCACTCAACAACAAGTGAAAGGCATGTTATTGATTGATGAAGTTCAAGGGACCAAGATTTACGCGAAAAGCGGCTGGGGTATGGATGTTAACCCGCAAGTGGGATGGTGGACAGGGTGGATAGAGCAAGCAAATGGCAAAGTCACGGCATTTTCATTGAATATGGAAATGAATCGGCCTGAGCATGCAGATGCCCGTAAGGCAATTGTTTATCAAGCCTTACAGCAACTGGATTTATTGGCGAATTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42827","NCBI_taxonomy_name":"Acinetobacter sp. NIPH 2100","NCBI_taxonomy_id":"1217708"}}}},"ARO_accession":"3001761","ARO_id":"38161","ARO_name":"OXA-306","CARD_short_name":"OXA-306","ARO_description":"OXA-306 is a beta-lactamase found in Acinetobacter spp.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46503":{"category_aro_accession":"3007714","category_aro_cvterm_id":"46503","category_aro_name":"OXA-286-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-286.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3497":{"model_id":"3497","model_name":"OXA-413","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"5692":{"protein_sequence":{"accession":"AJD07408.1","sequence":"MNIKTLLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEVHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEYHKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"KJ584922.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAACACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGTACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGTACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001604","ARO_id":"38004","ARO_name":"OXA-413","CARD_short_name":"OXA-413","ARO_description":"OXA-413 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3527":{"model_id":"3527","model_name":"OXA-460","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"5722":{"protein_sequence":{"accession":"ATL95930.1","sequence":"MKKITLFLLFLNLVFGQDKILNNWFKEYNTSGTFVFYDGKTWASNDFSRAMETFSPASTFKIFNALIALDSGVIKTKKEIFYHYRGEKVFLSSWAQDMNLSSAIKYSNVLAFKEVTRRIGIKTMQEYLNKLHYGNAKISKIDTFWLDNSLKISAKEQAILLFRLSQNSLPFSQEAMNSVKEMIYLKNMENLELFGKTGFNDEQKIAWIVGFVYLKDENKYKAFALNLDIDKFEDLYKREKILEKYLDELVKKS"},"dna_sequence":{"accession":"CP023866.1","fmin":"651045","fmax":"651807","strand":"+","sequence":"ATGAAAAAAATAACTTTATTTTTACTTTTCTTAAATTTAGTGTTTGGGCAAGATAAGATATTAAATAATTGGTTTAAAGAGTATAATACAAGCGGCACTTTTGTTTTTTATGATGGAAAAACTTGGGCGAGTAACGACTTTTCAAGGGCTATGGAGACTTTCTCTCCCGCTTCCACTTTTAAAATTTTTAATGCTCTAATTGCACTTGATAGTGGTGTGATAAAAACTAAAAAAGAAATTTTTTATCACTATAGAGGTGAAAAAGTATTTTTATCTTCTTGGGCGCAAGATATGAATTTAAGTTCAGCTATAAAATATTCTAATGTTCTTGCTTTTAAAGAAGTGACAAGAAGAATTGGTATCAAAACTATGCAAGAATATTTAAACAAGCTTCATTATGGTAATGCTAAAATTTCCAAGATCGATACTTTTTGGCTTGACAACTCACTAAAAATAAGCGCTAAAGAACAAGCAATTTTGCTTTTTAGACTTTCACAAAATAGCTTACCTTTTTCTCAAGAAGCAATGAATAGTGTTAAGGAAATGATTTATTTAAAAAATATGGAAAATTTAGAGCTTTTTGGAAAAACAGGTTTTAATGATGAGCAAAAAATTGCTTGGATTGTAGGTTTTGTGTATTTAAAAGATGAAAATAAATATAAGGCTTTCGCGCTAAATTTAGATATTGATAAATTTGAAGATTTATATAAAAGAGAAAAAATTTTAGAAAAATATTTAGATGAACTTGTAAAAAAAAGTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36772","NCBI_taxonomy_name":"Campylobacter jejuni","NCBI_taxonomy_id":"197"}}}},"ARO_accession":"3003616","ARO_id":"40226","ARO_name":"OXA-460","CARD_short_name":"OXA-460","ARO_description":"OXA-460 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46519":{"category_aro_accession":"3007730","category_aro_cvterm_id":"46519","category_aro_name":"OXA-61-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-61.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3554":{"model_id":"3554","model_name":"ARL-6","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"5749":{"protein_sequence":{"accession":"APY23865.1","sequence":"MKKFFTIFVLLCVCFAYTTATASAQGLTKLEHKNDATVGVYGINTATGQTYSHNADTRFAYASTFKAITSGLLLQQNSPEALNKTVTIKESDIVAYSPVTEQYVGKTMTLRQLISAAMLQSDNTASNIIMEQLGGLDQLSSRLQALGDTTTNPQRYEPELNNYDPQSTADTSTPRATAHNLQNLLTTDAVAPQQRKFLQNLMLNNKTGESLIKKGVPNSYKVGDKSGQGTTYGTRNDVAVIYPKHQTKPIILVVFTKHQQQDAQPQDELVAQAARHAIHQLD"},"dna_sequence":{"accession":"KY464892.1","fmin":"2236","fmax":"3085","strand":"+","sequence":"ATGAAAAAGTTTTTTACTATCTTTGTCTTACTCTGTGTTTGCTTCGCTTACACAACTGCTACTGCTTCAGCGCAAGGTTTAACTAAATTAGAACATAAAAATGATGCCACAGTAGGTGTTTATGGCATTAATACTGCTACTGGACAAACTTATTCGCACAACGCTGATACCCGTTTTGCTTATGCATCAACTTTTAAAGCCATTACGAGTGGGTTATTATTACAGCAAAATTCTCCTGAAGCATTAAACAAAACTGTAACAATAAAAGAATCAGATATCGTGGCATATTCACCTGTTACTGAACAATATGTTGGAAAAACAATGACCCTACGTCAACTCATTTCCGCTGCTATGTTACAGAGTGACAATACTGCTAGCAATATCATAATGGAACAACTCGGTGGTCTGGATCAGCTTTCGTCTCGCTTACAAGCACTCGGAGATACAACAACAAACCCACAACGTTATGAACCCGAATTAAATAACTATGATCCACAAAGTACGGCAGATACATCAACACCTCGTGCTACTGCCCATAATTTGCAAAATCTATTAACAACAGATGCCGTTGCACCACAACAGCGTAAGTTTTTACAAAATTTAATGTTGAACAATAAAACAGGTGAGAGTTTAATCAAAAAAGGTGTCCCTAACAGTTATAAAGTAGGTGACAAAAGTGGCCAAGGTACAACTTATGGCACGCGTAATGATGTTGCCGTCATCTATCCAAAACATCAAACAAAACCAATTATTTTAGTCGTCTTTACGAAACATCAGCAACAAGACGCACAACCACAAGATGAGTTAGTTGCACAAGCAGCACGTCATGCAATACATCAGCTCGATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42844","NCBI_taxonomy_name":"Staphylococcus arlettae","NCBI_taxonomy_id":"29378"}}}},"ARO_accession":"3004739","ARO_id":"42849","ARO_name":"ARL-6","CARD_short_name":"ARL-6","ARO_description":"ARL-6 is a beta-lactamase gene found in Staphylococcus arlettae.","ARO_category":{"42853":{"category_aro_accession":"3004742","category_aro_cvterm_id":"42853","category_aro_name":"ARL Beta-lactamase","category_aro_description":"ARL beta-lactamase is an AMR Gene Family associated with Staphylococcus arlettae.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4188":{"model_id":"4188","model_name":"ADC-114","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6563":{"protein_sequence":{"accession":"WP_125052776.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVKTDQQVLTFFKDWKPKNSIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_064673.1","fmin":"30","fmax":"1185","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAGTATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAATTTCCAGATGAAGTAAAAACAGATCAGCAAGTTTTAACATTTTTTAAAGACTGGAAACCTAAAAACTCAATCGGTGAATATCGACAATATTCAAACCCAAGCATTGGTTTATTTGGAAAAGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTAAATCCACAAAAATATCCAGCAGATATTCAACGGGCAATTAATGAAACACATCAGGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006292","ARO_id":"44754","ARO_name":"ADC-114","CARD_short_name":"ADC-114","ARO_description":"ADC-114 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3706":{"model_id":"3706","model_name":"Mycobacterium tuberculosis ponA1 mutations conferring resistance to rifabutin","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"9739":"G363D","9740":"Q365H","9749":"T658A","9753":"I41M","9755":"A516T"},"ReSeqTB-High":{"9739":"G363D","9749":"T658A","9758":"A516T","9759":"A516T","9760":"A516T","18566":"A516T"},"clinical":{"9739":"G363D","9740":"Q365H","9749":"T658A","9753":"I41M","9755":"A516T"},"ReSeqTB-Moderate":{"9740":"Q365H","9755":"A516T"},"ReSeqTB-Minimal":{"9753":"I41M","9738":"A516T","18561":"A516T"}},"48031":{"param_type":"duplication of peptide sequence","param_description":"A duplication is a sequence change between the translation initiation (start) and termination (stop) codon where, compared to a reference sequence, a copy of one or more amino acids is inserted directly C-terminal of the original copy of that sequence.","param_type_id":"48031","param_value":{"9738":"P627_P629dup","9758":"V624_P626dup","9759":"P627dup","9760":"P626_P628dup"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1275"},"41342":{"param_type":"deletion mutation from peptide sequence","param_description":"A peptide sequence change between the translation initiation (start) and termination (stop) codon where, compared to a reference sequence, one or more amino acids are deleted and therefore are not present. These represent in-frame deletions which do not result in frameshift variants and may include multiple amino acids. Format is given by [wildtype AA][position]del for a single peptide deletion or [wildtype AA][position]_[wildtype AA][position]del for a deleted peptide range, e.g. K527del or Q517_N518del.","param_type_id":"41342","param_value":{"18561":"P631del"}},"41344":{"param_type":"insertion mutation from peptide sequence","param_description":"A peptide sequence change between the translation initiation (start) and termination (stop) codon where, compared to the reference sequence, one or more amino acids are inserted. These represent in-frame insertions which do not result in frameshift variants and where the insertion is not a duplication of a sequence immediately N-terminal (5'), and are denoted with wildtype flanking residues. Format is given by [wildtype AA position]_[wildtype AA position]ins[AA sequence], e.g. K464_D465insE or P46_A47insYS.","param_type_id":"41344","param_value":{"18566":"P630_P631insPPW"}}},"model_sequences":{"sequence":{"8789":{"protein_sequence":{"accession":"YP_177687.1","sequence":"MVILLPMVTFTMAYLIVDVPKPGDIRTNQVSTILASDGSEIAKIVPPEGNRVDVNLSQVPMHVRQAVIAAEDRNFYSNPGFSFTGFARAVKNNLFGGDLQGGSTITQQYVKNALVGSAQHGWSGLMRKAKELVIATKMSGEWSKDDVLQAYLNIIYFGRGAYGISAASKAYFDKPVEQLTVAEGALLAALIRRPSTLDPAVDPEGAHARWNWVLDGMVETKALSPNDRAAQVFPETVPPDLARAENQTKGPNGLIERQVTRELLELFNIDEQTLNTQGLVVTTTIDPQAQRAAEKAVAKYLDGQDPDMRAAVVSIDPHNGAVRAYYGGDNANGFDFAQAGLQTGSSFKVFALVAALEQGIGLGYQVDSSPLTVDGIKITNVEGEGCGTCNIAEALKMSLNTSYYRLMLKLNGGPQAVADAAHQAGIASSFPGVAHTLSEDGKGGPPNNGIVLGQYQTRVIDMASAYATLAASGIYHPPHFVQKVVSANGQVLFDASTADNTGDQRIPKAVADNVTAAMEPIAGYSRGHNLAGGRDSAAKTGTTQFGDTTANKDAWMVGYTPSLSTAVWVGTVKGDEPLVTASGAAIYGSGLPSDIWKATMDGALKGTSNETFPKPTEVGGYAGVPPPPPPPEVPPSETVIQPTVEIAPGITIPIGPPTTITLAPPPPAPPAATPTPPP"},"dna_sequence":{"accession":"NC_000962.3","fmin":"53662","fmax":"55699","strand":"+","sequence":"GTGGTGATCCTGTTGCCGATGGTCACCTTCACGATGGCCTACCTGATCGTCGACGTTCCCAAGCCAGGTGACATCCGTACCAACCAGGTCTCCACGATCCTTGCCAGCGACGGCTCGGAAATCGCCAAAATTGTTCCGCCCGAAGGTAATCGGGTCGACGTCAACCTCAGCCAGGTGCCGATGCATGTGCGCCAGGCGGTGATTGCGGCCGAAGACCGCAATTTCTATTCGAATCCGGGATTCTCGTTCACCGGCTTCGCGCGGGCAGTCAAGAACAACCTGTTCGGCGGCGATCTGCAGGGCGGATCGACGATTACCCAGCAGTACGTCAAGAACGCGCTGGTCGGTTCCGCACAGCACGGGTGGAGCGGTCTGATGCGCAAGGCGAAAGAATTGGTCATCGCGACGAAGATGTCGGGGGAGTGGTCTAAAGACGATGTGCTGCAGGCGTATCTGAACATCATCTACTTCGGCCGGGGCGCCTACGGCATTTCGGCGGCGTCCAAGGCTTATTTCGACAAGCCCGTCGAGCAGCTGACCGTTGCCGAAGGGGCGTTGTTGGCAGCGCTGATTCGGCGGCCTTCGACGCTGGACCCGGCGGTCGACCCCGAAGGGGCCCATGCCCGCTGGAATTGGGTACTCGACGGCATGGTGGAAACCAAGGCTCTCTCGCCGAATGACCGTGCGGCGCAGGTGTTTCCCGAGACAGTGCCGCCCGATCTGGCCCGGGCAGAGAATCAGACCAAAGGACCCAACGGGCTGATCGAGCGGCAGGTGACAAGGGAGTTGCTCGAGCTGTTCAACATCGACGAGCAGACCCTCAACACCCAGGGGCTGGTGGTCACCACCACGATTGATCCGCAGGCCCAACGGGCGGCGGAGAAGGCGGTTGCGAAATACCTGGACGGGCAGGACCCCGACATGCGTGCCGCCGTGGTTTCCATCGACCCGCACAACGGGGCGGTGCGTGCGTACTACGGTGGCGACAATGCCAATGGCTTTGACTTCGCTCAAGCGGGATTGCAGACTGGATCGTCGTTTAAGGTGTTTGCTCTGGTGGCCGCCCTTGAGCAGGGGATCGGCCTGGGCTACCAGGTAGACAGCTCTCCGTTGACGGTCGACGGCATCAAGATCACCAACGTCGAGGGCGAGGGTTGCGGGACGTGCAACATCGCCGAGGCGCTCAAAATGTCGCTGAACACCTCCTACTACCGGCTGATGCTCAAGCTCAACGGCGGCCCACAGGCTGTGGCCGATGCCGCGCACCAAGCCGGCATTGCCTCCAGCTTCCCGGGCGTTGCGCACACGCTGTCCGAAGATGGCAAGGGTGGACCGCCCAACAACGGGATCGTGTTGGGCCAGTACCAAACCCGGGTGATCGACATGGCATCGGCGTATGCCACGTTGGCCGCGTCCGGTATCTACCACCCGCCGCATTTCGTACAGAAGGTGGTCAGTGCCAACGGCCAGGTCCTCTTCGACGCCAGCACCGCGGACAACACCGGCGATCAGCGCATCCCCAAGGCGGTAGCCGACAACGTGACTGCGGCGATGGAGCCGATCGCAGGTTATTCGCGTGGCCACAACCTAGCGGGTGGGCGGGATTCGGCGGCCAAGACCGGCACTACGCAATTTGGTGACACCACCGCGAACAAAGACGCCTGGATGGTCGGGTACACGCCGTCGTTGTCTACGGCTGTGTGGGTGGGCACCGTCAAGGGTGACGAGCCACTGGTAACCGCTTCGGGTGCAGCGATTTACGGCTCGGGCCTGCCGTCGGACATCTGGAAGGCAACCATGGACGGCGCCTTGAAGGGCACGTCGAACGAGACTTTCCCCAAACCGACCGAGGTCGGTGGTTATGCCGGTGTGCCGCCGCCGCCGCCGCCGCCGGAGGTACCACCTTCGGAGACCGTCATCCAGCCCACGGTCGAAATTGCGCCGGGGATTACCATCCCGATCGGTCCCCCGACCACCATTACCCTGGCGCCACCGCCCCCGGCCCCGCCCGCTGCGACTCCCACGCCGCCGCCGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3004960","ARO_id":"43146","ARO_name":"Mycobacterium tuberculosis ponA1 mutations conferring resistance to rifabutin","CARD_short_name":"Mtub_ponA1_RFB","ARO_description":"Mutations in ponA1 that contribute to or confer resistance to rifabutin antibiotic.","ARO_category":{"43145":{"category_aro_accession":"3004959","category_aro_cvterm_id":"43145","category_aro_name":"rifamycin resistant ponA1","category_aro_description":"Mutations in the ponA1 gene that can contribute to or confer resistance to rifamycin-class antibiotics.","category_aro_class_name":"AMR Gene Family"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36669":{"category_aro_accession":"3000530","category_aro_cvterm_id":"36669","category_aro_name":"rifabutin","category_aro_description":"Rifabutin is a semisynthetic rifamycin used in tuberculosis therapy. It inhibits DNA-dependent RNA synthesis.","category_aro_class_name":"Antibiotic"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3564":{"model_id":"3564","model_name":"BPU-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"5759":{"protein_sequence":{"accession":"ABV63006.2","sequence":"MKKKYIKRLFSCIMLMAFCISQPSSTEARSIAWSVDEFFKNREGTFVIQEVKEKSPWVYNKKRAKERFAPQSTFKVANALIGLQTGAVRDEYDIKYWDGVKREIDNWNRDHTLGSGMRDSVVWYYQAMARDIGEERMNHWVKAIHYGNKDISGGIDQFWLSSTLRISPIEQVRFLKQLYEETLPFDLKNMRTVKRMMVQEEEKHATLYGKTGSGSDIGWYVGFIKHEHKTYILATNIKGTGIEAKDITYRILKKYHLMEASV"},"dna_sequence":{"accession":"CP000813.4","fmin":"2349398","fmax":"2350187","strand":"-","sequence":"TTGAAGAAAAAGTATATAAAAAGGCTGTTTTCTTGCATCATGCTGATGGCATTTTGTATCAGCCAGCCATCATCAACTGAAGCAAGATCAATAGCGTGGTCTGTAGATGAATTCTTTAAAAATCGGGAAGGCACGTTTGTGATTCAAGAAGTAAAAGAAAAGTCCCCATGGGTGTATAACAAAAAAAGAGCGAAAGAGCGCTTTGCACCTCAATCGACATTTAAGGTAGCAAATGCCTTAATCGGACTCCAAACAGGCGCAGTGAGAGATGAATACGACATCAAATATTGGGATGGCGTAAAAAGAGAGATTGACAATTGGAATAGAGATCATACATTAGGATCTGGCATGAGAGATTCAGTCGTCTGGTACTATCAAGCCATGGCACGTGACATTGGAGAAGAACGCATGAATCATTGGGTGAAAGCTATTCATTATGGGAACAAAGACATATCTGGCGGAATCGATCAATTTTGGTTAAGCAGTACCCTACGAATTTCTCCCATCGAACAAGTTCGTTTTCTCAAACAGCTATATGAAGAGACTCTTCCATTTGACCTAAAGAACATGAGAACAGTCAAACGAATGATGGTACAAGAAGAAGAGAAACACGCCACCCTATACGGAAAAACAGGCTCCGGATCAGACATCGGCTGGTACGTAGGTTTTATCAAACATGAACACAAAACCTACATCCTCGCCACAAATATCAAAGGCACCGGCATAGAAGCAAAAGACATCACCTATCGCATTTTGAAAAAATATCATTTGATGGAAGCATCCGTTTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42872","NCBI_taxonomy_name":"Bacillus pumilus SAFR-032","NCBI_taxonomy_id":"315750"}}}},"ARO_accession":"3004759","ARO_id":"42871","ARO_name":"BPU-1","CARD_short_name":"BPU-1","ARO_description":"BPU-1 is a class D beta-lactamase found in Bacillus pumilus.","ARO_category":{"42870":{"category_aro_accession":"3004758","category_aro_cvterm_id":"42870","category_aro_name":"BPU Beta-lactamase","category_aro_description":"BPU is a class D beta lactamase gene family.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3570":{"model_id":"3570","model_name":"CIA-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"5766":{"protein_sequence":{"accession":"BAL40892.1","sequence":"MKKITFLLLMVSAFATAQKSVLDEKISAVIKDKKATVGVSVLGFENAFKYSKNGDKKLPLLSVFKFHLACAVLDMADKGKFSTDQKFLIKKSDLLENTWSPLREKFPEGNIELSLGEIITYTVAQSDNNTCDFLLRLIGGPQVVQHFMDSKGAKDLQIKYNEDDMHRDWKNQYGNESSTNATVSLLKKFYDGKLLTKKSTDFLMQIMLGTTTGTNKIVEQLPKSTPVAHKTGSSGKPDNILTVAENDMGIITLPNGKHYAIAVFVSNSTETEKVNTRMVSDISKIVWDNFNK"},"dna_sequence":{"accession":"AB639753.1","fmin":"0","fmax":"879","strand":"+","sequence":"ATGAAAAAAATAACATTTCTTTTACTGATGGTTTCTGCCTTTGCTACTGCACAGAAATCCGTACTTGACGAAAAAATCAGTGCTGTTATAAAAGATAAAAAAGCGACCGTAGGAGTTTCTGTTTTGGGTTTTGAGAATGCTTTCAAGTACAGTAAAAACGGAGATAAGAAACTGCCGTTACTCAGTGTTTTTAAATTTCACCTGGCCTGTGCTGTATTGGATATGGCAGATAAAGGTAAATTTTCAACAGATCAGAAGTTTTTAATAAAAAAATCAGATCTATTGGAAAATACATGGTCTCCGCTACGCGAAAAATTTCCGGAAGGAAATATTGAACTTTCTTTAGGAGAAATTATCACGTACACAGTTGCTCAAAGTGATAACAATACCTGTGATTTTCTTTTAAGATTGATAGGCGGTCCTCAGGTTGTTCAGCACTTCATGGATTCTAAAGGAGCAAAAGACCTTCAGATCAAATATAATGAGGACGACATGCACAGGGACTGGAAAAACCAATATGGGAACGAAAGCAGCACCAATGCGACTGTCTCACTATTGAAAAAATTCTATGATGGTAAGCTTCTTACAAAAAAATCGACGGATTTCCTGATGCAGATTATGTTGGGAACTACAACAGGAACCAATAAAATCGTTGAACAGTTACCCAAAAGTACGCCTGTTGCTCATAAAACGGGTTCTTCCGGAAAGCCGGACAATATACTTACTGTTGCAGAAAATGATATGGGGATTATTACCCTTCCTAACGGAAAGCATTATGCAATCGCTGTATTTGTAAGCAATTCAACGGAAACAGAAAAGGTAAATACAAGGATGGTTTCTGATATTTCAAAGATCGTTTGGGATAATTTTAATAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42883","NCBI_taxonomy_name":"Chryseobacterium indologenes NBRC 14944","NCBI_taxonomy_id":"1218103"}}}},"ARO_accession":"3004768","ARO_id":"42882","ARO_name":"CIA-1","CARD_short_name":"CIA-1","ARO_description":"CIA-1 is a class A beta-lactamase gene found in Chryseobacterium indologenes.","ARO_category":{"42881":{"category_aro_accession":"3004767","category_aro_cvterm_id":"42881","category_aro_name":"CIA beta-lactamase","category_aro_description":"CIA is a class A beta-lactamase gene family found in Chryseobacterium indologenes.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3604":{"model_id":"3604","model_name":"GOB-3","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"575"}},"model_sequences":{"sequence":{"5802":{"protein_sequence":{"accession":"AAF89147.1","sequence":"KEPENMPKEWNQTYEPFRIAGNLYYVGTYDLASYLIVTDKGNILINTGTAESLPIIKANIQKLGFNYKDIKILLLTQAHYDHTGALQDLKTETGAKFYADKADADVLRTGGNSDYEMGKYGVTFKPVTPDKTLKDQDKITLGNTILTLLHHPGHTKGSCSFIFETKDEKRKYRVLIANMPSIIVDKKFSEVTAYLNIQSDYAYTFKAMKNLDFDLWVASHASQFDLHEKRKEGDPYNPQLFMDKQSYFQNLN"},"dna_sequence":{"accession":"AF189291.1","fmin":"0","fmax":"756","strand":"+","sequence":"AAAGAACCTGAAAATATGCCCAAAGAATGGAACCAGACTTATGAACCCTTCAGAATTGCAGGTAATTTATATTACGTAGGAACCTATGATTTGGCTTCTTACCTTATTGTGACAGACAAAGGCAATATTCTCATTAATACAGGAACGGCAGAATCGCTTCCAATAATAAAAGCAAATATCCAAAAGCTCGGGTTTAATTATAAAGACATTAAGATCTTGCTGCTTACTCAGGCTCACTACGACCATACAGGTGCATTACAAGATCTTAAAACAGAAACCGGTGCAAAATTCTATGCCGATAAAGCAGATGCTGATGTCCTGAGAACAGGGGGAAATTCCGATTATGAAATGGGAAAATATGGGGTGACATTTAAACCTGTTACTCCGGATAAAACATTGAAAGATCAGGATAAAATAACACTGGGAAATACAATCCTGACTTTGCTTCATCATCCGGGACATACAAAAGGTTCCTGTAGTTTTATTTTTGAAACAAAAGACGAGAAGAGAAAATATAGAGTTTTGATAGCTAATATGCCCTCCATTATTGTTGATAAGAAATTTTCTGAAGTTACCGCATATCTAAATATTCAGTCCGATTATGCATATACTTTCAAAGCAATGAAGAATCTAGATTTTGACCTTTGGGTGGCATCACATGCAAGTCAGTTCGATCTACATGAAAAACGTAAAGAAGGAGATCCGTACAATCCGCAATTGTTTATGGATAAGCAAAGCTATTTTCAAAACCTTAAT","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36960","NCBI_taxonomy_name":"Elizabethkingia meningoseptica","NCBI_taxonomy_id":"238"}}}},"ARO_accession":"3004810","ARO_id":"42930","ARO_name":"GOB-3","CARD_short_name":"GOB-3","ARO_description":"GOB-3 is a class B beta-lactamase gene found in Elizabethkingia meningoseptica.","ARO_category":{"41376":{"category_aro_accession":"3004212","category_aro_cvterm_id":"41376","category_aro_name":"GOB beta-lactamase","category_aro_description":"The GOB family of beta-lactamases have been discovered in the Elizabethkingia meningoseptica and are classified as subclass B3 beta-lactamase. They confer resistance to cephalosporins, penicillins, and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3734":{"model_id":"3734","model_name":"Mycobacterium tuberculosis nat mutations conferring resistance to isoniazid","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"},"48039":{"param_type":"synonymous substitution for alternative promoter","param_description":"A synonymous or silent substitution in the coding DNA sequence of one gene which influences the promoter region of another gene. These substitutions do not change the amino acid sequence of a protein but may still influence the phenotype, including decreased susceptibility to antimicrobial compounds.","param_type_id":"48039","param_value":{"9578":"A196A"}},"snp":{"ReSeqTB-High":{"9578":"A516T","18569":"A516T"}},"41339":{"param_type":"nucleotide substitution in promoter region","param_description":"A nucleotide sequence change where, compared to a reference sequence, one nucleotide is replaced by one other nucleotide in the promoter region of a gene. These substitutions are indicated as upstream of the reference sequence transcription initiation site. Format is given by [-][position][wildtype][>][mutation], e.g. -11t>c or -15g>Var where Var represents any possible substitution.","param_type_id":"41339","param_value":{"18569":"-183g>a"}}},"model_sequences":{"sequence":{"8777":{"protein_sequence":{"accession":"YP_177989.1","sequence":"MALDLTAYFDRINYRGATDPTLDVLQDLVTVHSRTIPFENLDPLLGVPVDDLSPQALADKLVLRRRGGYCFEHNGLMGYVLAELGYRVRRFAARVVWKLAPDAPLPPQTHTLLGVTFPGSGGCYLVDVGFGGQTPTSPLRLETGAVQPTTHEPYRLEDRVDGFVLQAMVRDTWQTLYEFTTQTRPQIDLKVASWYASTHPASKFVTGLTAAVITDDARWNLSGRDLAVHRAGGTEKIRLADAAAVVDTLSERFGINVADIGERGALETRIDELLARQPGADAP"},"dna_sequence":{"accession":"NC_000962.3","fmin":"4007330","fmax":"4008182","strand":"-","sequence":"ATGGCACTGGATCTGACCGCGTACTTCGATCGCATCAACTATCGCGGCGCTACCGATCCAACCCTGGATGTTCTGCAGGATCTGGTGACCGTGCACAGTCGAACGATTCCGTTCGAGAACCTCGACCCGCTGCTGGGGGTGCCGGTCGACGACCTCAGTCCACAGGCGCTGGCCGACAAGCTGGTACTTCGGCGCCGAGGCGGGTACTGCTTTGAGCACAACGGGCTGATGGGTTATGTGCTGGCCGAACTCGGCTATCGGGTGCGCCGATTCGCCGCCCGCGTCGTCTGGAAGCTCGCGCCGGACGCGCCCCTGCCGCCGCAGACGCACACCCTGCTGGGGGTCACGTTCCCCGGCTCGGGCGGATGCTATCTCGTCGACGTCGGATTCGGCGGCCAAACACCGACCTCACCGCTTCGCCTCGAAACCGGCGCCGTCCAGCCGACAACGCACGAACCTTATCGGCTCGAGGACCGCGTCGACGGCTTTGTCTTGCAGGCGATGGTCCGGGACACATGGCAGACACTGTACGAATTCACCACCCAGACCCGCCCGCAGATCGATCTGAAAGTGGCCAGCTGGTACGCCTCAACACACCCGGCATCGAAGTTCGTCACGGGACTGACCGCCGCGGTGATCACCGACGACGCCCGGTGGAACCTATCTGGCCGCGACCTTGCCGTTCACCGTGCCGGTGGTACCGAGAAGATCCGCCTTGCCGATGCGGCAGCGGTTGTCGACACCCTGAGCGAACGGTTCGGGATCAACGTGGCAGATATCGGCGAGCGCGGCGCGCTCGAGACGCGCATCGACGAGCTATTGGCTCGGCAGCCAGGAGCCGATGCGCCGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3004930","ARO_id":"43116","ARO_name":"Mycobacterium tuberculosis nat mutations conferring resistance to isoniazid","CARD_short_name":"Mtub_nat_INH","ARO_description":"Mutations that occur in nat which through overexpression of the enzyme can result in or contribute to antibiotic resistance to isoniazid.","ARO_category":{"43096":{"category_aro_accession":"3004910","category_aro_cvterm_id":"43096","category_aro_name":"isoniazid resistant nat","category_aro_description":"Arylamine N-acetyltransferase catalyzes the transfer of the acetyl group from acetyl coenzyme A to the free amino group of arylamines and hydrazines. Reports have shown that overexpression of this enzyme may be responsible for increased resistance to isoniazid.","category_aro_class_name":"AMR Gene Family"},"36659":{"category_aro_accession":"3000520","category_aro_cvterm_id":"36659","category_aro_name":"isoniazid","category_aro_description":"Isoniazid is an organic compound that is the first-line anti tuberculosis medication in prevention and treatment. As a prodrug, it is activated by mycobacterial catalase-peroxidases such as M. tuberculosis KatG. Isoniazid inhibits mycolic acid synthesis, which prevents cell wall synthesis in mycobacteria.","category_aro_class_name":"Antibiotic"},"45734":{"category_aro_accession":"3007152","category_aro_cvterm_id":"45734","category_aro_name":"isoniazid-like antibiotic","category_aro_description":"A group of antibiotics containing isoniazid and its derivatives.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3418":{"model_id":"3418","model_name":"OXA-154","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"5613":{"protein_sequence":{"accession":"SNU87672.1","sequence":"MKRILSHWCRAAVVLRLASAVVAHGLLPSPAHALELSRASAAAAPSVAAPVHVTERADWGKFFAAENVKGTVVVLDGKTQTYQAYDSARAERRMSPASTYKIFNSLLALESGALDNERETIPWDGKPRRIKAWNAELNLRDAFRVSCYPCYQVVSHKIPRAYAQAKLDAVGYGNRTIGRVNDTYWVDDSLQISAREQVDFLQRLARGTLPFSARSQDIVRQISIVEANADYVLHGKTGWFVDKKPDIGWWVGWLERDGNLTMIALNIDMNGDADGPKRARIVREVLKNLKLI"},"dna_sequence":{"accession":"LT906435.1","fmin":"4449571","fmax":"4450450","strand":"-","sequence":"ATGAAACGAATTCTCTCTCACTGGTGTCGCGCGGCTGTCGTGCTGCGTCTGGCGTCGGCGGTCGTCGCGCATGGTCTGCTGCCCTCGCCAGCACACGCGCTGGAATTGTCGCGCGCGTCAGCCGCGGCAGCACCTTCCGTGGCAGCGCCCGTCCACGTGACCGAGCGTGCCGACTGGGGCAAGTTCTTTGCGGCGGAAAACGTGAAGGGCACGGTCGTCGTGCTCGACGGCAAGACACAGACGTATCAGGCGTACGACTCGGCGCGCGCCGAGCGGCGCATGTCCCCGGCGTCGACGTACAAGATTTTCAACAGTCTGCTGGCGCTGGAATCGGGTGCGCTGGACAACGAGCGCGAGACGATTCCGTGGGACGGCAAACCGCGCCGGATTAAGGCGTGGAATGCAGAATTGAATCTGCGCGACGCGTTTCGCGTGTCTTGCTACCCGTGCTATCAGGTCGTTTCGCACAAGATTCCGCGTGCGTATGCGCAGGCGAAGCTCGACGCCGTCGGGTACGGTAACCGGACCATCGGTCGGGTGAACGACACCTATTGGGTGGACGACAGTTTGCAGATCTCAGCGCGCGAGCAAGTCGACTTCCTGCAGCGTCTGGCGCGTGGCACGTTGCCGTTCTCCGCGCGTTCGCAGGACATCGTCCGGCAGATTTCCATCGTCGAAGCGAACGCCGACTATGTGCTGCACGGCAAGACCGGCTGGTTCGTCGACAAGAAGCCGGATATCGGCTGGTGGGTGGGCTGGCTGGAGCGTGACGGCAATCTGACGATGATCGCGCTGAACATCGACATGAACGGCGACGCCGACGGCCCGAAGCGCGCGCGTATCGTGCGTGAGGTGCTGAAGAACCTGAAGTTGATCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42786","NCBI_taxonomy_name":"Pandoraea sputorum","NCBI_taxonomy_id":"93222"}}}},"ARO_accession":"3001459","ARO_id":"37859","ARO_name":"OXA-154","CARD_short_name":"OXA-154","ARO_description":"OXA-154 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46520":{"category_aro_accession":"3007731","category_aro_cvterm_id":"46520","category_aro_name":"OXA-62-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-62.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3440":{"model_id":"3440","model_name":"OXA-273","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"5636":{"protein_sequence":{"accession":"ENW12288.1","sequence":"MTKKALFFAIGTMFLSACSFNTVEQHQIQSISTNKNSEKIKSLFDQAQTTGVLVIKHGRTEEVYGNDLKRASTEYVPASTFKMVNALIGLEHHKATPTEVFKWDGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMSKEVKRIGFGNADIGSKVDNFWLVGPLKITPQQEVQFAYKLANKTLPFSKNVQEQVQSMVFIEEKNGRKIYAKSGWGWDVDPEVGWFTGWVVQPQGEIIAFSLNLEMEKGIPSSIRKEITYKGLEQLGIL"},"dna_sequence":{"accession":"APQN01000012.1","fmin":"1170132","fmax":"1170954","strand":"+","sequence":"ATGACTAAAAAAGCTCTTTTCTTTGCCATTGGTACGATGTTTTTGTCTGCATGTTCTTTTAATACGGTAGAACAACATCAAATACAGTCAATTTCTACCAATAAAAACTCAGAGAAAATTAAATCGTTGTTTGATCAAGCACAAACTACAGGTGTTTTAGTTATAAAACATGGGCGAACAGAGGAAGTCTATGGCAATGATCTTAAAAGAGCATCAACCGAATATGTTCCCGCCTCTACCTTTAAAATGGTAAATGCTTTGATTGGACTTGAGCATCATAAAGCAACGCCAACTGAAGTGTTTAAATGGGATGGGCAAAAGCGTTTATTTCCCGATTGGGAAAAAGACATGACATTAGGCGATGCTATGAAAGCTTCTGCTATTCCAGTTTATCAGGAACTAGCTCGACGAATTGGCCTTGATCTTATGTCTAAAGAGGTAAAACGCATTGGTTTCGGTAATGCTGATATTGGTTCAAAAGTAGATAATTTTTGGCTTGTTGGCCCACTTAAAATTACACCTCAACAAGAAGTACAGTTTGCTTATAAATTAGCCAACAAAACTCTTCCCTTTAGCAAAAATGTACAAGAACAAGTTCAATCTATGGTGTTCATTGAAGAAAAAAATGGACGAAAAATTTATGCCAAAAGTGGTTGGGGATGGGATGTTGACCCAGAAGTTGGTTGGTTTACAGGCTGGGTAGTTCAACCTCAGGGAGAAATTATAGCTTTCTCACTTAATCTAGAAATGGAAAAAGGCATACCTAGCTCTATTCGAAAAGAAATTACTTATAAGGGATTGGAACAACTCGGTATTTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42803","NCBI_taxonomy_name":"Acinetobacter pittii ANC 3678","NCBI_taxonomy_id":"1217673"}}}},"ARO_accession":"3001729","ARO_id":"38129","ARO_name":"OXA-273","CARD_short_name":"OXA-273","ARO_description":"OXA-273 is a beta-lactamase found in Acinetobacter spp.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46495":{"category_aro_accession":"3007706","category_aro_cvterm_id":"46495","category_aro_name":"OXA-213-like beta-lactamase","category_aro_description":"OXA-213-like enzymes have been identified to be intrinsic to A. calcoaceticus and have been subsequently detected in A. pittii. Phylogenetic analysis of OXA-213-like proteins identified two distinct subgroups within the OXA family. The first group was linked to A. pittii and the second group to A. calcoaceticus. The carbapenemase activity of these OXAs may be related to the species-dependent effect.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3498":{"model_id":"3498","model_name":"OXA-414","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"5693":{"protein_sequence":{"accession":"AJD07401.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEVHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"KJ584914.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGTACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGACGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCATTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001605","ARO_id":"38005","ARO_name":"OXA-414","CARD_short_name":"OXA-414","ARO_description":"OXA-414 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3528":{"model_id":"3528","model_name":"OXA-461","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"5723":{"protein_sequence":{"accession":"AKI29921.1","sequence":"MKKITLFLLFLNLVFGQDKILNNWFKEYNTSGTFVFYDGKTWASNDFLRAMETFSPASTFKIFNALIALDSGVIKTKKEIFYHYRGEKVFLSSWAQDMNLSSAIKYSNVLAFKEVARRIGIKTMQEYLNKLHYGNAKISKIDTFWLDNSLKISAKEQAILLFRLSQNSLPFSQEAMNSVKEMIYLKNMENLELFGKTGFNDEQKIAWIVGFVYLKDENKYKAFALNLDIDKFEDLYKREKILEKYLDELVKKS"},"dna_sequence":{"accession":"KR061509.1","fmin":"0","fmax":"762","strand":"+","sequence":"ATGAAAAAAATAACTTTATTTTTACTTTTCTTAAATTTAGTGTTTGGGCAAGATAAGATATTAAATAATTGGTTTAAAGAGTATAATACAAGCGGCACTTTTGTTTTTTATGATGGAAAAACTTGGGCGAGTAACGACTTTTTAAGGGCTATGGAGACTTTCTCTCCCGCTTCCACTTTTAAAATTTTTAATGCTCTAATTGCACTTGATAGTGGTGTGATAAAAACTAAAAAAGAAATTTTTTATCACTATAGAGGTGAAAAAGTATTTTTATCTTCTTGGGCGCAAGATATGAATTTAAGTTCAGCTATAAAATATTCTAATGTTCTTGCTTTTAAAGAAGTGGCAAGAAGAATTGGTATCAAAACTATGCAAGAATATTTAAACAAGCTTCATTATGGTAATGCTAAAATTTCCAAGATCGATACTTTTTGGCTTGACAACTCACTAAAAATAAGCGCTAAAGAACAAGCAATTTTGCTTTTTAGACTTTCACAAAATAGCTTACCTTTTTCTCAAGAAGCAATGAATAGTGTTAAGGAAATGATTTATTTAAAAAATATGGAAAATTTAGAGCTTTTTGGAAAAACAGGTTTTAATGATGAGCAAAAAATTGCTTGGATTGTAGGTTTTGTGTATTTAAAAGATGAAAATAAATATAAGGCTTTCGCGCTAAATTTAGATATTGATAAATTTGAAGATTTATATAAAAGAGAAAAAATTTTAGAAAAATATTTAGATGAACTTGTAAAAAAAAGTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36772","NCBI_taxonomy_name":"Campylobacter jejuni","NCBI_taxonomy_id":"197"}}}},"ARO_accession":"3003617","ARO_id":"40227","ARO_name":"OXA-461","CARD_short_name":"OXA-461","ARO_description":"OXA-461 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46519":{"category_aro_accession":"3007730","category_aro_cvterm_id":"46519","category_aro_name":"OXA-61-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-61.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3555":{"model_id":"3555","model_name":"AST-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"575"}},"model_sequences":{"sequence":{"5750":{"protein_sequence":{"accession":"AAG44836.1","sequence":"MTFSALPFRRADRRRLLAAALAACALTLTAACDSGTVTVPVTDSVTTSAVADPRFAELETTSGARLGVFAVDTGSGRTVAHRADERFPMASTFKGLACGALLREHPLSTGYFDQVIHYSAAELVEYSPVTETRVETGMTVRELCDAAITVSDNTAGNQLLKLLGGPEGFTASLRSLGDATSRLDRWETDLNTAIPGDERDTTTPAALAADYRALVVGDVLGAPERDQLKAWLVANTTGATRIRAGLPADWTVGDKTGSPAYGSALDVAVAWPPGRAPIVIAVLSTKSEQDAEPDNALLAEATRVVVDALG"},"dna_sequence":{"accession":"AF279904.1","fmin":"159","fmax":"1092","strand":"+","sequence":"GTGACTTTCTCCGCTCTCCCCTTCCGCCGGGCCGACCGCCGGCGCCTGCTCGCCGCCGCGCTCGCGGCCTGCGCACTGACCCTGACGGCGGCCTGTGATTCCGGCACCGTCACCGTTCCGGTGACGGACTCGGTGACCACCTCGGCGGTGGCCGATCCCCGGTTCGCCGAACTGGAAACCACTTCCGGCGCCCGGCTGGGCGTGTTCGCCGTCGACACCGGCTCCGGGCGCACCGTCGCCCACCGCGCCGACGAACGGTTCCCGATGGCGTCCACGTTCAAGGGCCTGGCGTGCGGGGCGCTGCTGCGCGAGCATCCCCTGTCGACGGGCTACTTCGATCAGGTGATCCACTACTCCGCCGCCGAGCTGGTCGAGTATTCGCCGGTGACCGAGACCCGGGTCGAGACCGGCATGACGGTCCGGGAACTGTGCGACGCCGCGATCACGGTTTCCGACAACACGGCGGGCAATCAGTTGCTGAAACTGCTCGGTGGACCGGAGGGATTCACCGCGTCCCTGCGTTCCCTCGGCGACGCCACGTCGCGGCTGGACCGCTGGGAGACCGACCTGAACACCGCGATTCCCGGGGATGAGCGCGATACCACCACCCCGGCCGCGCTCGCCGCCGACTACCGCGCGCTCGTCGTCGGCGATGTCCTCGGCGCACCCGAACGCGACCAGCTGAAGGCATGGCTCGTCGCCAACACCACCGGTGCCACCCGGATTCGCGCGGGTCTGCCCGCGGACTGGACCGTCGGCGACAAGACCGGCAGCCCGGCCTACGGTTCGGCCCTCGATGTCGCGGTGGCCTGGCCGCCCGGTCGCGCGCCGATCGTCATCGCGGTGCTGTCGACTAAGTCCGAGCAGGACGCCGAACCCGACAACGCCCTGCTCGCCGAGGCCACCCGCGTGGTGGTCGACGCGCTCGGATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42852","NCBI_taxonomy_name":"Nocardia asteroides","NCBI_taxonomy_id":"1824"}}}},"ARO_accession":"3004740","ARO_id":"42850","ARO_name":"AST-1","CARD_short_name":"AST-1","ARO_description":"AST-1 is a broad-spectrum beta-lactamase gene found in Nocardia asteroides.","ARO_category":{"42851":{"category_aro_accession":"3004741","category_aro_cvterm_id":"42851","category_aro_name":"AST Beta-lactamase","category_aro_description":"A family of beta-lactamase known for their broad spectrum resistance profile.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3571":{"model_id":"3571","model_name":"CIA-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"575"}},"model_sequences":{"sequence":{"5767":{"protein_sequence":{"accession":"BAL40893.1","sequence":"MKKITFLILMVSAFATAQKSVLDEKISAVIKDKKATVGVSVLGFENAFKYSKNGDEKLPLLSVFKFHLACAVLDMADKGKFSTDQKFLIKKSDLLENTWSPLREKFPEGNIELSLGEIITYTVAQSDNNTCDFLLRLIGGPQVVQHFMDSKGAKDLQIKYNEDDMHRDWKNQYGNESSTNATVSLLKKFYDGKLLTKKSTDFLMQIMLGTTTGTNKIVEQLPKGTPVAHKTGSSGKPDNILAVAENDMGIITLPNGKHYAIAVFVSNSTETEKVNTRMVSDISKIVWDNFNK"},"dna_sequence":{"accession":"AB674566.1","fmin":"0","fmax":"879","strand":"+","sequence":"ATGAAAAAAATAACATTTCTTATACTGATGGTTTCTGCCTTTGCTACTGCACAGAAATCCGTACTTGACGAAAAAATCAGTGCTGTTATAAAAGATAAAAAAGCGACGGTAGGAGTTTCTGTTTTGGGTTTTGAGAATGCTTTCAAGTACAGTAAAAACGGAGATGAGAAGCTGCCGTTACTCAGCGTTTTTAAATTTCACCTGGCCTGTGCTGTATTGGATATGGCAGATAAAGGTAAATTTTCAACAGATCAGAAGTTTTTAATAAAAAAATCAGATCTATTGGAAAATACATGGTCTCCGCTACGCGAAAAATTTCCGGAAGGAAATATTGAACTTTCTTTAGGAGAAATTATCACGTACACAGTTGCTCAAAGTGATAACAATACCTGTGATTTTCTTTTAAGATTGATAGGCGGTCCTCAGGTTGTTCAGCACTTCATGGATTCTAAAGGAGCAAAAGATCTTCAGATCAAATATAATGAGGACGACATGCACAGGGACTGGAAAAACCAATATGGGAACGAAAGCAGCACCAATGCGACTGTCTCACTATTGAAAAAATTCTATGATGGTAAGCTTCTTACAAAAAAATCGACGGATTTCCTGATGCAGATTATGTTGGGAACTACAACAGGAACCAATAAAATCGTTGAACAGTTACCCAAAGGTACGCCTGTTGCTCATAAAACGGGTTCTTCCGGAAAGCCGGACAATATACTTGCTGTTGCAGAAAATGATATGGGGATTATTACCCTTCCCAACGGAAAGCATTATGCAATCGCTGTATTTGTAAGCAATTCAACGGAAACAGAAAAGGTAAATACAAGGATGGTTTCTGATATTTCAAAGATCGTTTGGGATAATTTTAATAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36916","NCBI_taxonomy_name":"Chryseobacterium indologenes","NCBI_taxonomy_id":"253"}}}},"ARO_accession":"3004769","ARO_id":"42884","ARO_name":"CIA-2","CARD_short_name":"CIA-2","ARO_description":"CIA-2 is a class A beta-lactamase gene found in Chryseobacterium indologenes.","ARO_category":{"42881":{"category_aro_accession":"3004767","category_aro_cvterm_id":"42881","category_aro_name":"CIA beta-lactamase","category_aro_description":"CIA is a class A beta-lactamase gene family found in Chryseobacterium indologenes.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3605":{"model_id":"3605","model_name":"GOB-4","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"575"}},"model_sequences":{"sequence":{"5803":{"protein_sequence":{"accession":"AAF89149.1","sequence":"KEPENMPKEWNQTYEPFRIAGNLYYVGTYDLASYLIVTDKGNILINTGTAESLPIIKANIQKLGFNYKDIKILLLTQAHYDHTGALQDLKTETAAKFYADKADADVLRTGGNSDYEMGKYGVTFKPVTPDKTLKDQDKITLGNTILTLLHHPGHTKGSCSFIFETKDEKRKYRVLIANMPSVIVDKKFSEVTAYPNIQSDYAYTFKAMKNLDFDLWVASHASQFDLHEKRKEGDPYNPQLFMDKQSYFQNLN"},"dna_sequence":{"accession":"AF189293.1","fmin":"0","fmax":"756","strand":"+","sequence":"AAAGAACCTGAAAATATGCCCAAAGAATGGAACCAGACTTATGAACCCTTCAGAATTGCAGGTAATTTATATTACGTAGGAACCTATGATTTGGCTTCTTACCTTATTGTGACAGACAAAGGCAATATTCTCATTAATACAGGAACGGCAGAATCGCTTCCAATAATAAAAGCAAATATCCAAAAGCTCGGGTTTAATTATAAAGACATTAAGATCTTGCTGCTTACTCAGGCTCACTACGACCATACAGGTGCATTACAAGATCTTAAAACAGAAACCGCTGCAAAATTCTATGCCGATAAAGCAGATGCTGATGTCCTGAGAACAGGGGGAAATTCCGATTATGAAATGGGAAAATATGGGGTGACATTTAAACCTGTTACTCCGGATAAAACATTGAAAGATCAGGATAAAATAACGCTGGGAAATACAATCCTGACTTTGCTTCATCATCCGGGACATACAAAAGGTTCCTGTAGTTTTATTTTTGAAACAAAAGACGAGAAGAGAAAATATAGAGTTTTGATAGCTAATATGCCCTCCGTTATTGTTGATAAGAAATTTTCTGAAGTTACCGCATATCCAAATATTCAGTCCGATTACGCATATACTTTCAAAGCAATGAAGAATCTAGATTTTGACCTTTGGGTGGCATCACATGCAAGTCAGTTCGATCTCCATGAAAAACGTAAAGAAGGAGATCCGTACAATCCGCAATTGTTTATGGATAAGCAAAGCTATTTCCAAAACCTTAAT","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36960","NCBI_taxonomy_name":"Elizabethkingia meningoseptica","NCBI_taxonomy_id":"238"}}}},"ARO_accession":"3004811","ARO_id":"42931","ARO_name":"GOB-4","CARD_short_name":"GOB-4","ARO_description":"GOB-4 is a class B beta-lactamase gene found in Elizabethkingia meningoseptica.","ARO_category":{"41376":{"category_aro_accession":"3004212","category_aro_cvterm_id":"41376","category_aro_name":"GOB beta-lactamase","category_aro_description":"The GOB family of beta-lactamases have been discovered in the Elizabethkingia meningoseptica and are classified as subclass B3 beta-lactamase. They confer resistance to cephalosporins, penicillins, and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3617":{"model_id":"3617","model_name":"IMI-8","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"5815":{"protein_sequence":{"accession":"AIY69088.1","sequence":"MSINAKKSKAAVFLSYFLIPISFYSQADTNAMDEIKKLETGFGGRVGVYALDTGSGKSFSYRANERFPLCSSFKGFLAAAVLKGSQDNQLNINEIVNYNKRSLEPHSPITQKYKENGMSLGDMAAAALQYSDNGAANIILERYIGGPEGMTNFMRSIGDEDFRLDRWELDLNTAIPGDERDTSTPAAVGKSLKNLALGNILNDHEKETYQTWLKGNTTGAARIRASVPSDWVVGDKTGTCGAYGTANDYAVVWPKNRAPLIISVYTTKSEKEAKHDEKVIEEASRIAITHLK"},"dna_sequence":{"accession":"KP081315.1","fmin":"0","fmax":"879","strand":"+","sequence":"ATGTCAATTAATGCAAAGAAAAGTAAAGCAGCTGTCTTTTTAAGCTATTTTTTAATCCCTATATCATTTTATTCACAGGCTGATACAAATGCCATGGATGAGATTAAGAAACTGGAAACAGGTTTTGGTGGCAGGGTTGGCGTCTACGCTTTAGACACTGGCTCTGGTAAATCATTTTCATACAGAGCGAATGAACGATTTCCTCTTTGTAGTTCTTTTAAAGGTTTTTTAGCCGCTGCTGTATTAAAGGGCTCGCAGGATAATCAACTGAATATTAATGAGATTGTAAATTATAATAAAAGAAGTTTAGAACCCCACTCCCCTATTACGCAAAAATATAAAGAAAACGGAATGTCTCTAGGTGATATGGCTGCTGCCGCTTTACAATATAGCGACAATGGTGCTGCTAATATTATTCTTGAGCGTTATATCGGTGGTCCTGAAGGTATGACTAATTTCATGCGGTCTATTGGAGATGAAGACTTTAGACTCGATCGTTGGGAGTTAGATCTAAATACAGCTATTCCTGGCGATGAACGTGACACTTCAACACCCGCAGCTGTAGGTAAAAGTTTAAAAAACCTTGCTCTGGGCAATATACTTAACGATCATGAAAAGGAAACATATCAGACATGGTTAAAGGGTAATACAACCGGCGCAGCGCGTATTCGTGCTAGCGTACCAAGCGACTGGGTCGTTGGCGATAAAACCGGTACTTGTGGAGCATACGGTACGGCAAATGATTATGCGGTTGTCTGGCCAAAAAACAGGGCTCCTCTTATCATTTCTGTGTACACTACAAAAAGTGAAAAAGAAGCAAAGCATGACGAGAAGGTAATCGAAGAAGCTTCAAGAATTGCAATTACACACCTTAAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3003142","ARO_id":"39719","ARO_name":"IMI-8","CARD_short_name":"IMI-8","ARO_description":"IMI-8 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36027":{"category_aro_accession":"3000018","category_aro_cvterm_id":"36027","category_aro_name":"IMI beta-lactamase","category_aro_description":"IMI beta-lactamases are a group of TEM-1-like beta-lactamase that are known to hydrolyze imipenem. IMI beta-lactamases are inhibited by clavulanic acid and tazobactam.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3419":{"model_id":"3419","model_name":"OXA-155","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"5614":{"protein_sequence":{"accession":"ALA99189.1","sequence":"MKRILSRWRRAAVVLRLASAVVAHGLLPSPAHALELSRASAAAAPSVAAPVHVTERADWGKFFAAENVKGTVVVLDGKTQTYQAYDSARAERRMSPASTYKIFNSLLALESGALDNERETIPWDGKPRRIKAWNAELNLRDAFRVSCYPCYQVVSHKIPRAYAQAKLDAVGYGNRTIGRVNDTYWVDDSLQISAREQVDFLQRLARGTLPFSARSQDIVRQISIVEANADYVLHGKTGWFVEKKPDIGWWVGWLERDGNLTMIALNIDMNGDADGPKRARIVREVLKNLKLI"},"dna_sequence":{"accession":"KP771983.1","fmin":"169","fmax":"1048","strand":"+","sequence":"ATGAAACGAATTCTCTCTCGCTGGCGTCGCGCGGCTGTCGTGCTGCGTCTGGCGTCGGCGGTCGTCGCGCATGGTCTGCTGCCCTCGCCAGCACACGCGCTGGAATTGTCGCGGGCGTCAGCCGCGGCGGCACCTTCCGTGGCAGCGCCCGTCCACGTGACCGAGCGTGCCGACTGGGGCAAGTTCTTTGCGGCGGAAAACGTGAAGGGCACGGTCGTCGTGCTCGACGGCAAGACACAGACGTATCAGGCGTACGACTCGGCGCGCGCCGAGCGGCGCATGTCCCCGGCGTCGACGTACAAGATATTCAACAGTCTGCTGGCGCTGGAATCGGGTGCGCTGGACAACGAGCGCGAGACGATTCCGTGGGACGGCAAACCGCGCCGGATTAAGGCGTGGAATGCAGAATTGAATCTGCGTGACGCGTTTCGTGTGTCTTGCTACCCGTGCTATCAGGTCGTTTCGCACAAGATTCCGCGTGCGTATGCGCAGGCGAAGCTCGACGCCGTCGGGTACGGTAACCGGACCATCGGTCGGGTGAACGACACCTATTGGGTGGACGACAGTTTGCAGATCTCGGCGCGCGAGCAAGTCGACTTCCTGCAGCGTCTGGCGCGTGGCACGTTGCCGTTCTCCGCGCGTTCGCAGGACATCGTCCGGCAGATTTCCATCGTCGAAGCGAACGCCGACTATGTGCTGCACGGCAAGACCGGCTGGTTCGTCGAGAAGAAGCCGGATATCGGCTGGTGGGTGGGCTGGCTGGAGCGTGACGGCAATCTGACGATGATCGCGCTGAACATCGACATGAACGGCGACGCCGACGGCCCGAAGCGTGCGCGTATCGTGCGTGAGGTGCTGAAGAACCTGAAGTTGATCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42786","NCBI_taxonomy_name":"Pandoraea sputorum","NCBI_taxonomy_id":"93222"}}}},"ARO_accession":"3001460","ARO_id":"37860","ARO_name":"OXA-155","CARD_short_name":"OXA-155","ARO_description":"OXA-155 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46520":{"category_aro_accession":"3007731","category_aro_cvterm_id":"46520","category_aro_name":"OXA-62-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-62.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3441":{"model_id":"3441","model_name":"OXA-275","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"5637":{"protein_sequence":{"accession":"ENV18923.1","sequence":"MSNYRFKSKIKSSVLIILSSVAFSGCVSNANLHDPASSQRTSEIPLLFNYAQTQAVFVTYDGTQFKRYGNDLNRAKTAYIPASTFKMLNALIGLQHAKATNTEVFKWNGEKRSFPAWEKDMTLAQAMQASAVPVYQELARRIGLDLMSKEVKRVGFGNTQIGQQVDNFWLVGPLKITPEQEAKFAFQLANKTLPFDDAVQQQVKDMLYVERRGDSKLYAKSGWGMDVEPQVGWYTGWVEQPNGQITAFALNMHMQTGDDPAERKQLTLSILDKLGLFFYLR"},"dna_sequence":{"accession":"APPJ01000001.1","fmin":"17227","fmax":"18073","strand":"+","sequence":"ATGAGTAATTACCGATTTAAATCTAAAATAAAAAGCAGTGTATTGATCATTCTGAGTAGTGTGGCATTTTCAGGTTGTGTTTCTAATGCCAATTTGCATGATCCAGCGTCATCACAAAGAACAAGTGAAATCCCGTTGTTGTTTAATTATGCGCAAACTCAAGCCGTCTTTGTGACTTATGATGGAACTCAATTTAAACGTTATGGGAATGATTTAAATAGAGCCAAGACTGCCTATATTCCAGCCTCTACTTTTAAAATGTTGAATGCCTTAATTGGTTTGCAACATGCGAAAGCGACGAATACAGAAGTATTTAAGTGGAATGGAGAAAAAAGATCTTTTCCTGCATGGGAAAAAGATATGACCTTGGCACAAGCAATGCAGGCTTCAGCCGTACCTGTATATCAGGAGTTGGCACGACGTATTGGCTTGGATTTGATGAGTAAAGAAGTCAAGCGTGTTGGTTTTGGCAATACACAAATTGGTCAACAGGTAGATAATTTCTGGCTAGTCGGCCCATTGAAAATTACCCCAGAGCAAGAAGCTAAATTTGCTTTTCAATTGGCAAACAAAACATTGCCTTTTGATGATGCTGTACAGCAACAAGTTAAAGATATGCTCTATGTCGAAAGACGGGGTGATTCCAAGCTTTATGCCAAAAGTGGATGGGGAATGGATGTGGAGCCACAAGTGGGTTGGTATACGGGATGGGTGGAACAGCCGAATGGTCAGATCACCGCTTTTGCTTTAAACATGCACATGCAGACAGGGGATGATCCTGCTGAACGCAAGCAACTGACATTAAGTATCTTGGATAAATTAGGCTTATTCTTTTATTTGAGATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42804","NCBI_taxonomy_name":"Acinetobacter guillouiae NIPH 991","NCBI_taxonomy_id":"1217656"}}}},"ARO_accession":"3001731","ARO_id":"38131","ARO_name":"OXA-275","CARD_short_name":"OXA-275","ARO_description":"OXA-275 is a beta-lactamase found in Acinetobacter spp.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46502":{"category_aro_accession":"3007713","category_aro_cvterm_id":"46502","category_aro_name":"OXA-274-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-274.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3470":{"model_id":"3470","model_name":"OXA-308","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"5664":{"protein_sequence":{"accession":"ENV32314.1","sequence":"MNKKLNLALLCFLSILCAACQSNQQLSANSHTENHNTRAAEISLLFDEMHTQAVFVTYDGQHFQSYGNALQRADTAYVPASTFKMLNALIGLQNHKATNTEVFKWDGQKRAMSIWEKDMTLSDAMKVSAVPVYQELARRIGLDLMQKEVTRVRYGNTDIGTVVDRFWLDGPLKITPKQEAQFAYQLATQQLPFDQNVQSQVKDMLYVESRGQSKLFAKSGLSMKNGQPDIGWYTGWVEQADGKIVAFSINMQMVQGLDVNSRQQATLDILDKLGIFFYL"},"dna_sequence":{"accession":"APPN01000080.1","fmin":"348498","fmax":"349338","strand":"-","sequence":"ATGAATAAAAAATTGAATTTGGCACTTTTGTGTTTTTTGAGTATTTTGTGTGCAGCTTGTCAGTCTAATCAACAACTGTCGGCTAATTCACATACTGAAAACCACAATACCCGTGCAGCAGAAATCTCGCTTCTTTTCGATGAGATGCATACTCAAGCAGTATTTGTGACCTATGACGGTCAGCATTTTCAGAGCTACGGTAATGCTTTACAAAGAGCAGATACTGCCTACGTTCCTGCTTCGACATTTAAAATGTTAAATGCATTGATTGGACTGCAAAATCATAAAGCAACCAACACCGAAGTCTTTAAATGGGATGGTCAAAAAAGGGCAATGTCGATCTGGGAAAAAGACATGACCTTATCCGATGCCATGAAAGTTTCAGCTGTACCGGTTTATCAAGAATTGGCGCGTCGTATTGGCTTGGATTTGATGCAAAAGGAAGTAACGCGGGTTAGATATGGCAATACGGATATCGGCACTGTTGTTGATCGTTTTTGGCTAGATGGACCACTGAAGATCACACCTAAACAAGAAGCCCAATTTGCATATCAATTGGCAACACAACAATTGCCATTTGATCAAAATGTGCAAAGCCAAGTTAAAGATATGTTGTATGTGGAAAGTCGAGGGCAATCCAAGCTTTTTGCCAAGTCTGGTTTGAGCATGAAAAATGGGCAACCTGACATCGGTTGGTATACGGGTTGGGTTGAACAAGCCGATGGCAAAATTGTGGCTTTTTCCATCAATATGCAAATGGTACAGGGGCTAGATGTCAATAGCCGTCAGCAGGCAACACTGGATATCTTAGATAAATTGGGCATATTTTTTTATTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41193","NCBI_taxonomy_name":"Acinetobacter gerneri DSM 14967 = CIP 107464 = MTCC 9824","NCBI_taxonomy_id":"1120926"}}}},"ARO_accession":"3001763","ARO_id":"38163","ARO_name":"OXA-308","CARD_short_name":"OXA-308","ARO_description":"OXA-308 is a beta-lactamase found in Acinetobacter spp.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3499":{"model_id":"3499","model_name":"OXA-416","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"5694":{"protein_sequence":{"accession":"AKH90740.1","sequence":"MRVLALSAVFLVASIIGMPAVAKEWQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGQTRDIATWNRDHNLITAMKYSVVPVYQEFARQIGEARMSKMLHAFDYGNEDISGNLDTFWLDGGIRISATEQISFLRKLYHNKLHVSERSQRIVKQAMLTEANADYIIRAKTGYSTRIEPKIGWWVGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP"},"dna_sequence":{"accession":"KP264119.1","fmin":"0","fmax":"798","strand":"+","sequence":"ATGCGTGTATTAGCCTTATCGGCTGTGTTTTTGGTGGCATCGATTATCGGAATGCCTGCGGTAGCAAAGGAATGGCAAGAAAACAAAAGTTGGAATGCTCACTTTACTGAACATAAATCACAGGGCGTAGTTGTGCTCTGGAATGAGAATAAGCAGCAAGGATTTACCAATAATCTTAAACGGGCGAACCAAGCATTTTTACCCGCATCTACCTTTAAAATTCCCAATAGCTTGATCGCCCTCGATTTGGGCGTGGTTAAGGATGAACACCAAGTCTTTAAGTGGGATGGACAGACGCGCGATATCGCCACTTGGAATCGCGATCATAATTTAATCACCGCGATGAAATATTCGGTTGTGCCTGTTTATCAAGAATTTGCCCGCCAAATTGGCGAGGCACGTATGAGCAAGATGCTGCACGCCTTCGATTATGGCAATGAGGACATTTCGGGCAATTTAGATACTTTTTGGCTTGATGGTGGCATTCGAATTTCGGCCACTGAGCAAATCAGCTTTTTAAGAAAGCTGTATCACAATAAGTTACACGTATCGGAGCGCAGCCAGCGTATCGTTAAACAAGCCATGCTTACTGAGGCGAATGCTGACTATATTATTCGGGCTAAAACGGGATACTCGACTAGAATCGAACCTAAGATTGGCTGGTGGGTCGGTTGGGTTGAGCTTGATGATAATGTGTGGTTTTTTGCGATGAATATGGATATGCCCACATCGGATGGTTTAGGGCTGCGCCAAGCCATCACAAAAGAAGTGCTCAAACAGGAGAAAATTATTCCCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39674","NCBI_taxonomy_name":"Shewanella xiamenensis","NCBI_taxonomy_id":"332186"}}}},"ARO_accession":"3001607","ARO_id":"38007","ARO_name":"OXA-416","CARD_short_name":"OXA-416","ARO_description":"OXA-416 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46510":{"category_aro_accession":"3007721","category_aro_cvterm_id":"46510","category_aro_name":"OXA-48-like beta-lactamase","category_aro_description":"OXA-48-type beta-lactamases are now routinely encountered in bacterial infections caused by carbapenam-resistant Enterobacterales. OXA-48-like proteins confer resistance to penicillin (which is efficiently hydrolyzed) and carbapenam antibiotics (which is more slowly broken down). The spectrum of activity of these variants varies, with some hydrolyzing expanded-spectrum oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3529":{"model_id":"3529","model_name":"OXA-464","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"480"}},"model_sequences":{"sequence":{"5724":{"protein_sequence":{"accession":"ANW35663.1","sequence":"MNKKIKLIFILIFSINLFANDVELENLFKKYQVEGTLVLESLNTKKVDIYNEKRANTSFSPASTFKIPNTLIALNEGVVNKDSIIVWDKKVREFDAWNKDQTLQSAFKSSCVWCYKEFASKIGVEKYKKYLKELNYGNKTIGKDVTDFWLDESLRITAFEEIRFLKQLQANNLAFKQEDINLLKELMIDEKSENYVVRAKTGWEGKYGWYVGYVETKNDVWFFALNIDTKTKEDLAKRKALTLEALKTKGIID"},"dna_sequence":{"accession":"KU721146.1","fmin":"0","fmax":"762","strand":"+","sequence":"ATGAATAAAAAAATAAAACTAATTTTTATTTTAATTTTTTCAATAAATTTATTTGCAAATGATGTGGAACTTGAAAATTTATTTAAAAAATACCAAGTTGAAGGAACTTTAGTATTAGAGTCTTTAAATACAAAAAAAGTAGATATTTATAATGAAAAGCGAGCAAATACATCGTTTTCTCCTGCTTCAACATTTAAAATACCAAATACTTTGATAGCTTTAAATGAAGGTGTTGTAAACAAAGATTCTATAATAGTTTGGGATAAAAAAGTAAGAGAATTTGATGCTTGGAATAAAGACCAAACTTTACAATCAGCTTTCAAAAGTTCATGCGTTTGGTGTTATAAAGAGTTCGCTTCAAAAATTGGAGTTGAAAAATATAAAAAGTATCTAAAAGAGCTTAATTATGGAAATAAAACAATAGGCAAAGATGTAACTGATTTTTGGTTGGATGAGAGTTTGAGAATTACAGCTTTTGAAGAGATAAGATTTTTAAAACAATTACAAGCAAACAATTTAGCTTTTAAACAAGAAGATATAAATCTTTTAAAAGAGTTGATGATTGATGAAAAAAGCGAAAATTATGTAGTTAGAGCAAAAACAGGTTGGGAAGGAAAATATGGTTGGTATGTTGGTTATGTTGAAACAAAAAATGATGTTTGGTTTTTTGCTTTAAATATCGACACAAAAACAAAAGAAGATTTAGCAAAAAGAAAAGCTTTAACTTTAGAAGCTTTAAAAACAAAAGGGATTATAGATTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42842","NCBI_taxonomy_name":"Aliarcobacter butzleri","NCBI_taxonomy_id":"28197"}}}},"ARO_accession":"3003620","ARO_id":"40230","ARO_name":"OXA-464","CARD_short_name":"OXA-464","ARO_description":"OXA-464 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3572":{"model_id":"3572","model_name":"CIA-3","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"540"}},"model_sequences":{"sequence":{"5768":{"protein_sequence":{"accession":"BAL40894.1","sequence":"MKKITFLLLMVSAFATAQKSVLDEKISAVIKDKKATVGVSVLGFENAFKYSKNGDEKLPLLSVFKFHLACAVLDMADKGKFSTYQKFLIKKSDLLENTWSPLREKFPEGNIELSLGEIITYTVAQSDNNTCDFLLRLIGGPQVVQHFMDSKGAKDLQIKYNEDDMHRDWKNQYGNESSTNATVSLLKKFYDGKLLTKKSTDFLMQIMLATTTGTNKIVEQLPKGTPVAHKTGSSGKPDNILTVAENDMGIITLPNGKHYAIAVFVSNSTETEKVNTRMVSDISKIVWDNFNK"},"dna_sequence":{"accession":"AB674567.1","fmin":"0","fmax":"879","strand":"+","sequence":"ATGAAAAAAATAACATTTCTTTTACTGATGGTTTCTGCCTTTGCTACTGCACAGAAATCCGTACTTGACGAAAAAATCAGTGCTGTTATAAAAGATAAAAAAGCGACGGTAGGAGTTTCTGTTTTGGGTTTTGAGAATGCTTTCAAGTACAGTAAAAACGGAGATGAGAAGCTGCCGTTACTCAGCGTTTTTAAATTTCACCTGGCCTGTGCTGTATTGGATATGGCAGATAAAGGTAAATTTTCAACATATCAGAAGTTTTTAATAAAAAAATCAGATCTATTGGAAAATACATGGTCTCCGCTACGCGAAAAATTTCCGGAAGGAAATATTGAACTTTCTTTAGGAGAAATTATCACGTACACAGTTGCTCAAAGTGATAACAATACCTGTGATTTTCTTTTAAGATTGATAGGCGGTCCTCAGGTTGTTCAGCACTTCATGGATTCTAAAGGAGCAAAAGATCTTCAGATCAAATATAATGAGGACGACATGCACCGGGACTGGAAAAACCAATATGGGAACGAAAGCAGCACCAATGCGACTGTCTCACTATTGAAAAAATTCTATGATGGTAAGCTTCTTACAAAAAAATCGACGGATTTCCTGATGCAGATTATGTTGGCAACTACAACAGGAACCAATAAAATCGTTGAACAGTTACCCAAAGGTACGCCTGTTGCTCATAAAACGGGTTCTTCCGGAAAGCCGGACAATATACTTACTGTTGCAGAAAATGATATGGGGATTATTACCCTTCCCAACGGAAAGCATTATGCAATCGCTGTATTTGTAAGCAATTCAACGGAAACAGAAAAGGTAAATACAAGGATGGTTTCTGATATTTCAAAGATCGTTTGGGATAATTTTAATAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36916","NCBI_taxonomy_name":"Chryseobacterium indologenes","NCBI_taxonomy_id":"253"}}}},"ARO_accession":"3004770","ARO_id":"42885","ARO_name":"CIA-3","CARD_short_name":"CIA-3","ARO_description":"CIA-3 is a class A beta-lactamase gene found in Chryseobacterium indologenes.","ARO_category":{"42881":{"category_aro_accession":"3004767","category_aro_cvterm_id":"42881","category_aro_name":"CIA beta-lactamase","category_aro_description":"CIA is a class A beta-lactamase gene family found in Chryseobacterium indologenes.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3606":{"model_id":"3606","model_name":"GOB-5","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"5804":{"protein_sequence":{"accession":"AAF89146.1","sequence":"KEPENMPKEWNQTYEPFRIAGNLYYVGTYDLASYLIVTDKGNILINTGTAESLPIIKANIQKLGFNYKDIKILLLTQAHYDHTGALQDLKTETAAKFYADKEDADVLRTGGKSDYEMGKYGVTFKPVTPDKTLKDQDKIKLGNTILTLLHHPGHTKGSCSFIFETKDEKRKYRVLIANMPSVIVDKKFSEVTAYPNIQSDYAYTFKAMKNLDFDLWVASHASQFDLHEKRKEGDPYNPQLFMDKQSYFQNLN"},"dna_sequence":{"accession":"AF189290.1","fmin":"0","fmax":"756","strand":"+","sequence":"AAAGAACCTGAAAATATGCCCAAAGAATGGAACCAGACTTATGAACCCTTCAGAATTGCAGGTAATTTATATTACGTAGGAACCTATGATTTGGCTTCTTACCTTATTGTGACAGACAAAGGCAATATTCTCATTAATACAGGAACGGCAGAATCGCTTCCAATAATAAAAGCAAATATCCAAAAGCTCGGGTTTAATTATAAAGACATTAAGATCTTGCTGCTTACTCAGGCTCACTACGACCATACAGGTGCATTACAAGATCTTAAAACAGAAACCGCTGCAAAATTCTATGCCGATAAAGAAGATGCTGATGTCCTGAGAACAGGGGGGAAGTCCGATTATGAAATGGGAAAATATGGTGTGACATTTAAACCTGTTACTCCGGATAAAACATTGAAAGATCAGGATAAAATAAAACTGGGAAATACAATCCTGACTTTGCTTCATCATCCCGGACATACAAAAGGTTCCTGTAGTTTTATTTTTGAAACAAAAGACGAGAAGAGAAAATATAGAGTTTTGATAGCTAATATGCCCTCCGTTATTGTTGATAAGAAATTTTCTGAAGTTACCGCATATCCAAATATTCAGTCCGATTATGCATATACTTTCAAAGCAATGAAGAATCTAGATTTTGACCTTTGGGTGGCATCACATGCAAGTCAGTTCGATCTGCATGAAAAACGTAAAGAAGGAGATCCGTACAATCCGCAATTGTTTATGGATAAGCAAAGCTATTTCCAAAACCTTAAT","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36960","NCBI_taxonomy_name":"Elizabethkingia meningoseptica","NCBI_taxonomy_id":"238"}}}},"ARO_accession":"3004812","ARO_id":"42932","ARO_name":"GOB-5","CARD_short_name":"GOB-5","ARO_description":"GOB-5 is a class B beta-lactamase gene found in Elizabethkingia meningoseptica.","ARO_category":{"41376":{"category_aro_accession":"3004212","category_aro_cvterm_id":"41376","category_aro_name":"GOB beta-lactamase","category_aro_description":"The GOB family of beta-lactamases have been discovered in the Elizabethkingia meningoseptica and are classified as subclass B3 beta-lactamase. They confer resistance to cephalosporins, penicillins, and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3420":{"model_id":"3420","model_name":"OXA-156","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"540"}},"model_sequences":{"sequence":{"5615":{"protein_sequence":{"accession":"SUA92210.1","sequence":"MKKTFSRWRRGALVLRILGALASPVVFATPGHAAEPVRPPSVHITERADWGKYFADEGVKGTVVVLDGRTQTYQAYDAARAERRLSPASTYKIFNSLLALESGAIDNEREVIPWDGKPRSMKAWNAALNLRDAFRVSCLPCYQILSHKIPRQYAQAKLNEVGYGNRTIGHAADTYWVDDSLQISAREQVDFLQRLAKGTLPFSARSQDIVRNISIVEANADYVLHGKTGWFTDKKPDIGWWVGWLERDGNLTMIALNIDIQSDADGPKRVRIVRSVLKDLKLI"},"dna_sequence":{"accession":"UGSJ01000001.1","fmin":"4174490","fmax":"4175342","strand":"+","sequence":"ATGAAAAAGACATTCTCCCGCTGGCGGCGCGGCGCGCTCGTGTTGCGCATCCTTGGCGCGCTGGCCTCGCCCGTGGTCTTCGCAACGCCGGGGCATGCCGCCGAACCCGTGCGTCCCCCTTCCGTACATATCACCGAGCGGGCCGATTGGGGGAAGTACTTTGCTGATGAAGGCGTCAAAGGCACCGTCGTCGTGCTCGACGGCCGCACGCAGACCTATCAGGCGTACGACGCCGCGCGCGCCGAGCGGCGCCTGTCGCCGGCATCAACCTACAAGATTTTCAACAGCTTGCTGGCGCTCGAATCGGGGGCGATCGACAACGAACGCGAAGTCATTCCCTGGGACGGCAAGCCGCGTAGCATGAAGGCGTGGAACGCGGCGCTCAACCTGCGGGACGCGTTCCGCGTGTCATGTCTGCCTTGCTATCAGATCCTCTCGCACAAGATCCCGCGTCAGTATGCGCAGGCCAAACTCAACGAGGTGGGCTATGGCAATCGCACGATCGGCCACGCCGCGGACACCTATTGGGTCGACGACAGCCTGCAGATTTCGGCGCGCGAACAGGTCGACTTCCTGCAGCGTTTGGCGAAGGGCACGCTGCCGTTCTCGGCGCGCTCGCAGGACATCGTGCGGAACATCTCGATCGTGGAAGCGAATGCCGACTACGTGCTGCACGGCAAGACGGGCTGGTTCACCGACAAGAAGCCCGACATCGGCTGGTGGGTGGGTTGGCTCGAGCGTGACGGCAACCTCACCATGATCGCCCTGAACATCGATATACAGTCGGATGCCGACGGGCCGAAGCGCGTGCGCATCGTCCGAAGCGTGCTCAAGGATCTGAAGTTGATCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42787","NCBI_taxonomy_name":"Pandoraea pulmonicola","NCBI_taxonomy_id":"93221"}}}},"ARO_accession":"3001461","ARO_id":"37861","ARO_name":"OXA-156","CARD_short_name":"OXA-156","ARO_description":"OXA-156 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46520":{"category_aro_accession":"3007731","category_aro_cvterm_id":"46520","category_aro_name":"OXA-62-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-62.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3442":{"model_id":"3442","model_name":"OXA-276","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"520"}},"model_sequences":{"sequence":{"5638":{"protein_sequence":{"accession":"ENV13583.1","sequence":"MKILILWPLLSYLSLTACSFPVSNSPSQITSTQSIQAIAKLFDQAQSSGVLVIQRGPHLQVYGNDLSRAHTEYVPASTFKIFNALIGLQHGKATTNEIFKWDGKKRSFAAWEKDMTLGQAMQASAVPVYQELARRIGLELMQQEVQRIQFGNQQIGHQVDNFWLVGPLKVTPKQEVEFASALAQEQLAFDPRVQQQVKTMLLLQERQAYRLYAKSGWGMDVEPQVGWLTGWIETPQDEIVAFSLNMQMQSNMDPAIRLKILQQALAELGLYPKAEG"},"dna_sequence":{"accession":"APPI01000013.1","fmin":"54643","fmax":"55474","strand":"-","sequence":"ATGAAAATTCTTATTTTGTGGCCTTTACTCAGTTACTTGAGCCTGACAGCCTGTAGCTTCCCTGTTTCAAATTCGCCCTCTCAAATCACTTCAACTCAATCTATTCAAGCTATTGCAAAGTTATTTGATCAGGCACAAAGCTCTGGCGTTTTAGTAATTCAACGGGGTCCACATCTACAGGTCTATGGCAATGATTTGAGTCGTGCACATACCGAATATGTTCCTGCTTCAACCTTTAAAATATTTAATGCTCTGATTGGCCTGCAACATGGTAAAGCCACGACCAATGAAATTTTTAAATGGGATGGCAAGAAGCGCAGTTTTGCAGCCTGGGAAAAAGACATGACTCTCGGCCAAGCCATGCAAGCTTCTGCTGTACCCGTCTATCAGGAACTGGCACGTCGCATTGGTCTGGAACTAATGCAACAGGAAGTACAACGTATTCAATTTGGTAATCAGCAGATTGGTCATCAGGTCGACAACTTCTGGTTAGTCGGACCTTTGAAAGTCACCCCGAAACAAGAAGTCGAATTTGCCTCTGCGCTTGCTCAAGAGCAGCTTGCCTTTGATCCTCGGGTTCAGCAGCAAGTTAAAACCATGTTACTGTTACAGGAGCGACAAGCTTATCGGCTTTATGCTAAATCCGGTTGGGGTATGGATGTGGAGCCGCAAGTCGGCTGGCTCACCGGTTGGATCGAAACACCTCAGGACGAAATCGTGGCATTTTCACTGAATATGCAGATGCAAAGTAATATGGATCCGGCGATCCGTCTTAAAATTTTGCAGCAGGCCTTGGCCGAATTAGGACTTTATCCAAAAGCTGAAGGGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42805","NCBI_taxonomy_name":"Acinetobacter schindleri NIPH 900","NCBI_taxonomy_id":"1217675"}}}},"ARO_accession":"3001732","ARO_id":"38132","ARO_name":"OXA-276","CARD_short_name":"OXA-276","ARO_description":"OXA-276 is a beta-lactamase found in Acinetobacter spp.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46489":{"category_aro_accession":"3007700","category_aro_cvterm_id":"46489","category_aro_name":"OXA-134-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-134.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3471":{"model_id":"3471","model_name":"OXA-336","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"5665":{"protein_sequence":{"accession":"AHN07452.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDVKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKNTPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"KF048907.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGTAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAAATACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAACAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001524","ARO_id":"37924","ARO_name":"OXA-336","CARD_short_name":"OXA-336","ARO_description":"OXA-336 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3503":{"model_id":"3503","model_name":"OXA-430","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"5837":{"protein_sequence":{"accession":"WP_063862927.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDDKAEKIKNLFNEAHTTGVLVIHQGQTQQSYGNDLARASTEYVPASTFKMLNALISLEHHKATTTEVFKWDGEKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_049717.1","fmin":"13","fmax":"838","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGACAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCATCAAGGTCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCAGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAATGGGATGGGGAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATAGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3003121","ARO_id":"39698","ARO_name":"OXA-430","CARD_short_name":"OXA-430","ARO_description":"OXA-430 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3216":{"model_id":"3216","model_name":"mphH","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"5321":{"protein_sequence":{"accession":"ACU86041.1","sequence":"MPEDLDALLDLAARHGLDLDGGTLRTEEIGLDFRVAFARAHDGGDWVLRLPRRPDVLERAAVEGRLLAMLAPHLDVAVPDWRISTSELIAYPLLPGSPGLTVAADGEVSWHVDMASTVYARSLGSVVAQLHAVDAEAAAATGIEVRSPAQVRGAWRQDLARVGAEFEIAPALRERWEAWLADDGCWPGHSVLTHGELYPAHTLVEDERITAVLDWTTAAVGDPAKDLMFHQVSAPSAIFEVALQAYAEGGGRPWPGLARHCTEMFSAAPLGYGLYALATGEAAHREAAAAALNPPEER"},"dna_sequence":{"accession":"CP001643.1","fmin":"2516712","fmax":"2517609","strand":"+","sequence":"ATGCCCGAGGACCTGGACGCACTGCTGGACCTCGCCGCCCGTCACGGCCTCGACCTCGACGGCGGCACGCTGCGCACCGAGGAGATCGGGCTGGACTTCCGGGTCGCATTCGCCCGCGCGCACGACGGCGGCGACTGGGTGCTGCGCCTCCCCCGCCGGCCCGACGTGCTCGAGCGCGCCGCGGTCGAGGGCCGGCTGCTGGCGATGCTCGCCCCGCACCTCGATGTCGCGGTGCCGGACTGGCGCATCAGCACCTCCGAGCTGATCGCCTACCCGCTGCTGCCGGGCAGTCCGGGGCTCACCGTCGCTGCGGACGGCGAGGTCTCCTGGCACGTCGACATGGCCTCGACCGTCTACGCCCGCTCCCTCGGGAGCGTGGTCGCGCAGCTGCATGCCGTGGATGCCGAGGCGGCCGCCGCCACCGGCATCGAGGTGCGCTCCCCCGCACAGGTGCGCGGGGCGTGGCGGCAGGACCTCGCACGCGTGGGCGCGGAGTTCGAGATCGCCCCGGCGCTGCGGGAGCGCTGGGAGGCCTGGCTCGCGGACGACGGCTGCTGGCCCGGGCACAGCGTGCTCACCCATGGCGAGCTCTATCCGGCCCACACCCTCGTCGAGGACGAGCGGATCACGGCAGTGCTCGACTGGACCACCGCCGCGGTGGGCGATCCCGCCAAGGACCTCATGTTCCACCAGGTCAGCGCCCCGTCGGCGATCTTCGAGGTGGCGCTGCAGGCGTACGCCGAGGGCGGCGGCCGCCCCTGGCCGGGGCTGGCACGGCACTGCACCGAGATGTTCTCCGCCGCGCCGCTGGGCTACGGGCTGTACGCGCTGGCCACCGGGGAGGCCGCTCATCGGGAGGCCGCCGCCGCGGCGCTGAACCCGCCCGAGGAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42602","NCBI_taxonomy_name":"Brachybacterium faecium DSM 4810","NCBI_taxonomy_id":"446465"}}}},"ARO_accession":"3004539","ARO_id":"42409","ARO_name":"mphH","CARD_short_name":"mphH","ARO_description":"A chromosomal macrolide 2'-phosphotransferase and resistance gene identified from a Brachybacterium faecium cave isolate.","ARO_category":{"36472":{"category_aro_accession":"3000333","category_aro_cvterm_id":"36472","category_aro_name":"macrolide phosphotransferase (MPH)","category_aro_description":"Macrolide phosphotransferases (MPH) are enzymes encoded by macrolide phosphotransferase genes (mph genes). These enzymes phosphorylate macrolides in GTP dependent manner at 2'-OH of desosamine sugar thereby inactivating them. Characterized MPH's are differentiated based on their substrate specificity.","category_aro_class_name":"AMR Gene Family"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3500":{"model_id":"3500","model_name":"OXA-417","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"530"}},"model_sequences":{"sequence":{"5695":{"protein_sequence":{"accession":"AIU44173.1","sequence":"MTKKALFFAIGTMFLSACSFNTVQQHQIQSISTNKNSEKIKSLFDQAQTEGVLVIKRGQTEEIYGNDLKRSSTEYVPASTFKMLNALIGLEHHKATPTEVFKWDGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMSNEVKRIGFGNADIGSKVDDFWLVGPLKITPQQEAQFAYELAHKTLPFSKNVQEQVQSMLFIEEKNGRKIYAKSGWGWDVEPQVGWLTGWVVQPQGKIVAFSLNLEMKKGIPSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"KM220587.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGACTAAAAAAGCTCTTTTCTTTGCCATTGGTACGATGTTTTTGTCGGCATGTTCTTTTAATACCGTACAACAACATCAAATACAGTCAATTTCTACCAATAAAAACTCAGAGAAAATTAAATCATTGTTTGATCAAGCACAAACTGAAGGTGTTTTAGTTATAAAACGTGGGCAAACAGAGGAAATCTATGGCAATGATCTTAAAAGATCATCAACCGAATATGTTCCCGCCTCTACCTTTAAAATGTTAAATGCTTTGATTGGACTTGAGCATCATAAAGCAACACCAACTGAAGTGTTTAAATGGGATGGGCAAAAGCGTTTGTTTCCTGATTGGGAAAAGGACATGACTCTAGGCGATGCGATGAAAGCTTCTGCTATTCCAGTTTATCAGGAACTAGCTCGACGAATTGGCCTTGATCTTATGTCTAATGAGGTAAAACGCATTGGTTTCGGTAATGCTGATATTGGTTCAAAAGTAGATGATTTTTGGCTTGTTGGTCCACTTAAAATTACACCTCAACAAGAAGCCCAGTTTGCTTATGAACTAGCCCATAAAACTCTTCCTTTTAGCAAGAATGTGCAAGAACAAGTTCAATCTATGCTGTTCATAGAAGAAAAAAATGGACGGAAAATTTATGCCAAAAGTGGTTGGGGATGGGATGTGGAGCCTCAAGTGGGCTGGTTAACAGGCTGGGTCGTTCAACCTCAAGGAAAAATTGTAGCGTTCTCACTCAATTTAGAAATGAAAAAAGGCATACCTAGTTCTATTCGAAAAGAAATTGCTTATAAGGGATTAGAGCAGCTAGGTATTTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39094","NCBI_taxonomy_name":"Acinetobacter calcoaceticus","NCBI_taxonomy_id":"471"}}}},"ARO_accession":"3001608","ARO_id":"38008","ARO_name":"OXA-417","CARD_short_name":"OXA-417","ARO_description":"OXA-417 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46495":{"category_aro_accession":"3007706","category_aro_cvterm_id":"46495","category_aro_name":"OXA-213-like beta-lactamase","category_aro_description":"OXA-213-like enzymes have been identified to be intrinsic to A. calcoaceticus and have been subsequently detected in A. pittii. Phylogenetic analysis of OXA-213-like proteins identified two distinct subgroups within the OXA family. The first group was linked to A. pittii and the second group to A. calcoaceticus. The carbapenemase activity of these OXAs may be related to the species-dependent effect.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3530":{"model_id":"3530","model_name":"OXA-465","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"440"}},"model_sequences":{"sequence":{"5725":{"protein_sequence":{"accession":"AKI29912.1","sequence":"MKKILLLFSLFYSFALANDKLKDFFKDYNTSGVFITFDGKHYASNDFKRAKEPFSPASTFKIFNALIALDNGVVKDTKEIFYHYKGEKVFLPSWKQDASLSSAIKRSQVPAFKELARKIGLKTMQESLNKLSYGNAKISKIDTFWLDNSLQISAKNQADLLFKLSQNSLPFSKKSQEEVKKIILFKEDKIQKIYAKTGFNDGINLAWIVGFIESKNKILSFALNVDIKDIKNIKIREELLEKYIYSLN"},"dna_sequence":{"accession":"KR061500.1","fmin":"0","fmax":"747","strand":"+","sequence":"TTGAAAAAAATACTTTTACTTTTTAGTCTTTTTTACTCTTTTGCTTTGGCAAATGATAAATTAAAAGATTTTTTTAAAGACTACAATACAAGCGGAGTTTTTATAACTTTTGATGGAAAACATTATGCAAGTAATGATTTTAAAAGAGCTAAAGAACCTTTTTCTCCTGCTTCGACTTTTAAAATTTTTAATGCTTTAATTGCGCTTGATAACGGTGTAGTTAAAGATACAAAGGAAATTTTTTATCATTATAAGGGTGAAAAAGTATTTTTGCCTTCTTGGAAACAAGATGCTAGTTTAAGCTCAGCCATAAAACGCTCTCAAGTGCCTGCTTTTAAAGAATTGGCAAGAAAAATAGGACTTAAAACCATGCAAGAAAGCTTAAATAAACTTTCCTATGGAAATGCAAAAATTTCAAAAATCGATACCTTTTGGTTGGATAATTCTTTACAAATTTCTGCAAAAAATCAAGCTGATTTGCTTTTTAAACTTTCACAAAATTCTTTACCTTTTTCCAAGAAAAGTCAAGAAGAAGTTAAAAAAATTATTCTTTTTAAAGAAGATAAAATCCAAAAAATTTATGCTAAAACAGGTTTTAATGATGGTATAAATTTGGCTTGGATTGTCGGATTTATAGAGAGTAAAAACAAAATTTTATCTTTTGCCTTAAATGTTGATATAAAGGACATTAAAAATATTAAAATAAGAGAAGAATTGCTAGAAAAATATATTTATTCTTTAAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36772","NCBI_taxonomy_name":"Campylobacter jejuni","NCBI_taxonomy_id":"197"}}}},"ARO_accession":"3003621","ARO_id":"40231","ARO_name":"OXA-465","CARD_short_name":"OXA-465","ARO_description":"OXA-465 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46491":{"category_aro_accession":"3007702","category_aro_cvterm_id":"46491","category_aro_name":"OXA-184-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-184.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3573":{"model_id":"3573","model_name":"CIA-4","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"560"}},"model_sequences":{"sequence":{"5769":{"protein_sequence":{"accession":"BAL40895.1","sequence":"MKKITFLILMVSAFATAQKSVLDEKISAVIKDKKATVGVSVLGFENAFKYSKNGDEKLPLLSVFKFHLACAVLDMADKGKFSTDQKFLIKKSDLLENTWSPLREKFPEGNIELSLGEIITYTVAQSDNNTCDFLLRLIGGPQVVQHFMDSKGAKDLQIKYNEDDMHRDWKNQYGNESSTNATVSLLKKFYDGKLLTKKSTDFLMQIMLGTTTGTNKIVEQLPKGTPVAHKTGSSGKPDNILTVAENDMGIITLPNGKHYAIAVFVSNSTETEKVNTRMVSDISKIVWDNFNK"},"dna_sequence":{"accession":"AB674568.1","fmin":"0","fmax":"879","strand":"+","sequence":"ATGAAAAAAATAACATTTCTTATACTGATGGTTTCTGCCTTTGCTACTGCACAGAAATCCGTACTTGACGAAAAAATCAGTGCTGTTATAAAAGATAAAAAAGCGACGGTAGGAGTTTCTGTTTTGGGTTTTGAGAATGCTTTCAAGTACAGTAAAAACGGAGATGAGAAGCTGCCGTTACTCAGCGTTTTTAAATTTCACCTGGCCTGTGCTGTATTGGATATGGCAGATAAAGGTAAATTTTCAACAGATCAGAAGTTTTTAATAAAAAAATCAGATCTATTGGAAAATACATGGTCTCCGCTACGCGAAAAATTTCCGGAAGGAAATATTGAACTTTCTTTAGGAGAAATTATCACGTACACAGTTGCTCAAAGTGATAACAATACCTGTGATTTTCTTTTAAGATTGATAGGCGGTCCTCAGGTTGTTCAGCACTTCATGGATTCTAAAGGAGCAAAAGATCTTCAGATCAAATATAATGAGGACGACATGCACAGGGACTGGAAAAACCAATATGGGAACGAAAGCAGCACCAATGCGACTGTCTCACTATTGAAAAAATTCTATGATGGTAAGCTTCTTACAAAAAAATCGACGGATTTCCTGATGCAGATTATGTTGGGAACTACAACAGGAACCAATAAAATCGTTGAACAGTTACCCAAAGGTACGCCTGTTGCTCATAAAACGGGTTCTTCCGGAAAGCCGGACAATATACTTACTGTTGCAGAAAATGATATGGGGATTATTACCCTTCCCAACGGAAAGCATTATGCAATCGCTGTATTTGTAAGCAATTCAACGGAAACAGAAAAGGTAAATACAAGGATGGTTTCTGATATTTCAAAGATCGTTTGGGATAATTTTAATAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36916","NCBI_taxonomy_name":"Chryseobacterium indologenes","NCBI_taxonomy_id":"253"}}}},"ARO_accession":"3004771","ARO_id":"42886","ARO_name":"CIA-4","CARD_short_name":"CIA-4","ARO_description":"CIA-4 is a class A beta-lactamase gene found in Chryseobacterium indologenes.","ARO_category":{"42881":{"category_aro_accession":"3004767","category_aro_cvterm_id":"42881","category_aro_name":"CIA beta-lactamase","category_aro_description":"CIA is a class A beta-lactamase gene family found in Chryseobacterium indologenes.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3607":{"model_id":"3607","model_name":"GOB-6","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"480"}},"model_sequences":{"sequence":{"5805":{"protein_sequence":{"accession":"AAF89148.1","sequence":"KEPENMPKEWNQTYEPFRIAGNLYYVGTYDLASYLIVTDKGNILINTGTAESLPIIKANIQKLGFNYKDIKILLLTQAHYDHTGALQDLKTETAAKFYADKADADVLRTGGNSDYEMGKYGVTFKPVTPDKTLKDQDKIKLGNITLTLLHHPGHTKGSCSFIFETKDEKRKYRVLIANMPSVIVDKKFSEVTAYPNIQSDYAYTFKAMKNLDFDLWVASHASQFDLHEKRKEGDPYNPQLFMDKQSYFQNLN"},"dna_sequence":{"accession":"AF189292.1","fmin":"0","fmax":"756","strand":"+","sequence":"AAAGAACCTGAAAATATGCCCAAAGAATGGAACCAGACTTATGAACCCTTCAGAATTGCAGGTAATTTATATTACGTAGGAACCTATGATTTGGCTTCTTACCTTATTGTGACAGACAAAGGCAATATTCTCATTAATACAGGAACGGCAGAATCGCTTCCAATAATAAAAGCAAATATCCAAAAGCTCGGGTTTAATTATAAAGACATTAAGATCTTGCTGCTTACTCAGGCTCACTACGACCATACAGGTGCATTACAAGATCTTAAAACAGAAACCGCTGCAAAATTCTATGCCGATAAAGCAGATGCTGATGTCCTGAGAACAGGGGGAAATTCCGATTATGAAATGGGAAAATATGGTGTGACATTTAAACCTGTTACTCCGGATAAAACATTGAAAGATCAGGATAAAATAAAACTGGGAAATATAACCCTGACTTTGCTTCATCATCCGGGACATACAAAAGGTTCCTGTAGTTTTATTTTTGAAACAAAAGACGAGAAGAGAAAATATAGAGTTTTGATAGCTAATATGCCCTCCGTTATTGTTGATAAGAAATTTTCTGAAGTTACCGCATATCCAAATATTCAGTCCGATTATGCATATACTTTCAAAGCAATGAAGAATCTAGATTTTGACCTTTGGGTGGCATCACATGCAAGTCAGTTCGATCTGCATGAAAAACGTAAAGAAGGAGATCCGTACAATCCGCAATTGTTTATGGATAAGCAAAGCTATTTCCAAAACCTTAAT","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36960","NCBI_taxonomy_name":"Elizabethkingia meningoseptica","NCBI_taxonomy_id":"238"}}}},"ARO_accession":"3004813","ARO_id":"42933","ARO_name":"GOB-6","CARD_short_name":"GOB-6","ARO_description":"GOB-6 is a class B beta-lactamase gene found in Elizabethkingia meningoseptica.","ARO_category":{"41376":{"category_aro_accession":"3004212","category_aro_cvterm_id":"41376","category_aro_name":"GOB beta-lactamase","category_aro_description":"The GOB family of beta-lactamases have been discovered in the Elizabethkingia meningoseptica and are classified as subclass B3 beta-lactamase. They confer resistance to cephalosporins, penicillins, and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3579":{"model_id":"3579","model_name":"CMY-135","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"740"}},"model_sequences":{"sequence":{"5777":{"protein_sequence":{"accession":"AKP17985.1","sequence":"MMKKSICCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAIIYEGKPYYFTWGKADIANNHLVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWRGISLLHLATYTAGGLPLQIPDDITDKAALLRFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQSEQKNYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIELAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPARVEAAWRILEKLQ"},"dna_sequence":{"accession":"KP981366.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGATATGCTGCGCACTGCTGCTGACAGCCTCTTTCTCCACGTTTGCTGCCGCAAAAACAGAACAACAAATTGCCGATATCGTTAACCGCACCATCACACCACTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTGGCGATTATCTACGAGGGGAAACCTTATTACTTTACCTGGGGTAAAGCCGATATCGCCAATAACCACCTAGTCACGCAGCAAACGCTGTTTGAGCTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGACGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCGGGGTATCAGCCTGCTGCACTTAGCCACCTATACAGCGGGTGGCCTGCCGCTGCAGATCCCCGATGACATTACGGATAAAGCCGCATTACTGCGCTTTTATCAAAACTGGCAACCACAATGGACTCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGTGCGCTGGCGGTGAAACCTTCAGGTATGAGCTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAAAGCGAACAAAAAAACTATGCCTGGGGCTATCGCGAAGGGAAGCCTGTGCACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATCGATATGGCCCGCTGGGTTCAGGCCAACATGGACGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGAGCTTGCGCAGTCTCGCTACTGGCGTATTGGTGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCAGCACCTGCCGTGAAAGCCTCATGGGTGCATAAAACAGGATCCACAGGCGGATTTGGCAGCTACGTTGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTAATGTTGGCAAACAAAAGCTACCCCAACCCGGCTCGCGTCGAGGCGGCCTGGCGCATTCTTGAAAAACTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3004778","ARO_id":"42893","ARO_name":"CMY-135","CARD_short_name":"CMY-135","ARO_description":"CMY-135 is a class C beta-lactamase that confers resistance to cephamycin.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4189":{"model_id":"4189","model_name":"ADC-115","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6564":{"protein_sequence":{"accession":"WP_001211215.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVKTDQQVLTFFKDWKPKNSIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRANPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTTGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_064674.1","fmin":"100","fmax":"1252","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAGTATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAATTTCCAGATGAAGTAAAAACAGATCAGCAAGTTTTAACATTTTTTAAAGACTGGAAACCTAAAAACTCAATCGGTGAATATCGACAATATTCAAACCCAAGCATTGGTTTATTTGGAAAAGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGCTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTAAATCCACAAAAATATCCAGCAGATATTCAACGGGCAATTAATGAAACACATCAGGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTACCGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006293","ARO_id":"44755","ARO_name":"ADC-115","CARD_short_name":"ADC-115","ARO_description":"ADC-115 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4231":{"model_id":"4231","model_name":"ADC-163","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6606":{"protein_sequence":{"accession":"WP_057093064.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANFNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPAPLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_056105.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCTTATTTGGAAAAGTTGTTGCTTTGTCTATGAATAAACCTTTCGATCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACTTCAACCCACAGAAATATCCGGCAGATATTCAACGGGCAATTAATGAAACACATCAAGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCACCTTTACAAACTTTATTAGACAGTAATTCAGAACAAATTGTGATGAAGCCTAATAAAGTGACTGCTATTTCAAAAGAGCCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACATATGTAGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006335","ARO_id":"44797","ARO_name":"ADC-163","CARD_short_name":"ADC-163","ARO_description":"ADC-163 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4232":{"model_id":"4232","model_name":"ADC-164","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6607":{"protein_sequence":{"accession":"WP_032068214.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGIIQNNKKYEMYYGLQSVQDKKALNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQCRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_056106.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCGTTATTAGAAAAATATGATGTGCCGGGTATGGCTGTGGGTATTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCTTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCCAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTAAATCCACAAAAATATCCAGCAGATATTCAACGGGCAATTAATGAAACACATCAGTGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCAACGGTTTCGGAACATATGTAGTGTTTATACCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006336","ARO_id":"44798","ARO_name":"ADC-164","CARD_short_name":"ADC-164","ARO_description":"ADC-164 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4014":{"model_id":"4014","model_name":"PDC-258","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"6379":{"protein_sequence":{"accession":"WP_109791192.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALTQDKMRLDDRASQHWPALQGSRFAGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_057590.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGACCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGCCGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005281","ARO_id":"43638","ARO_name":"PDC-258","CARD_short_name":"PDC-258","ARO_description":"PDC-258 is a class C beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4190":{"model_id":"4190","model_name":"ADC-116","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6565":{"protein_sequence":{"accession":"WP_017816757.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVKTDQQVLTFFKDWKPKNSIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGFYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_064675.1","fmin":"100","fmax":"1252","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAGTATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAATTTCCAGATGAAGTAAAAACAGATCAGCAAGTTTTAACATTTTTTAAAGACTGGAAACCTAAAAACTCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATACGGCGTCAAATCCACCTTACCGGATATGTTGAGTTTTATTCATGCCAACCTTAACCCACAAAAATATCCAGCAGATATTCAACGGGCAATTAATGAAACACATCAAGGGTTCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCAACGGTTTCGGAACATATGTGGTCTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCGTATGCAGTTTTAAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006294","ARO_id":"44756","ARO_name":"ADC-116","CARD_short_name":"ADC-116","ARO_description":"ADC-116 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3652":{"model_id":"3652","model_name":"CMY-136","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"5922":{"protein_sequence":{"accession":"AVR61040.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHVSPGQLDAEAHGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"MG844436.1","fmin":"6618","fmax":"7764","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCCATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3004854","ARO_id":"42990","ARO_name":"CMY-136","CARD_short_name":"CMY-136","ARO_description":"A CMY-2-like beta-lactamase which confers resistance to cephalosporin antibiotics, and is also capable of hydrolyzing the CMY-2 inhibitors ticarcillin and cloxacillin.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35980":{"category_aro_accession":"0000063","category_aro_cvterm_id":"35980","category_aro_name":"cefuroxime","category_aro_description":"Cefuroxime is a second-generation cephalosporin antibiotic with increased stability with beta-lactamases than first-generation cephalosporins. Cefuroxime is active against Gram-positive organisms but less active against methicillin-resistant strains.","category_aro_class_name":"Antibiotic"},"36989":{"category_aro_accession":"3000645","category_aro_cvterm_id":"36989","category_aro_name":"cefotaxime","category_aro_description":"Cefotaxime is a semisynthetic cephalosporin taken parenterally. It is resistant to most beta-lactamases and active against Gram-negative rods and cocci due to its aminothiazoyl and methoximino functional groups.","category_aro_class_name":"Antibiotic"},"40636":{"category_aro_accession":"3003927","category_aro_cvterm_id":"40636","category_aro_name":"ceftolozane","category_aro_description":"Ceftolozane is a fifth-generation cephalosporin antibiotic developed for the treatment of infections with gram-negative bacteria that have become resistant to conventional antibiotics.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3626":{"model_id":"3626","model_name":"LEN-37","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"576"}},"model_sequences":{"sequence":{"5824":{"protein_sequence":{"accession":"ALK01320.1","sequence":"MRYVRLCVISLLATLPLAVDAGPQPLEQIKQSESQLSGRVGMVEMDLASGRTLAAWRADERFPMVSTFKVLLCGAVLARVDAGVEQLDRRIHYRQQDLVDYSPVSEKHLVDGMTIGELCAAAITLSDNSAGNLLLATVGGPAGLTAFLRQIGDNVTRLDRWETALNEALPGDARDTTTPASMSATLRKLLTAQHLSARSQQQLLQWMVDDRVAGPLIRAVLPPGWFIADKTGAGERGARGIVALLGPDGKPERIVVIYLRDTPASMAERNQHIAGIGAALIEHWQR"},"dna_sequence":{"accession":"KR738739.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATGTTCGCCTTTGTGTTATCTCCCTGTTAGCCACCCTGCCACTGGCGGTAGACGCCGGTCCACAGCCGCTTGAGCAGATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTGGGGATGGTGGAAATGGATCTGGCCAGCGGCCGCACACTGGCCGCCTGGCGCGCCGATGAACGCTTTCCCATGGTGAGCACCTTTAAAGTGCTGCTGTGCGGCGCGGTGCTGGCGCGGGTGGATGCAGGGGTCGAACAACTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGTCGACGGGATGACGATCGGCGAACTCTGCGCCGCCGCCATCACCCTGAGCGATAACAGCGCTGGCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCGGGATTAACTGCCTTTCTACGCCAGATCGGTGACAACGTCACCCGTCTTGACCGCTGGGAAACGGCACTGAATGAGGCGCTTCCCGGCGACGCGCGCGACACCACCACCCCGGCCAGCATGTCCGCCACGCTGCGCAAACTACTGACCGCGCAGCATCTGAGCGCCCGTTCGCAACAGCAACTCCTGCAGTGGATGGTGGACGATCGGGTTGCCGGCCCGCTGATCCGCGCCGTGCTGCCGCCGGGCTGGTTTATCGCCGACAAAACCGGGGCTGGCGAACGGGGTGCGCGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAACCGGAGCGCATTGTGGTGATCTATCTGCGGGATACCCCGGCGAGTATGGCCGAGCGTAATCAACATATCGCCGGGATCGGCGCAGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42612","NCBI_taxonomy_name":"Klebsiella variicola","NCBI_taxonomy_id":"244366"}}}},"ARO_accession":"3004829","ARO_id":"42959","ARO_name":"LEN-37","CARD_short_name":"LEN-37","ARO_description":"LEN-37 is a Class A beta-lactamase gene found in Klebsiella variicola.","ARO_category":{"36236":{"category_aro_accession":"3000097","category_aro_cvterm_id":"36236","category_aro_name":"LEN beta-lactamase","category_aro_description":"LEN beta-lactamases are chromosomal class A beta-lactamases that confer resistance to ampicillin, amoxicillin, carbenicillin, and ticarcillin but not to extended-spectrum beta-lactams.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3636":{"model_id":"3636","model_name":"LEN-34","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"5907":{"protein_sequence":{"accession":"CTQ12020.1","sequence":"MRYVRLCVISLLATLPLAVYAGPQPLEQIKQSESQLSGRVGMVEMDLASGRTLAAWRADERFPMVSTFKVLLCGAVLARVDAGIEQLDRRIHYRQQDLVDYSPVSEKHLTDGMTIGELCAAAITLSDNSAGNLLLATVGGPAGLTAFLRQIGDNVTRLDRWETALNEALPGDARDTTTPASMAATLRKLLTAQHLSARSQQQLLQWMVDDRVAGPLIRAVLPPGWFIADKTGAGERGARGIVALLGPDGKPERIVVIYLRDTPASMAERNQHIAGIGAALIEHWQR"},"dna_sequence":{"accession":"CXPB01000032.1","fmin":"60038","fmax":"60899","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGTGTTATCTCCCTGTTAGCCACCCTGCCACTGGCGGTATACGCCGGTCCACAGCCGCTTGAGCAGATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTGGGGATGGTGGAAATGGATCTGGCCAGCGGCCGCACGCTGGCGGCCTGGCGCGCCGATGAACGCTTTCCCATGGTGAGCACCTTTAAAGTGCTGCTGTGCGGCGCGGTGCTGGCGCGGGTGGATGCCGGGATCGAACAACTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGATTACTCCCCGGTCAGCGAAAAACACCTTACCGACGGGATGACGATCGGCGAACTCTGCGCCGCCGCCATCACCCTGAGCGATAACAGCGCTGGCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCGGGATTAACTGCCTTTCTGCGCCAGATCGGTGACAACGTCACCCGTCTTGACCGCTGGGAAACGGCACTGAATGAGGCGCTTCCCGGCGACGCGCGCGACACCACCACCCCGGCCAGCATGGCCGCCACGCTGCGCAAACTACTGACCGCGCAGCATCTGAGCGCCCGTTCGCAACAGCAACTCCTGCAGTGGATGGTGGACGATCGGGTTGCCGGCCCGCTGATCCGCGCCGTGCTGCCGCCGGGCTGGTTTATCGCCGACAAAACCGGGGCTGGCGAACGGGGTGCGCGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAACCGGAGCGCATTGTGGTGATCTATCTGCGGGATACCCCGGCGAGTATGGCCGAGCGTAATCAACATATCGCCGGGATCGGCGCAGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42612","NCBI_taxonomy_name":"Klebsiella variicola","NCBI_taxonomy_id":"244366"}}}},"ARO_accession":"3004840","ARO_id":"42974","ARO_name":"LEN-34","CARD_short_name":"LEN-34","ARO_description":"A class-A beta-lactamase from Klebsiella variicola.","ARO_category":{"36236":{"category_aro_accession":"3000097","category_aro_cvterm_id":"36236","category_aro_name":"LEN beta-lactamase","category_aro_description":"LEN beta-lactamases are chromosomal class A beta-lactamases that confer resistance to ampicillin, amoxicillin, carbenicillin, and ticarcillin but not to extended-spectrum beta-lactams.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4191":{"model_id":"4191","model_name":"ADC-117","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6566":{"protein_sequence":{"accession":"WP_002157727.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_064676.1","fmin":"100","fmax":"1252","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAAGTTGTTGCTTTGTCTATGAATAAACCTTTTGATCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAGGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTTAACCCACAGAAATATCCGGCTGATATTCAAAGGGCAATTAATGAAACACATCAAGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCAACGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006295","ARO_id":"44757","ARO_name":"ADC-117","CARD_short_name":"ADC-117","ARO_description":"ADC-117 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3994":{"model_id":"3994","model_name":"TEM-231","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6358":{"protein_sequence":{"accession":"WP_104009855.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTIPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"NG_056418.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATACCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3005262","ARO_id":"43618","ARO_name":"TEM-231","CARD_short_name":"TEM-231","ARO_description":"TEM-231 is a beta-lactamase.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2907":{"model_id":"2907","model_name":"vmlR","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"5366":{"protein_sequence":{"accession":"NP_388442.1","sequence":"MKEIVTLTNVSYEVKDQTVFKHVNASVQQGDIIGIIGKNGAGKSTLLHLIHNDLAPAQGQILRKDIKLALVEQETAAYSFADQTPAEKKLLEKWHVPLRDFHQLSGGEKLKARLAKGLSEDADLLLLDEPTNHLDEKSLQFLIQQLKHYNGTVILVSHDRYFLDEAATKIWSLEDQTLIEFKGNYSGYMKFREKKRLTQQREYEKQQKMVERIEAQMNGLASWSEKAHAQSTKKEGFKEYHRVKAKRTDAQIKSKQKRLEKELEKAKAEPVTPEYTVRFSIDTTHKTGKRFLEVQNVTKAFGERTLFKNANFTIQHGEKVAIIGPNGSGKTTLLNIILGQETAEGSVWVSPSANIGYLTQEVFDLPLEQTPEELFENETFKARGHVQNLMRHLGFTAAQWTEPIKHMSMGERVKIKLMAYILEEKDVLILDEPTNHLDLPSREQLEETLSQYSGTLLAVSHDRYFLEKTTNSKLVISNNGIEKQLNDVPSERNEREELRLKLETERQEVLGKLSFMTPNDKGYKELDQAFNELTKRIKELDHQDKKD"},"dna_sequence":{"accession":"NC_000964.3","fmin":"604735","fmax":"606379","strand":"-","sequence":"ATGAAAGAGATCGTAACATTAACAAACGTTAGCTATGAAGTAAAGGATCAAACTGTTTTTAAACATGTAAACGCCAGTGTTCAGCAAGGAGATATCATTGGGATTATCGGCAAAAACGGCGCTGGGAAATCTACGTTGCTGCACCTCATTCACAATGACTTAGCCCCTGCACAGGGTCAAATCCTTCGGAAGGATATAAAACTGGCTTTGGTTGAACAGGAAACCGCGGCGTATTCCTTTGCGGATCAGACACCTGCCGAAAAGAAGTTACTGGAGAAATGGCATGTGCCTCTTCGTGATTTTCATCAGTTAAGCGGCGGTGAAAAACTGAAAGCGCGGCTGGCGAAAGGACTATCAGAGGATGCAGATCTGCTGCTGTTAGATGAACCGACAAACCACCTTGATGAAAAAAGCTTGCAATTTCTCATCCAACAGCTGAAACATTATAACGGCACTGTGATTCTCGTTTCTCACGATCGATATTTTTTAGACGAAGCCGCAACAAAAATATGGTCGCTTGAGGATCAGACGCTGATTGAATTCAAAGGGAATTACTCCGGGTATATGAAGTTCCGGGAGAAGAAAAGACTCACCCAGCAGCGTGAATATGAAAAGCAGCAAAAAATGGTTGAACGGATTGAAGCACAAATGAATGGGCTCGCTTCTTGGTCGGAAAAAGCCCATGCTCAATCGACGAAAAAGGAAGGGTTTAAAGAATATCACCGGGTAAAAGCGAAGCGTACGGATGCCCAGATAAAATCCAAGCAGAAGCGGCTTGAAAAAGAGCTTGAAAAAGCAAAGGCGGAACCCGTTACCCCAGAATATACAGTCCGCTTTTCAATCGATACAACCCACAAAACAGGAAAACGTTTTTTAGAAGTTCAGAATGTAACAAAAGCGTTTGGAGAAAGGACTCTCTTTAAAAACGCAAACTTTACAATTCAGCACGGCGAAAAGGTTGCGATCATAGGCCCCAATGGCAGCGGAAAAACGACATTACTGAACATCATTCTGGGACAGGAAACAGCAGAAGGAAGTGTATGGGTGTCGCCGTCCGCAAACATCGGCTATTTAACGCAGGAGGTGTTTGATTTGCCTTTAGAACAAACACCGGAAGAGTTATTTGAGAATGAAACATTCAAAGCAAGGGGGCACGTTCAAAATCTGATGAGGCACTTAGGTTTTACAGCCGCCCAATGGACTGAACCGATCAAGCATATGAGTATGGGTGAGCGTGTAAAGATCAAGCTGATGGCATATATTCTGGAGGAAAAAGACGTGCTGATTTTAGATGAGCCGACAAACCATCTCGACCTGCCGTCACGCGAACAGCTGGAAGAAACACTGTCACAATACAGCGGCACATTGCTGGCGGTTTCACATGACCGATACTTTCTCGAAAAAACAACAAACAGTAAACTCGTCATCTCAAACAACGGCATCGAAAAGCAGTTAAACGACGTTCCTTCAGAAAGAAATGAGCGGGAGGAGCTTCGGTTAAAGCTTGAGACAGAAAGACAAGAAGTGCTGGGAAAGCTCAGTTTTATGACGCCAAATGATAAAGGGTATAAGGAGCTTGATCAGGCTTTCAATGAGCTTACGAAACGAATAAAAGAGCTGGATCATCAAGACAAAAAAGACTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39579","NCBI_taxonomy_name":"Bacillus subtilis subsp. subtilis str. 168","NCBI_taxonomy_id":"224308"}}}},"ARO_accession":"3004476","ARO_id":"41736","ARO_name":"vmlR","CARD_short_name":"vmlR","ARO_description":"vmlR is an ABC-F ATPase ribosomal protection protein identified in Bacillus subtilus. Shown to confer resistance to lincomycin and streptogramin A virginiamycin. Described by Crowe-McAuliffe et al. 2018.","ARO_category":{"45630":{"category_aro_accession":"3007068","category_aro_cvterm_id":"45630","category_aro_name":"Miscellaneous ABC-F subfamily ATP-binding cassette ribosomal protection proteins","category_aro_description":"ABC-F subfamily ATP-binding cassette ribosomal protection proteins of unknown, unclear or miscellaneous classification which nevertheless confer resistance to antibiotics through ribosomal protection and not through antibiotic efflux. These proteins should be further reviewed to elucidate associated genes, their function, origin and classification.","category_aro_class_name":"AMR Gene Family"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"virginiamycin M1","category_aro_description":"Virginiamycin M1 is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37015":{"category_aro_accession":"3000671","category_aro_cvterm_id":"37015","category_aro_name":"tiamulin","category_aro_description":"Tiamulin is a pleuromutilin derivative currently used in veterinary medicine. It binds to the 23 rRNA of the 50S ribosomal subunit to inhibit protein translation.","category_aro_class_name":"Antibiotic"},"37021":{"category_aro_accession":"3000677","category_aro_cvterm_id":"37021","category_aro_name":"virginiamycin S2","category_aro_description":"Virginiamycin S2 is a streptogramin B antibiotic.","category_aro_class_name":"Antibiotic"},"37713":{"category_aro_accession":"3001314","category_aro_cvterm_id":"37713","category_aro_name":"retapamulin","category_aro_description":"Retapamulin is a semi-synthetic pleuromutilin antibiotic approved for the treatment of skin infections.","category_aro_class_name":"Antibiotic"},"46411":{"category_aro_accession":"3007636","category_aro_cvterm_id":"46411","category_aro_name":"iboxamycin","category_aro_description":"Iboxamycin is a fully synthetic lincosamide antibiotic. Like other lincosamides, it selectively targets the bacterial ribosome and prevents elongation of the peptide chain. Iboxamycin has been shown to  be effective against bacterial strains otherwise resistant to licosamide antibiotics.","category_aro_class_name":"Antibiotic"},"46413":{"category_aro_accession":"3007638","category_aro_cvterm_id":"46413","category_aro_name":"hygromycin A","category_aro_description":"Hygromycin A is an antibiotic produced by Streptomyces hygroscopicus. It inhibits translation by binding to the peptidyl transferase center on the large ribosomal subunit. This prevents the binding of aminoacyl-tRNA to the A-site. Not to confused with Hygromycin B, which is structurally distinct.","category_aro_class_name":"Antibiotic"},"46414":{"category_aro_accession":"3007639","category_aro_cvterm_id":"46414","category_aro_name":"A201A","category_aro_description":"A201A is a nucleoside antibiotic. It inhibits translation by binding to the peptidyl transferase center on the large ribosomal subunit. This prevents the binding of aminoacyl-tRNA to the A-site.","category_aro_class_name":"Antibiotic"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35952":{"category_aro_accession":"0000034","category_aro_cvterm_id":"35952","category_aro_name":"streptogramin A antibiotic","category_aro_description":"Streptogramin A antibiotics are cyclic polyketide peptide hybrids that bind to the ribosomal peptidyl transfer centre. Structural variation arises from substituting a proline for its desaturated derivative and by its substitution for Ala or Cys. Used alone, streptogramin A antibiotics are bacteriostatic, but is bactericidal when used with streptogramin B antibiotics.","category_aro_class_name":"Drug Class"},"35967":{"category_aro_accession":"0000050","category_aro_cvterm_id":"35967","category_aro_name":"streptogramin B antibiotic","category_aro_description":"Streptogramin B antibiotics are are cyclic hepta- or hexa-depsipeptides.  Type B streptogramins block the peptide exit tunnel of the 50S bacterial ribosome. The general composition of group B streptogramins is 3-hydroxypicolinic acid-L-Thr-D-aminobutyric acid (or D-Ala)-L-Pro-L-Phe (or 4-N-,N-(dimethylamino)-L-Phe)-X-L-phenylglycine. Used alone, streptogramin B antibiotics are bacteriostatic, but is bactericidal when used with streptogramin A antibiotics.","category_aro_class_name":"Drug Class"},"36012":{"category_aro_accession":"3000003","category_aro_cvterm_id":"36012","category_aro_name":"antibiotic without defined classification","category_aro_description":"These compounds are antibiotics of unique structure or origin, without a defined classification.","category_aro_class_name":"Drug Class"},"36174":{"category_aro_accession":"3000034","category_aro_cvterm_id":"36174","category_aro_name":"nucleoside antibiotic","category_aro_description":"Nucleoside antibiotics are made of modified nucleosides and nucleotides with wide-ranging activities and means of antibacterial effects. This drug class includes aminonucleoside antibiotics, which contain an amino group.","category_aro_class_name":"Drug Class"},"37014":{"category_aro_accession":"3000670","category_aro_cvterm_id":"37014","category_aro_name":"pleuromutilin antibiotic","category_aro_description":"Pleuromutilins are natural fungal products that target bacterial protein translation by binding the the 23S rRNA, blocking the ribosome P site at the 50S subunit. They are mostly used for agriculture and veterinary purposes.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3580":{"model_id":"3580","model_name":"DES-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"5778":{"protein_sequence":{"accession":"AAM45855.1","sequence":"MHSRSSYSRRYVLAGLCALPFASLSAGLIFNSSADAASLAAINGKTLQKKLAELEAASGGRLGVAARSSNGGKSLSYRGDERFPMCSTFKVLAVAALLRDKPGILEQRIHFAQIDIQPWSPVTEKHLEDGMTVAELCAAMLQHSDNTAANLVLAKLGGPQGLTSLARSFGDTTFRLDRWEVELNTAIPGDARDTTTPLAMCNTLNGLLCGNLLKAPARERLTGWMLGCATGAGRIPAGIPQGWRSAHKSGSGENGTANDVGVLLPPSNPGKATKPGKNKGKPLTVALYLTGSRLTGPENDKILASATRLVCAAEGLAMPLDNMY"},"dna_sequence":{"accession":"AF426161.1","fmin":"118","fmax":"1093","strand":"+","sequence":"ATGCATTCCCGTTCCAGTTATTCCAGGCGCTATGTGCTCGCGGGCCTGTGCGCCCTGCCTTTTGCCTCGCTGAGCGCAGGCCTTATTTTCAACAGCTCTGCTGATGCCGCCTCTCTTGCTGCAATTAACGGAAAAACCCTGCAAAAAAAGCTGGCCGAACTTGAGGCCGCAAGCGGCGGCAGGCTTGGCGTGGCTGCCCGGTCAAGCAATGGCGGCAAAAGCCTGTCTTACCGTGGGGACGAACGCTTTCCCATGTGCAGCACCTTTAAAGTGCTGGCAGTTGCGGCCCTTCTGCGGGACAAACCGGGCATTCTTGAACAGAGAATCCACTTTGCCCAAATCGACATCCAGCCCTGGTCGCCCGTTACAGAAAAGCACCTTGAAGACGGCATGACTGTGGCAGAATTGTGCGCCGCCATGCTCCAGCACAGCGACAACACGGCTGCCAACCTTGTGCTTGCCAAACTGGGCGGCCCGCAAGGCCTGACCTCCCTTGCCCGCAGTTTTGGCGACACAACGTTTCGCCTTGACCGCTGGGAAGTGGAACTGAATACGGCCATCCCCGGCGATGCGCGCGACACCACAACGCCCCTGGCCATGTGCAACACCCTGAACGGATTGCTGTGTGGCAACCTGCTGAAAGCGCCCGCACGCGAACGACTGACAGGCTGGATGCTGGGCTGCGCAACCGGGGCCGGGCGCATCCCCGCAGGAATTCCGCAGGGCTGGCGCTCTGCGCACAAAAGCGGCAGCGGAGAAAACGGCACCGCCAATGATGTAGGAGTATTGCTGCCGCCGAGCAACCCTGGCAAAGCCACAAAGCCCGGCAAGAACAAAGGCAAGCCGCTGACTGTGGCCCTCTACCTCACGGGATCGCGACTGACCGGGCCGGAAAACGACAAAATCCTTGCCAGTGCAACCCGCCTGGTCTGCGCCGCAGAAGGGCTTGCGATGCCGCTCGACAATATGTATTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42896","NCBI_taxonomy_name":"Desulfovibrio desulfuricans","NCBI_taxonomy_id":"876"}}}},"ARO_accession":"3004780","ARO_id":"42895","ARO_name":"DES-1","CARD_short_name":"DES-1","ARO_description":"DES-1 is a class A beta-lactamase gene found in Desulfovibrio desulfuricans.","ARO_category":{"42894":{"category_aro_accession":"3004779","category_aro_cvterm_id":"42894","category_aro_name":"DES beta-lactamase","category_aro_description":"DES is a class A beta-lactamase gene family found in Desulfovibrio desulfuricans.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2909":{"model_id":"2909","model_name":"OXA-664","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"4762":{"protein_sequence":{"accession":"EOR02560.1","sequence":"MWMLKTISCSVLSWMLLSACSQQTLKDQMQQPLMMQQPRLAELNHMFQAVDSAVVFVTYDGEKLQRFGNDLHRAETAYIPASTFKILNALIGLQQHKTTTTEVFVWDGKARALKSWERDMTLAEAMQVSAVPVYQTLARRIGLPLMQKELHRVDYGNAQIGTQVDRFWLDGPLKITPQQEAEFAYRLATQTLPFDIHVQQEVKEMLYVERRGVAKLYAKSGWGADVKPQVG"},"dna_sequence":{"accession":"AQFM01000048.1","fmin":"191231","fmax":"191927","strand":"-","sequence":"ATGTGGATGTTAAAAACGATATCTTGTTCAGTTTTAAGCTGGATGTTGTTAAGTGCATGCAGTCAGCAAACTCTGAAAGATCAAATGCAACAGCCATTGATGATGCAACAACCACGGTTAGCAGAGTTGAATCATATGTTTCAAGCAGTGGATAGCGCCGTGGTCTTTGTGACTTATGATGGGGAAAAATTACAGCGTTTTGGCAATGATTTGCATCGTGCCGAAACTGCCTATATACCAGCTTCAACTTTTAAAATACTAAATGCTTTAATTGGTTTGCAGCAGCATAAAACCACGACCACTGAAGTATTTGTATGGGATGGAAAAGCACGTGCATTGAAAAGTTGGGAACGGGATATGACTTTGGCAGAGGCGATGCAAGTCTCGGCAGTTCCCGTCTATCAAACCTTAGCGCGACGAATTGGTCTACCACTGATGCAAAAAGAGCTTCATCGTGTCGATTATGGAAATGCTCAGATTGGGACACAGGTTGATCGGTTTTGGTTAGATGGACCCTTAAAAATCACACCACAACAAGAAGCTGAATTTGCTTACAGACTTGCGACTCAGACTTTACCTTTTGATATACATGTGCAACAAGAGGTAAAGGAAATGCTTTATGTGGAGCGACGCGGTGTTGCTAAATTGTATGCTAAGTCAGGATGGGGAGCCGATGTAAAACCTCAGGTGGGTTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41739","NCBI_taxonomy_name":"Acinetobacter tandoii DSM 14970 = CIP 107469","NCBI_taxonomy_id":"1120927"}}}},"ARO_accession":"3004479","ARO_id":"41740","ARO_name":"OXA-664","CARD_short_name":"OXA-664","ARO_description":"Beta-lactamase found in Acinetobacter spp. efficiently inactivating carbapenems and amoxicillin conferring resistance to cephalosporins.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2910":{"model_id":"2910","model_name":"OXA-665","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4763":{"protein_sequence":{"accession":"EPF70268.1","sequence":"MKKNLFACLVLSTALTQVACSTLQTTADPSTQASTAQQSIKSYFDEVQTKGVIVIKQDGQLQTYGNDLSRANTEYVPASTFKILNALIGLENHKVTLNEVFKWDGQKRSFPTWEKDMNLAEAMKLSAVPVYQELARRIGVDLMAQEVKRLNFGNAQIGTQVDNFWLVGPLKVTPVQEVEFVEQLAHKQLPFKPEVQETVQQMILLQEVKGNKIYAKSGWGMDLDPQVGWLTGWVEQPNGKKVAFSLNMEMKPKMSGSIRNEITLKALENLGVI"},"dna_sequence":{"accession":"ATGI01000038.1","fmin":"274631","fmax":"275453","strand":"-","sequence":"ATGAAAAAAAATCTGTTTGCGTGTTTAGTACTATCTACAGCATTAACTCAAGTTGCTTGCTCTACACTGCAAACAACCGCTGATCCTTCTACGCAAGCATCTACTGCGCAGCAGTCAATCAAAAGCTATTTTGATGAAGTGCAGACGAAGGGCGTCATCGTCATTAAACAAGATGGACAACTGCAAACTTATGGTAATGATTTAAGCCGAGCCAATACTGAGTATGTTCCCGCTTCTACATTTAAAATCCTTAATGCTTTAATTGGATTAGAAAACCATAAAGTTACGCTAAATGAGGTTTTTAAATGGGATGGTCAAAAGCGCTCTTTTCCAACTTGGGAGAAGGATATGAACTTGGCTGAAGCAATGAAACTTTCAGCGGTACCTGTTTATCAGGAGCTGGCAAGACGTATTGGTGTGGACTTAATGGCACAAGAAGTAAAACGCCTTAACTTTGGTAATGCGCAAATCGGTACGCAAGTAGACAACTTTTGGTTGGTTGGCCCTTTGAAAGTTACACCAGTACAAGAGGTAGAGTTTGTTGAGCAACTTGCTCATAAGCAGTTGCCATTTAAGCCTGAAGTACAAGAGACAGTACAGCAGATGATTTTATTGCAGGAAGTTAAAGGCAATAAAATTTATGCAAAAAGTGGTTGGGGCATGGACCTAGATCCACAAGTCGGCTGGCTAACAGGCTGGGTAGAACAGCCTAACGGTAAAAAAGTCGCTTTTTCATTAAATATGGAAATGAAACCAAAGATGTCTGGTTCAATTCGTAATGAAATCACTCTAAAAGCACTTGAAAATCTAGGAGTTATTTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41191","NCBI_taxonomy_name":"Acinetobacter rudis CIP 110305","NCBI_taxonomy_id":"421052"}}}},"ARO_accession":"3004478","ARO_id":"41738","ARO_name":"OXA-665","CARD_short_name":"OXA-665","ARO_description":"Beta-lactamase found in Acinetobacter rudis efficiently inactivating carbapenems and amoxicillin conferring resistance to cephalosporins.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3421":{"model_id":"3421","model_name":"OXA-157","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"540"}},"model_sequences":{"sequence":{"5616":{"protein_sequence":{"accession":"ALA99191.1","sequence":"MMMLSRWRRSAVVLRIAAALLSPLAVAIPAHADAIANAANAVAPKIVERADWGKYFDAEGAKGTIIVLDGRTGGYQAYDSTRANQRMSPASTYKIFNSLLALESGALDNEREIIPWDGKPRSMKRWNAAMNLRDAFRVSCLPCYQVVSRKIARTYAQGKLDAVGYGNHTIGSAADAYWVDNSLQISAREQVVFLQRLARGQLPFSARTQDIVRQISIAEANMDYVLHGKTGWYVDGKHDIGWWVGWIERDGNITTVALNMDMRSDADAPKRARIARAVLKDLKLI"},"dna_sequence":{"accession":"KP771985.1","fmin":"172","fmax":"1030","strand":"+","sequence":"ATGATGATGCTTTCTCGCTGGCGTCGTAGCGCCGTTGTGCTGCGAATCGCCGCTGCACTGTTATCCCCGTTGGCGGTTGCGATACCGGCGCATGCGGACGCTATTGCCAATGCCGCTAATGCCGTAGCGCCGAAAATCGTGGAGCGGGCCGACTGGGGCAAGTACTTCGACGCCGAAGGCGCGAAGGGCACGATCATCGTGCTCGACGGCCGCACCGGGGGCTATCAGGCCTATGACAGCACTCGCGCGAATCAGCGCATGTCGCCAGCTTCAACGTACAAGATATTCAACAGTTTGCTGGCGCTGGAGTCTGGCGCACTCGACAACGAGCGCGAAATCATTCCTTGGGATGGCAAGCCACGTAGCATGAAGCGCTGGAACGCAGCAATGAATCTGCGCGATGCGTTCCGGGTGTCGTGTCTGCCGTGCTATCAGGTTGTGTCGCGCAAGATTGCGCGGACCTATGCGCAGGGCAAGCTCGATGCGGTGGGCTATGGCAATCACACCATCGGGTCCGCAGCGGATGCGTATTGGGTCGACAACAGCCTGCAAATTTCAGCGCGTGAGCAGGTGGTGTTTCTGCAACGGCTGGCGCGCGGGCAGTTGCCGTTCTCGGCGCGCACGCAGGACATCGTGCGGCAGATTTCGATTGCCGAAGCGAACATGGACTACGTCCTGCACGGCAAGACCGGCTGGTATGTCGATGGCAAGCACGACATTGGCTGGTGGGTCGGTTGGATCGAACGGGACGGCAATATCACCACGGTTGCGCTGAACATGGACATGCGCAGCGACGCCGACGCGCCCAAGCGTGCCCGGATTGCCCGTGCGGTGTTGAAGGATCTGAAGTTGATCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42788","NCBI_taxonomy_name":"Pandoraea norimbergensis","NCBI_taxonomy_id":"93219"}}}},"ARO_accession":"3001462","ARO_id":"37862","ARO_name":"OXA-157","CARD_short_name":"OXA-157","ARO_description":"OXA-157 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46520":{"category_aro_accession":"3007731","category_aro_cvterm_id":"46520","category_aro_name":"OXA-62-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-62.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2912":{"model_id":"2912","model_name":"OXA-274","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4764":{"protein_sequence":{"accession":"EPH38243.1","sequence":"MSNNLFKFKIKSSVLIILSSVAFSGCVSNANLHDPASSQRTSEIPLLFNYAQTQAVFVTYDGTQFKRYGNDLNRAKTAYIPASTFKMLNALIGLQHAKATNTEVFKWNGEKRSFPAWEKDMTLAQAMQASAVPVYQELARRIGLDLMSQEVKRVGFGNTQIGQQVDNFWLVGPLKITPEQEAKFAYQLAKKTLPFDDAVQQQVKDMLYVERRGDSKLYAKSGWGMDVEPQVGWYTGWIEQPNGQITAFALNMHMQTGDDPAERKQLTLSILDKLGLFFYLR"},"dna_sequence":{"accession":"ASQG01000007.1","fmin":"15484","fmax":"16330","strand":"+","sequence":"ATGAGTAATAACCTATTTAAATTTAAAATAAAAAGCAGTGTATTGATCATTCTGAGTAGTGTGGCATTTTCAGGTTGTGTTTCTAATGCCAATTTGCATGATCCAGCTTCATCACAAAGAACAAGTGAAATTCCGTTGTTGTTTAATTATGCGCAAACTCAAGCCGTCTTTGTGACTTATGATGGAACTCAATTTAAACGCTATGGGAATGATTTAAATAGAGCCAAGACTGCGTATATTCCGGCCTCTACTTTTAAAATGTTGAATGCCTTAATTGGTTTGCAACATGCGAAAGCGACAAATACAGAAGTATTTAAGTGGAATGGTGAAAAAAGATCTTTTCCTGCTTGGGAAAAAGATATGACCTTGGCACAAGCAATGCAGGCTTCCGCCGTACCTGTATATCAGGAGTTGGCACGACGTATTGGTTTGGATTTGATGAGTCAAGAAGTCAAACGTGTTGGTTTTGGTAATACACAAATTGGTCAACAGGTGGATAATTTCTGGTTGGTTGGTCCATTGAAAATCACCCCAGAGCAAGAAGCTAAATTTGCTTATCAATTGGCAAAGAAAACATTGCCTTTTGATGATGCTGTACAACAGCAAGTCAAAGATATGCTTTATGTCGAAAGACGTGGTGATTCCAAGCTCTATGCCAAAAGTGGCTGGGGAATGGATGTTGAGCCACAAGTGGGTTGGTATACAGGATGGATAGAACAGCCGAATGGTCAGATCACTGCTTTTGCTTTAAATATGCACATGCAGACAGGGGATGATCCTGCTGAACGTAAGCAACTGACATTAAGTATCTTAGATAAATTAGGCTTATTCTTTTATTTGAGATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41741","NCBI_taxonomy_name":"Acinetobacter guillouiae MSP4-18","NCBI_taxonomy_id":"1330038"}}}},"ARO_accession":"3001730","ARO_id":"38130","ARO_name":"OXA-274","CARD_short_name":"OXA-274","ARO_description":"OXA-274 is a beta-lactamase found in Acinetobacter spp.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46502":{"category_aro_accession":"3007713","category_aro_cvterm_id":"46502","category_aro_name":"OXA-274-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-274.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2913":{"model_id":"2913","model_name":"OXA-286","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"5902":{"protein_sequence":{"accession":"ENU21708.1","sequence":"MIMSKKLTCLALFTAIFFAIPMAACQSFSQQKQQLSTQKNEQQQISSLFQSAQTSGVLVIYDGKKIQSYGNDLDRAEQRYIPASTFKMLNALIGIQHHKTTPDEVFKWDGKKRAFSSWEKDLTLAEAMQASAVPVYQELARRIGLELMTREVKRVGYGNKNIGTQVDNFWLVGPLKITPVEEVRFAYALAKQKLPFDQPTQQQVKAMLLVDQIQGTKIYAKSGWGMDVSPQVGWWTGWIEQPNGKITAFSLNMQMSQPEHADARKAIVYQALQQLGLLAH"},"dna_sequence":{"accession":"APOI01000030.1","fmin":"189485","fmax":"190328","strand":"+","sequence":"ATGATCATGTCGAAAAAATTAACATGTCTGGCCCTGTTTACAGCCATCTTTTTTGCGATTCCCATGGCCGCTTGTCAAAGTTTTAGTCAACAAAAGCAACAGCTTTCGACACAGAAAAATGAACAGCAACAGATTTCAAGCTTATTTCAGAGTGCCCAAACCAGTGGTGTTTTGGTGATTTATGATGGCAAGAAAATTCAAAGCTATGGCAATGATCTTGATCGTGCAGAACAGCGCTATATTCCTGCCTCAACCTTTAAAATGCTAAATGCCTTGATTGGTATACAACATCATAAGACCACACCAGATGAAGTGTTTAAATGGGATGGCAAAAAGCGGGCATTCAGCAGTTGGGAAAAAGATTTAACCTTAGCTGAAGCGATGCAGGCATCGGCGGTACCTGTGTATCAGGAACTAGCAAGACGTATTGGCTTGGAGTTAATGACCCGTGAAGTGAAGCGTGTGGGTTATGGCAATAAAAATATTGGGACACAAGTTGATAATTTCTGGTTAGTTGGCCCATTAAAAATCACCCCCGTAGAAGAAGTTCGCTTTGCCTATGCGTTGGCAAAACAGAAATTGCCATTTGACCAGCCAACACAGCAACAAGTCAAAGCGATGTTATTGGTGGATCAGATTCAGGGAACTAAAATCTATGCAAAAAGTGGTTGGGGCATGGATGTTAGCCCGCAAGTGGGATGGTGGACAGGCTGGATTGAACAGCCAAATGGTAAGATCACAGCCTTCTCACTGAATATGCAAATGAGCCAGCCTGAGCATGCAGATGCACGTAAAGCGATTGTGTATCAAGCCTTGCAACAGTTGGGATTGTTAGCCCATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42970","NCBI_taxonomy_name":"Acinetobacter proteolyticus","NCBI_taxonomy_id":"1217713"}}}},"ARO_accession":"3001741","ARO_id":"38141","ARO_name":"OXA-286","CARD_short_name":"OXA-286","ARO_description":"OXA-286 is a beta-lactamase found in Acinetobacter spp.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46503":{"category_aro_accession":"3007714","category_aro_cvterm_id":"46503","category_aro_name":"OXA-286-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-286.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3443":{"model_id":"3443","model_name":"OXA-277","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"510"}},"model_sequences":{"sequence":{"5639":{"protein_sequence":{"accession":"ENV45890.1","sequence":"MKILILWPLLSCLSLTACSFAVSNSPSQITSTQSIQATAKLFDQAQSSGVLVIQRGPHLQVYGNDLSRAHTEYVPASTFKMFNALIGLQHGKATTNEIFKWDGKKRSFAAWEKDMTLGQAMQASAVPVYQELARRIGLELMQQEVQRIQFGNQQIGHQVDNFWLVGPLKITPKQEVEFASALAQEQLAFDPRVQQQVKTMLLLQERQAYRLYAKSGWGMDVEPQVGWLTGWIETPQDEIVVFSLNMQMQSNMDPAIRLKILQQALAELGLYPKAEA"},"dna_sequence":{"accession":"APPQ01000011.1","fmin":"9160","fmax":"9991","strand":"+","sequence":"ATGAAAATTCTTATTTTGTGGCCTTTACTCAGTTGCTTGAGCCTGACAGCTTGTAGCTTCGCTGTTTCAAATTCGCCCTCTCAAATCACTTCAACTCAATCTATTCAAGCTACTGCAAAGTTATTTGATCAGGCACAAAGCTCTGGCGTTTTAGTAATTCAACGGGGTCCACATCTACAGGTCTATGGCAATGATTTGAGTCGTGCACATACCGAATATGTTCCTGCTTCAACCTTTAAAATGTTTAATGCTCTGATTGGCCTGCAACATGGTAAAGCCACGACCAATGAAATTTTTAAATGGGATGGCAAGAAGCGCAGTTTTGCAGCCTGGGAAAAAGACATGACTCTCGGCCAAGCCATGCAAGCTTCTGCTGTACCCGTCTATCAGGAACTGGCACGTCGCATTGGTCTGGAACTAATGCAACAGGAAGTGCAACGTATTCAATTTGGTAATCAGCAGATTGGTCATCAGGTCGACAACTTCTGGTTAGTCGGACCTTTGAAAATCACCCCGAAACAAGAAGTCGAATTTGCCTCTGCGCTTGCTCAAGAGCAGCTTGCCTTTGATCCTCGGGTTCAGCAGCAAGTTAAAACCATGTTACTGTTACAGGAGCGACAAGCTTATCGGCTTTATGCTAAATCCGGTTGGGGTATGGATGTGGAGCCGCAAGTCGGCTGGCTCACCGGCTGGATTGAAACACCTCAGGACGAAATCGTGGTATTTTCACTGAATATGCAGATGCAAAGTAATATGGATCCGGCGATCCGTCTTAAAATTTTGCAGCAGGCCTTGGCTGAATTAGGGCTTTATCCGAAAGCTGAAGCGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42806","NCBI_taxonomy_name":"Acinetobacter schindleri CIP 107287","NCBI_taxonomy_id":"1217988"}}}},"ARO_accession":"3001733","ARO_id":"38133","ARO_name":"OXA-277","CARD_short_name":"OXA-277","ARO_description":"OXA-277 is a beta-lactamase found in Acinetobacter spp.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46489":{"category_aro_accession":"3007700","category_aro_cvterm_id":"46489","category_aro_name":"OXA-134-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-134.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3472":{"model_id":"3472","model_name":"OXA-337","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"5666":{"protein_sequence":{"accession":"RIL13772.1","sequence":"MNITALLLITSAIFISACSPYIVTANPNHSASKSDDKAEKIKNLFNEAHTTGVLVIHQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWNGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"PYSX01000023.1","fmin":"160178","fmax":"161003","strand":"+","sequence":"ATGAACATTACAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGACAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCATCAAGGTCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGAACGGGCAAAAAAGGCTGTTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCATTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001525","ARO_id":"37925","ARO_name":"OXA-337","CARD_short_name":"OXA-337","ARO_description":"OXA-337 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2960":{"model_id":"2960","model_name":"OXA-663","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"5348":{"protein_sequence":{"accession":"OWG16436.1","sequence":"MKTFAAYVIIACLSSKALAGSITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGIIGG"},"dna_sequence":{"accession":"JCMW02000002.1","fmin":"55721","fmax":"56522","strand":"-","sequence":"ATGAAAACATTTGCCGCATATGTAATTATCGCGTGTCTTTCGAGTAAGGCATTAGCTGGTTCAATTACAGAAAATACGTCTTGGAACAAAGAGTTCTCTGCCGAAGCCGTCAATGGTGTCTTCGTGCTTTGTAAAAGTAGCAGTAAATCCTGCGCTACCAATGACTTAGCTCGTGCATCAAAGGAATATCTTCCAGCATCAACATTTAAGATCCCCAACGCAATTATCGGCCTAGAAACTGGTGTCATAAAGAATGAGCATCAGGTTTTCAAATGGGACGGAAAGCCAAGAGCCATGAAGCAATGGGAAAGAGACTTGACCTTAAGAGGGGCAATACAAGTTTCAGCTGTTCCCGTATTTCAACAAATCGCCAGAGAAGTTGGCGAAGTAAGAATGCAGAAATACCTTAAAAAATTTTCCTATGGCAACCAGAATATCAGTGGTGGCATTGACAAATTCTGGTTGGAAGGCCAGCTTAGAATTTCCGCAGTTAATCAAGTGGAGTTTCTAGAGTCTCTATATTTAAATAAATTGTCAGCATCTAAAGAAAACCAGCTAATAGTAAAAGAGGCTTTGGTAACGGAGGCGGCACCTGAATATCTAGTGCATTCAAAAACTGGTTTTTCTGGTGTGGGAACTGAGTCAAATCCTGGTGTCGCATGGTGGGTTGGGTGGGTTGAGAAGGAGACAGAGGTTTACTTTTTCGCCTTTAACATGGATATAGACAACGAAAGTAAGTTGCCGCTAAGAAAATCCATTCCCACCAAAATCATGGAAAGTGAGGGCATCATTGGTGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42609","NCBI_taxonomy_name":"Klebsiella pneumoniae BIDMC 35","NCBI_taxonomy_id":"1328424"}}}},"ARO_accession":"3004489","ARO_id":"41930","ARO_name":"OXA-663","CARD_short_name":"OXA-663","ARO_description":"An OXA-10 family class beta-lactamase identified from a Klebsiella pneumoniae BIDMC 35 isolate.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46486":{"category_aro_accession":"3007697","category_aro_cvterm_id":"46486","category_aro_name":"OXA-10-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-10.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3501":{"model_id":"3501","model_name":"OXA-427","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"5696":{"protein_sequence":{"accession":"ARO85965.1","sequence":"MSRILLSSLLAAGLFCSLPASAATGCMLFADGSGKPFSAQGDCASQLPPASTFKIPLALMGYDSGFLVDEQLPALPFKAGDPDFLPEWKQTTTPSRWMTYSVIWYSQRLTEWLGAARFQQYVDRFDYGNRDLSGNPGKHDGLTQAWLSSSLAISPQEQARFLGKLVSGKLPVSAQTLQHTANILRQPDIDGWQIHGKTGTGYPKLLDGSLDRDQQIGWFVGWASKQDQKLIFVHTVIQKPGKQFASLRAREEVFAALPEQLKKL"},"dna_sequence":{"accession":"KX827604.1","fmin":"0","fmax":"795","strand":"+","sequence":"ATGTCCCGCATTCTGTTATCCAGCCTGCTTGCCGCCGGCCTCTTCTGCTCCCTGCCCGCCAGCGCCGCCACCGGCTGCATGCTGTTTGCCGATGGTAGCGGCAAGCCCTTCAGTGCCCAGGGTGACTGCGCCAGCCAGCTGCCTCCCGCCTCCACCTTCAAGATCCCGCTGGCGCTGATGGGCTATGACAGCGGCTTCCTGGTGGATGAGCAACTGCCAGCTCTGCCATTCAAAGCCGGTGACCCTGACTTCCTGCCGGAATGGAAACAGACCACCACCCCGAGCCGTTGGATGACCTATTCGGTGATCTGGTACTCCCAACGCCTCACCGAGTGGCTGGGGGCGGCGCGCTTCCAGCAATACGTGGACCGCTTCGACTACGGCAACCGGGATCTCTCGGGCAACCCGGGCAAACATGACGGCCTGACCCAAGCCTGGCTCAGTTCCAGCCTTGCCATCAGCCCCCAGGAGCAGGCACGCTTTCTCGGCAAACTGGTGAGCGGCAAGCTGCCGGTCTCCGCCCAGACGCTGCAGCACACGGCCAATATCCTGCGTCAGCCCGACATCGATGGCTGGCAGATCCATGGCAAGACCGGCACGGGCTATCCCAAACTGCTGGATGGCAGCCTCGACCGGGATCAGCAGATCGGCTGGTTCGTCGGCTGGGCCAGCAAGCAGGATCAGAAGCTCATCTTCGTCCACACCGTCATCCAGAAGCCTGGCAAGCAGTTTGCCTCCCTCAGGGCCAGGGAAGAGGTGTTTGCCGCACTGCCCGAACAGCTGAAGAAACTGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3003115","ARO_id":"39692","ARO_name":"OXA-427","CARD_short_name":"OXA-427","ARO_description":"OXA-427 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46508":{"category_aro_accession":"3007719","category_aro_cvterm_id":"46508","category_aro_name":"OXA-427-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-427.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3531":{"model_id":"3531","model_name":"OXA-466","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"5726":{"protein_sequence":{"accession":"AKI29913.1","sequence":"MKKILLLFSLFYSFALANDKLKDFFKDYNTSGVFITFDGKHYASNNFKRAKEPFSPASTFKIFNALIALDNGVVKDTKEIFYHYKGEKVFLPSWKQDASLRSAIKRSQVPAFKELARKIGLKTMQESLNKLSYGNTKISKIDTFWLDNSLQISAKNQADLLFKLSQNSLPFSKKSQEEVKKIILFKEDKIQKIYAKTGFNDGINLAWIVGFIESKNKILSFALNVDIKNIKNLKIREELLEKYIYSLN"},"dna_sequence":{"accession":"KR061501.1","fmin":"0","fmax":"747","strand":"+","sequence":"TTGAAAAAAATACTTTTACTTTTTAGTCTTTTTTACTCTTTTGCTTTGGCAAATGATAAATTAAAAGATTTTTTTAAAGACTACAATACAAGCGGAGTTTTTATAACTTTTGATGGAAAACATTATGCAAGTAATAATTTTAAAAGAGCTAAAGAACCTTTTTCTCCTGCTTCGACTTTTAAAATTTTTAATGCTTTAATTGCGCTTGATAATGGTGTAGTTAAAGATACAAAGGAAATTTTTTATCATTATAAGGGTGAAAAAGTATTTTTGCCCTCTTGGAAACAAGATGCTAGTTTAAGATCAGCCATAAAACGCTCTCAAGTGCCTGCTTTTAAAGAATTGGCAAGAAAAATAGGACTTAAAACCATGCAAGAAAGCTTAAATAAACTTTCCTATGGAAATACAAAAATTTCAAAAATCGATACCTTTTGGTTGGATAATTCTTTACAAATTTCTGCAAAAAATCAAGCTGATTTGCTTTTTAAACTTTCACAAAATTCTTTACCTTTTTCCAAGAAAAGTCAAGAAGAAGTTAAAAAAATTATTCTTTTTAAAGAAGATAAAATCCAAAAAATTTATGCTAAAACAGGTTTTAATGATGGTATAAATTTGGCTTGGATTGTTGGATTTATAGAGAGTAAAAACAAAATTTTATCTTTTGCCTTAAATGTTGATATAAAGAACATTAAAAATCTTAAAATAAGAGAAGAATTGCTAGAAAAATATATTTATTCTTTAAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36772","NCBI_taxonomy_name":"Campylobacter jejuni","NCBI_taxonomy_id":"197"}}}},"ARO_accession":"3003622","ARO_id":"40232","ARO_name":"OXA-466","CARD_short_name":"OXA-466","ARO_description":"OXA-466 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46491":{"category_aro_accession":"3007702","category_aro_cvterm_id":"46491","category_aro_name":"OXA-184-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-184.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3422":{"model_id":"3422","model_name":"OXA-158","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"5617":{"protein_sequence":{"accession":"ALA99192.1","sequence":"MKKTLSRWRRGALALRLLGALASPVVFAMPGHAAEPAHSSAVRIAERADWGKYFADEGVKGTVIVLDGRTQTYQAYDAARAERRMSPASTYKIFNSLLALESGALDNEREVIPWDGKPRRVKAWNAALDLRNAFRVSCLPCYQVVSHKIPRQYAQAKLNEAGYGNRTIGRAAHAYWIDDSLQISAREQVDFLQRLATGTLPFSARSQDIVRNISIVEANVDYVLHGKTGWFTEKKPDIGWWVGWLERDGNLTMIALNIDIQTDADAPKRARIVRNVLKDLKLI"},"dna_sequence":{"accession":"KP771986.1","fmin":"1028","fmax":"1880","strand":"+","sequence":"ATGAAAAAGACACTCTCTCGCTGGCGGCGCGGCGCGCTCGCGCTGCGCCTCCTCGGTGCGCTGGCCTCGCCCGTGGTCTTCGCAATGCCCGGACACGCCGCCGAACCCGCGCATTCTTCCGCGGTGCGCATCGCCGAGCGGGCCGACTGGGGCAAGTACTTTGCCGACGAAGGCGTCAAGGGCACGGTCATCGTGCTGGACGGCCGGACCCAGACCTATCAGGCTTACGATGCCGCACGCGCCGAGCGCCGCATGTCGCCCGCATCGACCTACAAGATATTCAACAGCCTGCTCGCGCTGGAGTCCGGCGCGCTCGACAACGAGCGCGAGGTCATCCCGTGGGACGGCAAGCCGCGTCGCGTCAAGGCGTGGAACGCCGCGCTCGATCTGCGCAACGCGTTTCGCGTGTCGTGCCTGCCTTGCTATCAGGTCGTCTCGCACAAGATCCCGCGCCAGTACGCGCAGGCCAAGCTCAACGAGGCGGGCTACGGCAATCGCACGATCGGCCGCGCCGCGCACGCCTACTGGATCGACGACAGCCTGCAGATTTCGGCGCGCGAGCAAGTCGACTTCCTGCAGCGTCTGGCCACGGGCACGCTGCCGTTCTCGGCGCGCTCGCAGGACATCGTGCGCAACATATCGATCGTCGAAGCGAACGTCGACTACGTGCTGCACGGCAAGACGGGCTGGTTTACCGAAAAGAAACCCGACATCGGGTGGTGGGTCGGCTGGCTCGAGCGTGACGGCAACCTCACCATGATCGCGTTGAACATCGACATTCAAACCGATGCCGACGCGCCAAAGCGCGCGCGCATCGTTCGCAACGTGCTCAAGGATCTGAAGCTGATCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42789","NCBI_taxonomy_name":"Pandoraea sp. Va8523","NCBI_taxonomy_id":"1705920"}}}},"ARO_accession":"3001463","ARO_id":"37863","ARO_name":"OXA-158","CARD_short_name":"OXA-158","ARO_description":"OXA-158 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46520":{"category_aro_accession":"3007731","category_aro_cvterm_id":"46520","category_aro_name":"OXA-62-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-62.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3654":{"model_id":"3654","model_name":"Neisseria gonorrhoeae gyrB conferring resistance to zoliflodacin","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1600"},"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"12582":"K450N","12583":"K450T","12584":"D429N"},"Curated-R":{"12582":"K450N","12583":"K450T","12584":"D429N"},"clinical":{"12582":"K450N","12583":"K450T","12584":"D429N"}}},"model_sequences":{"sequence":{"8367":{"protein_sequence":{"accession":"CNT74515.1","sequence":"MTEQKHEEYGADSIQVLEGLEAVRKRPGMYIGDTQDGSGLHHMVFEVLDNAIDEALAGHCDKITVTIHADHSVSVADNGRGMPTGIHPKEGRSAAEVIMTVLHAGGKFDNNSYKISGGLHGVGVSVVNALSDWVTLTIYRDGKEHFVRFVRGETEEPLKIVGDSDKKGTTVRFLAGTETFGNIEYSFDILAKRIRELSFLNNGVDIELTDERDGKHESFALSGGVAGFVQYMNRKKTPLHEKIFYAFGEKDGMSVECAMQWNDSYQESVQCFTNNIPQRDGGTHLTALRQVMTRTINSYIEANEVAKKAKVETAGDDMREGLTCVLSVKLPDPKFSSQTKDKLVSGEIGPVVNEVINQALTDFLEENPNEAKIITGKIVDAARAREAARKAREIPRRKGVMDGLGLPGKLADCQEKDPALSELYLVEGDSAGGSAMQGRDRKFQAILPLKGKILNVEKARFEKMLASQEVATLITALGAGIGKEEFNPEKLRYHRIIIMTDADVDGAHIRTLLLTFFYRQMPELVERGYIYIAQPPLYKAKYGKQERYLKDELEKDQWLLGLALEKAKIVSDGRTIEGAELADTAKQFLLAKTVIEQESRFVDELVLRAMLHASPIDLTSSENADKAVAELSGLLDEKEAALERIEGHEGHQFIKITRKLHGNVMVSYIEPKFLNSKAYQTLTQTAAALKGLVGEGAKLYKGENEYDADSFETALDILMSVAQKGMSIQRYKGLGEMNPEQLWETTMDPTVRRLLKVRIEDAIAADEVFVTLMGDEVEPRRAFIENNALIAQNIDA"},"dna_sequence":{"accession":"CQOZ01000008.1","fmin":"45893","fmax":"48284","strand":"-","sequence":"ATGACTGAACAAAAACACGAAGAATACGGCGCCGACAGCATCCAGGTGCTCGAAGGCTTGGAAGCGGTACGCAAACGCCCCGGCATGTACATCGGCGACACGCAGGACGGCAGCGGGCTGCACCATATGGTGTTTGAAGTATTGGACAACGCCATCGACGAAGCACTCGCCGGACATTGCGACAAAATCACGGTAACGATACACGCCGACCATTCCGTCAGCGTCGCCGACAACGGGCGCGGTATGCCCACCGGCATCCACCCGAAAGAAGGGCGTTCCGCCGCCGAAGTCATCATGACCGTCTTGCACGCGGGCGGCAAATTCGACAACAACAGCTACAAAATCTCCGGCGGCCTGCACGGCGTGGGCGTATCCGTCGTCAACGCGCTGTCCGACTGGGTAACGCTGACCATCTACCGCGACGGCAAAGAACACTTCGTCCGCTTCGTACGCGGCGAAACCGAAGAGCCGCTGAAAATTGTCGGCGATTCCGACAAAAAAGGCACGACCGTGCGCTTCCTCGCCGGCACGGAAACCTTCGGCAATATCGAATACAGCTTCGACATCCTCGCCAAACGTATTCGCGAACTTTCGTTCCTAAACAACGGCGTGGACATCGAATTGACCGACGAGCGCGACGGCAAGCACGAAAGCTTCGCCCTTTCCGGCGGCGTGGCGGGCTTCGTGCAATACATGAACCGCAAAAAAACGCCCTTGCACGAAAAAATCTTCTATGCGTTCGGCGAGAAAGACGGCATGAGCGTCGAATGCGCAATGCAATGGAACGACAGCTATCAGGAAAGCGTGCAGTGCTTCACCAACAACATCCCTCAGCGCGACGGCGGTACGCACCTGACCGCGCTGCGCCAAGTGATGACGCGCACCATCAACAGCTACATCGAAGCTAACGAAGTCGCCAAAAAAGCCAAAGTGGAAACCGCCGGCGACGATATGCGCGAAGGTTTGACCTGCGTGTTGTCCGTCAAACTGCCCGACCCCAAATTCTCATCCCAAACCAAAGACAAACTGGTTTCCGGCGAAATCGGCCCCGTTGTCAACGAAGTCATCAACCAAGCACTAACCGACTTCCTCGAAGAAAATCCGAACGAAGCCAAAATCATCACCGGCAAAATCGTCGATGCCGCCCGCGCACGCGAAGCCGCCCGCAAAGCCCGCGAAATCCCCCGCCGCAAAGGCGTGATGGACGGCTTGGGACTGCCCGGCAAACTCGCCGACTGCCAAGAAAAAGACCCTGCCCTGTCTGAACTCTACCTCGTCGAGGGCGACTCCGCAGGCGGTTCCGCCATGCAGGGCCGCGACCGCAAATTCCAAGCGATTTTGCCGCTCAAAGGTAAAATTTTGAACGTCGAAAAAGCACGTTTTGAAAAAATGCTCGCCAGCCAAGAGGTCGCCACCCTGATTACCGCGCTGGGTGCAGGCATCGGCAAAGAAGAGTTCAACCCTGAAAAACTACGCTACCACCGCATCATCATCATGACCGATGCCGACGTGGACGGTGCGCACATCCGCACCCTGCTCCTGACCTTCTTCTACCGCCAAATGCCCGAACTGGTCGAGCGCGGCTACATTTACATCGCCCAGCCGCCGCTCTACAAAGCCAAATACGGCAAGCAGGAGCGTTACCTCAAAGACGAACTGGAAAAAGACCAATGGCTGCTCGGCCTTGCCTTGGAAAAAGCCAAAATCGTTTCAGACGGCCGCACCATCGAAGGCGCAGAACTTGCCGACACCGCCAAACAATTCTTGTTGGCGAAAACCGTCATCGAACAGGAAAGCCGCTTCGTGGACGAACTCGTCCTGCGTGCCATGCTGCACGCGTCGCCCATTGATTTGACGTCGTCTGAAAACGCCGATAAAGCCGTTGCCGAACTTTCCGGTTTGCTTGACGAAAAAGAAGCCGCCCTCGAACGCATCGAAGGTCATGAAGGACACCAGTTCATCAAAATCACGCGCAAGCTGCACGGCAACGTCATGGTCAGCTACATCGAACCCAAGTTCCTCAACAGCAAAGCCTACCAAACCCTCACCCAAACCGCCGCCGCGCTCAAAGGCTTGGTCGGCGAGGGCGCCAAGCTCTACAAAGGCGAGAACGAGTACGACGCGGACAGCTTTGAAACCGCTTTGGACATCTTGATGAGCGTTGCCCAAAAAGGTATGTCCATCCAACGATACAAAGGTTTGGGCGAGATGAACCCCGAGCAGCTTTGGGAAACCACGATGGATCCCACCGTGCGCCGCCTGTTGAAAGTGCGCATCGAAGATGCCATTGCCGCCGACGAAGTGTTCGTTACCCTGATGGGCGACGAGGTCGAACCGCGCCGCGCCTTTATCGAAAACAATGCGCTGATTGCGCAAAATATCGACGCATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36806","NCBI_taxonomy_name":"Neisseria gonorrhoeae","NCBI_taxonomy_id":"485"}}}},"ARO_accession":"3004859","ARO_id":"42995","ARO_name":"Neisseria gonorrhoeae gyrB conferring resistance to zoliflodacin","CARD_short_name":"Ngon_gyrB_ZOL","ARO_description":"Point mutation in Neisseria gonorrhoea gyrase B decreases affinity to zoliflodacin antibiotic.","ARO_category":{"43187":{"category_aro_accession":"3005000","category_aro_cvterm_id":"43187","category_aro_name":"Zoliflodacin resistant gyrB","category_aro_description":"Point mutations in DNA gyrase subunit B (gyrB) of Neisseria gonorrhoeae can result in resistance to Zoliflodacin.","category_aro_class_name":"AMR Gene Family"},"42994":{"category_aro_accession":"3004858","category_aro_cvterm_id":"42994","category_aro_name":"Zoliflodacin","category_aro_description":"Experimental antibiotic in phase two trial for Neisseria gonorrhoeae treatment.","category_aro_class_name":"Antibiotic"},"45742":{"category_aro_accession":"3007160","category_aro_cvterm_id":"45742","category_aro_name":"zoliflodacin-like antibiotic","category_aro_description":"A group of antibiotics including the experimental compound zoliflodacin and its derivatives.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3444":{"model_id":"3444","model_name":"OXA-279","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"540"}},"model_sequences":{"sequence":{"5640":{"protein_sequence":{"accession":"ENU35234.1","sequence":"MPKILKHLGLCASVMIGLTLLGCQNLQAPTQSAVSKKHDQTEIASLFQHAQTVGVFVTYDGQTLQEYGNALSRSNTAYIPASTFKMLNALIGIQHHKSSPNEVFKWDGKKRAFASWEKDLTLAEAMQASAVPVYQELARRIGLELMANEVKRVGFGNAEIGTQVDDFWLVGPLKITPVEEVKFAYALAHKQLTFDQSVQEQVKQMVLVDEVKGTKIYAKSGWGMDVTPQVGWWTGWIEQPNGQVIAFSLNMQINNSKQGDARKAIVYQALQQLKLLETQ"},"dna_sequence":{"accession":"APOM01000058.1","fmin":"54862","fmax":"55702","strand":"-","sequence":"ATGCCAAAAATACTAAAACATCTTGGCCTTTGCGCATCTGTAATGATTGGACTGACGTTGCTAGGTTGCCAAAATTTGCAGGCCCCAACTCAAAGCGCCGTGTCAAAAAAACACGACCAAACCGAGATCGCTTCTTTATTCCAACATGCTCAAACTGTTGGCGTATTTGTTACATATGATGGGCAAACACTTCAAGAATATGGCAATGCGCTGAGTCGATCGAATACAGCTTATATTCCAGCCTCAACTTTCAAGATGTTAAATGCTCTGATTGGGATACAGCATCACAAAAGTTCGCCAAACGAAGTGTTTAAATGGGATGGCAAAAAGCGTGCTTTTGCGAGCTGGGAAAAAGATTTAACCTTAGCTGAGGCGATGCAGGCATCGGCAGTGCCTGTTTATCAAGAATTGGCTCGACGTATTGGTTTAGAGCTGATGGCGAACGAAGTGAAGCGAGTGGGCTTTGGCAATGCTGAGATCGGAACGCAAGTCGATGATTTTTGGTTGGTTGGTCCACTGAAGATTACCCCCGTTGAAGAAGTCAAATTTGCTTATGCTTTGGCTCATAAGCAGCTTACATTTGATCAATCTGTGCAGGAACAAGTGAAACAGATGGTTTTGGTTGATGAAGTTAAAGGAACCAAAATTTATGCCAAAAGTGGTTGGGGTATGGATGTAACGCCCCAAGTAGGTTGGTGGACAGGCTGGATTGAGCAACCGAATGGGCAGGTGATTGCATTTTCTTTAAATATGCAAATAAATAATTCTAAGCAGGGCGATGCGCGTAAAGCGATTGTTTATCAGGCATTACAACAATTGAAATTGTTAGAGACGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41200","NCBI_taxonomy_name":"Acinetobacter parvus DSM 16617 = CIP 108168","NCBI_taxonomy_id":"981333"}}}},"ARO_accession":"3001734","ARO_id":"38134","ARO_name":"OXA-279","CARD_short_name":"OXA-279","ARO_description":"OXA-279 is a beta-lactamase found in Acinetobacter spp.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3473":{"model_id":"3473","model_name":"OXA-339","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"5667":{"protein_sequence":{"accession":"AHN07456.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDDKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWNGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"KF048911.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGACAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTAATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGAACGGGCAAAAAAGGCTGTTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTTATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001527","ARO_id":"37927","ARO_name":"OXA-339","CARD_short_name":"OXA-339","ARO_description":"OXA-339 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3502":{"model_id":"3502","model_name":"OXA-429","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"5697":{"protein_sequence":{"accession":"AJG01375.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDKKAEKIKNLFNEAHTTGVLVIQQDQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLELLGIL"},"dna_sequence":{"accession":"KM979376.1","fmin":"20","fmax":"845","strand":"+","sequence":"ATGAATATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATAAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGACCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGACGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACGCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCCTTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGCATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACTATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3003120","ARO_id":"39697","ARO_name":"OXA-429","CARD_short_name":"OXA-429","ARO_description":"OXA-429 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3532":{"model_id":"3532","model_name":"OXA-470","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"520"}},"model_sequences":{"sequence":{"5727":{"protein_sequence":{"accession":"ALC79285.1","sequence":"MSKKNFILIFIFVILISCKNTEKISNETTLIDNIFTNSNAEGTLVIYNLNDDKYIIHNKERAEQRFYPASTFKIYNSLIGLNEKAVKDVDEVFYKYNGEKVFLESWAKDSNLRYAIKNSQVPAYKELARRIGLKKMKENIEKLDFGNKSIGDSVDTFWLEGPLEISAMEQIKLLTKLAQNELPYPIEIQKAVSDITILEQTYNYTLHGKTGLADSKNMTTEPIGWFVGWLEENDNIYVFALNIDNINSDDLAKRINIEKESLKALNLLK"},"dna_sequence":{"accession":"KR182163.1","fmin":"0","fmax":"810","strand":"+","sequence":"ATGTCTAAAAAAAATTTTATATTAATATTTATTTTTGTTATTTTAATATCTTGTAAAAATACAGAAAAAATATCAAATGAAACTACATTAATAGATAATATATTTACTAATAGCAATGCTGAAGGAACATTAGTTATATATAATTTAAATGATGATAAATATATAATTCATAATAAAGAAAGAGCTGAACAAAGATTTTATCCAGCATCAACATTTAAAATATATAATAGTTTAATAGGCTTAAATGAAAAAGCAGTTAAAGATGTAGATGAAGTATTTTATAAATATAATGGCGAAAAAGTTTTTCTTGAATCTTGGGCTAAGGACTCTAATTTAAGATATGCAATTAAAAATTCGCAAGTACCGGCATATAAAGAATTAGCAAGAAGAATAGGTCTTAAAAAGATGAAAGAGAATATAGAAAAACTAGATTTTGGTAATAAAAGTATAGGTGATAGTGTAGATACTTTTTGGCTTGAAGGACCTTTGGAAATAAGTGCGATGGAGCAAATTAAATTATTAACTAAATTAGCTCAAAATGAATTACCGTATCCTATAGAAATACAAAAAGCTGTTTCTGATATTACTATACTAGAGCAAACTTACAATTATACGCTTCATGGAAAAACTGGATTAGCTGATTCTAAAAACATGACAACTGAGCCTATTGGTTGGTTCGTAGGCTGGCTTGAAGAAAATGATAATATATATGTCTTTGCTTTAAATATTGATAATATAAATTCAGATGACCTTGCAAAAAGGATAAATATAGAAAAAGAAAGTTTAAAAGCATTAAATTTATTAAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36935","NCBI_taxonomy_name":"Brachyspira pilosicoli","NCBI_taxonomy_id":"52584"}}}},"ARO_accession":"3003626","ARO_id":"40236","ARO_name":"OXA-470","CARD_short_name":"OXA-470","ARO_description":"OXA-470 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46521":{"category_aro_accession":"3007732","category_aro_cvterm_id":"46521","category_aro_name":"OXA-63-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-63.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3574":{"model_id":"3574","model_name":"CKO-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"5770":{"protein_sequence":{"accession":"AAL85333.1","sequence":"MRNEEVISMWQRMKWGLCVLAALSGSAMAAPLTAQYVSAIAMQEEQRLHARIGIAVLDTATNSITHYRGEERFPLNSTHKPLLCAALLREVDRKALALSASMQFEPSQLVEYSPITEKHVAPDAMSWAQLCSAAVSYSDNTAANLIARKLNGPQAVTQFLRDSGDTITRLDRYEPELNSAIPGDERDSTTPVAIAQTLNTLLLGNVLQPSSREQLMQWMRDDKVADGLLRSVLPDGWKIADKTGAGDNGSRSIVSVVWPTSQKPLLVVIYITQTPATMAQRDAAIVRIGESLFSTLAVYD"},"dna_sequence":{"accession":"AF477396.1","fmin":"0","fmax":"903","strand":"+","sequence":"ATGAGAAACGAGGAAGTCATTAGTATGTGGCAACGGATGAAATGGGGTCTGTGTGTGCTGGCGGCACTCAGCGGTTCTGCGATGGCCGCACCGCTGACGGCGCAATACGTGTCGGCTATCGCGATGCAGGAAGAACAGCGTCTTCATGCCCGGATTGGCATTGCGGTACTTGATACGGCGACCAACAGTATCACCCATTATCGGGGAGAAGAACGGTTCCCGTTAAACAGTACGCACAAGCCGCTGTTATGCGCAGCGTTATTACGCGAAGTCGACAGGAAGGCGCTGGCGCTTTCTGCTTCAATGCAGTTTGAACCCTCACAACTGGTGGAGTATTCGCCGATTACTGAAAAACATGTGGCGCCAGACGCCATGAGCTGGGCGCAATTGTGCAGCGCGGCGGTAAGCTACAGCGATAACACGGCCGCCAATCTCATCGCCAGGAAGCTCAACGGGCCGCAGGCCGTCACGCAGTTTTTGCGTGATTCGGGGGATACGATAACCCGCCTCGATCGCTATGAGCCCGAACTGAACAGCGCCATTCCCGGTGATGAACGCGACTCCACGACGCCTGTCGCGATAGCGCAGACGCTCAATACGCTACTGCTGGGGAACGTGTTGCAGCCATCCTCAAGAGAGCAGCTTATGCAATGGATGCGGGACGACAAAGTGGCCGACGGTCTGCTGCGTTCGGTCTTGCCGGACGGCTGGAAAATCGCGGATAAAACCGGGGCGGGCGACAACGGCTCGCGTTCTATTGTCAGCGTTGTCTGGCCGACATCACAAAAACCTTTGCTCGTGGTTATCTATATTACACAAACTCCGGCGACAATGGCGCAGCGTGACGCCGCGATTGTCCGTATCGGGGAGTCGCTGTTTTCAACACTCGCAGTCTATGATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36934","NCBI_taxonomy_name":"Citrobacter koseri","NCBI_taxonomy_id":"545"}}}},"ARO_accession":"3004773","ARO_id":"42888","ARO_name":"CKO-1","CARD_short_name":"CKO-1","ARO_description":"CKO-1 is a class A beta-lactamase gene found in Citrobacter koseri.","ARO_category":{"42887":{"category_aro_accession":"3004772","category_aro_cvterm_id":"42887","category_aro_name":"CKO beta-lactamase","category_aro_description":"CKO is a class A beta-lactamase gene family found in Citrobacter koseri.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3608":{"model_id":"3608","model_name":"GOB-7","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"5806":{"protein_sequence":{"accession":"AAF89153.1","sequence":"KEPENMPKEWNQTYEPFRIAGNLYYVGTYDLASYLIVTDKGNILINTGTAESFPIIKGNIQKLGFNYKDIKILLLTQAHYDHTGALQDFKTETGAKFYADKADADVLRTGGKSDYELGKYGVTFKPVTPDKTLKDQDKITLGNTTLTLLHHPGHTKGSCSFIFETKDENRKYKILIANMPSIIVDKKFSEVTAYPGIQSDYAYTFKAMKNLDFDIWVASHASQFDLHTKRKEGDSYNPQLFMDKENYFKRLE"},"dna_sequence":{"accession":"AF189297.1","fmin":"0","fmax":"756","strand":"+","sequence":"AAAGAACCTGAGAATATGCCAAAAGAATGGAACCAGACTTATGAACCATTCAGAATTGCAGGTAATTTATATTACGTAGGAACCTATGATTTGGCGTCCTACCTTATTGTGACAGACAAAGGCAATATTCTCATTAATACAGGAACGGCAGAATCATTTCCAATAATAAAAGGAAATATTCAAAAGCTGGGGTTTAATTATAAAGACATTAAGATCTTGCTGCTTACTCAGGCTCATTATGACCATACAGGCGCGTTACAGGATTTTAAAACGGAAACCGGTGCGAAATTTTATGCCGATAAAGCAGATGCTGATGTCCTGAGAACAGGCGGAAAATCTGATTATGAATTAGGTAAATATGGTGTGACATTTAAACCTGTTACCCCAGACAAAACATTGAAGGATCAGGATAAAATAACATTGGGAAATACAACCCTGACTTTGCTTCACCATCCGGGACATACAAAAGGTTCCTGCAGTTTTATTTTTGAAACAAAAGATGAAAACAGGAAATACAAGATTTTAATAGCTAATATGCCTTCCATTATTGTTGATAAGAAATTTTCTGAAGTTACAGCATATCCAGGTATTCAGTCCGATTACGCATATACTTTCAAAGCGATGAAGAATCTGGATTTTGATATCTGGGTTGCCTCGCATGCAAGTCAGTTCGATTTGCATACCAAACGCAAAGAAGGTGACTCTTACAATCCACAGTTGTTTATGGATAAAGAGAATTATTTTAAAAGGCTCGAG","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36960","NCBI_taxonomy_name":"Elizabethkingia meningoseptica","NCBI_taxonomy_id":"238"}}}},"ARO_accession":"3004814","ARO_id":"42934","ARO_name":"GOB-7","CARD_short_name":"GOB-7","ARO_description":"GOB-7 is a class B beta-lactamase gene found in Elizabethkingia meningoseptica.","ARO_category":{"41376":{"category_aro_accession":"3004212","category_aro_cvterm_id":"41376","category_aro_name":"GOB beta-lactamase","category_aro_description":"The GOB family of beta-lactamases have been discovered in the Elizabethkingia meningoseptica and are classified as subclass B3 beta-lactamase. They confer resistance to cephalosporins, penicillins, and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3618":{"model_id":"3618","model_name":"IMP-49","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"5816":{"protein_sequence":{"accession":"AKO63210.1","sequence":"MKKLFVLCVFFLCNIAAADDSLPDLKIEKLEKGVYVHTSFEEVKGWGVFTKHGLVVLVKNDAYLIDTPITAKDTEKLVNWFIEHGYRIKGSISTHFHGDSTAGIEWLNSQSISTYASELTNELLKKDNKVQATNSFSGVSYSLIKNKIEVFYPGPGHTQDNVVVWLPEKKILFGGCFVKPDGLGNLGDANLEAWPKSAKILMSKYGKAKLVVSSHSEIGNASLLQRTWEQAVKGLNESKKPLQPSS"},"dna_sequence":{"accession":"KP681694.1","fmin":"0","fmax":"741","strand":"+","sequence":"ATGAAAAAATTATTTGTTTTATGTGTATTCTTCCTTTGCAACATTGCTGCTGCAGATGATTCTTTGCCTGATTTAAAAATTGAGAAGCTTGAAAAAGGCGTTTATGTTCATACTTCGTTTGAAGAAGTTAAAGGTTGGGGTGTATTCACAAAACACGGTTTAGTGGTTCTTGTAAAGAATGATGCTTATCTGATAGATACTCCAATTACCGCTAAAGATACTGAAAAATTAGTTAATTGGTTTATTGAGCACGGCTATAGAATCAAAGGCAGTATTTCCACACATTTCCATGGCGACAGTACGGCTGGAATAGAGTGGCTTAATTCTCAATCTATCTCCACGTATGCCTCTGAATTAACAAATGAACTTCTAAAAAAAGACAATAAGGTGCAAGCTACAAATTCTTTTAGTGGAGTTAGTTATTCACTTATCAAAAACAAAATTGAAGTTTTCTATCCAGGTCCAGGACACACTCAAGATAACGTAGTGGTTTGGTTACCTGAAAAGAAAATTTTATTCGGTGGTTGCTTTGTTAAACCGGACGGTCTTGGAAATTTAGGGGATGCAAATTTAGAAGCTTGGCCAAAGTCCGCTAAAATATTAATGTCTAAATATGGTAAAGCAAAACTGGTTGTTTCAAGTCATAGTGAAATTGGAAACGCATCACTCTTGCAGCGCACATGGGAGCAGGCTGTTAAAGGGTTAAATGAAAGTAAAAAACCGTTACAGCCAAGTAGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3003657","ARO_id":"40267","ARO_name":"IMP-49","CARD_short_name":"IMP-49","ARO_description":"IMP-49 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3623":{"model_id":"3623","model_name":"LEN-25","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"574"}},"model_sequences":{"sequence":{"5821":{"protein_sequence":{"accession":"ADW77562.1","sequence":"MRYVRLCVISLLATLPLAVDAGPQPLEQIKQSESQLSGRVGMVEMDLASGRTLAAWRADERFPMVSTFKVLLCGAVLARVDAGLEQLDRRIHYRQQDLVDYSPVSEKHLVDGMAIGELCAAAITLSDNSAGNLLLATVGGPAGLTAFLRQIGDNVTRLDRWETALNEALPGDARDTTTPASMAATLRKLLTAQHLSARSQQQLLQWMVDDRVAGPLIRAVLPPGWFIADKTGAGERGARGIVALLGPDGKPERIVVLYLRDTPASMAERNQHIAGIGAALIEHWQR"},"dna_sequence":{"accession":"HQ709169.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGTGTTATCTCCCTGTTAGCCACCCTGCCACTGGCGGTAGACGCCGGTCCACAGCCGCTTGAGCAGATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTGGGGATGGTGGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCGATGAACGCTTTCCCATGGTGAGCACCTTTAAAGTGCTGCTGTGCGGCGCGGTGCTGGCGCGGGTGGATGCCGGGCTCGAACAACTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGTCGACGGGATGGCGATCGGCGAACTCTGCGCCGCCGCCATCACCCTGAGCGATAACAGCGCTGGCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCGGGATTAACTGCCTTTCTGCGCCAGATCGGTGACAACGTCACCCGTCTTGACCGCTGGGAAACGGCACTGAATGAGGCGCTTCCCGGCGACGCGCGCGACACCACCACCCCGGCCAGCATGGCCGCCACGCTGCGCAAACTACTGACCGCGCAGCATCTGAGCGCCCGTTCGCAACAGCAACTCCTGCAGTGGATGGTGGACGATCGGGTTGCCGGCCCGCTGATCCGCGCCGTGCTGCCGCCGGGCTGGTTTATCGCCGACAAAACTGGGGCTGGCGAACGGGGTGCGCGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAACCGGAGCGCATTGTGGTGCTCTATCTGCGGGATACCCCGGCGAGTATGGCCGAGCGTAATCAACATATCGCCGGGATCGGCGCAGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002479","ARO_id":"38879","ARO_name":"LEN-25","CARD_short_name":"LEN-25","ARO_description":"LEN-25 is a beta-lactamase. From the Pasteur Institute list of LEN beta-lactamases.","ARO_category":{"36236":{"category_aro_accession":"3000097","category_aro_cvterm_id":"36236","category_aro_name":"LEN beta-lactamase","category_aro_description":"LEN beta-lactamases are chromosomal class A beta-lactamases that confer resistance to ampicillin, amoxicillin, carbenicillin, and ticarcillin but not to extended-spectrum beta-lactams.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2397":{"model_id":"2397","model_name":"pgpB","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"4612":{"protein_sequence":{"accession":"BAG33043.1","sequence":"MEYILEVERNLFLTLNGVQHPLLDGFFYLISAKWTWVIMSIAFLFFLFYKKPTKEALFIVGAVLLSVLICDQLSSSFFKPFFARFRPSHHPDFIDYVKTVYGYRGGKYGFISGHTTNYISLALFTSRIFRNKFYTWTIWSVVALVIYSRIYIGVHFITDIIPGIAVGLIVGHFVYKVYLYARSRWLGASCPAHPSAVYAGDSIRLWTLSLIGFVFAMLCMSRQLTEILQYYVFLLF"},"dna_sequence":{"accession":"AP009380.1","fmin":"573191","fmax":"573902","strand":"-","sequence":"TTGGAATACATTCTTGAAGTAGAAAGGAACCTCTTTTTGACTCTGAACGGAGTACAGCATCCTTTGTTGGACGGTTTTTTCTATTTGATCTCGGCCAAATGGACTTGGGTGATAATGTCCATCGCGTTTCTGTTCTTCCTTTTTTATAAGAAACCGACAAAGGAAGCTCTCTTCATCGTAGGAGCAGTCTTATTGAGCGTACTCATCTGCGATCAACTCTCCTCTTCTTTTTTCAAGCCTTTCTTCGCAAGATTCCGCCCTTCGCACCACCCTGATTTTATCGACTATGTGAAGACGGTCTACGGCTATCGGGGAGGAAAGTACGGATTTATCTCAGGGCATACGACGAACTACATATCGCTGGCATTATTTACGAGCCGTATTTTTCGGAATAAATTCTACACGTGGACGATCTGGAGCGTCGTCGCACTCGTCATCTATAGCCGTATTTATATCGGAGTGCATTTCATCACCGATATTATCCCGGGTATCGCCGTCGGACTTATCGTAGGACACTTTGTTTATAAAGTCTATCTGTATGCACGTTCCCGTTGGTTGGGAGCCTCATGCCCTGCCCATCCGTCGGCAGTCTATGCCGGCGATTCCATTCGGCTCTGGACACTTAGCCTCATCGGCTTTGTCTTTGCCATGCTGTGTATGTCCCGCCAGTTGACGGAGATACTACAGTACTATGTCTTCCTGCTCTTCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40629","NCBI_taxonomy_name":"Porphyromonas gingivalis ATCC 33277","NCBI_taxonomy_id":"431947"}}}},"ARO_accession":"3003920","ARO_id":"40628","ARO_name":"pgpB","CARD_short_name":"pgpB","ARO_description":"A gene that produces the protein lipid A 4'-phosphatase.","ARO_category":{"41451":{"category_aro_accession":"3004287","category_aro_cvterm_id":"41451","category_aro_name":"lipid A phosphatase","category_aro_description":"The antimicrobial activity of certain antibiotics, such as peptide antibiotics, is proposed to be initiated through binding to the lipid A moiety of lipopolysaccharides. Thus, covalent modification of Gram-negative bacterial lipid A by phosphatases is a mechanism to reduce the susceptibility of the bacteria to antibiotics.","category_aro_class_name":"AMR Gene Family"},"36593":{"category_aro_accession":"3000454","category_aro_cvterm_id":"36593","category_aro_name":"polymyxin B","category_aro_description":"Polymyxin B is mixture of mostly polymyxins B1 and B2, mainly used for resistant gram-negative infections. They are polypeptides with cationic detergent action on cell membranes.","category_aro_class_name":"Antibiotic"},"36969":{"category_aro_accession":"3000625","category_aro_cvterm_id":"36969","category_aro_name":"polymyxin B1","category_aro_description":"Polymyxin B1 is in the family of polymyxin lipopeptides with a 6-methyloctanoic acid acyl group. These antibiotics disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36970":{"category_aro_accession":"3000626","category_aro_cvterm_id":"36970","category_aro_name":"polymyxin B2","category_aro_description":"Polymyxin B2 is in the family of polymyxin lipopeptides with a 6-methylheptanoic acid acyl group. These antibiotics disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36971":{"category_aro_accession":"3000627","category_aro_cvterm_id":"36971","category_aro_name":"polymyxin B3","category_aro_description":"Polymyxin B3 is in the family of polymyxin lipopeptides with an octanoic acid acyl group. These antibiotics disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36972":{"category_aro_accession":"3000628","category_aro_cvterm_id":"36972","category_aro_name":"polymyxin B4","category_aro_description":"Polymyxin B4 is in the family of polymyxin lipopeptides with a heptanoic acid acyl group. These antibiotics disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3627":{"model_id":"3627","model_name":"SHV-4","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"5835":{"protein_sequence":{"accession":"SPD96731.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQLQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGASKRGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"LT985229.1","fmin":"36107","fmax":"36968","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTACTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACTGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTAGCAAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATCGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001063","ARO_id":"37443","ARO_name":"SHV-4","CARD_short_name":"SHV-4","ARO_description":"SHV-4 is an extended-spectrum beta-lactamase that has been found in clinical isolates.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3628":{"model_id":"3628","model_name":"Neisseria gonorrhoeae PBP2 conferring resistance to beta-lactam antibiotics","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"9277":"A501P","9289":"A501V","9292":"A311V","9290":"A501T","9294":"V316P","9296":"T483S","9350":"F504L","9361":"G542S","9352":"A510V","9362":"P551S","9353":"A516G","9363":"P551L","10520":"N513Y","10521":"G545S"},"Curated-R":{"9277":"A501P","9289":"A501V","9292":"A311V","9290":"A501T","9294":"V316P","9296":"T483S","9350":"F504L","9361":"G542S","9352":"A510V","9362":"P551S","9353":"A516G","9363":"P551L","10520":"N513Y","10521":"G545S","18564":"G545S"},"clinical":{"9277":"A501P","9289":"A501V","9292":"A311V","9290":"A501T","9294":"V316P","9296":"T483S","9350":"F504L","9361":"G542S","9352":"A510V","9362":"P551S","9353":"A516G","9363":"P551L","10520":"N513Y","10521":"G545S"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"},"41344":{"param_type":"insertion mutation from peptide sequence","param_description":"A peptide sequence change between the translation initiation (start) and termination (stop) codon where, compared to the reference sequence, one or more amino acids are inserted. These represent in-frame insertions which do not result in frameshift variants and where the insertion is not a duplication of a sequence immediately N-terminal (5'), and are denoted with wildtype flanking residues. Format is given by [wildtype AA position]_[wildtype AA position]ins[AA sequence], e.g. K464_D465insE or P46_A47insYS.","param_type_id":"41344","param_value":{"18564":"R345_D346insD"}}},"model_sequences":{"sequence":{"8380":{"protein_sequence":{"accession":"AAA25463.1","sequence":"MLIKSEYKPRMLPKEEQVKKPMTSNGRISFVLMAMAVLFACLIARGLYLQTVTYNFLKEQGDNRIVRTQALPATRGTVSDRNGAVLALSAPTESLFAVPKDMKEMPSAAQLERLSELVDVPVDVLRNKLEQKGKSFIWIKRQLDPKVAEEVKALGLENFVFEKELKRHYPMGNLFAHVIGFTDIDGKGQEGLELSLEDSLYGEDGAEVVLRDRQGNIVDSLDSPRNKAPQNGKDIILSLDQRIQTLAYEELNKAVEYHQAKAGTVVVLDARTGEILALANTPAYDPNRPGRADSEQRRNRAVTDMIEPGSAIKPFVIAKALDAGKTDLNERLNTQPYKIGPSPVRDTHVYPSLDVRGIMQKSSNVGTSKLSARFGAEEMYDFYHELGIGVRMHSGFPGETAGLLRNWRRWRPIEQATMSFGYGLQLSLLQLARAYTALTHDGVLLPLSFEKQAVAPQGKRIFKESTAREVRNLMVSVTEPGGTGTAGAVDGFDVGAKTGTARKFVNGRYADNKHVATFIGFAPAKNPRVIVAVTIDEPTAHGYYGGVVAGPPFKKIMGGSLNILGISPTKPLTAAAVKTPS"},"dna_sequence":{"accession":"M32091.1","fmin":"102","fmax":"1848","strand":"+","sequence":"ATGTTGATTAAAAGCGAATATAAGCCCCGGATGCTGCCCAAAGAAGAGCAGGTCAAAAAGCCGATGACCAGTAACGGACGGATTAGCTTCGTCCTGATGGCAATGGCGGTCTTGTTTGCCTGTCTGATTGCCCGCGGGCTGTATCTGCAGACGGTAACGTATAACTTTTTGAAAGAACAGGGCGACAACCGGATTGTGCGGACTCAAGCATTGCCGGCTACACGCGGTACGGTTTCGGACCGGAACGGTGCGGTTTTGGCGTTGAGCGCGCCGACGGAGTCCCTGTTTGCCGTGCCTAAAGATATGAAGGAAATGCCGTCTGCCGCCCAATTGGAACGCCTGTCCGAGCTTGTCGATGTGCCGGTCGATGTTTTGAGGAACAAACTCGAACAGAAAGGCAAGTCGTTTATTTGGATCAAGCGGCAGCTCGATCCCAAGGTTGCCGAAGAGGTCAAAGCCTTGGGTTTGGAAAACTTTGTATTTGAAAAAGAATTAAAACGCCATTACCCGATGGGCAACCTGTTTGCACACGTCATCGGATTTACCGATATTGACGGCAAAGGTCAGGAAGGTTTGGAACTTTCGCTTGAAGACAGCCTGTATGGCGAAGACGGCGCGGAAGTTGTTTTGCGGGACCGGCAGGGCAATATTGTGGACAGCTTGGACTCCCCGCGCAATAAAGCACCGCAAAACGGCAAAGACATCATCCTTTCCCTCGATCAGAGGATTCAGACCTTGGCCTATGAAGAGTTGAACAAGGCGGTCGAATACCATCAGGCAAAAGCCGGAACGGTGGTGGTTTTGGATGCCCGCACGGGGGAAATCCTCGCCTTGGCCAATACGCCCGCCTACGATCCCAACAGACCCGGCCGGGCAGACAGCGAACAGCGGCGCAACCGTGCCGTAACCGATATGATCGAACCTGGTTCGGCAATCAAACCGTTCGTGATTGCGAAGGCATTGGATGCGGGCAAAACCGATTTGAACGAACGGCTGAATACGCAGCCTTATAAAATCGGACCGTCTCCCGTGCGCGATACCCATGTTTACCCCTCTTTGGATGTGCGCGGCATTATGCAGAAATCGTCCAACGTCGGCACAAGCAAACTGTCTGCGCGTTTCGGCGCCGAAGAAATGTATGACTTCTATCATGAATTGGGCATCGGTGTGCGTATGCACTCGGGCTTTCCGGGGGAAACTGCAGGTTTGTTGAGAAATTGGCGCAGGTGGCGGCCCATCGAACAGGCGACGATGTCTTTCGGTTACGGTCTGCAATTGAGCCTGCTGCAATTGGCGCGCGCCTATACCGCACTGACGCACGACGGCGTTTTGCTGCCGCTCAGCTTTGAGAAGCAGGCGGTTGCGCCGCAAGGCAAACGCATATTCAAAGAATCGACCGCGCGCGAGGTACGCAATCTGATGGTTTCCGTAACCGAGCCGGGCGGCACCGGTACGGCGGGTGCGGTGGACGGTTTCGATGTCGGCGCTAAAACCGGCACGGCGCGCAAGTTCGTCAACGGGCGTTATGCCGACAACAAACACGTCGCTACCTTTATCGGTTTTGCCCCCGCCAAAAACCCCCGTGTGATTGTGGCGGTAACCATCGACGAACCGACTGCCCACGGCTATTACGGCGGCGTAGTGGCAGGGCCGCCCTTCAAAAAAATTATGGGCGGCAGCCTGAACATCTTGGGCATTTCCCCGACCAAGCCACTGACCGCCGCAGCCGTCAAAACACCGTCTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36806","NCBI_taxonomy_name":"Neisseria gonorrhoeae","NCBI_taxonomy_id":"485"}}}},"ARO_accession":"3004832","ARO_id":"42962","ARO_name":"Neisseria gonorrhoeae PBP2 conferring resistance to beta-lactam antibiotics","CARD_short_name":"Ngon_PBP2_BLA","ARO_description":"PBP2 is a penicillin-binding protein and beta-lactam resistance enzyme encoded by the penA gene, due to mutations can cause resistance to various drugs such as Penicillin and Ceftriaxone.","ARO_category":{"40661":{"category_aro_accession":"3003938","category_aro_cvterm_id":"40661","category_aro_name":"Penicillin-binding protein mutations conferring resistance to beta-lactam antibiotics","category_aro_description":"Mutations in PBP transpeptidases that change the affinity for penicillin thereby conferring resistance to penicillin antibiotics.","category_aro_class_name":"AMR Gene Family"},"35979":{"category_aro_accession":"0000062","category_aro_cvterm_id":"35979","category_aro_name":"ceftriaxone","category_aro_description":"Ceftriaxone is a third-generation cephalosporin antibiotic. The presence of an aminothiazolyl sidechain increases ceftriazone's resistance to beta-lactamases. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36990":{"category_aro_accession":"3000646","category_aro_cvterm_id":"36990","category_aro_name":"cefixime","category_aro_description":"Cefixime is a cephalosporin resistant to most beta-lactamases. It is active against many enterobacteria, but activity against staphylococci is poor.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3633":{"model_id":"3633","model_name":"OXA-724","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"5903":{"protein_sequence":{"accession":"CAB76928.1","sequence":"MSRLLLSGLLGAGLLFSLPASAATGCFLYADGNGQALSSEGDCSSQLPPASTFKIPLALMGYDSGFLVDEEHPALPFKPGYDDWLPAWRETTTPRRWETYSVVWFSQQITEWLGMERFQQYVDRFDYGNRDLSGNPGKHDGLTQAWLSSSLAISPQEQARFLGKMVSGKLPVSAQTLQYTANILKVSESDGWQIHGKTGMGYPKKLDGSLNREQQIGWFVGWASKPGKQLIFVHTVVQKPGKQFASLKAKEEVLAALPAKLKTL"},"dna_sequence":{"accession":"AJ276031.1","fmin":"111","fmax":"906","strand":"+","sequence":"ATGTCCCGCCTTCTCTTATCCGGCCTGCTCGGCGCAGGCCTGCTGTTCTCGCTGCCGGCCAGCGCCGCCACCGGCTGCTTTCTCTATGCCGACGGCAACGGCCAGGCCCTCTCCAGCGAAGGGGATTGTTCAAGCCAGCTGCCACCCGCGTCCACCTTCAAGATCCCGCTGGCGCTGATGGGCTACGACAGCGGCTTTCTGGTGGACGAAGAGCACCCGGCACTGCCTTTCAAGCCGGGTTACGACGACTGGCTGCCCGCCTGGCGGGAAACAACCACCCCGCGCCGCTGGGAAACCTACTCGGTGGTCTGGTTCTCCCAGCAGATCACCGAATGGCTGGGGATGGAGCGCTTCCAGCAGTACGTCGACCGTTTTGACTACGGCAACCGGGATCTCTCCGGCAATCCTGGCAAGCACGACGGTCTGACCCAGGCCTGGCTCAGTTCCAGCCTTGCCATCAGTCCACAGGAGCAGGCCCGCTTCCTCGGCAAGATGGTGAGCGGCAAGCTGCCGGTGTCGGCGCAAACCCTGCAGTACACCGCCAACATCCTCAAGGTGAGCGAGAGCGACGGCTGGCAGATCCACGGCAAGACCGGCATGGGCTACCCGAAGAAGCTGGATGGCAGCCTCAACCGGGAGCAGCAGATCGGCTGGTTCGTCGGCTGGGCCAGCAAGCCGGGCAAACAGCTGATCTTCGTCCATACCGTGGTGCAGAAACCCGGCAAACAGTTCGCCTCGCTCAAGGCCAAGGAAGAGGTGCTGGCCGCCCTGCCGGCCAAACTGAAAACCCTGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36810","NCBI_taxonomy_name":"Aeromonas hydrophila","NCBI_taxonomy_id":"644"}}}},"ARO_accession":"3004837","ARO_id":"42971","ARO_name":"OXA-724","CARD_short_name":"OXA-724","ARO_description":"An OXA-12-family class D beta-lactamase identified from Aeromonas hydrophila.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46488":{"category_aro_accession":"3007699","category_aro_cvterm_id":"46488","category_aro_name":"OXA-12-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-12.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3656":{"model_id":"3656","model_name":"Burkholderia dolosa gyrA conferring resistance to fluoroquinolones","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"9429":"G81D","9430":"T83I","9431":"D87H"},"Curated-R":{"9429":"G81D","9430":"T83I","9431":"D87H"},"clinical":{"9429":"G81D","9430":"T83I","9431":"D87H"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1700"}},"model_sequences":{"sequence":{"8366":{"protein_sequence":{"accession":"AJY14066.1","sequence":"MDQFAKETLPTSLEEEMRRSYLDYAMSVIVGRALPDVRDGLKPVHRRVLFAMHELNNDWNRAYKKSARIVGDVIGKYHPHGDTAVYDTIVRMAQDFSLRYMLIDGQGNFGSIDGDNAAAMRYTEIRMAKIGHELLADIDKETVDFEPNYDGNETQPSVLPSRIPNLLINGSSGIAVGMATNIPPHNLNEVVDACQHLLSNPDATVDELIEIIPAPDFPTAGIIYGVAGVRDGYRTGRGRVVMRAATHFEEIDRGQRMAIIVDELPYQVNKRSLLERIAELVNEKKLEGISDIRDESDKSGMRVVIELKRGEVPEVVLNNLYKATQLQDTFGMNMVALVDGQPKLLNLKEILQCFLSHRREVLTRRTIYELRKARERGHVLEGLAVALANIDEFIAIIKAAPTPPIAKQELMTKSWDSSLVREMLTRAESENAAAGGRAAYRPEGLNPAYGMQADGLYRLSDTQAQEILQMRLQRLTGLEQDKIIGEYREVMAQIADLLDILARPERITTMIGDELTTVKAEFGDARRSRIELNATELNTEDLITPQDMVVTMSHAGYVKSQPLSEYRAQKRGGRGKQATQMKEDDWIETLFIANTHDYMLCFSNRGRVYWIKVYEVPQGSRNSRGRPIVNMFPLQEGEKINVVLPVKEFSADKFVFMATSLGTVKKTPLEAFSRPMKKGIIAVGLDEGDYLIGASITDGAHDVMLFSDSGKAVRFDENDVRPMGREARGVRGMQLEDGQQVIALLVAGSEEQSVLTATENGFGKRTPITEYTRHGRGTKGMIAIQTSERNGKVVAATLVDPEDQIMLITTAGVLIRTRVSEIREMGRATQGVTLISLDEGTKLSGLQQIAEAEEGDGEADEASDGEA"},"dna_sequence":{"accession":"CP009795.1","fmin":"2298742","fmax":"2301346","strand":"-","sequence":"ATGGATCAATTCGCCAAAGAGACCCTGCCCACCTCCCTCGAGGAGGAAATGCGCCGTTCGTATCTCGATTACGCGATGAGCGTGATCGTCGGACGTGCCCTTCCGGATGTCCGCGATGGCCTGAAGCCCGTGCACCGGCGCGTACTGTTCGCGATGCACGAACTGAACAACGACTGGAACCGCGCGTACAAGAAATCGGCGCGTATCGTCGGCGACGTGATCGGTAAGTACCACCCGCACGGCGACACGGCGGTCTACGACACGATCGTGCGGATGGCGCAGGACTTCTCGCTGCGCTACATGCTGATCGACGGGCAGGGCAACTTCGGCTCGATCGACGGCGACAATGCGGCGGCGATGCGGTACACCGAAATTCGCATGGCGAAGATCGGGCACGAGCTGCTCGCCGACATCGACAAGGAAACGGTCGATTTCGAGCCGAACTACGACGGCAACGAAACGCAGCCGTCGGTCCTGCCGTCGCGGATCCCGAACCTGCTGATCAACGGCTCGTCGGGCATCGCCGTCGGCATGGCGACCAACATTCCGCCGCACAACCTGAACGAAGTCGTCGACGCGTGCCAGCACCTGCTGAGCAACCCCGACGCGACGGTCGACGAACTGATCGAGATCATCCCGGCGCCGGATTTCCCGACGGCCGGCATCATCTACGGCGTCGCCGGCGTGCGCGACGGCTACCGCACCGGCCGCGGCCGCGTCGTGATGCGCGCGGCCACGCACTTCGAGGAGATCGACCGCGGCCAGCGGATGGCGATCATCGTCGACGAGCTGCCGTACCAGGTCAACAAGCGCTCGCTGCTCGAGCGGATCGCCGAGCTCGTCAACGAGAAGAAGCTCGAAGGCATTTCCGATATCCGCGACGAATCCGACAAGAGCGGCATGCGGGTCGTGATCGAGCTCAAGCGCGGCGAAGTGCCGGAAGTGGTGCTGAACAACCTGTACAAGGCGACGCAGCTGCAGGACACGTTCGGCATGAACATGGTCGCGCTCGTCGACGGCCAGCCGAAGCTGCTGAACCTGAAGGAAATCCTGCAGTGCTTCCTGTCGCACCGGCGCGAAGTGCTGACGCGCCGCACGATCTACGAACTGCGCAAGGCGCGCGAGCGCGGCCACGTGCTCGAAGGTCTCGCGGTCGCGCTCGCGAACATCGACGAGTTCATCGCGATCATCAAGGCCGCGCCGACGCCGCCGATCGCGAAGCAGGAGCTGATGACGAAGTCGTGGGATTCGTCGCTCGTACGCGAGATGCTGACGCGCGCCGAATCCGAGAACGCGGCGGCGGGCGGCCGTGCCGCGTACCGTCCGGAAGGGCTGAATCCGGCGTACGGGATGCAGGCCGACGGGCTGTACAGGTTGTCCGACACGCAGGCGCAGGAAATCCTGCAGATGCGTCTGCAGCGCCTGACCGGCCTCGAGCAGGACAAGATCATCGGCGAGTATCGCGAAGTGATGGCGCAGATCGCCGATCTGCTCGACATCCTCGCGCGCCCGGAGCGCATCACGACGATGATCGGCGACGAGCTGACGACGGTGAAGGCCGAATTCGGCGATGCGCGCCGCTCGCGGATCGAGCTGAACGCGACCGAACTGAATACCGAAGACCTGATCACGCCGCAGGACATGGTCGTCACGATGTCGCATGCCGGCTACGTGAAGTCGCAGCCGCTGTCGGAGTACCGCGCGCAGAAGCGCGGCGGCCGCGGCAAGCAGGCGACGCAGATGAAGGAAGACGACTGGATCGAGACGCTCTTCATCGCGAATACGCACGACTACATGCTGTGCTTCTCGAACCGCGGTCGCGTGTACTGGATCAAGGTCTACGAGGTGCCGCAAGGTTCGCGCAACTCGCGCGGCCGTCCGATCGTCAACATGTTCCCGCTGCAGGAAGGCGAGAAGATCAACGTCGTGCTGCCGGTGAAGGAATTCTCGGCCGACAAGTTCGTGTTCATGGCGACGTCGCTCGGCACGGTCAAGAAGACGCCGCTCGAAGCGTTCAGCCGTCCGATGAAGAAGGGCATCATCGCGGTCGGCCTCGACGAGGGCGACTATCTGATCGGCGCGTCGATCACCGACGGCGCGCACGACGTGATGCTGTTCTCCGATTCGGGCAAGGCCGTGCGCTTCGACGAGAACGACGTGCGTCCGATGGGCCGCGAAGCGCGCGGCGTGCGCGGCATGCAGCTCGAGGACGGGCAGCAGGTCATCGCGCTGCTGGTCGCGGGCAGCGAGGAGCAGTCCGTGCTCACCGCAACCGAGAACGGCTTCGGCAAGCGTACGCCGATCACCGAGTACACGCGTCACGGCCGCGGCACGAAGGGTATGATCGCGATCCAGACCTCCGAGCGTAACGGCAAGGTCGTCGCTGCGACGCTCGTCGATCCGGAAGATCAGATCATGCTGATCACGACGGCCGGCGTGTTGATTCGCACGCGCGTTTCCGAGATCCGCGAGATGGGACGGGCGACGCAAGGTGTTACACTCATCAGTCTCGATGAGGGTACGAAGCTTTCGGGTCTGCAGCAGATTGCCGAGGCCGAAGAGGGCGATGGCGAAGCCGACGAGGCGTCGGACGGCGAAGCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42997","NCBI_taxonomy_name":"Burkholderia dolosa AU0158","NCBI_taxonomy_id":"350701"}}}},"ARO_accession":"3004860","ARO_id":"42996","ARO_name":"Burkholderia dolosa gyrA conferring resistance to fluoroquinolones","CARD_short_name":"Bdol_gyrA_FLO","ARO_description":"Point mutations in Burkholderia gyrA that confer resistance to ciprofloxacin, a fluoroquinolone antibiotic.","ARO_category":{"39876":{"category_aro_accession":"3003292","category_aro_cvterm_id":"39876","category_aro_name":"fluoroquinolone resistant gyrA","category_aro_description":"DNA gyrase is responsible for DNA supercoiling and consists of two alpha and two beta subunits. GyrA point mutations confer resistance by preventing fluoroquinolone antibiotics from binding the alpha-subunit.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3657":{"model_id":"3657","model_name":"NDM-15","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"5929":{"protein_sequence":{"accession":"AKF43458.1","sequence":"MELPNIMHPVAKLSTALAAALMLSGCMPGEIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGLVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASVRAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR"},"dna_sequence":{"accession":"KP735848.1","fmin":"0","fmax":"813","strand":"+","sequence":"ATGGAATTGCCCAATATTATGCACCCGGTCGCGAAGCTGAGCACCGCATTAGCCGCTGCATTGATGCTGAGCGGGTGCATGCCCGGTGAAATCCGCCCGACGATTGGCCAGCAAATGGAAACTGGCGACCAACGGTTTGGCGATCTGGTTTTCCGCCAGCTCGCACCGAATGTCTGGCAGCACACTTCCTATCTCGACATGCCGGGTTTCGGGGCAGTCGCTTCCAACGGTTTGATCGTCAGGGATGGCGGCCGCGTGCTGGTGGTCGATACCGCCTGGACCGATGACCAGACCGCCCAGATCCTCAACTGGATCAAGCAGGAGATCAACCTGCCGGTCGCGCTGGCGGTGGTGACTCACGCGCATCAGGACAAGATGGGCGGTATGGACGCGCTGCATGCGGCGGGGATTGCGACTTATGCCAATGCGTTGTCGAACCAGCTTGCCCCGCAAGAGGGGCTGGTTGCGGCGCAACACAGCCTGACTTTCGCCGCCAATGGCTGGGTCGAACCAGCAACCGCGCCCAACTTTGGCCCGCTCAAGGTATTTTACCCCGGCCCCGGCCACACCAGTGACAATATCACCGTTGGGATCGACGGCACCGACATCGCTTTTGGTGGCTGCCTGATCAAGGACAGCAAGGCCAAGTCGCTCGGCAATCTCGGTGATGCCGACACTGAGCACTACGCCGCGTCAGTGCGCGCGTTTGGTGCGGCGTTCCCCAAGGCCAGCATGATCGTGATGAGCCATTCCGCCCCCGATAGCCGCGCCGCAATCACTCATACGGCCCGCATGGCCGACAAGCTGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3003663","ARO_id":"40273","ARO_name":"NDM-15","CARD_short_name":"NDM-15","ARO_description":"New Delhi metallo-beta-lactamase-15 variant of NDM-1.","ARO_category":{"36196":{"category_aro_accession":"3000057","category_aro_cvterm_id":"36196","category_aro_name":"NDM beta-lactamase","category_aro_description":"NDM beta-lactamases or New Delhi metallo-beta-lactamases are class B beta-lactamases that confer resistance to a broad range of antibiotics including carbapenems, cephalosporins and penicillins.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3708":{"model_id":"3708","model_name":"Mycobacterium tuberculosis whib7 mutations confer resistance to kanamycin","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"41339":{"param_type":"nucleotide substitution in promoter region","param_description":"A nucleotide sequence change where, compared to a reference sequence, one nucleotide is replaced by one other nucleotide in the promoter region of a gene. These substitutions are indicated as upstream of the reference sequence transcription initiation site. Format is given by [-][position][wildtype][>][mutation], e.g. -11t>c or -15g>Var where Var represents any possible substitution.","param_type_id":"41339","param_value":{"13185":"-116a>g"}},"snp":{"ReSeqTB-Minimal":{"13185":"D87H"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"125"}},"model_sequences":{"sequence":{"8800":{"protein_sequence":{"accession":"YP_177940.1","sequence":"MSVLTVPRQTPRQRLPVLPCHVGDPDLWFADTPAGLEVAKTLCVSCPIRRQCLAAALQRAEPWGVWGGEIFDQGSIVSHKRPRGRPRKDAVA"},"dna_sequence":{"accession":"NC_000962.3","fmin":"3568400","fmax":"3568679","strand":"-","sequence":"GTGTCGGTACTGACAGTCCCCAGACAGACCCCCAGACAAAGATTGCCGGTTTTGCCGTGCCACGTCGGTGATCCCGATCTGTGGTTCGCCGATACCCCGGCCGGTCTCGAGGTAGCCAAGACACTGTGTGTGAGCTGCCCGATCAGGCGGCAGTGCTTGGCCGCGGCGCTTCAGCGGGCTGAACCCTGGGGCGTTTGGGGTGGTGAGATATTCGACCAAGGCTCGATCGTGAGTCACAAGCGTCCGCGCGGACGTCCGCGCAAGGATGCTGTTGCATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3004967","ARO_id":"43153","ARO_name":"Mycobacterium tuberculosis whib7 mutations confer resistance to kanamycin","CARD_short_name":"Mtub_whib7_KAN","ARO_description":"Mutations in whib7 that can contribute to or confer resistance to kanamycin.","ARO_category":{"43152":{"category_aro_accession":"3004966","category_aro_cvterm_id":"43152","category_aro_name":"Kanamycin resistant whib7","category_aro_description":"whib7 is a protein involved in transcriptional mechanisms. Mutations in the gene can cause resistance to kanamycin.","category_aro_class_name":"AMR Gene Family"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3735":{"model_id":"3735","model_name":"Mycobacterium tuberculosis sigI mutations conferring resistance to isoniazid","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"9592":"K270Q"},"ReSeqTB-High":{"9592":"K270Q"},"clinical":{"9592":"K270Q"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11358":{"protein_sequence":{"accession":"NP_215705.1","sequence":"MSQHDPVSAAWRAHRAYLVDLAFRMVGDIGVAEDMVQEAFSRLLRAPVGDIDDERGWLIVVTSRLCLDHIKSASTRRERPQDIAAWHDGDASVSSVDPADRVTLDDEVRLALLIMLERLGPAERVVFVLHEIFGLPYQQIATTIGSQASTCRQLAHRARRKINESRIAASVEPAQHRVVTRAFIEACSNGDLDTLLEVLDPGVAGEIDARKGVVVVGADRVGPTILRHWSHPATVLVAQPVCGQPAVLAFVNRALAGVLALSIEAGKITKIHVLVQPSTLDPLRAELGGG"},"dna_sequence":{"accession":"NC_000962.3","fmin":"1332091","fmax":"1332964","strand":"+","sequence":"ATGTCGCAACACGACCCGGTAAGTGCGGCCTGGCGGGCGCATCGGGCCTACCTGGTGGACCTCGCGTTTCGTATGGTAGGTGACATCGGCGTGGCCGAAGACATGGTGCAAGAGGCATTTTCCCGCTTGCTGCGGGCTCCGGTCGGCGACATCGACGACGAGCGTGGCTGGCTGATCGTGGTCACCAGCCGGCTGTGCCTGGATCACATCAAGTCGGCGTCGACACGCCGGGAGCGCCCGCAGGACATCGCCGCATGGCACGACGGTGACGCCAGCGTGTCATCGGTTGACCCGGCTGACCGGGTGACTCTCGACGACGAGGTCCGGCTGGCTTTGCTGATCATGCTCGAGCGCCTCGGCCCCGCGGAGCGGGTGGTGTTCGTGCTGCACGAGATCTTTGGGCTGCCCTACCAGCAAATCGCCACGACGATTGGCAGCCAGGCCTCCACATGCCGGCAGCTGGCTCATCGGGCCCGTCGCAAGATCAACGAATCGCGCATTGCGGCCAGCGTGGAGCCAGCCCAGCATCGCGTCGTCACCAGAGCTTTCATCGAAGCCTGCTCCAACGGAGACCTGGACACCCTGCTCGAGGTGCTGGATCCGGGTGTCGCCGGCGAGATCGACGCCCGCAAAGGCGTTGTCGTCGTGGGCGCGGATCGGGTTGGCCCGACCATCCTGCGCCACTGGAGTCACCCCGCCACCGTCCTGGTAGCCCAGCCGGTGTGCGGTCAACCGGCGGTGCTGGCCTTTGTCAACCGAGCGCTTGCCGGCGTGTTGGCCCTGTCGATCGAGGCCGGCAAGATCACAAAAATCCATGTCTTAGTGCAGCCTTCAACATTGGACCCGTTACGGGCCGAACTCGGCGGCGGTTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3004932","ARO_id":"43118","ARO_name":"Mycobacterium tuberculosis sigI mutations conferring resistance to isoniazid","CARD_short_name":"Mtub_sigI_INH","ARO_description":"Mycobacterium tuberculosis sigI mutations conferring resistance to isoniazid.","ARO_category":{"43099":{"category_aro_accession":"3004913","category_aro_cvterm_id":"43099","category_aro_name":"isoniazid resistant sigI","category_aro_description":"A sigma factor that acts as an initiation factor that promotes attachment of the RNA polymerase to specific initiation sites and then is released. Transcriptional analyses indicate that katG is also regulated by the sigma factor sigl and indicate resistance to isoniaizd.","category_aro_class_name":"AMR Gene Family"},"36659":{"category_aro_accession":"3000520","category_aro_cvterm_id":"36659","category_aro_name":"isoniazid","category_aro_description":"Isoniazid is an organic compound that is the first-line anti tuberculosis medication in prevention and treatment. As a prodrug, it is activated by mycobacterial catalase-peroxidases such as M. tuberculosis KatG. Isoniazid inhibits mycolic acid synthesis, which prevents cell wall synthesis in mycobacteria.","category_aro_class_name":"Antibiotic"},"45734":{"category_aro_accession":"3007152","category_aro_cvterm_id":"45734","category_aro_name":"isoniazid-like antibiotic","category_aro_description":"A group of antibiotics containing isoniazid and its derivatives.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3423":{"model_id":"3423","model_name":"OXA-185","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"5618":{"protein_sequence":{"accession":"AFO09969.1","sequence":"MKKILLLFSLFYSFALANDKLKDFFKDYNTSGVFITFDGKHYASNNFKRAKEPFSPASTFKIFNALIALDNGVVKDTKEIFYHYKGEKVFLPSWKQDASLSSAIKRSQVPAFKELARKIGLKTMQESLNKLSYGNTKISKIDTFWLDNSLQISAKNQADLLFKLSQNSLPFSKKSQEEVKKIILFKEDKIQKIYAKTGFNDGINLAWIVGFIESKNKILSFALNVDIKNIKNIKIREELLEKYIYSLN"},"dna_sequence":{"accession":"JQ396379.1","fmin":"0","fmax":"747","strand":"+","sequence":"TTGAAAAAAATACTTTTACTTTTTAGTCTTTTTTACTCTTTTGCTTTGGCAAATGATAAATTAAAAGATTTTTTTAAAGACTACAATACAAGCGGAGTTTTTATAACTTTTGATGGAAAACATTATGCAAGTAATAATTTTAAAAGAGCTAAAGAACCTTTTTCTCCTGCTTCGACTTTTAAAATTTTTAATGCTTTAATTGCGCTTGATAATGGTGTAGTTAAAGATACAAAGGAAATTTTTTATCATTATAAGGGTGAAAAAGTATTTTTGCCCTCTTGGAAACAAGATGCTAGTTTAAGCTCAGCCATAAAACGCTCTCAAGTGCCTGCTTTTAAAGAATTGGCAAGAAAAATAGGACTTAAAACCATGCAAGAAAGCTTAAATAAACTTTCCTATGGAAATACAAAAATTTCAAAAATCGATACCTTTTGGTTGGATAATTCTTTACAAATTTCTGCAAAAAATCAAGCTGATTTGCTTTTTAAACTTTCACAAAATTCTTTACCTTTTTCCAAGAAAAGTCAAGAAGAAGTTAAAAAAATTATTCTTTTTAAAGAAGATAAAATCCAAAAAATTTATGCTAAAACAGGTTTTAATGATGGTATAAATTTGGCTTGGATTGTTGGATTTATAGAGAGTAAAAACAAAATTTTATCTTTTGCCTTAAATGTTGATATAAAGAACATTAAAAATATTAAAATAAGAGAAGAATTGCTAGAAAAATATATTTATTCTTTAAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36772","NCBI_taxonomy_name":"Campylobacter jejuni","NCBI_taxonomy_id":"197"}}}},"ARO_accession":"3001477","ARO_id":"37877","ARO_name":"OXA-185","CARD_short_name":"OXA-185","ARO_description":"OXA-185 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46491":{"category_aro_accession":"3007702","category_aro_cvterm_id":"46491","category_aro_name":"OXA-184-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-184.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3445":{"model_id":"3445","model_name":"OXA-280","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"5641":{"protein_sequence":{"accession":"ENV74419.1","sequence":"MKTLQLGLIVLITTFGSACTIIRSPSIETAKNHEQQSAQQQIQQAFDQLQTTGVIVIKDKHGLHSYGNDLSRAQTPYVPASTFKMLNALIGLEHGKATSTEVFKWDGQKNSFPAWEKDMTLGQAMQASAVPVYQELARRIGLDLMQKEVQRIGYGNQQIGTVVDNFWLVGPLQITPVQEVLFVEKLANTQLAFKPDVQHTVQDMLLIEQKPNYKLYAKSGWGMDLEPQVGWWTGWVETATGEKVYFALNMHMKTGISASVREQLVKQSLTALGII"},"dna_sequence":{"accession":"APPZ01000001.1","fmin":"7525","fmax":"8353","strand":"+","sequence":"ATGAAAACTTTACAGTTGGGCCTCATCGTCCTCATTACTACCTTCGGTTCTGCATGTACCATAATAAGAAGCCCCTCCATAGAAACAGCTAAAAACCATGAGCAACAAAGTGCGCAGCAGCAGATCCAACAGGCCTTCGATCAACTCCAAACCACGGGGGTGATTGTCATAAAGGATAAGCATGGCTTACACAGCTACGGCAATGACTTGAGCCGTGCTCAGACACCCTATGTACCCGCCTCTACCTTTAAAATGCTGAATGCCTTAATCGGACTAGAACATGGTAAAGCAACCAGCACCGAGGTGTTTAAATGGGATGGTCAAAAGAACAGCTTCCCTGCTTGGGAAAAAGACATGACTTTAGGGCAAGCCATGCAAGCATCTGCCGTTCCTGTTTATCAGGAGCTAGCACGGCGCATTGGCCTAGATCTAATGCAAAAAGAAGTACAGCGCATTGGATATGGCAATCAACAGATTGGCACCGTTGTCGATAATTTTTGGTTAGTCGGTCCACTGCAAATTACGCCTGTTCAAGAAGTCCTTTTTGTAGAGAAGCTGGCCAATACGCAACTCGCTTTTAAGCCAGATGTGCAACATACCGTACAAGACATGCTGCTGATTGAACAAAAACCGAATTATAAACTCTACGCCAAATCTGGTTGGGGCATGGACCTAGAACCGCAAGTGGGCTGGTGGACAGGCTGGGTCGAAACAGCAACAGGTGAAAAAGTGTATTTTGCTTTGAATATGCATATGAAAACAGGAATTTCAGCCAGCGTGCGTGAGCAACTGGTCAAACAAAGTCTGACAGCACTGGGAATAATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42807","NCBI_taxonomy_name":"Acinetobacter johnsonii ANC 3681","NCBI_taxonomy_id":"1217662"}}}},"ARO_accession":"3001735","ARO_id":"38135","ARO_name":"OXA-280","CARD_short_name":"OXA-280","ARO_description":"OXA-280 is a beta-lactamase found in Acinetobacter spp.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46494":{"category_aro_accession":"3007705","category_aro_cvterm_id":"46494","category_aro_name":"OXA-211-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-211.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3474":{"model_id":"3474","model_name":"OXA-340","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"5668":{"protein_sequence":{"accession":"OTK94966.1","sequence":"MNIKALLLITSAIFISACSPYIVSANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWNGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NGCN01000023.1","fmin":"65770","fmax":"66595","strand":"-","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGTCTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGAACGGGCAAAAAAGGCTGTTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001528","ARO_id":"37928","ARO_name":"OXA-340","CARD_short_name":"OXA-340","ARO_description":"OXA-340 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3533":{"model_id":"3533","model_name":"OXA-471","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"5728":{"protein_sequence":{"accession":"ALC79286.1","sequence":"MSKKNFILIFIFVILISCKNTEKISNETTLIDNIFTNSNAEGTLVIYNLNDDKYIIHNKERAEQRFYPASTFKIYNSLIGLNEKAVKDVDEVFYKYNGEKVFLESWAKDSNLRYAIKNSQVPAYKELARRIGLKKMKENIEKLDFGNKSIGDSVDTFWLEGPLEISAMEQVKLLTKLAQNELPYPIEIQKAISDITILEQTYNYTLHGKTGLADSKNMTTEPIGWFVGWLEENDNIYVFALNIDNINSDDLAKRINIVKESLKALNLLK"},"dna_sequence":{"accession":"KR182164.1","fmin":"0","fmax":"810","strand":"+","sequence":"ATGTCTAAAAAAAATTTTATATTAATATTTATTTTTGTTATTTTAATATCTTGTAAAAATACAGAAAAAATATCAAATGAAACTACATTAATAGATAATATATTTACTAATAGCAATGCTGAAGGAACATTAGTTATATATAATTTAAATGATGATAAATATATAATTCATAATAAAGAAAGAGCTGAACAAAGATTTTATCCAGCATCAACATTTAAAATATATAATAGTTTAATAGGCTTAAATGAAAAAGCAGTTAAAGATGTAGATGAAGTATTTTATAAATATAATGGCGAAAAAGTTTTTCTCGAATCTTGGGCTAAAGACTCTAATTTAAGATATGCAATTAAAAATTCGCAAGTACCGGCATATAAAGAATTAGCAAGAAGAATAGGTCTTAAAAAGATGAAAGAGAATATAGAAAAACTAGATTTTGGTAATAAAAGTATAGGTGATAGTGTAGATACTTTTTGGCTTGAAGGACCTTTGGAAATAAGTGCGATGGAGCAAGTTAAATTATTAACTAAATTAGCTCAAAATGAATTACCGTATCCTATAGAAATACAAAAAGCTATTTCTGATATTACTATACTAGAGCAAACTTACAATTATACGCTTCATGGAAAAACTGGATTAGCTGATTCTAAAAACATGACAACTGAGCCTATTGGTTGGTTCGTAGGCTGGCTTGAAGAAAATGATAATATATACGTCTTTGCTTTAAATATTGATAATATCAATTCAGATGACCTTGCAAAAAGGATAAATATAGTAAAAGAAAGTTTAAAAGCATTAAATTTATTAAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36935","NCBI_taxonomy_name":"Brachyspira pilosicoli","NCBI_taxonomy_id":"52584"}}}},"ARO_accession":"3003627","ARO_id":"40237","ARO_name":"OXA-471","CARD_short_name":"OXA-471","ARO_description":"OXA-471 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46521":{"category_aro_accession":"3007732","category_aro_cvterm_id":"46521","category_aro_name":"OXA-63-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-63.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3575":{"model_id":"3575","model_name":"CME-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"5771":{"protein_sequence":{"accession":"CAB55427.1","sequence":"MKKIILLFILTSQLVLAQHTSILNDINAVTKDKKATVAVSVLGIENDFQFSNANGNLKMPMLSVFKFHIALAVLNQVDKGNLTLDQKILIKKSDLLENTWSPLREKYPDGNVELPLSEIITYTVAQSDNNGCDILLRLIGGTKTVQKLMDVNGIKNFQIKYNEEEMHKNDVKTLYANYTTTASMVKTLKAFYKGMFLSKRSTIFLMDIMTKTNTGMSKLPGLLPKVRMARKTGSSGKMKNGLTIAENDSGIVTLANGKHYAIAVFVKDSMESEEVNCGMIAQVSKIVWDALNKKK"},"dna_sequence":{"accession":"AJ006275.1","fmin":"71","fmax":"959","strand":"+","sequence":"ATGAAAAAAATTATACTCCTATTTATCTTGACAAGCCAGTTGGTGCTTGCTCAACATACTTCAATATTAAATGATATAAATGCTGTTACCAAAGACAAGAAAGCCACAGTAGCTGTTTCTGTTTTGGGGATAGAAAATGATTTTCAGTTTAGTAACGCCAATGGTAATTTGAAAATGCCGATGCTGAGTGTTTTTAAATTTCATATTGCATTGGCGGTTCTAAATCAGGTAGACAAAGGTAACCTTACCTTGGATCAGAAAATACTGATTAAAAAATCGGATCTATTAGAAAATACATGGTCACCACTTCGTGAGAAGTATCCGGATGGAAATGTAGAACTTCCTTTAAGCGAAATTATTACTTATACCGTAGCCCAAAGTGACAACAACGGATGCGACATACTATTAAGGCTAATTGGCGGGACTAAAACTGTTCAGAAATTAATGGATGTGAATGGTATAAAAAACTTTCAGATAAAATATAATGAGGAAGAAATGCATAAAAATGATGTAAAAACTCTTTATGCAAATTACACGACCACAGCATCTATGGTAAAAACTCTGAAAGCGTTCTATAAAGGAATGTTTTTATCAAAAAGATCCACAATTTTTCTAATGGATATTATGACTAAAACCAATACCGGAATGTCAAAGCTTCCGGGCTTGCTGCCAAAAGTTAGAATGGCCAGAAAAACAGGTTCTTCGGGTAAAATGAAAAACGGATTAACGATTGCTGAGAACGATTCAGGAATTGTAACTTTAGCAAATGGTAAACATTATGCAATTGCAGTATTTGTAAAGGACTCTATGGAAAGTGAGGAAGTCAATTGTGGAATGATTGCCCAGGTCTCGAAAATTGTCTGGGATGCTTTAAATAAAAAAAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36960","NCBI_taxonomy_name":"Elizabethkingia meningoseptica","NCBI_taxonomy_id":"238"}}}},"ARO_accession":"3004775","ARO_id":"42890","ARO_name":"CME-1","CARD_short_name":"CME-1","ARO_description":"CME-1 is a class A beta-lactamase gene belonging to Chryseobacterium meningosepticum.","ARO_category":{"42889":{"category_aro_accession":"3004774","category_aro_cvterm_id":"42889","category_aro_name":"CME beta-lactamase","category_aro_description":"CME is a class A beta-lactamase gene family belonging to Chryseobacterium meningosepticum.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3577":{"model_id":"3577","model_name":"CMY-132","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"5775":{"protein_sequence":{"accession":"AKZ20822.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKKLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"KP862820.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAAACTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3003652","ARO_id":"40262","ARO_name":"CMY-132","CARD_short_name":"CMY-132","ARO_description":"CMY-132 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3609":{"model_id":"3609","model_name":"GOB-8","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"575"}},"model_sequences":{"sequence":{"5807":{"protein_sequence":{"accession":"AAQ54756.1","sequence":"MRNFVILFFMFICLGLNAQVVKEPENMPKEWNQTYEPFRIAGNLYYVGTYDLASYLIVTDKGNILINTGTAESLPIIKANIQKLGFNYKDIKILLLTQAHYDHTGALQDLKTETGAKFYADKEDADVLRTGGKSDYEMGKYGVTFKPVTPDKTLKDQDKITLGNTILTLLHHPGHTKGSCSFIFETKDEKRKYRVLIANMPSVIVDKKFSEVTAYPNIQSDYAYTFKAMKNLDFDIWVASHASQFDLHEKRKEGDPYNPQLFMDKQSYFQNLNDLEKSYLNKRKKDSQDK"},"dna_sequence":{"accession":"AY348327.1","fmin":"0","fmax":"873","strand":"+","sequence":"ATGAGAAATTTTGTTATACTGTTTTTCATGTTCATTTGCTTGGGCTTGAATGCTCAGGTAGTAAAAGAACCTGAAAATATGCCCAAAGAATGGAACCAGACTTATGAACCCTTCAGAATTGCAGGTAATTTATATTACGTAGGAACCTATGATTTGGCTTCTTACCTTATTGTGACAGACAAAGGCAATATTCTCATTAATACAGGAACGGCAGAATCGCTTCCAATAATAAAAGCAAATATCCAAAAGCTCGGGTTTAATTATAAAGACATTAAGATCTTGCTGCTTACTCAGGCTCACTACGACCATACAGGTGCATTACAAGATCTTAAAACAGAAACCGGTGCAAAATTCTATGCCGATAAAGAAGATGCTGATGTCCTGAGAACAGGGGGGAAGTCCGATTATGAAATGGGAAAATATGGGGTGACATTTAAACCTGTTACTCCGGATAAAACATTGAAAGATCAGGATAAAATAACACTGGGAAATACAATCCTGACTTTGCTTCATCATCCCGGACATACAAAAGGTTCCTGTAGTTTTATTTTTGAAACAAAAGACGAGAAGAGAAAATATAGAGTTTTGATAGCTAATATGCCCTCCGTTATTGTTGATAAGAAATTTTCTGAAGTTACCGCATATCCAAATATTCAGTCCGATTATGCATATACTTTCAAAGCAATGAAGAATCTGGATTTTGATATTTGGGTGGCCTCCCATGCAAGTCAGTTCGATCTCCATGAAAAACGTAAAGAAGGAGATCCGTACAATCCGCAATTGTTTATGGATAAGCAAAGCTATTTCCAAAACCTTAATGATTTGGAAAAAAGCTATCTCAACAAAAGAAAAAAAGATTCCCAAGATAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36960","NCBI_taxonomy_name":"Elizabethkingia meningoseptica","NCBI_taxonomy_id":"238"}}}},"ARO_accession":"3004815","ARO_id":"42935","ARO_name":"GOB-8","CARD_short_name":"GOB-8","ARO_description":"GOB-8 is a class B beta-lactamase gene found in Elizabethkingia meningoseptica.","ARO_category":{"41376":{"category_aro_accession":"3004212","category_aro_cvterm_id":"41376","category_aro_name":"GOB beta-lactamase","category_aro_description":"The GOB family of beta-lactamases have been discovered in the Elizabethkingia meningoseptica and are classified as subclass B3 beta-lactamase. They confer resistance to cephalosporins, penicillins, and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3619":{"model_id":"3619","model_name":"IMP-52","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"495"}},"model_sequences":{"sequence":{"5817":{"protein_sequence":{"accession":"BAR80870.1","sequence":"MSKLSVFFIFLFCSIATAAESLPDLKIEKLDEGVYVHTSFEEVNGWGVVPKHGLVVLVNAEAYIIDTPFTAKDTEKLGTWFVERGYKIKGSISSHFHSDSTGGIEWLNSRSIPTYASELTNELLKKDGKVQATNSFSGVNYWLVKNKIEVFYPGPGHTPDNVVVWLPERKILFGGCFIKPYGLGNLGDANIEAWPKSAKLLKSKYGKAKLVVPSHSEVGDASLLKLTLEQAVKGLNESKKPSKPSN"},"dna_sequence":{"accession":"LC055762.1","fmin":"565","fmax":"1306","strand":"+","sequence":"ATGAGCAAGTTATCTGTATTCTTTATATTTTTGTTTTGCAGCATTGCTACCGCAGCAGAGTCTTTGCCAGATTTAAAAATTGAAAAGCTTGATGAAGGCGTTTATGTTCATACTTCGTTTGAAGAAGTTAACGGGTGGGGCGTTGTTCCTAAACATGGTTTGGTGGTTCTTGTAAATGCTGAGGCTTACATAATTGACACTCCATTTACGGCTAAAGATACTGAAAAGTTAGGCACTTGGTTTGTGGAGCGTGGCTATAAAATAAAAGGCAGCATTTCCTCTCATTTTCATAGCGACAGCACGGGCGGAATAGAGTGGCTTAATTCTCGATCTATCCCCACGTATGCATCTGAATTAACAAATGAACTGCTTAAAAAAGACGGTAAGGTTCAAGCCACAAATTCATTTAGCGGAGTTAACTATTGGCTAGTTAAAAATAAAATTGAAGTTTTTTATCCAGGCCCGGGACACACTCCAGATAACGTAGTGGTTTGGTTGCCTGAAAGGAAAATATTATTCGGTGGTTGTTTTATTAAACCGTACGGTTTAGGCAATTTGGGTGACGCAAATATAGAAGCTTGGCCAAAGTCCGCCAAATTATTAAAGTCCAAATATGGTAAGGCAAAACTGGTTGTTCCAAGTCACAGTGAAGTTGGAGACGCATCACTCTTGAAACTTACATTAGAGCAGGCGGTTAAAGGGTTAAACGAAAGTAAAAAACCATCAAAACCAAGCAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3004823","ARO_id":"42953","ARO_name":"IMP-52","CARD_short_name":"IMP-52","ARO_description":"IMP-52 is a class B metallo-beta-lactamase found in Escherichia coli.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3624":{"model_id":"3624","model_name":"LEN-35","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"575"}},"model_sequences":{"sequence":{"5822":{"protein_sequence":{"accession":"ALK01318.1","sequence":"MRYIRLCVISLLATLPLAVYAGPQPLEQIKQSESQLSGRVGMVEMDLASGRTLAAWRADERFPMVSTFKVLLCGAVLARVDAGLEQLDRRIHYRQQDLVDYSPVSEKHLTDGMTVGELCAAAITLSDNSAGNLLLATVGGPAGLTAFLRQIGDNVTRLDRWETALNEALPGDARDTTTPASMAATLRKLLTAQHLSARSQQQLLQWMVDDRVAGPLIRAVLPPGWFIADKTGAGERGARGIVALLGPDGKPERIVVIYLRDTPASMAERNQHIAGIGAALIEHWHD"},"dna_sequence":{"accession":"KR738737.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTGTTATCTCCCTGTTAGCCACCCTGCCACTGGCGGTATACGCCGGTCCACAGCCGCTTGAGCAGATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTGGGGATGGTGGAAATGGATCTGGCCAGCGGCCGCACGCTGGCGGCCTGGCGCGCCGATGAACGCTTTCCCATGGTGAGCACCTTTAAAGTGCTGCTGTGCGGCGCGGTGCTGGCGCGGGTGGATGCCGGGCTCGAACAACTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTACCGACGGGATGACGGTCGGCGAACTCTGCGCCGCCGCCATCACCCTGAGCGATAACAGCGCTGGCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCGGGATTAACTGCCTTTCTGCGCCAGATCGGTGACAACGTCACCCGTCTTGACCGCTGGGAAACGGCACTGAATGAGGCGCTTCCCGGCGACGCGCGCGACACCACCACCCCGGCCAGCATGGCTGCCACGCTGCGCAAACTACTGACCGCGCAGCATCTGAGCGCCCGTTCGCAACAGCAACTCCTGCAGTGGATGGTGGACGATCGGGTTGCCGGCCCGCTGATCCGCGCCGTGCTGCCGCCGGGCTGGTTTATCGCCGACAAAACCGGGGCTGGCGAACGGGGTGCGCGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAACCGGAGCGCATTGTGGTGATCTATCTGCGGGATACCCCGGCGAGTATGGCCGAGCGTAATCAACATATCGCCGGGATCGGCGCAGCGCTGATCGAGCACTGGCACGACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42612","NCBI_taxonomy_name":"Klebsiella variicola","NCBI_taxonomy_id":"244366"}}}},"ARO_accession":"3004827","ARO_id":"42957","ARO_name":"LEN-35","CARD_short_name":"LEN-35","ARO_description":"LEN-35 is a Class A beta-lactamase gene found in Klebsiella variicola.","ARO_category":{"36236":{"category_aro_accession":"3000097","category_aro_cvterm_id":"36236","category_aro_name":"LEN beta-lactamase","category_aro_description":"LEN beta-lactamases are chromosomal class A beta-lactamases that confer resistance to ampicillin, amoxicillin, carbenicillin, and ticarcillin but not to extended-spectrum beta-lactams.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3660":{"model_id":"3660","model_name":"NDM-19","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"5932":{"protein_sequence":{"accession":"ASC49561.1","sequence":"MELPNIMHPVAKLSTALAAALMLSGCMPGEIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMNALHAAGIATYANALSNQLAPQEGLVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASVRAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR"},"dna_sequence":{"accession":"MF370080.1","fmin":"0","fmax":"813","strand":"+","sequence":"ATGGAATTGCCCAATATTATGCACCCGGTCGCGAAGCTGAGCACCGCATTAGCCGCTGCATTGATGCTGAGCGGGTGCATGCCCGGTGAAATCCGCCCGACGATTGGCCAGCAAATGGAAACTGGCGACCAACGGTTTGGCGATCTGGTTTTCCGCCAGCTCGCACCGAATGTCTGGCAGCACACTTCCTATCTCGACATGCCGGGTTTCGGGGCAGTCGCTTCCAACGGTTTGATCGTCAGGGATGGCGGCCGCGTGCTGGTGGTCGATACCGCCTGGACCGATGACCAGACCGCCCAGATCCTCAACTGGATCAAGCAGGAGATCAACCTGCCGGTCGCGCTGGCGGTGGTGACTCACGCGCATCAGGACAAGATGGGCGGTATGAACGCGCTGCATGCGGCGGGGATTGCGACTTATGCCAATGCGTTGTCGAACCAGCTTGCCCCGCAAGAGGGGCTGGTTGCGGCGCAACACAGCCTGACTTTCGCCGCCAATGGCTGGGTCGAACCAGCAACCGCGCCCAACTTTGGCCCGCTCAAGGTATTTTACCCCGGCCCCGGCCACACCAGTGACAATATCACCGTTGGGATCGACGGCACCGACATCGCTTTTGGTGGCTGCCTGATCAAGGACAGCAAGGCCAAGTCGCTCGGCAATCTCGGTGATGCCGACACTGAGCACTACGCCGCGTCAGTGCGCGCGTTTGGTGCGGCGTTCCCCAAGGCCAGCATGATCGTGATGAGCCATTCCGCCCCCGATAGCCGCGCCGCAATCACTCATACGGCCCGCATGGCCGACAAGCTGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3004862","ARO_id":"43000","ARO_name":"NDM-19","CARD_short_name":"NDM-19","ARO_description":"A class B New Delhi metallo-beta-lactamase and NDM-1 variant.","ARO_category":{"36196":{"category_aro_accession":"3000057","category_aro_cvterm_id":"36196","category_aro_name":"NDM beta-lactamase","category_aro_description":"NDM beta-lactamases or New Delhi metallo-beta-lactamases are class B beta-lactamases that confer resistance to a broad range of antibiotics including carbapenems, cephalosporins and penicillins.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3217":{"model_id":"3217","model_name":"mphK","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"5320":{"protein_sequence":{"accession":"AJE92936.1","sequence":"MTNLNEKQLITEIVGLARSQGLTVHSENAQLNETGMDFQVVFAKDDTGMPWVLRKPRRSDVVERASAEGITLAFLRANLTADVPDWRIHTPELIAYPMLKGTPAAGIDLEQKQYVWNMDHQPPSDDFVRTLADILAELHGTDQISAGQSGIEVIRPEDFRQMTADSMVDVKNKLGVSTTLWERWQKWVDDDAYWPGFSSLIHGDLHPPHILIDQNGRVTGLLDWTEAKVADPAKDFVLYQTIFGEKETARLLEYYDQAGGRIWAKMQEHISEMQAAYPVEIAKLALQTQQEEHINMALEALGVTSD"},"dna_sequence":{"accession":"CP010314.1","fmin":"275837","fmax":"276758","strand":"+","sequence":"ATGACAAACCTTAACGAAAAACAGCTTATCACTGAGATTGTCGGGCTTGCACGCAGCCAAGGTTTGACGGTTCATTCTGAGAACGCGCAATTGAATGAAACCGGAATGGACTTTCAAGTTGTATTTGCCAAGGACGACACAGGTATGCCATGGGTGCTGCGAAAACCGCGGCGAAGTGATGTTGTGGAAAGAGCATCTGCAGAAGGCATAACGCTTGCCTTTCTCCGCGCGAATCTGACTGCTGATGTGCCGGATTGGAGAATTCATACACCGGAATTGATCGCTTACCCCATGTTAAAAGGAACGCCGGCTGCTGGAATTGACTTGGAACAAAAGCAATATGTATGGAATATGGATCATCAGCCGCCGTCAGACGACTTTGTCCGCACACTTGCCGACATACTGGCTGAATTACATGGCACGGATCAAATATCTGCTGGGCAATCCGGAATAGAAGTGATAAGGCCAGAAGATTTCAGGCAAATGACAGCAGACTCTATGGTTGATGTGAAGAATAAGCTTGGCGTATCTACGACGCTTTGGGAAAGATGGCAAAAGTGGGTAGATGATGATGCATACTGGCCGGGTTTCTCTTCTTTGATACACGGCGATCTCCACCCGCCGCATATCCTTATCGATCAAAATGGACGTGTCACAGGACTTCTGGATTGGACAGAAGCGAAGGTTGCTGACCCAGCCAAGGATTTTGTTCTTTATCAAACCATTTTCGGAGAAAAAGAAACTGCCCGTTTGCTTGAATACTATGATCAAGCAGGCGGCCGAATATGGGCAAAAATGCAGGAACACATCTCAGAGATGCAGGCGGCGTATCCGGTGGAAATCGCCAAGCTAGCTCTGCAAACACAGCAGGAGGAACACATCAATATGGCGCTGGAAGCACTTGGTGTAACATCGGATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42601","NCBI_taxonomy_name":"Bacillus subtilis subsp. subtilis","NCBI_taxonomy_id":"135461"}}}},"ARO_accession":"3004541","ARO_id":"42412","ARO_name":"mphK","CARD_short_name":"mphK","ARO_description":"A chromosomal macrolide phosphotransferase identified from Bacillus subtilis.","ARO_category":{"36472":{"category_aro_accession":"3000333","category_aro_cvterm_id":"36472","category_aro_name":"macrolide phosphotransferase (MPH)","category_aro_description":"Macrolide phosphotransferases (MPH) are enzymes encoded by macrolide phosphotransferase genes (mph genes). These enzymes phosphorylate macrolides in GTP dependent manner at 2'-OH of desosamine sugar thereby inactivating them. Characterized MPH's are differentiated based on their substrate specificity.","category_aro_class_name":"AMR Gene Family"},"35974":{"category_aro_accession":"0000057","category_aro_cvterm_id":"35974","category_aro_name":"telithromycin","category_aro_description":"Telithromycin is a semi-synthetic derivative of erythromycin. It is a 14-membered macrolide and is the first ketolide antibiotic to be used in clinics. Telithromycin binds the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2785":{"model_id":"2785","model_name":"Klebsiella pneumoniae OmpK37","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"4406":{"protein_sequence":{"accession":"CAA09666.1","sequence":"MKRKVLALVIPALLAAGAAHAAEIYNKDGNKLDLYGKVDGLHYFSSDSKKDGDQTYLRFGFKGETQINDILTGYGQWEYNVQANNTETSSDQAWTRLAFAGIKVGDYGSFDYGRNYGVLYDVEGWTDILPEFGGDSYTYADNFMAGRANGVATYRNSDFFGLVEGLNFALQYQGKNEGQNAQDINVGTNNRSSDSDVRFDNGDGFGLSTSYDFGMGISAAAAYTSSDRTNDQMTQTNARGDKAEAWTAGLKYDANDIYLATMYSETRNMTPYGNDGVANKTQNFEVTAQYQFDFGLRPAISYLQSKGKDLYNNGRYADKDLVKYMDVGATYYFNRNMSTYVDYKINLLDGNDKFYEDNGISTDNIVALGLVYQF"},"dna_sequence":{"accession":"AJ011502.1","fmin":"300","fmax":"1425","strand":"+","sequence":"ATGAAAAGAAAAGTACTGGCCCTCGTTATTCCGGCTTTATTAGCCGCCGGTGCCGCGCATGCGGCGGAAATTTATAATAAAGACGGGAATAAATTAGATCTCTATGGCAAGGTAGATGGTCTGCATTATTTCTCCAGCGACTCGAAAAAAGACGGCGATCAAACTTATTTACGTTTTGGCTTTAAAGGCGAAACCCAGATCAACGATATTCTTACCGGCTATGGCCAGTGGGAATATAACGTTCAGGCCAACAACACCGAGACCTCCAGCGATCAGGCGTGGACCCGTCTGGCATTCGCCGGTATCAAAGTGGGCGATTACGGCTCCTTCGACTACGGTCGTAACTACGGCGTGCTGTACGACGTTGAAGGCTGGACCGATATTCTGCCGGAGTTCGGCGGCGACTCCTACACCTATGCGGATAACTTTATGGCAGGCCGCGCCAACGGCGTCGCAACCTACCGCAACAGCGATTTTTTCGGTCTGGTGGAGGGTCTGAACTTCGCCCTGCAGTATCAGGGTAAAAACGAAGGCCAGAACGCGCAGGATATCAACGTCGGCACCAATAACCGCAGCAGCGACAGCGATGTTCGCTTCGACAATGGCGATGGTTTCGGCCTCTCTACTTCCTACGACTTCGGCATGGGCATCAGCGCGGCGGCAGCTTACACCTCGTCTGACCGTACTAACGATCAGATGACCCAGACCAACGCGCGCGGCGATAAAGCGGAAGCCTGGACCGCCGGCCTGAAGTACGACGCCAACGATATCTACCTGGCGACCATGTACTCTGAAACCCGCAATATGACCCCGTACGGCAATGACGGCGTGGCCAATAAAACACAAAACTTCGAAGTCACCGCGCAGTATCAGTTCGACTTCGGCCTGCGTCCGGCCATCTCCTACCTGCAGTCCAAAGGCAAAGATCTGTACAATAACGGCCGCTATGCCGATAAAGATCTGGTCAAATATATGGACGTTGGCGCGACCTATTACTTCAACCGTAATATGTCCACCTATGTTGATTACAAAATCAACCTGCTGGATGGTAACGACAAATTCTACGAAGACAACGGTATCTCTACCGATAACATCGTCGCCCTGGGCCTGGTTTACCAGTTCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3004122","ARO_id":"41247","ARO_name":"Klebsiella pneumoniae OmpK37","CARD_short_name":"Kpne_OmpK37","ARO_description":"Klebsiella pneumoniae outer membrane porin protein. Is preferentially detected in porin-deficient strains. Functional characterization of this new porin revealed a narrower pore than those of porins OmpK35 and OmpK36, which did not allow penetration by certain beta-lactams. Also, when a resistant strain expresses porin OmpK37 is less susceptible to cefotaxime and cefoxitin than when it is expressing either OmpK36 or OmpK35.","ARO_category":{"41445":{"category_aro_accession":"3004281","category_aro_cvterm_id":"41445","category_aro_name":"General Bacterial Porin with reduced permeability to beta-lactams","category_aro_description":"These are GBPs that are associated with decreased susceptibility to beta-lactams either through mutations in the porin protein, absence of the porin protein, or expression of the porin protein.","category_aro_class_name":"AMR Gene Family"},"35927":{"category_aro_accession":"0000008","category_aro_cvterm_id":"35927","category_aro_name":"cefoxitin","category_aro_description":"Cefoxitin is a cephamycin antibiotic often grouped with the second generation cephalosporins. Cefoxitin is bactericidal and acts by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. Cefoxitin's 7-alpha-methoxy group and 3' leaving group make it a poor substrate for most beta-lactamases.","category_aro_class_name":"Antibiotic"},"36989":{"category_aro_accession":"3000645","category_aro_cvterm_id":"36989","category_aro_name":"cefotaxime","category_aro_description":"Cefotaxime is a semisynthetic cephalosporin taken parenterally. It is resistant to most beta-lactamases and active against Gram-negative rods and cocci due to its aminothiazoyl and methoximino functional groups.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36383":{"category_aro_accession":"3000244","category_aro_cvterm_id":"36383","category_aro_name":"reduced permeability to antibiotic","category_aro_description":"Reduction in permeability to antibiotic, generally through reduced production of porins, can provide resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3634":{"model_id":"3634","model_name":"LEN-30","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"5905":{"protein_sequence":{"accession":"SLY33602.1","sequence":"MRYVRLCVISLLANLPLAVDAGPQPLEQIKQSESQLSGRVGMVEMDLASGRTLAAWRADERFPMVSTFKVLLCGAVLARVDAGLEQLDRRIHYRQQDLVDYSPVSEKHLTDGMTVGELCAAAITLSDNSAGNLLLATVGGPAGLTAFLRQIGDNVTRLDRWETALNEALPGDARDTTTPASMAATLRKLLTAQHLSARSQQQLLQWMVDDRVAGPLIRAVLPPGWFIADKTGAGERGARGIVALLGPDGKPERIVVIYLRDTPASMAERNQHIAGIGAALIEHWQR"},"dna_sequence":{"accession":"FWOA01000001.1","fmin":"576795","fmax":"577656","strand":"-","sequence":"ATGCGTTATGTTCGCCTGTGTGTTATCTCCCTGTTAGCCAACCTGCCACTGGCGGTAGACGCCGGTCCACAGCCGCTTGAGCAGATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTGGGGATGGTGGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCGATGAACGCTTTCCCATGGTGAGCACCTTTAAAGTGCTGCTGTGCGGCGCGGTGCTGGCGCGGGTGGATGCCGGGCTCGAACAACTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTACCGACGGGATGACGGTCGGCGAACTCTGCGCCGCCGCCATCACCCTGAGCGATAACAGCGCTGGCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCGGGATTAACTGCCTTTCTGCGCCAGATCGGTGACAACGTCACCCGTCTTGACCGCTGGGAAACGGCACTGAATGAGGCGCTTCCCGGCGACGCGCGCGACACCACCACCCCGGCCAGCATGGCCGCCACGCTGCGCAAACTACTGACCGCGCAGCATCTGAGCGCCCGTTCGCAACAGCAACTCCTGCAGTGGATGGTGGACGATCGGGTTGCCGGCCCGCTGATCCGCGCCGTGCTGCCGCCGGGCTGGTTTATCGCCGACAAAACCGGGGCTGGCGAACGGGGTGCGCGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAACCGGAGCGCATTGTGGTGATCTATCTGCGGGATACCCCGGCGAGTATGGCCGAGCGTAATCAACATATCGCCGGGATCGGCGCAGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3004838","ARO_id":"42972","ARO_name":"LEN-30","CARD_short_name":"LEN-30","ARO_description":"A class-A beta-lactamase from Klebsiella pneumoniae.","ARO_category":{"36236":{"category_aro_accession":"3000097","category_aro_cvterm_id":"36236","category_aro_name":"LEN beta-lactamase","category_aro_description":"LEN beta-lactamases are chromosomal class A beta-lactamases that confer resistance to ampicillin, amoxicillin, carbenicillin, and ticarcillin but not to extended-spectrum beta-lactams.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3651":{"model_id":"3651","model_name":"Mycobacterium tuberculosis 16S rRNA mutation conferring resistance to capreomycin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"13259":"a1401g","13334":"g1484t","14212":"c1402t","9447":"a514c"},"CRyPTIC-R":{"13259":"a1401g","13334":"g1484t","14212":"c1402t"},"clinical":{"13259":"a1401g","13334":"g1484t","14212":"c1402t","14742":"a1401g","14746":"c1402t","14757":"g1484t","9445":"a1401g","9446":"g1484t","9447":"a514c","9279":"a1401g"},"WHO-R":{"14742":"a1401g","14746":"c1402t","14757":"g1484t"},"ReSeqTB-High":{"9445":"a1401g","9446":"g1484t"},"ReSeqTB-Moderate":{"9447":"a514c"},"Curated-R":{"9279":"a1401g"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"41093","param_value":"2700"}},"model_sequences":{"sequence":{"8768":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"NC_000962.3","fmin":"1471845","fmax":"1473382","strand":"+","sequence":"TTTTGTTTGGAGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGGAAAGGTCTCTTCGGAGATACTCGAGTGGCGAACGGGTGAGTAACACGTGGGTGATCTGCCCTGCACTTCGGGATAAGCCTGGGAAACTGGGTCTAATACCGGATAGGACCACGGGATGCATGTCTTGTGGTGGAAAGCGCTTTAGCGGTGTGGGATGAGCCCGCGGCCTATCAGCTTGTTGGTGGGGTGACGGCCTACCAAGGCGACGACGGGTAGCCGGCCTGAGAGGGTGTCCGGCCACACTGGGACTGAGATACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCGACGCCGCGTGGGGGATGACGGCCTTCGGGTTGTAAACCTCTTTCACCATCGACGAAGGTCCGGGTTCTCTCGGATTGACGGTAGGTGGAGAAGAAGCACCGGCCAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGTGCGAGCGTTGTCCGGAATTACTGGGCGTAAAGAGCTCGTAGGTGGTTTGTCGCGTTGTTCGTGAAATCTCACGGCTTAACTGTGAGCGTGCGGGCGATACGGGCAGACTAGAGTACTGCAGGGGAGACTGGAATTCCTGGTGTAGCGGTGGAATGCGCAGATATCAGGAGGAACACCGGTGGCGAAGGCGGGTCTCTGGGCAGTAACTGACGCTGAGGAGCGAAAGCGTGGGGAGCGAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGGTGGGTACTAGGTGTGGGTTTCCTTCCTTGGGATCCGTGCCGTAGCTAACGCATTAAGTACCCCGCCTGGGGAGTACGGCCGCAAGGCTAAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGCGGAGCATGTGGATTAATTCGATGCAACGCGAAGAACCTTACCTGGGTTTGACATGCACAGGACGCGTCTAGAGATAGGCGTTCCCTTGTGGCCTGTGTGCAGGTGGTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTCTCATGTTGCCAGCACGTAATGGTGGGGACTCGTGAGAGACTGCCGGGGTCAACTCGGAGGAAGGTGGGGATGACGTCAAGTCATCATGCCCCTTATGTCCAGGGCTTCACACATGCTACAATGGCCGGTACAAAGGGCTGCGATGCCGCGAGGTTAAGCGAATCCTTAAAAGCCGGTCTCAGTTCGGATCGGGGTCTGCAACTCGACCCCGTGAAGTCGGAGTCGCTAGTAATCGCAGATCAGCAACGCTGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACGTCATGAAAGTCGGTAACACCCGAAGCCAGTGGCCTAACCCTCGGGAGGGAGCTGTCGAAGGTGGGATCGGCGATTGGGACGAAGTCGTAACAAGGTAGCCGTACCGGAAGGTGCGGCTGGATCACCTCCTTTCT","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3004853","ARO_id":"42989","ARO_name":"Mycobacterium tuberculosis 16S rRNA mutation conferring resistance to capreomycin","CARD_short_name":"Mtub_16S_CAP","ARO_description":"Point mutations in the 3' domain of 16S rRNA of Mycobacterium tuberculosis can confer resistance to capreomycin.","ARO_category":{"40277":{"category_aro_accession":"3003666","category_aro_cvterm_id":"40277","category_aro_name":"16s rRNA with mutation conferring resistance to aminoglycoside antibiotics","category_aro_description":"Point mutations in the 16S rRNA of bacteria can confer resistance to aminoglycosides.","category_aro_class_name":"AMR Gene Family"},"40875":{"category_aro_accession":"3003993","category_aro_cvterm_id":"40875","category_aro_name":"capreomycin","category_aro_description":"Capreomycin is an aminoglycoside antibiotic, capable of treating a large number of infections but in particular used for killing bacteria causing tuberculosis.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3653":{"model_id":"3653","model_name":"SCO-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6282":{"protein_sequence":{"accession":"ABL75133.1","sequence":"MTRSALLIPLTTAAIALNAISPVYASDTHSIDDTVKQVETTLGAKVGIAVLDTGSQRAWFHRADDRFPMASTSKALTCAALLDKGQSFMNKEALIKKADLDEYAPVTSGIVGKKVSAADLCSITMRTSDNTAVNKVLEILGGPQAVTAYLRKTGDNITRLDRNEPDLNEGTPGDVRDTTTPRAILETLNKLVLGPTLGSDERKQLTTWLESNEVGDPLLRAGVPSDWRVADRTGAGGNGTRGVIAVMWPPKHAPIIAAIYITQTKATMEERNAAIASIGKAIAAEVLE"},"dna_sequence":{"accession":"EF063111.1","fmin":"1121","fmax":"1988","strand":"+","sequence":"ATGACAAGATCTGCCCTTTTGATTCCACTCACCACGGCGGCTATCGCGCTAAACGCAATATCGCCGGTTTATGCGAGCGACACCCATTCTATTGATGATACCGTAAAACAGGTTGAAACCACGCTGGGAGCAAAAGTGGGTATAGCCGTCCTGGACACCGGGTCTCAACGTGCCTGGTTCCACCGTGCTGATGACCGTTTCCCGATGGCGAGCACATCCAAAGCTCTGACCTGTGCAGCGCTGTTGGATAAAGGTCAGAGCTTTATGAATAAAGAGGCCTTGATCAAAAAGGCGGACCTGGATGAATATGCACCAGTGACATCCGGCATAGTCGGCAAAAAAGTAAGTGCGGCTGACCTTTGCAGCATTACCATGCGTACAAGTGACAATACCGCCGTCAACAAAGTTCTTGAAATCCTGGGAGGACCGCAAGCTGTAACCGCTTATTTGCGCAAGACAGGTGATAACATTACTCGACTTGACAGAAATGAACCGGACCTCAACGAAGGAACGCCTGGAGACGTGCGCGACACGACAACGCCTCGCGCTATTCTCGAAACACTTAATAAACTGGTACTGGGCCCCACTCTTGGCTCTGACGAGCGAAAACAACTCACAACCTGGCTTGAAAGTAATGAGGTTGGTGACCCTTTGCTGCGCGCTGGAGTTCCTTCTGATTGGCGCGTCGCCGATCGAACTGGCGCTGGAGGTAACGGGACGCGTGGGGTGATTGCCGTCATGTGGCCGCCAAAACACGCGCCAATCATTGCTGCGATTTACATTACACAGACGAAAGCCACTATGGAGGAAAGGAACGCTGCCATCGCCTCTATTGGCAAAGCGATTGCTGCCGAAGTTCTGGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3004856","ARO_id":"42992","ARO_name":"SCO-1","CARD_short_name":"SCO-1","ARO_description":"Narrow-spectrum beta-lactamase isolated from several Acinetobacter spp. isolates from Argentina, as well as E. Coli. Hydrolyzes penicillins at a high level and cephalosporins and carbapenems at a very low level.","ARO_category":{"42991":{"category_aro_accession":"3004855","category_aro_cvterm_id":"42991","category_aro_name":"SCO beta-lactamase","category_aro_description":"SCOs are Class A beta-lactamases that confer resistance to a narrow range of penams, with some minor activity on cephalosporins and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35976":{"category_aro_accession":"0000059","category_aro_cvterm_id":"35976","category_aro_name":"cefepime","category_aro_description":"Cefepime (INN) is a fourth-generation cephalosporin antibiotic developed in 1994. It contains an aminothiazolyl group that decreases its affinity with beta-lactamases. Cefepime shows high binding affinity with penicillin-binding proteins and has an extended spectrum of activity against Gram-positive and Gram-negative bacteria, with greater activity against both Gram-negative and Gram-positive organisms than third-generation agents.","category_aro_class_name":"Antibiotic"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"35980":{"category_aro_accession":"0000063","category_aro_cvterm_id":"35980","category_aro_name":"cefuroxime","category_aro_description":"Cefuroxime is a second-generation cephalosporin antibiotic with increased stability with beta-lactamases than first-generation cephalosporins. Cefuroxime is active against Gram-positive organisms but less active against methicillin-resistant strains.","category_aro_class_name":"Antibiotic"},"35981":{"category_aro_accession":"0000064","category_aro_cvterm_id":"35981","category_aro_name":"amoxicillin","category_aro_description":"Amoxicillin is a moderate-spectrum, bacteriolytic, beta-lactam antibiotic used to treat bacterial infections caused by susceptible microorganisms. A derivative of penicillin, it has a wider range of treatment but remains relatively ineffective against Gram-negative bacteria. It is commonly taken with clavulanic acid, a beta-lactamase inhibitor. Like other beta-lactams, amoxicillin interferes with the synthesis of peptidoglycan.","category_aro_class_name":"Antibiotic"},"35995":{"category_aro_accession":"0000078","category_aro_cvterm_id":"35995","category_aro_name":"piperacillin","category_aro_description":"Piperacillin is an acetylureidopenicillin and has an extended spectrum of targets relative to other beta-lactam antibiotics. It inhibits cell wall synthesis in bacteria, and is usually taken with the beta-lactamase inhibitor tazobactam to overcome penicillin-resistant bacteria.","category_aro_class_name":"Antibiotic"},"36989":{"category_aro_accession":"3000645","category_aro_cvterm_id":"36989","category_aro_name":"cefotaxime","category_aro_description":"Cefotaxime is a semisynthetic cephalosporin taken parenterally. It is resistant to most beta-lactamases and active against Gram-negative rods and cocci due to its aminothiazoyl and methoximino functional groups.","category_aro_class_name":"Antibiotic"},"37084":{"category_aro_accession":"3000704","category_aro_cvterm_id":"37084","category_aro_name":"cefalotin","category_aro_description":"Cefalotin is a semisynthetic cephalosporin antibiotic activate against staphylococci. It is resistant to staphylococci beta-lactamases but hydrolyzed by enterobacterial beta-lactamases.","category_aro_class_name":"Antibiotic"},"40523":{"category_aro_accession":"3003832","category_aro_cvterm_id":"40523","category_aro_name":"ticarcillin","category_aro_description":"Ticarcillin is a carboxypenicillin used for the treatment of Gram-negative bacteria, particularly P. aeruginosa. Ticarcillin's antibiotic properties arise from its ability to prevent cross-linking of peptidoglycan during cell wall synthesis, when the bacteria try to divide, causing cell death.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3995":{"model_id":"3995","model_name":"TEM-232","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6359":{"protein_sequence":{"accession":"WP_109545059.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEESFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDSWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"NG_057472.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAAAGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATAGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3005263","ARO_id":"43619","ARO_name":"TEM-232","CARD_short_name":"TEM-232","ARO_description":"TEM-232 is a beta-lactamase.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3629":{"model_id":"3629","model_name":"Neisseria gonorrhoeae PBP1 conferring resistance to beta-lactam antibiotics","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"9243":"L421P"},"Curated-R":{"9243":"L421P"},"clinical":{"9243":"L421P"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1475"}},"model_sequences":{"sequence":{"5846":{"protein_sequence":{"accession":"AAB52541.1","sequence":"MIKKILTTCFGLVFGFCVFGVGLVAIAILVTYPKLPSLDSLQHYQPKMPLTIYSADGEVIGMYGEQRREFTKIGDFPEVLRNAVIAAEDKRFYRHWGVDVWGVARAAVGNVVSGSVQSGASTITQQVAKNFYLSSEKTFTRKFNEVLLAYKIEQSLSKDKILELYFNQIYLGQRAYGFASAAQIYFNKNVRDLTLAEAAMLAGLPKAPSAYNPIVNPERAKLRQKYILNNMLEEKMITVQQRDQALNEELHYERFVRKIDQSALYVAEMVRQELYEKYGEDAYTQGFKVYTTVRADHQKVATEALRKALRNFDRGSSYRGAENYIDLSKSEDVEETVSQYLSGLYTVDKMVPAVVLDVTKKKNVVIQLPGGRRVTLDRRALGFAARAVNNEKMGEDRIRRGAVIRVKNNGGRWAVVQEPLLQGALVSLDAKTGAVRALVGGYDFHSKTFNRAVQAMRQPGSTFKPFVYSAALSKGMTASTVVNDAPISLPGKGPNGSVWTPKNSDGRYSGYITLRQALTASKNMVSIRILMSIGVGYAQQYIRRFGFRSSELPASLSMALGTGETTPLKVAEAYSVFANGGYRVSSHVIDKIYDRDGRLRAQMQPLVAGQNAPQAIDPRNAYIMYKIMQDVVRVGTARGAAALGRTDIAGKTGTTNDNKDAWFVGFNPDVVTAVYIGFDKPKSMGRVGYGGTIAVPVWVDYMRFALKGKQGKGMKMPEGVVSSNGEYYMKERMVTDPGLTLDNSGIAPQPSRRAKEDDGGAAEGGRQAADDEVRQDMQETPVLPSNTGSKQQQLDSLF"},"dna_sequence":{"accession":"U80933.1","fmin":"122","fmax":"2519","strand":"+","sequence":"ATGATTAAAAAGATTTTAACGACTTGTTTTGGTTTGGTTTTTGGGTTTTGTGTATTTGGAGTGGGTTTGGTTGCCATTGCTATTTTGGTAACGTATCCGAAACTGCCGTCTTTGGATTCTTTGCAGCATTACCAGCCTAAAATGCCGTTGACTATTTATTCGGCGGATGGGGAAGTCATCGGTATGTATGGGGAGCAGCGGCGCGAATTTACAAAAATCGGCGATTTCCCAGAGGTGTTGCGGAATGCGGTTATCGCCGCCGAGGATAAACGCTTTTACCGGCATTGGGGGGTGGATGTTTGGGGTGTTGCCCGCGCTGCCGTCGGCAATGTCGTGTCCGGCAGCGTGCAGTCGGGTGCGAGTACGATTACGCAGCAGGTGGCGAAAAATTTTTATTTGAGCAGTGAAAAAACGTTCACACGCAAATTCAATGAGGTGTTGCTTGCCTATAAAATCGAGCAGTCTTTAAGCAAAGACAAAATCCTCGAGTTGTATTTCAATCAGATTTACCTCGGTCAGCGCGCCTATGGTTTTGCATCTGCCGCGCAAATCTATTTCAATAAGAATGTCCGAGATTTGACTTTGGCGGAAGCCGCCATGCTTGCGGGACTGCCCAAGGCTCCGTCTGCCTATAATCCGATTGTTAATCCAGAACGTGCCAAGTTGCGCCAGAAGTATATTTTGAACAATATGCTCGAGGAGAAGATGATTACCGTGCAACAGCGCGATCAGGCGTTGAATGAGGAACTGCATTACGAGCGGTTTGTTCGGAAAATCGATCAGAGTGCTTTATATGTGGCGGAAATGGTGCGTCAGGAACTGTATGAGAAATACGGTGAAGATGCCTATACGCAGGGTTTTAAGGTTTATACCACGGTCCGCGCCGATCATCAGAAGGTGGCAACCGAGGCATTGCGCAAGGCTCTACGGAATTTCGATCGCGGCAGCAGCTACCGCGGTGCGGAAAACTATATCGATTTGAGTAAGAGTGAAGATGTCGAGGAGACTGTCAGCCAGTATCTGTCGGGACTCTATACCGTCGATAAAATGGTTCCCGCCGTTGTGTTGGATGTGACTAAAAAGAAAAATGTCGTCATACAGCTGCCCGGCGGCAGGCGGGTTACGCTTGACAGGCGCGCCTTGGGTTTTGCGGCCCGCGCGGTCAATAATGAAAAAATGGGGGAGGACCGTATCCGCAGGGGCGCGGTCATCCGTGTCAAAAACAACGGCGGGCGTTGGGCGGTGGTTCAAGAGCCGTTGCTGCAGGGGGCTTTGGTTTCGCTGGATGCAAAAACCGGAGCTGTGCGCGCGCTGGTCGGCGGTTATGATTTTCACAGCAAAACATTCAATCGTGCCGTTCAGGCAATGCGGCAGCCGGGTTCGACCTTTAAGCCGTTTGTCTATTCGGCGGCATTATCTAAGGGGATGACCGCGTCCACAGTGGTTAACGATGCGCCGATTTCCCTGCCGGGGAAAGGGCCGAACGGTTCGGTTTGGACACCTAAAAATTCAGACGGCAGATATTCCGGCTACATTACTTTGAGACAGGCTCTGACGGCTTCCAAGAATATGGTTTCCATCCGTATTTTGATGTCTATCGGTGTCGGTTACGCGCAACAGTATATCCGGCGTTTCGGCTTCAGGTCGTCCGAGCTGCCGGCAAGCCTGTCTATGGCTTTAGGTACGGGCGAGACAACGCCGTTGAAAGTGGCGGAGGCATATAGCGTATTTGCGAACGGCGGATATAGGGTTTCTTCGCACGTAATCGATAAGATTTATGACAGAGACGGCAGGTTGCGCGCCCAAATGCAACCTTTGGTGGCCGGGCAAAATGCGCCTCAGGCAATCGATCCGCGCAATGCCTATATTATGTATAAGATTATGCAGGATGTGGTCCGTGTTGGTACGGCAAGGGGGGCAGCTGCGTTGGGAAGAACGGATATTGCCGGTAAAACGGGTACGACCAATGACAATAAGGATGCGTGGTTTGTCGGTTTTAACCCTGATGTGGTTACTGCCGTATATATCGGCTTCGACAAACCTAAGAGTATGGGGCGTGTCGGCTACGGCGGTACGATTGCGGTGCCGGTTTGGGTGGACTATATGCGTTTTGCGTTGAAAGGAAAGCAGGGCAAGGGGATGAAAATGCCTGAAGGTGTGGTCAGCAGCAATGGCGAATACTATATGAAGGAACGTATGGTAACCGATCCGGGCTTGACGCTGGACAACAGCGGTATTGCGCCGCAACCTTCCCGACGGGCAAAAGAAGATGACGGGGGCGCGGCAGAAGGCGGACGGCAGGCGGCGGATGACGAAGTCCGCCAAGATATGCAGGAAACGCCGGTGCTTCCGAGTAATACTGGTTCCAAACAGCAGCAGTTGGATTCCCTGTTTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36753","NCBI_taxonomy_name":"Neisseria meningitidis","NCBI_taxonomy_id":"487"}}}},"ARO_accession":"3004833","ARO_id":"42963","ARO_name":"Neisseria gonorrhoeae PBP1 conferring resistance to beta-lactam antibiotics","CARD_short_name":"Ngon_PBP1_BLA","ARO_description":"Point mutation in Neisseria gonorrhoea PBP1 (ponA) decreases affinity between beta-lactam antibiotic molecule and PBP1, thereby conferring resistance to beta-lactam antibiotics.","ARO_category":{"40661":{"category_aro_accession":"3003938","category_aro_cvterm_id":"40661","category_aro_name":"Penicillin-binding protein mutations conferring resistance to beta-lactam antibiotics","category_aro_description":"Mutations in PBP transpeptidases that change the affinity for penicillin thereby conferring resistance to penicillin antibiotics.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3329":{"model_id":"3329","model_name":"Mycoplasma genitalium parC mutations confers resistance to Moxifloxacin","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"8771":"G81C","8772":"D82N","8773":"S83R","8774":"S83I","8775":"D87N","8776":"D87H","8777":"D87Y","8778":"D87G","8779":"V103I","8784":"P62S","8785":"A67S","8786":"A66T","8787":"S83N","8788":"A119V"},"Curated-R":{"8771":"G81C","8772":"D82N","8773":"S83R","8774":"S83I","8775":"D87N","8776":"D87H","8777":"D87Y","8778":"D87G","8779":"V103I","8784":"P62S","8785":"A67S","8786":"A66T","8787":"S83N","8788":"A119V"},"clinical":{"8771":"G81C","8772":"D82N","8773":"S83R","8774":"S83I","8775":"D87N","8776":"D87H","8777":"D87Y","8778":"D87G","8779":"V103I","8784":"P62S","8785":"A67S","8786":"A66T","8787":"S83N","8788":"A119V"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1200"}},"model_sequences":{"sequence":{"5889":{"protein_sequence":{"accession":"WP_010869372.1","sequence":"MDQKNNNLFQKAIEEVFAVSFSKYAKYIIQDRALPDLRDGLKPVQRRILYGMFQMGLKPTTPYKKSARAVGEIMGKYHPHGDSSIYDAIIRMSQSWKNNWTTVSIHGNNGSVDGDNAAAMRYTETRLSLYGFELLKDIDKKLVSFINNFDDSEKEPTVLPTLLPNLFINGASGIAAGYATNIAPHNTNELLDSLCLRIDQPNCELKQILKIVKGPDFPTGGNVYFEKSLSDIYQAGKGKFIIQAKYEVNKNLNQIEITQIPYETLKANIVKQIEEIIFDNKLSAIESVIDSSDRNGIRIIIKHKDFLPAEKIMAFLFKHTQLQVNFNLNNTVIANRFPIQIGLLSYLDHFLKFCHELIINKAKYELELASKRLEIILGLIKAISIIDKIIKLIRSAVDKSDAREKLIDNFKFTFNQAEAIVSLRLYQLTNTDIFELNQEQNELEKTVISSEQLIASEKARNKLLKKQFEGYKKQFHQQRRSQICGFINQKKVEESELIENKTYGVLITKAGNYHKFESNQLLKSTTDFKSESDTIIFAQTIANTDQIFIVTSLGNIINIPVYKLAFNSKNKLASLVSKKPILLEYETIVFVGTMNSVNQPILVLTSKLGMVKRIDLTKLNIKPLKATLCISLRDKDHLVSAFLQQDDKLICLVSDHNYYTVFHTNEIPLISSKGMGVKGMKLKLEDQIKFVVAFEANEPLVMICSDGSVINLKQTELVVVSRMATAKKLPVKKAINYCFSDATNTQLINFQGKNGSKLITTSELNQMSKTAISQTRFNKLN"},"dna_sequence":{"accession":"NC_000908.2","fmin":"242223","fmax":"244569","strand":"+","sequence":"ATGGATCAAAAAAACAACAACCTCTTTCAAAAGGCAATTGAAGAAGTCTTTGCAGTTAGCTTTAGTAAGTATGCTAAATACATCATCCAAGATAGAGCTTTACCTGATCTAAGAGATGGGTTAAAACCAGTACAAAGACGGATCTTATATGGGATGTTTCAAATGGGCTTAAAACCCACCACTCCCTATAAAAAATCAGCCCGTGCTGTTGGGGAGATCATGGGGAAATACCACCCCCATGGTGATAGTTCCATTTATGATGCAATTATCAGAATGTCCCAAAGCTGAAAGAACAACTGAACAACTGTTTCTATCCATGGTAACAATGGTTCAGTGGATGGGGATAATGCTGCAGCAATGCGTTACACAGAAACCCGCTTAAGCTTGTATGGATTTGAACTATTAAAAGACATTGATAAAAAGTTAGTTAGTTTTATCAATAACTTTGATGATAGTGAAAAAGAACCAACGGTTTTACCAACCTTACTGCCTAACCTCTTTATCAATGGTGCGAGTGGGATAGCTGCTGGATATGCAACTAATATTGCTCCCCATAACACTAATGAACTATTAGATAGTCTTTGCTTGCGAATAGACCAACCTAATTGTGAACTTAAACAAATTTTAAAAATTGTTAAAGGTCCTGATTTTCCAACAGGGGGTAATGTTTATTTTGAAAAGAGTTTAAGTGATATTTATCAAGCAGGCAAAGGTAAATTTATTATCCAAGCTAAGTATGAAGTTAACAAGAACTTAAACCAGATTGAAATTACCCAAATCCCTTATGAAACACTGAAAGCTAACATTGTCAAACAAATTGAAGAGATTATCTTTGACAATAAACTATCTGCTATTGAAAGTGTCATTGATAGTTCAGATCGCAACGGCATTAGGATCATTATTAAACACAAGGACTTTTTGCCTGCTGAGAAGATCATGGCCTTTTTGTTTAAACACACCCAACTCCAAGTGAACTTTAACCTTAATAACACCGTGATTGCTAACCGCTTTCCCATCCAAATTGGTTTACTAAGTTACCTCGATCATTTTTTAAAGTTTTGTCATGAACTAATTATTAATAAAGCTAAGTATGAACTTGAGCTTGCAAGCAAGCGCTTGGAAATTATTTTAGGACTAATTAAAGCGATTAGTATCATTGATAAAATCATCAAATTAATTAGATCAGCAGTTGACAAAAGTGATGCAAGAGAAAAGTTAATTGATAACTTTAAATTTACTTTTAACCAAGCAGAGGCAATTGTTAGTTTGCGACTTTACCAACTAACTAACACTGATATTTTTGAACTTAACCAAGAACAAAATGAACTTGAAAAAACTGTGATTAGTTCAGAGCAACTAATTGCTAGTGAAAAAGCAAGAAACAAACTCCTAAAAAAACAGTTTGAAGGTTATAAAAAGCAGTTTCACCAGCAACGAAGGTCACAAATATGTGGCTTTATTAACCAAAAAAAGGTGGAGGAAAGTGAGCTAATTGAAAACAAAACTTATGGGGTTTTAATCACTAAAGCTGGTAACTACCATAAGTTTGAATCTAACCAACTATTAAAAAGCACCACTGATTTTAAAAGTGAGAGTGACACAATTATCTTTGCACAAACTATTGCTAATACCGACCAAATTTTTATTGTCACTTCACTAGGTAACATTATTAATATCCCTGTTTATAAATTAGCTTTCAATTCCAAAAATAAACTAGCAAGTTTAGTTAGTAAAAAACCAATCCTTTTGGAGTATGAAACGATTGTTTTTGTTGGAACAATGAACAGTGTAAACCAACCAATCCTTGTTTTAACTTCCAAACTAGGAATGGTTAAACGGATTGATTTAACCAAACTTAACATTAAGCCACTTAAAGCTACTTTGTGTATCTCACTCCGTGATAAAGACCATTTAGTAAGTGCATTTTTACAACAAGATGATAAACTGATCTGTTTAGTGTCTGATCACAACTATTACACTGTTTTTCACACCAATGAGATCCCATTAATTAGTAGTAAGGGGATGGGAGTGAAGGGGATGAAGTTAAAACTAGAGGATCAAATTAAGTTTGTTGTTGCTTTTGAAGCTAATGAACCGTTAGTGATGATATGTAGTGATGGTAGTGTCATTAACTTAAAACAAACTGAACTAGTTGTAGTTAGCAGGATGGCAACTGCAAAAAAACTGCCTGTTAAGAAAGCAATTAACTATTGTTTTAGTGATGCAACTAACACCCAGTTAATTAATTTTCAGGGTAAGAACGGTAGTAAATTAATTACAACTAGTGAACTGAACCAGATGAGTAAAACTGCAATTAGTCAAACCAGGTTTAACAAACTTAATTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42595","NCBI_taxonomy_name":"Mycoplasma genitalium","NCBI_taxonomy_id":"2097"}}}},"ARO_accession":"3004630","ARO_id":"42617","ARO_name":"Mycoplasma genitalium parC mutations confers resistance to Moxifloxacin","CARD_short_name":"Mgen_parC_MXF","ARO_description":"Mycoplasma genitalium exhibits multiple mutations in parC which confers resistance to Moxifloxacin.","ARO_category":{"36913":{"category_aro_accession":"3000619","category_aro_cvterm_id":"36913","category_aro_name":"fluoroquinolone resistant parC","category_aro_description":"ParC is a subunit of topoisomerase IV, which decatenates and relaxes DNA to allow access to genes for transcription or translation. Point mutations in ParC prevent fluoroquinolone antibiotics from inhibiting DNA synthesis, and confer low-level resistance. Higher-level resistance results from both gyrA and parC mutations.","category_aro_class_name":"AMR Gene Family"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3646":{"model_id":"3646","model_name":"Neisseria gonorrhoeae 23S rRNA with mutation conferring resistance to azithromycin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"41093","param_value":"5300"},"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"9356":"a2145g","9355":"c2600t","9358":"a2045g","9357":"c2597t","10522":"a2059g","10523":"c2611t"},"Curated-R":{"9356":"a2145g","9355":"c2600t","9358":"a2045g","9357":"c2597t","10522":"a2059g","10523":"c2611t"},"clinical":{"9356":"a2145g","9355":"c2600t","9358":"a2045g","9357":"c2597t","10522":"a2059g","10523":"c2611t"}}},"model_sequences":{"sequence":{"5918":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"NR_103957.1","fmin":"0","fmax":"2910","strand":"+","sequence":"TGAAATGATAGAGTCAAGTGAATAAGTGCATCAGGCGGATGCCTTGGCGATGATAGGCGACGAAGGACGTGTAAGCCTGCGAAAAGCGCGGGGGAGCTGGCAATAAAGCAATGATCCCGCGGTGTCCGAATGGGGAAACCCACTGCATTCTGTGCAGTATCCTAAGTTGAATACATAGGCTTAGAGAAGCGAACCCGGAGAACTGAACCATCTAAGTACCCGGAGGAAAAGAAATCAACCGAGATTCCGCAAGTAGTGGCGAGCGAACGCGGAGGAGCCTGTACGTAATAACTGTCGAGGTAGAAGAACAAGCTGGGAAGCTTGACCATAGCGGGTGACAGTCCCGTATTCGAAATCTCAACAGCGGTACTAAGCGTACGAAAAGTAGGGCGGGACACGTGAAATCCTGTCTGAATATGGGGGGACCATCCTCCAAGGCTAAATACTCATCATCGACCGATAGTGAACCAGTACCGTGAGGGAAAGGCGAAAAGAACCCCGGGAGGGGAGTGAAACAGAACCTGAAACCTGATGCATACAAACAGTGGGAGCGCCCTAGTGGTGTGACTGCGTACCTTTTGTATAATGGGTCAACGACTTACATTCAGTAGCGAGCTTAACCGGATAGGGGAGGCGTAGGGAAACCGAGTCTTAATAGGGCGATGAGTTGCTGGGTGTAGACCCGAAACCGAGTGATCTATCCATGGCCAGGTTGAAGGTGCCGTAACAGGTACTGGAGGACCGAACCCACGCATGTTGCAAAATGCGGGGATGAGCTGTGGGTAGGGGTGAAAGGCTAAACAAACTCGGAGATAGCTGGTTCTCCCCGAAAACTATTTAGGTAGTGCCTCGAGCAAGACACTGATGGGGGTAAAGCACTGTTATGGCTAGGGGGTTATTGCAACTTACCAACCCATGGCAAACTCAGAATACCATCAAGTGGTTCCTCGGGAGACAGACAGCGGGTGCTAACGTCCGTTGTCAAGAGGGAAACAACCCAGACCGCCGGCTAAGGTCCCAAATGATAGATTAAGTGGTAAACGAAGTGGGAAGGCACAGACAGCCAGGATGTTGGCTTAGAAGCAGCCATCATTTAAAGAAAGCGTAATAGCTCACTGGTCGAGTCGTCCTGCGCGGAAGATGTAACGGGGCTCAAATCTATAACCGAAGCTGCGGATGCCGGTTTACCGGCATGGTAGGGGAGCGTTCTGTAGGCTGATGAAGGTGCATTGTAAAGTGTGCTGGAGGTATCAGAAGTGCGAATGTTGACATGAGTAGCGATAAAGCGGGTGAAAAGCCCGCTCGCCGAAAGCCCAAGGTTTCCTACGCAACGTTCATCGGCGTAGGGTGAGTCGGCCCCTAAGGCGAGGCAGAAATGCGTAGTCGATGGGAAACAGGTTAATATTCCTGTACTTGATTCAAATGCGATGTGGGGACGGAGAAGGTTAGGTTGGCAAGCTGTTGGAATAGCTTGTTTAAGCCGGTAGGTGGAAGACTTAGGCAAATCCGGGTTTTCTTAACACCGAAGAAGTGATGACGAGTGTTTACGGACACGAAGCAACCGATACCACGCTTCCAGGAAAAGCCACTAAGCTTCAGTTTGAATCGAACCGTACCGCAAACCGACACAGGTGGGCAGGATGAGAATTCTAAGGCGCTTGAGAGAACTCGGGAGAAGGAACTCGGCAAATTGATACCGTAACTTCGGGAGAAGGTATGCCCTCTAAGGTTAAGGACTTGCTCCGTAAGCCCCGGAGGGTCGCAGAGAATAGGTGGCTGCGACTTGTTTATTAAAAACACGAGCACTCTTGCCAACACGAAAGTGGACGTATAGGGTGTAACGCCTGCCCGGTGCCGGAAGGTTAATTGAAGATGTGCAAGCATCGGATCGAAGCCCCGGTAAACGGCGGCCGTAACTATAACGGTCCTAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCCGCACGAATGGCGTAACGATGGCCACACTGTCTCCTCCCGAGACTCAGCGAAGTTGAAGTGGTTGTGAAGATGCAATCTACCCGCTGCTAGACGGAAAGACCCCGTGAACCTTTACTGTAGCTTTGCATTGGACTTTGAAGTCACTTGTGTAGGATAGGTGGAAGGCTTGGAAGCAAAGACGCCAGTCTCTGTGGAGTCGTCCTTGAAAATACCACCCTGGTGTCTTTGAGGTTCTAACCCAGACCCGTCATCCGGGTCGGGGACCGTGCATGGTAGGCAGTTTGACTGGGGCGGTCTCCTCCCAAAGCGTAACGGAGGAGTTCGAAGGTTACCTAGGTCCGGTCGGAAATCGGACTGATAGTGCAATGGCAAAAGGTAGCTTAACTGCGAGACCGACAAGTCGGGCAGGTGCGAAAGCAGGACATAGTGATCCGGTGGTTCTGTATGGAAGGGCCATCGCTCAACGGATAAAAGGTACTCCGGGGATAACAGGCTTGATTCCGCCCAAGAGTTCATATCGACGGCGGAGTTTGGCACCTCGATGTCGGCTCATCACATCCTGGGGCTGTAGTCGGTCCCAAGGGTATGGCTGTTCGCCATTTTAAAGTGGTACGTGAGTTGGGTTTAAAACGTCGTGAGACAGTTTGGTCCCTATCTGCAGTGGGCGTTGGAAGTTTGACGGGGGCTGCTCCTAGTACGAGAGGACCGGAGTGGACGAACCTCTGGTGTACCGGTTGTAACGCCAGTTGCATAGCCGGGTAGCTAAGTTCGGAAGAGATAAGCGCTGAAAGCATCTAAGCGCGAAACTCGCCTGAAGATGAGACTTCCCTTGCGGTTTAACCGCACTAAAGGGTCGTTCGAGACCAGGACGTTGATAGGTGGGGTGTGGAAGCGCGGTAACGCGTGAAGCTAACCCATACTAATTGCCCGTGAGGCTTGACTCT","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36806","NCBI_taxonomy_name":"Neisseria gonorrhoeae","NCBI_taxonomy_id":"485"}}}},"ARO_accession":"3004836","ARO_id":"42966","ARO_name":"Neisseria gonorrhoeae 23S rRNA with mutation conferring resistance to azithromycin","CARD_short_name":"Ngon_23S_AZM","ARO_description":"Point mutation in the 23S rRNA of Neisseria gonorrhoea shown to confer resistance to azithromycin, a macrolide type antibiotic.","ARO_category":{"41251":{"category_aro_accession":"3004125","category_aro_cvterm_id":"41251","category_aro_name":"23S rRNA with mutation conferring resistance to macrolide antibiotics","category_aro_description":"Nucleotide point mutations in the 23S rRNA subunit may confer resistance to macrolide antibiotics.","category_aro_class_name":"AMR Gene Family"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3649":{"model_id":"3649","model_name":"Neisseria gonorrhoeae mtrR with mutation conferring resistance","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"},"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"9273":"A39T","9274":"G45D"},"Curated-R":{"9273":"A39T","9274":"G45D"},"clinical":{"9273":"A39T","9274":"G45D"}}},"model_sequences":{"sequence":{"8361":{"protein_sequence":{"accession":"ACF30254.1","sequence":"MRKTKTEALKTKEHLMLAALETFYRKGIARTSLNEIAQAAGVTRGALYWHFKNKEDLFDALFQRICDDIENCIAQDAADAEGGSWTVFRHTLLHFFERLQSNDIYYKFHNILFLKCEHTEQNAAVIAIARKHQAIWREKITAVLTEAVENQDLADDLDKETAVIFIKSTLDGLIWRWFSSGESFDLGKTAPRIIGIMMDNLENHPCLRRK"},"dna_sequence":{"accession":"CP001050.1","fmin":"1332866","fmax":"1333499","strand":"+","sequence":"ATGAGAAAAACCAAAACCGAAGCCTTGAAAACCAAAGAACACCTGATGCTTGCCGCCTTGGAAACCTTTTACCGCAAAGGGATTGCCCGCACCTCGCTCAACGAAATCGCCCAAGCCGCCGGCGTAACGCGCGGCGCGCTCTATTGGCATTTCAAAAATAAGGAAGACTTGTTTGACGCGTTGTTCCAACGTATCTGCGACGACATCGAAAACTGCATCGCGCAAGATGCCGCAGATGCCGAAGGAGGTTCTTGGACGGTATTCCGCCACACGCTGCTGCACTTTTTCGAGCGGCTGCAAAGCAACGACATCTACTACAAATTCCACAACATCCTGTTTTTAAAATGCGAACACACGGAGCAAAACGCCGCCGTTATCGCCATTGCCCGCAAGCATCAGGCAATCTGGCGCGAGAAAATTACCGCCGTTTTGACCGAAGCGGTGGAAAATCAGGATTTGGCTGACGATTTGGACAAGGAAACGGCGGTCATCTTCATCAAATCGACGTTGGACGGGCTGATTTGGCGTTGGTTCTCTTCCGGCGAAAGTTTCGATTTGGGCAAAACCGCCCCGCGCATCATCGGGATAATGATGGACAACTTGGAAAACCATCCCTGCCTGCGCCGGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37080","NCBI_taxonomy_name":"Neisseria gonorrhoeae NCCP11945","NCBI_taxonomy_id":"521006"}}}},"ARO_accession":"3004851","ARO_id":"42987","ARO_name":"Neisseria gonorrhoeae mtrR with mutation conferring resistance","CARD_short_name":"Ngon_mtrR_AZM","ARO_description":"MtrR is a repressor of mtrCDE efflux pump expression, point mutations in mtrR confer resistance to azithromycin and other drugs.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"3631":{"model_id":"3631","model_name":"Neisseria gonorrhoeae pilQ gene conferring resistance to beta-lactam","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1400"},"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"9247":"E666K"},"Curated-R":{"9247":"E666K"},"clinical":{"9247":"E666K"}}},"model_sequences":{"sequence":{"5848":{"protein_sequence":{"accession":"VEG60537.1","sequence":"MNTKLTKIISGLFVATAAFQTASAGNITDIKVSSLPNKQKIVKVSFDKEIVNPTGFVTSSPARIALDFEQTGISMDQQVLEYADPLLSKISAAQNSSRARLVLNLNKPGQYNTEVRGNKVWIFINESDDTVSAPARPAVKAAPAAPAKQQAAAPFTESVVSVSAPFSPAKQQAAASAKQQAATPAKQTNIDFRKDGKNAGIIELAALGFAGQPDISQQHDHIIVTLKNHTLPTALQRSLDVADFKTPVQKVTLKRLNNDTQLIITTTGNWELVNKSAAPGYFTFQVLPKKQNLESGGVNNAPKTFTGRKISLDFQDVEIRTILQILAKESGMNIVASDSVNGKMTLSLKDVPWDQALDLVMQARNLDMRQQGNIVNIAPRDELLAKDKAFLQAEKDIADLGALYSQNFQLKYKNVEEFRSILRLDNADTTGNRNTLVSGRGSVLIDPATNTLIVTDTRSVIEKFRKLIDELDVPAQQVMIEARIVEAADGFSRDLGVKFGATGRKKLKNETSAFGWGVNSGFGGGDKWEAQTKINLPVAAAANSISLVRAISSGALNLELSASESLSKTKTLANPRVLTQNRKEAKIESGYEIPFTVTTASGGGNSTNTELKKAVLGLTVTPNITPDGQIIMTVKINKDSPAQCASGNNTILCISTKSLNTQAMVENGGTLIVGGIYEENNGNTLTKVPLLGDIPVIGNLFKTRGKKTDRRELLIFITPRIIDTAGNSLRY"},"dna_sequence":{"accession":"LR134358.1","fmin":"1478691","fmax":"1480887","strand":"+","sequence":"ATGAATACCAAACTGACAAAAATCATTTCCGGTCTCTTTGTCGCAACCGCCGCCTTTCAGACGGCATCGGCAGGAAACATTACAGACATCAAAGTTTCCTCCCTGCCCAACAAACAGAAAATCGTCAAAGTCAGCTTTGACAAAGAGATTGTCAACCCGACCGGCTTCGTAACCTCCTCACCGGCCCGCATCGCCTTGGACTTTGAACAAACCGGCATTTCCATGGATCAACAGGTACTCGAATATGCCGATCCTCTGTTGAGCAAAATCAGTGCCGCACAAAACAGCAGCCGTGCGCGTCTGGTTCTGAATTTGAACAAACCGGGCCAATACAATACCGAAGTACGCGGGAACAAAGTTTGGATATTCATTAACGAATCGGACGATACCGTGTCCGCCCCCGCCCGCCCAGCCGTAAAAGCCGCGCCTGCCGCACCGGCAAAACAACAGGCTGCCGCACCGTTTACCGAGTCCGTAGTATCCGTATCCGCACCGTTCAGCCCGGCAAAACAACAGGCAGCGGCATCGGCAAAACAACAGGCGGCGACACCGGCAAAACAAACCAATATCGATTTCCGCAAAGACGGCAAAAATGCCGGCATTATCGAATTGGCGGCATTGGGCTTTGCCGGGCAGCCCGACATCAGCCAACAGCACGACCACATCATCGTTACGCTGAAAAACCATACCCTGCCGACCGCGCTCCAACGCAGTTTGGATGTGGCAGACTTCAAAACACCGGTTCAAAAGGTTACGCTGAAACGCCTCAATAACGACACCCAGCTGATTATCACAACAACCGGCAACTGGGAACTCGTCAACAAATCCGCCGCGCCCGGATACTTTACCTTCCAAGTCCTGCCGAAAAAACAAAACCTCGAGTCAGGCGGCGTGAACAATGCGCCCAAAACCTTCACAGGCCGGAAAATCTCCCTTGACTTCCAAGATGTCGAAATCCGCACCATCCTGCAGATTTTGGCAAAAGAATCCGGGATGAACATTGTTGCCAGCGACTCCGTCAACGGCAAAATGACCCTCTCCCTCAAAGATGTGCCTTGGGATCAGGCTTTGGATTTGGTTATGCAGGCGCGCAACCTCGATATGCGCCAGCAAGGGAACATCGTCAACATCGCGCCCCGCGACGAGCTGCTTGCCAAAGACAAAGCCTTCTTACAGGCGGAAAAAGACATTGCCGATCTGGGCGCGCTGTATTCCCAAAACTTCCAATTGAAATACAAAAATGTGGAAGAATTCCGCAGCATCCTGCGTTTGGACAATGCCGACACGACCGGAAACCGCAACACGCTTGTCAGCGGCAGGGGCAGCGTGCTGATCGATCCCGCCACCAACACCCTGATTGTTACCGATACCCGCAGCGTCATCGAAAAATTCCGCAAACTGATTGACGAATTGGACGTACCCGCGCAACAAGTGATGATTGAGGCGCGTATCGTCGAAGCGGCAGACGGCTTCTCGCGCGATTTGGGCGTTAAGTTCGGCGCGACAGGCAGGAAAAAACTGAAAAATGAGACGAGCGCATTCGGCTGGGGCGTGAACTCCGGCTTCGGGGGCGGCGATAAATGGGAGGCCCAAACCAAAATCAACCTGCCGGTTGCCGCTGCCGCAAACAGCATTTCGCTGGTGCGCGCGATTTCCTCCGGCGCGTTGAATTTGGAATTGTCCGCATCCGAGTCGCTTTCAAAAACCAAAACGCTTGCCAATCCGCGCGTGCTGACCCAAAACCGCAAAGAGGCCAAAATCGAATCCGGTTACGAAATTCCTTTTACCGTAACTACAGCCTCGGGCGGCGGCAACTCTACCAACACGGAACTCAAAAAAGCCGTCTTGGGGCTGACCGTTACGCCGAACATCACGCCCGACGGACAAATCATCATGACCGTCAAAATCAACAAAGACTCGCCTGCACAATGTGCTTCAGGCAACAACACAATCCTATGTATTTCGACCAAAAGCCTGAATACGCAGGCTATGGTTGAAAACGGCGGCACTTTGATTGTCGGCGGTATTTATGAAGAAAACAACGGCAATACGCTGACCAAAGTCCCCCTGTTGGGCGACATCCCCGTTATCGGCAACCTCTTTAAAACACGCGGGAAAAAAACCGACCGCCGCGAACTGCTGATTTTCATTACCCCGAGGATTATAGATACGGCCGGCAACAGCCTGCGCTATTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36806","NCBI_taxonomy_name":"Neisseria gonorrhoeae","NCBI_taxonomy_id":"485"}}}},"ARO_accession":"3004835","ARO_id":"42965","ARO_name":"Neisseria gonorrhoeae pilQ gene conferring resistance to beta-lactam","CARD_short_name":"Ngon_pilQ_BLA","ARO_description":"PilQ is an important gonococcal outer membrane component, member of secretin protein family, and involved in Type IV pilus formation.","ARO_category":{"40661":{"category_aro_accession":"3003938","category_aro_cvterm_id":"40661","category_aro_name":"Penicillin-binding protein mutations conferring resistance to beta-lactam antibiotics","category_aro_description":"Mutations in PBP transpeptidases that change the affinity for penicillin thereby conferring resistance to penicillin antibiotics.","category_aro_class_name":"AMR Gene Family"},"35979":{"category_aro_accession":"0000062","category_aro_cvterm_id":"35979","category_aro_name":"ceftriaxone","category_aro_description":"Ceftriaxone is a third-generation cephalosporin antibiotic. The presence of an aminothiazolyl sidechain increases ceftriazone's resistance to beta-lactamases. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3709":{"model_id":"3709","model_name":"Mycobacterium tuberculosis whib7 mutation conferring resistance to streptomycin","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"41339":{"param_type":"nucleotide substitution in promoter region","param_description":"A nucleotide sequence change where, compared to a reference sequence, one nucleotide is replaced by one other nucleotide in the promoter region of a gene. These substitutions are indicated as upstream of the reference sequence transcription initiation site. Format is given by [-][position][wildtype][>][mutation], e.g. -11t>c or -15g>Var where Var represents any possible substitution.","param_type_id":"41339","param_value":{"13186":"-116a>g"}},"snp":{"ReSeqTB-High":{"13186":"E666K"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"125"}},"model_sequences":{"sequence":{"8798":{"protein_sequence":{"accession":"YP_177940.1","sequence":"MSVLTVPRQTPRQRLPVLPCHVGDPDLWFADTPAGLEVAKTLCVSCPIRRQCLAAALQRAEPWGVWGGEIFDQGSIVSHKRPRGRPRKDAVA"},"dna_sequence":{"accession":"NC_000962.3","fmin":"3568400","fmax":"3568679","strand":"-","sequence":"GTGTCGGTACTGACAGTCCCCAGACAGACCCCCAGACAAAGATTGCCGGTTTTGCCGTGCCACGTCGGTGATCCCGATCTGTGGTTCGCCGATACCCCGGCCGGTCTCGAGGTAGCCAAGACACTGTGTGTGAGCTGCCCGATCAGGCGGCAGTGCTTGGCCGCGGCGCTTCAGCGGGCTGAACCCTGGGGCGTTTGGGGTGGTGAGATATTCGACCAAGGCTCGATCGTGAGTCACAAGCGTCCGCGCGGACGTCCGCGCAAGGATGCTGTTGCATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3004968","ARO_id":"43154","ARO_name":"Mycobacterium tuberculosis whib7 mutation conferring resistance to streptomycin","CARD_short_name":"Mtub_whib7_STR","ARO_description":"Mutations in whib7 that can contribute to or confer resistance to streptomycin.","ARO_category":{"43151":{"category_aro_accession":"3004965","category_aro_cvterm_id":"43151","category_aro_name":"streptomycin resistant whib7","category_aro_description":"A protein involved in transcriptional mechanisms. Mutations in the gene can cause resistance to streptomycin.","category_aro_class_name":"AMR Gene Family"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3736":{"model_id":"3736","model_name":"Mycobacterium tuberculosis Rv0565c mutation conferring resistance to ethionamide","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"925"},"41339":{"param_type":"nucleotide substitution in promoter region","param_description":"A nucleotide sequence change where, compared to a reference sequence, one nucleotide is replaced by one other nucleotide in the promoter region of a gene. These substitutions are indicated as upstream of the reference sequence transcription initiation site. Format is given by [-][position][wildtype][>][mutation], e.g. -11t>c or -15g>Var where Var represents any possible substitution.","param_type_id":"41339","param_value":{"18570":"-27g>a"}},"snp":{"ReSeqTB-High":{"18570":"E666K"}}},"model_sequences":{"sequence":{"8884":{"protein_sequence":{"accession":"NP_215079.1","sequence":"MSVTPNAGCVDVVIVGAGISGLGAAYRIIERNPQLTYTILERRARIGGTWDLFRYPGVRSDSSIFTLSFPYEPWTREEGIADGAHIREYLTDMAHKYGIDRHIEFNSYVRAADWDSSTDTWTVTFEQNGVHKHYRSRFVFFGSGYYNYDEGYTPDFGGIEKFGGAVVHPQHWPEDLDYTGKKIVVIGSGATAVTLIPSLTDRAEKVTMLQRSPTYLISASKYSTFAAVVRKALPPKTSHLIVRMYNALLEAVFWFLSRKTPVFVKWLLRRTAIKNLPEGYDIETHFTPRYNPWDQRLCLIPDADLYNAITSGRAEVVTDHIDHFDATGIALKSGGHLDADIIVTATGLQLQALGGAAISLDGVEIDPRDRFVYKAHMLEDVPNLFWCVGYTNASWTLRADMTARATAKLLAHMAAHGHTRAAPHLGDEPMDEKPSWDIQAGYVKRAPYALPKSGTKRPWNVRQNYLADAIDYRFDRIEEAMVFGAA"},"dna_sequence":{"accession":"NC_000962.3","fmin":"656009","fmax":"657470","strand":"-","sequence":"ATGAGCGTGACTCCAAACGCCGGCTGTGTCGACGTCGTCATCGTCGGCGCCGGCATCTCCGGACTGGGCGCGGCCTACCGGATCATCGAACGCAACCCGCAGCTGACCTACACCATCCTGGAAAGGCGTGCGCGGATCGGCGGCACCTGGGATCTGTTCCGCTACCCCGGCGTGCGCTCCGACAGCAGCATCTTCACGCTGTCGTTTCCCTACGAGCCGTGGACCCGCGAAGAAGGCATCGCCGACGGCGCCCACATCCGCGAGTACCTCACCGACATGGCCCACAAGTACGGCATCGATCGCCACATCGAGTTCAACAGCTACGTTCGCGCAGCGGACTGGGACTCATCCACCGATACCTGGACCGTCACCTTCGAGCAGAACGGCGTGCACAAGCACTACCGCAGCCGGTTCGTGTTCTTCGGCAGCGGCTACTACAACTATGACGAGGGCTACACCCCCGACTTCGGAGGCATCGAGAAGTTTGGCGGCGCGGTAGTGCATCCCCAGCACTGGCCAGAGGATCTGGACTACACCGGCAAGAAGATCGTGGTGATCGGCAGCGGGGCCACCGCGGTCACACTGATCCCCTCGCTGACCGACCGGGCCGAAAAGGTAACCATGCTGCAGCGATCCCCGACCTACCTGATCTCGGCATCCAAATACAGCACGTTCGCCGCCGTTGTTCGTAAAGCGTTGCCTCCCAAAACTTCTCACTTGATTGTCCGAATGTACAACGCGTTATTGGAAGCGGTGTTCTGGTTCTTGTCCCGCAAGACACCGGTGTTCGTGAAATGGCTGCTGCGCCGTACCGCGATCAAAAATCTGCCCGAGGGCTACGACATCGAAACCCACTTCACGCCGCGGTACAACCCGTGGGATCAGCGACTGTGCCTGATCCCGGACGCCGACCTGTACAACGCCATCACCAGCGGCCGCGCCGAGGTGGTCACCGACCATATCGACCACTTCGACGCCACCGGTATTGCACTCAAATCCGGTGGGCACCTCGATGCGGACATTATCGTCACCGCCACCGGCCTGCAGTTGCAAGCGCTTGGCGGGGCCGCGATCAGCCTCGACGGCGTCGAGATCGACCCTCGGGATCGCTTTGTCTACAAGGCGCACATGCTCGAAGACGTGCCCAACCTGTTCTGGTGTGTGGGTTACACGAACGCGTCCTGGACGCTGCGCGCCGACATGACGGCCCGGGCGACGGCAAAACTACTGGCACACATGGCCGCCCATGGACACACGCGCGCCGCCCCGCACCTGGGCGACGAGCCGATGGACGAGAAACCGTCCTGGGACATTCAGGCCGGCTATGTGAAGCGGGCGCCGTACGCGCTGCCCAAGTCCGGCACCAAGCGGCCGTGGAATGTACGACAGAACTACTTGGCCGACGCCATCGACTACCGATTCGACCGCATCGAGGAGGCAATGGTGTTCGGCGCGGCATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3004955","ARO_id":"43141","ARO_name":"Mycobacterium tuberculosis Rv0565c mutation conferring resistance to ethionamide","CARD_short_name":"Mtub_Rv0565_ETO","ARO_description":"Mutations in a bacterial monooxygenase, Rv0565c, are significantly associated with ethionamide resistance as an activator of ethionamide.","ARO_category":{"43140":{"category_aro_accession":"3004954","category_aro_cvterm_id":"43140","category_aro_name":"Ethionamide resistant Rv0565c","category_aro_description":"Mycobacterial monoxygenase has been shown to confer resistance to ethionamide in recent literature.","category_aro_class_name":"AMR Gene Family"},"40067":{"category_aro_accession":"3003474","category_aro_cvterm_id":"40067","category_aro_name":"ethionamide","category_aro_description":"Ethionamide is a second-line antitubercular agent that inhibits mycolic acid synthesis.","category_aro_class_name":"Antibiotic"},"45738":{"category_aro_accession":"3007156","category_aro_cvterm_id":"45738","category_aro_name":"thioamide antibiotic","category_aro_description":"A group of antibiotics possessing the thioamide functional group.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3013":{"model_id":"3013","model_name":"ADC-68","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"4869":{"protein_sequence":{"accession":"AGL39360.1","sequence":"MRFKKISCLLLSPLFIFNTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGAYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKIIFPALGLKHSYVNVAKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"KC866352.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAATACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGCTTATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAGCTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTCCCTGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCTTATTTGGAAAAGTTGTTGCTTTGTCTATGAATAAACCTTTCGATCAAGTCTTAGAAAAAATAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTAGCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTAAATCCACAAAAATATCCGGCTGATATTCAACGTGCAATTAATGAAACACATCAGGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAGCCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCAACGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3004493","ARO_id":"42027","ARO_name":"ADC-68","CARD_short_name":"ADC-68","ARO_description":"A class C carbapenemase and extended-spectrum beta-lactamase identified from Acinetobacter baumannii.","ARO_category":{"42444":{"category_aro_accession":"3004545","category_aro_cvterm_id":"42444","category_aro_name":"ADC beta-lactamase with carbapenemase activity","category_aro_description":"ADC beta-lactamase enzymes with demonstrable carbapenemase activity, an exception amongst these enzymes.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3014":{"model_id":"3014","model_name":"IMP-55","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"475"}},"model_sequences":{"sequence":{"5347":{"protein_sequence":{"accession":"ALT07696.1","sequence":"MSKLSVFFIFLICSIATAAESLPDLKIEKLEEGVYVHTSFKEVNGWGVVPKHGLVVLVNAEAYLIDTPFTAKDTEKLVTWFVERGYKIKGSISSHFHSDSTGGIEWLNSRSIPTYASELTNELLKKDGKVQATNSFSGVNYWLVKNKIEVFYPGPGHTPDNVVVWLPERKIFFGGCFIKPYGLGKLGDANIEAWPKSAKLLKSKYGKAKLVVPSHSEVGDASLLKLTLEQAVKGLNESKKPSKPSN"},"dna_sequence":{"accession":"KU299753.1","fmin":"0","fmax":"741","strand":"+","sequence":"ATGAGCAAGTTATCTGTATTCTTTATATTTTTGATTTGCAGCATTGCTACCGCAGCAGAGTCTTTGCCAGATTTAAAAATTGAAAAGCTTGAAGAAGGCGTTTATGTTCATACTTCGTTTAAAGAAGTTAACGGGTGGGGCGTTGTTCCTAAACATGGTTTGGTGGTTCTTGTAAATGCTGAGGCTTACCTAATTGACACTCCATTTACGGCTAAAGATACTGAAAAGTTAGTCACTTGGTTTGTGGAGCGTGGCTATAAAATAAAAGGCAGCATTTCCTCTCATTTTCATAGCGACAGCACGGGCGGAATAGAGTGGCTTAATTCTCGATCTATCCCCACGTATGCATCTGAATTAACAAATGAACTGCTTAAAAAAGACGGTAAGGTTCAAGCCACAAATTCATTTAGCGGAGTTAACTATTGGCTAGTTAAAAATAAAATTGAAGTTTTTTATCCAGGCCCGGGACACACTCCAGATAACGTAGTGGTTTGGTTGCCTGAAAGGAAAATATTTTTCGGTGGTTGTTTTATTAAACCGTACGGTTTAGGCAAATTGGGTGACGCAAATATAGAAGCTTGGCCAAAGTCCGCCAAATTATTAAAGTCCAAATATGGTAAGGCAAAACTGGTTGTTCCAAGTCACAGTGAAGTTGGAGACGCATCACTCTTGAAACTTACATTAGAGCAGGCGGTTAAAGGGTTAAACGAAAGTAAAAAACCATCAAAACCAAGCAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3004494","ARO_id":"42028","ARO_name":"IMP-55","CARD_short_name":"IMP-55","ARO_description":"An IMP class B metallo-beta-lactamase enzyme identified from Acinetobacter baumannii.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3015":{"model_id":"3015","model_name":"IMP-56","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"5345":{"protein_sequence":{"accession":"ALT53802.1","sequence":"MKKLFVLCVFFLCNIAAADDSLPDLKIEKLEKGVYVHTSFEEVKGWGVVTKHGLVVLVKNDAYLIDTPITAKDTEKLVNWFIEHGYRIKGSISTHFHGDSTAGIEWLNSQSISTYASELTNELLKKDNKVQATNSFSGVSYSLIKNKIEVFYPGPGHTQDNVVVWLPEKKILFGGCFVKPDGLGNLGDANLEAWPKSAKILMSKYGKAKLVVSGHSEIGNASLLQRTWEQAVKGLNESKKPLQPSS"},"dna_sequence":{"accession":"KU315553.1","fmin":"0","fmax":"741","strand":"+","sequence":"ATGAAAAAATTATTTGTTTTATGTGTATTCTTCCTTTGCAACATTGCTGCTGCAGATGATTCTTTGCCTGATTTAAAAATTGAGAAGCTTGAAAAAGGCGTTTATGTTCATACTTCGTTTGAAGAAGTTAAAGGTTGGGGTGTAGTCACAAAACACGGTTTAGTGGTTCTTGTAAAGAATGATGCTTATCTGATAGATACTCCAATTACCGCTAAAGATACTGAAAAATTAGTTAATTGGTTTATTGAGCACGGCTATAGAATCAAAGGCAGTATTTCCACACATTTCCATGGCGACAGTACGGCTGGAATAGAGTGGCTTAATTCTCAATCTATCTCCACGTATGCCTCTGAATTAACAAATGAACTTCTAAAAAAAGACAATAAGGTGCAAGCTACAAATTCTTTTAGTGGAGTTAGTTATTCACTTATCAAAAACAAAATTGAAGTTTTCTATCCAGGTCCAGGACACACTCAAGATAACGTAGTGGTTTGGTTACCTGAAAAGAAAATTTTATTCGGTGGTTGCTTTGTTAAACCGGACGGTCTTGGAAATTTAGGGGATGCAAATTTAGAAGCTTGGCCAAAGTCCGCTAAAATATTAATGTCTAAATATGGTAAAGCAAAACTGGTTGTTTCAGGTCATAGTGAAATTGGAAACGCATCACTCTTGCAGCGCACATGGGAGCAGGCTGTTAAAGGGTTAAATGAAAGTAAAAAACCGTTACAGCCAAGTAGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3004495","ARO_id":"42029","ARO_name":"IMP-56","CARD_short_name":"IMP-56","ARO_description":"An IMP class B metallo-beta-lactamase enzyme identified from carbapenem-resistant Pseudomonas aeruginosa.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3424":{"model_id":"3424","model_name":"OXA-234","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"5619":{"protein_sequence":{"accession":"WP_038350216.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDVKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGLDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_050607.1","fmin":"100","fmax":"925","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGTAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAACAAAATATACGCAAAAAGTGGTTGGGGATTGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001496","ARO_id":"37896","ARO_name":"OXA-234","CARD_short_name":"OXA-234","ARO_description":"OXA-234 is a beta-lactamase found in Acinetobacter baumannii.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3446":{"model_id":"3446","model_name":"OXA-281","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"5642":{"protein_sequence":{"accession":"ENU38533.1","sequence":"MKTLQFGLIALITTFGSACTTISPSVETAKNHQQQSAQQQIQQAFDQLQTTGVIVIKDKHGLHSYGNDLSRAQTPYVPASTFKMLNALIGLEHGKATRTEVFKWDGQKRSFPAWEKDMTLGQAMQASAVPVYQELARRIGLDLMQKEVQRIGYGNQQIGTVVDNFWLVGPLQITPVQEVLFVEKLANTQLAFEPDVQHTVQDMLLIEQKPNYKLYAKSGWGMDLEPQVGWWTGWVETATGEKVYFALNMQMKTGISASVREQLVKQSLITLGII"},"dna_sequence":{"accession":"APON01000041.1","fmin":"10443","fmax":"11268","strand":"+","sequence":"ATGAAAACTTTACAATTTGGACTCATCGCCCTCATTACAACCTTCGGTTCTGCATGTACCACAATAAGCCCCTCAGTAGAAACAGCTAAAAATCACCAGCAACAAAGCGCGCAGCAGCAGATCCAACAGGCCTTCGATCAACTCCAAACCACTGGGGTGATTGTCATTAAGGATAAGCATGGCTTACACAGCTACGGCAATGACTTGAGCCGTGCTCAGACACCCTATGTACCCGCCTCTACCTTTAAAATGCTGAATGCCTTAATCGGACTAGAACATGGTAAAGCAACCAGAACCGAGGTGTTTAAATGGGATGGTCAAAAGCGCAGCTTCCCTGCCTGGGAAAAAGACATGACTTTAGGGCAAGCCATGCAAGCATCTGCCGTTCCCGTTTATCAGGAGCTTGCACGGCGTATTGGTCTAGACCTGATGCAAAAAGAAGTACAGCGCATTGGATATGGCAATCAACAGATTGGCACCGTTGTCGATAATTTTTGGTTAGTCGGTCCACTGCAAATTACGCCTGTTCAAGAAGTCCTTTTTGTAGAGAAGCTGGCCAATACACAACTCGCTTTTGAGCCAGATGTGCAACATACCGTACAAGACATGTTGCTGATTGAACAAAAACCGAATTATAAACTCTACGCCAAATCTGGTTGGGGCATGGACCTAGAACCGCAAGTGGGCTGGTGGACAGGCTGGGTCGAAACAGCAACAGGTGAAAAAGTGTATTTTGCTTTGAATATGCAGATGAAAACAGGAATTTCAGCCAGCGTGCGTGAGCAACTGGTCAAACAAAGTCTGATAACACTGGGGATAATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42808","NCBI_taxonomy_name":"Acinetobacter johnsonii CIP 64.6","NCBI_taxonomy_id":"1217663"}}}},"ARO_accession":"3001736","ARO_id":"38136","ARO_name":"OXA-281","CARD_short_name":"OXA-281","ARO_description":"OXA-281 is a beta-lactamase found in Acinetobacter spp.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46494":{"category_aro_accession":"3007705","category_aro_cvterm_id":"46494","category_aro_name":"OXA-211-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-211.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3475":{"model_id":"3475","model_name":"OXA-341","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"5669":{"protein_sequence":{"accession":"AHN07458.1","sequence":"MNIKAPLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNIFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYRSLEQLGIL"},"dna_sequence":{"accession":"KF048913.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACCCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATATATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATAGGCCTTGAGCACCATAAGGCAACCACTACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCCGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACGCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCCTTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAGAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001529","ARO_id":"37929","ARO_name":"OXA-341","CARD_short_name":"OXA-341","ARO_description":"OXA-341 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3504":{"model_id":"3504","model_name":"OXA-431","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"5699":{"protein_sequence":{"accession":"AJG01377.1","sequence":"MNIKALLLITSAIFISACSPYIVSTNPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"KM979378.1","fmin":"14","fmax":"839","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGTCTACTAATCCAAATCACAGTGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACTACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAACGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3003124","ARO_id":"39701","ARO_name":"OXA-431","CARD_short_name":"OXA-431","ARO_description":"OXA-431 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3534":{"model_id":"3534","model_name":"OXA-472","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"5729":{"protein_sequence":{"accession":"ALC79287.1","sequence":"MSKKNFILIFIFVILISCKNTEKISNETTLIDNIFTNSNAEGTLVIYNLNDDKYIIHNKERAELRFYQASTFKIYNSLIGLNEKAVKDVDEVFYKYNGEKVFLESWAKDSNLRYAIKNSQVPAYKELARRIGLKKMKENIEKLDFGNKSIGDSVDTFWLEGPLEISAMEQIKLLTKLAQNELPYPIEIQKAVSDITILEQTYNYTLHGKTGLADSKNMTTEPIGWFVGWLENDNIYVFALNIDNINSDDLAKRINIVKESLKALNLLK"},"dna_sequence":{"accession":"KR182165.1","fmin":"0","fmax":"807","strand":"+","sequence":"ATGTCTAAAAAAAATTTTATATTAATATTTATTTTTGTTATTTTAATATCTTGTAAAAATACAGAAAAAATATCAAATGAAACTACATTAATAGATAATATATTTACTAATAGCAATGCTGAAGGAACATTAGTTATATATAATTTAAATGATGATAAATATATAATTCATAATAAAGAAAGAGCTGAACTAAGATTTTATCAAGCATCAACATTTAAAATATATAATAGTTTAATAGGCTTAAATGAAAAAGCAGTTAAAGATGTAGATGAAGTATTTTATAAATATAATGGCGAAAAAGTTTTTCTTGAATCTTGGGCTAAGGACTCTAATTTAAGATATGCAATTAAAAATTCGCAAGTACCGGCATATAAAGAATTAGCAAGAAGAATAGGTCTTAAAAAGATGAAAGAGAATATAGAAAAACTAGATTTTGGTAATAAAAGTATAGGTGATAGTGTAGATACTTTTTGGCTTGAAGGACCTTTGGAAATAAGTGCGATGGAGCAAATTAAATTATTAACTAAATTAGCTCAAAATGAATTACCGTATCCTATAGAAATACAAAAAGCTGTTTCTGATATTACTATACTAGAGCAAACTTACAATTATACGCTTCATGGAAAAACTGGATTAGCTGATTCTAAAAACATGACAACTGAGCCTATTGGTTGGTTCGTAGGCTGGCTTGAAAATGATAATATATATGTCTTTGCTTTAAATATTGATAATATCAATTCAGATGACCTTGCAAAAAGGATAAATATAGTAAAAGAAAGTTTAAAAGCATTAAATTTATTAAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36935","NCBI_taxonomy_name":"Brachyspira pilosicoli","NCBI_taxonomy_id":"52584"}}}},"ARO_accession":"3003628","ARO_id":"40238","ARO_name":"OXA-472","CARD_short_name":"OXA-472","ARO_description":"OXA-472 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46521":{"category_aro_accession":"3007732","category_aro_cvterm_id":"46521","category_aro_name":"OXA-63-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-63.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3576":{"model_id":"3576","model_name":"CMH-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"5772":{"protein_sequence":{"accession":"AFI56422.1","sequence":"MMTKSLSCALLLSVACSAFAAPMSEKQLADVVERTVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSVSKTFTGVLGGDAIARKEISLADPVTKYWPELTGKQWQGIRLLDLATYTAGGLPLQVPDDVTDNASLLRFYQSWQPKWAPGTTRLYANTSIGLFGSLAVKPSGMCFEQAMAERVFKPLKLNHTWINVPHAEEPHYAWGYREGKAVHVSPGMLDAEAYGVKSNVKDMASWVMANMAPETLPQSTLQQGIALAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVDGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANKSYPNPVRVETAYRILDALQ"},"dna_sequence":{"accession":"JQ673557.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGACAAAATCCCTAAGCTGCGCGCTGCTGCTCAGCGTTGCCTGCTCTGCTTTTGCCGCGCCGATGTCAGAAAAACAGCTGGCTGACGTCGTGGAACGTACCGTTACGCCTCTGATGAAGGCGCAGGCCATACCCGGAATGGCCGTGGCCGTCATTTATCAGGGCCAGCCACACTATTTTACTTTCGGTAAAGCAGACGTCGCGGCGAATAAGCCCGTCACGCCGCAAACCTTATTTGAGCTGGGCTCCGTCAGCAAAACCTTCACCGGCGTGCTGGGTGGCGATGCCATTGCCCGCAAAGAGATTTCGCTGGCCGACCCGGTCACGAAATATTGGCCTGAATTGACGGGCAAGCAGTGGCAAGGCATTCGCCTGCTAGACCTGGCAACCTATACCGCAGGCGGATTGCCGTTGCAGGTACCGGATGATGTCACCGATAACGCCTCTCTGCTGCGTTTCTACCAGTCCTGGCAGCCAAAGTGGGCCCCGGGTACCACGCGTCTGTACGCCAACACCAGCATCGGTTTGTTTGGCTCACTGGCCGTTAAACCGTCCGGCATGTGCTTCGAGCAGGCCATGGCGGAGCGGGTCTTTAAGCCCCTGAAACTCAACCATACGTGGATAAACGTTCCACACGCTGAAGAACCGCACTACGCATGGGGTTATCGTGAGGGAAAAGCGGTCCACGTTTCGCCTGGTATGCTGGATGCAGAAGCCTATGGCGTGAAATCTAACGTCAAAGATATGGCGAGTTGGGTGATGGCCAATATGGCACCTGAGACACTCCCGCAGTCCACTCTGCAGCAGGGTATTGCGCTGGCGCAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAAGGGTTAGGCTGGGAGATGCTCAACTGGCCGGTCGATGCCAAAACCGTGGTGGATGGCAGCGATAATAAGGTCGCACTGGCGCCGTTGCCGGTCGCAGAAGTGAATCCTCCGGCTCCGCCAGTAAAAGCCTCCTGGGTGCATAAAACGGGCTCTACGGGTGGGTTTGGCAGCTACGTGGCGTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCAAATAAAAGCTATCCGAACCCGGTACGGGTGGAAACGGCTTACCGTATCCTCGACGCGCTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3004777","ARO_id":"42892","ARO_name":"CMH-1","CARD_short_name":"CMH-1","ARO_description":"CMH-1 is a class C beta-lactamase gene found in Enterobacter cloacae.","ARO_category":{"42891":{"category_aro_accession":"3004776","category_aro_cvterm_id":"42891","category_aro_name":"CMH beta-lactamase","category_aro_description":"CMH is a class C beta-lactamase gene family belonging to Enterobacter cloacae.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3578":{"model_id":"3578","model_name":"CMY-133","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"5776":{"protein_sequence":{"accession":"AKZ20821.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGNDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"KP862819.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAACGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3003653","ARO_id":"40263","ARO_name":"CMY-133","CARD_short_name":"CMY-133","ARO_description":"CMY-133 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3024":{"model_id":"3024","model_name":"KPC-24","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"575"}},"model_sequences":{"sequence":{"5343":{"protein_sequence":{"accession":"AKQ06274.1","sequence":"MSLYRPLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"KR052099.1","fmin":"5211","fmax":"6093","strand":"+","sequence":"ATGTCACTGTATCGCCCTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3004496","ARO_id":"42038","ARO_name":"KPC-24","CARD_short_name":"KPC-24","ARO_description":"A KPC class A beta-lactamase and carbapenemase identified from Chilean isolates of Klebsiella pneumoniae.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3610":{"model_id":"3610","model_name":"GOB-9","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"575"}},"model_sequences":{"sequence":{"5808":{"protein_sequence":{"accession":"AAT68576.1","sequence":"MRNFVILFFMFICLGLNAQVVKEPENMPKEWNQTYEPFRIAGNLYYVGTYDLASYLIVTDKGNILINTGTAESLPIIKANIQKLGFNYKDIKILLLTQAHYDHTGALQDLKTETGAKFYADKEDADVLRTGGKSDYEMGKYGVTFKPVTPDKTLKDQDKITLGNTILSLLHHPGHTKGSCSFIFETKDEKRKYRVLIANMPSVIVDKKFSEVTAYPNIQSDYAYTFKAMKNLDFDIWVASHASQFDLHEKRKEGDPYNPQLFMDKQSYFQNLNDLEKSYLNKIKKDSQDK"},"dna_sequence":{"accession":"AY647246.1","fmin":"0","fmax":"873","strand":"+","sequence":"ATGAGAAATTTTGTTATACTGTTTTTCATGTTCATTTGCTTGGGCTTGAATGCTCAGGTAGTAAAAGAACCTGAAAATATGCCCAAAGAATGGAACCAGACTTATGAACCCTTCAGAATTGCAGGTAATTTATATTACGTAGGAACCTATGATTTGGCTTCTTACCTTATTGTGACAGACAAAGGCAATATTCTCATTAATACAGGAACGGCAGAATCGCTTCCAATAATAAAAGCAAATATCCAAAAGCTCGGGTTTAATTATAAAGACATTAAGATCTTGCTGCTTACTCAGGCTCACTACGACCATACAGGTGCATTACAAGATCTTAAAACAGAAACCGGTGCAAAATTCTATGCCGATAAAGAAGATGCTGATGTCCTGAGAACAGGGGGGAAGTCCGATTATGAAATGGGAAAATATGGGGTGACATTTAAACCTGTTACTCCGGATAAAACATTGAAAGATCAGGATAAAATAACACTGGGAAATACAATCCTGAGTTTGCTTCATCATCCCGGACATACAAAAGGTTCCTGTAGTTTTATTTTTGAAACAAAAGACGAGAAGAGAAAATATAGAGTTTTGATAGCTAATATGCCCTCCGTTATTGTTGATAAGAAATTTTCTGAAGTTACCGCATATCCAAATATTCAGTCCGATTATGCATATACTTTCAAAGCAATGAAGAATCTGGATTTTGATATTTGGGTGGCCTCCCATGCAAGTCAGTTCGATCTCCATGAAAAACGTAAAGAAGGAGATCCGTACAATCCGCAATTGTTTATGGATAAGCAAAGCTATTTCCAAAACCTTAATGATTTGGAAAAAAGCTATCTCAACAAAATAAAAAAAGATTCCCAAGATAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36960","NCBI_taxonomy_name":"Elizabethkingia meningoseptica","NCBI_taxonomy_id":"238"}}}},"ARO_accession":"3004816","ARO_id":"42936","ARO_name":"GOB-9","CARD_short_name":"GOB-9","ARO_description":"GOB-9 is a class B beta-lactamase gene found in Elizabethkingia meningoseptica.","ARO_category":{"41376":{"category_aro_accession":"3004212","category_aro_cvterm_id":"41376","category_aro_name":"GOB beta-lactamase","category_aro_description":"The GOB family of beta-lactamases have been discovered in the Elizabethkingia meningoseptica and are classified as subclass B3 beta-lactamase. They confer resistance to cephalosporins, penicillins, and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3625":{"model_id":"3625","model_name":"LEN-36","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"576"}},"model_sequences":{"sequence":{"5823":{"protein_sequence":{"accession":"ALK01319.1","sequence":"MRYVRLCVISLLATLPLAVDAGPQPLEQIKQSESQLSGRVGMVEMDLASGHTLAAWRADERFPMVSTFKVLLCGAVLARVDAGVEQLDRRIHYRQQDLVDYSPVSEKHLTDGMTVGELCAAAITLSDNSAGNLLLATVGGPAGLTAFLRQIGDNVTRLDRWETALNEALPGDARDTTTPASMAATLRKLLTAQHLSARSQQQLLQWMVDDRVAGPLIRAVLPPGWFIADKTGAGERGARGIVALLGPDGKPERIVVIYLRDTPASMAERNQHIAGIGAALIEHWQR"},"dna_sequence":{"accession":"KR738738.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGTGTTATCTCCCTGTTAGCCACCCTGCCACTGGCGGTAGACGCCGGTCCACAGCCGCTTGAGCAGATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTGGGGATGGTGGAAATGGATCTGGCCAGCGGCCACACGCTGGCCGCCTGGCGCGCCGATGAACGCTTTCCCATGGTGAGCACCTTTAAAGTGCTGCTGTGCGGCGCGGTGCTGGCGCGGGTGGATGCAGGGGTCGAACAACTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTACCGACGGGATGACGGTCGGCGAACTCTGCGCCGCCGCCATCACCCTGAGCGATAACAGTGCTGGCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCGGGATTAACTGCCTTTCTGCGCCAGATCGGTGACAACGTCACCCGTCTTGACCGCTGGGAAACGGCACTGAATGAGGCGCTTCCCGGCGACGCACGCGACACCACCACCCCGGCCAGCATGGCCGCCACGCTGCGCAAACTACTGACCGCGCAGCATCTGAGCGCCCGTTCGCAACAGCAACTCCTGCAGTGGATGGTGGACGATCGGGTTGCCGGCCCGCTGATCCGCGCCGTGCTGCCGCCGGGCTGGTTTATCGCCGACAAGACCGGGGCTGGCGAACGGGGTGCGCGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAACCGGAGCGCATTGTGGTGATCTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGTAATCAACATATCGCCGGGATCGGCGCAGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42612","NCBI_taxonomy_name":"Klebsiella variicola","NCBI_taxonomy_id":"244366"}}}},"ARO_accession":"3004828","ARO_id":"42958","ARO_name":"LEN-36","CARD_short_name":"LEN-36","ARO_description":"LEN-36 is a class A beta-lactamase gene found in Klebsiella variicola.","ARO_category":{"36236":{"category_aro_accession":"3000097","category_aro_cvterm_id":"36236","category_aro_name":"LEN beta-lactamase","category_aro_description":"LEN beta-lactamases are chromosomal class A beta-lactamases that confer resistance to ampicillin, amoxicillin, carbenicillin, and ticarcillin but not to extended-spectrum beta-lactams.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3635":{"model_id":"3635","model_name":"LEN-32","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"5906":{"protein_sequence":{"accession":"CEL85185.1","sequence":"MRYVRLCVISLLATLPLAVDAGPQPLEQIKQSESQLSGRVGMVEMDLASGRTLAAWRADERFPVVSTFKVLLCGAVLARVDAGLEQLDRRIHYRQQDLVDYSPVSEKHLVDGMTIGELCAAAITLSDNSAGNLLLATVGGPAGLTAFLRQIGDNVTHLDRWETALNEALPGDARDTTTPASMAATLRKLLTAQHLSARSQQQLLQWMVDDRVAGPLIRAVLPPGWFIADKTGAGERGARGIVALLGPDGKPERIVVLYLRDTPASMAERNQHIAGIGAALIEHWQR"},"dna_sequence":{"accession":"CDMV01000010.1","fmin":"131908","fmax":"132769","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGTGTTATCTCCCTGTTAGCCACCCTGCCACTGGCGGTAGACGCCGGTCCACAGCCGCTTGAGCAGATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTGGGGATGGTGGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCGATGAACGCTTTCCCGTGGTGAGCACCTTTAAAGTGCTGCTGTGCGGCGCGGTGCTGGCGCGGGTGGATGCCGGGCTCGAACAACTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGTCGACGGGATGACGATCGGCGAACTCTGCGCCGCCGCCATCACCCTGAGCGATAACAGCGCTGGCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCGGGATTAACTGCCTTTCTGCGCCAGATCGGTGACAACGTCACCCATCTTGACCGCTGGGAAACGGCACTGAATGAGGCGCTTCCCGGCGACGCGCGCGACACCACCACCCCGGCCAGCATGGCCGCCACGCTGCGCAAACTACTGACCGCGCAGCATCTGAGCGCCCGTTCGCAACAGCAACTCCTGCAGTGGATGGTGGACGATCGGGTTGCCGGCCCGCTGATCCGCGCCGTGCTGCCGCCGGGCTGGTTTATCGCCGACAAAACCGGGGCTGGCGAACGGGGTGCGCGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAACCGGAGCGCATTGTGGTGCTCTATCTGCGGGATACCCCGGCGAGTATGGCCGAGCGTAATCAACATATCGCCGGGATCGGCGCAGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42612","NCBI_taxonomy_name":"Klebsiella variicola","NCBI_taxonomy_id":"244366"}}}},"ARO_accession":"3004839","ARO_id":"42973","ARO_name":"LEN-32","CARD_short_name":"LEN-32","ARO_description":"A class-A beta-lactamase from Klebsiella variicola.","ARO_category":{"36236":{"category_aro_accession":"3000097","category_aro_cvterm_id":"36236","category_aro_name":"LEN beta-lactamase","category_aro_description":"LEN beta-lactamases are chromosomal class A beta-lactamases that confer resistance to ampicillin, amoxicillin, carbenicillin, and ticarcillin but not to extended-spectrum beta-lactams.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3659":{"model_id":"3659","model_name":"NDM-18","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"5931":{"protein_sequence":{"accession":"APZ75411.1","sequence":"MELPNIMHPVAKLSTALAAALMLSGCMPGEIRPTIGQQMETGDQRFGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR"},"dna_sequence":{"accession":"KY503030.1","fmin":"0","fmax":"828","strand":"+","sequence":"ATGGAATTGCCCAATATTATGCACCCGGTCGCGAAGCTGAGCACCGCATTAGCCGCTGCATTGATGCTGAGCGGGTGCATGCCCGGTGAAATCCGCCCGACGATTGGCCAGCAAATGGAAACTGGCGACCAACGGTTTGGCGACCAACGGTTTGGCGATCTGGTTTTCCGCCAGCTCGCACCGAATGTCTGGCAGCACACTTCCTATCTCGACATGCCGGGTTTCGGGGCAGTCGCTTCCAACGGTTTGATCGTCAGGGATGGCGGCCGCGTGCTGGTGGTCGATACCGCCTGGACCGATGACCAGACCGCCCAGATCCTCAACTGGATCAAGCAGGAGATCAACCTGCCGGTCGCGCTGGCGGTGGTGACTCACGCGCATCAGGACAAGATGGGCGGTATGGACGCGCTGCATGCGGCGGGGATTGCGACTTATGCCAATGCGTTGTCGAACCAGCTTGCCCCGCAAGAGGGGATGGTTGCGGCGCAACACAGCCTGACTTTCGCCGCCAATGGCTGGGTCGAACCAGCAACCGCGCCCAACTTTGGCCCGCTCAAGGTATTTTACCCCGGCCCCGGCCACACCAGTGACAATATCACCGTTGGGATCGACGGCACCGACATCGCTTTTGGTGGCTGCCTGATCAAGGACAGCAAGGCCAAGTCGCTCGGCAATCTCGGTGATGCCGACACTGAGCACTACGCCGCGTCAGCGCGCGCGTTTGGTGCGGCGTTCCCCAAGGCCAGCATGATCGTGATGAGCCATTCCGCCCCCGATAGCCGCGCCGCAATCACTCATACGGCCCGCATGGCCGACAAGCTGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3004861","ARO_id":"42999","ARO_name":"NDM-18","CARD_short_name":"NDM-18","ARO_description":"A class B New Delhi metallo-beta-lactamase and NDM-1 variant.","ARO_category":{"36196":{"category_aro_accession":"3000057","category_aro_cvterm_id":"36196","category_aro_name":"NDM beta-lactamase","category_aro_description":"NDM beta-lactamases or New Delhi metallo-beta-lactamases are class B beta-lactamases that confer resistance to a broad range of antibiotics including carbapenems, cephalosporins and penicillins.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3742":{"model_id":"3742","model_name":"Mycobacterium tuberculosis ddlA mutations confer resistance to cycloserine","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"675"},"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"13184":"T365A"},"ReSeqTB-Minimal":{"13184":"T365A"},"clinical":{"13184":"T365A"}}},"model_sequences":{"sequence":{"8824":{"protein_sequence":{"accession":"NP_217497.1","sequence":"MSANDRRDRRVRVAVVFGGRSNEHAISCVSAGSILRNLDSRRFDVIAVGITPAGSWVLTDANPDALTITNRELPQVKSGSGTELALPADPRRGGQLVSLPPGAGEVLESVDVVFPVLHGPYGEDGTIQGLLELAGVPYVGAGVLASAVGMDKEFTKKLLAADGLPVGAYAVLRPPRSTLHRQECERLGLPVFVKPARGGSSIGVSRVSSWDQLPAAVARARRHDPKVIVEAAISGRELECGVLEMPDGTLEASTLGEIRVAGVRGREDSFYDFATKYLDDAAELDVPAKVDDQVAEAIRQLAIRAFAAIDCRGLARVDFFLTDDGPVINEINTMPGFTTISMYPRMWAASGVDYPTLLATMIETTLARGVGLH"},"dna_sequence":{"accession":"NC_000962.3","fmin":"3336795","fmax":"3337917","strand":"-","sequence":"GTGAGTGCTAACGACCGGCGTGATCGGCGTGTCCGCGTTGCCGTCGTGTTCGGCGGGCGCAGCAACGAGCACGCCATCTCGTGTGTGTCCGCCGGCAGCATCCTGCGCAACCTGGACTCGCGGCGGTTCGACGTGATCGCGGTGGGTATCACCCCGGCAGGTTCGTGGGTGCTCACCGACGCCAACCCCGACGCCCTGACGATCACCAACCGGGAGCTTCCTCAGGTCAAATCAGGATCGGGCACCGAGCTGGCGCTGCCGGCCGATCCGCGGCGTGGTGGCCAGTTGGTGTCGCTGCCGCCCGGGGCCGGCGAGGTTCTGGAGTCGGTCGACGTGGTGTTCCCGGTACTGCACGGCCCGTACGGCGAGGACGGCACGATCCAGGGACTGCTCGAACTCGCCGGGGTGCCCTACGTGGGCGCCGGTGTGCTGGCCAGTGCCGTCGGCATGGACAAGGAGTTCACCAAGAAGCTGCTCGCCGCCGATGGACTTCCGGTGGGTGCGTACGCGGTGCTGCGTCCGCCGCGGTCGACACTGCACCGCCAGGAGTGCGAACGGCTGGGCTTACCGGTGTTCGTCAAACCCGCCCGAGGCGGCTCGTCGATCGGTGTTAGCCGGGTGTCGAGTTGGGATCAACTGCCCGCCGCGGTCGCGCGGGCCCGCCGGCATGACCCTAAGGTCATCGTCGAGGCCGCGATCAGCGGCCGCGAGCTGGAATGCGGTGTGCTCGAAATGCCGGACGGCACACTGGAAGCCAGCACGCTGGGGGAGATCCGGGTGGCCGGGGTGCGGGGACGCGAGGACTCTTTCTACGACTTCGCAACCAAGTATCTCGACGACGCAGCCGAATTGGACGTGCCCGCCAAGGTCGATGACCAGGTCGCAGAGGCGATTCGTCAGCTGGCGATCCGGGCGTTCGCGGCTATCGACTGCCGGGGTCTGGCCAGGGTGGACTTCTTCCTCACCGACGACGGTCCGGTGATCAACGAGATCAACACGATGCCGGGATTCACCACGATCTCGATGTACCCGCGGATGTGGGCGGCCAGCGGTGTCGACTATCCGACCCTGCTGGCGACGATGATCGAGACGACATTGGCCCGCGGCGTGGGCCTGCACTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3004941","ARO_id":"43127","ARO_name":"Mycobacterium tuberculosis ddlA mutations confer resistance to cycloserine","CARD_short_name":"Mtub_ddlA_DCS","ARO_description":"Point mutations that occur within Mycobacterium tuberculosis ddlA gene resulting in resistance to cycloserine.","ARO_category":{"43125":{"category_aro_accession":"3004939","category_aro_cvterm_id":"43125","category_aro_name":"cycloserine resistant ddlA","category_aro_description":"ddlA catalyzes the ATP-driven ligation of two D-alanine molecules to form the D-alanyl-D-alanine dipeptide, key in forming the cell wall. Cycloserine has a similar structure to d-alanine and inhibits the growth of the cell wall.","category_aro_class_name":"AMR Gene Family"},"37140":{"category_aro_accession":"3000760","category_aro_cvterm_id":"37140","category_aro_name":"cycloserine","category_aro_description":"Cycloserine is an anti-mycobacterial agent, and is active against enterobacteria, streptococci, M. tuberculosis, Staphylococcus aureus, and many Gram-negative and Gram-positive bacteria. It inhibits cell wall biosynthesis.","category_aro_class_name":"Antibiotic"},"45736":{"category_aro_accession":"3007154","category_aro_cvterm_id":"45736","category_aro_name":"cycloserine-like antibiotic","category_aro_description":"A group of antibiotics including cycloserine and its derivatives.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3746":{"model_id":"3746","model_name":"Mycobacterium tuberculosis rpoC mutations confer resistance to rifampicin","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"9744":"V483G","9800":"N416S","9801":"V431M","9802":"G433S","9803":"P434L","9804":"K445R","9805":"F452S","9806":"V483A","9808":"W484G","9809":"D485Y","9810":"I491V","9811":"I491T","9812":"L507V","9813":"L516P","9815":"Q523E","9816":"H525Q","9817":"L527V","9823":"N698S","9824":"A734V","9825":"E750Q","9827":"P1040A","9828":"P1040S","9829":"P1040R","9830":"P1040L","9831":"E1092D","9832":"Q1110H","9833":"E1113G","9834":"Q1125H","9835":"T1230I","9837":"V1252L","9839":"G332S","9814":"V517L","9836":"V1252M"},"ReSeqTB-High":{"9744":"V483G","9800":"N416S","9801":"V431M","9802":"G433S","9803":"P434L","9804":"K445R","9805":"F452S","9806":"V483A","9808":"W484G","9809":"D485Y","9810":"I491V","9811":"I491T","9812":"L507V","9813":"L516P","9815":"Q523E","9816":"H525Q","9817":"L527V","9823":"N698S","9824":"A734V","9825":"E750Q","9827":"P1040A","9828":"P1040S","9829":"P1040R","9830":"P1040L","9832":"Q1110H","9833":"E1113G","9834":"Q1125H","9835":"T1230I","9837":"V1252L","9839":"G332S","9820":"G332S","9814":"V517L","9836":"V1252M"},"clinical":{"9744":"V483G","9800":"N416S","9801":"V431M","9802":"G433S","9803":"P434L","9804":"K445R","9805":"F452S","9806":"V483A","9808":"W484G","9809":"D485Y","9810":"I491V","9811":"I491T","9812":"L507V","9813":"L516P","9815":"Q523E","9816":"H525Q","9817":"L527V","9823":"N698S","9824":"A734V","9825":"E750Q","9827":"P1040A","9828":"P1040S","9829":"P1040R","9830":"P1040L","9831":"E1092D","9832":"Q1110H","9833":"E1113G","9834":"Q1125H","9835":"T1230I","9837":"V1252L","9839":"G332S","9814":"V517L","9836":"V1252M"},"ReSeqTB-Minimal":{"9831":"E1092D"}},"48039":{"param_type":"synonymous substitution for alternative promoter","param_description":"A synonymous or silent substitution in the coding DNA sequence of one gene which influences the promoter region of another gene. These substitutions do not change the amino acid sequence of a protein but may still influence the phenotype, including decreased susceptibility to antimicrobial compounds.","param_type_id":"48039","param_value":{"9820":"Y61Y"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1100"}},"model_sequences":{"sequence":{"8801":{"protein_sequence":{"accession":"NP_215182.1","sequence":"MLDVNFFDELRIGLATAEDIRQWSYGEVKKPETINYRTLKPEKDGLFCEKIFGPTRDWECYCGKYKRVRFKGIICERCGVEVTRAKVRRERMGHIELAAPVTHIWYFKGVPSRLGYLLDLAPKDLEKIIYFAAYVITSVDEEMRHNELSTLEAEMAVERKAVEDQRDGELEARAQKLEADLAELEAEGAKADARRKVRDGGEREMRQIRDRAQRELDRLEDIWSTFTKLAPKQLIVDENLYRELVDRYGEYFTGAMGAESIQKLIENFDIDAEAESLRDVIRNGKGQKKLRALKRLKVVAAFQQSGNSPMGMVLDAVPVIPPELRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLIDLGAPEIIVNNEKRMLQESVDALFDNGRRGRPVTGPGNRPLKSLSDLLKGKQGRFRQNLLGKRVDYSGRSVIVVGPQLKLHQCGLPKLMALELFKPFVMKRLVDLNHAQNIKSAKRMVERQRPQVWDVLEEVIAEHPVLLNRAPTLHRLGIQAFEPMLVEGKAIQLHPLVCEAFNADFDGDQMAVHLPLSAEAQAEARILMLSSNNILSPASGRPLAMPRLDMVTGLYYLTTEVPGDTGEYQPASGDHPETGVYSSPAEAIMAADRGVLSVRAKIKVRLTQLRPPVEIEAELFGHSGWQPGDAWMAETTLGRVMFNELLPLGYPFVNKQMHKKVQAAIINDLAERYPMIVVAQTVDKLKDAGFYWATRSGVTVSMADVLVPPRKKEILDHYEERADKVEKQFQRGALNHDERNEALVEIWKEATDEVGQALREHYPDDNPIITIVDSGATGNFTQTRTLAGMKGLVTNPKGEFIPRPVKSSFREGLTVLEYFINTHGARKGLADTALRTADSGYLTRRLVDVSQDVIVREHDCQTERGIVVELAERAPDGTLIRDPYIETSAYARTLGTDAVDEAGNVIVERGQDLGDPEIDALLAAGITQVKVRSVLTCATSTGVCATCYGRSMATGKLVDIGEAVGIVAAQSIGEPGTQLTMRTFHQGGVGEDITGGLPRVQELFEARVPRGKAPIADVTGRVRLEDGERFYKITIVPDDGGEEVVYDKISKRQRLRVFKHEDGSERVLSDGDHVEVGQQLMEGSADPHEVLRVQGPREVQIHLVREVQEVYRAQGVSIHDKHIEVIVRQMLRRVTIIDSGSTEFLPGSLIDRAEFEAENRRVVAEGGEPAAGRPVLMGITKASLATDSWLSAASFQETTRVLTDAAINCRSDKLNGLKENVIIGKLIPAGTGINRYRNIAVQPTEEARAAAYTIPSYEDQYYSPDFGAATGAAVPLDDYGYSDYR"},"dna_sequence":{"accession":"NC_000962.3","fmin":"763369","fmax":"767320","strand":"+","sequence":"GTGCTCGACGTCAACTTCTTCGATGAACTCCGCATCGGTCTTGCTACCGCGGAGGACATCAGGCAATGGTCCTATGGCGAGGTCAAAAAGCCGGAGACGATCAACTACCGCACGCTTAAGCCGGAGAAGGACGGCCTGTTCTGCGAGAAGATCTTCGGGCCGACTCGCGACTGGGAATGCTACTGCGGCAAGTACAAGCGGGTGCGCTTCAAGGGCATCATCTGCGAGCGCTGCGGCGTCGAGGTGACCCGCGCCAAGGTGCGTCGTGAGCGGATGGGCCACATCGAGCTTGCCGCGCCCGTCACCCACATCTGGTACTTCAAGGGTGTGCCCTCGCGGCTGGGGTATCTGCTGGACCTGGCCCCGAAGGACCTGGAGAAGATCATCTACTTCGCTGCCTACGTGATCACCTCGGTCGACGAGGAGATGCGCCACAATGAGCTCTCCACGCTCGAGGCCGAAATGGCGGTGGAGCGCAAGGCCGTCGAAGACCAGCGCGACGGCGAACTAGAGGCCCGGGCGCAAAAGCTGGAGGCCGACCTGGCCGAGCTGGAGGCCGAGGGCGCCAAGGCCGATGCGCGGCGCAAGGTTCGCGACGGCGGCGAGCGCGAGATGCGCCAGATCCGTGACCGCGCGCAGCGTGAGCTGGACCGGTTGGAGGACATCTGGAGCACTTTCACCAAGCTGGCGCCCAAGCAGCTGATCGTCGACGAAAACCTCTACCGCGAACTCGTCGACCGCTACGGCGAGTACTTCACCGGTGCCATGGGCGCGGAGTCGATCCAGAAGCTGATCGAGAACTTCGACATCGACGCCGAAGCCGAGTCGCTGCGGGATGTCATCCGAAACGGCAAGGGGCAGAAGAAGCTTCGCGCCCTCAAGCGGCTGAAGGTGGTTGCGGCGTTCCAACAGTCGGGCAACTCGCCGATGGGCATGGTGCTCGACGCCGTCCCGGTGATCCCGCCGGAGCTGCGCCCGATGGTGCAGCTCGACGGCGGCCGGTTCGCCACGTCCGACTTGAACGACCTGTACCGCAGGGTGATCAACCGCAACAACCGGCTGAAAAGGCTGATCGATCTGGGTGCGCCGGAAATCATCGTCAACAACGAGAAGCGGATGCTGCAGGAATCCGTGGACGCGCTGTTCGACAATGGCCGCCGCGGCCGGCCCGTCACCGGGCCGGGCAACCGTCCGCTCAAGTCGCTTTCCGATCTGCTCAAGGGCAAGCAGGGCCGGTTCCGGCAGAACCTGCTCGGCAAGCGTGTCGACTACTCGGGCCGGTCGGTCATCGTGGTCGGCCCGCAGCTCAAGCTGCACCAGTGCGGTCTGCCCAAGCTGATGGCGCTGGAGCTGTTCAAGCCGTTCGTGATGAAGCGGCTGGTGGACCTCAACCATGCGCAGAACATCAAGAGCGCCAAGCGCATGGTGGAGCGCCAGCGCCCCCAAGTGTGGGATGTGCTCGAAGAGGTCATCGCCGAGCACCCGGTGTTGCTGAACCGCGCACCCACCCTGCACCGGTTGGGTATCCAGGCCTTCGAGCCAATGCTGGTGGAAGGCAAGGCCATTCAGCTGCACCCGTTGGTGTGTGAGGCGTTCAATGCCGACTTCGACGGTGACCAGATGGCCGTGCACCTGCCTTTGAGCGCCGAAGCGCAGGCCGAGGCTCGCATTTTGATGTTGTCCTCCAACAACATCCTGTCGCCGGCATCTGGGCGTCCGTTGGCCATGCCGCGGCTGGACATGGTGACCGGGCTGTACTACCTGACCACCGAGGTCCCCGGGGACACCGGCGAATACCAGCCGGCCAGCGGGGATCACCCGGAGACTGGTGTCTACTCTTCGCCGGCCGAAGCGATCATGGCGGCCGACCGCGGTGTCTTGAGCGTGCGGGCCAAGATCAAGGTGCGGCTGACCCAGCTGCGGCCGCCGGTCGAGATCGAGGCCGAGCTATTCGGCCACAGCGGCTGGCAGCCGGGCGATGCGTGGATGGCCGAGACCACGCTGGGCCGGGTGATGTTCAACGAGCTGCTGCCGCTGGGTTATCCGTTCGTCAACAAGCAGATGCACAAGAAGGTGCAGGCCGCCATCATCAACGACCTGGCCGAGCGTTACCCGATGATCGTGGTCGCCCAGACCGTCGACAAGCTCAAGGACGCCGGCTTCTACTGGGCCACCCGCAGCGGCGTGACGGTGTCGATGGCCGACGTGCTGGTGCCGCCGCGCAAGAAGGAGATCCTCGACCACTACGAGGAGCGCGCGGACAAGGTCGAAAAGCAGTTCCAGCGTGGCGCTTTGAACCACGACGAGCGCAACGAGGCGCTGGTGGAGATTTGGAAGGAAGCCACCGACGAGGTCGGTCAGGCGTTGCGGGAGCACTACCCCGACGACAACCCGATCATCACCATCGTCGACTCCGGCGCCACCGGCAACTTCACCCAGACTCGAACGCTGGCCGGTATGAAGGGCCTGGTGACCAACCCGAAGGGTGAGTTCATCCCGCGTCCGGTCAAGTCCTCCTTCCGTGAGGGCCTGACCGTGCTGGAGTACTTCATCAACACCCACGGCGCTCGAAAGGGCTTGGCGGACACCGCGTTGCGCACCGCCGACTCCGGCTACCTGACCCGACGTCTGGTGGACGTGTCCCAGGACGTGATCGTGCGCGAGCACGACTGCCAGACCGAGCGCGGCATCGTCGTCGAGCTGGCCGAGCGTGCACCCGACGGCACGCTGATCCGCGACCCGTACATCGAAACCTCGGCCTACGCGCGGACCCTGGGCACCGACGCGGTCGACGAGGCCGGCAACGTCATCGTCGAGCGTGGTCAAGACCTGGGCGATCCGGAGATTGACGCTCTGTTGGCTGCTGGTATTACCCAGGTCAAGGTGCGTTCGGTGCTGACGTGTGCCACCAGCACCGGCGTGTGCGCGACCTGCTACGGGCGTTCCATGGCCACCGGCAAGCTGGTCGACATCGGTGAAGCCGTCGGCATCGTGGCCGCCCAGTCCATCGGCGAACCCGGCACCCAGCTGACCATGCGCACCTTCCACCAGGGTGGCGTCGGTGAGGACATCACCGGTGGTCTGCCCCGGGTGCAGGAGCTGTTCGAGGCCCGGGTACCGCGTGGCAAGGCGCCGATCGCCGACGTCACCGGCCGGGTTCGGCTCGAGGACGGCGAGCGGTTCTACAAGATCACCATCGTTCCTGACGACGGCGGTGAGGAAGTGGTCTACGACAAGATCTCCAAGCGGCAGCGGCTGCGGGTGTTCAAGCACGAAGACGGTTCCGAACGGGTGCTCTCCGATGGCGACCACGTCGAGGTGGGCCAGCAGCTGATGGAAGGCTCGGCCGACCCGCATGAGGTGCTGCGGGTGCAGGGCCCCCGCGAGGTGCAGATACACCTGGTTCGCGAGGTCCAGGAGGTCTACCGCGCCCAAGGTGTGTCGATCCACGACAAGCACATCGAGGTGATCGTTCGCCAGATGCTGCGCCGGGTGACCATCATCGACTCGGGCTCGACGGAGTTTTTGCCTGGCTCGCTGATCGACCGCGCGGAGTTCGAGGCAGAGAACCGCCGAGTGGTGGCCGAGGGCGGTGAGCCCGCGGCCGGCCGTCCGGTGCTGATGGGCATCACGAAGGCGTCGCTGGCCACCGACTCGTGGCTGTCGGCGGCGTCGTTCCAGGAGACCACTCGCGTGCTGACCGATGCGGCGATCAACTGCCGCAGCGATAAGCTCAACGGTCTGAAGGAAAACGTGATCATCGGCAAGCTGATCCCGGCCGGTACCGGTATCAACCGCTACCGCAACATCGCGGTGCAGCCCACCGAGGAGGCCCGCGCTGCGGCGTACACCATCCCGTCGTATGAGGATCAGTACTACAGCCCGGACTTCGGTGCGGCCACCGGTGCTGCCGTCCCGCTGGACGACTACGGCTACAGCGACTACCGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3004994","ARO_id":"43181","ARO_name":"Mycobacterium tuberculosis rpoC mutations confer resistance to rifampicin","CARD_short_name":"Mtub_rpoC_RIF","ARO_description":"Mutations in rpoC that contribute to or confer resistance to rifampicin antibiotic.","ARO_category":{"43182":{"category_aro_accession":"3004995","category_aro_cvterm_id":"43182","category_aro_name":"rifampicin resistant rpoC","category_aro_description":"rpoC catalyzes the transcription of DNA into RNA and mutations confer resistance to rifampicin.","category_aro_class_name":"AMR Gene Family"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36669":{"category_aro_accession":"3000530","category_aro_cvterm_id":"36669","category_aro_name":"rifabutin","category_aro_description":"Rifabutin is a semisynthetic rifamycin used in tuberculosis therapy. It inhibits DNA-dependent RNA synthesis.","category_aro_class_name":"Antibiotic"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3747":{"model_id":"3747","model_name":"Mycobacterium tuberculosis rpoA mutations confer resistance to rifampicin","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"9769":"V183A","9770":"V183G","9771":"T187A","9773":"G31S"},"ReSeqTB-High":{"9769":"V183A","9770":"V183G","9771":"T187A","9773":"G31S"},"clinical":{"9769":"V183A","9770":"V183G","9771":"T187A","9773":"G31S"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"8797":{"protein_sequence":{"accession":"NP_217974.1","sequence":"MLISQRPTLSEDVLTDNRSQFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFTTVPGVKEDVTEIILNLKSLVVSSEEDEPVTMYLRKQGPGEVTAGDIVPPAGVTVHNPGMHIATLNDKGKLEVELVVERGRGYVPAVQNRASGAEIGRIPVDSIYSPVLKVTYKVDATRVEQRTDFDKLILDVETKNSISPRDALASAGKTLVELFGLARELNVEAEGIEIGPSPAEADHIASFALPIDDLDLTVRSYNCLKREGVHTVGELVARTESDLLDIRNFGQKSIDEVKIKLHQLGLSLKDSPPSFDPSEVAGYDVATGTWSTEGAYDEQDYAETEQL"},"dna_sequence":{"accession":"NC_000962.3","fmin":"3877463","fmax":"3878507","strand":"-","sequence":"ATGCTGATCTCACAGCGCCCCACCCTGTCCGAGGACGTCCTCACCGACAACCGATCCCAGTTCGTGATCGAACCGCTGGAGCCGGGATTCGGCTACACCCTGGGCAATTCGCTGCGTCGCACCCTGCTGTCGTCGATTCCCGGAGCGGCCGTCACCAGCATTCGCATCGATGGTGTACTGCACGAATTCACCACGGTGCCCGGGGTCAAAGAAGATGTCACCGAGATCATCCTGAATCTCAAGAGCCTGGTGGTGTCCTCGGAGGAGGACGAGCCGGTCACCATGTACCTACGCAAGCAGGGTCCGGGTGAGGTTACCGCCGGCGACATCGTGCCGCCGGCCGGCGTCACCGTGCACAACCCCGGCATGCACATCGCCACGCTGAACGATAAGGGCAAGCTGGAAGTCGAGCTCGTCGTCGAGCGTGGCCGCGGCTATGTCCCGGCGGTGCAAAACCGGGCTTCGGGTGCCGAAATTGGGCGCATTCCAGTCGATTCCATCTACTCACCGGTGCTCAAAGTGACCTACAAGGTGGACGCCACCCGGGTCGAGCAGCGCACCGACTTCGACAAGCTGATCCTGGACGTGGAGACCAAGAATTCAATCAGCCCGCGCGACGCGCTGGCGTCGGCTGGCAAGACGCTGGTCGAGTTGTTCGGCCTGGCACGGGAACTCAACGTCGAGGCCGAAGGCATCGAGATCGGGCCGTCGCCGGCCGAGGCCGATCACATTGCGTCATTCGCCCTGCCGATCGACGACCTGGATCTGACGGTGCGGTCCTACAACTGCCTCAAGCGCGAGGGGGTGCACACCGTGGGCGAACTGGTGGCGCGCACCGAATCCGACCTGCTTGACATCCGCAACTTCGGTCAGAAGTCCATCGACGAGGTGAAGATCAAGCTGCACCAGCTGGGCCTGTCACTCAAGGACAGCCCGCCGAGCTTCGACCCCTCGGAGGTCGCGGGCTACGACGTCGCCACCGGCACCTGGTCGACCGAGGGCGCGTACGACGAGCAGGACTACGCCGAAACCGAACAGCTTTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3004999","ARO_id":"43186","ARO_name":"Mycobacterium tuberculosis rpoA mutations confer resistance to rifampicin","CARD_short_name":"Mtub_rpoA_RIF","ARO_description":"Mutations in rpoA that contribute to or confer resistance to rifampicin antibiotic.","ARO_category":{"43185":{"category_aro_accession":"3004998","category_aro_cvterm_id":"43185","category_aro_name":"rifampicin resistant rpoA","category_aro_description":"rpoA catalyzes the transcription of DNA into RNA and mutations confer resistance to rifampicin.","category_aro_class_name":"AMR Gene Family"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3425":{"model_id":"3425","model_name":"OXA-252","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"5620":{"protein_sequence":{"accession":"ASF15667.1","sequence":"MRVLALSAVFLVASIIGMPAVAKEWQENKSWNAHFTEHKSQGVVALWNENKQQGFTNNLKRANQAFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGQTRDIATWNRDHNLITAMKYSVVPVYQEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISATEQISFLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYSTRIEPKIGWWVGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP"},"dna_sequence":{"accession":"CP022089.2","fmin":"2724285","fmax":"2725083","strand":"-","sequence":"ATGCGTGTATTAGCCTTATCGGCTGTGTTTTTGGTGGCATCGATTATCGGAATGCCTGCGGTAGCAAAGGAATGGCAAGAAAACAAAAGTTGGAATGCTCACTTTACTGAACATAAATCACAGGGCGTAGTTGCGCTCTGGAATGAGAATAAGCAGCAAGGATTTACCAATAATCTTAAACGGGCGAACCAAGCATTTTTACCCGCATCTACCTTTAAAATTCCCAATAGCTTGATCGCCCTCGATTTGGGCGTGGTTAAGGATGAACACCAAGTCTTTAAGTGGGATGGACAGACGCGCGATATCGCCACTTGGAATCGCGATCATAATCTAATCACCGCGATGAAATATTCAGTTGTGCCTGTTTATCAAGAATTTGCCCGCCAAATTGGCGAGGCACGTATGAGCAAGATGCTACATGCTTTCGATTATGGTAATGAGGACATTTCGGGCAATGTAGACAGTTTCTGGCTCGACGGTGGTATTCGAATTTCGGCCACTGAGCAAATCAGCTTTTTAAGAAAGCTGTATCACAATAAGTTACACGTATCGGAGCGCAGCCAGCGTATTGTCAAACAAGCCATGCTGACCGAAGCCAATGGCGACTATATTATTCGGGCTAAAACTGGATACTCGACTAGAATCGAACCTAAGATTGGCTGGTGGGTCGGTTGGGTTGAACTGGATGATAATGTGTGGTTTTTTGCGATGAATATGGATATGCCCACATCGGATGGTTTAGGGCTGCGCCAAGCCATCACAAAAGAAGTGCTCAAACAGGAAAAAATTATTCCCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42790","NCBI_taxonomy_name":"Shewanella sp. FDAARGOS_354","NCBI_taxonomy_id":"1930557"}}}},"ARO_accession":"3001501","ARO_id":"37901","ARO_name":"OXA-252","CARD_short_name":"OXA-252","ARO_description":"OXA-252 is a beta-lactamase found in Shewanella spp.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46510":{"category_aro_accession":"3007721","category_aro_cvterm_id":"46510","category_aro_name":"OXA-48-like beta-lactamase","category_aro_description":"OXA-48-type beta-lactamases are now routinely encountered in bacterial infections caused by carbapenam-resistant Enterobacterales. OXA-48-like proteins confer resistance to penicillin (which is efficiently hydrolyzed) and carbapenam antibiotics (which is more slowly broken down). The spectrum of activity of these variants varies, with some hydrolyzing expanded-spectrum oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3447":{"model_id":"3447","model_name":"OXA-282","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"5643":{"protein_sequence":{"accession":"EKE23052.1","sequence":"MKILILLPLLSCLGLTACSLPVSSLLSQSTSTQSTQAIAQLFDQAQSAGVLVIQRGQQIQVYGNDLSRADTEYVPASTFKMLNALIGLQHGKATTNEIFKWDGKKRSFAAWEKDMTLGEAMQASAVPVYQELARRIGLELMQQEVQRIQFGNQQIGQQVDNFWLVGPLKVTPKQEVQFVSALAREQLAFDPQVQQQVKAMLFLQERKAYRLYVKSGWGMDVEPQVGWLTGWVETPQAEIVAFSLNMQMQNGIDPAIRLEILQQALAELGLYPKAEG"},"dna_sequence":{"accession":"AMFJ01001993.1","fmin":"70","fmax":"901","strand":"+","sequence":"ATGAAAATTCTGATTTTGCTGCCTTTACTTAGTTGCTTGGGCCTGACAGCGTGTAGCCTGCCCGTTTCATCTCTCCTATCTCAAAGCACTTCGACTCAATCGACTCAAGCCATTGCCCAATTATTTGATCAGGCGCAAAGCGCGGGTGTTCTAGTGATTCAGCGTGGTCAACAGATACAGGTTTATGGTAATGATTTAAGCCGTGCAGATACCGAATATGTTCCCGCCTCTACTTTTAAAATGCTCAATGCCCTGATTGGCCTGCAACATGGCAAAGCCACAACCAATGAAATTTTTAAATGGGATGGCAAGAAACGCAGTTTTGCAGCCTGGGAAAAAGACATGACTCTCGGCGAAGCCATGCAAGCTTCTGCTGTACCCGTGTATCAGGAACTGGCACGTCGCATTGGCCTTGAATTGATGCAACAGGAAGTACAACGCATCCAATTTGGTAATCAGCAGATTGGTCAACAGGTCGATAACTTCTGGTTGGTAGGCCCTTTGAAAGTTACTCCAAAACAGGAAGTCCAATTTGTTTCTGCGTTGGCCCGAGAGCAACTGGCCTTTGATCCTCAAGTCCAGCAACAAGTCAAAGCCATGTTATTTTTACAGGAGCGGAAAGCTTATCGACTATATGTCAAATCCGGTTGGGGCATGGATGTGGAACCGCAAGTCGGCTGGCTCACCGGCTGGGTTGAAACACCGCAGGCTGAAATCGTGGCATTTTCACTCAATATGCAGATGCAAAATGGTATAGATCCGGCGATCCGCCTTGAAATTTTGCAGCAGGCTTTGGCCGAATTAGGGCTTTATCCAAAAGCTGAAGGATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36791","NCBI_taxonomy_name":"uncultured bacterium","NCBI_taxonomy_id":"77133"}}}},"ARO_accession":"3001737","ARO_id":"38137","ARO_name":"OXA-282","CARD_short_name":"OXA-282","ARO_description":"OXA-282 is a beta-lactamase found in Acinetobacter spp.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46489":{"category_aro_accession":"3007700","category_aro_cvterm_id":"46489","category_aro_name":"OXA-134-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-134.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3476":{"model_id":"3476","model_name":"OXA-342","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"535"}},"model_sequences":{"sequence":{"5670":{"protein_sequence":{"accession":"AHN07460.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFREWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"KF048915.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCGAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACGCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCCTTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001530","ARO_id":"37930","ARO_name":"OXA-342","CARD_short_name":"OXA-342","ARO_description":"OXA-342 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3076":{"model_id":"3076","model_name":"dfrB4","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"150"}},"model_sequences":{"sequence":{"6117":{"protein_sequence":{"accession":"ABY55281.1","sequence":"MNEGKNEVSTSAAGRFAFPSNATFALGDRVRKKSGAAWQGRIVGWYCTTLTPEGYAVESESHPDSVQIYPMTALERVA"},"dna_sequence":{"accession":"EU339233.1","fmin":"164","fmax":"401","strand":"+","sequence":"ATGAATGAAGGAAAAAATGAGGTCAGTACTTCAGCTGCTGGCCGGTTCGCATTCCCATCAAACGCCACGTTTGCCTTGGGGGATCGCGTACGCAAGAAGTCTGGCGCTGCTTGGCAGGGGCGCATTGTCGGGTGGTACTGCACAACACTTACCCCTGAAGGCTACGCCGTCGAGTCCGAATCTCACCCAGACTCAGTCCAGATTTATCCCATGACTGCGCTTGAACGGGTGGCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3004498","ARO_id":"42133","ARO_name":"dfrB4","CARD_short_name":"dfrB4","ARO_description":"A trimethoprim-resistant dihydrofolate reductase characterized on a class I integron from an E. coli isolate.","ARO_category":{"37617":{"category_aro_accession":"3001218","category_aro_cvterm_id":"37617","category_aro_name":"trimethoprim resistant dihydrofolate reductase dfr","category_aro_description":"Alternative dihydropteroate synthase dfr present on plasmids produces alternate proteins that are less sensitive to trimethoprim from inhibiting its role in folate synthesis, thus conferring trimethoprim resistance.","category_aro_class_name":"AMR Gene Family"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3505":{"model_id":"3505","model_name":"OXA-432","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"540"}},"model_sequences":{"sequence":{"5700":{"protein_sequence":{"accession":"AJG01378.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASRSDDKAEKIKNLFNEAHTTGVLVIHQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWNGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"KM979379.1","fmin":"14","fmax":"839","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGTGCTTCAAGATCTGATGACAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCATCAAGGTCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGAACGGGCAAAAAAGGCTGTTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3003125","ARO_id":"39702","ARO_name":"OXA-432","CARD_short_name":"OXA-432","ARO_description":"OXA-432 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3535":{"model_id":"3535","model_name":"OXA-473","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"520"}},"model_sequences":{"sequence":{"5730":{"protein_sequence":{"accession":"ALC79288.1","sequence":"MSKKNFILIFIFVILISCKNTEKISNETTLIDNIFTNSNAEGTLVIYNLNDDKYIIHNKERAEQRFYPASTFKIYNSLIGLNEKAVKDVDEVFYKYNGEKVFLEFWAKDSNLRYAIKNSQVPAYKELARRIGLKKMKENIEKLDFGNKSIGDSVDTFWLEGPLEISAMEQVKLLTKLAQNELPYPIEIQKAISDITILEQTYNYTLHGKTGLADSKNMTTEPIGWFVGWLEENDNIYVFALNIDNINSDDLAKRINIVKESLKALNLLK"},"dna_sequence":{"accession":"KR182166.1","fmin":"0","fmax":"810","strand":"+","sequence":"ATGTCTAAAAAAAATTTTATATTAATATTTATTTTTGTTATTTTAATATCTTGTAAAAATACAGAAAAAATATCAAATGAAACTACATTAATAGATAATATATTTACTAATAGCAATGCTGAAGGAACATTAGTTATATATAATTTAAATGATGATAAATATATAATTCATAATAAAGAAAGAGCTGAACAAAGATTTTATCCAGCATCAACATTTAAAATATATAATAGTTTAATAGGCTTAAATGAAAAAGCAGTTAAAGATGTAGATGAAGTATTTTATAAATATAATGGCGAAAAAGTTTTTCTTGAATTTTGGGCTAAGGACTCTAATTTAAGATATGCAATTAAAAATTCGCAAGTACCGGCATATAAAGAATTAGCAAGAAGAATAGGTCTTAAAAAGATGAAAGAGAATATAGAAAAACTAGATTTTGGTAATAAAAGTATAGGTGATAGTGTAGATACTTTTTGGCTTGAAGGACCTTTGGAAATAAGTGCGATGGAGCAAGTTAAATTATTAACTAAATTAGCTCAAAATGAATTACCGTATCCTATAGAAATACAAAAAGCTATTTCTGATATTACTATACTAGAGCAAACTTACAATTATACGCTTCATGGAAAAACTGGATTAGCTGATTCTAAAAACATGACAACTGAGCCTATTGGTTGGTTCGTAGGCTGGCTTGAAGAAAATGATAATATATACGTCTTTGCTTTAAATATTGATAATATCAATTCAGATGACCTTGCAAAAAGGATAAATATAGTAAAAGAAAGTTTAAAAGCATTAAATTTATTAAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36935","NCBI_taxonomy_name":"Brachyspira pilosicoli","NCBI_taxonomy_id":"52584"}}}},"ARO_accession":"3003629","ARO_id":"40239","ARO_name":"OXA-473","CARD_short_name":"OXA-473","ARO_description":"OXA-473 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46521":{"category_aro_accession":"3007732","category_aro_cvterm_id":"46521","category_aro_name":"OXA-63-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-63.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4007":{"model_id":"4007","model_name":"PDC-438","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"6371":{"protein_sequence":{"accession":"WP_179284377.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRRYSNPSIDLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLNVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGMKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_070204.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGTCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCGCTATTCCAACCCGAGCATCGACCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCAACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGATGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005275","ARO_id":"43632","ARO_name":"PDC-438","CARD_short_name":"PDC-438","ARO_description":"PDC-438 is class C beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3712":{"model_id":"3712","model_name":"Mycobacterium tuberculosis ppsC mutations confer resistance to pyrazinamide","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"9707":"A957P","9708":"N1899S"},"ReSeqTB-Minimal":{"9707":"A957P","9708":"N1899S"},"clinical":{"9707":"A957P","9708":"N1899S"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"4250"}},"model_sequences":{"sequence":{"8791":{"protein_sequence":{"accession":"NP_217449.1","sequence":"MTAATPDRRAIITEALHKIDDLTARLEIAEKSSSEPIAVIGMGCRFPGGVNNPEQFWDLLCAGRSGIVRVPAQRWDADAYYCDDHTVPGTICSTEGGFLTSWQPDEFDAEFFSISPREAAAMDPQQRLLIEVAWEALEDAGVPQHTIRGTQTSVFVGVTAYDYMLTLAGRLRPVDLDAYIPTGNSANFAAGRLAYILGARGPAVVIDTACSSSLVAVHLACQSLRGRESDMALVGGTNLLLSPGPSIACSRWGMLSPEGRCKTFDASADGYVRGEGAAVVVLKRLDDAVRDGNRILAVVRGSAVNQDGASSGVTVPNGPAQQALLAKALTSSKLTAADIDYVEAHGTGTPLGDPIELDSLSKVFSDRAGSDQLVIGSVKTNLGHLEAAAGVAGLMKAVLAVHNGYIPRHLNFHQLTPHASEAASRLRIAADGIDWPTTGRPRRAGVSSFGVSGTNAHVVIEQAPDPMAAAGTEPQRGPVPAVSTLVVFGKTAPRVAATASVLADWLDGPGAAVPLADVAHTLNHHRARQTRFGTVAAVDRRQAVIGLRALAAGQSAPGVVAPREGSIGGGTVFVYSGRGSQWAGMGRQLLADEPAFAAAIAELEPEFVAQGGFSLRDVIAGGKELVGIEQIQLGLIGMQLALTALWRSYGVTPDAVIGHSMGEVAAAVVAGALTPAQGLRVTAVRSRLMAPLSGQGTMALLELDAEATEALIADYPEVSLGIYASPRQTVISGPPLLIDELIDKVRQQNGFATRVNIEVAPHNPAMDALQPAMRSELADLTPQPPTIPIISTTYADLGISLGSGPRFDAEHWATNMRNPVRFHQAIAHAGADHHTFIEISAHPLLTHSISDTLRASYDVDNYLSIGTLQRDAHDTLEFHTNLNTTHTTHPPQTPHPPEPHPVLPTTPWQHTQHWITATSAAYHRPDTHPLLGVGVTDPTNGTRVWESELDPDLLWLADHVIDDLVVLPGAAYAEIALAAATDTFAVEQDQPWMISELDLRQMLHVTPGTVLVTTLTGDEQRCQVEIRTRSGSSGWTTHATATVARAEPLAPLDHEGQRREVTTADLEDQLDPDDLYQRLRGAGQQHGPAFQGIVGLAVTQAGVARAQVRLPASARTGSREFMLHPVMMDIALQTLGATRTATDLAGGQDARQGPSSNSALVVPVRFAGVHVYGDITRGVRAVGSLAAAGDRLVGEVVLTDANGQPLLVVDEVEMAVLGSGSGATELTNRLFMLEWEPAPLEKTAEATGALLLIGDPAAGDPLLPALQSSLRDRITDLELASAADEATLRAAISRTSWDGIVVVCPPRANDESMPDEAQLELARTRTLLVASVVETVTRMGARKSPRLWIVTRGAAQFDAGESVTLAQTGLRGIARVLTFEHSELNTTLVDIEPDGTGSLAALAEELLAGSEADEVALRDGQRYVNRLVPAPTTTSGDLAAEARHQVVNLDSSGASRAAVRLQIDQPGRLDALNVHEVKRGRPQGDQVEVRVVAAGLNFSDVLKAMGVYPGLDGAAPVIGGECVGYVTAIGDEVDGVEVGQRVIAFGPGTFGTHLGTIADLVVPIPDTLADNEAATFGVAYLTAWHSLCEVGRLSPGERVLIHSATGGVGMAAVSIAKMIGARIYTTAGSDAKREMLSRLGVEYVGDSRSVDFADEILELTDGYGVDVVLNSLAGEAIQRGVQILAPGGRFIELGKKDVYADASLGLAALAKSASFSVVDLDLNLKLQPARYRQLLQHILQHVADGKLEVLPVTAFSLHDAADAFRLMASGKHTGKIVISIPQHGSIEAIAAPPPLPLVSRDGGYLIVGGMGGLGFVVARWLAEQGAGLIVLNGRSAPSDEVAAAIAELNASGSRIEVITGDITEPDTAERLVRAVEDAGFRLAGVVHSAMVLADEIVLNMTDSAARRVFAPKVTGSWRLHVATAARDVDWWLTFSSAAALLGTPGQGAYAAANSWVDGLVAHRRSAGLPAVGINWGPWADVGRAQFFKDLGVEMINAEQGLAAMQAVLTADRGRTGVFSLDARQWFQSFPAVAGSSLFAKLHDSAARKSGQRRGGGAIRAQLDALDAAERPGHLASAIADEIRAVLRSGDPIDHHRPLETLGLDSLMGLELRNRLEASLGITLPVALVWAYPTISDLATALCERMDYATPAAAQEISDTEPELSDEEMDLLADLVDASELEAATRGES"},"dna_sequence":{"accession":"NC_000962.3","fmin":"3255684","fmax":"3262251","strand":"+","sequence":"ATGACCGCAGCGACACCAGATCGCCGAGCGATCATCACCGAGGCGCTGCACAAGATCGATGATCTCACGGCGCGCCTGGAAATCGCCGAAAAATCCAGCAGCGAACCGATCGCGGTGATCGGCATGGGTTGCCGGTTCCCGGGCGGGGTCAACAACCCCGAACAGTTCTGGGATTTGTTGTGCGCCGGCCGAAGCGGCATCGTCCGGGTTCCCGCGCAGCGGTGGGACGCCGACGCCTACTACTGTGATGATCACACCGTGCCGGGGACCATCTGCAGCACCGAAGGCGGTTTTCTCACCAGCTGGCAGCCAGATGAGTTCGATGCGGAGTTCTTCTCAATCTCCCCGCGCGAAGCGGCGGCGATGGACCCGCAGCAGCGATTGTTGATTGAAGTTGCGTGGGAAGCGCTAGAAGACGCGGGCGTCCCGCAACACACCATTCGCGGTACGCAAACCTCGGTATTCGTCGGTGTCACCGCCTACGACTACATGCTCACGCTGGCGGGCCGGCTACGACCTGTTGACCTCGACGCGTACATCCCAACCGGGAACTCGGCGAACTTCGCCGCCGGACGGCTGGCCTACATCCTCGGGGCACGCGGACCCGCGGTGGTCATCGACACGGCCTGCTCATCGTCGTTGGTGGCGGTGCACCTGGCATGCCAGAGCCTGCGCGGGCGGGAAAGCGATATGGCGTTGGTGGGTGGAACCAACCTTTTGCTGAGCCCGGGACCCAGCATCGCTTGCTCGCGATGGGGGATGCTGTCACCGGAGGGGCGGTGCAAGACCTTCGATGCGTCCGCCGATGGATACGTGCGCGGCGAGGGTGCCGCGGTGGTGGTGCTCAAGCGGCTGGATGACGCGGTGCGCGACGGCAACCGCATTCTTGCCGTGGTACGCGGTTCGGCGGTCAACCAGGACGGTGCCAGCAGCGGAGTGACCGTTCCCAACGGGCCAGCGCAACAGGCGTTGCTCGCCAAAGCATTGACGTCGTCGAAGTTGACAGCGGCCGATATCGACTACGTCGAGGCCCATGGAACTGGTACTCCGCTGGGCGACCCGATCGAACTCGATTCACTGAGTAAGGTTTTCAGCGATCGAGCGGGTTCGGATCAGTTGGTGATTGGATCGGTGAAGACCAATCTCGGTCACCTGGAAGCGGCGGCCGGTGTCGCCGGGCTGATGAAAGCCGTGCTCGCGGTACACAACGGCTACATTCCGCGGCATCTTAACTTCCACCAGCTGACACCACATGCAAGTGAGGCCGCATCTCGGCTGAGGATCGCCGCCGATGGTATTGACTGGCCAACCACCGGTCGACCTCGCCGGGCGGGGGTGTCGTCGTTCGGCGTCAGTGGGACGAATGCACACGTGGTGATCGAGCAGGCACCCGATCCGATGGCCGCTGCGGGAACGGAGCCGCAGCGCGGCCCCGTTCCCGCGGTGTCGACGCTGGTGGTGTTCGGCAAGACCGCACCGCGGGTGGCTGCGACGGCATCGGTGCTGGCAGATTGGCTGGACGGCCCCGGCGCGGCGGTGCCGCTGGCCGATGTCGCGCACACCCTCAACCATCACCGGGCCCGTCAGACCAGGTTCGGCACGGTAGCCGCTGTCGATCGGCGCCAAGCGGTGATCGGGTTACGCGCGCTGGCCGCGGGTCAATCCGCCCCCGGGGTGGTGGCACCCCGCGAAGGCTCCATCGGAGGCGGCACGGTGTTCGTCTACTCGGGACGAGGATCGCAGTGGGCCGGAATGGGGCGCCAACTGCTGGCCGACGAGCCGGCATTCGCCGCTGCCATCGCCGAACTGGAGCCGGAATTCGTTGCTCAAGGCGGGTTTTCGCTGCGCGACGTGATCGCCGGCGGAAAAGAGTTGGTTGGCATCGAACAGATCCAGCTGGGACTGATCGGGATGCAGCTGGCGCTGACCGCGTTGTGGCGCTCATACGGCGTGACACCCGATGCGGTGATAGGTCACTCGATGGGCGAAGTGGCCGCCGCGGTGGTGGCCGGGGCGCTGACCCCGGCCCAGGGATTACGGGTGACCGCGGTCCGGTCGAGGCTGATGGCGCCGCTGTCCGGGCAGGGCACGATGGCGTTGCTGGAACTCGACGCCGAAGCCACTGAGGCGCTGATTGCCGACTACCCCGAGGTGAGCCTGGGGATCTATGCCTCCCCACGCCAAACCGTGATTTCCGGGCCGCCGCTATTGATCGACGAGCTCATCGACAAGGTGCGCCAACAGAACGGCTTCGCTACCCGAGTCAACATCGAGGTGGCCCCCCACAACCCGGCCATGGATGCACTGCAACCGGCGATGCGTTCGGAATTGGCCGATCTCACCCCGCAACCGCCGACCATCCCGATCATCTCCACCACCTACGCCGACCTCGGCATTTCCCTGGGTTCCGGCCCCAGGTTCGACGCCGAGCACTGGGCAACCAACATGCGCAACCCGGTACGGTTCCACCAGGCCATCGCTCATGCCGGCGCCGATCACCACACCTTCATCGAGATCAGCGCCCACCCGCTGCTGACCCACTCGATCAGCGACACCCTGCGCGCCAGCTACGATGTCGACAACTATCTGAGCATCGGCACCTTGCAACGCGACGCTCACGACACCCTCGAGTTCCACACGAACCTCAACACGACCCACACCACCCATCCCCCCCAGACTCCCCACCCCCCCGAACCCCACCCCGTGCTGCCCACCACCCCATGGCAGCACACCCAGCACTGGATCACCGCCACGTCGGCCGCTTACCACAGGCCCGACACCCACCCGTTGCTTGGCGTCGGTGTCACCGACCCCACTAACGGCACCCGGGTTTGGGAAAGCGAGCTCGACCCTGATCTGCTGTGGCTCGCCGATCACGTCATCGACGATCTCGTTGTGCTGCCCGGGGCGGCCTACGCTGAGATCGCGCTGGCGGCCGCGACCGACACCTTCGCAGTCGAGCAAGATCAGCCCTGGATGATCAGCGAGCTCGACCTTCGGCAGATGCTGCATGTGACCCCAGGCACCGTGTTGGTCACCACGCTCACCGGCGACGAGCAGCGATGCCAGGTCGAAATACGCACCCGCAGCGGGTCTTCGGGATGGACCACCCACGCCACCGCCACCGTTGCCCGCGCCGAGCCGTTAGCACCGCTGGATCACGAAGGACAGCGGCGCGAGGTAACCACTGCCGACCTCGAGGACCAACTGGATCCCGACGACCTGTATCAGCGCCTGCGCGGCGCCGGCCAACAGCACGGACCCGCGTTTCAAGGCATCGTGGGGCTGGCCGTCACGCAAGCTGGCGTGGCCCGTGCGCAAGTACGGCTACCCGCATCGGCCAGAACGGGTTCCCGTGAGTTCATGCTGCACCCGGTGATGATGGATATCGCGTTGCAGACACTGGGAGCCACCCGGACGGCGACCGATCTGGCCGGCGGCCAGGACGCCCGGCAGGGCCCATCTTCCAACTCGGCCTTGGTGGTACCGGTGCGTTTCGCCGGTGTCCACGTGTACGGCGATATCACCCGCGGGGTTCGCGCGGTCGGCTCTCTGGCCGCAGCCGGTGACCGGCTGGTCGGCGAGGTAGTCCTGACCGACGCGAATGGCCAACCGCTGCTGGTCGTCGATGAAGTCGAGATGGCGGTGCTCGGATCCGGCAGTGGCGCAACGGAACTCACCAACCGCCTATTCATGTTGGAGTGGGAGCCCGCACCGCTGGAAAAGACCGCCGAGGCTACGGGTGCCCTGTTGCTGATCGGTGACCCCGCCGCGGGTGACCCGCTGCTGCCCGCGCTGCAGTCGTCGCTGCGCGACCGCATCACCGACCTCGAGCTGGCATCCGCGGCCGACGAAGCCACGCTGCGCGCGGCGATCAGCCGAACCTCCTGGGACGGGATCGTTGTGGTCTGTCCGCCCCGAGCGAACGACGAATCGATGCCGGACGAGGCTCAACTGGAGTTGGCACGCACACGCACGCTGCTGGTCGCCAGCGTGGTCGAGACCGTGACGCGAATGGGTGCCCGCAAGAGCCCCCGACTGTGGATCGTCACCCGTGGCGCTGCACAGTTCGACGCAGGCGAGTCGGTCACGTTGGCGCAGACCGGCCTACGTGGCATCGCACGGGTGCTGACATTTGAGCATTCGGAGTTGAATACCACCCTCGTAGATATCGAACCGGACGGCACCGGCTCGCTGGCCGCCCTGGCCGAGGAGTTGCTTGCCGGTTCCGAGGCCGACGAGGTCGCCTTGCGCGACGGTCAACGCTATGTCAACCGGCTGGTGCCCGCACCCACCACGACCAGTGGTGATCTCGCCGCCGAAGCTCGCCACCAGGTGGTGAACCTGGACAGCTCGGGCGCTTCCAGGGCAGCTGTCCGACTGCAGATCGATCAACCCGGACGGCTGGACGCACTAAACGTTCACGAGGTGAAACGGGGCAGACCGCAAGGCGATCAAGTCGAGGTTCGCGTCGTCGCCGCCGGACTCAACTTCAGCGACGTGCTCAAAGCGATGGGCGTGTATCCGGGACTCGACGGTGCCGCGCCGGTGATCGGCGGCGAATGTGTCGGCTACGTGACGGCCATCGGTGACGAGGTTGACGGCGTCGAGGTCGGACAGCGAGTTATCGCATTCGGCCCTGGCACATTCGGGACCCATCTGGGGACCATCGCCGATCTCGTCGTCCCAATTCCGGACACGCTAGCCGACAACGAGGCGGCCACGTTCGGCGTCGCCTATCTCACCGCCTGGCACTCGCTGTGCGAGGTCGGGCGCCTATCCCCCGGCGAACGCGTGCTCATCCATTCCGCCACCGGCGGTGTTGGAATGGCGGCGGTCTCGATCGCGAAGATGATCGGCGCCCGCATCTACACGACGGCCGGTTCGGACGCCAAACGGGAAATGCTTTCCAGGCTCGGTGTCGAGTACGTCGGCGACTCGCGAAGCGTGGATTTCGCTGACGAGATCCTCGAGCTGACAGACGGCTACGGTGTGGACGTCGTTCTCAATTCGCTGGCGGGCGAGGCGATTCAACGCGGCGTGCAGATCCTTGCGCCCGGTGGCCGGTTCATCGAACTGGGCAAGAAGGACGTCTACGCCGATGCCAGCTTGGGCTTGGCCGCGCTAGCCAAGAGCGCGTCCTTCTCCGTGGTCGACCTCGACCTGAATCTCAAGCTGCAGCCGGCGCGCTACCGCCAACTCCTGCAACACATCCTGCAGCACGTGGCGGATGGCAAACTCGAGGTACTTCCCGTCACCGCATTTAGCCTGCACGATGCGGCCGACGCATTCCGGCTTATGGCATCCGGTAAACACACCGGCAAGATCGTCATCTCGATACCCCAGCACGGCAGCATCGAGGCGATCGCTGCCCCGCCACCACTTCCTCTGGTCAGCCGCGACGGCGGCTACCTCATCGTCGGCGGTATGGGTGGTCTCGGATTCGTCGTCGCGCGCTGGCTGGCTGAGCAAGGTGCGGGACTGATTGTCCTCAACGGACGCTCGGCCCCCAGCGACGAGGTGGCAGCCGCTATCGCGGAGCTGAACGCCTCCGGTAGCCGGATCGAGGTGATCACCGGCGACATCACCGAGCCAGACACCGCCGAGCGGCTGGTGCGGGCGGTCGAAGACGCCGGGTTCCGGCTGGCCGGGGTGGTGCACAGCGCGATGGTTCTCGCCGACGAGATCGTGTTGAACATGACCGATTCCGCCGCTCGGCGAGTGTTCGCCCCGAAGGTCACCGGCAGCTGGCGGCTTCATGTGGCCACCGCCGCGCGCGACGTCGACTGGTGGCTGACCTTCTCCTCGGCCGCCGCGCTGCTGGGCACTCCCGGGCAGGGCGCGTACGCCGCCGCCAACTCGTGGGTCGACGGCCTGGTCGCGCATCGGCGCTCGGCCGGACTTCCCGCTGTCGGGATCAACTGGGGCCCGTGGGCCGACGTTGGACGCGCGCAGTTCTTCAAAGACCTCGGGGTGGAGATGATCAACGCCGAGCAGGGGCTTGCCGCCATGCAGGCGGTACTCACCGCCGATCGCGGGCGCACCGGTGTGTTCAGCCTCGACGCGCGGCAGTGGTTCCAATCGTTCCCCGCTGTGGCGGGGTCCTCGCTGTTCGCGAAGCTGCATGACTCGGCGGCCCGCAAAAGTGGGCAGCGGCGCGGCGGGGGCGCGATTCGCGCTCAGCTAGACGCCCTCGACGCGGCCGAACGCCCAGGCCACCTCGCGTCCGCGATCGCCGACGAGATCCGTGCGGTGCTGCGCTCAGGCGATCCCATCGATCACCACCGACCGCTGGAAACCCTGGGACTCGACTCGCTGATGGGCCTGGAATTGCGCAATCGGCTGGAAGCAAGTCTGGGCATCACGTTGCCGGTCGCGTTGGTGTGGGCATACCCGACGATCAGCGATCTCGCGACCGCCCTGTGCGAACGAATGGACTACGCGACACCCGCGGCTGCGCAGGAGATTTCCGATACAGAACCCGAACTGTCCGACGAGGAGATGGATTTGCTCGCCGATCTGGTTGACGCCAGCGAGCTGGAAGCTGCGACGCGAGGCGAGTCATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3004975","ARO_id":"43162","ARO_name":"Mycobacterium tuberculosis ppsC mutations confer resistance to pyrazinamide","CARD_short_name":"Mtub_ppsC_PZA","ARO_description":"Mutations in ppsC can contribute to or confer resistance to pyrazinamide.","ARO_category":{"43189":{"category_aro_accession":"3005002","category_aro_cvterm_id":"43189","category_aro_name":"antibiotic resistant polyketide synthase genes","category_aro_description":"Genes ppsA-E constitute an operon encoding enzymes involved in the biosynthesis of phthiocerol dimycocerosate and other lipids in Mycobacterium tuberculosis. Mutations within this region can result in resistance to pyrazinamide.","category_aro_class_name":"AMR Gene Family"},"39997":{"category_aro_accession":"3003413","category_aro_cvterm_id":"39997","category_aro_name":"pyrazinamide","category_aro_description":"Pyrazinamide is an antimycobacterial. It is highly specific and active only against Mycobacterium tuberculosis. This compound is a prodrug and needs to be activated inside the cell. It interferes with the bacterium's ability to synthesize new fatty acids, causing cell death.","category_aro_class_name":"Antibiotic"},"45737":{"category_aro_accession":"3007155","category_aro_cvterm_id":"45737","category_aro_name":"pyrazine antibiotic","category_aro_description":"A group of antibiotics derived from pyrazine.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3738":{"model_id":"3738","model_name":"Mycobacterium tuberculosis mshC mutations conferring resistance to ethionamide","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"9518":"A403G"},"ReSeqTB-High":{"9518":"A403G"},"clinical":{"9518":"A403G"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"775"}},"model_sequences":{"sequence":{"8838":{"protein_sequence":{"accession":"NP_216646.1","sequence":"MQSWYCPPVPVLPGRGPQLRLYDSADRQVRPVAPGSKATMYVCGITPYDATHLGHAATYVTFDLIHRLWLDLGHELHYVQNITDIDDPLFERADRDGVDWRDLAQAEVALFCEDMAALRVLPPQDYVGATEAIAEMVELIEKMLACGAAYVIDREMGEYQDIYFRADATLQFGYESGYDRDTMLRLCEERGGDPRRPGKSDELDALLWRAARPGEPSWPSPFGPGRPGWHVECAAIALSRIGSGLDIQGGGSDLIFPHHEFTAAHAECVSGERRFARHYVHAGMIGWDGHKMSKSRGNLVLVSALRAQDVEPSAVRLGLLAGHYRADRFWSQQVLDEATARLHRWRTATALPAGPAAVDVVARVRRYLADDLDTPKAIAALDGWVTDAVEYGGHDAGAPKLVATAIDALLGVDL"},"dna_sequence":{"accession":"NC_000962.3","fmin":"2391214","fmax":"2392459","strand":"-","sequence":"ATGCAGTCGTGGTATTGCCCACCGGTTCCGGTGTTGCCGGGACGAGGCCCGCAGCTACGGCTGTACGACAGCGCCGACCGGCAGGTCCGTCCGGTGGCGCCCGGATCTAAGGCCACCATGTACGTCTGCGGGATCACGCCCTACGACGCCACGCATCTGGGCCATGCTGCCACCTATGTGACGTTCGACCTGATCCATCGGCTGTGGCTGGATCTCGGTCATGAATTGCACTATGTCCAGAACATCACCGACATCGACGATCCACTATTTGAGCGCGCGGATCGCGACGGTGTCGACTGGCGTGACCTTGCCCAAGCCGAGGTCGCCCTGTTCTGTGAGGACATGGCGGCGCTGCGGGTGCTACCACCGCAAGACTACGTGGGGGCCACCGAAGCGATTGCTGAAATGGTCGAGCTCATCGAAAAAATGCTGGCGTGCGGGGCGGCCTATGTCATAGACCGGGAAATGGGAGAGTACCAGGACATCTACTTCCGCGCTGACGCCACCCTGCAGTTCGGCTACGAGTCAGGGTATGACCGTGACACCATGCTGCGGCTGTGCGAGGAACGTGGCGGCGATCCGCGGCGCCCCGGCAAGAGCGACGAACTCGACGCGTTGTTGTGGCGGGCCGCGCGGCCCGGTGAGCCCAGCTGGCCGTCCCCGTTCGGGCCTGGCCGGCCAGGCTGGCATGTCGAGTGCGCAGCCATCGCGCTCAGTCGTATCGGAAGCGGCCTCGACATCCAGGGCGGTGGTAGCGATCTGATCTTTCCGCACCACGAGTTCACCGCTGCGCACGCCGAATGTGTCAGCGGCGAACGGCGATTCGCGCGGCACTACGTGCATGCCGGGATGATCGGCTGGGACGGGCACAAGATGTCAAAGAGCCGCGGCAACCTCGTGCTGGTGTCGGCGCTGCGTGCGCAGGACGTTGAGCCATCGGCGGTTCGGCTGGGTTTGCTCGCCGGACACTACCGAGCCGATCGGTTCTGGAGCCAGCAGGTGCTTGACGAGGCGACCGCCCGGCTGCACCGTTGGCGCACCGCAACCGCACTTCCCGCCGGTCCGGCCGCAGTTGACGTTGTCGCTCGGGTGCGCCGCTACCTGGCCGACGATCTCGATACGCCCAAAGCGATTGCCGCACTGGATGGTTGGGTCACCGATGCGGTGGAGTACGGCGGCCACGATGCCGGGGCGCCGAAGTTGGTGGCGACGGCGATCGATGCCCTGCTCGGGGTGGACCTGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3004934","ARO_id":"43120","ARO_name":"Mycobacterium tuberculosis mshC mutations conferring resistance to ethionamide","CARD_short_name":"Mtub_mshC_ETO","ARO_description":"Mutations that occur in mshC resulting in or contributing to conferring resistance to ethionamide.","ARO_category":{"43076":{"category_aro_accession":"3004890","category_aro_cvterm_id":"43076","category_aro_name":"ethionamide resistant mshC","category_aro_description":"Mutations that occur in mshC which is involved in the third step of mycothiol biosynthesis. It catalyzes the ATP-dependent condensation of GlcN-Ins and L-cysteine to form L-Cys-GlcN-Ins. The gene exhibits resistance to ethionamide.","category_aro_class_name":"AMR Gene Family"},"40067":{"category_aro_accession":"3003474","category_aro_cvterm_id":"40067","category_aro_name":"ethionamide","category_aro_description":"Ethionamide is a second-line antitubercular agent that inhibits mycolic acid synthesis.","category_aro_class_name":"Antibiotic"},"45738":{"category_aro_accession":"3007156","category_aro_cvterm_id":"45738","category_aro_name":"thioamide antibiotic","category_aro_description":"A group of antibiotics possessing the thioamide functional group.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3426":{"model_id":"3426","model_name":"OXA-259","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"540"}},"model_sequences":{"sequence":{"5621":{"protein_sequence":{"accession":"AGV04655.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"KF305666.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGTTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCATTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001715","ARO_id":"38115","ARO_name":"OXA-259","CARD_short_name":"OXA-259","ARO_description":"OXA-259 is a beta-lactamase found in Acinetobacter spp.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3448":{"model_id":"3448","model_name":"OXA-283","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"510"}},"model_sequences":{"sequence":{"5644":{"protein_sequence":{"accession":"ENU15301.1","sequence":"MKILILLPLLSCLGLTACSLPVSSLLSQSTSTQSTQAIAQLFDQAQSAGVLVIQRGQQIQVYGNDLSRADTEYVPASTFKMLNALIGLQHGKATTNEIFKWDGKKRSFAAWEKDMTLGEAMQASAVPVYQELARRIGLELMQQEVQRIQFGNQQIGQQVDNFWLVGPLKVTPKQEVQFVSALAREQLAFDPQVQQQVKAMLFLQERKAYRLYVKSGWGMDVEPQVGWLTGWVETPQAEIVAFSLNMQMRNGMDPAIRLEILQQALAELGLYPKAEG"},"dna_sequence":{"accession":"APOG01000008.1","fmin":"114899","fmax":"115730","strand":"+","sequence":"ATGAAAATTCTAATTTTGCTGCCTTTACTGAGTTGCTTGGGCCTGACAGCGTGTAGCCTGCCCGTTTCATCTCTCCTATCTCAAAGCACTTCGACTCAATCCACCCAAGCCATTGCCCAATTATTTGATCAGGCGCAAAGCGCGGGTGTTCTAGTGATTCAGCGTGGTCAACAGATACAGGTTTATGGTAATGATTTAAGCCGTGCAGATACCGAATATGTTCCCGCCTCTACTTTTAAAATGCTCAATGCCCTGATTGGCCTGCAACATGGCAAAGCCACAACCAATGAAATTTTTAAATGGGATGGCAAGAAACGCAGTTTTGCAGCCTGGGAAAAAGACATGACTCTCGGCGAAGCCATGCAAGCTTCTGCTGTACCCGTGTATCAGGAACTGGCACGTCGCATTGGCCTTGAATTGATGCAACAGGAAGTACAACGCATCCAATTTGGTAATCAGCAGATTGGTCAACAGGTCGATAACTTCTGGTTGGTAGGCCCTTTGAAAGTTACTCCAAAACAGGAAGTCCAATTTGTTTCTGCGTTGGCCCGAGAGCAACTGGCCTTTGATCCTCAAGTCCAGCAACAAGTCAAAGCCATGTTATTTTTACAGGAGCGGAAAGCTTATCGACTATATGTCAAATCCGGTTGGGGCATGGATGTGGAACCGCAAGTCGGCTGGCTCACCGGCTGGGTTGAAACACCGCAAGCCGAGATCGTGGCATTTTCACTGAATATGCAGATGCGAAATGGTATGGATCCGGCGATCCGCCTTGAAATTTTGCAGCAGGCTTTGGCCGAATTAGGGCTTTATCCAAAAGCTGAAGGATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42809","NCBI_taxonomy_name":"Acinetobacter sp. CIP A162","NCBI_taxonomy_id":"1144674"}}}},"ARO_accession":"3001738","ARO_id":"38138","ARO_name":"OXA-283","CARD_short_name":"OXA-283","ARO_description":"OXA-283 is a beta-lactamase found in Acinetobacter spp.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46489":{"category_aro_accession":"3007700","category_aro_cvterm_id":"46489","category_aro_name":"OXA-134-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-134.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3477":{"model_id":"3477","model_name":"OXA-343","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"540"}},"model_sequences":{"sequence":{"5671":{"protein_sequence":{"accession":"PCE45447.1","sequence":"MNIKALLLITSAIFISACSPYIVTTNPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNTDIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWIVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NWUK01000007.1","fmin":"12139","fmax":"12964","strand":"-","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTACTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATACAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGGTGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGATTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001531","ARO_id":"37931","ARO_name":"OXA-343","CARD_short_name":"OXA-343","ARO_description":"OXA-343 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3506":{"model_id":"3506","model_name":"OXA-433","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"540"}},"model_sequences":{"sequence":{"5701":{"protein_sequence":{"accession":"AJG01379.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDDKAEKIKNLFNEAHTTGVLVIHQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWNGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSDEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"KM979380.1","fmin":"25","fmax":"850","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGACAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCATCAAGGTCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGAACGGGCAAAAAAGGCTGTTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTGATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3003126","ARO_id":"39703","ARO_name":"OXA-433","CARD_short_name":"OXA-433","ARO_description":"OXA-433 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3536":{"model_id":"3536","model_name":"OXA-474","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"520"}},"model_sequences":{"sequence":{"5731":{"protein_sequence":{"accession":"ALC79289.1","sequence":"MSKKNFILIFIFVILISCKNTEKISNETTLIDNVFTNSNAEGTLVIYNLNDDKYIIHNKERAEQRFYPASTFKIYNSLIGLNEKAVKDVDEVFYKYNGEKVFLEFWAKDSNLRYAIKNSQVPAYKELARRIGLKKMKENIEKLDFGNKSIGDSVDTFWLEGPLEISAMEQVKLLTKLAQNELPYPIEIQKAVSDITILEQTYNYTLHGKTGLADSKNMTTEPIGWFVGWLEENDNIYVFALNIDNINSDDLAKRINIVKESLKALNLLK"},"dna_sequence":{"accession":"KR182167.1","fmin":"0","fmax":"810","strand":"+","sequence":"ATGTCTAAAAAAAATTTTATATTAATATTTATTTTTGTTATTTTAATATCTTGTAAAAATACAGAAAAAATATCAAATGAAACTACATTAATAGATAATGTATTTACTAATAGCAATGCTGAAGGAACATTAGTTATATATAATTTAAATGATGATAAATATATAATTCATAATAAAGAAAGAGCTGAACAAAGATTTTATCCAGCATCAACATTTAAAATATATAATAGTTTAATAGGCTTAAATGAAAAAGCAGTTAAAGATGTAGATGAAGTATTTTATAAATATAATGGCGAAAAAGTTTTTCTTGAATTTTGGGCTAAGGACTCTAATTTAAGATATGCAATTAAAAATTCGCAAGTACCGGCATATAAAGAATTAGCAAGAAGAATAGGTCTTAAAAAGATGAAAGAGAATATAGAAAAACTAGATTTTGGTAATAAAAGTATAGGTGATAGTGTAGATACTTTTTGGCTTGAAGGACCTTTGGAAATAAGTGCGATGGAGCAAGTTAAATTATTAACTAAATTAGCTCAAAATGAATTACCGTATCCTATAGAAATACAAAAAGCTGTTTCTGATATTACTATACTAGAGCAAACTTACAATTATACGCTTCATGGAAAAACTGGATTAGCTGATTCTAAAAACATGACAACTGAGCCTATTGGTTGGTTCGTAGGCTGGCTTGAAGAAAATGATAATATATATGTCTTTGCTTTAAATATTGATAATATCAATTCAGATGACCTTGCAAAAAGGATAAATATAGTAAAAGAAAGTTTAAAAGCATTAAATTTATTAAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36935","NCBI_taxonomy_name":"Brachyspira pilosicoli","NCBI_taxonomy_id":"52584"}}}},"ARO_accession":"3003631","ARO_id":"40241","ARO_name":"OXA-474","CARD_short_name":"OXA-474","ARO_description":"OXA-474 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46521":{"category_aro_accession":"3007732","category_aro_cvterm_id":"46521","category_aro_name":"OXA-63-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-63.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3637":{"model_id":"3637","model_name":"LEN-38","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"5908":{"protein_sequence":{"accession":"AZA07954.1","sequence":"MRYVRLCVISLLANLPLAVYAGPQPLEQIKQSESQLSGRVGMVEMDLASGRTLAAWRADERFPMVSTFKVLLCGAVLARVDAGVEQLDRRIHYRQQDLVDYSPVSEKHLVDGMTIGELCAAAITMSDNSAGNLLLATVGGPTGLTAFLRQIGDNVTRLDRWETALNEALPGDMRDTTTPASMAATLRKLLTAQHLSARSQQQLLQWMVDDRVAGPLIRAVLPAGWFIADKTGAGERGARGIVALLGPDGKAERIVVIYLRDTPASMAERNQHIAGIGAALIEHWQR"},"dna_sequence":{"accession":"MK161457.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGTGTTATCTCCCTGTTAGCCAACCTGCCACTAGCGGTATACGCCGGTCCACAGCCGCTTGAGCAGATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTGGGGATGGTGGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCGATGAACGCTTTCCCATGGTGAGCACCTTTAAAGTGCTGCTGTGCGGCGCGGTGCTGGCGCGGGTGGATGCCGGGGTCGAACAACTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGTCGACGGGATGACGATCGGCGAACTCTGCGCCGCCGCCATCACCATGAGCGATAACAGCGCTGGCAATCTGCTGCTGGCCACCGTCGGCGGCCCCACGGGATTGACCGCCTTTCTGCGCCAGATCGGTGACAACGTCACCCGTCTTGACCGCTGGGAAACGGCACTGAATGAGGCGCTTCCCGGCGACATGCGCGACACCACTACCCCGGCCAGCATGGCCGCCACGCTGCGTAAACTACTGACTGCGCAGCATCTGAGCGCCCGTTCACAGCAGCAGCTCCTGCAGTGGATGGTGGACGATCGGGTTGCCGGCCCGCTGATCCGCGCCGTGCTGCCGGCGGGCTGGTTTATCGCCGACAAGACCGGGGCTGGCGAACGGGGTGCGCGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAAGCGGAGCGCATTGTGGTGATCTATCTGCGGGATACCCCGGCGAGTATGGCCGAGCGTAATCAACATATCGCCGGGATCGGCGCAGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42976","NCBI_taxonomy_name":"Klebsiella variicola subsp. tropica","NCBI_taxonomy_id":"2489014"}}}},"ARO_accession":"3004841","ARO_id":"42975","ARO_name":"LEN-38","CARD_short_name":"LEN-38","ARO_description":"A class-A beta-lactamase from Klebsiella.","ARO_category":{"36236":{"category_aro_accession":"3000097","category_aro_cvterm_id":"36236","category_aro_name":"LEN beta-lactamase","category_aro_description":"LEN beta-lactamases are chromosomal class A beta-lactamases that confer resistance to ampicillin, amoxicillin, carbenicillin, and ticarcillin but not to extended-spectrum beta-lactams.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3713":{"model_id":"3713","model_name":"Mycobacterium tuberculosis ppsD mutations confer resistance to pyrazinamide","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"9709":"A437P","9710":"P563H","9711":"A1248T","9713":"M127I","9714":"I1508L","9715":"V1522A","9717":"E1823A","9718":"V295M"},"ReSeqTB-Minimal":{"9709":"A437P","9711":"A1248T","9715":"V1522A"},"clinical":{"9709":"A437P","9710":"P563H","9711":"A1248T","9713":"M127I","9714":"I1508L","9715":"V1522A","9717":"E1823A","9718":"V295M"},"ReSeqTB-High":{"9710":"P563H","9713":"M127I","9717":"E1823A","9718":"V295M"},"ReSeqTB-Moderate":{"9714":"I1508L"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"3575"}},"model_sequences":{"sequence":{"8793":{"protein_sequence":{"accession":"NP_217450.1","sequence":"MTSLAERAAQLSPNARAALARELVRAGTTFPTDICEPVAVVGIGCRFPGNVTGPESFWQLLADGVDTIEQVPPDRWDADAFYDPDPSASGRMTTKWGGFVSDVDAFDADFFGITPREAVAMDPQHRMLLEVAWEALEHAGIPPDSLSGTRTGVMMGLSSWDYTIVNIERRADIDAYLSTGTPHCAAVGRIAYLLGLRGPAVAVDTACSSSLVAIHLACQSLRLRETDVALAGGVQLTLSPFTAIALSKWSALSPTGRCNSFDANADGFVRGEGCGVVVLKRLADAVRDQDRVLAVVRGSATNSDGRSNGMTAPNALAQRDVITSALKLADVTPDSVNYVETHGTGTVLGDPIEFESLAATYGLGKGQGESPCALGSVKTNIGHLEAAAGVAGFIKAVLAVQRGHIPRNLHFTRWNPAIDASATRLFVPTESAPWPAAAGPRRAAVSSFGLSGTNAHVVVEQAPDTAVAAAGGMPYVSALNVSGKTAARVASAAAVLADWMSGPGAAAPLADVAHTLNRHRARHAKFATVIARDRAEAIAGLRALAAGQPRVGVVDCDQHAGGPGRVFVYSGQGSQWASMGQQLLANEPAFAKAVAELDPIFVDQVGFSLQQTLIDGDEVVGIDRIQPVLVGMQLALTELWRSYGVIPDAVIGHSMGEVSAAVVAGALTPEQGLRVITTRSRLMARLSGQGAMALLELDADAAEALIAGYPQVTLAVHASPRQTVIAGPPEQVDTVIAAVATQNRLARRVEVDVASHHPIIDPILPELRSALADLTPQPPSIPIISTTYESAQPVADADYWSANLRNPVRFHQAVTAAGVDHNTFIEISPHPVLTHALTDTLDPDGSHTVMSTMNRELDQTLYFHAQLAAVGVAASEHTTGRLVDLPPTPWHHQRFWVTDRSAMSELAATHPLLGAHIEMPRNGDHVWQTDVGTEVCPWLADHKVFGQPIMPAAGFAEIALAAASEALGTAADAVAPNIVINQFEVEQMLPLDGHTPLTTQLIRGGDSQIRVEIYSRTRGGEFCRHATAKVEQSPRECAHAHPEAQGPATGTTVSPADFYALLRQTGQHHGPAFAALSRIVRLADGSAETEISIPDEAPRHPGYRLHPVVLDAALQSVGAAIPDGEIAGSAEASYLPVSFETIRVYRDIGRHVRCRAHLTNLDGGTGKMGRIVLINDAGHIAAEVDGIYLRRVERRAVPLPLEQKIFDAEWTESPIAAVPAPEPAAETTRGSWLVLADATVDAPGKAQAKSMADDFVQQWRSPMRRVHTADIHDESAVLAAFAETAGDPEHPPVGVVVFVGGASSRLDDELAAARDTVWSITTVVRAVVGTWHGRSPRLWLVTGGGLSVADDEPGTPAAASLKGLVRVLAFEHPDMRTTLVDLDITQDPLTALSAELRNAGSGSRHDDVIAWRGERRFVERLSRATIDVSKGHPVVRQGASYVVTGGLGGLGLVVARWLVDRGAGRVVLGGRSDPTDEQCNVLAELQTRAEIVVVRGDVASPGVAEKLIETARQSGGQLRGVVHAAAVIEDSLVFSMSRDNLERVWAPKATGALRMHEATADCELDWWLGFSSAASLLGSPGQAAYACASAWLDALVGWRRASGLPAAVINWGPWSEVGVAQALVGSVLDTISVAEGIEALDSLLAADRIRTGVARLRADRALVAFPEIRSISYFTQVVEELDSAGDLGDWGGPDALADLDPGEARRAVTERMCARIAAVMGYTDQSTVEPAVPLDKPLTELGLDSLMAVRIRNGARADFGVEPPVALILQGASLHDLTADLMRQLGLNDPDPALNNADTIRDRARQRAAARHGAAMRRRPKPEVQGG"},"dna_sequence":{"accession":"NC_000962.3","fmin":"3262247","fmax":"3267731","strand":"+","sequence":"ATGACAAGTCTGGCGGAGCGCGCGGCGCAACTGTCGCCGAACGCGCGAGCGGCCCTGGCGCGCGAGCTCGTCCGTGCGGGTACGACCTTCCCGACCGACATCTGCGAGCCGGTGGCGGTGGTGGGCATCGGCTGTCGCTTTCCGGGGAATGTGACTGGGCCAGAGAGCTTTTGGCAGCTACTGGCCGACGGTGTGGACACAATCGAGCAGGTGCCGCCTGATCGGTGGGATGCGGACGCGTTCTACGATCCCGATCCTTCGGCGTCGGGTCGGATGACGACGAAATGGGGTGGTTTCGTTTCCGATGTCGACGCGTTCGACGCCGACTTTTTCGGAATCACTCCTCGGGAAGCCGTGGCGATGGACCCGCAGCATCGGATGCTGCTCGAGGTTGCCTGGGAAGCGTTGGAGCACGCGGGTATTCCGCCGGATTCCTTGAGCGGCACTCGAACCGGCGTGATGATGGGTCTGTCGTCGTGGGACTACACGATCGTCAATATCGAGCGCAGAGCCGACATCGACGCGTACCTGAGCACCGGAACCCCGCACTGTGCCGCGGTGGGGCGGATCGCGTATCTGTTGGGATTGCGTGGTCCGGCCGTCGCCGTAGATACCGCTTGTTCGTCGTCGCTGGTGGCAATTCACTTGGCGTGTCAGAGCCTTCGCCTGCGTGAAACCGACGTGGCATTGGCGGGCGGGGTGCAGCTCACCTTGTCACCGTTCACCGCCATCGCGCTGTCCAAGTGGTCGGCGCTGTCACCGACCGGCCGATGCAACAGCTTCGACGCCAACGCGGATGGATTCGTGCGCGGCGAGGGCTGCGGCGTGGTGGTGCTCAAGCGGTTGGCCGACGCGGTGCGCGACCAGGACCGGGTGCTTGCGGTGGTCCGCGGTTCGGCAACTAACTCCGATGGTCGGTCCAACGGCATGACCGCACCGAACGCGCTGGCGCAGCGTGACGTGATCACATCCGCCCTCAAGCTTGCGGATGTTACCCCTGACAGCGTGAACTATGTCGAAACACACGGCACCGGAACGGTGTTGGGGGACCCCATCGAGTTCGAGTCGCTGGCGGCCACTTATGGCCTGGGTAAAGGCCAGGGCGAGAGCCCGTGCGCATTGGGGTCGGTCAAGACCAACATCGGCCACCTGGAGGCGGCCGCCGGTGTGGCTGGATTCATCAAGGCGGTGCTGGCGGTGCAACGTGGGCACATTCCCCGCAACTTGCACTTCACCCGGTGGAACCCGGCCATCGACGCGTCGGCGACGCGGCTGTTCGTGCCGACCGAAAGCGCCCCGTGGCCGGCGGCTGCCGGTCCACGCAGGGCTGCGGTGTCATCGTTCGGCCTCAGCGGGACCAACGCGCACGTGGTGGTCGAGCAGGCACCCGACACCGCAGTAGCCGCAGCCGGCGGCATGCCGTATGTTTCGGCGCTGAACGTCTCCGGCAAGACGGCCGCGCGGGTGGCGTCGGCGGCGGCGGTGCTGGCCGACTGGATGTCGGGGCCGGGCGCGGCGGCACCACTGGCCGACGTGGCACACACGTTGAACCGGCACCGGGCCCGGCACGCCAAGTTCGCCACCGTCATCGCGCGTGACCGCGCCGAGGCGATCGCGGGGTTGCGAGCGCTGGCGGCCGGACAACCACGCGTTGGGGTGGTGGATTGCGACCAGCATGCCGGTGGGCCTGGCCGGGTTTTTGTGTATTCGGGTCAGGGCTCGCAGTGGGCGTCGATGGGCCAGCAGTTGCTGGCCAACGAACCGGCGTTCGCCAAGGCGGTAGCCGAGCTGGATCCGATATTCGTTGACCAGGTTGGCTTTTCGCTGCAGCAAACGCTTATCGACGGCGACGAGGTGGTGGGCATCGACCGCATCCAGCCGGTGCTGGTCGGGATGCAGTTGGCGCTGACCGAGTTATGGCGGTCCTATGGGGTGATTCCAGATGCCGTGATCGGGCACTCGATGGGTGAGGTGTCGGCGGCAGTGGTGGCCGGCGCGTTGACGCCCGAGCAGGGCTTGCGGGTCATCACCACCCGGTCGCGGTTGATGGCGCGGCTGTCGGGGCAGGGAGCGATGGCGCTGCTCGAGCTGGATGCCGACGCCGCCGAGGCGCTGATTGCCGGCTATCCGCAGGTGACGCTGGCGGTGCATGCGTCACCGCGCCAGACGGTGATCGCCGGGCCGCCCGAGCAGGTGGACACGGTGATCGCGGCGGTAGCGACGCAAAACCGGTTGGCGCGCCGCGTCGAAGTCGACGTGGCCTCCCATCACCCGATCATCGATCCCATACTGCCCGAGTTGCGAAGCGCGTTAGCGGATTTGACTCCGCAGCCGCCGAGCATCCCGATCATTTCCACTACGTACGAAAGCGCGCAGCCGGTGGCGGATGCCGACTATTGGTCGGCCAACCTGCGCAACCCGGTGCGATTCCACCAGGCCGTCACCGCCGCCGGTGTCGACCACAACACCTTCATCGAAATCAGCCCTCACCCCGTGCTCACGCACGCACTCACCGACACCCTGGATCCGGACGGCAGCCATACAGTCATGTCGACGATGAACCGCGAACTGGACCAGACGCTGTATTTCCACGCCCAACTCGCCGCGGTCGGTGTGGCTGCGTCCGAGCACACCACCGGTCGCCTTGTCGACCTGCCCCCCACACCGTGGCACCATCAGCGATTCTGGGTCACGGATCGTTCGGCGATGTCCGAGCTGGCCGCGACCCACCCGCTCCTGGGCGCGCACATCGAGATGCCGCGCAACGGAGACCATGTCTGGCAGACCGATGTCGGCACCGAGGTCTGTCCCTGGTTGGCAGACCACAAGGTGTTCGGTCAACCCATCATGCCGGCCGCGGGGTTCGCCGAGATCGCCTTGGCGGCGGCCAGCGAAGCCCTCGGCACAGCCGCCGACGCCGTCGCACCCAACATCGTGATCAACCAGTTCGAGGTGGAGCAGATGCTGCCCCTCGACGGCCACACGCCGCTAACGACGCAGTTAATTCGCGGCGGGGACAGCCAGATTCGGGTCGAGATCTATTCCCGCACGCGTGGCGGAGAGTTCTGCCGACACGCCACGGCCAAGGTTGAACAATCGCCGCGCGAATGTGCGCACGCGCACCCGGAAGCCCAAGGTCCCGCCACCGGGACAACAGTGTCGCCGGCCGATTTTTATGCCCTGCTCCGCCAAACCGGCCAACACCATGGTCCGGCGTTCGCGGCCTTAAGCCGGATCGTGCGCCTGGCCGATGGTTCCGCGGAAACCGAGATCAGCATTCCCGACGAGGCGCCGCGCCATCCCGGGTATCGGCTGCACCCCGTGGTATTGGATGCGGCATTGCAAAGCGTGGGTGCCGCGATACCCGACGGCGAGATCGCGGGGTCGGCGGAAGCCAGCTATCTGCCAGTGTCGTTCGAGACCATCCGGGTGTACCGCGACATCGGTCGGCACGTCAGGTGTCGTGCCCACCTGACAAACCTCGACGGCGGCACCGGAAAGATGGGCAGGATCGTCCTAATCAACGACGCCGGCCACATAGCGGCCGAAGTGGACGGCATCTATCTGCGTCGTGTCGAACGCCGTGCGGTACCCCTGCCACTAGAGCAGAAGATCTTCGATGCCGAATGGACCGAAAGCCCGATCGCAGCCGTGCCGGCTCCGGAGCCAGCTGCCGAGACGACGCGGGGAAGTTGGCTGGTACTCGCCGATGCAACGGTGGATGCGCCAGGCAAGGCCCAGGCCAAGTCGATGGCCGACGACTTCGTGCAGCAGTGGCGCTCACCGATGCGGCGGGTGCACACCGCCGATATCCACGACGAATCGGCGGTGCTGGCCGCATTTGCAGAAACGGCAGGCGATCCCGAGCACCCGCCGGTTGGCGTGGTGGTGTTCGTCGGCGGTGCCTCGAGTCGACTGGACGACGAGCTGGCGGCGGCGCGCGACACGGTGTGGTCGATCACCACGGTGGTTCGTGCGGTCGTCGGCACGTGGCACGGCCGATCACCGCGGCTATGGCTGGTCACCGGGGGCGGACTTTCCGTTGCCGACGACGAGCCGGGAACACCCGCGGCGGCTTCCTTGAAAGGGCTGGTGCGGGTGCTCGCCTTCGAGCACCCGGACATGCGCACCACCCTGGTCGATCTGGACATCACACAAGACCCGCTGACCGCGCTGAGCGCGGAACTGCGGAATGCCGGGAGTGGGTCGCGCCATGATGACGTGATCGCGTGGCGCGGCGAGCGCAGGTTCGTCGAACGGCTGTCGCGCGCCACGATCGATGTATCCAAAGGGCATCCGGTGGTGCGCCAGGGAGCGTCGTACGTCGTCACCGGCGGCCTCGGCGGTCTCGGCCTGGTCGTCGCTCGTTGGCTGGTGGACCGCGGCGCCGGCCGGGTGGTGCTGGGTGGCCGCAGCGATCCCACTGACGAGCAGTGCAACGTCCTGGCCGAACTGCAGACCCGCGCCGAGATCGTGGTTGTCCGTGGCGACGTGGCATCGCCGGGGGTGGCAGAAAAGCTGATTGAGACGGCCCGACAGTCTGGGGGCCAATTGCGCGGCGTCGTGCACGCCGCCGCGGTCATCGAAGACAGCCTGGTGTTCTCTATGAGCAGGGACAACCTAGAACGGGTGTGGGCACCCAAGGCCACCGGTGCGCTGCGCATGCACGAAGCCACCGCTGACTGCGAGCTCGACTGGTGGCTCGGATTCTCTTCCGCCGCTTCGCTATTGGGTTCTCCCGGGCAAGCGGCCTACGCGTGCGCCAGCGCGTGGCTGGACGCGCTGGTCGGATGGCGCAGGGCATCCGGCCTGCCGGCCGCGGTGATCAACTGGGGTCCGTGGTCGGAGGTAGGCGTCGCCCAGGCCTTGGTGGGCAGTGTTCTCGACACGATCAGTGTCGCAGAAGGCATCGAGGCTCTCGACTCATTGCTTGCCGCCGACCGGATCCGCACTGGAGTGGCTCGGCTGCGTGCCGATCGGGCCCTGGTCGCATTCCCGGAGATCCGCAGCATCAGCTACTTCACCCAGGTGGTCGAGGAGCTGGACTCGGCGGGTGACCTCGGCGACTGGGGCGGGCCCGACGCGCTTGCCGACCTCGACCCGGGCGAGGCGCGGCGCGCGGTGACCGAGCGGATGTGTGCGCGCATCGCTGCGGTGATGGGCTACACTGACCAGTCGACTGTCGAACCCGCCGTGCCCTTGGACAAGCCCCTGACCGAGCTGGGGCTGGATTCTCTGATGGCGGTACGAATACGCAACGGCGCGCGGGCGGATTTCGGCGTGGAACCGCCGGTAGCGCTGATACTGCAAGGCGCGTCCTTGCATGACCTGACGGCGGACTTAATGCGCCAACTCGGGCTCAATGATCCCGATCCGGCGCTCAACAACGCTGACACTATTCGCGACCGGGCGCGCCAGCGCGCGGCAGCGCGACACGGAGCCGCGATGCGGCGCCGACCTAAACCTGAAGTACAGGGAGGATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3004976","ARO_id":"43163","ARO_name":"Mycobacterium tuberculosis ppsD mutations confer resistance to pyrazinamide","CARD_short_name":"Mtub_ppsD_PZA","ARO_description":"Mutations in ppsD can contribute to or confer resistance to pyrazinamide.","ARO_category":{"43189":{"category_aro_accession":"3005002","category_aro_cvterm_id":"43189","category_aro_name":"antibiotic resistant polyketide synthase genes","category_aro_description":"Genes ppsA-E constitute an operon encoding enzymes involved in the biosynthesis of phthiocerol dimycocerosate and other lipids in Mycobacterium tuberculosis. Mutations within this region can result in resistance to pyrazinamide.","category_aro_class_name":"AMR Gene Family"},"39997":{"category_aro_accession":"3003413","category_aro_cvterm_id":"39997","category_aro_name":"pyrazinamide","category_aro_description":"Pyrazinamide is an antimycobacterial. It is highly specific and active only against Mycobacterium tuberculosis. This compound is a prodrug and needs to be activated inside the cell. It interferes with the bacterium's ability to synthesize new fatty acids, causing cell death.","category_aro_class_name":"Antibiotic"},"45737":{"category_aro_accession":"3007155","category_aro_cvterm_id":"45737","category_aro_name":"pyrazine antibiotic","category_aro_description":"A group of antibiotics derived from pyrazine.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3723":{"model_id":"3723","model_name":"Mycobacterium tuberculosis ahpC mutations confer resistance to isoniazid","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"41339":{"param_type":"nucleotide substitution in promoter region","param_description":"A nucleotide sequence change where, compared to a reference sequence, one nucleotide is replaced by one other nucleotide in the promoter region of a gene. These substitutions are indicated as upstream of the reference sequence transcription initiation site. Format is given by [-][position][wildtype][>][mutation], e.g. -11t>c or -15g>Var where Var represents any possible substitution.","param_type_id":"41339","param_value":{"13291":"-72c>t","13343":"-48g>a","13687":"-57c>t"}},"snp":{"CRyPTIC-R":{"13291":"V295M","13343":"V295M","13687":"G48A"},"ReSeqTB-High":{"9526":"V295M","13006":"C52T","13007":"C72T","13008":"C81T","13009":"G48A"},"param_value":{"13006":"C52T","13007":"C72T","13008":"C81T","13009":"G48A"},"clinical":{"13006":"C52T","13007":"C72T","13008":"C81T","13009":"G48A"}},"41345":{"param_type":"insertion mutation from nucleotide sequence","param_description":"A subtype of the insertion mutation detection model parameter used when a set of insertion mutations are reported in a nucleotide sequence format, encoded as [+]nt[position]:[nucleotides], for example +nt391:GG or +nt368:18. Such mutations may be of variable length, possibly causing a frameshift but not causing premature termination or a functional knockout.","param_type_id":"41345","param_value":{"9526":"+nt47:t"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"325"}},"model_sequences":{"sequence":{"8771":{"protein_sequence":{"accession":"NP_216944.1","sequence":"MPLLTIGDQFPAYQLTALIGGDLSKVDAKQPGDYFTTITSDEHPGKWRVVFFWPKDFTFVCPTEIAAFSKLNDEFEDRDAQILGVSIDSEFAHFQWRAQHNDLKTLPFPMLSDIKRELSQAAGVLNADGVADRVTFIVDPNNEIQFVSATAGSVGRNVDEVLRVLDALQSDELCACNWRKGDPTLDAGELLKASA"},"dna_sequence":{"accession":"NC_000962.3","fmin":"2726192","fmax":"2726780","strand":"+","sequence":"ATGCCACTGCTAACCATTGGCGATCAATTCCCCGCCTACCAGCTCACCGCTCTCATCGGCGGTGACCTGTCCAAGGTCGACGCCAAGCAGCCCGGCGACTACTTCACCACTATCACCAGTGACGAACACCCAGGCAAGTGGCGGGTGGTGTTCTTTTGGCCGAAAGACTTCACGTTCGTGTGCCCTACCGAGATCGCGGCGTTCAGCAAGCTCAATGACGAGTTCGAGGACCGCGACGCCCAGATCCTGGGGGTTTCGATTGACAGCGAATTCGCGCATTTCCAGTGGCGTGCACAGCACAACGACCTCAAAACGTTACCCTTCCCGATGCTCTCCGACATCAAGCGCGAACTCAGCCAAGCCGCAGGTGTCCTCAACGCCGACGGTGTGGCCGACCGCGTGACCTTTATCGTCGACCCCAACAACGAGATCCAGTTCGTCTCGGCCACCGCCGGTTCGGTGGGACGCAACGTCGATGAGGTACTGCGAGTGCTCGACGCCCTCCAGTCCGACGAGCTGTGCGCATGCAACTGGCGCAAGGGCGACCCGACGCTAGACGCTGGCGAACTCCTCAAGGCTTCGGCCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3004921","ARO_id":"43107","ARO_name":"Mycobacterium tuberculosis ahpC mutations confer resistance to isoniazid","CARD_short_name":"Mtub_ahpC_INH","ARO_description":"Mutations that occur in ahpC that result in ahpC overexpression thus conferring or contributing to resistance to isoniazid.","ARO_category":{"43080":{"category_aro_accession":"3004894","category_aro_cvterm_id":"43080","category_aro_name":"Isoniazid resistant ahpC","category_aro_description":"An alkyl hydroperoxide reductase that catalyzes the reduction of organic hydrogen peroxide to water and organic alcohols. Plays a role in protecting oxidative stress.","category_aro_class_name":"AMR Gene Family"},"36659":{"category_aro_accession":"3000520","category_aro_cvterm_id":"36659","category_aro_name":"isoniazid","category_aro_description":"Isoniazid is an organic compound that is the first-line anti tuberculosis medication in prevention and treatment. As a prodrug, it is activated by mycobacterial catalase-peroxidases such as M. tuberculosis KatG. Isoniazid inhibits mycolic acid synthesis, which prevents cell wall synthesis in mycobacteria.","category_aro_class_name":"Antibiotic"},"45734":{"category_aro_accession":"3007152","category_aro_cvterm_id":"45734","category_aro_name":"isoniazid-like antibiotic","category_aro_description":"A group of antibiotics containing isoniazid and its derivatives.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3128":{"model_id":"3128","model_name":"MCR-3.11","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"5342":{"protein_sequence":{"accession":"AUN87920.1","sequence":"MPSLIKIKIVPLMFFLALYFAFMLNWRGVLHFYEILYKLEDFKFGFAISLPILLVAALNFVFVPFSIRYLIKPFFALLIALSAIVSYTMMKYRVLFDQNMIQNIFETNQNEALAYLSLPIIVWVTIAGFIPAILLFFVEIEYEEKWFKGILTRALSMFASLIVIAVIAALYYQDYVSVGRNNSNLQREIVPANFVNSTVKYVYNRYLAEPIPFTTLGDDAKRDTNQSKPTLMFLVVGETARGKNFSMNGYEKDTNPFTSKSGGVISFNDVRSCGTATAVSVPCMFSNMGRKEFDDNRARNSEGLLDVLQKTGISIFWKENDGGCKGVCDRVPNIEIEPKDHPKFCDKNTCYDEVVLQDLDSEIAQMKGDKLVVFHLIGSHGPTYYKRYPDAHRQFTPDCPRSDIENCTDEELTNTYDNTIRYTDFVIGEMIAKLKTYEDKYNTALLYVSDHGESLGALGLYLHGTPYTFAPDDQTRVPMQVWMSPGFTKEKGVDMACLQQKAADTRYSHDNIFSSVLGIWDVKTSVYEKGLDIFSQCRNVQ"},"dna_sequence":{"accession":"MG489958.1","fmin":"0","fmax":"1626","strand":"+","sequence":"ATGCCTTCCCTTATAAAAATAAAAATTGTTCCGCTTATGTTCTTTTTGGCACTGTATTTTGCATTTATGCTGAACTGGCGTGGAGTTCTCCATTTTTACGAAATCCTTTACAAATTAGAAGATTTTAAGTTTGGTTTCGCCATTTCATTACCAATATTGCTTGTTGCAGCGCTTAACTTTGTATTTGTTCCATTTTCGATACGGTATTTAATAAAGCCTTTTTTTGCACTTCTTATCGCACTTAGTGCAATCGTTAGTTACACAATGATGAAGTATAGAGTCTTGTTTGATCAAAACATGATTCAGAATATTTTTGAAACCAATCAAAATGAGGCGTTAGCATATTTAAGCTTACCAATTATAGTATGGGTTACTATTGCTGGTTTTATCCCTGCCATTTTACTTTTCTTTGTTGAAATTGAATATGAGGAAAAATGGTTCAAAGGGATTCTAACTCGTGCCCTATCGATGTTTGCATCACTTATAGTGATTGCGGTTATTGCAGCACTATACTATCAAGATTATGTGTCAGTGGGGCGCAACAATTCAAACCTCCAGCGTGAGATTGTTCCAGCCAATTTCGTTAATAGTACCGTTAAATACGTTTACAATCGTTATCTTGCTGAACCAATCCCATTTACAACTTTAGGTGATGATGCAAAACGGGATACTAATCAAAGTAAGCCCACGTTGATGTTTCTGGTCGTTGGTGAAACCGCTCGTGGTAAAAATTTCTCGATGAATGGCTATGAGAAAGACACCAATCCATTTACCAGTAAATCTGGTGGCGTGATCTCCTTTAATGATGTTCGTTCGTGTGGGACTGCAACCGCTGTATCCGTCCCCTGCATGTTCTCCAATATGGGGAGAAAGGAGTTTGATGATAATCGCGCTCGCAATAGCGAGGGCCTGCTAGATGTGTTGCAAAAAACGGGGATCTCCATTTTTTGGAAGGAGAACGATGGAGGCTGCAAAGGCGTCTGCGACCGAGTACCTAACATCGAAATCGAACCAAAGGATCACCCTAAGTTCTGCGATAAAAACACATGCTATGACGAGGTTGTCCTTCAAGACCTCGATAGTGAAATTGCTCAAATGAAAGGGGATAAGCTGGTTGTCTTCCACCTGATAGGTAGCCATGGCCCAACCTACTACAAGCGCTACCCTGATGCTCATCGTCAGTTCACCCCTGACTGTCCACGCAGTGATATTGAAAACTGCACAGATGAAGAGCTCACCAACACCTATGACAACACCATCCGCTACACCGATTTCGTGATTGGAGAGATGATTGCCAAGTTGAAAACCTACGAAGATAAGTACAACACCGCGTTGCTCTACGTCTCCGATCATGGTGAATCACTGGGAGCATTAGGGCTTTACCTACACGGTACACCGTACACGTTTGCACCGGATGATCAGACCCGTGTTCCTATGCAGGTGTGGATGTCACCTGGATTTACCAAAGAGAAAGGCGTTGATATGGCGTGTTTGCAGCAGAAAGCCGCTGATACTCGTTACTCACACGATAATATTTTCTCATCTGTATTGGGTATCTGGGACGTCAAAACATCAGTTTACGAAAAGGGTCTAGATATTTTCAGTCAATGTCGTAATGTTCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3004500","ARO_id":"42205","ARO_name":"MCR-3.11","CARD_short_name":"MCR-3.11","ARO_description":"An MCR-3 phosphoethanolamine transferase and polymyxin resistance gene variant differing by 2 amino acid substitutions, identified from an Escherichia coli isolate.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3129":{"model_id":"3129","model_name":"MCR-6.1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"5341":{"protein_sequence":{"accession":"ASK49942.1","sequence":"MTQHSPWYRRPVNPYLLMSVVALFLSATANLTFFDKITNTYPMAQNAGFVISTALVLFGAMLLITVLLSYRYVLKPVLILLLIMGAVTSYFTDTYGTVYDTTMLQNALQTDQAESKDLMNMAFFVRIIGLGVLPSILVAWVKVDYPTLGKSLIQRAMTWGVAVVMALVPILAFSSHYASFFREHKPLRSYVNPVMPIYSVGKLASIEYKKATAPKDTIYHAKDAVQTTTPAERKPRLVVFVVGETARADHVQFNGYSRETFPQLAKIDNLANFSQVTSCGTSTAYSVPCMFSYLGQDDYDVDTAKYQENVLDTLDRLGVGILWRDNNSDSKGVMDKLPASQYFDYKSATNNTICNTNPYNECRDVGMLVGLDDYVSTNQGKDMLIMLHQMGNHGPAYFKRYDEQFAKYTPVCEGNELAKCEHQSLINAYDNALLATDDFIAKSIDWLKTHQANYDVAMLYVSDHGESLGENGVYLHGMPNAFAPKEQRAVPAFFWSNNPSFTPTASDTVLTHDAITPTLLKLFDVTADKVKDRTAFIR"},"dna_sequence":{"accession":"MF176240.1","fmin":"0","fmax":"1617","strand":"+","sequence":"ATGACACAGCATAGTCCTTGGTACCGCCGTCCGGTCAATCCCTATCTGTTGATGAGCGTGGTCGCTTTATTTTTGTCAGCGACAGCAAACCTAACTTTCTTTGATAAAATCACCAATACTTATCCGATGGCACAAAACGCAGGCTTTGTGATCTCAACGGCGCTTGTGCTATTTGGGGCGATGCTATTGATTACTGTGCTGTTATCGTATCGCTATGTGCTTAAGCCTGTGTTGATTTTGCTGCTTATCATGGGTGCGGTGACGAGCTATTTTACCGATACTTATGGCACCGTTTATGACACCACCATGCTCCAAAATGCCTTGCAAACTGACCAAGCCGAGTCTAAGGACTTGATGAATATGGCGTTTTTTGTGCGGATTATCGGGCTTGGCGTGTTGCCAAGTATCTTGGTGGCGTGGGTCAAGGTGGATTATCCGACATTGGGTAAGAGTCTGATTCAGCGTGCGATGACTTGGGGTGTGGCAGTGGTGATGGCACTTGTGCCGATTTTGGCATTTAGTAGTCACTACGCCAGTTTCTTTCGTGAACATAAGCCACTGCGTAGCTATGTCAATCCCGTGATGCCGATTTATTCAGTAGGTAAGCTTGCCAGTATTGAGTACAAAAAAGCCACCGCGCCAAAAGACACCATCTATCATGCCAAAGATGCTGTACAGACGACGACGCCTGCCGAGCGTAAGCCACGACTCGTGGTGTTCGTCGTCGGTGAGACGGCTCGAGCTGACCATGTGCAGTTTAATGGCTATAGTCGTGAGACTTTTCCGCAGCTTGCCAAGATTGACAACCTAGCCAATTTTAGCCAAGTGACATCGTGTGGCACATCGACGGCGTACTCTGTGCCGTGTATGTTCAGTTATCTGGGTCAAGATGACTATGATGTCGATACCGCCAAATACCAAGAAAACGTGCTGGATACGCTTGACCGACTGGGTGTGGGTATCCTGTGGCGGGATAATAATTCAGACTCAAAAGGCGTGATGGATAAACTGCCTGCTTCGCAGTATTTTGATTATAAATCAGCGACCAACAACACCATCTGTAACACCAATCCTTACAACGAATGTCGTGATGTCGGTATGTTGGTGGGGCTAGATGATTATGTGAGTACCAATCAAGGCAAAGATATGCTCATCATGCTACACCAAATGGGTAATCATGGGCCGGCGTACTTCAAGCGTTATGACGAGCAATTTGCCAAATACACCCCTGTGTGCGAAGGTAATGAACTTGCCAAGTGTGAACACCAATCGCTCATCAACGCCTATGATAATGCACTGCTTGCGACCGATGATTTTATCGCCAAAAGTATCGATTGGCTAAAAACGCATCAGGCCAACTATGATGTTGCCATGCTCTATGTCAGCGACCACGGCGAGAGTCTGGGTGAAAATGGCGTCTATCTGCATGGTATGCCAAATGCCTTTGCACCAAAAGAACAGCGAGCGGTACCGGCATTCTTTTGGTCAAATAATCCATCGTTCACGCCAACTGCCAGCGACACTGTGCTGACACATGATGCGATTACGCCGACTCTACTGAAGCTGTTTGATGTCACAGCGGATAAGGTCAAAGACCGCACCGCATTCATCCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42207","NCBI_taxonomy_name":"Moraxella sp. MSG47-C17","NCBI_taxonomy_id":"1935434"}}}},"ARO_accession":"3004501","ARO_id":"42206","ARO_name":"MCR-6.1","CARD_short_name":"MCR-6.1","ARO_description":"An MCR-2 phosphoethanolamine transferase and polymyxin resistance gene variant identified in Moraxella isolated from pigs in the United Kingdom.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3130":{"model_id":"3130","model_name":"MCR-2.2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"5339":{"protein_sequence":{"accession":"ASK49941.1","sequence":"MTSQHSWYRYSINPFVLMGLVALFLAATANLTFFEKAMAVYPVSDNLGFIISMAVALMGAMLLIVVLLSYRYVLKPVLILLLIMGAVTSYFTDTYGTVYDTTMLQNAMQTDQAESKDLMNLAFFVRIIGLGVLPSVLVAFAKVNYPTWGKGLIQRAMTWGVSLVLLLVPIGLFSSQYASFFRVHKPVRFYINPITPIYSVGKLASIEYKKATAPTDTIYHAKDAVQTTKPSERKPRLVVFVVGETARADHVQFNGYGRETFPQLAKVDGLANFSQVTSCGTSTAYSVPCMFSYLGQDDYDVDTAKYQENVLDTLDRLGVDILWRDNNSDSKGVMDKLPTTQYFDYKSATNNTICNTNPFNECRDVGMLVGLDDYVSANNGKDMLIMLHQMGNHGPAYFKRYDEQFAKFTPVCEGNELAKCEHQSLINAYDNALLATDDFIAKSIDWLKTHEANYDVAMLYVSDHGESLGENGVYLHGMPNAFAPKEQRAVPAFFWSNNTTFKPTASDTVLTHDAITPTLLKLFDVTADKVKDRTAFIQ"},"dna_sequence":{"accession":"MF176239.1","fmin":"0","fmax":"1617","strand":"+","sequence":"ATGACATCACAGCACTCTTGGTATCGCTACTCCATCAATCCTTTTGTACTGATGGGTTTGGTGGCGTTATTTTTGGCGGCAACAGCGAACCTGACATTTTTTGAAAAAGCGATGGCGGTCTATCCTGTATCGGATAACTTAGGCTTTATCATCTCAATGGCGGTTGCACTGATGGGTGCTATGCTATTGATTGTCGTGCTATTATCCTATCGCTATGTGCTAAAGCCTGTGCTGATTTTATTACTTATCATGGGTGCGGTGACGAGCTATTTTACCGATACTTATGGCACGGTCTATGATACCACCATGCTCCAAAATGCCATGCAAACCGACCAAGCTGAATCTAAAGACTTGATGAATTTGGCGTTTTTTGTGCGGATTATCGGGCTTGGCGTGTTGCCAAGTGTGTTGGTCGCATTTGCCAAAGTCAATTATCCAACATGGGGCAAAGGCCTGATTCAGCGTGCGATGACGTGGGGTGTCAGCCTTGTGCTGTTGCTTGTGCCGATTGGGCTATTTAGCAGTCAGTATGCGAGTTTCTTTCGGGTGCATAAGCCAGTGCGTTTTTATATCAATCCGATTACGCCGATTTATTCGGTGGGCAAGCTTGCCAGTATCGAGTACAAAAAAGCCACTGCACCAACAGACACCATCTATCATGCCAAAGATGCCGTGCAGACCACCAAGCCTAGCGAGCGTAAGCCACGCCTAGTAGTGTTCGTCGTCGGTGAGACGGCGCGTGCTGACCATGTGCAGTTCAATGGCTATGGCCGTGAGACTTTCCCACAGCTTGCCAAAGTTGATGGCTTGGCGAATTTTAGCCAAGTGACATCGTGTGGCACATCGACAGCGTATTCTGTGCCGTGTATGTTTAGCTATTTGGGTCAAGATGACTATGATGTCGATACCGCCAAATACCAAGAAAATGTGCTAGATACGCTTGACCGCTTGGGCGTGGATATCTTGTGGCGTGATAATAATTCAGACTCAAAAGGCGTGATGGATAAGCTACCTACCACGCAGTATTTTGATTATAAATCAGCGACCAACAACACCATCTGTAACACCAATCCCTTTAATGAATGCCGTGATGTCGGTATGCTTGTTGGGCTAGATGACTATGTCAGTGCCAATAATGGCAAAGATATGCTCATCATGCTACACCAAATGGGCAATCATGGGCCGGCGTACTTTAAGCGTTATGATGAGCAATTTGCCAAATTCACCCCTGTGTGCGAAGGCAATGAGCTTGCCAAATGCGAACACCAATCACTCATCAATGCCTATGATAATGCACTACTTGCCACCGATGATTTTATCGCCAAAAGTATCGATTGGCTAAAAACACATGAAGCAAACTACGATGTCGCTATGCTCTATGTCAGCGACCACGGCGAGAGCTTGGGCGAGAATGGTGTCTATCTGCATGGTATGCCAAATGCCTTTGCACCAAAAGAACAGCGAGCCGTGCCTGCGTTTTTTTGGTCAAATAATACGACATTCAAGCCAACTGCCAGCGACACTGTGCTGACGCATGATGCGATTACCCCGACATTGCTTAAGCTGTTTGATGTCACAGCCGACAAGGTCAAAGACCGCACGGCATTTATCCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42209","NCBI_taxonomy_name":"Moraxella pluranimalium","NCBI_taxonomy_id":"470453"}}}},"ARO_accession":"3004502","ARO_id":"42208","ARO_name":"MCR-2.2","CARD_short_name":"MCR-2.2","ARO_description":"An MCR-2 phosphoethanolamine transferase and polymyxin resistance gene variant identified in Moraxella isolated from pigs in Great Britain.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3131":{"model_id":"3131","model_name":"MCR-3.6","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"5338":{"protein_sequence":{"accession":"AST36140.1","sequence":"MPSLIKIKIVPLIFFLALYFAFMLNWRGVLHFYEILYKLEYFKFGFAISLPILLVAALNFVFVPFSIRYLVKPFFALLIALSAIVSYTMMKYRVLFDQNMIQNIFETNQNEALAYLNLPIIGWVTIAGFIPAILLFFVDIEYEEKWFKGILTRALSMFASLIVIAVIAALYYQDYVSVGRNNSNLQREIVPANFVNSTVKYVYNRYLAEPIPFTTLGDDAKRDTNQSKPTLMFLVVGETARGKNFSMNGYEKDTNPFTSKSGGVISFNDVRSCGTATAVSVPCMFSNMGRKEFDDNLARNSEGLLDVLQKTGVSIFWKENDGGCKGVCDRVPNIEIKPKDYPKFCDKNTCYDEVVLQDLDSEIAQMKGDKLVGFHLIGSHGPTYYKRYPDAHRQFTPDCPRSDIENCTDEELTNTYDNTIRYTDFVIAEMIAKLKTYEDKYNTALLYVSDHGESLGAMGLYLHGTPYKFAPDDQTRVPMQVWMSPGFIKEKGMNMECLQKNAAANRYSHDNIFSSVLGIWDVKTAIYEQELDIFKQCRNN"},"dna_sequence":{"accession":"MF598076.1","fmin":"0","fmax":"1623","strand":"+","sequence":"ATGCCTTCCCTTATAAAAATTAAAATTGTGCCGCTCATATTTTTTTTGGCACTGTATTTTGCATTTATGCTGAACTGGCGTGGAGTTCTCCATTTTTACGAAATCCTTTACAAATTAGAATATTTTAAGTTTGGTTTCGCCATTTCATTACCAATATTGCTTGTTGCAGCGCTTAACTTTGTATTTGTTCCATTTTCGATACGGTATTTAGTAAAGCCTTTTTTTGCACTTCTGATCGCACTTAGTGCAATCGTTAGTTACACAATGATGAAGTATAGAGTATTGTTTGATCAAAACATGATTCAGAATATTTTTGAAACCAATCAAAATGAGGCGTTAGCATATTTAAACTTACCAATTATAGGATGGGTTACTATTGCTGGTTTTATCCCTGCCATTTTACTTTTCTTTGTTGATATTGAATATGAGGAAAAATGGTTCAAAGGGATTCTAACTCGTGCCCTATCGATGTTTGCATCACTTATAGTGATTGCGGTTATTGCTGCACTATACTATCAAGATTATGTTTCAGTTGGGCGTAACAATTCAAACCTCCAGCGTGAAATTGTTCCAGCCAATTTCGTTAATAGTACCGTTAAATATGTTTACAATCGTTATCTTGCTGAACCAATCCCATTTACAACTTTAGGTGATGATGCAAAACGGGATACTAATCAAAGTAAGCCCACGTTGATGTTCCTGGTCGTTGGTGAAACCGCTCGCGGTAAAAATTTCTCGATGAATGGCTATGAGAAAGACACCAATCCATTTACCAGTAAATCTGGTGGCGTGATCTCCTTTAATGATGTTCGTTCGTGTGGGACTGCAACCGCTGTATCTGTCCCCTGCATGTTCTCCAATATGGGGAGAAAGGAGTTTGATGATAATCTCGCTCGTAATAGCGAGGGTTTGTTAGATGTGTTGCAGAAAACGGGGGTCTCCATTTTTTGGAAGGAGAACGATGGCGGCTGCAAAGGCGTCTGCGACCGAGTTCCTAACATCGAGATCAAACCGAAGGATTACCCAAAGTTCTGCGATAAAAACACATGCTATGACGAGGTTGTCCTTCAAGACCTCGACAGTGAAATTGCTCAAATGAAAGGGGATAAGCTGGTTGGCTTCCACCTGATAGGTAGCCATGGCCCAACCTACTACAAACGCTACCCTGATGCTCATCGTCAGTTCACTCCTGACTGTCCACGCAGTGATATTGAAAACTGCACAGATGAAGAGCTCACCAACACCTATGACAACACCATCCGCTACACGGATTTCGTGATTGCAGAGATGATTGCCAAGTTGAAAACCTACGAAGATAAGTACAACACCGCGTTGCTCTACGTCTCCGATCACGGTGAATCACTGGGAGCTATGGGGCTTTACCTGCACGGTACACCATACAAATTTGCACCGGATGATCAGACCCGCGTACCTATGCAGGTGTGGATGTCACCTGGTTTCATCAAAGAAAAAGGCATGAATATGGAATGTTTGCAGAAAAATGCCGCAGCCAATCGCTATTCTCATGACAACATATTTTCTTCTGTCCTGGGAATATGGGATGTGAAGACGGCTATCTACGAACAAGAATTAGATATCTTTAAGCAATGTCGGAATAATTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36947","NCBI_taxonomy_name":"Aeromonas allosaccharophila","NCBI_taxonomy_id":"656"}}}},"ARO_accession":"3004503","ARO_id":"42210","ARO_name":"MCR-3.6","CARD_short_name":"MCR-3.6","ARO_description":"An MCR-3 phosphoethanolamine transferase and polymyxin resistance gene variant identified in Aeromonas.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3132":{"model_id":"3132","model_name":"MCR-3.10","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"5337":{"protein_sequence":{"accession":"ATQ63376.1","sequence":"MPSLIKIKIVPLMFFLALYFAFMLNWRGVLHFYEILYKLEDFKFGFAISLPILLVAALNFVFVPFSIRYLIKPFFALLIALSAIVSYTMMKYRVLFDQNMIQNIFETNQNEALAYLSLPIIGWVTIAGFIPAILLFFVEIEYEEKWFKGILTRALSMFASLIVIAVIAALYYQDYVSVGRNNSNLQREIVPANFVNSTVKYVYNRYLAEPIPFTTLGDDAKRDTNQSKPTLMFLVVGETARGKNFSMNGYEKDTNPFTSKSGGVISFNDVRSCGTATAVSVPCMFSNMGRKEFDDNLARNSEGLLDVLQKTGVSIFWKENDGGCKGVCDRVPNIEIKPKDYPKFCDKNTCYDEVVLQELDSEIAQMKGDKLVGFHLIGSHGPTYYKRYPDAHRQFTPDCPRSDIENCTDEELTNTYDNTIRYTDFVIGEMIAKLKTYEDKYNTALLYVSDHGESLGALGLYLHGTPYKFAPDDQTRVPMQVWMSPGFTKEKGVDMACLQQKAADTRYSHDNIFSSVLGIWDVKTSVYEKGLDIFSQCRNVQ"},"dna_sequence":{"accession":"MG214531.1","fmin":"6792","fmax":"8418","strand":"+","sequence":"ATGCCTTCCCTTATAAAAATAAAAATTGTTCCGCTTATGTTCTTTTTGGCACTGTATTTTGCATTTATGCTGAACTGGCGTGGAGTTCTCCATTTTTACGAAATCCTTTACAAATTAGAAGATTTTAAGTTTGGTTTCGCCATTTCATTACCAATATTGCTTGTTGCAGCGCTTAACTTTGTATTTGTTCCATTTTCGATACGGTATTTAATAAAGCCTTTTTTTGCACTTCTTATCGCACTTAGTGCAATCGTTAGTTACACAATGATGAAGTATAGAGTCTTGTTTGATCAAAACATGATTCAGAATATTTTTGAAACCAATCAAAATGAGGCGTTAGCATATTTAAGCTTACCAATTATAGGATGGGTTACTATTGCTGGTTTTATCCCTGCCATTTTACTTTTCTTTGTTGAAATTGAATATGAGGAAAAATGGTTCAAAGGGATTCTAACTCGTGCCCTATCGATGTTTGCATCACTTATAGTGATTGCGGTTATTGCAGCACTATACTATCAAGATTATGTGTCAGTGGGGCGCAACAATTCAAACCTCCAGCGTGAGATTGTTCCAGCCAATTTCGTTAATAGTACCGTTAAATACGTTTACAATCGTTATCTTGCTGAACCAATCCCATTTACAACTTTAGGTGATGATGCAAAACGGGATACTAATCAAAGTAAGCCCACGTTGATGTTTCTGGTCGTTGGTGAAACCGCTCGTGGTAAAAATTTCTCGATGAATGGCTATGAGAAAGACACCAATCCATTTACCAGTAAATCTGGTGGCGTGATCTCCTTTAATGATGTTCGTTCGTGTGGGACTGCAACCGCTGTATCTGTCCCCTGCATGTTTTCCAATATGGGGAGAAAGGAGTTTGATGATAATCTCGCTCGTAATAGCGAGGGTTTGTTAGATGTGTTGCAGAAAACGGGGGTCTCCATTTTTTGGAAGGAGAACGATGGAGGCTGCAAAGGCGTCTGCGACCGAGTTCCTAACATCGAGATCAAACCGAAGGATTACCCAAAGTTCTGCGATAAAAACACATGCTATGACGAGGTTGTCCTTCAAGAGCTCGACAGTGAAATTGCTCAAATGAAAGGGGATAAGCTGGTTGGCTTCCACCTGATAGGTAGCCATGGCCCAACCTACTACAAGCGCTACCCTGATGCTCATCGTCAGTTCACCCCTGACTGTCCACGCAGTGATATTGAAAACTGCACAGATGAAGAGCTCACCAACACCTATGACAACACCATCCGCTACACCGATTTCGTGATTGGAGAGATGATTGCCAAGTTGAAAACCTACGAAGATAAGTACAACACCGCGTTGCTCTACGTCTCCGATCATGGTGAATCACTGGGAGCATTAGGGCTTTACCTACACGGTACACCGTACAAGTTTGCACCGGATGATCAGACCCGTGTTCCTATGCAGGTGTGGATGTCACCTGGATTTACCAAAGAGAAAGGCGTTGATATGGCGTGTTTGCAGCAGAAAGCCGCTGATACTCGTTACTCACACGATAATATTTTCTCATCTGTATTGGGTATCTGGGACGTCAAAACATCAGTTTACGAAAAGGGTCTAGATATTTTCAGTCAATGTCGTAATGTTCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36936","NCBI_taxonomy_name":"Aeromonas caviae","NCBI_taxonomy_id":"648"}}}},"ARO_accession":"3004504","ARO_id":"42212","ARO_name":"MCR-3.10","CARD_short_name":"MCR-3.10","ARO_description":"An MCR-3 phosphoethanolamine transferase and polymyxin (colistin) resistance gene variant identified from Aeromonas, Proteus and Escherichia coli.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3133":{"model_id":"3133","model_name":"MCR-3.5","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"5577":{"protein_sequence":{"accession":"ASU04896.1","sequence":"MPSLIKIKIVPLMFFLALYFAFVLNWRGVLHFYEILYKLEDFKFGFAISLPILLVAALNFVFVPFSIRYLIKPFFALLIALSAIVSYTMMKYRVLFDQNMIQNIFETNQNEALAYLSLPIIVWVTIAGFIPAILLFFVEIEYEEKWFKGILTRALSMFASLIVIAVIAALYYQDYVSVGRNNSNLQREIVPANFVNSTVKYVYNRYLAEPIPFTTLGDDAKRDTNQSKPTLMFLVVGETARGKNFSMNGYEKDTNPFTSKSGGVISFNDVRSCGTATAVSVPCMFSNMGRKEFDDNRARNSEGLLDVLQKTGISIFWKENDGGCKGVCDRVPNIEIEPKDHPKFCDKNTCYDEVVLQDLDSEIAQMKGDKLVGFHLIGSHGPTYYKRYPDAHRQFTPDCPRSDIENCTDEELTNTYDNTIRYTDFVIGEMIAKLKTYEDKYNTALLYVSDHGESLGELGLYLHGTPYQFAPDDQTRVPMQVWMSPGFIKEKGVDMACLQQKAADTRYSHDNIFSSVLGIWDVKTSVYEKGLDIFSQCRNVQ"},"dna_sequence":{"accession":"MF489760.1","fmin":"49179","fmax":"50805","strand":"+","sequence":"ATGCCTTCCCTTATAAAAATAAAAATTGTTCCGCTTATGTTCTTTTTGGCACTGTATTTTGCATTTGTGCTGAACTGGCGTGGAGTTCTCCATTTTTACGAAATCCTTTACAAATTAGAAGATTTTAAGTTTGGTTTCGCCATTTCATTACCAATATTGCTTGTTGCAGCGCTTAACTTTGTATTTGTTCCATTTTCGATACGGTATTTAATAAAGCCTTTTTTTGCACTTCTTATCGCACTTAGTGCAATCGTTAGTTACACAATGATGAAGTATAGAGTCTTGTTTGATCAAAACATGATTCAGAATATTTTTGAAACCAATCAAAATGAGGCGTTAGCATATTTAAGCTTACCAATTATAGTATGGGTTACTATTGCTGGTTTTATCCCTGCCATTTTACTTTTCTTTGTTGAAATTGAATATGAGGAAAAATGGTTCAAAGGGATTCTAACTCGTGCCCTATCGATGTTTGCATCACTTATAGTGATTGCGGTTATTGCAGCACTATACTATCAAGATTATGTGTCAGTGGGGCGCAACAATTCAAACCTCCAGCGTGAGATTGTTCCAGCCAATTTCGTTAATAGTACCGTTAAATACGTTTACAATCGTTATCTTGCTGAACCAATCCCATTTACAACTTTAGGTGATGATGCAAAACGGGATACTAATCAAAGTAAGCCCACGTTGATGTTTCTGGTCGTTGGTGAAACCGCTCGTGGTAAAAATTTCTCGATGAATGGCTATGAGAAAGACACCAATCCATTTACCAGTAAATCTGGTGGCGTGATCTCCTTTAATGATGTTCGTTCGTGTGGGACTGCAACCGCTGTATCCGTCCCCTGCATGTTCTCCAATATGGGGAGAAAGGAGTTTGATGATAATCGCGCTCGCAATAGCGAGGGCCTGCTAGATGTGTTGCAAAAAACGGGGATCTCCATTTTTTGGAAGGAGAACGATGGAGGCTGCAAAGGCGTCTGCGACCGAGTACCTAACATCGAAATCGAACCAAAGGATCACCCTAAGTTCTGCGATAAAAACACATGCTATGACGAGGTTGTCCTTCAAGACCTCGATAGTGAAATTGCTCAAATGAAAGGGGATAAGCTGGTTGGCTTCCACCTGATAGGTAGCCATGGCCCAACCTACTACAAGCGCTACCCTGATGCTCATCGTCAGTTCACCCCTGACTGTCCACGCAGTGATATTGAAAACTGCACAGATGAAGAGCTCACCAACACCTATGACAACACCATCCGCTACACCGATTTCGTGATTGGAGAGATGATTGCCAAGTTGAAAACCTACGAAGATAAGTACAACACCGCGTTGCTCTACGTCTCCGATCATGGTGAATCACTGGGAGAATTAGGGCTTTACCTACACGGTACACCGTACCAGTTTGCACCGGATGATCAGACCCGTGTTCCTATGCAGGTGTGGATGTCACCTGGATTTATCAAAGAGAAAGGCGTTGATATGGCGTGTTTGCAGCAGAAAGCCGCTGATACTCGTTACTCACACGATAATATTTTCTCATCTGTATTGGGTATCTGGGACGTCAAAACATCAGTTTACGAAAAGGGTCTAGATATTTTCAGTCAATGTCGTAATGTTCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3004505","ARO_id":"42213","ARO_name":"MCR-3.5","CARD_short_name":"MCR-3.5","ARO_description":"An MCR-3 phosphoethanolamine transferase and polymyxin (colistin) resistance gene variant identified from an extensively-resistant Escherichia coli clinical isolate.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3134":{"model_id":"3134","model_name":"MCR-1.10","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"5335":{"protein_sequence":{"accession":"ASK49940.1","sequence":"MVQHTSVWYRCSVSPFVLVASVSVFLTATANLTFFDKISQTYPIADNLGFVLTIAVVLFGAMLLITTLLSSYRYVLKPVLILLLIMGAVTSYFTDTYGTVYDTTMLQNALQTDQAETKDLLNAAFIMRIIGLGVLPSLLVAFVKVDYPTWGKGLVRRLGLIVASLALILLPVVAFSSHYASFFRVHKPLRSYVNPIMPIYSVGKLASIEYKKASAPKDTIYHAKDAVQATKPDTRKPRLVVFVVGETARADHVSFNGYERDTFPQLAKIDGVTNFSNVTSCGTSTAYSVPCMFSYLGADEYDVDTAKYQENVLDTLDRLGVSILWRDNNSDSKGVMDKLPKAQFADYKSATNNTICNTNPYNECRDVGMLVGLDDFVAANNGKDMLIMLHQMGNHGPAYFKRYDEKFAKFTPVCEGNELAKCEHQSLINAYDNALLATDDFITQSIQWLQTHSNAYDVSMLYVSDHGESLGENGVYLHGMPNAFAPKEQRSVPAFFWTDKQTGITPMATDTVLTHDAITPTLLKLFDVTADKVKDRTAFIR"},"dna_sequence":{"accession":"MF176238.1","fmin":"0","fmax":"1626","strand":"+","sequence":"ATGGTGCAGCATACTTCTGTGTGGTACCGATGCTCGGTCAGTCCGTTTGTTCTTGTGGCAAGTGTTTCCGTTTTCTTGACCGCGACCGCCAATCTTACCTTTTTTGATAAAATCAGCCAAACCTATCCCATCGCGGACAATCTCGGCTTTGTGCTGACGATCGCTGTCGTGCTCTTTGGCGCGATGCTACTGATCACCACACTGTTATCATCGTATCGCTATGTGCTAAAGCCTGTGTTGATTTTGCTATTAATCATGGGCGCGGTGACTAGTTATTTTACTGACACTTATGGCACGGTCTATGACACGACCATGCTCCAAAATGCCCTACAGACCGACCAAGCCGAGACCAAGGATCTATTAAACGCAGCGTTTATCATGCGTATCATTGGTTTGGGTGTACTACCAAGTTTGCTTGTGGCTTTTGTCAAGGTGGATTATCCGACTTGGGGCAAGGGTTTGGTGCGCCGATTGGGCTTGATCGTGGCAAGTCTTGCGCTGATTTTACTGCCTGTGGTGGCGTTCAGCAGTCATTATGCCAGTTTTTTTCGCGTGCATAAGCCGCTGCGTTCGTATGTCAATCCGATCATGCCAATCTACTCGGTGGGTAAGCTTGCCAGTATTGAGTATAAAAAAGCCAGTGCGCCAAAAGATACCATTTATCACGCCAAAGACGCGGTACAAGCAACCAAGCCTGATACGCGTAAGCCACGCCTAGTGGTGTTCGTCGTCGGTGAGACGGCACGCGCCGATCATGTCAGCTTCAATGGCTATGAGCGCGATACTTTCCCACAGCTTGCCAAGATCGATGGCGTGACCAATTTTAGCAATGTCACATCGTGCGGCACATCGACGGCGTATTCTGTGCCGTGTATGTTCAGCTATCTGGGCGCGGATGAGTATGATGTCGATACCGCCAAATACCAAGAAAATGTGCTTGATACGCTGGATCGTTTGGGCGTGAGCATCTTGTGGCGTGATAATAATTCGGACTCAAAAGGCGTGATGGATAAGCTGCCAAAAGCGCAATTTGCCGATTATAAATCCGCAACCAACAACACCATCTGCAACACCAATCCTTATAACGAATGCCGCGATGTCGGTATGCTCGTTGGCTTAGATGACTTTGTCGCTGCCAATAACGGCAAAGATATGCTGATCATGCTGCACCAAATGGGCAATCACGGGCCTGCGTATTTTAAGCGATATGATGAAAAGTTTGCCAAATTCACGCCAGTGTGTGAAGGTAATGAGCTTGCCAAGTGCGAACATCAGTCTTTGATCAATGCTTATGACAATGCCTTGCTTGCCACCGATGATTTCATCACTCAAAGTATCCAGTGGCTGCAGACGCACAGCAATGCCTATGATGTCTCGATGCTGTATGTCAGCGATCATGGCGAGAGTCTAGGTGAGAATGGTGTCTATCTACATGGTATGCCTAATGCCTTTGCACCAAAAGAACAGCGCAGTGTGCCTGCATTTTTCTGGACAGATAAGCAAACTGGCATCACGCCGATGGCGACCGATACTGTCCTGACCCATGATGCGATCACACCAACATTATTAAAGCTGTTCGATGTTACCGCAGATAAAGTCAAAGACCGCACCGCATTCATCCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42215","NCBI_taxonomy_name":"Moraxella sp. MSG13-C03","NCBI_taxonomy_id":"1935432"}}}},"ARO_accession":"3004506","ARO_id":"42214","ARO_name":"MCR-1.10","CARD_short_name":"MCR-1.10","ARO_description":"An MCR-1 phosphoethanolamine transferase and polymyxin (colistin) resistance gene variant identified from an Escherichia porcine isolate in Great Britain.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3135":{"model_id":"3135","model_name":"MCR-1.9","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"5334":{"protein_sequence":{"accession":"AVA31022.1","sequence":"MMQHTSVWYRRSVSPFVLVASVAVFLTATANLTFFDKISQTYPIADNLGFVLTIAVVLFGAMLLITTLLSSYRYVLKPVLILLLIMGAVTSYFTDTYGTVYDTTMLQNALQTDQAETKDLLNAAFIMRIIGLGVLPSLLVAFVKVDYPTWGKGLMRRLGLIVASLALILLPVVAFSSHYASFFRVHKPLRSYVNPIMPIYSVGKLASIEYKKASAPKDTIYHAKDAVQATKPDMRKPRLVVFVVGETARADHVSFNGYERDTFPQLAKIDGVTNFSNVTSCGTSTAYSVPCMFSYLGADEYDVDTAKYQENVLDTLDRLGVSILWRDNNSDSKGVMDKLPKAQFADYKSATNNAICNTNPYNECRDVGMLVGLDDFVAANNGKDMLIMLHQMGNHGPAYFKRYDEKFAKFTPACEGNELAKCEHQSLINAYDNALLATDDFIAQSIQWLQTHSNAYDVSMLYVSDHGESLGENGVYLHGMPNAFAPKEQRSVPAFFWTDKQTGITPMATDTVLTHDAITPTLLKLFDVTADKVKDRTAFIR"},"dna_sequence":{"accession":"KY780959.1","fmin":"0","fmax":"1626","strand":"+","sequence":"ATGATGCAGCATACTTCTGTGTGGTACCGACGCTCGGTCAGTCCGTTTGTTCTTGTGGCGAGTGTTGCCGTTTTCTTGACCGCGACCGCCAATCTTACCTTTTTTGATAAAATCAGCCAAACCTATCCCATCGCGGACAATCTCGGCTTTGTGCTGACGATCGCTGTCGTGCTCTTTGGCGCGATGCTACTGATCACCACGCTGTTATCATCGTATCGCTATGTGCTAAAGCCTGTGTTGATTTTGCTATTAATCATGGGCGCGGTGACCAGTTATTTTACTGACACTTATGGCACGGTCTATGATACGACCATGCTCCAAAATGCCCTACAGACCGACCAAGCCGAGACCAAGGATCTATTAAACGCAGCGTTTATCATGCGTATCATTGGTTTGGGTGTGCTACCAAGTTTGCTTGTGGCTTTTGTTAAGGTGGATTATCCGACTTGGGGCAAGGGTTTGATGCGCCGATTGGGCTTGATCGTGGCAAGTCTTGCGCTGATTTTACTGCCTGTGGTGGCGTTCAGCAGTCATTATGCCAGTTTCTTTCGCGTGCATAAGCCGCTGCGTAGCTATGTCAATCCGATCATGCCAATCTACTCGGTGGGTAAGCTTGCCAGTATTGAGTATAAAAAAGCCAGTGCGCCAAAAGATACCATTTATCACGCCAAAGACGCGGTACAAGCAACCAAGCCTGATATGCGTAAGCCACGCCTAGTGGTGTTCGTCGTCGGTGAGACGGCACGCGCCGATCATGTCAGCTTCAATGGCTATGAGCGCGATACTTTCCCACAGCTTGCCAAGATCGATGGCGTGACCAATTTTAGCAATGTCACATCGTGCGGCACATCGACGGCGTATTCTGTGCCGTGTATGTTCAGCTATCTGGGCGCGGATGAGTATGATGTCGATACCGCCAAATACCAAGAAAATGTGCTGGATACGCTGGATCGCTTGGGCGTAAGTATCTTGTGGCGTGATAATAATTCGGACTCAAAAGGCGTGATGGATAAGCTGCCAAAAGCGCAATTTGCCGATTATAAATCCGCGACCAACAACGCCATCTGCAACACCAATCCTTATAACGAATGCCGCGATGTCGGTATGCTCGTTGGCTTAGATGACTTTGTCGCTGCCAATAACGGCAAAGATATGCTGATCATGCTGCACCAAATGGGCAATCACGGGCCTGCGTATTTTAAGCGATATGATGAAAAGTTTGCCAAATTCACGCCAGCGTGTGAAGGTAATGAGCTTGCCAAGTGCGAACATCAGTCCTTGATCAATGCTTATGACAATGCCTTGCTTGCCACCGATGATTTCATCGCTCAAAGTATCCAGTGGCTGCAGACGCACAGCAATGCCTATGATGTCTCAATGCTGTATGTCAGCGATCATGGCGAAAGTCTGGGTGAGAACGGTGTCTATCTACATGGTATGCCAAATGCCTTTGCACCAAAAGAACAGCGCAGTGTGCCTGCATTTTTCTGGACGGATAAGCAAACTGGCATCACGCCAATGGCAACCGATACCGTCCTGACCCATGACGCGATCACGCCGACATTATTAAAGCTGTTTGATGTCACCGCGGACAAAGTCAAAGACCGCACCGCATTCATCCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3004507","ARO_id":"42216","ARO_name":"MCR-1.9","CARD_short_name":"MCR-1.9","ARO_description":"An MCR-1 phosphoethanolamine transferase and polymyxin resistance gene variant identified from an enterotoxigenic Escherichia coli clinical isolate.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3136":{"model_id":"3136","model_name":"MCR-3.9","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"5332":{"protein_sequence":{"accession":"AST36144.1","sequence":"MPSLIKIKIVPLIFFLALYFAFMLNWRGVLHFYEILYKLEDFKFGFAISLPILLVAALNFVFVPFSIRYLVKPFFALLIALSAIVSYTMMKYRVLFDQNMIQNIFETNQNEALAYLSLPIIGWVTIAGFIPAILLFFVEIEYEKKWFKGIITRALSMFASLIVIAVIAALYYQDYVSVGRNNSNLQREIVPANFVNSTVKYVYNRYLAEPIPFTTLGDDAKRDTNQSKPTLMFLVVGETARGKNFSMNGYEKDTNPFTSKSGGVISFNDVRSCGTATAVSVPCMFSNMGRKEFDDNLARNSEGLLDVLQKTGVSIFWKENDGGCKGVCDRVPNIEIKPKDYPKFCDKNTCYDEVVLQELDSEIAQMKGDKLVGFHLIGSHGPTYYKRYPDAHRQFTPDCPRSDIENCTDEELTNTYDNTIRYTDFVIGEMIAKLKTYEDKYNTALLYVSDHGESLGALGLYLHGTPYKFAPDDQTRVPMQVWMSPGFTKEKGVDMACLQQKAADTRYSHDNIFSSVLGIWDVKTSVYEKGLDIFSQCRNVQ"},"dna_sequence":{"accession":"MF598080.1","fmin":"0","fmax":"1626","strand":"+","sequence":"ATGCCTTCCCTTATAAAAATAAAAATTGTTCCGCTTATATTTTTTTTGGCACTGTATTTTGCATTTATGCTGAACTGGCGTGGAGTTCTCCATTTTTACGAAATCCTTTACAAATTAGAAGATTTTAAGTTTGGTTTCGCCATTTCATTACCAATATTGCTTGTTGCAGCGCTTAACTTTGTATTTGTTCCATTTTCGATACGGTATTTAGTAAAGCCTTTTTTTGCACTTCTGATCGCACTTAGTGCAATCGTTAGTTACACAATGATGAAGTATAGAGTCTTGTTTGATCAAAACATGATTCAGAATATTTTTGAAACCAATCAAAATGAGGCCTTAGCATATTTAAGCTTACCAATTATAGGATGGGTTACTATTGCTGGCTTTATCCCTGCCATTTTACTTTTCTTTGTTGAAATTGAATATGAGAAAAAATGGTTCAAAGGGATTATAACTCGTGCCCTATCGATGTTTGCATCACTTATAGTGATTGCGGTTATTGCAGCACTATACTATCAAGATTATGTGTCAGTGGGGCGCAACAATTCAAACCTCCAGCGTGAGATTGTTCCAGCCAATTTCGTTAATAGTACCGTTAAATACGTTTACAATCGTTATCTTGCTGAACCAATCCCATTTACAACTTTAGGTGATGATGCAAAACGGGATACTAATCAAAGTAAGCCCACGTTGATGTTTCTGGTCGTTGGTGAAACCGCTCGTGGTAAAAATTTCTCGATGAATGGCTATGAGAAAGATACCAACCCATTCACAAGTAAGTCTGGTGGTGTGATCTCCTTTAATGATGTTCGTTCGTGTGGGACTGCAACCGCTGTATCTGTCCCCTGCATGTTTTCCAATATGGGGAGAAAGGAGTTTGATGATAATCTCGCTCGTAATAGCGAGGGTTTGTTAGATGTGTTGCAGAAAACGGGGGTCTCCATTTTTTGGAAGGAGAACGATGGCGGCTGCAAAGGCGTCTGCGACCGAGTTCCTAACATCGAGATCAAACCGAAGGATTACCCAAAGTTCTGCGATAAAAACACATGCTATGACGAGGTTGTCCTTCAAGAGCTCGACAGTGAAATTGCTCAAATGAAAGGGGATAAGCTGGTTGGCTTCCACCTGATAGGTAGCCATGGCCCAACCTACTACAAGCGCTACCCTGATGCTCATCGTCAGTTCACCCCTGACTGTCCACGCAGTGATATTGAAAACTGCACAGATGAAGAGCTCACCAACACCTATGACAACACCATCCGCTACACCGATTTCGTGATTGGAGAGATGATTGCCAAGTTGAAAACCTACGAAGATAAGTACAACACCGCGTTGCTCTACGTCTCCGATCATGGTGAATCACTGGGAGCATTAGGGCTTTACCTACACGGTACACCGTACAAGTTTGCACCGGATGATCAGACCCGTGTTCCTATGCAGGTGTGGATGTCACCTGGATTTACCAAAGAGAAAGGCGTTGATATGGCGTGTTTGCAGCAGAAAGCCGCTGATACTCGTTACTCACACGATAATATTTTCTCATCTGTATTGGGTATCTGGGACGTCAAAACATCAGTTTACGAAAAGGGTCTAGATATTTTCAGTCAATGTCGTAATGTTCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36810","NCBI_taxonomy_name":"Aeromonas hydrophila","NCBI_taxonomy_id":"644"}}}},"ARO_accession":"3004508","ARO_id":"42217","ARO_name":"MCR-3.9","CARD_short_name":"MCR-3.9","ARO_description":"An MCR-3 polymyxin (incl. colistin) resistance gene variant isolated from an Aeromonas isolate.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3137":{"model_id":"3137","model_name":"MCR-3.8","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"5331":{"protein_sequence":{"accession":"AST36143.1","sequence":"MPSLIKIKIVPLIFFLALYFAFMLNWRGVLHFYEILYKLEDFKFGFAISLPILLVAALNFVFVPFSIRYLIKPFFALLIALSAIVSYTMMKYRVLFDQNMIQNIFETNQNEALAYLSLPIIGWVTIAGFIPAILLFFVEIEYEEKWFKGILTRALSMFASLIVIAVIAALYYQDYVSVGRNNSNLQREIVPANFVNSTVKYVYNRYLAEPIPFTTLGDDAKRDTNQSKPTLMFLVVGETARGKNFSMNGYEKDTNPFTSKSGGVISFNDVRSCGTATAVSVPCMFSNMGRKEFDDNLARNSEGLLDVLQKTGVSIFWKENDGGCKGVCDRVPNIEIKPKDYPKFCDKNTCYDEVVLQELDSEIAQMKGDKLVGFHLIGSHGPTYYKRYPDAHRQFTPDCPRSDIENCTDEELTNTYDNTIRYTDFVIAEMIAKLKTYEDKYNTALLYVSDHGESLGAMGLYLHGTPYKFAPDDQTRVPMQVWMSPGFIKEKGMNMECLQKNAAANRYSHDNIFSSVLGIWDVKTAIYEQELDIFKQCRNN"},"dna_sequence":{"accession":"MF598079.1","fmin":"0","fmax":"1623","strand":"+","sequence":"ATGCCTTCCCTTATAAAAATAAAAATTGTTCCGCTTATATTTTTTTTGGCACTGTATTTTGCATTTATGCTGAACTGGCGTGGAGTTCTCCATTTTTACGAAATCCTTTACAAATTAGAAGATTTTAAGTTTGGTTTCGCCATTTCATTACCAATATTGCTTGTTGCAGCGCTTAACTTTGTATTTGTTCCATTTTCGATACGGTATTTAATAAAGCCTTTTTTTGCACTTCTGATCGCACTTAGTGCAATCGTTAGTTACACAATGATGAAGTATAGAGTCTTGTTTGATCAAAACATGATTCAGAATATTTTTGAAACCAATCAAAATGAGGCGTTAGCATATTTAAGCTTACCAATCATAGGATGGGTTACTATTGCTGGTTTTATCCCTGCCATTTTACTTTTCTTTGTTGAAATTGAATATGAGGAAAAATGGTTCAAAGGGATTCTAACTCGTGCCCTATCGATGTTTGCATCACTTATAGTGATTGCGGTTATTGCAGCACTATACTATCAAGATTATGTGTCAGTGGGGCGAAACAATTCAAACCTCCAGCGTGAAATTGTTCCAGCCAATTTCGTTAATAGTACCGTTAAATACGTTTACAATCGTTATCTTGCTGAACCAATCCCATTTACAACTTTAGGTGATGATGCAAAACGGGATACTAATCAAAGTAAGCCCACGTTGATGTTTCTGGTCGTTGGTGAAACCGCTCGTGGTAAAAATTTCTCGATGAATGGCTATGAGAAAGACACCAATCCATTTACCAGTAAATCTGGTGGCGTGATCTCCTTTAATGATGTTCGTTCGTGTGGGACTGCAACCGCTGTATCTGTCCCCTGCATGTTCTCCAATATGGGGAGAAAGGAGTTTGATGATAATCTCGCTCGTAATAGCGAGGGTTTGTTAGATGTGTTGCAGAAAACGGGGGTCTCCATTTTTTGGAAGGAGAACGATGGCGGCTGCAAAGGCGTCTGCGACCGAGTTCCTAACATCGAGATCAAACCGAAGGATTACCCAAAGTTCTGCGATAAAAACACATGCTATGACGAGGTTGTCCTTCAAGAGCTCGACAGTGAAATTGCTCAAATGAAAGGGGATAAGCTGGTTGGCTTCCACCTCATAGGTAGCCATGGCCCAACCTACTACAAACGCTACCCTGATGCTCATCGTCAGTTCACTCCTGACTGTCCACGCAGTGATATTGAAAACTGCACAGATGAAGAGCTCACCAACACCTATGACAACACCATCCGCTACACCGATTTCGTGATTGCAGAGATGATTGCCAAGTTGAAAACCTACGAAGACAAGTACAACACCGCGTTGCTCTACGTCTCCGATCACGGTGAATCACTGGGAGCTATGGGGCTTTACCTGCACGGTACACCGTACAAATTTGCACCGGATGATCAGACCCGCGTACCTATGCAGGTGTGGATGTCGCCTGGTTTCATCAAAGAAAAAGGCATGAATATGGAATGTTTGCAGAAAAATGCCGCAGCCAATCGCTATTCTCATGACAACATATTTTCTTCTGTCCTGGGAATATGGGATGTGAAGACGGCTATCTACGAACAAGAATTAGATATCTTTAAGCAATGTCGGAATAATTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36810","NCBI_taxonomy_name":"Aeromonas hydrophila","NCBI_taxonomy_id":"644"}}}},"ARO_accession":"3004509","ARO_id":"42218","ARO_name":"MCR-3.8","CARD_short_name":"MCR-3.8","ARO_description":"An MCR-3 polymyxin (incl. colistin) resistance gene variant identified from an Aeromonas isolate.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3138":{"model_id":"3138","model_name":"MCR-3.7","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"5329":{"protein_sequence":{"accession":"AST36141.1","sequence":"MPSLIKIKIVPLIFFLALYFAFMLNWRGVLHFYEILYKLEDFKFGFAISLPILLVAALNFAFVPFSIRYLVKPFFALLIALSAIVSYTMMKYRVLFDQNMIQNIFETNQNEALAYLSLPIIGWVTIVGFIPAILLFFVEIEYEEKWFKGILTRVLSMFASLIVIAVIAALYYQDYVSVGRNNSNLQREIVPANFVNSTVKYVYNRYLAEPIPFTTLGDDAKRDTNKSKPTLMFLVVGETARGKNFSMNGYEKDTNPFTSKSGGVISFNDVRSCGTATAVSVPCMFSNMGRKEFDDNLARNSEGLLDVLQKTGVSIFWKENDGGCKGVCDRVPNIEVKPKDYPKFCDKNTCYDEVVLQDLDSEIAQMKGDKLVGFHLIGSHGPTYYKRYPDAHRQFTPDCPRSDIENCTDEELTNTYDNTIRYTDFVIAEMIAKLKTYEDKYNTALLYVSDHGESLGAMGLYLHGTPYKFAPDDQTRVPMQVWMSPGFTKEKGMNMECLQQKAADTRYSHDNIFSSVLGIWDVKTSVYEKGLDIFSQCRNVQ"},"dna_sequence":{"accession":"MF598077.1","fmin":"93","fmax":"1719","strand":"+","sequence":"ATGCCTTCCCTTATAAAAATAAAAATTGTGCCGCTCATATTTTTTTTGGCACTGTATTTTGCATTTATGCTGAACTGGCGTGGAGTTCTCCATTTTTACGAAATTCTTTATAAATTAGAAGATTTTAAATTTGGTTTCGCCATTTCATTACCAATATTGCTTGTTGCAGCGCTTAATTTTGCATTTGTTCCATTTTCGATACGGTATTTAGTAAAGCCTTTTTTTGCACTTCTTATCGCACTTAGCGCAATCGTTAGTTACACAATGATGAAGTATAGAGTCTTGTTTGATCAAAACATGATTCAGAATATTTTTGAAACCAATCAAAATGAGGCATTAGCATATTTAAGTTTGCCAATTATAGGATGGGTTACTATTGTTGGATTTATCCCTGCCATTTTACTTTTCTTTGTTGAAATTGAATATGAGGAAAAATGGTTTAAAGGGATTCTAACTCGCGTCCTATCGATGTTTGCATCCCTTATAGTGATTGCGGTTATTGCAGCACTATACTATCAAGATTATGTTTCAGTGGGGCGCAACAATTCAAACCTCCAGCGTGAAATTGTTCCGGCCAATTTTGTTAATAGTACCGTTAAATATGTTTATAATCGTTATCTTGCAGAACCAATCCCATTTACTACTTTAGGTGATGATGCAAAACGGGATACTAATAAAAGTAAGCCCACGTTGATGTTCCTGGTCGTTGGTGAAACTGCTCGTGGTAAAAATTTCTCGATGAATGGCTATGAGAAAGATACCAACCCATTTACCAGTAAATCTGGTGGTGTGATCTCCTTTAATGATGTTCGTTCGTGTGGGACAGCAACCGCTGTATCTGTCCCCTGCATGTTCTCCAATATGGGGAGAAAGGAGTTTGATGATAATCTCGCTCGTAATAGCGAGGGTTTGTTAGATGTGTTGCAGAAAACGGGGGTCTCCATTTTTTGGAAGGAGAACGATGGCGGCTGCAAAGGCGTCTGCGACCGAGTACCTAACATCGAGGTCAAACCGAAGGATTACCCAAAGTTCTGCGATAAAAATACATGCTATGACGAGGTTGTCCTTCAAGACCTCGATAGTGAAATTGCTCAAATGAAAGGGGATAAGCTGGTTGGCTTCCACCTGATAGGTAGCCATGGCCCAACCTACTACAAGCGCTATCCTGATGCTCATCGTCAGTTCACCCCTGACTGTCCACGCAGTGATATTGAAAACTGCACAGATGAAGAGCTCACCAACACCTATGACAACACCATCCGCTACACGGATTTCGTGATTGCAGAGATGATTGCCAAGTTGAAAACCTACGAAGATAAGTACAACACCGCGTTGCTCTACGTCTCCGATCATGGTGAATCACTGGGAGCTATGGGGCTTTACCTGCACGGTACACCGTACAAGTTTGCACCGGATGATCAGACCCGCGTACCTATGCAGGTGTGGATGTCACCTGGATTTACCAAAGAGAAAGGCATGAATATGGAATGTTTGCAGCAGAAAGCCGCTGATACTCGTTACTCACACGATAATATTTTCTCATCTGTATTGGGTATCTGGGACGTCAAAACATCAGTTTACGAAAAGGGTCTAGATATTTTCAGTCAATGTCGTAATGTTCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39526","NCBI_taxonomy_name":"Aeromonas media","NCBI_taxonomy_id":"651"}}}},"ARO_accession":"3004510","ARO_id":"42219","ARO_name":"MCR-3.7","CARD_short_name":"MCR-3.7","ARO_description":"An MCR polymyxin (colistin) resistance gene variant identified in Aeromonas.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3139":{"model_id":"3139","model_name":"MCR-3.2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"5328":{"protein_sequence":{"accession":"OYN70668.1","sequence":"MPSLIKIKIVPLMFFLALYFAFMLNWRGVLHFYEILYKLEDFKFGFAISLPILLVAALNFVFVPFSIRYLIKPFFALLIALSAIVSYTMMKYRVLFDQNMIQNIFETNQNEALAYLSLPIIVWVTIAGFIPAILLFFVEIEYEEKWFKGILTRALSMFASLIVIAVIAALYYQDYVSVGRNNSNLQREIVPANFVNSTVKYVYNRYLAEPIPFTTLGDDAKRDTNQSKPTLMFLVVGETARGKNFSMNGYEKDTNPFTSKSGGVISFNDVRSCGTATAVSVPCMFSNMGRKEFDDNRARNSEGLLDVLQKTGISIFWKENDGGCKGVCDRVPNIEIEPKDHPKFCDKNTCYDEVVLQDLDSEIAQMKGDKLVGFHLIGSHGPTYYKRYPDAHRQFTPDCPRSDIENCTDEELTNTYDNTIRYTDFVIGEMIAKLKTYEDKYNTALLYVSDHGESLGALGLYLHGTPYQFAPDDQTRVPMQVWMSPGFIKEKGVDMACLQQKAADTRYSHDNIFSSVLGIWDVKTSVYEKGLDIFSQCRNVQ"},"dna_sequence":{"accession":"NMWW01000143.1","fmin":"316","fmax":"1942","strand":"+","sequence":"ATGCCTTCCCTTATAAAAATAAAAATTGTTCCGCTTATGTTCTTTTTGGCACTGTATTTTGCATTTATGCTGAACTGGCGTGGAGTTCTCCATTTTTACGAAATCCTTTACAAATTAGAAGATTTTAAGTTTGGTTTCGCCATTTCATTACCAATATTGCTTGTTGCAGCGCTTAACTTTGTATTTGTTCCATTTTCGATACGGTATTTAATAAAGCCTTTTTTTGCACTTCTTATCGCACTTAGTGCAATCGTTAGTTACACAATGATGAAGTATAGAGTCTTGTTTGATCAAAACATGATTCAGAATATTTTTGAAACCAATCAAAATGAGGCGTTAGCATATTTAAGCTTACCAATTATAGTATGGGTTACTATTGCTGGTTTTATCCCTGCCATTTTACTTTTCTTTGTTGAAATTGAATATGAGGAAAAATGGTTCAAAGGGATTCTAACTCGTGCCCTATCGATGTTTGCATCACTTATAGTGATTGCGGTTATTGCAGCACTATACTATCAAGATTATGTGTCAGTGGGGCGCAACAATTCAAACCTCCAGCGTGAGATTGTTCCAGCCAATTTCGTTAATAGTACCGTTAAATACGTTTACAATCGTTATCTTGCTGAACCAATCCCATTTACAACTTTAGGTGATGATGCAAAACGGGATACTAATCAAAGTAAGCCCACGTTGATGTTTCTGGTCGTTGGTGAAACCGCTCGTGGTAAAAATTTCTCGATGAATGGCTATGAGAAAGACACCAATCCATTTACCAGTAAATCTGGTGGCGTGATCTCCTTTAATGATGTTCGTTCGTGTGGGACTGCAACCGCTGTATCCGTCCCCTGCATGTTCTCCAATATGGGGAGAAAGGAGTTTGATGATAATCGCGCTCGCAATAGCGAGGGCCTGCTAGATGTGTTGCAAAAAACGGGGATCTCCATTTTTTGGAAGGAGAACGATGGAGGCTGCAAAGGCGTCTGCGACCGAGTACCTAACATCGAAATCGAACCAAAGGATCACCCTAAGTTCTGCGATAAAAACACATGCTATGACGAGGTTGTCCTTCAAGACCTCGATAGTGAAATTGCTCAAATGAAAGGGGATAAGCTGGTTGGCTTCCACCTGATAGGTAGCCATGGCCCAACCTACTACAAGCGCTACCCTGATGCTCATCGTCAGTTCACCCCTGACTGTCCACGCAGTGATATTGAAAACTGCACAGATGAAGAGCTCACCAACACCTATGACAACACCATCCGCTACACCGATTTCGTGATTGGAGAGATGATTGCCAAGTTGAAAACCTACGAAGATAAGTACAACACCGCGTTGCTCTACGTCTCCGATCATGGTGAATCACTGGGAGCATTAGGGCTTTACCTACACGGTACACCGTACCAGTTTGCACCGGATGATCAGACCCGTGTTCCTATGCAGGTGTGGATGTCACCTGGATTTATCAAAGAGAAAGGCGTTGATATGGCGTGTTTGCAGCAGAAAGCCGCTGATACTCGTTACTCACACGATAATATTTTCTCATCTGTATTGGGTATCTGGGACGTCAAAACATCAGTTTACGAAAAGGGTCTAGATATTTTCAGTCAATGTCGTAATGTTCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3004511","ARO_id":"42220","ARO_name":"MCR-3.2","CARD_short_name":"MCR-3.2","ARO_description":"An MCR-3 polymyxin resistance gene variant identified in a colistin-resistant Salmonella isolate from Canada, located on an IncHI-2 plasmid.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3141":{"model_id":"3141","model_name":"MCR-1.6","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"5326":{"protein_sequence":{"accession":"AQK48217.1","sequence":"MMQHTSVWYRRSVSPFVLVASVAVFLTATANLTFFDKISQTYPIADNLGFVLTIAVVLFGAMLLITTLLSSYRYVLKPVLILLLIMGAVTSYFTDTYGTVYDTTMLQNALQTDQAETKDLLNAAFIMRIIGLGVLPSLLVAFVKVDYPTWGKGLMRRLGLIVASLALILLPVVAFSSHYASFFRVHKPLRSYVNPIMPIYSVGKLASIEYKKASAPKDTIYHAKDAVQATKPDMRKPRLVVFVVGETARADHVSFNGYERDTFPQLAKIDGVTNFSNVTSCGTSTAYSVPCMFSYLGADEYDVDTAKYQENVLDTLDRLGVSILWRDNNSDSKGVMDKLPKAQFADYKSATNNAICNTNPYNECRDVGMLVGLDDFVAANNGKDMLIMLHQMGNHGPAYFKRYDEKFAKFTPVCEGNELAKCEHQSLINAYDNALLATDDFIAQSIQWLQTHSNAYDVSMLYVSDHGESLGENGVYLHGMPNAFAPKEQRSVPAFFWTDKQTGITPMATDTVLTHDAITPTLLKLFDVTADKVKDHTAFIR"},"dna_sequence":{"accession":"KY352406.1","fmin":"4092","fmax":"5718","strand":"-","sequence":"ATGATGCAGCATACTTCTGTGTGGTACCGACGCTCGGTCAGTCCGTTTGTTCTTGTGGCGAGTGTTGCCGTTTTCTTGACCGCGACCGCCAATCTTACCTTTTTTGATAAAATCAGCCAAACCTATCCCATCGCGGACAATCTCGGCTTTGTGCTGACGATCGCTGTCGTGCTCTTTGGCGCGATGCTACTGATCACCACGCTGTTATCATCGTATCGCTATGTGCTAAAGCCTGTGTTGATTTTGCTATTAATCATGGGCGCGGTGACCAGTTATTTTACTGACACTTATGGCACGGTCTATGATACGACCATGCTCCAAAATGCCCTACAGACCGACCAAGCCGAGACCAAGGATCTATTAAACGCAGCGTTTATCATGCGTATCATTGGTTTGGGTGTGCTACCAAGTTTGCTTGTGGCTTTTGTTAAGGTGGATTATCCGACTTGGGGCAAGGGTTTGATGCGCCGATTGGGCTTGATCGTGGCAAGTCTTGCGCTGATTTTACTGCCTGTGGTGGCGTTCAGCAGTCATTATGCCAGTTTCTTTCGCGTGCATAAGCCGCTGCGTAGCTATGTCAATCCGATCATGCCAATCTACTCGGTGGGTAAGCTTGCCAGTATTGAGTATAAAAAAGCCAGTGCGCCAAAAGATACCATTTATCACGCCAAAGACGCGGTACAAGCAACCAAGCCTGATATGCGTAAGCCACGCCTAGTGGTGTTCGTCGTCGGTGAGACGGCACGCGCCGATCATGTCAGCTTCAATGGCTATGAGCGCGATACTTTCCCACAGCTTGCCAAGATCGATGGCGTGACCAATTTTAGCAATGTCACATCGTGCGGCACATCGACGGCGTATTCTGTGCCGTGTATGTTCAGCTATCTGGGCGCGGATGAGTATGATGTCGATACCGCCAAATACCAAGAAAATGTGCTGGATACGCTGGATCGCTTGGGCGTAAGTATCTTGTGGCGTGATAATAATTCGGACTCAAAAGGCGTGATGGATAAGCTGCCAAAAGCGCAATTTGCCGATTATAAATCCGCGACCAACAACGCCATCTGCAACACCAATCCTTATAACGAATGCCGCGATGTCGGTATGCTCGTTGGCTTAGATGACTTTGTCGCTGCCAATAACGGCAAAGATATGCTGATCATGCTGCACCAAATGGGCAATCACGGGCCTGCGTATTTTAAGCGATATGATGAAAAGTTTGCCAAATTCACGCCAGTGTGTGAAGGTAATGAGCTTGCCAAATGCGAACATCAGTCCTTGATCAATGCTTATGACAATGCCTTGCTTGCCACCGATGATTTCATCGCTCAAAGTATCCAGTGGCTGCAGACGCACAGCAATGCCTATGATGTCTCAATGCTGTATGTCAGCGATCATGGCGAAAGTCTGGGTGAGAACGGTGTCTATCTACATGGTATGCCAAATGCCTTTGCACCAAAAGAACAGCGCAGTGTGCCTGCATTTTTCTGGACGGATAAGCAAACTGGCATCACGCCAATGGCAACCGATACCGTCCTGACCCATGACGCGATCACGCCGACATTATTAAAGCTGTTTGATGTCACCGCGGACAAAGTCAAAGACCACACCGCATTCATCCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35732","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Typhimurium","NCBI_taxonomy_id":"90371"}}}},"ARO_accession":"3004513","ARO_id":"42222","ARO_name":"MCR-1.6","CARD_short_name":"MCR-1.6","ARO_description":"An MCR-1 polymyxin resistance gene variant identified from colistin-resistant Salmonella enterica (serovar typhimurium) isolate, carried by an IncP plasmid.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3142":{"model_id":"3142","model_name":"MCR-1.3","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"5324":{"protein_sequence":{"accession":"ANJ15621.1","sequence":"MMQHTSVWYRRSVSPFVLVASVAVFLTATANLTFFDKVSQTYPIADNLGFVLTIAVVLFGAMLLITTLLSSYRYVLKPVLILLLIMGAVTSYFTDTYGTVYDTTMLQNALQTDQAETKDLLNAAFIMRIIGLGVLPSLLVAFVKVDYPTWGKGLMRRLGLIVASLALILLPVVAFSSHYASFFRVHKPLRSYVNPIMPIYSVGKLASIEYKKASAPKDTIYHAKDAVQATKPDMRKPRLVVFVVGETARADHVSFNGYERDTFPQLAKIDGVTNFSNVTSCGTSTAYSVPCMFSYLGADEYDVDTAKYQENVLDTLDRLGVSILWRDNNSDSKGVMDKLPKAQFADYKSATNNAICNTNPYNECRDVGMLVGLDDFVAANNGKDMLIMLHQMGNHGPAYFKRYDEKFAKFTPVCEGNELAKCEHQSLINAYDNALLATDDFIAQSIQWLQTHSNAYDVSMLYVSDHGESLGENGVYLHGMPNAFAPKEQRSVPAFFWTDKQTGITPMATDTVLTHDAITPTLLKLFDVTADKVKDRTAFIR"},"dna_sequence":{"accession":"KU934208.1","fmin":"18647","fmax":"20273","strand":"+","sequence":"ATGATGCAGCATACTTCTGTGTGGTACCGACGCTCGGTCAGTCCGTTTGTTCTTGTGGCGAGTGTTGCCGTTTTCTTGACCGCGACCGCCAATCTTACCTTTTTTGATAAGGTCAGCCAAACCTATCCCATCGCGGACAATCTCGGCTTTGTGCTGACGATCGCTGTCGTGCTCTTTGGCGCGATGCTACTGATCACCACGCTGTTATCATCGTATCGCTATGTGCTAAAGCCTGTGTTGATTTTGCTATTAATCATGGGCGCGGTGACCAGTTATTTTACTGACACTTATGGCACGGTCTATGATACGACCATGCTCCAAAATGCCCTACAGACCGACCAAGCCGAGACCAAGGATCTATTAAACGCAGCGTTTATCATGCGTATCATTGGTTTGGGTGTGCTACCAAGTTTGCTTGTGGCTTTTGTTAAGGTGGATTATCCGACTTGGGGCAAGGGTTTGATGCGCCGATTGGGCTTGATCGTGGCAAGTCTTGCGCTGATTTTACTGCCTGTGGTGGCGTTCAGCAGTCATTATGCCAGTTTCTTTCGCGTGCATAAGCCGCTGCGTAGCTATGTCAATCCGATCATGCCAATCTACTCGGTGGGTAAGCTTGCCAGTATTGAGTATAAAAAAGCCAGTGCGCCAAAAGATACCATTTATCACGCCAAAGACGCGGTACAAGCAACCAAGCCTGATATGCGTAAGCCACGCCTAGTGGTGTTCGTCGTCGGTGAGACGGCACGCGCCGATCATGTCAGCTTCAATGGCTATGAGCGCGATACTTTCCCACAGCTTGCCAAGATCGATGGCGTGACCAATTTTAGCAATGTCACATCGTGCGGCACATCGACGGCGTATTCTGTGCCGTGTATGTTCAGCTATCTGGGCGCGGATGAGTATGATGTCGATACCGCCAAATACCAAGAAAATGTGCTGGATACGCTGGATCGCTTGGGCGTAAGTATCTTGTGGCGTGATAATAATTCGGACTCAAAAGGCGTGATGGATAAGCTGCCAAAAGCGCAATTTGCCGATTATAAATCCGCGACCAACAACGCCATCTGCAACACCAATCCTTATAACGAATGCCGCGATGTCGGTATGCTCGTTGGCTTAGATGACTTTGTCGCTGCCAATAACGGCAAAGATATGCTGATCATGCTGCACCAAATGGGCAATCACGGGCCTGCGTATTTTAAGCGATATGATGAAAAGTTTGCCAAATTCACGCCAGTGTGTGAAGGTAATGAGCTTGCCAAGTGCGAACATCAGTCCTTGATCAATGCTTATGACAATGCCTTGCTTGCCACCGATGATTTCATCGCTCAAAGTATCCAGTGGCTGCAGACGCACAGCAATGCCTATGATGTCTCAATGCTGTATGTCAGCGATCATGGCGAAAGTCTGGGTGAGAACGGTGTCTATCTACATGGTATGCCAAATGCCTTTGCACCAAAAGAACAGCGCAGTGTGCCTGCATTTTTCTGGACGGATAAGCAAACTGGCATCACGCCAATGGCAACCGATACCGTCCTGACCCATGACGCGATCACGCCGACATTATTAAAGCTGTTTGATGTCACCGCGGACAAAGTCAAAGACCGCACCGCATTCATCCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3004514","ARO_id":"42223","ARO_name":"MCR-1.3","CARD_short_name":"MCR-1.3","ARO_description":"An MCR-1 polymyxin resistance gene variant identified from a poultry Raoultella planticola isolate.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3143":{"model_id":"3143","model_name":"MCR-1.4","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"5323":{"protein_sequence":{"accession":"APM87143.1","sequence":"MMQHTSVWYRRSVSPFVLVASVAVFLTATANLTFFDKISQTYPIADNLGFVLTIAVVLFGAMLLITTLLSSYRYVLKPVLILLLIMGAVTSYFTDTYGTVYDTTMLQNALQTDQAETKDLLNAAFIMRIIGLGVLPSLLVAFVKVDYPTWGKGLMRRLGLIVASLALILLPVVAFSSHYASFFRVHKPLRSYVNPIMPIYSVGKLASIEYKKASAPKDTIYHAKDAVQATKPDMRKPRLVVFVVGETARADHVSFNGYERDTFPQLAKIDGVTNFSNVTSCGTSTAYSVPCMFSYLGADEYDVDTAKYQENVLDTLDRLGVSILWRDNNSDSKGVMDKLPKAQFADYKSATNNAICNTNPYNECRDVGMLVGLDDFVAANNGKDMLIMLHQMGNHGPAYFKRYDEKFAKFTPVCEGNELAKCEHQSLINAYDNALLATDNFIAQSIQWLQTHSNAYDVSMLYVSDHGESLGENGVYLHGMPNAFAPKEQRSVPAFFWTDKQTGITPMATDTVLTHDAITPTLLKLFDVTADKVKDRTAFIR"},"dna_sequence":{"accession":"KY041856.1","fmin":"0","fmax":"1626","strand":"+","sequence":"ATGATGCAGCATACTTCTGTGTGGTACCGACGCTCGGTCAGTCCGTTTGTTCTTGTGGCGAGTGTTGCCGTTTTCTTGACCGCGACCGCCAATCTTACCTTTTTTGATAAAATCAGCCAAACCTATCCCATCGCGGACAATCTCGGCTTTGTGCTGACGATCGCTGTCGTGCTCTTTGGCGCGATGCTACTGATCACCACGCTGTTATCATCGTATCGCTATGTGCTAAAGCCTGTGTTGATTTTGCTATTAATCATGGGCGCGGTGACCAGTTATTTTACTGACACTTATGGCACGGTCTATGATACGACCATGCTCCAAAATGCCCTACAGACCGACCAAGCCGAGACCAAGGATCTATTAAACGCAGCGTTTATCATGCGTATCATTGGTTTGGGTGTGCTACCAAGTTTGCTTGTGGCTTTTGTTAAGGTGGATTATCCGACTTGGGGCAAGGGTTTGATGCGCCGATTGGGCTTGATCGTGGCAAGTCTTGCGCTGATTTTACTGCCTGTGGTGGCGTTCAGCAGTCATTATGCCAGTTTCTTTCGCGTGCATAAGCCGCTGCGTAGCTATGTCAATCCGATCATGCCAATCTACTCGGTGGGTAAGCTTGCCAGTATTGAGTATAAAAAAGCCAGTGCGCCAAAAGATACCATTTATCACGCCAAAGACGCGGTACAAGCAACCAAGCCTGATATGCGTAAGCCACGCCTAGTGGTGTTCGTCGTCGGTGAGACGGCACGCGCCGATCATGTCAGCTTCAATGGCTATGAGCGCGATACTTTCCCACAGCTTGCCAAGATCGATGGCGTGACCAATTTTAGCAATGTCACATCGTGCGGCACATCGACGGCGTATTCTGTGCCGTGTATGTTCAGCTATCTGGGCGCGGATGAGTATGATGTCGATACCGCCAAATACCAAGAAAATGTGCTGGATACGCTGGATCGCTTGGGCGTAAGTATCTTGTGGCGTGATAATAATTCGGACTCAAAAGGCGTGATGGATAAGCTGCCAAAAGCGCAATTTGCCGATTATAAATCCGCGACCAACAACGCCATCTGCAACACCAATCCTTATAACGAATGCCGCGATGTCGGTATGCTCGTTGGCTTAGATGACTTTGTCGCTGCCAATAACGGCAAAGATATGCTGATCATGCTGCACCAAATGGGCAATCACGGGCCTGCGTATTTTAAGCGATATGATGAAAAGTTTGCCAAATTCACGCCAGTGTGTGAAGGTAATGAGCTTGCCAAGTGCGAACATCAGTCCTTGATCAATGCTTATGACAATGCCTTGCTTGCCACCGATAATTTCATCGCTCAAAGTATCCAGTGGCTGCAGACGCACAGCAATGCCTATGATGTCTCAATGCTGTATGTCAGCGATCATGGCGAAAGTCTGGGTGAGAACGGTGTCTATCTACATGGTATGCCAAATGCCTTTGCACCAAAAGAACAGCGCAGTGTGCCTGCATTTTTCTGGACGGATAAGCAAACTGGCATCACGCCAATGGCAACCGATACCGTCCTGACCCATGACGCGATCACGCCGACATTATTAAAGCTGTTTGATGTCACCGCGGACAAAGTCAAAGACCGCACCGCATTCATCCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3004515","ARO_id":"42224","ARO_name":"MCR-1.4","CARD_short_name":"MCR-1.4","ARO_description":"An MCR-1 polymyxin resistance gene variant identified from a colistin-resistant Escherichia coli isolate.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3145":{"model_id":"3145","model_name":"MCR-7.1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"5003":{"protein_sequence":{"accession":"AUR80098.1","sequence":"MRITLGVMKVNLLLVLFFALVLNWPFFLRFYSVISGLEHVRAGFVISVPLVLLAALNAVFIPFTFRWLLKPFFSLLILTGSIVSYAMLKYGVIFDASMIQNIVETNNSEATSYLNVPVVLWFLLTGVLPMVVLWSLKVRYPANWYKGLAIRAGALAFSLLFVGGVAALYYQDYVSIGRNHRILGKQIVPANYVNGIYKYARDVVFATPIPYQPLGTDAKVVAKGDKPTLMFLVVGETARGKNFSMNGYEKETNPFTSQAGGVISFKDVRSCGTATAVSVPCMFSNMGRKEFDDNRARNSEGLLDVLQRSGVSIFWKENDGGCKGVCDRVPNIEIKPKDHPQFCDKNTCYDEVVLQNLDDEVAQMKGDKLVGFHLIGSHRPPYHQRYPDKPPPFVPDCPRSDIENCSDEELVNTYDNTIRYTDFVIAEMITKLKKYEDKYNTALIYLSDHGESLGAMGLYLHGTPYKFAPDDQTRVPMQVWMSPGFAKEKGMDLNCLQQKAADNRYSHDNLFSSVLGIWDVSTAVYDKQLDIFSQCRTVQ"},"dna_sequence":{"accession":"MG267386.1","fmin":"23609","fmax":"25229","strand":"+","sequence":"ATGCGCATCACGCTCGGTGTGATGAAGGTGAATTTGTTGCTGGTGCTCTTTTTCGCACTGGTGCTGAACTGGCCTTTCTTTCTTCGTTTTTATTCTGTTATCAGTGGTCTGGAACATGTCCGGGCCGGTTTCGTTATCTCGGTTCCTCTGGTGCTGCTTGCCGCACTCAACGCCGTCTTTATCCCCTTTACCTTCCGCTGGTTGCTCAAGCCCTTCTTTTCGTTGTTGATCCTGACAGGCTCCATCGTCAGTTACGCCATGCTCAAATACGGCGTCATCTTCGATGCCAGCATGATCCAGAACATAGTGGAGACCAACAACAGTGAGGCGACCTCCTACCTGAATGTGCCGGTCGTGCTCTGGTTCCTGCTGACCGGTGTGTTGCCCATGGTGGTGCTCTGGTCGCTGAAGGTGCGCTATCCGGCAAACTGGTACAAGGGGCTGGCCATCAGGGCTGGTGCTCTGGCCTTCTCGCTGCTGTTCGTGGGAGGCGTTGCCGCACTTTACTATCAGGATTACGTCTCGATCGGCCGCAATCACCGGATCCTGGGCAAGCAGATAGTGCCGGCCAACTATGTCAACGGCATCTACAAATATGCCCGCGACGTGGTATTTGCTACCCCCATCCCTTATCAACCGCTGGGGACTGATGCCAAAGTCGTCGCCAAAGGGGATAAACCGACCCTGATGTTTCTGGTGGTGGGGGAGACAGCCCGCGGCAAGAACTTCTCGATGAACGGCTACGAGAAAGAGACCAACCCCTTTACCAGTCAGGCCGGGGGCGTGATCTCCTTCAAGGACGTGCGCTCTTGCGGCACGGCCACAGCGGTGTCGGTGCCCTGCATGTTCTCCAACATGGGGCGCAAGGAGTTTGATGACAACCGGGCCCGCAACAGCGAAGGCCTGCTCGATGTGCTGCAAAGAAGCGGGGTCTCCATCTTCTGGAAGGAGAACGACGGCGGCTGCAAAGGGGTGTGCGATCGGGTGCCCAACATCGAGATCAAGCCAAAAGATCACCCACAGTTCTGCGACAAGAACACCTGCTATGACGAGGTTGTACTGCAAAATCTCGACGACGAGGTGGCGCAGATGAAGGGCGACAAGCTGGTCGGTTTCCATCTGATCGGCAGCCACCGCCCGCCCTACCACCAACGCTATCCGGACAAACCACCCCCGTTCGTACCGGACTGCCCGCGCAGCGACATCGAGAACTGCAGCGATGAAGAGCTGGTCAACACCTATGACAACACCATCCGCTACACCGATTTTGTCATAGCAGAGATGATTACCAAGCTGAAAAAGTATGAAGATAAGTACAACACGGCGTTGATCTACCTCTCTGATCACGGCGAGTCGCTGGGTGCGATGGGGCTCTATCTGCATGGCACGCCCTACAAGTTTGCCCCTGACGACCAGACCCGGGTACCGATGCAGGTCTGGATGTCGCCGGGCTTTGCCAAAGAGAAGGGGATGGATCTGAACTGCCTGCAGCAAAAAGCGGCAGACAATCGCTACTCCCATGACAACCTCTTCTCCTCTGTGCTCGGGATCTGGGATGTCAGCACGGCGGTGTACGACAAGCAGCTCGATATTTTCAGCCAGTGCCGCACCGTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3004517","ARO_id":"42226","ARO_name":"MCR-7.1","CARD_short_name":"MCR-7.1","ARO_description":"A novel plasmid-mediated colistin-resistant phosphoethanolamine transferase identified from a poultry isolate of Klebsiella pneumoniae.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3744":{"model_id":"3744","model_name":"Mycobacterium tuberculosis ald mutations confer resistance to cycloserine","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"},"41339":{"param_type":"nucleotide substitution in promoter region","param_description":"A nucleotide sequence change where, compared to a reference sequence, one nucleotide is replaced by one other nucleotide in the promoter region of a gene. These substitutions are indicated as upstream of the reference sequence transcription initiation site. Format is given by [-][position][wildtype][>][mutation], e.g. -11t>c or -15g>Var where Var represents any possible substitution.","param_type_id":"41339","param_value":{"13240":"-32t>c"}},"snp":{"ReSeqTB-Minimal":{"13240":"G48A"}}},"model_sequences":{"sequence":{"8821":{"protein_sequence":{"accession":"NP_217296.1","sequence":"MRVGIPTETKNNEFRVAITPAGVAELTRRGHEVLIQAGAGEGSAITDADFKAAGAQLVGTADQVWADADLLLKVKEPIAAEYGRLRHGQILFTFLHLAASRACTDALLDSGTTSIAYETVQTADGALPLLAPMSEVAGRLAAQVGAYHLMRTQGGRGVLMGGVPGVEPADVVVIGAGTAGYNAARIANGMGATVTVLDINIDKLRQLDAEFCGRIHTRYSSAYELEGAVKRADLVIGAVLVPGAKAPKLVSNSLVAHMKPGAVLVDIAIDQGGCFEGSRPTTYDHPTFAVHDTLFYCVANMPASVPKTSTYALTNATMPYVLELADHGWRAACRSNPALAKGLSTHEGALLSERVATDLGVPFTEPASVLA"},"dna_sequence":{"accession":"NC_000962.3","fmin":"3086819","fmax":"3087935","strand":"+","sequence":"ATGCGCGTCGGTATTCCGACCGAGACCAAAAACAACGAATTCCGGGTGGCCATCACCCCGGCCGGCGTCGCGGAACTAACCCGTCGTGGCCATGAGGTGCTCATCCAGGCAGGTGCCGGAGAGGGCTCGGCTATCACCGACGCGGATTTCAAGGCGGCAGGCGCGCAACTGGTCGGCACCGCCGACCAGGTGTGGGCCGACGCTGATTTATTGCTCAAGGTCAAAGAACCGATAGCGGCGGAATACGGCCGCCTGCGACACGGGCAGATCTTGTTCACGTTCTTGCATTTGGCCGCGTCACGTGCTTGCACCGATGCGTTGTTGGATTCCGGCACCACGTCAATTGCCTACGAGACCGTCCAGACCGCCGACGGCGCACTACCCCTGCTTGCCCCGATGAGCGAAGTCGCCGGTCGACTCGCCGCCCAGGTTGGCGCTTACCACCTGATGCGAACCCAAGGGGGCCGCGGTGTGCTGATGGGCGGGGTGCCCGGCGTCGAACCGGCCGACGTCGTGGTGATCGGCGCCGGCACCGCCGGCTACAACGCAGCCCGCATCGCCAACGGCATGGGCGCGACCGTTACGGTTCTAGACATCAACATCGACAAACTTCGGCAACTCGACGCCGAGTTCTGCGGCCGGATCCACACTCGCTACTCATCGGCCTACGAGCTCGAGGGTGCCGTCAAACGTGCCGACCTGGTGATTGGGGCCGTCCTGGTGCCAGGCGCCAAGGCACCCAAATTAGTCTCGAATTCACTTGTCGCGCATATGAAACCAGGTGCGGTACTGGTGGATATAGCCATCGACCAGGGCGGCTGTTTCGAAGGCTCACGACCGACCACCTACGACCACCCGACGTTCGCCGTGCACGACACGCTGTTTTACTGCGTGGCGAACATGCCCGCCTCGGTGCCGAAGACGTCGACCTACGCGCTGACCAACGCGACGATGCCGTATGTGCTCGAGCTTGCCGACCATGGCTGGCGGGCGGCGTGCCGGTCGAATCCGGCACTAGCCAAAGGTCTTTCGACGCACGAAGGGGCGTTACTGTCCGAACGGGTGGCCACCGACCTGGGGGTGCCGTTCACCGAGCCCGCCAGCGTGCTGGCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3004945","ARO_id":"43131","ARO_name":"Mycobacterium tuberculosis ald mutations confer resistance to cycloserine","CARD_short_name":"Mtub_ald_DCS","ARO_description":"Mutations in the ald gene that contribute to or confer resistance to cycloserine.","ARO_category":{"43129":{"category_aro_accession":"3004943","category_aro_cvterm_id":"43129","category_aro_name":"cycloserine resistant ald","category_aro_description":"ald plays a role in cell wall synthesis as L-alanine is an important constituent of the peptidoglycan layer. Resistance due to mutations in ald can cause cycloserine to not function.","category_aro_class_name":"AMR Gene Family"},"37140":{"category_aro_accession":"3000760","category_aro_cvterm_id":"37140","category_aro_name":"cycloserine","category_aro_description":"Cycloserine is an anti-mycobacterial agent, and is active against enterobacteria, streptococci, M. tuberculosis, Staphylococcus aureus, and many Gram-negative and Gram-positive bacteria. It inhibits cell wall biosynthesis.","category_aro_class_name":"Antibiotic"},"45736":{"category_aro_accession":"3007154","category_aro_cvterm_id":"45736","category_aro_name":"cycloserine-like antibiotic","category_aro_description":"A group of antibiotics including cycloserine and its derivatives.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3427":{"model_id":"3427","model_name":"OXA-260","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"5622":{"protein_sequence":{"accession":"ENU54757.1","sequence":"MNIKAHLLITSAIFISACSPYIVTANPNHSASKSDVKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"APOR01000009.1","fmin":"341736","fmax":"342561","strand":"+","sequence":"ATGAACATTAAAGCACACTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGTAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAACAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42791","NCBI_taxonomy_name":"Acinetobacter baumannii NIPH 1362","NCBI_taxonomy_id":"1217642"}}}},"ARO_accession":"3001716","ARO_id":"38116","ARO_name":"OXA-260","CARD_short_name":"OXA-260","ARO_description":"OXA-260 is a beta-lactamase found in Acinetobacter spp.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3449":{"model_id":"3449","model_name":"OXA-284","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"5645":{"protein_sequence":{"accession":"ENX16434.1","sequence":"MKTLIFLPLLNCLSLTACTLPVSSSPSHITSTQSTQAIAQLFDQAQSSGVLVIQRGQQIQVYGNDLSRADTEYVPASTFKMLNALIGLQHGKATTNEIFKWDGKKRSFSAWEKDMTLGEAMQASAVPVYQELARRIGLELMQQEVQRIQFGNQQIGQQVDNFWLVGPLKITPKQEVEFVSALAREQLAFDPQVQQQVKAMLFLQERKAYRLYVKSGWGMDVEPQVGWLTGWVETPQAEIVAFSLNMQMQNGIDPAIRLEILQQALAELGLYPKAEG"},"dna_sequence":{"accession":"APRU01000004.1","fmin":"72684","fmax":"73515","strand":"+","sequence":"ATGAAAACTCTGATTTTTCTGCCTTTACTTAATTGCTTGAGCCTGACGGCGTGTACCTTACCCGTTTCATCTTCCCCATCTCATATCACTTCGACTCAATCGACTCAAGCCATTGCCCAATTATTTGATCAGGCGCAAAGCTCTGGCGTTTTAGTGATTCAGCGTGGTCAACAGATACAGGTCTATGGCAATGATTTAAGCCGTGCAGATACCGAATATGTTCCCGCCTCTACTTTTAAAATGCTCAATGCCCTGATTGGCCTGCAACATGGCAAAGCCACAACCAATGAAATTTTTAAATGGGATGGTAAGAAACGCAGTTTTTCAGCCTGGGAAAAAGATATGACTCTCGGTGAAGCCATGCAAGCGTCTGCTGTACCCGTCTATCAGGAACTGGCGCGTCGTATTGGCCTTGAACTGATGCAACAGGAAGTACAACGCATCCAATTTGGTAATCAGCAGATTGGTCAACAGGTCGATAACTTCTGGTTGGTAGGCCCTTTGAAAATCACTCCAAAACAGGAAGTCGAATTTGTTTCTGCGTTGGCCCGAGAGCAACTGGCCTTTGATCCTCAAGTCCAGCAACAAGTCAAAGCCATGTTATTTTTACAGGAGCGGAAAGCTTATCGACTATATGTCAAATCCGGTTGGGGCATGGATGTGGAACCGCAAGTCGGCTGGCTCACCGGCTGGGTTGAAACACCGCAGGCTGAAATCGTGGCATTTTCACTCAATATGCAGATGCAAAATGGTATAGATCCGGCGATCCGCCTTGAAATTTTGCAGCAGGCTTTGGCCGAATTAGGGCTTTATCCAAAAGCTGAAGGATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42810","NCBI_taxonomy_name":"Acinetobacter sp. CIP 51.11","NCBI_taxonomy_id":"1144670"}}}},"ARO_accession":"3001739","ARO_id":"38139","ARO_name":"OXA-284","CARD_short_name":"OXA-284","ARO_description":"OXA-284 is a beta-lactamase found in Acinetobacter spp.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46489":{"category_aro_accession":"3007700","category_aro_cvterm_id":"46489","category_aro_name":"OXA-134-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-134.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3478":{"model_id":"3478","model_name":"OXA-344","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"5672":{"protein_sequence":{"accession":"AHN07462.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDKKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"KF048917.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATAAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATAGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATAGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001532","ARO_id":"37932","ARO_name":"OXA-344","CARD_short_name":"OXA-344","ARO_description":"OXA-344 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3507":{"model_id":"3507","model_name":"OXA-437","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"5702":{"protein_sequence":{"accession":"AKL59536.1","sequence":"MKKFILPIFSISILVSLSACSSIKTKSEDNFHISSQQHEKAIKSYFDEAQTQGVIIIKEGKNLSTYGNALARANKEYVPASTFKMLNALIGLENHKATTNEIFKWDGKKRTYPMWEKDMTLGEAMALSAVPVYQELARRTGLELMQKEVKRVNFGNTNIGTQVDNFWLVGPLKITPVQEVNFADDLAHNRLPFKLETQEEVKKMLLIKEVNGSKIYAKSGWGMGVTPQVGWLTGWVEQANGKKISFSLNLEMKEGMSGSIRNEITYKSLENLGII"},"dna_sequence":{"accession":"KP410856.1","fmin":"0","fmax":"828","strand":"+","sequence":"ATGAAAAAATTTATACTTCCTATATTCAGCATTTCTATTCTAGTTTCTCTCAGTGCATGTTCATCTATTAAAACTAAATCTGAAGATAATTTTCATATTTCTTCTCAGCAACATGAAAAAGCTATTAAAAGCTATTTTGATGAAGCTCAAACACAGGGTGTAATTATTATTAAAGAGGGTAAAAATCTTAGCACCTATGGTAATGCTCTTGCACGAGCAAATAAAGAATATGTCCCTGCATCAACATTTAAGATGCTAAATGCTTTAATCGGGCTAGAAAATCATAAAGCAACAACAAATGAGATTTTCAAATGGGATGGTAAAAAAAGAACTTATCCTATGTGGGAGAAAGATATGACTTTAGGTGAGGCAATGGCATTGTCAGCAGTTCCAGTATATCAAGAGCTTGCAAGACGGACTGGCCTAGAGCTAATGCAGAAAGAAGTAAAGCGGGTTAATTTTGGAAATACAAATATTGGAACACAGGTCGATAATTTTTGGTTAGTTGGCCCCCTTAAAATTACACCAGTACAAGAAGTTAATTTTGCCGATGACCTTGCACATAACCGATTACCTTTTAAATTAGAAACTCAAGAAGAAGTTAAAAAAATGCTTCTAATTAAAGAAGTAAATGGTAGTAAGATTTATGCAAAAAGTGGATGGGGAATGGGTGTTACTCCACAGGTAGGTTGGTTGACTGGTTGGGTGGAGCAAGCTAATGGAAAAAAAATCTCCTTTTCGCTCAACTTAGAAATGAAAGAAGGAATGTCTGGTTCTATTCGTAATGAAATTACTTATAAGTCGCTAGAAAATCTTGGAATCATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3003593","ARO_id":"40203","ARO_name":"OXA-437","CARD_short_name":"OXA-437","ARO_description":"OXA-437 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46500":{"category_aro_accession":"3007711","category_aro_cvterm_id":"46500","category_aro_name":"OXA-24-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-24.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3537":{"model_id":"3537","model_name":"OXA-475","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"5732":{"protein_sequence":{"accession":"ALC79290.1","sequence":"MSKKNFILIFIFVILISCKNTEKISNETTLIDNIFTNSNAEGTLVIYNLNDDKYIIHNKERAEQRFYPASTFKIYNSLIGLNEKAVKDVDEVFYKYNGEKVFLESWAKDSNLRYAIKNSQVPAYKELARRIGLKKMKENIEKLDFGNKSIGDSVDTFWLEGPLEISAMEQVKLLTKLAQNELPYPIEIQKAVSDITILEQTYNYTLHGKTGLADSENMTTEPIGWFVGWLEENDNIYVFALNIDNINSDDLAKRINIVKEGLKALNLLK"},"dna_sequence":{"accession":"KR182168.1","fmin":"0","fmax":"810","strand":"+","sequence":"ATGTCTAAAAAAAATTTTATATTAATATTTATTTTTGTTATTTTAATATCTTGTAAAAATACAGAAAAAATATCAAATGAAACTACATTAATAGATAATATATTTACTAATAGCAATGCTGAAGGAACATTAGTTATATATAATTTAAATGATGATAAATATATAATTCATAATAAAGAAAGAGCTGAACAAAGATTTTATCCAGCATCAACATTTAAAATATATAATAGTTTAATAGGCTTAAATGAAAAAGCAGTTAAAGATGTAGATGAAGTATTTTATAAATATAATGGCGAAAAAGTTTTTCTTGAATCTTGGGCTAAGGACTCTAATTTAAGATATGCAATTAAAAATTCGCAAGTACCGGCATATAAAGAATTAGCAAGAAGAATAGGTCTTAAAAAGATGAAAGAGAATATAGAAAAACTAGATTTTGGTAATAAAAGTATAGGTGATAGTGTAGATACTTTTTGGCTTGAAGGACCTTTGGAAATAAGTGCGATGGAGCAAGTTAAATTATTAACTAAATTAGCTCAAAATGAATTACCGTATCCTATAGAAATACAAAAAGCTGTTTCTGATATTACTATACTAGAGCAAACTTACAATTATACGCTTCATGGAAAAACTGGATTAGCTGATTCTGAAAACATGACAACTGAGCCTATTGGTTGGTTCGTAGGCTGGCTTGAAGAAAATGATAATATATACGTCTTTGCTTTAAATATTGATAATATCAATTCAGATGACCTTGCAAAAAGGATAAATATAGTAAAAGAAGGTTTAAAAGCATTAAATTTATTAAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36935","NCBI_taxonomy_name":"Brachyspira pilosicoli","NCBI_taxonomy_id":"52584"}}}},"ARO_accession":"3003632","ARO_id":"40242","ARO_name":"OXA-475","CARD_short_name":"OXA-475","ARO_description":"OXA-475 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46521":{"category_aro_accession":"3007732","category_aro_cvterm_id":"46521","category_aro_name":"OXA-63-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-63.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3581":{"model_id":"3581","model_name":"DHA-9","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"8353":{"protein_sequence":{"accession":"AHL39320.1","sequence":"MTKSVSATLISALLAFSAPGFSAADNVAAVVDSTIKPLMAQQDIPGMAVAVSVKGKPYYFNYGFADIQAKQPVTENTLFELGSVSKTFTGVLGAVSVAKKEMALNDPAAKYQPELALPQWKGITLLDLATYTAGGLPLQVPDAVKSRADLLNFYQQWQPSRKPGDMRLYANSSIGLFGALTANAAGMPYEQLLTARILAPLGLSHTFITVPESAQSHYAYGYKNKKPVRVSPGQLDAESYGVKSASKDMLRWAEMNMEPSRAGNADLEMAMYLAQTRYYKTAAINQGLGWEMYDWPQQKDMIINGVTNEVALQPHPVTDNQVQPYNRASWVHKTGATTGFGAYVAFIPEKQVAIVILANKNYPNTERVKAAQAILSALE"},"dna_sequence":{"accession":"KJ207201.1","fmin":"951","fmax":"2091","strand":"+","sequence":"ATGACAAAATCTGTATCTGCAACACTGATTTCTGCCCTGCTGGCGTTTTCCGCCCCGGGGTTTTCTGCCGCTGATAATGTCGCAGCGGTGGTGGACAGCACCATTAAACCGCTGATGGCACAGCAGGATATTCCCGGGATGGCGGTTGCCGTCTCCGTAAAGGGTAAGCCCTATTATTTCAATTATGGTTTTGCCGATATTCAGGCAAAACAGCCGGTCACTGAAAATACACTATTTGAGCTCGGATCTGTAAGTAAAACTTTCACAGGTGTGCTGGGTGCGGTTTCTGTGGCGAAAAAAGAGATGGCGCTGAATGATCCGGCGGCAAAATACCAGCCGGAGCTGGCTCTGCCGCAGTGGAAGGGGATCACATTGCTGGATCTGGCTACCTATACCGCAGGCGGACTGCCGTTACAGGTGCCGGATGCGGTAAAAAGCCGTGCGGATCTGCTGAATTTCTATCAGCAGTGGCAGCCGTCCCGGAAACCGGGCGATATGCGTCTGTATGCAAACAGCAGTATCGGCCTGTTTGGTGCTCTGACCGCAAACGCGGCGGGGATGCCGTATGAGCAGTTGCTGACTGCACGGATCCTGGCACCGCTGGGGTTATCTCACACCTTTATTACTGTGCCGGAAAGTGCGCAAAGCCATTATGCGTACGGTTATAAAAACAAAAAACCGGTCCGCGTGTCGCCGGGACAGCTTGATGCGGAATCTTACGGCGTGAAATCCGCCTCAAAAGATATGCTGCGCTGGGCGGAAATGAATATGGAGCCGTCACGGGCCGGTAATGCGGATCTGGAAATGGCAATGTATCTTGCACAGACCCGCTACTATAAAACCGCCGCGATTAACCAGGGGCTGGGCTGGGAAATGTATGACTGGCCGCAGCAGAAAGATATGATCATTAACGGCGTGACCAACGAGGTCGCATTGCAGCCGCACCCGGTAACAGACAACCAGGTTCAGCCGTATAACCGTGCTTCCTGGGTGCATAAAACGGGGGCAACAACTGGTTTCGGCGCCTATGTGGCCTTTATTCCGGAAAAACAGGTGGCGATTGTGATTCTGGCGAATAAAAACTACCCGAATACCGAAAGAGTCAAAGCCGCACAGGCTATTTTGAGTGCACTGGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36917","NCBI_taxonomy_name":"Morganella morganii","NCBI_taxonomy_id":"582"}}}},"ARO_accession":"3002140","ARO_id":"38540","ARO_name":"DHA-9","CARD_short_name":"DHA-9","ARO_description":"DHA-9 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36207":{"category_aro_accession":"3000068","category_aro_cvterm_id":"36207","category_aro_name":"DHA beta-lactamase","category_aro_description":"DHA beta-lactamases are plasmid-mediated AmpC \u03b2-lactamases that confer resistance to cephamycins and oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3638":{"model_id":"3638","model_name":"LEN-39","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"5909":{"protein_sequence":{"accession":"AZA07955.1","sequence":"MRYVRLCVISLLATLPLAVYAGPQPLEQIKQSESQLSGRVGMVEMDLASGRTLAAWRADERFPMVSTFKVLLCGAVLARVDAGVEQLDRRIHYRQQDLVDYSPVSEKHLTDGMTVGELCAAAITMSDNSAGNLLLTTVGGPAGLTAFLRQIGDNVTRLDRWETALNEALPGDMRDTTTPASMAATLRKLLTAQHLSARSQQQLLQWMVDDRVAGPLIRAVLPAGWFIADKTGAGERGARGIVALLGPDGKAERIVVIYLRDTPASMAERNQHIAGIGAALIEHWQR"},"dna_sequence":{"accession":"MK161458.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGTGTTATCTCCCTGTTAGCCACCCTGCCACTGGCGGTATACGCCGGTCCACAGCCGCTTGAGCAGATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTGGGGATGGTGGAAATGGATCTGGCCAGCGGCCGCACTCTGGCGGCCTGGCGCGCCGATGAACGCTTTCCCATGGTGAGCACCTTTAAAGTGCTGCTATGCGGCGCGGTGCTGGCGCGGGTGGATGCCGGGGTCGAACAACTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTACCGACGGGATGACGGTCGGCGAACTCTGCGCCGCCGCCATCACCATGAGCGATAACAGCGCCGGCAATCTGCTGCTGACCACCGTCGGCGGCCCCGCGGGATTGACCGCCTTTCTGCGTCAGATCGGTGACAACGTCACTCGTCTTGACCGCTGGGAAACGGCACTGAATGAGGCGCTTCCCGGCGACATGCGCGACACCACTACCCCGGCCAGCATGGCCGCCACGCTGCGTAAACTACTGACCGCGCAGCATCTGAGCGCCCGTTCACAGCAGCAGCTCCTGCAGTGGATGGTGGACGATCGGGTTGCCGGCCCGCTGATCCGCGCCGTGCTGCCGGCGGGCTGGTTTATCGCCGACAAGACCGGGGCTGGCGAACGGGGTGCGCGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAAGCGGAGCGCATTGTGGTGATCTATCTGCGGGATACCCCGGCGAGTATGGCCGAGCGTAATCAACATATCGCCGGGATAGGCGCAGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42976","NCBI_taxonomy_name":"Klebsiella variicola subsp. tropica","NCBI_taxonomy_id":"2489014"}}}},"ARO_accession":"3004842","ARO_id":"42977","ARO_name":"LEN-39","CARD_short_name":"LEN-39","ARO_description":"A class-A broad-spectrum beta-lactamase identified from Klebsiella sp.","ARO_category":{"36236":{"category_aro_accession":"3000097","category_aro_cvterm_id":"36236","category_aro_name":"LEN beta-lactamase","category_aro_description":"LEN beta-lactamases are chromosomal class A beta-lactamases that confer resistance to ampicillin, amoxicillin, carbenicillin, and ticarcillin but not to extended-spectrum beta-lactams.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3662":{"model_id":"3662","model_name":"NDM-21","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"5935":{"protein_sequence":{"accession":"ATJ25942.1","sequence":"MELPNIMHPVAKLSTALAAALMLSGCMPGEIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPSFGAVASNGLIVRDGGRVLLVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGLVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR"},"dna_sequence":{"accession":"MG183694.1","fmin":"0","fmax":"813","strand":"+","sequence":"ATGGAATTGCCCAATATTATGCACCCGGTCGCGAAGCTGAGCACCGCATTAGCCGCTGCATTGATGCTGAGCGGGTGCATGCCCGGTGAAATCCGCCCGACGATTGGCCAGCAAATGGAAACTGGCGACCAACGGTTTGGCGATCTGGTTTTCCGCCAGCTCGCACCGAATGTCTGGCAGCACACTTCCTATCTCGACATGCCGAGTTTCGGGGCAGTCGCTTCCAACGGTTTGATCGTCAGGGATGGCGGCCGCGTGCTGTTGGTCGATACCGCCTGGACCGATGACCAGACCGCCCAGATCCTCAACTGGATCAAGCAGGAGATCAACCTGCCGGTCGCGCTGGCGGTGGTGACTCACGCGCATCAGGACAAGATGGGCGGTATGGACGCGCTGCATGCGGCGGGGATTGCGACTTATGCCAATGCGTTGTCGAACCAGCTTGCCCCGCAAGAGGGGCTGGTTGCGGCGCAACACAGCCTGACTTTCGCCGCCAATGGCTGGGTCGAACCAGCAACCGCGCCCAACTTTGGCCCGCTCAAGGTATTTTACCCCGGCCCCGGCCACACCAGTGACAATATCACCGTTGGGATCGACGGCACCGACATCGCTTTTGGTGGCTGCCTGATCAAGGACAGCAAGGCCAAGTCGCTCGGCAATCTCGGTGATGCCGACACTGAGCACTACGCCGCGTCAGCGCGCGCGTTTGGTGCGGCGTTCCCCAAGGCCAGCATGATCGTGATGAGCCATTCCGCCCCCGATAGCCGCGCCGCAATCACTCATACGGCCCGCATGGCCGACAAGCTGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3004864","ARO_id":"43002","ARO_name":"NDM-21","CARD_short_name":"NDM-21","ARO_description":"A class B New Delhi metallo-beta-lactamase and NDM-1 variant.","ARO_category":{"36196":{"category_aro_accession":"3000057","category_aro_cvterm_id":"36196","category_aro_name":"NDM beta-lactamase","category_aro_description":"NDM beta-lactamases or New Delhi metallo-beta-lactamases are class B beta-lactamases that confer resistance to a broad range of antibiotics including carbapenems, cephalosporins and penicillins.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3724":{"model_id":"3724","model_name":"Mycobacterium tuberculosis fabG1 mutations confer resistance to isoniazid","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"41339":{"param_type":"nucleotide substitution in promoter region","param_description":"A nucleotide sequence change where, compared to a reference sequence, one nucleotide is replaced by one other nucleotide in the promoter region of a gene. These substitutions are indicated as upstream of the reference sequence transcription initiation site. Format is given by [-][position][wildtype][>][mutation], e.g. -11t>c or -15g>Var where Var represents any possible substitution.","param_type_id":"41339","param_value":{"13398":"-15c>t","13400":"-8t>c","14182":"-8t>Var","14180":"-16a>Var","14181":"-15c>Var","14765":"-17g>t","14769":"-16a>g","14771":"-8t>c","14773":"-8t>g","14775":"-8t>a","13192":"-15c>t","13194":"-17t>g","13196":"-8c>t","13195":"-8t>a","13399":"-17g>t","14767":"-15c>t"}},"snp":{"CRyPTIC-R":{"13398":"G48A","13400":"G48A","13700":"G48A","14182":"G48A","14180":"G48A","14181":"G48A","13399":"G48A"},"WHO-R":{"14765":"G48A","14769":"G48A","14771":"G48A","14773":"G48A","14775":"G48A","14767":"G48A"},"ReSeqTB-High":{"13192":"G48A","13194":"G48A","13196":"G48A","13195":"G48A"}},"48039":{"param_type":"synonymous substitution for alternative promoter","param_description":"A synonymous or silent substitution in the coding DNA sequence of one gene which influences the promoter region of another gene. These substitutions do not change the amino acid sequence of a protein but may still influence the phenotype, including decreased susceptibility to antimicrobial compounds.","param_type_id":"48039","param_value":{"13700":"L203L"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"425"}},"model_sequences":{"sequence":{"8815":{"protein_sequence":{"accession":"NP_215999.1","sequence":"MTATATEGAKPPFVSRSVLVTGGNRGIGLAIAQRLAADGHKVAVTHRGSGAPKGLFGVECDVTDSDAVDRAFTAVEEHQGPVEVLVSNAGLSADAFLMRMTEEKFEKVINANLTGAFRVAQRASRSMQRNKFGRMIFIGSVSGSWGIGNQANYAASKAGVIGMARSIARELSKANVTANVVAPGYIDTDMTRALDERIQQGALQFIPAKRVGTPAEVAGVVSFLASEDASYISGAVIPVDGGMGMGH"},"dna_sequence":{"accession":"NC_000962.3","fmin":"1673439","fmax":"1674183","strand":"+","sequence":"GTGACTGCCACAGCCACTGAAGGGGCCAAACCCCCATTCGTATCCCGTTCAGTCCTGGTTACCGGAGGAAACCGGGGGATCGGGCTGGCGATCGCACAGCGGCTGGCTGCCGACGGCCACAAGGTGGCCGTCACCCACCGTGGATCCGGAGCGCCAAAGGGGCTGTTTGGCGTCGAATGTGACGTCACCGACAGCGACGCCGTCGATCGCGCCTTCACGGCGGTAGAAGAGCACCAGGGTCCGGTCGAGGTGCTGGTGTCCAACGCCGGCCTATCCGCGGACGCATTCCTCATGCGGATGACCGAGGAAAAGTTCGAGAAGGTCATCAACGCCAACCTCACCGGGGCGTTCCGGGTGGCTCAACGGGCATCGCGCAGCATGCAGCGCAACAAATTCGGTCGAATGATATTCATAGGTTCGGTCTCCGGCAGCTGGGGCATCGGCAACCAGGCCAACTACGCAGCCTCCAAGGCCGGAGTGATTGGCATGGCCCGCTCGATCGCCCGCGAGCTGTCGAAGGCAAACGTGACCGCGAATGTGGTGGCCCCGGGCTACATCGACACCGATATGACCCGCGCGCTGGATGAGCGGATTCAGCAGGGGGCGCTGCAATTTATCCCAGCGAAGCGGGTCGGCACCCCCGCCGAGGTCGCCGGGGTGGTCAGCTTCCTGGCTTCCGAGGATGCGAGCTATATCTCCGGTGCGGTCATCCCGGTCGACGGCGGCATGGGTATGGGCCACTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3004922","ARO_id":"43108","ARO_name":"Mycobacterium tuberculosis fabG1 mutations confer resistance to isoniazid","CARD_short_name":"Mtub_fabG1_INH","ARO_description":"Mutations that occur in fabG1 resulting in or contributing to resistance in isoniazid.","ARO_category":{"43081":{"category_aro_accession":"3004895","category_aro_cvterm_id":"43081","category_aro_name":"isoniazid resistant fabG1","category_aro_description":"fabG1 is involved in the fatty acid synthesis pathway, acting in the first reduction step for mycolic acid. It is associated with isoniazid resistance.","category_aro_class_name":"AMR Gene Family"},"36659":{"category_aro_accession":"3000520","category_aro_cvterm_id":"36659","category_aro_name":"isoniazid","category_aro_description":"Isoniazid is an organic compound that is the first-line anti tuberculosis medication in prevention and treatment. As a prodrug, it is activated by mycobacterial catalase-peroxidases such as M. tuberculosis KatG. Isoniazid inhibits mycolic acid synthesis, which prevents cell wall synthesis in mycobacteria.","category_aro_class_name":"Antibiotic"},"45734":{"category_aro_accession":"3007152","category_aro_cvterm_id":"45734","category_aro_name":"isoniazid-like antibiotic","category_aro_description":"A group of antibiotics containing isoniazid and its derivatives.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3740":{"model_id":"3740","model_name":"Mycobacterium tuberculosis ubiA mutations confer resistance to ethambutol","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"9500":"S173A","9502":"A237V","9503":"R240C","9501":"W175C"},"ReSeqTB-Moderate":{"9500":"S173A"},"clinical":{"9500":"S173A","9502":"A237V","9503":"R240C","9501":"W175C"},"ReSeqTB-High":{"9502":"A237V","9503":"R240C","9501":"W175C"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"8795":{"protein_sequence":{"accession":"NP_218323.1","sequence":"MSEDVVTQPPANLVAGVVKAIRPRQWVKNVLVLAAPLAALGGGVRYDYVEVLSKVSMAFVVFSLAASAVYLVNDVRDVEADREHPTKRFRPIAAGVVPEWLAYTVAVVLGVTSLAGAWMLTPNLALVMVVYLAMQLAYCFGLKHQAVVEICVVSSAYLIRAIAGGVATKIPLSKWFLLIMAFGSLFMVAGKRYAELHLAERTGAAIRKSLESYTSTYLRFVWTLSATAVVLCYGLWAFERDGYSGSWFAVSMIPFTIAILRYAVDVDGGLAGEPEDIALRDRVLQLLALAWIATVGAAVAFG"},"dna_sequence":{"accession":"NC_000962.3","fmin":"4268924","fmax":"4269833","strand":"-","sequence":"ATGAGTGAAGATGTGGTGACTCAACCTCCGGCAAACCTGGTCGCCGGGGTGGTCAAGGCGATCCGCCCGCGCCAGTGGGTGAAAAACGTGCTGGTGCTGGCCGCGCCGCTGGCCGCGTTGGGCGGCGGTGTCCGCTACGACTACGTCGAGGTGCTCAGCAAGGTGTCGATGGCCTTCGTGGTGTTCAGCCTGGCCGCCTCGGCGGTGTACCTCGTCAACGATGTGCGTGACGTCGAGGCAGACCGGGAGCACCCCACCAAAAGGTTCCGGCCGATCGCCGCCGGCGTGGTGCCCGAGTGGCTGGCGTACACCGTGGCGGTGGTACTGGGAGTGACATCGCTGGCCGGTGCCTGGATGCTGACCCCGAACCTGGCGCTGGTAATGGTCGTCTACCTCGCCATGCAGTTGGCGTATTGCTTTGGTCTCAAGCATCAAGCGGTGGTGGAAATCTGCGTCGTGTCGTCGGCGTATTTGATCCGCGCCATCGCCGGGGGCGTGGCCACCAAAATCCCGCTGTCCAAGTGGTTTTTGCTGATCATGGCATTCGGTTCGCTGTTCATGGTGGCCGGCAAGCGCTACGCCGAGCTGCATCTGGCCGAACGCACCGGCGCTGCGATCCGCAAGTCGCTGGAAAGCTACACCAGCACCTATCTGCGGTTCGTCTGGACGTTGTCGGCCACCGCGGTGGTCTTGTGCTACGGGCTGTGGGCTTTCGAGCGCGACGGCTACAGCGGGTCCTGGTTCGCGGTGTCGATGATTCCGTTCACCATCGCGATCCTGCGCTACGCGGTGGACGTCGATGGCGGCCTGGCCGGGGAGCCGGAAGATATCGCGCTGCGTGACCGGGTATTGCAGCTGCTGGCGCTGGCGTGGATAGCAACGGTTGGGGCCGCTGTTGCCTTCGGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3004950","ARO_id":"43136","ARO_name":"Mycobacterium tuberculosis ubiA mutations confer resistance to ethambutol","CARD_short_name":"Mtub_ubiA_EMB","ARO_description":"Mutations in the ubiA gene contribute to or confer resistance to ethambutol.","ARO_category":{"43135":{"category_aro_accession":"3004949","category_aro_cvterm_id":"43135","category_aro_name":"ethambutol resistant ubiA","category_aro_description":"DDPR synthase involved in arabinogalactan synthesis. Mutations can confer resistance to ethambutol.","category_aro_class_name":"AMR Gene Family"},"36636":{"category_aro_accession":"3000497","category_aro_cvterm_id":"36636","category_aro_name":"ethambutol","category_aro_description":"Ethambutol is an antimycobacterial drug prescribed to treat tuberculosis. It is usually given in combination with other tuberculosis drugs, such as isoniazid, rifampicin, and pyrazinamide. Ethambutol inhibits arabinosyl biosynthesis, disrupting mycobacterial cell wall formation.","category_aro_class_name":"Antibiotic"},"36666":{"category_aro_accession":"3000527","category_aro_cvterm_id":"36666","category_aro_name":"polyamine antibiotic","category_aro_description":"Polyamine antibiotics are organic compounds having two or more primary amino groups.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2614":{"model_id":"2614","model_name":"mphE","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"5079":{"protein_sequence":{"accession":"ABI20451.1","sequence":"MTIQDIQSLAEAHGLLLTDKMNFNEMGIDFKVVFALDTKGQQWLLRIPRRDGMREQIKKEKRILELVKKHLSVEVPDWRISSTELVAYPILKDNPVLNLDAETYEIIWNMDKDSPKYITSLAKTLFEIHSIPEKEVRENDLKIMKPSDLRPEIANNLQLVKSEIGISEQLETRYRKWLDNDVLWADFTQFIHGDLYAGHVLASKDGAVSGVIDWSTAHIDDPAIDFAGHVTLFGEESLKTLIIEYEKLGGKVWNKLYEQTLERAAASPLMYGLFALETQNESLIVGAKAQLGVI"},"dna_sequence":{"accession":"DQ839391.1","fmin":"12872","fmax":"13757","strand":"-","sequence":"ATGACAATTCAAGATATTCAATCACTTGCTGAAGCACACGGCTTGTTGCTTACGGACAAAATGAATTTCAATGAAATGGGCATTGATTTTAAGGTCGTTTTTGCTCTTGATACAAAGGGGCAACAATGGTTGCTGCGTATTCCTCGTCGTGATGGCATGAGGGAACAAATCAAGAAAGAAAAACGCATTTTAGAATTGGTAAAAAAACATCTTTCTGTAGAGGTTCCTGATTGGAGAATTTCATCTACAGAATTAGTGGCTTATCCCATACTTAAAGATAATCCTGTTTTAAATTTGGATGCTGAAACCTATGAAATAATTTGGAATATGGACAAAGATAGCCCGAAATACATAACATCTTTGGCAAAAACCTTATTTGAAATCCATAGTATTCCTGAAAAAGAAGTTCGGGAAAATGATTTGAAAATTATGAAACCTTCAGATTTAAGACCTGAAATAGCAAACAATTTGCAGTTAGTAAAATCTGAAATTGGTATAAGTGAGCAATTGGAAACCCGCTACAGAAAATGGTTGGATAATGATGTTCTATGGGCAGATTTCACCCAATTTATACATGGCGATTTATATGCTGGGCATGTACTAGCTTCAAAGGATGGAGCTGTTTCAGGCGTTATTGATTGGTCAACAGCCCATATAGATGACCCAGCGATTGATTTTGCTGGGCATGTAACTTTGTTTGGAGAAGAAAGCCTCAAAACTCTAATCATCGAGTATGAAAAACTAGGGGGTAAAGTTTGGAATAAACTATATGAACAGACTTTAGAAAGAGCAGCGGCCTCTCCTTTGATGTATGGTTTATTTGCCTTAGAAACTCAAAATGAAAGCCTTATCGTTGGAGCAAAAGCTCAGTTGGGAGTTATATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36791","NCBI_taxonomy_name":"uncultured bacterium","NCBI_taxonomy_id":"77133"}}}},"ARO_accession":"3003741","ARO_id":"40396","ARO_name":"mphE","CARD_short_name":"mphE","ARO_description":"mphE is a macrolide phosphotransferase and resistance gene identified on a plasmid, pRSB105.","ARO_category":{"36472":{"category_aro_accession":"3000333","category_aro_cvterm_id":"36472","category_aro_name":"macrolide phosphotransferase (MPH)","category_aro_description":"Macrolide phosphotransferases (MPH) are enzymes encoded by macrolide phosphotransferase genes (mph genes). These enzymes phosphorylate macrolides in GTP dependent manner at 2'-OH of desosamine sugar thereby inactivating them. Characterized MPH's are differentiated based on their substrate specificity.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4008":{"model_id":"4008","model_name":"PDC-284","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"6372":{"protein_sequence":{"accession":"WP_111672897.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDRAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDITQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_060554.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCGGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACTCATCGCGGTTACTACAAGGTCGGCGACATCACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATTCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005276","ARO_id":"43633","ARO_name":"PDC-284","CARD_short_name":"PDC-284","ARO_description":"PDC-284 is a class C beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3218":{"model_id":"3218","model_name":"mphN","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"5318":{"protein_sequence":{"accession":"AHE40505.1","sequence":"MNEFKRLAKNKGLDVLENSIVVNESGVDFQVAYAKDTLGSKWILRIPRRLDSMRSALKEKMALEIMEEHVSFQVPNWSIFDDELIAYKQLDGVPVATIDVEQQDYIWSFDKENTPQSYYQSLGKVLAELHTLPHRHFKEIGIKTLYARDLKSSMKIRMEKVRQKYHVNSELWERWQEWLANDSLWPSHVGVSHGDLHPGHILINKNFEVSGLIDWTEISIADTSVDFLSHLLLFGKDGLTKLLDAYDNAGGRTWSRMDEHIIELLTTSAITVAEFAEISDLQDMRETAAHMLAQNV"},"dna_sequence":{"accession":"KF648874.1","fmin":"4289","fmax":"5180","strand":"+","sequence":"ATGAACGAATTTAAACGGCTTGCAAAAAATAAAGGATTAGATGTGTTAGAGAATAGCATTGTGGTAAATGAATCGGGTGTTGATTTTCAAGTTGCTTATGCAAAAGATACGCTTGGTAGCAAGTGGATACTAAGAATTCCTCGAAGATTAGATTCGATGAGGAGCGCCTTGAAAGAAAAGATGGCACTAGAAATTATGGAAGAACATGTGAGTTTTCAAGTTCCAAATTGGTCGATTTTTGATGATGAACTAATTGCGTATAAGCAATTAGATGGTGTTCCGGTTGCAACAATTGATGTAGAGCAACAAGATTACATCTGGAGTTTTGACAAAGAGAATACACCACAATCTTACTATCAGTCATTAGGTAAAGTGTTGGCAGAACTACACACATTACCACATCGACACTTCAAAGAAATCGGTATCAAAACTCTATATGCTAGAGATTTAAAGAGTTCAATGAAGATACGGATGGAGAAGGTGAGACAGAAGTATCATGTGAATTCAGAGCTATGGGAGCGTTGGCAAGAATGGTTGGCGAATGATTCGCTATGGCCATCGCATGTAGGTGTAAGCCACGGGGATTTACACCCTGGCCACATACTAATAAATAAGAATTTTGAGGTCTCTGGTTTGATAGATTGGACAGAAATTAGTATTGCGGACACATCTGTGGATTTTCTATCACATCTATTACTGTTTGGTAAGGATGGTTTGACAAAGTTACTCGATGCTTACGACAATGCAGGCGGAAGAACATGGTCAAGAATGGATGAGCATATAATTGAGTTGTTAACAACCAGCGCAATAACTGTAGCTGAATTCGCAGAGATATCTGACCTACAAGATATGCGTGAAACAGCTGCTCATATGCTTGCACAAAATGTATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39580","NCBI_taxonomy_name":"Exiguobacterium sp. S3-2","NCBI_taxonomy_id":"1389960"}}}},"ARO_accession":"3004542","ARO_id":"42414","ARO_name":"mphN","CARD_short_name":"mphN","ARO_description":"A macrolide phosphotransferase identified on a plasmid in Exiguobacterium.","ARO_category":{"36472":{"category_aro_accession":"3000333","category_aro_cvterm_id":"36472","category_aro_name":"macrolide phosphotransferase (MPH)","category_aro_description":"Macrolide phosphotransferases (MPH) are enzymes encoded by macrolide phosphotransferase genes (mph genes). These enzymes phosphorylate macrolides in GTP dependent manner at 2'-OH of desosamine sugar thereby inactivating them. Characterized MPH's are differentiated based on their substrate specificity.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3219":{"model_id":"3219","model_name":"mphO","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"5085":{"protein_sequence":{"accession":"WP_050815728.1","sequence":"MTETSPSSPSSATADAGTPPPADLEQLLALAADHGLDLLGDSLRTEEIGLDFRVAFARSRDWQDWVLRIPRRAEVLARAAVEGRLLAHLAPHLDIAIPDWRISTERLIAYPLLPGTPGLTVSADGTVEWHVDMASTEYARALGTFLAQLHTVDPEEAAATGIPSRTPSEVRGVWREDLTRVAEAFPIAPALRERWEAWLAEDSYWPDRSVLTHGEVYPGHTLVEGERLSAVLDWTTASVGDPARDLMFHRSSAPPEAFAATLAAYVAGGGTLHPRLGEHAEEMFSASPLAYGLYALETGEEEHRAAAAAALDPPDAD"},"dna_sequence":{"accession":"NZ_AGSO01000004.1","fmin":"76478","fmax":"77432","strand":"+","sequence":"ATGACCGAGACCTCTCCCTCGAGCCCGTCGTCGGCCACGGCCGATGCCGGGACTCCCCCGCCCGCCGACCTCGAGCAGCTCCTCGCCCTCGCCGCCGATCACGGGCTCGACCTCCTCGGCGACTCGCTGCGCACCGAGGAGATCGGCCTCGACTTCCGCGTCGCCTTCGCCCGGTCGCGGGACTGGCAGGACTGGGTGCTGCGCATCCCCCGCCGCGCCGAGGTGCTGGCCCGCGCCGCGGTCGAGGGCCGGCTGCTCGCCCACCTCGCCCCGCACCTGGACATCGCGATCCCCGACTGGCGGATCAGCACGGAGCGCCTGATCGCCTATCCCCTCCTGCCCGGCACCCCGGGACTGACCGTCAGCGCCGACGGCACGGTCGAGTGGCACGTGGACATGGCCTCGACCGAGTACGCCCGCGCCCTCGGCACCTTCCTCGCCCAGCTCCACACCGTGGACCCCGAGGAGGCCGCCGCCACCGGGATCCCGTCCCGCACCCCGTCGGAGGTGCGCGGTGTATGGCGCGAGGACCTCACCCGGGTCGCGGAGGCCTTCCCCATCGCGCCGGCGCTGCGGGAGCGGTGGGAGGCGTGGCTGGCGGAGGACTCCTACTGGCCGGACCGCAGCGTGCTCACCCACGGTGAGGTGTACCCCGGCCACACCCTCGTCGAGGGCGAGCGGCTCAGCGCGGTGCTCGACTGGACCACGGCGTCCGTCGGCGATCCGGCGCGGGACCTCATGTTCCACCGCTCGAGCGCACCCCCGGAAGCCTTCGCGGCGACGCTCGCCGCCTACGTGGCCGGCGGCGGCACCCTCCACCCGCGGCTCGGCGAGCACGCCGAGGAGATGTTCTCCGCCTCCCCGCTCGCCTACGGGCTCTACGCGCTGGAGACCGGCGAGGAGGAGCACCGCGCCGCGGCGGCGGCCGCGCTCGACCCGCCGGACGCCGACTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42416","NCBI_taxonomy_name":"Brachybacterium paraconglomeratum","NCBI_taxonomy_id":"173362"}}}},"ARO_accession":"3004543","ARO_id":"42415","ARO_name":"mphO","CARD_short_name":"mphO","ARO_description":"A chromosomal macrolide phosphostransferase identified in Brachybacterium paraconglomeratum.","ARO_category":{"36472":{"category_aro_accession":"3000333","category_aro_cvterm_id":"36472","category_aro_name":"macrolide phosphotransferase (MPH)","category_aro_description":"Macrolide phosphotransferases (MPH) are enzymes encoded by macrolide phosphotransferase genes (mph genes). These enzymes phosphorylate macrolides in GTP dependent manner at 2'-OH of desosamine sugar thereby inactivating them. Characterized MPH's are differentiated based on their substrate specificity.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3220":{"model_id":"3220","model_name":"mphJ","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"5086":{"protein_sequence":{"accession":"ATL63232.1","sequence":"MSKNNVEHMLALAKNNGILVDPTTVKVNESGLDFLAIFASTIDGIPWVLRQPRRDDVVETARYEKRVLDLVAKHLRVEVPDWQVHTSEFIAYPILGGTPMATINMETKNYDWYLNPESLPELCIQTWAEALVELHGIHHDLARDAGIRVKQPSYARASLREKMNEIKRVFGVSGALWDRWQKWLADETFWPAHSALVHGDLHPGHILVAENGKVTGLLDWTEAEVSDPAIDFTVVYLLFGDTGLADFIQRYEKAGGRVWSRMHEHIVEMTAAYPVTLATFALKSGLEEFKIMARQALGVDENGKEITS"},"dna_sequence":{"accession":"KY753883.1","fmin":"0","fmax":"927","strand":"+","sequence":"ATGTCAAAAAACAATGTAGAGCACATGCTTGCACTCGCGAAAAATAACGGAATCCTGGTAGACCCCACTACCGTGAAAGTGAATGAATCCGGCTTGGATTTTCTTGCGATTTTTGCAAGTACGATAGATGGTATTCCATGGGTATTACGGCAACCGCGCCGGGACGATGTTGTGGAGACAGCGCGTTATGAGAAAAGGGTGCTAGATCTCGTTGCAAAACATCTGCGTGTCGAAGTACCGGATTGGCAGGTTCACACCTCTGAATTCATCGCTTATCCGATCCTGGGTGGCACACCGATGGCGACGATCAATATGGAAACCAAAAATTATGACTGGTATTTGAATCCCGAATCCCTACCCGAACTGTGCATCCAAACGTGGGCGGAAGCATTGGTGGAATTACACGGTATTCATCATGATCTCGCTCGAGATGCTGGTATCCGCGTCAAGCAGCCTAGCTATGCACGAGCAAGCCTTCGAGAAAAGATGAATGAAATCAAACGCGTCTTTGGCGTTTCTGGGGCGCTATGGGATCGATGGCAAAAATGGCTTGCAGATGAAACATTCTGGCCTGCTCACTCTGCACTTGTGCATGGTGACCTCCATCCGGGGCATATCCTGGTTGCTGAAAACGGCAAGGTAACAGGACTCCTGGATTGGACGGAGGCAGAAGTCTCTGACCCTGCTATTGATTTCACGGTCGTATACCTGTTGTTCGGAGATACTGGCTTGGCCGATTTCATCCAACGGTATGAGAAAGCAGGAGGCCGTGTATGGTCGCGTATGCATGAGCATATCGTCGAAATGACGGCTGCGTATCCCGTCACTCTTGCTACCTTCGCATTGAAATCAGGGCTGGAAGAGTTCAAGATCATGGCACGACAAGCTCTGGGTGTCGACGAGAACGGCAAAGAGATCACTTCCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41526","NCBI_taxonomy_name":"Brevibacillus brevis Vm4","NCBI_taxonomy_id":"1289602"}}}},"ARO_accession":"3004544","ARO_id":"42417","ARO_name":"mphJ","CARD_short_name":"mphJ","ARO_description":"A chromosomal macrolide phosphotransferase identified in Brevibacillus brevis VM4.","ARO_category":{"36472":{"category_aro_accession":"3000333","category_aro_cvterm_id":"36472","category_aro_name":"macrolide phosphotransferase (MPH)","category_aro_description":"Macrolide phosphotransferases (MPH) are enzymes encoded by macrolide phosphotransferase genes (mph genes). These enzymes phosphorylate macrolides in GTP dependent manner at 2'-OH of desosamine sugar thereby inactivating them. Characterized MPH's are differentiated based on their substrate specificity.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35974":{"category_aro_accession":"0000057","category_aro_cvterm_id":"35974","category_aro_name":"telithromycin","category_aro_description":"Telithromycin is a semi-synthetic derivative of erythromycin. It is a 14-membered macrolide and is the first ketolide antibiotic to be used in clinics. Telithromycin binds the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"36284":{"category_aro_accession":"3000145","category_aro_cvterm_id":"36284","category_aro_name":"tylosin","category_aro_description":"Tylosin is a 16-membered macrolide, naturally produced by Streptomyces fradiae. It interacts with the bacterial ribosome 50S subunit to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3252":{"model_id":"3252","model_name":"Campylobacter jejuni 23S rRNA with mutation conferring resistance to erythromycin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"41093","param_value":"5000"},"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"8568":"a2075g","8567":"a2074c"},"Curated-R":{"8568":"a2075g","8567":"a2074c"},"clinical":{"8568":"a2075g","8567":"a2074c"}}},"model_sequences":{"sequence":{"5105":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"NR_076226.1","fmin":"0","fmax":"2912","strand":"+","sequence":"AGCTACTAAGAGCGAATGGTGGATGCCTTGACTGGTAAAGGCGATGAAGGACGTACTAGACTGCGATAAGCTACGGGGAGCTGTCAAGAAGCTTTGATCCGTAGATTTCCGAATGGGGCAACCCAATGTATAGAGATATACATTACCTATATAGGAGCGAACGAGGGGAATTGAAACATCTTAGTACCCTCAGGAAAAGAAATCAATAGAGATTGCGTCAGTAGCGGCGAGCGAAAGCGCAAGAGGGCAAACCCAGTGCTTGCACTGGGGGTTGTAGGACTGCAATGTGCAAGAGCTGAGTTTAGCAGAACATTCTGGAAAGTATAGCCATAGAGGGTGATAGTCCCGTATGCGAAAAACAAAGCTTAGCTAGCAGTATCCTGAGTAGGGCGGGACACGAGGAATCCTGTCTGAATCCGGGTCGACCACGATCCAACCCTAAATACTAATACCAGATCGATAGTGCACAAGTACCGTGAGGGAAAGGTGAAAAGAACTGAGGTGATCAGAGTGAAATAGAACCTGAAACCATTTGCTTACAATCATTCAGAGCACTATGTAGCAATACAGTGTGATGGACTGCCTTTTGCATAATGAGCCTGCGAGTTGTGGTGTCTGGCAAGGTTAAGCAAACGCGAAGCCGTAGCGAAAGCGAGTCTGAATAGGGCGCTTAGTCAGATGCTGCAGACCCGAAACGAAGTGATCTATCCATGAGCAAGTTGAAGCTAGTGTAAGAACTAGTGGAGGACTGAACCCATAGGCGTTGAAAAGCCCCGGGATGACTTGTGGATAGGGGTGAAAGGCCAATCAAACTTCGTGATAGCTGGTTCTCTCCGAAATATATTTAGGTATAGCGTTGTGTCGTAATATAAGGGGGTAGAGCACTGAATGGGCTAGGGCATACACCAATGTACCAAACCCTATCAAACTCCGAATACCTTATATGTAATCACAGCAGTCAGGCGGCGAGTGATAAAATCCGTCGTCAAGAGGGAAACAACCCAGACTACCAGCTAAGGTCCCTAAATCTTACTTAAGTGGAAAACGATGTGAAGTTACTTAAACAACCAGGAGGTTGGCTTAGAAGCAGCCATCCTTTAAAGAAAGCGTAATAGCTCACTGGTCTAGTGATTTTGCGCGGAAAATATAACGGGGCTAAAGTAAGTACCGAAGCTGTAGACTTAGTTTACTAAGTGGTAGGAGAGCGTTCTATTTGCGTCGAAGGTATACCGGTAAGGAGTGCTGGAGCGAATAGAAGTGAGCATGCAGGCATGAGTAGCGATAATTAATGTGAGAATCATTAACGCCGTAAACCCAAGGTTTCCTACGCGATGCTCGTCATCGTAGGGTTAGTCGGGTCCTAAGTCGAGTCCGAAAGGGGTAGACGATGGCAAATTGGTTAATATTCCAATACCAACATTAGTGTGCGATGGAAGGACGCTTAGGGCTAAGGGGGCTAGCGGATGGAAGTGCTAGTCTAAGGTCGTAGGAGGTTATACAGGCAAATCCGTATAACAATACTCCGAGAACTGAAAGGCTTTTTGAAGTCTTCGGATGGATAGAAGAACCCCTGATGCCGTCGAGCCAAGAAAAGTTTCTAAGTTTAGCTAATGTTGCCCGTACCGTAAACCGACACAGGTGGGTGGGATGAGTATTCTAAGGCGCGTGGAAGAACTCTCTTTAAGGAACTCTGCAAAATAGCACCGTATCTTCGGTATAAGGTGTGGTTAGCTTTGTATTAGGATTTACTCTGAAAGCAAGGAAACTTACAACAAAGAGTCCCTCCCGACTGTTTACCAAAAACACAGCACTCTGCTAACTCGTAAGAGGATGTATAGGGTGTGACGCCTGCCCGGTGCTCGAAGGTTAATTGATGGGGTTAGCATTAGCGAAGCTCTTGATCGAAGCCCGAGTAAACGGCGGCCGTAACTATAACGGTCCTAAGGTAGCGAAATTCCTTGTCGGTTAAATACCGACCTGCATGAATGGCGTAACGAGATGGGAGCTGTCTCAAAGAGGGATCCAGTGAAATTGTAGTGGAGGTGAAAATTCCTCCTACCCGCGGCAAGACGGAAAGACCCCGTGGACCTTTACTACAGCTTGACACTGCTACTTGGATAAGAATGTGCAGGATAGGTGGGAGGCTTTGAGTATATGACGCCAGTTGTATATGAGCCATTGTTGAGATACCACTCTTTCTTATTTGGGTAGCTAACCAGCTTGAGTTATCCTCAAGTGGGACAATGTCTGGTGGGTAGTTTGACTGGGGCGGTCGCCTCCCAAATAATAACGGAGGCTTACAAAGGTTGGCTCAGAACGGTTGGAAATCGTTCGTAGAGTATAAAGGTATAAGCCAGCTTAACTGCAAGACATACAAGTCAAGCAGAGACGAAAGTCGGTCTTAGTGATCCGGTGGTTCTGTGTGGAAGGGCCATCGCTCAAAGGATAAAAGGTACCCCGGGGATAACAGGCTGATCTCCCCCAAGAGCTCACATCGACGGGGAGGTTTGGCACCTCGATGTCGGCTCATCGCATCCTGGGGCTGGAGCAGGTCCCAAGGGTATGGCTGTTCGCCATTTAAAGCGGTACGCGAGCTGGGTTCAGAACGTCGTGAGACAGTTCGGTCCCTATCTGCCGTGGGCGTAAGAAGATTGAAGAGATTTGACCCTAGTACGAGAGGACCGGGTTGAACAAACCACTGGTGTAGCTGTTGTTCTGCCAAGAGCATCGCAGCGTAGCTAAGTTTGGAAAGGATAAACGCTGAAAGCATCTAAGCGTGAAGCCAACTCTAAGATGAATCTTCTCTAAGCTCTCTAGAAGACTACTAGTTTGATAGGCTGGGTGTGTAATGGATGAAAGTCCTTTAGCTGACCAGTACTAATAGAGCGTTTGGCTTATCTTTAATAAAGCAT","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39578","NCBI_taxonomy_name":"Campylobacter jejuni subsp. jejuni","NCBI_taxonomy_id":"32022"}}}},"ARO_accession":"3004546","ARO_id":"42445","ARO_name":"Campylobacter jejuni 23S rRNA with mutation conferring resistance to erythromycin","CARD_short_name":"Cjej_23S_ERY","ARO_description":"Point mutations in the 23S ribosomal RNA domain of Campylobacter jejuni which confer resistance to macrolide antibiotics, including erythromycin.","ARO_category":{"41251":{"category_aro_accession":"3004125","category_aro_cvterm_id":"41251","category_aro_name":"23S rRNA with mutation conferring resistance to macrolide antibiotics","category_aro_description":"Nucleotide point mutations in the 23S rRNA subunit may confer resistance to macrolide antibiotics.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3256":{"model_id":"3256","model_name":"dfrA9","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"5112":{"protein_sequence":{"accession":"CAA40897.1","sequence":"MASLNMIVAVNKTGGIGFENQIPWHEPEDLKHFKAVTMNSVLIMGRKTFASLPKVLPGRLHVVVSKTVPPTQNTDQVVYVSTYQIAVRTASLLVDKPEYSQIFVIGGKSAYENLAAYVDKLYLTRVQLNTQQDTELDLSLFKSWKLVSEVPTITENKTKLIFQIWINPNPISEEPTC"},"dna_sequence":{"accession":"X57730.1","fmin":"725","fmax":"1259","strand":"+","sequence":"ATGGCTTCTCTAAACATGATTGTCGCTGTCAATAAGACAGGAGGTATCGGATTTGAAAATCAGATTCCGTGGCATGAACCAGAAGATTTAAAACACTTCAAAGCTGTTACAATGAACTCAGTTTTGATTATGGGTAGAAAAACTTTTGCCTCACTGCCTAAAGTGCTGCCCGGACGACTTCATGTGGTAGTCAGTAAAACAGTACCACCCACCCAGAACACTGATCAAGTTGTGTATGTAAGTACATACCAGATCGCAGTAAGAACTGCAAGCTTGTTGGTTGACAAACCAGAGTATTCTCAAATTTTTGTAATTGGTGGGAAGAGTGCGTACGAGAACTTAGCTGCCTACGTGGACAAACTCTACTTAACTAGAGTACAGCTCAACACACAACAAGACACTGAACTGGATTTATCCCTATTCAAGTCATGGAAACTCGTATCTGAGGTCCCGACCATTACTGAAAACAAAACAAAACTTATTTTCCAAATTTGGATTAACCCTAACCCTATTAGTGAGGAACCCACATGTTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3004548","ARO_id":"42451","ARO_name":"dfrA9","CARD_short_name":"dfrA9","ARO_description":"A dihydrofolate reductase and trimethoprim resistance gene identified from porcine isolates of Esherichia coli.","ARO_category":{"37617":{"category_aro_accession":"3001218","category_aro_cvterm_id":"37617","category_aro_name":"trimethoprim resistant dihydrofolate reductase dfr","category_aro_description":"Alternative dihydropteroate synthase dfr present on plasmids produces alternate proteins that are less sensitive to trimethoprim from inhibiting its role in folate synthesis, thus conferring trimethoprim resistance.","category_aro_class_name":"AMR Gene Family"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4192":{"model_id":"4192","model_name":"ADC-119","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6567":{"protein_sequence":{"accession":"WP_004712857.1","sequence":"MRFKKISCLLLSPLFIFSTSIYADNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSNTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPTDIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYVVLDAIKK"},"dna_sequence":{"accession":"NG_064677.1","fmin":"100","fmax":"1252","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGACAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCTGTAAATAGCAATACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAGTATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCTGGCCCACTCGATGCCCCAGCATACGGCGTCAAATCCACCTTACCGGATATGTTGAGTTTTATTCATGCCAACCTTAACCCACAGAAATATCCGACAGATATTCAACGGGCAATTAATGAAACACATCAAGGTCGCTATCAAGTAAATACCATGTATCAAGCGCTTGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCAACGGTTTCGGAACATATGTAGTGTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGTTGTGCTGGATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006296","ARO_id":"44758","ARO_name":"ADC-119","CARD_short_name":"ADC-119","ARO_description":"ADC-119 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4233":{"model_id":"4233","model_name":"ADC-165","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6608":{"protein_sequence":{"accession":"WP_001211239.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKVLKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPTDIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_056107.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACCCCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCATTATTAGAAAAATATGATGTGCCGGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGTGCTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATACGGCGTCAAATCCACCTTACCGGATATGTTGAGTTTTATTCATGCCAACCTTAACCCACAGAAATATCCGACAGATATTCAACGGGCAATTAATGAAACACATCAAGGTCGCTATCAAGTAAATACCATGTATCAAGCGCTTGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCAACGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006337","ARO_id":"44799","ARO_name":"ADC-165","CARD_short_name":"ADC-165","ARO_description":"ADC-165 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4129":{"model_id":"4129","model_name":"ACT-34","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6504":{"protein_sequence":{"accession":"WP_063857778.1","sequence":"MMMTKSLCCALLLSTSCSVLAIPMSEKQLAEVVERTVTPLMKAQAIPGMAVAVIYEGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIVRGEISLGDPVTKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMSYEQAITTRVFKPLKLDHTWINVPKAEEAHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVQDMASWVMVNMKPDSLQDNSLRKGLTLAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVEGSDNKVALAPLPAREVKPPVPPVNASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILSAL"},"dna_sequence":{"accession":"NG_048621.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGATGACTAAATCCCTTTGCTGCGCCCTGCTGCTCAGCACCTCCTGCTCGGTATTGGCTATCCCGATGTCAGAAAAACAGCTGGCTGAGGTGGTGGAACGGACCGTTACGCCGCTGATGAAAGCGCAGGCCATTCCGGGTATGGCGGTGGCGGTGATTTATGAGGGTCAGCCGCACTACTTCACCTTCGGTAAAGCCGATGTTGCGGCGAACAAACCTGTCACTCCACAAACCTTGTTCGAACTGGGTTCTATAAGTAAAACCTTCACCGGCGTACTCGGTGGCGATGCCATTGTTCGCGGTGAAATATCGCTGGGCGATCCGGTGACAAAATACTGGCCTGAGCTAACAGGCAAGCAGTGGCAGGGGATCCGCATGCTGGATCTGGCAACCTATACCGCAGGAGGTTTGCCGTTACAGGTACCGGATGAGGTCACGGATAACGCCTCTCTGTTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCGGGCACCACGCGTCTTTACGCCAATGCCAGCATCGGTCTTTTTGGCGCGCTGGCGGTCAAACCTTCCGGCATGAGCTATGAGCAGGCCATAACGACGCGGGTCTTTAAGCCGCTCAAGCTGGACCATACGTGGATTAACGTTCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGATACCGCGACGGTAAAGCGGTACACGTTTCGCCAGGAATGCTGGACGCTGAAGCCTATGGCGTAAAAACCAACGTGCAGGATATGGCAAGCTGGGTGATGGTCAACATGAAGCCGGACTCCCTTCAGGATAATTCACTCAGGAAAGGCCTTACCCTGGCGCAGTCTCGCTACTGGCGCGTGGGGGCCATGTATCAGGGGTTAGGCTGGGAAATGCTTAACTGGCCGGTCGATGCCAAAACCGTGGTTGAAGGTAGCGACAATAAGGTGGCACTGGCACCGCTGCCTGCGAGAGAAGTGAAACCACCGGTGCCCCCGGTCAACGCATCCTGGGTCCATAAAACAGGCTCTACCGGCGGGTTTGGCAGCTACGTGGCATTTATTCCTGAAAAGCAGCTCGGTATTGTGATGCTGGCAAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCGTATTTTGAGCGCGCTGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3001854","ARO_id":"38254","ARO_name":"ACT-34","CARD_short_name":"ACT-34","ARO_description":"ACT-34 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3996":{"model_id":"3996","model_name":"TEM-233","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6360":{"protein_sequence":{"accession":"WP_109791184.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEHLGRRIHYSQNDLVESPPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDEANRQIAEIGASLIKHW"},"dna_sequence":{"accession":"NG_057581.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTGGACGCCGGGCAAGAGCACCTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTCCCCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAAGCAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3005264","ARO_id":"43620","ARO_name":"TEM-233","CARD_short_name":"TEM-233","ARO_description":"TEM-233 is a beta-lactamase.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3285":{"model_id":"3285","model_name":"tet(49)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"5154":{"protein_sequence":{"accession":"AKQ05893.1","sequence":"MSAINKILVIGAGIAGPTVCYWLKRFGFSPTLIERSSKIRKGGQGLDVRGVAIDIVKRMGIYEKICNMRTQVELGRYVDARGNILHEEKGERFAFRQGEDVEINRGDLVEILIQTIEGVPCHFNQWIDGIKQSDNDVEVQFKDGRTEHYGLVIGADGLHSKTRRMVFNEDEYKLTNLGLYFSVFSIPNYLNLNHTEVQFEANQKLISLTSDKNPKMAEAAFCFRTQNVLNNIRDENEQQKFLRDTFQDFGWETSKILELMSDSDNFYFDSVTQVEMKSWTKGRVALLGDAGYSASPISGQGNNLALVGAYVFAGELKQAGGNYHRAFSRYNELLHSFVEANQKLGILVNESTLVYGEVSQEVAEERSNKIMQEVEIAANMISLPNYE"},"dna_sequence":{"accession":"KR857683.1","fmin":"0","fmax":"1164","strand":"+","sequence":"ATGTCTGCAATAAATAAAATTCTCGTAATAGGAGCCGGCATTGCTGGACCTACTGTTTGTTATTGGTTAAAAAGATTTGGCTTTTCTCCCACTCTAATTGAAAGGTCTTCCAAAATACGAAAAGGAGGGCAAGGATTGGATGTTCGGGGTGTTGCCATCGATATCGTTAAAAGAATGGGTATCTATGAGAAAATATGCAATATGCGCACCCAAGTGGAATTAGGACGGTATGTTGACGCCAGAGGCAATATCTTGCATGAAGAAAAAGGTGAAAGATTTGCCTTTAGGCAAGGTGAAGATGTTGAAATTAACCGCGGTGATTTAGTCGAAATACTGATACAGACTATTGAAGGTGTTCCCTGTCATTTCAATCAATGGATTGACGGTATTAAACAGAGTGATAATGATGTAGAAGTTCAATTTAAAGATGGTAGAACCGAACATTATGGCTTGGTTATTGGGGCTGATGGTTTACACTCAAAAACAAGACGTATGGTTTTCAATGAGGATGAATATAAATTAACTAACCTTGGTTTATATTTTAGCGTTTTTAGCATCCCAAATTATCTTAATTTGAACCACACCGAAGTTCAGTTCGAGGCCAATCAAAAACTTATATCTCTTACTAGTGATAAGAATCCTAAGATGGCTGAAGCCGCATTCTGCTTTCGTACACAAAATGTCTTAAATAATATTCGCGATGAAAATGAGCAACAGAAATTCCTACGCGATACTTTTCAAGATTTTGGCTGGGAAACGTCAAAAATACTTGAACTGATGTCTGATAGCGATAATTTTTATTTTGATTCAGTCACCCAGGTGGAAATGAAATCATGGACTAAAGGACGAGTGGCTTTGCTGGGAGATGCGGGTTACTCCGCATCTCCAATATCTGGTCAAGGTAATAATCTGGCACTAGTGGGAGCGTATGTTTTTGCAGGAGAACTAAAACAAGCAGGTGGCAATTATCATCGAGCATTTAGCCGTTATAATGAATTATTACACTCATTTGTTGAAGCCAATCAAAAATTGGGAATTTTGGTTAACGAATCAACTCTTGTTTATGGTGAAGTCTCTCAGGAGGTTGCAGAAGAAAGATCAAATAAGATTATGCAAGAGGTAGAAATCGCAGCGAATATGATTTCGTTACCTAATTATGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36791","NCBI_taxonomy_name":"uncultured bacterium","NCBI_taxonomy_id":"77133"}}}},"ARO_accession":"3004582","ARO_id":"42512","ARO_name":"tet(49)","CARD_short_name":"tet(49)","ARO_description":"A tetracycline inactivating enzyme. A flavoenzyme capable of degrading tetracycline antibiotics.","ARO_category":{"36176":{"category_aro_accession":"3000036","category_aro_cvterm_id":"36176","category_aro_name":"tetracycline inactivation enzyme","category_aro_description":"Enzymes or other gene products which hydroxylate tetracycline and other tetracycline derivatives. Hydroxylation inactivates tetracycline-like antibiotics, thus conferring resistance to these compounds.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"37012":{"category_aro_accession":"3000668","category_aro_cvterm_id":"37012","category_aro_name":"oxytetracycline","category_aro_description":"Oxytetracycline is a derivative of tetracycline with a 5-hydroxyl group. Its activity is similar to other tetracyclines.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4260":{"model_id":"4260","model_name":"ADC-195","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6635":{"protein_sequence":{"accession":"WP_140423305.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWQPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRANPGPLDAPAYGVKSTLPDMLSFIHANLTPQKYPTDIQRAINETHQGFYQVGTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKETAISKEPSVKMYHKTGSTSGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_065420.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCATTATTAGAAAAATATGATGTACCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAGCTAAAAAATACACCGATTGATCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGCAACCTCGCTTTACAATTTCCAGATGAAGTACAAACAGATCAACAAGTTTTAACTTTTTTCAAAGACTGGCAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTGGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGCTAACCCCGGCCCACTTGATGCCCCAGCATACGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTTACCCCACAGAAATATCCGACAGATATTCAACGGGCAATTAATGAAACACATCAAGGGTTCTATCAAGTCGGCACCATGTATCAGGCACTTGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGAGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCAGCGGTTTCGGAACATATGTGGTCTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006364","ARO_id":"44826","ARO_name":"ADC-195","CARD_short_name":"ADC-195","ARO_description":"ADC-195 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3257":{"model_id":"3257","model_name":"dfrB5","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"150"}},"model_sequences":{"sequence":{"8340":{"protein_sequence":{"accession":"AAX46054.1","sequence":"MDQGRSEVSNPVAGQFAFPSNAAFGMGDRVRKKSGAAWQGQIVGWYCTKLTPEGYAVESEAHPGSVQIYPVAALERIN"},"dna_sequence":{"accession":"AY943084.1","fmin":"2855","fmax":"3092","strand":"+","sequence":"ATGGACCAAGGCAGAAGTGAAGTCAGTAATCCAGTTGCTGGCCAGTTTGCGTTCCCTTCAAACGCCGCGTTCGGAATGGGAGATCGCGTGCGCAAGAAATCTGGCGCCGCTTGGCAAGGCCAGATTGTCGGGTGGTACTGCACAAAATTGACCCCTGAAGGGTACGCTGTCGAGTCTGAGGCTCACCCTGGCTCGGTACAGATTTATCCTGTTGCGGCACTGGAACGCATCAACTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3004549","ARO_id":"42452","ARO_name":"dfrB5","CARD_short_name":"dfrB5","ARO_description":"A dihydrofolate reductase and trimethoprim resistance gene identified from an integron in Pseudomonas aeruginosa.","ARO_category":{"37617":{"category_aro_accession":"3001218","category_aro_cvterm_id":"37617","category_aro_name":"trimethoprim resistant dihydrofolate reductase dfr","category_aro_description":"Alternative dihydropteroate synthase dfr present on plasmids produces alternate proteins that are less sensitive to trimethoprim from inhibiting its role in folate synthesis, thus conferring trimethoprim resistance.","category_aro_class_name":"AMR Gene Family"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4234":{"model_id":"4234","model_name":"ADC-166","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6609":{"protein_sequence":{"accession":"WP_101244937.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPINQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGHYQVNTMYQALGWEEFSYPAMLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYTVLNAIKK"},"dna_sequence":{"accession":"NG_056108.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTAGGTTCTGTTAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAGCTAAAAAATACACCGATTAACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTCCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCTTATTTGGAAAAGTTGTTGCTTTGTCTATGAATAAACCTTTCGATCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACTCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATACGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTTAACCCACAGAAATATCCGGCAGATATTCAACGGGCAATTAATGAAACACATCAGGGTCACTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAATGTTACAAACTTTACTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACGTATGTGGTGTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCGTATACAGTTTTAAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006338","ARO_id":"44800","ARO_name":"ADC-166","CARD_short_name":"ADC-166","ARO_description":"ADC-166 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3289":{"model_id":"3289","model_name":"tet(52)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"5158":{"protein_sequence":{"accession":"AKQ05896.1","sequence":"MSNVNKILVIGAGIAGPAACYWLRRFGFSPVLVERSASLRKGGHALDVRGVAIDLVKRMGIYQKIYNMRTQLEFGRHVDPEGNTLHEEKGERFGFREGQDVEIIRSDLVEILIDSIEGVPLQFNQTIESVKQTDAVVEVQFKDGRTEHFDLVIGADGLHSTTRRIVFDKHEYKLNDLGAYFSVFSIPNYLNLNNTEVQCEANQKLLSITSDKNRKMAEVAFSFRGQNVLNNVRDESEQRRVLRDTFQDFGWEAPRILELMSDSDDFYSDSFTQVIMKSWTKGRVALLGDAAYSASPISGQGNNLALVGAYVLAGELKQAGGNYKRAFDRYNEILRPFIEANQKLGVLVNESFLVRDEVSKEVAEERSNNIMEQVKIASNMIVLQDYANPH"},"dna_sequence":{"accession":"KR857686.1","fmin":"0","fmax":"1173","strand":"+","sequence":"ATGTCTAATGTGAATAAAATTCTCGTCATCGGGGCTGGCATTGCTGGCCCCGCGGCTTGTTATTGGTTAAGAAGATTCGGATTTTCTCCCGTCCTCGTAGAAAGATCTGCCAGTTTACGAAAAGGCGGTCATGCACTGGACGTTCGAGGTGTTGCAATAGACCTCGTCAAAAGAATGGGTATTTATCAGAAAATATATAATATGCGCACTCAGCTGGAGTTTGGGCGGCATGTTGACCCCGAAGGGAATACGCTTCATGAAGAGAAGGGCGAAAGATTTGGCTTTAGGGAAGGTCAAGATGTTGAAATTATCCGCAGTGATTTGGTCGAGATATTGATAGATTCCATTGAAGGCGTCCCCCTTCAGTTCAATCAAACGATTGAGAGCGTTAAACAGACTGATGCTGTTGTCGAAGTTCAATTTAAAGATGGCAGAACCGAACACTTCGATTTGGTTATCGGGGCTGACGGCTTGCACTCAACAACAAGACGTATCGTATTTGATAAACATGAATATAAATTAAATGACCTTGGTGCTTACTTTAGTGTTTTCAGTATTCCAAATTATCTAAATTTGAATAACACCGAAGTTCAGTGCGAAGCTAATCAAAAACTGTTATCTATAACGAGCGACAAGAACCGCAAGATGGCTGAGGTCGCATTCTCATTTCGTGGCCAGAATGTTTTGAATAATGTTCGTGATGAAAGCGAGCAACGGCGAGTCCTACGCGACACTTTTCAAGACTTTGGCTGGGAAGCACCAAGAATACTTGAACTGATGTCAGATAGTGATGATTTTTATTCTGATTCATTCACTCAGGTAATAATGAAATCATGGACTAAAGGTCGAGTTGCATTATTGGGAGATGCTGCGTACAGCGCGTCGCCAATATCGGGGCAAGGTAATAATCTGGCCCTGGTCGGCGCTTATGTTTTGGCAGGAGAACTAAAACAGGCAGGCGGCAATTATAAGCGGGCATTTGATCGTTATAATGAAATATTACGTCCATTTATTGAAGCTAATCAAAAATTGGGAGTCTTGGTTAACGAATCGTTTCTTGTTCGCGATGAAGTCTCTAAAGAGGTTGCGGAAGAACGGTCAAATAATATTATGGAACAGGTAAAAATCGCATCGAACATGATTGTGTTGCAGGATTACGCCAATCCGCACTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36791","NCBI_taxonomy_name":"uncultured bacterium","NCBI_taxonomy_id":"77133"}}}},"ARO_accession":"3004587","ARO_id":"42517","ARO_name":"tet(52)","CARD_short_name":"tet(52)","ARO_description":"A tetracycline inactivating enzyme. A flavoenzyme capable of degrading tetracycline antibiotics.","ARO_category":{"36176":{"category_aro_accession":"3000036","category_aro_cvterm_id":"36176","category_aro_name":"tetracycline inactivation enzyme","category_aro_description":"Enzymes or other gene products which hydroxylate tetracycline and other tetracycline derivatives. Hydroxylation inactivates tetracycline-like antibiotics, thus conferring resistance to these compounds.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"37012":{"category_aro_accession":"3000668","category_aro_cvterm_id":"37012","category_aro_name":"oxytetracycline","category_aro_description":"Oxytetracycline is a derivative of tetracycline with a 5-hydroxyl group. Its activity is similar to other tetracyclines.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3294":{"model_id":"3294","model_name":"erm(32)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"556"}},"model_sequences":{"sequence":{"5164":{"protein_sequence":{"accession":"CAB37345.2","sequence":"MRKNVVRYLRCPHCAAPLRSSDRTLRCENGHTFDVARQGYVNLLRRPTKLAADTTDMVAARAALLDSGHYAPLTERLAGTARRAAGAGAPDCVVDIGGGTGHHLARVLEEFEDAEGLLLDMSKPAVRRAARAHPRASSAVADVWDTLPLRDGAAAMALNVFAPRNPPEIRRILRPGGTLLVVTPQQDHLAELVDALGLLRVRDHKEGRLAEQLAPHFEAVGQERLRTTLRLDHDALGRVVAMGPSSWHQDPDELARRIAELPGIHEVTLSVTFTVCRPLP"},"dna_sequence":{"accession":"AJ009971.2","fmin":"1789","fmax":"2632","strand":"+","sequence":"ATGCGGAAGAACGTCGTGCGATATCTGCGCTGTCCGCACTGCGCAGCCCCTCTGCGGTCATCCGACCGCACCCTCCGCTGCGAAAACGGGCACACCTTCGACGTCGCCCGGCAGGGCTATGTGAATCTGCTCAGACGCCCGACGAAGCTCGCCGCCGACACCACCGACATGGTCGCCGCCCGGGCCGCGCTGCTGGACAGCGGGCATTACGCGCCGCTGACCGAGCGGCTGGCCGGGACGGCCCGGCGCGCGGCGGGCGCCGGGGCACCGGACTGCGTCGTGGACATCGGCGGGGGCACCGGTCACCATCTCGCCCGTGTCCTGGAGGAGTTCGAGGACGCCGAGGGACTCCTGCTGGACATGTCCAAGCCGGCCGTGCGCAGGGCCGCCCGCGCCCATCCCCGGGCCAGCTCCGCCGTCGCCGACGTATGGGACACACTTCCGCTGCGGGACGGGGCCGCCGCGATGGCCCTCAACGTCTTCGCCCCGCGCAACCCGCCGGAGATCCGCAGGATCCTCCGCCCCGGCGGCACCCTGCTGGTCGTCACGCCCCAGCAGGACCACCTCGCCGAACTCGTGGACGCGCTGGGGCTGTTGCGCGTACGGGACCACAAGGAGGGCCGGCTGGCCGAACAGCTCGCGCCGCACTTCGAGGCCGTCGGGCAGGAGCGGCTGCGGACCACTCTCCGCCTCGATCACGACGCGCTCGGCCGGGTGGTCGCCATGGGGCCCAGTTCCTGGCACCAGGACCCGGATGAACTGGCGCGGCGGATCGCGGAGTTGCCCGGCATCCACGAGGTCACGCTCTCGGTCACCTTCACCGTCTGCCGCCCTCTGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36838","NCBI_taxonomy_name":"Streptomyces fradiae","NCBI_taxonomy_id":"1906"}}}},"ARO_accession":"3004592","ARO_id":"42522","ARO_name":"erm(32)","CARD_short_name":"erm(32)","ARO_description":"erm(32) is a rRNA methyltransferase. Encodes methyltransferases that modify 23S rRNA.","ARO_category":{"36699":{"category_aro_accession":"3000560","category_aro_cvterm_id":"36699","category_aro_name":"Erm 23S ribosomal RNA methyltransferase","category_aro_description":"Erm proteins are part of the RNA methyltransferase family and methylate A2058 (E. coli nomenclature) of the 23S ribosomal RNA conferring degrees of resistance to Macrolides, Lincosamides and Streptogramin b. This is called the MLSb phenotype.","category_aro_class_name":"AMR Gene Family"},"37625":{"category_aro_accession":"3001226","category_aro_cvterm_id":"37625","category_aro_name":"narbomycin","category_aro_description":"Produced by Streptomyces narbonensis.","category_aro_class_name":"Antibiotic"},"37631":{"category_aro_accession":"3001232","category_aro_cvterm_id":"37631","category_aro_name":"methymycin","category_aro_description":"Produced by Streptomyces venezuelae ATCC 15439.","category_aro_class_name":"Antibiotic"},"37632":{"category_aro_accession":"3001233","category_aro_cvterm_id":"37632","category_aro_name":"pikromycin","category_aro_description":"Produced by Streptomyces venezuelae ATCC 15439.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4261":{"model_id":"4261","model_name":"ADC-196","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6636":{"protein_sequence":{"accession":"WP_145850033.1","sequence":"MRFKKISCLLLSPLFIFSTSIYADNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKIFFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHSNLNPQKYPKDIQRAINETHQGFYQVNTMYQALGWEDFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_065858.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGACAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCATTATTAGAAAAATATGATGTGCCGGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTTTTTTGACGATACGCCTGGTAAATATTGGAAAGAGCTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTCCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATACGGCGTCAAATCGACACTACCCGACATGCTGAGTTTTATTCATTCCAATCTGAACCCACAGAAATATCCGAAAGATATTCAACGTGCAATTAATGAAACACATCAAGGGTTCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGATTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCAACGGTTTCGGAACATATGTGGTCTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006365","ARO_id":"44827","ARO_name":"ADC-196","CARD_short_name":"ADC-196","ARO_description":"ADC-196 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3254":{"model_id":"3254","model_name":"NDM-11","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"5107":{"protein_sequence":{"accession":"AJE61443.1","sequence":"MELPNIMHPVAKLSTALAAALMLSGCMPGEIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGVVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR"},"dna_sequence":{"accession":"KP265939.1","fmin":"0","fmax":"813","strand":"+","sequence":"ATGGAATTGCCCAATATTATGCACCCGGTCGCGAAGCTGAGCACCGCATTAGCCGCTGCATTGATGCTGAGCGGGTGCATGCCCGGTGAAATCCGCCCGACGATTGGCCAGCAAATGGAAACTGGCGACCAACGGTTTGGCGATCTGGTTTTCCGCCAGCTCGCACCGAATGTCTGGCAGCACACTTCCTATCTCGACATGCCGGGTTTCGGGGCAGTCGCTTCCAACGGTTTGATCGTCAGGGATGGCGGCCGCGTGCTGGTGGTCGATACCGCCTGGACCGATGACCAGACCGCCCAGATCCTCAACTGGATCAAGCAGGAGATCAACCTGCCGGTCGCGCTGGCGGTGGTGACTCACGCGCATCAGGACAAGATGGGCGGTATGGACGCGCTGCATGCGGCGGGGATTGCGACTTATGCCAATGCGTTGTCGAACCAGCTTGCCCCGCAAGAGGGGGTGGTTGCGGCGCAACACAGCCTGACTTTCGCCGCCAATGGCTGGGTCGAACCAGCAACCGCGCCCAACTTTGGCCCGCTCAAGGTATTTTACCCCGGCCCCGGCCACACCAGTGACAATATCACCGTTGGGATCGACGGCACCGACATCGCTTTTGGTGGCTGCCTGATCAAGGACAGCAAGGCCAAGTCGCTCGGCAATCTCGGTGATGCCGACACTGAGCACTACGCCGCGTCAGCGCGCGCGTTTGGTGCGGCGTTCCCCAAGGCCAGCATGATCGTGATGAGCCATTCCGCCCCCGATAGCCGCGCCGCAATCACTCATACGGCCCGCATGGCCGACAAGCTGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002361","ARO_id":"38761","ARO_name":"NDM-11","CARD_short_name":"NDM-11","ARO_description":"NDM-11 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36196":{"category_aro_accession":"3000057","category_aro_cvterm_id":"36196","category_aro_name":"NDM beta-lactamase","category_aro_description":"NDM beta-lactamases or New Delhi metallo-beta-lactamases are class B beta-lactamases that confer resistance to a broad range of antibiotics including carbapenems, cephalosporins and penicillins.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3255":{"model_id":"3255","model_name":"dfrA6","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"5111":{"protein_sequence":{"accession":"ACY06082.1","sequence":"MKISIMAAVSENGVIGSGLDIPWHVYGEQLLFKAMTYNHWLLVGRKTFDSMGKLPNRKYAVVTRTEMVSNDPDVVYFTSVESALAYLDHTTTHVFVSGGGEIYKALIEQADVIHLSVIHKHISGDVFFPSVPQSFKQTFEQSFSSNIDYTYQIWTKG"},"dna_sequence":{"accession":"FJ905898.1","fmin":"328","fmax":"802","strand":"+","sequence":"ATGAAAATATCCATTATGGCAGCTGTTTCCGAGAATGGAGTAATTGGCTCTGGATTGGATATACCTTGGCATGTATATGGTGAGCAGCTCCTGTTCAAAGCTATGACTTACAATCATTGGCTTTTAGTCGGTCGTAAAACTTTCGACTCAATGGGTAAACTTCCGAATAGGAAATATGCTGTGGTTACTCGTACTGAAATGGTCTCGAATGATCCTGATGTTGTTTATTTCACAAGCGTTGAATCGGCATTAGCTTACTTAGACCACACGACAACACATGTCTTTGTTTCTGGTGGTGGTGAAATTTACAAAGCATTAATCGAACAAGCAGATGTTATCCATCTTTCAGTGATTCATAAGCACATCTCTGGCGACGTGTTTTTCCCTTCAGTTCCACAGAGTTTCAAGCAAACATTTGAGCAAAGTTTCAGTTCAAATATTGATTACACGTACCAAATTTGGACAAAGGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36789","NCBI_taxonomy_name":"Vibrio cholerae","NCBI_taxonomy_id":"666"}}}},"ARO_accession":"3004547","ARO_id":"42450","ARO_name":"dfrA6","CARD_short_name":"dfrA6","ARO_description":"A dihydrofolate reductase and antibiotic resistance gene identified from an integron in Vibrio cholerae.","ARO_category":{"37617":{"category_aro_accession":"3001218","category_aro_cvterm_id":"37617","category_aro_name":"trimethoprim resistant dihydrofolate reductase dfr","category_aro_description":"Alternative dihydropteroate synthase dfr present on plasmids produces alternate proteins that are less sensitive to trimethoprim from inhibiting its role in folate synthesis, thus conferring trimethoprim resistance.","category_aro_class_name":"AMR Gene Family"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3639":{"model_id":"3639","model_name":"LEN-40","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"5910":{"protein_sequence":{"accession":"AZA07956.1","sequence":"MRYVRLCVISLLANLPLAVYAGPQPLEQIKQSESQLSGRVGMVEMDLASGRTLAAWRADERFPMVSTFKVLLCGAVLARVDAGVEQLDRRIHYRQQDLVDYSPVSEKHLVDGMTIGELCAAAITMSDNSAGNLLLATVGGPVGLTAFLRQIGDNVTRLDRWETALNEALPGDARDTTTPASMAATLRKLLTAQHLSARSQQQLLQWMVDDRVAGPLIRAVLPAGWFIADKTGAGERGARGIVALLGPDGNAERIVVIYLRDTPASMAERNQHIAGIGAALIEHWQR"},"dna_sequence":{"accession":"MK161459.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGTGTTATCTCCCTGTTAGCCAACCTGCCACTAGCGGTATACGCCGGTCCACAGCCGCTTGAGCAGATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTGGGGATGGTGGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCGATGAACGCTTTCCCATGGTGAGCACCTTTAAAGTGCTGCTGTGCGGCGCGGTGCTGGCGCGGGTGGATGCCGGGGTCGAACAACTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGTCGACGGGATGACGATCGGCGAACTCTGCGCCGCCGCCATCACCATGAGCGATAACAGCGCCGGCAATCTGCTGCTGGCCACCGTCGGTGGCCCCGTGGGATTGACCGCCTTTCTGCGCCAGATCGGTGACAACGTCACCCGCCTTGACCGCTGGGAAACGGCACTGAATGAGGCGCTTCCCGGCGACGCGCGCGATACCACTACCCCGGCCAGCATGGCCGCCACGCTGCGCAAACTACTGACCGCGCAGCATCTGAGCGCCCGTTCGCAACAGCAGCTCCTGCAGTGGATGGTGGACGATCGGGTTGCCGGCCCGCTGATCCGCGCCGTGCTGCCGGCGGGCTGGTTTATCGCCGACAAAACCGGGGCTGGCGAACGGGGTGCGCGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAACGCGGAGCGCATTGTGGTGATCTATCTGCGGGATACCCCGGCGAGTATGGCCGAGCGTAATCAACATATCGCCGGGATCGGCGCAGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42976","NCBI_taxonomy_name":"Klebsiella variicola subsp. tropica","NCBI_taxonomy_id":"2489014"}}}},"ARO_accession":"3004843","ARO_id":"42978","ARO_name":"LEN-40","CARD_short_name":"LEN-40","ARO_description":"A class-A broad-spectrum beta-lactamase identified from Klebsiella sp.","ARO_category":{"36236":{"category_aro_accession":"3000097","category_aro_cvterm_id":"36236","category_aro_name":"LEN beta-lactamase","category_aro_description":"LEN beta-lactamases are chromosomal class A beta-lactamases that confer resistance to ampicillin, amoxicillin, carbenicillin, and ticarcillin but not to extended-spectrum beta-lactams.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3258":{"model_id":"3258","model_name":"dfrA27","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"5114":{"protein_sequence":{"accession":"ACD45689.1","sequence":"MKISLMAAKARNGVIGCGSDIPWNAKGEQLLFKAITYNQWLLVGRKTFEAMGALPNRKYAVVSRSGSVATNDDVVVFPSIEAAMRELKTLTNHVVVSGGGEIYKSLIAHADTLHISTIDSEPEGNVFFPEIPKEFNVVFEQEFHSNINYRYQIWQRG"},"dna_sequence":{"accession":"KP076293.1","fmin":"2347","fmax":"2821","strand":"+","sequence":"GTGAAAATATCACTAATGGCTGCAAAAGCAAGAAATGGGGTTATTGGCTGCGGCTCGGATATCCCGTGGAACGCTAAAGGTGAGCAGCTGCTTTTTAAAGCAATAACTTACAATCAATGGCTCTTAGTCGGCCGTAAAACATTTGAGGCAATGGGGGCTCTCCCAAATAGAAAGTATGCAGTTGTCAGCCGCTCAGGATCGGTAGCTACTAACGATGATGTGGTTGTGTTTCCATCTATAGAAGCAGCAATGAGGGAGCTAAAGACTCTTACGAACCATGTTGTTGTTTCTGGTGGTGGAGAGATCTACAAGAGTCTGATCGCCCATGCCGACACGCTACATATCTCGACAATAGATTCCGAGCCAGAGGGCAATGTTTTCTTTCCGGAAATCCCCAAAGAGTTCAATGTGGTGTTCGAGCAGGAATTTCATTCAAATATAAATTATCGCTATCAAATCTGGCAAAGGGGTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36920","NCBI_taxonomy_name":"Vibrio cholerae non-O1\/non-O139","NCBI_taxonomy_id":"156539"}}}},"ARO_accession":"3004550","ARO_id":"42453","ARO_name":"dfrA27","CARD_short_name":"dfrA27","ARO_description":"A dihydrofolate reductase and trimethoprim resistance gene from non-O1, non-O139 Vibrio cholerae.","ARO_category":{"37617":{"category_aro_accession":"3001218","category_aro_cvterm_id":"37617","category_aro_name":"trimethoprim resistant dihydrofolate reductase dfr","category_aro_description":"Alternative dihydropteroate synthase dfr present on plasmids produces alternate proteins that are less sensitive to trimethoprim from inhibiting its role in folate synthesis, thus conferring trimethoprim resistance.","category_aro_class_name":"AMR Gene Family"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3259":{"model_id":"3259","model_name":"dfrA28","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"5115":{"protein_sequence":{"accession":"CAT00035.1","sequence":"MKISLMAAKARNGVIGCGSDIPWNAKGEQLLFKAITYNQWLLVGRKTFEAMGALPNRKYAVVSRSGSVATNDDMVVFPSIEAAMGKLKTLTNHVVVSGGGEIYKSLIAHADTLHISTIDSEPEGNVFFPEIPKDFNVVFEQEFHSNINYRYQIWQRG"},"dna_sequence":{"accession":"FM877476.1","fmin":"115","fmax":"589","strand":"+","sequence":"GTGAAAATATCACTAATGGCTGCAAAAGCAAGAAATGGGGTTATTGGCTGCGGCTCTGATATCCCTTGGAACGCTAAAGGCGAGCAGCTGCTTTTTAAAGCAATAACTTACAATCAGTGGCTTTTAGTCGGCCGCAAAACATTTGAGGCAATGGGGGCTCTCCCAAATAGAAAGTATGCAGTTGTCAGCCGCTCAGGATCGGTAGCTACTAACGATGATATGGTTGTGTTTCCATCTATAGAAGCAGCAATGGGTAAGCTAAAGACTCTTACGAACCATGTTGTTGTTTCTGGTGGTGGAGAGATCTATAAGAGTCTGATCGCCCATGCCGACACGCTACATATTTCGACAATAGATTCCGAGCCAGAGGGCAATGTTTTCTTTCCGGAAATCCCCAAAGATTTCAATGTGGTGTTCGAGCAGGAATTTCATTCAAATATAAATTATCGATATCAAATCTGGCAAAGGGGTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36810","NCBI_taxonomy_name":"Aeromonas hydrophila","NCBI_taxonomy_id":"644"}}}},"ARO_accession":"3004551","ARO_id":"42454","ARO_name":"dfrA28","CARD_short_name":"dfrA28","ARO_description":"A dihydrofolate reductase and trimethoprim resistance gene from Aeromonas hydrophilia.","ARO_category":{"37617":{"category_aro_accession":"3001218","category_aro_cvterm_id":"37617","category_aro_name":"trimethoprim resistant dihydrofolate reductase dfr","category_aro_description":"Alternative dihydropteroate synthase dfr present on plasmids produces alternate proteins that are less sensitive to trimethoprim from inhibiting its role in folate synthesis, thus conferring trimethoprim resistance.","category_aro_class_name":"AMR Gene Family"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3260":{"model_id":"3260","model_name":"dfrA30","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"5116":{"protein_sequence":{"accession":"CAQ53849.2","sequence":"MKVSLMAARARNGVIGCGPHIPWSAKGEQLLFKALTYNQWLLVGRKTFESMGALPNRKYAVVTRSAWTANNDNVVVFPSIEEAMGGLAKLNGHVIVSGGGEIYRETLPMASTLHVSTIDIEPEGDVFFPNIPNFFEVVFEQHFSSNINYCYQIWKKG"},"dna_sequence":{"accession":"AM997279.2","fmin":"704","fmax":"1178","strand":"+","sequence":"GTGAAAGTATCATTAATGGCTGCAAGAGCGAGAAACGGAGTGATCGGTTGCGGTCCACACATACCCTGGTCCGCGAAAGGAGAGCAGCTACTCTTTAAAGCCCTGACGTACAACCAGTGGCTTTTGGTTGGCCGCAAGACGTTCGAATCAATGGGGGCGCTCCCCAACAGGAAATACGCGGTCGTTACTCGCTCAGCCTGGACGGCCAATAATGACAACGTAGTAGTATTCCCGTCGATCGAAGAGGCCATGGGCGGTCTAGCTAAACTCAACGGTCACGTTATAGTGTCTGGTGGCGGGGAGATTTACAGAGAAACGTTGCCCATGGCCTCTACGCTCCATGTATCGACGATCGACATTGAGCCAGAAGGGGATGTTTTCTTCCCGAATATTCCCAACTTCTTCGAAGTTGTTTTTGAGCAACATTTTAGTTCAAACATTAACTATTGCTATCAAATTTGGAAAAAGGGTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42456","NCBI_taxonomy_name":"Klebsiella sp. MB45","NCBI_taxonomy_id":"871235"}}}},"ARO_accession":"3004552","ARO_id":"42455","ARO_name":"dfrA30","CARD_short_name":"dfrA30","ARO_description":"A dihydrofolate reductase and trimethoprim resistance gene from Klebsiella pneumoniae.","ARO_category":{"37617":{"category_aro_accession":"3001218","category_aro_cvterm_id":"37617","category_aro_name":"trimethoprim resistant dihydrofolate reductase dfr","category_aro_description":"Alternative dihydropteroate synthase dfr present on plasmids produces alternate proteins that are less sensitive to trimethoprim from inhibiting its role in folate synthesis, thus conferring trimethoprim resistance.","category_aro_class_name":"AMR Gene Family"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3262":{"model_id":"3262","model_name":"dfrA29","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"5118":{"protein_sequence":{"accession":"ANN23980.1","sequence":"MAARAKNGVIGCGPNIPWSAKGEQLLFKALTYNQWLLVGRKTFESMGPLPNRKYAVVTRSNWTAANENVVVFPSIDEAMGRLGEITDHVIVAGGGEIYHETIPMASTLHVSTIDVEPEGDVFFPNIPGKFDVVFEQQFTSNINYCYQIWQKG"},"dna_sequence":{"accession":"KX118301.1","fmin":"131","fmax":"590","strand":"+","sequence":"ATGGCTGCAAGAGCGAAAAATGGCGTAATCGGTTGCGGTCCTAACATTCCTTGGTCTGCCAAAGGGGAACAGCTTCTTTTCAAAGCACTGACCTATAACCAATGGCTTTTGGTAGGGCGCAAAACATTTGAGTCTATGGGGCCGCTGCCCAATAGGAAATACGCGGTTGTTACCCGCTCAAACTGGACAGCGGCTAATGAAAACGTAGTGGTTTTCCCGTCGATTGACGAAGCGATGGGTAGATTAGGCGAGATCACTGACCATGTCATCGTCGCCGGTGGTGGAGAAATCTACCATGAAACGATACCCATGGCCTCTACTCTGCATGTGTCGACAATCGACGTTGAGCCAGAGGGAGACGTTTTCTTTCCGAACATTCCTGGGAAGTTTGATGTCGTTTTTGAGCAACAATTTACATCAAACATTAACTATTGCTATCAAATCTGGCAAAAGGGTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3004554","ARO_id":"42459","ARO_name":"dfrA29","CARD_short_name":"dfrA29","ARO_description":"A dihydrofolate reductase and trimethoprim resistance gene isolated from canine Escherichia coli infection.","ARO_category":{"37617":{"category_aro_accession":"3001218","category_aro_cvterm_id":"37617","category_aro_name":"trimethoprim resistant dihydrofolate reductase dfr","category_aro_description":"Alternative dihydropteroate synthase dfr present on plasmids produces alternate proteins that are less sensitive to trimethoprim from inhibiting its role in folate synthesis, thus conferring trimethoprim resistance.","category_aro_class_name":"AMR Gene Family"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3263":{"model_id":"3263","model_name":"dfrA32","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"5119":{"protein_sequence":{"accession":"ACZ52983.1","sequence":"MKISLISAVSENGVIGSGPDIPWSAKGEQLIFKALTYNQWLLVGRKTFDSMGVLPNRKYAVVSKNGISGSNENVLVFPSIENALQELSKITDHVYISGGGQIYESLIEKADIIHLSTIHVEVEGDIKFPILPEGFNLVFEQFFVSNINYTYQIWKKG"},"dna_sequence":{"accession":"GU067642.1","fmin":"534","fmax":"1008","strand":"+","sequence":"TTGAAAATTTCATTGATTTCTGCAGTGTCAGAAAATGGCGTAATCGGTAGTGGTCCTGATATTCCGTGGTCAGCAAAAGGTGAGCAGCTAATCTTTAAGGCGCTCACATACAATCAGTGGCTTCTTGTTGGAAGGAAAACATTTGACTCTATGGGAGTTCTTCCAAATCGCAAATATGCAGTAGTGTCAAAGAATGGAATTTCAGGGTCAAATGAAAACGTCTTGGTTTTTCCTTCAATAGAAAATGCTTTGCAAGAACTATCTAAAATTACAGATCATGTATATATTTCGGGTGGGGGGCAAATCTATGAAAGCCTTATTGAAAAAGCAGATATAATTCATCTATCTACTATTCATGTTGAGGTTGAAGGTGATATTAAATTCCCTATATTACCTGAAGGTTTCAACTTGGTTTTTGAACAGTTTTTTGTGTCTAATATAAATTATACATATCAAATTTGGAAAAAAGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35672","NCBI_taxonomy_name":"Salmonella enterica","NCBI_taxonomy_id":"28901"}}}},"ARO_accession":"3004555","ARO_id":"42460","ARO_name":"dfrA32","CARD_short_name":"dfrA32","ARO_description":"A dihydrofolate reductase and trimethoprim resistance gene identified from non-typhoidal multidrug-resistant Salmonella enterica.","ARO_category":{"37617":{"category_aro_accession":"3001218","category_aro_cvterm_id":"37617","category_aro_name":"trimethoprim resistant dihydrofolate reductase dfr","category_aro_description":"Alternative dihydropteroate synthase dfr present on plasmids produces alternate proteins that are less sensitive to trimethoprim from inhibiting its role in folate synthesis, thus conferring trimethoprim resistance.","category_aro_class_name":"AMR Gene Family"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3264":{"model_id":"3264","model_name":"dfrB7","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"150"}},"model_sequences":{"sequence":{"8341":{"protein_sequence":{"accession":"ADB54781.1","sequence":"MDQGSNEVGNPVAGQFSFPSNAAFSMGDRVRKKSGAAWQGQIVGWYCTKLTPEGYAVESEAHPGSVQIYPVAALERINGVQG"},"dna_sequence":{"accession":"GU295656.1","fmin":"1047","fmax":"1296","strand":"+","sequence":"ATGGACCAAGGTAGCAATGAAGTCGGTAATCCAGTTGCGGGCCAGTTTTCGTTCCCATCGAACGCCGCGTTTAGTATGGGAGATCGCGTGCGCAAGAAATCGGGCGCCGCTTGGCAAGGTCAGATTGTCGGGTGGTACTGCACAAAGTTGACCCCTGAAGGCTACGCTGTCGAGTCTGAGGCTCACCCTGGCTCGGTACAGATTTATCCTGTTGCGGCGCTTGAACGCATCAACGGAGTTCAAGGTTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36810","NCBI_taxonomy_name":"Aeromonas hydrophila","NCBI_taxonomy_id":"644"}}}},"ARO_accession":"3004556","ARO_id":"42461","ARO_name":"dfrB7","CARD_short_name":"dfrB7","ARO_description":"A dihydrofolate reductase and trimethoprim resistance gene identified on an integron in multidrug-resistant gram-negative bacteria.","ARO_category":{"37617":{"category_aro_accession":"3001218","category_aro_cvterm_id":"37617","category_aro_name":"trimethoprim resistant dihydrofolate reductase dfr","category_aro_description":"Alternative dihydropteroate synthase dfr present on plasmids produces alternate proteins that are less sensitive to trimethoprim from inhibiting its role in folate synthesis, thus conferring trimethoprim resistance.","category_aro_class_name":"AMR Gene Family"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3267":{"model_id":"3267","model_name":"Clostridioides difficile murG with mutation conferring resistance to vancomycin","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"8659":"P108L"},"Curated-R":{"8659":"P108L"},"clinical":{"8659":"P108L"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"5317":{"protein_sequence":{"accession":"AAK80188.1","sequence":"MKKLKIVMTGGGSAGHVTPNLALVPKLKELGYEIEYIGTKDGIERSIIEKENIKYNCISSGKLRRYIDIKNFSDPFKVILGIFQSVSILRKKKPNIVFSKGGFVSVPVVIAAHFCRIPVIAHESDITPGLANRIAVPYCTKVCATFPESLNNIKGNKGILTGTPIRDELFKGSKIKGLEICGFTGEKPVLMIIGGSLGSKIINDTVREALNKLIKKYDIVHICGKGNIDEALSKLKGYKQFDYISTELPHVMNAADLVISRAGANAIFELLALKKPNLLIPLSKKSSRGDQILNAMSFEKNGYSMVVQEDDLTPTLLVEKVIKLESDKEKYKKAMNSSPVKNGVENIIKVIDKYKKCKI"},"dna_sequence":{"accession":"AE001437.1","fmin":"2323780","fmax":"2324860","strand":"-","sequence":"ATGAAAAAACTGAAAATAGTAATGACGGGTGGAGGTTCTGCTGGACATGTTACCCCTAATTTAGCACTTGTGCCAAAACTAAAGGAGCTAGGATACGAAATAGAGTATATAGGAACAAAGGATGGGATAGAAAGAAGTATAATTGAAAAAGAAAATATAAAGTATAATTGTATATCCAGTGGAAAATTAAGAAGATATATTGATATTAAAAATTTTTCAGATCCTTTTAAGGTTATTTTAGGGATATTTCAATCTGTTAGTATATTAAGGAAGAAAAAGCCTAACATAGTCTTTTCTAAAGGAGGTTTTGTGTCAGTTCCTGTGGTTATAGCAGCACATTTTTGCAGAATACCGGTAATAGCTCATGAATCAGATATAACACCTGGACTTGCAAATAGGATAGCAGTTCCTTACTGCACAAAAGTTTGTGCTACATTTCCAGAATCTCTTAACAATATAAAAGGGAATAAGGGAATATTAACAGGTACTCCTATACGAGATGAGTTATTTAAGGGAAGTAAAATTAAGGGACTTGAAATATGTGGATTTACAGGTGAGAAGCCAGTACTTATGATTATAGGTGGAAGTTTAGGATCAAAGATTATAAATGATACAGTTCGTGAAGCTTTAAATAAGCTTATAAAAAAATATGATATAGTTCATATTTGTGGAAAGGGAAATATAGATGAAGCTTTAAGTAAACTTAAGGGGTATAAGCAATTTGACTATATATCAACTGAACTTCCTCATGTAATGAATGCTGCAGATTTAGTTATTTCAAGAGCAGGGGCTAATGCTATTTTTGAGCTTTTAGCATTAAAAAAGCCTAATTTATTGATCCCATTATCTAAAAAATCAAGCAGGGGAGATCAGATTTTAAATGCTATGTCATTTGAAAAAAATGGTTACAGTATGGTGGTTCAGGAAGATGACTTAACACCAACGTTGCTTGTAGAGAAGGTCATTAAACTTGAAAGCGATAAGGAAAAATACAAGAAAGCTATGAATTCAAGTCCTGTAAAAAATGGTGTGGAAAATATAATTAAAGTTATTGATAAATATAAAAAATGTAAAATATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42468","NCBI_taxonomy_name":"Clostridium acetobutylicum ATCC 824","NCBI_taxonomy_id":"272562"}}}},"ARO_accession":"3004561","ARO_id":"42467","ARO_name":"Clostridioides difficile murG with mutation conferring resistance to vancomycin","CARD_short_name":"Cdif_murG_VAN","ARO_description":"Mutations in murG which confer resistance to vancomycin in Clostridioides difficile.","ARO_category":{"42466":{"category_aro_accession":"3004560","category_aro_cvterm_id":"42466","category_aro_name":"murG transferase","category_aro_description":"murG acetylglucosaminyltransferase enzymes inhibited by vancomycin. Mutations in murG confer resistance to vancomycin through antibiotic target alteration.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3266":{"model_id":"3266","model_name":"CAM-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"5123":{"protein_sequence":{"accession":"AVX51087.1","sequence":"MKSTAIILFLLVFSLGVFGQTGDALKISQLSGDFYIFTTYQTYKDAKVSANGMYVVTDEGVVLIDTPWDETQLQPLLNYIKEKHNKDVVMSVSTHFHEDRTNGIEFLRTKGVKTYTTKKTDELSQKKGYERAEFLLEKDTEFKIGQYKFQTYYPGEGHAPDNIVVWFPNERILYGGCFIKSTEAEDIGNLSDANIDEWSNSIKNVQKKFKNPKFVIPGHDGWASTKSLKHTLKLIKKTRKK"},"dna_sequence":{"accession":"MG430339.1","fmin":"67103","fmax":"67829","strand":"+","sequence":"ATGAAATCAACTGCAATTATTTTATTTTTACTCGTTTTTTCGCTCGGCGTTTTCGGGCAAACGGGCGATGCGCTGAAAATCTCTCAACTGTCGGGCGATTTTTATATTTTTACGACTTATCAAACCTATAAAGACGCAAAAGTTTCCGCCAACGGAATGTATGTCGTGACCGACGAAGGCGTTGTTTTGATCGACACGCCGTGGGATGAAACTCAGCTTCAGCCGCTTCTCAATTACATCAAGGAAAAGCACAACAAGGATGTCGTGATGAGCGTTTCGACGCATTTTCACGAAGACCGCACGAACGGCATCGAATTTTTGAGGACAAAAGGCGTGAAAACCTACACGACCAAGAAAACCGACGAGCTTTCGCAGAAAAAAGGTTACGAACGCGCCGAATTTTTGCTCGAAAAAGACACGGAATTCAAGATCGGGCAATACAAATTTCAAACCTACTATCCCGGCGAAGGTCACGCGCCCGACAATATCGTGGTCTGGTTTCCGAACGAAAGAATTCTTTACGGCGGTTGTTTCATAAAAAGCACCGAAGCCGAAGACATCGGGAATTTGTCCGATGCAAATATCGATGAATGGTCAAACTCGATCAAAAACGTGCAGAAAAAATTCAAGAACCCGAAATTCGTAATTCCCGGTCACGACGGATGGGCAAGCACGAAATCACTCAAACACACATTAAAACTTATCAAGAAAACCCGTAAAAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3004559","ARO_id":"42465","ARO_name":"CAM-1","CARD_short_name":"CAM-1","ARO_description":"CAM-1 is a CAM (Central Alberta Metallo) beta-lactamase and carbapenemase identified from 4 clinical isolates of Pseudomonas aeruginosa from a Canadian hospital.","ARO_category":{"42464":{"category_aro_accession":"3004558","category_aro_cvterm_id":"42464","category_aro_name":"CAM beta-lactamase","category_aro_description":"CAM (Central Alberta Metallo) beta-lactamases are class B metallo-beta-lactamases and carbapenemases found to confer resistance to broad spectrum antibiotics in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35927":{"category_aro_accession":"0000008","category_aro_cvterm_id":"35927","category_aro_name":"cefoxitin","category_aro_description":"Cefoxitin is a cephamycin antibiotic often grouped with the second generation cephalosporins. Cefoxitin is bactericidal and acts by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. Cefoxitin's 7-alpha-methoxy group and 3' leaving group make it a poor substrate for most beta-lactamases.","category_aro_class_name":"Antibiotic"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"35990":{"category_aro_accession":"0000073","category_aro_cvterm_id":"35990","category_aro_name":"meropenem","category_aro_description":"Meropenem is an ultra-broad spectrum injectable antibiotic used to treat a wide variety of infections, including meningitis and pneumonia. It is a beta-lactam and belongs to the subgroup of carbapenem, similar to imipenem and ertapenem.","category_aro_class_name":"Antibiotic"},"36309":{"category_aro_accession":"3000170","category_aro_cvterm_id":"36309","category_aro_name":"imipenem","category_aro_description":"Imipenem is a broad-spectrum antibiotic and is usually taken with cilastatin, which prevents hydrolysis of imipenem by renal dehydropeptidase-I. It is resistant to hydrolysis by most other beta-lactamases. Notable exceptions are the KPC beta-lactamases and Ambler Class B enzymes.","category_aro_class_name":"Antibiotic"},"36984":{"category_aro_accession":"3000640","category_aro_cvterm_id":"36984","category_aro_name":"doripenem","category_aro_description":"Doripenem is a carbapenem with a broad range of activity against Gram-positive and Gram-negative bacteria, and along with meropenem, it is the most active beta-lactam antibiotic against Pseudomonas aeruginosa. It inhibits bacterial cell wall synthesis.","category_aro_class_name":"Antibiotic"},"36989":{"category_aro_accession":"3000645","category_aro_cvterm_id":"36989","category_aro_name":"cefotaxime","category_aro_description":"Cefotaxime is a semisynthetic cephalosporin taken parenterally. It is resistant to most beta-lactamases and active against Gram-negative rods and cocci due to its aminothiazoyl and methoximino functional groups.","category_aro_class_name":"Antibiotic"},"40636":{"category_aro_accession":"3003927","category_aro_cvterm_id":"40636","category_aro_name":"ceftolozane","category_aro_description":"Ceftolozane is a fifth-generation cephalosporin antibiotic developed for the treatment of infections with gram-negative bacteria that have become resistant to conventional antibiotics.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3270":{"model_id":"3270","model_name":"dfrA18","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"5832":{"protein_sequence":{"accession":"AAK64581.1","sequence":"MNKEIQFSMIVARGVNGEIGQDGDLPWHVEGVRLKEDLKRFKAITMGKTLVMGRKTFESIPNGLPGRNVIVLTREPYDKADITERGDGTFVAWGNSCHLFEVAEHLGVTEIIVAGGAEIYNLHKDVITKVFETKVLRAYPAADTHVDVFWESPGYDTEGRQWRVTSRGHIIENGSFTIATTYER"},"dna_sequence":{"accession":"AY034138.1","fmin":"7412","fmax":"7967","strand":"-","sequence":"ATGAATAAAGAAATTCAATTTTCAATGATTGTAGCGCGTGGTGTAAACGGTGAGATTGGTCAGGACGGCGACTTGCCTTGGCATGTCGAAGGAGTTCGGTTGAAAGAAGACCTCAAACGCTTCAAAGCGATCACTATGGGTAAGACACTCGTCATGGGCAGAAAGACCTTTGAGAGCATCCCCAATGGCCTGCCCGGACGCAACGTCATCGTGCTCACACGCGAGCCTTACGATAAAGCGGATATAACCGAACGTGGAGACGGCACCTTTGTAGCGTGGGGGAATAGCTGCCATCTGTTTGAAGTGGCCGAACACCTGGGCGTTACTGAGATCATCGTGGCGGGCGGTGCTGAAATCTATAATCTGCACAAAGACGTCATTACGAAGGTTTTTGAAACGAAGGTGTTGAGGGCGTATCCTGCAGCGGATACTCACGTAGACGTATTCTGGGAAAGTCCCGGATACGACACTGAAGGCCGACAATGGCGCGTAACGTCCAGAGGCCACATTATCGAAAACGGCAGTTTCACTATCGCGACGACGTATGAGCGATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39556","NCBI_taxonomy_name":"Vibrio cholerae MO10","NCBI_taxonomy_id":"345072"}}}},"ARO_accession":"3004568","ARO_id":"42475","ARO_name":"dfrA18","CARD_short_name":"dfrA18","ARO_description":"A trimethoprim-resistant dihydrofolate reductase identified from Vibrio cholerae.","ARO_category":{"37617":{"category_aro_accession":"3001218","category_aro_cvterm_id":"37617","category_aro_name":"trimethoprim resistant dihydrofolate reductase dfr","category_aro_description":"Alternative dihydropteroate synthase dfr present on plasmids produces alternate proteins that are less sensitive to trimethoprim from inhibiting its role in folate synthesis, thus conferring trimethoprim resistance.","category_aro_class_name":"AMR Gene Family"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3271":{"model_id":"3271","model_name":"ICR-Mo","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"5132":{"protein_sequence":{"accession":"WP_082741435.1","sequence":"MVHLDKVSNRMSVNNSRWLAWRQQGINAYVMMGIVALFLTLTANITFFDKATEVYPFAQHIGFIGSLPLVLFGVMLLVIVLLSYRYTLKAVLIFLLLTAAVTAYFTDTYGTVYDVNMLQNALQTDKAESADLFNVNFILRILLLGVLPSVWVAWQKVTFPPIKRSILQRGLTYLVSLGLVVLPILAMSKNYASFFREHKQLRSYTNPATPVYALGKLASIQLKQAQAPKTQIMHATDAVQVSNPTTRKPKLVVFVVGETARGDHVQLNGYNRTTFPQMAATAGVTNFNQVIACGTSTAYSVPCMFSYVGMKDYDVDTANYQENVLDTLHRLKVNILWRDNNSSSKGVTNRLPAADFVDYKTARNNTMCNTNPYGECRDVGMLVGLDDYVKQQANQNTLNQDTLIVLHQMGNHGPAYFKRYDKQFEKFTPVCQSNELAKCDPQSVINAFDNALLATDDFLAKTVNWLDKYDSTHQVAMLYVSDHGESLGENGIYLHGMPYKIAPKAQKHVASMFWAGKHSGIQAVPSNTELTHDAITPTLLKLFDVRAQTVQGKPLFIK"},"dna_sequence":{"accession":"NZ_CP014234.1","fmin":"1701629","fmax":"1703306","strand":"+","sequence":"TTGGTGCATTTAGATAAGGTGAGTAATCGTATGTCAGTGAATAACTCTCGATGGTTAGCATGGCGTCAGCAAGGTATTAATGCTTATGTGATGATGGGTATTGTCGCGCTATTTTTGACCCTAACCGCCAATATTACTTTCTTTGATAAAGCCACGGAAGTCTATCCGTTTGCCCAGCATATTGGGTTTATAGGCTCATTGCCGTTGGTGCTATTCGGTGTCATGCTACTGGTTATTGTGCTGCTCAGCTATCGTTACACCCTTAAAGCGGTATTGATTTTTTTGCTATTGACCGCGGCAGTCACGGCGTATTTTACTGATACTTATGGCACTGTCTATGATGTCAATATGCTACAAAACGCGCTACAAACCGATAAAGCAGAAAGCGCCGATTTGTTTAACGTCAATTTTATCTTACGCATTTTATTGCTTGGGGTATTGCCTAGTGTGTGGGTGGCGTGGCAAAAGGTCACATTTCCCCCCATCAAGCGCAGCATATTGCAGCGCGGCTTGACGTATTTGGTCAGCCTCGGTTTGGTAGTGTTACCGATTTTGGCAATGAGTAAAAATTACGCCAGTTTTTTCCGTGAACATAAACAGCTTCGTAGCTATACCAATCCTGCAACCCCTGTATATGCACTGGGTAAACTTGCCAGTATACAGCTCAAACAAGCACAAGCTCCCAAAACCCAAATCATGCATGCCACCGATGCGGTGCAGGTGAGTAATCCTACCACCCGTAAGCCAAAACTGGTGGTATTTGTAGTTGGAGAAACCGCGCGCGGCGACCATGTGCAGCTAAATGGGTATAACCGAACTACCTTCCCGCAGATGGCAGCGACGGCTGGGGTAACTAATTTTAACCAAGTCATCGCCTGCGGTACCTCAACCGCTTATTCGGTGCCTTGTATGTTTAGTTATGTCGGCATGAAAGACTACGATGTGGATACCGCCAACTACCAAGAAAACGTACTTGATACCTTACATCGCCTAAAGGTTAATATCTTGTGGCGTGATAACAACTCAAGCTCAAAAGGCGTCACTAATCGTTTGCCCGCGGCGGATTTTGTCGATTATAAAACTGCGCGCAACAATACGATGTGTAATACCAACCCCTATGGCGAGTGCCGCGATGTGGGTATGCTAGTAGGCTTAGATGACTACGTCAAACAACAAGCTAACCAAAATACGCTTAACCAGGATACCCTAATTGTGCTGCACCAAATGGGTAATCACGGACCTGCGTATTTTAAACGATATGATAAGCAATTTGAAAAATTCACCCCAGTCTGCCAAAGCAATGAACTTGCCAAATGCGACCCACAAAGCGTGATTAATGCCTTTGACAATGCGCTACTTGCCACCGATGACTTTTTGGCAAAAACGGTGAACTGGTTAGACAAATATGACAGCACCCACCAAGTAGCGATGCTGTATGTCAGTGACCACGGTGAAAGTCTGGGCGAAAACGGCATCTATTTACATGGTATGCCTTATAAAATCGCGCCTAAAGCGCAAAAACACGTCGCATCGATGTTTTGGGCAGGTAAACACTCAGGCATTCAAGCAGTGCCATCTAATACTGAGCTCACCCATGATGCCATTACCCCAACCTTGTTAAAACTGTTTGATGTGCGTGCGCAAACCGTACAAGGCAAACCTTTATTTATCAAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42478","NCBI_taxonomy_name":"Moraxella osloensis","NCBI_taxonomy_id":"34062"}}}},"ARO_accession":"3004569","ARO_id":"42477","ARO_name":"ICR-Mo","CARD_short_name":"ICR-Mo","ARO_description":"A chromosomally-encoded colistin resistance phosphoethanolamine (PEtN) transferase of Moraxella osloensis. ICR-Mo represents the closest known ortholog to the colistin resistance MCR-1 and MCR-2 PEtN transferases.","ARO_category":{"41681":{"category_aro_accession":"3004465","category_aro_cvterm_id":"41681","category_aro_name":"intrinsic colistin resistant phosphoethanolamine transferase","category_aro_description":"Chromosomally-encoded phosphoethanolamine (PEtN) transferases shown to confer resistance to polymyxin antibiotics, including colistin.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3272":{"model_id":"3272","model_name":"PNGM-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"5133":{"protein_sequence":{"accession":"AWN09461.1","sequence":"MAGGKVTSSTGIAPKRYVYYPGSEELGPDEIRVIACGTGMPTARRAQAAAAWVVELGNGDKFIVDIGSGSMANIQSLMIPANYLTKIFLTHLHTDHWGDLVSMWAGGWTAGRTDPLEVWGPSGSREDMGTKYAVEHMLKAYNWDYMTRAVTINPRPGDINVHEFDYRALNEVVYQENGVTFRSWPCIHAGDGPVSFALEWNGYKVVFGGDTAPNIWYPEYAKGADLAIHECWMTSDQMMTKYNQPAQLALRINLDFHTSAQSFGQIMNMVQPRHAVAYHFFNDDDTRYDIYTGVRENYAGPLSMATDMMVWNITRDAVTERMAVSPDHAWDVAGPSEDLAPDRNRASEYTQYILDGRLNVDEANAHWKQEFMGRTGLTTEDLGVGS"},"dna_sequence":{"accession":"MF445022.1","fmin":"0","fmax":"1161","strand":"+","sequence":"ATGGCAGGTGGAAAAGTAACCTCATCAACAGGTATCGCACCCAAACGGTACGTCTATTATCCAGGCAGTGAAGAATTGGGGCCCGATGAGATTCGGGTTATTGCTTGTGGCACAGGCATGCCTACGGCGCGTCGTGCTCAAGCAGCGGCCGCCTGGGTGGTAGAGCTAGGCAACGGTGACAAATTCATCGTCGACATTGGCAGCGGCTCAATGGCCAACATCCAATCGTTGATGATCCCGGCTAATTATTTGACCAAGATTTTTCTGACGCATTTGCACACCGACCACTGGGGCGACCTGGTGTCTATGTGGGCAGGCGGTTGGACAGCCGGGCGCACGGATCCGTTAGAGGTATGGGGACCAAGCGGTTCACGCGAAGATATGGGCACAAAGTACGCCGTCGAGCACATGCTCAAGGCGTACAATTGGGACTATATGACACGAGCCGTGACGATTAATCCCCGCCCCGGAGATATCAATGTTCACGAGTTCGACTATCGTGCCCTCAACGAGGTTGTCTATCAAGAGAACGGCGTCACTTTCCGCTCCTGGCCCTGTATTCACGCGGGAGACGGACCGGTCAGCTTTGCCCTAGAGTGGAATGGCTACAAGGTGGTTTTTGGCGGAGACACCGCCCCCAATATTTGGTACCCAGAATACGCCAAGGGTGCTGACCTGGCGATCCATGAGTGCTGGATGACCTCCGATCAAATGATGACAAAATATAACCAGCCGGCACAGCTTGCACTGCGCATCAATCTGGACTTTCACACCTCAGCGCAATCCTTTGGCCAGATTATGAATATGGTGCAGCCACGCCATGCCGTAGCCTATCACTTTTTCAACGATGATGACACGCGGTACGATATCTATACTGGCGTAAGAGAGAACTATGCCGGTCCCCTTTCAATGGCTACCGACATGATGGTGTGGAATATCACTCGAGACGCAGTCACCGAGCGTATGGCTGTCTCGCCGGATCATGCGTGGGATGTGGCAGGTCCTTCCGAAGATCTGGCGCCAGATCGGAATAGAGCCTCGGAGTACACGCAGTATATCCTCGACGGCCGTCTCAATGTCGACGAGGCCAATGCCCATTGGAAGCAGGAGTTCATGGGTCGTACTGGATTAACGACCGAGGATTTGGGAGTGGGAAGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36791","NCBI_taxonomy_name":"uncultured bacterium","NCBI_taxonomy_id":"77133"}}}},"ARO_accession":"3004571","ARO_id":"42480","ARO_name":"PNGM-1","CARD_short_name":"PNGM-1","ARO_description":"PNGM-1 is a subclass B3 metallo-beta-lactamase first identified from a deep-sea sediment meta-genome. PNGM-1 is shown to reduce susceptibility to extended- and broad-spectrum cephalosporins, carbapenems, and penicillins. PNGM-1 is a novel metallo-beta-lactamase which predates the current antibiotic era.","ARO_category":{"42479":{"category_aro_accession":"3004570","category_aro_cvterm_id":"42479","category_aro_name":"PNGM beta-lactamase","category_aro_description":"PNGM is a family of metallo-beta-lactamases first identified from a deep-sea sediment metagenome and shown to reduce antibiotic susceptibility by hydrolysis of penicillins, carbapenems and extended- and broad-spectrum cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3277":{"model_id":"3277","model_name":"Acinetobacter baumannii AbaF","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"5139":{"protein_sequence":{"accession":"ABO11759.2","sequence":"MTTTLKKVVAASMVGSVAEWYEFFLYGTASALVFGELFFQQTGNAIDGILAAFALYAVGFLARPLGGLVFGHYGDKIGRKKLLQISLIIVGITTFLMGCIPTFHQIGYWAPTLLVILRLIQGFAFGGEWGGAVILVSEHSPDDRRGYWASWPQTGVPLGNLVATLVLLLLSKNLSPEQFLDWGWRCAFWFSAVVVLIGLWIRKNVDDAEVFKEAQAKQQLLEKQQLGIIEVLKYHKKSVIAGIGARFAENILYYMVVTFSISYLKLVVHKDTSQILLLMFGAHLIHFFIIPFMGHLSDIFGRKPIYLIGAVLTAFWGFVGFPLMDTGNDWLIMLAIVLGLFIESMTYSPYSALMTELFPTHIRYTALSFCYQVAPIMAGSLAPLIALTLLKEFNSSIPISLYLVAASLISIVSILLVKETKGRSLAFKD"},"dna_sequence":{"accession":"CP000521.1","fmin":"1557233","fmax":"1558523","strand":"-","sequence":"ATGACGACAACACTAAAAAAGGTAGTCGCGGCCTCTATGGTCGGCTCCGTAGCAGAATGGTATGAATTTTTCCTTTATGGCACCGCTTCTGCCCTCGTCTTTGGCGAACTTTTCTTTCAACAAACTGGCAATGCTATAGATGGAATTTTGGCGGCCTTTGCTCTGTATGCCGTTGGCTTTTTAGCAAGACCTCTCGGTGGCCTCGTGTTTGGTCACTACGGCGATAAAATTGGGCGCAAGAAATTATTGCAAATTAGCCTGATCATTGTCGGTATCACTACTTTTTTAATGGGCTGTATTCCGACCTTTCATCAAATTGGCTATTGGGCTCCTACACTCCTAGTGATATTACGTTTAATTCAAGGTTTTGCTTTTGGTGGTGAATGGGGCGGCGCAGTTATTTTAGTTTCAGAGCACAGTCCAGATGATCGCAGAGGTTATTGGGCAAGCTGGCCACAAACTGGTGTACCGCTCGGAAATTTAGTAGCCACACTGGTTTTATTATTACTTTCAAAAAACCTCTCACCCGAACAATTTCTAGATTGGGGGTGGCGCTGTGCATTCTGGTTCTCAGCAGTCGTGGTACTGATTGGTTTATGGATTCGAAAAAATGTAGACGATGCCGAAGTGTTTAAAGAAGCACAGGCCAAACAACAGCTTCTTGAAAAGCAACAACTCGGGATTATTGAGGTTTTAAAATATCATAAGAAATCTGTTATTGCGGGTATCGGTGCCAGATTTGCAGAAAATATTTTGTACTATATGGTGGTTACTTTTTCGATCAGTTATTTAAAGTTAGTCGTCCATAAAGATACTTCGCAGATCTTACTGCTCATGTTCGGCGCTCATCTGATCCATTTCTTTATTATTCCTTTTATGGGGCATTTAAGCGATATATTTGGCCGTAAACCTATTTACCTTATTGGGGCTGTACTTACTGCTTTTTGGGGTTTTGTCGGCTTTCCTTTAATGGATACAGGCAATGACTGGCTCATTATGTTAGCAATTGTGCTTGGTTTATTTATTGAGTCCATGACCTACTCGCCTTACTCTGCGTTAATGACTGAGTTATTTCCAACTCACATCCGCTATACGGCGCTTTCATTTTGTTATCAAGTCGCACCCATTATGGCAGGTTCGCTTGCTCCATTAATTGCCCTAACATTACTCAAAGAATTTAATAGTTCGATTCCGATTTCTTTATATTTGGTTGCCGCAAGTCTGATTTCTATTGTCTCGATTTTGCTGGTGAAAGAAACCAAAGGCCGATCTCTAGCTTTTAAAGATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35522","NCBI_taxonomy_name":"Acinetobacter baumannii ATCC 17978","NCBI_taxonomy_id":"400667"}}}},"ARO_accession":"3004573","ARO_id":"42487","ARO_name":"Acinetobacter baumannii AbaF","CARD_short_name":"Abau_AbaF","ARO_description":"Expression of abaF in E. coli resulted in increased resistance to fosfomycin.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35944":{"category_aro_accession":"0000025","category_aro_cvterm_id":"35944","category_aro_name":"fosfomycin","category_aro_description":"Fosfomycin (also known as phosphomycin and phosphonomycin) is a broad-spectrum antibiotic produced by certain Streptomyces species. It is effective on gram positive and negative bacteria as it targets the cell wall, an essential feature shared by both bacteria. Its specific target is MurA (MurZ in E.coli), which attaches phosphoenolpyruvate (PEP) to UDP-N-acetylglucosamine, a step of commitment to cell wall synthesis. In the active site of MurA, the active cysteine molecule is alkylated which stops the catalytic reaction.","category_aro_class_name":"Antibiotic"},"45731":{"category_aro_accession":"3007149","category_aro_cvterm_id":"45731","category_aro_name":"phosphonic acid antibiotic","category_aro_description":"A group of antibiotics derived from phosphonic acids.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"3278":{"model_id":"3278","model_name":"Acinetobacter baumannii AbaQ","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"5314":{"protein_sequence":{"accession":"ACJ41547.2","sequence":"MDFEKDVIRTVTFKLIPALVILYLVAYIDRAAVGFAHLHMGADVGIGDAAYGLGAGLFFIGYFLFEVPSNLLLDKFGARKWFTRILLTWGLITMAMALIQGPKSFYLLRFLLGVAEAGFFPGVLYLITQWYPVRHRGKIMGMFVLSQPIAMMIAGPLAGLLLGMDGIANLHGWQWLFVAVGLPAVLLALPTFLWLPDNIDKVKWLSIEQKQWLKNELVKDEAEYDQTRHANPLHALKDKRVLLLALYYLPVTLSIYGLNLWLPTIIKQFGGGSDIQIGFLSSIPYIFGIIGLLIIPRSTDRLNDRYGHLSFLYALGACAMFLSGWLNSPVMQLAALAVVAFCLFSSTAVFWTLPGRFLTGASAAAGIALINSVGNLGGYVGPFGIGLLKEYTGNMAAGLYFLSIVMLFGLILTYIVYAKLERQKTQTVNIQKPL"},"dna_sequence":{"accession":"CP001182.2","fmin":"2255584","fmax":"2256889","strand":"-","sequence":"ATGGATTTCGAAAAGGATGTAATACGGACAGTCACGTTTAAGCTGATACCTGCATTAGTCATACTATATCTGGTGGCATACATTGATCGGGCCGCTGTCGGGTTTGCCCATCTGCATATGGGTGCCGATGTAGGAATTGGTGATGCTGCCTATGGCCTAGGAGCTGGCTTATTTTTTATTGGATATTTTCTTTTTGAAGTTCCAAGTAATTTGCTTTTAGACAAATTTGGTGCTCGTAAATGGTTTACCCGCATTTTATTAACATGGGGCCTCATCACCATGGCCATGGCGCTTATTCAAGGCCCTAAAAGTTTTTATCTCTTAAGGTTTTTACTCGGTGTAGCAGAGGCGGGTTTTTTCCCTGGTGTTTTATACCTAATTACGCAGTGGTATCCGGTGCGGCATCGCGGAAAAATTATGGGAATGTTTGTGCTTTCACAACCGATTGCCATGATGATTGCAGGGCCTTTAGCTGGTCTATTACTTGGAATGGATGGCATTGCAAATTTGCACGGCTGGCAATGGTTGTTTGTTGCAGTTGGCTTGCCCGCAGTTTTATTAGCTTTACCTACATTTCTGTGGCTGCCAGATAACATTGATAAAGTAAAATGGTTAAGCATTGAACAAAAACAATGGCTTAAAAATGAACTCGTTAAAGATGAAGCCGAATATGACCAAACCCGACATGCCAATCCACTACATGCTTTAAAAGACAAACGCGTACTTTTATTAGCACTTTACTACTTACCGGTAACTTTAAGTATTTATGGTTTAAATCTCTGGCTTCCTACCATTATTAAGCAATTTGGCGGAGGTAGTGATATTCAAATTGGGTTCTTATCTAGCATTCCCTATATTTTTGGAATTATTGGACTTCTCATTATTCCGCGTAGTACTGACCGCCTGAACGATCGTTACGGACACTTAAGTTTTCTGTATGCACTAGGTGCTTGTGCAATGTTTTTAAGTGGTTGGCTAAATTCTCCAGTTATGCAGTTGGCAGCTTTGGCTGTAGTTGCGTTCTGTCTATTTTCATCGACTGCCGTGTTTTGGACATTACCGGGTCGTTTCTTAACGGGTGCAAGTGCAGCGGCTGGTATCGCCTTAATTAACTCTGTTGGAAATTTAGGTGGCTATGTCGGTCCATTTGGCATCGGACTTTTAAAAGAATACACGGGAAATATGGCTGCTGGTTTGTATTTCTTATCTATCGTCATGCTTTTTGGCTTGATTCTGACTTACATCGTCTATGCCAAGCTCGAACGTCAAAAAACACAAACAGTGAATATTCAAAAGCCTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35531","NCBI_taxonomy_name":"Acinetobacter baumannii AB0057","NCBI_taxonomy_id":"480119"}}}},"ARO_accession":"3004574","ARO_id":"42490","ARO_name":"Acinetobacter baumannii AbaQ","CARD_short_name":"Abau_AbaQ","ARO_description":"AbaQ is an MFS transporter mainly involved in the extrusion of quinolone-type drugs in A. baumannii.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"3280":{"model_id":"3280","model_name":"Acinetobacter baumannii AmvA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"5144":{"protein_sequence":{"accession":"ACQ82816.1","sequence":"MQKKWLILTIIVLIYLPVTIDATVMHVATPSLSAALNLTANQLLWIIDIYSLIMAGLILPMGALGDRIGFKKLLFIGTAVFGVGSLAAAFSPTAYALIASRAILGLGAAMLIPATLSGIRNAFTEEKQRNFALGIWSTVGGGGAAFGPLVGGFVLEHFHWGAVFLINIPIILAVLVMIVMIIPKQQEKTDQPINLGQALVLVVAILSLIYSIKSAMYNFSVLTVVMFVVGISTLIHFIRSQKRATTPMIDLELFKHPVISTSIVMAVVSMIALVGFELLLSQELQFVHGFSPLQAAMFIIPFMIAISLGGPLAGICLNKWGLRRVSSLGILVSALSLWGLAQLNFSTDHFLAWTCMVFLGFSIEIALLASTAAIMSSVPPQKASAAGAIEGMAYELGAGLGVAIFGLMLSWFYSRSIILPAELPSNLIEKASISIGETMQLASNLENPLGGQLIVVAQQAFSYAHSWVLTLSAICFFLLTVFVWFSFPKKVN"},"dna_sequence":{"accession":"FJ911554.1","fmin":"176","fmax":"1655","strand":"+","sequence":"ATGCAAAAAAAATGGTTAATCCTGACAATTATCGTCCTCATTTATTTACCAGTTACGATTGATGCAACGGTGATGCATGTTGCAACACCATCTTTAAGTGCAGCATTGAATTTAACTGCCAATCAGCTTTTATGGATTATTGATATTTATTCGCTGATTATGGCGGGTTTGATTTTGCCGATGGGTGCACTCGGTGATCGTATTGGCTTTAAAAAATTATTATTTATTGGAACCGCAGTTTTTGGTGTGGGTTCGTTAGCTGCGGCTTTTTCTCCAACTGCCTATGCCTTAATTGCTTCTCGTGCTATTTTAGGCCTAGGGGCAGCTATGCTTATTCCTGCCACTTTATCCGGTATCCGTAATGCTTTTACCGAAGAAAAGCAGAGAAATTTTGCACTTGGTATTTGGTCTACAGTAGGTGGAGGTGGAGCAGCTTTTGGTCCATTAGTCGGTGGTTTTGTATTAGAACACTTCCATTGGGGAGCTGTATTCCTCATTAATATCCCGATTATTTTAGCCGTTCTAGTTATGATCGTGATGATCATTCCTAAACAACAAGAGAAAACTGATCAGCCAATTAACTTAGGGCAAGCTTTAGTTTTGGTTGTAGCAATTTTAAGCCTCATCTATTCAATTAAATCGGCTATGTATAACTTTTCGGTGCTCACGGTTGTGATGTTTGTGGTGGGTATAAGCACATTAATTCACTTCATTCGAAGCCAAAAAAGAGCTACGACACCAATGATTGATCTGGAGTTATTTAAACATCCAGTAATTTCTACAAGTATTGTTATGGCTGTTGTTTCCATGATTGCTTTGGTTGGCTTTGAATTATTACTGTCTCAAGAGTTGCAGTTTGTACACGGGTTTTCTCCATTACAGGCGGCGATGTTTATTATTCCATTTATGATTGCAATTAGTTTAGGTGGTCCATTAGCAGGTATTTGTTTAAATAAATGGGGTTTACGTAGAGTATCGAGCCTAGGTATTTTAGTGAGCGCGCTCAGTTTATGGGGGCTTGCTCAGCTTAATTTTTCAACCGACCACTTTTTAGCATGGACATGTATGGTCTTTTTGGGCTTTAGCATTGAGATTGCCTTACTTGCCTCAACTGCTGCCATTATGTCATCTGTGCCCCCTCAAAAGGCGAGTGCAGCAGGTGCTATTGAGGGAATGGCCTATGAGCTTGGCGCTGGCTTAGGTGTTGCTATTTTTGGTTTAATGTTGTCTTGGTTTTATAGCCGCTCAATTATTTTGCCAGCCGAGCTTCCGTCAAACTTAATTGAAAAAGCGAGTATCTCGATTGGAGAAACCATGCAATTAGCCTCTAATCTTGAAAATCCTTTAGGAGGGCAATTAATTGTAGTGGCGCAGCAAGCTTTTAGCTATGCCCATAGTTGGGTACTTACCCTCTCAGCGATCTGTTTCTTCCTTTTAACTGTATTTGTCTGGTTTAGTTTTCCGAAGAAAGTAAATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3004577","ARO_id":"42497","ARO_name":"Acinetobacter baumannii AmvA","CARD_short_name":"Abau_AmvA","ARO_description":"AmvA has 14 alpha-helical transmembrane segments, qualifying it as a member of the DHA2 transporter family of the major facilitator superfamily (MFS). When AmvA was expressed in E. coli,  the cells had at least four-fold decreased susceptibility to erythromycin, acridine orange, acriflavine, deoxycholate and methyl viologen. AmvA from the AC0037 strain of A. baumannii was tested.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35963":{"category_aro_accession":"0000045","category_aro_cvterm_id":"35963","category_aro_name":"acriflavine","category_aro_description":"Acriflavine is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"43746":{"category_aro_accession":"3005386","category_aro_cvterm_id":"43746","category_aro_name":"disinfecting agents and antiseptics","category_aro_description":"Disinfectants that can also interact with antimicrobial resistance mechanisms, e.g. molecule efflux, and thus are the targets of disinfectant resistance.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"3281":{"model_id":"3281","model_name":"Acinetobacter baumannii AbuO","model_type":"protein knockout model","model_type_id":"40354","model_description":"Protein Knockout Models (PKM) reflect resistance by the absence of a gene product, most often deletion of a gene involved in antibiotic import, such as Vibrio cholerae OmpT. Like Protein Homolog Models (PHMs), PKMs include a reference sequence and a bitscore cut-off for detection using BLASTP but instead are designed to only report lack of detection under Perfect or Strict criteria. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff. This model type is still under development and not currently supported by the Resistance Gene Identifier (RGI) software.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"5148":{"protein_sequence":{"accession":"WP_001985623.1","sequence":"MKIKLMLVAGLWSFTSSSFALDLVETYERAKLNDPTWQANQQQFEADQLNLGLATGALLPTVTLSGNITRNRQTVKRSNFPGVDQEGLSDALVSNTSTTKQATLSARQPLFRMDAWEGYKQVKTSVALSEITLRLQKQDHVLNVAEAYFNVLRQQALTAAYLQEEKALLEQLNMMNAKLKEGLVARSDVSEANAQYQNARANRIATNVQLLLAQEQLTEYIGPYQDKLAVLRSDFIFQKPYPAQLDEWLGLAQQQNLKIQQARLQKRYAEDQRRVEKAALYPQIDAVASYGYTKQTPETLISTDGKFDQVGVEMNWNLFNGGRTRTSIKKASVELNKAQAQLDAAIRRANVDVKSAFMQVDTDRAKLEARKAAMDSSALVSQASKASYNEGLKSMVDVLLAQRNAFSAKQDYLNAQYDYLLNVLRLKAAVGQLGEKDLVELNSWLTYQ"},"dna_sequence":{"accession":"NC_010410.1","fmin":"3570600","fmax":"3571947","strand":"-","sequence":"ATGAAAATAAAATTAATGCTTGTTGCGGGTTTATGGAGTTTTACATCGTCGAGTTTTGCTCTAGATTTAGTTGAAACTTATGAGCGCGCAAAACTAAATGATCCGACGTGGCAAGCGAATCAACAACAGTTTGAAGCAGATCAGCTTAATTTAGGCTTAGCAACAGGCGCTTTACTACCAACAGTTACATTATCTGGAAATATTACCCGTAATCGACAAACGGTAAAGCGTTCAAATTTTCCTGGTGTTGATCAGGAAGGACTTTCCGATGCTTTGGTAAGTAATACATCGACTACCAAACAGGCTACTTTATCTGCCCGTCAGCCTCTTTTTCGTATGGATGCATGGGAAGGTTATAAACAGGTTAAAACTTCGGTTGCCCTTAGTGAAATTACTTTAAGACTGCAAAAACAAGATCATGTTTTAAATGTAGCTGAAGCCTATTTTAATGTACTGCGTCAGCAGGCACTTACCGCTGCATATTTACAAGAAGAAAAAGCCTTGCTTGAACAGCTCAATATGATGAACGCCAAGCTTAAAGAAGGGTTGGTAGCACGTAGTGATGTGAGTGAAGCAAATGCCCAATATCAAAATGCCCGAGCCAACCGTATTGCTACCAATGTGCAGCTTTTATTGGCTCAAGAGCAACTAACTGAATATATTGGTCCGTATCAAGATAAGCTTGCTGTATTGAGAAGTGATTTTATCTTTCAAAAACCTTATCCGGCACAGCTCGATGAGTGGTTAGGATTAGCCCAACAGCAAAATTTAAAGATTCAGCAAGCACGTTTACAAAAGCGATATGCTGAAGATCAACGTCGTGTGGAAAAAGCTGCACTTTATCCACAGATAGATGCAGTAGCGAGTTATGGTTATACCAAACAAACGCCCGAAACGCTGATTTCGACTGATGGGAAGTTTGATCAGGTAGGGGTAGAGATGAACTGGAACTTATTTAATGGAGGCCGGACCCGAACTTCTATTAAAAAAGCCAGTGTGGAGTTAAATAAAGCGCAAGCCCAACTTGATGCGGCCATTCGCCGTGCCAATGTCGATGTGAAAAGTGCTTTTATGCAGGTAGATACCGACCGAGCAAAGCTTGAAGCAAGAAAGGCGGCAATGGACTCTTCAGCACTTGTTTCTCAAGCTTCAAAAGCAAGTTATAACGAAGGCTTAAAAAGTATGGTCGATGTTTTATTGGCGCAGCGTAATGCTTTTTCAGCAAAACAGGATTATCTTAATGCTCAGTATGACTATTTATTAAATGTATTACGTTTAAAAGCGGCTGTAGGTCAGCTAGGAGAAAAAGATCTAGTTGAATTAAATAGCTGGTTAACGTATCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3004578","ARO_id":"42502","ARO_name":"Acinetobacter baumannii AbuO","CARD_short_name":"Abau_AbuO","ARO_description":"AbuO is akin to the TolC outer membrane efflux protein. Deletion in A. baumannii results in increased susceptibility to antibiotics including amikacin, carbenicillin, ceftriaxone, meropenem, streptomycin, and tigecycline as well as disinfectants benzyalkonium chloride and chlorhexidine.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35961":{"category_aro_accession":"0000043","category_aro_cvterm_id":"35961","category_aro_name":"carbenicillin","category_aro_description":"Carbenicillin is a semi-synthetic antibiotic belonging to the carboxypenicillin subgroup of the penicillins. It has gram-negative coverage which includes Pseudomonas aeruginosa but limited gram-positive coverage. The carboxypenicillins are susceptible to degradation by beta-lactamase enzymes. Carbenicillin antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Antibiotic"},"35979":{"category_aro_accession":"0000062","category_aro_cvterm_id":"35979","category_aro_name":"ceftriaxone","category_aro_description":"Ceftriaxone is a third-generation cephalosporin antibiotic. The presence of an aminothiazolyl sidechain increases ceftriazone's resistance to beta-lactamases. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"35990":{"category_aro_accession":"0000073","category_aro_cvterm_id":"35990","category_aro_name":"meropenem","category_aro_description":"Meropenem is an ultra-broad spectrum injectable antibiotic used to treat a wide variety of infections, including meningitis and pneumonia. It is a beta-lactam and belongs to the subgroup of carbapenem, similar to imipenem and ertapenem.","category_aro_class_name":"Antibiotic"},"40514":{"category_aro_accession":"3003823","category_aro_cvterm_id":"40514","category_aro_name":"benzalkonium chloride","category_aro_description":"Benzalkonium chloride is a type of cationic surfactant. It is an organic salt called a quaternary ammonium compound. It has three main categories of use: as a biocide, a cationic surfactant, and as a phase transfer agent.","category_aro_class_name":"Antibiotic"},"45598":{"category_aro_accession":"3007039","category_aro_cvterm_id":"45598","category_aro_name":"chlorhexidine","category_aro_description":"Chlorhexidine is a disinfectant and antiseptic that is used for skin disinfection, including mouthwashes (chlorhexidine gluconate).","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"43746":{"category_aro_accession":"3005386","category_aro_cvterm_id":"43746","category_aro_name":"disinfecting agents and antiseptics","category_aro_description":"Disinfectants that can also interact with antimicrobial resistance mechanisms, e.g. molecule efflux, and thus are the targets of disinfectant resistance.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"3283":{"model_id":"3283","model_name":"Klebsiella pneumoniae KpnE","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"150"}},"model_sequences":{"sequence":{"5313":{"protein_sequence":{"accession":"BAH63251.1","sequence":"MFYWILLALAIIAEITGTLSMKWASVSGGHTGFILMLAMIALSYIFLAFAVKKIALGVAYALWEGIGILLITLFSVLLFDESLSLLKIAGLTTLVIGIVLIKSGTQKKASSQQEVAHAAV"},"dna_sequence":{"accession":"AP006725.1","fmin":"2483889","fmax":"2484252","strand":"+","sequence":"ATGTTTTATTGGATTTTATTAGCTTTAGCAATTATTGCTGAAATTACCGGCACCTTGTCTATGAAATGGGCAAGCGTGAGCGGCGGGCACACCGGCTTTATTTTAATGCTGGCCATGATTGCCCTGTCATATATTTTTCTTGCCTTTGCGGTTAAAAAGATTGCCCTCGGTGTGGCCTATGCGTTGTGGGAAGGGATCGGTATTTTACTGATTACCCTGTTCAGCGTGCTGCTGTTTGATGAGAGTCTGTCCCTGCTGAAAATAGCCGGCTTGACCACCCTGGTGATAGGGATCGTCTTAATTAAGTCCGGCACCCAGAAAAAAGCGTCTTCACAGCAGGAGGTGGCCCATGCAGCAGTTTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42598","NCBI_taxonomy_name":"Klebsiella pneumoniae subsp. pneumoniae NTUH-K2044","NCBI_taxonomy_id":"484021"}}}},"ARO_accession":"3004580","ARO_id":"42506","ARO_name":"Klebsiella pneumoniae KpnE","CARD_short_name":"Kpne_KpnE","ARO_description":"KpnE subunit of KpnEF resembles EbrAB from E. coli. Mutation in KpnEF resulted in increased susceptibility to cefepime, ceftriaxon, colistin, erythromycin, rifampin, tetracycline, and streptomycin as well as enhanced sensitivity toward sodium dodecyl sulfate, deoxycholate, dyes, benzalkonium chloride, chlorhexidine, and triclosan.","ARO_category":{"36004":{"category_aro_accession":"0010003","category_aro_cvterm_id":"36004","category_aro_name":"small multidrug resistance (SMR) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Small multidrug resistance (SMR) proteins are a relatively small family of transporters, restricted to prokaryotic cells. They are also the smallest multidrug transporters, with only four transmembrane alpha-helices and no significant extramembrane domain.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35976":{"category_aro_accession":"0000059","category_aro_cvterm_id":"35976","category_aro_name":"cefepime","category_aro_description":"Cefepime (INN) is a fourth-generation cephalosporin antibiotic developed in 1994. It contains an aminothiazolyl group that decreases its affinity with beta-lactamases. Cefepime shows high binding affinity with penicillin-binding proteins and has an extended spectrum of activity against Gram-positive and Gram-negative bacteria, with greater activity against both Gram-negative and Gram-positive organisms than third-generation agents.","category_aro_class_name":"Antibiotic"},"35979":{"category_aro_accession":"0000062","category_aro_cvterm_id":"35979","category_aro_name":"ceftriaxone","category_aro_description":"Ceftriaxone is a third-generation cephalosporin antibiotic. The presence of an aminothiazolyl sidechain increases ceftriazone's resistance to beta-lactamases. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"37250":{"category_aro_accession":"3000870","category_aro_cvterm_id":"37250","category_aro_name":"triclosan","category_aro_description":"Triclosan is a common antibacterial agent added to many consumer products as a biocide.  It is an inhibitor of fatty acid biosynthesis by blocking enoyl-carrier protein reductase (FabI).","category_aro_class_name":"Antibiotic"},"40514":{"category_aro_accession":"3003823","category_aro_cvterm_id":"40514","category_aro_name":"benzalkonium chloride","category_aro_description":"Benzalkonium chloride is a type of cationic surfactant. It is an organic salt called a quaternary ammonium compound. It has three main categories of use: as a biocide, a cationic surfactant, and as a phase transfer agent.","category_aro_class_name":"Antibiotic"},"45598":{"category_aro_accession":"3007039","category_aro_cvterm_id":"45598","category_aro_name":"chlorhexidine","category_aro_description":"Chlorhexidine is a disinfectant and antiseptic that is used for skin disinfection, including mouthwashes (chlorhexidine gluconate).","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"43746":{"category_aro_accession":"3005386","category_aro_cvterm_id":"43746","category_aro_name":"disinfecting agents and antiseptics","category_aro_description":"Disinfectants that can also interact with antimicrobial resistance mechanisms, e.g. molecule efflux, and thus are the targets of disinfectant resistance.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"3284":{"model_id":"3284","model_name":"tet(48)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"5151":{"protein_sequence":{"accession":"AKQ05892.1","sequence":"MTFLFKEFKGVFKMKKVLVVGAGVAGLAVCYWLKEFGFSPTLIEKSNALRKGGYGVDIFGIAVDIAKKMSVYEKICAMRTQLEHGFYVNADGHTLVEEQGEKFGFRQGEEVEILREDLIEILKQAIKDIPCHFNQRIKRIKQDGKHVEVTFKDNKTENYDLVIGADGVHSTTRAFTFDKEEYDLIDFGCYSAIFSLPNYLKLRQSEIAFDANQKFISVSSDKNPTIALASLMFHSNRGDNIRNEKDQKSFFKDAFIDLGWETNNLLQYMEESNDFYFDVATQIKMKSWTKGRIALVGDSGYCSTALSGQGTTTALVGAYILAGELKAANGNHITAFERYNMLLHPFVEANQELGAWINETFLLEDAVSKEAVEARTDNIIKKISAISNVIKLPEYSAYK"},"dna_sequence":{"accession":"KR857682.1","fmin":"0","fmax":"1200","strand":"+","sequence":"ATGACATTCCTATTTAAGGAATTTAAAGGTGTGTTTAAAATGAAAAAAGTACTAGTGGTTGGTGCAGGGGTTGCTGGATTGGCAGTTTGTTATTGGCTAAAGGAGTTTGGGTTTTCGCCTACATTAATTGAAAAAAGTAATGCTTTAAGGAAGGGTGGTTATGGAGTAGATATCTTTGGTATTGCTGTTGATATTGCTAAAAAAATGAGCGTTTATGAAAAAATATGTGCTATGCGCACCCAGTTAGAACACGGGTTTTATGTGAATGCTGATGGTCATACATTAGTTGAAGAACAAGGGGAAAAATTTGGTTTCAGGCAGGGTGAGGAAGTCGAAATTCTCCGAGAAGATTTAATTGAAATCTTAAAGCAAGCTATTAAAGATATTCCATGCCATTTTAATCAACGTATAAAGCGGATTAAGCAGGATGGTAAACATGTTGAAGTTACTTTTAAGGATAATAAGACTGAAAATTATGATTTAGTTATTGGCGCTGACGGGGTACATTCAACCACTAGAGCTTTTACTTTTGATAAAGAAGAGTATGATCTAATTGATTTTGGATGTTATTCTGCAATATTTAGCCTCCCAAATTATTTAAAATTGAGGCAAAGCGAAATAGCTTTTGATGCGAACCAAAAATTCATTTCTGTCAGTAGCGATAAAAACCCTACTATAGCTCTTGCATCCCTTATGTTCCATTCTAATCGTGGAGACAACATTCGCAATGAGAAGGACCAGAAAAGTTTTTTTAAAGATGCTTTTATTGATCTTGGATGGGAGACAAATAATCTACTTCAGTACATGGAAGAAAGTAATGATTTCTATTTCGATGTTGCTACTCAGATTAAAATGAAATCATGGACAAAAGGAAGAATTGCGTTGGTGGGTGATTCAGGTTATTGTTCAACCGCATTGTCTGGGCAAGGCACCACTACAGCACTTGTTGGAGCTTATATTTTGGCAGGAGAATTAAAAGCTGCAAATGGAAACCATATAACTGCTTTTGAACGCTATAATATGTTGCTACATCCATTTGTTGAAGCTAATCAAGAACTAGGAGCATGGATTAATGAAACGTTTCTTTTAGAAGACGCAGTATCTAAAGAAGCAGTAGAAGCAAGAACAGACAATATCATAAAGAAAATCAGCGCCATCTCGAATGTAATTAAATTACCTGAGTATTCAGCCTATAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36791","NCBI_taxonomy_name":"uncultured bacterium","NCBI_taxonomy_id":"77133"}}}},"ARO_accession":"3004581","ARO_id":"42510","ARO_name":"tet(48)","CARD_short_name":"tet(48)","ARO_description":"A tetracycline inactivating enzyme. A flavoenzyme capable of degrading tetracycline antibiotics.","ARO_category":{"36176":{"category_aro_accession":"3000036","category_aro_cvterm_id":"36176","category_aro_name":"tetracycline inactivation enzyme","category_aro_description":"Enzymes or other gene products which hydroxylate tetracycline and other tetracycline derivatives. Hydroxylation inactivates tetracycline-like antibiotics, thus conferring resistance to these compounds.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"37012":{"category_aro_accession":"3000668","category_aro_cvterm_id":"37012","category_aro_name":"oxytetracycline","category_aro_description":"Oxytetracycline is a derivative of tetracycline with a 5-hydroxyl group. Its activity is similar to other tetracyclines.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3286":{"model_id":"3286","model_name":"Klebsiella pneumoniae KpnF","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"150"}},"model_sequences":{"sequence":{"5312":{"protein_sequence":{"accession":"BAH63252.1","sequence":"MQQFEWIHAAWLAIAIVLEIIANVFLKFSDGFRRKIYGILSLAAVLGAFSALSQAVKGIDLSVAYALWGGFGIAATIAAGWVLFGQRLNNKGWAGVILLVAGMVLIKLA"},"dna_sequence":{"accession":"AP006725.1","fmin":"2484238","fmax":"2484568","strand":"+","sequence":"ATGCAGCAGTTTGAGTGGATCCACGCCGCCTGGCTGGCAATCGCCATTGTGCTGGAAATTATTGCCAACGTCTTTTTGAAGTTTTCCGACGGCTTCCGCCGCAAGATCTACGGCATCCTGTCCCTGGCGGCAGTATTGGGCGCGTTCAGCGCCCTGTCGCAGGCGGTTAAAGGGATCGATCTCTCGGTCGCCTATGCGCTGTGGGGCGGCTTCGGTATCGCGGCGACCATCGCCGCCGGCTGGGTGCTGTTTGGTCAGCGTCTGAATAACAAAGGCTGGGCGGGGGTTATCCTGCTGGTAGCCGGCATGGTGTTAATTAAACTCGCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42598","NCBI_taxonomy_name":"Klebsiella pneumoniae subsp. pneumoniae NTUH-K2044","NCBI_taxonomy_id":"484021"}}}},"ARO_accession":"3004583","ARO_id":"42513","ARO_name":"Klebsiella pneumoniae KpnF","CARD_short_name":"Kpne_KpnF","ARO_description":"KpnF subunit of KpnEF resembles EbrAB from E. coli. Mutation in KpnEF resulted in increased susceptibility to cefepime, ceftriaxon, colistin, erythromycin, rifampin, tetracycline, and streptomycin as well as enhanced sensitivity toward sodium dodecyl sulfate, deoxycholate, dyes, benzalkonium chloride, chlorhexidine, and triclosan.","ARO_category":{"36004":{"category_aro_accession":"0010003","category_aro_cvterm_id":"36004","category_aro_name":"small multidrug resistance (SMR) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Small multidrug resistance (SMR) proteins are a relatively small family of transporters, restricted to prokaryotic cells. They are also the smallest multidrug transporters, with only four transmembrane alpha-helices and no significant extramembrane domain.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35976":{"category_aro_accession":"0000059","category_aro_cvterm_id":"35976","category_aro_name":"cefepime","category_aro_description":"Cefepime (INN) is a fourth-generation cephalosporin antibiotic developed in 1994. It contains an aminothiazolyl group that decreases its affinity with beta-lactamases. Cefepime shows high binding affinity with penicillin-binding proteins and has an extended spectrum of activity against Gram-positive and Gram-negative bacteria, with greater activity against both Gram-negative and Gram-positive organisms than third-generation agents.","category_aro_class_name":"Antibiotic"},"35979":{"category_aro_accession":"0000062","category_aro_cvterm_id":"35979","category_aro_name":"ceftriaxone","category_aro_description":"Ceftriaxone is a third-generation cephalosporin antibiotic. The presence of an aminothiazolyl sidechain increases ceftriazone's resistance to beta-lactamases. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"37250":{"category_aro_accession":"3000870","category_aro_cvterm_id":"37250","category_aro_name":"triclosan","category_aro_description":"Triclosan is a common antibacterial agent added to many consumer products as a biocide.  It is an inhibitor of fatty acid biosynthesis by blocking enoyl-carrier protein reductase (FabI).","category_aro_class_name":"Antibiotic"},"40514":{"category_aro_accession":"3003823","category_aro_cvterm_id":"40514","category_aro_name":"benzalkonium chloride","category_aro_description":"Benzalkonium chloride is a type of cationic surfactant. It is an organic salt called a quaternary ammonium compound. It has three main categories of use: as a biocide, a cationic surfactant, and as a phase transfer agent.","category_aro_class_name":"Antibiotic"},"45598":{"category_aro_accession":"3007039","category_aro_cvterm_id":"45598","category_aro_name":"chlorhexidine","category_aro_description":"Chlorhexidine is a disinfectant and antiseptic that is used for skin disinfection, including mouthwashes (chlorhexidine gluconate).","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"43746":{"category_aro_accession":"3005386","category_aro_cvterm_id":"43746","category_aro_name":"disinfecting agents and antiseptics","category_aro_description":"Disinfectants that can also interact with antimicrobial resistance mechanisms, e.g. molecule efflux, and thus are the targets of disinfectant resistance.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"3287":{"model_id":"3287","model_name":"tet(50)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"5156":{"protein_sequence":{"accession":"AKQ05894.1","sequence":"MTKHIKILVIGVGVAGPAVAYWLKRFGFSPVLIEKSAAVRKGGQALDIRGIATHIAKEMGIYDQICNMRTQIKCGRYVDVKGNVLHEEQGETFGFRQDDEVEILRGDLVEILMKAIADIPCEFKQSVIKIEQNEDSVTVTYKDGRVENYDLVIAADGIHSATRGMVFSKNEYQLINLGSYVSAFTIPNYLGLDHMELLCESNHKLVTLQSDSQADKAMAGFMFRSKHVLEDIRDEQEQKHFLHASFQNFGWETQNILNRMPESDDFYFDAITQIKMKSWTKGRIALIGDAAYCPSPLSGQGNNLAFVGAYILAGELKKADGDYIQAFTRYNELLHPFVEANQQFGVWVSESFLLKDDEVSKEIAEARSNKILAMIKSVSNSINLPQYE"},"dna_sequence":{"accession":"KR857684.1","fmin":"0","fmax":"1167","strand":"+","sequence":"ATGACTAAACATATAAAAATTCTTGTAATAGGGGTTGGGGTTGCGGGCCCTGCAGTCGCTTATTGGTTAAAAAGATTTGGGTTTTCTCCGGTCTTAATTGAAAAATCAGCTGCCGTTAGAAAAGGGGGCCAGGCACTTGATATTCGCGGCATAGCCACACATATCGCTAAAGAAATGGGCATTTACGACCAGATATGTAACATGCGGACTCAAATAAAGTGTGGACGTTATGTGGATGTAAAGGGTAATGTTTTGCATGAAGAACAAGGTGAAACCTTTGGTTTCCGGCAAGATGACGAAGTTGAGATTCTTCGTGGAGACCTAGTTGAAATTCTAATGAAAGCAATTGCAGATATACCTTGTGAATTCAAACAATCCGTCATAAAAATTGAACAAAACGAAGATAGTGTAACTGTCACCTACAAAGATGGCAGAGTTGAAAATTATGACCTTGTGATCGCTGCCGATGGTATTCATTCTGCTACCAGGGGAATGGTTTTTAGTAAAAATGAATATCAGTTGATTAATCTCGGCTCCTACGTCAGCGCATTTACCATCCCAAATTATCTCGGTTTGGATCACATGGAACTCCTATGTGAATCAAATCATAAACTGGTTACTCTACAAAGCGACAGCCAAGCTGACAAAGCCATGGCGGGATTTATGTTCCGTTCAAAACATGTATTAGAAGATATTCGTGATGAGCAAGAACAAAAACATTTCTTACACGCCAGTTTTCAAAATTTCGGTTGGGAAACACAAAATATTTTAAATCGAATGCCAGAAAGCGATGACTTTTATTTTGACGCGATTACTCAAATCAAAATGAAAAGCTGGACTAAAGGCCGTATAGCCTTAATCGGCGATGCCGCTTATTGCCCCTCACCTTTATCAGGTCAGGGGAATAATTTAGCTTTTGTTGGCGCTTATATTTTGGCGGGTGAATTGAAAAAGGCTGATGGTGATTATATACAAGCATTTACCCGATATAACGAATTGCTACATCCCTTTGTTGAGGCTAACCAACAATTTGGTGTGTGGGTAAGCGAATCCTTTCTCCTAAAAGATGATGAAGTCTCTAAAGAGATTGCGGAAGCCCGTTCTAATAAAATTTTGGCAATGATAAAGTCAGTCTCTAATTCAATAAACTTGCCACAATACGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36791","NCBI_taxonomy_name":"uncultured bacterium","NCBI_taxonomy_id":"77133"}}}},"ARO_accession":"3004584","ARO_id":"42514","ARO_name":"tet(50)","CARD_short_name":"tet(50)","ARO_description":"A tetracycline inactivating enzyme. A flavoenzyme capable of degrading tetracycline antibiotics.","ARO_category":{"36176":{"category_aro_accession":"3000036","category_aro_cvterm_id":"36176","category_aro_name":"tetracycline inactivation enzyme","category_aro_description":"Enzymes or other gene products which hydroxylate tetracycline and other tetracycline derivatives. Hydroxylation inactivates tetracycline-like antibiotics, thus conferring resistance to these compounds.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"37012":{"category_aro_accession":"3000668","category_aro_cvterm_id":"37012","category_aro_name":"oxytetracycline","category_aro_description":"Oxytetracycline is a derivative of tetracycline with a 5-hydroxyl group. Its activity is similar to other tetracyclines.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3288":{"model_id":"3288","model_name":"tet(51)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"5157":{"protein_sequence":{"accession":"AKQ05895.1","sequence":"MPIINKILVIGAGIAGPAVCYWLRRFGFSPILVERCANLRKGGHAVDIRGVAIDLAKSMGIYKKICNMRTQVELGRYVDAEGNILHEEKGERFGFREGDDIEILRGDLVQILIDAMGDVPCHFNQWVESIKQRDNDVEVQFKDGRTELYDLVIGADGLHSTTRRMVFDKDEYKLTNLGAYFSAFSIPNYLNLNHTDVQFEANQKLISMASDKNPKIAITGFCFRAQNVLNNLRDENEQRRFLRDTFQDFGWETSKILELMSDSNDFYFDSFTQVKMKSWTKGRVALVGDAGYCASPFPGQGSNQALVGAYIFAGELKQAEGNYHRAFNRYNELLQPFVEANQKFGVLVNESFLVRDEVSKEVAEERSNKIMQEIKIVSNMISLPNYE"},"dna_sequence":{"accession":"KR857685.1","fmin":"0","fmax":"1164","strand":"+","sequence":"ATGCCTATCATAAATAAAATTCTGGTAATAGGAGCCGGCATTGCTGGACCCGCGGTTTGTTATTGGTTAAGAAGATTTGGCTTTTCTCCCATTTTAGTTGAAAGGTGTGCCAATTTACGAAAAGGAGGGCATGCTGTGGATATTCGAGGTGTTGCTATCGATCTTGCTAAAAGCATGGGTATTTATAAAAAAATATGCAATATGCGCACCCAGGTGGAATTAGGAAGGTATGTTGACGCCGAAGGTAATATCTTGCATGAAGAAAAAGGCGAAAGATTTGGCTTTAGGGAGGGTGATGATATTGAAATTCTCCGCGGTGATTTAGTTCAAATACTGATAGATGCCATGGGAGATGTTCCCTGTCATTTCAATCAATGGGTTGAGAGCATTAAGCAGAGGGATAATGATGTAGAGGTTCAATTTAAAGATGGTAGAACGGAACTTTACGATTTGGTTATCGGTGCTGATGGCTTGCATTCAACCACCAGAAGGATGGTTTTTGATAAGGATGAATATAAATTAACTAACCTTGGTGCATACTTTAGTGCTTTTAGTATTCCAAATTATCTTAATTTGAATCACACCGATGTGCAATTCGAGGCTAATCAAAAACTTATATCTATGGCTAGCGATAAGAACCCTAAAATTGCTATAACAGGATTCTGTTTCCGTGCACAGAATGTCTTGAATAATTTGCGCGATGAAAACGAGCAACGGAGATTTCTACGCGATACTTTTCAAGATTTTGGCTGGGAGACATCCAAAATACTTGAACTGATGTCAGATAGTAATGATTTTTATTTTGATTCATTCACTCAAGTGAAAATGAAGTCATGGACAAAAGGACGAGTTGCTTTGGTGGGCGATGCAGGTTACTGCGCATCCCCATTCCCTGGTCAAGGTAGTAATCAGGCACTGGTAGGTGCTTATATTTTTGCAGGAGAACTAAAACAGGCAGAAGGCAATTATCATCGAGCATTTAACCGTTATAATGAATTATTACAACCATTTGTTGAAGCCAATCAAAAATTTGGCGTCTTGGTTAACGAATCGTTTCTCGTTCGTGATGAAGTCTCTAAGGAGGTGGCAGAAGAAAGATCGAATAAGATTATGCAAGAGATAAAAATTGTATCGAATATGATTTCGTTGCCGAATTATGAATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36791","NCBI_taxonomy_name":"uncultured bacterium","NCBI_taxonomy_id":"77133"}}}},"ARO_accession":"3004586","ARO_id":"42516","ARO_name":"tet(51)","CARD_short_name":"tet(51)","ARO_description":"A tetracycline inactivating enzyme. A flavoenzyme capable of degrading tetracycline antibiotics.","ARO_category":{"36176":{"category_aro_accession":"3000036","category_aro_cvterm_id":"36176","category_aro_name":"tetracycline inactivation enzyme","category_aro_description":"Enzymes or other gene products which hydroxylate tetracycline and other tetracycline derivatives. Hydroxylation inactivates tetracycline-like antibiotics, thus conferring resistance to these compounds.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"37012":{"category_aro_accession":"3000668","category_aro_cvterm_id":"37012","category_aro_name":"oxytetracycline","category_aro_description":"Oxytetracycline is a derivative of tetracycline with a 5-hydroxyl group. Its activity is similar to other tetracyclines.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3290":{"model_id":"3290","model_name":"tet(53)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"5159":{"protein_sequence":{"accession":"AKQ05897.1","sequence":"MSTINKILVIGAGIAGPAVCYWLRRFGFSPVLIEKFANIRKEGQALDFRGVAIDIVKGMNIYEKMCNMHKQLEVGRYVDTEGNTLHEERGERFCFRQGEDVEIARGDFAEILTGAIEGIPCHFNQVIDSIKQSDDDVKVQFNDGRVEHYDLVIGADGIYSTTRGMVFDKDEYKLVNLGVCFGVFSILNYLNLSHTEVQCEANQKLISIWSHKNPKMAEVAFVFRTQNVLNNIRNKNEQQQLLRDAFQDFGWEASKILELMTGSDDFYFDSATQVKMKSWTKGRVALLGDAGYSASPLSGQGNYLALVGAYIFAGELKKADGNYTRAFSRYNELLHPLVEACHKLGVLVSESFLVPDEVSKEVAEERSNKILQEVKIVSNMISLPEYE"},"dna_sequence":{"accession":"KR857687.1","fmin":"0","fmax":"1164","strand":"+","sequence":"ATGTCTACTATAAATAAAATTCTCGTGATCGGAGCTGGTATTGCCGGACCCGCGGTTTGTTATTGGTTAAGAAGATTTGGCTTTTCTCCTGTCCTCATTGAAAAATTTGCCAATATACGAAAAGAAGGGCAGGCACTGGATTTTCGAGGCGTTGCGATCGACATCGTTAAAGGAATGAATATTTATGAGAAAATGTGCAATATGCACAAGCAGTTGGAGGTCGGGCGGTATGTGGACACAGAAGGCAATACCCTGCATGAAGAAAGAGGTGAAAGATTTTGCTTTAGACAAGGTGAAGACGTTGAAATTGCCCGCGGTGATTTCGCCGAAATACTGACGGGTGCCATTGAAGGTATTCCCTGTCATTTTAATCAAGTAATTGACAGCATTAAACAGAGTGACGATGATGTAAAAGTCCAGTTCAACGATGGCAGAGTCGAGCATTATGACTTGGTTATTGGTGCTGATGGCATATACTCGACAACGAGAGGTATGGTTTTTGATAAAGACGAATATAAATTAGTTAACCTTGGTGTGTGCTTTGGCGTATTTAGCATTCTGAATTATCTCAATTTGAGCCACACCGAAGTGCAGTGTGAGGCCAATCAAAAGCTGATATCTATCTGGAGCCACAAAAATCCCAAGATGGCTGAAGTTGCGTTTGTGTTCCGTACGCAGAATGTCTTGAATAACATTCGCAATAAAAACGAGCAGCAGCAACTCCTGCGTGATGCTTTTCAAGATTTTGGCTGGGAAGCATCAAAAATACTTGAGCTGATGACAGGTAGTGATGATTTTTATTTTGATTCAGCCACACAGGTAAAAATGAAATCGTGGACGAAAGGGCGGGTTGCTTTATTGGGTGATGCTGGTTACTCTGCATCTCCACTATCTGGTCAGGGTAATTATCTGGCACTGGTTGGCGCTTATATTTTTGCCGGAGAACTAAAAAAAGCAGATGGCAATTATACTCGTGCATTTAGTCGTTATAATGAATTATTACATCCACTCGTTGAAGCCTGTCACAAGTTGGGGGTCTTAGTTAGCGAATCGTTCCTCGTCCCAGATGAAGTCTCCAAAGAAGTTGCAGAAGAACGATCAAATAAGATTCTGCAAGAGGTGAAAATCGTATCGAATATGATTTCGTTGCCAGAGTATGAATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36791","NCBI_taxonomy_name":"uncultured bacterium","NCBI_taxonomy_id":"77133"}}}},"ARO_accession":"3004589","ARO_id":"42519","ARO_name":"tet(53)","CARD_short_name":"tet(53)","ARO_description":"A tetracycline inactivating enzyme. A flavoenzyme capable of degrading tetracycline antibiotics.","ARO_category":{"36176":{"category_aro_accession":"3000036","category_aro_cvterm_id":"36176","category_aro_name":"tetracycline inactivation enzyme","category_aro_description":"Enzymes or other gene products which hydroxylate tetracycline and other tetracycline derivatives. Hydroxylation inactivates tetracycline-like antibiotics, thus conferring resistance to these compounds.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36291":{"category_aro_accession":"3000152","category_aro_cvterm_id":"36291","category_aro_name":"minocycline","category_aro_description":"Minocycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"37012":{"category_aro_accession":"3000668","category_aro_cvterm_id":"37012","category_aro_name":"oxytetracycline","category_aro_description":"Oxytetracycline is a derivative of tetracycline with a 5-hydroxyl group. Its activity is similar to other tetracyclines.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3291":{"model_id":"3291","model_name":"Erm(48)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"5160":{"protein_sequence":{"accession":"CZT31773.1","sequence":"MNNKNPKDSQNFITSQKYINEILQNTNIESNDNIIEIGTGKGHFTKALLKISHFVTGIEIDRNLYYKLKKDTDLYDNLKLINKDVLRFQFHQNEPYKIFGSIPYNISTEIIKKILYESKSEFNYLIVELGFAKRLLNKKRALSLLLLPKMDVEILKIIPNVYFHPKPTVDSALILLKRHKPLVSEKDEKIYHFFVYRWVNKEYKKLFTKNQFNKTLNHANVQDINELSKEQFISIFNSYKLFN"},"dna_sequence":{"accession":"LT223129.1","fmin":"47369","fmax":"48101","strand":"+","sequence":"ATGAATAACAAAAACCCAAAAGATTCACAAAATTTTATAACATCTCAAAAATATATAAATGAAATCTTACAAAATACTAATATAGAATCAAATGACAATATCATTGAAATAGGAACAGGCAAGGGGCATTTTACAAAAGCATTATTAAAAATATCTCACTTTGTAACTGGAATAGAAATTGATAGGAATTTGTATTATAAATTAAAAAAAGACACTGACCTATATGATAATCTTAAATTAATCAATAAAGATGTATTGAGATTCCAATTTCATCAAAATGAACCTTATAAGATTTTTGGGAGTATTCCCTATAATATTAGTACAGAAATAATTAAAAAGATTTTGTATGAAAGTAAGTCAGAATTTAACTATCTAATTGTGGAGCTAGGATTTGCTAAACGTCTCTTAAATAAAAAAAGAGCGCTAAGTTTATTATTATTACCTAAAATGGATGTTGAAATTTTAAAAATAATCCCTAACGTTTATTTCCATCCTAAACCAACAGTAGATTCGGCACTAATTTTATTAAAACGACATAAGCCTTTAGTTTCAGAGAAAGATGAAAAGATATATCATTTTTTTGTATATAGATGGGTGAACAAAGAATATAAGAAACTGTTTACCAAAAATCAATTTAATAAAACATTGAATCATGCAAATGTGCAAGACATCAATGAATTATCAAAAGAACAATTTATATCTATTTTTAATAGTTATAAATTGTTTAATTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36844","NCBI_taxonomy_name":"Staphylococcus xylosus","NCBI_taxonomy_id":"1288"}}}},"ARO_accession":"3004094","ARO_id":"41202","ARO_name":"Erm(48)","CARD_short_name":"Erm(48)","ARO_description":"Erm(48) is a macrolide-lincosamide-streptogramin resistance gene identified on resistance plasmid pJW2311.","ARO_category":{"36699":{"category_aro_accession":"3000560","category_aro_cvterm_id":"36699","category_aro_name":"Erm 23S ribosomal RNA methyltransferase","category_aro_description":"Erm proteins are part of the RNA methyltransferase family and methylate A2058 (E. coli nomenclature) of the 23S ribosomal RNA conferring degrees of resistance to Macrolides, Lincosamides and Streptogramin b. This is called the MLSb phenotype.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"36722":{"category_aro_accession":"3000583","category_aro_cvterm_id":"36722","category_aro_name":"pristinamycin IA","category_aro_description":"Pristinamycin IA is a type B streptogramin antibiotic produced by Streptomyces pristinaespiralis. It binds to the P site of the 50S subunit of the bacterial ribosome, preventing the extension of protein chains.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35967":{"category_aro_accession":"0000050","category_aro_cvterm_id":"35967","category_aro_name":"streptogramin B antibiotic","category_aro_description":"Streptogramin B antibiotics are are cyclic hepta- or hexa-depsipeptides.  Type B streptogramins block the peptide exit tunnel of the 50S bacterial ribosome. The general composition of group B streptogramins is 3-hydroxypicolinic acid-L-Thr-D-aminobutyric acid (or D-Ala)-L-Pro-L-Phe (or 4-N-,N-(dimethylamino)-L-Phe)-X-L-phenylglycine. Used alone, streptogramin B antibiotics are bacteriostatic, but is bactericidal when used with streptogramin A antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3292":{"model_id":"3292","model_name":"tet(54)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"5161":{"protein_sequence":{"accession":"AKQ05898.1","sequence":"MSTIKKILVIGAGIAGTAVCYWLRRFGFYPVLIEKSACIRKGGQGLDIRGVAIDIVKKMVIYEQICKMRTQVECGRYVDVVGKTLHEEKGEKFAFRQDEDVEILRGDLIEILMKTIDDVPCHFNQSIDSIEQNDDDVIVYFKDARVEHYDLIIGADGIHSSIRRMVFDKDEYRLVNLAEAYFSIFSIPNYLNLSHTEVQCETNEKLVSITSDKDPKTAQVAFMFRSQHVWNNLRDEHEQMQFLRDIFHDFGWEAQKILELMPNSHDFYFDSVTQVKMRSWTKGQVALVGDASYSASPLSGQGNNLALVGAYILAGELKAAEGNYRLAFNRYNELLHPFVEANQQLGAWVSESFLVPDAVSKEVAEERSNRILQKVQIISNAIKLPEYE"},"dna_sequence":{"accession":"KR857688.1","fmin":"0","fmax":"1167","strand":"+","sequence":"ATGTCTACTATAAAAAAAATTCTCGTGATAGGAGCCGGTATTGCCGGTACTGCAGTCTGTTATTGGTTACGAAGATTTGGTTTTTATCCTGTATTAATTGAAAAATCTGCGTGTATACGAAAAGGCGGCCAAGGTTTGGATATTCGTGGGGTTGCAATCGATATCGTTAAAAAAATGGTTATTTATGAGCAAATATGCAAGATGCGCACGCAGGTAGAATGTGGTCGCTATGTGGATGTCGTAGGCAAAACACTACATGAAGAAAAAGGTGAAAAATTTGCCTTTAGGCAAGATGAAGATGTTGAAATTCTCCGCGGTGATTTAATCGAGATCCTAATGAAAACCATTGACGATGTTCCCTGTCATTTTAATCAATCCATTGACAGTATTGAACAGAATGACGATGACGTCATAGTTTATTTCAAAGATGCCAGAGTTGAGCACTATGATTTGATTATTGGCGCTGATGGGATACACTCATCGATCAGGCGCATGGTATTTGACAAAGATGAATATAGATTAGTTAATCTTGCAGAGGCGTACTTCAGTATATTTAGCATTCCGAATTATCTCAATTTAAGCCACACGGAAGTGCAGTGTGAGACTAATGAAAAATTGGTATCTATCACTAGCGATAAAGATCCCAAGACGGCTCAAGTTGCATTTATGTTCCGTTCGCAACATGTCTGGAATAATCTTCGCGATGAACACGAACAGATGCAATTTTTGCGGGATATTTTTCATGACTTTGGTTGGGAGGCGCAAAAAATACTTGAACTAATGCCAAATAGCCATGATTTTTATTTTGATTCAGTTACACAGGTGAAAATGCGTTCCTGGACCAAAGGACAAGTTGCTTTAGTAGGTGATGCGAGTTACTCTGCATCTCCACTATCGGGTCAAGGTAATAATCTGGCTCTAGTTGGTGCTTATATTTTGGCAGGAGAACTAAAAGCAGCGGAAGGAAATTATAGGCTCGCATTTAATCGTTATAATGAATTATTACATCCCTTCGTTGAGGCTAATCAACAGCTTGGAGCTTGGGTTAGCGAATCGTTTCTTGTCCCAGATGCAGTATCCAAAGAAGTTGCAGAAGAACGCTCAAACAGAATCCTGCAAAAAGTACAAATCATATCGAATGCGATCAAGCTGCCTGAGTATGAATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36791","NCBI_taxonomy_name":"uncultured bacterium","NCBI_taxonomy_id":"77133"}}}},"ARO_accession":"3004590","ARO_id":"42520","ARO_name":"tet(54)","CARD_short_name":"tet(54)","ARO_description":"A tetracycline inactivating enzyme. A flavoenzyme capable of degrading tetracycline antibiotics.","ARO_category":{"36176":{"category_aro_accession":"3000036","category_aro_cvterm_id":"36176","category_aro_name":"tetracycline inactivation enzyme","category_aro_description":"Enzymes or other gene products which hydroxylate tetracycline and other tetracycline derivatives. Hydroxylation inactivates tetracycline-like antibiotics, thus conferring resistance to these compounds.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"37012":{"category_aro_accession":"3000668","category_aro_cvterm_id":"37012","category_aro_name":"oxytetracycline","category_aro_description":"Oxytetracycline is a derivative of tetracycline with a 5-hydroxyl group. Its activity is similar to other tetracyclines.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3293":{"model_id":"3293","model_name":"tet(55)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"5162":{"protein_sequence":{"accession":"AKQ05899.1","sequence":"MPHTKKILVIGASIAGPALCYWLNHYGFQPTLVEKNQSTRKGGYAIDLRGIAVDVAKQMGIYDSVCAMRTSLQCVRYVDAAGNLLFEEHGEKGGFRQGDEVEIVRGDLVDILMKTITDIPCFYDHAIESLTQHDDHVTVQFKNGKTENYDLVIAADGLHSATRRMVFSKDDYHLRNLGCYISVFSIPNYLQLDHCETLLEAKQKLVSITSDKDSTKAFAGFMFRSSNSPNYIRDEASQKDFLRENFTNHGWESNKLLSLMNDANDFYFDAIMQVKMKDWTKGRIALVGDAGYTPSPLSGQGTSLALVGAYILAGELKTATDHVAAFARYNELLKPYVEANQAFGVWVSESFLADEPLSAEQAEERNNIVLGIMKKATHAIELPEY"},"dna_sequence":{"accession":"KR857689.1","fmin":"0","fmax":"1158","strand":"+","sequence":"ATGCCCCACACCAAAAAAATCCTAGTCATAGGTGCAAGTATCGCCGGCCCAGCATTATGCTACTGGCTAAACCACTACGGCTTCCAACCCACCCTCGTAGAAAAAAACCAATCAACAAGAAAAGGCGGATATGCAATCGATCTCCGCGGCATAGCAGTGGATGTCGCCAAACAAATGGGAATCTACGACTCAGTCTGCGCCATGCGTACCAGTCTGCAGTGCGTCCGCTATGTTGATGCGGCAGGAAATTTACTATTCGAAGAGCACGGCGAAAAAGGCGGTTTCAGGCAAGGCGATGAAGTAGAAATCGTGCGTGGTGATTTAGTGGATATCTTAATGAAAACCATTACGGATATTCCTTGTTTTTATGATCATGCAATCGAAAGTTTGACCCAGCATGATGATCATGTCACCGTGCAATTTAAAAATGGCAAAACCGAAAATTATGATTTAGTGATAGCGGCTGATGGTTTGCATTCTGCTACACGTCGTATGGTTTTCAGTAAAGATGACTATCATTTGCGAAATCTTGGTTGTTACATCAGTGTGTTTAGCATACCTAATTATTTGCAGCTGGATCACTGCGAGACACTATTAGAAGCCAAGCAAAAATTGGTTTCTATTACCAGTGATAAAGATTCTACTAAGGCCTTCGCTGGTTTTATGTTTCGTTCCAGTAATAGTCCAAACTACATTCGTGATGAAGCATCACAAAAAGATTTTCTAAGAGAAAATTTCACAAATCACGGCTGGGAATCAAATAAGCTATTGTCACTGATGAATGATGCCAATGATTTTTATTTTGATGCGATTATGCAGGTTAAAATGAAAGACTGGACTAAAGGGCGTATCGCGTTAGTGGGTGATGCTGGTTATACACCTTCACCCTTATCAGGGCAGGGAACCAGCCTCGCTTTGGTTGGGGCTTATATATTGGCGGGTGAATTGAAAACAGCTACTGATCATGTTGCGGCTTTTGCTCGATATAATGAGTTATTGAAGCCTTATGTTGAGGCTAATCAGGCGTTTGGGGTTTGGGTTAGTGAATCGTTTTTGGCGGATGAGCCTTTGTCTGCAGAGCAGGCGGAAGAGCGGAATAATATTGTTTTAGGGATAATGAAAAAAGCCACGCATGCGATCGAGTTGCCGGAGTATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36791","NCBI_taxonomy_name":"uncultured bacterium","NCBI_taxonomy_id":"77133"}}}},"ARO_accession":"3004591","ARO_id":"42521","ARO_name":"tet(55)","CARD_short_name":"tet(55)","ARO_description":"A tetracycline inactivating enzyme. A flavoenzyme capable of degrading tetracycline antibiotics.","ARO_category":{"36176":{"category_aro_accession":"3000036","category_aro_cvterm_id":"36176","category_aro_name":"tetracycline inactivation enzyme","category_aro_description":"Enzymes or other gene products which hydroxylate tetracycline and other tetracycline derivatives. Hydroxylation inactivates tetracycline-like antibiotics, thus conferring resistance to these compounds.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36291":{"category_aro_accession":"3000152","category_aro_cvterm_id":"36291","category_aro_name":"minocycline","category_aro_description":"Minocycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"37012":{"category_aro_accession":"3000668","category_aro_cvterm_id":"37012","category_aro_name":"oxytetracycline","category_aro_description":"Oxytetracycline is a derivative of tetracycline with a 5-hydroxyl group. Its activity is similar to other tetracyclines.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3990":{"model_id":"3990","model_name":"TEM-227","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6354":{"protein_sequence":{"accession":"WP_085562406.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDKLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVKYSPVTEKHLTNGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGASERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGTSLIKHW"},"dna_sequence":{"accession":"NG_054696.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATAAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTAAGTACTCACCAGTCACAGAAAAGCATCTTACGAATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCAGTGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTACCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3005258","ARO_id":"43614","ARO_name":"TEM-227","CARD_short_name":"TEM-227","ARO_description":"TEM-227 is a beta-lactamase.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4130":{"model_id":"4130","model_name":"ACT-39","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6505":{"protein_sequence":{"accession":"WP_063857782.1","sequence":"MMKKSLCCALLLGISCSALAAPVSEKQLAEVVANTVTPLMKAQSIPGMAVAVIYQGKPHYYTFGKADIAASKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNAALLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMGYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGILDAQAYGVKTNVQDMANWVMANMAPEKVADASLKQGISLAQSRYWRIGSMYQGLGWEMLNWPVEANTVIEGSDSKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANKSYPNPARVEAAYHILDALQ"},"dna_sequence":{"accession":"NG_048626.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCTCTTTGCTGCGCCCTGCTGCTCGGCATCTCTTGCTCTGCTCTCGCCGCGCCAGTGTCAGAAAAACAGCTGGCGGAGGTGGTCGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCGATTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGTAAACCGCACTATTACACGTTTGGCAAAGCCGATATCGCGGCCAGCAAACCCGTTACGCCTCAGACTCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGGGTTTTAGGAGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTGACGGGCAAGCAGTGGCAGGGGATTCGTATGCTGGATCTCGCAACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAATGCCGCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGTATCGGTCTTTTTGGCGCGCTGGCGGTCAAACCTTCCGGCATGGGCTATGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTTCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGAATACTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCGGAGAAGGTTGCTGATGCCTCACTTAAGCAGGGCATCTCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGATCGAGGGCAGCGACAGTAAGGTGGCGCTGGCACCGCTGCCCGTGGCAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGCTCTACTGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCGACGCGCTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40540","NCBI_taxonomy_name":"Enterobacter cloacae complex","NCBI_taxonomy_id":"354276"}}}},"ARO_accession":"3006234","ARO_id":"44696","ARO_name":"ACT-39","CARD_short_name":"ACT-39","ARO_description":"ACT-39 is a ACT beta-lactamase.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3297":{"model_id":"3297","model_name":"erm(46)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"5169":{"protein_sequence":{"accession":"AJF36617.1","sequence":"MPTYRSGRHELGQNFLTDRKAVDTIVDLVSRTDGPIIEIGSGGGALTLPLQALRRPITAIEIDPRHVQKLQHRVDPSTTVVHGDFLRYRLPRTPHTIVGNLPFHHTTAMLRRILHAEHWTASVLLVQWEVARRRAAVGGATMMTAQWWPWYDFGLAGRVSASAFTPRPGVDAGLMTIARRTVPLVDPALRPRYSTFVHTVFTSKGHGLHQILPRVAGDPEKAAVKKWLAGQRFRGTPLPRDLSPGQWSELFAIIDRRSPATDRKRAEYRR"},"dna_sequence":{"accession":"KM679362.1","fmin":"0","fmax":"813","strand":"+","sequence":"ATGCCTACCTACCGTTCCGGCCGTCACGAGCTCGGCCAGAACTTCCTCACGGACCGCAAAGCAGTCGATACGATCGTCGACCTCGTTTCTCGAACAGACGGCCCGATCATCGAAATCGGCTCCGGCGGTGGGGCGTTGACATTGCCCCTGCAGGCGCTGCGTCGACCGATCACAGCTATCGAGATCGATCCGCGACATGTGCAAAAGCTCCAACATCGCGTCGATCCGAGTACGACGGTCGTGCACGGCGACTTCCTGCGCTACCGACTGCCCCGAACACCGCACACCATCGTGGGGAACTTGCCGTTCCACCACACCACGGCGATGTTGCGGCGAATCCTCCACGCCGAACACTGGACAGCGTCGGTCCTGCTCGTGCAGTGGGAGGTTGCACGTCGTCGTGCGGCGGTCGGTGGCGCAACGATGATGACTGCGCAATGGTGGCCGTGGTACGACTTCGGCCTGGCCGGCCGTGTTTCCGCATCGGCGTTCACACCACGGCCGGGAGTCGATGCAGGGCTGATGACCATCGCTCGGCGGACCGTTCCACTCGTCGACCCCGCGCTACGTCCCCGATACAGCACCTTCGTCCACACCGTCTTCACCAGCAAGGGCCACGGCCTGCATCAGATCTTGCCGCGGGTGGCTGGCGATCCTGAGAAGGCCGCGGTTAAGAAGTGGCTCGCTGGCCAGCGATTTCGAGGCACACCGCTGCCGCGCGACCTCTCACCCGGACAATGGTCCGAGCTCTTCGCGATCATCGATCGACGCTCTCCGGCTACCGATCGGAAGCGGGCTGAGTACCGGCGATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36897","NCBI_taxonomy_name":"Rhodococcus hoagii","NCBI_taxonomy_id":"43767"}}}},"ARO_accession":"3004596","ARO_id":"42527","ARO_name":"erm(46)","CARD_short_name":"erm(46)","ARO_description":"erm(46) is transferable determinant that confers resistance to macrolides.","ARO_category":{"36699":{"category_aro_accession":"3000560","category_aro_cvterm_id":"36699","category_aro_name":"Erm 23S ribosomal RNA methyltransferase","category_aro_description":"Erm proteins are part of the RNA methyltransferase family and methylate A2058 (E. coli nomenclature) of the 23S ribosomal RNA conferring degrees of resistance to Macrolides, Lincosamides and Streptogramin b. This is called the MLSb phenotype.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35982":{"category_aro_accession":"0000065","category_aro_cvterm_id":"35982","category_aro_name":"clarithromycin","category_aro_description":"Clarithromycin is a methyl derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome and is used to treat pharyngitis, tonsillitis, acute maxillary sinusitis, acute bacterial exacerbation of chronic bronchitis, pneumonia (especially atypical pneumonias associated with Chlamydia pneumoniae or TWAR), and skin structure infections.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3298":{"model_id":"3298","model_name":"Klebsiella pneumoniae KpnG","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"5311":{"protein_sequence":{"accession":"EHL92831.1","sequence":"MSANAESQTPQQPGSKKGKRKGALLLLTLLFIIIAVAYGIYWFLVLRHYEETDDAYVAGNQVQIMAQVAGSVTKVWADNTDYVQKGDPLVTLDRTDAQQAFEKAKTQLAASVRQTRQQMINSKQLQANIDVKKTALSQAQADLNRRIPLGAANLIGREELQHARDTVASAQAELDVAIQQYNANQAIVLGTRLEQQPAVLQAATEVRNAWLALQRTQIVSPISGYVSRRSVQPGAQIGTTTPLMAVVPATNLWIDANFKETQLAHMRIGQPATVISDIYGDDVKYTGKVVGLDMGTGSAFSLLPAQNATGNWIKVVQRLPVRIELDEKQLAEHPLRIGLSTLVEVNTTDRDGEMLASQVRSSPVYESNAREIALDPVNKLIDEIIQANAG"},"dna_sequence":{"accession":"ACWO01000051.1","fmin":"22092","fmax":"23265","strand":"+","sequence":"ATGAGTGCAAATGCGGAGAGCCAAACCCCGCAGCAACCAGGCAGCAAAAAAGGAAAGCGTAAAGGCGCCCTTCTGTTGCTGACATTGCTCTTCATTATTATTGCCGTGGCATATGGGATTTACTGGTTTCTGGTACTGCGTCACTACGAAGAGACCGACGATGCCTACGTGGCAGGGAATCAGGTACAAATTATGGCTCAGGTCGCGGGCAGCGTGACCAAAGTCTGGGCTGACAACACGGACTACGTGCAGAAAGGCGATCCGCTGGTCACTCTCGATCGGACCGATGCCCAACAGGCGTTTGAAAAGGCTAAGACCCAACTGGCCGCCAGCGTCCGTCAGACCCGCCAGCAGATGATCAACAGCAAGCAGCTGCAGGCAAATATCGACGTCAAAAAAACCGCCCTCTCCCAGGCGCAGGCTGACCTGAACCGCCGCATCCCGCTGGGCGCCGCGAACCTCATTGGCCGCGAAGAGCTGCAGCACGCCCGCGATACCGTCGCCAGCGCACAGGCCGAACTCGACGTGGCAATCCAGCAGTACAACGCCAACCAGGCGATCGTGCTGGGCACCAGGCTGGAACAGCAGCCGGCGGTGCTCCAGGCGGCCACTGAAGTGCGTAACGCCTGGCTGGCCCTGCAGCGTACGCAGATCGTCAGCCCGATTAGCGGCTACGTTTCCCGTCGCTCGGTACAGCCTGGCGCGCAGATCGGCACCACCACGCCGCTGATGGCGGTGGTCCCGGCGACCAACCTGTGGATCGATGCTAACTTTAAAGAGACTCAGCTGGCGCATATGCGTATCGGCCAGCCGGCCACCGTGATCAGCGATATCTATGGCGATGACGTGAAATACACCGGTAAAGTGGTCGGTCTGGATATGGGTACCGGCAGCGCCTTCTCCCTGCTGCCGGCGCAGAATGCCACCGGCAACTGGATCAAAGTGGTACAGCGCCTGCCGGTTCGTATCGAGCTGGATGAAAAACAACTAGCGGAACACCCGCTGCGCATCGGCCTCTCGACGCTGGTGGAAGTCAACACCACCGATCGCGATGGTGAAATGCTGGCCAGCCAGGTGCGGAGCTCCCCGGTTTACGAGAGCAATGCCCGCGAAATCGCTCTCGATCCGGTTAATAAGCTGATAGACGAGATCATTCAGGCCAACGCCGGATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42597","NCBI_taxonomy_name":"Klebsiella sp. 4_1_44FAA","NCBI_taxonomy_id":"665944"}}}},"ARO_accession":"3004588","ARO_id":"42518","ARO_name":"Klebsiella pneumoniae KpnG","CARD_short_name":"Kpne_KpnG","ARO_description":"KpnG consists of ~390 residues and resembles EmrA of E. coli. Disruption of the pump components KpnG-KpnH signficantly decrease resistance to azithromycin, ceftazidime, ciprofloxacin, ertapenem, erythromycin, gentamicin, imipenem, ticarcillin, norfloxacin, polymyxin-B, piperacillin, spectinomycin, tobramycin, and streptomycin.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"35987":{"category_aro_accession":"0000070","category_aro_cvterm_id":"35987","category_aro_name":"ertapenem","category_aro_description":"Ertapenem is a carbapenem antibiotic and is highly resistant to beta-lactamases like other carbapenems. It inhibits bacterial cell wall synthesis.","category_aro_class_name":"Antibiotic"},"35995":{"category_aro_accession":"0000078","category_aro_cvterm_id":"35995","category_aro_name":"piperacillin","category_aro_description":"Piperacillin is an acetylureidopenicillin and has an extended spectrum of targets relative to other beta-lactam antibiotics. It inhibits cell wall synthesis in bacteria, and is usually taken with the beta-lactamase inhibitor tazobactam to overcome penicillin-resistant bacteria.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"36309":{"category_aro_accession":"3000170","category_aro_cvterm_id":"36309","category_aro_name":"imipenem","category_aro_description":"Imipenem is a broad-spectrum antibiotic and is usually taken with cilastatin, which prevents hydrolysis of imipenem by renal dehydropeptidase-I. It is resistant to hydrolysis by most other beta-lactamases. Notable exceptions are the KPC beta-lactamases and Ambler Class B enzymes.","category_aro_class_name":"Antibiotic"},"36593":{"category_aro_accession":"3000454","category_aro_cvterm_id":"36593","category_aro_name":"polymyxin B","category_aro_description":"Polymyxin B is mixture of mostly polymyxins B1 and B2, mainly used for resistant gram-negative infections. They are polypeptides with cationic detergent action on cell membranes.","category_aro_class_name":"Antibiotic"},"36969":{"category_aro_accession":"3000625","category_aro_cvterm_id":"36969","category_aro_name":"polymyxin B1","category_aro_description":"Polymyxin B1 is in the family of polymyxin lipopeptides with a 6-methyloctanoic acid acyl group. These antibiotics disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36970":{"category_aro_accession":"3000626","category_aro_cvterm_id":"36970","category_aro_name":"polymyxin B2","category_aro_description":"Polymyxin B2 is in the family of polymyxin lipopeptides with a 6-methylheptanoic acid acyl group. These antibiotics disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36971":{"category_aro_accession":"3000627","category_aro_cvterm_id":"36971","category_aro_name":"polymyxin B3","category_aro_description":"Polymyxin B3 is in the family of polymyxin lipopeptides with an octanoic acid acyl group. These antibiotics disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36972":{"category_aro_accession":"3000628","category_aro_cvterm_id":"36972","category_aro_name":"polymyxin B4","category_aro_description":"Polymyxin B4 is in the family of polymyxin lipopeptides with a heptanoic acid acyl group. These antibiotics disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"40523":{"category_aro_accession":"3003832","category_aro_cvterm_id":"40523","category_aro_name":"ticarcillin","category_aro_description":"Ticarcillin is a carboxypenicillin used for the treatment of Gram-negative bacteria, particularly P. aeruginosa. Ticarcillin's antibiotic properties arise from its ability to prevent cross-linking of peptidoglycan during cell wall synthesis, when the bacteria try to divide, causing cell death.","category_aro_class_name":"Antibiotic"},"46133":{"category_aro_accession":"3007382","category_aro_cvterm_id":"46133","category_aro_name":"gentamicin","category_aro_description":"Gentamicin is a commonly used aminoglycoside antibiotic derived from members of the Micromonospora genus of bacteria. It acts by binding the 30S ribosomal subunit, thus inhibiting protein synthesis. Gentamicin is typically used to treat Gram-negative infections of the repiratory and urinary tract, as well as infections of the bone and soft tissue. It also exhibits considerable nephrotoxicity and ototoxicity. Gentamicin is administered as a mixture of gentamicin type C (which makes about around 80% of the complex) and types A, B, and X (distributed in the remaining 20% of the complex).","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"3299":{"model_id":"3299","model_name":"Klebsiella pneumoniae KpnH","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"5310":{"protein_sequence":{"accession":"EOU56998.1","sequence":"MQQQKPLEGAQLVIMTIALSLATFMQVLDSTIANVAIPTIAGNLGSSLSQGTWVITSFGVANAISIPLTGWLAKRVGEVKLFLWSTIAFAIASWACGVSSSLNMLIFFRVIQGIVAGPLIPLSQSLLLNNYPPAKRSIALALWSMTVIVAPICGPILGGYISDNYHWGWIFFINVPIGVAVVLMTLQTLRGRETRTERRRIDAVGLALLVIGIGSLQIMLDRGKELDWFSSQEIIILTVVAVVAICFLIVWELTDDNPIVDLSLFKSRNFTIGCLCISLAYMLYFGAIVLLPQLLQEVYGYTATWAGLASAPVGIIPVILSPIIGRFAHKLDMRRLVTFSFIMYAVCFYWRAYTFEPGMDFGASAWPQFIQGFAVACFFMPLTTITLSGLPPERLAAASSLSNFTRTLAGSIGTSITTTMWTNRESMHHAQLTESVNPFNPNAQAMYSQLEGLGMTQQQASGWIAQQITNQGLIISANEIFWMSAGIFLILLGLVWFAKPPFGAGGGGGGAH"},"dna_sequence":{"accession":"ASTU01000063.1","fmin":"61248","fmax":"62787","strand":"+","sequence":"ATGCAACAGCAAAAACCGCTGGAAGGCGCGCAACTGGTCATTATGACGATTGCGCTGTCACTGGCGACATTCATGCAGGTGCTGGACTCCACCATTGCTAACGTGGCGATCCCCACTATCGCCGGGAATCTGGGCTCATCGCTCAGCCAGGGAACGTGGGTAATCACTTCTTTCGGGGTGGCGAATGCCATCTCGATCCCGCTTACCGGCTGGCTGGCAAAGCGCGTCGGGGAAGTGAAACTGTTCCTTTGGTCCACCATCGCCTTTGCTATTGCGTCGTGGGCGTGTGGTGTCTCCAGCAGCCTGAATATGCTGATCTTCTTCCGCGTGATTCAGGGGATTGTCGCCGGGCCGTTGATCCCGCTTTCGCAAAGTCTATTGCTGAATAACTACCCGCCAGCCAAACGCTCGATCGCGCTGGCGTTGTGGTCGATGACGGTGATTGTCGCGCCAATTTGCGGCCCGATCCTCGGCGGTTATATCAGCGATAATTACCACTGGGGCTGGATATTCTTCATCAACGTGCCGATTGGCGTGGCGGTGGTGTTGATGACACTGCAAACTCTGCGCGGACGTGAAACCCGCACCGAACGGCGGCGGATTGATGCCGTGGGGCTGGCACTGCTGGTTATTGGTATCGGCAGCCTGCAGATTATGCTCGACCGCGGTAAAGAGCTGGACTGGTTTTCATCACAGGAAATTATCATCCTTACCGTGGTGGCGGTGGTGGCTATCTGCTTCCTGATTGTCTGGGAGCTGACCGACGATAACCCGATAGTCGATCTGTCGTTGTTTAAGTCGCGCAACTTCACCATCGGCTGCTTGTGTATCAGCCTCGCGTATATGCTCTACTTCGGCGCTATTGTTCTGCTGCCGCAGTTGTTGCAGGAGGTCTACGGTTACACGGCGACCTGGGCAGGTTTGGCCTCTGCGCCGGTAGGGATTATTCCGGTGATCCTGTCGCCGATTATCGGCCGCTTCGCGCATAAACTGGATATGCGGCGGCTGGTAACCTTCAGCTTTATTATGTATGCCGTCTGCTTCTACTGGCGTGCCTATACCTTTGAACCAGGTATGGATTTTGGCGCGTCGGCCTGGCCGCAGTTTATCCAGGGGTTTGCGGTGGCCTGCTTCTTTATGCCGCTGACCACCATTACGCTGTCTGGTTTGCCACCGGAACGACTGGCGGCGGCATCGAGCCTCTCTAACTTTACGCGAACGCTGGCGGGGTCTATCGGCACGTCGATAACCACGACCATGTGGACCAACCGCGAGTCGATGCACCATGCGCAGTTGACTGAGTCGGTAAACCCGTTCAACCCGAATGCCCAGGCGATGTACAGTCAACTGGAAGGGCTTGGGATGACGCAACAGCAGGCATCAGGCTGGATTGCCCAGCAGATCACCAATCAGGGGCTGATTATTTCCGCCAATGAGATCTTCTGGATGTCAGCCGGGATATTCCTCATCCTGCTGGGGCTGGTGTGGTTTGCTAAACCGCCATTTGGCGCAGGTGGCGGCGGAGGCGGTGCGCACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42596","NCBI_taxonomy_name":"Escherichia coli KTE14","NCBI_taxonomy_id":"1169333"}}}},"ARO_accession":"3004597","ARO_id":"42528","ARO_name":"Klebsiella pneumoniae KpnH","CARD_short_name":"Kpne_KpnH","ARO_description":"KpnH consists of ~511 residues, resembles EmrB of E. coli, and is probably a translocase in the KpnGH-TolC efflux protein in K. pneumoniae. Disruption of the pump components KpnG-KpnH signficantly decrease resistance to azithromycin, ceftazidime, ciprofloxacin, ertapenem, erythromycin, gentamicin, imipenem, ticarcillin, norfloxacin, polymyxin-B, piperacillin, spectinomycin, tobramycin, and streptomycin.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"35987":{"category_aro_accession":"0000070","category_aro_cvterm_id":"35987","category_aro_name":"ertapenem","category_aro_description":"Ertapenem is a carbapenem antibiotic and is highly resistant to beta-lactamases like other carbapenems. It inhibits bacterial cell wall synthesis.","category_aro_class_name":"Antibiotic"},"35995":{"category_aro_accession":"0000078","category_aro_cvterm_id":"35995","category_aro_name":"piperacillin","category_aro_description":"Piperacillin is an acetylureidopenicillin and has an extended spectrum of targets relative to other beta-lactam antibiotics. It inhibits cell wall synthesis in bacteria, and is usually taken with the beta-lactamase inhibitor tazobactam to overcome penicillin-resistant bacteria.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"36309":{"category_aro_accession":"3000170","category_aro_cvterm_id":"36309","category_aro_name":"imipenem","category_aro_description":"Imipenem is a broad-spectrum antibiotic and is usually taken with cilastatin, which prevents hydrolysis of imipenem by renal dehydropeptidase-I. It is resistant to hydrolysis by most other beta-lactamases. Notable exceptions are the KPC beta-lactamases and Ambler Class B enzymes.","category_aro_class_name":"Antibiotic"},"36593":{"category_aro_accession":"3000454","category_aro_cvterm_id":"36593","category_aro_name":"polymyxin B","category_aro_description":"Polymyxin B is mixture of mostly polymyxins B1 and B2, mainly used for resistant gram-negative infections. They are polypeptides with cationic detergent action on cell membranes.","category_aro_class_name":"Antibiotic"},"36969":{"category_aro_accession":"3000625","category_aro_cvterm_id":"36969","category_aro_name":"polymyxin B1","category_aro_description":"Polymyxin B1 is in the family of polymyxin lipopeptides with a 6-methyloctanoic acid acyl group. These antibiotics disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36970":{"category_aro_accession":"3000626","category_aro_cvterm_id":"36970","category_aro_name":"polymyxin B2","category_aro_description":"Polymyxin B2 is in the family of polymyxin lipopeptides with a 6-methylheptanoic acid acyl group. These antibiotics disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36971":{"category_aro_accession":"3000627","category_aro_cvterm_id":"36971","category_aro_name":"polymyxin B3","category_aro_description":"Polymyxin B3 is in the family of polymyxin lipopeptides with an octanoic acid acyl group. These antibiotics disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36972":{"category_aro_accession":"3000628","category_aro_cvterm_id":"36972","category_aro_name":"polymyxin B4","category_aro_description":"Polymyxin B4 is in the family of polymyxin lipopeptides with a heptanoic acid acyl group. These antibiotics disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"40523":{"category_aro_accession":"3003832","category_aro_cvterm_id":"40523","category_aro_name":"ticarcillin","category_aro_description":"Ticarcillin is a carboxypenicillin used for the treatment of Gram-negative bacteria, particularly P. aeruginosa. Ticarcillin's antibiotic properties arise from its ability to prevent cross-linking of peptidoglycan during cell wall synthesis, when the bacteria try to divide, causing cell death.","category_aro_class_name":"Antibiotic"},"46133":{"category_aro_accession":"3007382","category_aro_cvterm_id":"46133","category_aro_name":"gentamicin","category_aro_description":"Gentamicin is a commonly used aminoglycoside antibiotic derived from members of the Micromonospora genus of bacteria. It acts by binding the 30S ribosomal subunit, thus inhibiting protein synthesis. Gentamicin is typically used to treat Gram-negative infections of the repiratory and urinary tract, as well as infections of the bone and soft tissue. It also exhibits considerable nephrotoxicity and ototoxicity. Gentamicin is administered as a mixture of gentamicin type C (which makes about around 80% of the complex) and types A, B, and X (distributed in the remaining 20% of the complex).","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"3300":{"model_id":"3300","model_name":"clcD","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"650"}},"model_sequences":{"sequence":{"5192":{"protein_sequence":{"accession":"AIX48090.1","sequence":"MQQKNKYIRIQEFLKQNKFPNYRMKQITNAIFPGRINNFNEITVLPKSLRDMLIEEFGESILNIVPLKAQQSTQVSKVLFGISGDEKIETVNMKYKAGWESFCISSQCGCNFGCKFCATGDIGLKRNLTSDEITDQILYFHLQGHSIDSISFMGMGEALANVQVFDALNVLTDPALFALSPRRLSISTIGIIPNIKKLTQNYPQVNLTFSLHSPFNEQRSELMPINERYPLSDVMDTLDEHIRVTSKKVYIAYIMLHGVNDSIEHAKEVVNLLRGRYRSGNLYHVNIIRYNPTISSRMRFEEANEKCLVNFYKELKSAGIKVTIRSQFGIDIDAACGQLYGNYQKTNSQ"},"dna_sequence":{"accession":"KM359438.1","fmin":"0","fmax":"1050","strand":"+","sequence":"ATGCAACAAAAAAATAAGTATATAAGAATTCAAGAGTTCTTGAAGCAGAATAAATTTCCTAATTATAGAATGAAACAAATTACAAATGCTATATTCCCAGGGAGAATAAATAATTTCAACGAAATAACGGTTCTTCCTAAATCACTAAGAGATATGTTAATTGAGGAGTTTGGAGAATCGATTTTAAATATTGTTCCTTTAAAAGCACAACAATCTACACAAGTTTCAAAAGTCTTATTTGGAATTTCAGGAGACGAAAAAATAGAAACGGTAAATATGAAATATAAAGCTGGTTGGGAGTCATTTTGTATATCATCGCAGTGCGGTTGTAATTTTGGTTGTAAATTTTGTGCAACTGGAGATATAGGTTTAAAACGTAACTTAACTTCAGATGAAATTACTGACCAGATTTTGTACTTTCACTTACAAGGGCATTCAATTGACAGTATTTCTTTTATGGGAATGGGAGAAGCATTAGCGAATGTACAAGTTTTTGATGCTTTAAATGTACTTACAGATCCTGCGTTGTTTGCTTTAAGTCCGCGTAGGTTATCTATATCCACTATAGGAATTATTCCAAACATTAAAAAATTGACTCAAAACTATCCGCAGGTCAACCTGACATTTTCATTACATTCTCCTTTTAATGAACAGCGAAGTGAGTTAATGCCAATTAATGAACGCTACCCATTATCAGATGTGATGGATACATTAGATGAGCATATACGAGTAACCTCAAAAAAAGTTTATATTGCTTATATTATGTTGCACGGAGTTAATGATTCTATTGAACATGCGAAAGAAGTCGTAAACCTTTTAAGAGGTAGATATAGGAGTGGGAACTTGTATCATGTGAACATCATTAGATATAACCCGACTATTAGTTCACGGATGCGGTTTGAAGAAGCAAATGAGAAATGTCTTGTCAACTTTTATAAAGAATTAAAGTCAGCAGGAATTAAAGTTACCATTAGAAGTCAATTTGGCATTGATATAGACGCTGCTTGCGGTCAATTGTATGGAAACTATCAAAAAACCAATAGCCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36807","NCBI_taxonomy_name":"Clostridioides difficile","NCBI_taxonomy_id":"1496"}}}},"ARO_accession":"3004599","ARO_id":"42532","ARO_name":"clcD","CARD_short_name":"clcD","ARO_description":"clcD gene can provide resistance to representatives of five of the six antibiotic groups previously shown to be affected by Cfr.  clcD was originally found in Clostridioides difficile and is cfr-like.","ARO_category":{"36341":{"category_aro_accession":"3000202","category_aro_cvterm_id":"36341","category_aro_name":"Cfr 23S ribosomal RNA methyltransferase","category_aro_description":"Cfr genes produce enzymes which catalyze the methylation of the 23S rRNA subunit at position 8 of adenine-2503. Methylation of 23S rRNA at this site confers resistance to some classes of antibiotics, including streptogramins, chloramphenicols, florfenicols, linezolids and clindamycin.","category_aro_class_name":"AMR Gene Family"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"35989":{"category_aro_accession":"0000072","category_aro_cvterm_id":"35989","category_aro_name":"linezolid","category_aro_description":"Linezolid is a synthetic antibiotic used for the treatment of serious infections caused by Gram-positive bacteria that are resistant to several other antibiotics. It inhibits protein synthesis by binding to domain V of the 23S rRNA of the 50S subunit of bacterial ribosomes.","category_aro_class_name":"Antibiotic"},"36600":{"category_aro_accession":"3000461","category_aro_cvterm_id":"36600","category_aro_name":"florfenicol","category_aro_description":"Florfenicol is a fluorine derivative of chloramphenicol, where the nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3) and the hydroxyl group (-OH), by a fluorine group (-F). The action mechanism is the same as chloramphenicol's, where the antibiotic binds to the 23S RNA of the 50S subunit of bacterial ribosomes to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"36723":{"category_aro_accession":"3000584","category_aro_cvterm_id":"36723","category_aro_name":"quinupristin","category_aro_description":"Quinupristin is a type B streptogramin and a semisynthetic derivative of pristinamycin 1A. It is a component of the drug Synercid and interacts with the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"37015":{"category_aro_accession":"3000671","category_aro_cvterm_id":"37015","category_aro_name":"tiamulin","category_aro_description":"Tiamulin is a pleuromutilin derivative currently used in veterinary medicine. It binds to the 23 rRNA of the 50S ribosomal subunit to inhibit protein translation.","category_aro_class_name":"Antibiotic"},"37018":{"category_aro_accession":"3000674","category_aro_cvterm_id":"37018","category_aro_name":"dalfopristin","category_aro_description":"Dalfopristin is a water-soluble semi-synthetic derivative of pristinamycin IIA. It is produced by Streptomyces pristinaespiralis and is used in combination with quinupristin in a 7:3 ratio. Both work together to inhibit protein synthesis, and is active against Gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"40952":{"category_aro_accession":"3004022","category_aro_cvterm_id":"40952","category_aro_name":"quinupristin-dalfopristin","category_aro_description":"An antibiotic cocktail of the streptogramin A dalfopristin and the streptogramin B quinupristin antibiotics. Used particularly to treat MRSA and vancomycin-resistant Enterococcus.","category_aro_class_name":"Antibiotic"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35952":{"category_aro_accession":"0000034","category_aro_cvterm_id":"35952","category_aro_name":"streptogramin A antibiotic","category_aro_description":"Streptogramin A antibiotics are cyclic polyketide peptide hybrids that bind to the ribosomal peptidyl transfer centre. Structural variation arises from substituting a proline for its desaturated derivative and by its substitution for Ala or Cys. Used alone, streptogramin A antibiotics are bacteriostatic, but is bactericidal when used with streptogramin B antibiotics.","category_aro_class_name":"Drug Class"},"35967":{"category_aro_accession":"0000050","category_aro_cvterm_id":"35967","category_aro_name":"streptogramin B antibiotic","category_aro_description":"Streptogramin B antibiotics are are cyclic hepta- or hexa-depsipeptides.  Type B streptogramins block the peptide exit tunnel of the 50S bacterial ribosome. The general composition of group B streptogramins is 3-hydroxypicolinic acid-L-Thr-D-aminobutyric acid (or D-Ala)-L-Pro-L-Phe (or 4-N-,N-(dimethylamino)-L-Phe)-X-L-phenylglycine. Used alone, streptogramin B antibiotics are bacteriostatic, but is bactericidal when used with streptogramin A antibiotics.","category_aro_class_name":"Drug Class"},"36218":{"category_aro_accession":"3000079","category_aro_cvterm_id":"36218","category_aro_name":"oxazolidinone antibiotic","category_aro_description":"Oxazolidinones are a class of synthetic antibiotics discovered the the 1980's.  They inhibit protein synthesis by binding to domain V of the 23S rRNA of the 50S subunit of bacterial ribosomes.  Linezolid is the only member of this class currently in clinical use.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"37014":{"category_aro_accession":"3000670","category_aro_cvterm_id":"37014","category_aro_name":"pleuromutilin antibiotic","category_aro_description":"Pleuromutilins are natural fungal products that target bacterial protein translation by binding the the 23S rRNA, blocking the ribosome P site at the 50S subunit. They are mostly used for agriculture and veterinary purposes.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3450":{"model_id":"3450","model_name":"OXA-285","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"5646":{"protein_sequence":{"accession":"ENX26326.1","sequence":"MKILILLPLLSCLGLTACTSPVSSFPSQITSTQSTQAIAQLFDQAQSSGVLVIQRGQKVQVYGNDLSRAGTEYVPASTFKMLNALIGLQHGKATTNEIFKWDGKKRSFAAWEKDMTLGEAMQASAVPVYQELARHIGLELMQQEVQRIQFGNQQIGQQVDNFWLVGPLKITPKQEVEFVSALAREQLAFDPQVQQQVKAMLLLQERQAYRLYAKSGWGMDVQPQVGWLTGWVETPQAEIVSFSLNMQMQNGMDPAIRLEILQQALAELGLYPKAEG"},"dna_sequence":{"accession":"APRY01000059.1","fmin":"64996","fmax":"65827","strand":"+","sequence":"ATGAAAATTCTGATTTTGCTACCTTTACTGAGTTGCTTGGGCCTGACAGCGTGTACCTCACCTGTTTCATCTTTCCCTTCTCAGATCACTTCAACTCAATCGACTCAAGCCATTGCCCAATTATTTGATCAGGCGCAAAGTTCTGGCGTTTTAGTGATTCAGCGTGGTCAAAAAGTACAGGTCTATGGCAATGATTTAAGCCGTGCAGGTACCGAATATGTTCCAGCCTCTACTTTCAAAATGCTCAATGCCCTGATTGGTCTACAACATGGTAAAGCCACAACCAATGAGATTTTTAAATGGGATGGCAAGAAACGCAGTTTTGCAGCCTGGGAAAAAGACATGACGCTCGGCGAAGCCATGCAAGCTTCTGCTGTACCCGTCTATCAGGAACTGGCACGTCATATTGGTTTGGAATTAATGCAGCAGGAAGTACAACGCATCCAATTTGGTAATCAGCAGATTGGTCAGCAGGTCGATAACTTCTGGTTGGTAGGCCCTTTGAAAATCACTCCAAAACAGGAAGTCGAATTTGTCTCTGCTCTAGCCCGAGAGCAACTAGCCTTTGATCCTCAAGTCCAGCAGCAAGTTAAAGCCATGTTACTTTTACAGGAACGGCAAGCTTATCGCCTATATGCCAAATCCGGTTGGGGCATGGATGTACAACCTCAAGTCGGCTGGCTTACCGGCTGGGTTGAAACACCGCAAGCCGAGATCGTGTCATTTTCACTGAATATGCAGATGCAAAATGGTATGGATCCGGCGATCCGCCTTGAAATTTTGCAGCAGGCTTTGGCCGAATTAGGGCTTTATCCAAAAGCTGAAGGATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42811","NCBI_taxonomy_name":"Acinetobacter sp. CIP 64.7","NCBI_taxonomy_id":"1144673"}}}},"ARO_accession":"3001740","ARO_id":"38140","ARO_name":"OXA-285","CARD_short_name":"OXA-285","ARO_description":"OXA-285 is a beta-lactamase found in Acinetobacter spp.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46489":{"category_aro_accession":"3007700","category_aro_cvterm_id":"46489","category_aro_name":"OXA-134-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-134.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3479":{"model_id":"3479","model_name":"OXA-345","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"5673":{"protein_sequence":{"accession":"AHN07463.1","sequence":"MNIKALLLITSAIFISACSPYIVSANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"KF048918.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGTCTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001533","ARO_id":"37933","ARO_name":"OXA-345","CARD_short_name":"OXA-345","ARO_description":"OXA-345 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3508":{"model_id":"3508","model_name":"OXA-438","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"5703":{"protein_sequence":{"accession":"AKL59521.1","sequence":"MRVLALSAVFLVASIIGMPAVAKEWQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGQTRDIATWNRDHNLITAMKYSVVPVYQEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISATEQISFLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYGYDTKIGWWVGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP"},"dna_sequence":{"accession":"KP410734.1","fmin":"0","fmax":"792","strand":"+","sequence":"ATGCGTGTATTAGCCTTATCGGCTGTGTTTTTGGTGGCATCGATTATCGGAATGCCTGCGGTAGCAAAGGAATGGCAAGAAAACAAAAGTTGGAATGCTCACTTTACTGAACATAAATCACAGGGCGTAGTTGTGCTCTGGAATGAGAATAAGCAGCAAGGATTTACCAATAATCTTAAACGGGCGAACCAAGCATTTTTACCCGCATCTACCTTTAAAATTCCCAATAGCTTGATCGCCCTCGATTTGGGCGTGGTTAAGGATGAACACCAAGTCTTTAAGTGGGATGGACAGACGCGCGATATCGCCACTTGGAATCGCGATCATAATCTAATCACCGCGATGAAATATTCAGTTGTGCCTGTTTATCAAGAATTTGCCCGCCAAATTGGCGAGGCACGTATGAGCAAGATGCTACATGCTTTCGATTATGGTAATGAGGACATTTCGGGCAATGTAGACAGTTTCTGGCTCGACGGTGGTATTCGAATTTCGGCCACGGAGCAAATCAGCTTTTTAAGAAAGCTGTATCACAATAAGTTACACGTATCGGAGCGCAGCCAGCGTATTGTCAAACAAGCCATGCTGACCGAAGCCAATGGCGACTATATTATTCGGGCTAAAACTGGATATGGATACGATACTAAGATTGGCTGGTGGGTCGGTTGGGTTGAACTTGATGATAATGTGTGGTTTTTTGCGATGAATATGGATATGCCCACATCGGATGGTTTAGGGCTGCGCCAAGCCATCACAAAAGAAGTGCTCAAACAGGAAAAAATTATTCCCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3003594","ARO_id":"40204","ARO_name":"OXA-438","CARD_short_name":"OXA-438","ARO_description":"OXA-438 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46510":{"category_aro_accession":"3007721","category_aro_cvterm_id":"46510","category_aro_name":"OXA-48-like beta-lactamase","category_aro_description":"OXA-48-type beta-lactamases are now routinely encountered in bacterial infections caused by carbapenam-resistant Enterobacterales. OXA-48-like proteins confer resistance to penicillin (which is efficiently hydrolyzed) and carbapenam antibiotics (which is more slowly broken down). The spectrum of activity of these variants varies, with some hydrolyzing expanded-spectrum oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3538":{"model_id":"3538","model_name":"OXA-476","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"5733":{"protein_sequence":{"accession":"ALC79291.1","sequence":"MSKKNFILIFIFVILISCKNTEKISNETTLIDNIFTNSNAEGTLVIYNLNDDKYIIHNKERAEQRFYPASTFKIYNSLIGLNEKAVKDVDEVFYKYNGEKVFLESWAKDSNLRYAIKNSQVPAYKELARRIGLKKMKENIEKLDFGNKSIGDNVDTFWLEGPLEISAMEQVKLLTKLAQNELPYPIEIQKAVSDITILEQTYNYTLHGKTGLADSENMTTEPIGWFVGWLEENDNIYVFALNIDNINSDDLAKRINIVKESLKALNLLK"},"dna_sequence":{"accession":"KR182169.1","fmin":"0","fmax":"810","strand":"+","sequence":"ATGTCTAAAAAAAATTTTATATTAATATTTATTTTTGTTATTTTAATATCTTGTAAAAATACAGAAAAAATATCAAATGAAACTACATTAATAGATAATATATTTACTAATAGCAATGCTGAAGGAACATTAGTTATATATAATTTAAATGATGATAAATATATAATTCATAATAAAGAAAGAGCTGAACAAAGATTTTATCCAGCATCAACATTTAAAATATATAATAGTTTAATAGGCTTAAATGAAAAAGCAGTTAAAGATGTAGATGAAGTATTTTATAAATATAATGGCGAAAAAGTTTTTCTTGAATCTTGGGCTAAGGACTCTAATTTAAGATATGCAATTAAAAATTCGCAAGTACCGGCATATAAAGAATTAGCAAGAAGAATAGGTCTTAAAAAGATGAAAGAGAATATAGAAAAACTAGATTTTGGTAATAAAAGTATAGGTGATAATGTAGATACTTTTTGGCTTGAAGGACCTTTGGAAATAAGTGCGATGGAGCAAGTTAAATTATTAACTAAATTAGCTCAAAATGAATTACCGTATCCTATAGAAATACAAAAAGCTGTTTCTGATATTACTATACTAGAGCAAACTTACAATTATACGCTTCATGGAAAAACTGGATTAGCTGATTCTGAAAACATGACAACTGAGCCTATTGGTTGGTTCGTAGGCTGGCTTGAAGAAAATGATAATATATATGTCTTTGCTTTAAATATTGATAATATCAATTCAGATGACCTTGCAAAAAGGATAAATATAGTAAAAGAAAGTTTAAAAGCATTAAATTTATTAAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36935","NCBI_taxonomy_name":"Brachyspira pilosicoli","NCBI_taxonomy_id":"52584"}}}},"ARO_accession":"3003633","ARO_id":"40243","ARO_name":"OXA-476","CARD_short_name":"OXA-476","ARO_description":"OXA-476 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46521":{"category_aro_accession":"3007732","category_aro_cvterm_id":"46521","category_aro_name":"OXA-63-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-63.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3582":{"model_id":"3582","model_name":"ERP-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"5780":{"protein_sequence":{"accession":"AAL86999.1","sequence":"MTILLQRRQLLVAGAALALTASLTPLNVFAAGDSLQRQLAALETEVNGRIGLSLIDSASQQAWSYRGDERFPLCSTFKLLLVAAVLKRSESQPALMQQTLHWTPADHLSYMPVTAKHPQGMTVSDLCAAALQYSDNLAANVLLTLLGGPASVTRLARSLGDSVTQLDRNEPTLNTAIPGDPRDTTTPLHMSHSVQQLLVKSGLQTAQQQQLIAWLKGNTTGKNAIAAALPAGWEIGDKTGSGGYGTTNDVAILWPPGKAPLILAIYFTQHAPEAKSRQDVLAKAAAIALKSVI"},"dna_sequence":{"accession":"AY077733.1","fmin":"0","fmax":"882","strand":"+","sequence":"ATGACGATTTTACTGCAACGCCGCCAGCTTCTGGTGGCGGGCGCGGCGCTGGCGCTGACCGCCTCGCTGACACCACTGAACGTATTTGCAGCAGGTGACTCGCTGCAGCGGCAGCTTGCCGCACTGGAAACGGAGGTGAATGGCCGTATCGGGCTGTCTCTGATCGACAGCGCCAGCCAGCAGGCGTGGAGCTATCGCGGTGACGAACGCTTTCCGCTGTGCAGCACCTTTAAACTGCTGCTGGTGGCTGCCGTTTTAAAACGCAGCGAGTCACAGCCCGCCCTGATGCAACAAACCCTGCACTGGACACCTGCGGATCACCTGAGCTATATGCCGGTAACGGCGAAGCATCCGCAGGGGATGACCGTCAGCGATCTGTGTGCAGCCGCGCTGCAGTACAGTGATAACCTGGCGGCCAACGTACTGTTGACACTGCTGGGGGGACCCGCGTCGGTGACCCGGCTGGCCCGCTCTTTAGGTGACAGTGTCACGCAGCTCGATCGTAATGAACCGACACTGAATACCGCGATCCCGGGCGATCCGCGTGACACCACCACGCCGCTGCACATGTCGCACAGCGTGCAGCAGTTGCTGGTGAAGTCGGGATTACAGACAGCACAGCAGCAGCAGCTGATCGCCTGGCTGAAGGGGAACACCACAGGGAAAAACGCCATTGCCGCAGCGCTGCCTGCGGGCTGGGAAATCGGGGATAAGACCGGCAGCGGGGGCTATGGCACAACCAACGATGTCGCCATCCTCTGGCCTCCGGGCAAGGCTCCGCTGATCCTGGCCATCTATTTTACCCAGCATGCCCCGGAGGCGAAGAGTCGTCAGGACGTGCTGGCGAAAGCGGCCGCCATTGCACTGAAATCTGTTATCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42899","NCBI_taxonomy_name":"Erwinia persicina","NCBI_taxonomy_id":"55211"}}}},"ARO_accession":"3004782","ARO_id":"42898","ARO_name":"ERP-1","CARD_short_name":"ERP-1","ARO_description":"ERP-1 is a class A beta-lactamase gene found in Erwinia persicina.","ARO_category":{"42897":{"category_aro_accession":"3004781","category_aro_cvterm_id":"42897","category_aro_name":"ERP beta-lactamase","category_aro_description":"ERP is a class A beta-lactamase gene family found in Erwinia persicina.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3663":{"model_id":"3663","model_name":"NDM-22","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"5936":{"protein_sequence":{"accession":"AWI33311.1","sequence":"MELPNIMHPVAKLSTALAAALMLSGCMPGEIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVLSHSAPDSRAAITHTARMADKLR"},"dna_sequence":{"accession":"MH243357.1","fmin":"0","fmax":"813","strand":"+","sequence":"ATGGAATTGCCCAATATTATGCACCCGGTCGCGAAGCTGAGCACCGCATTAGCCGCTGCATTGATGCTGAGCGGGTGCATGCCCGGTGAAATCCGCCCGACGATTGGCCAGCAAATGGAAACTGGCGACCAACGGTTTGGCGATCTGGTTTTCCGCCAGCTCGCACCGAATGTCTGGCAGCACACTTCCTATCTCGACATGCCGGGTTTCGGGGCAGTCGCTTCCAACGGTTTGATCGTCAGGGATGGCGGCCGCGTGCTGGTGGTCGATACCGCCTGGACCGATGACCAGACCGCCCAGATCCTCAACTGGATCAAGCAGGAGATCAACCTGCCGGTCGCGCTGGCGGTGGTGACTCACGCGCATCAGGACAAGATGGGCGGTATGGACGCGCTGCATGCGGCGGGGATTGCGACTTATGCCAATGCGTTGTCGAACCAGCTTGCCCCGCAAGAGGGGATGGTTGCGGCGCAACACAGCCTGACTTTCGCCGCCAATGGCTGGGTCGAACCAGCAACCGCGCCCAACTTTGGCCCGCTCAAGGTATTTTACCCCGGCCCCGGCCACACCAGTGACAATATCACCGTTGGGATCGACGGCACCGACATCGCTTTTGGTGGCTGCCTGATCAAGGACAGCAAGGCCAAGTCGCTCGGCAATCTCGGTGATGCCGACACTGAGCACTACGCCGCGTCAGCGCGCGCGTTTGGTGCGGCGTTCCCCAAGGCCAGCATGATCGTGCTGAGCCATTCCGCCCCCGATAGCCGCGCCGCAATCACTCATACGGCCCGCATGGCCGACAAGCTGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3004865","ARO_id":"43003","ARO_name":"NDM-22","CARD_short_name":"NDM-22","ARO_description":"A class B New Delhi metallo-beta-lactamase and NDM-1 variant.","ARO_category":{"36196":{"category_aro_accession":"3000057","category_aro_cvterm_id":"36196","category_aro_name":"NDM beta-lactamase","category_aro_description":"NDM beta-lactamases or New Delhi metallo-beta-lactamases are class B beta-lactamases that confer resistance to a broad range of antibiotics including carbapenems, cephalosporins and penicillins.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3715":{"model_id":"3715","model_name":"Mycobacterium tuberculosis mas mutations confer resistance to pyrazinamide","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"9639":"P398R","9640":"P495R","9642":"L98M","9644":"T2005P","9645":"S213C"},"ReSeqTB-High":{"9639":"P398R","9640":"P495R","9645":"S213C"},"clinical":{"9639":"P398R","9640":"P495R","9642":"L98M","9644":"T2005P","9645":"S213C"},"ReSeqTB-Minimal":{"9642":"L98M","9644":"T2005P"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"4180"}},"model_sequences":{"sequence":{"8835":{"protein_sequence":{"accession":"NP_217456.1","sequence":"MESRVTPVAVIGMGCRLPGGINSPDKLWESLLRGDDLVTEIPPDRWDADDYYDPEPGVPGRSVSRWGGFLDDVAGFDAEFFGISEREATSIDPQQRLLLETSWEAIEHAGLDPASLAGSSTAVFTGLTHEDYLVLTTTAGGLASPYVVTGLNNSVASGRIAHTLGLHGPAMTFDTACSSGLMAVHLACRSLHDGEADLALAGGCAVLLEPHASVAASAQGMLSSTGRCHSFDADADGFVRSEGCAMVLLKRLPDALRDGNRIFAVVRGTATNQDGRTETLTMPSEDAQVAVYRAALAAAGVQPETVGVVEAHGTGTPIGDPIEYRSLARVYGAGTPCALGSAKSNMGHSTASAGTVGLIKAILSLRHGVVPPLLHFNRLPDELSDVETGLFVPQAVTPWPNGNDHTPKRVAVSSFGMSGTNVHAIVEEAPAEASAPESSPGDAEVGPRLFMLSSTSSDALRQTARQLATWVEEHQDCVAASDLAYTLARGRAHRPVRTAVVAANLPELVEGLREVADGDALYDAAVGHGDRGPVWVFSGQGSQWAAMGTQLLASEPVFAATIAKLEPVIAAESGFSVTEAITAQQTVTGIDKVQPAVFAVQVALAATMEQTYGVRPGAVVGHSMGESAAAVVAGALSLEDAARVICRRSKLMTRIAGAGAMGSVELPAKQVNSELMARGIDDVVVSVVASPQSTVIGGTSDTVRDLIARWEQRDVMAREVAVDVASHSPQVDPILDDLAAALADIAPMTPKVPYYSATLFDPREQPVCDGAYWVDNLRNTVQFAAAVQAAMEDGYRVFAELSPHPLLTHAVEQTGRSLDMSVAALAGMRREQPLPHGLRGLLTELHRAGAALDYSALYPAGRLVDAPLPAWTHARLFIDDDGQEQRAQGACTITVHPLLGSHVRLTEEPERHVWQGDVGTSVLSWLSDHQVHNVAALPGAAYCEMALAAAAEVFGEAAEVRDITFEQMLLLDEQTPIDAVASIDAPGVVNFTVETNRDGETTRHATAALRAAEDDCPPPGYDITALLQAHPHAVNGTAMRESFAERGVTLGAAFGGLTTAHTAEAGAATVLAEVALPASIRFQQGAYRIHPALLDACFQSVGAGVQAGTATGGLLLPLGVRSLRAYGPTRNARYCYTRLTKAFNDGTRGGEADLDVLDEHGTVLLAVRGLRMGTGTSERDERDRLVSERLLTLGWQQRALPEVGDGEAGSWLLIDTSNAVDTPDMLASTLTDALKSHGPQGTECASLSWSVQDTPPNDQAGLEKLGSQLRGRDGVVIVYGPRVGDPDEHSLLAGREQVRHLVRITRELAEFEGELPRLFVVTRQAQIVKPHDSGERANLEQAGLRGLLRVISSEHPMLRTTLIDVDEHTDVERVAQQLLSGSEEDETAWRNGDWYVARLTPSPLGHEERRTAVLDPDHDGMRVQVRRPGDLQTLEFVASDRVPPGPGQIEVAVSMSSINFADVLIAFGRFPIIDDREPQLGMDFVGVVTAVGEGVTGHQVGDRVGGFSEGGCWRTFLTCDANLAVTLPPGLTDEQAITAATAHATAWYGLNDLAQIKAGDKVLIHSATGGVGQAAISIARAKGAEIFATAGNPAKRAMLRDMGVEHVYDSRSVEFAEQIRRDTDGYGVDIVLNSLTGAAQRAGLELLAFGGRFVEIGKADVYGNTRLGLFPFRRGLTFYYLDLALMSVTQPDRVRELLATVFKLTADGVLTAPQCTHYPLAEAADAIRAMSNAEHTGKLVLDVPRSGRRSVAVTPEQAPLYRRDGSYIITGGLGGLGLFFASKLAAAGCGRIVLTARSQPNPKARQTIEGLRAAGADIVVECGNIAEPDTADRLVSAATATGLPLRGVLHSAAVVEDATLTNITDELIDRDWSPKVFGSWNLHRATLGQPLDWFCLFSSGAALLGSPGQGAYAAANSWVDVFAHWRRAQGLPVSAIAWGAWGEVGRATFLAEGGEIMITPEEGAYAFETLVRHDRAYSGYIPILGAPWLADLVRRSPWGEMFASTGQRSRGPSKFRMELLSLPQDEWAGRLRRLLVEQASVILRRTIDADRSFIEYGLDSLGMLEMRTHVETETGIRLTPKVIATNNTARALAQYLADTLAEEQAAAPAAS"},"dna_sequence":{"accession":"NC_000962.3","fmin":"3276379","fmax":"3282715","strand":"-","sequence":"ATGGAATCACGTGTCACTCCCGTTGCGGTGATCGGGATGGGATGTCGGCTTCCTGGGGGGATCAACTCGCCCGACAAACTGTGGGAGTCGTTGCTGCGCGGTGATGACTTGGTCACCGAGATTCCGCCCGACCGCTGGGACGCCGACGACTATTACGACCCTGAGCCAGGGGTTCCCGGGCGGTCGGTGTCCCGGTGGGGTGGGTTCCTTGACGACGTCGCCGGTTTCGATGCTGAGTTCTTCGGGATTAGCGAGCGGGAAGCGACCTCGATCGATCCGCAGCAGCGGCTACTGCTGGAAACGTCGTGGGAGGCGATCGAGCATGCTGGTCTGGATCCGGCGTCGTTGGCCGGGTCCTCGACGGCCGTTTTTACTGGGCTGACCCACGAGGACTACCTGGTACTCACCACAACGGCGGGCGGTTTGGCCAGTCCATATGTGGTTACCGGCCTCAACAACAGTGTGGCGTCAGGGCGGATCGCGCACACATTGGGTCTACATGGTCCGGCGATGACGTTTGACACCGCGTGTTCTTCGGGTCTGATGGCGGTGCACCTGGCCTGCCGCAGCCTGCATGACGGCGAAGCTGACCTCGCTTTGGCGGGCGGTTGTGCGGTGCTGCTGGAGCCGCATGCCAGTGTGGCGGCGTCTGCGCAGGGCATGCTGTCGTCAACCGGTCGGTGCCATTCATTCGATGCTGACGCGGATGGGTTTGTGCGTTCCGAGGGCTGCGCGATGGTGTTGCTGAAGCGACTGCCGGATGCGCTGCGCGACGGTAATCGGATCTTCGCCGTGGTGCGTGGCACGGCCACCAATCAGGACGGCCGCACGGAGACGCTCACCATGCCGTCCGAGGACGCCCAGGTTGCCGTGTACCGTGCGGCGTTGGCGGCGGCGGGCGTGCAGCCCGAAACGGTCGGTGTGGTCGAGGCGCACGGCACCGGTACGCCAATCGGCGACCCGATTGAGTACCGCAGCCTGGCGCGGGTGTATGGCGCGGGCACCCCCTGCGCGCTTGGATCGGCCAAGAGCAACATGGGGCACAGCACGGCATCGGCGGGGACCGTCGGGCTGATCAAGGCAATTCTGTCACTGCGGCACGGGGTGGTGCCGCCGCTGCTGCATTTCAATCGGCTGCCCGATGAGCTTTCCGACGTCGAGACCGGGCTCTTTGTGCCGCAAGCGGTTACGCCGTGGCCCAACGGTAATGATCACACACCGAAGCGGGTCGCGGTGTCCTCGTTCGGGATGTCCGGGACCAACGTGCATGCCATCGTGGAAGAGGCCCCAGCAGAAGCTTCCGCACCCGAGAGTTCACCGGGCGACGCTGAGGTGGGCCCGCGGCTATTCATGCTGTCGTCCACGTCCAGCGACGCACTGCGCCAGACGGCCCGCCAACTAGCCACCTGGGTGGAAGAACACCAGGACTGCGTGGCGGCCTCGGATCTGGCCTACACGCTGGCGCGTGGCCGCGCGCACCGGCCGGTGCGCACCGCGGTGGTTGCCGCCAACCTGCCGGAGCTCGTCGAGGGTTTGCGCGAGGTGGCCGACGGTGACGCCCTCTATGACGCGGCGGTGGGACACGGTGATCGAGGACCGGTCTGGGTCTTCTCCGGGCAAGGGTCGCAGTGGGCGGCGATGGGCACGCAATTGCTCGCCAGCGAACCAGTGTTCGCGGCCACCATCGCCAAGCTGGAGCCGGTGATCGCCGCAGAATCGGGATTCTCGGTGACCGAGGCGATAACGGCGCAGCAGACCGTGACCGGAATCGACAAAGTGCAGCCGGCAGTGTTCGCCGTTCAGGTCGCGTTGGCCGCCACCATGGAGCAAACCTACGGAGTGCGGCCGGGCGCGGTCGTCGGACACTCGATGGGTGAGTCGGCCGCGGCCGTCGTCGCGGGGGCACTGTCGCTCGAGGACGCGGCGCGCGTCATTTGCCGCCGCTCGAAGCTGATGACCCGCATAGCCGGTGCTGGTGCCATGGGCTCGGTGGAATTGCCCGCCAAGCAAGTGAATTCGGAGCTGATGGCACGCGGAATCGACGATGTTGTGGTCTCGGTGGTGGCGTCCCCGCAATCCACGGTGATCGGCGGTACGAGCGACACCGTTCGTGACCTCATCGCCCGTTGGGAGCAGCGGGACGTGATGGCGCGCGAGGTGGCCGTCGACGTGGCGTCGCACTCGCCTCAAGTCGATCCGATACTCGACGATTTGGCCGCGGCGCTGGCGGACATTGCTCCGATGACGCCCAAGGTGCCGTACTACTCGGCGACCCTGTTCGACCCGCGCGAGCAGCCGGTGTGCGATGGCGCTTACTGGGTGGACAATCTGCGCAACACGGTGCAGTTCGCCGCGGCGGTGCAGGCTGCGATGGAGGACGGCTACCGGGTCTTCGCGGAGCTGTCGCCCCACCCGCTGCTTACCCACGCCGTCGAACAGACGGGCCGAAGCCTCGACATGTCGGTCGCCGCCCTGGCCGGCATGCGGCGAGAGCAGCCTCTGCCGCATGGTCTGCGCGGCTTGCTGACGGAGCTGCACCGCGCGGGCGCCGCTTTGGACTATTCGGCGCTGTATCCCGCTGGGCGGCTGGTGGATGCGCCGCTGCCGGCGTGGACCCACGCCCGCCTATTCATCGACGATGATGGGCAAGAACAGCGGGCACAAGGTGCCTGCACCATCACCGTGCATCCGTTGCTTGGCTCGCATGTGCGGCTGACTGAGGAACCTGAGCGCCACGTCTGGCAGGGCGACGTTGGCACCTCGGTGCTGTCCTGGCTCAGCGATCATCAGGTGCATAACGTTGCCGCCCTTCCCGGCGCCGCCTACTGCGAGATGGCTTTGGCTGCGGCCGCTGAGGTCTTCGGCGAAGCGGCTGAGGTTCGCGACATCACCTTTGAGCAGATGTTGTTGCTCGACGAGCAGACCCCGATCGACGCCGTCGCATCGATCGACGCGCCTGGTGTCGTCAACTTCACCGTGGAGACCAACCGGGACGGTGAAACCACCCGGCATGCCACCGCGGCGCTGCGCGCCGCCGAAGATGACTGCCCGCCGCCGGGGTACGACATCACCGCTCTGCTGCAGGCGCATCCGCACGCCGTGAACGGGACCGCCATGCGGGAATCGTTCGCCGAGCGTGGTGTTACTTTGGGCGCCGCGTTCGGTGGTCTGACCACCGCGCATACCGCCGAGGCGGGAGCCGCGACGGTGCTGGCCGAGGTCGCGCTGCCCGCGTCGATCCGGTTCCAGCAGGGCGCCTACCGAATCCACCCGGCGCTGCTGGACGCTTGTTTCCAGTCGGTCGGCGCGGGCGTCCAGGCCGGTACGGCCACTGGTGGCCTGCTGTTGCCGTTGGGTGTGCGCAGCCTGCGTGCCTACGGGCCTACCCGCAATGCCCGCTACTGCTACACGCGGTTGACCAAGGCCTTCAACGACGGGACCCGAGGTGGTGAGGCCGACCTCGACGTGCTGGACGAGCACGGGACCGTCCTGTTGGCCGTGCGTGGGCTACGCATGGGAACCGGGACCTCCGAACGCGACGAGCGTGACCGCCTAGTCAGCGAGCGGCTACTGACCCTCGGATGGCAGCAGCGAGCGCTGCCCGAGGTTGGCGACGGCGAGGCTGGATCGTGGCTATTGATCGACACTTCCAACGCCGTCGACACCCCCGACATGTTGGCTTCCACGTTGACGGACGCGCTGAAGTCCCACGGCCCCCAAGGCACCGAATGCGCCAGCCTGTCCTGGTCGGTCCAGGACACCCCGCCCAACGATCAAGCTGGCCTCGAAAAGCTGGGCAGCCAGCTGCGTGGCCGCGATGGTGTGGTGATCGTGTATGGGCCTCGCGTCGGCGACCCCGATGAGCACAGTCTGCTGGCCGGTCGTGAACAGGTCCGTCACCTGGTTCGGATCACCCGGGAACTGGCTGAATTCGAGGGCGAGCTGCCGCGCTTGTTCGTGGTGACCAGACAAGCCCAGATAGTGAAGCCGCACGACTCGGGAGAAAGAGCCAACCTGGAGCAGGCCGGCCTGCGTGGTCTGCTACGGGTGATCAGCAGTGAACATCCGATGCTGCGCACCACCTTGATCGATGTGGACGAACACACGGACGTTGAGCGGGTGGCCCAGCAGCTGCTGAGCGGATCGGAAGAGGACGAGACGGCCTGGCGGAATGGCGACTGGTATGTGGCCCGCTTGACCCCCAGTCCGCTGGGCCATGAAGAGCGGCGCACCGCGGTCTTGGATCCCGACCACGACGGTATGCGGGTGCAGGTCCGCAGGCCGGGAGACTTGCAAACGTTGGAATTCGTTGCGAGTGACCGAGTTCCGCCCGGCCCCGGGCAAATCGAAGTCGCGGTCAGCATGTCCAGCATCAACTTCGCCGACGTTTTGATCGCGTTTGGACGATTCCCCATTATCGATGACCGCGAGCCGCAGTTGGGTATGGATTTCGTCGGTGTGGTGACTGCGGTCGGGGAAGGTGTCACCGGTCACCAGGTCGGTGATCGTGTTGGCGGTTTCTCCGAAGGTGGCTGTTGGCGGACGTTCCTCACCTGTGACGCCAACCTCGCGGTCACGCTGCCGCCCGGCTTGACCGATGAGCAGGCGATCACGGCGGCCACCGCGCATGCCACCGCCTGGTATGGGCTCAACGACCTGGCTCAGATCAAGGCCGGTGACAAAGTGTTGATTCACTCCGCCACCGGCGGTGTGGGGCAGGCGGCCATATCGATTGCCCGCGCCAAGGGAGCGGAGATTTTCGCGACCGCCGGCAATCCCGCGAAGCGAGCCATGCTGCGCGACATGGGCGTCGAGCATGTCTACGATTCGCGCAGCGTCGAGTTCGCCGAGCAGATCCGGCGCGACACCGACGGGTACGGCGTGGATATCGTGCTGAACTCGCTGACCGGCGCCGCCCAACGTGCGGGGCTGGAGTTGTTGGCCTTCGGCGGACGCTTCGTCGAAATCGGCAAGGCCGACGTTTACGGCAACACCCGGCTGGGGCTGTTCCCGTTCCGTCGCGGACTGACCTTCTACTACTTGGACCTCGCGCTGATGTCGGTCACCCAGCCCGACCGGGTCCGTGAGTTGCTGGCCACGGTGTTCAAGCTCACCGCAGACGGGGTGCTGACCGCACCGCAATGCACTCATTACCCGTTGGCCGAGGCGGCCGACGCCATCCGGGCAATGAGCAACGCCGAGCACACCGGCAAACTCGTGCTCGACGTACCGCGTAGCGGCCGTAGAAGCGTGGCGGTCACCCCGGAGCAAGCTCCGCTGTACCGCCGCGACGGCTCCTACATCATCACCGGCGGCCTGGGTGGCCTCGGCCTGTTCTTCGCCTCGAAGCTGGCCGCGGCGGGCTGTGGCCGGATCGTGCTGACCGCACGTTCCCAGCCCAACCCCAAAGCGCGGCAGACCATCGAAGGCCTGCGCGCGGCTGGGGCCGACATCGTGGTGGAGTGTGGCAACATCGCCGAACCCGACACGGCGGACCGGCTGGTGAGTGCGGCGACCGCTACCGGGCTTCCGCTGCGCGGTGTGCTGCACTCGGCGGCGGTGGTCGAGGATGCCACGCTGACCAACATCACCGATGAGCTCATCGATCGCGACTGGTCGCCCAAGGTGTTCGGATCCTGGAACCTACACCGCGCCACCCTCGGTCAGCCGCTGGACTGGTTCTGCTTGTTCTCCTCGGGAGCGGCATTGCTCGGCTCGCCGGGTCAGGGCGCCTACGCGGCGGCCAACAGCTGGGTCGACGTCTTCGCGCACTGGCGCCGCGCCCAGGGCCTGCCGGTCAGCGCGATTGCGTGGGGTGCGTGGGGCGAGGTCGGCCGCGCCACGTTCTTGGCCGAGGGGGGCGAAATCATGATCACCCCGGAGGAAGGTGCGTATGCCTTCGAGACGCTCGTGCGCCACGACCGCGCCTACAGCGGTTACATTCCGATCCTCGGGGCGCCATGGCTGGCCGACCTTGTCCGACGCAGCCCGTGGGGTGAAATGTTCGCATCCACTGGGCAGCGGTCAAGGGGCCCAAGCAAATTCCGCATGGAGCTCCTTTCGCTGCCGCAAGATGAATGGGCCGGCCGGCTACGGCGTCTGCTGGTTGAGCAGGCCAGTGTGATCCTGCGTCGCACGATCGACGCTGACCGCTCATTCATCGAGTACGGCCTGGATTCGCTGGGCATGCTCGAGATGCGTACCCACGTTGAAACCGAGACCGGGATACGCCTGACCCCCAAGGTCATCGCCACAAACAACACCGCCCGCGCTTTGGCCCAGTACTTGGCGGACACGCTGGCCGAGGAGCAGGCGGCGGCACCGGCGGCATCATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3004978","ARO_id":"43165","ARO_name":"Mycobacterium tuberculosis mas mutations confer resistance to pyrazinamide","CARD_short_name":"Mtub_mas_PZA","ARO_description":"Mutations in mas that can contribute to or confer resistance to pyrazinamide.","ARO_category":{"43068":{"category_aro_accession":"3004882","category_aro_cvterm_id":"43068","category_aro_name":"pyrazinamide resistant mas","category_aro_description":"Mas is a multifunctional mycocerosic acid synthase membrane-associated mas. It catalyzes the elongation of N-fatty acyl-CoA with methylamalonyl-CoA as the elongating agent to form mycocerosyl fatty acids present in mycobacterium.","category_aro_class_name":"AMR Gene Family"},"39997":{"category_aro_accession":"3003413","category_aro_cvterm_id":"39997","category_aro_name":"pyrazinamide","category_aro_description":"Pyrazinamide is an antimycobacterial. It is highly specific and active only against Mycobacterium tuberculosis. This compound is a prodrug and needs to be activated inside the cell. It interferes with the bacterium's ability to synthesize new fatty acids, causing cell death.","category_aro_class_name":"Antibiotic"},"45737":{"category_aro_accession":"3007155","category_aro_cvterm_id":"45737","category_aro_name":"pyrazine antibiotic","category_aro_description":"A group of antibiotics derived from pyrazine.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3725":{"model_id":"3725","model_name":"Mycobacterium tuberculosis furA mutations confer resistance to isoniazid","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"12570":"A14V"},"ReSeqTB-Moderate":{"12570":"A14V"},"clinical":{"12570":"A14V"},"ReSeqTB-High":{"18571":"A14V"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"225"},"41339":{"param_type":"nucleotide substitution in promoter region","param_description":"A nucleotide sequence change where, compared to a reference sequence, one nucleotide is replaced by one other nucleotide in the promoter region of a gene. These substitutions are indicated as upstream of the reference sequence transcription initiation site. Format is given by [-][position][wildtype][>][mutation], e.g. -11t>c or -15g>Var where Var represents any possible substitution.","param_type_id":"41339","param_value":{"18571":"-26c>g"}}},"model_sequences":{"sequence":{"8817":{"protein_sequence":{"accession":"NP_216425.2","sequence":"MSSIPDYAEQLRTADLRVTRPRVAVLEAVNAHPHADTETIFGAVRFALPDVSRQAVYDVLHALTAAGLVRKIQPSGSVARYESRVGDNHHHIVCRSCGVIADVDCAVGEAPCLTASDHNGFLLDEAEVIYWGLCPDCSISDTSRSHP"},"dna_sequence":{"accession":"NC_000962.3","fmin":"2156148","fmax":"2156592","strand":"-","sequence":"GTGTCCTCTATACCGGACTACGCCGAACAGCTCCGGACGGCCGACCTGCGCGTGACCCGACCGCGCGTCGCCGTCCTGGAAGCAGTGAATGCGCATCCACACGCCGACACGGAAACGATTTTCGGTGCCGTGCGTTTTGCGCTGCCCGACGTATCCCGGCAAGCCGTGTACGACGTGCTGCATGCCCTGACCGCCGCGGGCTTGGTGCGAAAGATCCAACCCTCGGGCTCCGTCGCGCGCTACGAGTCCAGGGTCGGCGACAACCACCATCACATCGTCTGCCGGTCTTGCGGGGTTATCGCCGATGTCGACTGTGCTGTTGGCGAGGCACCCTGTCTGACGGCCTCGGACCATAACGGCTTCCTGTTGGACGAGGCGGAGGTCATCTACTGGGGTCTATGTCCTGATTGTTCGATATCCGACACTTCGCGATCACATCCGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3004923","ARO_id":"43109","ARO_name":"Mycobacterium tuberculosis furA mutations confer resistance to isoniazid","CARD_short_name":"Mtub_furA_INH","ARO_description":"Mutations that occur in furA that result in or contribute to antibiotic resistance to isoniazid.","ARO_category":{"43083":{"category_aro_accession":"3004897","category_aro_cvterm_id":"43083","category_aro_name":"isoniazid resistant furA","category_aro_description":"Transcriptional regulator furA, represses the transcription of the catalase-peroxidase gene katG and its own transcription by binding to the promoter region.","category_aro_class_name":"AMR Gene Family"},"36659":{"category_aro_accession":"3000520","category_aro_cvterm_id":"36659","category_aro_name":"isoniazid","category_aro_description":"Isoniazid is an organic compound that is the first-line anti tuberculosis medication in prevention and treatment. As a prodrug, it is activated by mycobacterial catalase-peroxidases such as M. tuberculosis KatG. Isoniazid inhibits mycolic acid synthesis, which prevents cell wall synthesis in mycobacteria.","category_aro_class_name":"Antibiotic"},"45734":{"category_aro_accession":"3007152","category_aro_cvterm_id":"45734","category_aro_name":"isoniazid-like antibiotic","category_aro_description":"A group of antibiotics containing isoniazid and its derivatives.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3750":{"model_id":"3750","model_name":"tet(57)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6041":{"protein_sequence":{"accession":"AJO67548.1","sequence":"MNKFAITALTITALDAMGIGLIMPVLPALLREYVSIEHLANHYGILLALYAIMQVFFAPLLGRWSDKFGRRPILLISLAGAALDYTLLALSSSLWMLYLGRLASGITGATGAVAASVIADHTQPQQRTKWFGRLGAAFGVGLIAGPAIGGFAGQLSPHLPFVIAAVLNACSFVVIWVIFKDQRKAVIQDAQHGDQPSPIPFMQIIKPIIQLLFVFFMAQLIGQIPATTWVLFTEGRFQWDSMQVGLSLAGLGVMHALFQAFVAGAIAKKFNEKVTIIVGFALDGSAFIILSLLAEGWLIYPTLILLAGGSIALPALQSLMSAQVNQANQGKLQGVLVSLTNATGVIGPLLFSVIFGQTLTMWDGWVWVIGAIMYVFLIVFILSFYRSSRPTIKQQTDN"},"dna_sequence":{"accession":"KP137702.1","fmin":"0","fmax":"1197","strand":"+","sequence":"ATGAATAAATTTGCGATCACAGCATTAACGATCACCGCCCTTGATGCGATGGGGATCGGGTTGATCATGCCAGTCTTACCAGCCTTACTCCGTGAATATGTCTCCATAGAACACTTGGCAAATCATTACGGCATCTTGTTGGCTTTATATGCCATCATGCAGGTATTTTTTGCCCCGCTACTTGGTAGATGGTCTGATAAATTCGGCCGCAGACCCATCTTGTTGATCTCCCTTGCAGGGGCAGCGCTGGACTACACTTTGTTGGCTTTATCCAGTTCACTATGGATGCTGTATTTAGGCCGCCTAGCCTCAGGGATCACTGGTGCAACAGGTGCGGTAGCCGCTTCTGTTATTGCCGACCATACACAGCCACAACAACGTACCAAGTGGTTTGGTCGTTTAGGGGCTGCGTTTGGCGTGGGTTTAATCGCCGGCCCTGCGATTGGCGGCTTTGCTGGGCAGTTATCTCCTCACTTGCCTTTTGTGATTGCGGCGGTCTTAAATGCATGCTCTTTTGTGGTGATTTGGGTTATTTTTAAAGATCAACGTAAGGCTGTCATACAGGATGCTCAACATGGAGATCAACCGTCGCCAATTCCCTTTATGCAAATAATAAAACCAATCATCCAGCTGCTTTTCGTCTTTTTTATGGCACAGCTCATTGGGCAGATCCCTGCCACTACTTGGGTGTTATTTACCGAAGGCCGCTTTCAGTGGGATAGCATGCAGGTTGGGCTGTCTTTAGCTGGCTTAGGCGTTATGCATGCCCTCTTCCAAGCCTTTGTTGCTGGCGCCATTGCCAAAAAATTCAATGAAAAGGTCACTATCATTGTCGGCTTTGCCCTAGATGGAAGCGCATTTATTATTTTGTCATTACTGGCAGAAGGTTGGTTGATTTACCCTACATTAATCTTACTCGCCGGTGGCAGTATCGCGTTACCCGCATTGCAAAGTTTGATGTCAGCTCAAGTCAACCAAGCTAACCAAGGAAAGCTCCAAGGGGTTTTAGTCAGTTTAACCAATGCCACAGGGGTCATTGGCCCATTATTATTTAGTGTTATTTTTGGCCAAACACTGACGATGTGGGATGGCTGGGTATGGGTGATTGGCGCGATAATGTATGTTTTCTTGATCGTATTTATTTTATCGTTTTATAGAAGCAGCAGACCGACAATTAAACAGCAGACCGACAATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42580","NCBI_taxonomy_name":"Providencia sp. Y14","NCBI_taxonomy_id":"1617397"}}}},"ARO_accession":"3005006","ARO_id":"43194","ARO_name":"tet(57)","CARD_short_name":"tet(57)","ARO_description":"A tetracycline efflux MFS Transporter from Providencia sp. Y14.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"3751":{"model_id":"3751","model_name":"TEM-181","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8385":{"protein_sequence":{"accession":"WP_000027060.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPVAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AM743197.2","fmin":"2076","fmax":"2937","strand":"-","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGTAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3001044","ARO_id":"37424","ARO_name":"TEM-181","CARD_short_name":"TEM-181","ARO_description":"TEM-181 is a beta-lactamase.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3754":{"model_id":"3754","model_name":"qacE","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"190"}},"model_sequences":{"sequence":{"6044":{"protein_sequence":{"accession":"AEH26330.1","sequence":"MKGWLFLVIAIVGEVIATSALKSSEGFTKLAPSAVVIIGYGIAFYFLSLVMKSIPVGVAYALWSGLGVVIITAIAWLLHGQKLDAWGFVGMGLIVSGVVVLNLLSKASAH"},"dna_sequence":{"accession":"HQ730118.1","fmin":"5174","fmax":"5507","strand":"+","sequence":"ATGAAAGGCTGGCTTTTTCTTGTTATCGCAATAGTTGGCGAAGTAATCGCAACATCCGCATTAAAATCTAGCGAGGGCTTTACTAAGCTTGCCCCTTCCGCCGTTGTCATAATCGGTTATGGCATCGCATTTTATTTTCTTTCTCTGGTTATGAAATCCATCCCTGTCGGTGTTGCTTATGCACTCTGGTCGGGACTCGGCGTCGTCATAATTACAGCCATTGCCTGGTTGCTTCATGGGCAAAAGCTTGATGCGTGGGGCTTTGTAGGTATGGGGCTCATAGTTAGTGGTGTAGTAGTTTTAAACTTGCTTTCCAAAGCAAGTGCCCACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3005009","ARO_id":"43197","ARO_name":"qacE","CARD_short_name":"qacE","ARO_description":"QacE is a resistance gene conferring resistance to antiseptics.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"43746":{"category_aro_accession":"3005386","category_aro_cvterm_id":"43746","category_aro_name":"disinfecting agents and antiseptics","category_aro_description":"Disinfectants that can also interact with antimicrobial resistance mechanisms, e.g. molecule efflux, and thus are the targets of disinfectant resistance.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"3755":{"model_id":"3755","model_name":"qacEdelta1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"190"}},"model_sequences":{"sequence":{"6045":{"protein_sequence":{"accession":"AAC44316.1","sequence":"MKGWLFLVIAIVGEVIATSALKSSEGFTKLAPSAVVIIGYGIAFYFLSLVLKSIPVGVAYAVWSGLGVVIITAIAWLLHGQKLDAWGFVGMGLIIAAFLLARSPSWKSLRRPTPW"},"dna_sequence":{"accession":"U49101.1","fmin":"1490","fmax":"1838","strand":"+","sequence":"ATGAAAGGCTGGCTTTTTCTTGTTATCGCAATAGTTGGCGAAGTAATCGCAACATCCGCATTAAAATCTAGCGAGGGCTTTACTAAGCTTGCCCCTTCCGCCGTTGTCATAATCGGTTATGGCATCGCATTTTATTTTCTTTCTCTGGTTCTGAAATCCATCCCTGTCGGTGTTGCTTATGCAGTCTGGTCGGGACTCGGCGTCGTCATAATTACAGCCATTGCCTGGTTGCTTCATGGGCAAAAGCTTGATGCGTGGGGCTTTGTAGGTATGGGGCTCATAATTGCTGCCTTTTTGCTCGCCCGATCCCCATCGTGGAAGTCGCTGCGGAGGCCGACGCCATGGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005010","ARO_id":"43198","ARO_name":"qacEdelta1","CARD_short_name":"qacEdelta1","ARO_description":"QacEdelta1 is a resistance gene conferring resistance to antiseptics. It is different from QacE only at the 3'-terminus.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"43746":{"category_aro_accession":"3005386","category_aro_cvterm_id":"43746","category_aro_name":"disinfecting agents and antiseptics","category_aro_description":"Disinfectants that can also interact with antimicrobial resistance mechanisms, e.g. molecule efflux, and thus are the targets of disinfectant resistance.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"3756":{"model_id":"3756","model_name":"IDC-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"775"}},"model_sequences":{"sequence":{"6046":{"protein_sequence":{"accession":"QIB98918.1","sequence":"MPRTESVPSKSLVVRTLLLVFACLFPMAVPAVEDSSRVRAAVDAAILPLMSQHDIPGMAVGLILDGQPYVVTYGVASKETNVPVAEATLFEIGSVSKVFTATLATYAQATGKLSLDDHPGKYLPHLKGAPIDQATLLHLGTYTAGGLPLQFPDEVTGEAAVMNYFRNWTPLAPPGTRREYSNASPGLLGVVAASALDDDFATLMQTTVFPAFGMTDSFIHVPDRKMPDYAWGYRKDRRVRVNEGPLDEQAYGVKTTVSDLLRFVQANIDPNSLEPSMRHAVEATQVGYFRAGTLVQGLGWEKYPYPVSREWLLGGNAKEMLFDPQPAYRLTDQTAGGQYLFNKTGSTGGFATYVAFVPARKIGIVMLANRSYPIPDRVEAAWMILEQLASGTDSN"},"dna_sequence":{"accession":"MN985649.1","fmin":"102","fmax":"1290","strand":"+","sequence":"ATGCCGAGAACTGAATCCGTGCCATCCAAGTCCCTTGTTGTTAGGACGCTGCTGCTCGTCTTCGCCTGCCTCTTTCCTATGGCAGTTCCAGCAGTCGAAGACTCCTCCCGTGTCCGCGCCGCCGTCGACGCCGCGATCCTGCCCTTAATGTCCCAGCATGACATCCCCGGCATGGCTGTCGGGCTGATCCTCGATGGCCAGCCCTATGTTGTTACGTATGGCGTCGCCTCGAAGGAAACCAACGTACCCGTAGCGGAGGCAACACTATTCGAGATCGGCTCCGTCAGCAAAGTCTTCACCGCAACGCTGGCCACCTACGCGCAAGCCACCGGCAAATTGTCCCTGGACGACCATCCGGGCAAGTACCTGCCGCATTTAAAAGGCGCGCCGATCGACCAAGCCACGTTGCTTCACCTGGGAACCTACACCGCCGGCGGACTGCCGTTGCAGTTCCCTGATGAGGTGACGGGAGAGGCGGCGGTGATGAACTACTTCCGCAACTGGACGCCGCTGGCTCCCCCGGGCACACGGCGCGAGTACTCCAACGCAAGCCCGGGCTTGCTCGGGGTTGTTGCGGCCAGCGCGCTGGATGACGATTTCGCGACGTTGATGCAAACGACGGTATTTCCCGCATTCGGCATGACGGACAGCTTCATTCACGTGCCGGACCGCAAGATGCCGGACTACGCGTGGGGCTATCGCAAGGACAGACGGGTCCGTGTGAACGAGGGGCCGCTTGACGAGCAGGCTTACGGCGTCAAGACGACGGTGTCGGACTTGCTCCGCTTCGTGCAGGCGAACATCGATCCGAACTCGCTCGAGCCGTCGATGCGCCACGCCGTCGAAGCCACGCAGGTCGGATACTTCCGCGCGGGGACTCTGGTGCAGGGCCTTGGGTGGGAAAAGTATCCGTACCCTGTCTCACGCGAATGGCTGCTCGGCGGCAACGCCAAGGAGATGCTTTTCGATCCACAGCCTGCCTATCGGCTGACGGACCAGACCGCAGGCGGACAGTATCTCTTTAACAAGACGGGATCGACCGGCGGCTTCGCCACTTACGTGGCATTCGTGCCCGCTAGGAAGATCGGGATCGTCATGCTGGCAAACCGGAGTTATCCAATTCCGGATCGCGTTGAGGCCGCCTGGATGATCTTGGAACAACTTGCATCGGGGACCGACTCAAATTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43201","NCBI_taxonomy_name":"sediment metagenome","NCBI_taxonomy_id":"749907"}}}},"ARO_accession":"3005012","ARO_id":"43200","ARO_name":"IDC-1","CARD_short_name":"IDC-1","ARO_description":"IDC-2 is an IDC beta-lactamase and an integron cephalosprinase.","ARO_category":{"43199":{"category_aro_accession":"3005011","category_aro_cvterm_id":"43199","category_aro_name":"IDC beta-lactamase","category_aro_description":"IDC beta-lactamases are class C beta-lactamases inc. cephalosporinases and carbapenemases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3757":{"model_id":"3757","model_name":"IDC-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"775"}},"model_sequences":{"sequence":{"6047":{"protein_sequence":{"accession":"QIB98910.1","sequence":"MPRTESVPSKSLVVRTLLLVFACLFPMAVPAVEDTSRVRTTVDAAILPLMSQHDIPGMVVGLILDGQPYVVTYGVASKEANVPVAEATLFEIGSVSKVFTATLAAYAQTTGKLSLDDHPGKYLPQLKGTPIDQATLLHLGTYTAGGLPLQFPDEVTGEVAVMDYFRNWTPLAPPGTRREYSNASPGLLGLVAASALDDDFATLMQSTVFPAFGMTDSFIHVPDRKMPDYAWGYRKDRPVRVNEGPLDEQAYGVKTTVSDLLRFVQANIDPSSLEPSMRRAVEATQVGYFRAGTLVQGLGWEKYPYPVSREWLLGGNAKEMLFDPQPAYRLTDQTAGERYLFNKTGSTGGFATYVAFVPARKIGIVMLANRSYPIPDRVEAAWIILEQLASGTDSN"},"dna_sequence":{"accession":"MN985646.1","fmin":"343","fmax":"1531","strand":"+","sequence":"ATGCCGAGAACTGAATCCGTGCCATCCAAGTCCCTTGTCGTTAGGACGCTGCTGCTCGTCTTCGCTTGCCTCTTTCCTATGGCAGTTCCAGCCGTCGAAGACACCTCCCGTGTCCGCACCACCGTCGACGCCGCGATCCTGCCCCTAATGTCCCAGCATGACATCCCCGGCATGGTTGTCGGGCTGATCCTCGATGGCCAGCCCTATGTTGTTACGTATGGCGTCGCCTCGAAGGAAGCCAACGTACCGGTAGCGGAGGCAACACTATTCGAGATCGGCTCCGTCAGCAAAGTCTTCACCGCAACGCTGGCCGCCTACGCGCAAACCACCGGCAAACTCTCCCTGGACGACCATCCGGGCAAGTACCTGCCGCAGTTGAAGGGCACGCCGATCGACCAAGCCACGTTGCTCCACTTGGGAACCTACACCGCCGGCGGACTGCCGTTGCAGTTCCCTGATGAGGTGACGGGAGAGGTGGCGGTGATGGACTACTTCCGCAACTGGACGCCGCTAGCTCCCCCGGGCACACGGCGCGAGTACTCCAACGCGAGCCCGGGCTTGCTCGGGCTTGTTGCGGCCAGCGCGCTGGATGACGATTTCGCGACGTTGATGCAATCGACGGTATTTCCAGCGTTCGGCATGACGGACAGCTTCATTCACGTGCCGGACCGCAAGATGCCGGACTACGCGTGGGGCTATCGCAAGGACAGACCGGTCCGTGTGAACGAGGGGCCGCTCGACGAGCAGGCTTACGGTGTCAAGACGACGGTGTCGGACTTGCTCCGCTTCGTGCAAGCAAACATCGATCCGAGTTCGCTCGAGCCGTCGATGCGCCGCGCCGTCGAAGCCACGCAGGTCGGATACTTCCGCGCGGGGACTCTGGTGCAGGGCCTTGGGTGGGAAAAGTATCCGTACCCTGTCTCACGCGAATGGCTGCTCGGTGGCAACGCCAAGGAGATGCTTTTCGATCCACAGCCTGCCTATCGGCTGACGGACCAAACCGCGGGCGAGCGGTATCTCTTTAACAAGACGGGATCGACCGGCGGCTTCGCCACTTACGTGGCGTTCGTGCCCGCTAGGAAGATCGGGATCGTCATGCTGGCAAACCGGAGTTATCCAATTCCGGATCGCGTTGAGGCCGCCTGGATCATTCTGGAACAACTTGCATCAGGGACCGACTCAAACTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43201","NCBI_taxonomy_name":"sediment metagenome","NCBI_taxonomy_id":"749907"}}}},"ARO_accession":"3005013","ARO_id":"43202","ARO_name":"IDC-2","CARD_short_name":"IDC-2","ARO_description":"IDC-2 is an IDC beta-lactamase and an integron cephalosprinase.","ARO_category":{"43199":{"category_aro_accession":"3005011","category_aro_cvterm_id":"43199","category_aro_name":"IDC beta-lactamase","category_aro_description":"IDC beta-lactamases are class C beta-lactamases inc. cephalosporinases and carbapenemases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3758":{"model_id":"3758","model_name":"VMB-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"6048":{"protein_sequence":{"accession":"QGQ32905.1","sequence":"MKYIILFLLLIPSIVFANNEGTKELKLKKLSDNVYQHISYKRVEPWGLIGASGLVVINGTEAHMIDTPWTTQGTKQLIEWIEAKGLTIKSAVVTHFHEDASGDIPLLNDLKIKTYATSLTNKLLKLNQKEVSSDEISSNTFEFIDGVASVFYPGAGHTEDNIVVWLPNEKILFGGCFVKSLKNKNLGYTGDANISEWPNSMQKVINRYPDAKLVVPGHGEVGDVSLLKHTQALALSAAASNKKINKD"},"dna_sequence":{"accession":"MN719868.1","fmin":"12","fmax":"756","strand":"+","sequence":"ATGAAGTATATTATTCTATTCCTTCTCTTGATTCCTTCTATTGTATTTGCAAACAACGAAGGCACTAAAGAACTTAAATTAAAAAAGTTAAGTGATAACGTTTATCAACATATTTCATATAAGAGGGTTGAGCCATGGGGTTTAATTGGAGCCTCAGGCTTAGTTGTTATTAATGGCACTGAAGCACATATGATTGATACACCTTGGACAACCCAAGGAACAAAACAACTAATTGAATGGATTGAGGCTAAAGGTCTAACTATAAAAAGTGCAGTAGTTACGCATTTTCATGAGGATGCTAGTGGTGATATACCACTTTTAAATGATTTGAAAATAAAAACGTATGCAACATCACTAACTAATAAGCTTCTTAAATTAAACCAAAAAGAAGTGTCTAGTGATGAAATATCAAGTAATACCTTTGAATTTATTGATGGTGTTGCTAGTGTATTTTATCCCGGAGCGGGGCATACAGAGGATAATATTGTTGTTTGGCTACCTAATGAAAAGATATTGTTTGGAGGTTGTTTTGTAAAAAGCCTTAAGAATAAAAATTTAGGTTATACAGGCGACGCAAATATTAGTGAATGGCCAAACTCTATGCAAAAAGTCATTAATCGTTATCCTGATGCCAAATTAGTTGTTCCAGGACATGGTGAAGTCGGAGATGTTAGCTTACTGAAGCATACTCAAGCATTAGCTTTGTCTGCAGCGGCCTCTAACAAGAAAATCAACAAGGACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43205","NCBI_taxonomy_name":"Vibrio alginolyticus","NCBI_taxonomy_id":"663"}}}},"ARO_accession":"3005015","ARO_id":"43204","ARO_name":"VMB-1","CARD_short_name":"VMB-1","ARO_description":"Vibrio metallo-B-lactamase 1, also known as VMB-1, is carbapenemase beta-lactamase that is found in plasmid pVB1796 from Vibrio alginolyticus.","ARO_category":{"43203":{"category_aro_accession":"3005014","category_aro_cvterm_id":"43203","category_aro_name":"VMB beta-lactamase","category_aro_description":"Vibro metallo-B-lactamase, also known as VMB is a carbapenemase beta-lactamase gene family.","category_aro_class_name":"AMR Gene Family"},"35979":{"category_aro_accession":"0000062","category_aro_cvterm_id":"35979","category_aro_name":"ceftriaxone","category_aro_description":"Ceftriaxone is a third-generation cephalosporin antibiotic. The presence of an aminothiazolyl sidechain increases ceftriazone's resistance to beta-lactamases. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"35981":{"category_aro_accession":"0000064","category_aro_cvterm_id":"35981","category_aro_name":"amoxicillin","category_aro_description":"Amoxicillin is a moderate-spectrum, bacteriolytic, beta-lactam antibiotic used to treat bacterial infections caused by susceptible microorganisms. A derivative of penicillin, it has a wider range of treatment but remains relatively ineffective against Gram-negative bacteria. It is commonly taken with clavulanic acid, a beta-lactamase inhibitor. Like other beta-lactams, amoxicillin interferes with the synthesis of peptidoglycan.","category_aro_class_name":"Antibiotic"},"35990":{"category_aro_accession":"0000073","category_aro_cvterm_id":"35990","category_aro_name":"meropenem","category_aro_description":"Meropenem is an ultra-broad spectrum injectable antibiotic used to treat a wide variety of infections, including meningitis and pneumonia. It is a beta-lactam and belongs to the subgroup of carbapenem, similar to imipenem and ertapenem.","category_aro_class_name":"Antibiotic"},"36309":{"category_aro_accession":"3000170","category_aro_cvterm_id":"36309","category_aro_name":"imipenem","category_aro_description":"Imipenem is a broad-spectrum antibiotic and is usually taken with cilastatin, which prevents hydrolysis of imipenem by renal dehydropeptidase-I. It is resistant to hydrolysis by most other beta-lactamases. Notable exceptions are the KPC beta-lactamases and Ambler Class B enzymes.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"36989":{"category_aro_accession":"3000645","category_aro_cvterm_id":"36989","category_aro_name":"cefotaxime","category_aro_description":"Cefotaxime is a semisynthetic cephalosporin taken parenterally. It is resistant to most beta-lactamases and active against Gram-negative rods and cocci due to its aminothiazoyl and methoximino functional groups.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3759":{"model_id":"3759","model_name":"APH(3')-VIb","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6049":{"protein_sequence":{"accession":"CAF29483.1","sequence":"MELPNIIQQFIGNSVLEPNKIGQSPSDVYSFNRNNETFFLKRSSTLYTETTYSVSREAKMLSWLSDKLKVPELIMTFQDEQFEFMITKAINAKSISALFLTEQELLAIYKETLNQLNAVAIIDCPFISSIDHRLKESKFFIDNQLLDEIDQDDFEAELWGDHKTYISLWNELNETRVEERLVFSHGDITDSNIFIDKSGEIYFLDLGRAGLADEFVDISFVERCLREDVSEETAKIFLKHLKNDMPDKRNYFLKLDELN"},"dna_sequence":{"accession":"AJ627643.4","fmin":"4933","fmax":"5713","strand":"+","sequence":"ATGGAATTGCCCAATATTATTCAACAATTTATTGGAAACAGCGTTTTAGAGCCAAATAAAATTGGTCAGTCGCCATCGGATGTTTATTCTTTTAATCGAAATAATGAAACTTTTTTTCTTAAGCGATCTAGCACTTTATATACAGAGACCACATACAGTGTCTCTCGTGAAGCGAAAATGTTGAGTTGGCTCTCTGATAAATTAAAGGTGCCTGAACTCATCATGACTTTTCAGGATGAGCAGTTTGAATTCATGATCACTAAAGCGATCAATGCAAAATCAATTTCAGCGCTTTTTTTAACAGAGCAAGAATTGCTTGCTATCTATAAGGAAACACTCAATCAGTTAAATGCAGTTGCTATTATTGATTGCCCATTTATTTCAAGCATTGATCATCGGTTAAAAGAGTCAAAATTTTTTATTGATAACCAACTCCTTGACGAGATAGATCAAGATGATTTTGAGGCTGAATTATGGGGAGACCATAAAACTTACATAAGTCTTTGGAATGAGTTAAATGAGACTCGTGTTGAAGAAAGATTGGTTTTTTCTCATGGCGATATCACGGATAGTAATATTTTTATAGATAAATCTGGTGAAATTTACTTTTTAGATCTTGGTCGTGCTGGATTAGCAGATGAATTTGTAGATATATCTTTTGTTGAACGTTGCCTAAGAGAGGATGTATCTGAGGAAACTGCTAAAATATTTTTAAAGCATTTAAAAAACGATATGCCTGACAAAAGGAATTATTTTTTAAAACTTGATGAATTGAATTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43206","NCBI_taxonomy_name":"Alcaligenes faecalis","NCBI_taxonomy_id":"511"}}}},"ARO_accession":"3002653","ARO_id":"39053","ARO_name":"APH(3')-VIb","CARD_short_name":"APH(3')-VIb","ARO_description":"APH(3')-VIb is a plasmid-encoded aminoglycoside phosphotransferase in K. pneumoniae and S. marcescens.","ARO_category":{"36265":{"category_aro_accession":"3000126","category_aro_cvterm_id":"36265","category_aro_name":"APH(3')","category_aro_description":"A category of aminoglycoside O-phosphotransferase enzymes with modification regiospecificity based at the 3'-hydroxyl group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics, specifically kanamycin and neomycin, by the ATP-dependent phosphorylation of the 3'-hydroxyl group of the compound.","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35940":{"category_aro_accession":"0000021","category_aro_cvterm_id":"35940","category_aro_name":"ribostamycin","category_aro_description":"Ribostamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Ribostamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35943":{"category_aro_accession":"0000024","category_aro_cvterm_id":"35943","category_aro_name":"butirosin","category_aro_description":"Butirosin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Butirosin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36996":{"category_aro_accession":"3000652","category_aro_cvterm_id":"36996","category_aro_name":"isepamicin","category_aro_description":"A semi-synthetic derivative of gentamicin B (hydroxyamino propionyl genamicin B). It is modified to combat microbial inactivation and has a slightly larger spectrum of activity compared to other aminoglycosides, including Ser marcescens, Enterobacteria, and K pneumoniae.","category_aro_class_name":"Antibiotic"},"36999":{"category_aro_accession":"3000655","category_aro_cvterm_id":"36999","category_aro_name":"gentamicin B","category_aro_description":"Gentamicin B is a semisynthetic aminoglycoside antibacterial.","category_aro_class_name":"Antibiotic"},"37001":{"category_aro_accession":"3000657","category_aro_cvterm_id":"37001","category_aro_name":"paromomycin","category_aro_description":"An aminoglycoside antibiotic used for the treatment of parasitic infections. It is similar to neomycin sharing a similar spectrum of activity, but its hydroxyl group at the 6'-position instead of an amino group makes it resistant to AAC(6') modifying enzymes.","category_aro_class_name":"Antibiotic"},"46133":{"category_aro_accession":"3007382","category_aro_cvterm_id":"46133","category_aro_name":"gentamicin","category_aro_description":"Gentamicin is a commonly used aminoglycoside antibiotic derived from members of the Micromonospora genus of bacteria. It acts by binding the 30S ribosomal subunit, thus inhibiting protein synthesis. Gentamicin is typically used to treat Gram-negative infections of the repiratory and urinary tract, as well as infections of the bone and soft tissue. It also exhibits considerable nephrotoxicity and ototoxicity. Gentamicin is administered as a mixture of gentamicin type C (which makes about around 80% of the complex) and types A, B, and X (distributed in the remaining 20% of the complex).","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3760":{"model_id":"3760","model_name":"CMY-150","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"782"}},"model_sequences":{"sequence":{"8391":{"protein_sequence":{"accession":"PUU64961.1","sequence":"MMKKSICCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAIIYEGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWRGISLLHLATYTAGGLPLQIPDDVTDKAELLRFYQNWQPQWTPGAKRLYANSSIGLFGALVVKHSGMSYEEAMTRRVLQPLKLAHTWITVPQSEQKNYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASLVQEKTLQQGIELAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPARVEAAWRILEKLQ"},"dna_sequence":{"accession":"QCWX01000028.1","fmin":"20234","fmax":"21380","strand":"-","sequence":"ATGATGAAAAAATCGATATGCTGCGCACTGCTGCTGACAGCCTCTTTCTCCACGTTTGCTGCCGCAAAAACAGAACAACAAATTGCCGATATCGTTAACCGCACCATCACACCACTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTGGCGATTATCTACGAGGGGAAACCTTATTACTTTACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGACGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCGGGGTATCAGCCTGCTGCACTTAGCCACCTATACAGCGGGTGGCCTGCCGCTGCAGATCCCCGATGACGTTACGGATAAAGCCGAATTACTGCGCTTTTATCAAAACTGGCAACCACAATGGACTCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGTGCGCTGGTGGTAAAACATTCAGGTATGAGCTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAAAGCGAACAAAAAAATTATGCCTGGGGCTATCGCGAAGGGAAGCCTGTACACGTTTCTCCGGGGCAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATCGATATGGCCCGCTGGGTTCAGGCCAACATGGACGCCAGCCTCGTTCAGGAGAAAACGCTCCAGCAGGGCATTGAGCTTGCGCAGTCTCGCTACTGGCGTATTGGTGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCAGCACCTGCCGTGAAAGCCTCATGGGTGCATAAAACAGGATCCACAGGCGGATTTGGCAGCTACGTTGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTAATGTTGGCAAACAAAAGCTACCCCAACCCGGCTCGCGTCGAGGCGGCCTGGCGCATTCTTGAAAAACTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3005016","ARO_id":"43207","ARO_name":"CMY-150","CARD_short_name":"CMY-150","ARO_description":"CMY-150 is a CMY-2 variant differing by 15 amino-acid substitutions. It confers higher resistance levels to ceftazidime and aztreonam compared to CMY-2.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3761":{"model_id":"3761","model_name":"LMB-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"6051":{"protein_sequence":{"accession":"AYD68552.1","sequence":"MTLAKSFRCFCLVTTLSSMAMLAGCGGTAPVTVLSPPPADWVNSCKDWDDWDKAGPPYRIYGNSYYVGTCGISAILITGDNGHILIDGATEAGAKVIAANIDRLGFSLRDVKLLLQSHEHFDHVAGLAQLQQQSGAKLLASPAAAPVLTSGVVAAADPQAGMHEPFPAVRVDGLVTAGQVVTLGKLSLLPVATPGHTPGALSWQWSSCEAGQCQVLVYADSLSPVSSDSYRFSEHLTYLNAYRASLHKLAALDCQILLTPHPSASNMRTRLQSSAGLTDTQGCVVYADAITQRLEQRLIKETTQ"},"dna_sequence":{"accession":"MH475146.1","fmin":"158348","fmax":"159263","strand":"+","sequence":"ATGACGTTAGCTAAAAGTTTTCGCTGTTTTTGCCTTGTAACTACATTAAGTTCGATGGCTATGCTGGCCGGTTGCGGCGGCACAGCCCCGGTAACAGTATTAAGCCCACCGCCAGCAGACTGGGTTAACAGCTGTAAAGACTGGGATGACTGGGACAAAGCCGGGCCGCCGTATCGGATTTATGGCAACAGTTACTATGTGGGCACCTGTGGTATCAGCGCTATTTTGATCACCGGTGATAACGGCCATATTCTGATCGATGGCGCCACTGAAGCGGGTGCAAAGGTAATTGCTGCCAATATCGACAGGCTGGGTTTTTCACTGCGTGATGTAAAGTTGCTACTGCAAAGCCATGAGCATTTCGATCATGTGGCCGGTTTGGCGCAGTTACAGCAACAAAGCGGCGCCAAACTGCTGGCATCGCCTGCAGCAGCACCGGTGTTAACCAGTGGCGTGGTAGCCGCTGCCGATCCGCAAGCGGGCATGCACGAGCCGTTTCCAGCCGTTAGGGTAGATGGCCTGGTTACAGCAGGCCAGGTGGTTACCCTGGGCAAGCTAAGCCTGCTGCCTGTGGCAACGCCGGGGCATACCCCTGGCGCCTTAAGCTGGCAGTGGAGCAGTTGCGAAGCCGGGCAGTGTCAGGTACTGGTGTACGCCGACAGCTTATCGCCGGTTAGCAGCGACAGTTATCGTTTTAGCGAGCACCTTACTTATCTCAATGCATACCGGGCCAGTTTGCATAAACTGGCAGCGCTTGATTGCCAGATCCTGCTTACGCCCCATCCGTCAGCCAGTAATATGCGTACGCGGCTGCAAAGCAGTGCAGGTTTAACAGATACCCAAGGCTGCGTAGTTTATGCAGACGCGATAACACAGCGGCTCGAGCAGCGTTTAATAAAGGAAACAACGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3005018","ARO_id":"43209","ARO_name":"LMB-1","CARD_short_name":"LMB-1","ARO_description":"LMB-1 is a subclass B3 metallo-beta-lactamase that confers resistance to penams, cephalosporins, and carbapenems.","ARO_category":{"43208":{"category_aro_accession":"3005017","category_aro_cvterm_id":"43208","category_aro_name":"LMB beta-lactamase","category_aro_description":"LMB is an AMR Gene family belonging to subclass B3 metallo-beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3762":{"model_id":"3762","model_name":"IMP-68","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"496"}},"model_sequences":{"sequence":{"6052":{"protein_sequence":{"accession":"ASU31903.1","sequence":"MKKLFVLCIFLFCSITAAGASLPDLKIEKLEEGVYVHTSFEEVNGWGVVSKHGLVVLVNTDAYLIDTPFTAKDTEKLVNWFVERGYKIKGSISSHFHSDSTGGIEWLNSQSIPTYASVLTNELLKKDGKVQAKNSFSGVSYWLVKNKIEVFYPGPGHTQDNVVVWLPKNKILFGGCFVKPYGLGNLDDANVEAWPHSAEKLISKYGNAKLVVPGHSDIGDASLLKLTWEQAVKGLNESKKSNTVH"},"dna_sequence":{"accession":"MF669572.1","fmin":"0","fmax":"738","strand":"+","sequence":"ATGAAAAAACTATTTGTTTTATGTATATTTTTGTTTTGTAGCATTACTGCCGCAGGAGCGTCTTTGCCTGATTTAAAAATTGAGAAGCTTGAAGAGGGTGTTTATGTTCATACATCGTTTGAAGAAGTTAACGGCTGGGGTGTTGTTTCTAAACACGGTTTGGTGGTTCTTGTAAATACTGACGCCTATCTGATTGACACTCCATTTACTGCTAAAGATACTGAAAAGTTAGTCAATTGGTTTGTGGAGCGCGGCTATAAAATCAAAGGCAGTATTTCCTCACATTTCCATAGCGACAGCACGGGTGGAATAGAGTGGCTTAATTCTCAATCTATTCCCACGTATGCATCTGTATTAACAAATGAACTTCTCAAAAAAGACGGTAAGGTGCAAGCTAAAAACTCATTTAGCGGAGTTAGCTATTGGCTAGTTAAAAATAAAATTGAAGTTTTTTATCCAGGCCCAGGGCACACTCAAGATAACGTAGTGGTTTGGCTACCTAAAAATAAAATCTTATTTGGTGGTTGTTTTGTTAAACCATATGGTCTTGGTAATCTAGATGACGCAAATGTTGAAGCATGGCCACATTCGGCTGAAAAATTAATATCTAAGTATGGTAATGCAAAACTGGTTGTTCCAGGCCATAGTGACATAGGAGATGCGTCGCTCTTGAAGCTTACGTGGGAACAGGCGGTAAAAGGGCTTAATGAAAGCAAAAAAAGTAACACTGTTCATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3005019","ARO_id":"43210","ARO_name":"IMP-68","CARD_short_name":"IMP-68","ARO_description":"IMP-68 is a subclass B1 metallo-beta-lactamase that confers resistance to carbapenems.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3765":{"model_id":"3765","model_name":"FosL1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"270"}},"model_sequences":{"sequence":{"6055":{"protein_sequence":{"accession":"QHR93773.1","sequence":"MLSGMNHLTLAVQSLERSVSFYKDTLGFRLAARWKNGAYLELGDLWLCLSLDDKRSAQPWPEYTHYAFSALEQDFSSFVAKLIQKGVVEWKKNRSEGNSFYFLDPDGHKLEVHVGNLESRLKQCRVHPYTDMEIFD"},"dna_sequence":{"accession":"MN464149.1","fmin":"528","fmax":"939","strand":"+","sequence":"ATGCTTTCTGGTATGAATCACCTAACGCTCGCGGTTCAGTCTTTGGAACGTAGCGTTTCTTTTTATAAAGACACCCTTGGCTTTCGTTTGGCAGCAAGATGGAAAAATGGCGCCTACCTTGAGCTCGGAGATTTATGGTTGTGTCTATCACTTGACGATAAAAGGTCTGCGCAGCCTTGGCCTGAATACACGCACTACGCTTTTTCTGCCTTGGAACAAGATTTCTCCTCCTTTGTTGCCAAGCTAATTCAAAAAGGCGTCGTTGAATGGAAGAAAAACAGAAGCGAAGGAAATTCTTTTTACTTTCTTGACCCTGATGGACATAAGCTAGAGGTTCACGTAGGTAATTTAGAGTCTCGCTTGAAGCAATGTCGTGTGCATCCATATACAGATATGGAAATATTTGACTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3005024","ARO_id":"43215","ARO_name":"FosL1","CARD_short_name":"FosL1","ARO_description":"FosL1 is related to FosA-like genes. It is a plasmid-encoded fosfomycin resistant gene found in E. coli.","ARO_category":{"36272":{"category_aro_accession":"3000133","category_aro_cvterm_id":"36272","category_aro_name":"fosfomycin thiol transferase","category_aro_description":"Catalyzes the addition of a thiol group from a nucleophilic molecule to fosfomycin.","category_aro_class_name":"AMR Gene Family"},"35944":{"category_aro_accession":"0000025","category_aro_cvterm_id":"35944","category_aro_name":"fosfomycin","category_aro_description":"Fosfomycin (also known as phosphomycin and phosphonomycin) is a broad-spectrum antibiotic produced by certain Streptomyces species. It is effective on gram positive and negative bacteria as it targets the cell wall, an essential feature shared by both bacteria. Its specific target is MurA (MurZ in E.coli), which attaches phosphoenolpyruvate (PEP) to UDP-N-acetylglucosamine, a step of commitment to cell wall synthesis. In the active site of MurA, the active cysteine molecule is alkylated which stops the catalytic reaction.","category_aro_class_name":"Antibiotic"},"45731":{"category_aro_accession":"3007149","category_aro_cvterm_id":"45731","category_aro_name":"phosphonic acid antibiotic","category_aro_description":"A group of antibiotics derived from phosphonic acids.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3763":{"model_id":"3763","model_name":"cfr(D)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6053":{"protein_sequence":{"accession":"AXY65402.1","sequence":"MLQKQLTKYQQIEKVLKECQQPNYRMKQILHCIFKEKKTDFNEMSVLPKNLRDTLTTEIGTSLLTVEPLIEQKSQQVRKVLFNLSGDNRIETVNMTYQAGWESFCISSQCGCNLGCQFCATGKIGLRKNLTAEEITDQVLYFLLKGHQIDSISFMGMGEPLANPHFFEALDIFMNPDMFQLSPRRLSVSTIGVIPKIKRLTAEYPQVHLTFSLHSPFDEERSQLMPINKSFPLLKVMDTLDEHIKVTSKKVYIAYILLPDVNDSLTHAVALADLLRSRYKKGKLYHVNLIRYNPTFDAPRTFKQVDEKQVKLFYQTLISKGINVTIRSQFGIEIDAACGQLYGNYEIKNKKTIQVND"},"dna_sequence":{"accession":"MG707078.1","fmin":"0","fmax":"1074","strand":"+","sequence":"ATGTTACAAAAACAATTAACTAAATATCAACAAATTGAAAAAGTTTTAAAAGAGTGTCAACAACCAAACTACCGAATGAAGCAAATTCTTCATTGTATTTTTAAAGAGAAAAAAACAGATTTCAATGAGATGTCTGTATTACCTAAAAATTTACGAGATACTTTAACAACAGAAATAGGAACATCACTTCTAACAGTTGAGCCCCTTATTGAACAGAAGTCGCAACAAGTGAGGAAAGTACTCTTTAATCTTTCTGGAGATAATCGCATTGAAACAGTCAACATGACCTATCAAGCTGGCTGGGAATCTTTTTGTATTTCATCTCAATGTGGCTGCAATCTAGGTTGTCAATTTTGCGCTACTGGAAAAATTGGCTTAAGAAAAAATTTAACGGCTGAGGAAATAACGGATCAAGTTCTCTACTTTCTTTTAAAAGGACACCAAATTGATAGTATTTCTTTTATGGGTATGGGAGAACCACTTGCTAACCCTCATTTTTTTGAGGCTTTAGATATTTTTATGAATCCTGATATGTTTCAACTGAGCCCTAGGCGTTTATCTGTTTCAACGATTGGTGTGATTCCTAAAATAAAACGACTAACAGCTGAATATCCACAAGTTCATTTAACTTTTTCTCTTCACTCACCTTTTGATGAAGAGAGAAGTCAGTTAATGCCGATTAATAAAAGTTTTCCCCTTTTAAAAGTGATGGATACTTTAGATGAACATATAAAAGTAACTTCAAAAAAAGTTTACATTGCTTATATTTTACTACCTGATGTGAACGATTCTTTGACTCATGCAGTTGCTTTAGCAGATTTACTTCGCTCTCGGTATAAAAAAGGAAAGCTGTATCATGTCAATCTCATCAGGTACAATCCTACTTTTGATGCACCAAGAACGTTCAAGCAAGTAGATGAAAAGCAAGTTAAACTGTTCTATCAAACCTTAATATCTAAAGGCATAAATGTCACTATTAGAAGTCAGTTTGGAATTGAAATTGATGCTGCCTGTGGCCAATTATATGGAAATTATGAGATTAAAAACAAAAAAACAATCCAAGTAAATGACTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36779","NCBI_taxonomy_name":"Enterococcus faecium","NCBI_taxonomy_id":"1352"}}}},"ARO_accession":"3005021","ARO_id":"43212","ARO_name":"cfr(D)","CARD_short_name":"cfr(D)","ARO_description":"cfr(D) is found in Enterococcus faecium. It confers resistance to vancomycin, teicoplanin, and linezolid.","ARO_category":{"36341":{"category_aro_accession":"3000202","category_aro_cvterm_id":"36341","category_aro_name":"Cfr 23S ribosomal RNA methyltransferase","category_aro_description":"Cfr genes produce enzymes which catalyze the methylation of the 23S rRNA subunit at position 8 of adenine-2503. Methylation of 23S rRNA at this site confers resistance to some classes of antibiotics, including streptogramins, chloramphenicols, florfenicols, linezolids and clindamycin.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"35948":{"category_aro_accession":"0000029","category_aro_cvterm_id":"35948","category_aro_name":"teicoplanin","category_aro_description":"Teicoplanin is a glycopeptide antibiotic used in the prophylaxis and treatment of serious infections caused by Gram-positive bacteria. Teicoplanin has a unique acyl-aliphatic chain, and binds to cell wall precursors to inhibit transglycosylation  and transpeptidation.","category_aro_class_name":"Antibiotic"},"35989":{"category_aro_accession":"0000072","category_aro_cvterm_id":"35989","category_aro_name":"linezolid","category_aro_description":"Linezolid is a synthetic antibiotic used for the treatment of serious infections caused by Gram-positive bacteria that are resistant to several other antibiotics. It inhibits protein synthesis by binding to domain V of the 23S rRNA of the 50S subunit of bacterial ribosomes.","category_aro_class_name":"Antibiotic"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"36218":{"category_aro_accession":"3000079","category_aro_cvterm_id":"36218","category_aro_name":"oxazolidinone antibiotic","category_aro_description":"Oxazolidinones are a class of synthetic antibiotics discovered the the 1980's.  They inhibit protein synthesis by binding to domain V of the 23S rRNA of the 50S subunit of bacterial ribosomes.  Linezolid is the only member of this class currently in clinical use.","category_aro_class_name":"Drug Class"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3766":{"model_id":"3766","model_name":"FRI-4","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"6056":{"protein_sequence":{"accession":"BAX00166.1","sequence":"MFFFKKSASTFIFLLCLPLNSFASQESNGVEQMRELETSFGGRIGVYILNTKNGKEFSYRQDERFPLCSSFKAFLAASVLKRTQDKSVSLDDMMEYSGRVMEKHSPVSEKYRETGASVQTLAKAAIQYSDNGASNLLMERYIGGPEGLTAFMRSTGDTDFRLDRWELELNSAIPGDERDTSTPKAVAISLNNIAFGSVLDAKNKSLLQDWLKGNTTGNARIRAAVPDKWVVGDKTGTCGLYGTANDIAILWPDANSPAVMAVYTTRPNQNDKHDETVIKNAAKIAINAVYGSTK"},"dna_sequence":{"accession":"LC178555.1","fmin":"0","fmax":"885","strand":"+","sequence":"ATGTTTTTTTTTAAAAAAAGTGCAAGTACATTTATTTTTTTGCTCTGCCTTCCATTGAACTCATTCGCCTCTCAGGAAAGTAATGGTGTTGAGCAAATGAGGGAATTGGAAACTTCTTTTGGGGGGCGAATAGGTGTTTATATTTTAAACACAAAAAATGGGAAAGAATTTTCCTACAGACAAGATGAGAGATTTCCTTTATGTAGTTCATTTAAGGCGTTCCTCGCTGCATCCGTATTAAAAAGAACCCAGGATAAATCTGTTTCTCTTGATGATATGATGGAATATTCTGGACGTGTTATGGAAAAGCATTCTCCTGTATCAGAAAAATACCGCGAAACAGGAGCAAGCGTGCAGACTTTGGCCAAGGCAGCAATTCAGTATAGTGACAATGGCGCTTCTAATCTATTAATGGAAAGATACATAGGAGGTCCTGAGGGTTTGACTGCATTTATGCGGTCAACGGGAGACACTGACTTCAGGCTTGATCGTTGGGAATTAGAATTAAACTCAGCTATTCCAGGCGATGAACGTGATACTTCCACTCCAAAAGCAGTGGCTATAAGCCTTAATAATATTGCTTTTGGTTCAGTACTCGATGCTAAAAATAAATCCTTGCTACAGGATTGGCTTAAAGGCAACACTACTGGTAATGCGCGAATTAGAGCTGCTGTTCCAGATAAGTGGGTTGTTGGCGATAAAACAGGCACCTGTGGTTTGTATGGTACAGCCAATGATATTGCTATTTTATGGCCAGATGCCAATTCACCTGCAGTTATGGCTGTCTACACAACACGTCCTAATCAAAACGACAAACATGACGAAACAGTTATAAAAAATGCTGCAAAAATAGCTATAAATGCAGTGTATGGGAGTACTAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36926","NCBI_taxonomy_name":"Enterobacter asburiae","NCBI_taxonomy_id":"61645"}}}},"ARO_accession":"3005027","ARO_id":"43218","ARO_name":"FRI-4","CARD_short_name":"FRI-4","ARO_description":"FRI-4 is a carbapenem-hydrolyzing Class A beta-lactamase gene found in Enterobacter asburiae.","ARO_category":{"42915":{"category_aro_accession":"3004796","category_aro_cvterm_id":"42915","category_aro_name":"FRI beta-lactamase","category_aro_description":"FRI is a carbapenem-Hydrolyzing Class A beta-Lactamase from Enterobacter cloacae.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3767":{"model_id":"3767","model_name":"FRI-5","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"6057":{"protein_sequence":{"accession":"AWA42532.1","sequence":"MFLCKKTSIMSFLLCLSFISFNSLATQENNSVAKMKELETAFGGRIGVYLLNTGNGKEFSYRQDERFPLCSSFKVFLAASVLKRIQSKSISLDDSVEYVGRVMEKHSPVSEKYREKGASVQTLAMAAIQYSDNGASNLLMERYIGGPEGLTAFMRSTGDTDFRLDRWELELNSAIPGDKRDTSTPKAVAMSLKNIAFGSILNAKNKALLQDWLKGNTTGNARVRAAVPDKWVVGDKTGTCGFYGTANDVAILWPDNNSPAVIAVYTTRPNQNDKHDETVIKNAAKIAIDSVYGSYK"},"dna_sequence":{"accession":"MH208723.1","fmin":"0","fmax":"891","strand":"+","sequence":"ATGTTTCTTTGCAAAAAAACAAGCATTATGTCTTTTCTGCTCTGCCTTTCTTTTATTTCATTTAACTCGCTTGCCACTCAGGAAAATAATAGTGTTGCTAAAATGAAGGAACTGGAGACTGCTTTCGGTGGTCGGATAGGTGTTTATCTTTTAAATACAGGGAATGGGAAAGAGTTTTCCTACAGACAGGATGAGAGATTTCCTTTGTGCAGTTCATTTAAGGTGTTTCTCGCTGCATCGGTGTTAAAAAGAATCCAGAGCAAATCTATTTCTCTTGATGATTCGGTGGAGTATGTCGGTCGTGTTATGGAAAAACATTCTCCTGTATCAGAAAAATATCGTGAAAAGGGAGCAAGCGTGCAGACTTTGGCTATGGCAGCAATTCAGTATAGTGACAATGGAGCTTCTAACCTGTTAATGGAAAGATACATCGGAGGTCCTGAAGGTTTAACTGCATTTATGCGGTCGACGGGAGATACTGACTTCAGGCTTGATCGCTGGGAATTAGAATTAAACTCAGCTATTCCAGGCGATAAACGTGACACATCCACTCCGAAAGCAGTAGCAATGAGCCTTAAAAATATTGCATTTGGTTCGATACTTAATGCTAAAAATAAAGCCTTACTGCAGGATTGGCTTAAAGGCAACACTACTGGTAATGCGCGAGTCAGAGCAGCTGTTCCAGATAAATGGGTTGTTGGCGATAAAACAGGTACCTGTGGTTTCTATGGTACAGCTAATGATGTTGCTATTTTATGGCCAGACAACAATTCACCTGCTGTTATCGCTGTGTATACAACGCGTCCTAATCAAAACGACAAGCATGATGAAACAGTAATTAAAAATGCCGCAAAAATAGCTATAGATTCGGTATATGGAAGTTATAAATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43220","NCBI_taxonomy_name":"Enterobacter cloacae complex sp.","NCBI_taxonomy_id":"2027919"}}}},"ARO_accession":"3005028","ARO_id":"43219","ARO_name":"FRI-5","CARD_short_name":"FRI-5","ARO_description":"FRI-5 is a carbapenem-hydrolyzing Class A beta-lactamase gene found in Enterobacter cloacae.","ARO_category":{"42915":{"category_aro_accession":"3004796","category_aro_cvterm_id":"42915","category_aro_name":"FRI beta-lactamase","category_aro_description":"FRI is a carbapenem-Hydrolyzing Class A beta-Lactamase from Enterobacter cloacae.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3768":{"model_id":"3768","model_name":"FRI-6","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"610"}},"model_sequences":{"sequence":{"6058":{"protein_sequence":{"accession":"AZK35806.1","sequence":"MFFFKKSASTFIFLLCLPLNSFASQESNGVEQMRELETSFGGRIGVYILNTKNGKEFSYRQDERFPLCSSFKAFLAASVLKRTQDKSVSLDDMMEYSGRVMEKHSPVSEKYRETGASVQTLAKAAIQYSDNGASNLLMERYIGGPEGLTAFMRSTGDTDFRLDRWELELNSAIPGDERDTSTPKAVAMSLNNIAFGSVLDAKNKSLLQDWLKGNTTGNARIRAAVPDKWVVGDKTGTCGFYGTANDIAILWPDANSPAVMAVYTTRPNQNDKHDETVIKNAAKIAINAVYGSTK"},"dna_sequence":{"accession":"MK248729.1","fmin":"0","fmax":"885","strand":"+","sequence":"ATGTTTTTTTTTAAAAAAAGTGCAAGTACATTTATTTTTTTGCTCTGTCTTCCATTGAACTCATTTGCCTCTCAGGAAAGTAATGGTGTTGAGCAAATGAGGGAATTGGAAACTTCTTTTGGGGGGCGGATAGGTGTTTATATTTTAAACACAAAAAATGGGAAAGAATTTTCCTACAGACAAGATGAGAGATTTCCTTTATGTAGTTCATTTAAGGCGTTCCTTGCTGCATCCGTATTAAAAAGAACTCAGGATAAATCTGTTTCTCTTGATGATATGATGGAATATTCTGGACGTGTTATGGAAAAGCATTCTCCTGTATCAGAAAAATACCGCGAAACAGGAGCAAGCGTGCAGACTTTGGCCAAGGCAGCAATTCAGTATAGTGACAATGGAGCTTCTAATCTATTAATGGAAAGATACATAGGAGGTCCTGAGGGTTTGACTGCATTTATGCGGTCAACGGGAGACACTGACTTCAGGCTTGATCGTTGGGAATTAGAATTAAACTCAGCTATTCCAGGCGATGAACGTGATACTTCCACTCCAAAAGCAGTGGCTATGAGTCTTAATAATATTGCTTTTGGTTCAGTACTCGATGCTAAAAATAAATCCTTGCTACAGGATTGGCTTAAAGGCAACACTACTGGTAATGCGCGAATTAGAGCTGCTGTTCCAGATAAGTGGGTTGTTGGCGATAAAACAGGCACCTGTGGTTTTTATGGTACAGCCAATGATATTGCTATTTTATGGCCAGATGCCAATTCACCTGCAGTTATGGCTGTCTACACAACACGTCCTAATCAAAACGACAAACATGACGAAACAGTTATAAAAAATGCTGCAAAAATAGCTATAAATGCAGTGTATGGGAGTACTAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3005029","ARO_id":"43221","ARO_name":"FRI-6","CARD_short_name":"FRI-6","ARO_description":"FRI-6 is a carbapenem-hydrolyzing Class A beta-lactamase gene found in Enterobacter cloacae.","ARO_category":{"42915":{"category_aro_accession":"3004796","category_aro_cvterm_id":"42915","category_aro_name":"FRI beta-lactamase","category_aro_description":"FRI is a carbapenem-Hydrolyzing Class A beta-Lactamase from Enterobacter cloacae.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3769":{"model_id":"3769","model_name":"FRI-7","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"610"}},"model_sequences":{"sequence":{"6059":{"protein_sequence":{"accession":"BBI97867.1","sequence":"MFFFKKSARTFIFLLCLPLNSFASQESNGVEQMRELETSFGGRIGVYILNTKNGKEFSYRQDERFPLCSSFKAFLAASVLKRTQDKSVSLDDMMEYSGRVMEKHSPVSEKYRETGASVQTLAKAAIQYSDNGASNLLMERYIGGPEGLTAFMRSTGDTDFRLDRWELELNSAIPGDERDTSTPKAVAMSLNNIAFGSVLDAKNKSLLQDWLKGNTTGNARIRAAVPDKWVVGDKTGTCGFYGTANDIAILWPDANSPAVMAVYTTRPNQNDKHDETVIKNAAKIAINAVYGSTK"},"dna_sequence":{"accession":"AP019534.1","fmin":"55764","fmax":"56649","strand":"+","sequence":"ATGTTTTTTTTTAAAAAAAGTGCACGTACATTTATTTTTTTGCTCTGTCTTCCATTGAACTCATTTGCCTCTCAGGAAAGTAATGGTGTTGAGCAAATGAGGGAATTGGAAACTTCTTTTGGGGGGCGGATAGGTGTTTATATTTTAAACACAAAAAATGGGAAAGAATTTTCCTACAGACAAGATGAGAGATTTCCTTTATGTAGTTCATTTAAGGCGTTCCTCGCTGCATCCGTATTAAAAAGAACTCAGGATAAATCTGTTTCTCTTGATGATATGATGGAATATTCTGGACGTGTTATGGAAAAGCATTCTCCTGTATCAGAAAAATACCGCGAAACAGGAGCAAGCGTGCAGACTTTGGCCAAGGCAGCAATTCAGTATAGTGACAATGGAGCTTCTAATCTATTAATGGAAAGATACATAGGAGGTCCTGAGGGTTTGACTGCATTTATGCGGTCAACGGGAGACACTGACTTCAGGCTTGATCGTTGGGAATTAGAATTAAACTCAGCTATTCCAGGCGATGAACGTGATACTTCCACTCCAAAAGCAGTGGCTATGAGCCTTAATAATATTGCTTTTGGTTCAGTACTCGATGCTAAAAATAAATCCTTGCTACAGGATTGGCTTAAAGGCAACACTACTGGTAATGCGCGAATTAGAGCTGCTGTTCCAGATAAGTGGGTTGTTGGCGATAAAACAGGCACCTGTGGTTTTTATGGTACAGCCAATGATATTGCTATTTTATGGCCAGATGCCAATTCACCTGCAGTTATGGCTGTCTACACAACACGTCCTAATCAAAACGACAAACATGACGAAACAGTTATAAAAAATGCTGCAAAAATAGCTATAAATGCAGTGTATGGAAGTACTAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36926","NCBI_taxonomy_name":"Enterobacter asburiae","NCBI_taxonomy_id":"61645"}}}},"ARO_accession":"3005030","ARO_id":"43222","ARO_name":"FRI-7","CARD_short_name":"FRI-7","ARO_description":"FRI-7 is a carbapenem-hydrolyzing Class A beta-lactamase gene found in Enterobacter asburiae.","ARO_category":{"42915":{"category_aro_accession":"3004796","category_aro_cvterm_id":"42915","category_aro_name":"FRI beta-lactamase","category_aro_description":"FRI is a carbapenem-Hydrolyzing Class A beta-Lactamase from Enterobacter cloacae.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3770":{"model_id":"3770","model_name":"FRI-8","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"615"}},"model_sequences":{"sequence":{"6060":{"protein_sequence":{"accession":"BBJ69931.1","sequence":"MLKKMRKNAIILSFSLCLPFASSNSFANQERNGLAQIKELETVFGGRIGVYLLNTENGKEFSYRQNERFPLCSSFKVFLAASVLKKTQDKSFSLNDTVEYSGRVMEKHSPVSEKYLETGASVQTLAMAAIQYSDNGASNLLMERYVGGPEGLTAFMRSTGDTEFRLDRWELELNSAIPGDKRDTSTPKAVAMSLKNIAFGSVLDAKNKALLQDWLQGNTTGNARVRAAVPDKWVVGDKTGTCGFYGTANDVAILWPDSNSPAVIAVYTTRTNQNDKHDETIIKNAAKIAINAVYGSYK"},"dna_sequence":{"accession":"AP019635.1","fmin":"146862","fmax":"147759","strand":"-","sequence":"ATGTTAAAAAAAATGCGAAAAAATGCGATTATTCTTTCTTTTTCGCTCTGCCTTCCTTTTGCTTCATCTAACTCATTTGCAAATCAGGAAAGGAATGGCCTGGCTCAAATTAAGGAACTGGAAACTGTTTTTGGAGGGCGGATAGGTGTTTATCTTTTAAATACAGAAAATGGGAAAGAGTTTTCCTACAGGCAAAATGAGAGATTTCCTTTATGCAGTTCATTTAAGGTGTTCTTAGCTGCATCCGTATTAAAAAAAACTCAGGATAAATCTTTTTCTCTTAATGATACGGTAGAGTATTCCGGTCGTGTTATGGAGAAGCATTCTCCTGTATCAGAAAAATACCTAGAAACGGGTGCAAGCGTTCAGACTTTGGCTATGGCAGCAATTCAGTACAGTGATAATGGAGCGTCTAATCTATTAATGGAAAGATACGTCGGAGGTCCTGAAGGTTTGACTGCATTTATGCGATCAACGGGAGACACGGAGTTCAGGCTTGATCGCTGGGAGTTAGAATTAAACTCAGCTATTCCAGGCGATAAACGTGATACTTCAACTCCGAAAGCAGTAGCAATGAGCCTAAAAAATATTGCATTTGGTTCTGTACTTGATGCTAAAAATAAAGCCTTACTGCAGGATTGGCTTCAAGGAAACACGACTGGCAATGCGCGAGTCAGAGCCGCAGTTCCTGATAAATGGGTTGTTGGCGATAAAACAGGCACCTGTGGTTTCTATGGTACAGCTAATGATGTTGCTATTTTATGGCCTGATTCCAATTCACCTGCTGTTATCGCTGTGTATACAACGCGTACTAATCAAAACGATAAACATGATGAAACAATAATTAAAAATGCTGCAAAAATTGCTATAAATGCAGTGTATGGAAGTTATAAATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43224","NCBI_taxonomy_name":"Enterobacter sp. 18A13","NCBI_taxonomy_id":"2565914"}}}},"ARO_accession":"3005031","ARO_id":"43223","ARO_name":"FRI-8","CARD_short_name":"FRI-8","ARO_description":"FRI-8 is a carbapenem-hydrolyzing Class A beta-lactamase gene found in Enterobacter sp. 18A13. It is from a plasmid.","ARO_category":{"42915":{"category_aro_accession":"3004796","category_aro_cvterm_id":"42915","category_aro_name":"FRI beta-lactamase","category_aro_description":"FRI is a carbapenem-Hydrolyzing Class A beta-Lactamase from Enterobacter cloacae.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3771":{"model_id":"3771","model_name":"FRI-9","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"605"}},"model_sequences":{"sequence":{"6061":{"protein_sequence":{"accession":"BBJ65425.1","sequence":"MFFLKKSASTFVFLLCLPLNSFASQESNGVEQMKELENSFGGRIGVYILNTKNGKEFSYRQDERFPLCSSFKAFLAASVLKRTQDKSVSLDDMMEYSGRVMEKHSPVSEKYRETGASVQTLAKAAIQYSDNGASNLLMERYIGGPEGLTAFMRSTGDTDFRLDRWELELNSAIPGDERDTSTPKTVAMSLNNIAFGSVLDAKNKSLLQDWLKGNTTGNARIRAAVPDKWVVGDKTGTCGFYGTANDIAILWPDANSPAVMAVYTTRPNQNDKHDETVIKNAAKIAINAVYGSTK"},"dna_sequence":{"accession":"AP019633.1","fmin":"117922","fmax":"118807","strand":"-","sequence":"ATGTTTTTTTTAAAAAAAAGTGCAAGTACATTTGTTTTTTTGCTCTGTCTTCCATTGAACTCATTCGCCTCCCAGGAAAGTAATGGTGTTGAGCAAATGAAGGAATTGGAAAATTCTTTTGGGGGGCGGATAGGTGTTTATATTTTAAACACAAAAAATGGGAAAGAATTTTCCTACAGACAAGATGAGAGATTTCCTTTATGTAGTTCATTTAAGGCGTTCCTCGCTGCATCCGTATTAAAAAGAACTCAGGATAAATCTGTTTCTCTTGATGATATGATGGAATATTCTGGACGTGTTATGGAAAAGCATTCTCCTGTATCAGAAAAATACCGCGAAACAGGAGCAAGCGTGCAGACTTTGGCCAAGGCAGCAATTCAGTATAGTGACAATGGAGCTTCTAATCTATTAATGGAAAGATACATAGGAGGTCCTGAGGGTTTGACTGCATTTATGCGGTCAACGGGAGACACTGACTTCAGGCTTGATCGTTGGGAATTAGAATTAAACTCAGCTATTCCAGGCGATGAACGTGATACTTCCACTCCAAAAACAGTGGCTATGAGCCTTAATAATATTGCTTTTGGTTCAGTACTCGATGCTAAAAATAAATCCTTGCTACAGGATTGGCTTAAAGGCAACACTACTGGTAATGCGCGAATTAGAGCTGCTGTTCCAGATAAGTGGGTTGTTGGCGATAAAACAGGCACCTGTGGTTTTTATGGTACAGCCAATGATATTGCTATTTTATGGCCAGATGCCAATTCACCTGCAGTTATGGCTGTCTACACAACACGTCCTAATCAAAACGACAAACATGACGAAACAGTTATAAAAAATGCTGCAAAAATAGCTATAAATGCAGTGTATGGAAGTACTAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36926","NCBI_taxonomy_name":"Enterobacter asburiae","NCBI_taxonomy_id":"61645"}}}},"ARO_accession":"3005032","ARO_id":"43225","ARO_name":"FRI-9","CARD_short_name":"FRI-9","ARO_description":"FRI-9 is a carbapenem-hydrolyzing Class A beta-lactamase gene found in Enterobacter asburiae.","ARO_category":{"42915":{"category_aro_accession":"3004796","category_aro_cvterm_id":"42915","category_aro_name":"FRI beta-lactamase","category_aro_description":"FRI is a carbapenem-Hydrolyzing Class A beta-Lactamase from Enterobacter cloacae.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3772":{"model_id":"3772","model_name":"FLC-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"615"}},"model_sequences":{"sequence":{"6062":{"protein_sequence":{"accession":"ATX60370.1","sequence":"MLKKMRKNAIILSFSLCLPFASSNSFANQERNGLAQIKELETVFGGRIGVYLLNTENGKEFSYRQNERFPLCSSFKVFLAASVLKKTQDKSFSLNDTVEYSDRVMEKHSPVSEKYLETGASVQTLAMAAIQYSDNGASNLLMERYVGGPEGLTAFMRSTGDTEFRLDRWELELNSAIPGDKRDTSTPKAVAMSLKNIAFGSVLDAKNKALLQDWLQGNTTGNARVRAAVPDKWVVGDKTGTCGFYGTANDVAILWPDSNSPAVIAVYTTRTNQNDKHDETIIKNAAKIAINAVYGSYK"},"dna_sequence":{"accession":"MG309750.1","fmin":"0","fmax":"897","strand":"+","sequence":"ATGTTAAAAAAAATGCGAAAAAATGCGATTATTCTTTCTTTTTCGCTCTGCCTTCCTTTTGCTTCATCTAACTCATTTGCAAATCAGGAAAGGAATGGCCTGGCTCAAATTAAGGAACTGGAAACTGTTTTTGGAGGGCGGATAGGTGTTTATCTTTTAAATACAGAAAATGGGAAAGAGTTTTCCTACAGGCAAAATGAGAGATTTCCTTTATGCAGTTCATTTAAGGTGTTCTTAGCTGCATCCGTATTAAAAAAAACTCAGGATAAATCTTTTTCTCTTAATGATACGGTAGAGTATTCCGATCGTGTTATGGAGAAGCATTCTCCTGTATCAGAAAAATACCTAGAAACGGGTGCAAGCGTTCAGACTTTGGCTATGGCAGCAATTCAGTACAGTGATAATGGAGCGTCTAATCTATTAATGGAAAGATACGTCGGAGGTCCTGAAGGTTTGACTGCATTTATGCGATCAACGGGAGACACGGAGTTCAGGCTTGATCGCTGGGAGTTAGAATTAAACTCAGCTATTCCAGGCGATAAACGTGATACTTCAACTCCGAAAGCAGTAGCAATGAGCCTAAAAAATATTGCATTTGGTTCTGTACTTGATGCTAAAAATAAAGCCTTACTGCAGGATTGGCTTCAAGGAAACACGACTGGCAATGCGCGAGTCAGAGCCGCAGTTCCTGATAAATGGGTTGTTGGCGATAAAACAGGCACCTGTGGTTTCTATGGTACAGCTAATGATGTTGCTATTTTATGGCCTGATTCCAATTCACCTGCTGTTATCGCTGTGTATACAACGCGTACTAATCAAAACGATAAACATGATGAAACAATAATTAAAAATGCTGCAAAAATTGCTATAAATGCAGTGTATGGAAGTTATAAATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3005033","ARO_id":"43226","ARO_name":"FLC-1","CARD_short_name":"FLC-1","ARO_description":"FLC-1 is part of the FRI beta-lactamase family. It is a class A carbapenem-hydrolyzing beta-lactamase from Enterobacter cloacae.","ARO_category":{"42915":{"category_aro_accession":"3004796","category_aro_cvterm_id":"42915","category_aro_name":"FRI beta-lactamase","category_aro_description":"FRI is a carbapenem-Hydrolyzing Class A beta-Lactamase from Enterobacter cloacae.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3773":{"model_id":"3773","model_name":"CTX-M-161","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6065":{"protein_sequence":{"accession":"AJU57235.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPEGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"KP128034.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTYGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGAAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGACTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3003169","ARO_id":"39746","ARO_name":"CTX-M-161","CARD_short_name":"CTX-M-161","ARO_description":"CTX-M-161 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3774":{"model_id":"3774","model_name":"CTX-M-162","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6066":{"protein_sequence":{"accession":"AKO63213.1","sequence":"MVKKSLSQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGDYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"KP681697.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGAGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGACTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3003646","ARO_id":"40256","ARO_name":"CTX-M-162","CARD_short_name":"CTX-M-162","ARO_description":"CTX-M-162 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3775":{"model_id":"3775","model_name":"CTX-M-163","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6067":{"protein_sequence":{"accession":"AKO63214.1","sequence":"MVKKSLSQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"KP681698.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGAGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3003647","ARO_id":"40257","ARO_name":"CTX-M-163","CARD_short_name":"CTX-M-163","ARO_description":"CTX-M-163 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3776":{"model_id":"3776","model_name":"CTX-M-164","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6068":{"protein_sequence":{"accession":"AKR53959.1","sequence":"MVKKSLRKFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAVAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"KP727571.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCAAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGTGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3003648","ARO_id":"40258","ARO_name":"CTX-M-164","CARD_short_name":"CTX-M-164","ARO_description":"CTX-M-164 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3777":{"model_id":"3777","model_name":"CTX-M-165","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6069":{"protein_sequence":{"accession":"AKR53960.1","sequence":"MMTQSIRRSMLTVMATLPLLFSSATLHAQASSVQQQLEALEKSSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKQSESDKHLLNQRVEIKKSDLVNYNPIAEKHVNGTMTLAELGAAALQYSDNTAMNKLIAHLGGPDKVTAFARSLGDETFRLDRTEPTLNTAIPGDPRDTTTPLAMAQTLKNLTLGKALAETQRAQLVTWLKGNTTGSASIRAGLPKSWVVGDKTGSGDYGTTNDIAVIWPENHAPLVLVTYFTQPEQKAESRRDILAAAAKIVTHGF"},"dna_sequence":{"accession":"KP727572.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGATGACTCAGAGCATTCGCCGCTCAATGTTAACGGTGATGGCGACGCTACCCCTGCTATTTAGCAGCGCAACGCTGCATGCGCAGGCTTCCAGCGTGCAACAGCAGCTGGAAGCCCTGGAGAAAAGTTCGGGAGGTCGGCTTGGCGTTGCGCTGATTAACACCGCCGATAATTCGCAGATTCTCTACCGTGCCGATGAACGTTTTGCGATGTGCAGTACCAGTAAGGTGATGGCGGCCGCGGCGGTGCTTAAACAGAGCGAGAGCGATAAGCACCTGCTAAATCAGCGCGTTGAAATCAAGAAGAGCGACCTGGTTAACTACAATCCCATTGCGGAGAAACACGTTAACGGCACGATGACGCTGGCTGAGCTTGGCGCAGCGGCGCTGCAGTATAGCGACAATACTGCCATGAATAAGCTGATTGCCCATCTGGGTGGTCCCGATAAAGTGACGGCGTTTGCTCGCTCGTTGGGTGATGAGACCTTCCGTCTGGACAGAACCGAGCCCACGCTCAATACCGCCATTCCAGGCGACCCGCGTGATACCACCACGCCGCTCGCGATGGCGCAGACCCTGAAAAATCTGACGCTGGGTAAAGCGCTGGCGGAAACTCAGCGGGCACAGTTGGTGACGTGGCTTAAGGGCAATACTACCGGTAGCGCGAGCATTCGGGCGGGTCTGCCGAAATCATGGGTAGTGGGCGATAAAACCGGCAGCGGAGATTATGGCACCACCAACGATATCGCGGTTATCTGGCCGGAAAACCACGCACCGCTGGTTCTGGTGACCTACTTTACCCAACCGGAGCAGAAGGCGGAAAGCCGTCGGGATATTCTGGCTGCGGCGGCGAAAATCGTAACCCACGGTTTCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3003649","ARO_id":"40259","ARO_name":"CTX-M-165","CARD_short_name":"CTX-M-165","ARO_description":"CTX-M-165 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3778":{"model_id":"3778","model_name":"CTX-M-166","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6070":{"protein_sequence":{"accession":"CFW94147.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAVAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVDGTMSLVELSAAALQYSDNVAMNKLISHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGDYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTNGL"},"dna_sequence":{"accession":"LN830266.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGTCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGAAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGTGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACTTGGTTAACTATAATCCGATTGCGGAAAAGCACGTCGATGGGACGATGTCACTGGTTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTTCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGTAATCTGACGCTGGGTAAAGCATTGGGTGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGACTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCAACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3003650","ARO_id":"40260","ARO_name":"CTX-M-166","CARD_short_name":"CTX-M-166","ARO_description":"CTX-M-166 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3780":{"model_id":"3780","model_name":"ADC-159","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"780"}},"model_sequences":{"sequence":{"6073":{"protein_sequence":{"accession":"ATP60652.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWEELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWQPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVAKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"MG229642.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACACCTGGTAAATATTGGGAAGAACTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGCAACCTAAAAACCCAATCGGTGAATATCGACAATATTCAAACCCAAGTATTGGCTTATTTGGAAAAGTTGTTGCTTTGTCTATGAATAAACCTTTCGATCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTAGCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTTAACCCACAGAAATATCCGGCTGATATTCAAAGGGCAATTAATGAAACACATCAAGGTCGCTATCAAGTAAATACCATGTATCAAGCGCTTGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCAACGGTTTCGGAACATATGTGGTCTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCGTATGCAGTTTTAAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005037","ARO_id":"43235","ARO_name":"ADC-159","CARD_short_name":"ADC-159","ARO_description":"ADC-159 is an ADC beta-lactamase and a ambler class C beta-lactamase.","ARO_category":{"40543":{"category_aro_accession":"3003846","category_aro_cvterm_id":"40543","category_aro_name":"ADC beta-lactamase without carbapenemase activity","category_aro_description":"ADC beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases with extended-spectrum resistance to cephalosporins but not to carbapenems. ADC beta-lactamases are found in Acinetobacter sp. and Oligella urethralis.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3781":{"model_id":"3781","model_name":"PDC-65","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"6074":{"protein_sequence":{"accession":"AIG20002.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGKPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"KJ949080.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCTTGGCCGTAGCCATCAGCCTGAAAGGAAAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATTCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005038","ARO_id":"43236","ARO_name":"PDC-65","CARD_short_name":"PDC-65","ARO_description":"PDC-65 is an ambler class C beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3782":{"model_id":"3782","model_name":"PDC-55","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"6075":{"protein_sequence":{"accession":"AIG19992.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFKRLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKRAREGDGA"},"dna_sequence":{"accession":"KJ949070.1","fmin":"0","fmax":"1215","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTAGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCAAACGGCTCATGGAGCAGCAACTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCCCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCATGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCGCTCGCGAGGGCGACGGAGCGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005039","ARO_id":"43237","ARO_name":"PDC-55","CARD_short_name":"PDC-55","ARO_description":"PDC-55 is an ambler class C beta-lactamase from Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3783":{"model_id":"3783","model_name":"YajC","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"200"}},"model_sequences":{"sequence":{"6076":{"protein_sequence":{"accession":"TKW44661.1","sequence":"MSFLIPAAYADAAAPAAAGPAGTGFEWVFLVGFLVIFYLMIWRPQAKRAKEHKNLLGNLQKGDEVVTSGGIAGKVTKVADDFVVVEVSDNVELKFQKAAIAATLPKGTLKAI"},"dna_sequence":{"accession":"VAOQ01003483.1","fmin":"0","fmax":"339","strand":"+","sequence":"ATGAGCTTTCTAATTCCCGCTGCCTACGCCGACGCAGCCGCTCCGGCAGCCGCTGGCCCGGCCGGCACCGGTTTCGAGTGGGTCTTCCTGGTTGGTTTCCTGGTCATCTTCTACCTGATGATCTGGCGTCCCCAGGCCAAGCGCGCCAAGGAACACAAGAACCTGCTGGGCAACCTGCAAAAAGGTGACGAAGTCGTCACTTCCGGCGGTATCGCCGGCAAGGTGACCAAGGTCGCCGACGATTTCGTCGTCGTCGAGGTCTCCGACAACGTCGAGCTGAAGTTCCAGAAGGCCGCGATTGCCGCGACCCTGCCGAAAGGCACCCTGAAAGCGATCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005040","ARO_id":"43238","ARO_name":"YajC","CARD_short_name":"YajC","ARO_description":"YajC interacts with the AcrAB-TolC efflux pump in a way that in uncharacterized but is shown to grant increased fitness in the presence of linezolid, rifampicin, and vancomycin.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35989":{"category_aro_accession":"0000072","category_aro_cvterm_id":"35989","category_aro_name":"linezolid","category_aro_description":"Linezolid is a synthetic antibiotic used for the treatment of serious infections caused by Gram-positive bacteria that are resistant to several other antibiotics. It inhibits protein synthesis by binding to domain V of the 23S rRNA of the 50S subunit of bacterial ribosomes.","category_aro_class_name":"Antibiotic"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"37084":{"category_aro_accession":"3000704","category_aro_cvterm_id":"37084","category_aro_name":"cefalotin","category_aro_description":"Cefalotin is a semisynthetic cephalosporin antibiotic activate against staphylococci. It is resistant to staphylococci beta-lactamases but hydrolyzed by enterobacterial beta-lactamases.","category_aro_class_name":"Antibiotic"},"37250":{"category_aro_accession":"3000870","category_aro_cvterm_id":"37250","category_aro_name":"triclosan","category_aro_description":"Triclosan is a common antibacterial agent added to many consumer products as a biocide.  It is an inhibitor of fatty acid biosynthesis by blocking enoyl-carrier protein reductase (FabI).","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36218":{"category_aro_accession":"3000079","category_aro_cvterm_id":"36218","category_aro_name":"oxazolidinone antibiotic","category_aro_description":"Oxazolidinones are a class of synthetic antibiotics discovered the the 1980's.  They inhibit protein synthesis by binding to domain V of the 23S rRNA of the 50S subunit of bacterial ribosomes.  Linezolid is the only member of this class currently in clinical use.","category_aro_class_name":"Drug Class"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"43746":{"category_aro_accession":"3005386","category_aro_cvterm_id":"43746","category_aro_name":"disinfecting agents and antiseptics","category_aro_description":"Disinfectants that can also interact with antimicrobial resistance mechanisms, e.g. molecule efflux, and thus are the targets of disinfectant resistance.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"4262":{"model_id":"4262","model_name":"ADC-197","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6637":{"protein_sequence":{"accession":"WP_150823452.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFIATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVKTDQQVLTFFKDWKPKNSIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTTGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_066477.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTATCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAGTATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAATTTCCAGATGAAGTAAAAACAGATCAGCAAGTTTTAACATTTTTTAAAGACTGGAAACCTAAAAACTCAATCGGTGAATATCGACAATATTCAAACCCAAGCATTGGTTTATTTGGAAAAGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTAAATCCACAAAAATATCCAGCAGATATTCAACGGGCAATTAATGAAACACATCAGGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTACCGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006366","ARO_id":"44828","ARO_name":"ADC-197","CARD_short_name":"ADC-197","ARO_description":"ADC-197 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3786":{"model_id":"3786","model_name":"cmlA9","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"6079":{"protein_sequence":{"accession":"ABZ01840.1","sequence":"MTTTRPAWAYTLPAALLLMAPFDILASLAMDIYLPVVPAMPGVLNTTPSIIQLTLSLYMVMLGVGQVIFGPLSDRVGRRPILLVGATAFVAASLGAACSSTALAFVAFRLVQAVGASAMLVATFATVRDVYANRPEGAVIYGLFSSMLAFVPALGPIAGALIGEFWGWQAIFITLAALASLALLNASFRWHETRPLDQARTQRSVLPIFASPAFWVYTVGFSAGMGTFFVFFSTAPRVLIGQAGYSEIGFSLAFATVALVMVTTTRFAKSFVAKWGIAGCVARGMALLVSGAILLGIGQLFGSPSFFSFILPMWVVAVGIVFTVSVTANGALAQFDDIAGSAVAFYFCIQSLIVSIVGTLAVTLLNGDTAWPVICYATAMAVLVSLGLALLRSRDAATEKSPVV"},"dna_sequence":{"accession":"AY963803.6","fmin":"24823","fmax":"26038","strand":"+","sequence":"ATGACCACCACACGCCCCGCGTGGGCCTATACGCTGCCGGCAGCCTTGCTGCTTATGGCTCCCTTCGACATCCTCGCCTCGCTGGCGATGGATATTTATCTTCCAGTCGTTCCGGCGATGCCGGGCGTCCTGAACACGACTCCATCCATAATCCAACTCACGTTGAGCCTCTACATGGTGATGCTCGGTGTGGGCCAAGTGATCTTTGGGCCACTCTCCGATCGCGTCGGGCGACGGCCGATCCTGCTTGTAGGCGCAACGGCTTTCGTTGCTGCGTCTCTGGGAGCGGCTTGTTCTTCAACTGCATTAGCCTTTGTTGCGTTTCGTCTGGTTCAGGCTGTTGGAGCATCGGCCATGCTGGTGGCCACCTTCGCGACCGTGCGCGACGTATATGCCAATCGTCCCGAAGGTGCCGTCATCTACGGCCTTTTCAGTTCGATGCTGGCGTTCGTGCCTGCGCTCGGCCCTATAGCCGGTGCGCTGATCGGCGAGTTTTGGGGATGGCAGGCGATCTTCATCACACTGGCTGCACTGGCTTCGCTCGCACTCTTAAACGCCAGTTTCAGGTGGCATGAAACCCGACCGTTGGATCAGGCCAGAACGCAACGATCTGTTTTGCCGATCTTCGCGAGTCCGGCCTTTTGGGTTTACACGGTCGGATTTAGTGCCGGCATGGGCACATTCTTCGTTTTCTTCTCGACAGCCCCCCGTGTTCTCATAGGCCAAGCCGGCTATTCCGAGATCGGATTTAGCTTGGCCTTCGCGACTGTCGCGCTGGTCATGGTCACGACAACCCGCTTCGCAAAGTCCTTCGTTGCCAAATGGGGTATCGCGGGATGCGTAGCGCGCGGGATGGCGTTGCTCGTTTCCGGCGCGATCCTGTTGGGGATCGGCCAACTTTTCGGATCGCCGTCATTTTTCAGCTTCATCCTGCCGATGTGGGTTGTCGCGGTCGGCATTGTCTTCACGGTGTCCGTTACCGCCAACGGCGCACTTGCGCAGTTCGACGACATCGCTGGATCAGCGGTTGCGTTCTACTTCTGCATCCAAAGCCTGATAGTCAGTATCGTCGGGACATTGGCGGTGACGCTGTTAAACGGCGATACAGCGTGGCCCGTGATTTGTTACGCCACGGCAATGGCAGTGCTGGTGTCGTTGGGGCTGGCGCTCCTTCGATCCCGTGATGCTGCCACCGAGAAGTCGCCAGTCGTCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35796","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Emek","NCBI_taxonomy_id":"286784"}}}},"ARO_accession":"3005043","ARO_id":"43241","ARO_name":"cmlA9","CARD_short_name":"cmlA9","ARO_description":"cmlA9 is a Major Facilitator Superfamily efflux gene that is found in Salmonella enterica.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"3787":{"model_id":"3787","model_name":"OmpA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6080":{"protein_sequence":{"accession":"CDO13836.1","sequence":"MRSFVTSWRILDDNEAQKMKKTAIAIAVALAGFATVAQAAPKDNTWYAGGKLGWSQYHDTGFYGNGFQNNNGPTRNDQLGAGAFGGYQVNPYLGFEMGYDWLGRMAYKGSVDNGAFKAQGVQLTAKLGYPITDDLDIYTRLGGMVWRADSKGNYASTGVSRSEHDTGVSPVFAGGVEWAVTRDIATRLEYQWVNNIGDAGTVGTRPDNGMLSLGVSYRFGQEDAAPVVAPAPAPAPEVATKHFTLKSDVLFNFNKATLKPEGQQALDQLYTQLSNMDPKDGSAVVLGYTDRIGSEAYNQQLSEKRAQSVVDYLVAKGIPAGKISARGMGESTPVTGNTCDNVKARAALIDCLAPDRRVEIEVKGYKEVVTQPAA"},"dna_sequence":{"accession":"FO834906.1","fmin":"2173974","fmax":"2175099","strand":"-","sequence":"GTGAGGTCTTTTGTAACTTCATGGCGAATTTTGGATGATAATGAGGCGCAAAAAATGAAAAAGACAGCTATCGCGATTGCAGTGGCACTGGCTGGCTTCGCTACCGTAGCGCAGGCCGCTCCGAAAGATAACACCTGGTATGCAGGTGGTAAACTGGGTTGGTCCCAGTATCACGACACCGGTTTCTACGGTAACGGTTTCCAGAACAACAACGGTCCGACCCGTAACGATCAGCTTGGTGCTGGTGCGTTCGGTGGTTACCAGGTTAACCCGTACCTCGGTTTCGAAATGGGTTATGACTGGCTGGGCCGTATGGCATATAAAGGCAGCGTTGACAACGGTGCTTTCAAAGCTCAGGGCGTTCAGCTGACCGCTAAACTGGGTTACCCGATCACTGACGATCTGGACATCTACACCCGTCTGGGCGGCATGGTTTGGCGCGCTGACTCCAAAGGCAACTACGCTTCTACCGGCGTTTCCCGTAGCGAACACGACACTGGCGTTTCCCCAGTATTTGCTGGCGGCGTAGAGTGGGCTGTTACTCGTGACATCGCTACCCGTCTGGAATACCAGTGGGTTAACAACATCGGCGACGCGGGCACTGTGGGTACCCGTCCTGATAACGGCATGCTGAGCCTGGGCGTTTCCTACCGCTTCGGTCAGGAAGATGCTGCACCGGTTGTTGCTCCGGCTCCGGCTCCGGCTCCGGAAGTGGCTACCAAGCACTTCACCCTGAAGTCTGACGTTCTGTTCAACTTCAACAAAGCTACCCTGAAACCGGAAGGTCAGCAGGCTCTGGATCAGCTGTACACTCAGCTGAGCAACATGGATCCGAAAGACGGTTCCGCTGTTGTTCTGGGCTACACCGACCGCATCGGTTCCGAAGCTTACAACCAGCAGCTGTCTGAGAAACGTGCTCAGTCCGTTGTTGACTACCTGGTTGCTAAAGGCATCCCGGCTGGCAAAATCTCCGCTCGCGGCATGGGTGAATCCACCCCGGTTACTGGCAACACCTGTGACAACGTGAAAGCTCGCGCTGCCCTGATCGATTGCCTGGCTCCGGATCGTCGTGTAGAGATCGAAGTTAAAGGCTACAAAGAAGTTGTAACTCAGCCGGCGGCTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3005044","ARO_id":"43242","ARO_name":"OmpA","CARD_short_name":"OmpA","ARO_description":"OmpA is a porin that confers resistance to beta-lactam antibiotics.","ARO_category":{"41446":{"category_aro_accession":"3004282","category_aro_cvterm_id":"41446","category_aro_name":"General Bacterial Porin with reduced permeability to peptide antibiotics","category_aro_description":"These are GBPs that are associated with decreased susceptibility to peptide antibiotics either through mutations in the porin protein, absence of the porin protein, or expression of the porin protein.","category_aro_class_name":"AMR Gene Family"},"36593":{"category_aro_accession":"3000454","category_aro_cvterm_id":"36593","category_aro_name":"polymyxin B","category_aro_description":"Polymyxin B is mixture of mostly polymyxins B1 and B2, mainly used for resistant gram-negative infections. They are polypeptides with cationic detergent action on cell membranes.","category_aro_class_name":"Antibiotic"},"37037":{"category_aro_accession":"3000693","category_aro_cvterm_id":"37037","category_aro_name":"defensin","category_aro_description":"Defensins are natural cationic peptides that have antibiotic properties. It is part of the innate immune system of plants and animals.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36383":{"category_aro_accession":"3000244","category_aro_cvterm_id":"36383","category_aro_name":"reduced permeability to antibiotic","category_aro_description":"Reduction in permeability to antibiotic, generally through reduced production of porins, can provide resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3788":{"model_id":"3788","model_name":"SatA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"350"}},"model_sequences":{"sequence":{"6081":{"protein_sequence":{"accession":"AAP26981.1","sequence":"MSLLIRELETNDLDNFPEIDDSFIVNARLMLSLSKVNRRIEYTVEDVPSYEKSYLQNDNEELVYNEYINKPNQIIYIALLHNQIIGFIVLKKNWNNYAYIEDITVDKKYRTLGVGKRLIAQAKQWAKEGNMPGIMLETQNNNVAACKFYEKCGFVIGGFDFLVYKGLNMTSDEVAIYWYLHFDS"},"dna_sequence":{"accession":"AE016879.1","fmin":"2933334","fmax":"2933889","strand":"+","sequence":"ATGAGCCTTTTAATTAGAGAGTTAGAAACAAATGATTTAGATAATTTCCCGGAGATTGATGACAGTTTTATAGTGAATGCTCGGTTAATGCTTTCTCTTTCAAAAGTAAATAGACGCATAGAATATACAGTAGAAGACGTTCCGAGTTATGAAAAAAGTTATTTACAAAATGATAATGAAGAACTGGTGTACAATGAATATATAAATAAGCCAAATCAAATAATTTACATAGCACTGTTACATAACCAAATTATTGGATTCATAGTATTGAAAAAGAATTGGAATAACTATGCTTACATAGAAGATATAACGGTGGATAAAAAATATCGTACACTCGGGGTTGGTAAAAGATTAATTGCTCAAGCAAAACAGTGGGCAAAAGAAGGCAACATGCCAGGTATCATGCTTGAAACGCAAAATAATAATGTCGCAGCATGTAAGTTCTATGAAAAATGCGGATTTGTAATTGGTGGATTTGATTTTCTTGTTTATAAAGGCTTAAATATGACAAGTGATGAAGTTGCAATTTATTGGTATTTGCATTTCGACTCTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43244","NCBI_taxonomy_name":"Bacillus anthracis str. Ames","NCBI_taxonomy_id":"198094"}}}},"ARO_accession":"3005045","ARO_id":"43243","ARO_name":"SatA","CARD_short_name":"SatA","ARO_description":"SatA is part of the Streptothricin acetyltransferase gene family. It confers resistance to nucleoside antibiotics.","ARO_category":{"37249":{"category_aro_accession":"3000869","category_aro_cvterm_id":"37249","category_aro_name":"streptothricin acetyltransferase (SAT)","category_aro_description":"AcetylCoA dependent acetyltransferase that acetylate streptothricins such as nourseothricin at position 16 (beta position of beta-lysine).","category_aro_class_name":"AMR Gene Family"},"35931":{"category_aro_accession":"0000012","category_aro_cvterm_id":"35931","category_aro_name":"streptothricin","category_aro_description":"Streptothricins are a group of N-glycoside antibiotics that include a carbamoylated D-glucosamine to which are attached a series of L-beta-lysine residues at position 2 and a streptolidine at position 1.  Streptothricins vary by the number of beta-lysine residues (from 1 (nourseothricin) to 7) and target protein synthesis in bacteria and eukaryotes.","category_aro_class_name":"Antibiotic"},"36174":{"category_aro_accession":"3000034","category_aro_cvterm_id":"36174","category_aro_name":"nucleoside antibiotic","category_aro_description":"Nucleoside antibiotics are made of modified nucleosides and nucleotides with wide-ranging activities and means of antibacterial effects. This drug class includes aminonucleoside antibiotics, which contain an amino group.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3789":{"model_id":"3789","model_name":"BLMT","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"200"}},"model_sequences":{"sequence":{"6084":{"protein_sequence":{"accession":"BAF34030.1","sequence":"MTDQATPNLPSRDFDSTAAFYERLGFGIVFRDAGWMILQRGDLMLEFFAHPGLDPLASWFSCCLRLDDLAEFYRQCKSVGIQETSSGYPRIHAPELQEWGGTMAALVDPDGTLLRLIQNELLAGIS"},"dna_sequence":{"accession":"AB255435.1","fmin":"117276","fmax":"117657","strand":"+","sequence":"ATGACCGACCAAGCGACGCCCAACCTGCCATCACGAGATTTCGATTCCACCGCCGCCTTCTATGAAAGGTTGGGCTTCGGAATCGTTTTCCGGGACGCCGGCTGGATGATCCTCCAGCGCGGGGATCTCATGCTGGAGTTCTTCGCCCACCCCGGGCTCGATCCCCTCGCGAGTTGGTTCAGCTGCTGCCTGAGGCTGGACGACCTCGCGGAGTTCTACCGGCAGTGCAAATCCGTCGGCATCCAGGAAACCAGCAGCGGCTATCCGCGCATCCATGCCCCCGAACTGCAGGAGTGGGGAGGCACGATGGCCGCTTTGGTCGACCCGGACGGGACGCTCCTGCGCCTGATACAGAACGAATTGCTTGCAGGCATCTCATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3005036","ARO_id":"43234","ARO_name":"BLMT","CARD_short_name":"BLMT","ARO_description":"BLMT is a bleomycin (Bm) resistance protein, encoded by the ble gene on the transposon Tn5. This protein confers a survival advantage to Escherichia coli host cells. BLMT confers resistance to bleomycin.","ARO_category":{"41420":{"category_aro_accession":"3004256","category_aro_cvterm_id":"41420","category_aro_name":"Bleomycin resistant protein","category_aro_description":"Bleomycin resistant proteins (BRP) confer resistance to bleomycin and to bleomycin-like molecules.","category_aro_class_name":"AMR Gene Family"},"35970":{"category_aro_accession":"0000053","category_aro_cvterm_id":"35970","category_aro_name":"bleomycin","category_aro_description":"Bleomycin is a family of glycopeptide antibiotics produced by the bacterium Streptomyces verticillus. Bleomycins, taken as a mixture, act by the induction of DNA and RNA strand breaks. In addition to its antibacterial activity, bleomycin is also used as an anticancer agent.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3790":{"model_id":"3790","model_name":"MecC-type methicillin resistance repressor MecI","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"200"}},"model_sequences":{"sequence":{"6085":{"protein_sequence":{"accession":"CCC86797.1","sequence":"MTREGYDISASEWEIMNTIWNKKLISANDVIEIVQKHKEWSPKTIRTLINRLYKKKFIDRTSRNKIFEYFPIVEEKDMKYKTSKVFLDKVYEGGLNSLVLNFVENEELSEDDIEELKNILNNKY"},"dna_sequence":{"accession":"FR821779.1","fmin":"39529","fmax":"39904","strand":"+","sequence":"ATGACACGTGAAGGCTATGATATATCAGCGTCAGAATGGGAAATAATGAATACGATTTGGAATAAAAAATTAATAAGTGCTAATGACGTTATAGAAATAGTACAAAAGCACAAGGAATGGAGTCCAAAAACAATAAGAACACTAATCAATCGTCTTTACAAAAAGAAATTCATAGATAGAACAAGTCGAAATAAAATTTTTGAATATTTCCCAATAGTAGAGGAAAAAGATATGAAGTACAAAACGTCTAAAGTGTTTTTGGATAAAGTGTATGAAGGTGGATTAAATTCATTAGTCTTAAATTTTGTTGAAAATGAAGAATTGTCCGAAGATGATATTGAAGAATTGAAAAATATATTAAATAATAAATATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42590","NCBI_taxonomy_name":"Staphylococcus aureus subsp. aureus LGA251","NCBI_taxonomy_id":"985006"}}}},"ARO_accession":"3005046","ARO_id":"43245","ARO_name":"MecC-type methicillin resistance repressor MecI","CARD_short_name":"MecI_rep","ARO_description":"This MecI is a methicillin-resistant repressor resembling MecC. It confers resistance to penams.","ARO_category":{"37589":{"category_aro_accession":"3001208","category_aro_cvterm_id":"37589","category_aro_name":"methicillin resistant PBP2","category_aro_description":"In methicillin sensitive S. aureus (MSSA), beta-lactams bind to native penicillin-binding proteins (PBPs) and disrupt synthesis of the cell membrane's peptidoglycan layer. In methicillin resistant S. aureus (MRSA), foreign PBP2a acquired by lateral gene transfer is able to perform peptidoglycan synthesis in the presence of beta-lactams.","category_aro_class_name":"AMR Gene Family"},"35934":{"category_aro_accession":"0000015","category_aro_cvterm_id":"35934","category_aro_name":"methicillin","category_aro_description":"Derived from penicillin to combat penicillin-resistance, methicillin is insensitive to beta-lactamases (also known as penicillinases) secreted by many penicillin-resistant bacteria. Methicillin is bactericidal, and acts by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3791":{"model_id":"3791","model_name":"eptB","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"6086":{"protein_sequence":{"accession":"CCI79240.1","sequence":"MPQRQAVFYSSFSRFACMKYIRTMTQQKLSFWLALYIGWFMNVAVFFRRFDGYAQEFTFWKGLSGVVELVATVFVTFFLLRLLSLFGRRIWRILATLIVLFSAAASYYMTFLNVVIGYGIIASVMTTDIDLSKEVIGWHLILWLVVVSAPPLLFIWSNRCRHTLLRQLRTPGQRVKNVLIVVLAGLIVWGPIRLLELRQHDVERHSEVDMPSYGGVIANSYLPSNWLSALGLYAWAQVDESSDNKSLINPAKKFTYVAPEGLDDTYVVFIIGETTRWDHMGILDYSRNTTPELEKEKNLVAFRGYLCDTATKLSLRCMFVREGGAEDNPQRTLKEQNVFAVLHQLGFSGNLYAMQSEMWFYSNTMANNIAYREQIGAEPRNRGKSVDDMLLVDEMKRGMAQGNASGKHLIILHTKGSHFNYTQRYPRSFAQWKPECVGVDNKCSKAELINSYDNSVTYVDHFIVSVLDQLRDKKAIVFYAADHGESINEREHLHGTPRKMAPPEQFRVPMMVWMSDKYLENPDHAAAFAHLQQQAAMKVPRRHVELYDTIMGCLGYTSPDGGINENNNWCRWKK"},"dna_sequence":{"accession":"FO203501.1","fmin":"5123640","fmax":"5125365","strand":"+","sequence":"GTGCCACAGCGTCAGGCGGTGTTTTATTCTTCTTTTTCCAGGTTTGCTTGCATGAAATATATTAGAACGATGACGCAGCAGAAGCTTAGTTTTTGGCTGGCGCTGTACATCGGCTGGTTTATGAACGTCGCCGTTTTTTTCCGGCGTTTCGATGGTTATGCTCAAGAGTTCACTTTCTGGAAAGGGCTTTCCGGTGTTGTTGAACTGGTTGCCACGGTATTTGTCACCTTCTTCCTGTTACGTCTTCTGTCGCTGTTCGGCCGCCGTATCTGGCGCATTCTGGCGACGCTGATTGTCCTGTTTTCCGCCGCGGCGAGTTACTACATGACGTTCCTCAATGTGGTGATTGGCTACGGGATTATCGCTTCGGTGATGACCACCGATATCGACCTGTCGAAAGAGGTCATCGGCTGGCACCTGATCCTCTGGCTGGTGGTGGTGAGCGCGCCGCCGTTGCTGTTCATCTGGAGCAACCGCTGCCGCCATACGCTGCTGCGCCAGCTGCGCACCCCGGGCCAGCGGGTTAAAAACGTGCTGATCGTGGTGCTGGCCGGACTGATTGTCTGGGGACCCATCCGCCTGCTAGAGCTGCGCCAGCATGATGTGGAGCGCCATTCGGAAGTGGATATGCCGAGCTATGGCGGGGTGATCGCCAACTCTTACCTGCCGTCGAACTGGTTGTCGGCGCTGGGACTGTACGCCTGGGCGCAGGTGGATGAATCCTCAGACAACAAATCGCTGATTAACCCGGCGAAGAAGTTCACCTACGTCGCGCCGGAAGGTCTGGATGATACCTACGTGGTGTTTATCATTGGCGAAACGACCCGCTGGGACCATATGGGCATCCTCGACTATAGCCGCAATACCACGCCAGAGCTGGAGAAAGAGAAGAATCTCGTCGCCTTCCGCGGTTACTTGTGCGATACCGCTACCAAACTGTCGTTACGCTGCATGTTTGTGCGCGAGGGCGGGGCGGAAGATAACCCCCAGCGGACGCTCAAAGAGCAGAATGTCTTTGCCGTGCTGCATCAGCTGGGCTTCAGCGGCAATCTGTACGCCATGCAGAGCGAGATGTGGTTCTACAGCAACACGATGGCCAACAATATCGCCTACCGCGAGCAGATTGGCGCCGAGCCGCGCAACCGCGGTAAGAGCGTTGACGATATGCTGCTGGTGGATGAGATGAAGCGCGGTATGGCGCAGGGCAACGCCTCCGGTAAGCATCTGATCATTCTCCACACCAAAGGCTCCCACTTTAACTACACCCAACGCTACCCGCGCAGCTTCGCCCAGTGGAAACCGGAGTGCGTCGGCGTCGACAACAAGTGCTCGAAAGCGGAACTGATCAATTCCTACGACAATAGCGTGACCTATGTCGATCACTTTATCGTCAGCGTCCTCGACCAGCTGCGGGATAAGAAAGCGATTGTGTTCTATGCCGCCGACCACGGGGAGTCGATTAACGAGCGTGAACACCTGCACGGTACGCCGCGCAAGATGGCGCCGCCGGAGCAGTTCCGCGTGCCGATGATGGTGTGGATGTCGGATAAGTACCTGGAAAATCCCGATCACGCCGCCGCGTTTGCCCATCTGCAGCAGCAGGCTGCGATGAAGGTGCCGCGCCGTCACGTCGAGCTGTACGACACCATTATGGGCTGCCTCGGCTATACCTCGCCGGATGGCGGGATCAATGAGAACAACAACTGGTGCCGGTGGAAAAAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43247","NCBI_taxonomy_name":"Klebsiella pneumoniae subsp. rhinoscleromatis SB3432","NCBI_taxonomy_id":"861365"}}}},"ARO_accession":"3005047","ARO_id":"43246","ARO_name":"eptB","CARD_short_name":"eptB","ARO_description":"eptB is a phosphoethanolamine transferase. It confers resistance to peptide antibiotics.","ARO_category":{"41433":{"category_aro_accession":"3004269","category_aro_cvterm_id":"41433","category_aro_name":"pmr phosphoethanolamine transferase","category_aro_description":"This family of phosphoethanolamine transferase catalyze the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine to lipid A, which impedes the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36593":{"category_aro_accession":"3000454","category_aro_cvterm_id":"36593","category_aro_name":"polymyxin B","category_aro_description":"Polymyxin B is mixture of mostly polymyxins B1 and B2, mainly used for resistant gram-negative infections. They are polypeptides with cationic detergent action on cell membranes.","category_aro_class_name":"Antibiotic"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3809":{"model_id":"3809","model_name":"ROB-3","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"620"}},"model_sequences":{"sequence":{"6104":{"protein_sequence":{"accession":"OOS23853.1","sequence":"MLNKLKIGTLLLLTLTLTACSPNSVHSVTSNPQPASAPVQQSATQATFQQTLANLEQQYQARIGVYVWDTETGHSLSYRADERFAYASTFKALLAGAVLQSLPEKDLNRTISYSQKDLVSYSPETQKYVGKGMTIAQLCEAAVRFSDNSATNLLLKELGGVEQYQRILRQLGDNVTHANRLEPDLNQAKPNDIRDTSTPKQMAMNLNAYLLGNTLTESQKTILWNWLDNNATGNPLIRAATPTSWKVYDKSGAGKYGVRNDIAVVRIPNRKPIVMAIMSTQFTEEAKFNNKLVEDAAKQVFHTLQLN"},"dna_sequence":{"accession":"MUYU01000013.1","fmin":"6897","fmax":"7821","strand":"-","sequence":"ATGTTGAATAAGTTAAAAATCGGCACATTATTATTGCTGACATTAACATTAACGGCTTGTTCGCCCAATTCTGTTCATTCGGTAACGTCTAATCCGCAGCCTGCTAGTGCGCCTGTGCAACAATCAGCCACACAAGCCACCTTTCAACAGACTTTGGCGAATTTGGAACAGCAGTATCAAGCCCGAATTGGCGTTTATGTATGGGATACAGAAACGGGACATTCTTTGTCTTATCGTGCAGATGAACGCTTTGCTTATGCGTCCACTTTCAAGGCGTTGTTGGCTGGGGCGGTGTTGCAATCGCTGCCTGAAAAAGATTTAAATCGTACCATTTCATACAGCCAAAAAGATTTGGTTAGTTATTCTCCCGAAACCCAAAAATACGTTGGCAAAGGCATGACGATTGCCCAATTATGTGAAGCAGCCGTGCGGTTTAGCGACAACAGCGCGACCAATTTGCTGCTCAAAGAATTGGGTGGCGTGGAACAATATCAACGTATTTTGCGACAATTAGGCGATAACGTAACCCATGCCAATCGGCTAGAACCCGATTTAAATCAAGCCAAACCCAACGATATTCGTGATACGAGTACACCCAAACAAATGGCGATGAATTTAAATGCGTATTTATTGGGCAACACATTAACCGAATCGCAAAAAACGATTTTGTGGAATTGGTTGGACAATAACGCAACAGGCAATCCATTGATTCGCGCTGCTACGCCAACATCGTGGAAAGTGTACGATAAAAGCGGGGCGGGTAAATATGGTGTACGCAATGATATTGCGGTGGTTCGCATACCAAATCGCAAACCGATTGTGATGGCAATCATGAGTACGCAATTTACCGAAGAAGCCAAATTCAACAATAAATTAGTAGAAGATGCAGCAAAGCAAGTATTTCATACTTTACAGCTCAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42209","NCBI_taxonomy_name":"Moraxella pluranimalium","NCBI_taxonomy_id":"470453"}}}},"ARO_accession":"3005073","ARO_id":"43278","ARO_name":"ROB-3","CARD_short_name":"ROB-3","ARO_description":"ROB-3 is a beta-lactamase from the blaROB AMR gene family. It was found in Moraxella pluranimalium.","ARO_category":{"39428":{"category_aro_accession":"3002994","category_aro_cvterm_id":"39428","category_aro_name":"ROB beta-lactamase","category_aro_description":"ROB beta-lactamases are a class A beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3792":{"model_id":"3792","model_name":"CrcB","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"250"}},"model_sequences":{"sequence":{"6087":{"protein_sequence":{"accession":"CCN31428.1","sequence":"MLNFTILIFVGGAFGAICRELLMLVVPRLSDGFPLDIFIANIIAAFLLGLCTSLYKRNRVNQYIHMMVATGIMGGLSTFSSFVSGAVEMMNEPLSALIAICYLVISLIVGFMAVELGLRLGSRVKPAPPMTHNRSTG"},"dna_sequence":{"accession":"HF536482.1","fmin":"4176809","fmax":"4177223","strand":"+","sequence":"GTGCTTAATTTTACTATTCTGATCTTTGTTGGCGGGGCGTTTGGCGCAATATGCCGCGAATTATTGATGTTGGTAGTGCCTCGCCTGAGCGATGGCTTTCCCCTGGATATCTTCATCGCCAATATTATTGCCGCTTTTTTGCTTGGTTTATGCACATCACTGTATAAAAGGAACCGGGTTAATCAGTACATCCATATGATGGTGGCTACGGGTATCATGGGAGGGCTATCAACCTTCTCCAGCTTTGTATCTGGCGCGGTGGAAATGATGAATGAGCCACTCAGCGCGCTGATCGCCATCTGTTATCTGGTTATCAGCCTGATAGTCGGTTTTATGGCTGTGGAGCTGGGGTTAAGACTGGGCTCCCGAGTAAAGCCTGCGCCGCCCATGACTCATAACAGATCGACTGGTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43250","NCBI_taxonomy_name":"Klebsiella pneumoniae subsp. pneumoniae Ecl8","NCBI_taxonomy_id":"1226680"}}}},"ARO_accession":"3005049","ARO_id":"43249","ARO_name":"CrcB","CARD_short_name":"CrcB","ARO_description":"CrcB is part of the Camphor Resistance Protein Family. It confers resistance to aminoglycoside antibiotics.","ARO_category":{"36251":{"category_aro_accession":"3000112","category_aro_cvterm_id":"36251","category_aro_name":"multidrug and toxic compound extrusion (MATE) transporter","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Multidrug and toxic compound extrusion (MATE) transporters utilize the cationic gradient across the membrane as an energy source. Although there is a diverse substrate specificity, almost all MATE transporters recognize fluoroquinolones. Arciflavine, ethidium and aminoglycosides are also good substrates.","category_aro_class_name":"AMR Gene Family"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"46133":{"category_aro_accession":"3007382","category_aro_cvterm_id":"46133","category_aro_name":"gentamicin","category_aro_description":"Gentamicin is a commonly used aminoglycoside antibiotic derived from members of the Micromonospora genus of bacteria. It acts by binding the 30S ribosomal subunit, thus inhibiting protein synthesis. Gentamicin is typically used to treat Gram-negative infections of the repiratory and urinary tract, as well as infections of the bone and soft tissue. It also exhibits considerable nephrotoxicity and ototoxicity. Gentamicin is administered as a mixture of gentamicin type C (which makes about around 80% of the complex) and types A, B, and X (distributed in the remaining 20% of the complex).","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"3793":{"model_id":"3793","model_name":"LpsB","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6088":{"protein_sequence":{"accession":"QFQ03949.1","sequence":"MKVMQLLPELNSGGVERGTLEIARALVAQGHQSLVVSNGGRLVSQLEAEGSTHLTLPIHKKSLSSLWQIRPLRQLIEEHQPDIVHVRSRVPAWLTHFALRKIPANKRPHLISTVHGFYSVNRYSAIMTQAEKVIAVSDSVVKYITGHYKNCPPQDIIRIYRGIDPAAFPHNYQPSAQWFNQVFNDFPELENKFLLCLPGRITRLKGHESLIELMQQLHSQYPQLHAVVVGGADVKKQAYLSELQNTIQSKGLADKITFVGHRSDIREWLAFSDIVLSLSNQAETFGRTALEALSVGTPVIGWNRGGVAEILSHVYPQGLVEAENEKALLEIVKHHIEQPQTVAPVTMFSLKDMCDQTLELYQSVLK"},"dna_sequence":{"accession":"CP045110.1","fmin":"521271","fmax":"522372","strand":"-","sequence":"ATGAAAGTGATGCAACTTCTCCCAGAACTCAATAGCGGTGGCGTAGAACGCGGCACACTGGAAATTGCACGTGCACTGGTTGCACAAGGTCATCAGTCTCTAGTTGTGTCTAATGGCGGGCGTTTGGTCTCACAACTTGAAGCTGAAGGTTCCACACACTTAACACTGCCGATTCATAAAAAATCATTGTCGAGCTTGTGGCAAATCCGTCCATTACGTCAGCTTATTGAAGAACACCAACCAGACATTGTACATGTGCGCTCTCGCGTACCTGCATGGCTAACCCACTTCGCTTTAAGAAAAATACCAGCGAATAAACGCCCTCACCTCATTAGCACGGTACATGGTTTCTATTCAGTTAATCGTTATAGTGCGATCATGACTCAGGCAGAAAAAGTGATCGCTGTTTCTGACAGCGTAGTTAAATACATCACAGGCCATTATAAAAACTGTCCACCACAAGATATTATCCGGATTTATCGAGGAATTGACCCTGCCGCTTTTCCGCATAACTATCAACCTTCAGCACAGTGGTTTAACCAAGTCTTTAACGACTTTCCCGAACTTGAAAATAAATTTTTACTTTGCCTACCTGGCCGTATTACTCGTTTAAAAGGACATGAAAGTTTAATTGAACTGATGCAGCAACTTCATTCGCAATATCCTCAACTGCATGCTGTTGTTGTAGGTGGGGCTGATGTAAAAAAACAAGCCTATTTAAGTGAGTTGCAAAACACCATTCAAAGCAAAGGACTTGCAGATAAAATTACATTTGTAGGACATCGCTCAGATATACGCGAATGGCTCGCTTTTAGCGATATAGTGCTCTCTCTATCCAATCAAGCAGAAACATTCGGTAGAACAGCATTAGAAGCGCTCTCTGTCGGTACGCCGGTCATTGGCTGGAACCGTGGAGGTGTTGCCGAGATTTTATCTCATGTGTACCCGCAGGGTCTTGTTGAAGCAGAAAATGAAAAAGCTTTATTAGAAATAGTAAAGCATCATATTGAACAACCTCAAACAGTCGCTCCTGTGACAATGTTTAGTTTAAAAGATATGTGTGACCAAACCCTTGAGCTATATCAAAGTGTATTGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005051","ARO_id":"43252","ARO_name":"LpsB","CARD_short_name":"LpsB","ARO_description":"LpsB is involved in lipopolysaccharide synthesis. It confers intrinsic resistance to colistin and other peptide antibiotics.","ARO_category":{"43251":{"category_aro_accession":"3005050","category_aro_cvterm_id":"43251","category_aro_name":"Intrinsic peptide antibiotic resistant Lps","category_aro_description":"LpsB is involved in lipopolysaccharide synthesis. It provides intrinsic resistance to colistin and other peptide antibiotics such as polymyxins.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"37037":{"category_aro_accession":"3000693","category_aro_cvterm_id":"37037","category_aro_name":"defensin","category_aro_description":"Defensins are natural cationic peptides that have antibiotic properties. It is part of the innate immune system of plants and animals.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36383":{"category_aro_accession":"3000244","category_aro_cvterm_id":"36383","category_aro_name":"reduced permeability to antibiotic","category_aro_description":"Reduction in permeability to antibiotic, generally through reduced production of porins, can provide resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3794":{"model_id":"3794","model_name":"LpsA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6089":{"protein_sequence":{"accession":"ABG48543.1","sequence":"MHNAAQHNYVISLTTEQKRRKHITEEFGKQNIPFEFFDAITPDIIEETAKKFNITLDRSPKAKLSDGEIGCALSHIVLWDLALENNLNYINIFEDDIHLGENAKELLEIDYISDDIHVLKLEANGKMFFKQPKSVKCDRNVYPMTVKQSGCAGYTVTAKGAKYLLELVKNKPLDVAVDSLVFEDFLHFKDYKIVQLSPGICVQDFVLHPDNPFESSLQEGRDRVHGNQRKFSILEKIKNEFGRVKIKMFGKQVPFK"},"dna_sequence":{"accession":"DQ647421.1","fmin":"0","fmax":"771","strand":"+","sequence":"ATGCATAATGCAGCTCAGCACAATTATGTTATCAGTTTAACTACTGAACAAAAACGCCGAAAACATATTACCGAAGAATTCGGTAAGCAGAATATTCCTTTCGAATTTTTTGATGCTATTACGCCCGACATTATTGAAGAAACCGCTAAAAAATTTAATATTACATTAGATCGCTCTCCTAAAGCCAAGTTGTCGGATGGGGAAATTGGTTGTGCATTAAGCCATATTGTTTTATGGGATTTAGCATTAGAAAATAATTTAAACTATATCAATATCTTTGAAGATGATATTCATTTGGGGGAAAATGCCAAAGAATTATTAGAAATTGATTATATTTCTGATGATATTCATGTTTTAAAATTAGAAGCAAATGGCAAGATGTTCTTTAAACAACCAAAATCTGTAAAATGCGATAGAAATGTTTATCCCATGACGGTAAAGCAATCAGGATGTGCAGGATATACTGTTACAGCAAAAGGGGCTAAATATTTGCTTGAATTAGTAAAAAATAAACCACTTGACGTGGCGGTTGATTCACTTGTTTTTGAGGATTTTTTACATTTTAAAGATTATAAAATAGTACAACTTTCTCCTGGTATTTGCGTTCAAGATTTTGTGTTACATCCAGATAATCCTTTTGAAAGCAGTTTACAAGAAGGACGAGATAGAGTACACGGAAATCAACGCAAGTTCTCTATTTTAGAAAAAATAAAAAATGAATTTGGACGAGTAAAAATAAAAATGTTTGGAAAACAAGTTCCATTTAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36768","NCBI_taxonomy_name":"Haemophilus influenzae","NCBI_taxonomy_id":"727"}}}},"ARO_accession":"3005052","ARO_id":"43253","ARO_name":"LpsA","CARD_short_name":"LpsA","ARO_description":"LpsA plays a role in Lipooligosaccharide biosynthesis. LpsA confers resistance to polymyxin antibiotics.","ARO_category":{"43251":{"category_aro_accession":"3005050","category_aro_cvterm_id":"43251","category_aro_name":"Intrinsic peptide antibiotic resistant Lps","category_aro_description":"LpsB is involved in lipopolysaccharide synthesis. It provides intrinsic resistance to colistin and other peptide antibiotics such as polymyxins.","category_aro_class_name":"AMR Gene Family"},"36593":{"category_aro_accession":"3000454","category_aro_cvterm_id":"36593","category_aro_name":"polymyxin B","category_aro_description":"Polymyxin B is mixture of mostly polymyxins B1 and B2, mainly used for resistant gram-negative infections. They are polypeptides with cationic detergent action on cell membranes.","category_aro_class_name":"Antibiotic"},"37037":{"category_aro_accession":"3000693","category_aro_cvterm_id":"37037","category_aro_name":"defensin","category_aro_description":"Defensins are natural cationic peptides that have antibiotic properties. It is part of the innate immune system of plants and animals.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36383":{"category_aro_accession":"3000244","category_aro_cvterm_id":"36383","category_aro_name":"reduced permeability to antibiotic","category_aro_description":"Reduction in permeability to antibiotic, generally through reduced production of porins, can provide resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3795":{"model_id":"3795","model_name":"ArnT","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"6090":{"protein_sequence":{"accession":"CDO12042.1","sequence":"MKSIRYGVSLIALFALYYLLPLNFRLLWQPDETRYAEISREMLATGDWVVPHFLGLRYFEKPIAGYWINSIGQWLFGHNNFGVRFGSVFAITMTALLVAWLAWRIFRDKRVAILSLIIFLTAMLVYAIGTYAVLDPMITLWLALAMCSFWGAVQAHSRSGKILGYVLLGVACGMGVMTKGFLALAVPVVGVLPWVIARKRWREVLTYGWLAVIVCTLVVLPWGLAIAQREPDFWRYFFWVEHIQRFAEKDAQHKAPFWYYIPFLIAGSLPWLALLPGALKRGWLERDEARGALYLLGWVAMPFLFFSIAKGKLPTYILPCFAPLSILMARYALEAAKTGAKALRINGMINLGVGLLGLIAVLVVSPWGFMHKPVWTKIELYKCLLAAIAFAVWALMGWLAMKDSGRRWSLAALCPLGLALLVGFAIPDRVIDSKQPQFLVDIVSESLQPSRYVLTNNVGIAGGLAWELKRSDIIMFDKQGELKYGLDWPDAQGSFVSQAGFADWLAAHRQQGPVSLVLLMDKGESMLDLPLPKPDNAYELGRVVFLQYLPQ"},"dna_sequence":{"accession":"FO834906.1","fmin":"304977","fmax":"306633","strand":"+","sequence":"ATGAAAAGCATTCGCTATGGCGTCTCTCTGATTGCGCTGTTTGCGCTGTATTATCTGCTGCCGCTCAATTTCCGTTTGCTCTGGCAACCCGACGAAACCCGCTACGCGGAGATCAGCCGTGAAATGCTGGCCACCGGCGACTGGGTGGTACCGCATTTTCTCGGCCTGCGCTACTTCGAAAAACCGATTGCCGGTTACTGGATCAACAGTATCGGTCAGTGGCTGTTTGGCCATAATAACTTCGGCGTACGCTTCGGGTCGGTCTTCGCCATCACCATGACCGCCCTGCTGGTGGCCTGGCTGGCGTGGCGGATCTTTCGTGATAAGCGGGTAGCTATCCTGTCGCTGATTATCTTCCTCACCGCGATGCTGGTGTATGCGATTGGCACCTATGCGGTGCTGGACCCGATGATCACCCTGTGGCTGGCGCTGGCGATGTGCAGCTTCTGGGGCGCGGTGCAGGCGCACAGCCGCAGCGGCAAAATACTGGGCTACGTGCTGCTGGGCGTCGCCTGCGGGATGGGGGTGATGACCAAGGGCTTCCTGGCGCTGGCGGTGCCGGTGGTGGGCGTTCTGCCGTGGGTGATCGCCCGTAAACGCTGGCGTGAAGTGCTGACCTACGGCTGGCTGGCGGTAATCGTCTGTACGCTGGTGGTGCTGCCCTGGGGGCTGGCTATCGCTCAGCGCGAGCCGGACTTCTGGCGCTACTTCTTCTGGGTCGAGCATATTCAGCGTTTTGCTGAAAAAGACGCCCAGCACAAAGCGCCGTTCTGGTACTACATCCCGTTCCTGATCGCCGGCAGTCTGCCGTGGCTGGCCCTGCTGCCGGGGGCGCTAAAGCGCGGCTGGCTTGAGCGCGATGAGGCCCGCGGCGCGCTGTATCTGTTAGGTTGGGTGGCGATGCCGTTCCTGTTCTTCAGTATCGCCAAAGGCAAACTGCCGACCTATATTCTGCCGTGCTTTGCGCCGCTGTCGATCCTGATGGCCCGCTACGCGCTGGAGGCCGCAAAGACCGGCGCGAAAGCGTTGCGCATCAACGGGATGATCAACCTGGGCGTTGGTTTGCTGGGGCTTATCGCCGTGCTGGTGGTCTCGCCGTGGGGCTTCATGCATAAGCCGGTGTGGACCAAGATTGAGCTGTATAAATGTCTGCTGGCGGCGATCGCTTTTGCCGTCTGGGCGCTGATGGGCTGGCTGGCGATGAAAGACTCTGGCCGCCGCTGGAGCCTCGCCGCGCTCTGTCCGCTCGGCCTGGCGCTGCTGGTGGGCTTCGCCATCCCGGACCGGGTTATCGACAGCAAACAGCCGCAGTTCCTCGTGGATATCGTCAGCGAATCCCTGCAGCCCAGCCGTTACGTCCTGACCAACAACGTTGGGATCGCCGGCGGCCTGGCCTGGGAGCTGAAGCGAAGCGATATTATTATGTTCGACAAACAGGGTGAGCTGAAGTACGGTCTCGACTGGCCGGATGCTCAGGGAAGCTTTGTCAGCCAGGCCGGTTTTGCCGACTGGCTGGCCGCGCATCGTCAGCAGGGGCCGGTCTCGCTGGTGCTGTTGATGGATAAAGGAGAGAGTATGCTCGACTTACCGTTACCGAAACCGGATAACGCCTACGAGCTGGGCCGGGTCGTTTTCCTTCAGTACCTGCCGCAATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3005053","ARO_id":"43254","ARO_name":"ArnT","CARD_short_name":"ArnT","ARO_description":"ArnT is involved in Cell Wall Biosynthesis, specifically 4-amino-4-deoxy-L-arabinose (Ara4N). It confers resistance to peptide antibiotics.","ARO_category":{"41433":{"category_aro_accession":"3004269","category_aro_cvterm_id":"41433","category_aro_name":"pmr phosphoethanolamine transferase","category_aro_description":"This family of phosphoethanolamine transferase catalyze the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine to lipid A, which impedes the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3785":{"model_id":"3785","model_name":"mlaD","model_type":"protein knockout model","model_type_id":"40354","model_description":"Protein Knockout Models (PKM) reflect resistance by the absence of a gene product, most often deletion of a gene involved in antibiotic import, such as Vibrio cholerae OmpT. Like Protein Homolog Models (PHMs), PKMs include a reference sequence and a bitscore cut-off for detection using BLASTP but instead are designed to only report lack of detection under Perfect or Strict criteria. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff. This model type is still under development and not currently supported by the Resistance Gene Identifier (RGI) software.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"6078":{"protein_sequence":{"accession":"VWQ04090.1","sequence":"MQTKKNEIWVGIFLLAALLAALFVCLKAANVTSIRTEPTYTLYATFDNIGGLKARSPVSIGGVVVGRVADITLDPKTYLPRVTLEIEQRYNHIPDTSSLSIRTSGLLGEQYLALNVGFEDPELGTAILKDGDTIQDTKSAMVLEDLIGQFLYGSKDDDNKNSGDAPAAAPGNNETTEPVGTTK"},"dna_sequence":{"accession":"LR730402.1","fmin":"3996374","fmax":"3996926","strand":"+","sequence":"ATGCAAACGAAAAAAAATGAAATTTGGGTGGGTATCTTTTTATTAGCAGCACTGCTTGCGGCGCTGTTTGTTTGCCTGAAGGCAGCGAACGTGACGTCTATACGTACTGAACCGACCTATACGCTTTATGCGACGTTCGATAACATTGGCGGCCTGAAAGCCCGCTCTCCGGTCAGCATTGGTGGCGTTGTTGTGGGCCGGGTGGCGGATATTACGCTGGACCCGAAAACCTATCTGCCGCGCGTAACGCTGGAAATTGAACAACGTTATAACCACATTCCTGATACCAGTTCGCTGAGCATTCGTACTTCCGGCCTGCTGGGGGAACAATATCTGGCATTAAACGTCGGTTTTGAAGACCCGGAACTGGGGACTGCTATCCTGAAGGATGGCGATACAATTCAGGACACCAAGTCTGCGATGGTGCTGGAAGATCTCATTGGTCAGTTCCTTTACGGTAGTAAAGACGATGACAATAAGAATAGTGGCGATGCGCCAGCTGCTGCGCCAGGTAATAATGAAACCACTGAACCTGTGGGTACAACGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3005042","ARO_id":"43240","ARO_name":"mlaD","CARD_short_name":"mlaD","ARO_description":"mlaD from the mla system is a gene proposed to play a part in the transport of phospholipids to the outer membrane. Insertions in mlaD are shown to confer resistance to linezolid.","ARO_category":{"36002":{"category_aro_accession":"0010001","category_aro_cvterm_id":"36002","category_aro_name":"ATP-binding cassette (ABC) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding\/hydrolysis to transport substrates across cell membranes.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"36218":{"category_aro_accession":"3000079","category_aro_cvterm_id":"36218","category_aro_name":"oxazolidinone antibiotic","category_aro_description":"Oxazolidinones are a class of synthetic antibiotics discovered the the 1980's.  They inhibit protein synthesis by binding to domain V of the 23S rRNA of the 50S subunit of bacterial ribosomes.  Linezolid is the only member of this class currently in clinical use.","category_aro_class_name":"Drug Class"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"3784":{"model_id":"3784","model_name":"mlaF","model_type":"protein knockout model","model_type_id":"40354","model_description":"Protein Knockout Models (PKM) reflect resistance by the absence of a gene product, most often deletion of a gene involved in antibiotic import, such as Vibrio cholerae OmpT. Like Protein Homolog Models (PHMs), PKMs include a reference sequence and a bitscore cut-off for detection using BLASTP but instead are designed to only report lack of detection under Perfect or Strict criteria. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff. This model type is still under development and not currently supported by the Resistance Gene Identifier (RGI) software.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6077":{"protein_sequence":{"accession":"VWQ04088.1","sequence":"MEQSVANLVDMRDVSFTRGNRCIFDNISLTVPRGKITAIMGPSGIGKTTLLRLIGGQIAPDHGEILFDGENIPAMSRSRLYTVRKRMSMLFQSGALFTDMNVFDNVAYPLREHTQLPAPLLHSTVMMKLEAVGLRGAAKLMPSELSGGMARRAALARAIALEPDLIMFDEPFVGQDPITMGVLVKLISELNSALGVTCVVVSHDVPEVLSIADHAWILADKKIVAHGSAQALQANPDPRVRQFLDGIADGPVPFRYPAGDYHADLLPGS"},"dna_sequence":{"accession":"LR730402.1","fmin":"3994770","fmax":"3995580","strand":"+","sequence":"ATGGAGCAGTCTGTGGCGAATTTAGTCGATATGCGCGATGTCAGTTTTACGCGTGGCAATCGCTGCATCTTCGATAATATTTCCCTGACCGTGCCGCGAGGGAAGATCACGGCGATCATGGGGCCATCGGGCATCGGTAAAACGACGCTACTCCGTCTGATTGGCGGGCAAATCGCACCAGATCATGGTGAGATCCTTTTCGATGGTGAGAATATTCCGGCGATGTCTCGTTCGCGCCTGTATACAGTGCGCAAACGGATGAGCATGTTATTTCAGTCCGGGGCGTTGTTCACTGATATGAACGTATTTGACAACGTCGCCTATCCACTGCGGGAACATACCCAACTTCCCGCACCATTGTTGCATAGTACGGTGATGATGAAGCTGGAGGCCGTGGGGCTGCGTGGAGCGGCTAAACTTATGCCTTCTGAACTTTCCGGTGGGATGGCGCGGCGTGCAGCGCTGGCACGTGCGATTGCGCTGGAGCCGGATCTCATCATGTTTGATGAGCCCTTTGTTGGGCAAGATCCCATTACCATGGGCGTGCTGGTGAAGCTGATTTCTGAGCTGAACAGCGCGCTGGGCGTGACTTGTGTGGTGGTTTCTCACGATGTGCCGGAAGTGTTAAGTATTGCGGATCACGCCTGGATCCTGGCGGACAAAAAAATTGTCGCTCATGGCAGTGCCCAGGCGTTGCAGGCGAATCCTGATCCGCGCGTACGTCAGTTTCTGGACGGGATAGCTGACGGGCCTGTTCCGTTCCGCTATCCTGCCGGCGATTATCACGCTGATCTTTTACCAGGGAGTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3005041","ARO_id":"43239","ARO_name":"mlaF","CARD_short_name":"mlaF","ARO_description":"mlaF from the mla system is a gene proposed to play a part in the transport of phospholipids to the outer membrane. Insertions in mlaF are shown to confer resistance to linezolid.","ARO_category":{"36002":{"category_aro_accession":"0010001","category_aro_cvterm_id":"36002","category_aro_name":"ATP-binding cassette (ABC) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding\/hydrolysis to transport substrates across cell membranes.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"36218":{"category_aro_accession":"3000079","category_aro_cvterm_id":"36218","category_aro_name":"oxazolidinone antibiotic","category_aro_description":"Oxazolidinones are a class of synthetic antibiotics discovered the the 1980's.  They inhibit protein synthesis by binding to domain V of the 23S rRNA of the 50S subunit of bacterial ribosomes.  Linezolid is the only member of this class currently in clinical use.","category_aro_class_name":"Drug Class"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"3799":{"model_id":"3799","model_name":"LptD","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1500"}},"model_sequences":{"sequence":{"6094":{"protein_sequence":{"accession":"AIA35096.1","sequence":"MKKRIPSLLATMIASALYSQQGLAADLATQCMLGVPSYDRPLVEGRPGDLPVTINADHAKGNYPDNAVFTGNVDINQGNSRLRADEVQLHQQQAAGQAQPVRTVDALGNVHYDDNQVILKGPKAWSNLNTKDTNVWQGDYQMVGRQGRGTADLMKQRGENRYTILENGSFTSCLPGSDTWSVVGSEVIHDREEQVAEIWNARFKLGSVPIFYSPYLQLPVGDKRRSGFLIPNAKYSTKNGVEFSLPYYWNIAPNFDATITPHYMNKRGGVMWENEFRYLTQLGSGLTEFDYLPSDKVYEDDHSSDSNSRRWLFYWNHSGVIDQVWRLNADYTKVSDPDYFNDFSSKYGSSTDGYATQKFSAGYVNQNFDATVSTKQFQVFDRESSNSYSAEPQLDVNYYQNDVGPFDTHLYGQVAHFVNSNNNMPEATRVHFEPTINLPLSNGWGSLNTEAKLLATHYQQSNLDKYNAANGTDYKESVSRVMPQFKVDGKMVFERDLQEGFTQTLEPRVQYLYVPYRDQSEIGNYDSTLLQSDYTGLFRDRTYSGLDRIASANQVTTGLTSRVYDAAAVERFNISVGQIYYFTESRTGDDNINWENNDTTGSLVWAGDTYWRIADEWGLRGGIQYDTRLDNVATGNGTIEYRRDENRLVQLNYRYASPEYIQATLPSYSTAAQYKQGISQVGMTASWPIVDRWSVVGAYYYDTNTRKAANQMLGVQYNSCCYAIRLGYERKVNGWNSNDNGGESKYDNTFGINIELRGLSSNYGLGTQQMLRSNILPYQSSL"},"dna_sequence":{"accession":"CP007727.1","fmin":"807206","fmax":"809555","strand":"-","sequence":"ATGAAAAAACGTATTCCCAGCCTCCTGGCTACGATGATTGCCAGCGCCTTGTATAGCCAACAAGGCCTCGCTGCCGATCTCGCAACGCAATGTATGCTTGGCGTGCCAAGCTATGATCGTCCGCTCGTGGAAGGTCGTCCTGGCGATCTGCCGGTGACGATTAACGCCGATCATGCGAAGGGCAACTACCCGGACAACGCCGTCTTTACCGGCAACGTCGATATTAACCAGGGGAATAGTCGCCTCCGCGCCGACGAAGTTCAGCTGCACCAGCAGCAGGCCGCGGGCCAGGCGCAGCCGGTGCGCACGGTGGACGCGCTGGGCAACGTGCATTACGACGATAACCAGGTGATCCTCAAAGGGCCAAAAGCCTGGTCGAATCTGAATACCAAAGATACCAACGTCTGGCAGGGCGATTATCAAATGGTCGGACGCCAGGGACGCGGCACCGCCGACCTGATGAAACAGCGCGGTGAAAACCGCTATACCATTCTCGAAAACGGCAGCTTTACCTCCTGTCTGCCGGGCTCCGACACCTGGAGCGTCGTCGGCAGCGAAGTTATCCACGATCGCGAAGAGCAGGTTGCCGAGATCTGGAACGCCCGCTTCAAGCTTGGCTCTGTGCCGATTTTCTATAGCCCCTACCTGCAGCTGCCGGTGGGCGATAAGCGTCGTTCAGGCTTCCTGATCCCGAACGCGAAATACAGCACCAAAAACGGCGTGGAATTCTCCCTGCCGTACTACTGGAACATCGCGCCAAACTTCGATGCCACCATTACTCCGCACTATATGAACAAACGCGGCGGCGTGATGTGGGAAAACGAGTTCCGCTATCTGACCCAGCTCGGCAGCGGCTTAACTGAATTCGACTACCTGCCGTCGGATAAAGTCTACGAAGACGACCACTCGAGCGACAGCAACAGCCGCCGCTGGCTGTTCTACTGGAACCACTCAGGGGTTATCGATCAGGTATGGCGTCTGAACGCTGACTACACCAAGGTCAGCGATCCTGACTACTTCAACGACTTCAGCTCGAAATATGGTTCCAGTACCGATGGCTATGCGACGCAGAAATTCAGCGCCGGTTACGTCAACCAGAACTTTGACGCCACGGTATCGACCAAACAGTTCCAGGTCTTTGACCGCGAATCGAGCAACTCCTATTCGGCTGAGCCGCAGCTCGACGTCAACTACTACCAGAATGATGTCGGTCCGTTCGATACCCATCTCTATGGACAGGTTGCCCATTTTGTTAACTCGAATAACAACATGCCGGAAGCGACCCGCGTTCACTTCGAACCGACGATCAACCTGCCGCTGTCCAACGGTTGGGGCAGTCTGAATACCGAAGCCAAGCTGCTGGCGACTCACTACCAGCAGAGCAACCTCGATAAGTACAATGCCGCCAACGGCACTGACTATAAAGAGTCCGTCAGCCGCGTAATGCCGCAGTTTAAAGTCGACGGCAAAATGGTCTTTGAACGCGACCTGCAGGAGGGATTCACCCAAACGCTGGAACCGCGCGTGCAGTATCTGTACGTGCCGTACCGCGATCAGAGTGAAATCGGCAACTACGACTCCACGCTGTTGCAGTCGGATTACACCGGTCTGTTCCGCGACCGTACCTATAGCGGTCTGGACCGCATCGCGTCGGCTAATCAGGTCACCACCGGGCTCACCTCGCGCGTGTATGATGCCGCCGCGGTGGAACGTTTTAATATTTCCGTTGGTCAAATCTACTATTTCACCGAGTCACGCACCGGTGATGACAACATCAACTGGGAGAACAACGATACCACGGGTTCACTGGTCTGGGCCGGCGATACCTACTGGCGCATTGCCGATGAATGGGGTCTGCGCGGAGGGATCCAGTACGATACGCGTCTGGATAACGTTGCCACTGGTAACGGCACCATTGAATACCGTCGCGATGAGAACCGCTTAGTTCAGCTTAACTATCGTTACGCCAGCCCGGAATATATTCAGGCCACGCTGCCGTCATATTCCACCGCGGCACAATATAAACAGGGTATTTCGCAGGTGGGGATGACCGCCAGTTGGCCGATTGTCGATCGCTGGTCCGTGGTCGGGGCCTACTACTACGATACTAATACCCGGAAAGCAGCAAACCAGATGTTGGGTGTGCAGTATAACTCCTGCTGCTACGCCATCCGTCTTGGCTACGAACGTAAAGTCAACGGCTGGAACAGCAACGACAACGGCGGCGAGAGCAAATACGATAACACCTTCGGAATCAATATCGAATTGCGCGGTCTGAGCTCTAACTACGGCCTCGGCACCCAGCAGATGCTGCGCTCGAACATTTTACCGTACCAGAGCTCCCTGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43262","NCBI_taxonomy_name":"Klebsiella pneumoniae subsp. pneumoniae KPNIH10","NCBI_taxonomy_id":"1094170"}}}},"ARO_accession":"3005059","ARO_id":"43261","ARO_name":"LptD","CARD_short_name":"LptD","ARO_description":"LptD is involved in LPS transport in a ABC Transporter efflux system. It confers resistance to rifamycin, aminocoumarin, and peptide antibiotics.","ARO_category":{"36002":{"category_aro_accession":"0010001","category_aro_cvterm_id":"36002","category_aro_name":"ATP-binding cassette (ABC) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding\/hydrolysis to transport substrates across cell membranes.","category_aro_class_name":"AMR Gene Family"},"36250":{"category_aro_accession":"3000111","category_aro_cvterm_id":"36250","category_aro_name":"novobiocin","category_aro_description":"Novobiocin is an aminocoumarin antibiotic produced by Streptomyces spheroides and Streptomyces niveus, and binds DNA gyrase subunit B inhibiting ATP-dependent DNA supercoiling.","category_aro_class_name":"Antibiotic"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36309":{"category_aro_accession":"3000170","category_aro_cvterm_id":"36309","category_aro_name":"imipenem","category_aro_description":"Imipenem is a broad-spectrum antibiotic and is usually taken with cilastatin, which prevents hydrolysis of imipenem by renal dehydropeptidase-I. It is resistant to hydrolysis by most other beta-lactamases. Notable exceptions are the KPC beta-lactamases and Ambler Class B enzymes.","category_aro_class_name":"Antibiotic"},"36593":{"category_aro_accession":"3000454","category_aro_cvterm_id":"36593","category_aro_name":"polymyxin B","category_aro_description":"Polymyxin B is mixture of mostly polymyxins B1 and B2, mainly used for resistant gram-negative infections. They are polypeptides with cationic detergent action on cell membranes.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36242":{"category_aro_accession":"3000103","category_aro_cvterm_id":"36242","category_aro_name":"aminocoumarin antibiotic","category_aro_description":"Aminocoumarin antibiotics bind DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling.","category_aro_class_name":"Drug Class"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"3800":{"model_id":"3800","model_name":"OXA-837","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6095":{"protein_sequence":{"accession":"QEE23059.1","sequence":"MKSRTEAQSLHAHGLYRRRLLQLAGGAALLPAARLALADVAPASAVAAPSEVARGDLMSHFRALDVDGCFALFDVKANRMTLVNASRAKTRMVPASTYKIPNSLIAFETGVVADPDQIQPYGGGKTRFPQWQRDMNLREAIAMSNVPVYQGIARRIGMQRMQTWVDRLDYGNRQLGKVVDQFWLRGPLAISAAEQTRFLARLAQGQLPASRLSQQWVREILRVEANDDHAIYAKTGWAMDAGLNHGWWVGWVERSGGVHAFALNMDLQREELAPKRMAIARAMMAELGVLPVENGQARKMS"},"dna_sequence":{"accession":"MN313890.1","fmin":"0","fmax":"906","strand":"+","sequence":"ATGAAGTCCCGTACCGAAGCGCAGTCCCTGCACGCGCATGGCCTGTATCGCCGCCGCCTGCTGCAACTGGCCGGCGGCGCCGCGCTGCTGCCTGCCGCGCGCCTGGCGCTGGCCGATGTCGCGCCGGCAAGCGCCGTCGCCGCGCCGAGCGAAGTCGCCCGCGGTGATTTGATGTCGCACTTTCGCGCGCTGGACGTCGACGGCTGTTTTGCGCTGTTCGACGTCAAGGCGAACCGGATGACGCTGGTCAACGCATCGCGTGCGAAGACGCGCATGGTGCCGGCGTCGACCTACAAGATTCCGAACAGCCTGATCGCCTTCGAGACCGGCGTGGTGGCCGATCCGGACCAGATCCAGCCATATGGCGGCGGCAAGACGCGCTTCCCGCAGTGGCAGCGCGACATGAATCTGCGCGAGGCGATCGCGATGTCGAATGTGCCGGTCTACCAGGGCATTGCCCGGCGGATCGGCATGCAGCGGATGCAGACGTGGGTCGACCGGCTCGACTATGGCAACCGGCAACTCGGGAAGGTGGTGGATCAGTTCTGGCTGCGCGGGCCGCTGGCGATCTCGGCGGCCGAACAGACGCGCTTTCTGGCGCGGCTGGCACAGGGCCAACTACCGGCGTCGCGCCTGAGCCAGCAATGGGTGCGCGAGATCCTGCGCGTCGAAGCCAATGACGATCACGCGATCTACGCCAAGACGGGCTGGGCGATGGATGCCGGGCTGAACCACGGCTGGTGGGTGGGGTGGGTCGAACGCAGCGGCGGCGTCCATGCCTTCGCGCTCAATATGGATCTGCAGCGCGAGGAACTGGCGCCAAAGCGCATGGCCATCGCACGGGCGATGATGGCGGAACTTGGCGTGTTGCCCGTGGAGAACGGGCAAGCGCGCAAGATGAGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43264","NCBI_taxonomy_name":"Cupriavidus gilardii","NCBI_taxonomy_id":"82541"}}}},"ARO_accession":"3005060","ARO_id":"43263","ARO_name":"OXA-837","CARD_short_name":"OXA-837","ARO_description":"A class D OXA-like beta-lactamase described in the emerging pathogen Cupriavidus gilardii.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3801":{"model_id":"3801","model_name":"AAC(3)-IVb","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6130":{"protein_sequence":{"accession":"QEQ43476.1","sequence":"MVTQLRALGVPPGAVLLVHASFRSIRPVQGGPQGLIEALREAAGPAGTLVMPSWGDDDDAPFDPAATPAAADLGAVADAFWRLPDVVRSHHPFAFAAAGPQAHRITADPLPLPPHIPASPVGRVHELDGQVLLLGVGHDANTTIHLAELMAGVPYGVPHHCTVLRDGKPARIDYLENDHCCQRFDLVDGWLKEKGLQREGPVGNAGARLMRARDIVDVVRQQLARDPLVFLHPPQVGCEECDAARRSVSTK"},"dna_sequence":{"accession":"MN366378.1","fmin":"0","fmax":"756","strand":"+","sequence":"TTGGTGACCCAGTTGCGCGCGCTCGGCGTGCCACCCGGCGCCGTGCTGCTGGTCCACGCGTCGTTCCGCTCGATCAGGCCCGTGCAAGGGGGCCCACAAGGATTGATCGAGGCGCTGCGGGAAGCGGCCGGCCCTGCCGGCACGCTGGTGATGCCGTCGTGGGGCGATGACGATGACGCGCCCTTCGACCCGGCCGCCACGCCGGCAGCGGCGGACCTTGGCGCGGTCGCCGATGCCTTCTGGCGACTGCCCGACGTGGTTCGCAGCCACCACCCGTTTGCCTTCGCGGCGGCGGGACCGCAGGCGCATCGAATCACCGCGGATCCCTTGCCGTTGCCGCCCCATATTCCGGCCAGCCCGGTCGGCCGCGTGCACGAGCTCGATGGACAGGTGCTGCTGCTTGGCGTGGGCCATGACGCCAACACCACGATCCATCTGGCCGAACTGATGGCCGGCGTGCCTTACGGCGTGCCGCATCACTGCACGGTGCTGCGGGACGGCAAGCCGGCTCGCATCGACTATCTCGAAAACGACCACTGCTGCCAGCGCTTCGATCTGGTGGACGGATGGCTCAAGGAAAAGGGCCTTCAGCGTGAAGGCCCAGTTGGCAATGCCGGCGCCCGCTTGATGCGGGCGCGGGACATCGTCGATGTCGTGCGGCAGCAGTTGGCTCGCGATCCGCTCGTCTTCCTGCATCCGCCTCAGGTTGGCTGCGAGGAGTGCGATGCCGCGCGGCGGTCGGTCAGCACCAAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43264","NCBI_taxonomy_name":"Cupriavidus gilardii","NCBI_taxonomy_id":"82541"}}}},"ARO_accession":"3005061","ARO_id":"43265","ARO_name":"AAC(3)-IVb","CARD_short_name":"AAC(3)-IVb","ARO_description":"A novel aminoglycoside resistance gene identified from Cupriavidus gilardii; AAC(3)-IVb \/ aacC10 is an aminoglycoside-3-N-acetyltransferase gene which confers resistance to gentamicin and tobramycin.","ARO_category":{"36461":{"category_aro_accession":"3000322","category_aro_cvterm_id":"36461","category_aro_name":"AAC(3)","category_aro_description":"A category of aminoglycoside N-acetyltransferase enzymes with modification regiospecificity based at the 3-amino group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics through acetylation of the 3-amino group of the compound.","category_aro_class_name":"AMR Gene Family"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"40942":{"category_aro_accession":"3004015","category_aro_cvterm_id":"40942","category_aro_name":"gentamicin A","category_aro_description":"Gentamicin A is part of a complex of broad spectrum aminoglycoside antibiotics. Gentamicin inhibits protein synthesis, resulting in bacterial cell death.","category_aro_class_name":"Antibiotic"},"46133":{"category_aro_accession":"3007382","category_aro_cvterm_id":"46133","category_aro_name":"gentamicin","category_aro_description":"Gentamicin is a commonly used aminoglycoside antibiotic derived from members of the Micromonospora genus of bacteria. It acts by binding the 30S ribosomal subunit, thus inhibiting protein synthesis. Gentamicin is typically used to treat Gram-negative infections of the repiratory and urinary tract, as well as infections of the bone and soft tissue. It also exhibits considerable nephrotoxicity and ototoxicity. Gentamicin is administered as a mixture of gentamicin type C (which makes about around 80% of the complex) and types A, B, and X (distributed in the remaining 20% of the complex).","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3802":{"model_id":"3802","model_name":"ANT(3'')-Ib","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6097":{"protein_sequence":{"accession":"QEQ43477.1","sequence":"MPPPANEPVPAEVQPILDVVVRALGDDIAGAYLFGSAIAGGLRPDSDVDLLVLTHRTMSRQSREDLVAALMEVSGARAGRGPARNAEVTVVVLGDIAPWRHPARSDFVYGEWLRDDFAAGVVPAPTADPDLTLVLATALQSHRALMGPGLAEFLPAIPYADIRRAMADSLPGLVANVRGDERNVMLTLARMWVTVATGDIVPKDAAADWLLPRLPPERRALLATARDAYRGHVADEAWHECRADVSEWVSEVSQAIARTLHDSVKA"},"dna_sequence":{"accession":"MN366379.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGCCACCGCCTGCGAACGAGCCCGTCCCGGCCGAAGTCCAGCCCATTCTCGATGTCGTGGTCCGCGCGCTGGGTGACGACATCGCCGGCGCGTACCTGTTCGGCTCCGCCATTGCAGGCGGGCTGCGGCCGGACAGCGATGTCGACCTGCTGGTGCTGACGCATCGAACGATGTCCCGGCAGAGCCGCGAGGATCTGGTGGCCGCGTTGATGGAAGTCTCCGGCGCGCGCGCGGGGCGGGGGCCGGCCCGCAATGCCGAGGTCACGGTCGTCGTGCTCGGCGACATCGCCCCGTGGCGCCACCCGGCGCGGAGCGACTTCGTCTACGGCGAATGGCTGCGCGACGATTTCGCAGCGGGCGTGGTGCCGGCGCCGACCGCCGATCCCGATCTGACGCTGGTGCTGGCCACGGCCTTGCAGAGCCACCGCGCATTGATGGGGCCGGGGCTTGCCGAATTTCTCCCCGCGATTCCTTACGCCGATATCCGGCGCGCGATGGCGGACAGCTTGCCGGGGCTGGTGGCCAACGTCCGCGGCGACGAACGCAACGTCATGCTGACGCTGGCCCGCATGTGGGTCACGGTTGCCACGGGCGACATCGTGCCGAAGGACGCGGCGGCCGATTGGCTGCTGCCGCGTCTGCCGCCGGAGCGGCGCGCGTTATTGGCGACGGCGCGCGACGCGTATCGCGGTCATGTCGCCGACGAAGCCTGGCACGAATGTCGGGCCGACGTCAGCGAATGGGTGAGCGAGGTCAGCCAGGCCATCGCGCGAACGCTCCACGACAGCGTCAAGGCATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43264","NCBI_taxonomy_name":"Cupriavidus gilardii","NCBI_taxonomy_id":"82541"}}}},"ARO_accession":"3005062","ARO_id":"43266","ARO_name":"ANT(3'')-Ib","CARD_short_name":"ANT(3'')-Ib","ARO_description":"A novel aminoglycoside 3''-adenyltransferase gene and aminoglycoside resistance gene identified from Cupriavidus gilardii. ANT(3'')-Ib \/ aadA32 confers resistance to spectinomycin and streptomycin.","ARO_category":{"41439":{"category_aro_accession":"3004275","category_aro_cvterm_id":"41439","category_aro_name":"ANT(3'')","category_aro_description":"A category of aminoglycoside O-nucleotidyltransferase enzymes with modification regiospecificity based at the 3''-hydroxyl group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics by transfer of an AMP group from an ATP substrate to the 3''-hydroxyl group of the compound.","category_aro_class_name":"AMR Gene Family"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3803":{"model_id":"3803","model_name":"cprR","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"6098":{"protein_sequence":{"accession":"AAG06465.1","sequence":"MHIHVLVVEDNFDLAGTVIDYLEAAGVVCDHARDGQAGLNLARANRYDVILLDIMLPRINGRQVCRQLREAGLQTPVLMLTALDTLQDKLDGFDAGADDYLLKPFELPELLVRLQALSRRRSGQAQRLQVDDLVMDLDSRQASRGGTPLALSPTAWKILECLMRASPALVTREQLGRSVWGDEPPESNTLNVHMHHLRSTVDKGFATPLIHTLHSVGFQLERK"},"dna_sequence":{"accession":"AE004091.2","fmin":"3450837","fmax":"3451509","strand":"+","sequence":"ATGCATATCCACGTACTCGTCGTCGAAGACAACTTCGATCTCGCCGGCACCGTCATCGACTACCTCGAGGCCGCCGGGGTGGTCTGCGATCACGCCCGCGACGGCCAGGCCGGCCTCAACCTGGCGCGCGCCAACCGCTACGACGTGATCCTGCTGGACATCATGCTGCCGCGCATCAACGGCCGGCAGGTCTGTCGCCAGCTGCGCGAAGCCGGCCTGCAGACCCCGGTACTCATGCTCACCGCCCTGGATACCCTGCAGGACAAGCTCGACGGCTTCGACGCCGGCGCCGACGACTACCTGCTCAAGCCCTTCGAACTGCCGGAGCTGCTGGTCCGCCTGCAAGCCCTCAGCCGGCGCCGCAGCGGCCAGGCCCAGCGCCTGCAGGTCGACGACCTGGTGATGGACCTCGACAGCCGCCAGGCCAGCCGCGGCGGCACGCCCCTGGCGCTGTCCCCCACCGCCTGGAAGATCCTTGAGTGCCTGATGCGCGCCAGCCCCGCGCTGGTCACCCGCGAGCAGCTGGGGCGCAGCGTCTGGGGCGACGAACCGCCGGAAAGCAACACCCTCAACGTGCACATGCACCACCTGCGCAGCACCGTCGACAAGGGGTTCGCCACCCCTCTGATCCATACCCTGCACAGCGTCGGCTTCCAGCTGGAGCGCAAATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36804","NCBI_taxonomy_name":"Pseudomonas aeruginosa PAO1","NCBI_taxonomy_id":"208964"}}}},"ARO_accession":"3005063","ARO_id":"43267","ARO_name":"cprR","CARD_short_name":"cprR","ARO_description":"cprR is one part of a two-component regulatory system. It with its counterpart cprS induce the Arn operon to confer resistance to peptide antibiotics.","ARO_category":{"41433":{"category_aro_accession":"3004269","category_aro_cvterm_id":"41433","category_aro_name":"pmr phosphoethanolamine transferase","category_aro_description":"This family of phosphoethanolamine transferase catalyze the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine to lipid A, which impedes the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36593":{"category_aro_accession":"3000454","category_aro_cvterm_id":"36593","category_aro_name":"polymyxin B","category_aro_description":"Polymyxin B is mixture of mostly polymyxins B1 and B2, mainly used for resistant gram-negative infections. They are polypeptides with cationic detergent action on cell membranes.","category_aro_class_name":"Antibiotic"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"3804":{"model_id":"3804","model_name":"cprS","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"6099":{"protein_sequence":{"accession":"AAG06466.1","sequence":"MKRGLSLIPIVGGGVTLILAGVLLVYTRMLGDYGETGALYLLSMMMEEEGLYFAQRYQEDPATPAPDSYYFKGSVGTAGLPPKLREMLDTPPYKSIGAMQLLGNWDDDDEEEDDDAPSDDAYVVVRQPLADGKTLYLYDNDAAGSIDTPLSDAIIDARVRQTWIVTLSVTLPSLAAVGLLVWFIVAPLRKLTRWSMTLDDLAPDSQRPRFNYRELNVLADTLWNSVTRIKDFSQREERFLRYASHELRTPLAVIGMNLELLDQPGRAPSPHALQRIRRSALGMQQMTETLLWLSRESGELRDDGHIEVGRLLEELLEEQQALSQRRGLTFHLDVEPHSLPQTRARIIIGNLLRNALQYSDEGVVEIVVRDRSLLISNPIGAAQGTEESMAFGYGLGLDLVQRLCQKSGWRLHYSSDEQRFRCELLFPATPD"},"dna_sequence":{"accession":"AE004091.2","fmin":"3451505","fmax":"3452801","strand":"+","sequence":"ATGAAACGCGGCCTGAGCCTGATCCCCATCGTCGGCGGCGGCGTCACCCTGATCCTCGCCGGGGTGTTGCTGGTCTACACGCGCATGCTCGGCGACTACGGCGAGACCGGCGCCCTCTACCTGCTCAGCATGATGATGGAAGAGGAAGGGCTGTACTTCGCCCAGCGCTACCAGGAAGACCCGGCTACGCCGGCGCCGGACAGCTACTACTTCAAGGGCAGCGTCGGCACCGCGGGGCTGCCGCCGAAACTCAGGGAGATGCTCGACACCCCGCCCTACAAGAGCATCGGCGCCATGCAACTGCTCGGCAACTGGGACGACGATGACGAAGAGGAGGATGACGACGCGCCCAGCGACGATGCCTACGTGGTGGTCCGCCAGCCACTGGCCGACGGCAAGACGCTCTACCTCTACGACAACGACGCCGCCGGCAGCATCGACACGCCGCTGTCCGACGCCATCATCGACGCCCGCGTCAGGCAGACCTGGATCGTCACCCTGTCGGTCACCCTGCCTTCGCTGGCCGCCGTCGGCCTGCTGGTCTGGTTCATCGTCGCGCCGTTGCGCAAGCTGACGCGCTGGTCGATGACCCTCGACGACCTCGCCCCGGACAGCCAGCGGCCGCGCTTCAACTACCGCGAACTCAACGTGCTGGCGGATACCCTGTGGAACAGCGTGACCCGGATCAAGGACTTCAGCCAGCGCGAGGAGCGCTTCCTGCGCTACGCCAGCCATGAGCTGCGCACCCCGCTGGCGGTGATCGGCATGAACCTGGAGTTGCTCGACCAACCCGGCCGCGCGCCCTCCCCGCATGCCTTGCAACGCATCCGCCGCTCGGCGCTGGGCATGCAGCAGATGACCGAGACCCTGCTCTGGCTCAGCCGCGAGAGCGGCGAACTGCGCGACGACGGACACATCGAGGTCGGCCGCCTGCTGGAGGAACTGCTCGAGGAACAGCAGGCGCTGAGCCAGCGCCGCGGCCTGACCTTCCACCTCGACGTGGAGCCACACAGCCTGCCGCAGACCCGCGCACGGATCATCATCGGCAACCTGCTGCGCAACGCCCTGCAGTACAGCGACGAGGGCGTGGTGGAAATCGTCGTGCGCGACCGCAGCCTGCTGATCAGCAACCCCATCGGTGCGGCCCAGGGCACGGAGGAGTCGATGGCGTTCGGTTATGGCCTGGGCCTCGACCTGGTCCAGCGCCTGTGCCAGAAGAGTGGCTGGCGCCTGCATTACAGCAGCGACGAGCAGCGCTTCCGCTGCGAGCTGCTGTTCCCCGCCACGCCGGACTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36804","NCBI_taxonomy_name":"Pseudomonas aeruginosa PAO1","NCBI_taxonomy_id":"208964"}}}},"ARO_accession":"3005064","ARO_id":"43268","ARO_name":"cprS","CARD_short_name":"cprS","ARO_description":"cprS is part of a two-component regulatory system that, with its counterpart cprR, induces the Arn operon in the presence of cationic peptides to confer resistance.","ARO_category":{"41433":{"category_aro_accession":"3004269","category_aro_cvterm_id":"41433","category_aro_name":"pmr phosphoethanolamine transferase","category_aro_description":"This family of phosphoethanolamine transferase catalyze the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine to lipid A, which impedes the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36593":{"category_aro_accession":"3000454","category_aro_cvterm_id":"36593","category_aro_name":"polymyxin B","category_aro_description":"Polymyxin B is mixture of mostly polymyxins B1 and B2, mainly used for resistant gram-negative infections. They are polypeptides with cationic detergent action on cell membranes.","category_aro_class_name":"Antibiotic"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"3805":{"model_id":"3805","model_name":"ParS","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"6100":{"protein_sequence":{"accession":"AAG05187.1","sequence":"MLRLFLRLYLLLALGFAAAIFVVDHVIDAFYDSIVENYHRDAVRGQAYSLVEKLAPLDQAGRQRQLEDWRPHYGLELSLTDARQAKLTQEEQALLDKNLLVVREDFTEFISRIDAGPQLLDIKLPPEPSLTPLFTVLAYILLGVLVGIALLVWVRPHWRDLETLRLAAQRFGDGDLSSRTRIFRRSDIRTLAQHFNQMADRIESLISNQRELTNAVSHELRTPISRLSFELEQLNKQVDAEVRHDLIEDMRADLGELEEMVSELLTYARLEHGNVGSHREIVDAASWLDSVVADVALEAEAAGVTCEISACQVEQIRIEPRFMARAVINLLRNAIRHAHSRVEIALLDQGDSCQIRVNDDGPGIPADARQKIFEPFSRLDDSRDRSTGGFGLGLAIVHRVAQWHGGYAEALETPQGGASFRLTWERPR"},"dna_sequence":{"accession":"AE004091.2","fmin":"1950438","fmax":"1951725","strand":"-","sequence":"ATGCTGCGCCTGTTCCTGCGCCTCTACCTGCTGCTGGCCCTGGGGTTCGCCGCCGCGATCTTCGTGGTCGACCATGTCATCGACGCGTTCTACGACAGCATCGTCGAGAACTATCACCGCGACGCCGTTCGCGGCCAGGCCTATTCGCTGGTGGAAAAGCTGGCCCCGCTGGACCAGGCCGGACGCCAGCGACAGCTCGAAGACTGGCGTCCCCACTACGGGCTCGAGCTGAGCCTGACGGATGCCAGGCAGGCGAAGCTGACGCAGGAAGAGCAGGCCCTCCTCGACAAGAACCTGCTGGTGGTACGCGAGGACTTCACGGAATTCATCAGCCGCATCGACGCGGGCCCGCAACTGCTCGACATCAAGCTGCCGCCGGAACCCTCGCTGACCCCACTATTCACCGTGCTGGCCTACATCCTGCTCGGCGTGCTGGTCGGCATCGCCCTGCTGGTATGGGTCCGCCCGCACTGGCGCGACCTCGAGACCCTGCGCCTGGCCGCGCAACGCTTCGGCGACGGCGACCTGTCATCGCGCACGCGCATTTTCCGACGCTCCGACATCCGCACCCTGGCCCAGCACTTCAACCAGATGGCCGACCGCATCGAAAGCCTGATCAGCAACCAGCGTGAACTGACCAACGCGGTATCCCACGAATTGCGCACGCCGATCTCCCGCCTGTCCTTCGAACTCGAGCAATTGAACAAGCAGGTCGACGCCGAAGTACGCCACGACCTGATAGAGGACATGCGCGCCGATCTCGGCGAACTGGAGGAAATGGTCTCCGAACTGCTGACCTACGCCCGCCTGGAGCACGGCAACGTCGGGAGCCACCGGGAAATCGTCGACGCCGCGAGCTGGCTGGATAGCGTCGTCGCCGACGTCGCCCTGGAAGCCGAAGCCGCCGGAGTCACCTGCGAGATCAGCGCCTGCCAGGTCGAACAGATCCGCATCGAGCCTCGCTTCATGGCGCGCGCAGTGATCAACCTGCTGCGCAACGCCATTCGCCACGCACACTCGCGCGTCGAAATCGCCCTCCTCGATCAAGGCGACAGCTGTCAGATACGGGTCAACGACGACGGCCCCGGGATACCGGCGGACGCCCGGCAGAAGATCTTCGAACCCTTTTCGCGCCTGGACGACAGCCGCGATCGCAGCACCGGCGGCTTCGGCCTGGGCCTGGCGATCGTCCACCGGGTCGCGCAATGGCACGGCGGCTATGCGGAAGCGCTGGAAACGCCGCAGGGAGGCGCCTCCTTCCGCCTGACCTGGGAGCGACCCCGTTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36804","NCBI_taxonomy_name":"Pseudomonas aeruginosa PAO1","NCBI_taxonomy_id":"208964"}}}},"ARO_accession":"3005067","ARO_id":"43271","ARO_name":"ParS","CARD_short_name":"ParS","ARO_description":"ParS is the sensor component of the two-component ParRS system. Alongside its counterpart ParR, it confers resistance to polycationic antibiotics though regulation of efflux pumps and porins.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"41442":{"category_aro_accession":"3004278","category_aro_cvterm_id":"41442","category_aro_name":"Outer Membrane Porin (Opr)","category_aro_description":"The Opr family consists of porins in Pseudomonas species, and other Gram-negative bacteria, that exhibit a variety of substrate selectivities.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35963":{"category_aro_accession":"0000045","category_aro_cvterm_id":"35963","category_aro_name":"acriflavine","category_aro_description":"Acriflavine is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35990":{"category_aro_accession":"0000073","category_aro_cvterm_id":"35990","category_aro_name":"meropenem","category_aro_description":"Meropenem is an ultra-broad spectrum injectable antibiotic used to treat a wide variety of infections, including meningitis and pneumonia. It is a beta-lactam and belongs to the subgroup of carbapenem, similar to imipenem and ertapenem.","category_aro_class_name":"Antibiotic"},"36309":{"category_aro_accession":"3000170","category_aro_cvterm_id":"36309","category_aro_name":"imipenem","category_aro_description":"Imipenem is a broad-spectrum antibiotic and is usually taken with cilastatin, which prevents hydrolysis of imipenem by renal dehydropeptidase-I. It is resistant to hydrolysis by most other beta-lactamases. Notable exceptions are the KPC beta-lactamases and Ambler Class B enzymes.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37007":{"category_aro_accession":"3000663","category_aro_cvterm_id":"37007","category_aro_name":"ofloxacin","category_aro_description":"Ofloxacin is a 6-fluoro, 7-piperazinyl quinolone with a methyl-substituted oxazine ring. It has a broad spectrum of activity including many enterobacteria and mycoplasma but most anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"46133":{"category_aro_accession":"3007382","category_aro_cvterm_id":"46133","category_aro_name":"gentamicin","category_aro_description":"Gentamicin is a commonly used aminoglycoside antibiotic derived from members of the Micromonospora genus of bacteria. It acts by binding the 30S ribosomal subunit, thus inhibiting protein synthesis. Gentamicin is typically used to treat Gram-negative infections of the repiratory and urinary tract, as well as infections of the bone and soft tissue. It also exhibits considerable nephrotoxicity and ototoxicity. Gentamicin is administered as a mixture of gentamicin type C (which makes about around 80% of the complex) and types A, B, and X (distributed in the remaining 20% of the complex).","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"43746":{"category_aro_accession":"3005386","category_aro_cvterm_id":"43746","category_aro_name":"disinfecting agents and antiseptics","category_aro_description":"Disinfectants that can also interact with antimicrobial resistance mechanisms, e.g. molecule efflux, and thus are the targets of disinfectant resistance.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"},"36383":{"category_aro_accession":"3000244","category_aro_cvterm_id":"36383","category_aro_name":"reduced permeability to antibiotic","category_aro_description":"Reduction in permeability to antibiotic, generally through reduced production of porins, can provide resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3806":{"model_id":"3806","model_name":"ParR","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"6101":{"protein_sequence":{"accession":"AAG05188.1","sequence":"MDCPTLSKVLLVEDDQKLARLIASFLSQHGFEVRQVHRGDAAFAAFLDFKPQVVVLDLMLPGQNGLQVCREIRRVANLPILILTAQEDDLDHILGLESGADDYVIKPIEPPVLLARLRALMRRHAPLPASPESLTFGKLNIDRRRREAELEGLGIELTTMEFELLWLLASQAGEILSRDEILNQIRGIGFDGLNRSVDVCISKLRNKLKDNPREPVRIKTVWGKGYLFNPLGWEL"},"dna_sequence":{"accession":"AE004091.2","fmin":"1951725","fmax":"1952433","strand":"-","sequence":"ATGGACTGCCCTACCCTCAGCAAGGTATTGCTCGTCGAAGACGACCAGAAGCTCGCCCGCCTGATCGCCAGTTTCCTTTCCCAGCATGGTTTCGAAGTGCGCCAGGTGCATCGCGGTGATGCCGCGTTCGCCGCCTTCCTCGACTTCAAGCCGCAAGTGGTGGTTCTCGACCTCATGCTCCCCGGACAGAATGGTCTGCAGGTGTGCCGGGAGATCCGCCGGGTCGCGAACCTGCCGATCCTCATACTCACCGCCCAGGAGGACGATCTCGATCACATCCTCGGCCTGGAGTCCGGCGCCGACGACTACGTGATCAAGCCGATCGAGCCACCGGTGCTGCTCGCCCGCCTGCGCGCCCTGATGCGCCGGCACGCGCCCCTTCCCGCGTCCCCGGAAAGCCTGACATTCGGCAAGCTGAACATCGACCGACGGCGGCGCGAAGCGGAACTCGAAGGCCTCGGCATCGAACTGACCACGATGGAGTTCGAGCTGCTCTGGCTGCTGGCCAGCCAGGCAGGGGAAATACTTTCCCGCGACGAGATCCTCAACCAGATCCGCGGCATCGGTTTCGACGGCCTGAACCGCAGCGTCGACGTCTGCATCAGCAAGCTGCGCAATAAACTGAAGGACAATCCGCGCGAGCCGGTCCGGATCAAGACTGTCTGGGGCAAGGGCTACCTGTTCAACCCGCTGGGCTGGGAGCTCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36804","NCBI_taxonomy_name":"Pseudomonas aeruginosa PAO1","NCBI_taxonomy_id":"208964"}}}},"ARO_accession":"3005068","ARO_id":"43272","ARO_name":"ParR","CARD_short_name":"ParR","ARO_description":"ParR is a component of the two-component sensor ParRS. Alongside its counterpart ParS, it confers resistance to polycationic antibiotics through the regulation of efflux components and porins.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"41442":{"category_aro_accession":"3004278","category_aro_cvterm_id":"41442","category_aro_name":"Outer Membrane Porin (Opr)","category_aro_description":"The Opr family consists of porins in Pseudomonas species, and other Gram-negative bacteria, that exhibit a variety of substrate selectivities.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35963":{"category_aro_accession":"0000045","category_aro_cvterm_id":"35963","category_aro_name":"acriflavine","category_aro_description":"Acriflavine is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35990":{"category_aro_accession":"0000073","category_aro_cvterm_id":"35990","category_aro_name":"meropenem","category_aro_description":"Meropenem is an ultra-broad spectrum injectable antibiotic used to treat a wide variety of infections, including meningitis and pneumonia. It is a beta-lactam and belongs to the subgroup of carbapenem, similar to imipenem and ertapenem.","category_aro_class_name":"Antibiotic"},"36309":{"category_aro_accession":"3000170","category_aro_cvterm_id":"36309","category_aro_name":"imipenem","category_aro_description":"Imipenem is a broad-spectrum antibiotic and is usually taken with cilastatin, which prevents hydrolysis of imipenem by renal dehydropeptidase-I. It is resistant to hydrolysis by most other beta-lactamases. Notable exceptions are the KPC beta-lactamases and Ambler Class B enzymes.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37007":{"category_aro_accession":"3000663","category_aro_cvterm_id":"37007","category_aro_name":"ofloxacin","category_aro_description":"Ofloxacin is a 6-fluoro, 7-piperazinyl quinolone with a methyl-substituted oxazine ring. It has a broad spectrum of activity including many enterobacteria and mycoplasma but most anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"46133":{"category_aro_accession":"3007382","category_aro_cvterm_id":"46133","category_aro_name":"gentamicin","category_aro_description":"Gentamicin is a commonly used aminoglycoside antibiotic derived from members of the Micromonospora genus of bacteria. It acts by binding the 30S ribosomal subunit, thus inhibiting protein synthesis. Gentamicin is typically used to treat Gram-negative infections of the repiratory and urinary tract, as well as infections of the bone and soft tissue. It also exhibits considerable nephrotoxicity and ototoxicity. Gentamicin is administered as a mixture of gentamicin type C (which makes about around 80% of the complex) and types A, B, and X (distributed in the remaining 20% of the complex).","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"43746":{"category_aro_accession":"3005386","category_aro_cvterm_id":"43746","category_aro_name":"disinfecting agents and antiseptics","category_aro_description":"Disinfectants that can also interact with antimicrobial resistance mechanisms, e.g. molecule efflux, and thus are the targets of disinfectant resistance.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"},"36383":{"category_aro_accession":"3000244","category_aro_cvterm_id":"36383","category_aro_name":"reduced permeability to antibiotic","category_aro_description":"Reduction in permeability to antibiotic, generally through reduced production of porins, can provide resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3807":{"model_id":"3807","model_name":"rsmA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"100"}},"model_sequences":{"sequence":{"6102":{"protein_sequence":{"accession":"AAC16242.1","sequence":"MLILTRRVGETLMVGDDVTVTVLGVKGNQVRIGVNAPKEVAVHREEIYQRIQKEKDQEPNH"},"dna_sequence":{"accession":"AF061757.1","fmin":"834","fmax":"1020","strand":"+","sequence":"ATGCTGATTCTGACTCGTCGGGTCGGAGAGACCCTGATGGTAGGTGACGACGTCACCGTGACGGTACTGGGTGTCAAAGGGAACCAGGTGCGCATCGGCGTCAACGCGCCGAAGGAAGTCGCCGTACACCGGGAGGAAATTTACCAGCGCATCCAGAAAGAGAAAGATCAAGAGCCAAACCATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005069","ARO_id":"43273","ARO_name":"rsmA","CARD_short_name":"rsmA","ARO_description":"rsmA is a gene that regulates virulence of Pseudomonas aeruginosa. However, its negative effect on MexEF-OprN overexpression has been noted to confer resistance to various antibiotics. It's Escherichia coli homolog is csrA.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"3810":{"model_id":"3810","model_name":"ROB-4","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"620"}},"model_sequences":{"sequence":{"6105":{"protein_sequence":{"accession":"OOS22656.1","sequence":"MLNKLKIGTLLLLTLTLTACSPNSVHSVTSNPQPASAPVQQSATQATFQQTLANLEQQYQARIGVYVWDTETGHSLSYRADERFAYASTFKALLAGAVLQSLPEKDLNRTISYSQKDLVSYSPETQKYVGKGMTIAQLCEAAVRFSDNSATNLLLKELGGVEQYQRILRQLGDNVTHANRLEPDLNQAKPNDIRDTSTPKQMAMNLNAYLLGNTLTESQKTILWNWLDNNATGNPLIRAATPTSWKVYDKSGAGKYGVRNDIAVVRIPNRKPIVMAIMSTQFTEEAKFNNKLVEDTAKQVFHTLQLN"},"dna_sequence":{"accession":"MUYV01000026.1","fmin":"80","fmax":"1004","strand":"-","sequence":"ATGTTAAATAAGTTAAAAATCGGCACATTATTATTGCTGACATTAACATTAACGGCTTGTTCGCCCAATTCTGTTCATTCGGTAACGTCTAATCCGCAGCCTGCTAGTGCGCCTGTGCAACAATCAGCCACACAAGCCACCTTTCAACAGACTTTGGCGAATTTGGAACAGCAGTATCAAGCCCGAATTGGCGTTTATGTATGGGATACAGAAACGGGACATTCTTTGTCTTATCGTGCAGATGAACGCTTTGCTTATGCGTCCACTTTCAAGGCGTTGTTGGCTGGGGCGGTGTTGCAATCGCTGCCTGAAAAAGATTTAAATCGTACCATTTCATATAGCCAAAAAGATTTGGTTAGTTATTCTCCCGAAACCCAAAAATACGTTGGCAAAGGCATGACGATTGCCCAATTATGTGAAGCAGCCGTGCGGTTTAGCGACAACAGCGCGACCAATTTGCTGCTCAAAGAATTGGGTGGCGTGGAACAATATCAACGTATTTTGCGACAATTAGGCGATAACGTAACCCATGCCAATCGGCTAGAACCCGATTTAAATCAAGCCAAACCCAACGATATTCGTGATACGAGTACACCCAAACAAATGGCGATGAATTTAAATGCGTATTTATTGGGCAACACATTAACCGAATCGCAAAAAACGATTTTGTGGAATTGGTTGGACAATAACGCAACAGGCAATCCATTGATTCGCGCTGCTACGCCAACATCGTGGAAAGTGTACGATAAAAGCGGGGCGGGTAAATATGGTGTACGCAATGATATTGCGGTGGTTCGCATACCAAATCGCAAACCGATTGTGATGGCAATCATGAGTACGCAATTTACCGAAGAAGCCAAATTCAACAATAAATTAGTAGAAGATACAGCAAAGCAAGTATTTCATACTTTACAGCTCAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43280","NCBI_taxonomy_name":"Moraxella porci DSM 25326","NCBI_taxonomy_id":"573983"}}}},"ARO_accession":"3005074","ARO_id":"43279","ARO_name":"ROB-4","CARD_short_name":"ROB-4","ARO_description":"ROB-4 is a beta-lactamase from the blaROB AMR gene family. It was found in Moraxella porci.","ARO_category":{"39428":{"category_aro_accession":"3002994","category_aro_cvterm_id":"39428","category_aro_name":"ROB beta-lactamase","category_aro_description":"ROB beta-lactamases are a class A beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3811":{"model_id":"3811","model_name":"ROB-5","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"620"}},"model_sequences":{"sequence":{"6106":{"protein_sequence":{"accession":"PNP96721.1","sequence":"MFNKLKIGTLLLLTLTACSPNSVHSVTSNPQPASAPVQQSATQATFQQTLANLEQQYQARIGVYVWDTETGHSLSYRADERFAYASTFKALLAGAVLQSLPEKDLNRTISYSQKDLVSYSPETQKYVGKGMTIAQLCEAAVRFSDNTATNLLLKELGGVEQYQRILRQLGDNVTHANRLEPDLNQAKPNDIRDTSTPKQMAMNLNAYLLGNTLTESQKTILWNWLDNNATGNPLIRAATPTSWKVYDKSGAGKYGVRNDIAVVRIPNRKPIVMAIMSTQFTEEAKFNNKLVEDAAKQVFHTLQLN"},"dna_sequence":{"accession":"LTCC01000022.1","fmin":"11001","fmax":"11919","strand":"-","sequence":"ATGTTTAATAAGTTAAAAATCGGCACATTATTATTGCTGACATTAACGGCTTGTTCGCCCAATTCTGTTCATTCGGTAACGTCTAATCCGCAGCCTGCTAGTGCGCCTGTGCAACAATCAGCCACACAAGCCACCTTTCAACAGACTTTGGCGAATTTGGAACAGCAGTATCAAGCCCGAATTGGCGTTTATGTATGGGATACAGAAACGGGACATTCTTTGTCTTATCGTGCAGATGAACGCTTTGCTTATGCGTCCACTTTCAAGGCGTTGTTGGCTGGGGCGGTGTTGCAATCGCTGCCTGAAAAAGATTTAAATCGTACCATTTCATATAGCCAAAAAGATTTGGTTAGTTATTCTCCCGAAACCCAAAAATACGTTGGCAAAGGCATGACGATTGCCCAATTATGTGAAGCAGCCGTGCGGTTTAGCGACAACACCGCGACCAATTTGCTGCTCAAAGAATTGGGTGGCGTGGAACAATATCAACGTATTTTGCGACAATTAGGCGATAACGTAACCCATGCCAATCGGCTAGAACCCGATTTAAATCAAGCCAAACCCAACGATATTCGTGATACGAGTACACCCAAACAAATGGCGATGAATTTAAATGCGTATTTATTGGGCAACACATTAACCGAATCGCAAAAAACGATTTTGTGGAATTGGTTGGACAATAACGCAACAGGCAATCCATTGATTCGCGCTGCTACGCCAACATCGTGGAAAGTGTACGATAAAAGCGGGGCGGGTAAATATGGTGTACGCAATGATATTGCGGTGGTTCGCATACCAAATCGCAAACCGATTGTGATGGCAATCATGAGTACGCAATTTACCGAAGAAGCCAAATTCAACAATAAATTAGTAGAAGATGCAGCAAAGCAAGTATTTCATACTTTACAGCTCAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43282","NCBI_taxonomy_name":"Moraxella sp. RCAD0137","NCBI_taxonomy_id":"1775913"}}}},"ARO_accession":"3005075","ARO_id":"43281","ARO_name":"ROB-5","CARD_short_name":"ROB-5","ARO_description":"ROB-5 is a class A beta-lactamase from the blaROB AMR gene family. It was found in Moraxella sp. RCAD0137.","ARO_category":{"39428":{"category_aro_accession":"3002994","category_aro_cvterm_id":"39428","category_aro_name":"ROB beta-lactamase","category_aro_description":"ROB beta-lactamases are a class A beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3812":{"model_id":"3812","model_name":"ROB-6","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"620"}},"model_sequences":{"sequence":{"6107":{"protein_sequence":{"accession":"AIW80558.1","sequence":"MLNKLKIGTLLLLTLTACLPNFVHSVTSNPQPASAPVQQSATQATFQQTSANLEQQYQARIGVYVWDTETGHSLSYRADERFAYASTFKALLAGAVLQSLPEKDLNRTISYSQKDLVSYSPETQKYVGKGMTIAQLCEAAVRFSDNSATNLLLKELGGVEQYQRILRQLGDNVTHTNRLEPDLNQAKPNDIRDTSTPKQMAMNLNAYLLGNTLTESQKTILWNWLDNNATGNPLIRAATPTSWKVYDKSGAGKYGVRNDIAVVRIPNRKPIVMAIMSTQFTEEAKFNNKLVEDAAKQVFHTLQLN"},"dna_sequence":{"accession":"KJ910989.1","fmin":"389","fmax":"1307","strand":"-","sequence":"ATGTTAAATAAGTTAAAAATCGGCACATTATTATTGCTGACATTAACGGCTTGTTTGCCCAATTTTGTTCATTCGGTAACGTCTAATCCGCAGCCTGCTAGTGCGCCTGTGCAACAATCAGCCACACAAGCCACCTTTCAACAGACTTCGGCGAATTTGGAACAGCAGTATCAAGCCCGAATTGGCGTTTATGTATGGGATACAGAAACGGGACATTCTTTGTCTTATCGTGCAGATGAACGCTTTGCTTATGCGTCCACTTTCAAGGCGTTGTTGGCTGGGGCGGTGTTGCAATCGCTGCCTGAAAAAGATTTAAATCGTACCATTTCATATAGCCAAAAAGATTTGGTTAGTTATTCTCCCGAAACCCAAAAATACGTTGGCAAAGGCATGACGATTGCCCAATTATGTGAAGCAGCCGTGCGGTTTAGCGACAACAGCGCGACCAATTTGCTGCTCAAAGAATTGGGTGGCGTGGAACAATATCAACGTATTTTGCGACAATTAGGCGATAACGTAACCCATACCAATCGGCTAGAACCCGATTTAAATCAAGCCAAACCCAACGATATTCGTGATACGAGTACACCCAAACAAATGGCGATGAATTTAAATGCGTATTTATTGGGCAACACATTAACCGAATCGCAAAAAACGATTTTGTGGAATTGGTTGGACAATAACGCAACAGGCAATCCATTGATTCGCGCTGCTACGCCAACATCGTGGAAAGTGTACGATAAAAGCGGGGCGGGTAAATATGGTGTACGCAATGATATTGCGGTGGTTCGCATACCAAATCGCAAACCGATTGTGATGGCAATCATGAGTACGCAATTTACCGAAGAAGCCAAATTCAACAATAAATTAGTAGAAGATGCAGCAAAGCAAGTATTTCATACTTTACAGCTCAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36791","NCBI_taxonomy_name":"uncultured bacterium","NCBI_taxonomy_id":"77133"}}}},"ARO_accession":"3005076","ARO_id":"43283","ARO_name":"ROB-6","CARD_short_name":"ROB-6","ARO_description":"ROB-6 is a class A beta-lactamase from the blaROB AMR gene family. It was first described by Clemente et al.","ARO_category":{"39428":{"category_aro_accession":"3002994","category_aro_cvterm_id":"39428","category_aro_name":"ROB beta-lactamase","category_aro_description":"ROB beta-lactamases are a class A beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3813":{"model_id":"3813","model_name":"ROB-7","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"620"}},"model_sequences":{"sequence":{"6108":{"protein_sequence":{"accession":"AIW80572.1","sequence":"MLNKLKIGTLLLLTLTACLPNSVLSVTSNPQPASAPVQQSATQATFQQTLANLEQQYQARIGVYVWDTETGHSLSYRADERFAYASTFKALLAGAVLQSLPEKDLNRTISYSQKDLVSYSPETQKYVGKGMTIAQLCEAAVRFSDNSATNLLLKELGGVEQYQRILRQLGDNVTHTNRLEPDLNQAKPNDIRDTSTPKQMAMNLNAYLLGNTLTESQKTILWNWLDNNATGNPLIRAATPTSWKVYDKSGAGKYGVRNDIAVVRIPNRKPIVMAIMSTQFTEEAKFNNKLVEDAAKQVFHTLQLN"},"dna_sequence":{"accession":"KJ910995.1","fmin":"281","fmax":"1199","strand":"-","sequence":"ATGTTAAATAAGTTAAAAATCGGCACATTATTATTGCTGACATTAACGGCTTGTTTGCCCAATTCTGTTCTTTCGGTAACGTCTAATCCGCAGCCTGCTAGTGCGCCTGTGCAACAATCAGCCACACAAGCCACCTTTCAACAGACTTTGGCGAATTTGGAACAGCAGTATCAAGCCCGAATTGGCGTTTATGTATGGGATACAGAAACGGGACATTCTTTGTCTTATCGTGCAGATGAACGCTTTGCTTATGCGTCCACTTTCAAGGCGTTGTTGGCTGGGGCGGTGTTGCAATCGCTGCCTGAAAAAGATTTAAATCGTACCATTTCATATAGCCAAAAAGATTTGGTTAGTTATTCTCCCGAAACCCAAAAATACGTTGGCAAAGGCATGACGATTGCCCAATTATGTGAAGCAGCCGTGCGGTTTAGCGACAACAGCGCGACCAATTTGCTGCTCAAAGAATTGGGTGGCGTGGAACAATATCAACGTATTTTGCGACAATTAGGCGATAACGTAACCCATACCAATCGGCTAGAACCCGATTTAAATCAAGCCAAACCCAACGATATTCGTGATACGAGTACACCCAAACAAATGGCGATGAATTTAAATGCGTATTTATTGGGCAACACATTAACCGAATCGCAAAAAACGATTTTGTGGAATTGGTTGGACAATAACGCAACAGGCAATCCATTGATTCGCGCTGCTACGCCAACATCGTGGAAAGTGTACGATAAAAGCGGGGCGGGTAAATATGGTGTACGCAATGATATTGCGGTGGTTCGCATACCAAATCGCAAACCGATTGTGATGGCAATCATGAGTACGCAATTTACCGAAGAAGCCAAATTCAACAATAAATTAGTAGAAGATGCAGCAAAGCAAGTATTTCATACTTTACAGCTCAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36791","NCBI_taxonomy_name":"uncultured bacterium","NCBI_taxonomy_id":"77133"}}}},"ARO_accession":"3005077","ARO_id":"43284","ARO_name":"ROB-7","CARD_short_name":"ROB-7","ARO_description":"ROB-7 is a class A beta-lactamase from the blaROB AMR gene family. It was first described by Clemente et al.","ARO_category":{"39428":{"category_aro_accession":"3002994","category_aro_cvterm_id":"39428","category_aro_name":"ROB beta-lactamase","category_aro_description":"ROB beta-lactamases are a class A beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3815":{"model_id":"3815","model_name":"ROB-8","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"620"}},"model_sequences":{"sequence":{"6110":{"protein_sequence":{"accession":"AIW80573.1","sequence":"MLNKLKIGTLLLLTLTACLPNSVPSVTSNPQPASAPVQQSATQATFQQTSANLEQQYQARIGVYVWDTETGHSLSYRADERFAYASTFKALLAGAVLQSLPEKDLNRTISYSQKDLVSYSPETQKYVGKGMTIAQLCEAAVRFSDNSATNLLLKELGGVEQYQRILRQLGDNVTHTNRLEPDLNQAKPNDIRDTSTPKQMAMNLNAYLLGNTLTESQKTILWNWLDNNATGNPLIRAATPTSWKVYDKSGAGKYGVRNDIAVVRIPNRKPIVMAIMSTQFTEEAKFNNKLVEDAAKQVFHTLQLN"},"dna_sequence":{"accession":"KJ910996.1","fmin":"200","fmax":"1118","strand":"+","sequence":"ATGTTAAATAAGTTAAAAATCGGCACATTATTATTGCTGACATTAACGGCTTGTTTGCCCAATTCTGTTCCTTCGGTAACGTCTAATCCGCAGCCTGCTAGTGCGCCTGTGCAACAATCAGCCACACAAGCCACCTTTCAACAGACTTCGGCGAATTTGGAACAGCAGTATCAAGCCCGAATTGGCGTTTATGTATGGGATACAGAAACGGGACATTCTTTGTCTTATCGTGCAGATGAACGCTTTGCTTATGCGTCCACTTTCAAGGCGTTGTTGGCTGGGGCGGTGTTGCAATCGCTGCCTGAAAAAGATTTAAATCGTACCATTTCATATAGCCAAAAAGATTTGGTTAGTTATTCTCCCGAAACCCAAAAATACGTTGGCAAAGGCATGACGATTGCCCAATTATGTGAAGCAGCCGTGCGGTTTAGCGACAACAGCGCGACCAATTTGCTGCTCAAAGAATTGGGTGGCGTGGAACAATATCAACGTATTTTGCGACAATTAGGCGATAACGTAACCCATACCAATCGGCTAGAACCCGATTTAAATCAAGCCAAACCCAACGATATTCGTGATACGAGTACACCCAAACAAATGGCGATGAATTTAAATGCGTATTTATTGGGCAACACATTAACCGAATCGCAAAAAACGATTTTGTGGAATTGGTTGGACAATAACGCAACAGGCAATCCATTGATTCGCGCTGCTACGCCAACATCGTGGAAAGTGTACGATAAAAGCGGGGCGGGTAAATATGGTGTACGCAATGATATTGCGGTGGTTCGCATACCAAATCGCAAACCGATTGTGATGGCAATCATGAGTACGCAATTTACCGAAGAAGCCAAATTCAACAATAAATTAGTAGAAGATGCAGCAAAGCAAGTATTTCATACTTTACAGCTCAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36791","NCBI_taxonomy_name":"uncultured bacterium","NCBI_taxonomy_id":"77133"}}}},"ARO_accession":"3005078","ARO_id":"43285","ARO_name":"ROB-8","CARD_short_name":"ROB-8","ARO_description":"ROB-8 is a class A beta-lactamase from the blaROB AMR gene family. It was first described by Clemente et al.","ARO_category":{"39428":{"category_aro_accession":"3002994","category_aro_cvterm_id":"39428","category_aro_name":"ROB beta-lactamase","category_aro_description":"ROB beta-lactamases are a class A beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3816":{"model_id":"3816","model_name":"ROB-10","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"620"}},"model_sequences":{"sequence":{"6112":{"protein_sequence":{"accession":"MWQ02887.1","sequence":"MFNKLKIGTLLLLTLTACSPNSVHSVTSNPQPASAPVQQSATQATFQQTLANLEQQYQARIGVYVWDTETGHSLSYRADERFAYASTFKALLAGAVLQSLPEKDLNRTISYSQKDLVSYSPETQKYVGKGMTIAQLCEAAVRFSDNSATNLLLKELGGVEQYQRILRQLGDNVTHANRLEPDLNQAKPNDIRDTSTPKQMAMNLNAYLLGNTLTESQKTILWNWLDNNATGNPLIRAATPTSWKVYDKSGAGKYGVRNDIAVVRIPNRKPIVMAIMSTQFTEEAKFNNKLVEDAAKQVFHTLQLN"},"dna_sequence":{"accession":"WIGU01000059.1","fmin":"11257","fmax":"12175","strand":"+","sequence":"ATGTTTAATAAGTTAAAAATCGGCACATTATTATTGCTGACATTAACGGCTTGTTCGCCCAATTCTGTTCATTCGGTAACGTCTAATCCGCAGCCTGCTAGTGCGCCTGTGCAACAATCAGCCACACAAGCCACCTTTCAACAGACTTTGGCGAATTTGGAACAGCAGTATCAAGCCCGAATTGGCGTTTATGTATGGGATACAGAAACGGGACATTCTTTGTCTTATCGTGCAGATGAACGCTTTGCTTATGCGTCCACTTTCAAGGCGTTGTTGGCTGGGGCGGTGTTGCAATCGCTGCCTGAAAAAGATTTAAATCGTACCATTTCATATAGCCAAAAAGATTTGGTTAGTTATTCTCCCGAAACCCAAAAATACGTTGGCAAAGGCATGACGATTGCCCAATTATGTGAAGCAGCCGTGCGGTTTAGCGACAACAGCGCGACCAATTTGCTGCTCAAAGAATTGGGTGGCGTGGAACAATATCAACGTATTTTGCGACAATTAGGCGATAACGTAACCCATGCCAATCGGCTAGAACCCGATTTAAACCAAGCCAAACCCAACGATATTCGTGATACGAGTACACCCAAACAAATGGCGATGAATTTAAATGCGTATTTATTGGGCAACACATTAACCGAATCGCAAAAAACGATTTTGTGGAATTGGTTGGACAATAACGCAACAGGCAATCCATTGATTCGCGCTGCTACGCCAACATCGTGGAAAGTGTACGATAAAAGCGGGGCGGGTAAATATGGTGTACGCAATGATATTGCGGTGGTTCGCATACCAAATCGCAAACCGATTGTGATGGCAATCATGAGTACGCAATTTACCGAAGAAGCCAAATTCAACAATAAATTAGTAGAAGATGCAGCAAAGCAAGTATTTCATACTTTACAGCTCAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43288","NCBI_taxonomy_name":"Glaesserella parasuis","NCBI_taxonomy_id":"738"}}}},"ARO_accession":"3005080","ARO_id":"43287","ARO_name":"ROB-10","CARD_short_name":"ROB-10","ARO_description":"ROB-10 is a class A beta-lactamase from the blaROB AMR gene family. It was found in Glaesserella parasuis.","ARO_category":{"39428":{"category_aro_accession":"3002994","category_aro_cvterm_id":"39428","category_aro_name":"ROB beta-lactamase","category_aro_description":"ROB beta-lactamases are a class A beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3817":{"model_id":"3817","model_name":"Thermus thermophilus uL3 mutations conferring resistance to pleuromutilin antibiotics","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"9963":"R144C","9964":"R144H"},"Curated-R":{"9963":"R144C","9964":"R144H"},"clinical":{"9963":"R144C","9964":"R144H"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"6113":{"protein_sequence":{"accession":"AAS81670.1","sequence":"MKGILGVKVGMTRIFRDDRAVPVTVILAGPCPVVQRRTPEKDGYTAVQLGFLPQNPKRVNRPLKGHFAKAGVEPVRILREIRDFNPEGDTVTVEIFKPGERVDVTGTSKGRGFAGVMKRWNFAGGPDSHGAHKIHRHPGSIGNRKTPGRVYKGKKMAGHYGAERVTVMNLEVVDVIPEENLLLVKGAVPGPNGGLVIVRETKKAAK"},"dna_sequence":{"accession":"AE017221.1","fmin":"1266022","fmax":"1266643","strand":"-","sequence":"GTGAAGGGCATCTTGGGCGTCAAGGTGGGCATGACCCGCATCTTCCGCGACGACCGCGCCGTCCCCGTCACGGTCATCCTTGCGGGGCCGTGCCCCGTGGTGCAGCGCCGCACCCCGGAGAAGGACGGCTACACCGCGGTGCAGCTGGGCTTCCTTCCCCAAAACCCCAAGCGGGTGAACCGCCCCCTTAAGGGGCACTTCGCCAAGGCCGGGGTGGAGCCCGTGCGCATCCTGCGGGAGATCCGGGACTTCAACCCCGAAGGCGACACGGTCACGGTGGAGATCTTCAAGCCCGGGGAGCGCGTGGACGTGACGGGCACCTCCAAGGGCCGGGGCTTCGCCGGCGTGATGAAGCGCTGGAACTTCGCGGGCGGCCCCGACTCCCACGGCGCCCACAAGATCCACCGCCACCCCGGCTCCATCGGGAACCGCAAGACCCCCGGTCGCGTCTACAAGGGCAAGAAGATGGCGGGCCACTACGGGGCCGAGCGCGTGACGGTCATGAACCTCGAGGTGGTGGACGTCATCCCCGAGGAGAACCTGCTTTTGGTCAAGGGGGCCGTCCCCGGTCCCAACGGCGGCCTGGTCATCGTCCGCGAGACCAAGAAGGCGGCCAAGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43290","NCBI_taxonomy_name":"Thermus thermophilus HB27","NCBI_taxonomy_id":"262724"}}}},"ARO_accession":"3005081","ARO_id":"43289","ARO_name":"Thermus thermophilus uL3 mutations conferring resistance to pleuromutilin antibiotics","CARD_short_name":"Tthe_uL3_PLM","ARO_description":"Thermus thermophilus ribosomal protein uL3 containing various mutations conferring resistance to tiamulin. Mutations in the ribosomal protein of uL3 acts by interfering with local rRNA conformation thus conferring resistance.","ARO_category":{"43291":{"category_aro_accession":"3005082","category_aro_cvterm_id":"43291","category_aro_name":"Ribosomal protein mutation conferring resistance to pleuromutilin antibiotics","category_aro_description":"Ribosomal protein mutations that interfere with the rRNA conformation at the active site thus conferring antibiotic resistance.","category_aro_class_name":"AMR Gene Family"},"37015":{"category_aro_accession":"3000671","category_aro_cvterm_id":"37015","category_aro_name":"tiamulin","category_aro_description":"Tiamulin is a pleuromutilin derivative currently used in veterinary medicine. It binds to the 23 rRNA of the 50S ribosomal subunit to inhibit protein translation.","category_aro_class_name":"Antibiotic"},"37014":{"category_aro_accession":"3000670","category_aro_cvterm_id":"37014","category_aro_name":"pleuromutilin antibiotic","category_aro_description":"Pleuromutilins are natural fungal products that target bacterial protein translation by binding the the 23S rRNA, blocking the ribosome P site at the 50S subunit. They are mostly used for agriculture and veterinary purposes.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3818":{"model_id":"3818","model_name":"Thermus thermophilus 23s rRNA conferring resistance to pleuromutilin antibiotics","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"41093","param_value":"5000"},"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"9966":"g2061t","9967":"a2451t","9969":"t2500a","9965":"g2061a","9968":"c2452t","9970":"t2504g"},"Curated-R":{"9966":"g2061t","9967":"a2451t","9969":"t2500a","9965":"g2061a","9968":"c2452t","9970":"t2504g"},"clinical":{"9966":"g2061t","9967":"a2451t","9969":"t2500a","9965":"g2061a","9968":"c2452t","9970":"t2504g"}}},"model_sequences":{"sequence":{"6116":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"AE017221.1","fmin":"1534489","fmax":"1537382","strand":"+","sequence":"GTCAAGATGGTAAGGGCCCACGGTGGATGCCTCGGCACCCGAGCCGATGAAGGACGTGGCTACCTGCGATAAGCCAGGGGGAGCCGGTAGCGGGCGTGGATCCCTGGATGTCCGAATGGGGGAACCCGGCCGGCGGGAACGCCGGTCACCGCGCTTTTTGCGCGGGGGGAACCTGGGGAACTGAAACATCTCAGTACCCAGAGGAGAGGAAAGAGAAATCGACTCCCTGAGTAGCGGCGAGCGAAAGGGGACCAGCCTAAACCGTCCGGCTTGTCCGGGCGGGGTCGTGGGGCCCTCGGACACCGAATCCCCAGCCTAGCCGAAGCTGTTGGGAAGCAGCGCCAGAGAGGGTGAAAGCCCCGTAGGCGAAAGGTGGGGGGATAGGTGAGGGTACCCGAGTACCCCGTGGTTCGTGGAGCCATGGGGGAATCTGGGCGGACCACCGCCTAAGGCTAAGTACTCCGGGTGACCGATAGCGCACCAGTACCGTGAGGGAAAGGTGAAAAGAACCCCGGGAGGGGAGTGAAATAGAGCCTGAAACCGTGGGCTTACAAGCAGTCACGGCCCCGCAAGGGGTTGTGGCGTGCCTATTGAAGCATGAGCCGGCGACTCACGGTCGTGGGCGAGCTTAAGCCGTTGAGGCGGAGGCGTAGGGAAACCGAGTCCGAACAGGGCGTCTAGTCCGCGGCCGTGGACCCGAAACCGGGCGAGCTAGCCCTGGCCAGGGTGAAGCTGGGGTGAGACCCAGTGGAGGCCCGAACCGGTGGGGGATGCAAACCCCTCGGATGAGCTGGGGCTAGGAGTGAAAAGCTAACCGAGCCCGGAGATAGCTGGTTCTCCCCGAAATGACTTTAGGGTCAGCCTCAGGCGCTGACTGGGGCCTGTAGAGCACTGATAGGGCTAGGGGGCCCACCAGCCTACCAAACCCTGTCAAACTCCGAAGGGTCCCAGGTGGAGCCTGGGAGTGAGGGCGCGAGCGATAACGTCCGCGTCCGAGCGCGGGAACAACCGAGACCGCCAGCTAAGGCCCCCAAGTCTGGGCTAAGTGGTAAAGGATGTGGCGCCGCGAAGACAGCCAGGAGGTTGGCTTAGAAGCAGCCATCCTTTAAAGAGTGCGTAATAGCTCACTGGTCGAGTGGCGCCGCGCCGAAAATGATCGGGGCTCAAGCCCAGCGCCGAAGCTGCGGGTCTGGGGGATGACCCCAGGCGGTAGGGGAGCGTTCCCGATGCCGATGAAGGCCGACCCGCGAGGGCGGCTGGAGGTAAGGGAAGTGCGAATGCCGGCATGAGTAACGATAAAGAGGGTGAGAATCCCTCTCGCCGTAAGCCCAAGGGTTCCTACGCAATGGTCGTCAGCGTAGGGTTAGGCGGGACCTAAGGTGAAGCCGAAAGGCGTAGCCGAAGGGCAGCCGGTTAATATTCCGGCCCTTCCCGCAGGTGCGATGGGGGGACGCTCTAGGCTAGGGGGACCGGAGCCATGGACGAGCCCGGCCAGAAGCGCAGGGTGGGAGGTAGGCAAATCCGCCTCCCAAAAGCTCTGCGTGGTGGGGAAGCCCGTACGGGTGACAACCCCCCGAAGCCAGGGAGCCAAGAAAAGCCTCTAAGCACAACCTGCGGGAACCCGTACCGCAAACCGACACAGGTGGGCGGGTGCAAGAGCACTCAGGCGCGCGGGAGAACCCTCGCCAAGGAACTCTGCAAGTTGGCCCCGTAACTTCGGGAGAAGGGGTGCTCCCTGGGGTGATGAGCTCCGGGGAGCCGCAGTGAACAGGCTCTGGCGACTGTTTACCAAAAACACAGCTCTCTGCGAACTCGTAAGAGGAGGTATAGGGAGCGACGCTTGCCCGGTGCCGGAAGGTCAAGGGGAGGGGTGCAAGCCCCGAACCGAAGCCCCGGTGAACGGCGGCCGTAACTATAACGGTCCTAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCTGCACGAAAAGCGTAACGACCGGAGCGCTGTCTCGGCGAGGGACCCGGTGAAATTGAACTGGCCGTGAAGATGCGGCCTACCCGTGGCAGGACGAAAAGACCCCGTGGAGCTTTACTGCAGCCTGGTGTTGGCTCTTGGTCGCGCCTGCGTAGGATAGGTGGGAGCCTGTGAACCCCCGCCTCCGGGTGGGGGGGAGGCGCCGGTGAAATACCACCCTGGCGCGGCTGGGGGCCTAACCCTCGGATGGGGGGACAGCGCTTGGCGGGCAGTTTGACTGGGGCGGTCGCCTCCTAAAAGGTAACGGAGGCGCCCAAAGGTCCCCTCAGGCGGGACGGAAATCCGCCGGAGAGCGCAAGGGTAGAAGGGGGCCTGACTGCGAGGCCTGCAAGCCGAGCAGGGGCGAAAGCCGGGCCTAGTGAACCGGTGGTCCCGTGTGGAAGGGCCATCGATCAACGGATAAAAGTTACCCCGGGGATAACAGGCTGATCTCCCCCGAGCGTCCACAGCGGCGGGGAGGTTTGGCACCTCGATGTCGGCTCGTCGCATCCTGGGGCTGAAGAAGGTCCCAAGGGTTGGGCTGTTCGCCCATTAAAGCGGCACGCGAGCTGGGTTCAGAACGTCGTGAGACAGTTCGGTCTCTATCCGCCACGGGCGCAGGAGGCTTGAGGGGGGCTCTTCCTAGTACGAGAGGACCGGAAGGGACGCACCTCTGGTTTCCCAGCTGTCCCTCCAGGGGCATAAGCTGGGTAGCCATGTGCGGAAGGGATAACCGCTGAAAGCATCTAAGCGGGAAGCCCGCCCCAAGATGAGGCCTCCCACGGCGTCAAGCCGGTAAGGACCCGGGAAGACGACCCGGTGGATGGGCCGGGGGTGTAAGCGCCGCGAGGCGTTGAGCCGACCGGTCCCAATCGTCCGAGGTCTTGACCCCTCC","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43290","NCBI_taxonomy_name":"Thermus thermophilus HB27","NCBI_taxonomy_id":"262724"}}}},"ARO_accession":"3005083","ARO_id":"43292","ARO_name":"Thermus thermophilus 23s rRNA conferring resistance to pleuromutilin antibiotics","CARD_short_name":"Tthe_23S_PLM","ARO_description":"Mutations in the 23s rRNA of Thermus thermophilus confers resistance to pleuromutilin antibiotics such as tiamulin.","ARO_category":{"41330":{"category_aro_accession":"3004178","category_aro_cvterm_id":"41330","category_aro_name":"23S rRNA with mutation conferring resistance to pleuromutilin antibiotics","category_aro_description":"Point mutations in the 23S rRNA subunit may confer resistance to pleuromutilin antibiotics.","category_aro_class_name":"AMR Gene Family"},"37015":{"category_aro_accession":"3000671","category_aro_cvterm_id":"37015","category_aro_name":"tiamulin","category_aro_description":"Tiamulin is a pleuromutilin derivative currently used in veterinary medicine. It binds to the 23 rRNA of the 50S ribosomal subunit to inhibit protein translation.","category_aro_class_name":"Antibiotic"},"37014":{"category_aro_accession":"3000670","category_aro_cvterm_id":"37014","category_aro_name":"pleuromutilin antibiotic","category_aro_description":"Pleuromutilins are natural fungal products that target bacterial protein translation by binding the the 23S rRNA, blocking the ribosome P site at the 50S subunit. They are mostly used for agriculture and veterinary purposes.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3819":{"model_id":"3819","model_name":"dfrA31","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"310"}},"model_sequences":{"sequence":{"6118":{"protein_sequence":{"accession":"BAD88719.1","sequence":"MKISIMAAVSENGVIGSGLDIPWHVQGEQLLFKAMTYNHWLLVGRKTFDSMGKLPNRKYAVVTRSEMVSNDPDVIYFTSIESALSYLDNTTTHVFVSGGGEIYKALIEQADVIHLSVIHKHISGDVFFPSVPQSFKQTFEQSFSSNIDYTYQIWAKG"},"dna_sequence":{"accession":"AB200915.1","fmin":"1831","fmax":"2305","strand":"-","sequence":"ATGAAAATATCCATTATGGCAGCAGTTTCTGAGAATGGAGTAATTGGCTCTGGATTGGATATACCTTGGCATGTACAAGGTGAGCAGCTCCTGTTCAAAGCTATGACTTACAATCATTGGCTTTTAGTCGGTCGTAAAACTTTCGACTCAATGGGTAAACTTCCCAATAGGAAATATGCTGTGGTTACTCGCTCAGAAATGGTCTCGAATGATCCAGATGTTATTTATTTCACCAGCATTGAATCGGCATTATCTTACTTAGACAATACGACAACACATGTCTTTGTTTCTGGTGGTGGTGAAATTTACAAAGCATTAATCGAACAAGCAGATGTTATCCATCTTTCAGTGATTCATAAGCACATCTCTGGCGACGTGTTTTTCCCTTCAGTTCCACAGAGTTTCAAACAAACATTTGAGCAAAGTTTCAGTTCAAATATTGATTACACGTACCAAATTTGGGCAAAGGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43295","NCBI_taxonomy_name":"Vibrio cholerae O1","NCBI_taxonomy_id":"127906"}}}},"ARO_accession":"3005084","ARO_id":"43294","ARO_name":"dfrA31","CARD_short_name":"dfrA31","ARO_description":"dfrA31 is an antibiotic resistance dihydrofolate reductase from an integron found from Vibrio cholerae.","ARO_category":{"37617":{"category_aro_accession":"3001218","category_aro_cvterm_id":"37617","category_aro_name":"trimethoprim resistant dihydrofolate reductase dfr","category_aro_description":"Alternative dihydropteroate synthase dfr present on plasmids produces alternate proteins that are less sensitive to trimethoprim from inhibiting its role in folate synthesis, thus conferring trimethoprim resistance.","category_aro_class_name":"AMR Gene Family"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3820":{"model_id":"3820","model_name":"AAC(3)-IIg","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6120":{"protein_sequence":{"accession":"QKT21444.1","sequence":"MNTRETIAADLSRLGVQSGALVMVHASLKAIGPVDGGAASIVSALLDAVGPTGSLMGYASWDRSPYEETLNGARMDAELRHRWPPFDPAISGTYRGFGLLNRFLLQTPGARRSAHPDASMVAVGPLAGTLTRPHELGQAFGPGSPLERFVERAGKVLLLGAPLDSVTVLHYAEAIARIPNKRRVSYEMPIRSEDGGVRWKRAEDFDSNGILDCFAIEGEPDAVETITNAYVELRRHREGLVGQAHCYLFEARDIVSFGVDYLQRHFGSP"},"dna_sequence":{"accession":"MT090547.1","fmin":"0","fmax":"810","strand":"+","sequence":"ATGAACACAAGGGAAACAATTGCGGCGGACCTTTCACGGCTGGGTGTCCAATCCGGCGCTCTCGTCATGGTTCACGCATCGCTGAAGGCGATCGGCCCCGTCGATGGAGGCGCAGCATCGATAGTGTCTGCCCTGCTCGATGCCGTCGGCCCCACTGGAAGCTTGATGGGATACGCCTCGTGGGACCGGTCGCCTTACGAAGAAACGCTCAATGGCGCACGGATGGATGCGGAACTGCGCCACCGATGGCCGCCGTTCGATCCAGCCATATCAGGCACGTATCGCGGCTTCGGCCTGCTCAACCGGTTCCTCCTCCAGACACCCGGCGCCCGGCGCAGCGCGCACCCGGATGCCTCGATGGTCGCGGTAGGGCCTCTGGCCGGCACTCTGACGCGGCCTCACGAACTTGGGCAGGCTTTCGGACCTGGATCGCCGCTGGAGCGTTTCGTCGAGCGTGCCGGAAAGGTTCTGTTGCTCGGAGCCCCGCTCGATTCCGTTACCGTCCTGCACTACGCCGAGGCCATTGCCCGCATCCCGAACAAGCGACGCGTGAGCTACGAAATGCCGATCCGCAGCGAGGACGGCGGAGTGAGATGGAAACGCGCCGAGGATTTCGACTCCAACGGCATTCTCGATTGTTTCGCTATCGAAGGAGAGCCGGACGCCGTCGAGACAATTACCAATGCCTATGTGGAGCTGCGACGCCATCGGGAGGGCTTGGTCGGTCAGGCGCACTGCTACTTGTTCGAAGCGCGGGATATCGTTTCGTTCGGTGTCGACTATCTTCAACGGCACTTTGGCTCGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3005085","ARO_id":"43296","ARO_name":"AAC(3)-IIg","CARD_short_name":"AAC(3)-IIg","ARO_description":"AAC(3)-IIg is part of the AAC(3) family. It was initially found in clinical isolates of Enterobacter cloacae.","ARO_category":{"36461":{"category_aro_accession":"3000322","category_aro_cvterm_id":"36461","category_aro_name":"AAC(3)","category_aro_description":"A category of aminoglycoside N-acetyltransferase enzymes with modification regiospecificity based at the 3-amino group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics through acetylation of the 3-amino group of the compound.","category_aro_class_name":"AMR Gene Family"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"46127":{"category_aro_accession":"3007377","category_aro_cvterm_id":"46127","category_aro_name":"6'-N-ethylnetilmicin","category_aro_description":"6'-N-ethylnetilmicin is an aminoglycoside antibiotic and a derivative of netilmicin.","category_aro_class_name":"Antibiotic"},"46128":{"category_aro_accession":"3007378","category_aro_cvterm_id":"46128","category_aro_name":"2'-N-ethylnetilmicin","category_aro_description":"2'-N-ethylnetilmicin is an aminoglycoside antibiotic and a derivative of netilmicin.","category_aro_class_name":"Antibiotic"},"46133":{"category_aro_accession":"3007382","category_aro_cvterm_id":"46133","category_aro_name":"gentamicin","category_aro_description":"Gentamicin is a commonly used aminoglycoside antibiotic derived from members of the Micromonospora genus of bacteria. It acts by binding the 30S ribosomal subunit, thus inhibiting protein synthesis. Gentamicin is typically used to treat Gram-negative infections of the repiratory and urinary tract, as well as infections of the bone and soft tissue. It also exhibits considerable nephrotoxicity and ototoxicity. Gentamicin is administered as a mixture of gentamicin type C (which makes about around 80% of the complex) and types A, B, and X (distributed in the remaining 20% of the complex).","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3798":{"model_id":"3798","model_name":"tet(X5)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"6093":{"protein_sequence":{"accession":"WP_150378267.1","sequence":"MTMRIDTDKQMNLLSDKNVAIIGGGPVGLTMAKLLQQNGIDVSVYERDNDREARIFGGTLDLHKGSGQEAMKKAGLLQTYYDLALPMGVNIADEKGNILSTKNVRPENRFDNPEINRNDLRTILLNSLQNDTVIWDRKLVTLEPDKEKWILTFEDKSSETADLVIIANGGMSKVRKFVTDTEVEETGTFNIQADIHQPEVNCPGFFQLCNGNRLMAAHQGNLLFANPNNNGALHFGISFKTPDEWKSKTRVDFQDRNSVVDFLLKKFSDWDERYKELIRLTSSFVGLATRIFPLDKSWKSKRPLPITMIGDAAHLMPPFAGQGVNSGLMDALILSDNLTNGKFNSIEEAIENYEQQMFAYGREAQAESIINETEMFSLDFSFQKLMNL"},"dna_sequence":{"accession":"NZ_CP040912.1","fmin":"84797","fmax":"85964","strand":"+","sequence":"ATGACAATGCGAATAGATACAGACAAACAAATGAATTTACTTAGTGATAAGAACGTTGCAATAATTGGTGGTGGACCCGTTGGACTGACTATGGCAAAATTATTACAGCAAAACGGCATAGACGTTTCAGTTTACGAAAGAGACAACGACCGAGAGGCAAGAATTTTTGGTGGAACCCTTGACCTACACAAAGGTTCAGGTCAGGAAGCAATGAAAAAAGCGGGATTGTTACAAACTTATTATGACTTAGCCTTACCAATGGGTGTAAATATTGCTGATGAAAAAGGCAATATTTTATCCACAAAAAATGTAAGACCCGAAAATCGTTTTGACAATCCTGAAATAAACAGAAATGACTTAAGGACTATCCTATTAAATAGTTTACAAAATGATACCGTCATTTGGGATAGAAAACTTGTTACCCTTGAACCTGATAAGGAGAAGTGGATACTAACTTTTGAGGATAAATCGAGTGAAACAGCAGATCTGGTTATTATTGCCAATGGTGGAATGTCTAAAGTAAGAAAATTTGTTACCGACACGGAAGTTGAAGAAACAGGTACTTTCAATATACAAGCCGATATTCATCAACCGGAGGTGAACTGTCCTGGATTTTTTCAGCTTTGCAATGGAAACCGGCTAATGGCTGCTCATCAAGGTAATTTATTATTTGCGAATCCTAATAATAATGGTGCATTGCATTTTGGAATAAGTTTTAAAACACCTGATGAATGGAAAAGCAAAACGCGGGTAGATTTTCAAGACAGAAATAGTGTCGTTGATTTTCTCCTGAAAAAATTTTCCGATTGGGACGAACGCTACAAAGAACTGATTCGTTTGACATCATCTTTTGTAGGGTTAGCGACACGAATATTTCCCTTAGATAAGTCTTGGAAAAGTAAGCGTCCATTACCCATAACGATGATTGGAGATGCTGCTCATTTGATGCCTCCTTTTGCAGGACAAGGCGTAAACAGTGGGTTGATGGATGCCTTGATATTGTCGGATAATCTGACCAATGGGAAATTTAACAGCATTGAAGAGGCTATTGAAAATTATGAACAGCAAATGTTTGCTTATGGAAGAGAAGCACAGGCAGAATCAATAATAAACGAAACGGAAATGTTCAGCCTCGACTTTTCTTTCCAAAAACTAATGAATCTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3005057","ARO_id":"43259","ARO_name":"tet(X5)","CARD_short_name":"tet(X5)","ARO_description":"Tet(X5) is a tetracycline inactivating enzyme. It is a variant of tet(X).","ARO_category":{"36176":{"category_aro_accession":"3000036","category_aro_cvterm_id":"36176","category_aro_name":"tetracycline inactivation enzyme","category_aro_description":"Enzymes or other gene products which hydroxylate tetracycline and other tetracycline derivatives. Hydroxylation inactivates tetracycline-like antibiotics, thus conferring resistance to these compounds.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36291":{"category_aro_accession":"3000152","category_aro_cvterm_id":"36291","category_aro_name":"minocycline","category_aro_description":"Minocycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"37012":{"category_aro_accession":"3000668","category_aro_cvterm_id":"37012","category_aro_name":"oxytetracycline","category_aro_description":"Oxytetracycline is a derivative of tetracycline with a 5-hydroxyl group. Its activity is similar to other tetracyclines.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3814":{"model_id":"3814","model_name":"ROB-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"620"}},"model_sequences":{"sequence":{"6111":{"protein_sequence":{"accession":"AWU47610.1","sequence":"MLNKLKIGTLLLLTLTACSPNSVHSVKSNPQPASAPVQQSATQATFQQTLANLEQQYQARIGVYVWDTETGHSLSYRADERFAYASTFKALLAGAVLQSLPEKDLNRTISYSQKDLVSYSPETQKYVGKGMTIAQLCEAAVRFSDNSATNLLLKELGGVEQYQRILRQLGDNVTHANRLEPDLNQAKPNDIRDTSTPKQMAMNLNAYLLGNTLTESQKTILWNWLDNNATGNPLIRAATPTSWKVYDKSGAGKKYGVRNDIAVVRIPNRKPIVMAIMSTQFTEEAKFNNKLVEDAAKQVFHTLQLN"},"dna_sequence":{"accession":"MH316128.1","fmin":"8","fmax":"929","strand":"-","sequence":"ATGTTAAATAAGTTAAAAATCGGCACATTATTATTGCTGACATTAACGGCTTGTTCGCCCAATTCTGTTCATTCGGTAAAGTCTAATCCGCAGCCTGCTAGTGCGCCTGTGCAACAATCAGCCACACAAGCCACCTTTCAACAGACTTTGGCGAATTTGGAACAGCAGTATCAAGCCCGAATTGGCGTTTATGTATGGGATACAGAAACGGGACATTCTTTGTCTTATCGTGCAGATGAACGCTTTGCTTATGCGTCCACTTTCAAGGCGTTGTTGGCTGGGGCGGTGTTGCAATCGCTGCCTGAAAAAGATTTAAATCGTACCATTTCATATAGCCAAAAAGATTTGGTTAGTTATTCTCCCGAAACCCAAAAATACGTTGGCAAAGGCATGACGATTGCCCAATTATGTGAAGCAGCCGTGCGGTTTAGCGACAACAGCGCGACCAATTTGCTGCTCAAAGAATTGGGTGGCGTGGAACAATATCAACGTATTTTGCGACAATTAGGCGATAACGTAACCCATGCCAATCGGCTAGAACCCGATTTAAATCAAGCCAAACCCAACGATATTCGTGATACGAGTACACCCAAACAAATGGCGATGAATTTAAATGCGTATTTATTGGGCAACACATTAACCGAATCGCAAAAAACGATTTTGTGGAATTGGTTGGACAATAACGCAACAGGCAATCCATTGATTCGCGCTGCTACGCCAACATCGTGGAAAGTGTACGATAAAAGCGGGGCGGGTAAAAAATATGGTGTACGCAATGATATTGCGGTGGTTCGCATACCAAATCGCAAACCGATTGTGATGGCAATCATGAGTACGCAATTTACCGAAGAAGCCAAATTCAACAATAAATTAGTAGAAGATGCAGCAAAGCAAGTATTTCATACTTTACAGCTCAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39540","NCBI_taxonomy_name":"Mannheimia haemolytica","NCBI_taxonomy_id":"75985"}}}},"ARO_accession":"3005079","ARO_id":"43286","ARO_name":"ROB-2","CARD_short_name":"ROB-2","ARO_description":"ROB-2 is an extended spectrum class A beta-lactamase from the blaROB AMR gene family It is described by Kadlec et al.","ARO_category":{"39428":{"category_aro_accession":"3002994","category_aro_cvterm_id":"39428","category_aro_name":"ROB beta-lactamase","category_aro_description":"ROB beta-lactamases are a class A beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3821":{"model_id":"3821","model_name":"msrF","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"900"}},"model_sequences":{"sequence":{"6121":{"protein_sequence":{"accession":"QHW12375.1","sequence":"MEQICFELENVEVTFLDKKILEIDRLAVHQFDRIGIVGKNGAGKSTLLKILGGIIKPTRGKVNRYIDYGYFEQVESPKVSMADPRLLGKLNVKVDSNNLSGGELTRLKIAQLFTDYYESLLIDEPTTHLDQDGISFLIDKLKYYYGALVLISHDRNLLDELVTTIWEIDDGMIKVYSGNYSEYLRQKKVEREQQAHDFDLYLKEKNRLEKAAKEKMNKAEKIANSSSMSKKESKAKANRMFESKSKGTSQKSLQRAAKAVEKRIEQLEVVDAPKEIHTIQFHQTHSTPPLHNKFPILGDRLTLQAGDKTLLEETSFQFPLGKTIAITGNNGSGKTTLIHHIIQKGEGITISPKAVIGFYEQMGYQFNEDKTVLSYMKARSDYDESKIRSVLHAMNFNGNDLKKNVRYLSGGEATRLVLCQLFLGRYNILILDEPTNFLDIFCIEALERFIEEYEGTIILISHDKKFVDHVSDTIYKIENKKLNLVN"},"dna_sequence":{"accession":"MN728682.1","fmin":"17386","fmax":"18847","strand":"+","sequence":"ATGGAACAAATATGTTTTGAATTAGAAAATGTTGAAGTAACTTTTTTAGATAAAAAAATATTGGAGATTGATCGCTTAGCTGTTCATCAGTTTGATCGAATAGGTATTGTTGGAAAAAATGGGGCAGGAAAAAGTACATTATTGAAAATACTTGGTGGTATTATTAAGCCTACTAGAGGAAAAGTAAATCGTTATATAGATTACGGATATTTTGAACAAGTAGAAAGTCCTAAAGTCAGTATGGCTGATCCACGCTTATTAGGAAAATTAAATGTAAAAGTAGATTCAAATAATCTAAGTGGTGGTGAACTAACAAGACTGAAAATTGCTCAATTATTTACAGACTATTATGAATCGTTGTTAATTGATGAGCCTACGACACATTTAGATCAAGATGGAATTTCATTTCTCATAGATAAATTAAAGTATTATTATGGTGCATTAGTTTTAATCAGTCATGACCGCAATCTACTAGATGAACTCGTTACTACTATATGGGAAATTGATGATGGTATGATTAAAGTATATTCTGGAAATTACAGTGAGTATTTGAGACAGAAGAAGGTGGAAAGAGAGCAACAAGCGCATGATTTCGATCTATATTTGAAAGAAAAGAATAGGCTTGAAAAAGCAGCTAAGGAAAAAATGAATAAAGCTGAAAAAATTGCCAATTCGTCTTCAATGTCAAAGAAAGAATCCAAAGCAAAGGCAAACCGTATGTTTGAATCAAAATCAAAAGGTACAAGTCAGAAATCACTACAACGAGCTGCAAAAGCTGTTGAAAAAAGAATAGAGCAACTTGAAGTAGTGGATGCACCTAAAGAAATTCACACAATTCAATTTCATCAGACTCACTCCACACCACCATTACACAACAAGTTTCCAATATTGGGAGATCGTTTAACTCTACAAGCAGGGGATAAAACACTCTTAGAAGAAACGAGTTTTCAATTTCCATTAGGAAAAACTATAGCAATTACAGGTAATAATGGTTCTGGTAAAACGACATTGATTCATCATATTATTCAAAAGGGTGAAGGTATTACTATATCTCCTAAAGCTGTGATTGGATTTTATGAACAAATGGGATATCAGTTCAATGAAGATAAAACTGTATTATCTTATATGAAAGCTAGAAGTGATTATGATGAAAGTAAAATACGTTCAGTTTTACACGCTATGAATTTCAATGGTAATGACTTGAAAAAGAATGTACGATATTTAAGTGGAGGAGAAGCAACTCGATTAGTATTATGTCAGCTTTTTTTAGGAAGATATAATATTTTGATTCTAGATGAGCCAACAAACTTTTTAGACATTTTTTGTATAGAAGCATTAGAGAGATTTATAGAAGAATATGAAGGGACTATTATTCTTATTTCGCATGATAAGAAGTTTGTAGATCATGTATCTGATACTATTTATAAAATAGAAAATAAAAAGTTGAATTTGGTAAATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43299","NCBI_taxonomy_name":"Macrococcus canis","NCBI_taxonomy_id":"1855823"}}}},"ARO_accession":"3005087","ARO_id":"43298","ARO_name":"msrF","CARD_short_name":"msrF","ARO_description":"msrF is an ABC-F binding cassette ribosomal protection protein. It confers resistance to macrolide antibiotics.","ARO_category":{"41695":{"category_aro_accession":"3004471","category_aro_cvterm_id":"41695","category_aro_name":"msr-type ABC-F protein","category_aro_description":"msr-type ABC-F subfamily ribosomal protection proteins expression in Staphylococci species and confer resistance to erythromycin and streptogramin B antibiotics through antibiotic target protection mechanisms.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3822":{"model_id":"3822","model_name":"msrH","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"900"}},"model_sequences":{"sequence":{"6122":{"protein_sequence":{"accession":"DAC81085.1","sequence":"MEQICFELENIELSYLDKKVLDIDRLAIHQFDRIGIVGRNGAGKSTLLKIIGGIINPSRGKVNQYVEYGYFEQLEGPIAKATNPRLLGKLQVKENASNLSGGEQTRLKLAQLFTHFYDALLIDEPTTHLDQDGISFLIEELKNYYGALILISHDRAFLDELVTTIWEIDEGTVKIYSGNYSDYMRQKQIERTQQVYNHEQFLKEKNRLEKASLEKMKKAEKIAKSTSMSKKESKAKPNRMFESKSKGTSQKSLQRAAKAIEQRINQLQVVEAPNDDYVIHFHSTNNISKLHNKFPIMGDCITLEIDDKVLLKETSFQFPLGKTIAITGKNGSGKTTLIRHIIENGEGITISPKAEIGIYEQMGYQFDEDKTVLSYIKDRSDYDESKIRSVLNAMSFTGNDLKKKVQNLSGGESIRLVLCQLFLGRYNILVLDEPTNFLDIFCIEALESILKEYKGTVIIISHDKKFVEHVSDIVYRIENQKLKLVN"},"dna_sequence":{"accession":"BK011995.1","fmin":"25516","fmax":"26977","strand":"+","sequence":"ATGGAACAAATATGTTTTGAATTAGAGAATATTGAATTAAGTTATTTAGATAAAAAAGTGTTGGATATTGATCGATTAGCTATTCATCAGTTTGATAGAATAGGTATTGTGGGAAGAAATGGAGCAGGAAAAAGTACATTATTGAAAATAATTGGTGGTATTATTAATCCTTCTAGAGGAAAGGTTAATCAATATGTAGAGTACGGGTATTTCGAACAATTAGAAGGTCCGATAGCTAAAGCAACTAATCCGCGCTTATTAGGTAAGTTGCAAGTAAAAGAGAACGCTAGTAATTTAAGTGGTGGTGAACAGACAAGGCTCAAACTTGCGCAATTATTTACCCATTTTTATGATGCGTTGTTAATTGATGAGCCTACAACACATTTGGATCAAGATGGTATCTCATTTCTTATCGAAGAACTTAAGAATTATTATGGTGCTTTAATTTTAATAAGTCATGATCGTGCATTTCTGGATGAACTTGTTACAACAATATGGGAAATTGATGAAGGTACAGTTAAAATATATTCTGGAAATTATAGTGATTATATGAGGCAGAAGCAAATAGAAAGAACGCAACAAGTTTACAATCATGAACAATTTTTGAAAGAAAAGAATAGGCTTGAAAAAGCATCACTAGAAAAAATGAAAAAAGCTGAAAAAATTGCTAAATCTACTTCGATGTCAAAGAAAGAGTCTAAGGCAAAGCCAAATCGTATGTTCGAATCAAAGTCGAAAGGCACAAGTCAGAAATCGTTACAACGTGCTGCAAAAGCAATCGAGCAAAGAATAAACCAACTGCAAGTTGTAGAAGCACCAAATGATGATTACGTCATTCATTTCCATTCGACTAATAATATATCAAAATTGCATAATAAATTTCCGATTATGGGGGATTGTATAACGCTAGAGATAGATGATAAAGTACTATTAAAAGAAACAAGTTTTCAATTTCCTTTAGGTAAAACAATAGCAATTACTGGTAAGAATGGTTCAGGTAAAACAACATTGATTCGTCATATTATTGAAAATGGTGAGGGTATCACTATTTCCCCAAAAGCAGAGATTGGAATATATGAACAAATGGGTTATCAGTTCGATGAAGATAAAACTGTTTTATCGTATATAAAAGATAGAAGTGATTATGATGAAAGTAAAATACGTTCTGTTCTTAATGCGATGAGTTTTACTGGTAATGACTTGAAGAAGAAAGTTCAAAACTTAAGTGGAGGAGAATCAATACGGTTAGTATTATGTCAACTTTTTTTAGGAAGGTATAATATTTTAGTTCTAGATGAGCCAACAAACTTTTTAGATATTTTTTGTATTGAAGCATTAGAGAGTATTTTAAAAGAATACAAAGGTACTGTAATTATTATTTCACATGATAAAAAATTTGTTGAACATGTTTCTGATATAGTTTATAGAATAGAAAACCAAAAATTGAAATTAGTAAATTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43299","NCBI_taxonomy_name":"Macrococcus canis","NCBI_taxonomy_id":"1855823"}}}},"ARO_accession":"3005088","ARO_id":"43300","ARO_name":"msrH","CARD_short_name":"msrH","ARO_description":"msrH is a ABC-F binding cassette ribosomal protection protein. It confers resistance to macrolide antibiotics.","ARO_category":{"41695":{"category_aro_accession":"3004471","category_aro_cvterm_id":"41695","category_aro_name":"msr-type ABC-F protein","category_aro_description":"msr-type ABC-F subfamily ribosomal protection proteins expression in Staphylococci species and confer resistance to erythromycin and streptogramin B antibiotics through antibiotic target protection mechanisms.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3823":{"model_id":"3823","model_name":"mef(D)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6123":{"protein_sequence":{"accession":"QHW12307.1","sequence":"MKNNKWKKKFIAIYIGQFFSLLSSAAVQFSIIWWLTDKTGGSPLVLTLAGLAGFLPQALAGPFAGTITDRYSRKLMMILADMTVALGSLILFISLYFYEINISFVILILAIRSLATAFHMPALQASIPLLVPEDDLTKAAGWGQTVSSISNITGPAVGMSILAASSIEWVLLLDVLGAVIASGILLFIYIPKIQNQNQQSIDSKGFFIEMKDGYNALVNHPILLKLTFVMTSVAVLYIPLGTYFPLITRNHFNKGVVEAGIVEIIFAVGLIIGGSFLGILGDKFNKINTMTTGILLMGIALFLTGILSPSLFYFFVVLAGLVGFSGPLFSAPFYALIQSEIEPHLLGRVFSFVTSISLLATPLGYVIAGLLIEITNVSTLFSIIGVLIIFNGIIINRLK"},"dna_sequence":{"accession":"MN728681.1","fmin":"17458","fmax":"18658","strand":"+","sequence":"GTGAAAAATAATAAATGGAAAAAGAAATTTATAGCAATATATATAGGGCAGTTCTTTTCTTTATTAAGTAGTGCTGCTGTACAATTCAGTATCATTTGGTGGTTAACAGATAAAACAGGAGGATCACCTCTTGTACTGACATTAGCAGGTCTTGCCGGTTTTTTACCACAAGCATTAGCAGGGCCATTTGCTGGAACAATTACGGATCGTTATTCAAGAAAATTAATGATGATTCTAGCAGATATGACAGTTGCATTGGGAAGTTTAATCTTATTTATTTCATTGTATTTTTATGAAATAAATATTTCATTTGTAATTTTAATATTAGCAATTCGCTCATTAGCAACGGCATTTCATATGCCTGCCCTGCAAGCATCTATTCCATTGCTTGTTCCTGAAGATGATCTTACTAAGGCCGCTGGATGGGGACAGACAGTAAGTTCTATATCAAATATAACAGGTCCCGCTGTAGGTATGTCAATACTTGCTGCAAGTTCTATAGAATGGGTTTTATTACTTGATGTTTTGGGAGCAGTGATAGCAAGTGGTATTTTACTATTCATTTACATTCCTAAAATTCAAAATCAAAATCAACAATCGATAGATTCTAAAGGGTTTTTTATTGAAATGAAGGATGGATATAACGCGCTTGTCAATCATCCAATCTTATTAAAACTAACGTTTGTTATGACATCTGTTGCAGTTTTATACATTCCGCTAGGTACTTATTTTCCTCTTATAACAAGGAATCACTTTAATAAGGGAGTTGTTGAAGCTGGAATCGTAGAGATTATTTTTGCTGTTGGACTAATTATTGGTGGTTCGTTCCTGGGAATACTTGGAGATAAATTTAATAAAATTAATACAATGACAACTGGAATATTGTTGATGGGAATTGCGTTATTTTTAACGGGTATTCTATCACCTTCTCTTTTCTATTTCTTTGTTGTTTTAGCTGGTTTAGTAGGATTTTCTGGGCCTTTATTTTCAGCACCGTTTTATGCATTAATCCAATCTGAAATTGAGCCTCATCTTTTAGGAAGAGTTTTTAGTTTCGTTACTAGTATCTCGTTATTAGCAACACCATTAGGATATGTTATTGCAGGATTATTGATAGAGATAACGAATGTATCTACACTATTTTCTATAATTGGAGTGTTGATTATTTTCAATGGAATTATTATTAATAGATTGAAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43299","NCBI_taxonomy_name":"Macrococcus canis","NCBI_taxonomy_id":"1855823"}}}},"ARO_accession":"3005089","ARO_id":"43301","ARO_name":"mef(D)","CARD_short_name":"mef(D)","ARO_description":"mef(D) is a major facilitator superfamily efflux pump protein. It works together with the msr proteins to confer resistance to macrolide antibiotics.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"3824":{"model_id":"3824","model_name":"RanB","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"6124":{"protein_sequence":{"accession":"ADZ12700.1","sequence":"MLKLSKRMLTSVGEYVLLLGKVIKRPQKHNIFFKLLMREINDLGVNSFGLVLFTSIFVGAVVAIQMYNNFKASTIPIPLYFIGYATKVVLILEFSPTIISLILAGKVGSYIASSIGTMRVTEQIDALDIMGVNSPNFLILPKIVANVIFNPLLIAISIVFGIYGGYLAGVATGNWTEADYITGIQRYIPDYFIWYAFFKTVVFAFLIATIPAYFGYNVKGGSLEVGRASTQAVVWTMVAIIIAELISTQLFLS"},"dna_sequence":{"accession":"CP002562.1","fmin":"1618244","fmax":"1619006","strand":"-","sequence":"ATGTTAAAGTTGTCAAAAAGAATGCTTACCTCTGTGGGAGAGTATGTTTTGTTACTAGGAAAAGTAATAAAACGCCCGCAGAAGCATAATATTTTTTTTAAACTCTTGATGAGAGAGATTAACGATTTAGGCGTTAACTCCTTTGGTTTGGTCTTATTTACTTCCATATTTGTGGGAGCTGTAGTCGCAATACAAATGTATAATAACTTTAAGGCTTCTACCATTCCCATTCCACTGTACTTCATAGGTTATGCTACTAAGGTGGTGCTTATTTTAGAGTTTTCGCCTACTATCATTAGTCTTATTTTGGCAGGTAAAGTAGGGTCTTACATCGCGTCTAGTATAGGAACGATGAGAGTGACGGAGCAGATAGACGCTTTAGATATTATGGGTGTTAATTCCCCCAACTTTTTGATTCTTCCAAAGATAGTAGCTAATGTTATTTTTAATCCGTTACTCATAGCCATTAGTATTGTTTTCGGTATTTATGGAGGTTATTTAGCAGGAGTTGCCACGGGCAATTGGACAGAAGCCGACTATATTACAGGGATACAAAGATATATTCCAGACTACTTTATATGGTATGCTTTTTTTAAAACGGTGGTGTTTGCGTTCCTTATTGCTACAATTCCAGCTTATTTTGGTTATAATGTAAAGGGAGGCTCTTTAGAAGTAGGTAGAGCTAGCACCCAAGCAGTAGTTTGGACTATGGTGGCAATTATTATTGCCGAACTTATATCAACCCAATTATTTTTAAGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43303","NCBI_taxonomy_name":"Riemerella anatipestifer RA-GD","NCBI_taxonomy_id":"992406"}}}},"ARO_accession":"3005090","ARO_id":"43302","ARO_name":"RanB","CARD_short_name":"RanB","ARO_description":"RanB is the determinant of antibiotic resistance within the RanARanB ABC-type efflux system. It confers resistance to aminoglycoside antibiotics.","ARO_category":{"36002":{"category_aro_accession":"0010001","category_aro_cvterm_id":"36002","category_aro_name":"ATP-binding cassette (ABC) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding\/hydrolysis to transport substrates across cell membranes.","category_aro_class_name":"AMR Gene Family"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"3825":{"model_id":"3825","model_name":"RanA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6125":{"protein_sequence":{"accession":"ADZ12699.1","sequence":"MIEVKDLRKSFNDVEVLKGITTTFETGKINLVIGQSGSGKTVFLKCLLNVFDPSSGDILFDGRNLSIMGRTEKQEIRSEIGTVFQGSALFDSMTVEENISFPLDMFTNLTYTEKRKRVKEVIGRVHLENANTKFPSEISGGMQKRVAIARAIVNNPKYLFCDEPNSGLDPNTAIVIDELIKEITEEYNTTTIINTHDMNSVLTIGEKIVYLRKGVKEWEGNKDLIIKAENEHLIDFVYSSALFKQVRETMLRNNQTNL"},"dna_sequence":{"accession":"CP002562.1","fmin":"1617468","fmax":"1618245","strand":"-","sequence":"ATGATTGAAGTTAAAGATTTAAGAAAAAGTTTTAATGATGTAGAGGTTCTCAAAGGAATTACTACTACTTTTGAAACAGGAAAAATAAACCTTGTCATTGGTCAATCGGGTTCTGGTAAAACAGTGTTTTTGAAGTGTTTACTCAATGTTTTTGACCCTTCTTCAGGAGATATTTTATTTGATGGAAGAAATCTAAGCATTATGGGGCGAACGGAAAAACAAGAAATTCGTTCTGAGATAGGCACGGTATTTCAAGGGAGTGCTTTATTTGACTCTATGACGGTAGAAGAAAATATATCTTTTCCTTTGGATATGTTTACCAATCTCACTTATACCGAAAAAAGAAAAAGAGTAAAAGAAGTAATTGGAAGAGTTCATTTAGAAAATGCTAACACCAAGTTTCCTTCTGAAATATCAGGCGGAATGCAAAAAAGAGTGGCAATAGCTCGTGCAATTGTGAACAATCCAAAATATCTCTTTTGTGACGAACCAAATTCTGGTTTAGACCCTAACACAGCCATTGTAATAGATGAGCTTATAAAAGAAATTACAGAGGAATATAATACTACGACGATTATCAACACCCACGATATGAACTCTGTACTTACTATAGGTGAGAAAATAGTTTATTTAAGAAAAGGTGTTAAAGAGTGGGAAGGTAACAAAGACCTTATTATCAAAGCAGAAAATGAGCATTTAATAGATTTTGTTTACTCTTCAGCTTTGTTTAAGCAAGTAAGGGAAACAATGTTAAGAAATAATCAAACTAATTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43303","NCBI_taxonomy_name":"Riemerella anatipestifer RA-GD","NCBI_taxonomy_id":"992406"}}}},"ARO_accession":"3005091","ARO_id":"43304","ARO_name":"RanA","CARD_short_name":"RanA","ARO_description":"RanA is a part of the RanARanB ABC-type efflux system. Alongside RanB, it confers resistance to aminoglycoside antibiotics.","ARO_category":{"36002":{"category_aro_accession":"0010001","category_aro_cvterm_id":"36002","category_aro_name":"ATP-binding cassette (ABC) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding\/hydrolysis to transport substrates across cell membranes.","category_aro_class_name":"AMR Gene Family"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"3826":{"model_id":"3826","model_name":"OXA-899","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"530"}},"model_sequences":{"sequence":{"6126":{"protein_sequence":{"accession":"QHT72949.1","sequence":"MMKRRHAATGALLAALATFAHAEHPICTIVADGATGKAVLQEGRCDERVTPASTFKLALAVMGFDHGFLKDEHTPVEHFRHGDPDWGGEAWHQPIDPALWLKYSVVWYSQRITHAMGAQTFQAYVRKLGYGNMDVSGDPGKNNGMDRSWITSSLKISPEEQVGFMRRIVNRQLPVSARTYEMVDRTVQTWQVPGGWSVHGKTGTAGPAPGNTSPDGTWDQAHAYGWFVGWARKGDKTYVFANLIQDDKVEPTSGGIRSRDALLARLPEVLAFAGQ"},"dna_sequence":{"accession":"MN968729.1","fmin":"0","fmax":"828","strand":"+","sequence":"ATGATGAAACGCCGCCACGCCGCCACCGGCGCCCTGCTTGCTGCGCTTGCAACCTTTGCCCACGCCGAGCACCCGATCTGCACGATCGTGGCCGATGGCGCGACGGGCAAGGCAGTCTTGCAAGAAGGCAGGTGCGACGAGCGCGTGACCCCCGCTTCCACCTTCAAGCTGGCGCTGGCCGTCATGGGCTTTGACCACGGCTTCCTGAAAGACGAGCACACCCCGGTGGAGCACTTCAGGCACGGTGACCCCGACTGGGGCGGCGAGGCTTGGCACCAGCCGATCGACCCGGCGCTGTGGCTCAAGTATTCGGTGGTCTGGTATTCGCAGCGCATTACGCATGCGATGGGCGCGCAGACCTTCCAGGCCTACGTGCGCAAGCTCGGCTACGGCAACATGGATGTGAGCGGCGATCCGGGCAAGAACAACGGCATGGACCGCTCGTGGATCACCTCGTCGCTGAAGATCTCGCCGGAGGAGCAAGTCGGCTTCATGCGCAGGATCGTCAACCGGCAGTTGCCGGTGTCGGCGCGCACCTACGAGATGGTCGACCGTACCGTGCAGACCTGGCAGGTGCCGGGCGGCTGGTCAGTGCACGGCAAGACGGGCACCGCCGGCCCTGCGCCGGGCAATACCTCGCCCGATGGCACGTGGGACCAGGCGCACGCTTACGGGTGGTTTGTCGGCTGGGCCAGGAAGGGCGACAAGACGTACGTGTTTGCCAACCTGATCCAGGACGACAAGGTTGAGCCGACCTCGGGCGGCATCCGCTCGCGCGATGCGCTGCTTGCGCGCCTGCCCGAAGTGCTTGCCTTTGCCGGGCAATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36921","NCBI_taxonomy_name":"Ralstonia pickettii","NCBI_taxonomy_id":"329"}}}},"ARO_accession":"3005093","ARO_id":"43306","ARO_name":"OXA-899","CARD_short_name":"OXA-899","ARO_description":"OXA-899 is a class D beta-lactamase and part of the OXA family. It confers resistance to B-lactams and was originally found in Ralstonia pikettii.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46497":{"category_aro_accession":"3007708","category_aro_cvterm_id":"46497","category_aro_name":"OXA-22-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-22.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3827":{"model_id":"3827","model_name":"OXA-898","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"530"}},"model_sequences":{"sequence":{"6127":{"protein_sequence":{"accession":"QHT72948.1","sequence":"MLSCCSKSFAFALMACLLATSAATARAELVVRNDLKRVFDAAGVSGTFVLMDISADRTYVVDPARAARRIHPASTFKIPNSLIAFDTGAVRDDHEVLPYGGKPQPFKQWEHDMALPEAIRLSAVPIYQEVARRVGFERMQAYVDAFDYGNRQLGGVIDQFWLRGPLEISALEEARFTSRMALKQLPVKPRTWDMVHRMLLIEQQGDAALYAKTGVATEYQPEIGWWVGWVERAGRVYAFALNIDMPREGDMAKRIPLGKQLMQALEVWPTL"},"dna_sequence":{"accession":"MN968728.1","fmin":"0","fmax":"816","strand":"+","sequence":"ATGCTGTCTTGCTGCTCGAAGTCCTTCGCGTTCGCCTTGATGGCCTGCCTGCTGGCAACAAGCGCCGCCACTGCCCGCGCTGAGCTGGTCGTGCGTAACGACCTCAAGCGCGTGTTCGACGCCGCCGGCGTCTCAGGCACCTTCGTGCTGATGGACATCAGCGCCGACCGGACCTATGTCGTCGACCCGGCGCGGGCCGCGCGACGCATCCATCCGGCCTCCACCTTCAAGATCCCGAACAGTCTGATCGCCTTCGACACCGGCGCCGTGCGCGACGACCACGAAGTGCTGCCCTACGGCGGCAAGCCGCAACCCTTCAAGCAGTGGGAGCACGACATGGCATTGCCCGAAGCGATTCGCCTATCCGCCGTGCCGATCTACCAGGAAGTGGCGCGCCGCGTGGGTTTCGAGCGCATGCAGGCCTACGTCGATGCGTTTGACTACGGCAATCGCCAGCTCGGCGGCGTGATCGACCAGTTCTGGCTGCGTGGCCCGCTGGAGATTTCTGCACTTGAAGAGGCGCGCTTCACCAGCCGCATGGCGCTCAAGCAGTTGCCGGTGAAGCCCCGCACGTGGGACATGGTCCACCGCATGCTGTTGATCGAGCAGCAGGGCGACGCCGCGCTGTATGCCAAGACAGGCGTTGCCACGGAGTATCAGCCGGAGATCGGCTGGTGGGTCGGTTGGGTCGAGCGTGCCGGGCGCGTGTATGCCTTCGCGCTGAACATCGACATGCCGCGCGAGGGCGACATGGCCAAGCGCATTCCGCTGGGCAAGCAGTTGATGCAGGCGCTGGAGGTGTGGCCGACGCTGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36921","NCBI_taxonomy_name":"Ralstonia pickettii","NCBI_taxonomy_id":"329"}}}},"ARO_accession":"3005094","ARO_id":"43307","ARO_name":"OXA-898","CARD_short_name":"OXA-898","ARO_description":"OXA-898 is a class D beta-lactamase from the OXA family. It confers resistance to B-lactams and was originally found in Ralstonia pikettii.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46518":{"category_aro_accession":"3007729","category_aro_cvterm_id":"46518","category_aro_name":"OXA-60-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-60.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3828":{"model_id":"3828","model_name":"GPC-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6128":{"protein_sequence":{"accession":"AWB15813.1","sequence":"MTITISRRQAMAGALLAIPAVSALTAGTSRAAGENLAQRLAALEARHGGRIGVAIHNLSTGARLGHNTDERFLMCSTFKALLAGHILVRVDRGEETLDRRIVVKEADLVDWSPVVEKRIGGDVISIAELCEATITLSDNAAANLLLAASGGPKAVTAFLRGLGDEVTRLDRTEPTLNYHETPGDERDTTTPSAMVETLRRLLFTDVLSARSKAQLAAWLIMNKTGDTRLRAGFPADWMTGDKTGTNGDKAGNANDVAVAWSPDRGAVIVAAFCEIPGISGDERNAVIAEIGRIAAEV"},"dna_sequence":{"accession":"MH211206.1","fmin":"0","fmax":"894","strand":"+","sequence":"ATGACGATAACCATTTCACGCCGCCAGGCCATGGCCGGCGCTCTTCTTGCCATTCCCGCGGTTTCTGCGCTGACGGCCGGCACCAGCCGCGCCGCCGGTGAGAACCTTGCGCAACGGCTTGCCGCATTAGAGGCACGCCACGGCGGGCGCATCGGCGTTGCAATACATAATCTTTCGACAGGCGCGCGGCTCGGTCACAACACGGACGAGCGTTTCCTGATGTGCAGCACCTTCAAGGCGCTGCTGGCGGGCCATATCCTCGTCCGGGTGGACCGCGGCGAGGAGACGCTGGACCGACGCATCGTCGTGAAGGAAGCGGATCTCGTGGATTGGTCGCCGGTGGTGGAAAAGCGCATCGGCGGGGATGTCATCTCTATTGCCGAACTCTGCGAGGCGACCATCACGCTCAGCGACAATGCCGCCGCCAACCTGCTGCTCGCCGCATCGGGCGGGCCTAAGGCCGTCACGGCGTTTCTGCGTGGCCTCGGCGATGAAGTGACGCGTCTCGACCGTACGGAGCCGACGCTCAACTACCACGAGACGCCGGGCGATGAGCGTGACACGACGACGCCGAGCGCCATGGTGGAGACGCTGCGCAGGCTGCTCTTCACGGACGTTCTGTCGGCGCGTTCGAAGGCGCAGCTTGCCGCCTGGCTGATAATGAACAAGACGGGCGACACGCGGCTGCGCGCTGGCTTCCCGGCAGACTGGATGACCGGCGACAAGACCGGCACCAACGGCGACAAGGCCGGAAACGCCAACGATGTCGCGGTCGCCTGGTCGCCGGATCGCGGTGCAGTCATTGTTGCCGCCTTCTGCGAAATCCCCGGCATTTCCGGTGACGAGCGCAATGCCGTTATTGCCGAAATCGGGCGCATCGCGGCAGAGGTCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005096","ARO_id":"43309","ARO_name":"GPC-1","CARD_short_name":"GPC-1","ARO_description":"GPC-1 is a class A beta-lactamase. It is part of the GPC beta-lactamase gene family. Originally found in Pseudomonas aeruginosa. Confers resistance to B-lactams.","ARO_category":{"43308":{"category_aro_accession":"3005095","category_aro_cvterm_id":"43308","category_aro_name":"GPC beta-lactamase","category_aro_description":"GPC is a class A beta-lactamase family. It is found initially in Pseudomonas aeruginosa. It confers resistance to B-lactams.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3829":{"model_id":"3829","model_name":"mecC-type BlaZ","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8358":{"protein_sequence":{"accession":"CBZ41939.1","sequence":"MKKLIILVVLALILSACNSKNSTNNDIEKIEKKYGANVGMYALNTQNGKELSFNENKRFAYASTLKTISSAMLLEQTPYNKLDKKIHINKDDIVPYSPVLEKYIGKEITLKKLIEATMLFSDNTANNKIIDELGGYGQVKTKLIDLGDTTTHPSRKEPDLNFYSPKDKRDTSTPLAYGKTLKKLIADGDLSKANKDFLLNLMFKNKSGDTLIKDGAPSNFKVMDKSGQALTYGSRNDVAFVYPDGQDKPIILVIFTNKDRKDGKPNDKIVSEVAEIVLKNINE"},"dna_sequence":{"accession":"FR823292.1","fmin":"795","fmax":"1647","strand":"-","sequence":"TTGAAAAAATTAATAATTTTAGTCGTGTTAGCGTTGATATTAAGTGCTTGTAATAGTAAGAATTCAACTAATAACGACATTGAAAAGATCGAAAAAAAATATGGTGCTAACGTAGGTATGTATGCTCTTAATACTCAAAATGGTAAAGAATTATCATTTAATGAAAATAAGCGTTTTGCATATGCTTCCACATTAAAAACTATAAGTAGCGCAATGCTGCTTGAACAAACACCTTACAACAAATTAGATAAAAAAATTCACATTAATAAAGATGATATTGTTCCATATTCACCAGTGTTAGAAAAATATATTGGCAAAGAGATAACTTTAAAAAAGCTTATAGAAGCTACCATGTTATTTAGCGATAACACGGCTAATAATAAAATTATCGATGAATTGGGAGGATATGGGCAAGTAAAAACGAAACTGATAGATTTAGGCGATACAACGACACATCCATCTAGAAAAGAACCAGACTTAAATTTTTATTCACCAAAGGATAAACGAGATACAAGTACTCCATTAGCCTATGGTAAAACTTTAAAGAAACTTATAGCTGATGGAGATCTTAGCAAAGCAAACAAAGATTTCTTACTTAATCTAATGTTCAAAAATAAAAGTGGCGATACATTAATTAAGGATGGTGCACCTTCAAACTTTAAAGTTATGGATAAGAGCGGTCAAGCACTAACATACGGTTCAAGAAACGATGTTGCGTTTGTTTATCCAGATGGACAAGATAAACCTATAATTCTGGTGATATTTACAAATAAAGATAGAAAAGATGGTAAACCTAATGACAAAATAGTAAGTGAGGTTGCTGAAATTGTACTAAAAAATATTAATGAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35508","NCBI_taxonomy_name":"Staphylococcus aureus","NCBI_taxonomy_id":"1280"}}}},"ARO_accession":"3005097","ARO_id":"43312","ARO_name":"mecC-type BlaZ","CARD_short_name":"mecC-type_BlaZ","ARO_description":"A blaZ-like beta-lactamase found in S. Aureus.","ARO_category":{"41361":{"category_aro_accession":"3004197","category_aro_cvterm_id":"41361","category_aro_name":"BlaZ beta-lactamase","category_aro_description":"BlaZ beta-lactamases are Class A beta-lactamases. These beta-lactamases are responsible for penicillin resistance in Staphylococcus aureus.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2323":{"model_id":"2323","model_name":"qacH","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"190"}},"model_sequences":{"sequence":{"6141":{"protein_sequence":{"accession":"CAA76544.1","sequence":"MPYLYLLLSIVSEVIGSAFLKSSDGFSKLYPTITTIISFLICFYFLSKTMQHLPLNITYASWAGLGLVLTTIVSVLIFKEQINLISIISIILIIFGVVLLNTFGSSH"},"dna_sequence":{"accession":"Y16945.1","fmin":"1861","fmax":"2185","strand":"+","sequence":"ATGCCATATTTATATTTGTTATTATCAATAGTCAGTGAAGTAATAGGCAGTGCATTTTTAAAATCTTCAGACGGTTTCTCAAAATTATATCCAACTATAACAACAATCATTTCATTCCTTATTTGTTTTTATTTTCTGAGTAAAACTATGCAACATTTACCACTTAATATTACTTACGCAAGTTGGGCAGGTTTAGGATTAGTATTAACAACAATTGTTTCAGTTCTTATTTTCAAAGAACAAATAAATTTAATAAGCATTATTTCAATTATTTTAATAATATTTGGTGTTGTTTTACTAAACACATTCGGATCATCACACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40387","NCBI_taxonomy_name":"Staphylococcus saprophyticus","NCBI_taxonomy_id":"29385"}}}},"ARO_accession":"3003836","ARO_id":"40527","ARO_name":"qacH","CARD_short_name":"qacH","ARO_description":"qacH is a subunit of the qac multidrug efflux pump in Staphylococcus saprophyticus.","ARO_category":{"36004":{"category_aro_accession":"0010003","category_aro_cvterm_id":"36004","category_aro_name":"small multidrug resistance (SMR) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Small multidrug resistance (SMR) proteins are a relatively small family of transporters, restricted to prokaryotic cells. They are also the smallest multidrug transporters, with only four transmembrane alpha-helices and no significant extramembrane domain.","category_aro_class_name":"AMR Gene Family"},"43746":{"category_aro_accession":"3005386","category_aro_cvterm_id":"43746","category_aro_name":"disinfecting agents and antiseptics","category_aro_description":"Disinfectants that can also interact with antimicrobial resistance mechanisms, e.g. molecule efflux, and thus are the targets of disinfectant resistance.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"3830":{"model_id":"3830","model_name":"qacL","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"180"}},"model_sequences":{"sequence":{"6142":{"protein_sequence":{"accession":"AAZ42322.1","sequence":"MKNWIFMAVAIFGEVIATSALKSSHGFTRLVPSVVVVAGYGLAFYFLSLALKSIPVGIAYAVWAGLGIVLVAAIAWIFHGQKLDFWAFIGMGLIVSGVAVLNLLSKVSAH"},"dna_sequence":{"accession":"DQ149925.1","fmin":"188","fmax":"521","strand":"+","sequence":"GTGAAGAACTGGATATTTATGGCTGTTGCAATCTTTGGCGAGGTCATCGCAACTTCCGCACTGAAGTCTAGCCATGGATTCACTAGGTTAGTTCCTTCCGTTGTAGTTGTGGCTGGCTACGGGCTTGCGTTCTATTTCTTGTCTCTCGCGCTCAAGTCCATTCCGGTCGGTATTGCTTACGCTGTATGGGCTGGGCTTGGCATCGTGCTTGTGGCAGCTATTGCTTGGATTTTCCATGGCCAAAAACTAGACTTCTGGGCGTTCATTGGCATGGGACTTATCGTCAGTGGCGTCGCCGTTCTAAACCTGCTATCCAAGGTCAGCGCACATTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36789","NCBI_taxonomy_name":"Vibrio cholerae","NCBI_taxonomy_id":"666"}}}},"ARO_accession":"3005098","ARO_id":"43313","ARO_name":"qacL","CARD_short_name":"qacL","ARO_description":"A subunit of the qac multidrug efflux pump in Vibrio cholerae.","ARO_category":{"36004":{"category_aro_accession":"0010003","category_aro_cvterm_id":"36004","category_aro_name":"small multidrug resistance (SMR) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Small multidrug resistance (SMR) proteins are a relatively small family of transporters, restricted to prokaryotic cells. They are also the smallest multidrug transporters, with only four transmembrane alpha-helices and no significant extramembrane domain.","category_aro_class_name":"AMR Gene Family"},"43746":{"category_aro_accession":"3005386","category_aro_cvterm_id":"43746","category_aro_name":"disinfecting agents and antiseptics","category_aro_description":"Disinfectants that can also interact with antimicrobial resistance mechanisms, e.g. molecule efflux, and thus are the targets of disinfectant resistance.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"3831":{"model_id":"3831","model_name":"23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(A)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"6143":{"protein_sequence":{"accession":"AAB60941.1","sequence":"MKQKNPKNTQNFITSKKHVKEILKYTNINKQDKIIEIGSGKGHFTKELVEMSQRVNAIEIDEGLCHATKKAVEPFQNIKVIHEDILKFSFPKNTDYKIFGNIPYNISTDIVKKIAFDSQAKYSYLIVERGFAKRLQNTQRALGLLLMVEMDIKILKKVPRAYFHPKPNVDSVLIVLERHKPFILKKDYKKYRFFVYKWVNREYHVLFTKNQLRQVLKHANVTDLDKLSNEQFLSVFNSYKLFQ"},"dna_sequence":{"accession":"AF002716.1","fmin":"210","fmax":"942","strand":"+","sequence":"ATGAAACAGAAAAACCCGAAAAATACGCAAAATTTCATTACATCTAAAAAGCATGTAAAGGAAATATTAAAATATACGAATATCAATAAACAAGATAAAATAATAGAAATTGGGTCAGGAAAAGGACATTTTACCAAGGAACTTGTGGAAATGAGTCAACGGGTGAATGCTATAGAGATTGATGAAGGTTTATGTCATGCCACGAAAAAAGCAGTTGAACCTTTTCAGAATATAAAAGTTATTCATGAGGATATTTTGAAGTTTAGCTTTCCTAAAAATACAGACTATAAAATATTTGGTAATATTCCCTACAATATTAGTACTGATATTGTAAAAAAGATTGCTTTTGATAGTCAAGCGAAATATAGCTACCTTATTGTAGAGAGGGGATTTGCTAAAAGGTTGCAAAATACCCAACGAGCTTTAGGTTTGCTGTTAATGGTGGAAATGGATATAAAAATTCTTAAAAAAGTGCCACGAGCATATTTTCACCCTAAGCCTAATGTAGATTCTGTATTGATTGTACTTGAAAGGCATAAACCATTTATTTTAAAGAAGGACTACAAAAAGTATAGATTTTTCGTTTATAAATGGGTAAACAGGGAATATCATGTTCTTTTTACTAAAAATCAATTAAGACAGGTGCTGAAGCATGCGAATGTTACTGATCTTGATAAATTATCCAATGAACAATTTTTGTCTGTTTTCAATAGTTACAAATTATTTCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36764","NCBI_taxonomy_name":"Streptococcus pyogenes","NCBI_taxonomy_id":"1314"}}}},"ARO_accession":"3005099","ARO_id":"43314","ARO_name":"23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(A)","CARD_short_name":"Spyo_ErmA_MLSb","ARO_description":"Variant of ErmA (ARO:3000347) found in Streptococcus pyogenes. Confers the MLSb phenotype.","ARO_category":{"36699":{"category_aro_accession":"3000560","category_aro_cvterm_id":"36699","category_aro_name":"Erm 23S ribosomal RNA methyltransferase","category_aro_description":"Erm proteins are part of the RNA methyltransferase family and methylate A2058 (E. coli nomenclature) of the 23S ribosomal RNA conferring degrees of resistance to Macrolides, Lincosamides and Streptogramin b. This is called the MLSb phenotype.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3832":{"model_id":"3832","model_name":"FosB2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"250"}},"model_sequences":{"sequence":{"6144":{"protein_sequence":{"accession":"AAP27834.1","sequence":"MLQGINHICFSVSNLEKSIEFYQKILQAKLLVKGRKLAYFDLNGLWIALNVEEDIPRNEIKQSYTHMAFTVTNEALDHLKEVLIQNDVNILPGRERDERDQRSLYFTDPDGHKFEFHTGTLQNRLEYYKEDKKHMTFYI"},"dna_sequence":{"accession":"AE016879.1","fmin":"3778398","fmax":"3778818","strand":"+","sequence":"ATGCTACAGGGCATTAACCATATTTGTTTTTCTGTATCAAACTTGGAAAAATCTATTGAATTCTATCAAAAAATACTTCAAGCAAAATTATTAGTAAAAGGTAGAAAATTAGCGTATTTTGATTTAAATGGATTATGGATTGCTTTAAATGTTGAAGAAGATATACCAAGAAATGAAATTAAGCAATCTTATACACATATGGCTTTCACTGTAACTAATGAAGCATTAGACCATTTAAAAGAAGTATTAATTCAAAATGATGTTAATATTTTACCTGGCCGAGAAAGAGATGAGAGAGACCAAAGATCTCTTTACTTTACAGATCCAGATGGCCATAAGTTTGAGTTCCACACTGGCACTTTGCAAAACCGGTTAGAGTACTATAAAGAAGATAAAAAACATATGACTTTTTACATATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43244","NCBI_taxonomy_name":"Bacillus anthracis str. Ames","NCBI_taxonomy_id":"198094"}}}},"ARO_accession":"3005100","ARO_id":"43315","ARO_name":"FosB2","CARD_short_name":"FosB2","ARO_description":"Subtype of FosB (ARO:3000172). Present in multiple species.","ARO_category":{"36272":{"category_aro_accession":"3000133","category_aro_cvterm_id":"36272","category_aro_name":"fosfomycin thiol transferase","category_aro_description":"Catalyzes the addition of a thiol group from a nucleophilic molecule to fosfomycin.","category_aro_class_name":"AMR Gene Family"},"35944":{"category_aro_accession":"0000025","category_aro_cvterm_id":"35944","category_aro_name":"fosfomycin","category_aro_description":"Fosfomycin (also known as phosphomycin and phosphonomycin) is a broad-spectrum antibiotic produced by certain Streptomyces species. It is effective on gram positive and negative bacteria as it targets the cell wall, an essential feature shared by both bacteria. Its specific target is MurA (MurZ in E.coli), which attaches phosphoenolpyruvate (PEP) to UDP-N-acetylglucosamine, a step of commitment to cell wall synthesis. In the active site of MurA, the active cysteine molecule is alkylated which stops the catalytic reaction.","category_aro_class_name":"Antibiotic"},"45731":{"category_aro_accession":"3007149","category_aro_cvterm_id":"45731","category_aro_name":"phosphonic acid antibiotic","category_aro_description":"A group of antibiotics derived from phosphonic acids.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3850":{"model_id":"3850","model_name":"PDC-63","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"6167":{"protein_sequence":{"accession":"AIG20000.1","sequence":"MRDTGFPCLCGIAASTLLFAATSAIAGEAPADRLKTLVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASLHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYTPGSQRLYSNPSIGLFGYLAARSLGQPFERIMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDKPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGSDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"KJ949078.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCGGATTCCCCTGCCTGTGCGGCATCGCCGCCTCCACACTGCTGTTCGCCGCCACCTCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGACACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGATATTCCGGGCCTGGCCGTGGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCTTCGAAAGAGGACGGTCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCTGCACTGGCCGGCGCTGCAAGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAAGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACACGCCGGGCAGCCAGCGCCTCTACTCCAACCCGAGCATCGGTCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGATCATGGAGCAGCAACTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAAGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCGGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGACTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATCCCAGGCAGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAATTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005124","ARO_id":"43341","ARO_name":"PDC-63","CARD_short_name":"PDC-63","ARO_description":"PDC-63 is an ambler class C beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3851":{"model_id":"3851","model_name":"PDC-57","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"6162":{"protein_sequence":{"accession":"AIG19994.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQNKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPKAALAQYAQGYGKDDRPLRAGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"KJ949072.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGAACAAGATGCGTCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCAAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGCCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCATGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005125","ARO_id":"43342","ARO_name":"PDC-57","CARD_short_name":"PDC-57","ARO_description":"PDC-57 is an ambler class C beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3834":{"model_id":"3834","model_name":"Mycobacterium tuberculosis katG mutations conferring resistance to prothionamide","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1500"},"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"10022":"A312P","10023":"N660D","10024":"S315T","10025":"S315N","10026":"A264V","10027":"L147P","10032":"D142G","10034":"M126I","10035":"W91R","10036":"S315G","10037":"G490S","10043":"N508D","10045":"G125S","10046":"Q127P","10048":"Q461P","10049":"E607A","10050":"H417Q","10051":"G111S","10052":"G33V","10040":"A110V"},"Curated-R":{"10022":"A312P","10023":"N660D","10024":"S315T","10025":"S315N","10026":"A264V","10027":"L147P","10032":"D142G","10034":"M126I","10035":"W91R","10036":"S315G","10037":"G490S","10043":"N508D","10045":"G125S","10046":"Q127P","10048":"Q461P","10049":"E607A","10050":"H417Q","10051":"G111S","10052":"G33V","12882":"G33V","12883":"G33V","12885":"G33V","12886":"G33V","12887":"G33V","12888":"G33V","12889":"G33V","12890":"G33V","10040":"A110V","12884":"A110V"},"clinical":{"10022":"A312P","10023":"N660D","10024":"S315T","10025":"S315N","10026":"A264V","10027":"L147P","10032":"D142G","10034":"M126I","10035":"W91R","10036":"S315G","10037":"G490S","10043":"N508D","10045":"G125S","10046":"Q127P","10048":"Q461P","10049":"E607A","10050":"H417Q","10051":"G111S","10052":"G33V","10040":"A110V"}},"40330":{"param_type":"multiple resistance variants","param_description":"A set of nucleotide or amino acid substitutions that are all required to confer resistance to an antibiotic drug or drug class, encoded as: [wild-type 1][position 1][mutation 1],[wild-type 2][position 2][mutation 2], etc. For example, D63Y,T142K.","param_type_id":"40330","param_value":{"12882":"C20R,S315T","12883":"S134S,T308P","12885":"S211G,S315T","12886":"S315T,V581G","12887":"S315T,G466R","12888":"G279V,L436P","12889":"P92S,S315T","12890":"V431A,G490S","12884":"T275A,S315T"}}},"model_sequences":{"sequence":{"8834":{"protein_sequence":{"accession":"NP_216424.1","sequence":"MPEQHPPITETTTGAASNGCPVVGHMKYPVEGGGNQDWWPNRLNLKVLHQNPAVADPMGAAFDYAAEVATIDVDALTRDIEEVMTTSQPWWPADYGHYGPLFIRMAWHAAGTYRIHDGRGGAGGGMQRFAPLNSWPDNASLDKARRLLWPVKKKYGKKLSWADLIVFAGNCALESMGFKTFGFGFGRVDQWEPDEVYWGKEATWLGDERYSGKRDLENPLAAVQMGLIYVNPEGPNGNPDPMAAAVDIRETFRRMAMNDVETAALIVGGHTFGKTHGAGPADLVGPEPEAAPLEQMGLGWKSSYGTGTGKDAITSGIEVVWTNTPTKWDNSFLEILYGYEWELTKSPAGAWQYTAKDGAGAGTIPDPFGGPGRSPTMLATDLSLRVDPIYERITRRWLEHPEELADEFAKAWYKLIHRDMGPVARYLGPLVPKQTLLWQDPVPAVSHDLVGEAEIASLKSQIRASGLTVSQLVSTAWAAASSFRGSDKRGGANGGRIRLQPQVGWEVNDPDGDLRKVIRTLEEIQESFNSAAPGNIKVSFADLVVLGGCAAIEKAAKAAGHNITVPFTPGRTDASQEQTDVESFAVLEPKADGFRNYLGKGNPLPAEYMLLDKANLLTLSAPEMTVLVGGLRVLGANYKRLPLGVFTEASESLTNDFFVNLLDMGITWEPSPADDGTYQGKDGSGKVKWTGSRVDLVFGSNSELRALVEVYGADDAQPKFVQDFVAAWDKVMNLDRFDVR"},"dna_sequence":{"accession":"NC_000962.3","fmin":"2153888","fmax":"2156111","strand":"-","sequence":"GTGCCCGAGCAACACCCACCCATTACAGAAACCACCACCGGAGCCGCTAGCAACGGCTGTCCCGTCGTGGGTCATATGAAATACCCCGTCGAGGGCGGCGGAAACCAGGACTGGTGGCCCAACCGGCTCAATCTGAAGGTACTGCACCAAAACCCGGCCGTCGCTGACCCGATGGGTGCGGCGTTCGACTATGCCGCGGAGGTCGCGACCATCGACGTTGACGCCCTGACGCGGGACATCGAGGAAGTGATGACCACCTCGCAGCCGTGGTGGCCCGCCGACTACGGCCACTACGGGCCGCTGTTTATCCGGATGGCGTGGCACGCTGCCGGCACCTACCGCATCCACGACGGCCGCGGCGGCGCCGGGGGCGGCATGCAGCGGTTCGCGCCGCTTAACAGCTGGCCCGACAACGCCAGCTTGGACAAGGCGCGCCGGCTGCTGTGGCCGGTCAAGAAGAAGTACGGCAAGAAGCTCTCATGGGCGGACCTGATTGTTTTCGCCGGCAACTGCGCGCTGGAATCGATGGGCTTCAAGACGTTCGGGTTCGGCTTCGGCCGGGTCGACCAGTGGGAGCCCGATGAGGTCTATTGGGGCAAGGAAGCCACCTGGCTCGGCGATGAGCGTTACAGCGGTAAGCGGGATCTGGAGAACCCGCTGGCCGCGGTGCAGATGGGGCTGATCTACGTGAACCCGGAGGGGCCGAACGGCAACCCGGACCCCATGGCCGCGGCGGTCGACATTCGCGAGACGTTTCGGCGCATGGCCATGAACGACGTCGAAACAGCGGCGCTGATCGTCGGCGGTCACACTTTCGGTAAGACCCATGGCGCCGGCCCGGCCGATCTGGTCGGCCCCGAACCCGAGGCTGCTCCGCTGGAGCAGATGGGCTTGGGCTGGAAGAGCTCGTATGGCACCGGAACCGGTAAGGACGCGATCACCAGCGGCATCGAGGTCGTATGGACGAACACCCCGACGAAATGGGACAACAGTTTCCTCGAGATCCTGTACGGCTACGAGTGGGAGCTGACGAAGAGCCCTGCTGGCGCTTGGCAATACACCGCCAAGGACGGCGCCGGTGCCGGCACCATCCCGGACCCGTTCGGCGGGCCAGGGCGCTCCCCGACGATGCTGGCCACTGACCTCTCGCTGCGGGTGGATCCGATCTATGAGCGGATCACGCGTCGCTGGCTGGAACACCCCGAGGAATTGGCCGACGAGTTCGCCAAGGCCTGGTACAAGCTGATCCACCGAGACATGGGTCCCGTTGCGAGATACCTTGGGCCGCTGGTCCCCAAGCAGACCCTGCTGTGGCAGGATCCGGTCCCTGCGGTCAGCCACGACCTCGTCGGCGAAGCCGAGATTGCCAGCCTTAAGAGCCAGATCCGGGCATCGGGATTGACTGTCTCACAGCTAGTTTCGACCGCATGGGCGGCGGCGTCGTCGTTCCGTGGTAGCGACAAGCGCGGCGGCGCCAACGGTGGTCGCATCCGCCTGCAGCCACAAGTCGGGTGGGAGGTCAACGACCCCGACGGGGATCTGCGCAAGGTCATTCGCACCCTGGAAGAGATCCAGGAGTCATTCAACTCCGCGGCGCCGGGGAACATCAAAGTGTCCTTCGCCGACCTCGTCGTGCTCGGTGGCTGTGCCGCCATAGAGAAAGCAGCAAAGGCGGCTGGCCACAACATCACGGTGCCCTTCACCCCGGGCCGCACGGATGCGTCGCAGGAACAAACCGACGTGGAATCCTTTGCCGTGCTGGAGCCCAAGGCAGATGGCTTCCGAAACTACCTCGGAAAGGGCAACCCGTTGCCGGCCGAGTACATGCTGCTCGACAAGGCGAACCTGCTTACGCTCAGTGCCCCTGAGATGACGGTGCTGGTAGGTGGCCTGCGCGTCCTCGGCGCAAACTACAAGCGCTTACCGCTGGGCGTGTTCACCGAGGCCTCCGAGTCACTGACCAACGACTTCTTCGTGAACCTGCTCGACATGGGTATCACCTGGGAGCCCTCGCCAGCAGATGACGGGACCTACCAGGGCAAGGATGGCAGTGGCAAGGTGAAGTGGACCGGCAGCCGCGTGGACCTGGTCTTCGGGTCCAACTCGGAGTTGCGGGCGCTTGTCGAGGTCTATGGCGCCGATGACGCGCAGCCGAAGTTCGTGCAGGACTTCGTCGCTGCCTGGGACAAGGTGATGAACCTCGACAGGTTCGACGTGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3005102","ARO_id":"43317","ARO_name":"Mycobacterium tuberculosis katG mutations conferring resistance to prothionamide","CARD_short_name":"Mtub_katG_PTO","ARO_description":"Mutations in Mycobacterium tuberculosis katG conferring resistance to prothionamide, an analogue of isoniazid.","ARO_category":{"43316":{"category_aro_accession":"3005101","category_aro_cvterm_id":"43316","category_aro_name":"prothionamide resistant katG","category_aro_description":"Mutations associated with katG conferring resistance to prothionamide, an analogue of isoniazid. Like isoniazid, prothionamide targets lnhA.","category_aro_class_name":"AMR Gene Family"},"40958":{"category_aro_accession":"3004025","category_aro_cvterm_id":"40958","category_aro_name":"prothionamide","category_aro_description":"Prothionamide is a thioamide derivative with antibacterial properties. It increases cell wall permeability and decreases cell wall damage resistance by inhibition of mycolic acid synthesis, resulting in cell death. It is particularly used to treat M. tuberculosis and M. leprae infections.","category_aro_class_name":"Antibiotic"},"45738":{"category_aro_accession":"3007156","category_aro_cvterm_id":"45738","category_aro_name":"thioamide antibiotic","category_aro_description":"A group of antibiotics possessing the thioamide functional group.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3836":{"model_id":"3836","model_name":"Mycobacterium tuberculosis ethA mutations conferring resistance to isoniazid","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"40394":{"param_type":"nonsense mutation","param_description":"A sequence change where, compared to a reference sequence, one codon is replaced by a termination codon through a nucleotide substitution. These are described as a substitution of the wildtype codon to a termination codon. Format is given as [wild type AA][position][Ter], for example Q42Ter where Q42 is a wildtype amino acid replaced by a premature termination codon.","param_type_id":"40394","param_value":{"10075":"R279Ter","10090":"E420Ter","10107":"W289Ter"}},"snp":{"Curated-R":{"10075":"A110V","10090":"A110V","10107":"A110V","10062":"P28S","10063":"L35R","10065":"D56Y","10066":"D58G","10067":"W69C","10068":"H102P","10070":"Y141N","10071":"T186P","10072":"T189R","10073":"Q246P","10076":"S329P","10078":"A341V","10079":"N345K","10081":"A352E","10083":"C403Y","10084":"F480S","10096":"L267V","10111":"V179F","10113":"A395D","10117":"Q254P","12891":"Q254P","12892":"Q254P","12893":"Q254P","12894":"Q254P","12895":"Q254P","12896":"Q254P","10064":"G42D","10082":"M372R"},"param_value":{"10062":"P28S","10063":"L35R","10065":"D56Y","10066":"D58G","10067":"W69C","10068":"H102P","10070":"Y141N","10071":"T186P","10072":"T189R","10073":"Q246P","10076":"S329P","10078":"A341V","10079":"N345K","10081":"A352E","10083":"C403Y","10084":"F480S","10096":"L267V","10111":"V179F","10113":"A395D","10117":"Q254P","10064":"G42D","10082":"M372R"},"clinical":{"10062":"P28S","10063":"L35R","10065":"D56Y","10066":"D58G","10067":"W69C","10068":"H102P","10070":"Y141N","10071":"T186P","10072":"T189R","10073":"Q246P","10076":"S329P","10078":"A341V","10079":"N345K","10081":"A352E","10083":"C403Y","10084":"F480S","10096":"L267V","10111":"V179F","10113":"A395D","10117":"Q254P","10064":"G42D","10082":"M372R"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"},"40330":{"param_type":"multiple resistance variants","param_description":"A set of nucleotide or amino acid substitutions that are all required to confer resistance to an antibiotic drug or drug class, encoded as: [wild-type 1][position 1][mutation 1],[wild-type 2][position 2][mutation 2], etc. For example, D63Y,T142K.","param_type_id":"40330","param_value":{"12891":"I161V,G324R","12892":"Q254P,S266R","12893":"S266R,M373T","12894":"S266R,P454L","12895":"R239Q,S266R","12896":"Q246R,L446P"}}},"model_sequences":{"sequence":{"8810":{"protein_sequence":{"accession":"NP_218371.1","sequence":"MTEHLDVVIVGAGISGVSAAWHLQDRCPTKSYAILEKRESMGGTWDLFRYPGIRSDSDMYTLGFRFRPWTGRQAIADGKPILEYVKSTAAMYGIDRHIRFHHKVISADWSTAENRWTVHIQSHGTLSALTCEFLFLCSGYYNYDEGYSPRFAGSEDFVGPIIHPQHWPEDLDYDAKNIVVIGSGATAVTLVPALADSGAKHVTMLQRSPTYIVSQPDRDGIAEKLNRWLPETMAYTAVRWKNVLRQAAVYSACQKWPRRMRKMFLSLIQRQLPEGYDVRKHFGPHYNPWDQRLCLVPNGDLFRAIRHGKVEVVTDTIERFTATGIRLNSGRELPADIIITATGLNLQLFGGATATIDGQQVDITTTMAYKGMMLSGIPNMAYTVGYTNASWTLKADLVSEFVCRLLNYMDDNGFDTVVVERPGSDVEERPFMEFTPGYVLRSLDELPKQGSRTPWRLNQNYLRDIRLIRRGKIDDEGLRFAKRPAPVGV"},"dna_sequence":{"accession":"NC_000962.3","fmin":"4326003","fmax":"4327473","strand":"-","sequence":"ATGACCGAGCACCTCGACGTTGTCATCGTGGGCGCTGGAATCTCCGGTGTCAGCGCGGCCTGGCACCTGCAGGACCGTTGCCCGACCAAGAGCTACGCCATCCTGGAAAAGCGGGAATCCATGGGCGGCACCTGGGATTTGTTCCGTTATCCCGGAATTCGCTCCGACTCCGACATGTACACGCTAGGTTTCCGATTCCGTCCCTGGACCGGACGGCAGGCGATCGCCGACGGCAAGCCCATCCTCGAGTACGTCAAGAGCACCGCGGCCATGTATGGAATCGACAGGCATATCCGGTTCCACCACAAGGTGATCAGTGCCGATTGGTCGACCGCGGAAAACCGCTGGACCGTTCACATCCAAAGCCACGGCACGCTCAGCGCCCTCACCTGCGAATTCCTCTTTCTGTGCAGCGGCTACTACAACTACGACGAGGGCTACTCGCCGAGATTCGCCGGCTCGGAGGATTTCGTCGGGCCGATCATCCATCCGCAGCACTGGCCCGAGGACCTCGACTACGACGCTAAGAACATCGTCGTGATCGGCAGTGGCGCAACGGCGGTCACGCTCGTGCCGGCGCTGGCGGACTCGGGCGCCAAGCACGTCACGATGCTGCAGCGCTCACCCACCTACATCGTGTCGCAGCCAGACCGGGACGGCATCGCCGAGAAGCTCAACCGCTGGCTGCCGGAGACCATGGCCTACACCGCGGTACGGTGGAAGAACGTGCTGCGCCAGGCGGCCGTGTACAGCGCCTGCCAGAAGTGGCCACGGCGCATGCGGAAGATGTTCCTGAGCCTGATCCAGCGCCAGCTACCCGAGGGGTACGACGTGCGAAAGCACTTCGGCCCGCACTACAACCCCTGGGACCAGCGATTGTGCTTGGTGCCCAACGGCGACCTGTTCCGGGCCATTCGTCACGGGAAGGTCGAGGTGGTGACCGACACCATTGAACGGTTCACCGCGACCGGAATCCGGCTGAACTCAGGTCGCGAACTGCCGGCTGACATCATCATTACCGCAACGGGGTTGAACCTGCAGCTTTTTGGTGGGGCGACGGCGACTATCGACGGACAACAAGTGGACATCACCACGACGATGGCCTACAAGGGCATGATGCTTTCCGGCATCCCCAACATGGCCTACACGGTTGGCTACACCAATGCCTCCTGGACGCTGAAGGCCGACCTGGTGTCGGAGTTTGTCTGTCGCTTGTTGAATTACATGGACGACAACGGTTTTGACACCGTGGTCGTCGAGCGACCGGGCTCAGATGTCGAAGAGCGGCCCTTCATGGAGTTCACCCCAGGTTACGTGCTGCGCTCGCTGGACGAGCTGCCCAAGCAGGGTTCGCGTACACCGTGGCGCCTGAATCAGAACTACCTACGTGACATCCGGCTCATCCGGCGCGGCAAGATCGACGACGAGGGTCTGCGGTTCGCCAAAAGGCCTGCCCCGGTGGGGGTTTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3005105","ARO_id":"43320","ARO_name":"Mycobacterium tuberculosis ethA mutations conferring resistance to isoniazid","CARD_short_name":"Mtub_ethA_INH","ARO_description":"Mutations in Mycobacterium tuberculosis ethA conferring resistance to isoniazid.","ARO_category":{"43318":{"category_aro_accession":"3005103","category_aro_cvterm_id":"43318","category_aro_name":"isoniazid resistant ethA","category_aro_description":"Mutations in ethA conferring resistance to isoniazid.","category_aro_class_name":"AMR Gene Family"},"36659":{"category_aro_accession":"3000520","category_aro_cvterm_id":"36659","category_aro_name":"isoniazid","category_aro_description":"Isoniazid is an organic compound that is the first-line anti tuberculosis medication in prevention and treatment. As a prodrug, it is activated by mycobacterial catalase-peroxidases such as M. tuberculosis KatG. Isoniazid inhibits mycolic acid synthesis, which prevents cell wall synthesis in mycobacteria.","category_aro_class_name":"Antibiotic"},"45734":{"category_aro_accession":"3007152","category_aro_cvterm_id":"45734","category_aro_name":"isoniazid-like antibiotic","category_aro_description":"A group of antibiotics containing isoniazid and its derivatives.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3837":{"model_id":"3837","model_name":"Mycobacterium tuberculosis ethA mutations conferring resistance to prothionamide","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"40394":{"param_type":"nonsense mutation","param_description":"A sequence change where, compared to a reference sequence, one codon is replaced by a termination codon through a nucleotide substitution. These are described as a substitution of the wildtype codon to a termination codon. Format is given as [wild type AA][position][Ter], for example Q42Ter where Q42 is a wildtype amino acid replaced by a premature termination codon.","param_type_id":"40394","param_value":{"10135":"R279Ter","10167":"W289Ter","10150":"E420Ter"}},"snp":{"Curated-R":{"10135":"M372R","10167":"M372R","10124":"P28S","10125":"L35R","10126":"G42D","10128":"D58G","10129":"W69C","10130":"H102P","10131":"Y141N","10132":"T186P","10133":"T189R","10136":"S329P","10138":"A341V","10139":"N345K","10141":"A352E","10142":"M372R","10143":"C403Y","10157":"L267V","10171":"V179F","10173":"A395D","10175":"Q246P","10178":"Q254P","12908":"Q254P","12909":"Q254P","12911":"Q254P","12912":"Q254P","12913":"Q254P","10150":"Q254P","10127":"D56Y","10144":"F480S","12910":"F480S"},"param_value":{"10124":"P28S","10125":"L35R","10126":"G42D","10128":"D58G","10129":"W69C","10130":"H102P","10131":"Y141N","10132":"T186P","10133":"T189R","10136":"S329P","10138":"A341V","10139":"N345K","10141":"A352E","10142":"M372R","10143":"C403Y","10157":"L267V","10171":"V179F","10173":"A395D","10175":"Q246P","10178":"Q254P","10127":"D56Y","10144":"F480S"},"clinical":{"10124":"P28S","10125":"L35R","10126":"G42D","10128":"D58G","10129":"W69C","10130":"H102P","10131":"Y141N","10132":"T186P","10133":"T189R","10136":"S329P","10138":"A341V","10139":"N345K","10141":"A352E","10142":"M372R","10143":"C403Y","10157":"L267V","10171":"V179F","10173":"A395D","10175":"Q246P","10178":"Q254P","10127":"D56Y","10144":"F480S"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"},"40330":{"param_type":"multiple resistance variants","param_description":"A set of nucleotide or amino acid substitutions that are all required to confer resistance to an antibiotic drug or drug class, encoded as: [wild-type 1][position 1][mutation 1],[wild-type 2][position 2][mutation 2], etc. For example, D63Y,T142K.","param_type_id":"40330","param_value":{"12908":"S266R,P454L","12909":"R239Q,S266R","12911":"I161V,G324R","12912":"S266R,M373T","12913":"Q254P,S266R","12910":"Q246R,L446P"}}},"model_sequences":{"sequence":{"8812":{"protein_sequence":{"accession":"NP_218371.1","sequence":"MTEHLDVVIVGAGISGVSAAWHLQDRCPTKSYAILEKRESMGGTWDLFRYPGIRSDSDMYTLGFRFRPWTGRQAIADGKPILEYVKSTAAMYGIDRHIRFHHKVISADWSTAENRWTVHIQSHGTLSALTCEFLFLCSGYYNYDEGYSPRFAGSEDFVGPIIHPQHWPEDLDYDAKNIVVIGSGATAVTLVPALADSGAKHVTMLQRSPTYIVSQPDRDGIAEKLNRWLPETMAYTAVRWKNVLRQAAVYSACQKWPRRMRKMFLSLIQRQLPEGYDVRKHFGPHYNPWDQRLCLVPNGDLFRAIRHGKVEVVTDTIERFTATGIRLNSGRELPADIIITATGLNLQLFGGATATIDGQQVDITTTMAYKGMMLSGIPNMAYTVGYTNASWTLKADLVSEFVCRLLNYMDDNGFDTVVVERPGSDVEERPFMEFTPGYVLRSLDELPKQGSRTPWRLNQNYLRDIRLIRRGKIDDEGLRFAKRPAPVGV"},"dna_sequence":{"accession":"NC_000962.3","fmin":"4326003","fmax":"4327473","strand":"-","sequence":"ATGACCGAGCACCTCGACGTTGTCATCGTGGGCGCTGGAATCTCCGGTGTCAGCGCGGCCTGGCACCTGCAGGACCGTTGCCCGACCAAGAGCTACGCCATCCTGGAAAAGCGGGAATCCATGGGCGGCACCTGGGATTTGTTCCGTTATCCCGGAATTCGCTCCGACTCCGACATGTACACGCTAGGTTTCCGATTCCGTCCCTGGACCGGACGGCAGGCGATCGCCGACGGCAAGCCCATCCTCGAGTACGTCAAGAGCACCGCGGCCATGTATGGAATCGACAGGCATATCCGGTTCCACCACAAGGTGATCAGTGCCGATTGGTCGACCGCGGAAAACCGCTGGACCGTTCACATCCAAAGCCACGGCACGCTCAGCGCCCTCACCTGCGAATTCCTCTTTCTGTGCAGCGGCTACTACAACTACGACGAGGGCTACTCGCCGAGATTCGCCGGCTCGGAGGATTTCGTCGGGCCGATCATCCATCCGCAGCACTGGCCCGAGGACCTCGACTACGACGCTAAGAACATCGTCGTGATCGGCAGTGGCGCAACGGCGGTCACGCTCGTGCCGGCGCTGGCGGACTCGGGCGCCAAGCACGTCACGATGCTGCAGCGCTCACCCACCTACATCGTGTCGCAGCCAGACCGGGACGGCATCGCCGAGAAGCTCAACCGCTGGCTGCCGGAGACCATGGCCTACACCGCGGTACGGTGGAAGAACGTGCTGCGCCAGGCGGCCGTGTACAGCGCCTGCCAGAAGTGGCCACGGCGCATGCGGAAGATGTTCCTGAGCCTGATCCAGCGCCAGCTACCCGAGGGGTACGACGTGCGAAAGCACTTCGGCCCGCACTACAACCCCTGGGACCAGCGATTGTGCTTGGTGCCCAACGGCGACCTGTTCCGGGCCATTCGTCACGGGAAGGTCGAGGTGGTGACCGACACCATTGAACGGTTCACCGCGACCGGAATCCGGCTGAACTCAGGTCGCGAACTGCCGGCTGACATCATCATTACCGCAACGGGGTTGAACCTGCAGCTTTTTGGTGGGGCGACGGCGACTATCGACGGACAACAAGTGGACATCACCACGACGATGGCCTACAAGGGCATGATGCTTTCCGGCATCCCCAACATGGCCTACACGGTTGGCTACACCAATGCCTCCTGGACGCTGAAGGCCGACCTGGTGTCGGAGTTTGTCTGTCGCTTGTTGAATTACATGGACGACAACGGTTTTGACACCGTGGTCGTCGAGCGACCGGGCTCAGATGTCGAAGAGCGGCCCTTCATGGAGTTCACCCCAGGTTACGTGCTGCGCTCGCTGGACGAGCTGCCCAAGCAGGGTTCGCGTACACCGTGGCGCCTGAATCAGAACTACCTACGTGACATCCGGCTCATCCGGCGCGGCAAGATCGACGACGAGGGTCTGCGGTTCGCCAAAAGGCCTGCCCCGGTGGGGGTTTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3005106","ARO_id":"43321","ARO_name":"Mycobacterium tuberculosis ethA mutations conferring resistance to prothionamide","CARD_short_name":"Mtub_ethA_PTO","ARO_description":"Mutations in Mycobacterium tuberculosis ethA conferring resistance to prothionamide, an analogue to isoniazid.","ARO_category":{"43319":{"category_aro_accession":"3005104","category_aro_cvterm_id":"43319","category_aro_name":"prothionamide resistant ethA","category_aro_description":"Mutations in ethA conferring resistance to prothionamide, an analogue of isoniazid.","category_aro_class_name":"AMR Gene Family"},"40958":{"category_aro_accession":"3004025","category_aro_cvterm_id":"40958","category_aro_name":"prothionamide","category_aro_description":"Prothionamide is a thioamide derivative with antibacterial properties. It increases cell wall permeability and decreases cell wall damage resistance by inhibition of mycolic acid synthesis, resulting in cell death. It is particularly used to treat M. tuberculosis and M. leprae infections.","category_aro_class_name":"Antibiotic"},"45738":{"category_aro_accession":"3007156","category_aro_cvterm_id":"45738","category_aro_name":"thioamide antibiotic","category_aro_description":"A group of antibiotics possessing the thioamide functional group.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3838":{"model_id":"3838","model_name":"Mycobacterium tuberculosis mshA mutations conferring resistance to prothionamide","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"10182":"F355S"},"Curated-R":{"10182":"F355S"},"clinical":{"10182":"F355S"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"900"}},"model_sequences":{"sequence":{"6150":{"protein_sequence":{"accession":"NP_215000.1","sequence":"MAGVRHDDGSGLIAQRRPVRGEGATRSRGPSGPSNRNVSAADDPRRVALLAVHTSPLAQPGTGDAGGMNVYMLQSALHLARRGIEVEIFTRATASADPPVVRVAPGVLVRNVVAGPFEGLDKYDLPTQLCAFAAGVLRAEAVHEPGYYDIVHSHYWLSGQVGWLARDRWAVPLVHTAHTLAAVKNAALADGDGPEPPLRTVGEQQVVDEADRLIVNTDDEARQVISLHGADPARIDVVHPGVDLDVFRPGDRRAARAALGLPVDERVVAFVGRIQPLKAPDIVLRAAAKLPGVRIIVAGGPSGSGLASPDGLVRLADELGISARVTFLPPQSHTDLATLFRAADLVAVPSYSESFGLVAVEAQACGTPVVAAAVGGLPVAVRDGITGTLVSGHEVGQWADAIDHLLRLCAGPRGRVMSRAAARHAATFSWENTTDALLASYRRAIGEYNAERQRRGGEVISDLVAVGKPRHWTPRRGVGA"},"dna_sequence":{"accession":"NC_000962.3","fmin":"575347","fmax":"576790","strand":"+","sequence":"ATGGCAGGTGTGCGGCACGATGACGGTTCAGGGTTGATCGCCCAGCGCCGTCCGGTCCGCGGCGAGGGTGCCACCCGCTCGCGCGGCCCATCCGGGCCATCCAATCGGAATGTTTCGGCAGCAGACGACCCGCGCCGGGTTGCGCTGCTGGCGGTGCACACCTCACCGCTGGCACAGCCGGGCACCGGTGACGCCGGCGGCATGAACGTCTACATGCTGCAAAGTGCGCTGCACCTGGCCCGTCGGGGCATCGAGGTGGAGATCTTCACCCGGGCCACCGCATCGGCAGATCCACCGGTGGTGCGGGTGGCACCCGGGGTGCTGGTGCGCAACGTGGTGGCGGGGCCCTTCGAGGGTTTGGACAAGTACGACCTGCCCACCCAGCTTTGTGCGTTCGCCGCCGGGGTGCTGCGCGCCGAGGCGGTCCACGAACCGGGTTACTACGACATCGTGCACTCGCACTACTGGCTGTCGGGTCAGGTCGGCTGGCTGGCGCGCGACCGCTGGGCGGTGCCGTTGGTGCACACCGCACACACGCTGGCCGCCGTGAAGAACGCGGCACTGGCCGACGGCGACGGACCCGAGCCGCCGCTGCGTACGGTCGGGGAGCAGCAGGTCGTCGACGAGGCGGATCGGTTGATCGTCAACACCGACGATGAAGCCAGGCAAGTGATTTCGCTTCATGGTGCCGATCCGGCACGAATCGACGTGGTCCATCCCGGTGTCGATCTGGACGTGTTCCGCCCGGGTGATCGGCGCGCGGCCCGGGCCGCGCTAGGACTACCAGTTGACGAGCGCGTGGTGGCCTTCGTCGGACGCATCCAGCCGCTGAAGGCACCCGACATTGTGCTGCGTGCGGCCGCCAAGTTGCCCGGGGTGCGCATCATCGTGGCCGGCGGACCGTCGGGCAGCGGTCTGGCTTCACCGGACGGACTGGTCCGGCTCGCCGACGAACTGGGCATCTCTGCACGGGTGACGTTTCTGCCGCCGCAGTCCCACACGGATCTGGCCACCTTGTTTCGGGCGGCGGACCTGGTTGCGGTGCCGAGCTACTCCGAGTCGTTCGGCCTGGTTGCTGTGGAGGCCCAAGCGTGCGGCACACCGGTGGTGGCCGCGGCGGTGGGCGGGCTGCCCGTCGCGGTGCGCGACGGGATCACCGGCACCCTGGTGTCCGGGCACGAGGTCGGTCAGTGGGCCGACGCCATCGATCACCTGCTGCGGTTGTGTGCCGGGCCACGGGGACGGGTGATGAGCCGGGCGGCGGCACGGCACGCCGCCACGTTCTCGTGGGAGAACACCACCGACGCGCTGTTGGCCAGTTATCGGCGTGCGATCGGCGAGTACAACGCCGAGCGCCAGCGCCGGGGCGGCGAGGTGATATCGGACCTGGTAGCGGTGGGCAAGCCCCGCCACTGGACGCCGCGTCGCGGGGTGGGCGCGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3005108","ARO_id":"43323","ARO_name":"Mycobacterium tuberculosis mshA mutations conferring resistance to prothionamide","CARD_short_name":"Mtub_mshA_PTO","ARO_description":"Mutations in Mycobacterium tuberculosis mshA conferring resistance to prothionamide, an analogue to isoniazid.","ARO_category":{"43322":{"category_aro_accession":"3005107","category_aro_cvterm_id":"43322","category_aro_name":"prothionamide resistant mshA","category_aro_description":"Mutations in mshA conferring resistance to prothionamide, an analogue of isoniazid.","category_aro_class_name":"AMR Gene Family"},"40958":{"category_aro_accession":"3004025","category_aro_cvterm_id":"40958","category_aro_name":"prothionamide","category_aro_description":"Prothionamide is a thioamide derivative with antibacterial properties. It increases cell wall permeability and decreases cell wall damage resistance by inhibition of mycolic acid synthesis, resulting in cell death. It is particularly used to treat M. tuberculosis and M. leprae infections.","category_aro_class_name":"Antibiotic"},"45738":{"category_aro_accession":"3007156","category_aro_cvterm_id":"45738","category_aro_name":"thioamide antibiotic","category_aro_description":"A group of antibiotics possessing the thioamide functional group.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3839":{"model_id":"3839","model_name":"blaS1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6151":{"protein_sequence":{"accession":"AAP97895.1","sequence":"MTNLSRRSVLIGSLAVMAAAGVRMPTASAAPVDDRIADLERRNNASIGIYAVDLDSNRTVAHRADDSFAMCSTFKAYLAARILRGAERGELSLDDRVFVDPAALLSNSPITETHAGGEMTLAELCQAALQRSDNAAANLLLKQIGGPAEITAFARSIGDQRTRLDRWETELNSAVPGDPRDTSTPAALAGGFRAVLTGDVLAPPQRQLLDEWMRANETSSLRAGLPDGWTSADKTGSGDYGSTNDVGIAYGPQGQRILLALMVRTRGDDPNADGFRPLIGELTALVLPELGVH"},"dna_sequence":{"accession":"AY332268.1","fmin":"926","fmax":"1808","strand":"+","sequence":"ATGACGAATCTCTCACGACGCAGTGTGTTGATCGGATCCCTGGCAGTGATGGCGGCCGCCGGTGTGCGTATGCCGACGGCTTCCGCCGCTCCCGTCGACGACCGGATCGCCGATCTCGAACGACGGAACAACGCATCCATCGGCATCTATGCCGTCGACCTCGATTCGAACCGTACGGTCGCGCACCGCGCCGACGACTCGTTCGCGATGTGCTCGACGTTCAAGGCCTACCTCGCGGCCCGGATCCTGCGGGGCGCCGAGCGCGGCGAGTTGTCGCTGGACGATCGTGTCTTCGTGGATCCCGCGGCGCTGCTGAGCAACTCGCCGATCACCGAGACACACGCAGGCGGCGAGATGACGCTGGCCGAGTTGTGCCAGGCGGCACTGCAGCGCAGCGACAACGCCGCGGCCAACCTGTTGCTCAAGCAGATCGGCGGGCCGGCCGAGATCACCGCGTTCGCGCGGTCGATCGGCGACCAGCGCACACGCCTGGACCGCTGGGAGACCGAACTGAACTCGGCGGTGCCCGGCGATCCGCGTGACACCAGCACCCCGGCCGCGCTGGCCGGTGGTTTCCGCGCCGTGCTGACCGGCGACGTGCTGGCCCCGCCGCAGCGTCAATTGCTCGACGAGTGGATGCGGGCCAACGAGACCTCCAGCCTGCGTGCGGGTTTGCCGGACGGCTGGACCAGTGCCGACAAGACCGGCAGCGGCGACTACGGATCCACCAACGATGTGGGTATCGCCTACGGCCCGCAGGGGCAGCGCATCCTGCTGGCGTTGATGGTGCGGACGCGCGGCGACGATCCGAACGCGGACGGGTTCCGGCCCCTCATCGGGGAACTCACCGCGCTGGTGCTGCCCGAACTCGGCGTGCACTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36769","NCBI_taxonomy_name":"Mycolicibacterium smegmatis MC2 155","NCBI_taxonomy_id":"246196"}}}},"ARO_accession":"3005111","ARO_id":"43326","ARO_name":"blaS1","CARD_short_name":"blaS1","ARO_description":"Predominant beta-lactamase in Mycolicibacterium smegmatis.","ARO_category":{"43325":{"category_aro_accession":"3005110","category_aro_cvterm_id":"43325","category_aro_name":"blaS","category_aro_description":"A class A beta-lactamase in Mycolicibacterium smegmatis.","category_aro_class_name":"AMR Gene Family"},"35927":{"category_aro_accession":"0000008","category_aro_cvterm_id":"35927","category_aro_name":"cefoxitin","category_aro_description":"Cefoxitin is a cephamycin antibiotic often grouped with the second generation cephalosporins. Cefoxitin is bactericidal and acts by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. Cefoxitin's 7-alpha-methoxy group and 3' leaving group make it a poor substrate for most beta-lactamases.","category_aro_class_name":"Antibiotic"},"35961":{"category_aro_accession":"0000043","category_aro_cvterm_id":"35961","category_aro_name":"carbenicillin","category_aro_description":"Carbenicillin is a semi-synthetic antibiotic belonging to the carboxypenicillin subgroup of the penicillins. It has gram-negative coverage which includes Pseudomonas aeruginosa but limited gram-positive coverage. The carboxypenicillins are susceptible to degradation by beta-lactamase enzymes. Carbenicillin antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Antibiotic"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35979":{"category_aro_accession":"0000062","category_aro_cvterm_id":"35979","category_aro_name":"ceftriaxone","category_aro_description":"Ceftriaxone is a third-generation cephalosporin antibiotic. The presence of an aminothiazolyl sidechain increases ceftriazone's resistance to beta-lactamases. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"35995":{"category_aro_accession":"0000078","category_aro_cvterm_id":"35995","category_aro_name":"piperacillin","category_aro_description":"Piperacillin is an acetylureidopenicillin and has an extended spectrum of targets relative to other beta-lactam antibiotics. It inhibits cell wall synthesis in bacteria, and is usually taken with the beta-lactamase inhibitor tazobactam to overcome penicillin-resistant bacteria.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"36983":{"category_aro_accession":"3000639","category_aro_cvterm_id":"36983","category_aro_name":"mezlocillin","category_aro_description":"Mezlocillin is a penicillin derivative taken parenterally.","category_aro_class_name":"Antibiotic"},"36990":{"category_aro_accession":"3000646","category_aro_cvterm_id":"36990","category_aro_name":"cefixime","category_aro_description":"Cefixime is a cephalosporin resistant to most beta-lactamases. It is active against many enterobacteria, but activity against staphylococci is poor.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3840":{"model_id":"3840","model_name":"AAC(6')-Ib-cr3","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"8752":{"protein_sequence":{"accession":"WP_071766621.1","sequence":"MTNSNDSVTLRLMTEHDLAMLYEWLNRSHIVEWWGGEEARPTLADVQEQYLPSVLAQESVTPYIAMLNGEPIGYAQSYVALGSGDGRWEEETDPGVRGIDQLLANASQLGKGLGTKLVRALVELLFNDPEVTKIQTDPSPSNLRAIRCYEKAGFERQGTVTTPYGPAVVMGQTRQAFERTRSDA"},"dna_sequence":{"accession":"NG_052123.1","fmin":"100","fmax":"655","strand":"+","sequence":"GTGACCAACAGCAACGATTCCGTCACACTGCGCCTCATGACTGAGCATGACCTTGCGATGCTCTATGAGTGGCTAAATCGATCTCATATCGTCGAGTGGTGGGGCGGAGAAGAAGCACGCCCGACACTTGCTGACGTACAGGAACAGTACTTGCCAAGCGTTTTAGCGCAAGAGTCCGTCACTCCATACATTGCAATGCTGAATGGAGAGCCGATTGGGTATGCCCAGTCGTACGTTGCTCTTGGAAGCGGGGACGGAAGGTGGGAAGAAGAAACCGATCCAGGAGTACGCGGAATAGACCAGTTACTGGCGAATGCATCACAACTGGGCAAAGGCTTGGGAACCAAGCTGGTTCGAGCTCTGGTTGAGTTGCTGTTCAATGATCCCGAGGTCACCAAGATCCAAACGGACCCGTCGCCGAGCAACTTGCGAGCGATCCGATGCTACGAGAAAGCGGGGTTTGAAAGGCAAGGTACCGTAACCACCCCATATGGTCCAGCCGTGGTAATGGGTCAAACACGCCAAGCATTCGAGCGAACACGCAGTGATGCCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39526","NCBI_taxonomy_name":"Aeromonas media","NCBI_taxonomy_id":"651"}}}},"ARO_accession":"3005112","ARO_id":"43327","ARO_name":"AAC(6')-Ib-cr3","CARD_short_name":"AAC(6')-Ib-cr3","ARO_description":"A fluoroquinolone-acetylating aminoglycoside acetyltransferase variant identified from Aeromonas. These proteins confer resistance to both fluoroquinolone and aminoglycoside antibiotics.","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"A category of aminoglycoside N-acetyltransferase enzymes with modification regiospecificity based at the 6'-amino group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics through acetylation of the 6-amino group of the compound.","category_aro_class_name":"AMR Gene Family"},"43328":{"category_aro_accession":"3005113","category_aro_cvterm_id":"43328","category_aro_name":"AAC(6')-Ib-cr","category_aro_description":"A subfamily of aminoglycoside 6'-N-acetyltransferases, AAC(6'), which doubly confer resistance to aminoglycoside and fluoroquinolone antibiotics through fluoroquinolone-acetylating activity.","category_aro_class_name":"AMR Gene Family"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3841":{"model_id":"3841","model_name":"AAC(6')-Ib-cr4","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"8753":{"protein_sequence":{"accession":"WP_065187000.1","sequence":"MTNSTDSVTLRLMTEHDLAMLYEWLNRSHIVEWWGGEEARPTLADVQEQYLPSVLAQESVTPYIAMLNGEPIGYAQSYVALGSGDGRWEEETDPGVRGIDQLLANASQLGKGLGTKLVRALVELLFNDPEVTKIQTDPSPSNLRAIRCYEKAGFERQGTVTTPYGPAVYMVQTRQAFERTRSDA"},"dna_sequence":{"accession":"NG_052463.1","fmin":"100","fmax":"655","strand":"+","sequence":"GTGACCAACAGCACCGATTCCGTCACACTGCGCCTCATGACTGAGCATGACCTTGCGATGCTCTATGAGTGGCTAAATCGATCTCATATCGTCGAGTGGTGGGGCGGAGAAGAAGCACGCCCGACACTTGCTGACGTACAGGAACAGTACTTGCCAAGCGTTTTAGCGCAAGAGTCCGTCACTCCATACATTGCAATGCTGAATGGAGAGCCGATTGGGTATGCCCAGTCGTACGTTGCTCTTGGAAGCGGGGACGGACGGTGGGAAGAAGAAACCGATCCAGGAGTACGCGGAATAGACCAGTTACTGGCGAATGCATCACAACTGGGCAAAGGCTTGGGAACCAAGCTGGTTCGAGCTCTGGTTGAGTTGCTGTTCAATGATCCCGAGGTCACCAAGATCCAAACGGACCCGTCGCCGAGCAACTTGCGAGCGATCCGATGCTACGAGAAAGCGGGGTTTGAGAGGCAAGGTACCGTAACCACCCCATATGGTCCAGCCGTGTACATGGTTCAAACACGCCAGGCATTCGAGCGAACACGCAGTGATGCCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43330","NCBI_taxonomy_name":"Enterobacter hormaechei subsp. steigerwaltii","NCBI_taxonomy_id":"299766"}}}},"ARO_accession":"3005114","ARO_id":"43329","ARO_name":"AAC(6')-Ib-cr4","CARD_short_name":"AAC(6')-Ib-cr4","ARO_description":"A fluoroquinolone-acetylating aminoglycoside acetyltransferase variant identified from Enterobacter. These proteins confer resistance to both fluoroquinolone and aminoglycoside antibiotics.","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"A category of aminoglycoside N-acetyltransferase enzymes with modification regiospecificity based at the 6'-amino group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics through acetylation of the 6-amino group of the compound.","category_aro_class_name":"AMR Gene Family"},"43328":{"category_aro_accession":"3005113","category_aro_cvterm_id":"43328","category_aro_name":"AAC(6')-Ib-cr","category_aro_description":"A subfamily of aminoglycoside 6'-N-acetyltransferases, AAC(6'), which doubly confer resistance to aminoglycoside and fluoroquinolone antibiotics through fluoroquinolone-acetylating activity.","category_aro_class_name":"AMR Gene Family"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3842":{"model_id":"3842","model_name":"AAC(6')-Ib-cr5","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"6155":{"protein_sequence":{"accession":"ABX24471.1","sequence":"MTNSNDSVTLRLMTEHDLAMLYEWLNRSHIVEWWGGEEARPTLADVQEQYLPSVLAQESVTPYIAMLNGEPIGYAQSYVALGSGDGRWEEETDPGVRGIDQLLANASQLGKGLGTKLVRALVELLFNDPEVTKIQTDPSPSNLRAIRCYEKAGFERQGTVTTPYGPAVYMVQTRQAFERTRSDA"},"dna_sequence":{"accession":"EU161636.1","fmin":"1021","fmax":"1576","strand":"+","sequence":"GTGACCAACAGCAACGATTCCGTCACACTGCGCCTCATGACTGAGCATGACCTTGCGATGCTCTATGAGTGGCTAAATCGATCTCATATCGTCGAGTGGTGGGGCGGAGAAGAAGCACGCCCGACACTTGCTGACGTACAGGAACAGTACTTGCCAAGCGTTTTAGCGCAAGAGTCCGTCACTCCATACATTGCAATGCTGAATGGAGAGCCGATTGGGTATGCCCAGTCGTACGTTGCTCTTGGAAGCGGGGACGGAAGGTGGGAAGAAGAAACCGATCCAGGAGTACGCGGAATAGACCAGTTACTGGCGAATGCATCACAACTGGGCAAAGGCTTGGGAACCAAGCTGGTTCGAGCTCTGGTTGAGTTGCTGTTCAATGATCCCGAGGTCACCAAGATCCAAACGGACCCGTCGCCGAGCAACTTGCGAGCGATCCGATGCTACGAGAAAGCGGGGTTTGAGAGGCAAGGTACCGTAACCACCCCATATGGTCCAGCCGTGTACATGGTTCAAACACGCCAGGCATTCGAGCGAACACGCAGTGATGCCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005115","ARO_id":"43331","ARO_name":"AAC(6')-Ib-cr5","CARD_short_name":"AAC(6')-Ib-cr5","ARO_description":"A fluoroquinolone-acetylating aminoglycoside acetyltransferase variant identified from Pseudomonas. These proteins confer resistance to both fluoroquinolone and aminoglycoside antibiotics.","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"A category of aminoglycoside N-acetyltransferase enzymes with modification regiospecificity based at the 6'-amino group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics through acetylation of the 6-amino group of the compound.","category_aro_class_name":"AMR Gene Family"},"43328":{"category_aro_accession":"3005113","category_aro_cvterm_id":"43328","category_aro_name":"AAC(6')-Ib-cr","category_aro_description":"A subfamily of aminoglycoside 6'-N-acetyltransferases, AAC(6'), which doubly confer resistance to aminoglycoside and fluoroquinolone antibiotics through fluoroquinolone-acetylating activity.","category_aro_class_name":"AMR Gene Family"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. 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Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3843":{"model_id":"3843","model_name":"AAC(6')-Ib-cr6","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"8754":{"protein_sequence":{"accession":"WP_063840320.1","sequence":"MTNCNDSVTLRLMTEHDLAMLYGWLNRSHIVEWWGGEEARPTLADVQEQYLPSVLAQESVTPYIAMLNGEPIGYAQSYVALGSGDGRWEEETDPGVRGIDQLLANASQLGKGLGTKLVRALVELLFNDPEVTKIQTDPSPSNLRAIRCYEKAGFERQGTVTTPYGPAVYMVQTRQAFERTRSDA"},"dna_sequence":{"accession":"NG_047292.1","fmin":"100","fmax":"655","strand":"+","sequence":"GTGACCAACTGCAACGATTCCGTCACACTGCGCCTCATGACTGAGCATGACCTTGCGATGCTCTATGGGTGGCTAAATCGATCTCATATCGTCGAGTGGTGGGGCGGAGAAGAAGCACGCCCGACACTTGCTGACGTACAGGAACAGTACTTGCCAAGCGTTTTAGCGCAAGAGTCCGTCACTCCATACATTGCAATGCTGAATGGAGAGCCGATTGGGTATGCCCAGTCGTACGTTGCTCTTGGAAGCGGGGACGGACGGTGGGAAGAAGAAACCGATCCAGGAGTACGCGGAATAGACCAGTTACTGGCGAATGCATCACAACTGGGCAAAGGCTTGGGAACCAAGCTGGTTCGAGCTCTGGTTGAGTTGCTGTTCAATGATCCCGAGGTCACCAAGATCCAAACGGACCCGTCGCCGAGCAACTTGCGAGCGATCCGATGCTACGAGAAAGCGGGGTTTGAGAGGCAAGGTACCGTAACCACCCCATATGGTCCAGCCGTGTACATGGTTCAAACACGCCAGGCATTCGAGCGAACACGCAGTGATGCCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3005116","ARO_id":"43332","ARO_name":"AAC(6')-Ib-cr6","CARD_short_name":"AAC(6')-Ib-cr6","ARO_description":"A fluoroquinolone-acetylating aminoglycoside acetyltransferase variant identified from Escherichia coli. These proteins confer resistance to both fluoroquinolone and aminoglycoside antibiotics.","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"A category of aminoglycoside N-acetyltransferase enzymes with modification regiospecificity based at the 6'-amino group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics through acetylation of the 6-amino group of the compound.","category_aro_class_name":"AMR Gene Family"},"43328":{"category_aro_accession":"3005113","category_aro_cvterm_id":"43328","category_aro_name":"AAC(6')-Ib-cr","category_aro_description":"A subfamily of aminoglycoside 6'-N-acetyltransferases, AAC(6'), which doubly confer resistance to aminoglycoside and fluoroquinolone antibiotics through fluoroquinolone-acetylating activity.","category_aro_class_name":"AMR Gene Family"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. 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Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3844":{"model_id":"3844","model_name":"AAC(6')-Ib-cr7","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"6157":{"protein_sequence":{"accession":"NON98701.1","sequence":"MTNSNDSVTLRLMTEHDLAMLYEWLNRSHIVEWWGGEEARPTLADVQEQYLPSVLAQESVTPYIAMLNGEPIGYAQSYVALGSGDGRWEEETDPGVRGIDQLLANASQLGKGLGTKLVRALVELLFNDPEVTKIQTDPSPSNLRAIRCYEKAGFERQGTVTTPYGPAVYMVQTRQAFERTRSVA"},"dna_sequence":{"accession":"JABGAB010000032.1","fmin":"11074","fmax":"11629","strand":"-","sequence":"GTGACCAACAGCAACGATTCCGTCACACTGCGCCTCATGACTGAGCATGACCTTGCGATGCTCTATGAGTGGCTAAATCGATCTCATATCGTCGAGTGGTGGGGCGGAGAAGAAGCACGCCCGACACTTGCTGACGTACAGGAACAGTACTTGCCAAGCGTTTTAGCGCAAGAGTCCGTCACTCCATACATTGCAATGCTGAATGGAGAGCCGATTGGGTATGCCCAGTCGTACGTTGCTCTTGGAAGCGGGGACGGACGGTGGGAAGAAGAAACCGATCCAGGAGTACGCGGAATAGACCAGTTACTGGCGAATGCATCACAACTGGGCAAAGGCTTGGGAACCAAGCTGGTTCGAGCTCTGGTTGAGTTGCTGTTCAATGATCCCGAGGTCACCAAGATCCAAACGGACCCGTCGCCGAGCAACTTGCGAGCGATCCGATGCTACGAGAAAGCGGGGTTTGAGAGGCAAGGTACCGTAACCACCCCATATGGTCCAGCCGTGTACATGGTTCAAACACGCCAGGCATTCGAGCGAACACGCAGTGTTGCCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3005117","ARO_id":"43333","ARO_name":"AAC(6')-Ib-cr7","CARD_short_name":"AAC(6')-Ib-cr7","ARO_description":"A fluoroquinolone-acetylating aminoglycoside acetyltransferase variant identified from Klebsiella. These proteins confer resistance to both fluoroquinolone and aminoglycoside antibiotics.","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"A category of aminoglycoside N-acetyltransferase enzymes with modification regiospecificity based at the 6'-amino group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics through acetylation of the 6-amino group of the compound.","category_aro_class_name":"AMR Gene Family"},"43328":{"category_aro_accession":"3005113","category_aro_cvterm_id":"43328","category_aro_name":"AAC(6')-Ib-cr","category_aro_description":"A subfamily of aminoglycoside 6'-N-acetyltransferases, AAC(6'), which doubly confer resistance to aminoglycoside and fluoroquinolone antibiotics through fluoroquinolone-acetylating activity.","category_aro_class_name":"AMR Gene Family"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3845":{"model_id":"3845","model_name":"AAC(6')-Ib-cr8","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"6158":{"protein_sequence":{"accession":"AZK52946.1","sequence":"MTNSNDSVTLRLMTEHDLAMLYECLNRSHIVEWWGGEEARPTLADVQEQYLPSVLAQESVTPYIAMLNGEPIGYAQSYVALGSGDGRWEEETDPGVRGIDQLLANASQLGKGLGTKLVRALVELLFNDPEVTKIQTDPSPSNLRAIRCYEKAGFERQGTVTTPYGPAVYMVQTREAFERTRSDA"},"dna_sequence":{"accession":"CP034250.1","fmin":"426089","fmax":"426644","strand":"-","sequence":"GTGACCAATAGCAACGATTCCGTCACACTGCGCCTCATGACTGAGCATGACCTTGCGATGCTCTATGAGTGCCTAAATCGATCTCATATCGTCGAGTGGTGGGGCGGAGAAGAAGCACGCCCGACACTTGCTGACGTACAGGAACAGTACTTGCCAAGCGTTTTAGCGCAAGAGTCCGTCACTCCATACATTGCAATGCTGAATGGAGAGCCGATTGGGTATGCCCAGTCGTACGTTGCTCTTGGAAGCGGGGACGGACGGTGGGAAGAAGAAACCGATCCAGGAGTACGCGGAATAGACCAGTTACTGGCGAATGCATCACAACTGGGCAAAGGCTTGGGAACCAAGCTGGTTCGAGCTCTGGTTGAGTTGCTGTTCAATGATCCCGAGGTCACCAAGATCCAAACGGACCCGTCGCCGAGCAACTTGCGAGCGATCCGATGCTACGAGAAAGCGGGGTTTGAGAGGCAAGGTACCGTAACCACCCCATATGGTCCAGCCGTGTACATGGTTCAAACACGCGAGGCATTCGAGCGAACACGCAGTGATGCCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35667","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Derby","NCBI_taxonomy_id":"28144"}}}},"ARO_accession":"3005118","ARO_id":"43334","ARO_name":"AAC(6')-Ib-cr8","CARD_short_name":"AAC(6')-Ib-cr8","ARO_description":"A fluoroquinolone-acetylating aminoglycoside acetyltransferase variant, identified from Salmonella. These variants confers resistance to both aminoglycoside and fluoroquinolone antibiotics.","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"A category of aminoglycoside N-acetyltransferase enzymes with modification regiospecificity based at the 6'-amino group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics through acetylation of the 6-amino group of the compound.","category_aro_class_name":"AMR Gene Family"},"43328":{"category_aro_accession":"3005113","category_aro_cvterm_id":"43328","category_aro_name":"AAC(6')-Ib-cr","category_aro_description":"A subfamily of aminoglycoside 6'-N-acetyltransferases, AAC(6'), which doubly confer resistance to aminoglycoside and fluoroquinolone antibiotics through fluoroquinolone-acetylating activity.","category_aro_class_name":"AMR Gene Family"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3846":{"model_id":"3846","model_name":"AAC(6')-Ib-cr9","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"6159":{"protein_sequence":{"accession":"AYD68572.1","sequence":"MKTFNDSVTLRLMTEHDLAMLYEWLNRSHIVEWWGGEEARPTLADVQEQYLPSVLAQESVTPYIAMLNGEPIGYAQSYVALGSGDGRWEEETDPGVRGIDQLLANASQLGKGLGTKLVRALVELLFNDPEVTKIQTDPSPSNLRAIRCYEKAGFERQGTVTTPYGPAVYMVQTRQAFERTRSDA"},"dna_sequence":{"accession":"MH569711.1","fmin":"1959","fmax":"2514","strand":"-","sequence":"ATGAAAACATTTAACGATTCCGTCACACTGCGCCTCATGACTGAGCATGACCTTGCGATGCTCTATGAGTGGCTAAATCGATCTCATATCGTCGAGTGGTGGGGCGGAGAAGAAGCACGCCCGACACTTGCTGACGTACAGGAACAGTACTTGCCAAGCGTTTTAGCGCAAGAGTCCGTCACTCCATACATTGCAATGCTGAATGGAGAGCCGATTGGGTATGCCCAGTCGTACGTTGCTCTTGGAAGCGGGGACGGAAGGTGGGAAGAAGAAACCGATCCAGGAGTACGCGGAATAGACCAGTTACTGGCGAATGCATCACAACTGGGCAAAGGCTTGGGAACCAAGCTGGTTCGAGCTCTGGTTGAGTTGCTGTTCAATGATCCCGAGGTCACCAAGATCCAAACGGACCCGTCGCCGAGCAACTTGCGAGCGATCCGATGCTACGAGAAAGCGGGGTTTGAGAGGCAAGGTACCGTAACCACCCCATATGGTCCAGCCGTGTACATGGTTCAAACACGCCAGGCATTCGAGCGAACACGCAGTGATGCCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36783","NCBI_taxonomy_name":"Serratia marcescens","NCBI_taxonomy_id":"615"}}}},"ARO_accession":"3005119","ARO_id":"43335","ARO_name":"AAC(6')-Ib-cr9","CARD_short_name":"AAC(6')-Ib-cr9","ARO_description":"A fluoroquinolone-acetylating aminoglycoside acetyltransferase variant, identified from Serratia. These variants confers resistance to both aminoglycoside and fluoroquinolone antibiotics.","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"A category of aminoglycoside N-acetyltransferase enzymes with modification regiospecificity based at the 6'-amino group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics through acetylation of the 6-amino group of the compound.","category_aro_class_name":"AMR Gene Family"},"43328":{"category_aro_accession":"3005113","category_aro_cvterm_id":"43328","category_aro_name":"AAC(6')-Ib-cr","category_aro_description":"A subfamily of aminoglycoside 6'-N-acetyltransferases, AAC(6'), which doubly confer resistance to aminoglycoside and fluoroquinolone antibiotics through fluoroquinolone-acetylating activity.","category_aro_class_name":"AMR Gene Family"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3848":{"model_id":"3848","model_name":"PDC-68","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"6161":{"protein_sequence":{"accession":"AIG20005.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDRAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"KJ949083.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCGGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACTCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATTCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005122","ARO_id":"43339","ARO_name":"PDC-68","CARD_short_name":"PDC-68","ARO_description":"PDC-68 is an ambler class C beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3849":{"model_id":"3849","model_name":"PDC-70","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"6169":{"protein_sequence":{"accession":"AIG20007.1","sequence":"MRDTKFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"KJ949085.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAAATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAACTGTTCCCAGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGATCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATTCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005123","ARO_id":"43340","ARO_name":"PDC-70","CARD_short_name":"PDC-70","ARO_description":"PDC-70 is an ambler class C beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3852":{"model_id":"3852","model_name":"PDC-66","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"6176":{"protein_sequence":{"accession":"AIG20003.1","sequence":"MRDTGFPCLCGIAASTLLFAATSAIAGEAPADRLKTLVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASLHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYTPGSQRLYSNPSIGLFGYLAARSLGQPFERIMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDKPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"KJ949081.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCGGATTCCCCTGCCTGTGCGGCATCGCCGCCTCCACACTGCTGTTCGCCGCCACCTCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGACACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGATATTCCGGGCCTGGCCGTGGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCTTCGAAAGAGGACGGTCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCTGCACTGGCCGGCGCTGCAAGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAAGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACACGCCGGGCAGCCAGCGCCTCTACTCCAACCCGAGCATCGGTCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGATCATGGAGCAGCAACTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCTCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAAGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCGGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGACTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATCCCAGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAATTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005126","ARO_id":"43343","ARO_name":"PDC-66","CARD_short_name":"PDC-66","ARO_description":"PDC-66 is an ambler class C beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3853":{"model_id":"3853","model_name":"PDC-14","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"6165":{"protein_sequence":{"accession":"ACX31164.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQSYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"GQ845017.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGTCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGAGCTACGGCAAGGACGACCGCCCCCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGATTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005127","ARO_id":"43344","ARO_name":"PDC-14","CARD_short_name":"PDC-14","ARO_description":"PDC-14 is an ambler class C beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3854":{"model_id":"3854","model_name":"PDC-47","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"6170":{"protein_sequence":{"accession":"AIG19984.1","sequence":"MRDTRFPCLCGIAASILLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGLVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFSDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"KJ949062.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCATACTGCTGTTCGCCACCACCCCGGCCATTGCCGACGAGGCCCCGGCAGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTTGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCTCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAACTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAAGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005128","ARO_id":"43345","ARO_name":"PDC-47","CARD_short_name":"PDC-47","ARO_description":"PDC-47 is an ambler class C beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3855":{"model_id":"3855","model_name":"PDC-51","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"6172":{"protein_sequence":{"accession":"AIG19988.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRAGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"KJ949066.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGCCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005129","ARO_id":"43346","ARO_name":"PDC-51","CARD_short_name":"PDC-51","ARO_description":"PDC-51 is an ambler class C beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3856":{"model_id":"3856","model_name":"OXA-846","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6173":{"protein_sequence":{"accession":"QEJ80883.1","sequence":"MRPLLFSALLLLSGHAQASEWNDSQAVDKLFGAAGVKGTFVLYDVQRQRYVGHDRERAETRFVPASTYKVANSLIGLSTGAVRSADEVLPYGGKPQRFKAWEHDMSLRDAIEASNVPVYQELARRIGLERMRANVSRLGYGNAEIGQVVDNFWLVGPLKISAMEQTRFLLRLAQGELPFPAPVQSTVRAMTLLESGPGWELHGKTGWCFDCTPELGWWVGWVKRNERLYGFALNIDMPGGEADIGKRVELGKASLKALGILP"},"dna_sequence":{"accession":"MN370854.1","fmin":"0","fmax":"789","strand":"+","sequence":"ATGCGCCCTCTCCTCTTCAGTGCCCTTCTCCTGCTTTCCGGGCATGCCCAGGCCAGCGAATGGAACGACAGCCAGGCCGTGGACAAGCTATTCGGCGCGGCCGGGGTGAAAGGCACCTTCGTCCTCTACGATGTGCAGCGGCAGCGCTATGTCGGCCATGACCGGGAGCGCGCGGAAACCCGCTTCGTTCCCGCTTCCACCTACAAGGTGGCGAACAGCCTGATCGGCTTATCCACAGGGGCGGTTAGATCCGCCGACGAGGTTCTTCCCTATGGCGGCAAGCCCCAGCGCTTCAAGGCCTGGGAGCACGACATGAGCCTGCGCGACGCAATCGAGGCATCGAACGTACCGGTCTACCAGGAACTGGCGCGGCGCATCGGCCTGGAGCGGATGCGCGCCAATGTCTCGCGTCTGGGTTACGGCAACGCGGAAATCGGCCAGGTTGTGGATAACTTCTGGTTGGTGGGACCGCTGAAGATCAGCGCGATGGAACAGACCCGCTTTCTGCTCCGACTGGCGCAGGGAGAATTGCCATTCCCCGCCCCGGTGCAGTCCACCGTGCGCGCCATGACCCTGCTGGAAAGCGGCCCGGGCTGGGAGCTGCACGGCAAGACCGGCTGGTGCTTCGACTGCACGCCGGAACTCGGCTGGTGGGTGGGCTGGGTGAAGCGCAACGAGCGGCTCTACGGCTTCGCCCTGAACATCGACATGCCCGGCGGCGAGGCCGACATCGGCAAGCGCGTCGAACTGGGCAAGGCCAGTCTCAAGGCTCTCGGGATACTGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005130","ARO_id":"43347","ARO_name":"OXA-846","CARD_short_name":"OXA-846","ARO_description":"OXA-846 is a class D beta-lactamase found in Pseudomonas aeruginosa. It is part of the OXA-50 family of oxacillin-hydrolyzing beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46513":{"category_aro_accession":"3007724","category_aro_cvterm_id":"46513","category_aro_name":"OXA-50-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-50.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3857":{"model_id":"3857","model_name":"NDM-29","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6177":{"protein_sequence":{"accession":"QFZ95817.1","sequence":"MELPNIMHPVAKLSTALAAALMLSGCMPGEIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMNALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR"},"dna_sequence":{"accession":"MN624980.1","fmin":"290","fmax":"1103","strand":"+","sequence":"ATGGAATTGCCCAATATTATGCACCCGGTCGCGAAGCTGAGCACCGCATTAGCCGCTGCATTGATGCTGAGCGGGTGCATGCCCGGTGAAATCCGCCCGACGATTGGCCAGCAAATGGAAACTGGCGACCAACGGTTTGGCGATCTGGTTTTCCGCCAGCTCGCACCGAATGTCTGGCAGCACACTTCCTATCTCGACATGCCGGGTTTCGGGGCAGTCGCTTCCAACGGTTTGATCGTCAGGGATGGCGGCCGCGTGCTGGTGGTCGATACCGCCTGGACCGATGACCAGACCGCCCAGATCCTCAACTGGATCAAGCAGGAGATCAACCTGCCGGTCGCGCTGGCGGTGGTGACTCACGCGCATCAGGACAAGATGGGCGGTATGAACGCGCTGCATGCGGCGGGGATTGCGACTTATGCCAATGCGTTGTCGAACCAGCTTGCCCCGCAAGAGGGGATGGTTGCGGCGCAACACAGCCTGACTTTCGCCGCCAATGGCTGGGTCGAACCAGCAACCGCGCCCAACTTTGGCCCGCTCAAGGTATTTTACCCCGGCCCCGGCCACACCAGTGACAATATCACCGTTGGGATCGACGGCACCGACATCGCTTTTGGTGGCTGCCTGATCAAGGACAGCAAGGCCAAGTCGCTCGGCAATCTCGGTGATGCCGACACTGAGCACTACGCCGCGTCAGCGCGCGCGTTTGGTGCGGCGTTCCCCAAGGCCAGCATGATCGTGATGAGCCATTCCGCCCCCGATAGCCGCGCCGCAATCACTCATACGGCCCGCATGGCCGACAAGCTGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3005131","ARO_id":"43348","ARO_name":"NDM-29","CARD_short_name":"NDM-29","ARO_description":"An NDM metallo-beta-lactamase variant reported in Klebsiella pneumoniae.","ARO_category":{"36196":{"category_aro_accession":"3000057","category_aro_cvterm_id":"36196","category_aro_name":"NDM beta-lactamase","category_aro_description":"NDM beta-lactamases or New Delhi metallo-beta-lactamases are class B beta-lactamases that confer resistance to a broad range of antibiotics including carbapenems, cephalosporins and penicillins.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3858":{"model_id":"3858","model_name":"PDC-11","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"6179":{"protein_sequence":{"accession":"ACX31161.1","sequence":"MRDTRFSCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"GQ845014.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCTCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005132","ARO_id":"43349","ARO_name":"PDC-11","CARD_short_name":"PDC-11","ARO_description":"PDC-11 is an ambler class C beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3859":{"model_id":"3859","model_name":"PDC-62","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"6182":{"protein_sequence":{"accession":"AIG19999.1","sequence":"MRHATILNLCGLAASTLFFATTSAFATAAPAERLKALVDAAVQPVMKANDIPGLAVAITLKGEPHYFSYGVASKEDARKVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASRHWPALQGSRFDGISLLDLGTYSAGGLPLQFPDAVQKDPAQIRDYYRQWQPTYAPGSHRQYSNPSIGLFGYLAARSLGQPFERSMERQLFPALGLEHTFIRVPAAQQGLYAQGYGKDDRPLRVGPGPLDAEAYGLKSSAADLLRFVEANLHPERLEKPWAQALDATHRGYYKVGDMTQGLGWEAYDWPIDLKRLQAGNSAPMALQAHKVARLPAPQALDGQRLLNKTGSTNGFGAYLAFIPGRDVGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLVR"},"dna_sequence":{"accession":"KJ949077.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCCATGCGACAATCCTCAACCTGTGCGGCCTCGCCGCTTCCACCCTGTTCTTCGCGACAACATCGGCCTTCGCCACGGCGGCGCCGGCGGAGCGCCTGAAGGCTCTGGTGGACGCCGCCGTGCAACCGGTCATGAAGGCCAATGATATCCCGGGACTGGCCGTCGCCATCACTCTCAAGGGCGAACCGCATTACTTCAGTTATGGGGTGGCCTCGAAGGAGGACGCCCGCAAGGTGACCCCCGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTACGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCGGCACTGGCCCGCCCTGCAGGGCAGCCGCTTCGACGGTATCAGCCTGCTCGACCTCGGCACCTACAGCGCTGGCGGCCTGCCGCTACAGTTCCCCGATGCGGTGCAGAAGGATCCGGCGCAGATCCGCGACTACTACCGCCAGTGGCAACCGACCTACGCCCCGGGCAGCCACCGCCAGTACTCCAACCCGAGCATCGGTCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCATTCGAGCGCAGCATGGAACGGCAGCTGTTCCCGGCGCTCGGCCTGGAGCACACCTTTATCCGGGTGCCCGCCGCGCAGCAGGGGCTGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTGCGGGTCGGACCCGGTCCGCTGGACGCCGAGGCCTACGGGCTGAAGTCCAGCGCTGCGGACCTGCTGCGCTTCGTCGAGGCCAACCTGCACCCCGAGCGCCTGGAGAAGCCCTGGGCGCAGGCCCTCGACGCCACCCATCGCGGCTACTACAAGGTGGGCGACATGACCCAGGGCCTGGGTTGGGAAGCCTACGATTGGCCGATCGACCTGAAGCGCCTGCAGGCGGGCAACTCGGCGCCGATGGCGCTACAGGCGCACAAGGTCGCCAGGTTGCCGGCGCCGCAAGCCCTGGACGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGTTTCGGCGCCTACCTGGCGTTCATCCCGGGACGCGACGTCGGCCTGGTGATCCTGGCCAATCGCAACTACCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAACAGCAGGCCAAGGTACCGCTGGTGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005133","ARO_id":"43350","ARO_name":"PDC-62","CARD_short_name":"PDC-62","ARO_description":"PDC-62 is an ambler class C beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3860":{"model_id":"3860","model_name":"PDC-43","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"6183":{"protein_sequence":{"accession":"AIG19980.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPVPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"KJ949058.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGTGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005134","ARO_id":"43351","ARO_name":"PDC-43","CARD_short_name":"PDC-43","ARO_description":"PDC-43 is an ambler class C beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3861":{"model_id":"3861","model_name":"PDC-54","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"6184":{"protein_sequence":{"accession":"AIG19991.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALTQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPSYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"KJ949069.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGACCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGTCCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCCCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005135","ARO_id":"43352","ARO_name":"PDC-54","CARD_short_name":"PDC-54","ARO_description":"PDC-54 is an ambler class C beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3862":{"model_id":"3862","model_name":"OXA-906","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"530"}},"model_sequences":{"sequence":{"6185":{"protein_sequence":{"accession":"QIC04089.1","sequence":"MRPLLFSALLLLSGHAQASEWNDSHAVDKLFGAAGVKGTFVLYDVQRQRYVGHDRERAETRFVPASTYKVANSLIGLSTGAVRSADEVLPYGGKPQRFKAWEHDMSLRDAIKASNVPVYQELARRIGLERMRANVSHLGYGNAEIGQVVDNFWLVGPLKISAMEQTRFLLRLAQGELPFPAPVQSTVRAMTLLESGPGWELHGKTGWCFDCTPELGWWVGWVKRNERLYGFALNIDMPGGEADIGKRVELGKASLKALGILP"},"dna_sequence":{"accession":"MT040744.1","fmin":"0","fmax":"789","strand":"+","sequence":"ATGCGCCCTCTCCTCTTCAGCGCCCTTCTCCTGCTCTCCGGGCATGCCCAGGCCAGCGAATGGAACGACAGCCACGCCGTGGACAAGCTATTCGGCGCGGCCGGGGTGAAAGGCACCTTCGTCCTCTACGATGTGCAGCGGCAGCGCTATGTCGGCCATGACCGGGAGCGCGCGGAAACTCGCTTCGTTCCTGCCTCCACCTACAAGGTGGCGAACAGCCTGATTGGCTTATCCACAGGGGCGGTTAGATCCGCCGACGAGGTTCTTCCCTATGGCGGCAAGCCCCAGCGCTTCAAGGCCTGGGAGCACGACATGAGCCTGCGCGACGCGATCAAGGCATCGAACGTACCGGTCTACCAGGAACTGGCGCGGCGCATCGGCCTGGAGCGGATGCGCGCCAATGTCTCGCACCTGGGTTATGGCAACGCGGAAATCGGCCAGGTTGTGGATAACTTCTGGTTGGTGGGACCGCTGAAGATCAGCGCGATGGAACAGACCCGCTTTCTGCTCCGACTGGCGCAGGGAGAATTGCCATTCCCCGCCCCGGTGCAGTCCACCGTGCGCGCCATGACCCTGCTGGAAAGCGGCCCGGGCTGGGAGCTGCACGGCAAGACCGGCTGGTGCTTCGACTGCACGCCGGAACTCGGCTGGTGGGTGGGCTGGGTGAAGCGCAACGAGCGGCTCTACGGCTTCGCCCTGAACATCGACATGCCCGGCGGCGAGGCCGACATCGGCAAGCGCGTCGAACTGGGCAAGGCCAGTCTCAAGGCTCTCGGGATACTGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005136","ARO_id":"43353","ARO_name":"OXA-906","CARD_short_name":"OXA-906","ARO_description":"OXA-906 is a class D beta-lactamase from the OXA-50 family found in Pseudomonas aeruginosa.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46513":{"category_aro_accession":"3007724","category_aro_cvterm_id":"46513","category_aro_name":"OXA-50-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-50.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3863":{"model_id":"3863","model_name":"PDC-59","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"6186":{"protein_sequence":{"accession":"AIG19996.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPITLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"KJ949074.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTTATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCCGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCACCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005137","ARO_id":"43354","ARO_name":"PDC-59","CARD_short_name":"PDC-59","ARO_description":"PDC-59 is an ambler class C beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3864":{"model_id":"3864","model_name":"OXA-850","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"527"}},"model_sequences":{"sequence":{"6188":{"protein_sequence":{"accession":"QEJ80887.1","sequence":"MRPLLFSALLLLSGHTQASEWNDSQAVDKLFGAAGVKGTFVLYDVQRQRYVGHDRERAETRFVPASTYKVANSLIGLSTGAVRSADEVLPYGGKPQRFKAWEHDMSLRDAIKASNVPVYQELARRIGLERMRANVSRLGYGNAEIGQVVDNFWLVGPLKISAMEQTHFLLRLAQGELPFPAPVQSTVRAMTLLESGPGWELHGKTGWCFDCTPELGWWVGWVKRNERLYGFALNIDMPGGEADIGKRVELGKASLKALGILP"},"dna_sequence":{"accession":"MN370858.1","fmin":"0","fmax":"789","strand":"+","sequence":"ATGCGCCCTCTCCTCTTCAGTGCCCTTCTCCTGCTTTCCGGGCATACCCAGGCCAGCGAATGGAACGACAGCCAGGCCGTGGACAAGCTATTCGGCGCGGCCGGGGTGAAAGGCACCTTCGTCCTCTACGATGTGCAGCGGCAGCGCTATGTCGGCCATGACCGGGAGCGCGCGGAAACCCGCTTCGTTCCCGCTTCCACCTACAAGGTGGCGAACAGCCTGATAGGCTTATCCACAGGGGCGGTTAGATCCGCCGACGAGGTTCTTCCCTATGGCGGCAAGCCCCAGCGCTTCAAGGCCTGGGAGCACGACATGAGCCTGCGCGACGCGATCAAGGCATCGAACGTACCGGTCTACCAGGAACTGGCGCGGCGCATCGGCCTGGAGCGGATGCGCGCCAATGTCTCGCGCCTGGGTTACGGCAACGCGGAAATCGGCCAGGTTGTGGATAACTTCTGGTTGGTGGGACCGCTGAAGATCAGCGCGATGGAACAGACCCACTTTCTGCTCCGACTGGCGCAGGGAGAATTGCCATTCCCCGCCCCGGTGCAGTCCACCGTGCGCGCCATGACCCTGCTGGAAAGCGGCCCGGGCTGGGAGCTGCACGGCAAGACCGGCTGGTGCTTCGACTGCACGCCGGAACTCGGCTGGTGGGTGGGCTGGGTGAAGCGCAACGAGCGGCTCTACGGCTTCGCCCTGAACATCGACATGCCCGGCGGCGAGGCCGACATCGGCAAGCGCGTCGAACTGGGCAAGGCCAGTCTCAAGGCTCTCGGGATACTGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005138","ARO_id":"43355","ARO_name":"OXA-850","CARD_short_name":"OXA-850","ARO_description":"Pseudomonas aeruginosa strain OXA-50 family oxacillin-hydrolyzing class D beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46513":{"category_aro_accession":"3007724","category_aro_cvterm_id":"46513","category_aro_name":"OXA-50-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-50.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3865":{"model_id":"3865","model_name":"PDC-67","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"795"}},"model_sequences":{"sequence":{"6189":{"protein_sequence":{"accession":"AIG20004.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKVRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"KJ949082.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGGTGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCATTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005139","ARO_id":"43356","ARO_name":"PDC-67","CARD_short_name":"PDC-67","ARO_description":"PDC-67 is an ambler class C beta-lactamase found in Pseudomonas aeruginosa strain 5065.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3866":{"model_id":"3866","model_name":"PDC-56","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"795"}},"model_sequences":{"sequence":{"6190":{"protein_sequence":{"accession":"AIG19993.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"KJ949071.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATTGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAACTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATTCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTACCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005140","ARO_id":"43357","ARO_name":"PDC-56","CARD_short_name":"PDC-56","ARO_description":"PDC-56 is an ambler class C beta-lactamase found in Pseudomonas aeruginosa strain 4883.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3867":{"model_id":"3867","model_name":"PDC-52","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"6191":{"protein_sequence":{"accession":"AIG19989.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTSGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"KJ949067.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAGCGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005141","ARO_id":"43358","ARO_name":"PDC-52","CARD_short_name":"PDC-52","ARO_description":"PDC-52 is an ambler class C beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3868":{"model_id":"3868","model_name":"PDC-44","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"6192":{"protein_sequence":{"accession":"AIG19981.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMAPQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"KJ949059.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGTCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCATGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCCGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005142","ARO_id":"43359","ARO_name":"PDC-44","CARD_short_name":"PDC-44","ARO_description":"PDC-44 is an ambler class C beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3869":{"model_id":"3869","model_name":"PDC-240","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"6193":{"protein_sequence":{"accession":"AUT06977.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRRYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRAGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"MG696099.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGTCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCGCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGCCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005143","ARO_id":"43360","ARO_name":"PDC-240","CARD_short_name":"PDC-240","ARO_description":"PDC-240 is an ambler class C beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4235":{"model_id":"4235","model_name":"ADC-167","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6610":{"protein_sequence":{"accession":"WP_002046804.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVKTDQQVLTFFKDWKPKNSIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLERTIFPELGLKYSYVNVPKTQIQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLKFINANLNPQKYPADIQRAINETHQGFYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_056109.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAGTATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAATTTCCAGATGAAGTAAAAACAGATCAGCAAGTTTTAACATTTTTTAAAGACTGGAAACCTAAAAACTCAATCGGTGAATATCGACAATATTCAAACCCAAGCATTGGTTTATTTGGAAAAGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAGAACTATTTTTCCAGAGCTTGGCTTAAAATATAGTTATGTAAATGTGCCTAAAACTCAGATACAAAACTATGCATTTGGTTATAACCAAGAAAATCAGCCGATTCGAGTTAATCCTGGTCCACTCGATGCACCAGCATACGGCGTTAAATCTACCTTACCTGATATGCTTAAGTTTATTAATGCCAACCTAAACCCACAAAAATATCCAGCAGATATTCAACGGGCAATTAATGAAACACATCAAGGGTTCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCAACGGTTTCGGAACATATGTGGTCTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCGTATGCAGTTTTAAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006339","ARO_id":"44801","ARO_name":"ADC-167","CARD_short_name":"ADC-167","ARO_description":"ADC-167 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3870":{"model_id":"3870","model_name":"PDC-61","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"6194":{"protein_sequence":{"accession":"AIG19998.1","sequence":"MRDTRFPCLCGIAASTLLFATTSAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALTQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQTLEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"KJ949076.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCTCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGACCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGTTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCACTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGACGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005144","ARO_id":"43361","ARO_name":"PDC-61","CARD_short_name":"PDC-61","ARO_description":"PDC-61 is an ambler class C beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3871":{"model_id":"3871","model_name":"PDC-45","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"6195":{"protein_sequence":{"accession":"AIG19982.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"KJ949060.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAACTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005145","ARO_id":"43362","ARO_name":"PDC-45","CARD_short_name":"PDC-45","ARO_description":"PDC-45 is an ambler class C beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3872":{"model_id":"3872","model_name":"PDC-49","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"6196":{"protein_sequence":{"accession":"AIG19986.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTYLDVPEAALAQYAQGYGKDDRPLRAGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"KJ949064.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCACGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCTACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGCCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCACTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005146","ARO_id":"43363","ARO_name":"PDC-49","CARD_short_name":"PDC-49","ARO_description":"PDC-49 is an ambler class C beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3873":{"model_id":"3873","model_name":"PDC-50","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"6197":{"protein_sequence":{"accession":"AIG19987.1","sequence":"MRNTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRAGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"KJ949065.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCAATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCACGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGCCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCACTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005147","ARO_id":"43364","ARO_name":"PDC-50","CARD_short_name":"PDC-50","ARO_description":"PDC-50 is an ambler class C beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3874":{"model_id":"3874","model_name":"PDC-48","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"6198":{"protein_sequence":{"accession":"AIG19985.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPIAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"KJ949063.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCAGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGTCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCATTGCCGAGCGGGTGAAGATCGCCTATGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005148","ARO_id":"43365","ARO_name":"PDC-48","CARD_short_name":"PDC-48","ARO_description":"PDC-48 is an ambler class C beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3875":{"model_id":"3875","model_name":"PAC-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"6199":{"protein_sequence":{"accession":"APM84516.1","sequence":"MRCNKNVLSVVLLGALSLSAGNAFGQVSQADVDAVIRPLMSKYKIPGMAVALSVDGQHTFYNYGVASKATGQAVTPTTLFEIGSLSKTFTATLASYAQGQGKLQWSDQASHYLPSLKGSAFDRVTLLNLATHTSGMPLFVPDEVTNQEQLMAWYQAWQPTAPIGSQRVYSNLGIGMLGLITAQSLQKPFSEAMEQDLLAPLGMKHSWVKVPENQMAEYAQGYNKLDEPVRVTPGPPDAEAYGLKSSSADLLRWLDLNMAITPPSPAWQQAITETHKGYYQTGEFTQALIWEYYPWPTTKETLLAGNSSERIMKGLGAKPLTPPQAGPEQAWYNKTGSTNGFSTYAVFIPGQKTALILLANKWYPNDARIEAAYELVQRLKK"},"dna_sequence":{"accession":"KY285014.1","fmin":"345","fmax":"1491","strand":"+","sequence":"ATGCGGTGTAACAAGAATGTTTTATCTGTGGTTCTGTTGGGCGCGCTGAGCCTCTCGGCGGGCAACGCCTTCGGTCAAGTATCACAAGCCGATGTCGATGCCGTCATCCGCCCCCTGATGAGCAAATATAAGATACCGGGAATGGCCGTGGCCCTCTCGGTGGATGGCCAACACACCTTTTACAACTACGGCGTGGCCTCCAAGGCGACAGGCCAGGCTGTCACCCCCACCACGCTCTTTGAGATCGGCTCCCTGAGCAAGACCTTCACCGCCACTCTGGCCAGCTATGCCCAGGGCCAGGGCAAATTGCAGTGGAGCGACCAGGCCAGCCACTATCTCCCCAGCCTCAAGGGGAGCGCCTTCGATCGGGTCACACTGCTCAATCTGGCCACCCACACCTCGGGCATGCCCCTCTTCGTCCCCGATGAAGTGACCAACCAGGAGCAGCTGATGGCCTGGTACCAGGCTTGGCAGCCGACAGCCCCCATAGGCAGCCAGCGGGTCTACTCCAACCTGGGGATCGGCATGCTGGGGTTGATCACGGCACAGAGCTTACAGAAACCCTTCAGTGAGGCGATGGAGCAGGATCTGCTCGCACCACTGGGCATGAAACACTCCTGGGTCAAGGTGCCGGAAAACCAGATGGCCGAGTATGCCCAGGGCTACAACAAACTGGATGAGCCGGTGCGCGTCACGCCGGGCCCTCCGGATGCAGAAGCCTATGGTTTGAAGTCCAGCAGTGCCGACCTGCTGCGCTGGCTCGATCTCAACATGGCCATCACGCCCCCGTCGCCCGCTTGGCAGCAGGCCATAACGGAGACCCACAAAGGGTATTACCAGACCGGGGAGTTTACCCAAGCCCTGATATGGGAGTACTACCCCTGGCCCACGACCAAAGAAACGTTGCTGGCGGGCAACAGCAGCGAGCGGATCATGAAGGGCCTGGGCGCCAAGCCCCTCACCCCACCCCAAGCAGGGCCAGAGCAGGCCTGGTATAACAAGACCGGCTCCACCAACGGCTTCTCCACCTATGCCGTGTTTATCCCGGGGCAAAAAACCGCACTCATACTGCTGGCCAACAAATGGTATCCGAACGATGCCCGTATCGAAGCGGCATATGAGCTGGTACAACGACTGAAAAAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005150","ARO_id":"43367","ARO_name":"PAC-1","CARD_short_name":"PAC-1","ARO_description":"PAC-1 is an ambler class C beta-lactamase from the PAC beta-lactamase family. It is found in Pseudomonas aeruginosa.","ARO_category":{"43366":{"category_aro_accession":"3005149","category_aro_cvterm_id":"43366","category_aro_name":"PAC beta-lactamase","category_aro_description":"PAC beta-lactamase is an inhibitior-resistant cephalosporin-hydrolyzing class C beta-lactamase.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3876":{"model_id":"3876","model_name":"PDC-53","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"6200":{"protein_sequence":{"accession":"AIG19990.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTNAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"KJ949068.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAACGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005151","ARO_id":"43368","ARO_name":"PDC-53","CARD_short_name":"PDC-53","ARO_description":"PDC-53 is an ambler class C beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3877":{"model_id":"3877","model_name":"PDC-72","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"6201":{"protein_sequence":{"accession":"AIG20009.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPRRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"KJ949087.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCGACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005152","ARO_id":"43369","ARO_name":"PDC-72","CARD_short_name":"PDC-72","ARO_description":"PDC-72 is an ambler class C beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3878":{"model_id":"3878","model_name":"PDC-69","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"6202":{"protein_sequence":{"accession":"AIG20006.1","sequence":"MRDTRFPCLCGIAASTLLFAATPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLLEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"KJ949084.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCGCCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCATTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCCTGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCTAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTATGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005153","ARO_id":"43370","ARO_name":"PDC-69","CARD_short_name":"PDC-69","ARO_description":"PDC-69 is an ambler class C beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3991":{"model_id":"3991","model_name":"TEM-228","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6355":{"protein_sequence":{"accession":"WP_164461302.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPATMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"NG_068038.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAACAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36806","NCBI_taxonomy_name":"Neisseria gonorrhoeae","NCBI_taxonomy_id":"485"}}}},"ARO_accession":"3005259","ARO_id":"43615","ARO_name":"TEM-228","CARD_short_name":"TEM-228","ARO_description":"TEM-228 is a beta lactamase.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3880":{"model_id":"3880","model_name":"PDC-23","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"6204":{"protein_sequence":{"accession":"CBZ41773.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDRAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPITLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"FR822747.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCGGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCCGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCACCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005155","ARO_id":"43372","ARO_name":"PDC-23","CARD_short_name":"PDC-23","ARO_description":"PDC-23 is an ambler class C beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3881":{"model_id":"3881","model_name":"PDC-28","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"6206":{"protein_sequence":{"accession":"AEM44533.1","sequence":"MRDTRFPCLCGIAASTLLLATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"JF326298.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGCTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAACTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005156","ARO_id":"43373","ARO_name":"PDC-28","CARD_short_name":"PDC-28","ARO_description":"PDC-28 is an ambler class C beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3882":{"model_id":"3882","model_name":"PDC-41","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"6207":{"protein_sequence":{"accession":"AIG19978.1","sequence":"MRHATILNLCGLAASTLFFATTSAFATEAPAERLKALVDAAVQPVMKANDIPGLAVAITLKGEPHYFSYGVASKEDARKVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASRHWPALQGSRFDGISLLDLGTYTAGGLPLQFPDAVQKDPAQIRDYYRQWQPTYAPGSHRQYSNPSIGLFGYLAARSLGQPFERSMERQLFPALGLEHTFIRVPAAQQGLYAQGYGKDDHPLRVGPGPLDAEAYGLKSSAADLLRFVEANLHPERLEKPWAQALDATHRGYYKVGDMTQGLGWEAYDWPIDLKRLQAGNSAPMALQAHKVARLPAPQALDGQRLLNKTGSTNGFGAYLAFIPGRDVGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLVR"},"dna_sequence":{"accession":"KJ949056.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCCATGCGACAATCCTCAACCTGTGCGGCCTCGCCGCTTCCACCCTGTTCTTCGCGACAACATCGGCCTTCGCCACGGAGGCGCCGGCGGAGCGCCTGAAGGCTCTGGTGGACGCCGCCGTGCAACCGGTCATGAAGGCCAATGATATCCCGGGACTGGCCGTCGCCATCACTCTCAAGGGCGAACCGCATTACTTCAGTTATGGGGTGGCCTCGAAGGAGGACGCCCGCAAGGTGACCCCCGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTACGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCGGCACTGGCCCGCCCTGCAGGGCAGCCGCTTCGACGGTATCAGCCTGCTCGACCTCGGCACCTACACCGCTGGCGGCCTGCCGCTACAGTTCCCCGATGCGGTGCAGAAGGATCCGGCGCAGATCCGCGACTATTACCGCCAGTGGCAACCGACCTACGCCCCGGGCAGCCACCGCCAGTACTCCAACCCGAGCATCGGTCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCATTCGAGCGCAGCATGGAACGGCAGCTGTTCCCGGCGCTCGGCCTGGAGCACACCTTTATCCGGGTGCCCGCCGCGCAGCAGGGGCTGTACGCCCAGGGCTACGGCAAGGACGACCACCCGCTGCGGGTCGGACCCGGTCCGCTGGACGCCGAGGCCTACGGGCTGAAGTCCAGCGCTGCGGACCTGCTGCGCTTCGTCGAGGCCAACCTGCACCCCGAGCGCCTGGAGAAGCCCTGGGCGCAGGCCCTCGACGCCACCCATCGCGGCTACTACAAGGTGGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGATTGGCCGATCGACCTGAAGCGCCTGCAGGCGGGCAACTCGGCGCCGATGGCGCTGCAGGCGCACAAGGTCGCCAGGTTGCCGGCGCCGCAAGCCCTGGACGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGTTTCGGCGCCTACCTGGCGTTCATCCCGGGACGCGACGTCGGCCTGGTGATCCTGGCCAATCGCAACTACCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAACAGCAGGCCAAGGTACCGCTGGTGCGTTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005157","ARO_id":"43374","ARO_name":"PDC-41","CARD_short_name":"PDC-41","ARO_description":"PDC-41 is an ambler class C beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3883":{"model_id":"3883","model_name":"OXA-668","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"580"}},"model_sequences":{"sequence":{"6209":{"protein_sequence":{"accession":"KEC85091.1","sequence":"MSNYRFKSKIKSSVLIILSSVAFSGCVSNANLHDPASSQRTSEIPLLFNYAQTQAVFVTYDGTQFKRYGNDLNRAKTAYIPASTFKMLNALIGLQHAKATNTEVFKWNGEKRSFPAWEKDMTLAQAMQASAVPVYQELARRIGLDLMSKEVKRVGFGNTQIGQQVDNFWLVGPLKITPEQEAKFAYQLAKKTLPFDDAVQQQVKDMLYVERRGDSKLYAKSGWGMDVEPQVGWYTGWVEQPNGQITAFALNMHMQTGDDPAERKQLTLSILDKLGLFFYLR"},"dna_sequence":{"accession":"JICM01000013.1","fmin":"60812","fmax":"61658","strand":"-","sequence":"ATGAGTAATTACCGATTTAAATCTAAAATAAAAAGCAGTGTATTGATCATTCTGAGTAGTGTGGCATTTTCAGGTTGTGTTTCTAATGCCAATTTGCATGATCCAGCGTCATCACAAAGAACAAGTGAAATCCCGTTGTTGTTTAATTATGCGCAAACTCAAGCCGTCTTTGTGACTTATGATGGAACTCAATTTAAACGTTATGGGAATGATTTAAATAGAGCCAAGACTGCCTATATTCCAGCCTCTACTTTTAAAATGTTGAATGCCTTAATTGGTTTGCAACATGCGAAAGCGACGAATACAGAAGTATTTAAGTGGAATGGAGAAAAAAGATCTTTTCCTGCATGGGAAAAAGATATGACCTTGGCACAAGCAATGCAGGCTTCAGCCGTACCTGTATATCAGGAGTTGGCACGACGTATTGGCTTGGATTTGATGAGTAAAGAAGTCAAGCGTGTTGGTTTTGGCAATACACAAATTGGTCAACAGGTAGATAATTTCTGGCTAGTCGGCCCATTGAAAATTACCCCAGAGCAAGAAGCTAAATTTGCTTATCAATTGGCAAAGAAAACATTGCCTTTTGATGATGCTGTACAGCAACAAGTTAAAGATATGCTCTATGTCGAAAGACGGGGTGATTCCAAGCTTTATGCCAAAAGTGGATGGGGAATGGATGTGGAGCCACAAGTGGGTTGGTATACGGGATGGGTGGAACAGCCGAATGGTCAGATCACCGCTTTTGCTTTAAATATGCACATGCAGACAGGGGATGATCCTGCTGAACGCAAGCAACTGACATTAAGTATCTTGGATAAATTAGGCTTATTCTTTTATTTGAGATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43376","NCBI_taxonomy_name":"Acinetobacter sp. ETR1","NCBI_taxonomy_id":"1485002"}}}},"ARO_accession":"3005158","ARO_id":"43375","ARO_name":"OXA-668","CARD_short_name":"OXA-668","ARO_description":"OXA-668 is a class D beta-lactamase from the OXA-274 family of OXA beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46502":{"category_aro_accession":"3007713","category_aro_cvterm_id":"46502","category_aro_name":"OXA-274-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-274.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3884":{"model_id":"3884","model_name":"OXA-818","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"560"}},"model_sequences":{"sequence":{"6210":{"protein_sequence":{"accession":"QBQ03043.1","sequence":"MNKYFTCYVVASLFLSGCTVQHNLINETQSQIVQGHNQVIHQYFDEKNTSGVLVIQADKKINLYGNALSRANTEYVPASTFKMLNALIGLENQKTDINEIFKWKGEKRSFTGWEKDMTLGEAMKLSAVPVYQELARRIGLDLMQKEVKRIGFGNAEIGQQVDNFWLVGPLKVTPIQEVEFVSQLAHTQLPFSEKVQANVKNMLLLEESNGYKIFGKTGWAMDIKPQVGWLTGWVEQPDGKIVAFALNMEMRSEMPASIRNELLMKSLKQLNII"},"dna_sequence":{"accession":"MK645930.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGAATAAATATTTTACTTGCTATGTGGTTGCTTCTCTTTTTCTTTCTGGTTGTACGGTTCAGCATAATTTAATAAATGAAACCCAGAGTCAGATTGTTCAAGGACATAATCAGGTGATTCATCAATACTTTGATGAAAAAAACACCTCAGGTGTGCTGGTTATTCAAGCAGATAAAAAAATTAATCTGTATGGTAATGCTCTAAGCCGCGCAAATACAGAATATGTGCCAGCCTCTACATTTAAAATGTTGAATGCCCTGATCGGATTGGAGAACCAGAAAACGGATATTAATGAAATATTTAAATGGAAGGGCGAGAAAAGGTCATTTACCGGTTGGGAAAAAGACATGACACTAGGAGAAGCCATGAAGCTTTCCGCAGTCCCAGTCTATCAGGAACTTGCGCGACGTATCGGTCTTGATCTCATGCAAAAAGAAGTAAAACGTATTGGTTTCGGTAATGCTGAAATTGGACAGCAGGTTGATAATTTCTGGTTGGTAGGGCCATTAAAGGTTACGCCTATTCAAGAGGTAGAGTTTGTTTCTCAATTGGCGCATACACAGCTTCCATTTAGTGAAAAAGTGCAGGCTAATGTAAAAAATATGCTTCTTTTAGAAGAGAGTAATGGCTACAAAATTTTTGGAAAGACCGGTTGGGCAATGGATATAAAACCACAAGTGGGCTGGTTGACCGGCTGGGTTGAGCAGCCAGATGGAAAAATTGTCGCTTTTGCATTAAATATGGAAATGCGGTCAGAAATGCCTGCATCTATACGTAATGAATTATTGATGAAATCATTAAAACAGCTGAATATTATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39672","NCBI_taxonomy_name":"Acinetobacter radioresistens","NCBI_taxonomy_id":"40216"}}}},"ARO_accession":"3005159","ARO_id":"43377","ARO_name":"OXA-818","CARD_short_name":"OXA-818","ARO_description":"OXA-818 is a class D beta-lactamase from the OXA-23 family of OXA beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46499":{"category_aro_accession":"3007710","category_aro_cvterm_id":"46499","category_aro_name":"OXA-23-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases, specifically imipenem, derived from OXA-23, first identified in Acinetobacter baumannii.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3885":{"model_id":"3885","model_name":"OXA-812","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"560"}},"model_sequences":{"sequence":{"6211":{"protein_sequence":{"accession":"QBQ03037.1","sequence":"MNKYFTCYVVASLFLSGCTVQHNLINETQSEIVQGHNQVIHQYFDEKNTSGVLVIQTDKKINLYGNALSRANTEYVPASTFKMLNALIGLENQKTDINEIFKWKGEKRSFIAWEKDMTLGEAMKLSAVPVYQELARRIGLDLMQKEVERIDFGNTEIGQQVDNFWLVGPLKVTPIQEVEFVSQLAHTQLPFSEKVQANVKNMLLLEESNGYKIFGKTGWAMDIKPQVGWLTGWVEQPDGKIVAFALNMEMRSEMPASIRNELLMKSLKQLNII"},"dna_sequence":{"accession":"MK645924.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGAATAAATATTTTACTTGCTATGTGGTTGCTTCTCTTTTTCTTTCTGGTTGTACGGTTCAGCATAATTTAATAAATGAAACCCAGAGTGAGATTGTTCAAGGACATAATCAGGTGATTCATCAATACTTTGATGAAAAAAACACCTCAGGTGTGCTGGTTATTCAAACAGATAAAAAAATTAATCTGTATGGTAATGCTCTAAGCCGTGCAAATACAGAATATGTGCCAGCCTCTACATTTAAAATGTTGAATGCCCTGATCGGATTGGAGAACCAGAAAACGGATATTAATGAAATATTTAAATGGAAGGGCGAGAAAAGGTCATTTATCGCTTGGGAAAAAGACATGACACTAGGAGAAGCCATGAAGCTTTCCGCAGTCCCAGTCTATCAAGAACTTGCAAGACGTATTGGTCTTGATCTCATGCAAAAAGAAGTAGAACGTATTGATTTCGGTAATACTGAAATTGGACAGCAGGTTGATAATTTCTGGTTGGTAGGGCCATTAAAGGTTACGCCTATTCAAGAGGTAGAGTTTGTTTCTCAATTGGCGCATACACAGCTTCCATTTAGTGAAAAAGTGCAGGCTAATGTAAAAAATATGCTTCTTTTAGAAGAGAGTAATGGCTACAAAATTTTTGGAAAGACTGGTTGGGCAATGGATATAAAACCACAAGTGGGCTGGTTGACCGGCTGGGTTGAGCAGCCAGATGGAAAAATTGTCGCTTTTGCATTAAATATGGAAATGCGGTCAGAAATGCCGGCATCTATACGTAATGAATTATTGATGAAATCATTAAAACAGCTGAATATTATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39672","NCBI_taxonomy_name":"Acinetobacter radioresistens","NCBI_taxonomy_id":"40216"}}}},"ARO_accession":"3005160","ARO_id":"43378","ARO_name":"OXA-812","CARD_short_name":"OXA-812","ARO_description":"OXA-812 is a class D beta-lactamase from the OXA-23 family of OXA beta-lactamases.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46499":{"category_aro_accession":"3007710","category_aro_cvterm_id":"46499","category_aro_name":"OXA-23-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases, specifically imipenem, derived from OXA-23, first identified in Acinetobacter baumannii.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4009":{"model_id":"4009","model_name":"PDC-105","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"6373":{"protein_sequence":{"accession":"WP_063864562.1","sequence":"MRDTRFSCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQTQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_049872.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCTCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGACACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATTCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005277","ARO_id":"43634","ARO_name":"PDC-105","CARD_short_name":"PDC-105","ARO_description":"PDC-105 is a class C beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3276":{"model_id":"3276","model_name":"Staphylococcus aureus LmrS","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"5623":{"protein_sequence":{"accession":"AAW38464.1","sequence":"MAKVELTTRRRNFIVAVMLISAFVAILNQTLLNTALPSIMRELNINESTSQWLVTGFMLVNGVMIPLTAYLMDRIKTRPLYLAAMGTFLLGSIVAALAPNFGVLMLARVIQAMGAGVLMPLMQFTLFTLFSKEHRGFAMGLAGLVIQFAPAIGPTVTGLIIDQASWRVPFIIIVGIAILAFVFGLVSISSYNEVKYTKLDKRSVMYSTIGFGLMLYAFSSAGDLGFTSPIVIGALILSMVIIYLFIRRQFNITNALLNLRVFKNRTFALCTISSMIIMMSMVGPALLIPLYVQNSLSLSALLSGLVIMPGAIINGIMSVFTGKFYDKYGPRPLIYTGFTILTITTIMLCFLHTDTSYTYLIVVYAIRMFSVSLLMMPINTTGINSLRNEEISHGTAIMNFGRVMAGSLGTALMVTLMSFGAKIFLSTSPSHLTATEIKQQSIAIGVDISFAFVAVLVMAAYVIALFIREPKEIESNRRKF"},"dna_sequence":{"accession":"CP000046.1","fmin":"2235374","fmax":"2236817","strand":"-","sequence":"ATGGCTAAAGTTGAATTAACAACCCGGAGACGAAACTTCATAGTTGCTGTTATGTTGATTAGTGCGTTTGTAGCTATTTTAAATCAAACATTATTAAATACAGCGTTACCTAGTATAATGAGAGAATTAAATATCAATGAAAGTACATCGCAATGGCTAGTTACTGGGTTTATGCTTGTTAATGGCGTCATGATACCTCTGACGGCATATCTAATGGATAGAATTAAAACTAGACCTTTATACTTAGCGGCGATGGGGACATTTTTATTAGGTTCTATTGTTGCAGCCTTAGCTCCGAATTTTGGAGTTTTAATGTTAGCTCGTGTAATTCAAGCGATGGGTGCAGGCGTACTTATGCCCTTAATGCAATTTACGTTATTTACATTGTTCAGTAAAGAACATCGAGGTTTTGCAATGGGACTAGCAGGTTTAGTAATTCAATTTGCACCAGCAATAGGACCTACAGTTACAGGATTAATTATTGATCAAGCGAGTTGGCGAGTTCCATTTATTATAATTGTAGGAATTGCTATACTTGCCTTTGTTTTCGGTTTGGTTTCAATCTCGAGTTACAATGAAGTGAAATATACGAAATTAGATAAGCGTTCAGTAATGTATTCAACTATTGGGTTCGGGTTAATGCTATACGCATTTAGTAGTGCAGGAGATTTAGGATTTACAAGTCCAATAGTAATAGGTGCGTTGATATTAAGTATGGTTATTATCTATTTATTTATACGTAGACAATTTAATATTACTAATGCACTTTTAAATTTAAGGGTTTTTAAAAATAGAACATTTGCATTATGTACGATTAGTTCAATGATTATAATGATGTCAATGGTTGGACCTGCGCTGCTTATACCGCTATATGTTCAAAACAGTTTATCTTTATCTGCCTTGTTATCAGGACTTGTTATCATGCCTGGTGCAATAATAAATGGTATTATGTCAGTTTTTACAGGTAAATTTTATGATAAGTATGGTCCTAGACCATTGATTTATACTGGTTTTACAATTTTAACAATTACTACAATTATGTTGTGTTTCTTGCATACAGACACATCTTATACGTATTTAATAGTCGTATATGCAATTAGAATGTTTTCAGTTTCTTTACTCATGATGCCGATAAATACTACAGGAATTAATTCTTTGAGAAATGAAGAAATCTCACATGGCACGGCTATTATGAACTTTGGTCGTGTAATGGCTGGTTCACTAGGCACAGCTTTAATGGTTACATTAATGAGTTTTGGTGCAAAAATATTTTTATCTACATCGCCATCGCATTTAACTGCAACTGAAATTAAACAGCAATCCATTGCTATAGGGGTGGATATCTCATTTGCTTTTGTAGCTGTGCTTGTTATGGCAGCTTATGTGATAGCACTTTTTATAAGAGAACCTAAAGAAATAGAAAGTAATAGAAGGAAATTTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35512","NCBI_taxonomy_name":"Staphylococcus aureus subsp. aureus COL","NCBI_taxonomy_id":"93062"}}}},"ARO_accession":"3004572","ARO_id":"42486","ARO_name":"Staphylococcus aureus LmrS","CARD_short_name":"Saur_LmrS","ARO_description":"MFS transporters are secondary active transporters with single-polypeptide chains containing 400-600 amino acids that transport small solutes across the membrane by using electrochemical gradients. LmrS has 14 transmembrane helices and, when expressed in E. coli, is capable of extruding a variety of antibiotics inclinding linezolid, trimethoprim, florfenicol, chlorampheniocol, erythromycin, streptomycin, kanamycin, and fusidic acid.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35989":{"category_aro_accession":"0000072","category_aro_cvterm_id":"35989","category_aro_name":"linezolid","category_aro_description":"Linezolid is a synthetic antibiotic used for the treatment of serious infections caused by Gram-positive bacteria that are resistant to several other antibiotics. It inhibits protein synthesis by binding to domain V of the 23S rRNA of the 50S subunit of bacterial ribosomes.","category_aro_class_name":"Antibiotic"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36600":{"category_aro_accession":"3000461","category_aro_cvterm_id":"36600","category_aro_name":"florfenicol","category_aro_description":"Florfenicol is a fluorine derivative of chloramphenicol, where the nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3) and the hydroxyl group (-OH), by a fluorine group (-F). The action mechanism is the same as chloramphenicol's, where the antibiotic binds to the 23S RNA of the 50S subunit of bacterial ribosomes to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36218":{"category_aro_accession":"3000079","category_aro_cvterm_id":"36218","category_aro_name":"oxazolidinone antibiotic","category_aro_description":"Oxazolidinones are a class of synthetic antibiotics discovered the the 1980's.  They inhibit protein synthesis by binding to domain V of the 23S rRNA of the 50S subunit of bacterial ribosomes.  Linezolid is the only member of this class currently in clinical use.","category_aro_class_name":"Drug Class"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"3886":{"model_id":"3886","model_name":"FosA7.5","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"280"}},"model_sequences":{"sequence":{"6213":{"protein_sequence":{"accession":"ANQ03635.1","sequence":"MLQSLNHLTLAVSNLQSSLTFWRDLLGLQLHAEWGTGAYLTCGDLWLCLSYDVSRSYVAPQKSDYTHYAFSIAPEDFEPFSYKLKQSGVTVWKDNKSEGQSFYFLDPDGHKLELHVGDLASRLAQCRERPYSGMRFGPGK"},"dna_sequence":{"accession":"CP015912.1","fmin":"3480172","fmax":"3480595","strand":"+","sequence":"ATGCTTCAATCTCTGAACCACTTAACGCTTGCTGTCAGTAATTTGCAAAGTAGCCTGACATTCTGGCGCGATTTGCTGGGGTTGCAGTTACATGCTGAGTGGGGTACAGGTGCTTACCTTACCTGTGGTGACCTTTGGCTCTGTCTTTCTTATGACGTATCCCGTAGCTACGTGGCCCCACAGAAAAGTGACTATACCCATTACGCATTCAGCATTGCGCCAGAAGATTTTGAGCCGTTCTCATATAAGCTGAAACAGTCGGGAGTGACGGTCTGGAAAGACAATAAAAGCGAAGGGCAATCTTTCTATTTTCTTGACCCGGATGGCCACAAGCTGGAGCTGCATGTGGGAGATTTAGCATCTCGACTGGCGCAGTGCCGGGAGAGGCCTTACTCTGGAATGCGTTTTGGTCCTGGTAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3005162","ARO_id":"43514","ARO_name":"FosA7.5","CARD_short_name":"FosA7.5","ARO_description":"FosA7.5 is a variant of the FosA7 gene. This gene is unique from FosA7 in that it is found in Escherichia coli as opposed to Salmonella enterica. It confers resistance to fosfomycin.","ARO_category":{"36272":{"category_aro_accession":"3000133","category_aro_cvterm_id":"36272","category_aro_name":"fosfomycin thiol transferase","category_aro_description":"Catalyzes the addition of a thiol group from a nucleophilic molecule to fosfomycin.","category_aro_class_name":"AMR Gene Family"},"35944":{"category_aro_accession":"0000025","category_aro_cvterm_id":"35944","category_aro_name":"fosfomycin","category_aro_description":"Fosfomycin (also known as phosphomycin and phosphonomycin) is a broad-spectrum antibiotic produced by certain Streptomyces species. It is effective on gram positive and negative bacteria as it targets the cell wall, an essential feature shared by both bacteria. Its specific target is MurA (MurZ in E.coli), which attaches phosphoenolpyruvate (PEP) to UDP-N-acetylglucosamine, a step of commitment to cell wall synthesis. In the active site of MurA, the active cysteine molecule is alkylated which stops the catalytic reaction.","category_aro_class_name":"Antibiotic"},"45731":{"category_aro_accession":"3007149","category_aro_cvterm_id":"45731","category_aro_name":"phosphonic acid antibiotic","category_aro_description":"A group of antibiotics derived from phosphonic acids.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3887":{"model_id":"3887","model_name":"dfrA35","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"6214":{"protein_sequence":{"accession":"ASF80997.1","sequence":"MISIVVAKSANHVIGVDNQLPWRLPSDLKWFKETTTGGVVVMGRKTFESIGKPLPDRINVIISKQPVPIEWASKVVWVNSIQQAMDYVRGLDGMIKTFIIGGSEIYRQFISLVDQVYLTEVGAEIEGDATFQPLDEHEWTLKTWWVVPDQSSKDQFRYQRKLYVRKVLDE"},"dna_sequence":{"accession":"KY887596.1","fmin":"137134","fmax":"137647","strand":"+","sequence":"ATGATTTCAATCGTCGTAGCCAAATCCGCCAATCACGTCATCGGGGTAGACAATCAATTACCGTGGCGATTGCCGTCCGATCTGAAGTGGTTTAAAGAAACGACCACTGGTGGGGTAGTTGTTATGGGACGCAAGACATTTGAATCCATCGGTAAGCCATTGCCGGATCGAATCAATGTGATCATTTCTAAACAACCAGTGCCGATCGAATGGGCAAGTAAGGTAGTTTGGGTTAACTCGATCCAGCAAGCGATGGACTATGTTCGCGGTCTGGATGGGATGATCAAAACATTTATTATTGGCGGGAGTGAGATTTATCGCCAATTTATCTCATTGGTCGATCAGGTGTATCTTACCGAAGTAGGTGCCGAAATAGAAGGCGACGCGACGTTTCAGCCGTTAGACGAACATGAATGGACGCTCAAAACTTGGTGGGTGGTTCCAGACCAATCATCCAAAGATCAATTCCGTTACCAACGTAAGCTCTACGTGAGGAAGGTGTTAGATGAATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3005164","ARO_id":"43516","ARO_name":"dfrA35","CARD_short_name":"dfrA35","ARO_description":"dfrA35 is a trimethoprim resistant dihydrofolate reductase gene found in the lncC plasmid pEc158 from E.coli.","ARO_category":{"37617":{"category_aro_accession":"3001218","category_aro_cvterm_id":"37617","category_aro_name":"trimethoprim resistant dihydrofolate reductase dfr","category_aro_description":"Alternative dihydropteroate synthase dfr present on plasmids produces alternate proteins that are less sensitive to trimethoprim from inhibiting its role in folate synthesis, thus conferring trimethoprim resistance.","category_aro_class_name":"AMR Gene Family"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3890":{"model_id":"3890","model_name":"CMY-134","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"775"}},"model_sequences":{"sequence":{"8392":{"protein_sequence":{"accession":"AKA60779.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRFYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"KP860987.1","fmin":"10","fmax":"1156","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGATTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3003654","ARO_id":"40264","ARO_name":"CMY-134","CARD_short_name":"CMY-134","ARO_description":"CMY-134 is a beta-lactamase found in Escherichia coli. It confers resistance to cephamycin.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3891":{"model_id":"3891","model_name":"CMY-143","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6252":{"protein_sequence":{"accession":"WP_071593223.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFDALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"NG_052047.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGACGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3005204","ARO_id":"43560","ARO_name":"CMY-143","CARD_short_name":"CMY-143","ARO_description":"CMY-143 is a beta-lactamase found in Escherichia coli. It confers resistance to cephamycin.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3892":{"model_id":"3892","model_name":"CMY-107","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"775"}},"model_sequences":{"sequence":{"8387":{"protein_sequence":{"accession":"WP_032494240.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDCAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"KR061886.1","fmin":"851","fmax":"1997","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTGTGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002119","ARO_id":"38519","ARO_name":"CMY-107","CARD_short_name":"CMY-107","ARO_description":"CMY-107 is a beta-lactamase found in Escherichia coli. It confers resistance to cephamycin.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3893":{"model_id":"3893","model_name":"CMY-158","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"775"}},"model_sequences":{"sequence":{"6254":{"protein_sequence":{"accession":"WP_122630836.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAMGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"NG_062242.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCATGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3005176","ARO_id":"43529","ARO_name":"CMY-158","CARD_short_name":"CMY-158","ARO_description":"CMY-158 is a beta-lactamase found in Escherichia coli. It confers resistance to cephamycin.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3894":{"model_id":"3894","model_name":"CMY-173","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"775"}},"model_sequences":{"sequence":{"6255":{"protein_sequence":{"accession":"WP_190259774.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYARGYREGKPVHSSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"NG_070783.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCAGGGGCTATCGCGAAGGGAAGCCCGTACACAGTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3005177","ARO_id":"43530","ARO_name":"CMY-173","CARD_short_name":"CMY-173","ARO_description":"CMY-173 is a beta-lactamase found in Escherichia coli. It confers resistance to cephamycin.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3896":{"model_id":"3896","model_name":"CMY-147","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6257":{"protein_sequence":{"accession":"WP_077767289.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHSSPGQLDAAAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"NG_052898.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACAGTTCTCCGGGACAACTTGACGCCGCAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3005180","ARO_id":"43533","ARO_name":"CMY-147","CARD_short_name":"CMY-147","ARO_description":"CMY-147 is a beta-lactamase found in Escherichia coli. It confers resistance to cephamycin.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3897":{"model_id":"3897","model_name":"CMY-146","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6258":{"protein_sequence":{"accession":"WP_075985683.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHSSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDNKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"NG_052648.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACAGTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAACAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3005181","ARO_id":"43534","ARO_name":"CMY-146","CARD_short_name":"CMY-146","ARO_description":"CMY-146 is a beta-lactamase found in Escherichia coli. It confers resistance to cephamycin.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3898":{"model_id":"3898","model_name":"CMY-156","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6259":{"protein_sequence":{"accession":"WP_104009849.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHSSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVAFAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"NG_056410.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACAGTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTCGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3005182","ARO_id":"43535","ARO_name":"CMY-156","CARD_short_name":"CMY-156","ARO_description":"CMY-156 is a beta-lactamase found in Escherichia coli. It confers resistance to cephamycin.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3899":{"model_id":"3899","model_name":"CMY-160","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6260":{"protein_sequence":{"accession":"WP_109791215.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHSSPGQLDAGAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"NG_057614.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACAGTTCTCCGGGACAACTTGACGCCGGAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3005183","ARO_id":"43536","ARO_name":"CMY-160","CARD_short_name":"CMY-160","ARO_description":"CMY-160 is a beta-lactamase found in Escherichia coli. It confers resistance to cephamycin.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3900":{"model_id":"3900","model_name":"CMY-162","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6261":{"protein_sequence":{"accession":"WP_111273851.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHVSPGQIDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"NG_060523.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAAATTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3005184","ARO_id":"43537","ARO_name":"CMY-162","CARD_short_name":"CMY-162","ARO_description":"CMY-162 is a beta-lactamase found in Escherichia coli. It confers resistance to cephamycin.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3901":{"model_id":"3901","model_name":"CMY-140","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6262":{"protein_sequence":{"accession":"WP_065102238.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDNKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"NG_050943.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAACAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3005185","ARO_id":"43538","ARO_name":"CMY-140","CARD_short_name":"CMY-140","ARO_description":"CMY-140 is a beta-lactamase found in Escherichia coli. It confers resistance to cephamycin.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3902":{"model_id":"3902","model_name":"CMY-164","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6263":{"protein_sequence":{"accession":"WP_140423307.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"NG_065422.1","fmin":"0","fmax":"1149","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3005186","ARO_id":"43539","ARO_name":"CMY-164","CARD_short_name":"CMY-164","ARO_description":"CMY-164 is a beta-lactamase found in Escherichia coli. It confers resistance to cephamycin.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4177":{"model_id":"4177","model_name":"ADC-101","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6552":{"protein_sequence":{"accession":"WP_068981608.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTMFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPKDIQLAINETHQGFYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKSNKVTAISKEPSVKMYHKTGSTSGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_051440.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCGGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACTGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTCCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATGTTTCCGGCTCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGCTGAGTTTTATTCATGCCAACCTCAACCCACAGAAATATCCGAAAGATATTCAACTTGCAATTAATGAAACACATCAAGGGTTCTATCAAGTAAATACCATGTATCAAGCGCTTGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAATCTAATAAAGTGACTGCTATTTCAAAAGAGCCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCAGCGGTTTCGGAACATATGTAGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006281","ARO_id":"44743","ARO_name":"ADC-101","CARD_short_name":"ADC-101","ARO_description":"ADC-101 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3903":{"model_id":"3903","model_name":"CMY-161","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6264":{"protein_sequence":{"accession":"WP_109545065.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRFEAAWRILEKLQ"},"dna_sequence":{"accession":"NG_057479.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTTTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3005187","ARO_id":"43540","ARO_name":"CMY-161","CARD_short_name":"CMY-161","ARO_description":"CMY-161 is a beta-lactamase found in Escherichia coli. It confers resistance to cephamycin.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3904":{"model_id":"3904","model_name":"CMY-165","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6265":{"protein_sequence":{"accession":"WP_148044406.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKEALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"NG_065862.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGAGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3005188","ARO_id":"43541","ARO_name":"CMY-165","CARD_short_name":"CMY-165","ARO_description":"CMY-165 is a beta-lactamase found in Escherichia coli. It confers resistance to cephamycin.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3905":{"model_id":"3905","model_name":"CMY-166","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6266":{"protein_sequence":{"accession":"WP_148044407.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKNYPIPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"NG_065863.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAACTATCCTATCCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3005189","ARO_id":"43542","ARO_name":"CMY-166","CARD_short_name":"CMY-166","ARO_description":"CMY-166 is a beta-lactamase found in Escherichia coli. It confers resistance to cephamycin.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3906":{"model_id":"3906","model_name":"CMY-149","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6267":{"protein_sequence":{"accession":"WP_085562396.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKYYARGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"NG_054682.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAATATTATGCCCGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3005190","ARO_id":"43543","ARO_name":"CMY-149","CARD_short_name":"CMY-149","ARO_description":"CMY-149 is a beta-lactamase found in Proteus mirabilis. It confers resistance to cephamycin.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3907":{"model_id":"3907","model_name":"CMY-139","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6268":{"protein_sequence":{"accession":"WP_063859815.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLTHTWITVPQNEQKDYAWGYREGKPVHSSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPALKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"NG_048807.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGACGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACAGTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCATTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3005191","ARO_id":"43544","ARO_name":"CMY-139","CARD_short_name":"CMY-139","ARO_description":"CMY-139 is a beta-lactamase found in Escherichia coli. It confers resistance to cephamycin.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3908":{"model_id":"3908","model_name":"CMY-148","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6269":{"protein_sequence":{"accession":"WP_085562395.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLTHTWITVPQNEQKDYAWGYREGKPVHSSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"NG_054681.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGACGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACAGTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3005192","ARO_id":"43545","ARO_name":"CMY-148","CARD_short_name":"CMY-148","ARO_description":"CMY-148 is a beta-lactamase found in Escherichia coli. It confers resistance to cephamycin.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3909":{"model_id":"3909","model_name":"CMY-163","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6270":{"protein_sequence":{"accession":"WP_111672906.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLTHTWITVPQNEQKDYAWGYREGKPVHSSPRQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"NG_060564.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGACGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACAGTTCTCCGAGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3005193","ARO_id":"43546","ARO_name":"CMY-163","CARD_short_name":"CMY-163","ARO_description":"CMY-163 is a beta-lactamase found in Escherichia coli. It confers resistance to cephamycin.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3910":{"model_id":"3910","model_name":"CMY-154","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6271":{"protein_sequence":{"accession":"WP_088245213.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGELAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHSSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"NG_055270.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGAGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACAGTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3005194","ARO_id":"43547","ARO_name":"CMY-154","CARD_short_name":"CMY-154","ARO_description":"CMY-154 is a beta-lactamase found in Escherichia coli. It confers resistance to cephamycin.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3911":{"model_id":"3911","model_name":"CMY-142","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6272":{"protein_sequence":{"accession":"WP_070064537.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSISLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"NG_051753.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTAGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3005195","ARO_id":"43548","ARO_name":"CMY-142","CARD_short_name":"CMY-142","ARO_description":"CMY-142 is a beta-lactamase found in Escherichia coli. It confers resistance to cephamycin.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3912":{"model_id":"3912","model_name":"CMY-141","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6273":{"protein_sequence":{"accession":"WP_065644637.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQLPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHSSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"NG_051215.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGCTCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACAGTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3005196","ARO_id":"43549","ARO_name":"CMY-141","CARD_short_name":"CMY-141","ARO_description":"CMY-141 is a beta-lactamase found in Escherichia coli. It confers resistance to cephamycin.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3913":{"model_id":"3913","model_name":"CMY-124","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6274":{"protein_sequence":{"accession":"WP_063859763.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGISLLHLATYTAGGLPLQIPDDVTDKAALLRFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHVTPGQLDAEAYGVKSNVTDMARWIQVNMDASRVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALHTVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"NG_048794.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCATTCTCCACGTTTGCCGCCGCCAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCAGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTACAGATAAAGCCGCATTACTGCGTTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACAGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGTTACTCCTGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAACGTTACCGATATGGCCCGTTGGATTCAGGTCAACATGGACGCCAGCCGCGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGTGACAGCAAAGTGGCATTGGCAGCGCTTCACACCGTTGAGGTAAACCCGCCCGCCCCGGCAGTGAAAGCCTCATGGGTGCATAAAACGGGATCCACTGGTGGATTTGGCAGCTACGTTGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43550","NCBI_taxonomy_name":"Citrobacter freundii complex","NCBI_taxonomy_id":"1344959"}}}},"ARO_accession":"3003132","ARO_id":"39709","ARO_name":"CMY-124","CARD_short_name":"CMY-124","ARO_description":"CMY-124 is a beta-lactamase found in Citrobacter freundii. It confers resistance to cephamycin.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3914":{"model_id":"3914","model_name":"CMY-125","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6275":{"protein_sequence":{"accession":"WP_063859768.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARSEIKLSDPVTKYWPELTGKQWQGISLLHLATYTAGGLPLQIPDDVTDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIISGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"NG_048795.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCAGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCAGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTACGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAGCGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3003133","ARO_id":"39710","ARO_name":"CMY-125","CARD_short_name":"CMY-125","ARO_description":"CMY-125 is a beta-lactamase found in Citrobacter freundii. It confers resistance to cephamycin.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3915":{"model_id":"3915","model_name":"CMY-145","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6276":{"protein_sequence":{"accession":"WP_075985684.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFTGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHSSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"NG_052649.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTACCGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACAGTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3005197","ARO_id":"43551","ARO_name":"CMY-145","CARD_short_name":"CMY-145","ARO_description":"CMY-145 is a beta-lactamase found in Escherichia coli. It confers resistance to cephamycin.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3916":{"model_id":"3916","model_name":"CMY-122","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6277":{"protein_sequence":{"accession":"WP_063859757.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHSVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGISLLHLATYTAGGLPLQIPDDVTDKAALLRFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTKRVLQPLKLAHTWITIPQNEQKDYAWGYREWKPVHVTPGQLDAEAYGVKSSVTDMARWVQVNMDASRVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"NG_048793.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCATTCTCCACGTTTGCCGCCGCCAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACTCAGTCACGCAGCAAACTCTGTTTGAGCTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCAGCCTGCTGCACTTAGCCACCTACACGGCAGGCGGCCTGCCGCTGCAGATCCCCGATGACGTTACGGATAAAGCCGCATTACTGCGTTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGTATGAGCTACGAAGAGGCAATGACCAAACGCGTCCTGCAGCCATTAAAACTGGCGCATACCTGGATTACGATTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAATGGAAGCCCGTACACGTTACTCCTGGACAACTTGATGCCGAAGCCTATGGCGTGAAATCCAGCGTTACCGATATGGCACGCTGGGTTCAGGTCAACATGGACGCCAGCCGCGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAATCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAGGCTGATTCGATCATCAACGGCAGTGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCGGCAGTGAAAGCCTCATGGGTGCATAAAACGGGATCCACTGGTGGATTTGGCAGCTACGTTGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37053","NCBI_taxonomy_name":"Citrobacter","NCBI_taxonomy_id":"544"}}}},"ARO_accession":"3003130","ARO_id":"39707","ARO_name":"CMY-122","CARD_short_name":"CMY-122","ARO_description":"CMY-122 is a beta-lactamase found in Citrobacter freundii. It confers resistance to cephamycin.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3917":{"model_id":"3917","model_name":"CMY-157","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6278":{"protein_sequence":{"accession":"WP_096807446.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNRPITQNTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTRYWPELTGKQWQNISLLHLATYTAGGLPLQIPDEVTDKTALLRFYQNWQPQWAPGAKRLYANSSIGLFGALAVKPSGMSYEGAMIRRVLQPLKLTHTWITVPQNEQRDYAWGYRDGKPVHVSPGQLDAEAYGVKSSIMDMARWVQVNMDASHVQEKTLQQGIGLAQSRYWRIGEMYQGLGWEMLNWPVKADTIINGSDSKIALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFIPEKNLGIVMLANKSYPNPARVDAAWRILEKLQ"},"dna_sequence":{"accession":"NG_055587.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCACTACTGCTGACAGCCTCTTTCTCAACGTTTGCCGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCGGTTATCTACCAGGGAAAACCGTATTACTTTACCTGGGGTAAAGCTGATATCGCCAATAATCGTCCGATTACACAGAACACACTGTTCGAACTCGGTTCAGTCAGTAAGACCTTCAATGGCGTGCTGGGCGGCGATGCTATCGCCCGCGGCGAAATCAAACTCAGCGATCCGGTCACCCGGTACTGGCCGGAACTCACAGGCAAACAGTGGCAGAACATTAGTCTGCTGCACTTAGCCACATACACGGCAGGTGGCCTGCCGCTTCAGATCCCCGACGAGGTGACGGATAAAACCGCATTGCTGCGCTTTTATCAAAACTGGCAACCCCAGTGGGCCCCGGGCGCTAAACGTCTCTATGCTAACTCCAGCATTGGTCTGTTTGGCGCACTGGCGGTGAAACCCTCTGGAATGAGCTACGAAGGGGCGATGATCAGACGCGTCCTGCAGCCATTAAAACTCACTCACACCTGGATTACCGTTCCGCAGAACGAGCAACGAGATTATGCCTGGGGCTATCGCGATGGCAAGCCCGTACATGTTTCGCCGGGCCAGCTTGATGCCGAAGCGTATGGTGTGAAATCCAGCATTATGGATATGGCTCGCTGGGTTCAGGTCAATATGGACGCCAGCCACGTGCAGGAGAAAACCCTGCAGCAGGGCATCGGGCTCGCACAGTCACGTTACTGGCGCATTGGTGAGATGTACCAGGGCTTAGGCTGGGAAATGCTTAACTGGCCGGTAAAAGCAGACACTATTATCAACGGCAGCGACAGTAAAATCGCTCTGGCGGCGCTTCCGGCCGTTGAGGTAAACCCACCTGCCCCCGCAGTAAAAGCCTCCTGGGTACATAAAACAGGTTCGACTGGCGGATTTGGTAGTTATGTGGCTTTTATTCCGGAGAAAAATCTTGGCATCGTGATGCTGGCCAATAAAAGCTACCCGAATCCTGCTCGCGTCGACGCGGCATGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43553","NCBI_taxonomy_name":"Citrobacter sp.","NCBI_taxonomy_id":"1896336"}}}},"ARO_accession":"3005198","ARO_id":"43552","ARO_name":"CMY-157","CARD_short_name":"CMY-157","ARO_description":"CMY-96 is a beta-lactamase found in Citrobacter sp. It confers resistance to cephamycin.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3918":{"model_id":"3918","model_name":"CMY-171","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6279":{"protein_sequence":{"accession":"WP_168247875.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPSMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"NG_068165.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGAGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3005199","ARO_id":"43554","ARO_name":"CMY-171","CARD_short_name":"CMY-171","ARO_description":"CMY-171 is a beta-lactamase found in Escherichia coli. It confers resistance to cephamycin.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3919":{"model_id":"3919","model_name":"CMY-155","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6280":{"protein_sequence":{"accession":"WP_094009802.1","sequence":"MMKKSLCCALLLTASLSTFAAAKTEPQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADITNNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGISLLHLATYTAGGLPLQIPDDVTDKAALLRFYQNWQPQWAPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKAVHVSPGQLDAEAYGVKSSVIDMARWVQVNMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNLVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"NG_055473.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTATCCACGTTTGCCGCCGCCAAAACAGAACCACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCTGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCACCAATAACCACCCAGTCACGCAGCAAACTCTGTTTGAGCTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCAGCCTGCTGCACTTAGCCACCTACACGGCAGGCGGCCTGCCGCTGCAGATCCCCGATGACGTTACGGATAAAGCCGCATTACTGCGTTTTTATCAAAACTGGCAGCCGCAATGGGCCCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACAGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGGCTGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGTCAACATGGACGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCAATCATCAACGGTAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGATCCACTGGAGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCTTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43556","NCBI_taxonomy_name":"Klebsiella sp. KF07","NCBI_taxonomy_id":"1727153"}}}},"ARO_accession":"3005200","ARO_id":"43555","ARO_name":"CMY-155","CARD_short_name":"CMY-155","ARO_description":"CMY-155 is a beta-lactamase found in Klebsiella sp. KF07. It confers resistance to cephamycin.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3920":{"model_id":"3920","model_name":"CMY-96","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6281":{"protein_sequence":{"accession":"WP_063859917.1","sequence":"MMKKSLCCALLLTASLSTFAAAKTEPQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADITNNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGISLLHLATYTAGGLPLQIPDDVTDKAALLRFYQNWQPQWAPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKAVHVSPGQLDAEAYGVKSSVIDMARWVQVNMDASRVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNLVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"NG_048893.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTATCCACGTTTGCCGCCGCCAAAACAGAACCACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCTGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCACCAATAACCACCCAGTCACGCAGCAAACTCTGTTTGAGCTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCAGCCTGCTGCACTTAGCCACCTACACGGCAGGCGGCCTGCCGCTGCAGATCCCCGATGACGTTACGGATAAAGCCGCATTACTGCGTTTTTATCAAAACTGGCAGCCGCAATGGGCCCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACAGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGGCTGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGTCAACATGGACGCCAGCCGCGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCAATCATCAACGGTAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGATCCACTGGAGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCTTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002109","ARO_id":"38509","ARO_name":"CMY-96","CARD_short_name":"CMY-96","ARO_description":"CMY-96 is a beta-lactamase found in Escherichia coli. It confers resistance to cephamycin.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3922":{"model_id":"3922","model_name":"SHV-205","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"540"}},"model_sequences":{"sequence":{"6285":{"protein_sequence":{"accession":"WP_122630863.1","sequence":"MRFIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDARVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"NG_062276.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTTTATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACATCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGCTCGAGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATCGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3005207","ARO_id":"43563","ARO_name":"SHV-205","CARD_short_name":"SHV-205","ARO_description":"A beta-lactamase gene found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3923":{"model_id":"3923","model_name":"SHV-222","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"540"}},"model_sequences":{"sequence":{"6286":{"protein_sequence":{"accession":"WP_122630876.1","sequence":"MRYFRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPVGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPMIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"NG_062294.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATTTTCGCCTGTGTATTATCTCTCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGTAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGATGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGAGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3005208","ARO_id":"43564","ARO_name":"SHV-222","CARD_short_name":"SHV-222","ARO_description":"A beta-lactamase gene from Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3924":{"model_id":"3924","model_name":"SHV-198","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"580"}},"model_sequences":{"sequence":{"6287":{"protein_sequence":{"accession":"WP_088245226.1","sequence":"MRYFRLCIISLLATLPLAVHASPQSLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPVGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"NG_055284.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATTTTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGTCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGTAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGGATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3005209","ARO_id":"43565","ARO_name":"SHV-198","CARD_short_name":"SHV-198","ARO_description":"A beta-lactamase gene from Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3925":{"model_id":"3925","model_name":"SHV-195","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"580"}},"model_sequences":{"sequence":{"6288":{"protein_sequence":{"accession":"WP_068981648.1","sequence":"MRYIRLCIISLLANLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALSGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"NG_051484.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCAACCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTTCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGGATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3005210","ARO_id":"43566","ARO_name":"SHV-195","CARD_short_name":"SHV-195","ARO_description":"Beta-lactamase gene from Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3926":{"model_id":"3926","model_name":"SHV-201","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"580"}},"model_sequences":{"sequence":{"6289":{"protein_sequence":{"accession":"WP_122630838.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWHADERFPMMSTFKVVLCGAVLARMDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"NG_062244.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCACGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGATGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATCGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3005211","ARO_id":"43567","ARO_name":"SHV-201","CARD_short_name":"SHV-201","ARO_description":"Beta-lactamase gene from Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3927":{"model_id":"3927","model_name":"SHV-212","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"580"}},"model_sequences":{"sequence":{"6290":{"protein_sequence":{"accession":"WP_122630867.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARMDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"NG_062284.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGATGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACATCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGAGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATCGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3005212","ARO_id":"43568","ARO_name":"SHV-212","CARD_short_name":"SHV-212","ARO_description":"A beta-lactamase gene from Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3928":{"model_id":"3928","model_name":"SHV-204","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6291":{"protein_sequence":{"accession":"WP_109791212.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDADDEQLERKIHYRQQDLVDYSPVSEKYLADGMTVGELCAAAITMSDNSAANLLLATVGGPVGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"NG_057611.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGATGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAATACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGTAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3005213","ARO_id":"43569","ARO_name":"SHV-204","CARD_short_name":"SHV-204","ARO_description":"A beta-lactamase gene from Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3929":{"model_id":"3929","model_name":"SHV-197","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"580"}},"model_sequences":{"sequence":{"6292":{"protein_sequence":{"accession":"WP_072081993.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNGAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"NG_052582.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACGGCGCCGCCAATCTGCTACTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGTAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3005214","ARO_id":"43570","ARO_name":"SHV-197","CARD_short_name":"SHV-197","ARO_description":"A beta-lactamase gene from Escherichia coli.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3930":{"model_id":"3930","model_name":"SHV-216","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"580"}},"model_sequences":{"sequence":{"6293":{"protein_sequence":{"accession":"WP_122630871.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAELTAFLRQIDDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"NG_062288.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACATCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGAATTGACTGCCTTTTTGCGCCAGATCGACGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3005215","ARO_id":"43571","ARO_name":"SHV-216","CARD_short_name":"SHV-216","ARO_description":"A beta-lactamase gene from Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3931":{"model_id":"3931","model_name":"CMY-121","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6294":{"protein_sequence":{"accession":"AIZ48988.1","sequence":"MKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYASGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"KM507172.1","fmin":"0","fmax":"1143","strand":"+","sequence":"ATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTCGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3003129","ARO_id":"39706","ARO_name":"CMY-121","CARD_short_name":"CMY-121","ARO_description":"CMY-121 is a beta-lactamase found in Escherichia coli. It confers resistance to cephamycin.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4236":{"model_id":"4236","model_name":"ADC-168","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6611":{"protein_sequence":{"accession":"WP_101244938.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEIYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTSGKYWKVLKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPTDIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_056110.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCATTATTAGAAAAATATGATGTGCCGGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATTTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGTCTGGTAAATATTGGAAAGTGCTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAATCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATACGGCGTCAAATCCACCTTACCGGATATGTTAAGTTTTATTCATGCCAACCTTAACCCACAGAAATATCCGACAGATATTCAACGGGCAATTAATGAAACACATCAAGGTCGCTATCAAGTAAATACCATGTATCAAGCGCTTGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCAACGGTTTCGGAACATATGTGGTCTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006340","ARO_id":"44802","ARO_name":"ADC-168","CARD_short_name":"ADC-168","ARO_description":"ADC-168 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4237":{"model_id":"4237","model_name":"ADC-169","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6612":{"protein_sequence":{"accession":"WP_001211212.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDRPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLSAIKK"},"dna_sequence":{"accession":"NG_056172.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCATTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATAGGCCTGGTAAATATTGGAAAGAACTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCTTATTTGGAAAAGTTGTTGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCTGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTTAACCCACAGAAATATCCGGCTGATATTCAAAGGGCAATTAATGAAACACATCAAGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCAACGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAACGCATTAAGGCAGCTTATGCTGTGCTGAGTGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006341","ARO_id":"44803","ARO_name":"ADC-169","CARD_short_name":"ADC-169","ARO_description":"ADC-169 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4238":{"model_id":"4238","model_name":"ADC-170","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6613":{"protein_sequence":{"accession":"WP_102607458.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTSIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWQPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVAKTQMQNYAFGYNQENQPIRANPGPLDAPAYGVKSTLPDMLKFIHANLNPQKYPTDIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTSGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKE"},"dna_sequence":{"accession":"NG_056175.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAACACATCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGCAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTGGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTAGCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGCTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGCTTAAGTTTATTCATGCCAATCTGAACCCACAGAAATATCCGACAGATATTCAACGTGCAATTAATGAAACACATCAAGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCAGCGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAACGCATTAAGGCAGCGTATGCAGTTTTAAATGCAATAAAGGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006342","ARO_id":"44804","ARO_name":"ADC-170","CARD_short_name":"ADC-170","ARO_description":"ADC-170 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3932":{"model_id":"3932","model_name":"CMY-152","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6295":{"protein_sequence":{"accession":"ARM19732.1","sequence":"MMKKSICCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAIIYEEKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWRGISLLHLATYTAGGLPLQIPDEVTDKAALLRFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQSEQKNYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIELAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPARVEAAWRILEKLQ"},"dna_sequence":{"accession":"KY978224.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGATATGCTGCGCGCTGCTGCTGACAGCCTCTTTCTCCACGTTTGCTGCCGCAAAAACAGAACAACAAATTGCCGATATCGTTAACCGCACCATCACACCACTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTGGCGATTATCTACGAGGAGAAACCTTATTACTTTACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAATTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGACGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCGGGGTATCAGCCTGCTGCACTTAGCCACCTATACAGCGGGTGGCCTACCGCTGCAGATCCCCGATGAAGTTACGGATAAAGCCGCATTACTGCGCTTTTATCAAAACTGGCAACCACAATGGACTCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGTGCGCTGGCGGTGAAACCTTCAGGTATGAGCTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAAAGCGAACAAAAAAATTATGCCTGGGGCTATCGCGAAGGGAAGCCTGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATCGATATGGCCCGCTGGGTTCAGGCCAACATGGACGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGAGCTTGCGCAGTCTCGTTACTGGCGTATTGGTGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCAGCACCTGCCGTGAAAGCCTCATGGGTGCATAAAACGGGATCCACAGGTGGATTTGGCAGCTACGTTGCCTTCGTTCCAGAAAAAAACCTTGGCATAGTGATGCTGGCAAACAAAAGCTACCCCAACCCGGCTCGCGTCGAGGCGGCCTGGCGCATTCTTGAAAAACTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3005216","ARO_id":"43572","ARO_name":"CMY-152","CARD_short_name":"CMY-152","ARO_description":"CMY-152 is a beta-lactamase found in Citrobacter freundii. It confers resistance to cephamycin.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3933":{"model_id":"3933","model_name":"CMY-97","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6296":{"protein_sequence":{"accession":"AFZ85213.1","sequence":"MMKKSICCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAIIYEGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWRGISLLHLATYTAGGLPLQIPDDVTEKAALLRFYQNWQPQWTPGAKRLYANSSIGLFGALVVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQSEQKNYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIELAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPARVEAAWRILEKLQ"},"dna_sequence":{"accession":"KC007363.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGATATGCTGCGCGCTGCTGCTGACAGCCTCTTTCTCCACGTTTGCTGCCGCAAAAACAGAACAACAAATTGCCGATATCGTTAACCGCACCATCACACCACTGATGCAGGAGCAGGCTATTCCGGGCATGGCCGTGGCAATTATCTACGAGGGGAAACCTTATTACTTTACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGACGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCGGGGTATCAGCCTGCTGCACTTAGCCACCTATACAGCGGGTGGCCTGCCGCTGCAGATCCCCGATGACGTTACGGAGAAAGCCGCATTACTGCGCTTTTATCAAAACTGGCAACCACAATGGACTCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGTGCGCTGGTGGTGAAACCTTCAGGTATGAGCTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAAAGCGAACAAAAAAATTATGCCTGGGGCTATCGCGAAGGGAAGCCTGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATCGATATGGCCCGCTGGGTTCAGGCCAACATGGACGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGAGCTTGCGCAGTCTCGCTACTGGCGTATTGGTGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCAGCACCTGCCGTGAAAGCCTCATGGGTGCATAAAACAGGATCCACAGGCGGATTTGGCAGCTACGTTGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTAATGTTGGCAAACAAAAGCTACCCCAACCCGGCTCGCGTAGAGGCGGCCTGGCGCATTCTTGAAAAACTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002110","ARO_id":"38510","ARO_name":"CMY-97","CARD_short_name":"CMY-97","ARO_description":"CMY-97 is a beta-lactamase found in Escherichia coli. It confers resistance to cephamycin.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3934":{"model_id":"3934","model_name":"CMY-151","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6297":{"protein_sequence":{"accession":"ARE65229.1","sequence":"MMKKSICCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAIIYEGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWRGISMLHLATYTAGGLPLQIPDDVTDKAELLRFYQNWQPQWTPGAKRLYANSSIGLFGALAVKSSGMSYEEAMTRRVLQPLKLAHTWITVPQSEQKNYAWGYLEGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIELAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPARVEAAWRILEKLQ"},"dna_sequence":{"accession":"KY780116.1","fmin":"0","fmax":"1146","strand":"-","sequence":"ATGATGAAAAAATCGATATGCTGCGCGCTGCTGCTGACAGCCTCTTTCTCCACGTTTGCTGCCGCAAAAACAGAACAACAAATTGCCGATATCGTTAACCGCACCATCACACCACTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTGGCGATTATCTACGAGGGGAAACCTTATTACTTTACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGACGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCGGGGTATCAGCATGCTGCACTTAGCCACCTATACAGCGGGTGGCCTGCCGCTGCAGATCCCCGATGACGTTACGGATAAAGCCGAATTACTGCGCTTTTATCAAAACTGGCAACCACAATGGACTCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGTGCGCTGGCGGTGAAATCTTCAGGTATGAGCTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAAAGCGAACAAAAAAACTATGCCTGGGGCTATCTCGAAGGGAAGCCTGTGCACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATCGATATGGCCCGCTGGGTTCAGGCCAACATGGACGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGAGCTTGCGCAGTCTCGCTACTGGCGTATTGGTGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGTGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCAGCACCTGCCGTGAAAGCCTCATGGGTGCATAAAACGGGATCCACAGGTGGATTTGGCAGCTACGTTGCCTTCGTTCCAGAAAAAAACCTTGGCATAGTGATGCTGGCAAACAAAAGCTATCCTAACCCGGCTCGCGTAGAGGCGGCCTGGCGCATTCTTGAAAAACTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3005217","ARO_id":"43573","ARO_name":"CMY-151","CARD_short_name":"CMY-151","ARO_description":"CMY-151 is a beta-lactamase found in Citrobacter freundii. It confers resistance to cephamycin.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3935":{"model_id":"3935","model_name":"CMY-128","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6298":{"protein_sequence":{"accession":"AKO62865.1","sequence":"MMKKSICCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQERAIPGMAVAIIYEGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWRGISLLHLATYTAGGLPLQIPDDVTDKTELLRFYQNWQPQWTPGAKRLYANSSIGLFGALVVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQSEQKNYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASLVQEKTLQQGIELAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPARVEAAWRILEKLQ"},"dna_sequence":{"accession":"KM985466.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGATATGCTGCGCACTGCTGCTGACAGCCTCTTTCTCCACGTTTGCTGCCGCAAAAACAGAACAACAAATTGCCGATATCGTTAACCGCACCATCACACCACTGATGCAGGAGCGGGCTATTCCGGGTATGGCCGTGGCGATTATCTACGAGGGGAAACCTTATTACTTTACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGACGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCGGGGTATCAGCCTGCTGCACTTAGCCACCTATACAGCGGGTGGCCTGCCGCTGCAGATCCCCGATGACGTTACGGATAAAACCGAATTACTGCGCTTTTATCAAAACTGGCAACCACAATGGACTCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGTGCGCTGGTAGTAAAACCTTCAGGTATGAGCTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAAAGCGAACAAAAAAATTATGCCTGGGGCTATCGCGAAGGGAAGCCTGTACACGTTTCTCCGGGGCAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATCGATATGGCCCGCTGGGTTCAGGCCAACATGGACGCCAGCCTCGTTCAGGAGAAAACGCTCCAGCAGGGCATTGAGCTTGCGCAGTCTCGCTACTGGCGTATTGGTGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCAGCACCTGCCGTGAAAGCCTCATGGGTGCATAAAACAGGATCCACAGGCGGATTTGGCAGCTACGTTGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTAATGTTGGCAAACAAAAGCTACCCCAACCCGGCTCGCGTCGAGGCGGCCTGGCGCATTCTTGAAAAACTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3003136","ARO_id":"39713","ARO_name":"CMY-128","CARD_short_name":"CMY-128","ARO_description":"CMY-128 is a beta-lactamase found in Citrobacter freundii. It confers resistance to cephamycin.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3936":{"model_id":"3936","model_name":"CMY-129","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6299":{"protein_sequence":{"accession":"AKO62866.1","sequence":"MMKKSLCCALLLTAPFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADITNNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGISLLHLATYTAGGLPLQIPDDVTDKAALLRFYQNWQPQWAPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKAVHVSPGQLDAEAYGVKSSVIDMARWVQVNMDANRVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"KM985467.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCCCTTTCTCCACGTTTGCCGCAGCCAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCACCAATAACCACCCAGTCACGCAGCAAACTCTGTTTGAGCTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCAGCCTGCTGCACTTAGCCACCTACACGGCAGGCGGCCTGCCGCTGCAGATCCCCGATGACGTTACGGATAAAGCCGCATTACTGCGTTTTTATCAAAACTGGCAGCCGCAATGGGCCCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACAGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGGCTGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGTGTTATTGATATGGCCCGCTGGGTTCAGGTCAACATGGACGCCAACCGCGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCAATCATCAACGGTAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCTGCCCCCGCTGTGAAAGCCTCATGGGTGCATAAAACGGGATCCACTGGAGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3003137","ARO_id":"39714","ARO_name":"CMY-129","CARD_short_name":"CMY-129","ARO_description":"CMY-129 is a beta-lactamase found in Citrobacter freundii. It confers resistance to cephamycin.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3992":{"model_id":"3992","model_name":"TEM-229","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6356":{"protein_sequence":{"accession":"WP_080699425.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRIDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPVAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRVVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"NG_056416.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTATTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGTAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTGTCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3005260","ARO_id":"43616","ARO_name":"TEM-229","CARD_short_name":"TEM-229","ARO_description":"TEM-229 is a beta-lactamase.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3993":{"model_id":"3993","model_name":"TEM-230","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6357":{"protein_sequence":{"accession":"WP_104009854.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKTGAGERGSRGIIAALGPDGKPSRIVVIYMTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"NG_056417.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAAACTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACATGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3005261","ARO_id":"43617","ARO_name":"TEM-230","CARD_short_name":"TEM-230","ARO_description":"TEM-230 is a beta-lactamase.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3937":{"model_id":"3937","model_name":"CMY-127","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6300":{"protein_sequence":{"accession":"AKO62864.1","sequence":"MMKKSLCCALLLTAPLSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAIAVIYQGKPYYFTWGKADITNNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYRPELTGKQWQGISLLHLATYTAGGLPLQIPDDVTDKAALLRFYQNWQPQWAPGAKRLYANSSIGLFGALAVNPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKAVHVSPGQLDAEAYGVKSSVIDMARWVQVNMDASRVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"KM985465.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCCCTTTATCCACGTTTGCCGCCGCCAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCTATTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCACCAATAACCACCCAGTCACGCAGCAAACTCTGTTTGAGCTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACCGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCAGCCTGCTGCACTTAGCCACCTACACGGCAGGCGGCCTGCCGCTGCAGATCCCCGATGACGTTACGGATAAAGCCGCATTACTGCGTTTTTATCAAAACTGGCAGCCGCAATGGGCCCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTTTTTGGCGCGCTGGCGGTGAACCCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACAGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGGCTGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGTGTTATTGATATGGCCCGCTGGGTTCAGGTCAACATGGACGCCAGCCGCGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGATGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGTAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGATCCACTGGAGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3003135","ARO_id":"39712","ARO_name":"CMY-127","CARD_short_name":"CMY-127","ARO_description":"CMY-127 is a beta-lactamase found in Citrobacter freundii. It confers resistance to cephamycin.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3938":{"model_id":"3938","model_name":"CMY-89","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6301":{"protein_sequence":{"accession":"CCK86742.1","sequence":"MMKKSLCCALLLTASFPTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAIIYEGKPYYFTWGKADIANKHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWRGISLLHLATYTAGGLPLQIPDDVTDKAELLRFYQNWQPQWTPGAKRLYANSSIGLFGALVVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQSEQKNYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIELAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPVPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"HE819403.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCGCTGCTGCTGACAGCCTCTTTCCCCACGTTTGCTGCCGCAAAAACAGAACAACAAATTGCCGATATCGTTAACCGCACCATCACACCACTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTGGCGATTATCTACGAGGGGAAACCTTATTACTTTACCTGGGGTAAAGCCGATATCGCCAATAAACACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGACGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCGGGGTATCAGCCTGCTGCACTTAGCCACCTATACAGCGGGTGGCCTGCCGCTGCAGATCCCCGATGACGTTACGGATAAAGCCGAATTACTGCGCTTTTATCAAAACTGGCAACCACAATGGACTCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGTGCGCTGGTGGTAAAACCTTCAGGTATGAGCTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAAAGCGAACAAAAAAATTATGCCTGGGGCTATCGCGAAGGGAAGCCTGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATCGATATGGCCCGCTGGGTTCAGGCCAACATGGACGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGAGCTTGCGCAGTCTCGCTACTGGCGTATTGGTGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCAGTACCTGCCGTGAAAGCCTCATGGGTGCATAAAACGGGATCCACAGGTGGATTTGGCAGCTACGTTGCCTTCGTTCCAGAAAAAAACCTTGGCATAGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGCGTCGAGGCGGCCTGGCGCATTCTTGAAAAACTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002102","ARO_id":"38502","ARO_name":"CMY-89","CARD_short_name":"CMY-89","ARO_description":"CMY-89 is a beta-lactamase found in Citrobacter freundii. It confers resistance to cephamycin.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3939":{"model_id":"3939","model_name":"CMY-153","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6302":{"protein_sequence":{"accession":"ARQ85812.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTIPPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"MF042206.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCCCCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3005218","ARO_id":"43574","ARO_name":"CMY-153","CARD_short_name":"CMY-153","ARO_description":"CMY-89 is a beta-lactamase found in Escherichia coli. It confers resistance to cephamycin.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3940":{"model_id":"3940","model_name":"CMY-130","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6303":{"protein_sequence":{"accession":"AKI06385.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQELAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"KP207589.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCTGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3003138","ARO_id":"39715","ARO_name":"CMY-130","CARD_short_name":"CMY-130","ARO_description":"CMY-130 is a beta-lactamase found in Escherichia coli. It confers resistance to cephamycin.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4131":{"model_id":"4131","model_name":"ACT-40","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6506":{"protein_sequence":{"accession":"WP_045328874.1","sequence":"MMKKSLCCALLLGISCSALATPVSEKQLAEVVANTVTPLMKAQSVPGMAVAVIYQGKPHYYTFGKADIAANKPVTPQTLFELGSISKTFTAVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMPYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPENVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVVEGSDSKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANTSYPNPARVEAAYHILEALQ"},"dna_sequence":{"accession":"NG_050703.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCCCTTTGCTGCGCCCTGCTGCTCGGCATCTCTTGCTCTGCTCTCGCCACGCCAGTGTCAGAAAAACAGCTGGCGGAGGTGGTCGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCTGTTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGAAAACCGCACTATTACACGTTTGGCAAGGCCGATATCGCGGCGAATAAACCCGTTACGCCTCAGACCCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGCCGTTTTAGGTGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTGACGGGCAAGCAGTGGCAGGGTATTCGTATGCTGGATCTCGCCACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTCAAACCTTCTGGCATGCCCTATGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTGCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGTATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCGGAGAACGTTGCTGATGCCTCACTTAAGCAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGGTCGAGGGCAGCGACAGTAAGGTAGCACTGGCGCCGTTGCCCGTGGCAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGCTCTACTGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATACAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCGAGGCGCTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40540","NCBI_taxonomy_name":"Enterobacter cloacae complex","NCBI_taxonomy_id":"354276"}}}},"ARO_accession":"3006235","ARO_id":"44697","ARO_name":"ACT-40","CARD_short_name":"ACT-40","ARO_description":"ACT-40 is a ACT beta-lactamase.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3941":{"model_id":"3941","model_name":"CMY-144","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6304":{"protein_sequence":{"accession":"APC23883.1","sequence":"MMKKSLCCALLLTVSFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEINLSDPVTKYWPELTGKQWQGISLLHLATYTAGGLPLQIPDDVTDKAALLRFYQNWQPQWAPGAKRLYANSSIGLFGALAVKPSGMSYEEAITRRVLQPLKLAHTWITVPQSEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSNVTDMARWVQVNMDASRVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFIPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"KY066478.1","fmin":"2087","fmax":"3233","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGTCTCATTCTCCACGTTTGCCGCCGCCAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACTCTGTTTGAGCTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAATCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCAGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTACAGATAAAGCCGCATTACTGCGTTTTTATCAAAACTGGCAGCCGCAATGGGCTCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGTGCGCTGGCGGTGAAACCCTCAGGTATGAGCTACGAAGAGGCAATCACCAGACGCGTCCTGCAGCCATTAAAACTGGCGCATACCTGGATTACAGTTCCGCAAAGCGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCTGTACACGTTTCTCCGGGACAACTTGATGCCGAAGCCTATGGCGTGAAATCCAACGTTACCGATATGGCACGCTGGGTTCAGGTCAACATGGACGCCAGCCGCGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGATGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGTAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGATCCACTGGAGGATTTGGCAGCTACGTAGCCTTCATTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3005219","ARO_id":"43575","ARO_name":"CMY-144","CARD_short_name":"CMY-144","ARO_description":"CMY-144 is a beta-lactamase found in Citrobacter freundii. It confers resistance to cephamycin.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3942":{"model_id":"3942","model_name":"CMY-138","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6305":{"protein_sequence":{"accession":"ALM96710.1","sequence":"MMKKSLYCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYARGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"KT997883.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATACTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCCGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3005220","ARO_id":"43576","ARO_name":"CMY-138","CARD_short_name":"CMY-138","ARO_description":"CMY-138 is a beta-lactamase found in Proteus mirabilis. It confers resistance to cephamycin.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3944":{"model_id":"3944","model_name":"OXA-544","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8393":{"protein_sequence":{"accession":"OPD39420.1","sequence":"MAIRIFAILFSIFSLATFAHAQEGTLERSDWRKFFSEFQAKGTIVVADERQADRAMLVFDPVRSKKRYSPASTFKILHTLFALDAGAVRDEFQIFRWDGVNRGFAGHNQDQDLRSAMRNSTVWVYELFAKEIGDDKARRYLKKIDYGNADPSTSNGDYWIEGSLAISAQEQIAFLRKLYRNELPFRVEHQRLVKDLMIVEAGRNWILRAKTGWEGRMGWWVGWVEWPTGSVFFALNIDTPNRMDDLFKREAIVRAILRSIEALPPNPAVNSDAAR"},"dna_sequence":{"accession":"LLMY01000078.1","fmin":"2375","fmax":"3203","strand":"+","sequence":"ATGGCAATCCGAATCTTCGCGATACTTTTCTCCATTTTTTCTCTTGCCACTTTCGCGCATGCGCAAGAAGGCACGCTAGAACGTTCTGACTGGAGGAAGTTTTTCAGCGAATTTCAAGCCAAAGGCACGATAGTTGTGGCAGACGAACGCCAAGCGGATCGTGCCATGTTGGTTTTTGATCCTGTGCGATCGAAGAAACGCTACTCGCCTGCATCGACATTCAAGATACTTCATACACTTTTTGCACTTGATGCAGGCGCTGTTCGTGATGAGTTCCAGATTTTTCGATGGGACGGCGTTAACAGGGGCTTTGCAGGCCACAATCAAGACCAAGATTTGCGATCAGCAATGCGGAATTCTACTGTTTGGGTGTATGAGCTATTTGCAAAGGAAATTGGTGATGACAAAGCTCGGCGCTATTTGAAGAAAATCGACTATGGCAACGCCGATCCTTCGACAAGTAATGGCGATTACTGGATAGAAGGCAGCCTTGCAATCTCGGCGCAGGAGCAAATTGCATTTCTCAGGAAGCTCTATCGTAACGAGCTGCCCTTTCGGGTAGAACATCAGCGCTTGGTCAAGGATCTCATGATTGTGGAAGCCGGTCGCAACTGGATACTGCGTGCAAAGACGGGCTGGGAAGGCCGTATGGGTTGGTGGGTAGGATGGGTTGAGTGGCCGACTGGCTCCGTATTCTTCGCACTGAATATTGATACGCCAAACAGAATGGATGATCTTTTCAAGAGGGAGGCAATCGTGCGGGCAATCCTTCGCTCTATTGAAGCGTTACCGCCCAACCCGGCAGTCAACTCGGACGCTGCGCGATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005222","ARO_id":"43578","ARO_name":"OXA-544","CARD_short_name":"OXA-544","ARO_description":"OXA-544 is a beta-lactamase in the OXA-2 family of OXA beta-lactamases that confers resistance to ampicillin and cephalothin.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46493":{"category_aro_accession":"3007704","category_aro_cvterm_id":"46493","category_aro_name":"OXA-2-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-2.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3945":{"model_id":"3945","model_name":"SHV-194","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"581"}},"model_sequences":{"sequence":{"6308":{"protein_sequence":{"accession":"WP_065419573.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTNQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"NG_051169.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAACCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGCATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3005223","ARO_id":"43579","ARO_name":"SHV-194","CARD_short_name":"SHV-194","ARO_description":"Beta-lactamase gene from Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3946":{"model_id":"3946","model_name":"SHV-220","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"577"}},"model_sequences":{"sequence":{"6309":{"protein_sequence":{"accession":"WP_109232473.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSPRLSVRSQRQLLQWMVDDGVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"NG_062292.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCCGCGTCTGAGCGTCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATGGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGCATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATATATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3005224","ARO_id":"43580","ARO_name":"SHV-220","CARD_short_name":"SHV-220","ARO_description":"Beta-lactamase gene from Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3947":{"model_id":"3947","model_name":"SHV-210","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"580"}},"model_sequences":{"sequence":{"6310":{"protein_sequence":{"accession":"WP_115196748.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDLVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"NG_062282.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTTGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCTGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGCATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3005225","ARO_id":"43581","ARO_name":"SHV-210","CARD_short_name":"SHV-210","ARO_description":"Beta-lactamase gene from Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3948":{"model_id":"3948","model_name":"SHV-208","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"580"}},"model_sequences":{"sequence":{"6311":{"protein_sequence":{"accession":"WP_122630865.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPADWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"NG_062280.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACATCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGAGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGACTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATCGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3005226","ARO_id":"43582","ARO_name":"SHV-208","CARD_short_name":"SHV-208","ARO_description":"A beta-lactamase gene found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3949":{"model_id":"3949","model_name":"SHV-206","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"580"}},"model_sequences":{"sequence":{"6312":{"protein_sequence":{"accession":"WP_004143591.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGLNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"NG_062278.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCTGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3005227","ARO_id":"43583","ARO_name":"SHV-206","CARD_short_name":"SHV-206","ARO_description":"A beta-lactamase gene from Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3950":{"model_id":"3950","model_name":"SHV-226","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"581"}},"model_sequences":{"sequence":{"6313":{"protein_sequence":{"accession":"WP_122630878.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGLGAALIEHWQR"},"dna_sequence":{"accession":"NG_062298.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGCATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGCTCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3005228","ARO_id":"43584","ARO_name":"SHV-226","CARD_short_name":"SHV-226","ARO_description":"A beta-lactamase gene found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3951":{"model_id":"3951","model_name":"SHV-196","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"580"}},"model_sequences":{"sequence":{"6314":{"protein_sequence":{"accession":"WP_069280714.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAEIGAALIEHWQR"},"dna_sequence":{"accession":"NG_051521.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATCGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGAGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3005229","ARO_id":"43585","ARO_name":"SHV-196","CARD_short_name":"SHV-196","ARO_description":"A beta-lactamase gene found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3952":{"model_id":"3952","model_name":"SHV-211","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"580"}},"model_sequences":{"sequence":{"6315":{"protein_sequence":{"accession":"WP_023341517.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGWALIEHWQR"},"dna_sequence":{"accession":"NG_062283.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGCATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCTGGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3005230","ARO_id":"43586","ARO_name":"SHV-211","CARD_short_name":"SHV-211","ARO_description":"A beta-lactamase gene found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3953":{"model_id":"3953","model_name":"SHV-219","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"580"}},"model_sequences":{"sequence":{"6316":{"protein_sequence":{"accession":"WP_122630874.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIARIGAALIEHWQR"},"dna_sequence":{"accession":"NG_062291.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACATCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGGATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCAGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3005231","ARO_id":"43587","ARO_name":"SHV-219","CARD_short_name":"SHV-219","ARO_description":"Beta-lactamase gene from Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3954":{"model_id":"3954","model_name":"SHV-199","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"580"}},"model_sequences":{"sequence":{"6317":{"protein_sequence":{"accession":"WP_094009815.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGSLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"NG_055503.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGATCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGCATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3005232","ARO_id":"43588","ARO_name":"SHV-199","CARD_short_name":"SHV-199","ARO_description":"A beta-lactamase gene found in Escherichia coli.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3955":{"model_id":"3955","model_name":"SHV-227","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"580"}},"model_sequences":{"sequence":{"6318":{"protein_sequence":{"accession":"WP_122630879.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAVTLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"NG_062299.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACATCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGTGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3005233","ARO_id":"43589","ARO_name":"SHV-227","CARD_short_name":"SHV-227","ARO_description":"Beta-lactamase gene from Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3956":{"model_id":"3956","model_name":"SHV-223","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"580"}},"model_sequences":{"sequence":{"6319":{"protein_sequence":{"accession":"WP_117241614.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQISDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"NG_062295.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCAGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCAGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCACTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGTTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGCATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3005234","ARO_id":"43590","ARO_name":"SHV-223","CARD_short_name":"SHV-223","ARO_description":"A beta-lactamase gene found in Klebsiella pneumonia.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3957":{"model_id":"3957","model_name":"SHV-214","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"580"}},"model_sequences":{"sequence":{"6321":{"protein_sequence":{"accession":"WP_122630869.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCVAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"NG_062286.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACATCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGTCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATCGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3005235","ARO_id":"43591","ARO_name":"SHV-214","CARD_short_name":"SHV-214","ARO_description":"A beta-lactamase gene found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3958":{"model_id":"3958","model_name":"SHV-207","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"580"}},"model_sequences":{"sequence":{"6322":{"protein_sequence":{"accession":"WP_064733493.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQHLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"NG_062279.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGCATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3005236","ARO_id":"43592","ARO_name":"SHV-207","CARD_short_name":"SHV-207","ARO_description":"A beta-lactamase gene found in Klebsiella penumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3959":{"model_id":"3959","model_name":"SHV-1b-b","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"580"}},"model_sequences":{"sequence":{"6323":{"protein_sequence":{"accession":"WP_063864669.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLTSGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"NG_050059.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGACCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGGATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3005237","ARO_id":"43593","ARO_name":"SHV-1b-b","CARD_short_name":"SHV-1b-b","ARO_description":"A beta-lactamase gene found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3960":{"model_id":"3960","model_name":"SHV-218","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"580"}},"model_sequences":{"sequence":{"6324":{"protein_sequence":{"accession":"WP_122630873.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDPASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATFGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"NG_062290.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCCGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGTATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCTTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGCATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAACACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3005238","ARO_id":"43594","ARO_name":"SHV-218","CARD_short_name":"SHV-218","ARO_description":"A beta-lactamase gene found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3961":{"model_id":"3961","model_name":"SHV-193","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"580"}},"model_sequences":{"sequence":{"6325":{"protein_sequence":{"accession":"WP_063864668.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADELFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"NG_050058.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACTCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCTCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3005239","ARO_id":"43595","ARO_name":"SHV-193","CARD_short_name":"SHV-193","ARO_description":"A beta-lactamase gene found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3962":{"model_id":"3962","model_name":"SHV-224","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"581"}},"model_sequences":{"sequence":{"6326":{"protein_sequence":{"accession":"WP_104159136.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAALARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"NG_062296.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGCGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATCGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3005240","ARO_id":"43596","ARO_name":"SHV-224","CARD_short_name":"SHV-224","ARO_description":"A beta-lactamase gene found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3963":{"model_id":"3963","model_name":"SHV-225","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"580"}},"model_sequences":{"sequence":{"6327":{"protein_sequence":{"accession":"WP_122630877.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMSVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"NG_062297.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGTCGGTCGGTGAACTCTGCGCTGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGCATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3005241","ARO_id":"43597","ARO_name":"SHV-225","CARD_short_name":"SHV-225","ARO_description":"A beta-lactamase gene found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3964":{"model_id":"3964","model_name":"SHV-209","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"580"}},"model_sequences":{"sequence":{"6328":{"protein_sequence":{"accession":"WP_122630866.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVDGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"NG_062281.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGACGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATCGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3005242","ARO_id":"43598","ARO_name":"SHV-209","CARD_short_name":"SHV-209","ARO_description":"A beta-lactamase gene found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3965":{"model_id":"3965","model_name":"SHV-215","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"580"}},"model_sequences":{"sequence":{"6329":{"protein_sequence":{"accession":"WP_122630870.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSAHSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"NG_062287.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCATTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3005243","ARO_id":"43599","ARO_name":"SHV-215","CARD_short_name":"SHV-215","ARO_description":"A beta-lactamase gene found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3966":{"model_id":"3966","model_name":"ADC-181","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"725"}},"model_sequences":{"sequence":{"6330":{"protein_sequence":{"accession":"AZK35803.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWQPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLGAPAYGVKSTLPDMLSFIHANLTPQKYPTDIQRAINETHQGFYQVGTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNRFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"MK248721.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCATTATTAGAAAAATATGATGTACCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAGCTAAAAAATACACCGATTGATCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGCAACCTCGCTTTACAATTTCCAGATGAAGTACAAACAGATCAACAAGTTTTAACTTTTTTCAAAGACTGGCAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTGGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTTGGTGCCCCAGCATACGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTTACCCCACAGAAATATCCGACAGATATTCAACGGGCAATTAATGAAACACATCAAGGGTTCTATCAAGTCGGCACCATGTATCAGGCACTTGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCAACCGTTTCGGAACATATGTGGTCTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005244","ARO_id":"43600","ARO_name":"ADC-181","CARD_short_name":"ADC-181","ARO_description":"ADC ortholog described by Nodari et al. 2020.","ARO_category":{"40543":{"category_aro_accession":"3003846","category_aro_cvterm_id":"40543","category_aro_name":"ADC beta-lactamase without carbapenemase activity","category_aro_description":"ADC beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases with extended-spectrum resistance to cephalosporins but not to carbapenems. ADC beta-lactamases are found in Acinetobacter sp. and Oligella urethralis.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3967":{"model_id":"3967","model_name":"ADC-182","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"725"}},"model_sequences":{"sequence":{"6331":{"protein_sequence":{"accession":"AZK35804.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWQPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPASPAYGVKSTLPDMLSFIHANLTPQKYPTDIQRAINETHQGFYQVGTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTTGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"MK248722.1","fmin":"0","fmax":"1161","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCATTATTAGAAAAATATGATGTACCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAGCTAAAAAATACACCGATTGATCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGCAACCTCGCTTTACAATTTCCAGATGAAGTACAAACAGATCAACAAGTTTTAACTTTTTTCAAAGACTGGCAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTGGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTTGATGCCCCAGCATCCCCAGCATACGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTTACCCCACAGAAATATCCGACAGATATTCAACGGGCAATTAATGAAACACATCAAGGGTTCTATCAAGTCGGCACCATGTATCAGGCACTTGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCACCGGTTTCGGAACATATGTGGTCTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005245","ARO_id":"43601","ARO_name":"ADC-182","CARD_short_name":"ADC-182","ARO_description":"ADC ortholog described by Nodari et al. 2020.","ARO_category":{"40543":{"category_aro_accession":"3003846","category_aro_cvterm_id":"40543","category_aro_name":"ADC beta-lactamase without carbapenemase activity","category_aro_description":"ADC beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases with extended-spectrum resistance to cephalosporins but not to carbapenems. ADC beta-lactamases are found in Acinetobacter sp. and Oligella urethralis.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3968":{"model_id":"3968","model_name":"ADC-183","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"725"}},"model_sequences":{"sequence":{"6332":{"protein_sequence":{"accession":"AZK35805.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWQPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLTPQKYPTDIQRAINETHQGFYQVGTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKETAISKEPSVKMYHKTGSTTGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"MK248723.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCATTATTAGAAAAATATGATGTACCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAGCTAAAAAATACACCGATTGATCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGCAACCTCGCTTTACAATTTCCAGATGAAGTACAAACAGATCAACAAGTTTTAACTTTTTTCAAAGACTGGCAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTGGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTTGATGCCCCAGCATACGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTTACCCCACAGAAATATCCGACAGATATTCAACGGGCAATTAATGAAACACATCAAGGGTTCTATCAAGTCGGCACCATGTATCAGGCACTTGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGAGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCACCGGTTTCGGAACATATGTGGTCTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005246","ARO_id":"43602","ARO_name":"ADC-183","CARD_short_name":"ADC-183","ARO_description":"ADC ortholog described by Nodari et al. 2020.","ARO_category":{"40543":{"category_aro_accession":"3003846","category_aro_cvterm_id":"40543","category_aro_name":"ADC beta-lactamase without carbapenemase activity","category_aro_description":"ADC beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases with extended-spectrum resistance to cephalosporins but not to carbapenems. ADC beta-lactamases are found in Acinetobacter sp. and Oligella urethralis.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3969":{"model_id":"3969","model_name":"SHV-228","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"580"}},"model_sequences":{"sequence":{"6333":{"protein_sequence":{"accession":"WP_122630880.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPAIMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"NG_062300.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGATCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3005247","ARO_id":"43603","ARO_name":"SHV-228","CARD_short_name":"SHV-228","ARO_description":"A beta-lactamase gene found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3970":{"model_id":"3970","model_name":"SHV-200","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"580"}},"model_sequences":{"sequence":{"6334":{"protein_sequence":{"accession":"WP_096807447.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGASKRGARGIVDLLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"NG_055588.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTACTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGATGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTAGCAAGCGGGGTGCGCGCGGGATTGTCGACCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3005248","ARO_id":"43604","ARO_name":"SHV-200","CARD_short_name":"SHV-200","ARO_description":"A beta-lactamase gene found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3971":{"model_id":"3971","model_name":"SHV-203","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"580"}},"model_sequences":{"sequence":{"6335":{"protein_sequence":{"accession":"WP_099156054.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMVSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLVDGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"NG_055668.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGGTGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGTCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3005249","ARO_id":"43605","ARO_name":"SHV-203","CARD_short_name":"SHV-203","ARO_description":"A beta-lactamase gene found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3972":{"model_id":"3972","model_name":"SHV-217","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"580"}},"model_sequences":{"sequence":{"6336":{"protein_sequence":{"accession":"WP_122630872.1","sequence":"MRYIRLCIISLLATLSLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"NG_062289.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGTCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATCGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3005250","ARO_id":"43606","ARO_name":"SHV-217","CARD_short_name":"SHV-217","ARO_description":"A beta-lactamase gene found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3973":{"model_id":"3973","model_name":"SHV-213","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"580"}},"model_sequences":{"sequence":{"6337":{"protein_sequence":{"accession":"WP_122630868.1","sequence":"MRYIRLCIISLLPTLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"NG_062285.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTACCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3005251","ARO_id":"43607","ARO_name":"SHV-213","CARD_short_name":"SHV-213","ARO_description":"A beta-lactamase gene found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3974":{"model_id":"3974","model_name":"SHV-221","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"580"}},"model_sequences":{"sequence":{"6338":{"protein_sequence":{"accession":"WP_122630875.1","sequence":"MRYIRLSIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIGMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"NG_062293.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGAGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGGAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGTTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGCATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3005252","ARO_id":"43608","ARO_name":"SHV-221","CARD_short_name":"SHV-221","ARO_description":"A beta-lactamase gene found in Klebsiella pneumonia.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3975":{"model_id":"3975","model_name":"SHV-202","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"580"}},"model_sequences":{"sequence":{"8394":{"protein_sequence":{"accession":"WP_122630839.1","sequence":"MVKRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQRERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"MF804906.1","fmin":"0","fmax":"867","strand":"+","sequence":"GTGGTTAAGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCGGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGGATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3005253","ARO_id":"43609","ARO_name":"SHV-202","CARD_short_name":"SHV-202","ARO_description":"A beta-lactamase gene found in Klebsiella pneumoniae.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3976":{"model_id":"3976","model_name":"TEM-5","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6340":{"protein_sequence":{"accession":"WP_109963600.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDSWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGTGKRGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"NG_068215.1","fmin":"100","fmax":"961","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATAGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAACCGGTAAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000877","ARO_id":"37257","ARO_name":"TEM-5","CARD_short_name":"TEM-5","ARO_description":"TEM-5 is an extended-spectrum beta-lactamase that has been found in clinical isolates.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4239":{"model_id":"4239","model_name":"ADC-171","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6614":{"protein_sequence":{"accession":"WP_031961878.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFNATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVKTDQQVLTFFKDWKPKNSIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNRGPLDAAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_056163.1","fmin":"100","fmax":"1255","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTAACGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAGTATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAATTTCCAGATGAAGTAAAAACAGATCAGCAAGTTTTAACATTTTTTAAAGACTGGAAACCTAAAAACTCAATCGGTGAATATCGACAATATTCAAACCCAAGCATTGGTTTATTTGGAAAAGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCGCGGCCCACTCGATGCCGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTAAATCCACAAAAATATCCAGCAGATATTCAACGGGCAATTAATGAAACACATCAGGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006343","ARO_id":"44805","ARO_name":"ADC-171","CARD_short_name":"ADC-171","ARO_description":"ADC-171 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4240":{"model_id":"4240","model_name":"ADC-172","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6615":{"protein_sequence":{"accession":"WP_032027415.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVKTDQQVLTFFKDWKPKNSIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNRGPLDAAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPKKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_056162.1","fmin":"100","fmax":"1255","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAGTATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAATTTCCAGATGAAGTAAAAACAGATCAGCAAGTTTTAACATTTTTTAAAGACTGGAAACCTAAAAACTCAATCGGTGAATATCGACAATATTCAAACCCAAGCATTGGTTTATTTGGAAAAGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCGCGGCCCACTCGATGCCGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTAAATCCACAAAAATATCCAGCAGATATTCAACGGGCAATTAATGAAACACATCAGGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAAAAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006344","ARO_id":"44806","ARO_name":"ADC-172","CARD_short_name":"ADC-172","ARO_description":"ADC-172 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3977":{"model_id":"3977","model_name":"TEM-9","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8462":{"protein_sequence":{"accession":"WP_102607453.1","sequence":"MSIQHFRVALIPFFAAFCFPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVKYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDSWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYMTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"NG_056168.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCTTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTAAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATAGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACATGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000881","ARO_id":"37261","ARO_name":"TEM-9","CARD_short_name":"TEM-9","ARO_description":"TEM-9 is an extended-spectrum beta-lactamase that has been found in clinical isolates.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3978":{"model_id":"3978","model_name":"TEM-31","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6342":{"protein_sequence":{"accession":"WP_165539487.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSCGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"NG_068213.1","fmin":"100","fmax":"961","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTTGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3000901","ARO_id":"37281","ARO_name":"TEM-31","CARD_short_name":"TEM-31","ARO_description":"TEM-31 is an inhibitor-resistant beta-lactamase that has been found in clinical isolates.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3979":{"model_id":"3979","model_name":"TEM-32","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6343":{"protein_sequence":{"accession":"WP_052944427.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMISTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTTPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"NG_050261.1","fmin":"100","fmax":"961","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATTAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGACGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36790","NCBI_taxonomy_name":"Shigella sonnei","NCBI_taxonomy_id":"624"}}}},"ARO_accession":"3000902","ARO_id":"37282","ARO_name":"TEM-32","CARD_short_name":"TEM-32","ARO_description":"TEM-32 is an inhibitor-resistant beta-lactamase that has been found in clinical isolates.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3980":{"model_id":"3980","model_name":"TEM-35","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6344":{"protein_sequence":{"accession":"WP_063864910.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMLSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERDRQIAEIGASLIKHW"},"dna_sequence":{"accession":"NG_050264.1","fmin":"13","fmax":"874","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGCTGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAGATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000905","ARO_id":"37285","ARO_name":"TEM-35","CARD_short_name":"TEM-35","ARO_description":"TEM-35 is an inhibitor-resistant beta-lactamase that has been found in clinical isolates.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3981":{"model_id":"3981","model_name":"TEM-36","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6345":{"protein_sequence":{"accession":"WP_075985685.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMVSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERDRQIAEIGASLIKHW"},"dna_sequence":{"accession":"NG_052650.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGGTGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAGATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000906","ARO_id":"37286","ARO_name":"TEM-36","CARD_short_name":"TEM-36","ARO_description":"TEM-36 is an inhibitor-resistant beta-lactamase that has been found in clinical isolates.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3982":{"model_id":"3982","model_name":"TEM-37","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6346":{"protein_sequence":{"accession":"WP_159373457.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMISTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERDRQIAEIGASLIKHW"},"dna_sequence":{"accession":"NG_068214.1","fmin":"100","fmax":"961","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATCAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAGATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000907","ARO_id":"37287","ARO_name":"TEM-37","CARD_short_name":"TEM-37","ARO_description":"TEM-37 is an inhibitor-resistant beta-lactamase that has been found in clinical isolates.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3983":{"model_id":"3983","model_name":"TEM-39","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6347":{"protein_sequence":{"accession":"WP_148044474.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMLSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRREPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERDRQIAEIGASLIKHW"},"dna_sequence":{"accession":"NG_065940.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGCTGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATCGTCGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAGATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000909","ARO_id":"37289","ARO_name":"TEM-39","CARD_short_name":"TEM-39","ARO_description":"TEM-39 is an inhibitor-resistant beta-lactamase that has been found in clinical isolates.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3985":{"model_id":"3985","model_name":"TEM-210","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6349":{"protein_sequence":{"accession":"WP_032072208.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIEMDLNSGKILESFRPEERFPMLSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"NG_050243.1","fmin":"100","fmax":"961","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAAATGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGCTGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001387","ARO_id":"37787","ARO_name":"TEM-210","CARD_short_name":"TEM-210","ARO_description":"TEM-210.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3986":{"model_id":"3986","model_name":"TEM-212","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6350":{"protein_sequence":{"accession":"WP_063864901.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVENSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"NG_050245.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGAACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36946","NCBI_taxonomy_name":"Providencia stuartii","NCBI_taxonomy_id":"588"}}}},"ARO_accession":"3001389","ARO_id":"37789","ARO_name":"TEM-212","CARD_short_name":"TEM-212","ARO_description":"TEM-212 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3987":{"model_id":"3987","model_name":"TEM-224","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6351":{"protein_sequence":{"accession":"WP_063864908.1","sequence":"MSIKHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVKYSPVTEKHLTDGMTVRELCSAAITMTDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDSWEPELNEAIPNDERDTTTPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"NG_050254.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTAAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTAAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGACTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATAGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGACGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3005255","ARO_id":"43611","ARO_name":"TEM-224","CARD_short_name":"TEM-224","ARO_description":"TEM-224 is a beta-lactamase.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3988":{"model_id":"3988","model_name":"TEM-225","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6352":{"protein_sequence":{"accession":"WP_075985686.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVKYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTTPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGASERGSRGIIAALGPDGKPSRIVVIYTTGSQVTMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"NG_052651.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTAAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGACGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCAGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGTAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3005256","ARO_id":"43612","ARO_name":"TEM-225","CARD_short_name":"TEM-225","ARO_description":"TEM-225 is a beta-lactamase.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3989":{"model_id":"3989","model_name":"TEM-226","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6353":{"protein_sequence":{"accession":"WP_085562398.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVKYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSVLPAGWFIADKSGASERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"NG_054684.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTAAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGTCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCAGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3005257","ARO_id":"43613","ARO_name":"TEM-226","CARD_short_name":"TEM-226","ARO_description":"TEM-226 is a beta lactamase.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3997":{"model_id":"3997","model_name":"TEM-234","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6361":{"protein_sequence":{"accession":"WP_109791210.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQSTMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"NG_057609.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGTCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005265","ARO_id":"43621","ARO_name":"TEM-234","CARD_short_name":"TEM-234","ARO_description":"TEM-234 is a beta-lactamase.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3998":{"model_id":"3998","model_name":"TEM-235","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6362":{"protein_sequence":{"accession":"WP_110174956.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIDDKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"NG_059898.1","fmin":"100","fmax":"961","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGATGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43623","NCBI_taxonomy_name":"mixed culture bacterium PE_gF3SD01_32","NCBI_taxonomy_id":"663178"}}}},"ARO_accession":"3005266","ARO_id":"43622","ARO_name":"TEM-235","CARD_short_name":"TEM-235","ARO_description":"TEM-235 is a beta-lactamase.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3999":{"model_id":"3999","model_name":"TEM-236","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6363":{"protein_sequence":{"accession":"WP_116786831.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDCWEPELNEAIPNDERDTTTPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"NG_061611.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATTGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGACGCCCGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3005267","ARO_id":"43624","ARO_name":"TEM-236","CARD_short_name":"TEM-236","ARO_description":"TEM-236 is a beta-lactamase.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4000":{"model_id":"4000","model_name":"TEM-237","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6364":{"protein_sequence":{"accession":"WP_122630841.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGGQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"NG_062250.1","fmin":"100","fmax":"961","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGGGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3005268","ARO_id":"43625","ARO_name":"TEM-237","CARD_short_name":"TEM-237","ARO_description":"TEM-237 is a beta-lactamase.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4001":{"model_id":"4001","model_name":"TEM-238","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6365":{"protein_sequence":{"accession":"WP_131419583.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMISTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRREPELNEAIPNDERDTTTPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"NG_067163.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATAAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTAGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGACGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3005269","ARO_id":"43626","ARO_name":"TEM-238","CARD_short_name":"TEM-238","ARO_description":"TEM-238 is a beta-lactamase.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4002":{"model_id":"4002","model_name":"TEM-240","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6366":{"protein_sequence":{"accession":"WP_150823495.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTTPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGEHGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"NG_066544.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGACGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCATGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42612","NCBI_taxonomy_name":"Klebsiella variicola","NCBI_taxonomy_id":"244366"}}}},"ARO_accession":"3005270","ARO_id":"43627","ARO_name":"TEM-240","CARD_short_name":"TEM-240","ARO_description":"TEM-240 is a beta-lactamase.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4003":{"model_id":"4003","model_name":"TEM-241","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6367":{"protein_sequence":{"accession":"WP_148044472.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDKLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLRNMGDHVTRLDHWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"NG_065938.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATAAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCGCAACATGGGGGATCATGTAACCCGCCTTGATCATTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005271","ARO_id":"43628","ARO_name":"TEM-241","CARD_short_name":"TEM-241","ARO_description":"TEM-241 is a beta-lactamase.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4004":{"model_id":"4004","model_name":"TEM-242","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6368":{"protein_sequence":{"accession":"WP_148044473.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVKYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDSWEPELNEAIPNDERDTTTPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"NG_065939.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTAAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATAGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGACGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36946","NCBI_taxonomy_name":"Providencia stuartii","NCBI_taxonomy_id":"588"}}}},"ARO_accession":"3005272","ARO_id":"43629","ARO_name":"TEM-242","CARD_short_name":"TEM-242","ARO_description":"TEM-242 is a beta-lactamase.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4005":{"model_id":"4005","model_name":"TEM-243","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6369":{"protein_sequence":{"accession":"WP_197749416.1","sequence":"MSIQHFRVARRPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"NG_071226.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCGAAGGCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3005273","ARO_id":"43630","ARO_name":"TEM-243","CARD_short_name":"TEM-243","ARO_description":"TEM-243 is a beta-lactamase.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4006":{"model_id":"4006","model_name":"PDC-225","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"6370":{"protein_sequence":{"accession":"WP_058169941.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_056103.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005274","ARO_id":"43631","ARO_name":"PDC-225","CARD_short_name":"PDC-225","ARO_description":"PDC-225 is a class C beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4015":{"model_id":"4015","model_name":"PDC-413","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"6380":{"protein_sequence":{"accession":"WP_168247897.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKHLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_068201.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGACGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAACTGTTCCCAGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCACCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATTCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005282","ARO_id":"43639","ARO_name":"PDC-413","CARD_short_name":"PDC-413","ARO_description":"PDC-413 is a class C beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4016":{"model_id":"4016","model_name":"PDC-264","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"6382":{"protein_sequence":{"accession":"WP_109791198.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQLPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_057596.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGCTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005284","ARO_id":"43641","ARO_name":"PDC-264","CARD_short_name":"PDC-264","ARO_description":"PDC-264 is a class C beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4017":{"model_id":"4017","model_name":"PDC-201","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"6383":{"protein_sequence":{"accession":"WP_087587966.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRRYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQVGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_054986.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGTCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCGCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGTCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005285","ARO_id":"43642","ARO_name":"PDC-201","CARD_short_name":"PDC-201","ARO_description":"PDC-201 is a class C beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4018":{"model_id":"4018","model_name":"PDC-346","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"6384":{"protein_sequence":{"accession":"WP_148044438.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIDLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_065898.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGACCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005286","ARO_id":"43643","ARO_name":"PDC-346","CARD_short_name":"PDC-346","ARO_description":"PDC-346 is a class C beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4019":{"model_id":"4019","model_name":"PDC-285","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"6385":{"protein_sequence":{"accession":"WP_073669325.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAAHSLGQPFKRLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_060555.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTAGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCACAGCCTGGGCCAGCCGTTCAAACGGCTCATGGAGCAGCAACTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCCCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCATGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005287","ARO_id":"43644","ARO_name":"PDC-285","CARD_short_name":"PDC-285","ARO_description":"PDC-285 is a class C beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4020":{"model_id":"4020","model_name":"PDC-337","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"6386":{"protein_sequence":{"accession":"WP_148044429.1","sequence":"MRDTRFPCLCGIAASTLLFAATPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAKGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQPKVPLKR"},"dna_sequence":{"accession":"NG_065889.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCGCCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCAAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGCCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005288","ARO_id":"43645","ARO_name":"PDC-337","CARD_short_name":"PDC-337","ARO_description":"PDC-337 is a class C beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4021":{"model_id":"4021","model_name":"PDC-212","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"6387":{"protein_sequence":{"accession":"WP_088245217.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLAIYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_055274.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGATCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005289","ARO_id":"43646","ARO_name":"PDC-212","CARD_short_name":"PDC-212","ARO_description":"PDC-212 is a class C beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4022":{"model_id":"4022","model_name":"PDC-352","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"6388":{"protein_sequence":{"accession":"WP_148044444.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRRYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALKGQRLLNKTGSTSGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_065904.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGTCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCGCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGAAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAGCGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005290","ARO_id":"43647","ARO_name":"PDC-352","CARD_short_name":"PDC-352","ARO_description":"PDC-352 is a class C beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4023":{"model_id":"4023","model_name":"PDC-464","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"6389":{"protein_sequence":{"accession":"WP_197749413.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRVSQHWPALQGSRFDGISLLDLATYTAGGLPLKFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTYLDVPEAALAQYAQGYGKDDRPLRAGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTSGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_071222.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTAGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGTCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGAAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCTACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCCCTACGGGCCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAGCGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005291","ARO_id":"43648","ARO_name":"PDC-464","CARD_short_name":"PDC-464","ARO_description":"PDC-464 is a class C beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4024":{"model_id":"4024","model_name":"PDC-19b","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"6390":{"protein_sequence":{"accession":"WP_023874922.1","sequence":"MRDTRFSCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTTTLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_049890.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCTCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCACCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005292","ARO_id":"43649","ARO_name":"PDC-19b","CARD_short_name":"PDC-19b","ARO_description":"PDC-19b is a class C beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4025":{"model_id":"4025","model_name":"PDC-380","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"6391":{"protein_sequence":{"accession":"WP_148044466.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPTDRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALTQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_065932.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGACGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGACCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGTTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005293","ARO_id":"43650","ARO_name":"PDC-380","CARD_short_name":"PDC-380","ARO_description":"PDC-380 is a class C beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4026":{"model_id":"4026","model_name":"PDC-461","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"6392":{"protein_sequence":{"accession":"WP_197749410.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRVSQHWPALQGSRFDGISLLDLATYTAGGLPLKFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRAGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_071219.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTAGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGTCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGAAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCCCTACGGGCCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005294","ARO_id":"43651","ARO_name":"PDC-461","CARD_short_name":"PDC-461","ARO_description":"PDC-461 is a class C beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4027":{"model_id":"4027","model_name":"PDC-19a","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"6393":{"protein_sequence":{"accession":"WP_003132320.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_049889.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCTTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATTCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37066","NCBI_taxonomy_name":"Pseudomonas","NCBI_taxonomy_id":"286"}}}},"ARO_accession":"3005295","ARO_id":"43652","ARO_name":"PDC-19a","CARD_short_name":"PDC-19a","ARO_description":"PDC-19a is a class C beta-lactamase found in Pseudomonas (multispecies).","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4028":{"model_id":"4028","model_name":"PDC-272","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"6394":{"protein_sequence":{"accession":"WP_109791204.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPTDRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_057603.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGACGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005296","ARO_id":"43653","ARO_name":"PDC-272","CARD_short_name":"PDC-272","ARO_description":"PDC-272 is a class C beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4029":{"model_id":"4029","model_name":"PDC-255","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"6395":{"protein_sequence":{"accession":"WP_109791189.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRRYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_057587.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCGCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005297","ARO_id":"43654","ARO_name":"PDC-255","CARD_short_name":"PDC-255","ARO_description":"PDC-255 is a class C beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4030":{"model_id":"4030","model_name":"PDC-293","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"6396":{"protein_sequence":{"accession":"WP_111672905.1","sequence":"MRDTRFPCLCGIAASTLLFAATPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_060563.1","fmin":"0","fmax":"1185","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCGCCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCATTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGCAACCACACAGGATCGCTAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTATGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005298","ARO_id":"43655","ARO_name":"PDC-293","CARD_short_name":"PDC-293","ARO_description":"PDC-293 is a class C beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4031":{"model_id":"4031","model_name":"PDC-183","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"6397":{"protein_sequence":{"accession":"WP_087587954.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPAPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_054969.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGCCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005299","ARO_id":"43656","ARO_name":"PDC-183","CARD_short_name":"PDC-183","ARO_description":"PDC-183 is a class C beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4032":{"model_id":"4032","model_name":"PDC-207","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"6398":{"protein_sequence":{"accession":"WP_058161279.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRRYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAESYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_054992.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGTCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCGCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAAGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005300","ARO_id":"43657","ARO_name":"PDC-207","CARD_short_name":"PDC-207","ARO_description":"PDC-207 is a class C beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4033":{"model_id":"4033","model_name":"PDC-306","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"6399":{"protein_sequence":{"accession":"WP_116786838.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYTQGYGKDDRPLRVGPGPLDAKGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_061625.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCTTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACACCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCAAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATTCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005301","ARO_id":"43658","ARO_name":"PDC-306","CARD_short_name":"PDC-306","ARO_description":"PDC-306 is a class C beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4034":{"model_id":"4034","model_name":"PDC-376","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"6400":{"protein_sequence":{"accession":"WP_148044462.1","sequence":"MRDTGFPCLCGIAASTLLFAATSAIAGEAPADRLKTLVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASLHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYTPGSQRLYSNPSIGLFGYLAARSLGQPFERIMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLVKPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGSDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_065928.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCGGATTCCCCTGCCTGTGCGGCATCGCCGCCTCCACACTGCTGTTCGCCGCCACCTCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGACACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGATATTCCGGGCCTGGCCGTGGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCTTCGAAAGAGGACGGTCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCTGCACTGGCCGGCGCTGCAAGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAAGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACACGCCGGGCAGCCAGCGCCTCTACTCCAACCCGAGCATCGGTCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGATCATGGAGCAGCAACTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGTCAAGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCGGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGACTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATCCCAGGCAGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005302","ARO_id":"43659","ARO_name":"PDC-376","CARD_short_name":"PDC-376","ARO_description":"PDC-376 is a class C beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4035":{"model_id":"4035","model_name":"PDC-117","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"6401":{"protein_sequence":{"accession":"WP_031687354.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLNRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_055481.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGTCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGAACAGGCCATGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005303","ARO_id":"43660","ARO_name":"PDC-117","CARD_short_name":"PDC-117","ARO_description":"PDC-117 is a class C beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4036":{"model_id":"4036","model_name":"PDC-231","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"6402":{"protein_sequence":{"accession":"WP_104009860.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALTQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_056423.1","fmin":"0","fmax":"1185","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGACCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTTCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005304","ARO_id":"43661","ARO_name":"PDC-231","CARD_short_name":"PDC-231","ARO_description":"PDC-231 is a class C beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4037":{"model_id":"4037","model_name":"PDC-104","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"6403":{"protein_sequence":{"accession":"WP_058129018.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTVTLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMVLQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_049871.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGTCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAACTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGTGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005305","ARO_id":"43662","ARO_name":"PDC-104","CARD_short_name":"PDC-104","ARO_description":"PDC-104 is a class C beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4038":{"model_id":"4038","model_name":"PDC-173","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"6404":{"protein_sequence":{"accession":"WP_099982812.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALTQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLPEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_055780.1","fmin":"0","fmax":"1170","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGACCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005306","ARO_id":"43663","ARO_name":"PDC-173","CARD_short_name":"PDC-173","ARO_description":"PDC-173 is a class C beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4039":{"model_id":"4039","model_name":"PDC-292","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"6405":{"protein_sequence":{"accession":"WP_111672904.1","sequence":"MRDTRFPCLCGIAASTLLFAATPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTKGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_060562.1","fmin":"0","fmax":"1173","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCGCCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCATTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAAAGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTATGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005307","ARO_id":"43664","ARO_name":"PDC-292","CARD_short_name":"PDC-292","ARO_description":"PDC-292 is a class C beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4040":{"model_id":"4040","model_name":"PDC-393","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"6406":{"protein_sequence":{"accession":"WP_164461297.1","sequence":"MRDTRFSCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_068033.1","fmin":"0","fmax":"1197","strand":"+","sequence":"ATGCGCGATACCAGATTCTCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCCGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACTCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACAACGGCTTCGGCGCCTACGTGGCGTTCATTCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005308","ARO_id":"43665","ARO_name":"PDC-393","CARD_short_name":"PDC-393","ARO_description":"PDC-393 is a class C beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4041":{"model_id":"4041","model_name":"PDC-119","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"6407":{"protein_sequence":{"accession":"WP_058128316.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPSPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_055483.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCACGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCAGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005309","ARO_id":"43666","ARO_name":"PDC-119","CARD_short_name":"PDC-119","ARO_description":"PDC-119 is a class C beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4042":{"model_id":"4042","model_name":"PDC-313","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"6408":{"protein_sequence":{"accession":"WP_122630851.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQAPEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_062264.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCCGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005310","ARO_id":"43667","ARO_name":"PDC-313","CARD_short_name":"PDC-313","ARO_description":"PDC-313 is a class C beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4043":{"model_id":"4043","model_name":"PDC-257","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"6409":{"protein_sequence":{"accession":"WP_109791191.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLRAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_057589.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCGGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005311","ARO_id":"43668","ARO_name":"PDC-257","CARD_short_name":"PDC-257","ARO_description":"PDC-257 is a class C beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4044":{"model_id":"4044","model_name":"PDC-429","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"6410":{"protein_sequence":{"accession":"WP_179284370.1","sequence":"MRDTRFPCLCGIAASTLLFAATPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDLAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_070195.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCGCCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTGGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCTGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005312","ARO_id":"43669","ARO_name":"PDC-429","CARD_short_name":"PDC-429","ARO_description":"PDC-429 is a class C beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4045":{"model_id":"4045","model_name":"PDC-449","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"6411":{"protein_sequence":{"accession":"WP_179284386.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPRDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_070215.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCTTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCGGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATTCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005313","ARO_id":"43670","ARO_name":"PDC-449","CARD_short_name":"PDC-449","ARO_description":"PDC-449 is a class C beta-lactamase found in Pseudomonas aeruginosa.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4046":{"model_id":"4046","model_name":"OXA-540","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"505"}},"model_sequences":{"sequence":{"8397":{"protein_sequence":{"accession":"AHN60085.1","sequence":"MAIRIFAILFSIFSLATFAHAQEGTLARSDWRKFFSEFQAKGTIVVADERQADRAMLVFDPVRSKKRYSPASTFKIPHTLFALDAGAVRDEFQIFRWDGVNRGFAGHNQDQDLRSAMRNSTVWVYELFAKEIGDDKARRYLKKIDYGNADPSTSNGDYWIEGSLAISAQEQIAFLRKLYRNELPFRVEHQRLVKDLMIVEAGRNWILRAKTGWEGRMGWWVGWVEWPTGSVFFALNIDTPNRMDDLFKREAIVRAILRSIEALPPNPAVNSDAAR"},"dna_sequence":{"accession":"KJ138219.1","fmin":"118","fmax":"946","strand":"+","sequence":"ATGGCAATCCGAATCTTCGCGATACTTTTCTCCATTTTTTCTCTTGCCACTTTCGCGCATGCGCAAGAAGGCACGCTAGCACGTTCTGACTGGAGGAAGTTTTTCAGCGAATTTCAAGCCAAAGGCACGATAGTTGTGGCAGACGAACGCCAAGCGGATCGTGCCATGTTGGTTTTTGATCCTGTGCGATCGAAGAAACGCTACTCGCCTGCATCGACATTCAAGATACCTCATACACTTTTTGCACTTGATGCAGGCGCTGTTCGTGATGAGTTCCAGATTTTTCGATGGGACGGCGTTAACAGGGGCTTTGCAGGCCACAATCAAGACCAAGATTTGCGATCAGCAATGCGGAATTCTACTGTTTGGGTGTATGAGCTATTTGCAAAGGAAATTGGTGATGACAAAGCTCGGCGCTATTTGAAGAAAATCGACTATGGCAACGCCGATCCTTCGACAAGTAATGGCGATTACTGGATAGAAGGCAGCCTTGCAATCTCGGCGCAGGAGCAAATTGCATTTCTCAGGAAGCTCTATCGTAACGAGCTGCCCTTTCGGGTAGAACATCAGCGCTTGGTCAAGGATCTCATGATTGTGGAAGCCGGTCGCAACTGGATACTGCGTGCAAAGACGGGCTGGGAAGGCCGTATGGGTTGGTGGGTAGGATGGGTTGAGTGGCCGACTGGCTCCGTATTCTTCGCACTGAATATTGATACGCCAAACAGAATGGATGATCTTTTCAAGAGGGAGGCAATCGTGCGGGCAATCCTTCGCTCTATTGAAGCGTTACCGCCCAACCCGGCAGTCAACTCGGACGCTGCGCGATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37076","NCBI_taxonomy_name":"Stenotrophomonas maltophilia","NCBI_taxonomy_id":"40324"}}}},"ARO_accession":"3005314","ARO_id":"43671","ARO_name":"OXA-540","CARD_short_name":"OXA-540","ARO_description":"OXA-540 is a beta-lactamase in the OXA-2 family of OXA beta-lactamases that confers resistance to ampicillin and cephalothin.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46493":{"category_aro_accession":"3007704","category_aro_cvterm_id":"46493","category_aro_name":"OXA-2-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-2.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4047":{"model_id":"4047","model_name":"OXA-779","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6413":{"protein_sequence":{"accession":"WP_122634438.1","sequence":"MAIRFFTILLSTFFLTSFVYAQEHVVIRSDWKKFFSDLQAEGAIVIADERQAKHTLSVFDQERAAKRYSPASTFKIPHTLFALDADAVRDEFQVFRWDGVNRSFAGHNQNQDLRSAMRNSTVWVYELFAKDIGEDKARRYLKQIDYGNVDPSTIKGDYWIDGNLKISAHEQILFLRKLYRNQLPFKVEHQRLVKDLMITEAGRSWILRAKTGWEGRFGWWVGWIEWPTGPVFFALNIDTPNRTDDLFKREAIARAILRSIDALPPN"},"dna_sequence":{"accession":"NG_062354.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGGCAATCCGATTCTTCACCATACTGCTATCCACCTTCTTTCTTACCTCATTCGTGTATGCGCAAGAACATGTGGTAATCCGTTCGGACTGGAAAAAGTTCTTCAGCGACCTCCAGGCCGAAGGTGCAATCGTTATTGCAGACGAACGTCAAGCGAAGCATACTTTATCGGTTTTTGATCAAGAGCGAGCGGCAAAGCGTTACTCGCCAGCTTCAACCTTCAAGATACCCCACACACTTTTTGCACTTGATGCAGACGCCGTTCGTGATGAGTTCCAGGTTTTTCGATGGGACGGCGTTAACCGAAGCTTTGCAGGTCACAATCAAAACCAAGATTTGCGATCAGCGATGCGAAATTCTACGGTTTGGGTTTATGAGCTGTTTGCAAAAGATATCGGAGAGGACAAAGCAAGACGTTATTTAAAGCAAATTGATTATGGCAACGTCGATCCTTCGACAATCAAGGGCGATTACTGGATAGATGGAAATCTTAAAATCTCAGCGCACGAACAGATTTTGTTTCTCAGAAAACTCTATCGAAATCAGTTACCATTTAAGGTGGAGCACCAGCGCTTGGTGAAAGATCTCATGATTACGGAAGCCGGGCGCAGTTGGATACTACGCGCAAAGACCGGCTGGGAAGGCAGGTTTGGCTGGTGGGTAGGGTGGATTGAATGGCCAACAGGCCCCGTATTCTTTGCGCTGAATATTGATACGCCAAACAGAACGGACGATCTTTTCAAAAGAGAGGCCATCGCACGGGCAATCCTTCGTTCTATTGACGCATTGCCACCCAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005315","ARO_id":"43672","ARO_name":"OXA-779","CARD_short_name":"OXA-779","ARO_description":"OXA-779 is a beta-lactamase in the OXA-46 family of OXA beta-lactamases that confers resistance to ampicillin and cephalothin.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46509":{"category_aro_accession":"3007720","category_aro_cvterm_id":"46509","category_aro_name":"OXA-46-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-46.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4048":{"model_id":"4048","model_name":"OXA-838","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"475"}},"model_sequences":{"sequence":{"6414":{"protein_sequence":{"accession":"QEJ74001.1","sequence":"MAIRIFAILFSIFSLATFAHAQEGTLERSDWRKFFSEFQAKGTIVVADERQADRAMLVFDPVRSKKRYSPASTFKIPHTLFALDAGAVRDEFQIFRWDGVNRGFAGHNQDQDLRSAMRNSTVWVYELFAKEIGDDKARRYLKKIDYGKADPSTSNGDYWIEGSLAISAQEQIAFLRKLYRNELPFRVEHQRLVKDLMIVEAGRNWILRAKTGWEGRMGWWVGWVEWPTGSVFFALNIDTPNRMDDLFKREAIVRAILRSIEALPPNPAVNSDAAR"},"dna_sequence":{"accession":"MN339504.1","fmin":"0","fmax":"828","strand":"+","sequence":"ATGGCAATCCGAATCTTCGCGATACTTTTCTCCATTTTTTCTCTTGCCACTTTCGCGCATGCGCAAGAAGGCACGCTAGAACGTTCTGACTGGAGGAAGTTTTTCAGCGAATTTCAAGCCAAAGGCACGATAGTTGTGGCAGACGAACGCCAAGCGGATCGTGCCATGTTGGTTTTTGATCCTGTGCGATCGAAGAAACGCTACTCGCCTGCATCGACATTCAAGATACCTCATACACTTTTTGCACTTGATGCAGGCGCTGTTCGTGATGAGTTCCAGATTTTTCGATGGGACGGCGTTAACAGGGGCTTTGCAGGCCACAATCAAGACCAAGATTTGCGATCAGCAATGCGGAATTCTACTGTTTGGGTGTATGAGCTATTTGCAAAGGAAATTGGTGATGACAAAGCTCGGCGCTATTTGAAGAAAATCGACTATGGCAAAGCCGATCCTTCGACAAGTAATGGCGATTACTGGATAGAAGGCAGCCTTGCAATCTCGGCGCAGGAGCAAATTGCATTTCTCAGGAAGCTCTATCGTAACGAGCTGCCCTTTCGGGTAGAACATCAGCGCTTGGTCAAGGATCTCATGATTGTGGAAGCCGGTCGCAACTGGATACTGCGTGCAAAGACGGGCTGGGAAGGCCGTATGGGTTGGTGGGTAGGATGGGTTGAGTGGCCGACTGGCTCCGTATTCTTCGCACTGAATATTGATACGCCAAACAGAATGGATGATCTTTTCAAGAGGGAGGCAATCGTGCGGGCAATCCTTCGCTCTATTGAAGCGTTACCGCCTAACCCGGCAGTCAACTCGGACGCTGCGCGATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005316","ARO_id":"43673","ARO_name":"OXA-838","CARD_short_name":"OXA-838","ARO_description":"OXA-838 is a beta-lactamase in the OXA-2 family of OXA beta-lactamases that confers resistance to ampicillin and cephalothin.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46493":{"category_aro_accession":"3007704","category_aro_cvterm_id":"46493","category_aro_name":"OXA-2-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-2.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4049":{"model_id":"4049","model_name":"OXA-539","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6415":{"protein_sequence":{"accession":"WP_071593233.1","sequence":"MAIRIFAILFSIFSLATFAHAQEGTLERSDWRKFFSEFQAKGTIVVADERQADRAMLVFDPVRSKKRYSPASTFKIPHTLFALDAGAVRDEFQIFRWDGVNRGFAGHNQDQDLRSAMRNSTVWVYELFAKEIGDDKARRYLKKIDYGNADDPSTSNGDYWIEGSLAISAQEQIAFLRKLYRNELPFRVEHQRLVKDLMIVEAGRNWILRAKTGWEGRMGWWVGWVEWPTGSVFFALNIDTPNRMDDLFKREAIVRAILRSIEALPPNPAVNSDAAR"},"dna_sequence":{"accession":"NG_052064.1","fmin":"0","fmax":"831","strand":"+","sequence":"ATGGCAATCCGAATCTTCGCGATACTTTTCTCCATTTTTTCTCTTGCCACTTTCGCGCATGCGCAAGAAGGCACGCTAGAACGTTCTGACTGGAGGAAGTTTTTCAGCGAATTTCAAGCCAAAGGCACGATAGTTGTGGCAGACGAACGCCAAGCGGATCGTGCCATGTTGGTTTTTGATCCTGTGCGATCGAAGAAACGCTACTCGCCTGCATCGACATTCAAGATACCTCATACACTTTTTGCACTTGATGCAGGCGCTGTTCGTGATGAGTTCCAGATTTTTCGATGGGACGGCGTTAACAGGGGCTTTGCAGGCCACAATCAAGACCAAGATTTGCGATCAGCAATGCGGAATTCTACTGTTTGGGTGTATGAGCTATTTGCAAAGGAAATTGGTGATGACAAAGCTCGGCGCTATTTGAAGAAAATCGACTATGGCAACGCCGATGATCCTTCGACAAGTAATGGCGATTACTGGATAGAAGGCAGCCTTGCAATCTCGGCGCAGGAGCAAATTGCATTTCTCAGGAAGCTCTATCGTAACGAGCTGCCCTTTCGGGTAGAACATCAGCGCTTGGTCAAGGATCTCATGATTGTGGAAGCCGGTCGCAACTGGATACTGCGTGCAAAGACGGGCTGGGAAGGCCGTATGGGTTGGTGGGTAGGATGGGTTGAGTGGCCGACTGGCTCCGTATTCTTCGCACTGAATATTGATACGCCAAACAGAATGGATGATCTTTTCAAGAGGGAGGCAATCGTGCGGGCAATCCTTCGCTCTATTGAAGCGTTACCGCCCAACCCGGCAGTCAACTCGGACGCTGCGCGATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005317","ARO_id":"43674","ARO_name":"OXA-539","CARD_short_name":"OXA-539","ARO_description":"OXA-539 is a beta-lactamase in the OXA-2 family of OXA beta-lactamases that confers resistance to ampicillin and cephalothin.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46493":{"category_aro_accession":"3007704","category_aro_cvterm_id":"46493","category_aro_name":"OXA-2-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-2.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4050":{"model_id":"4050","model_name":"OXA-543","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"505"}},"model_sequences":{"sequence":{"8395":{"protein_sequence":{"accession":"OPD39435.1","sequence":"MAIRIFAILFSIFSLATFAHAQEGTLERSDWRKFFSEFQAKGTIVVADERQADRAMLVFDPVRSKKRYSPASTFKIPHTLFALDAGAVRDEFQIFRWDGVNRGFAGHNQDQDLRSAMRNSTVWVYELFAKEIGDDKARRYLKKIDYGNADPSTSNGDYGIEGSLAISAQEQIAFLRKLYRNELPFRVEHQRLVKDLMIVEAGRNWILRAKTGWEGRMGWWVGWVEWPTGSVFFALNIDTPNRMDDLFKREAIVRAILRSIEALPPNPAVNSDAAR"},"dna_sequence":{"accession":"LLTZ01000057.1","fmin":"2151","fmax":"2979","strand":"+","sequence":"ATGGCAATCCGAATCTTCGCGATACTTTTCTCCATTTTTTCTCTTGCCACTTTCGCGCATGCGCAAGAAGGCACGCTAGAACGTTCTGACTGGAGGAAGTTTTTCAGCGAATTTCAAGCCAAAGGCACGATAGTTGTGGCAGACGAACGCCAAGCGGATCGTGCCATGTTGGTTTTTGATCCTGTGCGATCGAAGAAACGCTACTCGCCTGCATCGACATTCAAGATACCTCATACACTTTTTGCACTTGATGCAGGCGCTGTTCGTGATGAGTTCCAGATTTTTCGATGGGACGGCGTTAACAGGGGCTTTGCAGGCCACAATCAAGACCAAGATTTGCGATCAGCAATGCGGAATTCTACTGTTTGGGTGTATGAGCTATTTGCAAAGGAAATTGGTGATGACAAAGCTCGGCGCTATTTGAAGAAAATCGACTATGGCAACGCCGATCCTTCGACAAGTAATGGCGATTACGGGATAGAAGGCAGCCTTGCAATCTCGGCGCAGGAGCAAATTGCATTTCTCAGGAAGCTCTATCGTAACGAGCTGCCCTTTCGGGTAGAACATCAGCGCTTGGTCAAGGATCTCATGATTGTGGAAGCCGGTCGCAACTGGATACTGCGTGCAAAGACGGGCTGGGAAGGCCGTATGGGTTGGTGGGTAGGATGGGTTGAGTGGCCGACTGGCTCCGTATTCTTCGCACTGAATATTGATACGCCAAACAGAATGGATGATCTTTTCAAGAGGGAGGCAATCGTGCGGGCAATCCTTCGCTCTATTGAAGCGTTACCGCCCAACCCGGCAGTCAACTCGGACGCTGCGCGATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005318","ARO_id":"43675","ARO_name":"OXA-543","CARD_short_name":"OXA-543","ARO_description":"OXA-543 is a beta-lactamase in the OXA-2 family of OXA beta-lactamases that confers resistance to ampicillin and cephalothin.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46493":{"category_aro_accession":"3007704","category_aro_cvterm_id":"46493","category_aro_name":"OXA-2-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-2.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4051":{"model_id":"4051","model_name":"OXA-681","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6418":{"protein_sequence":{"accession":"WP_122630881.1","sequence":"MAIRIFAILFSIFSLATFAHAQEGTLERSDWRKFFSEFQAKGTIVVADERQADRAMLVFDPVRSKKRYSPASTFKIPHTLFALDAGAVRDEFQIFRWDGVNRGFAGHNQDQDLRSAMRNSTVWVYELFAKEIGDDKARRYLKKIDYGNADPSTSNGDYWKGSLAISAQEQIAFLRKLYRNELPFRVEHQRLVKDLMIVEAGRNWILRAKTGWEGRMGWWVGWVEWPTGSVFFALNIDTPNRMDDLFKREAIVRAILRSIEALPPNPAVNSDAAR"},"dna_sequence":{"accession":"NG_062301.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGGCAATCCGAATCTTCGCGATACTTTTCTCCATTTTTTCTCTTGCCACTTTCGCGCATGCGCAAGAAGGCACGCTAGAACGTTCTGACTGGAGGAAGTTTTTCAGCGAATTTCAAGCCAAAGGCACGATAGTTGTGGCAGACGAACGCCAAGCGGATCGTGCCATGTTGGTTTTTGATCCTGTGCGATCGAAGAAACGCTACTCGCCTGCATCGACATTCAAGATACCTCATACACTTTTTGCACTTGATGCAGGCGCTGTTCGTGATGAGTTCCAGATTTTTCGATGGGACGGCGTTAACAGGGGCTTTGCAGGCCACAATCAAGACCAAGATTTGCGATCAGCAATGCGGAATTCTACTGTTTGGGTGTATGAGCTATTTGCAAAGGAAATTGGTGATGACAAAGCTCGGCGCTATTTGAAGAAAATCGACTATGGCAACGCCGATCCTTCGACAAGTAATGGCGATTACTGGAAAGGCAGCCTTGCAATCTCGGCGCAGGAGCAAATTGCATTTCTCAGGAAGCTCTATCGTAACGAGCTGCCCTTTCGGGTAGAACATCAGCGCTTGGTCAAGGATCTCATGATTGTGGAAGCCGGTCGCAACTGGATACTGCGTGCAAAGACGGGCTGGGAAGGCCGTATGGGTTGGTGGGTAGGATGGGTTGAGTGGCCGACTGGCTCCGTATTCTTCGCACTGAATATTGATACGCCAAACAGAATGGATGATCTTTTCAAGAGGGAGGCAATCGTGCGGGCAATCCTTCGCTCTATTGAAGCGTTACCGCCCAACCCGGCAGTCAACTCGGACGCTGCGCGATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005319","ARO_id":"43676","ARO_name":"OXA-681","CARD_short_name":"OXA-681","ARO_description":"OXA-681 is a beta-lactamase in the OXA-2 family of OXA beta-lactamases that confers resistance to ampicillin and cephalothin.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46493":{"category_aro_accession":"3007704","category_aro_cvterm_id":"46493","category_aro_name":"OXA-2-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-2.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4052":{"model_id":"4052","model_name":"OXA-737","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6419":{"protein_sequence":{"accession":"WP_122630856.1","sequence":"MAIRIFAILFSIFSLATFAHAQEGTLERSDWRKFFSEFQAKGTIVVADERQADRAMLVFDPVRSKKRYSPASTFKIPHTLFALDAGAVRDEFQIFRWDGVNRGFAGHNQDQDLRSAMRNSTVWVYELFAKEIGDDKARRYLKKIDYGNPDPSTSNGDYWIEGSLAISAQEQIAFLRKLYRNELPFRVEHQRLVKDLMIVEAGRNWILRAKTGWEGRMGWWVGWVEWPTGSVFFALNIDTPNRMDDLFKREAIVRAILRSIEALPPNPAVNSDAAR"},"dna_sequence":{"accession":"NG_062269.1","fmin":"0","fmax":"828","strand":"+","sequence":"ATGGCAATCCGAATCTTCGCGATACTTTTCTCCATTTTTTCTCTTGCCACTTTCGCGCATGCGCAAGAAGGCACGCTAGAACGTTCTGACTGGAGGAAGTTTTTCAGCGAATTTCAAGCCAAAGGCACGATAGTTGTGGCAGACGAACGCCAAGCGGATCGTGCCATGTTGGTTTTTGATCCTGTGCGATCGAAGAAACGCTACTCGCCTGCATCGACATTCAAGATACCTCATACACTTTTTGCACTTGATGCAGGCGCTGTTCGTGATGAGTTCCAGATTTTTCGATGGGACGGCGTTAACAGGGGCTTTGCAGGCCACAATCAAGACCAAGATTTGCGATCAGCAATGCGGAATTCTACTGTTTGGGTGTATGAGCTATTTGCAAAGGAAATTGGTGATGACAAAGCTCGGCGCTATTTGAAGAAAATCGACTATGGCAACCCCGATCCTTCGACAAGTAATGGCGATTACTGGATAGAAGGCAGCCTTGCAATCTCGGCGCAGGAGCAAATTGCATTTCTCAGGAAGCTCTATCGTAACGAGCTGCCCTTTCGGGTAGAACATCAGCGCTTGGTCAAGGATCTCATGATTGTGGAAGCCGGTCGCAACTGGATACTGCGTGCAAAGACGGGCTGGGAAGGCCGTATGGGTTGGTGGGTAGGATGGGTTGAGTGGCCGACTGGCTCCGTATTCTTCGCACTGAATATTGATACGCCAAACAGAATGGATGATCTTTTCAAGAGGGAGGCAATCGTGCGGGCAATCCTTCGCTCTATTGAAGCGTTACCGCCCAACCCGGCAGTCAACTCGGACGCTGCGCGATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005320","ARO_id":"43677","ARO_name":"OXA-737","CARD_short_name":"OXA-737","ARO_description":"OXA-737 is a beta-lactamase in the OXA-2 family of OXA beta-lactamases that confers resistance to ampicillin and cephalothin.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46493":{"category_aro_accession":"3007704","category_aro_cvterm_id":"46493","category_aro_name":"OXA-2-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-2.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4053":{"model_id":"4053","model_name":"OXA-541","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8396":{"protein_sequence":{"accession":"CAQ77073.1","sequence":"MAIRIFAILFSIFSLATFAHAQEGTLERSDWRKFFSEFQAKGTIVVADERQADRAMLVFDPVRSKKRYSPASTFKIPHTLFALDAGAVRDEFQIFRWDGVNRGFAGHNQDQDLRSAMRNSTVWVYELFAKEIGDDKARRYLKKIDYGYADPSTSNGDYWIEGSLAISAQEQIAFLRKLYRNELPFRVEHQRLVKDLMIVEAGRNWILRAKTGWEGRMGWWVGWVEWPTGSVFFALNIDTPNRMDDLFKREAIVRAILRSIEALPPNPAVNSDAAR"},"dna_sequence":{"accession":"FM179467.1","fmin":"1938","fmax":"2766","strand":"+","sequence":"ATGGCAATCCGAATCTTCGCGATACTTTTCTCCATTTTTTCTCTTGCCACTTTCGCGCATGCGCAAGAAGGCACGCTAGAACGTTCTGACTGGAGGAAGTTTTTCAGCGAATTTCAAGCCAAAGGCACGATAGTTGTGGCAGACGAACGCCAAGCGGATCGTGCCATGTTGGTTTTTGATCCTGTGCGATCGAAGAAACGCTACTCGCCTGCATCGACATTCAAGATACCTCATACACTTTTTGCACTTGATGCAGGCGCTGTTCGTGATGAGTTCCAGATTTTTCGATGGGACGGCGTTAACAGGGGCTTTGCAGGCCACAATCAAGACCAAGATTTGCGATCAGCAATGCGGAATTCTACTGTTTGGGTGTATGAGCTATTTGCAAAGGAAATTGGTGATGACAAAGCTCGGCGCTATTTGAAGAAAATCGACTATGGCTACGCCGATCCTTCGACAAGTAATGGCGATTACTGGATAGAAGGCAGCCTTGCAATCTCGGCGCAGGAGCAAATTGCATTTCTCAGGAAGCTCTATCGTAACGAGCTGCCCTTTCGGGTAGAACATCAGCGCTTGGTCAAGGATCTCATGATTGTGGAAGCCGGTCGCAACTGGATACTGCGTGCAAAGACGGGCTGGGAAGGCCGTATGGGTTGGTGGGTAGGATGGGTTGAGTGGCCGACTGGCTCCGTATTCTTCGCACTGAATATTGATACGCCAAACAGAATGGATGATCTTTTCAAGAGGGAGGCAATCGTGCGGGCAATCCTTCGCTCTATTGAAGCGTTACCGCCCAACCCGGCAGTCAACTCGGACGCTGCGCGATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36803","NCBI_taxonomy_name":"Pseudomonas putida","NCBI_taxonomy_id":"303"}}}},"ARO_accession":"3005321","ARO_id":"43678","ARO_name":"OXA-541","CARD_short_name":"OXA-541","ARO_description":"OXA-541 is a beta-lactamase in the OXA-2 family of OXA beta-lactamases that confers resistance to ampicillin and cephalothin.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46493":{"category_aro_accession":"3007704","category_aro_cvterm_id":"46493","category_aro_name":"OXA-2-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-2.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4054":{"model_id":"4054","model_name":"OXA-835","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6421":{"protein_sequence":{"accession":"WP_148044422.1","sequence":"MAIRIFAILLSTFFLTSFVYAQEHVVIRSDWKKFFSDLQAEGAIVIADERQAKHTLSVFDQERAAKRYSPASTFKIPHTLFALDADAVRDEFQVFRWDGVNRSFAGHNQDQDLRSAMRNSTVWVYELFAKDIGEDKARRYLKQIDYGNVDPSTIKGDYWIDGNLKISAHEQILFLRKLYRNQLPFKVEHQRLVKDLMITEAGRSWILRAKTGWEGRFGWWVGWIEWPTGPVFFALNIDTPNRTDDLFKREAIARAILRSIDALPPN"},"dna_sequence":{"accession":"NG_065880.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGGCAATCCGAATCTTCGCCATACTGCTATCCACCTTCTTTCTTACCTCATTCGTGTATGCGCAAGAACATGTGGTAATCCGTTCGGACTGGAAAAAGTTCTTCAGCGACCTCCAGGCCGAAGGTGCAATCGTTATTGCAGACGAACGTCAAGCGAAGCATACTTTATCGGTTTTTGATCAAGAGCGAGCGGCAAAGCGTTACTCGCCAGCTTCAACCTTCAAGATACCCCACACACTTTTTGCACTTGATGCAGACGCCGTTCGTGATGAGTTCCAGGTTTTTCGATGGGACGGCGTTAACCGAAGCTTTGCAGGTCACAATCAAGACCAAGATTTGCGATCAGCGATGCGAAATTCTACGGTTTGGGTTTATGAGCTGTTTGCAAAAGATATCGGAGAGGACAAAGCAAGACGTTATTTAAAGCAAATTGATTATGGCAACGTCGATCCTTCGACAATCAAGGGCGATTACTGGATAGATGGAAATCTTAAAATCTCAGCGCACGAACAGATTTTGTTTCTCAGAAAACTCTATCGAAATCAGTTACCATTTAAGGTGGAGCACCAGCGCTTGGTGAAAGATCTCATGATTACGGAAGCCGGGCGCAGTTGGATACTACGCGCAAAGACCGGCTGGGAAGGCAGGTTTGGCTGGTGGGTAGGGTGGATTGAATGGCCAACAGGCCCCGTATTCTTTGCGCTGAATATTGATACGCCAAACAGAACGGACGATCTTTTCAAAAGAGAGGCCATCGCACGGGCAATCCTTCGTTCTATTGACGCATTGCCACCCAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005322","ARO_id":"43679","ARO_name":"OXA-835","CARD_short_name":"OXA-835","ARO_description":"OXA-835 is a beta-lactamase in the OXA-46 family of OXA beta-lactamases that confers resistance to ampicillin and cephalothin.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46509":{"category_aro_accession":"3007720","category_aro_cvterm_id":"46509","category_aro_name":"OXA-46-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-46.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4055":{"model_id":"4055","model_name":"OXA-926","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"6422":{"protein_sequence":{"accession":"WP_114268491.1","sequence":"MCNRILQVAAVSVVFLFSAPFATAHELCTLIADADSGRVLLQRGSACSGRVTPASTFKLAISLMGYDAGVLKDAAQPALSYQAGYPDWGGDAWRRDITPTTWIRNSVFWYSQQVVKRVGQERFAQYVKAFQYGNADVSAVPVDDPGQSGAWVMSSLRISPKEQLAFMRKIVRRQLPVSAHAFDMTALIANYGAPVDGWTVHGKTGTGSPGRNNRYDASRAYGWYVGWATKGARRLAFARLIQDEQAIKPNAGLRARDELLRLLPAIDH"},"dna_sequence":{"accession":"NG_070748.1","fmin":"0","fmax":"807","strand":"+","sequence":"ATGTGCAATCGCATCCTCCAGGTCGCTGCGGTATCAGTGGTCTTCCTTTTTTCAGCGCCTTTCGCGACCGCGCATGAGCTGTGCACGCTGATCGCCGATGCCGATTCCGGCAGGGTGCTTCTGCAGCGCGGCTCCGCCTGCTCCGGGCGCGTGACGCCTGCCTCGACTTTCAAGCTGGCCATCAGCCTCATGGGCTACGACGCAGGCGTGCTGAAGGATGCTGCACAGCCTGCCTTGTCGTATCAAGCGGGATATCCGGATTGGGGTGGTGATGCCTGGCGGCGCGACATCACGCCAACCACATGGATCAGGAACTCCGTCTTCTGGTACTCACAGCAGGTCGTGAAACGCGTGGGGCAGGAGCGCTTCGCGCAGTATGTGAAGGCCTTTCAATACGGCAATGCCGATGTCTCTGCCGTGCCGGTCGATGATCCTGGACAGAGCGGCGCCTGGGTGATGAGTTCACTGCGCATCTCCCCTAAGGAACAGCTTGCGTTCATGCGCAAGATCGTGCGCCGCCAGTTGCCGGTGAGTGCGCATGCCTTCGACATGACCGCCCTCATCGCGAACTACGGTGCACCGGTCGACGGCTGGACCGTGCATGGCAAGACGGGGACCGGCTCGCCGGGCCGCAACAATCGCTATGACGCAAGCCGCGCTTATGGCTGGTACGTAGGCTGGGCGACCAAGGGCGCGCGAAGGCTGGCATTTGCGCGCCTGATCCAGGACGAGCAGGCTATCAAGCCCAATGCGGGCCTGCGTGCGCGCGACGAGCTGCTTCGGCTTCTGCCAGCCATCGACCATTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37059","NCBI_taxonomy_name":"Klebsiella","NCBI_taxonomy_id":"570"}}}},"ARO_accession":"3005323","ARO_id":"43680","ARO_name":"OXA-926","CARD_short_name":"OXA-926","ARO_description":"OXA-926 is a class D beta-lactamase in the family of OXA beta-lactamases that confers resistance to ampicillin and cephalothin.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4104":{"model_id":"4104","model_name":"KPC-39","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"6478":{"protein_sequence":{"accession":"AYR04937.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSTIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKYSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"MK118771.1","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCACCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGTACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3005371","ARO_id":"43731","ARO_name":"KPC-39","CARD_short_name":"KPC-39","ARO_description":"Carbapenem-hydrolyzing class A beta-lactamase kpc-39 [Klebsiella pneumoniae] Accession: WP_128268237.1.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4056":{"model_id":"4056","model_name":"OXA-570","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"470"}},"model_sequences":{"sequence":{"6423":{"protein_sequence":{"accession":"WP_102607462.1","sequence":"MFARWSKTFALALTACAFVMGATQAHAELIVRDDLKRVFDEAGVTGTFVLMDISGNRTYVVDPARAARRIHPASTFKIPNSLIAFDTGAVRDDHEVIPYGGKPQPFKQWEKDMALPEAIRVSNVPIYQEVARRIGPARMQAYMDAFDYGNRQIGSVIDQFWLRGPLEISAFEEARFTSRLALKQLPVKPRTWDLVHRMLMIERQGDASLYAKTGVATEYQPEIGWWVGWVEREGKVYAFALNIDMPLEADMAKRILLGKRLMQALDVWPTP"},"dna_sequence":{"accession":"NG_056179.1","fmin":"0","fmax":"816","strand":"+","sequence":"ATGTTTGCTCGCTGGTCAAAGACCTTTGCGCTGGCCCTCACAGCCTGTGCTTTCGTGATGGGCGCCACTCAAGCGCACGCCGAGTTGATCGTGCGCGATGACCTTAAGCGCGTGTTTGATGAGGCCGGTGTTACGGGCACCTTCGTGCTGATGGACATCAGTGGTAATCGCACCTACGTTGTGGACCCGGCGCGCGCCGCACGGCGCATCCACCCTGCATCAACCTTCAAGATTCCCAACAGCCTGATCGCCTTCGATACGGGTGCCGTGCGTGACGATCACGAGGTGATCCCATACGGTGGCAAGCCACAGCCCTTCAAACAGTGGGAGAAGGACATGGCATTGCCCGAGGCGATCCGTGTATCCAACGTGCCCATCTATCAGGAAGTCGCGCGACGCATTGGCCCTGCGCGCATGCAGGCCTACATGGATGCCTTTGACTACGGCAACCGCCAGATCGGCAGCGTGATTGACCAGTTCTGGCTGCGTGGTCCATTGGAAATTTCCGCATTTGAAGAGGCGCGCTTCACCAGCCGTCTGGCGCTCAAGCAACTGCCGGTGAAGCCGCGCACCTGGGATCTGGTCCACCGCATGCTGATGATCGAGAGACAGGGCGATGCCTCGCTGTACGCCAAGACGGGGGTCGCCACCGAGTATCAGCCCGAGATCGGCTGGTGGGTGGGCTGGGTCGAGCGTGAGGGGAAGGTGTACGCGTTCGCCCTGAACATCGATATGCCGCTTGAGGCCGATATGGCCAAGCGCATCCTGCTGGGCAAACGGCTGATGCAGGCATTGGACGTGTGGCCAACACCCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43682","NCBI_taxonomy_name":"Ralstonia insidiosa","NCBI_taxonomy_id":"190721"}}}},"ARO_accession":"3005324","ARO_id":"43681","ARO_name":"OXA-570","CARD_short_name":"OXA-570","ARO_description":"OXA-570 is a beta-lactamase in the OXA-60 family of OXA beta-lactamases that confers resistance to ampicillin and cephalothin.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46518":{"category_aro_accession":"3007729","category_aro_cvterm_id":"46518","category_aro_name":"OXA-60-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-60.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4057":{"model_id":"4057","model_name":"OXA-573","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"6424":{"protein_sequence":{"accession":"WP_064808881.1","sequence":"MFPRWSKTFALALTAYAFVMGASQAHAELVVRDDLKRVFDEAGVTGTFVLMDIRGDRTYVVDPARAARRIHPASTFKIPNSLIAFDTGAVRDDQEVIPYGGKPQPFKQWEKDMALPEAIRVSNVPIYQEVARRIGPARMQAYVDAFDYGNRQIGSVIDQFWLRGPLEISAFEEARFTSRLALKQLPVKPRTWDLVHRMLLIEKQGDAALYAKTGVATEYQPEIGWWVGWVEREGKVYAFALNIDMPLEADMAKRIPLGKRLMQALEVWPTP"},"dna_sequence":{"accession":"NG_056182.1","fmin":"0","fmax":"816","strand":"+","sequence":"ATGTTCCCTCGCTGGTCAAAGACCTTTGCGCTGGCCCTCACAGCCTATGCGTTCGTGATGGGTGCCAGTCAGGCGCACGCCGAGCTGGTCGTGCGCGATGACCTCAAGCGCGTGTTCGACGAAGCCGGTGTTACCGGCACCTTCGTGCTGATGGACATCCGTGGTGATCGCACCTACGTGGTGGACCCGGCACGCGCCGCGCGGCGCATCCACCCTGCATCAACCTTCAAGATTCCCAACAGCCTGATCGCCTTCGATACGGGTGCCGTGCGTGACGACCAGGAGGTGATTCCATACGGTGGCAAGCCACAGCCCTTCAAACAGTGGGAGAAGGACATGGCATTGCCCGAGGCGATCCGCGTGTCGAACGTGCCGATCTACCAGGAGGTTGCGCGCCGTATCGGCCCCGCGCGCATGCAGGCCTATGTGGATGCCTTTGACTACGGCAACCGCCAGATCGGCAGCGTGATTGACCAGTTTTGGCTGCGTGGTCCATTGGAAATTTCCGCATTTGAAGAGGCGCGCTTCACCAGCCGCCTTGCGCTCAAGCAACTGCCGGTGAAGCCGCGCACGTGGGATCTGGTTCACCGCATGCTGCTGATCGAGAAACAGGGCGATGCCGCGCTGTACGCCAAGACGGGGGTCGCTACCGAGTATCAGCCCGAGATCGGCTGGTGGGTGGGCTGGGTCGAGCGTGAGGGGAAGGTGTACGCGTTCGCCCTGAACATCGACATGCCGCTTGAGGCCGACATGGCCAAGCGCATTCCGTTAGGAAAACGGCTGATGCAGGCATTGGAAGTGTGGCCAACACCCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43682","NCBI_taxonomy_name":"Ralstonia insidiosa","NCBI_taxonomy_id":"190721"}}}},"ARO_accession":"3005325","ARO_id":"43683","ARO_name":"OXA-573","CARD_short_name":"OXA-573","ARO_description":"OXA-573 is a beta-lactamase in the OXA-60 family of OXA beta-lactamases that confers resistance to ampicillin and cephalothin.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46518":{"category_aro_accession":"3007729","category_aro_cvterm_id":"46518","category_aro_name":"OXA-60-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-60.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4058":{"model_id":"4058","model_name":"OXA-571","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"6425":{"protein_sequence":{"accession":"WP_102607463.1","sequence":"MFSRWSKPFVLAATVCAMAMSAATAHAELIVRNDLKRVFDEAGVSGTFVLMDISADRTYVVDPARAARRIHPASTFKIPNSLIAFDTGAVRDDHEVLPYGGKPQPYKQWEHDMALPEAIRLSAVPIYQEVARRVGLERMQAYVDAFDYGNRQLGSVIDQFWLRGPLEISAFEEARFTSRMALKQLPVKPRTWDMVHRMLLIEQQGDAALYAKTGVATEYQPEIGWWVGWVERAGRVYAFALNIDMPREGDMAKRIPLGKQLMQALEVWPAP"},"dna_sequence":{"accession":"NG_056180.1","fmin":"0","fmax":"816","strand":"+","sequence":"ATGTTCTCTCGTTGGTCGAAACCTTTCGTGCTTGCCGCCACGGTGTGCGCCATGGCGATGAGCGCCGCCACTGCCCACGCCGAGCTCATCGTGCGCAACGATCTCAAGCGCGTGTTCGACGAGGCCGGCGTCTCCGGCACCTTCGTGCTGATGGATATCAGCGCCGACCGCACCTACGTCGTTGACCCGGCCCGCGCCGCGCGGCGTATCCATCCGGCCTCAACTTTCAAGATCCCGAACAGCCTCATCGCCTTCGACACGGGCGCAGTGCGTGACGATCATGAAGTGCTGCCATACGGCGGCAAGCCGCAGCCCTACAAGCAGTGGGAGCACGACATGGCGCTGCCCGAGGCGATCCGCCTGTCGGCCGTGCCGATCTACCAGGAAGTGGCGCGCCGCGTCGGCCTTGAGCGCATGCAGGCGTATGTCGATGCGTTCGACTATGGCAATCGCCAGCTTGGCAGCGTGATCGACCAGTTCTGGCTGCGCGGTCCGCTCGAAATCTCGGCGTTTGAAGAGGCGCGCTTCACCAGCCGCATGGCGCTCAAGCAGCTGCCGGTGAAGCCGCGCACGTGGGACATGGTCCATCGCATGCTGCTGATCGAGCAGCAAGGCGATGCCGCGCTGTACGCCAAGACCGGCGTCGCCACGGAATACCAGCCGGAGATCGGCTGGTGGGTCGGTTGGGTCGAGCGTGCCGGGCGCGTCTATGCCTTTGCGCTGAACATCGACATGCCGCGCGAGGGCGACATGGCCAAGCGCATTCCGCTGGGCAAGCAGTTGATGCAGGCGCTGGAGGTGTGGCCGGCACCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42837","NCBI_taxonomy_name":"Ralstonia mannitolilytica","NCBI_taxonomy_id":"105219"}}}},"ARO_accession":"3005326","ARO_id":"43684","ARO_name":"OXA-571","CARD_short_name":"OXA-571","ARO_description":"OXA-571 is a beta-lactamase in the OXA-60 family of OXA beta-lactamases that confers resistance to ampicillin and cephalothin.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46518":{"category_aro_accession":"3007729","category_aro_cvterm_id":"46518","category_aro_name":"OXA-60-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-60.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4059":{"model_id":"4059","model_name":"OXA-672","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"475"}},"model_sequences":{"sequence":{"8398":{"protein_sequence":{"accession":"WP_023271137.1","sequence":"MIMSKKLKCLTLFTAIFFAIPMAACQSFSQQKQQLSTQKNEQQQISSLFQSAQTSGVLVIYDGKKIQSYGNDIHRADQRYIPASTFKMLNALIGIQHHKTTPDEVFKWDGKKRAFSSWEKDLTLAEAMQASAVPVYQELARRIGLELMTREVKRVGYGNKNIGTQVDNFWLVGPLKITPVEEVRFAYALAKQKLPFDQPTQQQVKAMLLVDQIQGTKIYAKSGWGMDVSPQVGWWTGWIEQPNGKITAFSLNMQMSQPEHADARKAIVYQALQQLGLLAH"},"dna_sequence":{"accession":"AYEQ01000166.1","fmin":"161404","fmax":"162247","strand":"+","sequence":"ATGATCATGTCGAAAAAATTAAAATGTCTGACGCTGTTTACAGCCATCTTTTTTGCGATTCCCATGGCCGCTTGTCAAAGTTTTAGTCAACAAAAGCAACAGCTTTCGACACAGAAAAATGAACAGCAACAGATTTCAAGCTTATTTCAGAGTGCCCAAACCAGTGGTGTTTTGGTGATTTATGATGGCAAGAAAATTCAAAGCTATGGCAATGATATACATCGCGCAGATCAGCGCTATATTCCTGCCTCAACCTTTAAAATGCTAAACGCCTTGATTGGTATACAACATCATAAGACCACACCAGATGAAGTGTTTAAATGGGATGGCAAAAAGCGGGCATTCAGCAGTTGGGAAAAAGATTTAACCTTAGCTGAAGCGATGCAGGCATCGGCGGTACCTGTGTATCAAGAGTTGGCAAGACGTATTGGCTTGGAGTTAATGACCCGTGAAGTGAAGCGTGTGGGTTATGGCAATAAAAATATTGGGACACAAGTTGATAATTTCTGGTTAGTTGGCCCATTAAAAATCACCCCCGTAGAAGAAGTTCGCTTTGCCTATGCGTTGGCAAAACAGAAATTGCCATTTGACCAGCCAACACAGCAACAAGTCAAAGCGATGTTATTGGTGGATCAGATTCAGGGAACTAAAATCTATGCAAAAAGTGGTTGGGGCATGGATGTTAGCCCGCAAGTGGGATGGTGGACAGGCTGGATTGAACAGCCAAATGGTAAGATCACAGCCTTCTCACTGAATATGCAAATGAGCCAGCCTGAGCATGCAGATGCACGTAAAGCGATTGTGTATCAAGCCTTGCAACAGTTGGGATTGTTAGCCCATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42559","NCBI_taxonomy_name":"Acinetobacter gyllenbergii","NCBI_taxonomy_id":"134534"}}}},"ARO_accession":"3005327","ARO_id":"43685","ARO_name":"OXA-672","CARD_short_name":"OXA-672","ARO_description":"OXA-672 is a beta-lactamase in the OXA-286 family of OXA beta-lactamases that confers resistance to ampicillin and cephalothin.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46503":{"category_aro_accession":"3007714","category_aro_cvterm_id":"46503","category_aro_name":"OXA-286-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-286.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4060":{"model_id":"4060","model_name":"OXA-671","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"475"}},"model_sequences":{"sequence":{"8136":{"protein_sequence":{"accession":"WP_081401608.1","sequence":"MIMSKKLKCLTLFTAIFFAIPMAACQSLSQQKQQLTTEKNDQQQISSLFQSAQTSGVLVIYDGKKIQSYGNALDRAEQRYIPASTFKMLNALIGIQHHKTAPNEVFKWDGKKRAFSSWEKDLTLAEAMQASAVPVYQELARRIGLELMTREVKRVGYGNKNIGTQVDNFWLVGPLKITPVEEVRFAYALAKQKLPFDQPTQQQVKAMLLVDQIQDTKIYAKSGWGMDVSPQVGWWTGWIEQPNGKVIAFSLNMQMSQPEHADARKAIVYQALQQLGLLAT"},"dna_sequence":{"accession":"NG_062218.2","fmin":"100","fmax":"943","strand":"+","sequence":"ATGATCATGTCGAAAAAATTAAAATGTCTGACGCTTTTTACAGCCATCTTTTTTGCAATTCCTATGGCTGCTTGTCAAAGTTTAAGCCAACAAAAGCAACAGCTCACGACAGAAAAAAATGATCAGCAGCAGATCTCAAGTTTATTCCAGAGCGCTCAAACCAGTGGTGTTTTGGTGATTTATGACGGCAAGAAAATTCAAAGCTATGGCAATGCGCTTGATCGTGCAGAGCAGCGTTATATTCCCGCCTCAACCTTTAAAATGTTGAATGCTTTGATCGGGATACAACATCATAAGACTGCACCAAATGAAGTGTTTAAATGGGATGGAAAAAAGCGAGCATTTAGTAGCTGGGAAAAAGATTTAACCTTAGCTGAAGCGATGCAGGCATCGGCGGTACCCGTTTATCAAGAGTTGGCAAGACGGATTGGTTTAGAACTGATGACCCGTGAAGTGAAGCGTGTAGGTTATGGTAATAAAAATATTGGGACGCAAGTGGATAATTTCTGGTTAGTTGGTCCCTTAAAAATCACTCCCGTAGAGGAAGTTCGCTTTGCCTATGCATTAGCAAAACAGAAATTACCCTTTGATCAGCCGACACAGCAACAAGTCAAAGCGATGTTATTGGTGGATCAGATCCAGGATACCAAAATCTATGCCAAAAGCGGTTGGGGAATGGATGTCAGCCCGCAAGTGGGTTGGTGGACGGGGTGGATTGAACAGCCAAATGGTAAGGTCATTGCATTCTCATTGAATATGCAAATGAGCCAGCCTGAACATGCAGATGCACGTAAAGCGATTGTGTATCAAGCCTTGCAACAGTTGGGATTGTTAGCCACTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42559","NCBI_taxonomy_name":"Acinetobacter gyllenbergii","NCBI_taxonomy_id":"134534"}}}},"ARO_accession":"3005328","ARO_id":"43686","ARO_name":"OXA-671","CARD_short_name":"OXA-671","ARO_description":"OXA-671 is a beta-lactamase in the OXA-286 family of OXA beta-lactamases that confers resistance to ampicillin and cephalothin.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46503":{"category_aro_accession":"3007714","category_aro_cvterm_id":"46503","category_aro_name":"OXA-286-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-286.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4061":{"model_id":"4061","model_name":"OXA-673","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"8389":{"protein_sequence":{"accession":"WP_016162389.1","sequence":"MIMSKKLTCLALFTAIFFAIPMAACQSFSQQKQQLSTQKNEQQQISSLFQSAQTSGVLVIYDGKKIQSYGNDLDRAEQRYIPASTFKMLNALIGIQHHKTTPDEVFKWDGKKRAFSSWEKDLTLAEAMQASAVPVYQELARRIGLELMTREVKRVGYGNKNIGTQVDTFWLVGPLKITPVEEVRFAYALAKQKLPFDQPTQQQVKAMLLVDQIQGTKIYAKSGWGMDVSPQVGWLTGWIEQPNGKITAFSLNMQMSQPEHADARKVIVYQALQQLGLLAH"},"dna_sequence":{"accession":"AQFL01000004.1","fmin":"296446","fmax":"297289","strand":"-","sequence":"ATGATCATGTCGAAAAAATTAACATGTCTGGCCCTGTTTACAGCCATCTTTTTTGCGATTCCCATGGCCGCTTGTCAAAGTTTTAGTCAACAAAAGCAACAGCTTTCGACACAGAAAAATGAACAGCAACAGATTTCAAGCTTATTTCAGAGTGCCCAAACCAGTGGTGTTTTGGTGATTTATGATGGCAAGAAAATTCAAAGCTATGGCAATGATCTTGATCGTGCAGAACAGCGCTATATTCCTGCCTCAACCTTTAAAATGTTAAACGCCTTGATCGGCATACAGCATCATAAGACCACACCAGATGAAGTGTTTAAATGGGATGGTAAAAAGCGGGCATTCAGCAGTTGGGAAAAAGATTTAACCTTGGCTGAAGCCATGCAGGCATCGGCGGTACCTGTCTATCAGGAATTGGCACGACGTATTGGCTTAGAACTGATGACCCGTGAAGTGAAGCGTGTAGGTTATGGCAATAAAAATATCGGGACGCAAGTTGATACTTTCTGGTTGGTTGGCCCATTAAAAATCACCCCCGTAGAAGAAGTTCGCTTTGCCTATGCATTGGCAAAACAGAAGCTGCCATTTGACCAGCCAACGCAGCAACAAGTCAAAGCGATGTTATTGGTGGATCAGATTCAGGGAACTAAAATCTATGCCAAAAGTGGTTGGGGCATGGATGTTAGCCCTCAAGTGGGGTGGTTGACAGGCTGGATTGAACAGCCAAACGGTAAGATCACTGCCTTCTCGCTCAATATGCAAATGAGTCAGCCTGAACATGCAGATGCACGCAAAGTGATTGTGTATCAAGCCTTGCAACAGTTGGGATTGTTAGCCCATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"45627","NCBI_taxonomy_name":"unclassified Acinetobacter","NCBI_taxonomy_id":"196816"}}}},"ARO_accession":"3005329","ARO_id":"43687","ARO_name":"OXA-673","CARD_short_name":"OXA-673","ARO_description":"OXA-673 is a beta-lactamase in the OXA-286 family of OXA beta-lactamases that confers resistance to ampicillin and cephalothin.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46503":{"category_aro_accession":"3007714","category_aro_cvterm_id":"46503","category_aro_name":"OXA-286-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-286.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4062":{"model_id":"4062","model_name":"OXA-931","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"6429":{"protein_sequence":{"accession":"WP_190259776.1","sequence":"MKFKMKGLFCIILSSLAFSGCVYDSKLQRPVISERETEIPLLFNQAQTQAVFVTYDGIHLKSYGNDLSRAKTEYIPASTFKMLNALIGLQNAKATNTEVFHWNGEKRAFSAWEKDMTLAEAMQASAVPVYQELARRIGLELMREEVKRVGFGNAEIGQQVDNFWLVGPLKISPEQEVQFAYQLAMKQLPFDSNVQQQVKDMLYIERRGDSKLYAKSGWGMDVEPQVGWYTGWVEQPNGKVTAFALNMNMQAGNDPAERKQLTLSILDKLGLFFYLR"},"dna_sequence":{"accession":"NG_070786.1","fmin":"0","fmax":"831","strand":"+","sequence":"ATGAAGTTTAAAATGAAAGGTTTATTTTGTATCATCCTCAGTAGTTTGGCATTTTCAGGTTGTGTTTATGATTCAAAACTACAACGCCCAGTCATATCAGAGCGAGAAACTGAGATTCCTTTATTATTTAATCAAGCACAGACTCAAGCTGTGTTTGTTACTTATGATGGGATTCATCTAAAAAGTTATGGTAATGATCTAAGCCGAGCAAAGACTGAATATATTCCTGCATCTACATTTAAGATGTTGAATGCTTTAATTGGCTTGCAAAATGCAAAAGCAACCAATACTGAAGTATTTCATTGGAATGGTGAAAAGCGCGCTTTTTCAGCATGGGAAAAAGATATGACTTTGGCAGAAGCGATGCAGGCTTCAGCTGTTCCTGTATATCAAGAGCTTGCTCGACGTATTGGCTTGGAATTGATGCGTGAAGAAGTGAAGCGTGTAGGTTTTGGCAATGCGGAGATTGGTCAGCAAGTCGATAATTTTTGGTTGGTGGGTCCTTTAAAAATCTCCCCTGAACAAGAAGTTCAATTTGCCTATCAACTGGCAATGAAGCAATTGCCTTTTGATTCAAATGTACAGCAACAAGTCAAAGATATGCTTTATATCGAGAGACGTGGTGACAGTAAACTGTATGCTAAAAGTGGTTGGGGAATGGATGTTGAACCTCAAGTGGGTTGGTATACGGGATGGGTTGAACAACCCAATGGCAAGGTGACTGCATTTGCGTTAAATATGAACATGCAAGCAGGTAATGATCCAGCTGAACGTAAACAATTAACCTTAAGTATTTTGGACAAATTGGGTCTATTTTTTTATTTAAGATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39090","NCBI_taxonomy_name":"Acinetobacter bereziniae","NCBI_taxonomy_id":"106648"}}}},"ARO_accession":"3005330","ARO_id":"43689","ARO_name":"OXA-931","CARD_short_name":"OXA-931","ARO_description":"OXA-931 is a beta-lactamase in the OXA-229 family of OXA beta-lactamases that confers resistance to ampicillin and cephalothin.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46498":{"category_aro_accession":"3007709","category_aro_cvterm_id":"46498","category_aro_name":"OXA-229-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-229.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4063":{"model_id":"4063","model_name":"OXA-930","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"6430":{"protein_sequence":{"accession":"WP_151781119.1","sequence":"MKFKMKGLFCVILSSLAFSGCVYDSKLQRPVISERETEIPLLFNQAQTQAVFVTYDGIHLKSYGNDLSRAKTEYIPASTFKMLNALIGLQNAKATNTEVFHWNGEKRAFSAWEKDMTLAEAMQASAVPVYQELARRIGLELMREEVKRVGFGNAEIGQQVDNFWLVGPLKISPEQEVQFAYQLAMKQLPFDSNVQQQVKDMLYIERRGDSKLYAKSGWGMDVEPQVGWYTGWVEQPDGKVTAFALNMNMQAGDDPAERKQLTLSILDKLGLFFYLR"},"dna_sequence":{"accession":"NG_070785.1","fmin":"0","fmax":"831","strand":"+","sequence":"ATGAAGTTTAAAATGAAAGGTTTATTTTGTGTCATCCTCAGTAGTTTGGCATTTTCAGGTTGTGTTTATGATTCAAAACTACAACGCCCAGTCATATCAGAGCGAGAAACTGAGATTCCTTTATTATTTAATCAAGCACAGACTCAAGCTGTGTTTGTTACTTATGATGGGATTCATCTAAAAAGTTATGGTAATGATCTAAGCCGAGCAAAGACTGAATATATTCCTGCATCTACATTTAAGATGTTGAATGCTTTAATTGGCTTGCAAAATGCAAAAGCAACCAATACTGAAGTATTTCATTGGAATGGTGAAAAGCGCGCTTTTTCAGCATGGGAAAAAGATATGACTTTGGCAGAAGCGATGCAGGCTTCAGCTGTTCCCGTATATCAGGAGCTTGCTCGACGTATTGGCTTGGAATTGATGCGTGAAGAAGTGAAGCGTGTAGGTTTTGGCAATGCGGAGATTGGTCAGCAAGTCGATAATTTTTGGTTGGTGGGTCCTTTAAAAATCTCCCCTGAACAAGAAGTTCAATTTGCCTATCAACTGGCAATGAAGCAATTGCCTTTTGATTCAAATGTACAGCAACAAGTCAAAGATATGCTTTATATCGAGAGACGTGGTGACAGTAAACTGTATGCTAAAAGTGGTTGGGGAATGGATGTTGAACCTCAAGTGGGTTGGTATACGGGATGGGTTGAACAACCCGATGGCAAGGTGACTGCATTTGCGTTAAATATGAACATGCAAGCAGGTGATGATCCAGCTGAACGTAAACAATTAACCTTAAGTATTTTGGACAAATTGGGTCTATTTTTTTATTTAAGATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39090","NCBI_taxonomy_name":"Acinetobacter bereziniae","NCBI_taxonomy_id":"106648"}}}},"ARO_accession":"3005331","ARO_id":"43690","ARO_name":"OXA-930","CARD_short_name":"OXA-930","ARO_description":"OXA-930 is a beta-lactamase in the OXA-229 family of OXA beta-lactamases that confers resistance to ampicillin and cephalothin.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46498":{"category_aro_accession":"3007709","category_aro_cvterm_id":"46498","category_aro_name":"OXA-229-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-229.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4263":{"model_id":"4263","model_name":"ADC-198","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6638":{"protein_sequence":{"accession":"WP_150823453.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVKTDQQVLTFFKDWKPKNSIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDALAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTTTGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_066478.1","fmin":"0","fmax":"1155","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAGTATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAATTTCCAGATGAAGTAAAAACAGATCAGCAAGTTTTAACATTTTTTAAAGACTGGAAACCTAAAAACTCAATCGGTGAATATCGACAATATTCAAACCCAAGCATTGGTTTATTTGGAAAAGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCTAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTAAATCCACAAAAATATCCAGCAGATATTCAACGGGCAATTAATGAAACACATCAGGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTACTACCGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006367","ARO_id":"44829","ARO_name":"ADC-198","CARD_short_name":"ADC-198","ARO_description":"ADC-198 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4264":{"model_id":"4264","model_name":"ADC-199","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6639":{"protein_sequence":{"accession":"WP_114166683.1","sequence":"MQFKKISCLLLSPLFIFSTSIYADNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGFYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTTGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_066479.1","fmin":"0","fmax":"1167","strand":"+","sequence":"ATGCAATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGACAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCATTATTAGAAAAATATGATGTGCCGGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAGCTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTCCCAGATGAAGTACAAACAGATCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTGTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCCCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTTAACCCACAGAAATATCCGGCAGATATTCAACGGGCAATTAATGAAACACATCAAGGGTTCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTACCGGTTTCGGAACATATGTAGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006368","ARO_id":"44830","ARO_name":"ADC-199","CARD_short_name":"ADC-199","ARO_description":"ADC-199 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4064":{"model_id":"4064","model_name":"OXA-895","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"540"}},"model_sequences":{"sequence":{"6431":{"protein_sequence":{"accession":"WP_100886243.1","sequence":"MKFKMKGLFCVILSSLAFSGCVYDSKLQRPVISERETEIPLLFNQAQTQAVFVTYDGIHLKSYGNDLSRAKTEYIPASTFKMLNALIGLQNGKATNTEVFQWNGEKRAFSAWEKDMTLAEAMQASAVPVYQELARRIGLELMREEVKRVGFGNAEIGQQVDNFWLVGPLKISPEQEVQFAYQLAMKQLPFDSNVQQQVKDMLYIERRGDSKLYAKSGWGMDVEPQVGWYTGWVEQPNGKVTAFALNMNMQAGDDPAERKQLTLSILDKLGLFFYLR"},"dna_sequence":{"accession":"NG_067157.1","fmin":"0","fmax":"831","strand":"+","sequence":"ATGAAGTTTAAAATGAAAGGTTTATTTTGTGTCATCCTCAGTAGTTTGGCATTTTCAGGTTGTGTTTATGATTCAAAACTACAACGCCCAGTCATATCAGAGCGAGAAACTGAGATTCCTTTATTATTTAATCAAGCACAGACTCAAGCTGTGTTTGTTACTTATGATGGGATTCATCTAAAAAGTTATGGTAATGATCTAAGCCGAGCAAAGACTGAATATATTCCTGCATCTACATTTAAGATGTTGAATGCTTTAATTGGATTGCAAAATGGAAAAGCAACCAATACTGAAGTATTTCAGTGGAATGGTGAAAAGCGCGCTTTTTCAGCATGGGAAAAAGATATGACTTTGGCAGAAGCGATGCAGGCTTCAGCTGTTCCCGTATATCAGGAGCTTGCTCGACGTATTGGCTTGGAATTGATGCGTGAAGAAGTGAAGCGTGTAGGTTTTGGCAATGCGGAGATTGGTCAGCAAGTCGATAATTTTTGGTTGGTGGGTCCTTTAAAAATCTCCCCTGAACAAGAAGTTCAATTTGCCTATCAACTGGCAATGAAGCAATTGCCTTTTGATTCAAATGTACAGCAACAAGTCAAAGATATGCTTTATATCGAGAGACGTGGTGACAGTAAACTGTATGCTAAAAGTGGTTGGGGAATGGATGTTGAACCTCAAGTGGGTTGGTATACGGGATGGGTTGAACAACCCAATGGCAAGGTGACTGCATTTGCGTTAAATATGAACATGCAAGCAGGTGATGATCCAGCTGAACGTAAACAATTAACCTTAAGTATTTTGGACAAATTGGGTCTATTTTTTTATTTAAGATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39090","NCBI_taxonomy_name":"Acinetobacter bereziniae","NCBI_taxonomy_id":"106648"}}}},"ARO_accession":"3005332","ARO_id":"43691","ARO_name":"OXA-895","CARD_short_name":"OXA-895","ARO_description":"OXA-895 is a beta-lactamase in the OXA-229 family of OXA beta-lactamases that confers resistance to ampicillin and cephalothin.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46498":{"category_aro_accession":"3007709","category_aro_cvterm_id":"46498","category_aro_name":"OXA-229-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-229.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4065":{"model_id":"4065","model_name":"OXA-641","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6432":{"protein_sequence":{"accession":"WP_109545072.1","sequence":"MKHIFLVFLILCSNFALAEDKAISAIFSTEGVDGTIILKSLRGDKTITHNDARASRRFASASTFKIFNTLIAVQENVVSLSGTAFRWDGKTHDFPDWNRDQTLESAFKVSCVWCYQEIAKQVGEETYRRYLALARYGALSNVADSTTFWLDGSFTVSAVEQVALLKKIYLRELPFRDDAYDALKRVMLAEQTDSYKLYAKTGWAGRMNPQIGWYVGYVETSDDVWFFAINLTLRSETDLGLRQQITKAVLRAERIIP"},"dna_sequence":{"accession":"NG_057486.1","fmin":"0","fmax":"774","strand":"+","sequence":"ATGAAGCATATTTTTTTGGTCTTTCTGATTCTTTGCTCAAATTTTGCTCTCGCTGAGGACAAAGCTATTTCGGCTATTTTTTCCACAGAAGGTGTTGATGGGACCATCATTTTGAAGTCGTTGCGAGGAGATAAGACAATCACGCACAATGATGCACGCGCTTCTCGCCGATTCGCGTCAGCCTCGACTTTCAAGATATTCAACACGCTGATTGCAGTTCAAGAAAACGTGGTGAGTTTGTCGGGTACTGCATTCCGATGGGATGGAAAAACGCATGACTTCCCCGACTGGAACCGTGACCAAACACTTGAAAGCGCATTCAAAGTTTCTTGTGTGTGGTGCTATCAGGAAATCGCCAAGCAAGTGGGGGAAGAAACTTATCGACGCTATCTTGCGCTTGCAAGGTATGGTGCTCTGAGCAACGTGGCAGACAGTACAACCTTTTGGCTTGATGGCAGCTTTACGGTCAGCGCCGTCGAGCAAGTGGCTCTGTTGAAAAAAATCTATCTGCGAGAACTTCCGTTTCGCGATGACGCCTACGACGCTTTAAAGCGGGTGATGCTGGCAGAGCAGACTGACAGCTACAAGCTTTACGCAAAGACTGGCTGGGCAGGAAGAATGAACCCTCAAATTGGGTGGTACGTTGGATATGTTGAAACATCCGATGATGTATGGTTTTTTGCCATCAATTTGACCTTGAGGTCAGAAACTGACTTAGGTTTGCGCCAGCAAATAACAAAGGCTGTGCTTAGGGCTGAACGCATTATTCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36917","NCBI_taxonomy_name":"Morganella morganii","NCBI_taxonomy_id":"582"}}}},"ARO_accession":"3005333","ARO_id":"43692","ARO_name":"OXA-641","CARD_short_name":"OXA-641","ARO_description":"OXA-641 is a beta-lactamase in the OXA-372 family of OXA beta-lactamases that confers resistance to ampicillin and cephalothin.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46506":{"category_aro_accession":"3007717","category_aro_cvterm_id":"46506","category_aro_name":"OXA-372-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-372.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4066":{"model_id":"4066","model_name":"Trimethoprim-resistant dihydrofolate reductase DfrA42","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"8362":{"protein_sequence":{"accession":"WP_045475347.1","sequence":"MHKPTPLKRLSMILARDLNGAIGYEGSLAIKSDNDFAWYKKITKPFKHAVCGRVTYEEDLPDIVKKRHRFIIITRNPDKYASTPEAQYMTLSDALKELQVWDVPGHDIICLGGAEIYKALLPYVSTVYLTTFFSVADEADTYFNDFTDKWESVGATWFNDCYCTRLERVCQSTNNII"},"dna_sequence":{"accession":"HQ386845.2","fmin":"7728","fmax":"8262","strand":"+","sequence":"ATGCACAAACCAACCCCATTAAAACGGTTGTCGATGATACTTGCTCGTGACCTTAATGGTGCCATTGGTTACGAAGGTTCTTTGGCCATTAAATCGGACAATGATTTTGCGTGGTATAAGAAAATTACCAAACCATTTAAGCACGCTGTTTGTGGGCGAGTAACCTATGAGGAAGATTTGCCCGATATCGTCAAAAAACGCCACAGATTCATCATTATTACCCGTAATCCAGACAAGTACGCTAGTACTCCTGAAGCACAGTATATGACGCTCTCAGACGCGTTAAAAGAGTTACAAGTTTGGGACGTACCTGGTCACGACATTATCTGCTTAGGTGGTGCTGAAATTTACAAGGCATTATTGCCTTACGTTAGTACTGTTTACCTGACTACATTCTTTTCAGTAGCAGATGAAGCAGATACTTATTTCAATGACTTTACAGATAAATGGGAATCAGTAGGGGCCACTTGGTTTAACGACTGCTACTGCACCCGTCTGGAGCGTGTATGTCAATCTACAAACAATATTATCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36943","NCBI_taxonomy_name":"Proteus vulgaris","NCBI_taxonomy_id":"585"}}}},"ARO_accession":"3005334","ARO_id":"43693","ARO_name":"Trimethoprim-resistant dihydrofolate reductase DfrA42","CARD_short_name":"DfrA42_TMP","ARO_description":"DfrA42 is a dihydrofolate reductase that confers resistant to Trimethoprim.","ARO_category":{"37617":{"category_aro_accession":"3001218","category_aro_cvterm_id":"37617","category_aro_name":"trimethoprim resistant dihydrofolate reductase dfr","category_aro_description":"Alternative dihydropteroate synthase dfr present on plasmids produces alternate proteins that are less sensitive to trimethoprim from inhibiting its role in folate synthesis, thus conferring trimethoprim resistance.","category_aro_class_name":"AMR Gene Family"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4067":{"model_id":"4067","model_name":"OXA-496","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"6440":{"protein_sequence":{"accession":"WP_064483990.1","sequence":"MKILIFLPLLSCLSLTACSLPVSSSPSQITSTQSTQTIAQLFDQAQSSGVLGIQRGQQIQVYGNDLSRANTEYVPASTFKMLNALIGLQHGKATTNEIFKWDGKKRSFSAWEKDMTLGQAMQASAVPVYQELARRIGLELMQQEVQRIQFGNQQIGQQVDNFWLVGPLKVTPKQEVQFVSVLAREQLAFDPQVQQQVKAMLFLQERKAYRLYVKSGWGMDVEPQVGWLTGWVETPQAEIVAFSLNMQMQNGIDPAIRLEILQQALGELGLYPKVGQQSK"},"dna_sequence":{"accession":"NG_050781.1","fmin":"0","fmax":"840","strand":"+","sequence":"ATGAAAATTCTGATTTTTCTGCCTTTACTGAGTTGCTTGAGCCTGACAGCGTGTAGCCTGCCCGTTTCATCTTCCCCATCTCAGATCACTTCAACTCAATCTACCCAAACCATTGCCCAATTATTTGATCAGGCGCAAAGCTCTGGCGTTTTAGGGATTCAGCGTGGTCAACAGATACAGGTCTATGGTAATGATTTAAGTCGTGCAAATACCGAATATGTTCCTGCTTCTACTTTTAAAATGCTCAATGCCCTGATTGGCCTGCAACATGGCAAAGCTACAACCAATGAAATTTTTAAATGGGATGGCAAGAAACGCAGTTTTTCAGCTTGGGAAAAAGACATGACTCTCGGCCAAGCCATGCAAGCGTCTGCTGTACCCGTTTATCAGGAACTGGCACGTCGTATTGGCCTTGAACTGATGCAACAGGAAGTACAACGCATCCAATTTGGTAATCAGCAGATTGGTCAACAGGTCGATAACTTCTGGTTGGTAGGCCCTTTGAAAGTTACTCCAAAACAGGAAGTCCAATTTGTTTCTGTGTTGGCCCGAGAGCAACTGGCCTTTGATCCTCAAGTCCAGCAACAAGTCAAAGCCATGTTATTTTTACAGGAGCGGAAAGCTTATCGACTATATGTCAAATCCGGTTGGGGCATGGATGTGGAACCGCAAGTCGGCTGGCTCACCGGCTGGGTTGAAACACCGCAGGCTGAAATCGTGGCATTTTCACTCAATATGCAGATGCAAAATGGTATAGATCCGGCGATCCGCCTTGAAATTTTGCAGCAGGCTTTGGGCGAATTAGGGCTTTACCCAAAAGTGGGGCAGCAAAGCAAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36948","NCBI_taxonomy_name":"Acinetobacter lwoffii","NCBI_taxonomy_id":"28090"}}}},"ARO_accession":"3005335","ARO_id":"43694","ARO_name":"OXA-496","CARD_short_name":"OXA-496","ARO_description":"OXA-496 is a beta-lactamase in the OXA-134 family of OXA beta-lactamases that confers resistance to ampicillin and cephalothin.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46489":{"category_aro_accession":"3007700","category_aro_cvterm_id":"46489","category_aro_name":"OXA-134-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-134.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4068":{"model_id":"4068","model_name":"OXA-915","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"8390":{"protein_sequence":{"accession":"WP_168370988.1","sequence":"MKILILLPLFSCLGLTACSLPVSSSPSQITSTQSTQEAIAQLFDQAQSAGVLVIQRGQQIQVYGNDLGRADTEYVPASTFKMLNALIGLQHGKATTNEIFKWDGKKRSFTTWEKDMTLGEAMQASAVPVYQELARRIGLELMQQEVRRIQFGNQQIGQQVDNFWLVGPLKVTPKQEVQFVSALAREQLAFDPQVQQQVKAMLFLQERKAYRLYVKSGWGMDVEPQVGWLTGWVETPQAEIVTFSLNMQMQNGIDPAIRLEILQQALAELGLYPKAEG"},"dna_sequence":{"accession":"LC537318.1","fmin":"7282","fmax":"8116","strand":"+","sequence":"ATGAAAATTCTGATTTTGCTGCCTTTATTTAGTTGCTTGGGACTGACGGCGTGTAGTCTGCCCGTTTCATCCTCCCCCTCTCAGATCACTTCAACTCAATCGACTCAAGAAGCCATTGCCCAATTATTTGATCAGGCGCAAAGCGCTGGCGTTTTAGTGATTCAGCGTGGTCAGCAGATACAGGTCTATGGTAATGATTTAGGCCGTGCAGATACCGAATATGTTCCCGCCTCTACTTTTAAAATGCTCAATGCCCTGATTGGCCTGCAACATGGCAAAGCCACAACCAATGAAATTTTTAAATGGGATGGCAAGAAACGCAGCTTTACCACCTGGGAAAAAGACATGACTCTCGGCGAAGCCATGCAAGCTTCTGCTGTACCCGTGTATCAGGAACTGGCACGTCGCATTGGCCTTGAATTGATGCAACAGGAAGTGAGACGTATTCAATTCGGCAATCAGCAGATTGGTCAACAGGTCGATAACTTCTGGTTGGTAGGCCCTTTGAAAGTTACTCCAAAACAGGAAGTCCAATTTGTTTCTGCGTTGGCCCGAGAGCAACTGGCCTTTGATCCTCAAGTCCAGCAACAAGTCAAAGCCATGTTATTTTTACAGGAGCGGAAAGCTTATCGACTATATGTCAAATCCGGTTGGGGCATGGATGTGGAACCGCAAGTCGGCTGGCTCACCGGCTGGGTTGAAACACCGCAGGCTGAAATCGTGACATTTTCACTCAATATGCAGATGCAAAATGGTATAGATCCGGCGATCCGCCTTGAAATTTTGCAGCAGGCTTTGGCCGAATTAGGGCTTTATCCAAAAGCTGAAGGATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36948","NCBI_taxonomy_name":"Acinetobacter lwoffii","NCBI_taxonomy_id":"28090"}}}},"ARO_accession":"3005336","ARO_id":"43695","ARO_name":"OXA-915","CARD_short_name":"OXA-915","ARO_description":"OXA-915 is a beta-lactamase in the OXA-134 family of OXA beta-lactamases that confers resistance to ampicillin and cephalothin.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46489":{"category_aro_accession":"3007700","category_aro_cvterm_id":"46489","category_aro_name":"OXA-134-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-134.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4070":{"model_id":"4070","model_name":"OXA-648","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"6443":{"protein_sequence":{"accession":"WP_140423316.1","sequence":"MKILILLPLLSCLGLTACSLPVSSSPSQSTLTQSTQAIASLFDQAQSSGVLVIQRGQQLQIYGNDLSRANTEYVPASTFKIVNALIGLQHGKATANEIFKWDGKKRSFAAWEKDMTLGEAMQASAVPVYQELARRIGLELMQQEVQRIRFGNQQIGQQVDNFWLIGPLKISPKQEVEFVSALARGELPFDPQVQQQVKAMLLLQERQAYRLYAKSGWGMAVEPQVGWLTGWVEIPQGEIVAFSLNMQMQTNMNPAIRLEILQQALGELGLYPKAEQQSK"},"dna_sequence":{"accession":"NG_065434.1","fmin":"0","fmax":"840","strand":"+","sequence":"ATGAAAATTCTGATTTTGCTGCCTTTACTGAGTTGTTTGGGCCTGACAGCGTGTAGCCTGCCCGTTTCATCTTCCCCATCTCAAAGCACTTTGACTCAATCCACCCAAGCTATTGCCAGCTTATTTGATCAGGCACAAAGCTCTGGCGTTCTAGTGATTCAGCGTGGTCAACAGTTACAGATCTATGGCAATGATTTAAGCCGAGCAAATACCGAATATGTTCCTGCCTCAACCTTTAAAATAGTGAATGCCCTGATTGGCTTGCAGCATGGCAAAGCCACAGCCAATGAAATCTTTAAATGGGATGGCAAGAAACGCAGTTTTGCCGCCTGGGAAAAAGATATGACGCTCGGCGAGGCCATGCAAGCTTCTGCGGTACCGGTCTACCAGGAACTGGCACGTCGTATCGGTCTGGAATTGATGCAGCAGGAAGTGCAACGCATCCGGTTCGGCAATCAGCAGATTGGGCAGCAGGTCGATAACTTCTGGCTGATCGGGCCTCTAAAAATTAGCCCGAAACAGGAAGTCGAATTTGTCTCTGCTCTTGCTCGAGGAGAGCTCCCCTTTGATCCTCAAGTCCAGCAGCAAGTTAAAGCCATGTTACTTTTACAGGAACGGCAAGCTTATCGCCTGTATGCCAAATCCGGTTGGGGCATGGCTGTAGAACCGCAAGTTGGCTGGCTCACCGGGTGGGTCGAAATCCCTCAGGGGGAAATCGTGGCATTTTCCCTGAATATGCAAATGCAAACCAATATGAATCCAGCCATTCGCCTTGAAATTCTACAGCAGGCTCTGGGCGAATTAGGGCTTTACCCAAAAGCGGAGCAGCAAAGCAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36948","NCBI_taxonomy_name":"Acinetobacter lwoffii","NCBI_taxonomy_id":"28090"}}}},"ARO_accession":"3005338","ARO_id":"43697","ARO_name":"OXA-648","CARD_short_name":"OXA-648","ARO_description":"OXA-648 is a beta-lactamase in the OXA-134 family of OXA beta-lactamases that confers resistance to ampicillin and cephalothin.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46489":{"category_aro_accession":"3007700","category_aro_cvterm_id":"46489","category_aro_name":"OXA-134-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-134.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4071":{"model_id":"4071","model_name":"OXA-646","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"6444":{"protein_sequence":{"accession":"WP_039902635.1","sequence":"MKILILLPLLSCLGLTACTSPVSSFPSQITSTQSTQAIAQLFDQAQSSGVLVIQRGQKVQVYGNDLSRAGTEYVPASTFKMLNALIGLQHGKATTNEIFKWDGKKRSFAAWEKDMTLGEAMQASAVPVYQELARHIGLELMQQEVQRIQFGNQQIGQQVDNFWLVGPLKITPKQEVEFVSALAREQLAFDPQVQQQVKAMLLLQERQAYRLYAKSGWGMDVEPQVGWLTGWVETPQAEIVAFSLNMQMQTNMNPAIRLEILQQALGELGLYPKVGQQSK"},"dna_sequence":{"accession":"NG_065432.1","fmin":"0","fmax":"840","strand":"+","sequence":"ATGAAAATTCTGATTTTGCTACCTTTACTGAGTTGCTTGGGCCTGACAGCGTGTACCTCACCTGTTTCATCTTTCCCTTCTCAGATCACTTCAACTCAATCGACTCAAGCCATTGCCCAATTATTTGATCAGGCGCAAAGTTCTGGCGTTTTAGTGATTCAGCGTGGTCAAAAAGTACAGGTCTATGGCAATGATTTAAGCCGTGCAGGTACCGAATATGTTCCAGCCTCTACTTTCAAAATGCTCAATGCCCTGATTGGTCTACAACATGGTAAAGCCACAACCAATGAGATTTTTAAATGGGATGGCAAGAAACGCAGTTTTGCAGCCTGGGAAAAAGACATGACGCTCGGCGAAGCCATGCAAGCTTCTGCTGTACCCGTCTATCAGGAACTGGCACGTCATATTGGTTTGGAATTAATGCAGCAGGAAGTACAACGCATCCAATTTGGTAATCAGCAGATTGGTCAGCAGGTCGATAACTTCTGGTTGGTAGGTCCTTTGAAAATCACTCCAAAACAGGAAGTCGAATTTGTCTCTGCTCTAGCCCGAGAGCAACTAGCCTTTGATCCTCAAGTCCAGCAGCAAGTCAAAGCCATGTTACTTCTACAGGAACGGCAAGCTTATCGCCTGTATGCCAAATCCGGTTGGGGCATGGATGTAGAACCGCAAGTCGGCTGGCTCACCGGGTGGGTCGAAACACCGCAGGCTGAAATCGTGGCATTTTCTCTAAATATGCAAATGCAAACCAATATGAATCCAGCCATTCGCCTTGAAATTTTACAGCAGGCTCTGGGCGAATTAGGGCTTTACCCAAAAGTGGGGCAGCAAAGCAAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36948","NCBI_taxonomy_name":"Acinetobacter lwoffii","NCBI_taxonomy_id":"28090"}}}},"ARO_accession":"3005339","ARO_id":"43698","ARO_name":"OXA-646","CARD_short_name":"OXA-646","ARO_description":"OXA-646 is a beta-lactamase in the OXA-134 family of OXA beta-lactamases that confers resistance to ampicillin and cephalothin.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46489":{"category_aro_accession":"3007700","category_aro_cvterm_id":"46489","category_aro_name":"OXA-134-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-134.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4072":{"model_id":"4072","model_name":"OXA-649","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"520"}},"model_sequences":{"sequence":{"6445":{"protein_sequence":{"accession":"WP_109545071.1","sequence":"MKKFILPIFSISILLSLSACSSIQNKFEYTSDISDQQHGKAIKSYFDEAQTQGVIIIKEGKNISTYGNNLARAHTEYVPASTFKMLNALIGLENHKATTTEIFKWDGKKRSYPMWEKDMTLGDAMALSAVPVYQELARRTGLDLMQKEVKRVGFGNMNIGTQVDNFWLVGPLKITPIQEVNFADDLANNRLPFKLETQEEVKKMLLIKEVNGSKIYAKSGWGMDVTPQVGWLTGWVEKSNGEKVPFSLNLEMKQGMSGSIRNEITYKSLENLGII"},"dna_sequence":{"accession":"NG_057485.1","fmin":"0","fmax":"828","strand":"+","sequence":"ATGAAAAAATTTATACTTCCTATCTTCAGCATTTCTATTCTACTTTCTCTCAGTGCATGCTCATCTATTCAAAATAAATTTGAATATACTTCTGATATTTCTGATCAGCAGCATGGAAAAGCCATTAAAAGCTATTTTGATGAAGCTCAGACACAAGGTGTAATCATTATTAAAGAGGGAAAGAATATTAGTACCTATGGTAATAACCTGGCACGAGCACATACAGAATATGTCCCTGCATCAACATTTAAGATGCTAAATGCCTTAATTGGATTAGAAAATCATAAAGCTACAACAACTGAGATTTTCAAATGGGATGGTAAAAAAAGATCTTATCCTATGTGGGAAAAAGATATGACTTTAGGTGATGCCATGGCACTTTCAGCAGTTCCTGTATATCAAGAACTTGCAAGACGGACTGGTTTAGACCTAATGCAAAAAGAAGTCAAACGGGTTGGTTTTGGTAATATGAACATTGGAACACAAGTTGATAACTTCTGGTTGGTTGGCCCGCTTAAAATTACACCAATACAAGAGGTTAATTTTGCCGACGATCTCGCTAATAATCGATTACCCTTTAAATTAGAAACTCAAGAAGAAGTAAAAAAAATGCTTCTGATTAAAGAAGTCAATGGTAGTAAAATTTATGCGAAAAGCGGATGGGGAATGGATGTAACCCCTCAGGTAGGTTGGTTAACAGGTTGGGTAGAAAAATCTAATGGCGAAAAAGTTCCCTTTTCTCTAAACCTAGAAATGAAGCAAGGAATGTCTGGTTCTATTCGTAATGAAATTACTTATAAGTCATTAGAAAATTTAGGGATTATATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39090","NCBI_taxonomy_name":"Acinetobacter bereziniae","NCBI_taxonomy_id":"106648"}}}},"ARO_accession":"3005340","ARO_id":"43699","ARO_name":"OXA-649","CARD_short_name":"OXA-649","ARO_description":"OXA-649 is a beta-lactamase in the OXA-143 family of OXA beta-lactamases that confers resistance to ampicillin and cephalothin.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46490":{"category_aro_accession":"3007701","category_aro_cvterm_id":"46490","category_aro_name":"OXA-143-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-143.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4073":{"model_id":"4073","model_name":"OXA-897","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6446":{"protein_sequence":{"accession":"WP_164461290.1","sequence":"MKKFILPIFSISILVSLSACSSIKTKSEDNFHISSQQHEKAIKSYFDEAQTQGVIIIKEGKNLSTYGNALARANKEYVPASTFKMLIALIGLENHKATTNEIFKWDGKKRTYPMWEKDMTLGEAMALSAVPVYQELARRTGLELMQKEVKRVNFGNTNIGTQVDNFWLVGPLKITPVQEVNFADDLAHNRLPFKLETQEEVKKMLLIKEVNGSKIYAKSGWGMDVTPQVGWLTGWVEQANGKKIPFSLNLEMKEGMSGSIRNEITYKSLENLGII"},"dna_sequence":{"accession":"NG_068017.1","fmin":"0","fmax":"828","strand":"+","sequence":"ATGAAAAAATTTATACTTCCTATATTCAGCATTTCTATTCTAGTTTCTCTCAGTGCATGTTCATCTATTAAAACTAAATCTGAAGATAATTTTCATATTTCTTCTCAGCAACATGAAAAAGCTATTAAAAGCTATTTTGATGAAGCTCAAACACAGGGTGTAATTATTATTAAAGAGGGTAAAAATCTTAGCACCTATGGTAATGCTCTTGCACGAGCAAATAAAGAATATGTCCCTGCATCAACATTTAAGATGCTAATTGCTTTAATCGGGCTAGAAAATCATAAAGCAACAACAAATGAGATTTTCAAATGGGATGGTAAAAAAAGAACTTATCCTATGTGGGAGAAAGATATGACTTTAGGTGAGGCAATGGCATTGTCAGCAGTTCCAGTATATCAAGAGCTTGCAAGACGGACTGGCCTAGAGCTAATGCAGAAAGAAGTAAAGCGGGTTAATTTTGGAAATACAAATATTGGAACACAGGTCGATAATTTTTGGTTAGTTGGCCCCCTTAAAATTACACCAGTACAAGAAGTTAATTTTGCCGATGACCTTGCACATAACCGATTACCTTTTAAATTAGAAACTCAAGAAGAAGTTAAAAAAATGCTTCTAATTAAAGAAGTAAATGGTAGTAAGATTTATGCAAAAAGTGGATGGGGAATGGATGTTACTCCACAGGTAGGTTGGTTGACTGGTTGGGTGGAGCAAGCTAATGGAAAAAAAATCCCCTTTTCGCTCAACTTAGAAATGAAAGAAGGAATGTCTGGTTCTATTCGTAATGAAATTACTTATAAGTCGCTAGAAAATCTTGGAATCATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005341","ARO_id":"43700","ARO_name":"OXA-897","CARD_short_name":"OXA-897","ARO_description":"OXA-897 is a beta-lactamase in the OXA-24 family of OXA beta-lactamases that confers resistance to ampicillin and cephalothin.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46500":{"category_aro_accession":"3007711","category_aro_cvterm_id":"46500","category_aro_name":"OXA-24-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-24.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4074":{"model_id":"4074","model_name":"OXA-653","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6447":{"protein_sequence":{"accession":"WP_087554513.1","sequence":"MKKFILPIFSISILVSLSACSSIKTKSEDNFHISSQQHEKAIKSYFDEAQTQGVIIIKEGKNLSTYGNALARANKEYVPASTFKMLNALIGLENHKATTNEIFKWDGKKRTYPMWEKDMTLGEAMALSAVPVYQELARRTGLELMQKEVKRVNFGNTNIGTQVDNFWLVGPLKITPVQEVNFADDLAHNRLPFKLETQEEVKKMLLIKEVNGSKIYAKSGWRMDVTPQVGWLTGWVEQANGKKIPFSLNLEMKEGMSGSIRNEITYKSLENLGII"},"dna_sequence":{"accession":"NG_057615.1","fmin":"0","fmax":"828","strand":"+","sequence":"ATGAAAAAATTTATACTTCCTATATTCAGCATTTCTATTCTAGTTTCTCTCAGTGCATGTTCATCTATTAAAACTAAATCTGAAGATAATTTTCATATTTCTTCTCAGCAACATGAAAAAGCTATTAAAAGCTATTTTGATGAAGCTCAAACACAGGGTGTAATTATTATTAAAGAGGGTAAAAATCTTAGCACCTATGGTAATGCTCTTGCACGAGCAAATAAAGAATATGTCCCTGCATCAACATTTAAGATGCTAAATGCTTTAATCGGGCTAGAAAATCATAAAGCAACAACAAATGAGATTTTCAAATGGGATGGTAAAAAAAGAACTTATCCTATGTGGGAGAAAGATATGACTTTAGGTGAGGCAATGGCATTGTCAGCAGTTCCAGTATATCAAGAGCTTGCAAGACGGACTGGCCTAGAGCTAATGCAGAAAGAAGTAAAGCGGGTTAATTTTGGAAATACAAATATTGGAACACAGGTCGATAATTTTTGGTTAGTTGGCCCCCTTAAAATTACACCAGTACAAGAAGTTAATTTTGCCGATGACCTTGCACATAACCGATTACCTTTTAAATTAGAAACTCAAGAAGAAGTTAAAAAAATGCTTCTAATTAAAGAAGTAAATGGTAGTAAGATTTATGCAAAAAGTGGATGGAGAATGGATGTTACTCCACAGGTAGGTTGGTTGACTGGTTGGGTGGAGCAAGCTAATGGAAAAAAAATCCCCTTTTCGCTCAACTTAGAAATGAAAGAAGGAATGTCTGGTTCTATTCGTAATGAAATTACTTATAAGTCGCTAGAAAATCTTGGAATCATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37046","NCBI_taxonomy_name":"Acinetobacter","NCBI_taxonomy_id":"469"}}}},"ARO_accession":"3005342","ARO_id":"43701","ARO_name":"OXA-653","CARD_short_name":"OXA-653","ARO_description":"OXA-653 is a beta-lactamase in the OXA-24 family of OXA beta-lactamases that confers resistance to ampicillin and cephalothin.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46500":{"category_aro_accession":"3007711","category_aro_cvterm_id":"46500","category_aro_name":"OXA-24-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-24.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4075":{"model_id":"4075","model_name":"OXA-499","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"510"}},"model_sequences":{"sequence":{"6448":{"protein_sequence":{"accession":"WP_063864112.1","sequence":"MKKFILPIFSISTLLSLSACSSIQNKFENTSDISDQQHEKAIKSYFDEAQTQGVIIIKEGKNIRIYGNNLVRAHTEYVPASTFKMLNALIGLENHKATTTEIFKWDGKKRSYPMWEKDMTLGDAMALSAVPVYQELARRTGLDLMQKEVKRVGFGNMNIGTQVNNFWLVGPLKITPIQEANFADDLANNRLPFKLETQEEVKKMLLIKEVNGSKIYAKSGWGMDVTPQVGWLTGWVEKSNGEKVPFSLNLEMKQGMSGSIRNEITYKSLENLGII"},"dna_sequence":{"accession":"NG_049775.1","fmin":"0","fmax":"828","strand":"+","sequence":"ATGAAAAAATTTATACTTCCTATCTTCAGCATTTCTACTCTACTTTCTCTCAGTGCATGCTCATCTATTCAAAATAAATTTGAAAATACTTCTGATATTTCTGATCAGCAACATGAAAAAGCCATTAAAAGCTATTTTGATGAAGCTCAAACACAAGGTGTAATCATTATTAAAGAGGGAAAGAATATTAGAATCTATGGTAATAACCTGGTACGAGCACATACAGAATATGTCCCTGCGTCAACATTTAAGATGCTAAATGCCTTAATTGGATTAGAAAATCATAAAGCTACAACAACTGAGATTTTCAAATGGGATGGTAAAAAAAGATCTTATCCTATGTGGGAAAAAGATATGACTTTAGGTGATGCCATGGCACTTTCAGCAGTTCCTGTATATCAAGAACTTGCAAGACGGACTGGCTTAGATCTAATGCAAAAAGAAGTTAAACGGGTTGGTTTTGGTAATATGAACATCGGGACACAAGTTAATAACTTCTGGTTAGTTGGCCCCCTCAAGATTACACCAATACAAGAGGCTAATTTTGCCGATGATCTTGCGAATAATCGATTACCCTTTAAATTAGAAACTCAAGAAGAAGTAAAAAAAATGCTTCTGATTAAAGAAGTCAATGGTAGTAAAATTTATGCGAAAAGTGGATGGGGAATGGATGTGACCCCTCAAGTAGGTTGGTTAACAGGTTGGGTAGAAAAATCTAATGGCGAAAAAGTTCCCTTTTCTCTAAACCTAGAAATGAAGCAAGGAATGTCTGGTTCTATTCGTAATGAAATTACTTATAAATCATTAGAAAATTTAGGGATTATATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3005343","ARO_id":"43702","ARO_name":"OXA-499","CARD_short_name":"OXA-499","ARO_description":"OXA-499 is a beta-lactamase in the OXA-143 family of OXA beta-lactamases that confers resistance to ampicillin and cephalothin.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46490":{"category_aro_accession":"3007701","category_aro_cvterm_id":"46490","category_aro_name":"OXA-143-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-143.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4076":{"model_id":"4076","model_name":"OXA-825","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"510"}},"model_sequences":{"sequence":{"6449":{"protein_sequence":{"accession":"WP_140423318.1","sequence":"MKKFILPIFSISTLLSLSACSTIQNKFEKTSDISDQQHEKAIKSYFDEAQTQGVIIIKEGKNIRIYGNNLVRAHTEYVPASTFKMLNALIGLENHKATTTEIFKWDGKKRSYPIWEKDMTLGDAMALSAVPVYQELARRTGLDLMQKEVKRVGFGNMNIGTQVNNFWLVGPLKITPIQEANFVDDLANNRLPFKLETQEEVKKMLLIKEVNGSKIYAKSGWGMDVTPQVGWLTGWVEKSNGEKVPFSLNLEMKQGMSGSIRNEITYKSLENLGII"},"dna_sequence":{"accession":"NG_065436.1","fmin":"0","fmax":"828","strand":"+","sequence":"ATGAAAAAATTTATACTTCCTATCTTCAGCATTTCTACTCTACTTTCTCTCAGTGCATGCTCAACTATTCAAAATAAATTTGAAAAAACTTCTGATATTTCTGATCAGCAACATGAAAAAGCCATTAAAAGCTATTTTGATGAAGCTCAAACACAAGGTGTAATCATTATTAAAGAGGGAAAGAATATTAGAATCTATGGTAATAACCTGGTACGAGCACATACAGAATATGTCCCTGCGTCAACATTTAAGATGCTAAATGCCTTAATTGGATTAGAAAATCATAAAGCTACAACAACTGAGATTTTCAAATGGGATGGTAAAAAAAGATCTTATCCTATATGGGAAAAAGATATGACTTTAGGTGATGCCATGGCACTTTCAGCAGTTCCTGTATATCAAGAACTTGCAAGACGGACTGGCTTAGATCTAATGCAAAAAGAAGTTAAACGGGTTGGTTTTGGTAATATGAACATCGGGACACAAGTTAATAACTTCTGGTTAGTTGGCCCCCTCAAGATTACACCAATACAAGAGGCTAATTTTGTCGATGATCTTGCGAATAATCGATTACCCTTTAAATTAGAAACTCAAGAAGAAGTAAAAAAAATGCTTCTGATTAAAGAAGTCAATGGTAGTAAAATTTATGCGAAAAGTGGATGGGGAATGGATGTGACCCCTCAAGTAGGTTGGTTAACAGGTTGGGTAGAAAAATCTAATGGCGAAAAAGTTCCCTTTTCTCTAAACCTAGAAATGAAGCAAGGAATGTCTGGTTCTATTCGTAATGAAATTACTTATAAATCATTAGAAAATTTAGGGATTATATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005344","ARO_id":"43703","ARO_name":"OXA-825","CARD_short_name":"OXA-825","ARO_description":"OXA-825 is a beta-lactamase in the OXA-143 family of OXA beta-lactamases that confers resistance to ampicillin and cephalothin.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46490":{"category_aro_accession":"3007701","category_aro_cvterm_id":"46490","category_aro_name":"OXA-143-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-143.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4077":{"model_id":"4077","model_name":"Trimethoprim-resistant dihydrofolate reductase DfrA43","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"350"}},"model_sequences":{"sequence":{"6450":{"protein_sequence":{"accession":"WP_188331861.1","sequence":"MHMKMNIIVAMHEASRGIGINGELPWRIPEDMAHFARVTQKSVVIMGRKTWYSIPPKFRPLKNRLNIVLSRDPETRASIVSNTPGCMAFASLELCLQYLRQLHPSTIVFAIGGSSLYKEILAMQMLCERIYMTLVSGGPKTHSFDTFFPEIDETVYSKRICGGSGEHDDWKYKFVIYERPTSESVQSIETISQGH"},"dna_sequence":{"accession":"NG_070721.1","fmin":"100","fmax":"688","strand":"+","sequence":"ATGCACATGAAAATGAACATAATAGTCGCCATGCACGAGGCGTCTCGAGGAATCGGCATCAATGGAGAGTTGCCCTGGAGAATTCCAGAAGATATGGCCCACTTTGCAAGAGTTACACAAAAAAGTGTTGTAATTATGGGTCGAAAGACTTGGTACTCTATTCCGCCAAAGTTTAGACCACTCAAGAATCGCTTGAATATAGTGTTGTCTCGAGACCCTGAGACACGAGCTTCTATAGTGTCTAACACCCCAGGTTGCATGGCATTTGCATCGCTTGAGTTGTGTTTACAATACTTGAGACAACTGCACCCTTCGACCATCGTTTTTGCGATTGGCGGATCTTCACTATATAAGGAGATACTGGCCATGCAAATGCTCTGTGAACGAATTTACATGACACTTGTCTCGGGCGGTCCCAAAACCCATTCATTTGACACATTCTTTCCAGAAATAGACGAGACAGTATATTCAAAGAGAATTTGTGGAGGAAGTGGAGAACATGACGACTGGAAATACAAATTCGTTATTTACGAGAGACCCACCTCAGAAAGTGTTCAATCAATTGAGACAATCAGTCAAGGACATTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41223","NCBI_taxonomy_name":"Proteus penneri","NCBI_taxonomy_id":"102862"}}}},"ARO_accession":"3005345","ARO_id":"43704","ARO_name":"Trimethoprim-resistant dihydrofolate reductase DfrA43","CARD_short_name":"DfrA43_TMP","ARO_description":"DfrA43 is a dihydrofolate reductase that confers resistance to Trimethoprim. Originially described by Shi YZ et al, 2016, and isolated from Proteus penneri.","ARO_category":{"37617":{"category_aro_accession":"3001218","category_aro_cvterm_id":"37617","category_aro_name":"trimethoprim resistant dihydrofolate reductase dfr","category_aro_description":"Alternative dihydropteroate synthase dfr present on plasmids produces alternate proteins that are less sensitive to trimethoprim from inhibiting its role in folate synthesis, thus conferring trimethoprim resistance.","category_aro_class_name":"AMR Gene Family"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4078":{"model_id":"4078","model_name":"DfrA34","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"350"}},"model_sequences":{"sequence":{"6451":{"protein_sequence":{"accession":"WP_058652112.1","sequence":"MITACVAIDSDGGFGAQGTLPWAIPEEFAFYQEHVRGGICIIGGRSFNDLVHLSLSPKGGLYKKCLLRTTPHIVVSSSHELVYDPSIMALIEADRRHLDLYFVNTVDAAVKLAKGLGGMHANKDIHFIGGKRIYDAGLDYCDEVYTSILPAVYLNCDTFFPVEKLSRMFTPELYKTIPNQVHADIPVIKWTRKRA"},"dna_sequence":{"accession":"NG_062229.1","fmin":"100","fmax":"688","strand":"+","sequence":"ATGATCACAGCATGTGTAGCGATCGATAGCGATGGCGGTTTTGGTGCCCAGGGGACGCTTCCATGGGCAATACCAGAAGAATTTGCTTTTTACCAAGAGCATGTCAGGGGTGGTATCTGTATAATTGGCGGCAGATCGTTTAATGATCTAGTTCACTTATCGCTATCACCAAAGGGTGGTTTGTATAAAAAATGTCTACTCCGGACCACGCCACATATCGTAGTATCATCATCACACGAATTGGTGTACGATCCGTCGATAATGGCACTTATAGAGGCTGACAGGAGACATCTTGATCTGTACTTCGTGAACACCGTGGACGCTGCTGTTAAACTCGCAAAAGGGTTAGGTGGAATGCACGCGAATAAAGATATCCATTTCATTGGCGGTAAACGCATATATGATGCCGGTCTCGATTATTGTGACGAGGTATACACCTCAATATTACCGGCTGTGTATCTTAACTGCGACACATTCTTTCCTGTAGAAAAACTGTCGCGCATGTTTACACCAGAATTATACAAGACGATTCCTAACCAAGTTCATGCGGATATTCCTGTAATTAAATGGACCCGCAAGCGCGCATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35672","NCBI_taxonomy_name":"Salmonella enterica","NCBI_taxonomy_id":"28901"}}}},"ARO_accession":"3005346","ARO_id":"43705","ARO_name":"DfrA34","CARD_short_name":"DfrA34","ARO_description":"DfrA34 is a dihydrofolate reductase that confers resistant to Trimethoprim.","ARO_category":{"37617":{"category_aro_accession":"3001218","category_aro_cvterm_id":"37617","category_aro_name":"trimethoprim resistant dihydrofolate reductase dfr","category_aro_description":"Alternative dihydropteroate synthase dfr present on plasmids produces alternate proteins that are less sensitive to trimethoprim from inhibiting its role in folate synthesis, thus conferring trimethoprim resistance.","category_aro_class_name":"AMR Gene Family"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4079":{"model_id":"4079","model_name":"DfrA37","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"250"}},"model_sequences":{"sequence":{"6452":{"protein_sequence":{"accession":"WP_132586462.1","sequence":"MKLSLMAAISRNGVIGNGPDIPWSAKGEQLLFKAITYNQWILVGRKTFESMGALPNRKYAVVTRSNFTSDNENVIVFASIQDALSQLENMTNHVIVSGGGEIYKNLIDKVDTLHISTIDIEPEGDVYFPEIPSNFRPVFIQDFVSNINYSYQIWQKG"},"dna_sequence":{"accession":"NG_070720.1","fmin":"100","fmax":"574","strand":"+","sequence":"ATGAAACTATCTCTAATGGCAGCAATATCGAGGAATGGAGTCATCGGAAATGGACCTGATATTCCATGGAGCGCGAAAGGTGAGCAGCTTCTCTTTAAAGCTATTACATATAATCAATGGATTCTTGTTGGGCGTAAGACTTTCGAGTCAATGGGAGCGTTGCCCAATCGAAAATATGCTGTTGTAACTCGTTCAAACTTTACATCTGACAATGAGAACGTAATAGTCTTTGCATCTATTCAAGACGCTTTAAGCCAACTAGAAAATATGACAAACCACGTAATTGTTTCAGGTGGTGGGGAAATATACAAAAATCTGATCGATAAAGTCGATACATTACATATATCAACCATTGATATTGAGCCAGAAGGTGATGTTTACTTTCCAGAAATTCCCAGCAATTTTAGACCCGTTTTTATACAAGACTTCGTATCTAACATAAATTATAGTTATCAAATATGGCAAAAAGGTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43707","NCBI_taxonomy_name":"Rheinheimera sp. D18","NCBI_taxonomy_id":"2545632"}}}},"ARO_accession":"3005347","ARO_id":"43706","ARO_name":"DfrA37","CARD_short_name":"DfrA37","ARO_description":"DfrA37 is a dihydrofolate reductase that confers resistant to Trimethoprim.","ARO_category":{"37617":{"category_aro_accession":"3001218","category_aro_cvterm_id":"37617","category_aro_name":"trimethoprim resistant dihydrofolate reductase dfr","category_aro_description":"Alternative dihydropteroate synthase dfr present on plasmids produces alternate proteins that are less sensitive to trimethoprim from inhibiting its role in folate synthesis, thus conferring trimethoprim resistance.","category_aro_class_name":"AMR Gene Family"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4080":{"model_id":"4080","model_name":"DfrA36","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"350"}},"model_sequences":{"sequence":{"6453":{"protein_sequence":{"accession":"WP_000949574.1","sequence":"MLSKSDILLQFIYFYNTFIFLIAFFMKVSLIVAMDLEKGIGKNNDLMWHLPADMLFFKETTLNHIVVMGRKNFESIPERFRPLPNRENAILTRNTAFEAPNCTVFHSMEGCLKHYENEDKRTVFIIGGGQIYEEALEKNRVDEMFITFVDHTFGADTFFPSIDFSLWNEEVLRVHEADSKNAYNFTVKKFTKKLS"},"dna_sequence":{"accession":"NG_065842.1","fmin":"100","fmax":"688","strand":"+","sequence":"TTGCTTTCAAAAAGTGATATATTGCTTCAATTTATATACTTTTATAATACATTCATTTTTCTAATAGCGTTTTTCATGAAAGTAAGTTTGATAGTTGCAATGGATCTTGAAAAGGGCATTGGTAAAAACAACGATTTGATGTGGCATTTACCGGCCGATATGCTTTTTTTTAAAGAAACTACACTGAATCACATTGTGGTTATGGGTAGGAAAAATTTCGAATCAATCCCTGAAAGGTTTCGTCCACTTCCAAATCGGGAAAATGCAATATTAACTCGGAATACAGCTTTTGAAGCACCGAATTGTACTGTTTTTCACAGCATGGAAGGTTGCTTGAAACACTATGAGAACGAAGATAAGAGAACCGTTTTTATCATTGGTGGCGGACAAATATATGAGGAGGCTTTAGAAAAAAACAGGGTTGATGAAATGTTTATAACCTTTGTGGATCATACTTTTGGTGCGGATACATTTTTTCCTTCCATCGATTTTTCGCTTTGGAATGAAGAGGTGCTGCGTGTGCATGAAGCAGATTCTAAAAATGCGTATAATTTTACGGTCAAAAAATTCACTAAGAAGTTATCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3005348","ARO_id":"43708","ARO_name":"DfrA36","CARD_short_name":"DfrA36","ARO_description":"DfrA36 is a dihydrofolate reductase that confers resistant to Trimethoprim. Originally described by Wuthrich et al., 2019, and isolated from Escherichia coli.","ARO_category":{"37617":{"category_aro_accession":"3001218","category_aro_cvterm_id":"37617","category_aro_name":"trimethoprim resistant dihydrofolate reductase dfr","category_aro_description":"Alternative dihydropteroate synthase dfr present on plasmids produces alternate proteins that are less sensitive to trimethoprim from inhibiting its role in folate synthesis, thus conferring trimethoprim resistance.","category_aro_class_name":"AMR Gene Family"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4081":{"model_id":"4081","model_name":"DfrA38","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"6454":{"protein_sequence":{"accession":"WP_197749399.1","sequence":"MNCCIVVGIGRNREIGKNNDLPWHLPRDMQFFKETTTGHIVVMGRKNWESIPDKFRPLPNRVNIVLTRNKDYKAEGALVIHDWSELEQHLSADKTCFIIGGSEIFKQALDAGLVNEMYITHIDATFEGADVFFPYVNWENWTEEDILHYTKDEKNPYSFTIKKYSK"},"dna_sequence":{"accession":"NG_071175.1","fmin":"100","fmax":"601","strand":"+","sequence":"ATGAATTGTTGTATAGTAGTTGGAATTGGACGTAATCGTGAAATAGGAAAAAACAATGACTTACCTTGGCATCTACCAAGAGATATGCAGTTTTTTAAAGAGACAACAACTGGACATATTGTCGTTATGGGTAGAAAAAACTGGGAGTCTATTCCAGACAAATTTAGACCCTTACCCAATCGTGTGAATATTGTCCTTACCCGAAACAAAGATTACAAAGCCGAAGGAGCATTAGTTATTCATGATTGGTCAGAGTTAGAGCAACACCTTTCAGCAGATAAAACATGTTTCATTATCGGAGGCTCTGAAATCTTTAAACAAGCTTTAGATGCTGGTCTTGTCAATGAAATGTATATAACACATATCGATGCTACTTTTGAGGGCGCTGACGTTTTCTTCCCATACGTAAATTGGGAAAATTGGACTGAAGAGGATATTCTACATTATACAAAGGATGAGAAAAATCCTTATTCGTTTACCATTAAAAAGTATTCGAAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005349","ARO_id":"43709","ARO_name":"DfrA38","CARD_short_name":"DfrA38","ARO_description":"DfrA38 is a dihydrofolate reductase that confers resistant to Trimethoprim.","ARO_category":{"37617":{"category_aro_accession":"3001218","category_aro_cvterm_id":"37617","category_aro_name":"trimethoprim resistant dihydrofolate reductase dfr","category_aro_description":"Alternative dihydropteroate synthase dfr present on plasmids produces alternate proteins that are less sensitive to trimethoprim from inhibiting its role in folate synthesis, thus conferring trimethoprim resistance.","category_aro_class_name":"AMR Gene Family"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4082":{"model_id":"4082","model_name":"DfrB9","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"125"}},"model_sequences":{"sequence":{"6455":{"protein_sequence":{"accession":"WP_071846200.1","sequence":"MNQSSNCISTPVVGQFALPFQPTFGLGDRVRKKSGAAWQGKVVGWYCTKLTPEGYAVESEAHPGSVQIYPVAALERVA"},"dna_sequence":{"accession":"NG_052167.1","fmin":"100","fmax":"337","strand":"+","sequence":"ATGAATCAAAGTAGCAATTGCATCAGCACTCCAGTTGTTGGACAGTTTGCGCTGCCATTTCAACCCACGTTCGGCCTGGGAGATCGCGTACGCAAGAAGTCTGGCGCCGCTTGGCAAGGTAAAGTTGTCGGCTGGTACTGCACAAAATTAACCCCTGAAGGCTACGCGGTCGAGTCCGAAGCTCATCCAGGCTCAGTGCAGATTTATCCTGTGGCTGCGCTTGAACGCGTGGCCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3005350","ARO_id":"43710","ARO_name":"DfrB9","CARD_short_name":"DfrB9","ARO_description":"DfrB9 is a dihydrofolate reductase that confers resistant to Trimethoprim.","ARO_category":{"37617":{"category_aro_accession":"3001218","category_aro_cvterm_id":"37617","category_aro_name":"trimethoprim resistant dihydrofolate reductase dfr","category_aro_description":"Alternative dihydropteroate synthase dfr present on plasmids produces alternate proteins that are less sensitive to trimethoprim from inhibiting its role in folate synthesis, thus conferring trimethoprim resistance.","category_aro_class_name":"AMR Gene Family"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4178":{"model_id":"4178","model_name":"ADC-102","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6553":{"protein_sequence":{"accession":"WP_068981609.1","sequence":"MQFKKISCLLLSPLFIFSTSIYADNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTMFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPKDIQLAINETHQGFYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKSNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_051441.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCAATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGACAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCATTATTAGAAAAATATGATGTGCCGGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAGCTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTCCCAGATGAAGTACAAACAGATCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATGTTTCCGGCTCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGCTGAGTTTTATTCATGCCAACCTCAACCCACAGAAATATCCGAAAGATATTCAACTTGCAATTAATGAAACACATCAAGGGTTCTATCAAGTAAATACCATGTATCAAGCGCTTGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAATCTAATAAAGTGACTGCTATTTCAAAAGAGCCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCAACGGTTTCGGAACATATGTAGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006282","ARO_id":"44744","ARO_name":"ADC-102","CARD_short_name":"ADC-102","ARO_description":"ADC-102 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4179":{"model_id":"4179","model_name":"ADC-103","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6554":{"protein_sequence":{"accession":"WP_068981610.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDKPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFNQVLEKTIFPALGLKHSYVNIPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_051442.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATAAGCCTGGTAAATATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAAGTTGTTGCTTTGTCTATGAATAAACCTTTCAACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATATACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAATCCTGGTCCACTCGATGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTCAATCCACAGAAATATCCGGCTGATATTCAACGGGCAATTAATGAAACACATCAAGGTCGCTATCAAGTAAATACCATGTATCAAGCGCTTGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCGTATGCAGTTTTAAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006283","ARO_id":"44745","ARO_name":"ADC-103","CARD_short_name":"ADC-103","ARO_description":"ADC-103 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4083":{"model_id":"4083","model_name":"DfrA39","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"6456":{"protein_sequence":{"accession":"WP_149100971.1","sequence":"MNTPMIYISLIAAMGANRVIGNGPNIPWKIPGEQIIFRKITEGKVLVMGRKTFESIGKPLPNRKTLVISRNQHYKCQDCTVVKNLDEAIAIAKEFGNELFVAGGAEIYSLAMPVAHRIYLTEISKNFEGDVFFPEFNSADFRKISSEEVPASIPYTHSVYERKCG"},"dna_sequence":{"accession":"NG_070722.1","fmin":"100","fmax":"598","strand":"+","sequence":"ATGAATACTCCGATGATTTATATATCACTTATTGCTGCAATGGGAGCTAATCGAGTAATCGGTAATGGGCCTAATATCCCATGGAAAATTCCTGGCGAGCAGATAATATTTAGAAAAATCACAGAGGGTAAAGTTTTAGTGATGGGACGAAAAACATTTGAGTCTATTGGTAAACCTCTCCCAAATAGAAAAACTCTTGTTATTAGCCGCAATCAGCACTACAAGTGCCAAGATTGCACTGTAGTAAAGAACCTAGACGAAGCAATTGCTATCGCGAAGGAATTTGGAAATGAACTTTTCGTCGCAGGCGGTGCAGAAATCTACTCATTGGCTATGCCAGTGGCTCATCGCATTTACCTGACAGAAATTAGTAAAAATTTCGAGGGTGATGTATTTTTCCCTGAATTCAATTCCGCTGATTTTCGCAAAATATCCAGCGAGGAAGTACCCGCATCTATTCCTTATACGCACTCGGTCTATGAGCGAAAATGTGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005351","ARO_id":"43711","ARO_name":"DfrA39","CARD_short_name":"DfrA39","ARO_description":"DfrA39 is a dihydrofolate reductase that confers resistant to Trimethoprim.","ARO_category":{"37617":{"category_aro_accession":"3001218","category_aro_cvterm_id":"37617","category_aro_name":"trimethoprim resistant dihydrofolate reductase dfr","category_aro_description":"Alternative dihydropteroate synthase dfr present on plasmids produces alternate proteins that are less sensitive to trimethoprim from inhibiting its role in folate synthesis, thus conferring trimethoprim resistance.","category_aro_class_name":"AMR Gene Family"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4085":{"model_id":"4085","model_name":"dfr22","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"8135":{"protein_sequence":{"accession":"CAF31623.1","sequence":"MNPELVRIYLVAAMGANRVIGNGPDIPWKIPGEQKIFRRLTEGKVVVMGRKTFESIGKPLPNRRTVVLSRQASYSAAGCAVVSTLSQAIAIAAEHGKELYVAGGAEVYALALPRADGVFLSEVHQTFEGDAFFPVLDEAEFEVVSAETVQATITYTHSVYARRNG"},"dna_sequence":{"accession":"AJ628423.2","fmin":"324","fmax":"822","strand":"+","sequence":"ATGAACCCGGAATTGGTCCGCATTTATCTGGTCGCTGCCATGGGTGCCAATCGGGTTATTGGCAATGGCCCCGATATTCCCTGGAAAATCCCGGGTGAGCAAAAGATCTTTCGCAGGCTCACCGAGGGCAAAGTGGTCGTTATGGGCCGCAAGACGTTTGAGTCCATAGGCAAGCCCTTACCAAACCGCCGCACAGTGGTGCTCTCGCGCCAAGCCAGTTATAGCGCTGCTGGTTGTGCAGTTGTTTCAACGCTGTCGCAGGCTATTGCCATCGCAGCCGAACACGGCAAAGAGCTCTACGTGGCCGGCGGAGCCGAGGTATATGCACTGGCACTACCTCGTGCCGACGGCGTCTTTCTATCTGAGGTACATCAAACCTTCGAGGGTGACGCCTTCTTCCCTGTGCTCGACGAAGCAGAATTCGAGGTTGTCTCAGCCGAAACCGTTCAAGCCACAATCACGTACACGCACTCCGTCTATGCACGTCGTAACGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3005354","ARO_id":"43714","ARO_name":"dfr22","CARD_short_name":"dfr22","ARO_description":"Dfr22 is a dihydrofolate reductase that confers resistant to Trimethoprim. Originally detected by Grape et al., (2005) and isolated from Escherichia coli.","ARO_category":{"37617":{"category_aro_accession":"3001218","category_aro_cvterm_id":"37617","category_aro_name":"trimethoprim resistant dihydrofolate reductase dfr","category_aro_description":"Alternative dihydropteroate synthase dfr present on plasmids produces alternate proteins that are less sensitive to trimethoprim from inhibiting its role in folate synthesis, thus conferring trimethoprim resistance.","category_aro_class_name":"AMR Gene Family"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4088":{"model_id":"4088","model_name":"KPC-23","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"6464":{"protein_sequence":{"accession":"AWU66461.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGAYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKYSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"MH450213.1","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGCGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGTACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3005356","ARO_id":"43716","ARO_name":"KPC-23","CARD_short_name":"KPC-23","ARO_description":"Carbapenem-hydrolyzing class A beta-lactamase kpc-23 [Klebsiella pneumoniae] Accession: WP_111672911.1.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4089":{"model_id":"4089","model_name":"KPC-25","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"6493":{"protein_sequence":{"accession":"WP_065419571.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"NG_051167.1","fmin":"0","fmax":"888","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3005357","ARO_id":"43717","ARO_name":"KPC-25","CARD_short_name":"KPC-25","ARO_description":"Carbapenem-hydrolyzing class A beta-lactamase kpc-25 [Klebsiella pneumoniae] Accession: WP_065419571.1.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4090":{"model_id":"4090","model_name":"KPC-26","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"6462":{"protein_sequence":{"accession":"ANY26940.1","sequence":"MSLYRRLVLLSCLSWPLSGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"KX619622.1","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGTCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3005358","ARO_id":"43718","ARO_name":"KPC-26","CARD_short_name":"KPC-26","ARO_description":"Carbapenem-hydrolyzing class A beta-lactamase kpc-26 [Klebsiella pneumoniae] Accession: WP_068981634.1.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4091":{"model_id":"4091","model_name":"KPC-18","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"6463":{"protein_sequence":{"accession":"AKO63215.1","sequence":"MSLYRRLILLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"KP681699.1","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAATTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002328","ARO_id":"38728","ARO_name":"KPC-18","CARD_short_name":"KPC-18","ARO_description":"KPC-18 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4092":{"model_id":"4092","model_name":"KPC-27","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"6466":{"protein_sequence":{"accession":"AOR05747.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPRSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKYSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"KX828722.1","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGAGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGTACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3005359","ARO_id":"43719","ARO_name":"KPC-27","CARD_short_name":"KPC-27","ARO_description":"Carbapenem-hydrolyzing class A beta-lactamase kpc-27 [Klebsiella pneumoniae] Accession: WP_077064886.1.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4093":{"model_id":"4093","model_name":"KPC-29","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"6467":{"protein_sequence":{"accession":"AQM40193.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKDDKYSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"KY563764.1","fmin":"0","fmax":"891","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGGATGACAAGTACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3005360","ARO_id":"43720","ARO_name":"KPC-29","CARD_short_name":"KPC-29","ARO_description":"Carbapenem-hydrolyzing class A beta-lactamase kpc-29 [Klebsiella pneumoniae] Accession: WP_096807439.1.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4094":{"model_id":"4094","model_name":"KPC-28","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"6468":{"protein_sequence":{"accession":"APG42690.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYANDYAVVWPTGRAPIVLAVYTRAPNKDDKYSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"KY282958.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGTACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3005361","ARO_id":"43721","ARO_name":"KPC-28","CARD_short_name":"KPC-28","ARO_description":"Inhibitor-resistant class A extended-spectrum beta-lactamase kpc-28 [Escherichia coli] Accession: WP_072081992.1.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4095":{"model_id":"4095","model_name":"KPC-31","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"6469":{"protein_sequence":{"accession":"OKK72649.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARYTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKYSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"MAPH01000113.1","fmin":"8511","fmax":"9393","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCTATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGTACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3005362","ARO_id":"43722","ARO_name":"KPC-31","CARD_short_name":"KPC-31","ARO_description":"Inhibitor-resistant carbapenem-hydrolyzing class A beta-lactamase kpc-31 [Klebsiella] Accession: WP_073668892.1.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4096":{"model_id":"4096","model_name":"KPC-32","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"6470":{"protein_sequence":{"accession":"OKL07573.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARYTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGMANDYAVVWPTGRAPIVLAVYTRAPNKDDKYSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"MAPO01000050.1","fmin":"8511","fmax":"9393","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCTATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCATGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGTACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3005363","ARO_id":"43723","ARO_name":"KPC-32","CARD_short_name":"KPC-32","ARO_description":"Inhibitor-resistant carbapenem-hydrolyzing class A beta-lactamase kpc-32 [Klebsiella pneumoniae] Accession: WP_073800284.1.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4097":{"model_id":"4097","model_name":"KPC-30","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"6471":{"protein_sequence":{"accession":"AQT03460.1","sequence":"MSLYRHLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"KY646302.1","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCATCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3005364","ARO_id":"43724","ARO_name":"KPC-30","CARD_short_name":"KPC-30","ARO_description":"Inhibitor-resistant carbapenem-hydrolyzing class A beta-lactamase kpc-30 [Klebsiella pneumoniae] Accession: WP_085562399.1.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4098":{"model_id":"4098","model_name":"KPC-33","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"6472":{"protein_sequence":{"accession":"AUD37084.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARYTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"CP025144.1","fmin":"87792","fmax":"88674","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCTATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3005365","ARO_id":"43725","ARO_name":"KPC-33","CARD_short_name":"KPC-33","ARO_description":"Inhibitor-resistant class A extended-spectrum beta-lactamase kpc-33 [Klebsiella pneumoniae] Accession: WP_101140102.1.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4099":{"model_id":"4099","model_name":"KPC-34","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"6473":{"protein_sequence":{"accession":"AMS25623.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"KU985429.1","fmin":"0","fmax":"906","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3005366","ARO_id":"43726","ARO_name":"KPC-34","CARD_short_name":"KPC-34","ARO_description":"Carbapenem-hydrolyzing class A beta-lactamase kpc-34 [Klebsiella pneumoniae] Accession: WP_109545044.1.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4100":{"model_id":"4100","model_name":"KPC-35","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"6474":{"protein_sequence":{"accession":"AWR93230.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELEPNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"MH404098.1","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCCGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3005367","ARO_id":"43727","ARO_name":"KPC-35","CARD_short_name":"KPC-35","ARO_description":"Carbapenem-hydrolyzing class A beta-lactamase kpc-35 [Klebsiella pneumoniae] Accession: WP_111273852.1.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4101":{"model_id":"4101","model_name":"KPC-36","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"6475":{"protein_sequence":{"accession":"AXC08545.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLERWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKYSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"MH593787.1","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGAACGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGTACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3005368","ARO_id":"43728","ARO_name":"KPC-36","CARD_short_name":"KPC-36","ARO_description":"Carbapenem-hydrolyzing class A beta-lactamase kpc-36 [Klebsiella pneumoniae] Accession: WP_114699267.1.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4102":{"model_id":"4102","model_name":"KPC-37","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"6476":{"protein_sequence":{"accession":"AXL13972.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRRELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQLVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"MH718730.1","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCCGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGCTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3005369","ARO_id":"43729","ARO_name":"KPC-37","CARD_short_name":"KPC-37","ARO_description":"Carbapenem-hydrolyzing class A beta-lactamase kpc-37 [Klebsiella pneumoniae] Accession: WP_116786832.1.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4103":{"model_id":"4103","model_name":"KPC-38","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"6477":{"protein_sequence":{"accession":"AYP70144.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKYSEAVIAAAARLALEGLGANGQ"},"dna_sequence":{"accession":"MK098861.1","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGTACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGCCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3005370","ARO_id":"43730","ARO_name":"KPC-38","CARD_short_name":"KPC-38","ARO_description":"Carbapenem-hydrolyzing class A beta-lactamase kpc-38 [Klebsiella pneumoniae] Accession: WP_123002101.1.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4105":{"model_id":"4105","model_name":"KPC-40","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"6479":{"protein_sequence":{"accession":"RDT05676.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGSANDYAVVWPTGRAPIVLAVYTRAPNKDDKYSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"QRBR01000058.1","fmin":"6221","fmax":"7109","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCTCGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGTACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39098","NCBI_taxonomy_name":"Enterobacter hormaechei","NCBI_taxonomy_id":"158836"}}}},"ARO_accession":"3005372","ARO_id":"43732","ARO_name":"KPC-40","CARD_short_name":"KPC-40","ARO_description":"Inhibitor-resistant carbapenem-hydrolyzing class A beta-lactamase kpc-40 [Enterobacter hormaechei] Accession: WP_115470049.1.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4106":{"model_id":"4106","model_name":"KPC-41","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"6480":{"protein_sequence":{"accession":"QBC36180.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKPNKDDKYSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"MK497255.1","fmin":"0","fmax":"891","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTYTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGCCTAACAAGGATGACAAGTACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3005373","ARO_id":"43733","ARO_name":"KPC-41","CARD_short_name":"KPC-41","ARO_description":"Inhibitor-resistant carbapenem-hydrolyzing class A beta-lactamase kpc-41 [Klebsiella pneumoniae] Accession: WP_148044419.1.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4107":{"model_id":"4107","model_name":"KPC-42","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"6481":{"protein_sequence":{"accession":"QBC75465.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPAGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"MK467612.1","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCGCTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3005374","ARO_id":"43734","ARO_name":"KPC-42","CARD_short_name":"KPC-42","ARO_description":"Carbapenem-hydrolyzing class A beta-lactamase kpc-42 [Klebsiella pneumoniae] Accession: WP_136512070.1.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4108":{"model_id":"4108","model_name":"KPC-43","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"6482":{"protein_sequence":{"accession":"QBO66649.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLRKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"MK628511.1","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACGAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3005375","ARO_id":"43735","ARO_name":"KPC-43","CARD_short_name":"KPC-43","ARO_description":"Carbapenem-hydrolyzing class A beta-lactamase kpc-43 [Klebsiella pneumoniae] Accession: WP_136512071.1.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4109":{"model_id":"4109","model_name":"KPC-45","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"6483":{"protein_sequence":{"accession":"QDM39441.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDKPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"MN104596.1","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACAAACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3005376","ARO_id":"43736","ARO_name":"KPC-45","CARD_short_name":"KPC-45","ARO_description":"Carbapenem-hydrolyzing class A beta-lactamase kpc-45 [Enterobacter cloacae] Accession: WP_148044420.1.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4110":{"model_id":"4110","model_name":"KPC-46","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"6484":{"protein_sequence":{"accession":"QED08959.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELEPNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKYSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"MN267701.1","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCCGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGTACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3005377","ARO_id":"43737","ARO_name":"KPC-46","CARD_short_name":"KPC-46","ARO_description":"Inhibitor-resistant class A extended-spectrum beta-lactamase kpc-46 [Klebsiella pneumoniae] Accession: WP_148044421.1.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4111":{"model_id":"4111","model_name":"KPC-49","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"6485":{"protein_sequence":{"accession":"QFX75995.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDSWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKYSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"MN619655.1","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACAGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGTACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3005378","ARO_id":"43738","ARO_name":"KPC-49","CARD_short_name":"KPC-49","ARO_description":"Carbapenem-hydrolyzing class A beta-lactamase kpc-49 [Escherichia coli] Accession: WP_197749402.1.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4112":{"model_id":"4112","model_name":"KPC-50","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"6486":{"protein_sequence":{"accession":"QGJ02578.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKYSEAVEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"MN654342.1","fmin":"0","fmax":"891","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGTACAGCGAGGCCGTCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3005379","ARO_id":"43739","ARO_name":"KPC-50","CARD_short_name":"KPC-50","ARO_description":"Inhibitor-resistant class A beta-lactamase kpc-50 [Klebsiella pneumoniae] Accession: WP_171476788.1.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4265":{"model_id":"4265","model_name":"ADC-200","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6640":{"protein_sequence":{"accession":"WP_150823454.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVKTDQQVLTFFKDWKPKNSIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGTTTGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_066480.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAGTATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAATTTCCAGATGAAGTAAAAACAGATCAGCAAGTTTTAACATTTTTTAAAGACTGGAAACCTAAAAACTCAATCGGTGAATATCGACAATATTCAAACCCAAGCATTGGTTTATTTGGAAAAGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTAAATCCACAAAAATATCCAGCAGATATTCAACGGGCAATTAATGAAACACATCAGGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCACAACTACCGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006369","ARO_id":"44831","ARO_name":"ADC-200","CARD_short_name":"ADC-200","ARO_description":"ADC-200 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4266":{"model_id":"4266","model_name":"ADC-201","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6641":{"protein_sequence":{"accession":"WP_150823455.1","sequence":"MQFKKISCLLLPPLFIFSSSIYAGNTPKEQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSNTIFELGSVSKLFTATAGGYAKTKGTISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVKTDQQVLTFFKEWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPDLGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFINANLNPQKYPANIQRAINGTHQGFYQVGTMYQALGWEEFSYPAPLQTLLDSNSEQIVMKPNKVTAISKEPSVKMFHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_066481.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCAATTTAAAAAAATTTCTTGCTTACTTTTACCTCCTCTTTTTATTTTTAGTAGCTCAATTTATGCGGGTAATACACCAAAAGAGCAAGAGATCAAAAAACTGGTTGATCAAAACTTTAAGCCTTTATTAGAAAAATACGATGTGCCCGGTATGGCTGTGGGCGTTATTCAAAATAACAAAAAGTATGAAATGTATTATGGTCTACAATCCGTTCAAGATAAAAAAGCCGTTAATAGCAATACCATTTTTGAGCTAGGCTCGGTCAGTAAATTATTTACCGCTACAGCAGGCGGATATGCCAAAACAAAAGGAACAATCTCTTTTGATGATACGCCCGGAAAATATTGGAAAGAACTAAAAAATACACCGATTGATCAAGTGAATTTACTTCAACTTGCGACATATACCAGTGGCAACCTTGCCTTGCAATTTCCAGATGAAGTAAAAACAGATCAGCAAGTTTTAACGTTTTTCAAAGAATGGAAACCTAAAAACCCAATCGGTGAATATCGACAATATTCAAACCCAAGCATTGGTTTATTTGGAAAAGTTGTTGCTTTGTCTATGAATAAACCTTTTGACCAAGTCTTGGAAAAAACCATTTTTCCAGATCTTGGCTTAAAACATAGCTATGTAAATGTGCCTAAAACTCAAATGCAAAACTATGCATTTGGCTATAACCAAGAAAATCAGCCGATTCGCGTCAATCCTGGTCCACTCGATGCACCAGCATACGGCGTTAAATCTACCCTACCGGATATGCTGAGTTTTATTAATGCAAACCTAAATCCACAAAAATATCCAGCAAATATTCAACGTGCAATTAATGGAACACATCAAGGTTTCTACCAAGTGGGTACGATGTATCAAGCACTAGGTTGGGAAGAGTTTTCTTATCCAGCACCTTTACAAACTTTATTAGACAGTAATTCAGAACAAATCGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAACCTTCCGTTAAGATGTTCCACAAAACTGGATCGACTAACGGTTTTGGAACATATGTCGTGTTCATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACTAATAAACGTATTCCCAATGAAGAACGCATTAAAGCAGCTTATGCTGTGTTAAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3006370","ARO_id":"44832","ARO_name":"ADC-201","CARD_short_name":"ADC-201","ARO_description":"ADC-201 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4113":{"model_id":"4113","model_name":"KPC-51","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"6487":{"protein_sequence":{"accession":"QGT31448.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARNTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVHGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKNSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"MN725731.1","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCAATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGCATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGAACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3005380","ARO_id":"43740","ARO_name":"KPC-51","CARD_short_name":"KPC-51","ARO_description":"Inhibitor-resistant class A extended-spectrum beta-lactamase kpc-51 [Klebsiella pneumoniae] Accession: WP_158208923.1.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4114":{"model_id":"4114","model_name":"KPC-52","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"6488":{"protein_sequence":{"accession":"QGT31449.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARYTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"MN725732.1","fmin":"0","fmax":"885","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCTATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3005381","ARO_id":"43741","ARO_name":"KPC-52","CARD_short_name":"KPC-52","ARO_description":"Inhibitor-resistant class A extended-spectrum beta-lactamase kpc-52 [Klebsiella pneumoniae] Accession: WP_158208806.1.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4115":{"model_id":"4115","model_name":"KPC-54","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"6489":{"protein_sequence":{"accession":"QHA33651.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRSEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"MN854706.1","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCTCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3005382","ARO_id":"43742","ARO_name":"KPC-54","CARD_short_name":"KPC-54","ARO_description":"Carbapenem-hydrolyzing class A beta-lactamase kpc-54 [Klebsiella pneumoniae] Accession: WP_160164839.1.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4116":{"model_id":"4116","model_name":"KPC-55","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"6490":{"protein_sequence":{"accession":"QIS31290.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVNTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"MT028409.1","fmin":"14912","fmax":"15794","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCAACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3005383","ARO_id":"43743","ARO_name":"KPC-55","CARD_short_name":"KPC-55","ARO_description":"Carbapenem-hydrolyzing class A beta-lactamase kpc-55 [Klebsiella pneumoniae] Accession: WP_168247883.1.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4117":{"model_id":"4117","model_name":"KPC-56","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"6491":{"protein_sequence":{"accession":"QIC04092.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKYSEAVIAAAARLALEGLGVNWQ"},"dna_sequence":{"accession":"MT040751.1","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGTACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACTGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3005384","ARO_id":"43744","ARO_name":"KPC-56","CARD_short_name":"KPC-56","ARO_description":"Carbapenem-hydrolyzing class A beta-lactamase kpc-56 [Klebsiella pneumoniae] Accession: WP_087744800.1.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4118":{"model_id":"4118","model_name":"KPC-57","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"6492":{"protein_sequence":{"accession":"QJD09264.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARVTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"MT358626.1","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGTTACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39097","NCBI_taxonomy_name":"Klebsiella pneumoniae subsp. pneumoniae","NCBI_taxonomy_id":"72407"}}}},"ARO_accession":"3005385","ARO_id":"43745","ARO_name":"KPC-57","CARD_short_name":"KPC-57","ARO_description":"Inhibitor-resistant carbapenem-hydrolyzing class A beta-lactamase kpc-57 [Klebsiella pneumoniae] Accession: WP_171476789.1.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4122":{"model_id":"4122","model_name":"AAK-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"6497":{"protein_sequence":{"accession":"WP_194293132.1","sequence":"MRYIRLCIISLFATLPLAVHASPQPLQQITLRESQLSGRVGTIEMDLASGRTLTAWRADQRFPIMRTFTVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMPVGELCAAAITISDTSAANLLLATVGGPAGFTAFLRQIGDNVTRLHRWETELHAALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLLRSVLPAGWFIADKTGAGERGARGIVALLGPNHKAERIVVIYLRDTPASMAERNQQIAGIGAALLEHWQQ"},"dna_sequence":{"accession":"NG_070893.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTCGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTCAGCAAATTACACTACGCGAAAGCCAGCTGTCGGGCCGCGTCGGCACGATCGAAATGGATCTGGCCAGCGGCCGCACGCTCACCGCCTGGCGCGCCGATCAACGCTTTCCCATCATGCGCACCTTTACAGTCGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGCCGGTCGGCGAACTCTGCGCCGCCGCCATTACCATCAGCGATACCAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTCACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTCACCGCTGGGAAACGGAACTGCATGCGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTCACCAGCCAGCGTCTCAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGCTCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGACAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGCATTGTCGCCCTGCTTGGCCCGAATCACAAAGCAGAGCGCATTGTGGTCATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGCTCGAGCACTGGCAACAATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3006863","ARO_id":"45325","ARO_name":"AAK-1","CARD_short_name":"AAK-1","ARO_description":"AAK-1 is a AAK beta-lactamase.","ARO_category":{"43847":{"category_aro_accession":"3005387","category_aro_cvterm_id":"43847","category_aro_name":"AAK beta-lactamase","category_aro_description":"AAK beta-lactamases are a group of class A beta-lactamases found in Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4123":{"model_id":"4123","model_name":"ACC-1a","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6498":{"protein_sequence":{"accession":"WP_039189232.1","sequence":"MRKKMQNTLKLLSVITCLAATAQGALAANIDESKIKDTVDDLIQPLMQKNNIPGMSVAVTVNGKNYIYNYGLAAKQPQQPVTENTLFEVGSLSKTFAATLASYAQVSGKLSLDQSVSHYVPELRGSSFDHVSVLNVGTHTSGLQLFMPEDIKNTTQLMAYLKAWKPADAAGTHRVYSNIGTGLLGMIAAKSLGVSYEDAIEKTLLPQLGMHHSYLKVPADQMENYAWGYNKKDEPVHVNMEILGNEAYGIKTTSSDLLRYVQANMGQLKLDANAKMQQALTATHTGYFKSGEITQDLMWEQLPYPVSLPNLLTGNDMAMTKSVATPIVPPLPPQENVWINKTGSTNGFGAYIAFVPAKKMGIVMLANKNYSIDQRVTVAYKILSSLEGNK"},"dna_sequence":{"accession":"NG_048589.1","fmin":"0","fmax":"1173","strand":"+","sequence":"ATGCGTAAAAAAATGCAGAACACATTGAAGCTGTTATCCGTGATTACCTGTCTGGCAGCAACTGCCCAAGGTGCTCTGGCTGCTAATATCGATGAGAGCAAAATTAAAGACACCGTTGATGACCTGATCCAGCCGCTGATGCAGAAGAATAATATTCCCGGTATGTCGGTCGCAGTGACCGTCAACGGTAAAAACTACATTTATAACTATGGGTTAGCGGCAAAACAGCCTCAGCAGCCGGTTACGGAAAATACGTTATTTGAAGTGGGTTCGCTGAGTAAAACGTTTGCTGCCACCTTGGCGTCCTATGCGCAGGTGAGCGGTAAGCTGTCTTTGGATCAAAGCGTTAGCCATTACGTTCCAGAGTTGCGTGGCAGCAGCTTTGACCACGTTAGCGTACTCAATGTGGGCACGCATACCTCAGGCCTACAGCTATTTATGCCGGAAGATATTAAAAATACCACACAGCTGATGGCTTATCTAAAAGCATGGAAACCTGCCGATGCGGCTGGAACCCATCGCGTTTATTCCAATATCGGTACTGGTTTGCTAGGGATGATTGCGGCGAAAAGTCTGGGTGTGAGCTATGAAGATGCGATTGAGAAAACCCTCCTTCCTCAGTTAGGCATGCATCACAGCTACTTGAAGGTTCCGGCTGACCAGATGGAAAACTATGCGTGGGGCTACAACAAGAAAGATGAGCCAGTGCACGTGAATATGGAGATTTTGGGTAACGAAGCTTATGGTATCAAAACCACTTCCAGCGACTTGTTACGCTACGTGCAAGCCAATATGGGGCAGTTAAAGCTTGATGCTAATGCCAAGATGCAACAGGCTCTGACAGCCACCCACACCGGCTATTTCAAGTCGGGTGAGATTACTCAGGATCTGATGTGGGAGCAGCTGCCATATCCGGTTTCTCTGCCGAATTTGCTCACCGGTAACGATATGGCGATGACGAAAAGCGTGGCTACGCCGATTGTTCCGCCGTTACCGCCACAGGAAAATGTGTGGATTAATAAGACCGGATCAACTAACGGCTTCGGTGCCTATATTGCGTTTGTTCCTGCTAAGAAGATGGGGATCGTGATGCTGGCTAACAAAAACTACTCAATCGATCAGCGAGTGACGGTGGCGTATAAAATCCTGAGCTCGTTGGAAGGGAATAAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3006228","ARO_id":"44690","ARO_name":"ACC-1a","CARD_short_name":"ACC-1a","ARO_description":"ACC-1a is a ACC beta-lactamase.","ARO_category":{"36212":{"category_aro_accession":"3000073","category_aro_cvterm_id":"36212","category_aro_name":"ACC beta-lactamase","category_aro_description":"ACC beta-lactamases or Ambler class C beta-lactamases are AmpC beta-lactamases. They possess an interesting resistance phenotype due to their low activity against cephamycins.","category_aro_class_name":"AMR Gene Family"},"35976":{"category_aro_accession":"0000059","category_aro_cvterm_id":"35976","category_aro_name":"cefepime","category_aro_description":"Cefepime (INN) is a fourth-generation cephalosporin antibiotic developed in 1994. It contains an aminothiazolyl group that decreases its affinity with beta-lactamases. Cefepime shows high binding affinity with penicillin-binding proteins and has an extended spectrum of activity against Gram-positive and Gram-negative bacteria, with greater activity against both Gram-negative and Gram-positive organisms than third-generation agents.","category_aro_class_name":"Antibiotic"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"35995":{"category_aro_accession":"0000078","category_aro_cvterm_id":"35995","category_aro_name":"piperacillin","category_aro_description":"Piperacillin is an acetylureidopenicillin and has an extended spectrum of targets relative to other beta-lactam antibiotics. It inhibits cell wall synthesis in bacteria, and is usually taken with the beta-lactamase inhibitor tazobactam to overcome penicillin-resistant bacteria.","category_aro_class_name":"Antibiotic"},"36689":{"category_aro_accession":"3000550","category_aro_cvterm_id":"36689","category_aro_name":"aztreonam","category_aro_description":"Aztreonam was the first monobactam discovered, and is greatly effective against Gram-negative bacteria while inactive against Gram-positive bacteria. Artreonam is a poor substrate for beta-lactamases, and may even act as an inhibitor. In Gram-negative bacteria, Aztreonam interferes with filamentation, inhibiting cell division and leading to cell death.","category_aro_class_name":"Antibiotic"},"36989":{"category_aro_accession":"3000645","category_aro_cvterm_id":"36989","category_aro_name":"cefotaxime","category_aro_description":"Cefotaxime is a semisynthetic cephalosporin taken parenterally. It is resistant to most beta-lactamases and active against Gram-negative rods and cocci due to its aminothiazoyl and methoximino functional groups.","category_aro_class_name":"Antibiotic"},"40931":{"category_aro_accession":"3004004","category_aro_cvterm_id":"40931","category_aro_name":"cefotetan","category_aro_description":"Cefotetan is a cephamycin-class beta-lactam antibiotic that is highly resistant to beta-lactamases and effective against a wide range of gram-negative and gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"40941":{"category_aro_accession":"3004014","category_aro_cvterm_id":"40941","category_aro_name":"flomoxef","category_aro_description":"Flomoxef is an oxacephem antibiotic which was effective in preventing the growth of all ESBL-producing strains and is widely active against Gram-positive, Gram-negative, and anaerobic bacteria. It is sometimes classified as a second-generation or fourth-generation cephalosporin.","category_aro_class_name":"Antibiotic"},"40944":{"category_aro_accession":"3004017","category_aro_cvterm_id":"40944","category_aro_name":"moxalactam","category_aro_description":"Moxalactam (Latamoxef) is a broad spectrum cephalosporin (oxacephem) and beta-lactam antibiotic. Moxalactam binding to PBPs inhibits peptidoglycan cross-linkage in the cell wall, resulting in cell death. Moxalactam is proposed to be effective against meningitides as it passes the blood-brain barrier.","category_aro_class_name":"Antibiotic"},"42781":{"category_aro_accession":"3004726","category_aro_cvterm_id":"42781","category_aro_name":"cefpirome","category_aro_description":"Cefpirome is a fourth generation cephalosporin with activity against methicillin-susceptible Staphylococcus aureus, coagulase-negative staphylococci and viridans group streptococci, and in vitro activity towards Streptococcus pneumoniae.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4124":{"model_id":"4124","model_name":"ACC-1b","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6499":{"protein_sequence":{"accession":"WP_063857697.1","sequence":"MRKKMQNTLKLLSVITCLAATAQGALAANIDESKIKDTVDDLIQPLMQKNNIPGMSVAVTVNGKNYIYNYGLAAKQPQQPVTENTLFEVGSLSKTFAATLASYAQVSGKLSLDQSVSHYVPELRGSSFDHVSVLNVGTHTSGLQLFMPEDIKNTTQLMAYLKAWKPADAAGTHRVYSNIGTGLLGMIAAKSLGMSYEDAIEKTLLPQLGMHHSYLKVPADQMENYAWGYNKKDEPVHVNMEILGNEAYGIKTTSSDLLRYVQANMGQLKLDANAKMQQALTATHTGYFKSGEITQDLMWEQLPYPVSLPNLLTGNDMAMTKSVATPIVPPLPPQENVWINKTGSTNGFGAYIAFVPAKKMGIVMLANKNYSIDQRVTVAYKILSSLEGNK"},"dna_sequence":{"accession":"NG_048590.1","fmin":"0","fmax":"1173","strand":"+","sequence":"ATGCGTAAAAAAATGCAGAACACATTGAAGCTGTTATCCGTGATTACCTGTCTGGCAGCAACTGCCCAAGGTGCTCTGGCTGCTAATATCGATGAGAGCAAAATTAAAGACACCGTTGATGACCTGATCCAGCCGCTGATGCAGAAGAATAATATTCCCGGTATGTCGGTCGCAGTGACCGTCAACGGTAAAAACTACATTTATAACTATGGGTTAGCGGCAAAACAGCCTCAGCAGCCGGTTACGGAAAATACGTTATTTGAAGTGGGTTCGCTGAGTAAAACGTTTGCTGCCACCTTGGCGTCCTATGCGCAGGTGAGCGGTAAGCTGTCCTTGGATCAAAGCGTTAGCCATTACGTTCCAGAGTTGCGTGGCAGCAGCTTTGACCACGTTAGCGTACTCAATGTGGGCACGCATACCTCAGGCCTACAGCTATTTATGCCGGAAGATATTAAAAATACCACACAGCTGATGGCTTATCTAAAAGCATGGAAACCTGCCGATGCGGCTGGAACCCATCGCGTTTATTCCAATATCGGTACTGGTTTGCTAGGGATGATTGCGGCGAAAAGTCTGGGTATGAGCTATGAAGATGCGATTGAGAAAACCCTCCTTCCTCAGTTAGGCATGCATCACAGCTACTTGAAGGTTCCGGCTGACCAGATGGAAAACTATGCGTGGGGCTACAACAAGAAAGATGAGCCAGTGCACGTGAATATGGAGATTTTGGGTAACGAAGCTTATGGTATCAAAACCACTTCCAGCGACTTGTTACGCTACGTGCAAGCCAATATGGGGCAGTTAAAGCTTGATGCTAATGCCAAGATGCAACAGGCTCTGACAGCCACCCACACCGGCTATTTCAAATCGGGTGAGATTACTCAGGATCTGATGTGGGAGCAGCTGCCATATCCGGTTTCTCTGCCGAATTTGCTCACCGGTAACGATATGGCGATGACGAAAAGCGTGGCTACGCCGATTGTTCCGCCGTTACCGCCACAGGAAAATGTGTGGATTAATAAGACCGGATCAACTAACGGCTTCGGTGCCTATATTGCGTTTGTTCCTGCTAAGAAGATGGGGATCGTGATGCTGGCTAACAAAAACTACTCAATCGATCAGCGAGTGACGGTGGCGTATAAAATCCTGAGCTCGTTGGAAGGGAATAAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3006229","ARO_id":"44691","ARO_name":"ACC-1b","CARD_short_name":"ACC-1b","ARO_description":"ACC-1b is a ACC beta-lactamase.","ARO_category":{"36212":{"category_aro_accession":"3000073","category_aro_cvterm_id":"36212","category_aro_name":"ACC beta-lactamase","category_aro_description":"ACC beta-lactamases or Ambler class C beta-lactamases are AmpC beta-lactamases. They possess an interesting resistance phenotype due to their low activity against cephamycins.","category_aro_class_name":"AMR Gene Family"},"35976":{"category_aro_accession":"0000059","category_aro_cvterm_id":"35976","category_aro_name":"cefepime","category_aro_description":"Cefepime (INN) is a fourth-generation cephalosporin antibiotic developed in 1994. It contains an aminothiazolyl group that decreases its affinity with beta-lactamases. Cefepime shows high binding affinity with penicillin-binding proteins and has an extended spectrum of activity against Gram-positive and Gram-negative bacteria, with greater activity against both Gram-negative and Gram-positive organisms than third-generation agents.","category_aro_class_name":"Antibiotic"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"35995":{"category_aro_accession":"0000078","category_aro_cvterm_id":"35995","category_aro_name":"piperacillin","category_aro_description":"Piperacillin is an acetylureidopenicillin and has an extended spectrum of targets relative to other beta-lactam antibiotics. It inhibits cell wall synthesis in bacteria, and is usually taken with the beta-lactamase inhibitor tazobactam to overcome penicillin-resistant bacteria.","category_aro_class_name":"Antibiotic"},"36689":{"category_aro_accession":"3000550","category_aro_cvterm_id":"36689","category_aro_name":"aztreonam","category_aro_description":"Aztreonam was the first monobactam discovered, and is greatly effective against Gram-negative bacteria while inactive against Gram-positive bacteria. Artreonam is a poor substrate for beta-lactamases, and may even act as an inhibitor. In Gram-negative bacteria, Aztreonam interferes with filamentation, inhibiting cell division and leading to cell death.","category_aro_class_name":"Antibiotic"},"36989":{"category_aro_accession":"3000645","category_aro_cvterm_id":"36989","category_aro_name":"cefotaxime","category_aro_description":"Cefotaxime is a semisynthetic cephalosporin taken parenterally. It is resistant to most beta-lactamases and active against Gram-negative rods and cocci due to its aminothiazoyl and methoximino functional groups.","category_aro_class_name":"Antibiotic"},"40931":{"category_aro_accession":"3004004","category_aro_cvterm_id":"40931","category_aro_name":"cefotetan","category_aro_description":"Cefotetan is a cephamycin-class beta-lactam antibiotic that is highly resistant to beta-lactamases and effective against a wide range of gram-negative and gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"40941":{"category_aro_accession":"3004014","category_aro_cvterm_id":"40941","category_aro_name":"flomoxef","category_aro_description":"Flomoxef is an oxacephem antibiotic which was effective in preventing the growth of all ESBL-producing strains and is widely active against Gram-positive, Gram-negative, and anaerobic bacteria. It is sometimes classified as a second-generation or fourth-generation cephalosporin.","category_aro_class_name":"Antibiotic"},"40944":{"category_aro_accession":"3004017","category_aro_cvterm_id":"40944","category_aro_name":"moxalactam","category_aro_description":"Moxalactam (Latamoxef) is a broad spectrum cephalosporin (oxacephem) and beta-lactam antibiotic. Moxalactam binding to PBPs inhibits peptidoglycan cross-linkage in the cell wall, resulting in cell death. Moxalactam is proposed to be effective against meningitides as it passes the blood-brain barrier.","category_aro_class_name":"Antibiotic"},"42781":{"category_aro_accession":"3004726","category_aro_cvterm_id":"42781","category_aro_name":"cefpirome","category_aro_description":"Cefpirome is a fourth generation cephalosporin with activity against methicillin-susceptible Staphylococcus aureus, coagulase-negative staphylococci and viridans group streptococci, and in vitro activity towards Streptococcus pneumoniae.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4125":{"model_id":"4125","model_name":"ACC-1c","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6500":{"protein_sequence":{"accession":"WP_063857698.1","sequence":"MRKKMQNTLKLLSVITCLAATAQGALAANIDESKIKDTVDDLIQPLMQKNNIPGMSVAVTVNGKNYIYNYGLAAKQPQQPVTENTLFEVGSLSKTFAATLASYAQVSGKLSLDQSVSHYVPELRGSSFDHVSVLNVGTHTSGLQLFMPEDIKNTTQLMAYLKAWKPADAAGTHRVYSNIGTGLLGMIAAKSLGVSYEDAIEKTLLPQLGMHHSYLKVPADQMENYAWGYNKKDEPVHVNMEILGNEAYGIKTTSSDLLRYVQANMGQLKLDANAKMQQALTATHTGYFKSGEITQGLMWEQLPYPVSLPNLLTGNDMAMTKSVATPIVPPLPPQENVWINKTGSTNGFGAYIAFVPAKKMGIVMLANKNYSIDQRVTVAYKILSSLEGNK"},"dna_sequence":{"accession":"NG_048591.1","fmin":"0","fmax":"1173","strand":"+","sequence":"ATGCGTAAAAAAATGCAGAACACATTGAAGCTGTTATCCGTGATTACCTGTCTGGCAGCAACTGCCCAAGGTGCTCTGGCTGCTAATATCGATGAGAGCAAAATTAAAGACACCGTTGATGACCTGATCCAGCCGCTGATGCAGAAGAATAATATTCCCGGTATGTCGGTCGCAGTGACCGTCAACGGTAAAAACTACATTTACAACTATGGGTTAGCGGCAAAACAGCCTCAGCAGCCGGTTACGGAAAATACGTTATTTGAAGTGGGTTCGCTGAGTAAAACGTTTGCCGCCACCTTGGCGTCCTATGCGCAGGTGAGCGGTAAGCTGTCTTTGGATCAAAGCGTTAGCCATTACGTTCCAGAGTTGCGCGGCAGCAGCTTTGACCACGTTAGCGTACTCAATGTGGGCACGCATACCTCAGGCCTACAGCTATTTATGCCGGAAGATATTAAAAATACCACACAGCTGATGGCTTATCTAAAAGCATGGAAACCTGCCGATGCGGCTGGAACCCATCGCGTTTATTCCAATATCGGTACTGGTTTGCTAGGGATGATTGCGGCGAAAAGTCTGGGTGTGAGCTATGAAGATGCGATTGAGAAAACCCTCCTTCCTCAGTTAGGCATGCATCACAGCTACTTGAAGGTTCCGGCTGACCAGATGGAAAACTATGCGTGGGGCTACAACAAGAAAGATGAGCCAGTGCACGTGAATATGGAGATTTTGGGTAACGAAGCTTATGGTATCAAAACCACTTCCAGCGACTTGTTACGCTACGTGCAAGCCAATATGGGGCAGTTAAAGCTTGATGCTAATGCCAAGATGCAACAGGCTCTGACAGCCACCCACACCGGCTATTTCAAGTCGGGTGAGATTACTCAGGGTCTGATGTGGGAGCAGCTGCCATATCCGGTTTCTCTGCCGAATTTGCTCACCGGTAACGATATGGCGATGACGAAAAGCGTGGCTACGCCGATTGTTCCGCCGTTACCGCCACAGGAAAATGTGTGGATTAATAAGACCGGATCAACTAACGGCTTCGGTGCCTATATTGCGTTTGTTCCTGCTAAGAAGATGGGGATCGTGATGCTGGCTAACAAAAACTACTCAATCGATCAGCGAGTGACGGTGGCGTATAAAATCCTGAGCTCATTGGAAGGGAATAAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3006230","ARO_id":"44692","ARO_name":"ACC-1c","CARD_short_name":"ACC-1c","ARO_description":"ACC-1c is a ACC beta-lactamase.","ARO_category":{"36212":{"category_aro_accession":"3000073","category_aro_cvterm_id":"36212","category_aro_name":"ACC beta-lactamase","category_aro_description":"ACC beta-lactamases or Ambler class C beta-lactamases are AmpC beta-lactamases. They possess an interesting resistance phenotype due to their low activity against cephamycins.","category_aro_class_name":"AMR Gene Family"},"35976":{"category_aro_accession":"0000059","category_aro_cvterm_id":"35976","category_aro_name":"cefepime","category_aro_description":"Cefepime (INN) is a fourth-generation cephalosporin antibiotic developed in 1994. It contains an aminothiazolyl group that decreases its affinity with beta-lactamases. Cefepime shows high binding affinity with penicillin-binding proteins and has an extended spectrum of activity against Gram-positive and Gram-negative bacteria, with greater activity against both Gram-negative and Gram-positive organisms than third-generation agents.","category_aro_class_name":"Antibiotic"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"35995":{"category_aro_accession":"0000078","category_aro_cvterm_id":"35995","category_aro_name":"piperacillin","category_aro_description":"Piperacillin is an acetylureidopenicillin and has an extended spectrum of targets relative to other beta-lactam antibiotics. It inhibits cell wall synthesis in bacteria, and is usually taken with the beta-lactamase inhibitor tazobactam to overcome penicillin-resistant bacteria.","category_aro_class_name":"Antibiotic"},"36689":{"category_aro_accession":"3000550","category_aro_cvterm_id":"36689","category_aro_name":"aztreonam","category_aro_description":"Aztreonam was the first monobactam discovered, and is greatly effective against Gram-negative bacteria while inactive against Gram-positive bacteria. Artreonam is a poor substrate for beta-lactamases, and may even act as an inhibitor. In Gram-negative bacteria, Aztreonam interferes with filamentation, inhibiting cell division and leading to cell death.","category_aro_class_name":"Antibiotic"},"36989":{"category_aro_accession":"3000645","category_aro_cvterm_id":"36989","category_aro_name":"cefotaxime","category_aro_description":"Cefotaxime is a semisynthetic cephalosporin taken parenterally. It is resistant to most beta-lactamases and active against Gram-negative rods and cocci due to its aminothiazoyl and methoximino functional groups.","category_aro_class_name":"Antibiotic"},"40931":{"category_aro_accession":"3004004","category_aro_cvterm_id":"40931","category_aro_name":"cefotetan","category_aro_description":"Cefotetan is a cephamycin-class beta-lactam antibiotic that is highly resistant to beta-lactamases and effective against a wide range of gram-negative and gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"40941":{"category_aro_accession":"3004014","category_aro_cvterm_id":"40941","category_aro_name":"flomoxef","category_aro_description":"Flomoxef is an oxacephem antibiotic which was effective in preventing the growth of all ESBL-producing strains and is widely active against Gram-positive, Gram-negative, and anaerobic bacteria. It is sometimes classified as a second-generation or fourth-generation cephalosporin.","category_aro_class_name":"Antibiotic"},"40944":{"category_aro_accession":"3004017","category_aro_cvterm_id":"40944","category_aro_name":"moxalactam","category_aro_description":"Moxalactam (Latamoxef) is a broad spectrum cephalosporin (oxacephem) and beta-lactam antibiotic. Moxalactam binding to PBPs inhibits peptidoglycan cross-linkage in the cell wall, resulting in cell death. Moxalactam is proposed to be effective against meningitides as it passes the blood-brain barrier.","category_aro_class_name":"Antibiotic"},"42781":{"category_aro_accession":"3004726","category_aro_cvterm_id":"42781","category_aro_name":"cefpirome","category_aro_description":"Cefpirome is a fourth generation cephalosporin with activity against methicillin-susceptible Staphylococcus aureus, coagulase-negative staphylococci and viridans group streptococci, and in vitro activity towards Streptococcus pneumoniae.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4126":{"model_id":"4126","model_name":"ACC-1d","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6501":{"protein_sequence":{"accession":"WP_008815550.1","sequence":"MRKKMQNTLKLLSVITCLAATAQGALAANIDESKIKDTVDDLIQPLMQKNNIPGMSVAVTVNGKNYIYNYGLAAKQPQQSVTENTLFEVGSLSKTFAATLASYAQVSGKLSLDQSVSHYVPELRGSSFDHVSVLNVGTHTSGLQLFMPEDIKNTTQLMAYLKAWKPADAAGTHRVYSNIGTGLLGMIAAKSLGVSYEDAIEKTLLPQLGMHHSYLKVPADQMENYAWGYNKKDEPVHVNMEILGNEAYGIKTTSSDLLRYVQANMGQLKLDANAKMQQALTATHTGYFKSGEITQDLMWEQLPYPVSLPNLLTGNDMAMTKSVATPIVPPLPPQENVWINKTGSTNGFGAYIAFVPAKKMGIVMLANKNYSIDQRVTVAYKILSSLEGNK"},"dna_sequence":{"accession":"NG_048592.1","fmin":"0","fmax":"1173","strand":"+","sequence":"ATGCGTAAAAAAATGCAGAACACATTGAAGCTGTTATCCGTGATTACCTGTCTGGCAGCAACTGCCCAAGGTGCTCTGGCTGCTAATATCGATGAGAGCAAAATTAAAGACACCGTTGATGACCTGATCCAGCCGCTGATGCAGAAGAATAATATCCCCGGTATGTCGGTCGCAGTGACCGTCAACGGTAAAAACTACATTTATAACTATGGGTTAGCGGCAAAACAGCCTCAGCAGTCGGTTACGGAAAATACGTTATTTGAAGTGGGTTCGCTGAGTAAAACGTTTGCTGCCACCTTGGCGTCCTATGCGCAGGTGAGCGGTAAGCTGTCTTTGGATCAAAGCGTTAGCCATTACGTTCCAGAGTTGCGTGGCAGCAGCTTTGACCACGTTAGCGTACTCAATGTGGGCACGCATACCTCAGGCCTACAGCTATTTATGCCGGAAGATATTAAAAATACCACACAGCTGATGGCTTATCTAAAAGCATGGAAACCTGCCGATGCGGCTGGAACCCATCGCGTTTATTCCAATATCGGTACTGGTTTGCTAGGGATGATTGCGGCGAAAAGTCTGGGTGTGAGCTATGAAGATGCGATTGAGAAAACCCTCCTTCCTCAGTTAGGCATGCATCACAGCTACTTGAAGGTTCCGGCTGACCAGATGGAAAACTATGCGTGGGGCTACAACAAGAAAGATGAGCCAGTGCACGTGAATATGGAGATTTTGGGTAACGAAGCTTATGGTATCAAAACCACCTCCAGCGACTTGTTACGCTACGTGCAAGCCAATATGGGGCAGTTAAAGCTTGATGCTAATGCCAAGATGCAACAGGCTCTGACAGCCACCCACACCGGCTATTTCAAGTCGGGTGAGATTACTCAGGATCTGATGTGGGAGCAGCTGCCATATCCGGTTTCTCTGCCGAATTTGCTCACCGGTAACGATATGGCGATGACGAAAAGCGTGGCTACGCCGATTGTTCCCCCGTTACCGCCACAGGAAAATGTGTGGATTAATAAGACCGGATCAACTAACGGCTTCGGTGCCTATATTGCGTTTGTTCCTGCTAAGAAGATGGGGATCGTGATGCTGGCTAACAAAAACTACTCAATCGATCAGCGAGTGACGGTGGCGTATAAAATCCTGAGCTCATTGGAAGGGAATAAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36784","NCBI_taxonomy_name":"Hafnia alvei","NCBI_taxonomy_id":"569"}}}},"ARO_accession":"3006231","ARO_id":"44693","ARO_name":"ACC-1d","CARD_short_name":"ACC-1d","ARO_description":"ACC-1d is a ACC beta-lactamase.","ARO_category":{"36212":{"category_aro_accession":"3000073","category_aro_cvterm_id":"36212","category_aro_name":"ACC beta-lactamase","category_aro_description":"ACC beta-lactamases or Ambler class C beta-lactamases are AmpC beta-lactamases. They possess an interesting resistance phenotype due to their low activity against cephamycins.","category_aro_class_name":"AMR Gene Family"},"35976":{"category_aro_accession":"0000059","category_aro_cvterm_id":"35976","category_aro_name":"cefepime","category_aro_description":"Cefepime (INN) is a fourth-generation cephalosporin antibiotic developed in 1994. It contains an aminothiazolyl group that decreases its affinity with beta-lactamases. Cefepime shows high binding affinity with penicillin-binding proteins and has an extended spectrum of activity against Gram-positive and Gram-negative bacteria, with greater activity against both Gram-negative and Gram-positive organisms than third-generation agents.","category_aro_class_name":"Antibiotic"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"35995":{"category_aro_accession":"0000078","category_aro_cvterm_id":"35995","category_aro_name":"piperacillin","category_aro_description":"Piperacillin is an acetylureidopenicillin and has an extended spectrum of targets relative to other beta-lactam antibiotics. It inhibits cell wall synthesis in bacteria, and is usually taken with the beta-lactamase inhibitor tazobactam to overcome penicillin-resistant bacteria.","category_aro_class_name":"Antibiotic"},"36689":{"category_aro_accession":"3000550","category_aro_cvterm_id":"36689","category_aro_name":"aztreonam","category_aro_description":"Aztreonam was the first monobactam discovered, and is greatly effective against Gram-negative bacteria while inactive against Gram-positive bacteria. Artreonam is a poor substrate for beta-lactamases, and may even act as an inhibitor. In Gram-negative bacteria, Aztreonam interferes with filamentation, inhibiting cell division and leading to cell death.","category_aro_class_name":"Antibiotic"},"36989":{"category_aro_accession":"3000645","category_aro_cvterm_id":"36989","category_aro_name":"cefotaxime","category_aro_description":"Cefotaxime is a semisynthetic cephalosporin taken parenterally. It is resistant to most beta-lactamases and active against Gram-negative rods and cocci due to its aminothiazoyl and methoximino functional groups.","category_aro_class_name":"Antibiotic"},"40931":{"category_aro_accession":"3004004","category_aro_cvterm_id":"40931","category_aro_name":"cefotetan","category_aro_description":"Cefotetan is a cephamycin-class beta-lactam antibiotic that is highly resistant to beta-lactamases and effective against a wide range of gram-negative and gram-positive bacteria.","category_aro_class_name":"Antibiotic"},"40941":{"category_aro_accession":"3004014","category_aro_cvterm_id":"40941","category_aro_name":"flomoxef","category_aro_description":"Flomoxef is an oxacephem antibiotic which was effective in preventing the growth of all ESBL-producing strains and is widely active against Gram-positive, Gram-negative, and anaerobic bacteria. It is sometimes classified as a second-generation or fourth-generation cephalosporin.","category_aro_class_name":"Antibiotic"},"40944":{"category_aro_accession":"3004017","category_aro_cvterm_id":"40944","category_aro_name":"moxalactam","category_aro_description":"Moxalactam (Latamoxef) is a broad spectrum cephalosporin (oxacephem) and beta-lactam antibiotic. Moxalactam binding to PBPs inhibits peptidoglycan cross-linkage in the cell wall, resulting in cell death. Moxalactam is proposed to be effective against meningitides as it passes the blood-brain barrier.","category_aro_class_name":"Antibiotic"},"42781":{"category_aro_accession":"3004726","category_aro_cvterm_id":"42781","category_aro_name":"cefpirome","category_aro_description":"Cefpirome is a fourth generation cephalosporin with activity against methicillin-susceptible Staphylococcus aureus, coagulase-negative staphylococci and viridans group streptococci, and in vitro activity towards Streptococcus pneumoniae.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4127":{"model_id":"4127","model_name":"ACC-7","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6502":{"protein_sequence":{"accession":"WP_099156055.1","sequence":"MRKKMQNTLKLLSVITCLAATAQGAMAANIDESKIKDTVDSLIQPLMQKNNIPGMSVAVTIRGRNYIYNYGLAAKQPQQPVTKNTLFEVGSLSKTFAATLASYAQASGKLSLEQSVSHYVPELRGSSFDHVSVLNVGTHTSGLQLFMPEDIKNTTQLMTYLKAWKPADAAGTHRVYSNIGTGLLGMIAAKSLGVSYEDAIEQTILPLLGMNQTYLKVPADQMENYAWGYNKKDEPVHVNMEILGNEAYGIKTTSSDLLHYVQANMGQLKLDGNAKIQHALTATHTGYFKSGEITQDLMWEQLPYPVSLPNLLTGNDMAMTKSVATPIVPPLPPQENVWINKTGSTNGFGAYIAFVPAKKMGIVMLANKNYSIDQRVTVAYKILSSLEGNK"},"dna_sequence":{"accession":"NG_055669.1","fmin":"0","fmax":"1173","strand":"+","sequence":"ATGCGTAAAAAAATGCAGAACACCTTGAAGCTGTTATCCGTGATTACCTGTCTGGCAGCAACTGCCCAAGGCGCTATGGCTGCCAATATCGATGAGAGCAAAATTAAAGACACCGTCGATAGCCTGATCCAGCCGCTGATGCAGAAGAATAATATTCCCGGTATGTCGGTCGCAGTGACCATCAGAGGTAGGAACTATATTTATAACTACGGGTTAGCGGCAAAACAGCCTCAGCAGCCCGTGACGAAAAATACATTGTTTGAAGTGGGCTCTCTGAGTAAAACGTTTGCTGCCACTTTGGCTTCCTATGCGCAGGCGAGCGGTAAGCTGTCTTTGGAGCAAAGCGTGAGCCACTACGTTCCAGAACTGCGCGGCAGCAGCTTTGACCACGTTAGCGTACTCAATGTGGGTACGCATACCTCAGGTCTACAGCTGTTTATGCCGGAAGATATCAAGAACACCACACAGCTGATGACTTATCTAAAAGCATGGAAACCTGCTGATGCGGCTGGAACCCATCGCGTTTATTCCAATATCGGTACCGGTTTGCTAGGGATGATTGCGGCGAAAAGTCTGGGTGTGAGCTATGAAGATGCGATTGAGCAAACCATCCTTCCTCTATTAGGCATGAATCAAACCTACCTGAAGGTTCCGGCTGACCAGATGGAAAACTATGCGTGGGGCTACAACAAGAAAGATGAGCCAGTGCACGTCAATATGGAGATTTTGGGTAACGAAGCTTATGGCATCAAAACTACCTCCAGCGACTTGTTGCATTACGTGCAAGCCAATATGGGGCAGTTAAAGCTTGATGGTAATGCCAAGATCCAACATGCACTGACAGCCACCCACACCGGCTATTTCAAATCGGGTGAGATTACTCAGGATCTGATGTGGGAGCAGCTGCCATATCCAGTTTCTCTGCCGAATTTGCTCACTGGTAACGATATGGCGATGACGAAAAGCGTGGCTACGCCGATTGTTCCCCCGTTACCGCCACAGGAAAATGTGTGGATTAATAAGACCGGATCAACTAACGGCTTCGGTGCCTATATTGCGTTTGTTCCTGCTAAGAAGATGGGGATCGTGATGCTGGCTAACAAAAACTACTCAATCGATCAGCGAGTGACGGTGGCGTATAAAATCCTGAGCTCGTTGGAAGGGAATAAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36784","NCBI_taxonomy_name":"Hafnia alvei","NCBI_taxonomy_id":"569"}}}},"ARO_accession":"3006232","ARO_id":"44694","ARO_name":"ACC-7","CARD_short_name":"ACC-7","ARO_description":"ACC-7 is a ACC beta-lactamase.","ARO_category":{"36212":{"category_aro_accession":"3000073","category_aro_cvterm_id":"36212","category_aro_name":"ACC beta-lactamase","category_aro_description":"ACC beta-lactamases or Ambler class C beta-lactamases are AmpC beta-lactamases. They possess an interesting resistance phenotype due to their low activity against cephamycins.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4128":{"model_id":"4128","model_name":"ACC-8","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6503":{"protein_sequence":{"accession":"WP_188331862.1","sequence":"MQNTLKLLSVITCLAATVQGALAANIDESKIKDTVDDLIQPLMQKNNIPGMSVAVTVNGKNYIYNYGLAAKQPQQPVTENTLFEVGSLSKTFAATLASYAQVSGKLSLDQSVSHYVPELRGSSFDHVSVLNVGTHTSGLQLFMPEDIKNTTQLMAYLKAWKPADAAGTHRVYSNIGTGLLGMIAAKSLGVSYKDAIEKTLLPQLGMHHSYLKVPADQMENYAWGYNKKDEPVHVNMEILGNEAYGIKTTSSDLLRYVQANMGQLKLDANAKMQQALTATHTGYFKSGEITQDLMWEQLPYPVSLPNLLTGNDMAMTKSVATPIVPPLPPQENVWINKTGSTNGFGAYIAFVPAKKMGIVMLANKNYSIDQRVTVAYKILSSLEGNK"},"dna_sequence":{"accession":"NG_070728.1","fmin":"0","fmax":"1161","strand":"+","sequence":"ATGCAGAACACATTGAAGCTGTTATCCGTGATTACCTGTCTGGCAGCAACTGTCCAAGGTGCTCTGGCTGCTAATATCGATGAGAGCAAAATTAAAGACACCGTTGATGACCTGATCCAGCCGCTGATGCAGAAGAATAATATTCCCGGTATGTCGGTCGCAGTGACCGTCAACGGTAAAAACTACATTTATAACTATGGGTTAGCGGCAAAACAGCCTCAGCAGCCGGTTACGGAAAATACGTTATTTGAAGTGGGTTCGCTGAGTAAAACGTTTGCTGCCACCTTGGCGTCCTATGCGCAGGTGAGCGGTAAGCTGTCTTTGGATCAAAGCGTTAGCCATTACGTTCCAGAGTTGCGTGGCAGCAGCTTTGACCACGTTAGCGTACTCAATGTGGGCACGCATACCTCAGGCCTACAGCTATTTATGCCGGAAGATATTAAAAATACCACACAGCTGATGGCTTATCTAAAAGCATGGAAACCTGCCGATGCGGCTGGAACCCATCGCGTTTATTCCAATATCGGTACTGGTTTGCTAGGGATGATTGCGGCGAAAAGTCTGGGTGTGAGCTATAAAGATGCGATTGAGAAAACCCTCCTTCCTCAGTTAGGCATGCATCACAGCTACTTGAAGGTTCCGGCTGACCAGATGGAAAACTATGCGTGGGGCTACAACAAGAAAGATGAGCCAGTGCACGTGAATATGGAGATTTTGGGTAACGAAGCTTATGGTATCAAAACCACCTCCAGCGACTTGTTACGCTACGTGCAAGCCAATATGGGGCAGTTAAAGCTTGATGCTAATGCCAAGATGCAACAGGCTCTGACAGCCACCCACACCGGCTATTTCAAATCGGGTGAGATTACTCAGGATCTGATGTGGGAGCAGCTGCCATATCCGGTTTCTCTGCCGAATTTGCTCACCGGTAACGATATGGCGATGACGAAAAGCGTGGCTACGCCGATTGTTCCGCCGTTACCGCCACAGGAAAATGTGTGGATTAATAAGACCGGATCAACTAACGGCTTCGGTGCCTATATTGCGTTTGTTCCTGCTAAGAAGATGGGGATCGTGATGCTGGCTAACAAAAACTACTCAATCGATCAGCGAGTGACGGTGGCGTATAAAATCCTGAGCTCATTGGAAGGGAATAAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3006233","ARO_id":"44695","ARO_name":"ACC-8","CARD_short_name":"ACC-8","ARO_description":"ACC-8 is a ACC beta-lactamase.","ARO_category":{"36212":{"category_aro_accession":"3000073","category_aro_cvterm_id":"36212","category_aro_name":"ACC beta-lactamase","category_aro_description":"ACC beta-lactamases or Ambler class C beta-lactamases are AmpC beta-lactamases. They possess an interesting resistance phenotype due to their low activity against cephamycins.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4136":{"model_id":"4136","model_name":"ACT-45","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6511":{"protein_sequence":{"accession":"WP_032608349.1","sequence":"MMKKSLCCALLLGLSCSALAAPVSEKQLAEVVANTVTPLMKAQSVPGMAVAVIYQGKPHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMPYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGTLDAQAYGVKTNVQDMANWVMANMAPEKVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVVEGSDSKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANKSYPNPARVEAAYHILKALQ"},"dna_sequence":{"accession":"NG_050708.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCCCTTTGCTGCGCCCTGCTGCTGGGCCTCTCTTGCTCTGCTCTCGCCGCGCCAGTATCAGAAAAACAGCTGGCGGAGGTGGTCGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCTGTTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGAAAACCGCACTATTACACGTTTGGCAAGGCCGATATCGCGGCGAATAAACCCGTTACGCCTCAGACCCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGCGTTTTAGGTGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTGACGGGCAAGCAGTGGCAGGGTATTCGTATGCTGGATCTCGCCACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTCAAACCTTCCGGCATGCCCTATGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTTCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGAACGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCGGAAAAGGTTGCCGATGCCTCACTTAAGCAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGGTCGAAGGCAGCGACAGTAAGGTAGCGCTGGCGCCGTTACCCGTGGCAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGTTCTACTGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCAAGGCGCTTCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40540","NCBI_taxonomy_name":"Enterobacter cloacae complex","NCBI_taxonomy_id":"354276"}}}},"ARO_accession":"3006240","ARO_id":"44702","ARO_name":"ACT-45","CARD_short_name":"ACT-45","ARO_description":"ACT-45 is a ACT beta-lactamase.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4137":{"model_id":"4137","model_name":"ACT-46","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6512":{"protein_sequence":{"accession":"WP_045337464.1","sequence":"MMKKSLCCALLLGLSCSALAAPVSEKQLAEVVANTVTPLMIAQSVPGMAVAVIYQGKSHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMPYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPEKVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVVEGSDSKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANKSYPNPARVEAAYHILEALQ"},"dna_sequence":{"accession":"NG_050709.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCCCTTTGCTGCGCCCTGCTGCTCGGCCTCTCTTGCTCTGCTCTCGCCGCGCCAGTATCAGAAAAACAGCTGGCGGAGGTGGTCGCGAATACGGTTACCCCGCTGATGATAGCCCAGTCTGTTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGAAAATCGCACTATTACACGTTTGGCAAGGCCGATATCGCGGCGAATAAACCCGTTACGCCTCAGACCCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGCGTTTTAGGTGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTGACGGGCAAGCAGTGGCAGGGTATTCGTATGCTGGATCTCGCCACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTCAAACCTTCTGGCATGCCCTATGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTTCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGAATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCGGAGAAGGTTGCCGATGCCTCACTTAAGCAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGGTCGAAGGCAGCGACAGTAAGGTAGCGCTGGCGCCGTTACCCGTGGCAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGTTCTACTGGCGGATTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCGAGGCGCTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37055","NCBI_taxonomy_name":"Enterobacter","NCBI_taxonomy_id":"547"}}}},"ARO_accession":"3006241","ARO_id":"44703","ARO_name":"ACT-46","CARD_short_name":"ACT-46","ARO_description":"ACT-46 is a ACT beta-lactamase.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4138":{"model_id":"4138","model_name":"ACT-47","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6513":{"protein_sequence":{"accession":"WP_045309142.1","sequence":"MMKKSLCCALLLGISCSALAAPVSEKQLAEVVANTVTPLMKAQSIPGMAVAVIYQGKPHYYTFGKADIAASKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNAALLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMGYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPEKVADASLKQGISLAQSRYWRIGSMYQGLGWEMLNWPVEANTVIEGSDSKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANKSYPNPARVEAAYHILDALQ"},"dna_sequence":{"accession":"NG_050710.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCTCTTTGCTGCGCCCTGCTGCTCGGCATCTCTTGCTCTGCTCTCGCCGCGCCAGTGTCAGAAAAACAGCTGGCGGAGGTGGTCGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCGATTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGTAAACCGCACTATTACACGTTTGGCAAAGCCGATATCGCGGCCAGCAAACCCGTTACGCCTCAGACTCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGGGTTTTAGGTGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTGACGGGCAAGCAGTGGCAGGGGATTCGTATGCTGGATCTCGCAACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAATGCCGCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGTATCGGTCTTTTTGGCGCGCTGGCGGTCAAACCTTCCGGCATGGGCTATGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTTCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGAATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCGGAGAAGGTTGCTGATGCCTCACTTAAGCAGGGCATCTCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGATCGAGGGCAGCGACAGTAAGGTGGCGCTGGCACCGCTGCCCGTGGCAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGCTCTACTGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCGACGCGCTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37055","NCBI_taxonomy_name":"Enterobacter","NCBI_taxonomy_id":"547"}}}},"ARO_accession":"3006242","ARO_id":"44704","ARO_name":"ACT-47","CARD_short_name":"ACT-47","ARO_description":"ACT-47 is a ACT beta-lactamase.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4139":{"model_id":"4139","model_name":"ACT-48","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6514":{"protein_sequence":{"accession":"WP_045331469.1","sequence":"MMTKTLCCALLLSTSCSVLAAPLSEKQLAEVVERTVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVAKNKPVTPQTLFELGSISKTFTGVLGGDAVARGEISLGDPVTKYWPALTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDSASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMSYEQAITTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVQDMASWVMVNMKPETLQDTSLRQGITLAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVDGSDNKVALAPLPASEVNPPAPPVKASWVHKTGSTGGFGSYAAFIPEKSLGIVMLANKSYPNPARVEAAYRILDALQ"},"dna_sequence":{"accession":"NG_050711.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGACAAAAACCCTTTGCTGCGCCCTGCTGCTCAGCACCTCCTGCTCAGTATTGGCCGCACCGCTGTCAGAAAAACAGCTGGCTGAAGTGGTGGAGCGCACCGTTACGCCCCTGATGAAAGCGCAGGCTATTCCGGGTATGGCGGTGGCGGTGATTTATCAGGGCCAGCCGCACTACTTTACCTTCGGTAAAGCCGATGTTGCAAAGAACAAACCGGTTACCCCACAAACCCTGTTCGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTACTGGGTGGCGATGCCGTTGCTCGCGGTGAAATATCGCTGGGCGACCCCGTGACAAAGTACTGGCCCGCGCTGACAGGCAAGCAGTGGCAGGGGATCCGCATGCTGGATCTGGCCACCTATACCGCGGGAGGTCTGCCGCTACAGGTACCGGATGAGGTCACGGATAGCGCCTCTCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCGGGCACAACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGCGCGCTGGCGGTGAAGCCTTCCGGCATGAGCTATGAGCAGGCCATAACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTTCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGATACCGTGACGGTAAAGCGGTGCACGTTTCGCCGGGAATGCTCGATGCGGAAGCTTATGGCGTGAAAACCAACGTGCAGGATATGGCAAGCTGGGTGATGGTCAACATGAAGCCGGAAACCCTTCAGGATACGTCACTCAGGCAAGGCATTACCCTGGCGCAGTCTCGCTACTGGCGCGTGGGGGCCATGTACCAGGGATTAGGCTGGGAAATGCTTAACTGGCCGGTGGATGCCAAAACCGTGGTTGACGGCAGCGACAATAAGGTGGCGCTGGCGCCGCTGCCTGCGAGCGAAGTCAATCCGCCCGCGCCGCCGGTTAAGGCATCCTGGGTCCACAAAACGGGTTCAACCGGCGGGTTTGGCAGCTACGCGGCATTTATTCCGGAGAAAAGTCTCGGTATCGTGATGCTGGCGAATAAAAGCTACCCGAACCCGGCACGCGTTGAGGCGGCATACCGTATCCTCGACGCATTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37055","NCBI_taxonomy_name":"Enterobacter","NCBI_taxonomy_id":"547"}}}},"ARO_accession":"3006243","ARO_id":"44705","ARO_name":"ACT-48","CARD_short_name":"ACT-48","ARO_description":"ACT-48 is a ACT beta-lactamase.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4140":{"model_id":"4140","model_name":"ACT-49","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6515":{"protein_sequence":{"accession":"WP_045261282.1","sequence":"MMKKFLCCALLLSTSCSVLAAPMSEKQLADVVERNVTPLMKAQGIPGMAVAVIYQGQPHYFTFGKADIAANKSVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPDLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANSSIGLFGALAVKPSGMNYEQAMTTRVFKPLKLDHTWINVPKAEETHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVQDMASWVMANMAPDALQDTSLKQGITLAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVGGSDNKVALAPLPAREVSPPVPPVKASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILDALQ"},"dna_sequence":{"accession":"NG_050712.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATTCCTTTGCTGCGCCCTGCTGCTCAGCACATCCTGCTCTGTACTCGCCGCGCCGATGTCGGAAAAACAGCTGGCTGACGTGGTAGAACGCAACGTTACGCCCCTGATGAAAGCGCAGGGTATTCCAGGCATGGCGGTGGCCGTGATTTATCAGGGCCAGCCACACTACTTTACCTTTGGAAAGGCCGATATCGCGGCGAACAAATCCGTCACCCCGCAAACCCTGTTCGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTGCTGGGGGGCGATGCTATTGCCCGCGGCGAAATTTCGCTGGGCGATCCGGTAACCAAATATTGGCCTGATCTGACCGGCAAGCAGTGGCAAGGGATTCGCATGCTGGATCTGGCAACCTACACCGCCGGTGGCCTGCCTTTACAGGTGCCCGATGAGGTCACAGATAACGCATCCCTGCTGCGCTTCTATCAAAACTGGCAGCCTCAGTGGAAGCCGGGCACAACGCGTCTTTACGCCAACTCCAGCATCGGTCTTTTTGGCGCGCTGGCGGTCAAACCTTCCGGCATGAACTATGAGCAGGCCATGACGACGCGGGTCTTTAAGCCGCTCAAGCTGGATCATACCTGGATTAACGTTCCGAAAGCGGAGGAGACGCATTACGCCTGGGGATATCGTGACGGTAAAGCGGTCCACGTTTCACCGGGCATGCTGGACGCAGAGGCATATGGCGTGAAAACCAACGTGCAGGATATGGCGAGCTGGGTGATGGCCAATATGGCCCCTGACGCGCTGCAGGATACGTCCCTGAAGCAAGGCATTACGCTGGCGCAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAGGGGTTAGGTTGGGAGATGCTTAACTGGCCGGTCGATGCCAAAACCGTCGTCGGAGGCAGTGATAACAAGGTGGCGCTGGCACCGTTGCCTGCGAGAGAAGTGAGTCCACCCGTTCCCCCGGTTAAGGCCTCATGGGTGCACAAAACGGGCTCCACCGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGCTCGGCATTGTGATGCTGGCGAATAAAAGCTATCCGAACCCGGCGCGAGTTGAGGCGGCATACCGTATCCTCGACGCGCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3006244","ARO_id":"44706","ARO_name":"ACT-49","CARD_short_name":"ACT-49","ARO_description":"ACT-49 is a ACT beta-lactamase.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4141":{"model_id":"4141","model_name":"ACT-50","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6516":{"protein_sequence":{"accession":"WP_045286607.1","sequence":"MMKKSLSCALLLSVACSAFAAPMSEKQLAKVVERAVTPLMNAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTRYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDDVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMSFEEAMTKRVFKPLRLDHTWINVPKAEEAHYAWGYRDGKAVHVSPGMLDAEAYGIKTNVKDMASWVVANMAPDALQDSSLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVGGSDNKVALAPLPAREVNPPVPPVKASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVETAYRILDALQ"},"dna_sequence":{"accession":"NG_050713.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCCCTAAGTTGTGCCCTGCTGCTCAGCGTTGCCTGCTCTGCCTTCGCCGCCCCCATGTCAGAAAAACAGCTGGCTAAGGTGGTGGAGCGTGCCGTTACGCCGCTGATGAACGCGCAGGCCATTCCGGGTATGGCGGTGGCGGTAATTTATCAGGGTCAGCCGCACTACTTTACCTTTGGTAAAGCGGATGTCGCGGCGAATAAACCTGTTACGCCTCAAACCTTGTTCGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTATTGGGTGGCGATGCGATTGCTCGCGGTGAAATCTCACTGGGTGATCCAGTGACAAGGTACTGGCCTGAACTGACAGGAAAACAGTGGCAGGGCATTCGCATGCTGGATCTGGCAACCTATACCGCAGGGGGGTTGCCGTTACAGGTACCGGATGACGTCACTGATAACGCCTCTCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCGGGCACCACGCGTCTTTATGCCAACGCCAGCATCGGTCTTTTTGGTGCTCTCGCGGTTAAACCCTCCGGCATGAGTTTTGAAGAGGCCATGACGAAGCGGGTCTTTAAGCCGCTCAGGCTCGACCATACGTGGATTAACGTACCAAAAGCGGAAGAGGCGCATTACGCCTGGGGATACCGTGACGGTAAAGCGGTACACGTTTCTCCAGGGATGCTGGACGCTGAAGCCTATGGCATAAAAACCAACGTGAAAGATATGGCGAGCTGGGTGGTGGCAAACATGGCCCCCGATGCCCTTCAGGATAGCTCTCTCAAACAAGGGATAGCCCTGGCACAGTCCCGCTACTGGCGCGTGGGTGCCATGTATCAGGGGTTAGGCTGGGAAATGCTGAACTGGCCGGTCGATGCCAAAACCGTGGTCGGGGGCAGCGACAATAAGGTGGCGCTGGCGCCGTTGCCTGCCAGAGAAGTCAATCCCCCGGTACCGCCGGTTAAGGCCTCCTGGGTACACAAAACGGGTTCAACCGGTGGGTTTGGGAGCTACGTGGCATTTATTCCTGAAAAACAGCTCGGCATTGTGATGCTGGCGAATAAAAGCTATCCGAATCCGGCACGCGTTGAGACGGCATACCGTATCCTCGACGCGCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3006245","ARO_id":"44707","ARO_name":"ACT-50","CARD_short_name":"ACT-50","ARO_description":"ACT-50 is a ACT beta-lactamase.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4142":{"model_id":"4142","model_name":"ACT-51","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6517":{"protein_sequence":{"accession":"WP_045269678.1","sequence":"MKTKSLCCALMLSTSCSVLAAPMSEKQLSDVVERTVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQHWQPQWKPGTTRLYANASIGLFGALAVKPSGMSFEQAMTKRVFKPLKLDHTWINVPKEEEAHYAWGYRDGKATHVSPGMLDAEAYGVKTNVQDMASWVKANMNPDALPDSTLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVEAKTVVEGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKELGIVMLANKSYPNPARVEAAYRILSALQ"},"dna_sequence":{"accession":"NG_050714.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGAAGACAAAATCCCTTTGCTGTGCCCTGATGCTCAGCACCTCCTGCTCTGTTCTCGCCGCGCCGATGTCAGAGAAACAGCTGTCTGACGTGGTGGAACGTACCGTTACCCCCCTGATGAAAGCGCAAGCCATTCCGGGCATGGCGGTAGCGGTGATTTATCAGGGTCAGCCGCACTACTTTACCTTCGGAAAGGCCGATGTTGCGGCGAACAAACCTGTCACCCCGCAAACCCTGTTTGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTATTAGGTGGCGATGCGATTGCGCGCGGAGAAATATCGCTGGGCGACCCCGTGACAAAGTACTGGCCCGAGCTAACAGGCAAGCAGTGGCAGGGTATTCGCATGTTGGATCTGGCGACCTACACCGCGGGTGGCCTGCCGCTACAGGTGCCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGTTTCTATCAACACTGGCAACCGCAGTGGAAACCAGGCACAACGCGTCTTTATGCGAACGCCAGCATCGGGCTTTTTGGCGCCCTCGCGGTTAAACCCTCCGGTATGAGCTTTGAACAGGCCATGACGAAGCGGGTCTTCAAGCCACTCAAACTGGACCATACATGGATTAACGTTCCGAAAGAAGAAGAGGCGCATTACGCCTGGGGATACCGTGACGGTAAAGCAACCCACGTTTCACCGGGAATGCTGGATGCCGAAGCGTATGGTGTCAAAACCAACGTCCAGGATATGGCGAGCTGGGTGAAGGCCAACATGAACCCTGACGCCCTTCCGGATTCAACGTTGAAACAGGGTATTGCCCTGGCACAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCGGTAGAAGCCAAAACCGTCGTGGAGGGCAGCGATAACAAGGTGGCTCTTGCACCGTTACCGGTGGCAGAAGTGAACCCTCCAGCTCCGCCAGTAAAAGCATCATGGGTACATAAAACAGGCTCGACGGGTGGATTCGGCAGCTATGTCGCATTTATTCCTGAGAAGGAACTCGGCATTGTTATGCTGGCGAACAAGAGCTACCCGAACCCGGCGCGCGTGGAAGCGGCATACCGTATTCTGAGCGCTCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39773","NCBI_taxonomy_name":"Enterobacter kobei","NCBI_taxonomy_id":"208224"}}}},"ARO_accession":"3006246","ARO_id":"44708","ARO_name":"ACT-51","CARD_short_name":"ACT-51","ARO_description":"ACT-51 is a ACT beta-lactamase.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4143":{"model_id":"4143","model_name":"ACT-52","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6518":{"protein_sequence":{"accession":"WP_014882211.1","sequence":"MKTKSLCCALLLSTSCSVLAAPMSEKQLSDVVERTVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQHWQPQWKPGATRLYANASIGLFGALAVKPSGMSFEQAMTKRVFKPLKLDHTWINVPKEEEAHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVQDISSWVKANMNPAALPDSTLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVEAKTVVEGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKELGIVMLANKSYPNPARVEAAYRILSALQ"},"dna_sequence":{"accession":"NG_050715.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGAAGACAAAATCCCTTTGCTGTGCCCTGCTGCTCAGCACCTCCTGCTCTGTTCTCGCCGCGCCGATGTCAGAGAAACAGCTGTCTGACGTGGTGGAACGTACCGTTACCCCCCTGATGAAAGCGCAAGCCATTCCGGGCATGGCGGTAGCGGTGATTTATCAGGGTCAGCCGCACTACTTTACCTTCGGAAAGGCCGATGTTGCGGCGAACAAACCTGTCACCCCGCAAACCCTGTTTGAACTGGGCTCTATAAGTAAAACCTTCACCGGCGTATTAGGTGGCGATGCGATTGCGCGCGGAGAAATATCGCTGGGCGACCCCGTGACAAAGTACTGGCCCGAGCTAACAGGCAAGCAGTGGCAGGGTATTCGCATGTTGGATCTGGCGACCTACACCGCGGGTGGCCTGCCGCTACAGGTGCCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGTTTCTATCAACACTGGCAACCGCAGTGGAAACCAGGCGCAACGCGTCTTTATGCGAACGCCAGCATCGGGCTTTTTGGCGCCCTCGCGGTTAAACCCTCCGGTATGAGCTTTGAACAGGCCATGACGAAGCGGGTCTTCAAGCCACTCAAACTGGACCATACATGGATTAACGTTCCGAAAGAAGAAGAGGCGCATTACGCCTGGGGATACCGTGATGGTAAAGCGGTCCACGTTTCACCGGGAATGCTGGATGCCGAAGCGTATGGTGTCAAAACCAACGTCCAGGATATATCGAGCTGGGTGAAGGCCAACATGAACCCTGCCGCCCTTCCGGATTCAACGCTGAAACAGGGTATTGCCCTGGCACAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCGGTAGAAGCCAAAACCGTCGTGGAGGGCAGCGATAACAAGGTGGCTCTTGCACCGTTACCGGTGGCAGAAGTGAACCCTCCAGCTCCGCCAGTAAAAGCATCATGGGTACATAAAACAGGCTCGACGGGTGGATTCGGCAGCTATGTCGCATTTATTCCTGAGAAGGAACTCGGCATTGTTATGCTGGCGAACAAGAGCTACCCGAACCCGGCGCGCGTGGAAGCGGCATACCGTATTCTGAGCGCTCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40540","NCBI_taxonomy_name":"Enterobacter cloacae complex","NCBI_taxonomy_id":"354276"}}}},"ARO_accession":"3006247","ARO_id":"44709","ARO_name":"ACT-52","CARD_short_name":"ACT-52","ARO_description":"ACT-52 is a ACT beta-lactamase.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4144":{"model_id":"4144","model_name":"ACT-53","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6519":{"protein_sequence":{"accession":"WP_032644152.1","sequence":"MMTKTLCCALLLSTSCSALAGPLSEKQLAEVVEQTVTPLMKAQAIPGMAVAVIYEGQPHYFTFGKADVAKNKPVTPQTLFELGSISKTFTGVLGGDAVARGEISLGDPVTKYWPALTGKQWQGIRMLDLATYTAGGLPLQVPDDVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVQPSGMSYEQAITTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVQDMASWVMVNMKPEALQDTSLGQGITLAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVDGSDNKVALAPLPAREVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKNLGIVMLANKSYPNPARVEAAYRILDALQ"},"dna_sequence":{"accession":"NG_055522.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGACAAAAACTCTTTGCTGCGCCCTGCTGCTCAGCACCTCCTGCTCAGCGCTGGCTGGACCGCTGTCAGAAAAACAGCTGGCTGAAGTGGTGGAACAAACCGTTACGCCGTTAATGAAAGCGCAGGCCATTCCGGGTATGGCGGTGGCGGTGATTTATGAGGGTCAGCCGCACTACTTTACCTTTGGCAAAGCCGATGTCGCAAAGAACAAACCCGTTACCCCACAGACCCTGTTCGAGCTGGGATCTATAAGTAAAACCTTCACCGGCGTATTGGGTGGCGATGCCGTTGCTCGCGGTGAAATATCGCTGGGCGACCCTGTGACAAAGTACTGGCCCGCGCTGACAGGCAAGCAGTGGCAGGGGATCCGCATGCTGGATCTGGCCACCTATACCGCAGGAGGTCTGCCGCTACAGGTACCGGATGATGTCACGGATAATGCCTCTCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCGGGTACCACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGCGCGCTGGCGGTGCAGCCTTCCGGCATGAGCTATGAGCAGGCCATAACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTTCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGATACCGTGACGGTAAAGCGGTGCACGTTTCGCCGGGCATGCTCGACGCAGAAGCTTATGGCGTGAAAACCAACGTGCAGGATATGGCAAGCTGGGTGATGGTCAACATGAAGCCGGAAGCCCTTCAGGATACGTCGCTCGGGCAAGGTATCACCCTGGCGCAGTCTCGCTACTGGCGCGTGGGGGCGATGTACCAGGGCTTAGGCTGGGAAATGCTTAACTGGCCGGTCGATGCCAAAACCGTGGTTGACGGTAGCGACAATAAGGTGGCGCTGGCGCCGCTGCCTGCGAGGGAGGTGAATCCCCCAGCGCCGCCGGTTAAGGCATCCTGGGTCCATAAAACAGGCTCTACCGGCGGGTTTGGCAGCTACGTAGCATTTATTCCGGAGAAAAATCTCGGCATCGTGATGCTGGCGAATAAAAGCTATCCAAACCCTGCGCGGGTGGAGGCGGCGTACCGCATTCTCGACGCATTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40540","NCBI_taxonomy_name":"Enterobacter cloacae complex","NCBI_taxonomy_id":"354276"}}}},"ARO_accession":"3006248","ARO_id":"44710","ARO_name":"ACT-53","CARD_short_name":"ACT-53","ARO_description":"ACT-53 is a ACT beta-lactamase.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4145":{"model_id":"4145","model_name":"ACT-54","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6520":{"protein_sequence":{"accession":"WP_099156056.1","sequence":"MMKKSLCCALLLSTSCAALAAPMSETQLAKVVERTVTPLMKAQSIPGMAVAVIYQGQPHYFTFGKADVAANTPVTAQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPELTGKQWQGVRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQSWQPQWAPGTTRLYANASIGLFGALAVKPSGMRFEQAMTERVLKPLNLNHTWINVPKSEEQHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVKDMASWVMANMAPDGVQDASLKQGMVLAQSRYWRTGSMYQGLGWEMLNWPVEAKTVVEGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKELGIVMLANKSYPNPARVEAAYRILSALQ"},"dna_sequence":{"accession":"NG_055670.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCCCTGTGCTGCGCCCTGCTGCTCAGCACCTCCTGCGCTGCATTAGCCGCACCTATGTCAGAAACACAGCTGGCGAAGGTCGTGGAACGTACCGTTACGCCCCTGATGAAAGCGCAGTCTATTCCGGGTATGGCGGTCGCCGTGATCTATCAGGGCCAGCCGCACTACTTCACCTTCGGCAAGGCCGATGTCGCAGCGAACACACCCGTCACTGCACAAACGCTGTTTGAGCTGGGCTCAATCAGCAAAACCTTCACCGGCGTTCTGGGTGGCGATGCTATTGCTCGCGGTGAAATTTCGCTGGGCGATCCGGTGACCAAATACTGGCCTGAGCTGACCGGCAAACAGTGGCAGGGCGTTCGCATGCTGGACCTGGCAACCTATACTGCCGGTGGCCTGCCGTTACAGGTGCCCGATGAGGTTACCGATAATGCCTCGCTGCTGCGTTTTTACCAGTCCTGGCAACCACAGTGGGCGCCAGGCACCACGCGTCTTTATGCGAACGCCAGCATCGGTCTGTTTGGGGCTCTGGCGGTGAAACCTTCTGGCATGCGCTTTGAGCAGGCGATGACAGAGCGGGTCCTGAAGCCGCTTAACCTGAACCATACGTGGATTAACGTTCCGAAGTCAGAAGAACAGCATTACGCCTGGGGTTATCGTGACGGTAAAGCGGTTCACGTTTCGCCGGGCATGCTCGACGCCGAAGCGTATGGCGTGAAAACCAACGTGAAGGATATGGCGAGCTGGGTGATGGCTAACATGGCTCCCGATGGCGTACAGGATGCCTCACTGAAGCAGGGCATGGTGCTTGCACAGTCTCGCTACTGGCGCACAGGCTCGATGTACCAGGGCCTGGGCTGGGAGATGCTCAACTGGCCGGTAGAAGCCAAAACCGTGGTGGAGGGCAGCGACAACAAAGTAGCGCTTGCGCCGTTGCCCGTGGCAGAAGTAAACCCTCCTGCACCACCGGTAAAAGCGTCATGGGTACATAAAACAGGCTCGACGGGCGGATTTGGCAGCTACGTGGCATTTATTCCTGAGAAGGAACTCGGCATCGTTATGCTGGCGAACAAGAGCTACCCGAACCCGGCACGCGTGGAAGCGGCATACCGTATTCTGAGCGCTCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40540","NCBI_taxonomy_name":"Enterobacter cloacae complex","NCBI_taxonomy_id":"354276"}}}},"ARO_accession":"3006249","ARO_id":"44711","ARO_name":"ACT-54","CARD_short_name":"ACT-54","ARO_description":"ACT-54 is a ACT beta-lactamase.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4146":{"model_id":"4146","model_name":"ACT-55","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6521":{"protein_sequence":{"accession":"WP_047052637.1","sequence":"MMKKSLCCALLLGISCSALAAPVSEKQLAEVVANTVTPLMKAQSVPGMAVAVIYQGKPHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEITDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMSYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPENVADATLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVVGGSDSKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANKSYPNPARVEAAYHILEALQ"},"dna_sequence":{"accession":"NG_061414.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCCCTTTGCTGCGCCCTGCTGCTCGGCATCTCTTGCTCTGCTCTCGCCGCGCCAGTATCAGAAAAACAGCTGGCGGAGGTGGTCGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCTGTTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGAAAACCGCACTATTACACGTTTGGCAAGGCCGATATCGCGGCGAATAAACCCGTTACGCCTCAGACCCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGCGTTTTAGGTGGGGATGCCATTGCGCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTGACGGGCAAGCAGTGGCAGGGTATTCGTATGCTGGATCTCGCCACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGATCACGGATAACGCCTCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCAGGCACAACGCGTCTTTACGCCAATGCCAGCATCGGTCTTTTTGGCGCGCTGGCGGTCAAACCTTCCGGCATGTCCTATGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTGCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGTATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCGGAGAACGTTGCTGATGCCACACTTAAGCAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGGTCGGAGGCAGCGACAGTAAGGTAGCGCTGGCGCCGTTGCCCGTGGCAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGTTCTACTGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCGAGGCGTTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39098","NCBI_taxonomy_name":"Enterobacter hormaechei","NCBI_taxonomy_id":"158836"}}}},"ARO_accession":"3006250","ARO_id":"44712","ARO_name":"ACT-55","CARD_short_name":"ACT-55","ARO_description":"ACT-55 is a ACT beta-lactamase.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4147":{"model_id":"4147","model_name":"ACT-56","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6522":{"protein_sequence":{"accession":"WP_033487869.1","sequence":"MMKKSLCCALLLGISCSALATPVSEKQLAEVVANTVTPLMKAQSVPGMAVAVIYQGKPHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMPYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPENVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVVEGSDSKVALAPLPVVEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANTSYPNPARVEAAYHILEALQ"},"dna_sequence":{"accession":"NG_061415.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCCCTTTGCTGCGCCCTGCTGCTCGGCATCTCTTGCTCTGCTCTCGCCACGCCAGTGTCAGAAAAACAGCTGGCGGAGGTGGTAGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCTGTTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGAAAACCGCACTATTACACGTTTGGCAAGGCCGATATCGCGGCGAATAAACCCGTTACGCCTCAGACCCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGCGTTTTAGGTGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTGACGGGCAAGCAGTGGCAGGGTATTCGTATGCTGGATCTCGCCACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTCAAACCTTCTGGCATGCCCTATGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTGCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGTATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCGGAGAACGTTGCTGATGCCTCACTTAAGCAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGGTCGAGGGCAGCGACAGTAAGGTAGCGCTGGCGCCGTTGCCCGTGGTAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGCTCTACTGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATACAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCGAGGCGCTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40540","NCBI_taxonomy_name":"Enterobacter cloacae complex","NCBI_taxonomy_id":"354276"}}}},"ARO_accession":"3006251","ARO_id":"44713","ARO_name":"ACT-56","CARD_short_name":"ACT-56","ARO_description":"ACT-56 is a ACT beta-lactamase.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4148":{"model_id":"4148","model_name":"ACT-57","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6523":{"protein_sequence":{"accession":"WP_094935119.1","sequence":"MMTKSLCCALLLSTSCSVLAAPMSEKQLAEMVERTVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMSYEQAITTRVFKRLKLDHTWINVPKAEEAHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVKDMANWVMVNMKPDSLEDSSLRKGLTLAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVEGSDNKVALAPLPAREVNPPAPPVNASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILDALQ"},"dna_sequence":{"accession":"NG_061418.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGACTAAATCCCTTTGCTGCGCCCTGCTGCTCAGCACCTCCTGCTCGGTATTGGCTGCACCGATGTCAGAAAAACAGCTGGCTGAGATGGTGGAACGTACCGTTACGCCGCTGATGAAAGCGCAGGCCATTCCGGGTATGGCGGTGGCGGTGATTTATCAGGGTCAGCCGCACTACTTTACCTTCGGTAAAGCCGATGTTGCGGCGAACAAACCTGTCACCCCACAAACCTTATTCGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTACTGGGCGGCGATGCCATTGCTCGGGGTGAAATATCGCTGGGCGATCCGGTGACCAAATACTGGCCTGAACTGACAGGCAAGCAGTGGCAGGGGATCCGCATGCTGGATCTGGCAACCTATACCGCAGGAGGTTTGCCGTTACAGGTACCGGATGAGGTCACGGATAACGCCTCTCTGCTGCGCTTTTATCAAAACTGGCAGCCTCAGTGGAAGCCGGGCACCACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGCGCGCTGGCGGTCAAACCTTCCGGCATGAGCTATGAGCAGGCCATAACGACGCGGGTCTTTAAGCGGCTCAAGCTGGACCATACCTGGATTAACGTTCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGATACCGCGACGGTAAGGCGGTACACGTTTCGCCAGGAATGCTGGACGCTGAAGCCTATGGCGTAAAAACCAACGTGAAGGATATGGCAAACTGGGTGATGGTCAACATGAAGCCGGACTCGCTTGAGGATAGTTCACTCAGGAAAGGCCTTACCCTGGCGCAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAGGGGTTAGGCTGGGAAATGCTTAACTGGCCGGTCGATGCAAAAACCGTGGTTGAAGGTAGCGACAATAAGGTGGCGCTGGCACCGCTGCCTGCGAGAGAAGTGAATCCACCGGCGCCCCCGGTCAATGCGTCATGGGTCCATAAAACAGGCTCTACCGGCGGGTTTGGCAGCTACGTGGCATTTATTCCTGAAAAGCAGCTCGGCATTGTGATGCTGGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCGTATCCTCGACGCGCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40540","NCBI_taxonomy_name":"Enterobacter cloacae complex","NCBI_taxonomy_id":"354276"}}}},"ARO_accession":"3006252","ARO_id":"44714","ARO_name":"ACT-57","CARD_short_name":"ACT-57","ARO_description":"ACT-57 is a ACT beta-lactamase.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4149":{"model_id":"4149","model_name":"ACT-58","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6524":{"protein_sequence":{"accession":"WP_111965422.1","sequence":"MMTKSLCCALLLSTSSSVLAAPMSEKQLAEVVERTVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVAANKAVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMSYEQAITTRVFKPLKLDHTWINVPKTEEAHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVQDMASWVMVNMKPDSLPDTSLRQGIALAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVKGSDNKVALAPLTAREVNPPAPPVNASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYHILDALQ"},"dna_sequence":{"accession":"NG_061419.1","fmin":"2","fmax":"1148","strand":"+","sequence":"ATGATGACAAAATCCCTTTGCTGCGCCCTGCTGCTCAGCACCTCCAGCTCAGTATTGGCTGCCCCGATGTCAGAAAAACAGCTGGCTGAGGTGGTGGAACGCACCGTTACGCCACTGATGAAAGCGCAGGCCATTCCGGGCATGGCGGTGGCGGTGATTTATCAGGGTCAGCCGCACTACTTTACCTTCGGTAAAGCCGATGTTGCGGCAAACAAAGCTGTTACCCCACAAACCTTGTTCGAACTGGGTTCTATAAGTAAAACCTTCACCGGCGTATTGGGTGGCGATGCCATTGCTCGCGGTGAAATATCGCTGGGCGATCCGGTGACAAAATACTGGCCTGAGCTGACAGGCAAGCAGTGGCAGGGGATCCGCATGCTGGATCTGGCAACCTATACCGCAGGCGGTCTGCCGTTACAGGTACCGGATGAGGTCACGGATAACGCCTCTCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCGGGCACCACGCGTCTTTACGCCAATGCCAGCATCGGTCTTTTTGGCGCGCTGGCGGTCAAACCTTCCGGCATGAGCTATGAGCAGGCCATAACGACGCGGGTCTTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTTCCGAAAACGGAAGAGGCGCATTACGCCTGGGGATACCGCGACGGTAAAGCGGTCCACGTTTCGCCAGGAATGCTGGATGCAGAAGCCTATGGCGTAAAAACCAACGTGCAGGATATGGCAAGCTGGGTGATGGTTAATATGAAGCCAGACTCCCTCCCGGATACTTCACTCAGGCAAGGCATTGCCCTGGCGCAGTCTCGCTACTGGCGCGTGGGGGCCATGTATCAAGGGTTAGGTTGGGAAATGCTTAACTGGCCGGTCGATGCCAAAACCGTGGTTAAAGGTAGCGACAATAAGGTAGCGCTGGCACCGCTGACCGCGAGAGAAGTGAATCCGCCGGCACCGCCGGTCAACGCGTCCTGGGTCCATAAAACAGGCTCAACCGGCGGGTTTGGCAGCTACGTGGCATTTATTCCTGAAAAACAGCTCGGCATTGTGATGCTGGCGAATAAAAGCTATCCGAACCCTGCCCGCGTTGAGGCGGCATACCATATCCTCGACGCGCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40540","NCBI_taxonomy_name":"Enterobacter cloacae complex","NCBI_taxonomy_id":"354276"}}}},"ARO_accession":"3006253","ARO_id":"44715","ARO_name":"ACT-58","CARD_short_name":"ACT-58","ARO_description":"ACT-58 is a ACT beta-lactamase.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4150":{"model_id":"4150","model_name":"ACT-59","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6525":{"protein_sequence":{"accession":"WP_112792421.1","sequence":"MMKKTLCCAVLLGISCSALAAPVSEQQLAEVVAKTVTPLMKAQSIPGMAVAVIYQGKPHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDALARGEISLDDPVIKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDDASLLRFYQHWQPQWKPGTTRLYANASIGLFGALAVKPSGMRYEQAMTERVFKPLALHHTWINVPKAEEAHYAWGYRDGKAVHVSPGMLDAQAYGVKTNVQDMANWVMANMAPENVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEAKTVVDGSDSKVALAALPAVEINPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANKSYPNPARVEAAYHILDALQ"},"dna_sequence":{"accession":"NG_061401.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAAACCCTTTGCTGCGCCGTGCTGCTCGGCATCTCTTGCTCTGCCCTCGCCGCGCCAGTATCCGAACAACAGCTGGCGGAGGTGGTCGCGAAGACGGTTACGCCGCTGATGAAAGCCCAGTCTATTCCCGGTATGGCGGTGGCCGTTATTTATCAGGGTAAACCGCACTATTACACGTTTGGCAAGGCCGATATCGCAGCCAACAAACCGGTTACCCCTCAGACCCTGTTCGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTTTTAGGTGGGGATGCCCTTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGATCAAATACTGGCCTGAGCTGACGGGCAAGCAGTGGCAAGGGATTCGCATGCTGGATCTCGCGACCTACACCGCTGGCGGTCTGCCGCTACAGGTGCCCGATGAGGTGACGGATGACGCCTCCCTGCTGCGCTTCTATCAACACTGGCAGCCACAGTGGAAGCCAGGCACAACGCGCCTTTATGCCAACGCCAGCATCGGCCTGTTTGGTGCGCTGGCGGTTAAGCCTTCCGGCATGCGCTACGAGCAGGCGATGACCGAGCGAGTCTTCAAACCGCTGGCGCTGCATCACACCTGGATTAACGTGCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGCAAAGCGGTACACGTTTCGCCGGGGATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCAGAGAACGTTGCTGATGCCTCACTTAAGCAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGTTCAATGTACCAGGGCCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCAAAAACGGTGGTTGATGGCAGCGACAGTAAGGTGGCGCTGGCCGCCTTGCCTGCGGTCGAAATAAATCCTCCGGCTCCGCCTGTAAAAGCCTCCTGGGTGCACAAAACCGGCTCGACGGGCGGGTTCGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGCATCGTAATGCTCGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCGACGCGCTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39098","NCBI_taxonomy_name":"Enterobacter hormaechei","NCBI_taxonomy_id":"158836"}}}},"ARO_accession":"3006254","ARO_id":"44716","ARO_name":"ACT-59","CARD_short_name":"ACT-59","ARO_description":"ACT-59 is a ACT beta-lactamase.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4151":{"model_id":"4151","model_name":"ACT-60","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6526":{"protein_sequence":{"accession":"WP_111976052.1","sequence":"MMKKSLFCALLLGISCSALAAPVSEKQLAEVVANTVTPLMKAQSVPGMAVAVIYQGKPHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEITDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALTVKPSGMSYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPENVADATLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVVGGSDSKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANKSYPNPARVEAAYHILEALQ"},"dna_sequence":{"accession":"NG_061402.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCCCTTTTCTGCGCCCTGCTGCTCGGCATCTCTTGCTCTGCTCTCGCCGCGCCAGTATCAGAAAAACAGCTGGCGGAGGTGGTCGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCTGTTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGAAAACCGCACTATTACACGTTTGGCAAGGCCGATATCGCGGCGAATAAACCCGTTACGCCTCAGACCCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGCGTTTTAGGTGGGGATGCCATTGCGCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTGACGGGCAAGCAGTGGCAGGGTATTCGTATGCTGGATCTCGCCACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGATCACGGATAACGCCTCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCAGGCACAACGCGTCTTTACGCCAATGCCAGCATCGGTCTTTTTGGCGCGCTGACGGTCAAACCTTCCGGCATGTCCTATGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTGCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGTATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCGGAGAACGTTGCTGATGCCACACTTAAGCAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGGTCGGAGGCAGCGACAGTAAGGTAGCGCTGGCGCCGTTGCCCGTGGCAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGTTCTACTGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCGAGGCGTTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39098","NCBI_taxonomy_name":"Enterobacter hormaechei","NCBI_taxonomy_id":"158836"}}}},"ARO_accession":"3006255","ARO_id":"44717","ARO_name":"ACT-60","CARD_short_name":"ACT-60","ARO_description":"ACT-60 is a ACT beta-lactamase.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4152":{"model_id":"4152","model_name":"ACT-61","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6527":{"protein_sequence":{"accession":"WP_112017656.1","sequence":"MMKKSLCCALLLGLSCSALAAPVSEKQLAEVVANTITPLMKAQSVPGMAVAVIYQGKPHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMPYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPEKVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVVEGSDSKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANKSYPNPARVEAAYHILKALQ"},"dna_sequence":{"accession":"NG_061387.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCCCTTTGCTGCGCCCTGCTGCTGGGCCTCTCTTGCTCTGCTCTCGCCGCGCCAGTATCAGAAAAACAGCTGGCGGAGGTGGTCGCGAATACGATTACCCCGCTGATGAAAGCCCAGTCTGTTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGAAAACCGCACTATTACACGTTTGGCAAGGCCGATATCGCGGCGAATAAACCCGTTACGCCTCAGACCCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGCGTTTTAGGTGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTGACGGGCAAGCAGTGGCAGGGTATTCGTATGCTGGATCTCGCCACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTCAAACCTTCCGGCATGCCCTATGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTTCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGAATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCGGAAAAGGTTGCCGATGCCTCACTTAAGCAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGGTCGAAGGCAGCGACAGTAAGGTAGCGCTGGCGCCGTTACCCGTGGCAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGTTCTACTGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCAAGGCGCTTCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39098","NCBI_taxonomy_name":"Enterobacter hormaechei","NCBI_taxonomy_id":"158836"}}}},"ARO_accession":"3006256","ARO_id":"44718","ARO_name":"ACT-61","CARD_short_name":"ACT-61","ARO_description":"ACT-61 is a ACT beta-lactamase.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4153":{"model_id":"4153","model_name":"ACT-62","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6528":{"protein_sequence":{"accession":"WP_111967096.1","sequence":"MMKKSLSCALLLSASCSVLAAPMSEKQLAEVVERTVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEITLGDPVTKYWPELTGKQWQGIRMLDLATYTAGGLPLQAPDEVTDTASLLRFYQNWQPKWKPGTTRLYANTSIGLFGALAVKPSGMSYEQAMTTRVFKPLKLDHTWINVPKAEEAHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVQDMASWVMVNMMPDSLQDSPLKHGIALAQSRYWRVGAMYQGLGWEMLNWPVDAQTVVGGSDNKVALAPLPAREVNPPAPTVKASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILDALQ"},"dna_sequence":{"accession":"NG_061388.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCCCTAAGCTGTGCCCTGCTGCTCAGCGCCTCCTGCTCAGTATTAGCTGCACCGATGTCAGAAAAACAGCTGGCTGAGGTGGTGGAACGTACCGTTACGCCGCTGATGAAAGCGCAGGCCATCCCGGGTATGGCGGTGGCGGTGATTTATCAGGGTCAGCCGCACTACTTTACCTTCGGTAAAGCTGATGTTGCAGCGAACAAACCCGTCACCCCGCAAACCTTGTTCGAGCTGGGTTCGATAAGTAAAACCTTCACCGGCGTATTGGGTGGCGATGCGATTGCGCGCGGTGAAATAACGCTGGGCGATCCGGTGACCAAATACTGGCCTGAGCTCACGGGCAAGCAGTGGCAGGGCATTCGCATGCTGGATCTGGCAACCTACACCGCAGGCGGTCTGCCGTTGCAGGCGCCGGATGAGGTCACGGATACCGCCTCCCTGCTGCGCTTTTATCAAAACTGGCAGCCAAAGTGGAAGCCGGGCACCACGCGTCTTTACGCTAACACCAGCATCGGTCTTTTTGGCGCGCTGGCGGTCAAACCCTCCGGCATGAGCTATGAGCAGGCCATGACGACGCGGGTCTTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTCCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGATACCGTGACGGTAAAGCGGTCCACGTTTCGCCAGGGATGCTGGACGCGGAAGCCTATGGCGTAAAAACCAACGTGCAGGATATGGCAAGCTGGGTGATGGTCAACATGATGCCGGACTCCCTTCAGGATTCCCCACTGAAGCACGGTATTGCCCTGGCACAGTCTCGCTACTGGCGCGTGGGAGCCATGTATCAAGGATTGGGCTGGGAAATGCTGAACTGGCCGGTCGACGCCCAAACGGTGGTCGGGGGCAGCGACAATAAGGTGGCGCTGGCGCCGTTGCCTGCAAGAGAAGTGAATCCACCGGCACCAACGGTTAAGGCCTCCTGGGTCCATAAAACGGGCTCTACCGGCGGATTTGGCAGCTACGTGGCATTTATTCCTGAAAAGCAGCTCGGCATTGTGATGCTGGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCGTATCCTCGACGCGCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40540","NCBI_taxonomy_name":"Enterobacter cloacae complex","NCBI_taxonomy_id":"354276"}}}},"ARO_accession":"3006257","ARO_id":"44719","ARO_name":"ACT-62","CARD_short_name":"ACT-62","ARO_description":"ACT-62 is a ACT beta-lactamase.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4154":{"model_id":"4154","model_name":"ACT-63","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6529":{"protein_sequence":{"accession":"WP_112780466.1","sequence":"MMTKTLCCALLLSTSCSVLAAPLSEKQLAEVVERTVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVAKNKPVTPQTLFELGSISKTFTGVLGGDAVARGEISLGDPVTKYWPALTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDSASLLRFYQNWQPQWKSGTTRLYANASIGLFGALAVKPSGMSYEQAITTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVQDMASWVMVNMKPDAIQDTSLRQGITLAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVDGSDNKVALAPLPASEVNPPAPPVKASWVHKTGSTGGFGSYAAFIPEKSLGIVMLANKSYPNPARVEAAYRILDALQ"},"dna_sequence":{"accession":"NG_061406.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGACAAAAACCCTTTGCTGCGCCCTGCTGCTCAGCACCTCCTGCTCAGTATTGGCCGCACCGCTGTCAGAAAAACAGCTGGCTGAGGTGGTGGAGCGCACCGTTACGCCCCTGATGAAAGCGCAGGCTATTCCGGGTATGGCGGTGGCGGTGATTTATCAGGGCCAGCCGCACTACTTTACCTTCGGTAAAGCCGATGTTGCAAAGAACAAACCGGTTACCCCACAAACCCTGTTCGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTACTGGGTGGCGATGCCGTTGCTCGCGGTGAAATATCGCTGGGCGACCCCGTGACAAAGTACTGGCCCGCGCTGACAGGCAAGCAGTGGCAGGGGATCCGCATGCTGGATCTGGCCACCTATACCGCGGGAGGTCTGCCGCTACAGGTACCGGATGAGGTCACGGATAGCGCCTCTCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGTCGGGCACAACGCGTCTTTATGCCAACGCCAGCATCGGTCTTTTTGGCGCGCTGGCGGTGAAGCCTTCCGGCATGAGCTATGAGCAGGCCATAACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTTCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGATACCGTGACGGTAAAGCGGTGCACGTTTCGCCGGGAATGCTCGATGCGGAAGCTTATGGCGTGAAAACCAACGTGCAGGATATGGCAAGCTGGGTGATGGTCAACATGAAGCCGGACGCCATTCAGGATACGTCACTCAGGCAAGGCATTACCCTGGCGCAGTCTCGCTACTGGCGCGTGGGGGCCATGTACCAGGGATTAGGCTGGGAAATGCTTAACTGGCCGGTGGATGCCAAAACCGTGGTTGACGGCAGCGACAATAAGGTGGCGCTGGCGCCGCTGCCTGCGAGCGAAGTCAATCCGCCCGCGCCGCCGGTTAAGGCATCCTGGGTCCACAAAACGGGTTCAACCGGCGGGTTTGGCAGCTACGCGGCATTTATTCCGGAGAAAAGTCTCGGCATCGTGATGCTGGCGAATAAAAGCTACCCGAACCCGGCACGCGTTGAGGCGGCATACCGTATCCTCGACGCATTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40540","NCBI_taxonomy_name":"Enterobacter cloacae complex","NCBI_taxonomy_id":"354276"}}}},"ARO_accession":"3006258","ARO_id":"44720","ARO_name":"ACT-63","CARD_short_name":"ACT-63","ARO_description":"ACT-63 is a ACT beta-lactamase.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4155":{"model_id":"4155","model_name":"ACT-64","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6530":{"protein_sequence":{"accession":"WP_050861789.1","sequence":"MKTKSLCCALLLSTSCSVLAAPMSEKQLSDVVERTVTPLMKAQAIPGMAVAVIYQGHPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQDWQPQWKPGTTRLYANASIGLFGALAVKPSGMSFEQAMTKRVFKPLKLDHTWIDVPKEDEAHYAWGYRDGKTVHVSPGMLDAEAYGVKTNVQDMASWVKANMNPAALPDSTLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVEAKTVVEGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKELGIVMLANKSYPNPARVEAAYRILSALQ"},"dna_sequence":{"accession":"NG_061403.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGAAGACAAAATCTCTTTGCTGCGCCCTGCTGCTCAGCACCTCCTGCTCTGTTCTCGCCGCACCGATGTCAGAGAAACAGCTGTCTGACGTGGTGGAACGTACCGTTACCCCCCTGATGAAGGCGCAAGCCATTCCGGGCATGGCGGTGGCGGTGATTTATCAGGGTCATCCGCACTACTTTACCTTCGGAAAGGCCGATGTTGCGGCGAACAAACCTGTCACCCCGCAAACCCTGTTTGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTATTAGGTGGCGATGCGATTGCGCGCGGAGAAATATCGCTGGGCGACCCCGTGACAAAGTACTGGCCCGAGCTAACAGGCAAGCAGTGGCAGGGTATTCGCATGTTAGATCTGGCGACCTACACCGCGGGTGGCCTGCCGCTACAGGTGCCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGTTTCTATCAAGACTGGCAACCGCAGTGGAAACCAGGCACAACGCGTCTTTATGCGAACGCCAGCATCGGGCTTTTTGGCGCCCTCGCGGTTAAACCCTCCGGTATGAGCTTTGAACAGGCCATGACGAAGCGGGTCTTCAAGCCGCTCAAACTGGACCATACATGGATTGACGTTCCGAAAGAAGACGAGGCGCATTACGCCTGGGGATACCGTGATGGTAAAACGGTCCACGTTTCACCGGGAATGTTGGATGCCGAAGCGTATGGTGTCAAAACCAACGTCCAGGATATGGCGAGCTGGGTGAAGGCCAACATGAACCCTGCCGCCCTTCCGGATTCAACGTTGAAACAGGGTATTGCCTTGGCACAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCGGTAGAAGCCAAAACCGTCGTGGAGGGCAGCGATAACAAGGTGGCTCTTGCACCGTTACCGGTGGCAGAAGTGAACCCTCCAGCTCCGCCAGTAAAAGCATCATGGGTACATAAAACAGGCTCGACGGGTGGATTCGGCAGCTATGTCGCATTTATTCCTGAGAAGGAACTCGGCATTGTTATGCTGGCGAACAAGAGCTATCCGAACCCGGCGCGCGTGGAAGCGGCATACCGTATTCTGAGCGCTCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37055","NCBI_taxonomy_name":"Enterobacter","NCBI_taxonomy_id":"547"}}}},"ARO_accession":"3006259","ARO_id":"44721","ARO_name":"ACT-64","CARD_short_name":"ACT-64","ARO_description":"ACT-64 is a ACT beta-lactamase.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4156":{"model_id":"4156","model_name":"ACT-65","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6531":{"protein_sequence":{"accession":"WP_047726486.1","sequence":"MMKKSLCCALLLGISCSALATPVSEKQLAEVVANTVTPLMKAQSVPGMAVAVIYQGKPHYYTFGKADIAANKSVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMPYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPENVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVVEGSDSKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANTSYPNPARVEAAYHILEALQ"},"dna_sequence":{"accession":"NG_064665.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCCCTTTGCTGCGCCCTGCTGCTCGGCATCTCTTGCTCTGCTCTCGCCACGCCAGTGTCAGAAAAACAGCTGGCGGAGGTGGTTGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCTGTTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGAAAACCGCACTATTACACGTTTGGCAAGGCCGATATCGCGGCGAATAAATCCGTTACGCCTCAGACCCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGCGTTTTAGGTGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTGACGGGCAAGCAGTGGCAGGGTATTCGTATGCTGGATCTCGCCACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTCAAACCTTCTGGCATGCCCTATGAGCAAGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTGCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGATGGTAAAGCGGTGCGTGTTTCGCCGGGTATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCGGAGAACGTTGCTGATGCCTCACTTAAGCAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGGTCGAGGGCAGTGACAGTAAGGTAGCGCTGGCGCCGTTGCCCGTGGCAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGCTCTACTGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATACAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCGAGGCGCTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40540","NCBI_taxonomy_name":"Enterobacter cloacae complex","NCBI_taxonomy_id":"354276"}}}},"ARO_accession":"3006260","ARO_id":"44722","ARO_name":"ACT-65","CARD_short_name":"ACT-65","ARO_description":"ACT-65 is a ACT beta-lactamase.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4157":{"model_id":"4157","model_name":"ACT-66","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6532":{"protein_sequence":{"accession":"WP_032625176.1","sequence":"MMKKSLCCALLLGISCSALAAPVSEKQLAEVVANTITPLMKAQSIPGMAVAVIYQGKPHYYTFGKADIAASKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNAALLHFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMGYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPEKVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVIEGSDSKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQFGIVMLANKSYPNPARVEAAYHILDALQ"},"dna_sequence":{"accession":"NG_064666.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCTCTTTGCTGCGCCCTGCTGCTCGGCATCTCTTGCTCTGCTCTCGCCGCGCCAGTGTCAGAAAAACAGCTGGCGGAGGTGGTCGCGAATACGATTACCCCGCTGATGAAAGCCCAGTCGATTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGTAAACCGCACTATTACACGTTTGGCAAAGCCGATATCGCGGCCAGCAAACCCGTTACGCCTCAGACTCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGGGTTTTAGGAGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTAACGGGCAAGCAGTGGCAGGGGATTCGTATGCTGGATCTCGCAACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAATGCCGCCCTGCTGCACTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGTATCGGTCTTTTTGGCGCGCTGGCGGTCAAACCTTCCGGCATGGGCTATGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTTCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGAATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCGGAGAAGGTTGCTGATGCCTCACTTAAGCAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGATCGAGGGCAGCGACAGTAAGGTGGCGCTGGCACCGCTTCCCGTGGCAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGCTCTACTGGCGGGTTTGGCAGTTACGTGGCCTTTATTCCTGAAAAGCAGTTCGGTATTGTGATGCTCGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCGACGCGCTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39098","NCBI_taxonomy_name":"Enterobacter hormaechei","NCBI_taxonomy_id":"158836"}}}},"ARO_accession":"3006261","ARO_id":"44723","ARO_name":"ACT-66","CARD_short_name":"ACT-66","ARO_description":"ACT-66 is a ACT beta-lactamase.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4158":{"model_id":"4158","model_name":"ACT-67","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6533":{"protein_sequence":{"accession":"WP_063147148.1","sequence":"MMKKSLCCALLLGISCSALAAPVSEKQLAEVVANTVTPLMKAQSIPGMAVAVIYQGKPHYYTFGKADIAASKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNAALLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMGYERAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPEKVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVIEGSDSKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANKSYPNPARVEAAYHILDALQ"},"dna_sequence":{"accession":"NG_064667.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCTCTTTGCTGCGCCCTGCTGCTCGGCATCTCTTGCTCTGCTCTCGCCGCGCCAGTGTCAGAAAAACAGCTGGCGGAGGTGGTCGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCGATTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGTAAACCGCACTATTACACGTTTGGCAAAGCCGATATCGCGGCCAGCAAACCCGTTACGCCTCAGACTCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGGGTTTTAGGTGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTGACGGGCAAGCAGTGGCAGGGGATTCGTATGCTGGATCTCGCAACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAATGCCGCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGTATCGGTCTTTTTGGCGCGCTGGCGGTCAAACCTTCCGGCATGGGCTATGAGCGGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTTCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGAATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCGGAGAAGGTTGCTGATGCCTCACTTAAGCAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGATCGAGGGCAGCGACAGTAAGGTGGCGCTGGCACCGCTTCCCGTGGCAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGCTCTACTGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCGACGCGCTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40540","NCBI_taxonomy_name":"Enterobacter cloacae complex","NCBI_taxonomy_id":"354276"}}}},"ARO_accession":"3006262","ARO_id":"44724","ARO_name":"ACT-67","CARD_short_name":"ACT-67","ARO_description":"ACT-67 is a ACT beta-lactamase.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4159":{"model_id":"4159","model_name":"ACT-68","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6534":{"protein_sequence":{"accession":"WP_136512051.1","sequence":"MMMTKSLCCALLLSTSCSVLATPMSEKQLAEVVERTVTPLMKAQAIPGMAVAVIYEGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMSYEQAITTRVFKPLKLDHTWINVPKAEEAHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVQDMASWVMVNMKPDSLQDNSLRKGLTLAQSRYWGVGAMYQGLGWEMLNWPVDAKTVVEGSDNKVALAPLPAREVNPPALPVNASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILSAL"},"dna_sequence":{"accession":"NG_064668.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGATGACTAAATCCCTTTGCTGCGCCCTGCTGCTCAGCACCTCCTGCTCGGTATTGGCTACCCCGATGTCAGAAAAACAGCTGGCTGAGGTGGTGGAACGGACCGTTACGCCGCTGATGAAAGCGCAGGCCATTCCGGGTATGGCGGTGGCGGTGATTTATGAGGGTCAGCCGCACTACTTCACCTTCGGTAAAGCCGATGTTGCGGCGAACAAACCTGTCACTCCACAAACCTTGTTCGAACTGGGTTCTATAAGTAAAACCTTCACCGGCGTACTCGGTGGCGATGCCATTGCTCGCGGTGAAATATCGCTGGGCGATCCGGTGACAAAATACTGGCCTGAGCTGACAGGCAAGCAGTGGCAGGGGATCCGCATGCTGGATCTGGCAACCTATACCGCAGGAGGTTTGCCGTTACAGGTACCGGATGAGGTCACGGATAACGCCTCTCTGTTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCGGGCACCACGCGTCTTTACGCCAATGCCAGCATTGGTCTTTTTGGCGCGCTGGCGGTCAAACCTTCCGGCATGAGCTATGAGCAGGCCATAACGACGCGGGTCTTTAAGCCGCTCAAGCTGGACCATACGTGGATTAACGTTCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGATACCGCGACGGTAAAGCGGTACACGTTTCGCCAGGAATGCTGGACGCTGAAGCCTATGGCGTAAAAACCAACGTGCAGGATATGGCAAGCTGGGTGATGGTCAACATGAAGCCGGACTCCCTTCAGGATAATTCACTCAGGAAAGGCCTTACCCTGGCGCAGTCTCGCTACTGGGGCGTGGGGGCCATGTATCAGGGGTTAGGCTGGGAAATGCTTAACTGGCCGGTCGATGCCAAAACCGTGGTTGAAGGTAGCGACAATAAGGTTGCACTGGCACCGCTGCCTGCGAGAGAAGTGAATCCACCAGCGCTCCCGGTCAACGCATCCTGGGTCCATAAAACAGGCTCTACCGGCGGGTTTGGCAGCTACGTGGCATTTATTCCTGAAAAGCAGCTCGGTATTGTGATGCTGGCAAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCGTATTTTGAGCGCGCTGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36926","NCBI_taxonomy_name":"Enterobacter asburiae","NCBI_taxonomy_id":"61645"}}}},"ARO_accession":"3006263","ARO_id":"44725","ARO_name":"ACT-68","CARD_short_name":"ACT-68","ARO_description":"ACT-68 is a ACT beta-lactamase.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4160":{"model_id":"4160","model_name":"ACT-69","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6535":{"protein_sequence":{"accession":"WP_048209719.1","sequence":"MMKKSLCCALLLGLSCSALAAPVSEKQLAEVVANTVTPLMKAQSVPGMAVAVIYQGKSHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMPYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPEKVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVVEGSDSKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQVGIVMLANKSYPNPARVEAAYHILEALQ"},"dna_sequence":{"accession":"NG_065855.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCCCTTTGCTGCGCCCTGCTGCTGGGCCTCTCTTGCTCTGCTCTCGCCGCGCCAGTATCAGAAAAACAGCTGGCGGAGGTGGTCGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCTGTTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGAAAATCGCACTATTACACGTTTGGCAAGGCCGATATCGCGGCGAATAAACCCGTTACGCCTCAGACCCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGCGTTTTAGGTGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTGACGGGCAAGCAGTGGCAGGGTATTCGTATGCTGGATCTCGCCACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTCAAACCTTCCGGCATGCCCTATGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTTCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGAATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCGGAGAAGGTTGCCGATGCCTCACTTAAGCAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGGTCGAAGGCAGCGACAGTAAGGTAGCGCTGGCGCCGTTACCCGTGGCAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGTTCTACTGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGGTCGGTATTGTAATGCTCGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCGAGGCGCTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40540","NCBI_taxonomy_name":"Enterobacter cloacae complex","NCBI_taxonomy_id":"354276"}}}},"ARO_accession":"3006264","ARO_id":"44726","ARO_name":"ACT-69","CARD_short_name":"ACT-69","ARO_description":"ACT-69 is a ACT beta-lactamase.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4161":{"model_id":"4161","model_name":"ACT-70","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6536":{"protein_sequence":{"accession":"WP_047364854.1","sequence":"MMKKSLCCALLLGISCSALATPVSEKQLAEVVANTVTPLMKAQSVPGMAVAVIYQGKPHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALVVKPSGMPYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPENVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVVEGSDSKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANTSYPNPARVEAAYHILEALQ"},"dna_sequence":{"accession":"NG_065856.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCCCTTTGCTGCGCCCTGCTGCTCGGCATCTCTTGCTCTGCTCTCGCCACGCCAGTGTCAGAAAAACAGCTGGCGGAGGTGGTCGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCTGTTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGAAAACCGCACTATTACACGTTTGGCAAGGCCGATATCGCGGCGAATAAACCCGTTACGCCTCAGACCCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGCGTGTTAGGTGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTGACGGGCAAGCAGTGGCAGGGTATTCGTATGCTGGATCTCGCCACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGTGCGCTGGTGGTCAAACCTTCTGGCATGCCCTATGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTGCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGTATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCGGAGAACGTTGCTGATGCCTCACTTAAGCAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGGTCGAGGGCAGCGACAGTAAGGTAGCGCTGGCGCCGTTGCCCGTGGCAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGCTCTACTGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATACAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCGAGGCGCTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40540","NCBI_taxonomy_name":"Enterobacter cloacae complex","NCBI_taxonomy_id":"354276"}}}},"ARO_accession":"3006265","ARO_id":"44727","ARO_name":"ACT-70","CARD_short_name":"ACT-70","ARO_description":"ACT-70 is a ACT beta-lactamase.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4162":{"model_id":"4162","model_name":"ACT-72","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6537":{"protein_sequence":{"accession":"WP_045895620.1","sequence":"MMKKSLCCALLLGLSCSALAAPVSEKQLAEVVANTVTPLMKAQSVPGMAVAVIYQGKPHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDGPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMPYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPEKVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVVEGSDSKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANKSYPNPARVEAAYHILEALQ"},"dna_sequence":{"accession":"NG_065857.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCCCTTTGCTGCGCCCTGCTGCTGGGCCTCTCTTGCTCTGCTCTCGCCGCGCCAGTGTCAGAAAAACAGCTGGCGGAGGTGGTCGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCTGTTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGAAAACCGCACTATTACACGTTTGGCAAGGCCGATATCGCGGCGAATAAACCCGTTACGCCTCAGACCCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGCGTTTTAGGTGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGGTCCGGTGACCAGATACTGGCCACAGCTGACGGGCAAGCAGTGGCAGGGTATTCGTATGCTGGATCTCGCCACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTCAAACCTTCTGGCATGCCCTATGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTTCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGAATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCGGAGAAGGTTGCCGATGCCTCACTTAAGCAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGGTCGAAGGCAGCGACAGTAAGGTAGCGCTGGCGCCGTTACCCGTGGCAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGTTCTACTGGCGGATTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCGAGGCGCTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40540","NCBI_taxonomy_name":"Enterobacter cloacae complex","NCBI_taxonomy_id":"354276"}}}},"ARO_accession":"3006266","ARO_id":"44728","ARO_name":"ACT-72","CARD_short_name":"ACT-72","ARO_description":"ACT-72 is a ACT beta-lactamase.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4163":{"model_id":"4163","model_name":"ACT-73","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6538":{"protein_sequence":{"accession":"WP_152315464.1","sequence":"MMKKSLCCALLLGISCSALATPVSEKQLAEVVANTVTPLMKAQSVPGMAVAVIYQGKPHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMPYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPENVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVVEGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANTSYPNPARVEAAYHILEALQ"},"dna_sequence":{"accession":"NG_066689.2","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCCCTTTGCTGCGCCCTGCTGCTCGGCATCTCTTGCTCTGCTCTCGCCACGCCAGTGTCAGAAAAACAGCTGGCGGAGGTGGTAGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCTGTTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGAAAACCGCACTATTACACGTTTGGCAAGGCCGATATCGCGGCGAATAAACCCGTTACGCCTCAGACCCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGCGTGTTAGGTGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTGACGGGCAAGCAGTGGCAGGGTATTCGTATGCTGGATCTCGCCACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTCAAACCTTCTGGCATGCCCTATGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTGCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGTATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCACCGGAGAACGTTGCTGATGCCTCACTTAAACAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGGTCGAGGGCAGCGACAATAAGGTAGCGCTGGCGCCGTTGCCCGTGGCAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGCTCTACTGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATACAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCGAGGCGCTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3006267","ARO_id":"44729","ARO_name":"ACT-73","CARD_short_name":"ACT-73","ARO_description":"ACT-73 is a ACT beta-lactamase.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4164":{"model_id":"4164","model_name":"ACT-74","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6539":{"protein_sequence":{"accession":"WP_032652275.1","sequence":"MMKKSLCCALLLGISCSALATPVSEKQLAEVVANTVTPLMKAQSVPGMAVAVIYQGKPHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMPYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPEKVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVVEGSDSKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANTSYPNPARVEAAYHILEALQ"},"dna_sequence":{"accession":"NG_066690.1","fmin":"100","fmax":"1246","strand":"+","sequence":"ATGATGAAAAAATCCCTTTGCTGCGCCCTGCTGCTCGGCATCTCTTGCTCTGCTCTCGCCACGCCAGTGTCAGAAAAACAGCTGGCGGAGGTGGTCGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCTGTTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGAAAACCGCACTATTACACGTTTGGCAAGGCCGATATCGCGGCGAATAAACCCGTTACGCCTCAGACCCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGCGTTTTAGGTGGAGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTGACGGGCAAGCAGTGGCAGGGTATTCGTATGCTGGATCTCGCCACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTCAAACCTTCTGGCATGCCCTATGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTGCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGTATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCGGAGAAGGTTGCTGATGCCTCACTTAAGCAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGGTCGAGGGCAGCGACAGTAAGGTAGCGCTGGCGCCGTTGCCCGTGGCAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGCTCTACTGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATACAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCGAGGCGCTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40540","NCBI_taxonomy_name":"Enterobacter cloacae complex","NCBI_taxonomy_id":"354276"}}}},"ARO_accession":"3006268","ARO_id":"44730","ARO_name":"ACT-74","CARD_short_name":"ACT-74","ARO_description":"ACT-74 is a ACT beta-lactamase.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4165":{"model_id":"4165","model_name":"ACT-75","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6540":{"protein_sequence":{"accession":"WP_045347148.1","sequence":"MMKKSLCCALLLGLSCSALAAPVSEKQLAEVVANTVTPLMIAQSVPGMAVAVIYQGKSHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMPYEQAMTTRVLKPLKLDHTWINVPKAEEAHYARGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPEKVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVVEGSDSKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQVGIVMLANKSYPNPARVEAAYHILEALQ"},"dna_sequence":{"accession":"NG_066691.1","fmin":"100","fmax":"1246","strand":"+","sequence":"ATGATGAAAAAATCCCTTTGCTGCGCCCTGCTGCTCGGCCTCTCTTGCTCTGCTCTCGCCGCGCCAGTATCAGAAAAACAGCTGGCGGAGGTGGTCGCGAATACGGTTACCCCGCTGATGATAGCCCAGTCTGTTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGAAAATCGCACTATTACACGTTTGGCAAGGCCGATATCGCGGCGAATAAACCCGTTACGCCTCAGACCCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGCGTTTTAGGTGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTGACGGGCAAGCAGTGGCAGGGTATTCGTATGCTGGATCTCGCCACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTCAAACCTTCTGGCATGCCCTATGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTTCCGAAAGCGGAAGAGGCGCATTACGCCAGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGAATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCGGAGAAGGTTGCCGATGCCTCACTTAAGCAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGGTCGAAGGCAGCGACAGTAAGGTAGCGCTGGCGCCGTTACCCGTGGCAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCATGGGTCCATAAAACGGGTTCTACTGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGGTCGGTATTGTAATGCTCGCGAATAAAAGCTATCCGAATCCGGCACGCGTTGAGGCGGCATACCATATCCTCGAGGCGCTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39098","NCBI_taxonomy_name":"Enterobacter hormaechei","NCBI_taxonomy_id":"158836"}}}},"ARO_accession":"3006269","ARO_id":"44731","ARO_name":"ACT-75","CARD_short_name":"ACT-75","ARO_description":"ACT-75 is a ACT beta-lactamase.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4166":{"model_id":"4166","model_name":"ACT-76","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6541":{"protein_sequence":{"accession":"WP_126817982.1","sequence":"MMKKFLCCALLLSTSCSVLAAPMSEKQLADVVERNVTPLMKAQGIPGMAVAVIYQGQPHYFTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPDLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANSSIGLFGALAVKPSGMSYEQAMTTRVLKPLKLDHTWINVPKAEETHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVQDMASWVMANMAPDALQDTSLKQGITLAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVGGSDNMVALAPLPAREVSPPVPPVKASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILDALQ"},"dna_sequence":{"accession":"NG_066692.1","fmin":"100","fmax":"1246","strand":"+","sequence":"ATGATGAAAAAATTCCTTTGCTGCGCCCTGCTGCTCAGCACATCCTGCTCTGTACTCGCCGCGCCGATGTCGGAAAAACAGCTGGCTGACGTGGTAGAACGCAACGTTACGCCCCTGATGAAAGCGCAGGGTATTCCAGGCATGGCGGTGGCCGTGATTTATCAGGGCCAGCCACACTACTTTACCTTTGGAAAGGCCGATATCGCGGCGAACAAACCCGTCACCCCGCAAACCCTGTTCGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTGCTGGGGGGCGATGCTATTGCCCGCGGCGAAATTTCGCTGGGCGATCCGGTAACCAAATATTGGCCTGATCTGACCGGCAAGCAGTGGCAAGGGATTCGCATGCTGGATCTGGCAACCTACACCGCCGGTGGCCTGCCTTTACAGGTGCCCGATGAGGTCACAGATAACGCTTCCCTGCTGCGCTTCTATCAAAACTGGCAGCCTCAGTGGAAGCCGGGCACAACGCGTCTTTACGCCAACTCCAGCATCGGTCTTTTTGGCGCGCTGGCGGTCAAACCTTCCGGCATGAGCTATGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGATCATACCTGGATTAACGTTCCGAAAGCGGAGGAGACGCATTACGCCTGGGGATATCGTGACGGTAAAGCGGTCCACGTTTCACCGGGCATGCTGGACGCAGAGGCATATGGCGTGAAAACCAACGTGCAGGATATGGCGAGCTGGGTGATGGCCAATATGGCCCCTGACGCACTGCAGGATACGTCCCTGAAGCAAGGCATTACGCTGGCGCAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAGGGGTTAGGTTGGGAGATGCTTAACTGGCCGGTCGATGCCAAAACCGTCGTCGGAGGCAGTGATAACATGGTGGCGCTGGCACCGTTGCCTGCGAGAGAAGTGAGTCCACCCGTTCCCCCGGTTAAGGCCTCATGGGTGCACAAAACGGGCTCAACCGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGCTCGGCATTGTGATGCTGGCGAATAAAAGCTATCCGAATCCGGCGCGAGTTGAGGCGGCATACCGTATCCTCGACGCGCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37055","NCBI_taxonomy_name":"Enterobacter","NCBI_taxonomy_id":"547"}}}},"ARO_accession":"3006270","ARO_id":"44732","ARO_name":"ACT-76","CARD_short_name":"ACT-76","ARO_description":"ACT-76 is a ACT beta-lactamase.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4167":{"model_id":"4167","model_name":"ACT-77","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6542":{"protein_sequence":{"accession":"WP_060573544.1","sequence":"MMKKFLCCALLLSTSCSVLAAPMSEKQLADVVERNVTPLMKAQGIPGMAVAVIYQGQPHYFTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPDLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANSSIGLFGALAVKPSGMSYEQAMTTRVFKPLKLDHTWINVPKAEETHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVQDMASWVMANMAPDALQDTSLKQGITLAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVGGSDNKVALAPLPAREVSPPVPPVKASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILDALQ"},"dna_sequence":{"accession":"NG_067132.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATTCCTTTGCTGCGCCCTGCTGCTCAGCACATCCTGCTCTGTACTCGCCGCGCCGATGTCGGAAAAACAGCTGGCTGACGTGGTAGAACGCAACGTTACGCCCCTGATGAAAGCGCAGGGTATTCCAGGCATGGCGGTGGCCGTGATTTATCAGGGCCAGCCACACTACTTTACCTTTGGAAAGGCCGATATCGCGGCGAACAAACCCGTCACCCCGCAAACCCTGTTCGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTGCTGGGGGGCGATGCTATTGCCCGCGGCGAAATTTCGCTGGGCGATCCGGTAACCAAATATTGGCCTGATCTGACCGGCAAGCAGTGGCAAGGGATTCGCATGCTGGATCTGGCAACCTACACCGCCGGTGGCCTGCCTTTACAGGTGCCCGATGAGGTTACAGATAACGCTTCCCTGCTGCGCTTCTATCAAAACTGGCAGCCTCAGTGGAAGCCGGGCACAACGCGTCTTTACGCCAACTCCAGCATCGGTCTTTTTGGCGCGCTGGCGGTCAAACCTTCCGGCATGAGCTATGAGCAGGCCATGACGACGCGGGTCTTTAAGCCGCTCAAGCTGGATCATACCTGGATTAACGTTCCGAAAGCGGAGGAGACGCATTACGCCTGGGGATATCGTGACGGTAAAGCGGTCCACGTTTCACCGGGCATGCTGGACGCAGAGGCATATGGCGTGAAAACCAACGTGCAGGATATGGCGAGCTGGGTGATGGCCAATATGGCCCCTGACGCACTGCAGGATACGTCCCTGAAGCAAGGCATTACGCTGGCGCAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAGGGGTTAGGTTGGGAGATGCTTAACTGGCCGGTCGATGCCAAAACCGTCGTCGGAGGCAGTGATAACAAGGTGGCGCTGGCACCGTTGCCTGCGAGAGAAGTGAGTCCACCCGTTCCCCCGGTTAAGGCCTCATGGGTGCACAAAACGGGCTCCACCGGCGGGTTTGGCAGCTATGTGGCCTTTATTCCTGAAAAGCAGCTCGGCATTGTGATGCTGGCGAATAAAAGCTATCCGAACCCGGCGCGAGTTGAGGCGGCATACCGTATCCTCGACGCGCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37055","NCBI_taxonomy_name":"Enterobacter","NCBI_taxonomy_id":"547"}}}},"ARO_accession":"3006271","ARO_id":"44733","ARO_name":"ACT-77","CARD_short_name":"ACT-77","ARO_description":"ACT-77 is a ACT beta-lactamase.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4168":{"model_id":"4168","model_name":"ACT-78","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6543":{"protein_sequence":{"accession":"WP_164461280.1","sequence":"MMKKFLCCALLLSTSCSVLAAPMSEKQLADVVERNVTPLMKAQGIPGMAVAVIYQGQPHYFTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANSSIGLFGALAVKPSGMSYEQAMTARVFKPLKLDHTWINVPKAEETHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVQDMASWVMANMAPDALQDSSLKQGITLAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVGGSDNKVALAPLPAREVSPPVPPVKASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILDALQ"},"dna_sequence":{"accession":"NG_067972.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATTCCTTTGCTGCGCCCTGCTGCTCAGCACATCCTGCTCTGTACTCGCCGCGCCGATGTCGGAAAAACAGCTGGCTGACGTGGTAGAACGCAACGTTACGCCCCTGATGAAAGCGCAGGGTATTCCAGGCATGGCGGTGGCCGTGATTTATCAGGGCCAGCCACACTACTTTACCTTTGGAAAGGCCGATATCGCGGCGAACAAACCCGTCACCCCGCAAACCCTGTTCGAACTGGGCTCTATAAGTAAAACCTTCACCGGCGTGCTGGGGGGCGATGCTATTGCCCGCGGCGAAATTTCGCTGGGCGATCCGGTAACTAAATATTGGCCTGAACTGACCGGCAAGCAGTGGCAAGGGATTCGCATGCTGGATCTGGCAACCTACACCGCCGGTGGCCTGCCCTTACAGGTGCCCGATGAGGTTACAGATAACGCATCCCTGCTGCGCTTCTATCAAAACTGGCAGCCTCAGTGGAAGCCGGGCACAACGCGTCTTTACGCCAACTCCAGCATCGGTCTTTTTGGCGCGCTGGCGGTCAAACCTTCCGGCATGAGCTATGAGCAGGCCATGACGGCGCGGGTCTTTAAGCCGCTCAAGCTGGATCATACCTGGATTAACGTTCCGAAAGCGGAGGAGACGCATTACGCCTGGGGATATCGTGACGGTAAAGCGGTCCACGTTTCACCGGGCATGCTGGACGCAGAGGCATATGGCGTGAAAACCAACGTGCAGGATATGGCGAGCTGGGTGATGGCCAACATGGCCCCTGACGCACTGCAGGATTCGTCCCTGAAGCAAGGCATTACGCTGGCGCAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAGGGGTTAGGTTGGGAGATGCTTAACTGGCCGGTCGATGCCAAAACCGTCGTCGGAGGCAGTGATAACAAGGTGGCGCTGGCACCGTTGCCTGCGAGAGAAGTGAGTCCACCCGTTCCCCCGGTTAAGGCCTCATGGGTGCACAAAACGGGCTCCACCGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGCTCGGCATTGTGATGCTGGCGAATAAAAGCTATCCGAACCCGGCGCGAGTTGAGGCGGCATACCGTATCCTCGACGCGCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3006272","ARO_id":"44734","ARO_name":"ACT-78","CARD_short_name":"ACT-78","ARO_description":"ACT-78 is a ACT beta-lactamase.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4169":{"model_id":"4169","model_name":"ACT-79","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6544":{"protein_sequence":{"accession":"WP_164461281.1","sequence":"MMKKTLCCAVLLGISCSALAAPVSEQQLAEVVAKTVTPLMKAQSIPGMAVAVIYQGKPHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDALARGEISLDDPVTKYWPELTGKQWQGIRMLDLATYTAGGLPLQLPDEVTDDTSLLRFYQHWQPQWKPGTTRLYANASIGLFGALAVKPSGMRYEQAMTERVFKPLALHHTWINVPKAEEAHYAWGYRDGKAVHVSPGMLDAQAYGVKTNVQDMANWVMANMAPQNVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEAKTVVDGSDSKVALAALPAVEINPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANKSYPNPARVEAAYHILDALQ"},"dna_sequence":{"accession":"NG_067973.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAAACCCTTTGCTGCGCCGTGCTGCTCGGCATCTCTTGCTCTGCCCTCGCCGCGCCAGTGTCCGAACAACAGCTGGCGGAGGTGGTCGCGAAGACGGTTACGCCGCTGATGAAAGCCCAGTCTATTCCAGGTATGGCGGTGGCCGTTATTTATCAGGGTAAACCGCACTATTACACGTTTGGCAAGGCCGATATCGCAGCCAACAAACCGGTTACGCCTCAGACCCTGTTCGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTTTTAGGTGGGGATGCCCTTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAAATACTGGCCTGAGCTGACGGGCAAGCAGTGGCAAGGGATTCGGATGCTGGATCTCGCGACCTACACCGCTGGCGGTCTGCCGCTACAGTTGCCCGATGAGGTGACGGATGACACCTCCCTGCTGCGCTTCTATCAACACTGGCAGCCACAGTGGAAGCCAGGCACAACGCGCCTTTATGCCAACGCCAGCATCGGCCTGTTTGGTGCGCTGGCGGTTAAGCCTTCCGGCATGCGCTACGAGCAGGCGATGACCGAGCGAGTCTTCAAACCGCTGGCGCTGCATCACACCTGGATTAACGTGCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGCAAAGCGGTACACGTTTCGCCGGGGATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCACAGAACGTTGCTGATGCCTCACTTAAGCAGGGCATCGCGTTGGCGCAGTCGCGCTACTGGCGTATCGGTTCAATGTACCAGGGCCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCAAAAACGGTGGTTGATGGCAGCGACAGTAAGGTGGCGCTGGCCGCCTTGCCTGCGGTCGAAATAAATCCTCCGGCTCCGCCTGTAAAAGCCTCCTGGGTGCACAAAACCGGCTCGACGGGCGGGTTCGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGCATCGTGATGCTCGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCGACGCGCTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3006273","ARO_id":"44735","ARO_name":"ACT-79","CARD_short_name":"ACT-79","ARO_description":"ACT-79 is a ACT beta-lactamase.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4170":{"model_id":"4170","model_name":"ACT-80","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6545":{"protein_sequence":{"accession":"WP_164461282.1","sequence":"MMKKFLCCALLLSTSCSVLAAPMSEKQLADVVERNVTPLMKAQGIPGMAVAVIYQGQPHYFTFGKADTAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPDLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANSSIGLFGALAVKPSGMSYEQAMTTRVFKPLKLDHTWINVPKAEETHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVQDMASWVMANMAPDALQDTSLKQGITLAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVGGSDNKVALAPLPAREVSPPVPPVKASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILDALQ"},"dna_sequence":{"accession":"NG_067974.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATTCCTTTGCTGCGCCCTGCTGCTCAGCACATCCTGCTCTGTACTCGCCGCGCCGATGTCGGAAAAACAGCTGGCTGACGTGGTAGAACGCAACGTTACGCCCCTGATGAAAGCGCAGGGTATTCCAGGCATGGCGGTGGCCGTGATTTATCAGGGCCAGCCACACTACTTTACCTTTGGAAAGGCCGATACCGCGGCGAACAAACCCGTCACCCCGCAAACCCTGTTCGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTGCTGGGGGGCGATGCTATTGCCCGCGGCGAAATTTCGCTGGGCGATCCGGTAACCAAATATTGGCCTGATCTGACCGGCAAGCAGTGGCAAGGGATTCGCATGCTGGATCTGGCAACCTACACCGCCGGTGGCCTGCCTTTACAGGTGCCCGATGAGGTCACAGATAACGCTTCCCTGCTGCGCTTCTATCAAAACTGGCAGCCTCAGTGGAAGCCGGGCACAACGCGTCTTTACGCCAACTCCAGCATCGGTCTTTTTGGCGCGCTGGCGGTCAAACCTTCCGGCATGAGCTATGAGCAGGCCATGACGACGCGGGTCTTTAAGCCGCTCAAGCTGGATCATACCTGGATTAACGTTCCGAAAGCGGAGGAGACGCATTACGCCTGGGGATATCGTGACGGTAAAGCGGTCCACGTTTCACCGGGCATGCTGGACGCAGAGGCATATGGCGTGAAAACCAACGTGCAGGATATGGCGAGCTGGGTGATGGCCAATATGGCCCCTGACGCACTGCAGGATACGTCCCTGAAGCAAGGCATTACGCTGGCGCAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAGGGGTTAGGTTGGGAGATGCTTAACTGGCCGGTCGATGCCAAAACCGTCGTCGGAGGCAGTGATAACAAGGTGGCGCTGGCACCGTTGCCTGCGAGAGAAGTGAGTCCACCCGTTCCCCCGGTTAAGGCCTCATGGGTGCACAAAACGGGCTCAACCGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGCTCGGCATTGTGATGCTGGCGAATAAAAGCTATCCGAACCCGGCGCGAGTTGAGGCGGCATACCGTATCCTCGACGCGCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3006274","ARO_id":"44736","ARO_name":"ACT-80","CARD_short_name":"ACT-80","ARO_description":"ACT-80 is a ACT beta-lactamase.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4171":{"model_id":"4171","model_name":"ACT-81","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6546":{"protein_sequence":{"accession":"WP_164461283.1","sequence":"MMKKFLCCALLLSTSCSVLAAPMSEKQLADVVERNVTPLMKAQGIPGMAVAVIYQGQPHYFTFGKADIAANKSVTPRTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPDLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANSSIGLFGTLAVKPSGMNYEQAMTTRVFKPLKLDHTWINVPKAEETHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVQDMASWVMANMAPDALQDTSLKQGITLAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVGGSDNKVALAPLPAREVSPPVPPVKASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVETAYRILDALQ"},"dna_sequence":{"accession":"NG_067975.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATTCCTTTGCTGCGCCCTGCTGCTCAGCACATCCTGCTCTGTACTCGCCGCGCCGATGTCGGAAAAACAGCTGGCTGACGTGGTAGAACGCAACGTTACGCCCCTGATGAAAGCGCAGGGTATTCCAGGCATGGCGGTGGCCGTGATTTATCAGGGCCAGCCACACTACTTTACCTTTGGAAAGGCCGATATCGCGGCGAACAAATCCGTCACCCCGCGAACCCTGTTCGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTGCTGGGGGGCGATGCTATTGCCCGCGGCGAAATTTCGCTGGGCGATCCGGTAACCAAATATTGGCCTGATCTGACCGGCAAGCAGTGGCAAGGGATTCGCATGCTGGATCTGGCAACCTACACCGCCGGTGGCCTGCCTTTACAGGTGCCCGATGAGGTTACAGATAACGCTTCCCTGCTGCGCTTTTATCAAAACTGGCAGCCTCAGTGGAAGCCGGGCACAACGCGTCTTTACGCCAACTCCAGCATCGGTCTTTTTGGCACGCTGGCGGTCAAACCTTCCGGCATGAACTATGAGCAGGCCATGACGACGCGGGTCTTTAAGCCGCTCAAGCTGGATCATACCTGGATTAACGTTCCGAAAGCGGAGGAGACGCATTACGCCTGGGGATATCGTGACGGTAAAGCGGTCCACGTTTCACCGGGCATGCTGGACGCAGAGGCATATGGCGTGAAAACCAACGTGCAGGATATGGCGAGCTGGGTGATGGCCAATATGGCCCCTGACGCACTGCAGGATACGTCCCTGAAGCAAGGCATTACGCTGGCGCAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAGGGGTTAGGTTGGGAGATGCTTAACTGGCCGGTCGATGCCAAAACCGTCGTCGGAGGCAGTGATAACAAGGTGGCACTGGCACCGTTGCCTGCGAGAGAAGTGAGTCCACCCGTTCCCCCGGTTAAGGCCTCATGGGTGCACAAAACGGGCTCAACCGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAACTCGGCATTGTAATGCTGGCGAATAAAAGCTATCCGAACCCGGCGCGAGTTGAGACGGCATACCGTATCCTCGACGCGCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3006275","ARO_id":"44737","ARO_name":"ACT-81","CARD_short_name":"ACT-81","ARO_description":"ACT-81 is a ACT beta-lactamase.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4172":{"model_id":"4172","model_name":"ACT-82","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6547":{"protein_sequence":{"accession":"WP_164461284.1","sequence":"MMKKFLCCALLLSTSCSVLAAPMSEKQLADVVERNVTPLMKAQGIPGMAVAVIYQGQPHYFTFGKADIAANKSVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPDLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPKWKPGTTRLYANSSIGLFGALAVKPSGMSYEQAMTTRVFKPLKLDHTWINVPKAEETHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVQDMASWVMANMAPDALQDTSLKQGITLAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVGGSDNKVALAPLPAREVSPPVPPVKASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILDALQ"},"dna_sequence":{"accession":"NG_067976.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATTCCTTTGCTGCGCCCTGCTGCTCAGCACATCCTGCTCTGTACTCGCCGCGCCGATGTCGGAAAAACAGCTGGCTGACGTGGTAGAACGCAACGTTACGCCCCTGATGAAAGCGCAGGGTATTCCAGGCATGGCGGTGGCCGTGATTTATCAGGGCCAGCCACACTACTTTACCTTTGGAAAGGCCGATATCGCGGCGAACAAATCCGTCACCCCGCAAACCCTGTTCGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTGCTGGGGGGCGATGCTATTGCCCGCGGCGAAATTTCGCTGGGCGATCCGGTAACCAAATATTGGCCTGATCTGACCGGCAAGCAGTGGCAAGGGATTCGCATGCTGGATCTGGCAACCTACACCGCCGGTGGCCTGCCTTTACAGGTGCCCGATGAGGTCACAGATAACGCATCCCTGCTGCGCTTCTATCAAAACTGGCAGCCTAAGTGGAAGCCGGGCACAACGCGTCTTTACGCCAACTCCAGCATCGGTCTTTTTGGCGCGCTGGCGGTCAAACCTTCCGGCATGAGCTATGAGCAGGCCATGACGACGCGGGTCTTTAAGCCGCTCAAGCTGGATCATACCTGGATTAACGTTCCGAAAGCGGAGGAGACGCATTACGCCTGGGGATATCGTGACGGTAAAGCGGTCCACGTTTCACCGGGCATGCTGGACGCAGAGGCATATGGCGTGAAAACCAACGTGCAGGATATGGCGAGCTGGGTGATGGCCAATATGGCCCCTGACGCGCTGCAGGATACGTCCCTGAAGCAAGGCATTACGCTGGCGCAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAGGGGTTAGGTTGGGAGATGCTTAACTGGCCGGTCGATGCCAAAACCGTCGTCGGAGGCAGTGATAACAAGGTGGCGCTGGCACCGTTGCCTGCGAGAGAAGTGAGTCCACCCGTTCCCCCGGTTAAGGCCTCATGGGTGCACAAAACGGGCTCAACCGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGCTCGGCATTGTGATGCTGGCGAATAAAAGCTATCCGAACCCGGCGCGAGTTGAGGCGGCATACCGTATCCTCGACGCGCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3006276","ARO_id":"44738","ARO_name":"ACT-82","CARD_short_name":"ACT-82","ARO_description":"ACT-82 is a ACT beta-lactamase.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4173":{"model_id":"4173","model_name":"ACT-83","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6548":{"protein_sequence":{"accession":"WP_164461285.1","sequence":"MMKKSLCCALLLGLSCSALAAPVSEKQLAEVVANTVTPLMKAQSVPGMAVAVIYQGKSHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDDASLLRFYQHWQPQWKPGTTRLYANASIGLFGALAVKPSGMRYEQAMTERVFKPLALHHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPEKVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVVEGSDSKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANKSYPNPARVEAAYHILEALQ"},"dna_sequence":{"accession":"NG_067977.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCCCTTTGCTGCGCCCTGCTGCTGGGCCTCTCTTGCTCTGCTCTCGCCGCGCCAGTATCAGAAAAACAGCTGGCGGAGGTGGTCGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCTGTTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGAAAATCGCACTATTACACGTTTGGCAAGGCCGATATCGCGGCGAATAAACCCGTTACGCCTCAGACCCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGCGTTTTAGGTGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCTGAGCTGACGGGCAAGCAGTGGCAAGGGATTCGAATGCTGGATCTCGCCACCTACACCGCAGGCGGTCTGCCGCTACAGGTGCCCGATGAGGTGACGGATGACGCCTCCCTGCTGCGCTTCTATCAACACTGGCAGCCACAGTGGAAGCCAGGCACAACGCGCCTTTATGCCAACGCCAGCATCGGCCTGTTTGGTGCGCTGGCGGTTAAGCCTTCCGGCATGCGCTACGAGCAGGCGATGACCGAGCGAGTATTCAAACCGCTGGCGCTGCATCACACCTGGATTAACGTGCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGAATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCGGAGAAGGTTGCCGATGCCTCACTTAAGCAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGGTCGAAGGCAGCGACAGTAAGGTAGCGCTGGCGCCGTTACCCGTGGCAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGTTCTACCGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCGAGGCGCTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39098","NCBI_taxonomy_name":"Enterobacter hormaechei","NCBI_taxonomy_id":"158836"}}}},"ARO_accession":"3006277","ARO_id":"44739","ARO_name":"ACT-83","CARD_short_name":"ACT-83","ARO_description":"ACT-83 is a ACT beta-lactamase.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4174":{"model_id":"4174","model_name":"ACT-84","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6549":{"protein_sequence":{"accession":"WP_072139974.1","sequence":"MMKKSLCCALLLGLSCSALAAPVSEKQLAEVVANTVTPLMKAQSVPGMAVAVIYQGKPHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDDASLLRFYQHWQPQWKPGTTRLYANASIGLFGALAVKPSGMRYEQAMTERVFKPLALHHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPEKVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVVEGSDSKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANKSYPNPARVEAAYHILEALQ"},"dna_sequence":{"accession":"NG_068161.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCCCTTTGCTGCGCCCTGCTGCTGGGCCTCTCTTGCTCTGCTCTCGCCGCGCCAGTGTCAGAAAAACAGCTGGCGGAGGTGGTCGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCTGTTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGAAAACCGCACTATTACACGTTTGGCAAGGCCGATATCGCGGCGAATAAACCCGTTACGCCTCAGACCCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGCGTTTTAGGTGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCTGAGCTGACGGGCAAGCAGTGGCAAGGGATTCGAATGCTGGATCTCGCCACCTACACCGCAGGCGGTCTGCCGCTACAGGTGCCCGATGAGGTGACGGATGACGCCTCCCTGCTGCGCTTCTATCAACACTGGCAGCCACAGTGGAAGCCAGGCACAACGCGCCTTTATGCCAACGCCAGCATCGGCCTGTTTGGTGCGCTGGCGGTTAAGCCTTCCGGCATGCGCTACGAGCAGGCGATGACCGAGCGAGTATTCAAACCGCTGGCGCTGCATCACACCTGGATTAACGTTCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGAATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCGGAGAAGGTTGCCGATGCCTCACTTAAGCAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGGTCGAAGGCAGCGACAGTAAGGTAGCGCTGGCGCCGTTACCCGTGGCAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGTTCTACCGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCGAGGCGCTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40540","NCBI_taxonomy_name":"Enterobacter cloacae complex","NCBI_taxonomy_id":"354276"}}}},"ARO_accession":"3006278","ARO_id":"44740","ARO_name":"ACT-84","CARD_short_name":"ACT-84","ARO_description":"ACT-84 is a ACT beta-lactamase.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4175":{"model_id":"4175","model_name":"ACT-87","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6550":{"protein_sequence":{"accession":"WP_121527365.1","sequence":"MKTKSLCCALLLSTSCSVLAAPMSEKQLSDVVERTVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPELTGKQWQGISMLDLATYTAGGLPLQVPDEVTDNASLLRFYQYWQPQWKPGATRLYANASIGLFGALAVKPSGMSFEQAMTKRVFKPLKLDHTWINVPKEEEAHYAWGYRDGKAIHVSPGMLDTEAYGVKTNIQDMASWLKANMNPDALSDSTLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVEAKTVVEGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKELGIVMLANKSYPNPARVEAAYRILSALQ"},"dna_sequence":{"accession":"NG_070175.1","fmin":"100","fmax":"1246","strand":"+","sequence":"ATGAAGACAAAATCCCTTTGCTGTGCCCTGCTGCTCAGCACCTCCTGCTCTGTTCTCGCCGCGCCGATGTCAGAGAAACAGCTGTCTGACGTGGTGGAACGTACCGTTACCCCCCTGATGAAAGCGCAAGCCATTCCGGGCATGGCGGTAGCGGTGATTTATCAGGGTCAGCCGCACTACTTTACCTTCGGAAAGGCCGATGTTGCGGCGAACAAACCTGTCACCCCGCAAACCCTGTTTGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTATTAGGTGGCGATGCGATTGCGCGCGGAGAAATATCGCTGGGCGACCCCGTGACAAAGTACTGGCCCGAGCTAACAGGCAAGCAGTGGCAGGGTATTAGCATGTTGGATCTGGCGACCTACACCGCGGGTGGCCTGCCGCTACAGGTGCCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGTTTCTATCAATACTGGCAACCGCAGTGGAAACCAGGCGCAACGCGTCTTTATGCGAACGCCAGCATCGGGCTTTTTGGCGCCCTCGCGGTTAAACCCTCCGGCATGAGCTTTGAACAGGCCATGACGAAGCGGGTCTTCAAGCCACTCAAACTGGACCATACATGGATTAACGTTCCGAAAGAAGAAGAGGCGCATTACGCCTGGGGATACCGTGATGGTAAAGCAATCCACGTTTCACCGGGAATGCTGGATACCGAAGCGTATGGTGTCAAAACCAACATCCAGGATATGGCGAGCTGGCTGAAGGCCAACATGAACCCTGACGCCCTTTCGGATTCAACGTTGAAACAGGGTATTGCCCTGGCACAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAGGGGCTGGGCTGGGAGATGCTCAACTGGCCGGTAGAAGCCAAAACCGTCGTGGAGGGCAGCGATAACAAGGTGGCTCTTGCACCGTTACCGGTGGCAGAAGTGAACCCTCCAGCTCCGCCAGTAAAAGCATCATGGGTACATAAAACAGGCTCGACGGGTGGATTCGGCAGCTATGTCGCATTTATTCCTGAAAAGGAACTCGGCATTGTTATGCTGGCGAACAAGAGCTACCCGAACCCGGCGCGCGTGGAAGCGGCATACCGTATTCTGAGCGCTCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39773","NCBI_taxonomy_name":"Enterobacter kobei","NCBI_taxonomy_id":"208224"}}}},"ARO_accession":"3006279","ARO_id":"44741","ARO_name":"ACT-87","CARD_short_name":"ACT-87","ARO_description":"ACT-87 is a ACT beta-lactamase.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4176":{"model_id":"4176","model_name":"ADC-100","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6551":{"protein_sequence":{"accession":"WP_068981607.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVKTDQQVLTFFKDWKPKNSIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPASAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTTGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_051439.1","fmin":"0","fmax":"1158","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAGTATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAATTTCCAGATGAAGTAAAAACAGATCAGCAAGTTTTAACATTTTTTAAAGACTGGAAACCTAAAAACTCAATCGGTGAATATCGACAATATTCAAACCCAAGCATTGGTTTATTTGGAAAAGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTAAATCCACAAAAATATCCAGCAGATATTCAACGGGCAATTAATGAAACACATCAGGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTACCGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006280","ARO_id":"44742","ARO_name":"ADC-100","CARD_short_name":"ADC-100","ARO_description":"ADC-100 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4193":{"model_id":"4193","model_name":"ADC-120","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6568":{"protein_sequence":{"accession":"WP_002126587.1","sequence":"MRFKKISYLLLPSLFIFNTSIYAGNTSKDQEIKQLIDQNFKPLLEKYNVPGMAVGIIQNNKKYETYYGLQSVQDKKAVNSNTIFELGSVSKLFTATAGAYAKNTGKISFDDTPGKYWKELKNTPINQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGEIVGLSMKQPFSQVLEKTIFPDLGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPANIQRAINETHQGHYQVNTMYQALGWEEFSYPAMLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYTVLNAIKK"},"dna_sequence":{"accession":"NG_064678.1","fmin":"100","fmax":"1252","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTACTTACTTTTACCTTCTCTTTTTATTTTTAATACCTCAATTTATGCGGGCAATACTTCTAAAGACCAAGAAATTAAACAATTGATAGATCAAAATTTTAAACCCTTATTAGAAAAATATAATGTACCGGGTATGGCGGTAGGTATTATTCAAAACAATAAAAAATATGAAACGTATTATGGCCTACAATCCGTTCAAGATAAAAAAGCTGTAAATAGCAATACCATTTTTGAGCTAGGTTCTGTCAGTAAGTTATTTACTGCGACGGCAGGTGCTTATGCAAAAAATACAGGAAAAATCTCTTTTGATGATACGCCGGGCAAATACTGGAAAGAGCTAAAAAATACACCGATTAACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTCGCTTTGCAATTCCCCGATGAAGTACAAACAGATCAACAGGTTTTAACTTTTTTTAAAGATTGGAAACCTAAAAACCCAATCGGTGAATATAGACAATATTCAAACCCAAGTATTGGCCTATTTGGGGAAATAGTTGGTTTATCAATGAAGCAGCCTTTTAGTCAGGTCTTGGAAAAAACGATTTTTCCGGACCTTGGCTTAAAACATAGCTATGTCAATGTGCCTAAAACTCAGATGCAAAACTATGCATTTGGTTATAACCAAGAAAATCAGCCAATTCGAGTTAACCCTGGCCCACTCGATGCCCCAGCATACGGCGTCAAATCGACCCTACCCGATATGCTGAGCTTTATTCATGCCAACCTGAATCCACAGAAATATCCGGCAAATATTCAACGGGCAATTAATGAAACACATCAGGGTCACTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAATGTTACAAACTTTACTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACGTATGTGGTGTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCGTATACAGTTTTAAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006297","ARO_id":"44759","ARO_name":"ADC-120","CARD_short_name":"ADC-120","ARO_description":"ADC-120 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4194":{"model_id":"4194","model_name":"ADC-121","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6569":{"protein_sequence":{"accession":"WP_005109685.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDKPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFGQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKE"},"dna_sequence":{"accession":"NG_064679.1","fmin":"100","fmax":"1252","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATAAGCCTGGTAAATATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCTTATTTGGAAAAGTTGTTGCTTTGTCTATGAATAAACCTTTCGGCCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACTCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTCAATCCACAGAAATATCCGGCTGATATTCAACGGGCAATTAATGAAACACATCAAGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAAATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCAACGGTTTCGGAACGTATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAACGCATTAAGGCAGCGTATGCAGTTTTAAATGCAATAAAGGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006298","ARO_id":"44760","ARO_name":"ADC-121","CARD_short_name":"ADC-121","ARO_description":"ADC-121 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4195":{"model_id":"4195","model_name":"ADC-122","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6570":{"protein_sequence":{"accession":"WP_005123276.1","sequence":"MRFKKISCLLLSPLFIFSTSIYADNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGLYQVNTMYQALGWEEFSYPAPLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_064680.1","fmin":"100","fmax":"1252","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGACAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTAGGTTCTGTTAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAGCTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTTGATGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTTAACCCACAGAAATATCCGGCTGATATTCAACGGGCAATTAATGAAACACATCAAGGTCTCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCACCTTTACAAACTTTATTAGACAGTAATTCAGAACAAATTGTGATGAAGCCTAATAAAGTGACTGCTATTTCAAAAGAGCCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACATATGTAGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006299","ARO_id":"44761","ARO_name":"ADC-122","CARD_short_name":"ADC-122","ARO_description":"ADC-122 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4196":{"model_id":"4196","model_name":"ADC-123","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6571":{"protein_sequence":{"accession":"WP_004840559.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGAYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQLLEKTIFPDLGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGHYQVNTMYQALGWEEFSYPAMLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYTVLNAIKK"},"dna_sequence":{"accession":"NG_064681.1","fmin":"100","fmax":"1252","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGCTTATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGGAAAGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAACTCTTAGAAAAAACTATTTTTCCAGATCTTGGCTTAAAACATAGCTATGTAAATGTTCCTAAAACTCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCAATTCGTGTTAACCCTGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTTAACCCACAGAAATATCCGGCTGATATTCAAAGGGCAATTAATGAAACACATCAGGGTCACTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAATGTTACAAACTTTACTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCAACGGTTTCGGAACGTATGTGGTGTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCGTATACAGTTTTAAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006300","ARO_id":"44762","ARO_name":"ADC-123","CARD_short_name":"ADC-123","ARO_description":"ADC-123 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4197":{"model_id":"4197","model_name":"ADC-125","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6572":{"protein_sequence":{"accession":"WP_005131186.1","sequence":"MRFKKISYLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDKPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWQPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_064682.1","fmin":"100","fmax":"1252","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTATCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGGCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATAAGCCTGGTAAATATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAATTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGCAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCAACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTAAATCCACAAAAATATCCGGCAGATATTCAACGTGCAATTAATGAAACACATCAGGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCTGTTAAGATGTACCATAAAACTGGCTCAACCAACGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006301","ARO_id":"44763","ARO_name":"ADC-125","CARD_short_name":"ADC-125","ARO_description":"ADC-125 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4198":{"model_id":"4198","model_name":"ADC-127","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6573":{"protein_sequence":{"accession":"WP_005046018.1","sequence":"MRFKKISYLILPSLFIFNTSIYAGNTSKEQDIKKVVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKSVNGNTIFELGSVSKLFTATAGGYAKTKGKISFNDTPGKYWKELKNTPIDRVNLLQLATYTSGNLGLQFPDEVQTDQQVLTFFKDWKPKNQIGEYRQYSNPSIGLFGKVVGLSMNQPFSQVLENTIFPSLHLKHSYVNVPKTQMQNYAFGYNQENQPIRVTPGPLDAPAYGVKSTLPDMLSFIDANLNPQKYPADIRRAIDETHKGFYQVGTMYQALGWEEFSYPAPLQTLLDSNSEQIVMKPNKVTAISKEPSIKMFHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_064683.1","fmin":"100","fmax":"1252","strand":"+","sequence":"ATGCGATTCAAAAAAATTTCTTACTTAATTCTACCTTCTCTTTTTATTTTTAATACCTCAATTTATGCAGGTAACACATCAAAAGAACAAGATATCAAGAAAGTTGTTGATCAAAACTTTAAACCACTATTAGAAAAATATGATGTTCCCGGTATGGCGGTTGGCGTCATCCAAAACAATAAAAAGTACGAAATGTATTATGGCCTACAATCGGTTCAAGATAAAAAATCTGTAAATGGCAATACGATTTTTGAGCTAGGTTCAGTCAGTAAATTATTTACTGCCACGGCAGGTGGATATGCCAAAACTAAAGGAAAAATCTCTTTTAACGACACCCCAGGAAAATACTGGAAAGAGCTAAAAAATACACCGATTGACCGAGTGAACCTACTTCAACTTGCGACCTATACGAGTGGCAACCTTGGCTTACAATTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCAAATTGGTGAATATAGACAATATTCAAACCCTAGTATTGGCCTATTTGGAAAAGTTGTAGGCTTATCGATGAACCAGCCTTTTAGTCAGGTTTTAGAAAATACAATTTTTCCGTCTCTTCACTTAAAACATAGCTATGTGAATGTTCCTAAAACTCAGATGCAAAACTATGCATTTGGCTATAACCAAGAAAATCAGCCTATTCGTGTGACCCCAGGCCCACTAGATGCCCCTGCCTACGGCGTTAAATCCACATTACCAGACATGCTTAGCTTTATTGATGCCAATCTAAATCCACAAAAATATCCGGCAGATATTCGACGCGCAATTGATGAGACTCATAAAGGTTTTTATCAAGTCGGTACGATGTATCAGGCGCTTGGTTGGGAAGAGTTTTCTTATCCAGCTCCTTTACAAACTTTATTAGACAGTAATTCTGAACAAATCGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAGCCTTCAATCAAGATGTTCCATAAAACTGGTTCAACTAACGGATTTGGAACTTATGTCGTGTTTATTCCCAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCCAATGAAGAACGCATTAAAGCAGCGTATGCAGTGTTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39094","NCBI_taxonomy_name":"Acinetobacter calcoaceticus","NCBI_taxonomy_id":"471"}}}},"ARO_accession":"3006302","ARO_id":"44764","ARO_name":"ADC-127","CARD_short_name":"ADC-127","ARO_description":"ADC-127 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4199":{"model_id":"4199","model_name":"ADC-128","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6574":{"protein_sequence":{"accession":"WP_004643536.1","sequence":"MRFKKISYLILPSLFIFNTSIYAGNTSKEQDIKKVVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKSVNGNTIFELGSVSKLFTATAGGYAKTKEKISFDDTPGKYWKELKNTPIDRVNLLQLATYTSGNLGLQFPDEVQTDQQVLTFFKDWKPKNQIGEYRQYSNPSIGLFGKVVGLSMNQPFSQVLEKTIFPSLHLKHSYVNVPKTQMQNYAFGYNQENQPIRVTPGPLDAPAYGVKSTLPDMLSFIDANLNPQKYPADIRRAIDETHKGFYQVGTMYQALGWEEFSYPAPLQTLLDSNSEQIVMKPNKVTAISKEPSIKMFHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_064684.1","fmin":"100","fmax":"1252","strand":"+","sequence":"ATGCGATTCAAAAAAATTTCTTACTTAATTCTACCTTCTCTTTTTATTTTTAATACCTCAATTTATGCAGGTAACACATCAAAAGAACAAGATATCAAGAAAGTTGTTGATCAGAACTTTAAACCATTATTAGAAAAATATGACGTTCCTGGTATGGCGGTTGGTGTCATCCAAAACAATAAAAAGTACGAAATGTATTATGGCCTACAATCAGTTCAAGATAAAAAATCCGTAAATGGCAATACGATTTTTGAACTAGGCTCAGTCAGTAAATTATTTACTGCGACGGCAGGTGGATATGCCAAAACTAAAGAAAAAATCTCTTTTGACGACACCCCAGGAAAATACTGGAAAGAGCTAAAAAATACACCGATTGACCGAGTAAACCTACTTCAACTTGCGACGTATACGAGTGGCAACCTTGGCTTACAATTCCCAGATGAAGTTCAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCAAATTGGTGAATATAGACAATATTCAAACCCTAGTATTGGCCTATTTGGAAAAGTTGTAGGCTTATCGATGAACCAGCCTTTTAGTCAGGTTTTAGAAAAGACAATTTTTCCGTCTCTTCACTTAAAACATAGCTATGTAAATGTGCCTAAAACTCAGATGCAAAACTATGCATTTGGCTATAACCAAGAAAATCAGCCGATTCGTGTGACCCCAGGCCCACTAGATGCGCCTGCCTACGGGGTTAAATCTACATTACCAGACATGCTTAGCTTTATTGATGCCAATCTAAATCCACAAAAATATCCGGCAGATATTCGACGCGCAATTGATGAGACTCATAAAGGTTTTTATCAAGTCGGTACGATGTATCAGGCGCTTGGTTGGGAAGAGTTTTCTTATCCAGCTCCTTTACAAACTTTATTAGACAGTAATTCTGAACAAATCGTGATGAAACCTAATAAAGTGACTGCTATTTCCAAAGAACCTTCAATCAAGATGTTCCATAAAACTGGTTCAACTAACGGATTTGGAACTTATGTCGTGTTTATTCCCAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAACGCATTAAAGCAGCTTATGCTGTACTAAATGCGATTAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39094","NCBI_taxonomy_name":"Acinetobacter calcoaceticus","NCBI_taxonomy_id":"471"}}}},"ARO_accession":"3006303","ARO_id":"44765","ARO_name":"ADC-128","CARD_short_name":"ADC-128","ARO_description":"ADC-128 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4200":{"model_id":"4200","model_name":"ADC-129","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6575":{"protein_sequence":{"accession":"WP_005039111.1","sequence":"MRFKKISYLILPSLFIFNTSIYAGNTSKEQDIKKVVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKSVNSNTIFELGSVSKLFTATAGGYAKTKGKISFEDTPGKYWKELKNTPIDRVNLLQLATYTSGNLGLQFPDEVQTDQQVLTFFKDWKPKNQIGEYRQYSNPSIGLFGKVVGLSMNQPFSQVLEKTIFPSLHLKHSYVNVPKTQMQNYAFGYNQENQPIRVTPGPLDAPAYGVKSTLPDMLSFIDANLNPQKYPADIRRAIDETHKGFYQVGTMYQALGWEEFSYPAPLQTLLDSNSEQIVMKPNKVTAISKEPSIKMFHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_064685.1","fmin":"100","fmax":"1252","strand":"+","sequence":"ATGCGATTCAAAAAAATTTCTTACTTAATTCTACCTTCTCTTTTTATTTTTAATACCTCAATTTATGCAGGTAACACATCAAAAGAACAAGATATCAAAAAGGTTGTTGATCAGAACTTTAAACCATTATTAGAAAAATATGATGTTCCTGGTATGGCGGTTGGTGTCATCCAAAACAATAAAAAGTACGAAATGTATTATGGCCTACAATCGGTTCAAGATAAAAAATCCGTAAATAGCAATACGATTTTTGAGCTAGGTTCAGTCAGTAAATTATTTACTGCGACGGCAGGTGGATATGCCAAAACGAAAGGAAAAATCTCTTTTGAAGACACCCCAGGAAAATACTGGAAAGAGTTAAAAAATACACCGATTGACCGAGTGAACCTACTTCAACTTGCAACCTATACGAGTGGCAACCTTGGCTTACAGTTTCCAGATGAAGTTCAAACAGACCAACAAGTTTTAACCTTTTTCAAAGACTGGAAACCTAAAAACCAAATTGGTGAATATAGACAATATTCAAACCCAAGTATTGGCCTATTTGGAAAAGTTGTAGGCTTATCGATGAACCAGCCTTTTAGTCAGGTTTTAGAAAAGACAATTTTTCCGTCTCTTCACTTAAAACATAGCTATGTGAATGTTCCTAAAACTCAGATGCAAAACTATGCATTTGGCTATAACCAAGAAAATCAGCCGATTCGTGTGACCCCAGGCCCACTAGATGCGCCTGCCTACGGCGTTAAATCTACATTACCAGACATGCTTAGCTTTATTGATGCCAATCTAAATCCACAAAAATATCCAGCAGATATTCGACGCGCAATTGATGAGACTCATAAAGGTTTTTATCAAGTAGGTACGATGTATCAGGCGCTTGGTTGGGAAGAGTTTTCTTATCCAGCTCCTTTACAAACTTTATTAGACAGTAATTCTGAACAAATCGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAACCTTCAATCAAGATGTTCCATAAAACAGGTTCAACTAACGGATTTGGAACTTATGTCGTGTTTATTCCCAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAACGCATTAAAGCGGCTTATGCTGTACTAAACGCGATTAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39094","NCBI_taxonomy_name":"Acinetobacter calcoaceticus","NCBI_taxonomy_id":"471"}}}},"ARO_accession":"3006304","ARO_id":"44766","ARO_name":"ADC-129","CARD_short_name":"ADC-129","ARO_description":"ADC-129 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4201":{"model_id":"4201","model_name":"ADC-130","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6576":{"protein_sequence":{"accession":"WP_004886093.1","sequence":"MRFKKISYLLLPSLFIFNTSIYAGNSSKDQEIKQLVDQNFKPLLEKYNVPGMAVGVIQNNKKYETYYGLQSVQDKKAVNSNTIFELGSVSKLFTATAGAYAKNTGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGEIVGLSMKQPFSQVLEKTIFPDLGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPANIQCAINETHQGRYQVNSMYQALGWEEFAYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYAVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_064686.1","fmin":"100","fmax":"1252","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTACTTACTTTTACCTTCTCTTTTTATTTTTAATACCTCAATTTATGCGGGCAATAGTTCTAAAGACCAAGAAATTAAACAATTGGTAGATCAAAATTTTAAACCCTTATTAGAAAAATATAATGTGCCGGGCATGGCGGTAGGTGTTATTCAAAACAATAAAAAATATGAAACGTATTATGGTCTACAATCCGTTCAAGATAAAAAAGCTGTAAATAGCAATACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACTGCGACGGCAGGTGCTTATGCAAAAAATACAGGAAAAATTTCTTTTGATGATACGCCGGGCAAATACTGGAAAGAGTTAAAAAACACCCCAATTGATCAGGTCAATTTACTTCAACTTGCCACCTATACAAGTGGTAACCTCGCCTTGCAATTCCCAGATGAAGTACAAACAGATCAACAGGTTTTAACTTTTTTTAAAGATTGGAAACCTAAAAACCCAATCGGTGAATATAGACAATATTCAAACCCAAGTATCGGTCTATTTGGGGAAATAGTTGGTTTATCAATGAAGCAGCCTTTTAGTCAGGTCTTGGAAAAAACGATTTTTCCGGACCTTGGCTTAAAACATAGCTATGTCAATGTGCCTAAAACTCAGATGCAAAACTATGCATTTGGTTATAACCAAGAAAATCAGCCAATTCGAGTTAACCCTGGCCCACTCGATGCCCCAGCATACGGCGTCAAATCGACCCTACCCGACATGCTGAGCTTTATTCATGCCAACCTGAATCCACAGAAATATCCGGCAAATATTCAATGTGCAATTAATGAGACACATCAAGGTCGCTATCAAGTAAATAGCATGTATCAGGCACTCGGTTGGGAAGAGTTTGCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTCATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAACCTTCAGTTAAGATGTACCACAAAACTGGTTCAACAAATGGTTTCGGAACCTATGCCGTATTTATACCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGCATTCCAAATGAAGAACGCATTAAAGCAGCTTATGCTGTGCTAAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37046","NCBI_taxonomy_name":"Acinetobacter","NCBI_taxonomy_id":"469"}}}},"ARO_accession":"3006305","ARO_id":"44767","ARO_name":"ADC-130","CARD_short_name":"ADC-130","ARO_description":"ADC-130 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4202":{"model_id":"4202","model_name":"ADC-131","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6577":{"protein_sequence":{"accession":"WP_004707701.1","sequence":"MRFKKISYLLLPSLFIFNTSIYAGNTSKDQEIKQLVDQNFKPLLEKYNVPGMAVGVIQNNKKYETYYGLQSVQDKKAVNSNTIFELGSVSKLFTATAGAYAKNTGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGVIVGLSMKQPFSQVLEKTIFPDLGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPANIQRAINETHQGRYQVNSMYQALGWEEFAYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKDNIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_064687.1","fmin":"100","fmax":"1252","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTACTTACTTTTACCTTCTCTTTTTATTTTTAATACCTCAATTTATGCGGGCAATACTTCTAAAGACCAAGAAATTAAACAATTGGTAGATCAAAATTTTAAGCCCTTATTAGAAAAATATAATGTGCCGGGTATGGCGGTAGGTGTTATTCAAAACAATAAAAAATATGAAACGTATTATGGTCTACAATCCGTTCAAGATAAAAAAGCTGTAAATAGCAATACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACTGCGACGGCAGGTGCTTATGCAAAAAATACAGGGAAAATTTCTTTTGATGATACGCCGGGCAAATACTGGAAAGAGTTAAAAAACACCCCAATTGATCAGGTCAATTTACTTCAACTTGCCACCTATACAAGTGGTAACCTCGCTTTGCAATTCCCAGATGAAGTACAAACAGATCAACAGGTTTTAACTTTTTTTAAAGATTGGAAACCTAAAAACCCAATCGGTGAATATAGACAATATTCAAACCCAAGTATTGGCCTATTTGGGGTAATAGTTGGTTTATCAATGAAGCAGCCTTTTAGTCAGGTCTTGGAAAAAACGATTTTTCCGGACCTTGGCTTAAAACATAGCTATGTCAATGTGCCTAAAACTCAGATGCAAAACTATGCATTTGGTTATAACCAAGAAAATCAGCCAATTCGAGTTAACCCTGGCCCACTCGATGCCCCAGCATACGGCGTCAAATCGACCCTACCCGACATGCTGAGCTTTATTCATGCCAACCTGAACCCACAGAAATATCCGGCAAATATTCAACGTGCAATTAATGAGACACATCAAGGTCGCTATCAAGTAAATAGCATGTATCAGGCACTCGGTTGGGAAGAGTTTGCTTATCCAGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAACCTTCAGTTAAGATGTACCACAAAACTGGTTCAACAAATGGTTTCGGAACCTATGTCGTATTTATTCCTAAAGACAATATTGGTTTAGTCATGTTAACCAATAAACGCATTCCAAATGAAGAACGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36949","NCBI_taxonomy_name":"Acinetobacter nosocomialis","NCBI_taxonomy_id":"106654"}}}},"ARO_accession":"3006306","ARO_id":"44768","ARO_name":"ADC-131","CARD_short_name":"ADC-131","ARO_description":"ADC-131 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4203":{"model_id":"4203","model_name":"ADC-132","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6578":{"protein_sequence":{"accession":"WP_005068074.1","sequence":"MRFNKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLDKYDVPGMAVGVIQNNKKYETYYGLQSVQDKKAVSSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPGLGLKHSYVNVPKNQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLKFINANLNPQKYPADIQRAINETHQGFYQVGIMYQALGWEEFSYPAPLQTLLDSNSEQIVMKPNKVTAISKEPSVKMFHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNGIKK"},"dna_sequence":{"accession":"NG_064688.1","fmin":"100","fmax":"1252","strand":"+","sequence":"ATGCGATTTAACAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCTTTATTAGATAAATATGATGTGCCGGGTATGGCCGTGGGCGTTATTCAGAATAATAAAAAATATGAAACGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAGTAGCAGTACCATTTTTGAACTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCAACGTATACAAGTGGTAACCTTGCCTTGCAGTTCCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAAGTTGTTGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGGCCTTGGCTTAAAACATAGCTATGTAAATGTACCGAAGAACCAGATGCAAAACTATGCTTTTGGCTATAATCAAGAAAATCAGCCAATTCGTGTTAACCCTGGTCCGCTAGATGCTCCAGCATACGGCGTCAAATCGACACTACCCGATATGCTTAAGTTTATTAATGCCAACCTAAATCCACAAAAATATCCAGCAGATATTCAACGTGCAATTAATGAAACACATCAAGGTTTCTATCAAGTCGGCATCATGTATCAAGCATTAGGTTGGGAAGAATTTTCTTATCCAGCGCCTTTACAAACTTTATTAGACAGTAATTCAGAACAAATTGTGATGAAGCCTAATAAAGTGACTGCCATTTCAAAAGAACCTTCAGTTAAGATGTTCCACAAAACTGGTTCAACCAATGGTTTCGGAACTTATGTCGTGTTCATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAACGCATTAAGGCAGCGTATGCCGTGTTAAATGGAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37046","NCBI_taxonomy_name":"Acinetobacter","NCBI_taxonomy_id":"469"}}}},"ARO_accession":"3006307","ARO_id":"44769","ARO_name":"ADC-132","CARD_short_name":"ADC-132","ARO_description":"ADC-132 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4204":{"model_id":"4204","model_name":"ADC-133","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6579":{"protein_sequence":{"accession":"WP_004700205.1","sequence":"MRFNKISCLLLFPLFIFNTSIYAGNTPKEQEIKKLVDQNFKPLLEKYNVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGAYAKNKGKISFEDKPSKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVSLSMNQPFSQVLEKTIFPDLGLKHSYVNVPKTQMQHYAFGYNQQNQPIRVNPGPLDGPAYGVKSTLPDMLGFVHANLNPQQYPADIQRAINETHQGFYQVDTMYQALGWEEFSYPATLQTLLDSNSDQIVMKPNKVTAISKEPSIKMFHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_064689.1","fmin":"100","fmax":"1252","strand":"+","sequence":"ATGCGATTTAACAAAATTTCTTGCTTACTTTTATTCCCTCTTTTTATTTTTAATACCTCAATTTATGCAGGGAATACACCAAAAGAGCAAGAAATTAAGAAACTGGTTGATCAAAATTTTAAACCGTTATTAGAAAAATATAATGTGCCGGGTATGGCGGTAGGTGTTATTCAAAACAATAAAAAATATGAAATGTATTATGGCCTTCAATCTGTTCAAGATAAAAAAGCTGTAAATAGCAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAACTATTTACCGCTACAGCAGGTGCTTATGCTAAGAATAAGGGAAAAATCTCTTTTGAAGATAAACCAAGTAAATACTGGAAAGAGCTAAAAAACACCCCGATTGATCAGGTCAATTTACTTCAACTTGCTACTTATACCAGTGGTAATCTTGCGCTACAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAGCCTAAAAATCCAATTGGTGAATATAGACAATATTCCAACCCAAGTATTGGCCTATTTGGAAAAGTTGTAAGCTTGTCAATGAATCAGCCTTTTAGTCAGGTTTTAGAAAAAACCATTTTTCCAGACCTTGGCTTAAAACATAGTTATGTCAATGTACCTAAAACTCAAATGCAACATTATGCATTTGGCTATAACCAACAAAATCAGCCGATTCGAGTCAACCCTGGTCCCTTAGATGGTCCAGCTTACGGCGTTAAATCGACTCTTCCAGACATGTTGGGGTTTGTTCATGCCAACCTGAACCCGCAGCAATATCCTGCTGATATTCAACGTGCAATTAATGAGACACATCAAGGTTTCTATCAAGTAGATACCATGTATCAGGCGCTTGGTTGGGAAGAGTTTTCTTACCCTGCAACCTTACAAACTTTATTAGACAGTAATTCTGACCAGATTGTGATGAAGCCTAATAAAGTCACTGCTATTTCTAAAGAACCTTCAATTAAAATGTTTCACAAAACTGGTTCAACCAATGGCTTTGGAACATACGTCGTATTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAACGAAGAACGCATTAAGGCGGCTTATGCTGTGCTAAATGCGATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37046","NCBI_taxonomy_name":"Acinetobacter","NCBI_taxonomy_id":"469"}}}},"ARO_accession":"3006308","ARO_id":"44770","ARO_name":"ADC-133","CARD_short_name":"ADC-133","ARO_description":"ADC-133 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4205":{"model_id":"4205","model_name":"ADC-134","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6580":{"protein_sequence":{"accession":"WP_005307218.1","sequence":"MQFNKISCLLLSPLFIFNTSIYAGNTPKEQEIKKLVDQNFKPLLEKYDVPGMAVGIIQNNKKYETYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKTKGTISFKDTPGKYWKELKNTPIDQVNLLQLATYTSGNLGLQFPDEVQTDQQVLTFFKDWKPKNSIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPDLGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFVNANLNPQKYPADIQHAINETHKGFYQVGTMYQALGWEEFSYPAPLQTLLDSNSEQIVMKPNKVTAISNEPSVKMFHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_064690.1","fmin":"100","fmax":"1252","strand":"+","sequence":"ATGCAATTTAACAAAATTTCTTGCTTACTTTTATCCCCTCTTTTTATTTTTAATACCTCAATTTATGCAGGGAATACACCAAAAGAGCAAGAAATTAAGAAACTGGTTGATCAAAATTTTAAACCGTTATTAGAAAAATATGATGTGCCTGGGATGGCTGTTGGCATCATCCAAAATAATAAAAAGTATGAAACGTATTATGGTCTACAATCCGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTCGGTTCAGTTAGTAAATTATTTACTGCTACAGCTGGTGGATATGCCAAAACAAAAGGAACAATTTCTTTTAAAGACACACCCGGAAAATATTGGAAAGAATTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTTGCTACTTATACAAGTGGCAACCTTGGCTTACAGTTTCCAGATGAAGTCCAAACAGATCAGCAAGTTTTAACTTTTTTCAAAGACTGGAAGCCTAAAAACTCAATCGGTGAATATCGACAATATTCAAATCCAAGCATTGGTTTATTTGGAAAAGTTGTTGCTTTGTCTATGAATAAACCTTTTGACCAAGTCTTAGAAAAAACCATTTTTCCAGATCTTGGCTTAAAACATAGCTATGTAAATGTGCCTAAAACTCAAATGCAAAACTATGCATTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCGCTAGATGCACCTGCGTACGGCGTTAAATCGACCTTACCTGATATGCTGAGTTTCGTTAATGCCAACCTCAACCCACAAAAATATCCGGCAGATATTCAACACGCAATTAATGAAACACATAAAGGTTTCTACCAAGTAGGTACGATGTATCAAGCATTAGGTTGGGAAGAGTTCTCTTATCCAGCACCGTTACAGACTTTATTAGACAGTAATTCAGAACAAATCGTGATGAAGCCTAATAAAGTGACAGCTATTTCAAATGAACCTTCAGTTAAGATGTTCCACAAAACTGGTTCAACCAACGGTTTTGGAACCTATGTCGTGTTTATTCCAAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCCAATGAAGAACGCATTAAAGCAGCGTATGCAGTGTTAAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42825","NCBI_taxonomy_name":"Acinetobacter sp. NIPH 542","NCBI_taxonomy_id":"1217688"}}}},"ARO_accession":"3006309","ARO_id":"44771","ARO_name":"ADC-134","CARD_short_name":"ADC-134","ARO_description":"ADC-134 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4206":{"model_id":"4206","model_name":"ADC-135","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6581":{"protein_sequence":{"accession":"WP_004790939.1","sequence":"MRFNKISCLLLSPLFIFNTSIYAENTPKEQEIKKLVDQNFKPLLEKYDVPGMAVGIIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKTKGIISFKDTPGKYWKELKNTPIDQVNLLQLATYTSGNLGLQFPDEVQTNQQVLTFFKDWKPKNSIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPDLGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFVNANLNPQKYPADIQRAINETHQGFYQVGTMYQALGWEEFSYPAPLQTLLDSNSEQIVMKSNKVTAISKEPSVKMFHKTGSTNGFGTYVVFIPKQNIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_064691.1","fmin":"100","fmax":"1252","strand":"+","sequence":"ATGCGATTTAACAAAATTTCTTGCTTACTTTTATCCCCTCTTTTTATTTTTAATACCTCAATTTATGCAGAGAATACACCCAAAGAGCAAGAAATTAAGAAACTGGTTGATCAAAATTTTAAACCTTTATTAGAAAAATATGATGTGCCCGGTATGGCTGTTGGCATCATCCAAAATAATAAAAAGTATGAAATGTATTATGGTCTACAATCCGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTCGGTTCAGTCAGTAAATTATTTACTGCTACAGCAGGTGGATATGCAAAAACAAAAGGAATAATTTCTTTTAAAGACACTCCCGGAAAATATTGGAAAGAATTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTTGCTACTTATACAAGTGGCAACCTTGGCTTACAGTTTCCAGATGAAGTCCAAACAAATCAGCAAGTTTTAACTTTTTTCAAAGACTGGAAGCCTAAAAACTCAATCGGTGAATATCGACAATATTCAAATCCAAGCATTGGTTTATTTGGAAAAGTTGTTGCTTTGTCTATGAACAAACCTTTCGACCAAGTCTTAGAAAAAACCATTTTTCCAGATCTTGGCTTAAAACATAGCTATGTAAATGTGCCTAAAACTCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCGCTAGATGCACCTGCGTACGGCGTTAAATCGACCTTACCTGATATGCTGAGTTTCGTTAATGCCAATCTAAATCCACAAAAATATCCAGCAGATATTCAACGCGCAATTAATGAAACACATCAAGGTTTCTACCAAGTGGGTACGATGTATCAAGCATTAGGTTGGGAAGAGTTCTCTTATCCAGCACCATTACAGACTTTATTAGACAGTAATTCAGAGCAAATCGTAATGAAATCTAATAAAGTGACAGCTATTTCGAAAGAACCTTCAGTTAAGATGTTCCACAAAACTGGTTCGACCAACGGTTTTGGAACATATGTTGTCTTTATTCCAAAGCAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAACGCATTAAAGCTGCCTATGCAGTGTTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37046","NCBI_taxonomy_name":"Acinetobacter","NCBI_taxonomy_id":"469"}}}},"ARO_accession":"3006310","ARO_id":"44772","ARO_name":"ADC-135","CARD_short_name":"ADC-135","ARO_description":"ADC-135 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4207":{"model_id":"4207","model_name":"ADC-136","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6582":{"protein_sequence":{"accession":"WP_016137488.1","sequence":"MRFNKISCLLLPPLFIFNTSIYAGNSPKEQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKNYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKTKGTISFKDTPGKYWKELKNTPIDQINLLQLATYTSGNLGLQFPDEVQTDQQVLTFFKDWKPKNSIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPDLGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFVKANLNPQKYPADIQHAINETHKGFYQVGTMYQALGWEEFSYPAPLQTLLDSNSEQIVMKPNKVTALSKEPSVKIYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_064692.1","fmin":"100","fmax":"1252","strand":"+","sequence":"ATGCGATTTAACAAAATTTCCTGCTTACTTTTACCCCCTCTTTTTATTTTTAATACCTCAATTTATGCGGGTAATTCACCAAAAGAGCAAGAAATTAAAAAACTGGTTGATCAAAACTTTAAACCATTATTAGAAAAATATGATGTGCCCGGAATGGCTGTTGGCGTCATTCAAAATAATAAAAACTATGAAATGTATTATGGTCTACAATCCGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTAGGTTCTGTTAGTAAATTATTTACCGCTACAGCAGGTGGATATGCCAAAACAAAAGGAACAATTTCTTTTAAAGACACACCTGGAAAATATTGGAAAGAATTAAAAAACACACCGATTGACCAAATTAATTTACTTCAACTTGCTACTTATACAAGTGGCAACCTTGGCTTACAGTTTCCAGATGAAGTCCAAACAGATCAGCAAGTTTTAACTTTTTTCAAAGACTGGAAGCCTAAAAACTCAATCGGTGAATATCGACAATATTCAAATCCAAGCATTGGTTTATTTGGAAAAGTTGTTGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACTATTTTTCCAGATCTTGGCTTAAAACATAGCTATGTAAATGTGCCTAAAACTCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCGCTAGATGCACCTGCGTACGGTGTTAAATCGACCTTACCTGATATGCTGAGTTTCGTTAAGGCCAATCTAAATCCACAAAAATATCCGGCAGATATTCAACACGCGATTAATGAAACACATAAAGGTTTCTATCAAGTAGGTACTATGTATCAAGCATTGGGTTGGGAAGAATTCTCTTATCCAGCACCTTTACAAACTTTATTAGACAGTAATTCAGAACAAATCGTGATGAAGCCTAATAAAGTGACTGCCCTTTCAAAAGAACCTTCAGTCAAGATTTACCACAAAACTGGTTCAACTAACGGCTTTGGAACATATGTTGTCTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCCAATGAAGAACGCATTAAAGCAGCGTATGCAGTATTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39094","NCBI_taxonomy_name":"Acinetobacter calcoaceticus","NCBI_taxonomy_id":"471"}}}},"ARO_accession":"3006311","ARO_id":"44773","ARO_name":"ADC-136","CARD_short_name":"ADC-136","ARO_description":"ADC-136 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4208":{"model_id":"4208","model_name":"ADC-137","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6583":{"protein_sequence":{"accession":"WP_016140427.1","sequence":"MQFKKISCLLLPPLFIFSSSIYAGNTPKEQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKTKGTISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVKTEQQVLTFFKEWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFTDLGLKHSYVNVPKTQMQNYAFGYSQENQPIRVNPGPLDAPAYGVKSTLPDMLSFINANLNPQKYPADIQRAINETHQGFYQVGTMYQALGWEEFSYPAPLQTLLDSNSEQIVMKPNKVTAISKEPSVKMFHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_064693.1","fmin":"100","fmax":"1252","strand":"+","sequence":"ATGCAATTTAAAAAAATTTCTTGCTTACTTTTACCGCCTCTTTTTATTTTTAGTAGCTCAATTTATGCGGGTAATACACCAAAAGAGCAAGAGATCAAAAAACTGGTTGATCAAAATTTTAAGCCTTTATTAGAAAAATATGATGTGCCCGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTACAATCCGTTCAAGATAAAAAAGCCGTTAATAGTAGTACCATTTTTGAGCTAGGCTCGGTCAGTAAATTATTTACCGCTACAGCAGGCGGATATGCCAAAACAAAAGGAACAATCTCTTTTGATGACACGCCCGGAAAATATTGGAAAGAACTAAAAAATACACCGATTGATCAAGTGAATTTACTTCAACTTGCGACATATACCAGTGGCAACCTTGCCTTGCAATTTCCAGATGAAGTAAAAACAGAACAGCAAGTTTTAACGTTTTTCAAAGAATGGAAACCTAAAAACCCAATCGGTGAATATCGACAATATTCAAATCCAAGCATTGGTTTATTTGGAAAAGTTGTTGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTGGAAAAAACCATTTTTACAGATCTTGGCTTAAAACATAGCTATGTAAATGTGCCTAAAACTCAAATGCAAAACTATGCATTTGGCTATAGCCAAGAAAATCAGCCGATTCGCGTTAATCCTGGTCCGCTCGATGCACCAGCATACGGCGTTAAATCTACCCTACCAGATATGCTGAGTTTTATTAATGCCAACCTGAACCCGCAGAAATATCCAGCAGATATTCAACGTGCAATTAATGAAACACATCAAGGTTTCTACCAAGTGGGTACGATGTATCAAGCACTAGGTTGGGAAGAGTTTTCTTATCCAGCACCTTTACAAACTTTATTAGACAGTAATTCAGAACAAATCGTGATGAAACCTAATAAAGTAACTGCTATTTCAAAAGAACCTTCCGTTAAGATGTTCCACAAAACTGGATCGACTAACGGTTTTGGAACATATGTCGTGTTCATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACTAATAAACGTATTCCCAATGAAGAACGCATTAAAGCAGCTTATGCTGTGTTAAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3006312","ARO_id":"44774","ARO_name":"ADC-137","CARD_short_name":"ADC-137","ARO_description":"ADC-137 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4209":{"model_id":"4209","model_name":"ADC-138","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6584":{"protein_sequence":{"accession":"WP_016146025.1","sequence":"MRFQKVSCLLLSPLFIFSTSIYAGNTPKEQEIKKLVDQNFKPLLEKYNVPGMAVGIIQNNKKYETYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKTKGTLSFEDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVKTDQQVLTFFKDWKPKNSIGEYRQYSNPSIGLFGKVVALSMNQSFDQVLEKTIFPDLGLKHSYVNVPKLQMQNYAFGYNQQNQPIRVNPGPLDAPAYGVKSTLPDMLSFINANLNPQKYPADIQRAINETHQGFYQVGTMYQALGWEEFSYPAPLQTLLDSNSEQIVMKPNKVTAISKEPTVKMFHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_064694.1","fmin":"100","fmax":"1252","strand":"+","sequence":"ATGCGATTCCAAAAAGTTTCTTGCTTACTTTTATCCCCTCTTTTTATTTTTAGCACCTCAATTTATGCAGGCAATACACCAAAAGAACAAGAAATCAAAAAACTGGTAGATCAAAACTTTAAGCCTTTATTAGAAAAATATAATGTGCCCGGTATGGCAGTTGGCATCATCCAGAATAATAAAAAGTATGAAACCTATTATGGTCTACAATCCGTTCAAGATAAAAAAGCTGTAAATAGCAGCACCATTTTTGAGCTAGGTTCAGTCAGTAAATTATTTACTGCGACAGCGGGTGGATATGCCAAAACAAAAGGAACCCTCTCTTTTGAAGACACGCCCGGAAAATATTGGAAAGAACTAAAAAACACACCGATTGATCAAGTTAACTTACTTCAACTTGCGACATATACCAGCGGCAACCTTGCTTTGCAATTTCCAGATGAAGTAAAAACAGATCAGCAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAATTCAATCGGTGAATACAGACAATATTCAAACCCAAGTATTGGTTTATTTGGAAAAGTTGTGGCTTTGTCTATGAATCAATCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCAGATCTTGGCTTAAAACATAGTTATGTCAATGTGCCTAAACTTCAAATGCAAAACTATGCATTTGGCTATAACCAACAAAATCAGCCCATTCGAGTTAACCCCGGCCCACTCGATGCACCAGCATACGGCGTCAAATCGACATTACCAGACATGCTGAGTTTTATTAATGCCAACCTCAACCCGCAGAAATATCCAGCAGATATTCAACGTGCAATTAATGAAACACATCAAGGTTTCTATCAAGTCGGCACAATGTATCAAGCACTTGGCTGGGAAGAATTTTCTTATCCAGCGCCTTTACAAACTTTATTAGACAGTAATTCAGAACAAATCGTGATGAAGCCTAATAAAGTGACTGCTATTTCAAAAGAACCTACCGTTAAGATGTTCCATAAAACTGGTTCAACAAATGGCTTTGGAACATATGTTGTGTTCATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAACGTATTAAGGCAGCGTATGCAGTTTTAAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42801","NCBI_taxonomy_name":"Acinetobacter lactucae","NCBI_taxonomy_id":"1785128"}}}},"ARO_accession":"3006313","ARO_id":"44775","ARO_name":"ADC-138","CARD_short_name":"ADC-138","ARO_description":"ADC-138 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4210":{"model_id":"4210","model_name":"ADC-139","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6585":{"protein_sequence":{"accession":"WP_032039838.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVKTDQQVLTFFKDWKPKNSIGEYRQYSNPSIGLFGKVVALSMNKPFDQALEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_064695.1","fmin":"100","fmax":"1252","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAGTATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAATTTCCAGATGAAGTAAAAACAGATCAGCAAGTTTTAACATTTTTTAAAGACTGGAAACCTAAAAACTCAATCGGTGAATATAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGCCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTAAATCCACAAAAATATCCAGCAGATATTCAACGGGCAATTAATGAAACACATCAGGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006314","ARO_id":"44776","ARO_name":"ADC-139","CARD_short_name":"ADC-139","ARO_description":"ADC-139 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4211":{"model_id":"4211","model_name":"ADC-140","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6586":{"protein_sequence":{"accession":"WP_001211209.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFNATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVKTDQQVLTFFKDWKPKNSIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTSGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_064696.1","fmin":"100","fmax":"1252","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTAACGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAGTATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAATTTCCAGATGAAGTAAAAACAGATCAGCAAGTTTTAACATTTTTTAAAGACTGGAAACCTAAAAACTCAATCGGTGAATATCGACAATATTCAAACCCAAGCATTGGTTTATTTGGAAAAGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTAAATCCACAAAAATATCCAGCAGATATTCAACGGGCAATTAATGAAACACATCAGGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAGCGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006315","ARO_id":"44777","ARO_name":"ADC-140","CARD_short_name":"ADC-140","ARO_description":"ADC-140 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4212":{"model_id":"4212","model_name":"ADC-141","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6587":{"protein_sequence":{"accession":"WP_032062810.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPCKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVKTDQQVLTFFKDWKPKNSIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTTGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_064697.1","fmin":"100","fmax":"1252","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTTGTAAGTATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAATTTCCAGATGAAGTAAAAACAGATCAGCAAGTTTTAACATTTTTTAAAGACTGGAAACCTAAAAACTCAATCGGTGAATATCGACAATATTCAAACCCAAGCATTGGTTTATTTGGAAAAGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTAAATCCACAAAAATATCCAGCAGATATTCAACGGGCAATTAATGAAACACATCAGGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTACCGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006316","ARO_id":"44778","ARO_name":"ADC-141","CARD_short_name":"ADC-141","ARO_description":"ADC-141 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4213":{"model_id":"4213","model_name":"ADC-143","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6588":{"protein_sequence":{"accession":"WP_033502167.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALKFPDEVKTDQQVLTFFKDWKPKNSIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTTGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_064698.1","fmin":"100","fmax":"1252","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAGTATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGAAATTTCCAGATGAAGTAAAAACAGATCAGCAAGTTTTAACATTTTTTAAAGACTGGAAACCTAAAAACTCAATCGGTGAATATCGACAATATTCAAACCCAAGCATTGGTTTATTTGGAAAAGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTAAATCCACAAAAATATCCAGCAGATATTCAACGGGCAATTAATGAAACACATCAGGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTACCGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006317","ARO_id":"44779","ARO_name":"ADC-143","CARD_short_name":"ADC-143","ARO_description":"ADC-143 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4214":{"model_id":"4214","model_name":"ADC-144","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6589":{"protein_sequence":{"accession":"WP_001211214.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVKTDQQVLTFFKDWKPKNSIGEYQQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_064699.1","fmin":"100","fmax":"1252","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAGTATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAATTTCCAGATGAAGTAAAAACAGATCAGCAAGTTTTAACATTTTTTAAAGACTGGAAACCTAAAAACTCAATCGGTGAATATCAACAATATTCAAACCCAAGCATTGGTTTATTTGGAAAAGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTAAATCCACAAAAATATCCAGCAGATATTCAACGGGCAATTAATGAAACACATCAGGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006318","ARO_id":"44780","ARO_name":"ADC-144","CARD_short_name":"ADC-144","ARO_description":"ADC-144 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4215":{"model_id":"4215","model_name":"ADC-145","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6590":{"protein_sequence":{"accession":"WP_039270258.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVKTDQQVLTFFKDWKPKNSIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIMMKPNKVTAISKEPSVKMYHKTGTTTGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_064700.1","fmin":"8","fmax":"1160","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAGTATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAATTTCCAGATGAAGTAAAAACAGATCAGCAAGTTTTAACATTTTTTAAAGACTGGAAACCTAAAAACTCAATCGGTGAATATCGACAATATTCAAACCCAAGCATTGGTTTATTTGGAAAAGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTAAATCCACAAAAATATCCAGCAGATATTCAACGGGCAATTAATGAAACACATCAGGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTATGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCACAACTACCGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006319","ARO_id":"44781","ARO_name":"ADC-145","CARD_short_name":"ADC-145","ARO_description":"ADC-145 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4216":{"model_id":"4216","model_name":"ADC-146","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6591":{"protein_sequence":{"accession":"WP_039258389.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTSGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVKTDQQVLTFFKDWKPKNSIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTTGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_064701.1","fmin":"65","fmax":"1217","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGTCTGGTAAGTATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAATTTCCAGATGAAGTAAAAACAGATCAGCAAGTTTTAACATTTTTTAAAGACTGGAAACCTAAAAACTCAATCGGTGAATATCGACAATATTCAAACCCAAGCATTGGTTTATTTGGAAAAGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTAAATCCACAAAAATATCCAGCAGATATTCAACGGGCAATTAATGAAACACATCAGGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTACCGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006320","ARO_id":"44782","ARO_name":"ADC-146","CARD_short_name":"ADC-146","ARO_description":"ADC-146 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4217":{"model_id":"4217","model_name":"ADC-147","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6592":{"protein_sequence":{"accession":"WP_044718369.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVKTDQQVLTFFKDWKPKNSIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTRYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTTGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_064702.1","fmin":"84","fmax":"1236","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAGTATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAATTTCCAGATGAAGTAAAAACAGATCAGCAAGTTTTAACATTTTTTAAAGACTGGAAACCTAAAAACTCAATCGGTGAATATCGACAATATTCAAACCCAAGCATTGGTTTATTTGGAAAAGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTAAATCCACAAAAATATCCAGCAGATATTCAACGGGCAATTAATGAAACACATCAGGGTCGCTATCAAGTAAATACCAGGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTACCGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006321","ARO_id":"44783","ARO_name":"ADC-147","CARD_short_name":"ADC-147","ARO_description":"ADC-147 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4218":{"model_id":"4218","model_name":"ADC-148","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6593":{"protein_sequence":{"accession":"WP_039246976.1","sequence":"MQFKKISYLLLPSLFIFNTSIYAGNTSKDQEIKQLIDQNFKPLLEKYNVPGMAVGVIQNNKKYETYYGLQSVQDKKAVNSNTIFELGSVSKLFTATAGAYAKNTGKISFNDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGEIVGLSMKQPFSQVLEKTIFPDLGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPANIQRAINETHQGRYQVNSMYQALGWEEFAYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYAVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_064703.1","fmin":"100","fmax":"1252","strand":"+","sequence":"ATGCAATTTAAAAAAATTTCTTACTTACTTTTACCTTCTCTTTTTATTTTTAATACCTCAATTTATGCGGGCAATACTTCTAAAGACCAAGAAATTAAACAATTGATAGATCAAAATTTTAAACCCTTATTAGAAAAATATAATGTGCCGGGTATGGCGGTAGGTGTTATTCAAAACAATAAAAAATATGAAACGTATTATGGTCTACAATCCGTTCAAGATAAAAAAGCTGTAAATAGCAATACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACTGCGACGGCAGGTGCTTATGCAAAAAATACAGGAAAAATCTCTTTTAATGATACGCCGGGCAAATACTGGAAAGAGTTAAAAAACACCCCAATTGATCAGGTCAATTTACTTCAACTTGCCACCTATACAAGTGGTAACCTCGCTTTGCAATTCCCAGATGAAGTACAAACAGATCAACAGGTTTTAACTTTTTTTAAAGATTGGAAACCTAAAAACCCAATCGGTGAATATAGACAATATTCAAACCCAAGTATTGGCCTATTTGGGGAAATAGTTGGTTTATCAATGAAGCAGCCTTTTAGTCAGGTCTTGGAAAAAACGATTTTTCCGGACCTTGGCTTAAAACATAGCTATGTCAATGTGCCTAAAACTCAGATGCAAAACTATGCATTTGGCTATAACCAAGAAAATCAGCCAATTCGAGTTAACCCTGGCCCACTCGATGCCCCAGCATACGGCGTCAAATCGACCCTACCCGACATGCTGAGCTTTATTCATGCCAACCTGAACCCACAGAAATATCCGGCAAATATTCAACGTGCAATTAATGAGACACATCAAGGTCGCTATCAAGTAAATAGCATGTATCAGGCACTCGGTTGGGAAGAGTTTGCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAACCTTCAGTTAAGATGTACCACAAAACTGGTTCAACAAATGGTTTCGGAACCTATGCCGTATTTATACCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGCATTCCAAATGAAGAACGCATTAAAGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36949","NCBI_taxonomy_name":"Acinetobacter nosocomialis","NCBI_taxonomy_id":"106654"}}}},"ARO_accession":"3006322","ARO_id":"44784","ARO_name":"ADC-148","CARD_short_name":"ADC-148","ARO_description":"ADC-148 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4219":{"model_id":"4219","model_name":"ADC-149","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6594":{"protein_sequence":{"accession":"WP_014207272.1","sequence":"MRFKKISCLLLSPLFIFSTSIYADNTPKDREIKKLVDQNFKPLLDKYDVPGMAVGVIQNNKKYETYYGLQSVQDKKAVSSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLGLQFPDEVQTDQQVLTFFKDWKPKNSIGEYRQYSNPSIGLFGKVVALSMNKPFDQLLEKTIFPDLGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFINANLNPQKYPKDIQRAINETHQGFYQVGTMYQALGWEEFSYPAPLQTLLDSNSEQIVMKPNKVTAISKEPSVKMFHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_064704.1","fmin":"100","fmax":"1252","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGACAATACACCAAAAGACCGAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCTTTATTAGATAAATATGATGTGCCGGGTATGGCCGTGGGCGTTATTCAGAATAATAAAAAATATGAAACGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAGTAGCAGTACCATTTTTGAACTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTTGCTACTTATACGAGTGGCAACCTTGGCTTACAGTTTCCAGATGAAGTCCAAACAGATCAGCAAGTTTTAACTTTTTTCAAAGACTGGAAGCCTAAAAACTCAATCGGTGAATATCGACAATATTCAAATCCAAGCATTGGTTTATTTGGAAAAGTTGTTGCATTGTCTATGAATAAACCTTTCGACCAACTCTTAGAAAAAACAATTTTTCCAGATCTTGGCTTAAAACATAGCTATGTAAATGTACCGAAGACCCAGATGCAAAACTATGCTTTTGGCTATAATCAAGAAAATCAGCCAATTCGTGTTAACCCTGGTCCGCTAGATGCTCCAGCATATGGGGTTAAATCGACCCTACCTGATATGCTGAGTTTCATTAATGCCAACCTCAACCCACAGAAATATCCGAAAGATATTCAACGTGCAATTAATGAAACACATCAAGGTTTCTATCAAGTCGGCACCATGTATCAAGCATTAGGTTGGGAAGAATTTTCTTATCCAGCGCCTTTACAAACTTTATTAGACAGTAATTCAGAACAAATTGTGATGAAGCCTAATAAAGTGACTGCTATTTCAAAAGAACCTTCAGTTAAGATGTTCCACAAAACTGGCTCAACCAATGGTTTCGGAACATATGTCGTGTTCATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAACGCATTAAAGCAGCGTATGCAGTATTAAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3006323","ARO_id":"44785","ARO_name":"ADC-149","CARD_short_name":"ADC-149","ARO_description":"ADC-149 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4220":{"model_id":"4220","model_name":"ADC-150","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6595":{"protein_sequence":{"accession":"WP_017386568.1","sequence":"MRFKKISCLLLPPLFIFSTSIYAGNTPKDREIKKLVDQNFKPLLDKYDVPGMAVGVIQNNKKYETYYGLQSVQDKKAVSSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNSIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPDLGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLKFINANLNTQKYPKDIQRAINETHQGFYQVGTMYQALGWEEFSYPAPLQTLLDSNSEQIVMKPNKVTAISKEPSVKMFHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNGIKK"},"dna_sequence":{"accession":"NG_064705.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGCTTACTTTTACCTCCTCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCGAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCTTTATTAGATAAATATGATGTGCCGGGTATGGCCGTGGGCGTTATTCAGAATAATAAAAAATATGAAACGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAGTAGCAGTACCATTTTTGAACTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATTTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCAACGTATACAAGTGGTAACCTTGCCTTGCAGTTCCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACTCAATCGGTGAATATAGACAATATTCAAATCCAAGCATTGGTTTATTTGGAAAAGTTGTGGCATTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCAGATCTTGGCTTAAAACATAGCTATGTAAATGTTCCTAAAACTCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCAATTCGTGTTAACCCTGGTCCGCTAGATGCTCCAGCATATGGGGTTAAATCGACGCTACCCGATATGCTTAAGTTTATTAATGCCAACCTCAACACACAGAAATATCCGAAAGATATTCAACGTGCAATTAATGAAACACATCAGGGTTTCTATCAAGTCGGCACCATGTATCAGGCACTTGGTTGGGAAGAATTTTCTTATCCAGCGCCTTTACAAACTTTATTAGACAGTAATTCAGAACAAATTGTGATGAAGCCTAATAAAGTGACTGCCATTTCAAAAGAACCTTCAGTTAAGATGTTCCACAAAACTGGTTCAACCAATGGTTTCGGAACTTATGTCGTGTTCATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAACGCATTAAGGCAGCGTATGCCGTGTTAAATGGAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37046","NCBI_taxonomy_name":"Acinetobacter","NCBI_taxonomy_id":"469"}}}},"ARO_accession":"3006324","ARO_id":"44786","ARO_name":"ADC-150","CARD_short_name":"ADC-150","ARO_description":"ADC-150 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4221":{"model_id":"4221","model_name":"ADC-151","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6596":{"protein_sequence":{"accession":"WP_063099318.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDREIKKLVDQNFKPLLDKYDVPGMAVGIIQNNKKYETYYGLQSVQDKKAVSSSTIFELGSVSKLFTATAGGYAKTKGTISFDDAPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVKTDQQVLTFFKDWKPKNSIGEYRQYSNPSIGLFGKVVALSMNKPFDQLLEKTIFPDLGLKHSYVNVPKTQMQNYAFGYNQENQPIRVIPGPLDAPAYGVKSTLPDMLKFINANLNPQKYPKDIQRAINETHQGFYQVGTMYQALGWEEFSYPAPLQTLLDSNSEQIVMKPNKVTAISKEPSVKMFHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_064706.1","fmin":"100","fmax":"1252","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCGAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCCTTATTAGATAAATATGATGTGCCGGGTATGGCCGTGGGCATTATTCAGAATAATAAAAAATATGAAACGTATTACGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAGTAGCAGTACCATTTTTGAACTAGGTTCTGTCAGTAAATTATTTACCGCAACTGCAGGTGGATATGCCAAAACAAAAGGAACAATCTCTTTTGATGACGCACCTGGCAAATATTGGAAAGAACTAAAAAATACACCGATTGATCAAGTTAACTTACTTCAACTCGCAACGTATACAAGCGGCAACCTTGCCTTGCAATTTCCAGATGAAGTAAAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACTCAATCGGTGAATATAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAAGTTGTTGCATTGTCTATGAATAAACCTTTCGACCAACTCTTAGAAAAAACAATTTTTCCAGATCTTGGCTTAAAACATAGCTATGTAAATGTACCGAAGACCCAGATGCAAAACTATGCTTTTGGCTATAATCAAGAAAATCAGCCAATTCGTGTTATCCCTGGTCCGTTAGATGCACCTGCGTACGGCGTCAAATCGACACTACCCGATATGCTTAAGTTTATTAATGCCAACCTCAACCCACAGAAATATCCGAAAGATATTCAACGTGCAATTAATGAAACACATCAAGGTTTCTATCAAGTCGGCACCATGTATCAGGCACTTGGTTGGGAAGAATTTTCTTATCCAGCGCCTTTACAAACTTTATTAGACAGTAATTCAGAACAAATTGTGATGAAGCCTAATAAAGTGACTGCCATTTCAAAAGAACCTTCAGTTAAGATGTTCCACAAAACTGGTTCAACCAATGGTTTCGGAACTTATGTCGTGTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTGACCAATAAACGTATTCCAAATGAAGAACGCATTAAGGCAGCGTATGCGGTGTTAAATGCAATAAAAAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3006325","ARO_id":"44787","ARO_name":"ADC-151","CARD_short_name":"ADC-151","ARO_description":"ADC-151 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4222":{"model_id":"4222","model_name":"ADC-152","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6597":{"protein_sequence":{"accession":"WP_001211233.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTSIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWQPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVAKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLKFIHANLNPQKYPTDIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTSGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKE"},"dna_sequence":{"accession":"NG_054691.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAACACATCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGCAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTGGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTAGCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGCTTAAGTTTATTCATGCCAATCTGAACCCACAGAAATATCCGACAGATATTCAACGTGCAATTAATGAAACACATCAAGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCAGCGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAACGCATTAAGGCAGCGTATGCAGTTTTAAATGCAATAAAGGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006326","ARO_id":"44788","ARO_name":"ADC-152","CARD_short_name":"ADC-152","ARO_description":"ADC-152 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4223":{"model_id":"4223","model_name":"ADC-153","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6598":{"protein_sequence":{"accession":"WP_099156045.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTSGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVKTDQQVLTFFKDWKPKNSIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_055657.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGTCTGGTAAGTATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAATTTCCAGATGAAGTAAAAACAGATCAGCAAGTTTTAACATTTTTTAAAGACTGGAAACCTAAAAACTCAATCGGTGAATATCGACAATATTCAAACCCAAGCATTGGTTTATTTGGAAAAGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTAAATCCACAAAAATATCCAGCAGATATTCAACGGGCAATTAATGAAACACATCAGGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006327","ARO_id":"44789","ARO_name":"ADC-153","CARD_short_name":"ADC-153","ARO_description":"ADC-153 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4224":{"model_id":"4224","model_name":"ADC-154","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6599":{"protein_sequence":{"accession":"WP_005138362.1","sequence":"MRFKKISCLLLSPLFIFNTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKVLKNTPIDQVNLLQLATYTSSNLALQFPDEVQTDQQVLTFFKDWQPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPTDIQRAINETHQGFYQLGTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKE"},"dna_sequence":{"accession":"NG_054996.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAATACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCATTATTAGAAAAATATGATGTACCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGTGCTAAAAAATACACCGATTGATCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTAGCAACCTCGCTTTACAATTTCCAGATGAAGTACAAACAGATCAACAAGTTTTAACTTTTTTCAAAGACTGGCAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTGGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTTGATGCCCCAGCATACGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTTAACCCACAGAAATATCCGACAGATATTCAACGGGCAATTAATGAAACACATCAAGGGTTCTATCAATTAGGAACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCAACGGTTTCGGAACATATGTGGTGTTTATTCCCAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAACGCATTAAGGCAGCGTATGCAGTTTTAAATGCAATAAAGGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006328","ARO_id":"44790","ARO_name":"ADC-154","CARD_short_name":"ADC-154","ARO_description":"ADC-154 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4225":{"model_id":"4225","model_name":"ADC-155","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6600":{"protein_sequence":{"accession":"WP_005128228.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTGTAGGYAKNKGKISFDDKPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYSADIQRAINETHQGRYQINTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLSAIKK"},"dna_sequence":{"accession":"NG_055285.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGGGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATAAGCCTGGTAAATATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAAGTTGTTGCTTTGTCTATGAATAAACCTTTCGATCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAGGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATACGGCGTCAAATCCACCTTACCGGATATGTTGAGTTTTATTCATGCCAATCTGAACCCACAAAAATATTCGGCAGATATTCAACGTGCAATTAATGAAACACATCAGGGTCGCTATCAAATAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAGCCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCAACGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAGTGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006329","ARO_id":"44791","ARO_name":"ADC-155","CARD_short_name":"ADC-155","ARO_description":"ADC-155 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4241":{"model_id":"4241","model_name":"ADC-173","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6616":{"protein_sequence":{"accession":"WP_032071188.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVKTDQQVLTFFKDWKPKNSIGEYRQYSNPSIGLFGKVVALSMNKPIDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNRGPLDAAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_056164.1","fmin":"100","fmax":"1255","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAGTATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAATTTCCAGATGAAGTAAAAACAGATCAGCAAGTTTTAACATTTTTTAAAGACTGGAAACCTAAAAACTCAATCGGTGAATATCGACAATATTCAAACCCAAGCATTGGTTTATTTGGAAAAGTTGTAGCTTTGTCTATGAATAAACCTATCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCGCGGCCCACTCGATGCCGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTAAATCCACAAAAATATCCAGCAGATATTCAACGGGCAATTAATGAAACACATCAGGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006345","ARO_id":"44807","ARO_name":"ADC-173","CARD_short_name":"ADC-173","ARO_description":"ADC-173 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4242":{"model_id":"4242","model_name":"ADC-174","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6617":{"protein_sequence":{"accession":"WP_114699268.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKVLKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPEYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGFYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTTGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_061390.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACCCCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCATTATTAGAAAAATATGATGTGCCGGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGTGCTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGTCCACTCGATGCCCCAGAATACGGCGTCAAATCCACCTTACCGGATATGTTGAGTTTTATTCATGCCAACCTCAACCCACAGAAATATCCGGCAGATATTCAACGGGCAATTAATGAAACACATCAAGGGTTCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCACCGGTTTCGGAACATATGTGGTCTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006346","ARO_id":"44808","ARO_name":"ADC-174","CARD_short_name":"ADC-174","ARO_description":"ADC-174 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4243":{"model_id":"4243","model_name":"ADC-175","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6618":{"protein_sequence":{"accession":"WP_001211208.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNRSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWQPKNPIGEYRQYSNPSIGLFRKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGFYQVNTMYQALGWEEFSYPATLQTLLDSSSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLDAIKK"},"dna_sequence":{"accession":"NG_061391.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATCGCAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGCAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTAGAAAGGTTGTGGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCATTTGGTTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCTGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTTAACCCACAGAAATATCCGGCTGATATTCAACGGGCAATTAATGAAACACATCAAGGGTTCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAGTTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCAACGGTTTCGGAACATATGTAGTGTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGGATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006347","ARO_id":"44809","ARO_name":"ADC-175","CARD_short_name":"ADC-175","ARO_description":"ADC-175 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4244":{"model_id":"4244","model_name":"ADC-176","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6619":{"protein_sequence":{"accession":"WP_001159761.1","sequence":"MQFKKISCLLLSPLFIFSTSIYADNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGFYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_061392.1","fmin":"0","fmax":"1167","strand":"+","sequence":"ATGCAATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGACAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCATTATTAGAAAAATATGATGTGCCGGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAGCTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTCCCAGATGAAGTACAAACAGATCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTGTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCCCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTTAACCCACAGAAATATCCGGCAGATATTCAACGGGCAATTAATGAAACACATCAAGGGTTCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACATATGTAGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006348","ARO_id":"44810","ARO_name":"ADC-176","CARD_short_name":"ADC-176","ARO_description":"ADC-176 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4245":{"model_id":"4245","model_name":"ADC-177","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6620":{"protein_sequence":{"accession":"WP_114699269.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALKFPDEVKTDQQVLTFFKDWKPKNSIGEYQQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTTGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_061393.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAGTATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGAAATTTCCAGATGAAGTAAAAACAGATCAGCAAGTTTTAACATTTTTTAAAGACTGGAAACCTAAAAACTCAATCGGTGAATATCAACAATATTCAAACCCAAGCATTGGTTTATTTGGAAAAGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTAAATCCACAAAAATATCCAGCAGATATTCAACGGGCAATTAATGAAACACATCAGGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTACCGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006349","ARO_id":"44811","ARO_name":"ADC-177","CARD_short_name":"ADC-177","ARO_description":"ADC-177 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4246":{"model_id":"4246","model_name":"ADC-178","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6621":{"protein_sequence":{"accession":"WP_114699270.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVKTDQQVLTFFKDWKPKNSIGEYRQYSNPSIGLFEKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_061394.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAGTATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAATTTCCAGATGAAGTAAAAACAGATCAGCAAGTTTTAACATTTTTTAAAGACTGGAAACCTAAAAACTCAATCGGTGAATATCGACAATATTCAAACCCAAGCATTGGTTTATTTGAAAAAGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTAAATCCACAAAAATATCCAGCAGATATTCAACGGGCAATTAATGAAACACATCAGGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006350","ARO_id":"44812","ARO_name":"ADC-178","CARD_short_name":"ADC-178","ARO_description":"ADC-178 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4247":{"model_id":"4247","model_name":"ADC-179","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6622":{"protein_sequence":{"accession":"WP_114699271.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDKPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQCRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_061395.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGACAAGCCTGGTAAATATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCCAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTAAATCCACAAAAATATCCAGCAGATATTCAACGGGCAATTAATGAAACACATCAGTGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCAACGGTTTCGGAACATATGTAGTGTTTATACCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006351","ARO_id":"44813","ARO_name":"ADC-179","CARD_short_name":"ADC-179","ARO_description":"ADC-179 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4248":{"model_id":"4248","model_name":"ADC-180","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6623":{"protein_sequence":{"accession":"WP_114699272.1","sequence":"MRFKKISCLLLSPLFIFSTSIYADNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSNTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQIQNYAFGYNQKNQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGFYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_061396.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGACAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCTGTAAATAGCAATACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAGTATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATACAAAACTATGCTTTTGGCTATAACCAAAAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGCTGAGTTTTATTCATGCCAATCTGAACCCACAGAAATATCCGGCTGATATTCAACGGGCAATTAATGAAACACATCAAGGGTTCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCAACGGTTTCGGAACATATGTAGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAAGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006352","ARO_id":"44814","ARO_name":"ADC-180","CARD_short_name":"ADC-180","ARO_description":"ADC-180 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4249":{"model_id":"4249","model_name":"ADC-184","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6624":{"protein_sequence":{"accession":"WP_059247009.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGIIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDKPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWQPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEETIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGFYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYIVFIPKENIGLVMLTNKRIPNEERIKAAYAVLSAIKK"},"dna_sequence":{"accession":"NG_064707.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCGTTATTAGAAAAATATGATGTGCCGGGTATGGCTGTGGGTATTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATAAGCCTGGTAAATATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAATTTACTTCAACTCGCGACGTATACAAGTGGCAACCTCGCTTTACAATTTCCAGATGAAGTACAAACAGATCAACAAGTTTTAACTTTTTTCAAAGACTGGCAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTGGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAGAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCATTTGGTTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCAACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTTAACCCACAGAAATATCCGGCTGATATTCAAAGGGCAATTAATGAAACACATCAAGGGTTCTATCAAGTAAATACCATGTATCAAGCGCTTGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAGCCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACATATATAGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAGTGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006353","ARO_id":"44815","ARO_name":"ADC-184","CARD_short_name":"ADC-184","ARO_description":"ADC-184 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4250":{"model_id":"4250","model_name":"ADC-185","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6625":{"protein_sequence":{"accession":"WP_001211210.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFNATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAVGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFINANLNPQKYPTDIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTTGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_064708.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCTCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTAACGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAGTATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTGTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATACGGCGTCAAATCCACCTTACCGGATATGTTGAGTTTTATTAATGCCAACCTTAACCCACAAAAATATCCGACAGATATTCAACGGGCAATTAATGAAACACATCAAGGTCGCTATCAAGTAAATACCATGTATCAAGCGCTTGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAGCCTAATAAAGTGACTGCTATTTCAAAAGAGCCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTACCGGTTTCGGAACATATGTAGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006354","ARO_id":"44816","ARO_name":"ADC-185","CARD_short_name":"ADC-185","ARO_description":"ADC-185 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4251":{"model_id":"4251","model_name":"ADC-186","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6626":{"protein_sequence":{"accession":"WP_072292271.1","sequence":"MQFKKISCLLLSPLFIFSTSIYADNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGFYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTSGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_064709.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCAATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGACAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCATTATTAGAAAAATATGATGTGCCGGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAGCTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTCCCAGATGAAGTACAAACAGATCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTGTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTTAACCCACAGAAATATCCGGCAGATATTCAACGGGCAATTAATGAAACACATCAAGGGTTCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAGCGGTTTCGGAACATATGTAGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006355","ARO_id":"44817","ARO_name":"ADC-186","CARD_short_name":"ADC-186","ARO_description":"ADC-186 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4252":{"model_id":"4252","model_name":"ADC-187","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6627":{"protein_sequence":{"accession":"WP_136512056.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNRSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWQPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLGAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGFYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNRFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLDAIKK"},"dna_sequence":{"accession":"NG_064710.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATCGCAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGCAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTGGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCATTTGGTTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGGTGCCCCTGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTTAACCCACAGAAATATCCGGCTGATATTCAACGGGCAATTAATGAAACACATCAAGGGTTCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCAACCGTTTCGGAACATATGTAGTGTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGGATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006356","ARO_id":"44818","ARO_name":"ADC-187","CARD_short_name":"ADC-187","ARO_description":"ADC-187 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4267":{"model_id":"4267","model_name":"ADC-202","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6642":{"protein_sequence":{"accession":"WP_150823456.1","sequence":"MRFKKISCLLLPPLFIFSTSIYAGNTQKEQEVKKLVDQNFKPLLDKYDVPGMAVGVIQNNKKYEIYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKAKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKTKNAIGEYRQYSNPSIGLFGKIVALSMNKPFDQVLEKTIFPPLHLKNSYVNVPKTQMQNYAYGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLTFINANLNPQKYPKDIQHAINETHQGFYQVGTMYQALGWEEFSYPAPLQTLLDSNSEQIVMKPNKVTAISKEPSVKMFHKTGSTNGFGSYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_066482.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGCTTACTTTTACCGCCTCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACAAAAAGAACAAGAAGTTAAAAAACTGGTAGATCAAAATTTTAAGCCTTTATTAGATAAATATGATGTGCCTGGTATGGCCGTGGGAGTCATTCAAAATAATAAAAAATATGAAATATATTATGGCCTACAATCCGTTCAGGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAACTAGGTTCGGTCAGTAAATTATTTACCGCTACAGCTGGTGGATATGCAAAAGCAAAAGGAAAAATCTCTTTTGATGACACACCCGGAAAATATTGGAAAGAACTAAAAAACACACCGATTGACCAAGTTAATCTACTTCAACTTGCGACGTATACAAGTGGCAACCTTGCTTTGCAATTTCCAGATGAAGTTCAAACAGACCAACAAGTTTTAACTTTTTTCAAAGATTGGAAAACTAAAAACGCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCTTATTTGGAAAAATTGTGGCTTTGTCTATGAATAAACCTTTTGACCAAGTCTTAGAAAAAACAATTTTTCCACCTCTCCATTTAAAAAATAGCTATGTAAATGTACCTAAAACTCAAATGCAAAATTATGCATATGGCTATAACCAAGAAAATCAGCCGATCCGAGTTAACCCTGGTCCGCTAGATGCCCCTGCGTACGGCGTTAAATCGACACTACCAGATATGCTGACTTTTATTAATGCCAACCTCAACCCACAGAAATATCCGAAAGATATTCAACATGCAATTAATGAAACACATCAAGGTTTCTATCAAGTCGGTACGATGTATCAAGCATTGGGTTGGGAAGAATTTTCTTATCCAGCGCCTTTACAAACTTTATTAGACAGTAATTCAGAGCAAATCGTGATGAAGCCTAATAAAGTGACTGCCATTTCCAAAGAACCTTCAGTTAAGATGTTCCACAAAACTGGCTCAACAAATGGCTTTGGATCTTATGTGGTGTTTATTCCAAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAACGCATTAAGGCAGCGTATGCAGTATTAAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3006371","ARO_id":"44833","ARO_name":"ADC-202","CARD_short_name":"ADC-202","ARO_description":"ADC-202 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4268":{"model_id":"4268","model_name":"ADC-203","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6643":{"protein_sequence":{"accession":"WP_032000414.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVSLSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVSAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_066483.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACCCCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTATCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCTGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTTAACCCACAGAAATATCCGGCTGATATTCAACGTGCAATTAATGAAACACATCAAGGTCGCTATCAAGTAAATACCATGTATCAAGCGCTTGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGTCTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACGTATGTGGTGTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006372","ARO_id":"44834","ARO_name":"ADC-203","CARD_short_name":"ADC-203","ARO_description":"ADC-203 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4269":{"model_id":"4269","model_name":"ADC-204","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6644":{"protein_sequence":{"accession":"WP_150823457.1","sequence":"MQFKKISCLLLSPLFIFSTSIYADNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFRKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGFYQVNTMYQALGWEEFSYPATLQTLLDSSSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_066484.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCAATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGACAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCATTATTAGAAAAATATGATGTGCCGGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAGCTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTCCCAGATGAAGTACAAACAGATCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTAGAAAGGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTGTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTTAACCCACAGAAATATCCGGCAGATATTCAACGGGCAATTAATGAAACACATCAAGGGTTCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAGTTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACATATGTAGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006373","ARO_id":"44835","ARO_name":"ADC-204","CARD_short_name":"ADC-204","ARO_description":"ADC-204 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4270":{"model_id":"4270","model_name":"ADC-205","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6645":{"protein_sequence":{"accession":"WP_150823458.1","sequence":"MRFKKISCLLLPPLFIFNTSIYAGNTPKEQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKSVNSNTIFELGSVSKLFTATAGGYAKTKGKISFEDTPGKYWKELKNTPIDQVNLLQLATYTSGNLGLQFPDEVQTDQQVLTFFKEWKPKNQIGEYRQYSNPSIGLFGKIVGLSMNQPFSHVLEKTIFPSLHLKNSYVNVPKTQMQNYAFGYNQKNQPIRVTPGPLDAPAYGVKSTLPDMLSFIDANLNPQKYPADIRRAIDETHKGFYQAGTMYQALGWEEFSYPAPLQTLLDSNSEQIVMKPNKVTAISKEPSIKMFHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_066485.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCCTGCTTACTTTTGCCGCCTCTTTTTATTTTTAATACCTCAATTTATGCAGGCAATACACCAAAAGAGCAAGAAATTAAAAAACTGGTTGATCAAAACTTTAAACCATTATTAGAAAAATATGATGTTCCTGGTATGGCGGTTGGTGTCATCCAAAACAATAAAAAGTACGAAATGTATTATGGACTACAATCGGTTCAAGATAAAAAATCCGTAAATAGCAATACCATTTTTGAGCTAGGTTCAGTCAGTAAATTATTTACTGCCACGGCAGGTGGATATGCCAAAACGAAAGGAAAAATCTCTTTTGAAGACACCCCAGGAAAATACTGGAAAGAGCTAAAAAATACACCGATTGACCAAGTTAACCTACTTCAACTGGCTACGTATACGAGTGGCAACCTTGGCTTACAATTCCCAGATGAAGTACAAACAGACCAGCAAGTTTTAACTTTTTTCAAAGAATGGAAACCTAAAAATCAAATCGGTGAATATCGACAATATTCAAACCCAAGTATTGGCTTATTTGGAAAAATTGTAGGCTTATCGATGAATCAGCCTTTTAGTCATGTTTTAGAAAAGACAATTTTTCCGTCTCTTCACTTAAAAAATAGCTATGTAAATGTGCCTAAAACTCAGATGCAAAACTATGCATTTGGCTATAACCAAAAAAATCAGCCGATTCGAGTTACCCCAGGCCCACTAGATGCGCCTGCCTACGGGGTTAAATCTACATTACCAGACATGCTTAGCTTTATTGATGCCAATCTAAATCCACAAAAATATCCGGCAGATATTCGACGCGCAATTGATGAGACTCATAAAGGTTTTTATCAAGCCGGTACGATGTATCAAGCATTAGGTTGGGAAGAGTTCTCTTATCCAGCACCTTTGCAAACTTTATTAGACAGTAATTCTGAACAAATCGTGATGAAGCCTAATAAAGTGACTGCCATTTCCAAAGAACCTTCAATCAAGATGTTCCATAAAACTGGTTCAACTAACGGATTTGGAACTTATGTCGTGTTTATTCCCAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGCATTCCAAATGAAGAACGTATTAAAGCGGCTTATGCTGTACTAAATGCGATTAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39094","NCBI_taxonomy_name":"Acinetobacter calcoaceticus","NCBI_taxonomy_id":"471"}}}},"ARO_accession":"3006374","ARO_id":"44836","ARO_name":"ADC-205","CARD_short_name":"ADC-205","ARO_description":"ADC-205 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4271":{"model_id":"4271","model_name":"ADC-206","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6646":{"protein_sequence":{"accession":"WP_150823459.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLDKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVSSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPDLGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLKFINANLNPQKYPADIQRAINETHQGFYQVGTMYQALGWEEFSYPAPLQTLLDSNSEQIVMKPNKVTAISKEPSVKMFHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_066486.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCTTTATTAGATAAATATGATGTGCCGGGTATGGCCGTGGGTGTTATTCAGAATAATAAAAAGTATGAAATGTATTATGGTCTACAATCTGTTCAAGATAAAAAAGCCGTAAGTAGCAGTACCATTTTTGAACTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCAACGTATACAAGTGGTAACCTTGCCTTGCAGTTCCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAAGTTGTTGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCAGATCTGGGATTAAAACATAGTTATGTAAATGTGCCTAAAACTCAGATGCAAAACTATGCTTTTGGCTATAATCAAGAAAATCAGCCAATTCGTGTTAACCCTGGTCCGCTAGATGCTCCAGCATACGGCGTTAAATCGACACTACCAGACATGCTTAAGTTTATTAATGCCAACCTAAATCCACAAAAATATCCAGCAGATATTCAACGTGCAATTAATGAAACACATCAAGGTTTCTATCAAGTCGGCACCATGTATCAAGCATTAGGTTGGGAAGAATTTTCTTATCCAGCGCCTTTACAAACTTTATTAGACAGTAATTCAGAACAAATTGTGATGAAGCCTAATAAAGTGACTGCTATTTCAAAAGAACCTTCAGTTAAGATGTTCCACAAAACTGGCTCAACCAATGGTTTCGGAACATATGTCGTGTTCATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAACGCATTAAAGCAGCGTATGCAGTATTAAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3006375","ARO_id":"44837","ARO_name":"ADC-206","CARD_short_name":"ADC-206","ARO_description":"ADC-206 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4272":{"model_id":"4272","model_name":"ADC-207","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6647":{"protein_sequence":{"accession":"WP_130173437.1","sequence":"MRFNKISYLLISPLFIFNTSIYAGNTPKEQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYETYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKTKGTIFFKDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQLLEKTIFPDLGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLKFINANLNPQKYPKDIQRAINETHQGFYQVGTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTTISKEPSVKMFHKTGSTNGFGTYVVFIPKENIGLVVLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_066487.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAACAAAATTTCTTACTTACTTATATCCCCTCTTTTTATTTTTAATACCTCAATTTATGCAGGGAATACACCAAAAGAGCAAGAAATTAAGAAACTAGTTGATCAAAATTTTAAACCGTTATTAGAAAAATATGATGTACCCGGTATGGCGGTTGGCGTCATCCAAAATAATAAAAAGTATGAAACGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTCGGTTCAGTCAGTAAATTATTTACCGCAACAGCAGGTGGATATGCCAAAACAAAAGGAACAATCTTTTTTAAAGACACACCCGGAAAATATTGGAAAGAACTAAAGAATACACCGATTGATCAGGTTAACTTACTTCAACTTGCTACCTATACAAGTGGTAACCTTGCTTTGCAATTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGGAAAGTTGTGGCTTTGTCTATGAATAAACCTTTCGACCAACTCTTAGAAAAAACTATTTTTCCAGATCTTGGCTTAAAACATAGCTATGTAAATGTTCCTAAAACTCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCAATTCGTGTTAACCCTGGCCCACTCGATGCTCCAGCATACGGCGTCAAATCGACGCTACCCGATATGCTTAAGTTTATTAATGCCAACCTCAACCCACAGAAATATCCGAAAGATATTCAACGTGCAATTAATGAAACACATCAAGGTTTCTATCAAGTCGGCACCATGTATCAAGCGCTTGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAAATTGTGATGAAGCCTAATAAAGTGACGACCATTTCTAAAGAACCTTCAGTTAAGATGTTCCACAAAACTGGCTCAACCAATGGTTTCGGAACTTATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCGTGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCAGTTTTAAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3006376","ARO_id":"44838","ARO_name":"ADC-207","CARD_short_name":"ADC-207","ARO_description":"ADC-207 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4273":{"model_id":"4273","model_name":"ADC-208","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6648":{"protein_sequence":{"accession":"WP_150823460.1","sequence":"MQFKKISCLLLPPLFIFSSSIYAGNTPKEQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSNTIFELGSVSKLFTATAGGYAKTKGTISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVKTDQQVLTFFKEWKPKNSIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPDLGLKHSYINLPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFINANLNPQKYPADIQRAINETHQGFYQVGTMYQALGWEEFSYPAPLQTLLDSNSEQIVMKPNKVTAISKEPSVKMFHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_066488.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCAATTTAAAAAAATTTCTTGCTTACTTTTACCTCCTCTTTTTATTTTTAGTAGCTCAATTTATGCGGGTAATACACCAAAAGAGCAAGAAATCAAAAAACTGGTTGATCAAAATTTTAAGCCTTTATTAGAAAAATATGATGTGCCCGGTATGGCTGTGGGCGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTACAATCCGTTCAAGATAAAAAAGCCGTTAATAGCAATACCATTTTTGAGCTAGGCTCGGTCAGTAAATTATTTACCGCTACAGCAGGCGGATATGCCAAAACAAAAGGAACAATCTCTTTTGATGACACGCCCGGAAAATATTGGAAAGAACTAAAAAATACACCGATTGATCAAGTGAATTTACTTCAACTTGCGACATATACCAGTGGCAACCTTGCCTTACAATTTCCAGATGAAGTAAAAACAGATCAACAAGTTTTAACGTTTTTCAAAGAATGGAAACCTAAAAACTCAATCGGTGAATATCGACAATATTCAAACCCAAGCATTGGTTTATTTGGAAAAGTTGTTGCTTTGTCTATGAATAAACCTTTTGACCAAGTCTTGGAAAAAACCATTTTTCCAGATCTTGGCTTAAAACATAGCTATATAAATTTGCCTAAAACTCAAATGCAAAACTATGCATTTGGCTATAACCAAGAAAATCAGCCGATTCGCGTTAATCCTGGTCCACTCGATGCGCCAGCATACGGCGTTAAATCTACCCTACCGGATATGCTGAGTTTTATTAATGCCAACCTAAATCCACAAAAATATCCAGCAGATATTCAACGTGCAATTAATGAAACACATCAAGGTTTCTACCAAGTGGGTACGATGTATCAAGCACTAGGTTGGGAAGAGTTTTCTTATCCAGCACCTTTACAAACTTTATTAGACAGTAATTCAGAACAAATCGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAACCTTCAGTTAAAATGTTCCACAAAACTGGCTCAACCAACGGTTTTGGAACATATGTCGTGTTCATTCCAAAAGAAAATATTGGTTTAGTCATGTTAACTAATAAACGTATTCCCAATGAAGAACGCATTAAAGCAGCTTATGCTGTGTTAAATGCGATTAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3006377","ARO_id":"44839","ARO_name":"ADC-208","CARD_short_name":"ADC-208","ARO_description":"ADC-208 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4274":{"model_id":"4274","model_name":"ADC-209","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6649":{"protein_sequence":{"accession":"WP_150823461.1","sequence":"MRFQKISCLLLSPLFIFSTSIYAGNTLKEQEIKKLVDQNFKPLLEKYNVPGMAVGIIQNNKKYETYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKTKRTLSFEDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKEWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPDLGLKHSYVSMPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFVNANLNPQKYPADIQRAINETHKGFYQVGTMYQALGWEEFFYPAPLQTLLDSNSEQIVMKPNKVTAISKEPSVKIFHKTGSTNGFGAYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_066489.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTCCAAAAAATTTCTTGCTTACTTTTATCCCCTCTTTTTATTTTTAGCACCTCAATTTATGCAGGTAATACACTAAAAGAACAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATAATGTGCCCGGTATGGCAGTTGGCATCATCCAGAATAATAAAAAGTATGAAACCTATTATGGTCTACAATCCGTTCAAGATAAAAAAGCTGTAAATAGCAGCACCATTTTTGAGCTAGGTTCAGTCAGTAAATTATTTACTGCGACGGCGGGTGGATATGCCAAAACAAAACGAACTCTCTCTTTTGAAGACACGCCCGGAAAATATTGGAAAGAACTAAAAAACACACCGATTGATCAAGTTAACTTACTTCAACTTGCGACATATACCAGCGGCAACCTTGCTTTGCAATTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGAATGGAAACCCAAAAACCCAATCGGTGAATATCGACAATATTCAAATCCAAGCATTGGTTTATTTGGAAAAGTTGTTGCTTTATCTATGAATAAACCTTTCGACCAAGTCTTGGAAAAAACCATTTTTCCAGATCTTGGCTTAAAACATAGTTATGTAAGTATGCCTAAAACTCAAATGCAAAACTATGCATTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCGCTAGATGCACCTGCGTACGGCGTGAAATCAACCTTACCGGATATGCTGAGTTTCGTTAACGCCAACCTCAACCCACAAAAATATCCGGCAGATATTCAACGCGCGATTAATGAAACGCATAAAGGCTTCTACCAAGTAGGCACGATGTATCAAGCATTAGGTTGGGAAGAGTTCTTTTATCCAGCACCTTTACAGACTTTATTAGACAGTAATTCAGAACAAATCGTGATGAAGCCTAATAAAGTGACTGCTATTTCAAAAGAACCCTCAGTTAAGATATTCCACAAAACTGGTTCAACCAACGGTTTTGGAGCCTATGTCGTGTTTATTCCAAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAACGTATTAAGGCAGCTTATGCTGTATTAAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3006378","ARO_id":"44840","ARO_name":"ADC-209","CARD_short_name":"ADC-209","ARO_description":"ADC-209 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4275":{"model_id":"4275","model_name":"ADC-210","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6650":{"protein_sequence":{"accession":"WP_150823462.1","sequence":"MQFKKISCLLLPPLFIFSSSIYAGNTPKEQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSNTIFELGSVSKLFTATAGGYAKTKGTISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVKTDQQVLTFFKEWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPDLGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFINANLNPQKYPANIQRAINETHQGFYQVGTMYQALGWEEFSYPALLQTLLDSNSEQIVMKPNKVTAISKEPSVKMFHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_066490.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCAATTTAAAAAAATTTCTTGCTTACTTTTACCTCCTCTTTTTATTTTTAGTAGCTCAATTTATGCGGGTAATACACCAAAAGAGCAAGAGATCAAAAAACTGGTTGATCAAAACTTTAAGCCTTTATTAGAAAAATACGATGTGCCCGGTATGGCTGTGGGCGTTATTCAAAATAACAAAAAGTATGAAATGTATTATGGTCTACAATCCGTTCAAGATAAAAAAGCCGTTAATAGCAATACCATTTTTGAGCTAGGCTCGGTCAGTAAATTATTTACCGCTACAGCAGGCGGATATGCCAAAACAAAAGGAACAATCTCTTTTGATGATACGCCCGGAAAATATTGGAAAGAACTAAAAAATACACCGATTGATCAAGTGAATTTACTTCAACTTGCGACATATACCAGTGGCAACCTTGCCTTGCAATTTCCAGATGAAGTAAAAACAGATCAGCAAGTTTTAACGTTTTTCAAAGAATGGAAACCTAAAAACCCAATCGGTGAATATCGACAATATTCAAACCCAAGCATTGGTTTATTTGGAAAAGTTGTTGCTTTGTCTATGAATAAACCTTTTGACCAAGTCTTGGAAAAAACCATTTTTCCAGATCTTGGCTTAAAACATAGCTATGTAAATGTGCCTAAAACTCAAATGCAAAACTATGCATTTGGCTATAACCAAGAAAATCAGCCGATTCGCGTCAATCCTGGTCCACTCGATGCACCAGCATACGGCGTTAAATCTACCCTACCGGATATGCTGAGTTTTATTAATGCAAACCTAAATCCACAAAAATATCCAGCAAATATTCAACGTGCAATTAATGAAACACATCAAGGTTTCTACCAAGTCGGCACCATGTATCAAGCACTAGGTTGGGAAGAGTTCTCTTATCCAGCACTTTTACAAACTTTATTAGACAGTAATTCAGAACAAATCGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAACCTTCCGTTAAGATGTTCCACAAAACTGGATCGACTAACGGTTTTGGAACATATGTCGTGTTCATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACTAATAAACGTATTCCCAATGAAGAACGCATTAAAGCAGCTTATGCTGTGTTAAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3006379","ARO_id":"44841","ARO_name":"ADC-210","CARD_short_name":"ADC-210","ARO_description":"ADC-210 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4276":{"model_id":"4276","model_name":"ADC-211","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6651":{"protein_sequence":{"accession":"WP_150823463.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFNATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAVGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPTDIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTTGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_066491.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCTCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTAACGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAGTATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTGTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATACGGCGTCAAATCCACCTTACCGGATATGTTGAGTTTTATTCATGCCAACCTTAACCCACAAAAATATCCGACAGATATTCAACGGGCAATTAATGAAACACATCAAGGTCGCTATCAAGTAAATACCATGTATCAAGCGCTTGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAGCCTAATAAAGTGACTGCTATTTCAAAAGAGCCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTACCGGTTTCGGAACATATGTAGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006380","ARO_id":"44842","ARO_name":"ADC-211","CARD_short_name":"ADC-211","ARO_description":"ADC-211 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4277":{"model_id":"4277","model_name":"ADC-212","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6652":{"protein_sequence":{"accession":"WP_031975357.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVKTDQQVLTFFKDWKPKNSIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYDFGYNQENQPIRVNPGPLDALAAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_066492.1","fmin":"85","fmax":"1240","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAGTATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAATTTCCAGATGAAGTAAAAACAGATCAGCAAGTTTTAACATTTTTTAAAGACTGGAAACCTAAAAACTCAATCGGTGAATATCGACAATATTCAAACCCAAGCATTGGTTTATTTGGAAAAGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGATTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCTAGCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTAAATCCACAAAAATATCCAGCAGATATTCAACGGGCAATTAATGAAACACATCAGGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006381","ARO_id":"44843","ARO_name":"ADC-212","CARD_short_name":"ADC-212","ARO_description":"ADC-212 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4278":{"model_id":"4278","model_name":"ADC-213","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6653":{"protein_sequence":{"accession":"WP_078230092.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVKTDQQVLTFFKDWKPKNSIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYDFGYNQENQPIRVNPGPLDSLAAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_066493.1","fmin":"99","fmax":"1254","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAGTATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAATTTCCAGATGAAGTAAAAACAGATCAGCAAGTTTTAACATTTTTTAAAGACTGGAAACCTAAAAACTCAATCGGTGAATATCGACAATATTCAAACCCAAGCATTGGTTTATTTGGAAAAGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGATTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATTCCCTAGCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTAAATCCACAAAAATATCCAGCAGATATTCAACGGGCAATTAATGAAACACATCAGGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006382","ARO_id":"44844","ARO_name":"ADC-213","CARD_short_name":"ADC-213","ARO_description":"ADC-213 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4279":{"model_id":"4279","model_name":"ADC-214","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6654":{"protein_sequence":{"accession":"WP_060454527.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTSIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWQPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVAKTQMQNYAFGYNQENQPIRVNPGPLDAPAYSVKSTLPDMLKFIHANLNPQKYPTDIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTTGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKE"},"dna_sequence":{"accession":"NG_066494.1","fmin":"86","fmax":"1238","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAACACATCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGCAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTGGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTAGCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATAGCGTCAAATCGACACTACCCGACATGCTTAAGTTTATTCATGCCAATCTGAACCCACAGAAATATCCGACAGATATTCAACGTGCAATTAATGAAACACATCAAGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCACCGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAACGCATTAAGGCAGCGTATGCAGTTTTAAATGCAATAAAGGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37046","NCBI_taxonomy_name":"Acinetobacter","NCBI_taxonomy_id":"469"}}}},"ARO_accession":"3006383","ARO_id":"44845","ARO_name":"ADC-214","CARD_short_name":"ADC-214","ARO_description":"ADC-214 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4280":{"model_id":"4280","model_name":"ADC-215","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6655":{"protein_sequence":{"accession":"WP_039098799.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTSIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWQPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVAKTQMQNYAFGYNQENQPIRANPAPLDASAYGVKSTLPDMLKFIHANLNPQKYPTDIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTTGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKE"},"dna_sequence":{"accession":"NG_066495.1","fmin":"86","fmax":"1238","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAACACATCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGCAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTGGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTAGCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGCTAACCCCGCCCCACTCGATGCCTCAGCATATGGCGTCAAATCGACACTACCCGACATGCTTAAGTTTATTCATGCCAATCTGAACCCACAGAAATATCCGACAGATATTCAACGTGCAATTAATGAAACACATCAAGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCACCGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAACGCATTAAGGCAGCGTATGCAGTTTTAAATGCAATAAAGGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006384","ARO_id":"44846","ARO_name":"ADC-215","CARD_short_name":"ADC-215","ARO_description":"ADC-215 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4281":{"model_id":"4281","model_name":"ADC-216","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6656":{"protein_sequence":{"accession":"WP_039211240.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGAYAKNKGKISFNDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVKTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKSFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQEKQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPAPLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_066496.1","fmin":"100","fmax":"1252","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGCTTATGCAAAAAATAAAGGAAAAATCTCTTTTAACGATACGCCTGGTAAATATTGGAAAGAGCTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTCCCAGATGAAGTAAAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTAGCTTTGTCTATGAATAAATCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAAACAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGTGTCAAATCGACACTACCCGACATGCTGAGTTTTATTCATGCCAACCTCAACCCACAGAAATATCCGGCAGATATTCAACGGGCAATTAATGAAACACATCAAGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCAGCACCTTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACGTATGTGGTCTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGCATTCCAAATGAAGAGCGTATTAAGGCAGCGTATGCAGTTTTAAATGCAATAAAAAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006385","ARO_id":"44847","ARO_name":"ADC-216","CARD_short_name":"ADC-216","ARO_description":"ADC-216 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4282":{"model_id":"4282","model_name":"ADC-217","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6657":{"protein_sequence":{"accession":"WP_060470109.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVKTDQQVLTFFKDWKPKNSIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQENTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTTGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_066497.1","fmin":"86","fmax":"1238","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAGTATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAATTTCCAGATGAAGTAAAAACAGATCAGCAAGTTTTAACATTTTTTAAAGACTGGAAACCTAAAAACTCAATCGGTGAATATCGACAATATTCAAACCCAAGCATTGGTTTATTTGGAAAAGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTAAATCCACAAAAATATCCAGCAGATATTCAACGGGCAATTAATGAAACACATCAGGGTCGCTATCAAGAAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTACCGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006386","ARO_id":"44848","ARO_name":"ADC-217","CARD_short_name":"ADC-217","ARO_description":"ADC-217 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4283":{"model_id":"4283","model_name":"ADC-218","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6658":{"protein_sequence":{"accession":"WP_078216190.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVKTDQQVLTFFKDWKPKNSIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYDFGYNQENQPIRVNPGPLDALAAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTTGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKE"},"dna_sequence":{"accession":"NG_066498.1","fmin":"99","fmax":"1254","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAGTATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAATTTCCAGATGAAGTAAAAACAGATCAGCAAGTTTTAACATTTTTTAAAGACTGGAAACCTAAAAACTCAATCGGTGAATATCGACAATATTCAAACCCAAGCATTGGTTTATTTGGAAAAGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGATTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCTAGCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTAAATCCACAAAAATATCCAGCAGATATTCAACGGGCAATTAATGAAACACATCAGGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCACCGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAACGCATTAAGGCAGCGTATGCAGTTTTAAATGCAATAAAGGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006387","ARO_id":"44849","ARO_name":"ADC-218","CARD_short_name":"ADC-218","ARO_description":"ADC-218 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4284":{"model_id":"4284","model_name":"ADC-219","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6659":{"protein_sequence":{"accession":"WP_039213353.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVKTDQQVLTFFKDWKPKNSIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNRGPLDAAPAYDVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_066499.1","fmin":"100","fmax":"1255","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAGTATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAATTTCCAGATGAAGTAAAAACAGATCAGCAAGTTTTAACATTTTTTAAAGACTGGAAACCTAAAAACTCAATCGGTGAATATCGACAATATTCAAACCCAAGCATTGGTTTATTTGGAAAAGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCGCGGCCCACTCGATGCCGCCCCAGCATATGACGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTAAATCCACAAAAATATCCAGCAGATATTCAACGGGCAATTAATGAAACACATCAGGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006388","ARO_id":"44850","ARO_name":"ADC-219","CARD_short_name":"ADC-219","ARO_description":"ADC-219 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4285":{"model_id":"4285","model_name":"ADC-220","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6660":{"protein_sequence":{"accession":"WP_087876534.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALKFPDEVKTDQQVLTFFKDWKPKNSIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYDFGYNQENQPIRVNPGPLDALAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_066500.1","fmin":"86","fmax":"1238","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAGTATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGAAATTTCCAGATGAAGTAAAAACAGATCAGCAAGTTTTAACATTTTTTAAAGACTGGAAACCTAAAAACTCAATCGGTGAATATCGACAATATTCAAACCCAAGCATTGGTTTATTTGGAAAAGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGATTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCTAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTAAATCCACAAAAATATCCAGCAGATATTCAACGGGCAATTAATGAAACACATCAGGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006389","ARO_id":"44851","ARO_name":"ADC-220","CARD_short_name":"ADC-220","ARO_description":"ADC-220 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4286":{"model_id":"4286","model_name":"ADC-221","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6661":{"protein_sequence":{"accession":"WP_156404644.1","sequence":"MRFKKISCLLLPPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLDKYNVPGMAVGVIQNNKKYETYYGLQSVQDKKAVSSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPSKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVAFSMNKPFDQVLEKTIFPGLGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLKFINANLNPQKYPADIQRAINETHKGFYQVGTMYQALGWEEFSYPAPLQTLLDSNSEQIVMKPNKVTAISKEPSVKMFHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_067133.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGCTTACTTTTACCTCCTCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCTTTATTAGATAAATATAATGTGCCGGGTATGGCTGTTGGCGTTATTCAGAATAATAAAAAATATGAAACGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAGTAGCAGTACCATTTTTGAACTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTAGTAAATATTGGAAAGAACTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCAACGTATACAAGTGGTAACCTTGCCTTGCAGTTCCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAAGTTGTTGCTTTCTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGGCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAATCAAGAAAATCAGCCAATTCGTGTTAACCCTGGTCCGCTAGATGCTCCAGCATACGGCGTCAAATCGACACTACCCGATATGCTTAAGTTTATTAATGCCAACCTAAATCCACAAAAATATCCAGCAGATATTCAACGTGCAATTAATGAAACACATAAAGGTTTCTATCAAGTCGGCACCATGTATCAAGCATTAGGTTGGGAAGAATTTTCTTATCCAGCGCCTTTACAAACTTTATTAGACAGTAATTCAGAGCAAATTGTGATGAAGCCTAATAAAGTGACTGCCATTTCAAAAGAACCTTCAGTTAAGATGTTCCACAAAACTGGTTCAACCAATGGTTTTGGAACATATGTCGTGTTCATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGCATTCCAAATGAAGAACGCATTAAAGCAGCGTATGCAGTATTAAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3006390","ARO_id":"44852","ARO_name":"ADC-221","CARD_short_name":"ADC-221","ARO_description":"ADC-221 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4287":{"model_id":"4287","model_name":"ADC-222","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6662":{"protein_sequence":{"accession":"WP_031960999.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKYSYVNVPKTQIQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLKFIHANLNPQKYPADIQRAINETHQGFYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_067193.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACCCCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCGGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTAGGTTCTGTTAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAGCTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTTGCTTTGTCTATGAATAAACCTTTCGATCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAATATAGTTATGTAAATGTGCCTAAAACTCAGATACAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAATCCTGGTCCACTCGATGCCCCAGCATATGGCGTCAAATCAACACTACCCGACATGCTTAAGTTTATTCATGCCAACCTTAACCCACAGAAATATCCGGCTGATATTCAAAGGGCAATTAATGAAACACATCAAGGGTTCTATCAAGTAAATACCATGTATCAAGCGCTTGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACGTATGTGGTCTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006391","ARO_id":"44853","ARO_name":"ADC-222","CARD_short_name":"ADC-222","ARO_description":"ADC-222 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4288":{"model_id":"4288","model_name":"ADC-223","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6663":{"protein_sequence":{"accession":"WP_064987478.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVKTDQQVLTFFKDWKPKNSIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPKVTAISKEPSVKMYHKTGSTTGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_067194.1","fmin":"0","fmax":"1149","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAGTATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAATTTCCAGATGAAGTAAAAACAGATCAGCAAGTTTTAACATTTTTTAAAGACTGGAAACCTAAAAACTCAATCGGTGAATATCGACAATATTCAAACCCAAGCATTGGTTTATTTGGAAAAGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTAAATCCACAAAAATATCCAGCAGATATTCAACGGGCAATTAATGAAACACATCAGGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTACCGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006392","ARO_id":"44854","ARO_name":"ADC-223","CARD_short_name":"ADC-223","ARO_description":"ADC-223 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4289":{"model_id":"4289","model_name":"ADC-224","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6664":{"protein_sequence":{"accession":"WP_064907831.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVKTDQQVLTFFKDWKPKNSIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNRGPLNAAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_067195.1","fmin":"0","fmax":"1155","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAGTATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAATTTCCAGATGAAGTAAAAACAGATCAGCAAGTTTTAACATTTTTTAAAGACTGGAAACCTAAAAACTCAATCGGTGAATATCGACAATATTCAAACCCAAGCATTGGTTTATTTGGAAAAGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCGCGGCCCACTCAATGCCGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTAAATCCACAAAAATATCCAGCAGATATTCAACGGGCAATTAATGAAACACATCAGGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006393","ARO_id":"44855","ARO_name":"ADC-224","CARD_short_name":"ADC-224","ARO_description":"ADC-224 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4290":{"model_id":"4290","model_name":"ADC-225","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6665":{"protein_sequence":{"accession":"WP_160164833.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVKTDQQVLTFFKDWKPKNSIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNRGPLNAAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIGMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_067196.1","fmin":"0","fmax":"1155","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAGTATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAATTTCCAGATGAAGTAAAAACAGATCAGCAAGTTTTAACATTTTTTAAAGACTGGAAACCTAAAAACTCAATCGGTGAATATCGACAATATTCAAACCCAAGCATTGGTTTATTTGGAAAAGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCGCGGCCCACTCAATGCCGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTAAATCCACAAAAATATCCAGCAGATATTCAACGGGCAATTAATGAAACACATCAGGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGGGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006394","ARO_id":"44856","ARO_name":"ADC-225","CARD_short_name":"ADC-225","ARO_description":"ADC-225 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4291":{"model_id":"4291","model_name":"ADC-226","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6666":{"protein_sequence":{"accession":"WP_001211224.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVKTDQQVLTFFKDWKPKNSIGEYRQYSNPSIGLFRKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSTSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_067197.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAGTATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAATTTCCAGATGAAGTAAAAACAGATCAGCAAGTTTTAACATTTTTTAAAGACTGGAAACCTAAAAACTCAATCGGTGAATATCGACAATATTCAAACCCAAGCATTGGTTTATTTAGAAAAGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTAAATCCACAAAAATATCCAGCAGATATTCAACGGGCAATTAATGAAACACATCAGGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTACTTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006395","ARO_id":"44857","ARO_name":"ADC-226","CARD_short_name":"ADC-226","ARO_description":"ADC-226 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4292":{"model_id":"4292","model_name":"ADC-227","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6667":{"protein_sequence":{"accession":"WP_160164834.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVKTDQQVLTFFKDWKPKNSIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNRGPLDAAPAYGVKSTLPDMLKFIHANLNPQKYPTDIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIWMKPNKVTAISKEPSVKMYHKTGSTTGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKE"},"dna_sequence":{"accession":"NG_067198.1","fmin":"0","fmax":"1155","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAGTATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAATTTCCAGATGAAGTAAAAACAGATCAGCAAGTTTTAACATTTTTTAAAGACTGGAAACCTAAAAACTCAATCGGTGAATATCGACAATATTCAAACCCAAGCATTGGTTTATTTGGAAAAGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCGCGGCCCACTCGATGCCGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGCTTAAGTTTATTCATGCCAATCTGAACCCACAGAAATATCCGACAGATATTCAACGTGCAATTAATGAAACACATCAAGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTTGGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCACCGGTTTCGGAACATATGTAGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAACGCATTAAGGCAGCGTATGCAGTTTTAAATGCAATAAAGGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006396","ARO_id":"44858","ARO_name":"ADC-227","CARD_short_name":"ADC-227","ARO_description":"ADC-227 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4293":{"model_id":"4293","model_name":"ADC-228","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6668":{"protein_sequence":{"accession":"WP_160164835.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVKTDQQVLTFFKDWKPKNSIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPILVNRGPLDAAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_067199.1","fmin":"0","fmax":"1155","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAGTATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAATTTCCAGATGAAGTAAAAACAGATCAGCAAGTTTTAACATTTTTTAAAGACTGGAAACCTAAAAACTCAATCGGTGAATATCGACAATATTCAAACCCAAGCATTGGTTTATTTGGAAAAGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCTAGTTAACCGCGGCCCACTCGATGCCGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTAAATCCACAAAAATATCCAGCAGATATTCAACGGGCAATTAATGAAACACATCAGGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006397","ARO_id":"44859","ARO_name":"ADC-228","CARD_short_name":"ADC-228","ARO_description":"ADC-228 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4294":{"model_id":"4294","model_name":"ADC-229","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6669":{"protein_sequence":{"accession":"WP_160164836.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVKTDQQVLTFFKDWKPKNSIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYDVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTTGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_067200.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAGTATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAATTTCCAGATGAAGTAAAAACAGATCAGCAAGTTTTAACATTTTTTAAAGACTGGAAACCTAAAAACTCAATCGGTGAATATCGACAATATTCAAACCCAAGCATTGGTTTATTTGGAAAAGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGACGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTAAATCCACAAAAATATCCAGCAGATATTCAACGGGCAATTAATGAAACACATCAGGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTACCGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006398","ARO_id":"44860","ARO_name":"ADC-229","CARD_short_name":"ADC-229","ARO_description":"ADC-229 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4295":{"model_id":"4295","model_name":"ADC-230","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6670":{"protein_sequence":{"accession":"WP_160164837.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTSIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWQPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVAKTQMQNYAFGYNQENQPIRVNPGPLDAPAYSVKSTLPDMLKFIHANLNPQKYPTDIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDNNSEQIVMKPNKVTAISKEPSVKMYHKTGSTTGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKE"},"dna_sequence":{"accession":"NG_067201.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAACACATCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGCAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTGGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTAGCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATAGCGTCAAATCGACACTACCCGACATGCTTAAGTTTATTCATGCCAATCTGAACCCACAGAAATATCCGACAGATATTCAACGTGCAATTAATGAAACACATCAAGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAATAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCACCGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAACGCATTAAGGCAGCGTATGCAGTTTTAAATGCAATAAAGGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006399","ARO_id":"44861","ARO_name":"ADC-230","CARD_short_name":"ADC-230","ARO_description":"ADC-230 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4296":{"model_id":"4296","model_name":"ADC-231","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6671":{"protein_sequence":{"accession":"WP_160164838.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALKFPDEVKTDQQVLTFFKDWKPKNSIGEYRQYSNPSIGLFRKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_067202.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAGTATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGAAATTTCCAGATGAAGTAAAAACAGATCAGCAAGTTTTAACATTTTTTAAAGACTGGAAACCTAAAAACTCAATCGGTGAATATCGACAATATTCAAACCCAAGCATTGGTTTATTTAGAAAAGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTAAATCCACAAAAATATCCAGCAGATATTCAACGGGCAATTAATGAAACACATCAGGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006400","ARO_id":"44862","ARO_name":"ADC-231","CARD_short_name":"ADC-231","ARO_description":"ADC-231 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4297":{"model_id":"4297","model_name":"ADC-232","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6672":{"protein_sequence":{"accession":"WP_064907116.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVKTDQQVLTFFKDWKPKNSIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNFAFGYNQENQPIRVNRGPLDAAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_067203.1","fmin":"0","fmax":"1155","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAGTATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAATTTCCAGATGAAGTAAAAACAGATCAGCAAGTTTTAACATTTTTTAAAGACTGGAAACCTAAAAACTCAATCGGTGAATATCGACAATATTCAAACCCAAGCATTGGTTTATTTGGAAAAGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTTTGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCGCGGCCCACTCGATGCCGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTAAATCCACAAAAATATCCAGCAGATATTCAACGGGCAATTAATGAAACACATCAGGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006401","ARO_id":"44863","ARO_name":"ADC-232","CARD_short_name":"ADC-232","ARO_description":"ADC-232 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4298":{"model_id":"4298","model_name":"ADC-233","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6673":{"protein_sequence":{"accession":"WP_031950434.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVKTDQQVLTFFKDWKPKNSIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNRGPLDAAPSYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_067204.1","fmin":"0","fmax":"1155","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAGTATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAATTTCCAGATGAAGTAAAAACAGATCAGCAAGTTTTAACATTTTTTAAAGACTGGAAACCTAAAAACTCAATCGGTGAATATCGACAATATTCAAACCCAAGCATTGGTTTATTTGGAAAAGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCGCGGCCCACTCGATGCCGCCCCATCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTAAATCCACAAAAATATCCAGCAGATATTCAACGGGCAATTAATGAAACACATCAGGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006402","ARO_id":"44864","ARO_name":"ADC-233","CARD_short_name":"ADC-233","ARO_description":"ADC-233 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4299":{"model_id":"4299","model_name":"ADC-234","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6674":{"protein_sequence":{"accession":"WP_159162532.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWQPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVPGPLDAPAYGVKSTLPDMLSFIHANLTPQKYPTDIQRAINETHQGFYQVGTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLDAIKK"},"dna_sequence":{"accession":"NG_067978.1","fmin":"10","fmax":"1159","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCATTATTAGAAAAATATGATGTACCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAGCTAAAAAATACACCGATTGATCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGCAACCTCGCTTTACAATTTCCAGATGAAGTACAAACAGATCAACAAGTTTTAACTTTTTTCAAAGACTGGCAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTGGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTCCCGGCCCACTTGATGCCCCAGCATACGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTTACCCCACAGAAATATCCGACAGATATTCAACGGGCAATTAATGAAACACATCAAGGGTTCTATCAAGTCGGCACCATGTATCAGGCACTTGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCAACGGTTTCGGAACATATGTGGTCTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGGATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006403","ARO_id":"44865","ARO_name":"ADC-234","CARD_short_name":"ADC-234","ARO_description":"ADC-234 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4300":{"model_id":"4300","model_name":"ADC-235","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6675":{"protein_sequence":{"accession":"WP_132038428.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWQPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPASPAYGVKSTLPDMLSFIHANLTPQKYPTDIQRAINETHQGFYQVGTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTTTGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_067979.1","fmin":"10","fmax":"1174","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCATTATTAGAAAAATATGATGTACCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAGCTAAAAAATACACCGATTGATCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGCAACCTCGCTTTACAATTTCCAGATGAAGTACAAACAGATCAACAAGTTTTAACTTTTTTCAAAGACTGGCAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTGGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTTGATGCCCCAGCATCCCCAGCATACGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTTACCCCACAGAAATATCCGACAGATATTCAACGGGCAATTAATGAAACACATCAAGGGTTCTATCAAGTCGGCACCATGTATCAGGCACTTGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCACCACCGGTTTCGGAACATATGTGGTCTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006404","ARO_id":"44866","ARO_name":"ADC-235","CARD_short_name":"ADC-235","ARO_description":"ADC-235 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4301":{"model_id":"4301","model_name":"ADC-236","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6676":{"protein_sequence":{"accession":"WP_176673601.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTSIDQVNLLQLATYTSGNLALRFPDEVQTDQQVLTFFKDWQPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVAKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLKFIHANLNPQKYPTDIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTTGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKE"},"dna_sequence":{"accession":"NG_070226.1","fmin":"100","fmax":"1252","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAACACATCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCGGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGCAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTGGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTAGCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGCTTAAGTTTATTCATGCCAATCTGAACCCACAGAAATATCCGACAGATATTCAACGTGCAATTAATGAAACACATCAAGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCACCGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAACGCATTAAGGCAGCGTATGCAGTTTTAAATGCAATAAAGGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006405","ARO_id":"44867","ARO_name":"ADC-236","CARD_short_name":"ADC-236","ARO_description":"ADC-236 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4302":{"model_id":"4302","model_name":"ADC-237","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6677":{"protein_sequence":{"accession":"WP_086262823.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGAYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPTDIQRAINETHQGFYQLETMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKE"},"dna_sequence":{"accession":"NG_071183.1","fmin":"100","fmax":"1252","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGCTTATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAGCTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTCCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACTCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATACGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTTAACCCACAGAAATATCCGACAGATATTCAACGGGCAATTAATGAAACACATCAAGGGTTCTATCAATTAGAAACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACATATGTCGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAACGCATTAAGGCAGCGTATGCAGTTTTAAATGCAATAAAGGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006406","ARO_id":"44868","ARO_name":"ADC-237","CARD_short_name":"ADC-237","ARO_description":"ADC-237 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4303":{"model_id":"4303","model_name":"ADC-238","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6678":{"protein_sequence":{"accession":"WP_002058891.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSITIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLSAIKK"},"dna_sequence":{"accession":"NG_071184.1","fmin":"100","fmax":"1252","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTACGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCATTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCTTATTTGGAAAAGTTGTTGCTTTGTCTATGAATAAACCTTTCGATCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCTGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTTAACCCACAGAAATATCCGGCTGATATTCAAAGGGCAATTAATGAAACACATCAAGGTCGCTATCAAGTAAATACCATGTATCAAGCGCTTGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCAACGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAGTGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006407","ARO_id":"44869","ARO_name":"ADC-238","CARD_short_name":"ADC-238","ARO_description":"ADC-238 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4304":{"model_id":"4304","model_name":"ADC-239","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6679":{"protein_sequence":{"accession":"WP_031981814.1","sequence":"MRFKKISYLLLPSLFIFNTSIYAGNTSKDQEIKQLVDQNFKPLLEKYNVPGMAVGVIQNNKKYETYYGLQSVQDKKAVNSNTIFELGSVSKLFTATAGAYAKNTGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGEIVGLSMKQPFSQVLEKTIFPDLGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPANIQRAINETHQGRYQVNSMYQALGWEEFAYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYAVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_071185.1","fmin":"100","fmax":"1252","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTACTTACTTTTACCTTCTCTTTTTATTTTTAATACCTCAATTTATGCGGGCAATACTTCTAAAGACCAAGAAATTAAACAATTGGTAGATCAAAATTTTAAACCCTTATTAGAAAAATATAATGTGCCGGGTATGGCGGTAGGTGTTATTCAAAACAATAAAAAATATGAAACGTATTATGGTCTACAATCCGTTCAAGATAAAAAAGCTGTAAATAGCAATACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACTGCGACGGCAGGTGCTTATGCAAAAAATACAGGAAAAATCTCTTTTGATGATACGCCGGGCAAATACTGGAAAGAGTTAAAAAACACCCCAATTGATCAGGTCAATTTACTTCAACTTGCCACCTATACAAGTGGTAACCTCGCTTTGCAATTCCCAGATGAAGTACAAACAGATCAACAGGTTTTAACTTTTTTTAAAGATTGGAAACCTAAAAACCCTATCGGTGAATATAGACAATATTCAAACCCAAGTATTGGCCTATTTGGGGAAATAGTTGGTTTATCAATGAAGCAGCCTTTTAGTCAGGTCTTGGAAAAAACGATTTTTCCGGACCTTGGCTTAAAACATAGCTATGTCAATGTGCCTAAAACTCAGATGCAAAACTATGCATTTGGCTATAACCAAGAAAATCAGCCAATTCGAGTTAACCCTGGCCCACTCGATGCCCCAGCATACGGCGTCAAATCGACCCTACCCGACATGCTGAGCTTTATTCATGCCAACCTGAACCCACAGAAATATCCGGCAAATATTCAACGTGCAATTAATGAGACACATCAAGGTCGCTATCAAGTAAATAGCATGTATCAGGCACTCGGTTGGGAAGAGTTTGCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAACCTTCAGTTAAGATGTACCACAAAACTGGTTCAACAAATGGTTTCGGAACCTATGCCGTATTTATACCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGCATTCCAAATGAAGAACGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40550","NCBI_taxonomy_name":"Acinetobacter calcoaceticus\/baumannii complex","NCBI_taxonomy_id":"909768"}}}},"ARO_accession":"3006408","ARO_id":"44870","ARO_name":"ADC-239","CARD_short_name":"ADC-239","ARO_description":"ADC-239 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4305":{"model_id":"4305","model_name":"ADC-24","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6680":{"protein_sequence":{"accession":"WP_136512061.1","sequence":"MRFKKISCLLLSPLFIFNTSIYAGNTSKEQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKKLKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNSIGEYRQYSNPSIGLFGKVVAVSMNKPFDQVLEKTIFPDLGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLKFINANLNPQKYPKDIQRAINETHQGFYQVGTMYQALGWEEFSYPALLQTLLDSNSEQIVMKPNKVTAISKEPSVKMFHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_064717.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGCTTACTTTTATCTCCTCTTTTTATTTTTAATACATCAATTTATGCGGGCAATACATCAAAAGAACAAGAAATTAAAAAACTGGTAGATCAGAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCTGTAAATAGCAGTACCATTTTTGAGCTAGGTTCAGTTAGTAAATTATTTACCGCAACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAAAACTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCAACGTATACAAGTGGTAACCTTGCCTTGCAGTTCCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACTCAATCGGTGAATATAGACAATATTCAAATCCAAGCATTGGTTTATTTGGAAAAGTTGTGGCAGTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCAGATCTTGGCTTAAAACATAGCTATGTAAATGTTCCTAAAACTCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCAATTCGTGTTAACCCTGGTCCACTAGATGCTCCAGCATATGGGGTTAAATCGACGCTACCCGATATGCTTAAGTTTATTAATGCCAACCTCAACCCACAGAAATATCCGAAAGATATTCAACGTGCAATTAATGAAACACATCAAGGTTTCTACCAAGTCGGCACGATGTATCAGGCACTTGGTTGGGAAGAATTTTCTTATCCAGCGCTTTTACAAACTTTATTAGACAGTAATTCAGAACAAATTGTGATGAAGCCTAATAAAGTGACTGCCATTTCAAAAGAACCTTCAGTTAAGATGTTCCACAAAACTGGTTCAACCAATGGTTTCGGAACTTATGTCGTGTTCATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAACGCATTAAGGCAGCGTATGCAGTATTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3006409","ARO_id":"44871","ARO_name":"ADC-24","CARD_short_name":"ADC-24","ARO_description":"ADC-24 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4306":{"model_id":"4306","model_name":"ADC-240","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6681":{"protein_sequence":{"accession":"WP_001211207.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNRSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWQPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGFYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTTGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLDAIKK"},"dna_sequence":{"accession":"NG_071186.1","fmin":"86","fmax":"1238","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATCGCAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGCAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTGGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCATTTGGTTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCTGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTTAACCCACAGAAATATCCGGCTGATATTCAACGGGCAATTAATGAAACACATCAAGGGTTCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCACCGGTTTCGGAACATATGTAGTGTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGGATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006410","ARO_id":"44872","ARO_name":"ADC-240","CARD_short_name":"ADC-240","ARO_description":"ADC-240 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4307":{"model_id":"4307","model_name":"ADC-241","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6682":{"protein_sequence":{"accession":"WP_001211198.1","sequence":"MRFKKISCLLFSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVAKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLSAIKK"},"dna_sequence":{"accession":"NG_071187.1","fmin":"100","fmax":"1252","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTCTCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCTTATTTGGAAAAGTTGTTGCTTTGTCTATGAATAAACCTTTCGATCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTAGCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTTAACCCACAGAAATATCCGGCTGATATTCAAAGGGCAATTAATGAAACACATCAAGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCAACGGTTTCGGAACATATGTCGTGTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAGTGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006411","ARO_id":"44873","ARO_name":"ADC-241","CARD_short_name":"ADC-241","ARO_description":"ADC-241 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4308":{"model_id":"4308","model_name":"ADC-242","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6683":{"protein_sequence":{"accession":"WP_047481394.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGIIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPTDIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_071188.1","fmin":"100","fmax":"1252","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCGTTATTAGAAAAATATGATGTGCCGGGTATGGCTGTGGGTATTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATACGGCGTCAAATCCACCTTACCGGATATGTTGAGTTTTATTCATGCCAACCTTAACCCACAAAAATATCCGACAGATATTCAACGGGCAATTAATGAAACACATCAAGGTCGCTATCAAGTAAATACCATGTATCAAGCGCTTGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAGCCTAATAAAGTGACTGCTATTTCAAAAGAGCCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACATATGTAGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006412","ARO_id":"44874","ARO_name":"ADC-242","CARD_short_name":"ADC-242","ARO_description":"ADC-242 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4309":{"model_id":"4309","model_name":"ADC-243","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6684":{"protein_sequence":{"accession":"WP_001211199.1","sequence":"MRFKKISCLLLPPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPINQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKFVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPTDIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLSAIKK"},"dna_sequence":{"accession":"NG_071189.1","fmin":"100","fmax":"1252","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGCTTACTTTTACCTCCTCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTAGGTTCTGTTAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAGCTAAAAAATACACCGATTAACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTCCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGTTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATACGGCGTCAAATCCACCTTACCGGATATGTTAAGTTTTATTCATGCCAACCTTAACCCACAGAAATATCCGACAGATATTCAACGGGCAATTAATGAAACACATCAAGGTCGCTATCAAGTAAATACCATGTATCAAGCGCTTGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCAACGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAGTGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006413","ARO_id":"44875","ARO_name":"ADC-243","CARD_short_name":"ADC-243","ARO_description":"ADC-243 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4310":{"model_id":"4310","model_name":"ADC-244","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6685":{"protein_sequence":{"accession":"WP_032017586.1","sequence":"MRFKKISCLLLSPLFIFSTSIYADNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHSNLNPQKYPKDIQRAINETHQGFYQVNTMYQALGWEDFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_071190.1","fmin":"100","fmax":"1252","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGACAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCATTATTAGAAAAATATGATGTGCCGGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAGCTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTCCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATACGGCGTCAAATCGACACTACCCGACATGCTGAGTTTTATTCATTCCAATCTGAACCCACAGAAATATCCGAAAGATATTCAACGTGCAATTAATGAAACACATCAAGGGTTCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGATTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCAACGGTTTCGGAACATATGTGGTCTTTATTCCTAAAGAAAACATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006414","ARO_id":"44876","ARO_name":"ADC-244","CARD_short_name":"ADC-244","ARO_description":"ADC-244 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4311":{"model_id":"4311","model_name":"ADC-245","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6686":{"protein_sequence":{"accession":"WP_032005249.1","sequence":"MRFNKISCLLLSPLFIFNTSIYAGNTSKEQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKKLKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNSIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPDLGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLKFINANLNPQKYPKDIQRAINETHQGFYQVGTMYQALGWEEFSYPALLQTLLDSNSEQIVMKPNKVTAISKEPSVKMFHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_071191.1","fmin":"100","fmax":"1252","strand":"+","sequence":"ATGCGATTTAACAAGATTTCTTGCTTACTTTTATCTCCTCTTTTTATTTTTAATACATCAATTTATGCGGGCAATACATCAAAAGAACAAGAAATTAAAAAACTGGTAGATCAGAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCTGTAAATAGCAGTACCATTTTTGAGCTAGGTTCAGTTAGTAAATTATTTACCGCAACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAAAACTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCAACGTATACAAGTGGTAACCTTGCCTTGCAGTTCCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACTCAATCGGTGAATATAGACAATATTCAAATCCAAGCATTGGTTTATTTGGAAAAGTTGTGGCATTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCAGATCTTGGCTTAAAACATAGCTATGTAAATGTTCCTAAAACTCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCAATTCGTGTTAACCCTGGTCCACTAGATGCTCCAGCATATGGGGTTAAATCGACGCTACCCGATATGCTTAAGTTTATTAATGCCAACCTCAACCCACAGAAATATCCGAAAGATATTCAACGTGCAATTAATGAAACACATCAAGGTTTCTACCAAGTCGGCACGATGTATCAGGCACTTGGTTGGGAAGAATTTTCTTATCCAGCGCTTTTACAAACTTTATTAGACAGTAATTCAGAACAAATTGTGATGAAGCCTAATAAAGTGACTGCCATTTCAAAAGAACCTTCAGTTAAGATGTTCCACAAAACTGGTTCAACCAATGGTTTCGGAACTTATGTCGTGTTCATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAACGCATTAAGGCAGCGTATGCAGTATTAAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40550","NCBI_taxonomy_name":"Acinetobacter calcoaceticus\/baumannii complex","NCBI_taxonomy_id":"909768"}}}},"ARO_accession":"3006415","ARO_id":"44877","ARO_name":"ADC-245","CARD_short_name":"ADC-245","ARO_description":"ADC-245 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4312":{"model_id":"4312","model_name":"ADC-246","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6687":{"protein_sequence":{"accession":"WP_031976577.1","sequence":"MRFKKISCLLLSPLFIFSTSIYADNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNEKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDKPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWQPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVAKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLSAIKK"},"dna_sequence":{"accession":"NG_071192.1","fmin":"100","fmax":"1252","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGACAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATGAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGACAAGCCTGGTAAATATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAATTTACTTCAACTCGCGACGTATACAAGTGGCAACCTCGCTTTACAATTTCCAGATGAAGTACAAACAGATCAACAAGTTTTAACTTTTTTCAAAGACTGGCAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTGGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTAGCTAAGACCCAGATGCAAAACTATGCATTTGGTTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTTAACCCACAGAAATATCCGGCTGATATTCAAAGGGCAATTAATGAAACACATCAAGGTCGCTATCAAGTAAATACCATGTATCAAGCGCTTGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCAACGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAGTGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006416","ARO_id":"44878","ARO_name":"ADC-246","CARD_short_name":"ADC-246","ARO_description":"ADC-246 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4313":{"model_id":"4313","model_name":"ADC-247","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6688":{"protein_sequence":{"accession":"WP_032058755.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWQPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIYANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKE"},"dna_sequence":{"accession":"NG_071193.1","fmin":"100","fmax":"1252","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCATTATTAGAAAAATATGATGTGCCGGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGCAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTGGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCCACCTTACCGGATATGTTGAGTTTTATTTATGCCAACCTTAACCCACAGAAATATCCGGCAGATATTCAACGTGCAATTAATGAAACACATCAGGGTCGCTATCAAGTAAATACCATGTATCAAGCGCTTGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCAACGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAACGCATTAAGGCAGCGTATGCAGTTTTAAATGCAATAAAGGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006417","ARO_id":"44879","ARO_name":"ADC-247","CARD_short_name":"ADC-247","ARO_description":"ADC-247 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4314":{"model_id":"4314","model_name":"ADC-248","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6689":{"protein_sequence":{"accession":"WP_021511005.1","sequence":"MRFKKISCLLLSPLFIFSTSIYADNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFKDTPGKYWKELKNTPINQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGHYQVNTMYQALGWEEFSYPAMLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYTVLNAIKK"},"dna_sequence":{"accession":"NG_071194.1","fmin":"100","fmax":"1252","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGACAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTAGGTTCTGTTAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTAAAGACACACCCGGAAAATATTGGAAAGAGCTAAAAAATACACCGATTAACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTCCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCTTATTTGGAAAAGTTGTTGCTTTGTCTATGAATAAACCTTTCGATCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACTCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATACGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTTAACCCACAGAAATATCCGGCAGATATTCAACGGGCAATTAATGAAACACATCAGGGTCACTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAATGTTACAAACTTTACTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACGTATGTGGTGTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCGTATACAGTTTTAAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006418","ARO_id":"44880","ARO_name":"ADC-248","CARD_short_name":"ADC-248","ARO_description":"ADC-248 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4315":{"model_id":"4315","model_name":"ADC-249","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6690":{"protein_sequence":{"accession":"WP_001211200.1","sequence":"MRFKKISCLLLSPLFIFSTSIYADNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPINQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGHYQVNTMYQALGWEEFSYPAMLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYTVLNAIKK"},"dna_sequence":{"accession":"NG_071195.1","fmin":"100","fmax":"1252","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGACAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTAGGTTCTGTTAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAGCTAAAAAATACACCGATTAACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTCCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCTTATTTGGAAAAGTTGTTGCTTTGTCTATGAATAAACCTTTCGATCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACTCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATACGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTTAACCCACAGAAATATCCGGCAGATATTCAACGGGCAATTAATGAAACACATCAGGGTCACTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAATGTTACAAACTTTACTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACGTATGTGGTGTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAAGCAGCGTATACAGTTTTAAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006419","ARO_id":"44881","ARO_name":"ADC-249","CARD_short_name":"ADC-249","ARO_description":"ADC-249 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4316":{"model_id":"4316","model_name":"ADC-250","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6691":{"protein_sequence":{"accession":"WP_086329657.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVKTDQQVLTFFKDWKPKNSIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDATPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_071196.1","fmin":"86","fmax":"1241","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAGTATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAATTTCCAGATGAAGTAAAAACAGATCAGCAAGTTTTAACATTTTTTAAAGACTGGAAACCTAAAAACTCAATCGGTGAATATCGACAATATTCAAACCCAAGCATTGGTTTATTTGGAAAAGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCACCCCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTAAATCCACAAAAATATCCAGCAGATATTCAACGGGCAATTAATGAAACACATCAGGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006420","ARO_id":"44882","ARO_name":"ADC-250","CARD_short_name":"ADC-250","ARO_description":"ADC-250 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4317":{"model_id":"4317","model_name":"ADC-251","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6692":{"protein_sequence":{"accession":"WP_086443396.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDRPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWQPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFINANLNPQKYPTDIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_071197.1","fmin":"100","fmax":"1252","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCATTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATAGGCCTGGTAAATATTGGAAAGAACTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGCAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCTTATTTGGAAAAGTTGTTGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATACGGCGTCAAATCCACCTTACCGGATATGTTGAGTTTTATTAATGCCAACCTTAACCCACAAAAATATCCGACAGATATTCAACGGGCAATTAATGAAACACATCAAGGTCGCTATCAAGTAAATACCATGTATCAAGCGCTTGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAGCCTAATAAAGTGACTGCTATTTCAAAAGAGCCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACATATGTAGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006421","ARO_id":"44883","ARO_name":"ADC-251","CARD_short_name":"ADC-251","ARO_description":"ADC-251 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4318":{"model_id":"4318","model_name":"ADC-252","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6693":{"protein_sequence":{"accession":"WP_086399847.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDREIKKLVDQNFKPLLDKYDVPGMAVGVIQNNKKYETYYGLQSVQDKKSVSSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKEWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQILEKTIFPGLGLKHSYVIVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLKFINANLNPQKYPKDIQRAINETHQGFYQVGTMYQALGWEEFSYPAPLQTLLDSNSEQIVMKPNKVTAISKEPSVKMFHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_071198.1","fmin":"100","fmax":"1252","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCTCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCGAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCTTTATTAGATAAATATGATGTGCCAGGTATGGCCGTGGGCGTTATTCAGAATAATAAAAAATATGAAACGTATTATGGTCTTCAATCTGTTCAAGATAAAAAATCCGTAAGTAGCAGTACCATTTTTGAACTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCAACGTATACAAGTGGTAACCTTGCCTTGCAGTTCCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGAATGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAAGTTGTTGCTTTGTCTATGAATAAACCTTTCGACCAAATCTTAGAAAAAACAATTTTTCCGGGCCTTGGCTTAAAACATAGCTATGTAATTGTACCGAAGACCCAGATGCAAAACTATGCTTTTGGCTATAATCAAGAAAATCAGCCAATTCGTGTTAACCCTGGTCCGTTAGATGCACCTGCGTACGGCGTCAAATCGACACTACCCGATATGCTTAAGTTTATTAATGCCAACCTCAACCCACAGAAATATCCGAAAGATATTCAACGTGCAATTAATGAAACACATCAGGGTTTCTATCAAGTCGGCACCATGTATCAGGCACTTGGTTGGGAAGAATTTTCTTATCCAGCGCCTTTACAAACTTTATTAGACAGTAATTCAGAACAAATTGTGATGAAGCCTAATAAAGTGACTGCCATTTCAAAAGAACCTTCAGTTAAGATGTTCCACAAAACTGGTTCAACCAATGGTTTCGGAACTTATGTCGTGTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTGACCAATAAACGTATTCCAAATGAAGAACGCATTAAGGCAGCGTATGCGGTGTTAAATGCAATAAAAAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3006422","ARO_id":"44884","ARO_name":"ADC-252","CARD_short_name":"ADC-252","ARO_description":"ADC-252 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4319":{"model_id":"4319","model_name":"ADC-253","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6694":{"protein_sequence":{"accession":"WP_086394244.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLDKYDVPGMAVGVIQNNKKYEMYYGLQSIQDKKAVSSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNSIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPDLGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNSGPLDAPAYGVKSTLPDMLKFINANLNPQKYPKDIQRAINETHQGFYHVGTMYQALGWEEFSYPAPLQTLLDSNSEQIVMKSNKVTAISKEPSVKMFHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_071199.1","fmin":"100","fmax":"1252","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCGTTATTAGATAAATATGATGTGCCGGGTATGGCCGTGGGTGTTATTCAGAATAATAAAAAGTATGAAATGTATTATGGTCTACAATCTATTCAAGATAAAAAAGCCGTAAGTAGCAGTACCATTTTTGAACTAGGTTCAGTTAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCAACGTATACAAGTGGTAACCTTGCCTTGCAGTTCCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACTCAATCGGTGAATATAGACAATATTCAAATCCAAGCATTGGTTTATTTGGAAAAGTTGTGGCATTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCAGATCTGGGCTTAAAACATAGCTATGTAAATGTTCCTAAAACTCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCAATTCGTGTTAACTCTGGTCCGCTAGATGCCCCAGCATACGGCGTCAAATCGACACTACCCGATATGCTTAAGTTTATTAATGCCAACCTCAACCCACAGAAATATCCGAAAGATATTCAACGTGCAATTAATGAAACACATCAAGGTTTCTATCATGTCGGCACCATGTATCAGGCACTTGGTTGGGAAGAATTTTCTTATCCAGCGCCTTTACAAACTTTATTAGACAGTAATTCAGAACAAATTGTGATGAAGTCTAATAAAGTGACTGCCATTTCAAAAGAACCTTCAGTTAAGATGTTCCACAAAACTGGTTCAACCAATGGTTTTGGAACTTATGTCGTATTCATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAACGCATTAAGGCAGCGTATGCCGTGTTAAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3006423","ARO_id":"44885","ARO_name":"ADC-253","CARD_short_name":"ADC-253","ARO_description":"ADC-253 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4320":{"model_id":"4320","model_name":"ADC-254","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6695":{"protein_sequence":{"accession":"WP_031996777.1","sequence":"MRFKKISCLLLPSLFIFNTSIYAGTISKDQEIKQLVDQNFKPLLEKYNVPGMAVGVIQNNKKYETYYGLQSVQDKKAVNSSTIFELGSVSKLFTATTGTYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPGEVQTDQQVLTFFKDWQSKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVTPGPLDAPAYGVKSTLPDMLNFIHANLNPQKYPADIQSAINETHQGFYQVGTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVSAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_071200.1","fmin":"100","fmax":"1252","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGCTTACTTTTACCTTCTCTTTTTATTTTTAATACCTCAATTTATGCAGGCACTATCTCTAAAGATCAAGAAATTAAACAATTAGTAGATCAAAACTTTAAACCCTTATTAGAAAAATATAATGTGCCGGGTATGGCGGTAGGCGTTATTCAAAATAATAAAAAGTATGAAACGTATTATGGTCTACAATCCGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTAGGTTCCGTTAGTAAATTATTTACCGCGACAACAGGTACTTATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAACACGCCAATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGCAACCTCGCTTTACAATTTCCAGGTGAAGTACAAACAGATCAACAAGTTTTAACTTTTTTCAAAGACTGGCAATCTAAAAATCCAATTGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTCAATGTGCCTAAAACTCAAATGCAAAACTATGCATTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTACCCCTGGCCCACTCGATGCTCCAGCATACGGTGTTAAATCAACTCTACCGGATATGCTTAATTTTATTCATGCCAACCTAAACCCACAGAAATATCCGGCAGATATTCAAAGCGCAATTAATGAAACACATCAAGGTTTCTATCAAGTAGGTACCATGTATCAGGCACTTGGTTGGGAAGAGTTTTCTTATCCTGCAACCTTACAAACTTTATTAGACAGTAATTCAGAACAAATTGTGATGAAACCTAATAAAGTGAGTGCTATTTCAAAAGAACCTTCAGTTAAGATGTACCATAAAACAGGTTCTACCAACGGTTTTGGAACGTATGTCGTATTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGCATTCCAAACGAAGAACGTATTAAGGCGGCTTATGCTGTGTTGAATGCGATAAAAAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006424","ARO_id":"44886","ARO_name":"ADC-254","CARD_short_name":"ADC-254","ARO_description":"ADC-254 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4321":{"model_id":"4321","model_name":"ADC-255","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6696":{"protein_sequence":{"accession":"WP_022575343.1","sequence":"MQFKKISYLLLPSLFIFNTSIYAGNTSKDQEIKQLIDQNFKPLLEKYNVPGMAVGVIQNNKKYETYYGLQSVQDKKAVNSNTIFELGSVSKLFTATAGAYAKNTGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGEIVGLSMKQPFSQVLEKTIFPDLGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNSMYQALGWEEFAYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_071201.1","fmin":"100","fmax":"1252","strand":"+","sequence":"ATGCAATTTAAAAAAATTTCTTACTTACTTTTACCTTCTCTTTTTATTTTTAATACCTCAATTTATGCGGGCAATACTTCTAAAGACCAAGAAATTAAACAATTGATAGATCAAAATTTTAAACCCTTATTAGAAAAATATAATGTGCCGGGTATGGCGGTAGGTGTTATTCAAAACAATAAAAAATATGAAACGTATTATGGCCTACAATCCGTTCAAGATAAAAAAGCTGTAAATAGCAATACCATTTTTGAGCTAGGTTCTGTCAGTAAGTTATTTACTGCGACGGCAGGTGCTTATGCAAAAAATACAGGAAAAATCTCTTTTGATGATACGCCGGGCAAATACTGGAAAGAGTTAAAAAACACCCCAATTGATCAGGTCAATTTACTTCAACTTGCCACCTATACAAGTGGTAACCTCGCCTTGCAATTCCCAGATGAAGTACAAACAGATCAACAGGTTTTAACTTTTTTTAAAGATTGGAAACCTAAAAACCCAATCGGTGAATATAGACAATATTCAAACCCAAGTATTGGCCTATTTGGGGAAATAGTTGGTTTATCAATGAAGCAGCCTTTTAGTCAGGTCTTGGAAAAAACGATTTTTCCGGACCTTGGCTTAAAACATAGCTATGTCAATGTGCCTAAAACTCAGATGCAAAACTATGCATTTGGCTATAACCAAGAAAATCAGCCAATTCGAGTTAACCCTGGCCCACTCGATGCCCCAGCATACGGCGTCAAATCGACCCTACCCGACATGCTGAGCTTTATTCATGCCAACCTGAACCCACAAAAATATCCGGCTGATATTCAACGGGCAATTAATGAGACACATCAAGGTCGCTATCAAGTAAATAGCATGTATCAGGCACTCGGTTGGGAAGAGTTTGCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTCATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAACCTTCAGTTAAGATGTACCACAAAACTGGTTCAACCAATGGTTTCGGAACCTATGTCGTCTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGCATTCCAAATGAAGAACGCATTAAGGCAGCTTATGCTGTGCTAAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36949","NCBI_taxonomy_name":"Acinetobacter nosocomialis","NCBI_taxonomy_id":"106654"}}}},"ARO_accession":"3006425","ARO_id":"44887","ARO_name":"ADC-255","CARD_short_name":"ADC-255","ARO_description":"ADC-255 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4322":{"model_id":"4322","model_name":"ADC-256","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6697":{"protein_sequence":{"accession":"WP_204376223.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKVLKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGFYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGTTSGFGTYVVFIPKENIGLVMLTNKRIPNKERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_073457.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACCCCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCATTATTAGAAAAATATGATGTGCCGGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGTGCTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGTCCACTCGATGCCCCAGCATACGGCGTCAAATCCACCTTACCGGATATGTTGAGTTTTATTCATGCCAACCTCAACCCACAGAAATATCCGGCAGATATTCAACGGGCAATTAATGAAACACATCAAGGGTTCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCACAACCAGCGGTTTCGGAACATATGTGGTCTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATAAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006426","ARO_id":"44888","ARO_name":"ADC-256","CARD_short_name":"ADC-256","ARO_description":"ADC-256 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4324":{"model_id":"4324","model_name":"ADC-29","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6699":{"protein_sequence":{"accession":"WP_069174569.1","sequence":"MQFKKISCLLLSPLFIFSTSIYADNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGFYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNRFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_051493.1","fmin":"100","fmax":"1252","strand":"+","sequence":"ATGCAATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGACAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCATTATTAGAAAAATATGATGTGCCGGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAGCTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTCCCAGATGAAGTACAAACAGATCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTGTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTTAACCCACAGAAATATCCGGCAGATATTCAACGGGCAATTAATGAAACACATCAAGGGTTCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACCGTTTCGGAACATATGTAGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006427","ARO_id":"44889","ARO_name":"ADC-29","CARD_short_name":"ADC-29","ARO_description":"ADC-29 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4325":{"model_id":"4325","model_name":"ADC-32","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6700":{"protein_sequence":{"accession":"WP_004739487.1","sequence":"MRFKKISCLLLSPLFIFSTSIYADNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPINQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKFVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPTDIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLSAIKK"},"dna_sequence":{"accession":"NG_050717.1","fmin":"100","fmax":"1252","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGACAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTAGGTTCTGTTAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAGCTAAAAAATACACCGATTAACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTCCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGTTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATACGGCGTCAAATCCACCTTACCGGATATGTTAAGTTTTATTCATGCCAACCTTAACCCACAGAAATATCCGACAGATATTCAACGGGCAATTAATGAAACACATCAAGGTCGCTATCAAGTAAATACCATGTATCAAGCGCTTGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCAACGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAGTGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006428","ARO_id":"44890","ARO_name":"ADC-32","CARD_short_name":"ADC-32","ARO_description":"ADC-32 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4326":{"model_id":"4326","model_name":"ADC-33","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6701":{"protein_sequence":{"accession":"WP_001211220.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVKTDQQVLTFFKDWKPKNSIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNRGPLDAAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_056059.1","fmin":"0","fmax":"1155","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAGTATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAATTTCCAGATGAAGTAAAAACAGATCAGCAAGTTTTAACATTTTTTAAAGACTGGAAACCTAAAAACTCAATCGGTGAATATCGACAATATTCAAACCCAAGCATTGGTTTATTTGGAAAAGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCGCGGCCCACTCGATGCCGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTAAATCCACAAAAATATCCAGCAGATATTCAACGGGCAATTAATGAAACACATCAGGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006429","ARO_id":"44891","ARO_name":"ADC-33","CARD_short_name":"ADC-33","ARO_description":"ADC-33 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4327":{"model_id":"4327","model_name":"ADC-38","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6702":{"protein_sequence":{"accession":"WP_063857799.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNRSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWQPKNPIGEYRQYSNPSIGLFRKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGFYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_048653.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACCCCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCGTTATTAGAAAAATATGATGTGCCGGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATCGCAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGCAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTAGAAAGGTTGTGGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCATTTGGTTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCTGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTTAACCCACAGAAATATCCGGCTGATATTCAACGGGCAATTAATGAAACACATCAAGGGTTCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCAACGGTTTCGGAACATATGTAGTGTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006430","ARO_id":"44892","ARO_name":"ADC-38","CARD_short_name":"ADC-38","ARO_description":"ADC-38 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4329":{"model_id":"4329","model_name":"ADC-51","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6704":{"protein_sequence":{"accession":"WP_063857805.1","sequence":"MRFKKISCLLLSPLFIFSTSIYADNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFRKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGFYQVNTMYQALGWEEFSYPATLQTLLDSSSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_048662.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGACAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCATTATTAGAAAAATATGATGTGCCGGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAGCTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTCCCAGATGAAGTACAAACAGATCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTAGAAAGGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTGTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTTAACCCACAGAAATATCCGGCAGATATTCAACGGGCAATTAATGAAACACATCAAGGGTTCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAGTTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACATATGTAGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006431","ARO_id":"44893","ARO_name":"ADC-51","CARD_short_name":"ADC-51","ARO_description":"ADC-51 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4330":{"model_id":"4330","model_name":"ADC-52","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6705":{"protein_sequence":{"accession":"WP_001211232.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTSIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWQPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVAKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLKFIHANLNPQKYPTDIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKE"},"dna_sequence":{"accession":"NG_048663.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAACACATCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGCAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTGGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTAGCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGCTTAAGTTTATTCATGCCAATCTGAACCCACAGAAATATCCGACAGATATTCAACGTGCAATTAATGAAACACATCAAGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCAACGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAACGCATTAAGGCAGCGTATGCAGTTTTAAATGCAATAAAGGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006432","ARO_id":"44894","ARO_name":"ADC-52","CARD_short_name":"ADC-52","ARO_description":"ADC-52 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4331":{"model_id":"4331","model_name":"ADC-53","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6706":{"protein_sequence":{"accession":"WP_063857806.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKVLKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGESRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRANPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPTDIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTTGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_048664.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACCCCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCGTTATTAGAAAAATATGATGTGCCGGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGTGCTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATCCAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGCTAACCCCGGCCCACTCGATGCCCCAGCATACGGTGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTTAACCCACAGAAATATCCGACAGATATTCAACGGGCAATTAATGAAACACATCAAGGTCGCTATCAAGTAAATACCATGTATCAAGCGCTTGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTACCGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGTATTAAGGCAGCGTATGCAGTTTTAAATGCAATAAAAAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006433","ARO_id":"44895","ARO_name":"ADC-53","CARD_short_name":"ADC-53","ARO_description":"ADC-53 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4332":{"model_id":"4332","model_name":"ADC-54","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6707":{"protein_sequence":{"accession":"WP_063857807.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKVLKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPTDIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYIVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_048665.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACCCCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCATTATTAGAAAAATATGATGTGCCGGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGTGCTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTAGCTTTGTCTATGAATAAACCTTTCGATCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATACGGCGTCAAATCCACCTTACCGGATATGTTGAGTTTTATTCATGCCAACCTTAACCCACAGAAATATCCGACAGATATTCAACGGGCAATTAATGAAACACATCAAGGTCGCTATCAAGTAAATACCATGTATCAAGCGCTTGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAGCCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACATATATAGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006434","ARO_id":"44896","ARO_name":"ADC-54","CARD_short_name":"ADC-54","ARO_description":"ADC-54 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4333":{"model_id":"4333","model_name":"ADC-57","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6708":{"protein_sequence":{"accession":"WP_001211226.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANFNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_051494.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCGGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCTTATTTGGAAAAGTTGTTGCTTTGTCTATGAATAAACCTTTCGATCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACTTCAACCCACAGAAATATCCGGCTGATATTCAACGGGCAATTAATGAAACACATCAAGGTCGCTATCAAGTAAATACCATGTATCAAGCGCTTGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAGCCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACATATGTAGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006435","ARO_id":"44897","ARO_name":"ADC-57","CARD_short_name":"ADC-57","ARO_description":"ADC-57 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4334":{"model_id":"4334","model_name":"ADC-63","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6709":{"protein_sequence":{"accession":"WP_063857812.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTGTAGGYAKNKGKISFDDKPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYSADIQRAINETHQGRYQINTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYVVLNAIKK"},"dna_sequence":{"accession":"NG_048673.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTTTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGGGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATAAGCCTGGTAAATATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAAGTTGTTGCTTTGTCTATGAATAAACCTTTCGATCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAGGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATACGGCGTCAAATCCACCTTACCGGATATGTTGAGTTTTATTCATGCCAATCTGAACCCACAAAAATATTCGGCAGATATTCAACGTGCAATTAATGAAACACATCAGGGTCGCTATCAAATAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAGCCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCAACGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGTTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006436","ARO_id":"44898","ARO_name":"ADC-63","CARD_short_name":"ADC-63","ARO_description":"ADC-63 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4335":{"model_id":"4335","model_name":"ADC-65","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6710":{"protein_sequence":{"accession":"WP_136512062.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVKTDQQVLTFFKDWKPKNSIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPASAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTTGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYVVLNAIKK"},"dna_sequence":{"accession":"NG_064718.1","fmin":"0","fmax":"1158","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAGTATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAATTTCCAGATGAAGTAAAAACAGATCAGCAAGTTTTAACATTTTTTAAAGACTGGAAACCTAAAAACTCAATCGGTGAATATCGACAATATTCAAACCCAAGCATTGGTTTATTTGGAAAAGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTAAATCCACAAAAATATCCAGCAGATATTCAACGGGCAATTAATGAAACACATCAGGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTACCGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGTTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006437","ARO_id":"44899","ARO_name":"ADC-65","CARD_short_name":"ADC-65","ARO_description":"ADC-65 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4336":{"model_id":"4336","model_name":"ADC-66","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6711":{"protein_sequence":{"accession":"WP_136512063.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGFQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGFYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYVVLNAIKK"},"dna_sequence":{"accession":"NG_064719.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTTTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTTTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGTCCACTCGATGCCCCAGCATATGGCGTCAAATCAACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTTAACCCACAGAAATATCCGGCTGATATTCAAAGGGCAATTAATGAAACACATCAAGGGTTCTATCAAGTAAATACCATGTATCAAGCGCTTGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACGTATGTGGTCTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGTTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006438","ARO_id":"44900","ARO_name":"ADC-66","CARD_short_name":"ADC-66","ARO_description":"ADC-66 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4337":{"model_id":"4337","model_name":"ADC-70","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6712":{"protein_sequence":{"accession":"WP_017480710.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDREIKKLVDQNFKPLLDKYDVPGMAVGVIQNNKKYETYYGLQSVQDKKSVSSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKEWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPGLGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFINANINPQKYPKDTQRAINETHQGFYQVGTMYQALGWEEFSYPAPLQTLLDSNSEQIVMKPNKVTAISKEPSVKMFHKTGSTNGFGSYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_051317.1","fmin":"100","fmax":"1252","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCGAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCTTTATTAGATAAATATGATGTGCCGGGTATGGCCGTGGGCGTTATTCAGAATAATAAAAAATATGAAACGTATTATGGTCTTCAATCTGTTCAAGATAAAAAATCCGTAAGTAGCAGTACCATTTTTGAACTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCAACGTATACAAGTGGTAACCTTGCCTTGCAGTTCCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGAATGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAAGTTGTTGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGGCCTTGGCTTAAAACATAGCTATGTAAATGTACCGAAGACCCAGATGCAAAACTATGCTTTTGGCTATAATCAAGAAAATCAGCCAATTCGTGTTAACCCCGGTCCGCTAGATGCTCCAGCATACGGTGTTAAATCGACCTTACCTGATATGCTGAGTTTCATTAATGCCAATATAAATCCACAAAAATATCCGAAAGATACTCAACGTGCAATTAATGAAACACATCAAGGTTTCTACCAAGTCGGCACGATGTATCAGGCACTTGGTTGGGAAGAATTTTCTTATCCAGCGCCTTTACAAACTTTATTAGACAGTAATTCAGAGCAAATCGTGATGAAGCCTAATAAAGTGACTGCCATTTCCAAAGAACCTTCAGTTAAGATGTTCCACAAAACTGGCTCAACAAATGGCTTTGGATCTTATGTGGTGTTTATTCCAAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAACGCATTAAGGCAGCGTATGCAGTATTAAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3006439","ARO_id":"44901","ARO_name":"ADC-70","CARD_short_name":"ADC-70","ARO_description":"ADC-70 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4338":{"model_id":"4338","model_name":"ADC-80","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6713":{"protein_sequence":{"accession":"WP_029424536.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKVLKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPTDIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYIVFIPKENIGLVMLTNKRIPNEERIKAAYAVLSAIKK"},"dna_sequence":{"accession":"NG_048686.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACCCCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCATTATTAGAAAAATATGATGTGCCGGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGTGCTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTAGCTTTGTCTATGAATAAACCTTTCGATCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATACGGCGTCAAATCCACCTTACCGGATATGTTGAGTTTTATTCATGCCAACCTTAACCCACAGAAATATCCGACAGATATTCAACGGGCAATTAATGAAACACATCAAGGTCGCTATCAAGTAAATACCATGTATCAAGCGCTTGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAGCCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACATATATAGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAGTGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37046","NCBI_taxonomy_name":"Acinetobacter","NCBI_taxonomy_id":"469"}}}},"ARO_accession":"3003886","ARO_id":"40585","ARO_name":"ADC-80","CARD_short_name":"ADC-80","ARO_description":"ADC-80 is a beta-lactamase found in Acinetobacter baumannii.","ARO_category":{"40543":{"category_aro_accession":"3003846","category_aro_cvterm_id":"40543","category_aro_name":"ADC beta-lactamase without carbapenemase activity","category_aro_description":"ADC beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases with extended-spectrum resistance to cephalosporins but not to carbapenems. ADC beta-lactamases are found in Acinetobacter sp. and Oligella urethralis.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4339":{"model_id":"4339","model_name":"ADC-83","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6714":{"protein_sequence":{"accession":"WP_068981615.1","sequence":"MRFKKISCLLLPSLFILNTSIYAGNTSKDQEIKQLVDQNFKPLLEKYNVPGMAVGVIQNNKKYEMYYGLQSVQDKKVVNSNTIFELGSVSKLFTATAGAYAKNKGKISFEDTPSKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWQPKNPIGEYRQYSNPSIGLFGKIVGLSMNQPFSQFLEKTIFPDLGLKHSYVNVPKTQIQNYAFGYNPENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQSAINETHKGFYQVGTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVSAISKEPSVKMFHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_051447.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGCTTACTTTTACCTTCTCTTTTTATTCTTAATACCTCAATTTATGCAGGTAATACCTCTAAAGATCAAGAAATTAAACAACTGGTAGATCAAAACTTTAAACCCTTATTAGAAAAATATAATGTGCCGGGTATGGCGGTAGGTGTTATTCAAAATAATAAAAAATATGAAATGTATTATGGTTTGCAGTCCGTTCAAGATAAAAAAGTCGTAAACAGCAATACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACTGCAACCGCAGGTGCCTATGCCAAAAATAAAGGAAAAATCTCTTTTGAAGACACACCAAGTAAATACTGGAAAGAACTCAAAAATACGCCAATTGATCAAGTTAACCTACTTCAACTTGCCACCTATACCAGTGGTAACCTTGCCCTTCAATTTCCAGATGAAGTACAAACAGATCAACAAGTTTTAACTTTTTTCAAAGACTGGCAACCTAAAAACCCAATTGGTGAATATAGACAATATTCAAACCCAAGTATTGGCCTATTTGGAAAAATTGTAGGCCTATCGATGAATCAGCCTTTTAGTCAGTTCCTAGAAAAGACAATTTTTCCAGACCTTGGCTTAAAACATAGCTATGTCAATGTGCCTAAAACCCAAATACAAAACTATGCATTTGGCTACAACCCAGAAAATCAGCCGATTCGCGTTAACCCCGGTCCACTCGATGCTCCAGCATACGGTGTTAAATCTACCTTGCCTGACATGCTAAGTTTTATTCATGCCAACCTGAACCCACAGAAATATCCGGCAGATATTCAAAGCGCAATTAATGAAACTCACAAAGGTTTCTATCAAGTAGGTACCATGTATCAAGCGCTTGGTTGGGAAGAGTTTTCTTATCCTGCAACCTTACAAACTTTATTAGACAGTAATTCAGAACAAATTGTGATGAAACCTAATAAAGTGAGTGCTATTTCAAAAGAACCTTCAGTTAAGATGTTCCATAAAACAGGTTCAACCAACGGTTTTGGAACCTATGTCGTATTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAACGTATTAAGGCTGCTTATGCTGTTTTGAATGCGATAAAAAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3006440","ARO_id":"44902","ARO_name":"ADC-83","CARD_short_name":"ADC-83","ARO_description":"ADC-83 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4340":{"model_id":"4340","model_name":"ADC-84","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6715":{"protein_sequence":{"accession":"WP_068981616.1","sequence":"MRFKKISCLLLPSLFILNTSIYAGNTSKDQGIKQLVDQNFKPLLEKYNVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSNTIFELGSVSKLFTATAGAYAKNKGKISFEDTPSKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKIVGLSMNQPFSQVLEKTIFPDLGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPTDIQSAINETHKGFYQVGTMYQALGWEEFSYPASLQTLLDSNSEQIVMKPNKVTAISNEPSVKMFHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_051448.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGCTTACTTTTACCTTCTCTTTTTATTCTTAATACCTCAATTTATGCAGGTAACACCTCTAAAGATCAAGGAATTAAACAACTGGTAGATCAAAACTTTAAACCCTTATTAGAAAAATATAATGTGCCGGGTATGGCAGTTGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGCTTGCAGTCCGTTCAAGATAAAAAAGCCGTAAATAGTAATACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACTGCAACCGCAGGTGCCTATGCCAAAAATAAAGGAAAAATCTCTTTTGAAGACACACCAAGTAAATACTGGAAAGAACTCAAAAATACGCCGATTGACCAAGTTAACCTACTTCAACTTGCCACCTATACCAGTGGTAACCTTGCCCTTCAATTTCCAGATGAAGTACAAACAGATCAACAAGTTTTAACTTTTTTCAAAGATTGGAAACCTAAAAACCCAATTGGTGAATATAGACAATATTCAAACCCAAGTATTGGCCTATTTGGAAAAATTGTAGGCCTATCGATGAATCAGCCTTTTAGTCAGGTTTTAGAAAAGACAATTTTTCCAGACCTTGGTTTAAAACATAGCTATGTCAATGTGCCTAAAACTCAAATGCAAAACTATGCATTTGGCTATAACCAAGAAAATCAGCCGATTCGCGTTAACCCCGGTCCACTCGATGCTCCAGCATATGGGGTTAAATCGACGCTACCAGATATGCTAAGTTTTATTCATGCCAACCTGAACCCACAGAAATATCCAACTGATATTCAAAGCGCAATTAATGAAACTCACAAAGGTTTCTACCAAGTAGGCACAATGTATCAAGCATTAGGTTGGGAAGAGTTCTCTTATCCAGCATCTTTACAGACTTTATTAGACAGTAATTCAGAACAAATCGTGATGAAGCCTAATAAAGTGACAGCTATTTCAAATGAACCTTCAGTTAAAATGTTTCACAAAACTGGTTCAACCAATGGCTTTGGAACATACGTCGTATTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAACGAAGAACGCATTAAGGCGGCTTATGCTGTGCTAAATGCGATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006441","ARO_id":"44903","ARO_name":"ADC-84","CARD_short_name":"ADC-84","ARO_description":"ADC-84 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4341":{"model_id":"4341","model_name":"ADC-85","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6716":{"protein_sequence":{"accession":"WP_068981617.1","sequence":"MRFNKISCLLLSPLFIFNTSIYAGNTPKEQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYETYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGAYAKNKGKISFKDTPGKYWKELKNTPIDQVNLLQLATYTSGNLGLQFPDEVQTDQQVLTFFKDWKPKSSIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPDLSLKHSYVNVPKTQMQNYAFGYNQQNQPIRVNPGPLDGPAYGVKSTLPDMLGFVHANLNPQQYPADIQRAINETHKGFYQVGTMYQALGWEEFSYPATLQTLLDSNSDQIVMKPNKVTAISKEPSVKIFHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_051449.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAACAAAATTTCTTGCTTACTTTTATCCCCTCTTTTTATTTTTAATACCTCAATTTATGCAGGTAATACACCAAAAGAGCAAGAAATTAAGAAACTGGTTGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTACCCGGTATGGCTGTTGGCGTCATCCAAAATAATAAAAAGTATGAAACGTATTATGGTTTACAATCCGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTCGGTTCAGTTAGTAAATTATTTACCGCTACAGCAGGTGCTTATGCTAAAAACAAGGGAAAAATCTCTTTTAAAGACACACCTGGAAAATATTGGAAAGAATTAAAAAACACACCGATTGATCAAGTTAACTTACTTCAACTTGCAACATATACAAGTGGCAACCTTGGCTTACAGTTTCCAGATGAAGTCCAAACAGATCAGCAAGTTTTAACTTTTTTCAAAGACTGGAAGCCTAAGAGCTCAATCGGTGAATATCGACAATATTCAAATCCAAGCATTGGTTTATTTGGAAAAGTTGTTGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACTATTTTTCCAGATCTTAGCTTAAAACATAGTTATGTAAATGTGCCTAAAACTCAGATGCAAAACTATGCATTTGGCTATAACCAACAAAATCAGCCGATTCGAGTTAACCCCGGCCCCTTAGATGGTCCAGCTTACGGCGTTAAATCGACACTACCAGACATGTTGGGGTTTGTTCATGCCAATCTGAACCCGCAGCAATATCCTGCTGATATTCAACGTGCAATTAATGAGACACACAAAGGTTTCTATCAAGTAGGTACGATGTATCAGGCGCTTGGTTGGGAAGAGTTTTCTTATCCGGCAACATTACAAACTCTATTAGACAGTAATTCTGACCAAATTGTGATGAAACCTAATAAAGTCACTGCTATTTCTAAAGAACCTTCAGTTAAGATTTTCCACAAAACTGGTTCAACCAATGGCTTCGGAACATACGTCGTATTTATTCCTAAAGAGAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAACGAAGAACGCATTAAAGCAGCGTATGCGGTGTTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3006442","ARO_id":"44904","ARO_name":"ADC-85","CARD_short_name":"ADC-85","ARO_description":"ADC-85 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4342":{"model_id":"4342","model_name":"ADC-86","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6717":{"protein_sequence":{"accession":"WP_068981618.1","sequence":"MRFKKISCLLLSPLFIFSTSIYADNTPKDQEIKKLVDQNFKPLLDKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKTKGTISFKDTTGKYWKELKNTPIDQVNLLQLATYTSGNLGLQFPDEVQTDQQVLTFFKDWKPKNSIGEYRQYSNPSIGLFGKVVALSMNKPFDQLLEKTIFPDLGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLKFINANLNPQKYPKDIQRAINETHQGFYQVGTMYQALGWEEFSYPAPLQTLLDSNSEQIVMKPNKVTAISKEPSVKMFHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_051450.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGACAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCTTTATTAGATAAATATGATGTGCCGGGTATGGCCGTGGGTGTTATTCAGAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTCGGTTCAGTTAGTAAATTATTTACCGCTACAGCAGGTGGATATGCCAAAACAAAAGGAACAATTTCTTTTAAAGACACAACCGGAAAATATTGGAAAGAATTAAAAAACACACCAATTGACCAAGTTAACTTACTTCAACTTGCTACTTATACGAGTGGCAACCTTGGCTTACAGTTTCCAGATGAAGTCCAAACAGATCAGCAAGTTTTAACTTTTTTCAAAGACTGGAAGCCTAAAAACTCAATCGGTGAATATCGACAATATTCAAATCCAAGCATTGGTTTATTTGGAAAAGTTGTTGCATTGTCTATGAATAAACCTTTCGACCAACTCTTAGAAAAAACAATTTTTCCAGATCTTGGCTTAAAACATAGCTATGTAAATGTACCGAAGACCCAGATGCAAAACTATGCTTTTGGCTATAATCAAGAAAATCAGCCAATTCGTGTTAACCCTGGTCCGTTAGATGCACCTGCGTACGGCGTCAAATCGACACTACCCGATATGCTTAAGTTTATTAATGCCAACCTCAACCCACAGAAATATCCGAAAGATATTCAACGTGCAATTAATGAAACACATCAGGGTTTCTATCAAGTCGGCACCATGTATCAGGCACTTGGTTGGGAAGAATTTTCTTATCCAGCGCCTTTACAAACTTTATTAGACAGTAATTCAGAACAAATTGTGATGAAGCCTAATAAAGTGACTGCCATTTCAAAAGAACCTTCAGTTAAGATGTTCCACAAAACTGGTTCAACCAATGGTTTCGGAACTTATGTCGTGTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTGACCAATAAACGTATTCCAAATGAAGAACGCATTAAGGCAGCGTATGCGGTGTTAAATGCAATAAAAAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3006443","ARO_id":"44905","ARO_name":"ADC-86","CARD_short_name":"ADC-86","ARO_description":"ADC-86 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4343":{"model_id":"4343","model_name":"ADC-87","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6718":{"protein_sequence":{"accession":"WP_068981619.1","sequence":"MRFKKISCLLLSPLFIFSTSIYADNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTEQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGEIVGLSMKQPFSQVLEKTIFPDLGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPANIQRAINETHQGRYQVNTMYQALGWEEFAYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_051451.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGACAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCATTATTAGAAAAATATGATGTGCCGGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAGCTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTCCCAGATGAAGTACAAACAGAACAACAGGTTTTAACTTTTTTTAAAGATTGGAAACCTAAAAACCCAATCGGTGAATATAGACAATATTCAAACCCAAGTATTGGCCTATTTGGGGAAATAGTTGGTTTATCAATGAAGCAGCCTTTTAGTCAGGTCTTGGAAAAAACGATTTTTCCGGACCTTGGCTTAAAACATAGCTATGTCAATGTGCCTAAAACTCAGATGCAAAACTATGCATTTGGTTATAACCAAGAAAATCAGCCAATTCGAGTTAACCCTGGCCCACTCGATGCCCCAGCATACGGCGTCAAATCGACCCTACCCGACATGCTGAGCTTTATTCATGCCAACCTGAACCCACAGAAATATCCGGCAAATATTCAACGTGCAATTAATGAGACGCATCAAGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTGCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAACCTTCAGTTAAGATGTACCACAAAACTGGCTCAACCAACGGTTTCGGAACCTATGTCGTATTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGCATTCCAAATGAAGAACGCATTAAAGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006444","ARO_id":"44906","ARO_name":"ADC-87","CARD_short_name":"ADC-87","ARO_description":"ADC-87 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4344":{"model_id":"4344","model_name":"ADC-88","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6719":{"protein_sequence":{"accession":"WP_001211221.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVKTDQQVLTFFKDWKPKNSIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPELGLKYSYVNVPKTQIQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLKFINANLNPQKYPADIQRAINETHQGFYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_051452.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGCGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAGTATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAATTTCCAGATGAAGTAAAAACAGATCAGCAAGTTTTAACATTTTTTAAAGACTGGAAACCTAAAAACTCAATCGGTGAATATCGACAATATTCAAACCCAAGCATTGGTTTATTTGGAAAAGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACTATTTTTCCAGAGCTTGGCTTAAAATATAGTTATGTAAATGTGCCTAAAACTCAGATACAAAACTATGCATTTGGTTATAACCAAGAAAATCAGCCGATTCGAGTTAATCCTGGTCCACTCGATGCACCAGCATACGGCGTTAAATCTACCTTACCTGATATGCTTAAGTTTATTAATGCCAACCTAAACCCACAAAAATATCCAGCAGATATTCAACGGGCAATTAATGAAACACATCAAGGGTTCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCAACGGTTTCGGAACATATGTGGTCTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCGTATGCAGTTTTAAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006445","ARO_id":"44907","ARO_name":"ADC-88","CARD_short_name":"ADC-88","ARO_description":"ADC-88 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4345":{"model_id":"4345","model_name":"ADC-89","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6720":{"protein_sequence":{"accession":"WP_068981620.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNRSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWQPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPEYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGFYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTTGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLDAIKK"},"dna_sequence":{"accession":"NG_051453.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATCGCAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGCAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTGGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCATTTGGTTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCTGAATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTTAACCCACAGAAATATCCGGCTGATATTCAACGGGCAATTAATGAAACACATCAAGGGTTCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCACCGGTTTCGGAACATATGTAGTGTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGGATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006446","ARO_id":"44908","ARO_name":"ADC-89","CARD_short_name":"ADC-89","ARO_description":"ADC-89 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4346":{"model_id":"4346","model_name":"ADC-90","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6721":{"protein_sequence":{"accession":"WP_068981621.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWQPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVAKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNLQKYPTDIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_051454.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCATTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGCAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTGGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTAGCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCGACACTACCTGACATGCTGAGTTTTATTCATGCCAATCTGAACCTACAGAAATATCCGACAGATATTCAACGGGCAATTAATGAAACACATCAAGGTCGCTATCAAGTAAATACCATGTATCAAGCGCTTGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAGCCTAATAAAGTGACTGCTATTTCAAAAGAGCCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACATATGTAGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006447","ARO_id":"44909","ARO_name":"ADC-90","CARD_short_name":"ADC-90","ARO_description":"ADC-90 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4347":{"model_id":"4347","model_name":"ADC-91","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6722":{"protein_sequence":{"accession":"WP_068981622.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKVLKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGESRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPTDIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTSGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_051455.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACCCCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCGTTATTAGAAAAATATGATGTGCCGGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGTGCTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATCCAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATACGGTGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTTAACCCACAGAAATATCCGACAGATATTCAACGGGCAATTAATGAAACACATCAAGGTCGCTATCAAGTAAATACCATGTATCAAGCGCTTGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAGCGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGTATTAAGGCAGCGTATGCAGTTTTAAATGCAATAAAAAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006448","ARO_id":"44910","ARO_name":"ADC-91","CARD_short_name":"ADC-91","ARO_description":"ADC-91 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4348":{"model_id":"4348","model_name":"ADC-92","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6723":{"protein_sequence":{"accession":"WP_068981623.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIHNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKVLKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGESRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPTDIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_051456.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACCCCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCGTTATTAGAAAAATATGATGTGCCGGGTATGGCTGTGGGTGTTATTCATAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGTGCTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATCCAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATACGGTGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTTAACCCACAGAAATATCCGACAGATATTCAACGGGCAATTAATGAAACACATCAAGGTCGCTATCAAGTAAATACCATGTATCAAGCGCTTGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGTATTAAGGCAGCGTATGCAGTTTTAAATGCAATAAAAAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006449","ARO_id":"44911","ARO_name":"ADC-92","CARD_short_name":"ADC-92","ARO_description":"ADC-92 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4349":{"model_id":"4349","model_name":"ADC-93","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6724":{"protein_sequence":{"accession":"WP_068981624.1","sequence":"MQFKKISCLLLSPLFIFSTSIYADNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSSIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGFYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_051457.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCAATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGACAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCATTATTAGAAAAATATGATGTGCCGGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTAGTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAGCTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTCCCAGATGAAGTACAAACAGATCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTGTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTTAACCCACAGAAATATCCGGCAGATATTCAACGGGCAATTAATGAAACACATCAAGGGTTCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACATATGTAGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006450","ARO_id":"44912","ARO_name":"ADC-93","CARD_short_name":"ADC-93","ARO_description":"ADC-93 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4350":{"model_id":"4350","model_name":"ADC-94","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6725":{"protein_sequence":{"accession":"WP_068981625.1","sequence":"MQFKKISCLLLSPLFIFSTSIYADNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGFYQVNTMYQALGWEEFSYPATLQTLLDSSSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_051458.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCAATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGACAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCATTATTAGAAAAATATGATGTGCCGGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAGCTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTCCCAGATGAAGTACAAACAGATCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTGTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTTAACCCACAGAAATATCCGGCAGATATTCAACGGGCAATTAATGAAACACATCAAGGGTTCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAGTTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACATATGTAGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006451","ARO_id":"44913","ARO_name":"ADC-94","CARD_short_name":"ADC-94","ARO_description":"ADC-94 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4351":{"model_id":"4351","model_name":"ADC-95","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6726":{"protein_sequence":{"accession":"WP_068981626.1","sequence":"MQFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGFYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_051459.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCAATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCATTATTAGAAAAATATGATGTGCCGGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAGCTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTCCCAGATGAAGTACAAACAGATCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTGTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTTAACCCACAGAAATATCCGGCAGATATTCAACGGGCAATTAATGAAACACATCAAGGGTTCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACATATGTAGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006452","ARO_id":"44914","ARO_name":"ADC-95","CARD_short_name":"ADC-95","ARO_description":"ADC-95 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4352":{"model_id":"4352","model_name":"ADC-96","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6727":{"protein_sequence":{"accession":"WP_068981627.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKVLKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGFYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_051460.1","fmin":"0","fmax":"1167","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACCCCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCATTATTAGAAAAATATGATGTGCCGGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGTGCTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGTCCACTCGATGCCCCAGCATACGGCGCCCCAGCATACGGCGTCAAATCCACCTTACCGGATATGTTGAGTTTTATTCATGCCAACCTCAACCCACAGAAATATCCGGCAGATATTCAACGGGCAATTAATGAAACACATCAAGGGTTCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCAACGGTTTCGGAACATATGTGGTCTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006453","ARO_id":"44915","ARO_name":"ADC-96","CARD_short_name":"ADC-96","ARO_description":"ADC-96 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4353":{"model_id":"4353","model_name":"ADC-97","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6728":{"protein_sequence":{"accession":"WP_068981628.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKE"},"dna_sequence":{"accession":"NG_051461.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCGGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCTTATTTGGAAAAGTTGTTGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCAACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTCAATCCACAGAAATATCCGGCTGATATTCAACGGGCAATTAATGAAACACATCAAGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAAATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCAACGGTTTCGGAACGTATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAACGCATTAAGGCAGCGTATGCAGTTTTAAATGCAATAAAGGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006454","ARO_id":"44916","ARO_name":"ADC-97","CARD_short_name":"ADC-97","ARO_description":"ADC-97 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4354":{"model_id":"4354","model_name":"ADC-98","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6729":{"protein_sequence":{"accession":"WP_068981629.1","sequence":"MRFKKNSCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGIIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDKPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_051462.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAAATTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCGTTATTAGAAAAATATGATGTGCCGGGTATGGCTGTGGGTATTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGACAAGCCTGGTAAATATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTAAATCCACAAAAATATCCAGCAGATATTCAACGGGCAATTAATGAAACACATCAGGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCAACGGTTTCGGAACATATGTAGTGTTTATACCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006455","ARO_id":"44917","ARO_name":"ADC-98","CARD_short_name":"ADC-98","ARO_description":"ADC-98 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4355":{"model_id":"4355","model_name":"ADC-99","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6730":{"protein_sequence":{"accession":"WP_068981630.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGIIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDKPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"NG_051463.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCGTTATTAGAAAAATATGATGTGCCGGGTATGGCTGTGGGTATTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGACAAGCCTGGTAAATATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTAAATCCACAAAAATATCCAGCAGATATTCAACGGGCAATTAATGAAACACATCAGGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCAACGGTTTCGGAACATATGTAGTGTTTATACCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006456","ARO_id":"44918","ARO_name":"ADC-99","CARD_short_name":"ADC-99","ARO_description":"ADC-99 is a ADC beta-lactamase.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4356":{"model_id":"4356","model_name":"AFM-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"6731":{"protein_sequence":{"accession":"WP_069953510.1","sequence":"MITKSNIARIGLPLALAMALPGCIPGEIRPSIGEQVDKGDQRFGDLVFRQLAPNVWQHTSFMDVPGFGAVSSNGLIVKDGERVLLVDTAWTDDQTSQILNWIKQEINLPVALAVVTHAHQDKMGGMGALHAEAIPTYANALSNQLAPQEGMTAAQHSLTFAANGWVDPATAPNFGPLRVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTERYAASARAFGAAFPKANTIAMSHSAPDSRAAITHTARMADKLR"},"dna_sequence":{"accession":"NG_063835.1","fmin":"0","fmax":"804","strand":"+","sequence":"ATGATTACGAAATCGAACATCGCGCGGATTGGCTTGCCGCTGGCTTTGGCCATGGCGCTGCCCGGCTGCATCCCCGGCGAGATCCGCCCGTCGATTGGTGAGCAGGTGGATAAGGGTGACCAGCGCTTCGGCGATCTGGTGTTCCGCCAGCTGGCGCCCAATGTGTGGCAACATACCTCGTTCATGGATGTGCCGGGCTTTGGCGCGGTTTCTTCCAACGGGCTGATCGTCAAGGATGGCGAACGGGTGCTGTTGGTCGATACCGCCTGGACCGATGATCAGACCAGCCAGATCCTCAACTGGATTAAGCAAGAGATCAATCTGCCGGTGGCGCTGGCGGTGGTCACCCACGCGCATCAGGACAAGATGGGCGGGATGGGCGCGCTGCACGCGGAGGCAATCCCCACTTACGCCAATGCCTTGTCGAACCAGCTTGCCCCGCAAGAGGGGATGACGGCGGCGCAGCACAGCCTGACCTTCGCCGCCAACGGCTGGGTCGACCCGGCGACCGCGCCCAATTTCGGGCCGCTCAGGGTGTTCTATCCCGGCCCCGGCCACACCAGTGACAATATCACCGTCGGGATCGATGGCACCGACATCGCCTTTGGCGGCTGCCTGATCAAAGACAGCAAGGCCAAGTCGCTCGGCAATCTCGGCGATGCCGACACCGAACGCTATGCCGCCTCGGCGCGCGCATTTGGTGCGGCTTTTCCGAAGGCGAACACGATTGCGATGAGCCATTCCGCGCCTGACAGCCGCGCCGCGATCACCCACACCGCGCGGATGGCCGACAAGCTGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43206","NCBI_taxonomy_name":"Alcaligenes faecalis","NCBI_taxonomy_id":"511"}}}},"ARO_accession":"3006890","ARO_id":"45352","ARO_name":"AFM-1","CARD_short_name":"AFM-1","ARO_description":"AFM-1 is a AFM beta-lactamase.","ARO_category":{"43848":{"category_aro_accession":"3005388","category_aro_cvterm_id":"43848","category_aro_name":"AFM beta-lactamase","category_aro_description":"AFM beta-lactamases are class B1 beta-lactamases found in proteobacteria like Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4357":{"model_id":"4357","model_name":"AFM-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"6732":{"protein_sequence":{"accession":"WP_204376224.1","sequence":"MITKSNIARIGLPLVLAMALPGCIPGEIRPSIGEQVDKGDQRFGDLVFRQLAPNVWQHTSFMDVPGFGAVSSNGLIVKDGERVLLVDTAWTDDQTSQILNWIKQEINLPVALAVVTHAHQDKMGGMGALHAEAIPTYANALSNQLAPQEGMTAAQHSLTFAANGWVDPATAPNFGPLRVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTERYAASARAFGAAFPKANTIAMSHSAPDSRAAITHTARMADKLR"},"dna_sequence":{"accession":"NG_073458.1","fmin":"0","fmax":"804","strand":"+","sequence":"ATGATTACGAAATCGAACATCGCGCGGATTGGCTTGCCGCTGGTTTTGGCCATGGCGCTGCCCGGCTGCATCCCCGGCGAGATCCGCCCGTCGATTGGTGAGCAGGTGGATAAGGGTGACCAGCGCTTCGGCGATCTGGTGTTCCGCCAGCTGGCGCCCAATGTGTGGCAACATACCTCGTTCATGGATGTGCCGGGCTTTGGCGCGGTTTCTTCCAACGGGCTGATCGTCAAGGATGGCGAACGGGTGCTGTTGGTCGATACCGCCTGGACCGATGATCAGACCAGCCAGATCCTCAACTGGATTAAGCAAGAGATCAATCTGCCGGTGGCGCTGGCGGTGGTCACCCACGCGCATCAGGACAAGATGGGCGGGATGGGCGCGCTGCACGCGGAGGCAATCCCCACTTACGCCAATGCCTTGTCGAACCAGCTTGCCCCGCAAGAGGGGATGACGGCGGCGCAGCACAGCCTGACCTTCGCCGCCAACGGCTGGGTCGACCCGGCGACCGCGCCCAATTTCGGGCCGCTCAGGGTGTTCTATCCCGGCCCCGGCCACACCAGTGACAATATCACCGTCGGGATCGATGGCACCGACATCGCCTTTGGCGGCTGCCTGATCAAAGACAGCAAGGCCAAGTCGCTCGGCAATCTCGGCGATGCCGACACCGAACGCTATGCCGCCTCGGCGCGCGCATTTGGTGCGGCTTTTCCGAAGGCGAACACGATTGCGATGAGCCATTCCGCGCCTGACAGCCGCGCCGCGATCACCCACACCGCGCGGATGGCCGACAAGCTGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006891","ARO_id":"45353","ARO_name":"AFM-2","CARD_short_name":"AFM-2","ARO_description":"AFM-2 is a AFM beta-lactamase.","ARO_category":{"43848":{"category_aro_accession":"3005388","category_aro_cvterm_id":"43848","category_aro_name":"AFM beta-lactamase","category_aro_description":"AFM beta-lactamases are class B1 beta-lactamases found in proteobacteria like Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4358":{"model_id":"4358","model_name":"ALG11-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"6733":{"protein_sequence":{"accession":"WP_122630833.1","sequence":"MAASAAVSLVVFLFVFVFTFAHAQDQPASWAQPQKPVRIFGNTWYVGTRGLSAILITSPTGAVLIDGAVREAASDIASNITSLGVRLEDIKLIVNSHAHNDHAGAIAELQRRTGATVAALPWSAEALRSGRKHQGDPQFESPTSPPDRVANVKTIQDGEVLRAGGVEVTAHKTAGHTPGGTTWTWRSCEENRCVDIVYADSLTAVSADGFRFTDNKTYPQAIDDFNKGYAFLRSASCDILVTPHPEASDFWGRIAKRDAGERDALIDRSQCARYADRADAQLQKRLATERAERPK"},"dna_sequence":{"accession":"NG_062237.1","fmin":"0","fmax":"888","strand":"+","sequence":"ATGGCCGCCTCGGCCGCCGTATCGCTCGTCGTGTTCCTGTTCGTGTTCGTGTTTACGTTCGCGCACGCGCAGGATCAGCCGGCCTCGTGGGCTCAGCCGCAGAAGCCCGTTCGCATCTTCGGCAACACTTGGTACGTAGGCACGCGCGGGCTGAGCGCCATTCTCATCACGTCGCCCACCGGCGCCGTGCTCATCGACGGAGCGGTGCGTGAAGCGGCGTCCGATATCGCCAGCAACATCACGTCGCTTGGCGTACGGCTCGAGGACATCAAACTGATCGTCAATTCGCATGCGCACAACGATCACGCCGGCGCGATTGCGGAACTACAGCGGCGGACGGGCGCCACGGTGGCCGCGCTGCCGTGGAGCGCGGAGGCGCTGCGAAGCGGACGGAAGCATCAGGGCGATCCGCAGTTCGAATCACCAACGTCACCTCCCGACCGCGTCGCCAACGTCAAGACGATCCAGGATGGCGAGGTGCTGCGTGCCGGAGGCGTGGAGGTCACGGCGCACAAGACCGCCGGCCATACGCCGGGCGGCACGACATGGACGTGGCGCTCGTGCGAGGAGAACAGGTGCGTCGACATCGTGTATGCCGACAGCCTGACCGCCGTTTCGGCCGATGGGTTCCGCTTCACCGACAACAAAACGTATCCGCAGGCGATCGACGATTTCAACAAAGGCTACGCGTTCCTGCGATCCGCGAGCTGCGACATCCTGGTGACGCCGCATCCGGAAGCCTCGGACTTCTGGGGCCGCATCGCCAAGCGCGACGCCGGAGAGCGCGATGCGCTGATCGATCGCTCGCAGTGCGCGCGTTATGCCGATCGCGCCGATGCGCAGTTGCAGAAACGCCTGGCGACGGAGCGCGCGGAGCGCCCGAAATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36791","NCBI_taxonomy_name":"uncultured bacterium","NCBI_taxonomy_id":"77133"}}}},"ARO_accession":"3006892","ARO_id":"45354","ARO_name":"ALG11-1","CARD_short_name":"ALG11-1","ARO_description":"ALG11-1 is a ALG11 beta-lactamase.","ARO_category":{"43849":{"category_aro_accession":"3005389","category_aro_cvterm_id":"43849","category_aro_name":"ALG11 beta-lactamase","category_aro_description":"ALG11 beta-lactamases are class B3 beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4359":{"model_id":"4359","model_name":"ALG6-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"650"}},"model_sequences":{"sequence":{"6734":{"protein_sequence":{"accession":"WP_122630832.1","sequence":"MSHGIPCAPSSRMETQMVSKMAMAAILLLAGPTAAAEVTPTTPIVCSMCEGWNRPQKPFKIYGNTWYVGTNDLSALLVTSPNGHVLLDGALPQSAPLIEANIQALGFKLKDVKLILNSHEHFDHAGGIPALQRASGATVAASIRGAKVLRAGTVGKDDPQFDPVKPFFLAKLEKVREVADGETLTAGDLRITAHYTPGHTPGGTSWTWTSCENGRCLNMVYADSLTPVSSEGFRFSGGNGAPDISSAFQATIDKVAALKCDVMVSNHPGFSQVMEKLAARTDANNTFIDPTGCRKYAAAASKRLANRLATEAKQKAAR"},"dna_sequence":{"accession":"NG_062236.1","fmin":"0","fmax":"957","strand":"+","sequence":"ATGAGCCACGGCATCCCGTGCGCCCCGAGTTCAAGAATGGAGACCCAGATGGTTTCGAAGATGGCGATGGCCGCAATCCTGCTGCTGGCCGGCCCGACTGCAGCTGCCGAGGTCACTCCCACCACGCCCATCGTGTGCTCGATGTGCGAAGGCTGGAACAGGCCGCAGAAGCCTTTCAAGATCTACGGCAACACCTGGTACGTCGGAACCAACGACCTGTCGGCGCTGCTGGTCACCAGCCCCAACGGCCATGTCCTGCTCGACGGCGCGCTGCCGCAGTCGGCGCCGCTGATCGAAGCGAACATCCAGGCGCTCGGCTTCAAGCTGAAGGACGTGAAGCTGATCCTCAACTCGCACGAGCACTTCGATCACGCAGGCGGCATACCGGCCCTGCAGCGCGCCAGTGGTGCGACCGTGGCGGCGAGCATCCGCGGGGCCAAGGTGCTGCGCGCGGGAACCGTGGGCAAGGACGATCCGCAGTTCGACCCGGTCAAGCCGTTCTTCCTGGCGAAGCTCGAGAAGGTGCGTGAAGTGGCCGATGGCGAGACGCTGACTGCCGGCGACCTGAGAATCACGGCGCACTACACGCCGGGCCATACGCCGGGCGGTACCAGCTGGACCTGGACCTCGTGCGAGAACGGCCGCTGCCTGAACATGGTGTACGCGGACAGCCTCACGCCGGTGTCGAGCGAGGGCTTTCGGTTCAGCGGCGGCAACGGCGCCCCCGACATCTCCAGCGCCTTCCAGGCCACCATCGACAAGGTCGCGGCCCTGAAGTGCGACGTGATGGTGTCGAACCATCCGGGCTTCTCGCAGGTCATGGAGAAGCTGGCTGCGCGCACGGATGCGAACAACACCTTCATCGATCCGACCGGCTGCCGGAAGTATGCGGCGGCCGCCTCGAAGCGGCTGGCGAACCGGCTGGCCACGGAGGCGAAGCAGAAGGCCGCCAGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36791","NCBI_taxonomy_name":"uncultured bacterium","NCBI_taxonomy_id":"77133"}}}},"ARO_accession":"3006893","ARO_id":"45355","ARO_name":"ALG6-1","CARD_short_name":"ALG6-1","ARO_description":"ALG6-1 is a ALG6 beta-lactamase.","ARO_category":{"43850":{"category_aro_accession":"3005390","category_aro_cvterm_id":"43850","category_aro_name":"ALG6 beta-lactamases","category_aro_description":"ALG6 beta-lactamases are class B3 beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4360":{"model_id":"4360","model_name":"ALI-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"375"}},"model_sequences":{"sequence":{"6735":{"protein_sequence":{"accession":"WP_026025287.1","sequence":"MFKLTLALLSSVIGFNAAAEPVVKPLQFEEITNNVFLVKSYREFKNLQSPKKPILVDANSLVYVDGKDAYLIDTPWNASNMPQLMTWIENRGLTLKKTVFSHFHEDQTGGLEYLQEHHFETYASALTNKFLKGDNKKATNHQFSGDNFVLLENKIEVFYPGGGHTKDNAVVWLPKEKVLLGGCLMRANEVNTIGWTGDADMKAWAGSAQKVLTKYPQANFVVPGHGNVGEGTSIISHTVDITGKI"},"dna_sequence":{"accession":"NG_057427.1","fmin":"100","fmax":"838","strand":"+","sequence":"ATGTTTAAACTTACTCTCGCATTACTAAGTTCGGTTATCGGCTTTAATGCAGCAGCAGAGCCTGTAGTTAAACCGCTTCAATTTGAAGAAATCACGAATAATGTGTTTTTAGTTAAATCGTATCGTGAATTTAAAAACTTACAGAGCCCAAAGAAACCTATTTTGGTCGATGCTAATTCTTTAGTGTATGTTGATGGAAAGGATGCGTATTTGATTGATACGCCATGGAATGCGTCGAACATGCCTCAGTTGATGACGTGGATTGAAAACAGAGGATTAACATTAAAGAAAACGGTCTTTTCTCATTTTCATGAAGATCAAACTGGTGGTTTAGAATACCTGCAAGAACATCACTTTGAGACTTACGCGTCTGCATTAACGAACAAATTTTTGAAAGGTGATAACAAGAAAGCGACGAATCATCAATTTTCAGGTGATAATTTTGTGTTGTTAGAAAATAAGATTGAAGTTTTCTATCCGGGAGGAGGCCATACTAAAGACAATGCGGTGGTATGGTTACCAAAAGAAAAAGTATTACTTGGCGGTTGTTTAATGCGAGCAAATGAGGTGAATACGATTGGGTGGACTGGTGATGCCGATATGAAAGCATGGGCGGGGTCTGCTCAAAAAGTCTTAACGAAATACCCTCAAGCAAATTTTGTTGTTCCTGGACACGGGAACGTTGGTGAAGGGACGAGTATTATTAGTCATACTGTCGATATTACCGGAAAAATTTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3006894","ARO_id":"45356","ARO_name":"ALI-1","CARD_short_name":"ALI-1","ARO_description":"ALI-1 is a ALI beta-lactamase.","ARO_category":{"43851":{"category_aro_accession":"3005391","category_aro_cvterm_id":"43851","category_aro_name":"ALI beta-lactamase","category_aro_description":"ALI beta-lactamases are class B1 beta-lactamases found in species of the Aliivibrio genus.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4361":{"model_id":"4361","model_name":"ALI-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"375"}},"model_sequences":{"sequence":{"6736":{"protein_sequence":{"accession":"WP_065597326.1","sequence":"MFKFITGIVVAFVSFNTLSAPMLKPLQFEEVTTNIFLVKSFREFKNLKSPDNPIIIDANSLIYIDSKDAYLIDTPWNAENMPQLMTWIENRDLTLKKTVFTHFHEDQTGGLEYLQEHGFDTYATKLTNTLLVKDNKKAANHELDAQESVLLDNKIEVFYPGPGHSKDNSVVWFPKEKVLLGGCLMRANEVNTIGWTGDADLAKWAQSAKNVLIKYPETKLVIPGHGDIGKGTSVISHTVNIAESL"},"dna_sequence":{"accession":"NG_059328.1","fmin":"100","fmax":"838","strand":"+","sequence":"ATGTTTAAGTTTATTACGGGTATAGTCGTTGCTTTTGTTAGTTTTAATACCTTGTCTGCACCAATGCTTAAGCCTCTTCAATTTGAAGAAGTCACGACCAATATTTTTTTGGTTAAGTCATTTCGAGAATTTAAAAATTTAAAAAGTCCGGATAACCCAATTATTATTGATGCTAACTCATTGATTTATATAGATAGTAAAGATGCGTATCTCATTGATACTCCATGGAATGCTGAAAATATGCCTCAATTGATGACATGGATTGAAAACAGAGATTTAACGCTTAAAAAAACAGTATTTACACATTTTCATGAAGATCAAACGGGTGGTTTAGAATATTTGCAAGAACATGGGTTTGATACTTATGCTACAAAATTAACCAATACACTGCTTGTTAAAGATAATAAAAAAGCGGCAAATCATGAGTTAGACGCTCAGGAATCTGTTTTATTGGATAATAAAATTGAGGTTTTTTATCCGGGACCAGGACATTCAAAAGATAACTCTGTTGTGTGGTTTCCTAAAGAAAAAGTGTTATTAGGTGGATGCCTAATGCGAGCGAATGAGGTGAACACCATTGGCTGGACAGGCGATGCAGACCTCGCTAAATGGGCTCAATCAGCCAAAAATGTGTTAATAAAATACCCTGAAACTAAATTGGTTATTCCTGGGCACGGAGATATCGGGAAAGGGACTAGTGTAATTTCTCATACTGTCAATATTGCTGAAAGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3006895","ARO_id":"45357","ARO_name":"ALI-2","CARD_short_name":"ALI-2","ARO_description":"ALI-2 is a ALI beta-lactamase.","ARO_category":{"43851":{"category_aro_accession":"3005391","category_aro_cvterm_id":"43851","category_aro_name":"ALI beta-lactamase","category_aro_description":"ALI beta-lactamases are class B1 beta-lactamases found in species of the Aliivibrio genus.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4362":{"model_id":"4362","model_name":"ANA-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"6737":{"protein_sequence":{"accession":"WP_041449074.1","sequence":"MRTLLARVVVLLLVPWSAARGEPETDLGDRVRARPLSAHAWLIRSVSALEGFGDVESNAVLVTGATESVLVDTPATDEQTAPVLAWAEKTLRRPVRHLIVTHWHADRMGGIGAARARQVATYAFGRTRALARQKGLVVPEHELGPAERLTLAGLSLATWYPGHGHTADNIVVWLPEDGVLVAGCFVKDAAAGTLGNVREADPVQWATGVAALRRRYPGARIVVPGHGAAGGSELLARTTALLEAHGSRGVPASGR"},"dna_sequence":{"accession":"NG_057424.1","fmin":"100","fmax":"868","strand":"+","sequence":"ATGCGAACGCTCCTCGCCCGCGTCGTCGTGCTGCTCCTCGTGCCCTGGTCCGCCGCGCGGGGGGAACCCGAGACCGACCTCGGCGACCGCGTCCGGGCGCGCCCGCTCTCGGCCCACGCCTGGCTGATCCGGTCGGTGAGCGCGCTCGAGGGCTTCGGCGACGTCGAGTCGAACGCGGTGCTGGTGACGGGGGCGACGGAGTCCGTGCTCGTCGACACCCCCGCCACGGACGAGCAGACCGCGCCCGTGCTCGCCTGGGCGGAGAAGACGCTGCGCCGACCGGTGCGCCACCTGATCGTCACCCACTGGCACGCCGACCGGATGGGCGGGATCGGCGCCGCGCGGGCGCGCCAGGTCGCGACCTACGCCTTCGGCAGGACCCGCGCGCTGGCGCGGCAGAAGGGGCTCGTGGTTCCGGAGCACGAGCTCGGACCCGCAGAGCGGCTCACGCTCGCGGGCCTATCTCTGGCGACCTGGTATCCCGGCCACGGGCACACCGCGGACAACATCGTCGTGTGGCTGCCCGAGGACGGGGTGCTCGTCGCGGGATGCTTCGTGAAGGACGCAGCGGCGGGGACGCTCGGCAACGTACGGGAGGCCGACCCCGTCCAGTGGGCGACCGGGGTGGCCGCCCTGCGGCGGCGCTACCCGGGGGCTCGTATCGTCGTCCCGGGCCACGGCGCGGCCGGAGGCTCCGAGCTGCTCGCCCGAACGACGGCGCTGCTCGAGGCGCACGGCAGTCGGGGAGTTCCGGCCTCAGGCCGGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3006896","ARO_id":"45358","ARO_name":"ANA-1","CARD_short_name":"ANA-1","ARO_description":"ANA-1 is a ANA beta-lactamase.","ARO_category":{"43852":{"category_aro_accession":"3005392","category_aro_cvterm_id":"43852","category_aro_name":"ANA beta-lactamase","category_aro_description":"ANA beta-lactamases are class B1 beta-lactamases found in Anaeromyxobacter.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4363":{"model_id":"4363","model_name":"AXC-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6738":{"protein_sequence":{"accession":"WP_020924773.1","sequence":"MLTRRTFIASAVLAGWIPALAHARTDKKTRWTRESLAAFQQGLAQVEAASRGRLGVALLDVGSGQAAGYRADERFLMLSSFKTLSAAYVLARADRGEDQLSRRIPITDADVREYSPVTRLHVGPRGMTLAELCEATITTSDNAAVNLMHKSYGGPQALTRYLRSLGDTVTRHDRYEPELNRPHPSEPQDTTTPQAMARTLDTLLFGDALKPQSRQQLQSWLLANTTGGKRLRAGMPADWKIGEKTGTYSKVGCNDAGFAQPPGAAPIIIAAYLETTAVPMEERDRCIAEVGRLVAALG"},"dna_sequence":{"accession":"NG_061617.1","fmin":"100","fmax":"997","strand":"+","sequence":"TTGCTGACCCGAAGAACCTTCATTGCCTCGGCCGTGCTGGCCGGTTGGATTCCTGCCCTTGCACACGCCCGCACGGATAAGAAAACTCGATGGACGCGCGAAAGTCTCGCGGCGTTCCAACAAGGCCTTGCCCAAGTGGAGGCCGCCAGCCGCGGACGGCTGGGAGTGGCCCTGCTGGACGTGGGCAGTGGGCAAGCCGCCGGCTATCGCGCCGACGAACGCTTCCTGATGCTCAGCTCCTTCAAGACGCTGTCCGCGGCCTACGTGCTGGCGCGGGCCGACCGTGGCGAGGACCAGCTGTCGCGCCGCATCCCGATCACCGACGCCGATGTCCGGGAGTATTCGCCGGTCACGCGGCTGCATGTCGGGCCGCGGGGAATGACGCTGGCCGAACTCTGTGAAGCGACGATCACCACCAGCGACAACGCGGCGGTCAACCTCATGCACAAGAGCTATGGCGGCCCGCAAGCCCTGACCCGCTACCTGCGCAGCCTGGGCGATACCGTCACGCGCCACGATCGCTACGAACCCGAATTGAACCGCCCGCACCCGAGCGAACCGCAGGACACCACCACCCCGCAGGCCATGGCGCGCACGCTGGATACGCTACTGTTCGGCGACGCGCTCAAGCCGCAATCGCGGCAGCAACTGCAATCCTGGCTGCTGGCCAACACGACGGGCGGCAAGCGCCTGCGCGCCGGCATGCCGGCGGATTGGAAGATCGGCGAGAAGACAGGCACCTATTCGAAGGTGGGCTGCAACGACGCCGGCTTCGCGCAACCGCCCGGCGCGGCGCCGATCATCATCGCGGCCTATCTGGAAACCACCGCGGTGCCGATGGAGGAGCGCGACCGCTGCATCGCCGAGGTCGGCAGGCTGGTGGCGGCATTGGGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36941","NCBI_taxonomy_name":"Achromobacter xylosoxidans","NCBI_taxonomy_id":"85698"}}}},"ARO_accession":"3006897","ARO_id":"45359","ARO_name":"AXC-1","CARD_short_name":"AXC-1","ARO_description":"AXC-1 is a AXC beta-lactamase.","ARO_category":{"43853":{"category_aro_accession":"3005393","category_aro_cvterm_id":"43853","category_aro_name":"AXC beta-lactamase","category_aro_description":"AXC beta-lactamases are class A beta-lactamase found in the Anaeromyxobacter genus.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4364":{"model_id":"4364","model_name":"AXC-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6739":{"protein_sequence":{"accession":"WP_100505522.1","sequence":"MLTRRTFIASAVLAGGMPALARARTDKKTRWTRDSLATFQQALAKLEAASRGRLGVALLDVGSGQAAGYRADERFLMLSSFKTLSAAYVLARADRGEDQLSRRIPITDADVQEYSPVTRLHVGPRGMTLAELCEATITTSDNAAVNLMHKSYGGPQALTRYLRGLGDTVTRHDRYEPELNRPHPSEPQDTTTPQAMARTLDTLLFGDALKPQSRQQLQSWLLANTTGGKRLRAGMPADWKIGEKTGTYSKVGCNDAGFAQPPGAAPIIIAAYLETTAVPMEERDRCIAEVGRLVAALG"},"dna_sequence":{"accession":"NG_066501.1","fmin":"0","fmax":"897","strand":"+","sequence":"TTGCTGACGAGAAGAACCTTCATCGCCTCGGCCGTGCTGGCCGGCGGGATGCCCGCCCTGGCGCGCGCCAGGACGGATAAGAAAACTCGATGGACGCGCGACAGTCTCGCGACATTCCAACAGGCCCTGGCCAAGCTGGAGGCGGCCAGCCGTGGCCGGCTGGGCGTGGCCCTGCTCGACGTGGGCAGCGGGCAGGCCGCCGGCTATCGCGCCGACGAACGTTTCCTGATGCTCAGTTCCTTCAAGACGCTGTCAGCGGCCTATGTGCTGGCGCGGGCCGACCGTGGCGAGGATCAGCTGTCGCGCCGCATCCCGATCACCGATGCCGATGTGCAGGAGTATTCGCCGGTCACGCGGCTGCATGTCGGGCCGCGAGGAATGACCTTGGCCGAACTCTGTGAAGCGACGATCACCACCAGCGACAACGCGGCGGTCAACCTCATGCACAAGAGCTATGGCGGCCCGCAGGCCCTGACCCGCTACCTGCGCGGCCTGGGCGATACCGTCACGCGTCATGATCGTTATGAACCCGAACTGAACCGCCCGCATCCGAGCGAGCCGCAAGACACCACCACTCCGCAGGCCATGGCGCGCACGCTGGACACGCTGTTGTTCGGCGACGCGCTCAAGCCGCAATCGCGGCAGCAACTGCAATCCTGGCTGCTGGCCAACACGACGGGTGGCAAGCGCCTGCGCGCCGGCATGCCGGCGGATTGGAAAATCGGCGAGAAGACCGGCACCTATTCGAAGGTGGGCTGCAACGACGCCGGCTTTGCGCAGCCGCCGGGCGCGGCGCCGATCATCATCGCGGCCTATCTGGAAACCACCGCGGTGCCGATGGAGGAGCGCGACCGCTGCATCGCCGAAGTCGGCAGGCTGGTGGCGGCATTGGGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39091","NCBI_taxonomy_name":"Achromobacter ruhlandii","NCBI_taxonomy_id":"72557"}}}},"ARO_accession":"3006898","ARO_id":"45360","ARO_name":"AXC-2","CARD_short_name":"AXC-2","ARO_description":"AXC-2 is a AXC beta-lactamase.","ARO_category":{"43853":{"category_aro_accession":"3005393","category_aro_cvterm_id":"43853","category_aro_name":"AXC beta-lactamase","category_aro_description":"AXC beta-lactamases are class A beta-lactamase found in the Anaeromyxobacter genus.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4365":{"model_id":"4365","model_name":"AXC-3","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6740":{"protein_sequence":{"accession":"WP_081330264.1","sequence":"MLTRRTFIASAVLAGGMPALARARTDKKTRWTRDSLATFQQALAKLEAASRGRLGVALLDVGSGQAAGYRADERFLMLSSFKTLSAAYVLARADRGEDQLSRRIPITDADVQEYSPVTRLHVGPRGMTLAELCEATITTSDNAAVNLMHKSYGGPQALTRYLRGLGDTVTRHDRYEPELNRPHPSEPQDTTTPRAMARTLDTLLFGDALKPQSRQQLQSWLLANTTGGKRLRAGMPADWRIGEKTGTYSKVGCNDAGFAQPPGAAPIIIAAYLETTAVPMEERDRCIAEVGRLVAALG"},"dna_sequence":{"accession":"NG_066502.1","fmin":"0","fmax":"897","strand":"+","sequence":"TTGCTGACGAGAAGAACTTTCATCGCCTCGGCCGTGCTGGCCGGCGGGATGCCCGCCCTGGCGCGCGCCAGGACGGATAAGAAAACTCGATGGACGCGCGACAGTCTCGCGACATTCCAACAGGCCCTGGCCAAGCTGGAGGCGGCCAGCCGTGGCCGGCTGGGCGTGGCCCTGCTCGACGTGGGCAGCGGGCAGGCCGCCGGCTATCGCGCCGACGAACGTTTTTTGATGCTCAGTTCCTTCAAGACGCTGTCGGCGGCCTATGTGCTGGCGCGGGCCGACCGTGGCGAGGATCAGCTGTCGCGCCGCATCCCGATCACCGATGCCGATGTGCAGGAGTATTCGCCGGTCACGCGGCTGCATGTCGGGCCGCGAGGAATGACCTTGGCCGAACTCTGTGAAGCGACGATCACCACCAGCGACAACGCGGCGGTCAACCTCATGCACAAGAGCTATGGCGGCCCGCAGGCCCTGACCCGCTACCTGCGCGGCCTGGGCGATACCGTCACGCGTCATGATCGTTATGAACCCGAACTGAACCGCCCGCATCCGAGCGAGCCGCAAGACACCACCACCCCGCGGGCCATGGCGCGCACGCTGGACACGCTATTGTTCGGCGACGCGCTCAAGCCGCAATCGCGGCAGCAATTGCAATCCTGGCTGCTGGCCAACACGACGGGCGGCAAGCGCCTGCGCGCCGGCATGCCGGCGGATTGGAGAATCGGCGAGAAGACCGGCACCTATTCAAAGGTGGGCTGCAACGACGCCGGCTTTGCGCAGCCGCCGGGCGCGGCGCCGATCATCATCGCGGCCTATCTGGAAACCACCGCGGTGCCGATGGAGGAGCGCGACCGCTGCATCGCCGAGGTCGGCAGGCTGGTGGCGGCATTGGGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39101","NCBI_taxonomy_name":"Achromobacter","NCBI_taxonomy_id":"222"}}}},"ARO_accession":"3006899","ARO_id":"45361","ARO_name":"AXC-3","CARD_short_name":"AXC-3","ARO_description":"AXC-3 is a AXC beta-lactamase.","ARO_category":{"43853":{"category_aro_accession":"3005393","category_aro_cvterm_id":"43853","category_aro_name":"AXC beta-lactamase","category_aro_description":"AXC beta-lactamases are class A beta-lactamase found in the Anaeromyxobacter genus.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4366":{"model_id":"4366","model_name":"AXC-4","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6741":{"protein_sequence":{"accession":"WP_150823464.1","sequence":"MLTRRTFIASAVLAGWIPALAHARTDKKTRWTRESLAAFQQGLAQVEAASRGRLGVALLDVGSGQAAGYRADERFLMLSSFKTLSAAYVLARADRGEDQLSRRIPITDADVREYSPVTRLHVGPRGMTLAELCEATITTSDNAAVNLMHKSYGGPQALTRYLRSLGDTVTRHDRYEPELNRPHPSEPQDTTTPQAMARTLDTLLFGDALKPQSRQQLQSWLLANTTGGKRLRAGMPADWKIGEKTGTYSKVGCNDAGFAQPPGAAPIIIAAYLETTAVPMEERDRCIAEVGRLVAAMG"},"dna_sequence":{"accession":"NG_066503.1","fmin":"0","fmax":"897","strand":"+","sequence":"TTGCTGACCCGAAGAACCTTCATTGCCTCGGCCGTGCTGGCCGGTTGGATTCCTGCCCTTGCACACGCCCGCACGGATAAGAAAACTCGATGGACGCGCGAAAGTCTCGCGGCGTTCCAACAAGGCCTTGCCCAAGTGGAGGCCGCCAGCCGCGGACGGCTGGGAGTGGCCCTGCTGGACGTGGGCAGTGGGCAAGCCGCCGGCTATCGCGCCGACGAACGCTTCCTGATGCTCAGCTCCTTCAAGACGCTGTCCGCGGCCTACGTGCTGGCGCGGGCCGACCGTGGCGAGGACCAGCTGTCGCGCCGCATCCCGATCACCGACGCCGATGTCCGGGAGTATTCGCCGGTCACGCGGCTGCATGTCGGGCCGCGGGGAATGACGCTGGCCGAACTCTGTGAAGCGACGATCACCACCAGCGACAACGCGGCGGTCAACCTCATGCACAAGAGCTATGGCGGCCCGCAAGCCCTGACCCGCTACCTGCGCAGCCTGGGCGATACCGTCACGCGCCACGATCGCTACGAACCCGAATTGAACCGCCCGCACCCGAGCGAACCGCAGGACACCACCACCCCGCAGGCCATGGCGCGCACGCTGGATACGCTACTGTTCGGCGACGCGCTCAAGCCGCAATCGCGGCAGCAACTGCAATCCTGGCTGCTGGCCAACACGACGGGCGGCAAGCGCCTGCGCGCCGGCATGCCGGCGGATTGGAAGATCGGCGAGAAGACAGGCACCTATTCGAAGGTGGGCTGCAACGACGCCGGCTTCGCGCAACCGCCCGGCGCGGCGCCGATCATCATCGCGGCCTATCTGGAAACCACCGCGGTGCCGATGGAGGAGCGCGACCGCTGCATCGCCGAGGTCGGCAGGCTGGTGGCGGCAATGGGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36941","NCBI_taxonomy_name":"Achromobacter xylosoxidans","NCBI_taxonomy_id":"85698"}}}},"ARO_accession":"3006900","ARO_id":"45362","ARO_name":"AXC-4","CARD_short_name":"AXC-4","ARO_description":"AXC-4 is a AXC beta-lactamase.","ARO_category":{"43853":{"category_aro_accession":"3005393","category_aro_cvterm_id":"43853","category_aro_name":"AXC beta-lactamase","category_aro_description":"AXC beta-lactamases are class A beta-lactamase found in the Anaeromyxobacter genus.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4367":{"model_id":"4367","model_name":"AXC-5","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6742":{"protein_sequence":{"accession":"WP_150823465.1","sequence":"MLTRRTFIASAVLAGWIPALAHARTDKKTRWTRESLAAFQQGLAQVEAASRGRLGVALLDVGSGQAAGYRADELFLMLSSFKTLSAAYVLARADRGEDQLSRRIPITDADVRGYSPVTRLHVGPRGMTLAELCEATITTSDNAAVNLMHKSYGGPQALTRYLRSLGDTVTRHDRYEPELNRPHPSEPQDTTTPQAMARTLDTLLFGDALKPQSRQQLQSWLLANTTGGKRLRAGMPADWKIGEKTGTYSKVGCNDAGFAQPPGAAPIIIAAYLETTAVPMEERDRCIAEVGRLVAALG"},"dna_sequence":{"accession":"NG_066504.1","fmin":"0","fmax":"897","strand":"+","sequence":"TTGCTGACCCGAAGAACCTTCATTGCCTCGGCCGTGCTGGCCGGTTGGATTCCTGCCCTTGCACACGCCCGCACGGATAAGAAAACTCGATGGACGCGCGAAAGTCTCGCGGCGTTCCAACAAGGCCTTGCCCAAGTGGAGGCCGCCAGCCGCGGACGGCTGGGAGTGGCCCTGCTGGACGTGGGCAGTGGGCAAGCCGCCGGCTATCGCGCCGACGAACTCTTCCTGATGCTCAGCTCCTTCAAGACGCTGTCCGCGGCCTACGTGCTGGCGCGGGCCGACCGTGGCGAGGACCAGCTGTCGCGCCGCATCCCGATCACCGACGCCGATGTCCGGGGGTATTCGCCGGTCACGCGGCTGCATGTCGGGCCGCGGGGAATGACGCTGGCCGAACTCTGTGAAGCGACGATCACCACCAGCGACAACGCGGCGGTCAACCTCATGCACAAGAGCTATGGCGGCCCGCAAGCCCTGACCCGCTACCTGCGCAGCCTGGGCGATACCGTCACGCGCCACGATCGCTACGAACCCGAATTGAACCGCCCGCACCCGAGCGAACCGCAGGACACCACCACCCCGCAGGCCATGGCGCGCACGCTGGATACGCTACTGTTCGGCGACGCGCTCAAGCCGCAATCGCGGCAGCAACTGCAATCCTGGCTGCTGGCCAACACGACGGGCGGCAAGCGCCTGCGCGCCGGCATGCCGGCGGATTGGAAGATCGGCGAGAAGACAGGCACCTATTCGAAGGTGGGCTGCAACGACGCCGGCTTCGCGCAACCGCCCGGCGCGGCGCCGATCATCATCGCGGCCTATCTGGAAACCACCGCGGTGCCGATGGAGGAGCGCGACCGCTGCATCGCCGAGGTCGGCAGGCTGGTGGCGGCATTGGGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36941","NCBI_taxonomy_name":"Achromobacter xylosoxidans","NCBI_taxonomy_id":"85698"}}}},"ARO_accession":"3006901","ARO_id":"45363","ARO_name":"AXC-5","CARD_short_name":"AXC-5","ARO_description":"AXC-5 is a AXC beta-lactamase.","ARO_category":{"43853":{"category_aro_accession":"3005393","category_aro_cvterm_id":"43853","category_aro_name":"AXC beta-lactamase","category_aro_description":"AXC beta-lactamases are class A beta-lactamase found in the Anaeromyxobacter genus.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4368":{"model_id":"4368","model_name":"BEL-4","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"6743":{"protein_sequence":{"accession":"WP_065158950.1","sequence":"MKLLLYPLLLFLVIPAFAQADFEHAISDLEAHNQAKIGVALVSENGNLIQGYRANERFAMCSTFKLPLAALVLSRIDAGEENPERKLHYDSAFLEEYAPAAKRYVATGYMTVTEAIQSALQLSDNAAANLLLKEVGGPPLLTKYFRSLGDKVSRLDRIEPTLNTNTPGDERDATTPMSMAQTVSKLIFGDTLTYKSKGQLRRLLIGNQTGDKTIRAGLPDSWVTGDKTGSCANGGRNDVAFFITTAGKKYVLSVYTNAPELQGEERALLIASVAKLARQYVVH"},"dna_sequence":{"accession":"NG_050978.1","fmin":"0","fmax":"852","strand":"+","sequence":"ATGAAACTGCTGCTCTACCCGTTATTGCTGTTCCTTGTCATTCCAGCCTTTGCCCAGGCGGACTTTGAACATGCCATTTCAGATCTTGAGGCGCACAATCAAGCCAAGATCGGAGTGGCCCTAGTTAGTGAAAATGGCAACCTGATTCAAGGGTATCGTGCGAATGAAAGGTTCGCGATGTGCTCAACTTTCAAGTTGCCGTTGGCCGCTCTTGTTCTGAGTCGCATTGACGCTGGGGAAGAGAATCCTGAGCGCAAGCTTCATTACGATTCCGCGTTCCTTGAAGAGTACGCCCCAGCCGCAAAACGGTATGTGGCAACTGGATATATGACTGTAACTGAGGCAATTCAATCCGCCCTCCAACTCAGCGACAATGCCGCAGCTAACCTGCTGTTAAAAGAGGTTGGCGGCCCACCTTTATTGACAAAGTATTTCCGTAGCCTGGGTGATAAAGTAAGTCGCCTTGATCGTATTGAACCGACTTTGAACACCAATACGCCCGGCGATGAAAGAGATGCAACAACGCCCATGTCCATGGCACAGACTGTGTCAAAGCTGATTTTTGGAGACACGTTGACATATAAATCCAAGGGGCAGCTAAGGCGATTACTCATCGGCAATCAGACCGGGGACAAAACCATTCGAGCTGGCTTGCCTGATTCATGGGTAACGGGTGACAAGACAGGCTCGTGTGCGAATGGCGGCCGTAACGATGTGGCGTTTTTTATAACCACTGCCGGAAAAAAATATGTTCTTTCTGTATATACCAATGCACCTGAATTGCAAGGCGAGGAAAGGGCGTTATTAATTGCTTCTGTAGCAAAGTTAGCACGTCAATATGTTGTTCACTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006154","ARO_id":"44616","ARO_name":"BEL-4","CARD_short_name":"BEL-4","ARO_description":"BEL-4 is a BEL beta-lactamase.","ARO_category":{"38784":{"category_aro_accession":"3002384","category_aro_cvterm_id":"38784","category_aro_name":"BEL beta-lactamase","category_aro_description":"BEL beta-lactamases are class A expanded-spectrum beta-lactamases that are inhibited by clavulanic acid. They are chromosomally encoded and hydrolyze most cephalosporins and aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4369":{"model_id":"4369","model_name":"BKC-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"6744":{"protein_sequence":{"accession":"WP_171476787.1","sequence":"MTITFSRRQAIAGALLAVPAVFTLAASAGAATGGLLEKRLAASAGAATGGLLEKRLAELEGRHKGRIGVAIHNLATGARIGHRADERFLMCSTFKALLAAHILARVDRKEETLDRRIVVGKSDLVDWSPVVETRVGGEGISIAELCEAAITLSDNAAANLLLSASGGPKAVTQFLRGFGDDVTRLDRTEPTLNYRETPDDERDTTTPAAMAETLRKLIIGDVLARGSKAQLAAWLVMNKTGDTRLRAGFPVDWTTGDKTGTNGDRHGNANDVAIAWSPDRGAVVVTAFCEIPGISGDERNAVIAEIGRIAAEA"},"dna_sequence":{"accession":"NG_068505.1","fmin":"0","fmax":"942","strand":"+","sequence":"ATGACGATCACATTTTCGCGCCGGCAGGCGATTGCCGGCGCTCTCCTTGCCGTTCCCGCCGTGTTCACGCTGGCCGCCAGCGCCGGGGCGGCCACGGGCGGCCTGCTGGAAAAGAGGCTGGCCGCCAGCGCCGGGGCGGCCACGGGCGGCCTGCTGGAAAAGAGGCTGGCCGAGCTGGAAGGGCGTCACAAGGGCCGCATCGGCGTTGCCATACATAATCTCGCAACGGGCGCCCGCATCGGCCACCGGGCGGACGAGCGCTTCCTGATGTGCAGCACCTTCAAGGCGTTGCTGGCGGCCCATATCCTCGCCCGCGTCGACAGGAAGGAAGAAACGCTCGACCGGCGGATCGTCGTCGGGAAATCCGATCTTGTGGACTGGTCGCCGGTGGTGGAAACCCGTGTCGGCGGCGAGGGCATCTCGATTGCCGAGCTTTGCGAGGCGGCGATCACGCTCAGCGACAACGCCGCGGCCAATCTCCTGCTGTCCGCCTCGGGCGGGCCGAAGGCCGTCACGCAGTTCCTGCGCGGTTTCGGCGACGACGTGACGCGCCTCGACCGCACCGAACCGACGCTCAACTATCGCGAGACGCCGGACGACGAGCGCGACACGACCACGCCCGCCGCCATGGCCGAGACGCTGCGCAAGCTGATCATCGGCGATGTCCTCGCGCGCGGCTCGAAGGCGCAGCTTGCCGCCTGGCTGGTGATGAACAAGACCGGCGACACGCGATTGCGCGCCGGCTTCCCGGTCGACTGGACGACCGGCGACAAGACCGGCACGAACGGCGACAGGCACGGCAACGCCAACGATGTCGCCATCGCCTGGTCGCCGGATCGCGGCGCGGTGGTCGTCACCGCTTTCTGCGAGATTCCCGGCATTTCCGGGGATGAGCGCAACGCCGTCATCGCCGAGATTGGTCGCATTGCCGCCGAGGCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39098","NCBI_taxonomy_name":"Enterobacter hormaechei","NCBI_taxonomy_id":"158836"}}}},"ARO_accession":"3006223","ARO_id":"44685","ARO_name":"BKC-2","CARD_short_name":"BKC-2","ARO_description":"BKC-2 is a BKC beta-lactamase.","ARO_category":{"42868":{"category_aro_accession":"3004756","category_aro_cvterm_id":"42868","category_aro_name":"BKC Beta-lactamase","category_aro_description":"BKC beta-lactamase is a class A beta-lactamase.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4370":{"model_id":"4370","model_name":"BlaB-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"6745":{"protein_sequence":{"accession":"WP_029729112.1","sequence":"MLKKIKISLILALGLTSLQAFGQENPDVKIEKLKDNLYVYTTYNTFNGTKYAANAVYLVTDKGVVVIDCPWGEDKFKSFTDEIYKKHGKKVIMNIATHSHDDRAGGLEYFGKIGAKTYSTKMTDSILAKENKPRAQYTFDNNKSFKVGKSEFQVYYPGKGHTADNVVVWFPKEKVLVGGCIIKSADSKDLGYIGEAYVNDWTQSVHNIQQKFSGAQYVVAGHDDWKDQRSIQHTLDLINEYQQKQKASN"},"dna_sequence":{"accession":"NG_048691.1","fmin":"100","fmax":"850","strand":"+","sequence":"ATGTTGAAAAAAATAAAAATAAGCTTGATTCTTGCTCTTGGGCTTACCAGTTTGCAGGCATTTGGACAGGAGAATCCTGATGTCAAAATTGAAAAGCTAAAAGATAATCTGTATGTATACACAACCTACAATACATTTAACGGGACTAAATATGCCGCAAATGCAGTATATCTGGTAACTGATAAGGGTGTTGTGGTTATAGACTGTCCGTGGGGAGAAGACAAATTTAAAAGCTTTACGGACGAGATTTATAAAAAACACGGAAAGAAAGTTATTATGAATATTGCAACACATTCTCATGATGATCGTGCCGGAGGTCTTGAATATTTTGGTAAAATAGGTGCAAAAACTTATTCTACTAAAATGACAGATTCTATTTTAGCAAAAGAGAATAAGCCAAGAGCACAATATACTTTTGACAATAATAAATCTTTCAAAGTAGGAAAATCCGAGTTTCAGGTTTACTATCCCGGAAAAGGGCACACAGCAGATAATGTGGTGGTATGGTTTCCAAAAGAAAAAGTATTGGTTGGAGGTTGTATTATAAAAAGTGCTGATTCAAAGGACCTGGGGTATATTGGAGAAGCATATGTAAACGACTGGACGCAGTCTGTACACAATATTCAACAAAAGTTTTCCGGTGCTCAGTACGTTGTTGCAGGGCATGATGATTGGAAAGATCAAAGATCAATACAACATACACTAGACTTAATCAATGAATATCAACAAAAACAAAAGGCTTCAAATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3005522","ARO_id":"43984","ARO_name":"BlaB-1","CARD_short_name":"BlaB-1","ARO_description":"BlaB-1 is a BlaB beta-lactamase.","ARO_category":{"41365":{"category_aro_accession":"3004201","category_aro_cvterm_id":"41365","category_aro_name":"BlaB beta-lactamase","category_aro_description":"BlaB beta-lactamases are class B beta-lactamases that are found in a variety of species and have the ability to hydrolyze penams and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4371":{"model_id":"4371","model_name":"BlaB-10","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"6746":{"protein_sequence":{"accession":"WP_063857822.1","sequence":"MKGLKGLLVLALGFTGLQVFGQQNPDIKIEKLKDNLYVYTTYNTFKGTKYAANAVYMVTDKGVVVIDSPWGEDKFKSFTDEIYKKHGKKVIMNIATHSHDDRAGGLEYFGKLGAKTYSTKMTDSILAKENKPRAKYTFDNNKSFKVGKTEFQVYYPGKGHTADNVVVWFPKDKVLVGGCIVKSGDSKDLGFIGEAYVNDWTQSIHNIQQKFPYVQYVVAGHDDWKDQTSIQHTLDLISEYQQKQKASN"},"dna_sequence":{"accession":"NG_048692.1","fmin":"0","fmax":"747","strand":"+","sequence":"ATGAAAGGATTAAAAGGGCTATTGGTTCTGGCTTTAGGCTTTACAGGACTACAGGTTTTTGGGCAACAGAACCCTGATATTAAAATTGAAAAATTAAAAGATAATTTATACGTCTATACAACCTATAATACCTTCAAAGGAACTAAATATGCGGCTAATGCGGTATATATGGTAACCGATAAAGGAGTAGTGGTTATAGACTCTCCATGGGGAGAAGATAAATTTAAAAGTTTTACAGACGAGATTTATAAAAAGCACGGAAAGAAAGTTATCATGAACATTGCAACCCACTCTCATGATGATAGAGCCGGAGGTCTTGAATATTTTGGTAAACTAGGTGCAAAAACTTATTCTACTAAAATGACAGATTCTATTTTAGCAAAAGAGAATAAGCCAAGAGCAAAGTACACTTTTGATAATAATAAATCTTTTAAAGTAGGAAAGACTGAGTTTCAGGTTTATTATCCGGGAAAAGGTCATACAGCAGATAATGTGGTTGTGTGGTTTCCTAAAGACAAAGTATTAGTAGGAGGCTGCATTGTAAAAAGTGGTGATTCGAAAGACCTTGGGTTTATTGGGGAAGCTTATGTAAACGACTGGACACAGTCCATACACAACATTCAGCAGAAATTTCCCTATGTTCAGTATGTCGTTGCAGGTCATGACGACTGGAAAGATCAAACATCAATACAACATACACTGGATTTAATCAGTGAATATCAACAAAAACAAAAGGCTTCAAATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36960","NCBI_taxonomy_name":"Elizabethkingia meningoseptica","NCBI_taxonomy_id":"238"}}}},"ARO_accession":"3005523","ARO_id":"43985","ARO_name":"BlaB-10","CARD_short_name":"BlaB-10","ARO_description":"BlaB-10 is a BlaB beta-lactamase.","ARO_category":{"41365":{"category_aro_accession":"3004201","category_aro_cvterm_id":"41365","category_aro_name":"BlaB beta-lactamase","category_aro_description":"BlaB beta-lactamases are class B beta-lactamases that are found in a variety of species and have the ability to hydrolyze penams and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4372":{"model_id":"4372","model_name":"BlaB-11","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"6747":{"protein_sequence":{"accession":"WP_063857823.1","sequence":"MLKKIKISLILALGLTSLQAFGQENPDVKIEKLKDNLYVYTTYNTFNGTKYAANAVYLVTDKGVVVIDCPWGEDKFKSFTDEIYKKHGKKVIMNIATHSHDDRAGGLEYFGKIGAKTYSTKMTDSILAKENKPRAQYTFDNNKSFKVGKSEFQVYYPGKGHTADNVVVWFPKEKVLVGGCIIKSADSKDLGYIGEAYVNDWTQSVHNIQQKFSGAQYVVAGHDDWKDQRSIQRTLDLINEYQQKQKASN"},"dna_sequence":{"accession":"NG_048693.1","fmin":"0","fmax":"750","strand":"+","sequence":"ATGTTGAAAAAAATAAAAATAAGCTTGATTCTTGCTCTTGGGCTTACCAGTCTGCAGGCATTTGGACAGGAGAATCCTGATGTCAAAATTGAAAAGCTAAAAGATAATCTGTATGTATACACAACCTACAATACATTTAACGGGACTAAATATGCCGCTAATGCAGTATATCTGGTAACTGATAAGGGTGTTGTGGTTATAGACTGTCCGTGGGGAGAAGACAAATTTAAAAGCTTTACGGACGAGATTTATAAAAAACACGGAAAGAAAGTTATTATGAATATTGCAACACATTCTCATGATGATCGTGCCGGAGGTCTTGAATATTTTGGTAAAATAGGTGCAAAAACTTATTCTACTAAAATGACAGATTCTATTTTAGCAAAAGAGAATAAGCCAAGAGCACAATATACTTTTGACAATAATAAATCTTTCAAAGTAGGAAAATCCGAGTTTCAGGTTTACTATCCCGGAAAAGGACACACAGCAGATAATGTGGTGGTATGGTTTCCAAAAGAAAAAGTATTGGTTGGAGGTTGTATTATAAAAAGCGCTGATTCAAAAGACCTGGGGTATATTGGAGAAGCATATGTAAACGACTGGACGCAGTCTGTACACAATATTCAACAAAAGTTTTCCGGTGCTCAGTACGTTGTTGCAGGGCATGATGATTGGAAAGATCAAAGATCAATACAACGTACACTAGACTTAATCAATGAATATCAACAAAAACAAAAGGCTTCAAATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3005524","ARO_id":"43986","ARO_name":"BlaB-11","CARD_short_name":"BlaB-11","ARO_description":"BlaB-11 is a BlaB beta-lactamase.","ARO_category":{"41365":{"category_aro_accession":"3004201","category_aro_cvterm_id":"41365","category_aro_name":"BlaB beta-lactamase","category_aro_description":"BlaB beta-lactamases are class B beta-lactamases that are found in a variety of species and have the ability to hydrolyze penams and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4373":{"model_id":"4373","model_name":"BlaB-12","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"6748":{"protein_sequence":{"accession":"WP_063857824.1","sequence":"MMKKMKWALVLALGLTGLNAFGQETPEVKIEKLKDNLYVYTTYNTFNGTKYAANAVYLVTSKGVVVIDSPWGEEKFKNFTDEIYKRHGKKVIMNIATHSHDDRAGGLEYFKSLGVKTYSTKMTDSILAKDNKPRAQYTFDNNKSFKVGKDEFQVYYPGKGHTADNVVVWFPKDKVLVGGCIIKSGDSKDLGFLGEAYVNDWTQSVHNIQKKFPNVQYVVAGHDDWKDQTAIQHTLDLISEYQQKQKASN"},"dna_sequence":{"accession":"NG_048694.1","fmin":"0","fmax":"750","strand":"+","sequence":"ATGATGAAGAAAATGAAATGGGCACTTGTTCTTGCTCTTGGACTTACAGGTTTAAATGCCTTCGGGCAGGAAACTCCTGAAGTAAAAATAGAAAAGCTAAAAGACAATTTATATGTTTATACAACATATAATACATTCAACGGAACCAAATACGCAGCTAATGCGGTATATCTGGTGACCAGTAAAGGGGTGGTTGTAATAGATTCTCCATGGGGTGAGGAAAAATTTAAAAACTTTACCGACGAAATTTATAAAAGACACGGAAAGAAAGTCATCATGAATATTGCAACCCATTCTCATGACGACCGTGCAGGAGGTTTGGAATATTTTAAAAGCTTAGGGGTAAAAACCTATTCTACTAAAATGACAGACTCTATTTTAGCGAAAGATAATAAGCCAAGAGCCCAGTATACTTTTGATAATAATAAATCATTTAAAGTAGGAAAGGATGAGTTTCAGGTCTATTATCCGGGAAAAGGACATACAGCTGACAATGTAGTGGTATGGTTCCCTAAAGATAAAGTACTGGTGGGAGGCTGTATTATAAAAAGCGGTGATTCCAAAGATCTTGGATTTTTGGGAGAAGCATATGTAAACGACTGGACACAGTCAGTACACAATATTCAGAAGAAATTTCCCAATGTACAATATGTTGTTGCAGGCCACGATGACTGGAAAGATCAGACCGCCATTCAGCATACACTGGATTTAATCAGTGAATATCAACAAAAACAAAAGGCTTCAAATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36960","NCBI_taxonomy_name":"Elizabethkingia meningoseptica","NCBI_taxonomy_id":"238"}}}},"ARO_accession":"3005525","ARO_id":"43987","ARO_name":"BlaB-12","CARD_short_name":"BlaB-12","ARO_description":"BlaB-12 is a BlaB beta-lactamase.","ARO_category":{"41365":{"category_aro_accession":"3004201","category_aro_cvterm_id":"41365","category_aro_name":"BlaB beta-lactamase","category_aro_description":"BlaB beta-lactamases are class B beta-lactamases that are found in a variety of species and have the ability to hydrolyze penams and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4374":{"model_id":"4374","model_name":"BlaB-13","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"6749":{"protein_sequence":{"accession":"WP_063857825.1","sequence":"MMKKMKWALVLALGLTGLNAFGQETPEVKIEKLKDNLYVYTTYNTFNGTKYAANAVYLVTSKGVVVIDSPWGEEKFKNFTDEIYKRHGKKVIMNIATHSHDDRAGGLEYFKSLGVKTYSTKMTDSILAKDNKPRAQYTFDNNKSFKVGKDEFQVYYPGKGHTADNVVVWFPKDKVLVGGCIIKSGDSKNLGFLGEAYVNDWTQSVHNIQKKFPNVQYVVAGHDDWKDQTAIQHTLDLISEYQQKQKASN"},"dna_sequence":{"accession":"NG_048695.1","fmin":"0","fmax":"750","strand":"+","sequence":"ATGATGAAGAAAATGAAATGGGCACTTGTTCTTGCTCTTGGACTTACAGGTTTAAATGCCTTCGGGCAGGAAACTCCTGAAGTAAAAATAGAAAAGCTAAAAGACAATTTATATGTTTATACAACATATAATACATTCAACGGAACCAAATACGCAGCTAATGCGGTATATCTGGTGACCAGTAAAGGGGTGGTTGTAATAGATTCTCCATGGGGTGAGGAAAAATTTAAAAACTTTACCGACGAAATTTATAAAAGACACGGAAAGAAAGTCATCATGAATATTGCAACACATTCTCATGACGACCGTGCAGGAGGTTTGGAATATTTTAAAAGCTTAGGGGTAAAAACCTATTCTACTAAAATGACAGACTCTATTTTAGCGAAAGATAATAAGCCAAGAGCCCAGTATACTTTTGATAATAATAAATCATTTAAAGTAGGAAAGGATGAGTTTCAGGTCTATTATCCGGGAAAAGGACATACAGCTGACAATGTAGTGGTATGGTTCCCTAAAGATAAAGTACTGGTGGGAGGCTGTATTATAAAAAGCGGTGATTCCAAAAATCTTGGATTTTTGGGAGAAGCATATGTAAACGACTGGACACAGTCAGTACACAATATTCAGAAGAAATTTCCCAATGTACAATATGTTGTTGCAGGCCACGATGACTGGAAAGATCAGACTGCCATTCAGCATACACTGGATTTAATCAGTGAATATCAACAAAAACAAAAGGCTTCAAATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36960","NCBI_taxonomy_name":"Elizabethkingia meningoseptica","NCBI_taxonomy_id":"238"}}}},"ARO_accession":"3005526","ARO_id":"43988","ARO_name":"BlaB-13","CARD_short_name":"BlaB-13","ARO_description":"BlaB-13 is a BlaB beta-lactamase.","ARO_category":{"41365":{"category_aro_accession":"3004201","category_aro_cvterm_id":"41365","category_aro_name":"BlaB beta-lactamase","category_aro_description":"BlaB beta-lactamases are class B beta-lactamases that are found in a variety of species and have the ability to hydrolyze penams and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4375":{"model_id":"4375","model_name":"BlaB-14","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"6750":{"protein_sequence":{"accession":"WP_034848068.1","sequence":"MKNIMRALILVFGFMSFFMFGQENPDVKIEKLRDNLYVYTTYNTFNGTKYAANAVYLVTDKGVVVIDCPWGEDKFKSFTDEIYKKHGKKVIMNIATHSHDDRAGGLEYFGKIGAKTYSTKMTDSILAKENKPRAQYTFDNNKSFKVGKSEFQVYYPGKGHTADNVVVWFPKEKVLVGGCIIKSADSKDLGYIGEAYVNDWTQSVHNIQQKFSGAQYVVAGHDDWKDQRSIQRTLDLINEYQQKQKASN"},"dna_sequence":{"accession":"NG_048696.1","fmin":"100","fmax":"847","strand":"+","sequence":"ATGAAGAATATAATGCGGGCACTGATCCTTGTTTTTGGTTTTATGAGTTTTTTTATGTTTGGACAGGAGAATCCTGACGTCAAAATTGAAAAGCTAAGAGATAATCTGTATGTATACACAACCTACAATACATTTAACGGGACTAAATATGCCGCTAATGCAGTATATCTGGTAACTGATAAGGGTGTTGTGGTTATAGACTGTCCGTGGGGAGAAGACAAATTTAAAAGCTTTACGGACGAGATTTATAAAAAACACGGAAAGAAAGTTATTATGAATATTGCAACACATTCTCATGATGATCGTGCCGGAGGTCTTGAATATTTTGGTAAAATAGGTGCAAAAACTTATTCTACTAAAATGACAGATTCTATTTTAGCAAAAGAGAATAAGCCAAGAGCACAATATACTTTTGACAATAATAAATCTTTCAAAGTAGGAAAATCCGAGTTTCAGGTTTACTATCCCGGAAAAGGACATACAGCAGATAATGTGGTGGTATGGTTTCCAAAAGAAAAAGTATTGGTTGGAGGTTGTATTATAAAAAGCGCTGATTCAAAAGACCTGGGGTATATTGGAGAAGCATATGTAAATGACTGGACGCAGTCTGTACACAATATTCAACAGAAGTTTTCCGGTGCTCAGTACGTTGTTGCGGGGCATGATGATTGGAAAGATCAAAGATCAATACAACGTACACTAGACTTAATCAATGAATATCAACAAAAACAAAAGGCTTCAAATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36960","NCBI_taxonomy_name":"Elizabethkingia meningoseptica","NCBI_taxonomy_id":"238"}}}},"ARO_accession":"3005527","ARO_id":"43989","ARO_name":"BlaB-14","CARD_short_name":"BlaB-14","ARO_description":"BlaB-14 is a BlaB beta-lactamase.","ARO_category":{"41365":{"category_aro_accession":"3004201","category_aro_cvterm_id":"41365","category_aro_name":"BlaB beta-lactamase","category_aro_description":"BlaB beta-lactamases are class B beta-lactamases that are found in a variety of species and have the ability to hydrolyze penams and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4376":{"model_id":"4376","model_name":"BlaB-15","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"6751":{"protein_sequence":{"accession":"WP_140423306.1","sequence":"MLKRIKGLLVLALGFTGLQVFGQQNPDIKIEKLKDNLYVYTTYNTFKGTKYAANAVYMVTDKGVVVIDSPWGEDKFKSFTDEIYKKHGKKVIMNIATHSHDDRAGGLEYFGKLGAKTYSTKMTDSILAKENKPRAKYTFDNNKSFKVGKTEFQVYYPGKGHTADNVVVWFPKDKVLVGGCIVKSGDSKDLGYIGEAYVNDWTQSIHNIQQKFPDVQYVVAGHDDWKDQTSIQHTLDLISDYQQKQKASN"},"dna_sequence":{"accession":"NG_065421.1","fmin":"0","fmax":"750","strand":"+","sequence":"ATGTTGAAAAGGATAAAAGGATTATTGGTTCTGGCCTTAGGTTTTACAGGGCTACAGGTTTTTGGGCAGCAAAATCCTGATATTAAAATTGAAAAATTAAAAGATAATTTATACGTCTATACAACCTATAATACCTTCAAAGGGACTAAATATGCAGCTAATGCGGTATATATGGTAACTGATAAAGGAGTAGTGGTGATAGACTCTCCATGGGGAGAAGATAAATTTAAAAGTTTTACAGACGAGATTTATAAAAAGCATGGAAAGAAAGTCATCATGAACATTGCTACTCACTCTCATGATGATAGAGCCGGAGGTCTTGAGTATTTTGGTAAATTAGGTGCAAAAACTTATTCCACTAAAATGACAGATTCTATCTTAGCAAAAGAGAATAAGCCAAGAGCAAAGTACACTTTTGATAATAATAAATCCTTTAAAGTAGGAAAGACTGAATTTCAGGTCTATTATCCGGGAAAAGGTCATACAGCAGATAATGTGGTGGTATGGTTCCCTAAAGACAAAGTATTAGTAGGAGGCTGCATTGTAAAAAGCGGTGATTCGAAAGACCTTGGGTACATTGGAGAAGCTTATGTAAATGACTGGACACAGTCCATACACAACATTCAGCAGAAATTTCCCGATGTTCAGTATGTCGTTGCAGGCCACGATGACTGGAAAGATCAAACATCAATACAACATACACTGGATTTAATCAGTGATTACCAACAAAAACAAAAGGCTTCAAATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3005528","ARO_id":"43990","ARO_name":"BlaB-15","CARD_short_name":"BlaB-15","ARO_description":"BlaB-15 is a BlaB beta-lactamase.","ARO_category":{"41365":{"category_aro_accession":"3004201","category_aro_cvterm_id":"41365","category_aro_name":"BlaB beta-lactamase","category_aro_description":"BlaB beta-lactamases are class B beta-lactamases that are found in a variety of species and have the ability to hydrolyze penams and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4377":{"model_id":"4377","model_name":"BlaB-16","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"6752":{"protein_sequence":{"accession":"WP_086980232.1","sequence":"MMKRLKGLLVLALGFTGLQVFGQENPDVKIEKLKDNLYVYTTYNSYKGVKYAANAVYIVTDKGVVVIDCPWGEEKFKSFTDEIYKKHGKKVIMNIATHSHDDRAGGLGYFKKIGAKTYSTKMTDSILAKENKPRAEYTFDNNKSFKVGKSEFQVYYPGKGHTADNVVVWFPKEKVLVGGCIIKSADSKDLGFIGEAYVNDWTQSVYNIQQKFSGAQYIVAGHDDWKDQRSIKHTLDLISEYQQKQKASN"},"dna_sequence":{"accession":"NG_067205.1","fmin":"0","fmax":"750","strand":"+","sequence":"ATGATGAAAAGATTAAAAGGATTATTGGTTCTGGCTTTAGGTTTTACAGGACTACAGGTTTTTGGACAGGAGAATCCTGATGTTAAAATTGAGAAACTAAAAGATAATCTGTATGTTTATACAACCTATAATTCCTATAAAGGAGTAAAGTATGCAGCTAATGCTGTATATATAGTAACGGATAAAGGAGTTGTAGTTATAGATTGCCCATGGGGAGAGGAGAAATTTAAAAGCTTTACGGACGAGATTTATAAAAAGCACGGAAAGAAAGTCATTATGAATATTGCTACTCATTCTCATGATGACCGTGCCGGAGGCTTGGGATATTTCAAAAAAATAGGTGCAAAAACTTATTCTACTAAAATGACAGATTCTATCTTAGCGAAAGAGAATAAGCCAAGAGCAGAATATACTTTTGATAATAATAAATCTTTTAAAGTAGGTAAATCTGAATTTCAGGTTTACTATCCGGGAAAAGGTCATACAGCAGATAATGTAGTGGTATGGTTTCCCAAAGAAAAAGTATTAGTTGGAGGCTGTATTATAAAGAGTGCTGATTCAAAAGACCTTGGGTTTATTGGAGAAGCTTATGTAAACGATTGGACACAGTCTGTATACAATATTCAGCAGAAGTTTTCCGGGGCTCAGTATATAGTCGCGGGGCATGATGACTGGAAAGACCAAAGATCAATAAAACATACACTGGACCTAATCAGTGAATACCAACAAAAACAAAAGGCTTCAAATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3005529","ARO_id":"43991","ARO_name":"BlaB-16","CARD_short_name":"BlaB-16","ARO_description":"BlaB-16 is a BlaB beta-lactamase.","ARO_category":{"41365":{"category_aro_accession":"3004201","category_aro_cvterm_id":"41365","category_aro_name":"BlaB beta-lactamase","category_aro_description":"BlaB beta-lactamases are class B beta-lactamases that are found in a variety of species and have the ability to hydrolyze penams and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4378":{"model_id":"4378","model_name":"BlaB-17","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"6753":{"protein_sequence":{"accession":"WP_021348010.1","sequence":"MLKKIKISLILALGLTSLQAFGQENPDVKIEKLRDNLYVYTTYNTFNGTKYAANAVYLVTDKGVVVIDCPWGEDKFKSFTDEIYKKHGKKVIMNIATHSHDDRAGGLEYFGKIGAKTYSTKMTDSILAKENKPRAQYTFDNNKSFKVGKSEFQVYYPGKGHTADNVVVWFPKEKVLVGGCIIKSADSKDLGYIGEAYVNDWTQSVHNIQQKFSGAQYVVAGHDDWKDQRSIQRTLDLINEYQQKQKASN"},"dna_sequence":{"accession":"NG_067206.1","fmin":"100","fmax":"850","strand":"+","sequence":"ATGTTGAAAAAAATAAAAATAAGCTTGATTCTTGCTCTTGGGCTTACCAGTCTGCAGGCATTTGGACAGGAGAATCCTGACGTCAAAATTGAAAAGCTAAGAGATAATCTGTATGTATACACAACCTACAATACATTTAACGGGACTAAATATGCCGCTAATGCAGTATATCTGGTAACTGATAAGGGTGTTGTGGTTATAGACTGTCCGTGGGGAGAAGACAAATTTAAAAGCTTTACGGACGAGATTTATAAAAAACACGGAAAGAAAGTTATTATGAATATTGCAACACATTCTCATGATGATCGTGCCGGAGGTCTTGAATATTTTGGTAAAATAGGTGCAAAAACTTATTCTACTAAAATGACAGATTCTATTTTAGCAAAAGAGAATAAGCCAAGAGCACAATATACTTTTGACAATAATAAATCTTTCAAAGTAGGAAAATCCGAGTTTCAGGTTTACTATCCCGGAAAAGGACACACAGCAGATAATGTGGTGGTATGGTTTCCAAAAGAAAAAGTATTGGTTGGAGGTTGTATTATAAAAAGTGCTGATTCAAAAGACCTGGGATATATTGGAGAAGCATATGTAAACGACTGGACGCAGTCTGTACACAATATTCAACAAAAGTTTTCCGGTGCTCAGTACGTTGTTGCGGGGCATGATGATTGGAAAGATCAAAGATCAATACAACGTACACTAGACTTAATCAATGAATATCAACAAAAACAAAAGGCTTCAAATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41081","NCBI_taxonomy_name":"Elizabethkingia anophelis","NCBI_taxonomy_id":"1117645"}}}},"ARO_accession":"3005530","ARO_id":"43992","ARO_name":"BlaB-17","CARD_short_name":"BlaB-17","ARO_description":"BlaB-17 is a BlaB beta-lactamase.","ARO_category":{"41365":{"category_aro_accession":"3004201","category_aro_cvterm_id":"41365","category_aro_name":"BlaB beta-lactamase","category_aro_description":"BlaB beta-lactamases are class B beta-lactamases that are found in a variety of species and have the ability to hydrolyze penams and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4379":{"model_id":"4379","model_name":"BlaB-18","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"6754":{"protein_sequence":{"accession":"WP_078691467.1","sequence":"MMKNIMRALILVFGFMSFFMFGQENPDVKIDKLKDNLYVYTTYNTFNGTKYAANAVYLVTDKGVVVIDCPWGEDKFKSFTDEIYKKHGKKVIMNIATHSHDDRAGGLEYFGKIGAKTYSTKMTDSILAKENKPRAQYTFDNNKSFKVGKSEFQVYYPGKGHTADNVVVWFPKEKVLVGGCIIKSADSKDLGYIGEAYVNDWTQSVHNIQQKFSGAQYVVAGHDDWKDQRSIQRTLDLINEYQQKQKASN"},"dna_sequence":{"accession":"NG_067207.1","fmin":"100","fmax":"850","strand":"+","sequence":"ATTATGAAGAATATAATGCGGGCACTGATCCTTGTTTTTGGTTTTATGAGTTTTTTTATGTTTGGACAGGAGAATCCTGACGTTAAAATTGATAAGCTAAAAGATAATCTGTATGTATACACAACCTACAATACATTTAACGGGACTAAATATGCCGCTAATGCAGTATATCTGGTAACTGATAAGGGTGTTGTGGTTATAGACTGTCCGTGGGGAGAAGACAAATTTAAAAGCTTTACGGACGAGATTTATAAAAAACACGGAAAGAAAGTTATTATGAATATTGCAACACATTCTCATGATGATCGTGCCGGAGGTCTTGAATATTTTGGTAAAATAGGTGCAAAAACTTATTCTACTAAAATGACAGATTCTATTTTAGCAAAAGAGAATAAGCCAAGAGCACAATATACTTTTGACAATAATAAATCTTTCAAAGTAGGAAAATCCGAGTTTCAGGTTTACTATCCCGGAAAAGGACATACAGCAGATAATGTGGTGGTATGGTTTCCAAAAGAAAAAGTATTGGTTGGAGGTTGTATTATAAAAAGCGCTGATTCAAAAGACCTGGGGTATATTGGAGAAGCATATGTAAACGACTGGACGCAGTCTGTACACAATATTCAACAAAAGTTTTCCGGTGCTCAGTACGTTGTTGCAGGGCATGATGATTGGAAAGATCAAAGATCAATACAACGTACACTAGACTTAATCAATGAATATCAACAAAAACAAAAGGCTTCAAATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41081","NCBI_taxonomy_name":"Elizabethkingia anophelis","NCBI_taxonomy_id":"1117645"}}}},"ARO_accession":"3005531","ARO_id":"43993","ARO_name":"BlaB-18","CARD_short_name":"BlaB-18","ARO_description":"BlaB-18 is a BlaB beta-lactamase.","ARO_category":{"41365":{"category_aro_accession":"3004201","category_aro_cvterm_id":"41365","category_aro_name":"BlaB beta-lactamase","category_aro_description":"BlaB beta-lactamases are class B beta-lactamases that are found in a variety of species and have the ability to hydrolyze penams and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4380":{"model_id":"4380","model_name":"BlaB-19","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"6755":{"protein_sequence":{"accession":"WP_019051344.1","sequence":"MMKKMKWALVLALGLTGLNAFGQETPEVKIEKLKDNLYVYTTYNTFNGTKYAANAVYLVTSKGVVVIDSPWGEEKFKNFTDEIYKRHGKKVIMNIATHSHDDRAGGLEYFKSLGAKTYSTKMTDSILAKDNKPRAQYTFDNNKSFKVGKDEFQVYYPGKGHTADNVVVWFPKDKVLVGGCIIKSGDSKDLGFLGEAYVNDWTQSVHNIQKKFPNVQYVVAGHDDWKDQTAIQHTLDLISEYQQKQKASN"},"dna_sequence":{"accession":"NG_067208.1","fmin":"100","fmax":"850","strand":"+","sequence":"ATGATGAAGAAAATGAAATGGGCACTTGTTCTTGCTCTTGGACTTACAGGTTTAAATGCCTTCGGGCAGGAAACTCCTGAAGTAAAAATAGAAAAGCTAAAAGACAATTTATATGTTTATACAACATATAATACATTCAACGGAACCAAATACGCAGCTAATGCGGTATATCTGGTGACCAGTAAAGGGGTGGTTGTAATAGATTCTCCATGGGGTGAGGAAAAATTTAAAAACTTTACCGACGAAATTTATAAAAGACACGGAAAGAAAGTGATCATGAATATTGCAACACACTCTCATGATGACCGTGCAGGAGGTTTGGAATATTTTAAAAGCTTAGGGGCAAAAACCTATTCTACTAAAATGACAGACTCTATTTTAGCGAAAGATAATAAGCCAAGAGCCCAGTATACTTTTGATAATAATAAATCATTTAAAGTAGGAAAGGATGAGTTTCAGGTCTATTATCCGGGAAAAGGACATACAGCTGACAATGTAGTGGTATGGTTCCCTAAAGATAAAGTACTGGTGGGCGGCTGTATTATAAAAAGTGGGGATTCCAAAGATCTTGGCTTTTTGGGAGAAGCATATGTAAACGACTGGACACAGTCAGTACACAATATTCAGAAGAAATTTCCCAATGTACAATATGTTGTTGCAGGCCACGATGACTGGAAAGATCAGACTGCCATTCAGCATACACTGGATTTAATCAGTGAATATCAACAAAAACAAAAGGCTTCAAATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36960","NCBI_taxonomy_name":"Elizabethkingia meningoseptica","NCBI_taxonomy_id":"238"}}}},"ARO_accession":"3005532","ARO_id":"43994","ARO_name":"BlaB-19","CARD_short_name":"BlaB-19","ARO_description":"BlaB-19 is a BlaB beta-lactamase.","ARO_category":{"41365":{"category_aro_accession":"3004201","category_aro_cvterm_id":"41365","category_aro_name":"BlaB beta-lactamase","category_aro_description":"BlaB beta-lactamases are class B beta-lactamases that are found in a variety of species and have the ability to hydrolyze penams and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4381":{"model_id":"4381","model_name":"BlaB-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"6756":{"protein_sequence":{"accession":"WP_063857826.1","sequence":"MLKKIKISLILALGLTSLQAFGQENPDVKIDKLKDNLYVYTTYNTFNGTKYAANAVYLVTDKGVVVIDCPWGEDKFKSFTDEIYKKHGKKVIMNIATHSHDDRAGGLEYFGKIGAKTYSTKMTDSILAKENKPRAQYTFDNNKSFKVGKSEFQVYYPGKGHTADNVVVWFPKEKVLVGGCIIKSADSKDLGYIGEAYVNDWTQSVHNIQQKFSGAQYVVAGHDDWKDQRSIQRTLDLINEYQQKQKASN"},"dna_sequence":{"accession":"NG_048697.1","fmin":"100","fmax":"850","strand":"+","sequence":"ATGTTGAAAAAAATAAAAATAAGCTTGATTCTTGCTCTTGGGCTTACCAGTCTGCAGGCATTTGGACAGGAGAATCCTGACGTTAAAATTGATAAGCTAAAAGATAATCTGTATGTATACACAACCTACAATACATTTAACGGGACTAAATATGCCGCTAATGCAGTATATCTGGTAACTGATAAGGGTGTTGTGGTTATAGACTGTCCGTGGGGAGAAGACAAATTTAAAAGCTTTACGGACGAGATTTATAAAAAACACGGAAAGAAAGTTATTATGAATATTGCAACACATTCTCATGATGATCGTGCCGGAGGTCTTGAATATTTTGGTAAAATAGGTGCAAAAACTTATTCTACTAAAATGACAGATTCTATTTTAGCAAAAGAGAATAAGCCAAGAGCACAATATACTTTTGACAATAATAAATCTTTCAAAGTAGGAAAATCCGAGTTTCAGGTTTACTATCCCGGAAAAGGACATACAGCAGATAATGTGGTGGTATGGTTTCCAAAAGAAAAAGTATTGGTTGGAGGTTGTATTATAAAAAGCGCTGATTCAAAAGACCTGGGGTATATTGGAGAAGCATATGTAAACGACTGGACGCAGTCTGTACACAATATTCAACAAAAGTTTTCCGGTGCTCAGTACGTTGTTGCAGGGCATGATGATTGGAAAGATCAAAGATCAATACAACGTACACTAGACTTAATCAATGAATATCAACAAAAACAAAAGGCTTCAAATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3005533","ARO_id":"43995","ARO_name":"BlaB-2","CARD_short_name":"BlaB-2","ARO_description":"BlaB-2 is a BlaB beta-lactamase.","ARO_category":{"41365":{"category_aro_accession":"3004201","category_aro_cvterm_id":"41365","category_aro_name":"BlaB beta-lactamase","category_aro_description":"BlaB beta-lactamases are class B beta-lactamases that are found in a variety of species and have the ability to hydrolyze penams and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4382":{"model_id":"4382","model_name":"BlaB-20","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"6757":{"protein_sequence":{"accession":"WP_101360538.1","sequence":"MMKNIMRALILVFGFMSFFMFGQENPDVKIEKLRDNLYVYTTYNTFNGTRYAANAVYLVTDKGVVVIDCPWGEDKFKSFTDEIYKKHGKKVIMNIATHSHDDRAGGLEYFGKIGAKTYSTKMTDSILAKENKPRAQYTFDNNKSFKVGKSEFQVYYPGKGHTADNVVVWFPKEKVLVGGCIIKSADSKDLGYIGEAYVNDWTQSVHNIQQKFSGAQYVVAGHDDWKDQRSIQRTLDLINEYQQKQKASN"},"dna_sequence":{"accession":"NG_067209.1","fmin":"100","fmax":"850","strand":"+","sequence":"ATTATGAAGAATATAATGCGGGCACTGATCCTTGTTTTTGGTTTTATGAGTTTTTTTATGTTTGGACAGGAGAATCCTGACGTCAAAATTGAAAAGCTAAGAGATAATCTGTATGTATACACAACCTACAATACATTTAACGGGACTAGATATGCCGCTAATGCAGTATATCTGGTAACTGATAAGGGTGTTGTGGTTATAGACTGTCCGTGGGGAGAAGACAAATTTAAAAGCTTTACGGACGAGATTTATAAAAAACACGGAAAGAAAGTTATTATGAATATTGCAACACATTCTCATGATGATCGTGCCGGAGGTCTTGAATATTTTGGTAAAATAGGTGCAAAAACTTATTCTACTAAAATGACAGATTCTATTTTAGCAAAAGAGAATAAGCCAAGAGCACAATATACTTTTGACAATAATAAATCTTTCAAAGTAGGAAAATCCGAGTTTCAGGTTTACTATCCCGGAAAAGGACATACAGCAGATAATGTGGTGGTATGGTTTCCAAAAGAAAAAGTATTGGTTGGAGGTTGTATTATAAAAAGCGCTGATTCAAAAGACCTGGGGTATATTGGAGAAGCATATGTAAATGACTGGACGCAGTCTGTACACAATATTCAACAGAAGTTTTCCGGTGCTCAGTACGTTGTTGCAGGGCATGATGATTGGAAAGATCAAAGATCAATACAACGTACACTAGACTTAATCAATGAATATCAACAAAAACAAAAGGCTTCAAATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41081","NCBI_taxonomy_name":"Elizabethkingia anophelis","NCBI_taxonomy_id":"1117645"}}}},"ARO_accession":"3005534","ARO_id":"43996","ARO_name":"BlaB-20","CARD_short_name":"BlaB-20","ARO_description":"BlaB-20 is a BlaB beta-lactamase.","ARO_category":{"41365":{"category_aro_accession":"3004201","category_aro_cvterm_id":"41365","category_aro_name":"BlaB beta-lactamase","category_aro_description":"BlaB beta-lactamases are class B beta-lactamases that are found in a variety of species and have the ability to hydrolyze penams and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4383":{"model_id":"4383","model_name":"BlaB-22","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"6758":{"protein_sequence":{"accession":"WP_068801164.1","sequence":"MMKRLKGLLVLALGFTGLQVFGQQNPDIKIEKLKDNLYVYTTYNTFKGTKYAANAVYMVTDKGVMVIDSPWGEDKFKSFTDEIYKKHGKKVIMNIATHSHDDRAGGLEYFGKLGAKTYSTKMTDSILAKENKPRAKYTFDNNKSFKVGKTEFQVYYPGKGHTADNVVVWFPKDKVLVGGCIVKSGDSKDLGYIGEAYVNDWTQSIHNIQQKFPDVQYVVAGHDDWKDQTSIQHTLDLISDYQQKQKASN"},"dna_sequence":{"accession":"NG_067211.1","fmin":"100","fmax":"850","strand":"+","sequence":"ATGATGAAAAGATTAAAAGGACTATTGGTTCTGGCCTTAGGTTTTACAGGGCTACAGGTTTTTGGGCAGCAAAATCCTGATATTAAAATTGAAAAATTAAAAGATAATTTATACGTCTATACAACCTATAATACCTTCAAAGGGACTAAATATGCAGCTAATGCGGTATATATGGTAACTGATAAAGGAGTAATGGTTATAGACTCTCCATGGGGAGAAGATAAATTTAAAAGTTTTACAGACGAGATTTATAAAAAGCACGGAAAGAAAGTCATCATGAACATTGCTACTCACTCTCATGATGATAGAGCCGGAGGTCTTGAGTATTTTGGTAAATTAGGTGCGAAAACTTATTCTACTAAAATGACAGATTCTATTTTAGCAAAAGAGAATAAGCCAAGAGCAAAGTACACTTTTGATAATAATAAATCCTTTAAAGTAGGAAAGACTGAGTTTCAGGTCTATTATCCGGGAAAAGGGCATACGGCAGATAATGTGGTGGTATGGTTCCCTAAAGACAAAGTATTAGTAGGAGGCTGCATTGTAAAAAGTGGTGATTCGAAAGACCTTGGATATATTGGAGAAGCTTATGTAAACGACTGGACACAGTCTATACACAATATTCAGCAGAAATTTCCCGATGTTCAGTATGTCGTTGCAGGCCACGATGACTGGAAAGATCAAACATCAATACAACATACACTGGATTTAATCAGTGATTACCAACAAAAACAAAAGGCTTCAAATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3005535","ARO_id":"43997","ARO_name":"BlaB-22","CARD_short_name":"BlaB-22","ARO_description":"BlaB-22 is a BlaB beta-lactamase.","ARO_category":{"41365":{"category_aro_accession":"3004201","category_aro_cvterm_id":"41365","category_aro_name":"BlaB beta-lactamase","category_aro_description":"BlaB beta-lactamases are class B beta-lactamases that are found in a variety of species and have the ability to hydrolyze penams and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4384":{"model_id":"4384","model_name":"BlaB-23","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"6759":{"protein_sequence":{"accession":"WP_069214019.1","sequence":"MMKKMKWALVLALGLTGLNAFGQETPEVKIEKLKDNLYVYTTYNTFNGTKYAANAVYLVTSKGVVVIDSPWGEEKFKNFTDEIYKRHGKKVIMNIATHSHDDRAGGLEYFKSLGAKTYSTKMTDSILAKDNKPRAQYTFDNNKSFKVGKDEFQIYYPGKGHTADNVVVWFPKDKVLVGGCIIKSGDSKDLGFLGEAYVNDWTQSVHNIQKKFPNVQYVVAGHDDWKDQTAIQHTLDLISEYQQKQKASN"},"dna_sequence":{"accession":"NG_067212.1","fmin":"100","fmax":"850","strand":"+","sequence":"ATGATGAAGAAAATGAAATGGGCACTTGTTCTTGCTCTTGGACTTACAGGTTTAAACGCCTTCGGGCAGGAAACTCCTGAAGTGAAAATAGAAAAGCTAAAAGACAATTTATATGTTTATACAACATATAATACATTCAACGGAACCAAATACGCAGCTAATGCGGTATATCTGGTGACCAGTAAAGGGGTGGTTGTAATAGATTCTCCATGGGGTGAGGAAAAATTTAAAAATTTTACTGACGAAATTTATAAAAGACATGGAAAGAAAGTCATCATGAATATTGCAACACATTCACATGACGACCGTGCAGGAGGCTTGGAATATTTTAAAAGCTTAGGGGCAAAAACCTATTCTACTAAAATGACGGACTCTATTTTAGCAAAAGATAATAAACCAAGAGCCCAATATACTTTTGACAATAATAAGTCATTCAAAGTAGGAAAGGATGAGTTTCAGATCTATTATCCGGGAAAAGGACATACAGCTGACAATGTAGTGGTATGGTTCCCTAAAGATAAAGTACTGGTGGGAGGCTGTATTATAAAAAGCGGTGATTCCAAAGATCTTGGATTTTTGGGAGAAGCATATGTAAACGACTGGACACAGTCAGTACACAATATTCAGAAGAAATTTCCCAATGTACAATATGTTGTTGCAGGCCACGATGACTGGAAAGATCAGACCGCCATTCAGCATACACTGGATTTAATCAGTGAATATCAACAAAAACAAAAGGCTTCAAATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36960","NCBI_taxonomy_name":"Elizabethkingia meningoseptica","NCBI_taxonomy_id":"238"}}}},"ARO_accession":"3005536","ARO_id":"43998","ARO_name":"BlaB-23","CARD_short_name":"BlaB-23","ARO_description":"BlaB-23 is a BlaB beta-lactamase.","ARO_category":{"41365":{"category_aro_accession":"3004201","category_aro_cvterm_id":"41365","category_aro_name":"BlaB beta-lactamase","category_aro_description":"BlaB beta-lactamases are class B beta-lactamases that are found in a variety of species and have the ability to hydrolyze penams and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4385":{"model_id":"4385","model_name":"BlaB-24","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"6760":{"protein_sequence":{"accession":"WP_078704370.1","sequence":"MMKRLKGLLVLALGFTGLQVFGQQNPDIKIEKLKDNLYVYTTYNTFKGTKYAANAVYMVTDKGVVVIDSPWGEDKFKSFTDEIYKKHGKKVIMNIATHSHDDRAGGLEYFGKLGAKTYSTKMTDSILAKENKPRAKYTFDNNKSFKVGKTEFQVYYPGKGHTADNVVVWFPKDKVLVGGCIVKSGDSKDLGYIGEAYVNDWTQSIHNIQQKFPDVQYVVAGHDDWKDQTSIQHTLDLISEYQQKQKASN"},"dna_sequence":{"accession":"NG_067213.1","fmin":"100","fmax":"850","strand":"+","sequence":"ATGATGAAAAGATTAAAAGGACTATTGGTTCTGGCCTTAGGTTTTACAGGGCTACAGGTTTTTGGGCAGCAAAATCCTGATATTAAAATTGAAAAATTAAAAGATAATTTATACGTCTATACAACCTATAATACCTTCAAAGGGACTAAATATGCAGCTAATGCGGTATATATGGTAACTGATAAAGGAGTAGTGGTTATAGACTCTCCATGGGGAGAAGATAAATTTAAAAGTTTTACAGACGAGATTTATAAAAAGCACGGAAAGAAAGTCATCATGAACATTGCTACTCACTCTCATGATGATAGAGCCGGAGGTCTGGAATATTTTGGTAAACTAGGTGCAAAAACTTATTCCACTAAAATGACAGATTCTATCTTAGCAAAAGAGAATAAGCCAAGAGCAAAGTACACTTTTGATAATAATAAATCCTTTAAAGTAGGAAAGACTGAATTTCAGGTCTATTATCCGGGAAAAGGTCATACAGCAGATAATGTGGTGGTATGGTTCCCTAAAGACAAAGTATTAGTAGGAGGCTGCATTGTAAAAAGCGGTGATTCGAAAGACCTTGGGTACATTGGAGAAGCTTATGTAAATGACTGGACACAGTCCATACACAACATTCAGCAGAAATTTCCCGATGTTCAGTATGTCGTTGCAGGTCATGACGACTGGAAGGATCAAACATCAATACAACATACACTGGATTTAATCAGTGAATATCAACAAAAACAAAAGGCTTCAAATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3005537","ARO_id":"43999","ARO_name":"BlaB-24","CARD_short_name":"BlaB-24","ARO_description":"BlaB-24 is a BlaB beta-lactamase.","ARO_category":{"41365":{"category_aro_accession":"3004201","category_aro_cvterm_id":"41365","category_aro_name":"BlaB beta-lactamase","category_aro_description":"BlaB beta-lactamases are class B beta-lactamases that are found in a variety of species and have the ability to hydrolyze penams and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4386":{"model_id":"4386","model_name":"BlaB-25","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"6761":{"protein_sequence":{"accession":"WP_078702010.1","sequence":"MMKRLKGLLVLALGFTGLQVFGQQNPDIKIEKLKDNLYVYTTYNTFKGTKYAANAVYMVTDKGVVVIDSPWGEDKFKSFTDEIYKKHGKKVIMNIATHSHDDRAGGLEYFGKLGAKTYSTKMTDSILAKENKPRAKYTFDNNKSFKVGKTEFQVYYPGKGHTADNVVVWFPKDKVLVGGCIVKSGDSKDLGYIGEAYVNDWTQSIHNIQQKFPDVQYVVAGHDDWKDQTSIQHTLDLISDYQQKQKASN"},"dna_sequence":{"accession":"NG_067214.1","fmin":"100","fmax":"850","strand":"+","sequence":"ATGATGAAAAGATTAAAAGGACTATTGGTTCTGGCCTTAGGTTTTACAGGGCTACAGGTTTTTGGGCAGCAAAATCCTGATATTAAAATTGAAAAATTAAAAGATAATTTATACGTCTATACAACCTATAATACCTTCAAAGGGACTAAATATGCAGCTAATGCGGTATATATGGTAACTGATAAAGGAGTCGTGGTTATAGACTCTCCATGGGGAGAAGATAAATTTAAAAGTTTTACAGACGAGATTTATAAAAAGCATGGAAAGAAAGTCATCATGAACATTGCTACTCACTCTCATGATGATAGAGCCGGAGGTCTTGAATATTTTGGTAAATTAGGTGCGAAAACTTATTCTACTAAAATGACAGATTCTATTTTAGCAAAAGAGAATAAGCCAAGAGCAAAGTACACTTTTGATAATAATAAATCCTTTAAAGTAGGAAAGACTGAGTTTCAGGTCTATTATCCGGGAAAAGGGCATACGGCAGATAATGTGGTGGTATGGTTCCCTAAAGACAAAGTATTAGTAGGAGGCTGCATTGTAAAAAGTGGTGATTCGAAAGACCTTGGATATATTGGAGAAGCTTATGTAAACGACTGGACACAGTCTATACACAATATTCAGCAGAAATTTCCCGATGTTCAGTATGTCGTTGCAGGCCACGATGACTGGAAAGATCAAACATCAATACAACATACACTAGATTTAATCAGTGATTACCAACAAAAACAAAAGGCTTCAAATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3005538","ARO_id":"44000","ARO_name":"BlaB-25","CARD_short_name":"BlaB-25","ARO_description":"BlaB-25 is a BlaB beta-lactamase.","ARO_category":{"41365":{"category_aro_accession":"3004201","category_aro_cvterm_id":"41365","category_aro_name":"BlaB beta-lactamase","category_aro_description":"BlaB beta-lactamases are class B beta-lactamases that are found in a variety of species and have the ability to hydrolyze penams and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4387":{"model_id":"4387","model_name":"BlaB-26","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"6762":{"protein_sequence":{"accession":"WP_065083535.1","sequence":"MMKRLKGLLVLALGFTGLQVFGQENPDVKIEKLKDNLYVYTTYNTFKGTKYAANAVYMVTDKGVVVIDSPWGEDKFKSFTDEIYKKHGKKVIMNIATHSHDDRAGGLEYFGKLGAKTYSTKMTDSILAKENKPRAKYTFDNNKSFKVGKTEFQVYYPGKGHTADNVVVWFPKDKVLVGGCIVKSGDSKDLGFIGEAYVNDWTQSIHNIQQKFPDVQYVVAGHDDWKDQTSIQHTLDLISEYQQKQKASN"},"dna_sequence":{"accession":"NG_067215.1","fmin":"100","fmax":"850","strand":"+","sequence":"ATGATGAAAAGATTAAAAGGATTATTGGTTCTGGCTTTAGGTTTTACAGGACTACAGGTTTTTGGACAGGAGAATCCTGATGTTAAAATTGAGAAACTAAAAGATAATCTGTATGTTTATACAACCTATAATACCTTTAAAGGAACTAAATATGCGGCTAATGCGGTATATATGGTAACGGATAAAGGAGTAGTGGTGATAGACTCTCCATGGGGAGAAGATAAATTTAAAAGTTTTACAGACGAGATTTATAAAAAGCACGGAAAGAAAGTCATCATGAACATTGCTACCCATTCTCATGACGATAGAGCCGGAGGTCTTGAATATTTTGGTAAACTAGGTGCAAAAACTTATTCTACTAAAATGACAGATTCTATTTTAGCAAAAGAGAATAAGCCAAGAGCAAAGTACACTTTTGATAATAATAAATCCTTTAAAGTAGGAAAGACTGAGTTTCAGGTCTATTATCCGGGAAAAGGTCATACAGCAGATAATGTGGTGGTATGGTTCCCTAAAGACAAAGTATTAGTGGGAGGCTGCATTGTAAAAAGTGGTGATTCGAAAGACCTTGGGTTTATTGGAGAAGCTTATGTAAACGACTGGACACAGTCTATACACAATATTCAGCAGAAATTTCCCGATGTTCAGTATGTTGTTGCAGGTCATGATGACTGGAAGGATCAAACATCAATACAGCATACATTGGATTTAATCAGTGAATATCAACAAAAACAAAAGGCTTCAAATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3005539","ARO_id":"44001","ARO_name":"BlaB-26","CARD_short_name":"BlaB-26","ARO_description":"BlaB-26 is a BlaB beta-lactamase.","ARO_category":{"41365":{"category_aro_accession":"3004201","category_aro_cvterm_id":"41365","category_aro_name":"BlaB beta-lactamase","category_aro_description":"BlaB beta-lactamases are class B beta-lactamases that are found in a variety of species and have the ability to hydrolyze penams and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4388":{"model_id":"4388","model_name":"BlaB-27","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"6763":{"protein_sequence":{"accession":"WP_078772815.1","sequence":"MMKGLKGLLVLALGFTGLQVFGQQNPDIKIEKLKDNLYVYTTYNTFKGTKYAANAVYMVTDKGVVVIDSPWGEDKFKSFTDEIYKKHGKKVIMNIATHSHDDRAGGLEYFGKLGAKTYSTKMTDSILAKENKPRAKYTFDNNKSFKVGKTEFQVYYPGKGHTADNVVVWFPKDKVLVGGCIVKSGDSKDLGFIGEAYVNDWTQSIHNIQQKFPDAQYVVAGHDDWKDQTSIQHTLDLISEYQQKQKASN"},"dna_sequence":{"accession":"NG_067980.2","fmin":"100","fmax":"850","strand":"+","sequence":"ATAATGAAAGGATTAAAAGGGCTATTGGTTCTGGCTTTAGGCTTTACAGGACTACAGGTTTTTGGGCAACAGAACCCTGATATTAAAATTGAAAAATTAAAAGATAATTTATACGTCTATACAACCTATAATACCTTCAAAGGGACTAAATATGCAGCTAATGCTGTATATATGGTAACCGATAAAGGAGTAGTGGTTATAGACTCCCCGTGGGGAGAAGATAAATTTAAAAGTTTTACAGACGAGATTTATAAAAAACACGGAAAGAAAGTTATCATGAACATTGCGACCCACTCTCATGATGATAGAGCCGGAGGTCTTGAATATTTTGGTAAACTAGGTGCAAAAACTTATTCTACTAAAATGACAGATTCTATTTTAGCAAAAGAGAATAAGCCAAGAGCAAAGTACACTTTTGATAATAATAAATCTTTTAAAGTAGGAAAAACTGAGTTTCAGGTCTATTATCCGGGAAAAGGTCATACAGCAGATAATGTGGTTGTATGGTTCCCTAAAGACAAAGTATTAGTAGGAGGCTGCATTGTAAAAAGTGGTGATTCGAAAGACCTTGGGTTTATTGGAGAAGCTTATGTAAACGACTGGACACAGTCCATACACAATATTCAGCAGAAATTTCCCGATGCTCAGTATGTCGTTGCAGGTCATGACGACTGGAAAGATCAAACATCAATACAACATACACTGGATTTAATCAGTGAATATCAACAAAAACAAAAGGCTTCAAATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3005540","ARO_id":"44002","ARO_name":"BlaB-27","CARD_short_name":"BlaB-27","ARO_description":"BlaB-27 is a BlaB beta-lactamase.","ARO_category":{"41365":{"category_aro_accession":"3004201","category_aro_cvterm_id":"41365","category_aro_name":"BlaB beta-lactamase","category_aro_description":"BlaB beta-lactamases are class B beta-lactamases that are found in a variety of species and have the ability to hydrolyze penams and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4389":{"model_id":"4389","model_name":"BlaB-28","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"6764":{"protein_sequence":{"accession":"WP_107808007.1","sequence":"MMKRLKGVLVLALGFTGLQVFGQQNPDIKIEKLKENLYVYTTYNTFKGTKYAANAVYMVTDKGVVVIDSPWGEDKFKSFTDEIYKKHGKKVIMNIATHSHDDRAGGFEYFGKLGAKTYSTKMTDSILAKENKPRAQYTFDNNKSFKVGKTEFQVYYPGKGHTADNVVVWFPKDKVLVGGCIVKSGDSKDLGFIGEAYVNDWTQSIHNIQQKFPDVQYVVAGHDDWKDQTSIQHTLDLISEYQQKQKASN"},"dna_sequence":{"accession":"NG_067981.1","fmin":"100","fmax":"850","strand":"+","sequence":"ATGATGAAAAGATTAAAAGGGGTATTGGTTCTGGCTTTAGGATTTACAGGACTACAGGTTTTTGGACAACAAAATCCTGATATTAAAATTGAAAAATTAAAAGAAAATTTATACGTTTATACAACCTATAATACATTCAAAGGAACTAAATATGCAGCTAATGCGGTATATATGGTAACTGATAAAGGAGTAGTGGTTATAGATTCTCCATGGGGAGAAGATAAATTTAAAAGTTTTACAGACGAGATTTATAAAAAACACGGAAAGAAAGTCATCATGAACATTGCTACTCATTCTCATGATGATAGAGCCGGAGGTTTTGAATATTTTGGTAAACTAGGTGCAAAAACTTATTCTACTAAAATGACAGACTCTATTTTAGCAAAAGAGAATAAGCCAAGAGCGCAGTATACTTTTGATAATAATAAATCCTTTAAAGTAGGTAAGACCGAATTTCAGGTTTATTATCCGGGAAAAGGTCATACAGCAGATAATGTGGTTGTGTGGTTCCCTAAAGACAAAGTATTAGTAGGAGGCTGCATTGTAAAAAGCGGTGATTCGAAAGACCTTGGGTTTATTGGAGAAGCTTATGTAAATGACTGGACACAATCCATACACAACATTCAGCAGAAATTTCCCGATGTTCAGTATGTCGTTGCAGGTCACGATGACTGGAAGGATCAAACATCAATACAACATACACTGGATTTAATCAGTGAATATCAACAAAAACAAAAGGCTTCAAATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3005541","ARO_id":"44003","ARO_name":"BlaB-28","CARD_short_name":"BlaB-28","ARO_description":"BlaB-28 is a BlaB beta-lactamase.","ARO_category":{"41365":{"category_aro_accession":"3004201","category_aro_cvterm_id":"41365","category_aro_name":"BlaB beta-lactamase","category_aro_description":"BlaB beta-lactamases are class B beta-lactamases that are found in a variety of species and have the ability to hydrolyze penams and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4390":{"model_id":"4390","model_name":"BlaB-29","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"6765":{"protein_sequence":{"accession":"WP_081318900.1","sequence":"MMKNIMRALILVFGFMSFFMFGQENPDVKIDKLKDNLYVYTTYNTFNGTKYAANAVYLVTDKGVVVIDCPWGEDKFKSFTDEIYKKHGKKVIMNIATHSHDDRAGGLEYFGKIGAKTYSTKMTDSILAKENKPRAQYTFDNNKSFKVGKSEFQVYYPGKGHTADNVVVWFPKEKVLAGGCIIKSADSKDLGYIGEAYVNDWTQSVHNIQQKFSGAQYVVAGHDDWKDQRSIQRTLDLINEYQQKQKASN"},"dna_sequence":{"accession":"NG_067982.1","fmin":"100","fmax":"850","strand":"+","sequence":"ATTATGAAGAATATAATGCGGGCACTGATCCTTGTTTTTGGTTTTATGAGTTTTTTTATGTTTGGACAGGAGAATCCTGACGTTAAAATTGATAAGCTAAAAGATAATCTGTATGTATACACAACCTACAATACATTTAACGGGACTAAATATGCCGCTAATGCAGTATATCTGGTAACTGATAAGGGTGTTGTGGTTATAGACTGTCCGTGGGGAGAAGACAAATTTAAAAGCTTTACGGACGAGATTTATAAAAAACACGGAAAGAAAGTTATTATGAATATTGCAACACATTCTCATGATGATCGTGCCGGAGGTCTTGAATATTTTGGTAAAATAGGTGCAAAAACTTATTCTACTAAAATGACAGATTCTATTTTAGCAAAAGAGAATAAGCCAAGAGCACAATATACATTTGACAATAATAAATCTTTCAAAGTAGGAAAATCCGAGTTTCAGGTTTACTATCCCGGAAAAGGACATACAGCAGATAATGTGGTGGTATGGTTTCCAAAAGAAAAAGTATTGGCTGGAGGTTGTATTATAAAAAGCGCTGATTCAAAAGACCTGGGGTATATTGGAGAAGCATATGTAAACGACTGGACGCAGTCTGTACACAATATTCAACAAAAGTTTTCCGGTGCTCAGTACGTTGTTGCAGGGCATGATGATTGGAAAGATCAAAGATCAATACAACGTACACTAGACTTAATCAATGAATATCAACAAAAACAAAAGGCTTCAAATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41081","NCBI_taxonomy_name":"Elizabethkingia anophelis","NCBI_taxonomy_id":"1117645"}}}},"ARO_accession":"3005542","ARO_id":"44004","ARO_name":"BlaB-29","CARD_short_name":"BlaB-29","ARO_description":"BlaB-29 is a BlaB beta-lactamase.","ARO_category":{"41365":{"category_aro_accession":"3004201","category_aro_cvterm_id":"41365","category_aro_name":"BlaB beta-lactamase","category_aro_description":"BlaB beta-lactamases are class B beta-lactamases that are found in a variety of species and have the ability to hydrolyze penams and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4391":{"model_id":"4391","model_name":"BlaB-3","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"6766":{"protein_sequence":{"accession":"WP_063857827.1","sequence":"MMKKMKWALVLALGLTGLNAFGQETPEVKIEKLKDNLYVYTTYNTFNGTKYAANAVYLVTSKGVVVIDSPWGEEKFKNFTDEIYKRHGKKVIMNIATHSHDDRAGGLEYFKSLGAKTYSTKMTDSILAKDNKPRAQYTFDNNKSFKVGKDEFQVYYPGKGHTADHVVVWFPKDKVLVGGCIIKSGDSKDLGFLGEAYVNDWTQSVHNIQKKFPNVQYVVAGHDDWKDQTAIQHTLDLISEYQQKQKASN"},"dna_sequence":{"accession":"NG_048698.1","fmin":"0","fmax":"750","strand":"+","sequence":"ATGATGAAGAAAATGAAATGGGCACTTGTTCTTGCTCTTGGACTTACAGGTTTAAATGCCTTCGGGCAGGAAACTCCTGAAGTAAAAATAGAAAAGCTAAAAGACAATTTATATGTTTATACAACATATAATACATTCAACGGAACCAAATACGCAGCTAATGCGGTATATCTGGTGACCAGTAAAGGGGTGGTTGTAATAGATTCTCCATGGGGTGAGGAAAAATTTAAAAACTTTACCGACGAAATTTATAAAAGACACGGAAAGAAAGTGATCATGAATATTGCAACACACTCTCATGATGACCGTGCAGGAGGTTTGGAATATTTTAAAAGCTTAGGGGCAAAAACCTATTCTACTAAAATGACAGACTCTATTTTAGCGAAAGATAATAAGCCAAGAGCCCAGTATACTTTTGATAATAATAAATCATTTAAAGTAGGAAAGGATGAGTTTCAGGTCTATTATCCGGGAAAAGGACATACAGCTGACCATGTAGTGGTATGGTTCCCTAAAGATAAAGTACTGGTGGGCGGCTGTATTATAAAAAGTGGGGATTCCAAAGATCTTGGCTTTTTGGGAGAAGCATATGTAAACGACTGGACACAGTCAGTACACAATATTCAGAAGAAATTTCCCAATGTACAATATGTTGTTGCAGGCCACGATGACTGGAAAGATCAGACTGCCATTCAGCATACACTGGATTTAATCAGTGAATATCAACAAAAACAAAAGGCTTCAAATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36960","NCBI_taxonomy_name":"Elizabethkingia meningoseptica","NCBI_taxonomy_id":"238"}}}},"ARO_accession":"3005543","ARO_id":"44005","ARO_name":"BlaB-3","CARD_short_name":"BlaB-3","ARO_description":"BlaB-3 is a BlaB beta-lactamase.","ARO_category":{"41365":{"category_aro_accession":"3004201","category_aro_cvterm_id":"41365","category_aro_name":"BlaB beta-lactamase","category_aro_description":"BlaB beta-lactamases are class B beta-lactamases that are found in a variety of species and have the ability to hydrolyze penams and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4392":{"model_id":"4392","model_name":"BlaB-30","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"6767":{"protein_sequence":{"accession":"WP_087094142.1","sequence":"MMKNIMRALILVFGFMSFFMFGQENPDVKIEKLKDNLYVYTTYNTFNGTKYAANAVYLVTDKGVVVIDCPWGEDKFKSFTDEIYKKHGKKVIMNIATHSHDDRAGGLEYFGKIGAKTYSTKMTDSILAKENKPRAQYTFDNNKSFKVGKSEFQVYYPGKGHTADNVVVWFPKEKVLVGGCIIKSADSKDLGYIGEAYVNDWTQSVHNIQQKFSGAQYVVAGHDDWKDQRSIQRTLDLINEYQQKQKASN"},"dna_sequence":{"accession":"NG_068164.1","fmin":"100","fmax":"850","strand":"+","sequence":"ATTATGAAGAATATAATGCGGGCACTGATCCTTGTTTTTGGTTTTATGAGTTTTTTTATGTTTGGACAGGAGAATCCTGACGTCAAAATTGAAAAGCTAAAAGATAATCTGTATGTATACACAACCTACAATACATTTAACGGGACTAAATATGCCGCTAATGCAGTATATCTGGTAACTGATAAGGGTGTTGTGGTTATAGACTGTCCGTGGGGAGAAGACAAATTTAAAAGCTTTACGGACGAGATTTATAAAAAACACGGAAAGAAAGTTATTATGAATATTGCAACACATTCTCATGATGATCGTGCCGGAGGTCTTGAATATTTTGGTAAAATAGGTGCAAAAACTTATTCTACTAAAATGACAGATTCTATTTTAGCAAAAGAGAATAAGCCAAGAGCACAATATACTTTTGACAATAATAAATCTTTCAAAGTAGGAAAATCCGAGTTTCAGGTTTACTATCCCGGAAAAGGACACACAGCAGATAATGTGGTGGTATGGTTTCCAAAAGAAAAAGTATTGGTTGGAGGTTGTATTATAAAAAGCGCTGATTCAAAAGACCTGGGATATATTGGAGAAGCATATGTAAATGACTGGACGCAGTCTGTACACAATATTCAACAGAAGTTTTCCGGTGCTCAGTACGTTGTTGCAGGGCATGATGATTGGAAAGATCAAAGATCAATACAACGTACACTAGACTTAATCAATGAATATCAACAAAAACAAAAGGCTTCAAATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41081","NCBI_taxonomy_name":"Elizabethkingia anophelis","NCBI_taxonomy_id":"1117645"}}}},"ARO_accession":"3005544","ARO_id":"44006","ARO_name":"BlaB-30","CARD_short_name":"BlaB-30","ARO_description":"BlaB-30 is a BlaB beta-lactamase.","ARO_category":{"41365":{"category_aro_accession":"3004201","category_aro_cvterm_id":"41365","category_aro_name":"BlaB beta-lactamase","category_aro_description":"BlaB beta-lactamases are class B beta-lactamases that are found in a variety of species and have the ability to hydrolyze penams and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4393":{"model_id":"4393","model_name":"BlaB-31","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"6768":{"protein_sequence":{"accession":"WP_078675249.1","sequence":"MLKKIKISLILALGLTSLQAFGQENPDVKIEKLKDNLYVYTTYNTFNGTKYAANAVYLVTDKGVVVIDCPWGEDKFKSFTDEIYKKHGKKVIMNIATHSHDDRAGGLEYFGKIGAKTYSTKMTDSILAKENKPRAQYTFDNNKSFKVGKSEFQVYYPGKGHTADNVLVWFPKEKVLVGGCIIKSADSKDLGYIGEAYVNDWTQSVHNIQQKFSGAQYVVAGHDDWKDQRSIQRTLDLINEYQQKQKASN"},"dna_sequence":{"accession":"NG_067216.1","fmin":"0","fmax":"750","strand":"+","sequence":"ATGTTGAAAAAAATAAAAATAAGCTTGATTCTTGCTCTTGGGCTTACCAGTCTGCAGGCATTTGGACAGGAGAATCCTGATGTCAAAATTGAAAAGCTAAAAGATAATCTGTATGTATACACAACCTACAATACATTTAACGGGACTAAATATGCCGCAAATGCAGTATATCTGGTAACTGATAAGGGTGTTGTGGTTATAGACTGTCCGTGGGGAGAAGACAAATTTAAAAGCTTTACGGACGAGATTTATAAAAAACACGGAAAGAAAGTTATTATGAATATTGCAACACATTCTCATGATGATCGTGCCGGAGGTCTTGAATATTTTGGTAAAATAGGTGCAAAAACTTATTCTACTAAAATGACAGATTCTATTTTAGCAAAAGAGAATAAGCCAAGAGCACAATATACTTTTGACAATAATAAATCTTTCAAAGTAGGAAAATCCGAGTTTCAGGTTTACTATCCCGGAAAAGGACATACAGCAGATAATGTGTTGGTATGGTTTCCAAAAGAAAAAGTATTGGTTGGAGGTTGTATTATAAAAAGCGCTGATTCAAAAGACCTGGGGTATATTGGAGAAGCATATGTAAACGACTGGACGCAGTCTGTACACAATATTCAACAAAAGTTTTCCGGTGCTCAGTACGTTGTTGCAGGGCATGATGATTGGAAAGATCAAAGATCAATACAACGTACACTAGACTTAATCAATGAATATCAACAAAAACAAAAGGCTTCAAATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3005545","ARO_id":"44007","ARO_name":"BlaB-31","CARD_short_name":"BlaB-31","ARO_description":"BlaB-31 is a BlaB beta-lactamase.","ARO_category":{"41365":{"category_aro_accession":"3004201","category_aro_cvterm_id":"41365","category_aro_name":"BlaB beta-lactamase","category_aro_description":"BlaB beta-lactamases are class B beta-lactamases that are found in a variety of species and have the ability to hydrolyze penams and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4394":{"model_id":"4394","model_name":"BlaB-32","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"6769":{"protein_sequence":{"accession":"WP_078723747.1","sequence":"MLKKIKISLILALGLTSLQAFGQENPDVKIEKLRDNLYVYTTYNTFNGTKYAANAVYLVTDKGVVVIDCPWGEDKFKSFTDEIYKKHGKKVIMNIATHSHDDRAGGLEYFGKIGAKTYSTKMTDSILAKENKPRAQYTFDNNKSFKVGKSEFQVYYPGKGHTADNVVVWFPKEKVLLGGCIIKSADSKDLGYIGEAYVNDWTQSVHNIQQKFSGAQYVVAGHDDWKDQRSIQRTLDLINEYQQKQKASN"},"dna_sequence":{"accession":"NG_067217.1","fmin":"100","fmax":"850","strand":"+","sequence":"ATGTTGAAAAAAATAAAAATAAGCTTGATTCTTGCTCTTGGGCTTACCAGTCTGCAGGCATTTGGACAGGAGAATCCTGACGTCAAAATTGAAAAGCTAAGAGATAATCTGTATGTATACACAACCTACAATACATTTAACGGGACTAAATATGCCGCTAATGCAGTATATCTGGTAACTGATAAGGGTGTTGTGGTTATAGACTGTCCGTGGGGAGAAGACAAATTTAAAAGCTTTACGGACGAGATTTATAAAAAACACGGAAAGAAAGTTATTATGAATATTGCAACACATTCTCATGATGATCGTGCCGGAGGTCTTGAATATTTTGGTAAAATAGGTGCAAAAACTTATTCTACTAAAATGACAGATTCTATTTTAGCAAAAGAGAATAAGCCAAGAGCACAATATACTTTTGACAATAATAAATCTTTCAAAGTAGGAAAATCCGAGTTTCAGGTTTACTATCCCGGAAAAGGACACACAGCAGATAATGTGGTGGTATGGTTTCCAAAAGAAAAAGTATTGCTTGGAGGTTGTATTATAAAAAGTGCTGATTCAAAAGACCTGGGATATATTGGAGAAGCATATGTAAACGACTGGACGCAGTCTGTACACAATATTCAACAAAAGTTTTCCGGTGCTCAGTACGTTGTTGCGGGGCATGATGATTGGAAAGATCAAAGATCAATACAACGTACACTAGACTTAATCAATGAATATCAACAAAAACAAAAGGCTTCAAATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41081","NCBI_taxonomy_name":"Elizabethkingia anophelis","NCBI_taxonomy_id":"1117645"}}}},"ARO_accession":"3005546","ARO_id":"44008","ARO_name":"BlaB-32","CARD_short_name":"BlaB-32","ARO_description":"BlaB-32 is a BlaB beta-lactamase.","ARO_category":{"41365":{"category_aro_accession":"3004201","category_aro_cvterm_id":"41365","category_aro_name":"BlaB beta-lactamase","category_aro_description":"BlaB beta-lactamases are class B beta-lactamases that are found in a variety of species and have the ability to hydrolyze penams and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4395":{"model_id":"4395","model_name":"BlaB-33","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"6770":{"protein_sequence":{"accession":"WP_065161001.1","sequence":"MLKKIKISLILALGLTSLQAFGQENPDVKIEKLKDNLYVYTTYNTFNGTKYAANAVYLVTDKGVVVIDCPWGEDKFKSFTDEIYKKHGKKVIINIATHSHDDRAGGLEYFGKIGAKTYSTKMTDSILAKENKPRAQYTFDNNKSFKVGKSEFQVYYPGKGHTADNVVVWFPKEKVLVGGCIIKSADSKDLGYIGEAYVNDWTQSVHNIQQKFSGAQYVVAGHDDWKDQRSIQHTLDLINEYQQKQKASN"},"dna_sequence":{"accession":"NG_067218.1","fmin":"100","fmax":"850","strand":"+","sequence":"ATGTTGAAAAAAATAAAAATAAGCTTGATTCTTGCTCTTGGGCTTACCAGTTTGCAGGCATTTGGACAGGAGAATCCTGATGTCAAAATTGAAAAGCTAAAAGATAATCTGTATGTATACACAACCTACAATACATTTAACGGGACTAAATATGCCGCAAATGCAGTATATCTGGTAACTGATAAGGGTGTTGTGGTTATAGACTGTCCGTGGGGAGAAGACAAATTTAAAAGCTTTACGGACGAGATTTATAAAAAACACGGAAAGAAAGTTATTATTAATATTGCAACACATTCTCATGATGATCGTGCCGGAGGTCTTGAATATTTTGGTAAAATAGGTGCAAAAACTTATTCTACTAAAATGACAGATTCTATTTTAGCAAAAGAGAATAAGCCAAGAGCACAATATACTTTTGACAATAATAAATCTTTCAAAGTAGGAAAATCCGAGTTTCAGGTTTACTATCCCGGAAAAGGGCACACAGCAGATAATGTGGTGGTATGGTTTCCAAAAGAAAAAGTATTGGTTGGAGGTTGTATTATAAAAAGTGCTGATTCAAAGGACCTGGGGTATATTGGAGAAGCATATGTAAACGACTGGACGCAGTCTGTACACAATATTCAACAAAAGTTTTCCGGTGCTCAGTACGTTGTTGCAGGGCATGATGATTGGAAAGATCAAAGATCAATACAACATACACTAGACTTAATCAATGAATATCAACAAAAACAAAAGGCTTCAAATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41081","NCBI_taxonomy_name":"Elizabethkingia anophelis","NCBI_taxonomy_id":"1117645"}}}},"ARO_accession":"3005547","ARO_id":"44009","ARO_name":"BlaB-33","CARD_short_name":"BlaB-33","ARO_description":"BlaB-33 is a BlaB beta-lactamase.","ARO_category":{"41365":{"category_aro_accession":"3004201","category_aro_cvterm_id":"41365","category_aro_name":"BlaB beta-lactamase","category_aro_description":"BlaB beta-lactamases are class B beta-lactamases that are found in a variety of species and have the ability to hydrolyze penams and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4396":{"model_id":"4396","model_name":"BlaB-34","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"6771":{"protein_sequence":{"accession":"WP_078678782.1","sequence":"MMKGLKGLLVLALGFTGLQVFGQQNPDIKIEKLKDNLYVYTTYNTFKGTKYAANAVYMVTDKGVVVIDSPWGEDKFKSFTDEIYKKHGKKVIMNIATHAHDDRAGGLEYFGKLGAKTYSTKMTDSILAKENKPRAKYTFDNNKSFKVGKTEFQVYYPGKGHTADNVVVWFPKDKVLVGGCIVKSGDSKDLGYIGEAYVNDWTQSIHNIQQKFPDVQYVVAGHDDWKDQTSIQHTLDLISDYQQKQKASN"},"dna_sequence":{"accession":"NG_067983.2","fmin":"100","fmax":"850","strand":"+","sequence":"ATAATGAAAGGATTAAAAGGGTTATTAGTTCTGGCCTTAGGTTTTACAGGGCTACAGGTTTTTGGGCAGCAAAATCCTGATATTAAAATTGAAAAATTAAAAGATAATTTATACGTCTATACAACCTATAATACCTTCAAAGGGACCAAATATGCAGCTAATGCGGTATATATGGTAACTGATAAAGGAGTCGTGGTGATAGACTCTCCATGGGGAGAAGATAAATTTAAAAGTTTTACAGACGAGATTTATAAAAAGCATGGAAAGAAAGTCATCATGAACATTGCTACTCACGCTCATGATGATAGAGCCGGAGGTCTTGAATATTTTGGTAAATTAGGTGCGAAAACTTATTCTACTAAAATGACAGATTCTATTTTAGCAAAAGAGAATAAGCCAAGAGCAAAGTACACTTTTGATAATAATAAATCCTTTAAAGTAGGAAAGACTGAGTTTCAGGTCTATTATCCGGGAAAAGGGCATACGGCAGATAATGTGGTGGTATGGTTCCCTAAAGACAAAGTATTAGTAGGAGGCTGCATTGTAAAAAGTGGTGATTCGAAAGACCTTGGATATATTGGAGAAGCTTATGTAAACGACTGGACACAGTCTATACATAATATTCAGCAAAAATTTCCCGATGTTCAGTATGTCGTTGCAGGCCACGATGACTGGAAAGATCAAACATCAATACAACATACATTGGATTTAATCAGTGATTACCAACAAAAACAAAAGGCTTCAAATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3005548","ARO_id":"44010","ARO_name":"BlaB-34","CARD_short_name":"BlaB-34","ARO_description":"BlaB-34 is a BlaB beta-lactamase.","ARO_category":{"41365":{"category_aro_accession":"3004201","category_aro_cvterm_id":"41365","category_aro_name":"BlaB beta-lactamase","category_aro_description":"BlaB beta-lactamases are class B beta-lactamases that are found in a variety of species and have the ability to hydrolyze penams and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4397":{"model_id":"4397","model_name":"BlaB-35","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"6772":{"protein_sequence":{"accession":"WP_078793100.1","sequence":"MMKKMKWALVLALGLTGLNAFGQETPEVKIEKLKDNLYVYTTYNTFNGTKYAANAVYLVTSKGVVVIDSPWGEEKFKNFTDEIYKRHGKKVIMNIATHSHDDRAGGLEYFKSLGAKTYSTKMTDSILAKDNKPRAQYTFDNNKSFKVGKDEFQVYYPGKGHTADNLVVWFPKDKVLVGGCIIKSGDSKDLGFLGEAYVNDWTQSVHNIQKKFPNVQYVVAGHDDWKDQTAIQHTLDLISEYQQKQKASN"},"dna_sequence":{"accession":"NG_067219.1","fmin":"100","fmax":"850","strand":"+","sequence":"ATGATGAAGAAAATGAAATGGGCACTTGTTCTTGCTCTTGGACTTACAGGTTTAAATGCCTTCGGGCAGGAAACTCCTGAAGTAAAAATAGAAAAGCTAAAAGACAATTTATATGTTTATACAACATATAATACATTCAACGGAACCAAATACGCAGCTAATGCGGTATATCTGGTGACCAGTAAAGGGGTGGTTGTAATAGATTCTCCATGGGGTGAGGAAAAATTTAAAAACTTTACCGACGAAATTTATAAAAGACACGGAAAGAAAGTCATCATGAATATTGCAACACATTCTCATGACGACCGTGCAGGAGGTTTGGAATATTTTAAAAGCTTAGGGGCAAAAACCTATTCTACTAAAATGACAGACTCTATTTTAGCGAAAGATAATAAGCCAAGAGCCCAGTATACTTTTGATAATAATAAATCATTTAAAGTAGGAAAGGATGAGTTTCAGGTCTATTATCCGGGAAAAGGACATACAGCTGACAATCTAGTGGTATGGTTCCCTAAAGATAAAGTACTGGTGGGAGGCTGTATTATAAAAAGTGGTGATTCCAAAGATCTTGGATTTTTGGGAGAAGCATATGTAAACGACTGGACACAGTCAGTACACAATATTCAGAAGAAATTTCCCAATGTACAATATGTTGTTGCAGGCCACGATGACTGGAAAGATCAGACTGCCATTCAGCATACACTGGATTTAATCAGTGAATATCAACAAAAACAAAAGGCTTCAAATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36960","NCBI_taxonomy_name":"Elizabethkingia meningoseptica","NCBI_taxonomy_id":"238"}}}},"ARO_accession":"3005549","ARO_id":"44011","ARO_name":"BlaB-35","CARD_short_name":"BlaB-35","ARO_description":"BlaB-35 is a BlaB beta-lactamase.","ARO_category":{"41365":{"category_aro_accession":"3004201","category_aro_cvterm_id":"41365","category_aro_name":"BlaB beta-lactamase","category_aro_description":"BlaB beta-lactamases are class B beta-lactamases that are found in a variety of species and have the ability to hydrolyze penams and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4398":{"model_id":"4398","model_name":"BlaB-36","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"6773":{"protein_sequence":{"accession":"WP_080889626.1","sequence":"MMKGLKGLLVLALGFTGLQVFGQQNPDIKIEKLKDNLYVYTTYNTFKGTKYAANAVYVVTDKGVVVIDSPWGEDKFKSFTDEIYKKHGKKVIMNIATHSHDDRAGGLEYFGKLGAKTYSTKMTDSILAKENKPRAQYTFDNNKSFKVGKTEFQVYYPGKGHTADNVVVWFPKDKVLVGGCIVKSGDSKDLGYIGEAYVNDWTQSIHNIQQKFPDVQYVVAGHDDWKDQTSIQHTLDLISDYQQKQKASN"},"dna_sequence":{"accession":"NG_067984.1","fmin":"100","fmax":"850","strand":"+","sequence":"ATAATGAAAGGATTAAAAGGGTTATTAGTTCTGGCCTTAGGTTTTACAGGGCTACAGGTTTTTGGGCAGCAAAATCCTGATATTAAAATTGAAAAATTAAAAGATAATTTATACGTCTATACAACCTATAATACCTTCAAAGGGACTAAATATGCAGCTAATGCGGTATATGTGGTAACCGATAAAGGAGTAGTGGTTATAGACTCTCCATGGGGAGAAGATAAATTTAAAAGTTTTACAGACGAGATTTATAAAAAGCACGGAAAGAAAGTCATCATGAACATTGCTACTCACTCTCATGATGATAGAGCCGGAGGTCTTGAATATTTTGGTAAACTAGGTGCAAAAACTTATTCCACTAAAATGACAGATTCTATTTTAGCAAAAGAGAATAAGCCTAGAGCACAGTACACTTTTGATAATAATAAATCCTTTAAAGTAGGAAAGACTGAGTTTCAGGTCTATTATCCGGGAAAAGGTCATACAGCAGATAATGTGGTTGTGTGGTTCCCTAAAGACAAAGTATTAGTAGGAGGCTGCATTGTAAAAAGCGGTGATTCGAAAGATCTTGGGTACATTGGAGAAGCTTATGTAAATGACTGGACACAGTCCATACATAATATTCAGCAGAAATTTCCCGATGTTCAGTATGTCGTTGCAGGCCACGATGACTGGAAAGATCAAACATCAATACAACATACACTGGATTTAATCAGTGATTACCAACAAAAACAAAAGGCTTCAAATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3005550","ARO_id":"44012","ARO_name":"BlaB-36","CARD_short_name":"BlaB-36","ARO_description":"BlaB-36 is a BlaB beta-lactamase.","ARO_category":{"41365":{"category_aro_accession":"3004201","category_aro_cvterm_id":"41365","category_aro_name":"BlaB beta-lactamase","category_aro_description":"BlaB beta-lactamases are class B beta-lactamases that are found in a variety of species and have the ability to hydrolyze penams and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4399":{"model_id":"4399","model_name":"BlaB-38","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"6774":{"protein_sequence":{"accession":"WP_078795346.1","sequence":"MLKKIKLTLILAFGFTSLQAFGQENPDVKIEKLKDNLYVYTTYNSYKGVKYAANAVYMVTDKGVVVIDCPWGEEKFKSFTDEIYKKHGKKVIMNIATHSHDDRAGGLGYFKKIGAKTYSTKMTDSILAKENKPRAEYTFDNNKSFKVGKSEFQVYYPGKGHTADNVVVWFPKEKVLVGGCIIKSADSKDLGFIGEAYVNDWTQSVHNIQQKFSGAQYIVAGHDDWKDQRSIQHTLDLISEYQQKQKASN"},"dna_sequence":{"accession":"NG_067220.1","fmin":"100","fmax":"850","strand":"+","sequence":"ATGTTGAAGAAAATAAAACTGACGTTGATTCTTGCTTTTGGGTTTACAAGTCTACAGGCATTTGGGCAGGAGAATCCTGATGTTAAAATTGAGAAACTAAAAGATAATCTGTATGTTTATACAACTTATAATTCCTATAAAGGAGTAAAGTATGCAGCTAATGCTGTATATATGGTAACGGATAAAGGAGTTGTAGTTATAGATTGCCCATGGGGAGAGGAGAAATTTAAAAGCTTTACGGACGAGATTTATAAAAAGCACGGAAAGAAAGTCATTATGAATATTGCTACTCATTCTCATGATGACCGTGCCGGAGGCTTGGGATATTTCAAAAAAATAGGTGCAAAAACCTATTCTACTAAAATGACAGATTCTATCTTAGCGAAAGAGAATAAGCCAAGAGCAGAATATACTTTTGATAATAATAAATCTTTTAAAGTAGGTAAATCTGAATTTCAGGTTTACTATCCGGGAAAAGGTCATACAGCAGATAATGTAGTGGTATGGTTTCCCAAAGAAAAAGTATTAGTTGGAGGCTGTATTATAAAGAGTGCTGATTCAAAAGACCTTGGGTTTATTGGAGAAGCTTATGTAAATGATTGGACACAGTCTGTACACAATATTCAGCAGAAGTTTTCCGGGGCTCAGTATATAGTCGCGGGGCATGATGACTGGAAAGATCAAAGATCAATACAACATACACTGGACCTGATCAGTGAATACCAACAAAAACAAAAGGCTTCAAATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3005551","ARO_id":"44013","ARO_name":"BlaB-38","CARD_short_name":"BlaB-38","ARO_description":"BlaB-38 is a BlaB beta-lactamase.","ARO_category":{"41365":{"category_aro_accession":"3004201","category_aro_cvterm_id":"41365","category_aro_name":"BlaB beta-lactamase","category_aro_description":"BlaB beta-lactamases are class B beta-lactamases that are found in a variety of species and have the ability to hydrolyze penams and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4400":{"model_id":"4400","model_name":"BlaB-39","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"6775":{"protein_sequence":{"accession":"WP_078778510.1","sequence":"MMKGLKGLLVLALGFTGLQVFGQQNPDIKIEKLKDNLYVYTTYNTFKGTKYAANAVYMVTDKGVVVIDSPWGEDKFKSFTDEIYKKHGKKVIMNIATHSHDDRAGGLGYFGKLGAKTYSTKMTDSILAKENKPRAKYTFDNNKSFKVGKTEFQVYYPGKGHTADNVVVWFPKDKVLVGGCIVKSGDSKDLGFIGEAYVNNWTQSIHNIQQKFPDVQYVVAGHDDWKDQTSIQHTLDLISEYQQKQKASN"},"dna_sequence":{"accession":"NG_067985.1","fmin":"100","fmax":"850","strand":"+","sequence":"ATAATGAAAGGATTAAAAGGGCTATTGGTTCTGGCTTTAGGTTTTACAGGACTACAGGTTTTTGGGCAACAGAACCCTGATATTAAAATTGAAAAATTAAAAGATAATTTATACGTCTATACAACTTATAATACCTTCAAAGGAACTAAATATGCGGCTAATGCGGTATATATGGTAACCGATAAAGGAGTAGTAGTTATAGACTCTCCATGGGGAGAAGATAAATTTAAAAGTTTTACAGACGAGATTTATAAAAAGCACGGTAAGAAAGTTATCATGAACATTGCGACCCACTCTCATGATGATAGAGCCGGAGGTCTTGGATATTTTGGTAAACTAGGTGCAAAAACTTATTCTACTAAAATGACAGATTCTATTTTAGCAAAAGAGAATAAGCCAAGAGCAAAATACACTTTTGATAATAATAAATCTTTTAAAGTAGGAAAGACTGAGTTTCAGGTCTATTATCCGGGAAAAGGTCATACAGCAGATAATGTGGTTGTGTGGTTCCCTAAAGACAAAGTATTAGTAGGAGGCTGCATTGTAAAAAGCGGTGATTCGAAAGACCTTGGGTTTATTGGAGAAGCTTATGTAAACAACTGGACACAGTCTATACACAACATTCAGCAGAAATTTCCCGATGTTCAGTATGTCGTTGCAGGTCATGACGACTGGAAAGATCAAACATCAATACAACATACACTGGATTTAATCAGTGAATATCAACAAAAACAAAAGGCTTCAAATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3005552","ARO_id":"44014","ARO_name":"BlaB-39","CARD_short_name":"BlaB-39","ARO_description":"BlaB-39 is a BlaB beta-lactamase.","ARO_category":{"41365":{"category_aro_accession":"3004201","category_aro_cvterm_id":"41365","category_aro_name":"BlaB beta-lactamase","category_aro_description":"BlaB beta-lactamases are class B beta-lactamases that are found in a variety of species and have the ability to hydrolyze penams and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4401":{"model_id":"4401","model_name":"BlaB-5","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"6776":{"protein_sequence":{"accession":"WP_063857828.1","sequence":"MLKRLKGLLVLALGFTGLQVFGQQNPDIKIEKLKDNLYVYTTYNTFKGTKYAANAVYMVTDKGVVVIDSPWGEDKFKSFTDEIYKKHGKKVIMNIATHSHDDRAGGLEYFGKLGAKTYSTKMTDSILAKENKPRAKYTFDNNKSFKVGNTEFQVYYPGKGHTADNVVVWFPKDKVLVGGCIVKSGDSKDLGYIGEAYVNDWTQSIHNIQQKFPDVQYVVAGHDDWKDQTSIQHTLDLISDYQQKQKASN"},"dna_sequence":{"accession":"NG_048699.1","fmin":"0","fmax":"750","strand":"+","sequence":"ATGTTGAAAAGATTAAAAGGATTATTGGTTCTGGCTTTAGGTTTTACAGGACTACAGGTTTTTGGACAGCAAAATCCTGATATTAAAATTGAAAAATTAAAAGATAATTTATACGTCTATACAACCTATAATACCTTTAAAGGAACTAAATATGCGGCTAATGCGGTATATATGGTAACGGATAAAGGAGTAGTGGTGATAGACTCTCCATGGGGAGAAGATAAATTTAAAAGTTTTACAGACGAGATTTATAAAAAGCACGGAAAGAAAGTCATCATGAACATTGCTACCCATTCTCATGACGATAGAGCCGGAGGTCTTGAATATTTTGGTAAACTAGGTGCAAAAACTTATTCTACTAAAATGACAGATTCTATTTTAGCAAAAGAGAATAAGCCAAGAGCAAAGTACACTTTTGATAATAATAAATCTTTTAAAGTAGGAAACACTGAGTTCCAGGTCTATTATCCGGGAAAAGGGCATACGGCAGATAATGTGGTGGTATGGTTCCCTAAAGACAAAGTATTAGTAGGAGGCTGCATTGTAAAAAGTGGTGATTCGAAAGACCTTGGATATATTGGAGAAGCTTATGTAAACGACTGGACACAGTCTATACACAATATTCAGCAGAAATTTCCCGATGTTCAGTATGTCGTTGCAGGCCACGATGACTGGAAAGATCAAACATCAATACAACATACACTGGATTTAATCAGTGATTACCAACAAAAACAAAAGGCTTCAAATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36960","NCBI_taxonomy_name":"Elizabethkingia meningoseptica","NCBI_taxonomy_id":"238"}}}},"ARO_accession":"3005553","ARO_id":"44015","ARO_name":"BlaB-5","CARD_short_name":"BlaB-5","ARO_description":"BlaB-5 is a BlaB beta-lactamase.","ARO_category":{"41365":{"category_aro_accession":"3004201","category_aro_cvterm_id":"41365","category_aro_name":"BlaB beta-lactamase","category_aro_description":"BlaB beta-lactamases are class B beta-lactamases that are found in a variety of species and have the ability to hydrolyze penams and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4402":{"model_id":"4402","model_name":"BlaB-6","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"6777":{"protein_sequence":{"accession":"WP_068791546.1","sequence":"MMKRLKGLLVLALGFTGLQVFGQQNPDIKIEKLKDNLYVYTTYNTFKGTKYAANAVYMVTDKGVVVIDSPWGEDKFKSFTDEIYKKHGKKVIMNIATHSHDDRAGGLEYFGKLGAKTYSTKMTDSILAKENKPRAKYTFDNNKSFKVGNTEFQVYYPGKGHTADNVVVWFPKDKVLVGGCIVKSGDSKDLGFIGEAYVNDWTQSIHNIQQKFPDVQYVVAGHDDWKDQTSIQHTLDLISEYQQKQKASN"},"dna_sequence":{"accession":"NG_068504.1","fmin":"100","fmax":"850","strand":"+","sequence":"ATGATGAAAAGATTAAAAGGATTATTGGTTCTGGCTTTAGGTTTTACAGGACTACAGGTTTTTGGACAGCAAAATCCTGATATTAAAATTGAAAAATTAAAAGATAATTTATACGTCTATACAACCTATAATACCTTTAAAGGAACTAAATATGCGGCTAATGCGGTATATATGGTAACGGATAAAGGAGTAGTGGTGATAGACTCTCCATGGGGAGAAGATAAATTTAAAAGTTTTACAGACGAGATTTATAAAAAGCACGGAAAGAAAGTCATCATGAACATTGCTACCCATTCTCATGACGATAGAGCCGGAGGTCTTGAATATTTTGGTAAACTAGGTGCAAAAACTTATTCTACTAAAATGACAGATTCTATTTTAGCAAAAGAGAATAAGCCAAGAGCAAAGTACACTTTTGATAATAATAAATCTTTTAAAGTAGGAAACACTGAGTTCCAGGTCTATTATCCGGGAAAAGGTCATACAGCAGATAATGTGGTTGTGTGGTTCCCTAAAGACAAAGTATTAGTAGGAGGCTGCATTGTAAAAAGCGGTGATTCGAAAGACCTTGGGTTTATTGGAGAAGCTTATGTAAACGACTGGACACAGTCCATACACAACATTCAGCAGAAATTTCCCGATGTTCAGTATGTCGTTGCAGGTCACGATGACTGGAAGGATCAAACATCAATACAGCATACACTGGATTTAATCAGTGAATATCAACAAAAACAAAAGGCTTCAAATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3005554","ARO_id":"44016","ARO_name":"BlaB-6","CARD_short_name":"BlaB-6","ARO_description":"BlaB-6 is a BlaB beta-lactamase.","ARO_category":{"41365":{"category_aro_accession":"3004201","category_aro_cvterm_id":"41365","category_aro_name":"BlaB beta-lactamase","category_aro_description":"BlaB beta-lactamases are class B beta-lactamases that are found in a variety of species and have the ability to hydrolyze penams and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4403":{"model_id":"4403","model_name":"BlaB-7","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"6778":{"protein_sequence":{"accession":"WP_063857829.1","sequence":"MKGLKGLLVLALGFTGLQVFGQQNPDIKIEKLKDNLYVYTTYNTFKGTKYAANAVYMVTDKGIVVIDSPWGEDKFKSFTDEIYKKHGKKVIMNIATHSHDDRAGGLEYFGKLGAKTYSTKMTDSILAKENKPRAKYTFDNNKSFKVGKTEFQVYYPGKGHTADNVVVWFPKDKVLVGGCIVKSGDSKDLGFIGEAYVNDWTQSIHNIQQKFPDVQYVVAGHDDWKDQTSIQHTLDLISEYQQKQKASN"},"dna_sequence":{"accession":"NG_048701.1","fmin":"0","fmax":"747","strand":"+","sequence":"ATGAAAGGATTAAAAGGGCTATTGGTTCTGGCTTTAGGTTTTACAGGACTACAGGTTTTTGGGCAACAGAACCCTGATATTAAAATTGAAAAATTAAAAGATAATTTATACGTCTATACAACCTATAATACCTTCAAAGGAACTAAATATGCGGCTAATGCGGTATATATGGTAACCGATAAAGGAATAGTGGTTATAGACTCTCCATGGGGAGAAGATAAATTTAAAAGTTTTACAGACGAGATTTATAAAAAGCACGGTAAGAAAGTTATCATGAACATTGCGACCCACTCTCATGATGATAGAGCCGGAGGTCTTGAATATTTTGGTAAACTAGGTGCAAAAACTTATTCTACTAAAATGACAGATTCTATTTTAGCAAAAGAGAATAAGCCAAGAGCAAAGTACACTTTTGATAATAATAAATCTTTTAAAGTAGGAAAGACTGAGTTTCAGGTCTATTATCCGGGAAAAGGTCATACAGCAGATAATGTGGTTGTGTGGTTCCCTAAAGACAAAGTATTAGTAGGAGGCTGCATTGTAAAAAGTGGTGATTCGAAAGACCTTGGGTTTATTGGAGAAGCTTATGTAAACGACTGGACACAGTCCATACACAATATTCAGCAGAAATTTCCCGATGTTCAGTATGTCGTTGCAGGTCATGACGACTGGAAAGATCAAACATCAATACAACATACACTGGATTTAATCAGTGAATATCAACAAAAACAAAAGGCTTCAAATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36960","NCBI_taxonomy_name":"Elizabethkingia meningoseptica","NCBI_taxonomy_id":"238"}}}},"ARO_accession":"3005555","ARO_id":"44017","ARO_name":"BlaB-7","CARD_short_name":"BlaB-7","ARO_description":"BlaB-7 is a BlaB beta-lactamase.","ARO_category":{"41365":{"category_aro_accession":"3004201","category_aro_cvterm_id":"41365","category_aro_name":"BlaB beta-lactamase","category_aro_description":"BlaB beta-lactamases are class B beta-lactamases that are found in a variety of species and have the ability to hydrolyze penams and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4404":{"model_id":"4404","model_name":"BlaB-8","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"6779":{"protein_sequence":{"accession":"WP_059324801.1","sequence":"MKGLKGLLVLALGFTGLQVFGQQNPDIKIEKLKDNLYVYTTYNTFKGTKYAANAVYMVTDKGVVVIDSPWGEDKFKSFTDEIYKKHGKKVIMNIATHSHDDRAGGLEYFGKLGAKTYSTKMTDSILAKENKPRAKYTFDNNKSFKVGKTEFQVYYPGKGHTADNVVVWFPKDKVLVGGCIVKSGDSKDLGFIGEAYVNDWTQSIHNIQQKFPDVQYVVAGHDDWKDQTSIQHTLDLISEYQQKQKASN"},"dna_sequence":{"accession":"NG_048702.1","fmin":"0","fmax":"747","strand":"+","sequence":"ATGAAAGGATTAAAAGGACTATTGGTTCTGGCTTTAGGTTTTACAGGACTACAGGTTTTTGGGCAACAGAACCCTGATATTAAAATTGAAAAATTAAAAGATAATTTATACGTCTATACAACATATAATACCTTCAAAGGAACTAAATATGCGGCTAATGCGGTATATATGGTAACCGATAAAGGAGTAGTGGTTATAGACTCTCCATGGGGAGAAGATAAATTTAAAAGTTTTACAGACGAGATTTATAAAAAGCACGGAAAGAAAGTTATCATGAACATTGCGACCCACTCTCATGATGATAGAGCCGGAGGTCTTGAATATTTTGGTAAACTAGGTGCAAAAACTTATTCTACTAAAATGACAGATTCTATTTTAGCAAAAGAGAATAAGCCAAGAGCAAAGTACACTTTTGATAATAATAAATCTTTTAAAGTAGGAAAGACTGAGTTTCAGGTCTATTATCCAGGAAAAGGTCATACAGCAGATAATGTGGTTGTATGGTTCCCTAAAGACAAAGTATTAGTAGGAGGCTGCATTGTAAAAAGCGGTGATTCGAAAGATCTTGGGTTTATTGGAGAAGCTTATGTAAACGACTGGACACAGTCCATACACAACATTCAGCAGAAATTTCCCGATGTTCAGTATGTCGTTGCAGGTCATGACGACTGGAAAGATCAAACATCAATACAACATACACTGGATTTAATCAGTGAATATCAACAAAAACAAAAGGCTTCAAATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36960","NCBI_taxonomy_name":"Elizabethkingia meningoseptica","NCBI_taxonomy_id":"238"}}}},"ARO_accession":"3005556","ARO_id":"44018","ARO_name":"BlaB-8","CARD_short_name":"BlaB-8","ARO_description":"BlaB-8 is a BlaB beta-lactamase.","ARO_category":{"41365":{"category_aro_accession":"3004201","category_aro_cvterm_id":"41365","category_aro_name":"BlaB beta-lactamase","category_aro_description":"BlaB beta-lactamases are class B beta-lactamases that are found in a variety of species and have the ability to hydrolyze penams and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4405":{"model_id":"4405","model_name":"BlaB-9","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"6780":{"protein_sequence":{"accession":"WP_059154943.1","sequence":"MKGLKGLLVLALGFTGLQVFGQQNPDIKIEKLKDNLYVYTTYNTFKGTKYAANAVYMVTDKGVVVIDSPWGEDKFKSFTDEIYKKHGKKVIMNIATHSHDDRAGGLEYFGKLGAKTYSTKMTDSILAKENKPRAKYTFDNNKSFKVGNTEFQVYYPGKGHTADNVVVWFPKDKVLVGGCIVKSGDSKDLGFIGEAYVNDWTQSIHNIQQKFPDVQYVVAGHDDWKDQTSIQHTLDLISEYQQKQKASN"},"dna_sequence":{"accession":"NG_048703.1","fmin":"0","fmax":"747","strand":"+","sequence":"ATGAAAGGATTAAAAGGGCTATTGGTTCTGGCTTTAGGCTTTACAGGACTACAGGTTTTTGGGCAACAGAACCCTGATATTAAAATTGAAAAATTAAAAGATAATTTATACGTCTATACAACCTATAATACCTTCAAAGGAACTAAATATGCGGCTAATGCGGTATATATGGTAACCGATAAAGGAGTAGTGGTGATAGACTCTCCATGGGGAGAAGATAAATTTAAAAGTTTTACAGACGAGATTTATAAAAAGCACGGAAAGAAAGTCATCATGAACATTGCTACACATTCTCATGACGATAGAGCCGGAGGTCTTGAATATTTTGGTAAACTAGGTGCAAAAACTTATTCTACTAAAATGACAGATTCTATTTTAGCAAAAGAGAATAAGCCAAGAGCAAAGTACACTTTTGATAATAATAAATCTTTTAAAGTAGGAAACACTGAGTTCCAGGTCTATTATCCGGGAAAAGGTCATACAGCAGATAATGTGGTGGTATGGTTCCCTAAAGACAAAGTATTAGTAGGAGGCTGCATTGTAAAAAGCGGTGATTCGAAAGACCTTGGGTTTATTGGGGAAGCTTATGTAAACGACTGGACACAGTCCATACACAACATTCAGCAGAAATTTCCCGATGTTCAGTATGTCGTTGCAGGTCATGACGACTGGAAAGATCAAACATCAATACAACATACACTGGATTTAATCAGTGAATATCAACAAAAACAAAAGGCTTCAAATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36960","NCBI_taxonomy_name":"Elizabethkingia meningoseptica","NCBI_taxonomy_id":"238"}}}},"ARO_accession":"3005557","ARO_id":"44019","ARO_name":"BlaB-9","CARD_short_name":"BlaB-9","ARO_description":"BlaB-9 is a BlaB beta-lactamase.","ARO_category":{"41365":{"category_aro_accession":"3004201","category_aro_cvterm_id":"41365","category_aro_name":"BlaB beta-lactamase","category_aro_description":"BlaB beta-lactamases are class B beta-lactamases that are found in a variety of species and have the ability to hydrolyze penams and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4406":{"model_id":"4406","model_name":"BSU-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6781":{"protein_sequence":{"accession":"WP_003235647.1","sequence":"MSKGKVQALFLSLIGAALLMTSSLQTPTEAEAAEKNINSKKLKVDEFFTDLDGTFILRDLKNEKTFVYNDQRAKQRFAPQSTFKVPNALIGLETGAVKDEYDIKYWDGVKRELDVWNQDHTLGSAMRYSVVWYYQAMARDIGEERMKEWIEKTGYGNQDISGGIDQFWLSSTLKISPLEQTDFMESLYKEKLPFDKSVMKTVKRMMIQEDEDHYTLYGKTGSGSGIGWYAGFVKTEHGAYSFVTNIDGTGTEAKSITMDILKKYVLH"},"dna_sequence":{"accession":"NG_050942.1","fmin":"100","fmax":"904","strand":"+","sequence":"TTGAGCAAGGGAAAGGTGCAAGCACTCTTTTTATCACTTATCGGTGCGGCTCTGCTCATGACATCAAGTTTACAGACACCTACAGAAGCTGAAGCTGCAGAGAAAAACATAAATTCGAAAAAGCTGAAGGTTGATGAGTTTTTCACAGATCTCGACGGCACTTTTATCTTGCGGGATTTAAAAAACGAAAAAACATTCGTCTACAACGATCAGCGCGCAAAACAAAGATTTGCGCCGCAGTCGACGTTTAAAGTTCCTAATGCGCTTATCGGATTAGAAACAGGCGCTGTTAAAGATGAATATGACATCAAATACTGGGATGGCGTGAAACGGGAACTTGACGTTTGGAACCAAGACCATACGCTCGGCTCTGCTATGAGATATTCAGTGGTTTGGTATTACCAAGCAATGGCCCGGGACATCGGAGAAGAGCGAATGAAGGAATGGATTGAAAAAACAGGTTACGGCAACCAAGACATCAGCGGCGGAATTGATCAATTCTGGCTAAGCAGCACTCTCAAAATCTCTCCTTTAGAACAAACAGATTTTATGGAATCGTTATACAAAGAAAAACTACCATTTGACAAAAGCGTCATGAAGACGGTAAAACGGATGATGATTCAAGAAGACGAAGACCACTATACGCTTTATGGAAAAACCGGTTCTGGCTCAGGCATCGGCTGGTATGCCGGCTTTGTTAAAACCGAGCACGGGGCGTACAGCTTCGTGACAAACATTGACGGAACCGGAACAGAAGCGAAAAGCATCACAATGGACATTTTGAAGAAATATGTTCTGCATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3006902","ARO_id":"45364","ARO_name":"BSU-1","CARD_short_name":"BSU-1","ARO_description":"BSU-1 is a BSU beta-lactamase.","ARO_category":{"43854":{"category_aro_accession":"3005394","category_aro_cvterm_id":"43854","category_aro_name":"BSU beta-lactamase","category_aro_description":"BSU beta-lactamases are class D beta-lactamases found in Bacillus inaquosorum.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4407":{"model_id":"4407","model_name":"BUT-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6782":{"protein_sequence":{"accession":"WP_104531864.1","sequence":"MMKKTLCCALVLSASFSAFAAQKTLSDKQLEEAVNQTLKPMITAQAIPGMAVAVIYQGKPHYFTYGVADIAKNQPVTTQTIFELGSVSKTFTGVLGGDIVARGEVKLSDPAMKYWPELTGKQWQGITLLDLATYTAGGLPLQVPDEVDNQAALLKFYQNWQPDWAPGTRRQYANSSIGLFGALAVKPSGMTFNDAMRQRVLQPLNLKHTWLTVPASEENHYAWGYRDGKAMHVGPGMLDTEAYGVKSTIEDMASWVQYNMNPQQVKQPTLQKGLEIAQSRYWRSGSMYQGLGWEMLNWPVAAATVINGSDNKVALAASPVTAIEPPVAPVKASLVHKTGSTNGFGAYVAFIPEKQIGIVMLANKMYPNTERVKAANTLLNTLQ"},"dna_sequence":{"accession":"NG_056481.1","fmin":"100","fmax":"1252","strand":"+","sequence":"ATGATGAAAAAAACACTCTGCTGCGCGCTGGTTCTGAGCGCCTCTTTCTCCGCCTTTGCTGCACAAAAAACATTGAGTGACAAACAGTTAGAAGAGGCTGTCAATCAAACGCTTAAACCGATGATTACAGCCCAGGCCATTCCCGGCATGGCGGTGGCGGTGATTTATCAGGGCAAGCCGCACTACTTTACCTACGGCGTGGCCGACATCGCGAAAAATCAGCCGGTGACGACACAGACGATTTTTGAGCTGGGCTCCGTGAGTAAAACTTTCACCGGCGTGCTGGGCGGCGATATCGTGGCGCGCGGGGAAGTGAAGCTGAGTGACCCGGCGATGAAATACTGGCCAGAACTGACGGGCAAGCAGTGGCAGGGCATCACGTTGCTGGATCTGGCGACCTACACCGCCGGCGGCTTGCCGTTGCAGGTGCCGGATGAGGTCGATAATCAGGCCGCGCTGCTGAAGTTTTACCAGAACTGGCAGCCGGACTGGGCGCCGGGAACCCGTCGTCAGTACGCCAACTCGAGCATTGGCCTGTTTGGTGCGTTGGCAGTGAAACCGTCCGGGATGACGTTTAACGATGCGATGCGCCAGCGCGTTCTGCAACCGCTGAACCTGAAACATACCTGGCTCACCGTTCCGGCCAGTGAAGAAAATCATTACGCCTGGGGCTATCGTGACGGCAAAGCCATGCACGTCGGGCCGGGCATGCTGGATACCGAAGCCTACGGTGTCAAATCCACCATCGAAGATATGGCGAGCTGGGTGCAATACAACATGAACCCGCAGCAGGTGAAACAGCCGACGCTGCAAAAAGGGCTGGAGATTGCGCAGTCGCGCTACTGGCGCAGCGGCAGTATGTATCAGGGCTTAGGCTGGGAAATGCTGAACTGGCCGGTTGCGGCGGCGACCGTCATTAACGGCAGCGATAACAAAGTGGCGCTGGCGGCTTCGCCCGTGACGGCCATTGAACCGCCGGTTGCGCCGGTGAAAGCTTCTCTGGTGCATAAAACCGGGTCGACCAACGGCTTCGGCGCGTACGTGGCGTTCATTCCTGAAAAACAAATCGGCATCGTGATGCTGGCTAACAAAATGTATCCGAATACCGAGCGGGTTAAAGCGGCAAATACTCTTCTCAACACGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41461","NCBI_taxonomy_name":"Buttiauxella agrestis","NCBI_taxonomy_id":"82977"}}}},"ARO_accession":"3005558","ARO_id":"44020","ARO_name":"BUT-2","CARD_short_name":"BUT-2","ARO_description":"BUT-2 is a BUT beta-lactamase.","ARO_category":{"41459":{"category_aro_accession":"3004293","category_aro_cvterm_id":"41459","category_aro_name":"BUT beta-lactamase","category_aro_description":"A class C beta-lactamase family of chromosome-encoded antibiotic resistance genes originally described from Buttiauxella spp.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4408":{"model_id":"4408","model_name":"CAR-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"6783":{"protein_sequence":{"accession":"WP_011094382.1","sequence":"MKNQRLTPLAAFLLLISVAATAHTLPSQGTETKGAETNSPAITSLTGCGPSSAINQFFNQFGSSGKMPAELGRWLNDAKAQAVEPYQVFDNVYYVGICWVSAWLIKTSEGPVLIDTLYGEFTDQLMDNIKKIGVEPSDIKMVLLTHGHFDHVGGVSKLKSLTNARFVMSEEGWKEAQADAKKTLGKPSAWAMPDPATTDILVKDGDALTVGDTTFHAYITPGHTWGTTSYVLDVKERNNTYHAITIGGLGLNAIDGPQQVEAYIRSIDRIKVMVEDSKHPITVHLTAHPFSNGQIEMQNQLKVHQPDQPHPMVDAKGLLKQLATLRAGAIERLAVEQARIQK"},"dna_sequence":{"accession":"NG_048712.1","fmin":"100","fmax":"1129","strand":"+","sequence":"ATGAAAAACCAACGTCTTACGCCCCTAGCAGCTTTCTTACTTTTAATCAGTGTGGCTGCTACGGCTCACACTCTCCCATCACAAGGTACAGAAACAAAAGGTGCAGAAACAAATAGTCCCGCCATCACCTCACTGACAGGGTGCGGTCCATCCTCAGCTATCAACCAATTTTTCAACCAATTTGGAAGCAGCGGTAAAATGCCTGCCGAACTTGGACGTTGGCTGAATGATGCAAAGGCCCAGGCCGTCGAACCCTATCAGGTATTTGACAATGTTTATTATGTCGGCATTTGTTGGGTCTCAGCCTGGCTCATCAAAACCAGCGAAGGCCCAGTACTAATAGATACGCTGTATGGAGAATTTACAGACCAGCTTATGGATAACATTAAAAAAATCGGCGTCGAGCCATCAGATATCAAAATGGTACTGCTAACACACGGACATTTTGATCATGTAGGCGGCGTATCTAAACTCAAGTCGTTAACCAACGCACGTTTTGTCATGTCTGAGGAAGGATGGAAGGAAGCGCAGGCTGATGCAAAAAAAACACTGGGGAAACCTAGCGCATGGGCAATGCCTGACCCAGCCACCACAGATATCTTGGTGAAAGACGGCGATGCGTTGACGGTGGGTGATACTACATTTCATGCCTACATTACCCCAGGCCACACTTGGGGCACCACATCTTATGTGCTTGATGTCAAAGAGAGGAATAACACCTATCACGCGATTACTATTGGCGGATTAGGATTAAATGCTATAGACGGTCCGCAACAGGTTGAGGCCTACATCCGAAGCATAGACCGTATTAAGGTGATGGTGGAAGATTCTAAGCACCCCATTACAGTCCATCTCACCGCGCATCCTTTTAGTAACGGTCAAATTGAAATGCAAAATCAACTAAAAGTACATCAGCCTGACCAACCACACCCCATGGTAGATGCAAAAGGGCTCCTCAAACAGTTGGCGACACTCCGCGCAGGAGCAATAGAACGACTGGCCGTTGAACAGGCACGGATTCAAAAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3006903","ARO_id":"45365","ARO_name":"CAR-1","CARD_short_name":"CAR-1","ARO_description":"CAR-1 is a CAR beta-lactamase.","ARO_category":{"43855":{"category_aro_accession":"3005395","category_aro_cvterm_id":"43855","category_aro_name":"CAR beta-lactamase","category_aro_description":"CAR beta-lactamases are class B3 beta-lactamases found in Pectobacterium atrosepticum.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4409":{"model_id":"4409","model_name":"CARB-11","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6784":{"protein_sequence":{"accession":"WP_063857838.1","sequence":"MKFLLAFSLLIPSVVFASSSKFQQVEQDVKAIEVSLSARIGVSVLDTQNGEYWDYNGNQRFPLTSTFKTIACAKLLYDAEQGKVNSNSTVEIKKADLVTYSPVIEKQVGQAITLDDACFATMTTSDNTAANIILSAVGGPKGVTDFLRQIGDKETRLDRIEPDLNEGKLGDLRDTTTPKAIASTLNKFLFGSALSEMNQKKLESWMVNNQVTGNLLRSVLPAGWNIADRSGAGGFGARSITAVVWSEHQAPIIVSIYLAQTQASMAERNDAIVKIGHSIFDVYTSQSR"},"dna_sequence":{"accession":"NG_048715.1","fmin":"0","fmax":"867","strand":"+","sequence":"ATGAAGTTTTTATTGGCATTTTCGCTTTTAATACCATCCGTGGTTTTTGCAAGTAGTTCAAAGTTTCAGCAAGTTGAACAAGACGTTAAGGCAATTGAAGTTTCTCTTTCTGCTCGTATAGGTGTTTCCGTTCTTGATACTCAAAATGGAGAATATTGGGATTACAATGGCAATCAGCGCTTCCCGTTAACAAGTACTTTTAAAACAATAGCTTGCGCTAAATTACTATATGATGCTGAGCAAGGAAAAGTTAATTCCAATAGTACAGTCGAGATTAAGAAAGCAGATCTTGTGACCTATTCCCCTGTAATAGAAAAGCAAGTAGGGCAGGCAATCACACTCGATGATGCGTGCTTCGCAACTATGACTACAAGTGATAATACTGCGGCAAATATCATCCTAAGTGCTGTAGGTGGCCCCAAAGGCGTTACTGATTTTTTAAGACAAATTGGGGACAAAGAGACTCGTCTAGACCGTATTGAGCCTGATTTAAATGAAGGTAAGCTCGGTGATTTGAGGGATACGACAACTCCTAAGGCAATAGCCAGTACTTTGAATAAATTTTTATTTGGTTCCGCGCTATCTGAAATGAACCAGAAAAAATTAGAGTCTTGGATGGTGAACAATCAAGTCACTGGTAATTTACTACGTTCAGTATTGCCGGCGGGATGGAACATTGCGGATCGCTCAGGTGCTGGCGGATTTGGTGCTCGGAGTATTACAGCAGTTGTGTGGAGTGAGCATCAAGCCCCAATTATTGTGAGCATCTATCTAGCTCAAACACAGGCTTCAATGGCAGAGCGAAATGATGCGATTGTTAAAATTGGTCATTCAATTTTTGACGTTTATACATCACAGTCGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005559","ARO_id":"44021","ARO_name":"CARB-11","CARD_short_name":"CARB-11","ARO_description":"CARB-11 is a CARB beta-lactamase.","ARO_category":{"36230":{"category_aro_accession":"3000091","category_aro_cvterm_id":"36230","category_aro_name":"CARB beta-lactamase","category_aro_description":"CARB beta-lactamases are class A lactamases that can hydrolyze carbenicillin. Many of the PSE beta-lactamases have been renamed as CARB-lactamases with the notable exception of PSE-2 which is now OXA-10.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4410":{"model_id":"4410","model_name":"CARB-24","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6785":{"protein_sequence":{"accession":"WP_031413517.1","sequence":"MKKLFLLVGLMVCSTVSYASKLNEDISLIEKQTSGRIGVSVWDTQTDERWDYRGDERFPLMSTFKTLACATMLSDMDSGKLNKNATAKIDERNIVVWSPVMDKLAGQSTRIEHACEAAMLMSDNTAANLVLNEIGGPKAVTLFLRSIGDKATRLDRLEPRLNEAKPGDKRDTTTPNAMVNTLHTLMEDNALSYESRTQLKIWMQDNKVSDSLMRSVLPKGWSIADRSGAGNHGSRGISAMIWKDNYKPVYISIYVTDTDLSLQARDQLIAQISQLILEHYKES"},"dna_sequence":{"accession":"NG_048727.1","fmin":"0","fmax":"852","strand":"+","sequence":"ATGAAAAAGTTATTCCTGTTGGTTGGGCTGATGGTTTGCTCAACTGTTAGTTACGCCTCCAAATTAAACGAAGACATCTCCCTCATCGAGAAACAAACATCTGGGCGAATTGGAGTGTCAGTCTGGGATACACAAACGGACGAGCGTTGGGATTATCGCGGAGACGAACGTTTCCCATTAATGAGCACATTTAAAACGTTAGCGTGTGCCACCATGCTAAGCGACATGGACAGCGGCAAACTCAACAAAAATGCCACAGCGAAAATCGATGAACGCAATATTGTGGTCTGGTCTCCGGTGATGGATAAACTGGCTGGACAAAGCACACGCATCGAACACGCTTGTGAAGCCGCCATGTTGATGAGCGACAACACCGCCGCGAACTTAGTGCTAAATGAAATTGGTGGTCCTAAAGCGGTCACGTTGTTTTTGCGCTCTATTGGCGACAAAGCAACGCGACTTGACCGATTGGAACCCCGTTTGAATGAAGCGAAACCGGGCGACAAGCGAGACACCACAACGCCTAACGCCATGGTAAACACCCTACATACCTTGATGGAAGATAACGCCCTATCTTACGAGTCACGCACACAGCTGAAAATCTGGATGCAAGACAACAAAGTATCGGATTCTCTCATGCGCTCTGTTCTGCCAAAAGGCTGGTCGATTGCAGACCGCTCTGGCGCAGGTAACCACGGTTCACGCGGCATTAGCGCGATGATCTGGAAAGACAACTACAAGCCGGTTTACATCAGTATTTACGTCACAGACACTGACCTTTCGCTTCAAGCTCGCGATCAGCTGATCGCGCAAATCAGCCAACTGATTTTAGAGCACTACAAAGAAAGTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39615","NCBI_taxonomy_name":"Vibrio parahaemolyticus","NCBI_taxonomy_id":"670"}}}},"ARO_accession":"3005560","ARO_id":"44022","ARO_name":"CARB-24","CARD_short_name":"CARB-24","ARO_description":"CARB-24 is a CARB beta-lactamase.","ARO_category":{"36230":{"category_aro_accession":"3000091","category_aro_cvterm_id":"36230","category_aro_name":"CARB beta-lactamase","category_aro_description":"CARB beta-lactamases are class A lactamases that can hydrolyze carbenicillin. Many of the PSE beta-lactamases have been renamed as CARB-lactamases with the notable exception of PSE-2 which is now OXA-10.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4411":{"model_id":"4411","model_name":"CARB-25","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6786":{"protein_sequence":{"accession":"WP_042771632.1","sequence":"MKKLFLLVGLMVCSTVSYASKLNEDISLIEKQTSGRIGVSVWDTQTDERWDYRGDERFPLMSTFKTLACATMLSDMDSGKLNKNATAKIDERNIVVWSPVMDKLAGQSTRIEHACEAAMLMSDNTAANLVLNEIGGPKAVTLFLRSIGDKATRLDRLEPRLNEAKPGDKRDTTTPNAMVNTLHTLMEDNALSYESRTQLKIWMQDNKVSDSLMRSVLPKGWSIADRSGAGNYGSRGISAMIWKDNYKPVYISIYVTDTDLSLQARDQLIAQISQLILDHYKES"},"dna_sequence":{"accession":"NG_048728.1","fmin":"0","fmax":"852","strand":"+","sequence":"ATGAAAAAGTTATTCCTGTTGGTTGGGCTGATGGTTTGCTCAACTGTTAGTTACGCCTCCAAATTAAACGAAGACATCTCCCTCATCGAGAAACAAACATCTGGGCGAATTGGAGTGTCAGTCTGGGATACACAAACGGACGAGCGTTGGGATTATCGCGGAGACGAACGTTTCCCATTAATGAGCACATTCAAAACGTTAGCGTGTGCCACCATGCTAAGCGACATGGACAGCGGCAAACTCAACAAAAATGCCACAGCGAAAATCGATGAACGCAATATTGTGGTTTGGTCTCCGGTGATGGATAAACTGGCTGGACAAAGCACGCGTATCGAACACGCTTGTGAGGCCGCCATGTTGATGAGCGACAACACCGCCGCGAACTTAGTGCTAAATGAAATTGGTGGTCCTAAAGCGGTCACGCTGTTTTTGCGATCTATTGGCGACAAAGCAACGCGACTTGACCGATTGGAACCCCGTTTGAATGAAGCAAAACCGGGCGACAAGCGAGACACCACAACGCCTAACGCCATGGTAAACACCCTACACACCTTGATGGAAGATAACGCCCTATCTTACGAGTCACGCACACAGCTGAAAATCTGGATGCAAGACAACAAAGTATCGGATTCTCTCATGCGCTCTGTTCTGCCAAAAGGCTGGTCGATTGCAGACCGCTCTGGCGCAGGTAACTACGGTTCACGCGGCATTAGCGCGATGATCTGGAAAGACAACTACAAGCCGGTTTACATCAGTATTTACGTCACAGACACCGACCTTTCGCTTCAAGCTCGCGATCAACTGATCGCGCAAATCAGCCAACTGATTTTAGATCACTACAAAGAAAGTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39615","NCBI_taxonomy_name":"Vibrio parahaemolyticus","NCBI_taxonomy_id":"670"}}}},"ARO_accession":"3005561","ARO_id":"44023","ARO_name":"CARB-25","CARD_short_name":"CARB-25","ARO_description":"CARB-25 is a CARB beta-lactamase.","ARO_category":{"36230":{"category_aro_accession":"3000091","category_aro_cvterm_id":"36230","category_aro_name":"CARB beta-lactamase","category_aro_description":"CARB beta-lactamases are class A lactamases that can hydrolyze carbenicillin. Many of the PSE beta-lactamases have been renamed as CARB-lactamases with the notable exception of PSE-2 which is now OXA-10.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4412":{"model_id":"4412","model_name":"CARB-26","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6787":{"protein_sequence":{"accession":"WP_029795186.1","sequence":"MKKLFLLVGLMVCSTVSYASKLNEDISLIEKQTSGRIGVSVWDTQTDERWDYRGDERFPLMSTFKTLACATMLSDMDSGKLNKNATAKIDERNIVVWSPVMDKLAGQSTRIEHACEAAMLRSDNTAANLVLNEIGGPKAVTLFLRSIGDKATRLDRLEPRLNEAKPGDKRDTTTPNAMVNTLHTLMEDNALSYESRTQLKIWMQDNKVSDSLMRSVLPKGWSIADRSGAGNYGSRGISAMIWKDNYKPVYISIYVTDTDLSLQARDQLIAQISQLILEHYKES"},"dna_sequence":{"accession":"NG_048729.1","fmin":"0","fmax":"852","strand":"+","sequence":"ATGAAAAAGTTATTCCTGTTGGTTGGGCTGATGGTTTGCTCAACTGTTAGTTACGCCTCCAAATTAAACGAAGACATCTCCCTCATCGAGAAACAAACATCTGGGCGAATTGGAGTGTCAGTCTGGGATACACAAACGGACGAGCGTTGGGATTATCGCGGAGACGAACGTTTCCCATTAATGAGCACATTCAAAACGTTAGCGTGTGCCACCATGCTAAGCGACATGGATAGCGGCAAACTCAACAAAAATGCCACAGCGAAAATCGATGAACGCAATATTGTGGTTTGGTCTCCGGTGATGGATAAACTGGCTGGACAAAGCACACGCATCGAACACGCTTGTGAAGCCGCCATGTTGAGGAGCGACAACACCGCCGCGAACTTAGTGCTAAATGAAATTGGTGGTCCTAAAGCGGTCACGTTGTTTTTGCGATCTATTGGCGACAAAGCAACGCGACTTGACCGATTGGAACCCCGTTTGAATGAAGCAAAACCGGGCGACAAGCGAGACACCACAACGCCTAACGCCATGGTAAACACCCTACATACCTTGATGGAAGATAACGCCCTATCTTACGAGTCACGCACACAGCTGAAAATCTGGATGCAAGACAACAAAGTATCGGATTCGCTCATGCGCTCTGTTCTGCCAAAAGGTTGGTCGATTGCAGACCGCTCTGGCGCAGGTAACTACGGTTCACGCGGCATTAGCGCGATGATTTGGAAAGACAACTACAAGCCGGTTTACATCAGTATTTACGTCACAGACACCGACCTTTCGCTTCAAGCTCGCGATCAACTGATCGCGCAAATCAGCCAACTGATTTTAGAGCACTACAAAGAAAGTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39615","NCBI_taxonomy_name":"Vibrio parahaemolyticus","NCBI_taxonomy_id":"670"}}}},"ARO_accession":"3005562","ARO_id":"44024","ARO_name":"CARB-26","CARD_short_name":"CARB-26","ARO_description":"CARB-26 is a CARB beta-lactamase.","ARO_category":{"36230":{"category_aro_accession":"3000091","category_aro_cvterm_id":"36230","category_aro_name":"CARB beta-lactamase","category_aro_description":"CARB beta-lactamases are class A lactamases that can hydrolyze carbenicillin. Many of the PSE beta-lactamases have been renamed as CARB-lactamases with the notable exception of PSE-2 which is now OXA-10.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4413":{"model_id":"4413","model_name":"CARB-27","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6788":{"protein_sequence":{"accession":"WP_025623492.1","sequence":"MKKLFLLVGLMVCSTVSYASKLNEDISLIEKQTSGRIGVSVWDTQTDERWDYRGDERFPLMSTFKTLACATMLSDMDSGKLNKNATAKIDERNIVVWSPVMDKLTGQSTRIEHACEAAMLMSDNTAANLVLNEIGGPKAVTLFLRSIGDKATRLDRLEPRLNEAKPGDKRDTTTPNAMVNTLHTLMEDNALSYESRTQLKIWMQDNKVSDSLMRSVLPKGWSIADRSGAGNYGSRGISAMIWKDNYKPVYISIYVTDTDLSLQARDQLIAQISQLILEHYKES"},"dna_sequence":{"accession":"NG_048730.1","fmin":"0","fmax":"852","strand":"+","sequence":"ATGAAAAAGTTATTCCTGTTGGTTGGGCTGATGGTTTGCTCAACTGTTAGTTACGCCTCCAAATTAAACGAAGACATCTCCCTCATCGAGAAACAAACATCTGGGCGAATTGGAGTGTCAGTCTGGGATACACAAACGGACGAGCGTTGGGATTATCGCGGAGACGAACGTTTCCCATTAATGAGCACATTCAAAACGTTAGCGTGTGCCACCATGCTAAGCGACATGGACAGCGGCAAACTCAACAAAAATGCCACAGCGAAAATCGATGAACGCAATATTGTGGTTTGGTCTCCGGTGATGGATAAACTGACTGGACAAAGCACACGTATCGAACACGCTTGTGAGGCCGCCATGTTGATGAGCGACAACACCGCCGCGAACTTAGTGCTAAATGAAATTGGTGGTCCTAAAGCGGTCACACTGTTTTTGCGCTCTATTGGCGACAAAGCAACGCGACTTGACCGATTGGAGCCCCGTTTGAATGAAGCAAAACCGGGCGACAAGCGAGACACCACAACGCCTAACGCCATGGTAAACACCCTACACACCTTGATGGAAGATAACGCCCTATCTTACGAGTCACGCACACAACTGAAAATCTGGATGCAAGACAACAAAGTATCGGATTCTCTCATGCGCTCTGTTCTACCAAAAGGCTGGTCGATTGCAGACCGCTCTGGCGCAGGTAACTACGGTTCACGCGGCATTAGCGCGATGATTTGGAAAGACAACTACAAGCCGGTTTACATCAGTATTTACGTCACAGACACCGACCTTTCGCTTCAAGCTCGCGATCAACTGATCGCGCAAATCAGCCAACTGATTTTAGAGCACTACAAAGAAAGTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39615","NCBI_taxonomy_name":"Vibrio parahaemolyticus","NCBI_taxonomy_id":"670"}}}},"ARO_accession":"3005563","ARO_id":"44025","ARO_name":"CARB-27","CARD_short_name":"CARB-27","ARO_description":"CARB-27 is a CARB beta-lactamase.","ARO_category":{"36230":{"category_aro_accession":"3000091","category_aro_cvterm_id":"36230","category_aro_name":"CARB beta-lactamase","category_aro_description":"CARB beta-lactamases are class A lactamases that can hydrolyze carbenicillin. Many of the PSE beta-lactamases have been renamed as CARB-lactamases with the notable exception of PSE-2 which is now OXA-10.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4414":{"model_id":"4414","model_name":"CARB-28","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6789":{"protein_sequence":{"accession":"WP_029839920.1","sequence":"MKKLFLLVGLMVCSTVSYASKLNEDISLIEKQTSGRIGVSVWDTQTDERWDYRGDERFPLMSTFKTLACATMLSDMDSGKLNKNATAKIDERNIVVWSPVMDKLAGQSTRIEHACEAAMLMSDNTAANLVLNEIGGPKAVTLFLRSIGDKATRLDRLEPRLNEAKPGDKRDTTTPNAMVNTLHTLMEDNALSYESRTQLKIWMQDNKVSDSLMRSVLPKDWSIADRSGAGNYGSRGISAMIWKDNYKPVYISIYVTDTDLSLQARDQLIAQISQLILEHYKES"},"dna_sequence":{"accession":"NG_048731.1","fmin":"0","fmax":"852","strand":"+","sequence":"ATGAAAAAGTTATTCCTGTTGGTTGGGCTGATGGTTTGCTCAACTGTTAGTTACGCCTCCAAATTAAACGAAGACATCTCCCTCATCGAGAAACAAACATCTGGGCGAATTGGAGTGTCAGTCTGGGATACACAAACGGACGAGCGTTGGGATTATCGCGGAGACGAACGTTTCCCATTAATGAGCACATTCAAAACGTTAGCGTGTGCCACCATGCTAAGCGACATGGACAGCGGCAAACTCAACAAAAATGCCACAGCGAAAATTGATGAACGCAATATTGTGGTTTGGTCTCCGGTGATGGATAAACTGGCTGGACAAAGCACACGCATCGAACACGCTTGTGAAGCCGCCATGTTGATGAGCGACAACACCGCCGCGAACTTAGTGCTAAATGAAATTGGTGGTCCTAAAGCGGTCACACTGTTTTTGCGCTCTATTGGCGACAAAGCAACGCGACTTGACCGATTGGAACCCCGTTTGAATGAAGCGAAACCGGGCGACAAGCGAGACACCACAACGCCTAACGCCATGGTAAACACCCTACATACCTTGATGGAAGATAACGCCCTATCTTACGAGTCACGCACACAGCTGAAAATCTGGATGCAAGACAACAAAGTATCGGATTCTCTCATGCGCTCTGTTCTGCCAAAAGACTGGTCGATTGCAGACCGCTCTGGCGCAGGTAACTACGGTTCACGCGGCATTAGCGCGATGATCTGGAAAGACAACTACAAGCCGGTTTACATCAGTATTTACGTCACAGACACCGACCTTTCGCTTCAAGCTCGCGATCAACTGATCGCGCAAATCAGCCAACTGATTTTAGAGCACTACAAAGAAAGTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39615","NCBI_taxonomy_name":"Vibrio parahaemolyticus","NCBI_taxonomy_id":"670"}}}},"ARO_accession":"3005564","ARO_id":"44026","ARO_name":"CARB-28","CARD_short_name":"CARB-28","ARO_description":"CARB-28 is a CARB beta-lactamase.","ARO_category":{"36230":{"category_aro_accession":"3000091","category_aro_cvterm_id":"36230","category_aro_name":"CARB beta-lactamase","category_aro_description":"CARB beta-lactamases are class A lactamases that can hydrolyze carbenicillin. Many of the PSE beta-lactamases have been renamed as CARB-lactamases with the notable exception of PSE-2 which is now OXA-10.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4415":{"model_id":"4415","model_name":"CARB-29","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6790":{"protein_sequence":{"accession":"WP_029834158.1","sequence":"MKKLFLLVGLMVCSTVSYASKLNEDISIIEKQTSGRIGVSVWDTQTDERWDYRGDERFPLMSTFKTLACATMLSDMDSGKLNKNATAKIDERNIVVWSPVMDKLAGQSTRIEHACEAAMLMSDNTAANLVLNEIGGPKAVTLFLRSIGDKATRLDRLEPRLNEAKPGDKRDTTTPNAMVNTLHTLMEDNALSYESRTQLKIWMQDNKVSDSLMRSVLPKGWSIADRSGAGNYGSRGISAMIWKDNYKPVYISIYVTDTDLSLQARDQLIAQISQLILEHYKES"},"dna_sequence":{"accession":"NG_048732.1","fmin":"0","fmax":"852","strand":"+","sequence":"ATGAAAAAGTTATTCCTGTTGGTTGGGCTGATGGTTTGCTCAACTGTTAGTTACGCGTCCAAATTAAACGAAGACATATCCATCATCGAGAAACAAACATCTGGGCGAATTGGAGTGTCAGTCTGGGATACACAAACGGACGAGCGTTGGGATTATCGCGGAGACGAACGTTTCCCATTAATGAGCACATTCAAAACGTTAGCGTGTGCCACCATGCTAAGCGACATGGACAGCGGCAAACTCAACAAAAATGCCACAGCGAAAATCGATGAACGCAATATTGTGGTTTGGTCTCCGGTGATGGATAAACTGGCTGGACAAAGCACACGTATCGAACACGCTTGTGAGGCCGCCATGTTGATGAGCGACAACACCGCCGCGAACTTAGTGCTAAATGAAATTGGTGGTCCTAAAGCGGTCACGCTGTTTTTGCGATCTATTGGCGACAAAGCAACGCGACTTGACCGATTGGAACCCCGTTTGAATGAAGCAAAACCGGGCGATAAGCGAGACACCACAACGCCTAACGCCATGGTAAACACCCTACATACCTTGATGGAAGATAACGCCCTATCTTACGAGTCACGCACACAGCTGAAAATCTGGATGCAAGACAACAAAGTATCGGATTCGCTCATGCGCTCTGTTCTGCCAAAAGGCTGGTCGATTGCAGACCGCTCTGGCGCAGGTAACTACGGTTCACGCGGCATTAGCGCGATGATCTGGAAAGACAACTACAAGCCGGTTTACATCAGTATTTACGTCACAGACACCGACCTTTCGCTTCAAGCTCGCGATCAACTGATCGCGCAAATCAGCCAACTGATTTTAGAGCACTACAAAGAAAGTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39615","NCBI_taxonomy_name":"Vibrio parahaemolyticus","NCBI_taxonomy_id":"670"}}}},"ARO_accession":"3005565","ARO_id":"44027","ARO_name":"CARB-29","CARD_short_name":"CARB-29","ARO_description":"CARB-29 is a CARB beta-lactamase.","ARO_category":{"36230":{"category_aro_accession":"3000091","category_aro_cvterm_id":"36230","category_aro_name":"CARB beta-lactamase","category_aro_description":"CARB beta-lactamases are class A lactamases that can hydrolyze carbenicillin. Many of the PSE beta-lactamases have been renamed as CARB-lactamases with the notable exception of PSE-2 which is now OXA-10.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4416":{"model_id":"4416","model_name":"CARB-30","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6791":{"protein_sequence":{"accession":"WP_005498292.1","sequence":"MKKLFLLVGLMVCSTVSYASKLNEDISLIEKQTSGRIGVSVWDTQMDERWDYRGDERFPLMSTFKTLACATMLSDMDSGKLNKNATAKIDERNIVVWSPVMDKLAGQSTRIEHACEAAMLMSDNSAANLVLNEIGGPKAVTLFLRSIGDKATRLDRLEPRLNEAKPGDKRDTTTPNAMVNTLHTLMEDNALSYESRTQLKIWMQDNKVSDSLMRSVLPKGWSIADRSGAGNYGSRGISAMIWKDNYKPVYISIYVTDTDLSLQARDQLIAQISQLILEHYKES"},"dna_sequence":{"accession":"NG_048734.1","fmin":"0","fmax":"852","strand":"+","sequence":"ATGAAAAAGTTATTCCTGTTGGTTGGGCTGATGGTTTGCTCAACTGTTAGTTACGCCTCCAAATTAAACGAAGACATCTCCCTCATCGAGAAACAAACATCTGGGCGAATTGGAGTGTCAGTCTGGGATACACAAATGGACGAGCGTTGGGATTATCGCGGAGACGAACGTTTCCCATTAATGAGCACATTCAAAACGTTAGCGTGTGCCACCATGCTAAGCGACATGGACAGCGGCAAACTCAACAAAAATGCCACAGCGAAAATCGATGAACGCAATATTGTGGTTTGGTCTCCGGTGATGGATAAACTGGCTGGACAAAGCACACGTATAGAACACGCTTGTGAAGCCGCCATGTTGATGAGTGACAACTCCGCCGCGAACTTAGTGCTAAATGAAATTGGTGGTCCTAAAGCGGTCACGCTGTTTTTGCGATCTATTGGCGACAAAGCAACGCGACTTGACCGATTGGAACCCCGTTTGAACGAAGCAAAACCGGGCGACAAGCGAGACACCACAACGCCTAACGCCATGGTAAACACCCTACACACCTTGATGGAAGATAACGCCCTATCTTACGAGTCACGCACACAGTTGAAAATCTGGATGCAAGACAACAAAGTATCGGATTCGCTCATGCGCTCTGTTCTGCCAAAAGGCTGGTCGATTGCAGACCGCTCTGGCGCAGGTAACTACGGTTCACGCGGCATTAGCGCGATGATTTGGAAAGACAACTACAAGCCGGTTTACATCAGTATTTACGTCACAGACACTGACCTTTCGCTTCAAGCTCGCGATCAACTGATCGCGCAAATCAGCCAACTGATTTTAGAGCACTACAAAGAAAGTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39615","NCBI_taxonomy_name":"Vibrio parahaemolyticus","NCBI_taxonomy_id":"670"}}}},"ARO_accession":"3005566","ARO_id":"44028","ARO_name":"CARB-30","CARD_short_name":"CARB-30","ARO_description":"CARB-30 is a CARB beta-lactamase.","ARO_category":{"36230":{"category_aro_accession":"3000091","category_aro_cvterm_id":"36230","category_aro_name":"CARB beta-lactamase","category_aro_description":"CARB beta-lactamases are class A lactamases that can hydrolyze carbenicillin. Many of the PSE beta-lactamases have been renamed as CARB-lactamases with the notable exception of PSE-2 which is now OXA-10.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4417":{"model_id":"4417","model_name":"CARB-31","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6792":{"protein_sequence":{"accession":"WP_025546314.1","sequence":"MKKLFLLVGLMVYSTVSYASKLNEDISLIEKQTSGRIGVSVWDTQTDERWDYRGDERFPLMSTFKTLACATMLSDMDSGKLNKNATAKIDERNIVVWSPVMDKLAGQSTRIEHACEAAMLMSDNTAANLVLNEIGGPKAVTLFLRSIGDKATRLDRLEPRLNEAKPGDKRDTTTPNAMVNTLHTLMEDNALSYESRTQLKIWMQDNKVSDSLMRSVLPKGWSIADRSGAGNYGSRGISAMIWKDNYKPVYISIYVTDTDLSLQARDQLIAQISQLILEHYKES"},"dna_sequence":{"accession":"NG_048735.1","fmin":"0","fmax":"852","strand":"+","sequence":"ATGAAAAAGTTATTCCTGTTGGTTGGGCTGATGGTTTACTCAACTGTTAGTTACGCCTCCAAATTAAACGAAGACATCTCCCTCATCGAGAAACAAACATCTGGGCGAATTGGAGTGTCAGTCTGGGATACACAAACGGACGAGCGTTGGGATTATCGCGGAGACGAACGTTTCCCATTAATGAGCACATTTAAAACGTTAGCGTGTGCCACCATGCTAAGCGACATGGACAGCGGCAAACTCAACAAAAATGCCACAGCGAAAATCGATGAACGCAATATTGTGGTTTGGTCTCCGGTGATGGATAAACTGGCAGGACAAAGCACACGTATCGAACACGCTTGTGAAGCCGCCATGTTGATGAGCGACAACACCGCCGCGAACTTAGTGCTAAATGAAATTGGTGGTCCTAAAGCGGTCACACTGTTTTTGCGCTCTATTGGCGACAAAGCAACGCGACTTGACCGATTGGAGCCCCGTTTGAATGAAGCAAAACCGGGCGACAAGCGAGACACCACAACGCCTAACGCCATGGTAAACACCCTACATACCTTGATGGAAGATAACGCCCTATCTTACGAGTCACGCACACAGCTGAAAATCTGGATGCAAGACAACAAAGTATCGGATTCGCTCATGCGCTCTGTTCTGCCAAAAGGCTGGTCGATTGCAGACCGCTCTGGCGCAGGTAACTACGGTTCACGCGGCATTAGCGCGATGATCTGGAAAGACAACTACAAGCCGGTTTACATCAGTATTTACGTCACAGACACCGACCTTTCGCTTCAAGCTCGCGATCAACTGATCGCGCAAATCAGCCAACTGATTTTAGAGCACTACAAAGAAAGTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39615","NCBI_taxonomy_name":"Vibrio parahaemolyticus","NCBI_taxonomy_id":"670"}}}},"ARO_accession":"3005567","ARO_id":"44029","ARO_name":"CARB-31","CARD_short_name":"CARB-31","ARO_description":"CARB-31 is a CARB beta-lactamase.","ARO_category":{"36230":{"category_aro_accession":"3000091","category_aro_cvterm_id":"36230","category_aro_name":"CARB beta-lactamase","category_aro_description":"CARB beta-lactamases are class A lactamases that can hydrolyze carbenicillin. Many of the PSE beta-lactamases have been renamed as CARB-lactamases with the notable exception of PSE-2 which is now OXA-10.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4418":{"model_id":"4418","model_name":"CARB-32","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6793":{"protein_sequence":{"accession":"WP_029837067.1","sequence":"MKKLFLLVGLMVCSTVSYASKLNEDISLIEKQTSGRIGVSVWDTQMDERWDYRGDERFPLMSTFKTLACATMLSDMDSGKLNKNATARIDERNIVVWSPVMDKLAGQSTRIEHACEAAMLMSDNTAANLVLNEIGGPKAVTLFLRSVGDKATRLDRLEPRLNEAKPGDKRDTTTPNAMVNTLHTLMEDNALSYESRTQLKIWMQDNKVSDSLMRSVLPKGWSIADRSGAGNYGSRGISAMIWKDNYKPVYISIYVTDTDLSLQARDQLIAQISQLILERYKES"},"dna_sequence":{"accession":"NG_048736.1","fmin":"0","fmax":"852","strand":"+","sequence":"ATGAAAAAGTTATTCCTGTTGGTTGGGCTGATGGTTTGCTCAACTGTTAGTTACGCCTCCAAATTAAACGAAGACATCTCCCTCATCGAGAAACAAACATCTGGGCGAATTGGAGTGTCAGTCTGGGATACACAAATGGACGAACGTTGGGATTATCGCGGAGACGAACGTTTCCCATTAATGAGCACATTCAAAACGTTAGCGTGTGCCACCATGCTAAGCGACATGGACAGCGGCAAACTCAACAAAAATGCCACAGCGAGAATCGATGAACGCAATATTGTGGTTTGGTCTCCGGTGATGGATAAACTGGCTGGACAAAGCACGCGTATCGAACACGCTTGTGAAGCCGCCATGTTGATGAGCGACAACACCGCCGCAAACTTAGTGCTAAATGAAATTGGTGGTCCTAAAGCGGTCACGCTGTTTTTGCGCTCTGTTGGCGACAAAGCAACGCGACTTGACCGATTGGAGCCCCGTTTGAACGAAGCAAAACCGGGCGACAAGCGAGACACCACAACGCCTAACGCCATGGTAAACACCCTACACACCTTGATGGAAGATAACGCCCTATCTTACGAGTCACGCACACAGCTGAAAATCTGGATGCAAGACAACAAAGTATCGGATTCTCTCATGCGCTCTGTTCTACCAAAAGGCTGGTCGATTGCAGACCGCTCTGGCGCAGGTAACTACGGTTCACGCGGCATTAGCGCGATGATTTGGAAAGACAACTACAAGCCGGTTTACATCAGTATTTACGTCACAGACACTGACCTTTCGCTTCAAGCTCGCGATCAACTGATCGCGCAAATCAGCCAACTGATTTTAGAGCGCTACAAAGAAAGTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39615","NCBI_taxonomy_name":"Vibrio parahaemolyticus","NCBI_taxonomy_id":"670"}}}},"ARO_accession":"3005568","ARO_id":"44030","ARO_name":"CARB-32","CARD_short_name":"CARB-32","ARO_description":"CARB-32 is a CARB beta-lactamase.","ARO_category":{"36230":{"category_aro_accession":"3000091","category_aro_cvterm_id":"36230","category_aro_name":"CARB beta-lactamase","category_aro_description":"CARB beta-lactamases are class A lactamases that can hydrolyze carbenicillin. Many of the PSE beta-lactamases have been renamed as CARB-lactamases with the notable exception of PSE-2 which is now OXA-10.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4419":{"model_id":"4419","model_name":"CARB-33","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6794":{"protein_sequence":{"accession":"WP_025535332.1","sequence":"MKKLFLLVGLMVCSTVSYASKLNEDISLIEKQTSGRIGVSVWDTQTDERWDYRGDERFPLMSTFKTLACATMLSDMESGKLNKNATAKIDERNIVVWSPVMDKLAGQSTRIEHACEAAMLMSDNTAANLVLNEIGGPKAVTLFLRSIGDKATRLDRLEPRLNEAKPGDKRDTTTPNAMVNTLHTLMEDNALSYESRTQLKIWMQDNKVSDSLMRSVLPKGWSIADRSGAGNYGSRGISAMIWKDNYKPVYISIYVTDTDLSLQARDQLIAQISQLILEHYKES"},"dna_sequence":{"accession":"NG_048737.1","fmin":"0","fmax":"852","strand":"+","sequence":"ATGAAAAAGTTATTCCTGTTGGTTGGGCTGATGGTTTGCTCAACTGTTAGTTACGCCTCCAAATTAAACGAAGACATCTCCCTCATCGAGAAACAAACATCTGGGCGAATTGGAGTGTCAGTCTGGGATACACAAACGGACGAGCGTTGGGATTATCGCGGAGACGAACGTTTCCCATTAATGAGCACATTCAAAACGTTAGCGTGTGCCACCATGCTAAGCGACATGGAGAGCGGCAAACTCAACAAAAATGCCACAGCGAAAATCGATGAACGCAATATTGTGGTTTGGTCTCCGGTGATGGATAAACTGGCTGGACAAAGCACACGTATCGAACACGCTTGTGAGGCCGCCATGTTGATGAGCGACAACACCGCCGCGAACTTAGTGCTAAATGAAATTGGTGGTCCTAAAGCGGTCACGCTGTTTTTGCGATCTATTGGCGACAAAGCAACGCGACTTGACCGATTGGAACCCCGTTTGAATGAAGCAAAACCGGGCGATAAGCGAGACACCACAACGCCTAACGCCATGGTAAACACCCTACATACCTTGATGGAAGATAACGCCCTATCTTACGAGTCACGCACACAGCTGAAAATCTGGATGCAAGACAACAAAGTATCGGATTCTCTCATGCGCTCTGTTCTGCCAAAAGGCTGGTCGATTGCAGACCGCTCTGGCGCAGGTAACTACGGTTCACGCGGCATTAGCGCGATGATCTGGAAAGACAACTACAAGCCGGTTTACATCAGTATTTACGTCACAGACACTGACCTTTCGCTTCAAGCTCGCGATCAACTGATCGCGCAAATCAGCCAACTGATTTTAGAGCACTACAAAGAAAGTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39615","NCBI_taxonomy_name":"Vibrio parahaemolyticus","NCBI_taxonomy_id":"670"}}}},"ARO_accession":"3005569","ARO_id":"44031","ARO_name":"CARB-33","CARD_short_name":"CARB-33","ARO_description":"CARB-33 is a CARB beta-lactamase.","ARO_category":{"36230":{"category_aro_accession":"3000091","category_aro_cvterm_id":"36230","category_aro_name":"CARB beta-lactamase","category_aro_description":"CARB beta-lactamases are class A lactamases that can hydrolyze carbenicillin. Many of the PSE beta-lactamases have been renamed as CARB-lactamases with the notable exception of PSE-2 which is now OXA-10.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4420":{"model_id":"4420","model_name":"CARB-34","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6795":{"protein_sequence":{"accession":"WP_029815111.1","sequence":"MKKLFLLVGLMVCSTVSYASKLNEDISLIEKQTSGRIGVSVWDTQTDERWDYRGDERFPLMSTFKTLACATMLSDMDSGKLNKNATAKIDERNIVVWSPVMDKLAGQSTRIEHACEAAMLMSDNTAANLVLNEIGGPKAVTLFLRSIGDKATRLDRLEPGLNEAKPGDKRDTTTPNAMVNTLHTLMEDNALSYESRTQLKIWMQDNKVSDSLMRSVLPKGWSIADRSGAGNYGSRGISAMIWKDNYKPVYISIYVTDTDLSLQARDQLIAQISQLILEHYKES"},"dna_sequence":{"accession":"NG_048738.1","fmin":"0","fmax":"852","strand":"+","sequence":"ATGAAAAAGTTATTCCTGTTGGTTGGGCTGATGGTTTGCTCAACTGTTAGTTACGCCTCCAAATTAAACGAAGACATCTCCCTCATCGAGAAACAAACATCTGGGCGAATTGGAGTGTCAGTCTGGGATACACAAACGGACGAGCGTTGGGATTATCGCGGAGACGAACGTTTCCCATTAATGAGCACATTCAAAACGTTAGCGTGTGCCACCATGCTAAGCGACATGGACAGCGGCAAACTCAACAAAAATGCCACAGCGAAAATCGATGAACGCAATATTGTGGTTTGGTCTCCGGTGATGGATAAACTGGCTGGACAAAGCACACGCATCGAACACGCTTGTGAGGCCGCCATGTTGATGAGCGACAACACCGCCGCGAACTTAGTGCTAAATGAAATTGGTGGTCCTAAAGCGGTGACGTTATTTTTGCGATCTATTGGCGACAAAGCAACGCGACTTGACCGATTGGAACCCGGTTTGAATGAAGCAAAACCGGGCGACAAGCGAGACACCACAACGCCTAACGCCATGGTAAACACCCTACACACCTTGATGGAAGATAACGCCCTATCTTACGAGTCACGCACACAGCTGAAAATCTGGATGCAAGACAACAAAGTATCGGATTCGCTCATGCGCTCTGTTCTACCAAAAGGCTGGTCGATTGCAGACCGCTCTGGCGCAGGTAACTACGGTTCACGCGGCATTAGCGCGATGATCTGGAAAGACAACTACAAGCCAGTTTACATCAGTATTTACGTCACAGACACTGACCTTTCGCTTCAAGCTCGCGATCAGCTGATCGCGCAAATCAGCCAACTGATTTTAGAGCACTACAAAGAAAGTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39615","NCBI_taxonomy_name":"Vibrio parahaemolyticus","NCBI_taxonomy_id":"670"}}}},"ARO_accession":"3005570","ARO_id":"44032","ARO_name":"CARB-34","CARD_short_name":"CARB-34","ARO_description":"CARB-34 is a CARB beta-lactamase.","ARO_category":{"36230":{"category_aro_accession":"3000091","category_aro_cvterm_id":"36230","category_aro_name":"CARB beta-lactamase","category_aro_description":"CARB beta-lactamases are class A lactamases that can hydrolyze carbenicillin. Many of the PSE beta-lactamases have been renamed as CARB-lactamases with the notable exception of PSE-2 which is now OXA-10.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4421":{"model_id":"4421","model_name":"CARB-35","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6796":{"protein_sequence":{"accession":"WP_025521699.1","sequence":"MKKLFLLVGLMVCSTVSYASKLNEDISLIEKQTSGRIGVSVWDTQTDERWDYRGDERFPLMSTFKTLACATMLSDMDSGKLNKNATAKIDERNIVVWSPVMDKLAGQSTRIEHACEAAMLMSDNTAANLVLNKIGGPKAVTLFLRSIGDKATRLDRLEPRLNEAKPGDKRDTTTPNAMVNTLHTLMEDNALSYESRTQLKIWMQDNKVSDSLMRSVLPKGWSIADRSGAGNYGSRGISAMIWKDNYKPVYISIYVTDTDLSLQARDQLIAQISQLILEHYKES"},"dna_sequence":{"accession":"NG_048739.1","fmin":"0","fmax":"852","strand":"+","sequence":"ATGAAAAAGTTATTCCTGTTGGTTGGGCTGATGGTTTGCTCAACTGTTAGTTACGCCTCCAAATTAAACGAAGACATCTCCCTCATCGAGAAACAAACATCTGGGCGAATTGGAGTGTCAGTCTGGGATACACAAACGGACGAGCGTTGGGATTATCGCGGAGACGAACGTTTCCCATTAATGAGCACATTCAAAACGTTAGCGTGTGCCACCATGCTAAGCGACATGGACAGCGGCAAACTCAACAAAAATGCCACAGCGAAAATCGATGAACGCAATATTGTGGTTTGGTCTCCGGTGATGGATAAACTGGCTGGACAAAGCACACGCATCGAACACGCTTGTGAGGCCGCCATGTTGATGAGCGACAACACCGCCGCGAACTTAGTGCTAAATAAAATTGGTGGTCCTAAAGCGGTCACGCTGTTTTTGCGATCTATTGGCGACAAAGCAACGCGACTTGACCGATTGGAACCCCGTTTGAATGAAGCAAAACCGGGCGACAAGCGAGACACCACAACGCCTAACGCCATGGTAAACACCCTACACACCTTGATGGAAGATAACGCCCTATCTTACGAGTCACGCACACAGCTGAAAATCTGGATGCAAGACAACAAAGTATCGGATTCTCTCATGCGCTCTGTTCTGCCAAAAGGCTGGTCGATTGCAGACCGCTCTGGCGCAGGTAACTACGGTTCACGCGGCATTAGCGCGATGATCTGGAAAGACAACTACAAGCCGGTTTACATCAGTATTTACGTCACAGACACTGACCTTTCGCTTCAAGCTCGCGATCAACTGATCGCGCAAATCAGCCAACTGATTTTAGAGCACTACAAAGAAAGTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39615","NCBI_taxonomy_name":"Vibrio parahaemolyticus","NCBI_taxonomy_id":"670"}}}},"ARO_accession":"3005571","ARO_id":"44033","ARO_name":"CARB-35","CARD_short_name":"CARB-35","ARO_description":"CARB-35 is a CARB beta-lactamase.","ARO_category":{"36230":{"category_aro_accession":"3000091","category_aro_cvterm_id":"36230","category_aro_name":"CARB beta-lactamase","category_aro_description":"CARB beta-lactamases are class A lactamases that can hydrolyze carbenicillin. Many of the PSE beta-lactamases have been renamed as CARB-lactamases with the notable exception of PSE-2 which is now OXA-10.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4422":{"model_id":"4422","model_name":"CARB-36","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6797":{"protein_sequence":{"accession":"WP_025525762.1","sequence":"MKKLFLLVGLMVCSTVSYASKLNEDISLIEKQTSGRIGVSVWDTQTDERWDYRGDERFPLMSTFKTLACATMLSDMDSGKLNKNATAKIDERNIVVWSPVMDKLAGQSTRIEHACEAAMLMSDNTAANLVLNEIGGPKAVTLFLRSIGDKATRLDRLEPRLNEAKPGDKRDTTTPNAMVNTLHSLMEDNALSYESRTQLKIWMQDNKVSDSLMRSVLPKGWSIADRSGAGNYGSRGISAMIWKDNYKPVYISIYVTDTDLSLQARDQLIAQISQLILEHYKES"},"dna_sequence":{"accession":"NG_048740.1","fmin":"0","fmax":"852","strand":"+","sequence":"ATGAAAAAGTTATTCCTGTTGGTTGGGCTGATGGTTTGCTCAACTGTTAGTTACGCCTCCAAATTAAACGAAGACATCTCCCTCATCGAGAAACAAACATCTGGGCGAATTGGAGTGTCAGTCTGGGATACACAAACGGACGAGCGTTGGGATTATCGCGGAGACGAACGTTTCCCATTAATGAGCACATTCAAAACGTTAGCGTGTGCCACCATGCTAAGCGACATGGACAGCGGCAAACTCAACAAAAATGCCACAGCGAAAATCGATGAACGCAATATTGTGGTTTGGTCTCCGGTGATGGATAAACTGGCTGGACAAAGCACACGTATCGAACACGCTTGTGAGGCCGCCATGTTGATGAGCGACAACACCGCCGCGAACTTAGTGCTAAATGAAATTGGTGGTCCTAAAGCGGTCACGCTGTTTTTGCGATCTATTGGTGACAAAGCAACGCGACTTGACCGATTGGAACCCCGTTTGAACGAAGCAAAACCGGGCGACAAGCGAGATACCACAACGCCTAACGCCATGGTAAACACCCTACACTCCTTGATGGAAGATAACGCCCTATCTTACGAGTCACGCACACAGCTGAAAATCTGGATGCAAGACAACAAAGTATCGGATTCGCTCATGCGCTCTGTTCTGCCAAAAGGCTGGTCGATTGCAGACCGCTCTGGCGCAGGTAACTACGGTTCACGCGGCATTAGCGCGATGATCTGGAAAGACAACTACAAGCCGGTTTACATCAGTATTTACGTCACAGACACTGACCTTTCGCTTCAAGCTCGCGATCAACTGATCGCGCAAATCAGCCAACTGATTTTAGAGCACTACAAAGAAAGTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39615","NCBI_taxonomy_name":"Vibrio parahaemolyticus","NCBI_taxonomy_id":"670"}}}},"ARO_accession":"3005572","ARO_id":"44034","ARO_name":"CARB-36","CARD_short_name":"CARB-36","ARO_description":"CARB-36 is a CARB beta-lactamase.","ARO_category":{"36230":{"category_aro_accession":"3000091","category_aro_cvterm_id":"36230","category_aro_name":"CARB beta-lactamase","category_aro_description":"CARB beta-lactamases are class A lactamases that can hydrolyze carbenicillin. Many of the PSE beta-lactamases have been renamed as CARB-lactamases with the notable exception of PSE-2 which is now OXA-10.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4423":{"model_id":"4423","model_name":"CARB-38","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6798":{"protein_sequence":{"accession":"WP_025551322.1","sequence":"MKKLFLLVGLMVCSTVSYASKLNEDISLIEKQTSGRIGVSVWDTQTDERWDYRGDERFPLMSTFKTLACATMLSDMDSGKLNKNATAKIDERNIVVWSPVMDKLAGQSTRIEHACEAAMLMSDNTAANLVLNEIGGPKAVTLFLRSIGDKATRLDRLEPRLNEAKPGDKRDTTTPNAMVNTLHTLMEDNALSYESRTQLKIWMQDNKVSDSLMRSVLPKGWSIADRSGAGNYGSLGISAMIWKDNYKPVYISIYVTDTDLSLQARDQLIAQISQLILEHYKES"},"dna_sequence":{"accession":"NG_048741.1","fmin":"0","fmax":"852","strand":"+","sequence":"ATGAAAAAGTTATTCCTGTTGGTTGGGCTGATGGTTTGCTCAACTGTTAGTTACGCCTCCAAATTAAACGAAGACATCTCCCTCATCGAGAAACAAACATCTGGGCGAATTGGAGTGTCAGTCTGGGATACACAAACGGACGAGCGTTGGGATTATCGCGGAGACGAACGTTTCCCATTAATGAGCACATTCAAAACGTTAGCGTGTGCCACCATGCTAAGCGACATGGACAGCGGCAAACTCAACAAAAATGCCACAGCGAAAATCGATGAACGCAATATTGTGGTTTGGTCTCCGGTGATGGATAAACTGGCTGGACAAAGCACACGCATCGAACACGCTTGTGAAGCCGCCATGTTGATGAGCGACAACACCGCCGCGAACTTAGTGTTAAATGAAATTGGTGGTCCTAAAGCGGTCACGCTGTTTTTGCGCTCTATTGGCGACAAAGCAACGCGACTTGACCGATTGGAACCCCGTTTGAATGAAGCAAAACCGGGCGACAAGCGAGACACCACAACGCCTAACGCCATGGTAAACACCCTACACACCTTGATGGAAGATAACGCCCTATCTTACGAGTCACGCACACAGCTGAAAATCTGGATGCAAGACAACAAAGTATCGGATTCTCTCATGCGCTCTGTTCTGCCAAAAGGCTGGTCGATTGCAGACCGCTCTGGCGCAGGTAACTACGGTTCACTCGGCATTAGCGCGATGATCTGGAAAGACAACTACAAGCCGGTTTACATCAGTATTTACGTCACAGACACAGACCTTTCGCTTCAAGCTCGCGATCAACTGATCGCGCAAATCAGCCAACTGATTTTAGAGCACTACAAAGAAAGTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39615","NCBI_taxonomy_name":"Vibrio parahaemolyticus","NCBI_taxonomy_id":"670"}}}},"ARO_accession":"3005573","ARO_id":"44035","ARO_name":"CARB-38","CARD_short_name":"CARB-38","ARO_description":"CARB-38 is a CARB beta-lactamase.","ARO_category":{"36230":{"category_aro_accession":"3000091","category_aro_cvterm_id":"36230","category_aro_name":"CARB beta-lactamase","category_aro_description":"CARB beta-lactamases are class A lactamases that can hydrolyze carbenicillin. Many of the PSE beta-lactamases have been renamed as CARB-lactamases with the notable exception of PSE-2 which is now OXA-10.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4424":{"model_id":"4424","model_name":"CARB-40","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6799":{"protein_sequence":{"accession":"WP_025816575.1","sequence":"MKKLFLLVGLMVCSTVSYASKLNEDISLIEKQTSGRIGVSVWDTQTDERWDYRGDERFPLMSTFKTLACATMLSDMDSGKLNKNATARINERNIVVWSPVMDKLAGQSTRIEHACEAAMLMSDNTAANLVLNEIGGPKAVTLFLRSIGDKATRLDRLEPRLNEAKPGDKRDTTTPNAMVNTLHTLMEDNALSYESRTQLKIWMQDNKVSDSLMRSVLPKGWSIADRSGAGNYGSRGISAMIWKDNYKPVYISIYVTDTDLSLQARDQLIAQISQLILEHYKES"},"dna_sequence":{"accession":"NG_048743.1","fmin":"0","fmax":"852","strand":"+","sequence":"ATGAAAAAGTTATTCCTGTTGGTTGGGCTGATGGTTTGCTCAACTGTTAGTTACGCCTCCAAATTAAACGAAGACATCTCCCTCATCGAGAAACAAACATCTGGACGAATTGGAGTGTCAGTCTGGGATACACAAACGGACGAGCGTTGGGATTATCGCGGAGACGAACGTTTCCCATTAATGAGCACATTCAAAACGTTAGCGTGTGCCACCATGCTAAGCGATATGGACAGCGGCAAACTCAACAAAAATGCCACAGCGAGAATCAATGAACGCAATATTGTGGTTTGGTCTCCGGTGATGGATAAACTGGCTGGACAAAGCACACGTATCGAACACGCTTGTGAAGCCGCCATGTTGATGAGCGACAACACCGCCGCGAACTTAGTGCTAAATGAAATTGGTGGTCCTAAAGCGGTCACACTGTTTTTGCGCTCTATTGGCGACAAAGCAACGCGACTTGACCGATTGGAACCCCGTTTGAATGAAGCAAAACCGGGCGACAAGCGAGACACCACAACGCCTAACGCCATGGTAAACACCCTACACACCTTGATGGAAGATAACGCCCTATCTTACGAGTCACGCACACAGCTGAAAATCTGGATGCAAGACAACAAAGTATCGGATTCGCTCATGCGCTCTGTTCTACCAAAAGGCTGGTCGATTGCAGACCGCTCTGGCGCAGGTAACTACGGTTCACGCGGCATTAGCGCGATGATTTGGAAAGACAACTACAAGCCGGTTTACATTAGTATTTACGTCACAGACACTGACCTTTCGCTTCAAGCTCGCGATCAACTGATCGCGCAAATCAGCCAACTGATTTTAGAGCACTACAAAGAAAGTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39615","NCBI_taxonomy_name":"Vibrio parahaemolyticus","NCBI_taxonomy_id":"670"}}}},"ARO_accession":"3005574","ARO_id":"44036","ARO_name":"CARB-40","CARD_short_name":"CARB-40","ARO_description":"CARB-40 is a CARB beta-lactamase.","ARO_category":{"36230":{"category_aro_accession":"3000091","category_aro_cvterm_id":"36230","category_aro_name":"CARB beta-lactamase","category_aro_description":"CARB beta-lactamases are class A lactamases that can hydrolyze carbenicillin. Many of the PSE beta-lactamases have been renamed as CARB-lactamases with the notable exception of PSE-2 which is now OXA-10.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4425":{"model_id":"4425","model_name":"CARB-41","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6800":{"protein_sequence":{"accession":"WP_025788060.1","sequence":"MKKLFLLVGLMVCSTVSYASKLNEDISLIEKQTSGRIGVSVWDTQTDERWDYRGDERFPLMSTFKTLACATMLSDMDSGKLNKNATAKIDERNIVVWSPVMDKLAGQSTRVEHACEAAMLMSDNTAANLVLNEIGGPKAVTLFLRSIGDKATRLDRLEPRLNEAKPGDKRDTTTPNAMVNTLHTLMEDNALSYESRTQLKIWMQDNKVSDSLMRSVLPKGWSIADRSGAGNYGSRGISAMIWKDNYKPVYISIYVTDTDLSLQARDQLIAQISQLILEHYKES"},"dna_sequence":{"accession":"NG_048744.1","fmin":"0","fmax":"852","strand":"+","sequence":"ATGAAAAAGTTATTCCTGTTGGTTGGGCTGATGGTTTGCTCAACTGTTAGTTACGCCTCCAAATTAAACGAAGACATCTCCCTCATCGAGAAACAAACATCTGGGCGAATTGGAGTGTCAGTCTGGGATACACAAACGGACGAGCGTTGGGATTATCGCGGAGACGAACGTTTCCCATTAATGAGCACATTCAAAACGTTAGCGTGTGCCACCATGCTAAGCGACATGGACAGCGGCAAACTCAACAAAAATGCCACAGCGAAAATCGATGAACGCAATATTGTGGTTTGGTCTCCGGTGATGGATAAACTGGCTGGACAAAGCACACGTGTCGAACACGCTTGTGAGGCTGCCATGTTGATGAGCGACAACACCGCCGCGAACTTAGTGCTAAATGAAATTGGTGGTCCTAAAGCGGTCACGCTGTTTTTGCGATCTATTGGCGACAAAGCAACGCGACTTGACCGATTGGAACCCCGTTTGAATGAAGCAAAACCGGGCGATAAGCGAGACACCACAACGCCTAACGCCATGGTAAACACCCTACATACCTTGATGGAAGATAACGCCCTATCTTACGAGTCACGCACACAGCTGAAAATCTGGATGCAAGACAACAAAGTATCGGATTCTCTCATGCGCTCTGTTCTGCCAAAAGGCTGGTCGATTGCAGACCGCTCTGGCGCAGGTAACTACGGTTCACGCGGCATTAGCGCGATGATCTGGAAAGACAACTACAAGCCGGTTTACATCAGTATTTACGTCACAGACACCGACCTTTCGCTTCAAGCTCGCGATCAACTGATCGCGCAAATCAGCCAACTGATTTTAGAGCACTACAAAGAAAGTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39615","NCBI_taxonomy_name":"Vibrio parahaemolyticus","NCBI_taxonomy_id":"670"}}}},"ARO_accession":"3005575","ARO_id":"44037","ARO_name":"CARB-41","CARD_short_name":"CARB-41","ARO_description":"CARB-41 is a CARB beta-lactamase.","ARO_category":{"36230":{"category_aro_accession":"3000091","category_aro_cvterm_id":"36230","category_aro_name":"CARB beta-lactamase","category_aro_description":"CARB beta-lactamases are class A lactamases that can hydrolyze carbenicillin. Many of the PSE beta-lactamases have been renamed as CARB-lactamases with the notable exception of PSE-2 which is now OXA-10.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4426":{"model_id":"4426","model_name":"CARB-42","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6801":{"protein_sequence":{"accession":"WP_005375420.1","sequence":"MKKLFLLAGLMVCSTLSYASQLNEDISLLEQQTSSRIGVSVWDTQADERWDYRGDERFPLMSTFKTLACAKMLSDMDSGKLSKNATAKVDERSIVVWSPVMDKLAGQNTRIEHACEAAMLMSDNTAANLVLNEIGGPKAVTMFLRTIGDKATRLDRIEPRLNEATPGDSRDTTTPNAILNTLRTLVEGETLSYESRVQLKIWMQDNKVSDSLMRSVLPTGWSIADRSGAGGHGSRGINAIIWKENHRPVYISIYVTETELSLQARDQLVAQISQLILQKYKDN"},"dna_sequence":{"accession":"NG_048745.1","fmin":"0","fmax":"852","strand":"+","sequence":"ATGAAAAAGTTATTTTTGTTGGCTGGGCTAATGGTTTGCTCAACCCTAAGTTACGCGTCCCAACTGAATGAGGACATTTCTCTCCTCGAGCAACAAACCTCAAGCAGAATTGGGGTGTCAGTTTGGGATACCCAAGCAGACGAGCGTTGGGATTACCGTGGCGATGAACGCTTCCCACTCATGAGCACATTCAAAACCCTAGCTTGTGCCAAAATGTTAAGTGATATGGACAGCGGTAAGCTAAGTAAAAATGCGACCGCAAAAGTCGATGAGCGCAGTATCGTTGTATGGTCTCCAGTGATGGATAAGCTCGCAGGCCAAAACACACGCATAGAGCACGCGTGTGAAGCCGCTATGTTAATGAGTGATAATACCGCAGCCAACTTAGTATTAAATGAAATTGGCGGCCCTAAGGCCGTAACAATGTTTCTGCGAACAATTGGAGATAAAGCAACGCGCCTAGACAGAATAGAACCTCGCTTGAACGAAGCCACACCAGGCGACAGCCGCGACACAACTACACCTAACGCCATACTAAACACTCTTCGAACTTTGGTCGAAGGCGAAACGTTGTCTTATGAGTCTCGTGTACAATTAAAAATCTGGATGCAGGACAACAAAGTTTCAGACTCGTTAATGCGTTCTGTATTACCAACAGGTTGGTCTATTGCAGACCGTTCTGGTGCGGGAGGTCATGGTTCGCGTGGCATTAACGCGATTATATGGAAGGAAAATCATCGACCTGTTTACATTAGTATTTATGTCACAGAAACCGAGCTCTCACTTCAAGCTAGGGACCAACTCGTTGCGCAGATAAGTCAGTTGATTTTACAAAAGTACAAAGACAATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37072","NCBI_taxonomy_name":"Vibrio","NCBI_taxonomy_id":"662"}}}},"ARO_accession":"3005576","ARO_id":"44038","ARO_name":"CARB-42","CARD_short_name":"CARB-42","ARO_description":"CARB-42 is a CARB beta-lactamase.","ARO_category":{"36230":{"category_aro_accession":"3000091","category_aro_cvterm_id":"36230","category_aro_name":"CARB beta-lactamase","category_aro_description":"CARB beta-lactamases are class A lactamases that can hydrolyze carbenicillin. Many of the PSE beta-lactamases have been renamed as CARB-lactamases with the notable exception of PSE-2 which is now OXA-10.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4427":{"model_id":"4427","model_name":"CARB-43","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6802":{"protein_sequence":{"accession":"WP_025794721.1","sequence":"MKKLFLLVGLMVCSTVSYASKLNEDISLIEKQTSGRIGVSVWDTQTDERWDYRGDERFPLMSTFKTLACATMLSDMDSGKLNKNATAKIDERNIVVWSPVMDKLAGQSTRIEHACEAAMLMSDNTAANLVLNEIGGPKAVTLFLRSIGDNATRLDRLEPRLNEAKPGDKRDTTTPNAMVNTLHTLMEDNALSYESRTQLKIWMQDNKVSDSLMRSVLPKGWSIADRSGAGNYGSRGISAMIWKDNYKPVYISIYVTDTDLSLQARDQLIAQISQLILEHYKES"},"dna_sequence":{"accession":"NG_048746.1","fmin":"0","fmax":"852","strand":"+","sequence":"ATGAAAAAGTTATTCCTGTTGGTTGGGCTGATGGTTTGCTCAACTGTTAGTTACGCCTCCAAATTAAACGAAGACATATCCCTCATCGAGAAACAAACATCTGGGCGAATTGGAGTGTCAGTCTGGGATACACAAACGGACGAGCGTTGGGATTATCGCGGAGACGAACGTTTCCCATTAATGAGCACATTCAAAACGTTAGCGTGTGCCACCATGCTAAGCGACATGGACAGCGGCAAACTCAACAAAAATGCCACAGCGAAAATCGATGAACGCAATATTGTGGTTTGGTCTCCGGTGATGGATAAACTGGCTGGACAAAGCACACGTATCGAACACGCTTGTGAGGCCGCCATGTTGATGAGCGACAACACCGCCGCGAACTTAGTGCTAAATGAAATTGGTGGTCCTAAAGCGGTCACGTTGTTTTTGCGATCTATTGGCGACAACGCAACGCGACTTGACCGATTGGAGCCCCGTTTAAACGAAGCAAAACCGGGCGACAAGCGAGACACCACAACGCCTAACGCTATGGTAAACACCCTACACACCTTGATGGAAGATAACGCCCTATCTTACGAGTCACGCACACAGCTGAAAATCTGGATGCAAGACAACAAAGTATCGGATTCTCTCATGCGCTCTGTTCTGCCAAAAGGCTGGTCGATTGCAGACCGCTCTGGCGCAGGTAACTACGGTTCACGCGGCATTAGCGCGATGATCTGGAAAGACAACTACAAGCCGGTTTACATCAGTATTTACGTCACAGACACTGACCTTTCGCTTCAAGCTCGCGATCAGCTGATCGCGCAAATCAGCCAACTGATTTTAGAGCACTACAAAGAAAGTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39615","NCBI_taxonomy_name":"Vibrio parahaemolyticus","NCBI_taxonomy_id":"670"}}}},"ARO_accession":"3005577","ARO_id":"44039","ARO_name":"CARB-43","CARD_short_name":"CARB-43","ARO_description":"CARB-43 is a CARB beta-lactamase.","ARO_category":{"36230":{"category_aro_accession":"3000091","category_aro_cvterm_id":"36230","category_aro_name":"CARB beta-lactamase","category_aro_description":"CARB beta-lactamases are class A lactamases that can hydrolyze carbenicillin. Many of the PSE beta-lactamases have been renamed as CARB-lactamases with the notable exception of PSE-2 which is now OXA-10.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4428":{"model_id":"4428","model_name":"CARB-44","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6803":{"protein_sequence":{"accession":"WP_042764055.1","sequence":"MKKLFLLVGLMVCSTVSYASKLNEDISLIEKQTSGRIGVSVWDTQTDERWDYRGDERFPLMSTFKTLACATMLSDMDSGKLNKNATAKIDERNIVVWSPVMDKLAGQSTRIEHACEAAMLMSDNTAANLVLNEIGGPKAVTLFLRSIGDKATRLDRLEPRLNEAKPGDKRDTTTPNAMVNTLHTLMEDNTLSYESRTQLKIWMQDNKVSDSLMRSVLPKGWSIADRSGAGNYGSRGISAMIWKDNYKPVYISIYVTDTDLSLQARDQLIAQISQLILEHYKES"},"dna_sequence":{"accession":"NG_048747.1","fmin":"100","fmax":"952","strand":"+","sequence":"ATGAAAAAGTTATTCCTGTTGGTTGGGCTGATGGTTTGCTCAACTGTTAGTTACGCCTCCAAATTAAACGAAGACATCTCCCTCATCGAGAAACAAACATCTGGGCGAATTGGAGTGTCAGTCTGGGATACACAAACGGACGAGCGTTGGGATTATCGCGGAGACGAACGTTTCCCATTAATGAGCACATTCAAAACGTTAGCGTGTGCCACCATGCTAAGCGACATGGATAGCGGCAAACTCAACAAAAATGCCACAGCGAAAATCGATGAACGCAATATTGTGGTTTGGTCTCCGGTGATGGATAAACTGGCTGGACAAAGCACACGTATCGAACACGCTTGTGAAGCCGCCATGTTGATGAGCGACAACACCGCCGCGAACTTAGTGCTAAATGAAATTGGTGGTCCTAAAGCGGTCACACTGTTTTTGCGCTCTATTGGCGACAAAGCAACGCGACTTGACCGATTGGAGCCCCGTTTGAATGAAGCAAAACCGGGCGACAAGCGAGACACCACAACGCCTAACGCCATGGTAAACACCCTACACACCTTGATGGAAGATAACACCCTATCTTACGAGTCACGCACACAGCTGAAAATCTGGATGCAAGACAACAAAGTATCGGATTCTCTCATGCGCTCTGTTCTGCCAAAAGGCTGGTCGATTGCAGACCGCTCTGGCGCAGGTAACTACGGTTCACGCGGCATTAGCGCGATGATCTGGAAAGACAACTACAAGCCGGTTTACATCAGTATTTACGTCACAGACACTGACCTTTCGCTTCAAGCTCGCGATCAACTGATCGCGCAAATCAGCCAACTGATTTTAGAGCACTACAAAGAAAGTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39615","NCBI_taxonomy_name":"Vibrio parahaemolyticus","NCBI_taxonomy_id":"670"}}}},"ARO_accession":"3005578","ARO_id":"44040","ARO_name":"CARB-44","CARD_short_name":"CARB-44","ARO_description":"CARB-44 is a CARB beta-lactamase.","ARO_category":{"36230":{"category_aro_accession":"3000091","category_aro_cvterm_id":"36230","category_aro_name":"CARB beta-lactamase","category_aro_description":"CARB beta-lactamases are class A lactamases that can hydrolyze carbenicillin. Many of the PSE beta-lactamases have been renamed as CARB-lactamases with the notable exception of PSE-2 which is now OXA-10.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4429":{"model_id":"4429","model_name":"CARB-45","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6804":{"protein_sequence":{"accession":"WP_047706904.1","sequence":"MKKLFLLVGLMVCSTVSYASKLNADISLIEKQTSGRIGVSVWDTQTDERWDYRGDERFPLMSTFKTLACATMLSDMDSGKLNKNATAKIDERNIVVWSPVMDKLAGQSTRIEHACEAAMLMSDNTAANLVLNEIGGPKAVTLFLRSIGDKATRLDRLEPGLNEAKPGDKRDTTTPNAMVNTLHTLMEDNALSYESRTQLKIWMQDNKVSDSLMRSVLPKGWSIADRSGAGNYGSRGISAMIWKDNYKPVYISIYVTDTDLSLQARDQLIAQISQLILEHYKES"},"dna_sequence":{"accession":"NG_048748.1","fmin":"100","fmax":"952","strand":"+","sequence":"ATGAAAAAGTTATTCCTGTTGGTTGGGCTGATGGTTTGCTCAACTGTTAGTTACGCCTCCAAATTAAACGCAGACATCTCCCTCATCGAGAAACAAACATCTGGGCGAATTGGAGTGTCAGTCTGGGATACACAAACGGACGAGCGTTGGGATTATCGCGGAGACGAACGTTTCCCATTAATGAGCACATTCAAAACGTTAGCGTGTGCCACCATGCTAAGCGACATGGACAGCGGCAAACTCAACAAAAATGCCACAGCGAAAATCGATGAACGCAATATTGTGGTTTGGTCTCCGGTGATGGATAAACTGGCTGGACAAAGCACACGCATCGAACACGCTTGTGAAGCCGCCATGTTGATGAGCGACAACACCGCCGCGAACTTAGTGCTAAATGAAATTGGTGGTCCTAAAGCGGTCACGCTGTTTTTGCGATCTATTGGCGACAAAGCAACGCGACTTGACCGATTGGAACCCGGTTTGAATGAAGCAAAACCGGGCGACAAGCGAGACACCACAACGCCTAACGCCATGGTAAACACCCTACACACCTTGATGGAAGATAACGCCCTATCTTACGAGTCACGCACACAGCTGAAAATCTGGATGCAAGACAACAAAGTATCGGATTCTCTCATGCGCTCTGTTCTGCCAAAAGGCTGGTCGATTGCAGACCGCTCTGGCGCAGGTAACTACGGTTCACGCGGCATTAGCGCGATGATCTGGAAAGACAACTACAAGCCGGTTTACATCAGTATTTACGTCACAGACACTGACCTTTCGCTTCAAGCTCGCGATCAGCTGATCGCGCAAATCAGCCAACTGATTTTAGAGCACTACAAAGAAAGTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39615","NCBI_taxonomy_name":"Vibrio parahaemolyticus","NCBI_taxonomy_id":"670"}}}},"ARO_accession":"3005579","ARO_id":"44041","ARO_name":"CARB-45","CARD_short_name":"CARB-45","ARO_description":"CARB-45 is a CARB beta-lactamase.","ARO_category":{"36230":{"category_aro_accession":"3000091","category_aro_cvterm_id":"36230","category_aro_name":"CARB beta-lactamase","category_aro_description":"CARB beta-lactamases are class A lactamases that can hydrolyze carbenicillin. Many of the PSE beta-lactamases have been renamed as CARB-lactamases with the notable exception of PSE-2 which is now OXA-10.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4430":{"model_id":"4430","model_name":"CARB-46","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6805":{"protein_sequence":{"accession":"WP_031847165.1","sequence":"MKKLFLLVGLMVCSTVSYASKLNEDISLIEKQTSGRIGVSVWDTQTDERWDYRGDERFPLMSTFKTLACATMLSDMDSGKLNKNATAKIDERNIVVWSPVMDKLAGQSTRIEHACEAAMLMSDNTAANLVLNEIGGPKAVTLFLRSIGDEATRLDRLEPRLNEAKPGDKRDTTTPNAMVNTLHTLMEDNALSYESRTQLKIWMQDNKVSDSLMRSVLPKGWSIADRSGAGNYGSRGISAMIWKDNYKPVYISIYVTDTDLSLQARDQLIAQISQLILEHYKES"},"dna_sequence":{"accession":"NG_048749.2","fmin":"100","fmax":"952","strand":"+","sequence":"ATGAAAAAGTTATTCCTGTTGGTTGGGCTGATGGTTTGCTCAACTGTTAGTTACGCCTCCAAATTAAACGAAGACATCTCCCTCATCGAGAAACAAACATCTGGGCGAATTGGAGTGTCAGTCTGGGATACACAAACGGACGAGCGTTGGGATTATCGCGGAGACGAACGTTTCCCATTAATGAGCACATTCAAAACGTTAGCGTGTGCCACCATGCTAAGCGACATGGACAGCGGCAAACTCAACAAAAATGCCACAGCGAAAATCGATGAACGCAATATTGTGGTTTGGTCTCCGGTGATGGATAAACTGGCTGGACAAAGCACACGTATCGAACACGCTTGTGAGGCCGCCATGTTGATGAGCGACAACACCGCCGCGAACTTAGTGCTAAATGAAATTGGTGGTCCTAAAGCGGTCACACTGTTTTTGCGCTCTATTGGCGACGAAGCAACGCGACTTGACCGATTGGAACCCCGTTTGAATGAAGCAAAACCGGGCGACAAGCGAGACACCACAACGCCTAACGCCATGGTAAACACCCTACACACCTTGATGGAAGATAACGCCCTATCTTACGAGTCACGCACACAGCTGAAAATCTGGATGCAAGACAACAAAGTATCGGATTCTCTCATGCGCTCTGTTCTGCCAAAAGGCTGGTCGATTGCAGACCGCTCTGGCGCAGGTAACTACGGTTCACGCGGCATTAGCGCGATGATCTGGAAAGACAACTACAAGCCGGTTTACATCAGTATTTACGTCACAGACACCGACCTTTCGCTTCAAGCTCGCGATCAACTGATCGCGCAAATCAGCCAACTGATTTTAGAGCACTACAAAGAAAGTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39615","NCBI_taxonomy_name":"Vibrio parahaemolyticus","NCBI_taxonomy_id":"670"}}}},"ARO_accession":"3005580","ARO_id":"44042","ARO_name":"CARB-46","CARD_short_name":"CARB-46","ARO_description":"CARB-46 is a CARB beta-lactamase.","ARO_category":{"36230":{"category_aro_accession":"3000091","category_aro_cvterm_id":"36230","category_aro_name":"CARB beta-lactamase","category_aro_description":"CARB beta-lactamases are class A lactamases that can hydrolyze carbenicillin. Many of the PSE beta-lactamases have been renamed as CARB-lactamases with the notable exception of PSE-2 which is now OXA-10.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4431":{"model_id":"4431","model_name":"CARB-47","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6806":{"protein_sequence":{"accession":"WP_031841337.1","sequence":"MKKLFLLVGLMVCSTVSYASKLNEDISLIEKQTSGRIGVSVWDTQTDERWDYRGDERFPLMSTFKTLACATMLSDMDSGKLNKNATAKIDESNIVVWSPVMDKLAGQSTRIEHACEAAMLMSDNTAANLVLNEIGGPKAVTLFLRSIGDKATRLDRLEPRLNEAKPGDKRDTTTPNAMVNTLHTLMEDNALSYESRTQLKIWMQDNKVSDSLMRSVLPKGWSIADRSGAGNYGSRGISAMIWKDNYKPVYISIYVTDTDLSLQARDQLIAQISQLILEHYKES"},"dna_sequence":{"accession":"NG_050564.1","fmin":"100","fmax":"952","strand":"+","sequence":"ATGAAAAAGTTATTCCTGTTGGTTGGGCTGATGGTTTGCTCAACTGTTAGTTACGCCTCCAAATTAAACGAAGACATCTCCCTCATCGAGAAACAAACATCTGGGCGAATTGGAGTGTCAGTCTGGGATACACAAACGGACGAGCGTTGGGATTATCGCGGAGACGAACGTTTCCCATTAATGAGCACATTCAAAACGTTAGCGTGTGCCACCATGCTAAGCGACATGGACAGCGGCAAACTCAACAAAAATGCCACAGCGAAAATCGATGAAAGCAATATTGTGGTTTGGTCTCCGGTGATGGATAAACTGGCTGGACAAAGCACACGCATCGAACACGCTTGTGAAGCCGCCATGTTGATGAGCGACAACACCGCCGCGAACTTAGTGCTAAATGAAATTGGTGGTCCTAAAGCGGTCACGCTGTTTTTGCGATCTATTGGCGACAAAGCAACGCGACTTGACCGATTGGAACCCCGTTTGAATGAAGCAAAACCGGGCGACAAGCGAGACACTACAACGCCTAACGCCATGGTAAACACCCTACACACCTTGATGGAAGATAACGCCCTATCTTACGAGTCACGCACACAGCTGAAAATCTGGATGCAAGACAACAAAGTATCGGATTCGCTCATGCGTTCTGTTCTGCCAAAAGGCTGGTCGATTGCAGACCGCTCTGGCGCAGGTAACTACGGTTCACGCGGCATTAGCGCGATGATCTGGAAAGACAACTACAAGCCGGTTTACATCAGTATTTACGTCACAGACACCGACCTTTCGCTTCAAGCTCGCGATCAACTGATCGCGCAAATCAGCCAACTGATTTTAGAGCACTACAAAGAAAGTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39615","NCBI_taxonomy_name":"Vibrio parahaemolyticus","NCBI_taxonomy_id":"670"}}}},"ARO_accession":"3005581","ARO_id":"44043","ARO_name":"CARB-47","CARD_short_name":"CARB-47","ARO_description":"CARB-47 is a CARB beta-lactamase.","ARO_category":{"36230":{"category_aro_accession":"3000091","category_aro_cvterm_id":"36230","category_aro_name":"CARB beta-lactamase","category_aro_description":"CARB beta-lactamases are class A lactamases that can hydrolyze carbenicillin. Many of the PSE beta-lactamases have been renamed as CARB-lactamases with the notable exception of PSE-2 which is now OXA-10.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4432":{"model_id":"4432","model_name":"CARB-48","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6807":{"protein_sequence":{"accession":"WP_025577435.1","sequence":"MKKLFLLVGLMVCSTVSYASKLNEDISLIEKQTSGRIGVSVWDTQTDERWDYRGDERFPLMSTFKTLACATMLSDMDSGKLNKNATAKIDERNIVVWSPVMDKLAGQNTRIEHACEAAMLMSDNTAANLVLNEIGGPKAVTLFLRSIGDKTTRLDRLEPRLNEAKPGDKRDTTTPNAMVNTLHTLMEDNALSYESRTQLKIWMQDNKVSDSLMRSVLPKGWSIADRSGAGNYGSRGISAMIWKDNYKPVYISIYVTDTDLSLQARDQLIAQISQLILEHYKES"},"dna_sequence":{"accession":"NG_050604.1","fmin":"100","fmax":"952","strand":"+","sequence":"ATGAAAAAGTTATTCCTGTTGGTTGGGCTGATGGTTTGCTCAACTGTTAGTTACGCCTCCAAATTAAACGAAGACATCTCCCTCATCGAGAAACAAACATCTGGGCGAATTGGAGTGTCAGTCTGGGATACACAAACGGACGAGCGTTGGGATTATCGCGGAGACGAACGTTTCCCATTAATGAGCACATTCAAAACGTTAGCGTGTGCCACCATGCTAAGCGACATGGACAGCGGCAAACTCAACAAAAATGCCACAGCGAAAATCGATGAACGCAATATTGTGGTTTGGTCTCCGGTGATGGATAAACTGGCTGGACAAAACACACGCATCGAACACGCTTGTGAAGCTGCCATGTTGATGAGCGACAACACCGCCGCGAACTTAGTGTTAAATGAAATTGGTGGTCCTAAAGCGGTCACGCTGTTTTTGCGCTCTATTGGCGACAAAACAACGCGACTTGACCGATTGGAGCCTCGTTTGAATGAAGCAAAACCGGGCGACAAGCGAGACACCACAACGCCTAACGCCATGGTAAACACCCTACACACCTTGATGGAAGATAACGCCCTATCTTACGAGTCACGCACACAGCTGAAAATCTGGATGCAAGACAACAAAGTATCGGATTCGCTCATGCGCTCTGTTCTGCCAAAAGGCTGGTCGATTGCAGACCGCTCTGGCGCAGGTAACTACGGTTCACGCGGCATTAGCGCGATGATCTGGAAAGACAACTACAAGCCGGTTTACATCAGTATTTACGTCACAGACACTGACCTTTCGCTTCAAGCTCGCGATCAACTGATCGCGCAAATCAGCCAACTGATTTTAGAGCACTACAAAGAAAGTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39615","NCBI_taxonomy_name":"Vibrio parahaemolyticus","NCBI_taxonomy_id":"670"}}}},"ARO_accession":"3005582","ARO_id":"44044","ARO_name":"CARB-48","CARD_short_name":"CARB-48","ARO_description":"CARB-48 is a CARB beta-lactamase.","ARO_category":{"36230":{"category_aro_accession":"3000091","category_aro_cvterm_id":"36230","category_aro_name":"CARB beta-lactamase","category_aro_description":"CARB beta-lactamases are class A lactamases that can hydrolyze carbenicillin. Many of the PSE beta-lactamases have been renamed as CARB-lactamases with the notable exception of PSE-2 which is now OXA-10.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4433":{"model_id":"4433","model_name":"CARB-49","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6808":{"protein_sequence":{"accession":"WP_068981631.1","sequence":"MDVRKHKASFFSVVITFLCLTLSLNANATDSVLEAVTNAETELGARIGLAVHDLETGKRWEHKSNERFPLTSTFKTLACANVLQRVDLGKERIDRVVRFSESNLVTYSPVTEKHVGKKGMSLAELCQATLSTSDNSAANFILQAIGGPKALTKFLRSIGDDTTRLDRWETELNEAVPGDKRDTTTPIAMVTTLEKLLIDETLSIKSRQQLESWLKGNEVGDALFRKGVPSDWIVADRTGAGGYGSRAITAVMWPPNRKPIVAALYITETDASFEERNAVIAKIGEQIAKTVLMENSRN"},"dna_sequence":{"accession":"NG_051466.1","fmin":"0","fmax":"897","strand":"+","sequence":"ATGGACGTACGTAAACACAAGGCTAGTTTTTTTAGCGTAGTAATTACTTTTTTATGTCTCACGCTATCATTAAATGCTAATGCAACAGACTCAGTACTTGAAGCGGTTACCAATGCTGAAACTGAATTAGGCGCTAGAATTGGTCTAGCTGTGCATGATTTGGAAACGGGAAAACGTTGGGAACATAAATCTAATGAACGTTTTCCTCTAACTAGTACCTTTAAAACACTTGCCTGTGCAAACGTTCTTCAAAGAGTTGATCTAGGTAAAGAAAGAATTGATAGAGTTGTGAGATTCTCTGAAAGCAATCTCGTTACATACTCACCTGTAACAGAAAAACATGTGGGTAAAAAAGGGATGTCGCTCGCAGAGCTGTGTCAGGCCACATTATCAACCAGTGATAATTCAGCTGCCAATTTTATTCTACAAGCGATTGGTGGACCTAAGGCTCTAACGAAATTTTTGCGTTCCATTGGCGACGATACTACGCGCCTTGATCGCTGGGAAACAGAACTTAACGAAGCGGTGCCTGGAGATAAGCGAGACACGACAACACCAATTGCAATGGTAACGACACTTGAAAAGTTACTAATTGACGAAACACTATCTATCAAATCTCGTCAACAACTAGAATCTTGGCTTAAAGGTAATGAGGTTGGCGATGCATTGTTTCGTAAAGGCGTTCCAAGTGACTGGATAGTAGCAGATAGAACAGGCGCTGGTGGTTATGGGTCGCGTGCTATTACTGCGGTGATGTGGCCTCCAAATCGCAAGCCTATCGTAGCCGCTCTATACATTACAGAGACAGACGCCTCGTTTGAAGAAAGAAATGCTGTCATTGCAAAAATTGGTGAGCAAATAGCGAAGACAGTATTAATGGAGAATAGCCGTAACTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005583","ARO_id":"44045","ARO_name":"CARB-49","CARD_short_name":"CARB-49","ARO_description":"CARB-49 is a CARB beta-lactamase.","ARO_category":{"36230":{"category_aro_accession":"3000091","category_aro_cvterm_id":"36230","category_aro_name":"CARB beta-lactamase","category_aro_description":"CARB beta-lactamases are class A lactamases that can hydrolyze carbenicillin. Many of the PSE beta-lactamases have been renamed as CARB-lactamases with the notable exception of PSE-2 which is now OXA-10.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4434":{"model_id":"4434","model_name":"CARB-50","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6809":{"protein_sequence":{"accession":"WP_128268233.1","sequence":"MDVRQHKASFFSVVITFLCLTLSLNANATDSVLEAVTNAETELGARIGLAAHDLETGKRWEHKSNERFPLSSTFKTLACANVLQRVDLGKERIDRVVRFSESNLVTYSPVTEKHVGKKGMSLAELCQATLSTSDNSAANFILQAIGGPKALTKFLRSIGDDTTRLDRWETELNEAVPGDKRDTTTPIAMVTTLEKLLIDETLSIKSRQQLESWLKGNEVGDALFRKGVPSDWIVADRTGAGGYGSRAITAVMWPPNRKPIVAALYITETDASFEERNAVIAKIGEQIAKTVLMENSRN"},"dna_sequence":{"accession":"NG_063836.1","fmin":"0","fmax":"897","strand":"+","sequence":"ATGGACGTACGTCAACACAAGGCTAGTTTTTTTAGCGTAGTAATTACTTTTTTATGTCTCACGCTATCATTAAATGCTAATGCAACAGACTCAGTACTTGAAGCGGTTACCAATGCTGAAACTGAATTAGGCGCTAGAATTGGTCTAGCTGCGCATGATTTGGAAACGGGAAAACGTTGGGAACATAAATCTAATGAACGTTTTCCTCTAAGTAGTACCTTTAAAACACTTGCCTGTGCAAACGTTCTTCAAAGAGTTGATCTAGGTAAAGAAAGAATTGATAGAGTTGTGAGATTCTCTGAAAGCAATCTCGTTACATACTCACCTGTAACAGAAAAACATGTGGGTAAAAAAGGGATGTCGCTCGCAGAGCTGTGTCAGGCCACATTATCAACCAGTGATAATTCAGCTGCCAATTTTATTCTACAAGCGATTGGGGGACCTAAGGCTCTAACGAAATTTTTGCGTTCCATTGGCGACGATACTACGCGCCTTGATCGCTGGGAAACAGAACTTAACGAAGCGGTGCCTGGAGATAAGCGAGACACGACAACACCAATTGCAATGGTAACGACACTTGAAAAGTTACTAATTGACGAAACACTATCTATCAAATCTCGTCAACAACTAGAATCTTGGCTTAAAGGTAATGAGGTTGGCGATGCATTGTTTCGTAAAGGCGTTCCAAGTGACTGGATAGTAGCAGATAGAACAGGCGCTGGTGGTTATGGGTCGCGTGCTATTACTGCGGTGATGTGGCCTCCAAATCGCAAGCCTATCGTAGCCGCTCTATACATTACAGAGACAGACGCCTCGTTTGAAGAAAGAAATGCTGTCATTGCAAAAATTGGTGAGCAAATAGCGAAGACAGTATTAATGGAGAATAGCCGTAACTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3005584","ARO_id":"44046","ARO_name":"CARB-50","CARD_short_name":"CARB-50","ARO_description":"CARB-50 is a CARB beta-lactamase.","ARO_category":{"36230":{"category_aro_accession":"3000091","category_aro_cvterm_id":"36230","category_aro_name":"CARB beta-lactamase","category_aro_description":"CARB beta-lactamases are class A lactamases that can hydrolyze carbenicillin. Many of the PSE beta-lactamases have been renamed as CARB-lactamases with the notable exception of PSE-2 which is now OXA-10.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4435":{"model_id":"4435","model_name":"CARB-51","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6810":{"protein_sequence":{"accession":"WP_150823466.1","sequence":"MKFLLAFSLLIPSVVFASSSKFQQVEQDVKAIEVSLSARIGVSVLDTQNGEYWDYNGNQRFPLTSTFKTIACAKLLYDAEQGKVNPNSTVEIKKADLVTYSPVIEKQVGQAITLDDACFATMTTSDNTAANIILSAVGGPKGVTDFLRQIGDKETRLDRIEPDLNEGKLGDLRDTTTPKAIASTLNKFLFGSALSEMNQKKLESWMVNNQVTDNLLRSVLPAGWNIADRSGAGGFGARSITAVVWSEHQAPIIVSIYLAQTQASMAERNDAIVKIGHSIFDVYTSQSR"},"dna_sequence":{"accession":"NG_066505.1","fmin":"48","fmax":"915","strand":"+","sequence":"ATGAAGTTTTTATTGGCATTTTCGCTTTTAATACCATCCGTGGTTTTTGCAAGTAGTTCAAAGTTTCAGCAAGTTGAACAAGACGTTAAGGCAATTGAAGTTTCTCTTTCTGCTCGTATAGGTGTTTCCGTTCTTGATACTCAAAATGGAGAATATTGGGATTACAATGGCAATCAGCGCTTCCCGTTAACAAGTACTTTTAAAACAATAGCTTGCGCTAAATTACTATATGATGCTGAGCAAGGAAAAGTTAATCCCAATAGTACAGTCGAGATTAAGAAAGCAGATCTTGTGACCTATTCCCCTGTAATAGAAAAGCAAGTAGGGCAGGCAATCACACTCGATGATGCGTGCTTCGCAACTATGACTACAAGTGATAATACTGCGGCAAATATCATCCTAAGTGCTGTAGGTGGCCCCAAAGGCGTTACTGATTTTTTAAGACAAATTGGGGACAAAGAGACTCGTCTAGACCGTATTGAGCCTGATTTAAATGAAGGTAAGCTCGGTGATTTGAGGGATACGACAACTCCTAAGGCAATAGCCAGTACTTTGAATAAATTTTTATTTGGTTCCGCGCTATCTGAAATGAACCAGAAAAAATTAGAGTCTTGGATGGTGAACAATCAAGTCACTGATAATTTACTACGTTCAGTATTGCCGGCGGGATGGAACATTGCGGATCGCTCAGGTGCTGGCGGATTTGGTGCTCGGAGTATTACAGCAGTTGTGTGGAGTGAGCATCAAGCCCCAATTATTGTGAGCATCTATCTAGCTCAAACACAGGCTTCAATGGCAGAGCGAAATGATGCGATTGTTAAAATTGGTCATTCAATTTTTGACGTTTATACATCACAGTCGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005585","ARO_id":"44047","ARO_name":"CARB-51","CARD_short_name":"CARB-51","ARO_description":"CARB-51 is a CARB beta-lactamase.","ARO_category":{"36230":{"category_aro_accession":"3000091","category_aro_cvterm_id":"36230","category_aro_name":"CARB beta-lactamase","category_aro_description":"CARB beta-lactamases are class A lactamases that can hydrolyze carbenicillin. Many of the PSE beta-lactamases have been renamed as CARB-lactamases with the notable exception of PSE-2 which is now OXA-10.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4436":{"model_id":"4436","model_name":"CARB-52","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6811":{"protein_sequence":{"accession":"WP_150823467.1","sequence":"MKLLLVFSLLIPSMVFANSSKFQQVEQDAKVIEASLSAHIGISVLDTQTGEYWDYNGNQRFPLTSTFKTIACAKLLYDAEQGEINPKSTIEIKKADLVTYSPVIEKQVGQAITLDDACFATMTTSDNAAANIILNALGGPESVTDFLRQIGDKETRLDRIESELNEGKLGDLRDTTTPNAIVNTLNELLFGSTLSQDGQKKLEYWMVNNQVTGNLLRSVLPEGWNIADRSGAGGFGARSITAVVWSEAQSPIIVSIYLAQTEASIADRNDAIVKIGRSIFEVYSSQSR"},"dna_sequence":{"accession":"NG_066506.1","fmin":"0","fmax":"867","strand":"+","sequence":"ATGAAGCTTTTACTGGTATTTTCGCTTTTAATACCGTCTATGGTGTTTGCAAATAGTTCAAAGTTTCAACAGGTTGAACAAGATGCTAAGGTAATTGAAGCATCTCTTTCTGCGCATATAGGGATTTCTGTTCTTGATACTCAAACTGGAGAGTATTGGGATTACAATGGCAATCAGCGTTTTCCTTTGACAAGTACTTTTAAAACAATAGCTTGTGCTAAATTATTATATGATGCTGAGCAAGGGGAAATAAACCCTAAGAGTACAATTGAGATCAAAAAAGCAGATCTTGTGACCTATTCTCCCGTAATAGAAAAGCAAGTAGGACAAGCAATAACGCTCGATGATGCGTGTTTTGCAACTATGACGACAAGTGATAATGCAGCAGCAAATATCATCCTAAATGCCCTAGGAGGTCCTGAAAGCGTGACGGATTTTCTAAGACAAATCGGAGATAAAGAAACCCGTCTAGACCGTATTGAATCTGAATTAAATGAAGGCAAGCTTGGTGATTTGAGGGATACGACAACTCCTAATGCAATAGTGAATACTTTAAATGAATTATTATTTGGTTCCACATTGTCTCAAGATGGCCAGAAAAAATTAGAGTATTGGATGGTGAATAATCAAGTCACTGGTAATTTATTGCGGTCAGTATTGCCAGAGGGATGGAATATTGCGGATCGTTCAGGTGCTGGCGGATTTGGTGCTCGGAGTATTACAGCCGTTGTTTGGAGTGAAGCTCAATCCCCAATCATAGTTAGTATCTATCTAGCGCAAACAGAGGCTTCAATAGCAGATCGAAATGATGCAATTGTTAAAATTGGTCGTTCAATTTTTGAAGTTTATTCATCACAATCGCGTTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005586","ARO_id":"44048","ARO_name":"CARB-52","CARD_short_name":"CARB-52","ARO_description":"CARB-52 is a CARB beta-lactamase.","ARO_category":{"36230":{"category_aro_accession":"3000091","category_aro_cvterm_id":"36230","category_aro_name":"CARB beta-lactamase","category_aro_description":"CARB beta-lactamases are class A lactamases that can hydrolyze carbenicillin. Many of the PSE beta-lactamases have been renamed as CARB-lactamases with the notable exception of PSE-2 which is now OXA-10.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4437":{"model_id":"4437","model_name":"CARB-53","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6812":{"protein_sequence":{"accession":"WP_188331863.1","sequence":"MKFLLAFSLLIPSVVFASSSKFQQVKQDVKAIEVSLSARIGVSVLDTQNGEYWDYNGNQRFPLTSTFKTIACAKLLYDAEQGKVNPNSTVEIKKADLVTYSPVIEKQVGQAITLDDACFATMTTSDNTAANIILSAVGGPKGVTDFLRQIGDKETRLDRIEPDLNEGKLGDLRDTTTPKAIASTLNKFLFGSALSEMNQKKLESWMVNNQVTGNLLRSVLPAGWNIADRSGAGGFGARSITAVVWSEHQAPIIVSIYLAQTQASMAERNDAIVKIGHSIFDVYTSQSR"},"dna_sequence":{"accession":"NG_070729.1","fmin":"0","fmax":"867","strand":"+","sequence":"ATGAAGTTTTTATTGGCATTTTCGCTTTTAATACCATCCGTGGTTTTTGCAAGTAGTTCAAAGTTTCAGCAAGTTAAACAAGACGTTAAGGCAATTGAAGTTTCTCTTTCTGCTCGTATAGGTGTTTCCGTTCTTGATACTCAAAATGGAGAATATTGGGATTACAATGGCAATCAGCGCTTCCCGTTAACAAGTACTTTTAAAACAATAGCTTGCGCTAAATTACTATATGATGCTGAGCAAGGAAAAGTTAATCCCAATAGTACAGTCGAGATTAAGAAAGCAGATCTTGTGACCTATTCCCCTGTAATAGAAAAGCAAGTAGGGCAGGCAATCACACTCGATGATGCGTGCTTCGCAACTATGACTACAAGTGATAATACTGCGGCAAATATCATCCTAAGTGCTGTAGGTGGCCCCAAAGGCGTTACTGATTTTTTAAGACAAATTGGGGACAAAGAGACTCGTCTAGACCGTATTGAGCCTGATTTAAATGAAGGTAAGCTCGGTGATTTGAGGGATACGACAACTCCTAAGGCAATAGCCAGTACTTTGAATAAATTTTTATTTGGTTCCGCGCTATCTGAAATGAACCAGAAAAAATTAGAGTCTTGGATGGTGAACAATCAAGTCACTGGTAATTTACTACGTTCAGTATTGCCGGCGGGATGGAACATTGCGGATCGCTCAGGTGCTGGCGGATTTGGTGCTCGGAGTATTACAGCAGTTGTGTGGAGTGAGCATCAAGCCCCAATTATTGTGAGCATCTATCTAGCTCAAACACAGGCTTCAATGGCAGAGCGAAATGATGCGATTGTTAAAATTGGTCATTCAATTTTTGACGTTTATACATCACAGTCGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005587","ARO_id":"44049","ARO_name":"CARB-53","CARD_short_name":"CARB-53","ARO_description":"CARB-53 is a CARB beta-lactamase.","ARO_category":{"36230":{"category_aro_accession":"3000091","category_aro_cvterm_id":"36230","category_aro_name":"CARB beta-lactamase","category_aro_description":"CARB beta-lactamases are class A lactamases that can hydrolyze carbenicillin. Many of the PSE beta-lactamases have been renamed as CARB-lactamases with the notable exception of PSE-2 which is now OXA-10.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4438":{"model_id":"4438","model_name":"CARB-54","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6813":{"protein_sequence":{"accession":"WP_179284317.1","sequence":"MNVRQHKASFFSVVITFLCLTLSLNANATDSVLEAVTNAETELGARIGLAAHDLETGKRWEHKSNERFPLSSTFKTLACANVLQRVDLGKERIDRVVRFSESNLVTYSPVTEKHVGKKGMSLAELCQATLSTSDNSAANFILQAIGGPKALTKFLRSIGDDTTRLDRWEPELNEAVPGDKRDTTTPIAMVTTLEKLLIDETLSIKSRQQLESWLKGNEVGDALFRKGVPSDWIVADRTGAGGYGSRAITAVMWPPNRKPIVAALYITETDASFEERNAVIAKIGEQIAKTVLMENSRN"},"dna_sequence":{"accession":"NG_070176.1","fmin":"100","fmax":"997","strand":"+","sequence":"ATGAACGTACGTCAACACAAGGCTAGTTTTTTTAGCGTAGTAATTACTTTTTTATGTCTCACGCTATCATTAAATGCTAATGCAACAGACTCAGTACTTGAAGCGGTTACCAATGCTGAAACTGAATTAGGCGCTAGAATTGGTCTAGCTGCGCATGATTTGGAAACGGGAAAACGTTGGGAACATAAATCTAATGAACGTTTTCCTCTAAGTAGTACCTTTAAAACACTTGCCTGTGCAAACGTTCTTCAAAGAGTTGATCTAGGTAAAGAAAGAATTGATAGAGTTGTGAGATTCTCTGAAAGCAATCTCGTTACATACTCACCTGTAACAGAAAAACATGTGGGTAAAAAAGGGATGTCGCTCGCAGAGCTGTGTCAGGCCACATTATCAACCAGTGATAATTCAGCTGCCAATTTTATTCTACAAGCGATTGGGGGACCTAAGGCTCTAACGAAATTTTTGCGTTCCATTGGCGACGATACTACGCGCCTTGATCGCTGGGAACCAGAACTTAACGAAGCGGTGCCTGGAGATAAGCGAGACACGACAACACCAATTGCAATGGTAACGACACTTGAAAAGTTACTAATTGACGAAACACTATCTATCAAATCTCGTCAACAACTAGAATCTTGGCTTAAAGGTAATGAGGTTGGCGATGCATTGTTTCGTAAAGGCGTTCCAAGTGACTGGATAGTAGCAGATAGAACAGGCGCTGGTGGTTATGGGTCGCGTGCTATTACTGCGGTGATGTGGCCTCCAAATCGCAAGCCTATCGTAGCCGCTCTATACATTACAGAGACAGACGCCTCGTTTGAAGAAAGAAATGCTGTCATTGCAAAAATTGGTGAGCAAATAGCGAAGACAGTATTAATGGAGAATAGCCGTAACTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3005588","ARO_id":"44050","ARO_name":"CARB-54","CARD_short_name":"CARB-54","ARO_description":"CARB-54 is a CARB beta-lactamase.","ARO_category":{"36230":{"category_aro_accession":"3000091","category_aro_cvterm_id":"36230","category_aro_name":"CARB beta-lactamase","category_aro_description":"CARB beta-lactamases are class A lactamases that can hydrolyze carbenicillin. Many of the PSE beta-lactamases have been renamed as CARB-lactamases with the notable exception of PSE-2 which is now OXA-10.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4439":{"model_id":"4439","model_name":"CARB-55","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6814":{"protein_sequence":{"accession":"WP_071846358.1","sequence":"MKFLWAFSHLIPSVVFASSSKFQQVEQDVKAIEVSLSARIGVSVYDTQNGEYWDYNGNQRFPLTSTFKTIACAKLLYDAEQGKVNPNSTVEIKKADLVTYSPVIEKQVGQAITLDDACFATMTTSDNTAANIILSAVGGPKGVTDFLRQIGDKETRLDRIEPDLNEGKLGDLRDTTTPKAIASTLNKFLFGSALSEMNQKKLESWMVNNQVTGNLLRSVLPAGWNIADRSGAGGFGARSITAVVWSEHQAPIIVSIYLAQTQASMAERNDAIVKIGHSIFDVYTSQSR"},"dna_sequence":{"accession":"NG_052478.1","fmin":"100","fmax":"967","strand":"+","sequence":"ATGAAGTTTTTATGGGCATTTTCGCATTTAATACCATCCGTGGTTTTTGCAAGTAGTTCAAAGTTTCAGCAAGTTGAACAAGACGTTAAGGCAATTGAAGTTTCTCTTTCTGCTCGTATAGGTGTTTCCGTTTATGATACTCAAAATGGAGAATATTGGGATTACAATGGCAATCAGCGCTTCCCGTTAACAAGTACTTTTAAAACAATAGCTTGCGCTAAATTACTATATGATGCTGAGCAAGGAAAAGTTAATCCCAATAGTACAGTCGAGATTAAGAAAGCAGATCTTGTGACCTATTCCCCTGTAATAGAAAAGCAAGTAGGGCAGGCAATCACACTCGATGATGCGTGCTTCGCAACTATGACTACAAGTGATAATACTGCGGCAAATATCATCCTAAGTGCTGTAGGTGGCCCCAAAGGCGTTACTGATTTTTTAAGACAAATTGGGGACAAAGAGACTCGTCTAGACCGTATTGAGCCTGATTTAAATGAAGGTAAGCTCGGTGATTTGAGGGATACGACAACTCCTAAGGCAATAGCCAGTACTTTGAATAAATTTTTATTTGGTTCCGCGCTATCTGAAATGAACCAGAAAAAATTAGAGTCTTGGATGGTGAACAATCAAGTCACTGGTAATTTACTACGTTCAGTATTGCCGGCGGGATGGAACATTGCGGATCGCTCAGGTGCTGGCGGATTTGGTGCTCGGAGTATTACAGCAGTTGTGTGGAGTGAGCATCAAGCCCCAATTATTGTGAGCATCTATCTAGCTCAAACACAGGCTTCAATGGCAGAGCGAAATGATGCGATTGTTAAAATTGGTCATTCAATTTTTGACGTTTATACATCACAGTCGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35672","NCBI_taxonomy_name":"Salmonella enterica","NCBI_taxonomy_id":"28901"}}}},"ARO_accession":"3005589","ARO_id":"44051","ARO_name":"CARB-55","CARD_short_name":"CARB-55","ARO_description":"CARB-55 is a CARB beta-lactamase.","ARO_category":{"36230":{"category_aro_accession":"3000091","category_aro_cvterm_id":"36230","category_aro_name":"CARB beta-lactamase","category_aro_description":"CARB beta-lactamases are class A lactamases that can hydrolyze carbenicillin. Many of the PSE beta-lactamases have been renamed as CARB-lactamases with the notable exception of PSE-2 which is now OXA-10.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4440":{"model_id":"4440","model_name":"CDD-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"6815":{"protein_sequence":{"accession":"WP_009901927.1","sequence":"MKRKKNFIWIAILLVGVVMVMYYAVKKHNDINQKTDKNYIKSELNKSKIKNNDKNKKESVNIVDYSDCFEGISGGAIFCNTKNKEYNIYNKELIETRRSPCSTFKIVSTLIGLEKGVINSKESVMGYDGTDYPNKNWNKNLSLEEAFKESCVWYYKKLINKVDAKSVQNILDDLKYGNCDISEWEGDLKNGKGHLNGFWLESSLQISPKEQVQTMAKIFEGDTNFKKEHINILRDIMKIDVNDKNINVYGKTGTGFDEKNKRVDAWFVGMLEREGDTYYFAIKSDDSNKEITGPKVKEIAINIIKKYYSVRE"},"dna_sequence":{"accession":"NG_065860.1","fmin":"100","fmax":"1039","strand":"+","sequence":"ATGAAAAGAAAAAAGAATTTTATTTGGATAGCTATCTTGTTGGTTGGTGTAGTTATGGTAATGTATTATGCAGTGAAAAAACATAACGATATAAATCAAAAAACTGATAAGAATTATATAAAATCTGAATTAAATAAATCTAAAATTAAAAATAATGATAAGAATAAAAAAGAAAGCGTTAATATAGTTGACTATAGTGATTGTTTTGAAGGTATTAGTGGAGGAGCTATTTTTTGTAATACTAAAAATAAAGAATATAATATATATAACAAAGAATTAATTGAAACAAGAAGGTCACCATGTTCTACTTTTAAAATAGTTTCAACTCTAATTGGTTTAGAAAAAGGGGTAATAAACTCAAAAGAATCAGTTATGGGGTATGATGGTACAGATTATCCAAATAAAAATTGGAATAAAAATCTTAGTTTAGAAGAGGCATTTAAGGAGTCTTGTGTTTGGTACTACAAAAAATTGATAAATAAAGTTGATGCTAAATCTGTCCAAAACATTTTAGATGATTTAAAGTATGGGAATTGCGATATTAGTGAATGGGAAGGAGATTTAAAAAATGGAAAGGGACATTTAAATGGATTTTGGTTAGAATCGTCATTACAAATATCTCCAAAAGAACAAGTGCAAACAATGGCAAAAATATTTGAGGGAGATACAAACTTTAAAAAAGAGCATATTAATATTTTAAGAGATATTATGAAAATAGATGTAAATGATAAAAACATAAATGTATATGGAAAAACTGGAACAGGATTTGATGAAAAAAATAAACGTGTGGATGCATGGTTTGTTGGTATGCTAGAGCGTGAAGGTGACACCTATTATTTTGCTATTAAATCAGATGATTCCAATAAAGAAATTACAGGGCCAAAGGTAAAGGAAATTGCAATTAATATAATTAAGAAATATTATAGTGTAAGGGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36807","NCBI_taxonomy_name":"Clostridioides difficile","NCBI_taxonomy_id":"1496"}}}},"ARO_accession":"3006904","ARO_id":"45366","ARO_name":"CDD-1","CARD_short_name":"CDD-1","ARO_description":"CDD-1 is a CDD beta-lactamase.","ARO_category":{"43856":{"category_aro_accession":"3005396","category_aro_cvterm_id":"43856","category_aro_name":"CDD beta-lactamase","category_aro_description":"CDD beta-lactamases are class D beta-lactamases found in Clostridioides difficile.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4441":{"model_id":"4441","model_name":"CDD-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"6816":{"protein_sequence":{"accession":"WP_021361759.1","sequence":"MKRKNNFIWIVILLVVVAMGVYYVGRKHNNTKQKHDKNHINSELNKSKVENKKEKINMVDYSDCFEGISGGAIFYNTKNKEYNIYNKELIETRRSPCSTFKIVSTLIGLEKGVINSKESVMGYDGTEYPNKNWNKNLSLEEAFKESCVWYYKKLIDKVDAKSVQNILDDLKYGNCDISEWEGDLKNGKGHLNGFWLESSLQISPKEQVQTMAKIFEGDTNFKKEHINILRDIMKIDVNDKNINVYGKTGTGFDEKNKRVDAWFVGMLEREGDTYYFAIKSDDSNKEITGPKVKEIAINIIKKYYSVRE"},"dna_sequence":{"accession":"NG_065861.1","fmin":"100","fmax":"1027","strand":"+","sequence":"ATGAAAAGAAAAAATAATTTTATTTGGATAGTTATTCTTCTAGTTGTTGTAGCTATGGGAGTATATTATGTAGGAAGAAAGCATAACAACACAAAACAAAAACATGATAAGAATCATATAAACTCTGAATTAAATAAATCCAAAGTTGAAAACAAAAAAGAAAAAATTAATATGGTTGACTATAGTGATTGTTTTGAAGGTATTAGTGGAGGAGCTATTTTTTATAATACTAAAAATAAAGAATATAATATATATAACAAAGAATTAATTGAAACAAGAAGGTCACCATGTTCTACTTTTAAAATAGTTTCAACTTTAATTGGTTTAGAAAAAGGGGTAATAAACTCAAAAGAATCAGTTATGGGATATGATGGTACAGAGTATCCAAATAAAAATTGGAATAAAAATCTTAGTTTAGAAGAGGCATTTAAGGAGTCTTGTGTTTGGTACTACAAAAAATTGATAGATAAAGTTGATGCTAAATCTGTCCAAAACATTTTAGATGATTTAAAGTATGGGAATTGCGATATTAGCGAATGGGAAGGCGATTTAAAAAATGGAAAGGGACATTTAAATGGATTTTGGTTAGAATCTTCATTACAAATATCTCCAAAAGAACAAGTGCAAACAATGGCAAAAATATTTGAGGGAGATACAAACTTTAAAAAAGAGCATATTAATATTTTAAGAGATATTATGAAAATAGATGTAAATGATAAAAACATAAATGTATATGGAAAAACTGGAACAGGATTTGATGAAAAAAATAAACGTGTGGATGCATGGTTTGTTGGTATGCTAGAGCGTGAAGGTGACACCTATTATTTTGCTATTAAATCAGATGATTCCAATAAAGAAATTACAGGGCCAAAGGTAAAGGAAATTGCAATTAATATAATTAAGAAATATTATAGTGTAAGGGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36807","NCBI_taxonomy_name":"Clostridioides difficile","NCBI_taxonomy_id":"1496"}}}},"ARO_accession":"3006905","ARO_id":"45367","ARO_name":"CDD-2","CARD_short_name":"CDD-2","ARO_description":"CDD-2 is a CDD beta-lactamase.","ARO_category":{"43856":{"category_aro_accession":"3005396","category_aro_cvterm_id":"43856","category_aro_name":"CDD beta-lactamase","category_aro_description":"CDD beta-lactamases are class D beta-lactamases found in Clostridioides difficile.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4442":{"model_id":"4442","model_name":"CepA-29","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"6817":{"protein_sequence":{"accession":"WP_063865204.1","sequence":"MQKRLIHLSIIFFLLCPALVVAQNSPLETQLKKAIEGKKAEIGIAVIIDGQDTITVNNDIHYPMMSVFKFHQALALADYMHHQKQPLKTRLLIKKSDLKPDTYSPLREIYPQGGIEMSIADLLKYTLQQSDNNACDILFNYQGGPDAVNKYLHSLGIRECAVIHTENDMHENLEFCYQNWTTPLAAAKLLEIFRNENLFDKEYKNFIYQTMVECQTGQDRLIAPLLDKKVTMGHKTGTGDRNAKGQQIGCNDIGFILLPDRHAYSIAVFVKDSEADNRENSEIIAEISRIVYEYVTQQID"},"dna_sequence":{"accession":"NG_050385.1","fmin":"100","fmax":"1003","strand":"+","sequence":"ATGCAAAAAAGACTTATACATTTATCCATTATCTTCTTTCTGCTATGTCCTGCCCTGGTAGTTGCGCAGAACAGTCCTCTTGAAACTCAACTCAAGAAAGCCATAGAAGGGAAAAAAGCCGAAATAGGAATTGCAGTCATTATCGACGGGCAAGATACGATAACAGTCAATAATGATATTCATTATCCCATGATGAGTGTTTTCAAATTTCATCAGGCATTGGCATTGGCCGATTACATGCATCATCAAAAGCAACCTTTGAAAACCCGGTTATTGATTAAAAAGTCGGATTTAAAGCCGGACACCTATAGTCCGCTTCGAGAAATATACCCACAGGGAGGAATCGAAATGAGCATTGCCGATCTACTGAAATATACGCTTCAGCAAAGTGACAATAATGCCTGCGATATTCTTTTTAATTATCAAGGTGGTCCGGATGCCGTGAATAAGTATCTTCATTCATTGGGAATTCGTGAATGTGCTGTCATCCATACAGAAAACGATATGCATGAGAATCTGGAGTTCTGTTACCAAAACTGGACTACTCCATTAGCAGCCGCCAAATTACTGGAAATATTTCGCAATGAAAACCTTTTTGACAAAGAATACAAGAATTTCATTTATCAAACAATGGTGGAATGTCAGACAGGACAAGACCGCCTGATTGCTCCACTGCTCGATAAAAAAGTAACAATGGGGCATAAAACCGGAACAGGCGACCGTAATGCGAAAGGACAACAGATCGGTTGCAATGACATCGGGTTTATTCTTCTTCCCGACAGACATGCCTATAGTATAGCCGTCTTCGTGAAAGATTCCGAAGCAGATAACAGAGAAAACAGTGAGATTATCGCAGAAATTTCGCGCATCGTTTACGAATACGTAACGCAACAGATAGATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35916","NCBI_taxonomy_name":"Bacteroides fragilis","NCBI_taxonomy_id":"817"}}}},"ARO_accession":"3006224","ARO_id":"44686","ARO_name":"CepA-29","CARD_short_name":"CepA-29","ARO_description":"CepA-29 is a CepA beta-lactamase.","ARO_category":{"41356":{"category_aro_accession":"3004192","category_aro_cvterm_id":"41356","category_aro_name":"CepA beta-lactamase","category_aro_description":"CepA beta-lactamases are Class A beta-lactamases found in Bateroides fragilis and have the ability to hydrolyze cephalosporin.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4443":{"model_id":"4443","model_name":"CepA-44","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"6818":{"protein_sequence":{"accession":"WP_032579291.1","sequence":"MQKRLIHLSIIFFLLCPALVVAQNSPLETQLKKAIEGKKAEIGIAVIIDGQDTITINNDIHYPMMSVFKFHQALALADYMHHQKQPLKTRLLIKKSDLKPDTYSPLRETYPQGGIEMSIADLLKYTLQQSDNNACDILFNYQGGPDAVNKYLHSLGIRECAVIHTENDMHENLEFCYQNWTTPLAAAKLLEIFRNENLFDKEYKNFIYQTMVECQTGQDRLIAPLLDKKVTMGHKTGTGDRNAKGQQIGCNDIGFILLPDGHAYSIAVFVKDSEADNRENSEIIAEISRIVYEYVKQQID"},"dna_sequence":{"accession":"NG_050386.1","fmin":"100","fmax":"1003","strand":"+","sequence":"ATGCAAAAAAGACTTATACATTTATCCATTATCTTCTTTCTGCTATGTCCTGCCCTGGTAGTTGCGCAGAACAGTCCTCTTGAAACTCAACTCAAGAAAGCCATAGAAGGGAAAAAAGCCGAAATAGGAATTGCAGTCATTATCGACGGGCAAGATACGATAACAATCAATAATGATATTCATTATCCCATGATGAGTGTTTTCAAATTTCATCAGGCATTGGCATTGGCCGATTACATGCATCATCAAAAGCAACCTTTGAAAACCCGGTTATTGATTAAAAAGTCGGATTTAAAGCCGGACACCTATAGTCCGCTTCGAGAAACATACCCACAGGGAGGAATCGAAATGAGCATTGCCGATCTACTGAAATATACGCTTCAGCAAAGTGACAATAATGCCTGCGATATTCTTTTTAATTATCAAGGTGGTCCGGATGCCGTGAATAAGTATCTTCATTCATTGGGAATTCGTGAATGTGCTGTCATCCATACAGAAAACGATATGCATGAGAATCTGGAGTTCTGTTACCAAAACTGGACTACTCCATTGGCAGCCGCCAAATTACTGGAAATATTTCGCAATGAAAACCTTTTTGACAAAGAATACAAGAATTTCATTTATCAAACAATGGTGGAATGTCAGACAGGACAAGACCGCCTGATTGCTCCACTGCTCGATAAAAAAGTAACAATGGGGCATAAAACCGGAACAGGCGACCGTAATGCGAAAGGGCAACAGATCGGTTGCAATGACATCGGGTTTATTCTTCTTCCCGACGGACATGCCTATAGCATAGCCGTCTTCGTGAAAGATTCCGAAGCAGATAACAGGGAAAACAGTGAGATTATCGCAGAAATTTCGCGCATCGTTTACGAATACGTAAAGCAACAGATAGATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35916","NCBI_taxonomy_name":"Bacteroides fragilis","NCBI_taxonomy_id":"817"}}}},"ARO_accession":"3006225","ARO_id":"44687","ARO_name":"CepA-44","CARD_short_name":"CepA-44","ARO_description":"CepA-44 is a CepA beta-lactamase.","ARO_category":{"41356":{"category_aro_accession":"3004192","category_aro_cvterm_id":"41356","category_aro_name":"CepA beta-lactamase","category_aro_description":"CepA beta-lactamases are Class A beta-lactamases found in Bateroides fragilis and have the ability to hydrolyze cephalosporin.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4444":{"model_id":"4444","model_name":"CepA-49","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"6819":{"protein_sequence":{"accession":"WP_008659027.1","sequence":"MQKRLIHLSIIFFLLCPALVVAQNSPLETQLKKAIEGKKAEIGIAVIIDGQDTITVNNDIHYPMMSVFKFHQALALADYMHHQKQPLETRLLIKKSDLKPDTYSPLRETYPQGGIEMSIADLLKYTLQQSDNNACDILFNYQGGPDAVNKYLHSLGIRECAVIHTENDMHKNLEFCYQNWTTPLAAAKLLEIFRNENLFDKEYKNFIYQTMVECQTGQDRLIAPLLDKKVTMGHKTGTGDRNAKGQQIGCNDIGFILLPDGHVYSIAVFVKDSEADNRENSEIIAEISHIVYEYVTQQID"},"dna_sequence":{"accession":"NG_050387.1","fmin":"100","fmax":"1003","strand":"+","sequence":"ATGCAAAAAAGACTTATACATTTATCCATTATCTTCTTTCTGCTATGTCCTGCCCTGGTAGTTGCGCAGAACAGTCCTCTTGAAACTCAACTAAAGAAAGCCATAGAAGGGAAAAAAGCCGAAATAGGAATTGCAGTCATTATCGACGGGCAAGATACGATAACAGTCAATAATGATATTCATTATCCCATGATGAGTGTTTTCAAATTTCATCAGGCATTGGCATTGGCCGATTACATGCATCATCAAAAGCAACCTTTGGAAACCCGGTTATTGATTAAAAAGTCGGATTTAAAGCCGGACACCTATAGTCCGCTTCGAGAAACATACCCACAGGGAGGAATCGAAATGAGCATTGCCGATCTACTGAAATATACGCTTCAGCAAAGTGACAATAATGCCTGCGATATTCTTTTTAATTATCAAGGTGGTCCGGATGCCGTGAATAAGTATCTTCATTCATTGGGAATTCGTGAATGTGCTGTCATCCATACAGAAAACGATATGCATAAGAATCTGGAGTTCTGTTACCAAAACTGGACTACTCCATTAGCAGCCGCCAAATTACTGGAAATATTTCGCAATGAAAACCTTTTTGACAAAGAATACAAGAATTTCATTTATCAAACAATGGTGGAATGTCAGACAGGACAAGACCGCCTGATTGCTCCACTGCTCGATAAAAAAGTAACAATGGGGCATAAAACCGGAACAGGCGACCGTAATGCGAAAGGACAACAGATCGGTTGCAATGACATCGGGTTTATTCTTCTTCCCGACGGACATGTCTATAGTATAGCCGTCTTCGTGAAAGATTCCGAAGCAGATAACAGAGAAAACAGTGAGATTATCGCAGAAATTTCGCACATCGTTTACGAATACGTAACGCAACAGATAGATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37050","NCBI_taxonomy_name":"Bacteroides","NCBI_taxonomy_id":"816"}}}},"ARO_accession":"3006226","ARO_id":"44688","ARO_name":"CepA-49","CARD_short_name":"CepA-49","ARO_description":"CepA-49 is a CepA beta-lactamase.","ARO_category":{"41356":{"category_aro_accession":"3004192","category_aro_cvterm_id":"41356","category_aro_name":"CepA beta-lactamase","category_aro_description":"CepA beta-lactamases are Class A beta-lactamases found in Bateroides fragilis and have the ability to hydrolyze cephalosporin.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4445":{"model_id":"4445","model_name":"CfiA10","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"6820":{"protein_sequence":{"accession":"WP_063865205.1","sequence":"MKTVFILISMLFPVAVMAQKSVKISDDISITQLSDKVYTYVSLAEIEGWGMVPSNGMIVINNHQAALLDTPINDAQTETLVNWVADSLHAKVTTFIPNHWHGDCIGGLGYLQKKGVQSYANQMTIDLAKEKGLPVPEHGFTDSLTVSLDGMPLQCYYLGGGHATDNIVVWLPTENILFGGCMLKDNQATSIGNISDADVTAWPKTLDKVKAKFPSARYVVPGHGDYGGTELIEHPKQIVNQYIESTSKP"},"dna_sequence":{"accession":"NG_050388.1","fmin":"0","fmax":"750","strand":"+","sequence":"ATGAAAACAGTATTTATCCTTATCTCCATGCTTTTCCCTGTCGCAGTTATGGCACAGAAAAGCGTAAAAATATCCGATGATATCAGTATCACCCAACTCTCGGACAAAGTGTACACTTATGTATCCCTCGCCGAAATCGAAGGATGGGGTATGGTACCTTCCAACGGAATGATTGTTATCAACAACCATCAGGCAGCGTTGCTGGACACACCGATCAATGACGCACAAACGGAAACGCTGGTCAACTGGGTAGCGGACTCTTTGCATGCTAAAGTCACCACGTTTATCCCGAACCACTGGCACGGCGATTGTATTGGCGGACTGGGTTACCTGCAAAAGAAAGGTGTCCAATCATACGCAAACCAGATGACGATAGACCTCGCCAAGGAAAAAGGATTGCCCGTACCGGAACATGGATTCACCGATTCACTGACCGTCAGTCTGGACGGCATGCCTCTCCAATGTTATTATTTAGGAGGCGGACATGCGACCGACAATATCGTGGTTTGGCTGCCGACAGAGAATATCCTTTTTGGCGGATGTATGCTTAAAGACAACCAGGCGACAAGCATCGGCAACATCTCGGACGCGGACGTGACGGCATGGCCGAAAACTCTCGATAAGGTAAAAGCCAAGTTCCCCTCGGCCCGCTACGTCGTGCCCGGACATGGCGACTATGGCGGAACCGAACTGATAGAGCATCCCAAGCAGATCGTGAACCAATATATAGAAAGCACCTCAAAGCCATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35916","NCBI_taxonomy_name":"Bacteroides fragilis","NCBI_taxonomy_id":"817"}}}},"ARO_accession":"3006906","ARO_id":"45368","ARO_name":"CfiA10","CARD_short_name":"CfiA10","ARO_description":"CfiA10 is a CfiA beta-lactamase.","ARO_category":{"41364":{"category_aro_accession":"3004200","category_aro_cvterm_id":"41364","category_aro_name":"CfiA beta-lactamase","category_aro_description":"CfiA beta-lactamases are chromosomal-encoded carbapenemase commonly found in Bacteroides fragilis isolates.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4446":{"model_id":"4446","model_name":"CfiA11","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"6821":{"protein_sequence":{"accession":"WP_063843236.1","sequence":"MKTVFILISMLFPVAVMAQKSVKISDDISITQLSDKVYTYVSLAEIEGWGMVPSNGMIVINNHQAALLDTPINDAQTETLVNWVTDSLHAKVTTFIPNHWHGDCIGGLGYLQKKGVRSYANQMTIDLAKEKGLPVPEHGFTDSLTVSLDGMPLQCYYLGGGHATDNIVVWLPTENILFGGCMLKDNQTTSIGNISDADVTAWPKTLDKVKAKFPSARYVVPGHGNYGGTELIEHTKQIVNQYIESTSKP"},"dna_sequence":{"accession":"NG_047630.1","fmin":"100","fmax":"850","strand":"+","sequence":"ATGAAAACAGTATTTATCCTTATCTCCATGCTTTTCCCTGTCGCAGTTATGGCACAGAAAAGCGTAAAAATATCCGATGACATCAGTATCACCCAACTCTCGGACAAAGTGTACACTTATGTATCCCTCGCCGAAATCGAAGGATGGGGTATGGTACCTTCCAACGGGATGATTGTTATCAACAACCACCAGGCAGCGTTGCTGGACACACCGATCAATGACGCACAAACGGAAACGCTGGTCAACTGGGTGACAGACTCTTTGCATGCCAAAGTCACCACGTTTATCCCGAACCACTGGCACGGCGATTGTATTGGCGGACTGGGTTACCTGCAAAAGAAAGGTGTCCGATCATACGCGAACCAGATGACGATAGACCTCGCCAAGGAAAAAGGATTGCCCGTACCGGAACATGGATTCACCGATTCACTGACCGTCAGCTTGGACGGCATGCCTCTCCAATGCTATTATTTAGGAGGCGGGCATGCGACCGACAATATCGTGGTTTGGCTGCCGACAGAGAATATCCTTTTTGGCGGATGTATGCTTAAAGACAACCAGACGACAAGCATCGGCAACATCTCGGACGCGGACGTGACGGCATGGCCGAAAACTCTCGATAAGGTAAAAGCCAAGTTCCCCTCGGCCCGCTACGTCGTGCCCGGACATGGTAACTATGGCGGAACCGAACTGATAGAGCATACCAAGCAGATCGTGAACCAATATATAGAAAGCACTTCAAAGCCATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35916","NCBI_taxonomy_name":"Bacteroides fragilis","NCBI_taxonomy_id":"817"}}}},"ARO_accession":"3006907","ARO_id":"45369","ARO_name":"CfiA11","CARD_short_name":"CfiA11","ARO_description":"CfiA11 is a CfiA beta-lactamase.","ARO_category":{"41364":{"category_aro_accession":"3004200","category_aro_cvterm_id":"41364","category_aro_name":"CfiA beta-lactamase","category_aro_description":"CfiA beta-lactamases are chromosomal-encoded carbapenemase commonly found in Bacteroides fragilis isolates.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4447":{"model_id":"4447","model_name":"CfiA14","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"6822":{"protein_sequence":{"accession":"WP_005780969.1","sequence":"MKTVFILISMLFPVAVMAQKSVKISDDISITQLSDKVYTYVSLAEIEGWGMVPSNGMIVINNHQAALLDTPINDAQTETLVNWVTDSLHAKVTTFIPNHWHGDCIGGLGYLQKKGVQSYANQMTIDLAKEKGLPVPEHGFTDSLTVSLDGMPLQCYYLGGGHATDNIVVWLPTENILFGGCMLKDNQATSIGNISDADVTAWPKTLDKVKAKFPSARYVVPGHGDYGGTELIEHTKQIVNQYIESTSKP"},"dna_sequence":{"accession":"NG_050390.1","fmin":"100","fmax":"850","strand":"+","sequence":"ATGAAAACAGTATTTATCCTTATCTCCATGCTTTTCCCTGTCGCAGTTATGGCACAGAAAAGCGTAAAAATATCCGATGACATCAGTATCACCCAACTCTCGGACAAAGTGTACACTTATGTATCCCTCGCCGAAATTGAAGGATGGGGCATGGTACCTTCCAACGGGATGATTGTTATCAACAACCACCAGGCAGCGTTGCTGGACACACCTATCAATGACGCACAAACGGAAACGCTGGTCAACTGGGTGACAGACTCTTTGCATGCCAAAGTCACCACGTTTATCCCGAACCACTGGCACGGCGATTGTATTGGCGGACTGGGTTACCTGCAAAAGAAAGGTGTCCAATCATACGCGAACCAGATGACGATAGACCTCGCCAAGGAAAAAGGGTTGCCCGTACCGGAACATGGATTCACCGATTCACTGACCGTCAGCCTGGACGGCATGCCTCTCCAATGTTATTATTTAGGAGGCGGACATGCGACCGACAATATCGTGGTTTGGCTGCCGACAGAGAATATCCTTTTTGGCGGATGTATGCTTAAAGACAACCAGGCGACAAGCATCGGCAATATCTCGGACGCGGACGTGACGGCATGGCCGAAAACTCTCGATAAGGTAAAAGCCAAGTTCCCCTCGGCCCGCTACGTCGTGCCCGGACATGGCGACTATGGCGGAACCGAACTGATAGAGCATACCAAGCAGATCGTGAACCAATATATAGAAAGCACTTCAAAGCCATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35916","NCBI_taxonomy_name":"Bacteroides fragilis","NCBI_taxonomy_id":"817"}}}},"ARO_accession":"3006908","ARO_id":"45370","ARO_name":"CfiA14","CARD_short_name":"CfiA14","ARO_description":"CfiA14 is a CfiA beta-lactamase.","ARO_category":{"41364":{"category_aro_accession":"3004200","category_aro_cvterm_id":"41364","category_aro_name":"CfiA beta-lactamase","category_aro_description":"CfiA beta-lactamases are chromosomal-encoded carbapenemase commonly found in Bacteroides fragilis isolates.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4448":{"model_id":"4448","model_name":"CfiA17","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"6823":{"protein_sequence":{"accession":"WP_085562389.1","sequence":"MKTVFILISMLFPVAVMAQKSVKISDDISITQLSDKVYTYVSLAEIEGWGMVPSNGIIVINNHRAALLDTPINDAQTETLVNWVTDSLHAKVTTFIPNHWHGDCIGGLGYLQKKGVQSYANQMTIDFAKEKGLPIPEHGFTDSLTVSLDGMPLQCYYLGGGHATDNIVVWLPTENILFGGCMLKDNQATSIGNISDADVTAWPKTLDKVKAKFPSARYVVPGHGDYGGTELIEHTKQIVNQYIESTSKP"},"dna_sequence":{"accession":"NG_054674.1","fmin":"0","fmax":"750","strand":"+","sequence":"ATGAAAACAGTATTTATCCTTATCTCCATGCTTTTCCCTGTCGCAGTTATGGCACAGAAAAGCGTAAAAATATCTGATGATATCAGTATCACCCAACTCTCGGATAAAGTGTACACTTATGTATCCCTCGCCGAAATCGAAGGATGGGGCATGGTACCTTCCAACGGAATAATTGTTATCAACAACCATCGGGCAGCGTTGCTGGACACACCGATCAATGACGCACAAACGGAAACACTGGTCAACTGGGTGACAGACTCTTTGCATGCCAAAGTCACCACGTTTATCCCGAACCACTGGCACGGCGATTGTATTGGCGGACTGGGTTACCTGCAAAAGAAAGGTGTCCAATCATACGCAAACCAGATGACGATAGACTTCGCTAAGGAAAAAGGATTGCCCATACCGGAACATGGATTCACCGATTCACTGACCGTCAGTCTGGACGGCATGCCTCTCCAATGTTATTATTTAGGAGGCGGACATGCGACCGACAATATCGTGGTTTGGCTGCCGACAGAGAATATCCTTTTTGGCGGATGTATGCTTAAAGACAACCAGGCGACAAGCATCGGCAACATCTCGGACGCGGACGTGACGGCATGGCCGAAAACTCTCGATAAGGTAAAAGCCAAGTTCCCCTCGGCCCGCTACGTCGTGCCCGGACATGGCGACTATGGCGGAACCGAACTGATAGAGCATACCAAGCAGATCGTGAACCAATATATAGAAAGCACTTCAAAGCCATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35916","NCBI_taxonomy_name":"Bacteroides fragilis","NCBI_taxonomy_id":"817"}}}},"ARO_accession":"3006909","ARO_id":"45371","ARO_name":"CfiA17","CARD_short_name":"CfiA17","ARO_description":"CfiA17 is a CfiA beta-lactamase.","ARO_category":{"41364":{"category_aro_accession":"3004200","category_aro_cvterm_id":"41364","category_aro_name":"CfiA beta-lactamase","category_aro_description":"CfiA beta-lactamases are chromosomal-encoded carbapenemase commonly found in Bacteroides fragilis isolates.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4449":{"model_id":"4449","model_name":"CfiA18","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"6824":{"protein_sequence":{"accession":"WP_085562388.1","sequence":"MKTVFILISMLFPVAVMAQKSVKISNDISITQLSDKVYTYVSLAEIEGWGMVPSNGMIVINNHQAALLDTPINDAQTETLVNWVADSLHAKVTTFIPNHWHGDCIGGLGYLQKKGVQSYANQMTIDLAKEKGLPVPEHGFTDSLTVSLDGMPLQCYYLGGGHATDNIVVWLPTENILFGGCMLKDNQATSIGNISDADVTAWPKTLDKVKAKFPSARYVVPGHGDYGGTELIEHTKQIVNQYIESTSKP"},"dna_sequence":{"accession":"NG_054673.1","fmin":"0","fmax":"750","strand":"+","sequence":"ATGAAAACAGTATTTATCCTTATCTCCATGCTTTTCCCTGTCGCAGTTATGGCACAGAAAAGCGTAAAAATATCCAATGATATCAGTATCACCCAACTCTCGGACAAAGTGTACACTTATGTATCCCTCGCCGAAATCGAAGGATGGGGTATGGTACCTTCCAACGGAATGATTGTTATCAACAACCATCAGGCAGCGTTGCTGGACACACCGATCAATGACGCACAAACGGAAACGCTGGTCAACTGGGTAGCGGACTCTTTGCATGCCAAAGTCACCACGTTTATCCCGAACCACTGGCACGGCGATTGTATTGGCGGACTGGGTTACCTGCAAAAGAAAGGTGTCCAATCATATGCAAACCAGATGACGATAGACCTCGCCAAGGAAAAAGGGTTGCCCGTACCGGAACATGGATTCACCGATTCACTGACCGTCAGCTTGGACGGCATGCCTCTCCAATGTTATTATTTAGGAGGCGGACATGCGACCGACAATATCGTGGTTTGGCTGCCGACAGAGAATATCCTTTTTGGCGGATGTATGCTTAAAGACAACCAGGCGACAAGCATCGGCAACATCTCGGACGCGGACGTGACGGCATGGCCGAAAACTCTCGATAAGGTAAAAGCCAAGTTCCCCTCGGCCCGCTACGTCGTGCCCGGACATGGCGACTATGGCGGAACCGAACTGATAGAGCATACCAAGCAGATCGTGAACCAATATATAGAAAGCACCTCAAAGCCATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35916","NCBI_taxonomy_name":"Bacteroides fragilis","NCBI_taxonomy_id":"817"}}}},"ARO_accession":"3006910","ARO_id":"45372","ARO_name":"CfiA18","CARD_short_name":"CfiA18","ARO_description":"CfiA18 is a CfiA beta-lactamase.","ARO_category":{"41364":{"category_aro_accession":"3004200","category_aro_cvterm_id":"41364","category_aro_name":"CfiA beta-lactamase","category_aro_description":"CfiA beta-lactamases are chromosomal-encoded carbapenemase commonly found in Bacteroides fragilis isolates.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4450":{"model_id":"4450","model_name":"CfiA19","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"6825":{"protein_sequence":{"accession":"WP_085562383.1","sequence":"MKTVFILISMLFPVAVMAQKSVKISDDISITQLSDKVYTYVSLAEIEGWGMVPSNGMIVINNHQAALLDTPINDAQTEMLVNWVTDSLHAKVTTFIPNHWHGDCIGGLGYLQKKGVRSYANQMTIDLAKEKGLPVPEHGFTDSLTVSLDGMPLQCYYLGGGHATDNIVVWLPTENILFGGCMLKDNQATSIGNISDADVTAWPKTLDKVKAKFPSARYVVPGHGDYGGTELIEHTKQIVNQYIESTSKP"},"dna_sequence":{"accession":"NG_054664.1","fmin":"0","fmax":"750","strand":"+","sequence":"ATGAAAACAGTATTTATCCTTATCTCCATGCTTTTCCCTGTCGCAGTTATGGCACAGAAAAGCGTAAAAATATCCGATGACATCAGTATCACCCAACTCTCGGACAAAGTGTACACTTATGTATCCCTCGCCGAAATCGAAGGATGGGGTATGGTACCTTCCAACGGGATGATTGTTATCAACAACCACCAGGCAGCGTTGCTGGACACACCGATCAATGACGCACAAACGGAAATGCTGGTCAACTGGGTGACAGACTCTTTGCATGCCAAAGTCACCACGTTTATCCCGAACCACTGGCACGGCGATTGTATTGGCGGACTGGGTTACCTGCAAAAGAAAGGTGTCCGATCATACGCGAACCAGATGACGATAGACCTCGCCAAGGAAAAAGGATTGCCCGTACCGGAACATGGATTCACCGATTCACTGACCGTCAGCTTGGACGGCATGCCTCTCCAATGCTATTATTTAGGAGGCGGGCATGCGACCGACAATATCGTGGTTTGGCTGCCGACAGAGAATATCCTTTTTGGCGGATGTATGCTTAAAGACAACCAGGCGACAAGCATCGGCAACATCTCGGACGCAGACGTGACGGCATGGCCGAAAACTCTCGATAAGGTAAAAGCCAAGTTCCCCTCGGCCCGCTACGTCGTGCCCGGACATGGCGACTATGGCGGAACCGAACTGATAGAGCATACCAAGCAGATCGTGAACCAATATATAGAAAGCACCTCAAAGCCATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35916","NCBI_taxonomy_name":"Bacteroides fragilis","NCBI_taxonomy_id":"817"}}}},"ARO_accession":"3006911","ARO_id":"45373","ARO_name":"CfiA19","CARD_short_name":"CfiA19","ARO_description":"CfiA19 is a CfiA beta-lactamase.","ARO_category":{"41364":{"category_aro_accession":"3004200","category_aro_cvterm_id":"41364","category_aro_name":"CfiA beta-lactamase","category_aro_description":"CfiA beta-lactamases are chromosomal-encoded carbapenemase commonly found in Bacteroides fragilis isolates.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4451":{"model_id":"4451","model_name":"CfiA2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"6826":{"protein_sequence":{"accession":"WP_015083750.1","sequence":"MKTVFILISMLFPVAVMAQKSVKISDDISITQLSDKVYTYVSLAEIEGWGMVPSNGMIVINNHQAALLDTPINDAQTETLVNWVADSLHAKVTTFIPNHWHGDCIGGLGYLQKKGVQSYANQMTIDLAKEKGLPVPEHGFTDSLTVSLDGMPLQCYYLGGGHATDNIVVWLPTENILFGGCMLKDNQATSIGNISDADVTAWPKTLDKVKAKFPSARYVVPGHGDYGGTELIEHTKQIVNQYIESTSKP"},"dna_sequence":{"accession":"NG_050391.1","fmin":"0","fmax":"750","strand":"+","sequence":"ATGAAAACAGTATTTATCCTTATCTCCATGCTTTTCCCTGTCGCAGTTATGGCACAGAAAAGCGTAAAAATATCCGATGATATCAGTATCACCCAACTCTCGGACAAAGTGTACACTTATGTATCCCTCGCCGAAATCGAAGGATGGGGTATGGTACCTTCCAACGGAATGATTGTTATCAACAACCATCAGGCAGCGTTGCTGGACACACCGATCAATGACGCACAAACGGAAACGCTGGTCAACTGGGTAGCGGACTCTTTGCATGCCAAAGTCACCACGTTTATCCCGAACCACTGGCACGGCGATTGTATTGGCGGACTGGGTTACCTGCAAAAGAAAGGTGTCCAATCATACGCAAACCAGATGACGATAGACCTCGCCAAGGAAAAAGGATTGCCCGTACCGGAACATGGATTCACCGATTCACTGACCGTCAGTCTGGACGGCATGCCTCTCCAATGTTATTATTTAGGAGGCGGACATGCGACCGACAATATCGTGGTTTGGCTGCCGACAGAGAATATCCTTTTTGGCGGATGTATGCTTAAAGACAACCAGGCGACAAGCATCGGCAACATCTCGGACGCGGACGTGACGGCATGGCCGAAAACTCTCGATAAGGTAAAAGCCAAGTTCCCCTCGGCCCGCTACGTCGTGCCCGGACATGGCGACTATGGCGGAACCGAACTGATAGAGCATACCAAGCAGATCGTGAACCAATATATAGAAAGCACTTCAAAGCCATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35916","NCBI_taxonomy_name":"Bacteroides fragilis","NCBI_taxonomy_id":"817"}}}},"ARO_accession":"3006912","ARO_id":"45374","ARO_name":"CfiA2","CARD_short_name":"CfiA2","ARO_description":"CfiA2 is a CfiA beta-lactamase.","ARO_category":{"41364":{"category_aro_accession":"3004200","category_aro_cvterm_id":"41364","category_aro_name":"CfiA beta-lactamase","category_aro_description":"CfiA beta-lactamases are chromosomal-encoded carbapenemase commonly found in Bacteroides fragilis isolates.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4452":{"model_id":"4452","model_name":"CfiA21","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"6827":{"protein_sequence":{"accession":"WP_085562390.1","sequence":"MKTVFILISMLFPVAVMAQKSVKISDDISITQLSDKVYTYVSLAEIEGWGMVPSNGIIVINNHRAALLDTPINDAQTETLVNWVADSLHAKVTTFIPNHWHGDCIGGLGYLQKKGVQSYANQMTIDLAKEKGLPVPEHGFTDSLTVSLDGTPLQCYYLGGGHATDNIVVWLPTENILFGGCMLKDNQTTSIGNISDADVTAWPKTLDKVKAKFPSARYVVPGHGDYGGTELIEHTKQIVNQYIESTSKP"},"dna_sequence":{"accession":"NG_054675.1","fmin":"0","fmax":"750","strand":"+","sequence":"ATGAAAACAGTATTTATCCTTATCTCCATGCTTTTCCCTGTCGCAGTTATGGCACAGAAAAGCGTAAAAATATCTGATGATATCAGTATCACCCAACTCTCGGATAAAGTGTACACTTATGTATCCCTCGCCGAAATCGAAGGATGGGGCATGGTACCTTCCAACGGAATAATTGTTATCAACAACCATCGGGCAGCGTTGCTGGACACACCAATCAATGACGCACAAACGGAAACGCTGGTCAACTGGGTGGCAGACTCTTTGCATGCCAAAGTCACCACGTTTATCCCGAACCACTGGCACGGCGATTGTATTGGCGGACTGGGTTACCTGCAAAAGAAAGGTGTCCAATCATACGCAAACCAGATGACGATAGACCTCGCCAAGGAAAAAGGATTGCCCGTACCGGAACATGGATTCACCGATTCACTGACCGTCAGTCTGGACGGCACGCCTCTCCAATGTTATTATTTAGGAGGCGGACATGCGACCGACAATATCGTGGTTTGGCTGCCGACAGAGAATATCCTTTTTGGCGGATGTATGCTTAAAGACAACCAAACGACAAGCATCGGCAACATCTCGGACGCGGACGTGACGGCATGGCCGAAAACTCTCGATAAGGTAAAAGCCAAGTTCCCCTCGGCCCGCTACGTCGTGCCCGGACATGGCGACTATGGCGGAACCGAACTGATAGAGCATACCAAGCAGATCGTGAACCAATATATAGAAAGCACCTCAAAGCCATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35916","NCBI_taxonomy_name":"Bacteroides fragilis","NCBI_taxonomy_id":"817"}}}},"ARO_accession":"3006913","ARO_id":"45375","ARO_name":"CfiA21","CARD_short_name":"CfiA21","ARO_description":"CfiA21 is a CfiA beta-lactamase.","ARO_category":{"41364":{"category_aro_accession":"3004200","category_aro_cvterm_id":"41364","category_aro_name":"CfiA beta-lactamase","category_aro_description":"CfiA beta-lactamases are chromosomal-encoded carbapenemase commonly found in Bacteroides fragilis isolates.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4453":{"model_id":"4453","model_name":"CfiA22","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"6828":{"protein_sequence":{"accession":"WP_085562385.1","sequence":"MKTVFILISMLFPVAVMAQKSVKISDDISITQLSDKVYTYVSLAEIEGWGMVPSNGMIVINNHQAALLDTPINDAQTEMLVNWVTDSLHAKVTTFIPNHWHGDCIGGLGYLQKKGVRSYANQMTIDLAKEKGLPVPEHGFTDSLTVSLDGMPLQCYYLGGGHATDNIVVWLPTENILFGGCMLKDNQTTSIGNISDADVTAWPKTLDKVKAKFPSARYVVPGHGNYGGTELIEHTKQIVNQYIESTSKP"},"dna_sequence":{"accession":"NG_054668.1","fmin":"0","fmax":"750","strand":"+","sequence":"ATGAAAACAGTATTTATCCTTATCTCCATGCTTTTCCCTGTCGCAGTTATGGCACAGAAAAGCGTAAAAATATCCGATGATATCAGTATCACCCAACTCTCGGACAAAGTGTACACTTATGTATCCCTCGCCGAAATCGAAGGATGGGGTATGGTACCTTCCAACGGGATGATTGTTATCAACAACCACCAGGCAGCGTTGCTGGACACACCGATCAATGACGCACAAACGGAAATGCTGGTCAACTGGGTGACAGACTCTTTGCATGCCAAAGTCACCACGTTTATCCCGAACCACTGGCACGGCGATTGTATTGGCGGACTGGGTTACCTGCAAAAGAAAGGTGTCCGATCATACGCGAACCAGATGACGATAGACCTCGCCAAGGAAAAAGGATTGCCCGTACCGGAACATGGATTCACCGATTCACTGACCGTCAGCTTGGACGGCATGCCTCTCCAATGCTATTATTTAGGAGGCGGGCATGCGACCGACAATATCGTGGTTTGGCTGCCGACAGAGAATATCCTTTTTGGCGGATGTATGCTTAAAGACAACCAGACGACAAGCATCGGCAACATCTCGGACGCGGACGTGACGGCATGGCCGAAAACTCTCGATAAGGTAAAAGCCAAGTTCCCCTCGGCCCGCTACGTCGTGCCCGGACATGGTAACTATGGCGGAACCGAACTGATAGAGCATACCAAGCAGATCGTGAACCAATATATAGAAAGCACTTCAAAGCCATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35916","NCBI_taxonomy_name":"Bacteroides fragilis","NCBI_taxonomy_id":"817"}}}},"ARO_accession":"3006914","ARO_id":"45376","ARO_name":"CfiA22","CARD_short_name":"CfiA22","ARO_description":"CfiA22 is a CfiA beta-lactamase.","ARO_category":{"41364":{"category_aro_accession":"3004200","category_aro_cvterm_id":"41364","category_aro_name":"CfiA beta-lactamase","category_aro_description":"CfiA beta-lactamases are chromosomal-encoded carbapenemase commonly found in Bacteroides fragilis isolates.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4454":{"model_id":"4454","model_name":"CfiA23","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"6829":{"protein_sequence":{"accession":"WP_085562386.1","sequence":"MKTVFILISMLFPVAVMAQKSVKISDDISITQLSDKVYTYVSLAEIEGWGMVPSNGMIVINNHQAALLDTPINDAQTEMLVNWVTDSLHAKVTTFIPNHWHGDCIGGLGYLQKKGVQSYANQMTIDLAKEKGLPVPEHGFTDSLTVSLDGMPLQCYYLGGGHATDNIVVWLPTENILFGGCMLKDNQATSIGNISDADVTAWPKTLDKVKAKFPSARYVVPGHGNYGGTELIEHTKQIVNQYIESTSKP"},"dna_sequence":{"accession":"NG_054669.1","fmin":"0","fmax":"750","strand":"+","sequence":"ATGAAAACAGTATTTATCCTTATCTCCATGCTTTTCCCTGTCGCAGTTATGGCACAGAAAAGCGTAAAAATATCCGATGATATCAGTATCACCCAACTCTCGGACAAAGTGTACACTTATGTATCCCTCGCCGAAATCGAAGGATGGGGTATGGTACCTTCCAACGGGATGATTGTTATCAACAACCACCAGGCAGCGTTGCTGGACACACCGATCAATGACGCACAAACGGAAATGCTGGTCAACTGGGTGACAGACTCTTTGCATGCCAAAGTCACCACGTTTATCCCGAACCACTGGCACGGCGATTGTATTGGAGGACTGGGTTACCTGCAAAAGAAAGGTGTCCAATCATACGCGAACCAGATGACGATAGACCTCGCCAAGGAAAAAGGATTGCCCGTACCGGAACATGGATTCACCGATTCACTGACCGTCAGCCTGGACGGCATGCCTCTCCAATGCTATTATTTAGGAGGCGGACATGCGACCGACAATATCGTGGTTTGGCTGCCGACAGAGAATATCCTTTTTGGTGGATGTATGCTTAAAGACAACCAGGCGACAAGCATCGGCAACATCTCGGACGCGGACGTGACGGCATGGCCGAAAACTCTCGATAAGGTAAAAGCCAAGTTCCCCTCAGCCCGCTACGTCGTGCCCGGACATGGTAACTATGGCGGAACCGAACTGATAGAGCATACCAAGCAGATCGTGAACCAATATATAGAAAGCACCTCAAAACCATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35916","NCBI_taxonomy_name":"Bacteroides fragilis","NCBI_taxonomy_id":"817"}}}},"ARO_accession":"3006915","ARO_id":"45377","ARO_name":"CfiA23","CARD_short_name":"CfiA23","ARO_description":"CfiA23 is a CfiA beta-lactamase.","ARO_category":{"41364":{"category_aro_accession":"3004200","category_aro_cvterm_id":"41364","category_aro_name":"CfiA beta-lactamase","category_aro_description":"CfiA beta-lactamases are chromosomal-encoded carbapenemase commonly found in Bacteroides fragilis isolates.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4455":{"model_id":"4455","model_name":"CfiA24","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"6830":{"protein_sequence":{"accession":"WP_085562387.1","sequence":"MKTVFILISMLFPVAVMAQKSVKISDDISITQLSDKVYTYVSLAEIEGWGMVPSNGIIVINNHRAALLDTPINDAQTETLVNWVTDSLHAKVTTFIPNHWHGDCIGGLGYLQKKGVQSYANQMTIDLAKEKGLPVPEHGFTDSLTVSLDGMPLQCYYLGGGHATDNIVVWLPTENILFGGCMLKDNQTTSIGNISDADVTAWPKTLDKVKAKFPSARYVVPGHGDYGGTELIEHTKQIVNQYIESTSKP"},"dna_sequence":{"accession":"NG_054670.1","fmin":"0","fmax":"750","strand":"+","sequence":"ATGAAAACAGTATTTATCCTTATCTCCATGCTTTTCCCTGTCGCAGTTATGGCACAGAAAAGCGTAAAAATATCCGATGATATCAGTATCACCCAACTCTCGGACAAAGTGTACACTTATGTATCCCTCGCCGAAATCGAAGGATGGGGCATGGTACCTTCCAACGGAATAATTGTTATCAACAACCATCGGGCAGCGTTGCTGGACACACCGATCAATGACGCACAAACGGAAACGCTGGTCAACTGGGTGACAGACTCTTTGCATGCCAAAGTCACCACGTTTATCCCGAACCACTGGCACGGCGATTGTATTGGCGGACTGGGTTACCTGCAAAAGAAAGGTGTCCAATCATACGCAAACCAGATGACGATAGACCTCGCCAAGGAAAAAGGATTGCCCGTACCGGAACATGGATTCACCGATTCACTGACCGTCAGTCTGGACGGCATGCCTCTCCAATGTTATTATTTAGGAGGCGGACATGCGACCGACAATATCGTGGTTTGGCTGCCGACAGAGAATATCCTTTTTGGCGGATGTATGCTTAAAGACAACCAAACGACAAGCATCGGCAACATCTCGGACGCGGACGTGACGGCATGGCCGAAAACTCTCGATAAGGTAAAAGCCAAGTTCCCCTCGGCCCGCTACGTCGTGCCCGGACATGGCGACTATGGCGGAACCGAACTGATAGAGCATACCAAGCAGATCGTGAACCAATATATAGAAAGCACCTCAAAGCCATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35916","NCBI_taxonomy_name":"Bacteroides fragilis","NCBI_taxonomy_id":"817"}}}},"ARO_accession":"3006916","ARO_id":"45378","ARO_name":"CfiA24","CARD_short_name":"CfiA24","ARO_description":"CfiA24 is a CfiA beta-lactamase.","ARO_category":{"41364":{"category_aro_accession":"3004200","category_aro_cvterm_id":"41364","category_aro_name":"CfiA beta-lactamase","category_aro_description":"CfiA beta-lactamases are chromosomal-encoded carbapenemase commonly found in Bacteroides fragilis isolates.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4456":{"model_id":"4456","model_name":"CfiA26","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"6831":{"protein_sequence":{"accession":"WP_197749417.1","sequence":"MKTVFILISMLFPVAVMAQKSVKISDDISITQLSDKVYTYVSLAEIEGWGMVPSNGMIVINNHQAALLDTPINDAQTETLVNWVTDSLHAKVTTFIPNHWHSDCIGGLGYLQKKGVQSYANQMTIDLAKEKGLPVPEHGFTDSLTVSLDGMPLQCYYLGGGHATDNIVVWLPTENILFGGCMLKDNQATSIGNISDADVTAWPKTLDKVKAKFPSARYVVPGHGDYGGTELIEHTKQIVNQYIESTSKP"},"dna_sequence":{"accession":"NG_071227.1","fmin":"0","fmax":"750","strand":"+","sequence":"ATGAAAACAGTATTTATCCTTATCTCCATGCTTTTCCCTGTCGCAGTTATGGCACAGAAAAGCGTAAAAATATCCGATGATATCAGTATCACCCAACTCTCGGACAAAGTGTACACTTATGTATCCCTCGCCGAAATCGAAGGATGGGGCATGGTACCTTCCAACGGGATGATTGTTATCAACAACCATCAGGCAGCGTTGCTGGACACACCGATCAATGACGCACAAACGGAAACGCTGGTCAACTGGGTGACAGACTCTTTGCATGCCAAAGTCACCACGTTTATCCCGAACCACTGGCACAGCGATTGTATTGGAGGACTGGGTTACCTGCAAAAGAAAGGTGTCCAATCATACGCAAACCAGATGACGATAGACCTCGCCAAGGAAAAAGGGTTGCCCGTACCGGAACATGGATTCACCGATTCACTGACCGTCAGTCTGGACGGCATGCCTCTCCAATGCTATTATTTAGGAGGCGGGCATGCGACCGACAATATCGTGGTTTGGCTGCCGACAGAGAATATCCTTTTTGGCGGATGTATGCTTAAAGACAACCAGGCGACAAGCATCGGCAACATCTCGGACGCAGACGTGACGGCATGGCCGAAAACTCTCGATAAGGTAAAAGCCAAGTTCCCCTCGGCCCGCTACGTCGTGCCCGGACATGGCGACTATGGCGGAACCGAACTGATAGAGCATACCAAGCAGATCGTGAACCAATATATAGAAAGCACCTCAAAGCCATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35916","NCBI_taxonomy_name":"Bacteroides fragilis","NCBI_taxonomy_id":"817"}}}},"ARO_accession":"3006917","ARO_id":"45379","ARO_name":"CfiA26","CARD_short_name":"CfiA26","ARO_description":"CfiA26 is a CfiA beta-lactamase.","ARO_category":{"41364":{"category_aro_accession":"3004200","category_aro_cvterm_id":"41364","category_aro_name":"CfiA beta-lactamase","category_aro_description":"CfiA beta-lactamases are chromosomal-encoded carbapenemase commonly found in Bacteroides fragilis isolates.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4457":{"model_id":"4457","model_name":"CfiA27","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"6832":{"protein_sequence":{"accession":"WP_197749418.1","sequence":"MKTVFILISMLFPVAVMAQKSVKISDDISITQLSDKVYTYVSLAEIEGWGMVPSNGMIVINNHQAALLDTPINDAQTEMLVNWVTDSLHAKVTTFIPNHWHGDCIGGLGYLQRKGVQSYANQMTIDLAKEKGLPVPEHGFTDSLTVSLDGMPLQCYYLGGGHATDNIVVWLPTENILFGGCMLKDNQTTSIGNISDADVTAWPKTLDKVKAKFPSARYVVPGHGNYGGTELIEHTKQIVNQYIESTSKP"},"dna_sequence":{"accession":"NG_071228.1","fmin":"0","fmax":"750","strand":"+","sequence":"ATGAAAACAGTATTTATCCTTATCTCCATGCTTTTCCCTGTCGCAGTTATGGCACAGAAAAGCGTAAAAATATCCGATGACATCAGTATCACCCAACTCTCGGACAAAGTGTACACTTATGTATCCCTCGCCGAAATCGAAGGATGGGGTATGGTACCTTCCAACGGGATGATTGTTATCAACAACCACCAGGCAGCGTTGCTGGACACACCGATCAATGACGCACAAACGGAAATGCTGGTCAACTGGGTGACAGACTCTTTGCATGCCAAAGTCACCACGTTTATCCCGAACCACTGGCACGGCGATTGTATTGGCGGACTGGGTTACCTGCAAAGGAAAGGTGTCCAATCATACGCGAACCAGATGACGATAGACCTCGCCAAGGAAAAAGGGTTGCCCGTACCGGAACATGGATTCACCGATTCACTGACCGTCAGCTTGGACGGCATGCCTCTCCAATGCTATTATTTAGGAGGCGGGCATGCGACCGACAATATCGTGGTTTGGCTGCCGACAGAGAATATCCTTTTTGGCGGATGTATGCTTAAAGACAACCAGACGACAAGCATCGGCAACATCTCGGACGCGGACGTGACGGCATGGCCGAAAACTCTCGATAAGGTAAAAGCCAAGTTCCCCTCGGCCCGCTACGTCGTGCCCGGACATGGTAACTATGGCGGAACCGAACTGATAGAGCATACCAAGCAGATCGTGAACCAATATATAGAAAGCACTTCAAAGCCATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35916","NCBI_taxonomy_name":"Bacteroides fragilis","NCBI_taxonomy_id":"817"}}}},"ARO_accession":"3006918","ARO_id":"45380","ARO_name":"CfiA27","CARD_short_name":"CfiA27","ARO_description":"CfiA27 is a CfiA beta-lactamase.","ARO_category":{"41364":{"category_aro_accession":"3004200","category_aro_cvterm_id":"41364","category_aro_name":"CfiA beta-lactamase","category_aro_description":"CfiA beta-lactamases are chromosomal-encoded carbapenemase commonly found in Bacteroides fragilis isolates.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4458":{"model_id":"4458","model_name":"CfiA4","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"6833":{"protein_sequence":{"accession":"WP_005821510.1","sequence":"MKTVFILISMLFPVAVMAQKSVKISDDISITQLSDKVYTYVSLAEIEGWGMVPSNGMIVINNHQAALLDTPINDAQTETLVNWVTDSLHAKVTTFIPNHWHGDCIGGLGYLQKKGVQSYANQMTIDLAKEKGLPVPEHGFTDSLTVSLDGMPLQCYYLGGGHATDNIVVWLPTENILFGGCMLKDNQTTSIGNISDADVTAWPKTLDKVKAKFPSARYVVPGHGNYGGTELIEHTKQIVNQYIESTSKP"},"dna_sequence":{"accession":"NG_050392.1","fmin":"0","fmax":"750","strand":"+","sequence":"ATGAAAACAGTATTTATCCTTATCTCCATGCTTTTCCCTGTCGCAGTTATGGCACAGAAAAGCGTAAAAATATCCGATGACATCAGTATCACCCAACTCTCGGACAAAGTGTACACTTATGTATCCCTCGCCGAAATCGAAGGATGGGGTATGGTACCTTCCAACGGGATGATTGTTATCAACAACCACCAGGCAGCGTTGCTGGACACACCGATCAATGACGCACAAACGGAAACGCTGGTCAACTGGGTGACAGACTCTTTGCATGCCAAAGTCACCACGTTTATCCCGAACCACTGGCACGGCGATTGTATTGGCGGACTGGGTTACCTGCAAAAGAAAGGTGTCCAATCATACGCGAACCAGATGACGATAGACCTCGCCAAGGAAAAAGGATTGCCCGTACCGGAACATGGATTCACCGATTCACTGACCGTCAGTCTGGACGGCATGCCTCTCCAATGCTATTATTTAGGAGGCGGGCATGCGACCGACAATATCGTGGTTTGGCTGCCGACAGAGAATATCCTTTTTGGCGGATGTATGCTTAAAGACAACCAGACGACAAGCATCGGCAACATCTCGGACGCGGACGTGACGGCATGGCCGAAAACTCTCGATAAGGTAAAAGCCAAGTTCCCCTCGGCCCGCTACGTCGTGCCCGGACATGGTAACTATGGCGGAACCGAACTGATAGAGCATACCAAGCAGATCGTGAACCAATATATAGAAAGCACTTCAAAGCCATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37050","NCBI_taxonomy_name":"Bacteroides","NCBI_taxonomy_id":"816"}}}},"ARO_accession":"3006919","ARO_id":"45381","ARO_name":"CfiA4","CARD_short_name":"CfiA4","ARO_description":"CfiA4 is a CfiA beta-lactamase.","ARO_category":{"41364":{"category_aro_accession":"3004200","category_aro_cvterm_id":"41364","category_aro_name":"CfiA beta-lactamase","category_aro_description":"CfiA beta-lactamases are chromosomal-encoded carbapenemase commonly found in Bacteroides fragilis isolates.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4459":{"model_id":"4459","model_name":"CfiA8","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"6834":{"protein_sequence":{"accession":"WP_063865206.1","sequence":"MKTVFILISMLFPVAVMAQKSVKISDDISITQLSDKVYTYVSLAEIEGWGMVPSNGMIVINNHQAALLDTPINDAQTETLVNWVADSLHAKVTTFIPNHWHGDCIGGLGYLQKKGVQSYANQMTIDLAKEKGLPVPEHGFTDSLTVSLDGMPLQCYYLGGGHATDNIVVWLPTENILFGGCMLKDNQATSIGNISDADVTAWPKTLDKVKAKFPSARYVVPGHGDYGGTELIEHTKQIVNQYIESTLKP"},"dna_sequence":{"accession":"NG_050393.1","fmin":"0","fmax":"750","strand":"+","sequence":"ATGAAAACAGTATTTATCCTTATCTCCATGCTTTTCCCTGTCGCAGTTATGGCACAGAAAAGCGTAAAAATATCCGATGATATCAGTATCACCCAACTCTCGGACAAAGTGTACACTTATGTATCCCTCGCCGAAATCGAAGGATGGGGTATGGTACCTTCCAACGGAATGATTGTTATCAACAACCATCAGGCAGCGTTGCTGGACACACCGATCAATGACGCACAAACGGAAACGCTGGTCAACTGGGTAGCGGACTCTTTGCATGCCAAAGTCACCACGTTTATCCCGAACCACTGGCACGGCGATTGTATTGGCGGACTGGGTTACCTGCAAAAGAAAGGTGTCCAATCATACGCAAACCAGATGACGATAGACCTCGCCAAGGAAAAAGGATTGCCCGTACCGGAACATGGATTCACCGATTCACTGACCGTCAGCTTGGACGGCATGCCTCTCCAATGTTATTATTTAGGAGGCGGACATGCGACCGACAATATCGTGGTTTGGCTGCCGACAGAGAATATCCTTTTTGGCGGATGTATGCTTAAAGACAACCAGGCGACAAGCATCGGCAACATCTCGGACGCGGACGTGACGGCATGGCCGAAAACTCTCGATAAGGTAAAAGCCAAGTTCCCCTCGGCCCGCTACGTCGTGCCCGGACATGGCGACTATGGCGGAACCGAACTGATAGAGCATACCAAGCAGATCGTGAACCAATATATAGAAAGCACCTTAAAGCCATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35916","NCBI_taxonomy_name":"Bacteroides fragilis","NCBI_taxonomy_id":"817"}}}},"ARO_accession":"3006920","ARO_id":"45382","ARO_name":"CfiA8","CARD_short_name":"CfiA8","ARO_description":"CfiA8 is a CfiA beta-lactamase.","ARO_category":{"41364":{"category_aro_accession":"3004200","category_aro_cvterm_id":"41364","category_aro_name":"CfiA beta-lactamase","category_aro_description":"CfiA beta-lactamases are chromosomal-encoded carbapenemase commonly found in Bacteroides fragilis isolates.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4460":{"model_id":"4460","model_name":"CfiA9","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"6835":{"protein_sequence":{"accession":"WP_063865207.1","sequence":"MKTVFILISMLFPVAVMAQKSVKISDDISITQLSDKVYTYVSLAEIEGWGMVPSNGMIVINNYQAALLDTPINDAQTETLVNWVADSLHAKVTTFIPNHWHGDCIGGLGYLQKKGVQSYANQMTIDLAKEKGLPVPEHGFTDSLTVSLDGMPLQCYYLGGGHATDNIVVWLPTENILFGGCMLKDNQATSIGNISDADVTAWPKTLDKVKAKFPSARYVVPGHGDYGGTELIEHTKQIVNQYIESTSKP"},"dna_sequence":{"accession":"NG_050394.1","fmin":"0","fmax":"750","strand":"+","sequence":"ATGAAAACAGTATTTATCCTTATCTCCATGCTTTTCCCTGTCGCAGTTATGGCACAGAAAAGCGTAAAAATATCCGATGATATCAGTATCACCCAACTCTCGGACAAAGTGTACACTTATGTATCCCTCGCCGAAATCGAAGGATGGGGTATGGTACCTTCCAACGGAATGATTGTTATCAACAACTATCAGGCAGCGTTGCTGGACACACCGATCAATGACGCACAAACGGAAACGCTGGTCAACTGGGTAGCGGACTCTTTGCATGCTAAAGTCACCACGTTTATCCCGAACCACTGGCACGGCGATTGTATTGGCGGACTGGGTTACCTGCAAAAGAAAGGTGTCCAATCATACGCAAACCAGATGACGATAGACCTCGCCAAGGAAAAAGGATTGCCCGTACCGGAACATGGATTCACCGATTCACTGACCGTCAGTCTGGACGGCATGCCTCTCCAATGTTATTATTTAGGAGGCGGACATGCGACCGACAATATCGTGGTTTGGCTGCCGACAGAGAATATCCTTTTTGGCGGATGTATGCTTAAAGACAACCAGGCGACAAGCATCGGCAACATCTCGGACGCGGACGTGACGGCATGGCCGAAAACTCTCGATAAGGTAAAAGCCAAGTTCCCCTCGGCCCGCTACGTCGTGCCCGGACATGGCGACTATGGCGGAACCGAACTGATAGAGCATACCAAGCAGATCGTGAACCAATATATAGAAAGCACCTCAAAGCCATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35916","NCBI_taxonomy_name":"Bacteroides fragilis","NCBI_taxonomy_id":"817"}}}},"ARO_accession":"3006921","ARO_id":"45383","ARO_name":"CfiA9","CARD_short_name":"CfiA9","ARO_description":"CfiA9 is a CfiA beta-lactamase.","ARO_category":{"41364":{"category_aro_accession":"3004200","category_aro_cvterm_id":"41364","category_aro_name":"CfiA beta-lactamase","category_aro_description":"CfiA beta-lactamases are chromosomal-encoded carbapenemase commonly found in Bacteroides fragilis isolates.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4461":{"model_id":"4461","model_name":"CMA-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6836":{"protein_sequence":{"accession":"WP_032974004.1","sequence":"MKSKVSALLMMIVLAGHAQAAPVAPPDAVVKPLMARYQIPGMAVAVSVNGETHFWHYGVASKATRKPVDEKTLFEIGSLSKTFTATLASGAQHEGKLDFSAPASQYLPALKGSAFDHVTLLNLATHTAGTPLFVPDAVKNTAQLMAWYRAWQPEKPVGTERVYSNLGIGLLGMITAKALDKPFSEAMEQGLLKGFGMTHTFINVPDAAMDDYAQGYNKDDKPVRVTPGPLDAESYGLKSGSADLLRYLQIQLGEQEVAPGWRQAINATHNGYYRSGEFTQGMMWEYYPWPSPLSRLVEGNSSQRIMKGLAATAIVPPQPAPEAAWYNKTGSTNGFSTYAVFIPEKRIALIMLANKWFPNDDRVKAAYAIIQQLDK"},"dna_sequence":{"accession":"NG_062222.1","fmin":"100","fmax":"1228","strand":"+","sequence":"ATGAAAAGCAAAGTCAGTGCGCTGTTAATGATGATAGTTCTCGCGGGCCATGCGCAGGCCGCGCCCGTTGCGCCACCGGATGCGGTCGTTAAGCCGTTGATGGCGCGTTACCAGATCCCGGGCATGGCGGTGGCGGTGTCGGTCAATGGCGAAACGCATTTCTGGCACTACGGCGTGGCGTCAAAAGCGACGCGCAAGCCGGTGGATGAAAAAACGCTTTTCGAAATCGGCTCGCTCAGTAAAACCTTTACCGCGACGCTCGCAAGCGGGGCGCAGCATGAGGGGAAACTGGATTTCAGCGCGCCCGCCAGCCAGTATCTTCCTGCACTGAAAGGCAGCGCGTTCGACCACGTGACGCTGCTGAACCTCGCCACGCACACCGCGGGAACGCCGCTCTTTGTGCCGGATGCGGTGAAAAACACCGCGCAGCTGATGGCATGGTATCGCGCCTGGCAGCCTGAAAAGCCGGTCGGCACCGAGCGCGTATACTCGAATCTCGGGATCGGGCTGCTCGGGATGATTACCGCGAAGGCGCTCGATAAACCGTTCAGCGAGGCGATGGAGCAGGGGCTGCTTAAGGGTTTCGGCATGACGCACACCTTTATCAACGTGCCGGATGCCGCGATGGACGACTACGCCCAGGGCTATAACAAAGACGACAAACCGGTGCGGGTGACGCCCGGCCCGCTGGATGCTGAATCCTATGGGCTGAAGTCCGGCAGCGCCGACCTGCTGCGTTATCTGCAAATTCAGCTTGGCGAGCAGGAGGTGGCGCCAGGCTGGCGTCAGGCGATTAACGCCACGCATAACGGCTACTACCGCAGCGGTGAGTTCACACAGGGAATGATGTGGGAATATTATCCGTGGCCATCGCCGCTCTCGCGCCTTGTTGAAGGCAACAGCAGCCAGCGCATCATGAAAGGGCTCGCGGCCACCGCTATTGTGCCGCCGCAGCCCGCACCAGAGGCCGCGTGGTATAACAAAACCGGTTCGACCAACGGGTTTTCCACTTACGCGGTGTTTATCCCTGAAAAGCGTATCGCGCTGATTATGCTCGCCAACAAGTGGTTCCCGAATGACGACCGCGTGAAGGCGGCGTATGCGATTATTCAGCAGCTTGATAAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3006922","ARO_id":"45384","ARO_name":"CMA-1","CARD_short_name":"CMA-1","ARO_description":"CMA-1 is a CMA beta-lactamase.","ARO_category":{"43857":{"category_aro_accession":"3005397","category_aro_cvterm_id":"43857","category_aro_name":"CMA beta-lactamase","category_aro_description":"CMA beta-lactamases are class C beta-lactamases found in Cronobacter malonaticus.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4462":{"model_id":"4462","model_name":"CMA-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6837":{"protein_sequence":{"accession":"WP_105620838.1","sequence":"MKSKVSALLMMIVLAGHAQAAPVAPPDAVVKPLMARYQIPGMAVAVSVNGETHFWHYGVASKATRKPVDEKTLFEIGSLSKTFTATLASAAQQEGKLDFSAPASQYLPALKGSAFDHVTLLNLATHTSGTPLFVPDAVKNTAQLMAWYRAWQPEKPVGTERVYSNLGIGLLGMITAKALDKPFSEAMEQGLLRDFGMTHTFINVPDAAMDDYAQGYNKDDKPVRVTPGPLDAESYGLKSGSADLLRYLQIQLGEQEVAPRWRQAINATHNGYYRSGEFTQGMMWEYYPWPSPLSRLVEGNSSQRIMKGLAATAIVPPQPAPEAAWYNKTGSTNGFSSYAVFIPEKRIALIMLANKWFPNDDRVKAAYAIIQQLDK"},"dna_sequence":{"accession":"NG_062212.1","fmin":"100","fmax":"1228","strand":"+","sequence":"ATGAAAAGCAAAGTCAGTGCGCTGTTAATGATGATAGTTCTCGCGGGCCATGCGCAGGCCGCGCCCGTTGCGCCACCGGATGCGGTCGTTAAGCCGTTGATGGCGCGTTACCAGATCCCGGGCATGGCGGTGGCGGTGTCGGTCAATGGCGAAACGCATTTCTGGCACTACGGCGTGGCGTCAAAAGCGACGCGCAAGCCGGTGGATGAAAAAACGCTTTTCGAAATCGGCTCGCTCAGTAAAACCTTTACCGCGACGCTCGCAAGCGCGGCGCAGCAAGAGGGCAAACTGGATTTCAGCGCGCCCGCCAGCCAGTATCTTCCTGCACTGAAAGGCAGCGCGTTCGACCACGTGACGCTGCTGAACCTTGCCACGCACACCTCGGGAACGCCGCTGTTTGTGCCGGATGCGGTGAAAAACACCGCGCAGCTGATGGCCTGGTATCGCGCCTGGCAACCTGAAAAGCCGGTCGGCACCGAGCGCGTATACTCGAATCTCGGGATCGGGCTGCTCGGGATGATTACCGCGAAGGCGCTCGATAAACCGTTCAGCGAGGCGATGGAGCAGGGGCTGCTCAGGGATTTCGGCATGACGCACACCTTTATCAACGTGCCGGATGCCGCGATGGACGACTACGCCCAGGGCTATAACAAAGACGACAAACCGGTGCGGGTGACGCCCGGCCCGCTGGATGCTGAATCCTATGGGCTGAAATCCGGCAGCGCCGACCTGCTGCGTTATCTGCAAATCCAGCTTGGCGAGCAGGAGGTGGCCCCTCGCTGGCGTCAGGCGATTAACGCCACGCACAACGGCTACTACCGCAGCGGTGAGTTCACACAGGGAATGATGTGGGAATATTATCCGTGGCCATCGCCGCTCTCGCGCCTTGTTGAAGGCAACAGCAGCCAGCGCATCATGAAAGGGCTCGCGGCCACCGCTATTGTGCCGCCGCAGCCCGCACCAGAGGCCGCGTGGTATAACAAAACCGGTTCGACCAACGGGTTTTCCTCTTACGCGGTGTTTATCCCTGAAAAGCGTATCGCGCTGATTATGCTCGCCAACAAGTGGTTCCCGAATGACGACCGCGTGAAGGCGGCGTATGCGATTATTCAGCAGCTTGATAAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3006923","ARO_id":"45385","ARO_name":"CMA-2","CARD_short_name":"CMA-2","ARO_description":"CMA-2 is a CMA beta-lactamase.","ARO_category":{"43857":{"category_aro_accession":"3005397","category_aro_cvterm_id":"43857","category_aro_name":"CMA beta-lactamase","category_aro_description":"CMA beta-lactamases are class C beta-lactamases found in Cronobacter malonaticus.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4463":{"model_id":"4463","model_name":"CME-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"6838":{"protein_sequence":{"accession":"WP_063859570.1","sequence":"MKKIILLFILTSQLVLAQHTSILNDINAVTKDKKATVAVSVLGIENDFQFSNANGNLKMPMLSVFKFHIALAVLNQVDKGNLTLDQKILIKKSDLLENTWSPLREKYPDGNVELPLSEIITYTVAQSDNNGCDILLRLIGGTKTVQKLMDVNGVKNFQIKYNEEEMHKNDVKTLYANYTTTASMVKTLKAFYKGMFLSKRSTIFLMDIMTKTNTGMSKLPGLLPKVRMARKTGSSGKMKNGLTIAENDSGIVTLANGKHYAIAVFVKDSMEGEEVNCGIIAQVSKIVWDALNKKNKP"},"dna_sequence":{"accession":"NG_048765.1","fmin":"0","fmax":"894","strand":"+","sequence":"ATGAAAAAAATTATACTCCTATTTATCTTGACAAGCCAGTTGGTGCTTGCTCAACATACTTCAATATTAAATGATATAAATGCTGTTACCAAAGACAAGAAAGCCACAGTAGCTGTTTCTGTTTTGGGGATAGAAAATGATTTTCAGTTTAGTAACGCCAATGGTAATTTGAAAATGCCGATGCTGAGTGTTTTTAAATTTCATATTGCATTGGCGGTTCTAAATCAGGTAGACAAAGGTAACCTTACCTTGGATCAGAAAATACTGATTAAAAAATCGGATCTATTAGAAAATACATGGTCACCACTTCGTGAGAAGTATCCGGATGGAAATGTAGAACTTCCTTTAAGCGAAATTATTACTTATACTGTAGCCCAAAGTGACAACAACGGATGCGACATACTATTAAGGCTAATTGGCGGGACTAAAACTGTTCAGAAATTAATGGATGTGAATGGTGTAAAAAACTTTCAGATAAAATATAATGAGGAAGAAATGCATAAAAATGATGTAAAAACTCTTTATGCAAATTACACAACTACAGCATCTATGGTAAAAACTCTGAAAGCGTTCTATAAAGGAATGTTTTTATCAAAAAGATCCACAATTTTTCTAATGGATATTATGACTAAAACCAATACCGGAATGTCAAAGCTTCCGGGCTTGCTGCCAAAAGTTAGAATGGCCAGAAAAACAGGTTCTTCGGGTAAAATGAAAAACGGATTAACGATTGCTGAGAACGATTCAGGAATTGTAACTTTAGCAAATGGTAAACATTATGCAATTGCAGTATTTGTAAAGGACTCTATGGAAGGTGAGGAAGTCAATTGTGGAATCATTGCCCAGGTCTCGAAAATTGTCTGGGATGCTTTAAATAAAAAAAATAAACCCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36960","NCBI_taxonomy_name":"Elizabethkingia meningoseptica","NCBI_taxonomy_id":"238"}}}},"ARO_accession":"3006155","ARO_id":"44617","ARO_name":"CME-2","CARD_short_name":"CME-2","ARO_description":"CME-2 is a CME beta-lactamase.","ARO_category":{"42889":{"category_aro_accession":"3004774","category_aro_cvterm_id":"42889","category_aro_name":"CME beta-lactamase","category_aro_description":"CME is a class A beta-lactamase gene family belonging to Chryseobacterium meningosepticum.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4464":{"model_id":"4464","model_name":"CMH-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"6839":{"protein_sequence":{"accession":"WP_063859588.1","sequence":"MMTKSLSCALLLSVACSAFAAPMSEKQLADVVERTVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSVSKTFTGVLGGDAIARKEISLADPVTKYWPELTGKQWQGIRLLDLATYTAGGLPLQVPDAVTDNASLLRFYQSWQPKWAPGTTRLYANTSIGLFGSLAVKPSGMRFEEAMTERVFKPLKLNHTWINVPHAEESHYAWGYREGKAVHVSPGMLDAEAYGVKSNVKDMASWVMANMAPETLPQSTLQQGIALAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVDGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANKSYPNPVRVETAYRILDALQ"},"dna_sequence":{"accession":"NG_048767.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGACAAAATCCCTAAGCTGCGCGCTGCTGCTCAGCGTTGCCTGCTCTGCTTTTGCCGCGCCGATGTCAGAAAAACAGCTGGCTGACGTCGTGGAACGTACCGTTACGCCTCTGATGAAGGCGCAGGCCATACCCGGAATGGCCGTGGCCGTCATTTATCAGGGCCAGCCACACTATTTTACTTTCGGTAAAGCAGACGTTGCGGCGAATAAGCCCGTCACGCCGCAAACCTTATTTGAGCTGGGCTCCGTCAGCAAAACCTTCACCGGCGTGCTGGGTGGCGATGCCATTGCCCGCAAAGAGATTTCGCTGGCCGACCCGGTCACAAAATATTGGCCTGAATTGACGGGCAAGCAGTGGCAAGGCATTCGCCTGCTAGACCTGGCAACCTATACCGCAGGTGGATTGCCGTTGCAGGTGCCGGATGCTGTCACCGATAACGCCTCTCTGCTGCGTTTCTACCAGTCCTGGCAGCCAAAGTGGGCCCCGGGTACTACGCGTCTGTACGCCAACACCAGCATCGGTTTGTTTGGCTCACTGGCGGTTAAACCTTCCGGCATGCGCTTTGAGGAGGCCATGACGGAGCGGGTCTTTAAGCCCCTGAAACTCAACCATACGTGGATAAACGTTCCACACGCTGAAGAGTCGCACTACGCATGGGGTTATCGTGAGGGAAAAGCGGTCCACGTTTCGCCTGGTATGCTGGATGCAGAAGCCTATGGCGTGAAATCTAACGTCAAAGATATGGCGAGCTGGGTGATGGCCAATATGGCACCTGAGACACTCCCGCAGTCCACTCTGCAGCAGGGTATTGCGCTGGCGCAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAAGGGTTAGGCTGGGAGATGCTCAACTGGCCGGTCGACGCCAAAACCGTGGTGGATGGCAGCGATAATAAGGTCGCACTGGCGCCGTTGCCGGTCGCAGAAGTGAATCCTCCGGCTCCGCCAGTAAAAGCCTCCTGGGTGCATAAAACGGGCTCTACGGGTGGGTTTGGCAGCTACGTGGCGTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCAAATAAAAGCTATCCGAACCCGGTACGGGTGGAAACGGCTTACCGTATCCTCGACGCGCTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3006854","ARO_id":"45316","ARO_name":"CMH-2","CARD_short_name":"CMH-2","ARO_description":"CMH-2 is a CMH beta-lactamase.","ARO_category":{"42891":{"category_aro_accession":"3004776","category_aro_cvterm_id":"42891","category_aro_name":"CMH beta-lactamase","category_aro_description":"CMH is a class C beta-lactamase gene family belonging to Enterobacter cloacae.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4465":{"model_id":"4465","model_name":"CMH-3","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"6840":{"protein_sequence":{"accession":"WP_045295573.1","sequence":"MMKKSLSCALLLSVACSAFAAPMSEKQLADVVERTVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSVSKTFTGVLGGDAIARKEISLADPVTKYWPELTGKQWQGIRLLDLATYTAGGLPLQVPDDVTDNASLLRFYQSWQPKWAPGTTRLYANTSIGLFGSLAVKPSGMRFEQAMAERVFKPLKLNHTWINVPHAEEPNYAWGYREGKAVHVSPGMLDAEAYGVKSNVKDMASWVMANMAPETLPQSTLQQGIALAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVDGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANKSYPNPVRVETAYRILETLQ"},"dna_sequence":{"accession":"NG_050719.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCCCTAAGCTGCGCCCTGCTGCTCAGCGTTGCCTGCTCTGCTTTTGCCGCACCGATGTCAGAAAAACAGCTGGCTGACGTCGTGGAACGTACCGTTACGCCCCTGATGAAGGCGCAGGCCATACCCGGAATGGCCGTGGCCGTCATTTATCAGGGCCAGCCACACTATTTTACTTTCGGTAAAGCAGACGTCGCGGCGAATAAGCCCGTCACGCCGCAAACCTTATTTGAGCTGGGCTCCGTCAGCAAAACCTTCACCGGCGTGCTGGGTGGCGATGCCATTGCCCGCAAAGAGATTTCGCTGGCCGACCCGGTCACGAAATATTGGCCTGAATTGACGGGCAAGCAGTGGCAAGGCATTCGCCTGCTCGACCTGGCAACCTATACCGCAGGCGGATTGCCGTTGCAGGTACCGGATGATGTCACCGATAACGCCTCTCTGCTGCGTTTCTACCAGTCCTGGCAGCCAAAGTGGGCCCCGGGTACCACGCGTCTGTACGCCAACACCAGCATCGGCCTGTTTGGCTCACTGGCCGTTAAACCGTCCGGCATGCGCTTCGAGCAGGCCATGGCGGAGCGGGTCTTTAAGCCCCTGAAACTCAACCATACGTGGATAAACGTTCCACACGCTGAAGAGCCCAACTACGCATGGGGTTATCGTGAGGGAAAAGCGGTCCACGTTTCGCCTGGTATGCTGGATGCAGAAGCCTATGGTGTGAAATCTAACGTCAAAGATATGGCGAGCTGGGTGATGGCCAATATGGCACCTGAGACACTCCCGCAGTCCACTCTGCAGCAGGGTATTGCGCTGGCGCAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAAGGGTTAGGCTGGGAGATGCTCAACTGGCCGGTCGACGCCAAAACCGTGGTGGATGGCAGCGATAATAAGGTTGCACTGGCGCCGTTGCCGGTCGCAGAAGTGAATCCTCCGGCTCCGCCAGTAAAAGCCTCCTGGGTGCATAAAACGGGCTCTACGGGTGGGTTTGGCAGCTACGTGGCGTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCAAATAAAAGTTATCCGAACCCGGTACGGGTGGAAACGGCTTACCGTATTCTCGAGACGCTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3006855","ARO_id":"45317","ARO_name":"CMH-3","CARD_short_name":"CMH-3","ARO_description":"CMH-3 is a CMH beta-lactamase.","ARO_category":{"42891":{"category_aro_accession":"3004776","category_aro_cvterm_id":"42891","category_aro_name":"CMH beta-lactamase","category_aro_description":"CMH is a class C beta-lactamase gene family belonging to Enterobacter cloacae.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4466":{"model_id":"4466","model_name":"CMH-4","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"6841":{"protein_sequence":{"accession":"WP_013095270.1","sequence":"MMKKSLSCALLLSVACSAFAAPMSEKQLADVVERTVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSVSKTFTGVLGGDAIARKEISLADPVTKYWPELTGKQWQGIRLLDLATYTAGGLPLQVPDDVTDNASLLRFYQSWQPKWAPGTTRLYANTSIGLFGSLAVKPSGMRFEQAMAERVFKPLKLNHTWINVPHAEEPHYAWGYREGKAVHVSPGMLDAEAYGVKSNVKDMASWVMANMAPETLPQSTLQQGIALAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVDGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANKSYPNPVRVETAYRILDALQ"},"dna_sequence":{"accession":"NG_061416.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCCCTAAGCTGCGCCCTGCTGCTCAGCGTTGCCTGCTCTGCTTTTGCCGCGCCGATGTCAGAAAAACAGCTGGCTGACGTCGTGGAACGTACCGTTACGCCCCTGATGAAGGCGCAGGCCATACCCGGAATGGCCGTGGCCGTCATTTATCAGGGCCAGCCACACTATTTTACTTTCGGTAAAGCAGACGTCGCGGCGAATAAGCCCGTCACGCCGCAAACCTTATTTGAACTGGGCTCCGTCAGTAAAACCTTCACTGGCGTGCTGGGTGGCGATGCCATTGCCCGCAAAGAGATTTCGCTGGCCGACCCGGTCACGAAATATTGGCCTGAATTGACGGGCAAGCAGTGGCAAGGCATTCGCCTGCTCGACCTGGCAACCTATACGGCAGGCGGATTGCCGTTGCAGGTACCGGATGATGTTACCGATAACGCCTCTCTGCTGCGTTTCTACCAGTCCTGGCAGCCAAAGTGGGCCCCGGGTACCACGCGTCTGTACGCCAACACCAGCATCGGCCTGTTTGGCTCACTGGCCGTTAAACCGTCCGGCATGCGCTTCGAGCAGGCCATGGCGGAGCGGGTCTTTAAGCCCCTGAAACTCAACCATACGTGGATAAACGTTCCACACGCTGAAGAGCCGCACTACGCATGGGGTTATCGTGAGGGAAAAGCGGTCCACGTTTCGCCTGGTATGCTGGATGCAGAAGCCTATGGTGTGAAATCTAACGTCAAAGATATGGCGAGCTGGGTGATGGCCAATATGGCACCTGAGACACTCCCGCAGTCCACTCTGCAGCAGGGTATTGCGCTGGCGCAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAAGGGTTAGGCTGGGAGATGCTCAACTGGCCGGTCGATGCCAAAACCGTGGTGGATGGCAGCGACAATAAGGTCGCACTGGCGCCGTTGCCGGTCGCAGAAGTGAATCCTCCGGCTCCGCCAGTAAAAGCCTCCTGGGTGCATAAAACGGGCTCTACGGGTGGGTTTGGCAGCTACGTGGCGTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCAAATAAAAGCTATCCGAACCCGGTACGGGTGGAAACGGCTTACCGTATCCTCGACGCGCTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3006856","ARO_id":"45318","ARO_name":"CMH-4","CARD_short_name":"CMH-4","ARO_description":"CMH-4 is a CMH beta-lactamase.","ARO_category":{"42891":{"category_aro_accession":"3004776","category_aro_cvterm_id":"42891","category_aro_name":"CMH beta-lactamase","category_aro_description":"CMH is a class C beta-lactamase gene family belonging to Enterobacter cloacae.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4467":{"model_id":"4467","model_name":"CMH-5","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"6842":{"protein_sequence":{"accession":"WP_046887417.1","sequence":"MMKKSLSCALLLSVACSAFAAPMSEKQLANVVERNVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSVSKTFTGVLGGDTIARKEISLADPVTKYWPELTGKQWQGIRLLDLATYTAGGLPLQVPDAVTDNASLLRFYQSWQPKWAPGTTRLYANTSIGLFGSLTVKPSGMRFEEAMTERVFKPLKLNHTWINIPHAEEPHYAWGYREGKAVHVSPGMLDAEAYGVKSNVKDMASWVMANMAPETIQQPSLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVDGSDNKVALAPLPAAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANKSYPNPLRVETAYRILDTLQ"},"dna_sequence":{"accession":"NG_061417.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCCCTAAGCTGTGCACTGTTGCTCAGCGTTGCCTGCTCTGCCTTTGCCGCGCCAATGTCAGAAAAACAGCTGGCTAACGTCGTGGAACGTAACGTTACGCCCCTGATGAAAGCGCAGGCCATACCCGGTATGGCCGTGGCTGTCATTTATCAGGGTCAGCCGCACTATTTTACTTTTGGTAAAGCAGACGTCGCAGCGAATAAGCCTGTCACACCGCAAACCTTATTTGAGCTGGGCTCCGTCAGCAAAACTTTCACCGGGGTGCTGGGTGGCGATACCATTGCCCGCAAAGAGATCTCGCTGGCCGACCCGGTCACGAAATATTGGCCTGAATTGACGGGCAAGCAGTGGCAGGGCATTCGCCTGCTCGATCTGGCAACTTATACCGCTGGTGGATTGCCGTTGCAGGTACCGGATGCTGTCACCGATAACGCCTCTCTGCTGCGTTTCTACCAGTCCTGGCAGCCAAAGTGGGCCCCGGGTACTACGCGTCTGTACGCCAACACCAGCATCGGTTTGTTTGGCTCACTGACGGTTAAACCTTCCGGCATGCGCTTTGAGGAGGCCATGACGGAGCGGGTCTTTAAGCCCCTGAAACTCAATCATACGTGGATAAACATTCCACACGCTGAGGAGCCGCATTACGCATGGGGTTATCGTGAGGGTAAAGCGGTCCACGTTTCGCCGGGTATGCTGGATGCAGAAGCCTATGGCGTGAAATCTAATGTCAAAGATATGGCGAGCTGGGTGATGGCCAATATGGCACCGGAGACAATCCAGCAGCCCTCTCTGAAGCAGGGTATTGCGCTGGCGCAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAAGGGTTAGGCTGGGAGATGCTCAACTGGCCGGTCGACGCCAAAACCGTGGTGGATGGCAGCGACAATAAGGTTGCACTGGCGCCGTTACCGGCAGCAGAAGTGAATCCTCCGGCTCCGCCTGTGAAAGCCTCATGGGTGCATAAAACGGGCTCTACGGGGGGGTTTGGCAGCTACGTGGCGTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATAAAAGCTATCCGAACCCGCTACGGGTGGAAACGGCTTACCGTATCCTCGACACGCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3006857","ARO_id":"45319","ARO_name":"CMH-5","CARD_short_name":"CMH-5","ARO_description":"CMH-5 is a CMH beta-lactamase.","ARO_category":{"42891":{"category_aro_accession":"3004776","category_aro_cvterm_id":"42891","category_aro_name":"CMH beta-lactamase","category_aro_description":"CMH is a class C beta-lactamase gene family belonging to Enterobacter cloacae.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4468":{"model_id":"4468","model_name":"CMH-6","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"6843":{"protein_sequence":{"accession":"WP_156404645.1","sequence":"MMKKSLSCALLLSVACSAFAAPMSKKQLADVVERTVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSVSKTFTGVLGGDAIARKEISLADPVTKYWPELTGKQWQSIRLLDLATYTAGGLPLQVPDDVTDNVSLLRFYQSWQPKWAPGTTRLYANTSIGLFGSLAVKPSGMRFEQAMAERVFKPLKLNHTWINVPHAEEPHYAWGYREGKAVHVSPGMLDAEAYGVKSNVKDMASWVMANMAPETLPQSTLQQGIALAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVDGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANKSYPNPVRVETAYRILETLQ"},"dna_sequence":{"accession":"NG_067134.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCCCTAAGCTGCGCGCTGCTGCTCAGCGTTGCCTGCTCTGCTTTTGCCGCGCCGATGTCAAAAAAACAGCTGGCTGACGTCGTGGAACGTACCGTTACGCCCCTGATGAAGGCGCAGGCCATACCCGGAATGGCCGTGGCCGTCATTTATCAGGGCCAGCCACACTATTTTACTTTCGGTAAAGCAGACGTCGCGGCGAATAAGCCCGTCACGCCGCAAACCTTATTTGAGCTGGGCTCCGTCAGCAAAACCTTCACCGGCGTGCTGGGTGGCGATGCCATTGCCCGCAAAGAGATTTCGCTGGCCGACCCGGTCACGAAATATTGGCCTGAATTGACGGGCAAGCAGTGGCAAAGCATTCGCCTGCTAGACCTGGCAACCTATACCGCAGGCGGATTGCCGTTGCAGGTACCGGATGATGTCACCGATAACGTCTCTCTGCTGCGTTTCTACCAGTCCTGGCAGCCAAAGTGGGCCCCGGGTACCACGCGTCTGTACGCCAACACCAGCATCGGTTTGTTTGGCTCACTGGCCGTCAAACCGTCCGGCATGCGCTTCGAGCAGGCCATGGCGGAGCGGGTCTTTAAGCCCCTGAAACTCAACCATACGTGGATAAACGTTCCACACGCTGAAGAGCCGCACTACGCATGGGGTTATCGTGAGGGAAAAGCGGTCCACGTTTCGCCTGGTATGCTGGATGCAGAAGCCTATGGCGTGAAATCTAACGTCAAAGATATGGCGAGCTGGGTGATGGCCAATATGGCACCTGAGACACTCCCGCAGTCCACTCTGCAGCAGGGTATTGCGCTGGCGCAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAAGGGTTAGGCTGGGAGATGCTCAACTGGCCGGTCGACGCCAAAACCGTGGTGGATGGCAGCGACAATAAGGTCGCACTGGCGCCGTTGCCGGTCGCAGAAGTGAATCCTCCGGCTCCGCCAGTAAAAGCCTCCTGGGTGCATAAAACGGGCTCTACGGGTGGGTTTGGCAGCTACGTGGCGTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCAAATAAAAGCTATCCGAACCCGGTACGGGTGGAAACGGCTTACCGTATTCTCGAGACGCTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3006858","ARO_id":"45320","ARO_name":"CMH-6","CARD_short_name":"CMH-6","ARO_description":"CMH-6 is a CMH beta-lactamase.","ARO_category":{"42891":{"category_aro_accession":"3004776","category_aro_cvterm_id":"42891","category_aro_name":"CMH beta-lactamase","category_aro_description":"CMH is a class C beta-lactamase gene family belonging to Enterobacter cloacae.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4469":{"model_id":"4469","model_name":"CMY-106","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6844":{"protein_sequence":{"accession":"WP_063859654.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGISLLHLATYTAGGLPLQIPDDVTDKAALLRFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHVTPGQLDAEAYGVKSNVTDMARWIQVNMDASRVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPTPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"NG_048776.1","fmin":"100","fmax":"1246","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTTACAGCCTCATTCTCCACGTTTGCCGCCGCCAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCAGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTACAGATAAAGCCGCATTACTGCGTTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACAGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGTTACTCCTGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAACGTTACCGATATGGCCCGTTGGATTCAGGTCAACATGGATGCCAGCCGCGTTCAGGAGAAAACGCTCCAGCAAGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGTAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCACCCCGGCAGTGAAAGCCTCATGGGTGCATAAAACGGGATCCACTGGTGGATTTGGCAGCTACGTTGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002118","ARO_id":"38518","ARO_name":"CMY-106","CARD_short_name":"CMY-106","ARO_description":"CMY-106 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4470":{"model_id":"4470","model_name":"CMY-109","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6845":{"protein_sequence":{"accession":"WP_032948363.1","sequence":"MMKKSICCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAIIYKGKPYYFTWGKADIANNHPVTQHTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWRGISLLHLATYTAGGLPLQIPDDITDKAALLRFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQSEQKNYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMAHWVQANMDASHVQEKTLQQGIELAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPARVEAAWRILEKLQ"},"dna_sequence":{"accession":"NG_048779.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGATATGCTGCGCACTGCTGCTGACAGCCTCTTTCTCCACGTTTGCTGCCGCAAAAACAGAACAACAAATTGCCGATATCGTTAACCGCACCATCACACCACTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTGGCGATTATCTACAAGGGGAAACCTTATTACTTTACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCATACGCTGTTTGAGCTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGACGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCGGGGTATCAGCCTGCTGCACTTAGCCACCTATACAGCGGGTGGCCTGCCGCTGCAGATCCCCGATGACATTACGGATAAAGCCGCATTACTGCGCTTTTATCAAAACTGGCAACCACAATGGACTCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGTGCGCTGGCGGTGAAACCTTCAGGTATGAGCTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAAAGCGAACAAAAAAACTATGCCTGGGGCTATCGCGAAGGGAAGCCTGTGCACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATCGATATGGCCCACTGGGTTCAGGCCAACATGGACGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGAGCTTGCGCAGTCTCGCTACTGGCGTATTGGTGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCAGCACCTGCCGTGAAAGCCTCATGGGTGCATAAAACAGGATCCACAGGCGGATTTGGCAGCTACGTTGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTAATGTTGGCAAACAAAAGCTATCCCAACCCGGCTCGCGTCGAGGCGGCCTGGCGCATTCTTGAAAAACTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002121","ARO_id":"38521","ARO_name":"CMY-109","CARD_short_name":"CMY-109","ARO_description":"CMY-109 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4471":{"model_id":"4471","model_name":"CMY-131","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6846":{"protein_sequence":{"accession":"WP_063859788.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGELAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHVSPRQLGAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"NG_048801.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGAGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGAGACAACTTGGCGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3003170","ARO_id":"39747","ARO_name":"CMY-131","CARD_short_name":"CMY-131","ARO_description":"CMY-131 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4472":{"model_id":"4472","model_name":"CMY-137","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6847":{"protein_sequence":{"accession":"WP_053390271.1","sequence":"MMKKSICCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAIIYQGKPYYFTWGKADIANNRPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTHYWPELTGKQWQGISLLHLATYTAGGLPLQVPDDVTDKAALLRFYQNWQPQWAPGAKRLYANSSIGLFGALAVKPSGMSYEEAMSKRVLHPLKLAHTWITVPQSEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMTRWVQANMDASQVQEKTLQQGIELAQSRYWRIGDMYQGLGWEMLNWPVKADSIISGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"NG_066695.1","fmin":"100","fmax":"1246","strand":"+","sequence":"ATGATGAAAAAATCGATATGCTGCGCGCTGCTGCTGACAGCTTCGTTCTCCACGTTTGCCGCCGCAAAAACAGAACAACAAATTGCCGATATCGTTAACCGCACCATCACACCGCTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCGATTATCTATCAGGGGAAACCTTATTACTTTACCTGGGGTAAAGCCGATATCGCCAATAACCGTCCAGTCACTCAACAAACGCTGTTTGAACTCGGATCGGTCAGTAAAACGTTCAACGGCGTGCTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGCATTACTGGCCTGAACTGACTGGTAAGCAGTGGCAGGGTATCAGCCTGCTGCACTTAGCCACCTACACGGCAGGCGGCCTGCCGCTTCAGGTTCCGGACGACGTTACGGATAAAGCCGCGTTACTACGCTTTTATCAAAACTGGCAGCCGCAATGGGCCCCAGGCGCTAAACGTCTTTATGCTAACTCCAGCATTGGTCTGTTTGGCGCCCTGGCAGTGAAACCCTCAGGCATGAGCTACGAAGAGGCGATGTCCAAACGCGTCCTGCACCCCTTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAGCGAACAAAAAGATTATGCCTGGGGTTATCGCGAAGGAAAGCCAGTGCATGTATCCCCTGGCCAACTTGATGCCGAAGCATACGGGGTGAAATCGAGCGTTATCGATATGACCCGTTGGGTTCAGGCCAACATGGACGCCAGCCAGGTTCAGGAGAAAACGCTCCAGCAGGGCATCGAGCTTGCGCAGTCACGTTACTGGCGTATTGGCGATATGTACCAGGGCCTGGGCTGGGAGATGCTGAACTGGCCGGTGAAGGCCGACTCGATAATTAGTGGTAGCGACAGCAAAGTGGCACTGGCAGCGCTTCCTGCCGTTGAGGTAAACCCGCCCGCGCCTGCCGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGCGGATTCGGCAGCTACGTTGCGTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAGAGCTACCCAAACCCTGTTCGCGTCGAGGCCGCCTGGCGCATTCTTGAAAAACTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37053","NCBI_taxonomy_name":"Citrobacter","NCBI_taxonomy_id":"544"}}}},"ARO_accession":"3006457","ARO_id":"44919","ARO_name":"CMY-137","CARD_short_name":"CMY-137","ARO_description":"CMY-137 is a CMY beta-lactamase.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4473":{"model_id":"4473","model_name":"CMY-159","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6848":{"protein_sequence":{"accession":"WP_122630837.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAIIYQGKPYYFTWGKADIANDRPVTRQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTQYWPELTGKQWQGISLLHLATYTAGGLPLQVPDDVTDKAALLRFYQNWQPQWVPGAKRLYANSSIGLFGALAVKPSGIGYEEAMTKRVLQPLKLAHTWITVPQSEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSSLVDMTRWVQANMDASQVQEKTLRQGIEIAQARYWHIGDMYQGLGWEMLNWPVNADSIINGSDSKVALAALPVVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPARVEAAWRILEKLQ"},"dna_sequence":{"accession":"NG_062243.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCGTTGCTGCTGACAGCCTCTTTCTCCACGTTTGCCGCCGCAAAAACAGAACAACAGATTGCCGATATCGTAAACCGTACCATCACACCGCTGATGCAAGAACAGGCTATTCCGGGTATGGCCGTAGCAATTATCTACCAGGGAAAACCCTATTACTTTACCTGGGGGAAAGCCGATATCGCCAATGACCGCCCCGTCACCCGGCAAACGCTGTTTGAGCTTGGATCGGTAAGTAAGACGTTTAACGGTGTGCTGGGCGGCGATGCTATCGCCCGTGGTGAAATTAAGCTCAGCGATCCGGTCACCCAATACTGGCCCGAATTAACTGGCAAACAATGGCAGGGTATCAGCCTGCTGCACCTGGCCACCTATACGGCGGGTGGTCTGCCGCTTCAGGTACCTGACGACGTTACAGATAAAGCGGCATTACTGCGCTTTTATCAAAACTGGCAGCCGCAATGGGTCCCGGGAGCTAAACGCCTGTATGCTAACTCCAGTATTGGTCTGTTTGGCGCACTGGCGGTGAAACCTTCAGGAATAGGCTATGAAGAGGCGATGACCAAACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCACAGAGCGAACAAAAGGATTATGCCTGGGGTTATCGCGAAGGGAAGCCCGTGCACGTATCTCCGGGTCAGCTTGATGCCGAAGCCTACGGGGTGAAATCCAGCCTTGTCGATATGACTCGTTGGGTTCAGGCCAACATGGACGCCAGCCAGGTGCAGGAGAAAACGCTCCGACAGGGAATTGAAATTGCACAGGCTCGTTACTGGCATATTGGCGACATGTACCAGGGATTAGGTTGGGAGATGCTGAACTGGCCGGTGAATGCCGACTCGATAATCAACGGTAGCGACAGTAAAGTCGCGTTAGCGGCGCTTCCCGTCGTTGAGGTCAATCCGCCCGCCCCTGCAGTGAAAGCCTCATGGGTGCACAAAACCGGCTCCACTGGCGGATTTGGCAGCTACGTTGCGTTCGTTCCGGAAAAAAATCTCGGCATCGTGATGCTGGCAAACAAAAGCTACCCAAACCCTGCTCGCGTCGAGGCCGCCTGGCGTATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3006458","ARO_id":"44920","ARO_name":"CMY-159","CARD_short_name":"CMY-159","ARO_description":"CMY-159 is a CMY beta-lactamase.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4474":{"model_id":"4474","model_name":"CMY-167","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6849":{"protein_sequence":{"accession":"WP_148044408.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLKIPDDVRDKAALLHFYQNWQPQWTPGAKRLYSNSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYARGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"NG_065864.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGAAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACTCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCCGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3006459","ARO_id":"44921","ARO_name":"CMY-167","CARD_short_name":"CMY-167","ARO_description":"CMY-167 is a CMY beta-lactamase.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4475":{"model_id":"4475","model_name":"CMY-168","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6850":{"protein_sequence":{"accession":"WP_156404646.1","sequence":"MMKKSICCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAIIYEGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWRGISLLHLATYTAGGLPLQIPDEVTDKAALLRFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQSEQKNYALGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIELAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPARVEAAWRILEKLQ"},"dna_sequence":{"accession":"NG_067135.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGATATGCTGCGCGCTGCTGCTGACAGCCTCTTTCTCCACGTTTGCTGCCGCAAAAACAGAACAACAAATTGCCGATATCGTTAACCGCACCATCACACCACTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTAGCGATTATCTACGAGGGGAAACCTTATTACTTTACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAATTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGACGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCGGGGTATCAGCCTGCTGCACTTAGCCACCTATACAGCGGGTGGCCTACCGCTGCAGATCCCCGATGAAGTTACGGATAAAGCCGCATTACTGCGCTTTTATCAAAACTGGCAACCACAATGGACTCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGTGCGCTGGCGGTGAAACCTTCAGGTATGAGCTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAAAGCGAACAAAAAAATTATGCCTTGGGCTATCGCGAAGGGAAGCCTGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATCGATATGGCCCGCTGGGTTCAGGCCAACATGGACGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGAGCTTGCGCAGTCTCGTTACTGGCGTATTGGTGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCAGCACCTGCCGTGAAAGCCTCATGGGTGCATAAAACGGGATCCACAGGTGGATTTGGCAGCTACGTTGCCTTCGTTCCAGAAAAAAACCTTGGCATAGTGATGCTGGCAAACAAAAGCTACCCCAACCCGGCTCGCGTCGAGGCGGCCTGGCGCATTCTTGAAAAACTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36946","NCBI_taxonomy_name":"Providencia stuartii","NCBI_taxonomy_id":"588"}}}},"ARO_accession":"3006460","ARO_id":"44922","ARO_name":"CMY-168","CARD_short_name":"CMY-168","ARO_description":"CMY-168 is a CMY beta-lactamase.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4476":{"model_id":"4476","model_name":"CMY-169","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6851":{"protein_sequence":{"accession":"WP_156404647.1","sequence":"MMKKSICCALLLTASFSKFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAIIYEGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWRGISLLHLATYTAGGLPLQIPDDVTDKAALLRFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQSEQKNYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIELAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAAVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPARVEAAWRILEKLQ"},"dna_sequence":{"accession":"NG_067136.1","fmin":"0","fmax":"1131","strand":"+","sequence":"ATGATGAAAAAATCGATATGCTGCGCGCTGCTGCTGACAGCCTCTTTCTCCAAGTTTGCTGCCGCAAAAACAGAACAACAAATTGCCGATATCGTTAACCGCACCATCACACCACTGATGCAGGAGCAGGCTATTCCGGGCATGGCCGTGGCAATTATCTACGAGGGGAAACCTTATTACTTTACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAATTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGACGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCGGGGTATCAGCCTGCTGCACTTAGCCACCTATACAGCGGGTGGCCTGCCGCTGCAGATCCCCGATGACGTTACGGATAAAGCCGCATTACTGCGCTTTTATCAAAACTGGCAACCACAATGGACTCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGTGCGCTGGCGGTGAAACCTTCAGGTATGAGCTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAAAGCGAACAAAAAAATTATGCCTGGGGCTATCGCGAAGGGAAGCCTGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATCGATATGGCCCGCTGGGTTCAGGCCAACATGGACGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGAGCTTGCGCAGTCTCGTTACTGGCGTATTGGTGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGGTAAACCCGCCAGCACCTGCCGTGAAAGCCTCATGGGTGCATAAAACGGGATCCACAGGTGGATTTGGCAGCTACGTTGCCTTCGTTCCAGAAAAAAACCTTGGCATAGTGATGCTGGCAAACAAAAGCTATCCTAACCCGGCTCGCGTAGAGGCGGCCTGGCGCATTCTTGAAAAACTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36944","NCBI_taxonomy_name":"Providencia rettgeri","NCBI_taxonomy_id":"587"}}}},"ARO_accession":"3006461","ARO_id":"44923","ARO_name":"CMY-169","CARD_short_name":"CMY-169","ARO_description":"CMY-169 is a CMY beta-lactamase.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4477":{"model_id":"4477","model_name":"CMY-170","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6852":{"protein_sequence":{"accession":"WP_156404648.1","sequence":"MMKKSICCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAIIYEGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWRGISLLHLATYTAGGLPLQIPDDVTDKAALLRFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQSEQKNYAWGYREGKPVHVSPEQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIELAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPARVEAAWRILEKLQ"},"dna_sequence":{"accession":"NG_067137.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGATATGCTGCGCGCTGCTGCTGACAGCCTCTTTCTCCACGTTTGCTGCCGCAAAAACAGAACAACAAATTGCCGATATCGTTAACCGCACCATCACACCACTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTGGCGATTATCTACGAGGGGAAACCTTATTACTTTACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGACGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCGGGGTATCAGCCTGCTGCACTTAGCCACCTATACAGCGGGTGGCCTGCCGCTGCAGATCCCCGATGACGTTACGGATAAAGCCGCATTACTGCGCTTTTATCAAAACTGGCAACCACAATGGACTCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGTGCGCTGGCGGTGAAACCTTCAGGTATGAGCTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAAAGCGAACAAAAAAATTATGCCTGGGGCTATCGCGAAGGGAAGCCTGTACACGTTTCTCCGGAACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATCGATATGGCCCGCTGGGTTCAGGCCAACATGGACGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGAGCTTGCGCAGTCTCGTTACTGGCGTATTGGTGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCAGCACCTGCCGTGAAAGCCTCATGGGTGCATAAAACGGGATCCACAGGTGGATTTGGCAGCTACGTTGCCTTCGTTCCAGAAAAAAACCTTGGCATAGTGATGCTGGCAAACAAAAGCTATCCTAACCCGGCTCGCGTAGAGGCGGCCTGGCGCATTCTTGAAAAACTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3006462","ARO_id":"44924","ARO_name":"CMY-170","CARD_short_name":"CMY-170","ARO_description":"CMY-170 is a CMY beta-lactamase.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4478":{"model_id":"4478","model_name":"CMY-174","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6853":{"protein_sequence":{"accession":"WP_200302238.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAARRILEKLQ"},"dna_sequence":{"accession":"NG_073459.1","fmin":"100","fmax":"1246","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCCGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3006463","ARO_id":"44925","ARO_name":"CMY-174","CARD_short_name":"CMY-174","ARO_description":"CMY-174 is a CMY beta-lactamase.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4479":{"model_id":"4479","model_name":"CMY-8b","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6854":{"protein_sequence":{"accession":"WP_063859897.1","sequence":"MQQRQSILWGAVATLMWAGLAHAGEASPVDPLRPVVDASIQPLLKEHRIPGMAVAVLKDGKAHYFNYGVANRESGASVSEQTLFEIGSVSKTLTATLGAYAVVKGAMQLDDKASRHAPWLKGSAFDSITMGELATYSAGGLPLQFPEEVDSSEKMRAYYRQWAPVYSPGSHRQYSNPSIGLFGHLAASSLKQPFAQLMEQTLLPGLGMHHTYVNVPKQAMASYAYGYSKEDKPIRVNPGMLADEAYGIKTSSADLLAFVKANIGGVDDKALQQAISLTHKGHYSVGGMTQGLGWESYAYPVTEQTLLAGNSAKVILEANPTAAPRESGSQVLFNKTGSTNGFGAYVAFVPARGIGIVMLANRNYPIPARVKAAHAILAQLAG"},"dna_sequence":{"accession":"NG_048887.1","fmin":"0","fmax":"1149","strand":"+","sequence":"ATGCAACAACGACAATCCATCCTGTGGGGGGCCGTGGCCACCCTGATGTGGGCCGGTCTGGCCCATGCAGGTGAGGCTTCACCGGTCGATCCCCTGCGCCCCGTGGTGGATGCCAGCATCCAGCCGCTGCTCAAGGAGCACAGGATCCCGGGCATGGCGGTGGCCGTGCTCAAGGATGGCAAGGCCCACTATTTCAATTACGGGGTGGCCAACCGGGAGAGCGGGGCCAGCGTCAGCGAGCAGACCCTGTTCGAGATAGGATCCGTGAGCAAGACCCTGACTGCGACCCTGGGGGCCTATGCGGTGGTCAAGGGAGCGATGCAGCTGGATGACAAGGCGAGCCGGCACGCGCCCTGGCTCAAGGGATCCGCCTTTGACAGCATCACCATGGGGGAGCTTGCCACCTACAGCGCCGGAGGCCTGCCACTGCAATTCCCCGAGGAGGTGGATTCATCCGAGAAGATGCGCGCCTACTACCGCCAGTGGGCCCCTGTCTATTCGCCGGGCTCCCATCGCCAGTACTCCAACCCCAGCATAGGGCTGTTCGGCCACCTGGCGGCGAGCAGCCTGAAGCAGCCATTTGCCCAGTTGATGGAGCAGACCCTGCTGCCCGGGCTCGGCATGCACCACACCTATGTCAATGTGCCGAAGCAGGCCATGGCGAGTTATGCCTATGGCTATTCGAAAGAGGACAAGCCCATCCGGGTCAACCCTGGCATGCTGGCGGACGAGGCCTACGGCATCAAGACCAGCTCGGCGGATCTGCTCGCCTTCGTGAAGGCCAACATCGGCGGGGTTGATGACAAGGCGTTGCAGCAGGCCATCTCCCTGACCCACAAAGGGCATTACTCGGTAGGCGGGATGACCCAGGGGCTGGGTTGGGAGAGTTACGCCTATCCCGTCACCGAGCAGACATTGCTGGCGGGCAATTCGGCCAAGGTGATCCTCGAAGCCAATCCGACGGCGGCTCCCCGGGAGTCGGGGAGCCAGGTGCTCTTCAACAAGACCGGCTCGACCAATGGCTTTGGCGCCTATGTGGCCTTCGTGCCGGCCAGGGGGATCGGCATCGTCATGCTGGCCAATCGCAACTATCCCATCCCGGCCAGGGTGAAGGCGGCCCACGCCATCCTGGCGCAGTTGGCCGGTTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3006464","ARO_id":"44926","ARO_name":"CMY-8b","CARD_short_name":"CMY-8b","ARO_description":"CMY-8b is a CMY beta-lactamase.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4480":{"model_id":"4480","model_name":"CRD3-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"575"}},"model_sequences":{"sequence":{"6855":{"protein_sequence":{"accession":"WP_122630831.1","sequence":"MFASLIALTLAAQQIIVPLGKTPRPIERPRAPIETAGPLWAEACGDSTDWDQPAPPVRIHGNTYLVGTCGISAILVTGSDGHVLIDGGTEKGAEVIAANIRELGFDLKDIKFLLISHEHFDHVGGIAQLQKLTGATLVASAPAAKVMNSGLPGTDDPQSGMHPPFAPANVGRVVKDSEDVRFGNLMLTAMTTPGHTPGALSWRWESCDGGVCRTMVYADSLSPVSRDDYKFSGHPAYLAAYRASIAKVAATRCEILLTPHPSASAMKERMTGKQALFDADGCRDYAAALTRRLDERLAKEKAK"},"dna_sequence":{"accession":"NG_062235.1","fmin":"0","fmax":"912","strand":"+","sequence":"ATGTTCGCTAGCCTGATCGCACTTACGCTCGCCGCCCAGCAAATCATCGTCCCGCTCGGCAAGACGCCTCGCCCGATCGAACGCCCGCGCGCACCGATCGAGACGGCCGGTCCGCTATGGGCCGAGGCATGCGGCGATTCCACCGATTGGGACCAGCCCGCGCCGCCGGTGCGAATCCATGGCAACACCTATCTGGTCGGCACCTGCGGCATTTCCGCGATCCTCGTGACCGGCAGCGACGGCCACGTCCTGATCGACGGCGGGACAGAGAAGGGCGCCGAAGTGATCGCCGCCAATATCCGCGAGCTCGGCTTCGACCTGAAGGACATCAAGTTTCTCCTCATCAGTCATGAGCATTTCGACCATGTCGGCGGGATCGCGCAGCTACAAAAATTGACCGGCGCAACGCTGGTCGCGTCCGCCCCGGCAGCGAAGGTGATGAACAGCGGCCTGCCGGGCACCGACGACCCGCAGTCCGGCATGCACCCGCCCTTCGCCCCCGCGAACGTCGGCCGGGTGGTGAAGGACAGCGAGGATGTCCGCTTCGGCAATCTGATGCTGACCGCAATGACCACGCCCGGCCATACGCCGGGCGCGTTGAGCTGGCGCTGGGAGAGTTGCGACGGCGGGGTTTGCAGGACGATGGTCTACGCCGATAGCCTCTCGCCTGTCAGCCGCGACGATTACAAGTTTTCCGGCCATCCAGCCTATCTCGCCGCCTACCGCGCCTCGATCGCCAAGGTCGCTGCCACCCGCTGCGAAATCTTGCTCACACCGCACCCTTCGGCCAGCGCGATGAAGGAGCGCATGACCGGCAAACAGGCCTTGTTCGATGCCGACGGCTGCCGGGATTATGCCGCCGCGCTTACCCGGCGCCTCGACGAGCGACTGGCCAAGGAGAAAGCGAAATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36791","NCBI_taxonomy_name":"uncultured bacterium","NCBI_taxonomy_id":"77133"}}}},"ARO_accession":"3006864","ARO_id":"45326","ARO_name":"CRD3-1","CARD_short_name":"CRD3-1","ARO_description":"CRD3-1 is a CRD3 beta-lactamase.","ARO_category":{"43858":{"category_aro_accession":"3005398","category_aro_cvterm_id":"43858","category_aro_name":"CRD3 beta-lactamase","category_aro_description":"CRD3 beta-lactamases are class B3 beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4481":{"model_id":"4481","model_name":"CRH-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6856":{"protein_sequence":{"accession":"WP_043592266.1","sequence":"MFKHLILFASLAAPLTQAVAADPLAVAADKLAKLERDFGGSIGVYAIDTGSGATVANRPNERFPMCSSFKGFLAAGVLAQSQDKPGLLDKRIRYSKAALPNWSPITTKHQASGMTVAELNAASVQYSDNGAANLLLKEINGPAALTAFMRSIGDASFRLDRREPELNSAIPGDPRDTSTPKAVAESAQKLALGKALPEPQRQQLADWLKGNTTGNARIRAAVPAGWEVGDKTGTCGVYGTANDFAVIWPPKRAPIVLAVYTKHAKKEAKHSDEVIAAAARAALEAFNVKK"},"dna_sequence":{"accession":"NG_054656.1","fmin":"100","fmax":"973","strand":"+","sequence":"ATGTTCAAGCATCTGATTTTATTCGCATCGCTGGCCGCGCCGCTAACCCAGGCCGTCGCCGCCGATCCGCTCGCCGTCGCCGCCGACAAGCTGGCCAAACTGGAACGCGACTTTGGCGGCAGCATCGGCGTCTACGCCATCGACACCGGCTCCGGCGCCACCGTGGCCAACCGCCCCAACGAACGCTTTCCCATGTGCAGCTCTTTCAAAGGCTTTCTGGCGGCGGGAGTGCTGGCGCAAAGTCAAGACAAACCCGGCCTGCTGGACAAACGCATCCGCTACAGCAAGGCGGCTCTGCCTAATTGGTCCCCGATTACCACCAAACACCAAGCAAGCGGCATGACCGTGGCCGAGCTCAACGCCGCCTCCGTGCAATACAGCGACAACGGCGCGGCCAACCTGCTGCTCAAGGAAATCAACGGCCCCGCCGCGCTGACCGCCTTCATGCGCTCCATCGGCGACGCCAGCTTCCGCCTGGATCGTCGGGAGCCGGAACTGAACTCCGCCATCCCCGGCGACCCGCGCGACACCTCCACCCCCAAAGCGGTGGCGGAAAGCGCGCAAAAACTGGCGCTGGGCAAGGCGCTGCCGGAACCGCAACGCCAACAGCTGGCGGACTGGCTGAAGGGCAACACCACCGGCAACGCCAGAATCCGCGCCGCGGTGCCGGCCGGCTGGGAAGTGGGAGACAAAACCGGCACTTGCGGCGTCTACGGCACCGCCAACGACTTCGCGGTGATCTGGCCGCCCAAGCGCGCGCCCATCGTGCTGGCGGTCTACACCAAGCACGCCAAGAAAGAAGCCAAGCACAGCGACGAAGTGATCGCCGCCGCGGCGCGGGCGGCGCTGGAAGCCTTTAACGTGAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3006865","ARO_id":"45327","ARO_name":"CRH-1","CARD_short_name":"CRH-1","ARO_description":"CRH-1 is a CRH beta-lactamase.","ARO_category":{"43859":{"category_aro_accession":"3005399","category_aro_cvterm_id":"43859","category_aro_name":"CRH beta-lactamase","category_aro_description":"CRH beta-lactamases are class A beta-lactamases found in Chromobacterium haemolyticum.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4482":{"model_id":"4482","model_name":"CRH-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"575"}},"model_sequences":{"sequence":{"6857":{"protein_sequence":{"accession":"WP_109545050.1","sequence":"MFKHLILFASLAAPLTQAVAADPLSVAADKLAKLERDFGGSIGVYAIDTGSGATVANRPNERFPLCSSFKGFLAAGVLAQSQEKPGLLDKRIRYSKTALPNWSPITTKHQASGMTVAELNAASVQYSDNGAANLLLKEINGPAALTAFMRSIGDASFRLDRLEPELNSAVPGDPRDTSTPKAVAESAQKLALGKALPEPQRQQLADWLKGNTTGNARIRAAVPAGWEVGDKTGTCGVYGTANDFAVIWPPKRAPIVLAVYTKHAKKEAKHSDEVIAAAARAALEAFNVKK"},"dna_sequence":{"accession":"NG_057456.1","fmin":"0","fmax":"873","strand":"+","sequence":"ATGTTCAAGCATCTGATTTTATTCGCATCGCTGGCCGCACCGCTGACCCAGGCCGTTGCGGCGGACCCGCTCTCCGTCGCCGCCGACAAGCTGGCCAAACTGGAACGGGATTTTGGCGGCAGCATCGGCGTCTACGCCATCGACACCGGCTCCGGCGCCACCGTGGCCAACCGTCCCAACGAACGCTTTCCCCTGTGCAGCTCTTTCAAAGGCTTTCTGGCGGCGGGAGTGCTGGCGCAAAGCCAAGAAAAACCCGGCCTGCTGGACAAACGCATCCGCTACAGCAAGACGGCTCTGCCTAATTGGTCCCCGATTACCACCAAACACCAGGCAAGCGGCATGACCGTGGCCGAGCTCAACGCCGCCTCCGTGCAATACAGCGACAACGGCGCGGCCAATCTGCTGCTCAAGGAAATCAACGGCCCCGCCGCGCTGACCGCCTTCATGCGCTCCATCGGCGACGCCAGCTTCCGCCTGGACCGCCTGGAGCCGGAACTGAACTCCGCCGTCCCCGGCGACCCGCGCGACACCTCCACGCCCAAAGCGGTGGCGGAAAGCGCGCAAAAACTGGCGCTGGGCAAGGCGCTGCCGGAACCGCAACGCCAACAGCTGGCGGACTGGCTGAAGGGCAACACCACCGGCAACGCCAGAATCCGCGCCGCGGTGCCGGCCGGCTGGGAAGTGGGGGACAAAACCGGCACTTGCGGCGTTTACGGCACCGCCAACGACTTCGCGGTGATCTGGCCGCCCAAGCGCGCGCCCATCGTGCTGGCGGTCTACACCAAGCACGCCAAGAAAGAAGCCAAGCACAGCGACGAAGTGATCGCCGCCGCGGCGCGGGCGGCGCTGGAAGCCTTTAACGTGAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3006866","ARO_id":"45328","ARO_name":"CRH-2","CARD_short_name":"CRH-2","ARO_description":"CRH-2 is a CRH beta-lactamase.","ARO_category":{"43859":{"category_aro_accession":"3005399","category_aro_cvterm_id":"43859","category_aro_name":"CRH beta-lactamase","category_aro_description":"CRH beta-lactamases are class A beta-lactamases found in Chromobacterium haemolyticum.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4483":{"model_id":"4483","model_name":"CRH-3","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6858":{"protein_sequence":{"accession":"WP_109545051.1","sequence":"MFKHLILLASITAPLTQAVAADPLSVAADKLAKLERDFGGSIGVYAIDTGSGATVANRPNERFPLCSSFKGFLAAGVLAQSQDKPGLLDKRIRYSKTALPNWSPITTKHQASGMTVAELNAASVQYSDNGAANLLLKEINGPAALTAFMRSIGDARFRLDRLEPELNSAIPGDPRDTSTPKAVAESAQKLALGKALPEPQRQRLADWLKGNTTGNARIRAAVPAGWEVGDKTGTCGVYGTANDFAVIWPPKRAPIVLAVYTKHAKKEAKHSDEVIAAAARAALEAFNVKK"},"dna_sequence":{"accession":"NG_057457.1","fmin":"0","fmax":"873","strand":"+","sequence":"ATGTTCAAGCATCTGATTTTATTAGCGTCTATAACCGCGCCGCTAACCCAGGCCGTTGCGGCGGACCCGCTCTCCGTCGCCGCCGACAAGCTGGCCAAACTGGAACGCGACTTTGGCGGCAGCATCGGCGTCTACGCCATCGACACCGGCTCCGGCGCCACCGTGGCCAACCGTCCCAACGAACGTTTTCCCCTGTGCAGCTCTTTCAAAGGCTTTCTGGCGGCGGGAGTGCTGGCGCAAAGCCAAGACAAACCCGGCCTGCTGGACAAACGCATCCGCTACAGCAAGACGGCTCTGCCTAATTGGTCCCCGATTACCACCAAACACCAGGCAAGCGGCATGACCGTGGCCGAGCTCAACGCCGCCTCCGTGCAATACAGCGACAACGGCGCGGCCAATCTGCTGCTCAAGGAAATCAACGGCCCCGCCGCGCTGACCGCCTTCATGCGCTCCATCGGCGACGCCCGCTTCCGCCTGGATCGTCTGGAGCCGGAACTGAACTCCGCCATCCCCGGCGACCCGCGCGACACCTCCACGCCCAAAGCGGTGGCGGAAAGCGCACAAAAACTGGCGCTGGGCAAGGCGCTGCCGGAACCGCAACGCCAACGGCTGGCGGACTGGCTGAAGGGCAACACCACCGGCAACGCCAGAATCCGCGCCGCGGTGCCGGCCGGCTGGGAAGTGGGGGACAAAACCGGCACTTGCGGCGTCTACGGCACCGCCAACGACTTCGCGGTGATCTGGCCGCCCAAGCGCGCGCCCATCGTGCTGGCGGTCTACACCAAGCACGCCAAGAAAGAAGCCAAGCACAGCGACGAAGTGATCGCCGCCGCCGCGCGGGCGGCGCTGGAAGCCTTTAACGTGAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3006867","ARO_id":"45329","ARO_name":"CRH-3","CARD_short_name":"CRH-3","ARO_description":"CRH-3 is a CRH beta-lactamase.","ARO_category":{"43859":{"category_aro_accession":"3005399","category_aro_cvterm_id":"43859","category_aro_name":"CRH beta-lactamase","category_aro_description":"CRH beta-lactamases are class A beta-lactamases found in Chromobacterium haemolyticum.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4484":{"model_id":"4484","model_name":"CRP-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"6859":{"protein_sequence":{"accession":"WP_043629745.1","sequence":"MRLSRRLVLLSCLLLPQAGFSAAMPANLADQKIARLERVFGGQIGVYALDTGSGAAVSYRADERFPLCSSFKGFLAASALAHSQSKPGFLDQILHYGKEELIAWSPISEKHQSSGMTVAGLCAATVQYSDNAAANVLMKQLDGPAGLTAFMRAIGDSTFRLDRWEPELNTAIPGDARDTSTPRAVAESLQKLTLGTALAAHQRQQLVDWLKGNTTGNQRIRAAVPAGWLVGDKTGTCGVYGTANDYAVIWPTGRAPIVMAVYTRASKKDIKHSDAVIADAAKAALEALGVMTR"},"dna_sequence":{"accession":"NG_054657.1","fmin":"100","fmax":"982","strand":"+","sequence":"ATGAGACTGTCCCGCCGCCTCGTTTTGCTGTCTTGCCTGCTATTGCCGCAGGCAGGCTTTTCCGCAGCCATGCCTGCCAATCTTGCCGACCAGAAAATAGCCAGGCTGGAGCGCGTTTTTGGCGGCCAGATCGGGGTGTATGCGCTGGATACCGGCTCAGGCGCCGCCGTGAGTTACCGCGCGGATGAGCGCTTCCCGCTGTGCAGCTCGTTCAAGGGTTTTCTGGCCGCCTCCGCGCTGGCGCATAGCCAGAGCAAACCGGGCTTTCTGGATCAAATCCTCCATTACGGCAAGGAAGAGCTGATAGCCTGGTCCCCCATCTCGGAGAAGCACCAGTCCAGCGGCATGACGGTAGCCGGCCTGTGCGCGGCCACTGTGCAGTACAGCGATAATGCAGCCGCCAATGTCTTGATGAAGCAGCTGGATGGCCCGGCCGGCCTGACGGCCTTCATGCGCGCCATCGGCGACAGCACCTTCCGCCTTGACCGCTGGGAGCCGGAGTTGAACACGGCCATACCCGGCGACGCGCGCGATACCTCCACCCCGCGCGCCGTGGCGGAAAGCCTGCAAAAACTGACCCTTGGCACGGCACTGGCGGCGCATCAGCGCCAGCAGCTGGTGGATTGGCTCAAAGGGAACACTACCGGCAACCAGCGCATTCGCGCCGCCGTGCCGGCCGGCTGGTTGGTGGGCGACAAAACCGGCACTTGCGGCGTGTACGGCACGGCCAATGATTACGCGGTGATCTGGCCCACTGGCCGCGCGCCCATCGTGATGGCGGTTTATACCCGCGCGTCCAAGAAAGACATCAAGCACAGCGATGCCGTCATTGCCGATGCGGCCAAGGCCGCGCTGGAAGCGCTAGGGGTGATGACGCGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3006868","ARO_id":"45330","ARO_name":"CRP-1","CARD_short_name":"CRP-1","ARO_description":"CRP-1 is a CRP beta-lactamase.","ARO_category":{"43860":{"category_aro_accession":"3005400","category_aro_cvterm_id":"43860","category_aro_name":"CRP beta-lactamase","category_aro_description":"CRP beta-lactamases are class A beta-lactamase found in Chromobacterium piscinae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4485":{"model_id":"4485","model_name":"CSA-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6860":{"protein_sequence":{"accession":"WP_007888761.1","sequence":"MKSKVSALLMMIVLAGHAQAAPVAPPDAVVKPLMARYQIPGMAVAVSVNGETHFWHYGVASKATRKPVDENTLFEIGSLSKTFTATLASKAQQDGKLDFSAPASQYLPALKGSAFDNVTLLNLATHTAGTPLFVPDAVKNTTQLMDWYRAWQPEKPVGTERVYSNLGIGLLGMITAKALDKPFSEAMEQGLLRDFGMTHTFINVPEAAMDNYAQGYNKDDKPVRVTPGPLDAESYGLKSGSADLLRYLQIQLGEQEVAPGWRQAINATHNGYYRSGEFTQGLMWEYYPWPSPLSRLVEGNSSQRIMKGLAATAIVPPQPAPQAAWYNKTGSTNGFSTYAVFIPEKRIALIMLANKWFPNDDRVKAAYTIIQELDK"},"dna_sequence":{"accession":"NG_062223.1","fmin":"100","fmax":"1228","strand":"+","sequence":"ATGAAAAGCAAAGTCAGTGCGCTGTTAATGATGATAGTTCTTGCGGGCCATGCGCAGGCCGCGCCCGTTGCGCCGCCGGATGCGGTCGTTAAGCCATTGATGGCGCGCTACCAGATCCCGGGCATGGCGGTGGCGGTGTCGGTTAACGGCGAAACGCATTTCTGGCATTACGGCGTGGCGTCAAAAGCGACCCGTAAGCCGGTGGATGAAAACACGCTTTTCGAAATCGGCTCGCTCAGTAAAACCTTTACCGCGACGCTCGCAAGCAAGGCGCAGCAAGACGGCAAACTGGATTTCAGCGCGCCCGCCAGCCAGTATCTTCCTGCACTGAAAGGCAGCGCATTCGATAACGTGACGCTGCTGAACCTCGCCACGCACACCGCGGGAACGCCGCTCTTTGTGCCGGATGCGGTGAAAAACACCACACAGCTGATGGACTGGTATCGCGCCTGGCAGCCTGAAAAGCCGGTCGGCACCGAGCGCGTTTACTCGAATCTCGGGATCGGGCTGCTCGGGATGATTACCGCGAAGGCGCTCGATAAGCCGTTCAGCGAGGCGATGGAGCAGGGGCTTCTCAGGGATTTCGGCATGACGCACACCTTTATCAACGTGCCGGAGGCCGCGATGGACAACTACGCCCAGGGCTATAACAAGGACGACAAACCGGTGCGGGTGACGCCCGGCCCGCTTGACGCCGAATCGTATGGGCTGAAATCCGGCAGCGCGGATCTGCTGCGTTATCTGCAAATCCAGCTTGGCGAGCAGGAGGTCGCGCCAGGCTGGCGTCAGGCGATTAACGCCACGCACAACGGCTACTACCGCAGCGGTGAGTTCACACAGGGGTTGATGTGGGAATACTATCCGTGGCCGTCGCCGCTCTCGCGCCTTGTTGAAGGCAACAGCAGCCAGCGCATCATGAAAGGGCTTGCGGCCACCGCGATCGTTCCGCCGCAGCCTGCGCCGCAGGCCGCGTGGTATAACAAAACCGGCTCGACCAACGGCTTTTCCACTTACGCAGTGTTTATCCCTGAGAAGCGTATCGCGCTGATTATGCTCGCCAACAAGTGGTTCCCGAATGACGACCGTGTTAAAGCGGCGTATACGATTATTCAGGAGCTTGATAAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43762","NCBI_taxonomy_name":"Cronobacter sakazakii","NCBI_taxonomy_id":"28141"}}}},"ARO_accession":"3006869","ARO_id":"45331","ARO_name":"CSA-1","CARD_short_name":"CSA-1","ARO_description":"CSA-1 is a CSA beta-lactamase.","ARO_category":{"43861":{"category_aro_accession":"3005401","category_aro_cvterm_id":"43861","category_aro_name":"CSA beta-lactamase","category_aro_description":"CSA beta-lactamases are class C beta-lactamases found in Cronobacter sakazakii.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4486":{"model_id":"4486","model_name":"CSA-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6861":{"protein_sequence":{"accession":"WP_004384957.1","sequence":"MKSKVSALLMMIVLAGHAQAAPVAPPDAVVKPLMARYQIPGMAVAVSVNGETHFWHYGVASKATRKPVDENTLFEIGSLSKTFTATLASKAQQDGKLDFSAPASQYLPALKGSAFDHVTLLNLATHTAGTPLFVPDAVKNTPQLMDWYRAWQPEKPVGTERVYSNLGIGLLGMITAKALDKPFSEAMEQGLLRDFGMTHTFINVPDAAMGDYAQGYNKDDKPVRVTPGPLDAESYGLKSGSADLLRYLQIQLGEQEVAPGWRQAINATHNGYYRSGEFTQGLMWEYYPWPSPLSRLVEGNSSQRIMKGLATTAIVPPQPAPQAAWYNKTGSTNGFSTYAVFIPEKRIALIMLANKWFPNDDRVKAAYAIIQELDK"},"dna_sequence":{"accession":"NG_062211.1","fmin":"100","fmax":"1228","strand":"+","sequence":"ATGAAAAGCAAAGTCAGTGCGCTGTTAATGATGATAGTTCTTGCGGGCCATGCGCAGGCCGCGCCCGTTGCGCCGCCGGATGCGGTCGTTAAGCCATTGATGGCGCGCTACCAGATCCCGGGCATGGCGGTGGCGGTGTCGGTTAACGGCGAAACGCATTTCTGGCATTACGGCGTGGCGTCAAAAGCGACGCGCAAGCCGGTGGATGAAAACACGCTTTTCGAAATCGGCTCGCTCAGTAAAACCTTTACCGCGACGCTCGCAAGCAAGGCGCAGCAAGACGGCAAGCTGGATTTCAGCGCGCCCGCCAGCCAGTATCTTCCTGCACTGAAAGGCAGCGCGTTCGACCACGTGACGCTGCTGAATCTCGCCACGCACACCGCGGGAACGCCGCTCTTTGTGCCCGATGCGGTGAAAAACACCCCACAGCTGATGGACTGGTATCGCGCCTGGCAGCCTGAAAAGCCGGTCGGCACAGAGCGCGTTTACTCGAATCTTGGGATAGGGCTGCTCGGGATGATTACCGCGAAGGCGCTCGATAAGCCGTTCAGCGAGGCGATGGAGCAGGGGCTGCTCAGGGATTTCGGCATGACGCACACCTTTATTAACGTGCCGGATGCCGCGATGGGCGACTACGCCCAGGGTTATAACAAAGACGACAAACCGGTGCGGGTGACGCCCGGCCCGCTTGACGCCGAATCGTATGGGCTGAAATCCGGCAGCGCGGATCTGCTGCGTTATCTGCAAATCCAGCTTGGCGAGCAGGAGGTCGCGCCAGGCTGGCGTCAGGCGATTAACGCCACGCACAACGGCTACTACCGCAGCGGTGAGTTCACGCAGGGATTGATGTGGGAATATTATCCGTGGCCGTCACCACTCTCGCGCCTTGTTGAAGGCAACAGCAGCCAGCGCATCATGAAAGGGCTTGCGACCACCGCGATCGTTCCGCCGCAGCCTGCGCCGCAGGCCGCGTGGTATAACAAAACCGGCTCGACCAACGGCTTTTCCACATACGCAGTGTTTATCCCTGAGAAGCGTATCGCGCTGATTATGCTCGCCAACAAGTGGTTCCCTAATGACGACCGCGTGAAAGCGGCGTATGCGATTATTCAGGAGCTTGATAAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43762","NCBI_taxonomy_name":"Cronobacter sakazakii","NCBI_taxonomy_id":"28141"}}}},"ARO_accession":"3006870","ARO_id":"45332","ARO_name":"CSA-2","CARD_short_name":"CSA-2","ARO_description":"CSA-2 is a CSA beta-lactamase.","ARO_category":{"43861":{"category_aro_accession":"3005401","category_aro_cvterm_id":"43861","category_aro_name":"CSA beta-lactamase","category_aro_description":"CSA beta-lactamases are class C beta-lactamases found in Cronobacter sakazakii.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4487":{"model_id":"4487","model_name":"CSP-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"6862":{"protein_sequence":{"accession":"WP_063859920.1","sequence":"MKKLTQMKKLTQMKKYFSFCLLGIFIFCFSQQNLKRDITKIIQGKNALVAVSVMNSKGKTEVNINGNKKVPMLSVFKFHIALAVLDLVDRGILDLEQNIFVKKSELLENTWSPIRDKYPNGNVNIPLREIIEHTVSQSDNNGCDILLRLIGGVDTVQKFIESKGIKDFAIKYNEEEMNKNGKSIYSNYTTANASSRLLQKFYNGEIISESSRDFLFRIMYETSTGADRLISLLPPDVIVAHKTGTSGIVSGIQAATNDVGIIILPDDEYYTISVFVINSKENTSTNEKIIADISKTVWDYYFQNK"},"dna_sequence":{"accession":"NG_048896.1","fmin":"100","fmax":"1018","strand":"+","sequence":"ATGAAAAAATTAACACAAATGAAAAAATTAACACAAATGAAAAAATATTTTTCTTTTTGTCTTTTGGGGATTTTTATTTTTTGTTTTTCTCAACAAAATTTAAAAAGAGATATCACAAAGATTATACAAGGCAAGAATGCCCTTGTGGCGGTATCTGTGATGAACTCAAAAGGGAAAACAGAAGTAAATATTAACGGAAACAAAAAAGTTCCGATGCTTAGTGTGTTCAAATTTCACATTGCATTGGCAGTTTTGGATTTGGTGGACAGAGGTATTTTGGATTTGGAACAAAATATTTTTGTCAAGAAATCAGAACTTTTGGAGAATACTTGGAGCCCCATTCGTGATAAATATCCGAATGGCAATGTGAATATCCCTTTGAGAGAAATCATAGAACACACTGTTTCTCAGAGTGATAACAATGGTTGTGACATTCTGCTGAGGTTGATTGGAGGAGTTGATACTGTCCAGAAATTCATCGAGAGCAAGGGTATCAAAGATTTTGCGATAAAATACAATGAAGAAGAAATGAATAAGAATGGGAAATCCATCTACTCAAACTATACAACCGCAAACGCCTCCAGCAGGCTTCTGCAAAAATTTTATAATGGTGAGATAATTTCCGAGTCTTCCAGAGATTTTCTATTCAGAATCATGTATGAGACTTCTACTGGAGCAGACAGGCTCATATCCCTGCTTCCTCCAGATGTTATCGTTGCCCATAAAACAGGGACTTCTGGCATTGTATCTGGAATTCAGGCTGCTACCAATGATGTGGGAATCATCATTTTACCTGATGACGAATACTACACCATATCTGTTTTTGTGATAAATTCCAAAGAAAATACATCAACTAACGAAAAAATAATTGCTGATATATCAAAAACAGTGTGGGATTATTATTTTCAAAATAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3006871","ARO_id":"45333","ARO_name":"CSP-1","CARD_short_name":"CSP-1","ARO_description":"CSP-1 is a CSP beta-lactamase.","ARO_category":{"43862":{"category_aro_accession":"3005402","category_aro_cvterm_id":"43862","category_aro_name":"CSP beta-lactamase","category_aro_description":"CSP beta-lactamases are class A beta-lactamases found in Capnocytophaga sputigena.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4488":{"model_id":"4488","model_name":"CTX-M-127","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6863":{"protein_sequence":{"accession":"WP_088245211.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDDVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"NG_055268.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATGACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001986","ARO_id":"38386","ARO_name":"CTX-M-127","CARD_short_name":"CTX-M-127","ARO_description":"CTX-M-127 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4489":{"model_id":"4489","model_name":"CTX-M-138","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6864":{"protein_sequence":{"accession":"WP_070064534.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAVAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVDGTMSLAELSAAALQYSDNVAMNKLISHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGDYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKSVTNGL"},"dna_sequence":{"accession":"NG_051737.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGTCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGAAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGTGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACTTGGTTAACTATAATCCGATTGCGGAAAAGCACGTCGATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTTCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGTAATCTGACGCTGGGTAAAGCATTGGGTGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGACTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAATCCGTCACCAACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001996","ARO_id":"38396","ARO_name":"CTX-M-138","CARD_short_name":"CTX-M-138","ARO_description":"CTX-M-138 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4490":{"model_id":"4490","model_name":"CTX-M-140","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6865":{"protein_sequence":{"accession":"WP_063108644.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPITEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"NG_068166.1","fmin":"100","fmax":"976","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTACCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGACTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3001998","ARO_id":"38398","ARO_name":"CTX-M-140","CARD_short_name":"CTX-M-140","ARO_description":"CTX-M-140 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4491":{"model_id":"4491","model_name":"CTX-M-143","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6866":{"protein_sequence":{"accession":"WP_156404649.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLSTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"NG_067138.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAGCACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002001","ARO_id":"38401","ARO_name":"CTX-M-143","CARD_short_name":"CTX-M-143","ARO_description":"CTX-M-143 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4492":{"model_id":"4492","model_name":"CTX-M-146","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6867":{"protein_sequence":{"accession":"WP_102607454.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAVAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVDGTMSLAELSAAALQYSDNVAMNKLISHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDRTGSGDYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTNGL"},"dna_sequence":{"accession":"NG_056169.1","fmin":"100","fmax":"976","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGTCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGAAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGTGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACTTGGTTAACTATAATCCGATTGCGGAAAAGCACGTCGATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTTCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGTAATCTGACGCTGGGTAAAGCATTGGGTGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAGAACCGGCAGCGGTGACTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCAACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002004","ARO_id":"38404","ARO_name":"CTX-M-146","CARD_short_name":"CTX-M-146","ARO_description":"CTX-M-146 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4493":{"model_id":"4493","model_name":"CTX-M-150","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6868":{"protein_sequence":{"accession":"WP_063859959.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGHTHGAASIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"NG_048936.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCCATACCCACGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTAATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002007","ARO_id":"38407","ARO_name":"CTX-M-150","CARD_short_name":"CTX-M-150","ARO_description":"CTX-M-150 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4494":{"model_id":"4494","model_name":"CTX-M-153","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6869":{"protein_sequence":{"accession":"WP_168247876.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFPMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"NG_068167.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTCCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002010","ARO_id":"38410","ARO_name":"CTX-M-153","CARD_short_name":"CTX-M-153","ARO_description":"CTX-M-153 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4495":{"model_id":"4495","model_name":"CTX-M-154","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6870":{"protein_sequence":{"accession":"WP_110093562.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAKLERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"NG_067221.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCAAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002011","ARO_id":"38411","ARO_name":"CTX-M-154","CARD_short_name":"CTX-M-154","ARO_description":"CTX-M-154 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4496":{"model_id":"4496","model_name":"CTX-M-167","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6871":{"protein_sequence":{"accession":"WP_063859974.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSCDYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"NG_048952.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCTGTGACTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3005590","ARO_id":"44052","ARO_name":"CTX-M-167","CARD_short_name":"CTX-M-167","ARO_description":"CTX-M-167 is a CTX-M beta-lactamase.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4497":{"model_id":"4497","model_name":"CTX-M-168","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6872":{"protein_sequence":{"accession":"WP_063859975.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEHTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"NG_048953.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACATACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGACTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3005591","ARO_id":"44053","ARO_name":"CTX-M-168","CARD_short_name":"CTX-M-168","ARO_description":"CTX-M-168 is a CTX-M beta-lactamase.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4498":{"model_id":"4498","model_name":"CTX-M-169","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6873":{"protein_sequence":{"accession":"WP_063859976.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPSLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"NG_048954.1","fmin":"100","fmax":"976","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGAAGACTGGGGGTGGCATTGATTAACACAGCGGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTCGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAGTCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTGGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCAGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAATGATATCGCGGTGATTTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTGGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3005592","ARO_id":"44054","ARO_name":"CTX-M-169","CARD_short_name":"CTX-M-169","ARO_description":"CTX-M-169 is a CTX-M beta-lactamase.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4499":{"model_id":"4499","model_name":"CTX-M-170","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6874":{"protein_sequence":{"accession":"WP_063859984.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGNSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"NG_048956.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCAACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3005593","ARO_id":"44055","ARO_name":"CTX-M-170","CARD_short_name":"CTX-M-170","ARO_description":"CTX-M-170 is a CTX-M beta-lactamase.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4500":{"model_id":"4500","model_name":"CTX-M-171","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6875":{"protein_sequence":{"accession":"WP_065419568.1","sequence":"MMTQSIRRSMLTVMATLPLLFSSATLHAQANSVQQQLEALEKSSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKQSESDKHLLNQSVEIKKSDLVNYNPIAEKHVNGTMTLAELGAAALQYSDNTAMNKLIAHLGGPDKVTAFARSLGDETFRLDRTEPTLNTAIPGDPRDTTTPLAMAQTLKNLTLGKALAETQRAQLVTWLKGNTTGSASIRAGLPKSWVVGDKTGSGDYGTTNDIAVIWPENHAPLVLVTYFTQPEQKAESRRDILAAAAKIVTHGF"},"dna_sequence":{"accession":"NG_051164.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGATGACTCAGAGCATTCGCCGCTCAATGTTAACGGTGATGGCGACGCTACCCCTGCTATTTAGCAGCGCAACGCTGCATGCGCAGGCGAACAGCGTGCAACAGCAGCTGGAAGCCCTGGAGAAAAGTTCGGGAGGTCGGCTTGGCGTTGCGCTGATTAACACCGCCGATAATTCGCAGATTCTCTACCGTGCCGATGAACGTTTTGCGATGTGCAGTACCAGTAAGGTGATGGCGGCCGCGGCGGTGCTTAAACAGAGCGAGAGCGATAAGCACCTGCTAAATCAGAGCGTTGAAATCAAGAAGAGCGACCTGGTTAACTACAATCCCATTGCGGAGAAACACGTTAACGGCACGATGACGCTGGCTGAGCTTGGCGCAGCGGCGCTGCAGTATAGCGACAATACTGCCATGAATAAGCTGATTGCCCATCTGGGTGGTCCCGATAAAGTGACGGCGTTTGCTCGCTCGTTGGGTGATGAGACCTTCCGTCTGGACAGAACCGAGCCCACGCTCAATACCGCCATTCCAGGCGACCCGCGTGATACCACCACGCCGCTCGCGATGGCGCAGACCCTGAAAAATCTGACGCTGGGTAAAGCGCTGGCGGAAACTCAGCGGGCACAGTTGGTGACGTGGCTTAAGGGCAATACTACCGGTAGCGCGAGCATTCGGGCGGGTCTGCCGAAATCATGGGTAGTGGGCGATAAAACCGGCAGCGGAGATTATGGCACCACCAACGATATCGCGGTTATCTGGCCGGAAAACCACGCACCGCTGGTTCTGGTGACCTACTTTACCCAACCGGAGCAGAAGGCGGAAAGCCGTCGGGATATTCTGGCTGCGGCGGCGAAAATCGTAACCCACGGTTTCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3005594","ARO_id":"44056","ARO_name":"CTX-M-171","CARD_short_name":"CTX-M-171","ARO_description":"CTX-M-171 is a CTX-M beta-lactamase.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4501":{"model_id":"4501","model_name":"CTX-M-172","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6876":{"protein_sequence":{"accession":"WP_063859993.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKPIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"NG_048957.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCCGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3005595","ARO_id":"44057","ARO_name":"CTX-M-172","CARD_short_name":"CTX-M-172","ARO_description":"CTX-M-172 is a CTX-M beta-lactamase.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4502":{"model_id":"4502","model_name":"CTX-M-173","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6877":{"protein_sequence":{"accession":"WP_063859998.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTTFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"NG_048958.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCACGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3005596","ARO_id":"44058","ARO_name":"CTX-M-173","CARD_short_name":"CTX-M-173","ARO_description":"CTX-M-173 is a CTX-M beta-lactamase.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4503":{"model_id":"4503","model_name":"CTX-M-174","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6878":{"protein_sequence":{"accession":"WP_063860005.1","sequence":"MVTKRVLRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGGYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"NG_048959.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCTACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGGCTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3005597","ARO_id":"44059","ARO_name":"CTX-M-174","CARD_short_name":"CTX-M-174","ARO_description":"CTX-M-174 is a CTX-M beta-lactamase.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4504":{"model_id":"4504","model_name":"CTX-M-175","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6879":{"protein_sequence":{"accession":"WP_063860009.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAVAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVDGTMSLTELSAAALQYSDNVAMNKLISHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGDYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTNGL"},"dna_sequence":{"accession":"NG_048960.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGTCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGAAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGTGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACTTGGTTAACTATAATCCGATTGCGGAAAAGCACGTCGATGGGACGATGTCACTGACTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTTCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGTAATCTGACGCTGGGTAAAGCATTGGGTGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGACTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCAACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3005598","ARO_id":"44060","ARO_name":"CTX-M-175","CARD_short_name":"CTX-M-175","ARO_description":"CTX-M-175 is a CTX-M beta-lactamase.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4505":{"model_id":"4505","model_name":"CTX-M-176","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6880":{"protein_sequence":{"accession":"WP_063860014.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFAQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"NG_048961.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCGCCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3005599","ARO_id":"44061","ARO_name":"CTX-M-176","CARD_short_name":"CTX-M-176","ARO_description":"CTX-M-176 is a CTX-M beta-lactamase.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4506":{"model_id":"4506","model_name":"CTX-M-177","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6881":{"protein_sequence":{"accession":"WP_063860019.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARLLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGDYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"NG_048962.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGGGTGGCATTGATTAACACAGCGGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACTGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGACTATGGCACCACCAATGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3005600","ARO_id":"44062","ARO_name":"CTX-M-177","CARD_short_name":"CTX-M-177","ARO_description":"CTX-M-177 is a CTX-M beta-lactamase.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4507":{"model_id":"4507","model_name":"CTX-M-178","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6882":{"protein_sequence":{"accession":"WP_104009847.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTSSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"NG_056408.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCAGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3005601","ARO_id":"44063","ARO_name":"CTX-M-178","CARD_short_name":"CTX-M-178","ARO_description":"CTX-M-178 is a CTX-M beta-lactamase.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4508":{"model_id":"4508","model_name":"CTX-M-179","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6883":{"protein_sequence":{"accession":"WP_063860025.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAVAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQTQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"NG_048963.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGTGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGACTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3005602","ARO_id":"44064","ARO_name":"CTX-M-179","CARD_short_name":"CTX-M-179","ARO_description":"CTX-M-179 is a CTX-M beta-lactamase.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4509":{"model_id":"4509","model_name":"CTX-M-180","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6884":{"protein_sequence":{"accession":"WP_063860034.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTSAASIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"NG_048964.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCAGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3005603","ARO_id":"44065","ARO_name":"CTX-M-180","CARD_short_name":"CTX-M-180","ARO_description":"CTX-M-180 is a CTX-M beta-lactamase.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4510":{"model_id":"4510","model_name":"CTX-M-181","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6885":{"protein_sequence":{"accession":"WP_063860035.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDHVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"NG_048965.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATCACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3005604","ARO_id":"44066","ARO_name":"CTX-M-181","CARD_short_name":"CTX-M-181","ARO_description":"CTX-M-181 is a CTX-M beta-lactamase.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4511":{"model_id":"4511","model_name":"CTX-M-182","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6886":{"protein_sequence":{"accession":"WP_063860036.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQRLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"NG_048966.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAGACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3005605","ARO_id":"44067","ARO_name":"CTX-M-182","CARD_short_name":"CTX-M-182","ARO_description":"CTX-M-182 is a CTX-M beta-lactamase.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4512":{"model_id":"4512","model_name":"CTX-M-183","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6887":{"protein_sequence":{"accession":"WP_064511490.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQKADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"NG_050812.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAAAGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3005606","ARO_id":"44068","ARO_name":"CTX-M-183","CARD_short_name":"CTX-M-183","ARO_description":"CTX-M-183 is a CTX-M beta-lactamase.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4513":{"model_id":"4513","model_name":"CTX-M-184","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6888":{"protein_sequence":{"accession":"WP_064511491.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADTSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"NG_050813.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATACTTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3005607","ARO_id":"44069","ARO_name":"CTX-M-184","CARD_short_name":"CTX-M-184","ARO_description":"CTX-M-184 is a CTX-M beta-lactamase.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4514":{"model_id":"4514","model_name":"CTX-M-185","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6889":{"protein_sequence":{"accession":"WP_065102278.1","sequence":"MMRKSVSRAILMTTACVSLLLASVPLYAQANDIQQKLAALEKSSGGRLGVALINTADNTQTLYRADERFAMCSTSKVMAAAAVLKQSETQKDLLSQRVEIKSSDLINYNPIAEKHVNGTMTLGELSAAALQYSDNTAMNKLIAHLGGPGKVTAFARVIGDDTFRLDRTEPTLNTAIPGDPRDTTTPLAMAQTLRNLTLGNALGDTQRAQLVTWLKGNTTGAASIQAGLPTSWVVGDKTGSGDYGTTNDIAVIWPEGRAPLVLVTYFTQPKPKAESRRDVLAAAARIVTDGY"},"dna_sequence":{"accession":"NG_050944.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGATGAGAAAAAGCGTAAGTCGGGCGATATTAATGACGACAGCCTGTGTTTCGCTGCTGTTGGCCAGTGTGCCGCTGTATGCCCAGGCGAACGATATTCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGGGGACGACTGGGTGTGGCGTTGATTAACACCGCCGATAACACGCAGACGCTCTACCGCGCCGACGAGCGTTTTGCTATGTGCAGCACCAGTAAAGTGATGGCGGCGGCGGCGGTGCTTAAGCAAAGTGAAACGCAAAAAGACTTACTGAGTCAGCGGGTTGAAATTAAGTCCTCAGACTTGATTAACTACAACCCAATCGCTGAAAAGCACGTCAATGGCACGATGACACTCGGGGAGCTGAGCGCGGCGGCGCTGCAGTACAGCGATAATACTGCCATGAATAAGCTGATTGCCCATCTCGGGGGGCCGGGTAAAGTGACGGCATTTGCTCGCGTGATTGGCGATGACACTTTCCGGCTCGATCGTACCGAGCCGACGCTCAACACCGCGATCCCCGGCGACCCGCGCGATACCACCACGCCGTTAGCGATGGCGCAGACTCTACGCAATCTCACATTGGGCAATGCCCTGGGTGACACTCAGCGTGCGCAGCTGGTGACGTGGCTGAAAGGCAACACCACCGGCGCTGCCAGCATTCAGGCAGGGCTACCCACATCGTGGGTTGTCGGGGATAAAACCGGCAGCGGCGATTATGGTACGACGAATGATATCGCGGTTATTTGGCCGGAAGGTCGCGCGCCGCTCGTTCTGGTGACTTACTTCACCCAGCCGAAGCCGAAGGCAGAGAGCCGTCGTGACGTGCTCGCTGCTGCCGCCAGAATTGTCACCGACGGTTATTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37060","NCBI_taxonomy_name":"Kluyvera","NCBI_taxonomy_id":"579"}}}},"ARO_accession":"3005608","ARO_id":"44070","ARO_name":"CTX-M-185","CARD_short_name":"CTX-M-185","ARO_description":"CTX-M-185 is a CTX-M beta-lactamase.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4515":{"model_id":"4515","model_name":"CTX-M-186","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6890":{"protein_sequence":{"accession":"WP_065419569.1","sequence":"MVKKSLRQFTLMATATVTLSLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"NG_051165.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTCGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3005609","ARO_id":"44071","ARO_name":"CTX-M-186","CARD_short_name":"CTX-M-186","ARO_description":"CTX-M-186 is a CTX-M beta-lactamase.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4516":{"model_id":"4516","model_name":"CTX-M-187","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6891":{"protein_sequence":{"accession":"WP_104009848.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTSSGDYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGS"},"dna_sequence":{"accession":"NG_056409.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTCATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCAGCAGCGGTGACTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCAGCGGCTAAAATCGTCACCGACGGTTCGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3005610","ARO_id":"44072","ARO_name":"CTX-M-187","CARD_short_name":"CTX-M-187","ARO_description":"CTX-M-187 is a CTX-M beta-lactamase.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4517":{"model_id":"4517","model_name":"CTX-M-188","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6892":{"protein_sequence":{"accession":"WP_068981632.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAATVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"NG_051467.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCACGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3005611","ARO_id":"44073","ARO_name":"CTX-M-188","CARD_short_name":"CTX-M-188","ARO_description":"CTX-M-188 is a CTX-M beta-lactamase.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4518":{"model_id":"4518","model_name":"CTX-M-189","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6893":{"protein_sequence":{"accession":"WP_068981633.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYGDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"NG_051468.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACGGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3005612","ARO_id":"44074","ARO_name":"CTX-M-189","CARD_short_name":"CTX-M-189","ARO_description":"CTX-M-189 is a CTX-M beta-lactamase.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4519":{"model_id":"4519","model_name":"CTX-M-190","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6894":{"protein_sequence":{"accession":"WP_069280706.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAVAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYTDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"NG_051509.1","fmin":"100","fmax":"976","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGTGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACACCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3005613","ARO_id":"44075","ARO_name":"CTX-M-190","CARD_short_name":"CTX-M-190","ARO_description":"CTX-M-190 is a CTX-M beta-lactamase.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4520":{"model_id":"4520","model_name":"CTX-M-191","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6895":{"protein_sequence":{"accession":"WP_102607451.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDDTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"NG_056165.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACGATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGACTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3005614","ARO_id":"44076","ARO_name":"CTX-M-191","CARD_short_name":"CTX-M-191","ARO_description":"CTX-M-191 is a CTX-M beta-lactamase.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4521":{"model_id":"4521","model_name":"CTX-M-192","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6896":{"protein_sequence":{"accession":"WP_102607452.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDRTGSGGYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"NG_056166.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAGGACCGGCAGCGGCGGCTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3005615","ARO_id":"44077","ARO_name":"CTX-M-192","CARD_short_name":"CTX-M-192","ARO_description":"CTX-M-192 is a CTX-M beta-lactamase.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4522":{"model_id":"4522","model_name":"CTX-M-193","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6897":{"protein_sequence":{"accession":"WP_077767290.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPITEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"NG_052899.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTACGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3005616","ARO_id":"44078","ARO_name":"CTX-M-193","CARD_short_name":"CTX-M-193","ARO_description":"CTX-M-193 is a CTX-M beta-lactamase.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4523":{"model_id":"4523","model_name":"CTX-M-194","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6898":{"protein_sequence":{"accession":"WP_077767291.1","sequence":"MVKKSLHQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"NG_052900.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCACCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3005617","ARO_id":"44079","ARO_name":"CTX-M-194","CARD_short_name":"CTX-M-194","ARO_description":"CTX-M-194 is a CTX-M beta-lactamase.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4524":{"model_id":"4524","model_name":"CTX-M-195","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6899":{"protein_sequence":{"accession":"WP_077767292.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYSPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGGYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"NG_052901.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAGTCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGGCTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3005618","ARO_id":"44080","ARO_name":"CTX-M-195","CARD_short_name":"CTX-M-195","ARO_description":"CTX-M-195 is a CTX-M beta-lactamase.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4525":{"model_id":"4525","model_name":"CTX-M-196","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6900":{"protein_sequence":{"accession":"WP_077767293.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGGYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAERRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"NG_052902.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGGCTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGCGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3005619","ARO_id":"44081","ARO_name":"CTX-M-196","CARD_short_name":"CTX-M-196","ARO_description":"CTX-M-196 is a CTX-M beta-lactamase.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4526":{"model_id":"4526","model_name":"CTX-M-197","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6901":{"protein_sequence":{"accession":"WP_085562400.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQVGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"NG_054686.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGGTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3005620","ARO_id":"44082","ARO_name":"CTX-M-197","CARD_short_name":"CTX-M-197","ARO_description":"CTX-M-197 is a CTX-M beta-lactamase.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4527":{"model_id":"4527","model_name":"CTX-M-198","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6902":{"protein_sequence":{"accession":"WP_085562401.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAALYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"NG_054687.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGGCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGACTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3005621","ARO_id":"44083","ARO_name":"CTX-M-198","CARD_short_name":"CTX-M-198","ARO_description":"CTX-M-198 is a CTX-M beta-lactamase.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4528":{"model_id":"4528","model_name":"CTX-M-199","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6903":{"protein_sequence":{"accession":"WP_087587947.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPITEKHVNGTMTLAELSAAALQYTDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"NG_054961.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTACCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACACCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3005622","ARO_id":"44084","ARO_name":"CTX-M-199","CARD_short_name":"CTX-M-199","ARO_description":"CTX-M-199 is a CTX-M beta-lactamase.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4529":{"model_id":"4529","model_name":"CTX-M-200","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6904":{"protein_sequence":{"accession":"WP_094009813.1","sequence":"MMTQSIRRSMLTVMATLPLLFSSATLHAQANSVQQQLEALEKSSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKQSESDKHLLNQRVEIKKSDLVNYNPIAEKHVNGTMTLAELGAAALQYSDNTAMNKLIAHLGGPDKVTAFARSLGDETFRLDRTEPTLNTAIPGDPRDTTTPLAMAQTLKNLTLGKALAETQRAQLVTWLKGNTTGSASIRAGLPKSWVVGDKTGIGDYGTTNDIAVIWPENHAPLVLVTYFTQPEQKAESRRDILAAAAKIVTHGF"},"dna_sequence":{"accession":"NG_055501.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGATGACTCAGAGCATTCGCCGCTCAATGTTAACGGTGATGGCGACGCTACCCCTGCTATTTAGCAGCGCAACGCTGCATGCGCAGGCGAACAGCGTGCAACAGCAGCTGGAAGCCCTGGAGAAAAGTTCGGGAGGTCGGCTTGGCGTTGCGCTGATTAACACCGCCGATAATTCGCAGATTCTCTACCGTGCCGATGAACGTTTTGCGATGTGCAGTACCAGTAAGGTGATGGCGGCCGCGGCGGTGCTTAAACAGAGCGAGAGCGATAAGCACCTGCTAAATCAGCGCGTTGAAATCAAGAAGAGCGACCTGGTTAACTACAATCCCATTGCGGAGAAACACGTTAACGGCACGATGACGCTGGCTGAGCTTGGCGCAGCGGCGCTGCAGTATAGCGACAATACTGCCATGAATAAGCTGATTGCCCATCTGGGTGGTCCCGATAAAGTGACGGCGTTTGCTCGCTCGTTGGGTGATGAGACCTTCCGTCTGGACAGAACCGAGCCCACGCTCAATACCGCCATTCCAGGCGACCCGCGTGATACCACCACGCCGCTCGCGATGGCGCAGACCCTGAAAAATCTGACGCTGGGTAAAGCGCTGGCGGAAACTCAGCGGGCACAGTTGGTGACGTGGCTTAAGGGCAATACTACCGGTAGCGCGAGCATTCGGGCGGGTCTGCCGAAATCATGGGTAGTGGGCGATAAAACCGGCATCGGAGATTATGGCACCACCAACGATATCGCGGTTATCTGGCCGGAAAACCACGCACCGCTGGTTCTGGTGACCTACTTTACCCAACCGGAGCAGAAGGCGGAAAGCCGTCGGGATATTCTGGCTGCGGCGGCGAAAATCGTAACCCACGGTTTCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3005623","ARO_id":"44085","ARO_name":"CTX-M-200","CARD_short_name":"CTX-M-200","ARO_description":"CTX-M-200 is a CTX-M beta-lactamase.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4530":{"model_id":"4530","model_name":"CTX-M-201","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6905":{"protein_sequence":{"accession":"WP_094009814.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVYYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"NG_055502.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTTACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGACTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3005624","ARO_id":"44086","ARO_name":"CTX-M-201","CARD_short_name":"CTX-M-201","ARO_description":"CTX-M-201 is a CTX-M beta-lactamase.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4531":{"model_id":"4531","model_name":"CTX-M-202","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6906":{"protein_sequence":{"accession":"WP_088245215.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVIYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"NG_055272.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCATTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3005625","ARO_id":"44087","ARO_name":"CTX-M-202","CARD_short_name":"CTX-M-202","ARO_description":"CTX-M-202 is a CTX-M beta-lactamase.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4532":{"model_id":"4532","model_name":"CTX-M-203","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6907":{"protein_sequence":{"accession":"WP_088245212.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDRTGSGDYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"NG_055269.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAGAACCGGCAGCGGTGACTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3005626","ARO_id":"44088","ARO_name":"CTX-M-203","CARD_short_name":"CTX-M-203","ARO_description":"CTX-M-203 is a CTX-M beta-lactamase.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4533":{"model_id":"4533","model_name":"CTX-M-204","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6908":{"protein_sequence":{"accession":"WP_088245225.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRIEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGDYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"NG_055283.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTATCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGACTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3005627","ARO_id":"44089","ARO_name":"CTX-M-204","CARD_short_name":"CTX-M-204","ARO_description":"CTX-M-204 is a CTX-M beta-lactamase.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4534":{"model_id":"4534","model_name":"CTX-M-205","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6909":{"protein_sequence":{"accession":"WP_099156053.1","sequence":"MMRKSVRRAILMTTACVSLLLASVPLCAQANDVQQKLAALEKSSGGRLGVALINTADNTQTLYRADERFAMCSTSKVMAAAAVLKQSETQKDLLSQRVEIKSSDLINYNPIAEKHVNGTMTLGELSAAALQYSDNTAMNKLIAHLGGPGKVTAFARAIGDDTFRLDRTEPTLNTAIPGDPRDTTTPLAMAQTLRNLTLGNALGDTQRAQLVTWLKGNTTGAASIQAGLPTSWVVGDKTGSGDYGTTNDIAVIWPEGRAPLVLVTYFTQPKPKAESRGDVLAAAARIVTDGY"},"dna_sequence":{"accession":"NG_055667.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGATGAGAAAAAGCGTAAGGCGGGCGATATTAATGACGACAGCCTGTGTTTCGCTGCTGTTGGCCAGTGTGCCGCTGTGTGCCCAGGCGAACGATGTTCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGGGGACGACTGGGTGTGGCGTTGATTAACACCGCCGATAACACGCAGACGCTCTACCGCGCCGACGAGCGTTTTGCTATGTGCAGCACCAGTAAAGTGATGGCGGCGGCGGCGGTGCTTAAGCAAAGTGAAACGCAAAAAGACTTACTGAGTCAGCGGGTTGAAATTAAGTCATCAGACTTGATTAACTACAACCCAATCGCTGAAAAGCACGTCAATGGCACGATGACACTCGGGGAGCTGAGCGCGGCGGCGCTGCAGTACAGCGATAATACTGCCATGAATAAGCTGATTGCCCATCTCGGGGGGCCGGGTAAAGTGACGGCATTTGCTCGTGCGATTGGCGATGACACTTTCCGGCTCGATCGTACCGAGCCGACGCTCAACACCGCGATCCCCGGCGACCCGCGCGATACCACCACGCCGTTAGCGATGGCGCAGACTCTACGCAATCTCACATTGGGCAATGCCCTGGGTGACACTCAGCGTGCGCAGCTGGTGACGTGGCTGAAAGGCAACACCACCGGCGCTGCCAGCATTCAGGCAGGGCTACCCACATCGTGGGTTGTCGGGGATAAAACCGGCAGCGGCGATTATGGTACGACGAATGATATCGCGGTTATTTGGCCGGAAGGTCGCGCGCCGCTCGTTCTGGTGACTTACTTCACCCAGCCGAAGCCGAAGGCAGAGAGCCGTGGTGACGTGCTCGCTGCTGCCGCCAGAATTGTCACCGACGGTTATTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36929","NCBI_taxonomy_name":"Kluyvera georgiana","NCBI_taxonomy_id":"73098"}}}},"ARO_accession":"3005628","ARO_id":"44090","ARO_name":"CTX-M-205","CARD_short_name":"CTX-M-205","ARO_description":"CTX-M-205 is a CTX-M beta-lactamase.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4535":{"model_id":"4535","model_name":"CTX-M-206","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6910":{"protein_sequence":{"accession":"WP_102607455.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPSLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGDYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"NG_056171.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGGGTGGCATTGATTAACACAGCGGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTCGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAGTCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTGGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCAGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGACTATGGCACCACCAATGATATCGCGGTGATTTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005629","ARO_id":"44091","ARO_name":"CTX-M-206","CARD_short_name":"CTX-M-206","ARO_description":"CTX-M-206 is a CTX-M beta-lactamase.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4536":{"model_id":"4536","model_name":"CTX-M-207","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6911":{"protein_sequence":{"accession":"WP_102607456.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAVAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGSYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"NG_056173.1","fmin":"100","fmax":"976","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGTGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTAGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3005630","ARO_id":"44092","ARO_name":"CTX-M-207","CARD_short_name":"CTX-M-207","ARO_description":"CTX-M-207 is a CTX-M beta-lactamase.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4537":{"model_id":"4537","model_name":"CTX-M-208","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6912":{"protein_sequence":{"accession":"WP_109545060.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAESIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"NG_057474.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGAGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3005631","ARO_id":"44093","ARO_name":"CTX-M-208","CARD_short_name":"CTX-M-208","ARO_description":"CTX-M-208 is a CTX-M beta-lactamase.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4538":{"model_id":"4538","model_name":"CTX-M-209","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6913":{"protein_sequence":{"accession":"WP_109545061.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVIWMKGNTTGAASIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"NG_057475.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGATATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3005632","ARO_id":"44094","ARO_name":"CTX-M-209","CARD_short_name":"CTX-M-209","ARO_description":"CTX-M-209 is a CTX-M beta-lactamase.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4539":{"model_id":"4539","model_name":"CTX-M-210","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6914":{"protein_sequence":{"accession":"WP_109545062.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTTDVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"NG_057476.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGACGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3005633","ARO_id":"44095","ARO_name":"CTX-M-210","CARD_short_name":"CTX-M-210","ARO_description":"CTX-M-210 is a CTX-M beta-lactamase.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4540":{"model_id":"4540","model_name":"CTX-M-211","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6915":{"protein_sequence":{"accession":"WP_109545063.1","sequence":"MVKKSKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGDYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"NG_057477.1","fmin":"0","fmax":"885","strand":"+","sequence":"ATGGTTAAAAAATCTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGACTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3005634","ARO_id":"44096","ARO_name":"CTX-M-211","CARD_short_name":"CTX-M-211","ARO_description":"CTX-M-211 is a CTX-M beta-lactamase.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4541":{"model_id":"4541","model_name":"CTX-M-212","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6916":{"protein_sequence":{"accession":"WP_109545064.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAVAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTETTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGDYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"NG_057478.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGGGTGGCATTGATTAACACAGCGGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGTGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGACGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGACTATGGCACCACCAATGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3005635","ARO_id":"44097","ARO_name":"CTX-M-212","CARD_short_name":"CTX-M-212","ARO_description":"CTX-M-212 is a CTX-M beta-lactamase.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4542":{"model_id":"4542","model_name":"CTX-M-213","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6917":{"protein_sequence":{"accession":"WP_106924209.1","sequence":"MVTKRMQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTEDNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFAREIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"NG_057473.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTGACAAAGAGAATGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGAAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGAGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGACTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"45690","NCBI_taxonomy_name":"Kluyvera genomosp. 2","NCBI_taxonomy_id":"2774054"}}}},"ARO_accession":"3005636","ARO_id":"44098","ARO_name":"CTX-M-213","CARD_short_name":"CTX-M-213","ARO_description":"CTX-M-213 is a CTX-M beta-lactamase.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4543":{"model_id":"4543","model_name":"CTX-M-214","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6918":{"protein_sequence":{"accession":"WP_109545069.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPITEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTAGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"NG_057483.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTACCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAGCTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCACAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGCAGGTGATAAGACCGGCAGCGGCGACTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3005637","ARO_id":"44099","ARO_name":"CTX-M-214","CARD_short_name":"CTX-M-214","ARO_description":"CTX-M-214 is a CTX-M beta-lactamase.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4544":{"model_id":"4544","model_name":"CTX-M-215","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6919":{"protein_sequence":{"accession":"WP_128268235.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDDTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAEHRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"NG_063838.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACGATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGACTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGCACCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3005638","ARO_id":"44100","ARO_name":"CTX-M-215","CARD_short_name":"CTX-M-215","ARO_description":"CTX-M-215 is a CTX-M beta-lactamase.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4545":{"model_id":"4545","model_name":"CTX-M-216","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6920":{"protein_sequence":{"accession":"WP_109791209.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDSL"},"dna_sequence":{"accession":"NG_057608.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACAGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3005639","ARO_id":"44101","ARO_name":"CTX-M-216","CARD_short_name":"CTX-M-216","ARO_description":"CTX-M-216 is a CTX-M beta-lactamase.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4546":{"model_id":"4546","model_name":"CTX-M-217","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6921":{"protein_sequence":{"accession":"WP_109791211.1","sequence":"MMRKSVRRAMLMTTACVSLLLASVPLCAQANDVQQKLAALEKSSGGRLGVALINTADNTQTLYRADERFAMCSTSKVMAAAAVLKQSETQKGLLSQRVEIKPSDLINYSPIAEKHVNGTMTFGELSAAALQYSDNTAMNKLIAHLGGPDKVTAFARTIGDDTFRLDRTEPTLNTAIPGDPRDTTTPLAMAQALRNLTLGNALGDTQRAQLVMWLKGNTTGAASIQAGLPTSWVVGDKTGSGGYGTTNDIAVIWPEGRAPLVLVTYFTQSEPKAESRRDVLAAAARIVTDGY"},"dna_sequence":{"accession":"NG_057610.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGATGAGAAAAAGCGTAAGGCGGGCGATGTTAATGACGACAGCCTGTGTTTCGCTGCTGTTGGCCAGTGTGCCGCTGTGTGCCCAGGCGAACGATGTTCAACAAAAGCTCGCGGCGCTGGAGAAAAGCAGCGGGGGACGACTGGGTGTGGCGTTGATTAACACCGCCGATAACACGCAGACGCTCTACCGCGCCGACGAGCGTTTTGCCATGTGCAGCACCAGTAAAGTGATGGCGGCAGCGGCGGTGCTTAAGCAAAGTGAAACGCAAAAGGGCTTGTTGAGTCAGCGGGTTGAAATTAAGCCCTCAGACTTGATTAACTACAGCCCCATTGCGGAAAAACACGTCAATGGCACGATGACATTCGGGGAGTTGAGCGCGGCGGCGCTACAGTACAGCGATAATACTGCCATGAATAAGCTGATTGCCCATCTCGGGGGGCCGGATAAAGTGACGGCATTTGCCCGTACGATTGGCGATGACACGTTCCGGCTCGATCGTACCGAGCCGACGCTCAACACCGCGATCCCCGGCGACCCGCGCGATACCACCACGCCGTTAGCGATGGCGCAGGCTCTGCGCAATCTGACGTTGGGCAATGCCCTGGGTGACACTCAGCGTGCGCAGCTGGTGATGTGGCTGAAAGGCAACACCACCGGCGCTGCCAGCATTCAGGCAGGGCTACCCACATCGTGGGTTGTCGGGGATAAAACCGGCAGCGGCGGTTATGGTACGACGAATGATATCGCGGTTATTTGGCCGGAAGGTCGCGCGCCGCTCGTTCTGGTGACTTACTTCACCCAGTCGGAGCCGAAGGCAGAGAGCCGTCGTGACGTGCTCGCTGCTGCCGCCAGAATTGTCACCGACGGTTATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36946","NCBI_taxonomy_name":"Providencia stuartii","NCBI_taxonomy_id":"588"}}}},"ARO_accession":"3005640","ARO_id":"44102","ARO_name":"CTX-M-217","CARD_short_name":"CTX-M-217","ARO_description":"CTX-M-217 is a CTX-M beta-lactamase.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4547":{"model_id":"4547","model_name":"CTX-M-218","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6922":{"protein_sequence":{"accession":"WP_109791214.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYTDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"NG_057613.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACACCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3005641","ARO_id":"44103","ARO_name":"CTX-M-218","CARD_short_name":"CTX-M-218","ARO_description":"CTX-M-218 is a CTX-M beta-lactamase.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4548":{"model_id":"4548","model_name":"CTX-M-219","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6923":{"protein_sequence":{"accession":"WP_110092882.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTESTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGDYGTTNDIAVIWPQGRAPLVLVIYFTQPQQNAESRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"NG_059336.1","fmin":"100","fmax":"976","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAGCTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAATCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCACAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTAGGTGATAAGACCGGCAGCGGCGACTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGATCTATTTTACCCAGCCGCAACAGAACGCAGAGAGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3005642","ARO_id":"44104","ARO_name":"CTX-M-219","CARD_short_name":"CTX-M-219","ARO_description":"CTX-M-219 is a CTX-M beta-lactamase.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4549":{"model_id":"4549","model_name":"CTX-M-220","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6924":{"protein_sequence":{"accession":"WP_111672902.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYSPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGDYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"NG_060560.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAGTCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGACTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3005643","ARO_id":"44105","ARO_name":"CTX-M-220","CARD_short_name":"CTX-M-220","ARO_description":"CTX-M-220 is a CTX-M beta-lactamase.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4550":{"model_id":"4550","model_name":"CTX-M-221","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6925":{"protein_sequence":{"accession":"WP_114699284.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTESTLNTAIPGDPRDTTTPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGDYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"NG_061413.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAATCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGACTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36783","NCBI_taxonomy_name":"Serratia marcescens","NCBI_taxonomy_id":"615"}}}},"ARO_accession":"3005644","ARO_id":"44106","ARO_name":"CTX-M-221","CARD_short_name":"CTX-M-221","ARO_description":"CTX-M-221 is a CTX-M beta-lactamase.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4551":{"model_id":"4551","model_name":"CTX-M-222","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6926":{"protein_sequence":{"accession":"WP_116786829.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAVAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVDGTMSLAELSAAALQYSDNVAMNKLISHVGGPASITAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGDYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTNGL"},"dna_sequence":{"accession":"NG_061609.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGTCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGAAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGTGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACTTGGTTAACTATAATCCGATTGCGGAAAAGCACGTCGATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTTCTCACGTTGGCGGCCCGGCTAGCATCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGTAATCTGACGCTGGGTAAAGCATTGGGTGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGACTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCAACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3005645","ARO_id":"44107","ARO_name":"CTX-M-222","CARD_short_name":"CTX-M-222","ARO_description":"CTX-M-222 is a CTX-M beta-lactamase.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4552":{"model_id":"4552","model_name":"CTX-M-223","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6927":{"protein_sequence":{"accession":"WP_122630862.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYSPIAEKHVNGTMTLAELSAAVLQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGGYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"NG_062275.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAGTCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGTGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGGCTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3005646","ARO_id":"44108","ARO_name":"CTX-M-223","CARD_short_name":"CTX-M-223","ARO_description":"CTX-M-223 is a CTX-M beta-lactamase.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4553":{"model_id":"4553","model_name":"CTX-M-224","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6928":{"protein_sequence":{"accession":"WP_094166899.1","sequence":"MVKKSLRLFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"NG_062241.1","fmin":"100","fmax":"976","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCTGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39773","NCBI_taxonomy_name":"Enterobacter kobei","NCBI_taxonomy_id":"208224"}}}},"ARO_accession":"3005647","ARO_id":"44109","ARO_name":"CTX-M-224","CARD_short_name":"CTX-M-224","ARO_description":"CTX-M-224 is a CTX-M beta-lactamase.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4554":{"model_id":"4554","model_name":"CTX-M-225","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6929":{"protein_sequence":{"accession":"WP_136512064.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPTSWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"NG_064720.1","fmin":"72","fmax":"948","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTACTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3005648","ARO_id":"44110","ARO_name":"CTX-M-225","CARD_short_name":"CTX-M-225","ARO_description":"CTX-M-225 is a CTX-M beta-lactamase.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4555":{"model_id":"4555","model_name":"CTX-M-226","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6930":{"protein_sequence":{"accession":"WP_136512065.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVTLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAVAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"NG_064721.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGACGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGTGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3005649","ARO_id":"44111","ARO_name":"CTX-M-226","CARD_short_name":"CTX-M-226","ARO_description":"CTX-M-226 is a CTX-M beta-lactamase.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4556":{"model_id":"4556","model_name":"CTX-M-227","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6931":{"protein_sequence":{"accession":"WP_148044409.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAVAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTSSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDRL"},"dna_sequence":{"accession":"NG_065865.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGTGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCAGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACCGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3005650","ARO_id":"44112","ARO_name":"CTX-M-227","CARD_short_name":"CTX-M-227","ARO_description":"CTX-M-227 is a CTX-M beta-lactamase.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4557":{"model_id":"4557","model_name":"CTX-M-228","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6932":{"protein_sequence":{"accession":"WP_148044410.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAANIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"NG_065866.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAACATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3005651","ARO_id":"44113","ARO_name":"CTX-M-228","CARD_short_name":"CTX-M-228","ARO_description":"CTX-M-228 is a CTX-M beta-lactamase.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4558":{"model_id":"4558","model_name":"CTX-M-229","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6933":{"protein_sequence":{"accession":"WP_148044411.1","sequence":"MMTQSIRRSMLTVMATLPLLFSSATLHAQANSVQQQLEALEKSSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKQSESDKHLLNQRVEIKKSDLVNYNPIAEKHVNGTMTLAELGAAALQYSDNTAMNKLIAHLGGPDKVTAFARSLGDETFRLDSTEPTLNTAPGDPRDTTTPLAMAQTLKNLTLGKALAETQRAQLVTWLKGNTTGSASIRAGLPKSWVVGDKTGSGDYGTTNDIAVIWPENHAPLVLVTYFTQPEQKAESRRDILAAAAKIVTHGF"},"dna_sequence":{"accession":"NG_065867.1","fmin":"0","fmax":"873","strand":"+","sequence":"ATGATGACTCAGAGCATTCGCCGCTCAATGTTAACGGTGATGGCGACGCTACCCCTGCTATTTAGCAGCGCAACGCTGCATGCGCAGGCGAACAGCGTGCAACAGCAGCTGGAAGCCCTGGAGAAAAGTTCGGGAGGTCGGCTTGGCGTTGCGCTGATTAACACCGCCGATAATTCGCAGATTCTCTACCGTGCCGATGAACGTTTTGCGATGTGCAGTACCAGTAAGGTGATGGCGGCCGCGGCGGTGCTTAAACAGAGCGAGAGCGATAAGCACCTGCTAAATCAGCGCGTTGAAATCAAGAAGAGCGACCTGGTTAACTACAATCCCATTGCGGAGAAACACGTTAACGGCACGATGACGCTGGCTGAGCTTGGCGCAGCGGCGCTGCAGTATAGCGACAATACTGCCATGAATAAGCTGATTGCCCATCTGGGTGGTCCCGATAAAGTGACGGCGTTTGCTCGCTCGTTGGGTGATGAGACCTTCCGTCTGGACAGCACCGAGCCCACGCTCAATACCGCCCCAGGCGACCCGCGTGATACCACCACGCCGCTCGCGATGGCGCAGACCCTGAAAAATCTGACGCTGGGTAAAGCGCTGGCGGAAACTCAGCGGGCACAGTTGGTGACGTGGCTTAAGGGCAATACTACCGGTAGCGCGAGCATTCGGGCGGGTCTGCCGAAATCATGGGTAGTGGGCGATAAAACCGGCAGCGGAGATTATGGCACCACCAACGATATCGCGGTTATCTGGCCGGAAAACCACGCACCGCTGGTTCTGGTGACCTACTTTACCCAACCGGAGCAGAAGGCGGAAAGCCGTCGGGATATTCTGGCTGCGGCGGCGAAAATCGTAACCCACGGTTTCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005652","ARO_id":"44114","ARO_name":"CTX-M-229","CARD_short_name":"CTX-M-229","ARO_description":"CTX-M-229 is a CTX-M beta-lactamase.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4559":{"model_id":"4559","model_name":"CTX-M-230","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6934":{"protein_sequence":{"accession":"WP_156404650.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAVAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNIAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"NG_067139.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGTGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACATCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3005653","ARO_id":"44115","ARO_name":"CTX-M-230","CARD_short_name":"CTX-M-230","ARO_description":"CTX-M-230 is a CTX-M beta-lactamase.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4560":{"model_id":"4560","model_name":"CTX-M-231","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6935":{"protein_sequence":{"accession":"WP_156404651.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTEDVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"NG_067140.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGAGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3005654","ARO_id":"44116","ARO_name":"CTX-M-231","CARD_short_name":"CTX-M-231","ARO_description":"CTX-M-231 is a CTX-M beta-lactamase.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4561":{"model_id":"4561","model_name":"CTX-M-232","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6936":{"protein_sequence":{"accession":"WP_156404652.1","sequence":"MVKKSLRQFTLMATTTVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"NG_067141.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGACAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3005655","ARO_id":"44117","ARO_name":"CTX-M-232","CARD_short_name":"CTX-M-232","ARO_description":"CTX-M-232 is a CTX-M beta-lactamase.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4562":{"model_id":"4562","model_name":"CTX-M-233","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6937":{"protein_sequence":{"accession":"WP_156404653.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDKTFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGGYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"NG_067142.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATAAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGGCTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3005656","ARO_id":"44118","ARO_name":"CTX-M-233","CARD_short_name":"CTX-M-233","ARO_description":"CTX-M-233 is a CTX-M beta-lactamase.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4563":{"model_id":"4563","model_name":"CTX-M-234","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6938":{"protein_sequence":{"accession":"WP_168247877.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFPMCSTSKVMAVAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMTLAELSAAALQYTDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"NG_068168.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTCCAATGTGCAGCACCAGTAAAGTGATGGCCGTGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACACCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3005657","ARO_id":"44119","ARO_name":"CTX-M-234","CARD_short_name":"CTX-M-234","ARO_description":"CTX-M-234 is a CTX-M beta-lactamase.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4564":{"model_id":"4564","model_name":"CTX-M-235","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6939":{"protein_sequence":{"accession":"WP_168247878.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLINYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"NG_068169.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGATTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGACTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3005658","ARO_id":"44120","ARO_name":"CTX-M-235","CARD_short_name":"CTX-M-235","ARO_description":"CTX-M-235 is a CTX-M beta-lactamase.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4565":{"model_id":"4565","model_name":"CTX-M-236","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6940":{"protein_sequence":{"accession":"WP_156658722.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASRVVGDKTGSGDYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"NG_068506.1","fmin":"100","fmax":"976","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCCGGGTTGTGGGGGATAAAACCGGCAGCGGTGACTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3005659","ARO_id":"44121","ARO_name":"CTX-M-236","CARD_short_name":"CTX-M-236","ARO_description":"CTX-M-236 is a CTX-M beta-lactamase.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4566":{"model_id":"4566","model_name":"CTX-M-237","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6941":{"protein_sequence":{"accession":"WP_188331864.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFVRQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"NG_070730.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGTCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3005660","ARO_id":"44122","ARO_name":"CTX-M-237","CARD_short_name":"CTX-M-237","ARO_description":"CTX-M-237 is a CTX-M beta-lactamase.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4567":{"model_id":"4567","model_name":"CTX-M-238","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6942":{"protein_sequence":{"accession":"WP_188331865.1","sequence":"MVKKSLRQFALMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"NG_070731.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCGCGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3005661","ARO_id":"44123","ARO_name":"CTX-M-238","CARD_short_name":"CTX-M-238","ARO_description":"CTX-M-238 is a CTX-M beta-lactamase.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4568":{"model_id":"4568","model_name":"CTX-M-239","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6943":{"protein_sequence":{"accession":"WP_188331866.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYGDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDRTGSGGYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"NG_070732.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACGGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAGGACCGGCAGCGGCGGCTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3005662","ARO_id":"44124","ARO_name":"CTX-M-239","CARD_short_name":"CTX-M-239","ARO_description":"CTX-M-239 is a CTX-M beta-lactamase.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4569":{"model_id":"4569","model_name":"CTX-M-240","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6944":{"protein_sequence":{"accession":"WP_182496339.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLSTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGGYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"NG_070733.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAGTACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGGCTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3005663","ARO_id":"44125","ARO_name":"CTX-M-240","CARD_short_name":"CTX-M-240","ARO_description":"CTX-M-240 is a CTX-M beta-lactamase.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4570":{"model_id":"4570","model_name":"CTX-M-241","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6945":{"protein_sequence":{"accession":"WP_188331867.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAVAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"NG_070734.1","fmin":"0","fmax":"870","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGTCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGACTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3005664","ARO_id":"44126","ARO_name":"CTX-M-241","CARD_short_name":"CTX-M-241","ARO_description":"CTX-M-241 is a CTX-M beta-lactamase.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4571":{"model_id":"4571","model_name":"CTX-M-242","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6946":{"protein_sequence":{"accession":"WP_190259775.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAKLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGGYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"NG_070784.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGAAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGGCTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3005665","ARO_id":"44127","ARO_name":"CTX-M-242","CARD_short_name":"CTX-M-242","ARO_description":"CTX-M-242 is a CTX-M beta-lactamase.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4572":{"model_id":"4572","model_name":"CTX-M-244","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6947":{"protein_sequence":{"accession":"WP_204376225.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSISKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"NG_073460.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCATCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3005666","ARO_id":"44128","ARO_name":"CTX-M-244","CARD_short_name":"CTX-M-244","ARO_description":"CTX-M-244 is a CTX-M beta-lactamase.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4573":{"model_id":"4573","model_name":"CTX-M-73","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6948":{"protein_sequence":{"accession":"WP_063860072.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAMQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"NG_049025.1","fmin":"100","fmax":"976","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGATGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGACTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3001934","ARO_id":"38334","ARO_name":"CTX-M-73","CARD_short_name":"CTX-M-73","ARO_description":"CTX-M-73 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4574":{"model_id":"4574","model_name":"CTX-M-97","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"6949":{"protein_sequence":{"accession":"WP_063860093.1","sequence":"MMTQSIGRSMLTVMATLPLLFSSATLHAQANSVQQQLEALEKSSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKQSESDKHLLNQRVEIKKSDLVNYNPIAEKHVNGTMTLAELGAAALQYSDNTAMNKLIAHLGGPDKVTAFARSLGDETFRLDRTEPTLNTAIPGDPRDTTTPLAMAQTLKNLTLGKALAETQRAQLVTWLKGNTTGSASIRAGLPKSWVVGDKTGSGDYGTTNDIAVIWPENHAPLVLVTYFTQPEQKAESRRDILAAAAKIVTHGF"},"dna_sequence":{"accession":"NG_049051.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGATGACTCAGAGCATTGGCCGCTCAATGTTAACGGTGATGGCGACGCTACCCCTGCTATTTAGCAGCGCAACGCTGCATGCGCAGGCGAACAGCGTGCAACAGCAGCTGGAAGCCCTGGAGAAAAGTTCGGGAGGTCGGCTTGGCGTTGCGCTGATTAACACCGCCGATAATTCGCAGATTCTCTACCGTGCCGATGAACGTTTTGCGATGTGCAGTACCAGTAAGGTGATGGCGGCCGCGGCGGTGCTTAAACAGAGCGAGAGCGATAAGCACCTGCTAAATCAGCGCGTTGAAATCAAGAAGAGCGACCTGGTTAACTACAATCCCATTGCGGAGAAACACGTTAACGGCACGATGACGCTGGCTGAGCTTGGCGCAGCGGCGCTGCAGTATAGCGACAATACTGCCATGAATAAGCTGATTGCCCATCTGGGTGGTCCCGATAAAGTGACGGCGTTTGCTCGCTCGTTGGGTGATGAGACCTTCCGTCTGGACAGAACCGAGCCCACGCTCAATACCGCCATTCCAGGCGACCCGCGTGATACCACCACGCCGCTCGCGATGGCGCAGACCCTGAAAAATCTGACGCTGGGTAAAGCGCTGGCGGAAACTCAGCGGGCACAGTTGGTGACGTGGCTTAAGGGCAATACTACCGGTAGCGCGAGCATTCGGGCGGGTCTGCCGAAATCATGGGTAGTGGGCGATAAAACCGGCAGCGGAGATTATGGCACCACCAACGATATCGCGGTTATCTGGCCGGAAAACCACGCACCGCTGGTTCTGGTGACCTACTTTACCCAACCGGAGCAGAAGGCGGAAAGCCGTCGGGATATTCTGGCTGCGGCGGCGAAAATCGTAACCCACGGTTTCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3005667","ARO_id":"44129","ARO_name":"CTX-M-97","CARD_short_name":"CTX-M-97","ARO_description":"CTX-M-97 is a CTX-M beta-lactamase.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4575":{"model_id":"4575","model_name":"CVI-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"6950":{"protein_sequence":{"accession":"WP_164461288.1","sequence":"MRTVFGFAGALLGLAAAACAAQGGLALKHLKGGVYVVEDGYYAKENSVVYVGAEHVTVVGATWTPDTARELARQIRAVTYKPIAEVVNPNYHPDRAGGNAYWKSIGARIVSTRQTADEMRRGWDEVVAFTRRGFPDYPALPVSLPDREHPGDFELQDGRIKAFHLGAAHTRDGIFIHFPQERVLYGNCILKQELGNLSYADLNEYPKTLERLKLSELDFDTVIAGHLDALHGPELIDHYQRLLKRQASDAAAERS"},"dna_sequence":{"accession":"NG_067986.1","fmin":"72","fmax":"840","strand":"+","sequence":"ATGCGCACAGTATTTGGATTCGCCGGCGCGCTGTTGGGCCTGGCGGCCGCCGCCTGCGCGGCGCAGGGCGGCCTGGCTCTCAAGCACCTGAAGGGCGGCGTGTACGTGGTGGAGGATGGCTATTACGCCAAGGAGAACTCGGTGGTCTATGTCGGCGCGGAGCACGTGACCGTGGTGGGCGCCACCTGGACGCCGGATACGGCCCGAGAGCTGGCGCGGCAGATACGCGCGGTCACCTACAAGCCGATCGCGGAAGTGGTCAATCCCAATTATCACCCCGACCGCGCCGGAGGGAACGCATACTGGAAGTCCATCGGCGCCCGCATCGTGTCGACCCGGCAGACCGCCGACGAGATGCGCCGGGGGTGGGACGAGGTCGTCGCCTTCACCCGCCGCGGCTTTCCCGATTATCCGGCGCTGCCCGTCTCGCTGCCGGACCGCGAGCATCCCGGCGATTTCGAGCTGCAGGATGGCAGGATCAAGGCTTTCCACCTGGGCGCTGCGCATACCCGCGATGGCATCTTCATCCATTTTCCGCAGGAGAGGGTGTTGTACGGCAACTGCATTCTCAAGCAGGAGCTGGGCAACCTGAGTTACGCCGACCTGAACGAATACCCGAAAACGCTGGAACGGCTCAAGCTCAGCGAGCTCGATTTCGATACGGTCATCGCCGGGCATCTCGACGCCTTGCATGGTCCGGAACTGATCGACCATTACCAGCGGCTGCTGAAGCGGCAGGCATCGGATGCCGCGGCCGAACGCAGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3006924","ARO_id":"45386","ARO_name":"CVI-1","CARD_short_name":"CVI-1","ARO_description":"CVI-1 is a CVI beta-lactamase.","ARO_category":{"43863":{"category_aro_accession":"3005403","category_aro_cvterm_id":"43863","category_aro_name":"CVI beta-lactamase","category_aro_description":"CVI beta-lactamases are a class B2 beta-lactamase found in Chromobacterium violaceum.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4576":{"model_id":"4576","model_name":"DHA-23","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6951":{"protein_sequence":{"accession":"WP_063860108.1","sequence":"MKKSLSATLISALLAFSAPGFSAADNVAAVVDSTIKPLMAQQDIPGMAVAVSVKGKPYYFNYGFADIQAKQPVTENTLFELGSVSKTFTGVLGAVSVAKKEMALNDPAAKYQPELALPQWKGITLLDLATYTAGGLPLQVPDAVKSRADLLNFYQQWQPSRKPGDMRLYANSSIGLFGALTANAAGMPYEQLLTARILAPLGLSHTFITVPESAQSQYAYGYKNKKPVRVSPGQLDAESYGVKSSSKDMLRWAEMNMEPSRAGNADLEMAMYLAQTRYYKTAAINQGLGWEMYDWPQQKDMIINGVTNEVALQPHPVTDNQVQPYNRASWVHKTGATTGFGAYVAFIPEKQVAIVILANKNYPNTERVKAAQAILSALE"},"dna_sequence":{"accession":"NG_049069.1","fmin":"0","fmax":"1140","strand":"+","sequence":"ATGAAAAAATCGTTATCTGCAACACTGATTTCCGCTCTGCTGGCGTTTTCCGCCCCGGGGTTTTCTGCCGCTGATAATGTCGCGGCGGTGGTGGACAGCACCATTAAACCGCTGATGGCACAGCAGGATATTCCCGGGATGGCGGTTGCCGTCTCCGTAAAGGGTAAGCCCTATTATTTCAATTATGGTTTTGCCGATATTCAGGCAAAACAGCCGGTCACTGAAAATACACTATTTGAGCTCGGATCTGTAAGTAAAACTTTCACAGGTGTGCTGGGTGCGGTTTCTGTGGCGAAAAAAGAGATGGCGCTGAATGATCCGGCGGCAAAATACCAGCCGGAGCTGGCTCTGCCGCAGTGGAAGGGGATCACATTGCTGGATCTGGCTACCTATACCGCAGGCGGACTGCCGTTACAGGTGCCGGATGCGGTAAAAAGCCGTGCGGATCTGCTGAATTTCTATCAGCAGTGGCAGCCGTCCCGGAAACCGGGCGATATGCGTCTGTATGCAAACAGCAGTATCGGCCTGTTTGGTGCTCTGACCGCAAACGCGGCGGGGATGCCGTATGAGCAGTTGCTGACTGCACGGATCCTGGCACCGCTGGGGTTATCTCACACCTTTATTACTGTGCCGGAAAGTGCGCAAAGCCAGTATGCGTACGGTTATAAAAACAAAAAACCGGTCCGCGTGTCGCCGGGACAGCTTGATGCGGAATCTTACGGCGTGAAATCCTCCTCAAAAGATATGCTGCGCTGGGCGGAAATGAATATGGAGCCGTCACGGGCCGGTAATGCGGATCTGGAAATGGCAATGTATCTCGCCCAGACCCGCTACTATAAAACCGCCGCGATTAACCAGGGGCTGGGCTGGGAAATGTATGACTGGCCGCAGCAGAAAGATATGATCATTAACGGTGTGACCAACGAGGTCGCATTGCAGCCGCATCCGGTAACAGACAACCAGGTTCAGCCGTATAACCGTGCTTCCTGGGTGCATAAAACGGGCGCAACAACTGGTTTCGGCGCCTATGTCGCCTTTATTCCGGAAAAACAGGTGGCGATTGTGATTCTGGCGAATAAAAACTACCCGAATACCGAAAGAGTCAAAGCTGCACAGGCTATTTTGAGTGCACTGGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002154","ARO_id":"38554","ARO_name":"DHA-23","CARD_short_name":"DHA-23","ARO_description":"DHA-23 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36207":{"category_aro_accession":"3000068","category_aro_cvterm_id":"36207","category_aro_name":"DHA beta-lactamase","category_aro_description":"DHA beta-lactamases are plasmid-mediated AmpC \u03b2-lactamases that confer resistance to cephamycins and oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4577":{"model_id":"4577","model_name":"DHA-24","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6952":{"protein_sequence":{"accession":"WP_063860114.1","sequence":"MKKSLSATLISALLAFSAPGFSAADNVAAVVDSTIKPLMAQQDIPGMAVAVSVKGKPYYFNYGFADIQAKQPVTENTLFELGSVSKTFTGVLGAVSVAKKEMALNDPAAKYQPELALPQWKGITLLDLATYTAGGLPLQVPDAVKSRADLLNFYQQWQPSRKPGDMRLYANSSIGLFGALTANAAGMPYEQLLTARILAPLGLSHTFITVPESAQSQYAYGYKNKKPVRVSPGQLDAESYGVKSASKDMLRWAEMNMEPSRAGNADLEMAMYLAQTRYYKTAAINQGLGWEMYDWPQQKDMIINGVTNEVALQPHPVTDNQVQPYNRASWVHKTGAATGFGAYVAFIPEKQVAIVILANKNYPNTERVKAAQAILSALE"},"dna_sequence":{"accession":"NG_049070.1","fmin":"0","fmax":"1140","strand":"+","sequence":"ATGAAAAAATCGTTATCTGCAACACTGATTTCCGCTCTGCTGGCGTTTTCCGCCCCGGGGTTTTCTGCCGCTGATAATGTCGCGGCGGTGGTGGACAGCACCATTAAACCGCTGATGGCACAGCAGGATATTCCCGGGATGGCGGTTGCCGTCTCCGTAAAGGGTAAGCCCTATTATTTCAATTATGGTTTTGCCGATATTCAGGCAAAACAGCCGGTCACTGAAAATACACTATTTGAGCTCGGATCTGTAAGTAAAACTTTCACAGGTGTGCTGGGTGCGGTTTCTGTGGCGAAAAAAGAGATGGCGCTGAATGATCCGGCGGCAAAATACCAGCCGGAGCTGGCTCTGCCGCAGTGGAAGGGGATCACATTGCTGGATCTGGCTACCTATACCGCAGGCGGACTGCCGTTACAGGTGCCGGATGCGGTAAAAAGCCGTGCGGATCTGCTGAATTTCTATCAGCAGTGGCAGCCGTCCCGGAAACCGGGCGATATGCGTCTGTATGCAAACAGCAGTATCGGCCTGTTTGGTGCTCTGACCGCAAACGCGGCGGGGATGCCGTATGAGCAGTTGCTGACTGCACGGATCCTGGCACCGCTGGGGTTATCTCACACCTTTATTACTGTGCCGGAAAGTGCGCAAAGCCAGTATGCGTACGGTTATAAAAACAAAAAACCGGTCCGCGTGTCGCCGGGACAGCTTGATGCGGAATCTTACGGCGTGAAATCCGCCTCAAAAGATATGCTGCGCTGGGCGGAAATGAATATGGAGCCGTCACGGGCCGGTAATGCGGATCTGGAAATGGCAATGTATCTCGCCCAGACCCGCTACTATAAAACCGCCGCGATTAACCAGGGGCTGGGCTGGGAAATGTATGACTGGCCGCAGCAGAAAGATATGATCATTAACGGTGTGACCAACGAGGTCGCATTGCAGCCGCATCCGGTAACAGACAACCAGGTTCAGCCGTATAACCGTGCTTCCTGGGTGCATAAAACGGGCGCAGCAACTGGTTTCGGCGCCTATGTCGCCTTTATTCCGGAAAAACAGGTGGCGATTGTGATTCTGGCGAATAAAAACTACCCGAATACCGAAAGAGTCAAAGCTGCACAGGCTATTTTGAGTGCGCTGGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3006465","ARO_id":"44927","ARO_name":"DHA-24","CARD_short_name":"DHA-24","ARO_description":"DHA-24 is a DHA beta-lactamase.","ARO_category":{"36207":{"category_aro_accession":"3000068","category_aro_cvterm_id":"36207","category_aro_name":"DHA beta-lactamase","category_aro_description":"DHA beta-lactamases are plasmid-mediated AmpC \u03b2-lactamases that confer resistance to cephamycins and oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4578":{"model_id":"4578","model_name":"DHA-25","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6953":{"protein_sequence":{"accession":"WP_077767294.1","sequence":"MKKSLSATLISALLAFSAPGFSAADNVAAVVDSTIKPLMAQQDIPGMAVAVSVKGKPYYFNYGFADIQAKQPVTENTLFELGSVSKTFTGVLGAVSVAKKEMALNDPAAKYQPELALPQWKGITLLDLATYTAGGLPLQVPDAVKSRADLLNFYQQWQPSRKPGDMRLYANSSIGLFGALTANAAGMPYEQLLTARILAPLGLSHTFITVPESAQSQYAYGYKNKKPVRVSPGQLDAESYGVKSDSKDMLRWAEMNMEPSRAGNADLEMAMYLAQTRYYKTAAINQGLGWEMYDWPQQKDMIINGVTNEVALQPHPVTDNQVQPYNRASWVHKTGATTGFGAYVAFIPEKQVAIVILANKNYPNTERVKAAQAILSALE"},"dna_sequence":{"accession":"NG_052903.1","fmin":"0","fmax":"1140","strand":"+","sequence":"ATGAAAAAATCGTTATCTGCAACACTGATTTCCGCTCTGCTGGCGTTTTCCGCCCCGGGGTTTTCTGCCGCTGATAATGTCGCGGCGGTGGTGGACAGCACCATTAAACCGCTGATGGCACAGCAGGATATTCCCGGGATGGCGGTTGCCGTCTCCGTAAAGGGTAAGCCCTATTATTTCAATTATGGTTTTGCCGATATTCAGGCAAAACAGCCGGTCACTGAAAATACACTATTTGAGCTCGGATCTGTAAGTAAAACTTTCACAGGTGTGCTGGGTGCGGTTTCTGTGGCGAAAAAAGAGATGGCGCTGAATGATCCGGCGGCAAAATACCAGCCGGAGCTGGCTCTGCCGCAGTGGAAGGGGATCACATTGCTGGATCTGGCTACCTATACCGCAGGCGGACTGCCGTTACAGGTGCCGGATGCGGTAAAAAGCCGTGCGGATCTGCTGAATTTCTATCAGCAGTGGCAGCCGTCCCGGAAACCGGGCGATATGCGTCTGTATGCAAACAGCAGTATCGGCCTGTTTGGTGCTCTGACCGCAAACGCGGCGGGGATGCCGTATGAGCAGTTGCTGACTGCACGGATCCTGGCACCGCTGGGGTTATCTCACACCTTTATTACTGTGCCGGAAAGTGCGCAAAGCCAGTATGCGTACGGTTATAAAAACAAAAAACCGGTCCGCGTGTCGCCGGGACAGCTTGATGCGGAATCTTACGGCGTGAAATCCGACTCAAAAGATATGCTGCGCTGGGCGGAAATGAATATGGAGCCGTCACGGGCCGGTAATGCGGATCTGGAAATGGCAATGTATCTCGCCCAGACCCGCTACTATAAAACCGCCGCGATTAACCAGGGGCTGGGCTGGGAAATGTATGACTGGCCGCAGCAGAAAGATATGATCATTAACGGTGTGACCAACGAGGTCGCATTGCAGCCGCATCCGGTAACAGACAACCAGGTTCAGCCGTATAACCGTGCTTCCTGGGTGCATAAAACGGGCGCAACAACTGGTTTCGGCGCCTATGTCGCCTTTATTCCGGAAAAACAGGTGGCGATTGTGATTCTGGCGAATAAAAACTACCCGAATACCGAAAGAGTCAAAGCTGCACAGGCTATTTTGAGTGCACTGGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3006466","ARO_id":"44928","ARO_name":"DHA-25","CARD_short_name":"DHA-25","ARO_description":"DHA-25 is a DHA beta-lactamase.","ARO_category":{"36207":{"category_aro_accession":"3000068","category_aro_cvterm_id":"36207","category_aro_name":"DHA beta-lactamase","category_aro_description":"DHA beta-lactamases are plasmid-mediated AmpC \u03b2-lactamases that confer resistance to cephamycins and oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4579":{"model_id":"4579","model_name":"DHA-26","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6954":{"protein_sequence":{"accession":"WP_109545068.1","sequence":"MKKSLSATLISALLAFSAPGFSAADNVAAVVDSTIKPLMAQQDIPGMAVAVSVKGKPYYFNYGFADIQAKQPVTENTLFELGSVSKTFTGVLGAVSVAKKEMALNDPAAKYQPELALPQWKGITLLDLATYTAGGLPLQVPDAVKSRADLLNFYQQWQPSRKPGDMRLYANSSIGLFGALTANAAGMPYEQLLTARILAPLGLSHTFITVPESAQSHYAYGYKNKKPVRVSPGQLDAESYGVKSASKDMLRWAEMNMEPSRAGNADLEMAMYLAQTRYYKTAAINQGLGWEMYDWPQQKDMIINGVTNEVALQPHPVTDNQVQPYNRASWVHKTGATTGFGAYVAFIPEKQVAIVILANKNYPNTERVKAAQAILSALE"},"dna_sequence":{"accession":"NG_057482.1","fmin":"0","fmax":"1140","strand":"+","sequence":"ATGAAAAAATCGTTATCTGCAACACTGATTTCCGCTCTGCTGGCGTTTTCCGCCCCGGGGTTTTCTGCCGCTGATAATGTCGCGGCGGTGGTGGACAGCACCATTAAACCGCTGATGGCACAGCAGGATATTCCCGGGATGGCGGTTGCCGTCTCCGTAAAGGGTAAGCCCTATTATTTCAATTATGGTTTTGCCGATATTCAGGCAAAACAGCCGGTCACTGAAAATACACTATTTGAGCTCGGATCTGTAAGTAAAACTTTCACAGGTGTGCTGGGTGCGGTTTCTGTGGCGAAAAAAGAGATGGCGCTGAATGATCCGGCGGCAAAATACCAGCCGGAGCTGGCTCTGCCGCAGTGGAAGGGGATCACATTGCTGGATCTGGCTACCTATACCGCAGGCGGACTGCCGTTACAGGTGCCGGATGCGGTAAAAAGCCGTGCGGATCTGCTGAATTTCTATCAGCAGTGGCAGCCGTCCCGGAAACCGGGCGATATGCGTCTGTATGCAAACAGCAGTATCGGCCTGTTTGGTGCTCTGACCGCAAACGCGGCGGGGATGCCGTATGAGCAGTTGCTGACTGCACGGATCCTGGCACCGCTGGGGTTATCTCACACCTTTATTACTGTGCCGGAAAGTGCGCAAAGCCATTATGCGTACGGTTATAAAAACAAAAAACCGGTCCGCGTGTCGCCGGGACAGCTTGATGCGGAATCTTACGGCGTGAAATCCGCCTCAAAAGATATGCTGCGCTGGGCGGAAATGAATATGGAGCCGTCACGGGCCGGTAATGCGGATCTGGAAATGGCAATGTATCTCGCCCAGACCCGCTACTATAAAACCGCCGCGATTAACCAGGGGCTGGGCTGGGAAATGTATGACTGGCCGCAGCAGAAAGATATGATCATTAACGGTGTGACCAACGAGGTCGCATTGCAGCCGCATCCGGTAACAGACAACCAGGTTCAGCCGTATAACCGTGCTTCCTGGGTGCATAAAACGGGCGCAACAACTGGTTTCGGCGCCTATGTCGCCTTTATTCCGGAAAAACAGGTGGCGATTGTGATTCTGGCGAATAAAAACTACCCGAATACCGAAAGAGTCAAAGCTGCACAGGCTATTTTGAGTGCACTGGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3006467","ARO_id":"44929","ARO_name":"DHA-26","CARD_short_name":"DHA-26","ARO_description":"DHA-26 is a DHA beta-lactamase.","ARO_category":{"36207":{"category_aro_accession":"3000068","category_aro_cvterm_id":"36207","category_aro_name":"DHA beta-lactamase","category_aro_description":"DHA beta-lactamases are plasmid-mediated AmpC \u03b2-lactamases that confer resistance to cephamycins and oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4580":{"model_id":"4580","model_name":"DHA-27","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6955":{"protein_sequence":{"accession":"WP_109545067.1","sequence":"MKKSLSATLISALLAFSAPGFSAADNVAAVVDSTIKPLMAQQDIPGMAVAVSVKGKPYYFNYGFADIQAKQPVTENTLFELGSVSKTFTGVLGAVSVAKKEMALNDPAAKYQPELALPQWKGITLLDLATYTAGGLPLQVPDAVKSRADLLNFYQQWQPSWKPGDMRLYANSSIGLFGALTANAAGMPYEQLLTARILAPLGLSHTFITVPESAQSQYAYGYKNKKPVRVSPGQLDAESYGVKSASKDMLRWAEMNMEPSRAGNADLEMAMYLAQTRYYKTAAINQGLGWEMYDWPQQKDMIINGVTNEVALQPHPVTDNQVQPYNRASWVHKTGATTGFGAYVAFIPEKQVAIVILANKNYPNTERVKAAQAILSALE"},"dna_sequence":{"accession":"NG_057481.1","fmin":"0","fmax":"1140","strand":"+","sequence":"ATGAAAAAATCGTTATCTGCAACACTGATTTCCGCTCTGCTGGCGTTTTCCGCCCCGGGGTTTTCTGCCGCTGATAATGTCGCGGCGGTGGTGGACAGCACCATTAAACCGCTGATGGCACAGCAGGATATTCCCGGGATGGCGGTTGCCGTCTCCGTAAAGGGTAAGCCCTATTATTTCAATTATGGTTTTGCCGATATTCAGGCAAAACAGCCGGTCACTGAAAATACACTATTTGAGCTCGGATCTGTAAGTAAAACTTTCACAGGTGTGCTGGGTGCGGTTTCTGTGGCGAAAAAAGAGATGGCGCTGAATGATCCGGCGGCAAAATACCAGCCGGAGCTGGCTCTGCCGCAGTGGAAGGGGATCACATTGCTGGATCTGGCTACCTATACCGCAGGCGGACTGCCGTTACAGGTGCCGGATGCGGTAAAAAGCCGTGCGGATCTGCTGAATTTCTATCAGCAGTGGCAGCCGTCCTGGAAACCGGGCGATATGCGTCTGTATGCAAACAGCAGTATCGGCCTGTTTGGTGCTCTGACCGCAAACGCGGCGGGGATGCCGTATGAGCAGTTGCTGACTGCACGGATCCTGGCACCGCTGGGGTTATCTCACACCTTTATTACTGTGCCGGAAAGTGCGCAAAGCCAGTATGCGTACGGTTATAAAAACAAAAAACCGGTCCGCGTGTCGCCGGGACAGCTTGATGCGGAATCTTACGGCGTGAAATCCGCCTCAAAAGATATGCTGCGCTGGGCGGAAATGAATATGGAGCCGTCACGGGCCGGTAATGCGGATCTGGAAATGGCAATGTATCTCGCCCAGACCCGCTACTATAAAACCGCCGCGATTAACCAGGGGCTGGGCTGGGAAATGTATGACTGGCCGCAGCAGAAAGATATGATCATTAACGGTGTGACCAACGAGGTCGCATTGCAGCCGCATCCGGTAACAGACAACCAGGTTCAGCCGTATAACCGTGCTTCCTGGGTGCATAAAACGGGCGCAACAACTGGTTTCGGCGCCTATGTCGCCTTTATTCCGGAAAAACAGGTGGCGATTGTGATTCTGGCGAATAAAAACTACCCGAATACCGAAAGAGTCAAAGCTGCACAGGCTATTTTGAGTGCACTGGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3006468","ARO_id":"44930","ARO_name":"DHA-27","CARD_short_name":"DHA-27","ARO_description":"DHA-27 is a DHA beta-lactamase.","ARO_category":{"36207":{"category_aro_accession":"3000068","category_aro_cvterm_id":"36207","category_aro_name":"DHA beta-lactamase","category_aro_description":"DHA beta-lactamases are plasmid-mediated AmpC \u03b2-lactamases that confer resistance to cephamycins and oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4581":{"model_id":"4581","model_name":"DHA-28","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6956":{"protein_sequence":{"accession":"WP_128268236.1","sequence":"MTKSLSATLISALLAFSAPGFSAADNVAAVVDSTIKPLMAQQDIPGMAVAVSVKGKPYYFNYGFADVQAKQPVTENTLFELGSVSKTFTGVLGAVSVAKKEMTLNDPAAKYQPELALPQWKGITLLDLATYTAGGLPLQVPDAVKNRADLLNFYQQWQPSWQPGDMRLYANSSIGLFGALTANAAGMPYEQLLTARILAPLGLSHTFITVPESAQSQYAYGYKNKKPVRVSPGQLDAESYGVKSASKDMLRWAEMNMEPSRTGNADLEMAMYLAQTRYYKTVAINQGLGWEMYDWPQQKDMIINGVTNEVALQPHPVTDNQVQPYNRASWVHKTGATTGFGAYVAFIPEKQVAIVILANKNYPNTERVKAAQAILSALE"},"dna_sequence":{"accession":"NG_063839.1","fmin":"0","fmax":"1140","strand":"+","sequence":"ATGACAAAATCATTATCTGCAACACTGATTTCCGCCCTGCTGGCGTTTTCCGCCCCGGGGTTTTCCGCCGCTGACAATGTCGCGGCGGTGGTGGACAGCACCATTAAACCGCTGATGGCACAGCAGGATATTCCCGGGATGGCGGTTGCCGTCTCTGTAAAGGGCAAGCCCTATTATTTCAATTACGGTTTTGCCGATGTTCAGGCAAAACAGCCGGTCACTGAAAATACACTATTTGAGCTCGGATCTGTAAGTAAAACTTTCACAGGTGTGCTGGGTGCGGTTTCTGTGGCGAAAAAAGAGATGACGCTGAATGATCCGGCGGCAAAATACCAGCCGGAGCTGGCTCTGCCGCAGTGGAAGGGGATCACGCTGCTGGATCTGGCCACCTATACCGCAGGCGGGCTGCCGTTACAGGTGCCGGACGCGGTGAAAAACCGTGCGGATCTGCTGAATTTCTATCAGCAGTGGCAGCCGTCATGGCAACCGGGCGATATGCGTCTGTATGCAAACAGCAGTATCGGCCTGTTTGGTGCTCTGACCGCCAACGCAGCGGGGATGCCGTATGAGCAGTTGCTGACTGCGCGGATCCTGGCACCGCTGGGATTATCTCACACCTTTATTACCGTGCCGGAAAGCGCGCAAAGCCAGTATGCATACGGTTATAAAAACAAAAAGCCGGTTCGCGTGTCACCGGGACAGCTTGATGCGGAATCTTACGGCGTGAAATCCGCTTCAAAAGATATGCTGCGCTGGGCGGAAATGAATATGGAGCCGTCACGGACCGGTAATGCGGATCTGGAAATGGCAATGTATCTTGCACAGACCCGCTACTATAAAACCGTCGCGATTAATCAGGGGCTGGGCTGGGAAATGTATGACTGGCCGCAGCAGAAAGATATGATCATTAACGGCGTGACCAACGAGGTCGCATTGCAGCCGCACCCGGTAACAGACAACCAGGTTCAGCCGTATAACCGTGCTTCCTGGGTGCATAAAACGGGGGCAACAACTGGTTTCGGCGCCTATGTGGCCTTTATTCCGGAAAAACAGGTGGCGATTGTGATTCTGGCGAATAAAAACTACCCGAATACCGAAAGAGTCAAAGCCGCACAGGCTATTTTGAGTGCACTGGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36917","NCBI_taxonomy_name":"Morganella morganii","NCBI_taxonomy_id":"582"}}}},"ARO_accession":"3006469","ARO_id":"44931","ARO_name":"DHA-28","CARD_short_name":"DHA-28","ARO_description":"DHA-28 is a DHA beta-lactamase.","ARO_category":{"36207":{"category_aro_accession":"3000068","category_aro_cvterm_id":"36207","category_aro_name":"DHA beta-lactamase","category_aro_description":"DHA beta-lactamases are plasmid-mediated AmpC \u03b2-lactamases that confer resistance to cephamycins and oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4582":{"model_id":"4582","model_name":"DHA-29","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6957":{"protein_sequence":{"accession":"WP_148044412.1","sequence":"MKKSLSATLISALLAFSAPGFSAADNVAAVVDSTIKPLMAQQDIPGMAVAVSVKGKPYYFNYGFADIQAKQPVTENTLFELGSVSKTFTGVLGAVSVAKKEMALNDPAAKYQPELALPQWKGITLLDLATYTAGGLPLLVPDAVKSRADLLNFYQQWQPSRKPGDMRLYANSSIGLFGALTANAAGMPYEQLLTARILAPLGLSHTFITVPESAQSQYAYGYKNKKPVRVSLGQLDAESYGVKSASKDMLRWAEMNMEPSRAGNADLEMAMYLAQTRYYKTAAINQGLGWEMYDWPQQKDMIINGVTNEVALQPHPVTDNQVQPYNRASWVHKTGATTGFGAYVAFIPEKQVAIVILANKNYPNTERVKAAQAILSALE"},"dna_sequence":{"accession":"NG_065868.1","fmin":"0","fmax":"1140","strand":"+","sequence":"ATGAAAAAATCGTTATCTGCAACACTGATTTCCGCTCTGCTGGCGTTTTCCGCCCCGGGGTTTTCTGCCGCTGATAATGTCGCGGCGGTGGTGGACAGCACCATTAAACCGCTGATGGCACAGCAGGATATTCCCGGGATGGCGGTTGCCGTCTCCGTAAAGGGTAAGCCCTATTATTTCAATTATGGTTTTGCCGATATTCAGGCAAAACAGCCGGTCACTGAAAATACACTATTTGAGCTCGGATCTGTAAGTAAAACTTTCACAGGTGTGCTGGGTGCGGTTTCTGTGGCGAAAAAAGAGATGGCGCTGAATGATCCGGCGGCAAAATACCAGCCGGAGCTGGCTCTGCCGCAGTGGAAGGGGATCACATTGCTGGATCTGGCTACCTATACCGCAGGCGGACTGCCGTTACTGGTGCCGGATGCGGTAAAAAGCCGTGCGGATCTGCTGAATTTCTATCAGCAGTGGCAGCCGTCCCGGAAACCGGGCGATATGCGTCTGTATGCAAACAGCAGTATCGGCCTGTTTGGTGCTCTGACCGCAAACGCGGCGGGGATGCCGTATGAGCAGTTGCTGACTGCACGGATCCTGGCACCGCTGGGGTTATCTCACACCTTTATTACTGTGCCGGAAAGTGCGCAAAGCCAGTATGCGTACGGTTATAAAAACAAAAAACCGGTCCGCGTGTCGCTGGGACAGCTTGATGCGGAATCTTACGGCGTGAAATCCGCCTCAAAAGATATGCTGCGCTGGGCGGAAATGAATATGGAGCCGTCACGGGCCGGTAATGCGGATCTGGAAATGGCAATGTATCTCGCCCAGACCCGCTACTATAAAACCGCCGCGATTAACCAGGGGCTGGGCTGGGAAATGTATGACTGGCCGCAGCAGAAAGATATGATCATTAACGGTGTGACCAACGAGGTCGCATTGCAGCCGCATCCGGTAACAGACAACCAGGTTCAGCCGTATAACCGTGCTTCCTGGGTGCATAAAACGGGCGCAACAACTGGTTTCGGCGCCTATGTCGCCTTTATTCCGGAAAAACAGGTGGCGATTGTGATTCTGGCGAATAAAAACTACCCGAATACCGAAAGAGTCAAAGCTGCACAGGCTATTTTGAGTGCACTGGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3006470","ARO_id":"44932","ARO_name":"DHA-29","CARD_short_name":"DHA-29","ARO_description":"DHA-29 is a DHA beta-lactamase.","ARO_category":{"36207":{"category_aro_accession":"3000068","category_aro_cvterm_id":"36207","category_aro_name":"DHA beta-lactamase","category_aro_description":"DHA beta-lactamases are plasmid-mediated AmpC \u03b2-lactamases that confer resistance to cephamycins and oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4583":{"model_id":"4583","model_name":"DHA-4","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6958":{"protein_sequence":{"accession":"WP_032097955.1","sequence":"MKKSLSATLISALLAFSAPGFSAADNVAAVVDSTIKPLMAQQDIPGMAVAVSVKGKPYYFNYGFADVQAKQPVTENTLFELGSVSKTFTGVLGAVSVAKKEMALNDPAAKYQPELALPQWKGITLLDLATYTAGGLPLQVPDAVKSRADLLNFYQQWQPSRKPGDMRLYANSSIGLFGALTANAAGMPYEQLLTARILAPLGLSHTFITVPESAQSQYAYGYKNKKPVRVSPGQLDAESYGVKSASKDMLRWAEMNMEPSRAGNADLEMAMYLAQTRYYKTAAINQGLGWEMYDWPQQKDMIINGVTNEVALQPHPVTDNQVQPYNRASWVHKTGATTGFGAYVAFIPEKQVAIVILANKNYPNTERVKAAQAILSALE"},"dna_sequence":{"accession":"NG_049072.1","fmin":"100","fmax":"1240","strand":"+","sequence":"ATGAAAAAATCGTTATCTGCAACACTGATTTCCGCCCTGCTGGCGTTTTCCGCCCCGGGGTTTTCTGCCGCTGATAATGTCGCGGCTGTGGTGGACAGCACCATTAAACCGCTGATGGCACAGCAGGACATTCCCGGGATGGCGGTTGCCGTCTCTGTAAAGGGCAAGCCCTATTATTTCAATTACGGTTTTGCCGATGTTCAGGCAAAACAACCGGTCACTGAAAATACACTATTTGAGCTCGGATCTGTAAGTAAAACTTTCACAGGTGTGCTGGGTGCGGTTTCTGTGGCGAAAAAAGAGATGGCGCTGAATGATCCGGCGGCAAAATACCAGCCGGAGCTGGCTCTGCCGCAGTGGAAGGGGATCACATTGCTGGATCTGGCTACCTATACCGCAGGCGGACTGCCGTTACAGGTGCCGGATGCGGTAAAAAGCCGTGCGGATCTGCTGAATTTCTATCAGCAGTGGCAGCCGTCCCGGAAACCGGGCGATATGCGTCTGTATGCAAACAGCAGTATCGGCCTGTTTGGTGCTCTGACCGCCAACGCGGCGGGGATGCCGTATGAGCAGTTGCTGACCGCGCGGATCCTGGCACCGCTGGGATTATCTCACACCTTTATTACCGTGCCGGAAAGCGCGCAAAGTCAGTATGCGTACGGTTATAAAAACAAAAAACCGGTCCGCGTGTCACCGGGACAGCTTGATGCGGAATCTTACGGTGTGAAATCCGCCTCAAAAGATATGCTGCGCTGGGCGGAAATGAATATGGAGCCGTCACGGGCCGGTAATGCGGATCTGGAAATGGCAATGTATCTCGCCCAGACCCGTTACTATAAAACCGCCGCGATTAATCAGGGGCTGGGCTGGGAAATGTATGACTGGCCGCAGCAGAAAGATATGATCATTAACGGCGTGACCAACGAGGTCGCATTGCAGCCGCACCCGGTAACAGACAACCAGGTTCAGCCGTATAACCGTGCTTCCTGGGTGCATAAAACGGGGGCAACAACGGGTTTCGGCGCCTATGTGGCCTTTATTCCGGAAAAACAGGTAGCGATTGTGATTCTGGCGAATAAAAACTACCCGAATACCGAAAGAGTCAAAGCCGCACAGGCTATTTTGAGTGCACTGGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36917","NCBI_taxonomy_name":"Morganella morganii","NCBI_taxonomy_id":"582"}}}},"ARO_accession":"3002137","ARO_id":"38537","ARO_name":"DHA-4","CARD_short_name":"DHA-4","ARO_description":"DHA-4 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36207":{"category_aro_accession":"3000068","category_aro_cvterm_id":"36207","category_aro_name":"DHA beta-lactamase","category_aro_description":"DHA beta-lactamases are plasmid-mediated AmpC \u03b2-lactamases that confer resistance to cephamycins and oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4584":{"model_id":"4584","model_name":"DHT2-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"6959":{"protein_sequence":{"accession":"WP_122630829.1","sequence":"MSSIVRGVRAAVVASAISLAAAFACLPLAAADATREPVLPQSGRYEVPDSWRQPIAPVRIADHTWYIGTENLSAVLVTTPQGAVLIDGGMPQAADMLLQRMRDVGIAPGDLRWILVSHAHADHAGPVAKVKRATGARIAANAESAAMLARGGTDDIHFGDDITFPPAQADRLLQDDEVVQVGGIALTGHVTPGHTPGSTSWTWTDTKDGKPVRIAYADSLSAPGYKLIGNPRMPRIVEMYEATFAKVRALPCDLLLTPHPDASGWTPADAANPHPSPKTCAAYADEMEAKFDAELAKQRAAK"},"dna_sequence":{"accession":"NG_062233.1","fmin":"0","fmax":"909","strand":"+","sequence":"ATGTCATCCATCGTTCGCGGCGTTCGCGCCGCCGTCGTCGCATCCGCCATTTCTCTTGCAGCCGCGTTCGCCTGCCTGCCGCTCGCCGCGGCGGATGCGACGCGCGAGCCCGTCCTCCCGCAAAGCGGTCGCTACGAAGTGCCGGACAGTTGGCGCCAGCCGATTGCCCCGGTCCGCATCGCCGACCACACCTGGTACATCGGCACCGAGAACCTGAGTGCGGTGCTCGTCACGACGCCGCAGGGCGCGGTGCTGATCGACGGCGGCATGCCGCAGGCCGCGGACATGCTGTTGCAACGCATGCGCGACGTCGGCATCGCGCCCGGCGACCTGCGCTGGATCCTGGTGTCGCACGCGCACGCGGACCATGCCGGCCCCGTCGCGAAGGTCAAGCGCGCGACCGGAGCCCGCATCGCCGCCAACGCCGAATCCGCCGCGATGCTCGCGCGCGGCGGTACCGACGACATCCACTTCGGCGACGACATCACCTTCCCGCCCGCGCAGGCCGATCGCCTGCTGCAGGACGACGAAGTCGTGCAGGTCGGCGGCATCGCGCTCACCGGTCACGTCACGCCCGGGCACACGCCGGGCAGCACGAGCTGGACGTGGACCGACACGAAGGACGGCAAGCCGGTGCGCATCGCGTACGCGGACAGCCTGTCCGCGCCGGGCTACAAGCTCATCGGCAATCCGCGCATGCCGCGCATCGTCGAGATGTACGAGGCCACGTTCGCGAAGGTGCGCGCCCTGCCCTGCGACCTGCTGCTCACGCCGCATCCGGATGCGAGCGGGTGGACGCCCGCGGATGCGGCGAACCCGCATCCCTCGCCGAAAACCTGCGCGGCCTACGCCGACGAAATGGAAGCGAAGTTCGACGCCGAACTCGCGAAACAACGTGCGGCGAAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36791","NCBI_taxonomy_name":"uncultured bacterium","NCBI_taxonomy_id":"77133"}}}},"ARO_accession":"3006872","ARO_id":"45334","ARO_name":"DHT2-1","CARD_short_name":"DHT2-1","ARO_description":"DHT2-1 is a DHT2 beta-lactamase.","ARO_category":{"43864":{"category_aro_accession":"3005404","category_aro_cvterm_id":"43864","category_aro_name":"DHT2 beta-lactamase","category_aro_description":"DHT2 beta-lactamases are class B3 beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4585":{"model_id":"4585","model_name":"EAM-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"575"}},"model_sequences":{"sequence":{"6960":{"protein_sequence":{"accession":"WP_122630825.1","sequence":"MSVKALFAALPLLIAACAAIPAPQVEDADAPPSPAPTETVVNAHEMQMAFLDACEPWDEWDKPAPPFQLMGNSWYVGTCGISAVLITGEDGHILIDSGVPEAAPLVLANIASLGFDAKDVRYLLMSHEHFDHVGAHAAIKEATGAQVLASVRAKPVLETGKVAADDPQAASGHPDMTPVKVDRVIGDGEILDLGNLRVTAHETPGHSPGALSWTWWSCSLPGEPPVCNRFAYVDSLSAVSADDYRFTDHPEMVRAFRTSIDKARMLQCEFLVTPHPSAGSMLDLMSGEHGLYLHKGCGFYAKRLSKRLDERLAKEAAE"},"dna_sequence":{"accession":"NG_062208.1","fmin":"0","fmax":"957","strand":"+","sequence":"ATGTCCGTTAAAGCGCTGTTCGCGGCCCTGCCCTTGCTCATCGCTGCTTGCGCGGCAATTCCAGCACCGCAAGTTGAAGATGCGGACGCGCCGCCCTCGCCCGCGCCAACGGAAACGGTGGTGAACGCCCACGAGATGCAGATGGCGTTTCTCGATGCGTGCGAGCCGTGGGACGAGTGGGACAAGCCCGCTCCACCGTTCCAATTGATGGGCAACAGCTGGTATGTCGGCACCTGCGGTATCTCGGCAGTCCTGATTACCGGCGAAGACGGACACATCCTGATCGACAGCGGCGTCCCCGAGGCCGCCCCGCTGGTCCTCGCGAACATCGCCTCGCTCGGTTTCGATGCGAAGGATGTGCGCTATCTCCTGATGAGCCATGAGCATTTCGACCATGTCGGCGCGCATGCCGCAATCAAGGAAGCGACAGGTGCGCAAGTGTTGGCTTCGGTAAGAGCCAAGCCCGTGCTCGAAACGGGGAAAGTCGCCGCCGACGATCCGCAGGCCGCATCCGGCCATCCAGACATGACCCCGGTAAAGGTCGACCGCGTGATCGGCGATGGGGAAATACTCGATCTCGGCAACCTGCGCGTTACGGCTCATGAAACGCCCGGCCATTCGCCCGGGGCGCTCAGCTGGACATGGTGGTCGTGTTCGCTCCCTGGCGAGCCGCCCGTGTGCAACCGCTTCGCCTATGTCGACAGCCTGTCCGCGGTTTCCGCAGACGATTACCGCTTCACCGATCACCCGGAGATGGTTCGCGCATTCCGGACCAGCATCGACAAGGCACGCATGCTCCAGTGTGAGTTTCTGGTGACACCGCACCCCTCGGCCGGGTCCATGCTCGACCTGATGAGCGGAGAACACGGGCTCTACCTGCACAAGGGCTGCGGCTTCTATGCAAAGCGGCTTAGCAAACGCCTCGATGAGCGCTTGGCCAAGGAAGCTGCCGAGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3006873","ARO_id":"45335","ARO_name":"EAM-1","CARD_short_name":"EAM-1","ARO_description":"EAM-1 is a EAM beta-lactamase.","ARO_category":{"43865":{"category_aro_accession":"3005405","category_aro_cvterm_id":"43865","category_aro_name":"EAM beta-lactamase","category_aro_description":"EAM beta-lactamase are class B3 beta-lactamases found in Qipengyuania aquimaris.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4586":{"model_id":"4586","model_name":"EBR-3","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"6961":{"protein_sequence":{"accession":"WP_150823468.1","sequence":"MKKIFSLIALIGSFAFGQIKPIQIDSINNNLFVYQTFNSFNGVEYNANGMYLVTNKGIVLFDVPWQKSQYQELNDMLQEKYNLPVIAVFATHSHDDRAGDLSFYNDLNIPTYATSLTNSKLKKEGKATSKFEIELGKTYKFGNEKFVVEYFGEGHTSDNVVVWFPKYKVLNGGCLIKGADAVNLGYTGEANVAEWPKTVHKLVAKHPTIKQVIPGHDNWKATGHIENTFKLLEKK"},"dna_sequence":{"accession":"NG_066507.1","fmin":"0","fmax":"708","strand":"+","sequence":"ATGAAAAAAATATTTTCACTTATTGCATTGATAGGAAGTTTTGCATTTGGTCAAATAAAACCAATTCAAATTGATTCGATTAATAATAATCTATTTGTTTATCAAACATTTAATTCGTTTAATGGTGTTGAGTATAATGCAAATGGAATGTATTTGGTAACGAATAAAGGAATTGTTTTGTTTGATGTTCCTTGGCAGAAATCGCAGTATCAAGAGTTAAATGATATGTTGCAAGAAAAGTATAATTTGCCAGTTATCGCTGTCTTTGCAACACATTCGCATGATGATAGAGCAGGAGATTTGAGTTTTTATAATGATTTGAATATTCCTACTTATGCAACTTCTCTAACCAATTCTAAATTAAAAAAGGAAGGAAAAGCAACTTCTAAATTTGAGATTGAATTAGGGAAAACATACAAATTTGGTAACGAAAAATTTGTTGTTGAATATTTTGGAGAAGGACATACTTCTGATAATGTTGTGGTTTGGTTTCCGAAATATAAAGTGTTGAACGGGGGTTGTTTGATAAAAGGTGCTGATGCTGTAAATTTAGGTTATACAGGCGAAGCTAATGTTGCTGAATGGCCAAAAACAGTACACAAATTAGTTGCAAAACATCCAACGATTAAACAAGTTATTCCAGGACATGACAATTGGAAAGCTACTGGACATATCGAAAATACGTTTAAACTTTTAGAAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41679","NCBI_taxonomy_name":"Empedobacter falsenii","NCBI_taxonomy_id":"343874"}}}},"ARO_accession":"3005461","ARO_id":"43923","ARO_name":"EBR-3","CARD_short_name":"EBR-3","ARO_description":"EBR-3 is a EBR beta-lactamase.","ARO_category":{"41368":{"category_aro_accession":"3004204","category_aro_cvterm_id":"41368","category_aro_name":"EBR beta-lactamase","category_aro_description":"EBR beta-lactamases are Class B beta-lactamases first isolated from Empedobacter brevis and are able to hydrolyze penicillins, cephalosporins, and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4587":{"model_id":"4587","model_name":"EBR-4","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"6962":{"protein_sequence":{"accession":"WP_114999921.1","sequence":"MKKLFSLIALIGSFAFGQIKPIQIDPINNNLFVYQTFNSFNGVEYNANGMYLVTNKGIVLFDVPWQKSQYQELNDMLQEKYNLPVIAVFATHSHDDRAGDLSFYNDLNIPTYATSLTNSKLKKEGKATSKFEIELGKTYKFGNEKFVVEYFGEGHTSDNVVVWFPKYKVLNGGCLIKGADAVNLGYTGEANVTEWPKTVQKLVTKHPKIKQVIPGHDNWKVTGHIENTFKLLEKK"},"dna_sequence":{"accession":"NG_073461.1","fmin":"0","fmax":"708","strand":"+","sequence":"ATGAAGAAATTATTTTCACTTATAGCATTGATAGGAAGTTTTGCATTTGGTCAAATAAAACCAATTCAGATTGATCCGATTAATAACAATTTATTTGTTTATCAAACATTCAATTCGTTTAATGGTGTTGAGTATAATGCAAATGGAATGTATTTGGTAACGAATAAAGGAATCGTTTTGTTTGATGTTCCTTGGCAGAAATCGCAATATCAAGAATTAAATGATATGTTGCAAGAAAAGTATAATTTGCCAGTTATCGCTGTGTTTGCAACACATTCGCATGATGATAGAGCAGGAGATTTAAGTTTTTATAATGATTTGAATATTCCTACTTATGCAACTTCTTTAACCAATTCTAAATTAAAAAAAGAAGGAAAAGCGACTTCGAAATTTGAGATTGAATTAGGAAAAACATACAAATTTGGTAATGAAAAATTTGTTGTTGAATATTTTGGTGAAGGACATACTTCTGATAATGTTGTGGTTTGGTTTCCAAAATATAAAGTGCTGAATGGAGGTTGTTTGATAAAAGGTGCTGACGCTGTAAATTTAGGTTACACAGGTGAAGCAAATGTTACTGAATGGCCAAAAACAGTACAGAAATTAGTTACAAAACATCCAAAAATTAAACAAGTTATTCCAGGTCATGATAATTGGAAAGTTACTGGACATATCGAAAATACGTTTAAACTTTTAGAAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41679","NCBI_taxonomy_name":"Empedobacter falsenii","NCBI_taxonomy_id":"343874"}}}},"ARO_accession":"3005462","ARO_id":"43924","ARO_name":"EBR-4","CARD_short_name":"EBR-4","ARO_description":"EBR-4 is a EBR beta-lactamase.","ARO_category":{"41368":{"category_aro_accession":"3004204","category_aro_cvterm_id":"41368","category_aro_name":"EBR beta-lactamase","category_aro_description":"EBR beta-lactamases are Class B beta-lactamases first isolated from Empedobacter brevis and are able to hydrolyze penicillins, cephalosporins, and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4588":{"model_id":"4588","model_name":"EC-13","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"725"}},"model_sequences":{"sequence":{"6963":{"protein_sequence":{"accession":"WP_063860228.1","sequence":"MFKTTLCALLITASCSTFAAPQQINDIVHRTITPLIEQQKIPGMAVAVIYQGKPYYFTWGYADIAKKQPVTQQTLFELGSVSKTFTGVLGGDAIARGEIKLSDPATKYWPELTAKQWNGITLLHLATYTAGGLPLQVPDEVKSSSDLLRFYQNWQPAWAPGTQRLYANSSIGLFGALAVKPSGLSFEQAMQTRVFQPLKLNHTWINVPPPEEKNYAWGYREGKAVHVSPGALDAEAYGVKSTIEDMARWVRSNMNPRDINDKTLQQGIQLAQSRYWQTGDMYQGLGWEMLDWPVNPDSIINGNGNKIALAAHPVKAITPPTPAVRASWVHKTGATGGFGSYVAFIPEKELGIVMLANKNYPNPARVAAAWQILNALQ"},"dna_sequence":{"accession":"NG_049079.1","fmin":"100","fmax":"1234","strand":"+","sequence":"ATGTTCAAAACGACGCTCTGCGCCTTATTAATTACCGCCTCTTGCTCCACATTTGCTGCCCCTCAACAAATCAACGATATTGTGCATCGCACAATTACCCCGCTTATAGAGCAACAAAAGATCCCCGGTATGGCGGTGGCGGTAATTTATCAGGGTAAACCTTATTACTTTACCTGGGGCTATGCGGACATCGCCAAAAAGCAGCCCGTCACACAGCAAACGTTGTTTGAGTTAGGTTCGGTCAGCAAAACATTTACGGGCGTGCTTGGTGGCGACGCTATTGCTCGAGGGGAAATCAAGTTAAGCGATCCCGCAACAAAATACTGGCCTGAACTTACCGCTAAACAGTGGAATGGGATCACACTATTACATCTTGCGACCTACACCGCTGGCGGCCTGCCATTGCAGGTGCCGGATGAAGTGAAATCCTCAAGCGACTTGCTGCGCTTCTATCAAAACTGGCAGCCTGCATGGGCTCCAGGAACACAACGTCTGTATGCCAACTCCAGTATCGGTTTGTTCGGCGCACTGGCTGTGAAGCCGTCTGGTTTGAGTTTTGAGCAGGCGATGCAAACTCGTGTCTTCCAGCCACTCAAACTCAACCATACGTGGATTAATGTACCTCCCCCAGAAGAAAAGAATTACGCCTGGGGATATCGCGAAGGTAAGGCAGTGCATGTTTCGCCAGGGGCGTTAGATGCTGAAGCTTATGGTGTGAAGTCGACCATTGAAGATATGGCCCGCTGGGTACGAAGCAATATGAATCCCCGTGATATCAACGACAAAACACTTCAGCAAGGGATACAACTGGCACAATCTCGCTACTGGCAAACCGGCGATATGTATCAGGGCCTGGGCTGGGAAATGCTGGACTGGCCGGTAAATCCTGACAGCATCATTAACGGCAATGGCAATAAAATTGCACTGGCAGCACACCCTGTAAAAGCGATTACGCCCCCAACTCCTGCAGTACGCGCATCATGGGTACATAAAACAGGGGCAACCGGCGGATTTGGTAGCTATGTCGCGTTTATTCCAGAAAAAGAGCTGGGTATAGTGATGCTGGCTAACAAAAACTATCCCAATCCAGCGAGAGTCGCCGCCGCCTGGCAGATTCTCAACGCTCTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3006874","ARO_id":"45336","ARO_name":"EC-13","CARD_short_name":"EC-13","ARO_description":"EC-13 is a EC beta-lactamase.","ARO_category":{"43866":{"category_aro_accession":"3005406","category_aro_cvterm_id":"43866","category_aro_name":"EC beta-lactamase","category_aro_description":"EC beta-lactamases are class C beta-lactamases found in Escherichia coli.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4589":{"model_id":"4589","model_name":"EC-14","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"725"}},"model_sequences":{"sequence":{"6964":{"protein_sequence":{"accession":"WP_063860233.1","sequence":"MFKTTLCALLITASCSTFAAPQQINDIVHRTITPLIEQQKIPGMAVAVIYQGKPYYFTWGYADIAKKQPVTQQTLFELGSVSKTFTGVLGGDAIARGEIKLSDPATKYWPELTAKQWNGITLLHLATYTAGGLPLQVPDEVKSSSDLLRFYQNWQPAWAPGTQRLYANSSIGLFGALAVKPSGLSFEQAMQTRVFQPLKLNHTWINVPPPEEKNYAWGYREGKAVHVSPGALDAEAYGVKSTIEDMARWVRSNMNPRDINDKTLQQGIQLAQSRYWQTGDMYQGLGWEMLDWPVNPDSIINGSGNKIALAAHPLKAITPPTPAVRASWVHKTGATGGFGSYVAFIPEKELGIVMLANKNYPNPARVAAAWQILNALQ"},"dna_sequence":{"accession":"NG_049080.1","fmin":"100","fmax":"1234","strand":"+","sequence":"ATGTTCAAAACGACGCTCTGCGCCTTATTAATTACCGCCTCTTGCTCCACATTTGCTGCCCCTCAACAAATCAACGATATTGTGCATCGCACAATTACCCCGCTTATAGAGCAACAAAAGATCCCCGGTATGGCGGTGGCGGTAATTTATCAGGGTAAACCTTATTACTTTACCTGGGGCTATGCGGACATCGCCAAAAAGCAGCCCGTCACACAGCAAACGTTGTTTGAGTTAGGTTCGGTCAGCAAAACATTTACGGGCGTGCTTGGTGGCGACGCTATTGCTCGAGGGGAAATCAAGTTAAGCGATCCCGCAACAAAATACTGGCCTGAACTTACCGCTAAACAGTGGAATGGGATCACACTATTACATCTTGCGACCTACACCGCTGGCGGCCTGCCATTGCAGGTGCCGGATGAAGTGAAATCCTCAAGCGACTTGCTGCGCTTCTATCAAAACTGGCAGCCTGCATGGGCTCCAGGAACACAACGTCTGTATGCCAACTCCAGTATCGGTTTGTTCGGCGCACTGGCTGTGAAGCCGTCTGGTTTGAGTTTTGAGCAGGCGATGCAAACTCGTGTCTTCCAGCCACTCAAACTCAACCATACGTGGATTAATGTACCTCCCCCAGAAGAAAAGAATTACGCCTGGGGATATCGCGAAGGTAAGGCAGTGCATGTTTCGCCAGGGGCGTTAGATGCTGAAGCTTATGGTGTGAAGTCGACCATTGAAGATATGGCCCGCTGGGTACGAAGCAATATGAATCCCCGTGATATCAACGACAAAACACTTCAGCAAGGGATACAACTGGCACAATCTCGCTACTGGCAAACCGGCGATATGTATCAGGGCCTGGGCTGGGAAATGCTGGACTGGCCGGTAAATCCTGACAGCATCATTAACGGCAGTGGCAATAAAATTGCACTGGCAGCACACCCTTTAAAAGCGATTACGCCCCCAACTCCTGCAGTACGCGCATCATGGGTACATAAAACAGGGGCAACCGGCGGATTTGGTAGCTATGTCGCGTTTATTCCAGAAAAAGAGCTGGGTATAGTGATGCTGGCTAACAAAAACTATCCCAATCCAGCGAGAGTCGCCGCCGCCTGGCAGATTCTCAACGCTCTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3006875","ARO_id":"45337","ARO_name":"EC-14","CARD_short_name":"EC-14","ARO_description":"EC-14 is a EC beta-lactamase.","ARO_category":{"43866":{"category_aro_accession":"3005406","category_aro_cvterm_id":"43866","category_aro_name":"EC beta-lactamase","category_aro_description":"EC beta-lactamases are class C beta-lactamases found in Escherichia coli.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4590":{"model_id":"4590","model_name":"EC-15","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"725"}},"model_sequences":{"sequence":{"6965":{"protein_sequence":{"accession":"WP_063610930.1","sequence":"MFKTTLCALLITASCSTFAAPQQINDIVHRTITPLIEQQKIPGMAVAVIYQGKPYYFTWGYADIAKKQPVTQQTLFELGSVSKTFTGVLGGDAIARGEIKLSDPATKYWPELTAKQWNGITLLHLATYTAGGLPLQVPDEVKSSSDLLRFYQNWQPAWAPGTQRLYANSSIGLFGALAVKPSGLSFEQAMQTRVFQPLKLNHTWINVPPPEEKNYAWGYREGKAVHVSPGALDAEAYGVKSTIEDMARWVRSNMNPRDINDKTLQQGIQLAQSRYWQTGDMYQGLGWEMLDWPVNPDSIINGSGNKIALAAPPVKAITPPTPAVRASWVHKTGATGGFGSYVAFIPEKELGIVMLANKNYPNPARVAAAWQILNALQ"},"dna_sequence":{"accession":"NG_049081.1","fmin":"100","fmax":"1234","strand":"+","sequence":"ATGTTCAAAACGACGCTCTGCGCCTTATTAATTACCGCCTCTTGCTCCACATTTGCTGCCCCTCAACAAATCAACGATATTGTGCATCGCACAATTACCCCGCTTATAGAGCAACAAAAGATCCCCGGTATGGCGGTGGCGGTAATTTATCAGGGTAAACCTTATTACTTTACCTGGGGCTATGCGGACATCGCCAAAAAGCAGCCCGTCACACAGCAAACGTTGTTTGAGTTAGGTTCGGTCAGCAAAACATTTACGGGCGTGCTTGGTGGCGACGCTATTGCTCGAGGGGAAATCAAGTTAAGCGATCCCGCAACAAAATACTGGCCTGAACTTACCGCTAAACAGTGGAATGGGATCACACTATTACATCTTGCGACCTACACCGCTGGCGGCCTGCCATTGCAGGTGCCGGATGAAGTGAAATCCTCAAGCGACTTGCTGCGCTTCTATCAAAACTGGCAGCCTGCATGGGCTCCAGGAACACAACGTCTGTATGCCAACTCCAGTATCGGTTTGTTCGGCGCACTGGCTGTGAAGCCGTCTGGTTTGAGTTTTGAGCAGGCGATGCAAACTCGTGTCTTCCAGCCACTCAAACTCAACCATACGTGGATTAATGTACCTCCCCCAGAAGAAAAGAATTACGCCTGGGGATATCGCGAAGGTAAGGCAGTGCATGTTTCGCCAGGGGCGTTAGATGCTGAAGCTTATGGTGTGAAGTCGACCATTGAAGATATGGCCCGCTGGGTACGAAGCAATATGAATCCCCGTGATATCAACGACAAAACACTTCAGCAAGGGATACAACTGGCACAATCTCGCTACTGGCAAACCGGCGATATGTATCAGGGCCTGGGCTGGGAAATGCTGGACTGGCCGGTAAATCCTGACAGCATCATTAACGGCAGTGGCAATAAAATTGCACTGGCAGCACCCCCTGTAAAAGCGATTACGCCCCCAACTCCTGCAGTACGCGCATCATGGGTACATAAAACAGGGGCAACCGGCGGATTTGGTAGCTATGTCGCGTTTATTCCAGAAAAAGAGCTGGGTATAGTGATGCTGGCTAACAAAAACTATCCCAATCCAGCGAGAGTCGCCGCCGCCTGGCAGATTCTCAACGCTCTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3006876","ARO_id":"45338","ARO_name":"EC-15","CARD_short_name":"EC-15","ARO_description":"EC-15 is a EC beta-lactamase.","ARO_category":{"43866":{"category_aro_accession":"3005406","category_aro_cvterm_id":"43866","category_aro_name":"EC beta-lactamase","category_aro_description":"EC beta-lactamases are class C beta-lactamases found in Escherichia coli.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4591":{"model_id":"4591","model_name":"EC-16","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"725"}},"model_sequences":{"sequence":{"6966":{"protein_sequence":{"accession":"WP_063860248.1","sequence":"MFKTTLCALLITASCSTFAAPQQINDIVHRTITPLIEQQKIPGMAVAVIYQGKPYYFTWGYADIAKKQPVTQQTLFELGSVSKTFTGVLGGDAIARGEIKLSDPATKYWPELTAKQWNGITLLHLATYTAGGLPLQVPDEVKSSSDLLRFYQNWQPAWAPGTQRLYANSSIGLFGALAVKPSGLSFEQAMQTRVFQPLKLNHTWINVPPPEEKNYAWGYREGKAVHVSPGALDAEAYGVKSTIEDMARWVRSNMNPRDINDKTLQQGIQLAQSRYWQTGDMYQGLGWEMLDWPVNPDSIINGCGNKIALAAHPVKAITPPTPAVRASWVHKTGATGGFGSYVAFIPEKELGIVMLANKNYPNPARVAAAWQILNALQ"},"dna_sequence":{"accession":"NG_049082.1","fmin":"100","fmax":"1234","strand":"+","sequence":"ATGTTCAAAACGACGCTCTGCGCCTTATTAATTACCGCCTCTTGCTCCACATTTGCTGCCCCTCAACAAATCAACGATATTGTGCATCGCACAATTACCCCGCTTATAGAGCAACAAAAGATCCCCGGTATGGCGGTGGCGGTAATTTATCAGGGTAAACCTTATTACTTTACCTGGGGCTATGCGGACATCGCCAAAAAGCAGCCCGTCACACAGCAAACGTTGTTTGAGTTAGGTTCGGTCAGCAAAACATTTACGGGCGTGCTTGGTGGCGACGCTATTGCTCGAGGGGAAATCAAGTTAAGCGATCCCGCAACAAAATACTGGCCTGAACTTACCGCTAAACAGTGGAATGGGATCACACTATTACATCTTGCGACCTACACCGCTGGCGGCCTGCCATTGCAGGTGCCGGATGAAGTGAAATCCTCAAGCGACTTGCTGCGCTTCTATCAAAACTGGCAGCCTGCATGGGCTCCAGGAACACAACGTCTGTATGCCAACTCCAGTATCGGTTTGTTCGGCGCACTGGCTGTGAAGCCGTCTGGTTTGAGTTTTGAGCAGGCGATGCAAACTCGTGTCTTCCAGCCACTCAAACTCAACCATACGTGGATTAATGTACCTCCCCCAGAAGAAAAGAATTACGCCTGGGGATATCGCGAAGGTAAGGCAGTGCATGTTTCGCCAGGGGCGTTAGATGCTGAAGCTTATGGTGTGAAGTCGACCATTGAAGATATGGCCCGCTGGGTACGAAGCAATATGAATCCCCGTGATATCAACGACAAAACACTTCAGCAAGGGATACAACTGGCACAATCTCGCTACTGGCAAACCGGCGATATGTATCAGGGCCTGGGCTGGGAAATGCTGGACTGGCCGGTAAATCCTGACAGCATCATTAACGGCTGTGGCAATAAAATTGCACTGGCAGCACACCCTGTAAAAGCGATTACGCCCCCAACTCCTGCAGTACGCGCATCATGGGTACATAAAACAGGGGCAACCGGCGGATTTGGTAGCTATGTCGCGTTTATTCCAGAAAAAGAGCTGGGTATAGTGATGCTGGCTAACAAAAACTATCCCAATCCAGCGAGAGTCGCCGCCGCCTGGCAGATTCTCAACGCTCTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3006877","ARO_id":"45339","ARO_name":"EC-16","CARD_short_name":"EC-16","ARO_description":"EC-16 is a EC beta-lactamase.","ARO_category":{"43866":{"category_aro_accession":"3005406","category_aro_cvterm_id":"43866","category_aro_name":"EC beta-lactamase","category_aro_description":"EC beta-lactamases are class C beta-lactamases found in Escherichia coli.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4592":{"model_id":"4592","model_name":"EC-18","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"725"}},"model_sequences":{"sequence":{"6967":{"protein_sequence":{"accession":"WP_063860256.1","sequence":"MFKTTLCALLITASCSTFAAPQQINDIVHRTITPLIEQQKIPGMAVAVIYQGKPYYFTWGYADIAKKQPVTQQTLFELGSVSKTFTGVLGGDAIARGEIKLSDPTTKYWPELTAKQWNGITLLHLATYTAGGLPLQVPDEVKSSSDLLRFYQNWQPTWAPGTQRLYANSSIGLFGALAVKPSGLSFEQAMQTRVFQPLKLNHTWINVPPPEEKNYAWGYREGKAVHVSPGALDAEAYGVKSTIEDMARWVRSNMNPRDINDKTLQQGIQLAQSRYWQTGDMYQGLGWEMLDWPVNPDSIINGSGNKIALAAHPVKAITPPTPAVRASWVHKTGATGGFGSYVAFIPEKELGIVMLANKNYPNPARFAAAWQILNALQ"},"dna_sequence":{"accession":"NG_049083.1","fmin":"100","fmax":"1234","strand":"+","sequence":"ATGTTCAAAACGACGCTCTGCGCCTTATTAATTACCGCCTCTTGCTCCACATTTGCTGCCCCTCAACAAATCAACGATATTGTGCATCGCACAATTACCCCGCTTATAGAGCAACAAAAGATCCCCGGTATGGCGGTGGCGGTAATTTATCAGGGTAAACCTTATTACTTTACCTGGGGCTATGCGGACATCGCCAAAAAGCAGCCCGTCACACAGCAAACGTTGTTTGAGTTAGGTTCGGTCAGCAAAACATTTACGGGCGTGCTTGGTGGCGACGCTATTGCTCGAGGGGAAATCAAGTTAAGCGATCCCACAACAAAATACTGGCCTGAACTTACCGCTAAACAGTGGAATGGGATCACACTATTACATCTCGCAACCTACACTGCTGGCGGCCTGCCATTGCAGGTGCCGGATGAGGTGAAATCCTCAAGCGACTTGCTGCGCTTCTATCAAAACTGGCAGCCTACATGGGCGCCAGGAACACAACGTCTGTATGCCAACTCCAGTATCGGTTTGTTCGGCGCACTGGCTGTGAAGCCGTCTGGTTTGAGTTTTGAGCAGGCGATGCAAACACGTGTCTTCCAGCCACTCAAACTCAACCATACGTGGATTAATGTACCTCCCCCAGAAGAAAAGAATTACGCCTGGGGATATCGCGAAGGTAAGGCAGTGCATGTTTCGCCAGGGGCGTTAGATGCTGAAGCTTATGGTGTGAAGTCGACCATTGAAGATATGGCCCGCTGGGTACGAAGCAATATGAATCCCCGTGATATCAACGACAAAACACTTCAGCAAGGGATACAACTGGCACAATCTCGCTACTGGCAAACCGGCGATATGTATCAGGGCCTGGGCTGGGAAATGCTGGACTGGCCGGTAAATCCTGACAGCATCATTAACGGCAGTGGCAATAAAATTGCACTGGCAGCACACCCTGTAAAAGCGATTACGCCCCCAACTCCTGCAGTACGCGCATCATGGGTACATAAAACAGGGGCAACCGGCGGATTTGGTAGCTATGTCGCGTTTATTCCAGAAAAAGAGCTGGGTATAGTGATGCTGGCTAACAAAAACTATCCCAATCCAGCGAGATTCGCCGCCGCCTGGCAGATTCTCAACGCTCTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3006878","ARO_id":"45340","ARO_name":"EC-18","CARD_short_name":"EC-18","ARO_description":"EC-18 is a EC beta-lactamase.","ARO_category":{"43866":{"category_aro_accession":"3005406","category_aro_cvterm_id":"43866","category_aro_name":"EC beta-lactamase","category_aro_description":"EC beta-lactamases are class C beta-lactamases found in Escherichia coli.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4593":{"model_id":"4593","model_name":"EC-19","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"725"}},"model_sequences":{"sequence":{"6968":{"protein_sequence":{"accession":"WP_063860263.1","sequence":"MFKTTLCTLLITASCSTFAAPQQINDIVHRTITPLIEQQKIPGMAVAVIYQGKPYYFTWGYADIAKKQPVTQQTLFELGSVSKTFTGVLGGDAIARGEIKLSDPTTKYWPELTAKQWNGITLLHLATYTAGGLPLQVPDEVKSSSDLLRFYQNWQPAWAPGTQRLYANSSIGLFGALAVKPSGLSFEQAMKTRVFQPLKLNHTWINVPSAEEKNYAWGYREGKAVHVSPGALDAEAYGVKSTIEDMARWVQSNLKPFDINEKTLQQGIQLAQSRYWQTGDMYQGLGWEMLDWPLNPDIIINGSDNKIALAARPVKPITPPTPAVRASWVHKTGATGGFGSYVAFIPEKELGIVMLANKNYPNPARFAAAWQILNALQ"},"dna_sequence":{"accession":"NG_049084.1","fmin":"100","fmax":"1234","strand":"+","sequence":"ATGTTCAAAACGACGCTCTGCACCTTATTAATTACCGCCTCTTGCTCCACATTTGCCGCCCCTCAACAAATCAACGATATTGTGCATCGCACAATTACCCCGCTTATAGAGCAACAAAAGATCCCCGGTATGGCGGTGGCGGTAATTTATCAGGGTAAACCTTATTACTTTACCTGGGGCTATGCGGACATCGCCAAAAAGCAGCCCGTCACACAGCAAACGTTGTTTGAGTTAGGTTCGGTCAGCAAAACATTTACGGGCGTGCTTGGTGGCGACGCTATTGCTCGAGGGGAAATCAAGTTAAGCGATCCCACAACAAAATACTGGCCTGAACTTACCGCTAAACAGTGGAATGGGATCACACTATTACATCTCGCAACCTACACCGCTGGCGGCCTGCCATTGCAGGTGCCGGATGAGGTGAAATCCTCAAGCGACTTGCTGCGCTTCTATCAAAACTGGCAGCCTGCATGGGCTCCAGGAACACAACGTCTGTATGCCAACTCCAGTATCGGTTTGTTCGGCGCACTGGCTGTGAAGCCGTCTGGTTTGAGTTTTGAGCAGGCGATGAAAACTCGTGTCTTCCAGCCACTCAAACTCAATCATACGTGGATTAATGTACCGTCCGCAGAAGAAAAGAACTACGCCTGGGGATATCGCGAAGGTAAGGCAGTACATGTTTCGCCAGGGGCGTTAGATGCTGAAGCTTATGGTGTGAAGTCGACCATTGAAGATATGGCCCGCTGGGTGCAAAGCAATTTAAAACCATTTGATATCAATGAGAAAACACTTCAACAAGGGATACAACTGGCACAATCTCGCTACTGGCAAACCGGCGATATGTATCAGGGTCTGGGCTGGGAAATGCTGGACTGGCCGCTAAATCCTGACATCATCATTAACGGCAGTGACAATAAAATTGCACTGGCAGCACGCCCCGTAAAACCGATTACGCCCCCAACTCCTGCAGTACGCGCATCATGGGTACATAAAACGGGGGCGACCGGCGGATTTGGTAGCTATGTCGCGTTTATTCCAGAAAAAGAGCTGGGTATCGTGATGCTGGCTAACAAAAACTATCCCAATCCAGCGAGATTCGCCGCCGCCTGGCAGATTCTCAACGCTCTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3006879","ARO_id":"45341","ARO_name":"EC-19","CARD_short_name":"EC-19","ARO_description":"EC-19 is a EC beta-lactamase.","ARO_category":{"43866":{"category_aro_accession":"3005406","category_aro_cvterm_id":"43866","category_aro_name":"EC beta-lactamase","category_aro_description":"EC beta-lactamases are class C beta-lactamases found in Escherichia coli.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4594":{"model_id":"4594","model_name":"EC-5","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"725"}},"model_sequences":{"sequence":{"6969":{"protein_sequence":{"accession":"WP_001443153.1","sequence":"MFKTTLCTLLITASCSTFAAPQQINDIVHRTITPLIEQQKIPGMAVAVIYQGKPYYFTWGYADIAKKQPVTQQTLFELGSVSKTFTGVLGGDAIARGEIKLSDPTTKYWPELTAKQWNGITLLHLATYTAGGLPLQVPDEVKSSSDLLRFYQNWQPAWAPGTQRLYANSSIGLFGALAVKPSGLSFEQAMKTRVFQPLKLNHTWINVPSAEEKNYAWGYREGKAVHVSPGALDAEAYGVKSTIEDMARWVQSNLKPLDINEKTLQQGIQLAQSRYWQTGDMYQGLGWEMLDWPVNPDIIINGSDNKIALAARPVKPITPPTPAVRASWVHKTGATGGFGSYVAFIPEKELGIVMLANKNYPNPARVAAAWQILNALQ"},"dna_sequence":{"accession":"NG_049085.1","fmin":"100","fmax":"1234","strand":"+","sequence":"ATGTTCAAAACGACGCTCTGCACCTTATTAATTACCGCCTCTTGCTCCACATTTGCCGCCCCTCAACAAATCAACGATATTGTGCATCGCACAATTACCCCGCTTATAGAGCAACAAAAGATCCCCGGTATGGCGGTAGCGGTAATTTATCAGGGTAAACCTTATTACTTTACCTGGGGCTATGCGGACATCGCCAAAAAGCAGCCCGTCACACAGCAAACGTTGTTTGAGTTAGGTTCGGTCAGCAAAACATTTACGGGCGTGCTTGGTGGCGACGCTATTGCTCGAGGGGAAATCAAGTTAAGCGATCCCACAACAAAATACTGGCCTGAACTTACCGCTAAACAGTGGAATGGGATCACACTATTACATCTCGCAACCTACACCGCTGGCGGCCTGCCATTGCAGGTGCCGGATGAGGTGAAATCCTCAAGCGACTTGCTGCGCTTCTATCAAAACTGGCAGCCTGCATGGGCTCCAGGAACACAACGTCTGTATGCCAACTCCAGTATCGGTTTGTTCGGCGCACTGGCTGTGAAGCCGTCTGGTTTGAGTTTTGAGCAGGCGATGAAAACTCGTGTCTTCCAGCCACTCAAACTCAATCATACGTGGATTAATGTACCGTCCGCAGAAGAAAAGAACTACGCCTGGGGATATCGCGAAGGTAAGGCAGTACATGTTTCGCCAGGGGCGTTAGATGCTGAAGCTTATGGTGTGAAGTCGACCATTGAAGATATGGCCCGCTGGGTGCAAAGCAATTTAAAACCCCTTGATATCAATGAGAAAACACTTCAACAAGGGATACAACTGGCACAATCTCGCTACTGGCAAACCGGCGATATGTATCAGGGTCTGGGCTGGGAAATGCTGGACTGGCCGGTAAATCCTGACATCATCATTAACGGCAGTGACAATAAAATTGCACTGGCAGCACGCCCCGTAAAACCGATTACGCCCCCAACTCCTGCAGTACGCGCATCATGGGTACATAAAACGGGGGCGACCGGCGGATTTGGTAGCTATGTCGCGTTTATTCCAGAAAAAGAGCTGGGTATCGTGATGCTGGCTAACAAAAACTACCCCAATCCAGCGAGAGTCGCCGCCGCCTGGCAGATTCTCAACGCTCTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40458","NCBI_taxonomy_name":"Escherichia","NCBI_taxonomy_id":"561"}}}},"ARO_accession":"3006880","ARO_id":"45342","ARO_name":"EC-5","CARD_short_name":"EC-5","ARO_description":"EC-5 is a EC beta-lactamase.","ARO_category":{"43866":{"category_aro_accession":"3005406","category_aro_cvterm_id":"43866","category_aro_name":"EC beta-lactamase","category_aro_description":"EC beta-lactamases are class C beta-lactamases found in Escherichia coli.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4595":{"model_id":"4595","model_name":"EC-8","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"725"}},"model_sequences":{"sequence":{"6970":{"protein_sequence":{"accession":"WP_063860454.1","sequence":"MFKTTLCALLITASCSTFAAPQQINDIVHRTITPLIEQQKIPGMAVAVIYQGKPYYFTWGYADIAKKQPVTQQTLFELGSVSKTFTGVLGGDAIARGEIKLSDPATKYWPELTAKQWNGITLLHLATYTAGGLPLQVPDDVKSSSDLLRFYQNWQPAWAPGTQRLYANSSIGLFGALAVKPSGLSFEQAMQTRVFQPLKLNHTWINVPPAEEKNYAWGYREGKAVHVSPGALDAEAYGVKSTIEDMARWVQSNLKPLDITEKTLQQGIQLAQSRYWQTGDMYQGLGWEMLDWPVNPDSIINGSDNKIALAARPVKAITPPTPAVRASWVHKTGATGGFGSYVAFIPEKELGIVMLANKNYPNPARVTAAWQILNALQ"},"dna_sequence":{"accession":"NG_049086.1","fmin":"100","fmax":"1234","strand":"+","sequence":"ATGTTCAAAACGACGCTCTGCGCCTTATTAATTACCGCCTCTTGCTCCACATTTGCCGCCCCTCAACAAATCAACGATATTGTGCATCGCACAATTACCCCGCTTATAGAGCAACAAAAGATCCCCGGTATGGCGGTGGCGGTAATTTATCAGGGTAAACCTTATTACTTTACCTGGGGCTATGCGGACATCGCCAAAAAGCAGCCCGTCACACAGCAAACGTTGTTTGAGTTAGGTTCGGTCAGCAAAACATTTACGGGCGTGCTTGGTGGCGACGCTATTGCACGAGGGGAAATCAAGTTAAGCGATCCCGCGACAAAATACTGGCCTGAACTTACCGCTAAACAATGGAATGGGATCACACTATTACATCTTGCGACCTACACCGCTGGCGGCCTGCCATTGCAGGTGCCGGATGACGTTAAATCCTCAAGCGACTTGCTGCGCTTCTATCAAAACTGGCAGCCTGCATGGGCTCCAGGAACACAACGTCTGTATGCCAACTCCAGTATCGGTTTGTTCGGCGCACTGGCTGTGAAGCCGTCTGGTTTGAGTTTTGAGCAGGCGATGCAAACTCGTGTCTTCCAGCCACTCAAACTCAACCATACGTGGATTAATGTACCGCCCGCAGAAGAAAAGAATTACGCCTGGGGATATCGCGAAGGTAAGGCAGTGCATGTTTCGCCAGGGGCGTTAGATGCTGAAGCTTATGGTGTGAAGTCGACCATTGAAGATATGGCCCGCTGGGTGCAAAGCAATTTAAAACCCCTTGATATCACTGAGAAAACGCTTCAACAAGGGATACAACTGGCACAATCTCGCTACTGGCAAACCGGCGATATGTATCAGGGCCTGGGCTGGGAAATGCTGGACTGGCCGGTAAATCCTGACAGCATCATTAACGGCAGTGACAATAAAATTGCACTGGCAGCACGCCCCGTAAAAGCGATTACGCCCCCAACTCCTGCAGTGCGCGCATCATGGGTACATAAAACAGGGGCGACCGGCGGATTTGGTAGCTATGTCGCGTTTATTCCAGAAAAAGAGCTGGGTATCGTGATGCTGGCTAACAAAAACTATCCCAATCCAGCGAGAGTCACTGCCGCCTGGCAGATTCTCAACGCTCTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3006881","ARO_id":"45343","ARO_name":"EC-8","CARD_short_name":"EC-8","ARO_description":"EC-8 is a EC beta-lactamase.","ARO_category":{"43866":{"category_aro_accession":"3005406","category_aro_cvterm_id":"43866","category_aro_name":"EC beta-lactamase","category_aro_description":"EC beta-lactamases are class C beta-lactamases found in Escherichia coli.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4596":{"model_id":"4596","model_name":"ECM-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"6971":{"protein_sequence":{"accession":"WP_122630824.1","sequence":"MFARTGAGLALAAACLAGCAPPIQSRPDLPAPEQVTPQQWAAGCEPWDDWDKPAPPYRIHGSTYYVGTCGITAILVAGPAGHLLIDSGTEAGAKVVLDNIGKVGFRPDEIASLLHSHEHFDHTGGHARVKQASGAHIVASPAAAPALRSGLSIAEDPQYGLHEPMAPVAVDVLVRGGETVRSETATLTAIATPGHTPGALSWTWRSCDAAGDCLDVVYADSLSAISREGYRFADHPAYVAAFRAGLQRLRETACDLLLTPHPSASEMVARAASGTLAGGMSCAAYADAAEARLDARLAEEADG"},"dna_sequence":{"accession":"NG_062207.1","fmin":"18","fmax":"930","strand":"+","sequence":"ATGTTCGCTAGAACCGGAGCCGGCCTCGCACTTGCGGCCGCGTGCCTCGCCGGCTGCGCACCGCCGATCCAGTCCCGTCCCGACCTGCCCGCGCCCGAGCAGGTTACGCCGCAGCAATGGGCTGCCGGTTGCGAGCCGTGGGACGATTGGGACAAGCCCGCCCCGCCCTACCGCATCCACGGCTCGACCTATTATGTCGGCACTTGCGGCATCACGGCGATCCTCGTCGCGGGGCCGGCCGGACACCTGCTGATCGACAGCGGGACCGAGGCGGGCGCCAAAGTGGTGCTCGACAACATCGGCAAGGTCGGTTTCCGCCCCGACGAGATCGCCAGCCTGCTGCACAGCCACGAACATTTCGACCACACCGGCGGCCATGCGCGCGTCAAGCAAGCCAGCGGCGCGCATATCGTCGCTTCGCCCGCTGCCGCGCCTGCGCTACGCAGCGGCCTGAGCATTGCCGAAGATCCGCAATACGGACTGCACGAACCGATGGCGCCGGTGGCTGTCGACGTGCTGGTCCGCGGCGGCGAGACGGTGCGCAGCGAAACCGCCACGCTCACCGCGATCGCCACGCCGGGGCACACGCCGGGCGCGCTGAGCTGGACATGGCGCTCGTGCGACGCGGCGGGTGACTGCCTCGACGTGGTCTATGCCGACTCGCTCTCCGCGATCAGCCGCGAAGGATACCGCTTTGCCGACCATCCCGCCTATGTCGCCGCGTTCCGCGCCGGATTGCAGCGGCTGCGCGAAACCGCCTGCGACCTGCTGCTGACCCCGCACCCCTCCGCGAGCGAGATGGTCGCGCGCGCGGCGAGCGGAACGCTGGCCGGCGGGATGAGCTGCGCCGCCTATGCCGATGCCGCCGAGGCCCGGCTCGATGCGCGGTTGGCGGAGGAAGCGGATGGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3006882","ARO_id":"45344","ARO_name":"ECM-1","CARD_short_name":"ECM-1","ARO_description":"ECM-1 is a ECM beta-lactamase.","ARO_category":{"43867":{"category_aro_accession":"3005407","category_aro_cvterm_id":"43867","category_aro_name":"ECM beta-lactamase","category_aro_description":"ECM beta-lactamases are class B3 beta-lactamases found in Qipengyuania citrea.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4597":{"model_id":"4597","model_name":"ECV-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"6972":{"protein_sequence":{"accession":"WP_015266427.1","sequence":"MYYSLLISAFLLSISACGGKSEKLQEHLVAEQTSTFTEKEVYSSDKLIIKQVSPHTYVHVSFLDTDTFGKVACNGMIVISDGEAVVFDTPSTSNETSELLSFLEEEKLQVNAVVATHFHLDCLGGLEAFHARNIPSYAFKNTLSLASQHDFPQPQKGFSDELTLKVGTKAVFVHYFGEGHTQDNVIGYFPDDQVLFGGCLIKANGAGKGNLEDANVEAWPVTVNKISTAYPNLRLVIPGHGNWGDKTLLHYTETLFK"},"dna_sequence":{"accession":"NG_059320.1","fmin":"100","fmax":"874","strand":"+","sequence":"ATGTATTACAGCCTCCTTATTTCAGCATTTCTCTTATCCATATCCGCTTGCGGAGGAAAAAGTGAAAAATTACAGGAACATCTTGTTGCTGAGCAAACCTCCACTTTTACTGAAAAAGAGGTCTATTCATCGGATAAACTCATTATCAAACAAGTCAGTCCCCATACTTATGTTCACGTTTCCTTTCTGGACACCGACACCTTCGGAAAAGTAGCCTGCAACGGGATGATCGTCATCAGTGATGGAGAAGCTGTCGTATTCGACACCCCAAGTACCTCAAATGAGACCAGTGAACTTCTTTCATTTTTGGAAGAGGAGAAGCTACAGGTCAACGCTGTAGTAGCGACACATTTTCACTTGGATTGCCTGGGTGGACTTGAAGCATTTCACGCCAGGAACATTCCGTCATATGCCTTTAAAAACACCCTATCTTTAGCATCTCAGCATGACTTCCCACAACCCCAAAAGGGCTTTTCTGACGAGCTGACCTTAAAAGTAGGCACTAAAGCAGTCTTTGTTCACTATTTTGGGGAAGGACATACCCAAGACAATGTAATTGGATACTTCCCTGATGACCAAGTGCTGTTTGGCGGGTGTCTCATCAAAGCTAATGGTGCTGGAAAAGGTAACCTCGAAGATGCCAATGTCGAGGCTTGGCCGGTCACCGTGAACAAAATCAGTACCGCTTATCCAAACCTTCGGCTAGTCATTCCAGGACATGGCAATTGGGGCGACAAAACCTTACTGCATTACACCGAAACCCTCTTCAAATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3006883","ARO_id":"45345","ARO_name":"ECV-1","CARD_short_name":"ECV-1","ARO_description":"ECV-1 is a ECV beta-lactamase.","ARO_category":{"43868":{"category_aro_accession":"3005408","category_aro_cvterm_id":"43868","category_aro_name":"ECV beta-lactamase","category_aro_description":"ECV beta-lactamases are class B1 beta-lactamases found in Echinicola vietnamensis.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4598":{"model_id":"4598","model_name":"EFM-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"6973":{"protein_sequence":{"accession":"WP_122630822.1","sequence":"MSARCLPALTLPLALAACAPPIQTPDPLPPREIVTPQQWAQQCTDWDEWDKPAPPYRIHGSTYYVGTCGIAAILVAGDGGHILIDSGTEAGADVVLDNVGKLGFRPNEIASLLHSHEHFDHTGGHALVRRESGAHVVASPQAAPVLRTGEDDPADPQHGLHDAMEPVPVDVIVRDGETVRSESATLTAIATPGHTPGALSWAWQSCDEAGDCLSIVYADSLSPISRKGYRFGDHPEYLEGFRAGLEKLRAVDCDILLTPHPSASDMVTRAAAGSMVGGMSCVDYADAVEARLDARLVEEAGD"},"dna_sequence":{"accession":"NG_062204.1","fmin":"0","fmax":"909","strand":"+","sequence":"ATGTCCGCTAGATGCCTGCCCGCGCTGACGCTGCCGCTGGCCCTTGCGGCTTGCGCCCCGCCGATCCAGACGCCCGATCCACTGCCCCCGCGCGAAATCGTCACGCCGCAGCAATGGGCGCAGCAATGCACCGACTGGGACGAATGGGACAAACCCGCCCCGCCCTACCGCATCCACGGATCGACCTATTACGTGGGCACTTGCGGCATCGCCGCGATCCTCGTCGCGGGCGACGGCGGCCATATCCTGATCGATAGCGGGACCGAGGCGGGCGCGGATGTGGTGCTCGACAACGTCGGCAAGCTCGGCTTCCGTCCCAACGAGATCGCCAGCCTGCTGCACAGCCACGAACATTTCGACCACACCGGTGGGCACGCGCTGGTCAGGCGGGAAAGCGGCGCCCATGTCGTTGCCTCGCCGCAGGCCGCGCCGGTCCTGCGTACCGGCGAAGACGACCCCGCCGATCCCCAGCACGGCCTGCACGATGCGATGGAGCCGGTGCCGGTCGATGTCATCGTGCGCGACGGTGAAACCGTGCGCAGCGAAAGCGCGACGCTTACCGCGATCGCGACCCCGGGGCACACGCCGGGGGCGTTGAGCTGGGCATGGCAATCCTGCGATGAGGCAGGTGATTGCCTTTCGATAGTCTATGCCGATTCGCTTTCGCCGATCAGCCGCAAAGGCTATCGCTTCGGCGACCACCCCGAGTACCTCGAGGGCTTCCGTGCCGGCCTCGAAAAGCTCCGTGCGGTCGATTGCGACATCCTGCTCACCCCGCATCCCTCGGCCAGCGACATGGTGACACGCGCCGCTGCGGGATCGATGGTCGGGGGCATGAGCTGCGTGGACTATGCCGATGCGGTCGAAGCGCGGCTCGACGCGCGGCTGGTGGAGGAAGCGGGTGACTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3006884","ARO_id":"45346","ARO_name":"EFM-1","CARD_short_name":"EFM-1","ARO_description":"EFM-1 is a EFM beta-lactamase.","ARO_category":{"43869":{"category_aro_accession":"3005409","category_aro_cvterm_id":"43869","category_aro_name":"EFM beta-lactamase","category_aro_description":"EFM beta-lactamases are class B3 beta-lactamase found in Qipengyuania flava.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4599":{"model_id":"4599","model_name":"ELM-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"575"}},"model_sequences":{"sequence":{"6974":{"protein_sequence":{"accession":"WP_081853183.1","sequence":"MPMEQALFVRIARALAASLITLSAVAFAQEPKVDIPADQQAFVDICKPWDEWDKPAPPFEIYRDTYYVGTCGIAAILITDEEGHILIDSGTEAGADVVMANVAALGFDLKDVRYLLYSHEHFDHVGGMAKLQRATGALVVASKAAEPVLTSGEDSLADPQHGMHEPFEGVAVGRIMAAGDILELGGTTIRAIETPGHTPGAMSWWWQECKERCENIVYADSLSPISRDDYRFGDHPEYVAAYRAGLVALGREDCTVLLTPHPSHSRMIRRMQEGDLIENRQGTRPCARYAGQKLLDLETRLSNETLSEEDRAQ"},"dna_sequence":{"accession":"NG_062206.1","fmin":"0","fmax":"942","strand":"+","sequence":"ATGCCAATGGAGCAAGCTTTGTTCGTTAGGATTGCGCGTGCACTTGCCGCATCGCTCATTACCCTTTCCGCTGTCGCTTTTGCGCAAGAGCCGAAGGTGGATATCCCCGCCGATCAACAGGCTTTTGTCGATATCTGCAAGCCATGGGACGAATGGGACAAACCTGCCCCACCCTTCGAGATTTACCGCGACACCTATTATGTCGGGACCTGCGGCATCGCCGCGATTCTTATCACCGATGAGGAGGGCCATATCCTGATCGACAGCGGGACCGAGGCAGGCGCGGATGTGGTCATGGCCAATGTGGCGGCGCTGGGCTTTGACCTTAAAGATGTGCGCTATCTTTTGTATAGCCACGAACACTTCGACCACGTCGGCGGCATGGCAAAGCTTCAACGCGCAACCGGCGCACTGGTGGTCGCTTCAAAAGCCGCAGAGCCCGTGCTGACATCAGGCGAAGATTCGCTGGCGGACCCGCAGCACGGGATGCACGAACCGTTCGAAGGGGTTGCCGTAGGACGGATCATGGCCGCAGGAGACATCCTAGAGCTGGGCGGCACCACCATTCGTGCGATCGAAACACCCGGCCACACCCCTGGCGCGATGAGCTGGTGGTGGCAGGAATGCAAGGAACGCTGCGAGAATATCGTCTACGCCGACAGCCTTTCTCCCATCAGCCGCGATGACTACCGATTTGGCGATCACCCCGAATATGTCGCCGCATACCGCGCCGGACTGGTCGCATTGGGGCGTGAGGACTGCACCGTTTTGCTGACCCCGCACCCTTCGCACAGCCGCATGATCCGCCGGATGCAAGAGGGTGATCTGATCGAAAACAGGCAAGGGACGCGGCCATGTGCCCGCTATGCAGGGCAAAAGCTGCTCGACCTTGAAACGCGACTTTCCAATGAAACGCTATCCGAAGAAGATCGGGCCCAATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3006885","ARO_id":"45347","ARO_name":"ELM-1","CARD_short_name":"ELM-1","ARO_description":"ELM-1 is a ELM beta-lactamase.","ARO_category":{"43870":{"category_aro_accession":"3005410","category_aro_cvterm_id":"43870","category_aro_name":"ELM beta-lactamase","category_aro_description":"ELM beta-lactamases are class B3 beta-lactamases found in Erythrobacter longus.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4600":{"model_id":"4600","model_name":"EVM-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"6975":{"protein_sequence":{"accession":"WP_122630823.1","sequence":"MSVKFLVPIAFALSGCAVLPPPIQTPEPLPPAEEVQPEQWAATCEPWDDWDKPAPPYRIFGSTYYVGTCGISAILIAGDDGHILIDSGTEEGAEVVMDNIQKLGFRLNEIASILHSHEHFDHVGGLAKLRAATGAHIVSSAEAAKVLSTGEDHPEDPQFGVHEPMEPVQVDVIVEDGDTVRTETATVTAHATPGHSPGALSWTWVSCSLPGEPPACSRIAYVDSLSAVSSDDYRFTDHPEVVAAFRTSIDKVRSLPCDILLTPHPSSSQLIERLRTGTLGAPGKCATYAAQLGDKLDERLAKENP"},"dna_sequence":{"accession":"NG_062205.1","fmin":"0","fmax":"918","strand":"+","sequence":"ATGTCCGTTAAGTTCCTCGTCCCCATCGCTTTCGCTTTGTCGGGCTGCGCAGTCCTGCCTCCACCGATCCAGACGCCGGAGCCTCTGCCTCCGGCCGAAGAGGTCCAGCCTGAACAATGGGCGGCTACCTGCGAGCCTTGGGATGATTGGGACAAACCCGCCCCGCCCTATCGTATCTTCGGTTCGACCTATTATGTCGGCACCTGCGGCATTTCCGCGATCCTCATAGCAGGCGACGATGGACACATCCTGATCGACAGCGGGACCGAGGAAGGCGCCGAGGTCGTCATGGACAACATCCAGAAGCTGGGCTTCCGGCTCAACGAGATCGCGAGCATCCTCCACAGCCACGAACATTTCGACCATGTCGGCGGTCTGGCCAAACTTCGCGCCGCGACCGGGGCGCATATCGTTTCATCGGCGGAAGCAGCGAAGGTGCTCTCGACGGGAGAGGACCATCCGGAGGACCCGCAGTTCGGGGTCCATGAGCCGATGGAGCCGGTGCAGGTCGATGTCATCGTCGAAGACGGAGACACGGTACGCACAGAGACCGCTACGGTCACGGCACATGCGACGCCCGGCCACAGTCCGGGCGCACTCAGTTGGACCTGGGTGAGTTGCAGCCTGCCGGGCGAACCGCCAGCCTGCAGCAGGATCGCCTATGTCGACAGTCTGTCGGCCGTTTCTTCCGATGACTATCGCTTTACCGACCACCCCGAGGTCGTGGCCGCATTCCGCACCAGCATAGACAAGGTACGGTCCCTGCCCTGCGATATCCTCCTCACTCCGCATCCCTCTTCCAGCCAATTGATCGAGCGGTTGCGCACCGGGACGCTTGGCGCACCGGGCAAATGTGCCACCTATGCGGCGCAACTCGGCGATAAGCTCGACGAACGGCTTGCGAAAGAAAACCCGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3006886","ARO_id":"45348","ARO_name":"EVM-1","CARD_short_name":"EVM-1","ARO_description":"EVM-1 is a EVM beta-lactamase.","ARO_category":{"43871":{"category_aro_accession":"3005411","category_aro_cvterm_id":"43871","category_aro_name":"EVM beta-lactamase","category_aro_description":"EVM beta-lactamases are class B3 beta-lactamases found in Qipengyuania vulgaris.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4601":{"model_id":"4601","model_name":"FIA-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"475"}},"model_sequences":{"sequence":{"6976":{"protein_sequence":{"accession":"WP_041258349.1","sequence":"MRFLFILLASTLFTHLAVAQAAQKPPLRVSRLSDRVFVHTTYGMYQGEPVPSNGLIVRTDDGVVLLDTGWDTEGNTDNTRQLLRWVADSLRLPVRLCIVTHSHDDKVGGIVELQKAGIRVVSTPLTAQKTVKQGYPSPDGILPADTTFTIGNVPIRTYFPGEGHTVDNIVVWLPSERILHGGCFVKSVAAFGMGYVGESNLTAWSGSIRNVKKRFGNARIVVPGHEEWTGPQALDHTLRLLEKYNANRH"},"dna_sequence":{"accession":"NG_057437.1","fmin":"100","fmax":"850","strand":"+","sequence":"ATGCGTTTTCTGTTCATTCTGCTTGCTAGCACTTTATTTACTCACTTAGCCGTAGCGCAGGCGGCCCAGAAGCCGCCGCTGCGAGTGAGTCGGTTGAGCGATCGGGTGTTTGTCCATACGACTTACGGCATGTATCAGGGCGAGCCGGTGCCGTCCAACGGGCTCATTGTCCGCACCGACGACGGCGTGGTGCTGCTGGACACGGGCTGGGATACCGAGGGTAATACCGACAACACCCGGCAGCTACTCCGCTGGGTGGCCGACAGTCTGCGCCTCCCCGTCCGGCTGTGCATCGTGACGCACTCCCACGACGATAAAGTGGGCGGCATCGTCGAGCTGCAAAAGGCGGGTATCCGGGTGGTGAGTACGCCGCTGACTGCGCAGAAAACTGTGAAACAGGGCTATCCCTCGCCCGACGGCATCCTGCCCGCCGACACTACGTTTACGATCGGCAATGTACCCATCCGCACTTATTTTCCGGGTGAAGGCCATACGGTCGACAACATCGTGGTGTGGCTCCCGAGCGAGCGCATTCTGCACGGCGGCTGCTTCGTCAAGAGTGTGGCGGCCTTCGGGATGGGCTACGTCGGCGAGTCGAACCTGACCGCCTGGAGTGGCTCGATCCGGAACGTAAAAAAGCGTTTCGGCAACGCCCGCATCGTCGTGCCCGGCCACGAAGAATGGACTGGCCCGCAGGCGCTCGACCACACGTTGCGCCTATTGGAAAAATACAACGCCAATCGTCATTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3006887","ARO_id":"45349","ARO_name":"FIA-1","CARD_short_name":"FIA-1","ARO_description":"FIA-1 is a FIA beta-lactamase.","ARO_category":{"43872":{"category_aro_accession":"3005412","category_aro_cvterm_id":"43872","category_aro_name":"FIA beta-lactamase","category_aro_description":"FIA beta-lactamases are class B1 beta-lactamases found in Fibrella aestuarina.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4602":{"model_id":"4602","model_name":"FOX-12","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6977":{"protein_sequence":{"accession":"WP_063860495.1","sequence":"MQQRRAFALLTLGSLLLAPCTYARGEAPLTAAVDGIIQPMLKEYRIPGMAVAVLKDGKAHYFNYGVANRESGQRVSEQTLFEIGSVSKTLTATLGAYAAVKGGFELDDKVSQHAPWLKGSAFDGVTMAELATYSAGGLPLQFPDEVDSNDKMRTYYRHWSPVYPAGTHRQYSNPSIGLFGHLAANSLGQPFEQLMSQTLLPKLGLHHTYIQVPESAIANYAYGYSKEDKPVRVTPGVLAAEAYGIKTGSADLLKFTEANMGYQGDAALKSAIALTHTGFYSVGDMTQGLGWESYAYPLTEQALLAGNSSFQANPVTRFAVPKAMGEQRLYNKTGSTGGFGAYVAFVPARGIAIVMLANRNYPIEARVKAAHAILSQLAE"},"dna_sequence":{"accession":"NG_049100.1","fmin":"0","fmax":"1140","strand":"+","sequence":"ATGCAACAACGACGTGCGTTCGCGCTACTGACGCTGGGTAGCCTGCTGCTAGCCCCTTGTACTTATGCCCGCGGGGAGGCTCCGCTGACCGCCGCTGTGGACGGCATTATCCAGCCGATGCTCAAGGAGTATCGGATCCCGGGGATGGCGGTCGCCGTGCTGAAAGATGGCAAGGCCCACTATTTCAACTATGGGGTTGCCAACCGCGAGAGTGGTCAGCGCGTCAGCGAGCAGACCCTGTTCGAGATTGGCTCGGTCAGCAAGACCCTGACCGCGACCCTCGGTGCCTATGCTGCGGTCAAGGGGGGCTTTGAGCTGGATGACAAGGTGAGCCAGCACGCCCCCTGGCTCAAAGGTTCCGCCTTTGATGGTGTGACCATGGCCGAGCTTGCCACCTACAGTGCGGGTGGTTTGCCGCTGCAGTTCCCCGATGAGGTGGATTCGAATGACAAGATGCGCACTTACTATCGGCACTGGTCACCGGTTTATCCGGCGGGGACCCATCGCCAGTATTCCAACCCCAGCATAGGCCTGTTTGGTCACCTGGCCGCAAATAGTCTGGGCCAGCCATTTGAGCAACTGATGAGCCAGACCCTGCTGCCCAAGCTGGGTTTGCACCACACCTATATTCAGGTGCCGGAGTCGGCCATAGCGAACTATGCCTACGGCTATTCGAAGGAAGATAAGCCCGTCCGGGTCACTCCGGGCGTGCTGGCGGCCGAGGCTTACGGGATCAAGACCGGCTCGGCGGATCTGCTGAAGTTTACCGAGGCCAACATGGGGTATCAGGGAGATGCCGCGCTAAAAAGCGCGATCGCGCTGACCCATACCGGTTTCTACTCGGTGGGAGACATGACTCAGGGGCTGGGTTGGGAGAGCTACGCCTATCCGTTGACCGAGCAGGCGCTGCTGGCGGGCAACTCGAGCTTCCAGGCCAATCCGGTTACGCGCTTTGCGGTGCCCAAAGCGATGGGCGAGCAGCGGCTCTATAACAAGACGGGCTCGACTGGCGGCTTTGGCGCCTATGTGGCGTTCGTGCCCGCCAGAGGGATCGCCATCGTCATGCTGGCCAATCGCAACTATCCCATCGAGGCCAGGGTGAAGGCGGCTCACGCCATCCTGAGTCAGTTGGCCGAGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36936","NCBI_taxonomy_name":"Aeromonas caviae","NCBI_taxonomy_id":"648"}}}},"ARO_accession":"3002165","ARO_id":"38565","ARO_name":"FOX-12","CARD_short_name":"FOX-12","ARO_description":"FOX-12 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36206":{"category_aro_accession":"3000067","category_aro_cvterm_id":"36206","category_aro_name":"FOX beta-lactamase","category_aro_description":"FOX beta-lactamases are plasmid-encoded AmpC-type beta-lactamase which conferred resistance to broad-spectrum cephalosporins and cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4603":{"model_id":"4603","model_name":"FOX-13","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6978":{"protein_sequence":{"accession":"WP_063860496.1","sequence":"MQQRRAFALLTLGSLLLAPCTYAGGEAPLTAAVDGIIQPMLKEYRIPGMAVAVLKDGKAHYFNYGVANRESGQRVNEQTLFEIGSVSKTLTATLGAYAAVKGGFELDDKVSQHGPWLKGSALDGVTMAELATYSAGGLPLQFPDEVDSNDKMRTYYQSWSPVYPAGTHRQYSNPSIGLFGHLAANSLGQPFEQLMSQTLLPKLGLHHTYIQVPESAMVNYAYGYSKEDKPVRVTPGVLAAEAYGIKTGSADLLKFVEANMGYQGDAAVKSAIALTHTGFYSVGEMTQGLGWESYAYPVTEQTLLAGNSPAVSFQANPVTRFAVPKAMGEQRLYNKTGSTGGFGAYVAFVPARGIAIVMLANRNYPIEARVKAAHAILSQLNE"},"dna_sequence":{"accession":"NG_049101.1","fmin":"0","fmax":"1149","strand":"+","sequence":"ATGCAACAACGACGTGCGTTCGCGCTACTGACGCTGGGTAGCCTGCTGCTAGCCCCTTGTACTTATGCCGGCGGGGAGGCTCCGCTGACCGCCGCTGTGGACGGCATTATCCAGCCGATGCTCAAGGAGTATCGGATCCCGGGGATGGCGGTCGCCGTGCTGAAAGATGGCAAGGCCCACTATTTCAACTATGGGGTTGCCAACCGCGAGAGCGGCCAGCGGGTCAATGAGCAGACCCTGTTCGAGATTGGCTCGGTCAGCAAGACCCTGACAGCGACCCTCGGAGCCTATGCCGCGGTCAAGGGGGGCTTTGAGCTGGATGACAAGGTGAGCCAGCACGGCCCTTGGCTCAAAGGTTCCGCCTTGGATGGTGTGACCATGGCCGAGCTTGCCACCTACAGTGCGGGTGGTTTGCCGCTGCAGTTCCCCGATGAGGTAGATTCGAATGACAAGATGCGCACTTACTATCAGAGCTGGTCACCGGTTTATCCGGCAGGGACCCATCGCCAGTATTCCAACCCCAGCATAGGCCTGTTTGGTCACCTGGCCGCAAATAGTCTGGGCCAGCCATTTGAGCAACTGATGAGCCAGACCCTGCTGCCCAAGCTGGGTTTGCACCACACCTATATCCAGGTGCCGGAGTCGGCCATGGTGAACTATGCCTACGGCTATTCGAAGGAAGATAAGCCCGTCCGGGTCACTCCGGGTGTGCTGGCGGCCGAGGCTTACGGGATCAAGACCGGCTCGGCGGATCTGCTGAAGTTTGTCGAGGCCAACATGGGGTATCAGGGAGATGCCGCGGTAAAAAGCGCAATCGCGCTGACCCACACCGGTTTCTACTCGGTGGGAGAAATGACCCAGGGATTAGGATGGGAGAGTTATGCCTATCCGGTGACCGAGCAGACATTGCTGGCGGGCAATTCACCAGCGGTGAGCTTCCAGGCCAATCCGGTTACGCGCTTTGCGGTGCCCAAAGCGATGGGCGAGCAGCGGCTCTATAACAAGACGGGCTCGACTGGCGGCTTTGGCGCCTATGTGGCGTTCGTGCCCGCCAGAGGGATAGCCATCGTCATGCTGGCCAATCGCAACTATCCCATCGAGGCCAGGGTGAAGGCGGCTCACGCCATCCTGAGTCAGTTGAACGAGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36944","NCBI_taxonomy_name":"Providencia rettgeri","NCBI_taxonomy_id":"587"}}}},"ARO_accession":"3006471","ARO_id":"44933","ARO_name":"FOX-13","CARD_short_name":"FOX-13","ARO_description":"FOX-13 is a FOX beta-lactamase.","ARO_category":{"36206":{"category_aro_accession":"3000067","category_aro_cvterm_id":"36206","category_aro_name":"FOX beta-lactamase","category_aro_description":"FOX beta-lactamases are plasmid-encoded AmpC-type beta-lactamase which conferred resistance to broad-spectrum cephalosporins and cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4604":{"model_id":"4604","model_name":"FOX-14","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6979":{"protein_sequence":{"accession":"WP_064511492.1","sequence":"MQQRRAFALLTLGSLLLAPCTYAGGEAPLTAAVDGIIQPMLKEYRIPGMAVAVLKDGKAHYFNYGVANRESGQRVNEQTLFEIGSVSKTLTATLGAYAAVKGGFELDDKVSQHGPWLKGSALDGVTMAELATYSAGGLPLQFPDEVDSNDKMRTYYQSWSPVYPAGTHRQYSNPSIGLFGHLAANSLGQPFEQLMSQTLLPKLGLHHTYIQVPESAMVNYAYGYSKEDKPVRVTPGVLAAEAYGIKTGSADLLKFVEANMGYQGDAAVKSAIALTHTGFYSVGEMTQGLGWESYAYPVTEQTLLAGNSPAVSFQANPVTRFAVPKAMGEQRLYNKTGSTGGFGAYVAFVPARGIAIVMLANRNYPIEARVKAAHAILSQLAE"},"dna_sequence":{"accession":"NG_050814.1","fmin":"0","fmax":"1149","strand":"+","sequence":"ATGCAACAACGACGTGCGTTCGCGCTACTGACGCTGGGTAGCCTGCTGCTAGCCCCTTGTACTTATGCCGGCGGGGAGGCTCCGCTGACCGCCGCTGTGGACGGCATTATCCAGCCGATGCTCAAGGAGTATCGGATCCCGGGGATGGCGGTCGCCGTGCTGAAAGATGGCAAGGCCCACTATTTCAACTATGGGGTTGCCAACCGCGAGAGCGGCCAGCGGGTCAATGAGCAGACCCTGTTCGAGATTGGCTCGGTCAGCAAGACCCTGACAGCGACCCTCGGAGCCTATGCCGCGGTCAAGGGGGGCTTTGAGCTGGATGACAAGGTGAGCCAGCACGGCCCTTGGCTCAAAGGTTCCGCCTTGGATGGTGTGACCATGGCCGAGCTTGCCACCTACAGTGCGGGTGGTTTGCCGCTGCAGTTCCCCGATGAGGTAGATTCGAATGACAAGATGCGCACTTACTATCAGAGCTGGTCACCGGTTTATCCGGCAGGGACCCATCGCCAGTATTCCAACCCCAGCATAGGCCTGTTTGGTCACCTGGCCGCAAATAGTCTGGGCCAGCCATTTGAGCAACTGATGAGCCAGACCCTGCTGCCCAAGCTGGGTTTGCACCACACCTATATCCAGGTGCCGGAGTCGGCCATGGTGAACTATGCCTACGGCTATTCGAAGGAAGATAAGCCCGTCCGGGTCACTCCGGGTGTGCTGGCGGCCGAGGCTTACGGGATCAAGACCGGCTCGGCGGATCTGCTGAAGTTTGTCGAGGCCAACATGGGGTATCAGGGAGATGCCGCGGTAAAAAGCGCAATCGCGCTGACCCACACCGGTTTCTACTCGGTGGGAGAAATGACCCAGGGATTAGGATGGGAGAGTTATGCCTATCCGGTGACCGAGCAGACATTGCTGGCGGGCAATTCACCAGCGGTGAGCTTCCAGGCCAATCCGGTTACGCGCTTTGCGGTGCCCAAAGCGATGGGCGAGCAGCGGCTCTATAACAAGACGGGCTCGACTGGCGGCTTTGGCGCCTATGTGGCGTTCGTGCCCGCCAGAGGGATAGCCATCGTCATGCTGGCCAATCGCAACTATCCCATCGAGGCCAGGGTGAAGGCGGCTCACGCCATCCTGAGTCAGTTGGCCGAGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006472","ARO_id":"44934","ARO_name":"FOX-14","CARD_short_name":"FOX-14","ARO_description":"FOX-14 is a FOX beta-lactamase.","ARO_category":{"36206":{"category_aro_accession":"3000067","category_aro_cvterm_id":"36206","category_aro_name":"FOX beta-lactamase","category_aro_description":"FOX beta-lactamases are plasmid-encoded AmpC-type beta-lactamase which conferred resistance to broad-spectrum cephalosporins and cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4605":{"model_id":"4605","model_name":"FOX-15","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6980":{"protein_sequence":{"accession":"WP_096807445.1","sequence":"MQQRRALALLTLGSLLLTPCTYARGEAPLTATVDGAIQPMLKEYRIPGMAVAVLKDGKAHYFNYGVANRESGQHVSEQTLFEIGSVSKTLTATLGAYAAVKGGFELDDKVSQHAPWLKGSAFDGVTMAELATYSAGGLPLQFPDEVDLNDKMQTYYRSWSPVYPAGTHRQYSNPSIGLFGHLAANSLGQPFEQLMSQTLLPKLGLHHTYIQVPESAMANYAYGYSKEDKPIRVTPGVLAAEAYGIKTGSADLLKFTEANMGYQGDATVKSAIALTHTGFYSVGEMTQGLGWESYAYPVTEQALLAGNSPAVSFQANPVTRFAVPKAMGEQRLYNKTGSTGGFGAYVAFVPARGIAIVMLANRNYPIEARVKAAHAILSQLAE"},"dna_sequence":{"accession":"NG_059334.1","fmin":"0","fmax":"1149","strand":"+","sequence":"ATGCAACAACGACGTGCGCTCGCGCTACTGACGCTGGGTAGCCTGCTGCTAACCCCTTGTACTTATGCCCGTGGGGAGGCCCCGCTGACCGCCACTGTGGATGGCGCCATCCAGCCGATGCTCAAGGAGTATCGGATCCCGGGGATGGCGGTCGCCGTACTGAAAGATGGCAAGGCCCACTATTTCAACTATGGGGTGGCCAACCGCGAGAGTGGTCAGCACGTCAGCGAGCAGACTCTGTTCGAGATTGGCTCGGTCAGCAAGACCCTGACCGCGACCCTTGGCGCCTATGCCGCAGTCAAGGGGGGCTTTGAGCTGGATGACAAGGTGAGCCAGCACGCCCCCTGGCTCAAAGGTTCCGCCTTTGATGGTGTGACCATGGCCGAGCTTGCCACCTACAGTGCGGGTGGTTTGCCGCTGCAGTTCCCCGATGAGGTAGATTTGAATGACAAGATGCAAACTTACTATCGGAGCTGGTCACCGGTTTATCCGGCGGGGACTCATCGCCAGTATTCCAACCCCAGCATAGGCCTGTTTGGTCACCTGGCCGCAAATAGTCTGGGCCAGCCATTTGAGCAACTGATGAGCCAGACCCTGCTGCCCAAACTGGGTTTGCACCACACCTATATCCAGGTGCCGGAGTCGGCCATGGCGAACTATGCCTACGGCTATTCGAAGGAAGATAAGCCTATCCGGGTCACTCCGGGCGTGCTGGCTGCCGAGGCTTACGGGATCAAGACCGGCTCGGCGGATCTGCTGAAGTTTACCGAGGCCAACATGGGGTATCAGGGAGATGCCACGGTAAAAAGCGCGATCGCGCTGACCCACACCGGTTTCTACTCGGTGGGAGAAATGACCCAAGGACTGGGCTGGGAGAGCTACGCCTATCCGGTGACCGAGCAGGCGTTGCTGGCGGGCAACTCCCCGGCGGTGAGCTTCCAGGCCAATCCGGTTACGCGCTTTGCGGTGCCCAAAGCGATGGGTGAGCAGCGGCTCTATAACAAAACGGGCTCGACCGGCGGCTTTGGCGCCTATGTGGCGTTCGTGCCCGCCAGAGGGATCGCCATCGTCATGCTGGCCAATCGCAACTATCCCATCGAGGCCAGGGTGAAGGCAGCTCACGCCATCCTGAGTCAGTTGGCCGAGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3006473","ARO_id":"44935","ARO_name":"FOX-15","CARD_short_name":"FOX-15","ARO_description":"FOX-15 is a FOX beta-lactamase.","ARO_category":{"36206":{"category_aro_accession":"3000067","category_aro_cvterm_id":"36206","category_aro_name":"FOX beta-lactamase","category_aro_description":"FOX beta-lactamases are plasmid-encoded AmpC-type beta-lactamase which conferred resistance to broad-spectrum cephalosporins and cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4606":{"model_id":"4606","model_name":"FOX-16","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6981":{"protein_sequence":{"accession":"WP_109545066.1","sequence":"MQQRCAFALLTLVSLLLAPCTYASGEAPLTATVDGIIQPMLKEYRIPGMAVAVLKDGKAHYFNYGVANRESGQRVSEQTLFEIGSVSKTLTATLGAYAAVKGGFVLDDNVSQHAPWLKGSALDGVTMAELATYSAGGLPLQFPDEVDSNDKMRTYYRSWSPVYPAGTHRQYSNPSIGLFGHLAANSLGQPFEQLMSQTLLPKLGLHHTYIQVPESAIANYAYGYSKEDKPVRVTPGVLAAEAYGIKTGSADLLKFAEANMGYQGDAAVKSAIALTHTGFYSVGDMTQGLGWESYAYPVTEQTLLAGNSPAVSFQANPVTRFAVPKAMGEQRLYNKTGSTGGFGAYVAFVPARGIAIVMLANRNYPIEARVKAAHAILSQLAE"},"dna_sequence":{"accession":"NG_057480.1","fmin":"0","fmax":"1149","strand":"+","sequence":"ATGCAACAAAGATGTGCGTTCGCGCTACTGACGCTGGTTAGCCTGCTGCTAGCCCCTTGTACTTATGCCAGCGGGGAGGCCCCGCTGACCGCCACTGTGGACGGCATTATCCAGCCGATGCTCAAGGAGTATCGGATCCCGGGGATGGCGGTCGCCGTACTGAAAGATGGCAAGGCCCACTATTTCAACTATGGGGTTGCCAACCGCGAGAGTGGCCAGCGCGTCAGCGAGCAGACCCTGTTCGAGATTGGCTCGGTCAGCAAGACCCTGACCGCGACCCTCGGTGCCTATGCCGCGGTCAAGGGGGGCTTTGTGCTGGATGACAATGTGAGCCAGCACGCCCCTTGGCTCAAAGGTTCCGCCTTGGATGGTGTGACCATGGCCGAGCTTGCCACCTACAGTGCGGGTGGTTTGCCGCTGCAGTTCCCCGATGAGGTAGATTCGAATGACAAGATGCGCACTTACTATCGGAGCTGGTCACCGGTTTATCCGGCGGGGACCCATCGCCAGTATTCCAACCCCAGCATAGGCCTGTTTGGTCACCTGGCCGCAAATAGTCTGGGCCAGCCATTTGAGCAACTGATGAGCCAGACCCTGCTGCCCAAGCTGGGTTTGCACCACACCTATATTCAGGTGCCGGAGTCGGCCATAGCGAACTATGCCTACGGCTATTCGAAGGAAGATAAGCCCGTCCGGGTCACTCCGGGCGTGCTGGCGGCCGAGGCTTACGGGATCAAGACCGGCTCGGCGGATCTGCTGAAGTTTGCCGAGGCAAACATGGGGTATCAGGGAGATGCCGCGGTAAAAAGCGCGATCGCGCTGACCCACACCGGTTTCTACTCGGTGGGAGACATGACTCAGGGACTGGGCTGGGAGAGTTACGCCTATCCGGTGACCGAGCAGACATTGCTGGCGGGCAATTCACCAGCGGTGAGCTTCCAGGCCAATCCGGTTACGCGCTTTGCGGTGCCCAAAGCGATGGGCGAGCAGCGGCTCTATAACAAGACGGGCTCGACTGGCGGCTTTGGCGCCTATGTGGCGTTCGTGCCCGCCAGAGGGATCGCCATCGTCATGCTGGCCAATCGCAACTATCCCATCGAGGCTAGGGTGAAGGCGGCTCACGCCATCCTGAGTCAGTTGGCCGAGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3006474","ARO_id":"44936","ARO_name":"FOX-16","CARD_short_name":"FOX-16","ARO_description":"FOX-16 is a FOX beta-lactamase.","ARO_category":{"36206":{"category_aro_accession":"3000067","category_aro_cvterm_id":"36206","category_aro_name":"FOX beta-lactamase","category_aro_description":"FOX beta-lactamases are plasmid-encoded AmpC-type beta-lactamase which conferred resistance to broad-spectrum cephalosporins and cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4607":{"model_id":"4607","model_name":"FOX-17","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"6982":{"protein_sequence":{"accession":"WP_168247879.1","sequence":"MQQRRAFALLTLGSLLLAPCTYASGEAPLTATVDGIIQPMLKEYRIPGIAVAVLKDGKAHYFNYGVANRESGQRVSEQTLFEIGSVSKTLTATLGAYAAVKGGFVLDDKVSQHAPWLKGSALDGVTMAELATYSAGGLPLQFPDKVDSNDKMQTYYRSWSPVYPAGTHRQYSNPSIGLFGHLAANSLGQPFEQLMSQTLLPKLGLHHTYIQVPESAMANYAYGYSKEDKPIRVTPGVLAAEAYGIKTSSADLLKFAEANMGYQGDALVKSAIALTHTGFYSVGEMTQGLGWESYDYPVTEQVLLAGNSPAVSFQANPVTRFAVPKAMGEQRLYNKTGSTGGFGAYVAFVPARGIAIVMLANRNYPIEARVKAAHAILSQLAE"},"dna_sequence":{"accession":"NG_068170.1","fmin":"0","fmax":"1149","strand":"+","sequence":"ATGCAACAACGACGTGCGTTCGCGCTACTGACGCTGGGTAGCCTGCTGCTAGCCCCTTGTACTTATGCCAGCGGGGAGGCCCCGCTGACCGCCACTGTGGACGGCATTATCCAGCCGATGCTCAAGGAGTATCGGATCCCGGGGATAGCGGTCGCCGTACTGAAAGATGGCAAGGCCCACTATTTCAACTATGGGGTTGCCAACCGCGAGAGTGGCCAGCGCGTCAGCGAGCAGACCCTGTTCGAGATTGGCTCGGTCAGCAAGACCCTGACCGCGACCCTCGGTGCCTATGCTGCGGTCAAGGGGGGCTTTGTGCTGGATGACAAGGTGAGCCAGCACGCCCCCTGGCTCAAAGGTTCCGCCTTGGATGGTGTGACCATGGCCGAGCTTGCCACCTACAGTGCGGGTGGTTTGCCGCTGCAGTTCCCCGATAAGGTGGATTCGAATGACAAGATGCAAACTTACTATCGGAGCTGGTCACCGGTTTATCCGGCAGGGACTCATCGCCAGTATTCCAACCCCAGCATAGGCCTGTTTGGTCACCTGGCCGCAAATAGTCTGGGCCAGCCATTTGAGCAACTGATGAGCCAGACCCTGCTGCCCAAGCTGGGTTTGCACCACACCTATATCCAGGTGCCGGAGTCGGCCATGGCGAACTATGCCTACGGCTATTCGAAGGAAGATAAGCCCATCCGGGTCACTCCGGGCGTGCTGGCGGCCGAGGCTTACGGGATCAAGACCAGCTCGGCGGATCTGCTGAAGTTTGCCGAGGCAAACATGGGGTATCAGGGAGATGCCCTGGTAAAAAGCGCAATCGCGCTGACCCACACCGGTTTCTACTCGGTGGGGGAAATGACCCAGGGGCTGGGCTGGGAGAGTTACGACTATCCCGTCACCGAGCAGGTGCTGCTGGCGGGCAACTCCCCGGCGGTGAGCTTCCAGGCCAATCCGGTTACGCGCTTTGCGGTGCCCAAAGCGATGGGCGAGCAGCGGCTCTATAACAAGACGGGCTCGACTGGCGGCTTTGGCGCCTATGTGGCGTTCGTGCCCGCCAGAGGGATCGCCATCGTCATGCTGGCCAATCGCAACTATCCCATCGAGGCCAGGGTGAAGGCGGCTCACGCCATCCTGAGTCAGTTGGCCGAGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36946","NCBI_taxonomy_name":"Providencia stuartii","NCBI_taxonomy_id":"588"}}}},"ARO_accession":"3006475","ARO_id":"44937","ARO_name":"FOX-17","CARD_short_name":"FOX-17","ARO_description":"FOX-17 is a FOX beta-lactamase.","ARO_category":{"36206":{"category_aro_accession":"3000067","category_aro_cvterm_id":"36206","category_aro_name":"FOX beta-lactamase","category_aro_description":"FOX beta-lactamases are plasmid-encoded AmpC-type beta-lactamase which conferred resistance to broad-spectrum cephalosporins and cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4608":{"model_id":"4608","model_name":"FRI-10","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"6983":{"protein_sequence":{"accession":"WP_204376226.1","sequence":"MFFFKKSASTFIFFLCLPLNSFASQESNSIEQMRELEASFGGRIGVYILNTKNGKEFSYRQDERFPLCSSFKAFLAASVLKKTQEKSVSLDDMMEYSGRVMEKHSPVSEKYRKTGASVRTLAKAAIQYSDNGASNLLMERYIGGPEGLTAFMRSTGDTDFRLDRWELELNSAIPSDERDTSTPKAVAMSLKNIAFGSVLDAKNKLLLQEWLKGNTTGNARIRAAVPDKWDVGDKTGTCGFYGTANDVAILWPDANSPAVMAVYTTRPNQNDKHDEAVIKNAAKIAINAVYGSYK"},"dna_sequence":{"accession":"NG_073462.1","fmin":"0","fmax":"885","strand":"+","sequence":"ATGTTTTTTTTTAAAAAAAGTGCAAGTACATTTATTTTTTTCCTCTGTCTTCCATTGAACTCATTCGCCTCTCAGGAAAGTAATAGTATTGAGCAAATGAGGGAATTGGAAGCTTCTTTTGGGGGGCGGATAGGTGTTTATATTTTAAACACAAAAAATGGGAAAGAATTTTCCTACAGACAAGATGAGAGATTTCCTTTATGTAGTTCATTTAAGGCATTCCTCGCTGCATCCGTATTAAAAAAAACTCAGGAGAAATCTGTTTCTCTTGATGATATGATGGAATATTCTGGACGTGTTATGGAAAAGCATTCTCCTGTGTCAGAAAAATACCGCAAAACAGGAGCAAGCGTGCGGACTTTGGCGAAGGCAGCAATTCAGTACAGTGACAATGGAGCTTCTAATCTATTAATGGAAAGATACATAGGAGGTCCTGAGGGTTTGACTGCATTTATGCGGTCAACGGGAGACACTGACTTCAGGCTTGATCGTTGGGAATTAGAATTAAACTCAGCTATTCCAAGCGATGAACGAGATACTTCAACTCCAAAAGCAGTGGCAATGAGCCTTAAAAATATTGCTTTTGGTTCAGTACTCGATGCTAAAAATAAATTATTGCTGCAGGAATGGCTTAAAGGCAACACTACTGGTAATGCGCGAATTAGAGCTGCGGTTCCAGATAAGTGGGATGTTGGCGATAAAACAGGCACCTGTGGTTTTTATGGTACAGCCAATGATGTTGCTATTTTATGGCCAGACGCTAATTCACCTGCAGTTATGGCTGTCTACACAACACGTCCTAATCAAAACGACAAACATGACGAAGCAGTAATTAAAAATGCTGCAAAAATAGCTATAAATGCAGTGTATGGAAGTTATAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3006227","ARO_id":"44689","ARO_name":"FRI-10","CARD_short_name":"FRI-10","ARO_description":"FRI-10 is a FRI beta-lactamase.","ARO_category":{"42915":{"category_aro_accession":"3004796","category_aro_cvterm_id":"42915","category_aro_name":"FRI beta-lactamase","category_aro_description":"FRI is a carbapenem-Hydrolyzing Class A beta-Lactamase from Enterobacter cloacae.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4609":{"model_id":"4609","model_name":"GES-25","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"6984":{"protein_sequence":{"accession":"WP_063860510.1","sequence":"MRFIHALLLAGIAHSAHASEKLTFKTDLERLEREKAAQIGVAIVDPQGEIVAGHRMAQRFAMCSTFKFPLAALVFERIDSGTERGDRKLSYGPDMIVEWSPATERFLASGHMTVLEAAQAAVQLSDNGATNLLLREIGGPAAMTQYFRKIGDSVSRLDRKEPEMSDNTPGDLRDTTTPIAMARTVAKVLYGGALTSTSTHTIERWLIGNQTGDATLRAGFPKDWVVGEKTGTCANGGRNDIGFFKAQERDYAVAVYTTAPKLSAVERDELVASVGQVITQLILSTDK"},"dna_sequence":{"accession":"NG_049128.1","fmin":"0","fmax":"864","strand":"+","sequence":"ATGCGCTTCATTCACGCACTATTACTGGCAGGGATCGCTCACTCTGCACATGCGTCGGAAAAATTAACCTTCAAGACCGATCTTGAGAGGCTAGAGCGCGAAAAAGCAGCTCAGATCGGTGTTGCGATCGTCGATCCCCAAGGAGAGATCGTCGCGGGCCACCGAATGGCGCAGCGTTTTGCAATGTGCTCAACGTTCAAGTTTCCGCTAGCCGCGCTGGTCTTTGAAAGAATTGACTCAGGCACCGAGCGGGGGGATCGAAAACTTTCATATGGGCCGGACATGATCGTCGAATGGTCTCCTGCCACGGAGCGGTTTCTAGCATCGGGACACATGACGGTTCTCGAGGCAGCGCAAGCTGCGGTGCAGCTTAGCGACAATGGGGCTACTAACCTCTTACTGAGAGAAATTGGCGGACCTGCTGCAATGACGCAGTATTTTCGTAAAATTGGCGACTCTGTGAGTCGGCTAGACCGGAAAGAGCCGGAGATGAGCGACAACACACCTGGCGACCTCAGAGATACAACTACGCCTATTGCTATGGCACGTACTGTGGCAAAAGTCCTCTATGGCGGCGCACTGACGTCCACCTCGACCCACACCATTGAGAGGTGGCTGATCGGAAACCAAACGGGAGACGCGACACTACGAGCGGGTTTTCCTAAAGATTGGGTTGTTGGAGAGAAAACTGGTACCTGCGCCAACGGGGGCCGGAACGACATTGGTTTTTTTAAAGCCCAGGAGAGAGATTACGCTGTAGCGGTGTATACAACGGCCCCGAAACTATCGGCCGTAGAACGTGACGAATTAGTTGCCTCTGTCGGTCAAGTTATTACACAACTCATCCTGAGCACGGACAAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3003185","ARO_id":"39762","ARO_name":"GES-25","CARD_short_name":"GES-25","ARO_description":"GES-25 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36205":{"category_aro_accession":"3000066","category_aro_cvterm_id":"36205","category_aro_name":"GES beta-lactamase","category_aro_description":"GES beta-lactamases or Guiana extended-spectrum beta-lactamases are related to the other plasmid-located class A beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4610":{"model_id":"4610","model_name":"GES-27","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"6985":{"protein_sequence":{"accession":"WP_063860512.1","sequence":"MRFIHALLLAGIAHSAYASEKLTFKTDLEKLEREKAAQIGVAIVDPQGEIVAGHRMAQRFAMCSTFKFPLAALVFERIDSGTERGDRKLSYGPDMIVEWSPATERFLASGHMTVLEAAQAAVQLSDNGATNLLLREIGGPAAMTQYFRKIGDSVSRLDRKEQEMSDNTPGDLRDTTTPIAMARTVAKVLYGGALTSTSTHTIERWLIGNQTGDATLRAGFPKDWVVGEKTGTCANGGRNDIGFFKAQERDYAVAVYTTAPKLSAVERDELVASVGQVITQLILSTDK"},"dna_sequence":{"accession":"NG_049130.1","fmin":"0","fmax":"864","strand":"+","sequence":"ATGCGCTTCATTCACGCACTATTACTGGCAGGGATCGCTCACTCTGCATATGCGTCGGAAAAATTAACCTTCAAGACCGATCTTGAGAAGCTAGAGCGCGAAAAAGCAGCTCAGATCGGTGTTGCGATCGTCGATCCCCAAGGAGAGATCGTCGCGGGCCACCGAATGGCGCAGCGTTTTGCAATGTGCTCAACGTTCAAGTTTCCGCTAGCCGCGCTGGTCTTTGAAAGAATTGACTCAGGCACCGAGCGGGGGGATCGAAAACTTTCATATGGGCCGGACATGATCGTCGAATGGTCTCCTGCCACGGAGCGGTTTCTAGCATCGGGACACATGACGGTTCTCGAGGCAGCGCAAGCTGCGGTGCAGCTTAGCGACAATGGGGCTACTAACCTCTTACTGAGAGAAATTGGCGGACCTGCTGCAATGACGCAGTATTTTCGTAAAATTGGCGACTCTGTGAGTCGGCTAGACCGGAAAGAGCAGGAGATGAGCGACAACACACCTGGCGACCTCAGAGATACAACTACGCCTATTGCTATGGCACGTACTGTGGCTAAAGTCCTCTATGGCGGCGCACTGACGTCCACCTCGACCCACACCATTGAGAGGTGGCTGATCGGAAACCAAACGGGAGACGCGACACTACGAGCGGGTTTTCCTAAAGATTGGGTTGTTGGAGAGAAAACTGGTACCTGCGCCAACGGGGGCCGGAACGACATTGGTTTTTTTAAAGCCCAGGAGAGAGATTACGCTGTAGCGGTGTATACAACGGCCCCGAAACTATCGGCCGTAGAACGTGACGAATTAGTTGCCTCTGTCGGTCAAGTTATTACACAACTCATCCTGAGCACGGACAAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006156","ARO_id":"44618","ARO_name":"GES-27","CARD_short_name":"GES-27","ARO_description":"GES-27 is a GES beta-lactamase.","ARO_category":{"36205":{"category_aro_accession":"3000066","category_aro_cvterm_id":"36205","category_aro_name":"GES beta-lactamase","category_aro_description":"GES beta-lactamases or Guiana extended-spectrum beta-lactamases are related to the other plasmid-located class A beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4611":{"model_id":"4611","model_name":"GES-28","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"6986":{"protein_sequence":{"accession":"WP_063860513.1","sequence":"MRFIHALLLAGIAHSAYASEKLTFKTDLEKLEREKAAQIGVAIVDPQGEIVAGHRMAQRFAMCSTFKFPLAALVFERIDSGTERGDRKLSYGPDMIVEWSPATERFLASGHMTVLEAAQAAVQLSDNGATNLLLREIGGPAAMTQYFRKIGDSVSRLDRKEPEMSDNTPGDLRNTTTPIAMARTVAKVLYGGALTSTSTHTIERWLIGNQTGDATLRAGFPKDWVVGEKTGTCANGGRNDIGFFKAQERDYAVAVYTTAPKLSAVERDELVASVGQVITQLILSTDK"},"dna_sequence":{"accession":"NG_049131.1","fmin":"0","fmax":"864","strand":"+","sequence":"ATGCGCTTCATTCACGCACTATTACTGGCAGGGATCGCTCACTCTGCATATGCGTCGGAAAAATTAACCTTCAAGACCGATCTTGAGAAGCTAGAGCGCGAAAAAGCAGCTCAGATCGGTGTTGCGATCGTCGATCCCCAAGGAGAGATCGTCGCGGGCCACCGAATGGCGCAGCGTTTTGCAATGTGCTCAACGTTCAAGTTTCCGCTAGCCGCGCTGGTCTTTGAAAGAATTGACTCAGGCACCGAGCGGGGGGATCGAAAACTTTCATATGGGCCGGACATGATCGTCGAATGGTCTCCTGCCACGGAGCGGTTTCTAGCATCGGGACACATGACGGTTCTCGAGGCAGCGCAAGCTGCGGTGCAGCTTAGCGACAATGGGGCTACTAACCTCTTACTGAGAGAAATTGGCGGACCTGCTGCAATGACGCAGTATTTTCGTAAAATTGGCGACTCTGTGAGTCGGCTAGACCGGAAAGAGCCGGAGATGAGCGACAACACACCTGGCGACCTCAGAAATACAACTACGCCTATTGCTATGGCACGTACTGTGGCTAAAGTCCTCTATGGCGGCGCACTGACGTCCACCTCGACCCACACCATTGAGAGGTGGCTGATCGGAAACCAAACGGGAGACGCGACACTACGAGCGGGTTTTCCTAAAGATTGGGTTGTTGGAGAGAAAACTGGTACCTGCGCCAACGGGGGCCGGAACGACATTGGTTTTTTTAAAGCCCAGGAGAGAGATTACGCTGTAGCGGTGTATACAACGGCCCCGAAACTATCGGCCGTAGAACGTGACGAATTAGTTGCCTCTGTCGGTCAAGTTATTACACAACTCATCCTGAGCACGGACAAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006157","ARO_id":"44619","ARO_name":"GES-28","CARD_short_name":"GES-28","ARO_description":"GES-28 is a GES beta-lactamase.","ARO_category":{"36205":{"category_aro_accession":"3000066","category_aro_cvterm_id":"36205","category_aro_name":"GES beta-lactamase","category_aro_description":"GES beta-lactamases or Guiana extended-spectrum beta-lactamases are related to the other plasmid-located class A beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4612":{"model_id":"4612","model_name":"GES-29","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"6987":{"protein_sequence":{"accession":"WP_063860514.1","sequence":"MRFIHALLLAGIAHSAYASEKLTFKTDLEKLEREKAAQIGVAIVDPQGEIVAGHRMAQRFAMCSTFKFPLAALVFERIDSGTERGDRKLSYGPDMIVEWSPATERFLASGHMTVLEAAQAAVQLSDNGATNLLLREIGGPAAMTQYFRKIGDSVSRLDRKEAEMSDNTPGDLRDTTTPIAMARTVAKVLYGGALTSTSTHTIERWLIGNQTGDATLRAGFPKDWVVGEKTGTCANGGRNDIGFFKAQERDYAVAVYTTAPKLSAVERDELVASVGQVITQLILSTDK"},"dna_sequence":{"accession":"NG_049132.1","fmin":"0","fmax":"864","strand":"+","sequence":"ATGCGCTTCATTCACGCACTATTACTGGCAGGGATCGCTCACTCTGCATATGCGTCGGAAAAATTAACCTTCAAGACCGATCTTGAGAAGCTAGAGCGCGAAAAAGCAGCTCAGATCGGTGTTGCGATCGTCGATCCCCAAGGAGAGATCGTCGCGGGCCACCGAATGGCGCAGCGTTTTGCAATGTGCTCAACGTTCAAGTTTCCGCTAGCCGCGCTGGTCTTTGAAAGAATTGACTCAGGCACCGAGCGGGGGGATCGAAAACTTTCATATGGGCCGGACATGATCGTCGAATGGTCTCCTGCCACGGAGCGGTTTCTAGCATCGGGACACATGACGGTTCTCGAGGCAGCGCAAGCTGCGGTGCAGCTTAGCGACAATGGGGCTACTAACCTCTTACTGAGAGAAATTGGCGGACCTGCTGCAATGACGCAGTATTTTCGTAAAATTGGCGACTCTGTGAGTCGGCTAGACCGGAAAGAGGCGGAGATGAGCGACAACACACCTGGCGACCTCAGAGATACAACTACGCCTATTGCTATGGCACGTACTGTGGCTAAAGTCCTCTATGGCGGCGCACTGACGTCCACCTCGACCCACACCATTGAGAGGTGGCTGATCGGAAACCAAACGGGAGACGCGACACTACGAGCGGGTTTTCCTAAAGATTGGGTTGTTGGAGAGAAAACTGGTACCTGCGCCAACGGGGGCCGGAACGACATTGGTTTTTTTAAAGCCCAGGAGAGAGATTACGCTGTAGCGGTGTATACAACGGCCCCGAAACTATCGGCCGTAGAACGTGACGAATTAGTTGCCTCTGTCGGTCAAGTTATTACACAACTCATCCTGAGCACGGACAAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006158","ARO_id":"44620","ARO_name":"GES-29","CARD_short_name":"GES-29","ARO_description":"GES-29 is a GES beta-lactamase.","ARO_category":{"36205":{"category_aro_accession":"3000066","category_aro_cvterm_id":"36205","category_aro_name":"GES beta-lactamase","category_aro_description":"GES beta-lactamases or Guiana extended-spectrum beta-lactamases are related to the other plasmid-located class A beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4613":{"model_id":"4613","model_name":"GES-30","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"6988":{"protein_sequence":{"accession":"WP_063860516.1","sequence":"MRFIHALLLAGIAHSAYASEKLTFKTDLEKLECEKAAQIGVAIVDPQGEIVAGHRMAQRFAMCSTFKFPLAALVFERIDSGTERGDRKLSYGPDMIVEWSPATERFLASGHMTVLEAAQAAVQLSDNGATNLLLREIGGPAAMTQYFRKIGDSVSRLDRKEPEMSDNTPGDLRDTTTPIAMARTVAKVLYGGALTSTSTHTIERWLIGNQTGDATLRAGFPKDWVVGEKTGTCANGGRNDIGFFKAQERDYAVAVYTTAPKLSAVERDELVASVGQVITQLILSTDK"},"dna_sequence":{"accession":"NG_049134.1","fmin":"0","fmax":"864","strand":"+","sequence":"ATGCGCTTCATTCACGCACTATTACTGGCAGGGATCGCTCACTCTGCATATGCGTCGGAAAAATTAACCTTCAAGACCGATCTTGAGAAGCTAGAGTGCGAAAAAGCAGCTCAGATCGGTGTTGCGATCGTCGATCCCCAAGGAGAGATCGTCGCGGGCCACCGAATGGCGCAGCGTTTTGCAATGTGCTCAACGTTCAAGTTTCCGCTAGCCGCGCTGGTCTTTGAAAGAATTGACTCAGGCACCGAGCGGGGGGATCGAAAACTTTCATATGGGCCGGACATGATCGTCGAATGGTCTCCTGCCACGGAGCGGTTTCTAGCATCGGGACACATGACGGTTCTCGAGGCAGCGCAAGCTGCGGTGCAGCTTAGCGACAATGGGGCTACTAACCTCTTACTGAGAGAAATTGGCGGACCTGCTGCAATGACGCAGTATTTTCGTAAAATTGGCGACTCTGTGAGTCGGCTAGACCGGAAAGAGCCGGAGATGAGCGACAACACACCTGGCGACCTCAGAGATACAACTACGCCTATTGCTATGGCACGTACTGTGGCTAAAGTCCTCTATGGCGGCGCACTGACGTCCACCTCGACCCACACCATTGAGAGGTGGCTGATCGGAAACCAAACGGGAGACGCGACACTACGAGCGGGTTTTCCTAAAGATTGGGTTGTTGGAGAGAAAACTGGTACCTGCGCCAACGGGGGCCGGAACGACATTGGTTTTTTTAAAGCCCAGGAGAGAGATTACGCTGTAGCGGTGTATACAACGGCCCCGAAACTATCGGCCGTAGAACGTGACGAATTAGTTGCCTCTGTCGGTCAAGTTATTACACAACTCATCCTGAGCACGGACAAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006159","ARO_id":"44621","ARO_name":"GES-30","CARD_short_name":"GES-30","ARO_description":"GES-30 is a GES beta-lactamase.","ARO_category":{"36205":{"category_aro_accession":"3000066","category_aro_cvterm_id":"36205","category_aro_name":"GES beta-lactamase","category_aro_description":"GES beta-lactamases or Guiana extended-spectrum beta-lactamases are related to the other plasmid-located class A beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4614":{"model_id":"4614","model_name":"GES-31","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"6989":{"protein_sequence":{"accession":"WP_063860517.1","sequence":"MRFIHALLLAGIAHSAYASEKLTFKTDLEKLEREKAAEIGVAIVDPQGEIVAGHRMAQRFAMCSTFKFPLAALVFERIDSGTERGDRKLSYGPDMIVKWSPATERFLASGHMTVLEAAQAAVQLSDNGATNLLLREIGGPAAMTQYFRKIGDSVSRLDRKEPEMGDNTPGDLRDTTTPIAMARTVAKVLYGGALTSTSTHTIERWLIGNQTGDATLRAGFPKDWVVGEKTGTCANGGRNDIGFFKAQERDYAVAVYTTAPKLSAVERDELVASVGQVITQLILSTDK"},"dna_sequence":{"accession":"NG_049135.1","fmin":"0","fmax":"864","strand":"+","sequence":"ATGCGCTTCATTCACGCACTATTACTGGCAGGGATCGCTCACTCTGCATATGCGTCGGAAAAATTAACCTTCAAGACCGATCTTGAGAAGCTAGAGCGCGAAAAAGCAGCTGAGATCGGTGTTGCGATCGTCGATCCCCAAGGAGAGATCGTCGCGGGCCACCGAATGGCGCAGCGTTTTGCAATGTGCTCAACGTTCAAGTTTCCGCTAGCCGCGCTGGTCTTTGAAAGAATTGACTCAGGCACCGAGCGGGGGGATCGAAAACTTTCATATGGGCCGGACATGATCGTCAAATGGTCTCCTGCCACGGAGCGGTTTCTAGCATCGGGACACATGACGGTTCTCGAGGCAGCGCAAGCTGCGGTGCAGCTTAGCGACAATGGGGCTACTAACCTCTTACTGAGAGAAATTGGCGGACCTGCTGCAATGACGCAGTATTTTCGTAAAATTGGCGACTCTGTGAGTCGGCTAGACCGGAAAGAGCCGGAGATGGGCGACAACACACCTGGCGACCTCAGAGATACAACTACGCCTATTGCTATGGCACGTACTGTGGCTAAAGTCCTCTATGGCGGCGCACTGACGTCCACCTCGACCCACACCATTGAGAGGTGGCTGATCGGAAACCAAACGGGAGACGCGACGCTACGAGCGGGTTTTCCTAAAGATTGGGTTGTTGGAGAGAAAACTGGTACCTGCGCCAACGGGGGCCGGAACGACATTGGTTTTTTTAAAGCCCAGGAGAGAGATTACGCTGTAGCGGTGTATACAACGGCCCCGAAACTATCGGCCGTAGAACGTGACGAATTAGTTGCCTCTGTCGGTCAAGTTATTACACAACTCATCCTGAGCACGGACAAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36936","NCBI_taxonomy_name":"Aeromonas caviae","NCBI_taxonomy_id":"648"}}}},"ARO_accession":"3006160","ARO_id":"44622","ARO_name":"GES-31","CARD_short_name":"GES-31","ARO_description":"GES-31 is a GES beta-lactamase.","ARO_category":{"36205":{"category_aro_accession":"3000066","category_aro_cvterm_id":"36205","category_aro_name":"GES beta-lactamase","category_aro_description":"GES beta-lactamases or Guiana extended-spectrum beta-lactamases are related to the other plasmid-located class A beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4615":{"model_id":"4615","model_name":"GES-32","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"6990":{"protein_sequence":{"accession":"WP_069280709.1","sequence":"MRFIHALFLAGIAHSASASENLTFRTDLEKLEREKAAEIGVAIVDPQGQIVAGHRIEQRFAMCSTFKFPLAALVFERIDSGTERGDRKLSYGRDMIVKWSPAAERFLASGHMTVLEAAQAAVQLSDNGATNLLLREIGGPAAMTQYFRKIGDSVSRLDRKEPEMGDNTPGDLRDTTTPIAMARTVAKVLYGGALTPTSTHTIERWLIGNQTGDATLRAGFPKDWVIGEKTGTCANGGRNDIGFFKAQDRDYAVAVYTTAPKLSAEQRDELVASVGQVITQLILSTDK"},"dna_sequence":{"accession":"NG_051512.1","fmin":"0","fmax":"864","strand":"+","sequence":"ATGCGCTTCATTCACGCACTATTCCTGGCAGGGATCGCTCACTCTGCATCTGCGTCGGAAAACTTAACCTTCAGGACCGATCTTGAGAAGCTAGAGCGCGAGAAAGCAGCTGAGATCGGTGTTGCGATCGTCGATCCCCAAGGACAGATCGTCGCGGGCCACCGAATCGAGCAGCGTTTTGCAATGTGCTCTACGTTCAAGTTTCCGCTAGCCGCGCTGGTCTTTGAAAGAATTGACTCAGGCACCGAGCGGGGGGATCGAAAACTTTCGTACGGGCGGGACATGATCGTCAAATGGTCTCCTGCCGCGGAGCGGTTTCTCGCATCGGGACATATGACGGTTCTCGAGGCAGCGCAAGCGGCGGTGCAGCTCAGCGACAATGGGGCTACTAACCTCTTACTGAGAGAAATTGGCGGACCTGCTGCAATGACGCAGTATTTTCGTAAAATTGGCGACTCTGTGAGTCGGCTAGACCGGAAAGAGCCGGAGATGGGCGACAACACACCTGGCGACCTCAGAGATACAACCACGCCTATTGCTATGGCACGTACTGTGGCTAAAGTCCTCTATGGCGGCGCACTGACGCCCACCTCGACCCACACAATTGAGAGGTGGCTGATCGGAAACCAAACGGGAGACGCGACATTACGAGCGGGTTTTCCTAAAGATTGGGTTATTGGAGAGAAAACCGGCACCTGCGCCAACGGGGGCCGGAACGACATTGGGTTTTTTAAAGCCCAGGACAGAGATTACGCTGTAGCGGTGTATACAACGGCCCCGAAACTATCGGCCGAACAACGTGACGAATTAGTTGCCTCTGTCGGTCAAGTTATTACGCAACTCATCCTGAGCACGGACAAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006161","ARO_id":"44623","ARO_name":"GES-32","CARD_short_name":"GES-32","ARO_description":"GES-32 is a GES beta-lactamase.","ARO_category":{"36205":{"category_aro_accession":"3000066","category_aro_cvterm_id":"36205","category_aro_name":"GES beta-lactamase","category_aro_description":"GES beta-lactamases or Guiana extended-spectrum beta-lactamases are related to the other plasmid-located class A beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4616":{"model_id":"4616","model_name":"GES-33","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"6991":{"protein_sequence":{"accession":"WP_085562419.1","sequence":"MRFIHALLLAGIAHSAYASEKLTFKTDLEKLEREKAAQIGVAIVDPQGEIVAGHRMAQRFAMCSTFKFPLAALVFERIDSGTERGDRKLSYGPDMIVKWSPATERFLASGHMTVLEAAQAAVQLSDNGATNLLLREIGGPAAMTQYFRKIGDSVSRLDRKEPEMSDNTPGDLRDTTTPIAMARTVAKVLYGGALTSTSTHTIERWLIGNQTGDATLRAGFPKDWVVGEKTGACANGGRNDIGFFKAQERDYAVAVYTTAPKLSAVERDELVASVGQVITQLILSTDK"},"dna_sequence":{"accession":"NG_054709.1","fmin":"0","fmax":"864","strand":"+","sequence":"ATGCGCTTCATTCACGCACTATTACTGGCAGGGATCGCTCACTCTGCATATGCGTCGGAAAAATTAACCTTCAAGACCGATCTTGAGAAGCTAGAGCGCGAAAAAGCAGCTCAGATCGGTGTTGCGATCGTCGATCCCCAAGGAGAGATCGTCGCGGGCCACCGAATGGCGCAGCGTTTTGCAATGTGCTCAACGTTCAAGTTTCCGCTAGCCGCGCTGGTCTTTGAAAGAATTGACTCAGGCACCGAGCGGGGGGATCGAAAACTTTCATATGGGCCGGACATGATCGTCAAATGGTCTCCTGCCACGGAGCGGTTTCTAGCATCGGGACACATGACGGTTCTCGAGGCAGCGCAAGCTGCGGTGCAGCTTAGCGACAATGGGGCTACTAACCTCTTACTGAGAGAAATTGGCGGACCTGCTGCAATGACGCAGTATTTTCGTAAAATTGGCGACTCTGTGAGTCGGCTAGACCGGAAAGAGCCGGAGATGAGCGACAACACACCTGGCGACCTCAGAGATACAACTACGCCTATTGCTATGGCACGTACTGTGGCTAAAGTCCTCTATGGCGGCGCACTGACGTCCACCTCGACCCACACCATTGAGAGGTGGCTGATCGGAAACCAAACGGGAGACGCGACACTACGAGCGGGTTTTCCTAAAGATTGGGTTGTTGGAGAGAAAACTGGTGCCTGCGCCAACGGGGGCCGGAACGACATTGGTTTTTTTAAAGCCCAGGAGAGAGATTACGCTGTAGCGGTGTATACAACGGCCCCGAAACTATCGGCCGTAGAACGTGACGAATTAGTTGCCTCTGTCGGTCAAGTTATTACACAACTCATCCTGAGCACGGACAAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006162","ARO_id":"44624","ARO_name":"GES-33","CARD_short_name":"GES-33","ARO_description":"GES-33 is a GES beta-lactamase.","ARO_category":{"36205":{"category_aro_accession":"3000066","category_aro_cvterm_id":"36205","category_aro_name":"GES beta-lactamase","category_aro_description":"GES beta-lactamases or Guiana extended-spectrum beta-lactamases are related to the other plasmid-located class A beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4617":{"model_id":"4617","model_name":"GES-34","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"6992":{"protein_sequence":{"accession":"WP_102607460.1","sequence":"MRFIHALLLAGIAHSAYASEKLTFKTDLEKLEREKAAQIGVAIVDPQGEIVAGHRMAQRFAMCSTFKFPLAALVFERIDSGTERGDRKLSYGPDMIVKWSPATERFLASGHMTVLEAAQAAVQLSDNGATNLLLREIGGPAAMTQYFRKIGDSVSRLDRNEPEMSDNTPGDLRDTTTPIAMARTVAKVLYGGALTSTSTHTIERWLIGNQTGDATLRAGFPKDWVVGEKTGTCANGGRNDIGFFKAQERDYAVAVYTTAPKLSAVERDELVASVGQVITQLILSTDK"},"dna_sequence":{"accession":"NG_056177.1","fmin":"0","fmax":"864","strand":"+","sequence":"ATGCGCTTCATTCACGCACTATTACTGGCAGGGATCGCTCACTCTGCATATGCGTCGGAAAAATTAACCTTCAAGACCGATCTTGAGAAGCTAGAGCGCGAAAAAGCAGCTCAGATCGGTGTTGCGATCGTCGATCCCCAAGGAGAGATCGTCGCGGGCCACCGAATGGCGCAGCGTTTTGCAATGTGCTCAACGTTCAAGTTTCCGCTAGCCGCGCTGGTCTTTGAAAGAATTGACTCAGGCACCGAGCGGGGGGATCGAAAACTTTCATATGGGCCGGACATGATCGTCAAATGGTCTCCTGCCACGGAGCGGTTTCTAGCATCGGGACACATGACGGTTCTCGAGGCAGCGCAAGCTGCGGTGCAGCTTAGCGACAATGGGGCTACTAACCTCTTACTGAGAGAAATTGGCGGACCTGCTGCAATGACGCAGTATTTTCGTAAAATTGGCGACTCTGTGAGTCGGCTAGACCGGAATGAGCCGGAGATGAGCGACAACACACCTGGCGACCTCAGAGATACAACTACGCCTATTGCTATGGCACGTACTGTGGCTAAAGTCCTCTATGGCGGCGCACTGACGTCCACCTCGACCCACACCATTGAGAGGTGGCTGATCGGAAACCAAACGGGAGACGCGACACTACGAGCGGGTTTTCCTAAAGATTGGGTTGTTGGAGAGAAAACTGGTACCTGCGCCAACGGGGGCCGGAACGACATTGGTTTTTTTAAAGCCCAGGAGAGAGATTACGCTGTAGCGGTGTATACAACGGCCCCGAAACTATCGGCCGTAGAACGTGACGAATTAGTTGCCTCTGTCGGTCAAGTTATTACACAACTCATCCTGAGCACGGACAAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006163","ARO_id":"44625","ARO_name":"GES-34","CARD_short_name":"GES-34","ARO_description":"GES-34 is a GES beta-lactamase.","ARO_category":{"36205":{"category_aro_accession":"3000066","category_aro_cvterm_id":"36205","category_aro_name":"GES beta-lactamase","category_aro_description":"GES beta-lactamases or Guiana extended-spectrum beta-lactamases are related to the other plasmid-located class A beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4618":{"model_id":"4618","model_name":"GES-35","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"6993":{"protein_sequence":{"accession":"WP_111273848.1","sequence":"MRFIHALLLAGIAHSAYASEKLTFKTDLEKLEREKAAQIGVAIVDPQGEIVAGHRMAQRFAMCSTFKFPLAALVFERIDSGTERGDRKLSYGPDMIVEWSPATERFLASGHMTVLEAAQAAVQLSDNGATNLLLREIGGPAAMTQYFRKIGDSVSRLDRKEPELGDNTPGDLRDTTTPIAMARTVAKILYGGALTSTSTHTIERWLIGNQTGDATLRAGFPKDWVVGEKTGTCANGARNDIGFFKAQERDYAVAVYTTAPKLSAVERDELVASVGQVITQLILSTDK"},"dna_sequence":{"accession":"NG_060520.1","fmin":"0","fmax":"864","strand":"+","sequence":"ATGCGCTTCATTCACGCACTATTACTGGCAGGGATCGCTCACTCTGCATATGCGTCGGAAAAATTAACCTTCAAGACCGATCTTGAGAAGCTAGAGCGCGAAAAAGCAGCTCAGATCGGTGTTGCGATCGTCGATCCCCAAGGAGAGATCGTCGCGGGCCACCGAATGGCGCAGCGTTTTGCAATGTGCTCAACGTTCAAGTTTCCGCTAGCCGCGCTGGTCTTTGAAAGAATTGACTCAGGCACCGAGCGGGGGGATCGAAAACTTTCATATGGGCCGGACATGATCGTCGAATGGTCTCCTGCCACGGAGCGGTTTCTAGCATCGGGACACATGACGGTTCTCGAGGCAGCGCAAGCTGCGGTGCAGCTTAGCGACAATGGGGCTACTAACCTCTTACTGAGAGAAATTGGCGGACCTGCTGCAATGACGCAGTATTTTCGTAAAATTGGCGACTCTGTGAGTCGGCTAGACCGGAAAGAGCCGGAGTTGGGCGACAACACACCTGGCGACCTCAGAGATACAACTACGCCTATTGCTATGGCACGTACTGTGGCTAAAATCCTCTATGGCGGCGCACTGACGTCCACCTCGACCCACACCATTGAGAGGTGGCTGATCGGAAACCAAACGGGAGACGCGACACTACGAGCGGGTTTTCCTAAAGATTGGGTTGTTGGAGAGAAAACTGGTACCTGCGCCAACGGGGCCCGGAACGACATTGGTTTTTTTAAAGCCCAGGAGAGAGATTACGCTGTAGCGGTGTATACAACGGCCCCGAAACTATCGGCCGTAGAACGTGACGAATTAGTTGCCTCTGTCGGTCAAGTTATTACACAACTCATCCTGAGCACGGACAAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006164","ARO_id":"44626","ARO_name":"GES-35","CARD_short_name":"GES-35","ARO_description":"GES-35 is a GES beta-lactamase.","ARO_category":{"36205":{"category_aro_accession":"3000066","category_aro_cvterm_id":"36205","category_aro_name":"GES beta-lactamase","category_aro_description":"GES beta-lactamases or Guiana extended-spectrum beta-lactamases are related to the other plasmid-located class A beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4619":{"model_id":"4619","model_name":"GES-36","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"6994":{"protein_sequence":{"accession":"WP_111273849.1","sequence":"MRFIHALLLAGIAHSAYASEKLTFKTDLEKLEREKAAQIGVAIVDPQGEIVAGHRMAQRFAMCSTFKFPLAALVFERIDSGTERGDRKLSYGPDMIVEWSPATERFLASGHMTVLEAAQAAVQLSDNGATNLLLREIGGPAAMTQYFRKIGDSVSRLDRKEPKMSDNTPGDLRDTTTPIAMARTVAKVLYGGALTSTSTHTIERWLIGNQTGDATLRAGFPKDWVVGEKTGTCANGGRNDIGFFKAQERDYAVAVYTTAPKLSAVERDELVASVGQVITQLILSTDK"},"dna_sequence":{"accession":"NG_060521.1","fmin":"0","fmax":"864","strand":"+","sequence":"ATGCGCTTCATTCACGCACTATTACTGGCAGGGATCGCTCACTCTGCATATGCGTCGGAAAAATTAACCTTCAAGACCGATCTTGAGAAGCTAGAGCGCGAAAAAGCAGCTCAGATCGGTGTTGCGATCGTCGATCCCCAAGGAGAGATCGTCGCGGGCCACCGAATGGCGCAGCGTTTTGCAATGTGCTCAACGTTCAAGTTTCCGCTAGCCGCGCTGGTCTTTGAAAGAATTGACTCAGGCACCGAGCGGGGGGATCGAAAACTTTCATATGGGCCGGACATGATCGTCGAATGGTCTCCTGCCACGGAGCGGTTTCTAGCATCGGGACACATGACGGTTCTCGAGGCAGCGCAAGCTGCGGTGCAGCTTAGCGACAATGGGGCTACTAACCTCTTACTGAGAGAAATTGGCGGACCTGCTGCAATGACGCAGTATTTTCGTAAAATTGGCGACTCTGTGAGTCGGCTAGACCGGAAAGAGCCGAAGATGAGCGACAACACACCTGGCGACCTCAGAGATACAACTACGCCTATTGCTATGGCACGTACTGTGGCTAAAGTCCTCTATGGCGGCGCACTGACGTCCACCTCGACCCACACCATTGAGAGGTGGCTGATCGGAAACCAAACGGGAGACGCGACACTACGAGCGGGTTTTCCTAAAGATTGGGTTGTTGGAGAGAAAACTGGTACCTGCGCCAACGGGGGCCGGAACGACATTGGTTTTTTTAAAGCCCAGGAGAGAGATTACGCTGTAGCGGTGTATACAACGGCCCCGAAACTATCGGCCGTAGAACGTGACGAATTAGTTGCCTCTGTCGGTCAAGTTATTACACAACTCATCCTGAGCACGGACAAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006165","ARO_id":"44627","ARO_name":"GES-36","CARD_short_name":"GES-36","ARO_description":"GES-36 is a GES beta-lactamase.","ARO_category":{"36205":{"category_aro_accession":"3000066","category_aro_cvterm_id":"36205","category_aro_name":"GES beta-lactamase","category_aro_description":"GES beta-lactamases or Guiana extended-spectrum beta-lactamases are related to the other plasmid-located class A beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4620":{"model_id":"4620","model_name":"GES-37","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"6995":{"protein_sequence":{"accession":"WP_111273850.1","sequence":"MRFIHALLLAGIAHSAYASEKLTFKTDLEKLEREKAAQIGVAIVDPQGEIVAGHRMAQRFAMCSTFKFPLAALVFERIDSGTERGDRKLSYGPDMIVEWSPATERFLASGHMTVLEAAQAAVQLSDNGATNLLLREIGGPAAMTQYFRKIGDSVSRLDRKETEMSDNTPGDLRDTTTPIAMARTVAKVLYGGALTSTSTHTIERWLIGNQTGDATLRAGFPKDWVVGEKTGTCANGGRNDIGFFKAQERDYAVAVYTTAPKLSAVERDELVASVGQVITQLILSTDK"},"dna_sequence":{"accession":"NG_060522.1","fmin":"0","fmax":"864","strand":"+","sequence":"ATGCGCTTCATTCACGCACTATTACTGGCAGGGATCGCTCACTCTGCATATGCGTCGGAAAAATTAACCTTCAAGACCGATCTTGAGAAGCTAGAGCGCGAAAAAGCAGCTCAGATCGGTGTTGCGATCGTCGATCCCCAAGGAGAGATCGTCGCGGGCCACCGAATGGCGCAGCGTTTTGCAATGTGCTCAACGTTCAAGTTTCCGCTAGCCGCGCTGGTCTTTGAAAGAATTGACTCAGGCACCGAGCGGGGGGATCGAAAACTTTCATATGGGCCGGACATGATCGTCGAATGGTCTCCTGCCACGGAGCGGTTTCTAGCATCGGGACACATGACGGTTCTCGAGGCAGCGCAAGCTGCGGTGCAGCTTAGCGACAATGGGGCTACTAACCTCTTACTGAGAGAAATTGGCGGACCTGCTGCAATGACGCAGTATTTTCGTAAAATTGGCGACTCTGTGAGTCGGCTAGACCGGAAAGAGACGGAGATGAGCGACAACACACCTGGCGACCTCAGAGATACAACTACGCCTATTGCTATGGCACGTACTGTGGCTAAAGTCCTCTATGGCGGCGCACTGACGTCCACCTCGACCCACACCATTGAGAGGTGGCTGATCGGAAACCAAACGGGAGACGCGACACTACGAGCGGGTTTTCCTAAAGATTGGGTTGTTGGAGAGAAAACTGGTACCTGCGCCAACGGGGGCCGGAACGACATTGGTTTTTTTAAAGCCCAGGAGAGAGATTACGCTGTAGCGGTGTATACAACGGCCCCGAAACTATCGGCCGTAGAACGTGACGAATTAGTTGCCTCTGTCGGTCAAGTTATTACACAACTCATCCTGAGCACGGACAAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006166","ARO_id":"44628","ARO_name":"GES-37","CARD_short_name":"GES-37","ARO_description":"GES-37 is a GES beta-lactamase.","ARO_category":{"36205":{"category_aro_accession":"3000066","category_aro_cvterm_id":"36205","category_aro_name":"GES beta-lactamase","category_aro_description":"GES beta-lactamases or Guiana extended-spectrum beta-lactamases are related to the other plasmid-located class A beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4621":{"model_id":"4621","model_name":"GES-38","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"6996":{"protein_sequence":{"accession":"WP_122630826.1","sequence":"MRFIHALLLAGIAHSAYASEKLTFKTDLEKLEREKAAQIGVAIVDPQGEIVAGHRMAQRFAMCSTFKFPLAALVFERIDSGTERGDRKLSYGPDMIVKWSPATERFLASGHMTVLEAAQAAVQLSDNGATNLLLREIGGPAAMTQYFRKIGDSVSRLDRKEPEMGDNTPGDLRDTTTPIAMARTVAKVLYGGALTSTSTHTIERWLIGNQTGDATLRAGFPKDWVVGEKTGTCANGAQNDIGFFKAQERDYAVAVYTTAPKLSAVERDELVASVGQVITQLILSTDK"},"dna_sequence":{"accession":"NG_062215.1","fmin":"0","fmax":"864","strand":"+","sequence":"ATGCGCTTCATTCACGCACTATTACTGGCAGGGATCGCTCACTCTGCATATGCGTCGGAAAAATTAACCTTCAAGACCGATCTTGAGAAGCTAGAGCGCGAAAAAGCAGCTCAGATCGGTGTTGCGATCGTCGATCCCCAAGGAGAGATCGTCGCGGGCCACCGAATGGCGCAGCGTTTTGCAATGTGCTCAACGTTCAAGTTTCCGCTAGCCGCGCTGGTCTTTGAAAGAATTGACTCAGGCACCGAGCGGGGGGATCGAAAACTTTCATATGGGCCGGACATGATCGTCAAATGGTCTCCTGCCACGGAGCGGTTTCTAGCATCGGGACACATGACGGTTCTCGAGGCAGCGCAAGCTGCGGTGCAGCTTAGCGACAATGGGGCTACTAACCTCTTACTGAGAGAAATTGGCGGACCTGCTGCAATGACGCAGTATTTTCGTAAAATTGGCGACTCTGTGAGTCGGCTAGACCGGAAAGAGCCGGAGATGGGCGACAACACACCTGGCGACCTCAGAGATACAACTACGCCTATTGCTATGGCACGTACTGTGGCTAAAGTCCTCTATGGCGGCGCACTGACGTCCACCTCGACCCACACCATTGAGAGGTGGCTGATCGGAAACCAAACGGGAGACGCGACACTACGAGCGGGTTTTCCTAAAGATTGGGTTGTTGGAGAGAAAACTGGTACCTGCGCCAACGGGGCCCAGAACGACATTGGTTTTTTTAAAGCCCAGGAGAGAGATTACGCTGTAGCGGTGTATACAACGGCCCCGAAACTATCGGCCGTAGAACGTGACGAATTAGTTGCCTCTGTCGGTCAAGTTATTACACAACTCATCCTGAGCACGGACAAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006167","ARO_id":"44629","ARO_name":"GES-38","CARD_short_name":"GES-38","ARO_description":"GES-38 is a GES beta-lactamase.","ARO_category":{"36205":{"category_aro_accession":"3000066","category_aro_cvterm_id":"36205","category_aro_name":"GES beta-lactamase","category_aro_description":"GES beta-lactamases or Guiana extended-spectrum beta-lactamases are related to the other plasmid-located class A beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4622":{"model_id":"4622","model_name":"GES-39","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"6997":{"protein_sequence":{"accession":"WP_122630827.1","sequence":"MRFIHALLLAGIAHSAYASEKLTFKTDLEKLEREKAAQIGVAIVDPQGEIVAGHRMAQRFAMCSTFKFPLAALVFERIDSGTERGDRKLSYGPDMIVGWSPATERFLASGHMTVLEAAQAAVQLSDNGATNLLLREIGGPAAMTQYFRKIGDSVSRLDRKEPEMSDNTPGDLRDTTTPIAMARTVAKVLYGGALTSTSTHTIERWLIGNQTGDATLRAGFPKDWVVGEKTGTCANGGRNDIGFFKAQERDYAVAVYTTAPKLSAVERDELVASVGQVITQLILSTDK"},"dna_sequence":{"accession":"NG_062216.1","fmin":"0","fmax":"864","strand":"+","sequence":"ATGCGCTTCATTCACGCACTATTACTGGCAGGGATCGCTCACTCTGCATATGCGTCGGAAAAATTAACCTTCAAGACCGATCTTGAGAAGCTAGAGCGCGAAAAAGCAGCTCAGATCGGTGTTGCGATCGTCGATCCCCAAGGAGAGATCGTCGCGGGCCACCGAATGGCGCAGCGTTTTGCAATGTGCTCAACGTTCAAGTTTCCGCTAGCCGCGCTGGTCTTTGAAAGAATTGACTCAGGCACCGAGCGGGGGGATCGAAAACTTTCATATGGGCCGGACATGATCGTCGGATGGTCTCCTGCCACGGAGCGGTTTCTAGCATCGGGACACATGACGGTTCTCGAGGCAGCGCAAGCTGCGGTGCAGCTTAGCGACAATGGGGCTACTAACCTCTTACTGAGAGAAATTGGCGGACCTGCTGCAATGACGCAGTATTTTCGTAAAATTGGCGACTCTGTGAGTCGGCTAGACCGGAAAGAGCCGGAGATGAGCGACAACACACCTGGCGACCTCAGAGATACAACTACGCCTATTGCTATGGCACGTACTGTGGCTAAAGTCCTCTATGGCGGCGCACTGACGTCCACCTCGACCCACACCATTGAGAGGTGGCTGATCGGAAACCAAACGGGAGACGCGACACTACGAGCGGGTTTTCCTAAAGATTGGGTTGTTGGAGAGAAAACTGGTACCTGCGCCAACGGGGGCCGGAACGACATTGGTTTTTTTAAAGCCCAGGAGAGAGATTACGCTGTAGCGGTGTATACAACGGCCCCGAAACTATCGGCCGTAGAACGTGACGAATTAGTTGCCTCTGTCGGTCAAGTTATTACACAACTCATCCTGAGCACGGACAAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006168","ARO_id":"44630","ARO_name":"GES-39","CARD_short_name":"GES-39","ARO_description":"GES-39 is a GES beta-lactamase.","ARO_category":{"36205":{"category_aro_accession":"3000066","category_aro_cvterm_id":"36205","category_aro_name":"GES beta-lactamase","category_aro_description":"GES beta-lactamases or Guiana extended-spectrum beta-lactamases are related to the other plasmid-located class A beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4623":{"model_id":"4623","model_name":"GES-40","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"6998":{"protein_sequence":{"accession":"WP_123002100.1","sequence":"MRFIHALLLAAIAHSAYASEKLTFKTDLEKLEREKAAQIGVAIVDPQGEIVAGHRMAQRFAMCSTFKFPLAALVFERIDSGTERGDRKLSYGPDMIVEWSPATERFLASGHMTVLEAAQAAVQLSDNGATNLLLREIGGPAAMTQYFRKIGDSVSRLDRKEPEMSDNTPGDLRDTTTPIAMARTVAKVLYGGALTSTSTHTIERWLIGNQTGDATLRAGFPKDWVVGEKTGTCANGARNDIGFFKAQERDYAVAVYTTAPKLSAVERDELVASVGQVITQLILSTDK"},"dna_sequence":{"accession":"NG_062356.1","fmin":"0","fmax":"864","strand":"+","sequence":"ATGCGCTTCATTCACGCACTATTACTGGCAGCGATCGCTCACTCTGCATATGCGTCGGAAAAATTAACCTTCAAGACCGATCTTGAGAAGCTAGAGCGCGAAAAAGCAGCTCAGATCGGTGTTGCGATCGTCGATCCCCAAGGAGAGATCGTCGCGGGCCACCGAATGGCGCAGCGTTTTGCAATGTGCTCAACGTTCAAGTTTCCGCTAGCCGCGCTGGTCTTTGAAAGAATTGACTCAGGCACCGAGCGGGGGGATCGAAAACTTTCATATGGGCCGGACATGATCGTCGAATGGTCTCCTGCCACGGAGCGGTTTCTAGCATCGGGACACATGACGGTTCTCGAGGCAGCGCAAGCTGCGGTGCAGCTTAGCGACAATGGGGCTACTAACCTCTTACTGAGAGAAATTGGCGGACCTGCTGCAATGACGCAGTATTTTCGTAAAATTGGCGACTCTGTGAGTCGGCTAGACCGGAAAGAGCCGGAGATGAGCGACAACACACCTGGCGACCTCAGAGATACAACTACGCCTATTGCTATGGCACGTACTGTGGCTAAAGTCCTCTATGGCGGCGCACTGACGTCCACCTCGACCCACACCATTGAGAGGTGGCTGATCGGAAACCAAACGGGAGACGCGACACTACGAGCGGGTTTTCCTAAAGATTGGGTTGTTGGAGAGAAAACTGGTACCTGCGCCAACGGGGCCCGGAACGACATTGGTTTTTTTAAAGCCCAGGAGAGAGATTACGCTGTAGCGGTGTATACAACGGCCCCGAAACTATCGGCCGTAGAACGTGACGAATTAGTTGCCTCTGTCGGTCAAGTTATTACACAACTCATCCTGAGCACGGACAAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006169","ARO_id":"44631","ARO_name":"GES-40","CARD_short_name":"GES-40","ARO_description":"GES-40 is a GES beta-lactamase.","ARO_category":{"36205":{"category_aro_accession":"3000066","category_aro_cvterm_id":"36205","category_aro_name":"GES beta-lactamase","category_aro_description":"GES beta-lactamases or Guiana extended-spectrum beta-lactamases are related to the other plasmid-located class A beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4624":{"model_id":"4624","model_name":"GES-41","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"6999":{"protein_sequence":{"accession":"WP_135350920.1","sequence":"MRFIHALFLAGIAHSASASENLTFRTDLEKLEREKAAEIGVAIVDPQGQIVAGHRIEQRFAMCSTFKFPLAALVFERIDSGTERGDRKLSYGRDMIVEWSPAAERFLASGHMTVLEAAQAAVQLSDNGATNLLLREIGGPAAMTQYFRKIGDSVSRLDRKEPEMSDNTPGDLRDTTTPIAMARTVAKVLYGGALTPTSTHTIERWLIGNQTGDATLRAGFPKDWVIGEKTGTCANGGRNDIGFFKAQDRDYAVAVYTTAPKLSAEQRDELVASVGQVITQLILSTDK"},"dna_sequence":{"accession":"NG_065425.1","fmin":"0","fmax":"864","strand":"+","sequence":"ATGCGCTTTATTCACGCACTATTCCTGGCAGGGATCGCTCACTCTGCATCTGCGTCGGAAAACTTAACCTTCAGGACCGATCTTGAGAAGCTAGAGCGCGAGAAAGCAGCTGAGATCGGTGTTGCGATCGTCGATCCCCAAGGACAGATCGTCGCGGGCCACCGAATCGAGCAGCGTTTTGCAATGTGCTCTACGTTCAAGTTTCCGCTAGCCGCGCTGGTCTTTGAAAGAATTGACTCAGGCACCGAGCGGGGGGATCGAAAACTTTCGTACGGGCGGGACATGATCGTCGAATGGTCTCCTGCCGCGGAGCGGTTTCTCGCATCGGGACATATGACGGTTCTCGAGGCAGCGCAAGCGGCGGTGCAGCTCAGCGACAATGGGGCTACTAACCTCTTACTGAGAGAAATTGGCGGACCTGCTGCAATGACGCAGTATTTTCGTAAAATTGGCGACTCTGTGAGTCGGCTAGACCGGAAAGAGCCGGAGATGAGCGACAACACACCTGGCGACCTCAGAGATACAACCACGCCTATTGCTATGGCACGTACTGTGGCTAAAGTCCTCTATGGCGGCGCACTGACGCCCACCTCGACCCACACAATTGAGAGGTGGCTGATCGGAAACCAAACGGGAGACGCGACATTACGAGCGGGTTTTCCTAAAGATTGGGTTATTGGAGAGAAAACCGGCACCTGCGCCAACGGGGGCCGGAACGACATTGGGTTTTTTAAAGCCCAGGACAGAGATTACGCTGTAGCGGTGTATACAACGGCCCCGAAACTATCGGCCGAACAACGTGACGAATTAGTTGCCTCTGTCGGTCAAGTTATTACGCAACTCATCCTAAGTACGGACAAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006170","ARO_id":"44632","ARO_name":"GES-41","CARD_short_name":"GES-41","ARO_description":"GES-41 is a GES beta-lactamase.","ARO_category":{"36205":{"category_aro_accession":"3000066","category_aro_cvterm_id":"36205","category_aro_name":"GES beta-lactamase","category_aro_description":"GES beta-lactamases or Guiana extended-spectrum beta-lactamases are related to the other plasmid-located class A beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4625":{"model_id":"4625","model_name":"GES-42","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"7000":{"protein_sequence":{"accession":"WP_148044413.1","sequence":"MRFIHALLLAGIAHSAYASEKLTFKTDLEKLEREKAAQIGVAIVDPQGEIVAGHRMAQRFAMCSTFKFPLAALVFERIDSGTERGDRKLSYGPDMIVEWSPATERFLASGHMTVLEAAQAAVQLSDNGATNLLLREIGGPAAMTQYFRKIGDSVSRLDRKERKEPEMSDNTPGDLRDTTTPIAMARTVAKVLYGGALTSTSTHTIERWLIGNQTGDATLRAGFPKDWVVGEKTGTCANGGRNDIGFFKAQERDYAVAVYTTAPKLSAVERDELVASVGQVITQLILSTDK"},"dna_sequence":{"accession":"NG_065870.1","fmin":"0","fmax":"873","strand":"+","sequence":"ATGCGCTTCATTCACGCACTATTACTGGCAGGGATCGCTCACTCTGCATATGCGTCGGAAAAATTAACCTTCAAGACCGATCTTGAGAAGCTAGAGCGCGAAAAAGCAGCTCAGATCGGTGTTGCGATCGTCGATCCCCAAGGAGAGATCGTCGCGGGCCACCGAATGGCGCAGCGTTTTGCAATGTGCTCAACGTTCAAGTTTCCGCTAGCCGCGCTGGTCTTTGAAAGAATTGACTCAGGCACCGAGCGGGGGGATCGAAAACTTTCATATGGGCCGGACATGATCGTCGAATGGTCTCCTGCCACGGAGCGGTTTCTAGCATCGGGACACATGACGGTTCTCGAGGCAGCGCAAGCTGCGGTGCAGCTTAGCGACAATGGGGCTACTAACCTCTTACTGAGAGAAATTGGCGGACCTGCTGCAATGACGCAGTATTTTCGTAAAATTGGCGACTCTGTGAGTCGGCTAGACCGGAAAGAGCGGAAAGAGCCGGAGATGAGCGACAACACACCTGGCGACCTCAGAGATACAACTACGCCTATTGCTATGGCACGTACTGTGGCTAAAGTCCTCTATGGCGGCGCACTGACGTCCACCTCGACCCACACCATTGAGAGGTGGCTGATCGGAAACCAAACGGGAGACGCGACACTACGAGCGGGTTTTCCTAAAGATTGGGTTGTTGGAGAGAAAACTGGTACCTGCGCCAACGGGGGCCGGAACGACATTGGTTTTTTTAAAGCCCAGGAGAGAGATTACGCTGTAGCGGTGTATACAACGGCCCCGAAACTATCGGCCGTAGAACGTGACGAATTAGTTGCCTCTGTCGGTCAAGTTATTACACAACTCATCCTGAGCACGGACAAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006171","ARO_id":"44633","ARO_name":"GES-42","CARD_short_name":"GES-42","ARO_description":"GES-42 is a GES beta-lactamase.","ARO_category":{"36205":{"category_aro_accession":"3000066","category_aro_cvterm_id":"36205","category_aro_name":"GES beta-lactamase","category_aro_description":"GES beta-lactamases or Guiana extended-spectrum beta-lactamases are related to the other plasmid-located class A beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4626":{"model_id":"4626","model_name":"GES-43","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"7001":{"protein_sequence":{"accession":"WP_148044414.1","sequence":"MRFIYALLLAGIAHSAYASEKLTFKTDLEKLEREKAAQIGVAIVDPQGEIVAGHRMAQRFAMCSTFKFPLAALVFERIDSGTERGDRKLSYGPDMIVEWSPATERFLASGHMTVLEAAQAAVQLSDNGATNLLLREIGGPAAMTQYFRKIGDSVSRLDRKESEMSDNTPGDLRDTTTPIAMARTVAKVLYGGALTSTSTHTIERWLIGNQTGDATLRAGFPKDWVVGEKTGTCANGGRNDIGFFKAQERDYAVAVYTTAPKLSAVERDELVASVGQVITQLILSTDK"},"dna_sequence":{"accession":"NG_065871.1","fmin":"0","fmax":"864","strand":"+","sequence":"ATGCGCTTCATTTACGCACTATTACTGGCAGGGATCGCTCACTCTGCATATGCGTCGGAAAAATTAACCTTCAAGACCGATCTTGAGAAGCTAGAGCGCGAAAAAGCAGCTCAGATCGGTGTTGCGATCGTCGATCCCCAAGGAGAGATCGTCGCGGGCCACCGAATGGCGCAGCGTTTTGCAATGTGCTCAACGTTCAAGTTTCCGCTAGCCGCGCTGGTCTTTGAAAGAATTGACTCAGGCACCGAGCGGGGGGATCGAAAACTTTCATATGGGCCGGACATGATCGTCGAATGGTCTCCTGCCACGGAGCGGTTTCTAGCATCGGGACACATGACGGTTCTCGAGGCAGCGCAAGCTGCGGTGCAGCTTAGCGACAATGGGGCTACTAACCTCTTACTGAGAGAAATTGGCGGACCTGCTGCAATGACGCAGTATTTTCGTAAAATTGGCGACTCTGTGAGTCGGCTAGACCGGAAAGAGTCGGAGATGAGCGACAACACACCTGGCGACCTCAGAGATACAACTACGCCTATTGCTATGGCACGTACTGTGGCTAAAGTCCTCTATGGCGGCGCACTGACGTCCACCTCGACCCACACCATTGAGAGGTGGCTGATCGGAAACCAAACGGGAGACGCGACACTACGAGCGGGTTTTCCTAAAGATTGGGTTGTTGGAGAGAAAACTGGTACCTGCGCCAACGGGGGCCGGAACGACATTGGTTTTTTTAAAGCCCAGGAGAGAGATTACGCTGTAGCGGTGTATACAACGGCCCCGAAACTATCGGCCGTAGAACGTGACGAATTAGTTGCCTCTGTCGGTCAAGTTATTACACAACTCATCCTGAGCACGGACAAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006172","ARO_id":"44634","ARO_name":"GES-43","CARD_short_name":"GES-43","ARO_description":"GES-43 is a GES beta-lactamase.","ARO_category":{"36205":{"category_aro_accession":"3000066","category_aro_cvterm_id":"36205","category_aro_name":"GES beta-lactamase","category_aro_description":"GES beta-lactamases or Guiana extended-spectrum beta-lactamases are related to the other plasmid-located class A beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4627":{"model_id":"4627","model_name":"GES-44","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"7002":{"protein_sequence":{"accession":"WP_188331868.1","sequence":"MRFIHALFLAGIAHSASASENLTFKTDLEKLEREKAAQIGVAIVDPQGQIVAGHRMAQRFAMCSTFKFPLAALVFERIDSGTERGDRKLSYGPDMIVEWSPATERFLASGHMTVLEAAQAAVQLSDNGATNLLLREIGGPAAMTQYFRKIGDSVSRLDRKEPEMGDNTPGDLRDTTTPIAMARTVAKVLYGGALTSTSTHTIERWLIGNQTGDATLRAGFPKDWVVGEKTGTCANGGRNDIGFFKAQDRDYAVAVYTTAPKLSAEQRDELVASVGQVITQLILSTDK"},"dna_sequence":{"accession":"NG_070735.1","fmin":"0","fmax":"864","strand":"+","sequence":"ATGCGCTTCATTCATGCACTATTCCTGGCAGGGATCGCTCACTCTGCATCTGCGTCGGAAAACTTAACCTTCAAGACCGATCTTGAGAAGTTAGAGCGCGAAAAAGCAGCTCAGATCGGTGTTGCGATCGTCGATCCCCAAGGACAGATCGTCGCGGGCCACCGAATGGCGCAGCGTTTTGCAATGTGTTCTACGTTCAAGTTTCCGCTAGCCGCGCTGGTCTTTGAAAGAATTGACTCAGGCACCGAGCGAGGGGATCGAAAACTTTCGTATGGGCCGGACATGATCGTCGAATGGTCTCCTGCCACGGAGCGGTTTCTAGCATCGGGACACATGACGGTTCTCGAGGCAGCGCAAGCGGCGGTGCAGCTCAGCGACAATGGGGCTACTAACCTCTTACTGAGAGAAATTGGCGGACCTGCTGCAATGACGCAGTATTTTCGCAAAATTGGCGACTCTGTGAGTAGGCTAGACCGGAAAGAGCCGGAGATGGGCGACAACACACCTGGCGACCTCAGAGATACAACTACGCCTATTGCTATGGCACGTACTGTGGCTAAAGTCCTCTATGGCGGCGCACTGACGTCCACTTCGACCCACACCATTGAGAGGTGGCTGATCGGAAACCAAACGGGAGACGCGACATTACGAGCGGGTTTTCCTAAAGATTGGGTTGTTGGAGAAAAAACCGGTACCTGCGCCAACGGTGGCCGGAACGACATTGGTTTTTTTAAAGCCCAGGACAGAGATTACGCTGTAGCGGTGTATACAACGGCCCCGAAACTATCGGCCGAACAACGTGACGAATTAGTTGCCTCTGTCGGTCAAGTTATTACGCAACTCATCCTGAGCACGGACAAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006173","ARO_id":"44635","ARO_name":"GES-44","CARD_short_name":"GES-44","ARO_description":"GES-44 is a GES beta-lactamase.","ARO_category":{"36205":{"category_aro_accession":"3000066","category_aro_cvterm_id":"36205","category_aro_name":"GES beta-lactamase","category_aro_description":"GES beta-lactamases or Guiana extended-spectrum beta-lactamases are related to the other plasmid-located class A beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4628":{"model_id":"4628","model_name":"GES-45","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"7003":{"protein_sequence":{"accession":"WP_188331869.1","sequence":"MRFIHALLLAGIAHSAYASEKLTFKTDLEKLEREKAAQIGVAIVDPQGEIVAGHRMAQRFAMCSTFKFPLAALVFERIDSGTERGDRKLSYGPDMIVEWSPATERFLASGHMTVLEAAQAAVQLSDNGATNLLLREIGGPAAMTQYFRKIGDSVSRLDRKEPEMGDNTPGDLRDTTTPIAMARTVAKVLYGGALTSTSTHTIERWLIGNQTGDATLRAGFPKDWVVGEKTGACANGGRNDIGFFKAQERDYAVAVYTTAPKLSAVERDELVASVGQVITQLILSTDK"},"dna_sequence":{"accession":"NG_070736.1","fmin":"0","fmax":"864","strand":"+","sequence":"ATGCGCTTCATTCACGCACTATTACTGGCAGGGATCGCTCACTCTGCATATGCGTCGGAAAAATTAACCTTCAAGACCGATCTTGAGAAGCTAGAGCGCGAAAAAGCAGCTCAGATCGGTGTTGCGATCGTCGATCCCCAAGGAGAGATCGTCGCGGGCCACCGAATGGCGCAGCGTTTTGCAATGTGCTCAACGTTCAAGTTTCCGCTAGCCGCGCTGGTCTTTGAAAGAATTGACTCAGGCACCGAGCGGGGGGATCGAAAACTTTCATATGGGCCGGACATGATCGTCGAATGGTCTCCTGCCACGGAGCGGTTTCTAGCATCGGGACACATGACGGTTCTCGAGGCAGCGCAAGCTGCGGTGCAGCTTAGCGACAATGGGGCTACTAACCTCTTACTGAGAGAAATTGGCGGACCTGCTGCAATGACGCAGTATTTTCGTAAAATTGGCGACTCTGTGAGTCGGCTAGACCGGAAAGAGCCGGAGATGGGCGACAACACACCTGGCGACCTCAGAGATACAACTACGCCTATTGCTATGGCACGTACTGTGGCTAAAGTCCTCTATGGCGGCGCACTGACGTCCACCTCGACCCACACCATTGAGAGGTGGCTGATCGGAAACCAAACGGGAGACGCGACACTACGAGCGGGTTTTCCTAAAGATTGGGTTGTTGGAGAGAAAACTGGTGCCTGCGCCAACGGGGGCCGGAACGACATTGGTTTTTTTAAAGCCCAGGAGAGAGATTACGCTGTAGCGGTGTATACAACGGCCCCGAAACTATCGGCCGTAGAACGTGACGAATTAGTTGCCTCTGTCGGTCAAGTTATTACACAACTCATCCTGAGCACGGACAAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006174","ARO_id":"44636","ARO_name":"GES-45","CARD_short_name":"GES-45","ARO_description":"GES-45 is a GES beta-lactamase.","ARO_category":{"36205":{"category_aro_accession":"3000066","category_aro_cvterm_id":"36205","category_aro_name":"GES beta-lactamase","category_aro_description":"GES beta-lactamases or Guiana extended-spectrum beta-lactamases are related to the other plasmid-located class A beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4629":{"model_id":"4629","model_name":"GES-46","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"7004":{"protein_sequence":{"accession":"WP_197749401.1","sequence":"MRFIHALLLAGIAHSAYASEKLTFKTDLEKLEREKAAQIGVAIVDPQGEIVAGHRMAQRFAMCSTFKFPLAALVFERIDSGTERGDRKLSYGPDMIVKWSPATERFLASGHMTVLEAAQAAVQLSDNGATNLLLREIGGPAAMTQYFRKIGDSVSRLDRNEPEMGDNTPGDLRDTTTPIAMARTVAKVLYGGALTSTSTHTIERWLIGNQTGDATLRAGFPKDWVVGEKTGTCANGGRNDIGFFKAQERDYAVAVYTTAPKLSAVERDELVASVGQVITQLILSTDK"},"dna_sequence":{"accession":"NG_071202.1","fmin":"0","fmax":"864","strand":"+","sequence":"ATGCGCTTCATTCACGCACTATTACTGGCAGGGATCGCTCACTCTGCATATGCGTCGGAAAAATTAACCTTCAAGACCGATCTTGAGAAGCTAGAGCGCGAAAAAGCAGCTCAGATCGGTGTTGCGATCGTCGATCCCCAAGGAGAGATCGTCGCGGGCCACCGAATGGCGCAGCGTTTTGCAATGTGCTCAACGTTCAAGTTTCCGCTAGCCGCGCTGGTCTTTGAAAGAATTGACTCAGGCACCGAGCGGGGGGATCGAAAACTTTCATATGGGCCGGACATGATCGTCAAATGGTCTCCTGCCACGGAGCGGTTTCTAGCATCGGGACACATGACGGTTCTCGAGGCAGCGCAAGCTGCGGTGCAGCTTAGCGACAATGGGGCTACTAACCTCTTACTGAGAGAAATTGGCGGACCTGCTGCAATGACGCAGTATTTTCGTAAAATTGGCGACTCTGTGAGTCGGCTAGACCGGAATGAGCCGGAGATGGGCGACAACACACCTGGCGACCTCAGAGATACAACTACGCCTATTGCTATGGCACGTACTGTGGCTAAAGTCCTCTATGGCGGCGCACTGACGTCCACCTCGACCCACACCATTGAGAGGTGGCTGATCGGAAACCAAACGGGAGACGCGACACTACGAGCGGGTTTTCCTAAAGATTGGGTTGTTGGAGAGAAAACTGGTACCTGCGCCAACGGGGGCCGGAACGACATTGGTTTTTTTAAAGCCCAGGAGAGAGATTACGCTGTAGCGGTGTATACAACGGCCCCGAAACTATCGGCCGTAGAACGTGACGAATTAGTTGCCTCTGTCGGTCAAGTTATTACACAACTCATCCTGAGCACGGACAAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006175","ARO_id":"44637","ARO_name":"GES-46","CARD_short_name":"GES-46","ARO_description":"GES-46 is a GES beta-lactamase.","ARO_category":{"36205":{"category_aro_accession":"3000066","category_aro_cvterm_id":"36205","category_aro_name":"GES beta-lactamase","category_aro_description":"GES beta-lactamases or Guiana extended-spectrum beta-lactamases are related to the other plasmid-located class A beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4630":{"model_id":"4630","model_name":"GIL-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7005":{"protein_sequence":{"accession":"WP_063860521.1","sequence":"MPHFRLALIPLLTAFCLPAFAHPTTLNKVKEAESQLTARVGYAELDLTSGEILESYRLQERFPMMSTFKVLLCGAVLARVDAGKERLDRRIPFSRRDLVEYSPVTEKHLTDGMTVGELCDAAITMSDNTAANLLLTAIGGPQGLTAFLRTTGDRVTRLDRWEPELNEALPGDKRDTTTPENMAQTLRQLLTGKILTTTSQQQLTHWMVTDKVAGPLLRSVLPAGWFIADKTGAGARGSRGIVAALGPDGKPSRIVVIYITESQATMAERNRQIAGIGATLIQHWDE"},"dna_sequence":{"accession":"NG_049142.1","fmin":"100","fmax":"961","strand":"+","sequence":"ATGCCCCACTTTCGTCTGGCCCTTATCCCATTACTTACCGCATTTTGTCTGCCCGCGTTTGCCCACCCGACAACGCTGAATAAAGTCAAAGAAGCAGAAAGCCAGCTCACCGCACGCGTCGGTTATGCCGAGCTGGATCTCACCAGCGGCGAGATTCTGGAAAGCTATCGCCTGCAAGAGCGTTTTCCTATGATGAGTACATTTAAGGTTTTACTCTGCGGCGCGGTGCTCGCACGCGTTGACGCAGGAAAAGAGCGGCTGGATCGTCGCATCCCATTCAGCCGGCGTGATCTGGTCGAATACTCGCCGGTTACAGAAAAACACCTGACCGATGGCATGACCGTCGGCGAATTATGCGATGCCGCCATCACCATGAGCGATAACACGGCGGCGAATCTACTGCTTACGGCCATCGGCGGTCCGCAAGGATTAACCGCGTTTCTGCGCACAACCGGCGATCGGGTGACCCGACTCGACCGCTGGGAACCCGAATTGAACGAAGCGCTACCCGGCGATAAACGCGATACGACGACACCTGAAAATATGGCGCAAACGTTGCGCCAACTGCTCACCGGAAAAATCTTGACGACGACATCACAGCAGCAACTCACCCACTGGATGGTGACGGATAAAGTCGCGGGGCCACTGTTGCGCTCGGTACTTCCGGCAGGCTGGTTTATAGCCGATAAAACAGGTGCCGGGGCACGCGGTTCTCGCGGGATCGTCGCGGCGTTAGGGCCGGACGGTAAGCCTTCCCGTATCGTGGTGATTTACATCACCGAAAGCCAGGCAACAATGGCGGAGCGAAACAGACAGATTGCGGGGATTGGGGCGACGCTGATCCAACACTGGGATGAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3006888","ARO_id":"45350","ARO_name":"GIL-1","CARD_short_name":"GIL-1","ARO_description":"GIL-1 is a GIL beta-lactamase.","ARO_category":{"43873":{"category_aro_accession":"3005413","category_aro_cvterm_id":"43873","category_aro_name":"GIL beta-lactamase","category_aro_description":"GIL-beta-lactamases are class A beta-lactamases found in Citrobacter gillenii.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4631":{"model_id":"4631","model_name":"GMB-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"475"}},"model_sequences":{"sequence":{"7006":{"protein_sequence":{"accession":"WP_204376227.1","sequence":"MLNFVFALFTAFTAFSAFALDQKAFDEQFAVKELAKDTYQVTDKFYHDSNVLVARMPDGTVVIASSPFETVGAQLMMDWIKEKWDPKRIVAVNTHFHSDGTGGNEAYKQAGAEIWASDLTWRLHRQSTKKDQQALADGFKSKPELRDRILKRKTVHANRTFKSKEGKIFDFGGEKVELIFPGEGHTSDNSVVYLPQRKVLFGGCLIRSAKHDIGYLGDAVVKPWAETVRNVQKLKPEIVIPGHGPVGGPELLTRTIDLAEKEAAKGTTKN"},"dna_sequence":{"accession":"NG_073463.1","fmin":"0","fmax":"813","strand":"+","sequence":"ATGCTCAATTTCGTCTTCGCGCTGTTCACCGCGTTCACCGCGTTCAGCGCCTTTGCCTTAGATCAGAAAGCGTTCGATGAACAGTTCGCCGTGAAGGAACTCGCCAAAGACACGTATCAGGTCACCGATAAATTCTATCACGACTCCAACGTTTTGGTGGCGCGCATGCCCGATGGAACTGTGGTGATTGCATCGAGTCCGTTTGAAACGGTGGGTGCGCAACTGATGATGGATTGGATCAAAGAGAAATGGGATCCAAAGCGCATCGTCGCGGTGAACACTCATTTTCATTCTGACGGCACCGGCGGAAATGAAGCGTATAAACAAGCAGGGGCGGAAATCTGGGCCAGTGATTTGACTTGGCGTCTGCACCGACAGAGCACAAAGAAAGACCAGCAGGCATTGGCTGACGGATTTAAATCCAAGCCCGAACTGCGCGATCGAATCTTAAAAAGAAAGACCGTGCACGCCAACCGCACGTTTAAGTCGAAGGAAGGCAAGATCTTCGACTTCGGCGGTGAAAAGGTTGAACTGATTTTTCCGGGTGAAGGGCACACCTCAGACAATTCGGTGGTCTATCTTCCTCAGCGAAAAGTCCTTTTCGGGGGATGCCTCATCCGCTCGGCCAAACATGACATCGGATATCTCGGTGATGCGGTTGTGAAGCCCTGGGCAGAAACCGTGCGCAACGTGCAGAAGCTAAAACCTGAGATTGTGATTCCGGGACACGGTCCCGTGGGCGGGCCAGAACTTTTGACCCGCACCATTGATCTTGCAGAAAAGGAAGCCGCGAAGGGCACAACGAAGAATTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3006889","ARO_id":"45351","ARO_name":"GMB-1","CARD_short_name":"GMB-1","ARO_description":"GMB-1 is a GMB beta-lactamase.","ARO_category":{"43874":{"category_aro_accession":"3005414","category_aro_cvterm_id":"43874","category_aro_name":"GMB beta-lactamase","category_aro_description":"GMB beta-lactamases are class B1 beta-lactamases found in Citrobacter freundii.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4632":{"model_id":"4632","model_name":"GOB-19","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7007":{"protein_sequence":{"accession":"WP_086979105.1","sequence":"MRNFATLFFLSVCLSLNLNAQVVKEPENMPKEWNQTYEPFRIAGNLYYVGTYDLASYLIVTDKGNILINTGTAESLPIIKGNIQKLGFNYKDIKILLLTQAHYDHTGALEDFKTETGAKFYADKADADVLKTGGKSDYEMGKYGVTFKPITPDRTLKDQDKITLGNTTLTLLHHPGHTKGSCSFIFETKDEKRKYRVLIANMPSIIVDKKFSEVTAYPNIQSDYAYTFGAMKKLDFDLWVASHASQFDLHEKRKEGDPYNPQLFMDKQSYFQNLNDLEKSYLDKIKKDSQDK"},"dna_sequence":{"accession":"NG_067222.1","fmin":"0","fmax":"879","strand":"+","sequence":"ATGAGAAATTTTGCTACACTGTTTTTTCTGTCAGTTTGTTTGAGTTTGAATTTGAACGCTCAGGTAGTAAAAGAACCTGAGAATATGCCTAAAGAATGGAATCAGACTTATGAACCATTCAGAATTGCAGGTAACCTGTATTACGTAGGGACCTATGATTTAGCTTCTTACCTTATTGTGACGGACAAAGGCAATATTCTCATTAATACAGGAACGGCAGAATCGCTTCCAATAATAAAAGGCAATATTCAAAAGCTGGGGTTTAATTATAAAGACATTAAGATCTTGCTGCTTACCCAGGCTCATTATGACCATACAGGTGCGTTAGAGGATTTTAAAACAGAAACCGGTGCAAAATTCTATGCAGATAAAGCAGATGCTGATGTCCTGAAAACAGGGGGTAAGTCCGATTATGAAATGGGAAAATATGGTGTGACATTTAAACCTATTACTCCGGACAGAACGTTAAAAGATCAGGATAAAATAACACTGGGAAATACAACCCTGACTTTGCTTCATCACCCGGGACATACAAAAGGTTCCTGCAGTTTTATTTTTGAAACAAAAGACGAAAAGAGAAAGTATAGAGTTCTGATAGCTAATATGCCCTCTATTATTGTTGATAAGAAATTTTCTGAAGTTACAGCATATCCGAATATTCAGTCCGATTATGCTTATACCTTTGGTGCAATGAAAAAGCTTGATTTTGATCTTTGGGTGGCATCGCATGCAAGTCAGTTTGATCTGCATGAAAAACGTAAAGAAGGAGATCCGTACAATCCACAATTGTTTATGGATAAACAAAGCTATTTCCAAAACCTTAATGATTTGGAGAAAAGCTATCTCGACAAAATAAAAAAAGATTCACAAGATAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3005668","ARO_id":"44130","ARO_name":"GOB-19","CARD_short_name":"GOB-19","ARO_description":"GOB-19 is a GOB beta-lactamase.","ARO_category":{"41376":{"category_aro_accession":"3004212","category_aro_cvterm_id":"41376","category_aro_name":"GOB beta-lactamase","category_aro_description":"The GOB family of beta-lactamases have been discovered in the Elizabethkingia meningoseptica and are classified as subclass B3 beta-lactamase. They confer resistance to cephalosporins, penicillins, and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4633":{"model_id":"4633","model_name":"GOB-20","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7008":{"protein_sequence":{"accession":"WP_009089555.1","sequence":"MRNFVILFFMFICLGLNAQVVKEPENMPKEWNQTYEPFRIAGNLYYVGTYDLASYLIVTDKGNILINTGTAESLPIIKANIQKLGFNYKDIKILLLTQAHYDHTGALQDLKTETGAKFYADKEDADVLRTGGKSDYEMGKYGVTFKPVTPDKTLKDQDKITLGNTILTLLHHPGHTKGSCSFIFETKDEKRKYRVLIANMPSVIVDKKFSEVTAYPNIQSDYAYTFKAMKNLDFDIWVASHASQFDLHEKRKEGDPYNPQLFMDKQSYFQNLNDLEKSYLNKIKKDSQDK"},"dna_sequence":{"accession":"NG_067987.1","fmin":"100","fmax":"973","strand":"+","sequence":"ATGAGAAATTTTGTTATACTGTTTTTCATGTTCATTTGCTTGGGCTTGAATGCTCAGGTAGTAAAAGAACCTGAAAATATGCCCAAAGAATGGAACCAGACTTATGAACCCTTCAGAATTGCAGGTAATTTATATTACGTAGGAACCTATGATTTGGCTTCTTACCTTATTGTGACAGACAAAGGCAATATTCTCATTAATACAGGAACGGCAGAATCGCTTCCAATAATAAAAGCAAATATCCAAAAGCTCGGGTTTAATTATAAAGACATTAAGATCTTGCTGCTTACTCAGGCTCACTACGACCATACAGGTGCATTACAAGATCTTAAAACAGAAACCGGTGCAAAATTCTATGCCGATAAAGAAGATGCTGATGTCCTGAGAACAGGGGGGAAGTCCGATTATGAAATGGGAAAATATGGGGTGACATTTAAACCTGTTACTCCGGATAAAACATTGAAAGATCAGGATAAAATAACACTGGGAAATACAATCCTGACTTTGCTTCATCATCCCGGACATACAAAAGGTTCCTGTAGTTTTATTTTTGAAACAAAAGACGAGAAGAGAAAATATAGAGTTTTGATAGCTAATATGCCCTCCGTTATTGTTGATAAGAAATTTTCTGAAGTTACCGCATATCCAAATATTCAGTCCGATTATGCATATACTTTCAAAGCAATGAAGAATCTGGATTTTGATATTTGGGTGGCCTCCCATGCAAGTCAGTTCGATCTCCATGAAAAACGTAAAGAAGGAGATCCGTACAATCCGCAATTGTTTATGGATAAGCAAAGCTATTTCCAAAACCTTAATGATTTGGAAAAAAGCTATCTCAACAAAATAAAAAAAGATTCCCAAGATAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3005669","ARO_id":"44131","ARO_name":"GOB-20","CARD_short_name":"GOB-20","ARO_description":"GOB-20 is a GOB beta-lactamase.","ARO_category":{"41376":{"category_aro_accession":"3004212","category_aro_cvterm_id":"41376","category_aro_name":"GOB beta-lactamase","category_aro_description":"The GOB family of beta-lactamases have been discovered in the Elizabethkingia meningoseptica and are classified as subclass B3 beta-lactamase. They confer resistance to cephalosporins, penicillins, and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4634":{"model_id":"4634","model_name":"GOB-21","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7009":{"protein_sequence":{"accession":"WP_024566153.1","sequence":"MRNFATLFFMFVCLGLNAQVVKEPENMPKEWNQTYEPFRIAGNLYYVGTYDLASYLIVTDKGNILINTGTAESLPIIKANIQKLGFNYKDIKILLLTQAHYDHTGALQDLKTETAAKFYADKADADVLRTGGNSDYEMGKYGVTFKPVTPDKTLKDQDKIKLGNTILTLLHHPGHTKGSCSFIFETKDEKRKYRVLIANMPSVIVDKKFSEVTAYPNIQSDYAYTFKAMKNLDFDLWVASHASQFDLHEKRKEGDPYNPQLFMDKQSYFQNLNDLEKSYLDKIKKDSQDK"},"dna_sequence":{"accession":"NG_067988.1","fmin":"100","fmax":"973","strand":"+","sequence":"ATGAGAAATTTTGCTACACTGTTTTTCATGTTCGTTTGCTTGGGCTTGAATGCTCAGGTAGTAAAAGAACCTGAAAATATGCCCAAAGAATGGAACCAGACTTATGAACCCTTCAGAATTGCAGGTAATTTATATTACGTAGGAACCTATGATTTGGCTTCTTACCTTATTGTGACAGACAAAGGCAATATTCTCATTAATACAGGAACGGCAGAATCGCTTCCAATAATAAAAGCAAATATCCAAAAGCTCGGGTTTAATTATAAAGACATTAAGATCTTGCTGCTTACTCAGGCTCACTACGACCATACAGGTGCATTACAAGATCTTAAAACAGAAACCGCTGCAAAATTCTATGCCGATAAAGCAGATGCTGATGTCCTGAGAACAGGGGGAAATTCCGATTATGAAATGGGAAAATATGGTGTGACATTTAAACCTGTTACTCCGGATAAAACATTGAAAGATCAGGATAAAATAAAACTGGGAAATACAATCCTGACTTTGCTTCATCATCCGGGACATACAAAAGGTTCCTGTAGTTTTATTTTTGAAACAAAAGACGAGAAGAGAAAATATAGAGTTTTGATAGCTAATATGCCCTCCGTTATTGTTGATAAGAAATTTTCTGAAGTTACCGCATATCCAAATATTCAGTCCGATTATGCATATACTTTCAAAGCAATGAAGAATCTAGATTTTGACCTTTGGGTGGCATCACATGCAAGTCAGTTCGATCTGCATGAAAAACGTAAAGAAGGAGATCCGTACAATCCGCAATTGTTTATGGATAAGCAAAGCTATTTCCAAAACCTTAATGATTTGGAAAAAAGCTATCTCGACAAAATAAAAAAAGATTCACAAGATAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41081","NCBI_taxonomy_name":"Elizabethkingia anophelis","NCBI_taxonomy_id":"1117645"}}}},"ARO_accession":"3005670","ARO_id":"44132","ARO_name":"GOB-21","CARD_short_name":"GOB-21","ARO_description":"GOB-21 is a GOB beta-lactamase.","ARO_category":{"41376":{"category_aro_accession":"3004212","category_aro_cvterm_id":"41376","category_aro_name":"GOB beta-lactamase","category_aro_description":"The GOB family of beta-lactamases have been discovered in the Elizabethkingia meningoseptica and are classified as subclass B3 beta-lactamase. They confer resistance to cephalosporins, penicillins, and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4635":{"model_id":"4635","model_name":"GOB-22","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7010":{"protein_sequence":{"accession":"WP_019050927.1","sequence":"MRNLVILFFLLITFSWKAQVVKEPENTNEEWSRSYEPFRIAGNLYYVGTYDLASYLIVTDKGNILINTGLAGSLPMIKENIKKLGFNYKDIKILLLTQAHYDHTGALKDLQTETGAKFYADSADADVLKTGGKSDYEMGKYGATFKPIKPDILLKDQDKIKLGNTTLTLLHHPGHTKGSCSFIFETKDENRNYKVLIANMPSVIVDRKFSEIKDYPNIQADYAYTFKAMKKLDFDLWVASHASQFDLHTKHKEGDPYNPQVFMDKANYFAFLNSLETDYLEKIKNDSQKK"},"dna_sequence":{"accession":"NG_067989.1","fmin":"100","fmax":"973","strand":"+","sequence":"ATGAGAAACCTTGTAATTTTATTTTTTTTACTAATCACTTTCAGCTGGAAAGCTCAGGTTGTTAAAGAACCGGAAAATACAAATGAAGAATGGTCCCGATCATATGAGCCATTCAGAATTGCGGGTAACTTATACTATGTAGGAACTTACGATCTGGCTTCTTATTTAATAGTTACCGATAAAGGAAATATTCTCATTAATACAGGATTGGCTGGTTCTCTTCCTATGATAAAAGAGAATATTAAAAAACTGGGATTCAATTATAAAGACATTAAAATTCTGCTTTTAACCCAGGCGCATTATGATCATACAGGTGCATTAAAAGATTTGCAAACAGAAACAGGTGCGAAATTTTATGCAGACAGTGCTGATGCTGATGTATTGAAAACGGGCGGTAAATCCGATTATGAAATGGGGAAATACGGGGCAACCTTTAAGCCGATTAAGCCTGATATCCTGTTGAAAGATCAGGATAAAATAAAACTGGGGAATACAACCTTAACTTTACTTCATCATCCGGGGCACACAAAAGGTTCATGCAGTTTTATATTTGAAACAAAGGATGAAAACAGAAATTATAAAGTGCTGATAGCCAATATGCCATCGGTTATAGTTGACCGTAAGTTTTCCGAAATAAAAGATTACCCTAATATTCAGGCCGATTATGCTTATACATTTAAAGCCATGAAAAAACTGGATTTTGATCTTTGGGTCGCTTCACATGCGAGTCAGTTTGATTTACATACAAAACATAAAGAGGGAGACCCTTATAACCCACAGGTATTTATGGATAAGGCCAATTATTTTGCATTCCTCAATAGCCTGGAAACAGATTATCTGGAAAAAATTAAAAACGACTCACAAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36960","NCBI_taxonomy_name":"Elizabethkingia meningoseptica","NCBI_taxonomy_id":"238"}}}},"ARO_accession":"3005671","ARO_id":"44133","ARO_name":"GOB-22","CARD_short_name":"GOB-22","ARO_description":"GOB-22 is a GOB beta-lactamase.","ARO_category":{"41376":{"category_aro_accession":"3004212","category_aro_cvterm_id":"41376","category_aro_name":"GOB beta-lactamase","category_aro_description":"The GOB family of beta-lactamases have been discovered in the Elizabethkingia meningoseptica and are classified as subclass B3 beta-lactamase. They confer resistance to cephalosporins, penicillins, and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4636":{"model_id":"4636","model_name":"GOB-23","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7011":{"protein_sequence":{"accession":"WP_078795634.1","sequence":"MRNFAILFFLSVCLSLNAQVVKEPENMPKEWNQTYEPFRIAGNLYYVGTYDLASYLIVTDKGNILINTGTAESLPIIKGNIQKLGFNYKDIKILLLTQAHYDHTGALEDFKTETGAKFYADKADADVLKTGGKSDYEMGKYGVTFKPITPDRALKDQDKITLANTTLTLLHHPGHTKGSCSFIFETKDEKRKYRVLIANMPSIIVDKKFSEVTAYPNIQSDYAYTFGAMKKLDFDLWVASHASQFDLHEKRKEGDPYNPQLFMDKQSYFQNLNDLEKSYLDKIKKDSQDK"},"dna_sequence":{"accession":"NG_067990.1","fmin":"100","fmax":"973","strand":"+","sequence":"ATGAGAAATTTTGCTATACTGTTTTTTCTGTCAGTTTGTTTGAGTTTGAATGCTCAGGTAGTAAAAGAACCTGAAAATATGCCCAAAGAATGGAATCAGACTTATGAACCATTCAGAATTGCAGGTAACTTATATTACGTAGGAACCTATGATTTGGCTTCTTACCTTATTGTGACGGACAAAGGCAATATTCTCATTAATACAGGAACGGCAGAATCGCTTCCTATAATAAAAGGCAATATTCAAAAGCTGGGTTTTAATTATAAAGACATTAAGATCTTGCTGCTTACCCAGGCTCATTATGACCATACAGGTGCGTTAGAGGATTTTAAAACAGAAACCGGTGCAAAATTCTATGCCGATAAAGCAGATGCTGATGTCCTGAAAACAGGGGGTAAGTCCGATTATGAAATGGGAAAATATGGTGTGACATTTAAACCTATTACTCCGGATAGAGCGTTAAAAGATCAGGATAAAATAACACTGGCAAATACAACCCTGACTTTGCTTCATCACCCGGGACATACAAAAGGTTCCTGCAGTTTTATTTTTGAAACAAAAGACGAGAAGAGAAAGTATAGAGTTCTGATAGCTAATATGCCCTCTATTATTGTTGATAAGAAATTTTCTGAAGTTACAGCATATCCGAATATTCAGTCCGATTATGCTTATACCTTTGGTGCAATGAAAAAACTTGATTTTGATCTTTGGGTGGCATCGCATGCAAGTCAGTTTGATCTGCATGAAAAACGTAAAGAAGGAGATCCGTACAATCCACAATTGTTTATGGATAAGCAAAGCTATTTCCAAAACCTTAATGATTTGGAGAAAAGCTATCTCGACAAAATAAAAAAAGATTCACAAGATAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3005672","ARO_id":"44134","ARO_name":"GOB-23","CARD_short_name":"GOB-23","ARO_description":"GOB-23 is a GOB beta-lactamase.","ARO_category":{"41376":{"category_aro_accession":"3004212","category_aro_cvterm_id":"41376","category_aro_name":"GOB beta-lactamase","category_aro_description":"The GOB family of beta-lactamases have been discovered in the Elizabethkingia meningoseptica and are classified as subclass B3 beta-lactamase. They confer resistance to cephalosporins, penicillins, and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4637":{"model_id":"4637","model_name":"GOB-24","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7012":{"protein_sequence":{"accession":"WP_101360689.1","sequence":"MRNFATLFFMFICLGLNAQVVKEPENMPKEWNQAYEPFRIAGNLYYVGTYDLASYLIVTGKGNILINTGTAESLPIIKANIQKLGFNYKGIKILLLTQAHYDHTGALQDFKTETAAKFYVDKADVDVLRTGGKSDYEMGKYGVTFKPVTPDKTLKDQDKIKLGNITLTLLHHPGHTKGSCSFIFETKDEKRKYRVLIANMPSVIVDKKFSEVTAYPNIQSDYAYTFGVMKKLDFDIWVASHASQFDLHEKRKEGDPYNPQLFMDKQSYFQNLNDLEKSYLNKIKKDSQDK"},"dna_sequence":{"accession":"NG_067991.1","fmin":"100","fmax":"973","strand":"+","sequence":"ATGAGAAATTTTGCTACACTGTTTTTCATGTTCATTTGCTTGGGCTTGAATGCTCAGGTAGTAAAAGAACCTGAAAATATGCCCAAAGAATGGAACCAGGCTTATGAACCATTCAGAATTGCAGGTAATTTATATTACGTAGGAACCTATGATTTGGCTTCTTACCTTATTGTGACAGGCAAAGGCAATATTCTCATTAATACAGGAACGGCAGAATCGCTTCCAATAATAAAAGCAAATATCCAAAAGCTCGGGTTTAATTATAAAGGCATTAAGATCTTGCTGCTTACTCAGGCTCACTACGACCATACAGGTGCATTACAGGATTTTAAAACAGAAACCGCTGCAAAATTCTATGTCGATAAAGCAGATGTTGATGTCCTGAGAACAGGGGGGAAGTCCGATTATGAAATGGGAAAATATGGTGTGACATTTAAACCTGTTACTCCGGATAAAACATTGAAAGATCAGGATAAAATAAAACTGGGAAATATAACCCTGACTTTGCTTCATCATCCGGGACATACAAAAGGTTCCTGTAGTTTTATTTTTGAAACAAAAGACGAGAAGAGAAAATATAGAGTTTTGATAGCTAATATGCCCTCCGTTATTGTTGATAAGAAATTTTCTGAAGTTACCGCATATCCAAATATTCAGTCCGATTATGCTTATACCTTTGGTGTTATGAAAAAGCTGGATTTTGATATTTGGGTGGCCTCCCATGCAAGTCAGTTCGATCTCCATGAAAAACGTAAAGAAGGAGATCCGTACAATCCGCAATTGTTTATGGATAAGCAAAGCTATTTCCAAAACCTTAATGATTTGGAAAAAAGCTATCTCAACAAAATAAAAAAAGATTCACAAGATAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41081","NCBI_taxonomy_name":"Elizabethkingia anophelis","NCBI_taxonomy_id":"1117645"}}}},"ARO_accession":"3005673","ARO_id":"44135","ARO_name":"GOB-24","CARD_short_name":"GOB-24","ARO_description":"GOB-24 is a GOB beta-lactamase.","ARO_category":{"41376":{"category_aro_accession":"3004212","category_aro_cvterm_id":"41376","category_aro_name":"GOB beta-lactamase","category_aro_description":"The GOB family of beta-lactamases have been discovered in the Elizabethkingia meningoseptica and are classified as subclass B3 beta-lactamase. They confer resistance to cephalosporins, penicillins, and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4638":{"model_id":"4638","model_name":"GOB-25","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7013":{"protein_sequence":{"accession":"WP_059345125.1","sequence":"MRNFATLFFLSVCLSLNLNLNAQVVKEPENMPKEWNQTYEPFRIAGNLYYVGTYDLTSYLIVTDKGNILINTGTAESLPIIKGNIQKLGFNYKDIKILLLTQAHYDHTGALEDFKTETGAKFYADKADADVLRTGGKSDYELGKYGVTFKPITPDRTLKDQDKITLGNTTLTLLHHPGHTKGSCSFIFETKDEKRKYRVLIANMPSIIVDKKFSEVTAYPNIQSDYAYTFGAMKKLDFDLWVASHASQFDLHEKRKEGDPYNPQLFMDKQSYFQNLNDLEKSYLDKIKKDSQDK"},"dna_sequence":{"accession":"NG_067992.1","fmin":"100","fmax":"985","strand":"+","sequence":"ATGAGAAATTTTGCTACACTGTTTTTTCTGTCAGTTTGTTTGAGTTTGAATTTGAATTTGAATGCTCAGGTAGTAAAAGAACCTGAGAATATGCCTAAAGAATGGAATCAGACTTATGAACCATTCAGAATTGCAGGGAACCTATATTACGTAGGAACCTATGATTTGACTTCTTACCTTATTGTGACGGACAAAGGCAATATTCTCATTAATACAGGTACAGCAGAATCGCTTCCAATAATAAAAGGCAATATTCAAAAGCTGGGTTTTAATTATAAAGACATTAAGATCTTGCTGCTTACCCAGGCTCATTATGACCATACAGGTGCGTTAGAGGATTTTAAAACAGAAACTGGTGCAAAATTCTATGCTGATAAAGCAGATGCTGATGTCCTGAGAACAGGGGGTAAGTCCGATTATGAATTGGGAAAATATGGTGTGACATTTAAACCTATTACTCCGGATAGAACGTTAAAAGATCAGGATAAAATAACACTGGGAAATACAACCCTGACTTTGCTTCATCACCCGGGACATACAAAAGGTTCCTGCAGTTTTATTTTTGAAACAAAAGACGAGAAGAGAAAGTATAGAGTTCTGATAGCTAATATGCCCTCTATTATTGTTGATAAGAAATTTTCTGAAGTTACAGCATATCCGAATATTCAGTCCGATTATGCTTATACCTTTGGTGCTATGAAAAAGCTTGATTTTGATCTTTGGGTAGCATCGCATGCAAGTCAGTTCGATCTGCATGAAAAACGTAAAGAAGGGGATCCGTACAATCCACAATTGTTTATGGATAAGCAAAGCTATTTCCAAAACCTTAATGATTTGGAGAAAAGCTATCTCGACAAAATAAAAAAAGATTCACAAGATAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3005674","ARO_id":"44136","ARO_name":"GOB-25","CARD_short_name":"GOB-25","ARO_description":"GOB-25 is a GOB beta-lactamase.","ARO_category":{"41376":{"category_aro_accession":"3004212","category_aro_cvterm_id":"41376","category_aro_name":"GOB beta-lactamase","category_aro_description":"The GOB family of beta-lactamases have been discovered in the Elizabethkingia meningoseptica and are classified as subclass B3 beta-lactamase. They confer resistance to cephalosporins, penicillins, and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4639":{"model_id":"4639","model_name":"GOB-26","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7014":{"protein_sequence":{"accession":"WP_024567831.1","sequence":"MRNFATLFFLSVCLSLNLNAQVVKEPENMPKEWNQAYEPFRIAGNLYYVGTYDLASYLIVTDKGNILINTGTAESLPIIKGNIQKLGFNYKDIKILLLTQAHYDHTGALEDFKTETGAKFYADKADADVLRTGGKSDYELGKYGVTFKPITPDRTLKDQDKITLGNTTLTLLHHPGHTKGSCSFIFDTKDEKRKYRVLIANMPSIIVDKKFSEVTAYPNIQSDYAYTFGAMKKLDFDLWVASHASQFDLHEKRKEGDPYNPQLFMDKQNYFQSLNNLEKSYLDKIKKDSQDK"},"dna_sequence":{"accession":"NG_067993.1","fmin":"100","fmax":"979","strand":"+","sequence":"ATGAGAAATTTTGCTACACTGTTTTTTCTGTCAGTTTGTTTGAGTTTGAATTTGAACGCTCAGGTAGTAAAAGAACCTGAGAATATGCCTAAAGAATGGAATCAGGCTTATGAACCATTCAGAATTGCAGGTAACCTATATTACGTAGGAACCTATGATTTGGCTTCTTACCTTATTGTGACGGACAAAGGCAATATTCTCATTAATACAGGTACGGCAGAATCGCTTCCAATAATAAAAGGCAATATTCAAAAGCTGGGGTTTAATTATAAAGACATTAAGATCTTGCTGCTTACCCAGGCTCATTATGACCATACAGGTGCGTTAGAGGATTTTAAAACAGAAACCGGTGCAAAATTCTATGCAGATAAAGCAGATGCTGATGTCCTGAGAACAGGGGGTAAGTCCGACTATGAATTGGGAAAATATGGTGTGACATTTAAACCTATTACTCCGGATAGAACGTTAAAAGACCAGGATAAAATAACACTGGGAAATACAACCCTGACTTTGCTTCATCACCCGGGACATACAAAAGGTTCCTGCAGTTTTATTTTTGACACAAAAGACGAGAAGAGAAAGTATAGAGTTCTGATAGCTAATATGCCCTCTATTATTGTTGATAAGAAATTTTCTGAAGTTACAGCATATCCGAATATTCAGTCCGATTATGCTTATACCTTTGGTGCAATGAAAAAGCTTGATTTTGATCTTTGGGTAGCATCGCATGCAAGTCAGTTCGATCTGCATGAAAAACGTAAAGAAGGAGATCCGTACAACCCACAATTGTTTATGGATAAGCAAAACTATTTCCAAAGTCTTAATAATCTGGAGAAAAGCTATCTTGATAAAATTAAAAAAGATTCACAAGATAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41081","NCBI_taxonomy_name":"Elizabethkingia anophelis","NCBI_taxonomy_id":"1117645"}}}},"ARO_accession":"3005675","ARO_id":"44137","ARO_name":"GOB-26","CARD_short_name":"GOB-26","ARO_description":"GOB-26 is a GOB beta-lactamase.","ARO_category":{"41376":{"category_aro_accession":"3004212","category_aro_cvterm_id":"41376","category_aro_name":"GOB beta-lactamase","category_aro_description":"The GOB family of beta-lactamases have been discovered in the Elizabethkingia meningoseptica and are classified as subclass B3 beta-lactamase. They confer resistance to cephalosporins, penicillins, and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4640":{"model_id":"4640","model_name":"GOB-27","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7015":{"protein_sequence":{"accession":"WP_069213816.1","sequence":"MRNFAILFFLLITFSWKAQVVKEPENTNEEWSRSYEPFRIAGNLYYVGTYDLASYLIVTDKGNILINTGLAGSLPMIKENIKKLGFNYKDIKILLLTQAHYDHTGALKDLQTETGAKFYADSADADVLKTGGKSDYEMGKYGATFKPIKPDILLKDQDKIKLGNTTLTLLHHPGHTKGSCSFIFETKDENRNYKVLIANMPSVIVDRKFSEIKDYPNIQADYAYTFKAMKKLDFDLWVASHASQFDLHTKHKEGDLYNPQVFMDKANYFAFLNSLETDYLEKIKNDSQKK"},"dna_sequence":{"accession":"NG_067994.1","fmin":"100","fmax":"973","strand":"+","sequence":"ATGAGAAACTTTGCAATTTTATTTTTTTTACTGATCACTTTCAGCTGGAAAGCACAGGTTGTTAAAGAACCGGAAAATACAAATGAAGAATGGTCCCGATCATATGAGCCATTCAGAATTGCGGGTAACTTATACTATGTAGGAACTTACGATCTGGCATCTTATTTAATAGTTACCGATAAAGGAAATATTCTCATTAATACAGGATTGGCTGGTTCTCTTCCTATGATAAAAGAGAATATTAAAAAACTGGGATTCAATTATAAAGACATCAAAATTCTGCTTTTAACCCAGGCGCATTATGATCATACAGGTGCATTAAAAGATTTGCAAACAGAAACAGGTGCGAAATTTTATGCAGACAGTGCTGATGCTGATGTATTGAAAACGGGCGGTAAATCCGATTATGAAATGGGGAAATACGGGGCAACCTTTAAGCCGATTAAGCCTGATATCCTGTTGAAAGATCAGGATAAAATAAAACTGGGGAATACAACCTTAACTTTACTTCATCATCCGGGGCACACAAAAGGTTCATGCAGTTTTATATTTGAAACAAAGGATGAAAACAGAAATTACAAAGTGCTGATAGCCAATATGCCATCGGTTATAGTTGACCGTAAGTTTTCCGAAATAAAAGATTACCCTAATATTCAGGCCGATTATGCTTATACATTTAAAGCCATGAAAAAACTGGATTTTGATCTTTGGGTCGCTTCACATGCAAGTCAGTTTGATTTACATACAAAACATAAAGAGGGAGACCTTTATAACCCACAGGTATTTATGGATAAGGCCAATTATTTTGCATTCCTCAATAGCCTGGAAACAGATTATCTGGAAAAAATTAAAAACGACTCACAAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36960","NCBI_taxonomy_name":"Elizabethkingia meningoseptica","NCBI_taxonomy_id":"238"}}}},"ARO_accession":"3005676","ARO_id":"44138","ARO_name":"GOB-27","CARD_short_name":"GOB-27","ARO_description":"GOB-27 is a GOB beta-lactamase.","ARO_category":{"41376":{"category_aro_accession":"3004212","category_aro_cvterm_id":"41376","category_aro_name":"GOB beta-lactamase","category_aro_description":"The GOB family of beta-lactamases have been discovered in the Elizabethkingia meningoseptica and are classified as subclass B3 beta-lactamase. They confer resistance to cephalosporins, penicillins, and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4641":{"model_id":"4641","model_name":"GOB-28","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7016":{"protein_sequence":{"accession":"WP_087093762.1","sequence":"MRNFATLFFMFICLGLNAQVVKEPENMPKEWNQAYEPFRIAGNLYYVGTYDLASYLIVTDKGNILINTGTAESLPIIKANIQKLGFNYKGIKILLLTQAHYDHTGALQDFKTETAAKFYADKADADVLRTGGKSDYEMGKYGVTFKPVTPDNTLKDQDKITLGNITLTLLHHPGHTKGSCSFIFETKDEKRKYRVLIANMPSVIVDKKFSEVTAYPNIQSDYAYTFGVMKKLDFDIWVASHASQFDLHEKRKEGDPYNPQLFMDKQSYFQNLNDLEKSYLNKIKKDSQDK"},"dna_sequence":{"accession":"NG_068171.1","fmin":"100","fmax":"973","strand":"+","sequence":"ATGAGAAATTTTGCTACACTGTTTTTCATGTTCATTTGCTTGGGCTTGAATGCTCAGGTAGTAAAAGAACCTGAAAATATGCCCAAAGAATGGAACCAGGCTTATGAACCATTCAGAATTGCAGGTAATTTATATTACGTAGGAACCTATGATTTGGCTTCTTACCTTATTGTGACAGACAAAGGCAATATTCTCATTAATACAGGAACGGCAGAATCGCTTCCAATAATAAAAGCAAATATCCAAAAGCTCGGGTTTAATTATAAAGGCATTAAGATCTTGCTGCTTACTCAGGCTCACTACGACCATACAGGTGCATTACAGGATTTTAAAACAGAAACCGCTGCAAAATTCTATGCCGATAAAGCAGATGCTGATGTCCTGAGAACAGGGGGGAAGTCCGATTATGAAATGGGAAAATATGGTGTGACATTTAAACCTGTTACTCCGGATAATACATTGAAAGATCAGGATAAAATAACACTGGGAAATATAACCCTGACTTTGCTTCATCATCCCGGACATACAAAAGGTTCCTGTAGTTTTATTTTTGAAACAAAAGACGAGAAGAGAAAATATAGAGTTTTGATAGCTAATATGCCCTCCGTTATTGTTGATAAGAAATTTTCTGAAGTTACCGCATATCCAAATATTCAGTCCGATTATGCTTATACCTTTGGTGTTATGAAAAAGCTGGATTTTGATATTTGGGTGGCCTCCCATGCAAGTCAGTTCGATCTCCATGAAAAACGTAAAGAAGGAGATCCGTACAATCCGCAATTGTTTATGGATAAGCAAAGCTATTTCCAAAACCTTAATGATTTGGAAAAAAGCTATCTCAACAAAATAAAAAAAGATTCCCAAGATAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41081","NCBI_taxonomy_name":"Elizabethkingia anophelis","NCBI_taxonomy_id":"1117645"}}}},"ARO_accession":"3005677","ARO_id":"44139","ARO_name":"GOB-28","CARD_short_name":"GOB-28","ARO_description":"GOB-28 is a GOB beta-lactamase.","ARO_category":{"41376":{"category_aro_accession":"3004212","category_aro_cvterm_id":"41376","category_aro_name":"GOB beta-lactamase","category_aro_description":"The GOB family of beta-lactamases have been discovered in the Elizabethkingia meningoseptica and are classified as subclass B3 beta-lactamase. They confer resistance to cephalosporins, penicillins, and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4642":{"model_id":"4642","model_name":"GOB-29","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7017":{"protein_sequence":{"accession":"WP_078678126.1","sequence":"MRNFVTLFFLLVCLSLNAQVVKEPENMPKEWNQTYEPFRIAGNLYYVGTYDLASYLIVTDKGNILINTGTAESFPIIKGNIQKLGFNYKDIKILLLTQAHYDHTGALQDFKTETGAKFYADKADADVLRTGGKSDYELGKYGVTFKPVTPDKTLKDQDKITLGNTTLTLLHHPGHTKGSCSFIFETKDENRKYKILIANMPSIIVDKKFSEVTAYPGIQSDYAYTFKAMKNLDFDVWVASHASQFDLHTKRKEGDSYNPQLFMDKKNYFKRLERLENNYFEKIKEDSKDK"},"dna_sequence":{"accession":"NG_067995.1","fmin":"100","fmax":"973","strand":"+","sequence":"ATGAGAAATTTTGTTACACTATTTTTTCTGTTAGTTTGTTTGAGCTTGAATGCTCAGGTCGTAAAAGAACCTGAGAATATGCCAAAAGAATGGAACCAGACTTATGAACCATTCAGAATTGCAGGTAATTTATATTACGTAGGAACCTATGATTTGGCGTCCTACCTTATTGTGACAGACAAAGGCAATATTCTCATTAATACAGGAACGGCAGAATCATTTCCAATAATAAAAGGAAATATTCAAAAGCTGGGGTTTAATTATAAAGACATTAAGATCTTGCTGCTTACTCAGGCTCATTATGACCATACAGGCGCGTTACAGGATTTTAAAACGGAAACCGGTGCGAAATTTTATGCCGATAAAGCAGATGCTGATGTCCTGAGAACAGGCGGAAAATCTGATTATGAATTAGGTAAATATGGTGTGACATTTAAACCTGTTACCCCAGACAAAACATTGAAGGATCAGGATAAAATAACATTGGGAAATACAACCCTGACTTTGCTTCACCATCCGGGACATACAAAAGGTTCCTGCAGTTTTATTTTTGAAACAAAAGATGAAAACAGGAAATACAAGATTTTAATAGCTAATATGCCTTCCATTATTGTTGATAAGAAATTTTCTGAAGTTACAGCATATCCAGGTATTCAGTCCGATTACGCATATACTTTCAAAGCGATGAAGAATCTAGATTTTGATGTCTGGGTTGCCTCGCATGCAAGTCAGTTCGATTTGCACACCAAACGCAAAGAAGGTGACTCTTACAATCCACAGTTGTTTATGGATAAAAAGAATTATTTTAAAAGGCTCGAGCGTTTGGAAAATAATTATTTTGAAAAGATTAAAGAAGATTCAAAGGATAAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3005678","ARO_id":"44140","ARO_name":"GOB-29","CARD_short_name":"GOB-29","ARO_description":"GOB-29 is a GOB beta-lactamase.","ARO_category":{"41376":{"category_aro_accession":"3004212","category_aro_cvterm_id":"41376","category_aro_name":"GOB beta-lactamase","category_aro_description":"The GOB family of beta-lactamases have been discovered in the Elizabethkingia meningoseptica and are classified as subclass B3 beta-lactamase. They confer resistance to cephalosporins, penicillins, and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4643":{"model_id":"4643","model_name":"GOB-30","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7018":{"protein_sequence":{"accession":"WP_078676551.1","sequence":"MRNFATLFFMFICLGLNAQVVKEPENMPKEWNQAYEPFRIAGNLYYVGTYDLASYLIVTDKGNILINTGTAESFPIIKANIQKLGFNYKDIKILLLTQAHYDHTGALQDFKTETAAKFYVDKADVDVLRTGGKSDYEMGKYGVTFKPVTPDKTLKDQDKIKLGNITLTLLHHPGHTKGSCSFIFETKDEKRKYRVLIANMPSVIVDKKFSEVTAYPNIQSDYAYTFGVMKKLDFDIWVASHASQFDLHEKRKEGDPYNPQLFMDKQSYFQNLNDLEKSYLNKIKKDSQDK"},"dna_sequence":{"accession":"NG_067996.1","fmin":"100","fmax":"973","strand":"+","sequence":"ATGAGAAATTTTGCTACACTGTTTTTCATGTTCATTTGCTTGGGCTTGAATGCTCAGGTAGTAAAAGAACCTGAAAATATGCCCAAAGAATGGAATCAGGCTTATGAACCATTCAGAATTGCAGGTAATTTATATTACGTAGGAACCTATGATTTGGCTTCTTACCTTATTGTGACAGACAAAGGCAATATTCTCATTAATACAGGAACGGCAGAATCGTTTCCAATAATAAAAGCAAATATCCAAAAGCTCGGGTTTAATTATAAAGACATTAAGATCTTGCTGCTTACTCAGGCTCACTACGACCATACAGGTGCATTACAGGATTTTAAAACAGAAACCGCTGCAAAATTCTATGTCGATAAAGCAGATGTTGATGTCCTGAGAACAGGGGGGAAGTCCGATTATGAAATGGGAAAATATGGTGTGACATTTAAACCTGTTACTCCGGATAAAACATTGAAAGATCAGGATAAAATAAAACTGGGAAATATAACCCTGACTTTGCTTCATCATCCGGGACATACAAAAGGTTCCTGTAGTTTTATTTTTGAAACAAAAGACGAGAAGAGAAAATATAGAGTTTTGATAGCTAATATGCCCTCCGTTATTGTTGATAAGAAATTTTCTGAAGTTACCGCATATCCAAATATTCAGTCCGATTATGCTTATACCTTTGGTGTTATGAAAAAGCTGGATTTTGATATTTGGGTGGCCTCCCATGCAAGTCAGTTCGATCTCCATGAAAAACGTAAAGAAGGAGATCCGTACAATCCGCAATTGTTTATGGATAAGCAAAGCTATTTCCAAAACCTTAATGATTTGGAAAAAAGCTATCTCAACAAAATAAAAAAAGATTCACAAGATAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41081","NCBI_taxonomy_name":"Elizabethkingia anophelis","NCBI_taxonomy_id":"1117645"}}}},"ARO_accession":"3005679","ARO_id":"44141","ARO_name":"GOB-30","CARD_short_name":"GOB-30","ARO_description":"GOB-30 is a GOB beta-lactamase.","ARO_category":{"41376":{"category_aro_accession":"3004212","category_aro_cvterm_id":"41376","category_aro_name":"GOB beta-lactamase","category_aro_description":"The GOB family of beta-lactamases have been discovered in the Elizabethkingia meningoseptica and are classified as subclass B3 beta-lactamase. They confer resistance to cephalosporins, penicillins, and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4644":{"model_id":"4644","model_name":"GOB-31","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7019":{"protein_sequence":{"accession":"WP_078703439.1","sequence":"MRNFVTLFFLLVCLSLNAQVVKEPENMPKEWNQTYEPFRIAGNLYYVGTYDLASYLIVTDKGNILINTGTAESFPIIKGNIQKLGFNYKDIKILLLTQAHYDHTGALQDFKTETGAKFYADKADADVLRTGGKSDYELGKYGVTFKPVTPDKTLKDQDKITLGNTTLTLLHHPGHTKGSCSFIFETKDKNRKYKVLIANMPSIIVDKKFSEVTAYPCIQSDYAYTFKAMKNLDFDVWVASHASQFDLHTKRKEGDSYNPQLFMDKENYFKRLERLENNYFEKIKEDSKDK"},"dna_sequence":{"accession":"NG_067997.1","fmin":"100","fmax":"973","strand":"+","sequence":"ATGAGAAATTTTGTTACACTATTTTTTCTGTTAGTTTGTTTGAGCTTGAATGCTCAGGTCGTAAAAGAACCTGAGAATATGCCCAAAGAATGGAACCAGACTTATGAGCCATTCAGAATTGCAGGTAATTTATATTACGTAGGAACCTATGATTTGGCGTCCTACCTTATTGTGACAGACAAAGGCAATATTCTCATTAATACAGGAACGGCAGAATCATTTCCAATAATAAAAGGAAATATTCAAAAGCTGGGGTTTAATTATAAAGACATTAAGATCTTGCTGCTTACTCAGGCTCATTATGACCATACAGGCGCGTTACAGGATTTTAAAACGGAAACCGGTGCGAAATTTTATGCCGATAAAGCAGATGCTGATGTCCTGAGAACAGGCGGAAAATCTGATTATGAATTAGGTAAATATGGTGTGACATTTAAACCTGTTACCCCAGACAAAACATTGAAGGATCAGGATAAAATAACATTGGGAAATACAACCCTGACTTTGCTTCACCATCCGGGACATACAAAAGGTTCCTGCAGTTTTATTTTTGAAACAAAAGATAAAAACAGAAAATACAAGGTTTTAATAGCTAATATGCCTTCCATTATTGTTGATAAGAAATTTTCTGAAGTTACAGCATATCCATGTATTCAGTCCGATTACGCATATACTTTCAAAGCGATGAAGAATCTGGATTTTGATGTCTGGGTTGCCTCGCATGCAAGTCAGTTCGATTTGCATACCAAACGCAAAGAAGGTGACTCTTACAATCCACAGTTGTTTATGGATAAAGAGAATTATTTTAAAAGGCTTGAGCGTTTGGAAAATAATTATTTTGAAAAGATTAAAGAAGATTCAAAGGATAAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3005680","ARO_id":"44142","ARO_name":"GOB-31","CARD_short_name":"GOB-31","ARO_description":"GOB-31 is a GOB beta-lactamase.","ARO_category":{"41376":{"category_aro_accession":"3004212","category_aro_cvterm_id":"41376","category_aro_name":"GOB beta-lactamase","category_aro_description":"The GOB family of beta-lactamases have been discovered in the Elizabethkingia meningoseptica and are classified as subclass B3 beta-lactamase. They confer resistance to cephalosporins, penicillins, and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4645":{"model_id":"4645","model_name":"GOB-32","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7020":{"protein_sequence":{"accession":"WP_065081961.1","sequence":"MRNFATLFFLSVCLSLNLNAQIVKEPENMPKEWNQAYEPFRIAGNLYYVGTYDLASYLIVTDKGNILINTGTAESLPIIKDNIQKLGFNYKDIKILLLTQAHYDHTGALEDFKTETGAKFYADKADADVLRTGGKSDYELGKYGVTFKPITPDRTLKDQDKITLGNTTLTLLHHPGHTKGSCSFIFETKDEKRKYRVLIANMPSIIVDKKFSEVTAYPNIQSDYAYTFGAMKKLDFDLWVASHASQFDLHEKRKEGDPYNPQLFMDKQSYFQNLNDLEKSYLDKIKKDSQDK"},"dna_sequence":{"accession":"NG_067998.1","fmin":"100","fmax":"979","strand":"+","sequence":"ATGAGAAATTTTGCTACACTGTTTTTTCTGTCAGTTTGTTTGAGTTTGAATTTGAATGCTCAGATAGTAAAAGAACCTGAGAATATGCCTAAAGAATGGAATCAGGCTTATGAACCATTCAGAATTGCAGGTAACCTGTATTACGTAGGAACTTATGATTTGGCTTCTTACCTTATTGTGACGGACAAAGGCAATATTCTCATTAATACAGGAACGGCAGAATCGCTTCCAATAATAAAAGACAATATTCAAAAGCTGGGGTTTAATTATAAAGACATTAAGATCTTGCTGCTTACCCAGGCTCATTATGACCATACAGGTGCGTTAGAGGATTTTAAAACAGAAACCGGTGCAAAATTCTATGCAGATAAAGCAGATGCTGATGTCCTGAGAACAGGGGGTAAGTCCGATTATGAATTGGGAAAATATGGTGTGACATTTAAACCTATTACTCCGGATAGAACGTTAAAAGATCAGGATAAAATAACACTGGGAAATACAACCCTGACTTTGCTTCATCACCCGGGACATACAAAAGGTTCCTGCAGTTTTATTTTTGAAACAAAAGATGAGAAGAGAAAGTATAGAGTTCTGATAGCTAATATGCCCTCTATTATTGTTGATAAGAAATTTTCTGAAGTTACAGCATATCCGAATATTCAGTCCGATTATGCTTATACCTTTGGTGCAATGAAAAAGCTTGATTTTGACCTTTGGGTGGCATCGCATGCAAGTCAGTTCGATCTGCATGAAAAACGTAAAGAAGGAGATCCGTACAATCCACAATTGTTTATGGATAAGCAAAGCTATTTCCAAAACCTTAATGATTTGGAGAAAAGCTATCTCGACAAAATAAAAAAAGATTCACAAGATAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3005681","ARO_id":"44143","ARO_name":"GOB-32","CARD_short_name":"GOB-32","ARO_description":"GOB-32 is a GOB beta-lactamase.","ARO_category":{"41376":{"category_aro_accession":"3004212","category_aro_cvterm_id":"41376","category_aro_name":"GOB beta-lactamase","category_aro_description":"The GOB family of beta-lactamases have been discovered in the Elizabethkingia meningoseptica and are classified as subclass B3 beta-lactamase. They confer resistance to cephalosporins, penicillins, and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4646":{"model_id":"4646","model_name":"GOB-33","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7021":{"protein_sequence":{"accession":"WP_078797000.1","sequence":"MKRITTLLFLLVCFGWNAQVVKEPENTPKEWSQNYEPFRIAGNLYYVGTYDLASYLIVTDKGNILINTGLAGSLSTIKENIAKLGFNYKDIKILLLTQAHYDHTGALMDFKTETDAKFYADAADADVLRTGGQSDYEMGKYGATFKPIIPDRTLKNLDKIKLGNTTLTMLHHPGHTKGSCSFVFDTNDGKRKYRVLIANMPSIIVDNKFSEVTEYPNIQSDYAYTFNAMKKLDFDIWVASHASQFDLHEKRKEGEPYNPKLFMDKQNYFQSLNNLEKSYLDKIKKDLQDK"},"dna_sequence":{"accession":"NG_067999.1","fmin":"100","fmax":"973","strand":"+","sequence":"ATGAAAAGAATAACGACTTTACTTTTTCTGTTAGTATGTTTTGGATGGAATGCTCAGGTTGTAAAAGAGCCTGAAAATACACCAAAAGAATGGTCTCAGAATTATGAACCATTCAGGATAGCAGGTAACCTGTATTACGTAGGAACTTATGATCTGGCTTCTTACCTAATCGTTACAGATAAAGGAAATATTCTGATCAATACAGGACTAGCTGGCTCTCTTTCTACAATAAAAGAGAACATTGCTAAATTAGGATTCAATTATAAAGACATCAAGATTCTGCTTCTCACACAGGCTCATTATGACCATACAGGTGCGTTAATGGACTTTAAAACAGAAACAGATGCGAAATTTTATGCAGATGCTGCAGATGCAGATGTTCTGAGAACAGGCGGGCAGTCTGATTATGAAATGGGAAAATATGGTGCAACTTTTAAACCTATTATTCCGGATCGTACGTTAAAAAATCTGGATAAAATAAAATTAGGGAATACAACACTTACGATGCTCCATCATCCAGGACATACAAAAGGTTCCTGTAGTTTTGTATTTGATACAAACGATGGGAAAAGAAAATACAGAGTGCTTATAGCCAATATGCCTTCCATTATTGTTGATAATAAATTCTCTGAAGTTACAGAATATCCGAATATTCAGTCCGATTATGCTTATACCTTTAATGCGATGAAAAAGCTGGATTTTGATATTTGGGTAGCATCGCATGCAAGCCAGTTCGATCTGCATGAAAAACGCAAAGAAGGAGAGCCGTACAACCCAAAATTGTTTATGGATAAGCAAAACTATTTCCAAAGCCTTAATAATCTGGAGAAAAGCTATCTTGATAAAATTAAAAAAGATTTACAAGATAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3005682","ARO_id":"44144","ARO_name":"GOB-33","CARD_short_name":"GOB-33","ARO_description":"GOB-33 is a GOB beta-lactamase.","ARO_category":{"41376":{"category_aro_accession":"3004212","category_aro_cvterm_id":"41376","category_aro_name":"GOB beta-lactamase","category_aro_description":"The GOB family of beta-lactamases have been discovered in the Elizabethkingia meningoseptica and are classified as subclass B3 beta-lactamase. They confer resistance to cephalosporins, penicillins, and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4647":{"model_id":"4647","model_name":"GOB-34","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7022":{"protein_sequence":{"accession":"WP_107809858.1","sequence":"MKRITTLLFLLVCFGWNAQVVKEPENTPKEWSQNYEPFRIAGNLYYVGTYDLASYLIVTDKGNILINTGLTGSLSTIKENIAKLGFNYKDIKILLLTQAHYDHTGALMDFKTETGAKFYADAADADVLRTGGQSDYEMGKYGATFKPIIPDRTLKNLDKIKLGNTTLTMLHHPGHTKGSCSFVFNTRDGKRKYRVLIANMPSVIVDNKFSEVTAYPNIQSDYAYTFKAMKKLDFDIWVASHASQFDLHEKRKEGAPYNPQLFMDKQSYFQNLNDLEKSYLDKIQKDSQDK"},"dna_sequence":{"accession":"NG_068000.1","fmin":"100","fmax":"973","strand":"+","sequence":"ATGAAAAGAATAACGACTTTACTTTTTCTACTGGTTTGTTTTGGCTGGAATGCTCAGGTTGTAAAAGAACCTGAAAATACACCAAAAGAATGGTCTCAGAATTATGAACCATTCAGAATTGCAGGTAATCTGTATTACGTAGGAACTTATGATTTGGCTTCTTACCTAATCGTTACAGATAAAGGAAATATTCTGATCAATACAGGACTAACAGGCTCTCTTTCTACAATAAAAGAGAACATTGCTAAATTAGGATTCAATTATAAAGATATCAAGATTCTGCTTCTCACACAGGCTCATTATGACCATACAGGTGCATTAATGGACTTTAAAACAGAAACAGGTGCAAAATTTTATGCAGATGCTGCAGATGCAGATGTTCTGAGAACAGGCGGGCAGTCTGATTATGAAATGGGAAAATATGGTGCAACTTTTAAACCTATTATCCCGGATCGAACGTTGAAAAATCTGGATAAAATAAAATTAGGAAATACAACGCTTACGATGCTCCATCATCCTGGGCATACAAAAGGTTCCTGTAGTTTTGTGTTTAATACAAGAGATGGAAAAAGAAAATACAGAGTGCTTATAGCCAATATGCCTTCCGTAATTGTTGATAATAAATTTTCTGAAGTTACGGCATATCCAAATATTCAGTCCGATTATGCTTACACCTTTAAAGCCATGAAAAAGCTGGATTTTGATATTTGGGTAGCATCGCATGCAAGTCAGTTCGATCTGCATGAAAAACGTAAGGAAGGGGCTCCCTACAATCCACAATTGTTTATGGATAAACAAAGCTATTTCCAAAACCTTAATGATCTGGAGAAAAGCTATCTCGACAAAATTCAAAAAGATTCACAGGATAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3005683","ARO_id":"44145","ARO_name":"GOB-34","CARD_short_name":"GOB-34","ARO_description":"GOB-34 is a GOB beta-lactamase.","ARO_category":{"41376":{"category_aro_accession":"3004212","category_aro_cvterm_id":"41376","category_aro_name":"GOB beta-lactamase","category_aro_description":"The GOB family of beta-lactamases have been discovered in the Elizabethkingia meningoseptica and are classified as subclass B3 beta-lactamase. They confer resistance to cephalosporins, penicillins, and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4648":{"model_id":"4648","model_name":"GOB-35","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7023":{"protein_sequence":{"accession":"WP_078779188.1","sequence":"MKRITTLLFLLVCFGWNAQTVKEPENTPKEWSQNYEPFRIAGNLYYVGTYDLASYLIVTDKGNILINTGLAGSLSTIKENIAKLGFNYKDIKILLLTQAHYDHTGALMDFKTETGAKFYADAADADVLRTGGQSDYEMGKYGATFKPIIPDRTLKNLDKIKLGNTTLTMLHHPGHTKGSCSFVFDTNDGKRKYRVLIANMPSIIVDNKFSEVTAYPNIQSDYAYTFNAMKKLDFDIWVASHASQFDLHEKRKEGEPYNPQLFMDKQNYFQNLNNLEQSYRDKIKKDSQDK"},"dna_sequence":{"accession":"NG_068001.1","fmin":"100","fmax":"973","strand":"+","sequence":"ATGAAAAGAATAACGACTTTACTTTTTCTGTTAGTATGTTTTGGCTGGAATGCTCAGACTGTTAAAGAACCTGAAAATACACCAAAAGAATGGTCTCAAAATTATGAACCATTCAGGATAGCAGGTAACCTGTATTACGTAGGAACTTATGATTTGGCTTCTTACCTAATCGTTACAGATAAAGGAAATATTCTGATCAATACAGGACTAGCAGGCTCTCTTTCTACAATAAAAGAGAACATTGCTAAATTAGGATTCAATTATAAAGATATCAAGATTCTGCTTCTCACACAGGCTCATTATGACCATACAGGTGCGTTAATGGACTTTAAAACAGAAACGGGTGCGAAATTTTATGCAGATGCTGCAGATGCAGATGTTCTGAGAACAGGCGGGCAGTCTGATTATGAAATGGGAAAATATGGTGCAACTTTTAAACCCATTATCCCAGATCGTACGTTAAAAAATCTGGATAAAATAAAATTAGGGAATACAACACTTACGATGCTACATCATCCTGGGCATACAAAAGGTTCTTGTAGTTTTGTATTTGATACAAACGATGGGAAAAGAAAATACAGAGTGCTTATAGCCAATATGCCTTCCATTATTGTTGATAATAAATTCTCTGAAGTTACGGCATATCCGAATATTCAGTCCGATTATGCTTATACCTTTAATGCGATGAAAAAGCTGGATTTTGATATTTGGGTAGCATCGCATGCAAGTCAGTTCGATCTGCATGAAAAACGCAAAGAAGGAGAGCCATACAACCCACAATTGTTTATGGATAAGCAAAACTATTTCCAAAACCTTAATAATCTGGAGCAAAGCTATCGCGATAAAATTAAAAAAGATTCACAAGATAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3005684","ARO_id":"44146","ARO_name":"GOB-35","CARD_short_name":"GOB-35","ARO_description":"GOB-35 is a GOB beta-lactamase.","ARO_category":{"41376":{"category_aro_accession":"3004212","category_aro_cvterm_id":"41376","category_aro_name":"GOB beta-lactamase","category_aro_description":"The GOB family of beta-lactamases have been discovered in the Elizabethkingia meningoseptica and are classified as subclass B3 beta-lactamase. They confer resistance to cephalosporins, penicillins, and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4649":{"model_id":"4649","model_name":"GOB-36","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7024":{"protein_sequence":{"accession":"WP_078722646.1","sequence":"MKRITTLLFLLVCFGWNAQTVKEPENTPKEWSQNYEPFRIAGNLYYVGTYDLASYLIVTDKGNILINTGLAGSLSTIKENIAKLEFNYKDIKILLLTQAHYDHTGALMDFKTETGAKFYADAADADVLRTGGQSDYEMGKYGATFKPIIPDRTLKNLDKIKLGNTTLTMLHHPGHTKGSCSFVFDTNDGKRKYRVLIANMPSIIIDNKFSEVTAYPNIQSDYAYTFNAMKKLDFDIWVASHASQFDLHEKRKEREPYNPQLFMDKQNYFQSLNNLEKSYLDKIKKDSQDK"},"dna_sequence":{"accession":"NG_068002.1","fmin":"100","fmax":"973","strand":"+","sequence":"ATGAAAAGAATAACGACTTTACTTTTTCTGTTAGTATGTTTTGGCTGGAATGCTCAGACTGTTAAAGAACCTGAAAATACACCAAAAGAATGGTCTCAAAATTATGAACCATTCAGGATAGCAGGTAACCTGTATTACGTAGGAACTTATGATCTGGCTTCTTACCTAATCGTTACAGATAAAGGAAATATTCTAATCAATACAGGACTAGCAGGCTCTCTTTCTACAATAAAAGAGAACATTGCTAAATTAGAATTCAATTATAAAGATATCAAGATTCTGCTTCTCACACAGGCTCATTATGACCATACAGGTGCGTTAATGGACTTTAAAACAGAAACAGGTGCAAAATTTTATGCAGATGCTGCAGATGCAGATGTTCTGAGAACAGGCGGGCAGTCTGATTATGAAATGGGAAAATATGGTGCAACTTTTAAACCTATTATCCCGGATCGTACGTTAAAAAATCTGGATAAAATAAAATTAGGAAATACAACACTTACGATGCTCCATCATCCTGGGCATACAAAAGGTTCCTGTAGTTTTGTATTTGATACAAACGATGGGAAAAGAAAATACAGAGTGCTTATAGCCAATATGCCTTCCATTATTATTGATAATAAATTCTCTGAAGTTACAGCATATCCGAATATTCAGTCCGATTATGCTTATACCTTTAATGCGATGAAAAAGCTGGACTTTGATATTTGGGTAGCATCGCATGCAAGTCAGTTCGACCTGCATGAAAAACGCAAAGAAAGAGAGCCGTACAACCCACAATTGTTTATGGATAAGCAAAACTATTTCCAAAGCCTTAATAATCTGGAGAAAAGCTATCTTGATAAAATTAAAAAAGATTCACAAGATAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3005685","ARO_id":"44147","ARO_name":"GOB-36","CARD_short_name":"GOB-36","ARO_description":"GOB-36 is a GOB beta-lactamase.","ARO_category":{"41376":{"category_aro_accession":"3004212","category_aro_cvterm_id":"41376","category_aro_name":"GOB beta-lactamase","category_aro_description":"The GOB family of beta-lactamases have been discovered in the Elizabethkingia meningoseptica and are classified as subclass B3 beta-lactamase. They confer resistance to cephalosporins, penicillins, and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4650":{"model_id":"4650","model_name":"GOB-37","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7025":{"protein_sequence":{"accession":"WP_059323095.1","sequence":"MKRITTLLFLLVCFGWNAQTVKEPENTPKEWSQNYEPFRIAGNLYYVGTYDLASYLIVTDKGNILINTGLAGSLSTIKENIAKLGFNYKDIKILLLTQAHYDHTGALMDFKTETGAKFYADAADADVLRTGGQSDYEMGKYGATFKPIIPDRTLKNLDKIKLGNTTLTMLHHPGHTKGSCSFVFDTNDGKRKYRVLIANMPSIIVDNKFSEVTAYPNIQSDYAYTFNAMKKLDFDIWVASHASQFDLHEKRKGGEPYNPQLFMDKQNYFQSLNNLEKSYLDKIKKDSQDK"},"dna_sequence":{"accession":"NG_068003.1","fmin":"100","fmax":"973","strand":"+","sequence":"ATGAAAAGAATAACGACTTTACTTTTTCTGTTAGTATGTTTTGGCTGGAATGCTCAGACTGTTAAAGAACCTGAAAATACACCAAAAGAATGGTCTCAAAATTATGAACCATTCAGGATAGCAGGTAACCTGTATTACGTAGGAACTTATGATTTGGCTTCTTACCTAATCGTTACAGATAAAGGAAATATTCTGATCAATACAGGACTAGCAGGCTCTCTTTCTACAATAAAAGAGAACATTGCTAAATTAGGATTCAATTATAAAGACATCAAGATTCTGCTTCTCACACAGGCTCATTATGACCATACAGGTGCGTTAATGGACTTTAAAACAGAAACGGGTGCGAAATTTTATGCAGATGCTGCAGATGCAGATGTTCTGAGAACAGGCGGGCAGTCTGATTATGAAATGGGAAAATATGGTGCAACTTTTAAACCTATTATCCCGGATCGTACGTTAAAAAATCTGGATAAAATAAAATTAGGAAATACAACACTTACTATGCTCCATCATCCTGGACATACAAAAGGTTCCTGTAGTTTTGTATTTGATACAAACGATGGGAAAAGAAAATACAGAGTGCTTATAGCCAATATGCCTTCCATTATTGTTGATAATAAATTCTCTGAAGTTACAGCATATCCGAATATTCAGTCCGATTATGCTTATACCTTTAATGCGATGAAAAAGCTGGACTTTGATATTTGGGTAGCATCACATGCAAGTCAGTTCGATCTGCATGAAAAACGCAAAGGAGGAGAGCCGTACAACCCACAATTGTTTATGGATAAGCAAAACTATTTCCAAAGCCTTAATAATCTGGAGAAAAGCTATCTTGATAAAATTAAAAAAGATTCACAAGATAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3005686","ARO_id":"44148","ARO_name":"GOB-37","CARD_short_name":"GOB-37","ARO_description":"GOB-37 is a GOB beta-lactamase.","ARO_category":{"41376":{"category_aro_accession":"3004212","category_aro_cvterm_id":"41376","category_aro_name":"GOB beta-lactamase","category_aro_description":"The GOB family of beta-lactamases have been discovered in the Elizabethkingia meningoseptica and are classified as subclass B3 beta-lactamase. They confer resistance to cephalosporins, penicillins, and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4651":{"model_id":"4651","model_name":"GOB-38","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7026":{"protein_sequence":{"accession":"WP_058879139.1","sequence":"MRNFVILFFMFICLGLNAQVVKEPENMPKEWNQTYEPFRIAGNLYYVGTYDLASYLIVTDKGNILINTGTAESLPIIKANIQKLGFNYKDIKILLLTQAHYDHTGALQDLKTETGAKFYADKEDADVLRTGGKSDYEMGKYGVTFKPVTPDKTLKDQDKITLGNTILTLLHHPGHTKGSCSFIFETKDEKRKYRVLIANMPSVIVDKKFSEVTAYPNIQSDYAYTFKAMKNLDFDLWVASHASQFDLHEKRKEGDPYNPQLFMDKQSYFQNLNDLEKSYLDKIKKDSQDK"},"dna_sequence":{"accession":"NG_068004.1","fmin":"100","fmax":"973","strand":"+","sequence":"ATGAGAAATTTTGTTATACTGTTTTTCATGTTCATTTGCTTGGGCTTGAATGCTCAGGTAGTAAAAGAACCTGAAAATATGCCCAAAGAATGGAACCAGACTTATGAACCCTTCAGAATTGCAGGTAATTTATATTACGTAGGAACCTATGATTTGGCTTCTTACCTTATTGTGACAGACAAAGGCAATATTCTCATTAATACAGGAACGGCAGAATCGCTTCCAATAATAAAAGCAAATATCCAAAAGCTCGGGTTTAATTATAAAGACATTAAGATCTTGCTGCTTACTCAGGCTCACTACGACCATACAGGTGCATTACAAGATCTTAAAACAGAAACCGGTGCAAAATTCTATGCCGATAAAGAAGATGCTGATGTCCTGAGAACAGGGGGGAAGTCCGATTATGAAATGGGAAAATATGGGGTGACATTTAAACCTGTTACTCCGGATAAAACATTGAAAGATCAGGATAAAATAACGCTGGGAAATACAATCCTGACTTTGCTTCATCATCCGGGACATACAAAAGGTTCCTGTAGTTTTATTTTTGAAACAAAAGACGAGAAGAGAAAATATAGAGTTTTGATAGCTAATATGCCCTCCGTTATTGTTGATAAGAAATTTTCTGAAGTTACCGCATATCCAAATATTCAGTCCGATTACGCATATACTTTCAAAGCAATGAAGAATCTAGATTTTGACCTTTGGGTGGCCTCCCATGCAAGTCAGTTCGATCTCCATGAAAAACGTAAAGAAGGAGATCCGTACAATCCGCAATTGTTTATGGATAAGCAAAGCTATTTCCAAAACCTTAATGATTTGGAAAAAAGCTATCTCGACAAAATAAAAAAAGATTCACAAGATAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41081","NCBI_taxonomy_name":"Elizabethkingia anophelis","NCBI_taxonomy_id":"1117645"}}}},"ARO_accession":"3005687","ARO_id":"44149","ARO_name":"GOB-38","CARD_short_name":"GOB-38","ARO_description":"GOB-38 is a GOB beta-lactamase.","ARO_category":{"41376":{"category_aro_accession":"3004212","category_aro_cvterm_id":"41376","category_aro_name":"GOB beta-lactamase","category_aro_description":"The GOB family of beta-lactamases have been discovered in the Elizabethkingia meningoseptica and are classified as subclass B3 beta-lactamase. They confer resistance to cephalosporins, penicillins, and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4652":{"model_id":"4652","model_name":"GOB-39","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7027":{"protein_sequence":{"accession":"WP_031257659.1","sequence":"MRNFATLFFMFVCLGLNAQVVKEPENMPKEWNQTYEPFRIAGNLYYVGTYDLASYLIVTDKGNILINTGTAESLPIIKANIQKLGFNYKDIKILLLTQAHYDHTGALQDLKTETAAKFYADKADADVLRTGGNSDYEMGKYGVTFKPVTLDKTLKDQDKIKLGNTILTLLHHPGHTKGSCSFIFETKDEKRKYRVLIANMPSVIVDKKFSEVTAYPNIQSDYAYTFKAMKNLDFDLWVASHASQFDLHEKRKEGDPYNPQLFMDKQSYFQNLNDLEKSYLDKIKKDSQDK"},"dna_sequence":{"accession":"NG_068005.1","fmin":"100","fmax":"973","strand":"+","sequence":"ATGAGAAATTTTGCTACACTGTTTTTCATGTTCGTTTGCTTGGGCTTGAATGCTCAGGTAGTAAAAGAACCTGAAAATATGCCCAAAGAATGGAACCAGACTTATGAACCCTTCAGAATTGCAGGTAATTTATATTACGTAGGAACCTATGATTTGGCTTCTTACCTTATTGTGACAGACAAAGGCAATATTCTCATTAATACAGGAACGGCAGAATCGCTTCCAATAATAAAAGCAAATATCCAAAAGCTCGGGTTTAATTATAAAGACATTAAGATCTTGCTGCTTACTCAGGCTCACTACGACCATACAGGTGCATTACAAGATCTTAAAACAGAAACCGCTGCAAAATTCTATGCCGATAAAGCAGATGCTGATGTCCTGAGAACAGGGGGAAATTCCGATTATGAAATGGGAAAATATGGTGTGACATTTAAACCTGTTACTCTGGATAAAACATTGAAAGATCAGGATAAAATAAAACTGGGAAATACAATCCTGACTTTGCTTCATCATCCGGGACATACAAAAGGTTCCTGTAGTTTTATTTTTGAAACAAAAGACGAGAAGAGAAAATATAGAGTTTTGATAGCTAATATGCCCTCCGTTATTGTTGATAAGAAATTTTCTGAAGTTACCGCATATCCAAATATTCAGTCCGATTATGCATATACTTTCAAAGCAATGAAGAATCTAGATTTTGACCTTTGGGTGGCATCACATGCAAGTCAGTTCGATCTGCATGAAAAACGTAAAGAAGGAGATCCGTACAATCCGCAATTGTTTATGGATAAGCAAAGCTATTTCCAAAACCTTAATGATTTGGAAAAAAGCTATCTCGACAAAATAAAAAAAGATTCACAAGATAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41081","NCBI_taxonomy_name":"Elizabethkingia anophelis","NCBI_taxonomy_id":"1117645"}}}},"ARO_accession":"3005688","ARO_id":"44150","ARO_name":"GOB-39","CARD_short_name":"GOB-39","ARO_description":"GOB-39 is a GOB beta-lactamase.","ARO_category":{"41376":{"category_aro_accession":"3004212","category_aro_cvterm_id":"41376","category_aro_name":"GOB beta-lactamase","category_aro_description":"The GOB family of beta-lactamases have been discovered in the Elizabethkingia meningoseptica and are classified as subclass B3 beta-lactamase. They confer resistance to cephalosporins, penicillins, and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4653":{"model_id":"4653","model_name":"GOB-40","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7028":{"protein_sequence":{"accession":"WP_034845394.1","sequence":"MRNFATLFFMFICLGLNAQVVKEPENMPKEWNQAYEPFRIAGNLYYVGTYDLASYLIVTDKGNILINTGTAESFSIIKANIQKLGFNYKDIKILLLTQAHYDHTGALQDFKTETAAKFYADKADVDVLRTGGKSDYEMGKYGVTFKPVTPDKTLKDQDKIKLGNITLTLLHHPGHTKGSCSFIFETKDEKRKYRVLIANMPSVIVDKKFSEVTAYPNIQSDYAYTFGVMKKLDFDIWVASHASQFDLHEKRKEGDPYNPQLFMDKQSYFQNLNDLEKSYLNKIKKDSQDK"},"dna_sequence":{"accession":"NG_068006.1","fmin":"100","fmax":"973","strand":"+","sequence":"ATGAGAAATTTTGCTACACTGTTTTTCATGTTCATTTGCTTGGGCTTGAATGCTCAGGTAGTAAAAGAACCTGAAAATATGCCCAAAGAATGGAACCAGGCTTATGAACCATTCAGAATTGCAGGTAATTTATATTACGTAGGAACCTATGATTTGGCTTCTTACCTTATTGTGACAGACAAAGGCAATATTCTCATTAATACAGGAACGGCAGAATCGTTTTCAATAATAAAAGCAAATATCCAAAAGCTCGGGTTTAATTATAAAGACATTAAGATCTTGCTGCTTACTCAGGCTCACTACGACCATACAGGTGCATTACAGGATTTTAAAACAGAAACCGCTGCAAAATTCTATGCCGATAAAGCAGATGTTGATGTCCTGAGAACAGGGGGGAAGTCCGATTATGAAATGGGAAAATATGGTGTGACATTTAAACCTGTTACTCCGGATAAAACATTGAAAGATCAGGATAAAATAAAACTGGGAAATATAACCCTGACTTTGCTTCATCATCCGGGACATACAAAAGGTTCCTGTAGTTTTATTTTTGAAACAAAAGACGAGAAGAGAAAATATAGAGTTTTGATAGCTAATATGCCCTCCGTTATTGTTGATAAGAAATTTTCTGAAGTTACCGCATATCCAAATATTCAGTCCGATTATGCTTATACCTTTGGTGTTATGAAAAAGCTGGATTTTGATATTTGGGTGGCCTCCCATGCAAGTCAGTTCGATCTCCATGAAAAACGTAAAGAAGGAGATCCGTACAATCCGCAATTGTTTATGGATAAGCAAAGCTATTTCCAAAACCTTAATGATTTGGAAAAAAGCTATCTCAACAAAATAAAAAAAGATTCACAAGATAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41081","NCBI_taxonomy_name":"Elizabethkingia anophelis","NCBI_taxonomy_id":"1117645"}}}},"ARO_accession":"3005689","ARO_id":"44151","ARO_name":"GOB-40","CARD_short_name":"GOB-40","ARO_description":"GOB-40 is a GOB beta-lactamase.","ARO_category":{"41376":{"category_aro_accession":"3004212","category_aro_cvterm_id":"41376","category_aro_name":"GOB beta-lactamase","category_aro_description":"The GOB family of beta-lactamases have been discovered in the Elizabethkingia meningoseptica and are classified as subclass B3 beta-lactamase. They confer resistance to cephalosporins, penicillins, and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4654":{"model_id":"4654","model_name":"GOB-41","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7029":{"protein_sequence":{"accession":"WP_078395323.1","sequence":"MRNFATLFFMFICLGLNAQVVKEPENMPKEWNQAYEPFRIAGNLYYVGTYDLASYLIVTDKGNILINTGTAESLPIIKANIQKLGFNYKDIKILLLTQAHYDHTGALQDFKTETAAKFYADKADADVLRTGGKSDYEMGKYGVTFKPVTPDNTLKDQDKITLGNITLTLLHHPGHTKGSCSFIFETKDEKRKYRVLIANMPSVIVDKKFSEVTAYPNIQSDYAYTFGVMKKLDFDIWVASHASQFDLHEKRKEGDPYNPQLFMDKQSYFQNLNDLEKSYLNKIKKDSQDK"},"dna_sequence":{"accession":"NG_068007.1","fmin":"100","fmax":"973","strand":"+","sequence":"ATGAGAAATTTTGCTACACTGTTTTTCATGTTCATTTGCTTGGGCTTGAATGCTCAGGTAGTAAAAGAACCTGAAAATATGCCCAAAGAATGGAACCAGGCTTATGAACCATTCAGAATTGCAGGTAATTTATATTACGTAGGAACCTATGATTTGGCTTCTTACCTTATTGTGACAGACAAAGGCAATATTCTCATTAATACAGGAACGGCAGAATCGCTTCCAATAATAAAAGCAAATATCCAAAAGCTCGGGTTTAATTATAAAGACATTAAGATCTTGCTGCTTACTCAGGCTCACTACGACCATACAGGTGCATTACAGGATTTTAAAACAGAAACCGCTGCAAAATTCTATGCCGATAAAGCAGATGCTGATGTCCTGAGAACAGGGGGGAAGTCCGATTATGAAATGGGAAAATATGGTGTGACATTTAAACCTGTTACTCCGGATAATACATTGAAAGATCAGGATAAAATAACACTGGGAAATATAACCCTGACTTTGCTTCATCATCCCGGACATACAAAAGGTTCCTGTAGTTTTATTTTTGAAACAAAAGACGAGAAGAGAAAATATAGAGTTTTGATAGCTAATATGCCCTCCGTTATTGTTGATAAGAAATTTTCTGAAGTTACCGCATATCCAAATATTCAGTCCGATTATGCTTATACCTTTGGTGTTATGAAAAAGCTGGATTTTGATATTTGGGTGGCCTCCCATGCAAGTCAGTTCGATCTCCATGAAAAACGTAAAGAAGGAGATCCGTACAATCCGCAATTGTTTATGGATAAGCAAAGCTATTTCCAAAACCTTAATGATTTGGAAAAAAGCTATCTCAACAAAATAAAAAAAGATTCCCAAGATAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41081","NCBI_taxonomy_name":"Elizabethkingia anophelis","NCBI_taxonomy_id":"1117645"}}}},"ARO_accession":"3005690","ARO_id":"44152","ARO_name":"GOB-41","CARD_short_name":"GOB-41","ARO_description":"GOB-41 is a GOB beta-lactamase.","ARO_category":{"41376":{"category_aro_accession":"3004212","category_aro_cvterm_id":"41376","category_aro_name":"GOB beta-lactamase","category_aro_description":"The GOB family of beta-lactamases have been discovered in the Elizabethkingia meningoseptica and are classified as subclass B3 beta-lactamase. They confer resistance to cephalosporins, penicillins, and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4655":{"model_id":"4655","model_name":"GOB-42","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7030":{"protein_sequence":{"accession":"WP_047034183.1","sequence":"MRNFATLFFMFVCLGLNAQVVKEPENMPKEWNQTYEPFRIAGNLYYVGTYDLASYLIVTDKGNILINTGTAESLPIIKANIQKLGFNYKDIKILLLTQAHYDHTGALQDLKTETAAKFYADKADADVLRTGGNSDYEMGKYGVTFKPVTPDKTLKDQDKIKLGNTILTLLHHPGHTKGSCSFIFETKDEKRKYRVLIANMPSIIVDKKFSEVTAYPNIQSDYAYAFKAMKNLDFDLWVASHASQFDLHEKRKEGDPYNPQLFMDKQSYFQNLNDLEKSYLDKIKKDSQGK"},"dna_sequence":{"accession":"NG_068008.2","fmin":"100","fmax":"973","strand":"+","sequence":"ATGAGAAATTTTGCTACACTGTTTTTCATGTTCGTTTGCTTGGGCTTGAATGCTCAGGTAGTAAAAGAACCTGAAAATATGCCCAAAGAATGGAACCAGACTTATGAACCCTTCAGAATTGCAGGTAATTTATATTACGTAGGAACCTATGATTTGGCTTCTTACCTTATTGTGACAGACAAAGGCAATATTCTCATTAATACAGGAACGGCAGAATCGCTTCCAATAATAAAAGCAAATATCCAAAAGCTCGGGTTTAATTATAAAGACATTAAGATCTTGCTGCTTACTCAGGCTCACTACGACCATACAGGTGCATTACAAGATCTTAAAACAGAAACCGCTGCAAAATTCTATGCCGATAAAGCAGATGCTGATGTCCTGAGAACAGGGGGAAATTCCGATTATGAAATGGGAAAATATGGTGTGACATTTAAACCTGTTACTCCGGATAAAACATTGAAAGATCAGGATAAAATAAAACTGGGAAATACAATCCTGACTTTGCTTCATCATCCGGGACATACAAAAGGTTCCTGTAGTTTTATTTTTGAAACAAAAGACGAGAAGAGAAAATATAGAGTTTTGATAGCTAATATGCCCTCTATTATTGTTGATAAGAAATTTTCTGAAGTTACCGCATATCCAAATATTCAGTCCGATTATGCATATGCTTTCAAAGCAATGAAGAATCTGGATTTTGACCTTTGGGTGGCATCACATGCAAGTCAGTTCGATCTGCATGAAAAACGTAAAGAAGGAGATCCGTACAATCCGCAATTGTTTATGGATAAGCAAAGCTATTTCCAAAACCTTAATGATTTGGAAAAAAGCTATCTCGACAAAATAAAAAAAGATTCACAAGGTAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41081","NCBI_taxonomy_name":"Elizabethkingia anophelis","NCBI_taxonomy_id":"1117645"}}}},"ARO_accession":"3005691","ARO_id":"44153","ARO_name":"GOB-42","CARD_short_name":"GOB-42","ARO_description":"GOB-42 is a GOB beta-lactamase.","ARO_category":{"41376":{"category_aro_accession":"3004212","category_aro_cvterm_id":"41376","category_aro_name":"GOB beta-lactamase","category_aro_description":"The GOB family of beta-lactamases have been discovered in the Elizabethkingia meningoseptica and are classified as subclass B3 beta-lactamase. They confer resistance to cephalosporins, penicillins, and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4656":{"model_id":"4656","model_name":"GOB-43","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7031":{"protein_sequence":{"accession":"WP_078407131.1","sequence":"MRNFATLFFMFICLGLNAQVVKEPENMPKEWNQAYEPFRIAGNLYYVGTYDLASYLIVTDKGNILINTGTAESLPIIKANIQKLGFNYKDIKILLLTQAHYDHTGALQDFKTETAAKFYADKADADVLKTGGKSDYEMGKYGVTFKPVTPDKTLKDQDKIKLGNITLTLLHHPGHTKGSCSFIFETKDEKRKYRVLIANMPSVIVDKKFSEVTAYPNIQSDYAYTFGVMKKLDFDIWVASHASQFDLHEKRKEGDPYNPQLFMDKQSYFQNLNDLEKSYLNKIKKDSQDK"},"dna_sequence":{"accession":"NG_068009.1","fmin":"100","fmax":"973","strand":"+","sequence":"ATGAGAAATTTTGCTACACTGTTTTTCATGTTCATTTGCTTGGGCTTGAATGCTCAGGTAGTAAAAGAACCTGAAAATATGCCCAAAGAATGGAACCAGGCTTATGAACCATTCAGAATTGCAGGTAATTTATATTACGTAGGAACCTATGATTTGGCTTCTTACCTTATTGTGACAGACAAAGGCAATATTCTCATTAATACAGGAACGGCAGAATCGCTTCCAATAATAAAAGCAAATATCCAAAAGCTCGGGTTTAATTATAAAGACATTAAGATCTTGCTGCTTACTCAGGCTCACTACGACCATACAGGTGCATTACAGGATTTTAAAACAGAAACCGCTGCAAAATTCTATGCCGATAAAGCAGATGCTGATGTCCTGAAAACAGGGGGGAAGTCCGATTATGAAATGGGAAAATATGGTGTGACATTTAAACCTGTTACTCCGGATAAAACATTGAAAGATCAGGATAAAATAAAACTGGGAAATATAACCCTGACTTTGCTTCATCATCCGGGACATACAAAAGGTTCCTGTAGTTTTATTTTTGAAACAAAAGACGAGAAGAGAAAATATAGAGTTTTGATAGCTAATATGCCCTCCGTTATTGTTGATAAGAAATTTTCTGAAGTTACCGCATATCCAAATATTCAGTCCGATTATGCTTATACCTTTGGTGTTATGAAAAAGCTGGATTTTGATATTTGGGTGGCCTCCCATGCAAGTCAGTTCGATCTCCATGAAAAACGTAAAGAAGGAGATCCGTACAATCCGCAATTGTTTATGGATAAGCAAAGCTATTTCCAAAACCTTAATGATTTGGAAAAAAGCTATCTCAACAAAATAAAAAAAGATTCCCAAGATAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41081","NCBI_taxonomy_name":"Elizabethkingia anophelis","NCBI_taxonomy_id":"1117645"}}}},"ARO_accession":"3005692","ARO_id":"44154","ARO_name":"GOB-43","CARD_short_name":"GOB-43","ARO_description":"GOB-43 is a GOB beta-lactamase.","ARO_category":{"41376":{"category_aro_accession":"3004212","category_aro_cvterm_id":"41376","category_aro_name":"GOB beta-lactamase","category_aro_description":"The GOB family of beta-lactamases have been discovered in the Elizabethkingia meningoseptica and are classified as subclass B3 beta-lactamase. They confer resistance to cephalosporins, penicillins, and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4657":{"model_id":"4657","model_name":"GOB-44","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7032":{"protein_sequence":{"accession":"WP_078793281.1","sequence":"MRNFAILFFLLITFSWKAQVVKEPENTNEEWSRSYEPFRIAGNLYYVGTYDLASYLIVTDKGNILINTGLAGSLPMIKENIKKLGFNYKDIKILLLTQAHYDHTGALKDLQTETGAKLYADSADADVLKTGGKSDYEMGKYGATFKPIKPDILLKDQDKIKLGNTTLTLLHHPGHTKGSCSFIFETKDENRNYKVLIANMPSVIVDRKFSEIKDYPNIQADYAYTFKAMKKLDFDLWVASHASQFDLHTKHKEGDPYNPQVFMDKANYFAFLNSLETDYLEKIKNDSQKK"},"dna_sequence":{"accession":"NG_068010.1","fmin":"100","fmax":"973","strand":"+","sequence":"ATGAGAAACTTTGCAATTTTATTTTTTTTACTGATCACTTTCAGCTGGAAAGCACAGGTTGTTAAAGAACCGGAAAATACAAATGAAGAATGGTCCCGATCATATGAGCCATTCAGAATTGCGGGTAACTTATACTATGTAGGAACTTACGATCTGGCATCTTATTTAATAGTTACCGATAAAGGAAATATTCTCATTAATACAGGATTGGCTGGTTCTCTTCCTATGATAAAAGAGAATATTAAAAAACTGGGATTCAATTATAAAGACATTAAAATTCTGCTTTTAACCCAGGCGCATTATGATCATACAGGTGCATTAAAAGATTTGCAGACAGAAACAGGTGCAAAACTTTATGCAGACAGTGCTGATGCTGATGTATTGAAAACGGGCGGTAAATCCGATTATGAAATGGGGAAATACGGGGCAACCTTTAAGCCGATTAAGCCTGATATCCTGTTGAAAGATCAGGATAAAATAAAACTGGGGAATACAACCTTAACTTTACTTCATCATCCGGGGCACACAAAAGGTTCATGCAGTTTTATATTTGAAACAAAGGATGAAAACAGAAATTATAAAGTGCTGATAGCCAATATGCCATCGGTTATAGTTGACCGTAAGTTTTCCGAAATAAAAGATTACCCTAATATTCAGGCCGATTATGCTTATACATTTAAAGCCATGAAAAAACTGGATTTTGATCTTTGGGTCGCTTCACATGCAAGTCAGTTTGATTTACATACAAAACATAAAGAGGGAGACCCTTATAACCCACAGGTATTTATGGATAAGGCCAATTATTTTGCATTCCTCAATAGCCTGGAAACAGATTATCTGGAAAAAATTAAAAACGACTCACAAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36960","NCBI_taxonomy_name":"Elizabethkingia meningoseptica","NCBI_taxonomy_id":"238"}}}},"ARO_accession":"3005693","ARO_id":"44155","ARO_name":"GOB-44","CARD_short_name":"GOB-44","ARO_description":"GOB-44 is a GOB beta-lactamase.","ARO_category":{"41376":{"category_aro_accession":"3004212","category_aro_cvterm_id":"41376","category_aro_name":"GOB beta-lactamase","category_aro_description":"The GOB family of beta-lactamases have been discovered in the Elizabethkingia meningoseptica and are classified as subclass B3 beta-lactamase. They confer resistance to cephalosporins, penicillins, and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4658":{"model_id":"4658","model_name":"GOB-45","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7033":{"protein_sequence":{"accession":"WP_102793805.1","sequence":"MRNFATLFFMFICLGLNAQVVKEPENMPKEWNQAYEPFRIAGNLYYVGTYDLASYLIVTDKGNILINTGTAESLPIIKANIQKLGFNYKDIKILLLTQAHYDHTGALQDFKTETAAKFYADKADVDVLRTGGKSDYEMGKYGVTFKPVTPDKTLKDQDKIKLGNITLTLLHHPGHTKGSCSFIFETKDEKRKYRVLIANMPSVIVDKKFSEVTAYPNIQSDYAYTFGVMKKLDFDIWVASHASQFDLHEKRKEGDPYNPQLFMDKQSYFQNLNDLEKSYLNKIKKDSQDK"},"dna_sequence":{"accession":"NG_068172.1","fmin":"100","fmax":"973","strand":"+","sequence":"ATGAGAAATTTTGCTACACTGTTTTTCATGTTCATTTGCTTGGGCTTGAATGCTCAGGTAGTAAAAGAACCTGAAAATATGCCCAAAGAATGGAACCAGGCTTATGAACCATTCAGAATTGCAGGTAATTTATATTACGTAGGAACCTATGATTTGGCTTCTTACCTTATTGTGACAGACAAAGGCAATATTCTCATTAATACAGGAACGGCAGAATCGCTTCCAATAATAAAAGCAAATATCCAAAAGCTCGGGTTTAATTATAAAGACATTAAGATCTTGCTGCTTACTCAGGCTCACTACGACCATACAGGTGCATTACAGGATTTTAAAACAGAAACCGCTGCAAAATTCTATGCCGATAAAGCAGATGTTGATGTCCTGAGAACAGGGGGGAAGTCCGATTATGAAATGGGAAAATATGGTGTGACATTTAAACCTGTTACTCCGGATAAAACATTGAAAGATCAGGATAAAATAAAACTGGGAAATATAACCCTGACTTTGCTTCATCATCCGGGACATACAAAAGGTTCCTGTAGTTTTATTTTTGAAACAAAAGACGAGAAGAGAAAATATAGAGTTTTGATAGCTAATATGCCCTCCGTTATTGTTGATAAGAAATTTTCTGAAGTTACCGCATATCCAAATATTCAGTCCGATTATGCTTATACCTTTGGTGTTATGAAAAAGCTGGATTTTGATATTTGGGTGGCCTCCCATGCAAGTCAGTTCGATCTCCATGAAAAACGTAAAGAAGGAGATCCGTACAATCCGCAATTGTTTATGGATAAGCAAAGCTATTTCCAAAACCTTAATGATTTGGAAAAAAGCTATCTCAACAAAATAAAAAAAGATTCCCAAGATAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41081","NCBI_taxonomy_name":"Elizabethkingia anophelis","NCBI_taxonomy_id":"1117645"}}}},"ARO_accession":"3005694","ARO_id":"44156","ARO_name":"GOB-45","CARD_short_name":"GOB-45","ARO_description":"GOB-45 is a GOB beta-lactamase.","ARO_category":{"41376":{"category_aro_accession":"3004212","category_aro_cvterm_id":"41376","category_aro_name":"GOB beta-lactamase","category_aro_description":"The GOB family of beta-lactamases have been discovered in the Elizabethkingia meningoseptica and are classified as subclass B3 beta-lactamase. They confer resistance to cephalosporins, penicillins, and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4659":{"model_id":"4659","model_name":"GOB-46","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7034":{"protein_sequence":{"accession":"WP_078769980.1","sequence":"MRNFAILFFLLITFSWKAQVVKEPENTNEEWSRSYEPFRIAGNLYYVGTYDLASYLIVTDKGNILINTGLAGSLPMIKENIKKLGFNYKDIKILLLTQAHYDHTGALKDLQTETGAKLYADRADADVLKTGGKSDYEMGKYGATFKPIKPDILLKDQDKIKLGNTTLTLLHHPGHTKGSCSFIFETKDENRNYKVLIANMPSVIVDRKFSEIKDYPNIQADYAYTFKAMKKLDFDLWVASHASQFDLHTKHKEGDPYNPQVFMDKANYFAFLNSLETDYLEKIKNDSQKK"},"dna_sequence":{"accession":"NG_068011.1","fmin":"100","fmax":"973","strand":"+","sequence":"ATGAGAAACTTTGCAATTTTATTTTTTTTACTGATCACTTTCAGCTGGAAAGCACAGGTTGTTAAAGAACCGGAAAATACAAATGAAGAATGGTCCCGATCATATGAGCCATTCAGAATTGCGGGTAACTTATACTATGTAGGAACTTACGATCTGGCATCTTATTTAATAGTTACCGATAAAGGAAATATTCTCATTAATACAGGATTGGCTGGTTCTCTTCCTATGATAAAAGAGAATATTAAAAAACTGGGATTCAATTATAAAGACATTAAAATTCTGCTTTTAACCCAGGCGCATTATGATCATACAGGTGCATTAAAAGATTTGCAGACAGAAACAGGTGCAAAACTTTATGCAGACAGAGCTGATGCTGATGTATTGAAAACGGGCGGTAAATCCGATTATGAAATGGGGAAATACGGGGCAACCTTTAAGCCGATTAAGCCTGATATCCTGTTGAAAGATCAGGATAAAATAAAACTGGGGAATACAACCTTAACTTTACTTCATCATCCGGGGCACACAAAAGGTTCATGCAGTTTTATATTTGAAACAAAGGATGAAAACAGAAATTACAAAGTGCTGATAGCCAATATGCCATCGGTTATAGTTGACCGTAAGTTTTCCGAAATAAAAGATTACCCTAATATTCAGGCCGATTATGCTTATACATTTAAAGCCATGAAAAAACTGGATTTTGATCTTTGGGTCGCTTCACATGCAAGTCAGTTTGATTTACATACAAAACATAAAGAGGGAGACCCTTATAACCCACAGGTATTTATGGATAAGGCCAATTATTTTGCATTCCTCAATAGCCTGGAAACAGATTATCTGGAAAAAATTAAAAACGACTCACAAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36960","NCBI_taxonomy_name":"Elizabethkingia meningoseptica","NCBI_taxonomy_id":"238"}}}},"ARO_accession":"3005695","ARO_id":"44157","ARO_name":"GOB-46","CARD_short_name":"GOB-46","ARO_description":"GOB-46 is a GOB beta-lactamase.","ARO_category":{"41376":{"category_aro_accession":"3004212","category_aro_cvterm_id":"41376","category_aro_name":"GOB beta-lactamase","category_aro_description":"The GOB family of beta-lactamases have been discovered in the Elizabethkingia meningoseptica and are classified as subclass B3 beta-lactamase. They confer resistance to cephalosporins, penicillins, and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4660":{"model_id":"4660","model_name":"GOB-48","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7035":{"protein_sequence":{"accession":"WP_078724262.1","sequence":"MRNFATLFFMFVCLGLNAQVVKEPENMPKEWNQTYEPFRIAGNLYYVGTYDLASYLIVTDKGNILINTGTAESLPIIKANIQKLGFNYKDIKILLLTQAHYDHTGALQDLKTETGAKFYADKADADVLRTGGNSDYEMGKYGVTFKPVTPDKTLKDQDKITLGNTILTLLHHPGHTKGSCSFIFETKDEKRKYRVLIANMPSVIVDKKFSEVTAYPNIQSDYAYTFKAMKNLDFDLWVASHASQFDLHEKRKEGDPYNPQLFMDKQSYFQNLNDLEKSYLDKIKKDSQDK"},"dna_sequence":{"accession":"NG_068012.1","fmin":"100","fmax":"973","strand":"+","sequence":"ATGAGAAATTTTGCTACACTGTTTTTCATGTTCGTTTGCTTGGGCTTGAATGCTCAGGTAGTAAAAGAACCTGAAAATATGCCCAAAGAATGGAACCAGACTTATGAACCCTTCAGAATTGCAGGTAATTTATATTACGTAGGAACCTATGATTTGGCTTCTTACCTTATTGTGACAGACAAAGGCAATATTCTCATTAATACAGGAACGGCAGAATCGCTTCCAATAATAAAAGCAAATATCCAAAAGCTCGGGTTTAATTATAAAGACATTAAGATCTTGCTGCTTACTCAGGCTCACTACGACCATACAGGTGCATTACAAGATCTTAAAACAGAAACCGGTGCAAAATTCTATGCCGATAAAGCAGATGCTGATGTCCTGAGAACAGGGGGAAATTCCGATTATGAAATGGGAAAATATGGGGTGACATTTAAACCTGTTACTCCGGATAAAACATTGAAAGATCAGGATAAAATAACGCTGGGAAATACAATCCTGACTTTGCTTCATCATCCGGGACATACAAAAGGTTCCTGTAGTTTTATTTTTGAAACAAAAGACGAGAAGAGAAAATATAGAGTTTTGATAGCTAATATGCCCTCCGTTATTGTTGATAAGAAATTTTCTGAAGTTACCGCATATCCAAATATTCAGTCCGATTACGCATATACTTTCAAAGCAATGAAGAATCTAGATTTTGACCTTTGGGTGGCATCACATGCAAGTCAGTTCGATCTGCATGAAAAACGTAAAGAAGGAGATCCGTACAATCCGCAATTGTTTATGGATAAGCAAAGCTATTTCCAAAACCTTAATGATTTGGAAAAAAGCTATCTCGACAAAATAAAAAAAGATTCACAAGATAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41081","NCBI_taxonomy_name":"Elizabethkingia anophelis","NCBI_taxonomy_id":"1117645"}}}},"ARO_accession":"3005696","ARO_id":"44158","ARO_name":"GOB-48","CARD_short_name":"GOB-48","ARO_description":"GOB-48 is a GOB beta-lactamase.","ARO_category":{"41376":{"category_aro_accession":"3004212","category_aro_cvterm_id":"41376","category_aro_name":"GOB beta-lactamase","category_aro_description":"The GOB family of beta-lactamases have been discovered in the Elizabethkingia meningoseptica and are classified as subclass B3 beta-lactamase. They confer resistance to cephalosporins, penicillins, and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4661":{"model_id":"4661","model_name":"GOB-49","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7036":{"protein_sequence":{"accession":"WP_045183849.1","sequence":"MRNFVTLFFLLVCLSLNAQVVKEPENMPKEWNQTYEPFRIAGNLYYVGTYDLASYLIVTDKGNILINTGTAESFPIIKGNIQKLGFNYKDIKILLLTQAHYDHTGALRDFKTETGAKFYADKADADVLRTGGKSDYELGKYGVTFKPVTPDKTLKDQDKITLGNTTLTLLHHPGHTKGSCSFIFETKDENRKYKILIANMPSIIVDKKFSEVTAYPGIQSDYAYTFKAMKNLDFDVWVASHASQFDLHTKRKEGDSYNPQLFMDKKNYFKRLERLENNYFEKIKEDSKDK"},"dna_sequence":{"accession":"NG_068013.1","fmin":"100","fmax":"973","strand":"+","sequence":"ATGAGAAATTTTGTTACACTATTTTTTCTGTTAGTTTGTTTGAGCTTGAATGCTCAGGTCGTAAAAGAACCTGAGAATATGCCAAAAGAATGGAACCAGACTTATGAACCATTCAGAATTGCAGGTAATTTATATTACGTAGGAACCTATGATTTGGCGTCCTACCTTATTGTGACAGACAAAGGCAATATTCTCATTAATACAGGAACGGCAGAATCATTTCCAATAATAAAAGGAAATATTCAAAAGCTGGGGTTTAATTATAAAGACATTAAGATCTTGCTGCTTACTCAGGCTCATTATGACCATACAGGCGCGTTACGGGATTTTAAAACGGAAACCGGTGCGAAATTTTATGCCGATAAAGCAGATGCTGATGTCCTGAGAACAGGCGGAAAATCTGATTATGAATTAGGTAAATATGGTGTGACATTTAAACCTGTTACCCCAGACAAAACATTGAAGGATCAGGATAAAATAACATTGGGAAATACAACCCTGACTTTGCTTCACCATCCGGGACATACAAAAGGTTCCTGCAGTTTTATTTTTGAAACAAAAGATGAAAACAGGAAATACAAGATTTTAATAGCTAATATGCCTTCCATTATTGTTGATAAGAAATTTTCTGAAGTTACAGCATATCCAGGTATTCAGTCCGATTACGCATATACTTTCAAAGCGATGAAGAATCTAGATTTTGATGTCTGGGTTGCCTCGCATGCAAGTCAGTTCGATTTGCACACCAAACGCAAAGAAGGTGACTCTTACAATCCACAGTTGTTTATGGATAAAAAGAATTATTTTAAAAGGCTCGAGCGTTTGGAAAATAATTATTTTGAAAAGATTAAAGAAGATTCAAAGGATAAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3005697","ARO_id":"44159","ARO_name":"GOB-49","CARD_short_name":"GOB-49","ARO_description":"GOB-49 is a GOB beta-lactamase.","ARO_category":{"41376":{"category_aro_accession":"3004212","category_aro_cvterm_id":"41376","category_aro_name":"GOB beta-lactamase","category_aro_description":"The GOB family of beta-lactamases have been discovered in the Elizabethkingia meningoseptica and are classified as subclass B3 beta-lactamase. They confer resistance to cephalosporins, penicillins, and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4662":{"model_id":"4662","model_name":"GOB-50","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7037":{"protein_sequence":{"accession":"WP_078675023.1","sequence":"MRNFVILFFMFICLGLNAQVVKEPENMPKEWNQTYEPFRIAGNLYYVGTYDLASYLIVTDKGNILINTGTAESLPIIKANIQKLGFNYKDIKILLLTQAHYDHTGALQDLKTETGAKFYADKADADVLRTGGKSDYEMGKYGVTFKPVTPDKTLKDQDKITLGNTILTLLHHPGHTKGSCSFIFETKDEKRKYRVLIANMPSVIVDKKFSEVTAYPNIQSDYAYTFKAMKNLDFDLWVASHASQFDLHEKRKEGDPYNPQLFMDKQSYFQNLNDLEKSYLDKIKKDSQDK"},"dna_sequence":{"accession":"NG_068014.1","fmin":"100","fmax":"973","strand":"+","sequence":"ATGAGAAATTTTGTTATACTGTTTTTCATGTTCATTTGCTTGGGCTTGAATGCTCAGGTAGTAAAAGAACCTGAAAATATGCCCAAAGAATGGAACCAGACTTATGAACCCTTCAGAATTGCAGGTAATTTATATTACGTAGGAACCTATGATTTGGCTTCTTACCTTATTGTGACAGACAAAGGCAATATTCTCATTAATACAGGAACGGCAGAATCGCTTCCAATAATAAAAGCAAATATCCAAAAGCTCGGGTTTAATTATAAAGACATTAAGATCTTGCTGCTTACTCAGGCTCACTACGACCATACAGGTGCATTACAAGATCTTAAAACAGAAACCGGTGCAAAATTCTATGCCGATAAAGCAGATGCTGATGTCCTGAGAACAGGGGGGAAGTCCGATTATGAAATGGGAAAATATGGGGTGACATTTAAACCTGTTACTCCGGATAAAACATTGAAAGATCAGGATAAAATAACACTGGGAAATACAATCCTGACTTTGCTTCATCATCCGGGACATACAAAAGGTTCCTGTAGTTTTATTTTTGAAACAAAAGACGAGAAGAGAAAATATAGAGTTTTGATAGCTAATATGCCCTCCGTTATTGTTGATAAGAAATTTTCTGAAGTTACCGCATATCCAAATATTCAGTCCGATTACGCATATACTTTCAAAGCAATGAAGAATCTAGATTTTGACCTTTGGGTGGCATCACATGCAAGTCAGTTCGATCTGCATGAAAAACGTAAAGAAGGAGATCCGTACAATCCGCAATTGTTTATGGATAAGCAAAGCTATTTCCAAAACCTTAATGATTTGGAAAAAAGCTATCTCGACAAAATAAAAAAAGATTCACAAGATAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41081","NCBI_taxonomy_name":"Elizabethkingia anophelis","NCBI_taxonomy_id":"1117645"}}}},"ARO_accession":"3005698","ARO_id":"44160","ARO_name":"GOB-50","CARD_short_name":"GOB-50","ARO_description":"GOB-50 is a GOB beta-lactamase.","ARO_category":{"41376":{"category_aro_accession":"3004212","category_aro_cvterm_id":"41376","category_aro_name":"GOB beta-lactamase","category_aro_description":"The GOB family of beta-lactamases have been discovered in the Elizabethkingia meningoseptica and are classified as subclass B3 beta-lactamase. They confer resistance to cephalosporins, penicillins, and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4663":{"model_id":"4663","model_name":"GOB-51","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7038":{"protein_sequence":{"accession":"WP_078402651.1","sequence":"MKRITTLLFLLVCFGWNAQVVKEPENTPKEWSQNYEPFRIAGNLYYVGTYDLASYLIVTDKGNILINTGLAGSLSTIKENIAKLGFNYKDIKILLLTQAHYDHTGALMDFKTETGAKFYADAADADVLRTGGQSDYEMGKYGATFKPIIPDRTLKNLDKIKLGNTTLTMLHHPGHTKGSCSFVFDTNDGKRKYRVLIANMPSIIVDNKFSEVTAYPNIQSDYAYTFNAMKKLDFDIWVASHASQFDLHEKRKEGEPYNPQLFMDKQSYFQNLNDLEKSYLDKIKKDSQDK"},"dna_sequence":{"accession":"NG_068015.1","fmin":"100","fmax":"973","strand":"+","sequence":"ATGAAAAGAATAACGACTTTACTTTTTCTGTTAGTATGTTTTGGCTGGAATGCTCAGGTTGTAAAAGAGCCTGAAAATACACCAAAAGAATGGTCTCAAAATTATGAACCATTCAGGATAGCAGGTAACTTGTATTACGTAGGAACTTATGACCTGGCTTCTTATCTAATCGTTACAGATAAAGGAAATATTCTGATCAATACAGGACTAGCAGGCTCTCTTTCTACAATAAAAGAGAATATTGCTAAATTAGGATTCAATTATAAAGATATCAAGATTCTGCTTCTCACACAGGCTCATTATGACCATACAGGTGCGTTAATGGACTTTAAAACAGAAACAGGTGCGAAATTTTATGCAGATGCTGCAGATGCAGATGTTCTGAGAACAGGCGGGCAGTCTGATTATGAAATGGGAAAATATGGTGCAACTTTTAAACCTATTATTCCGGATCGTACGTTAAAAAATCTGGATAAAATAAAATTAGGAAATACAACACTTACGATGCTCCATCATCCTGGGCATACAAAAGGTTCCTGTAGTTTTGTATTTGATACAAACGATGGGAAAAGAAAATACAGAGTGCTTATAGCCAATATGCCTTCCATTATTGTTGATAATAAATTCTCTGAAGTTACAGCATATCCGAATATTCAGTCCGATTATGCTTATACCTTTAATGCGATGAAAAAACTGGATTTTGATATTTGGGTAGCATCGCATGCAAGTCAGTTCGACCTGCATGAAAAACGCAAAGAAGGAGAGCCGTACAACCCACAATTGTTTATGGATAAGCAAAGCTATTTCCAAAACCTTAATGATCTGGAGAAAAGCTATCTTGATAAAATTAAAAAAGATTCACAAGATAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3005699","ARO_id":"44161","ARO_name":"GOB-51","CARD_short_name":"GOB-51","ARO_description":"GOB-51 is a GOB beta-lactamase.","ARO_category":{"41376":{"category_aro_accession":"3004212","category_aro_cvterm_id":"41376","category_aro_name":"GOB beta-lactamase","category_aro_description":"The GOB family of beta-lactamases have been discovered in the Elizabethkingia meningoseptica and are classified as subclass B3 beta-lactamase. They confer resistance to cephalosporins, penicillins, and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4664":{"model_id":"4664","model_name":"GRD23-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"425"}},"model_sequences":{"sequence":{"7039":{"protein_sequence":{"accession":"WP_122630835.1","sequence":"MKQILIFLLAVFIPTSFVFAGDPLPDLKIKQLDDGVYLHTSFQVFSGVVMGSNGLVVLDHNDAYIVDTPWSAEDTEKLLSWIKANGFSVKGSISTHSHDDRTAGIALLNSKAIPTYASKMTNGFLEKAGKAQAKNSFDSKDFWWVKDQVEVFYPGAGHAPDNLVVWLPKQKILFGGCLIRAKEAKNLGNVADAVIGEWPRSAEKLQEKYGNAKVVVPGHGEVGDVSLLEHTKELAAASARK"},"dna_sequence":{"accession":"NG_062239.1","fmin":"0","fmax":"726","strand":"+","sequence":"ATGAAGCAAATATTAATTTTTCTGTTAGCGGTATTCATTCCGACAAGCTTTGTTTTTGCTGGTGATCCGCTGCCAGATTTGAAAATCAAGCAGCTGGATGACGGCGTTTATCTGCATACGTCTTTCCAGGTTTTTAGTGGGGTTGTGATGGGCTCGAATGGATTGGTGGTGCTGGATCACAATGATGCCTATATCGTCGATACGCCATGGTCTGCGGAAGACACGGAAAAGCTTCTGAGTTGGATTAAGGCGAATGGCTTTTCCGTTAAAGGCAGCATTTCGACCCATTCGCACGATGATCGAACCGCCGGTATTGCATTGCTCAATTCGAAAGCCATTCCCACATACGCTTCGAAAATGACCAATGGATTTCTTGAGAAAGCCGGTAAGGCGCAGGCCAAAAATTCATTCGATAGCAAGGATTTCTGGTGGGTAAAAGACCAAGTGGAAGTCTTCTACCCCGGTGCAGGTCACGCACCCGACAATTTGGTTGTGTGGCTGCCCAAGCAAAAAATTCTATTTGGCGGCTGTCTGATTCGCGCAAAAGAAGCTAAAAATCTTGGCAATGTCGCCGATGCAGTTATTGGGGAGTGGCCTAGGTCGGCCGAAAAACTGCAGGAAAAATATGGAAACGCCAAGGTCGTCGTTCCGGGGCACGGTGAGGTTGGCGATGTATCGTTGTTGGAGCACACAAAGGAGCTGGCTGCGGCGAGTGCTAGAAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36791","NCBI_taxonomy_name":"uncultured bacterium","NCBI_taxonomy_id":"77133"}}}},"ARO_accession":"3006925","ARO_id":"45387","ARO_name":"GRD23-1","CARD_short_name":"GRD23-1","ARO_description":"GRD23-1 is a GRD23 beta-lactamase.","ARO_category":{"43875":{"category_aro_accession":"3005415","category_aro_cvterm_id":"43875","category_aro_name":"GRD23 beta-lactamase","category_aro_description":"GRD23 beta-lactamases are class B1 beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4665":{"model_id":"4665","model_name":"GRD33-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7040":{"protein_sequence":{"accession":"WP_122630834.1","sequence":"MAAMAAVAAVLLGVFAFAHAQDQPALWTQPQQPVRIIGNAWYVGTRGLSAILITSPTGAVLIDGAMRESADDIAKNITSLGVRLEDVKLIVNSHAHNDHAGGIAELQRRTGATVAALPWSAEALRSGRKHQGDPQFDTQTPPPDRVPKVKTIRDGEALHAGGVTITAHKTGGHTPGSTSWTWRSCEENRCVDIVYADSITAVSADGFRFTDNKTYPQAIDDFNKGYAFLRSASCDILVTPHPEASDFWGRIAKRDAGERDALIDRSQCARYADRADAQLQKRLATERAK"},"dna_sequence":{"accession":"NG_062238.1","fmin":"0","fmax":"870","strand":"+","sequence":"ATGGCCGCCATGGCCGCCGTGGCTGCCGTACTGCTCGGCGTGTTTGCATTCGCGCACGCGCAGGATCAGCCGGCCTTGTGGACTCAACCGCAGCAGCCCGTTCGCATCATTGGCAACGCCTGGTACGTCGGCACGCGCGGGCTGAGCGCCATTCTCATCACGTCGCCCACCGGCGCCGTGCTCATCGACGGAGCGATGCGTGAATCGGCGGACGATATCGCCAAGAACATCACGAGCCTCGGTGTACGGCTCGAGGACGTCAAGCTGATCGTCAATTCGCATGCGCACAACGATCATGCTGGCGGGATCGCGGAACTTCAGCGGCGTACGGGCGCCACGGTGGCCGCGCTGCCCTGGAGCGCGGAGGCGCTGCGAAGCGGACGGAAGCATCAGGGCGATCCGCAGTTCGACACACAAACGCCTCCTCCCGATCGTGTCCCCAAGGTCAAAACGATTCGGGATGGCGAGGCGCTTCATGCCGGTGGCGTGACGATCACGGCGCACAAGACCGGCGGCCACACGCCAGGCAGCACGTCATGGACGTGGCGCTCGTGCGAGGAGAACCGGTGCGTCGACATCGTGTATGCCGACAGCATCACTGCCGTCTCGGCGGATGGATTCCGCTTCACCGACAACAAGACGTATCCGCAGGCGATCGACGACTTCAACAAGGGCTACGCGTTCCTGCGATCGGCGAGTTGCGACATCCTGGTGACACCGCACCCCGAAGCCTCGGACTTCTGGGGGCGGATCGCCAAACGTGACGCCGGAGAGCGCGATGCGCTGATCGATCGCTCGCAGTGCGCGCGCTATGCCGATCGTGCCGACGCGCAACTCCAGAAACGCCTCGCGACGGAGCGCGCGAAATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36791","NCBI_taxonomy_name":"uncultured bacterium","NCBI_taxonomy_id":"77133"}}}},"ARO_accession":"3006926","ARO_id":"45388","ARO_name":"GRD33-1","CARD_short_name":"GRD33-1","ARO_description":"GRD33-1 is a GRD33 beta-lactamase.","ARO_category":{"43876":{"category_aro_accession":"3005416","category_aro_cvterm_id":"43876","category_aro_name":"GRD33 beta-lactamase","category_aro_description":"GRD33 beta-lactamases are class B3 beta-lactamase.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4666":{"model_id":"4666","model_name":"IMI-12","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"7041":{"protein_sequence":{"accession":"WP_064190970.1","sequence":"MSLNVKPSRIAILFSSCLVSISFFSQANTKGIDEIKNLETDFNGRIGVYALDTGSGKSFSYKANERFPLCSSFKGFLAAAVLKGSQDNQLNLNQIVNYNTRSLEFHSPITTKYKDNGMSLGDMAAAALQYSDNGATNIILERYIGGPEGMTKFMRSIGDKDFRLDRWELDLNTAIPGDERDTSTPAAVAKSLKTLALGNILNEREKETYQTWLKGNTTGAARIRASVPSDWVVGDKTGSCGAYGTANDYAVVWPKNRAPLIISVYTTKNEKEAKHDDKVIAEASRIAIDNLK"},"dna_sequence":{"accession":"NG_050720.1","fmin":"0","fmax":"879","strand":"+","sequence":"ATGTCACTTAATGTAAAACCAAGTAGAATAGCCATCTTGTTTAGCTCTTGTTTAGTTTCAATATCATTTTTCTCACAGGCCAATACAAAGGGCATCGATGAGATTAAGAACCTTGAAACAGATTTCAATGGTAGAATTGGTGTCTACGCTTTAGACACTGGCTCAGGTAAATCATTTTCATACAAAGCAAATGAACGATTTCCATTATGTAGTTCTTTCAAAGGTTTTTTAGCTGCTGCTGTATTAAAAGGCTCTCAAGATAATCAACTAAATCTTAATCAGATCGTGAATTACAATACAAGAAGTTTAGAGTTCCATTCACCCATCACAACTAAATATAAAGATAATGGAATGTCATTAGGTGATATGGCTGCTGCCGCTTTACAATATAGCGACAATGGTGCTACTAATATTATTCTTGAACGATATATCGGTGGTCCTGAGGGTATGACTAAATTCATGCGGTCGATTGGAGATAAAGATTTTAGACTCGATCGTTGGGAGTTAGATCTAAACACAGCTATTCCTGGCGATGAACGTGACACATCTACACCTGCAGCAGTAGCTAAGAGCCTGAAAACCCTTGCTCTGGGTAACATACTTAATGAGCGTGAAAAGGAAACCTATCAGACATGGTTAAAGGGTAACACAACCGGTGCAGCACGTATTCGTGCTAGCGTACCAAGCGATTGGGTAGTTGGCGATAAAACTGGTAGTTGCGGAGCATACGGTACGGCAAATGATTATGCGGTAGTCTGGCCAAAGAACCGAGCTCCTCTTATAATTTCTGTATACACTACAAAAAACGAAAAAGAAGCCAAGCATGACGATAAAGTAATCGCAGAAGCTTCAAGAATCGCAATTGATAACCTTAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40540","NCBI_taxonomy_name":"Enterobacter cloacae complex","NCBI_taxonomy_id":"354276"}}}},"ARO_accession":"3006176","ARO_id":"44638","ARO_name":"IMI-12","CARD_short_name":"IMI-12","ARO_description":"IMI-12 is a IMI beta-lactamase.","ARO_category":{"36027":{"category_aro_accession":"3000018","category_aro_cvterm_id":"36027","category_aro_name":"IMI beta-lactamase","category_aro_description":"IMI beta-lactamases are a group of TEM-1-like beta-lactamase that are known to hydrolyze imipenem. IMI beta-lactamases are inhibited by clavulanic acid and tazobactam.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4667":{"model_id":"4667","model_name":"IMI-13","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"7042":{"protein_sequence":{"accession":"WP_094009809.1","sequence":"MSLNAKPSRIGILFSSCLVLISFFSQANTKGIDEIKSLETDFNGRIGVYALDTGSGKSFSYRANERFPLCSSFKGFLAAAVLKGSQDNQLNLNQIVNYSTRSLEFHSPITTKYKDNGMSLGDMAAAALQYSDNGATNIILERFIGGPEGMTKFMRSIGDEVFRLDRWELDLNTAIPGDERDTSTPAAIGKSLENLALGNILSEREKETYQTWLKGNTTGATRIRASVPSDWVVGDKTGSCGAYGTANDYAVVWPKNRAPLIISVYTTKNQKEAKHDDKVIAEASRIAIDNLK"},"dna_sequence":{"accession":"NG_055491.1","fmin":"0","fmax":"879","strand":"+","sequence":"ATGTCACTTAATGCAAAACCAAGTAGAATAGGCATCCTGTTTAGCTCTTGTTTAGTTTTAATATCATTTTTCTCACAAGCCAATACAAAGGGCATCGATGAGATTAAAAGCCTTGAGACAGATTTCAATGGGAGGATTGGTGTCTACGCTTTGGACACTGGCTCGGGTAAATCATTTTCGTACAGAGCAAATGAACGATTTCCATTATGTAGTTCTTTTAAAGGTTTTTTAGCTGCTGCTGTATTAAAAGGTTCTCAAGATAATCAACTTAATCTTAATCAGATCGTAAACTATAGCACAAGAAGTTTAGAGTTCCATTCCCCCATTACAACTAAATATAAAGATAATGGAATGTCATTAGGTGATATGGCTGCTGCCGCTTTACAATATAGCGACAATGGTGCTACTAATATTATCCTTGAACGTTTTATCGGTGGTCCTGAGGGTATGACTAAATTCATGCGGTCGATTGGAGATGAAGTTTTTAGACTCGATCGTTGGGAGTTAGATCTAAACACAGCTATTCCAGGCGATGAACGTGATACATCTACACCTGCAGCAATAGGTAAGAGCCTGGAAAACCTTGCTCTGGGTAACATACTTAGTGAACGTGAAAAGGAAACCTATCAGACATGGTTAAAGGGTAACACAACCGGCGCAACGCGTATTCGTGCTAGCGTACCAAGCGATTGGGTTGTTGGCGATAAAACTGGTAGTTGCGGGGCATACGGTACGGCAAATGATTATGCAGTAGTGTGGCCAAAGAACCGGGCTCCTCTTATAATTTCTGTATACACTACAAAAAACCAAAAAGAAGCTAAGCATGACGATAAAGTAATAGCAGAAGCTTCAAGAATTGCAATTGACAACCTTAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36926","NCBI_taxonomy_name":"Enterobacter asburiae","NCBI_taxonomy_id":"61645"}}}},"ARO_accession":"3006177","ARO_id":"44639","ARO_name":"IMI-13","CARD_short_name":"IMI-13","ARO_description":"IMI-13 is a IMI beta-lactamase.","ARO_category":{"36027":{"category_aro_accession":"3000018","category_aro_cvterm_id":"36027","category_aro_name":"IMI beta-lactamase","category_aro_description":"IMI beta-lactamases are a group of TEM-1-like beta-lactamase that are known to hydrolyze imipenem. IMI beta-lactamases are inhibited by clavulanic acid and tazobactam.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4668":{"model_id":"4668","model_name":"IMI-14","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"7043":{"protein_sequence":{"accession":"WP_077064887.1","sequence":"MSLNVKPSRIAILFSSCLVSISFFSQANTKGIDEIKDLETDFNGRIGVYALDTGSGKSFSYKANERFPLCSSFKGFLAAAVLKGSQDNQLNLNQIVNYNTRSLEFHSPITTKYKDNGMSLGDMAAAALQYSDNGATNIILERYIGGPEGMTKFMRSIGDKDFRLDRWELDLNTAIPGDERDTSTPAAVAKSLKTLALGNILNEREKETYQTWLKGNTTGAARIRASVPSDWVVGDKTGSCGAYGTANDYAVVWPKNRAPLIISVYTTKNEKEAMHEDKVIAEASRIAIDNLK"},"dna_sequence":{"accession":"NG_052863.1","fmin":"0","fmax":"879","strand":"+","sequence":"ATGTCACTTAATGTAAAACCAAGTAGAATAGCCATCTTGTTTAGCTCTTGTTTAGTTTCAATATCATTTTTCTCACAGGCCAATACAAAGGGCATCGATGAGATTAAAGACCTTGAAACAGATTTCAATGGTAGAATTGGTGTCTACGCTTTAGACACTGGCTCAGGCAAATCATTTTCATACAAAGCAAATGAACGATTTCCATTATGTAGTTCTTTCAAAGGTTTTTTAGCTGCTGCTGTATTAAAAGGCTCTCAAGATAATCAACTAAATCTTAATCAGATCGTGAATTATAATACAAGAAGTTTAGAGTTCCATTCACCCATCACAACTAAATATAAAGATAATGGAATGTCATTAGGTGATATGGCTGCTGCAGCTTTACAATATAGCGACAATGGTGCTACTAATATTATCCTTGAACGATATATCGGTGGTCCTGAGGGTATGACTAAATTCATGCGGTCGATTGGAGATAAAGATTTTAGACTCGATCGTTGGGAGTTAGATCTAAACACAGCTATTCCTGGCGATGAACGTGACACATCTACACCTGCAGCAGTAGCTAAGAGCCTGAAAACCCTTGCACTGGGTAACATACTCAATGAGCGTGAAAAGGAAACCTATCAGACATGGTTAAAGGGTAACACAACCGGTGCAGCGCGTATTCGTGCTAGCGTACCAAGCGATTGGGTAGTTGGCGATAAAACTGGTAGTTGCGGTGCATACGGTACGGCAAATGATTATGCGGTAGTCTGGCCAAAGAACCGAGCTCCTCTTATAATTTCTGTATACACTACAAAAAACGAAAAAGAAGCCATGCATGAGGATAAAGTAATCGCAGAAGCTTCAAGAATCGCAATTGATAACCTTAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39098","NCBI_taxonomy_name":"Enterobacter hormaechei","NCBI_taxonomy_id":"158836"}}}},"ARO_accession":"3006178","ARO_id":"44640","ARO_name":"IMI-14","CARD_short_name":"IMI-14","ARO_description":"IMI-14 is a IMI beta-lactamase.","ARO_category":{"36027":{"category_aro_accession":"3000018","category_aro_cvterm_id":"36027","category_aro_name":"IMI beta-lactamase","category_aro_description":"IMI beta-lactamases are a group of TEM-1-like beta-lactamase that are known to hydrolyze imipenem. IMI beta-lactamases are inhibited by clavulanic acid and tazobactam.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4669":{"model_id":"4669","model_name":"IMI-15","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"7044":{"protein_sequence":{"accession":"WP_085562404.1","sequence":"MSLNVKPSRIAILFSSCLVSISFFSQANTKGIDEIKDLETDFNGRIGVYALDTGSGKSFSYKANERFPLCSSFKGFLAAAVLKGSQDNQLNLNQIVNYNTRSLEFHSPITTKYKDNGMSLGDMAAAALQYSDNGATNIILERYIGGPEGMTKFMRSIGDKDFRLDRWELDLNTAIPGDERDTSTPAAVAKSLKTLALGNILNEREKETYQTWLKGNTTGAARIRASVPSDWVVGDKTGSCGAYGTANDYAVVWPKNRAPLIISVYTTKTKKEAKHEDKVIAEASRIAIDNLK"},"dna_sequence":{"accession":"NG_054694.1","fmin":"0","fmax":"879","strand":"+","sequence":"ATGTCACTTAATGTAAAACCAAGTAGAATAGCCATCTTGTTTAGCTCTTGTTTAGTTTCAATATCATTTTTCTCACAGGCCAATACAAAGGGCATCGATGAGATTAAAGACCTTGAAACAGATTTCAATGGTAGAATTGGTGTCTACGCTTTAGACACTGGCTCAGGCAAATCATTTTCATACAAAGCAAATGAACGATTTCCATTATGTAGTTCTTTCAAAGGTTTTTTAGCTGCTGCTGTATTAAAAGGCTCTCAAGATAATCAACTAAATCTTAATCAGATCGTAAATTATAATACAAGAAGTTTAGAGTTCCATTCACCCATCACAACTAAATATAAAGATAATGGAATGTCATTAGGTGATATGGCTGCTGCAGCTTTACAATATAGCGACAATGGTGCTACTAATATTATCCTTGAACGATATATCGGTGGTCCTGAGGGTATGACTAAATTCATGCGGTCGATTGGAGATAAAGATTTTAGACTCGATCGTTGGGAGTTAGATCTAAACACAGCTATTCCTGGCGATGAACGTGACACATCTACACCTGCAGCAGTAGCTAAGAGCCTGAAAACCCTTGCACTGGGTAACATACTCAATGAGCGTGAAAAGGAAACCTATCAGACATGGTTAAAGGGTAACACAACCGGTGCAGCGCGTATTCGTGCTAGCGTACCAAGCGATTGGGTAGTTGGCGATAAAACTGGTAGTTGCGGTGCATACGGTACGGCAAATGATTATGCGGTAGTCTGGCCAAAGAACCGAGCTCCTCTTATAATTTCTGTATACACTACAAAAACGAAAAAAGAAGCCAAGCATGAGGATAAAGTAATCGCAGAAGCTTCAAGAATCGCAATTGATAACCTTAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3006179","ARO_id":"44641","ARO_name":"IMI-15","CARD_short_name":"IMI-15","ARO_description":"IMI-15 is a IMI beta-lactamase.","ARO_category":{"36027":{"category_aro_accession":"3000018","category_aro_cvterm_id":"36027","category_aro_name":"IMI beta-lactamase","category_aro_description":"IMI beta-lactamases are a group of TEM-1-like beta-lactamase that are known to hydrolyze imipenem. IMI beta-lactamases are inhibited by clavulanic acid and tazobactam.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4670":{"model_id":"4670","model_name":"IMI-16","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"7045":{"protein_sequence":{"accession":"WP_094009816.1","sequence":"MSLNVKPSRIAILFSSCLVSISFFSQANTKGIDDIKNLETDFNGRIGVYALDTGSGKSFSYKANERFPLCSSFKGFLAAAVLKRSQDNQLSLNQIVNYNTRTLEFHSPITTKYKDNGMSLGDMAAAALQYSDNGATNIILERYIGGPEGMTKFMRSIGDEDFRLDRWELDLNTAIPGDERDTSTPAAVAKSLKTIALGNILSEREKETYQTWLKGNTTGAARIRASVPSDWVVGDKTGSCGAYGTANDYAVVWPKNRAPLIISVYTTKYEKEAKHEDKVIAEASRIAIDNLK"},"dna_sequence":{"accession":"NG_055504.1","fmin":"0","fmax":"879","strand":"+","sequence":"ATGTCACTTAATGTAAAACCAAGCAGAATAGCCATCTTGTTTAGCTCTTGTTTAGTTTCAATATCATTTTTCTCACAGGCCAATACAAAGGGCATCGATGATATTAAAAACCTTGAAACAGATTTCAATGGTAGAATTGGTGTCTACGCTTTAGACACTGGCTCAGGTAAATCATTTTCGTACAAAGCAAATGAACGATTTCCATTATGTAGTTCTTTCAAAGGTTTTTTAGCTGCTGCTGTATTAAAACGCTCTCAAGATAATCAACTCAGTCTTAATCAGATCGTGAATTACAATACAAGAACTTTAGAGTTCCATTCACCCATCACAACTAAATATAAAGATAATGGAATGTCATTAGGTGATATGGCTGCTGCCGCTTTACAATATAGTGACAATGGTGCTACTAATATTATTCTTGAACGTTATATCGGTGGTCCTGAGGGTATGACTAAATTCATGCGGTCGATTGGAGATGAAGATTTTAGACTCGATCGTTGGGAGTTAGATCTAAACACAGCTATTCCAGGCGATGAACGTGACACATCTACACCTGCAGCAGTAGCCAAGAGCCTGAAAACCATTGCTCTGGGTAACATACTTAGTGAGCGTGAAAAGGAAACATATCAGACATGGTTAAAGGGTAACACAACCGGTGCAGCGCGTATTCGTGCTAGCGTACCAAGCGATTGGGTAGTTGGCGATAAAACTGGTAGTTGCGGAGCATACGGTACTGCAAATGATTATGCGGTAGTCTGGCCAAAGAACCGGGCTCCTCTTATAATTTCTGTATACACTACAAAATACGAAAAAGAAGCCAAGCATGAGGATAAAGTAATCGCAGAAGCTTCAAGAATCGCAATTGATAACCTTAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3006180","ARO_id":"44642","ARO_name":"IMI-16","CARD_short_name":"IMI-16","ARO_description":"IMI-16 is a IMI beta-lactamase.","ARO_category":{"36027":{"category_aro_accession":"3000018","category_aro_cvterm_id":"36027","category_aro_name":"IMI beta-lactamase","category_aro_description":"IMI beta-lactamases are a group of TEM-1-like beta-lactamase that are known to hydrolyze imipenem. IMI beta-lactamases are inhibited by clavulanic acid and tazobactam.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4671":{"model_id":"4671","model_name":"IMI-17","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"7046":{"protein_sequence":{"accession":"WP_100086555.1","sequence":"MSLNVKPSKIAILFISCLFSISFFSQANTKGIDEIKNLETDFNGRVGVYALDTGSGKSFSYKANERFPLCSSFKGFLAAAVLKGSQDNQLNLNQIVNYNTRSLEFHSPITTKYKDNGMSLGDMAAAALQYSDNGATNIILERYIGGPEGMTKFMRSIGDEDFRLDRWELDLNTAIPGDERDTSTPAAVAKSLKTLALGNILSEREKETYQTWLKGNTTGAARIRASVPSDWVVGDKTGSCGAYGTANDYAVVWPKNRAPLIISVYTTKNEKEAKHEDKVIAEASRIAIDNLK"},"dna_sequence":{"accession":"NG_055819.1","fmin":"0","fmax":"879","strand":"+","sequence":"ATGTCACTTAATGTAAAACCAAGTAAAATAGCCATCTTGTTTATCTCTTGTTTATTTTCAATATCATTTTTCTCACAGGCCAATACAAAGGGTATCGATGAGATTAAAAACCTTGAAACAGATTTCAATGGTAGAGTTGGTGTCTACGCTTTAGACACTGGCTCAGGTAAATCATTTTCGTACAAAGCAAATGAACGATTTCCATTATGTAGTTCTTTCAAAGGCTTTTTAGCTGCTGCTGTATTAAAAGGCTCTCAAGATAATCAACTCAATCTTAATCAGATCGTGAATTACAATACAAGAAGTTTAGAGTTCCATTCACCCATCACAACTAAATATAAAGATAATGGAATGTCATTAGGTGATATGGCTGCTGCCGCTTTACAATATAGCGACAATGGTGCTACTAATATTATTCTTGAACGTTATATCGGTGGTCCTGAGGGTATGACTAAATTCATGCGGTCGATTGGAGATGAAGATTTTAGACTCGATCGTTGGGAGTTAGATCTAAACACAGCTATTCCAGGCGATGAACGTGACACATCTACGCCTGCAGCAGTAGCTAAGAGCCTGAAAACTCTTGCTCTGGGTAACATACTTAGTGAGCGTGAAAAGGAAACCTATCAGACATGGTTAAAGGGTAACACAACCGGTGCAGCGCGTATTCGTGCTAGCGTACCAAGCGATTGGGTAGTTGGCGATAAAACTGGTAGTTGCGGAGCATACGGTACTGCAAATGATTATGCGGTAGTCTGGCCAAAGAACCGGGCTCCTCTTATAATTTCTGTATACACAACAAAAAACGAAAAAGAAGCCAAGCATGAGGATAAAGTAATCGCAGAAGCTTCAAGAATCGCAATTGATAACCTTAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3006181","ARO_id":"44643","ARO_name":"IMI-17","CARD_short_name":"IMI-17","ARO_description":"IMI-17 is a IMI beta-lactamase.","ARO_category":{"36027":{"category_aro_accession":"3000018","category_aro_cvterm_id":"36027","category_aro_name":"IMI beta-lactamase","category_aro_description":"IMI beta-lactamases are a group of TEM-1-like beta-lactamase that are known to hydrolyze imipenem. IMI beta-lactamases are inhibited by clavulanic acid and tazobactam.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4672":{"model_id":"4672","model_name":"IMI-18","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"7047":{"protein_sequence":{"accession":"WP_136512067.1","sequence":"MSLNVKPSRIAILFSSCLVSISFFSQANTKGIDDIKNLETDFNGRIGVYALDTGSGKSFSYKANERFPLCSSFKGFLAAAVLKRSQDNQLSLNQIVNYNTRSLEFHSPITTKYKDNGMSLGDMAAAALQYSDNGATNIILERYIGGPEGMTKFMRSIGDEDFRLDRWELDLNTAIPGDERDTSTPAAVAKSLKTIALGNILSEREKETYQTWLKGNTTGAARIRASVPSDWVVGDKTGSCGAYGTANDYAVVWPKNRAPLIISVYTTKYEKEAKHEDKVIAEASRIAIDNLK"},"dna_sequence":{"accession":"NG_064723.1","fmin":"0","fmax":"879","strand":"+","sequence":"ATGTCACTTAATGTAAAACCAAGCAGAATAGCCATCTTGTTTAGCTCTTGTTTAGTTTCAATATCATTTTTCTCACAGGCCAATACAAAGGGCATCGATGATATTAAAAACCTTGAAACAGATTTCAATGGTAGAATTGGTGTCTACGCTTTAGACACTGGCTCAGGTAAATCATTTTCGTACAAAGCAAATGAACGATTTCCATTATGTAGTTCTTTCAAAGGTTTTTTAGCTGCTGCTGTATTAAAACGCTCTCAAGATAATCAACTCAGTCTTAATCAGATCGTGAATTACAATACAAGAAGTTTAGAGTTCCATTCACCCATCACAACTAAATATAAAGATAATGGAATGTCATTAGGTGATATGGCTGCTGCCGCTTTACAATATAGTGACAATGGTGCTACTAATATTATTCTTGAACGTTATATCGGTGGTCCTGAGGGTATGACTAAATTCATGCGGTCGATTGGAGATGAAGATTTTAGACTCGATCGTTGGGAGTTAGATCTAAACACAGCTATTCCAGGCGATGAACGTGACACATCTACACCTGCAGCAGTAGCTAAGAGCCTGAAAACCATTGCTCTGGGTAACATACTTAGTGAGCGTGAAAAGGAAACATATCAGACATGGTTAAAGGGTAACACAACCGGTGCAGCGCGTATTCGTGCTAGCGTACCAAGCGATTGGGTAGTTGGCGATAAAACTGGTAGTTGCGGAGCATACGGTACTGCAAATGATTATGCGGTAGTCTGGCCAAAGAACCGGGCTCCTCTTATAATTTCTGTATACACTACGAAATACGAAAAAGAAGCCAAGCATGAGGATAAAGTAATCGCAGAAGCTTCAAGAATCGCAATTGATAACCTTAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3006182","ARO_id":"44644","ARO_name":"IMI-18","CARD_short_name":"IMI-18","ARO_description":"IMI-18 is a IMI beta-lactamase.","ARO_category":{"36027":{"category_aro_accession":"3000018","category_aro_cvterm_id":"36027","category_aro_name":"IMI beta-lactamase","category_aro_description":"IMI beta-lactamases are a group of TEM-1-like beta-lactamase that are known to hydrolyze imipenem. IMI beta-lactamases are inhibited by clavulanic acid and tazobactam.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4673":{"model_id":"4673","model_name":"IMI-19","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"7048":{"protein_sequence":{"accession":"WP_140423310.1","sequence":"MSLNVKPSRIAILFSSCLVSISFFSQANTKGIDDIKNLETDFNGRIGVYALDTGSGKSFTYKANERFPLCSSFKGFLAAAVLKRSQDNQLSLNQIVNYNTRTLEFHSPITTKYKDNGMSLGDMAAAALQYSDNGATNIILERYIGGPEGMTKFMRSIGDEDFRLDRWELDLNTAIPGDERDTSTPAAVAKSLKTIALGNILSEREKETYQTWLKGNTTGAARIRASVPSDWVVGDKTGSCGAYGTANDYAVVWPKNRAPLIISVYTTKYEKEAKHEDKVIAEASRIAIDNLK"},"dna_sequence":{"accession":"NG_065426.1","fmin":"0","fmax":"879","strand":"+","sequence":"ATGTCACTTAATGTAAAACCAAGCAGAATAGCCATCTTGTTTAGCTCTTGTTTAGTTTCAATATCATTTTTCTCACAGGCCAATACAAAGGGCATCGATGATATTAAAAACCTTGAAACAGATTTCAATGGTAGAATTGGTGTCTACGCTTTAGACACTGGCTCAGGTAAATCATTTACGTACAAAGCAAATGAACGATTTCCATTATGTAGTTCTTTCAAAGGTTTTTTAGCTGCTGCTGTATTAAAACGCTCTCAAGATAATCAACTCAGTCTTAATCAGATCGTGAATTACAATACAAGAACTTTAGAGTTCCATTCACCCATCACAACTAAATATAAAGATAATGGAATGTCATTAGGTGATATGGCTGCTGCCGCTTTACAATATAGTGACAATGGTGCTACTAATATTATTCTTGAACGTTATATCGGTGGTCCTGAGGGTATGACTAAATTCATGCGGTCGATTGGAGATGAAGATTTTAGACTCGATCGTTGGGAGTTAGATCTAAACACAGCTATTCCAGGCGATGAACGTGACACATCTACACCTGCAGCAGTAGCCAAGAGCCTGAAAACCATTGCTCTGGGTAACATACTTAGTGAGCGTGAAAAGGAAACATATCAGACATGGTTAAAGGGTAACACAACCGGTGCAGCGCGTATTCGTGCTAGCGTACCAAGCGATTGGGTAGTTGGCGATAAAACTGGTAGTTGCGGAGCATACGGTACTGCAAATGATTATGCGGTAGTCTGGCCAAAGAACCGGGCTCCTCTTATAATTTCTGTATACACTACAAAATACGAAAAAGAAGCCAAGCATGAGGATAAAGTAATCGCAGAAGCTTCAAGAATCGCAATTGATAACCTTAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3006183","ARO_id":"44645","ARO_name":"IMI-19","CARD_short_name":"IMI-19","ARO_description":"IMI-19 is a IMI beta-lactamase.","ARO_category":{"36027":{"category_aro_accession":"3000018","category_aro_cvterm_id":"36027","category_aro_name":"IMI beta-lactamase","category_aro_description":"IMI beta-lactamases are a group of TEM-1-like beta-lactamase that are known to hydrolyze imipenem. IMI beta-lactamases are inhibited by clavulanic acid and tazobactam.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4674":{"model_id":"4674","model_name":"IMI-20","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"7049":{"protein_sequence":{"accession":"WP_194293133.1","sequence":"MSLNVKPSRIAILFSSFLVSISFFSQANTKGIDEIKNLETDFNGRIGVYALDTGSGKSFSYKANERFPLCSSFKGFLAAAVLKGSQDNQLNLNQIVNYNTRSLEFYSPITTKYKDNGMSLGDMAAAALQYSDNGATNIILERYIGGPEGMTKFMRSIGDKDFRLDRWELDLNTAIPGDERDTSTPAAVAKSLKTLALGNILNEREKETYQTWLKGNTTGAARIRASVPSDWVVGDKTGSCGAYGTANDYAVVWPKNRAPLIISVYTTKNEKEAKHEDKVIAEASRIAIDNLK"},"dna_sequence":{"accession":"NG_070894.1","fmin":"0","fmax":"879","strand":"+","sequence":"ATGTCACTTAATGTAAAACCAAGTAGAATAGCCATCTTGTTTAGCTCTTTTTTAGTTTCAATATCATTTTTCTCACAGGCCAATACAAAGGGAATCGATGAGATTAAAAACCTTGAAACAGATTTCAATGGTAGAATTGGTGTCTACGCTTTAGACACTGGCTCAGGTAAATCATTTTCGTACAAAGCAAATGAACGATTTCCATTATGTAGTTCTTTCAAAGGTTTTTTAGCTGCTGCTGTATTAAAAGGCTCTCAAGATAATCAACTAAATCTTAATCAGATCGTGAATTATAATACAAGAAGTTTAGAGTTCTATTCACCCATCACAACTAAATATAAAGATAATGGAATGTCATTAGGTGATATGGCTGCTGCCGCTTTACAATATAGCGACAATGGTGCTACTAATATTATTCTTGAACGATATATCGGTGGTCCTGAGGGTATGACTAAATTCATGCGGTCGATTGGAGATAAAGATTTTAGACTCGATCGTTGGGAGTTAGATCTAAACACAGCAATTCCTGGCGATGAACGTGACACATCTACACCTGCAGCAGTAGCTAAGAGCCTGAAAACCCTTGCTCTGGGTAACATACTTAATGAGCGTGAAAAGGAAACCTATCAGACATGGTTAAAGGGTAACACAACCGGTGCAGCGCGTATTCGTGCTAGCGTACCAAGCGATTGGGTAGTTGGCGATAAAACTGGTAGTTGCGGAGCATACGGTACGGCAAATGATTATGCGGTAGTCTGGCCAAAGAACCGAGCTCCTCTTATAATTTCTGTATACACTACAAAAAACGAAAAAGAAGCCAAGCATGAGGATAAAGTAATCGCAGAAGCTTCAAGAATCGCAATTGATAACCTTAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3006184","ARO_id":"44646","ARO_name":"IMI-20","CARD_short_name":"IMI-20","ARO_description":"IMI-20 is a IMI beta-lactamase.","ARO_category":{"36027":{"category_aro_accession":"3000018","category_aro_cvterm_id":"36027","category_aro_name":"IMI beta-lactamase","category_aro_description":"IMI beta-lactamases are a group of TEM-1-like beta-lactamase that are known to hydrolyze imipenem. IMI beta-lactamases are inhibited by clavulanic acid and tazobactam.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4675":{"model_id":"4675","model_name":"IMI-21","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"7050":{"protein_sequence":{"accession":"WP_204376228.1","sequence":"MSLNVKPSRIGILFSSCLVLISFFSQANTKGIDEIKSLETDFNGRIGVYALDTGSGKSFSYRANERFPLCSSFKGFLAAAVLKGSQDNQLNLNQIVNYSTRSLEFHSPITTKYKDNGMSLGDMAAAALQYSDNGATNIILERYIGGPEGMTKFMRSIGDEVFRLDRWELDLNTAIPGDERDTSTPAAIGKSLENLALGNILSEREKETYQTWLKGNTTGATRIRASVPSDWVVGDKTGSCGAYGTANDYAVVWPKNRAPLIISVYTTKNQKEAKHDDKVIAEASRIAIDNLK"},"dna_sequence":{"accession":"NG_073464.1","fmin":"0","fmax":"879","strand":"+","sequence":"ATGTCACTTAATGTAAAACCAAGTAGAATAGGCATCCTGTTTAGCTCTTGTTTAGTTTTAATATCATTTTTCTCACAAGCCAATACAAAGGGCATCGATGAGATTAAAAGCCTTGAGACAGATTTCAATGGGAGGATTGGTGTCTACGCTTTGGACACTGGCTCGGGTAAATCATTTTCGTACAGAGCAAATGAACGATTTCCATTATGTAGTTCTTTTAAAGGTTTTTTAGCTGCTGCTGTATTAAAAGGTTCTCAAGATAATCAACTTAATCTTAATCAGATTGTAAATTATAGCACAAGAAGTTTAGAGTTCCATTCCCCCATTACAACTAAATATAAAGATAATGGAATGTCATTAGGTGATATGGCTGCTGCCGCTTTACAATATAGCGACAATGGTGCTACTAATATTATTCTTGAACGTTATATCGGTGGTCCTGAGGGTATGACTAAATTCATGCGGTCGATTGGAGATGAAGTTTTTAGACTCGATCGTTGGGAGTTAGATCTAAACACAGCTATTCCAGGCGATGAACGTGATACATCCACACCTGCAGCAATAGGTAAGAGCCTGGAAAACCTTGCTCTGGGTAACATACTTAGTGAACGTGAAAAGGAAACCTATCAGACATGGTTAAAGGGTAACACAACCGGCGCAACGCGTATTCGTGCTAGCGTACCAAGCGATTGGGTTGTTGGCGATAAAACTGGTAGTTGCGGAGCATACGGTACGGCAAATGATTATGCAGTAGTGTGGCCAAAGAACCGGGCTCCTCTTATAATTTCTGTATACACGACAAAAAACCAAAAAGAAGCTAAGCATGACGATAAAGTAATAGCAGAAGCTTCAAGAATTGCAATTGACAACCTTAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36926","NCBI_taxonomy_name":"Enterobacter asburiae","NCBI_taxonomy_id":"61645"}}}},"ARO_accession":"3006185","ARO_id":"44647","ARO_name":"IMI-21","CARD_short_name":"IMI-21","ARO_description":"IMI-21 is a IMI beta-lactamase.","ARO_category":{"36027":{"category_aro_accession":"3000018","category_aro_cvterm_id":"36027","category_aro_name":"IMI beta-lactamase","category_aro_description":"IMI beta-lactamases are a group of TEM-1-like beta-lactamase that are known to hydrolyze imipenem. IMI beta-lactamases are inhibited by clavulanic acid and tazobactam.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4676":{"model_id":"4676","model_name":"IMI-5","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"7051":{"protein_sequence":{"accession":"WP_085562405.1","sequence":"MSTTLRKSKPAFLLGSFLMSISLYSYANENGIDEIKNLEKKFNGRIGVYALDTGSGKSFAYRANERFPLCSSFKGFLAASVLKGSQDKQLNFSEIVNYNTRSLEPNSPITAKYKEQGMPLGEMAAAALQYSDNAATNIILERYIGGPVGMTKFMRSIGDEEFRLDRYELDLNTAIPGDERDTSTPEAVGKSLKNLALGNILNDSEKETYQTWLKGNTTGAARIRSSVPREWVVGDKTGTCGAYGTANDYAVVWPDDRAPLIISVYTTKYEKDAKHEEEFIAEASRIAIKTLN"},"dna_sequence":{"accession":"NG_054695.1","fmin":"100","fmax":"979","strand":"+","sequence":"ATGTCAACAACCTTAAGAAAAAGCAAACCTGCTTTTCTTCTTGGCTCTTTTTTAATGTCGATATCTTTGTATTCATATGCGAATGAAAATGGCATAGATGAGATAAAGAATCTTGAAAAAAAATTTAATGGAAGGATTGGTGTCTACGCTTTAGACACAGGCTCTGGCAAATCATTTGCATACAGAGCGAATGAACGCTTTCCTCTGTGCAGTTCATTTAAAGGTTTTTTAGCTGCTTCTGTATTAAAAGGTTCTCAAGATAAGCAACTTAACTTTAGCGAGATCGTAAATTACAATACAAGAAGTTTAGAACCCAATTCTCCCATCACGGCAAAATATAAAGAGCAAGGAATGCCACTTGGAGAAATGGCTGCTGCAGCTTTACAATATAGTGACAATGCTGCTACCAATATTATTCTTGAACGTTATATCGGTGGTCCTGTAGGTATGACTAAGTTCATGCGGTCGATCGGAGATGAAGAATTTAGACTAGATCGTTATGAACTAGATCTTAATACGGCTATTCCAGGAGATGAACGAGACACATCAACACCTGAAGCAGTGGGTAAAAGCTTAAAAAACCTCGCTCTGGGCAATATACTTAATGACAGTGAAAAAGAAACATATCAGACATGGTTAAAGGGTAATACAACAGGTGCAGCGCGCATTCGTTCTAGCGTACCGCGCGAATGGGTAGTTGGCGATAAAACTGGTACCTGTGGAGCATACGGTACGGCAAATGATTATGCGGTAGTCTGGCCAGATGACAGGGCACCACTTATCATTTCCGTATACACTACAAAATATGAAAAAGATGCCAAGCATGAAGAGGAATTTATTGCAGAAGCTTCAAGAATTGCGATTAAAACCCTTAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3001862","ARO_id":"38262","ARO_name":"IMI-5","CARD_short_name":"IMI-5","ARO_description":"IMI-5 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36027":{"category_aro_accession":"3000018","category_aro_cvterm_id":"36027","category_aro_name":"IMI beta-lactamase","category_aro_description":"IMI beta-lactamases are a group of TEM-1-like beta-lactamase that are known to hydrolyze imipenem. IMI beta-lactamases are inhibited by clavulanic acid and tazobactam.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4677":{"model_id":"4677","model_name":"IMI-6","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"7052":{"protein_sequence":{"accession":"WP_063860570.1","sequence":"MSLNVKPSRIAILFISCLFSISFFSQANTKGIDEIKNLETDFNGRVGVYALDTGSGKSFSYKANERFPLCSSFKGFLAAAVLKGSQDNQLNLNQIVNYNTRSLEFHSPITTKYKDNGMSLGDMAAAALQYSDNGATNIILERYIGGPEGMTKFMRSIGDEDFRLDRWELDLNTAIPGDERDTSTPAAVAKSLKTLALGNILSEREKETYQTWLKGNTTGAARIRASVPSDWVVGDKTGSCGAYGTANDYAVVWPKNRAPLIISVYTTKNEKEAKHEDKVIAEASRIAIDNLK"},"dna_sequence":{"accession":"NG_049168.1","fmin":"100","fmax":"979","strand":"+","sequence":"ATGTCACTTAATGTAAAACCAAGTAGAATAGCCATCTTGTTTATCTCTTGTTTATTTTCAATATCATTTTTCTCACAGGCCAATACAAAGGGTATCGATGAGATTAAAAACCTTGAAACAGATTTCAATGGTAGAGTTGGTGTCTACGCTTTAGACACTGGCTCAGGTAAATCATTTTCGTACAAAGCAAATGAACGATTTCCATTATGTAGTTCTTTCAAAGGCTTTTTAGCTGCTGCTGTATTAAAAGGCTCTCAAGATAATCAACTCAATCTTAATCAGATCGTGAATTACAATACAAGAAGTTTAGAGTTCCATTCACCCATCACAACTAAATATAAAGATAATGGAATGTCATTAGGTGATATGGCTGCTGCCGCTTTACAATATAGCGACAATGGTGCTACTAATATTATTCTTGAACGTTATATCGGTGGTCCTGAGGGTATGACTAAATTCATGCGGTCGATTGGAGATGAAGATTTTAGACTCGATCGTTGGGAGTTAGATCTAAACACAGCTATTCCAGGCGATGAACGTGACACATCTACACCTGCAGCAGTAGCTAAGAGCCTGAAAACTCTTGCTCTGGGTAACATACTTAGTGAGCGTGAAAAGGAAACCTATCAGACATGGTTAAAGGGTAACACAACCGGTGCAGCGCGTATTCGTGCTAGCGTACCAAGCGATTGGGTAGTTGGCGATAAAACTGGTAGTTGCGGAGCATACGGTACTGCAAATGATTATGCGGTAGTCTGGCCAAAGAACCGGGCTCCTCTTATAATTTCTGTATACACAACAAAAAACGAAAAAGAAGCCAAGCATGAGGATAAAGTAATCGCAGAAGCTTCAAGAATCGCAATTGATAACCTTAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"45686","NCBI_taxonomy_name":"Raoultella ornithinolytica","NCBI_taxonomy_id":"54291"}}}},"ARO_accession":"3001863","ARO_id":"38263","ARO_name":"IMI-6","CARD_short_name":"IMI-6","ARO_description":"IMI-6 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36027":{"category_aro_accession":"3000018","category_aro_cvterm_id":"36027","category_aro_name":"IMI beta-lactamase","category_aro_description":"IMI beta-lactamases are a group of TEM-1-like beta-lactamase that are known to hydrolyze imipenem. IMI beta-lactamases are inhibited by clavulanic acid and tazobactam.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4678":{"model_id":"4678","model_name":"IMI-9","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"7053":{"protein_sequence":{"accession":"WP_060571602.1","sequence":"MSLNVKPSRIAILFSSCLVSISFFSQANTKGIDEIKNLETDFNGRIGVYALDTGSGKSFSYKANERFPLCSSFKGFLAAAVLKGSQDNQLNLNQIVNYNTRSLEFHSPITTKYKDNGMSLGDMAAAALQYSDNGATNIILERYIGGPEGMTKFMRSIGDKDFRLDRWELDLNTAIPGDERDTSTPAAVAKSVKTLALGNILNEREKETYQTWLKGNTTGAARIRASVPSDWVVGDKTGSCGAYGTANDYAVVWPKNRAPLIISVYTTKNEKEAKHDDKVIAEASRIAIDNLK"},"dna_sequence":{"accession":"NG_049171.1","fmin":"100","fmax":"979","strand":"+","sequence":"ATGTCACTTAATGTAAAACCAAGTAGAATAGCCATCTTGTTTAGCTCTTGTTTAGTTTCAATATCATTTTTCTCACAGGCCAATACAAAGGGCATCGATGAGATTAAAAACCTTGAAACAGATTTCAATGGTAGAATTGGTGTCTACGCTTTAGACACTGGCTCAGGTAAATCATTTTCATACAAAGCAAATGAACGATTTCCATTATGTAGTTCTTTCAAAGGTTTTTTAGCTGCTGCTGTATTAAAAGGCTCTCAAGATAATCAACTAAATCTTAATCAGATCGTGAATTACAATACAAGAAGTTTAGAGTTCCATTCACCCATCACAACTAAATATAAAGATAATGGAATGTCATTAGGTGATATGGCTGCTGCCGCTTTACAATATAGCGACAATGGTGCTACTAATATTATTCTTGAACGATATATCGGTGGTCCTGAGGGTATGACTAAATTCATGCGGTCGATTGGAGATAAAGATTTTAGACTCGATCGTTGGGAGTTAGATCTAAACACAGCTATTCCTGGCGATGAACGTGACACATCTACACCTGCAGCAGTAGCTAAGAGCGTGAAAACCCTTGCTCTGGGTAACATACTTAATGAGCGTGAAAAGGAAACCTATCAGACATGGTTAAAGGGTAACACAACCGGTGCAGCACGTATTCGTGCTAGCGTACCAAGCGATTGGGTAGTTGGCGATAAAACTGGTAGTTGCGGAGCATACGGTACGGCAAATGATTATGCGGTAGTCTGGCCAAAGAACCGAGCTCCTCTTATAATTTCTGTATACACTACAAAAAACGAAAAAGAAGCCAAGCATGACGATAAAGTAATCGCAGAAGCTTCAAGAATCGCAATTGATAACCTTAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3003143","ARO_id":"39720","ARO_name":"IMI-9","CARD_short_name":"IMI-9","ARO_description":"IMI-9 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36027":{"category_aro_accession":"3000018","category_aro_cvterm_id":"36027","category_aro_name":"IMI beta-lactamase","category_aro_description":"IMI beta-lactamases are a group of TEM-1-like beta-lactamase that are known to hydrolyze imipenem. IMI beta-lactamases are inhibited by clavulanic acid and tazobactam.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4679":{"model_id":"4679","model_name":"IMP-17","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"7054":{"protein_sequence":{"accession":"WP_063860577.1","sequence":"MKKLFVLCVCFFCSITAAGAALPDLKIEKLEEGVFVHTSFEEVNGWGVVTKHGLVVLVNTDAYLIDTPFTATDTEKLVNWFVERGYEIKGTISSHFHSDSTGGIEWLNSQSIPTYASELTNELLKKSGKVQAKYSFSGVSYWLVKNKIEVFYPGPGHTQDNLVVWLPESEILFGGCFIKPHGLGNLGDANLEAWPKSAKILMSKYGKAKLVVSSHSEKGDASLMKRTWEQALKGLKESKKTSSPSN"},"dna_sequence":{"accession":"NG_049180.1","fmin":"100","fmax":"841","strand":"+","sequence":"ATGAAGAAATTATTTGTTTTATGTGTATGCTTCTTTTGTAGCATTACTGCCGCAGGAGCGGCTTTACCTGATTTAAAAATCGAGAAGCTTGAAGAAGGTGTTTTTGTTCATACATCGTTCGAAGAGGTTAACGGTTGGGGGGTTGTTACTAAACACGGTTTAGTGGTGCTTGTAAACACAGACGCCTATCTAATTGACACTCCATTTACTGCTACAGACACTGAAAAATTAGTCAATTGGTTTGTGGAGCGCGGCTATGAAATCAAAGGCACTATTTCATCACATTTCCATAGCGACAGCACAGGAGGAATAGAGTGGCTTAATTCTCAATCTATTCCCACGTATGCATCTGAATTAACAAATGAACTTTTGAAAAAATCCGGTAAGGTACAAGCTAAATATTCATTTAGCGGAGTTAGCTATTGGCTAGTTAAAAATAAAATTGAAGTTTTCTACCCTGGCCCAGGTCACACTCAAGATAACCTAGTGGTTTGGTTGCCTGAAAGTGAAATTTTATTCGGTGGTTGCTTTATTAAACCTCACGGTCTTGGCAATTTAGGTGACGCAAATTTAGAAGCTTGGCCAAAGTCCGCCAAAATATTAATGTCTAAATATGGCAAAGCAAAGCTTGTTGTTTCAAGTCATAGTGAAAAAGGGGACGCATCACTAATGAAACGTACATGGGAACAAGCCCTTAAAGGGCTTAAAGAAAGTAAAAAAACATCATCACCAAGTAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002208","ARO_id":"38608","ARO_name":"IMP-17","CARD_short_name":"IMP-17","ARO_description":"IMP-17 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4680":{"model_id":"4680","model_name":"IMP-23","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"7055":{"protein_sequence":{"accession":"WP_063860582.1","sequence":"MKKLFVLCVCFLCSITAAGAALPDLKIEKLEEGVYVHTSFEEVNGWGVFSKHGLVVLVNTDAYLIDTPFTATDTEKLVNWFVERGYKIKGTISSHFHSDSTGGIEWLNSQSIPTYASELTNELLKKDGKVQAKNSFSGVSYWLVKNKIEVFYPGPGHTQDNVVVWLPEKKILFGGCFVKPDGLGNLGDANLEAWPKSAKILMSKYGKAKLVVSSHSEIGDASLLKRTWEQAVKGLNESKKPSQPSN"},"dna_sequence":{"accession":"NG_049187.1","fmin":"0","fmax":"741","strand":"+","sequence":"ATGAAGAAATTATTTGTTTTATGTGTATGCTTCCTTTGTAGCATTACTGCCGCAGGAGCGGCTTTGCCTGATTTAAAAATCGAGAAGCTTGAAGAAGGTGTTTATGTTCATACATCGTTCGAAGAAGTTAACGGTTGGGGTGTTTTTTCTAAACACGGTTTGGTGGTTCTTGTAAACACTGACGCCTATCTGATTGACACTCCATTTACTGCTACAGATACTGAAAAGTTAGTCAATTGGTTTGTGGAGCGCGGCTATAAAATCAAAGGCACTATTTCCTCACATTTCCATAGCGACAGCACAGGGGGAATAGAGTGGCTTAATTCTCAATCTATTCCCACGTATGCATCTGAATTAACAAATGAACTTCTTAAAAAAGACGGTAAGGTGCAAGCTAAAAACTCATTTAGCGGAGTTAGTTATTGGCTAGTTAAAAATAAAATTGAAGTTTTTTATCCCGGCCCGGGGCACACTCAAGATAACGTAGTGGTTTGGTTACCTGAAAAGAAAATTTTATTCGGTGGTTGTTTTGTTAAACCGGACGGTCTTGGTAATTTGGGTGACGCAAATTTAGAAGCTTGGCCAAAGTCCGCCAAAATATTAATGTCTAAATATGGTAAAGCAAAACTGGTTGTTTCAAGTCATAGTGAAATTGGGGACGCATCACTCTTGAAACGTACATGGGAACAGGCTGTTAAAGGGCTAAATGAAAGTAAAAAACCATCACAGCCAAGTAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3002214","ARO_id":"38614","ARO_name":"IMP-23","CARD_short_name":"IMP-23","ARO_description":"IMP-23 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4681":{"model_id":"4681","model_name":"IMP-39","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"7056":{"protein_sequence":{"accession":"WP_136512068.1","sequence":"MKKLFVLCVCFLCSITAAGAALPDLKIEKLEEGVYVHTSFEEVNGWGVVSKHGLVVLVNTDAYLIDTPFTATDTEKLVNWFVERGYKIKGTISSHFHSDSTGGIEWLNSQSIPTYASELTNELLKKDGKVQAKHSFSGVSYWLVKNKIEVFYPGPGHTQDNVVVWLPENKILFGGCFVKPHGLGNLGDANLEAWPKSAKILMSKYGKAKLVVSSHSETGGASLLKRTWEQALKGLKESKKPSPPSN"},"dna_sequence":{"accession":"NG_064724.1","fmin":"0","fmax":"741","strand":"+","sequence":"ATGAAGAAATTATTTGTTTTATGTGTATGCTTCCTTTGTAGCATTACTGCCGCAGGAGCGGCTTTGCCTGATTTAAAAATCGAGAAGCTTGAAGAAGGTGTTTATGTTCATACATCGTTCGAAGAAGTTAACGGTTGGGGTGTTGTTTCTAAACACGGATTGGTGGTTCTTGTAAACACTGACGCCTATCTGATTGACACTCCATTTACTGCTACAGATACTGAAAAGTTAGTCAATTGGTTTGTGGAGCGCGGCTATAAAATCAAAGGCACTATTTCCTCACATTTCCATAGCGACAGCACAGGGGGAATAGAGTGGCTTAATTCTCAATCTATTCCCACGTATGCATCTGAATTAACAAATGAACTTCTTAAAAAAGACGGTAAGGTGCAAGCTAAACACTCATTTAGCGGAGTTAGTTATTGGCTAGTCAAAAATAAAATTGAAGTTTTTTATCCTGGCCCAGGCCACACTCAAGATAACGTAGTGGTTTGGTTACCTGAAAATAAAATTTTATTCGGTGGTTGCTTTGTTAAACCTCACGGTCTTGGTAATTTGGGTGACGCAAATTTAGAAGCTTGGCCAAAGTCCGCCAAAATATTAATGTCTAAATATGGTAAAGCAAAACTTGTTGTTTCAAGTCATAGTGAAACTGGGGGCGCATCACTATTGAAACGTACATGGGAACAGGCTCTTAAAGGGCTTAAAGAAAGTAAAAAGCCATCACCGCCAAGTAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002230","ARO_id":"38630","ARO_name":"IMP-39","CARD_short_name":"IMP-39","ARO_description":"IMP-39 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4682":{"model_id":"4682","model_name":"IMP-46","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"7057":{"protein_sequence":{"accession":"WP_136512069.1","sequence":"MKKLFVLCVFLLCNIATAEDSLPDLKIDKLEEGVYVHTSFEEVKGWNVVTKHGLVVLVKNDAYLIDTPITVKDTEKLVNWLVERGYKIKGSISTHFHDDSSAGIEWLNSQSIPTYASRLTNELRKKGGKPQATNSFDGVSYSLIKNKIEVFYPGPGHTQDNVVVWLPEKKILFGGCFVKPDGLGYLGDANLEAWPKSAKILMSKYAKAKLVVSSHSEIGDTSLLKRTWEQAVKGLNESKKP"},"dna_sequence":{"accession":"NG_064725.1","fmin":"0","fmax":"726","strand":"+","sequence":"ATGAAAAAATTATTTGTTTTATGTGTATTCTTGCTTTGTAACATTGCTACTGCAGAAGATTCTTTGCCTGATTTAAAAATTGATAAGCTTGAAGAAGGAGTTTATGTTCATACTTCGTTTGAAGAAGTTAAAGGTTGGAATGTAGTCACAAAACACGGTCTGGTGGTTCTTGTAAAAAATGACGCCTATCTGATTGATACTCCAATTACTGTTAAAGATACTGAAAAATTAGTCAATTGGTTGGTTGAGCGTGGCTATAAAATCAAAGGCAGTATTTCAACACATTTCCATGATGATAGTTCAGCTGGAATAGAATGGCTTAATTCTCAATCTATTCCCACGTATGCATCGAGATTAACAAATGAACTTCGTAAAAAAGGCGGCAAGCCGCAAGCTACTAACTCTTTTGATGGCGTTAGTTATTCACTCATTAAAAACAAGATTGAAGTTTTTTATCCAGGCCCAGGGCACACTCAAGATAACGTAGTAGTTTGGTTACCTGAAAAGAAAATTTTATTCGGTGGTTGTTTTGTTAAACCGGACGGTCTTGGATATTTGGGGGACGCAAATTTAGAGGCTTGGCCAAAGTCCGCTAAAATATTAATGTCTAAATATGCTAAGGCAAAACTGGTCGTTTCAAGTCACAGTGAAATTGGGGATACATCACTCTTGAAACGTACATGGGAACAAGCTGTTAAAGGGCTAAATGAAAGTAAAAAGCCATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36803","NCBI_taxonomy_name":"Pseudomonas putida","NCBI_taxonomy_id":"303"}}}},"ARO_accession":"3002237","ARO_id":"38637","ARO_name":"IMP-46","CARD_short_name":"IMP-46","ARO_description":"IMP-46 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4683":{"model_id":"4683","model_name":"IMP-53","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"7058":{"protein_sequence":{"accession":"WP_063860614.1","sequence":"MSKLFVFFMFLFCSITAAGESLPDLKIEKLDEGVYVHTSFEEVNGWGVIPKHGLVVLVNTDAYLIDTPFTAKDTENLVNWFVERGYRIKGSISSHFHSDSTGGIEWLNSQSIPTYASELTNELLKKDGKVQAKYSFSGVSYWLVKKKIEVFYPGSGHAPDNVVVWLPENRVLFGGCFVKPYGLGNLGDANLEAWPKSAKLLMSKYSKAKLVVPGHSDIGDSSLLKLTWEQTVKGFNESKKSTTAH"},"dna_sequence":{"accession":"NG_049215.1","fmin":"100","fmax":"838","strand":"+","sequence":"ATGAGCAAGTTATTTGTATTCTTTATGTTTTTGTTTTGTAGCATTACTGCCGCAGGAGAGTCTTTGCCAGATTTAAAAATTGAGAAGCTTGACGAAGGCGTTTATGTTCATACTTCGTTTGAAGAAGTTAACGGTTGGGGTGTTATTCCTAAACACGGCTTGGTGGTTCTTGTAAATACTGATGCCTATCTGATAGACACTCCATTTACTGCTAAAGATACTGAAAATTTAGTTAATTGGTTTGTTGAGCGCGGCTATAGAATAAAAGGCAGTATTTCCTCACATTTCCATAGCGACAGCACGGGTGGAATAGAGTGGCTTAATTCTCAATCTATCCCCACGTATGCATCTGAATTAACAAATGAACTTCTTAAAAAAGACGGTAAGGTACAAGCTAAATATTCATTTAGCGGAGTTAGCTATTGGCTAGTTAAGAAAAAGATTGAAGTTTTTTATCCTGGTTCAGGGCACGCTCCAGATAACGTAGTGGTTTGGCTGCCTGAAAATAGAGTTTTGTTCGGTGGTTGTTTTGTTAAACCCTACGGTCTAGGTAATTTGGGTGACGCAAATTTAGAAGCTTGGCCAAAATCCGCCAAATTATTAATGTCAAAATATAGTAAGGCAAAACTGGTTGTACCAGGTCATAGTGACATAGGAGATTCGTCGCTCTTGAAGCTTACATGGGAGCAGACGGTAAAAGGATTCAATGAAAGCAAAAAAAGTACCACTGCACATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005463","ARO_id":"43925","ARO_name":"IMP-53","CARD_short_name":"IMP-53","ARO_description":"IMP-53 is a IMP beta-lactamase.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4684":{"model_id":"4684","model_name":"IMP-54","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"7059":{"protein_sequence":{"accession":"WP_063860615.1","sequence":"MKKLFVLCVFFFCNIAVAEESLPDLKIEKLEEGVYVHTSFEEVKGWSVVTKHGLVVLVKNDAYLIDTPVTAKDTEKLVNWFVERGYKIKGSISTHFHGDSTAGIEWLNSQSIPTYASELTNELLKKDNKVQAKHSFNGVSYSLIKNKIEVFYPGPGHTQDNVVVWLPEKKILFGGCFVKPDGLGYLGDANLEAWPKSAKILMSKYGKAKLVVSSHSDIGDVSLLKRTWEQAVKGLNESKKSSQPSD"},"dna_sequence":{"accession":"NG_049216.1","fmin":"0","fmax":"741","strand":"+","sequence":"ATGAAAAAATTATTTGTTTTATGTGTATTCTTCTTCTGCAACATTGCAGTTGCAGAAGAATCTTTGCCTGATTTAAAAATTGAGAAGCTTGAAGAAGGCGTTTATGTTCATACTTCGTTTGAAGAAGTTAAAGGTTGGAGTGTGGTCACTAAACACGGTTTGGTGGTTCTTGTGAAAAATGACGCCTATCTGATTGATACTCCAGTTACTGCTAAAGATACTGAAAAATTAGTCAATTGGTTTGTTGAGCGGGGCTATAAAATCAAAGGCAGTATTTCCACACATTTCCATGGTGACAGTACGGCTGGAATAGAGTGGCTTAATTCTCAATCTATCCCCACATATGCTTCTGAATTAACAAATGAACTTCTTAAAAAAGACAATAAGGTACAAGCTAAACACTCTTTTAATGGGGTTAGTTATTCACTAATTAAAAACAAAATTGAAGTTTTTTATCCAGGCCCAGGGCACACTCAAGATAACGTAGTGGTTTGGTTACCTGAAAAGAAAATTTTATTCGGTGGTTGCTTTGTTAAACCGGACGGTCTTGGCTATTTGGGGGACGCAAATTTAGAAGCTTGGCCAAAGTCCGCTAAAATATTAATGTCTAAATATGGTAAAGCAAAACTAGTTGTGTCGAGTCATAGTGATATTGGAGATGTATCACTCTTGAAACGTACATGGGAGCAGGCTGTTAAAGGGCTGAATGAAAGTAAAAAATCATCACAGCCAAGCGACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005464","ARO_id":"43926","ARO_name":"IMP-54","CARD_short_name":"IMP-54","ARO_description":"IMP-54 is a IMP beta-lactamase.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4685":{"model_id":"4685","model_name":"IMP-58","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"7060":{"protein_sequence":{"accession":"WP_063860618.1","sequence":"MKKLFVLCVFLFCSITAAGESLPDLKIEKLEEGVYVHTSFEEVNGWGVFSKHGLVILVNTDAYLIDTPFTAKDTEKLVTWFVERGYKIKGSISSHFHSDSTGGIEWLNSQSIPTYASELTNDLLKQNGKVQAKNSFSGVSYWLVKNKIEVFYPGPGHTQDNVVVWLPEKKILFGGCFVKPYGLGNLDDANVVAWPHSAEILMSRYGNAKLVVPSHSDIGDASLLKLTWEQAVKGLKESKKPSEPSN"},"dna_sequence":{"accession":"NG_049219.1","fmin":"0","fmax":"741","strand":"+","sequence":"ATGAAGAAATTATTTGTTTTATGTGTGTTTTTGTTTTGTAGCATTACTGCCGCAGGAGAGTCTTTGCCCGATTTAAAAATTGAAAAGCTTGAAGAAGGTGTTTATGTTCATACATCGTTTGAAGAAGTTAATGGTTGGGGCGTTTTTTCTAAACACGGTTTGGTTATTCTTGTGAATACTGACGCCTATCTGATTGACACTCCATTCACGGCTAAAGATACTGAAAAGTTAGTCACCTGGTTTGTGGAGCGCGGCTATAAAATCAAAGGTAGCATTTCCTCACATTTCCATAGCGACAGCACGGGTGGAATAGAGTGGCTTAATTCTCAATCAATTCCCACGTATGCATCTGAATTAACAAATGACCTTCTTAAACAAAACGGTAAGGTACAAGCTAAAAACTCATTTAGCGGAGTTAGTTATTGGTTAGTTAAAAATAAAATTGAAGTTTTCTATCCCGGCCCCGGGCACACTCAAGATAACGTAGTGGTTTGGTTGCCTGAAAAGAAAATTTTATTTGGTGGGTGCTTTGTTAAACCGTACGGTCTTGGAAATCTCGATGACGCAAATGTTGTAGCATGGCCACATTCTGCTGAAATATTAATGTCTAGGTATGGTAATGCAAAACTGGTTGTTCCAAGCCATAGTGACATCGGAGATGCGTCGCTCTTGAAGCTTACATGGGAGCAGGCTGTTAAAGGGCTAAAAGAAAGTAAAAAACCATCGGAGCCAAGTAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36803","NCBI_taxonomy_name":"Pseudomonas putida","NCBI_taxonomy_id":"303"}}}},"ARO_accession":"3005465","ARO_id":"43927","ARO_name":"IMP-58","CARD_short_name":"IMP-58","ARO_description":"IMP-58 is a IMP beta-lactamase.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4686":{"model_id":"4686","model_name":"IMP-59","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"7061":{"protein_sequence":{"accession":"WP_094009805.1","sequence":"MSKLSVFFIFLFCSIATAAEPLPDLKIEKLDEGVYVHTSFEEVNGWGVVPKHGLVVLVDAEAYLIDTPFTAKDTEKLVTWFVERGYKIKGSISSHFHSDSTGGIEWLNSQSIPTYASELTNELLKKDGKVQAKNSFGGVNYWLVKNKIEVFYPGPGHTPDNLVVWLPERKILFGGCFIKPYGLGYLGDANLEAWPKSAKLLISKYGKAKLVVPSHSEAGDASLLKLTLEQAVKGLNESKKPSKLSN"},"dna_sequence":{"accession":"NG_055477.1","fmin":"0","fmax":"741","strand":"+","sequence":"ATGAGCAAGTTATCTGTATTCTTTATATTTTTGTTTTGTAGCATTGCTACCGCAGCAGAGCCTTTGCCAGATTTAAAAATTGAAAAACTTGATGAAGGCGTTTATGTTCATACTTCGTTTGAAGAAGTTAACGGGTGGGGCGTTGTTCCTAAACATGGTTTGGTTGTTCTTGTAGATGCTGAAGCTTATCTAATTGACACTCCATTTACGGCTAAAGATACTGAAAAGTTAGTCACTTGGTTTGTGGAACGTGGCTATAAAATAAAAGGCAGTATTTCCTCTCATTTTCATAGTGACAGCACGGGCGGAATAGAGTGGCTTAATTCTCAATCCATCCCCACGTATGCGTCTGAATTAACTAATGAGCTGCTTAAAAAAGACGGTAAGGTTCAAGCTAAAAATTCATTTGGCGGGGTTAACTATTGGCTAGTTAAAAATAAAATTGAAGTTTTTTATCCAGGCCCAGGACACACTCCAGATAACCTAGTAGTTTGGCTGCCTGAAAGGAAAATATTATTCGGTGGTTGTTTTATTAAACCGTACGGTCTAGGTTATTTGGGTGACGCAAATTTAGAAGCTTGGCCAAAGTCCGCTAAATTATTAATATCCAAATATGGTAAGGCAAAACTGGTTGTTCCAAGTCACAGTGAAGCTGGAGACGCATCACTCTTGAAACTTACATTAGAGCAGGCGGTTAAAGGGTTAAACGAAAGTAAAAAACCATCAAAACTAAGCAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3005466","ARO_id":"43928","ARO_name":"IMP-59","CARD_short_name":"IMP-59","ARO_description":"IMP-59 is a IMP beta-lactamase.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4687":{"model_id":"4687","model_name":"IMP-60","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"7062":{"protein_sequence":{"accession":"WP_065102288.1","sequence":"MSKLSVFFIFLFCSIATAAESLPDLKIEKLDEGVYVHTSFEEVNGWGVVPKHGLVVLVNAEAYLIDTPFTAKDTEKLVTWFVERGYKIKGSISSHFHSDSTGGIEWLNSRSIPTYASELTNELLKKDGKVQATNSFSGVNYWLVKNKIEVFYPGPGHTPDNVVVWLPKRKILFGGCFIKPYGLGNLGDANIEAWPKSAKLLKSKYGKAKLVVPSHSEVGDASLLKLTLEQAVKGLNESKKPSKPSN"},"dna_sequence":{"accession":"NG_050945.1","fmin":"0","fmax":"741","strand":"+","sequence":"ATGAGCAAGTTATCTGTATTCTTTATATTTTTGTTTTGCAGCATTGCTACCGCAGCAGAGTCTTTGCCAGATTTAAAAATTGAAAAGCTTGATGAAGGCGTTTATGTTCATACTTCGTTTGAAGAAGTTAACGGGTGGGGCGTTGTTCCTAAACATGGTTTGGTGGTTCTTGTAAATGCTGAGGCTTACCTAATTGACACTCCATTTACGGCTAAAGATACTGAAAAGTTAGTCACTTGGTTTGTGGAGCGTGGCTATAAAATAAAAGGCAGCATTTCCTCTCATTTTCATAGCGACAGCACGGGCGGAATAGAGTGGCTTAATTCTCGATCTATCCCCACGTATGCATCTGAATTAACAAATGAACTGCTTAAAAAAGACGGTAAGGTTCAAGCCACAAATTCATTTAGCGGAGTTAACTATTGGCTAGTTAAAAATAAAATTGAAGTTTTTTATCCAGGCCCGGGACACACTCCAGATAACGTAGTGGTTTGGTTGCCTAAAAGGAAAATATTATTCGGTGGTTGTTTTATTAAACCGTACGGTTTAGGCAATTTGGGTGACGCAAATATAGAAGCTTGGCCAAAGTCCGCCAAATTATTAAAGTCCAAATATGGTAAGGCAAAACTGGTTGTTCCAAGTCACAGTGAAGTTGGAGACGCATCACTCTTGAAACTTACATTAGAGCAGGCGGTTAAAGGGTTAAACGAAAGTAAAAAACCATCAAAACCAAGCAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3005467","ARO_id":"43929","ARO_name":"IMP-60","CARD_short_name":"IMP-60","ARO_description":"IMP-60 is a IMP beta-lactamase.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4688":{"model_id":"4688","model_name":"IMP-61","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"7063":{"protein_sequence":{"accession":"WP_065419570.1","sequence":"MSKLSVFFIFLFCSIATAAESLPDLKIEKLDEGVYVHTSFEEVNGWGVVPKHGLVVLVNAEAYLIDTPFTAKDTEKLVTWFVERGYKIKGSISSHFHSDSTGGIEWLISRSIPTYASELTNELLKKDGKVQATNSFSGVNYWLVKNKIEVFYPGPGHTPDNVVVWLPERKILFGGCFIKPYGLGNLGDANIEAWPKSAKLLKSKYGKAKLVVPSHSEVGDASLLKLTLEQAVKGLNESKKPSKPSN"},"dna_sequence":{"accession":"NG_051166.1","fmin":"0","fmax":"741","strand":"+","sequence":"ATGAGCAAGTTATCTGTATTCTTTATATTTTTGTTTTGCAGCATTGCTACCGCAGCAGAGTCTTTGCCAGATTTAAAAATTGAAAAGCTTGATGAAGGCGTTTATGTTCATACTTCGTTTGAAGAAGTTAACGGGTGGGGCGTTGTTCCTAAACATGGTTTGGTGGTTCTTGTAAATGCTGAGGCTTACCTAATTGACACTCCATTTACGGCTAAAGATACTGAAAAGTTAGTCACTTGGTTTGTGGAGCGTGGCTATAAAATAAAAGGCAGCATTTCCTCTCATTTTCATAGCGACAGCACGGGCGGAATAGAGTGGCTTATTTCTCGATCTATCCCCACGTATGCATCTGAATTAACAAATGAACTGCTTAAAAAAGACGGTAAGGTTCAAGCCACAAATTCATTTAGCGGAGTTAACTATTGGCTAGTTAAAAATAAAATTGAAGTTTTTTATCCAGGCCCGGGACACACTCCAGATAACGTAGTGGTTTGGTTGCCTGAAAGGAAAATATTATTCGGTGGTTGTTTTATTAAACCGTACGGTTTAGGCAATTTGGGTGACGCAAATATAGAAGCTTGGCCAAAGTCCGCCAAATTATTAAAGTCCAAATATGGTAAGGCAAAACTGGTTGTTCCAAGTCACAGTGAAGTTGGAGACGCATCACTCTTGAAACTTACATTAGAGCAGGCGGTTAAAGGGTTAAACGAAAGTAAAAAACCATCAAAACCAAGCAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005468","ARO_id":"43930","ARO_name":"IMP-61","CARD_short_name":"IMP-61","ARO_description":"IMP-61 is a IMP beta-lactamase.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4689":{"model_id":"4689","model_name":"IMP-62","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"7064":{"protein_sequence":{"accession":"WP_069280710.1","sequence":"MNKLSVFFMFMFCSITAAGESLPDLKIEKLDEGVYVHTSFEEVNGWGVVPKHGLVVLVNTEAYLIDTPFTAKDTEKLVTWFVERGYKIKGSISSHFHSDSTGGIEWLNSQSIPTYASELTNELLKKDGKVQAKNSFSGGSYWLVNNKIEVFYPGPGHTPDNVVVWLPENRVLFGGCFVKPYGLGNLGDANLEAWPKSAKILMSKYGKAKLVVSGHSETGNASLLKLTWEQAVKGLKESKKPSLPSN"},"dna_sequence":{"accession":"NG_051513.1","fmin":"0","fmax":"741","strand":"+","sequence":"ATGAACAAGTTATCTGTATTCTTTATGTTTATGTTTTGTAGCATTACTGCCGCAGGAGAGTCTTTGCCAGATTTAAAAATTGAGAAGCTTGACGAAGGTGTTTATGTTCATACTTCGTTTGAAGAAGTTAACGGTTGGGGTGTTGTTCCTAAACACGGCTTGGTGGTTCTTGTAAATACTGAGGCCTATCTGATTGACACTCCATTTACGGCAAAAGATACTGAAAAGTTAGTCACTTGGTTTGTGGAGCGCGGCTATAAAATAAAAGGCAGTATTTCCTCTCATTTTCATAGCGACAGCACGGGCGGAATAGAGTGGCTTAATTCTCAATCTATCCCCACGTATGCATCTGAATTAACAAATGAACTTCTTAAAAAAGACGGTAAGGTACAAGCTAAAAATTCATTTAGCGGAGGTAGCTATTGGCTAGTTAATAATAAGATTGAAGTTTTTTATCCTGGTCCAGGGCACACTCCAGATAACGTAGTGGTTTGGCTACCTGAAAATAGAGTTTTGTTCGGTGGTTGTTTTGTTAAACCGTACGGTCTTGGTAATTTGGGTGACGCAAATTTAGAAGCTTGGCCAAAGTCCGCCAAAATATTAATGTCTAAATATGGTAAAGCAAAGTTGGTTGTTTCAGGTCATAGTGAAACTGGGAACGCATCACTCTTGAAACTTACTTGGGAGCAGGCTGTTAAAGGGCTAAAAGAAAGTAAAAAACCATCACTGCCAAGTAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005469","ARO_id":"43931","ARO_name":"IMP-62","CARD_short_name":"IMP-62","ARO_description":"IMP-62 is a IMP beta-lactamase.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4690":{"model_id":"4690","model_name":"IMP-63","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"7065":{"protein_sequence":{"accession":"WP_071593225.1","sequence":"MKKLFVLCIFLFLSITASGEVLPDLKIEKLEEGVYLHTSFEEVSGWGVVTKHGLVVLVNNDAYLIDTPFTNKDTEKLVAWFVGRGFTIKGSVSSHFHSDSTGGIEWLNSQSIPTYASELTNELLKKNGKVQATNSFSGVSYWLVKNKIEIFYPGPGHTQDNVVVWLPENKILFGGCFVKPDGLGNLDDANLKAWPKSAKILMSKYGKAKLVVSSHSEIGNASLLKLTWEQAVKGLKESKKPLLPSN"},"dna_sequence":{"accession":"NG_052049.1","fmin":"0","fmax":"741","strand":"+","sequence":"ATGAAGAAATTATTTGTTTTATGCATTTTTTTGTTTTTAAGTATTACTGCCTCAGGTGAGGTTTTGCCTGATTTGAAAATTGAGAAGCTTGAAGAGGGTGTTTATCTTCATACATCTTTTGAAGAGGTTAGCGGTTGGGGTGTTGTTACTAAACATGGTTTGGTAGTTCTTGTAAATAATGACGCCTATCTAATTGACACTCCATTTACAAATAAAGATACTGAAAAATTAGTTGCTTGGTTTGTAGGGCGCGGCTTTACAATAAAGGGAAGTGTTTCCTCACATTTTCATAGCGACAGTACGGGTGGAATAGAGTGGCTTAATTCTCAATCTATTCCCACGTATGCATCTGAGTTAACAAATGAACTTCTGAAAAAGAACGGTAAGGTGCAAGCTACAAATTCATTTAGCGGGGTTAGTTATTGGCTAGTTAAAAATAAAATTGAAATTTTTTATCCCGGCCCAGGACATACTCAAGATAACGTAGTGGTTTGGCTACCTGAAAACAAAATTTTATTCGGTGGTTGTTTTGTTAAACCGGACGGTCTTGGTAATTTGGATGACGCAAATTTAAAAGCTTGGCCAAAGTCCGCAAAAATATTAATGTCTAAATATGGTAAAGCAAAGTTAGTTGTTTCAAGTCATAGTGAAATTGGGAACGCATCACTCTTGAAACTTACTTGGGAGCAGGCTGTTAAAGGGCTAAAAGAAAGTAAAAAACCATTACTGCCAAGTAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37066","NCBI_taxonomy_name":"Pseudomonas","NCBI_taxonomy_id":"286"}}}},"ARO_accession":"3005470","ARO_id":"43932","ARO_name":"IMP-63","CARD_short_name":"IMP-63","ARO_description":"IMP-63 is a IMP beta-lactamase.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4691":{"model_id":"4691","model_name":"IMP-64","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"7066":{"protein_sequence":{"accession":"WP_071593226.1","sequence":"MKKLFVLCVFVFCSITVAAETLPNLRVEKLEEGVYVHTSYEEVKGWGVVTKHGLVVLIGADAYLIDTPFTAKDTEKLVNWFVERGYKIKGTVSSHFHSDSTGGIEWLNSQSIPTYASELTNELLKKDGKVQAKNSFDGVSYWLAKDKIEVFYPGPGHTQDNVVVWLPEKEILFGGCFVKPHGLGNLGDANLEAWPESAKILMEKYGKAKLVVSGHSETGDATHLKRTWEQAVKGLKESKKTLQPSN"},"dna_sequence":{"accession":"NG_054710.1","fmin":"100","fmax":"841","strand":"+","sequence":"ATGAAAAAATTATTTGTTTTATGTGTCTTTGTCTTTTGTAGTATTACTGTCGCAGCTGAGACTTTGCCTAATTTGAGAGTTGAAAAGCTTGAAGAAGGTGTTTATGTTCATACATCGTATGAAGAAGTTAAAGGTTGGGGTGTTGTTACTAAACACGGTTTGGTGGTTCTCATAGGCGCTGACGCCTATCTGATTGATACTCCATTTACTGCTAAAGATACTGAAAAGTTAGTCAATTGGTTTGTGGAGCGCGGCTATAAAATAAAAGGCACTGTTTCCTCACATTTCCATAGCGACAGTACGGGGGGAATAGAGTGGCTTAACTCTCAGTCTATCCCCACGTATGCGTCTGAATTAACGAATGAACTTCTGAAAAAAGACGGTAAGGTTCAAGCCAAAAACTCATTTGACGGGGTTAGTTATTGGCTGGCGAAAGATAAAATAGAAGTGTTTTATCCTGGCCCTGGCCACACTCAAGACAACGTAGTAGTTTGGCTGCCTGAAAAGGAAATATTATTTGGCGGTTGCTTTGTTAAGCCTCACGGCCTTGGTAATTTGGGTGACGCAAATTTAGAGGCTTGGCCAGAGTCCGCCAAAATATTGATGGAAAAATATGGTAAAGCAAAGCTGGTTGTTTCAGGTCATAGCGAAACCGGAGACGCGACACACTTGAAGCGTACCTGGGAGCAGGCTGTTAAAGGACTTAAAGAAAGTAAAAAGACATTGCAGCCAAGCAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3005471","ARO_id":"43933","ARO_name":"IMP-64","CARD_short_name":"IMP-64","ARO_description":"IMP-64 is a IMP beta-lactamase.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4692":{"model_id":"4692","model_name":"IMP-65","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"7067":{"protein_sequence":{"accession":"WP_150823469.1","sequence":"MKKLFVLCVFFFCNIAVAEESLPDLKIEKLEEGVYVHTSFEEVKGWSVVTKHGLVVLVKNDAYLIDTPITAKDTEKLVNWFVERGYKIKGSISTHFHGDSAAGIEWLNSQSIPTYASELTNELLKKDNKVQAKHSFNGVSYSLIKNKIEVFYPGPGHTQDNVVVWLPEKKILFGGCFVKPDGLGYLGDANLEAWPKSAKILMSKYGKAKLVVSSHSDIGDVSLLKRTWEQAVKGLNESKKSSQPSD"},"dna_sequence":{"accession":"NG_066508.1","fmin":"0","fmax":"741","strand":"+","sequence":"ATGAAAAAATTATTTGTTTTATGTGTATTCTTCTTCTGCAACATTGCAGTTGCAGAAGAATCTTTGCCTGATTTAAAAATTGAGAAGCTTGAAGAAGGCGTTTATGTTCATACTTCGTTTGAAGAAGTTAAAGGTTGGAGTGTGGTCACTAAACACGGTTTGGTGGTTCTTGTGAAAAATGACGCCTATCTGATTGATACTCCAATTACTGCTAAAGATACTGAAAAATTAGTCAATTGGTTTGTTGAGCGGGGCTATAAAATCAAAGGCAGTATTTCCACACATTTCCATGGTGACAGTGCGGCTGGAATAGAGTGGCTTAATTCTCAATCTATCCCCACATATGCTTCTGAATTAACAAATGAACTTCTTAAAAAAGACAATAAGGTACAAGCTAAACACTCTTTTAATGGGGTTAGTTATTCACTAATTAAAAACAAAATTGAAGTTTTTTATCCAGGCCCAGGGCACACTCAAGATAACGTAGTGGTTTGGTTACCTGAAAAGAAAATTTTATTCGGTGGTTGCTTTGTTAAACCGGACGGTCTTGGCTATTTGGGGGACGCAAATTTAGAAGCTTGGCCAAAGTCCGCTAAAATATTAATGTCTAAATATGGTAAAGCAAAACTAGTTGTGTCGAGTCATAGTGATATTGGAGATGTATCACTCTTGAAACGTACATGGGAGCAGGCTGTTAAAGGGCTGAATGAAAGTAAAAAATCATCACAGCCAAGCGACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005472","ARO_id":"43934","ARO_name":"IMP-65","CARD_short_name":"IMP-65","ARO_description":"IMP-65 is a IMP beta-lactamase.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4693":{"model_id":"4693","model_name":"IMP-66","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"7068":{"protein_sequence":{"accession":"WP_085562391.1","sequence":"MSKLSVFFIFLFCSIATAAESLPDLKIEKLDEGVYVHTSFEEVNGWGFVPKHGLVVLVNAEAYLIDTPFTAKDTEKLVTWFVERGYKIKGSISSHFHSDSTGGIEWLNSRSIPTYASELTNELLKKDGKVQATNSFSGVNYWLVKNKIEVFYPGPGHTPDNVVVWLPERKILFGGCFIKPYGLGNLGDANIEAWPKSAKLLKSKYGKAKLVVPSHSEVGDASLLKLTLEQAVKGLNESKKPSKPSN"},"dna_sequence":{"accession":"NG_054676.1","fmin":"0","fmax":"741","strand":"+","sequence":"ATGAGCAAGTTATCTGTATTCTTTATATTTTTGTTTTGCAGCATTGCTACCGCAGCAGAGTCTTTGCCAGATTTAAAAATTGAAAAGCTTGATGAAGGCGTTTATGTTCATACTTCGTTTGAAGAAGTTAACGGGTGGGGCTTTGTTCCTAAACATGGTTTGGTGGTTCTTGTAAATGCTGAGGCTTACCTAATTGACACTCCATTTACGGCTAAAGATACTGAAAAGTTAGTCACTTGGTTTGTGGAGCGTGGCTATAAAATAAAAGGCAGCATTTCCTCTCATTTTCATAGCGACAGCACGGGCGGAATAGAGTGGCTTAATTCTCGATCTATCCCCACGTATGCATCTGAATTAACAAATGAACTGCTTAAAAAAGACGGTAAGGTTCAAGCCACAAATTCATTTAGCGGAGTTAACTATTGGCTAGTTAAAAATAAAATTGAAGTTTTTTATCCAGGCCCGGGACACACTCCAGATAACGTAGTGGTTTGGTTGCCTGAAAGGAAAATATTATTCGGTGGTTGTTTTATTAAACCGTACGGTTTAGGCAATTTGGGTGACGCAAATATAGAAGCTTGGCCAAAGTCCGCCAAATTATTAAAGTCCAAATATGGTAAGGCAAAACTGGTTGTTCCAAGTCACAGTGAAGTTGGAGACGCATCACTCTTGAAACTTACATTAGAGCAGGCGGTTAAAGGGTTAAACGAAAGTAAAAAACCATCAAAACCAAGCAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3005473","ARO_id":"43935","ARO_name":"IMP-66","CARD_short_name":"IMP-66","ARO_description":"IMP-66 is a IMP beta-lactamase.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4694":{"model_id":"4694","model_name":"IMP-67","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"7069":{"protein_sequence":{"accession":"WP_088245214.1","sequence":"MKKLFVLCVFVFCSITVAGETLPNLRVEKLEEGVYVHTSYEEVKGWGVVTKHGLVVLIGADAYLIDTPFTAKDTEKLVNWFVERGYKIKGTVSSHFHSDSTGGIEWLNSQSIPTYASELTNELLKKDGKVQAKNSFDGVSYWLAKDKIEVFYPGPGHTQDNVVVWLPEKEILFGGCFVKPHGLGNLGDANLEAWPESAKILMEKYGKAKLVVSGHSETGDSTHLKRTWEQAVKGLKESKKTLQPSN"},"dna_sequence":{"accession":"NG_055271.1","fmin":"0","fmax":"741","strand":"+","sequence":"ATGAAAAAATTATTTGTTTTATGTGTCTTTGTCTTTTGTAGTATTACTGTCGCAGGTGAGACTTTGCCTAATTTGAGAGTTGAAAAGCTTGAAGAAGGTGTTTATGTTCATACATCGTATGAAGAAGTTAAAGGTTGGGGTGTTGTTACTAAACACGGTTTGGTGGTTCTCATAGGCGCTGACGCCTATCTGATTGATACTCCATTTACTGCTAAAGATACTGAAAAGTTAGTCAATTGGTTTGTGGAGCGCGGCTATAAAATAAAAGGCACTGTTTCCTCACATTTCCATAGCGACAGTACGGGGGGAATAGAGTGGCTTAACTCTCAGTCTATCCCCACGTATGCGTCTGAATTAACGAATGAACTTCTGAAAAAAGACGGTAAGGTTCAAGCCAAAAACTCATTTGACGGGGTTAGTTATTGGCTGGCGAAAGATAAAATAGAAGTGTTTTATCCTGGCCCTGGCCACACTCAAGACAACGTAGTAGTTTGGCTGCCTGAAAAGGAAATATTATTTGGCGGTTGCTTTGTTAAGCCTCACGGCCTTGGTAATTTGGGTGACGCAAATTTAGAGGCTTGGCCAGAGTCCGCCAAAATATTGATGGAAAAATATGGTAAAGCAAAGCTGGTTGTTTCAGGTCATAGCGAAACCGGAGACTCGACACACTTGAAGCGTACCTGGGAGCAGGCTGTTAAAGGACTTAAAGAAAGTAAAAAGACATTGCAGCCAAGCAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36944","NCBI_taxonomy_name":"Providencia rettgeri","NCBI_taxonomy_id":"587"}}}},"ARO_accession":"3005474","ARO_id":"43936","ARO_name":"IMP-67","CARD_short_name":"IMP-67","ARO_description":"IMP-67 is a IMP beta-lactamase.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4695":{"model_id":"4695","model_name":"IMP-69","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"7070":{"protein_sequence":{"accession":"WP_099156051.1","sequence":"MKKLFVLCVCFLCSITAAGATLPDLKIEKLEEGVYVHTSFEEVNGWGVVSKHGLVVLVNTDAYLIDTPFTATDTEKLVNWFVERGYKIKGTISSHFHSDSTGGIEWLNSQSIPTYASELTNELLKKDGKVQAKNSFSGVSYWLVKNKIEVFYPGPGHTQDNVVVWLPEKKILFGGCFVKPDGLGNLGDANLEAWPKSAKILMSKYGKAKLVVSSHSEIGDASLLKRTWEQAVKGLNESKKPSQPSN"},"dna_sequence":{"accession":"NG_055665.1","fmin":"0","fmax":"741","strand":"+","sequence":"ATGAAGAAATTATTTGTTTTATGTGTATGCTTCCTTTGTAGCATTACTGCCGCAGGAGCGACTTTGCCTGATTTAAAAATCGAGAAGCTTGAAGAAGGTGTTTATGTTCATACATCGTTCGAAGAAGTTAACGGTTGGGGTGTTGTTTCTAAACACGGTTTGGTGGTTCTTGTAAACACTGACGCCTATCTGATTGACACTCCATTTACTGCTACAGATACTGAAAAGTTAGTCAATTGGTTTGTGGAGCGCGGCTATAAAATCAAAGGCACTATTTCCTCACATTTCCATAGCGACAGCACAGGGGGAATAGAGTGGCTTAATTCTCAATCTATTCCCACGTATGCATCTGAATTAACAAATGAACTTCTTAAAAAAGACGGTAAGGTGCAAGCTAAAAACTCATTTAGCGGAGTTAGTTATTGGCTAGTTAAAAATAAAATTGAAGTTTTTTATCCCGGCCCGGGGCACACTCAAGATAACGTAGTGGTTTGGTTACCTGAAAAGAAAATTTTATTCGGTGGTTGTTTTGTTAAACCGGACGGTCTTGGTAATTTGGGTGACGCAAATTTAGAAGCTTGGCCAAAGTCCGCCAAAATATTAATGTCTAAATATGGTAAAGCAAAACTGGTTGTTTCAAGTCATAGTGAAATTGGGGACGCATCACTCTTGAAACGTACATGGGAACAGGCTGTTAAAGGGCTAAATGAAAGTAAAAAACCATCACAGCCAAGTAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37065","NCBI_taxonomy_name":"Providencia","NCBI_taxonomy_id":"586"}}}},"ARO_accession":"3005475","ARO_id":"43937","ARO_name":"IMP-69","CARD_short_name":"IMP-69","ARO_description":"IMP-69 is a IMP beta-lactamase.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4696":{"model_id":"4696","model_name":"IMP-70","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"7071":{"protein_sequence":{"accession":"WP_102607459.1","sequence":"MSKLSVFFIFLFCSIATAAESLPDLKIEKLDEGVYVHTSFEEVNGWGVVPKHGLVVLVNAEAYLIDTPFTAKDTEKLVTWFVERGYKIKGSISSHFHSDSTGGIEWLNSRSIPTYASELTNELLKKDGKVQATNSFSGVNYWLVKNKIEVFYPGPGHTPDNVVVWLPERKILFGGCFIKPYGLGNLGDANIEAWPKSAKLLKSKYGKAKLVVPSHSEVGDASLLKLTIEQAVKGLNESKKPSKPSN"},"dna_sequence":{"accession":"NG_056176.1","fmin":"0","fmax":"741","strand":"+","sequence":"ATGAGCAAGTTATCTGTATTCTTTATATTTTTGTTTTGTAGCATTGCTACCGCAGCAGAGTCTTTACCAGATTTAAAAATTGAAAAGCTTGATGAAGGCGTTTATGTTCATACTTCGTTTGAAGAAGTTAACGGGTGGGGCGTTGTTCCTAAACATGGTTTGGTGGTTCTTGTAAATGCTGAGGCTTATCTAATTGACACTCCATTTACGGCTAAAGATACTGAAAAGTTAGTCACTTGGTTTGTGGAGCGTGGCTATAAAATAAAAGGCAGTATTTCCTCTCATTTTCATAGCGACAGCACGGGCGGAATAGAGTGGCTTAATTCTCGATCTATCCCCACGTATGCATCTGAATTAACAAATGAACTGCTTAAAAAAGACGGCAAGGTTCAAGCTACAAATTCATTTAGCGGAGTTAACTATTGGCTAGTTAAAAATAAAATTGAAGTTTTTTATCCAGGCCCGGGACACACTCCAGATAACGTAGTGGTTTGGCTGCCTGAAAGGAAAATATTATTCGGTGGTTGTTTTATTAAACCGTACGGTTTAGGCAATTTGGGTGACGCAAATATAGAAGCTTGGCCAAAGTCCGCCAAATTATTAAAGTCCAAATATGGTAAGGCAAAACTGGTTGTTCCAAGTCACAGTGAAGTTGGAGACGCATCACTCTTGAAACTTACAATAGAGCAGGCGGTTAAAGGGTTAAACGAAAGTAAAAAACCATCAAAACCAAGCAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005476","ARO_id":"43938","ARO_name":"IMP-70","CARD_short_name":"IMP-70","ARO_description":"IMP-70 is a IMP beta-lactamase.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4697":{"model_id":"4697","model_name":"IMP-71","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"7072":{"protein_sequence":{"accession":"WP_104009852.1","sequence":"MKKLFVLCVFFLCNIAAADDSLPDLKIEKLEKGVYVHTSFEEVKGWGVFAKHGLVVLVKNDAYLIDTPITAKDTEKLVNWFIEHGYRIKGSISTHFHGDSTAGIEWLNSQSISTYASELTNELLKKDNKVQATNSFSGVSYSLIKNKIEVFYPGPGHTQDNVVVWLPEKKILFGGCFVKPDGLGNLGDANLEAWPKSAKILMSKYGKAKLVVSSHSEIGNASLLQRTWEQAVKGLNESKKPLQPSS"},"dna_sequence":{"accession":"NG_056414.1","fmin":"0","fmax":"741","strand":"+","sequence":"ATGAAAAAATTATTTGTTTTATGTGTATTCTTCCTTTGCAACATTGCTGCTGCAGATGATTCTTTGCCTGATTTAAAAATTGAGAAGCTTGAAAAAGGCGTTTATGTTCATACTTCGTTTGAAGAAGTTAAAGGTTGGGGTGTATTCGCAAAACACGGTTTAGTGGTTCTTGTAAAGAATGATGCTTATCTGATAGATACTCCAATTACCGCTAAAGATACTGAAAAATTAGTTAATTGGTTTATTGAGCACGGCTATAGAATCAAAGGCAGTATTTCCACACATTTCCATGGCGACAGTACGGCTGGAATAGAGTGGCTTAATTCTCAATCTATCTCCACGTATGCCTCTGAATTAACAAATGAACTTCTAAAAAAAGACAATAAGGTGCAAGCTACAAATTCTTTTAGTGGAGTTAGTTATTCACTTATCAAAAACAAAATTGAAGTTTTCTATCCAGGTCCAGGACACACTCAAGATAACGTAGTGGTTTGGTTACCTGAAAAGAAAATTTTATTCGGTGGTTGCTTTGTTAAACCGGACGGTCTTGGAAATTTAGGGGATGCAAATTTAGAAGCTTGGCCAAAGTCCGCTAAAATATTAATGTCTAAATATGGTAAAGCAAAACTGGTTGTTTCAAGTCATAGTGAAATTGGAAACGCATCACTCTTGCAGCGCACATGGGAGCAGGCTGTTAAAGGGTTAAATGAAAGTAAAAAACCGTTACAGCCAAGTAGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005477","ARO_id":"43939","ARO_name":"IMP-71","CARD_short_name":"IMP-71","ARO_description":"IMP-71 is a IMP beta-lactamase.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4698":{"model_id":"4698","model_name":"IMP-73","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"7073":{"protein_sequence":{"accession":"WP_109545053.1","sequence":"MKKLSVFFMFLFCSIAASGEALPDLKIEKLDEGVYVHTSFEEVNGWGVAPKHGLVVLVNTDAYLIDTPFTAKDTEKLVTWFVERGYKIKGSISSHFHSDSTGGIEWLNSQSIPTYASELTNELLKKDGKVQAKNSFSGASYWLVKKKIEIFYPGPGHTPDNVVVWLPEHRVLFGGCFVKPYGLGNLGDANLEAWPKSAKLLVSKYGKAKLVVPSHSEVGDASLLKRTLEQAVKGLNESKKLSKPSN"},"dna_sequence":{"accession":"NG_057463.1","fmin":"0","fmax":"741","strand":"+","sequence":"ATGAAAAAGTTATCAGTATTCTTTATGTTTTTGTTTTGTAGCATTGCTGCCTCAGGAGAGGCTTTGCCAGATTTAAAAATTGAGAAGCTTGACGAAGGCGTTTATGTTCATACTTCGTTTGAGGAAGTTAACGGCTGGGGCGTGGCTCCTAAACACGGCTTGGTGGTTCTTGTAAATACTGACGCTTATTTGATTGACACTCCATTTACAGCTAAAGATACTGAAAAGTTAGTTACTTGGTTTGTAGAGCGCGGCTATAAAATAAAAGGCAGTATCTCCTCTCATTTTCATAGCGACAGCACGGGCGGAATAGAGTGGCTTAATTCTCAATCTATTCCAACATATGCATCTGAATTAACAAATGAACTTCTTAAAAAAGACGGTAAGGTACAAGCTAAAAATTCATTTAGCGGAGCCAGCTATTGGTTAGTTAAGAAAAAGATTGAAATTTTTTATCCTGGCCCAGGGCACACTCCAGATAACGTAGTGGTTTGGCTACCTGAACATAGAGTTTTGTTTGGTGGTTGTTTTGTTAAACCGTATGGTCTAGGTAATTTGGGTGACGCAAATTTAGAAGCTTGGCCAAAGTCTGCCAAATTATTAGTGTCCAAATATGGTAAGGCAAAACTGGTTGTTCCAAGTCACAGTGAAGTTGGAGATGCATCACTCTTGAAACGTACATTAGAACAGGCTGTTAAAGGATTAAACGAAAGTAAAAAGCTATCAAAACCAAGTAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005478","ARO_id":"43940","ARO_name":"IMP-73","CARD_short_name":"IMP-73","ARO_description":"IMP-73 is a IMP beta-lactamase.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4699":{"model_id":"4699","model_name":"IMP-74","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"7074":{"protein_sequence":{"accession":"WP_109791207.1","sequence":"MKKLFVLCIFLFCSITAAGESLPDLKIEKLEDGVYVHTSFEEVNGWGVFTKHGLVFLVNTDAYLIDTPFAAKDTEKLVNWFVERGYKIKGSISSHFHSDSSGGIEWLNSQSIPTYASELTNELLKKNGKVQAKNSFSGVSYWLLKNKIEIFYPGPGHTQDNVVVWLPEKKILFGGCFVKPYGLGNLDDANVEAWPHSAEILMSRYGNAKLVVPSHSDVGDASLLKLTWEQAVKGLKESKKPSQPSN"},"dna_sequence":{"accession":"NG_057606.1","fmin":"0","fmax":"741","strand":"+","sequence":"ATGAAAAAATTATTTGTTTTATGTATCTTTTTGTTTTGTAGCATTACTGCCGCAGGAGAGTCTTTGCCTGATTTAAAAATTGAGAAGCTTGAAGACGGTGTTTATGTTCATACATCGTTTGAAGAAGTTAACGGTTGGGGTGTTTTTACTAAACACGGTTTGGTGTTTCTTGTAAACACAGACGCCTATCTGATTGACACTCCATTTGCTGCTAAAGACACTGAAAAGTTAGTAAATTGGTTTGTGGAGCGCGGTTATAAAATAAAAGGCAGTATTTCCTCACATTTTCATAGCGACAGCTCGGGTGGAATAGAATGGCTTAACTCTCAATCTATTCCCACGTATGCATCTGAATTAACAAACGAACTTCTTAAAAAGAACGGTAAGGTGCAAGCTAAAAACTCATTTAGCGGAGTTAGTTATTGGCTACTTAAAAATAAAATTGAAATTTTTTATCCGGGCCCTGGGCACACTCAAGATAATGTAGTGGTTTGGTTGCCTGAAAAGAAAATTTTATTTGGTGGGTGTTTTGTTAAACCGTACGGTCTTGGAAATCTCGATGATGCAAATGTTGAAGCGTGGCCACATTCTGCTGAAATATTAATGTCTAGGTATGGTAATGCAAAACTGGTTGTTCCAAGCCATAGTGACGTCGGAGATGCGTCGCTCTTGAAGCTTACATGGGAGCAGGCTGTTAAAGGGCTAAAAGAAAGTAAAAAACCATCACAGCCAAGTAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37066","NCBI_taxonomy_name":"Pseudomonas","NCBI_taxonomy_id":"286"}}}},"ARO_accession":"3005479","ARO_id":"43941","ARO_name":"IMP-74","CARD_short_name":"IMP-74","ARO_description":"IMP-74 is a IMP beta-lactamase.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4700":{"model_id":"4700","model_name":"IMP-75","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"7075":{"protein_sequence":{"accession":"WP_109791208.1","sequence":"MKKLFVLCVFFLCNIAAADDSLPDLKIEKLEKGVYVHTSFEEVKGWGVFAKHGLVVLVKNDAYLIDTPITAKDTEKLVNWFIEHGYRIKGSISTHFHGDSTAGIEWLNSQSISTYASELTNELLKKDNKVQATNSFSGVSYSLIKNKIEVFYPGPGHTQDNVVVWLPEKKILFGGCFVKPDGLGNLGDANLEAWPKSAKILMSKYGKAKLVVPSHSEIGNASLLQRTWEQAVKGLNESKKPLQPSS"},"dna_sequence":{"accession":"NG_057607.1","fmin":"0","fmax":"741","strand":"+","sequence":"ATGAAAAAATTATTTGTTTTATGTGTATTCTTCCTTTGCAACATTGCTGCTGCAGATGATTCTTTGCCTGATTTAAAAATTGAGAAGCTTGAAAAAGGCGTTTATGTTCATACTTCGTTTGAAGAAGTTAAAGGTTGGGGTGTATTCGCAAAACACGGTTTAGTGGTTCTTGTAAAGAATGATGCTTATCTGATAGATACTCCAATTACCGCTAAAGATACTGAAAAATTAGTTAATTGGTTTATTGAGCACGGCTATAGAATCAAAGGCAGTATTTCCACACATTTCCATGGCGACAGTACGGCTGGAATAGAGTGGCTTAATTCTCAATCTATCTCCACGTATGCCTCTGAATTAACAAATGAACTTCTAAAAAAAGACAATAAGGTGCAAGCTACAAATTCTTTTAGTGGAGTTAGTTATTCACTTATCAAAAACAAAATTGAAGTTTTCTATCCAGGTCCAGGACACACTCAAGATAACGTAGTGGTTTGGTTACCTGAAAAGAAAATTTTATTCGGTGGTTGCTTTGTTAAACCGGACGGTCTTGGAAATTTAGGGGATGCAAATTTAGAAGCTTGGCCAAAGTCCGCTAAAATATTAATGTCTAAATATGGTAAAGCAAAACTGGTTGTTCCAAGTCATAGTGAAATTGGAAACGCATCACTCTTGCAGCGCACATGGGAGCAGGCTGTTAAAGGGTTAAATGAAAGTAAAAAACCGTTACAGCCAAGTAGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005480","ARO_id":"43942","ARO_name":"IMP-75","CARD_short_name":"IMP-75","ARO_description":"IMP-75 is a IMP beta-lactamase.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4701":{"model_id":"4701","model_name":"IMP-76","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"7076":{"protein_sequence":{"accession":"WP_114699280.1","sequence":"MSKLSVFFIFLFCSIATAAESLPDLKIEKLDEGVYVHTSFEEVNGWGVAPKHGLVVLVNAEAYLIDTPFTAKDTEKLVTWFVERGYKIKGSISSHFHSDSTGGIEWLNSRSIPTYASELTNELLKKDGKVQATNSFSGVNYWLVKNKIEVFYPGPGHTPDNVVVWLPERKILFGGCFIKPYGLGNLGDANIEAWPKSAKLLKSKYGKAKLVVPSHSEVGDASLLKLTLEQAVKGLNESKKPSKPSN"},"dna_sequence":{"accession":"NG_061409.1","fmin":"0","fmax":"741","strand":"+","sequence":"ATGAGCAAGTTATCTGTATTCTTTATATTTTTGTTTTGCAGCATTGCTACCGCAGCAGAGTCTTTGCCAGATTTAAAAATTGAAAAGCTTGATGAAGGCGTTTATGTTCATACTTCGTTTGAAGAAGTTAACGGGTGGGGCGTTGCTCCTAAACATGGTTTGGTGGTTCTTGTAAATGCTGAGGCTTACCTAATTGACACTCCATTTACGGCTAAAGATACTGAAAAGTTAGTCACTTGGTTTGTGGAGCGTGGCTATAAAATAAAAGGCAGCATTTCCTCTCATTTTCATAGCGACAGCACGGGCGGAATAGAGTGGCTTAATTCTCGATCTATCCCCACGTATGCATCTGAATTAACAAATGAACTGCTTAAAAAAGACGGTAAGGTTCAAGCCACAAATTCATTTAGCGGAGTTAACTATTGGCTAGTTAAAAATAAAATTGAAGTTTTTTATCCAGGCCCGGGACACACTCCAGATAACGTAGTGGTTTGGTTGCCTGAAAGGAAAATATTATTCGGTGGTTGTTTTATTAAACCGTACGGTTTAGGCAATTTGGGTGACGCAAATATAGAAGCTTGGCCAAAGTCCGCCAAATTATTAAAGTCCAAATATGGTAAGGCAAAACTGGTTGTTCCAAGTCACAGTGAAGTTGGAGACGCATCACTCTTGAAACTTACATTAGAGCAGGCGGTTAAAGGGTTAAACGAAAGTAAAAAACCATCAAAACCAAGCAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005481","ARO_id":"43943","ARO_name":"IMP-76","CARD_short_name":"IMP-76","ARO_description":"IMP-76 is a IMP beta-lactamase.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4702":{"model_id":"4702","model_name":"IMP-77","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"7077":{"protein_sequence":{"accession":"WP_114699281.1","sequence":"MSKLSVFFIFLFCSIATAAESLPDLKIEKLDEGVYVHTSFEEVNGWGVFPKHGLVVLVNAEAYLIDTPFTAKDTEKLVTWFVERGYKIKGSISSHFHSDSTGGIEWLNSRSIPTYASELTNELLKKDGKVQATNSFSGVNYWLVKNKIEVFYPGPGHTPDNVVVWLPERKILFGGCFIKPYGLGNLGDANIEAWPKSAKSLKSKYGKAKLVVPSHSEVGDASLLKLTLEQAVKGLNESKKPSKPSN"},"dna_sequence":{"accession":"NG_061410.1","fmin":"0","fmax":"741","strand":"+","sequence":"ATGAGCAAGTTATCTGTATTCTTTATATTTTTGTTTTGCAGCATTGCTACCGCAGCAGAGTCTTTGCCAGATTTAAAAATTGAAAAGCTTGATGAAGGCGTTTATGTTCATACTTCGTTTGAAGAAGTTAACGGGTGGGGCGTTTTTCCTAAACATGGTTTGGTGGTTCTTGTAAATGCTGAGGCTTACCTAATTGACACTCCATTTACGGCTAAAGATACTGAAAAGTTAGTCACTTGGTTTGTGGAGCGTGGCTATAAAATAAAAGGCAGCATTTCCTCTCATTTTCATAGCGACAGCACGGGCGGAATAGAGTGGCTTAATTCTCGATCTATCCCCACGTATGCATCTGAATTAACAAATGAACTGCTTAAAAAAGACGGTAAGGTTCAAGCCACAAATTCATTTAGCGGAGTTAACTATTGGCTAGTTAAAAATAAAATTGAAGTTTTTTATCCAGGCCCGGGACACACTCCAGATAACGTAGTGGTTTGGTTGCCTGAAAGGAAAATATTATTCGGTGGTTGTTTTATTAAACCGTACGGTTTAGGCAATTTGGGTGACGCAAATATAGAAGCTTGGCCAAAGTCCGCCAAATCATTAAAGTCCAAATATGGTAAGGCAAAACTGGTTGTTCCAAGTCACAGTGAAGTTGGAGACGCATCACTCTTGAAACTTACATTAGAGCAGGCGGTTAAAGGGTTAAACGAAAGTAAAAAACCATCAAAACCAAGCAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005482","ARO_id":"43944","ARO_name":"IMP-77","CARD_short_name":"IMP-77","ARO_description":"IMP-77 is a IMP beta-lactamase.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4703":{"model_id":"4703","model_name":"IMP-78","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"7078":{"protein_sequence":{"accession":"WP_114699282.1","sequence":"MSKLSVFFIFLFCSIATAAESLPDLKIEKLDEGVYVHTSFEEVNGWGVFPKHGLVVLVNAEAYLIDTPFTAKDTEKLVTWFVERGYKIKGSISSHFHSDSTGGIEWLNSRSIPTYASELTNELLKKDGKVQATNSFSGVNYWLVKNKIEVFYPGPGHTPDNVVVWLPERKILFGGCFIKPYGLGNLGDANIEAWPKSAKLLKSKYGKAKLVVPGHSEVGDASLLKLTLEQAVKGLNESKKPSKPSN"},"dna_sequence":{"accession":"NG_061411.1","fmin":"0","fmax":"741","strand":"+","sequence":"ATGAGCAAGTTATCTGTATTCTTTATATTTTTGTTTTGCAGCATTGCTACCGCAGCAGAGTCTTTGCCAGATTTAAAAATTGAAAAGCTTGATGAAGGCGTTTATGTTCATACTTCGTTTGAAGAAGTTAACGGGTGGGGCGTTTTTCCTAAACATGGTTTGGTGGTTCTTGTAAATGCTGAGGCTTACCTAATTGACACTCCATTTACGGCTAAAGATACTGAAAAGTTAGTCACTTGGTTTGTGGAGCGTGGCTATAAAATAAAAGGCAGCATTTCCTCTCATTTTCATAGCGACAGCACGGGCGGAATAGAGTGGCTTAATTCTCGATCTATCCCCACGTATGCATCTGAATTAACAAATGAACTGCTTAAAAAAGACGGTAAGGTTCAAGCCACAAATTCATTTAGCGGAGTTAACTATTGGCTAGTTAAAAATAAAATTGAAGTTTTTTATCCAGGCCCGGGACACACTCCAGATAACGTAGTGGTTTGGTTGCCTGAAAGGAAAATATTATTCGGTGGTTGTTTTATTAAACCGTACGGTTTAGGCAATTTGGGTGACGCAAATATAGAAGCTTGGCCAAAGTCCGCCAAATTATTAAAGTCCAAATATGGTAAGGCAAAACTGGTTGTTCCAGGTCACAGTGAAGTTGGAGACGCATCACTCTTGAAACTTACATTAGAGCAGGCGGTTAAAGGGTTAAACGAAAGTAAAAAACCATCAAAACCAAGCAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005483","ARO_id":"43945","ARO_name":"IMP-78","CARD_short_name":"IMP-78","ARO_description":"IMP-78 is a IMP beta-lactamase.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4704":{"model_id":"4704","model_name":"IMP-79","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"7079":{"protein_sequence":{"accession":"WP_116786839.1","sequence":"MSKLSVFFIFLFCSIATAAESLPDLKIEKLDEGVYVHTSFEEVNGWGVVPKHGLVVLVNAEAYLIDTPFTAKDTEKLVTWFVERGYKIKGSISSHFHSDSTGGIEWLNSRSIPTYASELTNELLKKDGKVQATNSFSGVNYWLVKNKIEVFYPGPGHTPDNVVVWLPERKILFGGCFIKPYGLGNLGDANIEAWPKSARLLKSKYGKAKLVVPSHSEVGDASLLKLTLEQAVKGLNESKKPSKPSN"},"dna_sequence":{"accession":"NG_061626.1","fmin":"0","fmax":"741","strand":"+","sequence":"ATGAGCAAGTTATCTGTATTCTTTATATTTTTGTTTTGCAGCATTGCTACCGCAGCAGAGTCTTTGCCAGATTTAAAAATTGAAAAGCTTGATGAAGGCGTTTATGTTCATACTTCGTTTGAAGAAGTTAACGGGTGGGGCGTTGTTCCTAAACATGGTTTGGTGGTTCTTGTAAATGCTGAGGCTTATCTAATTGACACTCCATTTACGGCTAAAGATACTGAAAAGTTAGTCACTTGGTTTGTGGAGCGTGGCTATAAAATAAAAGGCAGTATTTCCTCTCATTTTCATAGCGACAGCACGGGCGGAATAGAGTGGCTTAATTCTCGATCTATCCCCACGTATGCATCTGAATTAACAAATGAACTGCTTAAAAAAGACGGTAAGGTTCAAGCCACAAATTCATTTAGCGGAGTTAACTATTGGCTAGTTAAAAATAAAATTGAAGTTTTTTATCCAGGCCCGGGACACACTCCAGATAACGTAGTGGTTTGGCTGCCTGAAAGGAAAATATTATTCGGTGGTTGTTTTATTAAACCGTACGGTTTAGGCAATTTGGGTGACGCAAATATAGAAGCTTGGCCAAAGTCCGCCAGATTATTAAAGTCCAAATATGGTAAGGCAAAACTGGTTGTTCCAAGTCACAGTGAAGTTGGAGACGCATCACTCTTGAAACTTACATTAGAGCAGGCGGTTAAAGGATTAAACGAAAGTAAAAAACCATCAAAACCAAGCAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005484","ARO_id":"43946","ARO_name":"IMP-79","CARD_short_name":"IMP-79","ARO_description":"IMP-79 is a IMP beta-lactamase.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4705":{"model_id":"4705","model_name":"IMP-80","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"7080":{"protein_sequence":{"accession":"WP_122630861.1","sequence":"MSKLSVFFIFLFCSIATAAESLPDLKIEKLDEGVYVHTSFEEVNGWGVFPKHGLVVLVNAEAYLIDTPFTAKDTEKLVTWFVERGYKIKGSISSHFHSDSTGGIEWLNSRSIPTYASELTNELLKKDGKVQATNSFSGVNYWLVKNKIEVFYPGPGHTPDNVVVWLPERKILFGGCFIKPYGLGNLGDANIEAWPKSAKLLKSKYGKAKLVVPAHSEVGDASLLKLTLEQAVKGLNESKKPSKPSN"},"dna_sequence":{"accession":"NG_062274.1","fmin":"0","fmax":"741","strand":"+","sequence":"ATGAGCAAGTTATCTGTATTCTTTATATTTTTGTTTTGCAGCATTGCTACCGCAGCAGAGTCTTTGCCAGATTTAAAAATTGAAAAGCTTGATGAAGGCGTTTATGTTCATACTTCGTTTGAAGAAGTTAACGGGTGGGGCGTTTTTCCTAAACATGGTTTGGTGGTTCTTGTAAATGCTGAGGCTTACCTAATTGACACTCCATTTACGGCTAAAGATACTGAAAAGTTAGTCACTTGGTTTGTGGAGCGTGGCTATAAAATAAAAGGCAGCATTTCCTCTCATTTTCATAGCGACAGCACGGGCGGAATAGAGTGGCTTAATTCTCGATCTATCCCCACGTATGCATCTGAATTAACAAATGAACTGCTTAAAAAAGACGGTAAGGTTCAAGCCACAAATTCATTTAGCGGAGTTAACTATTGGCTAGTTAAAAATAAAATTGAAGTTTTTTATCCAGGCCCGGGACACACTCCAGATAACGTAGTGGTTTGGTTGCCTGAAAGGAAAATATTATTCGGTGGTTGTTTTATTAAACCGTACGGTTTAGGCAATTTGGGTGACGCAAATATAGAAGCTTGGCCAAAGTCCGCCAAATTATTAAAGTCCAAATATGGTAAGGCAAAACTGGTTGTTCCAGCTCACAGTGAAGTTGGAGACGCATCACTCTTGAAACTTACATTAGAGCAGGCGGTTAAAGGGTTAAACGAAAGTAAAAAACCATCAAAACCAAGCAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005485","ARO_id":"43947","ARO_name":"IMP-80","CARD_short_name":"IMP-80","ARO_description":"IMP-80 is a IMP beta-lactamase.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4706":{"model_id":"4706","model_name":"IMP-81","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"7081":{"protein_sequence":{"accession":"WP_148044415.1","sequence":"MSKLFVFCMFLFCSITAAGESLPDLKIEKLDEGVYVHTSFEEVNGWGVVPKHGLVVLVNTDAYLIDTPFTAKDTEKLVTWFVERGYKIKGSVSSHFHSDSTGGIEWLNSQSIPTYASELTNELLKKDGKVQAKNSFSGVSYWLVKNKVEIFYPGPGHTPDNVVVWLPENRVLFGGCFVKPYGLGNLGDANLEAWPKSAKLLMSKYGKAKLVVPSHSEVGDASLLKLTLVQAVKGLNESKKPSKPSN"},"dna_sequence":{"accession":"NG_065947.1","fmin":"0","fmax":"741","strand":"+","sequence":"ATGAGCAAGTTATTTGTATTCTGTATGTTTTTGTTTTGTAGCATTACAGCCGCAGGAGAGTCTTTGCCAGATTTAAAAATTGAGAAGCTTGACGAAGGGGTTTATGTTCATACTTCGTTTGAAGAAGTTAACGGTTGGGGTGTTGTTCCTAAGCACGGCTTGGTGGTTCTTGTAAATACTGATGCCTATTTGATTGATACTCCATTTACGGCTAAAGATACTGAAAAGTTAGTCACTTGGTTTGTGGAGCGCGGCTATAAAATAAAAGGTAGTGTTTCCTCTCATTTTCATAGCGACAGTACGGGCGGAATAGAGTGGCTTAATTCTCAATCTATCCCCACGTATGCATCAGAATTAACAAATGAACTCCTTAAAAAAGACGGTAAGGTACAAGCTAAAAATTCATTTAGCGGAGTTAGTTATTGGCTAGTTAAGAATAAGGTTGAAATTTTTTATCCTGGTCCTGGGCACACTCCAGATAACGTAGTGGTTTGGTTACCTGAAAATAGAGTTTTGTTCGGTGGTTGTTTTGTTAAACCGTACGGTCTTGGTAATTTGGGTGATGCAAATTTAGAAGCTTGGCCAAAGTCAGCCAAATTATTAATGTCCAAATATGGTAAAGCAAAACTGGTTGTTCCAAGTCACAGTGAAGTTGGAGACGCATCGCTCTTGAAGCTTACATTAGTACAGGCGGTTAAAGGTTTAAATGAAAGTAAAAAACCATCAAAACCAAGTAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36791","NCBI_taxonomy_name":"uncultured bacterium","NCBI_taxonomy_id":"77133"}}}},"ARO_accession":"3005486","ARO_id":"43948","ARO_name":"IMP-81","CARD_short_name":"IMP-81","ARO_description":"IMP-81 is a IMP beta-lactamase.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4707":{"model_id":"4707","model_name":"IMP-82","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"7082":{"protein_sequence":{"accession":"WP_148044416.1","sequence":"MSKLFVFFMFLFCSITAAGESLPDLKIEKLDEGVYVHTSFEEVNGWGVVPKHGLVVLVNTDAYLIDTPFTAKDTENLVNWFVERGYKIKGSISSHFHSDSTGGIEWLNSQSIPTYASELTNELLKKDGKVQAKNSFSGVSYWLVKKKIEVFYPGPGHAPDNVVVWLPENRVLFGGCFVKPYGLGNLGDANLEAWPKSAKLLMSKYSKAKLVVPSHSDIGDSSLLKLTWEQTVKGFNERKKSTTAH"},"dna_sequence":{"accession":"NG_065873.1","fmin":"0","fmax":"738","strand":"+","sequence":"ATGAGCAAGTTATTTGTATTCTTTATGTTTTTGTTTTGTAGCATTACTGCCGCAGGAGAGTCTTTGCCAGATTTAAAAATTGAGAAGCTTGACGAAGGCGTTTATGTTCATACTTCGTTTGAGGAAGTTAACGGTTGGGGTGTTGTTCCTAAACACGGCTTGGTGGTTCTTGTAAATACTGATGCCTATCTAATAGACACTCCATTTACTGCTAAAGATACTGAAAATTTAGTTAATTGGTTTGTTGAGCGCGGCTATAAAATCAAAGGCAGTATTTCCTCACATTTCCATAGCGACAGCACGGGTGGAATAGAGTGGCTTAATTCTCAATCTATCCCCACGTATGCATCTGAATTAACAAATGAACTTCTTAAAAAAGACGGTAAGGTACAAGCTAAAAATTCATTTAGCGGAGTTAGCTATTGGCTAGTTAAGAAAAAGATTGAAGTTTTTTATCCTGGTCCAGGGCACGCTCCAGATAACGTAGTGGTTTGGCTGCCTGAAAATAGAGTTTTGTTCGGTGGTTGTTTTGTTAAACCCTACGGTCTAGGTAATTTGGGTGACGCCAATTTAGAAGCTTGGCCAAAATCCGCCAAATTATTAATGTCAAAATATAGTAAGGCAAAACTGGTTGTTCCAAGTCATAGTGACATAGGAGATTCGTCGCTCTTGAAGCTTACATGGGAGCAGACGGTAAAAGGATTCAATGAAAGAAAAAAAAGTACCACTGCACATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005487","ARO_id":"43949","ARO_name":"IMP-82","CARD_short_name":"IMP-82","ARO_description":"IMP-82 is a IMP beta-lactamase.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4708":{"model_id":"4708","model_name":"IMP-83","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"7083":{"protein_sequence":{"accession":"WP_148044417.1","sequence":"MKKLFVLCVFFLCNIAAADDSLPDLKIEKLEKGVYVHTSFEEVKGWGVVTKHGLVVLVKNDAYLIDTPVTAKDTEKLVNWFIEHGYRIKGSISTHFHGDSTAGIEWLNSQSISTYASELTNELLKKDNKVQATNSFSGVSYSLIKNKIEVFYPGPGHTQDNVVVWLPEKKILFGGCFVKPDGLGNLGDANLEAWPKSAKILMSKYGKAKLVVSSHSEIGNASLLQRTWEQAVKGLNESKKPLQPSS"},"dna_sequence":{"accession":"NG_065874.1","fmin":"0","fmax":"741","strand":"+","sequence":"ATGAAAAAATTATTTGTTTTATGTGTATTCTTCCTTTGCAACATTGCTGCTGCAGATGATTCTTTGCCTGATTTAAAAATTGAGAAGCTTGAAAAAGGCGTTTATGTTCATACTTCGTTTGAAGAAGTTAAAGGTTGGGGTGTAGTCACAAAACACGGTTTAGTGGTTCTTGTAAAGAATGATGCTTATCTGATAGATACTCCAGTTACCGCTAAAGATACTGAAAAATTAGTTAATTGGTTTATTGAGCACGGCTATAGAATCAAAGGCAGTATTTCCACACATTTCCATGGCGACAGTACGGCTGGAATAGAGTGGCTTAATTCTCAATCTATCTCCACGTATGCCTCTGAATTAACAAATGAACTTCTAAAAAAAGACAATAAGGTGCAAGCTACAAATTCTTTTAGTGGAGTTAGTTATTCACTTATCAAAAACAAAATTGAAGTTTTCTATCCAGGTCCAGGACACACTCAAGATAACGTAGTGGTTTGGTTACCTGAAAAGAAAATTTTATTCGGTGGTTGCTTTGTTAAACCGGACGGTCTTGGAAATTTAGGGGATGCAAATTTAGAAGCTTGGCCAAAGTCCGCTAAAATATTAATGTCTAAATATGGTAAAGCAAAACTGGTTGTTTCAAGTCATAGTGAAATTGGAAACGCATCACTCTTGCAGCGCACATGGGAGCAGGCTGTTAAAGGGTTAAATGAAAGTAAAAAACCGTTACAGCCAAGTAGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005488","ARO_id":"43950","ARO_name":"IMP-83","CARD_short_name":"IMP-83","ARO_description":"IMP-83 is a IMP beta-lactamase.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4709":{"model_id":"4709","model_name":"IMP-84","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"7084":{"protein_sequence":{"accession":"WP_148044418.1","sequence":"MKKLFVLCVCFFCSITAAGAALPDLKIEKLEEGVFVHTSFEEVNGWGVFTKHGLVVLVNTDAYLIDTPFTATDTEKLVNWFVERGYEIKGTISSHFHSDSTGGIEWLNSQSIPTYASELTNELLKKSGKVQAKYSFSEVSYWLVKNKIEVFYPGPGHTQDNLVVWLPESKILFGGCFIKPHGLGNLGDANLEAWPKSAKILMSKYGKAKLVVSSHSEKGDASLMKRTWEQALKGLKESKKTSSPSN"},"dna_sequence":{"accession":"NG_065875.1","fmin":"0","fmax":"741","strand":"+","sequence":"ATGAAGAAATTATTTGTTTTATGTGTATGCTTCTTTTGTAGCATTACTGCCGCAGGAGCGGCTTTACCTGATTTAAAAATCGAGAAGCTTGAAGAAGGTGTTTTTGTTCATACATCGTTCGAAGAGGTTAACGGTTGGGGGGTTTTTACTAAACACGGTTTAGTGGTGCTTGTAAACACAGACGCCTATCTAATTGACACTCCATTTACTGCTACAGACACTGAAAAATTAGTCAATTGGTTTGTGGAGCGCGGCTATGAAATCAAAGGCACTATTTCATCACATTTCCATAGCGACAGCACAGGAGGAATAGAGTGGCTTAATTCTCAATCTATTCCCACGTATGCATCTGAATTAACAAATGAACTTTTGAAAAAATCCGGTAAGGTACAAGCTAAATATTCATTTAGCGAAGTTAGCTATTGGCTAGTTAAAAATAAAATTGAAGTTTTCTACCCTGGCCCAGGTCACACTCAAGATAACCTAGTGGTTTGGTTGCCTGAAAGTAAAATTTTATTCGGTGGTTGCTTTATTAAACCTCACGGTCTTGGCAATTTAGGTGACGCAAATTTAGAAGCTTGGCCAAAGTCCGCCAAAATATTAATGTCTAAATATGGCAAAGCAAAGCTTGTTGTTTCAAGTCATAGTGAAAAAGGGGACGCATCACTAATGAAACGTACATGGGAACAAGCCCTTAAAGGGCTTAAAGAAAGTAAAAAAACATCATCACCAAGTAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005489","ARO_id":"43951","ARO_name":"IMP-84","CARD_short_name":"IMP-84","ARO_description":"IMP-84 is a IMP beta-lactamase.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4710":{"model_id":"4710","model_name":"IMP-85","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"7085":{"protein_sequence":{"accession":"WP_152315465.1","sequence":"MSKLFVFFMFLFCSITAAAESLPDLKIEKLDEGVYVHTSFEEVNGWGVVPKHGLVVLVNTEAYLIDTPFTAKDTEKLVTWFVERGYKIKGSISSHFHSDSTGGIEWLNSQSIPTYASELTNELLKKDGKVQAKNSFSGASYWLVKKKIEVFYPGPGHTPDNVVVWLPENRVLFGGCFVKPYGLGNLGDANVEAWPKSAKLLMSKYGKAKLVVPSHSEVGDASLLKRTLEQAVKGLNESKKPSKPGN"},"dna_sequence":{"accession":"NG_066696.1","fmin":"0","fmax":"741","strand":"+","sequence":"ATGAGCAAGTTATTTGTATTCTTTATGTTTTTGTTTTGTAGCATTACTGCCGCAGCAGAGTCTTTGCCAGATTTAAAAATTGAGAAGCTTGACGAAGGCGTTTATGTTCATACTTCGTTTGAAGAAGTTAACGGTTGGGGTGTTGTTCCTAAACACGGCTTGGTGGTTCTTGTAAATACTGAGGCCTATCTGATTGACACTCCATTTACGGCTAAAGATACTGAAAAGTTAGTCACTTGGTTTGTGGAACGCGGCTATAAAATAAAAGGCAGTATTTCCTCTCATTTTCATAGCGACAGCACGGGCGGAATAGAGTGGCTTAATTCTCAATCTATCCCCACGTATGCATCTGAATTAACAAATGAACTTCTTAAAAAAGACGGTAAAGTACAAGCTAAAAATTCATTTAGCGGAGCTAGCTATTGGCTAGTTAAGAAAAAGATTGAAGTTTTTTATCCTGGTCCAGGGCACACTCCAGATAACGTAGTGGTTTGGCTACCTGAAAATAGAGTTTTGTTCGGTGGTTGTTTTGTTAAACCGTACGGTCTAGGTAATTTGGGTGACGCAAATGTAGAAGCTTGGCCAAAGTCCGCCAAATTATTAATGTCCAAATATGGTAAGGCAAAACTGGTAGTTCCAAGTCACAGTGAAGTTGGAGACGCATCACTCTTGAAACGTACATTAGAACAGGCGGTTAAAGGGTTAAACGAAAGTAAAAAACCATCAAAACCAGGTAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005490","ARO_id":"43952","ARO_name":"IMP-85","CARD_short_name":"IMP-85","ARO_description":"IMP-85 is a IMP beta-lactamase.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4711":{"model_id":"4711","model_name":"IMP-88","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"7086":{"protein_sequence":{"accession":"WP_188331870.1","sequence":"MSKLSVFFIFLFCSIATAAESLPDLKIEKLDEGVYVHTSFEEVNGWGVFPKHGLVVLVNAEAYLIDTPFTAKDTEKLVTWFVERGYKIKGSISSHFHSDSTGGIEWLNSRSIPTYASELTNELLKKHGKVQATNSFSGVNYWLVKNKIEVFYPGPGHTPDNVVVWLPERKILFGGCFIKPYGLGNLGDANIEAWPKSAKLLKSKYGKAKLVVPSHSEVGDASLLKLTLEQAVKGLNESKKPSKPSN"},"dna_sequence":{"accession":"NG_070737.1","fmin":"0","fmax":"741","strand":"+","sequence":"ATGAGCAAGTTATCTGTATTCTTTATATTTTTGTTTTGCAGCATTGCTACCGCAGCAGAGTCTTTGCCAGATTTAAAAATTGAAAAGCTTGATGAAGGCGTTTATGTTCATACTTCGTTTGAAGAAGTTAACGGGTGGGGCGTTTTTCCTAAACATGGTTTGGTGGTTCTTGTAAATGCTGAGGCTTACCTAATTGACACTCCATTTACGGCTAAAGATACTGAAAAGTTAGTCACTTGGTTTGTGGAGCGTGGCTATAAAATAAAAGGCAGCATTTCCTCTCATTTTCATAGCGACAGCACGGGCGGAATAGAGTGGCTTAATTCTCGATCTATCCCCACGTATGCATCTGAATTAACAAATGAACTGCTTAAAAAACACGGTAAGGTTCAAGCCACAAATTCATTTAGCGGAGTTAACTATTGGCTAGTTAAAAATAAAATTGAAGTTTTTTATCCAGGCCCGGGACACACTCCAGATAACGTAGTGGTTTGGTTGCCTGAAAGGAAAATATTATTCGGTGGTTGTTTTATTAAACCGTACGGTTTAGGCAATTTGGGTGACGCAAATATAGAAGCTTGGCCAAAGTCCGCCAAATTATTAAAGTCCAAATATGGTAAGGCAAAACTGGTTGTTCCAAGTCACAGTGAAGTTGGAGACGCATCACTCTTGAAACTTACATTAGAGCAGGCGGTTAAAGGGTTAAACGAAAGTAAAAAACCATCAAAACCAAGCAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005491","ARO_id":"43953","ARO_name":"IMP-88","CARD_short_name":"IMP-88","ARO_description":"IMP-88 is a IMP beta-lactamase.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4712":{"model_id":"4712","model_name":"IMP-89","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"7087":{"protein_sequence":{"accession":"WP_181727105.1","sequence":"MSKLSVFFIFLFCNIATAAEPLPDLKIEKLDEGVYVHTSFEEVNGWGVFPKHGLVVLVDAEAYLIDTPFTAKDTEKLVTWFVERGYKIKGSISSHFHSDSTGGIEWLNSQSIPTYASELTNELLKKDGKVQAKNSFGGVNYWLVKNKIEVFYPGPGHTPDNLVVWLPERKILFGGCFIKPYGLGNLGDANLEAWPKSAKLLISKYGKAKLVVPSHSEAGDASLLKLTLEQAVKGLNESKKPSKLSN"},"dna_sequence":{"accession":"NG_070738.1","fmin":"100","fmax":"841","strand":"+","sequence":"ATGAGCAAGTTATCTGTATTCTTTATATTTTTGTTTTGTAACATTGCTACCGCAGCAGAGCCTTTGCCAGATTTAAAAATTGAAAAACTTGATGAAGGCGTTTATGTTCATACTTCGTTTGAAGAAGTTAACGGGTGGGGCGTTTTTCCTAAACATGGTTTGGTTGTTCTTGTAGATGCTGAAGCTTATCTAATTGACACTCCATTTACGGCTAAAGATACTGAAAAGTTAGTCACTTGGTTTGTGGAACGTGGCTATAAAATAAAAGGCAGTATTTCCTCTCATTTTCATAGTGACAGCACGGGCGGAATAGAGTGGCTTAATTCTCAATCCATCCCCACGTATGCGTCTGAATTAACTAATGAGCTGCTTAAAAAAGACGGTAAGGTTCAAGCTAAAAATTCATTTGGCGGGGTTAACTATTGGCTAGTTAAAAATAAAATTGAAGTTTTTTATCCAGGCCCAGGACACACTCCAGATAACCTAGTAGTTTGGCTGCCTGAAAGGAAAATATTATTCGGTGGTTGTTTTATTAAACCGTACGGTCTAGGTAATTTGGGTGACGCAAATTTAGAAGCTTGGCCAAAGTCCGCTAAATTATTAATATCCAAATATGGTAAGGCAAAACTGGTTGTTCCAAGTCACAGTGAAGCTGGAGACGCATCACTCTTGAAACTTACATTAGAGCAGGCGGTTAAAGGGTTAAACGAAAGTAAAAAACCATCAAAACTAAGCAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36803","NCBI_taxonomy_name":"Pseudomonas putida","NCBI_taxonomy_id":"303"}}}},"ARO_accession":"3005492","ARO_id":"43954","ARO_name":"IMP-89","CARD_short_name":"IMP-89","ARO_description":"IMP-89 is a IMP beta-lactamase.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4713":{"model_id":"4713","model_name":"IND-16","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"7088":{"protein_sequence":{"accession":"WP_052769157.1","sequence":"MKKSIQFFIVSMLLSPFANAQVKDFVIEPPIKSNLYIYKTFGVFGGKEYSANAAYLKTKKGVILFDVPWEKVQYQSLMDTIKKRHNLPVIAVFATHSHDDRAGDLSFFNNKGIKTYATLKTNEFLKKDGKATSTEIIQTGKPYHIGGEEFVVDFLGEGHTADNVVVWFPKYNVLDGGCLVKSNSATDLGYIKEANVEQWPKTMNKLKTKYSKATLIIPGHDEWKGGGHVEHTLELLNKK"},"dna_sequence":{"accession":"NG_054943.1","fmin":"0","fmax":"720","strand":"+","sequence":"ATGAAAAAAAGCATTCAATTTTTTATTGTTTCCATGTTGTTGAGCCCTTTTGCCAATGCACAGGTAAAAGATTTTGTAATTGAGCCACCTATTAAATCCAATCTATATATTTACAAGACTTTTGGAGTATTCGGAGGTAAAGAATATTCTGCCAATGCAGCCTATCTTAAGACTAAAAAAGGTGTAATTCTGTTTGATGTACCCTGGGAAAAAGTACAGTATCAAAGCCTGATGGATACCATCAAAAAACGTCATAACTTACCGGTAATTGCCGTATTTGCTACGCATTCCCATGATGACCGTGCAGGAGACTTAAGCTTTTTCAATAATAAAGGCATTAAGACGTATGCTACCCTGAAAACCAATGAGTTTCTGAAGAAAGATGGAAAAGCAACATCCACAGAGATCATCCAAACCGGAAAACCTTATCACATTGGCGGAGAAGAATTTGTGGTCGATTTTCTTGGTGAAGGACATACTGCTGATAATGTAGTGGTATGGTTTCCAAAATATAATGTTTTGGATGGCGGATGTCTTGTAAAAAGTAATTCTGCTACTGACTTAGGATACATTAAAGAAGCCAATGTAGAACAATGGCCCAAGACGATGAATAAATTAAAAACCAAATATTCAAAAGCCACATTAATTATTCCCGGGCATGATGAATGGAAAGGGGGTGGACATGTTGAACACACTTTAGAGCTTTTGAACAAAAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39102","NCBI_taxonomy_name":"Chryseobacterium","NCBI_taxonomy_id":"59732"}}}},"ARO_accession":"3005493","ARO_id":"43955","ARO_name":"IND-16","CARD_short_name":"IND-16","ARO_description":"IND-16 is a IND beta-lactamase.","ARO_category":{"36199":{"category_aro_accession":"3000060","category_aro_cvterm_id":"36199","category_aro_name":"IND beta-lactamase","category_aro_description":"IND beta-lactamases are class B carbapenem-hydrolyzing beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4714":{"model_id":"4714","model_name":"KLUC-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"7089":{"protein_sequence":{"accession":"WP_061284984.1","sequence":"MVKKSLRQFALLAATVFPLLAGSVSLQAQTLSVEQKLAALEQRSGGRLGVALIDTADGSQILYRGDERFAMCSTSKVMAAAAVLKQSESQHDLLNQRIEIKKGDLTNYNPIAEKHVGGSMSLSELSAAALQYSDNVAMNKLIAQLGGPQGVTAFARKIGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDAQRAQLVTWMKGNTTGTASIQAGLPASWVVGDKTGSGDYGTTNDIAVIWPKDRAPLVLVTYFTQPQPEAESRRDVLASAAKIVTEGL"},"dna_sequence":{"accession":"NG_049241.1","fmin":"100","fmax":"976","strand":"+","sequence":"ATGGTTAAAAAATCATTACGCCAGTTTGCGCTGTTGGCCGCGACGGTTTTTCCGCTGCTGGCAGGCAGCGTATCGCTACAGGCACAAACGCTAAGCGTAGAGCAGAAACTTGCGGCTTTAGAGCAGCGTTCAGGGGGACGGCTTGGGGTCGCGTTGATAGATACTGCGGATGGTTCGCAAATTCTCTATCGTGGCGATGAGCGTTTCGCGATGTGTAGTACCAGCAAAGTGATGGCCGCTGCCGCGGTGCTAAAGCAAAGTGAAAGTCAGCACGATCTTTTAAATCAGCGCATTGAGATCAAAAAGGGTGACCTGACTAACTATAACCCGATTGCGGAAAAACATGTCGGTGGGTCGATGTCGTTGTCTGAGCTCAGCGCCGCGGCCTTGCAGTACAGCGATAACGTGGCGATGAATAAGCTTATCGCTCAACTGGGTGGCCCGCAGGGGGTTACCGCGTTTGCCCGTAAGATTGGGGATGAGACGTTTCGTCTCGATCGCACGGAACCGACGCTGAACACTGCAATTCCCGGCGATCCACGCGATACCACATCACCACGGGCTATGGCACAAACGCTGCGCAACCTGACGCTGGGAAAAGCGCTTGGTGACGCTCAAAGGGCGCAGTTGGTGACCTGGATGAAAGGGAATACGACTGGAACGGCCAGTATTCAGGCTGGACTACCGGCTTCGTGGGTGGTGGGTGATAAAACCGGCAGCGGTGATTACGGCACCACCAACGACATTGCGGTGATTTGGCCGAAAGATCGTGCACCATTGGTTTTGGTTACCTACTTCACGCAGCCTCAGCCTGAGGCGGAAAGCCGTCGTGATGTATTAGCCTCGGCGGCGAAAATCGTCACTGAGGGATTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3006927","ARO_id":"45389","ARO_name":"KLUC-1","CARD_short_name":"KLUC-1","ARO_description":"KLUC-1 is a KLUC beta-lactamase.","ARO_category":{"43877":{"category_aro_accession":"3005417","category_aro_cvterm_id":"43877","category_aro_name":"KLUC beta-lactamase","category_aro_description":"KLUC beta-lactamases are class A beta-lactamases found in Kluyvera cryocrescens, Escherichia coli and Enterobacteriaceae.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4715":{"model_id":"4715","model_name":"KLUC-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"7090":{"protein_sequence":{"accession":"WP_032491875.1","sequence":"MVKKSLRQFALLAATVFPLLAGSVSLQAQTLSVEQKLAALEQRSGGRLGVALIDTADGSQILYRGDERFAMCSTSKVMAAAAVLKQSESQHDLLNQRIEIKKGDLTNYNPIAEKHVGRSMSLSELSAAALQYSDNVAMNKLIAQLGGPQGVTAFARKIGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDAQRAQLVTWMKGNTTGTASIQAGLPASWVVGDKTGSGDYGTTNDIAVIWPKDRAPLVLVTYFTQPQPEAESRRDVLASAAKIVTEGL"},"dna_sequence":{"accession":"NG_049242.1","fmin":"100","fmax":"976","strand":"+","sequence":"ATGGTTAAAAAATCATTACGCCAGTTTGCGCTGTTGGCCGCGACGGTTTTTCCGCTGCTGGCAGGCAGCGTATCGCTACAGGCACAAACGCTAAGCGTAGAGCAGAAACTTGCGGCTTTAGAGCAGCGTTCAGGGGGACGGCTTGGGGTCGCGTTGATAGATACTGCGGATGGTTCGCAAATTCTCTATCGTGGCGATGAGCGTTTCGCGATGTGTAGTACCAGCAAAGTGATGGCCGCTGCCGCGGTGCTAAAGCAAAGTGAAAGTCAGCACGATCTTTTAAATCAGCGCATTGAGATCAAAAAGGGTGACCTGACTAACTATAACCCGATTGCGGAAAAACATGTCGGTAGGTCGATGTCGTTGTCTGAGCTCAGCGCCGCGGCCTTGCAGTACAGCGATAACGTGGCGATGAATAAGCTTATCGCTCAACTGGGTGGCCCGCAGGGGGTTACCGCGTTTGCCCGTAAGATTGGGGATGAGACGTTTCGTCTCGATCGCACGGAACCGACGCTGAACACTGCAATTCCCGGCGATCCACGCGATACCACATCACCACGGGCTATGGCACAAACGCTGCGCAACCTGACGCTGGGAAAAGCGCTTGGTGACGCTCAAAGGGCGCAGTTGGTGACCTGGATGAAAGGGAATACGACTGGAACGGCCAGTATTCAGGCTGGACTACCGGCTTCGTGGGTGGTGGGCGATAAAACCGGCAGCGGTGATTACGGCACCACCAACGACATTGCGGTGATTTGGCCGAAAGATCGTGCACCATTGGTTTTGGTTACCTACTTCACGCAGCCTCAGCCTGAGGCGGAAAGCCGTCGTGATGTATTAGCCTCGGCGGCGAAAATCGTCACTGAGGGATTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3006928","ARO_id":"45390","ARO_name":"KLUC-2","CARD_short_name":"KLUC-2","ARO_description":"KLUC-2 is a KLUC beta-lactamase.","ARO_category":{"43877":{"category_aro_accession":"3005417","category_aro_cvterm_id":"43877","category_aro_name":"KLUC beta-lactamase","category_aro_description":"KLUC beta-lactamases are class A beta-lactamases found in Kluyvera cryocrescens, Escherichia coli and Enterobacteriaceae.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4716":{"model_id":"4716","model_name":"KLUC-3","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"7091":{"protein_sequence":{"accession":"WP_032495491.1","sequence":"MVKKSLRQFALLAATVFPLLASSVSLQAQTLSVEQKLAALEQRSGGRLGVALIDTADGSQILYRGDERFAMCSTSKVMAAAAVLKQSESQHDLLNQRIEIKKGDLTNYNPIAEKHVGGSMSLSELSAAALQYSDNVAMNKLIAQLGGPQGVTAFARKIGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDAQRAQLVTWMKGNTTGTASIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLVLVTYFTQPQPEAESRRDVLASAAKIVTEGL"},"dna_sequence":{"accession":"NG_062209.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCATTACGCCAGTTTGCGCTGTTGGCCGCGACGGTCTTTCCGCTGCTGGCAAGCAGCGTATCGCTACAGGCACAAACGCTAAGCGTAGAGCAGAAACTTGCGGCTTTAGAGCAGCGTTCAGGGGGACGGCTTGGGGTCGCGTTGATAGATACTGCGGATGGTTCGCAAATTCTCTATCGTGGCGATGAGCGTTTCGCGATGTGTAGTACCAGCAAAGTGATGGCCGCTGCCGCGGTGCTAAAGCAAAGTGAAAGTCAGCACGATCTTTTAAATCAGCGCATTGAGATCAAAAAGGGTGACCTGACTAACTATAACCCGATTGCGGAAAAACATGTCGGTGGGTCGATGTCGTTGTCTGAGCTCAGCGCCGCGGCCTTGCAGTACAGCGATAACGTGGCGATGAATAAGCTTATCGCTCAACTGGGTGGCCCGCAGGGGGTTACCGCGTTTGCCCGTAAGATTGGGGATGAGACGTTTCGTCTCGATCGCACGGAACCGACGCTGAACACTGCAATTCCCGGCGATCCACGCGATACCACATCACCACGGGCTATGGCACAAACGCTGCGCAACCTGACGCTGGGAAAAGCGCTTGGTGACGCTCAAAGGGCGCAGTTGGTGACCTGGATGAAAGGGAATACGACTGGAACGGCCAGTATTCAGGCTGGACTACCGGCTTCGTGGGTGGTGGGCGATAAAACCGGCAGCGGTGGTTACGGCACCACCAACGACATTGCGGTGATTTGGCCGAAAGATCGTGCACCATTGGTTTTGGTTACCTACTTCACGCAGCCTCAGCCTGAGGCGGAAAGCCGTCGTGATGTATTAGCCTCGGCGGCGAAAATCGTCACTGAGGGATTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3006929","ARO_id":"45391","ARO_name":"KLUC-3","CARD_short_name":"KLUC-3","ARO_description":"KLUC-3 is a KLUC beta-lactamase.","ARO_category":{"43877":{"category_aro_accession":"3005417","category_aro_cvterm_id":"43877","category_aro_name":"KLUC beta-lactamase","category_aro_description":"KLUC beta-lactamases are class A beta-lactamases found in Kluyvera cryocrescens, Escherichia coli and Enterobacteriaceae.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4717":{"model_id":"4717","model_name":"KLUC-4","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"7092":{"protein_sequence":{"accession":"WP_032495492.1","sequence":"MVKKSLRQFALLAATVFPLLASSVSLQAQTLSVEQKLAALEQRSGGRLGVALIDTADGSQILYRGDERFAMCSTSKVMAAAAVLKQSESQHDLLNQRIEIKKGDLTNYNPIAEKHVGGSMSLSELSAAALQYSDNVAMNKLIAQLGGPQGVTAFARKIGDETFRLDLTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDAQRAQLVTWMKGNTTGTASIQAGLPASWVVGDKTGSGDYGTTNDIAVIWPKDRAPLVLVTYFTQPQPEAESRRDVLASAAKIVTEGL"},"dna_sequence":{"accession":"NG_062210.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCATTACGCCAGTTTGCGCTGTTGGCCGCGACGGTCTTTCCGCTGCTGGCAAGCAGCGTATCGCTACAGGCACAAACGCTAAGCGTAGAGCAGAAACTTGCGGCTTTAGAGCAGCGTTCAGGGGGACGGCTTGGGGTCGCGCTGATAGATACTGCGGATGGTTCGCAAATTCTCTATCGTGGCGATGAGCGTTTCGCGATGTGTAGTACCAGCAAAGTGATGGCCGCTGCCGCGGTGCTAAAGCAAAGTGAAAGTCAGCACGATCTTTTAAATCAGCGCATTGAGATCAAAAAGGGTGACCTGACTAACTATAACCCGATTGCGGAAAAACATGTCGGTGGGTCGATGTCGTTGTCTGAGCTCAGCGCCGCGGCCTTGCAGTACAGCGATAACGTGGCGATGAATAAGCTTATCGCTCAACTGGGTGGCCCGCAGGGGGTTACCGCGTTTGCCCGTAAGATTGGGGATGAGACGTTTCGTCTCGATCTCACGGAACCGACGCTGAACACTGCAATTCCCGGCGATCCACGCGATACCACATCACCACGGGCTATGGCACAAACGCTGCGCAACCTGACGCTGGGAAAAGCGCTTGGTGACGCTCAAAGGGCGCAGTTGGTGACCTGGATGAAAGGGAATACGACTGGAACGGCCAGTATTCAGGCTGGACTACCGGCTTCGTGGGTGGTGGGCGATAAAACCGGCAGCGGTGATTACGGCACCACCAACGACATTGCGGTGATTTGGCCGAAAGATCGTGCACCTTTGGTTTTGGTTACCTACTTCACGCAGCCTCAGCCTGAGGCGGAAAGCCGTCGTGATGTATTAGCCTCGGCGGCGAAAATCGTCACTGAGGGATTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3006930","ARO_id":"45392","ARO_name":"KLUC-4","CARD_short_name":"KLUC-4","ARO_description":"KLUC-4 is a KLUC beta-lactamase.","ARO_category":{"43877":{"category_aro_accession":"3005417","category_aro_cvterm_id":"43877","category_aro_name":"KLUC beta-lactamase","category_aro_description":"KLUC beta-lactamases are class A beta-lactamases found in Kluyvera cryocrescens, Escherichia coli and Enterobacteriaceae.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4718":{"model_id":"4718","model_name":"KLUC-5","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"7093":{"protein_sequence":{"accession":"WP_100663667.1","sequence":"MVKKSLRQFALLAATVFPLLASSVSLQAQTLSVEQKLAALEQRSGGRLGVALIDTADGSQILYRGDERFAMCSTSKVMAAAAVLKQSESQHDLLNQRIEIKKGDLTNYNPIAEKHVGGSMSLSELSAAALQYSDNVAMNKLIAQLGGPQGVTAFARKIGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDAQRAQLVTWMKGNTTGTASIQAGLPASWVVGDKTGSGDYGTTNDIAVIWPKDRAPLVLVTYFTQPQPEAESRRDVLASAAKIVTEGL"},"dna_sequence":{"accession":"NG_062249.1","fmin":"100","fmax":"976","strand":"+","sequence":"ATGGTTAAAAAATCATTACGCCAGTTTGCGCTGTTGGCCGCGACGGTCTTTCCGCTGCTGGCAAGCAGCGTATCGCTACAGGCACAAACGCTAAGCGTAGAGCAGAAACTTGCGGCTTTAGAGCAGCGTTCAGGGGGACGGCTTGGGGTCGCGTTGATAGATACTGCGGATGGTTCGCAAATTCTCTATCGTGGCGATGAGCGTTTCGCGATGTGTAGTACCAGCAAAGTGATGGCCGCTGCCGCGGTGCTAAAGCAAAGTGAAAGTCAGCACGATCTTTTAAATCAGCGCATTGAGATCAAAAAGGGTGACCTGACTAACTATAACCCGATTGCGGAAAAACATGTCGGTGGGTCGATGTCGTTGTCTGAGCTCAGCGCCGCGGCCTTGCAGTACAGCGATAACGTGGCGATGAATAAGCTTATCGCTCAACTGGGTGGCCCGCAGGGGGTTACCGCGTTTGCCCGTAAGATTGGGGATGAGACGTTTCGTCTCGATCGCACGGAACCGACGCTGAACACTGCAATTCCCGGCGATCCACGCGATACCACATCACCACGGGCTATGGCACAAACGCTGCGCAACCTGACGCTGGGAAAAGCGCTTGGTGACGCTCAAAGGGCGCAGTTGGTGACCTGGATGAAAGGGAATACGACTGGAACGGCCAGTATTCAGGCTGGACTACCGGCTTCGTGGGTGGTGGGCGATAAAACCGGCAGCGGTGATTACGGCACCACCAACGACATTGCGGTGATTTGGCCGAAAGATCGTGCACCATTGGTTTTGGTTACCTACTTCACGCAGCCTCAGCCTGAGGCGGAAAGCCGTCGTGATGTATTAGCCTCGGCGGCGAAAATCGTCACTGAGGGATTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"45686","NCBI_taxonomy_name":"Raoultella ornithinolytica","NCBI_taxonomy_id":"54291"}}}},"ARO_accession":"3006931","ARO_id":"45393","ARO_name":"KLUC-5","CARD_short_name":"KLUC-5","ARO_description":"KLUC-5 is a KLUC beta-lactamase.","ARO_category":{"43877":{"category_aro_accession":"3005417","category_aro_cvterm_id":"43877","category_aro_name":"KLUC beta-lactamase","category_aro_description":"KLUC beta-lactamases are class A beta-lactamases found in Kluyvera cryocrescens, Escherichia coli and Enterobacteriaceae.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4719":{"model_id":"4719","model_name":"KPC-21","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"7094":{"protein_sequence":{"accession":"WP_063860711.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPRSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"NG_049254.1","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGAGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3003145","ARO_id":"39722","ARO_name":"KPC-21","CARD_short_name":"KPC-21","ARO_description":"KPC-21 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4720":{"model_id":"4720","model_name":"KPC-44","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"7095":{"protein_sequence":{"accession":"WP_140423311.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"NG_065427.1","fmin":"0","fmax":"927","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3006186","ARO_id":"44648","ARO_name":"KPC-44","CARD_short_name":"KPC-44","ARO_description":"KPC-44 is a KPC beta-lactamase.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4721":{"model_id":"4721","model_name":"KPC-58","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"7096":{"protein_sequence":{"accession":"WP_179284320.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDNRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"NG_070177.1","fmin":"0","fmax":"906","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAACCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3006187","ARO_id":"44649","ARO_name":"KPC-58","CARD_short_name":"KPC-58","ARO_description":"KPC-58 is a KPC beta-lactamase.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4722":{"model_id":"4722","model_name":"KPC-59","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"7097":{"protein_sequence":{"accession":"WP_179284322.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQADLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"NG_070178.1","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGACTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3006188","ARO_id":"44650","ARO_name":"KPC-59","CARD_short_name":"KPC-59","ARO_description":"KPC-59 is a KPC beta-lactamase.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4723":{"model_id":"4723","model_name":"KPC-60","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"7098":{"protein_sequence":{"accession":"WP_179284324.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVTELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"NG_070179.1","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGACGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3006189","ARO_id":"44651","ARO_name":"KPC-60","CARD_short_name":"KPC-60","ARO_description":"KPC-60 is a KPC beta-lactamase.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4724":{"model_id":"4724","model_name":"KPC-61","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"7099":{"protein_sequence":{"accession":"WP_179284328.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNPAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKYSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"NG_070180.1","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACCCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGTACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3006190","ARO_id":"44652","ARO_name":"KPC-61","CARD_short_name":"KPC-61","ARO_description":"KPC-61 is a KPC beta-lactamase.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4725":{"model_id":"4725","model_name":"KPC-62","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"7100":{"protein_sequence":{"accession":"WP_204376229.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELEQNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKYSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"NG_073465.1","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCAGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGTACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3006191","ARO_id":"44653","ARO_name":"KPC-62","CARD_short_name":"KPC-62","ARO_description":"KPC-62 is a KPC beta-lactamase.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4726":{"model_id":"4726","model_name":"KPC-63","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"7101":{"protein_sequence":{"accession":"WP_204376230.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVSGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKYSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"NG_073466.1","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTCTGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGTACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3006192","ARO_id":"44654","ARO_name":"KPC-63","CARD_short_name":"KPC-63","ARO_description":"KPC-63 is a KPC beta-lactamase.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4727":{"model_id":"4727","model_name":"KPC-64","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"7102":{"protein_sequence":{"accession":"WP_204376231.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGAANDYAVVWPTGRAPIVLAVHTRAPNKDDKYSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"NG_073467.1","fmin":"0","fmax":"885","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCGCGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCCACACCCGGGCGCCTAACAAGGATGACAAGTACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3006193","ARO_id":"44655","ARO_name":"KPC-64","CARD_short_name":"KPC-64","ARO_description":"KPC-64 is a KPC beta-lactamase.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4728":{"model_id":"4728","model_name":"KPC-65","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"7103":{"protein_sequence":{"accession":"WP_204376232.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTYTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKYSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"NG_073468.1","fmin":"0","fmax":"888","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGTACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3006194","ARO_id":"44656","ARO_name":"KPC-65","CARD_short_name":"KPC-65","ARO_description":"KPC-65 is a KPC beta-lactamase.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4729":{"model_id":"4729","model_name":"KPC-66","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"7104":{"protein_sequence":{"accession":"WP_188331871.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKYSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"NG_070739.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGTACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3006195","ARO_id":"44657","ARO_name":"KPC-66","CARD_short_name":"KPC-66","ARO_description":"KPC-66 is a KPC beta-lactamase.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4730":{"model_id":"4730","model_name":"KPC-71","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"7105":{"protein_sequence":{"accession":"WP_194293134.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"NG_070895.1","fmin":"0","fmax":"885","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3006196","ARO_id":"44658","ARO_name":"KPC-71","CARD_short_name":"KPC-71","ARO_description":"KPC-71 is a KPC beta-lactamase.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4731":{"model_id":"4731","model_name":"KPC-72","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"7106":{"protein_sequence":{"accession":"WP_188331872.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSDIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"NG_070740.1","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGACATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3006197","ARO_id":"44659","ARO_name":"KPC-72","CARD_short_name":"KPC-72","ARO_description":"KPC-72 is a KPC beta-lactamase.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4732":{"model_id":"4732","model_name":"KPC-73","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"7107":{"protein_sequence":{"accession":"WP_188331873.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"NG_070741.1","fmin":"0","fmax":"894","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3006198","ARO_id":"44660","ARO_name":"KPC-73","CARD_short_name":"KPC-73","ARO_description":"KPC-73 is a KPC beta-lactamase.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4733":{"model_id":"4733","model_name":"KPC-74","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"7108":{"protein_sequence":{"accession":"WP_188331874.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"NG_070742.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3006199","ARO_id":"44661","ARO_name":"KPC-74","CARD_short_name":"KPC-74","ARO_description":"KPC-74 is a KPC beta-lactamase.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4734":{"model_id":"4734","model_name":"KPC-75","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"7109":{"protein_sequence":{"accession":"WP_188331875.1","sequence":"MSLYRRLVLLSCFSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"NG_070743.1","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTTTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3006200","ARO_id":"44662","ARO_name":"KPC-75","CARD_short_name":"KPC-75","ARO_description":"KPC-75 is a KPC beta-lactamase.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4735":{"model_id":"4735","model_name":"KPC-76","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"7110":{"protein_sequence":{"accession":"WP_194293135.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARYTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"NG_070896.1","fmin":"100","fmax":"1003","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCTATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3006201","ARO_id":"44663","ARO_name":"KPC-76","CARD_short_name":"KPC-76","ARO_description":"KPC-76 is a KPC beta-lactamase.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4736":{"model_id":"4736","model_name":"KPC-77","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"7111":{"protein_sequence":{"accession":"WP_194293136.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDPWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"NG_070897.1","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCCCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3006202","ARO_id":"44664","ARO_name":"KPC-77","CARD_short_name":"KPC-77","ARO_description":"KPC-77 is a KPC beta-lactamase.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4737":{"model_id":"4737","model_name":"KPC-78","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"7112":{"protein_sequence":{"accession":"WP_197749403.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARATSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"NG_071204.1","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGCTACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3006203","ARO_id":"44665","ARO_name":"KPC-78","CARD_short_name":"KPC-78","ARO_description":"KPC-78 is a KPC beta-lactamase.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4738":{"model_id":"4738","model_name":"KPC-79","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"7113":{"protein_sequence":{"accession":"WP_197749404.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"NG_071205.1","fmin":"100","fmax":"1003","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3006204","ARO_id":"44666","ARO_name":"KPC-79","CARD_short_name":"KPC-79","ARO_description":"KPC-79 is a KPC beta-lactamase.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4739":{"model_id":"4739","model_name":"KPC-80","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"7114":{"protein_sequence":{"accession":"WP_204376233.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"NG_073469.1","fmin":"0","fmax":"891","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3006205","ARO_id":"44667","ARO_name":"KPC-80","CARD_short_name":"KPC-80","ARO_description":"KPC-80 is a KPC beta-lactamase.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4740":{"model_id":"4740","model_name":"KPC-81","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"7115":{"protein_sequence":{"accession":"WP_204376234.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"NG_073470.1","fmin":"0","fmax":"879","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3006206","ARO_id":"44668","ARO_name":"KPC-81","CARD_short_name":"KPC-81","ARO_description":"KPC-81 is a KPC beta-lactamase.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4741":{"model_id":"4741","model_name":"KPC-82","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"7116":{"protein_sequence":{"accession":"WP_202781289.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSDSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"NG_073471.1","fmin":"0","fmax":"888","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36934","NCBI_taxonomy_name":"Citrobacter koseri","NCBI_taxonomy_id":"545"}}}},"ARO_accession":"3006207","ARO_id":"44669","ARO_name":"KPC-82","CARD_short_name":"KPC-82","ARO_description":"KPC-82 is a KPC beta-lactamase.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4743":{"model_id":"4743","model_name":"LEN-27","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"7118":{"protein_sequence":{"accession":"WP_008804981.1","sequence":"MRYVRLCVISLLATLPLAVDAGPQPLEQIKQSESQLSGRVGMVEMDLASGRTLAAWRADERFPMVSTFKVLLCGAVLARVDAGLEQLDRRIHYRQQDLVDYSPVSEKHLTDGMTIGELCAAAITLSDNSAGNLLLATVGGPAGLTAFLRQIGDNVTRLDRWETALNEALPGDARDTTTPASMAATLRKLLTAQHLSARSQQQLLQWMVDDRVAGPLIRAVLPPGWFIADKTGAGERGARGIVALLGPDGKPERIVVIYLRDTPASMAERNQHIAGIGAALIEHWQR"},"dna_sequence":{"accession":"NG_068509.1","fmin":"100","fmax":"961","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGTGTTATCTCCCTGTTAGCCACCCTGCCACTGGCGGTAGACGCCGGTCCACAGCCGCTTGAGCAGATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTGGGGATGGTGGAAATGGATCTGGCCAGCGGCCGCACGCTGGCGGCCTGGCGCGCCGATGAACGCTTTCCCATGGTGAGCACCTTTAAAGTGCTGCTGTGCGGCGCGGTGCTGGCGCGGGTGGATGCCGGGCTCGAACAACTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTACCGACGGGATGACGATCGGCGAACTCTGCGCCGCCGCCATCACCCTGAGCGATAACAGCGCTGGCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCGGGATTAACTGCCTTTCTGCGCCAGATCGGTGACAACGTCACCCGTCTTGACCGCTGGGAAACGGCACTGAATGAGGCGCTTCCCGGCGACGCGCGCGACACCACCACCCCGGCCAGCATGGCCGCCACGCTGCGCAAACTACTGACCGCGCAGCATCTGAGCGCCCGTTCGCAACAGCAACTCCTGCAGTGGATGGTGGACGATCGGGTTGCCGGCCCGCTGATCCGCGCCGTGCTGCCGCCGGGCTGGTTTATCGCCGACAAAACCGGGGCTGGCGAACGGGGTGCGCGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAACCGGAGCGCATTGTGGTGATCTATCTGCGGGATACCCCGGCGAGTATGGCCGAGCGTAATCAACATATCGCCGGGATCGGCGCAGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37059","NCBI_taxonomy_name":"Klebsiella","NCBI_taxonomy_id":"570"}}}},"ARO_accession":"3006932","ARO_id":"45394","ARO_name":"LEN-27","CARD_short_name":"LEN-27","ARO_description":"LEN-27 is a LEN beta-lactamase.","ARO_category":{"36236":{"category_aro_accession":"3000097","category_aro_cvterm_id":"36236","category_aro_name":"LEN beta-lactamase","category_aro_description":"LEN beta-lactamases are chromosomal class A beta-lactamases that confer resistance to ampicillin, amoxicillin, carbenicillin, and ticarcillin but not to extended-spectrum beta-lactams.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4744":{"model_id":"4744","model_name":"LEN-28","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"7119":{"protein_sequence":{"accession":"WP_012541790.1","sequence":"MRYVRLCVISLLANLPLAVDAGPQPLEQIKQSESQLSGRVGMVEMDLASGRTLAAWRADERFPMVSTFKVLLCGAVLARVDAGLEQLDRRIHYRQQDLVDYSPVSEKHLVDGMTIGELCAAAITLSDNSAGNLLLATVGGPAGLTAFLRQIGDNVTRLDRWETALNEALPGDARDTTTPASMAATLRKLLTAQHLSPRSQQQLLQWMVDDRVAGPLIRAVLPAGWFIADKTGAGERGARGIVALLGPDGKPERIVVIYLRDTPASMAERNQHIAGIGAALIEHWQR"},"dna_sequence":{"accession":"NG_060510.1","fmin":"100","fmax":"961","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGTGTTATCTCCCTGTTAGCCAACCTGCCACTGGCGGTAGACGCCGGTCCACAGCCGCTTGAGCAGATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTGGGGATGGTGGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCGATGAACGCTTTCCCATGGTGAGCACCTTTAAAGTGCTGCTGTGCGGCGCGGTGCTGGCGCGGGTGGATGCCGGGCTCGAACAACTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGTCGACGGGATGACGATCGGCGAACTCTGCGCCGCCGCCATCACCCTGAGCGATAACAGCGCTGGCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCGGGATTAACTGCCTTTCTGCGCCAGATCGGTGACAACGTCACCCGTCTTGACCGCTGGGAAACGGCACTGAATGAGGCGCTTCCCGGCGACGCGCGCGACACCACCACCCCGGCCAGCATGGCCGCCACGCTGCGCAAACTACTGACCGCGCAGCATCTGAGCCCCCGTTCGCAACAGCAACTCCTGCAGTGGATGGTGGACGATCGGGTTGCCGGCCCGCTGATCCGCGCCGTGCTGCCGGCGGGCTGGTTTATCGCCGACAAGACCGGGGCTGGCGAACGGGGTGCGCGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAACCGGAGCGCATTGTGGTGATCTATCTGCGGGATACCCCGGCGAGTATGGCCGAGCGTAATCAACATATCGCCGGGATCGGCGCAGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42612","NCBI_taxonomy_name":"Klebsiella variicola","NCBI_taxonomy_id":"244366"}}}},"ARO_accession":"3006933","ARO_id":"45395","ARO_name":"LEN-28","CARD_short_name":"LEN-28","ARO_description":"LEN-28 is a LEN beta-lactamase.","ARO_category":{"36236":{"category_aro_accession":"3000097","category_aro_cvterm_id":"36236","category_aro_name":"LEN beta-lactamase","category_aro_description":"LEN beta-lactamases are chromosomal class A beta-lactamases that confer resistance to ampicillin, amoxicillin, carbenicillin, and ticarcillin but not to extended-spectrum beta-lactams.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4745":{"model_id":"4745","model_name":"LEN-31","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"7120":{"protein_sequence":{"accession":"WP_016160983.1","sequence":"MRYVRLCVISLLATLPLAVDAGPQPLEQIKQSESQLSGRVGMVEMDLASGRTLAAWRADERFPMVSTFKVLLCGAVLARVDAGVEQLDRRIHYRQQDLVDYSPVSEKHLTDGMTVGELCAAAITLSDNSAGNLLLATVGGPAGLTAFLRQIGDNVTHLDRWETALNEALPGDARDTTTPASMAATLRKLLTAQHLSARSQQQLLQWMVDDRVAGPLIRAVLPPGWFIADKTGAGERGARGIVALLGPDGKPERIVVIYLRDTPASMAERNQHIAGIGAALIEHWQR"},"dna_sequence":{"accession":"NG_050605.1","fmin":"100","fmax":"961","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGTGTTATCTCCCTGTTAGCCACCCTGCCACTGGCGGTAGACGCCGGTCCACAGCCGCTTGAGCAGATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTGGGGATGGTGGAAATGGATCTGGCCAGCGGCCGCACGCTGGCGGCCTGGCGCGCCGATGAACGCTTTCCCATGGTGAGCACCTTTAAAGTGCTGCTGTGCGGCGCGGTGCTGGCGCGGGTGGATGCAGGGGTCGAACAACTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTACCGACGGGATGACGGTCGGCGAACTCTGCGCCGCCGCCATCACCCTGAGCGATAACAGTGCTGGCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCGGGATTAACTGCCTTTCTGCGCCAGATCGGTGACAACGTCACCCATCTTGACCGCTGGGAAACGGCACTGAATGAGGCGCTTCCCGGCGACGCACGCGACACCACCACCCCGGCCAGCATGGCCGCCACGCTGCGCAAACTACTGACCGCGCAGCATCTGAGCGCCCGTTCGCAACAGCAACTCCTGCAGTGGATGGTGGACGATCGGGTTGCCGGCCCGCTGATCCGCGCCGTGCTGCCGCCGGGCTGGTTTATCGCCGACAAGACCGGGGCTGGCGAACGGGGTGCGCGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAACCGGAGCGCATTGTGGTGATCTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGTAATCAACATATCGCCGGGATCGGCGCAGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37059","NCBI_taxonomy_name":"Klebsiella","NCBI_taxonomy_id":"570"}}}},"ARO_accession":"3006934","ARO_id":"45396","ARO_name":"LEN-31","CARD_short_name":"LEN-31","ARO_description":"LEN-31 is a LEN beta-lactamase.","ARO_category":{"36236":{"category_aro_accession":"3000097","category_aro_cvterm_id":"36236","category_aro_name":"LEN beta-lactamase","category_aro_description":"LEN beta-lactamases are chromosomal class A beta-lactamases that confer resistance to ampicillin, amoxicillin, carbenicillin, and ticarcillin but not to extended-spectrum beta-lactams.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4746":{"model_id":"4746","model_name":"LHK-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7121":{"protein_sequence":{"accession":"WP_081666691.1","sequence":"MKKRITPFSRFASKGLFACSTGMLLVTVAHAANTAAAGMDAMIQTVMQAHQIPGMAIAIIQSGKTTYHNYGVASRETGQPVRETTLFEIGSLSKPFTALIAQRAETEGRIDLSAPASRYVTALRGSAFDRITLRQLGTYSAGGLPLQFPDNVTTPADVLAYYRHWQPVHPAGTTRLYSNPSIGLMGLAASLATGESFAGLLGTTVLQPLGMNSTYLQMPPEARSRYAMGYTAAGKPVRVNPGPLDEETYGVKSTTADMAGFLLAHMDPARSKGALRSALQQTRVPVYCAGQTRQGLGWESYQDWKNLDVLLAGNSNQMVFEPQPVKACPAGTMNEPDVWVNKTGSTAGFGAYAVFLPARQTGIVILANRNYPIADRIRLAHGILTALH"},"dna_sequence":{"accession":"NG_056482.1","fmin":"0","fmax":"1167","strand":"+","sequence":"ATGAAAAAACGGATTACCCCATTTTCCCGCTTTGCATCAAAAGGCCTTTTCGCCTGTAGCACAGGCATGTTGCTGGTGACGGTGGCACATGCTGCCAATACAGCAGCAGCCGGCATGGATGCCATGATACAAACCGTGATGCAGGCACACCAGATTCCGGGCATGGCCATTGCCATCATCCAGTCAGGCAAGACCACTTATCACAATTATGGTGTCGCCTCCCGCGAAACCGGCCAGCCGGTCCGGGAAACCACCCTGTTTGAAATCGGCTCCCTTTCCAAACCGTTTACTGCACTGATCGCCCAGCGGGCTGAAACCGAAGGCCGGATTGACCTGTCTGCACCGGCCAGCCGCTACGTTACCGCCCTGCGGGGCAGTGCATTCGACCGGATCACCCTCAGGCAGCTCGGTACTTATAGCGCAGGCGGATTACCGCTCCAGTTTCCTGACAATGTCACCACCCCGGCAGATGTGCTGGCTTATTACCGGCATTGGCAACCTGTCCATCCGGCAGGCACCACCCGGCTGTATTCCAATCCGAGCATTGGCCTGATGGGGCTGGCTGCCAGCCTGGCAACCGGAGAGTCCTTTGCCGGCCTGCTCGGGACAACGGTGCTGCAACCCCTCGGCATGAACTCGACCTATCTGCAAATGCCCCCGGAGGCCCGTTCACGTTATGCCATGGGTTATACCGCCGCCGGGAAACCGGTCAGGGTCAACCCCGGTCCGCTGGATGAGGAAACCTACGGCGTCAAGTCCACAACCGCAGACATGGCCGGATTTTTATTGGCGCATATGGACCCTGCACGCAGCAAAGGTGCATTGCGGTCGGCATTACAGCAAACACGTGTACCGGTTTATTGCGCCGGACAGACCCGGCAAGGACTGGGCTGGGAAAGTTATCAAGACTGGAAAAACCTCGACGTGCTGCTGGCGGGAAATTCAAATCAAATGGTGTTTGAGCCGCAGCCGGTGAAAGCCTGTCCTGCCGGCACCATGAATGAGCCCGATGTGTGGGTCAACAAGACCGGTTCTACTGCGGGATTCGGCGCTTATGCCGTATTCCTGCCTGCCCGACAAACCGGCATTGTCATCCTGGCCAACCGTAATTACCCGATTGCAGACCGTATCCGGCTCGCTCACGGAATTTTGACCGCATTGCACTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41458","NCBI_taxonomy_name":"Laribacter hongkongensis","NCBI_taxonomy_id":"168471"}}}},"ARO_accession":"3006935","ARO_id":"45397","ARO_name":"LHK-1","CARD_short_name":"LHK-1","ARO_description":"LHK-1 is a LHK beta-lactamase.","ARO_category":{"43878":{"category_aro_accession":"3005418","category_aro_cvterm_id":"43878","category_aro_name":"LHK beta-lactamase","category_aro_description":"LHK beta-lactamases are class C beta-lactamases found in Laribacter hongkongensis.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4747":{"model_id":"4747","model_name":"LHK-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7122":{"protein_sequence":{"accession":"WP_104531865.1","sequence":"MKKRITPFSRFASKGLFACSAGMLLVTVAHAANTAAAPAGVDAMVQTVMQAHQIPGMAIAIIQPGKTSYHNYGVASRETGQPVRETTLFEIGSLSKPFTALVAQRAETEGRIDLSAPASRYVAALRGSAFDRITLRQLGTYSAGGLPLQFPDNVTTPADMLAYYQHWQPVHPAGTTRLYSNPSIGLMGLAASQATGESFAGLLGTTVLQPLGMNSTYLQVPPEARSRYAMGYTAAGKPVRVSPGPLDEETYGIKSTTADMAGFLLAHMDPARSKDALRSALQQRAPVYCAGQTRQGLGWESYQDWKNLDVLLAGNSNQMVFEPQPVKACPAGTMNEPDVWVNKTGSTAGFGAYAVFLPARQTGIVILANRNYPITDRIRLAHGILTALH"},"dna_sequence":{"accession":"NG_056483.1","fmin":"0","fmax":"1170","strand":"+","sequence":"ATGAAAAAACGGATTACCCCATTTTCCCGATTTGCATCAAAAGGCCTTTTCGCCTGTAGCGCAGGCATGTTGCTGGTGACGGTGGCACATGCCGCCAATACGGCAGCAGCGCCAGCCGGTGTGGATGCCATGGTCCAAACCGTGATGCAGGCACACCAGATTCCGGGCATGGCCATTGCCATCATCCAGCCAGGCAAGACCTCTTATCACAATTATGGTGTCGCCTCCCGCGAAACCGGCCAGCCGGTCCGGGAAACCACTCTGTTTGAAATCGGCTCCCTTTCCAAACCGTTTACTGCACTGGTCGCCCAGCGGGCCGAAACCGAAGGCCGGATTGACCTGTCTGCACCGGCCAGCCGCTACGTTGCCGCCCTGCGAGGCAGTGCATTCGACCGGATCACCCTCAGGCAGCTCGGTACTTATAGCGCAGGCGGATTACCGCTCCAGTTTCCTGACAATGTCACCACCCCGGCAGACATGCTGGCTTATTACCAGCATTGGCAACCTGTCCATCCGGCAGGTACCACCCGGCTGTATTCCAATCCGAGCATTGGCCTGATGGGGCTGGCTGCCAGTCAGGCAACCGGAGAGTCCTTTGCCGGCCTGCTCGGGACAACGGTGCTGCAACCTCTCGGCATGAACTCGACCTATCTGCAAGTGCCCCCGGAGGCCCGTTCACGTTATGCCATGGGTTATACCGCCGCCGGGAAACCGGTCAGGGTCAGCCCCGGTCCGCTGGATGAGGAAACCTACGGCATCAAGTCCACAACCGCAGACATGGCCGGATTTTTACTGGCGCATATGGACCCTGCGCGCAGCAAAGATGCATTGCGGTCGGCATTACAGCAACGTGCACCGGTTTATTGCGCCGGACAGACCCGGCAAGGACTGGGCTGGGAAAGTTATCAAGACTGGAAAAACCTAGACGTGCTGCTGGCGGGAAATTCAAATCAAATGGTGTTTGAACCGCAGCCGGTAAAAGCCTGTCCTGCCGGCACCATGAATGAGCCCGATGTGTGGGTCAACAAGACCGGTTCTACTGCGGGATTCGGCGCTTATGCCGTATTCCTGCCTGCCCGACAGACCGGCATTGTCATCCTGGCCAACCGTAATTACCCGATTACAGACCGTATCCGGCTCGCTCACGGGATTTTGACCGCATTGCACTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41458","NCBI_taxonomy_name":"Laribacter hongkongensis","NCBI_taxonomy_id":"168471"}}}},"ARO_accession":"3006936","ARO_id":"45398","ARO_name":"LHK-2","CARD_short_name":"LHK-2","ARO_description":"LHK-2 is a LHK beta-lactamase.","ARO_category":{"43878":{"category_aro_accession":"3005418","category_aro_cvterm_id":"43878","category_aro_name":"LHK beta-lactamase","category_aro_description":"LHK beta-lactamases are class C beta-lactamases found in Laribacter hongkongensis.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4748":{"model_id":"4748","model_name":"LHK-3","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7123":{"protein_sequence":{"accession":"WP_104531866.1","sequence":"MKKRITPFSRFASKGLFACSAGMLLVTVAHAANMAAAPAGMDAMVQTVMQAHQIPGMAIAIIQPGKTTYHNYGVASRETGQPVRETTLFEIGSLSKPFTALVAQRAETEGRIDLSAPASRYVTALRGSAFDRITLRQLGTYSAGGLPLQFPDNVTTPADVLAYYRHWQPVHPAGSTRLYSNPSIGLMGLAASQATGESFAGLLGTTVLQPLGMNSTYLQVPPEARSRYAMGYTAAGKPVRVNPGPLDEETYGVKSTTADMAGFLLAHMDPARSKGALRSALQQTRVPVYCAGQTRQGLGWESYQDWKNLDVLLAGNSNQMVFEPQPVKACLAGTMNEPDVWVNKTGSTAGFGAYAVFLPARQTGIVILANRNYPIADRIRLAHGILTALH"},"dna_sequence":{"accession":"NG_056484.1","fmin":"0","fmax":"1173","strand":"+","sequence":"ATGAAAAAACGGATTACCCCATTTTCCCGATTTGCATCAAAAGGCCTTTTCGCCTGTAGCGCAGGCATGTTGCTGGTGACGGTGGCACATGCCGCCAATATGGCAGCAGCACCAGCCGGCATGGATGCCATGGTACAAACCGTGATGCAGGCACACCAGATTCCGGGCATGGCCATTGCCATCATCCAGCCAGGAAAGACCACTTATCACAATTATGGTGTCGCCTCCCGCGAAACCGGCCAGCCGGTCCGGGAAACCACCCTGTTTGAAATCGGCTCCCTTTCCAAACCGTTTACTGCACTGGTCGCCCAGCGGGCTGAAACCGAAGGCCGGATTGACCTGTCTGCACCGGCCAGCCGCTACGTTACCGCCCTGCGGGGCAGTGCATTCGACCGGATCACCCTCAGGCAGCTCGGTACTTATAGTGCAGGCGGATTACCGCTCCAGTTTCCTGACAATGTCACTACCCCGGCAGATGTACTGGCTTATTACCGCCATTGGCAACCTGTCCATCCGGCAGGTAGCACCCGGCTGTATTCCAATCCGAGCATTGGCCTGATGGGGCTGGCTGCCAGTCAGGCAACCGGAGAGTCCTTTGCCGGCCTGCTCGGGACAACGGTGCTGCAACCCCTCGGCATGAACTCGACCTATCTGCAAGTGCCCCCGGAGGCCCGTTCACGTTATGCCATGGGTTATACCGCCGCCGGGAAACCGGTCAGGGTCAACCCCGGTCCGCTGGATGAGGAAACCTACGGCGTCAAGTCCACAACCGCAGACATGGCCGGATTTTTACTGGCGCATATGGACCCTGCGCGCAGCAAAGGTGCATTGCGGTCGGCATTACAGCAAACACGTGTACCGGTTTATTGTGCCGGACAGACCCGGCAAGGACTGGGCTGGGAAAGTTATCAAGACTGGAAAAACCTCGACGTGCTGCTGGCGGGAAATTCAAATCAAATGGTGTTTGAACCGCAGCCGGTAAAAGCCTGTCTTGCCGGCACCATGAATGAGCCTGATGTGTGGGTCAACAAGACCGGTTCTACTGCGGGATTCGGCGCTTATGCCGTATTCCTGCCTGCCCGACAGACCGGCATTGTCATCCTGGCCAACCGTAATTACCCGATTGCAGACCGTATCCGGCTCGCTCACGGAATTTTGACCGCATTGCACTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41458","NCBI_taxonomy_name":"Laribacter hongkongensis","NCBI_taxonomy_id":"168471"}}}},"ARO_accession":"3006937","ARO_id":"45399","ARO_name":"LHK-3","CARD_short_name":"LHK-3","ARO_description":"LHK-3 is a LHK beta-lactamase.","ARO_category":{"43878":{"category_aro_accession":"3005418","category_aro_cvterm_id":"43878","category_aro_name":"LHK beta-lactamase","category_aro_description":"LHK beta-lactamases are class C beta-lactamases found in Laribacter hongkongensis.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4749":{"model_id":"4749","model_name":"LHK-4","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7124":{"protein_sequence":{"accession":"WP_104531867.1","sequence":"MKKRITPFSRFASKGLSACSAGMLLVTVAHAANTAAAPAGVDAMVQTVMQAHQIPGMAIAIIQPGKTTYHNYGVASRETGQPVRETTLFEIGSLSKPFTALVAQRAETEGRIDLSAPASRYVTALRGSAFDRITLRQLGTYSAGGLPLQFPDNVTTPADVLAYYRHWQPVHPAGSTRLYSNPSIGLMGLAASQATGESFAGLLGTTVLQPLGMNSTYLQVPPEARSRYAMGYTAAGKPVRVNPGPLDEETYGVKSTTADMAGFLLAHMDPARSKGALRSALQQTRVPVYCAGQTRQGLGWESYQDWKNLDVLLAGNSNQMVFEPQPVKACLAGTMNEPDVWVNKTGSTAGFGAYAVFLPARQTGIVILANRNYPIADRIRLAHGILTALH"},"dna_sequence":{"accession":"NG_056485.1","fmin":"0","fmax":"1173","strand":"+","sequence":"ATGAAAAAACGGATTACCCCATTTTCCCGATTTGCATCAAAAGGCCTTTCCGCCTGTAGCGCAGGCATGTTGCTGGTGACGGTGGCACATGCCGCCAATACGGCAGCAGCACCAGCCGGTGTGGATGCCATGGTCCAAACCGTGATGCAGGCACACCAGATTCCGGGCATGGCCATTGCCATCATCCAGCCAGGAAAGACCACTTATCACAATTATGGTGTCGCCTCCCGCGAAACCGGCCAGCCGGTCCGGGAAACCACCCTGTTTGAAATCGGCTCCCTTTCCAAACCGTTTACTGCACTGGTCGCCCAGCGGGCTGAAACCGAAGGCCGGATTGACCTGTCTGCACCGGCCAGCCGCTACGTTACCGCCCTGCGGGGCAGTGCATTCGACCGGATCACCCTCAGGCAGCTCGGTACTTATAGTGCAGGCGGATTACCGCTCCAGTTTCCTGACAATGTCACTACCCCGGCAGATGTACTGGCTTATTACCGCCATTGGCAACCTGTCCATCCGGCAGGTAGCACCCGGCTGTATTCCAATCCGAGCATTGGCCTGATGGGGCTGGCTGCCAGTCAGGCAACCGGAGAGTCCTTTGCCGGCCTGCTCGGGACAACGGTGCTGCAACCCCTCGGCATGAACTCGACCTATCTGCAAGTGCCCCCGGAGGCCCGTTCACGTTATGCCATGGGTTATACCGCCGCCGGGAAACCGGTCAGGGTCAACCCCGGTCCGCTGGATGAGGAAACCTACGGCGTCAAGTCCACAACCGCAGACATGGCCGGATTTTTACTGGCGCATATGGACCCTGCGCGCAGCAAAGGTGCATTGCGGTCGGCATTACAGCAAACACGTGTACCGGTTTATTGTGCCGGACAGACCCGGCAAGGACTGGGCTGGGAAAGTTATCAAGACTGGAAAAACCTCGACGTGCTGCTGGCGGGAAATTCAAATCAAATGGTGTTTGAACCGCAGCCGGTAAAAGCCTGTCTTGCCGGCACCATGAATGAGCCTGATGTGTGGGTCAACAAGACCGGTTCTACTGCGGGATTCGGCGCTTATGCCGTATTCCTGCCTGCCCGACAGACCGGCATTGTCATCCTGGCCAACCGTAATTACCCGATTGCAGACCGTATCCGGCTCGCTCACGGGATTTTGACCGCATTGCACTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41458","NCBI_taxonomy_name":"Laribacter hongkongensis","NCBI_taxonomy_id":"168471"}}}},"ARO_accession":"3006938","ARO_id":"45400","ARO_name":"LHK-4","CARD_short_name":"LHK-4","ARO_description":"LHK-4 is a LHK beta-lactamase.","ARO_category":{"43878":{"category_aro_accession":"3005418","category_aro_cvterm_id":"43878","category_aro_name":"LHK beta-lactamase","category_aro_description":"LHK beta-lactamases are class C beta-lactamases found in Laribacter hongkongensis.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4750":{"model_id":"4750","model_name":"LHK-5","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7125":{"protein_sequence":{"accession":"WP_104531868.1","sequence":"MKKRITPFSRFASKGLSACSAGMLLVTVAHAANTAAAPAGMDAMVQTVMQAHQIPGMAIAIIQPGKTTYHNYGVASRETGQPVRETTLFEIGSLSKPFTALVAQRAETEGRIDLSAPASRYVTALRGSAFDRITLRQLGTYSAGGLPLQFPDNVTTPADVLAYYRHWQPVHPAGTTRLYSNPSIGLMGLAASLATGESFAGLLGTTVLQPLGMNSTYLQVPPEARSRYAMGYTAAGKPVRVNPGPLDEETYGVKSTTADMVGFLLAHMDPARSKGALRSALQQTRVPVYCAGQTRQGLGWESYQDWKNLDMLLAGNSNQMVFEPQLVKACPAGTMNEPNVWVNKTGSTAGFGAYAVFLPARQTGIVILANRNYPIADRIRLAHGILTALH"},"dna_sequence":{"accession":"NG_056486.1","fmin":"0","fmax":"1173","strand":"+","sequence":"ATGAAAAAACGGATTACCCCATTTTCCCGATTTGCATCAAAAGGCCTTTCCGCCTGTAGCGCAGGCATGTTGCTGGTGACGGTGGCACATGCCGCCAATACGGCAGCAGCGCCAGCCGGCATGGATGCCATGGTCCAAACCGTGATGCAGGCACACCAGATTCCGGGCATGGCCATTGCCATCATCCAGCCTGGCAAGACCACTTATCACAATTATGGTGTCGCCTCCCGCGAAACCGGCCAGCCGGTCCGGGAAACCACCCTGTTTGAAATCGGCTCCCTTTCCAAACCGTTTACTGCACTGGTCGCCCAGCGGGCTGAAACCGAAGGCCGGATTGACCTGTCTGCACCGGCCAGCCGCTACGTTACCGCCCTGCGGGGCAGTGCATTCGACCGGATCACCCTCAGGCAGCTCGGTACTTATAGCGCAGGCGGATTACCGCTCCAGTTTCCTGACAATGTCACCACCCCGGCAGATGTGCTGGCTTATTACCGGCATTGGCAACCTGTCCATCCGGCAGGCACCACCCGGCTGTATTCCAATCCGAGCATTGGCCTGATGGGGCTGGCTGCCAGCCTGGCAACCGGAGAGTCCTTTGCCGGCCTGCTCGGGACAACGGTGCTGCAACCCCTCGGCATGAACTCGACCTATCTGCAAGTGCCCCCGGAGGCCCGTTCACGTTATGCCATGGGTTATACCGCCGCCGGGAAACCGGTCAGGGTCAACCCCGGTCCGCTGGATGAGGAAACCTACGGCGTCAAGTCCACAACCGCAGACATGGTCGGATTTTTATTGGCGCATATGGACCCTGCACGCAGCAAAGGTGCATTGCGGTCGGCATTACAGCAAACACGTGTACCGGTTTATTGCGCCGGACAGACCCGGCAAGGACTGGGCTGGGAAAGTTATCAAGACTGGAAAAACCTCGACATGCTGCTGGCGGGAAATTCAAATCAAATGGTGTTTGAACCGCAGCTGGTAAAAGCCTGTCCTGCCGGCACCATGAATGAGCCCAATGTGTGGGTCAACAAGACCGGTTCTACTGCGGGATTCGGCGCTTATGCCGTATTCCTGCCTGCCCGACAAACCGGCATTGTCATCCTGGCCAACCGTAATTACCCGATTGCAGACCGTATCCGGCTCGCTCACGGAATTTTGACCGCATTGCACTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41458","NCBI_taxonomy_name":"Laribacter hongkongensis","NCBI_taxonomy_id":"168471"}}}},"ARO_accession":"3006939","ARO_id":"45401","ARO_name":"LHK-5","CARD_short_name":"LHK-5","ARO_description":"LHK-5 is a LHK beta-lactamase.","ARO_category":{"43878":{"category_aro_accession":"3005418","category_aro_cvterm_id":"43878","category_aro_name":"LHK beta-lactamase","category_aro_description":"LHK beta-lactamases are class C beta-lactamases found in Laribacter hongkongensis.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4751":{"model_id":"4751","model_name":"LHK-6","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7126":{"protein_sequence":{"accession":"WP_104531869.1","sequence":"MKKRITPFSRFASKGLSACSAGMLLVTVAHAANTAAAPAGMDAMVQTVMQAHQIPGMAIAIIQPGKTTYHNYGIASRETGQPVRETTLFEIGSLSKPFTALVAQRAETEGRIDLSAPASRYVTALRGSAFDRITLRQLGTYSAGELPLQFPDNVTTPADVLAYYRHWQPVHPAGTTRLYSNPSIGLMGLAASQATGESFAGLLGTTVLQPLGMNSTYLQVPPEARSRYAMGYTAAGKPVRVSPGPLDEETYGVKSTTADMAGFLLAHMDPARSKGALRSALQQTRVPVYCAGQTRQGLGWESYQDWKNLDVLLAGNSNQMVFEPQPVKACLAGTSNEPDVWVNKTGSTAGFGAYAVFLPARQAGIVILANRNYPIADRIRLAHGILTALH"},"dna_sequence":{"accession":"NG_056487.1","fmin":"0","fmax":"1173","strand":"+","sequence":"ATGAAAAAACGGATTACCCCATTTTCCCGATTTGCATCAAAAGGCCTTTCCGCCTGTAGCGCAGGCATGTTGCTGGTGACGGTGGCACATGCCGCCAATACGGCAGCAGCGCCAGCCGGCATGGATGCCATGGTCCAAACCGTGATGCAGGCACACCAGATTCCGGGCATGGCCATTGCCATCATCCAGCCAGGAAAGACCACTTATCACAATTATGGTATCGCCTCCCGCGAAACCGGCCAGCCGGTCCGGGAAACCACCCTGTTTGAAATCGGCTCCCTTTCCAAACCGTTTACTGCACTGGTCGCCCAGCGGGCTGAAACCGAAGGCCGGATTGACCTGTCTGCACCGGCCAGCCGCTACGTTACCGCCCTGCGGGGCAGTGCATTCGACCGGATCACCCTCAGGCAGCTCGGTACTTATAGTGCAGGCGAATTGCCGCTCCAGTTTCCTGACAATGTCACCACCCCGGCAGACGTGCTGGCTTATTACCGCCATTGGCAACCTGTCCATCCGGCAGGTACCACCCGGCTGTATTCCAATCCGAGCATTGGCCTGATGGGGCTGGCTGCCAGTCAGGCAACCGGAGAGTCCTTTGCCGGCCTGCTCGGGACAACGGTGCTGCAACCCCTCGGCATGAACTCGACCTATCTGCAAGTGCCTCCGGAGGCCCGTTCACGTTATGCCATGGGTTATACCGCCGCCGGGAAACCGGTCAGGGTCAGCCCCGGTCCGCTGGATGAGGAAACCTACGGCGTCAAGTCCACAACCGCAGACATGGCCGGATTTTTATTGGCGCATATGGACCCTGCGCGCAGCAAAGGTGCATTGCGGTCGGCATTACAGCAAACACGTGTACCGGTTTATTGCGCCGGACAGACCCGGCAAGGACTGGGCTGGGAAAGTTATCAAGACTGGAAAAACCTCGACGTGCTGCTGGCGGGAAATTCAAATCAAATGGTGTTTGAACCGCAGCCGGTAAAAGCCTGTCTTGCCGGCACCTCGAATGAGCCCGACGTATGGGTCAACAAGACAGGTTCTACTGCGGGATTCGGCGCTTATGCCGTATTCCTGCCTGCCCGACAGGCCGGCATTGTCATCCTAGCCAACCGTAATTACCCGATTGCAGACCGTATCCGGCTCGCTCACGGAATTTTGACCGCATTGCACTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41458","NCBI_taxonomy_name":"Laribacter hongkongensis","NCBI_taxonomy_id":"168471"}}}},"ARO_accession":"3006940","ARO_id":"45402","ARO_name":"LHK-6","CARD_short_name":"LHK-6","ARO_description":"LHK-6 is a LHK beta-lactamase.","ARO_category":{"43878":{"category_aro_accession":"3005418","category_aro_cvterm_id":"43878","category_aro_name":"LHK beta-lactamase","category_aro_description":"LHK beta-lactamases are class C beta-lactamases found in Laribacter hongkongensis.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4752":{"model_id":"4752","model_name":"LRG-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"7127":{"protein_sequence":{"accession":"WP_063860827.1","sequence":"MNSIFSLSRRKYLLAAAGLTIAALFPPSVVLAEQPATLAAQLSALEASANGRLGVALIDSGSSRQLSYRGEERFAMASTFKALAAAAVLQRSVEQPALLNKRIIYQQSELITYSPVTEKHLQQGMTVAELCAAAVELSDNTAGNILLREIGGPQGITQLARRLGDNQTRLDRREPALNSAIPGDVRDTSTPLAMAGNLNQLALGKALPSAQQQLLIQWLKQSKTGAQSIRAGVPQGWQVGDKTGAGGYGTTNDLAILWPPQGKPLVLAVYFTQHNPQAEARRDVLASATRLVLAAWEKQ"},"dna_sequence":{"accession":"NG_049283.1","fmin":"100","fmax":"1000","strand":"+","sequence":"ATGAATAGCATCTTTTCCCTGTCCCGCCGTAAATACTTACTGGCCGCCGCCGGACTGACCATCGCCGCGCTATTTCCGCCATCCGTGGTGCTGGCCGAACAACCAGCAACGCTGGCGGCTCAGCTCAGCGCACTGGAGGCATCGGCCAATGGCCGTCTCGGTGTGGCGCTGATTGACAGCGGATCTTCACGCCAGCTGAGTTATCGCGGGGAAGAGCGTTTCGCCATGGCCAGTACGTTTAAAGCGCTTGCCGCCGCCGCCGTGCTGCAACGCAGTGTTGAACAGCCCGCACTGCTGAATAAACGCATTATTTATCAACAGAGCGAACTGATCACTTACTCGCCGGTAACCGAAAAGCATCTGCAACAGGGCATGACCGTCGCGGAACTCTGTGCTGCGGCAGTTGAACTCAGTGATAACACGGCGGGGAATATTCTGCTGCGGGAAATAGGGGGGCCGCAAGGGATTACCCAACTGGCACGCCGTTTAGGTGATAATCAGACGCGTCTTGACCGCCGGGAACCCGCGTTAAACAGCGCGATTCCGGGTGATGTACGTGATACTTCAACACCTCTGGCGATGGCCGGGAATTTAAATCAGCTGGCGCTGGGCAAGGCGTTACCCTCCGCTCAGCAACAGCTGCTGATTCAGTGGCTAAAGCAGAGCAAAACCGGGGCGCAGAGCATTCGTGCCGGGGTGCCGCAAGGCTGGCAAGTGGGTGATAAAACCGGGGCGGGAGGCTACGGCACGACTAACGATCTGGCAATCCTCTGGCCACCACAGGGTAAACCGCTGGTGCTGGCCGTCTATTTCACCCAGCATAATCCGCAGGCTGAGGCACGCCGCGATGTGCTGGCCAGCGCCACCAGGCTGGTACTGGCGGCGTGGGAAAAACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36791","NCBI_taxonomy_name":"uncultured bacterium","NCBI_taxonomy_id":"77133"}}}},"ARO_accession":"3006941","ARO_id":"45403","ARO_name":"LRG-1","CARD_short_name":"LRG-1","ARO_description":"LRG-1 is a LRG beta-lactamase.","ARO_category":{"43879":{"category_aro_accession":"3005419","category_aro_cvterm_id":"43879","category_aro_name":"LRG beta-lactamase","category_aro_description":"LRG beta-lactamases are class A beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4753":{"model_id":"4753","model_name":"LUS-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"7128":{"protein_sequence":{"accession":"WP_041881964.1","sequence":"MKGFFRIKSVVCGVFLLMISVNAFAQKSELREKLQRIVNAHSATIGFSLTDLRNGDTLTVNGTKHLPMQSVYKFHLALAVLDQVDQGKLKLDQKIMVKKSDLLPDTWSPLRDKYPNGEVEIPLSEILSFTVSQSDNNGCDILFRLIGGPAKVNRYIHHLGIKDVAITATEEQMHQNDQIQFTNWTTPQAATELLGLFYAKKILSPASHEFLCKVMTETSTGADKIKGLLPAGTLAAHKTGSSGANKSGLTAASNDIGIVTLPDGKHFAVAAFVSMTKEDEKATDLIIAELTKASWDYLTTGKP"},"dna_sequence":{"accession":"NG_055472.1","fmin":"100","fmax":"1012","strand":"+","sequence":"ATGAAAGGATTTTTTAGAATAAAGAGCGTGGTTTGCGGAGTGTTTTTACTGATGATTTCAGTCAATGCTTTTGCTCAGAAAAGTGAACTACGGGAAAAGCTTCAGCGTATTGTCAATGCACATTCAGCGACCATTGGATTCTCGCTGACAGATCTCCGGAATGGAGATACCTTAACGGTTAACGGTACAAAACATTTACCCATGCAAAGTGTCTATAAATTTCATCTTGCACTTGCCGTTTTAGATCAGGTTGATCAGGGTAAGTTAAAGCTGGATCAGAAAATAATGGTTAAAAAAAGTGACTTGTTACCAGATACCTGGAGCCCGTTAAGAGATAAATACCCGAACGGAGAAGTTGAAATTCCTTTGTCAGAAATTTTAAGTTTTACAGTTTCGCAAAGTGATAACAATGGTTGTGATATCCTGTTCAGGTTGATTGGCGGCCCTGCAAAAGTAAACCGGTATATTCATCATCTTGGGATAAAAGATGTAGCCATTACAGCTACTGAAGAACAAATGCACCAGAATGACCAGATCCAGTTTACCAATTGGACTACCCCTCAGGCTGCTACAGAGTTACTGGGACTGTTTTATGCTAAAAAAATACTTTCTCCGGCATCCCATGAATTTTTATGTAAGGTCATGACCGAAACGTCTACCGGAGCTGACAAAATTAAAGGTTTATTGCCTGCAGGTACTTTAGCCGCCCATAAAACCGGTAGCTCAGGCGCTAATAAATCAGGGCTGACAGCAGCTTCCAATGATATTGGCATTGTAACTCTTCCTGACGGAAAACATTTTGCCGTTGCTGCATTCGTGTCTATGACTAAAGAAGATGAAAAAGCAACTGACCTGATTATTGCAGAGCTTACTAAAGCGAGCTGGGATTACCTGACCACAGGGAAACCATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3006942","ARO_id":"45404","ARO_name":"LUS-1","CARD_short_name":"LUS-1","ARO_description":"LUS-1 is a LUS beta-lactamase.","ARO_category":{"43880":{"category_aro_accession":"3005420","category_aro_cvterm_id":"43880","category_aro_name":"LUS beta-lactamase","category_aro_description":"LUS beta-lactamases are class A beta-lactamases found in Pedobacter lusitanus.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4754":{"model_id":"4754","model_name":"LUT-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"575"}},"model_sequences":{"sequence":{"7129":{"protein_sequence":{"accession":"WP_010798607.1","sequence":"MNVILNRRTFLLASAVVSASYSLGTLAGANRDDASFQDRLAKLEQQLNGRLGVCAIDTANGAQLGYRANERFAMNSTFKVMLASAFLARSQDEPGLLEERLTYTRADLVTYSPVTEKHVSTGMTVAELCAAGIQYSDNTAANVLMKKLGGPEAVTAFARSIGDTHFRLDRWETELNSAIPGDPRDTSTPQAMAMSLQRLALGDMLAADKQHQLQAWLKGNTTGGKRIRAGVPAGWQVGDKTGTGDYGSANDVAILWPPRRAPVVLALYSALENQQAEARNDVLADAARIVAEWVTG"},"dna_sequence":{"accession":"NG_049284.1","fmin":"0","fmax":"891","strand":"+","sequence":"ATGAATGTCATCCTGAACCGTCGAACGTTTTTATTGGCTAGCGCTGTGGTGTCTGCGTCTTATTCGCTAGGTACGCTGGCTGGCGCTAATCGGGATGATGCTTCCTTTCAAGATCGGCTGGCTAAGTTGGAGCAGCAGCTGAACGGACGGCTTGGAGTATGCGCCATCGATACCGCAAATGGAGCACAGTTGGGCTATCGCGCCAATGAGCGGTTTGCCATGAACAGCACGTTCAAGGTCATGCTCGCCTCAGCGTTTCTCGCCCGAAGCCAAGACGAACCGGGGCTCCTCGAAGAACGGCTCACGTACACCCGGGCCGATCTGGTCACATACTCTCCCGTGACGGAAAAGCACGTTTCCACTGGGATGACCGTTGCCGAATTGTGCGCCGCAGGCATTCAGTACAGTGATAACACCGCGGCCAATGTGCTCATGAAAAAGCTGGGGGGCCCTGAAGCGGTCACCGCATTTGCCCGTTCGATAGGCGATACGCATTTTCGCCTCGATCGGTGGGAAACCGAACTCAATTCGGCTATTCCGGGAGATCCTCGTGATACGAGCACCCCTCAGGCCATGGCAATGAGCCTGCAACGTCTGGCATTGGGTGACATGCTGGCTGCGGATAAACAGCATCAGTTGCAGGCGTGGTTGAAAGGCAATACCACAGGTGGCAAGCGTATCCGGGCCGGGGTACCGGCTGGCTGGCAGGTAGGCGATAAGACAGGTACGGGTGATTACGGCTCGGCCAACGACGTGGCTATCCTCTGGCCGCCTCGCCGTGCACCCGTTGTGCTGGCTCTCTATTCCGCTCTTGAAAACCAGCAGGCGGAAGCGCGCAATGACGTACTGGCCGATGCGGCGCGCATTGTGGCTGAATGGGTGACAGGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37066","NCBI_taxonomy_name":"Pseudomonas","NCBI_taxonomy_id":"286"}}}},"ARO_accession":"3006943","ARO_id":"45405","ARO_name":"LUT-1","CARD_short_name":"LUT-1","ARO_description":"LUT-1 is a LUT beta-lactamase.","ARO_category":{"43881":{"category_aro_accession":"3005421","category_aro_cvterm_id":"43881","category_aro_name":"LUT beta-lactamase","category_aro_description":"LUT beta-lactamases are class A beta lactamases found in Pseudomonas luteola.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4755":{"model_id":"4755","model_name":"LUT-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"575"}},"model_sequences":{"sequence":{"7130":{"protein_sequence":{"accession":"WP_063860828.1","sequence":"MNVILNRRTFLLTSAVVSASYSLGTLAGANRDDASFQDRLAKLEQQLNGRLGVCAIDTANGAQLGYRANERFAMNSTFKVMLASAFLARSQDEPGLLEERLTYTRADLVTYSPVTEKHVSTGMTVAELCAAGIQYSDNTAANVLMKKLGGPEAVTAFARSIGDTHFRLDRWETELNSAIPGDPRDTSTPQAMAMSLQRLALGDMLAADKQHQLQAWLKGNTTGGKRIRAGVPAGWQVGDKTGTGDYGSANDVAILWPPRRTPVVLALYSALENQQAEARNDVLADAARIVAEWVTG"},"dna_sequence":{"accession":"NG_049285.1","fmin":"0","fmax":"891","strand":"+","sequence":"ATGAATGTCATCCTGAACCGTCGAACGTTTTTATTGACTAGCGCTGTGGTGTCTGCGTCTTATTCGCTAGGTACGCTGGCTGGCGCTAATCGGGATGATGCTTCCTTTCAAGATCGGCTGGCTAAGTTGGAGCAGCAGCTGAACGGACGGCTTGGAGTATGCGCCATCGATACCGCAAATGGAGCACAGTTGGGCTATCGCGCCAATGAGCGGTTTGCCATGAACAGCACGTTCAAGGTCATGCTCGCCTCAGCGTTTCTCGCCCGAAGCCAAGACGAACCGGGGCTCCTCGAAGAACGGCTCACGTACACCCGGGCCGATCTGGTCACATACTCTCCCGTGACGGAAAAGCACGTTTCCACTGGGATGACCGTTGCCGAATTGTGCGCCGCAGGCATTCAGTACAGTGATAACACCGCGGCCAATGTGCTCATGAAAAAGCTGGGGGGCCCTGAAGCGGTCACCGCATTTGCCCGTTCGATAGGCGATACGCATTTTCGCCTCGATCGGTGGGAAACCGAACTCAATTCGGCTATTCCGGGAGATCCTCGTGATACGAGTACCCCTCAGGCCATGGCAATGAGCCTGCAACGTCTGGCATTGGGTGACATGCTGGCTGCGGATAAACAGCATCAGTTGCAGGCGTGGTTGAAAGGCAATACCACAGGTGGCAAGCGTATCCGGGCCGGGGTACCGGCTGGCTGGCAGGTAGGCGATAAGACAGGTACGGGTGATTACGGCTCGGCCAACGACGTGGCTATCCTCTGGCCGCCTCGCCGTACACCCGTTGTGCTGGCTCTCTATTCCGCTCTTGAAAACCAGCAGGCGGAAGCGCGCAATGACGTGCTGGCCGATGCGGCGCGCATTGTGGCTGAATGGGTGACAGGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3006944","ARO_id":"45406","ARO_name":"LUT-2","CARD_short_name":"LUT-2","ARO_description":"LUT-2 is a LUT beta-lactamase.","ARO_category":{"43881":{"category_aro_accession":"3005421","category_aro_cvterm_id":"43881","category_aro_name":"LUT beta-lactamase","category_aro_description":"LUT beta-lactamases are class A beta lactamases found in Pseudomonas luteola.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4756":{"model_id":"4756","model_name":"LUT-3","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"575"}},"model_sequences":{"sequence":{"7131":{"protein_sequence":{"accession":"WP_063860829.1","sequence":"MNVILNRRTFLLASAVVSASYSLGTLAGANRDDASFQDRLAKLEQKLNGRLGVCAIDTANGAQLGYRANERFAMNSTFKVMLASAFLARSQDEPGLLEERLMYTRADLVTYSPVTEKHVSTGMTVAELCAAGIQYSDNTAANVLMKKLGGPEAVTAFARSIGDTHFRLDRWETELNSAIPGDPRDTSTPQAMAMSLQRLALGDMLAADKQHQLQAWLKGNTTGGKRIRAGVPAGWQVGDKTGTGDYGSANDVAILWPPRRAPVVLALYSALENQQAEARNDVLADAARIVAEWVTG"},"dna_sequence":{"accession":"NG_049286.1","fmin":"0","fmax":"891","strand":"+","sequence":"ATGAATGTCATCCTGAACCGTCGAACGTTTTTATTGGCTAGCGCTGTGGTGTCTGCGTCTTATTCGCTAGGTACGCTGGCTGGCGCTAATCGGGATGATGCTTCCTTTCAAGATCGGCTGGCTAAGTTGGAGCAGAAGCTGAACGGACGGCTTGGAGTATGCGCCATCGATACCGCAAATGGAGCACAGCTGGGCTATCGCGCCAATGAGCGGTTTGCCATGAACAGCACGTTCAAGGTCATGCTCGCTTCAGCGTTTCTCGCCCGAAGCCAAGACGAACCGGGGCTCCTCGAAGAACGGCTCATGTACACCCGGGCCGATCTGGTCACATACTCTCCCGTGACGGAAAAGCACGTTTCCACTGGGATGACCGTTGCCGAATTGTGCGCCGCAGGCATTCAGTACAGTGATAACACCGCGGCCAATGTGCTCATGAAAAAGCTGGGGGGCCCTGAAGCGGTCACCGCATTTGCCCGTTCGATAGGCGATACGCATTTTCGCCTCGATCGGTGGGAAACCGAACTCAATTCGGCTATTCCGGGAGATCCTCGTGATACGAGTACCCCTCAGGCCATGGCAATGAGCCTGCAACGTCTGGCATTGGGTGACATGCTGGCTGCGGATAAACAGCATCAGTTGCAGGCGTGGTTGAAAGGCAATACCACAGGTGGCAAGCGTATCCGGGCCGGGGTACCGGCTGGCTGGCAGGTAGGCGATAAGACAGGTACGGGTGATTACGGCTCGGCCAACGACGTGGCTATCCTCTGGCCGCCTCGCCGTGCACCCGTTGTGCTGGCTCTCTATTCCGCTCTTGAAAACCAGCAGGCGGAAGCGCGCAATGACGTGCTGGCCGATGCGGCGCGCATTGTGGCTGAATGGGTGACAGGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37066","NCBI_taxonomy_name":"Pseudomonas","NCBI_taxonomy_id":"286"}}}},"ARO_accession":"3006945","ARO_id":"45407","ARO_name":"LUT-3","CARD_short_name":"LUT-3","ARO_description":"LUT-3 is a LUT beta-lactamase.","ARO_category":{"43881":{"category_aro_accession":"3005421","category_aro_cvterm_id":"43881","category_aro_name":"LUT beta-lactamase","category_aro_description":"LUT beta-lactamases are class A beta lactamases found in Pseudomonas luteola.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4757":{"model_id":"4757","model_name":"LUT-4","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"575"}},"model_sequences":{"sequence":{"7132":{"protein_sequence":{"accession":"WP_063860830.1","sequence":"MNVILNRRTFLLASAVVSASYSLGTLAGANRDDASFQDRLAKLEQKLNGRLGVCAIDTANGAQLGYRANERFAMNSTFKVMLASAFLARSQDEPGLLEERLTYTRADLVTYSPVTEKHVSTGMTVAELCAAGIQYSDNTAANVLMKKLGGPEAVTAFARSIGDTHFRLDRWETELNSAIPGDPRDTSTPQAMAMSLQRLALGDMLAADKQHQLQAWLKGNTTGGKRIRAGVPAGWQVGDKTGTGDYGSANDVAILWPPRRAPVVLALYSALESQQAEARNDVLADAARIVAEWVTG"},"dna_sequence":{"accession":"NG_049287.1","fmin":"0","fmax":"891","strand":"+","sequence":"ATGAATGTCATCCTGAACCGCCGAACGTTTTTATTGGCTAGCGCTGTGGTGTCTGCGTCTTATTCGCTAGGTACGCTGGCTGGCGCTAATCGGGATGACGCTTCCTTTCAAGATCGGCTGGCTAAGTTGGAGCAGAAGCTGAACGGACGGCTTGGGGTATGCGCCATCGATACCGCAAATGGAGCACAGTTGGGCTATCGCGCCAATGAGCGGTTTGCCATGAACAGCACGTTCAAGGTCATGCTCGCCTCAGCGTTTCTCGCCCGAAGCCAAGACGAACCGGGGCTCCTCGAAGAGCGGCTCACGTACACCCGGGCCGATCTGGTCACATACTCTCCCGTGACGGAAAAGCACGTTTCCACTGGGATGACCGTTGCCGAATTGTGCGCCGCAGGCATTCAGTACAGTGATAACACCGCGGCCAATGTGCTCATGAAAAAGCTGGGGGGCCCTGAAGCGGTCACCGCATTTGCCCGTTCGATAGGCGATACGCATTTTCGCCTCGATCGGTGGGAAACCGAACTCAATTCGGCTATTCCGGGAGATCCTCGTGATACGAGTACCCCTCAGGCCATGGCAATGAGCCTGCAACGTCTGGCATTGGGTGACATGCTGGCTGCGGATAAACAGCATCAGTTGCAGGCGTGGTTGAAAGGCAATACCACAGGTGGCAAGCGTATCCGGGCCGGGGTACCGGCTGGCTGGCAGGTAGGCGATAAGACAGGTACAGGTGATTACGGCTCGGCCAACGACGTGGCTATCCTCTGGCCGCCTCGCCGTGCACCCGTTGTGCTGGCTCTCTATTCCGCTCTTGAAAGCCAGCAGGCGGAAGCGCGCAATGACGTACTGGCCGATGCGGCGCGCATTGTGGCTGAATGGGTGACAGGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3006946","ARO_id":"45408","ARO_name":"LUT-4","CARD_short_name":"LUT-4","ARO_description":"LUT-4 is a LUT beta-lactamase.","ARO_category":{"43881":{"category_aro_accession":"3005421","category_aro_cvterm_id":"43881","category_aro_name":"LUT beta-lactamase","category_aro_description":"LUT beta-lactamases are class A beta lactamases found in Pseudomonas luteola.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4758":{"model_id":"4758","model_name":"LUT-5","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"575"}},"model_sequences":{"sequence":{"7133":{"protein_sequence":{"accession":"WP_063860831.1","sequence":"MNVILNRRTFLLASAVVSASYSLGTLAGANRDDASFQDRLAKLEQKLNGRLGVCAIDTADGAQLGYRANERFAMNSTFKVMLASAFLAQSQDEPGLLEERLTYTRADLVTYSPVTEKHVATGMTVAELCAAGIQYSDNTAANVLMKKLGGPEAVTAFARSIGDTHFRLDRWETELNSAIPGDPRDTSTPQAMAMSLQRLALGDMLAADKQHQLQAWLKGNTTGGKRIRAGVPAGWQVGDKTGTGDYGSANDVAILWPPRRAPVVLALYSALENQQAEARNDVLADAARIVAEWVTG"},"dna_sequence":{"accession":"NG_049288.1","fmin":"0","fmax":"891","strand":"+","sequence":"ATGAATGTCATCCTGAACCGTCGAACGTTTTTATTGGCTAGCGCTGTGGTGTCTGCGTCTTATTCGCTAGGTACGCTGGCTGGCGCTAATCGGGATGATGCTTCCTTTCAAGATCGGCTGGCTAAGTTAGAGCAGAAGCTGAACGGACGGCTTGGGGTATGCGCCATCGATACCGCAGATGGAGCACAGTTGGGCTATCGCGCCAATGAGCGGTTTGCCATGAACAGCACGTTCAAGGTCATGCTCGCTTCAGCGTTTCTCGCCCAAAGCCAAGACGAACCGGGGCTCCTCGAAGAGCGGCTCACGTACACCCGGGCCGATCTGGTCACATACTCTCCAGTGACGGAAAAGCACGTTGCCACTGGGATGACCGTTGCCGAGTTGTGCGCCGCAGGCATTCAGTACAGTGATAACACCGCGGCCAATGTGCTCATGAAAAAGCTGGGGGGCCCTGAAGCGGTCACCGCATTTGCCCGCTCGATAGGAGATACGCATTTTCGCCTCGATCGATGGGAAACCGAACTCAATTCGGCTATTCCGGGAGATCCTCGTGATACGAGTACCCCTCAGGCCATGGCAATGAGTCTGCAACGTCTGGCATTGGGTGACATGCTGGCTGCGGATAAACAGCATCAGTTGCAGGCGTGGTTGAAAGGCAATACCACGGGTGGCAAGCGTATCCGGGCCGGGGTACCGGCTGGCTGGCAGGTAGGCGATAAGACAGGTACGGGTGATTACGGCTCGGCCAACGACGTGGCTATCCTCTGGCCGCCTCGCCGTGCACCCGTTGTGCTGGCTCTCTATTCCGCTCTTGAAAACCAGCAGGCGGAAGCGCGCAATGACGTACTGGCCGATGCGGCACGCATTGTGGCTGAATGGGTGACAGGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3006947","ARO_id":"45409","ARO_name":"LUT-5","CARD_short_name":"LUT-5","ARO_description":"LUT-5 is a LUT beta-lactamase.","ARO_category":{"43881":{"category_aro_accession":"3005421","category_aro_cvterm_id":"43881","category_aro_name":"LUT beta-lactamase","category_aro_description":"LUT beta-lactamases are class A beta lactamases found in Pseudomonas luteola.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4759":{"model_id":"4759","model_name":"LUT-6","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"575"}},"model_sequences":{"sequence":{"7134":{"protein_sequence":{"accession":"WP_063860832.1","sequence":"MNVILNRRTFLLASAVVSASYSLGTLAGANRDDASFQDRLAKLEQKLNGRLGVCAIDTADGAQLGYRANERFAMNSTFKVMLASAFLARSQDEPGLLEERLTYTRADLVTYSPVTEKHVSTGMTVAELCAAGIQYSDNTAANVLMKKLGGPEAVTAFARSIGDTHFRLDRWETELNSAIPGDPRDTSTPQAMAMSLQRLALSDMLAADKQHQLQAWLKGNTTGGKRIRAGVPAGWQVGDKTGTGDYGSANDVAILWPPRRAPVVLALYSALESQQAEARNDVLADAARIVAEWVTG"},"dna_sequence":{"accession":"NG_049289.1","fmin":"0","fmax":"891","strand":"+","sequence":"ATGAATGTCATCCTGAACCGTCGAACGTTTTTATTGGCTAGCGCTGTGGTGTCTGCGTCTTATTCGCTAGGTACGCTGGCTGGCGCTAATCGGGATGATGCTTCCTTTCAAGATCGGCTGGCTAAGTTGGAGCAGAAGCTGAACGGACGGCTTGGGGTATGCGCCATCGATACCGCAGATGGAGCACAGTTGGGCTATCGCGCCAATGAGCGGTTTGCCATGAACAGCACGTTCAAGGTCATGCTCGCTTCAGCGTTTCTCGCCCGAAGCCAAGACGAACCGGGGCTCCTCGAAGAGCGGCTCACGTACACCCGGGCCGATCTGGTCACATACTCTCCCGTGACGGAAAAGCACGTTTCCACTGGGATGACCGTTGCCGAATTGTGCGCCGCAGGTATTCAGTACAGTGATAACACCGCGGCCAATGTGCTCATGAAAAAGCTGGGGGGCCCTGAAGCGGTCACCGCATTTGCCCGCTCGATAGGCGATACGCATTTTCGCCTCGATCGATGGGAAACCGAGCTCAATTCGGCTATTCCGGGAGATCCTCGTGATACGAGTACCCCTCAGGCCATGGCAATGAGTCTGCAACGTCTGGCATTGAGTGACATGCTGGCTGCGGATAAACAGCATCAGTTGCAGGCGTGGTTGAAAGGCAATACCACGGGTGGCAAGCGTATCCGGGCCGGAGTACCGGCTGGCTGGCAGGTAGGCGATAAGACAGGTACGGGTGATTACGGCTCGGCCAACGACGTGGCTATCCTCTGGCCGCCTCGCCGTGCACCCGTTGTGCTGGCTCTCTATTCCGCTCTTGAAAGCCAGCAGGCGGAAGCTCGCAATGACGTACTGGCCGATGCGGCGCGCATTGTGGCTGAATGGGTGACAGGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3006948","ARO_id":"45410","ARO_name":"LUT-6","CARD_short_name":"LUT-6","ARO_description":"LUT-6 is a LUT beta-lactamase.","ARO_category":{"43881":{"category_aro_accession":"3005421","category_aro_cvterm_id":"43881","category_aro_name":"LUT beta-lactamase","category_aro_description":"LUT beta-lactamases are class A beta lactamases found in Pseudomonas luteola.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4760":{"model_id":"4760","model_name":"MAL-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"7135":{"protein_sequence":{"accession":"WP_063860833.1","sequence":"MRNEEVISMWQRMKWGLCVLAALSGSAMAAPLTAQYVSTIATQEEQRLHARIGIAVLDTATNSITHYRGEERFPLNSTHKPLLCAALLREVDRKALALSASTQFESSQLVEYSPITEKHVAPDAMSWAQLCSAAVSYSDNTAANLIARKLNGPQAVTQFLRDSGDTITRLDRYEPELNSAIPGDERDSTTPVAIAQTLNTLLLGNVLQPSSREQLMQWMRDDKVADGLLRSVLPDGWKIADKTGAGDNGSRSIVSVVWPTSQKPLLVVIYITQTPATMAQRDAAIVRIGESLFSTLAVYD"},"dna_sequence":{"accession":"NG_049290.1","fmin":"11","fmax":"914","strand":"+","sequence":"ATGAGAAACGAGGAAGTCATTAGTATGTGGCAACGGATGAAATGGGGTTTGTGTGTGCTGGCGGCACTCAGCGGTTCTGCGATGGCCGCACCGCTGACGGCGCAATACGTGTCGACTATCGCGACGCAGGAAGAACAGCGTCTTCATGCCCGGATTGGCATTGCGGTACTTGATACGGCGACCAACAGTATCACCCATTATCGGGGAGAAGAACGGTTCCCGTTAAACAGTACGCACAAGCCGCTGTTATGCGCAGCGTTATTACGCGAAGTCGACAGGAAGGCGCTGGCGCTTTCTGCTTCAACGCAGTTTGAATCCTCGCAGCTGGTGGAGTATTCGCCGATTACTGAAAAACATGTGGCGCCAGACGCCATGAGCTGGGCGCAATTGTGCAGCGCGGCGGTAAGCTACAGCGATAACACGGCCGCCAATCTCATCGCCAGGAAGCTCAACGGGCCGCAGGCCGTCACGCAGTTTTTGCGTGATTCGGGGGATACAATAACCCGCCTCGATCGCTATGAGCCTGAACTGAACAGCGCCATTCCCGGCGATGAACGCGACTCCACGACGCCTGTCGCGATAGCGCAGACGCTCAATACGCTACTGCTGGGGAACGTGTTGCAGCCATCCTCAAGAGAGCAGCTTATGCAGTGGATGCGGGACGACAAAGTGGCTGACGGTCTGCTGCGTTCGGTCTTGCCGGATGGCTGGAAAATCGCGGATAAAACCGGGGCGGGCGACAACGGCTCGCGTTCTATTGTCAGCGTTGTCTGGCCGACATCACAAAAACCTCTGCTCGTGGTTATCTATATTACACAAACTCCGGCGACAATGGCGCAGCGTGACGCCGCGATTGTCCGCATCGGGGAGTCGCTGTTTTCAACACTCGCAGTCTATGATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36934","NCBI_taxonomy_name":"Citrobacter koseri","NCBI_taxonomy_id":"545"}}}},"ARO_accession":"3006949","ARO_id":"45411","ARO_name":"MAL-1","CARD_short_name":"MAL-1","ARO_description":"MAL-1 is a MAL beta-lactamase.","ARO_category":{"43882":{"category_aro_accession":"3005422","category_aro_cvterm_id":"43882","category_aro_name":"MAL beta-lactamase","category_aro_description":"MAL beta-lactamase are class A beta-lactamases found in Citrobacter koseri.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4761":{"model_id":"4761","model_name":"MAL-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"7136":{"protein_sequence":{"accession":"WP_063860834.1","sequence":"MRNEEVISMWQRMKWGLCVLALSGSAMAAPLTAQYVSAIATQEEQRLHARIGIAVLDTATNSITHYRGEERFPLNSTHKPLLCAALLREVDRKALALSASTQFEPSQLVEYSPITEKHVAPDAMNWAQLCSAAVSYSDNTAANLIARKLNGPQAVTQFLRDSGDTITRLDRYEPELNSAIPGDERDSTTPVAIAKTLNTLLLGNVLQPSSREQLMQWMRDDKVADGLLRSVLPDGWKIADKTGAGDNGSRSIVSVVWPTSQKPLLVVIYITQTPATMAQRDAAIVRIGESLFSTLAVYD"},"dna_sequence":{"accession":"NG_049291.1","fmin":"2","fmax":"902","strand":"+","sequence":"ATGAGAAATGAGGAAGTCATTAGTATGTGGCAACGGATGAAATGGGGTCTGTGTGTGCTGGCACTCAGCGGTTCTGCGATGGCCGCACCGCTGACGGCGCAATACGTGTCGGCTATCGCGACGCAGGAAGAACAGCGTCTTCATGCCCGGATTGGCATTGCGGTACTTGATACGGCGACCAACAGTATCACCCATTATCGGGGAGAAGAACGGTTCCCGTTAAACAGTACGCACAAGCCGCTGTTATGCGCAGCGTTATTACGCGAAGTCGACAGGAAGGCGCTGGCGCTTTCTGCTTCAACGCAGTTTGAACCCTCGCAGCTGGTGGAGTATTCGCCGATTACTGAAAAACATGTGGCGCCAGACGCCATGAACTGGGCGCAATTGTGCAGCGCGGCGGTAAGCTACAGCGATAACACGGCCGCCAATCTCATCGCCAGGAAGCTCAACGGGCCGCAGGCCGTCACGCAGTTTTTGCGTGATTCGGGGGATACGATAACCCGCCTCGATCGCTATGAGCCCGAACTGAACAGCGCCATTCCCGGTGATGAACGCGACTCCACGACGCCTGTCGCGATAGCGAAGACGCTCAATACGCTACTGCTGGGGAATGTGTTGCAGCCATCCTCAAGAGAGCAGCTTATGCAATGGATGCGGGACGACAAAGTGGCTGACGGTCTGCTGCGTTCGGTCTTGCCGGACGGCTGGAAAATCGCGGATAAAACCGGGGCGGGCGACAACGGTTCGCGTTCTATTGTCAGCGTTGTCTGGCCGACATCACAAAAACCTTTGCTCGTGGTTATCTATATTACACAAACTCCGGCGACAATGGCGCAGCGTGACGCCGCGATTGTCCGCATCGGGGAGTCGCTGTTTTCAACACTCGCAGTCTATGATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36934","NCBI_taxonomy_name":"Citrobacter koseri","NCBI_taxonomy_id":"545"}}}},"ARO_accession":"3006950","ARO_id":"45412","ARO_name":"MAL-2","CARD_short_name":"MAL-2","ARO_description":"MAL-2 is a MAL beta-lactamase.","ARO_category":{"43882":{"category_aro_accession":"3005422","category_aro_cvterm_id":"43882","category_aro_name":"MAL beta-lactamase","category_aro_description":"MAL beta-lactamase are class A beta-lactamases found in Citrobacter koseri.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4762":{"model_id":"4762","model_name":"MBL1b","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"575"}},"model_sequences":{"sequence":{"8101":{"protein_sequence":{"accession":"WP_063860835.1","sequence":"MKRLILAAAASLLALASAAHADDMPANWTKPTKPYRVVGNIYYVGTEGISSWLITSSEGHVVLHGGPNAETGKLVERNITALGFQLADLKILINTHAHYDHAGGLAQLKADTGAKLWISRDDAPAMAAGHHIGDNIYGPTPMPAAKPDRSFGDQTKLKLGEIAMVAHLTPGHTIGCTSWTTAVVEKGRPLTVTFPCSLSVAGNVLVGNKTHRTIVADYRASFAKLRAIPTDVMLPAHEEQGNLLAKRQKQLRGDPNAFVDPGELARFVDASEAAFNKELARQQAAGPKP"},"dna_sequence":{"accession":"NG_049292.1","fmin":"0","fmax":"870","strand":"+","sequence":"ATGAAGCGCCTGATCCTGGCCGCCGCTGCGTCGCTGTTGGCTCTGGCCTCGGCGGCCCACGCCGACGACATGCCGGCCAACTGGACCAAGCCGACCAAGCCCTACCGTGTGGTCGGCAACATCTATTACGTCGGCACCGAGGGCATCTCGTCCTGGCTGATCACGTCGTCCGAGGGCCATGTGGTGCTGCACGGCGGGCCGAACGCCGAGACGGGCAAGCTGGTCGAGCGCAACATCACGGCGCTGGGCTTCCAGCTTGCGGACCTGAAGATCCTGATCAACACCCACGCCCACTACGATCACGCCGGCGGTCTGGCGCAGTTGAAGGCCGACACCGGCGCCAAGCTGTGGATCTCGCGCGACGACGCCCCGGCCATGGCGGCGGGCCACCACATCGGCGACAATATCTATGGCCCAACGCCGATGCCGGCCGCCAAGCCCGACAGGAGCTTCGGCGACCAGACCAAGCTGAAGCTGGGCGAGATCGCCATGGTCGCCCACCTGACGCCGGGCCACACCATTGGCTGCACCAGCTGGACCACGGCCGTGGTCGAGAAGGGGCGGCCGCTGACCGTCACCTTCCCGTGCTCGCTGTCGGTGGCAGGCAATGTGCTCGTGGGCAACAAGACCCACCGGACCATCGTCGCCGACTATCGCGCCAGCTTCGCCAAGCTGCGCGCCATTCCTACCGACGTGATGCTGCCCGCGCACGAAGAGCAGGGGAACCTGCTGGCCAAGCGCCAGAAGCAGCTGCGCGGTGATCCCAACGCCTTTGTCGACCCAGGCGAGCTTGCCCGGTTCGTCGACGCCTCCGAAGCCGCCTTCAACAAGGAGCTCGCGCGCCAGCAGGCGGCGGGGCCCAAGCCATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39075","NCBI_taxonomy_name":"Caulobacter vibrioides","NCBI_taxonomy_id":"155892"}}}},"ARO_accession":"3006951","ARO_id":"45413","ARO_name":"MBL1b","CARD_short_name":"MBL1b","ARO_description":"MBL1b is a MBL beta-lactamase.","ARO_category":{"43883":{"category_aro_accession":"3005423","category_aro_cvterm_id":"43883","category_aro_name":"MBL beta-lactamase","category_aro_description":"MBL beta-lactamases are class B3 beta-lactamases found in Caulobacter vibrioides.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4763":{"model_id":"4763","model_name":"MIR-18","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"8102":{"protein_sequence":{"accession":"WP_063860839.1","sequence":"MMTKSLSCALLLSVASSAFAAPMSEKQLAEVVERTVTPLMNAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEIALGDPVAKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDTASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMSYEQAMTTRVFKPLKLDHTWINVPKAEEAHYAWGYREGKAVHVSPGMLDAEAYGVKTNVKDMASWLIANMKPDSLEAPSLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVGGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILDALQ"},"dna_sequence":{"accession":"NG_049302.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGACAAAATCCCTAAGCTGTGCCCTGCTGCTCAGCGTCGCCAGCTCTGCATTCGCCGCACCGATGTCCGAAAAACAGCTGGCTGAGGTGGTGGAACGTACCGTTACGCCGCTGATGAACGCGCAGGCCATTCCGGGTATGGCGGTGGCGGTAATTTATCAGGGTCAGCCACACTACTTTACCTTCGGTAAAGCCGATGTTGCGGCGAACAAACCCGTCACCCCGCAAACCCTGTTTGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTACTGGGCGGCGATGCCATTGCCCGGGGTGAAATAGCGCTGGGCGATCCGGTAGCAAAATACTGGCCTGAGCTCACGGGCAAGCAGTGGCAGGGCATTCGCATGCTGGATCTGGCAACCTATACCGCAGGCGGTCTGCCGTTACAGGTGCCGGATGAGGTCACGGATACCGCCTCTCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCGGGCACCACGCGTCTTTACGCTAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTCAAACCTTCCGGCATGAGCTATGAGCAGGCCATGACGACGCGGGTCTTTAAACCCCTCAAGCTGGACCATACCTGGATTAACGTCCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGATACCGTGAGGGTAAAGCGGTCCACGTTTCGCCAGGGATGCTGGACGCGGAAGCCTATGGCGTAAAAACTAACGTGAAGGATATGGCGAGCTGGCTGATAGCCAACATGAAGCCGGATTCTCTTGAGGCTCCCTCACTCAAGCAAGGCATTGCTCTGGCGCAGTCTCGCTACTGGCGCGTGGGGGCTATGTATCAGGGGCTGGGCTGGGAGATGCTCAACTGGCCGGTCGATGCCAAAACCGTCGTCGGAGGCAGTGATAACAAGGTGGCGCTGGCACCATTGCCCGTGGCAGAAGTGAATCCACCCGCGCCGCCGGTCAAGGCCTCCTGGGTCCATAAAACAGGCTCGACGGGCGGGTTTGGCAGCTACGTGGCATTTATTCCTGAAAAGCAGCTCGGCATTGTGATGCTGGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCGTATCCTCGACGCGCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"45472","NCBI_taxonomy_name":"Enterobacter sp. ET82","NCBI_taxonomy_id":"1546034"}}}},"ARO_accession":"3003139","ARO_id":"39716","ARO_name":"MIR-18","CARD_short_name":"MIR-18","ARO_description":"MIR-18 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36197":{"category_aro_accession":"3000058","category_aro_cvterm_id":"36197","category_aro_name":"MIR beta-lactamase","category_aro_description":"MIR beta-lactamases are plasmid-mediated beta-lactamases that confer resistance to oxyimino- and alpha-methoxy beta-lactams.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4764":{"model_id":"4764","model_name":"MIR-19","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"8104":{"protein_sequence":{"accession":"WP_045354584.1","sequence":"MMTKSLSCALLLSVASSAFAAPMSEKQLAEVVERTVTPLMNAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEIALGDPVAKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDTASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMSYEQAMTTRVFKPLKLDHTWINVPKAEEAHYAWGYREGKAVHVSPGMLDAEAYGVKTNVKDMASWLIANMKPDSLQAPSLKQGIALAQSRYWCVGAMYQGLGWEMLNWPVDAKTVVGGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILDALQ"},"dna_sequence":{"accession":"NG_050721.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGACAAAATCCCTAAGCTGTGCCCTGCTGCTCAGCGTCGCCAGTTCTGCATTCGCCGCACCGATGTCCGAAAAACAGCTGGCTGAGGTGGTGGAACGTACCGTTACGCCGCTGATGAACGCGCAGGCCATTCCGGGTATGGCGGTGGCGGTAATTTATCAGGGTCAGCCACACTACTTTACCTTCGGTAAAGCCGATGTTGCGGCGAACAAACCCGTCACCCCGCAAACCCTGTTTGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTACTGGGCGGCGATGCCATTGCCCGGGGTGAAATAGCGCTGGGCGATCCGGTAGCAAAATACTGGCCTGAGCTCACGGGCAAGCAGTGGCAGGGCATTCGCATGCTGGATCTGGCAACCTATACCGCAGGCGGTCTGCCGTTACAGGTGCCGGATGAGGTCACGGATACCGCCTCTCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCGGGCACCACGCGTCTTTACGCTAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTCAAACCTTCCGGCATGAGCTATGAGCAGGCCATGACGACGCGGGTCTTTAAACCCCTCAAGCTGGACCATACCTGGATTAACGTCCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGATACCGTGAGGGTAAAGCGGTCCACGTTTCGCCAGGGATGCTGGACGCGGAAGCCTATGGCGTAAAAACTAACGTGAAGGATATGGCGAGCTGGCTGATAGCCAACATGAAGCCGGATTCTCTTCAGGCTCCCTCACTCAAGCAAGGCATTGCTCTGGCGCAGTCTCGCTACTGGTGCGTGGGGGCTATGTATCAGGGGTTGGGCTGGGAGATGCTCAACTGGCCGGTCGATGCCAAAACCGTCGTCGGAGGCAGTGATAACAAGGTGGCGCTGGCACCATTGCCCGTGGCAGAAGTGAATCCACCCGCGCCGCCGGTCAAGGCCTCCTGGGTCCATAAAACAGGCTCGACGGGCGGGTTTGGCAGCTACGTGGCATTTATTCCTGAAAAGCAGCTCGGCATTGTGATGCTGGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCGTATCCTCGACGCGCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40540","NCBI_taxonomy_name":"Enterobacter cloacae complex","NCBI_taxonomy_id":"354276"}}}},"ARO_accession":"3006859","ARO_id":"45321","ARO_name":"MIR-19","CARD_short_name":"MIR-19","ARO_description":"MIR-19 is a MIR beta-lactamase.","ARO_category":{"36197":{"category_aro_accession":"3000058","category_aro_cvterm_id":"36197","category_aro_name":"MIR beta-lactamase","category_aro_description":"MIR beta-lactamases are plasmid-mediated beta-lactamases that confer resistance to oxyimino- and alpha-methoxy beta-lactams.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4765":{"model_id":"4765","model_name":"MIR-20","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"8105":{"protein_sequence":{"accession":"WP_044597278.1","sequence":"MMTKSLSCALLLSVTSAAFAAPMSETQLAEVVERTVTPLMNAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEIALGDPVAKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDTASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMSYEQAMTTRVFKPLKLDHTWINVPKAEEAHYAWGYREGKAVHVSPGMLDAEAYGVKTNVKDMASWLIANMKPDSLQAPSLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVGGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILDALQ"},"dna_sequence":{"accession":"NG_050722.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGACAAAATCCCTAAGCTGTGCCCTGCTGCTCAGCGTCACCAGCGCTGCATTCGCCGCACCGATGTCCGAAACACAGCTGGCTGAGGTGGTGGAACGTACCGTTACGCCGCTGATGAACGCGCAGGCCATTCCGGGTATGGCGGTGGCGGTAATTTATCAGGGTCAGCCACACTACTTTACCTTCGGTAAAGCCGATGTTGCGGCGAACAAACCCGTCACCCCGCAAACCCTGTTTGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTACTGGGCGGCGATGCCATTGCCCGGGGTGAAATAGCGCTGGGCGATCCGGTAGCAAAATACTGGCCTGAGCTCACGGGCAAGCAGTGGCAGGGCATTCGCATGCTGGATCTGGCAACCTATACCGCAGGCGGTCTGCCGTTACAGGTGCCGGATGAGGTCACGGATACCGCCTCTCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCGGGCACCACGCGTCTTTACGCTAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTTAAACCTTCCGGCATGAGCTATGAGCAGGCCATGACGACGCGGGTCTTTAAACCCCTCAAGCTGGACCATACCTGGATTAACGTCCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGATACCGTGAGGGTAAAGCGGTCCACGTTTCGCCAGGGATGCTGGACGCGGAAGCCTATGGCGTAAAAACTAACGTGAAGGATATGGCGAGCTGGCTGATAGCCAACATGAAGCCGGATTCTCTTCAGGCTCCCTCACTCAAGCAAGGCATTGCTCTGGCGCAGTCTCGCTACTGGCGCGTGGGGGCCATGTATCAGGGGTTGGGCTGGGAGATGCTCAACTGGCCGGTCGATGCCAAAACCGTCGTCGGAGGCAGTGATAACAAGGTGGCGCTGGCACCATTGCCCGTGGCAGAAGTGAATCCACCCGCGCCGCCGGTCAAAGCCTCCTGGGTCCATAAAACAGGCTCGACGGGCGGGTTTGGCAGCTACGTGGCATTTATTCCTGAAAAGCAGCTCGGCATTGTGATGCTGGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCGTATCCTCGACGCGCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37055","NCBI_taxonomy_name":"Enterobacter","NCBI_taxonomy_id":"547"}}}},"ARO_accession":"3006860","ARO_id":"45322","ARO_name":"MIR-20","CARD_short_name":"MIR-20","ARO_description":"MIR-20 is a MIR beta-lactamase.","ARO_category":{"36197":{"category_aro_accession":"3000058","category_aro_cvterm_id":"36197","category_aro_name":"MIR beta-lactamase","category_aro_description":"MIR beta-lactamases are plasmid-mediated beta-lactamases that confer resistance to oxyimino- and alpha-methoxy beta-lactams.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4766":{"model_id":"4766","model_name":"MIR-21","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"8106":{"protein_sequence":{"accession":"WP_045372339.1","sequence":"MMTKSLSCALLLSVTSSAFAAPMSEKQLAEVVERTVTPLMNAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEIALGDPVAKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDTASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMSYEQAMTTRVFKPLKLDHTWINVPKAEEAHYAWGYREGKAVHVSPGMLDAEAYGVKTNVKDMASWVIANMKPDSLQAPSLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVGGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILDALQ"},"dna_sequence":{"accession":"NG_050723.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGACAAAATCCCTAAGCTGTGCCCTGCTGCTCAGCGTCACCAGCTCTGCATTCGCCGCACCGATGTCCGAAAAACAGCTGGCTGAGGTGGTGGAACGTACCGTTACGCCGCTGATGAACGCGCAGGCCATTCCGGGTATGGCGGTGGCGGTAATTTATCAGGGTCAGCCACACTACTTTACCTTCGGTAAAGCCGATGTTGCGGCGAACAAACCCGTCACCCCGCAAACCCTGTTTGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTACTGGGCGGCGATGCCATTGCCCGAGGTGAAATAGCGCTGGGCGATCCGGTAGCAAAATACTGGCCTGAGCTCACGGGCAAACAGTGGCAGGGCATTCGCATGCTGGATCTGGCAACCTATACCGCAGGCGGTCTGCCGTTACAGGTGCCGGATGAGGTCACGGATACCGCTTCTCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCGGGCACCACGCGTCTTTACGCTAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTTAAACCTTCCGGCATGAGCTATGAGCAGGCCATGACGACGCGGGTCTTTAAACCCCTCAAGCTGGACCATACCTGGATTAACGTCCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGATACCGTGAGGGTAAAGCGGTCCACGTTTCGCCAGGGATGCTGGACGCGGAAGCCTATGGCGTAAAAACTAACGTGAAGGATATGGCGAGCTGGGTGATAGCCAACATGAAGCCGGATTCTCTTCAGGCTCCCTCACTCAAGCAAGGCATTGCTCTGGCGCAGTCTCGCTACTGGCGCGTGGGGGCTATGTATCAGGGGTTGGGCTGGGAGATGCTCAACTGGCCGGTCGATGCCAAAACCGTCGTCGGAGGCAGTGATAACAAGGTGGCGCTGGCACCATTGCCCGTGGCAGAAGTGAATCCACCCGCACCGCCGGTCAAAGCCTCCTGGGTCCATAAAACAGGCTCGACGGGCGGGTTTGGCAGCTACGTGGCATTTATTCCTGAAAAGCAGCTCGGCATTGTGATGCTGGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCGTATCCTTGACGCGCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40540","NCBI_taxonomy_name":"Enterobacter cloacae complex","NCBI_taxonomy_id":"354276"}}}},"ARO_accession":"3006861","ARO_id":"45323","ARO_name":"MIR-21","CARD_short_name":"MIR-21","ARO_description":"MIR-21 is a MIR beta-lactamase.","ARO_category":{"36197":{"category_aro_accession":"3000058","category_aro_cvterm_id":"36197","category_aro_name":"MIR beta-lactamase","category_aro_description":"MIR beta-lactamases are plasmid-mediated beta-lactamases that confer resistance to oxyimino- and alpha-methoxy beta-lactams.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4767":{"model_id":"4767","model_name":"MIR-22","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"8107":{"protein_sequence":{"accession":"WP_099156057.1","sequence":"MMTKSLSCALLLSVTSSAFAAPMSEKQLAEVVERTVTPLMNAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEVALGDPVAKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDTASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMSYEQAMTTRVFKPLKLDHTWINVPKAEEAHYAWGYREGKAVHVSPGMLDAEAYGVKTNVKDMASWVIANMKPDSLQAPSLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVGGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILDALQ"},"dna_sequence":{"accession":"NG_055671.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGACAAAATCCCTAAGCTGTGCCCTGCTGCTCAGCGTCACCAGCTCTGCATTCGCCGCACCGATGTCCGAAAAACAGCTGGCTGAGGTGGTGGAACGTACCGTTACGCCGCTGATGAACGCGCAGGCCATTCCGGGTATGGCGGTGGCGGTAATTTATCAGGGTCAGCCACACTACTTTACCTTCGGTAAAGCCGATGTTGCGGCGAACAAACCCGTCACCCCGCAAACCCTGTTTGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTACTGGGCGGCGATGCCATTGCCCGGGGTGAAGTAGCGCTGGGCGATCCGGTAGCAAAATACTGGCCTGAGCTCACGGGCAAGCAGTGGCAGGGCATTCGCATGCTGGATCTGGCAACCTATACCGCAGGCGGTCTGCCGTTACAGGTGCCGGATGAGGTCACGGATACCGCCTCTCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCGGGCACCACGCGTCTTTACGCTAACGCCAGCATCGGTCTTTTTGGTGCGTTGGCGGTTAAACCTTCCGGCATGAGCTATGAGCAGGCCATGACGACGCGGGTCTTTAAACCCCTCAAGCTGGACCATACCTGGATTAACGTCCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGATACCGTGAGGGTAAAGCGGTCCACGTTTCGCCAGGGATGCTGGACGCGGAAGCCTATGGCGTAAAAACTAACGTGAAGGATATGGCGAGCTGGGTGATAGCCAACATGAAGCCGGATTCTCTTCAGGCTCCCTCACTCAAGCAAGGCATTGCTCTGGCGCAGTCTCGCTACTGGCGCGTGGGGGCTATGTATCAGGGGTTAGGCTGGGAGATGCTCAACTGGCCGGTCGATGCCAAAACCGTCGTCGGAGGCAGTGATAACAAGGTGGCGCTGGCACCATTGCCCGTGGCAGAAGTGAATCCACCCGCGCCGCCGGTTAAGGCCTCCTGGGTCCATAAAACAGGCTCGACGGGTGGGTTTGGCAGCTACGTGGCATTTATTCCTGAAAAGCAGCTCGGCATTGTGATGCTGGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCGTATCCTCGACGCGCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40540","NCBI_taxonomy_name":"Enterobacter cloacae complex","NCBI_taxonomy_id":"354276"}}}},"ARO_accession":"3006862","ARO_id":"45324","ARO_name":"MIR-22","CARD_short_name":"MIR-22","ARO_description":"MIR-22 is a MIR beta-lactamase.","ARO_category":{"36197":{"category_aro_accession":"3000058","category_aro_cvterm_id":"36197","category_aro_name":"MIR beta-lactamase","category_aro_description":"MIR beta-lactamases are plasmid-mediated beta-lactamases that confer resistance to oxyimino- and alpha-methoxy beta-lactams.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4768":{"model_id":"4768","model_name":"MIR-7","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"8108":{"protein_sequence":{"accession":"WP_045409557.1","sequence":"MMTKSLSCALLLSVASAAFAAPMSEKQLAEVVERTVTPLMNAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEIALGDPVAKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDTASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMSYEQAMTTRVFKPLKLDHTWINVPKAEEAHYAWGYREGKAVHVSPGMLDAEAYGVKTNVKDMASWLIANMKPDSLQAPSLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVGGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILDALQ"},"dna_sequence":{"accession":"NG_049308.1","fmin":"100","fmax":"1246","strand":"+","sequence":"ATGATGACAAAATCCCTAAGCTGTGCCCTGCTGCTCAGCGTCGCCAGCGCTGCATTCGCCGCACCGATGTCCGAAAAACAGCTGGCTGAGGTGGTGGAACGTACCGTTACGCCGCTGATGAACGCGCAGGCCATTCCGGGTATGGCGGTGGCGGTAATTTATCAGGGTCAGCCACACTACTTTACCTTCGGTAAAGCCGATGTTGCGGCGAACAAACCCGTCACCCCGCAAACCCTGTTTGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTACTGGGCGGCGATGCCATTGCCCGGGGTGAAATAGCGCTGGGCGATCCGGTAGCAAAATACTGGCCTGAGCTCACGGGCAAGCAGTGGCAGGGCATTCGCATGCTGGATCTGGCAACCTATACCGCAGGCGGTCTGCCGTTACAGGTGCCGGATGAGGTCACGGATACCGCCTCTCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCGGGTACCACGCGTCTTTACGCTAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTTAAACCTTCCGGCATGAGCTATGAGCAGGCCATGACGACGCGGGTCTTTAAACCCCTCAAGCTGGACCATACCTGGATTAACGTCCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGATACCGTGAGGGTAAAGCGGTCCACGTTTCGCCAGGGATGCTGGACGCGGAAGCCTATGGCGTAAAAACTAACGTGAAGGATATGGCGAGCTGGCTGATAGCCAACATGAAGCCGGATTCTCTTCAGGCTCCCTCACTCAAGCAAGGCATTGCTCTGGCGCAGTCTCGCTACTGGCGCGTGGGGGCTATGTATCAGGGGCTGGGCTGGGAGATGCTCAACTGGCCGGTCGATGCCAAAACCGTCGTCGGAGGCAGTGATAACAAGGTGGCGCTGGCACCATTGCCCGTGGCAGAAGTGAATCCACCCGCGCCGCCGGTCAAAGCCTCCTGGGTCCATAAAACAGGCTCGACGGGCGGGTTTGGCAGCTACGTGGCATTTATTCCTGAAAAGCAGCTCGGCATTGTGATGCTGGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCGTATCCTCGACGCGCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40540","NCBI_taxonomy_name":"Enterobacter cloacae complex","NCBI_taxonomy_id":"354276"}}}},"ARO_accession":"3002172","ARO_id":"38572","ARO_name":"MIR-7","CARD_short_name":"MIR-7","ARO_description":"MIR-7 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36197":{"category_aro_accession":"3000058","category_aro_cvterm_id":"36197","category_aro_name":"MIR beta-lactamase","category_aro_description":"MIR beta-lactamases are plasmid-mediated beta-lactamases that confer resistance to oxyimino- and alpha-methoxy beta-lactams.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4769":{"model_id":"4769","model_name":"MOC-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8109":{"protein_sequence":{"accession":"WP_060874262.1","sequence":"MYKFLSSILLLASTTFVFAQSKPLKVEKLQDNIYVYITYQMYNGVEYSSNALYIVTDEGAILIDTPWDKEQNDPLVEHIRKQHNKEVKWVITTHFHEDRSGGLDYFRKAGAETYTYALTNEILKNRNEPQAEFTFGKEKHFTFGKEEIVVYFLGEGHSKDNTVVWFPKEKVLYGGCLIKSAEATDIGYIGDGNTDAWPATIKAVKSKFKQAKTVIPGHDNWNQSGHIENTERILSAYNAQKVKNNKQI"},"dna_sequence":{"accession":"NG_051495.1","fmin":"0","fmax":"747","strand":"+","sequence":"ATGTACAAATTTTTAAGCAGTATTTTACTACTTGCATCTACGACTTTCGTATTCGCTCAATCCAAACCCTTAAAGGTTGAAAAACTACAGGATAACATCTATGTTTACATTACGTATCAAATGTATAACGGTGTGGAATATTCGTCCAATGCCTTATATATAGTAACAGATGAGGGAGCGATTCTAATCGATACGCCTTGGGATAAAGAGCAAAATGACCCTTTAGTAGAACATATCAGAAAACAACACAACAAAGAGGTAAAATGGGTGATTACGACACACTTTCATGAAGATCGCTCAGGAGGATTGGACTATTTCAGAAAAGCAGGGGCTGAAACCTATACTTATGCATTAACGAATGAAATTCTCAAAAACAGAAATGAACCCCAAGCAGAATTTACTTTTGGCAAGGAAAAACATTTCACTTTTGGCAAAGAAGAGATCGTAGTTTATTTTTTAGGAGAAGGGCATAGCAAGGATAATACAGTAGTATGGTTTCCAAAAGAAAAAGTTTTATACGGAGGTTGTTTGATTAAAAGTGCTGAAGCAACAGACATTGGTTATATTGGAGATGGTAATACTGATGCATGGCCTGCAACAATCAAAGCAGTTAAAAGCAAGTTTAAACAAGCGAAAACAGTAATTCCAGGGCATGATAATTGGAATCAATCCGGTCATATCGAGAATACAGAACGCATTTTATCAGCTTACAATGCACAAAAAGTAAAAAACAACAAGCAAATATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"45473","NCBI_taxonomy_name":"Myroides odoratus","NCBI_taxonomy_id":"256"}}}},"ARO_accession":"3006952","ARO_id":"45414","ARO_name":"MOC-1","CARD_short_name":"MOC-1","ARO_description":"MOC-1 is a MOC beta-lactamase.","ARO_category":{"43884":{"category_aro_accession":"3005424","category_aro_cvterm_id":"43884","category_aro_name":"MOC beta-lactamase","category_aro_description":"MOC beta-lactamases are class B1 beta-lactamase found in Myroides odoratus.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4770":{"model_id":"4770","model_name":"MOR-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"8110":{"protein_sequence":{"accession":"WP_063860842.1","sequence":"MTKSVSATLISALLAFSAPGFSAADNVAAVVDSTIKPLMAQQDIPGMAVAVSVKGKPYYFNYGFADVQAKQPVTENTLFELGSVSKTFTGVLGAVSVAKKEMTLNDPAEKYQPELALPQWKGITLLDLATYTAGGLPLQVPDAVKSRADLLNFYQQWQPSRKPGDMRLYANSSIGLFGALTANAAGMPYEQLLTARILAPLGLSHTFITVPESAQSQYAYGYKNKKPVRVSPGQLDAESYGVKSASKDMLRWAEMNMEPSRAGNADLEMAMYLAQTRYYKTAAINQGLGWEMYDWPQQKDMIINGVTNEVALQPHPVTDNQVQPYNRASWVHKTGATTGFGAYVAFIPEKQVAIVILANKNYPNTERVKAAQAILSALE"},"dna_sequence":{"accession":"NG_049310.1","fmin":"100","fmax":"1240","strand":"+","sequence":"ATGACAAAATCTGTATCTGCAACACTGATTTCCGCCCTGCTGGCATTTTCCGCCCCGGGGTTTTCTGCCGCTGATAATGTCGCGGCGGTGGTGGACAGCACCATTAAACCGCTGATGGCACAGCAGGATATTCCCGGGATGGCGGTTGCCGTCTCCGTAAAGGGTAAGCCCTATTATTTCAATTACGGTTTTGCCGATGTTCAGGCAAAACAGCCTGTCACTGAAAATACACTATTTGAGCTCGGATCTGTAAGTAAAACTTTCACAGGTGTGCTGGGTGCGGTTTCCGTGGCGAAAAAAGAGATGACGCTGAATGACCCGGCAGAAAAATACCAGCCGGAGCTGGCTCTGCCGCAGTGGAAGGGGATCACGCTGCTGGATCTGGCCACCTACACCGCAGGCGGGCTGCCGTTACAGGTACCGGATGCGGTGAAAAGCCGTGCGGATCTGCTGAATTTCTATCAGCAGTGGCAGCCGTCCCGGAAACCGGGCGATATGCGTCTGTATGCAAACAGCAGTATCGGCCTGTTTGGTGCTCTGACCGCCAACGCAGCGGGGATGCCGTATGAGCAGTTGCTGACTGCACGGATCCTGGCACCGCTGGGGTTATCTCACACCTTTATTACTGTGCCGGAAAGCGCGCAAAGCCAGTATGCGTACGGTTATAAAAACAAAAAACCGGTCCGCGTGTCGCCGGGACAGCTTGATGCGGAATCTTACGGCGTGAAATCCGCCTCAAAAGATATGCTGCGCTGGGCGGAAATGAATATGGAGCCGTCACGGGCCGGTAATGCGGATCTGGAAATGGCAATGTATCTCGCCCAGACCCGCTACTATAAAACCGCCGCGATTAACCAGGGGCTGGGCTGGGAAATGTATGACTGGCCGCAGCAGAAAGATATGATCATTAACGGTGTGACCAACGAGGTCGCATTGCAGCCGCACCCGGTAACAGACAACCAGGTTCAGCCGTATAACCGTGCTTCCTGGGTGCATAAAACGGGGGCAACAACTGGTTTCGGCGCCTATGTGGCCTTTATTCCGGAAAAACAGGTGGCGATTGTGATTCTGGCGAATAAAAACTACCCGAATACCGAAAGAGTCAAAGCCGCACAGGCTATTTTGAGTGCACTGGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36917","NCBI_taxonomy_name":"Morganella morganii","NCBI_taxonomy_id":"582"}}}},"ARO_accession":"3006953","ARO_id":"45415","ARO_name":"MOR-2","CARD_short_name":"MOR-2","ARO_description":"MOR-2 is a MOR beta-lactamase.","ARO_category":{"43885":{"category_aro_accession":"3005425","category_aro_cvterm_id":"43885","category_aro_name":"MOR beta-lactamase","category_aro_description":"MOR beta-lactamases are class C beta-lactamases found in Morganella morganii.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4771":{"model_id":"4771","model_name":"MOX-10","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"8111":{"protein_sequence":{"accession":"WP_063860843.1","sequence":"MQQRQSFLWGAVATLMWAGLAHAGETSPVDPLRPVVDASIQPLLKEHRIPGMAVAVLKDGKAHYFNYGVADRERAVGVSEQTLFEIGSVSKPLTATLGAYAVVKGAMQLDDKASRHAPWLKGSAFDSITMGELATYSAGGLPLQFPEEVDSLEKMQAYYRQWTPAYSPGSHRQYSNPSIGLFGHLAASSLKQPFAQLMEQTLLPGLGLHHTYVNVPKQAMASYAYGYSKEDKPIRVSPGMLADEAYGIKTSSADLLRFVKANISGVDDKALQQAISLTHKGHYSVGGMTQGLGWESYAYPVSEQILLAGNSAKVILEANPTAAPRESGSQMLFNKTGSTSGFGAYVAFVPAKGIGIVMLANRNYPIPARVKAAHAILTQLAR"},"dna_sequence":{"accession":"NG_049312.1","fmin":"0","fmax":"1149","strand":"+","sequence":"ATGCAACAACGACAATCCTTCCTGTGGGGGGCCGTGGCCACCCTGATGTGGGCCGGTCTGGCCCATGCAGGTGAGACTTCACCGGTCGATCCCCTGCGCCCCGTGGTGGATGCCAGCATCCAGCCGCTGCTCAAGGAGCACAGGATCCCGGGCATGGCGGTGGCCGTGCTCAAGGATGGCAAGGCCCACTATTTCAACTACGGTGTGGCCGATCGGGAGCGCGCGGTCGGTGTCAGCGAGCAGACCCTGTTCGAGATAGGCTCCGTGAGCAAGCCCCTGACCGCGACCCTAGGAGCCTATGCGGTGGTCAAGGGAGCGATGCAACTGGATGACAAGGCGAGCCGGCACGCCCCCTGGCTCAAGGGATCCGCCTTTGACAGCATCACCATGGGGGAGCTGGCTACCTACAGCGCGGGCGGCTTGCCGCTGCAATTCCCCGAGGAGGTGGATTCGCTCGAGAAGATGCAGGCCTACTACCGCCAGTGGACCCCAGCCTACTCGCCGGGTTCCCATCGCCAGTACTCTAACCCCAGCATAGGGCTGTTCGGCCACCTGGCGGCGAGCAGCCTGAAGCAGCCGTTTGCCCAGTTGATGGAGCAGACGCTCCTGCCGGGGCTTGGCCTGCACCACACCTATGTCAATGTGCCGAAGCAGGCCATGGCGAGTTATGCCTATGGCTATTCGAAAGAGGACAAGCCCATCAGGGTCAGCCCCGGCATGCTGGCGGACGAGGCCTACGGCATCAAGACCAGCTCGGCGGATCTGCTGCGCTTTGTGAAGGCCAACATCAGCGGGGTTGATGACAAGGCGTTGCAGCAGGCCATCTCCCTGACCCACAAAGGGCACTACTCGGTAGGCGGGATGACCCAGGGACTGGGTTGGGAGAGTTACGCCTATCCCGTCAGCGAGCAGATATTGCTGGCGGGCAATTCGGCCAAGGTGATCCTCGAAGCCAATCCGACGGCGGCGCCCCGGGAGTCGGGGAGCCAGATGCTCTTCAACAAGACCGGCTCGACCAGCGGCTTCGGCGCCTATGTGGCCTTCGTGCCGGCCAAAGGGATCGGCATCGTCATGCTGGCCAACCGCAACTATCCTATCCCGGCCAGGGTGAAAGCGGCCCACGCCATCCTGACGCAACTGGCCAGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36936","NCBI_taxonomy_name":"Aeromonas caviae","NCBI_taxonomy_id":"648"}}}},"ARO_accession":"3003140","ARO_id":"39717","ARO_name":"MOX-10","CARD_short_name":"MOX-10","ARO_description":"MOX-10 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36222":{"category_aro_accession":"3000083","category_aro_cvterm_id":"36222","category_aro_name":"MOX beta-lactamase","category_aro_description":"MOX beta-lactamases are plasmid-mediated AmpC-type beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4772":{"model_id":"4772","model_name":"MOX-11","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"8112":{"protein_sequence":{"accession":"WP_063860844.1","sequence":"MQQRQSFLWGAVATLMWAGLAHAGETSPVDPLRPVVDASIQPLLKEHRIPGMAVAVLKDGKAHYFNYGVADRERAVGVSEQTLFEIGSVSKPLTATLGAYAVVKGAMQLDDKASRHAPWLKGSAFDSITMGELATYSAGGLPLQFPEEVDSLEKMQAYYRQWTPAYSPGSHRQYSNPSIGLFGHLAASSLKQPFAQLMEQTLLPGLGLHHTYVNVPKQAMASYAYGYSKEDKPIRVSPGMLADEAYGIKTSSADLLRFVKANISGVDDKALQQAISLTHKGHYSVGGMTQGLGWERYAYPVSEQTLLAGNSAKVILEANPTAAPRESGSQMLFNKTGSTSGFGAYVAFVPAKGIGIVMLANRNYPIPARVKAAHAILTQLAR"},"dna_sequence":{"accession":"NG_049313.1","fmin":"0","fmax":"1149","strand":"+","sequence":"ATGCAACAACGACAATCCTTCCTGTGGGGGGCCGTGGCCACCCTGATGTGGGCCGGTCTGGCCCATGCAGGTGAGACTTCACCGGTCGATCCCCTGCGCCCCGTGGTGGATGCCAGCATCCAGCCGCTGCTCAAGGAGCACAGGATCCCGGGCATGGCGGTGGCCGTGCTCAAGGATGGCAAGGCCCACTATTTCAACTACGGTGTGGCCGATCGGGAGCGCGCGGTCGGTGTCAGCGAGCAGACCCTGTTCGAGATAGGCTCCGTGAGCAAGCCCCTGACCGCGACCCTAGGAGCCTATGCGGTGGTCAAGGGAGCGATGCAACTGGATGACAAGGCGAGCCGGCACGCCCCCTGGCTCAAGGGATCCGCCTTTGACAGCATCACCATGGGGGAGCTGGCTACCTACAGCGCGGGCGGCTTGCCGCTGCAATTCCCCGAGGAGGTGGATTCGCTCGAGAAGATGCAGGCCTACTACCGCCAGTGGACCCCAGCCTACTCGCCGGGTTCCCATCGCCAGTACTCTAACCCCAGCATAGGGCTGTTCGGCCACCTGGCGGCGAGCAGCCTGAAGCAGCCGTTTGCCCAGTTGATGGAGCAGACGCTCCTGCCGGGGCTTGGCCTGCACCACACCTATGTCAATGTGCCGAAGCAGGCCATGGCGAGTTATGCCTATGGCTATTCGAAAGAGGACAAGCCCATCAGGGTCAGCCCCGGCATGCTGGCGGACGAGGCCTACGGCATCAAGACCAGCTCGGCGGATCTGCTGCGCTTTGTGAAGGCCAACATCAGCGGGGTTGATGACAAGGCGTTGCAGCAGGCCATCTCCCTGACCCACAAAGGGCACTACTCGGTAGGCGGGATGACCCAGGGACTGGGTTGGGAGCGTTACGCCTATCCCGTCAGCGAGCAGACATTGCTGGCGGGCAATTCGGCCAAGGTGATCCTCGAAGCCAATCCGACGGCGGCGCCCCGGGAGTCGGGGAGCCAGATGCTCTTCAACAAGACCGGCTCGACCAGCGGCTTCGGCGCCTATGTGGCCTTCGTGCCGGCCAAAGGGATCGGCATCGTCATGCTGGCCAACCGCAACTATCCTATCCCGGCCAGGGTGAAAGCGGCCCACGCCATCCTGACGCAACTGGCCAGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39526","NCBI_taxonomy_name":"Aeromonas media","NCBI_taxonomy_id":"651"}}}},"ARO_accession":"3003141","ARO_id":"39718","ARO_name":"MOX-11","CARD_short_name":"MOX-11","ARO_description":"MOX-11 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36222":{"category_aro_accession":"3000083","category_aro_cvterm_id":"36222","category_aro_name":"MOX beta-lactamase","category_aro_description":"MOX beta-lactamases are plasmid-mediated AmpC-type beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4773":{"model_id":"4773","model_name":"MOX-12","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"8121":{"protein_sequence":{"accession":"WP_043155783.1","sequence":"MQQRQSILWGALATLMWAGLAHAGDKAATDPLRPVVDASIRPLLKEHRIPGMAVAVLKDGKAHYFNYGVADRERAVGVSEQTLFEIGSVSKTLTATLGAYAVVQGGFELDDKASLFAPWLKGSAFDNITMGELATYSAGGLPLQFPEEVDSLEKMQAYYRQWTPAYSPGSHRQYANPSIGLFGYLAASSMKQPFDRLMEQTILPGLGLYHTYLNVPEQAMGHYAYGYSKEDKPIRVTPGMLADEAYGIKTSSADLLRFVKANISGVDNAAMQQAIDLTHQGQYAVGEMTQGLGWERYAYPVSEQTLLAGNSPAMIYNTNPAAPAPAAAGHPVLFNKTGSTNGFGAYVAFVPAKGIGVVMLANRNYPNEARIKAAHAILTKLAR"},"dna_sequence":{"accession":"NG_049314.1","fmin":"100","fmax":"1252","strand":"+","sequence":"ATGCAACAACGACAATCCATCCTGTGGGGCGCTCTGGCCACCCTGATGTGGGCCGGCCTGGCTCATGCCGGTGACAAGGCGGCGACCGATCCCCTGCGCCCCGTGGTGGATGCCAGCATCCGGCCGCTGCTCAAGGAGCACAGGATCCCGGGCATGGCGGTGGCCGTGCTCAAGGATGGCAAGGCCCACTATTTCAACTACGGTGTGGCCGATCGGGAGCGCGCGGTCGGTGTCAGCGAGCAGACCCTGTTCGAGATAGGCTCCGTGAGCAAGACCCTGACCGCGACGCTGGGGGCCTACGCCGTGGTGCAGGGGGGCTTCGAGCTCGATGACAAGGCGAGTCTGTTCGCCCCCTGGCTCAAGGGATCCGCCTTTGACAACATCACCATGGGGGAGCTGGCTACCTACAGCGCAGGCGGCTTGCCGCTGCAATTCCCCGAGGAGGTGGATTCGCTCGAGAAGATGCAGGCCTACTACCGCCAGTGGACCCCAGCCTACTCGCCGGGTTCCCATCGCCAGTACGCCAACCCCAGCATCGGGCTCTTTGGCTATCTGGCGGCGAGCAGCATGAAGCAGCCGTTCGATCGCCTGATGGAGCAGACGATCCTGCCGGGGCTTGGCCTGTACCATACCTACCTCAATGTGCCCGAGCAGGCCATGGGGCACTACGCCTACGGCTACTCGAAGGAGGACAAGCCCATCCGCGTCACTCCCGGCATGCTGGCGGACGAGGCCTACGGCATCAAGACCAGCTCGGCGGATCTGCTGCGCTTTGTGAAGGCGAACATCAGCGGGGTGGATAATGCGGCCATGCAGCAGGCCATCGACCTGACTCACCAGGGCCAGTATGCGGTGGGGGAGATGACCCAGGGACTGGGCTGGGAGCGTTACGCCTATCCCGTCAGCGAGCAGACGCTGCTGGCGGGCAACTCCCCGGCGATGATTTATAATACGAACCCGGCGGCGCCCGCGCCCGCTGCGGCAGGGCACCCTGTGCTCTTCAACAAGACCGGCTCGACCAACGGCTTCGGGGCCTATGTGGCCTTCGTGCCGGCCAAAGGGATCGGCGTCGTCATGCTGGCCAATCGCAACTACCCCAACGAGGCGCGCATCAAGGCGGCTCACGCCATCCTGACGAAACTGGCCAGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37047","NCBI_taxonomy_name":"Aeromonas","NCBI_taxonomy_id":"642"}}}},"ARO_accession":"3006477","ARO_id":"44939","ARO_name":"MOX-12","CARD_short_name":"MOX-12","ARO_description":"MOX-12 is a MOX beta-lactamase.","ARO_category":{"36222":{"category_aro_accession":"3000083","category_aro_cvterm_id":"36222","category_aro_name":"MOX beta-lactamase","category_aro_description":"MOX beta-lactamases are plasmid-mediated AmpC-type beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4774":{"model_id":"4774","model_name":"MOX-13","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"8113":{"protein_sequence":{"accession":"WP_096807444.1","sequence":"MQQRQSILWGALATLMWAGLAHAGDKAATDPLRPVVDASIRPLLKEHRILGMAVAVLKDGKAHYFNYGVADRERAVGVSEQTLFEIGSVSKTLTATLGAYAVVQGSFELDDKASLFASWLKGSAFDNITMGELATYSAGGLPLQFPEEVDSLEKMQAYYRQWTPAYSPGSHRQYANPSIGLFGYLAASSMKQPFDRLMEQTILPGLGLYHTYLNVPEQAMGHYAYGYSKEDKPIRVTPGMLADEAYGIKTSSADLLRFVKANISGVDNAAMQQAIDLTHQGQYAVGEMTQGLGWERYAYPVSEQTLLAGNSPAMIYNANPAAPAPAATGHPVLFNKTGSTNGFGAYVAFVPAKGIGIVMLANRNYPNEARIKAAHAILTQLAR"},"dna_sequence":{"accession":"NG_055585.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCAACAACGACAATCCATCCTGTGGGGCGCTCTGGCCACCCTGATGTGGGCCGGTCTGGCTCATGCCGGTGACAAGGCGGCGACCGATCCCCTGCGCCCCGTGGTGGATGCCAGCATCCGGCCGCTGCTCAAGGAGCACAGGATCCTGGGCATGGCGGTGGCCGTGCTCAAGGATGGCAAGGCCCACTATTTCAACTACGGTGTGGCCGATCGGGAGCGCGCAGTCGGTGTCAGCGAGCAGACCCTGTTCGAGATAGGTTCCGTGAGCAAGACCCTGACCGCGACGCTGGGGGCCTACGCCGTGGTGCAGGGGAGCTTCGAGCTCGATGACAAGGCGAGTCTGTTCGCCTCCTGGCTCAAGGGATCCGCCTTTGACAACATCACCATGGGGGAGCTGGCTACCTACAGCGCGGGCGGCTTGCCGCTGCAATTCCCCGAGGAGGTGGATTCGCTCGAGAAGATGCAGGCCTACTACCGCCAGTGGACCCCAGCCTACTCGCCGGGTTCCCATCGCCAGTACGCCAACCCCAGCATCGGGCTCTTTGGCTATCTGGCGGCGAGCAGCATGAAGCAGCCGTTCGATCGCCTGATGGAGCAGACGATCCTGCCGGGGCTTGGCCTGTACCATACCTACCTCAATGTGCCCGAGCAGGCCATGGGGCACTACGCCTACGGCTACTCGAAGGAGGACAAGCCCATCCGCGTCACTCCCGGCATGCTGGCGGACGAGGCCTACGGCATCAAGACCAGCTCGGCGGATCTGCTGCGCTTTGTGAAGGCCAACATCAGCGGGGTGGATAATGCGGCCATGCAGCAGGCCATCGATCTGACTCACCAGGGCCAGTATGCGGTGGGGGAGATGACCCAGGGACTGGGCTGGGAGCGTTACGCCTATCCCGTCAGCGAGCAGACGCTGCTGGCGGGCAACTCCCCGGCGATGATTTACAATGCCAACCCGGCGGCGCCCGCGCCCGCTGCAACAGGGCACCCTGTGCTCTTCAACAAGACCGGCTCGACCAACGGCTTCGGGGCCTATGTGGCTTTCGTGCCGGCCAAAGGGATCGGCATCGTCATGCTGGCCAATCGCAACTACCCCAACGAGGCGCGCATCAAGGCGGCCCACGCCATCCTGACGCAACTGGCCAGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43553","NCBI_taxonomy_name":"Citrobacter sp.","NCBI_taxonomy_id":"1896336"}}}},"ARO_accession":"3006478","ARO_id":"44940","ARO_name":"MOX-13","CARD_short_name":"MOX-13","ARO_description":"MOX-13 is a MOX beta-lactamase.","ARO_category":{"36222":{"category_aro_accession":"3000083","category_aro_cvterm_id":"36222","category_aro_name":"MOX beta-lactamase","category_aro_description":"MOX beta-lactamases are plasmid-mediated AmpC-type beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4775":{"model_id":"4775","model_name":"MOX-14","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"8114":{"protein_sequence":{"accession":"WP_156404654.1","sequence":"MQQRQSILWGAVATLMWAGLAHAGEASPVDPLRPVVDASIQPLLKEHRIPGMAVAVLKDGKAHYFNYGVANRESGAGVSEQTLFEIGSVSKTLTATLGAYAVVKGAMQLDDKASRHAPWLKGSAFDSITMGELATYSAGGLPLQFPEEVDSSEKMRAYYRQWAPVYSPGSHRQYSNPSIGLFGHLAASSLKQPFAPLMEQTLLPGLGMHHTYVNVPKQAMASYAYGYSKEDKPIRVNPGMLADEAYGIKTSSADLLRFVKANIGGVDDKALQQAISLPHQGHYSVGGMTQGLGWESYAYPVTEQTLLAGNSAKVILEANPTAAPRESGSQVLFNKTGSTNGFGAYVAFVPARGIGIVMLANRNYPIEARIKAAHAILAQLAG"},"dna_sequence":{"accession":"NG_067143.1","fmin":"0","fmax":"1149","strand":"+","sequence":"ATGCAACAACGACAATCCATCCTGTGGGGGGCCGTGGCCACCCTGATGTGGGCCGGTCTGGCCCATGCAGGTGAGGCTTCACCGGTCGATCCCCTGCGCCCCGTGGTGGATGCCAGCATCCAGCCGCTGCTCAAGGAGCACAGGATCCCGGGCATGGCGGTGGCCGTGCTCAAGGATGGCAAGGCCCACTACTTCAATTACGGGGTGGCCAACCGGGAGAGCGGGGCCGGCGTCAGCGAGCAGACCCTGTTCGAGATAGGATCCGTGAGCAAGACCCTGACTGCGACCCTGGGGGCCTATGCGGTGGTCAAGGGAGCGATGCAGCTGGATGACAAGGCGAGCCGGCACGCGCCCTGGCTCAAGGGATCCGCCTTTGACAGCATCACCATGGGGGAGCTTGCCACCTACAGCGCCGGAGGCCTGCCACTGCAATTCCCCGAGGAGGTGGATTCATCCGAGAAGATGCGCGCCTACTACCGCCAGTGGGCCCCTGTCTATTCGCCGGGCTCCCATCGCCAGTACTCCAACCCCAGCATAGGGCTGTTCGGCCACCTGGCGGCGAGCAGCCTGAAGCAGCCGTTTGCCCCCTTGATGGAGCAGACCCTGCTGCCCGGGCTCGGCATGCACCACACCTATGTCAATGTGCCGAAGCAGGCCATGGCGAGTTATGCCTATGGCTATTCGAAAGAGGACAAGCCCATCCGTGTCAACCCTGGCATGCTGGCGGACGAGGCCTATGGCATCAAGACCAGCTCGGCGGATCTGCTGCGTTTTGTGAAGGCCAACATCGGCGGGGTTGATGACAAGGCGTTGCAGCAGGCCATCTCCCTGCCCCACCAAGGGCATTACTCGGTAGGCGGGATGACCCAGGGGCTGGGTTGGGAGAGTTACGCCTATCCCGTCACCGAGCAGACATTGCTGGCGGGCAATTCGGCCAAGGTGATCCTCGAAGCCAATCCGACGGCGGCGCCCCGGGAGTCGGGGAGCCAGGTGCTCTTCAACAAGACCGGCTCGACCAATGGCTTTGGCGCCTATGTGGCCTTCGTGCCGGCCAGGGGGATCGGCATCGTCATGCTGGCCAATCGCAACTACCCCATCGAGGCGCGCATCAAGGCGGCCCACGCCATCCTGGCGCAGTTGGCCGGTTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3006479","ARO_id":"44941","ARO_name":"MOX-14","CARD_short_name":"MOX-14","ARO_description":"MOX-14 is a MOX beta-lactamase.","ARO_category":{"36222":{"category_aro_accession":"3000083","category_aro_cvterm_id":"36222","category_aro_name":"MOX beta-lactamase","category_aro_description":"MOX beta-lactamases are plasmid-mediated AmpC-type beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4776":{"model_id":"4776","model_name":"MYO-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8115":{"protein_sequence":{"accession":"WP_081048762.1","sequence":"MKILLAFFLLSSLTFISCKESSSNHNQANQENKKEIINKPLTDSLIVYQTENLIINKLSNHIYEHISFLNTDDFGKVACNGMLVLNENKVVVFDTPTDDKSSLELINFVTNTLKSEIIGLIPTHFHDDCIGGITEFENHNIQTYVSKETIELLKDNGQEFSNPTKDFDNSLTLDIGNKKVYAEYFGEGHTKDNVVGYFPEDNAVFGGCLIKEIDASKGYLGDANIKEWSTTVEKVKLKYPNAKIVIPGHGKWGGIELFDYTIKLFE"},"dna_sequence":{"accession":"NG_059325.1","fmin":"100","fmax":"901","strand":"+","sequence":"ATGAAAATATTATTAGCATTCTTTCTTCTTTCAAGTTTGACTTTTATTTCTTGCAAAGAATCATCCTCTAACCACAATCAGGCAAATCAAGAAAACAAGAAGGAAATAATCAATAAACCTTTAACCGACAGCTTGATAGTCTATCAAACCGAAAATCTGATAATTAACAAACTCTCAAATCACATTTATGAACATATTTCCTTTTTAAATACGGACGATTTTGGAAAAGTTGCCTGCAATGGAATGTTAGTTTTAAATGAGAATAAAGTAGTTGTTTTTGATACACCAACAGACGACAAAAGTTCGTTAGAGTTAATAAATTTTGTAACGAATACATTAAAAAGTGAAATTATAGGGCTAATTCCAACTCATTTTCACGATGATTGTATTGGTGGAATAACGGAATTTGAAAACCATAATATTCAAACCTATGTCTCTAAAGAAACTATAGAATTATTAAAAGATAACGGTCAAGAATTCTCTAATCCAACTAAAGATTTTGACAATAGTCTCACATTAGATATCGGAAACAAGAAAGTTTATGCGGAATATTTTGGAGAAGGGCACACTAAAGATAATGTTGTGGGCTATTTCCCAGAAGATAACGCAGTATTCGGTGGATGCTTGATAAAGGAAATTGACGCGAGTAAAGGATATTTAGGAGATGCAAATATTAAAGAATGGTCAACAACAGTAGAAAAAGTAAAACTCAAATATCCCAATGCTAAAATTGTAATACCAGGACACGGAAAATGGGGTGGAATTGAATTATTTGACTACACAATAAAACTATTTGAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39072","NCBI_taxonomy_name":"Myroides odoratimimus","NCBI_taxonomy_id":"76832"}}}},"ARO_accession":"3006954","ARO_id":"45416","ARO_name":"MYO-1","CARD_short_name":"MYO-1","ARO_description":"MYO-1 is a MYO beta-lactamase.","ARO_category":{"43886":{"category_aro_accession":"3005426","category_aro_cvterm_id":"43886","category_aro_name":"MYO beta-lactamase","category_aro_description":"MYO beta-lactamases are class B1 beta-lactamases found in Myroides odoratimimus.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4777":{"model_id":"4777","model_name":"MYX-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8116":{"protein_sequence":{"accession":"WP_011550565.1","sequence":"MTLFPLRWFCAGALLITLSTACTRSTPAATVERNIPVKAQSQGPDEYVLADDVSVRKLAPGVWLHITVVTLEPFGRVSTNGLIIEDGETSLLVDTGWDARQGALLLDWARDTLRRPVRAAVVTHFHEDRLGGVPALAPHGIPVHGLEETARIATSLGLPGPTETFAKTSTVDSLELFFPGAGHAKDNIVVWHRDSGVLFGGCFVKDGASTNLGNVADADVAAWPASLSRTRQRFPEARVVVPGHGQPGGPELLGHTEALLR"},"dna_sequence":{"accession":"NG_057453.1","fmin":"100","fmax":"886","strand":"+","sequence":"ATGACGTTGTTTCCTCTTCGTTGGTTTTGTGCCGGTGCTCTTCTCATCACCCTGAGCACCGCCTGCACCCGCTCCACGCCGGCCGCGACGGTGGAGCGGAACATCCCCGTGAAGGCGCAGTCCCAGGGTCCGGACGAATACGTGCTGGCGGATGACGTGAGCGTGCGGAAGCTCGCGCCTGGCGTGTGGCTGCACATCACGGTGGTGACGTTGGAGCCATTCGGCCGCGTCTCCACCAACGGGCTCATCATCGAGGACGGTGAAACGTCCTTGCTGGTCGACACGGGCTGGGATGCACGGCAGGGCGCGCTACTGCTCGACTGGGCCCGGGACACGCTTCGGCGTCCGGTCCGCGCGGCGGTGGTGACGCACTTCCATGAAGATCGCCTCGGTGGTGTTCCGGCGCTCGCCCCGCATGGCATCCCCGTCCATGGCTTGGAGGAGACGGCACGGATTGCCACGTCCCTGGGCCTGCCAGGCCCCACGGAGACCTTCGCCAAGACGAGCACGGTGGACTCCCTGGAGCTCTTCTTCCCGGGGGCGGGCCACGCGAAGGACAACATCGTCGTGTGGCACCGGGACAGCGGCGTGCTGTTCGGCGGCTGCTTCGTGAAGGACGGCGCCTCGACGAACCTGGGCAACGTGGCGGACGCGGACGTAGCGGCCTGGCCCGCGAGCCTGTCGCGGACGCGGCAGCGGTTTCCGGAGGCGCGCGTGGTGGTCCCGGGTCACGGACAGCCCGGTGGGCCGGAGCTGCTGGGCCACACGGAAGCGCTGCTCCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"45474","NCBI_taxonomy_name":"Myxococcus","NCBI_taxonomy_id":"32"}}}},"ARO_accession":"3006955","ARO_id":"45417","ARO_name":"MYX-1","CARD_short_name":"MYX-1","ARO_description":"MYX-1 is a MYX beta-lactamase.","ARO_category":{"43887":{"category_aro_accession":"3005427","category_aro_cvterm_id":"43887","category_aro_name":"MYX beta-lactamase","category_aro_description":"MYX beta-lactamases are class B1 beta-lactamases found in Myxococcus.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4778":{"model_id":"4778","model_name":"NDM-26","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8117":{"protein_sequence":{"accession":"WP_156404655.1","sequence":"MELPNIMHPVAKLSTALAAALMLSGCMPGEIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLLVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGLVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLSDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR"},"dna_sequence":{"accession":"NG_067144.1","fmin":"0","fmax":"813","strand":"+","sequence":"ATGGAATTGCCCAATATTATGCACCCGGTCGCGAAGCTGAGCACCGCATTAGCCGCTGCATTGATGCTGAGCGGGTGCATGCCCGGTGAAATCCGCCCGACGATTGGCCAGCAAATGGAAACTGGCGACCAACGGTTTGGCGATCTGGTTTTCCGCCAGCTCGCACCGAATGTCTGGCAGCACACTTCCTATCTCGACATGCCGGGTTTCGGGGCAGTCGCTTCCAACGGTTTGATCGTCAGGGATGGCGGCCGCGTGCTGTTGGTCGATACCGCCTGGACCGATGACCAGACCGCCCAGATCCTCAACTGGATCAAGCAGGAGATCAACCTGCCGGTCGCGCTGGCGGTGGTGACTCACGCGCATCAGGACAAGATGGGCGGTATGGACGCGCTGCATGCGGCGGGGATTGCGACTTATGCCAATGCGTTGTCGAACCAGCTTGCCCCGCAAGAGGGGCTGGTTGCGGCGCAACACAGCCTGACTTTCGCCGCCAATGGCTGGGTCGAACCAGCAACCGCGCCCAACTTTGGCCCGCTCAAGGTATTTTACCCCGGCCCCGGCCACACCAGTGACAATATCACCGTTGGGATCGACGGCACCGACATCGCTTTTGGTGGCTGCCTGATCAAGGACAGCAAGGCCAAGTCGCTCGGCAATCTCAGTGATGCCGACACTGAGCACTACGCCGCGTCAGCGCGCGCGTTTGGTGCGGCGTTCCCCAAGGCCAGCATGATCGTGATGAGCCATTCCGCCCCCGATAGCCGCGCCGCAATCACTCATACGGCCCGCATGGCCGACAAGCTGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3004869","ARO_id":"43007","ARO_name":"NDM-26","CARD_short_name":"NDM-26","ARO_description":"A class B New Delhi metallo-beta-lactamase and NDM-1 variant.","ARO_category":{"36196":{"category_aro_accession":"3000057","category_aro_cvterm_id":"36196","category_aro_name":"NDM beta-lactamase","category_aro_description":"NDM beta-lactamases or New Delhi metallo-beta-lactamases are class B beta-lactamases that confer resistance to a broad range of antibiotics including carbapenems, cephalosporins and penicillins.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4779":{"model_id":"4779","model_name":"NDM-30","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8118":{"protein_sequence":{"accession":"WP_197749405.1","sequence":"MELPNIMHPVAKLSTALAAALMLSGCMPGEIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGYADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR"},"dna_sequence":{"accession":"NG_071206.1","fmin":"0","fmax":"813","strand":"+","sequence":"ATGGAATTGCCCAATATTATGCACCCGGTCGCGAAGCTGAGCACCGCATTAGCCGCTGCATTGATGCTGAGCGGGTGCATGCCCGGTGAAATCCGCCCGACGATTGGCCAGCAAATGGAAACTGGCGACCAACGGTTTGGCGATCTGGTTTTCCGCCAGCTCGCACCGAATGTCTGGCAGCACACTTCCTATCTCGACATGCCGGGTTTCGGGGCAGTCGCTTCCAACGGTTTGATCGTCAGGGATGGCGGCCGCGTGCTGGTGGTCGATACCGCCTGGACCGATGACCAGACCGCCCAGATCCTCAACTGGATCAAGCAGGAGATCAACCTGCCGGTCGCGCTGGCGGTGGTGACTCACGCGCATCAGGACAAGATGGGCGGTATGGACGCGCTGCATGCGGCGGGGATTGCGACTTATGCCAATGCGTTGTCGAACCAGCTTGCCCCGCAAGAGGGGATGGTTGCGGCGCAACACAGCCTGACTTTCGCCGCCAATGGCTGGGTCGAACCAGCAACCGCGCCCAACTTTGGCCCGCTCAAGGTATTTTACCCCGGCCCCGGCCACACCAGTGACAATATCACCGTTGGGATCGACGGCACCGACATCGCTTTTGGTGGCTGCCTGATCAAGGACAGCAAGGCCAAGTCGCTCGGCAATCTCGGTTATGCCGACACTGAGCACTACGCCGCGTCAGCGCGCGCGTTTGGTGCGGCGTTCCCCAAGGCCAGCATGATCGTGATGAGCCATTCCGCCCCCGATAGCCGCGCCGCAATCACTCATACGGCCCGCATGGCCGACAAGCTGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3005700","ARO_id":"44162","ARO_name":"NDM-30","CARD_short_name":"NDM-30","ARO_description":"NDM-30 is a NDM beta-lactamase.","ARO_category":{"36196":{"category_aro_accession":"3000057","category_aro_cvterm_id":"36196","category_aro_name":"NDM beta-lactamase","category_aro_description":"NDM beta-lactamases or New Delhi metallo-beta-lactamases are class B beta-lactamases that confer resistance to a broad range of antibiotics including carbapenems, cephalosporins and penicillins.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4780":{"model_id":"4780","model_name":"NDM-31","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8103":{"protein_sequence":{"accession":"WP_197749406.1","sequence":"MELPNIMHPVAKLSTALAAALMLSGCMPGEIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVETATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR"},"dna_sequence":{"accession":"NG_071207.1","fmin":"0","fmax":"813","strand":"+","sequence":"ATGGAATTGCCCAATATTATGCACCCGGTCGCGAAGCTGAGCACCGCATTAGCCGCTGCATTGATGCTGAGCGGGTGCATGCCCGGTGAAATCCGCCCGACGATTGGCCAGCAAATGGAAACTGGCGACCAACGGTTTGGCGATCTGGTTTTCCGCCAGCTCGCACCGAATGTCTGGCAGCACACTTCCTATCTCGACATGCCGGGTTTCGGGGCAGTCGCTTCCAACGGTTTGATCGTCAGGGATGGCGGCCGCGTGCTGGTGGTCGATACCGCCTGGACCGATGACCAGACCGCCCAGATCCTCAACTGGATCAAGCAGGAGATCAACCTGCCGGTCGCGCTGGCGGTGGTGACTCACGCGCATCAGGACAAGATGGGCGGTATGGACGCGCTGCATGCGGCGGGGATTGCGACTTATGCCAATGCGTTGTCGAACCAGCTTGCCCCGCAAGAGGGGATGGTTGCGGCGCAACACAGCCTGACTTTCGCCGCCAATGGCTGGGTCGAAACAGCAACCGCGCCCAACTTTGGCCCGCTCAAGGTATTTTACCCCGGCCCCGGCCACACCAGTGACAATATCACCGTTGGGATCGACGGCACCGACATCGCTTTTGGTGGCTGCCTGATCAAGGACAGCAAGGCCAAGTCGCTCGGCAATCTCGGTGATGCCGACACTGAGCACTACGCCGCGTCAGCGCGCGCGTTTGGTGCGGCGTTCCCCAAGGCCAGCATGATCGTGATGAGCCATTCCGCCCCCGATAGCCGCGCCGCAATCACTCATACGGCCCGCATGGCCGACAAGCTGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39583","NCBI_taxonomy_name":"Citrobacter werkmanii","NCBI_taxonomy_id":"67827"}}}},"ARO_accession":"3005701","ARO_id":"44163","ARO_name":"NDM-31","CARD_short_name":"NDM-31","ARO_description":"NDM-31 is a NDM beta-lactamase.","ARO_category":{"36196":{"category_aro_accession":"3000057","category_aro_cvterm_id":"36196","category_aro_name":"NDM beta-lactamase","category_aro_description":"NDM beta-lactamases or New Delhi metallo-beta-lactamases are class B beta-lactamases that confer resistance to a broad range of antibiotics including carbapenems, cephalosporins and penicillins.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4781":{"model_id":"4781","model_name":"OHIO-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"8119":{"protein_sequence":{"accession":"WP_063860895.1","sequence":"MRYFRLCIISLLATLPLRVHAGPQPLEQIKLSESQLSGSVGMIEMDLARPGTLTAWRADERFPMMSTFKVVLCGAGLARVDAGDEQLERKIHYRRQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLPAVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTARSMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGRLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIAGALIEHWQR"},"dna_sequence":{"accession":"NG_049352.1","fmin":"100","fmax":"961","strand":"+","sequence":"ATGCGTTATTTTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGCGGGTACACGCCGGACCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCAGCGTAGGCATGATAGAAATGGATCTGGCCAGGCCCGGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGGTCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCGACAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGCCAGCCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCGCCCGCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACGTTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGGATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGCCGGGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"45475","NCBI_taxonomy_name":"Plasmid PDS075","NCBI_taxonomy_id":"2474"}}}},"ARO_accession":"3006956","ARO_id":"45418","ARO_name":"OHIO-1","CARD_short_name":"OHIO-1","ARO_description":"OHIO-1 is a OHIO beta-lactamase.","ARO_category":{"43888":{"category_aro_accession":"3005428","category_aro_cvterm_id":"43888","category_aro_name":"OHIO beta-lactamase","category_aro_description":"OHIO beta-lactamases are class A beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4782":{"model_id":"4782","model_name":"OKP-A-17","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"8120":{"protein_sequence":{"accession":"WP_023289605.1","sequence":"MRYVRLCLFSLIAALPLAVFASPPPLEQVTRSESQLAGRVGYVEMDLASGRTLAAWRASERFPLMSTFKVLLCGAVLARVDAGDEQLDRRIRYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAGNLLLKSVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDVRDTTTPASMAATLRKLLTSHALSARSQQQLLQWMVDDQVAGPLIRAVLPAGWFIADKTGAGERGSRGIVALLGPNGKAERIVVIYLRDTPATMAERNQQIARIGAALIEHWQR"},"dna_sequence":{"accession":"NG_049361.1","fmin":"100","fmax":"961","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGCCTTTTCTCCCTGATTGCCGCCCTGCCACTGGCGGTATTCGCCAGCCCTCCGCCGCTTGAGCAAGTTACACGCAGCGAAAGTCAGCTGGCGGGCCGCGTGGGCTATGTTGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCAGTGAGCGCTTTCCGCTGATGAGCACCTTTAAAGTGCTGCTCTGCGGCGCGGTGCTGGCCCGGGTGGATGCCGGAGACGAACAGCTGGATCGGCGGATCCGCTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGCCGACGGGATGACCGTTGGCGAACTCTGCGCCGCCGCCATCACCATGAGCGACAACAGCGCCGGCAATCTGCTGTTGAAGAGCGTTGGCGGCCCCGCGGGATTGACCGCTTTTCTGCGCCAGATCGGTGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAGCTCAATGAAGCGCTTCCCGGCGACGTGCGCGACACCACCACCCCAGCCAGCATGGCCGCCACCCTGCGCAAGCTGCTAACCAGCCACGCGCTGAGCGCCCGTTCGCAGCAGCAGCTGCTGCAGTGGATGGTGGACGACCAGGTGGCCGGCCCGCTGATCCGCGCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAAACCGGGGCCGGCGAGCGGGGCTCACGCGGCATTGTCGCCCTCCTCGGCCCGAACGGCAAAGCGGAGCGCATCGTGGTGATCTATCTGCGGGATACGCCGGCGACCATGGCCGAGCGTAACCAGCAGATCGCCAGAATAGGCGCGGCGCTGATCGAGCACTGGCAGCGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43789","NCBI_taxonomy_name":"Klebsiella quasipneumoniae","NCBI_taxonomy_id":"1463165"}}}},"ARO_accession":"3006141","ARO_id":"44603","ARO_name":"OKP-A-17","CARD_short_name":"OKP-A-17","ARO_description":"OKP-A-17 is a OKP beta-lactamase.","ARO_category":{"38817":{"category_aro_accession":"3002417","category_aro_cvterm_id":"38817","category_aro_name":"OKP beta-lactamase","category_aro_description":"OKP beta-lactamases are chromosomal class A beta-lactamase that confer resistance to penicillins and early cephalosporins in Klebsiella pneumoniae. OKP beta-lactamases can be subdivided into two groups: OKP-A and OKP-B which diverge by about 4.2%.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4783":{"model_id":"4783","model_name":"OKP-B-16","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"7158":{"protein_sequence":{"accession":"WP_064183695.1","sequence":"MRYFRLCLISLIAALPLAVFASPQPLEQIKISESQLAGRVGYVEMDLASGRTLAAWRASERFPLMSTFKVLLCGAVLARVDAGDEQLDRRIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAGNLLLKIVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDVRDTTTPASMATTLRKLLTTPSLSARSQQQLLQWMVDDRVAGPLIRAVLPAGWFIADKTGAGERGSRGIVALLGPDGKAERIVVIYLRDTPATMVERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"NG_067146.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATTTTCGCCTGTGCCTTATCTCCCTGATTGCCGCCCTGCCACTGGCGGTATTCGCCAGCCCTCAGCCGCTTGAGCAGATTAAAATCAGCGAAAGTCAGCTGGCGGGCCGGGTGGGCTATGTTGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCAGTGAGCGCTTTCCGCTGATGAGCACCTTTAAAGTGCTGCTCTGCGGCGCGGTGCTGGCCCGGGTGGATGCCGGCGACGAACAGCTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGCCGACGGGATGACCGTTGGCGAACTCTGCGCCGCCGCCATCACCATGAGCGACAACAGCGCCGGCAATCTGCTGTTGAAGATCGTCGGCGGCCCCGCGGGATTGACCGCTTTTCTGCGCCAGATCGGTGACAACGTCACCCGTCTTGACCGCTGGGAAACGGAACTCAATGAGGCGCTTCCCGGCGACGTGCGCGACACCACCACCCCGGCCAGCATGGCCACCACCCTGCGCAAGCTGCTAACCACCCCCTCTCTGAGCGCCCGTTCGCAGCAGCAGCTGCTGCAGTGGATGGTTGACGACCGGGTGGCCGGCCCGTTGATCCGCGCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAAACCGGGGCCGGTGAGCGGGGCTCACGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAAGCGGAGCGTATCGTGGTGATCTATCTGCGTGATACCCCGGCGACCATGGTCGAGCGTAACCAGCAGATCGCCGGGATAGGCGCGGCGCTGATCGAGCACTGGCAGCGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43789","NCBI_taxonomy_name":"Klebsiella quasipneumoniae","NCBI_taxonomy_id":"1463165"}}}},"ARO_accession":"3006142","ARO_id":"44604","ARO_name":"OKP-B-16","CARD_short_name":"OKP-B-16","ARO_description":"OKP-B-16 is a OKP beta-lactamase.","ARO_category":{"38817":{"category_aro_accession":"3002417","category_aro_cvterm_id":"38817","category_aro_name":"OKP beta-lactamase","category_aro_description":"OKP beta-lactamases are chromosomal class A beta-lactamase that confer resistance to penicillins and early cephalosporins in Klebsiella pneumoniae. OKP beta-lactamases can be subdivided into two groups: OKP-A and OKP-B which diverge by about 4.2%.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4784":{"model_id":"4784","model_name":"OKP-B-21","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"7159":{"protein_sequence":{"accession":"WP_087833272.1","sequence":"MRYVRLCLISLIAALPLAVFASPQPLEQIKISEGQLAGRVGYVEMDLASGRTLAAWRASERFPLMSTFKVLLCGAVLARVDAGDEQLDRRIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAGNLLLKSVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDVRDTTTPASMATTLRKLLTTPSLSARSQQQLLQWMVDDQVAGPLIRAVLPAGWFIADKTGAGERGSRGIVALLGPDGKAERIVVIYLRDTAATMAERNEQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"NG_067147.1","fmin":"100","fmax":"961","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGCCTTATCTCACTGATTGCCGCCCTGCCACTGGCGGTATTCGCCAGCCCTCAGCCGCTTGAGCAGATTAAAATCAGCGAAGGTCAGCTGGCGGGCCGGGTGGGCTATGTTGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCAGTGAGCGCTTTCCGCTGATGAGCACCTTTAAAGTGCTGCTCTGCGGCGCTGTGCTGGCCCGGGTGGATGCCGGCGACGAACAGCTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGCCGACGGGATGACCGTTGGCGAACTCTGCGCCGCCGCCATCACCATGAGCGACAACAGCGCCGGCAATCTGCTGTTGAAGAGCGTCGGCGGCCCCGCGGGATTGACCGCTTTTCTGCGCCAGATCGGTGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTCAATGAGGCGCTTCCCGGCGACGTGCGCGACACCACCACCCCGGCCAGCATGGCCACCACCCTGCGCAAGTTGCTAACCACCCCCTCTCTGAGCGCCCGTTCGCAGCAGCAGCTGCTGCAGTGGATGGTGGACGACCAGGTGGCCGGCCCGTTGATCCGCGCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAAACCGGGGCCGGTGAGCGGGGCTCACGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAAGCGGAGCGTATCGTGGTGATCTATCTGCGGGATACCGCGGCGACCATGGCCGAACGTAACGAGCAGATCGCCGGGATAGGCGCGGCGCTGATCGAGCACTGGCAGCGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43789","NCBI_taxonomy_name":"Klebsiella quasipneumoniae","NCBI_taxonomy_id":"1463165"}}}},"ARO_accession":"3006143","ARO_id":"44605","ARO_name":"OKP-B-21","CARD_short_name":"OKP-B-21","ARO_description":"OKP-B-21 is a OKP beta-lactamase.","ARO_category":{"38817":{"category_aro_accession":"3002417","category_aro_cvterm_id":"38817","category_aro_name":"OKP beta-lactamase","category_aro_description":"OKP beta-lactamases are chromosomal class A beta-lactamase that confer resistance to penicillins and early cephalosporins in Klebsiella pneumoniae. OKP beta-lactamases can be subdivided into two groups: OKP-A and OKP-B which diverge by about 4.2%.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4785":{"model_id":"4785","model_name":"OKP-B-22","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"7160":{"protein_sequence":{"accession":"WP_122543028.1","sequence":"MRYVRLCLISLIAALPLAVFASPQPLEQIKISESQLAGRVGYVEMDLASGRTLAAWRASERFPLMSTFKVLLCGAVLARVDAGDEQLDRRIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAGNLLLKSVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDVRDTTTPASMATTLRKLLTTPSLSARSQQQLLQWMVDDRVAGPLIRAVLPAGWFIADKTGAGERGSRGIVALLGPDGKAERIVVIYLRDTAATMTERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"NG_067148.1","fmin":"100","fmax":"961","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGCCTTATCTCCCTGATTGCCGCCCTGCCACTGGCGGTATTCGCCAGCCCTCAGCCGCTTGAGCAGATTAAAATCAGCGAAAGTCAGCTGGCGGGCCGGGTGGGCTATGTTGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCAGTGAGCGCTTTCCGCTGATGAGCACCTTTAAAGTGCTGCTCTGCGGCGCGGTGCTGGCCCGGGTGGATGCCGGCGACGAACAGCTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGCCGACGGGATGACCGTTGGCGAACTCTGCGCCGCCGCCATCACCATGAGCGACAACAGCGCCGGCAATCTGCTGTTGAAGAGCGTCGGCGGCCCCGCGGGATTGACCGCTTTTCTGCGCCAGATCGGTGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTCAATGAGGCGCTTCCCGGCGACGTGCGCGACACCACCACCCCGGCCAGCATGGCCACCACCCTGCGCAAGCTGCTAACCACCCCCTCTCTGAGCGCCCGTTCGCAGCAGCAGCTGCTGCAGTGGATGGTGGACGACCGGGTGGCCGGCCCGTTGATCCGCGCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAAACCGGGGCCGGTGAGCGGGGCTCACGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAAGCGGAGCGTATCGTGGTGATCTATCTACGGGATACCGCGGCGACCATGACCGAACGTAACCAGCAGATCGCCGGGATAGGCGCGGCGCTGATCGAGCACTGGCAGCGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43789","NCBI_taxonomy_name":"Klebsiella quasipneumoniae","NCBI_taxonomy_id":"1463165"}}}},"ARO_accession":"3006144","ARO_id":"44606","ARO_name":"OKP-B-22","CARD_short_name":"OKP-B-22","ARO_description":"OKP-B-22 is a OKP beta-lactamase.","ARO_category":{"38817":{"category_aro_accession":"3002417","category_aro_cvterm_id":"38817","category_aro_name":"OKP beta-lactamase","category_aro_description":"OKP beta-lactamases are chromosomal class A beta-lactamase that confer resistance to penicillins and early cephalosporins in Klebsiella pneumoniae. OKP beta-lactamases can be subdivided into two groups: OKP-A and OKP-B which diverge by about 4.2%.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4786":{"model_id":"4786","model_name":"OKP-B-23","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"7161":{"protein_sequence":{"accession":"WP_023318187.1","sequence":"MRYVRLYLISLIAALPLAVFASPQPLEQIKISESQLAGRVGYVEMDLASGRTLAAWRASERFPLMSTFKVLLCGAVLARVDAGDEQLDRRIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAGNLLLKIVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDVRDTTTPASMATTLRKLLTTPSLSARSQQQLLQWMVDDRVAGPLIRAVLPAGWFIADKTGAGERGSRGIVALLGPDGKAERIVVIYLRDTAATMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"NG_050606.1","fmin":"100","fmax":"961","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTACCTTATCTCCCTGATTGCCGCCCTGCCACTGGCGGTATTCGCCAGCCCTCAGCCGCTTGAGCAGATTAAAATCAGCGAAAGTCAGCTGGCGGGCCGGGTGGGCTATGTTGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCAGTGAGCGCTTTCCGCTGATGAGCACCTTTAAAGTGCTGCTCTGCGGCGCGGTGCTGGCCCGGGTGGATGCCGGCGACGAACAGCTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGCCGACGGGATGACCGTTGGCGAACTCTGCGCCGCCGCCATCACCATGAGCGACAACAGCGCCGGCAATCTGCTGTTGAAGATCGTCGGCGGCCCCGCGGGATTGACCGCTTTTCTGCGCCAGATCGGTGACAACGTCACCCGTCTTGACCGCTGGGAAACGGAACTCAATGAGGCGCTTCCCGGCGACGTGCGCGACACCACCACCCCGGCCAGCATGGCCACCACCCTGCGCAAGCTGCTAACCACCCCCTCTCTGAGCGCCCGTTCGCAGCAGCAGCTGCTGCAGTGGATGGTTGACGACCGGGTGGCCGGCCCGTTGATCCGCGCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAAACCGGGGCCGGTGAGCGGGGCTCACGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAAGCGGAGCGTATCGTGGTGATCTATCTGCGGGATACCGCAGCGACCATGGCCGAACGTAACCAGCAGATCGCCGGGATAGGCGCGGCGCTGATCGAACACTGGCAGCGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37059","NCBI_taxonomy_name":"Klebsiella","NCBI_taxonomy_id":"570"}}}},"ARO_accession":"3006145","ARO_id":"44607","ARO_name":"OKP-B-23","CARD_short_name":"OKP-B-23","ARO_description":"OKP-B-23 is a OKP beta-lactamase.","ARO_category":{"38817":{"category_aro_accession":"3002417","category_aro_cvterm_id":"38817","category_aro_name":"OKP beta-lactamase","category_aro_description":"OKP beta-lactamases are chromosomal class A beta-lactamase that confer resistance to penicillins and early cephalosporins in Klebsiella pneumoniae. OKP beta-lactamases can be subdivided into two groups: OKP-A and OKP-B which diverge by about 4.2%.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4787":{"model_id":"4787","model_name":"OKP-B-24","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"7162":{"protein_sequence":{"accession":"WP_156404657.1","sequence":"MRYVRLCLISLIAALPLAVFASPQPLEQIKISESQLAGRVGYVEMDLASGRTLAAWRASERFPLMSTFKVLLCGAVLARVDAGDEQLDRRIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNTAGNLLLKIVSGPAGLTAFLRQFGDNVTRLDRWETELNEALPGDVRDTTTPASMATTLRKLLTTPSLSARSQQQLLQWMVDDRVAGPLIRAVLPAGWFIADKTGAGERGSRGIVALLGPDGKAERIVVIYLRDTPATMVERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"NG_067149.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGCCTTATCTCCCTGATTGCCGCCCTGCCACTGGCGGTATTCGCCAGCCCTCAGCCGCTTGAGCAGATTAAAATCAGCGAAAGTCAGCTGGCGGGCCGGGTGGGCTATGTTGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCAGTGAGCGCTTTCCGCTGATGAGCACCTTTAAAGTGCTGCTCTGCGGCGCGGTGCTGGCCCGGGTGGATGCCGGCGACGAACAGCTGGATCGGCGGATCCACTACCGTCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGCCGACGGGATGACCGTTGGCGAACTCTGCGCCGCCGCCATCACCATGAGCGACAACACCGCCGGCAATCTGCTGTTGAAGATCGTCAGCGGCCCCGCGGGATTGACCGCTTTTCTGCGCCAGTTCGGTGACAACGTCACCCGTCTTGACCGCTGGGAAACGGAACTCAATGAGGCGCTTCCCGGCGACGTGCGCGACACCACCACCCCGGCCAGCATGGCCACCACCCTGCGCAAGCTGCTAACCACCCCCTCTCTGAGCGCCCGTTCGCAGCAGCAGCTGCTGCAGTGGATGGTGGACGACCGGGTGGCCGGCCCGTTGATCCGCGCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAAACCGGGGCCGGTGAGCGGGGCTCACGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAAGCGGAGCGTATCGTGGTGATCTATCTGCGTGATACCCCGGCGACCATGGTCGAGCGTAACCAGCAGATCGCCGGGATAGGCGCGGCGCTGATCGAGCACTGGCAGCGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43789","NCBI_taxonomy_name":"Klebsiella quasipneumoniae","NCBI_taxonomy_id":"1463165"}}}},"ARO_accession":"3006146","ARO_id":"44608","ARO_name":"OKP-B-24","CARD_short_name":"OKP-B-24","ARO_description":"OKP-B-24 is a OKP beta-lactamase.","ARO_category":{"38817":{"category_aro_accession":"3002417","category_aro_cvterm_id":"38817","category_aro_name":"OKP beta-lactamase","category_aro_description":"OKP beta-lactamases are chromosomal class A beta-lactamase that confer resistance to penicillins and early cephalosporins in Klebsiella pneumoniae. OKP beta-lactamases can be subdivided into two groups: OKP-A and OKP-B which diverge by about 4.2%.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4788":{"model_id":"4788","model_name":"OKP-B-34","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"7163":{"protein_sequence":{"accession":"WP_087771722.1","sequence":"MRYVRLCLISLIAALPLAVFASPQPLEQIKISESQLAGRVGYVEMDLASGRTLAAWRASERFPLMSTFKVLLCGAVLARVDAGDEQLDRRIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNTAGNLLLKIVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDVRDTTTPASMATTLRKLLTTPSLSARSQQQLLQWMVDDRVAGPLIRAVLPAGWFIADKTGAGERGSRGIVALLGPDGKAERIVVIYLRDTAATMAERNQQIAVIGAALIEHWQR"},"dna_sequence":{"accession":"NG_067150.1","fmin":"100","fmax":"961","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGCCTTATCTCCCTGATTGCCGCCCTGCCACTGGCGGTATTCGCCAGCCCTCAGCCGCTTGAGCAGATTAAAATCAGCGAAAGTCAGCTGGCGGGCCGGGTGGGCTATGTTGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCAGTGAGCGCTTTCCGCTGATGAGCACCTTTAAAGTGCTGCTCTGCGGCGCGGTGCTGGCCCGGGTGGATGCCGGCGACGAACAGCTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGCCGACGGGATGACCGTTGGCGAACTCTGCGCCGCCGCCATCACCATGAGCGACAACACCGCCGGCAATCTGCTGTTGAAGATCGTCGGCGGCCCCGCGGGATTGACCGCTTTTCTGCGCCAGATCGGTGACAACGTCACCCGTCTTGACCGCTGGGAAACGGAACTCAATGAGGCGCTTCCCGGCGACGTGCGCGACACCACCACCCCGGCCAGCATGGCCACCACCCTGCGCAAGCTGCTAACCACCCCCTCTCTGAGCGCCCGTTCGCAGCAGCAGCTGCTGCAGTGGATGGTTGACGACCGGGTGGCCGGCCCGTTGATCCGCGCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAAACCGGGGCCGGTGAGCGGGGCTCACGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAAGCGGAGCGTATCGTGGTGATCTATCTGCGGGATACCGCAGCGACCATGGCCGAACGTAACCAGCAGATCGCCGTGATAGGCGCGGCGCTGATCGAGCACTGGCAGCGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37059","NCBI_taxonomy_name":"Klebsiella","NCBI_taxonomy_id":"570"}}}},"ARO_accession":"3006147","ARO_id":"44609","ARO_name":"OKP-B-34","CARD_short_name":"OKP-B-34","ARO_description":"OKP-B-34 is a OKP beta-lactamase.","ARO_category":{"38817":{"category_aro_accession":"3002417","category_aro_cvterm_id":"38817","category_aro_name":"OKP beta-lactamase","category_aro_description":"OKP beta-lactamases are chromosomal class A beta-lactamase that confer resistance to penicillins and early cephalosporins in Klebsiella pneumoniae. OKP beta-lactamases can be subdivided into two groups: OKP-A and OKP-B which diverge by about 4.2%.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4789":{"model_id":"4789","model_name":"OKP-B-36","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"7164":{"protein_sequence":{"accession":"WP_060655783.1","sequence":"MRYVRLCLISLITALPLAVFASPQPLEQIKISESQLAGRVGYVEMDLASGRTLAAWRASERFPLMSTFKVLLCGAVLARVDAGDEQLDRRIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAGNLLLKIVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDVRDTTTPASMATTLRKLLTTPSLSARSQQQLLQWMVDDRVAGPLIRAVLPAGWFIADKTGAGERGSRGIVALLGPDGKAERIVVIYLRDTAATMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"NG_067151.1","fmin":"100","fmax":"961","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGCCTTATCTCCCTGATTACCGCCCTGCCACTGGCGGTATTCGCCAGCCCTCAGCCGCTTGAGCAGATTAAAATCAGCGAAAGTCAGCTGGCGGGCCGGGTGGGCTATGTTGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCAGTGAGCGCTTTCCGCTGATGAGCACCTTTAAAGTGCTGCTCTGCGGCGCGGTGCTGGCCCGGGTGGATGCCGGCGACGAACAGCTGGATCGGCGGATTCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGCCGACGGGATGACCGTTGGCGAACTCTGCGCCGCCGCCATCACCATGAGCGACAACAGCGCCGGCAATCTGCTGTTGAAGATCGTCGGCGGCCCTGCGGGATTGACCGCTTTTCTGCGCCAGATCGGTGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTCAATGAGGCGCTTCCCGGCGACGTGCGCGACACCACCACCCCGGCCAGCATGGCCACCACCCTGCGCAAGTTGCTAACCACCCCCTCTCTGAGCGCCCGTTCGCAGCAGCAGCTGCTGCAGTGGATGGTGGACGACCGGGTGGCCGGCCCGTTGATCCGCGCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAAACCGGGGCCGGTGAGCGGGGCTCACGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAAGCGGAGCGTATCGTGGTGATCTATCTGCGGGATACCGCGGCGACCATGGCCGAACGTAACCAGCAGATCGCCGGGATAGGCGCGGCGCTGATCGAGCACTGGCAGCGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43789","NCBI_taxonomy_name":"Klebsiella quasipneumoniae","NCBI_taxonomy_id":"1463165"}}}},"ARO_accession":"3006148","ARO_id":"44610","ARO_name":"OKP-B-36","CARD_short_name":"OKP-B-36","ARO_description":"OKP-B-36 is a OKP beta-lactamase.","ARO_category":{"38817":{"category_aro_accession":"3002417","category_aro_cvterm_id":"38817","category_aro_name":"OKP beta-lactamase","category_aro_description":"OKP beta-lactamases are chromosomal class A beta-lactamase that confer resistance to penicillins and early cephalosporins in Klebsiella pneumoniae. OKP beta-lactamases can be subdivided into two groups: OKP-A and OKP-B which diverge by about 4.2%.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4790":{"model_id":"4790","model_name":"OKP-B-40","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"7165":{"protein_sequence":{"accession":"WP_114508147.1","sequence":"MRYVRLCLISLIAALPLAVFASPQPLEQIKISESQLAGRVGYVEMDLASGRTLAAWRASERFPLMSTFKVLLCGAVLARVDAGDEQLDRRIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNTAGNLLLKIVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDVRDTTTPASMATTLRRLLTTPSLSARSQQQLLQWMVDDRVAGPLIRAVLPAGWFIADKTGAGERGSRGIVALLGPDGKAERIVVIYLRDTAATMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"NG_067152.1","fmin":"100","fmax":"961","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGCCTTATCTCCCTGATTGCCGCCCTGCCACTGGCGGTATTCGCCAGCCCTCAGCCGCTTGAGCAGATTAAAATCAGCGAAAGTCAGCTGGCGGGCCGGGTGGGCTATGTTGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCAGTGAGCGCTTTCCGCTGATGAGCACCTTTAAAGTGCTGCTCTGCGGCGCGGTGCTGGCCCGGGTGGATGCCGGCGACGAACAGCTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGCCGACGGGATGACCGTTGGCGAACTCTGCGCCGCCGCCATCACCATGAGCGACAACACCGCCGGCAATCTGCTGTTGAAGATCGTCGGCGGCCCCGCGGGATTGACCGCTTTTCTGCGCCAGATCGGTGACAACGTCACCCGTCTTGACCGCTGGGAAACGGAACTCAATGAGGCGCTTCCCGGCGACGTGCGCGACACCACCACCCCGGCCAGCATGGCCACCACCCTGCGCAGGCTGCTAACCACCCCCTCTCTGAGCGCCCGTTCGCAGCAGCAGCTGCTGCAGTGGATGGTGGACGACCGGGTGGCCGGCCCGTTGATCCGCGCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAAACCGGGGCCGGTGAGCGGGGCTCACGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAAGCGGAGCGTATCGTGGTGATCTATCTACGGGATACCGCGGCGACCATGGCCGAACGTAACCAGCAGATCGCCGGGATAGGCGCGGCGCTGATCGAGCACTGGCAGCGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43789","NCBI_taxonomy_name":"Klebsiella quasipneumoniae","NCBI_taxonomy_id":"1463165"}}}},"ARO_accession":"3006149","ARO_id":"44611","ARO_name":"OKP-B-40","CARD_short_name":"OKP-B-40","ARO_description":"OKP-B-40 is a OKP beta-lactamase.","ARO_category":{"38817":{"category_aro_accession":"3002417","category_aro_cvterm_id":"38817","category_aro_name":"OKP beta-lactamase","category_aro_description":"OKP beta-lactamases are chromosomal class A beta-lactamase that confer resistance to penicillins and early cephalosporins in Klebsiella pneumoniae. OKP beta-lactamases can be subdivided into two groups: OKP-A and OKP-B which diverge by about 4.2%.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4791":{"model_id":"4791","model_name":"OKP-B-41","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"7166":{"protein_sequence":{"accession":"WP_049003700.1","sequence":"MRYVRLCLISLIAALPLAVFASPQPLEQIKISEGQLAGRVGYVEMDLASGRTLAAWRASERFPLMSTFKVLLCGAVLARVDAGDEQLDRRIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAGNLLLKIVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDVRDTTTPASMATTLRKLLTTPSLSARSQQQLLQWMVDDRVAGPLIRAVLPAGWFIADKTGAGERGSRGIVALLGPDGKAERIVVIYLRDTAATMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"NG_067153.1","fmin":"100","fmax":"961","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGCCTTATCTCCCTGATTGCCGCCCTGCCACTGGCGGTATTCGCCAGCCCTCAGCCGCTTGAGCAGATTAAAATCAGCGAAGGTCAGCTGGCGGGCCGGGTGGGCTATGTTGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCAGTGAGCGCTTTCCGCTGATGAGCACCTTTAAAGTGCTGCTCTGCGGCGCGGTGCTGGCCCGGGTGGATGCCGGCGACGAACAGCTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGCCGACGGGATGACCGTTGGCGAACTCTGCGCCGCCGCCATCACCATGAGCGACAACAGCGCCGGCAATCTGCTGTTGAAGATCGTCGGCGGCCCTGCGGGATTGACCGCTTTTCTGCGCCAGATCGGTGACAACGTCACCCGTCTTGACCGCTGGGAAACGGAACTCAATGAGGCGCTTCCCGGCGACGTGCGCGACACCACCACCCCGGCCAGCATGGCCACCACCCTGCGCAAGCTGCTAACCACCCCCTCTCTGAGCGCCCGCTCGCAGCAGCAGCTGCTGCAGTGGATGGTTGACGACCGGGTGGCCGGCCCGTTGATCCGCGCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAAACCGGGGCCGGTGAGCGGGGCTCACGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAAGCGGAGCGTATCGTGGTGATCTATCTGCGGGATACCGCAGCGACCATGGCCGAACGTAACCAGCAGATCGCCGGGATAGGCGCGGCGCTGATCGAACACTGGCAGCGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43789","NCBI_taxonomy_name":"Klebsiella quasipneumoniae","NCBI_taxonomy_id":"1463165"}}}},"ARO_accession":"3006150","ARO_id":"44612","ARO_name":"OKP-B-41","CARD_short_name":"OKP-B-41","ARO_description":"OKP-B-41 is a OKP beta-lactamase.","ARO_category":{"38817":{"category_aro_accession":"3002417","category_aro_cvterm_id":"38817","category_aro_name":"OKP beta-lactamase","category_aro_description":"OKP beta-lactamases are chromosomal class A beta-lactamase that confer resistance to penicillins and early cephalosporins in Klebsiella pneumoniae. OKP beta-lactamases can be subdivided into two groups: OKP-A and OKP-B which diverge by about 4.2%.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4792":{"model_id":"4792","model_name":"OKP-B-45","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"7167":{"protein_sequence":{"accession":"WP_048324114.1","sequence":"MRYVRLCLISLIAALPLAVFASPQPLEQIKISEGQLAGRVGYVEMDLASGRTLAAWRASERFPLMSTFKVLLCGAVLARVDAGDEQLDRRIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNTAGNLLLKIVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDVRDTTTPASMATTLRKLLTTPSLSARSQQQLLQWMVDDRVAGPLIRAVLPAGWFIADKTGAGERGSRGIVALLGPDGKAERIVVIYLRDTPATMVERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"NG_067154.1","fmin":"100","fmax":"961","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGCCTTATCTCCCTGATTGCCGCCCTGCCACTGGCGGTATTCGCCAGCCCTCAGCCGCTTGAGCAGATTAAAATCAGCGAAGGTCAGCTGGCGGGCCGGGTGGGCTATGTTGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCAGTGAGCGCTTTCCGCTGATGAGCACCTTTAAAGTGCTGCTCTGCGGCGCGGTGCTGGCCCGGGTGGATGCCGGCGACGAACAGCTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGCCGACGGGATGACCGTTGGCGAACTCTGCGCCGCCGCCATCACCATGAGCGACAACACCGCCGGCAATCTGCTGTTGAAGATCGTCGGCGGCCCCGCGGGATTGACCGCTTTTCTGCGCCAGATCGGTGACAACGTCACCCGTCTTGACCGCTGGGAAACGGAACTCAATGAGGCGCTTCCCGGCGACGTGCGCGACACCACCACCCCGGCCAGCATGGCCACCACCCTGCGCAAGCTGCTAACCACCCCCTCTCTGAGCGCCCGTTCGCAGCAGCAGCTGCTGCAGTGGATGGTTGACGACCGGGTGGCCGGCCCGTTGATCCGCGCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAAACCGGGGCCGGTGAGCGGGGCTCACGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAAGCGGAGCGTATCGTGGTGATCTATCTGCGTGATACCCCGGCGACCATGGTCGAGCGTAACCAGCAGATCGCCGGGATAGGCGCGGCGCTGATCGAGCACTGGCAGCGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43789","NCBI_taxonomy_name":"Klebsiella quasipneumoniae","NCBI_taxonomy_id":"1463165"}}}},"ARO_accession":"3006151","ARO_id":"44613","ARO_name":"OKP-B-45","CARD_short_name":"OKP-B-45","ARO_description":"OKP-B-45 is a OKP beta-lactamase.","ARO_category":{"38817":{"category_aro_accession":"3002417","category_aro_cvterm_id":"38817","category_aro_name":"OKP beta-lactamase","category_aro_description":"OKP beta-lactamases are chromosomal class A beta-lactamase that confer resistance to penicillins and early cephalosporins in Klebsiella pneumoniae. OKP beta-lactamases can be subdivided into two groups: OKP-A and OKP-B which diverge by about 4.2%.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4793":{"model_id":"4793","model_name":"OKP-C-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"7168":{"protein_sequence":{"accession":"WP_136034107.1","sequence":"MRYVRLCVISLLASLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVLLCGAVLARVDAGDEQLERRIHYRQQDLVAYSPVSEKHLADGMTVGELCTAAITMSDNSAANLLLGTVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTAQHLSARSQQQLLQWMVDDRVAGPLIRAVVPPGWFIADKTGAGERGARGIVALLGPDGKPERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"NG_067155.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATGTTCGCCTGTGTGTTATCTCCCTGTTAGCCTCCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTGGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTACTGCTCTGCGGCGCGGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGACGGATCCATTACCGCCAGCAGGATCTGGTGGCTTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGGATGACGGTCGGCGAACTCTGCACCGCCGCCATCACTATGAGCGATAATAGCGCCGCCAATCTGCTGCTGGGCACCGTCGGCGGCCCTGCGGGATTGACTGCCTTTCTGCGCCAGATCGGTGACAACGTCACGCGCCTTGACCGCTGGGAAACAGAACTGAATGAGGCGCTTCCCGGCGACGCGCGCGACACCACCACCCCGGCCAGCATGGCCGCCACGCTGCGTAAACTACTGACCGCACAACATCTGAGCGCCCGTTCGCAACAGCAGCTTCTGCAGTGGATGGTAGACGATCGGGTTGCCGGCCCGCTGATCCGCGCCGTAGTGCCGCCGGGCTGGTTTATCGCCGATAAGACCGGGGCTGGCGAACGGGGTGCGCGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAACCGGAGCGCATTGTGGTGATCTATCTGCGGGATACCCCGGCGAGTATGGCCGAGCGTAACCAGCAGATCGCCGGGATAGGTGCCGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3006152","ARO_id":"44614","ARO_name":"OKP-C-1","CARD_short_name":"OKP-C-1","ARO_description":"OKP-C-1 is a OKP beta-lactamase.","ARO_category":{"38817":{"category_aro_accession":"3002417","category_aro_cvterm_id":"38817","category_aro_name":"OKP beta-lactamase","category_aro_description":"OKP beta-lactamases are chromosomal class A beta-lactamase that confer resistance to penicillins and early cephalosporins in Klebsiella pneumoniae. OKP beta-lactamases can be subdivided into two groups: OKP-A and OKP-B which diverge by about 4.2%.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4794":{"model_id":"4794","model_name":"OKP-D-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"7169":{"protein_sequence":{"accession":"WP_080897395.1","sequence":"MRYVHLCVISLFACLPLPLFAGPQPLEQIKISESQLSGRVGYVEMDLASGRTLAAWRADERFPLTSTFKVLLCGAVLARVDAGVERLDRRIHYRQQDLVAYSPVSEKHLADGMTVGELCAAAITMSDNSAGNLLLDTLGGPAGLTAFLRTIGDNVTRLDRRETQLNEALPGDVRDTTTPASMAATLRKLLTAKHLSARSQQQLVQWMVDDRVAGPLIRAVLPAGWFIADKTGAGERGARGIVALLGPDGKAERIVVIYMRDTPATIAERNQQIAAIGAALIEHWQR"},"dna_sequence":{"accession":"NG_067156.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATGTTCACCTGTGTGTTATCTCCCTGTTCGCCTGCCTGCCACTGCCGCTATTCGCCGGTCCACAGCCGCTCGAGCAGATAAAAATAAGCGAAAGCCAGCTGTCGGGCCGCGTGGGCTATGTCGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCGATGAACGTTTTCCGCTCACCAGCACCTTTAAAGTCCTGCTCTGCGGCGCGGTGCTGGCCCGGGTGGATGCCGGGGTCGAACGACTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGCGTATTCCCCGGTCAGCGAAAAACACCTTGCCGACGGGATGACGGTCGGCGAACTCTGCGCCGCCGCCATCACCATGAGCGATAACAGTGCCGGCAATCTGCTGCTGGACACCCTCGGCGGTCCGGCGGGATTGACGGCTTTTCTGCGCACTATTGGTGACAACGTCACGCGCCTTGACCGCCGGGAAACGCAACTGAATGAGGCGCTGCCCGGCGACGTGCGCGACACCACCACCCCGGCCAGCATGGCCGCCACGCTGCGCAAACTACTGACCGCGAAGCATCTGAGCGCCCGTTCGCAACAGCAGCTCGTGCAGTGGATGGTGGACGATCGGGTTGCCGGCCCGCTGATCCGCGCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAAACCGGGGCTGGCGAACGGGGTGCGCGCGGCATCGTCGCCCTGCTCGGCCCGGACGGCAAAGCGGAGCGCATTGTGGTGATTTATATGCGGGATACGCCGGCGACCATCGCCGAGCGTAACCAGCAGATCGCCGCTATCGGCGCGGCGCTGATCGAGCACTGGCAGCGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3006153","ARO_id":"44615","ARO_name":"OKP-D-1","CARD_short_name":"OKP-D-1","ARO_description":"OKP-D-1 is a OKP beta-lactamase.","ARO_category":{"38817":{"category_aro_accession":"3002417","category_aro_cvterm_id":"38817","category_aro_name":"OKP beta-lactamase","category_aro_description":"OKP beta-lactamases are chromosomal class A beta-lactamase that confer resistance to penicillins and early cephalosporins in Klebsiella pneumoniae. OKP beta-lactamases can be subdivided into two groups: OKP-A and OKP-B which diverge by about 4.2%.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4795":{"model_id":"4795","model_name":"ORN-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"575"}},"model_sequences":{"sequence":{"7170":{"protein_sequence":{"accession":"WP_004862397.1","sequence":"MRQYRFALLPLLAALALPGWAHEATVTTVKQAESQLQGRVGYAELDLASGQLLSGYRAGERFPMMSTFKVLLCGAVLSRVDTGEEQLDRRIHYRQQDLVEYSPVTEKHLADGLTVGELCAAAITLSDNTAANLLLTTLGGPQGLTTFLRHSGDQTSRLDRWETELNEARPGDVRDTTTPEAMARTLRNLLTGRVLSPASQQQLQRWMVEDKVAGPLLRSALPAGWFIADKTGAGNRGSRGIIAALGPDGKAARIVVIYLTATPASMDERNKQIAAIGETLVRHWSKDDKRP"},"dna_sequence":{"accession":"NG_049386.1","fmin":"100","fmax":"976","strand":"+","sequence":"ATGCGTCAATATCGATTCGCCCTTCTGCCATTGTTAGCCGCCCTGGCGCTCCCCGGTTGGGCGCATGAAGCCACGGTGACGACGGTTAAACAAGCCGAAAGCCAGCTGCAGGGCCGGGTCGGCTACGCCGAACTGGATTTAGCTTCCGGCCAACTGCTGTCCGGCTATCGCGCTGGCGAACGCTTCCCGATGATGAGCACCTTTAAAGTGCTGCTCTGCGGCGCAGTCTTGTCGCGCGTCGATACCGGTGAAGAACAGCTCGATCGCCGTATCCATTACCGGCAGCAGGATCTGGTGGAATACTCGCCGGTGACGGAGAAGCATCTTGCCGATGGGCTCACCGTGGGCGAACTGTGCGCGGCCGCCATTACCCTGAGCGATAATACGGCGGCAAACCTGCTGTTGACCACTCTCGGCGGCCCGCAGGGGCTGACCACGTTCCTGCGCCACAGCGGCGACCAGACTTCGCGACTCGACCGGTGGGAAACGGAACTCAATGAAGCGCGGCCGGGCGATGTGCGTGATACGACGACTCCGGAAGCGATGGCCAGGACACTGCGAAATCTGTTGACCGGCCGCGTGCTTTCCCCCGCCTCGCAGCAGCAGTTGCAACGCTGGATGGTAGAGGACAAAGTTGCGGGGCCGCTGTTGCGCTCTGCGCTGCCGGCGGGCTGGTTTATTGCCGATAAGACCGGAGCCGGCAATCGCGGCTCGCGCGGAATCATCGCCGCTCTCGGTCCGGACGGTAAAGCCGCGCGCATCGTGGTGATTTATTTAACCGCAACCCCGGCCTCAATGGATGAGCGCAATAAACAGATTGCGGCCATCGGTGAAACGCTGGTCAGGCACTGGTCCAAAGACGATAAAAGACCCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41224","NCBI_taxonomy_name":"Raoultella","NCBI_taxonomy_id":"160674"}}}},"ARO_accession":"3006957","ARO_id":"45419","ARO_name":"ORN-1","CARD_short_name":"ORN-1","ARO_description":"ORN-1 is a ORN beta-lactamase.","ARO_category":{"43889":{"category_aro_accession":"3005429","category_aro_cvterm_id":"43889","category_aro_name":"ORN beta-lactamase","category_aro_description":"ORN beta-lactamases are class A beta-lactamases found in Raoultella ornithinolytica.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4796":{"model_id":"4796","model_name":"ORN-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"575"}},"model_sequences":{"sequence":{"7171":{"protein_sequence":{"accession":"WP_063860932.1","sequence":"MRQYRLALLPLLAALALPGWAHEATVTTVKQAESQLQGRVGYAELDLASGQLLSGYRAGERFPMMSTFKVLLCGAVLSRVDTGEEQLDRRIHYRQQDLVEYSPVTEKHLADGLTVGELCAAAITLSDNTAANLLLTTLGGPQGLTTFLRHSGDQTSRLDRWETELNEARPGDVRDTTTPEAMARTLRNLLTGRVLSPASQQQLQRWMVEDKVAGPLLRSALPAGWFIADKTGAGNRGSRGIIAALGPDGKAARIVVIYLTATPASMDERNKQIAAIGETLVRHWSKDDKRP"},"dna_sequence":{"accession":"NG_049387.1","fmin":"100","fmax":"976","strand":"+","sequence":"ATGCGTCAATATCGACTCGCCCTTCTGCCATTGTTAGCCGCCCTGGCGCTCCCCGGTTGGGCGCATGAAGCCACGGTGACGACGGTTAAACAAGCCGAAAGCCAGCTGCAGGGCCGGGTCGGCTACGCCGAACTGGATTTAGCTTCCGGCCAACTGCTGTCCGGCTATCGCGCTGGCGAACGCTTCCCGATGATGAGCACCTTTAAAGTGCTGCTCTGCGGCGCAGTCTTGTCGCGCGTCGATACCGGTGAAGAACAGCTCGATCGCCGTATCCATTACCGGCAGCAGGATCTGGTGGAATACTCGCCGGTGACGGAGAAGCATCTTGCCGATGGGCTCACCGTGGGCGAACTGTGCGCGGCCGCCATTACCCTGAGCGATAATACGGCGGCAAACCTGCTGTTGACCACTCTCGGCGGCCCGCAGGGGCTGACCACGTTCCTGCGCCACAGCGGCGACCAGACTTCGCGACTCGACCGGTGGGAAACGGAACTCAATGAAGCGCGGCCGGGCGATGTGCGTGATACGACGACTCCGGAAGCGATGGCCAGGACACTGCGAAATCTGTTGACCGGCCGCGTGCTTTCCCCCGCCTCGCAGCAGCAGTTGCAACGCTGGATGGTAGAGGACAAAGTTGCGGGGCCGCTGTTGCGCTCTGCGCTGCCGGCGGGCTGGTTTATTGCCGATAAGACCGGAGCCGGCAATCGCGGCTCGCGCGGAATCATCGCCGCTCTCGGTCCGGACGGTAAAGCCGCGCGCATCGTGGTGATTTATTTAACCGCAACCCCGGCCTCAATGGATGAGCGCAATAAACAGATTGCGGCCATCGGTGAAACGCTGGTCAGGCACTGGTCCAAAGACGATAAAAGACCCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3006958","ARO_id":"45420","ARO_name":"ORN-2","CARD_short_name":"ORN-2","ARO_description":"ORN-2 is a ORN beta-lactamase.","ARO_category":{"43889":{"category_aro_accession":"3005429","category_aro_cvterm_id":"43889","category_aro_name":"ORN beta-lactamase","category_aro_description":"ORN beta-lactamases are class A beta-lactamases found in Raoultella ornithinolytica.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4797":{"model_id":"4797","model_name":"ORN-3","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"575"}},"model_sequences":{"sequence":{"7172":{"protein_sequence":{"accession":"WP_063860933.1","sequence":"MRQYRFALLPLLAALALPGWAHEATVTTVKQAESQLQGRVGYAELDLASGQLLSGYCAGERFPMMSTFKVLLCGAVLSRVDTGEEQLDRRIHYRQQDLVEYSPVTEKHLADGLTVGELCAAAITLSDNTAANLLLTTLGGPQGLTTFLRHSGDQTSRLDRWETELNEARPGDVRDTTTPEAMARTLRNLLTGRVLSPASQQQLQRWMVEDKVAGPLLRSALPAGWFIADKTGAGNRGSRGIIAALGPDGKAARIVVIYLTATPASMDERNKQIAAIGETLVRHWSKDDKRP"},"dna_sequence":{"accession":"NG_049388.1","fmin":"100","fmax":"976","strand":"+","sequence":"ATGCGTCAATATCGATTCGCCCTTCTGCCATTGTTAGCCGCCCTGGCGCTCCCCGGTTGGGCGCATGAAGCCACGGTGACGACGGTTAAACAAGCCGAAAGCCAGCTGCAGGGCCGGGTCGGCTACGCCGAACTGGATTTAGCTTCCGGCCAACTGCTGTCCGGCTATTGCGCTGGCGAACGCTTCCCGATGATGAGCACCTTTAAAGTGCTGCTCTGCGGCGCAGTCTTGTCGCGCGTCGATACCGGTGAAGAACAGCTCGATCGCCGTATCCATTACCGGCAGCAGGATCTGGTGGAATACTCGCCGGTGACGGAGAAGCATCTTGCCGATGGGCTCACCGTGGGCGAACTGTGCGCGGCCGCCATTACCCTGAGCGATAATACGGCGGCAAACCTGCTGTTGACCACTCTCGGCGGCCCGCAGGGGCTGACCACGTTCCTGCGCCACAGCGGCGACCAGACTTCGCGACTCGACCGGTGGGAAACGGAACTCAATGAAGCGCGGCCGGGCGATGTGCGTGATACGACGACTCCGGAAGCGATGGCCAGGACACTGCGAAATCTGTTGACCGGCCGCGTGCTTTCCCCCGCCTCGCAGCAGCAGTTGCAACGCTGGATGGTAGAGGACAAAGTTGCGGGGCCGCTGTTGCGCTCAGCGCTGCCGGCGGGCTGGTTTATTGCCGATAAGACCGGAGCCGGCAACCGCGGCTCGCGCGGAATCATCGCCGCTCTCGGTCCGGACGGTAAAGCCGCGCGCATCGTGGTGATTTATTTAACCGCAACCCCGGCCTCAATGGATGAGCGCAATAAACAGATTGCGGCCATCGGTGAAACGCTGGTCAGGCACTGGTCCAAAGACGATAAAAGACCCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3006959","ARO_id":"45421","ARO_name":"ORN-3","CARD_short_name":"ORN-3","ARO_description":"ORN-3 is a ORN beta-lactamase.","ARO_category":{"43889":{"category_aro_accession":"3005429","category_aro_cvterm_id":"43889","category_aro_name":"ORN beta-lactamase","category_aro_description":"ORN beta-lactamases are class A beta-lactamases found in Raoultella ornithinolytica.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4798":{"model_id":"4798","model_name":"ORN-4","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"575"}},"model_sequences":{"sequence":{"7173":{"protein_sequence":{"accession":"WP_063860934.1","sequence":"MRQYRFALLPLLAALALPGWAHEATVTTVKQAESQLQGRVGYAELDLASGQLLSGYRAGERFPMMSTFKVLLCGAVLSRVDTGEEQLDRRIHYRQQDLVEYSPVTEKHLADGLNVGELCAAAITLSDNTAANLLLTTLGGPQGLTTFLRHSGDQTSRLDRWETELNEARPGDVRDTTTPEAMARTLRNLLTGRVLSPASQQQLQRWMVEDKVAGPLLRSALPAGWFIADKTGAGNRGSRGIIAALGPDGKAARIVVIYLTATPASMDERNKQIAAIGETLVRHWSKDDKRP"},"dna_sequence":{"accession":"NG_049389.1","fmin":"100","fmax":"976","strand":"+","sequence":"ATGCGTCAATATCGATTCGCCCTTCTGCCATTGTTAGCCGCCCTGGCGCTCCCCGGTTGGGCGCATGAAGCCACGGTGACGACGGTTAAACAAGCCGAAAGCCAGCTGCAGGGCCGGGTCGGCTACGCCGAACTGGATTTAGCTTCCGGCCAACTGCTGTCCGGCTATCGCGCTGGCGAACGCTTCCCGATGATGAGCACCTTTAAAGTGCTGCTCTGCGGCGCAGTCTTGTCGCGCGTCGATACCGGTGAAGAACAGCTCGATCGCCGTATCCATTACCGGCAGCAGGATCTGGTGGAATACTCGCCGGTGACGGAGAAGCATCTTGCCGATGGGCTCAACGTGGGCGAACTGTGCGCGGCCGCCATTACCCTGAGCGATAATACGGCGGCAAACCTGCTGTTGACCACTCTCGGCGGCCCGCAGGGGCTGACCACGTTCCTGCGCCACAGCGGCGACCAGACTTCGCGACTCGACCGGTGGGAAACGGAACTCAATGAAGCGCGGCCGGGCGATGTGCGTGATACGACGACTCCGGAAGCGATGGCCAGGACACTGCGAAATCTGTTGACCGGCCGCGTGCTTTCCCCCGCCTCGCAGCAGCAGTTGCAACGCTGGATGGTAGAGGACAAAGTTGCGGGGCCGCTGTTGCGCTCTGCGCTGCCGGCGGGCTGGTTTATTGCCGATAAGACCGGAGCCGGCAATCGCGGCTCGCGCGGAATCATCGCCGCTCTCGGTCCGGACGGTAAAGCCGCGCGCATCGTGGTGATTTATTTAACCGCAACCCCGGCCTCAATGGATGAGCGCAATAAACAGATTGCGGCCATCGGTGAAACGCTGGTCAGGCACTGGTCCAAAGACGATAAAAGACCCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3006960","ARO_id":"45422","ARO_name":"ORN-4","CARD_short_name":"ORN-4","ARO_description":"ORN-4 is a ORN beta-lactamase.","ARO_category":{"43889":{"category_aro_accession":"3005429","category_aro_cvterm_id":"43889","category_aro_name":"ORN beta-lactamase","category_aro_description":"ORN beta-lactamases are class A beta-lactamases found in Raoultella ornithinolytica.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4799":{"model_id":"4799","model_name":"ORN-5","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"575"}},"model_sequences":{"sequence":{"7174":{"protein_sequence":{"accession":"WP_063860935.1","sequence":"MRQYRFALLPLLAALALPGWAHEATVTTVKQAESQLQGRVGYAELDLASGQLLSGYRAGERFPMMSTFKVLLCGAVLSRVDTGEEQLDRRIHYRQQDLVEYSPVTEKHLADGLTVGELCAAAITLSDNTAANLLLTTIGGPQGLTTFLRHSGDQTSRLDRWETELNEARPGDVRDTTTPEAMARTLRNLLTGRVLSPASQQQLQRWMVEDKVAGPLLRSALPAGWFIADKTGAGNRGSRGIIAALGPDGKAARIVVIYLTATPASMDERNKQIAAIGETLVRHWSKDDKRP"},"dna_sequence":{"accession":"NG_049390.1","fmin":"100","fmax":"976","strand":"+","sequence":"ATGCGTCAATATCGATTCGCCCTTCTGCCATTGTTAGCCGCCCTGGCGCTCCCCGGTTGGGCGCATGAAGCCACGGTGACGACGGTTAAACAAGCCGAAAGCCAGCTGCAGGGCCGGGTCGGCTACGCCGAACTGGATTTAGCTTCCGGCCAACTGCTGTCCGGCTATCGCGCTGGCGAACGCTTCCCGATGATGAGCACCTTTAAAGTGCTGCTCTGCGGCGCAGTCTTGTCGCGCGTCGATACCGGTGAAGAACAGCTCGATCGCCGTATCCATTACCGGCAGCAGGATCTGGTGGAATACTCGCCGGTGACGGAGAAGCATCTTGCCGATGGGCTCACCGTGGGCGAACTGTGCGCGGCCGCCATTACCCTGAGCGATAATACGGCGGCAAACCTGCTGTTGACCACTATCGGCGGCCCGCAGGGGCTGACCACGTTCCTGCGCCACAGCGGCGACCAGACTTCGCGACTCGACCGGTGGGAAACGGAACTCAATGAAGCGCGGCCGGGCGATGTGCGTGATACGACGACTCCGGAAGCGATGGCCAGGACACTGCGAAATCTGTTGACCGGCCGCGTGCTTTCCCCCGCCTCGCAGCAGCAGTTGCAACGCTGGATGGTAGAGGACAAAGTTGCGGGGCCGCTGTTGCGCTCTGCGCTGCCGGCGGGCTGGTTTATTGCCGATAAGACCGGAGCCGGCAATCGCGGCTCGCGCGGAATCATCGCCGCTCTCGGTCCGGACGGTAAAGCCGCGCGCATCGTGGTGATTTATTTAACCGCAACCCCGGCCTCAATGGATGAGCGCAATAAACAGATTGCGGCCATCGGTGAAACGCTGGTCAGGCACTGGTCCAAAGACGATAAAAGACCCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3006961","ARO_id":"45423","ARO_name":"ORN-5","CARD_short_name":"ORN-5","ARO_description":"ORN-5 is a ORN beta-lactamase.","ARO_category":{"43889":{"category_aro_accession":"3005429","category_aro_cvterm_id":"43889","category_aro_name":"ORN beta-lactamase","category_aro_description":"ORN beta-lactamases are class A beta-lactamases found in Raoultella ornithinolytica.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4800":{"model_id":"4800","model_name":"ORN-6","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"575"}},"model_sequences":{"sequence":{"7175":{"protein_sequence":{"accession":"WP_063860936.1","sequence":"MRQYRFALLPLLAALALPGWAHEATVTTVKQAESQLQGRVGYAELDLASGQLLSGYRAGERFPMMSTFKVLLCGAVLSRVDTGEEQLDRRIHYRQQDLVEYSPVTEKHLADGLTVGELCAAAITLSDNTAANLLLTTLGGPQGLTTFLRHSGDQTSRLDRWETELNEARPGDVRDTTTPEAMARILRNLLTGRVLSPASQQQLQRWMVEDKVAGPLLRSALPAGWFIADKTGAGNRGSRGIIAALGPDGKAARIVVIYLTATPASMDERNKQIAAIGETLVRHWSKDDKRP"},"dna_sequence":{"accession":"NG_049391.1","fmin":"100","fmax":"976","strand":"+","sequence":"ATGCGTCAATATCGATTCGCCCTTCTGCCATTGTTAGCCGCCCTGGCGCTCCCCGGTTGGGCGCATGAAGCCACGGTGACGACGGTTAAACAAGCCGAAAGCCAGCTGCAGGGCCGGGTCGGCTACGCCGAACTGGATTTAGCTTCCGGCCAACTGCTGTCCGGCTATCGCGCTGGCGAACGCTTCCCGATGATGAGCACCTTTAAAGTGCTGCTCTGCGGCGCAGTCTTGTCGCGCGTCGATACCGGTGAAGAACAGCTCGATCGCCGTATCCATTACCGGCAGCAGGATCTGGTGGAATACTCGCCGGTGACGGAGAAGCATCTTGCCGATGGGCTCACCGTGGGCGAACTGTGCGCGGCCGCCATTACCCTGAGCGATAATACGGCGGCAAACCTGCTGTTGACCACTCTCGGCGGCCCGCAGGGGCTGACCACGTTCCTGCGCCACAGCGGCGACCAGACTTCGCGACTCGACCGGTGGGAAACGGAACTCAATGAAGCGCGGCCGGGCGATGTGCGTGATACGACGACTCCGGAAGCGATGGCCAGGATACTGCGAAATCTGTTGACCGGCCGCGTGCTTTCCCCTGCCTCGCAGCAGCAGTTGCAACGCTGGATGGTAGAGGACAAAGTTGCGGGGCCGCTGTTGCGCTCAGCGCTGCCGGCGGGCTGGTTTATTGCCGATAAGACCGGAGCCGGCAACCGCGGCTCGCGCGGAATCATCGCCGCTCTCGGTCCGGACGGTAAAGCCGCGCGCATCGTGGTGATTTATTTAACCGCAACCCCGGCCTCAATGGATGAGCGCAATAAACAGATTGCGGCCATCGGTGAAACGCTGGTCAGGCACTGGTCCAAAGACGATAAAAGACCCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3006962","ARO_id":"45424","ARO_name":"ORN-6","CARD_short_name":"ORN-6","ARO_description":"ORN-6 is a ORN beta-lactamase.","ARO_category":{"43889":{"category_aro_accession":"3005429","category_aro_cvterm_id":"43889","category_aro_name":"ORN beta-lactamase","category_aro_description":"ORN beta-lactamases are class A beta-lactamases found in Raoultella ornithinolytica.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4801":{"model_id":"4801","model_name":"ORR-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7176":{"protein_sequence":{"accession":"WP_109545042.1","sequence":"MLKKNFKPLFFYLCFWMSLAACQSQSFGGLQFPKIVYQSEDLKVVQIAPDTFVHTSYLATQQWGKVPCNGMIVRHQREAMVFDTPTDEASSEALIHWIKNELKAEIKWVVPTHFHDDNLGGLPAFHRDKIMSIAYYRTQNLSKKHRKPQTITTFSATDSTWNLGGAKIQIGYYGKGHTEDNIVVYFPKDQVLFGGCLVKELGAGKGNLSDAFPKEWSATIQKVKHAYPEAKIVVPGHGKIGDKALLDYTAQLFKP"},"dna_sequence":{"accession":"NG_059317.1","fmin":"100","fmax":"868","strand":"+","sequence":"ATGCTGAAAAAGAATTTTAAACCATTATTTTTTTATTTATGCTTTTGGATGAGTTTGGCGGCGTGTCAATCTCAGTCTTTTGGAGGGCTTCAGTTCCCTAAAATAGTTTATCAATCCGAGGATTTAAAGGTGGTTCAGATTGCGCCTGATACTTTTGTCCATACGTCTTATTTAGCCACCCAGCAATGGGGAAAAGTGCCTTGTAATGGTATGATTGTCAGACATCAACGAGAAGCGATGGTTTTTGATACGCCCACAGATGAAGCCTCTTCGGAAGCTTTAATCCATTGGATTAAAAACGAACTGAAAGCCGAAATAAAATGGGTGGTGCCGACGCATTTTCACGATGATAATTTGGGCGGATTACCAGCGTTTCATCGGGATAAGATAATGTCTATTGCATATTATAGAACTCAAAACTTATCTAAAAAGCATCGAAAACCACAGACTATTACTACCTTTTCAGCTACAGATTCAACTTGGAATTTGGGAGGTGCAAAAATCCAAATAGGTTATTATGGAAAAGGACATACGGAGGATAATATAGTTGTGTATTTTCCAAAGGATCAAGTGTTATTTGGTGGCTGTTTGGTAAAAGAATTGGGGGCAGGTAAAGGTAATTTGTCTGATGCTTTCCCTAAGGAATGGTCGGCAACCATTCAAAAAGTGAAACACGCCTATCCAGAAGCGAAAATTGTGGTGCCTGGACATGGCAAAATAGGGGACAAAGCGCTATTGGACTACACGGCGCAACTTTTCAAACCATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3006963","ARO_id":"45425","ARO_name":"ORR-1","CARD_short_name":"ORR-1","ARO_description":"ORR-1 is a ORR beta-lactamase.","ARO_category":{"43890":{"category_aro_accession":"3005430","category_aro_cvterm_id":"43890","category_aro_name":"ORR beta-lactamase","category_aro_description":"ORR beta-lactamases are class B1 beta-lactamases found in Ornithobacterium rhinotracheale.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4802":{"model_id":"4802","model_name":"OXA-114b","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7177":{"protein_sequence":{"accession":"WP_006384924.1","sequence":"MTVRRLSCALGAALSLSALGGGPVQAAVLCTVVADAADGRILFQQGTQQACAERYTPASTFKLAIALMGADAGILQGPHEPVWNYQPAYPDWGGDAWRQPTDPARWIKYSVVWYSQLTAKALGQDRFQRYTSAFGYGNADVSGEPGKHNGTDGAWIISSLRISPLEQLAFLRKLVNRQLPVKAAAYELAENLFEAGQADGWRLYGKTGTGSPGSNGVYTAANAYGWFVGWARKDGRQLVYARLLQDERATQPNAGLRARDELVRDWPAMAGAWRP"},"dna_sequence":{"accession":"NG_049408.1","fmin":"0","fmax":"828","strand":"+","sequence":"ATGACCGTTCGACGCCTTTCGTGCGCCCTTGGCGCAGCCCTTTCCCTGTCCGCGCTGGGCGGCGGCCCCGTCCAGGCCGCCGTCCTGTGCACCGTGGTGGCCGACGCCGCCGACGGCCGCATCCTGTTCCAGCAAGGCACGCAGCAGGCCTGCGCCGAGCGCTACACGCCGGCCTCGACCTTCAAGCTGGCCATCGCCCTGATGGGCGCCGACGCCGGCATCCTGCAAGGCCCGCACGAGCCGGTCTGGAACTACCAGCCCGCCTATCCCGACTGGGGCGGCGACGCCTGGCGCCAGCCCACCGATCCGGCGCGCTGGATCAAGTATTCGGTGGTCTGGTATTCACAGCTGACGGCCAAGGCGCTGGGACAGGACCGCTTCCAGCGCTACACCAGCGCGTTCGGATACGGCAATGCGGACGTCTCGGGCGAGCCCGGCAAGCACAACGGCACCGACGGCGCGTGGATCATCTCGTCGCTGCGCATTTCGCCGCTGGAACAACTGGCTTTCCTGCGCAAGCTGGTGAATCGGCAATTGCCGGTCAAGGCCGCCGCCTATGAGCTTGCCGAAAACCTCTTCGAGGCGGGCCAGGCCGATGGCTGGCGCCTGTATGGCAAGACCGGCACCGGGTCGCCCGGCAGCAACGGCGTCTACACGGCGGCCAATGCCTACGGCTGGTTCGTCGGCTGGGCGCGCAAGGATGGCCGCCAGCTGGTGTACGCCCGCCTGCTGCAGGATGAGCGCGCCACCCAGCCCAACGCCGGCCTGCGCGCCCGCGACGAGCTGGTGCGCGACTGGCCGGCCATGGCCGGCGCGTGGCGCCCGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36941","NCBI_taxonomy_name":"Achromobacter xylosoxidans","NCBI_taxonomy_id":"85698"}}}},"ARO_accession":"3005702","ARO_id":"44164","ARO_name":"OXA-114b","CARD_short_name":"OXA-114b","ARO_description":"OXA-114b is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46487":{"category_aro_accession":"3007698","category_aro_cvterm_id":"46487","category_aro_name":"OXA-114-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-114.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4803":{"model_id":"4803","model_name":"OXA-114c","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7178":{"protein_sequence":{"accession":"WP_054448427.1","sequence":"MTVRRLSCALGAALSLSALGGGPVQAAVLCTVVADAADGRILFQQSTQQACAERYTPASTFKLAIALMGADAGILQGPHEPVWNYQPAYPDWGGDAWRQPTDPARWIKYSVVWYSQLTAKALGQDRFQRYTSAFGYGNADVSGEPGKHNGTDGAWIISSLRISPLEQLAFLRKLVNRQLPVKAAAYELADNLFEVGQADGWRLYGKTGTGSPGSNGVYTAANAYGWFVGWARKDGRQLVYARLLQDERATRPNAGLRARDELVRDWPAKAGAWRP"},"dna_sequence":{"accession":"NG_049409.1","fmin":"0","fmax":"828","strand":"+","sequence":"ATGACCGTTCGACGCCTTTCGTGCGCCCTTGGCGCAGCCCTTTCCCTGTCCGCGCTGGGCGGCGGCCCCGTCCAGGCCGCCGTCCTGTGCACCGTGGTGGCCGACGCCGCCGACGGCCGCATCCTGTTCCAGCAAAGCACGCAGCAGGCCTGCGCCGAGCGCTACACGCCGGCCTCGACCTTCAAGCTGGCCATCGCCCTGATGGGCGCCGACGCCGGCATCCTGCAAGGCCCGCACGAGCCGGTCTGGAACTACCAGCCCGCCTATCCCGACTGGGGCGGCGACGCCTGGCGCCAGCCCACCGATCCGGCGCGCTGGATCAAGTATTCGGTGGTCTGGTATTCACAGCTGACGGCCAAGGCGCTGGGACAGGACCGCTTCCAGCGCTACACCAGCGCGTTCGGATACGGCAATGCGGACGTCTCGGGCGAGCCCGGCAAGCACAACGGCACCGACGGCGCGTGGATCATCTCGTCGCTGCGCATTTCGCCGCTGGAACAACTGGCTTTCCTGCGCAAGCTGGTGAACCGGCAATTGCCGGTCAAGGCCGCCGCCTATGAGCTGGCCGACAACCTCTTCGAGGTGGGCCAGGCCGATGGCTGGCGCCTGTATGGCAAGACCGGCACCGGTTCGCCCGGCAGCAACGGCGTCTACACGGCGGCCAATGCCTACGGCTGGTTCGTCGGCTGGGCGCGCAAGGATGGCCGCCAGCTGGTGTACGCCCGCCTGCTGCAGGATGAGCGCGCCACCCGGCCCAACGCCGGCCTGCGCGCCCGCGACGAGCTGGTGCGCGACTGGCCGGCCAAGGCCGGCGCGTGGCGCCCGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36941","NCBI_taxonomy_name":"Achromobacter xylosoxidans","NCBI_taxonomy_id":"85698"}}}},"ARO_accession":"3005703","ARO_id":"44165","ARO_name":"OXA-114c","CARD_short_name":"OXA-114c","ARO_description":"OXA-114c is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46487":{"category_aro_accession":"3007698","category_aro_cvterm_id":"46487","category_aro_name":"OXA-114-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-114.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4804":{"model_id":"4804","model_name":"OXA-114d","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7179":{"protein_sequence":{"accession":"WP_063860980.1","sequence":"MTVRRLSCALGAALSLSALGGGPVQAAVLCTVVADAADGRILFQQGTQQACAERYTPGSTFKLAIALMGADAGILQGPHEPVWNYQPAYPDWGGDAWRQPTDPARWIKYSVVWYSQLTAKALGQDRFQRYTSAFGYGNADVSGEPGKHNGTDGAWIISSLRISPLEQLAFLRKLVNRQLPVKAAAYELAENLFEAGQADGWRLYGKTGTGSPGSNGVYTAANAYGWFVGWARKDGRQLVYARLLQDERATQPNAGLRARDELVRDWPAMAGAWRP"},"dna_sequence":{"accession":"NG_049410.1","fmin":"0","fmax":"828","strand":"+","sequence":"ATGACCGTTCGACGCCTTTCGTGCGCCCTTGGCGCAGCCCTTTCCCTGTCCGCGCTGGGCGGCGGCCCCGTCCAGGCCGCCGTCCTGTGCACCGTGGTGGCCGACGCCGCCGACGGCCGCATCCTGTTCCAGCAAGGCACGCAGCAGGCCTGCGCCGAGCGCTACACGCCGGGCTCGACCTTCAAGCTGGCCATCGCCCTGATGGGCGCCGACGCCGGCATCCTGCAAGGCCCGCACGAGCCGGTCTGGAACTACCAGCCCGCCTATCCCGACTGGGGCGGCGACGCCTGGCGCCAGCCCACCGATCCGGCGCGCTGGATCAAGTATTCGGTGGTCTGGTATTCACAGCTGACGGCCAAGGCGCTGGGACAGGACCGCTTCCAGCGCTACACCAGCGCGTTCGGATACGGCAATGCGGACGTCTCGGGCGAGCCCGGCAAGCACAACGGCACCGACGGCGCGTGGATCATCTCGTCGCTGCGCATTTCGCCGCTGGAACAACTGGCTTTCCTGCGCAAGCTGGTGAATCGGCAATTGCCGGTCAAGGCCGCCGCCTATGAGCTTGCCGAAAACCTCTTCGAGGCGGGCCAGGCCGATGGCTGGCGCCTGTATGGCAAGACCGGCACCGGGTCGCCCGGCAGCAACGGCGTCTACACGGCGGCCAATGCCTACGGCTGGTTCGTCGGCTGGGCGCGCAAGGATGGCCGCCAGCTGGTGTACGCCCGCCTGCTGCAGGATGAGCGCGCCACCCAGCCCAACGCCGGCCTGCGCGCCCGCGACGAGCTGGTGCGCGACTGGCCGGCCATGGCCGGCGCGTGGCGCCCGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36941","NCBI_taxonomy_name":"Achromobacter xylosoxidans","NCBI_taxonomy_id":"85698"}}}},"ARO_accession":"3005704","ARO_id":"44166","ARO_name":"OXA-114d","CARD_short_name":"OXA-114d","ARO_description":"OXA-114d is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46487":{"category_aro_accession":"3007698","category_aro_cvterm_id":"46487","category_aro_name":"OXA-114-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-114.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4805":{"model_id":"4805","model_name":"OXA-114e","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7180":{"protein_sequence":{"accession":"WP_049058560.1","sequence":"MTVRRLSCALGAALSLSALGGGPVQAAVLCTVVADAADGRILFQQGTQQACAERYTPASTFKLAIALMGADAGILQGPHEPVWNYQPAYPDWGGDAWRQPTDPARWIKYSVVWYSQLTAMALGQDRFQRYTSAFGYGNADVSGEPGKHNGTDGAWIISSLRISPLEQLAFLRKLVNRQLPVKAAAYELAENLFEVGQADGWRLYGKTGTGSPGSNGVYTAANAYGWFVGWARKDGRQLVYARLLQDERATQPNAGLRARDELVRDWPAMAGAWRP"},"dna_sequence":{"accession":"NG_049411.1","fmin":"0","fmax":"828","strand":"+","sequence":"ATGACCGTTCGACGCCTTTCGTGCGCCCTTGGCGCAGCCCTTTCCCTGTCCGCGCTGGGCGGCGGCCCCGTCCAGGCCGCCGTCCTGTGCACCGTGGTGGCCGACGCCGCCGACGGCCGCATCCTGTTCCAGCAAGGCACGCAGCAGGCCTGCGCCGAGCGCTACACGCCGGCCTCGACCTTCAAGCTGGCCATCGCCCTGATGGGCGCCGACGCCGGCATCCTGCAAGGCCCGCACGAGCCGGTCTGGAACTACCAGCCCGCCTATCCCGACTGGGGCGGCGACGCCTGGCGCCAGCCCACCGATCCGGCGCGCTGGATCAAGTATTCGGTGGTCTGGTATTCACAGCTGACGGCCATGGCGCTGGGACAGGACCGCTTCCAGCGCTACACCAGCGCGTTCGGATACGGCAATGCGGACGTCTCGGGCGAGCCCGGCAAGCACAACGGCACCGACGGCGCGTGGATCATCTCGTCGCTGCGCATTTCGCCGCTGGAACAACTGGCTTTCCTGCGCAAGCTGGTGAATCGGCAATTGCCGGTCAAGGCCGCCGCCTATGAGCTGGCCGAAAACCTCTTCGAGGTGGGCCAGGCCGATGGCTGGCGCCTGTATGGCAAGACCGGCACCGGGTCGCCCGGCAGCAACGGCGTCTACACGGCGGCCAATGCCTACGGCTGGTTCGTCGGCTGGGCGCGCAAGGATGGCCGCCAGCTGGTGTACGCCCGCCTGCTGCAGGATGAGCGCGCCACCCAGCCCAACGCCGGCCTGCGCGCCCGCGACGAGCTGGTGCGCGACTGGCCGGCCATGGCCGGCGCGTGGCGCCCGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36941","NCBI_taxonomy_name":"Achromobacter xylosoxidans","NCBI_taxonomy_id":"85698"}}}},"ARO_accession":"3005705","ARO_id":"44167","ARO_name":"OXA-114e","CARD_short_name":"OXA-114e","ARO_description":"OXA-114e is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46487":{"category_aro_accession":"3007698","category_aro_cvterm_id":"46487","category_aro_name":"OXA-114-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-114.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4806":{"model_id":"4806","model_name":"OXA-114f","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7181":{"protein_sequence":{"accession":"WP_024069684.1","sequence":"MTVRRLSCALGAALSLSALGGGPVQAAVLCTVVADAADGRILFQQGTQQACAERYTPASTFKLAIALMGADAGILQGPHEPVWNYQPAYPDWGGDAWRQPTDPARWIKYSVVWYSQLTAKALGQDRFQRYTSAFGYGNADVSGEPGKHNGTDGAWIISSLRISPLEQLAFLRKLVNRQLPVKAAAYELAENLFEVGQADGWRLYGKTGTGSPGSNGVYTAANAYGWFVGWARKDGRQLVYARLLQDERATRPNAGLRARDELVRDWPAMAGAWRP"},"dna_sequence":{"accession":"NG_049412.1","fmin":"0","fmax":"828","strand":"+","sequence":"ATGACCGTTCGACGCCTTTCGTGCGCCCTTGGCGCAGCCCTTTCCCTGTCCGCGCTGGGCGGCGGCCCCGTCCAGGCCGCCGTCCTGTGCACCGTGGTGGCCGACGCCGCCGACGGCCGCATCCTGTTCCAGCAAGGCACGCAGCAGGCCTGCGCCGAGCGCTACACGCCGGCCTCGACCTTCAAGCTGGCCATCGCCCTGATGGGCGCCGACGCCGGCATCCTGCAAGGCCCGCACGAGCCGGTCTGGAACTACCAGCCCGCCTATCCCGACTGGGGCGGCGACGCCTGGCGCCAGCCCACCGATCCGGCGCGCTGGATCAAGTATTCGGTGGTCTGGTATTCACAGCTGACGGCCAAGGCGCTGGGACAGGACCGCTTCCAGCGCTACACCAGCGCGTTCGGCTACGGCAATGCGGACGTCTCGGGCGAGCCCGGCAAGCATAACGGCACCGACGGCGCGTGGATCATCTCGTCGCTGCGCATTTCGCCGCTGGAACAACTGGCTTTCCTGCGCAAGCTGGTGAATCGGCAATTGCCGGTCAAGGCCGCCGCCTATGAGCTTGCCGAAAACCTCTTCGAGGTGGGCCAGGCCGATGGCTGGCGCCTGTATGGCAAGACCGGCACCGGGTCGCCCGGCAGCAACGGCGTCTACACGGCGGCCAATGCCTACGGCTGGTTCGTCGGCTGGGCGCGCAAGGATGGCCGCCAGCTGGTGTACGCCCGCCTGCTGCAGGATGAGCGCGCCACCCGGCCCAACGCCGGCCTGCGCGCCCGCGACGAGCTGGTGCGCGACTGGCCGGCCATGGCCGGCGCGTGGCGCCCGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36941","NCBI_taxonomy_name":"Achromobacter xylosoxidans","NCBI_taxonomy_id":"85698"}}}},"ARO_accession":"3005706","ARO_id":"44168","ARO_name":"OXA-114f","CARD_short_name":"OXA-114f","ARO_description":"OXA-114f is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46487":{"category_aro_accession":"3007698","category_aro_cvterm_id":"46487","category_aro_name":"OXA-114-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-114.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4807":{"model_id":"4807","model_name":"OXA-114g","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7182":{"protein_sequence":{"accession":"WP_063861000.1","sequence":"MTVRRLSCALGAALSLSALGGGPVQAAVLCTVVADAADGRILFQQGTQQACAERYTPASTFKLAIALMGADAGILQGPHEPVWNYQPAYPDWGGDAWRQPTDPARWIKYSVVWYSQLTAKALGQDRFQRYTSAFGYGNADVSGEPGRHNGTDGAWIISSLRISPLEQLAFLRKVVNRQLPVKAAAYELADNLFEVGQADGWRLYGKTGTGSPGSNGVYTAANAYGWFVGWARKDGRQLVYARLLQDERATQPNAGLRARDELVRDWPAMAGAWRP"},"dna_sequence":{"accession":"NG_049413.1","fmin":"0","fmax":"828","strand":"+","sequence":"ATGACCGTTCGACGCCTTTCGTGCGCCCTTGGCGCAGCCCTTTCCCTGTCCGCGCTGGGCGGCGGCCCCGTCCAGGCCGCCGTCCTGTGCACCGTGGTGGCCGACGCCGCCGACGGCCGCATCCTGTTCCAGCAAGGCACGCAGCAGGCCTGCGCCGAGCGCTACACGCCGGCCTCGACCTTCAAGCTGGCCATCGCCCTGATGGGCGCCGACGCCGGCATCCTGCAAGGCCCGCACGAGCCGGTCTGGAACTACCAGCCCGCCTATCCCGACTGGGGCGGCGACGCCTGGCGCCAGCCCACCGATCCGGCGCGCTGGATCAAGTATTCGGTGGTCTGGTATTCACAGCTGACGGCCAAGGCGCTGGGACAGGACCGCTTCCAGCGCTACACCAGCGCGTTCGGCTACGGCAATGCGGACGTCTCCGGCGAGCCCGGCAGGCACAACGGCACCGACGGCGCGTGGATCATCTCGTCGCTGCGCATTTCGCCGCTGGAACAACTGGCTTTCCTGCGCAAGGTGGTGAACCGGCAATTGCCGGTCAAGGCCGCCGCCTATGAGCTGGCGGACAACCTCTTCGAGGTGGGCCAGGCCGATGGCTGGCGCCTGTATGGCAAGACCGGCACCGGGTCGCCCGGCAGCAACGGCGTCTACACGGCGGCCAATGCCTACGGCTGGTTCGTCGGCTGGGCTCGCAAGGATGGCCGCCAACTGGTGTACGCCCGCCTGCTGCAGGACGAGCGCGCCACCCAGCCCAACGCCGGCCTGCGCGCCCGCGACGAGCTGGTGCGCGACTGGCCGGCCATGGCCGGCGCGTGGCGCCCGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36941","NCBI_taxonomy_name":"Achromobacter xylosoxidans","NCBI_taxonomy_id":"85698"}}}},"ARO_accession":"3005707","ARO_id":"44169","ARO_name":"OXA-114g","CARD_short_name":"OXA-114g","ARO_description":"OXA-114g is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46487":{"category_aro_accession":"3007698","category_aro_cvterm_id":"46487","category_aro_name":"OXA-114-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-114.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4808":{"model_id":"4808","model_name":"OXA-114h","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7183":{"protein_sequence":{"accession":"WP_053498400.1","sequence":"MTVRRLSCALGAALSLCALGGGPVQAAVLCTVVADAADGRILFQQGTQQACAERYTPASTFKLAIALMGADAGILQGPHEPVWNYQPAYPDWGGDAWRQPTDPARWIKYSVVWYSQLTAKALGQDRFQRYTSAFGYGNADVSGEPGKHNGTDGAWIISSLRISPLEQLAFLRKLVNRQLPVKAAAYELAENLFEVGQADGWRLYGKTGTGSPGSNGVYTAANAYGWFVGWARKDGRQLVYARLLQDERATRPNAGLRARDELVRDWPAMAGAWRP"},"dna_sequence":{"accession":"NG_064730.1","fmin":"0","fmax":"828","strand":"+","sequence":"ATGACCGTTCGACGCCTTTCGTGCGCCCTTGGCGCAGCCCTTTCCCTGTGCGCGCTGGGCGGCGGCCCCGTCCAGGCCGCCGTCCTGTGCACCGTGGTGGCCGACGCCGCCGACGGCCGCATCCTGTTCCAGCAAGGCACGCAGCAGGCCTGCGCCGAGCGCTACACGCCGGCCTCGACCTTCAAGCTGGCCATCGCCCTGATGGGCGCCGACGCCGGCATCCTGCAAGGCCCGCACGAGCCGGTCTGGAACTACCAGCCCGCCTATCCCGACTGGGGCGGCGACGCCTGGCGCCAGCCCACCGATCCGGCGCGCTGGATCAAGTATTCGGTGGTCTGGTATTCACAGCTGACGGCCAAGGCGCTGGGACAGGACCGCTTCCAGCGCTACACCAGCGCGTTCGGCTACGGCAATGCGGACGTCTCGGGCGAGCCCGGCAAGCACAACGGCACCGACGGCGCGTGGATCATCTCGTCGCTGCGCATTTCGCCGCTGGAACAACTGGCTTTCCTGCGCAAGCTGGTGAATCGGCAATTGCCGGTCAAGGCCGCCGCCTATGAGCTTGCCGAAAACCTCTTCGAGGTGGGCCAGGCCGATGGCTGGCGCCTGTATGGCAAAACCGGCACCGGGTCGCCCGGCAGCAACGGCGTCTACACGGCGGCCAATGCCTACGGCTGGTTCGTCGGCTGGGCGCGCAAGGATGGCCGCCAGCTGGTGTACGCCCGCCTGCTGCAGGATGAGCGCGCCACCCGGCCCAACGCCGGCCTGCGCGCCCGCGACGAGCTGGTGCGCGACTGGCCGGCCATGGCCGGCGCGTGGCGCCCGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36941","NCBI_taxonomy_name":"Achromobacter xylosoxidans","NCBI_taxonomy_id":"85698"}}}},"ARO_accession":"3005708","ARO_id":"44170","ARO_name":"OXA-114h","CARD_short_name":"OXA-114h","ARO_description":"OXA-114h is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46487":{"category_aro_accession":"3007698","category_aro_cvterm_id":"46487","category_aro_name":"OXA-114-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-114.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4809":{"model_id":"4809","model_name":"OXA-114i","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7184":{"protein_sequence":{"accession":"WP_026382828.1","sequence":"MTVRRLSCALGAALSLSALGGGPVQAAVLCTVVADAADGRILFQQGTQQACAERYTPASTFKLAIALMGADAGILQGPHEPVWNYQPAYPDWGGDAWRQPTDPARWIKYSVVWYSQLTAKALGQDRFQRYTSAFGYGNADVSGEPGKHNGTDGAWIISSLRISPLEQLAFLRKVVNRQLPVKAAAYELADNLFEVGQADGWRLYGKTGTGSPGSNGVYTAANAYGWFVGWARKDGRQLVYARLLQDERATQPNAGLRARDELVRDWPAMAGAWRP"},"dna_sequence":{"accession":"NG_064731.1","fmin":"0","fmax":"828","strand":"+","sequence":"ATGACCGTTCGACGCCTTTCGTGCGCCCTTGGCGCAGCCCTTTCCCTGTCCGCGCTGGGCGGCGGCCCCGTCCAGGCCGCCGTCCTGTGCACCGTGGTGGCCGACGCCGCCGACGGCCGCATCCTGTTCCAGCAAGGCACGCAGCAGGCCTGCGCCGAGCGCTACACGCCGGCCTCGACCTTCAAGCTGGCCATCGCCCTGATGGGCGCCGACGCCGGCATCCTGCAAGGCCCGCACGAGCCGGTCTGGAACTACCAGCCCGCCTATCCCGACTGGGGCGGCGACGCCTGGCGCCAGCCCACCGATCCGGCGCGCTGGATCAAGTATTCGGTGGTCTGGTATTCACAGCTGACGGCCAAGGCGCTGGGACAGGACCGCTTCCAGCGCTACACCAGCGCGTTCGGCTACGGCAATGCGGACGTCTCGGGCGAGCCCGGCAAGCACAACGGCACCGACGGCGCGTGGATCATCTCGTCGCTGCGCATTTCGCCGCTGGAACAACTGGCTTTCCTGCGCAAGGTGGTGAACCGGCAATTGCCGGTCAAGGCCGCCGCCTATGAGCTGGCGGACAACCTCTTCGAGGTGGGCCAGGCCGATGGCTGGCGCCTGTATGGCAAGACCGGCACCGGGTCGCCCGGCAGCAACGGCGTCTACACGGCGGCCAATGCCTACGGCTGGTTCGTCGGCTGGGCTCGCAAGGATGGCCGCCAACTGGTGTACGCCCGCCTGCTGCAGGACGAGCGCGCCACCCAGCCCAACGCCGGCCTGCGCGCCCGCGACGAGCTGGTGCGCGACTGGCCGGCCATGGCCGGCGCGTGGCGCCCGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39101","NCBI_taxonomy_name":"Achromobacter","NCBI_taxonomy_id":"222"}}}},"ARO_accession":"3005709","ARO_id":"44171","ARO_name":"OXA-114i","CARD_short_name":"OXA-114i","ARO_description":"OXA-114i is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46487":{"category_aro_accession":"3007698","category_aro_cvterm_id":"46487","category_aro_name":"OXA-114-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-114.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4810":{"model_id":"4810","model_name":"OXA-114j","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7185":{"protein_sequence":{"accession":"WP_054437016.1","sequence":"MTVRRLSCALGAALSLSALGGGPVQAAVLCTVVADAADGRILFQQGTQQACAERYTPASTFKLAIALMGADAGILQGPHEPVWNYQPAYPDWGGDAWRQPTDPARWIKYSVVWYSQLTAKALGQDRFQRYTSAFGYGNADVSGEPGKHNGTDGAWIISSLRISPLEQLAFLRKLVNRQLPVKAAAYELAENLFEVGQADGWRLFGKTGTGSPGSNGVYTAANAYGWFVGWARKDGRQLVYARLLQDERATRPNAGLRARDELVRDWPAMAGAWRP"},"dna_sequence":{"accession":"NG_064732.1","fmin":"0","fmax":"828","strand":"+","sequence":"ATGACCGTTCGACGCCTTTCGTGCGCCCTTGGCGCAGCCCTTTCCCTGTCCGCGCTGGGCGGCGGCCCCGTCCAGGCCGCCGTCCTGTGCACCGTGGTGGCCGACGCCGCCGACGGCCGCATCCTGTTCCAGCAAGGCACGCAGCAGGCCTGCGCCGAGCGCTACACGCCGGCCTCGACCTTCAAGCTGGCCATCGCCCTGATGGGCGCCGACGCCGGCATCCTGCAAGGCCCGCACGAGCCGGTCTGGAACTACCAGCCCGCCTATCCCGACTGGGGCGGCGACGCCTGGCGCCAGCCCACCGATCCGGCGCGCTGGATCAAGTATTCGGTGGTCTGGTATTCACAGCTGACGGCCAAGGCGCTGGGACAGGACCGCTTCCAGCGCTACACCAGCGCGTTCGGCTACGGCAATGCGGACGTCTCGGGCGAGCCCGGCAAGCACAACGGCACCGACGGCGCGTGGATCATCTCGTCGCTGCGCATTTCGCCGCTGGAACAACTGGCTTTCCTGCGCAAGCTGGTGAATCGGCAATTGCCGGTCAAGGCCGCCGCCTATGAGCTTGCCGAAAACCTCTTCGAGGTGGGCCAGGCCGATGGCTGGCGCCTGTTTGGCAAGACCGGCACCGGGTCGCCCGGCAGCAACGGCGTCTACACGGCGGCCAATGCCTACGGCTGGTTCGTCGGCTGGGCGCGCAAGGATGGCCGCCAGCTGGTGTACGCCCGCCTGCTGCAGGATGAGCGCGCCACCCGGCCCAACGCCGGCCTGCGCGCCCGCGACGAGCTGGTGCGCGACTGGCCGGCCATGGCCGGCGCGTGGCGCCCGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36941","NCBI_taxonomy_name":"Achromobacter xylosoxidans","NCBI_taxonomy_id":"85698"}}}},"ARO_accession":"3005710","ARO_id":"44172","ARO_name":"OXA-114j","CARD_short_name":"OXA-114j","ARO_description":"OXA-114j is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46487":{"category_aro_accession":"3007698","category_aro_cvterm_id":"46487","category_aro_name":"OXA-114-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-114.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4811":{"model_id":"4811","model_name":"OXA-114k","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7186":{"protein_sequence":{"accession":"WP_136512073.1","sequence":"MTVRRLSCALGAALSLSALGGGPVQAAVLCTVVADAADGRILFQQGTQQACAERYTPASTFKLAIALMGADAGILQGPHEPVWNYQPAYPDWGGDAWRQPTDPARWIKYSVVWYSQLTAKALGQDCFQRYTSAFGYGNADVSGEPGKHNGTDGAWIISSLRISPLEQLAFLRKVVNRQLPVKAAAYELADNLFEVGQADGWRLYGKTGTGSPGSNGVYTAANAYGWFVGWARKDGRQLVYARLLQDERATQPNAGLRARDELVRDWPAMAGAWRP"},"dna_sequence":{"accession":"NG_064733.1","fmin":"0","fmax":"828","strand":"+","sequence":"ATGACCGTTCGACGCCTTTCGTGCGCCCTTGGCGCAGCCCTTTCCCTGTCCGCGCTGGGCGGCGGCCCCGTCCAGGCCGCCGTCCTGTGCACCGTGGTGGCCGACGCCGCCGACGGCCGCATCCTGTTCCAGCAAGGCACGCAGCAGGCCTGCGCCGAGCGCTACACGCCGGCCTCGACCTTCAAGCTGGCCATCGCCCTGATGGGCGCCGACGCCGGCATCCTGCAAGGCCCGCACGAGCCGGTCTGGAACTACCAGCCCGCCTATCCCGACTGGGGCGGCGACGCCTGGCGCCAGCCCACCGATCCGGCGCGCTGGATCAAGTATTCGGTGGTCTGGTATTCACAGCTGACGGCCAAGGCGCTGGGACAGGACTGCTTCCAGCGCTACACCAGCGCGTTCGGCTACGGCAATGCGGACGTCTCCGGCGAGCCCGGCAAGCACAACGGCACCGACGGCGCGTGGATCATCTCGTCGCTGCGCATTTCGCCGCTGGAACAACTGGCTTTCCTGCGCAAGGTGGTGAACCGGCAATTGCCGGTCAAGGCCGCCGCCTATGAGCTGGCGGACAACCTCTTCGAGGTGGGCCAGGCCGATGGCTGGCGCCTGTATGGCAAGACCGGCACCGGTTCGCCCGGCAGCAACGGCGTCTACACGGCGGCCAATGCCTACGGCTGGTTCGTCGGCTGGGCTCGCAAGGATGGCCGCCAACTGGTGTACGCCCGCCTGCTGCAGGACGAGCGCGCCACCCAGCCCAACGCCGGCCTGCGCGCCCGCGACGAGCTGGTGCGCGACTGGCCGGCCATGGCCGGCGCGTGGCGCCCGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36941","NCBI_taxonomy_name":"Achromobacter xylosoxidans","NCBI_taxonomy_id":"85698"}}}},"ARO_accession":"3005711","ARO_id":"44173","ARO_name":"OXA-114k","CARD_short_name":"OXA-114k","ARO_description":"OXA-114k is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46487":{"category_aro_accession":"3007698","category_aro_cvterm_id":"46487","category_aro_name":"OXA-114-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-114.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4812":{"model_id":"4812","model_name":"OXA-114l","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7187":{"protein_sequence":{"accession":"WP_054517040.1","sequence":"MTVRRLSCALGAALSLSALGGGPVQAAVLCTVVADAADGRILFQQGTQQACAERYTPASTFKLAIALMGADAGILQGPHEPVWNYQPAYPDWGGDAWRQPTDPARWIKYSVVWYSQLTAKALGQDRFQRYTSAFGYGNADVSGEPGKHNGTDGAWIISSLRISPLEQLAFLRKLVNRQLPVKAAAYELADNLFEAGQADGWRLYGKTGTGSPGSNGVYTAANAYGWFVGWARKDGRQLVYARLLQDERATRPNAGLRARDELVRDWPAMAGAWRP"},"dna_sequence":{"accession":"NG_064734.1","fmin":"0","fmax":"828","strand":"+","sequence":"ATGACCGTTCGACGCCTTTCGTGCGCCCTTGGCGCAGCCCTTTCCCTGTCCGCGCTGGGCGGCGGCCCCGTCCAGGCCGCCGTCCTGTGCACCGTGGTGGCCGACGCCGCCGACGGCCGCATCCTGTTCCAGCAAGGCACGCAGCAGGCCTGCGCCGAGCGCTACACGCCGGCCTCGACCTTCAAGCTGGCCATCGCCCTGATGGGCGCCGACGCCGGCATCCTGCAAGGCCCGCACGAGCCGGTCTGGAACTACCAGCCCGCCTATCCCGACTGGGGCGGCGACGCCTGGCGCCAGCCCACCGATCCGGCGCGCTGGATCAAGTATTCGGTGGTCTGGTATTCACAGCTGACGGCCAAGGCGCTGGGACAGGACCGCTTCCAGCGCTACACCAGCGCGTTCGGCTACGGCAATGCGGACGTCTCGGGCGAGCCCGGCAAGCACAACGGCACCGACGGCGCGTGGATCATCTCGTCGCTGCGCATTTCGCCGCTGGAACAACTGGCTTTCCTGCGCAAGCTGGTGAACCGGCAATTGCCGGTCAAGGCCGCCGCCTATGAGCTGGCCGACAACCTCTTCGAGGCGGGCCAGGCCGATGGCTGGCGCCTGTATGGCAAGACCGGCACCGGTTCGCCCGGCAGCAACGGCGTCTACACGGCGGCCAATGCCTACGGCTGGTTCGTCGGCTGGGCGCGCAAGGATGGCCGCCAGCTGGTGTACGCCCGCCTGCTGCAGGATGAGCGCGCCACCCGGCCCAACGCCGGCCTGCGCGCCCGCGACGAGCTGGTGCGCGACTGGCCGGCCATGGCCGGCGCGTGGCGCCCGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36941","NCBI_taxonomy_name":"Achromobacter xylosoxidans","NCBI_taxonomy_id":"85698"}}}},"ARO_accession":"3005712","ARO_id":"44174","ARO_name":"OXA-114l","CARD_short_name":"OXA-114l","ARO_description":"OXA-114l is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46487":{"category_aro_accession":"3007698","category_aro_cvterm_id":"46487","category_aro_name":"OXA-114-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-114.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4813":{"model_id":"4813","model_name":"OXA-114m","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7188":{"protein_sequence":{"accession":"WP_054471662.1","sequence":"MTVRRLSCALGAALSLSALGGGPVQAAVLCTVVADAADGRILFQQGTQQACAERYTPASTFKLAIALMGADAGILQGPHEPVWNYQPAYPDWGGDAWRQPTDPARWIKYSVVWYSQLTAKALGQDRFQRYTSAFGYGNADVSGEPGKHNGTDGAWIISSLRISPLEQLAFLRKLVNRQLPVKAAAYELADNLFEVGQADGWRLYGKTGTGSPGSNGVYTAANAYGWFVGWARKDGRQLVYARLLQDERATRPNAGLRARDELVRDWPAMAGAWRP"},"dna_sequence":{"accession":"NG_064735.1","fmin":"0","fmax":"828","strand":"+","sequence":"ATGACCGTTCGACGCCTTTCGTGCGCCCTTGGCGCAGCCCTTTCCCTGTCCGCGCTGGGCGGCGGCCCCGTCCAGGCCGCCGTCCTGTGCACCGTGGTGGCCGACGCCGCCGACGGCCGCATCCTGTTCCAGCAAGGCACGCAGCAGGCCTGCGCCGAGCGCTACACGCCGGCCTCGACCTTCAAGCTGGCCATCGCCCTGATGGGCGCCGACGCCGGCATCCTGCAAGGCCCGCACGAGCCGGTCTGGAACTACCAGCCCGCCTATCCCGACTGGGGCGGCGACGCCTGGCGCCAGCCCACCGATCCGGCGCGCTGGATCAAGTATTCGGTGGTCTGGTATTCACAGCTGACGGCCAAGGCGCTGGGACAGGACCGCTTCCAGCGCTACACCAGCGCGTTCGGCTACGGCAATGCGGACGTCTCGGGCGAGCCCGGCAAGCACAACGGCACCGACGGCGCGTGGATCATCTCGTCGCTGCGCATTTCGCCGCTGGAACAACTGGCTTTCCTGCGCAAGCTGGTGAATCGGCAATTGCCGGTCAAGGCCGCCGCCTATGAGCTGGCGGACAACCTCTTCGAGGTGGGCCAGGCCGATGGCTGGCGCCTGTATGGCAAGACCGGCACCGGTTCGCCCGGCAGCAACGGCGTCTACACGGCGGCCAATGCCTACGGCTGGTTCGTCGGCTGGGCGCGCAAGGATGGCCGCCAGCTGGTGTACGCCCGCCTGCTGCAGGATGAGCGCGCCACCCGGCCCAACGCCGGCCTGCGCGCCCGCGACGAGCTGGTGCGCGACTGGCCGGCCATGGCCGGCGCGTGGCGCCCGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36941","NCBI_taxonomy_name":"Achromobacter xylosoxidans","NCBI_taxonomy_id":"85698"}}}},"ARO_accession":"3005713","ARO_id":"44175","ARO_name":"OXA-114m","CARD_short_name":"OXA-114m","ARO_description":"OXA-114m is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46487":{"category_aro_accession":"3007698","category_aro_cvterm_id":"46487","category_aro_name":"OXA-114-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-114.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4814":{"model_id":"4814","model_name":"OXA-114n","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7189":{"protein_sequence":{"accession":"WP_136512074.1","sequence":"MTVRRLSCALGAALSLSALGGGPVQAAVLCTVVADAADGRILFQQGTQQACAERYTPASTFKVAIALMGADAGILQGPHEPVWNYQPAYPDWGGDAWRQPTDPARWIKYSVVWYSQLTAKALGQDRFQRYTSAFGYGNADVSGEPGKHNGTDGAWIISSLRISPLEQLAFLRRLVNRQLPVKAAAYELAENLFEVGQADGWRLFGKTGTGSPGSNGVYTAANAYGWFVGWARKDGRQLVYARLLQDERATRPNAGLRARDELVRDWPAMAGAWRP"},"dna_sequence":{"accession":"NG_064736.1","fmin":"0","fmax":"828","strand":"+","sequence":"ATGACCGTTCGACGCCTTTCGTGCGCCCTTGGCGCAGCCCTTTCCCTGTCCGCGCTGGGCGGCGGCCCCGTCCAGGCCGCCGTCCTGTGCACCGTGGTGGCCGACGCCGCCGACGGCCGCATCCTGTTCCAGCAAGGCACGCAACAGGCCTGCGCCGAGCGCTACACGCCAGCCTCGACCTTCAAGGTGGCCATTGCCCTGATGGGCGCCGACGCCGGCATCCTGCAAGGCCCGCACGAGCCGGTCTGGAACTACCAGCCCGCCTATCCCGACTGGGGCGGCGACGCCTGGCGCCAGCCCACCGATCCGGCGCGCTGGATCAAGTATTCGGTGGTCTGGTATTCACAGCTGACGGCCAAGGCGCTGGGACAGGACCGCTTCCAGCGCTACACCAGCGCGTTCGGCTACGGCAATGCGGACGTCTCGGGCGAGCCCGGCAAGCACAACGGCACCGACGGCGCGTGGATCATCTCGTCGCTGCGCATTTCGCCGCTGGAACAACTGGCTTTCCTGCGCAGGCTGGTGAACCGGCAATTGCCGGTCAAGGCCGCCGCCTATGAGCTTGCCGAAAACCTCTTCGAGGTGGGCCAGGCCGATGGCTGGCGCCTGTTTGGCAAGACCGGCACCGGGTCGCCCGGCAGCAACGGCGTCTACACGGCGGCCAATGCCTACGGCTGGTTCGTCGGCTGGGCGCGCAAGGATGGCCGCCAGCTGGTGTACGCCCGCCTGCTGCAGGATGAGCGCGCCACCCGGCCCAACGCCGGCCTGCGCGCCCGCGACGAGCTGGTGCGCGACTGGCCGGCCATGGCCGGCGCGTGGCGCCCGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36941","NCBI_taxonomy_name":"Achromobacter xylosoxidans","NCBI_taxonomy_id":"85698"}}}},"ARO_accession":"3005714","ARO_id":"44176","ARO_name":"OXA-114n","CARD_short_name":"OXA-114n","ARO_description":"OXA-114n is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46487":{"category_aro_accession":"3007698","category_aro_cvterm_id":"46487","category_aro_name":"OXA-114-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-114.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4815":{"model_id":"4815","model_name":"OXA-114p","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7190":{"protein_sequence":{"accession":"WP_076412384.1","sequence":"MTVRRLSCALGAALSLSALGGGPVQAAVLCTVVADAADGRILFQQGTQQACAERYTPASTFKLAIALMGADADILQGPHEPVWNYQPAYPDWGGDVWRQPTDPARWIQYSVVWYSQLIAKALGQDRFQRYTSAFGYGNADVSGEPGKHNGTDGAWIISSLRISPLEQLAFLRRLVNRQLPVKAAAYELADNLFEVGQADGWRLYGKTGTGSPGSDGVYTAANAYGWFVGWARKDGRQLVYARLLQDERATRPNAGLRARDELVRDWPAMAGAWRP"},"dna_sequence":{"accession":"NG_064737.1","fmin":"0","fmax":"828","strand":"+","sequence":"ATGACCGTTCGACGCCTTTCGTGCGCCCTTGGCGCAGCCCTTTCCCTGTCCGCGCTGGGCGGCGGCCCCGTCCAGGCCGCCGTCCTGTGCACCGTGGTGGCCGACGCCGCCGACGGCCGCATCCTGTTCCAGCAAGGCACGCAACAGGCCTGCGCCGAGCGCTACACGCCAGCTTCGACCTTCAAGCTGGCCATTGCCCTGATGGGCGCCGACGCCGACATCCTGCAAGGCCCGCACGAGCCGGTCTGGAACTACCAGCCTGCCTATCCCGACTGGGGCGGCGACGTCTGGCGCCAGCCCACCGACCCGGCGCGCTGGATCCAGTATTCGGTGGTCTGGTATTCACAGCTGATCGCCAAGGCGCTGGGACAGGACCGCTTCCAGCGCTACACCAGCGCATTCGGCTACGGCAATGCGGACGTCTCGGGCGAGCCCGGCAAGCACAACGGCACCGACGGCGCGTGGATCATCTCGTCGCTGCGCATTTCGCCGCTGGAACAACTGGCTTTCCTGCGCAGGCTGGTGAACCGGCAATTGCCAGTCAAGGCCGCCGCCTATGAGCTGGCCGACAACTTGTTCGAGGTGGGCCAGGCCGATGGCTGGCGCCTGTATGGCAAGACCGGCACCGGTTCGCCCGGCAGCGATGGCGTCTACACGGCGGCCAATGCCTACGGCTGGTTCGTCGGCTGGGCGCGCAAGGATGGCCGCCAGCTGGTGTACGCCCGCCTGCTGCAGGATGAGCGCGCCACCCGGCCCAACGCCGGCCTGCGCGCCCGCGACGAGCTGGTGCGCGACTGGCCGGCCATGGCCGGCGCGTGGCGCCCGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36941","NCBI_taxonomy_name":"Achromobacter xylosoxidans","NCBI_taxonomy_id":"85698"}}}},"ARO_accession":"3005715","ARO_id":"44177","ARO_name":"OXA-114p","CARD_short_name":"OXA-114p","ARO_description":"OXA-114p is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46487":{"category_aro_accession":"3007698","category_aro_cvterm_id":"46487","category_aro_name":"OXA-114-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-114.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4816":{"model_id":"4816","model_name":"OXA-114q","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7191":{"protein_sequence":{"accession":"WP_136512075.1","sequence":"MTVRRLSCALGAALSLSALGGGPVQAAVLCTVVADAADGRILFQQSTQQACAERYTPASTFKLAIALMGADAGILQGPHEPVWNYQPAYPDWGGDAWRQPTDPARWIKYSVVWYSQLTAKALGQDRFQRYTSAFGYGNADVSGEPGKHNGTDGAWIISSLRISPLEQLAFLRKLVNRQLPVKAAAYELAENLFEVGQADGWRLYGKTGTGSPGSNGVYTAANAYGWFVGWARKDGRQLVYARLLQDERATRPNAGLRARDELVRDWPAKAGAWRP"},"dna_sequence":{"accession":"NG_064738.1","fmin":"0","fmax":"828","strand":"+","sequence":"ATGACCGTTCGACGCCTTTCGTGCGCCCTTGGCGCAGCCCTTTCCCTGTCCGCGCTGGGCGGCGGCCCCGTCCAGGCCGCCGTCCTGTGCACCGTGGTGGCCGACGCCGCCGACGGCCGCATCCTGTTCCAGCAAAGCACGCAGCAGGCCTGCGCCGAGCGCTACACGCCGGCCTCGACCTTCAAGCTGGCCATCGCCCTGATGGGCGCCGACGCCGGCATCCTGCAAGGCCCGCACGAGCCGGTCTGGAACTACCAGCCCGCCTATCCCGACTGGGGCGGCGACGCCTGGCGCCAGCCCACCGATCCGGCGCGCTGGATCAAGTATTCGGTGGTCTGGTATTCACAGCTGACGGCCAAGGCGCTGGGACAGGACCGCTTCCAGCGCTACACCAGCGCGTTCGGATACGGCAATGCGGACGTCTCGGGCGAGCCCGGCAAGCACAACGGCACCGACGGCGCGTGGATCATCTCGTCGCTGCGCATTTCGCCGCTGGAACAACTGGCTTTCCTGCGCAAGCTGGTGAACCGGCAATTGCCGGTCAAGGCCGCCGCCTATGAGCTGGCCGAAAACCTCTTCGAGGTGGGCCAGGCCGATGGCTGGCGCCTGTATGGCAAGACCGGCACCGGTTCGCCCGGCAGCAACGGCGTCTACACGGCGGCCAATGCCTACGGCTGGTTCGTCGGCTGGGCGCGCAAGGATGGCCGCCAGCTGGTGTACGCCCGCCTGCTGCAGGATGAGCGCGCCACCCGGCCCAACGCCGGCCTGCGCGCCCGCGACGAGCTGGTGCGCGACTGGCCGGCCAAGGCCGGCGCGTGGCGCCCGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36941","NCBI_taxonomy_name":"Achromobacter xylosoxidans","NCBI_taxonomy_id":"85698"}}}},"ARO_accession":"3005716","ARO_id":"44178","ARO_name":"OXA-114q","CARD_short_name":"OXA-114q","ARO_description":"OXA-114q is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46487":{"category_aro_accession":"3007698","category_aro_cvterm_id":"46487","category_aro_name":"OXA-114-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-114.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4817":{"model_id":"4817","model_name":"OXA-114r","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7192":{"protein_sequence":{"accession":"WP_136512076.1","sequence":"MTVRRLSCALGAALSLSALGGGPVQAAVLCTVVADAADGRILFQQGAQQACAERYTPASTFKLAIALMGADAGILQGPHEPVWNYQPAYPDWGGDAWRQPTDPARWIKYSVVWYSQLTAKALGQDRFQRYTSAFGYGNADVSGEPGKHNGTDGAWIISSLRISPLEQLAFLRKLVNRQLPVKAAAYELAENLFEAGQADGWRLYGKTGTGSPGSNGVYTAANAYGWFVGWARKDGRQLVYARLLQDERATRPNAGLRARDELVRDWPAMAGAWRP"},"dna_sequence":{"accession":"NG_064739.1","fmin":"0","fmax":"828","strand":"+","sequence":"ATGACCGTTCGACGCCTTTCGTGCGCCCTTGGCGCAGCCCTTTCCCTGTCCGCGCTGGGCGGCGGCCCCGTCCAGGCCGCCGTCCTGTGCACCGTGGTGGCCGACGCCGCCGACGGCCGCATCCTGTTCCAGCAAGGCGCGCAGCAGGCCTGCGCCGAGCGCTACACGCCGGCCTCGACCTTCAAGCTGGCCATCGCCCTGATGGGCGCCGACGCCGGCATCCTGCAAGGCCCGCACGAGCCGGTCTGGAACTACCAGCCCGCCTATCCCGACTGGGGCGGCGACGCCTGGCGCCAGCCCACCGATCCGGCGCGCTGGATCAAGTATTCGGTGGTCTGGTATTCACAGCTGACGGCCAAGGCGCTGGGACAGGACCGCTTCCAGCGCTACACCAGCGCGTTCGGCTACGGCAATGCGGACGTCTCGGGCGAGCCCGGCAAGCACAACGGCACCGACGGCGCGTGGATCATCTCGTCGCTGCGCATTTCGCCGCTGGAACAACTGGCTTTCCTGCGCAAGCTGGTGAACCGGCAATTGCCGGTCAAGGCCGCCGCTTATGAGCTTGCCGAAAACCTCTTCGAGGCGGGCCAGGCCGATGGCTGGCGCCTGTATGGCAAAACCGGCACCGGGTCGCCCGGCAGCAACGGCGTCTACACGGCGGCCAATGCCTACGGCTGGTTCGTCGGCTGGGCGCGCAAGGATGGCCGCCAGCTGGTGTACGCCCGCCTGCTGCAGGATGAGCGCGCCACCCGGCCCAACGCCGGCCTGCGCGCCCGCGACGAGCTGGTGCGCGACTGGCCGGCCATGGCCGGCGCGTGGCGCCCGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36941","NCBI_taxonomy_name":"Achromobacter xylosoxidans","NCBI_taxonomy_id":"85698"}}}},"ARO_accession":"3005717","ARO_id":"44179","ARO_name":"OXA-114r","CARD_short_name":"OXA-114r","ARO_description":"OXA-114r is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46487":{"category_aro_accession":"3007698","category_aro_cvterm_id":"46487","category_aro_name":"OXA-114-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-114.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4818":{"model_id":"4818","model_name":"OXA-114s","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7193":{"protein_sequence":{"accession":"WP_136512077.1","sequence":"MTVRRLSCALGAALSLCALGGGPVQAAVLCTVVADAADGRILFQQGTQQACAERYTPASTFKLAIALMGADAGILQGPHEPVWNYQPAYPDWGGDAWRQPTDPARWIKYSVVWYSQLTAKALGQDRFQRYTSAFGYGNADVSGEPGKHNGTDGAWIISSLRISPLEQLAFLRKLVNRQLPVKAAAYELADNLFEVGQADGWRLYGKTGTGSPGSNGVYTAANAYGWFVGWARKDGRQLVYARLLQDERATRSNAGLRARDELVRDWPAMAGAWRP"},"dna_sequence":{"accession":"NG_064740.1","fmin":"0","fmax":"828","strand":"+","sequence":"ATGACCGTTCGACGCCTTTCGTGCGCCCTTGGCGCAGCCCTTTCCCTATGCGCGCTGGGCGGCGGCCCCGTCCAGGCCGCCGTCCTGTGCACCGTGGTGGCCGACGCCGCCGACGGCCGCATCCTGTTCCAGCAAGGCACGCAGCAGGCCTGCGCCGAGCGCTACACGCCGGCCTCGACCTTCAAGCTGGCCATCGCCCTGATGGGCGCCGACGCCGGCATCCTGCAAGGCCCGCACGAGCCGGTCTGGAACTACCAGCCCGCCTATCCCGACTGGGGCGGCGACGCCTGGCGCCAGCCCACCGATCCGGCGCGCTGGATCAAGTATTCGGTGGTCTGGTATTCACAGCTGACGGCCAAGGCGCTGGGACAGGACCGCTTCCAGCGCTACACCAGTGCGTTCGGCTACGGCAATGCGGACGTCTCGGGCGAGCCCGGCAAGCACAACGGCACCGACGGCGCGTGGATCATCTCGTCGCTGCGCATTTCGCCGCTGGAACAACTGGCTTTCCTGCGCAAGCTGGTGAATCGGCAATTGCCGGTCAAGGCCGCCGCTTATGAGCTGGCCGACAACCTCTTCGAGGTGGGCCAGGCCGATGGCTGGCGCCTGTATGGCAAAACCGGCACCGGGTCGCCCGGCAGCAACGGCGTCTACACGGCGGCCAATGCCTACGGTTGGTTCGTCGGCTGGGCGCGCAAGGATGGCCGCCAGCTGGTGTACGCCCGCCTGCTGCAGGATGAGCGCGCCACCCGGTCCAACGCCGGCCTGCGCGCCCGCGACGAGCTGGTGCGCGACTGGCCGGCCATGGCCGGCGCGTGGCGCCCGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36941","NCBI_taxonomy_name":"Achromobacter xylosoxidans","NCBI_taxonomy_id":"85698"}}}},"ARO_accession":"3005718","ARO_id":"44180","ARO_name":"OXA-114s","CARD_short_name":"OXA-114s","ARO_description":"OXA-114s is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46487":{"category_aro_accession":"3007698","category_aro_cvterm_id":"46487","category_aro_name":"OXA-114-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-114.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4819":{"model_id":"4819","model_name":"OXA-114t","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7194":{"protein_sequence":{"accession":"WP_136512078.1","sequence":"MTVRRLSCALGAALSLSALGGGPVQAAVLCTVVADAADGRILFQQGTQQACAERYTPASTFKLAIALMGADAGILQGPHEPVWNYQPAYPDWGGDAWRQPTDPARWIKYSVVWYSQLTAKALGQDRFQRYTSAFGYGNADVSGEPGKHNGTDGAWIISSLRISPLEQLAFLRKVVNRQLPVKAAAYELADNLFEVGQADGWRLYGKTGTGSPGSNGVYTAANAYGWFVGWARKDGRQLVYARLLQDERATRPNAGLRARDELVRDWPAMAGAWRP"},"dna_sequence":{"accession":"NG_064741.1","fmin":"0","fmax":"828","strand":"+","sequence":"ATGACCGTTCGACGCCTTTCGTGCGCCCTTGGCGCAGCCCTTTCCCTGTCCGCGCTGGGCGGCGGCCCCGTCCAGGCCGCCGTCCTGTGCACCGTGGTGGCCGACGCCGCCGACGGCCGCATCCTGTTCCAGCAAGGCACGCAGCAGGCCTGCGCCGAGCGCTACACGCCGGCCTCGACCTTCAAGCTGGCCATCGCCCTGATGGGCGCCGACGCCGGCATCCTGCAAGGCCCGCACGAGCCGGTCTGGAACTACCAGCCCGCCTATCCCGACTGGGGCGGCGACGCCTGGCGCCAGCCCACCGATCCGGCACGCTGGATCAAGTATTCGGTGGTCTGGTATTCACAGCTGACGGCCAAGGCGCTGGGACAGGACCGCTTCCAGCGCTACACCAGCGCGTTCGGCTACGGCAATGCGGACGTCTCCGGCGAGCCCGGCAAGCACAACGGCACCGACGGCGCGTGGATCATCTCGTCGCTGCGCATTTCGCCGCTGGAACAACTGGCTTTCCTGCGCAAGGTGGTGAACCGGCAATTGCCGGTCAAGGCCGCCGCCTATGAGCTGGCGGACAACCTCTTCGAGGTGGGCCAGGCCGATGGCTGGCGCCTGTATGGCAAGACCGGCACCGGGTCGCCCGGCAGCAACGGCGTCTACACGGCGGCCAATGCCTACGGCTGGTTCGTCGGCTGGGCGCGCAAGGATGGCCGCCAGCTGGTGTACGCCCGCCTGCTGCAGGATGAGCGCGCCACCCGGCCCAACGCCGGCCTGCGCGCCCGCGACGAGCTGGTGCGCGACTGGCCGGCCATGGCCGGCGCGTGGCGCCCGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36941","NCBI_taxonomy_name":"Achromobacter xylosoxidans","NCBI_taxonomy_id":"85698"}}}},"ARO_accession":"3005719","ARO_id":"44181","ARO_name":"OXA-114t","CARD_short_name":"OXA-114t","ARO_description":"OXA-114t is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46487":{"category_aro_accession":"3007698","category_aro_cvterm_id":"46487","category_aro_name":"OXA-114-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-114.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4820":{"model_id":"4820","model_name":"OXA-114u","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7195":{"protein_sequence":{"accession":"WP_136512079.1","sequence":"MTVRRLSCALGAAISLSALGGGPVQAAVLCTVVADAADGRILFQQGTRQACAERYTPASTFKLAIALMGADAGILQGPHEPVWNYQPAYPDWGGDAWRQPTDPARWIQYSVVWYSQLIAKALGQDRFQRYASAFGYGNADVSGEPGKHNGTDGAWIISSLRISPLEQLAFLRRLVNRELPVKAAAYELADNLFEVGQADGWRLYGKTGTGSPGGNGVYTAANAYGWFVGWARKDGRQLVYARLLQDEHATRPNAGLRARDELMRDWPAMAGAWRP"},"dna_sequence":{"accession":"NG_064742.1","fmin":"0","fmax":"828","strand":"+","sequence":"ATGACCGTTCGACGCCTTTCGTGCGCCCTTGGCGCAGCCATTTCCCTGTCCGCGCTGGGCGGCGGCCCCGTCCAGGCCGCCGTCCTGTGCACCGTGGTGGCCGACGCCGCCGACGGCCGCATCCTGTTCCAGCAAGGCACGCGGCAGGCCTGCGCCGAGCGCTACACGCCGGCCTCGACCTTCAAGCTGGCCATTGCCCTGATGGGCGCCGACGCCGGCATCCTGCAAGGCCCGCACGAGCCGGTCTGGAACTACCAGCCCGCCTATCCCGACTGGGGCGGCGACGCCTGGCGCCAGCCCACCGACCCGGCGCGCTGGATCCAGTATTCGGTGGTCTGGTATTCACAGCTGATCGCCAAGGCGCTGGGACAGGACCGCTTCCAGCGCTACGCCAGCGCATTCGGCTACGGCAATGCGGACGTCTCGGGCGAGCCCGGCAAGCACAACGGCACCGACGGCGCGTGGATCATCTCGTCGCTGCGCATTTCGCCGCTGGAACAACTGGCTTTCCTGCGCAGGCTGGTGAACCGGGAGTTGCCGGTCAAGGCCGCCGCCTATGAGCTGGCCGACAACTTGTTCGAGGTGGGCCAGGCCGATGGCTGGCGCCTGTATGGCAAGACCGGCACCGGTTCGCCCGGCGGCAACGGCGTCTACACGGCGGCCAATGCCTACGGCTGGTTCGTCGGCTGGGCGCGCAAGGATGGCCGCCAGCTGGTGTACGCCCGCCTGCTGCAGGATGAGCACGCCACCCGGCCCAATGCCGGCCTGCGCGCCCGCGACGAGCTGATGCGCGACTGGCCGGCCATGGCCGGCGCGTGGCGCCCGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36941","NCBI_taxonomy_name":"Achromobacter xylosoxidans","NCBI_taxonomy_id":"85698"}}}},"ARO_accession":"3005720","ARO_id":"44182","ARO_name":"OXA-114u","CARD_short_name":"OXA-114u","ARO_description":"OXA-114u is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46487":{"category_aro_accession":"3007698","category_aro_cvterm_id":"46487","category_aro_name":"OXA-114-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-114.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4821":{"model_id":"4821","model_name":"OXA-114v","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7196":{"protein_sequence":{"accession":"WP_136512080.1","sequence":"MTVRRLSCALGAALSLSALGGGPVQAAVLCTVVADAADGRILFQQGTQQACAERYTPASTFKLAIALMGADAGILQGPHEPVWNYQPAYPDWGGDAWRQPTDPARWIKYSVVWYSQLTAKALGQDRFQRYTSAFGYGNADVSGEPGKHNGTDGAWIISSLRISPLEQLAFLRRLVNRQLPVKAAAYELAENLFEAGQADGWRLYGKTGTGSPGSNGVYTAANAYGWFVGWARKDGRQLVYARLLQDERATQPNAGLRARDELVRDWPAMAGAWRP"},"dna_sequence":{"accession":"NG_064743.1","fmin":"0","fmax":"828","strand":"+","sequence":"ATGACCGTTCGACGCCTTTCGTGCGCCCTTGGCGCAGCCCTTTCCCTGTCCGCGCTGGGCGGCGGCCCCGTCCAGGCCGCCGTCCTGTGCACCGTGGTGGCCGACGCCGCCGACGGCCGCATCCTGTTCCAGCAAGGCACGCAGCAGGCCTGCGCCGAGCGCTACACGCCGGCCTCGACCTTCAAGCTGGCCATCGCCCTGATGGGCGCCGACGCAGGCATCCTGCAAGGCCCGCACGAGCCGGTCTGGAACTACCAGCCCGCCTATCCCGACTGGGGCGGCGACGCCTGGCGCCAGCCCACCGATCCGGCGCGCTGGATCAAGTATTCGGTGGTCTGGTATTCACAGCTGACGGCCAAGGCGCTGGGACAGGACCGCTTCCAGCGCTACACCAGCGCGTTCGGCTACGGCAATGCAGACGTCTCGGGCGAGCCCGGCAAGCATAACGGCACCGACGGCGCGTGGATCATCTCGTCGCTGCGCATTTCGCCGCTGGAACAACTGGCTTTCCTGCGCAGGCTGGTGAATCGGCAATTGCCGGTCAAGGCCGCCGCCTATGAGCTTGCCGAAAACCTCTTCGAGGCGGGCCAGGCCGATGGCTGGCGCCTGTATGGCAAGACCGGCACCGGGTCGCCCGGCAGCAACGGCGTCTACACGGCGGCCAATGCCTACGGCTGGTTCGTCGGCTGGGCGCGCAAGGATGGCCGCCAGCTGGTGTACGCCCGCCTGCTGCAGGATGAGCGCGCCACCCAGCCCAACGCCGGCCTGCGCGCCCGCGACGAGCTGGTGCGCGACTGGCCGGCCATGGCCGGCGCGTGGCGCCCGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36941","NCBI_taxonomy_name":"Achromobacter xylosoxidans","NCBI_taxonomy_id":"85698"}}}},"ARO_accession":"3005721","ARO_id":"44183","ARO_name":"OXA-114v","CARD_short_name":"OXA-114v","ARO_description":"OXA-114v is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46487":{"category_aro_accession":"3007698","category_aro_cvterm_id":"46487","category_aro_name":"OXA-114-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-114.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4822":{"model_id":"4822","model_name":"OXA-114w","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7197":{"protein_sequence":{"accession":"WP_136512081.1","sequence":"MTVRRLSCALGAALSLSALGGGPVQAAVLCTVVADAADGRILFQQGTQQACAERYTPASTFKLAIALMGADAGILQGPHEPVWNYQPAYPDWGGDAWRQPTDPARWIKYSVVWYSQLTAKALGQDRFQRYTSAFGYGNADVSGEPGKHNGTDGAWIISSLRISPLEQLAFLRKLVNRQLPVKAAAYELADNLFEVGQADGWRLYGKTGTGSPGSNGVYTAANAYGWFVGWARKDGRQLVYARLLQDERATQPNAGLRARDELVRDWPAMAGAWRP"},"dna_sequence":{"accession":"NG_064744.1","fmin":"0","fmax":"828","strand":"+","sequence":"ATGACCGTTCGACGCCTTTCGTGCGCCCTTGGCGCAGCCCTTTCCCTGTCCGCGCTGGGCGGCGGCCCCGTCCAGGCCGCCGTCCTGTGCACCGTGGTGGCCGACGCCGCCGACGGCCGCATCCTGTTTCAGCAAGGCACGCAGCAGGCCTGCGCCGAGCGCTACACGCCGGCCTCGACCTTCAAGCTGGCCATCGCCCTGATGGGCGCCGACGCCGGCATCCTGCAAGGCCCGCACGAGCCGGTCTGGAACTACCAGCCCGCCTATCCCGACTGGGGCGGCGACGCCTGGCGCCAGCCCACCGATCCGGCGCGCTGGATCAAGTATTCGGTGGTCTGGTATTCACAGCTGACGGCCAAGGCGCTGGGACAGGACCGCTTCCAGCGCTACACCAGCGCGTTCGGCTACGGCAATGCGGACGTCTCCGGCGAGCCCGGCAAGCACAACGGCACCGACGGCGCGTGGATCATTTCGTCGCTGCGCATTTCGCCGCTGGAACAACTGGCTTTCCTGCGCAAGCTGGTGAACCGGCAATTGCCGGTCAAGGCCGCCGCCTATGAGCTGGCGGACAACCTCTTCGAGGTGGGCCAGGCCGATGGCTGGCGCCTGTATGGCAAGACCGGCACCGGGTCGCCCGGCAGCAACGGCGTCTACACGGCGGCCAATGCCTACGGCTGGTTCGTCGGCTGGGCGCGCAAGGATGGCCGCCAACTGGTGTACGCCCGCCTGCTGCAGGACGAGCGCGCCACCCAGCCCAACGCCGGCCTGCGCGCCCGCGACGAGCTGGTGCGCGACTGGCCGGCCATGGCCGGCGCGTGGCGCCCGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36941","NCBI_taxonomy_name":"Achromobacter xylosoxidans","NCBI_taxonomy_id":"85698"}}}},"ARO_accession":"3005722","ARO_id":"44184","ARO_name":"OXA-114w","CARD_short_name":"OXA-114w","ARO_description":"OXA-114w is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46487":{"category_aro_accession":"3007698","category_aro_cvterm_id":"46487","category_aro_name":"OXA-114-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-114.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4823":{"model_id":"4823","model_name":"OXA-114x","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7198":{"protein_sequence":{"accession":"WP_136512082.1","sequence":"MTVRRLSCALGAALSLSALGGDPVQAAVLCTVVADAADGRILFQQGTQQACAERYTPASTFKLAIALMGADAGILQGPHEPVWNYQPAYPDWGGDAWRQPTDPARWIKYSVVWYSQLTAKALGQDRFQRYTSAFGYGNADVSGEPGKHNGTDGAWIISSLRISPLEQLAFLRKLVNRQLPVKAAAYELAENLFEAGQADGWRLYGKTGTGSPGSNGVYTAANAYGWFVGWARKDGRQLVYARLLQDERATRPNAGLRARDELVRDWPAMAGAWRP"},"dna_sequence":{"accession":"NG_064745.1","fmin":"0","fmax":"828","strand":"+","sequence":"ATGACCGTTCGACGCCTTTCGTGCGCCCTTGGCGCAGCCCTTTCCCTGTCCGCGCTGGGCGGCGACCCCGTCCAGGCCGCCGTCCTGTGCACCGTGGTGGCCGACGCCGCCGACGGCCGCATCCTGTTCCAGCAAGGCACGCAGCAGGCCTGCGCCGAGCGCTACACGCCGGCCTCGACCTTCAAGCTGGCCATCGCCCTGATGGGCGCCGACGCCGGCATCCTGCAAGGCCCGCACGAGCCGGTCTGGAACTACCAGCCCGCCTATCCCGACTGGGGCGGCGACGCCTGGCGCCAGCCCACCGATCCGGCGCGCTGGATCAAGTATTCGGTGGTCTGGTATTCACAGCTGACGGCCAAGGCGCTGGGACAGGACCGCTTCCAGCGCTACACCAGCGCGTTCGGCTACGGCAATGCGGACGTCTCGGGCGAGCCCGGCAAGCATAACGGCACCGACGGCGCGTGGATCATCTCGTCGCTGCGCATTTCGCCGCTGGAACAACTGGCTTTCCTGCGCAAGCTGGTGAATCGGCAATTGCCGGTCAAGGCCGCCGCCTATGAGCTTGCCGAAAACCTCTTCGAGGCGGGCCAGGCCGATGGCTGGCGCCTGTATGGCAAGACCGGCACCGGGTCGCCCGGCAGCAACGGCGTCTACACGGCGGCCAATGCCTACGGCTGGTTCGTCGGCTGGGCGCGCAAGGATGGCCGCCAGCTGGTGTACGCCCGCCTGCTGCAGGATGAGCGCGCCACCCGGCCCAACGCCGGCCTGCGCGCCCGCGACGAGCTGGTGCGCGACTGGCCGGCCATGGCCGGCGCGTGGCGCCCGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36941","NCBI_taxonomy_name":"Achromobacter xylosoxidans","NCBI_taxonomy_id":"85698"}}}},"ARO_accession":"3005723","ARO_id":"44185","ARO_name":"OXA-114x","CARD_short_name":"OXA-114x","ARO_description":"OXA-114x is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46487":{"category_aro_accession":"3007698","category_aro_cvterm_id":"46487","category_aro_name":"OXA-114-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-114.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4824":{"model_id":"4824","model_name":"OXA-159","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7199":{"protein_sequence":{"accession":"WP_063861087.1","sequence":"MKKTLSRWRRGALALRLLGALASPVVFAMPGHAAEPAHSSAVRIAERADWGKYFADEGVKGTVIVLDGRTQTYQAYDAARAERRMSPASTYKIFNSLLALESGALDNEREVIPWDGKPRRVKAWNAALDLRNAFRVSCLPCYQVVSHKIPRQYAQAKLNEAGYGNRTIGRAAHAYWIDDSLQISAREQVDFLQRLATGALPFSARSQDIVRNISIVEANVDYVLHGKTGWFTEKKPDIGWWVGWLERDGNLTMIALNIDIQTDADAPKRARIVRNVLKDLKLI"},"dna_sequence":{"accession":"NG_049458.1","fmin":"100","fmax":"952","strand":"+","sequence":"ATGAAAAAGACACTCTCTCGCTGGCGGCGCGGCGCGCTCGCGCTGCGCCTCCTCGGTGCGCTGGCCTCGCCCGTGGTCTTCGCAATGCCCGGACACGCCGCCGAACCCGCGCATTCTTCCGCGGTGCGCATCGCCGAGCGGGCCGACTGGGGCAAGTACTTTGCCGACGAAGGCGTCAAGGGCACGGTCATCGTGCTGGACGGCCGGACCCAGACCTATCAGGCTTACGATGCCGCACGCGCCGAGCGCCGCATGTCGCCCGCATCGACCTACAAGATATTCAACAGCCTGCTCGCGCTGGAGTCCGGCGCGCTCGACAACGAGCGCGAGGTCATCCCGTGGGACGGCAAGCCGCGTCGCGTCAAGGCGTGGAACGCCGCGCTCGACCTGCGCAACGCGTTTCGCGTGTCGTGCCTGCCTTGCTATCAGGTCGTCTCGCACAAGATCCCGCGCCAGTACGCGCAGGCCAAGCTCAACGAGGCGGGCTACGGCAATCGCACAATCGGCCGCGCCGCGCACGCCTACTGGATCGACGACAGCCTGCAGATTTCGGCGCGCGAGCAAGTCGACTTCCTGCAGCGTCTGGCCACGGGTGCGCTGCCGTTCTCGGCGCGCTCGCAGGACATCGTGCGCAACATATCGATCGTCGAAGCGAACGTCGACTACGTGCTGCACGGCAAGACGGGCTGGTTTACCGAAAAGAAACCCGACATCGGGTGGTGGGTCGGCTGGCTCGAGCGTGACGGCAACCTCACCATGATCGCGTTGAACATCGACATTCAAACCGATGCCGACGCGCCAAAGCGCGCGCGCATCGTTCGCAACGTGCTCAAGGATCTGAAGCTGATCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3001464","ARO_id":"37864","ARO_name":"OXA-159","CARD_short_name":"OXA-159","ARO_description":"OXA-159 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46520":{"category_aro_accession":"3007731","category_aro_cvterm_id":"46520","category_aro_name":"OXA-62-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-62.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4825":{"model_id":"4825","model_name":"OXA-193","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7200":{"protein_sequence":{"accession":"WP_002783228.1","sequence":"MKKITLFLLFLNLVFGQDKILNNWFKEYNTSGTFVFYDGKTWASNDFSRAMETFSPASTFKIFNALIALDSGVIKTKKEIFYHYRGEKVFLSSWAQDMNLSSAIKYSNVLAFKEVARRIGIKTMQEYLNKLHYGNAKISKIDTFWLDNSLKISAKEQAILLFRLSQNSLPFSQEAMNSVKEMIYLKNMENLELFGKTGFNDEQKIAWIVGFVYLKDENKYKAFALNLDIDKFEDLYKREKILEKYLDELVKKVKNDG"},"dna_sequence":{"accession":"NG_049489.1","fmin":"100","fmax":"874","strand":"+","sequence":"ATGAAAAAAATAACTTTATTTTTACTTTTCTTAAATTTAGTGTTTGGGCAAGATAAGATATTAAATAATTGGTTTAAAGAGTATAATACAAGCGGCACTTTTGTTTTTTATGATGGAAAAACTTGGGCGAGTAACGACTTTTCAAGGGCTATGGAGACTTTCTCTCCCGCTTCCACTTTTAAAATTTTTAATGCTCTAATTGCACTTGATAGTGGTGTGATAAAAACTAAAAAAGAAATTTTTTATCACTATAGAGGTGAAAAAGTATTTTTATCTTCTTGGGCGCAAGATATGAATTTAAGTTCAGCTATAAAATATTCTAATGTTCTTGCTTTTAAAGAAGTGGCAAGAAGAATTGGTATCAAAACTATGCAAGAATATTTAAACAAGCTTCATTATGGTAATGCTAAAATTTCCAAGATCGATACTTTTTGGCTTGACAACTCACTAAAAATAAGCGCTAAAGAACAAGCAATTTTGCTTTTTAGACTTTCACAAAATAGCTTACCTTTTTCTCAAGAAGCAATGAATAGTGTTAAGGAAATGATTTATTTAAAAAATATGGAAAATTTAGAGCTTTTTGGAAAAACAGGTTTTAATGATGAGCAAAAAATTGCTTGGATTGTAGGTTTTGTGTATTTAAAAGATGAAAATAAATATAAGGCTTTCGCGCTAAATTTAGATATTGATAAATTTGAAGATTTATATAAAAGAGAAAAAATTTTAGAAAAATATTTAGATGAACTTGTAAAAAAAGTTAAAAATGATGGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37052","NCBI_taxonomy_name":"Campylobacter","NCBI_taxonomy_id":"194"}}}},"ARO_accession":"3001478","ARO_id":"37878","ARO_name":"OXA-193","CARD_short_name":"OXA-193","ARO_description":"OXA-193 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46519":{"category_aro_accession":"3007730","category_aro_cvterm_id":"46519","category_aro_name":"OXA-61-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-61.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4826":{"model_id":"4826","model_name":"OXA-307","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7201":{"protein_sequence":{"accession":"WP_032879257.1","sequence":"MSKKLKCLALLTPLILILPLTACQSPSQKKQQVVSLQNEQQRVANLFQQAQTTGVLVIYDGKQIQTYGNATRRADQRFIPASTFKILNALIGIQHHKTTPNEVFKWDGQKRAFSSWEKDLSLAEAMQASAVPVYQELARRIGLELMTREVKRVGYGNKHIGTQVDNFWLVGPLKITPVEEVRFVYALAKQKLPFDQSTQQQVKDMLLVDEHQGTKIYAKSGWGMDVTPQVGWWTGWIEQPNGKIIAFSLNMQMSQPAHADARKVIVYQALQELGLLAN"},"dna_sequence":{"accession":"NG_050611.1","fmin":"100","fmax":"937","strand":"+","sequence":"ATGTCGAAAAAATTAAAATGCCTAGCGCTACTTACGCCATTAATTTTGATCCTTCCATTGACTGCTTGTCAGAGTCCTAGCCAAAAAAAACAGCAAGTCGTGTCATTGCAAAATGAGCAACAGCGGGTGGCGAATTTATTCCAGCAGGCGCAAACCACAGGGGTTTTGGTCATCTATGATGGCAAACAAATTCAAACATACGGCAATGCGACACGCCGTGCAGATCAACGTTTTATCCCAGCCTCAACCTTTAAAATACTGAATGCACTGATTGGTATACAGCATCATAAAACCACGCCAAATGAAGTCTTTAAATGGGATGGTCAAAAACGTGCATTTAGCAGTTGGGAAAAAGATTTAAGTTTGGCTGAAGCTATGCAGGCATCGGCTGTACCTGTCTATCAGGAGCTAGCACGACGCATTGGTCTAGAACTCATGACCCGTGAGGTGAAGCGTGTTGGCTATGGCAATAAACATATTGGAACCCAAGTCGATAATTTTTGGTTGGTCGGGCCTTTGAAAATTACACCTGTAGAAGAAGTTCGATTTGTCTATGCATTGGCAAAGCAAAAACTACCGTTTGACCAGTCAACTCAACAGCAAGTGAAAGACATGTTATTGGTGGATGAGCATCAAGGGACCAAGATTTATGCCAAGAGCGGTTGGGGTATGGACGTTACCCCACAGGTCGGATGGTGGACTGGCTGGATTGAACAGCCAAATGGCAAAATCATTGCATTTTCACTGAATATGCAAATGAGCCAGCCTGCGCATGCAGATGCGCGTAAAGTGATTGTTTATCAAGCATTACAAGAGCTGGGATTGTTAGCCAATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39512","NCBI_taxonomy_name":"Acinetobacter colistiniresistens","NCBI_taxonomy_id":"70345"}}}},"ARO_accession":"3001762","ARO_id":"38162","ARO_name":"OXA-307","CARD_short_name":"OXA-307","ARO_description":"OXA-307 is a beta-lactamase found in Acinetobacter spp.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46503":{"category_aro_accession":"3007714","category_aro_cvterm_id":"46503","category_aro_name":"OXA-286-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-286.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4827":{"model_id":"4827","model_name":"OXA-395","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7202":{"protein_sequence":{"accession":"WP_015649877.1","sequence":"MRPLLFSALLLLSGHAQASEWNDSQAVDKLFGAAGVKGTFVLYDVQRQRYVGHDRERAETRFVPASTYKVANSLIGLSTGAVKSADEVLPYGGKPQRFKAWEHDMSLRDAIKASNVPVYQELARRIGLERMRANVSRLGYGNAEIGQVVDNFWLVGPLKISAMEQTRFLLRLAQGELPFPAPVQSTVRAMTLLESGPGWELHGKTGWCFDCTPELGWWVGWVKRNERLYGFALNIDMPGGEADIGKRVELGKASLKALGILP"},"dna_sequence":{"accession":"NG_049684.1","fmin":"0","fmax":"789","strand":"+","sequence":"ATGCGCCCTCTCCTCTTCAGCGCCCTTCTCCTGCTCTCCGGGCATGCCCAGGCCAGCGAATGGAACGACAGCCAGGCCGTGGACAAGCTATTCGGCGCGGCCGGGGTGAAAGGCACCTTCGTCCTCTACGATGTGCAGCGGCAGCGCTATGTCGGCCATGACCGGGAGCGCGCGGAAACTCGCTTCGTTCCTGCCTCCACCTACAAGGTGGCGAACAGCCTGATTGGCTTATCCACAGGGGCGGTTAAATCCGCCGACGAGGTTCTTCCCTATGGCGGCAAGCCCCAGCGCTTCAAGGCCTGGGAGCACGACATGAGCCTGCGCGACGCGATCAAGGCATCGAACGTACCGGTCTACCAGGAACTGGCGCGACGCATCGGCCTGGAGCGGATGCGCGCCAATGTCTCGCGCCTGGGTTACGGCAACGCGGAAATCGGCCAGGTTGTGGATAACTTCTGGTTGGTGGGACCGCTGAAGATCAGCGCGATGGAACAGACCCGCTTTCTGCTCCGACTGGCGCAGGGAGAATTGCCATTCCCCGCCCCGGTGCAGTCCACCGTGCGCGCCATGACCCTGCTGGAAAGCGGCCCGGGCTGGGAGCTGCACGGCAAGACCGGCTGGTGCTTCGACTGCACGCCGGAACTCGGCTGGTGGGTGGGCTGGGTGAAGCGCAACGAGCGGCTCTACGGCTTCGCCCTGAACATCGACATGCCCGGCGGCGAGGCCGACATCGGCAAGCGCGTCGAACTGGGCAAGGCCAGTCTCAAGGCTCTCGGGATACTGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37066","NCBI_taxonomy_name":"Pseudomonas","NCBI_taxonomy_id":"286"}}}},"ARO_accession":"3001581","ARO_id":"37981","ARO_name":"OXA-395","CARD_short_name":"OXA-395","ARO_description":"OXA-395 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46513":{"category_aro_accession":"3007724","category_aro_cvterm_id":"46513","category_aro_name":"OXA-50-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-50.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4828":{"model_id":"4828","model_name":"OXA-396","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7203":{"protein_sequence":{"accession":"WP_016852290.1","sequence":"MRPLLLSALLLLSGHTQASEWNDSQAVDKLFGAAGVKGTFVLYDVQRQRYVGHDRERAETRFVPASTYKVANSLIGLSTGAVRSADEVLPYGGKPQRFKAWEHDMSLREAIKASNVPVYQELARRIGLERMRANVSRLGYGNAEIGQVVDNFWLVGPLKISAMEQTHFLLRLAQGELPFPAPVQSTVRAMTLLESGPGWELHGKTGWCFDCTPELGWWVGWVKRNERLYGFALNIDMPGGEADIGKRVELGKASLKALGILP"},"dna_sequence":{"accession":"NG_049685.1","fmin":"0","fmax":"789","strand":"+","sequence":"ATGCGCCCTCTCCTCTTGAGTGCCCTTCTCCTGCTTTCCGGGCATACCCAGGCCAGCGAATGGAACGACAGCCAGGCCGTGGACAAGCTATTCGGCGCGGCCGGGGTGAAAGGCACCTTCGTCCTCTACGATGTGCAGCGGCAGCGCTATGTCGGCCATGACCGGGAGCGCGCGGAAACCCGCTTCGTTCCCGCTTCCACCTACAAGGTGGCGAACAGCCTGATCGGCTTATCCACAGGGGCGGTTAGATCCGCCGACGAGGTTCTTCCCTATGGCGGCAAGCCCCAGCGCTTCAAGGCCTGGGAGCACGACATGAGCCTGCGCGAGGCGATCAAGGCATCGAACGTACCGGTCTACCAGGAACTGGCGCGGCGCATCGGCCTGGAGCGGATGCGCGCCAATGTCTCGCGCCTGGGTTACGGCAACGCGGAAATCGGCCAGGTTGTGGATAACTTCTGGTTGGTGGGACCGCTGAAGATCAGCGCGATGGAACAGACCCACTTTCTGCTCCGACTGGCGCAGGGAGAATTGCCATTCCCCGCCCCGGTGCAGTCCACCGTGCGCGCCATGACCCTGCTGGAAAGCGGCCCGGGCTGGGAGCTGCACGGCAAGACCGGCTGGTGCTTCGACTGCACGCCGGAACTCGGCTGGTGGGTGGGCTGGGTGAAGCGCAACGAGCGGCTCTACGGCTTCGCCCTGAACATCGACATGCCCGGCGGCGAGGCCGACATCGGCAAGCGCGTCGAACTGGGCAAGGCCAGTCTCAAGGCTCTCGGGATACTGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37066","NCBI_taxonomy_name":"Pseudomonas","NCBI_taxonomy_id":"286"}}}},"ARO_accession":"3001582","ARO_id":"37982","ARO_name":"OXA-396","CARD_short_name":"OXA-396","ARO_description":"OXA-396 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46513":{"category_aro_accession":"3007724","category_aro_cvterm_id":"46513","category_aro_name":"OXA-50-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-50.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4829":{"model_id":"4829","model_name":"OXA-489","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7204":{"protein_sequence":{"accession":"WP_002791310.1","sequence":"MKKITLFLLFLNLVFGQDKILNNWFKEYNTSGTFVFYDGKTWASNDFSRAMETFSPASTFKIFNALIALDSGVIKTKKEIFYHYRGEKVFLSSWAQDMNLSSAIKYSNVLAFKEVARRIGIKTMQEYLDKLHYGNAKISKIDTFWLDNSLKISAKEQAILLFRLSQNSLPFSQEAMNSVKEMIYLKNMENLELFGKTGFNDEQKIAWIVGFVYLKDENKYKAFALNLDIDKFEDLYKREKILEKYLDELVKKVKNDG"},"dna_sequence":{"accession":"NG_049769.1","fmin":"100","fmax":"874","strand":"+","sequence":"ATGAAAAAAATAACTTTATTTTTACTTTTCTTAAATTTAGTGTTTGGGCAAGATAAGATATTAAATAATTGGTTTAAAGAGTATAATACAAGCGGCACTTTTGTTTTTTATGATGGAAAAACTTGGGCGAGTAACGACTTTTCAAGGGCTATGGAGACTTTCTCTCCCGCTTCCACTTTTAAAATTTTTAATGCTCTAATTGCACTTGATAGTGGTGTGATAAAAACTAAAAAAGAAATTTTTTATCACTATAGAGGTGAAAAAGTATTTTTATCTTCTTGGGCGCAAGATATGAATTTAAGTTCAGCTATAAAATATTCTAATGTTCTTGCTTTTAAAGAAGTGGCAAGAAGAATTGGTATCAAAACTATGCAAGAATATTTAGACAAGCTTCATTATGGTAATGCTAAAATTTCCAAGATCGATACTTTTTGGCTTGACAACTCACTAAAAATAAGCGCTAAAGAACAAGCAATTTTGCTTTTTAGACTTTCACAAAATAGCTTACCTTTTTCTCAAGAAGCAATGAATAGTGTTAAGGAAATGATTTATTTAAAAAATATGGAAAATTTAGAGCTTTTTGGAAAAACAGGTTTTAATGATGAGCAAAAAATTGCTTGGATTGTAGGTTTTGTGTATTTAAAAGATGAAAATAAATATAAGGCTTTCGCGCTAAATTTAGATATTGATAAATTTGAAGATTTATATAAAAGAGAAAAAATTTTAGAAAAATATTTAGATGAACTTGTAAAAAAAGTTAAAAATGATGGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37052","NCBI_taxonomy_name":"Campylobacter","NCBI_taxonomy_id":"194"}}}},"ARO_accession":"3005724","ARO_id":"44186","ARO_name":"OXA-489","CARD_short_name":"OXA-489","ARO_description":"OXA-489 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46519":{"category_aro_accession":"3007730","category_aro_cvterm_id":"46519","category_aro_name":"OXA-61-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-61.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4830":{"model_id":"4830","model_name":"OXA-491","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7205":{"protein_sequence":{"accession":"WP_020848173.1","sequence":"MNKKIKLIFILIFSINLFANDVELENLFKKYQVEGTLVLESLNTKKVDIYNEKRANTSFSPASTFKIPNTLIALNEGVVNKDSIIVWDKKVREFDAWNKDQTLQSAFKSSCVWCYKEFASKIGVEKYSKYLKELNYGNKTIGKDVTDFWLDESLRITAFEEIRFLKQLQANNLAFKQEDINLLKELMIDEKSENYVVRAKTGWEGKYGWYVGYVETKNDVWFFALNIDTKTKEDLAKRKALTLEALKTKGIIN"},"dna_sequence":{"accession":"NG_049771.1","fmin":"100","fmax":"862","strand":"+","sequence":"ATGAATAAAAAAATAAAACTAATTTTTATTTTAATTTTTTCAATAAATTTATTTGCAAATGATGTGGAACTTGAAAATTTATTTAAAAAATACCAAGTTGAAGGAACTTTAGTATTAGAGTCTTTAAATACAAAAAAAGTAGATATTTATAATGAAAAGAGAGCAAATACATCATTTTCTCCTGCTTCAACATTTAAAATACCAAATACTTTGATAGCTTTAAATGAAGGTGTTGTAAACAAAGATTCTATAATAGTTTGGGATAAAAAAGTAAGAGAATTTGATGCTTGGAATAAAGACCAAACTTTACAATCAGCTTTCAAAAGTTCATGTGTTTGGTGTTATAAAGAGTTCGCTTCAAAAATTGGAGTTGAAAAATATAGTAAGTATCTAAAAGAGCTTAATTATGGAAATAAAACAATAGGCAAAGATGTAACTGATTTTTGGTTGGATGAGAGTTTGAGAATTACAGCTTTTGAAGAGATAAGATTTTTAAAACAATTACAAGCAAACAATTTAGCTTTTAAACAAGAAGATATAAATCTTTTAAAAGAGTTGATGATTGATGAAAAAAGCGAAAATTATGTAGTTAGAGCAAAAACAGGTTGGGAAGGAAAATATGGTTGGTATGTTGGTTATGTTGAAACAAAAAATGATGTTTGGTTTTTTGCTTTAAATATCGACACAAAAACAAAAGAAGATTTAGCAAAAAGAAAAGCTTTAACTTTAGAAGCTTTAAAAACAAAAGGTATTATAAATTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3005725","ARO_id":"44187","ARO_name":"OXA-491","CARD_short_name":"OXA-491","ARO_description":"OXA-491 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4831":{"model_id":"4831","model_name":"OXA-493","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7206":{"protein_sequence":{"accession":"WP_012662081.1","sequence":"MKKIFLLFGLFCSFALANENLKDLFKDYNESGVFIAYDGKNYYSNDFKKANKRILPASTFKIFNALIALNEGVVKDTNEIFYHYKGEKVFLPSWKNNANLALAMQRSQLPAYKELARKIGLEKMQKNLNKLNYGNQKISKIDEFWIDDSLQISLKEQATLLFKLANLTLDYPKHIQEEVINIIKLKENDHYELFAKTGWGLRQYGQIVGFIKSKKSDKIYAFALNMNISDFNKLYLREEIVQLYLDQL"},"dna_sequence":{"accession":"NG_049772.1","fmin":"100","fmax":"847","strand":"+","sequence":"ATGAAAAAAATATTTTTGCTTTTTGGTCTTTTTTGCTCTTTTGCTTTGGCAAATGAAAATTTAAAAGATCTTTTTAAAGATTATAATGAAAGTGGAGTTTTTATAGCTTATGATGGTAAAAATTATTATAGCAATGACTTTAAAAAAGCAAACAAACGCATTTTACCTGCCTCTACTTTTAAAATTTTCAATGCCTTAATCGCACTTAATGAAGGTGTTGTGAAAGATACTAATGAAATTTTTTATCATTACAAAGGTGAAAAAGTATTTTTACCATCTTGGAAAAATAATGCAAACTTAGCTTTAGCTATGCAAAGATCACAACTACCTGCTTATAAAGAACTAGCTAGAAAAATAGGCTTAGAAAAAATGCAAAAAAACTTAAATAAACTTAATTATGGCAACCAAAAAATAAGTAAAATAGATGAGTTTTGGATAGATGATTCTTTACAAATTAGTCTTAAAGAACAAGCTACTTTACTTTTTAAGCTTGCCAATTTAACACTAGACTACCCTAAACATATACAAGAAGAAGTGATTAATATCATCAAGTTAAAAGAAAATGATCATTATGAACTTTTTGCAAAAACAGGTTGGGGTCTTAGACAATATGGACAAATCGTAGGTTTTATAAAAAGTAAAAAAAGTGACAAAATTTACGCTTTTGCTTTAAATATGAATATAAGTGATTTTAACAAGCTTTATCTAAGAGAAGAAATAGTACAACTGTATCTAGATCAATTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37052","NCBI_taxonomy_name":"Campylobacter","NCBI_taxonomy_id":"194"}}}},"ARO_accession":"3005726","ARO_id":"44188","ARO_name":"OXA-493","CARD_short_name":"OXA-493","ARO_description":"OXA-493 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46511":{"category_aro_accession":"3007722","category_aro_cvterm_id":"46511","category_aro_name":"OXA-493-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-493.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4832":{"model_id":"4832","model_name":"OXA-494","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7207":{"protein_sequence":{"accession":"WP_003118452.1","sequence":"MRPLLFSALLLLSGHTQASEWNDSQAVDKLFGAAGVKGTFVLYDVQRQRYVGHDRERAETRFVPASTYKVANSLIGLSTGAVRSADEVLPYGGKPQRFKAWEHDMSLREAIKASNVPVYQELARRIGLERMRANVSRLGYGNAEIGQVVDNFWLVGPLKISAMEQTHFLLRLAQGELPFPAPVQSTVRAMTLLESGPGWELHGKTGWCFDCTPELGWWVGWVKRNERLYGFALNIDMPGGEADIGKRVELGKASLKALGILP"},"dna_sequence":{"accession":"NG_049773.1","fmin":"100","fmax":"889","strand":"+","sequence":"ATGCGCCCCCTCCTCTTCAGTGCCCTTCTCCTGCTTTCCGGGCATACCCAGGCCAGCGAATGGAACGACAGCCAGGCCGTGGACAAGCTATTCGGCGCGGCCGGGGTGAAAGGCACCTTCGTCCTCTACGATGTGCAGCGGCAGCGCTATGTCGGCCATGACCGGGAGCGCGCGGAAACCCGCTTCGTTCCCGCTTCCACCTACAAGGTGGCGAACAGCCTGATCGGCTTATCCACAGGGGCGGTTAGATCCGCCGACGAGGTTCTTCCCTATGGCGGCAAGCCCCAGCGCTTCAAGGCCTGGGAGCACGACATGAGCCTGCGCGAGGCGATCAAGGCATCGAACGTACCGGTCTACCAGGAACTGGCGCGGCGCATCGGCCTGGAGCGGATGCGCGCCAATGTCTCGCGCCTGGGTTACGGCAACGCGGAAATCGGCCAGGTTGTGGATAACTTCTGGTTGGTGGGACCGCTGAAGATCAGCGCGATGGAACAGACCCACTTTCTGCTCCGACTGGCGCAGGGAGAATTGCCATTCCCCGCCCCGGTGCAGTCCACCGTGCGCGCCATGACCCTGCTGGAAAGCGGCCCGGGCTGGGAGCTGCACGGCAAGACCGGCTGGTGCTTCGACTGCACGCCGGAACTCGGCTGGTGGGTGGGCTGGGTGAAGCGCAACGAGCGGCTCTACGGCTTCGCCCTGAACATCGACATGCCCGGCGGCGAGGCCGACATCGGCAAGCGCGTCGAACTGGGCAAGGCCAGTCTCAAGGCTCTCGGGATACTGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37066","NCBI_taxonomy_name":"Pseudomonas","NCBI_taxonomy_id":"286"}}}},"ARO_accession":"3005727","ARO_id":"44189","ARO_name":"OXA-494","CARD_short_name":"OXA-494","ARO_description":"OXA-494 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46513":{"category_aro_accession":"3007724","category_aro_cvterm_id":"46513","category_aro_name":"OXA-50-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-50.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4833":{"model_id":"4833","model_name":"OXA-497","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7208":{"protein_sequence":{"accession":"WP_058061931.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSTSKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRIGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_049774.1","fmin":"100","fmax":"925","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGTTCACCTTATATAGTGACTGCTAATCCAAATCACAGCACTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACTACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTATTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005728","ARO_id":"44190","ARO_name":"OXA-497","CARD_short_name":"OXA-497","ARO_description":"OXA-497 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4834":{"model_id":"4834","model_name":"OXA-498","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7209":{"protein_sequence":{"accession":"WP_063454569.1","sequence":"MKTLQLGLIALITTFGSACTTINPSVETAKNQQQQSAQQQIQQAFDQLQTTGVIVIKDKHGLHSYGNDLSRAQTPYVPASTFKMLNALIGLEHGKATSTEVFKWDGQKNSFPAWEKDMTLGQAMQASAVPVYQELARRIGLDLMQKEVQRIGYGNQKIGTVVDNFWLVGPLQITPVQEVLFVEKLANTKLAFKPDVQHAVQDMLLIEQKSNYKLYAKSGWGMDLEPQVGWWTGWVETSTGEKVYFALNMHMKTGISASAREQLVKQSLTALGII"},"dna_sequence":{"accession":"NG_068178.1","fmin":"100","fmax":"925","strand":"+","sequence":"ATGAAAACTTTACAGTTGGGCCTCATCGCCCTCATTACAACCTTCGGTTCCGCATGTACTACTATAAACCCCTCAGTAGAAACAGCTAAAAACCAACAGCAACAAAGTGCGCAGCAGCAGATCCAACAAGCCTTCGATCAACTCCAAACCACGGGGGTGATTGTCATAAAGGATAAGCATGGCTTACACAGCTACGGCAATGACTTGAGCCGTGCTCAGACACCCTATGTACCCGCCTCTACCTTTAAAATGCTGAATGCCTTAATCGGACTAGAACATGGTAAAGCAACCAGCACCGAGGTGTTTAAATGGGATGGTCAAAAGAACAGCTTCCCTGCTTGGGAAAAAGACATGACTTTAGGGCAAGCCATGCAAGCATCTGCCGTTCCTGTTTATCAGGAGCTTGCACGGCGCATTGGCCTAGACCTAATGCAAAAAGAAGTACAGCGCATTGGATATGGCAATCAAAAGATTGGCACCGTTGTCGATAATTTTTGGTTAGTCGGTCCACTGCAAATTACGCCTGTTCAAGAAGTCCTTTTTGTGGAGAAACTGGCCAATACAAAACTCGCTTTTAAGCCCGACGTGCAACATGCAGTACAAGATATGCTGCTGATTGAACAAAAATCGAATTATAAACTCTACGCCAAATCAGGCTGGGGTATGGACCTAGAACCGCAAGTGGGCTGGTGGACAGGCTGGGTCGAAACTTCAACAGGTGAAAAAGTGTATTTTGCTTTGAATATGCATATGAAAACAGGGATTTCAGCCAGCGCGCGTGAGCAACTGGTCAAACAAAGTCTGACAGCGTTGGGAATAATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39092","NCBI_taxonomy_name":"Acinetobacter johnsonii","NCBI_taxonomy_id":"40214"}}}},"ARO_accession":"3005729","ARO_id":"44191","ARO_name":"OXA-498","CARD_short_name":"OXA-498","ARO_description":"OXA-498 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46494":{"category_aro_accession":"3007705","category_aro_cvterm_id":"46494","category_aro_name":"OXA-211-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-211.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4835":{"model_id":"4835","model_name":"OXA-500","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7210":{"protein_sequence":{"accession":"WP_002121386.1","sequence":"MTKKALFFAIGTMFLSACSFNTVEQHQIQSISTNKNSEKIKSLFDQAQTTGVLVIKRGQTEEVYGNDLKRASTEYVPASTFKMLNALIGLEHHKATPTEVFKWDGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMSKEVKRIGFGNADIGSKVDDFWLVGPLKITPQQEAQFAYELAHKTLPFSKNMQEQVQSMLFIEEKNGRKIYAKSGWGWDVEPQVGWLTGWVVQPQGEIIAFSLNLEMKKGIPSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"NG_049778.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGACTAAAAAAGCTCTTTTCTTTGCCATTGGTACGATGTTTTTGTCTGCATGTTCTTTTAATACGGTAGAACAACATCAAATACAGTCAATTTCTACCAATAAAAACTCAGAGAAAATTAAATCGTTGTTTGATCAAGCACAAACTACAGGTGTTTTAGTTATAAAACGTGGGCAAACAGAGGAAGTCTATGGCAATGATCTTAAAAGAGCATCAACCGAATATGTTCCCGCCTCTACCTTTAAAATGTTAAATGCTTTGATTGGACTTGAGCATCATAAAGCAACACCAACTGAAGTGTTTAAATGGGATGGGCAAAAGCGTTTATTTCCCGATTGGGAAAAAGATATGACATTAGGCGATGCGATGAAAGCTTCTGCTATTCCAGTTTATCAGGAACTAGCTCGACGAATTGGCCTTGATCTTATGTCTAAAGAGGTAAAACGCATTGGTTTCGGTAATGCTGATATTGGTTCAAAAGTAGATGATTTTTGGCTTGTTGGTCCACTTAAAATTACACCTCAACAAGAAGCCCAGTTTGCTTATGAACTAGCCCATAAAACTCTTCCTTTTAGCAAAAATATGCAAGAACAAGTTCAATCTATGCTGTTCATAGAAGAAAAAAATGGACGGAAAATTTATGCCAAAAGTGGTTGGGGATGGGATGTGGAGCCTCAAGTGGGCTGGTTAACAGGCTGGGTCGTTCAACCACAAGGAGAAATTATAGCTTTCTCACTTAATTTAGAAATGAAAAAAGGCATACCTAGCTCTATTCGAAAAGAAATTGCTTATAAGGGATTGGAACAACTCGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40550","NCBI_taxonomy_name":"Acinetobacter calcoaceticus\/baumannii complex","NCBI_taxonomy_id":"909768"}}}},"ARO_accession":"3005730","ARO_id":"44192","ARO_name":"OXA-500","CARD_short_name":"OXA-500","ARO_description":"OXA-500 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46495":{"category_aro_accession":"3007706","category_aro_cvterm_id":"46495","category_aro_name":"OXA-213-like beta-lactamase","category_aro_description":"OXA-213-like enzymes have been identified to be intrinsic to A. calcoaceticus and have been subsequently detected in A. pittii. Phylogenetic analysis of OXA-213-like proteins identified two distinct subgroups within the OXA family. The first group was linked to A. pittii and the second group to A. calcoaceticus. The carbapenemase activity of these OXAs may be related to the species-dependent effect.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4836":{"model_id":"4836","model_name":"OXA-501","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7211":{"protein_sequence":{"accession":"WP_063864113.1","sequence":"MTKKALFFAIGTMFLSACSFNTVEQHQIQSISTNKNSEKIKSLFDQAQTTGVLVIKHGQTEEVYGNDLKRASTEYVPASTFKMLNALIGLEHHKATPTEVFKWDGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMSKEVKRIGFGNADIGSKVDDFWLVGPLKITPQQEAQFAYELAHKTLPFSKNVQEQVQSMVFIEEKNGRKIYAKSGWGWDVEPQVGWLTGWVVQPQGEIVAFSLNLEMKKGIPSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"NG_049779.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGACTAAAAAAGCTCTTTTCTTTGCCATTGGTACGATGTTTTTGTCTGCATGTTCTTTTAATACGGTAGAACAACATCAAATACAGTCAATTTCTACCAATAAAAACTCAGAGAAAATTAAATCGTTGTTTGATCAAGCACAAACTACAGGTGTTTTAGTTATAAAACATGGGCAAACAGAGGAAGTCTATGGCAATGATCTTAAAAGAGCATCAACCGAATATGTTCCCGCCTCTACCTTTAAAATGTTAAATGCTTTGATTGGACTTGAGCATCATAAAGCAACACCAACTGAAGTGTTTAAATGGGATGGGCAAAAGCGTTTGTTTCCTGATTGGGAAAAGGACATGACTCTAGGCGATGCGATGAAAGCTTCTGCTATTCCAGTTTATCAGGAACTAGCTCGACGAATTGGCCTTGATCTTATGTCTAAAGAGGTAAAACGCATTGGTTTCGGTAATGCTGATATTGGTTCAAAAGTAGATGATTTTTGGCTTGTTGGTCCACTTAAAATTACACCTCAACAAGAAGCCCAGTTTGCTTATGAACTAGCCCATAAAACTCTTCCTTTTAGCAAAAATGTGCAAGAACAAGTTCAATCTATGGTGTTCATAGAAGAAAAAAATGGACGAAAAATTTATGCCAAAAGTGGTTGGGGATGGGATGTGGAGCCTCAAGTGGGCTGGTTAACAGGCTGGGTCGTTCAACCTCAAGGAGAAATTGTAGCGTTCTCACTCAATTTAGAAATGAAAAAAGGCATACCTAGTTCTATTCGAAAAGAAATTGCTTATAAGGGATTGGAACAACTCGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3005731","ARO_id":"44193","ARO_name":"OXA-501","CARD_short_name":"OXA-501","ARO_description":"OXA-501 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46495":{"category_aro_accession":"3007706","category_aro_cvterm_id":"46495","category_aro_name":"OXA-213-like beta-lactamase","category_aro_description":"OXA-213-like enzymes have been identified to be intrinsic to A. calcoaceticus and have been subsequently detected in A. pittii. Phylogenetic analysis of OXA-213-like proteins identified two distinct subgroups within the OXA family. The first group was linked to A. pittii and the second group to A. calcoaceticus. The carbapenemase activity of these OXAs may be related to the species-dependent effect.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4837":{"model_id":"4837","model_name":"OXA-502","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7212":{"protein_sequence":{"accession":"WP_032003497.1","sequence":"MTKKALFFAIGTMFLSACSFNTVQQHQIQSISTNKNSEKIKSLFDQAQTEGVLVIKRGQTEEIYGNDLKRSSTEYVPASTFKMLNALIGLEHHKATPTEVFKWDGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMSKEVKRIGFGNADIGSKVDDFWLVGPLKITPQQEAQFAYELAHKTLPFSKNVQEQVQSMLFIEEKNGRKIYAKSGWGWDVEPQVGWLTGWVVQPQGEIVAFSLNLEMKKGIPSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"NG_049780.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGACTAAAAAAGCTCTTTTCTTTGCCATTGGTACGATGTTTTTGTCGGCATGTTCTTTTAATACCGTACAACAACATCAAATACAGTCAATTTCTACCAATAAAAACTCAGAGAAAATTAAATCATTGTTTGATCAAGCACAAACTGAAGGTGTTTTAGTTATAAAACGTGGGCAAACAGAGGAAATCTATGGCAATGATCTTAAAAGATCATCAACCGAATATGTTCCCGCCTCTACCTTTAAAATGTTAAATGCTTTGATTGGACTTGAGCATCATAAAGCAACACCAACTGAAGTGTTTAAATGGGATGGGCAAAAGCGTTTATTTCCCGATTGGGAAAAAGACATGACATTAGGCGATGCGATGAAAGCTTCTGCTATTCCAGTCTATCAGGAACTAGCTCGACGAATTGGCCTTGATCTTATGTCTAAAGAGGTAAAACGCATTGGTTTCGGTAATGCTGATATTGGTTCAAAAGTAGATGATTTTTGGCTTGTTGGTCCACTTAAAATTACACCTCAACAAGAAGCCCAGTTTGCTTATGAACTAGCCCATAAAACTCTTCCTTTTAGCAAGAATGTGCAAGAACAAGTTCAATCTATGCTGTTCATAGAAGAAAAAAATGGACGGAAAATTTATGCCAAAAGTGGTTGGGGATGGGATGTGGAGCCTCAAGTGGGCTGGTTAACAGGCTGGGTCGTTCAACCTCAAGGAGAAATTGTAGCGTTCTCACTCAATTTAGAAATGAAAAAAGGCATACCTAGTTCTATTCGAAAAGAAATTGCTTATAAGGGATTAGAGCAGCTAGGTATTTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40550","NCBI_taxonomy_name":"Acinetobacter calcoaceticus\/baumannii complex","NCBI_taxonomy_id":"909768"}}}},"ARO_accession":"3005732","ARO_id":"44194","ARO_name":"OXA-502","CARD_short_name":"OXA-502","ARO_description":"OXA-502 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46495":{"category_aro_accession":"3007706","category_aro_cvterm_id":"46495","category_aro_name":"OXA-213-like beta-lactamase","category_aro_description":"OXA-213-like enzymes have been identified to be intrinsic to A. calcoaceticus and have been subsequently detected in A. pittii. Phylogenetic analysis of OXA-213-like proteins identified two distinct subgroups within the OXA family. The first group was linked to A. pittii and the second group to A. calcoaceticus. The carbapenemase activity of these OXAs may be related to the species-dependent effect.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4838":{"model_id":"4838","model_name":"OXA-503","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7213":{"protein_sequence":{"accession":"WP_063864114.1","sequence":"MTKKALFFAIGTMFLSACSFNTVQQHQIQSISTNKNSEKIKSLFDQAQNEGVLVIKRGQTEEIYGNDLKRSSTEYVPASTFKMLNALIGLEHHKATPTEVFKWDGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMSKEVKRIGFGNADIGSKVDDFWLVGPLKITPQQEAQFAYELAHKTLPFSKNVQEQVQSMLFIEEKNGRKIYAKSGWGWDVEPQVGWLTGWVVQPQGKIVAFSLNLEMKKGIPSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"NG_049781.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGACTAAAAAAGCTCTTTTCTTTGCCATTGGTACGATGTTTTTGTCGGCATGTTCTTTTAATACCGTACAACAACATCAAATACAGTCAATTTCTACCAATAAAAACTCAGAGAAAATTAAATCATTGTTTGATCAAGCACAAAATGAAGGTGTTTTAGTTATAAAACGTGGGCAAACAGAGGAAATCTATGGCAATGATCTTAAAAGATCATCAACCGAATATGTTCCCGCCTCTACCTTTAAAATGTTAAATGCTTTGATTGGACTTGAGCATCATAAAGCAACACCAACTGAAGTGTTTAAATGGGATGGGCAAAAGCGTTTGTTTCCTGATTGGGAAAAGGACATGACTCTAGGCGATGCGATGAAAGCTTCTGCTATTCCAGTTTATCAGGAACTAGCTCGACGAATTGGCCTTGATCTTATGTCTAAAGAGGTAAAACGCATTGGTTTCGGTAATGCTGATATTGGTTCAAAAGTAGATGATTTTTGGCTTGTTGGTCCACTTAAAATTACACCTCAACAAGAAGCCCAGTTTGCTTATGAACTAGCCCATAAAACTCTTCCTTTTAGCAAGAATGTGCAAGAACAAGTTCAATCTATGCTGTTCATAGAAGAAAAAAATGGACGGAAAATTTATGCCAAAAGTGGTTGGGGATGGGATGTGGAGCCTCAAGTGGGCTGGTTAACAGGCTGGGTCGTTCAACCTCAAGGAAAAATTGTAGCGTTCTCACTCAATTTAGAAATGAAAAAAGGCATACCTAGTTCTATTCGAAAAGAAATTGCTTATAAGGGATTAGAGCAGCTAGGTATTTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3005733","ARO_id":"44195","ARO_name":"OXA-503","CARD_short_name":"OXA-503","ARO_description":"OXA-503 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46495":{"category_aro_accession":"3007706","category_aro_cvterm_id":"46495","category_aro_name":"OXA-213-like beta-lactamase","category_aro_description":"OXA-213-like enzymes have been identified to be intrinsic to A. calcoaceticus and have been subsequently detected in A. pittii. Phylogenetic analysis of OXA-213-like proteins identified two distinct subgroups within the OXA family. The first group was linked to A. pittii and the second group to A. calcoaceticus. The carbapenemase activity of these OXAs may be related to the species-dependent effect.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4839":{"model_id":"4839","model_name":"OXA-504","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7214":{"protein_sequence":{"accession":"WP_063864115.1","sequence":"MPRMLLSSLLAAGLFCALPASAASGCMLFADGTGKPVSTQGDCAAQLTPASTFKIPLALMGYDSGFLVDEQLPALPFKAGDPDFLPEWKQTTTPSSWMQFSVIWYSQRLTEWLGEARFQHYVDSFDYGNRDLEGNPGKHDGLTQAWLSASLAISPQEQARFLGKMVSGKLPVSAQTLRHTANLMRQPDIDGWQIHGKTGMGYPKLLDGSLDREQQIGWFVGWASKQDKTLIFVHTVIQTPGKQFASLRAREEVFAALPARLKTL"},"dna_sequence":{"accession":"NG_049782.1","fmin":"0","fmax":"795","strand":"+","sequence":"ATGCCCCGTATGCTGTTGTCCAGTCTGCTTGCTGCTGGCCTCTTCTGTGCACTGCCTGCCAGCGCCGCTTCTGGCTGCATGCTGTTTGCCGACGGCACCGGCAAACCCGTCAGCACCCAGGGGGACTGTGCCGCCCAGTTGACCCCGGCCTCCACCTTCAAGATCCCGCTGGCACTGATGGGCTATGACAGCGGCTTCCTGGTGGATGAACAACTGCCTGCCCTGCCGTTCAAGGCCGGTGATCCTGATTTCCTGCCGGAGTGGAAACAGACCACCACCCCGAGCAGCTGGATGCAATTCTCGGTCATCTGGTACTCGCAGCGCCTCACCGAGTGGCTGGGAGAGGCTCGCTTCCAGCACTACGTGGACAGCTTCGACTACGGCAACCGGGATCTCGAAGGCAACCCGGGCAAGCACGACGGTCTGACCCAGGCCTGGCTCAGCGCCAGCCTCGCCATCAGCCCCCAGGAGCAAGCCCGCTTCCTTGGCAAGATGGTGAGCGGCAAGCTGCCGGTCTCCGCCCAGACCCTGCGCCATACCGCCAACCTGATGCGTCAGCCCGACATCGACGGTTGGCAGATCCACGGCAAGACCGGCATGGGTTACCCCAAGCTGCTGGATGGCAGCTTGGACAGGGAGCAGCAGATCGGCTGGTTCGTCGGCTGGGCCAGCAAACAGGACAAGACGCTCATCTTCGTCCACACCGTCATCCAGACGCCGGGCAAGCAGTTCGCTTCCCTCAGGGCCAGGGAGGAGGTGTTCGCCGCCCTGCCGGCCCGGTTGAAGACACTCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36936","NCBI_taxonomy_name":"Aeromonas caviae","NCBI_taxonomy_id":"648"}}}},"ARO_accession":"3005734","ARO_id":"44196","ARO_name":"OXA-504","CARD_short_name":"OXA-504","ARO_description":"OXA-504 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4840":{"model_id":"4840","model_name":"OXA-505","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7215":{"protein_sequence":{"accession":"WP_063864118.1","sequence":"MRVLALSTVFLVASIIGMPAVAKEWQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGQTRDIATWNRDHNLITAMKYSVVPVYQEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISATEQISFLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYSTRIEPKIGWWVGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP"},"dna_sequence":{"accession":"NG_049783.1","fmin":"0","fmax":"798","strand":"+","sequence":"ATGCGTGTATTAGCCTTATCGACTGTGTTTTTGGTGGCATCGATTATCGGAATGCCTGCGGTAGCAAAGGAATGGCAAGAAAACAAAAGTTGGAATGCTCACTTTACTGAACATAAATCACAGGGCGTAGTTGTGCTCTGGAATGAGAATAAGCAGCAAGGATTTACCAATAATCTTAAACGGGCGAACCAAGCATTTTTACCCGCATCTACCTTTAAAATTCCCAATAGCTTGATCGCCCTCGATTTGGGCGTGGTTAAGGATGAACACCAAGTCTTTAAGTGGGATGGACAGACGCGCGATATCGCCACTTGGAATCGCGATCATAATCTAATCACCGCGATGAAATATTCAGTTGTGCCTGTTTATCAAGAATTTGCCCGCCAAATTGGCGAGGCACGTATGAGCAAGATGCTACATGCTTTCGATTATGGTAATGAGGACATTTCGGGCAATGTAGACAGTTTCTGGCTCGACGGTGGTATTCGAATTTCGGCCACGGAGCAAATCAGCTTTTTAAGAAAGCTGTATCACAATAAGTTACACGTATCGGAGCGCAGCCAGCGTATTGTCAAACAAGCCATGCTGACCGAAGCCAATGGTGACTATATTATTCGGGCTAAAACTGGATACTCGACTAGAATCGAACCTAAGATTGGCTGGTGGGTCGGTTGGGTTGAACTTGATGATAATGTGTGGTTTTTTGCGATGAATATGGATATGCCCACATCGGATGGTTTAGGGCTGCGCCAAGCCATCACAAAAGAAGTGCTCAAACAGGAAAAAATTATTCCCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3005735","ARO_id":"44197","ARO_name":"OXA-505","CARD_short_name":"OXA-505","ARO_description":"OXA-505 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46510":{"category_aro_accession":"3007721","category_aro_cvterm_id":"46510","category_aro_name":"OXA-48-like beta-lactamase","category_aro_description":"OXA-48-type beta-lactamases are now routinely encountered in bacterial infections caused by carbapenam-resistant Enterobacterales. OXA-48-like proteins confer resistance to penicillin (which is efficiently hydrolyzed) and carbapenam antibiotics (which is more slowly broken down). The spectrum of activity of these variants varies, with some hydrolyzing expanded-spectrum oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4841":{"model_id":"4841","model_name":"OXA-506","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7216":{"protein_sequence":{"accession":"WP_032007272.1","sequence":"MTKKALFFAIGTMFLSACSFNTVQQHQIQSISTNKNSEKIKSLFDQAQTEGVLVIKRGQTEEIYGNDLKRSSTEYVPASTFKMLNALIGLEHHKATPTEVFKWDGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMSKEVKRIGFGNADIGSKVDDFWLVGPLKITPQQEAQFAYELAHKTLPFSKNVQEQVQSMLFIEEKNGRKIYAKSGWGWDVEPQVGWLTGWVVQPQGKIVAFSLNLEMKKGIPSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"NG_049784.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGACTAAAAAAGCTCTTTTCTTTGCCATTGGTACGATGTTTTTGTCGGCATGTTCTTTTAATACCGTACAACAACATCAAATACAGTCAATTTCTACCAATAAAAACTCAGAGAAAATTAAATCATTGTTTGATCAAGCACAAACTGAAGGTGTTTTAGTTATAAAACGTGGGCAAACAGAGGAAATCTATGGCAATGATCTTAAAAGATCATCAACCGAATATGTTCCCGCCTCTACCTTTAAAATGTTAAATGCTTTGATTGGACTTGAGCATCATAAAGCAACACCAACTGAAGTGTTTAAATGGGATGGGCAAAAGCGTTTGTTTCCTGATTGGGAAAAGGACATGACTCTAGGCGATGCGATGAAAGCTTCTGCTATTCCAGTTTATCAGGAACTAGCTCGACGAATTGGCCTTGATCTTATGTCTAAAGAGGTAAAACGCATTGGTTTCGGTAATGCTGATATTGGTTCAAAAGTAGATGATTTTTGGCTTGTTGGTCCACTTAAAATTACACCTCAACAAGAAGCCCAGTTTGCTTATGAACTAGCCCATAAAACTCTTCCTTTTAGCAAGAATGTGCAAGAACAAGTTCAATCTATGCTGTTCATAGAAGAAAAAAATGGACGGAAAATTTATGCCAAAAGTGGTTGGGGATGGGATGTGGAGCCTCAAGTGGGCTGGTTAACAGGCTGGGTCGTTCAACCTCAAGGAAAAATTGTAGCGTTCTCACTCAATTTAGAAATGAAAAAAGGCATACCTAGTTCTATTCGAAAAGAAATTGCTTATAAGGGATTAGAGCAGCTAGGTATTTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37046","NCBI_taxonomy_name":"Acinetobacter","NCBI_taxonomy_id":"469"}}}},"ARO_accession":"3005736","ARO_id":"44198","ARO_name":"OXA-506","CARD_short_name":"OXA-506","ARO_description":"OXA-506 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46495":{"category_aro_accession":"3007706","category_aro_cvterm_id":"46495","category_aro_name":"OXA-213-like beta-lactamase","category_aro_description":"OXA-213-like enzymes have been identified to be intrinsic to A. calcoaceticus and have been subsequently detected in A. pittii. Phylogenetic analysis of OXA-213-like proteins identified two distinct subgroups within the OXA family. The first group was linked to A. pittii and the second group to A. calcoaceticus. The carbapenemase activity of these OXAs may be related to the species-dependent effect.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4842":{"model_id":"4842","model_name":"OXA-507","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7217":{"protein_sequence":{"accession":"WP_063864138.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDDKAEKIKNLFNEAHTTGVLVIHQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGEKRLFPEWEKNMTLGDAMKASAILVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_049785.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGACAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCATCAAGGTCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAATGGGATGGGGAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCTGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTCTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005737","ARO_id":"44199","ARO_name":"OXA-507","CARD_short_name":"OXA-507","ARO_description":"OXA-507 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4843":{"model_id":"4843","model_name":"OXA-508","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7218":{"protein_sequence":{"accession":"WP_063864150.1","sequence":"MNIKTLLLITSAIFISACSPYIVTANPNHSASKSDVKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_049786.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAACACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGTAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAACAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005738","ARO_id":"44200","ARO_name":"OXA-508","CARD_short_name":"OXA-508","ARO_description":"OXA-508 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4844":{"model_id":"4844","model_name":"OXA-509","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7219":{"protein_sequence":{"accession":"WP_063864158.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKTTTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAILVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_049787.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCCCTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTCTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGACAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGACGCTATGAAAGCTTCCGCTATTCTGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCATTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005739","ARO_id":"44201","ARO_name":"OXA-509","CARD_short_name":"OXA-509","ARO_description":"OXA-509 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4845":{"model_id":"4845","model_name":"OXA-510","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7220":{"protein_sequence":{"accession":"WP_068981635.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANNTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_051470.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAATACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005740","ARO_id":"44202","ARO_name":"OXA-510","CARD_short_name":"OXA-510","ARO_description":"OXA-510 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4846":{"model_id":"4846","model_name":"OXA-511","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7221":{"protein_sequence":{"accession":"WP_068981636.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKNKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_051471.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCCCTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAAATAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTAGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAACAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005741","ARO_id":"44203","ARO_name":"OXA-511","CARD_short_name":"OXA-511","ARO_description":"OXA-511 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4847":{"model_id":"4847","model_name":"OXA-512","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7222":{"protein_sequence":{"accession":"WP_063864184.1","sequence":"MKLLKILSLVCLSISIGACAEHSMSRAKTSTFPQVNNSIIDQNVQALFNEISADAVFVTYDGQNIKKYGTHLDRAKTAYIPASTFKIANALIGLENHKATSTEIFKWDGKPRFFKEWDKDFTLGEAMQASTVPVYQELARRIGPSLMQSELQRIGYGNMQIGTEVDQFWLKGPLTITPIQEVKFVYDLAQGQLPFKPEVQQQVKEMLYVERRGENSLYAKSGWGMAVDPQVGWYVGFVEKADGQVVAFALNMQMKAGDDSALRKQLSLDVLDKLGVFHYL"},"dna_sequence":{"accession":"NG_049789.1","fmin":"0","fmax":"843","strand":"+","sequence":"ATGAAATTATTAAAAATATTGAGTTTAGTTTGCTTAAGCATAAGTATTGGGGCTTGTGCTGAGCATAGTATGAGTCGAGCAAAAACAAGTACATTCCCACAAGTGAATAACTCAATCATCGATCAGAATGTTCAAGCGCTTTTTAATGAAATCTCAGCTGATGCTGTGTTTGTCACATATGATGGTCAAAATATTAAAAAATATGGCACGCATTTAGACCGAGCAAAAACAGCTTATATTCCTGCATCTACATTTAAAATTGCCAATGCACTAATTGGTTTAGAAAATCATAAAGCAACATCTACAGAAATATTTAAGTGGGATGGAAAGCCACGTTTTTTTAAAGAATGGGACAAAGATTTTACTTTGGGCGAAGCCATGCAAGCATCTACAGTGCCTGTATATCAAGAATTGGCACGTCGTATTGGTCCAAGCTTAATGCAAAGTGAATTGCAACGTATTGGTTATGGCAATATGCAAATAGGCACGGAAGTTGATCAATTTTGGTTGAAAGGGCCTTTGACAATTACACCTATACAAGAAGTAAAGTTTGTGTATGATTTAGCCCAAGGGCAATTGCCTTTTAAACCTGAAGTTCAGCAACAAGTGAAAGAGATGTTGTATGTAGAGCGCAGAGGGGAGAATAGTCTATATGCTAAAAGTGGCTGGGGAATGGCTGTAGACCCGCAAGTGGGTTGGTATGTGGGTTTTGTTGAAAAGGCAGATGGGCAAGTGGTGGCATTTGCTTTAAATATGCAAATGAAAGCTGGTGATGATAGTGCTCTACGTAAACAATTGTCTTTAGATGTGCTAGATAAGTTGGGTGTTTTTCATTATTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005742","ARO_id":"44204","ARO_name":"OXA-512","CARD_short_name":"OXA-512","ARO_description":"OXA-512 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46517":{"category_aro_accession":"3007728","category_aro_cvterm_id":"46517","category_aro_name":"OXA-58-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-58.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4848":{"model_id":"4848","model_name":"OXA-513","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7223":{"protein_sequence":{"accession":"WP_063864194.1","sequence":"MTVRRFSCALGAALSLSALAGVPARAAVLCTVVADAADGRIVFQQGTQAACAERYTPASTFKLPIALMGADAGILQGPHAPVWNYQPGYPDWGGDAWRQPTDPARWIKYSVVWYSQLTARALGQERFQRYASAFQYGNEDVSGEPGKHNGLDGAWINSSLRISPLEQLAFLRKLVNRQLPLKPAAYDLAETLFDAGEAGGWRLYGKTGTGSPGSNGVYTPDNAYGWFVGWARKDGRQLVFARLLQDEKATKPNAGLRARDDLMRDWPAMADAPRQ"},"dna_sequence":{"accession":"NG_049790.1","fmin":"0","fmax":"828","strand":"+","sequence":"ATGACCGTTCGACGTTTTTCGTGCGCCCTGGGCGCAGCCCTTTCCCTGTCCGCGCTGGCGGGCGTCCCCGCCCGCGCGGCGGTTTTGTGCACCGTGGTGGCCGACGCCGCCGACGGCCGCATCGTGTTCCAGCAAGGCACGCAGGCGGCCTGCGCCGAGCGCTACACGCCGGCCTCGACCTTCAAGCTGCCGATCGCGCTGATGGGCGCGGACGCGGGCATCCTGCAAGGCCCGCACGCGCCGGTCTGGAACTACCAGCCGGGCTACCCCGACTGGGGCGGCGACGCCTGGCGCCAGCCGACGGACCCGGCGCGCTGGATCAAGTATTCGGTGGTCTGGTATTCGCAGCTGACCGCCAGGGCGCTGGGGCAGGAGCGCTTCCAGCGCTACGCCTCGGCCTTCCAGTACGGCAACGAGGACGTCTCGGGCGAGCCCGGCAAGCACAACGGCCTGGATGGCGCGTGGATCAACTCGTCGCTGCGCATTTCGCCGCTGGAGCAACTGGCGTTCCTGCGCAAGCTGGTCAACCGGCAATTGCCGCTCAAGCCCGCGGCCTACGATCTGGCCGAGACGCTGTTCGACGCCGGCGAGGCCGGCGGCTGGCGCCTGTATGGCAAGACCGGCACCGGCTCGCCGGGCAGCAACGGCGTCTACACGCCGGACAACGCCTACGGCTGGTTCGTCGGCTGGGCGCGCAAGGACGGCCGCCAGCTGGTGTTCGCCCGCCTGCTGCAGGACGAGAAGGCCACCAAACCCAACGCCGGCCTGCGCGCCCGCGATGACCTGATGCGCGACTGGCCGGCCATGGCCGACGCGCCCCGCCAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42556","NCBI_taxonomy_name":"Achromobacter insuavis","NCBI_taxonomy_id":"1287735"}}}},"ARO_accession":"3005743","ARO_id":"44205","ARO_name":"OXA-513","CARD_short_name":"OXA-513","ARO_description":"OXA-513 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46505":{"category_aro_accession":"3007716","category_aro_cvterm_id":"46505","category_aro_name":"OXA-364-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-364.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4849":{"model_id":"4849","model_name":"OXA-514","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7224":{"protein_sequence":{"accession":"WP_094009803.1","sequence":"MRVLALSAVFLVASIIGMPAVAKEWQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGQTRDIATWNRDHNLITAMKYSVVPVYQEFARQIGEARMSKMLHAFDYGNEDISGNLDTFWLDGGIRISATEQISFLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYSTRIEPKIGWWVGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP"},"dna_sequence":{"accession":"NG_055475.1","fmin":"0","fmax":"798","strand":"+","sequence":"ATGCGTGTATTAGCCTTATCGGCTGTGTTTTTGGTGGCATCGATTATCGGAATGCCTGCGGTAGCAAAGGAATGGCAAGAAAACAAAAGTTGGAATGCTCACTTTACTGAACATAAATCACAGGGCGTAGTTGTGCTCTGGAATGAGAATAAGCAGCAAGGATTTACCAATAATCTTAAACGGGCGAACCAAGCATTTTTACCCGCATCTACCTTTAAAATTCCCAATAGCTTGATCGCCCTCGATTTGGGCGTGGTTAAGGATGAACACCAAGTCTTTAAGTGGGATGGACAGACGCGCGATATCGCCACTTGGAATCGCGATCATAATTTAATCACCGCGATGAAATATTCGGTTGTGCCTGTTTATCAAGAATTTGCCCGCCAAATTGGCGAGGCACGTATGAGCAAGATGCTGCACGCCTTCGATTATGGCAATGAGGACATTTCGGGCAATTTAGATACTTTTTGGCTTGATGGTGGCATTCGAATTTCGGCCACTGAGCAAATCAGCTTTTTAAGAAAGCTGTATCACAATAAGTTACACGTATCGGAGCGCAGCCAGCGTATTGTCAAACAAGCCATGCTGACCGAAGCCAATGGCGACTATATTATTCGGGCTAAAACGGGATACTCGACTAGAATCGAACCTAAGATTGGCTGGTGGGTCGGTTGGGTTGAACTTGATGATAATGTGTGGTTTTTTGCGATGAATATGGATATGCCCACATCGGATGGTTTAGGGCTGCGCCAAGCCATCACAAAAGAAGTGCTCAAACAGGAGAAAATTATTCCCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3005744","ARO_id":"44206","ARO_name":"OXA-514","CARD_short_name":"OXA-514","ARO_description":"OXA-514 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46510":{"category_aro_accession":"3007721","category_aro_cvterm_id":"46510","category_aro_name":"OXA-48-like beta-lactamase","category_aro_description":"OXA-48-type beta-lactamases are now routinely encountered in bacterial infections caused by carbapenam-resistant Enterobacterales. OXA-48-like proteins confer resistance to penicillin (which is efficiently hydrolyzed) and carbapenam antibiotics (which is more slowly broken down). The spectrum of activity of these variants varies, with some hydrolyzing expanded-spectrum oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4850":{"model_id":"4850","model_name":"OXA-515","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7225":{"protein_sequence":{"accession":"WP_094009804.1","sequence":"MRVLALSAVFLVASIIGMPAVAKEWQENKSWNAHFTEHKSQGVVALWNENKQQGFTNNLKRANQAFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGQTRDIATWNRDHNLITAMKYSVVPVYQEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISATEQISFLRKLYHNKLHVSERSQRIVKQAMLTEANSDYIIRAKTGYSTRIEPKIGWWVGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP"},"dna_sequence":{"accession":"NG_055476.1","fmin":"0","fmax":"798","strand":"+","sequence":"ATGCGTGTATTAGCCTTATCGGCTGTGTTTTTGGTGGCATCGATTATCGGCATGCCTGCGGTAGCAAAGGAATGGCAAGAAAACAAAAGTTGGAATGCTCACTTTACTGAACATAAATCACAGGGCGTAGTTGCGCTCTGGAATGAGAATAAGCAGCAAGGATTTACCAATAATCTTAAACGGGCGAACCAAGCATTTTTACCCGCATCTACCTTTAAAATTCCCAATAGCTTGATCGCCCTCGATTTGGGCGTGGTTAAGGATGAACACCAAGTCTTTAAGTGGGATGGACAGACGCGCGATATCGCCACTTGGAATCGCGATCATAATCTAATCACCGCGATGAAATATTCAGTTGTGCCTGTTTATCAAGAATTTGCCCGCCAAATTGGCGAGGCACGTATGAGCAAGATGCTACATGCTTTCGATTATGGTAATGAGGACATTTCGGGCAATGTAGACAGTTTCTGGCTCGACGGTGGTATTCGAATTTCGGCCACTGAGCAAATCAGCTTTTTAAGAAAGCTGTATCACAATAAGTTACACGTATCGGAGCGCAGCCAGCGTATTGTCAAACAAGCCATGCTGACCGAAGCCAATAGCGACTATATTATTCGGGCTAAAACGGGATACTCGACTAGAATCGAACCTAAGATTGGCTGGTGGGTCGGTTGGGTTGAACTTGATGATAATGTGTGGTTTTTTGCGATGAATATGGATATGCCCACATCGGATGGTTTAGGGCTGCGCCAAGCCATCACAAAAGAAGTGCTCAAACAGGAAAAAATTATTCCCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3005745","ARO_id":"44207","ARO_name":"OXA-515","CARD_short_name":"OXA-515","ARO_description":"OXA-515 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46510":{"category_aro_accession":"3007721","category_aro_cvterm_id":"46510","category_aro_name":"OXA-48-like beta-lactamase","category_aro_description":"OXA-48-type beta-lactamases are now routinely encountered in bacterial infections caused by carbapenam-resistant Enterobacterales. OXA-48-like proteins confer resistance to penicillin (which is efficiently hydrolyzed) and carbapenam antibiotics (which is more slowly broken down). The spectrum of activity of these variants varies, with some hydrolyzing expanded-spectrum oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4851":{"model_id":"4851","model_name":"OXA-516","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7226":{"protein_sequence":{"accession":"WP_063864208.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDKKAEKIKNLFNEAHTTGVLVIQQDQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKNMTLGDAMKASALPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_049791.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAATATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATAAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGACCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACTACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTCTTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005746","ARO_id":"44208","ARO_name":"OXA-516","CARD_short_name":"OXA-516","ARO_description":"OXA-516 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4852":{"model_id":"4852","model_name":"OXA-517","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7227":{"protein_sequence":{"accession":"WP_085562384.1","sequence":"MRVLALSAVFLVASIIGMPAVAKEWQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGQTRDIATWNRDHNLITAMKYSVVPVYQEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISATEQISFLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYSTKPKIGWWVGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP"},"dna_sequence":{"accession":"NG_054666.1","fmin":"0","fmax":"792","strand":"+","sequence":"ATGCGTGTATTAGCCTTATCGGCTGTGTTTTTGGTGGCATCGATTATCGGAATGCCTGCGGTAGCAAAGGAATGGCAAGAAAACAAAAGTTGGAATGCTCACTTTACTGAACATAAATCACAGGGCGTAGTTGTGCTCTGGAATGAGAATAAGCAGCAAGGATTTACCAATAATCTTAAACGGGCGAACCAAGCATTTTTACCCGCATCTACCTTTAAAATTCCCAATAGCTTGATCGCCCTCGATTTGGGCGTGGTTAAGGATGAACACCAAGTCTTTAAGTGGGATGGACAGACGCGCGATATCGCCACTTGGAATCGCGATCATAATCTAATCACCGCGATGAAATATTCAGTTGTGCCTGTTTATCAAGAATTTGCCCGCCAAATTGGCGAGGCACGTATGAGCAAGATGCTACATGCTTTCGATTATGGTAATGAGGACATTTCGGGCAATGTAGACAGTTTCTGGCTCGACGGTGGTATTCGAATTTCGGCCACGGAGCAAATCAGCTTTTTAAGAAAGCTGTATCACAATAAGTTACACGTATCGGAGCGCAGCCAGCGTATTGTCAAACAAGCCATGCTGACCGAAGCCAATGGTGACTATATTATTCGGGCTAAAACTGGATACTCGACTAAACCTAAGATTGGCTGGTGGGTCGGTTGGGTTGAACTTGATGATAATGTGTGGTTTTTTGCGATGAATATGGATATGCCCACATCGGATGGTTTAGGGCTGCGCCAAGCCATCACAAAAGAAGTGCTCAAACAGGAAAAAATTATTCCCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3005747","ARO_id":"44209","ARO_name":"OXA-517","CARD_short_name":"OXA-517","ARO_description":"OXA-517 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46510":{"category_aro_accession":"3007721","category_aro_cvterm_id":"46510","category_aro_name":"OXA-48-like beta-lactamase","category_aro_description":"OXA-48-type beta-lactamases are now routinely encountered in bacterial infections caused by carbapenam-resistant Enterobacterales. OXA-48-like proteins confer resistance to penicillin (which is efficiently hydrolyzed) and carbapenam antibiotics (which is more slowly broken down). The spectrum of activity of these variants varies, with some hydrolyzing expanded-spectrum oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4853":{"model_id":"4853","model_name":"OXA-518","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7228":{"protein_sequence":{"accession":"WP_063864216.1","sequence":"MKKIFLLFGLFCSFALANENLKDLFKDYNESGVFIAYDGKNYYSNDFKKANKRILPASTFKIFNALIALNEDVVKDTNEIFYHYKGEKVFLPSWKNNANLALAMQRSQLPAYKELARKIGLEKMQKNLNKLNYGNQKISKIDEFWIDDSLQISLKEQATLLFKLANLTLDYPKHIQEEVINIIKLKENDHYELFAKTGWGLRQYGQIVGFIKSKKSDKIYAFALNMNISDFNKLYLREEIVQLYLDQL"},"dna_sequence":{"accession":"NG_049792.1","fmin":"0","fmax":"747","strand":"+","sequence":"ATGAAAAAAATATTTTTGCTTTTTGGTCTTTTTTGCTCTTTTGCTTTGGCAAATGAAAATTTAAAAGATCTTTTTAAAGATTATAATGAAAGTGGAGTTTTTATAGCTTATGATGGTAAAAATTATTATAGCAATGACTTTAAAAAAGCAAACAAACGCATTTTACCTGCCTCTACTTTTAAAATTTTCAATGCCTTAATCGCACTTAATGAAGATGTTGTGAAAGATACTAATGAAATTTTTTATCATTACAAAGGTGAAAAAGTATTTTTACCATCTTGGAAAAATAATGCAAACTTAGCTTTAGCTATGCAAAGATCACAACTACCTGCTTATAAAGAACTAGCTAGAAAAATAGGCTTAGAAAAAATGCAAAAAAACTTAAATAAACTTAATTATGGCAACCAAAAAATAAGTAAAATAGATGAGTTTTGGATAGATGATTCTTTACAAATTAGTCTTAAAGAACAAGCTACTTTACTTTTTAAGCTTGCCAATTTAACACTAGATTACCCTAAACATATACAAGAAGAAGTGATTAATATCATCAAGTTAAAAGAAAATGATCATTATGAACTTTTTGCAAAAACAGGTTGGGGTCTTAGACAATATGGACAAATCGTAGGTTTTATAAAAAGTAAAAAAAGTGACAAAATTTACGCTTTTGCTTTAAATATGAATATAAGTGATTTTAACAAGCTTTATCTAAGAGAAGAAATAGTACAACTGTATCTAGATCAATTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3005748","ARO_id":"44210","ARO_name":"OXA-518","CARD_short_name":"OXA-518","ARO_description":"OXA-518 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46511":{"category_aro_accession":"3007722","category_aro_cvterm_id":"46511","category_aro_name":"OXA-493-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-493.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4854":{"model_id":"4854","model_name":"OXA-519","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7229":{"protein_sequence":{"accession":"WP_094009808.1","sequence":"MRVLALSAVFLVASIIGMPAVAKEWQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGQTRDIATWNRDHNLITAMKYSVLPVYQEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISATEQISFLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYSTRIEPKIGWWVGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP"},"dna_sequence":{"accession":"NG_055490.1","fmin":"0","fmax":"798","strand":"+","sequence":"ATGCGTGTATTAGCCTTATCGGCTGTGTTTTTGGTGGCATCGATTATCGGAATGCCTGCGGTAGCAAAGGAATGGCAAGAAAACAAAAGTTGGAATGCTCACTTTACTGAACATAAATCACAGGGCGTAGTTGTGCTCTGGAATGAGAATAAGCAGCAAGGATTTACCAATAATCTTAAACGGGCGAACCAAGCATTTTTACCCGCATCTACCTTTAAAATTCCCAATAGCTTGATCGCCCTCGATTTGGGCGTGGTTAAGGATGAACACCAAGTCTTTAAGTGGGATGGACAGACGCGCGATATCGCCACTTGGAATCGCGATCATAATCTAATCACCGCGATGAAATATTCAGTTTTGCCTGTTTATCAAGAATTTGCCCGCCAAATTGGCGAGGCACGTATGAGCAAGATGCTACATGCTTTCGATTATGGTAATGAGGACATTTCGGGCAATGTAGACAGTTTCTGGCTCGACGGTGGTATTCGAATTTCGGCCACGGAGCAAATCAGCTTTTTAAGAAAGCTGTATCACAATAAGTTACACGTATCGGAGCGCAGCCAGCGTATTGTCAAACAAGCCATGCTGACCGAAGCCAATGGTGACTATATTATTCGGGCTAAAACTGGATACTCGACTAGAATCGAACCTAAGATTGGCTGGTGGGTCGGTTGGGTTGAACTTGATGATAATGTGTGGTTTTTTGCGATGAATATGGATATGCCCACATCGGATGGTTTAGGGCTGCGCCAAGCCATCACAAAAGAAGTGCTCAAACAGGAAAAAATTATTCCCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3005749","ARO_id":"44211","ARO_name":"OXA-519","CARD_short_name":"OXA-519","ARO_description":"OXA-519 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46510":{"category_aro_accession":"3007721","category_aro_cvterm_id":"46510","category_aro_name":"OXA-48-like beta-lactamase","category_aro_description":"OXA-48-type beta-lactamases are now routinely encountered in bacterial infections caused by carbapenam-resistant Enterobacterales. OXA-48-like proteins confer resistance to penicillin (which is efficiently hydrolyzed) and carbapenam antibiotics (which is more slowly broken down). The spectrum of activity of these variants varies, with some hydrolyzing expanded-spectrum oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4855":{"model_id":"4855","model_name":"OXA-520","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7230":{"protein_sequence":{"accession":"WP_065159014.1","sequence":"MKTFAAYVIIACLSSTALAGSITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFGLEGQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGIIGG"},"dna_sequence":{"accession":"NG_050979.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGAAAACATTTGCCGCATATGTAATTATCGCGTGTCTTTCGAGTACGGCATTAGCTGGTTCAATTACAGAAAATACGTCTTGGAACAAAGAGTTCTCTGCCGAAGCCGTCAATGGTGTCTTCGTGCTTTGTAAAAGTAGCAGTAAATCCTGCGCTACCAATGACTTAGCTCGTGCATCAAAGGAATATCTTCCAGCATCAACATTTAAGATCCCCAACGCAATTATCGGCCTAGAAACTGGTGTCATAAAGAATGAGCATCAGGTTTTCAAATGGGACGGAAAGCCAAGAGCCATGAAGCAATGGGAAAGAGACTTGACCTTAAGAGGGGCAATACAAGTTTCAGCTGTTCCCGTATTTCAACAAATCGCCAGAGAAGTTGGCGAAGTAAGAATGCAGAAATACCTTAAAAAATTTTCCTATGGCAACCAGAATATCAGTGGTGGCATTGACAAATTCGGGTTGGAAGGCCAGCTTAGAATTTCCGCAGTTAATCAAGTGGAGTTTCTAGAGTCTCTATATTTAAATAAATTGTCAGCATCTAAAGAAAACCAGCTAATAGTAAAAGAGGCTTTGGTAACGGAGGCGGCACCTGAATATCTAGTGCATTCAAAAACTGGTTTTTCTGGTGTGGGAACTGAGTCAAATCCTGGTGTCGCATGGTGGGTTGGGTGGGTTGAGAAGGAGACAGAGGTTTACTTTTTCGCCTTTAACATGGATATAGACAACGAAAGTAAGTTGCCGCTAAGAAAATCCATTCCCACCAAAATCATGGAAAGTGAGGGCATCATTGGTGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005750","ARO_id":"44212","ARO_name":"OXA-520","CARD_short_name":"OXA-520","ARO_description":"OXA-520 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46486":{"category_aro_accession":"3007697","category_aro_cvterm_id":"46486","category_aro_name":"OXA-10-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-10.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4856":{"model_id":"4856","model_name":"OXA-521","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7231":{"protein_sequence":{"accession":"WP_065419572.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAILVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWIVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_051168.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCCCTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCTAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGATAGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAACAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005751","ARO_id":"44213","ARO_name":"OXA-521","CARD_short_name":"OXA-521","ARO_description":"OXA-521 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4857":{"model_id":"4857","model_name":"OXA-522","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7232":{"protein_sequence":{"accession":"WP_068981637.1","sequence":"MTKKALFFAIGTMFLSACSFNTVQQHQIQSISTNKNSEKIKSLFDQAQTEGVLVIKRGQTEEIYGNDLKRSSTEYVPASTFKMLNALIGLEHHKATPTEVFKWDGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMSKEVKRIGFGNADIGSKVDDFWLVGPLKITPQQKAQFAYELAHKTLPFSKNVQEQVQSMLFIEEKNGRKIYAKSGWGWDVEPQVGWLTGWVVQPQGKIVAFSLNLEMKKGIPSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"NG_051472.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGACTAAAAAAGCTCTTTTCTTTGCCATTGGTACGATGTTTTTGTCGGCATGTTCTTTTAATACCGTACAACAACATCAAATACAGTCAATTTCTACCAATAAAAACTCAGAGAAAATTAAATCATTGTTTGATCAAGCACAAACTGAAGGTGTTTTAGTTATAAAACGTGGGCAAACAGAGGAAATCTATGGCAATGATCTTAAAAGATCATCAACCGAATATGTTCCCGCCTCTACCTTTAAAATGTTAAATGCTTTGATTGGACTTGAGCATCATAAAGCAACACCAACTGAAGTGTTTAAATGGGATGGGCAAAAGCGTTTGTTTCCTGATTGGGAAAAGGACATGACTCTAGGCGATGCGATGAAAGCTTCTGCTATTCCAGTTTATCAGGAACTAGCTCGACGAATTGGCCTTGATCTTATGTCTAAAGAGGTAAAACGCATTGGTTTCGGTAATGCTGATATTGGTTCAAAAGTAGATGATTTTTGGCTTGTTGGTCCACTTAAAATTACACCTCAACAAAAAGCCCAGTTTGCTTATGAACTAGCCCATAAAACTCTTCCTTTTAGCAAGAATGTGCAAGAACAAGTTCAATCTATGCTGTTCATAGAAGAAAAAAATGGACGGAAAATTTATGCCAAAAGTGGTTGGGGATGGGATGTGGAGCCTCAAGTGGGCTGGTTAACAGGCTGGGTCGTTCAACCTCAAGGAAAAATTGTAGCGTTCTCACTCAATTTAGAAATGAAAAAAGGCATACCTAGTTCTATTCGAAAAGAAATTGCTTATAAGGGATTAGAGCAGCTAGGTATTTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3005752","ARO_id":"44214","ARO_name":"OXA-522","CARD_short_name":"OXA-522","ARO_description":"OXA-522 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46495":{"category_aro_accession":"3007706","category_aro_cvterm_id":"46495","category_aro_name":"OXA-213-like beta-lactamase","category_aro_description":"OXA-213-like enzymes have been identified to be intrinsic to A. calcoaceticus and have been subsequently detected in A. pittii. Phylogenetic analysis of OXA-213-like proteins identified two distinct subgroups within the OXA family. The first group was linked to A. pittii and the second group to A. calcoaceticus. The carbapenemase activity of these OXAs may be related to the species-dependent effect.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4858":{"model_id":"4858","model_name":"OXA-523","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7233":{"protein_sequence":{"accession":"WP_068981638.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKTTTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAFPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_051473.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCCCTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTCTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGACAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGACGCTATGAAAGCTTCCGCTTTTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCATTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005753","ARO_id":"44215","ARO_name":"OXA-523","CARD_short_name":"OXA-523","ARO_description":"OXA-523 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4859":{"model_id":"4859","model_name":"OXA-524","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7234":{"protein_sequence":{"accession":"WP_068981639.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDVKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKTTTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_051474.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCCCTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGTAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGACAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGACGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCATTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005754","ARO_id":"44216","ARO_name":"OXA-524","CARD_short_name":"OXA-524","ARO_description":"OXA-524 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4860":{"model_id":"4860","model_name":"OXA-525","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7235":{"protein_sequence":{"accession":"WP_068981640.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDVKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYLPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAISVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_051475.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGTAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATCTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTTCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAACAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005755","ARO_id":"44217","ARO_name":"OXA-525","CARD_short_name":"OXA-525","ARO_description":"OXA-525 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4861":{"model_id":"4861","model_name":"OXA-526","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7236":{"protein_sequence":{"accession":"WP_068981641.1","sequence":"MTKKALFFAISTMFLSACSFNTVQQHQIQSISTNKNSEKIKSLFDQAQTEGVLVIKRGQIEEVYGNDPKRASTDYVPASTFKMLNALIGLEHHKATPTEVFKWDGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMSKEVKRIGFGNADIGSKVDDFWLVGPLKITPQQEAQFAYELAHKTLPFSKNVQEQVQSMLFIEEKNGRKIYAKSGWGWDVEPQVGWLTGWVVQPQGEIVAFSLNLEMKKGIPSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"NG_051476.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGACTAAAAAAGCTCTTTTCTTTGCCATTAGTACGATGTTTTTGTCGGCATGTTCTTTTAATACCGTACAACAACATCAAATACAGTCAATTTCTACCAATAAAAACTCAGAGAAAATTAAATCATTGTTTGATCAAGCACAAACTGAAGGTGTTTTAGTTATAAAACGTGGGCAAATAGAGGAAGTCTATGGCAATGATCCTAAAAGAGCATCAACCGACTATGTTCCCGCCTCTACCTTTAAAATGTTAAATGCTTTGATTGGACTTGAGCATCATAAAGCAACACCAACTGAAGTGTTTAAATGGGATGGGCAAAAGCGTTTATTTCCCGATTGGGAAAAAGACATGACATTAGGCGATGCGATGAAAGCTTCTGCTATTCCAGTTTATCAGGAACTAGCTCGACGAATTGGCCTTGATCTTATGTCTAAAGAGGTAAAACGCATTGGTTTCGGTAATGCTGATATTGGTTCAAAAGTAGATGATTTTTGGCTTGTTGGTCCACTTAAAATTACACCTCAACAAGAAGCCCAGTTTGCTTATGAACTAGCCCATAAAACTCTTCCTTTTAGCAAGAATGTGCAAGAACAAGTTCAATCTATGCTGTTCATAGAAGAAAAAAATGGACGGAAAATTTATGCCAAAAGTGGTTGGGGATGGGATGTGGAGCCTCAAGTGGGCTGGTTAACAGGCTGGGTCGTTCAACCTCAAGGAGAAATTGTAGCGTTCTCACTCAATTTAGAAATGAAAAAAGGCATACCTAGTTCTATTCGAAAAGAAATTGCTTATAAGGGATTAGAGCAGCTAGGTATTTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3005756","ARO_id":"44218","ARO_name":"OXA-526","CARD_short_name":"OXA-526","ARO_description":"OXA-526 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46495":{"category_aro_accession":"3007706","category_aro_cvterm_id":"46495","category_aro_name":"OXA-213-like beta-lactamase","category_aro_description":"OXA-213-like enzymes have been identified to be intrinsic to A. calcoaceticus and have been subsequently detected in A. pittii. Phylogenetic analysis of OXA-213-like proteins identified two distinct subgroups within the OXA family. The first group was linked to A. pittii and the second group to A. calcoaceticus. The carbapenemase activity of these OXAs may be related to the species-dependent effect.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4862":{"model_id":"4862","model_name":"OXA-527","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7237":{"protein_sequence":{"accession":"WP_068981642.1","sequence":"MNIKTILLVTSTLLISACSPYIVTANPNNSALKADEKAQKIKDIFEEAHTTGVLVIQQGQTQQSYGNDLTRASTEYVPASTFKMLNALIGLEHHKVTTTEIFKWDKKKRLFPEWERDMTLGDAMKASAIPVYQDLARRIGLELMSAEVKRVNYGNTNIGTQVDNFWLVGPLKITPQQEAQFAYRLANKTLPFSQNVQEQVQSMLFIEEKNGNKIYAKSGWGWDIDPQVGWLTGWVVQPKGNIVAFSLNLEMKKGIPSSVRKEITYKSLEKLGIL"},"dna_sequence":{"accession":"NG_051477.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAATATTAAAACTATCTTATTGGTAACAAGCACTCTTCTTATTTCTGCCTGCTCACCTTATATAGTGACAGCAAATCCAAATAATAGTGCTTTAAAAGCAGATGAAAAAGCGCAGAAAATTAAAGACATCTTTGAAGAAGCACATACAACTGGTGTTTTAGTTATTCAACAAGGTCAAACACAACAAAGCTATGGTAACGATCTTACTCGAGCTTCAACAGAGTATGTACCGGCTTCAACATTTAAAATGCTTAATGCTTTAATCGGCCTTGAGCACCATAAGGTAACCACAACAGAAATATTCAAATGGGATAAAAAAAAGCGACTCTTTCCTGAATGGGAAAGGGATATGACGCTAGGCGATGCTATGAAGGCTTCTGCTATTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTGCTGAGGTAAAACGAGTAAATTATGGTAATACTAATATTGGCACCCAAGTCGATAATTTTTGGCTTGTCGGCCCTTTAAAGATTACGCCTCAACAAGAAGCACAATTTGCCTATAGGTTAGCTAACAAAACCCTTCCATTTAGTCAAAATGTACAAGAACAAGTTCAATCCATGCTTTTCATAGAAGAAAAAAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATATAGACCCACAGGTGGGTTGGTTAACTGGCTGGGTGGTCCAACCTAAAGGGAATATTGTAGCGTTCTCGCTCAATTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTACAAAAGCTTAGAAAAATTAGGTATTTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3005757","ARO_id":"44219","ARO_name":"OXA-527","CARD_short_name":"OXA-527","ARO_description":"OXA-527 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4863":{"model_id":"4863","model_name":"OXA-528","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7238":{"protein_sequence":{"accession":"WP_068981643.1","sequence":"MNIKALSLITSAIFISACSPYIVTANPNHSASKSDDKAEKIKNLFNEAHTTGVLVIHQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWNGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_051478.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTCACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGACAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCATCAAGGTCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGAACGGGCAAAAAAGGCTGTTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005758","ARO_id":"44220","ARO_name":"OXA-528","CARD_short_name":"OXA-528","ARO_description":"OXA-528 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4864":{"model_id":"4864","model_name":"OXA-529","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7239":{"protein_sequence":{"accession":"WP_068981644.1","sequence":"MNIKALLLITSTIFISACSPYIVTANPNHSTSKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEIFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARHIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_051479.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCACTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCACTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAATATTTAAGTGGGACGGGCAAAAAAGGCTGTTCCCAGAATGGGAAAAGGACATGACCCTAGGTGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCATATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACGCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005759","ARO_id":"44221","ARO_name":"OXA-529","CARD_short_name":"OXA-529","ARO_description":"OXA-529 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4865":{"model_id":"4865","model_name":"OXA-530","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7240":{"protein_sequence":{"accession":"WP_068981645.1","sequence":"MNIKTLLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEVHSTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_051480.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAACACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGTACACTCTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCAACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005760","ARO_id":"44222","ARO_name":"OXA-530","CARD_short_name":"OXA-530","ARO_description":"OXA-530 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4866":{"model_id":"4866","model_name":"OXA-531","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7241":{"protein_sequence":{"accession":"WP_068981646.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDKKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEIFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSLKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_051481.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATAAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAATATTTAAGTGGGACGGGCAAAAAAGGCTGTTCCCAGAATGGGAAAAGGACATGACCCTAGGTGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCTAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCATTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005761","ARO_id":"44223","ARO_name":"OXA-531","CARD_short_name":"OXA-531","ARO_description":"OXA-531 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4867":{"model_id":"4867","model_name":"OXA-532","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7242":{"protein_sequence":{"accession":"WP_068981647.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_051482.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACTACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAACGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005762","ARO_id":"44224","ARO_name":"OXA-532","CARD_short_name":"OXA-532","ARO_description":"OXA-532 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4868":{"model_id":"4868","model_name":"OXA-533","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7243":{"protein_sequence":{"accession":"WP_068611377.1","sequence":"MTKKALFFAIGTMFLSACSFNTVQQHQIQSISTNKNSEKIKSLFDQAQTEGVLVIKRGQIEEVYGNDLKRASTEYVPASTFKMLNALIGLEHHKATPTEVFKWDGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMSKEVKRIGFGNADIGSKVDDFWLVGPLKITPQQEAQFAYELAHKTLPFSKNVQEQVQSMLFIEEKNGRKIYAKSGWGWDVDPQVGWFTGWVVQPQGEIIAFSLNLEMKKGIPSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"NG_051483.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGACTAAAAAAGCTCTTTTCTTTGCCATTGGTACGATGTTTTTGTCGGCATGTTCTTTTAATACCGTACAACAACATCAAATACAGTCAATTTCTACCAATAAAAACTCAGAGAAAATTAAATCATTGTTTGATCAAGCACAAACTGAAGGTGTTTTAGTTATAAAACGTGGGCAAATAGAGGAAGTCTATGGCAATGATCTTAAAAGAGCATCAACCGAATATGTTCCCGCCTCTACCTTTAAAATGTTAAATGCTTTGATTGGACTTGAGCATCATAAAGCAACACCAACTGAAGTGTTTAAATGGGATGGGCAAAAACGTTTATTTCCTGATTGGGAAAAGGACATGACTCTAGGCGATGCGATGAAAGCTTCTGCTATTCCAGTTTATCAGGAACTAGCTCGACGAATTGGCCTTGATCTTATGTCTAAAGAGGTAAAACGCATTGGTTTCGGTAATGCTGATATTGGTTCAAAAGTAGATGATTTTTGGCTTGTTGGTCCACTTAAAATTACACCTCAACAAGAAGCCCAGTTTGCTTATGAACTAGCCCATAAAACTCTTCCTTTTAGCAAAAATGTGCAAGAACAAGTTCAATCTATGCTGTTCATAGAAGAAAAAAATGGACGAAAAATTTATGCCAAAAGTGGTTGGGGATGGGATGTTGACCCACAAGTTGGTTGGTTTACAGGCTGGGTAGTTCAACCTCAGGGAGAAATTATAGCTTTCTCACTTAATTTAGAAATGAAGAAAGGCATACCTAGTTCTATTCGAAAAGAAATTGCTTATAAAGGATTAGAGCAGCTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3005763","ARO_id":"44225","ARO_name":"OXA-533","CARD_short_name":"OXA-533","ARO_description":"OXA-533 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46495":{"category_aro_accession":"3007706","category_aro_cvterm_id":"46495","category_aro_name":"OXA-213-like beta-lactamase","category_aro_description":"OXA-213-like enzymes have been identified to be intrinsic to A. calcoaceticus and have been subsequently detected in A. pittii. Phylogenetic analysis of OXA-213-like proteins identified two distinct subgroups within the OXA family. The first group was linked to A. pittii and the second group to A. calcoaceticus. The carbapenemase activity of these OXAs may be related to the species-dependent effect.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4869":{"model_id":"4869","model_name":"OXA-534","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7244":{"protein_sequence":{"accession":"WP_069280711.1","sequence":"MKNTIHINFAIFLIIANIIYSSASASTDISTVASPLFEGTEGCFLLYDASTNAEIAQFNKAKCATQMAPDSTFKIALSLMAFDAEIIDQKTIFKWDKTPKGMEIWNSNHTPKTWMQFSVVWVSQEITQKIGLNKIKNYLKDFDYGNQDFSGDKERNNGLTEAWLESSLKISPEEQIQFLRKIINHNLPVKNSAIENTIENMYLQDLDNSTKLYGKTGAGFTANRTLQNGWFEGFIISKSGHKYFFVSALTGNLGSNLTSSIKAKKNAITILNTLNL"},"dna_sequence":{"accession":"NG_051517.1","fmin":"0","fmax":"831","strand":"+","sequence":"ATGAAAAACACAATACATATCAACTTCGCTATTTTTTTAATAATTGCAAATATTATCTACAGCAGCGCCAGTGCATCAACAGATATCTCTACTGTTGCATCTCCATTATTTGAAGGAACTGAAGGTTGTTTTTTACTTTACGATGCATCCACAAACGCTGAAATTGCTCAATTCAATAAAGCAAAGTGTGCAACGCAAATGGCACCAGATTCAACTTTCAAGATCGCATTATCACTTATGGCATTTGATGCGGAAATAATAGATCAGAAAACCATATTCAAATGGGATAAAACCCCCAAAGGAATGGAGATCTGGAACAGCAATCATACACCAAAGACGTGGATGCAATTTTCTGTTGTTTGGGTTTCGCAAGAAATAACCCAAAAAATTGGATTAAATAAAATCAAGAATTATCTCAAAGATTTTGATTATGGAAATCAAGACTTCTCTGGAGATAAAGAAAGAAACAACGGATTAACAGAAGCATGGCTCGAAAGTAGCTTAAAAATTTCACCAGAAGAACAAATTCAATTCCTGCGTAAAATTATTAATCACAATCTCCCAGTTAAAAACTCAGCCATAGAAAACACCATAGAGAACATGTATCTACAAGATCTGGATAATAGTACAAAACTGTATGGGAAAACTGGTGCAGGATTCACAGCAAATAGAACCTTACAAAACGGATGGTTTGAAGGGTTTATTATAAGCAAATCAGGACATAAATATTTTTTTGTGTCCGCACTTACAGGAAACTTGGGGTCGAATTTAACATCAAGCATAAAAGCCAAGAAAAATGCGATCACCATTCTAAACACACTAAATTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3005764","ARO_id":"44226","ARO_name":"OXA-534","CARD_short_name":"OXA-534","ARO_description":"OXA-534 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46485":{"category_aro_accession":"3007696","category_aro_cvterm_id":"46485","category_aro_name":"OXA-1-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-1.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4870":{"model_id":"4870","model_name":"OXA-536","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7245":{"protein_sequence":{"accession":"WP_070064535.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDVKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLVHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_051751.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGTAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGTGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAACAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005765","ARO_id":"44227","ARO_name":"OXA-536","CARD_short_name":"OXA-536","ARO_description":"OXA-536 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4871":{"model_id":"4871","model_name":"OXA-537","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7246":{"protein_sequence":{"accession":"WP_070064536.1","sequence":"MKTLILLPLLSCLSLTACSLPVSNSSSQITSTQSIQTIAKLFDQAQSSGVLVIQRGPHLQVYGNDLSRAHTEYIPASTFKMLNALIGLQHGKATTNEIFKWDGKKRSFAAWEKDLTLAEAMQASAVPVYQELARRIGLELMQQEVQRIRFGNQQIGQHIDNFWLVGPLKITPEQEVEFASALAQEQLAFDPQVQQQVKAMLLLQERQAYRLYAKSGWGMDVEPQVGWLTGWIETPQDEIVAFSLNMQMQSNMDPAIRLKILQQALAELGLYPKAEG"},"dna_sequence":{"accession":"NG_051752.1","fmin":"0","fmax":"831","strand":"+","sequence":"ATGAAAACTCTTATTTTGTTGCCTTTACTTAGTTGCTTGAGCCTGACAGCCTGTAGCTTGCCTGTTTCAAATTCGTCCTCTCAAATCACTTCAACTCAATCTATTCAAACCATTGCCAAATTATTTGATCAGGCACAAAGCTCTGGCGTTTTAGTAATTCAACGGGGCCCACATCTACAGGTCTATGGCAATGATTTGAGTCGTGCACATACCGAATATATTCCTGCTTCAACCTTTAAAATGCTCAATGCCCTGATTGGCCTGCAACATGGTAAAGCCACGACCAATGAAATCTTTAAATGGGATGGCAAGAAGCGCAGTTTTGCAGCCTGGGAAAAAGACCTGACCCTAGCCGAGGCCATGCAAGCTTCTGCTGTACCCGTCTATCAGGAACTGGCACGTCGCATTGGTCTGGAACTAATGCAACAGGAAGTGCAACGCATTCGATTTGGTAATCAGCAGATTGGTCAGCATATCGACAACTTCTGGTTAGTCGGACCTTTGAAAATCACCCCGGAACAAGAAGTCGAATTTGCCTCTGCGCTTGCTCAAGAGCAACTTGCCTTTGATCCTCAAGTCCAGCAACAAGTCAAAGCCATGTTACTGTTACAGGAGCGACAAGCTTATCGACTATATGCCAAATCTGGTTGGGGTATGGATGTGGAGCCGCAAGTCGGCTGGCTCACCGGCTGGATCGAAACACCTCAGGACGAAATCGTGGCATTTTCACTGAATATGCAGATGCAAAGTAATATGGATCCGGCGATCCGTCTTAAAATTTTGCAGCAGGCCTTGGCCGAATTAGGGCTTTATCCGAAAGCTGAAGGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39096","NCBI_taxonomy_name":"Acinetobacter schindleri","NCBI_taxonomy_id":"108981"}}}},"ARO_accession":"3005766","ARO_id":"44228","ARO_name":"OXA-537","CARD_short_name":"OXA-537","ARO_description":"OXA-537 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46489":{"category_aro_accession":"3007700","category_aro_cvterm_id":"46489","category_aro_name":"OXA-134-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-134.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4872":{"model_id":"4872","model_name":"OXA-538","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7247":{"protein_sequence":{"accession":"WP_071593227.1","sequence":"MRVLALSAVFLVASIIGMPAVAKEWQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGQTRDIATWNRDHNLITAMKYSVVPVYQEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISATEQISFLRKLYHNKLHVSERSQRIVKQAMLTEANADYIIRAKTGYSGRIEPKFGWWVGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP"},"dna_sequence":{"accession":"NG_052051.1","fmin":"23","fmax":"821","strand":"+","sequence":"ATGCGTGTATTAGCCTTATCGGCTGTGTTTTTGGTGGCATCGATTATCGGAATGCCTGCGGTAGCAAAGGAATGGCAAGAAAACAAAAGTTGGAATGCTCACTTTACTGAACATAAATCACAGGGCGTAGTTGTGCTCTGGAATGAGAATAAGCAGCAAGGATTTACCAATAATCTTAAACGGGCGAACCAAGCATTTTTACCCGCATCTACCTTTAAAATTCCCAATAGCTTGATCGCCCTCGATTTGGGCGTGGTTAAGGATGAACACCAAGTCTTTAAGTGGGATGGACAGACGCGCGATATCGCCACTTGGAATCGCGATCATAATCTAATCACCGCGATGAAATATTCAGTTGTGCCTGTTTATCAAGAATTTGCCCGCCAAATTGGCGAGGCACGTATGAGCAAGATGCTACATGCTTTCGATTATGGTAATGAGGACATTTCGGGCAATGTAGACAGTTTCTGGCTCGACGGTGGTATTCGAATTTCGGCCACGGAGCAAATCAGCTTTTTAAGAAAGCTGTATCACAATAAGTTACACGTATCGGAGCGCAGCCAGCGTATTGTCAAACAAGCCATGCTGACCGAGGCGAATGCTGATTATATTATTCGGGCGAAAACCGGTTATTCAGGCAGAATTGAGCCGAAATTCGGTTGGTGGGTCGGTTGGGTTGAACTTGATGATAATGTGTGGTTTTTTGCGATGAATATGGATATGCCCACATCGGATGGTTTAGGGCTGCGCCAAGCCATCACAAAAGAAGTGCTCAAACAGGAGAAAATTATTCCCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39674","NCBI_taxonomy_name":"Shewanella xiamenensis","NCBI_taxonomy_id":"332186"}}}},"ARO_accession":"3005767","ARO_id":"44229","ARO_name":"OXA-538","CARD_short_name":"OXA-538","ARO_description":"OXA-538 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46510":{"category_aro_accession":"3007721","category_aro_cvterm_id":"46510","category_aro_name":"OXA-48-like beta-lactamase","category_aro_description":"OXA-48-type beta-lactamases are now routinely encountered in bacterial infections caused by carbapenam-resistant Enterobacterales. OXA-48-like proteins confer resistance to penicillin (which is efficiently hydrolyzed) and carbapenam antibiotics (which is more slowly broken down). The spectrum of activity of these variants varies, with some hydrolyzing expanded-spectrum oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4873":{"model_id":"4873","model_name":"OXA-542","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7248":{"protein_sequence":{"accession":"WP_109545048.1","sequence":"MKKVVFPILSIFTLFSLNACSSVQTASESTISAYNQQSKETIKKYFDDAQTQGVIVIKDNNHLAIYGNNLTRAHTQYVPASTFKMLNALIGLENNKVTTDELFKWDGNKKAFPIWEKDMNLDEAMKLSAVPVYQELAKRIGIDLMQKEVKRVNFGNANIGTKVDNFWLVGPLKITPIQEVKFADDLAHNKLPFKIETQETVKNMLLIKEINGSKIYAKSGWGMDVTPQVGWLTGWVEQPTGKIISFSLNLEMKNNMTGSIRNEITYKALENLGII"},"dna_sequence":{"accession":"NG_057454.1","fmin":"0","fmax":"828","strand":"+","sequence":"ATGAAAAAAGTTGTATTTCCTATATTGAGTATCTTTACTTTATTTTCTCTGAATGCGTGTTCATCGGTTCAGACAGCATCCGAAAGTACTATTTCAGCTTACAATCAACAGAGTAAAGAAACTATAAAAAAATATTTTGATGATGCTCAAACACAAGGTGTAATTGTTATTAAAGATAATAATCATCTTGCGATATATGGTAATAATTTAACACGAGCACATACACAATATGTTCCAGCATCAACTTTTAAAATGTTGAACGCTTTAATTGGATTAGAAAATAATAAAGTAACCACGGATGAACTGTTTAAGTGGGATGGTAATAAAAAAGCTTTCCCAATTTGGGAAAAAGATATGAACTTAGATGAGGCGATGAAATTATCAGCAGTTCCTGTATATCAAGAACTTGCAAAACGTATTGGTATAGATTTAATGCAGAAAGAAGTAAAACGGGTTAATTTTGGTAATGCTAATATTGGAACTAAAGTTGATAATTTTTGGTTAGTTGGCCCTTTGAAGATTACACCTATTCAAGAAGTTAAATTTGCTGATGATCTTGCACATAACAAATTACCTTTCAAAATTGAAACTCAAGAAACAGTTAAAAATATGCTTCTAATTAAAGAAATTAATGGAAGTAAAATTTATGCAAAAAGTGGTTGGGGAATGGATGTTACACCTCAAGTGGGTTGGTTAACTGGTTGGGTAGAACAGCCTACAGGGAAGATAATTTCATTTTCATTAAATTTAGAAATGAAAAATAATATGACAGGTTCTATTCGCAATGAAATTACATATAAAGCATTAGAGAATCTTGGTATCATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3005768","ARO_id":"44230","ARO_name":"OXA-542","CARD_short_name":"OXA-542","ARO_description":"OXA-542 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4874":{"model_id":"4874","model_name":"OXA-545","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7249":{"protein_sequence":{"accession":"WP_085562402.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWVVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_054692.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCCCTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGGTAGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAACAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005769","ARO_id":"44231","ARO_name":"OXA-545","CARD_short_name":"OXA-545","ARO_description":"OXA-545 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4875":{"model_id":"4875","model_name":"OXA-546","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7250":{"protein_sequence":{"accession":"WP_087587945.1","sequence":"MRVLALSAVFLVASIIGMPAVAKEWQENKSWNAHFTEHKSQGVVALWNENKQQGFTNNLKRANQAFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGQTRDIATWNRDHNLITAMKYSVVPVYQEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISAIEQISFLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYSTRIEPKIGWWVGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP"},"dna_sequence":{"accession":"NG_054959.1","fmin":"0","fmax":"798","strand":"+","sequence":"ATGCGTGTATTAGCCTTATCGGCTGTGTTTTTGGTGGCATCGATTATCGGAATGCCTGCGGTAGCAAAGGAATGGCAAGAAAACAAAAGTTGGAATGCTCACTTTACTGAACATAAATCACAGGGCGTAGTTGCGCTCTGGAATGAGAATAAGCAGCAAGGATTTACCAATAATCTTAAACGGGCGAACCAAGCATTTTTACCCGCATCTACCTTTAAAATTCCCAATAGCTTGATCGCCCTCGATTTGGGCGTGGTTAAGGATGAACACCAAGTCTTTAAGTGGGATGGACAGACGCGCGATATCGCCACTTGGAATCGCGATCATAATCTAATCACCGCGATGAAATATTCGGTTGTGCCTGTTTATCAAGAATTTGCCCGCCAAATTGGCGAGGCACGTATGAGCAAGATGCTACATGCTTTCGATTATGGTAATGAGGACATTTCGGGCAATGTAGACAGTTTCTGGCTCGACGGTGGTATTCGAATTTCGGCCATTGAGCAAATCAGCTTTTTAAGAAAGCTGTATCACAATAAGTTACACGTATCGGAGCGCAGTCAGCGCATCGTGAAACAAGCCATGCTGACCGAAGCCAATGGCGACTATATTATTCGGGCTAAAACTGGATACTCGACTAGAATCGAACCTAAGATTGGCTGGTGGGTCGGTTGGGTTGAACTTGATGATAATGTGTGGTTTTTTGCGATGAATATGGATATGCCCACATCGGATGGTTTAGGGCTGCGCCAAGCCATCACAAAAGAAGTGCTCAAACAGGAAAAAATTATTCCCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39674","NCBI_taxonomy_name":"Shewanella xiamenensis","NCBI_taxonomy_id":"332186"}}}},"ARO_accession":"3005770","ARO_id":"44232","ARO_name":"OXA-546","CARD_short_name":"OXA-546","ARO_description":"OXA-546 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46510":{"category_aro_accession":"3007721","category_aro_cvterm_id":"46510","category_aro_name":"OXA-48-like beta-lactamase","category_aro_description":"OXA-48-type beta-lactamases are now routinely encountered in bacterial infections caused by carbapenam-resistant Enterobacterales. OXA-48-like proteins confer resistance to penicillin (which is efficiently hydrolyzed) and carbapenam antibiotics (which is more slowly broken down). The spectrum of activity of these variants varies, with some hydrolyzing expanded-spectrum oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4876":{"model_id":"4876","model_name":"OXA-547","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7251":{"protein_sequence":{"accession":"WP_085562403.1","sequence":"MRVLALSAVFLVASIIGMPAVAREWQENKSWNVHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGQTRDIATWNRDHNLITAMKYSVVPVYQEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISAIEQISFLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYSTRIEPKIGWWVGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP"},"dna_sequence":{"accession":"NG_054693.1","fmin":"18","fmax":"816","strand":"+","sequence":"ATGCGTGTATTAGCCTTATCGGCTGTGTTTTTGGTGGCATCGATTATCGGAATGCCTGCGGTAGCAAGGGAATGGCAAGAAAACAAAAGTTGGAATGTTCACTTTACTGAACATAAATCACAGGGCGTAGTTGTGCTCTGGAATGAGAATAAGCAGCAAGGATTTACCAATAATCTTAAACGGGCGAACCAAGCATTTTTACCCGCATCTACATTTAAAATTCCCAATAGCTTGATCGCCCTCGATTTGGGCGTGGTTAAGGATGAACACCAAGTCTTTAAGTGGGATGGACAGACGCGCGATATCGCCACTTGGAATCGCGATCATAATCTAATCACCGCGATGAAATATTCGGTTGTGCCTGTTTATCAAGAATTTGCCCGCCAAATTGGCGAGGCACGTATGAGCAAGATGCTACATGCTTTCGATTATGGTAATGAGGACATTTCGGGCAATGTAGACAGTTTCTGGCTCGACGGTGGTATTCGAATTTCGGCCATTGAGCAAATCAGCTTTTTAAGAAAGCTGTATCACAATAAGTTACACGTATCGGAGCGCAGTCAGCGCATCGTGAAACAAGCCATGCTGACCGAAGCCAATGGCGACTATATTATTCGGGCTAAAACTGGATACTCGACTAGAATCGAACCTAAGATTGGCTGGTGGGTCGGTTGGGTTGAACTTGATGATAATGTGTGGTTTTTTGCGATGAATATGGATATGCCCACATCGGATGGTTTAGGGCTGCGCCAAGCCATCACAAAAGAAGTGCTCAAACAGGAAAAAATTATTCCCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37068","NCBI_taxonomy_name":"Shewanella","NCBI_taxonomy_id":"22"}}}},"ARO_accession":"3005771","ARO_id":"44233","ARO_name":"OXA-547","CARD_short_name":"OXA-547","ARO_description":"OXA-547 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46510":{"category_aro_accession":"3007721","category_aro_cvterm_id":"46510","category_aro_name":"OXA-48-like beta-lactamase","category_aro_description":"OXA-48-type beta-lactamases are now routinely encountered in bacterial infections caused by carbapenam-resistant Enterobacterales. OXA-48-like proteins confer resistance to penicillin (which is efficiently hydrolyzed) and carbapenam antibiotics (which is more slowly broken down). The spectrum of activity of these variants varies, with some hydrolyzing expanded-spectrum oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4877":{"model_id":"4877","model_name":"OXA-548","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7252":{"protein_sequence":{"accession":"WP_087587939.1","sequence":"MRSFAISTVLVMSSLLASSIIAAPTFASTAVKKEWQETRSWDAIFTQHQAEPQQAKLQKTKLQQTSGVVALWNENKQQGYTNNLKRANQGFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGKSRDIATWNRDHNLITGMKYSVVPVYQEFARQIGEARMSKMIASFDYGNEDISGNLDSFWLDGGIRISATEQIDFLRRLYYNKIHASERSQRIVKQAMLTEANSDYIIRAKTGYAVRAEPSIGWWVGWIELDDNVWFFAMNMDIPDAAGLPLRQAITKEVLKLEHVIP"},"dna_sequence":{"accession":"NG_054953.1","fmin":"0","fmax":"873","strand":"+","sequence":"ATGCGTTCGTTTGCCATATCGACTGTGTTGGTGATGTCCTCACTGTTAGCGTCGTCAATCATTGCCGCCCCGACTTTTGCCTCAACCGCGGTGAAGAAGGAGTGGCAAGAAACCCGCAGTTGGGATGCCATTTTTACTCAGCATCAAGCTGAACCGCAACAAGCTAAACTGCAAAAAACTAAGCTCCAACAAACCTCGGGCGTGGTAGCACTATGGAACGAAAACAAGCAACAGGGATATACCAACAATCTTAAACGTGCCAATCAAGGTTTTTTACCTGCATCGACCTTTAAAATCCCTAACAGTTTGATTGCGCTTGATCTCGGTGTGGTGAAGGATGAACATCAAGTGTTTAAGTGGGATGGTAAAAGCCGTGATATTGCCACTTGGAATCGTGACCACAACTTGATTACCGGGATGAAGTATTCGGTGGTGCCAGTCTATCAAGAGTTTGCCCGCCAAATTGGTGAGGCGCGAATGTCGAAGATGATCGCCTCTTTCGATTATGGTAATGAGGATATCTCGGGTAACTTAGATAGCTTTTGGCTTGATGGTGGTATTCGGATATCGGCCACTGAGCAAATCGATTTCCTGCGCCGACTTTATTACAACAAAATACACGCTTCAGAGCGCAGTCAACGCATCGTTAAGCAAGCCATGCTCACCGAGGCGAATTCTGATTATATTATCCGCGCAAAAACCGGTTATGCGGTCAGAGCTGAGCCAAGCATTGGCTGGTGGGTTGGTTGGATAGAACTCGATGATAATGTGTGGTTTTTTGCAATGAATATGGATATCCCTGATGCCGCAGGTTTGCCATTGCGCCAAGCCATTACTAAAGAAGTATTAAAACTGGAACACGTAATTCCTTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3005772","ARO_id":"44234","ARO_name":"OXA-548","CARD_short_name":"OXA-548","ARO_description":"OXA-548 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46515":{"category_aro_accession":"3007726","category_aro_cvterm_id":"46515","category_aro_name":"OXA-548-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-548.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4878":{"model_id":"4878","model_name":"OXA-549","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7253":{"protein_sequence":{"accession":"WP_087587940.1","sequence":"MRSFAISTVLGMSSLLASSIIAAPTFASTAVKKEWQETRSWDAIFTQHQVEPQQAKLQKTKLQQTSGVVALWNENKQQGYTNNLKRANQGFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGKSRDIATWNRDHNLITGMKYSVVPVYQEFARQIGEARMSKMIASFDYGNETISGNLDSFWLDGGIRISATEQIDFLRRLYHNKVHASERSQRIVKQAMLTEANSDYIIRAKTGYAVRAEPSIGWWVGWVELDDNVWFFAMNMDIPDAAGLPLRQAITKEVLKLEHVIP"},"dna_sequence":{"accession":"NG_054954.1","fmin":"0","fmax":"873","strand":"+","sequence":"ATGCGTTCGTTCGCCATATCGACTGTGTTGGGGATGTCCTCACTGTTAGCGTCGTCAATCATTGCCGCCCCGACTTTTGCCTCAACAGCGGTGAAGAAGGAGTGGCAAGAAACCCGTAGTTGGGATGCCATTTTTACTCAGCACCAAGTTGAACCGCAACAAGCTAAACTGCAAAAAACTAAGCTCCAACAAACCTCGGGCGTGGTAGCACTATGGAACGAAAACAAGCAACAGGGATATACCAACAATCTTAAACGTGCCAATCAAGGTTTTTTACCTGCATCGACCTTTAAAATCCCTAACAGTCTGATTGCGCTAGATCTCGGTGTGGTGAAGGATGAACATCAAGTGTTTAAGTGGGATGGTAAAAGCCGTGATATTGCCACTTGGAATCGTGACCACAACTTGATTACCGGGATGAAGTATTCGGTTGTGCCAGTCTATCAAGAGTTTGCCCGCCAAATTGGTGAGGCGCGAATGTCGAAGATGATCGCCTCTTTCGATTATGGTAATGAGACTATCTCGGGTAACTTAGATAGCTTTTGGCTTGATGGTGGTATTCGGATATCGGCTACTGAGCAAATTGATTTCCTGCGCCGGCTTTATCACAACAAGGTACACGCTTCAGAGCGCAGTCAACGCATCGTTAAGCAAGCCATGCTCACCGAGGCGAATTCTGACTATATTATCCGCGCAAAAACCGGTTATGCGGTCAGAGCTGAGCCAAGCATTGGCTGGTGGGTTGGTTGGGTAGAGCTCGATGATAATGTGTGGTTTTTTGCAATGAATATGGATATCCCCGACGCTGCAGGTTTGCCATTGCGTCAAGCCATTACTAAGGAAGTATTAAAACTGGAACACGTAATTCCTTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3005773","ARO_id":"44235","ARO_name":"OXA-549","CARD_short_name":"OXA-549","ARO_description":"OXA-549 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46515":{"category_aro_accession":"3007726","category_aro_cvterm_id":"46515","category_aro_name":"OXA-548-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-548.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4879":{"model_id":"4879","model_name":"OXA-550","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7254":{"protein_sequence":{"accession":"WP_087587941.1","sequence":"MRSFAISTVLVMSSLLASSIIAAPTFASTAVKKEWQETRSWDAIFTQHQVEPQQAKLQKTKLQQTSGVVALWNENKQQGYTNNLKRANQGFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGKSRDIVTWNRDHSLITGMKYSVVPVYQEFARQIGEARMSKMIASFDYGNEDISGNLDSFWLDGGIRISATEQIDFLRRLYYNKIHASERSQRIVKQAMLTEANSDYIIRAKTGYAVRAEPSIGWWVGWVELDDNVWFFAMNMDIPDAAGLPLRQAITKEVLKLEHVIP"},"dna_sequence":{"accession":"NG_054955.1","fmin":"0","fmax":"873","strand":"+","sequence":"ATGCGTTCGTTCGCCATATCGACTGTGTTGGTGATGTCCTCACTGTTAGCGTCGTCAATCATTGCCGCCCCGACTTTTGCCTCAACAGCGGTGAAGAAGGAGTGGCAAGAAACCCGTAGTTGGGATGCCATTTTTACTCAGCACCAAGTTGAACCGCAACAAGCTAAACTGCAAAAAACTAAGCTCCAACAAACCTCGGGCGTGGTAGCACTATGGAACGAAAACAAGCAACAGGGATATACCAACAATCTTAAACGTGCCAATCAAGGTTTTTTACCTGCATCGACCTTTAAAATCCCTAACAGTTTGATTGCGCTAGATCTCGGTGTGGTGAAGGATGAACATCAAGTGTTTAAGTGGGATGGTAAAAGCCGTGATATTGTCACTTGGAATCGTGACCACAGCTTGATTACCGGGATGAAGTATTCGGTGGTGCCAGTCTATCAAGAGTTTGCCCGCCAAATTGGTGAGGCGCGAATGTCGAAGATGATCGCCTCTTTCGATTATGGTAATGAGGATATCTCGGGTAACTTAGATAGCTTTTGGCTTGATGGCGGTATTCGGATATCGGCCACTGAGCAAATCGATTTCCTGCGCCGACTTTATTACAACAAAATACACGCTTCAGAGCGCAGTCAACGCATCGTTAAGCAAGCCATGCTCACCGAGGCGAATTCTGATTATATTATCCGCGCAAAAACCGGTTATGCGGTCAGAGCTGAGCCAAGCATTGGCTGGTGGGTGGGTTGGGTAGAACTCGATGATAATGTGTGGTTTTTTGCAATGAATATGGACATCCCAGATGCCGCAGGTTTGCCATTGCGCCAAGCCATTACTAAGGAAGTATTAAAACTGGAACACGTAATTCCTTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3005774","ARO_id":"44236","ARO_name":"OXA-550","CARD_short_name":"OXA-550","ARO_description":"OXA-550 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46515":{"category_aro_accession":"3007726","category_aro_cvterm_id":"46515","category_aro_name":"OXA-548-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-548.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4880":{"model_id":"4880","model_name":"OXA-551","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7255":{"protein_sequence":{"accession":"WP_087587942.1","sequence":"MRSFAISTVLVMSSLLASSTIAAPTFASTAAKTEWQETRSWDAIFTQHQVEPQQAKQQQAKPQKTKSQQASGVVVLWNENKQQGYTNNLKRANQGFLPASTFKIPNSLIALELGVVKDEHQVFKWDGKSRDIATWNRDHNLITGMKYSVVPVYQEFARQIGEARMSKMIASFDYGNEDISGNLDSFWLDGGIRISATEQIDFLRRLYHNKIHASERSQRIVKQAMLTEANSDYIIRAKTGYAVRAEPSIGWWVGWVELDNNVWFFAMNMDIPDAAGLPLRQAITKEVLKLEHVIP"},"dna_sequence":{"accession":"NG_054956.1","fmin":"0","fmax":"888","strand":"+","sequence":"ATGCGTTCGTTCGCCATATCGACTGTGTTGGTGATGTCCTCACTGTTAGCGTCGTCAACCATAGCTGCCCCAACTTTTGCCTCAACAGCGGCGAAGACAGAGTGGCAAGAAACCCGCAGTTGGGATGCCATTTTTACTCAGCACCAAGTTGAACCGCAACAAGCTAAGCAACAACAAGCTAAACCGCAAAAAACTAAGTCCCAACAAGCCTCTGGAGTGGTGGTGCTGTGGAACGAAAACAAGCAACAGGGATATACCAACAATCTTAAACGTGCCAATCAAGGTTTTTTACCGGCATCGACCTTTAAAATCCCCAATAGCTTGATTGCGCTCGAGTTGGGTGTGGTGAAGGATGAGCACCAAGTGTTTAAATGGGATGGTAAAAGTCGTGATATCGCCACTTGGAATCGTGATCATAACTTGATTACTGGGATGAAGTATTCGGTTGTGCCCGTCTATCAAGAGTTTGCCCGCCAAATTGGTGAGGCGAGGATGTCGAAGATGATCGCCTCCTTCGATTATGGCAATGAGGATATCTCGGGTAACTTAGATAGCTTTTGGCTCGATGGCGGTATTCGGATTTCGGCCACTGAGCAAATTGATTTCCTGCGTCGGCTTTATCACAACAAGATCCACGCTTCAGAACGCAGTCAACGAATTGTTAAGCAGGCTATGCTCACCGAGGCGAATTCTGACTATATTATCCGCGCAAAAACCGGCTATGCGGTCAGAGCTGAGCCAAGTATTGGCTGGTGGGTGGGTTGGGTAGAACTCGATAATAATGTGTGGTTTTTTGCAATGAATATGGATATACCCGACGCCGCAGGTTTGCCATTGCGTCAAGCCATCACTAAAGAAGTTTTAAAACTGGAACACGTTATTCCTTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3005775","ARO_id":"44237","ARO_name":"OXA-551","CARD_short_name":"OXA-551","ARO_description":"OXA-551 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46515":{"category_aro_accession":"3007726","category_aro_cvterm_id":"46515","category_aro_name":"OXA-548-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-548.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4881":{"model_id":"4881","model_name":"OXA-552","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7256":{"protein_sequence":{"accession":"WP_087587943.1","sequence":"MRSFAISTVLVMSSLLASSIIAAPTFASTAVKKEWQETRSWDAIFTQHQVEPQQAKLQKTKLQQTSGVVALWNENKQQGYTNNLKRANQGFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGKSRDIATWNRDHNLITGMKYSVVPVYQEFARQIGEARMSKMIASFDYGNETISGNLDSFWLDGGIRISATEQIDFLRRLYHNKVHASERSQRIVKQAMLTEANSDYIIRAKTGYAVRAEPSIGWWVGWVELDDNVWFFAMNMDIPDAAGLPLRQAITKEVLKLEHVIP"},"dna_sequence":{"accession":"NG_054957.1","fmin":"0","fmax":"873","strand":"+","sequence":"ATGCGTTCGTTCGCCATATCGACTGTGTTGGTGATGTCCTCACTGTTAGCGTCGTCAATCATTGCCGCCCCGACTTTTGCCTCAACAGCGGTGAAGAAGGAGTGGCAAGAAACCCGTAGTTGGGATGCCATTTTTACTCAGCACCAAGTTGAACCGCAACAAGCTAAACTGCAAAAAACTAAGCTCCAACAAACCTCGGGCGTGGTAGCACTATGGAACGAAAACAAGCAACAGGGATATACCAACAATCTTAAACGTGCCAATCAAGGTTTTTTACCTGCATCGACCTTTAAAATCCCTAACAGTCTGATTGCGCTAGATCTCGGTGTGGTGAAGGATGAACATCAAGTGTTTAAGTGGGATGGTAAAAGCCGTGATATTGCCACTTGGAATCGTGACCACAACTTGATTACCGGGATGAAGTATTCGGTTGTGCCAGTCTATCAAGAGTTTGCCCGCCAAATTGGTGAGGCGCGAATGTCGAAGATGATCGCCTCTTTCGATTATGGTAATGAGACTATCTCGGGTAACTTAGATAGCTTTTGGCTTGATGGTGGTATTCGGATATCGGCTACTGAGCAAATTGATTTCCTGCGCCGGCTTTATCACAACAAGGTACACGCTTCAGAGCGCAGTCAACGCATCGTTAAGCAAGCCATGCTCACCGAGGCGAATTCTGACTATATTATCCGCGCAAAAACCGGTTATGCGGTCAGAGCTGAGCCAAGCATTGGCTGGTGGGTTGGTTGGGTAGAGCTCGATGATAATGTGTGGTTTTTTGCAATGAATATGGATATCCCCGACGCTGCAGGTTTGCCATTGCGTCAAGCCATTACTAAGGAAGTATTAAAACTGGAACACGTAATTCCTTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37068","NCBI_taxonomy_name":"Shewanella","NCBI_taxonomy_id":"22"}}}},"ARO_accession":"3005776","ARO_id":"44238","ARO_name":"OXA-552","CARD_short_name":"OXA-552","ARO_description":"OXA-552 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46515":{"category_aro_accession":"3007726","category_aro_cvterm_id":"46515","category_aro_name":"OXA-548-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-548.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4882":{"model_id":"4882","model_name":"OXA-553","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7257":{"protein_sequence":{"accession":"WP_087587944.1","sequence":"MRSFAISTVLVMSSLLASSIIAAPTFASTAVKKEWQETRSWDAIFTQHQVEPQQAKQQQAKPQKTKSQQTSGVVALWNENKQQGYTNNLKRANQGFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGKSRDIATWNRDHNLITGMKYSVVPVYQEFARQIGEARMSKMIASFDYGNEDISGNLDSFWLDGGIRISATEQIDFLRRLYYNKIHASERSQRIVKQAMLTEANSDYIIRAKTGYAVRAEPSIGWWVGWIELDDNVWFFAMNMDIPDAAGLPLRQAITKEVLKLEHVIP"},"dna_sequence":{"accession":"NG_054958.1","fmin":"0","fmax":"888","strand":"+","sequence":"ATGCGTTCGTTCGCCATATCGACTGTGTTGGTGATGTCCTCACTGTTAGCGTCGTCAATCATTGCCGCCCCGACTTTTGCCTCAACAGCGGTGAAGAAGGAGTGGCAAGAAACCCGCAGTTGGGATGCCATTTTTACTCAGCACCAAGTTGAACCGCAACAAGCTAAGCAACAACAAGCTAAACCGCAAAAAACTAAGTCCCAACAAACCTCGGGCGTGGTAGCACTATGGAACGAAAACAAGCAACAGGGATATACCAACAATCTTAAACGTGCCAATCAAGGTTTTTTACCTGCATCGACCTTTAAAATCCCTAACAGTTTGATTGCGCTTGATCTCGGTGTGGTGAAGGATGAACATCAAGTGTTTAAGTGGGATGGTAAAAGCCGTGATATTGCCACTTGGAATCGTGACCACAACTTGATTACCGGGATGAAGTATTCGGTGGTGCCAGTCTATCAAGAGTTTGCCCGCCAAATTGGTGAGGCGCGAATGTCGAAGATGATCGCCTCTTTCGATTATGGTAATGAGGATATCTCGGGTAACTTAGATAGCTTTTGGCTTGATGGTGGTATTCGGATATCGGCCACTGAGCAAATCGATTTCCTGCGCCGACTTTATTACAACAAAATACACGCTTCAGAGCGCAGTCAACGCATCGTTAAGCAAGCCATGCTCACCGAGGCGAATTCTGATTATATTATCCGCGCAAAAACCGGTTATGCGGTCAGAGCTGAGCCAAGCATTGGCTGGTGGGTTGGTTGGATAGAACTCGATGATAATGTGTGGTTTTTTGCAATGAATATGGATATCCCTGATGCCGCAGGTTTGCCATTGCGCCAAGCCATTACTAAAGAAGTATTAAAACTGGAACACGTAATTCCTTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3005777","ARO_id":"44239","ARO_name":"OXA-553","CARD_short_name":"OXA-553","ARO_description":"OXA-553 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46515":{"category_aro_accession":"3007726","category_aro_cvterm_id":"46515","category_aro_name":"OXA-548-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-548.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4883":{"model_id":"4883","model_name":"OXA-554","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7258":{"protein_sequence":{"accession":"WP_085562408.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDDKAEKIKNLFNEAHTTGVLVIHQGQTQQSYGNDLARASTEYVPTSTFKMLNALIGLEHHKATTTEVFKWNGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_054698.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGACAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCATCAAGGTCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTACTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGAACGGGCAAAAAAGGCTGTTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACGCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005778","ARO_id":"44240","ARO_name":"OXA-554","CARD_short_name":"OXA-554","ARO_description":"OXA-554 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4884":{"model_id":"4884","model_name":"OXA-555","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7259":{"protein_sequence":{"accession":"WP_085562409.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEVHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_054699.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGTACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005779","ARO_id":"44241","ARO_name":"OXA-555","CARD_short_name":"OXA-555","ARO_description":"OXA-555 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4885":{"model_id":"4885","model_name":"OXA-556","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7260":{"protein_sequence":{"accession":"WP_085562410.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSDSKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_054700.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGATTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005780","ARO_id":"44242","ARO_name":"OXA-556","CARD_short_name":"OXA-556","ARO_description":"OXA-556 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4886":{"model_id":"4886","model_name":"OXA-557","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7261":{"protein_sequence":{"accession":"WP_085562411.1","sequence":"MNIKALLLITSAIFISACSPYIVSANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPHGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_054701.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGTCTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCATGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005781","ARO_id":"44243","ARO_name":"OXA-557","CARD_short_name":"OXA-557","ARO_description":"OXA-557 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4887":{"model_id":"4887","model_name":"OXA-558","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7262":{"protein_sequence":{"accession":"WP_085562412.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKTTTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWIVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_054702.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTCTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGACAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGACGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGATTGTTCAGCCTCAAGGAAATATTGTAGCATTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005782","ARO_id":"44244","ARO_name":"OXA-558","CARD_short_name":"OXA-558","ARO_description":"OXA-558 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4888":{"model_id":"4888","model_name":"OXA-559","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7263":{"protein_sequence":{"accession":"WP_085562413.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNGLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_054703.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGGTCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGACGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAACGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005783","ARO_id":"44245","ARO_name":"OXA-559","CARD_short_name":"OXA-559","ARO_description":"OXA-559 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4889":{"model_id":"4889","model_name":"OXA-560","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7264":{"protein_sequence":{"accession":"WP_085562414.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDDKAEKIKNLFNEAHTTGVLVIHQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWNGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_054704.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGACAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCATCAAGGTCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGAACGGGCAAAAAAGGCTGTTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCATTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005784","ARO_id":"44246","ARO_name":"OXA-560","CARD_short_name":"OXA-560","ARO_description":"OXA-560 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4890":{"model_id":"4890","model_name":"OXA-561","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7265":{"protein_sequence":{"accession":"WP_085562415.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEVHTTGVLVIHQGQTQQSYGNDLTRASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSEEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFTLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_054705.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGTACACACTACGGGTGTTTTAGTTATCCATCAAGGTCAAACTCAACAAAGCTATGGTAATGATCTTACTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTGAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCACCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005785","ARO_id":"44247","ARO_name":"OXA-561","CARD_short_name":"OXA-561","ARO_description":"OXA-561 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4891":{"model_id":"4891","model_name":"OXA-562","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7266":{"protein_sequence":{"accession":"WP_085562416.1","sequence":"MNIKALLLITSAIFSSACSPYIVSANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQEEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_054706.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTAGTTCAGCCTGCTCACCTTATATAGTGTCTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACTACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGCCCTTTAAAAATTACGCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCCTTTAGCCAAAAAGTCCAAGAAGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005786","ARO_id":"44248","ARO_name":"OXA-562","CARD_short_name":"OXA-562","ARO_description":"OXA-562 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4892":{"model_id":"4892","model_name":"OXA-563","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7267":{"protein_sequence":{"accession":"WP_085562417.1","sequence":"MTKKALFFAIGTMFLSACSFNTVEQHQIQSISTNKNSEKIKSLFDQAQTTGVLVIKRGQTEEVYGNDLKRASTEYVPASTFKMLNALIGLEHHKATPTEVFKWDGQKHLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMSKEVKRIGFGNADIGSKVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSKNVQEQVQSMVFIEEKNGRKIYAKSGWGWDVDPQVGWFTGWVVQPQGEIVAFSLNLEMKKGIPSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"NG_054707.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGACTAAAAAAGCTCTTTTCTTTGCCATTGGTACGATGTTTTTGTCTGCATGTTCTTTTAATACGGTAGAACAACATCAAATACAGTCAATTTCTACCAATAAAAACTCAGAGAAAATTAAATCGTTGTTTGATCAAGCACAAACTACAGGTGTTTTAGTTATAAAACGTGGGCAAACGGAGGAAGTCTATGGCAATGATCTTAAAAGAGCATCAACCGAATATGTTCCCGCCTCTACCTTTAAAATGTTAAATGCTTTGATTGGACTTGAACATCATAAAGCAACACCAACTGAAGTGTTTAAATGGGATGGGCAAAAGCATTTATTTCCCGATTGGGAAAAAGACATGACCTTAGGCGATGCTATGAAGGCTTCTGCTATTCCAGTTTATCAGGAACTAGCTCGACGAATTGGCCTTGATCTTATGTCTAAAGAGGTAAAGCGTATTGGTTTCGGTAATGCTGATATTGGTTCAAAAGTAGATAATTTTTGGCTTGTTGGCCCACTTAAAATTACACCACAACAAGAAGCGCAGTTTGCTTACAAATTAGCCAATAAAACTCTTCCCTTTAGCAAAAATGTACAAGAGCAAGTTCAATCTATGGTGTTCATAGAAGAAAAAAATGGACGAAAAATTTATGCCAAAAGTGGTTGGGGATGGGATGTTGACCCACAAGTTGGTTGGTTTACAGGCTGGGTAGTTCAACCTCAGGGAGAAATTGTAGCGTTCTCACTCAATTTAGAAATGAAGAAAGGCATACCTAGTTCTATTCGAAAAGAAATTGCTTATAAGGGATTAGAGCAGCTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3005787","ARO_id":"44249","ARO_name":"OXA-563","CARD_short_name":"OXA-563","ARO_description":"OXA-563 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46495":{"category_aro_accession":"3007706","category_aro_cvterm_id":"46495","category_aro_name":"OXA-213-like beta-lactamase","category_aro_description":"OXA-213-like enzymes have been identified to be intrinsic to A. calcoaceticus and have been subsequently detected in A. pittii. Phylogenetic analysis of OXA-213-like proteins identified two distinct subgroups within the OXA family. The first group was linked to A. pittii and the second group to A. calcoaceticus. The carbapenemase activity of these OXAs may be related to the species-dependent effect.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4893":{"model_id":"4893","model_name":"OXA-564","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7268":{"protein_sequence":{"accession":"WP_085562418.1","sequence":"MTKKALFFAIGTMFLSACSFNTVQQHQIQSISTNKNSEKIKSLFDQAQTEGVLVIKRGQTEEIYGNDLKRSSTEYVPASTFKMLNALIGLEHHKATPTEVFKWDGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMSKEVKRIGFGNADIGSKVDDFWLVGPLKITPQQEAQFAYELAHKTLPFSKNVQEQVQSMLFIEEKNGQKIYAKSGWGWDVEPQVGWLTGWVVQPQGEIVAFSLNLEMKKGIPSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"NG_054708.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGACTAAAAAAGCTCTTTTCTTTGCCATTGGTACGATGTTTTTGTCGGCATGTTCTTTTAATACCGTACAACAACATCAAATACAGTCAATTTCTACCAATAAAAACTCAGAGAAAATTAAATCATTGTTTGATCAAGCACAAACTGAAGGTGTTTTAGTTATAAAACGTGGGCAAACAGAGGAAATCTATGGCAATGATCTTAAAAGATCATCAACCGAATATGTTCCCGCCTCTACCTTTAAAATGTTAAATGCTTTGATTGGACTTGAGCATCATAAAGCAACACCAACTGAAGTGTTTAAATGGGATGGGCAAAAGCGTTTGTTTCCTGATTGGGAAAAGGACATGACTCTAGGCGATGCGATGAAAGCTTCTGCTATTCCAGTTTATCAGGAACTAGCTCGACGAATTGGCCTTGATCTTATGTCTAAAGAGGTAAAACGCATTGGTTTCGGTAATGCTGATATTGGTTCAAAAGTAGATGATTTTTGGCTTGTTGGTCCACTTAAAATTACACCTCAACAAGAAGCCCAGTTTGCTTATGAACTAGCCCATAAAACTCTTCCTTTTAGCAAGAATGTGCAAGAACAAGTTCAATCTATGCTGTTCATAGAAGAAAAAAATGGACAGAAAATTTATGCCAAAAGTGGTTGGGGATGGGATGTGGAGCCTCAAGTGGGCTGGTTAACAGGCTGGGTCGTTCAACCTCAAGGAGAAATTGTAGCGTTCTCACTCAATTTAGAAATGAAAAAAGGCATACCTAGTTCTATTCGAAAAGAAATTGCTTATAAGGGATTAGAGCAGCTAGGTATTTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3005788","ARO_id":"44250","ARO_name":"OXA-564","CARD_short_name":"OXA-564","ARO_description":"OXA-564 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46495":{"category_aro_accession":"3007706","category_aro_cvterm_id":"46495","category_aro_name":"OXA-213-like beta-lactamase","category_aro_description":"OXA-213-like enzymes have been identified to be intrinsic to A. calcoaceticus and have been subsequently detected in A. pittii. Phylogenetic analysis of OXA-213-like proteins identified two distinct subgroups within the OXA family. The first group was linked to A. pittii and the second group to A. calcoaceticus. The carbapenemase activity of these OXAs may be related to the species-dependent effect.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4894":{"model_id":"4894","model_name":"OXA-565","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7269":{"protein_sequence":{"accession":"WP_085562421.1","sequence":"MNKYFTCYVVASLFLSGCTVQHNLINKTQSQIVQGHNQVIHQYFDEKNTSGVLVIQADKKINLYGNALSRANTEYVPASTFKMLNALIGLENQKTDINEIFKWKGEKRSFTAWEKDMTLGEAMKLSAVPVYQELARRIGLDLMQKEVKRIGFGNAEIGQQVDNFWLVGPLKVTPIQEVEFVSQLAHTQLPFSEKVQANVKNMLLLEESNGYKIFGKTGWAMDIKPQVGWLTGWVEQPDGKIVTFALNMEMRSEMPASIRNELLMKSLKQLNII"},"dna_sequence":{"accession":"NG_054712.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGAATAAATATTTTACTTGCTATGTGGTTGCTTCTCTTTTTCTTTCTGGTTGTACGGTTCAGCATAATTTAATAAATAAAACCCAGAGTCAGATTGTTCAAGGACATAATCAGGTGATTCATCAATACTTTGATGAAAAAAACACCTCAGGTGTGCTGGTTATTCAAGCAGATAAAAAAATTAATCTATATGGTAATGCTCTAAGCCGCGCAAATACAGAATATGTGCCAGCCTCTACATTTAAAATGTTGAATGCCCTGATCGGATTGGAGAACCAGAAAACGGATATTAATGAAATATTTAAATGGAAGGGCGAGAAAAGGTCATTTACCGCTTGGGAAAAAGACATGACACTAGGAGAAGCCATGAAGCTTTCCGCAGTCCCAGTCTATCAGGAACTTGCGCGACGTATCGGTCTTGATCTCATGCAAAAAGAAGTAAAACGTATTGGTTTCGGTAATGCTGAAATTGGACAGCAGGTTGATAATTTCTGGTTGGTAGGGCCATTAAAGGTTACGCCTATTCAAGAGGTAGAGTTTGTTTCTCAATTGGCGCATACACAGCTTCCATTTAGTGAAAAAGTGCAGGCTAATGTAAAAAATATGCTTCTTTTAGAAGAGAGTAATGGCTACAAAATTTTTGGAAAGACCGGTTGGGCAATGGATATAAAACCACAAGTGGGCTGGTTGACCGGCTGGGTTGAGCAGCCAGATGGAAAAATTGTCACTTTTGCATTAAATATGGAAATGCGGTCAGAAATGCCTGCATCTATACGTAATGAATTATTGATGAAATCATTAAAACAGCTGAATATTATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005789","ARO_id":"44251","ARO_name":"OXA-565","CARD_short_name":"OXA-565","ARO_description":"OXA-565 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46499":{"category_aro_accession":"3007710","category_aro_cvterm_id":"46499","category_aro_name":"OXA-23-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases, specifically imipenem, derived from OXA-23, first identified in Acinetobacter baumannii.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4895":{"model_id":"4895","model_name":"OXA-566","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7270":{"protein_sequence":{"accession":"WP_094009811.1","sequence":"MRVLALSAVFLVASIIGMPAVAKEWQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGQTRDIATWNRDHNLITAMKYSVVPVYQEFARQIGEARMSKMLHDFDYGNEDISGNVDSFWLDGGIRISATEQISFLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYSTRIEPKIGWWVGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP"},"dna_sequence":{"accession":"NG_055499.1","fmin":"0","fmax":"798","strand":"+","sequence":"ATGCGTGTATTAGCCTTATCGGCTGTGTTTTTGGTGGCATCGATTATCGGAATGCCTGCGGTAGCAAAGGAATGGCAAGAAAACAAAAGTTGGAATGCTCACTTTACTGAACATAAATCACAGGGCGTAGTTGTGCTCTGGAATGAGAATAAGCAGCAAGGATTTACCAATAATCTTAAACGGGCGAACCAAGCATTTTTACCCGCATCTACCTTTAAAATTCCCAATAGCTTGATCGCCCTCGATTTGGGCGTGGTTAAGGATGAACACCAAGTCTTTAAGTGGGATGGACAGACGCGCGATATCGCCACTTGGAATCGCGATCATAATCTAATCACCGCGATGAAATATTCAGTTGTGCCTGTTTATCAAGAATTTGCCCGCCAAATTGGCGAGGCACGTATGAGCAAGATGCTACATGATTTCGATTATGGTAATGAGGACATTTCGGGCAATGTAGACAGTTTCTGGCTCGACGGTGGTATTCGAATTTCGGCCACGGAGCAAATCAGCTTTTTAAGAAAGCTGTATCACAATAAGTTACACGTATCGGAGCGCAGCCAGCGTATTGTCAAACAAGCCATGCTGACCGAAGCCAATGGTGACTATATTATTCGGGCTAAAACTGGATACTCGACTAGAATCGAACCTAAGATTGGCTGGTGGGTCGGTTGGGTTGAACTTGATGATAATGTGTGGTTTTTTGCGATGAATATGGATATGCCCACATCGGATGGTTTAGGGCTGCGCCAAGCCATCACAAAAGAAGTGCTCAAACAGGAAAAAATTATTCCCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3005790","ARO_id":"44252","ARO_name":"OXA-566","CARD_short_name":"OXA-566","ARO_description":"OXA-566 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46510":{"category_aro_accession":"3007721","category_aro_cvterm_id":"46510","category_aro_name":"OXA-48-like beta-lactamase","category_aro_description":"OXA-48-type beta-lactamases are now routinely encountered in bacterial infections caused by carbapenam-resistant Enterobacterales. OXA-48-like proteins confer resistance to penicillin (which is efficiently hydrolyzed) and carbapenam antibiotics (which is more slowly broken down). The spectrum of activity of these variants varies, with some hydrolyzing expanded-spectrum oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4896":{"model_id":"4896","model_name":"OXA-567","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7271":{"protein_sequence":{"accession":"WP_099156052.1","sequence":"MRVLALSAVFLVASIIGMPAVAKEWQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGQTRDIATWNRDHNLITAMKYSVVPVYQEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISATEQISFLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYDTKIGKIGWWVGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP"},"dna_sequence":{"accession":"NG_055666.1","fmin":"0","fmax":"795","strand":"+","sequence":"ATGCGTGTATTAGCCTTATCGGCTGTGTTTTTGGTGGCATCGATTATCGGAATGCCTGCGGTAGCAAAGGAATGGCAAGAAAACAAAAGTTGGAATGCTCACTTTACTGAACATAAATCACAGGGCGTAGTTGTGCTCTGGAATGAGAATAAGCAGCAAGGATTTACCAATAATCTTAAACGGGCGAACCAAGCATTTTTACCCGCATCTACCTTTAAAATTCCCAATAGCTTGATCGCCCTCGATTTGGGCGTGGTTAAGGATGAACACCAAGTCTTTAAGTGGGATGGACAGACGCGCGATATCGCCACTTGGAATCGCGATCATAATCTAATCACCGCGATGAAATATTCAGTTGTGCCTGTTTATCAAGAATTTGCCCGCCAAATTGGCGAGGCACGTATGAGCAAGATGCTACATGCTTTCGATTATGGTAATGAGGACATTTCGGGCAATGTAGACAGTTTCTGGCTCGACGGTGGTATTCGAATTTCGGCCACGGAGCAAATCAGCTTTTTAAGAAAGCTGTATCACAATAAGTTACACGTATCGGAGCGCAGCCAGCGTATTGTCAAACAAGCCATGCTGACCGAAGCCAATGGCGACTATATTATTCGGGCTAAAACTGGATACGATACTAAGATTGGTAAGATTGGCTGGTGGGTCGGTTGGGTTGAACTTGATGATAATGTGTGGTTTTTTGCGATGAATATGGATATGCCCACATCGGATGGTTTAGGGCTGCGCCAAGCCATCACAAAAGAAGTGCTCAAACAGGAAAAAATTATTCCCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3005791","ARO_id":"44253","ARO_name":"OXA-567","CARD_short_name":"OXA-567","ARO_description":"OXA-567 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46510":{"category_aro_accession":"3007721","category_aro_cvterm_id":"46510","category_aro_name":"OXA-48-like beta-lactamase","category_aro_description":"OXA-48-type beta-lactamases are now routinely encountered in bacterial infections caused by carbapenam-resistant Enterobacterales. OXA-48-like proteins confer resistance to penicillin (which is efficiently hydrolyzed) and carbapenam antibiotics (which is more slowly broken down). The spectrum of activity of these variants varies, with some hydrolyzing expanded-spectrum oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4897":{"model_id":"4897","model_name":"OXA-568","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7272":{"protein_sequence":{"accession":"WP_099337823.1","sequence":"MKTIMLLVLCSSLMLMACTSPTTSLSTPSQHVQTQQAQVIAELFNQAQTQGVLVIQHGAKVQSYGNDLSRADTEYVPASTFKMLNALIGLQHHKANIEEVFKWDGKKRSFPAWEKDMTLGEAMQASAVPVYQELARRIGLELMQQEVRRIKFGNQKIGQQVDNFWLVGPLKITPKQEADFVARLAQQQLAFDPLVQQQVKQMLLLQQRQGYRLYAKSGWGMDLEPQVGWLTGWIETPDAEIVAFSLNMQMYNSTNPAIRLEILQQALAELGLYPKA"},"dna_sequence":{"accession":"NG_055785.1","fmin":"100","fmax":"931","strand":"+","sequence":"ATGAAAACAATAATGCTTCTGGTGCTGTGCAGCAGCCTTATGCTGATGGCTTGTACCTCACCTACGACATCTTTATCTACACCATCACAGCATGTCCAGACCCAACAGGCACAAGTAATCGCGGAATTATTTAATCAAGCTCAGACTCAAGGGGTTTTAGTCATTCAGCATGGCGCTAAGGTACAAAGCTATGGCAATGACTTAAGCCGTGCAGATACCGAATATGTGCCCGCCTCCACTTTTAAAATGCTGAATGCCTTGATTGGATTACAACATCACAAAGCCAACATAGAGGAAGTGTTTAAATGGGATGGCAAGAAACGTAGCTTTCCGGCCTGGGAAAAGGACATGACCTTGGGCGAAGCTATGCAGGCCTCTGCTGTACCTGTCTATCAGGAGCTGGCACGCCGTATTGGTCTGGAGCTCATGCAACAGGAAGTGCGACGGATCAAATTTGGTAATCAAAAGATTGGGCAACAAGTCGATAACTTCTGGTTAGTGGGCCCCTTAAAAATCACTCCTAAACAGGAGGCCGATTTTGTCGCTCGCCTGGCTCAACAGCAATTGGCTTTTGATCCTCTGGTTCAGCAACAAGTGAAACAGATGTTACTCTTGCAACAAAGACAGGGTTATCGTCTCTATGCCAAATCTGGCTGGGGAATGGATCTTGAACCACAAGTCGGCTGGTTGACAGGCTGGATTGAAACTCCAGACGCTGAAATCGTGGCATTCTCACTGAATATGCAGATGTATAATTCGACGAATCCGGCAATTCGCCTAGAAATTTTACAACAGGCGCTGGCTGAATTAGGGCTTTATCCAAAAGCATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3005792","ARO_id":"44254","ARO_name":"OXA-568","CARD_short_name":"OXA-568","ARO_description":"OXA-568 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4898":{"model_id":"4898","model_name":"OXA-569","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7273":{"protein_sequence":{"accession":"WP_102607461.1","sequence":"MMKLRHAATGALLAALATFAHAERTICTIVADAATGKVVLHEGQCAERVTPASTFKLALAVMGYDHGFLKDEHAPIEHMKAGDPDWGGEAWHQPIDPTLWLKYSVVWYSQRITHAMGAQTLHAYLRKFDYGNMDASGDPGKNNGLDRSWITSSLKISPEEQVGFMRKIVNRQLPVSAHTYEMVERAVQTWPVPGGWTVQGKTGTAGPGPGNTSPDGTWDQAHAYGWFVGWAKKGTGDDSRTYVFANLIQDDKLEPTSGGLRSRDALLARLPEVLALASH"},"dna_sequence":{"accession":"NG_056178.1","fmin":"0","fmax":"840","strand":"+","sequence":"ATGATGAAACTCCGCCACGCCGCGACCGGCGCCCTGCTGGCCGCGCTTGCCACCTTTGCCCATGCCGAGCGCACGATCTGCACGATCGTTGCCGATGCCGCCACCGGCAAGGTTGTTCTGCACGAAGGCCAGTGCGCCGAACGTGTCACGCCTGCATCTACCTTCAAGCTGGCGCTGGCCGTGATGGGCTACGACCACGGTTTCCTGAAGGACGAGCACGCCCCCATCGAGCACATGAAGGCTGGCGACCCCGATTGGGGTGGCGAGGCCTGGCACCAGCCCATCGACCCCACGCTGTGGCTCAAGTACTCCGTGGTCTGGTATTCGCAGCGCATCACGCATGCGATGGGTGCGCAGACGCTGCATGCGTATCTGCGCAAATTCGACTACGGCAACATGGACGCGAGCGGCGACCCGGGGAAGAACAACGGTCTGGACCGCTCGTGGATCACCTCGTCGCTGAAGATCTCGCCGGAGGAGCAGGTGGGCTTCATGCGCAAGATCGTCAACCGCCAGTTGCCAGTGTCTGCGCATACGTATGAGATGGTCGAGCGCGCGGTGCAGACCTGGCCGGTGCCGGGTGGCTGGACTGTGCAGGGCAAAACGGGCACTGCTGGGCCGGGCCCCGGCAATACGTCGCCCGATGGCACGTGGGATCAGGCACACGCTTATGGCTGGTTTGTCGGCTGGGCGAAGAAGGGCACGGGTGACGACAGTCGGACCTACGTGTTTGCGAACCTGATCCAGGACGACAAGCTTGAGCCGACATCGGGGGGCTTGCGCTCGCGCGATGCGCTGCTGGCGCGCCTGCCGGAAGTGCTGGCCCTTGCGAGTCACTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43682","NCBI_taxonomy_name":"Ralstonia insidiosa","NCBI_taxonomy_id":"190721"}}}},"ARO_accession":"3005793","ARO_id":"44255","ARO_name":"OXA-569","CARD_short_name":"OXA-569","ARO_description":"OXA-569 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46497":{"category_aro_accession":"3007708","category_aro_cvterm_id":"46497","category_aro_name":"OXA-22-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-22.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4899":{"model_id":"4899","model_name":"OXA-572","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7274":{"protein_sequence":{"accession":"WP_102607464.1","sequence":"MMKLRHAATGAFLAALATFAHAEHPICTLVADAATGKVVVQEGKCNERVTPASTFKLALAVMGYDAGFLKDPHTPVEHFRRGDPDWGGQPWRQPVDPTLWLKYSVVWYSQRITHAMGAQTFASYVRKLDYGNMDVSGDPGKNNGLDRSWITSSLKISPEEQVGFLRRLVNRQLPVSAQTYEMVDRIVQTWQVPGGWAVQGKTGTAGPAPGNTSADGTWDQAHAYGWFVGWAKKGGQTYVFANLIQDDKIEPTSGGIRSRDAMLARLAQVLAAAKP"},"dna_sequence":{"accession":"NG_056181.1","fmin":"0","fmax":"828","strand":"+","sequence":"ATGATGAAACTCCGCCACGCCGCCACGGGCGCCTTCCTTGCCGCGCTGGCCACCTTCGCCCATGCCGAACACCCTATCTGCACGCTCGTTGCCGATGCAGCCACGGGCAAGGTCGTCGTGCAGGAGGGCAAGTGCAACGAGCGCGTGACGCCGGCGTCCACCTTCAAGCTGGCGCTGGCCGTCATGGGTTACGACGCCGGCTTCCTGAAAGATCCGCACACGCCGGTCGAACACTTCAGGCGCGGCGACCCCGACTGGGGCGGCCAGCCGTGGCGCCAGCCTGTCGACCCGACGCTGTGGCTCAAGTATTCGGTGGTCTGGTATTCCCAGCGCATCACCCACGCGATGGGCGCGCAGACGTTCGCCTCGTACGTGCGCAAGCTCGACTACGGCAACATGGATGTGAGCGGCGACCCGGGCAAGAACAACGGCCTGGACCGCTCGTGGATCACCTCGTCGCTGAAGATCTCGCCCGAGGAGCAGGTCGGCTTTCTGCGCCGGCTCGTCAACCGGCAGTTGCCGGTGTCGGCGCAGACGTACGAGATGGTCGACCGCATCGTGCAGACGTGGCAGGTGCCGGGCGGCTGGGCCGTGCAGGGCAAGACGGGCACGGCGGGCCCGGCACCGGGCAATACCTCGGCCGACGGCACGTGGGATCAGGCGCACGCTTACGGCTGGTTTGTCGGCTGGGCGAAGAAAGGAGGCCAGACCTACGTGTTTGCGAACCTGATCCAGGACGACAAGATCGAGCCCACCTCGGGCGGCATCCGCTCGCGCGATGCGATGCTGGCGCGCCTGGCGCAGGTGCTGGCTGCCGCCAAGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42837","NCBI_taxonomy_name":"Ralstonia mannitolilytica","NCBI_taxonomy_id":"105219"}}}},"ARO_accession":"3005794","ARO_id":"44256","ARO_name":"OXA-572","CARD_short_name":"OXA-572","ARO_description":"OXA-572 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46497":{"category_aro_accession":"3007708","category_aro_cvterm_id":"46497","category_aro_name":"OXA-22-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-22.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4900":{"model_id":"4900","model_name":"OXA-574","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7275":{"protein_sequence":{"accession":"WP_064808581.1","sequence":"MMKLRHAATGALLAALATFAHAERTICTIVADAATGKVVLHEGQCAERVTPASTFKLALAVMGYDHGFLRDEHTPIEHMKAGDPDWGGEAWHQPIDPTLWLKYSVVWYSQRITHAMGAQTLHAYLRKFDYGNMDASGDPGKNNGLDRSWITSSLKISPEEQVGFMRKIVNRQLPVSAHTYEMVDRTVQTWPVPGGWAVQGKTGTAGPGPGNTSPDGTWDQAHAYGWFVGWAKKGTGDDSRTYVFANLIQDDKLEPTSGGLRSRDALLARLPEVLALASH"},"dna_sequence":{"accession":"NG_056183.1","fmin":"0","fmax":"840","strand":"+","sequence":"ATGATGAAACTCCGCCACGCCGCGACCGGCGCCCTGCTGGCCGCGCTTGCCACCTTTGCCCATGCCGAGCGCACGATCTGCACGATCGTTGCCGATGCCGCCACCGGCAAGGTTGTTCTGCACGAAGGCCAGTGCGCCGAACGCGTCACGCCTGCGTCCACCTTCAAGCTGGCGCTGGCGGTCATGGGCTACGACCACGGTTTCCTGAGGGACGAGCACACCCCCATCGAGCACATGAAGGCTGGCGACCCCGATTGGGGTGGCGAGGCCTGGCACCAGCCCATCGACCCCACGCTGTGGCTCAAGTACTCCGTGGTCTGGTATTCGCAGCGCATCACGCATGCGATGGGTGCGCAGACGCTGCATGCGTATCTGCGCAAATTCGACTACGGCAACATGGACGCGAGCGGCGATCCGGGGAAGAACAACGGCCTGGACCGCTCGTGGATCACCTCGTCGCTGAAGATCTCGCCGGAGGAGCAGGTGGGCTTCATGCGCAAGATCGTCAACCGCCAGTTGCCGGTGTCTGCGCATACGTATGAGATGGTGGACCGTACGGTGCAGACCTGGCCGGTGCCGGGTGGCTGGGCTGTGCAGGGCAAAACGGGCACTGCTGGGCCGGGCCCCGGCAATACGTCGCCCGATGGCACGTGGGATCAGGCACACGCTTATGGCTGGTTTGTCGGCTGGGCGAAGAAGGGCACGGGTGACGACAGTCGGACCTACGTGTTTGCGAACCTGATCCAGGACGACAAGCTTGAGCCGACATCGGGGGGCTTGCGCTCGCGCGATGCGCTGCTGGCGCGCCTGCCGGAAGTGCTGGCCCTTGCGAGCCACTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43682","NCBI_taxonomy_name":"Ralstonia insidiosa","NCBI_taxonomy_id":"190721"}}}},"ARO_accession":"3005795","ARO_id":"44257","ARO_name":"OXA-574","CARD_short_name":"OXA-574","ARO_description":"OXA-574 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46497":{"category_aro_accession":"3007708","category_aro_cvterm_id":"46497","category_aro_name":"OXA-22-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-22.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4901":{"model_id":"4901","model_name":"OXA-575","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7276":{"protein_sequence":{"accession":"WP_104009853.1","sequence":"MKLSKLYILTVLIGFGLSGVACQHIHTPVSFNQIENDQTKQIASLFENVQTTGVLITFDGQAYKAYGNDLNRARTAYIPASTFKILNALIGIEHDKTSPNEVFKWDGQKRAFESWEKDLTLAEAMQASAVPVYQALAQRIGLDLMAKEVKRVGFGNTRIGTQVDNFWLIGPLKITPIEEAQFAYRLAKRELPFTQDTQKQVIDMLLVDEIRGTKVYAKSGWGMDITPQVGWWTGWIEDPNGKVIAFSLNMEMNQPAHAAARKEIVYQALTQLKLL"},"dna_sequence":{"accession":"NG_056415.1","fmin":"0","fmax":"828","strand":"+","sequence":"ATGAAGCTATCAAAATTATACATCCTCACTGTGCTCATAGGGTTTGGATTAAGCGGTGTCGCCTGCCAGCATATCCATACTCCAGTCTCGTTCAATCAAATTGAAAACGATCAAACAAAGCAGATCGCTTCCTTGTTTGAGAATGTTCAAACAACAGGCGTTCTGATTACCTTTGATGGACAGGCGTATAAAGCATACGGTAATGATCTGAATCGTGCCAGAACTGCGTATATCCCAGCATCTACTTTCAAAATATTAAATGCTTTGATTGGCATTGAACATGATAAAACTTCACCAAATGAAGTATTTAAGTGGGATGGTCAGAAGCGTGCTTTTGAAAGTTGGGAAAAAGATCTGACTTTAGCTGAAGCCATGCAAGCTTCTGCTGTACCTGTTTATCAAGCGCTTGCCCAGAGAATCGGATTGGATTTGATGGCAAAGGAAGTCAAAAGAGTCGGCTTCGGTAATACACGCATCGGAACACAAGTTGATAACTTCTGGCTCATTGGACCTTTAAAGATCACGCCAATCGAAGAAGCACAATTTGCTTACAGGCTTGCAAAACGGGAACTACCGTTTACCCAAGACACTCAAAAGCAAGTGATTGATATGCTGCTGGTGGATGAAATACGGGGAACTAAAGTTTACGCCAAAAGTGGTTGGGGAATGGATATTACCCCACAAGTAGGATGGTGGACTGGATGGATTGAAGATCCGAACGGAAAAGTGATCGCTTTTTCTCTCAATATGGAAATGAATCAACCTGCGCATGCAGCTGCACGTAAAGAAATTGTTTATCAGGCACTTACGCAATTGAAATTATTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36938","NCBI_taxonomy_name":"Acinetobacter haemolyticus","NCBI_taxonomy_id":"29430"}}}},"ARO_accession":"3005796","ARO_id":"44258","ARO_name":"OXA-575","CARD_short_name":"OXA-575","ARO_description":"OXA-575 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46496":{"category_aro_accession":"3007707","category_aro_cvterm_id":"46496","category_aro_name":"OXA-214-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-214.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4902":{"model_id":"4902","model_name":"OXA-576","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7277":{"protein_sequence":{"accession":"WP_087696200.1","sequence":"MKKITLFLLFLNLVFGQDKILNNWFKEYNTSGTFVFYDGKTWASNDFSRAMETFSPASTFKIFNALIALDSGVIKTKKEIFYHYRGEKVFLSSWAQDMNLSSAIKYSNVLAFKEVARRIGIKTMQEYLNKLHYGNAKISKIDTFWLDNSLKISAKEQAILLFKLSQNSLPFSKKSQEEVKKIILFKEDKIQKIYAKTGFNDGINLAWIVGFIESKNKILSFALNVDIKNIKNLKIREELLEKYIYSLN"},"dna_sequence":{"accession":"NG_066510.1","fmin":"0","fmax":"747","strand":"+","sequence":"ATGAAAAAAATAACTTTATTTTTACTTTTCTTAAATTTAGTGTTTGGGCAAGATAAGATATTAAATAATTGGTTTAAAGAGTATAATACAAGCGGCACTTTTGTTTTTTATGATGGAAAAACTTGGGCGAGTAACGACTTTTCAAGGGCTATGGAGACTTTCTCTCCCGCTTCCACTTTTAAAATTTTTAATGCTCTAATTGCACTTGATAGTGGTGTGATAAAAACTAAAAAAGAAATTTTTTATCACTATAGAGGTGAAAAAGTATTTTTATCTTCTTGGGCGCAAGATATGAATTTAAGTTCAGCTATAAAATATTCTAATGTTCTTGCTTTTAAAGAAGTGGCAAGAAGAATTGGTATCAAAACTATGCAAGAATATTTAAACAAGCTTCATTATGGTAATGCTAAAATTTCCAAGATCGATACTTTTTGGCTTGATAACTCACTAAAAATAAGCGCTAAAGAACAAGCAATTTTGCTTTTTAAACTTTCACAAAATTCTTTACCTTTTTCCAAGAAAAGTCAAGAAGAAGTTAAAAAAATTATTCTTTTTAAAGAAGATAAAATCCAAAAAATTTATGCTAAAACAGGTTTTAATGATGGTATAAATTTGGCTTGGATTGTTGGATTTATAGAGAGTAAAAACAAAATTTTATCTTTTGCCTTAAATGTTGATATAAAGAACATTAAAAATCTTAAAATAAGAGAAGAATTGCTAGAAAAATATATTTATTCTTTAAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36772","NCBI_taxonomy_name":"Campylobacter jejuni","NCBI_taxonomy_id":"197"}}}},"ARO_accession":"3005797","ARO_id":"44259","ARO_name":"OXA-576","CARD_short_name":"OXA-576","ARO_description":"OXA-576 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4903":{"model_id":"4903","model_name":"OXA-577","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7278":{"protein_sequence":{"accession":"WP_109545091.1","sequence":"MKKITLFLLFLNLVFGQDKILNNWFKEYNTSGTFVFYDGKTWASNDFSRAMETFSPASTFKIFNALIALDSGVIKTKKEIFYHYRGEKVFLSSWAQDMNLSSAIKYSNVLAFKEVTRRIGIKTMQEYLNKLHYGNAKISKIDTFWLDNSLKISAKEQAILLFRLSQNSLPFSQEAMNSVKEMIYLKNMENLELFGKTGFNDEQKIAWIVGFVYLKDENKYKAFALNLDIDKFEDLYKREKILEKYLDELVKKVKNDG"},"dna_sequence":{"accession":"NG_057525.1","fmin":"0","fmax":"774","strand":"+","sequence":"ATGAAAAAAATAACTTTATTTTTACTTTTCTTAAATTTAGTGTTTGGGCAAGATAAGATATTAAATAATTGGTTTAAAGAGTATAATACAAGCGGCACTTTTGTTTTTTATGATGGAAAAACTTGGGCGAGTAACGACTTTTCAAGGGCTATGGAGACTTTCTCTCCCGCTTCCACTTTTAAAATTTTTAATGCTCTAATTGCACTTGATAGTGGTGTGATAAAAACTAAAAAAGAAATTTTTTATCACTATAGAGGTGAAAAAGTATTTTTATCTTCTTGGGCGCAAGATATGAATTTAAGTTCAGCTATAAAATATTCTAATGTTCTTGCTTTTAAAGAAGTGACAAGAAGAATTGGTATCAAAACTATGCAAGAATATTTAAACAAGCTTCATTATGGTAATGCTAAAATTTCCAAGATCGATACTTTTTGGCTTGACAACTCACTAAAAATAAGCGCTAAAGAACAAGCAATTTTGCTTTTTAGACTTTCACAAAATAGCTTACCTTTTTCTCAAGAAGCAATGAATAGTGTTAAGGAAATGATTTATTTAAAAAATATGGAAAATTTAGAGCTTTTTGGAAAAACAGGTTTTAATGATGAGCAAAAAATTGCTTGGATTGTAGGTTTTGTGTATTTAAAAGATGAAAATAAATATAAGGCTTTCGCGCTAAATTTAGATATTGATAAATTTGAAGATTTATATAAAAGAGAAAAAATTTTAGAAAAATATTTAGATGAACTTGTAAAAAAAGTTAAAAATGATGGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36772","NCBI_taxonomy_name":"Campylobacter jejuni","NCBI_taxonomy_id":"197"}}}},"ARO_accession":"3005798","ARO_id":"44260","ARO_name":"OXA-577","CARD_short_name":"OXA-577","ARO_description":"OXA-577 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46519":{"category_aro_accession":"3007730","category_aro_cvterm_id":"46519","category_aro_name":"OXA-61-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-61.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4904":{"model_id":"4904","model_name":"OXA-578","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7279":{"protein_sequence":{"accession":"WP_002812372.1","sequence":"MKKITLFLLFLNLVFGQDKILNNWFKEYNTSGTFVFYDGKTWASNDFSRAMETFSPASTFKIFNALIALDSGVIKTKKEIFYHYRGEKVFLSSWVQDMNLSSAIKYSNVLAFKEVARRIGIKTMQEYLNKLHYGNAKISKIDTFWLDNSLKISAKEQAILLFRLSQNSLPFSQEAMNSVKEMIYLKNMENLELFGKTGFNDEQKIAWIVGFVYLKDENKYKAFALNLDIDKFEDLYKREKILEKYLDELVKKVKNDG"},"dna_sequence":{"accession":"NG_057512.1","fmin":"0","fmax":"774","strand":"+","sequence":"ATGAAAAAAATAACTTTATTTTTACTTTTCTTAAATTTAGTGTTTGGGCAAGATAAGATATTAAATAATTGGTTTAAAGAGTATAATACAAGCGGCACTTTTGTTTTTTATGATGGAAAAACTTGGGCGAGTAACGACTTTTCAAGGGCTATGGAGACTTTCTCTCCCGCTTCCACTTTTAAAATTTTTAATGCTCTAATTGCACTTGATAGTGGTGTGATAAAAACTAAAAAAGAAATTTTTTATCACTATAGAGGTGAAAAAGTATTTTTATCTTCTTGGGTGCAAGATATGAATTTAAGTTCAGCTATAAAATATTCTAATGTTCTTGCTTTTAAAGAAGTGGCAAGAAGAATTGGTATCAAAACTATGCAAGAATATTTAAACAAGCTTCATTATGGTAATGCTAAAATTTCCAAGATCGATACTTTTTGGCTTGACAACTCACTAAAAATAAGCGCTAAAGAACAAGCAATTTTACTTTTTAGACTTTCACAAAATAGCTTACCTTTTTCTCAAGAAGCAATGAATAGTGTTAAGGAAATGATTTATTTAAAAAATATGGAAAATTTAGAGCTTTTTGGAAAAACAGGTTTTAATGATGAGCAAAAAATTGCTTGGATTGTAGGTTTTGTGTATTTAAAAGATGAAAATAAATATAAGGCTTTCGCGCTAAATTTAGATATTGATAAATTTGAAGATTTATATAAAAGAGAAAAAATTTTAGAAAAATATTTAGATGAACTTGTAAAAAAAGTTAAAAATGATGGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37052","NCBI_taxonomy_name":"Campylobacter","NCBI_taxonomy_id":"194"}}}},"ARO_accession":"3005799","ARO_id":"44261","ARO_name":"OXA-578","CARD_short_name":"OXA-578","ARO_description":"OXA-578 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46519":{"category_aro_accession":"3007730","category_aro_cvterm_id":"46519","category_aro_name":"OXA-61-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-61.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4905":{"model_id":"4905","model_name":"OXA-579","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7280":{"protein_sequence":{"accession":"WP_002837769.1","sequence":"MKKITLFLLFLNLVFGQDKILNNWFKEYNTSGTFVFYDGKTWASNDFSRAMETFSPASTFKIFNALIALDSCVIKTKKEIFYHYRGEKVFLSSWAQDMNLSSAIKYSNVLAFKEVARRIGIKTMQEYLNKLHYGNAKISKIDTFWLDNSLKISAKEQAILLFRLSQNSLPFSQEAMNSVKEMIYLKNMENLELFGKTGFNDEQKIAWIVGFVYLKDENKYKAFALNLDIDKFEDLYKREKILEKYLDELVKKVKNDG"},"dna_sequence":{"accession":"NG_057514.1","fmin":"0","fmax":"774","strand":"+","sequence":"ATGAAAAAAATAACTTTATTTTTACTTTTCTTAAATTTAGTGTTTGGGCAAGATAAGATATTAAATAATTGGTTTAAAGAGTATAATACAAGCGGCACTTTTGTTTTTTATGATGGAAAAACTTGGGCGAGTAACGACTTTTCAAGGGCTATGGAGACTTTCTCTCCCGCTTCCACTTTTAAAATTTTTAATGCTCTAATTGCACTTGATAGTTGTGTGATAAAAACTAAAAAAGAAATTTTTTATCACTATAGAGGTGAAAAAGTATTTTTATCTTCTTGGGCGCAAGATATGAATTTAAGTTCAGCTATAAAATATTCTAATGTTCTTGCTTTTAAAGAAGTGGCAAGAAGAATTGGTATCAAAACTATGCAAGAATATTTAAACAAGCTTCATTATGGTAATGCTAAAATTTCCAAGATCGATACTTTTTGGCTTGACAACTCACTAAAAATAAGCGCTAAAGAACAAGCAATTTTGCTTTTTAGACTTTCACAAAATAGCTTACCTTTTTCTCAAGAAGCAATGAATAGTGTTAAGGAAATGATTTATTTAAAAAATATGGAAAATTTAGAGCTTTTTGGAAAAACAGGTTTTAATGATGAGCAAAAAATTGCTTGGATCGTAGGTTTTGTGTATTTAAAAGATGAAAATAAATATAAGGCTTTCGCGCTAAATTTAGATATTGATAAATTTGAAGATTTATATAAAAGAGAAAAAATTTTAGAAAAATATTTAGATGAACTTGTAAAAAAAGTTAAAAATGATGGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37052","NCBI_taxonomy_name":"Campylobacter","NCBI_taxonomy_id":"194"}}}},"ARO_accession":"3005800","ARO_id":"44262","ARO_name":"OXA-579","CARD_short_name":"OXA-579","ARO_description":"OXA-579 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46519":{"category_aro_accession":"3007730","category_aro_cvterm_id":"46519","category_aro_name":"OXA-61-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-61.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4906":{"model_id":"4906","model_name":"OXA-580","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7281":{"protein_sequence":{"accession":"WP_025006557.1","sequence":"MKKITLFLLFLNLVFGQDKILNNWFKEYNTSGTFVFYDGKTWASNDFSRAMETFSPTSTFKIFNALIALDSGVIKTKKEIFYHYRGEKVFLSSWAQDMNLSSAIKYSNVLAFKEVARRIGIKTMQEYLNKLHYGNAKISKIDTFWLDNSLKISAKEQAILLFRLSQNSLPFSQEAMNSVKEMIYLKNMENLELFGKTGFNDEQKIAWIVGFVYLKDENKYKAFALNLDIDKFEDLYKREKILEKYLDELVKKVKNDG"},"dna_sequence":{"accession":"NG_057516.1","fmin":"0","fmax":"774","strand":"+","sequence":"ATGAAAAAAATAACTTTATTTTTACTTTTCTTAAATTTAGTGTTTGGGCAAGATAAGATATTAAATAATTGGTTTAAAGAGTATAATACAAGCGGCACTTTTGTTTTTTATGATGGAAAAACTTGGGCGAGTAACGACTTTTCAAGGGCTATGGAGACTTTCTCTCCCACTTCCACTTTTAAAATTTTTAATGCTCTAATTGCACTTGATAGTGGTGTGATAAAAACTAAAAAAGAAATTTTTTATCACTATAGAGGTGAAAAAGTATTTTTATCTTCTTGGGCGCAAGATATGAATTTAAGTTCAGCTATAAAATATTCTAATGTTCTTGCTTTTAAAGAAGTGGCAAGAAGAATTGGTATCAAAACTATGCAAGAATATTTAAACAAGCTTCATTATGGTAATGCTAAAATTTCCAAGATCGATACTTTTTGGCTTGACAACTCACTAAAAATAAGCGCTAAAGAACAAGCAATTTTGCTTTTTAGACTTTCACAAAATAGCTTACCTTTTTCTCAAGAAGCAATGAATAGTGTTAAGGAAATGATTTATTTAAAAAATATGGAAAATTTAGAGCTTTTTGGAAAAACAGGTTTTAATGATGAGCAAAAAATTGCTTGGATTGTAGGTTTTGTGTATTTAAAAGATGAAAATAAATATAAGGCTTTCGCGCTAAATTTAGATATTGATAAATTTGAAGATTTATATAAAAGAGAAAAAATTTTAGAAAAATATTTAGATGAACTTGTAAAAAAAGTTAAAAATGATGGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36772","NCBI_taxonomy_name":"Campylobacter jejuni","NCBI_taxonomy_id":"197"}}}},"ARO_accession":"3005801","ARO_id":"44263","ARO_name":"OXA-580","CARD_short_name":"OXA-580","ARO_description":"OXA-580 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46519":{"category_aro_accession":"3007730","category_aro_cvterm_id":"46519","category_aro_name":"OXA-61-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-61.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4907":{"model_id":"4907","model_name":"OXA-581","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7282":{"protein_sequence":{"accession":"WP_052788887.1","sequence":"MKKITLFLLFLNLVFGQDKILNNWFKEYNTSGTFVFYDGKTWASNDFSRAMETFSPASTFKIFNALIALDSGVIKTKKEIFYHYRGEKVFLSSWAQDMNLSSAIKYSNVLAFKEVARRIGIKTMQEYLNKLHYGNAKISKIDTFWLDNSLKISAKEQAILLFRLSQNRLPFSQEAMNSVKEMIYLKNMENLELFGKTGFNDEQKIAWIVGFVYLKDENKYKAFALNLDIDKFEDLYKREKILEKYLDELVKKVKNDG"},"dna_sequence":{"accession":"NG_057517.1","fmin":"0","fmax":"774","strand":"+","sequence":"ATGAAAAAAATAACTTTATTTTTACTTTTCTTAAATTTAGTGTTTGGGCAAGATAAGATATTAAATAATTGGTTTAAAGAGTATAATACAAGCGGCACTTTTGTTTTTTATGATGGAAAAACTTGGGCGAGTAACGACTTTTCAAGGGCTATGGAGACTTTCTCTCCCGCTTCCACTTTTAAAATTTTTAATGCTCTAATTGCACTTGATAGTGGTGTGATAAAAACTAAAAAAGAAATTTTTTATCACTATAGAGGTGAAAAAGTATTTTTATCTTCTTGGGCGCAAGATATGAATTTAAGTTCAGCTATAAAATATTCTAATGTTCTTGCTTTTAAAGAAGTGGCAAGAAGAATTGGTATCAAAACTATGCAAGAATATTTAAACAAGCTTCATTATGGTAATGCTAAAATTTCCAAGATCGATACTTTTTGGCTTGACAACTCACTAAAAATAAGCGCTAAAGAACAAGCAATTTTGCTTTTTAGACTTTCACAAAATAGATTACCTTTTTCTCAAGAAGCAATGAATAGTGTTAAGGAAATGATTTATTTAAAAAATATGGAAAATTTAGAGCTTTTTGGAAAAACAGGTTTTAATGATGAGCAAAAAATTGCTTGGATTGTAGGTTTTGTGTATTTAAAAGATGAAAATAAATATAAGGCTTTCGCGCTAAATTTAGATATTGATAAATTTGAAGATTTATATAAAAGAGAAAAAATTTTAGAAAAATATTTAGATGAACTTGTAAAAAAAGTTAAAAATGATGGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36772","NCBI_taxonomy_name":"Campylobacter jejuni","NCBI_taxonomy_id":"197"}}}},"ARO_accession":"3005802","ARO_id":"44264","ARO_name":"OXA-581","CARD_short_name":"OXA-581","ARO_description":"OXA-581 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46519":{"category_aro_accession":"3007730","category_aro_cvterm_id":"46519","category_aro_name":"OXA-61-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-61.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4908":{"model_id":"4908","model_name":"OXA-582","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7283":{"protein_sequence":{"accession":"WP_109545107.1","sequence":"MKKITLFLLFLNLVFGQDKILNNWFKEYNTSGTFVFYDGKTWASNDFSRAMETFSPASTFKIFNALIALDSGVIKTKKEIFYHYRGEKVFLSSWAQDMNLSSAIKYSNVLAFKEVARRIGIKTMQEYLNKLHYGNAKISKIDTFWLDNSLKISAKEQAILLFRLSQNILPFSQEAMNSVKEMIYLKNMENLELFGKTGFNDEQKIAWIVGFVYLKDENKYKAFALNLDIDKFEDLYKREKILEKYLDELVKKVKNDG"},"dna_sequence":{"accession":"NG_057541.1","fmin":"0","fmax":"774","strand":"+","sequence":"ATGAAAAAAATAACTTTATTTTTACTTTTCTTAAATTTAGTGTTTGGGCAAGATAAGATATTAAATAATTGGTTTAAAGAGTATAATACAAGCGGCACTTTTGTTTTTTATGATGGAAAAACTTGGGCGAGTAACGACTTTTCAAGGGCTATGGAGACTTTCTCTCCCGCTTCCACTTTTAAAATTTTTAATGCTCTAATTGCACTTGATAGTGGTGTGATAAAAACTAAAAAAGAAATTTTTTATCACTATAGAGGTGAAAAAGTATTTTTATCTTCTTGGGCGCAAGATATGAATTTAAGTTCAGCTATAAAATATTCTAATGTTCTTGCTTTTAAAGAAGTGGCAAGAAGAATTGGTATCAAAACTATGCAAGAATATTTAAACAAGCTTCATTATGGTAATGCTAAAATTTCCAAGATCGATACTTTTTGGCTTGACAACTCACTAAAAATAAGCGCTAAAGAACAAGCAATTTTGCTTTTTAGACTTTCACAAAATATCTTACCTTTTTCTCAAGAAGCAATGAATAGTGTTAAGGAAATGATTTATTTAAAAAATATGGAAAATTTAGAGCTTTTTGGAAAAACAGGTTTTAATGATGAGCAAAAAATTGCTTGGATTGTAGGTTTTGTGTATTTAAAAGATGAAAATAAATATAAGGCTTTCGCGCTAAATTTAGATATTGATAAATTTGAAGATTTATATAAAAGAGAAAAAATTTTAGAAAAATATTTAGATGAACTTGTAAAAAAAGTTAAAAATGATGGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36772","NCBI_taxonomy_name":"Campylobacter jejuni","NCBI_taxonomy_id":"197"}}}},"ARO_accession":"3005803","ARO_id":"44265","ARO_name":"OXA-582","CARD_short_name":"OXA-582","ARO_description":"OXA-582 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46519":{"category_aro_accession":"3007730","category_aro_cvterm_id":"46519","category_aro_name":"OXA-61-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-61.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4909":{"model_id":"4909","model_name":"OXA-583","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7284":{"protein_sequence":{"accession":"WP_052781249.1","sequence":"MKKITLFLLFLNLVFGQDKILNNWFKEYNTSGTFVFYDGKTWASNDFSRAMETFSPASTFKIFNALIALDSGVIKTKKEIFYHYRGEKVFLSSWAQDMNLSSAIKYSNVLAFKEVARRIGIKTMQEYLNKLHYGNAKISKIDTFWLDNSLKISAKEQAILLFKLSQNSLPFSQEAMNSVKEMIYLKNMENLELFGKTGFNDEQKIAWIVGFVYLKDENKYKAFALNLDIDKFEDLYKREKILEKYLDELVKKVKNDG"},"dna_sequence":{"accession":"NG_057519.1","fmin":"0","fmax":"774","strand":"+","sequence":"ATGAAAAAAATAACTTTATTTTTACTTTTCTTAAATTTAGTGTTTGGGCAAGATAAGATATTAAATAATTGGTTTAAAGAGTATAATACAAGCGGCACTTTTGTTTTTTATGATGGAAAAACTTGGGCGAGTAACGACTTTTCAAGGGCTATGGAGACTTTCTCTCCCGCTTCCACTTTTAAAATTTTTAATGCTCTAATTGCACTTGATAGTGGTGTGATAAAAACTAAAAAAGAAATTTTTTATCACTATAGAGGTGAAAAAGTATTTTTATCTTCTTGGGCGCAAGATATGAATTTAAGTTCAGCTATAAAATATTCTAATGTTCTTGCTTTTAAAGAAGTGGCAAGAAGAATTGGTATCAAAACTATGCAAGAATATTTAAACAAGCTTCATTATGGTAATGCTAAAATTTCCAAGATCGATACTTTTTGGCTTGATAACTCACTAAAAATAAGCGCTAAAGAACAAGCAATTTTGCTTTTTAAACTTTCACAAAATTCTTTACCTTTTTCTCAAGAAGCAATGAATAGTGTTAAGGAAATGATTTATTTAAAAAATATGGAAAATTTAGAGCTTTTTGGAAAAACAGGTTTTAATGATGAGCAAAAAATTGCTTGGATTGTAGGTTTTGTGTATTTAAAAGATGAAAATAAATATAAGGCTTTCGCGCTAAATTTAGATATTGATAAATTTGAAGATTTATATAAAAGAGAAAAAATTTTAGAAAAATATTTAGATGAACTTGTAAAAAAAGTTAAAAATGATGGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36772","NCBI_taxonomy_name":"Campylobacter jejuni","NCBI_taxonomy_id":"197"}}}},"ARO_accession":"3005804","ARO_id":"44266","ARO_name":"OXA-583","CARD_short_name":"OXA-583","ARO_description":"OXA-583 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46519":{"category_aro_accession":"3007730","category_aro_cvterm_id":"46519","category_aro_name":"OXA-61-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-61.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4910":{"model_id":"4910","model_name":"OXA-584","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7285":{"protein_sequence":{"accession":"WP_109545088.1","sequence":"MKKITLFLLFLNLVFGQDKILNNWFKEYNTSGTFVFYDGKTWASNDFSRAMETFSPASTFKIFNALIALDSGVIKTKKEIFYHYRGEKVFLSSWAQDMNLSSAIKYSNVLAFKEVARRIGIKTMQEYLNKLHYGNAKISKIDTFWLDNSLKISAKEQAILLFRLSQNSLPFSQEAMNSVKEMIYLKNMENLELFGKTGFNDEQKIAWIVGFVYLKDENKYKAFALNLNIDKFEDLYKREKILEKYLDELVKKVKNDG"},"dna_sequence":{"accession":"NG_057522.1","fmin":"0","fmax":"774","strand":"+","sequence":"ATGAAAAAAATAACTTTATTTTTACTTTTCTTAAATTTAGTGTTTGGGCAAGATAAGATATTAAATAATTGGTTTAAAGAGTATAATACAAGCGGCACTTTTGTTTTTTATGATGGAAAAACTTGGGCGAGTAACGACTTTTCAAGGGCTATGGAGACTTTCTCTCCCGCTTCCACTTTTAAAATTTTTAATGCTCTAATTGCACTTGATAGTGGTGTGATAAAAACTAAAAAAGAAATTTTTTATCACTATAGAGGTGAAAAAGTATTTTTATCTTCTTGGGCGCAAGATATGAATTTAAGTTCAGCTATAAAATATTCTAATGTTCTTGCTTTTAAAGAAGTGGCAAGAAGAATTGGTATCAAAACTATGCAAGAATATTTAAACAAGCTTCATTATGGTAATGCTAAAATTTCCAAGATCGATACTTTTTGGCTTGACAACTCACTAAAAATAAGCGCTAAAGAACAAGCAATTTTGCTTTTTAGACTTTCACAAAATAGCTTACCTTTTTCTCAAGAAGCAATGAATAGTGTTAAGGAAATGATTTATTTAAAAAATATGGAAAATTTAGAGCTTTTTGGAAAAACAGGTTTTAATGATGAGCAAAAAATTGCTTGGATTGTAGGTTTTGTGTATTTAAAAGATGAAAATAAATATAAGGCTTTCGCGCTAAATTTAAATATTGATAAATTTGAAGATTTATATAAAAGAGAAAAAATTTTAGAAAAATATTTAGATGAACTTGTAAAAAAAGTTAAAAATGATGGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36772","NCBI_taxonomy_name":"Campylobacter jejuni","NCBI_taxonomy_id":"197"}}}},"ARO_accession":"3005805","ARO_id":"44267","ARO_name":"OXA-584","CARD_short_name":"OXA-584","ARO_description":"OXA-584 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46519":{"category_aro_accession":"3007730","category_aro_cvterm_id":"46519","category_aro_name":"OXA-61-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-61.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4911":{"model_id":"4911","model_name":"OXA-585","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7286":{"protein_sequence":{"accession":"WP_109545089.1","sequence":"MKKITLFLLFLNLVFGQDKILNNWFKEYNTSGTFVFYDGKTWASNDFSRAMETFSPASTFKIFNALIALDSGVIKTKKEIFYHYRGEKVFLSSWAQDMNLSSAIKYSNVLAFKEVARRIGIKTMQEYLNKLHYGNAKISKIDTFWLDNSLKISAKEQAILLFRLSQNSLPFSQEAMNSVKEMIYLKNMENLELFGKTGFNDEQKITWIVGFVYLKDENKYKAFALNLDIDKFEDLYKREKILEKYLDELVKKVKNDG"},"dna_sequence":{"accession":"NG_057523.1","fmin":"0","fmax":"774","strand":"+","sequence":"ATGAAAAAAATAACTTTATTTTTACTTTTCTTAAATTTAGTGTTTGGGCAAGATAAGATATTAAATAATTGGTTTAAAGAGTATAATACAAGCGGCACTTTTGTTTTTTATGATGGAAAAACTTGGGCGAGTAACGACTTTTCAAGGGCTATGGAGACTTTCTCTCCCGCTTCCACTTTTAAAATTTTTAATGCTCTAATTGCACTTGATAGTGGTGTGATAAAAACTAAAAAAGAAATTTTTTATCACTATAGAGGTGAAAAAGTATTTTTATCTTCTTGGGCGCAAGATATGAATTTAAGTTCAGCTATAAAATATTCTAATGTTCTTGCTTTTAAAGAAGTGGCAAGAAGAATTGGTATCAAAACTATGCAAGAATATTTAAACAAGCTTCATTATGGTAATGCTAAAATTTCCAAGATCGATACTTTTTGGCTTGACAACTCACTAAAAATAAGCGCTAAAGAACAAGCAATTTTGCTTTTTAGACTTTCACAAAATAGCTTACCTTTTTCTCAAGAAGCAATGAATAGTGTTAAGGAAATGATTTATTTAAAAAATATGGAAAATTTAGAGCTTTTTGGAAAAACAGGTTTTAATGATGAGCAAAAAATTACTTGGATTGTAGGTTTTGTGTATTTAAAAGATGAAAATAAATATAAGGCTTTCGCGCTAAATTTAGATATTGATAAATTTGAAGATTTATATAAAAGAGAAAAAATTTTAGAAAAATATTTAGATGAACTTGTAAAAAAAGTTAAAAATGATGGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36772","NCBI_taxonomy_name":"Campylobacter jejuni","NCBI_taxonomy_id":"197"}}}},"ARO_accession":"3005806","ARO_id":"44268","ARO_name":"OXA-585","CARD_short_name":"OXA-585","ARO_description":"OXA-585 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46519":{"category_aro_accession":"3007730","category_aro_cvterm_id":"46519","category_aro_name":"OXA-61-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-61.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4912":{"model_id":"4912","model_name":"OXA-586","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7287":{"protein_sequence":{"accession":"WP_109545090.1","sequence":"MKKITLFLLFLNLVFGQDKILNNWFKEYNTSGTFVFYDGKTWASNDFSRAMETFSPASTFKIFNALIALDSGVIKTKKEIFYHYRGEKVFLSSWAQDMNLSSAIKYSNVLAFKEVARRIGIKTMQEYLNKLHYDNAKISKIDTFWLDNSLKISAKEQAILLFRLSQNSLPFSQEAMNSVKEMIYLKNMENLELFGKTGFNDEQKIAWIVGFVYLKDENKYKAFALNLDIDKFEDLYKREKILEKYLDELVKKVKNDG"},"dna_sequence":{"accession":"NG_057524.1","fmin":"0","fmax":"774","strand":"+","sequence":"ATGAAAAAAATAACTTTATTTTTACTTTTCTTAAATTTAGTGTTTGGGCAAGATAAGATATTAAATAATTGGTTTAAAGAGTATAATACAAGCGGCACTTTTGTTTTTTATGATGGAAAAACTTGGGCGAGTAACGACTTTTCAAGGGCTATGGAGACTTTCTCTCCCGCTTCCACTTTTAAAATTTTTAATGCTCTAATTGCACTTGATAGTGGTGTGATAAAAACTAAAAAAGAAATTTTTTATCACTATAGAGGTGAAAAAGTATTTTTATCTTCTTGGGCGCAAGATATGAATTTAAGTTCAGCTATAAAATATTCTAATGTTCTTGCTTTTAAAGAAGTGGCAAGAAGAATTGGTATCAAAACTATGCAAGAATATTTAAACAAGCTTCATTATGATAATGCTAAAATTTCCAAGATCGATACTTTTTGGCTTGACAACTCACTAAAAATAAGCGCTAAAGAACAAGCAATTTTGCTTTTTAGACTTTCACAAAATAGCTTACCTTTTTCTCAAGAAGCAATGAATAGTGTTAAGGAAATGATTTATTTAAAAAATATGGAAAATTTAGAGCTTTTTGGAAAAACAGGTTTTAATGATGAGCAAAAAATTGCTTGGATTGTAGGTTTTGTGTATTTAAAAGATGAAAATAAATATAAGGCTTTCGCGCTAAATTTAGATATTGATAAATTTGAAGATTTATATAAAAGAGAAAAAATTTTAGAAAAATATTTAGATGAACTTGTAAAAAAAGTTAAAAATGATGGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36772","NCBI_taxonomy_name":"Campylobacter jejuni","NCBI_taxonomy_id":"197"}}}},"ARO_accession":"3005807","ARO_id":"44269","ARO_name":"OXA-586","CARD_short_name":"OXA-586","ARO_description":"OXA-586 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46519":{"category_aro_accession":"3007730","category_aro_cvterm_id":"46519","category_aro_name":"OXA-61-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-61.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4913":{"model_id":"4913","model_name":"OXA-587","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7288":{"protein_sequence":{"accession":"WP_109545092.1","sequence":"MKKITLFLLFLNLVFGQDKILNNWFKEYNTSGTFVFYDGKTWASNDFSRAMETFSPASTFKIFNALIALDSGVIKTKKEIFYHYRGEKVFLSSWAQDMNLSSAIKYSNVLAFKEVARRIGIKTMQEYLNKLHYGNAKISKIDTFWLDNSPKISAKEQAILLFRLSQNSLPFSQEAMNSVKEMIYLKNMENLELFGKTGFNDEQKIAWIVGFVYLKDENKYKAFALNLDIDKFEDLYKREKILEKYLDELVKKVKNDG"},"dna_sequence":{"accession":"NG_057526.1","fmin":"0","fmax":"774","strand":"+","sequence":"ATGAAAAAAATAACTTTATTTTTACTTTTCTTAAATTTAGTGTTTGGGCAAGATAAGATATTAAATAATTGGTTTAAAGAGTATAATACAAGCGGCACTTTTGTTTTTTATGATGGAAAAACTTGGGCGAGTAACGACTTTTCAAGGGCTATGGAGACTTTCTCTCCCGCTTCCACTTTTAAAATTTTTAATGCTCTAATTGCACTTGATAGTGGTGTGATAAAAACTAAAAAAGAAATTTTTTATCACTATAGAGGTGAAAAAGTATTTTTATCTTCTTGGGCGCAAGATATGAATTTAAGTTCAGCTATAAAATATTCTAATGTTCTTGCTTTTAAAGAAGTGGCAAGAAGAATTGGTATCAAAACTATGCAAGAATATTTAAACAAGCTTCATTATGGTAATGCTAAAATTTCCAAGATCGATACTTTTTGGCTTGACAACTCACCAAAAATAAGCGCTAAAGAACAAGCAATTTTGCTTTTTAGACTTTCACAAAATAGCTTACCTTTTTCTCAAGAAGCAATGAATAGTGTTAAGGAAATGATTTATTTAAAAAATATGGAAAATTTAGAGCTTTTTGGAAAAACAGGTTTTAATGATGAGCAAAAAATTGCTTGGATTGTAGGTTTTGTGTATTTAAAAGATGAAAATAAATATAAGGCTTTCGCGCTAAATTTAGATATTGATAAATTTGAAGATTTATATAAAAGAGAAAAAATTTTAGAAAAATATTTAGATGAACTTGTAAAAAAAGTTAAAAATGATGGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36772","NCBI_taxonomy_name":"Campylobacter jejuni","NCBI_taxonomy_id":"197"}}}},"ARO_accession":"3005808","ARO_id":"44270","ARO_name":"OXA-587","CARD_short_name":"OXA-587","ARO_description":"OXA-587 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46519":{"category_aro_accession":"3007730","category_aro_cvterm_id":"46519","category_aro_name":"OXA-61-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-61.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4914":{"model_id":"4914","model_name":"OXA-588","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7289":{"protein_sequence":{"accession":"WP_109545095.1","sequence":"MKKITLFLLFLNLVFGQDKILNNWFKEYNTSGTFVFYDGKTWASNDFSRAMETFSPASTFKIFNTLIALDSGVIKTKKEIFYHYRGEKVFLSSWAQDMNLSSAIKYSNVLAFKEVARRIGIKTMQEYLNKLHYGNAKISKIDTFWLDNSLKISAKEQAILLFRLSQNSLPFSQEAMNSVKEMIYLKNMENLELFGKTGFNDEQKIAWIVGFVYLKDENKYKAFALNLDIDKFEDLYKREKILEKYLDELVKKVKNDG"},"dna_sequence":{"accession":"NG_057529.1","fmin":"0","fmax":"774","strand":"+","sequence":"ATGAAAAAAATAACTTTATTTTTACTTTTCTTAAATTTAGTGTTTGGGCAAGATAAGATATTAAATAATTGGTTTAAAGAGTATAATACAAGCGGCACTTTTGTTTTTTATGATGGAAAAACTTGGGCGAGTAACGACTTTTCAAGGGCTATGGAGACTTTCTCTCCCGCTTCCACTTTTAAAATTTTTAATACTCTAATTGCACTTGATAGTGGTGTGATAAAAACTAAAAAAGAAATTTTTTATCACTATAGAGGTGAAAAAGTATTTTTATCTTCTTGGGCGCAAGATATGAATTTAAGTTCAGCTATAAAATATTCTAATGTTCTTGCTTTTAAAGAAGTGGCAAGAAGAATTGGTATCAAAACTATGCAAGAATATTTAAACAAGCTTCATTATGGTAATGCTAAAATTTCCAAGATCGATACTTTTTGGCTTGACAACTCACTAAAAATAAGCGCTAAAGAACAAGCAATTTTGCTTTTTAGACTTTCACAAAATAGCTTACCTTTTTCTCAAGAAGCAATGAATAGTGTTAAGGAAATGATTTATTTAAAAAATATGGAAAATTTAGAGCTTTTTGGAAAAACAGGTTTTAATGATGAGCAAAAAATTGCTTGGATTGTAGGTTTTGTGTATTTAAAAGATGAAAATAAATATAAGGCTTTCGCGCTAAATTTAGATATTGATAAATTTGAAGATTTATATAAAAGAGAAAAAATTTTAGAAAAATATTTAGATGAACTTGTAAAAAAAGTTAAAAATGATGGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36772","NCBI_taxonomy_name":"Campylobacter jejuni","NCBI_taxonomy_id":"197"}}}},"ARO_accession":"3005809","ARO_id":"44271","ARO_name":"OXA-588","CARD_short_name":"OXA-588","ARO_description":"OXA-588 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46519":{"category_aro_accession":"3007730","category_aro_cvterm_id":"46519","category_aro_name":"OXA-61-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-61.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4915":{"model_id":"4915","model_name":"OXA-589","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7290":{"protein_sequence":{"accession":"WP_109545096.1","sequence":"MKKITLFLLFLNLVFGQDKILNNWFKEYNTSGTFVFYDGKTWASNDFSRAMETFSPASTFKIFNALIALDSGVIKTKKEIFYHYRGEKVFLSSWAQDMNLSSAIKYSNVLAFKEVARRIGIKTMQEYLNKLHYGNAKISKIDTFWLDNSLKISAKEQAILLFRLSQNSLPFSQEAMNSVKEIIYLKNMENLELFGKTGFNDEQKIAWIVGFVYLKDENKYKAFALNLDIDKFEDLYKREKILEKYLDELVKKVKNDG"},"dna_sequence":{"accession":"NG_057530.1","fmin":"0","fmax":"774","strand":"+","sequence":"ATGAAAAAAATAACTTTATTTTTACTTTTCTTAAATTTAGTGTTTGGGCAAGATAAGATATTAAATAATTGGTTTAAAGAGTATAATACAAGCGGCACTTTTGTTTTTTATGATGGAAAAACTTGGGCGAGTAACGACTTTTCAAGGGCTATGGAGACTTTCTCTCCCGCTTCCACTTTTAAAATTTTTAATGCTCTAATTGCACTTGATAGTGGTGTGATAAAAACTAAAAAAGAAATTTTTTATCACTATAGAGGTGAAAAAGTATTTTTATCTTCTTGGGCGCAAGATATGAATTTAAGTTCAGCTATAAAATATTCTAATGTTCTTGCTTTTAAAGAAGTGGCAAGAAGAATTGGTATCAAAACTATGCAAGAATATTTAAACAAGCTTCATTATGGTAATGCTAAAATTTCCAAGATCGATACTTTTTGGCTTGACAACTCACTAAAAATAAGCGCTAAAGAACAAGCAATTTTGCTTTTTAGACTTTCACAAAATAGCTTACCTTTTTCTCAAGAAGCAATGAATAGTGTTAAGGAAATTATTTATTTAAAAAATATGGAAAATTTAGAGCTTTTTGGAAAAACAGGTTTTAATGATGAGCAAAAAATTGCTTGGATTGTAGGTTTTGTGTATTTAAAAGATGAAAATAAATATAAGGCTTTCGCGCTAAATTTAGATATTGATAAATTTGAAGATTTATATAAAAGAGAAAAAATTTTAGAAAAATATTTAGATGAACTTGTAAAAAAAGTTAAAAATGATGGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36772","NCBI_taxonomy_name":"Campylobacter jejuni","NCBI_taxonomy_id":"197"}}}},"ARO_accession":"3005810","ARO_id":"44272","ARO_name":"OXA-589","CARD_short_name":"OXA-589","ARO_description":"OXA-589 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46519":{"category_aro_accession":"3007730","category_aro_cvterm_id":"46519","category_aro_name":"OXA-61-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-61.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4916":{"model_id":"4916","model_name":"OXA-590","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7291":{"protein_sequence":{"accession":"WP_109545103.1","sequence":"MKKITLFLLFLNLVFGQDKILNNWFKEYNTRGTFVFYDGKTWASNDFSRAMETFSPASTFKIFNALIALDSGVIKTKKEIFYHYRGEKVFLSSWAQDMNLSSAIKYSNVLAFKEVARRIGIKTMQEYLNKLHYGNAKISKIDTFWLDNSLKISAKEQAILLFRLSQNSLPFSQEAMNSVKEMIYLKNMENLELFGKTGFNDEQKIAWIVGFVYLKDENKYKAFALNLDIDKFEDLYKREKILEKYLDELVKKVKNDG"},"dna_sequence":{"accession":"NG_057537.1","fmin":"0","fmax":"774","strand":"+","sequence":"ATGAAAAAAATAACTTTATTTTTACTTTTCTTAAATTTAGTGTTTGGGCAAGATAAGATATTAAATAATTGGTTTAAAGAGTATAATACAAGAGGCACTTTTGTTTTTTATGATGGAAAAACTTGGGCGAGTAACGACTTTTCAAGGGCTATGGAGACTTTCTCTCCCGCTTCCACTTTTAAAATTTTTAATGCTCTAATTGCACTTGATAGTGGTGTGATAAAAACTAAAAAAGAAATTTTTTATCACTATAGAGGTGAAAAAGTATTTTTATCTTCTTGGGCGCAAGATATGAATTTAAGTTCAGCTATAAAATATTCTAATGTTCTTGCTTTTAAAGAAGTGGCAAGAAGAATTGGTATCAAAACTATGCAAGAATATTTAAACAAGCTTCATTATGGTAATGCTAAAATTTCCAAGATCGATACTTTTTGGCTTGACAACTCACTAAAAATAAGCGCTAAAGAACAAGCAATTTTGCTTTTTAGACTTTCACAAAATAGCTTACCTTTTTCTCAAGAAGCAATGAATAGTGTTAAGGAAATGATTTATTTAAAAAATATGGAAAATTTAGAGCTTTTTGGAAAAACAGGTTTTAATGATGAGCAAAAAATTGCTTGGATTGTAGGTTTTGTGTATTTAAAAGATGAAAATAAATATAAGGCTTTCGCGCTAAATTTAGATATTGATAAATTTGAAGATTTATATAAAAGAGAAAAAATTTTAGAAAAATATTTAGATGAGCTTGTAAAAAAAGTTAAAAATGATGGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36772","NCBI_taxonomy_name":"Campylobacter jejuni","NCBI_taxonomy_id":"197"}}}},"ARO_accession":"3005811","ARO_id":"44273","ARO_name":"OXA-590","CARD_short_name":"OXA-590","ARO_description":"OXA-590 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46519":{"category_aro_accession":"3007730","category_aro_cvterm_id":"46519","category_aro_name":"OXA-61-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-61.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4917":{"model_id":"4917","model_name":"OXA-591","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7292":{"protein_sequence":{"accession":"WP_002889704.1","sequence":"MKKITLFLLFLNLVFGQDKILNNWFKEYNTSGTFVFYDGKTWASNDFSRAMETFSPASTFKIFNALIALDSGVIKTKKEIFYHYRGEKVFLSSWAQDMNLSSAIKYSNVLAFKEVARRIGIKTMQEYLNKLHYGNAKISKIDTFWLDNSLKISAKEQAILLFRLSQNSLPFSQEAMNSVKEMICLKNMENLELFGKTGFNDEQKIAWIVGFVYLKDENKYKAFALNLDIDKFEDLYKREKILEKYLDELVKKVKNDG"},"dna_sequence":{"accession":"NG_057511.1","fmin":"0","fmax":"774","strand":"+","sequence":"ATGAAAAAAATAACTTTATTTTTACTTTTCTTAAATTTAGTGTTTGGGCAAGATAAGATATTAAATAATTGGTTTAAAGAGTATAATACAAGCGGCACTTTTGTTTTTTATGATGGAAAAACTTGGGCGAGTAACGACTTTTCAAGGGCTATGGAGACTTTCTCTCCCGCTTCCACTTTTAAAATTTTTAATGCTCTAATTGCACTTGATAGTGGTGTGATAAAAACTAAAAAAGAAATTTTTTATCACTATAGAGGTGAAAAAGTATTTTTATCTTCTTGGGCGCAAGATATGAATTTAAGTTCAGCTATAAAATATTCTAATGTTCTTGCTTTTAAAGAAGTGGCAAGAAGAATTGGTATCAAAACTATGCAAGAATATTTAAACAAGCTTCATTATGGTAATGCTAAAATTTCCAAGATCGATACTTTTTGGCTTGACAACTCACTAAAAATAAGCGCTAAAGAACAAGCAATTTTGCTTTTTAGACTTTCACAAAATAGCTTACCTTTTTCTCAAGAAGCAATGAATAGTGTTAAGGAAATGATTTGTTTAAAAAATATGGAAAATTTAGAGCTTTTTGGAAAAACAGGTTTTAATGATGAGCAAAAAATTGCTTGGATTGTAGGTTTTGTGTATTTAAAAGATGAAAATAAATATAAGGCTTTCGCGCTAAATTTAGATATTGATAAATTTGAAGATTTATATAAAAGAGAAAAAATTTTAGAAAAATATTTAGATGAACTTGTAAAAAAAGTTAAAAATGATGGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37052","NCBI_taxonomy_name":"Campylobacter","NCBI_taxonomy_id":"194"}}}},"ARO_accession":"3005812","ARO_id":"44274","ARO_name":"OXA-591","CARD_short_name":"OXA-591","ARO_description":"OXA-591 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46519":{"category_aro_accession":"3007730","category_aro_cvterm_id":"46519","category_aro_name":"OXA-61-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-61.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4918":{"model_id":"4918","model_name":"OXA-592","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7293":{"protein_sequence":{"accession":"WP_002857546.1","sequence":"MKKITLFLLFLNLVFGQDKVLNNWFKEYNTSGTFVFYDGKTWASNDFSRAMETFSPASTFKIFNALIALDSGVIKTKKEIFYHYRGEKVFLSSWAQDMNLSSAIKYSNVLAFKEVARRIGIKTMQEYLNKLHYGNAKISKIDTFWLDNSLKISAKEQAILLFRLSQNSLPFSQEAMNSVKEMIYLKNMENLELFGKTGFNDEQKIAWIVGFVYLKDENKYKAFALNLDIDKFEDLYKREKILEKYLDELVKKVKNDG"},"dna_sequence":{"accession":"NG_057515.1","fmin":"0","fmax":"774","strand":"+","sequence":"ATGAAAAAAATAACTTTATTTTTACTTTTCTTAAATTTAGTGTTTGGGCAAGATAAGGTATTAAATAATTGGTTTAAAGAGTATAATACAAGCGGCACTTTTGTTTTTTATGATGGAAAAACTTGGGCGAGTAACGACTTTTCAAGGGCTATGGAGACTTTCTCTCCCGCTTCCACTTTTAAAATTTTTAATGCTCTAATTGCACTTGATAGTGGTGTGATAAAAACTAAAAAAGAAATTTTTTATCACTATAGAGGTGAAAAAGTATTTTTATCTTCTTGGGCGCAAGATATGAATTTAAGTTCAGCTATAAAATATTCTAATGTTCTTGCTTTTAAAGAAGTGGCAAGAAGAATTGGTATCAAAACTATGCAAGAATATTTAAACAAGCTTCATTATGGTAATGCTAAAATTTCCAAGATCGATACTTTTTGGCTTGACAACTCACTAAAAATAAGCGCTAAAGAACAAGCAATTTTGCTTTTTAGACTTTCACAAAATAGCTTACCTTTTTCTCAAGAAGCAATGAATAGTGTTAAGGAAATGATTTATTTAAAAAATATGGAAAATTTAGAGCTTTTTGGAAAAACAGGTTTTAATGATGAGCAAAAAATTGCTTGGATTGTAGGTTTTGTGTATTTAAAAGATGAAAATAAATATAAGGCTTTCGCGCTAAATTTAGATATTGATAAATTTGAAGATTTATATAAAAGAGAAAAAATTTTAGAAAAATATTTAGATGAACTTGTAAAAAAAGTTAAAAATGATGGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36772","NCBI_taxonomy_name":"Campylobacter jejuni","NCBI_taxonomy_id":"197"}}}},"ARO_accession":"3005813","ARO_id":"44275","ARO_name":"OXA-592","CARD_short_name":"OXA-592","ARO_description":"OXA-592 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46519":{"category_aro_accession":"3007730","category_aro_cvterm_id":"46519","category_aro_name":"OXA-61-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-61.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4919":{"model_id":"4919","model_name":"OXA-593","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7294":{"protein_sequence":{"accession":"WP_109545097.1","sequence":"MKKITLFLLFLNLVFGQDKILNNWFKEYNTSGTFVFYDGKTWASNDFSRAMETFSPASTFKIFNALIALDSGVIKTKKEIFYHYRGEKVFLSSWAQDMNLSSAIKYSNVLAFKEVVRRIGIKTMQEYLDKLHYGNAKISKIDTFWLDNSLKISAKEQAILLFRLSQNSLPFSQEAMNSVKEMIYLKNMENLELFGKTGFNDEQKIAWIVGFVYLKDENKYKAFALNLDIDKFEDLYKREKILEKYLDELVKKVKNDG"},"dna_sequence":{"accession":"NG_057531.1","fmin":"0","fmax":"774","strand":"+","sequence":"ATGAAAAAAATAACTTTATTTTTACTTTTCTTAAATTTAGTGTTTGGGCAAGATAAGATATTAAATAATTGGTTTAAAGAGTATAATACAAGCGGCACTTTTGTTTTTTATGATGGAAAAACTTGGGCGAGTAACGACTTTTCAAGGGCTATGGAGACTTTCTCTCCCGCTTCCACTTTTAAAATTTTTAATGCTCTAATTGCACTTGATAGTGGTGTGATAAAAACTAAAAAAGAAATTTTTTATCACTATAGAGGTGAAAAAGTATTTTTATCTTCTTGGGCGCAAGATATGAATTTAAGTTCAGCTATAAAATATTCTAATGTTCTTGCTTTTAAAGAAGTGGTAAGAAGAATTGGTATCAAAACTATGCAAGAATATTTAGACAAGCTTCATTATGGTAATGCTAAAATTTCCAAGATCGATACTTTTTGGCTTGACAACTCACTAAAAATAAGCGCTAAAGAACAAGCAATTTTGCTTTTTAGACTTTCACAAAATAGCTTACCTTTTTCTCAAGAAGCAATGAATAGTGTTAAGGAAATGATTTATTTAAAAAATATGGAAAATTTAGAGCTTTTTGGAAAAACAGGTTTTAATGATGAGCAAAAAATTGCTTGGATTGTAGGTTTTGTGTATTTAAAAGATGAAAATAAATATAAGGCTTTCGCGCTAAATTTAGATATTGATAAATTTGAAGATTTATATAAAAGAGAAAAAATTTTAGAAAAATATTTAGATGAACTTGTAAAAAAAGTTAAAAATGATGGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36772","NCBI_taxonomy_name":"Campylobacter jejuni","NCBI_taxonomy_id":"197"}}}},"ARO_accession":"3005814","ARO_id":"44276","ARO_name":"OXA-593","CARD_short_name":"OXA-593","ARO_description":"OXA-593 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46519":{"category_aro_accession":"3007730","category_aro_cvterm_id":"46519","category_aro_name":"OXA-61-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-61.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4920":{"model_id":"4920","model_name":"OXA-594","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7295":{"protein_sequence":{"accession":"WP_044600959.1","sequence":"MKKITLFLLFLNLVFGQDKILNNWFKEYNTSGTFVFYDGKTWASNDFSRAMETFSPASTFKIFNALIALDSGVIKTKKEIFYHYRGEKVFLSSWAQDMNLSSAIKYSNVLAFKEVARRIGIKTMQEYLNKLHYGNAKISKIDTFWLDNSLKISTKEQAILLFRLSQNSLPFSQEAMNSVKEMIYLKNMENLELFGKTGFNDEQKIAWIVGFVYLKDENKYKAFALNLDIDKFEDLYKREKILEKYLDELVKKVKNDG"},"dna_sequence":{"accession":"NG_057508.1","fmin":"0","fmax":"774","strand":"+","sequence":"ATGAAAAAAATAACTTTATTTTTACTTTTCTTAAATTTAGTGTTTGGGCAAGATAAGATATTAAATAATTGGTTTAAAGAGTATAATACAAGCGGCACTTTTGTTTTTTATGATGGAAAAACTTGGGCGAGTAACGACTTTTCAAGGGCTATGGAGACTTTCTCTCCCGCTTCCACTTTTAAAATTTTTAATGCTCTAATTGCACTTGATAGTGGTGTGATAAAAACTAAAAAAGAAATTTTTTATCACTATAGAGGTGAAAAAGTATTTTTATCTTCTTGGGCGCAAGATATGAATTTAAGTTCAGCTATAAAATATTCTAATGTTCTTGCTTTTAAAGAAGTGGCAAGAAGAATTGGTATCAAAACTATGCAAGAATATTTAAACAAGCTTCATTATGGTAATGCTAAAATTTCCAAGATCGATACTTTTTGGCTTGACAACTCACTAAAAATAAGCACTAAAGAACAAGCAATTTTGCTTTTTAGACTTTCACAAAATAGCTTACCTTTTTCTCAAGAAGCAATGAATAGTGTTAAGGAAATGATTTATTTAAAAAATATGGAAAATTTAGAGCTTTTTGGAAAAACAGGTTTTAATGATGAGCAAAAAATTGCTTGGATTGTAGGTTTTGTGTATTTAAAAGATGAAAATAAATATAAGGCTTTCGCGCTAAATTTAGATATTGATAAATTTGAAGATTTATATAAAAGAGAAAAAATTTTAGAAAAATATTTAGATGAGCTTGTAAAAAAAGTTAAAAATGATGGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37052","NCBI_taxonomy_name":"Campylobacter","NCBI_taxonomy_id":"194"}}}},"ARO_accession":"3005815","ARO_id":"44277","ARO_name":"OXA-594","CARD_short_name":"OXA-594","ARO_description":"OXA-594 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46519":{"category_aro_accession":"3007730","category_aro_cvterm_id":"46519","category_aro_name":"OXA-61-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-61.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4921":{"model_id":"4921","model_name":"OXA-595","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7296":{"protein_sequence":{"accession":"WP_002824679.1","sequence":"MKKITLFLLFLNLVFGQDKILNNWFKEYNTSGTFVFYDGKTWASNDFSRAMETFSPASTFKIFNALIALDSGVIKTKKEIFYHYRGEKVFLSSWAQDMNLSSAIKYSNVLAFKEVARRIGIKTMQEYLNKLHYGNAKISKIDTFWLDNSLKISVKEQAILLFRLSQNSLPFSQEAMNSVKEMIYLKNMENLELFGKTGFNDEQKIAWIVGFVYLKDENKYKAFALNLDIDKFEDLYKREKILEKYLDELVKKVKNDG"},"dna_sequence":{"accession":"NG_057513.1","fmin":"0","fmax":"774","strand":"+","sequence":"ATGAAAAAAATAACTTTATTTTTACTTTTCTTAAATTTAGTGTTTGGGCAAGATAAGATATTAAATAATTGGTTTAAAGAGTATAATACAAGCGGCACTTTTGTTTTTTATGATGGAAAAACTTGGGCGAGTAACGACTTTTCAAGGGCTATGGAGACTTTCTCTCCCGCTTCCACTTTTAAAATTTTTAATGCTCTAATTGCACTTGATAGTGGTGTGATAAAAACTAAAAAAGAAATTTTTTATCACTATAGAGGTGAAAAAGTATTTTTATCTTCTTGGGCGCAAGATATGAATTTAAGTTCAGCTATAAAATATTCTAATGTTCTTGCTTTCAAAGAAGTGGCAAGAAGAATTGGTATCAAAACTATGCAAGAATATTTAAACAAGCTTCATTATGGTAATGCTAAAATTTCCAAGATCGATACTTTTTGGCTTGACAACTCACTAAAAATAAGCGTTAAAGAACAAGCAATTTTGCTTTTTAGACTTTCACAAAATAGCTTACCTTTTTCTCAAGAAGCAATGAATAGTGTTAAGGAAATGATTTATTTAAAAAATATGGAAAATTTAGAGCTTTTTGGAAAAACAGGTTTTAATGATGAGCAAAAAATTGCTTGGATTGTAGGTTTTGTGTATTTAAAAGATGAAAATAAATATAAGGCTTTCGCGCTAAATTTAGATATTGATAAATTTGAAGATTTATATAAAAGAGAAAAAATTTTAGAAAAATATTTAGATGAACTTGTAAAAAAAGTTAAAAATGATGGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37052","NCBI_taxonomy_name":"Campylobacter","NCBI_taxonomy_id":"194"}}}},"ARO_accession":"3005816","ARO_id":"44278","ARO_name":"OXA-595","CARD_short_name":"OXA-595","ARO_description":"OXA-595 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46519":{"category_aro_accession":"3007730","category_aro_cvterm_id":"46519","category_aro_name":"OXA-61-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-61.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4922":{"model_id":"4922","model_name":"OXA-596","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7297":{"protein_sequence":{"accession":"WP_109545093.1","sequence":"MKKITLFLLFLNLVFGQDKILNNWFKEYNTSGTFVFYDGKTWASNDFSRTMETFSPASTFKIFNALIALDSGVIKTKKEIFYHYRGEKVFLSSWAQDMNLSSAIKYSNVLAFKEVARRIGIKTMQEYLNKLHYGNAKISKIDTFWLDNSLKISAKEQAILLFRLSQNSLPFSQEAMNSVKEMICLKNMENLELFGKTGFNDEQKIAWIVGFVYLKDENKYKAFALNLDIDKFEDLYKREKILEKYLDELVKKVKNDG"},"dna_sequence":{"accession":"NG_057527.1","fmin":"0","fmax":"774","strand":"+","sequence":"ATGAAAAAAATAACTTTATTTTTACTTTTCTTAAATTTAGTGTTTGGGCAAGATAAGATATTAAATAATTGGTTTAAAGAGTATAATACAAGCGGCACTTTTGTTTTTTATGATGGAAAAACTTGGGCGAGTAACGACTTTTCAAGGACTATGGAGACTTTCTCTCCCGCTTCCACTTTTAAAATTTTTAATGCTCTAATTGCACTTGATAGTGGTGTGATAAAAACTAAAAAAGAAATTTTTTATCACTATAGAGGTGAAAAAGTATTTTTATCTTCTTGGGCGCAAGATATGAATTTAAGTTCAGCTATAAAATATTCTAATGTTCTTGCTTTTAAAGAAGTGGCAAGAAGAATTGGTATCAAAACTATGCAAGAATATTTAAACAAGCTTCATTATGGTAATGCTAAAATTTCCAAGATCGATACTTTTTGGCTTGACAACTCACTAAAAATAAGCGCTAAAGAACAAGCAATTTTGCTTTTTAGACTTTCACAAAATAGCTTACCTTTTTCTCAAGAAGCAATGAATAGTGTTAAGGAAATGATTTGTTTAAAAAATATGGAAAATTTAGAGCTTTTTGGAAAAACAGGTTTTAATGATGAGCAAAAAATTGCTTGGATTGTAGGTTTTGTGTATTTAAAAGATGAAAATAAATATAAGGCTTTCGCGCTAAATTTAGATATTGATAAATTTGAAGATTTATATAAAAGAGAAAAAATTTTAGAAAAATATTTAGATGAACTTGTAAAAAAAGTTAAAAATGATGGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36772","NCBI_taxonomy_name":"Campylobacter jejuni","NCBI_taxonomy_id":"197"}}}},"ARO_accession":"3005817","ARO_id":"44279","ARO_name":"OXA-596","CARD_short_name":"OXA-596","ARO_description":"OXA-596 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46519":{"category_aro_accession":"3007730","category_aro_cvterm_id":"46519","category_aro_name":"OXA-61-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-61.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4923":{"model_id":"4923","model_name":"OXA-597","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7298":{"protein_sequence":{"accession":"WP_052800105.1","sequence":"MKKITLFLLFLNLVFGQDKVLNNWFKEYNTSGTFVFYDGKTWASNDFSRAMETFSPASTFKIFNALIALDSGVIKTKKEIFYHYRGEKVFLSSWAQDINLSSAIKYSNVLAFKEVARRIGIKTMQEYLNKLHYGNAKISKIDTFWLDNSLKISAKEQAILLFRLSQNSLPFSQEAMNSVKEMIYLKNMENLELFGKTGFNDEQKIAWIVGFVYLKDENKYKAFALNLDIDKFEDLYKREKILEKYLDELVKKVKNDG"},"dna_sequence":{"accession":"NG_057520.1","fmin":"0","fmax":"774","strand":"+","sequence":"ATGAAAAAAATAACTTTATTTTTACTTTTCTTAAATTTAGTGTTTGGGCAAGATAAGGTATTAAATAATTGGTTTAAAGAGTATAATACAAGCGGCACTTTTGTTTTTTATGATGGAAAAACTTGGGCGAGTAACGACTTTTCAAGGGCTATGGAGACTTTCTCTCCCGCTTCCACTTTTAAAATTTTTAATGCTCTAATTGCACTTGATAGTGGTGTGATAAAAACTAAAAAAGAAATTTTTTATCACTATAGAGGTGAAAAAGTATTTTTATCTTCTTGGGCGCAAGATATAAATTTAAGTTCAGCTATAAAATATTCTAATGTTCTTGCTTTTAAAGAAGTGGCAAGAAGAATTGGTATCAAAACTATGCAAGAATATTTAAACAAGCTTCATTATGGTAATGCTAAAATTTCCAAGATCGATACTTTTTGGCTTGACAACTCACTAAAAATAAGCGCTAAAGAACAAGCAATTTTGCTTTTTAGACTTTCACAAAATAGCTTACCTTTTTCTCAAGAAGCAATGAATAGTGTTAAGGAAATGATTTATTTAAAAAATATGGAAAATTTAGAGCTTTTTGGAAAAACAGGTTTTAATGATGAGCAAAAAATTGCTTGGATTGTAGGTTTTGTGTATTTAAAAGATGAAAATAAATATAAGGCTTTCGCGCTAAATTTAGATATTGATAAATTTGAAGATTTATATAAAAGAGAAAAAATTTTAGAAAAATATTTAGATGAACTTGTAAAAAAAGTTAAAAATGATGGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36772","NCBI_taxonomy_name":"Campylobacter jejuni","NCBI_taxonomy_id":"197"}}}},"ARO_accession":"3005818","ARO_id":"44280","ARO_name":"OXA-597","CARD_short_name":"OXA-597","ARO_description":"OXA-597 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46519":{"category_aro_accession":"3007730","category_aro_cvterm_id":"46519","category_aro_name":"OXA-61-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-61.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4924":{"model_id":"4924","model_name":"OXA-598","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7299":{"protein_sequence":{"accession":"WP_109545101.1","sequence":"MKKITLFLLFLNLVFGQDKILNNWFKEYNTSGTFVFYDGKTWASNDFSRAMETFSPASTFKIFNALIALDSGVIKTKKEIFYHYRGEKVFLSSWAQDMNLSSAIKYSNVLAFKEVARRIGIKTMQEYLNKLHYGNAKISKIDTFWLDNSLKISAKEQAILLFRLSQNSLPSQEAMNSVKEMIYLKNMENLELFGKTGFNDEQKIAWIVGFVYLKDENKYKAFALNLDIDKFEDLYKREKILEKYLDELVKKVKNDG"},"dna_sequence":{"accession":"NG_057535.1","fmin":"0","fmax":"771","strand":"+","sequence":"ATGAAAAAAATAACTTTATTTTTACTTTTCTTAAATTTAGTGTTTGGGCAAGATAAGATATTAAATAATTGGTTTAAAGAGTATAATACAAGCGGCACTTTTGTTTTTTATGATGGAAAAACTTGGGCGAGTAACGACTTTTCAAGGGCTATGGAGACTTTCTCTCCCGCTTCCACTTTTAAAATTTTTAATGCTCTAATTGCACTTGATAGTGGTGTGATAAAAACTAAAAAAGAAATTTTTTATCACTATAGAGGTGAAAAAGTATTTTTATCTTCTTGGGCGCAAGATATGAATTTAAGTTCAGCTATAAAATATTCTAATGTTCTTGCTTTTAAAGAAGTGGCAAGAAGAATTGGTATCAAAACTATGCAAGAATATTTAAACAAGCTTCATTATGGTAATGCTAAAATTTCCAAGATCGATACTTTTTGGCTTGACAACTCACTAAAAATAAGCGCTAAAGAACAAGCAATTTTGCTTTTTAGACTTTCACAAAATAGCTTACCTTCTCAAGAAGCAATGAATAGTGTTAAGGAAATGATTTATTTAAAAAATATGGAAAATTTAGAGCTTTTTGGAAAAACAGGTTTTAATGATGAGCAAAAAATTGCTTGGATTGTAGGTTTTGTGTATTTAAAAGATGAAAATAAATATAAGGCTTTCGCGCTAAATTTAGATATTGATAAATTTGAAGATTTATATAAAAGAGAAAAAATTTTAGAAAAATATTTAGATGAACTTGTAAAAAAAGTTAAAAATGATGGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36772","NCBI_taxonomy_name":"Campylobacter jejuni","NCBI_taxonomy_id":"197"}}}},"ARO_accession":"3005819","ARO_id":"44281","ARO_name":"OXA-598","CARD_short_name":"OXA-598","ARO_description":"OXA-598 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46519":{"category_aro_accession":"3007730","category_aro_cvterm_id":"46519","category_aro_name":"OXA-61-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-61.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4925":{"model_id":"4925","model_name":"OXA-599","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7300":{"protein_sequence":{"accession":"WP_109545098.1","sequence":"MKKITLFLLFLNLVFGQDKILNNWFKEYNTSGTFVFYDGKTWASNDFSRAMETFSPASTFKIFNALIALDSGVIKTKKEIFYHYRGEKVFLSSWAQDMNLSSAIKYSNVLAFKEVARRIGIKTMQEYLDKLHYGNAKISKIDTFWLDNSLKISAKEQATLLFRLSQNSLPFSQEAMNSVKEMIYLKNMENLELFGKTGFNDEQKIAWIVGFVYLKDENKYKAFALNLDIDKFEDLYKREKILEKYLDELVKKVKNDG"},"dna_sequence":{"accession":"NG_057532.1","fmin":"0","fmax":"774","strand":"+","sequence":"ATGAAAAAAATAACTTTATTTTTACTTTTCTTAAATTTAGTGTTTGGGCAAGATAAGATATTAAATAATTGGTTTAAAGAGTATAATACAAGCGGCACTTTTGTTTTTTATGATGGAAAAACTTGGGCGAGTAACGACTTTTCAAGGGCTATGGAGACTTTCTCTCCCGCTTCCACTTTTAAAATTTTTAATGCTCTAATTGCACTTGATAGTGGTGTGATAAAAACTAAAAAAGAAATTTTTTATCACTATAGAGGTGAAAAAGTATTTTTATCTTCTTGGGCGCAAGATATGAATTTAAGTTCAGCTATAAAATATTCTAATGTTCTTGCTTTTAAAGAAGTGGCAAGAAGAATTGGTATCAAAACTATGCAAGAATATTTAGACAAGCTTCATTATGGTAATGCTAAAATTTCCAAGATCGATACTTTTTGGCTTGACAACTCACTAAAAATAAGCGCTAAAGAACAAGCAACTTTGCTTTTTAGACTTTCACAAAATAGCTTACCTTTTTCTCAAGAAGCAATGAATAGTGTTAAGGAAATGATTTATTTAAAAAATATGGAAAATTTAGAGCTTTTTGGAAAAACAGGTTTTAATGATGAGCAAAAAATTGCTTGGATTGTAGGTTTTGTGTATTTAAAAGATGAAAATAAATATAAGGCTTTCGCGCTAAATTTAGATATTGATAAATTTGAAGATTTATATAAAAGAGAAAAAATTTTAGAAAAATATTTAGATGAACTTGTAAAAAAAGTTAAAAATGATGGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36772","NCBI_taxonomy_name":"Campylobacter jejuni","NCBI_taxonomy_id":"197"}}}},"ARO_accession":"3005820","ARO_id":"44282","ARO_name":"OXA-599","CARD_short_name":"OXA-599","ARO_description":"OXA-599 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46519":{"category_aro_accession":"3007730","category_aro_cvterm_id":"46519","category_aro_name":"OXA-61-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-61.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4926":{"model_id":"4926","model_name":"OXA-600","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7301":{"protein_sequence":{"accession":"WP_109545094.1","sequence":"MKKITLFLLFLNLVFGQDKILNNWFKEYNTSGTFVFYDGKTWASNDFSRAMETFSPASTFKIFNALIALDSGVIKTKKEIFYHYTGEKVFLSSWAQDMNLSSAIKYSNVLAFKEVARRIGIKTMQEYLNKLHYGNAKISKIDTFWLDNSLKISAKEQAILLFRLSQNSLPFSQEAMNSVKEMIYLKNMENLELFGKTGFNDGQKIAWIVGFVYLKDENKYKAFALNLDIDKFEDLYKREKILEKYLDELVKKVKNDG"},"dna_sequence":{"accession":"NG_057528.1","fmin":"0","fmax":"774","strand":"+","sequence":"ATGAAAAAAATAACTTTATTTTTACTTTTCTTAAATTTAGTGTTTGGGCAAGATAAGATATTAAATAATTGGTTTAAAGAGTATAATACAAGCGGCACTTTTGTTTTTTATGATGGAAAAACTTGGGCGAGTAACGACTTTTCAAGGGCTATGGAGACTTTCTCTCCCGCTTCCACTTTTAAAATTTTTAATGCTCTAATTGCACTTGATAGTGGTGTGATAAAAACTAAAAAAGAAATTTTTTATCACTATACAGGTGAAAAAGTATTTTTATCTTCTTGGGCGCAAGATATGAATTTAAGTTCAGCTATAAAATATTCTAATGTTCTTGCTTTTAAAGAAGTGGCAAGAAGAATTGGTATCAAAACTATGCAAGAATATTTAAACAAGCTTCATTATGGTAATGCTAAAATTTCCAAGATCGATACTTTTTGGCTTGACAACTCACTAAAAATAAGCGCTAAAGAACAAGCAATTTTGCTTTTTAGACTTTCACAAAATAGCTTACCTTTTTCTCAAGAAGCAATGAATAGTGTTAAGGAAATGATTTATTTAAAAAATATGGAAAATTTAGAGCTTTTTGGAAAAACAGGTTTTAATGATGGGCAAAAAATTGCTTGGATTGTAGGTTTTGTGTATTTAAAAGATGAAAATAAATATAAGGCTTTCGCGCTAAATTTAGATATTGATAAATTTGAAGATTTATATAAAAGAGAAAAAATTTTAGAAAAATATTTAGATGAACTTGTAAAAAAAGTTAAAAATGATGGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36772","NCBI_taxonomy_name":"Campylobacter jejuni","NCBI_taxonomy_id":"197"}}}},"ARO_accession":"3005821","ARO_id":"44283","ARO_name":"OXA-600","CARD_short_name":"OXA-600","ARO_description":"OXA-600 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46519":{"category_aro_accession":"3007730","category_aro_cvterm_id":"46519","category_aro_name":"OXA-61-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-61.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4927":{"model_id":"4927","model_name":"OXA-601","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7302":{"protein_sequence":{"accession":"WP_052803794.1","sequence":"MKKITLFLLFLNLVFGQDKILNNWFKEYNTSGTFVFYDGKTWASNDFSRAMETFSPASTFKIFNALIALDSGVIKTKKEIFYHYRGEKVFLSSWAQDMNLSSAIKYSNVLAFKEVARRIGIKTMQEYLNKLHYGNAKISKIDTFWLDNSLKISVKEQAILLFRLSQNSLPFSQEAMNSVKEMIYLKNMENLELFGKTGFNDEQKIAWIVGFVYLKDENKYKAFALNLDIDKFEDLYKREKILEKYLDELVKKS"},"dna_sequence":{"accession":"NG_057521.1","fmin":"0","fmax":"762","strand":"+","sequence":"ATGAAAAAAATAACTTTATTTTTACTTTTCTTAAATTTAGTGTTTGGGCAAGATAAGATATTAAATAATTGGTTTAAAGAGTATAATACAAGCGGCACTTTTGTTTTTTATGATGGAAAAACTTGGGCGAGTAACGACTTTTCAAGGGCTATGGAGACTTTCTCTCCCGCTTCCACTTTTAAAATTTTTAATGCTCTAATTGCACTTGATAGTGGTGTGATAAAAACTAAAAAAGAAATTTTTTATCACTATAGAGGTGAAAAAGTATTTTTATCTTCTTGGGCGCAAGATATGAATTTAAGTTCAGCTATAAAATATTCTAATGTTCTTGCTTTTAAAGAAGTGGCAAGAAGAATTGGTATCAAAACTATGCAAGAATATTTAAACAAGCTTCATTATGGTAATGCTAAAATTTCCAAGATCGATACTTTTTGGCTTGACAACTCACTAAAAATAAGCGTTAAAGAACAAGCAATTTTGCTTTTTAGACTTTCACAAAATAGCTTACCTTTTTCTCAAGAAGCAATGAATAGTGTTAAGGAAATGATTTATTTAAAAAATATGGAAAATTTAGAGCTTTTTGGAAAAACAGGTTTTAATGATGAGCAAAAAATTGCTTGGATTGTAGGTTTTGTGTATTTAAAAGATGAAAATAAATATAAGGCTTTCGCGCTAAATTTAGATATTGATAAATTTGAAGATTTATATAAAAGAGAAAAAATTTTAGAAAAATATTTAGATGAACTTGTAAAAAAAAGTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36772","NCBI_taxonomy_name":"Campylobacter jejuni","NCBI_taxonomy_id":"197"}}}},"ARO_accession":"3005822","ARO_id":"44284","ARO_name":"OXA-601","CARD_short_name":"OXA-601","ARO_description":"OXA-601 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46519":{"category_aro_accession":"3007730","category_aro_cvterm_id":"46519","category_aro_name":"OXA-61-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-61.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4928":{"model_id":"4928","model_name":"OXA-602","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7303":{"protein_sequence":{"accession":"WP_109545105.1","sequence":"MKKITLFLLFLNLVFGQDKILNNWFKEYNTSGTFVFYDGKTWASNDFSRAMETFSPASTFKIFNALIALDSGVIKTKKEIFYHYRGEKVFLSSWAQDMNLSSAIKYSNVLAFKEVARRIGIKTMQEYLNKLHYGNAKISKIDTFWLDNSLKISAKEQAILLFRLSQNSLPFSQEAINSVKEMIYLKNMENLELFGKTGFNDEQKIAWIVGFVYLKDENKYKAFALNLDIDKFEDLYKREKILEKYLDELVKKS"},"dna_sequence":{"accession":"NG_057539.1","fmin":"0","fmax":"762","strand":"+","sequence":"ATGAAAAAAATAACTTTATTTTTACTTTTCTTAAATTTAGTGTTTGGGCAAGATAAGATATTAAATAATTGGTTTAAAGAGTATAATACAAGCGGCACTTTTGTTTTTTATGATGGAAAAACTTGGGCGAGTAACGACTTTTCAAGGGCTATGGAGACTTTCTCTCCCGCTTCCACTTTTAAAATTTTTAATGCTTTAATTGCACTTGATAGTGGTGTGATAAAAACTAAAAAAGAAATTTTTTATCACTATAGAGGTGAAAAAGTATTTTTATCTTCTTGGGCGCAAGATATGAATTTAAGTTCAGCTATAAAATATTCTAATGTTCTTGCTTTTAAAGAAGTGGCAAGAAGAATTGGTATCAAAACTATGCAAGAATATTTAAACAAGCTTCATTATGGTAATGCTAAAATTTCCAAGATCGATACTTTTTGGCTTGACAACTCACTAAAAATAAGCGCTAAAGAACAAGCAATTTTGCTTTTTAGACTTTCACAAAATAGCTTACCTTTTTCTCAAGAAGCAATCAATAGTGTTAAGGAAATGATTTATTTAAAAAATATGGAAAATTTAGAGCTTTTTGGAAAAACAGGTTTTAATGATGAGCAAAAAATTGCTTGGATTGTAGGTTTTGTGTATTTAAAAGATGAAAATAAATATAAGGCTTTCGCGCTAAATTTAGATATTGATAAATTTGAAGATTTATATAAAAGAGAAAAAATTTTAGAAAAATATTTAGATGAACTTGTAAAAAAAAGTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36772","NCBI_taxonomy_name":"Campylobacter jejuni","NCBI_taxonomy_id":"197"}}}},"ARO_accession":"3005823","ARO_id":"44285","ARO_name":"OXA-602","CARD_short_name":"OXA-602","ARO_description":"OXA-602 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46519":{"category_aro_accession":"3007730","category_aro_cvterm_id":"46519","category_aro_name":"OXA-61-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-61.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4929":{"model_id":"4929","model_name":"OXA-603","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7304":{"protein_sequence":{"accession":"WP_053921012.1","sequence":"MKKITLFLLFLNLVFGQDKILNNWFKEYNTSGTFVFYDGKTWASNDFSRAMETFSPASTFKIFNALIALDSGVIKTKKEIFYHYRGEKVFLSSWAQDMNLSSAIKYSNVLAFKEVARRIGIKTMQEYLNKLHYGNAKISKIDTFWLDNSLKISAKEQAILLFRLSQNSLPFSQEAMNSVKEMIYLKNMENLELFGKTGFNDEQKIAWIVGFVYLKDENKYKVFALNLDIDKFEDLYKREKILEKYLDELVKKS"},"dna_sequence":{"accession":"NG_057507.1","fmin":"0","fmax":"762","strand":"+","sequence":"ATGAAAAAAATAACTTTATTTTTACTTTTCTTAAATTTAGTGTTTGGGCAAGATAAGATATTAAATAATTGGTTTAAAGAGTATAATACAAGCGGCACTTTTGTTTTTTATGATGGAAAAACTTGGGCGAGTAACGACTTTTCAAGGGCTATGGAGACTTTCTCTCCCGCTTCCACTTTTAAAATTTTTAATGCTCTAATTGCACTTGATAGTGGTGTGATAAAAACTAAAAAAGAAATTTTTTATCACTATAGAGGTGAAAAAGTATTTTTATCTTCTTGGGCGCAAGATATGAATTTAAGTTCAGCTATAAAATATTCTAATGTTCTTGCTTTTAAAGAAGTGGCAAGAAGAATTGGTATCAAAACTATGCAAGAATATTTAAACAAGCTTCATTATGGTAATGCTAAAATTTCCAAGATCGATACTTTTTGGCTTGACAACTCACTAAAAATAAGCGCTAAAGAACAAGCAATTTTGCTTTTTAGACTTTCACAAAATAGCTTACCTTTTTCTCAAGAAGCAATGAATAGTGTTAAGGAAATGATTTATTTAAAAAATATGGAAAATTTAGAGCTTTTTGGAAAAACAGGTTTTAATGATGAGCAAAAAATTGCTTGGATTGTAGGTTTTGTGTATTTAAAAGATGAAAATAAATATAAGGTTTTCGCGCTAAATTTAGATATTGATAAATTTGAAGATTTATATAAAAGAGAAAAAATTTTAGAAAAATATTTAGATGAACTTGTAAAAAAAAGTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36772","NCBI_taxonomy_name":"Campylobacter jejuni","NCBI_taxonomy_id":"197"}}}},"ARO_accession":"3005824","ARO_id":"44286","ARO_name":"OXA-603","CARD_short_name":"OXA-603","ARO_description":"OXA-603 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46519":{"category_aro_accession":"3007730","category_aro_cvterm_id":"46519","category_aro_name":"OXA-61-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-61.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4930":{"model_id":"4930","model_name":"OXA-604","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7305":{"protein_sequence":{"accession":"WP_109545104.1","sequence":"MKKITLFLLFLNLVFGQDKILNNWFKEYNTSGTFVFYDGKTWASNDFSRAMETFSPASTFKIFNALIALDSGVIKTKKEIFYHYRGGKVFLSSWAQDMNLSSAIKYSNVLAFKEVARRIGIKTMQEYLNKLHYGNAKISKIDTFWLDNSLKISAKEQAILLFRLSQNSLPFSQEAINSVKEMIYLKNMENLELFGKTGFNDEQKIAWIVGFVYLKDENKYKAFALNLDIDKFEDLYKREKILEKYLDELVKKS"},"dna_sequence":{"accession":"NG_057538.1","fmin":"0","fmax":"762","strand":"+","sequence":"ATGAAAAAAATAACTTTATTTTTACTTTTCTTAAATTTAGTGTTTGGGCAAGATAAGATATTAAATAATTGGTTTAAAGAGTATAATACAAGCGGCACTTTTGTTTTTTATGATGGAAAAACTTGGGCGAGTAACGACTTTTCAAGGGCTATGGAGACTTTCTCTCCCGCTTCCACTTTTAAAATTTTTAATGCTCTAATTGCACTTGATAGTGGTGTGATAAAAACTAAAAAAGAAATTTTTTATCACTATAGAGGTGGAAAAGTATTTTTATCTTCTTGGGCGCAAGATATGAATTTAAGTTCAGCTATAAAATATTCTAATGTTCTTGCTTTTAAAGAAGTGGCAAGAAGAATTGGTATCAAAACTATGCAAGAATATTTAAACAAGCTTCATTATGGTAATGCTAAAATTTCCAAGATCGATACTTTTTGGCTTGACAACTCACTAAAAATAAGCGCTAAAGAACAAGCAATTTTGCTTTTTAGACTTTCACAAAATAGCTTACCTTTTTCTCAAGAAGCAATAAATAGTGTTAAGGAAATGATTTATTTAAAAAATATGGAAAATTTAGAGCTTTTTGGAAAAACAGGTTTTAATGATGAGCAAAAAATTGCTTGGATTGTAGGTTTTGTGTATTTAAAAGATGAAAATAAATATAAGGCTTTCGCGCTAAATTTAGATATTGATAAATTTGAAGATTTATATAAAAGAGAAAAAATTTTAGAAAAATATTTAGATGAACTTGTAAAAAAAAGTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36772","NCBI_taxonomy_name":"Campylobacter jejuni","NCBI_taxonomy_id":"197"}}}},"ARO_accession":"3005825","ARO_id":"44287","ARO_name":"OXA-604","CARD_short_name":"OXA-604","ARO_description":"OXA-604 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46519":{"category_aro_accession":"3007730","category_aro_cvterm_id":"46519","category_aro_name":"OXA-61-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-61.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4931":{"model_id":"4931","model_name":"OXA-605","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7306":{"protein_sequence":{"accession":"WP_109545108.1","sequence":"MKKITLFLLFLNLVFGQDKILNNWFKEYNTSGTFVFYDGKTWASNDFSRAMETFSPASTFKIFNALIALDSGVIKTKKEIFYHYRGEKVFLSSWAQDMNLSSAIKYSNVLAFKEVTRRIGIKTMQEYLNKLHYGNAKISKIDTFWLDNSLKISAKEQAILLFRLSQNSLPFSQEAMNSVKEMIYLKNMENLELFGKTGFNDEQKIAWIVGFVYLKDENKYKAFALNLDIDKFEDLYKREKILEKYLDELVKKKLKMMASEYFVKCKNT"},"dna_sequence":{"accession":"NG_057542.1","fmin":"0","fmax":"807","strand":"+","sequence":"ATGAAAAAAATAACTTTATTTTTACTTTTCTTAAATTTAGTGTTTGGGCAAGATAAGATATTAAATAATTGGTTTAAAGAGTATAATACAAGCGGCACTTTTGTTTTTTATGATGGAAAAACTTGGGCGAGTAACGACTTTTCAAGGGCTATGGAGACTTTCTCTCCCGCTTCCACTTTTAAAATTTTTAATGCTCTAATTGCACTTGATAGTGGTGTGATAAAAACTAAAAAAGAAATTTTTTATCACTATAGAGGTGAAAAAGTATTTTTATCTTCTTGGGCGCAAGATATGAATTTAAGTTCAGCTATAAAATATTCTAATGTTCTTGCTTTTAAAGAAGTGACAAGAAGAATTGGTATCAAAACTATGCAAGAATATTTAAACAAGCTTCATTATGGTAATGCTAAAATTTCCAAGATCGATACTTTTTGGCTTGACAACTCACTAAAAATAAGCGCTAAAGAACAAGCAATTTTGCTTTTTAGACTTTCACAAAATAGCTTACCTTTTTCTCAAGAAGCAATGAATAGTGTTAAGGAAATGATTTATTTAAAAAATATGGAAAATTTAGAGCTTTTTGGAAAAACAGGTTTTAATGATGAGCAAAAAATTGCTTGGATTGTAGGTTTTGTGTATTTAAAAGATGAAAATAAATATAAGGCTTTCGCGCTAAATTTAGATATTGATAAATTTGAAGATTTATATAAAAGAGAAAAAATTTTAGAAAAATATTTAGATGAACTTGTAAAAAAAAAGTTAAAAATGATGGCTAGTGAGTATTTCGTAAAATGCAAAAATACTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36772","NCBI_taxonomy_name":"Campylobacter jejuni","NCBI_taxonomy_id":"197"}}}},"ARO_accession":"3005826","ARO_id":"44288","ARO_name":"OXA-605","CARD_short_name":"OXA-605","ARO_description":"OXA-605 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46519":{"category_aro_accession":"3007730","category_aro_cvterm_id":"46519","category_aro_name":"OXA-61-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-61.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4932":{"model_id":"4932","model_name":"OXA-606","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7307":{"protein_sequence":{"accession":"WP_109545106.1","sequence":"MKKITLFLLFLNLVFGQDKILNNWFKEYNTSGTFVFYDGKTWASNDFSRAMETFSPASTFKIFNALIALDSGVIKTKKEIFYHYRGEKVFLSSWAQDMNLSSAIKYSNVLAFKEVARRIGIKTMQEYLNKLHYGNAKISKIDTFWLDNSLKISAKEQAILLFRLSQNSLPFSQEAMNSVKEMIYLKNMENLELFGKTGFNDEQKIAWIVGFVYLKDENKYKVFALNLDIDKFEDLYKREKILEKYLDELVKKKYLIV"},"dna_sequence":{"accession":"NG_057540.1","fmin":"0","fmax":"774","strand":"+","sequence":"ATGAAAAAAATAACTTTATTTTTACTTTTCTTAAATTTAGTGTTTGGGCAAGATAAGATATTAAATAATTGGTTTAAAGAGTATAATACAAGCGGCACTTTTGTTTTTTATGATGGAAAAACTTGGGCGAGTAACGACTTTTCAAGGGCTATGGAGACTTTCTCTCCCGCTTCCACTTTTAAAATTTTTAATGCTCTAATTGCACTTGATAGTGGTGTGATAAAAACTAAAAAAGAAATTTTTTATCACTATAGAGGTGAAAAAGTATTTTTATCTTCTTGGGCGCAAGATATGAATTTAAGTTCAGCTATAAAATATTCTAATGTTCTTGCTTTTAAAGAAGTGGCAAGAAGAATTGGTATCAAAACTATGCAAGAATATTTAAACAAGCTTCATTATGGTAATGCTAAAATTTCCAAGATCGATACTTTTTGGCTTGACAACTCACTAAAAATAAGCGCTAAAGAACAAGCAATTTTGCTTTTTAGACTTTCACAAAATAGCTTACCTTTTTCTCAAGAAGCAATGAATAGTGTTAAGGAAATGATTTATTTAAAAAATATGGAAAATTTAGAGCTTTTTGGAAAAACAGGTTTTAATGATGAGCAAAAAATTGCTTGGATTGTAGGTTTTGTGTATTTAAAAGATGAAAATAAATATAAGGTTTTCGCGCTAAATTTAGATATTGATAAATTTGAAGATTTATATAAAAGAGAAAAAATTTTAGAAAAATATTTAGATGAACTTGTAAAAAAAAAATACTTAATTGTATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36772","NCBI_taxonomy_name":"Campylobacter jejuni","NCBI_taxonomy_id":"197"}}}},"ARO_accession":"3005827","ARO_id":"44289","ARO_name":"OXA-606","CARD_short_name":"OXA-606","ARO_description":"OXA-606 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46519":{"category_aro_accession":"3007730","category_aro_cvterm_id":"46519","category_aro_name":"OXA-61-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-61.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4933":{"model_id":"4933","model_name":"OXA-607","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7308":{"protein_sequence":{"accession":"WP_109545102.1","sequence":"MKKITLFLLFLNLKILNNWFKEYNTSGTFVFYDGKTWASNDFSRAMETFSPASTFKIFNALIALDSGVIKTKKEIFYHYRGEKVFLSSWAQDMNLSSAIKYSNVLAFKEVARRIGIKTMQEYLNKLHYGNAKISKIDTFWLDNSLKISAKEQAILLFRLSQNSLPFSQEAMNSVKEMIYLKNMENLELFGKTGFNDEQKIAWIVGFVYLKDENKYKAFALNLDIDKFEDLYKREKILEKYLDELVKKVKNDG"},"dna_sequence":{"accession":"NG_057536.1","fmin":"0","fmax":"759","strand":"+","sequence":"ATGAAAAAAATAACTTTATTTTTACTTTTCTTAAATTTAAAGATATTAAATAATTGGTTTAAAGAGTATAATACAAGCGGCACTTTTGTTTTTTATGATGGAAAAACTTGGGCGAGTAACGACTTTTCAAGGGCTATGGAGACTTTCTCTCCCGCTTCCACTTTTAAAATTTTTAATGCTCTAATTGCACTTGATAGTGGTGTGATAAAAACTAAAAAAGAAATTTTTTATCACTATAGAGGTGAAAAAGTATTTTTATCTTCTTGGGCGCAAGATATGAATTTAAGTTCAGCTATAAAATATTCTAATGTTCTTGCTTTTAAAGAAGTGGCAAGAAGAATTGGTATCAAAACTATGCAAGAATATTTAAACAAGCTTCATTATGGTAATGCTAAAATTTCCAAGATCGATACTTTTTGGCTTGACAACTCACTAAAAATAAGCGCTAAAGAACAAGCAATTTTGCTTTTTAGACTTTCACAAAATAGCTTACCTTTTTCTCAAGAAGCAATGAATAGTGTTAAGGAAATGATTTATTTAAAAAATATGGAAAATTTAGAGCTTTTTGGAAAAACAGGTTTTAATGATGAGCAAAAAATTGCTTGGATTGTAGGTTTTGTGTATTTAAAAGATGAAAATAAATATAAGGCTTTCGCGCTAAATTTAGATATTGATAAATTTGAAGATTTATATAAAAGAGAAAAAATTTTAGAAAAATATTTAGATGAACTTGTAAAAAAAGTTAAAAATGATGGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36772","NCBI_taxonomy_name":"Campylobacter jejuni","NCBI_taxonomy_id":"197"}}}},"ARO_accession":"3005828","ARO_id":"44290","ARO_name":"OXA-607","CARD_short_name":"OXA-607","ARO_description":"OXA-607 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46519":{"category_aro_accession":"3007730","category_aro_cvterm_id":"46519","category_aro_name":"OXA-61-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-61.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4934":{"model_id":"4934","model_name":"OXA-608","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7309":{"protein_sequence":{"accession":"WP_109545087.1","sequence":"MKKITLFLLFLNLVFGQDKILNNWFKEYNTSGTFVFYDGKTWASNDFSRAMETFSPASTFKIFNALIALDSGVIKTKKEIFYHYRGEKVFLSSWAQDMNLSSAIKYSNVLAFKEVARRIGIKTMQEYLNKLHYGNAKISKIDTFWLDNSLKISAKEQAILLFRLSQNSLPFSQEAMNSVKEMIYLKNMENLELFGKTGFNDEQKIAWIVGFVYLKDENKYKTFALNLDIDKFEDLYKREKILEKYLDELVKKVKNDG"},"dna_sequence":{"accession":"NG_057509.1","fmin":"0","fmax":"774","strand":"+","sequence":"ATGAAAAAAATAACTTTATTTTTACTTTTCTTAAATTTAGTGTTTGGGCAAGATAAGATATTAAATAATTGGTTTAAAGAGTATAATACAAGCGGCACTTTTGTTTTTTATGATGGAAAAACTTGGGCGAGTAACGACTTTTCAAGGGCTATGGAGACTTTCTCTCCCGCTTCCACTTTTAAAATTTTTAATGCTCTAATTGCACTTGATAGTGGTGTGATAAAAACTAAAAAAGAAATTTTTTATCACTATAGAGGTGAAAAAGTATTTTTATCTTCTTGGGCGCAAGATATGAATTTAAGTTCAGCTATAAAATATTCTAATGTTCTTGCTTTTAAAGAAGTGGCAAGAAGAATTGGTATCAAAACTATGCAAGAATATTTAAACAAGCTTCATTATGGTAATGCTAAAATTTCCAAGATCGATACTTTTTGGCTTGACAACTCACTAAAAATAAGCGCTAAAGAACAAGCAATTTTGCTTTTTAGACTTTCACAAAATAGCTTACCTTTTTCTCAAGAAGCAATGAATAGTGTTAAGGAAATGATTTATTTAAAAAATATGGAAAATTTAGAGCTTTTTGGAAAAACAGGTTTTAATGATGAGCAAAAAATTGCTTGGATTGTAGGTTTTGTGTATTTAAAAGATGAAAATAAATATAAGACTTTCGCGCTAAATTTAGATATTGATAAATTTGAAGATTTATATAAAAGAGAAAAAATTTTAGAAAAATATTTAGATGAACTTGTAAAAAAAGTTAAAAATGATGGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36772","NCBI_taxonomy_name":"Campylobacter jejuni","NCBI_taxonomy_id":"197"}}}},"ARO_accession":"3005829","ARO_id":"44291","ARO_name":"OXA-608","CARD_short_name":"OXA-608","ARO_description":"OXA-608 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46519":{"category_aro_accession":"3007730","category_aro_cvterm_id":"46519","category_aro_name":"OXA-61-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-61.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4935":{"model_id":"4935","model_name":"OXA-609","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7310":{"protein_sequence":{"accession":"WP_052798312.1","sequence":"MKKITLFLLFLNLVFGQDKILNNWFKEYNTSGTFVFYDGKTWASNDFSRAMETFSPASTFKIFNALIALDSGVIKTKKEIFYHYRGEKVFLSSWAQDMNLSSAIKYSNVLAFKEVARRIGIKTMQEYLNKLHYGNAKISKIDTFWLDNSLKISAKEQAILLFRLSQNSLPFSQEAMNSVKEMIYLKNMENLELFGKTGFNDEQKIAWIVGFVYLKDENKYKAFALNLDIDKFEDLYKREKILEKYLDELVKKVKNDD"},"dna_sequence":{"accession":"NG_057518.1","fmin":"0","fmax":"774","strand":"+","sequence":"ATGAAAAAAATAACTTTATTTTTACTTTTCTTAAATTTAGTGTTTGGGCAAGATAAGATATTAAATAATTGGTTTAAAGAGTATAATACAAGCGGCACTTTTGTTTTTTATGATGGAAAAACTTGGGCGAGTAACGACTTTTCAAGGGCTATGGAGACTTTCTCTCCCGCTTCCACTTTTAAAATTTTTAATGCTCTAATTGCACTTGATAGTGGTGTGATAAAAACTAAAAAAGAAATTTTTTATCACTATAGAGGTGAAAAAGTATTTTTATCTTCTTGGGCGCAAGATATGAATTTAAGTTCAGCTATAAAATATTCTAATGTTCTTGCTTTTAAAGAAGTGGCAAGAAGAATTGGTATCAAAACTATGCAAGAATATTTAAACAAGCTTCATTATGGTAATGCTAAAATTTCCAAGATCGATACTTTTTGGCTTGACAACTCACTAAAAATAAGCGCTAAAGAACAAGCAATTTTGCTTTTTAGACTTTCACAAAATAGCTTACCTTTTTCTCAAGAAGCAATGAATAGTGTTAAGGAAATGATTTATTTAAAAAATATGGAAAATTTAGAGCTTTTTGGAAAAACAGGTTTTAATGATGAGCAAAAAATTGCTTGGATTGTAGGTTTTGTGTATTTAAAAGATGAAAATAAATATAAGGCTTTCGCGCTAAATTTAGATATTGATAAATTTGAAGATTTATATAAAAGAGAAAAAATTTTAGAAAAATATTTAGATGAACTTGTAAAAAAAGTTAAAAATGATGACTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36772","NCBI_taxonomy_name":"Campylobacter jejuni","NCBI_taxonomy_id":"197"}}}},"ARO_accession":"3005830","ARO_id":"44292","ARO_name":"OXA-609","CARD_short_name":"OXA-609","ARO_description":"OXA-609 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46519":{"category_aro_accession":"3007730","category_aro_cvterm_id":"46519","category_aro_name":"OXA-61-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-61.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4936":{"model_id":"4936","model_name":"OXA-610","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7311":{"protein_sequence":{"accession":"WP_109545099.1","sequence":"MKKITLFLLFLNLVFGQDKILNNWFKEYNTSGTFVFYDGKTWASNDFSRAMETFSPASTFKIFNALIALDSGVIKTKKEIFYHYRGEKVFLSSWAQDMNLSSAIKYSNVLAFKEVARRIGIKTMQEYLNKLHYGNAKISKIDTFWLDNSLKISAKEQAILLFRLSQNSLPFSQEAMNSVKEMIYLKNMENLELFGKTGFNDEQKIAWIVGFVYLKDENKYKAFALNLDIDKFEDLYKREKILEKYLDELVKKVKNDS"},"dna_sequence":{"accession":"NG_057533.1","fmin":"0","fmax":"774","strand":"+","sequence":"ATGAAAAAAATAACTTTATTTTTACTTTTCTTAAATTTAGTGTTTGGGCAAGATAAGATATTAAATAATTGGTTTAAAGAGTATAATACAAGCGGCACTTTTGTTTTTTATGATGGAAAAACTTGGGCGAGTAACGACTTTTCAAGGGCTATGGAGACTTTCTCTCCCGCTTCCACTTTTAAAATTTTTAATGCTCTAATTGCACTTGATAGTGGTGTGATAAAAACTAAAAAAGAAATTTTTTATCACTATAGAGGTGAAAAAGTATTTTTATCTTCTTGGGCGCAAGATATGAATTTAAGTTCAGCTATAAAATATTCTAATGTTCTTGCTTTTAAAGAAGTGGCAAGAAGAATTGGTATCAAAACTATGCAAGAATATTTAAACAAGCTTCATTATGGTAATGCTAAAATTTCCAAGATCGATACTTTTTGGCTTGACAACTCACTAAAAATAAGCGCTAAAGAACAAGCAATTTTGCTTTTTAGACTTTCACAAAATAGCTTACCTTTTTCTCAAGAAGCAATGAATAGTGTTAAGGAAATGATTTATTTAAAAAATATGGAAAATTTAGAGCTTTTTGGAAAAACAGGTTTTAATGATGAGCAAAAAATTGCTTGGATTGTAGGTTTTGTGTATTTAAAAGATGAAAATAAATATAAGGCTTTCGCGCTAAATTTAGATATTGATAAATTTGAAGATTTATATAAAAGAGAAAAAATTTTAGAAAAATATTTAGATGAACTTGTAAAAAAAGTTAAAAATGATAGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36772","NCBI_taxonomy_name":"Campylobacter jejuni","NCBI_taxonomy_id":"197"}}}},"ARO_accession":"3005831","ARO_id":"44293","ARO_name":"OXA-610","CARD_short_name":"OXA-610","ARO_description":"OXA-610 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46519":{"category_aro_accession":"3007730","category_aro_cvterm_id":"46519","category_aro_name":"OXA-61-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-61.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4937":{"model_id":"4937","model_name":"OXA-611","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7312":{"protein_sequence":{"accession":"WP_052788483.1","sequence":"MKKITLFLLFLNLVFGQDKILNNWFKEYNTSGTFVFYDGKTWVSNDFSRAMETFSPASTFKIFNALIALDSGVIKTKKEIFYHYRGEKVFLSSWAQDMNLSSAIKYSNVLAFKEVARRIGIKTMQEYLNKLHYGNAKISKIDTFWLDNSLKISAKEQAILLFRLSQNSLPFSQEAMNSVKEMIYLKNMENLELFGKTGFNDEQKIAWIVGFVYLKDENKYKAFALNLDIDKFEDLYKREKILEKYLDELVKKVKNDG"},"dna_sequence":{"accession":"NG_057510.1","fmin":"0","fmax":"774","strand":"+","sequence":"ATGAAAAAAATAACTTTATTTTTACTTTTCTTAAATTTAGTGTTTGGGCAAGATAAGATATTAAATAATTGGTTTAAAGAGTATAATACAAGCGGCACTTTTGTTTTTTATGATGGAAAAACTTGGGTGAGTAACGACTTTTCAAGGGCTATGGAGACTTTCTCTCCCGCTTCCACTTTTAAAATTTTTAATGCTCTAATTGCACTTGATAGTGGTGTGATAAAAACTAAAAAAGAAATTTTTTATCACTATAGAGGTGAAAAAGTATTTTTATCTTCTTGGGCGCAAGATATGAATTTAAGTTCAGCTATAAAATATTCTAATGTTCTTGCTTTTAAAGAAGTGGCAAGAAGAATTGGTATCAAAACTATGCAAGAATATTTAAACAAGCTTCATTATGGTAATGCTAAAATTTCCAAGATCGATACTTTTTGGCTTGACAACTCACTAAAAATAAGCGCTAAAGAACAAGCAATTTTGCTTTTTAGACTTTCACAAAATAGCTTACCTTTTTCTCAAGAAGCAATGAATAGTGTTAAGGAAATGATTTATTTAAAAAATATGGAAAATTTAGAGCTTTTTGGAAAAACAGGTTTTAATGATGAGCAAAAAATTGCTTGGATTGTAGGTTTTGTGTATTTAAAAGATGAAAATAAATATAAGGCTTTCGCGCTAAATTTAGATATTGATAAATTTGAAGATTTATATAAAAGAGAAAAAATTTTAGAAAAATATTTAGATGAACTTGTAAAAAAAGTTAAAAATGATGGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36772","NCBI_taxonomy_name":"Campylobacter jejuni","NCBI_taxonomy_id":"197"}}}},"ARO_accession":"3005832","ARO_id":"44294","ARO_name":"OXA-611","CARD_short_name":"OXA-611","ARO_description":"OXA-611 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46519":{"category_aro_accession":"3007730","category_aro_cvterm_id":"46519","category_aro_name":"OXA-61-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-61.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4938":{"model_id":"4938","model_name":"OXA-612","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7313":{"protein_sequence":{"accession":"WP_109545100.1","sequence":"MKKITLFLLFLNLVFGQDKILNNWFKEYNTSGTFVFYDGKTWGSNDFSRAMETFSPASTFKIFNALIALDSGVIKTKKEIFYHYRGEKVFLSSWAQDMNLSSAIKYSNVLAFKEVARRIGIKTMQEYLNKLHYGNAKISKIDTFWLDNSLKISAKEQAILLFRLSQNSLPFSQEAMNSVKEMIYLKNMENLELFGKTGFNDEQKIAWIVGFVYLKDENKYKAFALNLDIDKFEDLYKREKILEKYLDELVKKVKNDG"},"dna_sequence":{"accession":"NG_057534.1","fmin":"0","fmax":"774","strand":"+","sequence":"ATGAAAAAAATAACTTTATTTTTACTTTTCTTAAATTTAGTGTTTGGGCAAGATAAGATATTAAATAATTGGTTTAAAGAGTATAATACAAGCGGCACTTTTGTTTTTTATGATGGAAAAACTTGGGGGAGTAACGACTTTTCAAGGGCTATGGAGACTTTCTCTCCCGCTTCCACTTTTAAAATTTTTAATGCTCTAATTGCACTTGATAGTGGTGTGATAAAAACTAAAAAAGAAATTTTTTATCACTATAGAGGTGAAAAAGTATTTTTATCTTCTTGGGCGCAAGATATGAATTTAAGTTCAGCTATAAAATATTCTAATGTTCTTGCTTTTAAAGAAGTGGCAAGAAGAATTGGTATCAAAACTATGCAAGAATATTTAAACAAGCTTCATTATGGTAATGCTAAAATTTCCAAGATCGATACTTTTTGGCTTGACAACTCACTAAAAATAAGCGCTAAAGAACAAGCAATTTTGCTTTTTAGACTTTCACAAAATAGCTTACCTTTTTCTCAAGAAGCAATGAATAGTGTTAAGGAAATGATTTATTTAAAAAATATGGAAAATTTAGAGCTTTTTGGAAAAACAGGTTTTAATGATGAGCAAAAAATTGCTTGGATTGTAGGTTTTGTGTATTTAAAAGATGAAAATAAATATAAGGCTTTCGCGCTAAATTTAGATATTGATAAATTTGAAGATTTATATAAAAGAGAAAAAATTTTAGAAAAATATTTAGATGAACTTGTAAAAAAAGTTAAAAATGATGGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36772","NCBI_taxonomy_name":"Campylobacter jejuni","NCBI_taxonomy_id":"197"}}}},"ARO_accession":"3005833","ARO_id":"44295","ARO_name":"OXA-612","CARD_short_name":"OXA-612","ARO_description":"OXA-612 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46519":{"category_aro_accession":"3007730","category_aro_cvterm_id":"46519","category_aro_name":"OXA-61-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-61.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4939":{"model_id":"4939","model_name":"OXA-613","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7314":{"protein_sequence":{"accession":"WP_109545111.1","sequence":"MRNFIVFILFLNIAIGEDKILGNFFKDCNTSGTFIVFDGKNYASNDFQRAKQTFSPASTFKIFNALIALDNGVVRDTKEIFYHYKGEKVFLPSWKQDASLSSAIKRSQVPAFKELARKIGLKTMQEGLNKLSYGNTKISKIDTFWLDNSLQISAKNQADLLFKLSQNSLPFSKKSQEEVKEIILFKEDKIQKIYAKTGFNDNINLAWIVGFVKTENKILSFALNVDIKDIKNIKIREELLNKYLANFFQQ"},"dna_sequence":{"accession":"NG_057547.1","fmin":"0","fmax":"753","strand":"+","sequence":"ATGAGAAATTTTATTGTATTTATATTGTTTTTGAATATAGCCATTGGAGAGGATAAAATACTTGGTAATTTTTTTAAAGATTGTAATACAAGTGGGACTTTTATAGTCTTTGATGGAAAAAATTATGCAAGTAATGATTTTCAAAGAGCTAAACAAACCTTTTCTCCTGCTTCAACTTTTAAAATTTTTAATGCTTTAATTGCACTTGATAATGGTGTAGTTAGAGATACAAAGGAAATTTTCTATCATTATAAGGGTGAAAAAGTATTTTTGCCCTCTTGGAAACAAGATGCTAGTTTAAGCTCAGCCATAAAACGCTCTCAAGTGCCTGCTTTTAAAGAATTGGCAAGAAAAATAGGACTTAAAACCATGCAAGAAGGCTTAAATAAACTTTCTTATGGAAATACAAAAATTTCAAAAATCGATACCTTTTGGTTGGATAATTCTTTACAAATTTCTGCAAAAAATCAAGCTGATTTGCTTTTTAAACTTTCGCAAAATTCTTTACCTTTTTCCAAAAAAAGTCAAGAAGAAGTTAAAGAAATTATTCTTTTTAAGGAAGATAAAATCCAAAAAATTTATGCTAAAACAGGTTTTAATGATAATATCAATTTAGCTTGGATTGTTGGATTTGTAAAGACTGAAAACAAAATTTTATCTTTTGCTTTAAATGTTGATATAAAGGACATTAAAAATATTAAAATAAGGGAAGAATTATTAAATAAGTATTTAGCTAATTTTTTCCAACAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36772","NCBI_taxonomy_name":"Campylobacter jejuni","NCBI_taxonomy_id":"197"}}}},"ARO_accession":"3005834","ARO_id":"44296","ARO_name":"OXA-613","CARD_short_name":"OXA-613","ARO_description":"OXA-613 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46491":{"category_aro_accession":"3007702","category_aro_cvterm_id":"46491","category_aro_name":"OXA-184-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-184.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4940":{"model_id":"4940","model_name":"OXA-614","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7315":{"protein_sequence":{"accession":"WP_070233680.1","sequence":"MRNFIVFILFLNIAIGEDKILGNFFKDCNTSGTFIVFDGKNYASNDFQRAKQTFSPASTFKIFNALIALDNGVVRDTKEIFYHYKGEKVFLPSWKQDASLSSAIKRSQVPAFKELARKIGLKTMQEGLNKLSYGNTKISKIDTFWLDNSLQISAKNQADLLFKLSQNSLPFSKKSQEEVKEIILFKEDKIQKIYAKTGFNDNINLAWIVGFVKTENKILSFALNVDIKDIKNIKIREELLNKYLANFSNNNRIKSFY"},"dna_sequence":{"accession":"NG_057546.1","fmin":"0","fmax":"774","strand":"+","sequence":"ATGAGAAATTTTATTGTATTTATATTGTTTTTGAATATAGCCATTGGAGAGGATAAAATACTTGGTAATTTTTTTAAAGATTGTAATACAAGTGGGACTTTTATAGTCTTTGATGGAAAAAATTATGCAAGTAATGATTTTCAAAGAGCTAAACAAACCTTTTCTCCTGCTTCAACTTTTAAAATTTTTAATGCTTTAATTGCACTTGATAATGGTGTAGTTAGAGATACAAAGGAAATTTTCTATCATTATAAGGGTGAAAAAGTATTTTTGCCCTCTTGGAAACAAGATGCTAGTTTAAGCTCAGCCATAAAACGCTCTCAAGTGCCTGCTTTTAAAGAATTGGCAAGAAAAATAGGACTTAAAACCATGCAAGAAGGCTTAAATAAACTTTCTTATGGAAATACAAAAATTTCAAAAATCGATACCTTTTGGTTGGATAATTCTTTACAAATTTCTGCAAAAAATCAAGCTGATTTGCTTTTTAAACTTTCGCAAAATTCTTTACCTTTTTCCAAAAAAAGTCAAGAAGAAGTTAAAGAAATTATTCTTTTTAAGGAAGATAAAATCCAAAAAATTTATGCTAAAACAGGTTTTAATGATAATATCAATTTAGCTTGGATTGTTGGATTTGTAAAGACTGAAAACAAAATTTTATCTTTTGCTTTAAATGTTGATATAAAGGACATTAAAAATATTAAAATAAGGGAAGAATTATTAAATAAGTATTTAGCTAATTTTTCCAACAATAATAGGATTAAAAGCTTTTACTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37052","NCBI_taxonomy_name":"Campylobacter","NCBI_taxonomy_id":"194"}}}},"ARO_accession":"3005835","ARO_id":"44297","ARO_name":"OXA-614","CARD_short_name":"OXA-614","ARO_description":"OXA-614 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46491":{"category_aro_accession":"3007702","category_aro_cvterm_id":"46491","category_aro_name":"OXA-184-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-184.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4941":{"model_id":"4941","model_name":"OXA-615","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7316":{"protein_sequence":{"accession":"WP_109545115.1","sequence":"MRNFIVFILFLNIAIGEDKILGNFFKDCNTSGTFIVFDGKNYASNDFQRAKQAFSPASTFKIFNALIALDNGVVRDTKEIFYHYKGEKVFLPSWKQDASLSSAIKRSQVPAFKELARKIGLKTMQEGLNKLSYGNTKISKIDTFWLDNSLQISAKNQADLLFKLSQNSLPFSKKSQEEVKEIILFKEDKIQKIYAKTGFNDNINLAWIVGFVKTENKILSFALNVDIKDIKNIKIREELLNKYLANFSNNNRIKSFY"},"dna_sequence":{"accession":"NG_057552.1","fmin":"0","fmax":"774","strand":"+","sequence":"ATGAGAAATTTTATTGTATTTATATTGTTTTTGAATATAGCCATTGGAGAGGATAAAATACTTGGTAATTTTTTTAAAGATTGTAATACAAGTGGGACTTTTATAGTCTTTGATGGAAAAAATTATGCAAGTAATGATTTTCAAAGAGCTAAACAAGCCTTTTCTCCTGCTTCAACTTTTAAAATTTTTAATGCTTTAATTGCACTTGATAATGGTGTAGTTAGAGATACAAAGGAAATTTTCTATCATTATAAGGGTGAAAAAGTATTTTTGCCCTCTTGGAAACAAGATGCTAGTTTAAGCTCAGCCATAAAACGCTCTCAAGTGCCTGCTTTTAAAGAATTGGCAAGAAAAATAGGACTTAAAACCATGCAAGAAGGCTTAAATAAACTTTCTTATGGAAATACAAAAATTTCAAAAATCGATACCTTTTGGCTCGATAATTCTTTACAAATTTCTGCAAAAAATCAAGCTGATTTGCTTTTTAAACTTTCGCAAAATTCTTTACCTTTTTCCAAAAAAAGTCAAGAAGAAGTTAAAGAAATTATTCTTTTTAAGGAAGATAAAATCCAAAAAATTTATGCTAAAACAGGTTTTAATGATAATATCAATTTAGCTTGGATTGTTGGATTTGTAAAGACTGAAAACAAAATTTTATCTTTTGCTTTAAATGTTGATATAAAGGACATTAAAAATATTAAAATAAGGGAAGAATTATTAAATAAGTATTTAGCTAATTTTTCCAACAATAATAGGATTAAAAGCTTTTACTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36772","NCBI_taxonomy_name":"Campylobacter jejuni","NCBI_taxonomy_id":"197"}}}},"ARO_accession":"3005836","ARO_id":"44298","ARO_name":"OXA-615","CARD_short_name":"OXA-615","ARO_description":"OXA-615 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46491":{"category_aro_accession":"3007702","category_aro_cvterm_id":"46491","category_aro_name":"OXA-184-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-184.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4942":{"model_id":"4942","model_name":"OXA-616","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7317":{"protein_sequence":{"accession":"WP_109545110.1","sequence":"MRNFIVFIMFLNIAIGEDKILGNFFKDYNTSGTFIVFDGKNYASNDFKRAKKAFSPASTFKIFNALIALDNGVVRDTKEIFYHYKGEKVFLPSWKQDASLSSAIKRSQVPAFKELARKIGLKTMQESLNKLSYGNAKISKIDTFWLDNSLQISAKNQADLLFKLSQNSLPFSKKNQEEVKEIILFKEDKIQKIYVKTGFNDSINLAWIVGFVKTKNKILSFALNVDIKDIKNIKIREELLEKYLAIITN"},"dna_sequence":{"accession":"NG_057545.1","fmin":"0","fmax":"750","strand":"+","sequence":"ATGAGAAATTTTATTGTATTTATAATGTTTTTGAATATAGCCATTGGAGAGGATAAAATACTTGGTAATTTTTTTAAAGATTATAATACAAGTGGGACTTTTATAGTTTTTGATGGAAAAAATTATGCAAGTAATGATTTTAAAAGAGCTAAAAAAGCTTTTTCTCCTGCTTCAACTTTTAAAATTTTTAATGCTTTAATTGCACTTGATAATGGTGTAGTTAGAGATACAAAGGAAATTTTTTATCATTATAAGGGCGAAAAAGTATTTTTGCCCTCTTGGAAACAAGATGCTAGTTTAAGCTCAGCCATAAAACGTTCTCAAGTGCCTGCTTTTAAAGAATTGGCAAGAAAAATAGGACTTAAAACCATGCAAGAAAGCTTAAATAAACTTTCTTATGGAAATGCAAAAATTTCAAAAATCGATACCTTTTGGCTAGATAATTCTTTACAAATTTCTGCAAAAAATCAAGCTGATTTACTTTTTAAACTTTCGCAAAATTCTTTACCTTTTTCTAAAAAAAATCAAGAAGAAGTTAAAGAAATTATTCTTTTTAAGGAAGATAAAATCCAAAAAATTTATGTTAAAACAGGTTTTAATGATAGTATAAATTTAGCTTGGATTGTTGGATTTGTAAAGACTAAAAATAAAATTTTATCTTTTGCTTTAAATGTTGATATAAAGGACATTAAAAATATTAAAATAAGAGAAGAATTGCTAGAAAAATATCTAGCAATCATAACAAATTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36772","NCBI_taxonomy_name":"Campylobacter jejuni","NCBI_taxonomy_id":"197"}}}},"ARO_accession":"3005837","ARO_id":"44299","ARO_name":"OXA-616","CARD_short_name":"OXA-616","ARO_description":"OXA-616 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46491":{"category_aro_accession":"3007702","category_aro_cvterm_id":"46491","category_aro_name":"OXA-184-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-184.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4943":{"model_id":"4943","model_name":"OXA-617","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7318":{"protein_sequence":{"accession":"WP_109545114.1","sequence":"MRNFIVFILFLNIAIGEDKILGNFFKDYNTSGTFIVFDGKNYASNDFKRAKKAFSPASTFKIFNALIALDNGVVRDTKEIFYHYKGEKVFLPSWKQDASLSSAIKRSQVPAFKELARKIGLKTMQESLNKLSYGNAKISKIDTFWLDNSLQISAKNQADLLFKLSQNSLPFSKKIQEEVKEIILFKENKIQKIYAKTGFNDNINLAWIVGFVKTENKILSFALNVDIKDIKNIKIREELLNKYLANFFNNNRIKSFY"},"dna_sequence":{"accession":"NG_057550.1","fmin":"0","fmax":"774","strand":"+","sequence":"ATGAGAAATTTTATTGTATTTATATTGTTTTTGAATATAGCCATTGGAGAGGATAAAATACTTGGTAATTTTTTTAAAGATTATAATACAAGTGGGACTTTTATAGTTTTTGATGGAAAAAATTATGCAAGTAATGATTTTAAAAGAGCTAAAAAAGCTTTTTCTCCTGCTTCAACTTTTAAAATTTTTAATGCTTTAATTGCACTTGATAATGGTGTAGTTAGAGATACAAAGGAAATTTTTTATCATTATAAGGGCGAAAAAGTATTTTTGCCCTCTTGGAAACAAGATGCTAGTTTAAGCTCAGCCATAAAACGTTCTCAAGTGCCTGCTTTTAAAGAATTGGCAAGAAAAATAGGACTTAAAACTATGCAAGAAAGCTTAAATAAACTTTCTTATGGAAATGCAAAAATTTCAAAAATCGATACCTTTTGGCTAGATAATTCTTTACAAATTTCTGCAAAAAATCAAGCTGATTTACTTTTTAAACTTTCGCAAAATTCTTTACCTTTTTCTAAAAAAATTCAAGAAGAAGTTAAAGAAATTATTCTTTTTAAGGAAAATAAAATCCAAAAAATTTATGCTAAAACAGGTTTTAATGATAATATCAATTTAGCTTGGATTGTTGGATTTGTAAAGACTGAAAACAAAATTTTATCTTTTGCTTTAAATGTTGATATAAAGGACATTAAAAATATTAAAATAAGGGAAGAATTATTAAATAAGTATTTAGCTAATTTTTTCAACAATAATAGGATTAAAAGCTTTTACTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36772","NCBI_taxonomy_name":"Campylobacter jejuni","NCBI_taxonomy_id":"197"}}}},"ARO_accession":"3005838","ARO_id":"44300","ARO_name":"OXA-617","CARD_short_name":"OXA-617","ARO_description":"OXA-617 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46491":{"category_aro_accession":"3007702","category_aro_cvterm_id":"46491","category_aro_name":"OXA-184-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-184.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4944":{"model_id":"4944","model_name":"OXA-618","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7319":{"protein_sequence":{"accession":"WP_109545113.1","sequence":"MRNFIVFILFLNIAIGEDKILGNFFKDYNTSGTFMVFDGKNYASNDFKRAKKAFSPASTFKIFNALIALDNGVVRDTKEIFYHYKGEKVFLPSWKQDASLSSAIKRSQVPAFKELARKIGLKTMQESLNKLSYGNAKISKIDTFWLDNSLQISAKNQVDLLFKLSQNSLPFSKKIQEEVKEIILFKEDKIQKIYAKTGFNDNINLAWIVGFVKTENKILSFALNVDIKDIKNIKIREELLNKYLANFFNNNRIKSFY"},"dna_sequence":{"accession":"NG_057549.1","fmin":"0","fmax":"774","strand":"+","sequence":"ATGAGAAATTTTATTGTATTTATATTGTTTTTGAATATAGCCATTGGAGAGGATAAAATACTTGGTAATTTTTTTAAAGATTATAATACAAGCGGGACTTTTATGGTTTTTGATGGAAAAAATTATGCAAGTAATGATTTTAAAAGAGCTAAAAAAGCTTTTTCTCCTGCTTCAACTTTTAAAATTTTTAATGCTTTAATTGCACTTGATAATGGTGTAGTTAGAGATACAAAGGAAATTTTTTATCATTATAAGGGCGAAAAAGTATTTTTGCCCTCTTGGAAACAAGATGCTAGTTTAAGCTCAGCCATAAAACGTTCTCAAGTGCCTGCTTTTAAAGAATTGGCAAGAAAAATAGGACTTAAAACCATGCAAGAAAGCTTAAATAAACTTTCTTATGGAAATGCAAAAATTTCAAAAATCGATACCTTTTGGCTAGATAATTCTTTACAAATTTCTGCAAAAAATCAAGTTGATTTACTTTTTAAACTTTCGCAAAATTCTTTACCTTTTTCTAAAAAAATTCAAGAAGAAGTTAAAGAAATTATTCTTTTTAAGGAAGATAAAATCCAAAAAATTTATGCTAAAACAGGTTTTAATGATAATATCAATTTAGCTTGGATTGTTGGATTTGTAAAGACTGAAAACAAAATTTTATCTTTTGCTTTAAATGTTGATATAAAGGACATTAAAAATATTAAAATAAGGGAAGAATTATTAAATAAGTATTTAGCTAATTTTTTCAACAATAATAGGATTAAAAGCTTTTACTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36772","NCBI_taxonomy_name":"Campylobacter jejuni","NCBI_taxonomy_id":"197"}}}},"ARO_accession":"3005839","ARO_id":"44301","ARO_name":"OXA-618","CARD_short_name":"OXA-618","ARO_description":"OXA-618 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46491":{"category_aro_accession":"3007702","category_aro_cvterm_id":"46491","category_aro_name":"OXA-184-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-184.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4945":{"model_id":"4945","model_name":"OXA-619","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7320":{"protein_sequence":{"accession":"WP_109545075.1","sequence":"MRNFIVFILFLNIAIGEDKILGNFFKDCNTSGTFIVFDGKNYASNDFKRAKQAFSPASTFKIFNALIALDNGVVRDTKEIFYHYKGEKVFLPSWKQDASLSSAIKRSQVPAFKELARKIGLKTMQESLNKLSYGNAKISKIDTFWLDNSLQISAKNQADLLFKLSQNSLPFSKKIQEEVKEIILFKEDKIQKIYAKTGFNDNINLAWIVGFVKTENKILSFALNVDIKDIKNIKIREELLNKYLANFSNNNRIKSFY"},"dna_sequence":{"accession":"NG_057491.1","fmin":"0","fmax":"774","strand":"+","sequence":"ATGAGAAATTTTATTGTATTTATATTGTTTTTGAATATAGCCATTGGAGAGGATAAAATACTTGGTAATTTTTTTAAAGATTGTAATACAAGTGGGACTTTTATAGTCTTTGATGGAAAAAATTATGCAAGTAATGATTTTAAAAGAGCTAAACAAGCCTTTTCTCCTGCTTCAACTTTTAAAATTTTTAATGCTTTAATTGCACTTGATAATGGTGTAGTTAGAGATACAAAGGAAATTTTTTATCATTATAAGGGCGAAAAAGTATTTTTGCCCTCTTGGAAACAAGATGCTAGTTTAAGCTCAGCTATAAAACGCTCTCAAGTGCCTGCTTTTAAAGAATTGGCAAGAAAAATAGGACTTAAAACCATGCAAGAAAGCTTAAATAAACTTTCTTATGGAAATGCAAAAATTTCAAAAATCGATACCTTTTGGCTCGATAATTCTTTACAAATTTCTGCAAAAAATCAAGCTGATTTACTTTTTAAACTTTCGCAAAATTCTTTACCTTTTTCTAAAAAAATTCAAGAAGAAGTTAAAGAAATTATTCTTTTTAAGGAAGATAAAATCCAAAAAATTTATGCTAAAACAGGTTTTAATGATAATATCAATTTAGCTTGGATTGTTGGATTTGTAAAGACTGAAAACAAAATTTTATCTTTTGCCTTAAATGTTGATATAAAGGACATTAAAAATATTAAAATAAGGGAAGAATTATTAAATAAGTATTTAGCTAATTTTTCCAACAATAATAGGATTAAAAGCTTTTACTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36772","NCBI_taxonomy_name":"Campylobacter jejuni","NCBI_taxonomy_id":"197"}}}},"ARO_accession":"3005840","ARO_id":"44302","ARO_name":"OXA-619","CARD_short_name":"OXA-619","ARO_description":"OXA-619 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46491":{"category_aro_accession":"3007702","category_aro_cvterm_id":"46491","category_aro_name":"OXA-184-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-184.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4946":{"model_id":"4946","model_name":"OXA-620","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7321":{"protein_sequence":{"accession":"WP_109545076.1","sequence":"MRNFIVFILFLNIAIGEDKILGNFFKDCNTSGTFIVFDGKNYASNDFKRAKQAFSPASTFKIFNALIALDNGVVRDTKEIFYHYKGEKVFLPSWKQDASLSSAIKRSQVPAFKELARKIGLKTMQESLNKLSYGNAKISKIDTFWLDNSLQISAKNQADLLFKLSQNSLPFSKKSQEEVKEIILFKEDKIQKIYAKTGFNDNINLAWIVGFVKTENKILSFALNVDIKDIKNIKIREELLNKYLANFSNNNRIKSFY"},"dna_sequence":{"accession":"NG_057492.1","fmin":"0","fmax":"774","strand":"+","sequence":"ATGAGAAATTTTATTGTATTTATATTGTTTTTGAATATAGCCATTGGAGAGGATAAAATACTTGGTAATTTTTTTAAAGATTGTAATACAAGTGGGACTTTTATAGTCTTTGATGGAAAAAATTATGCAAGTAATGATTTTAAAAGAGCTAAACAAGCCTTTTCTCCTGCTTCAACTTTTAAAATTTTTAATGCTTTAATTGCACTTGATAATGGTGTAGTTAGAGATACAAAGGAAATTTTTTATCATTATAAGGGCGAAAAAGTATTTTTGCCCTCTTGGAAACAAGATGCTAGTTTAAGCTCAGCTATAAAACGCTCTCAAGTGCCTGCTTTTAAAGAATTGGCAAGAAAAATAGGACTTAAAACCATGCAAGAAAGCTTAAATAAACTTTCTTATGGAAATGCAAAAATTTCAAAAATCGATACCTTTTGGCTCGATAATTCTTTACAAATTTCTGCAAAAAATCAAGCTGATTTGCTTTTTAAACTTTCGCAAAATTCTTTACCTTTTTCCAAAAAAAGTCAAGAAGAAGTTAAAGAAATTATTCTTTTTAAGGAAGATAAAATCCAAAAAATTTATGCTAAAACAGGTTTTAATGATAATATCAATTTAGCTTGGATTGTTGGATTTGTAAAGACTGAAAACAAAATTTTATCTTTTGCTTTAAATGTTGATATAAAGGACATTAAAAATATTAAAATAAGGGAAGAATTATTAAATAAGTATTTAGCTAATTTTTCCAACAATAATAGGATTAAAAGCTTTTACTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36772","NCBI_taxonomy_name":"Campylobacter jejuni","NCBI_taxonomy_id":"197"}}}},"ARO_accession":"3005841","ARO_id":"44303","ARO_name":"OXA-620","CARD_short_name":"OXA-620","ARO_description":"OXA-620 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46491":{"category_aro_accession":"3007702","category_aro_cvterm_id":"46491","category_aro_name":"OXA-184-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-184.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4947":{"model_id":"4947","model_name":"OXA-621","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7322":{"protein_sequence":{"accession":"WP_109545116.1","sequence":"MRDFIVFIWFLNIAIGEDKILGNFFKDYNTSGTFIVFDGKNYASNDFQRAKQAFSPASTFKIFNALIALDNGVVRDTKEIFYHYKGEKVFLPSWKQDASLSSAIKRSQVPVFKELARKIGLKTMQESLNKLSYGNAKISKIDTFWLDNSLQISAKNQADLLFKLSQNSLPFSKKNQEEVKEIILFKEDKIQKIYAKTGFNDNINLAWIVGFVKTENKILSFALNVDIKDIKNIKIREELLNKYLANFSNNNRIKSFY"},"dna_sequence":{"accession":"NG_057553.1","fmin":"0","fmax":"774","strand":"+","sequence":"ATGAGAGATTTTATTGTATTTATATGGTTTTTGAATATAGCCATTGGAGAGGATAAAATACTTGGTAATTTTTTTAAAGATTATAATACAAGTGGGACTTTTATAGTCTTTGATGGAAAAAATTATGCAAGTAATGATTTTCAAAGAGCTAAACAAGCCTTTTCTCCTGCTTCAACTTTTAAAATTTTTAATGCTTTAATTGCACTTGATAATGGTGTAGTTAGAGATACAAAGGAAATTTTTTATCATTATAAGGGCGAAAAAGTATTTTTGCCCTCTTGGAAACAAGATGCTAGTTTAAGCTCAGCTATAAAACGCTCTCAAGTACCTGTTTTTAAAGAATTGGCAAGAAAAATAGGACTTAAAACCATGCAAGAAAGCTTAAATAAACTTTCTTATGGAAATGCAAAAATTTCAAAAATCGATACTTTTTGGCTAGATAATTCTTTACAAATTTCTGCAAAAAATCAAGCTGATTTACTTTTTAAACTTTCGCAAAATTCTTTACCTTTTTCTAAAAAAAATCAAGAAGAAGTTAAAGAAATTATTCTTTTTAAGGAAGATAAAATCCAAAAAATTTATGCTAAAACAGGTTTTAATGATAATATCAATTTAGCTTGGATTGTTGGATTTGTAAAGACTGAAAACAAAATTTTATCTTTTGCTTTAAATGTTGATATAAAGGACATTAAAAATATTAAAATAAGGGAAGAATTATTAAATAAGTATTTAGCTAATTTTTCCAACAATAATAGGATTAAAAGCTTTTACTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36772","NCBI_taxonomy_name":"Campylobacter jejuni","NCBI_taxonomy_id":"197"}}}},"ARO_accession":"3005842","ARO_id":"44304","ARO_name":"OXA-621","CARD_short_name":"OXA-621","ARO_description":"OXA-621 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46491":{"category_aro_accession":"3007702","category_aro_cvterm_id":"46491","category_aro_name":"OXA-184-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-184.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4948":{"model_id":"4948","model_name":"OXA-622","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7323":{"protein_sequence":{"accession":"WP_109545112.1","sequence":"MRNFIVFILFLNIAIGEDKILGNFFKDYNTSGTFIVFDGKNYASNDFKRAKKAFSPASTFKIFNALIALDNGVVRDTKEIFYHYKGEKVFLPSWKQDASLSSAIKCSQVPAFKELARNIGLKTMQESLNKLSYGNTKISKIDTFWLDNSLQISAKNQADLLFKLSQNSLPFSKKNQEEVKEIILFKEDKIQKIYAKTGFNDNINLAWIVGFVKIKNKILSFALNVDIKDIKNIKIREELLNKYLANFFNNNRIKSFY"},"dna_sequence":{"accession":"NG_057548.1","fmin":"0","fmax":"774","strand":"+","sequence":"ATGAGAAATTTTATTGTATTTATATTGTTTTTGAATATAGCCATTGGAGAGGATAAAATACTTGGTAATTTTTTTAAAGATTATAATACAAGTGGGACTTTTATAGTCTTTGATGGAAAAAATTATGCAAGTAATGATTTTAAAAGAGCTAAAAAAGCTTTTTCTCCTGCTTCAACTTTTAAAATTTTTAATGCTTTAATTGCACTTGATAATGGTGTAGTTAGAGACACAAAGGAAATTTTTTATCATTATAAGGGCGAAAAAGTATTTTTGCCCTCTTGGAAACAAGATGCTAGTTTAAGCTCAGCCATAAAATGCTCTCAAGTGCCTGCTTTTAAAGAATTGGCAAGAAACATAGGACTTAAAACTATGCAAGAAAGCTTAAATAAACTTTCTTATGGAAATACAAAAATTTCAAAAATCGATACCTTTTGGCTAGATAATTCTTTACAAATTTCTGCAAAAAATCAAGCTGATTTACTTTTTAAACTTTCGCAAAATTCTTTACCTTTTTCTAAAAAAAATCAAGAAGAAGTTAAAGAAATTATTCTTTTTAAGGAAGATAAAATCCAAAAAATTTATGCTAAAACAGGTTTTAATGATAATATCAATTTAGCTTGGATTGTTGGATTTGTAAAGATTAAAAACAAAATTTTATCTTTTGCTTTAAATGTTGATATAAAGGACATTAAAAATATTAAAATAAGGGAAGAATTATTAAATAAGTATTTAGCTAATTTTTTCAACAATAATAGGATTAAAAGCTTTTACTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36772","NCBI_taxonomy_name":"Campylobacter jejuni","NCBI_taxonomy_id":"197"}}}},"ARO_accession":"3005843","ARO_id":"44305","ARO_name":"OXA-622","CARD_short_name":"OXA-622","ARO_description":"OXA-622 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46491":{"category_aro_accession":"3007702","category_aro_cvterm_id":"46491","category_aro_name":"OXA-184-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-184.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4949":{"model_id":"4949","model_name":"OXA-623","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7324":{"protein_sequence":{"accession":"WP_002936877.1","sequence":"MKKIILFLWILNFAFGQDKILEDFFKDYNTSGTFIVFDGKNYASNDFQRAKQTFSPASTFKIFNALIALDNGVIKDTKEIFYHYKGEKVFLPSWKQDASLSSAIKRSQVPAFKELARKIGLKTMQESLNKLSYGNAKISKIDTFWLDNSLQISAKNQADLLFKLSQNSLPFSNKSQEEVKKLLLFKENKIQKIYAKTGFNDNINLAWIVGFVKTKNKILSFALNVDIKDIKNIKIREKLLEKYIYSLN"},"dna_sequence":{"accession":"NG_057493.1","fmin":"0","fmax":"747","strand":"+","sequence":"ATGAAAAAAATCATCTTGTTTTTATGGATTTTAAATTTTGCCTTTGGACAAGATAAAATATTAGAAGATTTTTTTAAAGATTATAATACAAGTGGGACTTTTATAGTCTTTGATGGAAAAAATTATGCAAGTAATGATTTTCAAAGAGCAAAACAAACCTTTTCTCCTGCTTCAACTTTTAAAATTTTTAATGCTTTAATTGCGCTTGATAATGGTGTAATTAAAGATACAAAGGAAATTTTTTATCATTATAAGGGCGAAAAAGTATTTTTGCCCTCTTGGAAACAAGATGCTAGTTTAAGCTCAGCCATAAAACGCTCTCAAGTGCCTGCTTTTAAAGAATTGGCAAGAAAAATAGGACTTAAAACCATGCAAGAAAGCTTAAATAAACTTTCTTATGGAAATGCAAAAATTTCAAAAATCGATACTTTTTGGCTGGATAATTCTTTGCAAATTTCTGCAAAAAATCAAGCTGATTTACTTTTTAAACTTTCACAAAATTCTTTACCCTTTTCCAATAAAAGTCAAGAAGAAGTCAAAAAACTTCTTCTTTTTAAAGAAAATAAAATACAAAAAATTTATGCTAAAACAGGTTTTAATGATAATATAAATTTAGCTTGGATTGTTGGATTCGTAAAGACTAAAAACAAAATTTTATCTTTTGCTTTAAATGTTGATATAAAGGACATTAAAAATATTAAAATAAGAGAAAAATTGCTAGAAAAATATATTTATTCTTTAAATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37052","NCBI_taxonomy_name":"Campylobacter","NCBI_taxonomy_id":"194"}}}},"ARO_accession":"3005844","ARO_id":"44306","ARO_name":"OXA-623","CARD_short_name":"OXA-623","ARO_description":"OXA-623 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46491":{"category_aro_accession":"3007702","category_aro_cvterm_id":"46491","category_aro_name":"OXA-184-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-184.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4950":{"model_id":"4950","model_name":"OXA-624","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7325":{"protein_sequence":{"accession":"WP_088303859.1","sequence":"MRNFIVFILFLNIAIGEDKILGNFFKDYNTSGTFIVFDGKNYASNDFKRAKKAFSPASTFKIFNALIALDNGVVRDTKEIFYHYKGEKVFLPSWKQDASLSSAIKCSQVPAFKELARNIGLKTMQESLNKLSYGNTKISKIDTFWLDNSLQISAKNQADLLFKLSQNSLPFSKKNQEEVKKIILFKEDKIQKIYAKTGFNDNINLAWIVGFVKIKNKILSFALNVDIKDIKNIKIREELLNKYLANFFNNNRIKSFY"},"dna_sequence":{"accession":"NG_057551.1","fmin":"0","fmax":"774","strand":"+","sequence":"ATGAGAAATTTTATTGTATTTATATTGTTTTTGAATATAGCCATTGGAGAGGATAAAATACTTGGTAATTTTTTTAAAGATTATAATACAAGTGGGACTTTTATAGTCTTTGATGGAAAAAATTATGCAAGTAATGATTTTAAAAGAGCTAAAAAAGCTTTTTCTCCTGCTTCAACTTTTAAAATTTTTAATGCTTTAATTGCACTTGATAATGGTGTAGTTAGAGACACAAAGGAAATTTTTTATCATTATAAGGGCGAAAAAGTATTTTTGCCCTCTTGGAAACAAGATGCTAGTTTAAGCTCAGCCATAAAATGCTCTCAAGTGCCTGCTTTTAAAGAATTGGCAAGAAACATAGGACTTAAAACTATGCAAGAAAGCTTAAATAAACTTTCTTATGGAAATACAAAAATTTCAAAAATCGATACCTTTTGGCTAGATAATTCTTTACAAATTTCTGCAAAAAATCAAGCTGATTTACTTTTTAAACTTTCGCAAAATTCTTTACCTTTTTCTAAAAAAAATCAAGAAGAAGTTAAAAAAATTATTCTTTTTAAGGAAGATAAAATCCAAAAAATTTATGCTAAAACAGGTTTTAATGATAATATCAATTTAGCTTGGATTGTTGGATTTGTAAAGATTAAAAACAAAATTTTATCTTTTGCTTTAAATGTTGATATAAAGGACATTAAAAATATTAAAATAAGGGAAGAATTATTAAATAAGTATTTAGCTAATTTTTTCAACAATAATAGGATTAAAAGCTTTTACTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36772","NCBI_taxonomy_name":"Campylobacter jejuni","NCBI_taxonomy_id":"197"}}}},"ARO_accession":"3005845","ARO_id":"44307","ARO_name":"OXA-624","CARD_short_name":"OXA-624","ARO_description":"OXA-624 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46491":{"category_aro_accession":"3007702","category_aro_cvterm_id":"46491","category_aro_name":"OXA-184-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-184.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4951":{"model_id":"4951","model_name":"OXA-625","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7326":{"protein_sequence":{"accession":"WP_052794776.1","sequence":"MKKILLLFSLFYSFALANDKLKDFFKDYNTSGVFITFDGKHYASNDFKRAKEPFSPASTFKIFNALIALDNGVVKDTKEIFYHYKGEKVFLPSWKQDASLSSAIKRSQVPAFKELARKIGLKTMQESLNKLSYGNAKISKIDTFWLDNSLQISAKNQADLLFKLSQNSLPFSKKSQEEVKKIILFKEDKIQKIYAKTGFNDGINLAWIVGFIESKNKILSFALNVDIKNIKNLKIREELLEKYIYSLN"},"dna_sequence":{"accession":"NG_057505.1","fmin":"0","fmax":"747","strand":"+","sequence":"TTGAAAAAAATACTTTTACTTTTTAGTCTTTTTTACTCTTTTGCTTTGGCAAATGATAAATTAAAAGATTTTTTTAAAGACTACAATACAAGCGGAGTTTTTATAACTTTTGATGGAAAACATTATGCAAGTAATGATTTTAAAAGAGCTAAAGAACCTTTTTCTCCTGCTTCGACTTTTAAAATTTTTAATGCTTTAATTGCGCTTGATAACGGTGTAGTTAAAGATACAAAGGAAATTTTTTATCATTATAAGGGTGAAAAAGTATTTTTGCCTTCTTGGAAACAAGATGCTAGTTTAAGCTCAGCCATAAAACGCTCTCAAGTGCCTGCTTTTAAAGAATTGGCAAGAAAAATAGGACTTAAAACCATGCAAGAAAGCTTAAATAAACTTTCCTATGGAAATGCGAAAATTTCAAAAATCGATACCTTTTGGTTGGATAATTCTTTACAAATTTCTGCAAAAAATCAAGCTGATTTGCTTTTTAAACTTTCACAAAATTCTTTACCTTTTTCCAAGAAAAGTCAAGAAGAAGTTAAAAAAATTATTCTTTTTAAAGAAGATAAAATCCAAAAAATTTATGCTAAAACAGGTTTTAATGATGGTATAAATTTGGCTTGGATTGTCGGATTTATAGAGAGTAAAAACAAAATTTTATCTTTTGCCTTAAATGTTGATATAAAGAATATTAAAAATCTTAAAATAAGAGAAGAATTGCTAGAAAAATATATTTATTCTTTAAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36772","NCBI_taxonomy_name":"Campylobacter jejuni","NCBI_taxonomy_id":"197"}}}},"ARO_accession":"3005846","ARO_id":"44308","ARO_name":"OXA-625","CARD_short_name":"OXA-625","ARO_description":"OXA-625 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46491":{"category_aro_accession":"3007702","category_aro_cvterm_id":"46491","category_aro_name":"OXA-184-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-184.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4952":{"model_id":"4952","model_name":"OXA-626","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7327":{"protein_sequence":{"accession":"WP_109545080.1","sequence":"MKKILLLFSLFYSFALANDKLKDFFKDYNTSGVFITFDGKHYASNNFKRAKEPFSPASTFKIFNALIALDNGIVKDTKEIFYHYKGEKVFLPSWKQDASLSSAIKRSQVPAFKELARKIGLKTMQESLNKLSYGNAKISKIDTFWLDNSLQISAKNQADLLFKLSQNSLPFSKKSQEEVKKIILFKEDKIQKIYAKTGFNDGINLAWIVGFIESKNKILSFALNVDIKNIKNLKIREELLEKYIYSLN"},"dna_sequence":{"accession":"NG_057497.1","fmin":"0","fmax":"747","strand":"+","sequence":"TTGAAAAAAATACTTTTACTTTTTAGTCTTTTTTACTCTTTTGCTTTGGCAAATGATAAATTAAAAGATTTTTTTAAAGACTACAATACAAGCGGAGTTTTTATAACTTTTGATGGAAAACATTATGCAAGTAATAATTTTAAAAGAGCTAAAGAACCTTTTTCTCCTGCTTCGACTTTTAAAATTTTTAATGCTTTAATTGCGCTTGATAATGGTATAGTTAAAGATACAAAGGAAATTTTTTATCATTATAAGGGTGAAAAAGTATTTTTGCCCTCTTGGAAACAAGATGCTAGTTTAAGCTCAGCCATAAAACGCTCTCAAGTGCCTGCTTTTAAAGAATTGGCAAGAAAAATAGGACTTAAAACCATGCAAGAAAGCTTAAATAAACTTTCCTATGGAAATGCAAAAATTTCAAAAATCGATACCTTTTGGTTGGATAATTCTTTACAAATTTCTGCAAAAAATCAAGCTGATTTGCTTTTTAAACTTTCACAAAATTCTTTACCTTTTTCCAAGAAAAGTCAAGAAGAAGTTAAAAAAATTATTCTTTTTAAAGAAGATAAAATCCAAAAAATTTATGCTAAAACAGGTTTTAATGATGGTATAAATTTGGCTTGGATTGTCGGATTTATAGAGAGTAAAAACAAAATTTTATCTTTTGCCTTAAATGTTGATATAAAGAATATTAAAAATCTTAAAATAAGAGAAGAATTGCTAGAAAAATATATTTATTCTTTAAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36772","NCBI_taxonomy_name":"Campylobacter jejuni","NCBI_taxonomy_id":"197"}}}},"ARO_accession":"3005847","ARO_id":"44309","ARO_name":"OXA-626","CARD_short_name":"OXA-626","ARO_description":"OXA-626 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46491":{"category_aro_accession":"3007702","category_aro_cvterm_id":"46491","category_aro_name":"OXA-184-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-184.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4953":{"model_id":"4953","model_name":"OXA-627","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7328":{"protein_sequence":{"accession":"WP_109545081.1","sequence":"MKKILLLFSLFYSFALANDKLKDFFKDYNTSGVFITFDGKHYASNNFKRAKEPFSPASTFKIFNALIALDNGVVKDTKEIFYHYKGEKVFLPSWKQDAGLSSAIKRSQVPAFKELARKIGLKTMQESLNKLSYGNTKISKIDTFWLDNSLQISAKNQADLLFKLSQNSLPFSKKSQEEVKKIILFKEDKIQKIYAKTGFNDGINLAWIVGFIESKNKILSFALNVDIKNIKNLKIREELLEKYIYSLN"},"dna_sequence":{"accession":"NG_057498.1","fmin":"0","fmax":"747","strand":"+","sequence":"TTGAAAAAAATACTTTTACTTTTTAGTCTTTTTTACTCTTTTGCTTTGGCAAATGATAAATTAAAAGATTTTTTTAAAGACTACAATACAAGCGGAGTTTTTATAACTTTTGATGGAAAACATTATGCAAGTAATAATTTTAAAAGAGCTAAAGAACCTTTTTCTCCTGCTTCGACTTTTAAAATTTTTAATGCTTTAATTGCGCTTGATAATGGTGTAGTTAAAGATACAAAGGAAATTTTTTATCATTATAAGGGTGAAAAAGTATTTTTGCCCTCTTGGAAACAAGATGCTGGTTTAAGCTCAGCCATAAAACGCTCTCAAGTGCCTGCTTTTAAAGAATTGGCAAGAAAAATAGGACTTAAAACCATGCAAGAAAGCTTAAATAAACTTTCCTATGGAAATACAAAAATTTCAAAAATCGATACCTTTTGGTTGGATAATTCTTTACAAATTTCTGCAAAAAATCAAGCTGATTTGCTTTTTAAACTTTCACAAAATTCTTTACCTTTTTCCAAGAAAAGTCAAGAAGAAGTTAAAAAAATTATTCTTTTTAAAGAAGATAAAATCCAAAAAATTTATGCTAAAACAGGTTTTAATGATGGTATAAATTTGGCTTGGATTGTTGGATTTATAGAGAGTAAAAACAAAATTTTATCTTTTGCCTTAAATGTTGATATAAAGAACATTAAAAATCTTAAAATAAGAGAAGAATTGCTAGAAAAATATATTTATTCTTTAAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37052","NCBI_taxonomy_name":"Campylobacter","NCBI_taxonomy_id":"194"}}}},"ARO_accession":"3005848","ARO_id":"44310","ARO_name":"OXA-627","CARD_short_name":"OXA-627","ARO_description":"OXA-627 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46491":{"category_aro_accession":"3007702","category_aro_cvterm_id":"46491","category_aro_name":"OXA-184-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-184.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4954":{"model_id":"4954","model_name":"OXA-628","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7329":{"protein_sequence":{"accession":"WP_109545083.1","sequence":"MKKILLLFSLFYSFALANDKLKDFFKDYNTSGVFITFDGKHYASNNFKRAKEPFSPASTFKIFNALIALDNGVVKDTKEIFYHYKGEKVFLPSWKQDASLSSAIKRSQVPAFKELARKIGLKTMQESLNKLSCGNTKISKIDTFWLDNSLQISAKNQADLLFKLSQNSLPFSKKSQEEVKKIILFKEDKIQKIYAKTGFNDGINLAWIVGFIESKNKILSFALNVDIKNIKNLKIREELLEKYIYSLN"},"dna_sequence":{"accession":"NG_057500.1","fmin":"0","fmax":"747","strand":"+","sequence":"TTGAAAAAAATACTTTTACTTTTTAGTCTTTTTTACTCTTTTGCTTTGGCAAATGATAAATTAAAAGATTTTTTTAAAGACTACAATACAAGCGGAGTTTTTATAACTTTTGATGGAAAACATTATGCAAGTAATAATTTTAAAAGAGCTAAAGAACCTTTTTCTCCTGCTTCGACTTTTAAAATTTTTAATGCTTTAATTGCGCTTGATAATGGTGTAGTTAAAGATACAAAGGAAATTTTTTATCATTATAAGGGTGAAAAAGTATTTTTGCCCTCTTGGAAACAAGATGCTAGTTTAAGCTCAGCCATAAAACGCTCTCAAGTGCCTGCTTTTAAAGAATTGGCAAGAAAAATAGGACTTAAAACCATGCAAGAAAGCTTAAATAAACTTTCCTGTGGAAATACAAAAATTTCAAAAATCGATACCTTTTGGTTGGATAATTCTTTACAAATTTCTGCAAAAAATCAAGCTGATTTGCTTTTTAAACTTTCACAAAATTCTTTACCTTTTTCCAAGAAAAGTCAAGAAGAAGTTAAAAAAATTATTCTTTTTAAAGAAGATAAAATCCAAAAAATTTATGCTAAAACAGGTTTTAATGATGGTATAAATTTGGCTTGGATTGTTGGATTTATAGAGAGTAAAAACAAAATTTTATCTTTTGCCTTAAATGTTGATATAAAGAACATTAAAAATCTTAAAATAAGAGAAGAATTGCTAGAAAAATATATTTATTCTTTAAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36772","NCBI_taxonomy_name":"Campylobacter jejuni","NCBI_taxonomy_id":"197"}}}},"ARO_accession":"3005849","ARO_id":"44311","ARO_name":"OXA-628","CARD_short_name":"OXA-628","ARO_description":"OXA-628 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46491":{"category_aro_accession":"3007702","category_aro_cvterm_id":"46491","category_aro_name":"OXA-184-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-184.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4955":{"model_id":"4955","model_name":"OXA-629","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7330":{"protein_sequence":{"accession":"WP_057036510.1","sequence":"MKKILLLFSLFYSFALANDKLKDFFKDYNTSGVFITFDGKHYASNNFKRAKEPFSPASTFKIFNALIALDNGVVKDTKEIFYHYKGEKVFLPSWKQDASLSSAIKRSQVPAFKELARKIGLKTMQESLNKLSYGNTKISKIDTFWLDNSLQISAKNQADLLFKLSQNSLPFSKKSQEEVKKIILFKEDKIQKIYAKTGFNDGINLAWIVGFIESKTKFLSFALNVDIKNIKNLKIREELLEKYIYSLN"},"dna_sequence":{"accession":"NG_057501.1","fmin":"0","fmax":"747","strand":"+","sequence":"TTGAAAAAAATACTTTTACTTTTTAGTCTTTTTTACTCTTTTGCTTTGGCAAATGATAAATTAAAAGATTTTTTTAAAGACTACAATACAAGCGGAGTTTTTATAACTTTTGATGGAAAACATTATGCAAGTAATAATTTTAAAAGAGCTAAAGAACCTTTTTCTCCTGCTTCGACTTTTAAAATTTTTAATGCTTTAATTGCGCTTGATAATGGTGTAGTTAAAGATACAAAGGAAATTTTTTATCATTATAAGGGTGAAAAAGTATTTTTGCCCTCTTGGAAACAAGATGCTAGTTTAAGCTCAGCCATAAAACGCTCTCAAGTGCCTGCTTTTAAAGAATTGGCAAGAAAAATAGGACTTAAAACCATGCAAGAAAGCTTAAATAAACTTTCCTATGGAAATACAAAAATTTCAAAAATCGATACCTTTTGGTTGGATAATTCTTTACAAATTTCTGCAAAAAATCAAGCTGATTTGCTTTTTAAACTTTCACAAAATTCTTTACCTTTTTCCAAGAAAAGTCAAGAAGAAGTTAAAAAAATTATTCTTTTTAAAGAAGATAAAATCCAAAAAATTTATGCTAAAACAGGTTTTAATGATGGTATAAATTTGGCTTGGATTGTTGGATTTATAGAGAGTAAAACAAAATTTTTATCTTTTGCCTTAAATGTTGATATAAAGAACATTAAAAATCTTAAAATAAGAGAAGAATTGCTAGAAAAATATATTTATTCTTTAAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36772","NCBI_taxonomy_name":"Campylobacter jejuni","NCBI_taxonomy_id":"197"}}}},"ARO_accession":"3005850","ARO_id":"44312","ARO_name":"OXA-629","CARD_short_name":"OXA-629","ARO_description":"OXA-629 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46491":{"category_aro_accession":"3007702","category_aro_cvterm_id":"46491","category_aro_name":"OXA-184-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-184.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4956":{"model_id":"4956","model_name":"OXA-630","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7331":{"protein_sequence":{"accession":"WP_109545085.1","sequence":"MKKILLLFSLFYSFALANDKLKDFFKDYNTSGVFITFDGKHYASNNFKRAKEPFSPASTFKIFNALIALDNGVVKDTKEIFYHYKGEKVFLPSWKQDASLRSAIKRSQVPAFKELARKIGLKTMQESLNKLSYGNTKISKIDTFWLDNSLQISAKNQADLLFKLSQNSLPFSKKSQEEVKKIILFKEDKIQKIYAKTGFNDGINLAWIVGFMESKNKILSFALNVDIKNIKNLKIREELLEKYIYSLN"},"dna_sequence":{"accession":"NG_057503.1","fmin":"0","fmax":"747","strand":"+","sequence":"TTGAAAAAAATACTTTTACTTTTTAGTCTTTTTTACTCTTTTGCTTTGGCAAATGATAAATTAAAAGATTTTTTTAAAGACTACAATACAAGCGGAGTTTTTATAACTTTTGATGGAAAACATTATGCAAGTAATAATTTTAAAAGAGCTAAAGAACCTTTTTCTCCTGCTTCGACTTTTAAAATTTTTAATGCTTTAATTGCGCTTGATAATGGTGTAGTTAAAGATACAAAGGAAATTTTTTATCATTATAAGGGTGAAAAAGTATTTTTGCCCTCTTGGAAACAAGATGCTAGTTTAAGATCAGCCATAAAACGCTCTCAAGTGCCTGCTTTTAAAGAATTGGCAAGAAAAATAGGACTTAAAACCATGCAAGAAAGCTTAAATAAACTTTCCTATGGAAATACAAAAATTTCAAAAATCGATACCTTTTGGTTGGATAATTCTTTACAAATTTCTGCAAAAAATCAAGCTGATTTGCTTTTTAAACTTTCACAAAATTCTTTACCTTTTTCCAAGAAAAGTCAAGAAGAAGTTAAAAAAATTATTCTTTTTAAAGAAGATAAAATCCAAAAAATTTATGCTAAAACAGGTTTTAATGATGGTATAAATTTGGCTTGGATTGTTGGATTTATGGAGAGTAAAAACAAAATTTTATCTTTTGCCTTAAATGTTGATATAAAGAACATTAAAAATCTTAAAATAAGAGAAGAATTGCTAGAAAAATATATTTATTCTTTAAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36772","NCBI_taxonomy_name":"Campylobacter jejuni","NCBI_taxonomy_id":"197"}}}},"ARO_accession":"3005851","ARO_id":"44313","ARO_name":"OXA-630","CARD_short_name":"OXA-630","ARO_description":"OXA-630 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46491":{"category_aro_accession":"3007702","category_aro_cvterm_id":"46491","category_aro_name":"OXA-184-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-184.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4957":{"model_id":"4957","model_name":"OXA-631","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7332":{"protein_sequence":{"accession":"WP_109545079.1","sequence":"MKKILLLFSLFYSFALANDKLKDFFKDYNTSGVFITFDGKHYASNDFKRAKEPFSPASTFKIFNALIALDNGIVKDTKEIFYHYKGEKVFLPSWKQDASLSSAIKRSQVPAFKELARKIGLKTMQESLNKLSYGNTKISKIDTFWLDNSLQISAKNQADLLFKLSQNSLPFSKKSQEEVKKIILFKEDKIQKIYAKTGFNDGINLAWIVGFIESKNKILSFALNVDIKDIKNIKIREELLEKYIYSLN"},"dna_sequence":{"accession":"NG_057496.1","fmin":"0","fmax":"747","strand":"+","sequence":"TTGAAAAAAATACTTTTACTTTTTAGTCTTTTTTACTCTTTTGCTTTGGCAAATGATAAATTAAAAGATTTTTTTAAAGACTACAATACAAGCGGAGTTTTTATAACTTTTGATGGAAAACATTATGCAAGTAATGATTTTAAAAGAGCTAAAGAACCTTTTTCTCCTGCTTCGACTTTTAAAATTTTTAATGCTTTAATTGCGCTTGATAACGGTATAGTTAAAGATACAAAGGAAATTTTTTATCATTATAAGGGTGAAAAAGTATTTTTGCCTTCTTGGAAACAAGATGCTAGTTTAAGCTCAGCCATAAAACGCTCTCAAGTGCCTGCTTTTAAAGAATTGGCAAGAAAAATAGGACTTAAAACCATGCAAGAAAGCTTAAATAAACTTTCCTATGGAAATACAAAAATTTCAAAAATCGATACCTTTTGGTTGGATAATTCTTTACAAATTTCTGCAAAAAATCAAGCTGATTTGCTTTTTAAACTTTCACAAAATTCTTTACCTTTTTCCAAGAAAAGTCAAGAAGAAGTTAAAAAAATTATTCTTTTTAAAGAAGATAAAATCCAAAAAATTTATGCTAAAACAGGTTTTAATGATGGTATAAATTTGGCTTGGATTGTTGGATTTATAGAGAGTAAAAACAAAATTTTATCTTTTGCTTTAAATGTTGATATAAAGGACATTAAAAATATTAAAATAAGAGAAGAATTGCTAGAAAAATATATTTATTCTTTAAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36772","NCBI_taxonomy_name":"Campylobacter jejuni","NCBI_taxonomy_id":"197"}}}},"ARO_accession":"3005852","ARO_id":"44314","ARO_name":"OXA-631","CARD_short_name":"OXA-631","ARO_description":"OXA-631 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46491":{"category_aro_accession":"3007702","category_aro_cvterm_id":"46491","category_aro_name":"OXA-184-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-184.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4958":{"model_id":"4958","model_name":"OXA-632","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7333":{"protein_sequence":{"accession":"WP_109545086.1","sequence":"MKKILLLFSLFYSFALANDKLKDFFKDYNTSGVFITFDGKHYASNNFKRAKEPFSPASTFKIFNALIALDNGIVKDTKEIFYHYKGEKVFLPSWKQDASLSSAIKRSQVPAFKELARKIGLKTMQESLNKLSYGNTKISKIDTFWLDNSLQISAKNQADLLFKLSQNSLPFSKKSQEEVKKIILFKEDKIQKIYAKTGFNDGINLAWIVGFIESKNKILSFALNVDIKDIKNIKIREELLEKYIYSLN"},"dna_sequence":{"accession":"NG_057506.1","fmin":"0","fmax":"747","strand":"+","sequence":"TTGAAAAAAATACTTTTACTTTTTAGTCTTTTTTACTCTTTTGCTTTGGCAAATGATAAATTAAAAGATTTTTTTAAAGACTACAATACAAGCGGAGTTTTTATAACTTTTGATGGAAAACATTATGCAAGTAATAATTTTAAAAGAGCTAAAGAACCTTTTTCTCCTGCTTCGACTTTTAAAATTTTTAATGCTTTAATTGCGCTTGATAACGGTATAGTTAAAGATACAAAGGAAATTTTTTATCATTATAAGGGTGAAAAAGTATTTTTGCCTTCTTGGAAACAAGATGCTAGTTTAAGCTCAGCCATAAAACGCTCTCAAGTGCCTGCTTTTAAAGAATTGGCAAGAAAAATAGGACTTAAAACCATGCAAGAAAGCTTAAATAAACTTTCCTATGGAAATACAAAAATTTCAAAAATCGATACCTTTTGGTTGGATAATTCTTTACAAATTTCTGCAAAAAATCAAGCTGATTTGCTTTTTAAACTTTCACAAAATTCTTTACCTTTTTCCAAGAAAAGTCAAGAAGAAGTTAAAAAAATTATTCTTTTTAAAGAAGATAAAATCCAAAAAATTTATGCTAAAACAGGTTTTAATGATGGTATAAATTTGGCTTGGATTGTTGGATTTATAGAGAGTAAAAACAAAATTTTATCTTTTGCTTTAAATGTTGATATAAAGGACATTAAAAATATTAAAATAAGAGAAGAATTGCTAGAAAAATATATTTATTCTTTAAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36772","NCBI_taxonomy_name":"Campylobacter jejuni","NCBI_taxonomy_id":"197"}}}},"ARO_accession":"3005853","ARO_id":"44315","ARO_name":"OXA-632","CARD_short_name":"OXA-632","ARO_description":"OXA-632 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46491":{"category_aro_accession":"3007702","category_aro_cvterm_id":"46491","category_aro_name":"OXA-184-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-184.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4959":{"model_id":"4959","model_name":"OXA-633","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7334":{"protein_sequence":{"accession":"WP_109545082.1","sequence":"MKKILLLFSLFYSFALANDKLKDFFKDYNTSGVFITFDGKHYASNNFKRAKEPFSPASTFKIFNALIALDNGVVKDTKEIFYHYKGEKVFLPSWKQDASLRSAIKRSQVPAFKELARKIGLKTMQESLNKLSYGNTKISKIDTFWLDNSLQISAKNQADLLFKLSQNSLPFSKKSQEEVKKIILFKEDKIQKIYAKTGFNDNINLAWIVGFVKTKNKILSFALNVDIKNIKNLKIREELLEKYIYSLN"},"dna_sequence":{"accession":"NG_057499.1","fmin":"0","fmax":"747","strand":"+","sequence":"TTGAAAAAAATACTTTTACTTTTTAGTCTTTTTTACTCTTTTGCTTTGGCAAATGATAAATTAAAAGATTTTTTTAAAGACTACAATACAAGCGGAGTTTTTATAACTTTTGATGGAAAACATTATGCAAGTAATAATTTTAAAAGAGCTAAAGAACCTTTTTCTCCTGCTTCGACTTTTAAAATTTTTAATGCTTTAATTGCGCTTGATAATGGTGTAGTTAAAGATACAAAGGAAATTTTTTATCATTATAAGGGTGAAAAAGTATTTTTGCCCTCTTGGAAACAAGATGCTAGTTTAAGATCAGCCATAAAACGCTCTCAAGTGCCTGCTTTTAAAGAATTGGCAAGAAAAATAGGACTTAAAACCATGCAAGAAAGCTTAAATAAACTTTCCTATGGAAATACAAAAATTTCAAAAATCGATACCTTTTGGTTGGATAATTCTTTACAAATTTCTGCAAAAAATCAAGCTGATTTGCTTTTTAAACTTTCACAAAATTCTTTACCTTTTTCCAAGAAAAGTCAAGAAGAAGTTAAAAAAATTATTCTTTTTAAAGAAGATAAAATCCAAAAAATTTATGCTAAAACAGGTTTTAATGATAATATAAATTTAGCTTGGATTGTTGGATTCGTAAAGACTAAAAACAAAATTTTATCTTTTGCCTTAAATGTTGATATAAAGAACATTAAAAATCTTAAAATAAGAGAAGAATTGCTAGAAAAATATATTTATTCTTTAAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36772","NCBI_taxonomy_name":"Campylobacter jejuni","NCBI_taxonomy_id":"197"}}}},"ARO_accession":"3005854","ARO_id":"44316","ARO_name":"OXA-633","CARD_short_name":"OXA-633","ARO_description":"OXA-633 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46491":{"category_aro_accession":"3007702","category_aro_cvterm_id":"46491","category_aro_name":"OXA-184-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-184.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4960":{"model_id":"4960","model_name":"OXA-634","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7335":{"protein_sequence":{"accession":"WP_109545084.1","sequence":"MKKYFYFLVFFYSFALANDKLKDFFKDYNTSGVFITFDGKHYASNNFKRAKEPFSPASTFKIFNALIALDNGVVKDTKEIFYHYKGEKVFLPSWKQDASLSSAIKRSQVPAFKELARKIGLKTMQESLNKLSYGNTKISKIDTFWLDNSLQISAKNQADLLFKLSQNSLPFSKKSQEEVKKIILFKEDKIQKIYAKTGFNDGINLAWIVGFIESKNKILSFALNVDIKNIKNLKIREELLEKYIYSLN"},"dna_sequence":{"accession":"NG_057502.1","fmin":"0","fmax":"747","strand":"+","sequence":"TTGAAAAAATACTTTTACTTTTTAGTCTTTTTTTACTCTTTTGCTTTGGCAAATGATAAATTAAAAGATTTTTTTAAAGACTACAATACAAGCGGAGTTTTTATAACTTTTGATGGAAAACATTATGCAAGTAATAATTTTAAAAGAGCTAAAGAACCTTTTTCTCCTGCTTCGACTTTTAAAATTTTTAATGCTTTAATTGCGCTTGATAATGGTGTAGTTAAAGATACAAAGGAAATTTTTTATCATTATAAGGGTGAAAAAGTATTTTTGCCCTCTTGGAAACAAGATGCTAGTTTAAGCTCAGCCATAAAACGCTCTCAAGTGCCTGCTTTTAAAGAATTGGCAAGAAAAATAGGACTTAAAACCATGCAAGAAAGCTTAAATAAACTTTCCTATGGAAATACAAAAATTTCAAAAATCGATACCTTTTGGCTGGATAATTCTTTACAAATTTCTGCAAAAAATCAAGCTGATTTGCTTTTTAAACTTTCACAAAATTCTTTACCTTTTTCCAAGAAAAGTCAAGAAGAAGTTAAAAAAATTATTCTTTTTAAAGAAGATAAAATCCAAAAAATTTATGCTAAAACAGGTTTTAATGATGGTATAAATTTGGCTTGGATTGTTGGATTTATAGAGAGTAAAAACAAAATTTTATCTTTTGCCTTAAATGTTGATATAAAGAACATTAAAAATCTTAAAATAAGAGAAGAATTGCTAGAAAAATATATTTATTCTTTAAATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36772","NCBI_taxonomy_name":"Campylobacter jejuni","NCBI_taxonomy_id":"197"}}}},"ARO_accession":"3005855","ARO_id":"44317","ARO_name":"OXA-634","CARD_short_name":"OXA-634","ARO_description":"OXA-634 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46491":{"category_aro_accession":"3007702","category_aro_cvterm_id":"46491","category_aro_name":"OXA-184-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-184.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4961":{"model_id":"4961","model_name":"OXA-635","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7336":{"protein_sequence":{"accession":"WP_109545078.1","sequence":"MKKIILFLWILNFAFGQDKILEDFFKDYNTSGIFIIFDGKNYASNDFQRAKQTFSPASTFKIFNALIALDNGVVKDTKEIFYHYKGEKVFLSSWKQDASLSSAIKRSQVPAFKELARKIGLKTMQESLNKLSYGNAKISKIDTFWLDNSLQISAKNQADLLFKLSQNSLPFSKKSQEEVKKLLLFKENKIQKIYAKTGFNDNINLAWIVGFVKTKNKILSFALNVDIKHVKNIKIREELLEKYLAIITN"},"dna_sequence":{"accession":"NG_057495.1","fmin":"0","fmax":"750","strand":"+","sequence":"ATGAAAAAAATCATCTTGTTTTTATGGATTTTAAATTTTGCCTTTGGACAAGATAAAATATTAGAAGATTTTTTTAAAGATTATAATACAAGTGGGATTTTTATAATCTTTGATGGAAAAAATTATGCAAGTAATGATTTTCAAAGAGCAAAACAAACCTTTTCTCCTGCTTCAACTTTTAAAATTTTTAATGCTTTAATTGCGCTTGATAATGGTGTAGTTAAAGATACAAAGGAAATTTTTTATCATTATAAGGGCGAAAAAGTATTTTTGTCCTCTTGGAAACAAGATGCTAGTTTAAGCTCAGCCATAAAACGCTCTCAAGTGCCTGCTTTTAAAGAATTAGCAAGAAAAATAGGACTTAAAACCATGCAAGAAAGCTTAAATAAACTTTCTTATGGAAATGCAAAAATTTCAAAAATCGATACCTTTTGGCTGGATAATTCTTTGCAAATTTCTGCAAAAAATCAAGCTGATTTACTTTTTAAACTTTCACAAAATTCTTTACCTTTTTCCAAGAAAAGTCAAGAAGAAGTTAAAAAACTTCTTCTTTTTAAAGAAAATAAAATACAAAAAATTTATGCCAAAACAGGTTTTAATGATAATATAAATTTAGCTTGGATTGTTGGATTCGTAAAGACTAAAAACAAAATTTTATCTTTTGCTTTAAATGTTGATATAAAGCACGTTAAAAATATTAAAATAAGAGAAGAATTGCTAGAAAAATATCTAGCAATCATAACAAATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36772","NCBI_taxonomy_name":"Campylobacter jejuni","NCBI_taxonomy_id":"197"}}}},"ARO_accession":"3005856","ARO_id":"44318","ARO_name":"OXA-635","CARD_short_name":"OXA-635","ARO_description":"OXA-635 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46491":{"category_aro_accession":"3007702","category_aro_cvterm_id":"46491","category_aro_name":"OXA-184-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-184.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4962":{"model_id":"4962","model_name":"OXA-636","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7337":{"protein_sequence":{"accession":"WP_109545077.1","sequence":"MKKIILFLWILNFAFGQDKILEDFFKDYNTSGIFIIFDGKNYASNDFQRAKQAFSPASTFKIFNALIALDNGVVKDTKEIFYHYKGEKVFLPSWKQDASLSSAIKRSQVPAFKELARKIGLKTMQESLNKLSYGNAKISKIDTFWLDNSLQISAKNQADLLFKLSQNSLPFSKKSQEEVKKLLLFKENKIQKIYAKTGFNDNINLAWIVGFVKTKNKILSFALNVDIKHVKNIKIREELLEKYLAIITN"},"dna_sequence":{"accession":"NG_057494.1","fmin":"0","fmax":"750","strand":"+","sequence":"ATGAAAAAAATCATCTTGTTTTTATGGATTTTAAATTTTGCCTTTGGACAAGATAAAATATTAGAAGATTTTTTTAAAGATTATAATACAAGTGGGATTTTTATAATCTTTGATGGAAAAAATTATGCAAGTAATGATTTTCAAAGAGCTAAACAAGCCTTTTCTCCTGCTTCAACTTTTAAAATTTTTAATGCTTTAATTGCGCTTGATAATGGTGTAGTTAAAGATACAAAGGAAATTTTTTATCATTATAAGGGCGAAAAAGTATTTTTGCCCTCTTGGAAACAAGATGCTAGTTTAAGCTCAGCCATAAAACGCTCTCAAGTGCCTGCTTTTAAAGAATTAGCAAGAAAAATAGGACTTAAAACCATGCAAGAAAGCTTAAATAAACTTTCTTATGGAAATGCAAAAATTTCAAAAATCGATACCTTTTGGCTGGATAATTCTTTGCAAATTTCTGCAAAAAATCAAGCTGATTTACTTTTTAAACTTTCACAAAATTCTTTACCTTTTTCCAAGAAAAGTCAAGAAGAAGTTAAAAAACTTCTTCTTTTTAAAGAAAATAAAATACAAAAAATTTATGCCAAAACAGGTTTTAATGATAATATAAATTTAGCTTGGATTGTTGGATTCGTAAAGACTAAAAACAAAATTTTATCTTTTGCTTTAAATGTTGATATAAAGCACGTTAAAAATATTAAAATAAGAGAAGAATTGCTAGAAAAATATCTAGCAATCATAACAAATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36772","NCBI_taxonomy_name":"Campylobacter jejuni","NCBI_taxonomy_id":"197"}}}},"ARO_accession":"3005857","ARO_id":"44319","ARO_name":"OXA-636","CARD_short_name":"OXA-636","ARO_description":"OXA-636 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46491":{"category_aro_accession":"3007702","category_aro_cvterm_id":"46491","category_aro_name":"OXA-184-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-184.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4963":{"model_id":"4963","model_name":"OXA-637","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7338":{"protein_sequence":{"accession":"WP_052858477.1","sequence":"MRNFIVFILFLNIAIGEDKILGNFFKDCNTSGTFIVFDGKNYASNDFQRAKQTFSPASTFKIFNALIALDNGVVRDTKEIFYHYKGEKVFLPSWKQDASLSSAIKRSQVPAFKELARKIGLKTMQEGLNKLSYGNTKISKIDTFWLDNSLQISAKNQADLLFKLSQNSLPFSKKSQEEVKEIILFKEDKIQKIYAKTGFNDNINLAWIVGFVKTENKILSFALNVDIKDIKNIKIREELLEKYLAIITN"},"dna_sequence":{"accession":"NG_057490.1","fmin":"0","fmax":"750","strand":"+","sequence":"ATGAGAAATTTTATTGTATTTATATTGTTTTTGAATATAGCCATTGGAGAGGATAAAATACTTGGTAATTTTTTTAAAGATTGTAATACAAGTGGGACTTTTATAGTCTTTGATGGAAAAAATTATGCAAGTAATGATTTTCAAAGAGCTAAACAAACCTTTTCTCCTGCTTCAACTTTTAAAATTTTTAATGCTTTAATTGCACTTGATAATGGTGTAGTTAGAGATACAAAGGAAATTTTCTATCATTATAAGGGTGAAAAAGTATTTTTGCCCTCTTGGAAACAAGATGCTAGTTTAAGCTCAGCCATAAAACGCTCTCAAGTGCCTGCTTTTAAAGAATTGGCAAGAAAAATAGGACTTAAAACCATGCAAGAAGGCTTAAATAAACTTTCTTATGGAAATACAAAAATTTCAAAAATCGATACCTTTTGGTTGGATAATTCTTTACAAATTTCTGCAAAAAATCAAGCTGATTTGCTTTTTAAACTTTCGCAAAATTCTTTACCTTTTTCCAAAAAAAGTCAAGAAGAAGTTAAAGAAATTATTCTTTTTAAGGAAGATAAAATCCAAAAAATTTATGCTAAAACAGGTTTTAATGATAATATCAATTTAGCTTGGATTGTTGGATTTGTAAAGACTGAAAACAAAATTTTATCTTTTGCTTTAAATGTTGATATAAAGGACATTAAAAATATTAAAATAAGGGAAGAATTGCTAGAAAAATATCTAGCAATCATAACAAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37052","NCBI_taxonomy_name":"Campylobacter","NCBI_taxonomy_id":"194"}}}},"ARO_accession":"3005858","ARO_id":"44320","ARO_name":"OXA-637","CARD_short_name":"OXA-637","ARO_description":"OXA-637 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46491":{"category_aro_accession":"3007702","category_aro_cvterm_id":"46491","category_aro_name":"OXA-184-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-184.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4964":{"model_id":"4964","model_name":"OXA-638","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7339":{"protein_sequence":{"accession":"WP_044779552.1","sequence":"MRNFIVFILFLNIAIGEDKILGNFFKDCNTSGTFIVFDGKNYASNDFKRAKQAFSPASTFKIFNALIALDNGVVRDTKEIFYHYKGEKVFLPSWKQDASLSSAIKRSQVPAFKELARKIGLKTMQESLNKLSYGNAKISKIDTFWLDNSLQISAKNQADLLFKLSQNSLPFSKKSQEEVKEIILFKEDKIQKIYAKTGFNDNINLAWIVGFVKTENKILSFALNVDIKDIKNIKIREELLEKYLAIITN"},"dna_sequence":{"accession":"NG_057544.1","fmin":"0","fmax":"750","strand":"+","sequence":"ATGAGAAATTTTATTGTATTTATATTGTTTTTGAATATAGCCATTGGAGAGGATAAAATACTTGGTAATTTTTTTAAAGATTGTAATACAAGTGGGACTTTTATAGTCTTTGATGGAAAAAATTATGCAAGTAATGATTTTAAAAGAGCTAAACAAGCCTTTTCTCCTGCTTCAACTTTTAAAATTTTTAATGCTTTAATTGCACTTGATAATGGTGTAGTTAGAGATACAAAGGAAATTTTTTATCATTATAAGGGCGAAAAAGTATTTTTGCCCTCTTGGAAACAAGATGCTAGTTTAAGCTCAGCTATAAAACGCTCTCAAGTGCCTGCTTTTAAAGAATTGGCAAGAAAAATAGGACTTAAAACCATGCAAGAAAGCTTAAATAAACTTTCTTATGGAAATGCAAAAATTTCAAAAATCGATACCTTTTGGCTCGATAATTCTTTACAAATTTCTGCAAAAAATCAAGCTGATTTGCTTTTTAAACTTTCGCAAAATTCTTTACCTTTTTCCAAAAAAAGTCAAGAAGAAGTTAAAGAAATTATTCTTTTTAAGGAAGATAAAATCCAAAAAATTTATGCTAAAACAGGTTTTAATGATAATATCAATTTAGCTTGGATTGTTGGATTTGTAAAGACTGAAAACAAAATTTTATCTTTTGCTTTAAATGTTGATATAAAGGACATTAAAAATATTAAAATAAGAGAAGAATTGCTAGAAAAATATCTAGCAATCATAACAAATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37052","NCBI_taxonomy_name":"Campylobacter","NCBI_taxonomy_id":"194"}}}},"ARO_accession":"3005859","ARO_id":"44321","ARO_name":"OXA-638","CARD_short_name":"OXA-638","ARO_description":"OXA-638 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46491":{"category_aro_accession":"3007702","category_aro_cvterm_id":"46491","category_aro_name":"OXA-184-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-184.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4965":{"model_id":"4965","model_name":"OXA-639","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7340":{"protein_sequence":{"accession":"WP_053872444.1","sequence":"MRNFIVFILFLNIAIGEDKILGNFFKDCNTSGVFITFDGKHYASNDFKRAKQAFSPASTFKIFNALIALDNGVVRDTKEIFYHYKGEKVFLPSWKQDASLSSAIKRSQVPAFKELARKIGLKTMQEGLNKLSYGNTKISKIDTFWLDNSLQISAKNQADLLFKLSQNSLPFSKKSQEEVKEIILFKEDKIQKIYAKTGFNDNINLAWIVGFVKTENKILSFALNVDIKDIKNIKIREELLEKYLAIITN"},"dna_sequence":{"accession":"NG_057504.1","fmin":"0","fmax":"750","strand":"+","sequence":"ATGAGAAATTTTATTGTATTTATATTGTTTTTGAATATAGCCATTGGAGAGGATAAAATACTTGGTAATTTTTTTAAAGATTGCAATACAAGTGGAGTTTTTATAACTTTTGATGGAAAACATTATGCAAGTAATGATTTTAAAAGAGCTAAACAAGCCTTTTCTCCTGCTTCAACTTTTAAAATTTTTAATGCTTTAATTGCACTTGATAATGGTGTAGTTAGAGATACAAAGGAAATTTTTTATCATTATAAGGGCGAAAAAGTATTTTTGCCCTCTTGGAAACAAGATGCTAGTTTAAGCTCAGCCATAAAACGCTCTCAAGTGCCTGCTTTTAAAGAATTGGCAAGAAAAATAGGACTTAAAACCATGCAAGAAGGCTTAAATAAACTTTCTTATGGAAATACAAAAATTTCAAAAATCGATACCTTTTGGTTGGATAATTCTTTACAAATTTCTGCAAAAAATCAAGCTGATTTGCTTTTTAAACTTTCGCAAAATTCTTTACCTTTTTCCAAAAAAAGTCAAGAAGAAGTTAAAGAAATTATTCTTTTTAAGGAAGATAAAATCCAAAAAATTTATGCTAAAACAGGTTTTAATGATAATATCAATTTAGCTTGGATTGTTGGATTTGTAAAGACTGAAAACAAAATTTTATCTTTTGCTTTAAATGTTGATATAAAGGACATTAAAAATATTAAAATAAGGGAAGAATTGCTAGAAAAATATCTAGCAATCATAACAAATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36772","NCBI_taxonomy_name":"Campylobacter jejuni","NCBI_taxonomy_id":"197"}}}},"ARO_accession":"3005860","ARO_id":"44322","ARO_name":"OXA-639","CARD_short_name":"OXA-639","ARO_description":"OXA-639 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46491":{"category_aro_accession":"3007702","category_aro_cvterm_id":"46491","category_aro_name":"OXA-184-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-184.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4966":{"model_id":"4966","model_name":"OXA-640","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7341":{"protein_sequence":{"accession":"WP_109545109.1","sequence":"MRNFIVFILFLNIAIGEDKILGNFFKDCNTSGVFITFDGKHYASNDFKRAKQAFSPASTFKIFNALIALDNDVVRDTKEIFYHYKGEKVFLPSWKQDASLSSAIKRSQVPAFKELARKIGLKTMQEGLNKLSYGNTKISKIDTFWLDNSLQISAKNQADLLFKLSQNSLPFSKKSQEEVKEIILFKEDKIQKIYAKTGFNDNINLAWIVGFVKTENKILSFALNVDIKDIKNIKIREELLEKYLAIITN"},"dna_sequence":{"accession":"NG_057543.1","fmin":"0","fmax":"750","strand":"+","sequence":"ATGAGAAATTTTATTGTATTTATATTGTTTTTGAATATAGCCATTGGAGAGGATAAAATACTTGGTAATTTTTTTAAAGATTGCAATACAAGTGGAGTTTTTATAACTTTTGATGGAAAACATTATGCAAGTAATGATTTTAAAAGAGCTAAACAAGCCTTTTCTCCTGCTTCAACTTTTAAAATTTTTAATGCTTTAATTGCACTTGATAATGATGTAGTTAGAGATACAAAGGAAATTTTTTATCATTATAAGGGCGAAAAAGTATTTTTGCCCTCTTGGAAACAAGATGCTAGTTTAAGCTCAGCCATAAAACGCTCTCAAGTGCCTGCTTTTAAAGAATTGGCAAGAAAAATAGGACTTAAAACCATGCAAGAAGGCTTAAATAAACTTTCTTATGGAAATACAAAAATTTCAAAAATCGATACCTTTTGGTTGGATAATTCTTTACAAATTTCTGCAAAAAATCAAGCTGATTTGCTTTTTAAACTTTCGCAAAATTCTTTACCTTTTTCCAAAAAAAGTCAAGAAGAAGTTAAAGAAATTATTCTTTTTAAGGAAGATAAAATCCAAAAAATTTATGCTAAAACAGGTTTTAATGATAATATCAATTTAGCTTGGATTGTTGGATTTGTAAAGACTGAAAACAAAATTTTATCTTTTGCTTTAAATGTTGATATAAAGGACATTAAAAATATTAAAATAAGGGAAGAATTGCTAGAAAAATATCTAGCAATCATAACAAATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36772","NCBI_taxonomy_name":"Campylobacter jejuni","NCBI_taxonomy_id":"197"}}}},"ARO_accession":"3005861","ARO_id":"44323","ARO_name":"OXA-640","CARD_short_name":"OXA-640","ARO_description":"OXA-640 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46491":{"category_aro_accession":"3007702","category_aro_cvterm_id":"46491","category_aro_name":"OXA-184-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-184.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4967":{"model_id":"4967","model_name":"OXA-642","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7342":{"protein_sequence":{"accession":"WP_014206564.1","sequence":"MTKKALFFAIGTMFLSACSFNTVQQHQIQSISTNKNSEKIKSLFDQAQTEGVLVIKRGQIEEIYGNDLKRSSTEYVPASTFKMLNALIGLEHHKATPTEVFKWDGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMSKEVKRISFGNADIGSTVDDFWLVGPLKITPQQEAQFAYELAHKTLPFSKNMQEQVQSMLFIEEKNGRKIYAKSGWGWDVDPQVGWFTGWVVQPQGEIVAFSLNLEMKKGIPSSIRKEITYKGLEQLGIL"},"dna_sequence":{"accession":"NG_057487.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGACTAAAAAAGCTCTTTTCTTTGCCATTGGTACGATGTTTTTGTCGGCATGTTCTTTTAATACCGTACAACAACATCAAATACAGTCAATTTCTACCAATAAAAACTCAGAGAAAATTAAATCATTGTTTGATCAAGCACAAACTGAAGGTGTTTTAGTTATAAAACGTGGGCAAATAGAGGAAATCTATGGCAATGATCTTAAAAGATCATCAACCGAATATGTTCCCGCCTCTACCTTTAAAATGTTAAATGCTTTGATTGGACTTGAGCATCACAAAGCAACACCAACTGAAGTGTTTAAATGGGATGGGCAAAAGCGTTTATTTCCCGATTGGGAAAAAGACATGACATTAGGCGATGCGATGAAAGCTTCTGCTATTCCAGTTTATCAGGAACTAGCTCGACGAATTGGCCTTGATCTTATGTCTAAAGAGGTAAAACGCATTAGTTTCGGTAATGCTGATATTGGTTCAACAGTAGATGATTTTTGGCTTGTTGGTCCACTTAAAATTACACCTCAACAAGAAGCCCAGTTTGCTTATGAACTAGCCCATAAAACTCTTCCTTTTAGCAAAAATATGCAAGAACAAGTTCAATCTATGCTGTTCATAGAAGAAAAAAATGGACGAAAAATTTATGCCAAAAGTGGTTGGGGATGGGATGTTGACCCACAAGTTGGTTGGTTTACAGGCTGGGTAGTTCAACCACAAGGAGAAATTGTAGCGTTCTCACTTAATTTAGAAATGAAGAAAGGCATACCTAGTTCTATTCGAAAAGAAATTACTTATAAAGGATTAGAGCAGCTAGGTATTTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40550","NCBI_taxonomy_name":"Acinetobacter calcoaceticus\/baumannii complex","NCBI_taxonomy_id":"909768"}}}},"ARO_accession":"3005862","ARO_id":"44324","ARO_name":"OXA-642","CARD_short_name":"OXA-642","ARO_description":"OXA-642 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46495":{"category_aro_accession":"3007706","category_aro_cvterm_id":"46495","category_aro_name":"OXA-213-like beta-lactamase","category_aro_description":"OXA-213-like enzymes have been identified to be intrinsic to A. calcoaceticus and have been subsequently detected in A. pittii. Phylogenetic analysis of OXA-213-like proteins identified two distinct subgroups within the OXA family. The first group was linked to A. pittii and the second group to A. calcoaceticus. The carbapenemase activity of these OXAs may be related to the species-dependent effect.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4968":{"model_id":"4968","model_name":"OXA-643","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7343":{"protein_sequence":{"accession":"WP_140423312.1","sequence":"MKNLQLGLIVLITTFGSACTTISPSVETAKNQQQQSAQQQIQQAFDQLQTTGVIVIKDKHGLHSYGNDLSRAQTPYVPASTFKMLNALIGLEYGKATSTEVFKWDGQKRSFPAWEKDMTLGQAMQASAVPVYQELARRIGLDLMKKEVQRIGYGNQQIGTVVDNFWLVGPLQITPVQEILFVEKLANTQLAFKPDVQHAVQDMLLIEQKPNYKLYAKSGWGMDLEPQVGWWTGWVETATGEKVYFALNMHMKTGISASEREQLVKQSLTALGII"},"dna_sequence":{"accession":"NG_065429.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAAAAATTTACAGTTGGGACTCATCGTCCTCATTACAACCTTCGGTTCCGCATGTACAACAATAAGCCCCTCCGTAGAAACAGCTAAAAACCAACAGCAACAAAGTGCGCAGCAGCAGATCCAACAAGCCTTCGATCAACTCCAAACCACAGGGGTGATTGTCATAAAGGATAAGCATGGCTTACACAGCTACGGCAATGACTTGAGCCGTGCTCAGACACCCTATGTACCCGCCTCTACCTTTAAAATGCTGAATGCCTTAATCGGACTAGAATATGGTAAAGCAACCAGCACCGAGGTATTTAAATGGGATGGTCAAAAGCGCAGCTTCCCTGCTTGGGAAAAAGACATGACTTTAGGGCAAGCCATGCAAGCATCTGCCGTTCCCGTTTATCAGGAGCTAGCACGGCGCATTGGCCTAGACCTGATGAAAAAAGAAGTACAGCGCATTGGATATGGCAATCAACAGATTGGCACCGTTGTCGATAATTTTTGGTTAGTCGGTCCACTGCAAATTACGCCTGTTCAAGAAATCCTTTTTGTAGAGAAGCTGGCCAATACACAACTCGCTTTTAAACCCGATGTACAACATGCAGTACAAGACATGCTGCTGATTGAACAAAAACCGAATTATAAACTCTACGCCAAATCTGGTTGGGGCATGGACCTAGAACCGCAAGTGGGCTGGTGGACAGGCTGGGTCGAAACAGCAACAGGTGAAAAAGTGTATTTTGCTTTGAATATGCATATGAAAACAGGGATTTCAGCCAGCGAGCGTGAGCAACTGGTCAAACAAAGTCTGACAGCACTGGGAATAATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39092","NCBI_taxonomy_name":"Acinetobacter johnsonii","NCBI_taxonomy_id":"40214"}}}},"ARO_accession":"3005863","ARO_id":"44325","ARO_name":"OXA-643","CARD_short_name":"OXA-643","ARO_description":"OXA-643 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46494":{"category_aro_accession":"3007705","category_aro_cvterm_id":"46494","category_aro_name":"OXA-211-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-211.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4969":{"model_id":"4969","model_name":"OXA-644","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7344":{"protein_sequence":{"accession":"WP_140423313.1","sequence":"MKNLQLGLIVLITTFGSACTTISPSVETAKNQQQQSAQQQIQQAFDQLQTTGVIVIKDKHGLHSYGNDLSRAQTPYVPASTFKMLNALIGLEHGKATSTEVFKWDGQKRSFPAWEKDMTLGQAMQASAVPVYQELARRIGLDLMKKEVQRIGYGNQQIGTVVDNFWLVGPLQITPVQEVLFVEKLANTQLAFKPDVQHTVQDMLLIEQKPNYKLYAKSGWGMDLEPQVGWWTGWVETATSEKVYFALNMHMKTGISASVREQLVKQSLTALGII"},"dna_sequence":{"accession":"NG_065430.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAAAAATTTACAGTTGGGACTCATCGTCCTCATTACAACCTTCGGTTCCGCATGTACAACAATAAGCCCCTCCGTAGAAACAGCTAAAAACCAACAGCAACAAAGTGCTCAGCAGCAGATCCAACAGGCCTTCGATCAACTCCAAACCACGGGGGTGATTGTCATTAAGGATAAGCATGGCTTACACAGCTACGGCAATGACTTGAGCCGTGCTCAGACACCCTATGTACCCGCCTCTACCTTTAAAATGCTGAATGCCTTAATCGGACTAGAACATGGTAAAGCAACCAGCACCGAGGTATTTAAATGGGATGGTCAAAAGCGCAGCTTCCCTGCTTGGGAAAAAGACATGACTTTAGGGCAAGCCATGCAAGCATCTGCCGTTCCCGTTTATCAGGAGCTAGCACGGCGCATTGGCCTAGACCTGATGAAAAAAGAAGTGCAACGCATTGGATATGGCAATCAACAGATTGGCACCGTTGTCGATAATTTTTGGTTAGTCGGTCCACTGCAAATTACGCCTGTTCAAGAAGTCCTTTTTGTAGAGAAGCTGGCCAATACACAACTCGCTTTTAAGCCAGATGTGCAACATACCGTACAAGACATGCTGCTGATTGAACAAAAACCGAATTATAAACTCTACGCCAAATCTGGTTGGGGCATGGACCTAGAACCGCAAGTGGGCTGGTGGACAGGCTGGGTCGAAACAGCAACAAGTGAAAAAGTGTATTTTGCTTTGAATATGCATATGAAAACGGGAATTTCAGCCAGCGTACGTGAGCAACTGGTCAAACAAAGTCTGACAGCACTGGGGATAATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39092","NCBI_taxonomy_name":"Acinetobacter johnsonii","NCBI_taxonomy_id":"40214"}}}},"ARO_accession":"3005864","ARO_id":"44326","ARO_name":"OXA-644","CARD_short_name":"OXA-644","ARO_description":"OXA-644 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46494":{"category_aro_accession":"3007705","category_aro_cvterm_id":"46494","category_aro_name":"OXA-211-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-211.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4970":{"model_id":"4970","model_name":"OXA-645","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7345":{"protein_sequence":{"accession":"WP_140423314.1","sequence":"MKNLQLGLIALITTFGSACTTISPSVETAKNQQQQSAQQQIQQAFDQLQTTGVIVIKDKHGLRSYGNDLSRAQTAYVPASTFKMLNALIGLEHGKATSTEVFKWDGQKRSFPAWEKDMTLGQAMQASAVPVYQELARRIGLDLMQKEVQRIGYGNQRIGTVVDNFWLVGPLQITPVQEVLFVEKLANTQLAFEPDVQHTVQDMLLIEQKPNYKLYAKSGWGMDLEPQVGWWTGWVETATGEKVYFALNMQMKTGISASVREQLVKQSLTALGII"},"dna_sequence":{"accession":"NG_065431.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAAAAATTTACAGTTGGGCCTCATCGCCCTCATTACAACCTTCGGTTCCGCATGTACCACAATAAGCCCCTCCGTAGAAACAGCTAAAAACCAACAGCAACAAAGTGCGCAGCAGCAGATCCAACAGGCCTTCGATCAACTCCAAACCACTGGGGTGATTGTCATTAAGGATAAGCATGGCTTACGCAGCTACGGCAATGACTTGAGCCGTGCTCAGACAGCCTATGTACCCGCCTCTACCTTTAAAATGCTGAATGCCTTAATCGGACTAGAACATGGTAAAGCAACCAGCACTGAGGTGTTTAAATGGGATGGTCAAAAGCGTAGTTTCCCTGCCTGGGAAAAAGACATGACTTTAGGGCAAGCCATGCAAGCATCTGCTGTTCCCGTTTATCAGGAGCTTGCACGGCGCATTGGTCTAGACCTGATGCAAAAAGAAGTACAGCGCATTGGATATGGCAATCAACGGATTGGCACCGTTGTCGATAATTTTTGGTTAGTCGGTCCACTGCAAATTACGCCTGTTCAAGAAGTCCTTTTTGTAGAGAAGCTGGCCAATACACAACTCGCTTTTGAGCCAGATGTGCAACATACCGTACAAGACATGTTGCTGATTGAACAAAAACCGAATTATAAACTCTATGCCAAATCTGGTTGGGGCATGGACCTAGAACCGCAAGTGGGCTGGTGGACAGGCTGGGTCGAAACAGCAACAGGTGAAAAAGTGTATTTTGCTTTGAATATGCAGATGAAAACAGGAATTTCAGCCAGCGTGCGTGAGCAACTGGTCAAACAAAGTCTAACAGCACTGGGGATAATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39092","NCBI_taxonomy_name":"Acinetobacter johnsonii","NCBI_taxonomy_id":"40214"}}}},"ARO_accession":"3005865","ARO_id":"44327","ARO_name":"OXA-645","CARD_short_name":"OXA-645","ARO_description":"OXA-645 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46494":{"category_aro_accession":"3007705","category_aro_cvterm_id":"46494","category_aro_name":"OXA-211-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-211.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4971":{"model_id":"4971","model_name":"OXA-650","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7346":{"protein_sequence":{"accession":"WP_140423317.1","sequence":"MKNLQLGLIALITTFGSACTTINPSVETAKNHQQQSAQQQIQQAFNQLQTTGVIVIKDKHGLHSYGNDLSRAQTPYVPASTFKMLNALIGLEHGKATSTEVFKWDGQKRSFPAWEKDMTLGQAMQASAVPVYQELARRIGLDLMQKEVQRIGYGNQQIGTVVDNFWLVGPLQITPIQEVLFVEKLANTKLAFKPDVQHAVQDMLLIEQKPNYKLYAKSGWGMDLEPQVGWWTGWVETATGAKVYFALNMQMKTGISASVREQLVKQSLTALGII"},"dna_sequence":{"accession":"NG_065435.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAAAAATTTACAGTTGGGCCTCATCGCCCTCATTACAACCTTCGGTTCCGCATGTACCACAATAAACCCCTCCGTAGAAACAGCTAAAAATCACCAACAACAAAGCGCGCAGCAGCAGATCCAACAAGCCTTCAATCAACTCCAAACCACGGGGGTGATTGTCATTAAGGATAAACATGGCTTGCACAGCTACGGCAATGACTTGAGCCGTGCTCAGACACCCTATGTACCGGCCTCTACCTTTAAAATGCTGAATGCCTTAATCGGACTAGAACATGGTAAAGCAACCAGCACCGAGGTGTTTAAATGGGATGGTCAAAAGCGCAGCTTCCCTGCTTGGGAAAAAGACATGACTTTAGGCCAAGCCATGCAAGCATCTGCCGTTCCCGTTTATCAGGAGCTTGCACGGCGCATTGGCCTAGACCTGATGCAAAAAGAAGTGCAGCGCATTGGATATGGCAATCAACAGATTGGCACCGTTGTCGATAATTTTTGGTTAGTCGGTCCACTGCAAATTACGCCTATTCAAGAAGTCCTTTTTGTGGAGAAACTAGCCAATACAAAACTCGCTTTTAAGCCCGACGTGCAACATGCAGTACAAGACATGCTGCTGATTGAACAAAAACCGAATTATAAACTCTATGCAAAATCAGGCTGGGGCATGGACCTAGAACCGCAAGTAGGCTGGTGGACAGGCTGGGTCGAAACAGCAACAGGTGCAAAAGTGTATTTTGCTTTGAATATGCAGATGAAAACGGGAATTTCAGCCAGCGTGCGTGAGCAACTGGTCAAACAAAGCCTGACAGCACTGGGGATAATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39092","NCBI_taxonomy_name":"Acinetobacter johnsonii","NCBI_taxonomy_id":"40214"}}}},"ARO_accession":"3005866","ARO_id":"44328","ARO_name":"OXA-650","CARD_short_name":"OXA-650","ARO_description":"OXA-650 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46494":{"category_aro_accession":"3007705","category_aro_cvterm_id":"46494","category_aro_name":"OXA-211-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-211.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4972":{"model_id":"4972","model_name":"OXA-651","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7347":{"protein_sequence":{"accession":"WP_058870660.1","sequence":"MKTLQFGLIALITTFGSACTTISPSVETAKNHQQQSAQQQIQQAFDQLQTTGVIVIKDKHGLRSYGNDLSRAQTAYVPASTFKMLNALIGLEHGKATSTEVFKWDGQKRSFPAWEKDMTLGQAMQASAVPVYQELARRIGLDLMQKEVQRIGYGNQQIGTVVDNFWLVGPLQITPVQEVLFVEKLANTQLAFKPDVQHTVQDMLLIEQKPNYKLYAKSGWGMDLEPQVGWWTGWVETATGEKVYFALNMHMKTGISASVREQLVKQSLTALGII"},"dna_sequence":{"accession":"NG_059326.1","fmin":"100","fmax":"925","strand":"+","sequence":"ATGAAAACTTTACAATTTGGACTCATCGCCCTCATTACAACCTTCGGTTCTGCATGTACCACAATAAGCCCCTCAGTAGAAACAGCTAAAAATCACCAGCAACAAAGCGCGCAGCAGCAGATCCAACAGGCCTTCGATCAACTCCAAACCACTGGGGTGATTGTCATTAAGGATAAGCATGGCTTACGCAGCTACGGCAATGACTTGAGCCGTGCTCAGACAGCCTATGTACCCGCCTCTACCTTTAAAATGCTGAATGCCTTAATCGGACTAGAACATGGTAAAGCAACCAGCACTGAGGTGTTTAAATGGGATGGTCAAAAGCGTAGTTTCCCTGCCTGGGAAAAAGACATGACTTTAGGGCAAGCCATGCAAGCATCTGCTGTTCCCGTTTATCAGGAGCTTGCACGGCGCATTGGTCTAGACCTGATGCAAAAAGAAGTACAGCGCATTGGATATGGCAATCAACAGATTGGCACCGTTGTCGATAATTTTTGGTTAGTCGGTCCACTGCAAATTACGCCTGTGCAAGAAGTCCTTTTTGTAGAGAAGCTGGCCAATACGCAACTCGCTTTTAAGCCAGATGTGCAACATACCGTACAAGACATGCTGCTGATTGAACAAAAACCGAATTATAAACTCTACGCCAAATCTGGTTGGGGCATGGACCTAGAACCGCAAGTGGGCTGGTGGACAGGCTGGGTCGAAACAGCAACAGGTGAAAAAGTGTATTTTGCTTTGAATATGCATATGAAAACAGGAATTTCAGCCAGCGTGCGTGAGCAACTGGTCAAACAAAGTCTGACAGCACTGGGAATAATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39092","NCBI_taxonomy_name":"Acinetobacter johnsonii","NCBI_taxonomy_id":"40214"}}}},"ARO_accession":"3005867","ARO_id":"44329","ARO_name":"OXA-651","CARD_short_name":"OXA-651","ARO_description":"OXA-651 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46494":{"category_aro_accession":"3007705","category_aro_cvterm_id":"46494","category_aro_name":"OXA-211-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-211.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4973":{"model_id":"4973","model_name":"OXA-652","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7348":{"protein_sequence":{"accession":"WP_058951457.1","sequence":"MKNLQLGLIVLITTFGSACTTISPSVETAKNQHQQSAQQQIQQAFDQLQTTGVIVIKDKYGLHSYGNDLSRAQTPYVPASTFKMLNALIGLEHGKATSTEVFKWDGQKRSFPAWEKDMTLGQAMQASAVPVYQELARRIGLDLMQKEVQRIGYGNQQIGTVVDNFWLVGPLQITPVQEVLFVEKLANTQLAFEPDVQHTVQDMLLIEQKPNYKLYAKSGWGMDLEPQVGWWTGWVETATGEKVYFALNMQMKTGISASVREQLVKQSLTALGII"},"dna_sequence":{"accession":"NG_059327.1","fmin":"100","fmax":"925","strand":"+","sequence":"ATGAAAAATTTACAGTTGGGACTCATCGTCCTCATTACAACCTTCGGTTCCGCATGTACAACAATAAGCCCCTCCGTAGAAACAGCTAAAAACCAACATCAGCAAAGCGCGCAGCAGCAGATCCAACAAGCCTTCGATCAACTCCAAACCACTGGGGTGATTGTCATTAAGGACAAGTATGGCTTACACAGCTACGGCAATGACTTGAGCCGTGCTCAGACACCCTATGTACCGGCCTCTACCTTTAAAATGCTGAATGCCTTAATCGGACTAGAACATGGTAAAGCAACCAGCACCGAGGTGTTTAAATGGGATGGTCAAAAGCGTAGTTTCCCTGCCTGGGAAAAAGACATGACTTTAGGGCAAGCCATGCAAGCATCTGCTGTTCCCGTTTATCAGGAGCTTGCACGGCGCATTGGTCTAGACCTGATGCAAAAAGAAGTACAGCGCATTGGATATGGCAATCAACAGATTGGCACCGTTGTCGATAATTTTTGGTTAGTCGGTCCACTGCAAATTACACCTGTTCAAGAAGTCCTTTTTGTAGAGAAGCTGGCCAATACACAACTCGCTTTTGAGCCAGATGTGCAACATACCGTACAAGACATGTTGCTGATTGAACAAAAACCGAATTATAAACTCTACGCCAAATCTGGTTGGGGCATGGACCTAGAACCGCAAGTGGGCTGGTGGACAGGCTGGGTCGAAACAGCAACAGGTGAAAAAGTGTATTTTGCTTTGAATATGCAGATGAAAACAGGAATTTCAGCCAGCGTGCGTGAGCAACTGGTCAAACAAAGTCTAACAGCACTGGGGATAATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39092","NCBI_taxonomy_name":"Acinetobacter johnsonii","NCBI_taxonomy_id":"40214"}}}},"ARO_accession":"3005868","ARO_id":"44330","ARO_name":"OXA-652","CARD_short_name":"OXA-652","ARO_description":"OXA-652 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46494":{"category_aro_accession":"3007705","category_aro_cvterm_id":"46494","category_aro_name":"OXA-211-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-211.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4974":{"model_id":"4974","model_name":"OXA-654","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7349":{"protein_sequence":{"accession":"WP_109791216.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDVKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAVPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_057616.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGTAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTGTTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAACAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005869","ARO_id":"44331","ARO_name":"OXA-654","CARD_short_name":"OXA-654","ARO_description":"OXA-654 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4975":{"model_id":"4975","model_name":"OXA-655","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7350":{"protein_sequence":{"accession":"WP_122630842.1","sequence":"MKTFAAYVIIACLSSTALAGSITENMSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSALPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGIIGG"},"dna_sequence":{"accession":"NG_062252.1","fmin":"100","fmax":"901","strand":"+","sequence":"ATGAAAACATTTGCCGCATATGTAATTATCGCGTGTCTTTCGAGTACGGCATTAGCTGGTTCAATTACAGAAAATATGTCTTGGAACAAAGAGTTCTCTGCCGAAGCCGTCAATGGTGTCTTCGTGCTTTGTAAAAGTAGCAGTAAATCCTGCGCTACCAATGACTTAGCTCGTGCATCAAAGGAATATCTTCCAGCATCAACATTTAAGATCCCCAACGCAATTATCGGCCTAGAAACTGGTGTCATAAAGAATGAGCATCAGGTTTTCAAATGGGACGGAAAGCCAAGAGCCATGAAGCAATGGGAAAGAGACTTGACCTTAAGAGGGGCAATACAAGTTTCAGCTCTTCCCGTATTTCAACAAATCGCCAGAGAAGTTGGCGAAGTAAGAATGCAGAAATACCTTAAAAAATTTTCCTATGGCAACCAGAATATCAGTGGTGGCATTGACAAATTCTGGTTGGAAGGCCAGCTTAGAATTTCCGCAGTTAATCAAGTGGAGTTTCTAGAGTCTCTATATTTAAATAAATTGTCAGCATCTAAAGAAAACCAGCTAATAGTAAAAGAGGCTTTGGTAACGGAGGCGGCACCTGAATATCTAGTGCATTCAAAAACTGGTTTTTCTGGTGTGGGAACTGAGTCAAATCCTGGTGTCGCATGGTGGGTTGGGTGGGTTGAGAAGGAGACAGAGGTTTACTTTTTCGCCTTTAACATGGATATAGACAACGAAAGTAAGTTGCCGCTAAGAAAATCCATTCCCACCAAAATCATGGAAAGTGAGGGCATCATTGGTGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3005870","ARO_id":"44332","ARO_name":"OXA-655","CARD_short_name":"OXA-655","ARO_description":"OXA-655 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46486":{"category_aro_accession":"3007697","category_aro_cvterm_id":"46486","category_aro_name":"OXA-10-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-10.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4976":{"model_id":"4976","model_name":"OXA-656","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7351":{"protein_sequence":{"accession":"WP_122630843.1","sequence":"MKTFAAYVIIACLSSTALAGSITENMSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGIIGG"},"dna_sequence":{"accession":"NG_062253.1","fmin":"100","fmax":"901","strand":"+","sequence":"ATGAAAACATTTGCCGCATATGTAATTATCGCGTGTCTTTCGAGTACGGCATTAGCTGGTTCAATTACAGAAAATATGTCTTGGAACAAAGAGTTCTCTGCCGAAGCCGTCAATGGTGTCTTCGTGCTTTGTAAAAGTAGCAGTAAATCCTGCGCTACCAATGACTTAGCTCGTGCATCAAAGGAATATCTTCCAGCATCAACATTTAAGATCCCCAACGCAATTATCGGCCTAGAAACTGGTGTCATAAAGAATGAGCATCAGGTTTTCAAATGGGACGGAAAGCCAAGAGCCATGAAGCAATGGGAAAGAGACTTGACCTTAAGAGGGGCAATACAAGTTTCAGCTGTTCCCGTATTTCAACAAATCGCCAGAGAAGTTGGCGAAGTAAGAATGCAGAAATACCTTAAAAAATTTTCCTATGGCAACCAGAATATCAGTGGTGGCATTGACAAATTCTGGTTGGAAGGCCAGCTTAGAATTTCCGCAGTTAATCAAGTGGAGTTTCTAGAGTCTCTATATTTAAATAAATTGTCAGCATCTAAAGAAAACCAGCTAATAGTAAAAGAGGCTTTGGTAACGGAGGCGGCACCTGAATATCTAGTGCATTCAAAAACTGGTTTTTCTGGTGTGGGAACTGAGTCAAATCCTGGTGTCGCATGGTGGGTTGGGTGGGTTGAGAAGGAGACAGAGGTTTACTTTTTCGCCTTTAACATGGATATAGACAACGAAAGTAAGTTGCCGCTAAGAAAATCCATTCCCACCAAAATCATGGAAAGTGAGGGCATCATTGGTGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3005871","ARO_id":"44333","ARO_name":"OXA-656","CARD_short_name":"OXA-656","ARO_description":"OXA-656 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46486":{"category_aro_accession":"3007697","category_aro_cvterm_id":"46486","category_aro_name":"OXA-10-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-10.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4977":{"model_id":"4977","model_name":"OXA-657","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7352":{"protein_sequence":{"accession":"WP_111672907.1","sequence":"MNKYFTCYVVASLFLSGCTVQHNLINETPSQIVQGHNQVIHQYFDEKNTSGVLVIQTDKKINLYGNALSRANTEYVPASTFKMLNALIGLENQKTDINEIFKWKGEKRSFTAWEKDMTLGEAMKLSAVPVYQELARRIGLDLMQKEVKRIGFGNAEIGQQVDNFWLVGPLKVTPIQEVEFVSQLAHTQLPFSEKVQANVKNMLLLEESNGYKIFGKTGWAMGIKPQVGWLTGWVEQPDGKIVAFALNMEMRSEMPASIRNELLMKSLKQLNII"},"dna_sequence":{"accession":"NG_060565.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGAATAAATATTTTACTTGCTATGTGGTTGCTTCTCTTTTTCTTTCTGGTTGTACGGTTCAGCATAATTTAATAAATGAAACCCCGAGTCAGATTGTTCAAGGACATAATCAGGTGATTCATCAATACTTTGATGAAAAAAACACCTCAGGTGTGCTGGTTATTCAAACAGATAAAAAAATTAATCTATATGGTAATGCTCTAAGCCGCGCAAATACAGAATATGTGCCAGCCTCTACATTTAAAATGTTGAATGCCCTGATCGGATTGGAGAACCAGAAAACGGATATTAATGAAATATTTAAATGGAAGGGCGAGAAAAGGTCATTTACCGCTTGGGAAAAAGACATGACACTAGGAGAAGCCATGAAGCTTTCTGCAGTCCCAGTCTATCAGGAACTTGCGCGACGTATCGGTCTTGATCTCATGCAAAAAGAAGTAAAACGTATTGGTTTCGGTAATGCTGAAATTGGACAGCAGGTTGATAATTTCTGGTTGGTAGGACCATTAAAGGTTACGCCTATTCAAGAGGTAGAGTTTGTTTCCCAATTAGCACATACACAGCTTCCATTTAGTGAAAAAGTGCAGGCTAATGTAAAAAATATGCTTCTTTTAGAAGAGAGTAATGGCTACAAAATTTTTGGAAAGACTGGTTGGGCAATGGGTATAAAACCACAAGTGGGCTGGTTGACCGGCTGGGTTGAGCAGCCAGATGGAAAAATTGTCGCTTTTGCATTAAATATGGAAATGCGGTCAGAAATGCCGGCATCTATACGTAATGAATTATTGATGAAATCATTAAAACAGCTGAATATTATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005872","ARO_id":"44334","ARO_name":"OXA-657","CARD_short_name":"OXA-657","ARO_description":"OXA-657 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46499":{"category_aro_accession":"3007710","category_aro_cvterm_id":"46499","category_aro_name":"OXA-23-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases, specifically imipenem, derived from OXA-23, first identified in Acinetobacter baumannii.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4978":{"model_id":"4978","model_name":"OXA-658","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7353":{"protein_sequence":{"accession":"WP_070210118.1","sequence":"MRNFIVFILFLNIAIGEDKILGNFFKDYNTSGTFIVFDGKNYASNDFQRAKQAFSPASTFKIFNALIALDNGVVRDTKEIFYHYKGEKVFLPSWKQDASLSSAIKRSQVPAFKELARKIGLKTMQESLNKLSYGNAKISKIDTFWLDNSLQISAKNQADLLFKFSQNSLPFSKKIQEEVKEIILFKEDKIQKIYAKTGFNDNINLAWIVGFVKTENKILSFALNVDIKDIKNIKIRENY"},"dna_sequence":{"accession":"NG_061408.1","fmin":"0","fmax":"720","strand":"+","sequence":"ATGAGAAATTTTATTGTATTTATATTGTTTTTGAATATAGCCATTGGAGAGGATAAAATACTTGGTAATTTTTTTAAAGATTATAATACAAGTGGGACTTTTATAGTCTTTGATGGAAAAAATTATGCAAGTAATGATTTTCAAAGAGCTAAACAAGCCTTTTCTCCTGCTTCAACTTTTAAAATTTTTAATGCTTTAATTGCGCTTGATAATGGTGTAGTTAGAGATACAAAGGAAATTTTTTATCATTATAAGGGCGAAAAAGTATTTTTGCCCTCTTGGAAACAAGATGCTAGTTTAAGCTCAGCTATAAAACGCTCTCAAGTGCCTGCTTTTAAAGAATTGGCAAGAAAAATAGGACTTAAAACCATGCAAGAAAGCTTAAATAAACTTTCTTATGGAAATGCAAAAATTTCAAAAATCGATACTTTTTGGCTAGATAATTCTTTACAAATTTCTGCAAAAAATCAAGCTGATTTACTTTTTAAATTTTCGCAAAATTCTTTACCTTTTTCTAAAAAAATTCAAGAAGAAGTTAAAGAAATTATTCTTTTTAAGGAAGATAAAATCCAAAAAATTTATGCTAAAACAGGTTTTAATGATAATATCAATTTAGCTTGGATTGTTGGATTTGTAAAGACTGAAAACAAAATTTTATCTTTTGCTTTAAATGTTGATATAAAGGACATTAAAAATATTAAAATAAGGGAAAATTATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37052","NCBI_taxonomy_name":"Campylobacter","NCBI_taxonomy_id":"194"}}}},"ARO_accession":"3005873","ARO_id":"44335","ARO_name":"OXA-658","CARD_short_name":"OXA-658","ARO_description":"OXA-658 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46491":{"category_aro_accession":"3007702","category_aro_cvterm_id":"46491","category_aro_name":"OXA-184-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-184.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4979":{"model_id":"4979","model_name":"OXA-659","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7354":{"protein_sequence":{"accession":"WP_114699276.1","sequence":"MQPKSIILFFYGYILFFRRQKITLFLLFLNLVFGQDKILNNWFKEYNTSGTFVFYDGKTWASNDFSRAMETFSPASTFKIFNALIALDSGVIKTKKEIFYHYRGEKVFLSSWAQDMNLSSAIKYSNVLAFKEVARRIGIKTMQEYLNKLHYGNAKISKIDTFWLDNSLKISAKEQAILLFRLSQNSLPFSQEAMNSVKEMICLKNMENLELFGKTGFNDEQKIAWIVGFVYLKDENKYKAFALNLDIDKFEDLYKREKILEKYLDELVKKVKNDG"},"dna_sequence":{"accession":"NG_061400.1","fmin":"0","fmax":"828","strand":"+","sequence":"ATGCAACCAAAAAGTATCATTTTATTTTTCTATGGTTACATTTTATTTTTCCGCCGACAAAAAATAACTTTATTTTTACTTTTCTTAAATTTAGTGTTTGGGCAAGATAAGATATTAAATAATTGGTTTAAAGAGTATAATACAAGCGGCACTTTTGTTTTTTATGATGGAAAAACTTGGGCGAGTAACGACTTTTCAAGGGCTATGGAGACTTTCTCTCCCGCTTCCACTTTTAAAATTTTTAATGCTCTAATTGCACTTGATAGTGGTGTGATAAAAACTAAAAAAGAAATTTTTTATCACTATAGAGGTGAAAAAGTATTTTTATCTTCTTGGGCGCAAGATATGAATTTAAGTTCAGCTATAAAATATTCTAATGTTCTTGCTTTTAAAGAAGTGGCAAGAAGAATTGGTATCAAAACTATGCAAGAATATTTAAACAAGCTTCATTATGGTAATGCTAAAATTTCCAAGATCGATACTTTTTGGCTTGACAACTCACTAAAAATAAGCGCTAAAGAACAAGCAATTTTGCTTTTTAGACTTTCACAAAATAGCTTACCTTTTTCTCAAGAAGCAATGAATAGTGTTAAGGAAATGATTTGTTTAAAAAATATGGAAAATTTAGAGCTTTTTGGAAAAACAGGTTTTAATGATGAGCAAAAAATTGCTTGGATTGTAGGTTTTGTGTATTTAAAAGATGAAAATAAATATAAGGCTTTCGCGCTAAATTTAGATATTGATAAATTTGAAGATTTATATAAAAGAGAAAAAATTTTAGAAAAATATTTAGATGAACTTGTAAAAAAAGTTAAAAATGATGGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36772","NCBI_taxonomy_name":"Campylobacter jejuni","NCBI_taxonomy_id":"197"}}}},"ARO_accession":"3005874","ARO_id":"44336","ARO_name":"OXA-659","CARD_short_name":"OXA-659","ARO_description":"OXA-659 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46519":{"category_aro_accession":"3007730","category_aro_cvterm_id":"46519","category_aro_name":"OXA-61-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-61.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4980":{"model_id":"4980","model_name":"OXA-660","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7355":{"protein_sequence":{"accession":"WP_114699279.1","sequence":"MKKITLFLLFLNLVFGQDKILNNWFKEYNTSGTFVFYDGKTWASNDFSRAMETFSPASTFKIFNALIALDSGVIKTKKEIFYHYRGEKVFLSSWAQDMNLSSAIKYSNVLAFKEVARRIGIKTMQEYLNKLHYGNAKISKIDTFWLDNSLKISAKEQAILLFRLSQNSLPFSQEAMNSVKEMICLKNMENLELFGKTGFNDEQKIAWIVGFVYLKDENKYKAFALNLDIDKFEDLCKNT"},"dna_sequence":{"accession":"NG_061407.1","fmin":"0","fmax":"720","strand":"+","sequence":"ATGAAAAAAATAACTTTATTTTTACTTTTCTTAAATTTAGTGTTTGGGCAAGATAAGATATTAAATAATTGGTTTAAAGAGTATAATACAAGCGGCACTTTTGTTTTTTATGATGGAAAAACTTGGGCGAGTAACGACTTTTCAAGGGCTATGGAGACTTTCTCTCCCGCTTCCACTTTTAAAATTTTTAATGCTCTAATTGCACTTGATAGTGGTGTGATAAAAACTAAAAAAGAAATTTTTTATCACTATAGAGGTGAAAAAGTATTTTTATCTTCTTGGGCGCAAGATATGAATTTAAGTTCAGCTATAAAATATTCTAATGTTCTTGCTTTTAAAGAAGTGGCAAGAAGAATTGGTATCAAAACTATGCAAGAATATTTAAACAAGCTTCATTATGGTAATGCTAAAATTTCCAAGATCGATACTTTTTGGCTTGACAACTCACTAAAAATAAGCGCTAAAGAACAAGCAATTTTGCTTTTTAGACTTTCACAAAATAGCTTACCTTTTTCTCAAGAAGCAATGAATAGTGTTAAGGAAATGATTTGTTTAAAAAATATGGAAAATTTAGAGCTTTTTGGAAAAACAGGTTTTAATGATGAGCAAAAAATTGCTTGGATTGTAGGTTTTGTGTATTTAAAAGATGAAAATAAATATAAGGCTTTCGCGCTAAATTTAGATATTGATAAATTTGAAGATTTATGCAAAAATACTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36772","NCBI_taxonomy_name":"Campylobacter jejuni","NCBI_taxonomy_id":"197"}}}},"ARO_accession":"3005875","ARO_id":"44337","ARO_name":"OXA-660","CARD_short_name":"OXA-660","ARO_description":"OXA-660 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46519":{"category_aro_accession":"3007730","category_aro_cvterm_id":"46519","category_aro_name":"OXA-61-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-61.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4981":{"model_id":"4981","model_name":"OXA-661","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7356":{"protein_sequence":{"accession":"WP_114699273.1","sequence":"MRKNLKVALLCSSLCLSLGLVACHSLNSELQIAEQQKQQQKISKLFVNAKTEGVFVTYDGQKIHEYGNALNRAQTSYIPASTFKMLNALIGIQHHKTTPNEVFKWNGEKRRFKSWEKDLTLTEAIQASAVPIYQELARRIGLDMMASEVKRIGFGNSDIGNQVDNFWLVGPLKITPIQEVRFAYALANEQLAFDIPVQQQVKQMLLVDQVNGTKVYAKSGWGMDVEPQVGWWTGWVEQPDGKITAFSLNMEMNKTEHVEARKTIVYEALQQLGLIQH"},"dna_sequence":{"accession":"NG_061397.1","fmin":"0","fmax":"834","strand":"+","sequence":"ATGCGAAAAAATCTCAAAGTTGCTCTGCTATGTAGTTCGTTATGCTTAAGTTTAGGCTTGGTTGCTTGTCACAGCTTAAATTCAGAGCTGCAGATTGCAGAACAGCAAAAGCAACAACAAAAAATTTCTAAGCTATTTGTGAATGCCAAAACAGAAGGCGTATTTGTCACTTATGACGGTCAAAAGATACATGAATATGGGAATGCCTTAAATCGGGCTCAAACCTCTTATATCCCTGCATCTACTTTTAAAATGCTCAATGCTTTGATTGGCATCCAACACCATAAAACGACACCAAATGAAGTTTTTAAATGGAATGGAGAAAAGCGTAGATTTAAGAGCTGGGAAAAAGATTTGACTTTAACTGAAGCGATCCAAGCATCCGCTGTTCCTATTTATCAAGAATTAGCCAGACGAATAGGTTTAGATATGATGGCATCTGAAGTTAAAAGAATAGGCTTTGGAAATTCAGATATAGGCAATCAGGTCGATAATTTTTGGTTGGTTGGCCCATTAAAAATTACACCTATTCAAGAAGTCAGATTTGCCTACGCGTTGGCAAATGAGCAATTGGCGTTTGACATTCCTGTTCAGCAGCAAGTTAAGCAAATGTTATTGGTGGATCAGGTGAATGGGACAAAAGTTTATGCGAAAAGTGGTTGGGGAATGGATGTTGAGCCACAAGTGGGATGGTGGACAGGATGGGTAGAGCAGCCTGATGGTAAAATAACTGCATTTTCTCTAAATATGGAGATGAATAAAACTGAACATGTGGAGGCTCGGAAAACGATTGTTTATGAGGCATTGCAGCAGTTAGGTTTAATTCAGCATTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42947","NCBI_taxonomy_name":"Acinetobacter venetianus","NCBI_taxonomy_id":"52133"}}}},"ARO_accession":"3005876","ARO_id":"44338","ARO_name":"OXA-661","CARD_short_name":"OXA-661","ARO_description":"OXA-661 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46501":{"category_aro_accession":"3007712","category_aro_cvterm_id":"46501","category_aro_name":"OXA-266-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-266.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4982":{"model_id":"4982","model_name":"OXA-662","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7357":{"protein_sequence":{"accession":"WP_114699274.1","sequence":"MKTLQFGFIALITTFSSACTTISPSVETAKNQQQQSAQQQIQQAFDQLQTTGVIVIKDKHGLHSYGNDLSRAQTPYVPASTFKMLNALIGLEHGKATSTEVFKWDGQKRSFPAWEKDMTLGQAMQASAVPVYQELARRIGLDLMQKEVQRIRYGNQQIGTVVDNFWLVGPLQITPVQEVLFVEKLANTQLAFKPDVQHAVQDLLLIEQKPNYKLYAKSGWGMDLEPQVGWWTGWVETATGEKVYFALNMHMKTGISASVREQLVKQSLTALGII"},"dna_sequence":{"accession":"NG_061398.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAAAACTTTACAATTTGGATTCATCGCCCTCATTACAACCTTCAGTTCCGCATGTACCACAATAAGCCCCTCCGTAGAAACAGCTAAAAACCAACAGCAACAAAGTGCGCAGCAGCAGATCCAACAGGCCTTCGATCAACTCCAAACCACTGGGGTGATTGTCATTAAGGATAAGCACGGCTTACACAGCTACGGCAATGACTTGAGCCGTGCTCAGACACCCTATGTACCCGCCTCTACCTTTAAAATGCTGAATGCCTTAATCGGACTAGAACATGGTAAAGCAACCAGCACTGAGGTGTTTAAATGGGATGGTCAAAAGCGCAGCTTCCCTGCTTGGGAAAAAGATATGACTTTAGGGCAAGCCATGCAAGCATCTGCCGTTCCCGTTTATCAGGAGCTAGCACGGCGCATTGGTCTAGACCTAATGCAAAAAGAAGTACAGCGCATTCGATATGGCAATCAACAGATTGGCACCGTTGTCGATAATTTTTGGTTAGTCGGCCCACTGCAAATTACGCCTGTTCAAGAAGTCCTTTTTGTAGAGAAGCTGGCCAATACCCAACTCGCTTTTAAGCCCGACGTGCAACATGCAGTACAAGACCTGCTGCTGATTGAACAAAAACCGAATTATAAACTTTATGCAAAATCAGGCTGGGGCATGGACCTAGAACCGCAAGTCGGCTGGTGGACAGGCTGGGTCGAAACAGCAACAGGTGAAAAAGTGTATTTTGCTTTGAATATGCATATGAAAACAGGAATTTCAGCCAGCGTGCGTGAGCAACTGGTCAAACAAAGTCTGACAGCACTGGGGATAATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39092","NCBI_taxonomy_name":"Acinetobacter johnsonii","NCBI_taxonomy_id":"40214"}}}},"ARO_accession":"3005877","ARO_id":"44339","ARO_name":"OXA-662","CARD_short_name":"OXA-662","ARO_description":"OXA-662 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46494":{"category_aro_accession":"3007705","category_aro_cvterm_id":"46494","category_aro_name":"OXA-211-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-211.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4983":{"model_id":"4983","model_name":"OXA-666","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7358":{"protein_sequence":{"accession":"WP_092689909.1","sequence":"MQQGLFYFGWLLLLTQLSACHMNMAQMSDPSVQKVVSKAIFERSEEIKALFNAANTSAVFMTYDGQQFHYYGNALARAKNAYIPASTFKMLNALIALQHHKVTTSEVFEWKGEKRSFSAWEKDMNLAQAMQASAVPVYQELARRIGLELMQKEVSRLGFGNQKIGQQVDNFWLVGPLKVTPEQEVKFVYQLATEQLLFDVKVQKQVKEMLYIERRGDTKLYAKSGWGMDVKPQVGWYTGWVEQPNGQITAFVLNLEMHDGDDVGERKQLTLDVLDKLGLFFYLH"},"dna_sequence":{"accession":"NG_062232.1","fmin":"100","fmax":"955","strand":"+","sequence":"ATGCAACAGGGGTTATTTTACTTCGGCTGGTTATTACTTTTAACGCAATTAAGTGCTTGCCACATGAACATGGCGCAGATGTCTGATCCATCCGTACAAAAGGTGGTTTCGAAGGCAATATTTGAACGCTCAGAAGAGATTAAGGCATTATTCAACGCTGCAAATACATCAGCCGTTTTTATGACTTATGACGGTCAGCAGTTTCATTATTATGGTAATGCTTTGGCCCGTGCTAAGAATGCCTATATTCCAGCTTCAACATTTAAAATGTTAAATGCATTGATTGCTCTTCAGCATCATAAAGTAACTACTTCCGAAGTGTTTGAATGGAAGGGTGAAAAGCGTTCATTTTCTGCGTGGGAAAAAGACATGAACTTGGCGCAAGCCATGCAAGCTTCAGCAGTTCCAGTGTATCAAGAGCTTGCTAGACGTATTGGGTTAGAGTTGATGCAGAAAGAAGTTTCTCGACTTGGTTTTGGCAATCAAAAAATTGGTCAACAGGTGGATAATTTTTGGCTGGTTGGCCCTTTAAAAGTAACCCCAGAACAAGAAGTAAAATTTGTTTATCAACTGGCAACAGAGCAATTACTTTTTGATGTAAAAGTACAAAAACAGGTCAAAGAAATGCTTTATATTGAGCGTCGTGGTGATACAAAACTATATGCAAAAAGTGGTTGGGGAATGGATGTAAAGCCCCAAGTGGGGTGGTACACAGGGTGGGTTGAACAACCCAATGGACAGATCACCGCTTTTGTTTTAAATTTGGAAATGCATGATGGCGATGATGTAGGCGAACGTAAGCAGCTTACTTTGGATGTGTTAGATAAGTTAGGATTATTCTTTTATTTACACTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3005878","ARO_id":"44340","ARO_name":"OXA-666","CARD_short_name":"OXA-666","ARO_description":"OXA-666 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4984":{"model_id":"4984","model_name":"OXA-667","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7359":{"protein_sequence":{"accession":"WP_096735335.1","sequence":"MSNYRFKSKIKSSVLIILSSVAFSGCVSNANLHDPASSQRISEIPLLFNYAQTQAVFVTYDGTQFKRYGNDLNRAKTAYIPASTFKMLNALIGLQHAKATNTEVFKWNGEKRSFPAWEKDMTLAQAMQASAVPVYQELARRIGLDLMSKEVKRVGFGNTQIGQQVDNFWLVGPLKITPEQEAKFAYQLANKTLPFDDAVQQQVKDMLYVERRGDSKLYAKSGWGMDVEPQVGWYTGWVEQPNGQITAFALNMHMQTGDDPAERKQLTLSILDKLGLFFYLR"},"dna_sequence":{"accession":"NG_062225.1","fmin":"100","fmax":"946","strand":"+","sequence":"ATGAGTAATTACCGATTTAAATCTAAAATAAAAAGCAGTGTATTGATCATTCTGAGTAGTGTGGCATTTTCAGGTTGTGTTTCTAATGCCAATTTGCATGATCCAGCGTCATCACAAAGAATAAGTGAAATCCCGTTGTTGTTTAATTATGCGCAAACTCAAGCCGTCTTTGTGACTTATGATGGAACTCAATTTAAACGTTATGGGAATGATTTAAATAGAGCCAAGACTGCCTATATTCCAGCCTCTACTTTTAAAATGTTGAATGCCTTAATTGGTTTGCAACATGCGAAAGCGACGAATACAGAAGTATTTAAGTGGAATGGAGAAAAAAGATCTTTTCCTGCATGGGAAAAAGATATGACCTTGGCACAAGCAATGCAGGCTTCAGCCGTACCTGTATATCAGGAGTTGGCACGACGTATTGGCTTGGATTTGATGAGTAAAGAAGTCAAGCGTGTTGGTTTTGGCAATACACAAATTGGTCAACAGGTAGATAATTTCTGGCTAGTCGGCCCATTGAAAATTACCCCAGAACAAGAAGCTAAATTTGCTTATCAATTGGCAAACAAAACATTGCCTTTTGATGATGCTGTACAGCAACAAGTTAAAGATATGCTCTATGTCGAAAGACGGGGTGATTCCAAGCTTTATGCCAAAAGTGGATGGGGAATGGATGTGGAGCCACAAGTGGGGTGGTACACAGGATGGGTGGAACAGCCGAATGGTCAGATCACTGCTTTTGCTTTAAACATGCACATGCAGACAGGGGATGATCCTGCTGAACGCAAGCAACTGACATTAAGTATCTTGGATAAATTAGGCTTATTCTTTTATTTGAGATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42558","NCBI_taxonomy_name":"Acinetobacter guillouiae","NCBI_taxonomy_id":"106649"}}}},"ARO_accession":"3005879","ARO_id":"44341","ARO_name":"OXA-667","CARD_short_name":"OXA-667","ARO_description":"OXA-667 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46502":{"category_aro_accession":"3007713","category_aro_cvterm_id":"46502","category_aro_name":"OXA-274-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-274.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4985":{"model_id":"4985","model_name":"OXA-669","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7360":{"protein_sequence":{"accession":"WP_056517622.1","sequence":"MSNNIFKIKSSVLIILSSLAFSGCVSKLNLYDPASSQRTSEIPLLFNYAQTQAVFVTYDGTQFKRYGNDLNRAKTAYIPASTFKMLNALIGLQHAKTTNTEVFKWNGEKRSFPAWEKDMTLAGAMQASAVPVYQELARRIGLDLMSQEVKRVGFGNTQIGQQVDNFWLVGPLKITPEQEAKFAYQLAKKTLPFDDAVQQQVKDMLYVERRGDSKLYAKSGWGMDVEPQVGWYTGWIEQPNGQITAFALNMHMQTGDDPAERKQLTLSILDKLGLFFYLR"},"dna_sequence":{"accession":"NG_062227.1","fmin":"100","fmax":"940","strand":"+","sequence":"ATGAGTAATAACATATTTAAAATAAAAAGCAGTGTATTGATCATCCTGAGTAGTTTGGCTTTTTCAGGTTGTGTTTCGAAGCTTAATTTGTATGATCCAGCTTCATCACAAAGAACAAGTGAAATTCCGTTGTTGTTTAATTATGCGCAAACTCAAGCCGTCTTTGTGACTTATGACGGAACTCAATTTAAACGCTATGGGAATGATTTAAATAGAGCCAAGACTGCGTATATTCCAGCCTCTACTTTTAAAATGTTGAATGCCTTAATTGGTTTGCAACATGCGAAAACGACAAATACAGAAGTATTTAAGTGGAATGGTGAAAAAAGATCTTTTCCTGCTTGGGAAAAAGATATGACCTTGGCAGGAGCAATGCAGGCTTCCGCCGTACCTGTATATCAGGAGTTGGCACGACGTATTGGTTTGGATTTGATGAGTCAAGAAGTCAAACGTGTTGGTTTTGGTAATACACAAATTGGTCAACAGGTGGATAATTTCTGGTTGGTTGGTCCATTGAAAATCACCCCAGAGCAAGAAGCTAAATTTGCTTATCAATTGGCAAAGAAAACATTGCCTTTTGATGATGCTGTACAACAGCAAGTCAAAGATATGCTTTATGTCGAAAGACGTGGTGATTCCAAGCTCTATGCCAAAAGTGGCTGGGGAATGGATGTTGAGCCACAAGTGGGTTGGTATACAGGATGGATAGAACAGCCGAATGGTCAGATCACCGCTTTTGCTTTAAATATGCACATGCAGACAGGGGATGATCCTGCTGAACGTAAGCAACTGACATTAAGTATCTTAGATAAATTAGGCTTATTCTTTTATTTGAGATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3005880","ARO_id":"44342","ARO_name":"OXA-669","CARD_short_name":"OXA-669","ARO_description":"OXA-669 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46502":{"category_aro_accession":"3007713","category_aro_cvterm_id":"46502","category_aro_name":"OXA-274-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-274.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4986":{"model_id":"4986","model_name":"OXA-670","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7361":{"protein_sequence":{"accession":"WP_016651348.1","sequence":"MSKKLKCLALLTPLILILPLTACQSSSQKKQQVVSLNEQQRVANLFQQAQTIGVLVIYDGKQIQTYGNATRRADQRFIPASTFKILNALIGIQHHKTTPNEVFKWDGQKRAFSSWEKDLSLAEAMQASAVPVYQELARRIGLELMTREVKRVGYGNKNIGTQVDNFWLVGPLKITPVEEVRFVYALAKQKLPFDQSTQQQVKGMLLVDEHQGTKIYAKSGWGMDVTPQVGWWTGWIEQPNGKIIAFSLNMQMSQPEHADARKVIVYQALQELGLLAN"},"dna_sequence":{"accession":"NG_062219.1","fmin":"100","fmax":"934","strand":"+","sequence":"ATGTCGAAAAAATTAAAATGCCTAGCGCTTCTTACGCCATTAATTTTGATCCTTCCATTGACTGCTTGTCAGAGTTCTAGCCAAAAAAAACAGCAAGTCGTGTCATTAAATGAGCAACAGCGGGTGGCGAATTTATTCCAGCAGGCGCAAACAATAGGGGTTTTGGTCATCTATGATGGCAAACAAATTCAAACATACGGCAATGCAACACGCCGTGCAGATCAACGTTTTATCCCAGCCTCAACCTTTAAAATACTGAATGCACTGATTGGTATACAGCATCATAAAACCACGCCAAATGAAGTCTTTAAATGGGATGGTCAAAAACGTGCCTTTAGCAGTTGGGAAAAAGATTTAAGTTTAGCTGAAGCTATGCAGGCATCGGCTGTACCTGTCTATCAGGAGCTAGCGCGACGCATTGGTCTAGAACTCATGACCCGTGAGGTGAAGCGTGTTGGCTATGGCAATAAAAATATTGGAACCCAAGTCGATAATTTTTGGTTGGTCGGGCCTTTGAAAATTACACCTGTAGAAGAAGTTCGATTTGTCTATGCATTGGCCAAGCAAAAACTACCGTTTGACCAGTCAACTCAACAGCAAGTGAAAGGCATGTTATTGGTGGATGAGCATCAGGGAACCAAGATCTATGCCAAGAGCGGTTGGGGCATGGACGTTACCCCGCAGGTTGGATGGTGGACAGGTTGGATTGAACAGCCAAATGGCAAAATCATTGCATTTTCACTGAATATGCAAATGAGCCAACCTGAGCATGCAGATGCACGTAAAGTGATTGTTTATCAAGCATTGCAAGAGCTGGGATTGTTAGCCAATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39512","NCBI_taxonomy_name":"Acinetobacter colistiniresistens","NCBI_taxonomy_id":"70345"}}}},"ARO_accession":"3005881","ARO_id":"44343","ARO_name":"OXA-670","CARD_short_name":"OXA-670","ARO_description":"OXA-670 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46503":{"category_aro_accession":"3007714","category_aro_cvterm_id":"46503","category_aro_name":"OXA-286-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-286.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4987":{"model_id":"4987","model_name":"OXA-674","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7362":{"protein_sequence":{"accession":"WP_081406929.1","sequence":"MMMSKKLKCLAFFTAIFFAIPMTACQSFSQQKQQLSTQKNEQQQISSLFQSAQTSGVLVIYDGKKIQSYGNDVHRAEQRYIPASTFKMLNALIGIQHHKTTPDEVFKWDGKKRAFSSWEKDLTLAEAMQASAVPVYQELARRIGLELMSREVKRVGYGNKNIGTQVDNFWLVGPLKITPVEEVRFAYALAKQKLPFDQPTQQQVKAMLLVDQIQGTKIYAKSGWGMDVSPQVGWWTGWIEQPNGKITAFSLNMQMSQPEHADARKAIVYQALQELGLLAH"},"dna_sequence":{"accession":"NG_062226.1","fmin":"100","fmax":"943","strand":"+","sequence":"ATCATGATGTCGAAAAAATTAAAATGTCTGGCCTTTTTTACAGCCATCTTTTTTGCAATTCCCATGACTGCTTGTCAAAGTTTTAGCCAACAAAAGCAACAGCTCTCGACACAAAAAAATGAGCAGCAGCAGATCTCAAGTTTATTCCAGAGTGCCCAAACCAGTGGTGTTTTGGTGATTTATGATGGTAAGAAAATTCAAAGCTATGGCAATGACGTACATCGTGCAGAACAGCGCTATATTCCTGCCTCAACCTTTAAAATGTTAAACGCCTTGATCGGAATACAGCATCATAAGACCACACCAGATGAAGTGTTTAAATGGGACGGCAAAAAGCGGGCATTTAGCAGTTGGGAAAAAGATTTAACCTTAGCTGAGGCGATGCAGGCATCGGCGGTACCTGTCTATCAAGAATTGGCAAGACGTATTGGCTTGGAACTGATGAGCCGTGAAGTAAAGCGTGTGGGTTATGGTAATAAAAATATCGGGACACAAGTCGATAATTTCTGGTTAGTTGGCCCCTTAAAAATCACTCCCGTAGAAGAAGTTCGCTTTGCCTATGCGCTGGCAAAACAGAAACTGCCCTTTGACCAGCCAACGCAGCAACAAGTCAAAGCGATGTTATTGGTGGATCAGATTCAGGGTACCAAAATCTATGCCAAAAGTGGTTGGGGAATGGATGTCAGCCCGCAAGTGGGATGGTGGACAGGCTGGATTGAACAGCCAAATGGCAAGATCACTGCATTTTCACTCAATATGCAAATGAGCCAGCCTGAGCATGCAGATGCACGTAAGGCGATTGTGTATCAAGCCTTGCAGGAGTTGGGATTGTTAGCCCATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3005882","ARO_id":"44344","ARO_name":"OXA-674","CARD_short_name":"OXA-674","ARO_description":"OXA-674 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46503":{"category_aro_accession":"3007714","category_aro_cvterm_id":"46503","category_aro_name":"OXA-286-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-286.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4988":{"model_id":"4988","model_name":"OXA-675","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7363":{"protein_sequence":{"accession":"WP_122630857.1","sequence":"MKNTIHINFAIFLIIANIIYSSARASTDISTVASQLFEGTEGCFLLYDASTNAEIAQFNKAKCSAQMAPDSTFKIALSLMAFDAEIIDQKTIFKWDKIPKGMEIWNSNHTPKTWMQFSVVWVSQEITQKIGLNKIKNYLKDFDYGNQDFSGDKERNNGLTEAWLESSLKISPEEQIQFLRKIINHNLPVRNSAIENTIDNMYLQDLENSTKLYGKTGAGFTANRTLQNGWFEGFIISKSGRKYVFVSALTGNLGSNLTSSIKAKKNAITILNTLNL"},"dna_sequence":{"accession":"NG_062270.1","fmin":"0","fmax":"831","strand":"+","sequence":"ATGAAAAACACAATACATATCAACTTCGCTATTTTTTTAATAATTGCAAATATTATCTACAGCAGCGCCAGAGCATCAACAGATATCTCTACTGTTGCATCTCAATTATTTGAAGGAACTGAAGGTTGTTTTTTACTTTACGATGCATCCACAAACGCTGAAATTGCTCAATTCAATAAAGCAAAGTGTTCAGCGCAAATGGCACCAGATTCAACTTTCAAAATCGCATTATCACTTATGGCATTTGATGCAGAAATAATAGATCAGAAAACCATATTCAAATGGGATAAAATCCCAAAAGGAATGGAAATTTGGAACAGCAATCATACACCAAAGACGTGGATGCAATTTTCTGTTGTTTGGGTTTCGCAAGAAATAACCCAAAAAATTGGATTAAATAAAATTAAGAATTATCTCAAAGATTTTGATTATGGAAATCAAGACTTCTCGGGAGATAAAGAAAGAAACAATGGATTAACAGAAGCATGGCTCGAAAGTAGCTTAAAAATTTCACCGGAAGAACAAATTCAATTCCTGCGTAAAATTATTAATCACAATCTTCCAGTTAGAAATTCAGCCATAGAAAACACCATAGATAACATGTATCTACAAGATCTGGAGAATAGTACAAAACTGTATGGGAAAACTGGTGCAGGATTCACAGCAAATAGAACCCTACAAAACGGATGGTTTGAAGGGTTTATCATAAGCAAATCAGGACGTAAATATGTTTTTGTGTCCGCACTTACAGGAAACTTGGGGTCGAATTTAACATCAAGCATAAAAGCCAAGAAAAATGCAATTACCATTCTAAACACACTAAATTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005883","ARO_id":"44345","ARO_name":"OXA-675","CARD_short_name":"OXA-675","ARO_description":"OXA-675 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46485":{"category_aro_accession":"3007696","category_aro_cvterm_id":"46485","category_aro_name":"OXA-1-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-1.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4989":{"model_id":"4989","model_name":"OXA-676","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7364":{"protein_sequence":{"accession":"WP_122630858.1","sequence":"MKTFAAYVITACLSSTALASSITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNNLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLSLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEDQLRISAVNQVEFLESLFLNKLSASKENQLIVKKALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKGTEVYFFAFNMDIDNENKLPLRKSIPTKIMASEGIIGG"},"dna_sequence":{"accession":"NG_062271.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGAAAACATTTGCCGCATATGTAATTACTGCGTGTCTTTCAAGTACGGCATTAGCTAGTTCAATTACAGAAAATACGTCTTGGAACAAAGAGTTCTCTGCCGAAGCCGTCAATGGTGTTTTCGTGCTTTGTAAAAGTAGCAGTAAATCCTGCGCTACCAATAACTTAGCTCGTGCATCAAAGGAATATCTTCCAGCATCAACATTTAAGATCCCCAACGCAATTATCGGCCTAGAAACTGGTGTCATAAAGAATGAGCATCAGGTTTTCAAATGGGACGGAAAGCCAAGAGCCATGAAACAATGGGAAAGAGACTTGAGCTTAAGAGGGGCAATACAAGTTTCAGCGGTTCCCGTATTTCAACAAATCGCCAGAGAAGTTGGCGAAGTAAGAATGCAGAAATACCTTAAAAAATTTTCATATGGCAACCAGAATATCAGTGGTGGCATTGACAAATTCTGGTTGGAGGATCAGCTAAGAATTTCCGCAGTTAATCAAGTGGAGTTTCTAGAGTCTCTATTTTTAAATAAATTGTCAGCATCAAAAGAAAATCAGCTAATAGTAAAAAAGGCTTTGGTAACGGAGGCTGCGCCTGAATATCTTGTGCATTCAAAAACTGGTTTTTCTGGTGTGGGAACTGAGTCAAATCCTGGTGTCGCATGGTGGGTTGGTTGGGTTGAGAAGGGAACAGAGGTTTACTTTTTCGCCTTTAACATGGATATAGACAACGAAAATAAGTTGCCGCTAAGAAAATCCATTCCCACCAAAATCATGGCAAGTGAGGGCATCATTGGTGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005884","ARO_id":"44346","ARO_name":"OXA-676","CARD_short_name":"OXA-676","ARO_description":"OXA-676 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46486":{"category_aro_accession":"3007697","category_aro_cvterm_id":"46486","category_aro_name":"OXA-10-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-10.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4990":{"model_id":"4990","model_name":"OXA-677","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7365":{"protein_sequence":{"accession":"WP_122630859.1","sequence":"MKTFAAYVIIACLSSTALAGSITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAFPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGIIGG"},"dna_sequence":{"accession":"NG_062272.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGAAAACATTTGCCGCATATGTAATTATCGCGTGTCTTTCAAGTACGGCATTAGCTGGTTCAATTACAGAAAATACGTCTTGGAACAAAGAGTTCTCTGCCGAAGCCGTCAATGGTGTCTTCGTGCTTTGTAAAAGTAGCAGTAAATCCTGCGCTACCAATGACTTAGCTCGTGCATCAAAGGAATATCTTCCAGCATCAACATTTAAGATCCCCAACGCAATTATCGGCCTAGAAACTGGTGTCATAAAGAATGAGCATCAGGTTTTCAAATGGGACGGAAAGCCAAGAGCCATGAAGCAATGGGAAAGAGACTTGACCTTAAGAGGGGCAATACAAGTTTCAGCTTTTCCCGTATTTCAACAAATCGCCAGAGAAGTTGGCGAAGTAAGAATGCAGAAATACCTTAAAAAATTTTCCTATGGCAACCAGAATATCAGTGGTGGCATTGACAAATTCTGGTTGGAAGGCCAGCTTAGAATTTCCGCAGTTAATCAAGTGGAGTTTCTAGAGTCTCTATATTTAAATAAATTGTCAGCATCTAAAGAAAACCAGCTAATAGTAAAAGAGGCTTTGGTAACGGAGGCGGCACCTGAATATCTAGTGCATTCAAAAACTGGTTTTTCTGGTGTGGGAACTGAGTCAAATCCTGGTGTCGCATGGTGGGTTGGGTGGGTTGAGAAGGAGACAGAGGTTTACTTTTTCGCCTTTAACATGGATATAGACAACGAAAGTAAGTTGCCGCTAAGAAAATCCATTCCCACCAAAATCATGGAAAGTGAGGGCATCATTGGTGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005885","ARO_id":"44347","ARO_name":"OXA-677","CARD_short_name":"OXA-677","ARO_description":"OXA-677 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46486":{"category_aro_accession":"3007697","category_aro_cvterm_id":"46486","category_aro_name":"OXA-10-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-10.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4991":{"model_id":"4991","model_name":"OXA-678","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7366":{"protein_sequence":{"accession":"WP_122630860.1","sequence":"MTKKALFFAISTIFLSACSFNTVQQHQIHAISTHKNSEEIKSLFDQAQTTGVLVIKRGNTEEIYGNDLKRASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFFDWEKDMTLGDAMKASAIPVYQELARRIGLDLMSKEVKRIGFGNADIGSKVDNFWLVGPLKITPQQEAQFAYELAHKTLPFSKNVQEQVQSMVFVEEKNGRKIYAKSGWGWDVEPQVGWLTGWVVQPQGEIVAFSLNLEMKKGTPSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"NG_062273.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGACTAAAAAAGCTCTTTTCTTTGCCATTAGTACCATATTTTTGTCAGCATGTTCTTTCAATACAGTACAACAGCACCAAATACACGCTATTTCTACACATAAAAATTCAGAAGAAATAAAATCACTGTTTGATCAAGCACAGACCACAGGTGTTTTGGTTATTAAGCGCGGAAATACAGAGGAAATTTATGGGAATGATCTAAAAAGGGCATCAACCGAATATGTCCCTGCATCTACCTTTAAAATGCTAAATGCTTTAATTGGTCTTGAACATCATAAAGCAACAACAACTGAAGTGTTCAAATGGGATGGACAAAAGCGTTTATTTTTTGATTGGGAAAAGGATATGACTCTGGGTGATGCCATGAAAGCTTCTGCTATTCCCGTGTATCAAGAACTAGCTCGACGAATTGGCCTTGATCTTATGTCCAAAGAGGTCAAGCGTATTGGTTTCGGTAATGCTGATATTGGTTCAAAAGTAGATAATTTTTGGCTTGTCGGTCCACTCAAAATTACGCCTCAACAGGAAGCACAGTTTGCTTATGAATTAGCACATAAAACTCTTCCTTTTAGCAAAAATGTACAAGAACAAGTTCAATCTATGGTGTTCGTAGAAGAAAAAAACGGACGTAAAATTTACGCTAAAAGCGGTTGGGGATGGGATGTGGAACCTCAAGTGGGCTGGTTAACAGGCTGGGTCGTTCAACCACAAGGAGAAATTGTAGCGTTCTCACTCAATTTAGAAATGAAAAAAGGAACACCTAGTTCTATTCGAAAAGAAATTGCTTATAAAGGATTAGAGCAGCTAGGTATTTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3005886","ARO_id":"44348","ARO_name":"OXA-678","CARD_short_name":"OXA-678","ARO_description":"OXA-678 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46495":{"category_aro_accession":"3007706","category_aro_cvterm_id":"46495","category_aro_name":"OXA-213-like beta-lactamase","category_aro_description":"OXA-213-like enzymes have been identified to be intrinsic to A. calcoaceticus and have been subsequently detected in A. pittii. Phylogenetic analysis of OXA-213-like proteins identified two distinct subgroups within the OXA family. The first group was linked to A. pittii and the second group to A. calcoaceticus. The carbapenemase activity of these OXAs may be related to the species-dependent effect.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4992":{"model_id":"4992","model_name":"OXA-679","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7367":{"protein_sequence":{"accession":"WP_122634439.1","sequence":"MRTRLFPLLSISISIFLSACSSPFIEPKDILPISTTDQTQQAIGSYFDEAQTQGVIVIKDGHNIDTYGNDLTRANTLYVPASTFKMLNALIGLENNKATVDEVFKWDGKKRSYSIWEKDMNLGEAMKLSAVPVYQELAKRIGVDLMQKEVKRVKFGNSNIGTKVDDFWLVGPLKITPIQEVEFADKLAHQELPFKQQVQKQVQDMLLIKEVEGNKIYAKSGWGMNVTPQVGWLTGWVEQPNGKKIAFSLNIEMKPNMPGSVRNEIALKSLKRLGII"},"dna_sequence":{"accession":"NG_062355.1","fmin":"0","fmax":"831","strand":"+","sequence":"GTGAGAACACGTTTATTTCCTTTATTAAGTATATCTATTTCAATTTTTTTAAGTGCGTGCTCCTCTCCATTTATCGAACCTAAAGACATCCTGCCTATTTCTACTACTGATCAAACTCAACAAGCGATTGGCTCCTATTTTGATGAAGCTCAGACACAGGGTGTTATTGTCATTAAGGATGGGCACAATATTGATACTTATGGTAATGATTTAACCCGAGCCAATACATTGTATGTACCTGCATCAACTTTTAAGATGTTAAATGCTTTAATTGGTTTGGAAAACAATAAAGCTACAGTCGATGAAGTTTTTAAATGGGATGGGAAAAAGCGTTCATATTCTATATGGGAAAAAGATATGAATTTGGGTGAAGCCATGAAGTTATCAGCGGTTCCTGTATATCAAGAACTCGCAAAACGGATAGGCGTAGATCTAATGCAAAAAGAAGTAAAAAGAGTCAAATTTGGTAATTCAAATATTGGGACAAAAGTTGATGACTTTTGGTTGGTAGGCCCATTAAAGATTACTCCTATTCAAGAAGTTGAGTTTGCTGACAAACTTGCCCATCAAGAGCTACCATTCAAACAGCAAGTACAAAAACAAGTCCAAGATATGCTGTTAATAAAGGAAGTAGAGGGTAACAAAATTTATGCAAAGAGCGGGTGGGGAATGAATGTCACCCCTCAAGTAGGCTGGTTAACAGGTTGGGTGGAACAACCTAACGGGAAAAAAATAGCTTTTTCATTGAACATTGAGATGAAACCAAACATGCCTGGTTCAGTCCGTAATGAAATAGCTCTTAAATCATTAAAACGCTTAGGTATTATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39094","NCBI_taxonomy_name":"Acinetobacter calcoaceticus","NCBI_taxonomy_id":"471"}}}},"ARO_accession":"3005887","ARO_id":"44349","ARO_name":"OXA-679","CARD_short_name":"OXA-679","ARO_description":"OXA-679 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46522":{"category_aro_accession":"3007733","category_aro_cvterm_id":"46522","category_aro_name":"OXA-679-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-679.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4993":{"model_id":"4993","model_name":"OXA-680","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7368":{"protein_sequence":{"accession":"WP_122630864.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALISLEHHKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_062277.1","fmin":"11","fmax":"836","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTCTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCAGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGACGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005888","ARO_id":"44350","ARO_name":"OXA-680","CARD_short_name":"OXA-680","ARO_description":"OXA-680 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4994":{"model_id":"4994","model_name":"OXA-682","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7369":{"protein_sequence":{"accession":"WP_122630884.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALISLEHHKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_062304.1","fmin":"13","fmax":"838","strand":"+","sequence":"ATGAACATTAAAGCCCTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTCTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCAGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGACGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCCTTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005889","ARO_id":"44351","ARO_name":"OXA-682","CARD_short_name":"OXA-682","ARO_description":"OXA-682 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4995":{"model_id":"4995","model_name":"OXA-683","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7370":{"protein_sequence":{"accession":"WP_122630885.1","sequence":"MNFQALLLITSAIFISACSPYIVTANPNYSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNNLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRIGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGISSSVRKEITYRSLEQLGIL"},"dna_sequence":{"accession":"NG_062305.1","fmin":"13","fmax":"838","strand":"+","sequence":"ATGAACTTTCAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATTACAGTGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATAATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATAGGCCTTGAGCACCATAAGGCAACCACTACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTATTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAACAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATATCTAGCTCTGTTCGAAAAGAGATTACTTATAGAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005890","ARO_id":"44352","ARO_name":"OXA-683","CARD_short_name":"OXA-683","ARO_description":"OXA-683 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4996":{"model_id":"4996","model_name":"OXA-684","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7371":{"protein_sequence":{"accession":"WP_122630886.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDDKAEKIKNLFNEAHTTGVLVIHQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRIGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGISSSVRKEITYRSLEQLGIL"},"dna_sequence":{"accession":"NG_062306.1","fmin":"29","fmax":"854","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGACAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCATCAAGGTCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATAGGCCTTGAGCACCATAAGGCAACCACTACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTATTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAACAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATATCTAGCTCTGTTCGAAAAGAGATTACTTATAGAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005891","ARO_id":"44353","ARO_name":"OXA-684","CARD_short_name":"OXA-684","ARO_description":"OXA-684 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4997":{"model_id":"4997","model_name":"OXA-685","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7372":{"protein_sequence":{"accession":"WP_122630887.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGEKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_062307.1","fmin":"39","fmax":"864","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAATGGGATGGGGAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGTGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATAGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005892","ARO_id":"44354","ARO_name":"OXA-685","CARD_short_name":"OXA-685","ARO_description":"OXA-685 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4998":{"model_id":"4998","model_name":"OXA-686","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7373":{"protein_sequence":{"accession":"WP_122630888.1","sequence":"MNIKALLLITSAIFISACSPYIVIANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKTTTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADISTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_062308.1","fmin":"13","fmax":"838","strand":"+","sequence":"ATGAACATTAAAGCCCTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGATTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTCTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGACAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGACGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCAGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCATTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005893","ARO_id":"44355","ARO_name":"OXA-686","CARD_short_name":"OXA-686","ARO_description":"OXA-686 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4999":{"model_id":"4999","model_name":"OXA-687","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7374":{"protein_sequence":{"accession":"WP_122630889.1","sequence":"MNIKALLLITSAIFISACSPYIVIANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKTTTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_062309.1","fmin":"13","fmax":"838","strand":"+","sequence":"ATGAACATTAAAGCCCTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGATTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTCTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGACAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGACGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCATTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005894","ARO_id":"44356","ARO_name":"OXA-687","CARD_short_name":"OXA-687","ARO_description":"OXA-687 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5000":{"model_id":"5000","model_name":"OXA-688","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7375":{"protein_sequence":{"accession":"WP_122630890.1","sequence":"MNIKTLLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEVHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_062310.1","fmin":"31","fmax":"856","strand":"+","sequence":"ATGAACATTAAAACACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGTACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACGCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCCTTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005895","ARO_id":"44357","ARO_name":"OXA-688","CARD_short_name":"OXA-688","ARO_description":"OXA-688 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5001":{"model_id":"5001","model_name":"OXA-689","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7376":{"protein_sequence":{"accession":"WP_122630891.1","sequence":"MNIKTLLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEVHTKGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIAVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_062311.1","fmin":"14","fmax":"839","strand":"+","sequence":"ATGAACATTAAAACACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGTACACACTAAGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTGCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005896","ARO_id":"44358","ARO_name":"OXA-689","CARD_short_name":"OXA-689","ARO_description":"OXA-689 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5002":{"model_id":"5002","model_name":"OXA-690","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7377":{"protein_sequence":{"accession":"WP_122630892.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDKKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWNGQKRLFPEWEKDMTLGDAMKASAIPIYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWNVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_062312.1","fmin":"11","fmax":"836","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATAAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGAACGGGCAAAAAAGGCTGTTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGATTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAAAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGAATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005897","ARO_id":"44359","ARO_name":"OXA-690","CARD_short_name":"OXA-690","ARO_description":"OXA-690 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5003":{"model_id":"5003","model_name":"OXA-691","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7378":{"protein_sequence":{"accession":"WP_122630893.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVIQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_062313.1","fmin":"13","fmax":"838","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGACGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTATTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005898","ARO_id":"44360","ARO_name":"OXA-691","CARD_short_name":"OXA-691","ARO_description":"OXA-691 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5004":{"model_id":"5004","model_name":"OXA-692","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7379":{"protein_sequence":{"accession":"WP_122630894.1","sequence":"MNIKTLLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEVHSTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAITVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_062314.1","fmin":"13","fmax":"838","strand":"+","sequence":"ATGAACATTAAAACACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGTACACTCTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCAACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTACGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGTAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005899","ARO_id":"44361","ARO_name":"OXA-692","CARD_short_name":"OXA-692","ARO_description":"OXA-692 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5005":{"model_id":"5005","model_name":"OXA-693","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7380":{"protein_sequence":{"accession":"WP_122630895.1","sequence":"MNIKTLLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEVHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEKNGNKIYTKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_062315.1","fmin":"13","fmax":"838","strand":"+","sequence":"ATGAACATTAAAACACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGTACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACACAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005900","ARO_id":"44362","ARO_name":"OXA-693","CARD_short_name":"OXA-693","ARO_description":"OXA-693 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5006":{"model_id":"5006","model_name":"OXA-694","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7381":{"protein_sequence":{"accession":"WP_122630896.1","sequence":"MNIKALLLITSAIFISACSPYIVSANPNHSASKSDEKAEKIKNLFNEAHTTCVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_062316.1","fmin":"27","fmax":"852","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGTCTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGTGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACTACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005901","ARO_id":"44363","ARO_name":"OXA-694","CARD_short_name":"OXA-694","ARO_description":"OXA-694 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5007":{"model_id":"5007","model_name":"OXA-695","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7382":{"protein_sequence":{"accession":"WP_122630897.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGILVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWNGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_062317.1","fmin":"18","fmax":"843","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGTTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTATTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGAACGGGCAAAAAAGGCTGTTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005902","ARO_id":"44364","ARO_name":"OXA-695","CARD_short_name":"OXA-695","ARO_description":"OXA-695 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5008":{"model_id":"5008","model_name":"OXA-696","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7383":{"protein_sequence":{"accession":"WP_122630898.1","sequence":"MNIKTLLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEVHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEIFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSLKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_062318.1","fmin":"12","fmax":"837","strand":"+","sequence":"ATGAACATTAAAACACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGTACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAATATTTAAGTGGGACGGGCAAAAAAGGCTGTTCCCAGAATGGGAAAAGGACATGACCCTAGGTGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCTAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005903","ARO_id":"44365","ARO_name":"OXA-696","CARD_short_name":"OXA-696","ARO_description":"OXA-696 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5009":{"model_id":"5009","model_name":"OXA-697","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7384":{"protein_sequence":{"accession":"WP_122630899.1","sequence":"MNFQALLLITSAIFISAYSPYIVTANPNYSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRIGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGISSSVRKEITYRSLEQLGIL"},"dna_sequence":{"accession":"NG_062319.1","fmin":"36","fmax":"861","strand":"+","sequence":"ATGAACTTTCAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTACTCACCTTATATAGTGACTGCTAATCCAAATTACAGTGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATAGGCCTTGAGCACCATAAGGCAACCACTACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTATTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAACAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATATCTAGCTCTGTTCGAAAAGAGATTACTTATAGAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005904","ARO_id":"44366","ARO_name":"OXA-697","CARD_short_name":"OXA-697","ARO_description":"OXA-697 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5010":{"model_id":"5010","model_name":"OXA-698","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7385":{"protein_sequence":{"accession":"WP_122630900.1","sequence":"MNIKALLLITSAIFISACSPYIVSANPNHSASKSDDKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_062320.1","fmin":"26","fmax":"851","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGTCTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGACAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACTACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTGGGTTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005905","ARO_id":"44367","ARO_name":"OXA-698","CARD_short_name":"OXA-698","ARO_description":"OXA-698 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5011":{"model_id":"5011","model_name":"OXA-699","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7386":{"protein_sequence":{"accession":"WP_122630901.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLERHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_062321.1","fmin":"15","fmax":"840","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCGCCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGGTGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005906","ARO_id":"44368","ARO_name":"OXA-699","CARD_short_name":"OXA-699","ARO_description":"OXA-699 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5012":{"model_id":"5012","model_name":"OXA-700","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7387":{"protein_sequence":{"accession":"WP_122630902.1","sequence":"MNIKALLLITSAIFISACSPYIVTTNPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNTDIGTQVDNFWLMGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQENIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_062322.1","fmin":"12","fmax":"837","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTACTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATACAGATATCGGTACCCAAGTCGATAATTTTTGGCTGATGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGAGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005907","ARO_id":"44369","ARO_name":"OXA-700","CARD_short_name":"OXA-700","ARO_description":"OXA-700 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5013":{"model_id":"5013","model_name":"OXA-701","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7388":{"protein_sequence":{"accession":"WP_122630903.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFTYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_062323.1","fmin":"17","fmax":"842","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTACTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005908","ARO_id":"44370","ARO_name":"OXA-701","CARD_short_name":"OXA-701","ARO_description":"OXA-701 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5014":{"model_id":"5014","model_name":"OXA-702","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7389":{"protein_sequence":{"accession":"WP_122630904.1","sequence":"MNIKTLLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEVHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMINALIGLEHHKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_062324.1","fmin":"13","fmax":"838","strand":"+","sequence":"ATGAACATTAAAACACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGTACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGATTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCGCAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCATTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005909","ARO_id":"44371","ARO_name":"OXA-702","CARD_short_name":"OXA-702","ARO_description":"OXA-702 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5015":{"model_id":"5015","model_name":"OXA-703","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7390":{"protein_sequence":{"accession":"WP_122630905.1","sequence":"MNIKALLFITSAIFISACSPYIVTANPNHSASKSDDKAEKIKNLFNEAHTTGVLVIHQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWNGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLMGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_062325.1","fmin":"16","fmax":"841","strand":"+","sequence":"ATGAACATTAAAGCACTCTTATTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGACAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCATCAAGGTCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGAACGGGCAAAAAAGGCTGTTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGATGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005910","ARO_id":"44372","ARO_name":"OXA-703","CARD_short_name":"OXA-703","ARO_description":"OXA-703 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5016":{"model_id":"5016","model_name":"OXA-704","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7391":{"protein_sequence":{"accession":"WP_122630906.1","sequence":"MNIKTLLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEVHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWRWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_062326.1","fmin":"16","fmax":"841","strand":"+","sequence":"ATGAACATTAAAACACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGTACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGAGATGGGATGTAGACCCACAAGTAGGCTGGTTAACKGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005911","ARO_id":"44373","ARO_name":"OXA-704","CARD_short_name":"OXA-704","ARO_description":"OXA-704 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5017":{"model_id":"5017","model_name":"OXA-705","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7392":{"protein_sequence":{"accession":"WP_122630907.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHITGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_062327.1","fmin":"25","fmax":"850","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGTTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACATTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005912","ARO_id":"44374","ARO_name":"OXA-705","CARD_short_name":"OXA-705","ARO_description":"OXA-705 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5018":{"model_id":"5018","model_name":"OXA-706","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7393":{"protein_sequence":{"accession":"WP_122630908.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDKKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWNGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFGQKVQHEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_062328.1","fmin":"17","fmax":"842","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATAAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGAACGGGCAAAAAAGGCTGTTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTGGCCAAAAAGTCCAACATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005913","ARO_id":"44375","ARO_name":"OXA-706","CARD_short_name":"OXA-706","ARO_description":"OXA-706 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5019":{"model_id":"5019","model_name":"OXA-707","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7394":{"protein_sequence":{"accession":"WP_122630909.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDKKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHYKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_062329.1","fmin":"24","fmax":"849","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATAAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTTAAAATGCTTAATGCTTTGATCGGCCTTGAGCATTATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCCGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACGCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCCTTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005914","ARO_id":"44376","ARO_name":"OXA-707","CARD_short_name":"OXA-707","ARO_description":"OXA-707 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5020":{"model_id":"5020","model_name":"OXA-708","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7395":{"protein_sequence":{"accession":"WP_122630916.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDDKAEKIKNLFNEAHTTGVLVIHQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWNGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYTKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_062336.1","fmin":"19","fmax":"844","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGACAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACAGGTGTTTTAGTTATCCATCAAGGTCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGAACGGGCAAAAAAGGCTGTTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACACAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005915","ARO_id":"44377","ARO_name":"OXA-708","CARD_short_name":"OXA-708","ARO_description":"OXA-708 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5021":{"model_id":"5021","model_name":"OXA-709","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7396":{"protein_sequence":{"accession":"WP_122630917.1","sequence":"MNIKALLLITSAIFISACSPYIVSANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_062337.1","fmin":"11","fmax":"836","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGTCTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACTACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACGCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCATTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005916","ARO_id":"44378","ARO_name":"OXA-709","CARD_short_name":"OXA-709","ARO_description":"OXA-709 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5022":{"model_id":"5022","model_name":"OXA-710","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7397":{"protein_sequence":{"accession":"WP_122630918.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDKKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWNGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_062338.1","fmin":"21","fmax":"846","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATAAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGAACGGGCAAAAAAGGCTGTTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGTTGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005917","ARO_id":"44379","ARO_name":"OXA-710","CARD_short_name":"OXA-710","ARO_description":"OXA-710 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5023":{"model_id":"5023","model_name":"OXA-711","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7398":{"protein_sequence":{"accession":"WP_122630919.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDKKAEKIKNLFNEAHTTGVLVIQQGQTQKSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_062339.1","fmin":"21","fmax":"846","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATAAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAAAAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005918","ARO_id":"44380","ARO_name":"OXA-711","CARD_short_name":"OXA-711","ARO_description":"OXA-711 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5024":{"model_id":"5024","model_name":"OXA-712","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7399":{"protein_sequence":{"accession":"WP_122630920.1","sequence":"MNIKTLLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_062340.1","fmin":"28","fmax":"853","strand":"+","sequence":"ATGAACATTAAAACACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGACGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCATTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005919","ARO_id":"44381","ARO_name":"OXA-712","CARD_short_name":"OXA-712","ARO_description":"OXA-712 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5025":{"model_id":"5025","model_name":"OXA-713","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7400":{"protein_sequence":{"accession":"WP_122630921.1","sequence":"MNIKTLLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALISLEHHKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_062341.1","fmin":"14","fmax":"839","strand":"+","sequence":"ATGAACATTAAAACACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTCTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCAGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGACGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005920","ARO_id":"44382","ARO_name":"OXA-713","CARD_short_name":"OXA-713","ARO_description":"OXA-713 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5026":{"model_id":"5026","model_name":"OXA-714","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7401":{"protein_sequence":{"accession":"WP_122630922.1","sequence":"MNIKALLLITSAIFISACSPYIVSANPNHSASKSDDKAEKIKNLFNEAHTTGVLVIHQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGEKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_062342.1","fmin":"21","fmax":"846","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGTCTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGACAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCATCAAGGTCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAATGGGATGGGGAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATAGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005921","ARO_id":"44383","ARO_name":"OXA-714","CARD_short_name":"OXA-714","ARO_description":"OXA-714 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5027":{"model_id":"5027","model_name":"OXA-715","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7402":{"protein_sequence":{"accession":"WP_016685888.1","sequence":"MNIKTLLLITSAIFISACSPYIVSANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFTYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_062343.1","fmin":"13","fmax":"838","strand":"+","sequence":"ATGAACATTAAAACACTCTTACTTATAACAAGCGCTATCTTTATTTCAGCCTGCTCACCTTATATAGTGTCTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCATCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACTACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTACTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005922","ARO_id":"44384","ARO_name":"OXA-715","CARD_short_name":"OXA-715","ARO_description":"OXA-715 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5028":{"model_id":"5028","model_name":"OXA-716","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7403":{"protein_sequence":{"accession":"WP_031998610.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDKKAEKIKNLFNEAHTTGVLIIQQDQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLELLGIL"},"dna_sequence":{"accession":"NG_062344.1","fmin":"12","fmax":"837","strand":"+","sequence":"ATGAATATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATAAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAATTATCCAACAAGACCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGACGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACGCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGCATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACTATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005923","ARO_id":"44385","ARO_name":"OXA-716","CARD_short_name":"OXA-716","ARO_description":"OXA-716 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5029":{"model_id":"5029","model_name":"OXA-717","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7404":{"protein_sequence":{"accession":"WP_032018141.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKTTTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_062345.1","fmin":"12","fmax":"837","strand":"+","sequence":"ATGAACATTAAAGCCCTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTCTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGACAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGACGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCATTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005924","ARO_id":"44386","ARO_name":"OXA-717","CARD_short_name":"OXA-717","ARO_description":"OXA-717 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5030":{"model_id":"5030","model_name":"OXA-718","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7405":{"protein_sequence":{"accession":"WP_122630910.1","sequence":"MNIKALLLITSAIFISACSPYIVTTNPNHSASKSDEKAEKIKNLFNETHTTGVLVIHQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWNGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVTPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_062330.1","fmin":"11","fmax":"836","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTACTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAACACACACTACGGGTGTTTTAGTTATCCATCAAGGTCAAACTCAACAAAGCTACGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGAACGGGCAAAAAAGGCTGTTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAACCCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005925","ARO_id":"44387","ARO_name":"OXA-718","CARD_short_name":"OXA-718","ARO_description":"OXA-718 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5031":{"model_id":"5031","model_name":"OXA-719","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7406":{"protein_sequence":{"accession":"WP_122630911.1","sequence":"MNIKTLLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEVHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_062331.1","fmin":"8","fmax":"833","strand":"+","sequence":"ATGAACATTAAAACACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGTACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTGGGTTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005926","ARO_id":"44388","ARO_name":"OXA-719","CARD_short_name":"OXA-719","ARO_description":"OXA-719 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5032":{"model_id":"5032","model_name":"OXA-720","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7407":{"protein_sequence":{"accession":"WP_122630912.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKNMTLGDAMKTSAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_062332.1","fmin":"19","fmax":"844","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGTTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAACTTCTGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCATTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005927","ARO_id":"44389","ARO_name":"OXA-720","CARD_short_name":"OXA-720","ARO_description":"OXA-720 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5033":{"model_id":"5033","model_name":"OXA-721","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7408":{"protein_sequence":{"accession":"WP_122630913.1","sequence":"MNIKALLLITSAIFISACSPYIVSANPNHSASKSDEKAEKIKNLFNEAHTMGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWNGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_062333.1","fmin":"11","fmax":"836","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGTCTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTATGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGAACGGGCAAAAAAGGCTGTTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005928","ARO_id":"44390","ARO_name":"OXA-721","CARD_short_name":"OXA-721","ARO_description":"OXA-721 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5034":{"model_id":"5034","model_name":"OXA-722","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7409":{"protein_sequence":{"accession":"WP_122630914.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHITGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFTLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_062334.1","fmin":"12","fmax":"837","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGTTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACATTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCACCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005929","ARO_id":"44391","ARO_name":"OXA-722","CARD_short_name":"OXA-722","ARO_description":"OXA-722 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5035":{"model_id":"5035","model_name":"OXA-723","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7410":{"protein_sequence":{"accession":"WP_122630915.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDKKAEKIKNLFNEAHTTGVLVIQQDQTQQSYGNDLARASTEYVPASTFKMLNALIGFEHHKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLELLGIL"},"dna_sequence":{"accession":"NG_062335.1","fmin":"17","fmax":"842","strand":"+","sequence":"ATGAATATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATAAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGACCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCTTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGACGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACGCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCCTTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGCATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACTATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005930","ARO_id":"44392","ARO_name":"OXA-723","CARD_short_name":"OXA-723","ARO_description":"OXA-723 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5036":{"model_id":"5036","model_name":"OXA-726","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7411":{"protein_sequence":{"accession":"WP_101150415.1","sequence":"MSRLLLSGLLGAGLLFSLPASAATGCFLYADGNGQTLSSEGDCSSQLPPASTFKIPLALMGYDSGFLVDEEHPALPFKPGYDDWLPAWRETTTPRRWETYSVVWFSQQITEWLGMERFQQYVDRFDYGNRDLSGNPGKHDGLTQAWLSASLAISPQEQARFLGKMVSGKLPVSAQTLQYTANILKVSEIDGWQIHGKTGMGYPKKLDGSLNRDQQIGWFVGWASKPGKQLIFVHTVVQKPGKQFASLKAKEEVLAALPAKLKTL"},"dna_sequence":{"accession":"NG_062247.1","fmin":"100","fmax":"895","strand":"+","sequence":"ATGTCCCGCCTTCTGTTATCCGGCCTGCTCGGCGCAGGCCTGCTGTTCTCGCTGCCGGCCAGCGCCGCCACCGGCTGTTTTCTCTATGCCGACGGCAACGGCCAGACCCTCTCCAGCGAAGGGGATTGTTCAAGCCAGCTGCCACCCGCGTCCACCTTCAAGATCCCGCTGGCGCTGATGGGCTACGACAGTGGCTTTCTGGTGGACGAAGAGCACCCGGCACTGCCTTTCAAGCCGGGTTACGACGACTGGCTGCCCGCCTGGCGGGAAACCACCACCCCGCGCCGCTGGGAAACCTACTCGGTGGTCTGGTTCTCCCAGCAGATCACCGAATGGCTGGGGATGGAGCGCTTCCAGCAGTACGTCGACCGTTTTGACTACGGCAACCGGGATCTCTCCGGCAATCCTGGCAAGCACGACGGTCTGACCCAGGCCTGGCTCAGTGCCAGCCTTGCCATCAGTCCACAGGAGCAGGCCCGCTTCCTCGGCAAGATGGTGAGCGGCAAGCTGCCGGTGTCGGCGCAAACCCTGCAGTACACCGCCAACATCCTCAAGGTGAGCGAGATCGACGGCTGGCAGATCCACGGCAAGACCGGCATGGGCTACCCGAAGAAGCTGGATGGCAGCCTCAACCGCGATCAGCAGATCGGCTGGTTCGTCGGCTGGGCCAGCAAGCCGGGCAAGCAGCTCATCTTCGTCCATACCGTGGTGCAGAAACCCGGCAAGCAGTTCGCCTCGCTCAAGGCCAAGGAAGAGGTGCTGGCCGCCCTGCCGGCCAAACTGAAAACCCTGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36810","NCBI_taxonomy_name":"Aeromonas hydrophila","NCBI_taxonomy_id":"644"}}}},"ARO_accession":"3005931","ARO_id":"44393","ARO_name":"OXA-726","CARD_short_name":"OXA-726","ARO_description":"OXA-726 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46488":{"category_aro_accession":"3007699","category_aro_cvterm_id":"46488","category_aro_name":"OXA-12-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-12.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5037":{"model_id":"5037","model_name":"OXA-727","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7412":{"protein_sequence":{"accession":"WP_114272532.1","sequence":"MKKTLFFAVSAWMLSACSGGVMMSADNQQKSPFISSKTEDSRIQQILQLFNEAGAQAVFVTFDGTVLKRYGNDLTRAQTEYIPASTFKMLNALIGLQHDKATSTEVFKWNGEKRSFPAWEKDMTLAQAMQASAVPVYQELARRIGLELMQQEVRRAGFGNADIGKQVDNFWLVGPLKITPEQEARFAYGLATEQLGFDTAVQKQVKDMLYIEGRGDAKLYAKSGWGMDVNPQVGWYTGWVDDGHGKVTAFALNMQMEQGDDVGERKQLTLDVLDKLGVFFYLR"},"dna_sequence":{"accession":"NG_061621.1","fmin":"0","fmax":"852","strand":"+","sequence":"ATGAAAAAAACACTGTTTTTTGCAGTTTCAGCGTGGATGCTGAGCGCATGTTCCGGGGGAGTCATGATGTCTGCGGACAATCAGCAGAAGTCACCATTCATATCTTCAAAGACAGAAGACAGTCGGATACAGCAGATCCTACAGCTGTTTAATGAAGCAGGTGCGCAGGCTGTTTTTGTCACTTTTGATGGCACTGTACTTAAACGTTATGGCAATGATTTAACACGTGCTCAGACTGAGTATATTCCTGCATCCACTTTTAAAATGCTGAATGCTTTGATTGGTTTGCAGCATGATAAAGCGACTTCGACAGAAGTTTTTAAATGGAATGGTGAAAAACGCTCTTTTCCTGCGTGGGAAAAGGACATGACTTTAGCTCAGGCGATGCAGGCTTCAGCTGTACCGGTCTATCAGGAACTGGCAAGACGGATAGGGCTTGAACTGATGCAGCAGGAAGTCCGGCGTGCCGGTTTTGGTAATGCAGACATTGGGAAGCAGGTTGATAACTTCTGGCTGGTGGGGCCACTGAAAATCACGCCTGAACAGGAGGCTCGATTTGCGTATGGACTTGCGACTGAGCAGCTGGGTTTTGATACTGCTGTACAAAAGCAGGTGAAAGATATGCTGTATATAGAAGGTCGTGGAGATGCGAAGCTGTATGCTAAAAGTGGCTGGGGCATGGATGTGAACCCTCAGGTGGGCTGGTATACCGGTTGGGTGGATGATGGTCATGGCAAGGTGACGGCTTTTGCTTTGAATATGCAGATGGAGCAGGGTGATGATGTTGGAGAAAGAAAACAGTTGACTCTGGATGTACTGGATAAATTGGGTGTGTTTTTTTATTTAAGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37046","NCBI_taxonomy_name":"Acinetobacter","NCBI_taxonomy_id":"469"}}}},"ARO_accession":"3005932","ARO_id":"44394","ARO_name":"OXA-727","CARD_short_name":"OXA-727","ARO_description":"OXA-727 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46523":{"category_aro_accession":"3007734","category_aro_cvterm_id":"46523","category_aro_name":"OXA-727-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-727.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5038":{"model_id":"5038","model_name":"OXA-728","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7413":{"protein_sequence":{"accession":"WP_116786835.1","sequence":"MKKTLFFAVSAWMLSACSGGIMMSGDNQKKSPFISSKTEDSRIQQIPQLFNEAGTQAVFVTFDGTVLKRYGNDLTRAQTEYIPASTFKMLNALIGLQHGKATATEVFKWNGEKRSFPAWEKDMTLAQAMQASAVPVYQELARRIGLELMQQEVRRAGFGNADIGKQVDNFWLVGPLKVTPEQEARFAYGLATEQLGFDTAVQKQVKDMLYIEGRGDVKLYAKSGWGMDVNPQVGWYTGWVDDGHGKVTAFALNMQMEQGDDVGERKQLTLDVLDKLGVFFYLH"},"dna_sequence":{"accession":"NG_061622.1","fmin":"0","fmax":"852","strand":"+","sequence":"ATGAAAAAAACACTGTTTTTTGCAGTTTCAGCGTGGATGCTGAGCGCATGTTCCGGGGGAATCATGATGTCTGGGGACAATCAGAAGAAGTCACCATTCATATCTTCAAAGACAGAAGACAGTCGGATACAGCAGATCCCACAGCTGTTTAATGAAGCAGGTACACAGGCTGTTTTTGTCACTTTTGATGGCACTGTACTTAAACGTTATGGCAATGATTTAACACGTGCTCAGACTGAGTATATTCCTGCGTCCACTTTTAAAATGCTGAATGCTTTGATTGGTTTACAGCATGGTAAAGCGACAGCGACAGAAGTTTTTAAATGGAACGGTGAAAAACGCTCTTTTCCTGCGTGGGAAAAGGATATGACTTTAGCTCAGGCGATGCAGGCCTCAGCTGTTCCGGTCTATCAGGAGCTGGCAAGACGAATTGGACTTGAACTGATGCAGCAGGAAGTCCGACGTGCTGGTTTTGGTAATGCAGACATTGGGAAGCAGGTTGATAACTTCTGGCTGGTGGGACCTTTGAAAGTCACGCCTGAACAGGAAGCCCGATTTGCTTATGGACTTGCGACTGAGCAGCTGGGTTTTGATACTGCTGTACAAAAGCAGGTGAAAGATATGCTGTATATAGAAGGTCGTGGAGATGTGAAGCTGTATGCTAAAAGTGGCTGGGGCATGGATGTGAACCCTCAGGTGGGGTGGTATACCGGTTGGGTGGATGATGGTCATGGCAAGGTGACGGCTTTTGCTTTGAATATGCAGATGGAGCAGGGTGATGATGTCGGGGAAAGAAAACAGCTGACTTTGGATGTGCTGGATAAACTAGGTGTGTTTTTTTATTTGCATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3005933","ARO_id":"44395","ARO_name":"OXA-728","CARD_short_name":"OXA-728","ARO_description":"OXA-728 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46523":{"category_aro_accession":"3007734","category_aro_cvterm_id":"46523","category_aro_name":"OXA-727-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-727.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5039":{"model_id":"5039","model_name":"OXA-729","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7414":{"protein_sequence":{"accession":"WP_114699266.1","sequence":"MNKGLHRKRLSKRLLLPMLLCLLAQQTQAVAAEQTKVSDVGSEVTAEGWQEVRRWDKLFESAGVKGSLLLWDQKRSLGLSNNLSRAAEGFIPASTFKIPSSLIALETGAVRDETSRFSWDGKVREIAAWNRDQSFRTAMKYSVVPVYQQLAREIGPKVMAAMVRQLKYGNQDIGGQADSFWLDGQLRITAFQQVDFLRQLHDNKLPVSERSQRIVKQMMLTEASTDYIIRAKTGYGVRRTPAIGWWVGWLELDDNTVYFAVNLDLASASQLPLRQQLVKQVLKQEQLLP"},"dna_sequence":{"accession":"NG_061383.1","fmin":"100","fmax":"970","strand":"+","sequence":"ATGAATAAAGGTTTGCACAGAAAGCGCCTGAGTAAGCGTTTGCTGCTGCCCATGTTGCTGTGTTTATTGGCTCAACAAACGCAGGCTGTGGCAGCTGAGCAGACCAAGGTCAGTGACGTCGGCTCTGAGGTCACGGCCGAGGGTTGGCAAGAGGTACGCCGCTGGGACAAACTGTTCGAATCCGCAGGTGTTAAAGGCAGTTTACTGCTTTGGGATCAAAAGCGTTCTTTGGGGCTCTCCAACAATCTAAGTCGCGCCGCCGAAGGCTTTATTCCGGCTTCCACCTTCAAGATCCCCTCCAGCCTTATTGCGTTGGAAACCGGGGCGGTGCGCGATGAAACCAGTCGTTTTAGCTGGGACGGAAAGGTTCGTGAAATTGCCGCCTGGAACAGGGACCAGAGTTTTCGCACCGCAATGAAGTACTCTGTGGTGCCTGTATATCAGCAGTTGGCCAGGGAGATAGGCCCCAAAGTGATGGCAGCTATGGTGCGGCAGCTGAAATATGGCAATCAGGATATCGGTGGCCAAGCGGACAGCTTCTGGCTCGACGGCCAACTGAGAATTACAGCATTTCAACAAGTGGATTTTCTAAGGCAACTGCATGACAACAAGTTGCCTGTGTCCGAGCGCAGCCAGCGAATTGTCAAACAGATGATGCTGACCGAAGCGAGTACTGACTATATCATTCGTGCCAAGACAGGCTATGGTGTGCGGCGTACGCCGGCCATAGGTTGGTGGGTCGGTTGGTTGGAGTTGGACGACAACACTGTCTATTTCGCCGTTAACCTGGATCTGGCCTCGGCCAGCCAGTTACCGTTGCGCCAACAACTGGTGAAACAGGTGCTCAAGCAGGAACAGCTGCTGCCTTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36891","NCBI_taxonomy_name":"Shewanella algae","NCBI_taxonomy_id":"38313"}}}},"ARO_accession":"3005934","ARO_id":"44396","ARO_name":"OXA-729","CARD_short_name":"OXA-729","ARO_description":"OXA-729 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46516":{"category_aro_accession":"3007727","category_aro_cvterm_id":"46516","category_aro_name":"OXA-55-like beta-lactamase","category_aro_description":"A subfamily of carbapanem-hydrolyzing class D OXA beta-lactamases derived from OXA-55.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5040":{"model_id":"5040","model_name":"OXA-730","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7415":{"protein_sequence":{"accession":"WP_116786836.1","sequence":"MRTRLFPLLSISISIFLSACSSPFIEPKDILPISTTDQTQQAIGSYFDEAQTQGVIVIKDGHNIDTYGNDLTRANTLYVPASTFKMLNALIGLENNKATVDEVFKWDGKKRSYSIWEKDMNLGEAMKLSAVPVYQELAKRIGVDLMQKEVKRVKFGNSNIGIKVDDFWLVGPLKITPIQEVEFADKLAHQELPFKQQVQKQVQDMLLIKEVEGNKIYAKSGWGMNVTPQVGWLTGWVEQPNGKKIAFSLNIEMKPNMPGSVRNEIALKSLKRLGII"},"dna_sequence":{"accession":"NG_061623.1","fmin":"0","fmax":"831","strand":"+","sequence":"GTGAGAACACGTTTATTTCCTTTATTAAGTATATCTATTTCAATTTTTTTAAGTGCGTGCTCCTCTCCATTTATCGAACCTAAAGACATCCTGCCTATTTCTACTACTGATCAAACTCAACAAGCGATTGGCTCCTATTTTGATGAAGCTCAGACACAGGGTGTTATTGTCATTAAGGATGGGCACAATATTGATACTTATGGTAATGATTTAACCCGAGCCAATACATTGTATGTACCTGCATCAACTTTTAAGATGTTAAATGCTTTAATTGGTTTGGAAAACAATAAAGCTACAGTCGATGAAGTTTTTAAATGGGATGGGAAAAAGCGTTCATATTCTATATGGGAAAAAGATATGAATTTGGGTGAAGCCATGAAGTTATCAGCGGTTCCTGTATATCAAGAACTCGCAAAACGGATAGGCGTAGATCTAATGCAAAAAGAAGTAAAAAGAGTCAAATTTGGTAATTCAAATATTGGGATAAAAGTTGATGACTTTTGGTTGGTAGGCCCATTAAAGATTACTCCTATTCAAGAAGTTGAGTTTGCTGACAAACTTGCCCATCAAGAGCTACCATTCAAACAGCAAGTACAAAAACAAGTCCAAGATATGCTGTTAATAAAGGAAGTAGAGGGTAACAAAATTTATGCAAAGAGCGGGTGGGGAATGAATGTCACCCCTCAAGTAGGCTGGTTAACAGGTTGGGTGGAACAACCTAACGGGAAAAAAATAGCTTTTTCATTGAACATTGAGATGAAACCAAACATGCCTGGTTCAGTCCGTAATGAAATAGCTCTTAAATCATTAAAACGCTTAGGTATTATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39094","NCBI_taxonomy_name":"Acinetobacter calcoaceticus","NCBI_taxonomy_id":"471"}}}},"ARO_accession":"3005935","ARO_id":"44397","ARO_name":"OXA-730","CARD_short_name":"OXA-730","ARO_description":"OXA-730 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46522":{"category_aro_accession":"3007733","category_aro_cvterm_id":"46522","category_aro_name":"OXA-679-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-679.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5041":{"model_id":"5041","model_name":"OXA-731","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7416":{"protein_sequence":{"accession":"WP_116786833.1","sequence":"MRALALSAVLLVASIIGMPAEAKEWKETQSWNTHFTEHKTQGVVVLWNENKQQGYTNDLKRANQAFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGQTRDIAAWNRDHDLITAMKYSVVPVYQEFARKIGQARMNKMLHAFDYGNEDISGNLDSFWLDGGIRISAIQQIEFLRKLYHNKLHVSERSQRIVKQAMLTEANADYIIRAKTGYSVRIEPKIGWWVGWVELDDNVWFFATNMDMPTSDGLGLRQTITKEVLKQEKIIP"},"dna_sequence":{"accession":"NG_061613.1","fmin":"0","fmax":"798","strand":"+","sequence":"ATGCGTGCATTAGCCTTATCGGCTGTGTTGTTAGTGGCATCGATTATCGGAATGCCTGCGGAAGCAAAGGAGTGGAAAGAAACTCAGAGTTGGAATACTCACTTTACAGAACATAAAACCCAAGGCGTGGTTGTGCTCTGGAACGAGAATAAACAGCAGGGTTATACCAACGATCTTAAACGGGCGAACCAAGCATTTTTACCCGCATCGACCTTTAAAATTCCCAATAGCTTGATTGCACTCGATTTAGGTGTGGTTAAGGATGAGCACCAAGTCTTTAAATGGGATGGACAGACGCGTGATATCGCCGCCTGGAACCGCGACCATGACTTAATTACCGCAATGAAATATTCGGTTGTGCCTGTGTATCAAGAATTTGCTCGCAAAATCGGCCAAGCACGTATGAATAAGATGTTGCATGCCTTCGATTATGGCAATGAGGATATTTCGGGCAATTTAGACAGCTTTTGGCTCGATGGTGGCATTCGGATTTCGGCCATCCAGCAAATCGAATTTTTACGCAAGCTGTACCACAACAAGTTGCATGTCTCGGAGCGTAGTCAGCGTATCGTTAAACAAGCCATGCTGACCGAGGCGAATGCTGATTATATTATTCGGGCGAAAACCGGTTATTCAGTCAGAATTGAGCCGAAAATCGGTTGGTGGGTGGGTTGGGTCGAACTCGATGATAATGTGTGGTTCTTCGCGACCAATATGGATATGCCAACTTCGGATGGTTTAGGACTGCGTCAAACCATCACTAAAGAAGTGTTGAAGCAGGAAAAAATTATTCCCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41536","NCBI_taxonomy_name":"Shewanella sp.","NCBI_taxonomy_id":"50422"}}}},"ARO_accession":"3005936","ARO_id":"44398","ARO_name":"OXA-731","CARD_short_name":"OXA-731","ARO_description":"OXA-731 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46510":{"category_aro_accession":"3007721","category_aro_cvterm_id":"46510","category_aro_name":"OXA-48-like beta-lactamase","category_aro_description":"OXA-48-type beta-lactamases are now routinely encountered in bacterial infections caused by carbapenam-resistant Enterobacterales. OXA-48-like proteins confer resistance to penicillin (which is efficiently hydrolyzed) and carbapenam antibiotics (which is more slowly broken down). The spectrum of activity of these variants varies, with some hydrolyzing expanded-spectrum oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5042":{"model_id":"5042","model_name":"OXA-732","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7417":{"protein_sequence":{"accession":"WP_072678505.1","sequence":"MTIRIFAIFFSTLIFATFAHAQEGTLERSDWKKFFDDYQAKGTIVVADERQADRILSVFDQARATKRYSPASTFKIPHTLFALDVGAVRDEFQVFRWDGIKRSFAGHNQDQNLRSAMRNSTVWVYELFAREIGEEKAKRYLKQIGYGNADPSTSKGDYWIDGTLEISAYEQISFLRKLYRNELPFRVEHQRLVKDLMITEAGRNWILRAKTGWEGRFGWWVGWVEWPTGAVFFALNIDTPNRMDDLFKREAIVRAILHSIDALPPN"},"dna_sequence":{"accession":"NG_061615.1","fmin":"100","fmax":"901","strand":"+","sequence":"ATGACAATCCGAATCTTTGCAATATTTTTCTCCACTCTTATTTTTGCCACTTTCGCGCATGCACAAGAAGGCACGCTAGAACGTTCTGACTGGAAGAAGTTCTTCGACGATTACCAAGCCAAAGGCACGATAGTTGTGGCAGACGAACGTCAAGCAGATCGCATCCTATCGGTTTTTGATCAAGCACGGGCGACAAAACGTTACTCGCCTGCATCAACATTCAAGATTCCACACACACTTTTTGCACTTGATGTAGGTGCTGTTCGTGATGAGTTCCAGGTTTTCCGATGGGACGGTATTAAACGAAGCTTTGCAGGACACAATCAAGACCAAAACTTGCGATCAGCTATGCGAAACTCTACGGTCTGGGTTTATGAGCTATTTGCAAGAGAGATCGGTGAGGAAAAAGCCAAACGCTATTTAAAGCAAATAGGTTATGGCAACGCCGACCCTTCGACAAGCAAAGGCGATTATTGGATAGATGGCACTCTAGAAATTTCTGCGTACGAACAGATTTCGTTTCTCAGAAAACTCTATCGAAATGAATTGCCATTTCGGGTAGAGCATCAGCGCTTGGTCAAAGATCTCATGATTACGGAAGCCGGGCGCAACTGGATTCTGCGCGCAAAGACTGGCTGGGAAGGTAGGTTTGGCTGGTGGGTGGGATGGGTTGAGTGGCCTACCGGCGCCGTATTCTTCGCATTGAATATCGATACGCCAAACAGAATGGATGATCTTTTCAAAAGAGAGGCAATCGTGCGGGCAATCCTCCACTCTATCGACGCGTTGCCGCCCAACTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005937","ARO_id":"44399","ARO_name":"OXA-732","CARD_short_name":"OXA-732","ARO_description":"OXA-732 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5043":{"model_id":"5043","model_name":"OXA-733","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7418":{"protein_sequence":{"accession":"WP_122630844.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDVKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAFPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_062257.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGTAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTTTTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAACAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005938","ARO_id":"44400","ARO_name":"OXA-733","CARD_short_name":"OXA-733","ARO_description":"OXA-733 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5044":{"model_id":"5044","model_name":"OXA-734","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7419":{"protein_sequence":{"accession":"WP_122630853.1","sequence":"MNIKTLLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEVHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLELLGIL"},"dna_sequence":{"accession":"NG_062266.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAACACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGTACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGCATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACTATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005939","ARO_id":"44401","ARO_name":"OXA-734","CARD_short_name":"OXA-734","ARO_description":"OXA-734 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5045":{"model_id":"5045","model_name":"OXA-735","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7420":{"protein_sequence":{"accession":"WP_122630854.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDKKAEKIKNLFNEAHTTGVLVIQQDQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKQVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQSQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_062267.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAATATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATAAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGACCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGACGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGCAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACGCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCCTTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGTCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005940","ARO_id":"44402","ARO_name":"OXA-735","CARD_short_name":"OXA-735","ARO_description":"OXA-735 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5046":{"model_id":"5046","model_name":"OXA-736","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7421":{"protein_sequence":{"accession":"WP_122630855.1","sequence":"MKTFAAYVITACLSSTALASSITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNNLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLSLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGSQNISGGIDKFWLEDQLRISAVNQVEFLESLFLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKGTEVYFFAFNMDIDNENKLPLRKSIPTKIMASEGIIGG"},"dna_sequence":{"accession":"NG_062268.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGAAAACATTTGCCGCATATGTAATTACTGCGTGTCTTTCAAGTACGGCATTAGCTAGTTCAATTACAGAAAATACGTCTTGGAACAAAGAGTTCTCTGCCGAAGCCGTCAATGGTGTTTTCGTGCTTTGTAAAAGTAGCAGTAAATCCTGCGCTACCAATAACTTAGCTCGTGCATCAAAGGAATATCTTCCAGCATCAACATTTAAGATCCCCAACGCAATTATCGGCCTAGAAACTGGTGTCATAAAGAATGAGCATCAGGTTTTCAAATGGGACGGAAAGCCAAGAGCCATGAAACAATGGGAAAGAGACTTGAGCTTAAGAGGGGCAATACAAGTTTCAGCGGTTCCCGTATTTCAACAAATCGCCAGAGAAGTTGGCGAAGTAAGAATGCAGAAATACCTTAAAAAATTTTCATATGGCAGCCAGAATATCAGTGGTGGCATTGACAAATTCTGGTTGGAGGATCAGCTAAGAATTTCCGCAGTTAATCAAGTGGAGTTTCTAGAGTCTCTATTTTTAAATAAATTGTCAGCATCAAAAGAAAATCAGCTAATAGTAAAAGAGGCTTTGGTAACGGAGGCTGCGCCTGAATATCTTGTGCATTCAAAAACTGGTTTTTCTGGTGTGGGAACTGAGTCAAATCCTGGTGTCGCATGGTGGGTTGGTTGGGTTGAGAAGGGAACAGAGGTTTACTTTTTCGCCTTTAACATGGATATAGACAACGAAAATAAGTTGCCGCTAAGAAAATCCATTCCCACCAAAATCATGGCAAGTGAGGGCATCATTGGTGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3005941","ARO_id":"44403","ARO_name":"OXA-736","CARD_short_name":"OXA-736","ARO_description":"OXA-736 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46486":{"category_aro_accession":"3007697","category_aro_cvterm_id":"46486","category_aro_name":"OXA-10-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-10.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5047":{"model_id":"5047","model_name":"OXA-738","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7422":{"protein_sequence":{"accession":"WP_128268238.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDDKAEKIKNLFNEAHTTGVLVIHQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_063842.1","fmin":"49","fmax":"874","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGACAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCATCAAGGTCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005942","ARO_id":"44404","ARO_name":"OXA-738","CARD_short_name":"OXA-738","ARO_description":"OXA-738 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5048":{"model_id":"5048","model_name":"OXA-739","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7423":{"protein_sequence":{"accession":"WP_114225343.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWNGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNVDIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_063843.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATAAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGTTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGAACGGGCAAAAAAGGCTGTTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGTAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005943","ARO_id":"44405","ARO_name":"OXA-739","CARD_short_name":"OXA-739","ARO_description":"OXA-739 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5049":{"model_id":"5049","model_name":"OXA-740","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7424":{"protein_sequence":{"accession":"WP_128268239.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDEKGEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVSWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_063844.1","fmin":"40","fmax":"865","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGGAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAAGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005944","ARO_id":"44406","ARO_name":"OXA-740","CARD_short_name":"OXA-740","ARO_description":"OXA-740 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5050":{"model_id":"5050","model_name":"OXA-741","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7425":{"protein_sequence":{"accession":"WP_128268240.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGISSSVRKEITYRSLEQLGIL"},"dna_sequence":{"accession":"NG_063845.1","fmin":"39","fmax":"864","strand":"+","sequence":"ATGAACATTAAAGCCCTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTCTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTCAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGACGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGGCTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAACAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATATCTAGCTCTGTTCGAAAAGAGATTACTTATAGAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005945","ARO_id":"44407","ARO_name":"OXA-741","CARD_short_name":"OXA-741","ARO_description":"OXA-741 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5051":{"model_id":"5051","model_name":"OXA-742","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7426":{"protein_sequence":{"accession":"WP_128268241.1","sequence":"MNIKTLLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEVHSTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_063846.1","fmin":"33","fmax":"858","strand":"+","sequence":"ATGAACATTAAAACACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGTACACTCTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAACAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005946","ARO_id":"44408","ARO_name":"OXA-742","CARD_short_name":"OXA-742","ARO_description":"OXA-742 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5052":{"model_id":"5052","model_name":"OXA-743","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7427":{"protein_sequence":{"accession":"WP_128268242.1","sequence":"MNIKTLLLITSAIFISACSPYIVTANPNHSASKSVEKAEKIKNLFNEVHSTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_063847.1","fmin":"18","fmax":"843","strand":"+","sequence":"ATGAACATTAAAACACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGTTGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGTACACTCTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAACAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005947","ARO_id":"44409","ARO_name":"OXA-743","CARD_short_name":"OXA-743","ARO_description":"OXA-743 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5053":{"model_id":"5053","model_name":"OXA-744","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7428":{"protein_sequence":{"accession":"WP_128268243.1","sequence":"MNIKALLLITSTIFISACSPYIVTANPNHSTSKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEIFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNAVIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSLKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEMTYKSLEQLGIL"},"dna_sequence":{"accession":"NG_063848.1","fmin":"39","fmax":"864","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCACTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCACTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAATATTTAAGTGGGACGGGCAAAAAAGGCTGTTCCCAGAATGGGAAAAGGACATGACCCTAGGTGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGTTATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCTAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATGACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005948","ARO_id":"44410","ARO_name":"OXA-744","CARD_short_name":"OXA-744","ARO_description":"OXA-744 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5054":{"model_id":"5054","model_name":"OXA-745","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7429":{"protein_sequence":{"accession":"WP_128268244.1","sequence":"MNIKALLLITSAIFISACSPYIVTTNPNHSASKSDEKAEKIKNLFNETHTTGVLVIHQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKTTTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_063849.1","fmin":"33","fmax":"858","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTACTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAACACACACTACGGGTGTTTTAGTTATCCATCAAGGTCAAACTCAACAAAGCTACGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGACAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGACGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACGCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCATTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005949","ARO_id":"44411","ARO_name":"OXA-745","CARD_short_name":"OXA-745","ARO_description":"OXA-745 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5055":{"model_id":"5055","model_name":"OXA-746","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7430":{"protein_sequence":{"accession":"WP_128268245.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDKKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHYKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_063850.1","fmin":"23","fmax":"848","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATAAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTTAAAATGCTTAATGCTTTGATCGGCCTTGAGCATTATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCCGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005950","ARO_id":"44412","ARO_name":"OXA-746","CARD_short_name":"OXA-746","ARO_description":"OXA-746 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5056":{"model_id":"5056","model_name":"OXA-747","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7431":{"protein_sequence":{"accession":"WP_128268246.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPIHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_063851.1","fmin":"25","fmax":"850","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGTTCACCTTATATAGTGACTGCTAATCCAATTCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTGGGTTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005951","ARO_id":"44413","ARO_name":"OXA-747","CARD_short_name":"OXA-747","ARO_description":"OXA-747 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5057":{"model_id":"5057","model_name":"OXA-748","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7432":{"protein_sequence":{"accession":"WP_128268247.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSNEVKHVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_063852.1","fmin":"40","fmax":"865","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGTTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCATGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCTCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005952","ARO_id":"44414","ARO_name":"OXA-748","CARD_short_name":"OXA-748","ARO_description":"OXA-748 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5058":{"model_id":"5058","model_name":"OXA-749","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7433":{"protein_sequence":{"accession":"WP_128268248.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNANIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_063853.1","fmin":"29","fmax":"854","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGTTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAAATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTGGGTTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005953","ARO_id":"44415","ARO_name":"OXA-749","CARD_short_name":"OXA-749","ARO_description":"OXA-749 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5059":{"model_id":"5059","model_name":"OXA-750","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7434":{"protein_sequence":{"accession":"WP_128268249.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSIRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_063854.1","fmin":"14","fmax":"839","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGTTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCATTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTATTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005954","ARO_id":"44416","ARO_name":"OXA-750","CARD_short_name":"OXA-750","ARO_description":"OXA-750 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5060":{"model_id":"5060","model_name":"OXA-751","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7435":{"protein_sequence":{"accession":"WP_128268250.1","sequence":"MNIKALLLITSAIFISACSPYIVTANLNHSASKSDKKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWNGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_063855.1","fmin":"13","fmax":"838","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCTAAATCACAGCGCTTCAAAATCTGATAAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGAACGGGCAAAAAAGGCTGTTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005955","ARO_id":"44417","ARO_name":"OXA-751","CARD_short_name":"OXA-751","ARO_description":"OXA-751 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5061":{"model_id":"5061","model_name":"OXA-752","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7436":{"protein_sequence":{"accession":"WP_128268251.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDKKAEKNKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWNGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_063856.1","fmin":"13","fmax":"838","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATAAAAAAGCAGAGAAAAATAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGAACGGGCAAAAAAGGCTGTTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005956","ARO_id":"44418","ARO_name":"OXA-752","CARD_short_name":"OXA-752","ARO_description":"OXA-752 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5062":{"model_id":"5062","model_name":"OXA-753","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7437":{"protein_sequence":{"accession":"WP_128268252.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDKKAEKIKNLFNEAHTTGVLVIQQDQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWNGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_063857.1","fmin":"39","fmax":"864","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATAAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGACCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGAACGGGCAAAAAAGGCTGTTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCCCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005957","ARO_id":"44419","ARO_name":"OXA-753","CARD_short_name":"OXA-753","ARO_description":"OXA-753 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5063":{"model_id":"5063","model_name":"OXA-754","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7438":{"protein_sequence":{"accession":"WP_128268253.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDKKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWNGQKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_063858.1","fmin":"29","fmax":"854","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATAAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGAACGGGCAAAAAAGGCTGTTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGTTGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005958","ARO_id":"44420","ARO_name":"OXA-754","CARD_short_name":"OXA-754","ARO_description":"OXA-754 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5064":{"model_id":"5064","model_name":"OXA-755","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7439":{"protein_sequence":{"accession":"WP_128268254.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDKKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKILNALIGLEHHKATTTEVFKWNGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVIQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_063859.1","fmin":"13","fmax":"838","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATAAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATACTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGAACGGGCAAAAAAGGCTGTTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTATTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005959","ARO_id":"44421","ARO_name":"OXA-755","CARD_short_name":"OXA-755","ARO_description":"OXA-755 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5065":{"model_id":"5065","model_name":"OXA-756","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7440":{"protein_sequence":{"accession":"WP_128268255.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDKKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHYKATTTEVFKWNGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_063860.1","fmin":"40","fmax":"865","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATAAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACTATAAGGCAACCACCACAGAAGTATTTAAGTGGAACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTTATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005960","ARO_id":"44422","ARO_name":"OXA-756","CARD_short_name":"OXA-756","ARO_description":"OXA-756 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5066":{"model_id":"5066","model_name":"OXA-757","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7441":{"protein_sequence":{"accession":"WP_128268256.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDDKAEKIKNLFNEAHTTGVLVIHQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEIFKWDGQKRLFPEWEKDMPLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_063861.1","fmin":"40","fmax":"865","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGACAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCATCAAGGTCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAATATTTAAGTGGGACGGGCAAAAAAGGCTGTTCCCAGAATGGGAAAAGGACATGCCCCTAGGTGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005961","ARO_id":"44423","ARO_name":"OXA-757","CARD_short_name":"OXA-757","ARO_description":"OXA-757 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5067":{"model_id":"5067","model_name":"OXA-758","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7442":{"protein_sequence":{"accession":"WP_128268257.1","sequence":"MNIKALLLITSAIFISACSPYIVTTNPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNTDIGTQVDNFWLMGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLSIL"},"dna_sequence":{"accession":"NG_063862.1","fmin":"43","fmax":"868","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTACTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATACAGATATCGGTACCCAAGTCGATAATTTTTGGCTGATGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAAGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005962","ARO_id":"44424","ARO_name":"OXA-758","CARD_short_name":"OXA-758","ARO_description":"OXA-758 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5068":{"model_id":"5068","model_name":"OXA-759","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7443":{"protein_sequence":{"accession":"WP_128268258.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDDKAEKIKNLFNEAQTTGVLVIHQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWNGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_063863.1","fmin":"40","fmax":"865","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGACAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACAAACTACGGGTGTTTTAGTTATCCATCAAGGTCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACTTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGAACGGGCAAAAAAGGCTGTTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATTGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005963","ARO_id":"44425","ARO_name":"OXA-759","CARD_short_name":"OXA-759","ARO_description":"OXA-759 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5069":{"model_id":"5069","model_name":"OXA-760","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7444":{"protein_sequence":{"accession":"WP_128268259.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDDKAEKIKNLFNEAHTTGVLVIHQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWNGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEKKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_063864.1","fmin":"29","fmax":"854","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGACAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCATCAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGAACGGGCAAAAAAGGCTGTTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAAAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005964","ARO_id":"44426","ARO_name":"OXA-760","CARD_short_name":"OXA-760","ARO_description":"OXA-760 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5070":{"model_id":"5070","model_name":"OXA-761","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7445":{"protein_sequence":{"accession":"WP_128268260.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKNGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_063865.1","fmin":"14","fmax":"839","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGTTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCATTCTCCCTTAACTTAGAAATGAAAAATGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005965","ARO_id":"44427","ARO_name":"OXA-761","CARD_short_name":"OXA-761","ARO_description":"OXA-761 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5071":{"model_id":"5071","model_name":"OXA-762","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7446":{"protein_sequence":{"accession":"WP_128268261.1","sequence":"MNIKALLFITSAIFISACSPYIVTANPNHSASKSDDKAEKIKNLFNEAHTTGVLVIHQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWNGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_063866.1","fmin":"24","fmax":"849","strand":"+","sequence":"ATGAACATTAAAGCACTCTTATTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGACAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCATCAAGGTCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGAACGGGCAAAAAAGGCTGTTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005966","ARO_id":"44428","ARO_name":"OXA-762","CARD_short_name":"OXA-762","ARO_description":"OXA-762 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5072":{"model_id":"5072","model_name":"OXA-763","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7447":{"protein_sequence":{"accession":"WP_128268262.1","sequence":"MNIKALLLITSTIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALISLEHHKATTTEVFKWDGQKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_063867.1","fmin":"13","fmax":"838","strand":"+","sequence":"ATGAACATTAAAGCCCTCTTACTTATAACAAGCACTATTTTTATTTCAGCCTGCTCACCCTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTCTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCAGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCCTTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005967","ARO_id":"44429","ARO_name":"OXA-763","CARD_short_name":"OXA-763","ARO_description":"OXA-763 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5073":{"model_id":"5073","model_name":"OXA-764","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7448":{"protein_sequence":{"accession":"WP_128268263.1","sequence":"MTIKALLLITSAIFISACSPYIVSANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWNGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWIVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_063868.1","fmin":"47","fmax":"872","strand":"+","sequence":"ATGACCATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGTCTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGAACGGGCAAAAAAGGCTGTTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGATTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005968","ARO_id":"44430","ARO_name":"OXA-764","CARD_short_name":"OXA-764","ARO_description":"OXA-764 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5074":{"model_id":"5074","model_name":"OXA-765","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7449":{"protein_sequence":{"accession":"WP_128268264.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSTSKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWNGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_063869.1","fmin":"13","fmax":"838","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGTTCACCTTATATAGTGACTGCTAATCCAAATCACAGCACTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGAACGGGCAAAAAAGGCTGTTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005969","ARO_id":"44431","ARO_name":"OXA-765","CARD_short_name":"OXA-765","ARO_description":"OXA-765 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5075":{"model_id":"5075","model_name":"OXA-766","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7450":{"protein_sequence":{"accession":"WP_128268265.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFREWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLDQLGIL"},"dna_sequence":{"accession":"NG_063870.1","fmin":"40","fmax":"865","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCGAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACGCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCCTTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGACCAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005970","ARO_id":"44432","ARO_name":"OXA-766","CARD_short_name":"OXA-766","ARO_description":"OXA-766 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5076":{"model_id":"5076","model_name":"OXA-767","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7451":{"protein_sequence":{"accession":"WP_128268266.1","sequence":"MNIKALLLITSAIFISACSPYIVTTNPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNTDIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWIVQPQGNIVAFSFNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_063871.1","fmin":"36","fmax":"861","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTACTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATACAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGGTGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGATTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCTTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005971","ARO_id":"44433","ARO_name":"OXA-767","CARD_short_name":"OXA-767","ARO_description":"OXA-767 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5077":{"model_id":"5077","model_name":"OXA-768","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7452":{"protein_sequence":{"accession":"WP_128268267.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDKKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWGVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_063872.1","fmin":"12","fmax":"837","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATAAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATAGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGGTGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005972","ARO_id":"44434","ARO_name":"OXA-768","CARD_short_name":"OXA-768","ARO_description":"OXA-768 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5078":{"model_id":"5078","model_name":"OXA-769","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7453":{"protein_sequence":{"accession":"WP_128268268.1","sequence":"MNIKALLLITSAIFISACSPYIVSANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_063873.1","fmin":"18","fmax":"843","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGTCTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAATGGGATGGGCAAAAAAGGCTGTTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTACAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005973","ARO_id":"44435","ARO_name":"OXA-769","CARD_short_name":"OXA-769","ARO_description":"OXA-769 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5079":{"model_id":"5079","model_name":"OXA-770","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7454":{"protein_sequence":{"accession":"WP_128268269.1","sequence":"MNIKALLLITSAIFISACSPYIVSANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_063874.1","fmin":"33","fmax":"858","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGTCTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005974","ARO_id":"44436","ARO_name":"OXA-770","CARD_short_name":"OXA-770","ARO_description":"OXA-770 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5080":{"model_id":"5080","model_name":"OXA-771","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7455":{"protein_sequence":{"accession":"WP_128268270.1","sequence":"MNIKTLLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEVHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_063875.1","fmin":"35","fmax":"860","strand":"+","sequence":"ATGAACATTAAAACACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGTACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGACAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005975","ARO_id":"44437","ARO_name":"OXA-771","CARD_short_name":"OXA-771","ARO_description":"OXA-771 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5081":{"model_id":"5081","model_name":"OXA-772","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7456":{"protein_sequence":{"accession":"WP_128268271.1","sequence":"MNIKAPLLITSAIFIPACSPYIVTANPNHSASKSDEKAEKIKNIFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLKHHKATTTEVFKWDGQKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_063876.1","fmin":"42","fmax":"867","strand":"+","sequence":"ATGAACATTAAAGCACCCTTACTTATAACAAGCGCTATTTTTATTCCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATATATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTAAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCCGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTGGGTTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005976","ARO_id":"44438","ARO_name":"OXA-772","CARD_short_name":"OXA-772","ARO_description":"OXA-772 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5082":{"model_id":"5082","model_name":"OXA-773","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7457":{"protein_sequence":{"accession":"WP_128268272.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSNEKAEKIKNLFNKAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHRATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_063877.1","fmin":"23","fmax":"848","strand":"+","sequence":"ATGAATATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTAATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACAAAGCACACACTACGGGTGTCTTAGTTATCCAGCAAGGGCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAGGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGACGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005977","ARO_id":"44439","ARO_name":"OXA-773","CARD_short_name":"OXA-773","ARO_description":"OXA-773 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5083":{"model_id":"5083","model_name":"OXA-774","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7458":{"protein_sequence":{"accession":"WP_128268273.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_063878.1","fmin":"22","fmax":"847","strand":"+","sequence":"ATGAACATTAAAGCCCTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005978","ARO_id":"44440","ARO_name":"OXA-774","CARD_short_name":"OXA-774","ARO_description":"OXA-774 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5084":{"model_id":"5084","model_name":"OXA-775","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7459":{"protein_sequence":{"accession":"WP_128268274.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDKKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKDMALGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKIAPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_063879.1","fmin":"13","fmax":"838","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATAAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATAGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGGCCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTGCTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005979","ARO_id":"44441","ARO_name":"OXA-775","CARD_short_name":"OXA-775","ARO_description":"OXA-775 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5085":{"model_id":"5085","model_name":"OXA-776","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7460":{"protein_sequence":{"accession":"WP_128268275.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSEDKAEKIKNLFNEAHTTGVLVIHQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGEKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_063880.1","fmin":"15","fmax":"840","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGTGCTTCAAAATCTGAGGACAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCATCAAGGTCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAATGGGATGGGGAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005980","ARO_id":"44442","ARO_name":"OXA-776","CARD_short_name":"OXA-776","ARO_description":"OXA-776 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5086":{"model_id":"5086","model_name":"OXA-777","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7461":{"protein_sequence":{"accession":"WP_122630923.1","sequence":"MTKKALFFAIGTMFLSACSFNTVEQHQIQSISTNKNSKKIKSLFDQAQTEGVLVIKHGQTEEVYGNDLKRASTEYVPASTFKMVNALIGLEHHKATPTEVFKWDGQKRLFPDWEKDMTLGDAMKASAIPVYRELARRIGLDLMSKEVKRIGFGNADIGSKVDNFWLVGPLKITPQQEVQFAYKLAHKTLPFSKNVQEQVQSMLFIEEKNGRKIYAKSGWGWDVEPQVGWFTGWVVQPQGEIVAFSLNLEMKKGIPSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"NG_062346.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGACTAAAAAAGCTCTTTTCTTTGCCATTGGTACGATGTTTTTATCGGCATGTTCTTTTAATACGGTAGAACAGCATCAAATACAGTCAATTTCTACCAATAAAAACTCAAAGAAAATTAAATCATTGTTTGATCAAGCACAAACTGAAGGTGTTTTAGTTATAAAACATGGGCAAACAGAGGAAGTCTATGGCAATGATCTTAAAAGAGCATCAACCGAATATGTTCCCGCCTCTACCTTTAAAATGGTAAATGCTTTGATTGGACTTGAGCATCATAAAGCAACGCCAACTGAAGTGTTTAAATGGGATGGGCAAAAGCGTTTATTTCCCGATTGGGAAAAAGACATGACATTAGGCGATGCGATGAAAGCTTCTGCTATTCCAGTTTATCGGGAACTAGCTCGACGAATTGGCCTTGATCTTATGTCTAAAGAGGTAAAACGCATTGGTTTCGGTAATGCTGATATTGGTTCAAAAGTAGATAATTTTTGGCTTGTTGGCCCACTTAAAATTACACCTCAACAAGAAGTACAGTTTGCTTATAAATTAGCCCACAAAACTCTTCCCTTTAGCAAAAATGTACAAGAACAAGTTCAATCTATGCTGTTCATAGAAGAAAAAAATGGACGAAAAATTTATGCCAAAAGTGGTTGGGGATGGGATGTGGAGCCTCAAGTGGGCTGGTTTACAGGCTGGGTAGTTCAACCACAAGGAGAAATTGTAGCGTTCTCACTCAATTTAGAAATGAAGAAAGGCATACCTAGTTCTATTCGAAAAGAAATTGCTTATAAGGGATTAGAGCAGCTAGGTATTTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3005981","ARO_id":"44443","ARO_name":"OXA-777","CARD_short_name":"OXA-777","ARO_description":"OXA-777 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46495":{"category_aro_accession":"3007706","category_aro_cvterm_id":"46495","category_aro_name":"OXA-213-like beta-lactamase","category_aro_description":"OXA-213-like enzymes have been identified to be intrinsic to A. calcoaceticus and have been subsequently detected in A. pittii. Phylogenetic analysis of OXA-213-like proteins identified two distinct subgroups within the OXA family. The first group was linked to A. pittii and the second group to A. calcoaceticus. The carbapenemase activity of these OXAs may be related to the species-dependent effect.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5087":{"model_id":"5087","model_name":"OXA-778","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7462":{"protein_sequence":{"accession":"WP_122630924.1","sequence":"MTKKALFFAIGTMFLSACSFNTVEQHQIQSISTNKNSEKIKSLFDQAQTEGVLVIKRGQIEEVYGNDLKRASTEYVPASTFKMLNALIGLEHHKATPTEVFKWDGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLNLMSKEVKRIGFGNADIGSKVDNFWLVGPLKITPQQEAQFAYKLAHKTLPFSKNMQEQVQSMLFIEEKNGRKIYAKSGWGWDVEPQVGWLTGWVVQPQGEIIAFSLNLEMKKGIPSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"NG_062347.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGACTAAAAAAGCTCTTTTCTTTGCCATTGGTACGATGTTTTTATCGGCATGTTCTTTTAATACGGTAGAACAGCATCAAATACAGTCAATTTCTACCAATAAAAACTCAGAGAAAATTAAATCATTGTTTGATCAAGCACAAACTGAAGGTGTTTTAGTTATAAAACGTGGGCAAATAGAGGAAGTCTATGGCAATGATCTTAAAAGAGCATCAACCGAATATGTTCCCGCCTCTACCTTTAAAATGTTAAATGCTTTGATTGGACTTGAGCATCATAAAGCAACACCAACTGAAGTGTTTAAATGGGATGGGCAAAAGCGTTTATTTCCCGATTGGGAAAAAGACATGACATTAGGCGATGCGATGAAAGCTTCTGCTATTCCAGTTTATCAGGAACTAGCTCGACGAATTGGCCTTAATCTTATGTCTAAAGAGGTAAAACGTATTGGTTTCGGTAATGCTGATATTGGTTCAAAAGTAGATAATTTTTGGCTTGTTGGCCCACTTAAAATTACACCACAACAAGAAGCGCAGTTTGCTTACAAATTAGCCCACAAAACTCTTCCCTTTAGCAAAAATATGCAAGAACAAGTTCAATCTATGCTGTTCATAGAAGAAAAAAATGGACGGAAAATTTATGCCAAAAGTGGTTGGGGATGGGATGTGGAGCCTCAAGTGGGCTGGTTAACAGGCTGGGTCGTTCAACCACAAGGAGAAATTATAGCTTTCTCACTTAATTTAGAAATGAAAAAAGGCATACCTAGCTCTATTCGAAAAGAAATTGCTTATAAGGGATTGGAACAACTCGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3005982","ARO_id":"44444","ARO_name":"OXA-778","CARD_short_name":"OXA-778","ARO_description":"OXA-778 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46495":{"category_aro_accession":"3007706","category_aro_cvterm_id":"46495","category_aro_name":"OXA-213-like beta-lactamase","category_aro_description":"OXA-213-like enzymes have been identified to be intrinsic to A. calcoaceticus and have been subsequently detected in A. pittii. Phylogenetic analysis of OXA-213-like proteins identified two distinct subgroups within the OXA family. The first group was linked to A. pittii and the second group to A. calcoaceticus. The carbapenemase activity of these OXAs may be related to the species-dependent effect.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5088":{"model_id":"5088","model_name":"OXA-780","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7463":{"protein_sequence":{"accession":"WP_049637206.1","sequence":"MPRMLLSGLLAAGLFCALPASAASGCMLFADGTGKPVSTQGDCAAQLTPASTFKIPLALMGYDSGFLVDEQLPALPFKAGDPDFLPEWKQTTTPSSWMKNSVIWYSQRLTEWLGEARFQHYVDSFDYGNRDLEGNPGKHDGLTQAWLSASLAISPQEQARFLGKMVSGKLPVSAQTLRHTANLMRQPDIDGWQIHGKTGMGYPKLLDGSLDREQQIGWFVGWASKQGKTLIFVHTVIQKPGKQFASLRAREEVFAALPARLKTL"},"dna_sequence":{"accession":"NG_063881.1","fmin":"100","fmax":"895","strand":"+","sequence":"ATGCCCCGTATGCTGTTGTCCGGTCTGCTTGCTGCTGGCCTCTTCTGTGCACTGCCTGCCAGCGCCGCTTCTGGCTGCATGCTGTTTGCGGATGGAACCGGCAAACCCGTCAGCACCCAGGGGGACTGTGCCGCCCAGTTGACCCCGGCCTCCACCTTCAAGATCCCGCTGGCACTGATGGGCTATGACAGCGGCTTCCTGGTGGATGAACAACTGCCGGCCCTGCCGTTCAAGGCCGGTGATCCTGATTTCCTGCCGGAGTGGAAACAGACCACCACCCCGAGCAGCTGGATGAAGAACTCCGTCATCTGGTATTCCCAGCGCCTCACCGAGTGGCTGGGAGAGGCTCGCTTCCAGCACTACGTGGACAGCTTCGACTACGGCAACCGGGATCTCGAAGGCAACCCGGGCAAGCACGACGGTCTGACCCAGGCCTGGCTCAGCGCCAGCCTCGCCATCAGCCCCCAGGAGCAAGCCCGCTTCCTTGGCAAGATGGTGAGCGGCAAGCTGCCGGTCTCCGCCCAGACCCTGCGCCATACCGCCAACCTGATGCGTCAGCCCGACATCGACGGTTGGCAGATCCACGGCAAGACCGGCATGGGTTACCCCAAGCTGCTGGATGGCAGCCTGGACAGGGAGCAGCAGATCGGCTGGTTCGTCGGCTGGGCCAGCAAACAGGGCAAGACGCTCATCTTCGTCCACACCGTCATCCAGAAGCCGGGCAAGCAGTTCGCTTCCCTCAGGGCCAGGGAGGAGGTGTTCGCCGCCCTGCCGGCCCGGTTGAAGACACTCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37047","NCBI_taxonomy_name":"Aeromonas","NCBI_taxonomy_id":"642"}}}},"ARO_accession":"3005983","ARO_id":"44445","ARO_name":"OXA-780","CARD_short_name":"OXA-780","ARO_description":"OXA-780 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5089":{"model_id":"5089","model_name":"OXA-781","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7464":{"protein_sequence":{"accession":"WP_128268276.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALISLEHHKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGISSSVRKEITYRSLEQLGIL"},"dna_sequence":{"accession":"NG_063882.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCCCTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTCTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCAGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGACGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATATCTAGCTCTGTTCGAAAAGAGATTACTTATAGAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005984","ARO_id":"44446","ARO_name":"OXA-781","CARD_short_name":"OXA-781","ARO_description":"OXA-781 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5090":{"model_id":"5090","model_name":"OXA-782","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7465":{"protein_sequence":{"accession":"WP_128268277.1","sequence":"MNIKALLLITSAIFISACSPYIVTTNPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHRATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_063883.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTACTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAGGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGACGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005985","ARO_id":"44447","ARO_name":"OXA-782","CARD_short_name":"OXA-782","ARO_description":"OXA-782 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5091":{"model_id":"5091","model_name":"OXA-783","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7466":{"protein_sequence":{"accession":"WP_128268278.1","sequence":"MKKITLFLLFLNLVFGQDKILNNWFKEYNTSGTFVFYDGKTWASNDFSRAMETFSPASTFKIFNALIALDNGVVKNIKEIFYHYKGEKVFLPSWKQDASLSSAIKRSQVPAFKELARKIGLKTMQESLNKLSYGNAKISKIDTFWLDNSLQISAKNQADLLFKLSQNSLPFSKKSQEEVKKLLLFKENKIQKIYAKTGFNDNINLAWIVGFVKTKNKILSFALNVDIKHIKNIKIREELLEKYLAIITN"},"dna_sequence":{"accession":"NG_063884.1","fmin":"0","fmax":"750","strand":"+","sequence":"ATGAAAAAAATAACTTTATTTTTACTTTTCTTAAATTTAGTGTTTGGGCAAGATAAGATATTAAATAATTGGTTTAAAGAGTATAATACAAGCGGCACTTTTGTTTTTTATGATGGAAAAACTTGGGCGAGTAACGACTTTTCAAGGGCTATGGAGACTTTCTCTCCCGCTTCCACTTTTAAAATTTTTAATGCTTTAATTGCGCTTGATAATGGTGTAGTTAAAAATATAAAGGAAATTTTTTATCATTATAAGGGCGAAAAAGTATTTTTGCCCTCTTGGAAACAAGATGCTAGTTTAAGCTCAGCCATAAAACGCTCTCAAGTGCCTGCTTTTAAAGAATTGGCAAGAAAAATAGGACTTAAAACCATGCAAGAAAGCTTAAATAAACTTTCTTATGGAAATGCAAAAATTTCAAAAATCGATACCTTTTGGCTGGATAATTCTTTGCAAATTTCTGCAAAAAATCAAGCTGATTTACTTTTTAAACTTTCACAAAATTCTTTACCTTTTTCCAAGAAAAGTCAAGAAGAAGTTAAAAAACTTCTTCTTTTTAAAGAAAATAAAATACAAAAAATTTATGCCAAAACAGGTTTTAATGATAATATAAATTTAGCTTGGATTGTTGGATTCGTAAAGACTAAAAACAAAATTTTATCTTTTGCTTTAAATGTTGATATAAAGCACATTAAAAATATTAAAATAAGAGAAGAATTGCTAGAAAAATATCTAGCAATTATAACAAATTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36835","NCBI_taxonomy_name":"Campylobacter coli","NCBI_taxonomy_id":"195"}}}},"ARO_accession":"3005986","ARO_id":"44448","ARO_name":"OXA-783","CARD_short_name":"OXA-783","ARO_description":"OXA-783 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46491":{"category_aro_accession":"3007702","category_aro_cvterm_id":"46491","category_aro_name":"OXA-184-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-184.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5092":{"model_id":"5092","model_name":"OXA-784","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7467":{"protein_sequence":{"accession":"WP_065980086.1","sequence":"MKKITLFLLFLNLVFGQDKILNNWFKEYNTSGTFVFYDGKTWASNDFSRTMETFSPASTFKIFNALIALDSGVIKTKKEIFYHYRGEKVFLSSWAQDMNLSSAIKYSNVLAFKEVARRIGIKTMQEYLNKLHYGNAKISKIDTFWLDNSLKISAKEQAILLFRLSQNSLPFSQEAINSVKEMIYLKNMENLELFGKTGFNDEQKIAWIVGFVYLKDENKYKAFALNLDIDKFEDLYKREKILEKYLDELVKKVKNDG"},"dna_sequence":{"accession":"NG_063885.1","fmin":"0","fmax":"774","strand":"+","sequence":"ATGAAAAAAATAACTTTATTTTTACTTTTCTTAAATTTAGTGTTTGGGCAAGATAAGATATTAAATAATTGGTTTAAAGAGTATAATACAAGCGGCACTTTTGTTTTTTATGATGGAAAAACTTGGGCGAGTAACGACTTTTCAAGGACTATGGAGACTTTCTCTCCCGCTTCCACTTTTAAAATTTTTAATGCTCTAATTGCACTTGATAGTGGTGTGATAAAAACTAAAAAAGAAATTTTTTATCACTATAGAGGTGAAAAAGTATTTTTATCTTCTTGGGCGCAAGATATGAATTTAAGTTCAGCTATAAAATATTCTAATGTTCTTGCTTTTAAAGAAGTGGCAAGAAGAATTGGTATCAAAACTATGCAAGAATATTTAAACAAGCTTCATTATGGTAATGCTAAAATTTCCAAGATCGATACTTTTTGGCTTGACAACTCACTAAAAATAAGCGCTAAAGAACAAGCAATTTTGCTTTTTAGACTTTCACAAAATAGCTTACCTTTTTCTCAAGAAGCAATAAATAGTGTTAAGGAAATGATTTATTTAAAAAATATGGAAAATTTAGAGCTTTTTGGAAAAACAGGTTTTAATGATGAGCAAAAAATTGCTTGGATTGTAGGTTTTGTGTATTTAAAAGATGAAAATAAATATAAGGCTTTCGCGCTAAATTTAGATATTGATAAATTTGAAGATTTATATAAAAGAGAAAAAATTTTAGAAAAATATTTAGATGAACTTGTAAAAAAAGTTAAAAATGATGGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37052","NCBI_taxonomy_name":"Campylobacter","NCBI_taxonomy_id":"194"}}}},"ARO_accession":"3005987","ARO_id":"44449","ARO_name":"OXA-784","CARD_short_name":"OXA-784","ARO_description":"OXA-784 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46519":{"category_aro_accession":"3007730","category_aro_cvterm_id":"46519","category_aro_name":"OXA-61-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-61.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5093":{"model_id":"5093","model_name":"OXA-785","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7468":{"protein_sequence":{"accession":"WP_126205827.1","sequence":"MKKILLLFSLFYSFALANDKLKDFFKDYNTSGVFITFDGKHYASNDFKRAKEPFSPASTFKIFNALIALDNGVVKDTKEIFYHYKGEKVFLPSWKQDASLSSAIKRSQVPAFKELARKIGLKTMQESLNKLSYGNAKISKIDTFWLDNSLQISAKNQADLLFKLSQNSLPFSKKSQEEVKKIILFKEDKIQKIYAKTGFNDGVNLAWIVGFIESKNKILSFALNVDIKNIKNLKIREELLEKYIYSLN"},"dna_sequence":{"accession":"NG_063886.1","fmin":"0","fmax":"747","strand":"+","sequence":"TTGAAAAAAATACTTTTACTTTTTAGTCTTTTTTACTCTTTTGCTTTGGCAAATGATAAATTAAAAGATTTTTTTAAAGACTACAATACAAGCGGAGTTTTTATAACTTTTGATGGAAAACATTATGCAAGTAATGATTTTAAAAGAGCTAAAGAACCTTTTTCTCCTGCTTCGACTTTTAAAATTTTTAATGCTTTAATTGCGCTTGATAACGGTGTAGTTAAAGATACAAAGGAAATTTTTTATCATTATAAGGGTGAAAAAGTATTTTTGCCTTCTTGGAAACAAGATGCTAGTTTAAGCTCAGCCATAAAACGCTCTCAAGTGCCTGCTTTTAAAGAATTGGCAAGAAAAATAGGACTTAAAACCATGCAAGAAAGCTTAAATAAACTTTCCTATGGAAATGCAAAAATTTCAAAAATCGATACCTTTTGGTTGGATAATTCTTTACAAATTTCTGCAAAAAATCAAGCTGATTTGCTTTTTAAACTTTCACAAAATTCTTTACCTTTTTCCAAGAAAAGTCAAGAAGAAGTTAAAAAAATTATTCTTTTTAAAGAAGATAAAATCCAAAAAATTTATGCTAAAACAGGTTTTAATGATGGTGTAAATTTGGCTTGGATTGTCGGATTTATAGAGAGTAAAAACAAAATTTTATCTTTTGCCTTAAATGTTGATATAAAGAATATTAAAAATCTTAAAATAAGAGAAGAATTACTAGAAAAATATATTTATTCTTTAAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36772","NCBI_taxonomy_name":"Campylobacter jejuni","NCBI_taxonomy_id":"197"}}}},"ARO_accession":"3005988","ARO_id":"44450","ARO_name":"OXA-785","CARD_short_name":"OXA-785","ARO_description":"OXA-785 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46491":{"category_aro_accession":"3007702","category_aro_cvterm_id":"46491","category_aro_name":"OXA-184-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-184.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5094":{"model_id":"5094","model_name":"OXA-786","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7469":{"protein_sequence":{"accession":"WP_128268279.1","sequence":"MKKITLFLLFLNLVFGQDKILNNWFKEYNTSGTFVFYDGKTWASNDFSRAMETFSPASTFKIFNALIALDSGVIKTKKEIFYHYRGEKVFLSSWAQDMNLSSAIKYSNVLAFKEVARRIGIKTMQEYLNKLHYGNAKISKIDTFWLDNSLKISAKEQAILLFRLSQNSLPFSQEAMNSVKEMIYLKNMENLELFGKTGFNDEQKIAWIVGFVYLKDENKYKAFALNLDIDKFEDLYKREKNFRKIFR"},"dna_sequence":{"accession":"NG_063887.1","fmin":"0","fmax":"744","strand":"+","sequence":"ATGAAAAAAATAACTTTATTTTTACTTTTCTTAAATTTAGTGTTTGGGCAAGATAAGATATTAAATAATTGGTTTAAAGAGTATAATACAAGCGGCACTTTTGTTTTTTATGATGGAAAAACTTGGGCGAGTAACGACTTTTCAAGGGCTATGGAGACTTTCTCTCCCGCTTCCACTTTTAAAATTTTTAATGCTCTAATTGCACTTGATAGTGGTGTGATAAAAACTAAAAAAGAAATTTTTTATCACTATAGAGGTGAAAAAGTATTTTTATCTTCTTGGGCGCAAGATATGAATTTAAGTTCAGCTATAAAATATTCTAATGTTCTTGCTTTTAAAGAAGTGGCAAGAAGAATTGGTATCAAAACTATGCAAGAATATTTAAACAAGCTTCATTATGGTAATGCTAAAATTTCCAAGATCGATACTTTTTGGCTTGACAACTCACTAAAAATAAGCGCTAAAGAACAAGCAATTTTGCTTTTTAGACTTTCACAAAATAGCTTACCTTTTTCTCAAGAAGCAATGAATAGTGTTAAGGAAATGATTTATTTAAAAAATATGGAAAATTTAGAGCTTTTTGGAAAAACAGGTTTTAATGATGAGCAAAAAATTGCTTGGATTGTAGGTTTTGTGTATTTAAAAGATGAAAATAAATATAAGGCTTTCGCGCTAAATTTAGATATTGATAAATTTGAAGATTTATATAAAAGAGAAAAAAATTTTAGAAAAATATTTAGATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36772","NCBI_taxonomy_name":"Campylobacter jejuni","NCBI_taxonomy_id":"197"}}}},"ARO_accession":"3005989","ARO_id":"44451","ARO_name":"OXA-786","CARD_short_name":"OXA-786","ARO_description":"OXA-786 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46519":{"category_aro_accession":"3007730","category_aro_cvterm_id":"46519","category_aro_name":"OXA-61-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-61.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5095":{"model_id":"5095","model_name":"OXA-787","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7470":{"protein_sequence":{"accession":"WP_136512083.1","sequence":"MPLRLPLRALGAALSLFALAGAPARAAVLCTVVADAADGRIVFQQGTQAACAERYTPASTFKLPIALMGADAGILQGPHAPVWNYQPGYPDWGGDAWRQPTDPARWIKYSVVWYSQLTARALGQERFQRYASAFQYGNEDVSGEPGKHNGLDGAWINSSLRISPLEQLAFLRKLVNRQLPLKPAAYDLAETLFDAGEAGGWRLYGKTGTGSPGSNGVYTPDNAYGWFVGWARKDGRQLVFARLLQDEKATRPNAGLRARDKLLREWPAMADAPRQ"},"dna_sequence":{"accession":"NG_064748.1","fmin":"0","fmax":"828","strand":"+","sequence":"ATGCCCCTCCGACTCCCTTTGCGCGCCCTCGGCGCGGCCCTGTCCCTGTTCGCGCTGGCCGGCGCCCCCGCCCGCGCGGCGGTTTTGTGCACCGTGGTGGCCGACGCCGCCGACGGCCGCATCGTGTTCCAGCAAGGCACGCAGGCGGCCTGCGCCGAGCGCTACACGCCCGCCTCGACCTTCAAGCTGCCGATCGCGCTGATGGGCGCGGACGCGGGCATCCTGCAAGGCCCGCACGCGCCAGTCTGGAACTACCAGCCGGGCTACCCCGACTGGGGCGGCGACGCCTGGCGCCAGCCGACGGACCCGGCGCGCTGGATCAAGTATTCGGTGGTCTGGTACTCACAACTGACCGCCCGGGCGCTGGGGCAGGAGCGCTTCCAGCGCTACGCCTCGGCCTTCCAGTACGGCAACGAGGACGTCTCGGGCGAGCCCGGCAAGCACAACGGCCTGGACGGCGCGTGGATCAACTCGTCGCTGCGCATTTCGCCGCTGGAGCAACTGGCGTTCCTGCGCAAGCTGGTCAACCGCCAATTGCCGCTCAAGCCCGCGGCCTACGATCTGGCCGAGACGCTGTTCGACGCCGGCGAGGCCGGCGGCTGGCGCCTGTATGGCAAGACCGGCACCGGCTCGCCGGGCAGCAACGGCGTCTACACGCCGGACAACGCCTACGGCTGGTTCGTCGGCTGGGCGCGCAAGGACGGCCGCCAACTGGTGTTCGCGCGCCTGCTGCAGGACGAGAAAGCCACCCGGCCCAATGCCGGCCTGCGCGCCCGCGACAAGCTGTTGCGCGAGTGGCCAGCCATGGCCGACGCGCCCCGCCAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42832","NCBI_taxonomy_name":"Achromobacter dolens","NCBI_taxonomy_id":"1287738"}}}},"ARO_accession":"3005990","ARO_id":"44452","ARO_name":"OXA-787","CARD_short_name":"OXA-787","ARO_description":"OXA-787 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46505":{"category_aro_accession":"3007716","category_aro_cvterm_id":"46505","category_aro_name":"OXA-364-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-364.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5096":{"model_id":"5096","model_name":"OXA-788","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7471":{"protein_sequence":{"accession":"WP_136512084.1","sequence":"MRVLALSAVFLVASIIGMPAVAKEWQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGQTRDIATWNRDHNLITAMKYSVLPVYQEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISATEQISFLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYDTKIGWWVGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP"},"dna_sequence":{"accession":"NG_064749.1","fmin":"0","fmax":"786","strand":"+","sequence":"ATGCGTGTATTAGCCTTATCGGCTGTGTTTTTGGTGGCATCGATTATCGGAATGCCTGCGGTAGCAAAGGAATGGCAAGAAAACAAAAGTTGGAATGCTCACTTTACTGAACATAAATCACAGGGCGTAGTTGTGCTCTGGAATGAGAATAAGCAGCAAGGATTTACCAATAATCTTAAACGGGCGAACCAAGCATTTTTACCCGCATCTACCTTTAAAATTCCCAATAGCTTGATCGCCCTCGATTTGGGCGTGGTTAAGGATGAACACCAAGTCTTTAAGTGGGATGGACAGACGCGCGATATCGCCACTTGGAATCGCGATCATAATCTAATCACCGCGATGAAATATTCAGTTTTGCCTGTTTATCAAGAATTTGCCCGCCAAATTGGCGAGGCACGTATGAGCAAGATGCTACATGCTTTCGATTATGGTAATGAGGACATTTCGGGCAATGTAGACAGTTTCTGGCTCGACGGTGGTATTCGAATTTCGGCCACGGAGCAAATCAGCTTTTTAAGAAAGCTGTATCACAATAAGTTACACGTATCGGAGCGCAGCCAGCGTATTGTCAAACAAGCCATGCTGACCGAAGCCAATGGCGACTATATTATTCGGGCTAAAACTGGATACGATACTAAGATTGGCTGGTGGGTCGGTTGGGTTGAACTTGATGATAATGTGTGGTTTTTTGCGATGAATATGGATATGCCCACATCGGATGGTTTAGGGCTGCGCCAAGCCATCACAAAAGAAGTGCTCAAACAGGAAAAAATTATTCCCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36946","NCBI_taxonomy_name":"Providencia stuartii","NCBI_taxonomy_id":"588"}}}},"ARO_accession":"3005991","ARO_id":"44453","ARO_name":"OXA-788","CARD_short_name":"OXA-788","ARO_description":"OXA-788 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46510":{"category_aro_accession":"3007721","category_aro_cvterm_id":"46510","category_aro_name":"OXA-48-like beta-lactamase","category_aro_description":"OXA-48-type beta-lactamases are now routinely encountered in bacterial infections caused by carbapenam-resistant Enterobacterales. OXA-48-like proteins confer resistance to penicillin (which is efficiently hydrolyzed) and carbapenam antibiotics (which is more slowly broken down). The spectrum of activity of these variants varies, with some hydrolyzing expanded-spectrum oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5097":{"model_id":"5097","model_name":"OXA-789","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7472":{"protein_sequence":{"accession":"WP_054500785.1","sequence":"MPLRLPLRALGAALSLFALAGAPARAAVLCTVVADAADGRIVFQQGTQAACAERYTPASTFKLPIALMGADAGILQGPHAPVWNYQPGYPDWGGDAWRQPTDPARWIKYSVVWYSQLTARALGQERFQRYASAFQYGNEDVSGEPGKHNGLDGAWINSSLRISPLEQLAFLRKLVNRQLPLKPAAYDLAETLFDAGEAGGWRLYGKTGTGSPGSNGVYTPDNAYGWFVGWARKDGRQLVFARLLQDEKATRPNAGLRARDELLREWPAMADAPRQ"},"dna_sequence":{"accession":"NG_064750.1","fmin":"0","fmax":"828","strand":"+","sequence":"ATGCCCCTCCGACTCCCTTTGCGCGCCCTCGGCGCGGCCCTGTCCCTGTTCGCGCTGGCCGGCGCCCCCGCCCGCGCGGCGGTTTTGTGCACCGTGGTGGCCGACGCCGCCGACGGCCGCATCGTGTTCCAGCAAGGCACGCAGGCGGCCTGCGCCGAGCGCTACACGCCCGCCTCGACCTTCAAGCTGCCGATCGCGCTGATGGGCGCGGACGCGGGCATCCTGCAAGGCCCGCACGCGCCAGTCTGGAACTACCAGCCGGGCTACCCCGACTGGGGCGGCGACGCCTGGCGCCAGCCGACGGACCCGGCGCGCTGGATCAAGTATTCGGTGGTCTGGTACTCACAACTGACCGCCCGGGCGCTGGGGCAGGAGCGCTTCCAGCGCTACGCCTCGGCCTTCCAGTACGGCAACGAGGACGTCTCGGGCGAGCCCGGCAAGCACAACGGCCTGGACGGCGCGTGGATCAACTCGTCGCTGCGCATTTCGCCGCTGGAGCAACTGGCGTTCCTGCGCAAGCTGGTCAACCGCCAATTGCCGCTCAAGCCCGCGGCCTACGATCTGGCCGAGACGCTGTTCGACGCCGGCGAGGCCGGCGGCTGGCGCCTGTATGGCAAGACCGGCACCGGCTCGCCGGGCAGCAACGGCGTCTACACGCCGGACAACGCCTACGGCTGGTTCGTCGGCTGGGCGCGCAAGGACGGCCGCCAACTGGTGTTCGCGCGCCTGCTGCAGGACGAGAAAGCCACCCGGCCCAATGCCGGCCTGCGCGCCCGCGACGAGCTGTTGCGCGAGTGGCCAGCCATGGCCGACGCGCCCCGCCAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42832","NCBI_taxonomy_name":"Achromobacter dolens","NCBI_taxonomy_id":"1287738"}}}},"ARO_accession":"3005992","ARO_id":"44454","ARO_name":"OXA-789","CARD_short_name":"OXA-789","ARO_description":"OXA-789 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46505":{"category_aro_accession":"3007716","category_aro_cvterm_id":"46505","category_aro_name":"OXA-364-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-364.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5098":{"model_id":"5098","model_name":"OXA-793","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7473":{"protein_sequence":{"accession":"WP_136512085.1","sequence":"MRVLALSAVFLVASIIGMPAVAKEWQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGQTRDIATWNRDHNLITAMKYSVVPVYQEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISATEQISFLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYSTRPKIGWWVGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP"},"dna_sequence":{"accession":"NG_064751.1","fmin":"0","fmax":"792","strand":"+","sequence":"ATGCGTGTATTAGCCTTATCGGCTGTGTTTTTGGTGGCATCGATTATCGGAATGCCTGCGGTAGCAAAGGAATGGCAAGAAAACAAAAGTTGGAATGCTCACTTTACTGAACATAAATCACAGGGCGTAGTTGTGCTCTGGAATGAGAATAAGCAGCAAGGATTTACCAATAATCTTAAACGGGCGAACCAAGCATTTTTACCCGCATCTACCTTTAAAATTCCCAATAGCTTGATCGCCCTCGATTTGGGCGTGGTTAAGGATGAACACCAAGTCTTTAAGTGGGATGGACAGACGCGCGATATCGCCACTTGGAATCGCGATCATAATCTAATCACCGCGATGAAATATTCAGTTGTGCCTGTTTATCAAGAATTTGCCCGCCAAATTGGCGAGGCACGTATGAGCAAGATGCTACATGCTTTCGATTATGGTAATGAGGACATTTCGGGCAATGTAGACAGTTTCTGGCTCGACGGTGGTATTCGAATTTCGGCCACGGAGCAAATCAGCTTTTTAAGAAAGCTGTATCACAATAAGTTACACGTATCGGAGCGCAGCCAGCGTATTGTCAAACAAGCCATGCTGACCGAAGCCAATGGTGACTATATTATTCGGGCTAAAACTGGATACTCGACTAGACCTAAGATTGGCTGGTGGGTCGGTTGGGTTGAACTTGATGATAATGTGTGGTTTTTTGCGATGAATATGGATATGCCCACATCGGATGGTTTAGGGCTGCGCCAAGCCATCACAAAAGAAGTGCTCAAACAGGAAAAAATTATTCCCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3005993","ARO_id":"44455","ARO_name":"OXA-793","CARD_short_name":"OXA-793","ARO_description":"OXA-793 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46510":{"category_aro_accession":"3007721","category_aro_cvterm_id":"46510","category_aro_name":"OXA-48-like beta-lactamase","category_aro_description":"OXA-48-type beta-lactamases are now routinely encountered in bacterial infections caused by carbapenam-resistant Enterobacterales. OXA-48-like proteins confer resistance to penicillin (which is efficiently hydrolyzed) and carbapenam antibiotics (which is more slowly broken down). The spectrum of activity of these variants varies, with some hydrolyzing expanded-spectrum oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5099":{"model_id":"5099","model_name":"OXA-794","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7474":{"protein_sequence":{"accession":"WP_136512086.1","sequence":"MKTFAAYVIIACLSSTALAGSITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFCLEGQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGIIGG"},"dna_sequence":{"accession":"NG_064752.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGAAAACATTTGCCGCATATGTAATTATCGCGTGTCTTTCGAGTACGGCATTAGCTGGTTCAATTACAGAAAATACGTCTTGGAACAAAGAGTTCTCTGCCGAAGCCGTCAATGGTGTCTTCGTGCTTTGTAAAAGTAGCAGTAAATCCTGCGCTACCAATGACTTAGCTCGTGCATCAAAGGAATATCTTCCAGCATCAACATTTAAGATCCCCAACGCAATTATCGGCCTAGAAACTGGTGTCATAAAGAATGAGCATCAGGTTTTCAAATGGGACGGAAAGCCAAGAGCCATGAAGCAATGGGAAAGAGACTTGACCTTAAGAGGGGCAATACAAGTTTCAGCTGTTCCCGTATTTCAACAAATCGCCAGAGAAGTTGGCGAAGTAAGAATGCAGAAATACCTTAAAAAATTTTCCTATGGCAACCAGAATATCAGTGGTGGCATTGACAAATTCTGTTTGGAAGGCCAGCTTAGAATTTCCGCAGTTAATCAAGTGGAGTTTCTAGAGTCTCTATATTTAAATAAATTGTCAGCATCTAAAGAAAACCAGCTAATAGTAAAAGAGGCTTTGGTAACGGAGGCGGCACCTGAATATCTAGTGCATTCAAAAACTGGTTTTTCTGGTGTGGGAACTGAGTCAAATCCTGGTGTCGCATGGTGGGTTGGGTGGGTTGAGAAGGAGACAGAGGTTTACTTTTTCGCCTTTAACATGGATATAGACAACGAAAGTAAGTTGCCGCTAAGAAAATCCATTCCCACCAAAATCATGGAAAGTGAGGGCATCATTGGTGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005994","ARO_id":"44456","ARO_name":"OXA-794","CARD_short_name":"OXA-794","ARO_description":"OXA-794 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46486":{"category_aro_accession":"3007697","category_aro_cvterm_id":"46486","category_aro_name":"OXA-10-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-10.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5100":{"model_id":"5100","model_name":"OXA-795","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7475":{"protein_sequence":{"accession":"WP_136512087.1","sequence":"MKTFAAYVIIACLSSTALAGSITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKLEGQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGIIGG"},"dna_sequence":{"accession":"NG_064753.1","fmin":"0","fmax":"795","strand":"+","sequence":"ATGAAAACATTTGCCGCATATGTAATTATCGCGTGTCTTTCGAGTACGGCATTAGCTGGTTCAATTACAGAAAATACGTCTTGGAACAAAGAGTTCTCTGCCGAAGCCGTCAATGGTGTCTTCGTGCTTTGTAAAAGTAGCAGTAAATCCTGCGCTACCAATGACTTAGCTCGTGCATCAAAGGAATATCTTCCAGCATCAACATTTAAGATCCCCAACGCAATTATCGGCCTAGAAACTGGTGTCATAAAGAATGAGCATCAGGTTTTCAAATGGGACGGAAAGCCAAGAGCCATGAAGCAATGGGAAAGAGACTTGACCTTAAGAGGGGCAATACAAGTTTCAGCTGTTCCCGTATTTCAACAAATCGCCAGAGAAGTTGGCGAAGTAAGAATGCAGAAATACCTTAAAAAATTTTCCTATGGCAACCAGAATATCAGTGGTGGCATTGACAAATTGGAAGGCCAGCTTAGAATTTCCGCAGTTAATCAAGTGGAGTTTCTAGAGTCTCTATATTTAAATAAATTGTCAGCATCTAAAGAAAACCAGCTAATAGTAAAAGAGGCTTTGGTAACGGAGGCGGCACCTGAATATCTAGTGCATTCAAAAACTGGTTTTTCTGGTGTGGGAACTGAGTCAAATCCTGGTGTCGCATGGTGGGTTGGGTGGGTTGAGAAGGAGACAGAGGTTTACTTTTTCGCCTTTAACATGGATATAGACAACGAAAGTAAGTTGCCGCTAAGAAAATCCATTCCCACCAAAATCATGGAAAGTGAGGGCATCATTGGTGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005995","ARO_id":"44457","ARO_name":"OXA-795","CARD_short_name":"OXA-795","ARO_description":"OXA-795 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46486":{"category_aro_accession":"3007697","category_aro_cvterm_id":"46486","category_aro_name":"OXA-10-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-10.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5101":{"model_id":"5101","model_name":"OXA-796","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7476":{"protein_sequence":{"accession":"WP_110612827.1","sequence":"MKNTIHINFAIFLIIANIIYSSASASTDISTVASPLFEGTEGCFLLYDVSTNAEIAQFNKAKCATQMAPDSTFKIALSLMAFDAEIIDQKTIFKWDKTPKGMEIWNSNHTPKTWMQFSVVWVSQEITQKIGLNKIKNYLKDFDYGNQDFSGDKERNNGLTEAWLESSLKISPEEQIQFLRKIINHNLPVKNSAIENTIENMYLQDLDNSTKLYGKTGAGFTANRTLQNGWFEGFIISKSGHKYVFVSALTGNLGSNLTSSIKAKKNAITILNTLNL"},"dna_sequence":{"accession":"NG_064754.1","fmin":"100","fmax":"931","strand":"+","sequence":"ATGAAAAACACAATACATATCAACTTCGCTATTTTTTTAATAATTGCAAATATTATCTACAGCAGCGCCAGTGCATCAACAGATATCTCTACTGTTGCATCTCCATTATTTGAAGGAACTGAAGGTTGTTTTTTACTTTACGATGTATCCACAAACGCTGAAATTGCTCAATTCAATAAAGCAAAGTGTGCAACGCAAATGGCACCAGATTCAACTTTCAAGATCGCATTATCACTTATGGCATTTGATGCGGAAATAATAGATCAGAAAACCATATTCAAATGGGATAAAACCCCCAAAGGAATGGAGATCTGGAACAGCAATCATACACCAAAGACGTGGATGCAATTTTCTGTTGTTTGGGTTTCGCAAGAAATAACCCAAAAAATTGGATTAAATAAAATCAAGAATTATCTCAAAGATTTTGATTATGGAAATCAAGACTTCTCTGGAGATAAAGAAAGAAACAACGGATTAACAGAAGCATGGCTCGAAAGTAGCTTAAAAATTTCACCAGAAGAACAAATTCAATTCCTGCGTAAAATTATTAATCACAATCTCCCAGTTAAAAACTCAGCCATAGAAAACACCATAGAGAACATGTATCTACAAGATCTGGATAATAGTACAAAACTGTATGGGAAAACTGGTGCAGGATTCACAGCAAATAGAACCTTACAAAACGGATGGTTTGAAGGGTTTATTATAAGCAAATCAGGACATAAATATGTTTTTGTGTCCGCACTTACAGGAAACTTGGGGTCGAATTTAACATCAAGCATAAAAGCCAAGAAAAATGCGATCACCATTCTAAACACACTAAATTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"45688","NCBI_taxonomy_name":"Proteus sp. VIITMP5","NCBI_taxonomy_id":"1009030"}}}},"ARO_accession":"3005996","ARO_id":"44458","ARO_name":"OXA-796","CARD_short_name":"OXA-796","ARO_description":"OXA-796 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46485":{"category_aro_accession":"3007696","category_aro_cvterm_id":"46485","category_aro_name":"OXA-1-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-1.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5102":{"model_id":"5102","model_name":"OXA-797","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7477":{"protein_sequence":{"accession":"WP_136512088.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHRKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_064755.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCGTAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005997","ARO_id":"44459","ARO_name":"OXA-797","CARD_short_name":"OXA-797","ARO_description":"OXA-797 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5103":{"model_id":"5103","model_name":"OXA-798","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7478":{"protein_sequence":{"accession":"WP_136512089.1","sequence":"MNIKAPLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNIFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHYKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRIGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGISSSVRKEITYRSLEQLGIL"},"dna_sequence":{"accession":"NG_064756.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACCCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATATATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCATTATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCCGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTATTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAACAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATATCTAGCTCTGTTCGAAAAGAGATTACTTATAGAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005998","ARO_id":"44460","ARO_name":"OXA-798","CARD_short_name":"OXA-798","ARO_description":"OXA-798 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5104":{"model_id":"5104","model_name":"OXA-799","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7479":{"protein_sequence":{"accession":"WP_136512090.1","sequence":"MNIKALLLITSAIFISACSPYIVTTNPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNPLIGLEHHRATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_064757.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTACTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATCCTTTGATCGGCCTTGAGCACCATAGGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGACGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3005999","ARO_id":"44461","ARO_name":"OXA-799","CARD_short_name":"OXA-799","ARO_description":"OXA-799 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5105":{"model_id":"5105","model_name":"OXA-800","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7480":{"protein_sequence":{"accession":"WP_136512091.1","sequence":"MNIKALLLITSAIFISACSPYIVSANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGISSSVRKEITYRSLEQLGIL"},"dna_sequence":{"accession":"NG_064758.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGTCTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACTACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAACAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATATCTAGCTCTGTTCGAAAAGAGATTACTTATAGAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006000","ARO_id":"44462","ARO_name":"OXA-800","CARD_short_name":"OXA-800","ARO_description":"OXA-800 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5106":{"model_id":"5106","model_name":"OXA-801","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7481":{"protein_sequence":{"accession":"WP_136512092.1","sequence":"MTKKALFFAISAIFLSACSFNTVQQHQIHAISTHKNSEEIKSLFDQAQTTGVLVIKRGQTEEIYGNDLKRASTEYVPASTFKMLNALIGLEHHKATTTEMFKWDGQKRLFPDWEKDMTLGEAMKASAIPVYQELARRIGLDLMSKEVKRIGFGNADIGSKVDNFWLVGPLKITPQQETQFAYELAHKTLPFSKNVQEQVQSMVFVEEKNGRKIYAKSGWGLDMDPQVGWLTGWVVQPQGEIVAFSLNLEMKKGIPSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"NG_064759.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGACTAAAAAAGCTCTTTTCTTTGCTATTAGTGCCATATTTTTGTCAGCATGTTCTTTCAATACAGTACAACAGCACCAAATACACGCTATTTCTACTCATAAAAATTCAGAAGAAATTAAATCACTGTTTGATCAGGCACAGACCACGGGAGTTTTAGTGATTAAGCGTGGGCAAACCGAAGAAATTTATGGCAATGATCTTAAAAGAGCATCAACCGAATATGTTCCCGCCTCTACATTTAAAATGCTAAATGCTTTAATTGGACTTGAACATCATAAAGCAACGACAACTGAAATGTTCAAATGGGATGGACAAAAGCGTTTATTTCCTGATTGGGAAAAGGATATGACTCTGGGTGAGGCCATGAAAGCTTCTGCTATTCCTGTCTATCAAGAACTAGCGCGAAGAATTGGCCTTGATCTTATGTCCAAAGAGGTCAAGCGTATTGGTTTCGGTAATGCTGATATTGGTTCAAAAGTAGATAATTTTTGGCTTGTTGGTCCCCTTAAAATTACACCTCAGCAAGAAACCCAATTTGCTTATGAATTAGCACATAAAACTCTTCCCTTTAGCAAAAATGTACAAGAACAAGTTCAATCTATGGTGTTCGTAGAAGAAAAAAACGGACGTAAAATTTACGCTAAAAGCGGTTGGGGATTGGATATGGATCCTCAAGTTGGCTGGTTAACAGGCTGGGTCGTTCAACCACAAGGAGAAATTGTGGCATTCTCGCTCAATTTAGAAATGAAAAAAGGCATACCTAGTTCTATCCGAAAAGAAATTGCTTATAAGGGATTAGAGCAGCTAGGTATTTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3006001","ARO_id":"44463","ARO_name":"OXA-801","CARD_short_name":"OXA-801","ARO_description":"OXA-801 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46495":{"category_aro_accession":"3007706","category_aro_cvterm_id":"46495","category_aro_name":"OXA-213-like beta-lactamase","category_aro_description":"OXA-213-like enzymes have been identified to be intrinsic to A. calcoaceticus and have been subsequently detected in A. pittii. Phylogenetic analysis of OXA-213-like proteins identified two distinct subgroups within the OXA family. The first group was linked to A. pittii and the second group to A. calcoaceticus. The carbapenemase activity of these OXAs may be related to the species-dependent effect.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5107":{"model_id":"5107","model_name":"OXA-802","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7482":{"protein_sequence":{"accession":"WP_136512093.1","sequence":"MTKRALFFAISTIFLSACSFNTVQQHQIHTISTHKNSEEIKSLFDQAQTTGVLVIKRGQTEEIYGNDLKRASTEYVPASTFKMLNALIGLEHHKATTTEMFKWDGQKRLFPDWEKDMTLGEAMKASAIPVYQELARRIGLDLMSKEVKRIGFGNADIGSKVDNFWLVGPLKITPQQEVQFAYELAHKTLPFSKNVQEQVQSMVLVEEKNGRKIYAKSGWGWDVDPQVGWLTGWVVQPQGEIVAFSLNLEMKKGTPSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"NG_064760.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGACTAAAAGAGCTCTTTTCTTTGCTATTAGTACCATATTTTTGTCAGCATGTTCTTTCAATACAGTACAACAGCACCAAATACACACTATTTCTACTCATAAAAATTCAGAAGAAATTAAATCACTGTTTGATCAGGCACAGACCACGGGAGTTTTAGTGATTAAGCGTGGGCAAACCGAAGAAATTTATGGCAATGATCTTAAAAGAGCATCAACCGAATATGTTCCCGCCTCTACCTTTAAAATGTTAAATGCTTTGATTGGACTTGAGCACCATAAAGCGACGACAACTGAAATGTTCAAATGGGATGGACAAAAGCGTTTGTTTCCTGATTGGGAAAAAGATATGACTCTGGGTGAGGCGATGAAAGCTTCTGCTATTCCTGTCTATCAAGAACTAGCTCGACGAATTGGCCTTGATCTTATGTCCAAAGAAGTCAAACGTATTGGTTTCGGTAATGCCGATATTGGTTCAAAAGTAGATAATTTTTGGCTTGTCGGTCCACTCAAAATTACGCCTCAGCAGGAAGTACAGTTTGCTTATGAATTAGCCCATAAAACTCTTCCCTTTAGCAAAAATGTACAAGAACAAGTTCAATCTATGGTGCTCGTAGAAGAAAAAAACGGGCGTAAAATTTACGCTAAAAGCGGTTGGGGATGGGATGTGGATCCTCAAGTGGGCTGGTTAACAGGCTGGGTCGTTCAACCACAAGGTGAAATTGTGGCATTCTCGCTCAATTTAGAAATGAAAAAAGGAACACCTAGTTCTATTCGAAAAGAAATTGCTTATAAAGGATTAGAGCAGCTAGGTATTTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3006002","ARO_id":"44464","ARO_name":"OXA-802","CARD_short_name":"OXA-802","ARO_description":"OXA-802 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46495":{"category_aro_accession":"3007706","category_aro_cvterm_id":"46495","category_aro_name":"OXA-213-like beta-lactamase","category_aro_description":"OXA-213-like enzymes have been identified to be intrinsic to A. calcoaceticus and have been subsequently detected in A. pittii. Phylogenetic analysis of OXA-213-like proteins identified two distinct subgroups within the OXA family. The first group was linked to A. pittii and the second group to A. calcoaceticus. The carbapenemase activity of these OXAs may be related to the species-dependent effect.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5108":{"model_id":"5108","model_name":"OXA-803","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7483":{"protein_sequence":{"accession":"WP_136512094.1","sequence":"MTKKALFFAIGTMFLSACSFNTVQQHQIQSISTNKNSEKIKSLFDQAQTEGVLVIKRGQIEEVYGNDLKRASTEYVPASTFKMLNALIGLEHHKATPTEVFKWDGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMSKEVKRIGFGNADIGSKVDDFWLVGPLKITPQQEAQFAYELAHKTLPFSKNVQEQVQSMLFIEEKNGRKIYAKSGWGWNVEPQVGWLTGWVVQPQGEIIAFSLNLEMKKGIPSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"NG_064761.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGACTAAAAAAGCTCTTTTCTTTGCCATTGGTACGATGTTTTTGTCGGCATGTTCTTTTAATACCGTACAACAACATCAAATACAGTCAATTTCTACCAATAAAAACTCAGAGAAAATTAAATCATTGTTTGATCAAGCACAAACTGAAGGTGTTTTAGTTATAAAACGTGGGCAAATAGAGGAAGTCTATGGCAATGATCTTAAAAGAGCATCAACCGAATATGTTCCCGCCTCTACCTTTAAAATGTTAAATGCTTTGATTGGACTTGAGCATCATAAAGCAACACCAACTGAAGTGTTTAAATGGGATGGGCAAAAACGTTTATTTCCTGATTGGGAAAAGGACATGACTCTAGGCGATGCGATGAAAGCTTCTGCTATTCCAGTTTATCAGGAACTAGCTCGACGAATTGGCCTTGATCTTATGTCTAAAGAGGTAAAACGCATTGGTTTCGGTAATGCTGATATTGGTTCAAAAGTAGATGATTTTTGGCTTGTTGGTCCACTTAAAATTACACCTCAACAAGAAGCCCAGTTTGCTTATGAACTAGCCCATAAAACTCTTCCTTTTAGCAAAAATGTGCAAGAACAAGTTCAATCTATGCTGTTCATAGAAGAAAAAAATGGACGAAAAATTTATGCCAAAAGTGGTTGGGGATGGAATGTGGAGCCTCAAGTGGGCTGGTTAACAGGCTGGGTCGTTCAACCTCAAGGAGAAATTATAGCGTTCTCACTTAATTTAGAAATGAAAAAAGGCATACCTAGTTCTATTCGAAAAGAAATTGCTTATAAAGGATTGGAACAACTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3006003","ARO_id":"44465","ARO_name":"OXA-803","CARD_short_name":"OXA-803","ARO_description":"OXA-803 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46495":{"category_aro_accession":"3007706","category_aro_cvterm_id":"46495","category_aro_name":"OXA-213-like beta-lactamase","category_aro_description":"OXA-213-like enzymes have been identified to be intrinsic to A. calcoaceticus and have been subsequently detected in A. pittii. Phylogenetic analysis of OXA-213-like proteins identified two distinct subgroups within the OXA family. The first group was linked to A. pittii and the second group to A. calcoaceticus. The carbapenemase activity of these OXAs may be related to the species-dependent effect.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5109":{"model_id":"5109","model_name":"OXA-804","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7484":{"protein_sequence":{"accession":"WP_136512095.1","sequence":"MTKKALFFAIGTMFLSACSFNTVQQHQIQSISTNKNSEKIKSLFDQAQTEGVLVIKRGQTEEIYGNDLKRSSTEYVPASTFKMLNALIGLEHHKATPTEVFKWDGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMSKEVKRIGFGNADIGSKVDDFWLVGPLKITPQQEVRFAYKLANKTLPFSKNVQEQVQSMVFIEEKNGRKIYAKSGWGWDVDPEVGWFTGWVVQPQGEIIAFSLNLEMKKGIPSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"NG_064762.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGACTAAAAAAGCTCTTTTCTTTGCCATTGGTACGATGTTTTTGTCGGCATGTTCTTTTAATACCGTACAACAACATCAAATACAGTCAATTTCTACCAATAAAAACTCAGAGAAAATTAAATCATTGTTTGATCAAGCACAAACTGAAGGTGTTTTAGTTATAAAACGTGGGCAAACAGAGGAAATCTATGGCAATGATCTTAAAAGATCATCAACCGAATATGTTCCCGCCTCTACCTTTAAAATGTTAAATGCTTTGATTGGACTTGAGCATCATAAAGCAACACCAACTGAAGTGTTTAAATGGGATGGGCAAAAGCGTTTGTTTCCTGATTGGGAAAAGGACATGACTCTAGGCGATGCGATGAAAGCTTCTGCTATTCCAGTTTATCAGGAACTAGCTCGACGAATTGGCCTTGATCTTATGTCTAAAGAGGTAAAACGCATTGGTTTCGGTAATGCTGATATTGGTTCAAAAGTAGATGATTTTTGGCTTGTTGGTCCACTTAAAATTACACCTCAACAAGAAGTACGGTTTGCTTATAAATTAGCCAACAAAACTCTTCCCTTTAGCAAAAATGTACAAGAACAAGTTCAATCTATGGTGTTCATTGAAGAAAAAAATGGACGAAAAATTTATGCCAAAAGTGGTTGGGGATGGGATGTTGACCCAGAAGTTGGTTGGTTTACAGGCTGGGTAGTTCAACCTCAGGGAGAAATTATAGCTTTCTCACTTAATTTAGAAATGAAGAAAGGCATACCTAGTTCTATTCGAAAAGAAATTGCTTATAAGGGATTAGAGCAGCTAGGTATTTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3006004","ARO_id":"44466","ARO_name":"OXA-804","CARD_short_name":"OXA-804","ARO_description":"OXA-804 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46495":{"category_aro_accession":"3007706","category_aro_cvterm_id":"46495","category_aro_name":"OXA-213-like beta-lactamase","category_aro_description":"OXA-213-like enzymes have been identified to be intrinsic to A. calcoaceticus and have been subsequently detected in A. pittii. Phylogenetic analysis of OXA-213-like proteins identified two distinct subgroups within the OXA family. The first group was linked to A. pittii and the second group to A. calcoaceticus. The carbapenemase activity of these OXAs may be related to the species-dependent effect.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5110":{"model_id":"5110","model_name":"OXA-805","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7485":{"protein_sequence":{"accession":"WP_136512096.1","sequence":"MYKKVLVVATATLFLSACSSNTVKQHQIHSISANKKSEEIKSLFDQAQTTGVLVVKRGQTEEIYGNDLKRASTEYVPASTFKMLNALIGLEHHKATTTEIFKWDGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMSKEVKRIGFGNADIGSKVDNFWLVGPLKITPEQETQFAYKLANKTLPFSKNVQEQVQSMVFIEEKNGRKIYAKSGWGWDVEPQVGWLTGWVVQPQGEIVAFSLNLEMKKGIPSSIRKEIAYKGLEQLGVL"},"dna_sequence":{"accession":"NG_064763.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGTATAAAAAAGTCCTTGTCGTTGCAACAGCTACTCTATTTTTATCTGCCTGCTCTTCTAACACGGTAAAACAACATCAAATACATTCTATTTCCGCCAATAAAAAATCAGAAGAAATTAAATCTCTGTTTGATCAGGCACAGACCACAGGAGTTTTAGTGGTTAAGCGTGGGCAAACCGAAGAAATTTATGGCAATGATCTTAAAAGAGCATCAACCGAATATGTTCCCGCCTCTACCTTTAAAATGCTAAATGCTTTAATTGGACTTGAACATCATAAAGCAACGACAACTGAAATATTTAAATGGGATGGGCAAAAGCGTTTATTTCCTGATTGGGAAAAGGATATGACTCTAGGCGATGCTATGAAAGCTTCTGCTATTCCAGTTTATCAAGAACTAGCGCGAAGAATTGGACTTGATCTTATGTCTAAAGAGGTAAAACGTATTGGTTTCGGTAATGCTGATATTGGTTCAAAAGTAGATAATTTTTGGCTTGTCGGTCCACTTAAAATTACACCTGAGCAAGAAACCCAATTTGCTTATAAATTAGCTAATAAAACTCTTCCATTTAGTAAAAATGTACAAGAACAAGTCCAATCAATGGTGTTTATAGAAGAAAAAAATGGACGTAAAATTTATGCTAAAAGTGGTTGGGGATGGGATGTTGAACCACAAGTTGGCTGGTTAACCGGCTGGGTCGTTCAACCACAAGGAGAAATTGTGGCATTCTCACTCAATTTAGAAATGAAAAAAGGAATTCCTAGTTCTATTCGAAAAGAAATTGCTTATAAAGGATTAGAACAACTCGGTGTTTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3006005","ARO_id":"44467","ARO_name":"OXA-805","CARD_short_name":"OXA-805","ARO_description":"OXA-805 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46495":{"category_aro_accession":"3007706","category_aro_cvterm_id":"46495","category_aro_name":"OXA-213-like beta-lactamase","category_aro_description":"OXA-213-like enzymes have been identified to be intrinsic to A. calcoaceticus and have been subsequently detected in A. pittii. Phylogenetic analysis of OXA-213-like proteins identified two distinct subgroups within the OXA family. The first group was linked to A. pittii and the second group to A. calcoaceticus. The carbapenemase activity of these OXAs may be related to the species-dependent effect.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5111":{"model_id":"5111","model_name":"OXA-806","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7486":{"protein_sequence":{"accession":"WP_136512097.1","sequence":"MNKYFTCYVVASLFLSGCTVQHNLINKTQSQIVQGHNQVIHQYFDEKNTSGVLVIQADKKINLYGNALSRANTEYVPASTFKMLNALIGLENQKTDINEIFKWKGEKRSFTAWEKDMTLGEAMKLSAVPVYQELARRIGLDLMQKEVKRIGFGNAEIGQQVDNFWLVGPLKVTPIQEVEFVSQLAHTQLPFSEKVQANVKNMLLLEESNGYKIFGKTGWAMDIKPQVGWLTGWVEQPDGKIVAFALNMEMRSGMPASIRNELLMKSLKQLNII"},"dna_sequence":{"accession":"NG_064764.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGAATAAATATTTTACTTGCTATGTGGTTGCTTCTCTTTTTCTTTCTGGTTGTACGGTTCAGCATAATTTAATAAATAAAACCCAGAGTCAGATTGTTCAAGGACATAATCAGGTGATTCATCAATACTTTGATGAAAAAAACACCTCAGGTGTGCTGGTTATTCAAGCAGATAAAAAAATTAATCTGTATGGTAATGCTCTAAGCCGCGCAAATACAGAATATGTGCCAGCCTCTACATTTAAAATGTTGAATGCCCTGATCGGATTGGAGAACCAGAAAACGGATATTAATGAAATATTTAAATGGAAGGGCGAGAAAAGGTCATTTACCGCTTGGGAAAAAGACATGACACTAGGAGAAGCCATGAAGCTTTCCGCAGTCCCAGTCTATCAGGAACTTGCGCGACGTATCGGTCTTGATCTCATGCAAAAAGAAGTAAAACGTATTGGTTTCGGTAATGCTGAAATTGGACAGCAGGTTGATAATTTCTGGTTGGTAGGGCCATTAAAGGTTACGCCTATTCAAGAGGTAGAGTTTGTTTCTCAATTGGCGCATACACAGCTTCCATTTAGTGAAAAAGTGCAGGCTAATGTAAAAAATATGCTTCTTTTAGAAGAGAGTAATGGCTACAAAATTTTTGGAAAGACTGGTTGGGCAATGGATATAAAACCACAAGTGGGCTGGTTGACCGGCTGGGTTGAGCAGCCAGATGGAAAAATTGTCGCTTTTGCACTAAATATGGAAATGCGGTCAGGAATGCCTGCATCTATACGTAATGAATTATTGATGAAATCATTAAAACAGCTGAATATTATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39672","NCBI_taxonomy_name":"Acinetobacter radioresistens","NCBI_taxonomy_id":"40216"}}}},"ARO_accession":"3006006","ARO_id":"44468","ARO_name":"OXA-806","CARD_short_name":"OXA-806","ARO_description":"OXA-806 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46499":{"category_aro_accession":"3007710","category_aro_cvterm_id":"46499","category_aro_name":"OXA-23-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases, specifically imipenem, derived from OXA-23, first identified in Acinetobacter baumannii.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5112":{"model_id":"5112","model_name":"OXA-807","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7487":{"protein_sequence":{"accession":"WP_136512098.1","sequence":"MNKYFTCYVVASLFLSGCTVQHNLINKTQSQIVQGHNQVIHQYFDEKNTSGVLVIQADKKINLYGNALSRANTEYVPASTFKMLNALIGLENQKTDINEIFKWKGEKRSFTGWEKDMTLGEAMKLSAVPVYQELARRIGLDLMQKEVKRIGFGNAEIGQQVDNFWLVGPLKVTPIQEVEFVSQLAHTQLPFSEKVQANVKNMLLLEESNGYKIFGKTGWAMDIKPQVGWLTGWVEQPDGKIVTFALNMEMRSEMPASIRNELLMKSLKQLNII"},"dna_sequence":{"accession":"NG_064765.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGAATAAATATTTTACTTGCTATGTGGTTGCTTCTCTTTTTCTTTCTGGTTGTACGGTTCAGCATAATTTAATAAATAAAACCCAGAGTCAGATTGTTCAAGGACATAATCAGGTGATTCATCAATACTTTGATGAAAAAAACACCTCAGGTGTGCTGGTTATTCAAGCAGATAAAAAAATTAATCTGTATGGTAATGCTCTAAGCCGCGCAAATACAGAATATGTGCCAGCCTCTACATTTAAAATGTTGAATGCCCTGATCGGATTGGAGAACCAGAAAACGGATATTAATGAAATATTTAAATGGAAGGGCGAGAAAAGGTCATTTACCGGTTGGGAAAAAGACATGACACTAGGAGAAGCCATGAAGCTTTCCGCAGTCCCAGTCTATCAGGAACTTGCGCGACGTATCGGTCTTGATCTCATGCAAAAAGAAGTAAAACGTATTGGTTTCGGTAATGCTGAAATTGGACAGCAGGTTGATAATTTCTGGTTGGTAGGGCCATTAAAGGTTACGCCTATTCAAGAGGTAGAGTTTGTTTCTCAATTGGCGCATACACAGCTTCCATTTAGTGAAAAAGTGCAGGCTAATGTAAAAAATATGCTTCTTTTAGAAGAGAGTAATGGCTACAAAATTTTTGGAAAGACCGGTTGGGCAATGGATATAAAACCACAAGTGGGCTGGTTGACCGGCTGGGTTGAGCAGCCAGATGGAAAAATTGTCACTTTTGCATTAAATATGGAAATGCGGTCAGAAATGCCTGCATCTATACGTAATGAATTATTGATGAAATCATTAAAACAGCTGAATATTATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39672","NCBI_taxonomy_name":"Acinetobacter radioresistens","NCBI_taxonomy_id":"40216"}}}},"ARO_accession":"3006007","ARO_id":"44469","ARO_name":"OXA-807","CARD_short_name":"OXA-807","ARO_description":"OXA-807 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46499":{"category_aro_accession":"3007710","category_aro_cvterm_id":"46499","category_aro_name":"OXA-23-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases, specifically imipenem, derived from OXA-23, first identified in Acinetobacter baumannii.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5113":{"model_id":"5113","model_name":"OXA-808","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7488":{"protein_sequence":{"accession":"WP_136512099.1","sequence":"MNKYFTCYVVASLFLSGCTVQHNLINETQSQIVQGHNQVIHQYFDEKNTSGVLVIQADKKINLYGNALSRANTEYVPASTFKMLNALIGLENQKTDINEIFKWKGEKRSFTGWEKDMTLGEAMKLSAVPVYQELARRIGLDLMQKEVKRIGFGNAEIGQQVDNFWLVGPLKVTPIQEVEFVSQLAHTQLPFSEKVQANVKNMLLLEESNGYKIFGKTGWAMDIKPQVGWLTGWVEQPDGKIVTFALNMEMRSEMPASILNELLMKSLKQLNII"},"dna_sequence":{"accession":"NG_064766.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGAATAAATATTTTACTTGCTATGTGGTTGCTTCTCTTTTTCTTTCTGGTTGTACGGTTCAGCATAATTTAATAAATGAAACCCAGAGTCAGATTGTTCAAGGACATAATCAGGTGATTCATCAATACTTTGATGAAAAAAACACCTCAGGTGTGCTGGTTATTCAAGCAGATAAAAAAATTAATCTGTATGGTAATGCTCTAAGCCGCGCAAATACAGAATATGTGCCAGCCTCTACATTTAAAATGTTGAATGCCCTGATCGGATTGGAGAACCAGAAAACGGATATTAATGAAATATTTAAATGGAAGGGCGAGAAAAGGTCATTTACCGGTTGGGAAAAAGACATGACACTAGGAGAAGCCATGAAGCTTTCCGCAGTCCCAGTCTATCAGGAACTTGCGCGACGTATCGGTCTTGATCTCATGCAAAAAGAAGTAAAACGTATTGGTTTCGGTAATGCTGAAATTGGACAGCAGGTTGATAATTTCTGGTTGGTAGGGCCATTAAAGGTTACGCCTATTCAAGAGGTAGAGTTTGTTTCTCAATTGGCGCATACACAGCTTCCATTTAGTGAAAAAGTGCAGGCTAATGTAAAAAATATGCTTCTTTTAGAAGAGAGTAATGGCTACAAAATTTTTGGAAAGACCGGTTGGGCAATGGATATAAAACCACAAGTGGGCTGGTTGACCGGCTGGGTTGAGCAGCCAGATGGAAAAATTGTCACTTTTGCATTAAATATGGAAATGCGGTCAGAAATGCCTGCATCTATACTTAATGAATTATTGATGAAATCATTAAAACAGCTGAATATTATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39672","NCBI_taxonomy_name":"Acinetobacter radioresistens","NCBI_taxonomy_id":"40216"}}}},"ARO_accession":"3006008","ARO_id":"44470","ARO_name":"OXA-808","CARD_short_name":"OXA-808","ARO_description":"OXA-808 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46499":{"category_aro_accession":"3007710","category_aro_cvterm_id":"46499","category_aro_name":"OXA-23-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases, specifically imipenem, derived from OXA-23, first identified in Acinetobacter baumannii.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5114":{"model_id":"5114","model_name":"OXA-809","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7489":{"protein_sequence":{"accession":"WP_136512100.1","sequence":"MNKYFTYYVFASLFLSGCTVQHNLINDAQSQIVQGHNQVIHQYFDEKNTSGVLVIQTDKKINLYGNALSRANTEYVPASTFKMLNALIGLENQKTDINEIFKWKGEKRSFIAWEKDMTLGEAMKLSAVPVYQELARRIGLDLMQKEVERIDFGNTEIGQQVDNFWLVGPLKVTPIQEVEFVSQLAHTQLPFSEKVQANVKNMLLLEESNGYKIFGKTGWAMDIKPQVGWLTGWVEQPDGKIVAFALNMEMRSEMPASIRNELLMKSLKQLNII"},"dna_sequence":{"accession":"NG_064767.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGAATAAATATTTTACTTACTATGTGTTTGCTTCTCTTTTTCTTTCTGGTTGTACGGTTCAGCATAACTTAATAAATGACGCTCAGAGTCAGATTGTTCAAGGACATAATCAGGTGATTCATCAATACTTTGATGAAAAAAACACCTCAGGTGTGCTGGTTATTCAAACAGATAAAAAAATTAATCTGTATGGTAATGCTCTAAGCCGCGCAAATACAGAATATGTGCCAGCCTCTACATTTAAAATGTTGAATGCCCTGATCGGATTGGAGAACCAGAAAACGGATATTAATGAAATATTTAAATGGAAGGGCGAGAAAAGGTCATTTATCGCTTGGGAAAAAGACATGACACTAGGAGAAGCCATGAAGCTTTCCGCAGTCCCAGTCTATCAGGAACTTGCAAGACGTATTGGTCTTGATCTCATGCAAAAAGAAGTAGAACGTATTGATTTCGGTAATACTGAAATTGGACAGCAGGTTGATAATTTCTGGTTGGTAGGGCCATTAAAGGTCACGCCTATTCAAGAGGTAGAGTTTGTTTCTCAATTGGCACATACACAGCTTCCATTTAGTGAAAAAGTGCAGGCTAATGTAAAAAATATGCTTCTTTTAGAAGAGAGTAATGGCTACAAAATTTTTGGAAAGACTGGTTGGGCAATGGATATAAAACCACAAGTGGGCTGGTTGACCGGCTGGGTTGAGCAGCCAGATGGAAAAATTGTCGCTTTTGCATTAAATATGGAAATGCGGTCAGAAATGCCGGCATCTATACGTAATGAATTATTGATGAAATCATTAAAACAGCTGAATATTATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39672","NCBI_taxonomy_name":"Acinetobacter radioresistens","NCBI_taxonomy_id":"40216"}}}},"ARO_accession":"3006009","ARO_id":"44471","ARO_name":"OXA-809","CARD_short_name":"OXA-809","ARO_description":"OXA-809 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46499":{"category_aro_accession":"3007710","category_aro_cvterm_id":"46499","category_aro_name":"OXA-23-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases, specifically imipenem, derived from OXA-23, first identified in Acinetobacter baumannii.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5115":{"model_id":"5115","model_name":"OXA-810","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7490":{"protein_sequence":{"accession":"WP_136512101.1","sequence":"MNKYFTCYVVASLFLSGCTVQHNLINETPSQIVQGHNQVIHQYFDEKNTSGVLVIQTDKKINLYGNALSRANTEYVPASTFKMLNALIGLENQKTDINEIFKWKGEKRSFTAWEKDMTLGEAMKLSAVPVYQELARRIGLDLMQKEVKRIGFGNAEIGQQVDNFWLVGPLKVTPIQEVEFVSQLAHTQLPFSEKVQANVKNMLLLEENNGYKIFGKTGWAMDIKPQVGWLTGWVEQPDGKIVAFALNMEMRSEMPASIRNELLMKSLKQLNII"},"dna_sequence":{"accession":"NG_064768.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGAATAAATATTTTACTTGCTATGTGGTTGCTTCTCTTTTTCTTTCTGGTTGTACGGTTCAGCATAATTTAATAAATGAAACCCCGAGTCAGATTGTTCAAGGACATAATCAGGTGATTCATCAATACTTTGATGAAAAAAACACCTCAGGTGTGCTGGTTATTCAAACAGATAAAAAAATTAATCTATATGGTAATGCTCTAAGCCGCGCAAATACAGAATATGTGCCAGCCTCTACATTTAAAATGTTGAATGCCCTGATCGGATTGGAGAACCAGAAAACGGATATTAATGAAATATTTAAATGGAAGGGCGAGAAAAGGTCATTTACCGCTTGGGAAAAAGACATGACACTAGGAGAAGCCATGAAGCTTTCTGCAGTCCCAGTCTATCAGGAACTTGCGCGACGTATCGGTCTTGATCTCATGCAAAAAGAAGTAAAACGTATTGGTTTCGGTAATGCTGAAATTGGACAGCAGGTTGATAATTTCTGGTTGGTAGGACCATTAAAGGTTACGCCTATTCAAGAGGTAGAGTTTGTTTCCCAATTAGCACATACACAGCTTCCATTTAGTGAAAAAGTGCAGGCTAATGTAAAAAATATGCTACTTCTAGAAGAGAATAATGGCTACAAGATTTTTGGAAAGACTGGTTGGGCAATGGATATAAAACCACAAGTGGGCTGGTTGACCGGCTGGGTTGAGCAGCCAGATGGAAAAATTGTCGCTTTTGCATTAAATATGGAAATGCGGTCAGAAATGCCGGCATCTATACGTAATGAATTATTGATGAAATCATTAAAACAGCTAAATATTATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39672","NCBI_taxonomy_name":"Acinetobacter radioresistens","NCBI_taxonomy_id":"40216"}}}},"ARO_accession":"3006010","ARO_id":"44472","ARO_name":"OXA-810","CARD_short_name":"OXA-810","ARO_description":"OXA-810 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46499":{"category_aro_accession":"3007710","category_aro_cvterm_id":"46499","category_aro_name":"OXA-23-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases, specifically imipenem, derived from OXA-23, first identified in Acinetobacter baumannii.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5116":{"model_id":"5116","model_name":"OXA-811","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7491":{"protein_sequence":{"accession":"WP_136512102.1","sequence":"MNKYFTCYVFASLFLSGCTVQHNLINETPSQIVQGHNQVIHQYFDEKNTSGVLVIQTDKKINLYGNALSRANTEYVPASTFKMLNALIGLENQKTDINEIFKWKGEKRSFTAWEKDMTLGEAMKLSAVPVYQELARRIGLDLMQKEVKRIGFGNAEIGQQVDNFWLVGPLKVTPIQEVEFVSQLAHTQLPFSEKVQANVKNMLLLEESNGYKIFGKTGWAMDIKPQVGWLTGWVEQPDGKIVAFALNMEMRSGMPASIRNELLMKSLKQLNII"},"dna_sequence":{"accession":"NG_064769.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGAATAAATATTTTACTTGCTATGTGTTTGCTTCTCTTTTTCTTTCTGGTTGTACGGTTCAGCATAATTTAATAAATGAAACCCCGAGTCAGATTGTTCAAGGACATAATCAGGTGATTCATCAATACTTTGATGAAAAAAACACCTCAGGTGTGCTGGTTATTCAAACAGATAAAAAAATTAATCTGTATGGTAATGCTCTAAGCCGCGCAAATACAGAATATGTGCCAGCCTCTACATTTAAAATGTTGAATGCCCTGATCGGACTGGAGAACCAGAAAACGGATATTAATGAAATATTTAAATGGAAGGGCGAGAAAAGGTCATTTACCGCTTGGGAAAAAGACATGACACTAGGAGAAGCCATGAAGCTTTCTGCAGTCCCAGTCTATCAGGAACTTGCGCGACGTATCGGTCTTGATCTCATGCAAAAAGAAGTAAAACGTATTGGTTTCGGTAATGCTGAAATTGGACAGCAGGTTGATAATTTCTGGTTGGTAGGGCCATTAAAGGTTACGCCTATTCAAGAGGTAGAGTTTGTTTCTCAATTGGCGCATACACAGCTTCCATTTAGTGAAAAAGTGCAGGCTAATGTAAAAAATATGCTACTTCTAGAAGAGAGTAATGGCTACAAAATTTTTGGAAAGACTGGTTGGGCAATGGATATAAAACCACAAGTGGGCTGGTTGACCGGCTGGGTTGAGCAGCCAGATGGAAAAATTGTCGCTTTTGCACTAAATATGGAAATGCGGTCAGGAATGCCTGCATCTATACGTAATGAATTATTGATGAAATCATTAAAACAGCTGAATATTATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39672","NCBI_taxonomy_name":"Acinetobacter radioresistens","NCBI_taxonomy_id":"40216"}}}},"ARO_accession":"3006011","ARO_id":"44473","ARO_name":"OXA-811","CARD_short_name":"OXA-811","ARO_description":"OXA-811 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46499":{"category_aro_accession":"3007710","category_aro_cvterm_id":"46499","category_aro_name":"OXA-23-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases, specifically imipenem, derived from OXA-23, first identified in Acinetobacter baumannii.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5117":{"model_id":"5117","model_name":"OXA-813","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7492":{"protein_sequence":{"accession":"WP_005404206.1","sequence":"MNKYFTCYVFASLFLSGCTVQHNLINETPSQIAQGHNQVIHQYFDEKNTSGVLVIQTDKKINLYGNALSRANTEYVPASTFKMLNALIGLENQKTDINEIFKWKGEKRSFTAWEKDMTLGEAMKLSAVPVYQELARRIGLDLMQKEVKRIGFGNAEIGQQVDNFWLVGPLKVTPIQEVEFVSQLAHTQLPFSEKVQANVKNMLLLEESNGYKIFGKTGWAMDIKPQVGWLTGWVEQPDGKIVAFALNMEMRSEMPASIRNELLMKSLKQLNII"},"dna_sequence":{"accession":"NG_064771.1","fmin":"100","fmax":"922","strand":"+","sequence":"ATGAATAAATATTTTACTTGCTATGTGTTTGCTTCTCTTTTTCTTTCTGGTTGTACGGTTCAGCATAATTTAATAAATGAAACCCCGAGTCAGATTGCTCAAGGACATAATCAGGTGATTCATCAATACTTTGATGAAAAAAACACCTCAGGTGTGCTGGTTATTCAAACAGATAAAAAAATTAATCTGTATGGTAATGCTCTAAGCCGCGCAAATACAGAATATGTGCCAGCCTCTACATTTAAAATGTTGAATGCCCTGATCGGATTGGAGAACCAGAAAACGGATATTAATGAAATATTTAAATGGAAGGGCGAGAAAAGGTCATTTACCGCTTGGGAAAAAGACATGACACTAGGAGAAGCCATGAAGCTTTCCGCAGTCCCAGTCTATCAGGAACTTGCGCGACGTATCGGTCTTGATCTCATGCAAAAAGAAGTAAAACGTATTGGTTTCGGTAATGCTGAAATTGGACAGCAGGTTGATAATTTCTGGTTGGTAGGGCCATTAAAGGTTACGCCTATTCAAGAGGTAGAGTTTGTTTCTCAATTGGCGCATACACAGCTTCCATTTAGTGAAAAAGTGCAGGCTAATGTAAAAAATATGCTTCTTTTAGAAGAGAGTAATGGCTACAAAATTTTTGGAAAGACTGGTTGGGCAATGGATATAAAACCACAAGTGGGCTGGTTGACCGGCTGGGTTGAGCAGCCAGATGGAAAAATTGTCGCTTTTGCATTAAATATGGAAATGCGGTCAGAAATGCCGGCATCTATACGTAATGAATTATTGATGAAATCATTAAAACAGCTGAATATTATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37046","NCBI_taxonomy_name":"Acinetobacter","NCBI_taxonomy_id":"469"}}}},"ARO_accession":"3006012","ARO_id":"44474","ARO_name":"OXA-813","CARD_short_name":"OXA-813","ARO_description":"OXA-813 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46499":{"category_aro_accession":"3007710","category_aro_cvterm_id":"46499","category_aro_name":"OXA-23-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases, specifically imipenem, derived from OXA-23, first identified in Acinetobacter baumannii.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5118":{"model_id":"5118","model_name":"OXA-814","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7493":{"protein_sequence":{"accession":"WP_005405613.1","sequence":"MNKYFTCYVVASLFLSGCTVQHNLINETQSQIVQGHNQVIHQYFDEKNTSGVLVIQADKKINLYGNALSRANTEYVPASTFKMLNALIGLENQKTDINEIFKWKGEKRSFTGWEKDMTLGEAMKLSAVPVYQELARRIGLDLMQKEVKRIGFGNAEIGQQVDNFWLVGPLKVTPIQEVEFVSQLAHTQLPFSEKVQANVKNMLLLEESNGYKIFGKTGWAMDIKPQVGWLTGWVEQPDGKIVTFALNMEMRSEMPASIRNELLMKSLKQLNII"},"dna_sequence":{"accession":"NG_064772.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGAATAAATATTTTACTTGCTATGTGGTTGCTTCTCTTTTTCTTTCTGGTTGTACGGTTCAGCATAATTTAATAAATGAAACCCAGAGTCAGATTGTTCAAGGACATAATCAGGTGATTCATCAATACTTTGATGAAAAAAACACCTCAGGTGTGCTGGTTATTCAAGCAGATAAAAAAATTAATCTGTATGGTAATGCTCTAAGCCGCGCAAATACAGAATATGTGCCAGCCTCTACATTTAAAATGTTGAATGCCCTGATCGGATTGGAGAACCAGAAAACGGATATTAATGAAATATTTAAATGGAAGGGCGAGAAAAGGTCATTTACCGGTTGGGAAAAAGACATGACACTAGGAGAAGCCATGAAGCTTTCCGCAGTCCCAGTCTATCAGGAACTTGCGCGACGTATCGGTCTTGATCTCATGCAAAAAGAAGTAAAACGTATTGGTTTCGGTAATGCTGAAATTGGACAGCAGGTTGATAATTTCTGGTTGGTAGGGCCATTAAAGGTTACGCCTATTCAAGAGGTAGAGTTTGTTTCTCAATTGGCGCATACACAGCTTCCATTTAGTGAAAAAGTGCAGGCTAATGTAAAAAATATGCTTCTTTTAGAAGAGAGTAATGGCTACAAAATTTTTGGAAAGACCGGTTGGGCAATGGATATAAAACCACAAGTGGGCTGGTTGACCGGCTGGGTTGAGCAGCCAGATGGAAAAATTGTCACTTTTGCATTAAATATGGAAATGCGGTCAGAAATGCCTGCATCTATACGTAATGAATTATTGATGAAATCATTAAAACAGCTGAATATTATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39672","NCBI_taxonomy_name":"Acinetobacter radioresistens","NCBI_taxonomy_id":"40216"}}}},"ARO_accession":"3006013","ARO_id":"44475","ARO_name":"OXA-814","CARD_short_name":"OXA-814","ARO_description":"OXA-814 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46499":{"category_aro_accession":"3007710","category_aro_cvterm_id":"46499","category_aro_name":"OXA-23-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases, specifically imipenem, derived from OXA-23, first identified in Acinetobacter baumannii.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5119":{"model_id":"5119","model_name":"OXA-815","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7494":{"protein_sequence":{"accession":"WP_111280830.1","sequence":"MNKYFTCYVVASLFLSGCTVQHNLINETQSQIVQGHNQVIHQYFDEKNTSGVLVIQTDKKINLYGNALSRANTEYVPASTFKMLNALIGLENQKTDINEIFKWKGEKRSFTAWEKDMTLGEAMKLSAVPVYQELARRIGLDLMQKEVERIDFGNAEIGQQVDNFWLIGPLKVTPIQEVEFVSQLAHTQLPFSEKVQANVKNMLLLEENNGYKIFGKTGWAMDIKPQVGWLTGWVEQPDGKIVAFALNMEMRSEMPASIRNELLMKSLKQLNII"},"dna_sequence":{"accession":"NG_064773.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGAATAAATATTTTACTTGCTATGTGGTTGCTTCTCTTTTTCTTTCTGGTTGTACGGTTCAGCATAATTTAATAAATGAAACCCAGAGTCAGATTGTTCAAGGACATAATCAGGTGATTCATCAATACTTTGATGAAAAAAACACCTCAGGTGTGCTGGTTATTCAAACAGATAAAAAAATTAATTTGTATGGTAATGCTCTAAGCCGCGCAAATACAGAATATGTGCCAGCCTCTACATTTAAAATGTTGAATGCCCTGATCGGATTGGAGAACCAGAAAACGGATATTAATGAAATATTTAAATGGAAGGGCGAGAAAAGGTCATTTACCGCTTGGGAAAAAGACATGACACTAGGAGAAGCCATGAAGCTTTCTGCAGTCCCAGTCTATCAGGAACTTGCAAGACGTATCGGTCTTGATCTCATGCAAAAAGAAGTAGAACGTATTGATTTCGGTAATGCTGAAATTGGACAGCAGGTTGACAATTTCTGGTTGATAGGCCCATTAAAGGTCACGCCTATTCAAGAGGTAGAGTTTGTTTCTCAATTGGCACATACACAGCTTCCATTTAGTGAAAAAGTGCAGGCTAATGTAAAAAATATGCTACTTCTAGAAGAGAATAATGGCTACAAGATTTTTGGAAAGACTGGTTGGGCAATGGATATAAAACCACAAGTGGGCTGGTTGACCGGCTGGGTTGAGCAGCCAGATGGAAAAATTGTCGCTTTTGCATTAAATATGGAAATGCGGTCAGAAATGCCGGCATCTATACGTAATGAATTATTGATGAAATCATTAAAACAGCTAAATATTATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39672","NCBI_taxonomy_name":"Acinetobacter radioresistens","NCBI_taxonomy_id":"40216"}}}},"ARO_accession":"3006014","ARO_id":"44476","ARO_name":"OXA-815","CARD_short_name":"OXA-815","ARO_description":"OXA-815 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46499":{"category_aro_accession":"3007710","category_aro_cvterm_id":"46499","category_aro_name":"OXA-23-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases, specifically imipenem, derived from OXA-23, first identified in Acinetobacter baumannii.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5120":{"model_id":"5120","model_name":"OXA-816","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7495":{"protein_sequence":{"accession":"WP_026444036.1","sequence":"MNKYFTCYVVASLFLSGCTVQHNLINETQSQIVQGHNQVIHQYFDEKNTSGVLVIQTDKKINLYGNALSRANTEYVPASTFKMLNALIGLENQKTDINEIFKWKGEKRSFIAWEKDMTLGEAMKLSAVPVYQELARRIGLDLMQKEVERIDFGNTEIGQQVDNFWLVGPLKVTPIQEVEFVSQLAHTQLPFSEKVQANVKNMLLLEESNGYKIFGKTGWAMDIKPQVGWLTGWVEQPDGKIVAFALNMEMRSEMPASIRNELLMKSLKQLNII"},"dna_sequence":{"accession":"NG_064774.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGAATAAATATTTTACTTGCTATGTGGTTGCTTCTCTTTTTCTTTCTGGTTGTACGGTTCAGCATAATTTAATAAATGAAACCCAGAGTCAGATTGTTCAAGGACATAATCAGGTGATTCATCAATACTTTGATGAAAAAAACACCTCAGGTGTGCTGGTTATTCAAACAGATAAAAAAATTAATCTGTATGGTAATGCTCTAAGCCGTGCAAATACAGAATATGTGCCAGCCTCTACATTTAAAATGTTGAATGCCCTGATCGGATTGGAGAACCAGAAAACGGATATTAATGAAATATTTAAATGGAAGGGCGAGAAAAGGTCATTTATCGCTTGGGAAAAAGACATGACACTAGGAGAAGCCATGAAGCTTTCCGCAGTCCCAGTCTATCAAGAACTTGCAAGACGTATTGGTCTTGATCTCATGCAAAAAGAAGTAGAACGTATTGATTTCGGTAATACTGAAATTGGACAGCAGGTTGATAATTTCTGGTTGGTAGGGCCATTAAAGGTTACGCCTATTCAAGAGGTAGAGTTTGTTTCTCAATTGGCGCATACACAGCTTCCATTTAGTGAAAAAGTGCAGGCTAATGTAAAAAATATGCTTCTTTTAGAAGAGAGTAATGGCTACAAAATTTTTGGAAAGACTGGTTGGGCAATGGATATAAAACCACAAGTGGGCTGGTTGACCGGCTGGGTTGAGCAGCCAGATGGAAAAATTGTCGCTTTTGCATTAAATATGGAAATGCGGTCAGAAATGCCGGCATCTATACGTAATGAATTATTGATGAAATCATTAAAACAGCTGAATATTATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37046","NCBI_taxonomy_name":"Acinetobacter","NCBI_taxonomy_id":"469"}}}},"ARO_accession":"3006015","ARO_id":"44477","ARO_name":"OXA-816","CARD_short_name":"OXA-816","ARO_description":"OXA-816 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46499":{"category_aro_accession":"3007710","category_aro_cvterm_id":"46499","category_aro_name":"OXA-23-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases, specifically imipenem, derived from OXA-23, first identified in Acinetobacter baumannii.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5121":{"model_id":"5121","model_name":"OXA-817","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7496":{"protein_sequence":{"accession":"WP_075040046.1","sequence":"MNKYFTCYVVASLFLSGCTVQHNLINETQSQIVQGHNQVIHQYFDEKNTSGVLVIQTDKKINLYGNALSRANTEYVPASTFKMLNALIGLENQKTDINEIFKWKGEKRSFTTWEKDMTLGEAMKLSAVPVYQELARRIGLDLMQKEVERIDFGNAEIGQQVDNFWLIGPLKVTPIQEVEFVSQLAHTQLPFSEKVQANVKNMLLLEENNGYKIFGKTGWAMDIKPQVGWLTGWVEQPDGKIVAFALNMEMRSEMPASIRNELLMKSLKQLNII"},"dna_sequence":{"accession":"NG_064775.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGAATAAATATTTTACTTGCTATGTGGTTGCTTCTCTTTTTCTTTCTGGTTGTACGGTTCAGCATAATTTAATAAATGAAACCCAGAGTCAGATTGTTCAAGGACATAATCAGGTGATTCATCAATACTTTGATGAAAAAAACACCTCAGGTGTGCTGGTTATTCAAACAGATAAAAAAATTAATTTGTATGGTAATGCTCTAAGCCGCGCAAATACAGAATATGTGCCAGCCTCTACATTTAAAATGTTGAATGCCCTGATCGGATTGGAGAACCAGAAAACGGATATTAATGAAATATTTAAATGGAAGGGCGAGAAAAGGTCATTTACCACTTGGGAAAAAGACATGACACTAGGAGAAGCCATGAAGCTTTCTGCAGTCCCAGTCTATCAGGAACTTGCAAGACGTATCGGTCTTGATCTCATGCAAAAAGAAGTAGAACGTATTGATTTCGGTAATGCTGAAATTGGACAGCAGGTTGACAATTTCTGGTTGATAGGCCCATTAAAGGTCACGCCTATTCAAGAGGTAGAGTTTGTTTCTCAATTGGCACATACACAGCTTCCATTTAGTGAAAAAGTGCAGGCTAATGTAAAAAATATGCTACTTCTAGAAGAGAATAATGGCTACAAGATTTTTGGAAAGACTGGTTGGGCAATGGATATAAAACCACAAGTGGGCTGGTTGACCGGCTGGGTTGAGCAGCCAGATGGAAAAATTGTCGCTTTTGCATTAAATATGGAAATGCGGTCAGAAATGCCTGCATCTATACGTAATGAATTATTGATGAAATCATTAAAACAGCTGAATATTATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39672","NCBI_taxonomy_name":"Acinetobacter radioresistens","NCBI_taxonomy_id":"40216"}}}},"ARO_accession":"3006016","ARO_id":"44478","ARO_name":"OXA-817","CARD_short_name":"OXA-817","ARO_description":"OXA-817 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46499":{"category_aro_accession":"3007710","category_aro_cvterm_id":"46499","category_aro_name":"OXA-23-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases, specifically imipenem, derived from OXA-23, first identified in Acinetobacter baumannii.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5122":{"model_id":"5122","model_name":"OXA-819","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7497":{"protein_sequence":{"accession":"WP_032053762.1","sequence":"MTKKALFFAISTIFLSACSFNTVQQHQIHAISTHKNSEEIKSLFDQAQTTGVLVIKRGQTEEIYGNNLKRASTEYVPASTFKMLNALIGLEHHKATTTEMFKWDGQKRLFPDWEKDMTLGEAMKASAIPVYQELARRIGLDLMSKEVKRIGFGNADIGSKVDNFWLVGPLKITPQQETQFAYELAHKTLPFSKNVQEQVQSMVFVEEKNGRKIYAKSGWGWDVEPQVGWLTGWVVQPQGEIVAFSLNLEMKKGTPSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"NG_064777.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGACTAAAAAAGCTCTTTTCTTTGCTATTAGTACCATATTTTTGTCAGCATGTTCTTTCAATACAGTACAACAGCACCAAATACACGCTATTTCTACTCATAAAAATTCAGAAGAAATTAAATCACTGTTTGATCAGGCACAGACCACGGGAGTTTTAGTGATTAAGCGTGGGCAAACCGAAGAAATTTATGGCAATAATCTTAAAAGAGCATCAACCGAATATGTTCCCGCCTCTACATTTAAAATGCTAAATGCTTTAATTGGACTTGAACATCATAAAGCAACGACAACTGAAATGTTCAAATGGGATGGACAAAAGCGTTTATTTCCTGATTGGGAAAAGGATATGACTCTGGGTGAGGCCATGAAAGCTTCTGCTATTCCTGTCTATCAAGAACTAGCGCGAAGAATTGGCCTTGATCTTATGTCCAAAGAGGTCAAGCGTATTGGTTTCGGTAATGCTGATATTGGTTCAAAAGTAGATAATTTTTGGCTTGTCGGTCCCCTTAAAATTACACCTCAGCAAGAAACCCAGTTTGCTTATGAATTAGCCCATAAAACTCTTCCCTTTAGCAAAAATGTACAAGAACAAGTTCAATCTATGGTGTTCGTAGAAGAAAAAAACGGACGTAAAATTTACGCTAAAAGCGGTTGGGGATGGGATGTTGAACCACAAGTTGGCTGGTTAACAGGCTGGGTCGTTCAACCACAAGGAGAAATTGTAGCGTTCTCACTCAATTTAGAAATGAAAAAAGGAACACCTAGTTCTATTCGAAAAGAAATTGCTTATAAAGGATTAGAGCAGCTAGGTATTTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40550","NCBI_taxonomy_name":"Acinetobacter calcoaceticus\/baumannii complex","NCBI_taxonomy_id":"909768"}}}},"ARO_accession":"3006017","ARO_id":"44479","ARO_name":"OXA-819","CARD_short_name":"OXA-819","ARO_description":"OXA-819 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46495":{"category_aro_accession":"3007706","category_aro_cvterm_id":"46495","category_aro_name":"OXA-213-like beta-lactamase","category_aro_description":"OXA-213-like enzymes have been identified to be intrinsic to A. calcoaceticus and have been subsequently detected in A. pittii. Phylogenetic analysis of OXA-213-like proteins identified two distinct subgroups within the OXA family. The first group was linked to A. pittii and the second group to A. calcoaceticus. The carbapenemase activity of these OXAs may be related to the species-dependent effect.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5123":{"model_id":"5123","model_name":"OXA-820","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7498":{"protein_sequence":{"accession":"WP_032057042.1","sequence":"MTKKALFFAIGTMFLSACSFNTVEQHQIQSISTNKNSEKIKSLFDQAQTEGVLVIKRGQIEEVYGNDLKRASTEYVPASTFKMLNALIGLEHHKATPTEVFKWDGQKRLFPDWEKDMTLGDAMKASTIPVYQELARRIGLDLMSKEIKRISFGNADIGSKVDDFWLVGPLKITPQQEAQFAYELAHKTLPFSKNVQEQVQSMLFIEEKNGRKIYAKSGWGWDVEPQVGWLTGWVVQPQGKIVAFSLNLEMKKGIPSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"NG_064778.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGACTAAAAAAGCTCTTTTCTTTGCCATTGGTACGATGTTTTTATCGGCATGTTCTTTTAATACGGTAGAACAGCATCAAATACAGTCAATTTCTACCAATAAAAACTCAGAGAAAATTAAATCGTTGTTTGATCAAGCACAAACTGAAGGTGTTTTAGTTATAAAACGTGGGCAAATAGAGGAAGTCTATGGCAATGATCTTAAAAGAGCATCAACCGAATATGTTCCCGCCTCTACCTTTAAAATGTTAAATGCTTTGATTGGACTTGAGCATCATAAAGCAACACCAACTGAAGTGTTTAAATGGGATGGGCAAAAGCGTTTATTTCCCGATTGGGAAAAAGACATGACATTAGGCGATGCGATGAAAGCTTCTACTATTCCAGTTTATCAGGAACTAGCTCGACGAATTGGCCTTGATCTTATGTCTAAAGAGATAAAACGCATTAGTTTCGGTAATGCTGATATTGGTTCAAAAGTAGATGATTTTTGGCTTGTTGGTCCACTTAAAATTACACCTCAACAAGAAGCCCAGTTTGCTTATGAACTAGCCCATAAAACTCTTCCTTTTAGCAAGAATGTGCAAGAACAAGTTCAATCTATGCTGTTCATAGAAGAAAAAAATGGACGGAAAATTTATGCCAAAAGTGGTTGGGGATGGGATGTGGAGCCTCAAGTGGGCTGGTTAACAGGCTGGGTCGTTCAACCTCAAGGAAAAATTGTAGCGTTCTCACTCAATTTAGAAATGAAAAAAGGCATACCTAGTTCTATTCGAAAAGAAATTGCTTATAAGGGATTAGAGCAGCTAGGTATTTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40550","NCBI_taxonomy_name":"Acinetobacter calcoaceticus\/baumannii complex","NCBI_taxonomy_id":"909768"}}}},"ARO_accession":"3006018","ARO_id":"44480","ARO_name":"OXA-820","CARD_short_name":"OXA-820","ARO_description":"OXA-820 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46495":{"category_aro_accession":"3007706","category_aro_cvterm_id":"46495","category_aro_name":"OXA-213-like beta-lactamase","category_aro_description":"OXA-213-like enzymes have been identified to be intrinsic to A. calcoaceticus and have been subsequently detected in A. pittii. Phylogenetic analysis of OXA-213-like proteins identified two distinct subgroups within the OXA family. The first group was linked to A. pittii and the second group to A. calcoaceticus. The carbapenemase activity of these OXAs may be related to the species-dependent effect.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5124":{"model_id":"5124","model_name":"OXA-821","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7499":{"protein_sequence":{"accession":"WP_057061999.1","sequence":"MTKKALFFAISTMFLSACSFNTVQQHQIQSISTNKNSEKIKSLFDQAQTEGVLVIKRGQTEEIYGNDLKRSSTEYVPASTFKMLNALIGLEHHKATPTEVFKWDGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMSKEVKRIGFGNADIGSKVDDFWLVGPLKITPQQEAQFAYELAHKTLPFSKNVQEEVQSMLFIEEKNGRKIYAKSGWGWDVEPQVGWLTGWVVQPQGEIVAFSLNLEMKKGIPSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"NG_064779.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGACTAAAAAAGCTCTTTTCTTTGCCATTAGTACGATGTTTTTGTCGGCATGTTCTTTTAATACCGTACAACAACATCAAATACAGTCAATTTCTACCAATAAAAACTCAGAGAAAATTAAATCATTGTTTGATCAAGCACAAACTGAAGGTGTTTTAGTTATAAAACGTGGGCAAACAGAGGAAATCTATGGCAATGATCTTAAAAGATCATCAACCGAATATGTTCCCGCCTCTACCTTTAAAATGTTAAATGCATTGATTGGACTTGAGCATCATAAAGCAACACCAACTGAAGTGTTTAAATGGGATGGGCAAAAGCGTTTGTTTCCTGATTGGGAAAAGGACATGACTCTAGGCGATGCGATGAAAGCTTCTGCTATTCCAGTTTATCAGGAACTAGCTCGACGAATTGGCCTTGATCTTATGTCTAAAGAGGTAAAACGCATTGGTTTCGGTAATGCTGATATTGGTTCAAAAGTAGATGATTTTTGGCTTGTTGGTCCACTTAAAATTACACCTCAACAAGAAGCCCAGTTTGCTTATGAACTAGCCCATAAAACTCTTCCTTTTAGCAAGAATGTGCAAGAAGAAGTTCAATCTATGCTGTTCATAGAAGAAAAAAATGGACGGAAAATTTATGCCAAAAGTGGTTGGGGATGGGATGTGGAGCCTCAAGTGGGCTGGTTAACAGGCTGGGTCGTTCAACCTCAAGGAGAAATTGTAGCGTTCTCACTCAATTTAGAAATGAAAAAAGGCATACCTAGTTCTATTCGAAAAGAAATTGCTTATAAGGGATTAGAGCAGCTAGGTATTTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3006019","ARO_id":"44481","ARO_name":"OXA-821","CARD_short_name":"OXA-821","ARO_description":"OXA-821 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46495":{"category_aro_accession":"3007706","category_aro_cvterm_id":"46495","category_aro_name":"OXA-213-like beta-lactamase","category_aro_description":"OXA-213-like enzymes have been identified to be intrinsic to A. calcoaceticus and have been subsequently detected in A. pittii. Phylogenetic analysis of OXA-213-like proteins identified two distinct subgroups within the OXA family. The first group was linked to A. pittii and the second group to A. calcoaceticus. The carbapenemase activity of these OXAs may be related to the species-dependent effect.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5125":{"model_id":"5125","model_name":"OXA-822","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7500":{"protein_sequence":{"accession":"WP_133973918.1","sequence":"MYKKVLIVATSILFLSACSSNTVEQHQIYSISANKNSEEIKSLFDQAQTTGVLVIKREQKEEIYGNDLKRASTEYVPASTFKMLNALIGLEHHKATATEVFKWDGQKRLFPDWEKDMTLGNAMKASAIPVYQELARRIGLDLMSKEVKRIGFGNANIGSKVDNFWLVGPLKITPQQEAQFAYQLAHKTLPFSKDVQEQVQSMVFIEEKNGRRIYAKSGWGWDVEPQVGWLTGWVVQPQGEIVAFSLNLEMKKGTPSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"NG_066712.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGTATAAAAAAGTCCTTATCGTTGCAACAAGCATCCTATTTTTATCTGCCTGTTCTTCTAATACGGTGGAACAACATCAAATATATTCTATTTCTGCCAATAAAAATTCAGAAGAAATTAAATCACTGTTTGATCAAGCGCAGACCACAGGCGTTTTGGTTATTAAGCGAGAGCAAAAAGAAGAAATTTATGGCAATGACCTTAAAAGAGCATCAACTGAATATGTTCCAGCTTCTACCTTTAAAATGTTAAATGCTTTAATTGGACTTGAACACCATAAGGCAACTGCAACTGAAGTGTTTAAATGGGATGGGCAAAAACGTTTATTTCCTGACTGGGAAAAAGATATGACTCTGGGCAATGCCATGAAAGCTTCTGCTATTCCAGTTTATCAAGAATTAGCCCGACGAATTGGTCTAGACCTTATGTCTAAAGAGGTGAAACGAATTGGTTTCGGTAATGCCAATATTGGTTCAAAAGTAGATAATTTTTGGCTTGTTGGTCCACTAAAAATCACACCTCAACAAGAAGCCCAGTTTGCTTATCAATTGGCCCATAAAACACTTCCATTCAGCAAAGATGTACAAGAACAAGTTCAATCAATGGTGTTCATCGAGGAAAAGAATGGACGTAGAATTTATGCCAAAAGTGGTTGGGGATGGGATGTTGAACCACAAGTTGGTTGGTTAACAGGCTGGGTCGTTCAACCACAAGGAGAAATTGTGGCATTCTCACTTAATTTAGAAATGAAAAAAGGAACTCCTAGCTCTATTCGCAAAGAAATTGCTTATAAAGGCTTAGAACAATTAGGGATTCTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39094","NCBI_taxonomy_name":"Acinetobacter calcoaceticus","NCBI_taxonomy_id":"471"}}}},"ARO_accession":"3006020","ARO_id":"44482","ARO_name":"OXA-822","CARD_short_name":"OXA-822","ARO_description":"OXA-822 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46495":{"category_aro_accession":"3007706","category_aro_cvterm_id":"46495","category_aro_name":"OXA-213-like beta-lactamase","category_aro_description":"OXA-213-like enzymes have been identified to be intrinsic to A. calcoaceticus and have been subsequently detected in A. pittii. Phylogenetic analysis of OXA-213-like proteins identified two distinct subgroups within the OXA family. The first group was linked to A. pittii and the second group to A. calcoaceticus. The carbapenemase activity of these OXAs may be related to the species-dependent effect.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5126":{"model_id":"5126","model_name":"OXA-823","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7501":{"protein_sequence":{"accession":"WP_136512103.1","sequence":"MKTFAAYVIIACLSSTALAGSITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLESQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGIIGG"},"dna_sequence":{"accession":"NG_064780.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGAAAACATTTGCCGCATATGTAATTATCGCGTGTCTTTCGAGTACGGCATTAGCTGGTTCAATTACAGAAAATACGTCTTGGAACAAAGAGTTCTCTGCCGAAGCCGTCAATGGTGTCTTCGTGCTTTGTAAAAGTAGCAGTAAATCCTGCGCTACCAATGACTTAGCTCGTGCATCAAAGGAATATCTTCCAGCATCAACATTTAAGATCCCCAACGCAATTATCGGCCTAGAAACTGGTGTCATAAAGAATGAGCATCAGGTTTTCAAATGGGACGGAAAGCCAAGAGCCATGAAGCAATGGGAAAGAGACTTGACCTTAAGAGGGGCAATACAAGTTTCAGCTGTTCCCGTATTTCAACAAATCGCCAGAGAAGTTGGCGAAGTAAGAATGCAGAAATACCTTAAAAAATTTTCCTATGGCAACCAGAATATCAGTGGTGGCATTGACAAATTCTGGTTGGAAAGCCAGCTTAGAATTTCCGCAGTTAATCAAGTGGAGTTTCTAGAGTCTCTATATTTAAATAAATTGTCAGCATCTAAAGAAAACCAGCTAATAGTAAAAGAGGCTTTGGTAACGGAGGCGGCACCTGAATATCTAGTGCATTCAAAAACTGGTTTTTCTGGTGTGGGAACTGAGTCAAATCCTGGTGTCGCATGGTGGGTTGGGTGGGTTGAGAAGGAGACAGAGGTTTACTTTTTCGCCTTTAACATGGATATAGACAACGAAAGTAAGTTGCCGCTAAGAAAATCCATTCCCACCAAAATCATGGAAAGTGAGGGCATCATTGGTGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006021","ARO_id":"44483","ARO_name":"OXA-823","CARD_short_name":"OXA-823","ARO_description":"OXA-823 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46486":{"category_aro_accession":"3007697","category_aro_cvterm_id":"46486","category_aro_name":"OXA-10-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-10.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5127":{"model_id":"5127","model_name":"OXA-824","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7502":{"protein_sequence":{"accession":"WP_136512104.1","sequence":"MKTFAAYVIIACLSSTALAGSITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGKQNISGGIDKFWLEGQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGIIGG"},"dna_sequence":{"accession":"NG_064781.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGAAAACATTTGCCGCATATGTAATTATCGCGTGTCTTTCGAGTACGGCATTAGCTGGTTCAATTACAGAAAATACGTCTTGGAACAAAGAGTTCTCTGCCGAAGCCGTCAATGGTGTCTTCGTGCTTTGTAAAAGTAGCAGTAAATCCTGCGCTACCAATGACTTAGCTCGTGCATCAAAGGAATATCTTCCAGCATCAACATTTAAGATCCCCAACGCAATTATCGGCCTAGAAACTGGTGTCATAAAGAATGAGCATCAGGTTTTCAAATGGGACGGAAAGCCAAGAGCCATGAAGCAATGGGAAAGAGACTTGACCTTAAGAGGGGCAATACAAGTTTCAGCTGTTCCCGTATTTCAACAAATCGCCAGAGAAGTTGGCGAAGTAAGAATGCAGAAATACCTTAAAAAATTTTCCTATGGCAAACAGAATATCAGTGGTGGCATTGACAAATTCTGGTTGGAAGGCCAGCTTAGAATTTCCGCAGTTAATCAAGTGGAGTTTCTAGAGTCTCTATATTTAAATAAATTGTCAGCATCTAAAGAAAACCAGCTAATAGTAAAAGAGGCTTTGGTAACGGAGGCGGCACCTGAATATCTAGTGCATTCAAAAACTGGTTTTTCTGGTGTGGGAACTGAGTCAAATCCTGGTGTCGCATGGTGGGTTGGGTGGGTTGAGAAGGAGACAGAGGTTTACTTTTTCGCCTTTAACATGGATATAGACAACGAAAGTAAGTTGCCGCTAAGAAAATCCATTCCCACCAAAATCATGGAAAGTGAGGGCATCATTGGTGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006022","ARO_id":"44484","ARO_name":"OXA-824","CARD_short_name":"OXA-824","ARO_description":"OXA-824 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46486":{"category_aro_accession":"3007697","category_aro_cvterm_id":"46486","category_aro_name":"OXA-10-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-10.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5128":{"model_id":"5128","model_name":"OXA-826","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7503":{"protein_sequence":{"accession":"WP_140423319.1","sequence":"MTKKALFFAIGTMFLSACSFNTVEQHQTQSISTNKNSEKIKSLFDQAQTEGVLVIKRGQIEEVYGNDLKRASTEYVPASTFKMLNALIGLEHHKATPTEVFKWDGQKRLFPDWEKDMTLGDAMKAYAIPVYQELARRIGLDLMSKEVKRIGFGNADIGSKVDDFWLVGPLKITPQQEAQFAYELAHKTLPFSKNMQEQVQSMLFIEEKNGRKIYAKSGWGWDVEPQVGWLTGWVVQPQGEIIAFSLNLEMKKGIPSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"NG_065437.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGACTAAAAAAGCTCTTTTCTTTGCCATTGGTACGATGTTTTTATCGGCATGTTCTTTTAATACGGTAGAACAGCATCAAACACAGTCAATTTCTACCAATAAAAACTCAGAGAAAATTAAATCATTGTTTGATCAAGCACAAACTGAAGGTGTTTTAGTTATAAAACGTGGGCAAATAGAGGAAGTCTATGGCAATGATCTTAAAAGAGCATCAACCGAATATGTTCCCGCCTCTACCTTTAAAATGTTAAATGCTTTGATTGGACTTGAGCATCATAAAGCAACACCAACTGAAGTGTTTAAATGGGATGGGCAAAAGCGTTTATTTCCCGATTGGGAAAAAGACATGACATTAGGCGATGCGATGAAAGCTTATGCTATTCCAGTTTATCAGGAACTAGCTCGACGAATTGGCCTTGATCTTATGTCTAAAGAGGTAAAACGCATTGGTTTCGGTAATGCTGATATTGGTTCAAAAGTAGATGATTTTTGGCTTGTTGGTCCACTTAAAATTACACCTCAACAAGAAGCCCAGTTTGCTTATGAACTAGCCCATAAAACTCTTCCTTTTAGCAAAAATATGCAAGAACAAGTTCAATCTATGCTGTTCATAGAAGAAAAAAATGGACGAAAAATTTATGCCAAAAGTGGTTGGGGATGGGATGTGGAGCCTCAAGTGGGCTGGTTAACAGGCTGGGTCGTTCAACCACAAGGAGAAATTATAGCTTTCTCACTTAATTTAGAAATGAAAAAAGGCATACCTAGCTCTATTCGAAAAGAAATTGCTTATAAGGGATTGGAACAACTCGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3006023","ARO_id":"44485","ARO_name":"OXA-826","CARD_short_name":"OXA-826","ARO_description":"OXA-826 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46495":{"category_aro_accession":"3007706","category_aro_cvterm_id":"46495","category_aro_name":"OXA-213-like beta-lactamase","category_aro_description":"OXA-213-like enzymes have been identified to be intrinsic to A. calcoaceticus and have been subsequently detected in A. pittii. Phylogenetic analysis of OXA-213-like proteins identified two distinct subgroups within the OXA family. The first group was linked to A. pittii and the second group to A. calcoaceticus. The carbapenemase activity of these OXAs may be related to the species-dependent effect.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5129":{"model_id":"5129","model_name":"OXA-827","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7504":{"protein_sequence":{"accession":"WP_140423320.1","sequence":"MKTFAAYVIIACLSSTALAGSITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKGTEVYFFAFNMDIDNENKLPLRKSIPTKIMASEGIIGG"},"dna_sequence":{"accession":"NG_065438.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGAAAACATTTGCCGCATATGTAATTATCGCGTGTCTTTCGAGTACGGCATTAGCTGGTTCAATTACAGAAAATACGTCTTGGAACAAAGAGTTCTCTGCCGAAGCCGTCAATGGTGTCTTCGTGCTTTGTAAAAGTAGCAGTAAATCCTGCGCTACCAATGACTTAGCTCGTGCATCAAAGGAATATCTTCCAGCATCAACATTTAAGATCCCCAACGCAATTATCGGCCTAGAAACTGGTGTCATAAAGAATGAGCATCAGGTTTTCAAATGGGACGGAAAGCCAAGAGCCATGAAGCAATGGGAAAGAGACTTGACCTTAAGAGGGGCAATACAAGTTTCAGCTGTTCCCGTATTTCAACAAATCGCCAGAGAAGTTGGCGAAGTAAGAATGCAGAAATACCTTAAAAAATTTTCCTATGGCAACCAGAATATCAGTGGTGGCATTGACAAATTCTGGTTGGAAGGCCAGCTTAGAATTTCCGCAGTTAATCAAGTGGAGTTTCTAGAGTCTCTATATTTAAATAAATTGTCAGCATCTAAAGAAAACCAGCTAATAGTAAAAGAGGCTTTGGTAACGGAGGCGGCACCTGAATATCTAGTGCATTCAAAAACTGGTTTTTCTGGTGTGGGAACTGAGTCAAATCCTGGTGTCGCATGGTGGGTTGGTTGGGTTGAGAAGGGAACAGAGGTTTACTTTTTCGCCTTTAACATGGATATAGACAACGAAAATAAGTTGCCGCTAAGAAAATCCATTCCCACCAAAATCATGGCAAGTGAGGGCATCATTGGTGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006024","ARO_id":"44486","ARO_name":"OXA-827","CARD_short_name":"OXA-827","ARO_description":"OXA-827 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46486":{"category_aro_accession":"3007697","category_aro_cvterm_id":"46486","category_aro_name":"OXA-10-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-10.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5130":{"model_id":"5130","model_name":"OXA-828","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7505":{"protein_sequence":{"accession":"WP_140423321.1","sequence":"MNIKTLLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEVHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKKVKRVGYGNADIGTQVDNFWLVGPLNITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_065439.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAACACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGTACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGAAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAATATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006025","ARO_id":"44487","ARO_name":"OXA-828","CARD_short_name":"OXA-828","ARO_description":"OXA-828 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5131":{"model_id":"5131","model_name":"OXA-829","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7506":{"protein_sequence":{"accession":"WP_140423322.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDVKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAVPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGLDVNLQVGWLTGWVVQPQGNIVAFSLNLEIKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_065440.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGTAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTGTTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAACAAAATATACGCAAAAAGTGGTTGGGGATTGGATGTAAACCTACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATAAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006026","ARO_id":"44488","ARO_name":"OXA-829","CARD_short_name":"OXA-829","ARO_description":"OXA-829 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5132":{"model_id":"5132","model_name":"OXA-830","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7507":{"protein_sequence":{"accession":"WP_152315468.1","sequence":"MTPILLRGLLAAGLLFALPAAANDGCFLFADGSGKTLSREGACSMRLPPASTFKIPLALMGYDSGYLVDEQRPALPFKPGYNGWLPAWHETTTPSRWMTYSVVWFSQLMTEWLGMPRLQHYVDQFDYGNRDLSGHPGKQDGLTQAWLSSSLQISPEEQARFLGRMLEGKLPVAASTLQHTANLLKVSEIDGWQIHGKTGMGYPKKLDGSLNRQRQIGWFVGWASKGSERRIFVHTVIQPPGKQFASLKAKEEVLAALPAKLAEQAN"},"dna_sequence":{"accession":"NG_066713.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGACCCCCATTCTGCTGCGTGGCCTATTGGCCGCCGGTCTGCTTTTCGCCCTGCCAGCGGCCGCCAACGATGGCTGCTTCCTGTTTGCCGATGGCAGTGGCAAGACGCTCTCCCGTGAGGGCGCGTGCAGCATGCGTCTCCCACCGGCATCGACCTTCAAGATCCCGCTGGCCCTGATGGGCTATGACAGCGGCTATCTGGTTGATGAACAGCGGCCCGCGCTCCCCTTCAAGCCCGGTTATAACGGCTGGCTGCCCGCCTGGCACGAGACCACCACCCCGAGCCGCTGGATGACCTACTCGGTGGTGTGGTTCTCCCAGTTGATGACCGAGTGGCTCGGCATGCCGCGCCTTCAGCATTACGTCGACCAATTCGACTACGGCAACCGGGATCTCAGCGGCCATCCGGGCAAACAGGATGGCCTGACCCAGGCCTGGCTCAGCAGCAGCCTGCAAATCAGCCCCGAAGAGCAGGCCCGCTTCCTCGGCCGCATGCTGGAAGGCAAGTTGCCGGTGGCGGCGAGCACCCTGCAACATACCGCCAATCTCCTCAAGGTGAGCGAGATCGACGGCTGGCAGATCCATGGCAAGACCGGCATGGGCTATCCCAAGAAACTCGATGGCAGCCTCAACCGGCAACGACAGATCGGCTGGTTTGTCGGCTGGGCCAGCAAGGGCAGCGAACGACGCATCTTCGTGCATACCGTGATCCAGCCGCCCGGCAAGCAGTTCGCCTCGCTCAAAGCCAAGGAGGAGGTGCTGGCCGCCCTACCGGCCAAGCTGGCTGAGCAAGCTAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3006027","ARO_id":"44489","ARO_name":"OXA-830","CARD_short_name":"OXA-830","ARO_description":"OXA-830 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5133":{"model_id":"5133","model_name":"OXA-831","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7508":{"protein_sequence":{"accession":"WP_140423323.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIQVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_065441.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCAGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGGTGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006028","ARO_id":"44490","ARO_name":"OXA-831","CARD_short_name":"OXA-831","ARO_description":"OXA-831 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5134":{"model_id":"5134","model_name":"OXA-832","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7509":{"protein_sequence":{"accession":"WP_086264536.1","sequence":"MTKKALFFAIGTMFLSACSFDTVEQHQIQSISTNKNSEKIQSLFDQAQTTGILIIKRGQTEEVYGNDLKRASTEYVPASTFKMLNALIGLEHHKATPTEVFKWDGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMSKEVKRIGFGNADIGSKIDNFWLVGPLKITPQQEAQFAYELAHKTLPFSKNVQEQVQSLLFIEEKNGRKIYAKSGWGWDVEPQVGWFTGWVVQPQGEIVAFALNLEMKKGIPSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"NG_065442.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGACTAAAAAAGCTCTTTTCTTTGCCATTGGTACGATGTTTTTATCGGCGTGTTCTTTTGATACCGTAGAACAACATCAAATACAGTCAATTTCTACCAATAAAAACTCAGAGAAAATTCAATCATTGTTTGATCAAGCACAAACTACAGGTATTTTAATTATAAAACGTGGCCAAACAGAGGAAGTCTATGGCAATGATCTTAAAAGAGCATCAACCGAATATGTTCCCGCCTCTACCTTTAAAATGTTAAATGCTTTGATCGGACTTGAGCATCATAAAGCAACACCAACTGAAGTATTTAAATGGGATGGGCAAAAGCGTTTATTTCCCGATTGGGAAAAAGACATGACATTAGGCGATGCTATGAAAGCTTCTGCTATTCCAGTTTATCAGGAACTAGCTCGACGAATTGGTCTTGATCTTATGTCTAAAGAGGTGAAGCGTATTGGTTTCGGTAATGCTGATATTGGTTCAAAAATAGATAATTTTTGGCTTGTTGGCCCACTTAAAATTACACCTCAACAAGAAGCCCAGTTTGCTTATGAACTAGCCCATAAAACTCTTCCCTTTAGCAAAAATGTGCAAGAACAAGTTCAATCTCTGTTGTTCATAGAAGAAAAAAATGGACGAAAAATTTATGCTAAAAGTGGTTGGGGATGGGATGTGGAACCACAAGTTGGTTGGTTTACAGGCTGGGTGGTTCAACCACAAGGAGAAATTGTAGCGTTCGCACTTAATTTAGAAATGAAAAAAGGAATACCTAGTTCTATTCGAAAAGAAATTGCTTATAAAGGATTAGAACAATTAGGTATTTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3006029","ARO_id":"44491","ARO_name":"OXA-832","CARD_short_name":"OXA-832","ARO_description":"OXA-832 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46495":{"category_aro_accession":"3007706","category_aro_cvterm_id":"46495","category_aro_name":"OXA-213-like beta-lactamase","category_aro_description":"OXA-213-like enzymes have been identified to be intrinsic to A. calcoaceticus and have been subsequently detected in A. pittii. Phylogenetic analysis of OXA-213-like proteins identified two distinct subgroups within the OXA family. The first group was linked to A. pittii and the second group to A. calcoaceticus. The carbapenemase activity of these OXAs may be related to the species-dependent effect.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5135":{"model_id":"5135","model_name":"OXA-833","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7510":{"protein_sequence":{"accession":"WP_140423324.1","sequence":"MRVLALSAVFLVASIIGMPAVAKEWQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGQTRDIAAWNRDHDLITAMKYSVVPVYQEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISATQQIAFLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYSTSIEPKIGWWVGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLTQEKIIP"},"dna_sequence":{"accession":"NG_065443.1","fmin":"26","fmax":"824","strand":"+","sequence":"ATGCGTGTATTAGCCTTATCGGCTGTGTTTTTGGTGGCATCGATTATCGGAATGCCAGCGGTAGCAAAGGAATGGCAAGAAAACAAAAGTTGGAATGCTCACTTTACTGAACATAAATCACAGGGCGTAGTTGTGCTCTGGAATGAGAATAAGCAGCAAGGATTTACCAATAATCTTAAACGGGCGAACCAAGCATTTTTACCCGCATCTACCTTTAAAATTCCCAATAGCTTGATCGCCCTCGATTTGGGCGTGGTTAAGGATGAACACCAAGTCTTTAAGTGGGATGGACAGACGCGTGATATCGCCGCTTGGAATCGTGACCATGACTTAATTACCGCGATGAAGTACTCAGTTGTGCCTGTTTATCAAGAATTTGCCCGCCAAATTGGTGAGGCACGTATGAGTAAAATGCTGCACGCCTTCGATTATGGCAATGAGGATATCTCGGGCAATGTAGACAGTTTTTGGCTCGATGGTGGTATTCGCATTTCGGCTACCCAGCAAATCGCTTTTTTACGCAAGCTGTATCACAACAAGCTGCACGTTTCTGAGCGTAGTCAGCGCATCGTGAAACAAGCCATGCTGACCGAAGCCAATGGCGACTATATTATTCGGGCTAAAACGGGATACTCGACTAGTATCGAACCTAAGATTGGCTGGTGGGTTGGTTGGGTTGAACTTGATGATAATGTGTGGTTTTTTGCGATGAATATGGATATGCCCACATCGGATGGTTTAGGGCTGCGCCAAGCCATCACAAAAGAAGTGCTCACACAGGAGAAAATTATTCCCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3006030","ARO_id":"44492","ARO_name":"OXA-833","CARD_short_name":"OXA-833","ARO_description":"OXA-833 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46510":{"category_aro_accession":"3007721","category_aro_cvterm_id":"46510","category_aro_name":"OXA-48-like beta-lactamase","category_aro_description":"OXA-48-type beta-lactamases are now routinely encountered in bacterial infections caused by carbapenam-resistant Enterobacterales. OXA-48-like proteins confer resistance to penicillin (which is efficiently hydrolyzed) and carbapenam antibiotics (which is more slowly broken down). The spectrum of activity of these variants varies, with some hydrolyzing expanded-spectrum oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5136":{"model_id":"5136","model_name":"OXA-834","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7511":{"protein_sequence":{"accession":"WP_125052736.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDVKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIQVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGLDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_065444.1","fmin":"100","fmax":"925","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGTAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCAAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAACAAAATATACGCAAAAAGTGGTTGGGGATTGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006031","ARO_id":"44493","ARO_name":"OXA-834","CARD_short_name":"OXA-834","ARO_description":"OXA-834 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5137":{"model_id":"5137","model_name":"OXA-836","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7512":{"protein_sequence":{"accession":"WP_148044423.1","sequence":"MKTFAAYVIIACLSSTALAGSITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFKIPSAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGIIGG"},"dna_sequence":{"accession":"NG_065881.1","fmin":"0","fmax":"807","strand":"+","sequence":"ATGAAAACATTTGCCGCATATGTAATTATCGCGTGTCTTTCGAGTACGGCATTAGCTGGTTCAATTACAGAAAATACGTCTTGGAACAAAGAGTTCTCTGCCGAAGCCGTCAATGGTGTCTTCGTGCTTTGTAAAAGTAGCAGTAAATCCTGCGCTACCAATGACTTAGCTCGTGCATCAAAGGAATATCTTCCAGCATCAACATTTAAGATCCCCAGCGCAATTATCGGCCTAGAAACTGGTGTCATAAAGAATGAGCATCAGGTTTTCAAATGGGACGGAAAGCCAAGAGCCATGAAGCAATGGGAAAGAGACTTGACCTTAAGAGGGGCAATACAAGTTTCAGCTGTTCCCGTATTTCAACAAATCGCCAGAGAAGTTGGCGAAGTAAGAATGCAGAAATACCTTAAAAAATTTTCCTATGGCAACCAGAATATCAGTGGTGGCATTGACAAATTCTGGTTGGAAGGCCAGCTTAGAATTTCCGCAGTTAATCAAGTGGAGTTTCTAGAGTCTCTATATTTAAATAAATTGTCAGCATCTAAAGAAAACCAGCTAATAGTAAAAGAGGCTTTGGTAACGGAGGCGGCACCTGAATATCTAGTGCATTCAAAAACTGGAACTGGTTTTTCTGGTGTGGGAACTGAGTCAAATCCTGGTGTCGCATGGTGGGTTGGGTGGGTTGAGAAGGAGACAGAGGTTTACTTTTTCGCCTTTAACATGGATATAGACAACGAAAGTAAGTTGCCGCTAAGAAAATCCATTCCCACCAAAATCATGGAAAGTGAGGGCATCATTGGTGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006032","ARO_id":"44494","ARO_name":"OXA-836","CARD_short_name":"OXA-836","ARO_description":"OXA-836 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46486":{"category_aro_accession":"3007697","category_aro_cvterm_id":"46486","category_aro_name":"OXA-10-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-10.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5138":{"model_id":"5138","model_name":"OXA-839","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7513":{"protein_sequence":{"accession":"WP_150823471.1","sequence":"MTVRRLSCALGAALSLCALGGGPVQAAVLCTVVADAADGRILFQQGTQQACAERYTPASTFKLAIALMGADAGILQGPHEPVWNYQPAYPDWGGDAWRQPTDPARWIKYSVVWYSQLTAKALGQDRFQRYTSAFGYGNADVSGEPGKHNGTDGAWIISSLRISPLEQLAFLRKLVNRQLPVKAAAYELAENLFEVGQADGWRLYGKTGTGSPGSNGVYTAANAYGWFVGWARKDGRQLVYARLLQDERATQPNAGLRARDELVRDWPAMAGAWRP"},"dna_sequence":{"accession":"NG_066512.1","fmin":"0","fmax":"828","strand":"+","sequence":"ATGACCGTTCGACGCCTTTCGTGCGCCCTTGGCGCAGCCCTTTCCCTGTGCGCGCTGGGCGGCGGCCCCGTCCAGGCCGCCGTCCTGTGCACCGTGGTGGCCGACGCCGCCGACGGCCGCATCCTGTTCCAGCAAGGCACGCAGCAGGCCTGCGCCGAGCGCTACACGCCGGCCTCGACCTTCAAGCTGGCCATCGCCCTGATGGGCGCCGACGCCGGCATCCTGCAAGGCCCGCACGAGCCGGTCTGGAACTACCAGCCCGCCTATCCCGACTGGGGCGGCGACGCCTGGCGCCAGCCCACCGATCCGGCGCGCTGGATCAAGTATTCGGTGGTCTGGTATTCACAGCTGACGGCCAAGGCGCTGGGACAGGACCGCTTCCAGCGCTACACCAGCGCGTTCGGCTACGGCAATGCGGACGTCTCGGGCGAGCCCGGCAAGCATAACGGCACCGACGGCGCGTGGATCATCTCGTCGCTGCGCATTTCGCCGCTGGAACAACTGGCTTTCCTGCGCAAGCTGGTGAATCGGCAATTGCCGGTCAAGGCCGCCGCCTATGAGCTTGCCGAAAACCTCTTCGAGGTGGGCCAGGCCGATGGCTGGCGCCTGTATGGCAAGACCGGCACCGGGTCGCCCGGCAGCAACGGCGTCTACACGGCGGCCAATGCCTACGGCTGGTTCGTCGGCTGGGCGCGCAAGGATGGCCGCCAGCTGGTGTACGCCCGCCTGCTGCAGGACGAGCGCGCCACCCAGCCCAACGCCGGCTTGCGCGCCCGCGACGAGCTGGTGCGCGACTGGCCGGCCATGGCTGGCGCGTGGCGCCCGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36941","NCBI_taxonomy_name":"Achromobacter xylosoxidans","NCBI_taxonomy_id":"85698"}}}},"ARO_accession":"3006033","ARO_id":"44495","ARO_name":"OXA-839","CARD_short_name":"OXA-839","ARO_description":"OXA-839 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46487":{"category_aro_accession":"3007698","category_aro_cvterm_id":"46487","category_aro_name":"OXA-114-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-114.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5139":{"model_id":"5139","model_name":"OXA-840","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7514":{"protein_sequence":{"accession":"WP_150823472.1","sequence":"MTKKALFFAIGMMFLSACSFNTVEQHQIQSISTNKNSEKIKSLFDQAQTTGVLVIKRGQTEEVYGNDLKRASTEYVPASTFKMLNALIGLEHHKATPTEVFKWDVQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMSKEVKRIGFGNADIGSKVDDFWLVGPLKITPQQEAQFAYELAHKTLPFSKNMQEQVQSMLFIEEKNGRKIYAKSGWGWDVEPQVGWLTGWVVQPQGEIIAFSLNLEMKKGIPSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"NG_066513.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGACTAAAAAAGCTCTTTTCTTTGCCATTGGTATGATGTTTTTGTCTGCATGTTCTTTTAATACGGTAGAACAACATCAAATACAGTCAATTTCTACCAATAAAAACTCAGAGAAAATTAAATCGTTGTTTGATCAAGCACAAACTACAGGTGTTTTAGTTATAAAACGTGGGCAAACAGAGGAAGTCTATGGCAATGATCTTAAAAGAGCATCAACCGAATATGTTCCCGCCTCTACCTTTAAAATGTTAAATGCTTTGATAGGACTTGAGCATCATAAAGCAACACCAACTGAAGTGTTTAAATGGGATGTGCAAAAGCGTTTATTTCCCGATTGGGAAAAAGACATGACATTAGGCGATGCTATGAAAGCTTCTGCTATTCCAGTTTATCAGGAACTAGCTCGACGAATTGGCCTTGATCTTATGTCTAAAGAGGTAAAACGCATTGGTTTCGGTAATGCTGATATTGGTTCAAAAGTAGATGATTTTTGGCTTGTTGGTCCACTTAAAATTACCCCTCAACAAGAAGCCCAGTTTGCTTATGAACTAGCCCATAAAACTCTTCCTTTTAGCAAAAATATGCAAGAACAAGTTCAATCTATGCTGTTCATAGAAGAAAAAAATGGACGGAAAATTTATGCCAAAAGTGGTTGGGGATGGGATGTGGAGCCTCAAGTGGGCTGGTTAACAGGCTGGGTCGTTCAACCACAAGGAGAAATTATAGCTTTCTCACTTAATTTAGAAATGAAAAAAGGCATACCTAGCTCTATTCGAAAAGAAATTGCTTATAAGGGATTGGAACAACTCGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3006034","ARO_id":"44496","ARO_name":"OXA-840","CARD_short_name":"OXA-840","ARO_description":"OXA-840 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46495":{"category_aro_accession":"3007706","category_aro_cvterm_id":"46495","category_aro_name":"OXA-213-like beta-lactamase","category_aro_description":"OXA-213-like enzymes have been identified to be intrinsic to A. calcoaceticus and have been subsequently detected in A. pittii. Phylogenetic analysis of OXA-213-like proteins identified two distinct subgroups within the OXA family. The first group was linked to A. pittii and the second group to A. calcoaceticus. The carbapenemase activity of these OXAs may be related to the species-dependent effect.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5140":{"model_id":"5140","model_name":"OXA-841","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7515":{"protein_sequence":{"accession":"WP_150823473.1","sequence":"MTKKALFFAISTIFLSACSFNTVQQHQIHPISTHKNSEEIKSLFDQAQTTGVLVIKHGNTEEIYGNDLKRASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMSKEVKRIGFGNADIGSKVDNFWLIGPLKITPQQEAQFAYELAHKTLPFSKNVQEQVQSMVFVEEKNGRKIYAKSGWGWDVEPQVGWLTGWVVQPQGEIVAFSLNLEMKKGTPSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"NG_066514.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGACTAAAAAAGCTCTTTTCTTTGCCATTAGTACCATATTTTTGTCAGCATGTTCTTTCAATACAGTACAACAGCATCAAATACACCCTATTTCTACCCATAAAAATTCAGAAGAAATAAAATCACTGTTTGATCAAGCACAGACCACAGGTGTTTTGGTTATTAAGCACGGAAATACAGAGGAAATTTATGGTAATGATCTTAAAAGAGCATCAACCGAATATGTCCCCGCATCTACTTTTAAAATGTTAAATGCTCTAATTGGTCTTGAACATCATAAAGCAACAACAACTGAAGTGTTCAAATGGGATGGACAAAAGCGTTTATTTCCTGATTGGGAAAAGGATATGACTCTAGGTGATGCCATGAAAGCTTCTGCTATTCCTGTGTATCAAGAACTAGCTCGACGAATTGGCCTTGATCTTATGTCCAAAGAGGTCAAGCGTATTGGTTTCGGTAATGCTGATATTGGTTCAAAAGTAGATAATTTTTGGCTTATCGGTCCACTCAAAATTACGCCTCAACAGGAAGCACAGTTTGCTTATGAATTAGCACATAAAACTCTTCCCTTTAGCAAAAATGTACAAGAACAAGTTCAATCTATGGTGTTCGTAGAAGAAAAAAACGGACGTAAAATTTACGCTAAAAGCGGTTGGGGATGGGATGTGGAACCTCAAGTGGGCTGGTTAACAGGCTGGGTCGTTCAACCACAAGGAGAAATTGTAGCGTTCTCACTCAATTTAGAAATGAAAAAAGGAACACCTAGTTCTATTCGAAAAGAAATTGCTTATAAAGGATTAGAGCAGCTAGGTATTTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3006035","ARO_id":"44497","ARO_name":"OXA-841","CARD_short_name":"OXA-841","ARO_description":"OXA-841 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46495":{"category_aro_accession":"3007706","category_aro_cvterm_id":"46495","category_aro_name":"OXA-213-like beta-lactamase","category_aro_description":"OXA-213-like enzymes have been identified to be intrinsic to A. calcoaceticus and have been subsequently detected in A. pittii. Phylogenetic analysis of OXA-213-like proteins identified two distinct subgroups within the OXA family. The first group was linked to A. pittii and the second group to A. calcoaceticus. The carbapenemase activity of these OXAs may be related to the species-dependent effect.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5141":{"model_id":"5141","model_name":"OXA-842","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7516":{"protein_sequence":{"accession":"WP_087088911.1","sequence":"MTKKALFLAISTIFLSACSFNTVQQHQIHAISTDKNSEEIKSLFDQAQTTGVLVIKRGNTEEIYGNDLKRASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMSKEVKRIGFGNSDIGSKVDNFWLVGPLKITPQQEAQFAYELAHKTLPFSKNVQEQVQSMVFVEEKNGRKIYAKSGWGWDVEPQVGWFTGWVVQPQGEIVAFSLNLEMKKGIPSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"NG_066515.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGACTAAAAAAGCTCTTTTCCTTGCTATTAGTACCATATTTTTGTCAGCATGTTCTTTCAATACAGTACAACAGCATCAAATACACGCTATTTCTACCGATAAAAATTCAGAAGAAATTAAATCACTGTTTGATCAAGCACAGACCACTGGTGTTTTGGTTATTAAGCGCGGAAATACAGAGGAAATTTATGGCAATGATCTAAAAAGAGCATCAACCGAATATGTCCCTGCATCTACCTTTAAAATGCTAAATGCTTTAATTGGTCTTGAACATCATAAAGCAACAACAACAGAAGTGTTTAAATGGGATGGACAAAAGCGTTTATTTCCTGATTGGGAAAAAGATATGACCTTAGGTGATGCCATGAAAGCTTCTGCTATTCCTGTGTATCAAGAACTAGCTCGACGAATTGGCCTTGATCTTATGTCCAAAGAGGTTAAGCGTATTGGTTTCGGTAATTCTGATATTGGTTCAAAAGTAGATAATTTTTGGCTTGTTGGCCCCCTCAAAATTACGCCTCAACAGGAAGCACAGTTTGCTTATGAATTAGCCCACAAAACTCTTCCCTTTAGCAAAAATGTACAAGAACAAGTTCAATCTATGGTGTTCGTAGAAGAAAAAAATGGACGAAAAATTTATGCCAAAAGTGGTTGGGGATGGGATGTGGAGCCTCAAGTGGGCTGGTTTACAGGCTGGGTCGTTCAACCTCAAGGAGAAATTGTAGCGTTCTCACTCAATTTAGAAATGAAGAAAGGCATACCTAGTTCTATTCGAAAAGAAATTGCTTATAAGGGATTAGAGCAGCTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3006036","ARO_id":"44498","ARO_name":"OXA-842","CARD_short_name":"OXA-842","ARO_description":"OXA-842 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46495":{"category_aro_accession":"3007706","category_aro_cvterm_id":"46495","category_aro_name":"OXA-213-like beta-lactamase","category_aro_description":"OXA-213-like enzymes have been identified to be intrinsic to A. calcoaceticus and have been subsequently detected in A. pittii. Phylogenetic analysis of OXA-213-like proteins identified two distinct subgroups within the OXA family. The first group was linked to A. pittii and the second group to A. calcoaceticus. The carbapenemase activity of these OXAs may be related to the species-dependent effect.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5142":{"model_id":"5142","model_name":"OXA-843","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7517":{"protein_sequence":{"accession":"WP_150823474.1","sequence":"MTKKALFFAISTIFLSACSFNTVQHHQIHTISTHKNSEEIKSLFDQAQTTGVLVIKRGNTEEIYGNDLKRASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMSKEVKRIGFGNTDIGSKVDNFWLVGPLKITPQQEAQFAYELAHKTLPFSKNVQEQVQSMVFVEEKNGRKIYAKSGWGWDVEPQVGWLTGWVVQPQGEIVAFSLNLEMKKGTPSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"NG_066516.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGACTAAAAAAGCTCTTTTCTTTGCCATTAGTACCATATTTTTGTCAGCATGTTCTTTCAATACAGTACAACATCACCAAATACACACTATTTCTACTCATAAAAATTCAGAAGAAATAAAATCACTGTTTGATCAAGCACAGACCACAGGTGTTTTGGTTATTAAGCGCGGAAATACAGAGGAAATTTATGGCAATGATCTAAAAAGGGCATCAACTGAATATGTCCCTGCATCTACCTTTAAAATGTTAAATGCTCTAATTGGTCTTGAACATCATAAAGCAACAACCACTGAAGTGTTCAAATGGGATGGACAAAAGCGTTTATTTCCTGATTGGGAAAAGGATATGACTCTAGGTGATGCCATGAAAGCTTCTGCTATTCCTGTGTATCAAGAACTAGCTCGACGAATTGGCCTTGATCTTATGTCCAAAGAGGTCAAGCGTATTGGTTTCGGTAATACTGATATTGGTTCAAAAGTAGATAATTTTTGGCTTGTCGGTCCACTCAAAATTACGCCTCAACAGGAAGCACAGTTTGCTTATGAATTAGCACATAAAACTCTTCCCTTTAGCAAAAATGTACAAGAACAAGTTCAATCTATGGTGTTCGTAGAAGAAAAAAACGGACGTAAAATTTACGCTAAAAGCGGTTGGGGATGGGATGTGGAGCCTCAAGTGGGCTGGTTAACAGGCTGGGTCGTTCAACCACAAGGAGAAATTGTAGCGTTCTCTCTCAATTTAGAAATGAAAAAAGGAACACCCAGTTCTATTCGAAAAGAAATTGCTTATAAAGGATTAGAACAGCTAGGTATTTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3006037","ARO_id":"44499","ARO_name":"OXA-843","CARD_short_name":"OXA-843","ARO_description":"OXA-843 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46495":{"category_aro_accession":"3007706","category_aro_cvterm_id":"46495","category_aro_name":"OXA-213-like beta-lactamase","category_aro_description":"OXA-213-like enzymes have been identified to be intrinsic to A. calcoaceticus and have been subsequently detected in A. pittii. Phylogenetic analysis of OXA-213-like proteins identified two distinct subgroups within the OXA family. The first group was linked to A. pittii and the second group to A. calcoaceticus. The carbapenemase activity of these OXAs may be related to the species-dependent effect.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5143":{"model_id":"5143","model_name":"OXA-844","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7518":{"protein_sequence":{"accession":"WP_150823475.1","sequence":"MYKKALIVATSLLFLSACSSNTVEQHQIYSIAANKNSEKIKSLFDQAQTTGVLVIKRGQKEEIYGNDVKRASTEYVPASTFKMLNALIGLEHHKATATEVFKWDGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMSQEVKRIGFGNANIGSKVDNFWLVGPLKITPQQETQFAYQLAHKTLPFSKDVQEQVQTMVFIEEKNGRKIYAKSGWGWDVEPQVGWLTGWVVQPQGEIVAFSLNLEMKKGTPSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"NG_066517.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGTATAAAAAAGCCCTTATCGTTGCAACAAGCCTCCTATTTTTATCTGCCTGTTCTTCTAATACGGTGGAACAACATCAAATATATTCTATTGCTGCCAATAAAAATTCAGAAAAAATTAAATCGCTGTTTGATCAAGCACAGACCACTGGTGTTTTGGTTATTAAGCGAGGGCAAAAAGAAGAAATTTATGGCAATGACGTTAAAAGAGCATCAACTGAATATGTCCCTGCTTCTACTTTTAAAATGTTAAATGCTTTAATTGGACTTGAACACCATAAGGCAACTGCAACTGAAGTGTTTAAATGGGATGGGCAAAAACGTTTATTTCCTGATTGGGAAAAAGATATGACGCTGGGCGATGCCATGAAAGCTTCTGCTATTCCAGTTTATCAAGAATTAGCCCGACGAATTGGTCTAGATCTTATGTCTCAAGAGGTGAAACGAATTGGTTTCGGTAATGCCAATATTGGTTCAAAAGTAGATAATTTTTGGCTTGTTGGTCCTCTAAAAATTACACCTCAACAAGAAACCCAGTTTGCTTATCAATTGGCCCATAAAACACTTCCATTTAGTAAAGATGTACAAGAACAAGTTCAAACAATGGTGTTCATAGAGGAAAAGAATGGACGTAAGATTTATGCCAAAAGTGGTTGGGGATGGGATGTTGAACCACAAGTGGGTTGGTTAACAGGCTGGGTCGTTCAACCACAAGGAGAAATTGTGGCATTCTCGCTTAATTTAGAAATGAAAAAAGGAACTCCTAGCTCTATTCGCAAAGAGATTGCCTATAAAGGCTTAGAACAATTAGGGATTCTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39094","NCBI_taxonomy_name":"Acinetobacter calcoaceticus","NCBI_taxonomy_id":"471"}}}},"ARO_accession":"3006038","ARO_id":"44500","ARO_name":"OXA-844","CARD_short_name":"OXA-844","ARO_description":"OXA-844 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46495":{"category_aro_accession":"3007706","category_aro_cvterm_id":"46495","category_aro_name":"OXA-213-like beta-lactamase","category_aro_description":"OXA-213-like enzymes have been identified to be intrinsic to A. calcoaceticus and have been subsequently detected in A. pittii. Phylogenetic analysis of OXA-213-like proteins identified two distinct subgroups within the OXA family. The first group was linked to A. pittii and the second group to A. calcoaceticus. The carbapenemase activity of these OXAs may be related to the species-dependent effect.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5144":{"model_id":"5144","model_name":"OXA-845","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7519":{"protein_sequence":{"accession":"WP_150823476.1","sequence":"MKLSKLYTLTVLIGFGLSGVACQHIYTPVSFNQIENDQTKQIASLFENVQTTGVLITFDGQEHKAYGNDLNRAKTAYIPASTFKILNALIGIEHDKTSPNEVFKWDGQKRAFESWEKDLTLAEAMQASAVPVYQALGQRIGLDLMAKEVKRVGFGNTRIGTQVDNFWLIGPLKITPIEEAQFAYRLAKQELPFTPKTQQQVIDMLLVDEIRGTKVYAKSGWGMDITPQVGWWTGWIEDPNGKVIAFSLNMEMNQPTHAAARKEIVYQALTQLKLL"},"dna_sequence":{"accession":"NG_066518.1","fmin":"0","fmax":"828","strand":"+","sequence":"ATGAAGCTATCAAAATTATACACCCTCACTGTGCTCATAGGATTTGGATTAAGCGGTGTCGCCTGCCAGCATATCTATACTCCAGTCTCGTTCAATCAAATTGAAAACGATCAAACAAAGCAGATCGCTTCCTTGTTTGAGAATGTTCAAACAACTGGTGTTCTAATTACCTTTGATGGACAGGAGCATAAAGCATACGGTAATGATCTGAATCGTGCCAAAACTGCGTATATCCCAGCATCTACTTTCAAAATATTAAATGCTTTGATTGGTATTGAACATGATAAAACTTCACCAAATGAAGTATTTAAGTGGGATGGTCAGAAGCGTGCTTTTGAAAGTTGGGAAAAAGATCTGACTTTAGCTGAAGCCATGCAAGCTTCTGCTGTACCTGTTTATCAAGCGCTTGGCCAGAGAATCGGATTGGATTTGATGGCAAAGGAAGTCAAAAGAGTCGGCTTCGGTAATACACGCATCGGAACACAAGTTGATAACTTCTGGCTCATTGGACCTTTAAAGATCACGCCAATCGAAGAAGCTCAATTTGCTTACAGGCTAGCAAAACAGGAGTTACCGTTTACCCCAAAAACACAACAGCAAGTGATTGATATGCTGTTGGTGGATGAAATACGGGGAACTAAAGTTTACGCCAAAAGTGGTTGGGGAATGGATATTACCCCGCAAGTAGGATGGTGGACTGGATGGATTGAAGATCCGAACGGAAAAGTGATCGCTTTTTCTCTCAATATGGAAATGAATCAACCTACACATGCAGCTGCACGTAAAGAAATTGTTTATCAGGCACTTACGCAATTGAAATTATTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36938","NCBI_taxonomy_name":"Acinetobacter haemolyticus","NCBI_taxonomy_id":"29430"}}}},"ARO_accession":"3006039","ARO_id":"44501","ARO_name":"OXA-845","CARD_short_name":"OXA-845","ARO_description":"OXA-845 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46496":{"category_aro_accession":"3007707","category_aro_cvterm_id":"46496","category_aro_name":"OXA-214-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-214.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5145":{"model_id":"5145","model_name":"OXA-847","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7520":{"protein_sequence":{"accession":"WP_010793618.1","sequence":"MRPLLFSALLLLSGHTQASEWNDSQAVDKLFGAAGVKGTFVLYDVQRQCYVGHDRERAETRFVPASTYKVANSLIGLSTGAVRSADEVLPYGGKPQRFKAWEHDMSLREAIKASNVPVYQELARRIGLERMRANVSRLGYGNAEIGQVVDNFWLVGPLKISAMEQTHFLLRLAQGELPFPAPVQSTVRAMTLLESGPGWELHGKTGWCFDCTPELGWWVGWVKRNERLYGFALNIDMPGGEADIGKRVELGKASLKALGILP"},"dna_sequence":{"accession":"NG_066520.1","fmin":"0","fmax":"789","strand":"+","sequence":"ATGCGCCCCCTCCTCTTCAGTGCCCTTCTCCTGCTTTCCGGGCATACCCAGGCCAGCGAATGGAACGACAGCCAGGCCGTGGACAAGCTATTCGGCGCGGCCGGGGTGAAAGGCACCTTCGTCCTCTACGATGTGCAGCGGCAGTGCTATGTCGGCCATGACCGGGAGCGCGCGGAAACCCGCTTCGTTCCCGCTTCCACCTACAAGGTGGCGAACAGCCTGATCGGCTTATCCACAGGGGCGGTTAGATCCGCCGACGAGGTTCTTCCCTATGGCGGCAAGCCCCAGCGCTTCAAGGCCTGGGAGCACGACATGAGCCTGCGCGAGGCGATCAAGGCATCGAACGTACCGGTCTACCAGGAACTGGCGCGGCGCATCGGCCTGGAGCGGATGCGCGCCAATGTCTCGCGCCTGGGTTACGGCAACGCGGAAATCGGCCAGGTTGTGGATAACTTCTGGTTGGTGGGACCGCTGAAGATCAGCGCGATGGAACAGACCCACTTTCTGCTCCGACTGGCGCAGGGAGAATTGCCATTCCCCGCCCCGGTGCAGTCCACCGTGCGCGCCATGACCCTGCTGGAAAGCGGCCCGGGCTGGGAGCTGCACGGCAAGACCGGCTGGTGCTTCGACTGCACGCCGGAACTCGGCTGGTGGGTGGGCTGGGTGAAGCGCAACGAGCGGCTCTACGGCTTCGCCCTGAACATCGACATGCCCGGCGGCGAGGCCGACATCGGCAAGCGCGTCGAACTGGGCAAGGCCAGTCTCAAGGCTCTCGGGATACTGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37066","NCBI_taxonomy_name":"Pseudomonas","NCBI_taxonomy_id":"286"}}}},"ARO_accession":"3006040","ARO_id":"44502","ARO_name":"OXA-847","CARD_short_name":"OXA-847","ARO_description":"OXA-847 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46513":{"category_aro_accession":"3007724","category_aro_cvterm_id":"46513","category_aro_name":"OXA-50-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-50.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5146":{"model_id":"5146","model_name":"OXA-848","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7521":{"protein_sequence":{"accession":"WP_019485147.1","sequence":"MRPLLFSALLLLSGHAQASEWNDSRAVDKLFGAAGVKGTFVLYDVQRQRYVGHDRERAETRFVPASTYKVANSLIGLSTGAVKSADEVLPYGGKPQRFKAWEHDMSLRDAIKASNVPVYQELARRIGLERMRANVSRLGYGNAEIGQVVDNFWLVGPLKISAMEQTRFLLRLAQGELPFPAPVQSTVRAMTLLESGPGWELHGKTGWCFDCTPELGWWVGWVKRNERLYGFALNIDMPGGEADIGKRVELGKASLKALGILP"},"dna_sequence":{"accession":"NG_066521.1","fmin":"0","fmax":"789","strand":"+","sequence":"ATGCGCCCTCTCCTCTTCAGCGCCCTTCTCCTGCTCTCCGGGCATGCCCAGGCCAGCGAATGGAACGACAGCCGGGCCGTGGACAAGCTATTCGGAGCGGCCGGTGTGAAAGGCACCTTCGTCCTCTACGATGTGCAGCGGCAGCGCTATGTCGGCCATGACCGGGAGCGCGCGGAAACTCGCTTCGTTCCTGCCTCCACCTACAAGGTGGCGAACAGCCTGATTGGCTTATCCACAGGGGCGGTTAAATCCGCCGACGAGGTTCTTCCCTATGGCGGCAAGCCCCAGCGCTTCAAGGCCTGGGAGCACGACATGAGCCTGCGCGACGCGATCAAGGCATCGAACGTACCGGTCTACCAGGAACTGGCGCGACGCATCGGCCTGGAGCGGATGCGCGCCAATGTCTCGCGCCTGGGTTACGGCAACGCGGAAATCGGCCAGGTTGTGGATAACTTCTGGTTGGTGGGACCGCTGAAGATCAGCGCGATGGAACAGACCCGCTTTCTGCTCCGACTGGCGCAGGGAGAATTGCCATTCCCCGCCCCGGTGCAGTCCACCGTGCGCGCCATGACCCTGCTGGAAAGCGGCCCGGGCTGGGAGCTGCACGGCAAGACCGGCTGGTGCTTCGACTGCACGCCGGAACTCGGCTGGTGGGTGGGCTGGGTGAAGCGCAACGAGCGGCTCTACGGCTTCGCCCTGAACATCGACATGCCCGGCGGCGAGGCCGACATCGGCAAGCGCGTCGAACTGGGCAAGGCCAGTCTCAAGGCTCTCGGGATACTGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006041","ARO_id":"44503","ARO_name":"OXA-848","CARD_short_name":"OXA-848","ARO_description":"OXA-848 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46513":{"category_aro_accession":"3007724","category_aro_cvterm_id":"46513","category_aro_name":"OXA-50-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-50.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5147":{"model_id":"5147","model_name":"OXA-849","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7522":{"protein_sequence":{"accession":"WP_150823477.1","sequence":"MRPLLISALLLLSGHAQASEWNDSQAVDKLFGAAGVKGTFVLYDVQRQRYVGHDRERAETRFVPASTYKVANSLIGLSTGAVRSADEVLPYGGKPQRFKAWEHDMSLRDAIEASNVPVYQELARRIGLERMRANVSRLGYGNAEIGQVVDNFWLVGPLKISAMEQTRFLLRLAQGELPFPAPVQSTVRAMTLLESGPGWELHGKTGWCFDCTPELGWWVGWVKRNERLYGFALNIDMPGGEADIGKRVELGKASLKALGILP"},"dna_sequence":{"accession":"NG_066522.1","fmin":"0","fmax":"789","strand":"+","sequence":"ATGCGCCCTCTCCTCATCAGTGCCCTTCTCCTGCTTTCCGGGCATGCCCAGGCCAGCGAATGGAACGACAGCCAGGCCGTGGACAAGCTATTCGGCGCGGCCGGGGTGAAAGGCACCTTCGTCCTCTACGATGTGCAGCGGCAGCGCTATGTCGGCCATGACCGGGAGCGCGCGGAAACCCGCTTCGTTCCCGCTTCCACCTACAAGGTGGCGAACAGCCTGATCGGCTTATCCACAGGGGCGGTTAGATCCGCCGACGAGGTTCTTCCCTATGGCGGCAAGCCCCAGCGCTTCAAGGCCTGGGAGCACGACATGAGCCTGCGCGACGCAATCGAGGCATCGAACGTACCGGTCTACCAGGAACTGGCGCGGCGCATCGGCCTGGAGCGGATGCGCGCCAATGTCTCGCGTCTGGGTTACGGCAACGCGGAAATCGGCCAGGTTGTGGATAACTTCTGGTTGGTGGGACCGCTGAAGATCAGCGCGATGGAACAGACCCGCTTTCTGCTCCGACTGGCGCAGGGAGAATTGCCATTCCCCGCCCCGGTGCAGTCCACCGTGCGCGCCATGACCCTGCTGGAAAGCGGCCCGGGCTGGGAGCTGCACGGCAAGACCGGCTGGTGCTTCGACTGCACGCCGGAACTCGGCTGGTGGGTGGGCTGGGTGAAGCGCAACGAGCGGCTCTACGGCTTCGCCCTGAACATCGACATGCCCGGCGGCGAGGCCGACATCGGCAAGCGCGTCGAACTGGGCAAGGCCAGTCTCAAGGCTCTCGGGATACTGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006042","ARO_id":"44504","ARO_name":"OXA-849","CARD_short_name":"OXA-849","ARO_description":"OXA-849 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46513":{"category_aro_accession":"3007724","category_aro_cvterm_id":"46513","category_aro_name":"OXA-50-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-50.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5148":{"model_id":"5148","model_name":"OXA-851","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7523":{"protein_sequence":{"accession":"WP_014603442.1","sequence":"MRPLLFSALLLLSGHAQASEWNDSQAVDKLFGAAGVKGTFVLYDVQRQRYVGHDRERAETRFVPASTYKVANSLIGLSTGAVRSADEVLPYGGKPQRFKAWEHDMSLRDAIKASNVPVYQELARRIGLERMRANVSRLGYGNAEIGQVVDNFWLVGPLKISAMEQTRFLLRLAQGELPFPAPVQSTVRAMTLLESGPGWELHGKTGWCFDCTPELGWWVGWVKRNERLYGFALNIDMPGGEADIGKRVELGKASLKALGILP"},"dna_sequence":{"accession":"NG_066524.1","fmin":"0","fmax":"789","strand":"+","sequence":"ATGCGCCCTCTCCTCTTCAGCGCCCTTCTCCTGCTCTCCGGGCATGCCCAGGCCAGCGAATGGAACGACAGCCAGGCCGTGGACAAGCTATTCGGCGCGGCCGGGGTGAAAGGCACCTTCGTCCTCTACGATGTGCAGCGGCAGCGCTATGTCGGCCACGACCGGGAGCGCGCGGAAACTCGCTTCGTTCCCGCTTCCACCTACAAGGTGGCGAACAGCCTGATCGGCTTATCCACAGGGGCGGTTAGATCCGCCGACGAGGTTCTTCCCTATGGCGGCAAACCCCAGCGCTTCAAGGCCTGGGAGCACGACATGAGCCTGCGCGACGCGATCAAGGCATCGAACGTACCGGTCTACCAGGAACTGGCGCGGCGCATCGGCCTGGAGCGGATGCGCGCCAATGTCTCGCGCCTGGGTTACGGCAACGCGGAAATCGGCCAGGTTGTGGATAACTTCTGGTTGGTGGGACCGCTGAAGATCAGCGCGATGGAACAGACCCGCTTTCTGCTCCGACTGGCGCAGGGAGAATTGCCATTCCCCGCCCCAGTGCAGTCCACCGTGCGCGCCATGACCCTGCTGGAAAGCGGCCCGGGCTGGGAGCTGCACGGCAAGACCGGCTGGTGCTTCGACTGCACGCCGGAACTCGGCTGGTGGGTGGGCTGGGTGAAGCGCAACGAGCGGCTCTACGGCTTCGCCCTGAACATCGACATGCCCGGCGGCGAGGCCGACATCGGCAAGCGCGTCGAACTGGGCAAGGCCAGTCTCAAGGCTCTCGGGATACTGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006043","ARO_id":"44505","ARO_name":"OXA-851","CARD_short_name":"OXA-851","ARO_description":"OXA-851 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46513":{"category_aro_accession":"3007724","category_aro_cvterm_id":"46513","category_aro_name":"OXA-50-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-50.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5149":{"model_id":"5149","model_name":"OXA-852","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7524":{"protein_sequence":{"accession":"WP_152315469.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFREWEKDMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_066714.1","fmin":"13","fmax":"838","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCGAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006044","ARO_id":"44506","ARO_name":"OXA-852","CARD_short_name":"OXA-852","ARO_description":"OXA-852 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5150":{"model_id":"5150","model_name":"OXA-853","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7525":{"protein_sequence":{"accession":"WP_114252036.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDDKAEKIKNLFNEAHTTGVLVIHQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGEKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_066715.1","fmin":"28","fmax":"853","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGTGCTTCGAAATCTGATGACAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCATCAAGGTCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAATGGGATGGGGAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATAGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006045","ARO_id":"44507","ARO_name":"OXA-853","CARD_short_name":"OXA-853","ARO_description":"OXA-853 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5151":{"model_id":"5151","model_name":"OXA-854","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7526":{"protein_sequence":{"accession":"WP_114158997.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSEDKAEKIKNLFNEAHTTGVLVIHQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGEKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_066716.1","fmin":"13","fmax":"838","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGTGCTTCAAAATCTGAGGACAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCATCAAGGTCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAATGGGATGGGGAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATAGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006046","ARO_id":"44508","ARO_name":"OXA-854","CARD_short_name":"OXA-854","ARO_description":"OXA-854 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5152":{"model_id":"5152","model_name":"OXA-855","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7527":{"protein_sequence":{"accession":"WP_032061328.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWNGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_066717.1","fmin":"24","fmax":"849","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGTTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGAACGGGCAAAAAAGGCTGTTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006047","ARO_id":"44509","ARO_name":"OXA-855","CARD_short_name":"OXA-855","ARO_description":"OXA-855 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5153":{"model_id":"5153","model_name":"OXA-856","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7528":{"protein_sequence":{"accession":"WP_001021774.1","sequence":"MNIKALLLITSAIFISACSPYIVSANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_066718.1","fmin":"18","fmax":"843","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGTCTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006048","ARO_id":"44510","ARO_name":"OXA-856","CARD_short_name":"OXA-856","ARO_description":"OXA-856 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5154":{"model_id":"5154","model_name":"OXA-857","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7529":{"protein_sequence":{"accession":"WP_152315470.1","sequence":"MNIKTLLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEVHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEYHKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_066719.1","fmin":"27","fmax":"852","strand":"+","sequence":"ATGAACATTAAAACACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGTACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGTACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006049","ARO_id":"44511","ARO_name":"OXA-857","CARD_short_name":"OXA-857","ARO_description":"OXA-857 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5155":{"model_id":"5155","model_name":"OXA-858","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7530":{"protein_sequence":{"accession":"WP_152315471.1","sequence":"MNIKAHLLITSAIFISACSPYIVTANPNHSASKSDKKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWNGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_066720.1","fmin":"30","fmax":"855","strand":"+","sequence":"ATGAACATTAAAGCACACTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATAAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGAACGGGCAAAAAAGGCTGTTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006050","ARO_id":"44512","ARO_name":"OXA-858","CARD_short_name":"OXA-858","ARO_description":"OXA-858 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5156":{"model_id":"5156","model_name":"OXA-859","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7531":{"protein_sequence":{"accession":"WP_152315472.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDKKAEKIKNLFNEAHTTGVLVIQQDQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKDMTLGYAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_066721.1","fmin":"15","fmax":"840","strand":"+","sequence":"ATGAATATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATAAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGACCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACTACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCTATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006051","ARO_id":"44513","ARO_name":"OXA-859","CARD_short_name":"OXA-859","ARO_description":"OXA-859 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5157":{"model_id":"5157","model_name":"OXA-860","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7532":{"protein_sequence":{"accession":"WP_152315473.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDKKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEIFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_066722.1","fmin":"12","fmax":"837","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATAAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAATATTTAAGTGGGACGGGCAAAAAAGGCTGTTCCCAGAATGGGAAAAGGACATGACCCTAGGTGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006052","ARO_id":"44514","ARO_name":"OXA-860","CARD_short_name":"OXA-860","ARO_description":"OXA-860 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5158":{"model_id":"5158","model_name":"OXA-861","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7533":{"protein_sequence":{"accession":"WP_152315474.1","sequence":"MNIKTLLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNKVHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEYHKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGGLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_066723.1","fmin":"31","fmax":"856","strand":"+","sequence":"ATGAACATTAAAACACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACAAAGTACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGTACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCGGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006053","ARO_id":"44515","ARO_name":"OXA-861","CARD_short_name":"OXA-861","ARO_description":"OXA-861 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5159":{"model_id":"5159","model_name":"OXA-862","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7534":{"protein_sequence":{"accession":"WP_152315475.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDDKAEKIKNLFNEAHTTGVLVIHQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_066724.1","fmin":"28","fmax":"853","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGACAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCATCAAGGTCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACGCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCCTTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATCTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006054","ARO_id":"44516","ARO_name":"OXA-862","CARD_short_name":"OXA-862","ARO_description":"OXA-862 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5160":{"model_id":"5160","model_name":"OXA-863","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7535":{"protein_sequence":{"accession":"WP_152315476.1","sequence":"MNIKALLLITSAIFISACSPYLVTANPNHSASKSNEKAEKIKNLFNKAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHRATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_066725.1","fmin":"14","fmax":"839","strand":"+","sequence":"ATGAATATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATCTAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTAATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACAAAGCACACACTACGGGTGTCTTAGTTATCCAGCAAGGGCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAGGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGACGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006055","ARO_id":"44517","ARO_name":"OXA-863","CARD_short_name":"OXA-863","ARO_description":"OXA-863 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5161":{"model_id":"5161","model_name":"OXA-864","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7536":{"protein_sequence":{"accession":"WP_152315477.1","sequence":"MNIKTLLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEVHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_066726.1","fmin":"13","fmax":"838","strand":"+","sequence":"ATGAACATTAAAACACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGTACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCCTTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006056","ARO_id":"44518","ARO_name":"OXA-864","CARD_short_name":"OXA-864","ARO_description":"OXA-864 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5162":{"model_id":"5162","model_name":"OXA-865","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7537":{"protein_sequence":{"accession":"WP_152315478.1","sequence":"MNIKAPLLITSAIFIPACSPYIVTANPNHSASKSDEKAEKIKNIFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_066727.1","fmin":"42","fmax":"867","strand":"+","sequence":"ATGAACATTAAAGCACCCTTACTTATAACAAGCGCTATTTTTATTCCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATATATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCCGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTGGGTTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006057","ARO_id":"44519","ARO_name":"OXA-865","CARD_short_name":"OXA-865","ARO_description":"OXA-865 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5163":{"model_id":"5163","model_name":"OXA-866","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7538":{"protein_sequence":{"accession":"WP_152315479.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKTTTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_066728.1","fmin":"30","fmax":"855","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTCTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGACAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGACGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCATTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006058","ARO_id":"44520","ARO_name":"OXA-866","CARD_short_name":"OXA-866","ARO_description":"OXA-866 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5164":{"model_id":"5164","model_name":"OXA-867","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7539":{"protein_sequence":{"accession":"WP_152315480.1","sequence":"MNIKTLLLITSAIFISACSPYIVSANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLERHKATTTEVFKWDGQKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFTYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_066729.1","fmin":"47","fmax":"872","strand":"+","sequence":"ATGAACATTAAAACACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGTCTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCATCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCGCCATAAGGCAACCACTACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTACTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006059","ARO_id":"44521","ARO_name":"OXA-867","CARD_short_name":"OXA-867","ARO_description":"OXA-867 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5165":{"model_id":"5165","model_name":"OXA-868","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7540":{"protein_sequence":{"accession":"WP_152315481.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDDKAEKIKNLFNEALTTGVLVIHQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGEKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_066730.1","fmin":"23","fmax":"848","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGACAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACTCACTACGGGTGTTTTAGTTATCCATCAAGGTCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAATGGGATGGGGAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATAGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006060","ARO_id":"44522","ARO_name":"OXA-868","CARD_short_name":"OXA-868","ARO_description":"OXA-868 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5166":{"model_id":"5166","model_name":"OXA-869","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7541":{"protein_sequence":{"accession":"WP_152315482.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELISKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_066731.1","fmin":"34","fmax":"859","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATATCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGGTGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006061","ARO_id":"44523","ARO_name":"OXA-869","CARD_short_name":"OXA-869","ARO_description":"OXA-869 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5167":{"model_id":"5167","model_name":"OXA-870","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7542":{"protein_sequence":{"accession":"WP_152315483.1","sequence":"MNIQALLLITSAIFISACSPYIVSANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_066732.1","fmin":"34","fmax":"859","strand":"+","sequence":"ATGAACATTCAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGTCTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACTACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006062","ARO_id":"44524","ARO_name":"OXA-870","CARD_short_name":"OXA-870","ARO_description":"OXA-870 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5168":{"model_id":"5168","model_name":"OXA-871","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7543":{"protein_sequence":{"accession":"WP_152315484.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQDQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFSEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_066733.1","fmin":"34","fmax":"859","strand":"+","sequence":"ATGAATATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGACCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACTACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCTCGGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACGCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCCTTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGTTGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAACTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006063","ARO_id":"44525","ARO_name":"OXA-871","CARD_short_name":"OXA-871","ARO_description":"OXA-871 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5169":{"model_id":"5169","model_name":"OXA-872","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7544":{"protein_sequence":{"accession":"WP_152315485.1","sequence":"MNIKTLLLITSAIFISACSPYIVSANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIRLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFTYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_066734.1","fmin":"34","fmax":"859","strand":"+","sequence":"ATGAACATTAAAACACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGTCTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCATCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACTACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTAGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTACTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006064","ARO_id":"44526","ARO_name":"OXA-872","CARD_short_name":"OXA-872","ARO_description":"OXA-872 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5170":{"model_id":"5170","model_name":"OXA-873","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7545":{"protein_sequence":{"accession":"WP_152315486.1","sequence":"MNIKALLLITSAIFISACSPYIVTANSNHSASKSDDKAEKIKNLFNEAHTTGVLVIHQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWNGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_066735.1","fmin":"16","fmax":"841","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATTCAAATCACAGTGCTTCAAAATCTGATGACAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCATCAAGGTCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGAACGGGCAAAAAAGGCTGTTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006065","ARO_id":"44527","ARO_name":"OXA-873","CARD_short_name":"OXA-873","ARO_description":"OXA-873 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5171":{"model_id":"5171","model_name":"OXA-874","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7546":{"protein_sequence":{"accession":"WP_152315487.1","sequence":"MNIKALLLITSTIFISACSPYIVTANPNHSTSKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEIFKWNGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_066736.1","fmin":"40","fmax":"865","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCACTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCACTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAATATTTAAGTGGAACGGGCAAAAAAGGCTGTTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTTATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGCGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006066","ARO_id":"44528","ARO_name":"OXA-874","CARD_short_name":"OXA-874","ARO_description":"OXA-874 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5172":{"model_id":"5172","model_name":"OXA-875","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7547":{"protein_sequence":{"accession":"WP_152315488.1","sequence":"MNIKALLLITSTIFISACSPYIVTANPNHSTSKSDEKAEKIKNLFNEAHTTGVLVIQQDQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEIFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSLKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_066737.1","fmin":"42","fmax":"867","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCACTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCACTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGACCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAATATTTAAGTGGGACGGGCAAAAAAGGCTGTTCCCAGAATGGGAAAAGGACATGACCCTAGGTGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCTAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006067","ARO_id":"44529","ARO_name":"OXA-875","CARD_short_name":"OXA-875","ARO_description":"OXA-875 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5173":{"model_id":"5173","model_name":"OXA-876","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7548":{"protein_sequence":{"accession":"WP_152315489.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDVKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIPIYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_066738.1","fmin":"40","fmax":"865","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGTAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCCAATTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAACAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCATTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006068","ARO_id":"44530","ARO_name":"OXA-876","CARD_short_name":"OXA-876","ARO_description":"OXA-876 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5174":{"model_id":"5174","model_name":"OXA-877","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7549":{"protein_sequence":{"accession":"WP_152315490.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEIKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_066739.1","fmin":"35","fmax":"860","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATCAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006069","ARO_id":"44531","ARO_name":"OXA-877","CARD_short_name":"OXA-877","ARO_description":"OXA-877 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5175":{"model_id":"5175","model_name":"OXA-878","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7550":{"protein_sequence":{"accession":"WP_152315491.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALISLEHHKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVNNFWLVGPLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGISSSVRKEITYRSLEQLGIL"},"dna_sequence":{"accession":"NG_066740.1","fmin":"40","fmax":"865","strand":"+","sequence":"ATGAACATTAAAGCCCTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTCTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCAGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGACGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCAATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATATCTAGCTCTGTTCGAAAAGAGATTACTTATAGAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006070","ARO_id":"44532","ARO_name":"OXA-878","CARD_short_name":"OXA-878","ARO_description":"OXA-878 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5176":{"model_id":"5176","model_name":"OXA-879","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7551":{"protein_sequence":{"accession":"WP_152315492.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSTSKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEIFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSLKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_066741.1","fmin":"44","fmax":"869","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGTTCACCTTATATAGTGACTGCTAATCCAAATCACAGCACTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAATATTTAAGTGGGACGGGCAAAAAAGGCTGTTCCCAGAATGGGAAAAGGACATGACCCTAGGTGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCTAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006071","ARO_id":"44533","ARO_name":"OXA-879","CARD_short_name":"OXA-879","ARO_description":"OXA-879 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5177":{"model_id":"5177","model_name":"OXA-880","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7552":{"protein_sequence":{"accession":"WP_152315493.1","sequence":"MNIKTLLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEVHTTGVLVIQQGQTQQSYGNNLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_066742.1","fmin":"39","fmax":"864","strand":"+","sequence":"ATGAACATTAAAACACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGTACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATAATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAGAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006072","ARO_id":"44534","ARO_name":"OXA-880","CARD_short_name":"OXA-880","ARO_description":"OXA-880 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5178":{"model_id":"5178","model_name":"OXA-881","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7553":{"protein_sequence":{"accession":"WP_152315494.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALISLEHHKATTTEVFKWDGKKRLFPEWEKNMTLGDAMKTSAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_066743.1","fmin":"27","fmax":"852","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGTTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCAGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAACTTCTGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCATTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006073","ARO_id":"44535","ARO_name":"OXA-881","CARD_short_name":"OXA-881","ARO_description":"OXA-881 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5179":{"model_id":"5179","model_name":"OXA-882","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7554":{"protein_sequence":{"accession":"WP_152315495.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQWNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_066744.1","fmin":"29","fmax":"854","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGGTGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAATGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006074","ARO_id":"44536","ARO_name":"OXA-882","CARD_short_name":"OXA-882","ARO_description":"OXA-882 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5180":{"model_id":"5180","model_name":"OXA-883","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7555":{"protein_sequence":{"accession":"WP_152315496.1","sequence":"MNIKTLLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWNGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQHEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_066745.1","fmin":"11","fmax":"836","strand":"+","sequence":"ATGAACATTAAAACACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGAACGGGCAAAAAAGGCTGTTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAACATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006075","ARO_id":"44537","ARO_name":"OXA-883","CARD_short_name":"OXA-883","ARO_description":"OXA-883 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5181":{"model_id":"5181","model_name":"OXA-884","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7556":{"protein_sequence":{"accession":"WP_152315497.1","sequence":"MNIKAPLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNIFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_066746.1","fmin":"12","fmax":"837","strand":"+","sequence":"ATGAACATTAAAGCACCCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATATATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATAGGCCTTGAGCACCATAAGGCAACCACTACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCCGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACGCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCCTTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006076","ARO_id":"44538","ARO_name":"OXA-884","CARD_short_name":"OXA-884","ARO_description":"OXA-884 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5182":{"model_id":"5182","model_name":"OXA-885","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7557":{"protein_sequence":{"accession":"WP_152315498.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDDKAEKIKNLFNEAHTTGVLVIHQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRIGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVIQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_066747.1","fmin":"42","fmax":"867","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGACAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCATCAAGGTCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATAGGCCTTGAGCACCATAAGGCAACCACTACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTATTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAACAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTATTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006077","ARO_id":"44539","ARO_name":"OXA-885","CARD_short_name":"OXA-885","ARO_description":"OXA-885 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5183":{"model_id":"5183","model_name":"OXA-886","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7558":{"protein_sequence":{"accession":"WP_152315499.1","sequence":"MNIKTLLLITSAIFISACSPYIVTANPNHSASKFDEKAEKIKNLFNEVHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_066748.1","fmin":"11","fmax":"836","strand":"+","sequence":"ATGAACATTAAAACACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATTTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGTACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGTAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACGCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCCTTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006078","ARO_id":"44540","ARO_name":"OXA-886","CARD_short_name":"OXA-886","ARO_description":"OXA-886 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5184":{"model_id":"5184","model_name":"OXA-887","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7559":{"protein_sequence":{"accession":"WP_152315500.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDKKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKDMTLGDVMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLSFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_066749.1","fmin":"12","fmax":"837","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATAAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTGTTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGTTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTTCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006079","ARO_id":"44541","ARO_name":"OXA-887","CARD_short_name":"OXA-887","ARO_description":"OXA-887 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5185":{"model_id":"5185","model_name":"OXA-888","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7560":{"protein_sequence":{"accession":"WP_152315501.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDKKAEKIKNLFNEAHTTGVLIIQQDQTQQSYGNDLARASTEYVPASTFKMLNALIGLENHKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLELLGIL"},"dna_sequence":{"accession":"NG_066750.1","fmin":"32","fmax":"857","strand":"+","sequence":"ATGAATATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATAAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAATTATCCAACAAGACCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGAACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGACGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACGCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGCATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACTATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006080","ARO_id":"44542","ARO_name":"OXA-888","CARD_short_name":"OXA-888","ARO_description":"OXA-888 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5186":{"model_id":"5186","model_name":"OXA-889","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7561":{"protein_sequence":{"accession":"WP_152315502.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGILVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMYKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_066751.1","fmin":"45","fmax":"870","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTATTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTATAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGGTGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006081","ARO_id":"44543","ARO_name":"OXA-889","CARD_short_name":"OXA-889","ARO_description":"OXA-889 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5187":{"model_id":"5187","model_name":"OXA-890","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7562":{"protein_sequence":{"accession":"WP_152315503.1","sequence":"MNIKALLLITSAIFISACSPYIVTAKPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKTTTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_066752.1","fmin":"31","fmax":"856","strand":"+","sequence":"ATGAACATTAAAGCCCTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAAACCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTCTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGACAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGACGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006082","ARO_id":"44544","ARO_name":"OXA-890","CARD_short_name":"OXA-890","ARO_description":"OXA-890 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5188":{"model_id":"5188","model_name":"OXA-891","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7563":{"protein_sequence":{"accession":"WP_152315504.1","sequence":"MNVKALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_066753.1","fmin":"15","fmax":"840","strand":"+","sequence":"ATGAACGTTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGACGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCATTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006083","ARO_id":"44545","ARO_name":"OXA-891","CARD_short_name":"OXA-891","ARO_description":"OXA-891 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5189":{"model_id":"5189","model_name":"OXA-892","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7564":{"protein_sequence":{"accession":"WP_152315505.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGILVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_066754.1","fmin":"30","fmax":"855","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTATTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGGTGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006084","ARO_id":"44546","ARO_name":"OXA-892","CARD_short_name":"OXA-892","ARO_description":"OXA-892 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5190":{"model_id":"5190","model_name":"OXA-893","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7565":{"protein_sequence":{"accession":"WP_194293137.1","sequence":"MNKYFTCYVVASLFLSGCTVQHNLINETPSQIVQGHNQVIHQYFDEKNTSGVLVIQTDKKINLYGNALSRANTEYVPASTFKMLNALIGLENQKTDINEIFKWKGEKRSFTAWEKDMTLGEAMKLSAVPVYQELARRIGLDLMQKEVKRIGFGNAEIGQQVDNFWLVGPLKVTPIQEVEFVSQLAHTQLPFSEKVQANVKNMLLLEESNGYKIFGKTGWAMDIKPQVGWLTGWVEQPDGKIVAFALNMEMRSEMPASIRNVLLMKSLKQLNII"},"dna_sequence":{"accession":"NG_070898.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGAATAAATATTTTACTTGCTATGTGGTTGCTTCTCTTTTTCTTTCTGGTTGTACGGTTCAGCATAATTTAATAAATGAAACCCCGAGTCAGATTGTTCAAGGACATAATCAGGTGATTCATCAATACTTTGATGAAAAAAACACCTCAGGTGTGCTGGTTATTCAAACAGATAAAAAAATTAATCTATATGGTAATGCTCTAAGCCGCGCAAATACAGAATATGTGCCAGCCTCTACATTTAAAATGTTGAATGCCCTGATCGGATTGGAGAACCAGAAAACGGATATTAATGAAATATTTAAATGGAAGGGCGAGAAAAGGTCATTTACCGCTTGGGAAAAAGACATGACACTAGGAGAAGCCATGAAGCTTTCTGCAGTCCCAGTCTATCAGGAACTTGCGCGACGTATCGGTCTTGATCTCATGCAAAAAGAAGTAAAACGTATTGGTTTCGGTAATGCTGAAATTGGACAGCAGGTTGATAATTTCTGGTTGGTAGGACCATTAAAGGTTACGCCTATTCAAGAGGTAGAGTTTGTTTCCCAATTAGCACATACACAGCTTCCATTTAGTGAAAAAGTGCAGGCTAATGTAAAAAATATGCTTCTTTTAGAAGAGAGTAATGGCTACAAAATTTTTGGAAAGACTGGTTGGGCAATGGATATAAAACCACAAGTGGGCTGGTTGACCGGCTGGGTTGAGCAGCCAGATGGAAAAATTGTCGCTTTTGCATTAAATATGGAAATGCGGTCAGAAATGCCGGCATCTATACGTAATGTATTATTGATGAAATCATTAAAACAGCTGAATATTATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006085","ARO_id":"44547","ARO_name":"OXA-893","CARD_short_name":"OXA-893","ARO_description":"OXA-893 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46499":{"category_aro_accession":"3007710","category_aro_cvterm_id":"46499","category_aro_name":"OXA-23-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases, specifically imipenem, derived from OXA-23, first identified in Acinetobacter baumannii.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5191":{"model_id":"5191","model_name":"OXA-894","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7566":{"protein_sequence":{"accession":"WP_144376393.1","sequence":"MRVLALSAVFLVASIIGMPAVAKEWQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGQTRDIATWNRDHNLITAMKYSVVPVYQEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISAIEQISFLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYSTRIEPKIGWWVGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP"},"dna_sequence":{"accession":"NG_066755.1","fmin":"0","fmax":"798","strand":"+","sequence":"ATGCGTGTATTAGCCTTATCGGCTGTGTTTTTGGTGGCATCGATTATCGGAATGCCTGCGGTAGCAAAGGAATGGCAAGAAAACAAAAGTTGGAATGCTCACTTTACTGAACATAAATCACAGGGCGTAGTTGTGCTCTGGAATGAGAATAAGCAGCAAGGATTTACCAATAATCTTAAACGGGCGAACCAAGCATTTTTACCCGCATCTACCTTTAAAATTCCCAATAGCTTGATCGCCCTCGATTTGGGCGTGGTTAAGGATGAACACCAAGTCTTTAAGTGGGATGGACAGACGCGCGATATCGCCACTTGGAATCGCGATCATAATCTAATCACCGCGATGAAATATTCAGTTGTGCCTGTTTATCAAGAATTTGCCCGCCAAATTGGCGAGGCACGTATGAGCAAGATGCTACATGCTTTCGATTATGGTAATGAGGACATTTCGGGCAATGTAGACAGTTTCTGGCTCGACGGTGGTATTCGAATTTCGGCCATTGAGCAAATCAGCTTTTTAAGAAAGCTGTATCACAATAAGTTACACGTATCGGAGCGCAGTCAGCGCATCGTGAAACAAGCCATGCTGACCGAAGCCAATGGCGACTATATTATTCGGGCTAAAACTGGATACTCGACTAGAATCGAACCTAAGATTGGCTGGTGGGTCGGTTGGGTTGAACTTGATGATAATGTGTGGTTTTTTGCGATGAATATGGATATGCCCACATCGGATGGTTTAGGGCTGCGCCAAGCCATCACAAAAGAAGTGCTCAAACAGGAAAAAATTATTCCCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39674","NCBI_taxonomy_name":"Shewanella xiamenensis","NCBI_taxonomy_id":"332186"}}}},"ARO_accession":"3006086","ARO_id":"44548","ARO_name":"OXA-894","CARD_short_name":"OXA-894","ARO_description":"OXA-894 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46510":{"category_aro_accession":"3007721","category_aro_cvterm_id":"46510","category_aro_name":"OXA-48-like beta-lactamase","category_aro_description":"OXA-48-type beta-lactamases are now routinely encountered in bacterial infections caused by carbapenam-resistant Enterobacterales. OXA-48-like proteins confer resistance to penicillin (which is efficiently hydrolyzed) and carbapenam antibiotics (which is more slowly broken down). The spectrum of activity of these variants varies, with some hydrolyzing expanded-spectrum oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5192":{"model_id":"5192","model_name":"OXA-896","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7567":{"protein_sequence":{"accession":"WP_156404658.1","sequence":"MKKILLLHMLVFVSATLPISSVASDEVETLKCTIIADAITGNTLYETGECARRVSPCSSFKLPLAIMGFDSGILQSPKSPTWELKPEYNPSPRDRTYKQVYPALWQSDSVVWFSQQLTSRLGVDRFTEYVKKFEYGNQDVSGDSGKHNGLTQSWLMSSLTISPKEQIQFLLRFVAHKLPVSEAAYDMAYATIPQYQAAEGWAVHGKSGSGWLRDNNGKINESRPQGWFVGWAEKNGRQVVFARLEIGKEKSDIPGGSKAREDIPVELPVLMGNK"},"dna_sequence":{"accession":"NG_067158.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAAAAAAATTTTGCTGCTGCATATGTTGGTGTTCGTTTCCGCCACTCTCCCAATCAGTTCCGTGGCTTCTGATGAGGTTGAAACGCTTAAATGCACCATCATCGCAGACGCCATTACCGGAAATACCTTATATGAGACCGGAGAATGTGCCCGTCGTGTGTCTCCGTGCTCGTCTTTTAAACTTCCATTGGCAATCATGGGGTTTGATAGTGGAATCTTGCAGTCGCCAAAATCACCTACGTGGGAATTGAAGCCGGAATACAACCCGTCTCCGAGAGATCGCACATACAAACAAGTCTATCCGGCGCTATGGCAAAGCGACTCTGTTGTCTGGTTCTCGCAGCAATTAACAAGCCGTCTGGGAGTTGATCGGTTCACGGAATACGTAAAGAAATTTGAGTACGGTAATCAAGATGTTTCCGGTGACTCGGGGAAGCATAACGGCTTGACCCAGTCATGGCTGATGTCGTCGCTCACCATATCTCCCAAGGAGCAAATTCAGTTTCTTCTACGCTTTGTCGCGCATAAGCTGCCTGTATCCGAAGCGGCTTATGACATGGCGTATGCCACAATCCCGCAGTACCAGGCAGCCGAAGGATGGGCTGTACATGGAAAAAGCGGCAGCGGCTGGCTTCGGGACAATAACGGCAAGATAAATGAAAGTCGTCCGCAGGGCTGGTTCGTGGGCTGGGCTGAAAAAAACGGACGGCAAGTTGTTTTCGCCCGATTGGAAATAGGAAAGGAAAAGTCCGATATTCCCGGCGGGTCTAAAGCACGAGAGGATATTCCCGTGGAATTACCCGTGTTGATGGGTAACAAATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3006087","ARO_id":"44549","ARO_name":"OXA-896","CARD_short_name":"OXA-896","ARO_description":"OXA-896 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46524":{"category_aro_accession":"3007735","category_aro_cvterm_id":"46524","category_aro_name":"OXA-9-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-9.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5193":{"model_id":"5193","model_name":"OXA-900","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7568":{"protein_sequence":{"accession":"WP_178317675.1","sequence":"MRLFVISAVLVMSSISAFPVFAASSPQKEWQETRSWDASFTQHQAKGVVVLWNENKQQGFTNNLKRANQGFLPASTFKIPNSLIALDLGMVKDEHQVFKWDGKNRDIAAWNRDHNLISAMKYSVVPIYQEFARQIGDARMGKMIAVFDYGNEDISGNLDSFWLDGGIRISAKEQIDFLRRLYHNKLHVSERSQRIVKQAMLTEANSDYIIRAKTGYAVRAEPSIGWWVGWVELDDNVWFFAMNMDMPSADGLALRQAITKEVLRQEKIIP"},"dna_sequence":{"accession":"NG_070745.1","fmin":"0","fmax":"813","strand":"+","sequence":"ATGCGTTTGTTCGTCATCTCGGCGGTATTGGTGATGTCCTCCATCTCAGCTTTCCCTGTTTTTGCTGCTAGCTCGCCCCAAAAAGAGTGGCAAGAAACCCGCAGTTGGGATGCCAGTTTTACTCAGCACCAAGCTAAAGGCGTGGTGGTGTTATGGAATGAAAATAAACAACAGGGATTCACTAATAATCTTAAACGCGCCAATCAAGGTTTTTTACCTGCATCGACGTTTAAAATTCCCAACAGTTTGATTGCTCTCGATTTAGGGATGGTGAAAGATGAGCACCAAGTTTTTAAGTGGGATGGTAAAAATCGTGATATTGCCGCCTGGAATCGTGACCATAATTTGATTAGCGCCATGAAGTATTCGGTTGTGCCCATCTACCAAGAGTTTGCTCGCCAAATAGGTGATGCTCGCATGGGGAAGATGATCGCTGTTTTTGATTATGGCAATGAGGATATCTCAGGCAATTTAGACAGTTTTTGGTTAGATGGAGGCATTCGGATCTCAGCCAAAGAGCAAATCGATTTCCTACGTCGGCTTTATCATAACAAGTTGCATGTTTCCGAGAGAAGTCAGCGTATTGTTAAGCAAGCCATGCTGACTGAAGCCAATAGTGACTATATTATCCGCGCAAAAACGGGTTATGCCGTAAGGGCCGAACCGAGCATTGGTTGGTGGGTCGGTTGGGTAGAACTCGATGATAATGTATGGTTTTTTGCAATGAATATGGATATGCCATCAGCGGATGGTTTGGCACTGCGCCAAGCCATTACAAAAGAAGTACTCAGGCAGGAAAAGATTATCCCCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3006088","ARO_id":"44550","ARO_name":"OXA-900","CARD_short_name":"OXA-900","ARO_description":"OXA-900 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5194":{"model_id":"5194","model_name":"OXA-901","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7569":{"protein_sequence":{"accession":"WP_031757092.1","sequence":"MRPLLFSALLLLSGHAQASEWNNSRAVDKLFGAAGVKGTFVLYDVQRQRYVGHDRERAETRFVPASTYKVANSLIGLSTGAVRSADEVLPYGGKPQRFKAWEHDMSLRDAIKASNVPVYQELARRIGLERMRANVSRLGYGNAEIGQVVDNFWLVGPLKISAMEQTRFLLRLAQGELPFPAPVQSTVRAMTLLESGPGWELHGKTGWCFDCTPELGWWVGWVKRNERLYGFALNIDMPGGEADIGKRVELGKASLKALGILP"},"dna_sequence":{"accession":"NG_068020.1","fmin":"0","fmax":"789","strand":"+","sequence":"ATGCGCCCTCTCCTCTTCAGCGCCCTTCTCCTGCTCTCCGGGCATGCCCAGGCCAGCGAATGGAACAACAGCCGGGCCGTGGACAAGCTATTCGGAGCGGCCGGTGTGAAAGGCACCTTCGTCCTTTACGATGTGCAGCGGCAGCGCTATGTCGGCCATGACCGGGAGCGCGCGGAAACCCGCTTCGTTCCCGCTTCCACCTACAAGGTGGCGAACAGCCTGATCGGCTTATCCACAGGGGCGGTTAGATCCGCCGACGAGGTTCTTCCCTATGGCGGCAAACCCCAGCGCTTCAAGGCCTGGGAGCACGACATGAGCCTGCGCGACGCGATCAAGGCATCGAACGTACCGGTCTACCAGGAACTGGCGCGGCGCATCGGCCTGGAGCGGATGCGCGCCAATGTCTCGCGCCTGGGTTACGGCAACGCGGAAATCGGCCAGGTTGTGGATAACTTCTGGTTGGTGGGACCGCTGAAGATCAGCGCGATGGAGCAGACCCGCTTTCTGCTCCGACTGGCGCAGGGAGAATTGCCATTCCCCGCCCCGGTGCAGTCCACCGTGCGCGCCATGACCCTGCTGGAAAGCGGCCCGGGCTGGGAGCTGCACGGCAAGACCGGCTGGTGCTTCGACTGCACGCCGGAACTCGGCTGGTGGGTGGGCTGGGTGAAGCGCAACGAGCGGCTCTACGGCTTCGCCCTGAACATCGACATGCCCGGCGGCGAGGCCGACATCGGCAAGCGCGTCGAACTGGGCAAGGCCAGTCTCAAGGCTCTCGGGATACTGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006089","ARO_id":"44551","ARO_name":"OXA-901","CARD_short_name":"OXA-901","ARO_description":"OXA-901 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46513":{"category_aro_accession":"3007724","category_aro_cvterm_id":"46513","category_aro_name":"OXA-50-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-50.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5195":{"model_id":"5195","model_name":"OXA-902","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7570":{"protein_sequence":{"accession":"WP_024916334.1","sequence":"MRPLFFSALLLLFSGHAQASEWNDSQAVDKLFGAAGVKGTFVLYDVQRQRYVGHDRGRAETRFVPASTYKVANSLIGLSTGAVKSADEVLPYGGKPQRFKAWEHDMSLRDAIKASNVPVYQELARRIGLERMRANVSRLGYGNAEIGQVVDNFWLVGPLKISAMEQTRFLLRLAQGELPFPAPVQSTVRAMTLLESGPGWELHGKTGWCFDCTPELGWWVGWVKRNERLYGFALNIDMPGGEADIGKRVELGKASLKALGILP"},"dna_sequence":{"accession":"NG_068021.1","fmin":"0","fmax":"792","strand":"+","sequence":"ATGCGCCCTCTCTTCTTCAGCGCCCTTCTCCTACTCTTCTCCGGGCATGCCCAGGCCAGCGAATGGAACGACAGCCAGGCTGTGGACAAGCTCTTCGGCGCGGCCGGGGTGAAAGGCACCTTCGTCCTCTACGATGTGCAGCGGCAGCGCTATGTCGGCCATGACCGGGGACGCGCGGAAACCCGCTTCGTTCCCGCTTCCACCTACAAGGTGGCGAACAGCCTGATCGGCTTATCCACAGGGGCGGTTAAATCCGCCGACGAGGTTCTTCCCTATGGCGGCAAGCCCCAGCGGTTCAAGGCCTGGGAACACGACATGAGCCTGCGCGACGCGATCAAGGCATCGAACGTACCGGTCTACCAGGAGCTGGCGCGACGCATCGGCCTGGAACGGATGCGCGCCAATGTTTCCCGCCTGGGTTACGGCAATGCGGAAATCGGCCAGGTTGTGGATAACTTCTGGCTGGTGGGACCGCTGAAGATCAGCGCGATGGAGCAGACCCGCTTTCTGCTCCGACTGGCACAGGGAGAATTGCCATTCCCCGCCCCGGTGCAGTCCACCGTGCGCGCCATGACCCTGCTGGAAAGCGGCCCGGGCTGGGAGCTGCACGGCAAGACCGGCTGGTGCTTCGACTGCACGCCGGAACTCGGCTGGTGGGTAGGCTGGGTGAAGCGCAACGAGCGGCTCTATGGCTTCGCCTTGAACATCGACATGCCCGGCGGCGAGGCCGACATCGGCAAGCGCGTCGAACTGGGCAAGGCCAGTCTCAAGGCCCTCGGGATACTGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006090","ARO_id":"44552","ARO_name":"OXA-902","CARD_short_name":"OXA-902","ARO_description":"OXA-902 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46513":{"category_aro_accession":"3007724","category_aro_cvterm_id":"46513","category_aro_name":"OXA-50-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-50.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5196":{"model_id":"5196","model_name":"OXA-903","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7571":{"protein_sequence":{"accession":"WP_164461291.1","sequence":"MRPLLFSALLLLSGHTQASEWNDSQAVDKLFGAAGVKGTFVLYDVQRQCYVGHDRERAETRFVPASTYKVSNSLIGLSTGAVRSADEVLPYGGKPQRFKAWEHDMSLREAIKASNVPVYQELARRIGLERMRANVSRLGYGNAEIGQVVDNFWLVGPLKISAMEQTRFLLRLAQGELPFPAPVQSTVRAMTLLESGPGWELHGKTGWCFDCTPELGWWVGWVKRNERLYGFALNIDMPGGEADIGKRVELGKASLKALGILP"},"dna_sequence":{"accession":"NG_068022.1","fmin":"0","fmax":"789","strand":"+","sequence":"ATGCGCCCTCTCCTCTTCAGTGCCCTTCTCCTGCTTTCCGGGCATACCCAGGCCAGCGAATGGAACGACAGCCAGGCCGTGGACAAGCTATTCGGCGCGGCCGGGGTGAAAGGCACCTTCGTCCTCTACGATGTGCAGCGGCAGTGCTATGTCGGCCATGACCGGGAGCGCGCGGAAACCCGCTTCGTTCCCGCTTCCACCTACAAGGTGTCGAACAGCCTGATCGGCTTATCCACAGGGGCGGTTAGATCCGCCGACGAGGTTCTTCCCTATGGCGGCAAGCCCCAGCGCTTCAAGGCCTGGGAGCACGACATGAGCCTGCGCGAGGCGATCAAGGCATCGAACGTACCGGTCTACCAGGAACTGGCGCGGCGCATCGGCCTGGAGCGGATGCGCGCCAATGTCTCGCGCCTGGGTTACGGCAACGCGGAAATCGGCCAGGTTGTGGATAACTTCTGGTTGGTGGGACCGCTGAAGATCAGCGCGATGGAACAGACCCGCTTTCTGCTCCGACTGGCGCAGGGAGAATTGCCATTCCCCGCCCCGGTGCAGTCCACCGTGCGCGCCATGACCCTGCTGGAAAGCGGCCCGGGCTGGGAGCTGCACGGCAAGACCGGCTGGTGCTTCGACTGCACGCCGGAGCTCGGCTGGTGGGTGGGCTGGGTGAAGCGCAACGAGCGGCTCTACGGCTTCGCCCTGAACATCGACATGCCCGGCGGCGAGGCCGACATCGGCAAGCGCGTCGAACTGGGCAAGGCCAGTCTCAAGGCTCTCGGGATACTGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006091","ARO_id":"44553","ARO_name":"OXA-903","CARD_short_name":"OXA-903","ARO_description":"OXA-903 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46513":{"category_aro_accession":"3007724","category_aro_cvterm_id":"46513","category_aro_name":"OXA-50-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-50.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5197":{"model_id":"5197","model_name":"OXA-904","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7572":{"protein_sequence":{"accession":"WP_003122322.1","sequence":"MRPLLFSALLLLSGHTQASEWNDSQAVDKLFGAAGVKGTFVLYDVQRQRYVGHDRERAETRFVPASTYKVANSLIGLSTGAVRSADEVLPYGGKPQRFKAWEHDMSLREAIKASNVPVYQELARRIGLERMRANVSRLGYGNAEIGQVVDNFWLVGPLKISAMEQTRFLLRLAQGELPFPAPVQSTVRAMTLLESGPGWELHGKTGWCFDCTPELGWWVGWVKRNERLYGFALNIDMPGGEADIGKRVELGKASLKALGILP"},"dna_sequence":{"accession":"NG_068023.1","fmin":"0","fmax":"789","strand":"+","sequence":"ATGCGCCCTCTCCTCTTCAGTGCCCTTCTCCTGCTTTCCGGGCATACCCAGGCCAGCGAATGGAACGACAGCCAGGCCGTGGACAAGCTATTCGGCGCGGCCGGGGTGAAAGGCACCTTCGTCCTCTACGATGTGCAGCGGCAGCGCTATGTCGGCCATGACCGGGAGCGCGCGGAAACCCGCTTCGTTCCCGCTTCCACCTACAAGGTGGCGAACAGCCTGATCGGCTTATCCACAGGGGCGGTTAGATCCGCCGACGAGGTTCTTCCCTATGGCGGCAAGCCCCAGCGCTTCAAGGCCTGGGAGCACGACATGAGCCTGCGCGAGGCGATCAAGGCATCGAACGTACCGGTCTACCAGGAACTGGCGCGGCGCATCGGCCTGGAGCGGATGCGCGCCAATGTCTCGCGCCTGGGTTACGGCAACGCGGAAATCGGCCAGGTTGTGGATAACTTCTGGTTGGTGGGACCGCTGAAGATCAGCGCGATGGAACAGACCCGCTTTCTGCTCCGACTGGCGCAGGGAGAATTGCCATTCCCCGCCCCGGTGCAGTCCACCGTGCGCGCCATGACCCTGCTGGAAAGCGGCCCGGGCTGGGAGCTGCACGGCAAGACCGGCTGGTGCTTCGACTGCACGCCGGAACTCGGCTGGTGGGTGGGCTGGGTGAAGCGCAACGAGCGGCTCTACGGCTTCGCCCTGAACATCGACATGCCCGGCGGCGAGGCCGACATCGGCAAGCGCGTCGAACTGGGCAAGGCCAGTCTCAAGGCTCTCGGGATACTGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006092","ARO_id":"44554","ARO_name":"OXA-904","CARD_short_name":"OXA-904","ARO_description":"OXA-904 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46513":{"category_aro_accession":"3007724","category_aro_cvterm_id":"46513","category_aro_name":"OXA-50-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-50.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5198":{"model_id":"5198","model_name":"OXA-905","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7573":{"protein_sequence":{"accession":"WP_003161096.1","sequence":"MRPLLFSALLLLSGHAQASEWNDSQAVDKLFGAAGVKGTFVLYDVQRQRYVGHDRERAETRFVPASTYKVANSLIGLSTGAVRSADEVLPYGGKPQRFKAWEHDMSLRDAIKASNVPVYQELARRIGLERMRANVSRLGYGNAEIGQAVDNFWLVGPLKISAMEQTRFLLRLAQGELPFPAPVQSTVRAMTLLESGPGWELHGKTGWCFDCTPELGWWVGWVKRNERLYGFALNIDMPGGEADIGKRVELGKASLKALGILP"},"dna_sequence":{"accession":"NG_068024.1","fmin":"0","fmax":"789","strand":"+","sequence":"ATGCGCCCTCTCCTCTTCAGCGCCCTTCTCCTGCTCTCCGGGCATGCCCAGGCCAGCGAATGGAACGACAGCCAGGCCGTGGACAAGCTATTCGGAGCGGCCGGTGTGAAAGGCACCTTCGTCCTCTACGATGTGCAGCGGCAGCGCTATGTCGGCCATGACCGGGAGCGCGCGGAAACCCGCTTCGTTCCCGCTTCCACCTACAAGGTGGCGAACAGCCTGATCGGCTTATCCACAGGGGCGGTTAGATCCGCCGACGAGGTTCTTCCCTATGGCGGCAAACCCCAGCGCTTCAAGGCCTGGGAGCACGACATGAGCCTGCGCGACGCGATCAAGGCATCGAACGTACCGGTCTACCAGGAACTGGCGCGGCGCATCGGCCTGGAGCGGATGCGCGCCAATGTCTCGCGCCTGGGTTACGGCAACGCGGAAATCGGCCAGGCTGTGGATAACTTCTGGTTGGTGGGACCGCTGAAGATCAGCGCGATGGAACAGACCCGCTTTCTGCTCCGACTGGCGCAGGGAGAATTGCCATTCCCCGCCCCGGTGCAGTCCACCGTGCGCGCCATGACCCTGCTGGAAAGCGGCCCGGGCTGGGAGCTGCACGGCAAGACCGGCTGGTGCTTCGACTGCACGCCGGAACTCGGCTGGTGGGTGGGCTGGGTGAAGCGCAACGAGCGGCTCTACGGCTTCGCCCTGAACATCGACATGCCCGGCGGCGAGGCCGACATCGGCAAGCGCGTCGAACTGGGCAAGGCCAGTCTCAAGGCTCTCGGGATACTGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37066","NCBI_taxonomy_name":"Pseudomonas","NCBI_taxonomy_id":"286"}}}},"ARO_accession":"3006093","ARO_id":"44555","ARO_name":"OXA-905","CARD_short_name":"OXA-905","ARO_description":"OXA-905 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46513":{"category_aro_accession":"3007724","category_aro_cvterm_id":"46513","category_aro_name":"OXA-50-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-50.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5199":{"model_id":"5199","model_name":"OXA-907","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7574":{"protein_sequence":{"accession":"WP_164461292.1","sequence":"MRPLLFSALLLLSGHAQASEWNDSQAVDKLFGAAGVKGTFVLYDVQRQRYVGHDRERAETRFVPASTYKVANSLIGLSIGAVKSADEVLPYGGKPQRFKAWEHDMSLRDAIKASNVPVYQELARRIGLERMRANVSRLGYGNAEIGQVVDNFWLVGPLKISAMEQTRFLLRLAQGELPFPAPVQSTVRAMTLLESGPGWELHGKTGWCFDCTPELGWWVGWVKRNERLYGFALNIDMPGGEADIGKRVELGKASLKALGILP"},"dna_sequence":{"accession":"NG_068026.1","fmin":"0","fmax":"789","strand":"+","sequence":"ATGCGCCCTCTCCTCTTCAGCGCCCTTCTCCTGCTCTCCGGGCATGCCCAGGCCAGCGAATGGAACGACAGCCAGGCCGTGGACAAGCTATTCGGCGCGGCCGGGGTGAAAGGCACCTTCGTCCTCTACGATGTGCAGCGGCAGCGCTATGTCGGCCATGACCGGGAGCGCGCGGAAACTCGCTTCGTTCCTGCCTCCACCTACAAGGTGGCGAACAGCCTGATTGGCTTATCCATAGGGGCGGTTAAATCCGCCGACGAGGTTCTTCCCTATGGCGGCAAGCCCCAGCGCTTCAAGGCCTGGGAGCACGACATGAGCCTGCGCGACGCGATCAAGGCATCGAACGTACCGGTCTACCAGGAACTGGCGCGACGCATCGGCCTGGAGCGGATGCGCGCCAATGTCTCGCGCCTGGGTTACGGCAACGCGGAAATCGGCCAGGTTGTGGATAACTTCTGGTTGGTGGGACCGCTGAAGATCAGCGCGATGGAACAGACCCGCTTTCTGCTCCGACTGGCGCAGGGAGAATTGCCATTCCCCGCCCCGGTGCAGTCCACCGTGCGCGCCATGACCCTGCTGGAAAGCGGCCCGGGCTGGGAGCTGCACGGCAAGACCGGCTGGTGCTTCGACTGCACGCCGGAACTCGGCTGGTGGGTGGGCTGGGTGAAGCGCAACGAGCGGCTCTACGGCTTCGCCCTGAACATCGACATGCCCGGCGGCGAGGCCGACATCGGCAAGCGCGTCGAACTGGGCAAGGCCAGTCTCAAGGCTCTCGGGATACTGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006094","ARO_id":"44556","ARO_name":"OXA-907","CARD_short_name":"OXA-907","ARO_description":"OXA-907 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46513":{"category_aro_accession":"3007724","category_aro_cvterm_id":"46513","category_aro_name":"OXA-50-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-50.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5200":{"model_id":"5200","model_name":"OXA-908","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7575":{"protein_sequence":{"accession":"WP_031694184.1","sequence":"MRPLLFSALLLLSGHAQASEWNDSQAVDKLFGAAGVKGTFVLYDVQRQRYVGHDRERAETRFVPASTYKVANSLIGLSTGAVKSADEVLPYGGKPQRFKAWEHDMSLRDAIKASNVPVYQELARRIGLERMHANVSRLGYGNAEIGQAVDNFWLVGPLKISAMEQTRFLLRLAQGELPFPAPVQSTVRAMTLLESGPGWELHGKTGWCFDCTPELGWWVGWVKRNERLYGFALNIDMPGGEADIGKRVELGKASLKALGILP"},"dna_sequence":{"accession":"NG_068027.1","fmin":"0","fmax":"789","strand":"+","sequence":"ATGCGCCCTCTCCTCTTCAGCGCCCTTCTCCTGCTCTCCGGGCATGCCCAGGCCAGCGAATGGAACGACAGCCAGGCCGTGGACAAGCTATTCGGCGCGGCCGGGGTGAAAGGCACCTTCGTCCTCTACGATGTGCAGCGGCAGCGCTATGTCGGCCACGACCGGGAGCGCGCGGAAACTCGCTTCGTTCCCGCTTCCACCTACAAGGTGGCGAACAGCCTGATTGGCTTATCCACAGGGGCGGTTAAATCCGCCGACGAGGTTCTTCCCTATGGCGGCAAGCCCCAGCGCTTCAAGGCCTGGGAGCACGACATGAGCCTGCGCGACGCGATCAAGGCATCGAACGTACCGGTCTACCAGGAACTGGCGCGGCGCATCGGCCTGGAGCGGATGCACGCCAATGTCTCGCGCCTGGGTTACGGCAACGCGGAAATCGGCCAGGCTGTGGATAACTTCTGGTTGGTGGGACCGCTGAAGATCAGCGCGATGGAACAGACCCGCTTTCTGCTCCGACTGGCGCAGGGAGAATTGCCATTCCCCGCCCCGGTGCAGTCCACCGTGCGCGCCATGACCCTGCTGGAAAGCGGCCCGGGCTGGGAGCTGCACGGCAAGACCGGCTGGTGCTTCGACTGCACGCCGGAACTCGGCTGGTGGGTGGGCTGGGTGAAGCGCAACGAGCGGCTCTACGGCTTCGCCCTGAACATCGACATGCCCGGCGGCGAGGCCGACATCGGCAAGCGCGTCGAACTGGGCAAGGCCAGTCTCAAGGCTCTCGGGATACTGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006095","ARO_id":"44557","ARO_name":"OXA-908","CARD_short_name":"OXA-908","ARO_description":"OXA-908 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46513":{"category_aro_accession":"3007724","category_aro_cvterm_id":"46513","category_aro_name":"OXA-50-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-50.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5201":{"model_id":"5201","model_name":"OXA-909","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7576":{"protein_sequence":{"accession":"WP_162278338.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDDKAEKIKNLFNEAHTTGVLVIHQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGEKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWYVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_068181.1","fmin":"100","fmax":"925","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGACAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCATCAAGGTCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAATGGGATGGGGAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATAGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGTATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006096","ARO_id":"44558","ARO_name":"OXA-909","CARD_short_name":"OXA-909","ARO_description":"OXA-909 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5202":{"model_id":"5202","model_name":"OXA-910","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7577":{"protein_sequence":{"accession":"WP_162280230.1","sequence":"MNIKTLLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEVHTKGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKDMALGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_068028.1","fmin":"100","fmax":"925","strand":"+","sequence":"ATGAACATTAAAACACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGTACACACTAAGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGGCCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006097","ARO_id":"44559","ARO_name":"OXA-910","CARD_short_name":"OXA-910","ARO_description":"OXA-910 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5203":{"model_id":"5203","model_name":"OXA-911","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7578":{"protein_sequence":{"accession":"WP_168247884.1","sequence":"MNKYFTCYVVASLFLSGCTVQHNLINETPSQIVQGHNQVIHQYFDEKNTSGVLVIQTDKKINLYGNALSRANTEYVPASTFKMLNALIGLENQKTDINEIFKWKGEKRSFTAWEKDMTLGEAMKLSAVPVYQELARRIGLDLMQKEVKRIGFGNAEIGQQVDNFWLVGPLKVTPIQEVEFVSQLAHTQLPFSEKVQANVKNMLLLEESNGYKIFGKTGWAMDIKKPQVGWLTGWVEQPDGKIVAFALNMEMRSEMPASIRNELLMKSLKQLNII"},"dna_sequence":{"accession":"NG_068182.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAATAAATATTTTACTTGCTATGTGGTTGCTTCTCTTTTTCTTTCTGGTTGTACGGTTCAGCATAATTTAATAAATGAAACCCCGAGTCAGATTGTTCAAGGACATAATCAGGTGATTCATCAATACTTTGATGAAAAAAACACCTCAGGTGTGCTGGTTATTCAAACAGATAAAAAAATTAATCTATATGGTAATGCTCTAAGCCGCGCAAATACAGAATATGTGCCAGCCTCTACATTTAAAATGTTGAATGCCCTGATCGGATTGGAGAACCAGAAAACGGATATTAATGAAATATTTAAATGGAAGGGCGAGAAAAGGTCATTTACCGCTTGGGAAAAAGACATGACACTAGGAGAAGCCATGAAGCTTTCTGCAGTCCCAGTCTATCAGGAACTTGCGCGACGTATCGGTCTTGATCTCATGCAAAAAGAAGTAAAACGTATTGGTTTCGGTAATGCTGAAATTGGACAGCAGGTTGATAATTTCTGGTTGGTAGGACCATTAAAGGTTACGCCTATTCAAGAGGTAGAGTTTGTTTCCCAATTAGCACATACACAGCTTCCATTTAGTGAAAAAGTGCAGGCTAATGTAAAAAATATGCTTCTTTTAGAAGAGAGTAATGGCTACAAAATTTTTGGAAAGACTGGTTGGGCAATGGATATAAAAAAACCACAAGTGGGCTGGTTGACCGGCTGGGTTGAGCAGCCAGATGGAAAAATTGTCGCTTTTGCATTAAATATGGAAATGCGGTCAGAAATGCCGGCATCTATACGTAATGAATTATTGATGAAATCATTAAAACAGCTGAATATTATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006098","ARO_id":"44560","ARO_name":"OXA-911","CARD_short_name":"OXA-911","ARO_description":"OXA-911 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46499":{"category_aro_accession":"3007710","category_aro_cvterm_id":"46499","category_aro_name":"OXA-23-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases, specifically imipenem, derived from OXA-23, first identified in Acinetobacter baumannii.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5204":{"model_id":"5204","model_name":"OXA-912","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7579":{"protein_sequence":{"accession":"WP_040068451.1","sequence":"MSRLLLSSLLAAGLLAALPASAASGCFLYADGNGQTLSSEGDCSSQLPPASTFKIPLALMGYDSGYLVDEEHPALPYKPSYDGWLPAWRETTTPRRWETYSVVWFSQQITEWLGMERFQQYVDRFDYGNRDLSGNPGKHDGLTQAWLSSSLAISPEEQARFLGKMLSGKLPVSAQTLQYTANILKVSEIDGWQIHGKTGMGYPKKLDGSLNRDQQIGWFVGWASKPGKQLIFVHTVVQKPGKQFASLKAKEEVLAALPAQLKKQ"},"dna_sequence":{"accession":"NG_068183.1","fmin":"0","fmax":"795","strand":"+","sequence":"ATGTCCCGCCTGCTTCTCTCCAGCCTGCTGGCTGCCGGTCTGCTCGCAGCCCTGCCTGCCTCCGCCGCCAGCGGCTGCTTTCTCTATGCTGACGGCAACGGCCAGACCCTCTCCAGCGAAGGGGACTGCTCCAGCCAGCTGCCACCCGCGTCCACCTTCAAGATCCCGCTGGCGCTGATGGGTTACGACAGTGGCTATCTGGTGGATGAAGAGCATCCGGCACTGCCTTACAAACCGAGCTATGACGGCTGGCTGCCCGCCTGGCGTGAAACCACCACCCCGCGCCGCTGGGAAACCTACTCGGTGGTCTGGTTCTCCCAGCAGATCACCGAATGGCTGGGGATGGAGCGCTTCCAGCAATATGTCGACCGCTTCGACTACGGCAATCGGGATCTCTCCGGTAATCCGGGCAAACATGATGGCCTGACCCAGGCCTGGCTCAGCTCCAGCCTCGCCATCAGTCCGGAGGAGCAGGCCCGCTTCCTCGGCAAGATGCTGAGCGGCAAGCTTCCGGTCTCTGCGCAGACCCTGCAGTACACCGCCAATATCCTCAAGGTGAGCGAGATCGACGGCTGGCAGATCCACGGCAAAACCGGCATGGGCTACCCGAAGAAGCTGGATGGCAGCCTCAACCGCGATCAGCAGATCGGCTGGTTCGTCGGCTGGGCCAGCAAACCGGGCAAACAGCTGATCTTCGTCCATACCGTGGTGCAAAAGCCCGGCAAGCAGTTCGCCTCCCTCAAGGCAAAAGAGGAGGTGCTGGCCGCCCTGCCTGCACAACTTAAAAAGCAGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37047","NCBI_taxonomy_name":"Aeromonas","NCBI_taxonomy_id":"642"}}}},"ARO_accession":"3006099","ARO_id":"44561","ARO_name":"OXA-912","CARD_short_name":"OXA-912","ARO_description":"OXA-912 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46488":{"category_aro_accession":"3007699","category_aro_cvterm_id":"46488","category_aro_name":"OXA-12-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-12.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5205":{"model_id":"5205","model_name":"OXA-913","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7580":{"protein_sequence":{"accession":"WP_031691948.1","sequence":"MRPLLFSALLLLSGHAQASEWNDSRAVDKLFGAAGVKGTFVLYDVQRQRYVGHDRERAETRFVPASTYKVANSLIGLSTGAVRSADEVLPYGGKPQRFNAWEHDMSLRDAIKASNVPVYQELARRIGLERMRANVSRLGYGNAEIGQVVDNFWLVGPLKISAMEQTRFLLRLAQGELPFPAPVQSTVRAMTLLESGPGWELHGKTGWCFDCTPELGWWVGWVKRNERLYGFALNIDMPGGEADIGKRVELGKASLKALGILP"},"dna_sequence":{"accession":"NG_068184.1","fmin":"0","fmax":"789","strand":"+","sequence":"ATGCGCCCTCTCCTCTTCAGCGCCCTTCTCCTGCTCTCCGGGCATGCCCAGGCCAGCGAATGGAACGACAGCCGGGCCGTGGACAAGCTATTCGGAGCGGCCGGTGTGAAAGGCACCTTCGTCCTTTACGATGTGCAGCGGCAGCGCTATGTCGGCCATGACCGGGAGCGCGCGGAAACCCGCTTCGTTCCCGCTTCCACCTACAAGGTGGCGAACAGCCTTATCGGCTTATCCACAGGGGCGGTTAGATCCGCCGACGAGGTTCTTCCCTATGGCGGCAAACCCCAGCGCTTCAACGCCTGGGAGCACGACATGAGCCTGCGCGACGCGATCAAGGCATCGAACGTACCGGTCTACCAGGAACTGGCGCGGCGCATCGGCCTGGAGCGGATGCGCGCCAATGTCTCGCGCCTGGGTTACGGCAACGCGGAAATCGGCCAGGTTGTGGATAACTTCTGGTTGGTGGGACCGCTGAAGATCAGCGCGATGGAGCAGACCCGCTTTCTGCTCCGACTGGCGCAGGGAGAATTGCCATTCCCCGCCCCGGTGCAGTCCACCGTGCGCGCCATGACCCTGCTGGAAAGCGGCCCGGGCTGGGAGCTGCACGGCAAGACCGGCTGGTGCTTCGACTGCACGCCGGAACTCGGCTGGTGGGTGGGCTGGGTGAAGCGCAACGAGCGGCTCTACGGCTTCGCCCTGAACATCGACATGCCCGGCGGCGAGGCCGACATCGGCAAGCGCGTCGAACTGGGCAAGGCCAGTCTCAAGGCTCTCGGGATACTGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37066","NCBI_taxonomy_name":"Pseudomonas","NCBI_taxonomy_id":"286"}}}},"ARO_accession":"3006100","ARO_id":"44562","ARO_name":"OXA-913","CARD_short_name":"OXA-913","ARO_description":"OXA-913 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46513":{"category_aro_accession":"3007724","category_aro_cvterm_id":"46513","category_aro_name":"OXA-50-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-50.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5206":{"model_id":"5206","model_name":"OXA-914","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7581":{"protein_sequence":{"accession":"WP_023132404.1","sequence":"MRPLLFSALLLLSGHTQASEWNDSQAVDKLFGAAGVKGTFVLYDVQRQRYVGHDRERAETRFVPASTYKVANSLIGLSTGAVRSADEVLPYGGKPQRFKAWEHDMSLRDAIKASNVPVYQELARRIGLERMRANVSRLSYGNAEIGQVVDNFWLVGPLKISAMEQTRFLLRLAQGELPFPAPVQSTVRAMTLLESGPGWELHGKTGWCFDCTPELGWWVGWVKRNERLYGFALNIDMPGGEADIGKRVELGKASLKALGILP"},"dna_sequence":{"accession":"NG_068185.1","fmin":"0","fmax":"789","strand":"+","sequence":"ATGCGCCCCCTCCTCTTCAGTGCCCTTCTCCTGCTTTCCGGGCATACCCAGGCCAGCGAATGGAACGACAGCCAGGCCGTGGACAAGCTATTCGGCGCGGCCGGGGTGAAAGGCACCTTCGTCCTCTACGATGTGCAGCGGCAGCGCTATGTCGGCCATGACCGGGAGCGCGCGGAAACCCGCTTCGTTCCCGCTTCCACCTACAAGGTGGCGAACAGCCTGATCGGCTTATCCACAGGGGCGGTTAGATCCGCCGACGAGGTTCTTCCCTATGGCGGCAAGCCCCAGCGCTTCAAGGCCTGGGAGCACGACATGAGCCTGCGCGACGCGATTAAGGCATCGAACGTACCGGTCTACCAGGAACTGGCGCGGCGCATCGGCCTGGAGCGGATGCGCGCCAATGTCTCGCGCCTGAGTTACGGCAACGCGGAAATCGGCCAGGTTGTGGATAACTTCTGGTTGGTGGGACCGCTGAAGATCAGCGCGATGGAACAGACCCGCTTTCTGCTCCGACTGGCGCAGGGAGAATTGCCATTCCCCGCCCCGGTGCAGTCCACCGTGCGCGCCATGACCCTGCTGGAAAGCGGCCCGGGCTGGGAGCTGCACGGCAAGACCGGCTGGTGCTTCGACTGCACGCCGGAACTCGGCTGGTGGGTGGGCTGGGTGAAGCGCAACGAGCGGCTCTACGGCTTCGCCCTGAACATCGACATGCCCGGCGGCGAGGCCGACATCGGCAAGCGCGTCGAACTGGGCAAGGCCAGTCTCAAGGCTCTCGGGATACTGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006101","ARO_id":"44563","ARO_name":"OXA-914","CARD_short_name":"OXA-914","ARO_description":"OXA-914 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46513":{"category_aro_accession":"3007724","category_aro_cvterm_id":"46513","category_aro_name":"OXA-50-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-50.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5207":{"model_id":"5207","model_name":"OXA-916","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7582":{"protein_sequence":{"accession":"WP_171476790.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDVKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIAVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_068510.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGTAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTGCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAACAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006102","ARO_id":"44564","ARO_name":"OXA-916","CARD_short_name":"OXA-916","ARO_description":"OXA-916 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5208":{"model_id":"5208","model_name":"OXA-917","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7583":{"protein_sequence":{"accession":"WP_161507793.1","sequence":"MSRILLSSLLAAGLFCSLPASAATGCMLFADGSGKPFSAQGDCASQLPPASTFKIPLALMGYDSGFLVDEQLPALPFKAGDPDFLPEWKQTTTPSRWMTYSVIWYSQRLTEWLGAARFQQYVDRFDYGNRDLSGNPGKHDGLTQAWLSSSLAISPQEQARFLGKLVSGKLPVSAQTLQHTANILRQPDIDGWQIHGKTGMGYPKLLDGSLDRDQQIGWFVGWASKQDQKLIFVHTVIQKPGKQFASLRAREEVFAALPEQLKKL"},"dna_sequence":{"accession":"NG_070181.1","fmin":"0","fmax":"795","strand":"+","sequence":"ATGTCCCGCATTCTGTTATCCAGCCTGCTTGCCGCCGGCCTCTTCTGCTCCCTGCCCGCCAGCGCCGCCACCGGCTGCATGCTGTTTGCCGATGGTAGCGGCAAGCCCTTCAGTGCCCAGGGTGACTGCGCCAGCCAGCTGCCTCCCGCCTCCACCTTCAAGATCCCGCTGGCGCTGATGGGCTATGACAGCGGCTTCCTGGTGGATGAGCAACTGCCAGCTCTGCCATTCAAAGCCGGTGACCCTGACTTCCTGCCGGAATGGAAACAGACCACCACCCCGAGCCGTTGGATGACCTATTCGGTGATCTGGTACTCCCAACGCCTCACCGAGTGGCTGGGGGCGGCGCGCTTCCAGCAATACGTGGACCGCTTCGACTACGGCAACCGGGATCTCTCGGGCAACCCGGGCAAACATGACGGCCTGACCCAAGCCTGGCTCAGTTCCAGCCTTGCCATCAGCCCCCAGGAGCAGGCACGCTTTCTCGGCAAACTGGTGAGCGGCAAGCTGCCGGTCTCCGCCCAGACGCTGCAGCACACGGCCAATATCCTGCGTCAGCCCGACATCGATGGCTGGCAGATCCATGGCAAGACCGGCATGGGCTATCCCAAACTGCTGGATGGCAGCCTCGACCGGGATCAGCAGATCGGCTGGTTCGTCGGCTGGGCCAGCAAGCAGGATCAGAAGCTCATCTTCGTCCACACCGTCATCCAGAAGCCTGGCAAGCAGTTTGCCTCCCTCAGGGCCAGGGAAGAGGTGTTTGCCGCACTGCCCGAACAGCTGAAGAAACTGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006103","ARO_id":"44565","ARO_name":"OXA-917","CARD_short_name":"OXA-917","ARO_description":"OXA-917 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46508":{"category_aro_accession":"3007719","category_aro_cvterm_id":"46508","category_aro_name":"OXA-427-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-427.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5209":{"model_id":"5209","model_name":"OXA-918","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7584":{"protein_sequence":{"accession":"WP_179284333.1","sequence":"MRVLALSAVFLVASIIGMPAVAKEWQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFKITNSLIALDLGVVKDEHQVFKWDGQTRDIATWNRDHNLITAMKYSVVPVYQEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISATEQISFLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYSTRIEPKIGWWVGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP"},"dna_sequence":{"accession":"NG_070182.1","fmin":"0","fmax":"798","strand":"+","sequence":"ATGCGTGTATTAGCCTTATCGGCTGTGTTTTTGGTGGCATCGATTATCGGAATGCCTGCGGTAGCAAAGGAATGGCAAGAAAACAAAAGTTGGAATGCTCACTTTACTGAACATAAATCACAGGGCGTAGTTGTGCTCTGGAATGAGAATAAGCAGCAAGGATTTACCAATAATCTTAAACGGGCGAACCAAGCATTTTTACCCGCATCTACCTTTAAAATTACCAATAGCTTGATCGCCCTCGATTTGGGCGTGGTTAAGGATGAACACCAAGTCTTTAAGTGGGATGGACAGACGCGCGATATCGCCACTTGGAATCGCGATCATAATCTAATCACCGCGATGAAATATTCAGTTGTGCCTGTTTATCAAGAATTTGCCCGCCAAATTGGCGAGGCACGTATGAGCAAGATGCTACATGCTTTCGATTATGGTAATGAGGACATTTCGGGCAATGTAGACAGTTTCTGGCTCGACGGTGGTATTCGAATTTCGGCCACGGAGCAAATCAGCTTTTTAAGAAAGCTGTATCACAATAAGTTACACGTATCGGAGCGCAGCCAGCGTATTGTCAAACAAGCCATGCTGACCGAAGCCAATGGTGACTATATTATTCGGGCTAAAACTGGATACTCGACTAGAATCGAACCTAAGATTGGCTGGTGGGTCGGTTGGGTTGAACTTGATGATAATGTGTGGTTTTTTGCGATGAATATGGATATGCCCACATCGGATGGTTTAGGGCTGCGCCAAGCCATCACAAAAGAAGTGCTCAAACAGGAAAAAATTATTCCCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3006104","ARO_id":"44566","ARO_name":"OXA-918","CARD_short_name":"OXA-918","ARO_description":"OXA-918 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46510":{"category_aro_accession":"3007721","category_aro_cvterm_id":"46510","category_aro_name":"OXA-48-like beta-lactamase","category_aro_description":"OXA-48-type beta-lactamases are now routinely encountered in bacterial infections caused by carbapenam-resistant Enterobacterales. OXA-48-like proteins confer resistance to penicillin (which is efficiently hydrolyzed) and carbapenam antibiotics (which is more slowly broken down). The spectrum of activity of these variants varies, with some hydrolyzing expanded-spectrum oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5210":{"model_id":"5210","model_name":"OXA-919","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7585":{"protein_sequence":{"accession":"WP_007879679.1","sequence":"MQRTIKAAFGLAGGTLLAMLALQGQASAAGQKLTCMIILNANSGEVIAKEGEICDKRNSPASTFKVPLALMGFESGILKDSHNPSWPYKEGYPAWRESWKQSVDPTYWEDQSVVWFSQELTRKLGKEKFQEYTDQLNYGNRDLRGDPGKNNGMLRSWISSSLTISPNEQADFLMKMVNNKLPFSEAAMTKTMAILPSHKLSNGWTAHGKTGSAFETGPKGKPDRRRQFGWYVGWAEKGDEKVVFVRLNRNMLAHNAGMGPVTRDEQWSILEKTLK"},"dna_sequence":{"accession":"NG_070746.1","fmin":"100","fmax":"928","strand":"+","sequence":"ATGCAAAGAACGATCAAAGCGGCTTTCGGATTGGCAGGCGGCACCTTGCTTGCGATGCTCGCCCTGCAAGGGCAGGCCTCGGCTGCAGGTCAAAAACTCACCTGCATGATCATCCTCAATGCGAACAGCGGTGAGGTCATCGCCAAAGAGGGCGAGATTTGCGACAAGCGCAACAGCCCGGCATCAACCTTCAAAGTGCCATTGGCGCTGATGGGTTTTGAAAGCGGCATATTAAAAGATAGCCACAACCCGTCCTGGCCTTACAAGGAGGGTTATCCGGCGTGGCGTGAATCCTGGAAACAATCTGTCGATCCGACCTATTGGGAAGACCAGTCGGTAGTCTGGTTCTCACAGGAGCTGACGCGGAAGCTCGGAAAAGAAAAGTTTCAGGAATACACAGACCAGCTCAATTACGGCAATCGTGATCTGCGTGGCGATCCGGGCAAGAATAACGGCATGTTGCGCTCATGGATTTCCTCGTCGCTGACAATATCGCCCAATGAGCAGGCGGATTTTCTGATGAAAATGGTCAATAACAAGCTGCCGTTCTCGGAAGCTGCAATGACCAAAACCATGGCCATTCTGCCCAGCCATAAGCTTTCAAACGGCTGGACAGCTCATGGCAAAACCGGTTCGGCGTTTGAAACAGGTCCCAAGGGCAAGCCGGATCGGCGTCGTCAATTTGGCTGGTATGTCGGATGGGCTGAGAAAGGCGATGAAAAAGTCGTATTTGTGCGCCTGAACCGAAATATGCTGGCGCATAATGCGGGTATGGGGCCGGTGACGCGTGACGAGCAATGGTCGATACTGGAAAAGACACTTAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3006105","ARO_id":"44567","ARO_name":"OXA-919","CARD_short_name":"OXA-919","ARO_description":"OXA-919 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5211":{"model_id":"5211","model_name":"OXA-920","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7586":{"protein_sequence":{"accession":"WP_179284336.1","sequence":"MRVLALSAVFLVASIIGMPAVAKEWQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGQTRDIATWNRDHNLITAMKYSVVPVYQEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISATEQISFLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYSTRIESKIGWWVGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP"},"dna_sequence":{"accession":"NG_070183.1","fmin":"0","fmax":"798","strand":"+","sequence":"ATGCGTGTATTAGCCTTATCGGCTGTGTTTTTGGTGGCATCGATTATCGGAATGCCTGCGGTAGCAAAGGAATGGCAAGAAAACAAAAGTTGGAATGCTCACTTTACTGAACATAAATCACAGGGCGTAGTTGTGCTCTGGAATGAGAATAAGCAGCAAGGATTTACCAATAATCTTAAACGGGCGAACCAAGCATTTTTACCCGCATCTACCTTTAAAATTCCCAATAGCTTGATCGCCCTCGATTTGGGCGTGGTTAAGGATGAACACCAAGTCTTTAAGTGGGATGGACAGACGCGCGATATCGCCACTTGGAATCGCGATCATAATCTAATCACCGCGATGAAATATTCAGTTGTGCCTGTTTATCAAGAATTTGCCCGCCAAATTGGCGAGGCACGTATGAGCAAGATGCTACATGCTTTCGATTATGGTAATGAGGACATTTCGGGCAATGTAGACAGTTTCTGGCTCGACGGTGGTATTCGAATTTCGGCCACGGAGCAAATCAGCTTTTTAAGAAAGCTGTATCACAATAAGTTACACGTATCGGAGCGCAGCCAGCGTATTGTCAAACAAGCCATGCTGACCGAAGCCAATGGTGACTATATTATTCGGGCTAAAACTGGATACTCGACTAGAATCGAATCTAAGATTGGCTGGTGGGTCGGTTGGGTTGAACTTGATGATAATGTGTGGTTTTTTGCGATGAATATGGATATGCCCACATCGGATGGTTTAGGGCTGCGCCAAGCCATCACAAAAGAAGTGCTCAAACAGGAAAAAATTATTCCCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3006106","ARO_id":"44568","ARO_name":"OXA-920","CARD_short_name":"OXA-920","ARO_description":"OXA-920 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46510":{"category_aro_accession":"3007721","category_aro_cvterm_id":"46510","category_aro_name":"OXA-48-like beta-lactamase","category_aro_description":"OXA-48-type beta-lactamases are now routinely encountered in bacterial infections caused by carbapenam-resistant Enterobacterales. OXA-48-like proteins confer resistance to penicillin (which is efficiently hydrolyzed) and carbapenam antibiotics (which is more slowly broken down). The spectrum of activity of these variants varies, with some hydrolyzing expanded-spectrum oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5212":{"model_id":"5212","model_name":"OXA-921","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7587":{"protein_sequence":{"accession":"WP_179284339.1","sequence":"MKNTIHINFAIFLIIANIIYSSASASTDISTVASQLFEGTEGCFLLYDASTNAEIAQFNKAKCAAQMAPDSTFKIALSLMAFDADIIDQKTIFKWDKIPKRMEIWNSNHTPKTWMQFSVVWVSQEITQKIGLNKIKNYLKDFDYGNQDFSGDKERNNGLTEAWLESSLKISPEEQIQFLRKIINHNLPVRNSAIENTIDNMYLQDLENSTKLYGKTGAGFTANRTLQNGWFEGFIISKSGHKYVFVSALTGNLGSNLTSSIKAKKNAITILNTLNL"},"dna_sequence":{"accession":"NG_070184.1","fmin":"0","fmax":"831","strand":"+","sequence":"ATGAAAAACACAATACATATCAACTTCGCTATTTTTTTAATAATTGCAAATATTATCTACAGCAGCGCCAGTGCATCAACAGATATCTCTACTGTTGCATCTCAATTATTTGAAGGAACTGAAGGTTGTTTTTTACTTTACGATGCATCCACAAACGCTGAAATTGCTCAATTCAATAAAGCAAAGTGTGCAGCGCAAATGGCACCAGATTCAACTTTCAAGATCGCATTATCACTTATGGCATTTGATGCGGATATAATAGATCAGAAAACCATATTCAAATGGGATAAAATCCCAAAAAGAATGGAAATTTGGAACAGCAATCATACACCAAAGACGTGGATGCAATTTTCTGTTGTTTGGGTTTCGCAAGAAATAACCCAAAAAATTGGATTAAATAAAATCAAGAATTATCTCAAAGATTTTGATTATGGAAATCAAGACTTCTCGGGAGATAAAGAAAGAAACAACGGATTAACAGAAGCATGGCTCGAAAGTAGCTTAAAAATTTCACCAGAAGAACAAATTCAATTCCTGCGTAAAATTATTAATCACAATCTTCCAGTTAGAAATTCAGCCATAGAAAACACCATAGATAACATGTATCTACAAGATCTGGAGAATAGTACAAAACTGTATGGGAAAACTGGTGCAGGATTCACAGCAAATAGAACCCTACAAAACGGATGGTTTGAAGGGTTTATCATAAGCAAATCAGGACATAAATATGTTTTTGTGTCCGCACTTACAGGAAACTTGGGGTCGAATTTAACATCAAGCATAAAAGCCAAGAAAAATGCAATCACCATTCTAAACACACTAAATTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43789","NCBI_taxonomy_name":"Klebsiella quasipneumoniae","NCBI_taxonomy_id":"1463165"}}}},"ARO_accession":"3006107","ARO_id":"44569","ARO_name":"OXA-921","CARD_short_name":"OXA-921","ARO_description":"OXA-921 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46485":{"category_aro_accession":"3007696","category_aro_cvterm_id":"46485","category_aro_name":"OXA-1-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-1.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5213":{"model_id":"5213","model_name":"OXA-922","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7588":{"protein_sequence":{"accession":"WP_188331876.1","sequence":"MRVLALSAVFLVASIIGMPAVAKEWQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGQTRDIAAWNRDHDLITAMKYSVVPVYQEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISAIQQIAFLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYSTGIEPKIGWWVGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP"},"dna_sequence":{"accession":"NG_070747.1","fmin":"0","fmax":"798","strand":"+","sequence":"ATGCGTGTATTAGCCTTATCGGCTGTGTTTTTGGTGGCATCGATTATCGGAATGCCAGCGGTAGCAAAGGAATGGCAAGAAAACAAAAGTTGGAATGCTCACTTTACTGAACATAAATCACAGGGCGTAGTTGTGCTCTGGAATGAGAATAAGCAGCAAGGATTTACCAATAATCTTAAACGGGCGAACCAAGCATTTTTACCCGCATCTACCTTTAAAATTCCCAATAGCTTGATCGCCCTCGATTTGGGCGTGGTTAAGGATGAACACCAAGTCTTTAAGTGGGATGGACAGACGCGTGATATCGCCGCTTGGAATCGTGACCATGACTTAATTACCGCGATGAAGTACTCAGTTGTGCCTGTTTATCAAGAATTTGCCCGCCAAATTGGTGAGGCACGTATGAGTAAAATGCTGCACGCCTTCGATTATGGCAATGAGGATATCTCGGGCAATGTAGACAGTTTTTGGCTCGATGGTGGTATTCGCATTTCGGCTATCCAGCAAATCGCTTTTTTACGCAAGCTGTATCACAACAAGCTGCACGTTTCTGAGCGTAGTCAGCGCATCGTGAAACAAGCCATGCTGACCGAAGCCAATGGCGACTATATTATTCGGGCTAAAACGGGATACTCGACTGGAATCGAACCTAAGATTGGCTGGTGGGTTGGTTGGGTTGAACTTGATGATAATGTGTGGTTTTTTGCGATGAATATGGATATGCCCACATCGGATGGTTTAGGGCTGCGCCAAGCCATCACAAAAGAAGTGCTCAAACAGGAGAAAATTATTCCCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39773","NCBI_taxonomy_name":"Enterobacter kobei","NCBI_taxonomy_id":"208224"}}}},"ARO_accession":"3006108","ARO_id":"44570","ARO_name":"OXA-922","CARD_short_name":"OXA-922","ARO_description":"OXA-922 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46510":{"category_aro_accession":"3007721","category_aro_cvterm_id":"46510","category_aro_name":"OXA-48-like beta-lactamase","category_aro_description":"OXA-48-type beta-lactamases are now routinely encountered in bacterial infections caused by carbapenam-resistant Enterobacterales. OXA-48-like proteins confer resistance to penicillin (which is efficiently hydrolyzed) and carbapenam antibiotics (which is more slowly broken down). The spectrum of activity of these variants varies, with some hydrolyzing expanded-spectrum oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5214":{"model_id":"5214","model_name":"OXA-923","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7589":{"protein_sequence":{"accession":"WP_179284342.1","sequence":"MRVLALSAVFLVASIIGMPAVAKEWQENKSWNAYFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGQTRDIAAWNRDHDLITAMKYSVVPVYQEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISATQQIAFLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYSTRIEPKIGWWVGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP"},"dna_sequence":{"accession":"NG_070185.1","fmin":"0","fmax":"798","strand":"+","sequence":"ATGCGTGTATTAGCCTTATCGGCTGTGTTTTTGGTGGCATCGATTATCGGAATGCCAGCGGTAGCAAAGGAATGGCAAGAAAACAAAAGTTGGAATGCTTACTTTACTGAACATAAATCACAGGGCGTAGTTGTGCTCTGGAATGAGAATAAGCAGCAAGGATTTACCAATAATCTTAAACGGGCGAACCAAGCATTTTTACCCGCATCTACCTTTAAAATTCCCAATAGCTTGATCGCCCTCGATTTGGGCGTGGTTAAGGATGAACACCAAGTCTTTAAGTGGGATGGACAGACGCGTGATATCGCCGCTTGGAATCGTGACCATGACTTAATTACCGCGATGAAGTACTCAGTTGTGCCTGTTTATCAAGAATTTGCCCGCCAAATTGGTGAGGCACGTATGAGTAAAATGCTGCACGCCTTCGATTATGGCAATGAGGATATCTCGGGCAATGTAGACAGTTTTTGGCTCGATGGTGGTATTCGCATTTCGGCTACCCAGCAAATCGCTTTTTTACGCAAGCTGTATCACAACAAGCTGCACGTTTCTGAGCGTAGTCAGCGCATCGTGAAACAAGCCATGCTGACCGAAGCCAATGGCGACTATATTATTCGGGCTAAAACGGGATACTCGACTAGAATCGAACCTAAGATTGGCTGGTGGGTTGGTTGGGTTGAACTTGATGATAATGTGTGGTTTTTTGCGATGAATATGGATATGCCCACATCGGATGGTTTAGGGCTGCGCCAAGCCATCACAAAAGAAGTGCTCAAACAGGAGAAAATTATTCCCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39773","NCBI_taxonomy_name":"Enterobacter kobei","NCBI_taxonomy_id":"208224"}}}},"ARO_accession":"3006109","ARO_id":"44571","ARO_name":"OXA-923","CARD_short_name":"OXA-923","ARO_description":"OXA-923 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46510":{"category_aro_accession":"3007721","category_aro_cvterm_id":"46510","category_aro_name":"OXA-48-like beta-lactamase","category_aro_description":"OXA-48-type beta-lactamases are now routinely encountered in bacterial infections caused by carbapenam-resistant Enterobacterales. OXA-48-like proteins confer resistance to penicillin (which is efficiently hydrolyzed) and carbapenam antibiotics (which is more slowly broken down). The spectrum of activity of these variants varies, with some hydrolyzing expanded-spectrum oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5215":{"model_id":"5215","model_name":"OXA-924","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7590":{"protein_sequence":{"accession":"WP_179284345.1","sequence":"MRVLALSAVFLVASIIGMPAVAKEWQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGQTRDIAAWNRDHDLITAMKYSVVPVYQEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISATQQIAFLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYSTEIEPKIGWWVGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP"},"dna_sequence":{"accession":"NG_070186.1","fmin":"0","fmax":"798","strand":"+","sequence":"ATGCGTGTATTAGCCTTATCGGCTGTGTTTTTGGTGGCATCGATTATCGGAATGCCAGCGGTAGCAAAGGAATGGCAAGAAAACAAAAGTTGGAATGCTCACTTTACTGAACATAAATCACAGGGCGTAGTTGTGCTCTGGAATGAGAATAAGCAGCAAGGATTTACCAATAATCTTAAACGGGCGAACCAAGCATTTTTACCCGCATCTACCTTTAAAATTCCCAATAGCTTGATCGCCCTCGATTTGGGCGTGGTTAAGGATGAACACCAAGTCTTTAAGTGGGATGGACAGACGCGTGATATCGCCGCTTGGAATCGTGACCATGACTTAATTACCGCGATGAAGTACTCAGTTGTGCCTGTTTATCAAGAATTTGCCCGCCAAATTGGTGAGGCACGTATGAGTAAAATGCTGCACGCCTTCGATTATGGCAATGAGGATATCTCGGGCAATGTAGACAGTTTTTGGCTCGATGGTGGTATTCGCATTTCGGCTACCCAGCAAATCGCTTTTTTACGCAAGCTGTATCACAACAAGCTGCACGTTTCTGAGCGTAGTCAGCGCATCGTGAAACAAGCCATGCTGACCGAAGCCAATGGCGACTATATTATTCGGGCTAAAACGGGATACTCGACTGAAATCGAACCTAAGATTGGCTGGTGGGTTGGTTGGGTTGAACTTGATGATAATGTGTGGTTTTTTGCGATGAATATGGATATGCCCACATCGGATGGTTTAGGGCTGCGCCAAGCCATCACAAAAGAAGTGCTCAAACAGGAGAAAATTATTCCCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3006110","ARO_id":"44572","ARO_name":"OXA-924","CARD_short_name":"OXA-924","ARO_description":"OXA-924 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46510":{"category_aro_accession":"3007721","category_aro_cvterm_id":"46510","category_aro_name":"OXA-48-like beta-lactamase","category_aro_description":"OXA-48-type beta-lactamases are now routinely encountered in bacterial infections caused by carbapenam-resistant Enterobacterales. OXA-48-like proteins confer resistance to penicillin (which is efficiently hydrolyzed) and carbapenam antibiotics (which is more slowly broken down). The spectrum of activity of these variants varies, with some hydrolyzing expanded-spectrum oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5216":{"model_id":"5216","model_name":"OXA-925","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7591":{"protein_sequence":{"accession":"WP_100507493.1","sequence":"MTVRLVSRALGAVLFASALTLPARADVLCTLVADAADGRILFQQGTRQDCTQRYTPASTFKLPIALMGADAGILQGPHQPVWNYQPAYPDWGGEAWRQPTDPARWIKYSVVWYSQLTARALGQERFQRYTSAFGYGNADVSGEPGKHNGTDGAWIISSLHISPFEQVDFLRKFVNRQLPVKAAAYDLAENLFEVGEADGWRLYGKTGTGSPGSHGVYTPANAYGWFVGWARKDDRQLVFARLLQDEGATQPNAGLRARDGLMRDWAAMVAAPRK"},"dna_sequence":{"accession":"NG_070187.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGACAGTTCGACTCGTTTCGCGCGCCCTGGGCGCAGTCCTCTTTGCGTCCGCCCTGACCCTGCCCGCCCGGGCGGACGTCCTGTGCACCCTGGTGGCCGACGCCGCCGACGGCCGCATCCTGTTCCAGCAGGGCACGCGGCAGGACTGCACGCAGCGCTACACCCCCGCCTCGACCTTCAAGCTGCCCATCGCCCTGATGGGCGCGGATGCCGGCATCCTGCAGGGCCCGCACCAGCCCGTCTGGAACTACCAGCCCGCTTATCCCGACTGGGGCGGCGAGGCCTGGCGCCAGCCCACCGATCCGGCTCGCTGGATCAAGTATTCGGTGGTCTGGTACTCGCAGTTGACCGCCAGGGCGCTGGGGCAGGAGCGCTTCCAGCGCTACACCTCCGCGTTCGGTTATGGCAACGCGGACGTCTCGGGTGAACCCGGCAAGCACAACGGCACCGATGGCGCGTGGATCATCTCCTCGCTGCACATTTCGCCGTTTGAGCAGGTGGACTTCCTGCGCAAGTTCGTCAACCGGCAACTGCCCGTCAAGGCGGCTGCCTATGACCTGGCCGAGAACCTGTTCGAGGTCGGCGAAGCCGACGGCTGGCGCCTGTACGGCAAGACCGGAACCGGCTCGCCCGGCAGCCACGGCGTCTACACGCCGGCCAACGCCTATGGCTGGTTCGTCGGCTGGGCGCGCAAGGACGACCGCCAACTGGTGTTTGCCCGCCTGCTGCAGGACGAGGGGGCGACCCAGCCCAATGCCGGCCTGCGCGCCCGCGACGGCCTGATGCGCGACTGGGCCGCCATGGTCGCGGCGCCCCGCAAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39091","NCBI_taxonomy_name":"Achromobacter ruhlandii","NCBI_taxonomy_id":"72557"}}}},"ARO_accession":"3006111","ARO_id":"44573","ARO_name":"OXA-925","CARD_short_name":"OXA-925","ARO_description":"OXA-925 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5217":{"model_id":"5217","model_name":"OXA-927","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7592":{"protein_sequence":{"accession":"WP_047480628.1","sequence":"MNIKTLLLITSAIFISACSPYIVTANLNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_073472.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAACACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCTAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGACGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCATTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006112","ARO_id":"44574","ARO_name":"OXA-927","CARD_short_name":"OXA-927","ARO_description":"OXA-927 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5218":{"model_id":"5218","model_name":"OXA-928","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7593":{"protein_sequence":{"accession":"WP_188331877.1","sequence":"MKTFAAYVIIACLSSTALAGSITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGTASNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGIIGG"},"dna_sequence":{"accession":"NG_070749.1","fmin":"0","fmax":"786","strand":"+","sequence":"ATGAAAACATTTGCCGCATATGTAATTATCGCGTGTCTTTCGAGTACGGCATTAGCTGGTTCAATTACAGAAAATACGTCTTGGAACAAAGAGTTCTCTGCCGAAGCCGTCAATGGTGTCTTCGTGCTTTGTAAAAGTAGCAGTAAATCCTGCGCTACCAATGACTTAGCTCGTGCATCAAAGGAATATCTTCCAGCATCAACATTTAAGATCCCCAACGCAATTATCGGCCTAGAAACTGGTGTCATAAAGAATGAGCATCAGGTTTTCAAATGGGACGGAAAGCCAAGAGCCATGAAGCAATGGGAAAGAGACTTGACCTTAAGAGGGGCAATACAAGTTTCAGCTGTTCCCGTATTTCAACAAATCGCCAGAGAAGTTGGCGAAGTAAGAATGCAGAAATACCTTAAAAAATTTTCCTATGGCAACCAGAATATCAGTGGTGGCATTGACAAATTCTGGTTGGAAGGCCAGCTTAGAATTTCCGCAGTTAATCAAGTGGAGTTTCTAGAGTCTCTATATTTAAATAAATTGTCAGCATCTAAAGAAAACCAGCTAATAGTAAAAGAGGCTTTGGTAACGGAGGCGGCACCTGAATATCTAGTGCATTCAAAAACGGGAACTGCGTCAAATCCTGGTGTCGCATGGTGGGTTGGGTGGGTTGAGAAGGAGACAGAGGTTTACTTTTTCGCCTTTAACATGGATATAGACAACGAAAGTAAGTTGCCGCTAAGAAAATCCATTCCCACCAAAATCATGGAAAGTGAGGGCATCATTGGTGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006113","ARO_id":"44575","ARO_name":"OXA-928","CARD_short_name":"OXA-928","ARO_description":"OXA-928 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46486":{"category_aro_accession":"3007697","category_aro_cvterm_id":"46486","category_aro_name":"OXA-10-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-10.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5219":{"model_id":"5219","model_name":"OXA-929","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7594":{"protein_sequence":{"accession":"WP_188331878.1","sequence":"MRVLALSAVFLVASIIGMPAVAKEWQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGQTRDIATWNRDHNLITAMKYSVVPVYQEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISATEQISFLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYSAKIGWWVGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP"},"dna_sequence":{"accession":"NG_070750.1","fmin":"0","fmax":"786","strand":"+","sequence":"ATGCGTGTATTAGCCTTATCGGCTGTGTTTTTGGTGGCATCGATTATCGGAATGCCTGCGGTAGCAAAGGAATGGCAAGAAAACAAAAGTTGGAATGCTCACTTTACTGAACATAAATCACAGGGCGTAGTTGTGCTCTGGAATGAGAATAAGCAGCAAGGATTTACCAATAATCTTAAACGGGCGAACCAAGCATTTTTACCCGCATCTACCTTTAAAATTCCCAATAGCTTGATCGCCCTCGATTTGGGCGTGGTTAAGGATGAACACCAAGTCTTTAAGTGGGATGGACAGACGCGCGATATCGCCACTTGGAATCGCGATCATAATCTAATCACCGCGATGAAATATTCAGTTGTGCCTGTTTATCAAGAATTTGCCCGCCAAATTGGCGAGGCACGTATGAGCAAGATGCTACATGCTTTCGATTATGGTAATGAGGACATTTCGGGCAATGTAGACAGTTTCTGGCTCGACGGTGGTATTCGAATTTCGGCCACGGAGCAAATCAGCTTTTTAAGAAAGCTGTATCACAATAAGTTACACGTATCGGAGCGCAGCCAGCGTATTGTCAAACAAGCCATGCTGACCGAAGCCAATGGTGACTATATTATTCGGGCTAAAACTGGATACTCGGCTAAGATTGGCTGGTGGGTCGGTTGGGTTGAACTTGATGATAATGTGTGGTTTTTTGCGATGAATATGGATATGCCCACATCGGATGGTTTAGGGCTGCGCCAAGCCATCACAAAAGAAGTGCTCAAACAGGAAAAAATTATTCCCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3006114","ARO_id":"44576","ARO_name":"OXA-929","CARD_short_name":"OXA-929","ARO_description":"OXA-929 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46510":{"category_aro_accession":"3007721","category_aro_cvterm_id":"46510","category_aro_name":"OXA-48-like beta-lactamase","category_aro_description":"OXA-48-type beta-lactamases are now routinely encountered in bacterial infections caused by carbapenam-resistant Enterobacterales. OXA-48-like proteins confer resistance to penicillin (which is efficiently hydrolyzed) and carbapenam antibiotics (which is more slowly broken down). The spectrum of activity of these variants varies, with some hydrolyzing expanded-spectrum oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5220":{"model_id":"5220","model_name":"OXA-932","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7595":{"protein_sequence":{"accession":"WP_121331722.1","sequence":"MKTFAAYVITACLSSTALASSITENTFWNKEFSAEAVNGVFVLCKSSSKSCATNNLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLSLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLGSLFLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKGTEVYFFAFNMDIDNENKLPLRKSIPTKIMASEGIIGG"},"dna_sequence":{"accession":"NG_070899.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGAAAACATTTGCCGCATATGTAATTACTGCGTGTCTTTCAAGTACGGCATTAGCTAGTTCAATTACAGAAAATACGTTTTGGAACAAAGAGTTCTCTGCCGAAGCCGTCAATGGTGTTTTCGTGCTTTGTAAAAGTAGCAGTAAATCCTGCGCTACCAATAACTTAGCTCGTGCATCAAAGGAATATCTTCCAGCATCAACATTTAAGATCCCCAACGCAATTATCGGCCTAGAAACTGGTGTCATAAAGAATGAGCATCAGGTTTTCAAATGGGACGGAAAGCCAAGAGCCATGAAACAATGGGAAAGAGACTTGAGCTTAAGAGGGGCAATACAAGTTTCAGCGGTTCCCGTATTTCAACAAATCGCCAGAGAAGTTGGCGAAGTAAGAATGCAGAAATATCTTAAAAAATTTTCATATGGTAACCAGAATATCAGTGGTGGCATTGACAAATTCTGGTTGGAGGGTCAGCTTAGAATTTCCGCAGTTAATCAAGTGGAGTTTCTAGGGTCTCTATTTTTAAATAAATTGTCAGCATCAAAAGAAAATCAGCTAATAGTAAAAGAGGCTTTGGTAACGGAGGCTGCGCCTGAATATCTTGTGCATTCAAAAACTGGTTTTTCTGGTGTGGGAACTGAGTCAAATCCTGGTGTCGCATGGTGGGTTGGCTGGGTTGAGAAGGGAACAGAGGTTTACTTTTTCGCCTTTAACATGGATATAGACAACGAAAATAAGTTGCCGCTAAGAAAATCCATTCCCACCAAAATCATGGCAAGTGAGGGCATCATTGGTGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"45686","NCBI_taxonomy_name":"Raoultella ornithinolytica","NCBI_taxonomy_id":"54291"}}}},"ARO_accession":"3006115","ARO_id":"44577","ARO_name":"OXA-932","CARD_short_name":"OXA-932","ARO_description":"OXA-932 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46486":{"category_aro_accession":"3007697","category_aro_cvterm_id":"46486","category_aro_name":"OXA-10-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-10.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5221":{"model_id":"5221","model_name":"OXA-935","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7596":{"protein_sequence":{"accession":"WP_141989064.1","sequence":"MKTFAAYVIIACLSSTALAGSITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKSWLEDQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGIIGG"},"dna_sequence":{"accession":"NG_070900.1","fmin":"100","fmax":"901","strand":"+","sequence":"ATGAAAACATTTGCCGCATATGTAATTATCGCGTGTCTTTCGAGTACGGCATTAGCTGGTTCAATTACAGAAAATACGTCTTGGAACAAAGAGTTCTCTGCCGAAGCCGTCAATGGTGTCTTCGTGCTTTGTAAAAGTAGCAGTAAATCCTGCGCTACCAATGACTTAGCTCGTGCATCAAAGGAATATCTTCCAGCATCAACATTTAAGATCCCCAACGCAATTATCGGCCTAGAAACTGGTGTCATAAAGAATGAGCATCAGGTTTTCAAATGGGACGGAAAGCCAAGAGCCATGAAGCAATGGGAAAGAGACTTGACCTTAAGAGGGGCAATACAAGTTTCAGCTGTTCCCGTATTTCAACAAATCGCCAGAGAAGTTGGCGAAGTAAGAATGCAGAAATACCTTAAAAAATTTTCCTATGGCAACCAGAATATCAGTGGTGGCATTGACAAATCCTGGTTGGAAGACCAGCTTAGAATTTCCGCAGTTAATCAAGTGGAGTTTCTAGAGTCTCTATATTTAAATAAATTGTCAGCATCTAAAGAAAACCAGCTAATAGTAAAAGAGGCTTTGGTAACGGAGGCGGCACCTGAATATCTAGTGCATTCAAAAACTGGTTTTTCTGGTGTGGGAACTGAGTCAAATCCTGGTGTCGCATGGTGGGTTGGGTGGGTTGAGAAGGAGACAGAGGTTTACTTTTTCGCCTTTAACATGGATATAGACAACGAAAGTAAGTTGCCGCTAAGAAAATCCATTCCCACCAAAATCATGGAAAGTGAGGGCATCATTGGTGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006116","ARO_id":"44578","ARO_name":"OXA-935","CARD_short_name":"OXA-935","ARO_description":"OXA-935 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46486":{"category_aro_accession":"3007697","category_aro_cvterm_id":"46486","category_aro_name":"OXA-10-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-10.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5222":{"model_id":"5222","model_name":"OXA-937","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7597":{"protein_sequence":{"accession":"WP_034081711.1","sequence":"MRPLLFSALLLLSGHTQASEWNDSQAVDKLFGAAGVKGTFVLYDVQRQRYVGHDRERAETRFVPASTYKVANSLIGLSTGAVRSADEVLPYGGKPQRFKAWEHDMSLRDAIKASNVPVYQELARRIGLERMRANVSRLGYGNAEIGQVVDNFWLVGPLKISAMEQTRFLIRLAQGELPFPAPVQSTVRAMTLLESGPGWELHGKTGWCFDCTPELGWWVGWVKRNERLYGFALNIDMPGGEADIGKRVELGKASLKALGILP"},"dna_sequence":{"accession":"NG_071209.1","fmin":"0","fmax":"789","strand":"+","sequence":"ATGCGCCCCCTCCTCTTCAGTGCCCTTCTCCTGCTTTCCGGGCATACCCAGGCCAGCGAATGGAACGACAGCCAGGCCGTGGACAAGCTATTCGGCGCGGCCGGGGTGAAAGGCACCTTCGTCCTCTACGATGTGCAGCGGCAGCGCTATGTCGGCCATGACCGGGAGCGCGCGGAAACCCGCTTCGTTCCCGCTTCCACCTACAAGGTGGCGAACAGCCTGATCGGCTTATCCACAGGGGCGGTTAGATCCGCCGACGAGGTTCTTCCCTATGGCGGCAAGCCCCAGCGCTTCAAGGCCTGGGAGCACGACATGAGCCTGCGCGACGCGATTAAGGCATCGAACGTACCGGTCTACCAGGAACTGGCGCGGCGCATCGGCCTGGAGCGGATGCGCGCCAATGTCTCGCGCCTGGGTTACGGCAACGCGGAAATCGGCCAGGTTGTGGATAACTTCTGGTTGGTGGGACCGCTGAAGATCAGCGCGATGGAACAGACCCGCTTTCTGATCCGACTGGCGCAGGGAGAATTGCCATTCCCCGCCCCGGTGCAGTCCACCGTGCGCGCCATGACCCTGCTGGAAAGCGGCCCGGGCTGGGAGCTGCACGGCAAGACCGGCTGGTGCTTCGACTGCACGCCGGAACTCGGCTGGTGGGTGGGCTGGGTGAAGCGCAACGAGCGGCTCTACGGCTTCGCCCTGAACATCGACATGCCCGGCGGCGAGGCCGACATCGGCAAGCGCGTCGAACTGGGCAAGGCCAGTCTCAAGGCTCTCGGGATACTGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006117","ARO_id":"44579","ARO_name":"OXA-937","CARD_short_name":"OXA-937","ARO_description":"OXA-937 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46513":{"category_aro_accession":"3007724","category_aro_cvterm_id":"46513","category_aro_name":"OXA-50-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-50.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5223":{"model_id":"5223","model_name":"OXA-938","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7598":{"protein_sequence":{"accession":"WP_086263559.1","sequence":"MNIKTLLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEVHTTGVLVIQQDQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_071210.1","fmin":"100","fmax":"925","strand":"+","sequence":"ATGAACATTAAAACACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGTACACACTACGGGTGTTTTAGTTATCCAACAAGACCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCCGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006118","ARO_id":"44580","ARO_name":"OXA-938","CARD_short_name":"OXA-938","ARO_description":"OXA-938 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5224":{"model_id":"5224","model_name":"OXA-939","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7599":{"protein_sequence":{"accession":"WP_086261538.1","sequence":"MNIKALLLITSAIFISACSPYIVSANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEIFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_071211.1","fmin":"100","fmax":"925","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGTCTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAATATTTAAGTGGGACGGGCAAAAAAGGCTGTTCCCAGAATGGGAAAAGGACATGACCCTAGGTGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006119","ARO_id":"44581","ARO_name":"OXA-939","CARD_short_name":"OXA-939","ARO_description":"OXA-939 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5225":{"model_id":"5225","model_name":"OXA-940","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7600":{"protein_sequence":{"accession":"WP_086442870.1","sequence":"MNIKTLLLITSAIFISACSPYIVTANPNHSTSKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEIFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"NG_071212.1","fmin":"100","fmax":"925","strand":"+","sequence":"ATGAACATTAAAACACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCACTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAATATTTAAGTGGGACGGGCAAAAAAGGCTGTTCCCAGAATGGGAAAAGGACATGACCCTAGGTGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006120","ARO_id":"44582","ARO_name":"OXA-940","CARD_short_name":"OXA-940","ARO_description":"OXA-940 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5226":{"model_id":"5226","model_name":"OXA-941","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7601":{"protein_sequence":{"accession":"WP_086395021.1","sequence":"MTKKALFFAIGTMFLSACSFNTVEQHQIQSISTNKNSEKIKSLFDQAQTTGVLIIKRGQTEEVYGNDLKRASTEYVPASTFKMLNALIGLEHHKATPTEVFKWDGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMSKEVKRIGFGNADIGSKVDDFWLVGPLKITPQQEAQFAYELAHKTLPFSKNMQEQVQSMLVIEEKNGRKIYAKSGWGWDVEPQVGWLTGWVVQPQGEIIAFSLNLEMKKSIPSSIRKEIAYKALEQLGIL"},"dna_sequence":{"accession":"NG_071213.1","fmin":"100","fmax":"922","strand":"+","sequence":"ATGACTAAAAAAGCTCTTTTCTTTGCCATTGGTACGATGTTTTTGTCTGCATGTTCTTTTAATACGGTAGAACAGCATCAAATACAGTCAATTTCTACCAATAAAAACTCAGAGAAAATTAAATCGTTGTTTGATCAAGCACAAACTACAGGTGTTTTAATTATAAAACGTGGGCAAACAGAGGAAGTCTATGGCAATGATCTTAAAAGAGCATCAACCGAATATGTTCCCGCCTCTACCTTTAAAATGTTAAATGCTTTGATTGGACTTGAACATCATAAAGCAACACCAACTGAAGTGTTTAAATGGGATGGGCAAAAGCGTTTATTTCCCGATTGGGAAAAAGACATGACCTTAGGTGATGCTATGAAGGCTTCTGCTATTCCAGTTTATCAGGAACTAGCTCGACGAATTGGCCTTGATCTTATGTCTAAAGAGGTAAAACGCATTGGTTTCGGTAATGCTGATATTGGTTCAAAAGTAGATGATTTTTGGCTTGTTGGTCCACTTAAAATTACACCTCAACAAGAAGCCCAGTTTGCTTATGAACTAGCCCATAAAACTCTTCCTTTTAGCAAAAATATGCAAGAACAAGTTCAATCTATGCTGGTCATAGAAGAAAAAAATGGACGGAAAATTTATGCCAAAAGTGGTTGGGGATGGGATGTGGAGCCTCAAGTGGGCTGGTTAACAGGCTGGGTCGTTCAACCACAAGGAGAAATTATAGCTTTCTCACTTAATTTAGAAATGAAAAAAAGCATACCTAGCTCTATTCGAAAAGAAATTGCTTATAAGGCATTAGAACAACTCGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3006121","ARO_id":"44583","ARO_name":"OXA-941","CARD_short_name":"OXA-941","ARO_description":"OXA-941 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46495":{"category_aro_accession":"3007706","category_aro_cvterm_id":"46495","category_aro_name":"OXA-213-like beta-lactamase","category_aro_description":"OXA-213-like enzymes have been identified to be intrinsic to A. calcoaceticus and have been subsequently detected in A. pittii. Phylogenetic analysis of OXA-213-like proteins identified two distinct subgroups within the OXA family. The first group was linked to A. pittii and the second group to A. calcoaceticus. The carbapenemase activity of these OXAs may be related to the species-dependent effect.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5227":{"model_id":"5227","model_name":"OXA-942","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7602":{"protein_sequence":{"accession":"WP_078225401.1","sequence":"MTKKALFFAIGTMFLSACSFNTVEQHQIQSISTNKNSEKIKSLFDQAQTEGVLVIKRGQIEEVYGNNLKRASTEYVPASTFKMLNALIGLEHHKATPIEVFKWDGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMSKEVKRIGFGNADIGSKVDNFWLVGPLKITPQQEAQFAYKLAHKTLPFSKNVQEQVQSMVFIEEKNGRKIYAKSGWGWDVDPQVGWFTGWVVQPQGEIVAFSLNLEMKKGIPSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"NG_071214.1","fmin":"100","fmax":"922","strand":"+","sequence":"ATGACTAAAAAAGCTCTTTTCTTTGCCATTGGTACGATGTTTTTGTCTGCATGTTCTTTTAATACGGTAGAACAACATCAAATACAGTCAATTTCTACCAATAAAAACTCAGAGAAAATTAAATCATTGTTTGATCAAGCACAAACTGAAGGTGTTTTAGTTATAAAACGTGGGCAAATAGAGGAAGTCTATGGCAATAATCTTAAAAGAGCATCAACCGAATATGTTCCCGCCTCTACCTTTAAAATGTTAAATGCTTTGATTGGACTTGAGCATCATAAAGCAACACCAATTGAAGTGTTTAAATGGGATGGGCAAAAGCGTTTATTTCCCGATTGGGAAAAAGACATGACATTAGGCGATGCTATGAAAGCTTCTGCTATTCCAGTTTATCAGGAACTAGCTCGACGAATTGGCCTTGATCTTATGTCTAAAGAGGTAAAACGCATTGGTTTCGGTAATGCTGATATTGGTTCAAAAGTAGATAATTTTTGGCTTGTTGGCCCCCTTAAAATTACACCACAACAAGAAGCGCAGTTTGCTTACAAATTAGCCCACAAAACTCTTCCTTTTAGCAAAAATGTACAAGAGCAAGTTCAATCTATGGTGTTCATAGAAGAAAAAAATGGACGAAAAATTTATGCCAAAAGTGGTTGGGGATGGGATGTTGACCCACAAGTTGGTTGGTTTACAGGCTGGGTAGTTCAACCACAAGGAGAAATTGTAGCGTTCTCACTCAATTTAGAAATGAAAAAAGGCATACCTAGTTCTATTCGAAAAGAAATTGCTTATAAGGGATTAGAGCAGCTAGGTATTTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3006122","ARO_id":"44584","ARO_name":"OXA-942","CARD_short_name":"OXA-942","ARO_description":"OXA-942 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46495":{"category_aro_accession":"3007706","category_aro_cvterm_id":"46495","category_aro_name":"OXA-213-like beta-lactamase","category_aro_description":"OXA-213-like enzymes have been identified to be intrinsic to A. calcoaceticus and have been subsequently detected in A. pittii. Phylogenetic analysis of OXA-213-like proteins identified two distinct subgroups within the OXA family. The first group was linked to A. pittii and the second group to A. calcoaceticus. The carbapenemase activity of these OXAs may be related to the species-dependent effect.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5228":{"model_id":"5228","model_name":"OXA-943","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7603":{"protein_sequence":{"accession":"WP_086398931.1","sequence":"MTKKALFFAIGTMFLSACSFNTVEQHQIQSISTNKNSEKIKSLFDQAQTTGVLIIKRGQTEEVYGNDLKRASTEYVPASTFKMLNALIGLEHHKATPTEVFKWDGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMSKEVKRIGFGNADIGSKVDDFWLVGPLKITPQQEAQFAYELAHKTLPFSKNVQEQVQSMLFIEEKNGRKIYAKSGWGWDVEPQVGWLTGWVVQPQGEIVAFSLNLEMKKGIPSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"NG_071215.1","fmin":"100","fmax":"922","strand":"+","sequence":"ATGACTAAAAAAGCTCTTTTCTTTGCCATTGGTACGATGTTTTTGTCTGCATGTTCTTTTAATACGGTAGAACAGCATCAAATACAGTCAATTTCTACCAATAAAAACTCAGAGAAAATTAAATCGTTGTTTGATCAAGCACAAACTACAGGTGTTTTAATTATAAAACGTGGGCAAACAGAGGAAGTCTATGGCAATGATCTTAAAAGAGCATCAACCGAATATGTTCCCGCCTCTACCTTTAAAATGTTAAATGCTTTGATTGGACTTGAACATCATAAAGCAACACCAACTGAAGTGTTTAAATGGGATGGGCAAAAGCGTTTATTTCCCGATTGGGAAAAAGACATGACCTTAGGTGATGCTATGAAGGCTTCTGCTATTCCAGTTTATCAGGAACTAGCTCGACGAATTGGCCTTGATCTTATGTCTAAAGAGGTAAAACGCATTGGTTTCGGTAATGCTGATATTGGTTCAAAAGTAGATGATTTTTGGCTTGTTGGTCCACTTAAAATTACACCTCAACAAGAAGCCCAGTTTGCTTATGAACTAGCCCATAAAACTCTTCCTTTTAGCAAGAATGTGCAAGAACAAGTTCAATCTATGCTGTTCATAGAAGAAAAAAATGGACGGAAAATTTATGCCAAAAGTGGTTGGGGATGGGATGTGGAGCCTCAAGTGGGCTGGTTAACAGGCTGGGTCGTTCAACCTCAAGGAGAAATTGTAGCGTTCTCACTCAATTTAGAAATGAAAAAAGGCATACCTAGTTCTATTCGAAAAGAAATTGCTTATAAGGGATTGGAACAACTCGGTATTTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3006123","ARO_id":"44585","ARO_name":"OXA-943","CARD_short_name":"OXA-943","ARO_description":"OXA-943 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46495":{"category_aro_accession":"3007706","category_aro_cvterm_id":"46495","category_aro_name":"OXA-213-like beta-lactamase","category_aro_description":"OXA-213-like enzymes have been identified to be intrinsic to A. calcoaceticus and have been subsequently detected in A. pittii. Phylogenetic analysis of OXA-213-like proteins identified two distinct subgroups within the OXA family. The first group was linked to A. pittii and the second group to A. calcoaceticus. The carbapenemase activity of these OXAs may be related to the species-dependent effect.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5229":{"model_id":"5229","model_name":"OXA-945","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7604":{"protein_sequence":{"accession":"WP_204376235.1","sequence":"MKKFILPIFSISTLLSLSACSSIQTKFEDTFHTSDQQHEKAIKSYFDEAQTQGVIVIKEGKNISTYGNNLARAHTEYVPASTFKMLNALIGLENHKATTAEIFKWDGKKRSYPMWEKDMTLGDAMALSAVPVYQELARRTGLDLMQKEVKRVGFGNMNIGTQVDNFWLVGPLKITPIQEVNFADDLANNRLPFKLETQEKVRKMLLIKEVNGSKIYAKSGWGMDVTPQVGWLTGWVEKSNGEKVPFSLNLEMKQGMSGSIRNEITYKSLENLGII"},"dna_sequence":{"accession":"NG_073473.1","fmin":"0","fmax":"828","strand":"+","sequence":"ATGAAAAAATTTATACTTCCTATATTCAGCATTTCTACGTTACTTTCTCTCAGTGCATGCTCATCTATTCAAACTAAATTTGAAGATACCTTTCATACTTCTGATCAGCAACATGAAAAAGCCATTAAAAGCTATTTTGATGAAGCTCAAACACAGGGTGTAATCGTTATTAAAGAGGGAAAAAATATTAGTACCTATGGTAATAATCTGGCACGAGCACATACTGAATATGTCCCTGCATCAACATTTAAGATGCTAAATGCCTTAATTGGACTAGAAAATCATAAAGCTACAACAGCTGAGATTTTCAAATGGGATGGTAAAAAAAGATCTTATCCTATGTGGGAAAAAGATATGACTTTAGGTGATGCCATGGCCCTTTCAGCAGTTCCTGTATATCAAGAACTTGCAAGACGGACTGGTTTAGACCTAATGCAAAAAGAAGTTAAACGGGTTGGTTTTGGTAATATGAACATTGGAACACAAGTTGATAATTTCTGGTTGGTTGGCCCTCTTAAAATTACACCAATACAAGAGGTTAATTTTGCCGATGATCTCGCGAATAATCGATTACCCTTTAAATTAGAAACTCAAGAAAAAGTAAGAAAAATGCTTCTGATTAAAGAAGTCAATGGTAGTAAAATTTATGCGAAAAGCGGATGGGGAATGGATGTAACCCCTCAAGTAGGTTGGTTAACAGGTTGGGTAGAAAAATCTAATGGCGAAAAAGTTCCCTTTTCTCTAAACTTAGAAATGAAGCAAGGAATGTCTGGTTCTATTCGTAATGAAATTACTTATAAATCATTAGAAAATTTAGGGATTATATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39090","NCBI_taxonomy_name":"Acinetobacter bereziniae","NCBI_taxonomy_id":"106648"}}}},"ARO_accession":"3006124","ARO_id":"44586","ARO_name":"OXA-945","CARD_short_name":"OXA-945","ARO_description":"OXA-945 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46490":{"category_aro_accession":"3007701","category_aro_cvterm_id":"46490","category_aro_name":"OXA-143-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-143.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5230":{"model_id":"5230","model_name":"OXA-946","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7605":{"protein_sequence":{"accession":"WP_204376236.1","sequence":"MRTRLFPLLSISISIFLSACSSPFIEPKDILPISTTDQTQQAIGSYFDEAQTQGVIVIKDGHNIDTYGNDLTRANTLYVPASTFKMLNALIGLENNKATVDEVFKWDGKKRSYSIWEKDMNLGEAMKLSAVPVYQELAKRIGVDLMQKEVKRVKFGNSNIGTKVDDFWLVGPLKITPIQEVEFADKLAHQELPFKQQVQKQVQDMLLIKEVEGNKIYAKSGWGMNVTPQVGWLTGWVEQPNGKKIAFSLNIKMKPNMPGSVRNEIALKSLKRLGII"},"dna_sequence":{"accession":"NG_073474.1","fmin":"0","fmax":"831","strand":"+","sequence":"GTGAGAACACGTTTATTTCCTTTATTAAGTATATCTATTTCAATTTTTTTAAGTGCGTGCTCCTCTCCATTTATCGAACCTAAAGACATCCTGCCTATTTCTACTACTGATCAAACTCAACAAGCGATTGGCTCTTATTTTGATGAAGCTCAGACACAGGGTGTTATTGTCATTAAGGATGGGCACAATATTGATACTTATGGTAATGATTTAACCCGAGCCAATACATTGTATGTACCTGCATCAACTTTTAAGATGTTAAATGCTTTAATTGGTTTGGAAAACAATAAAGCTACAGTCGATGAAGTTTTTAAATGGGATGGGAAAAAGCGTTCATATTCTATATGGGAAAAAGATATGAATTTGGGTGAAGCCATGAAGTTATCAGCGGTTCCTGTATATCAAGAACTCGCAAAACGGATAGGCGTAGATCTAATGCAAAAAGAAGTAAAAAGAGTCAAATTTGGTAATTCAAATATTGGGACAAAAGTTGATGACTTTTGGTTGGTAGGCCCATTAAAGATTACTCCTATTCAAGAAGTTGAGTTTGCTGACAAACTTGCCCATCAAGAGCTACCATTCAAACAGCAAGTACAAAAACAAGTCCAAGATATGCTGTTAATAAAGGAAGTAGAGGGTAACAAAATTTATGCAAAGAGCGGGTGGGGAATGAATGTCACCCCTCAAGTAGGCTGGTTAACAGGTTGGGTGGAACAACCTAACGGGAAAAAAATAGCTTTTTCATTGAACATTAAGATGAAACCAAACATGCCTGGTTCAGTCCGTAATGAAATAGCTCTTAAATCATTAAAACGCTTAGGTATTATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39094","NCBI_taxonomy_name":"Acinetobacter calcoaceticus","NCBI_taxonomy_id":"471"}}}},"ARO_accession":"3006125","ARO_id":"44587","ARO_name":"OXA-946","CARD_short_name":"OXA-946","ARO_description":"OXA-946 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46522":{"category_aro_accession":"3007733","category_aro_cvterm_id":"46522","category_aro_name":"OXA-679-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-679.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5231":{"model_id":"5231","model_name":"OXA-947","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7606":{"protein_sequence":{"accession":"WP_204376237.1","sequence":"MRTRLFPLSISISIFLSACSSPFIGPKDILPISTTDQTQQAIGSYFDEAQTQGVIVIKDDQDIDTYGNDLTRANTQYVPASTFKMLNALIGLENNKATVDEVFKWDGKKRSYSIWEKDMNLGEAMKLSAVPVYQELAKRIGVDLMQKEVKRVKFGNSNIGPKVDDFWLVGPLKITPIQEVEFANKLAHQELPFKQQVQKQVQDMLLIDEVDGNKIYAKSGWGMNVTPQVGWLTGWVEQPNGKKIAFSLNIEMKPNMPGSVRNEIALKSLKKLGII"},"dna_sequence":{"accession":"NG_073475.1","fmin":"0","fmax":"828","strand":"+","sequence":"GTGCGAACACGTCTATTTCCTTTAAGTATATCTATTTCAATTTTTTTAAGTGCATGCTCCTCTCCATTTATCGGACCTAAAGACATCCTGCCTATTTCTACTACTGATCAAACTCAACAAGCGATTGGCTCCTATTTTGATGAAGCTCAGACTCAGGGAGTTATTGTTATTAAGGATGATCAAGATATTGATACTTATGGTAATGATTTAACCCGAGCCAATACACAATATGTACCTGCGTCAACTTTTAAGATGTTAAATGCTTTAATTGGTTTGGAAAACAATAAAGCTACAGTCGATGAAGTTTTTAAATGGGATGGGAAAAAGCGTTCATATTCTATATGGGAAAAAGATATGAATTTGGGTGAAGCCATGAAGTTATCAGCGGTTCCTGTATATCAAGAACTCGCAAAACGGATAGGCGTAGATCTAATGCAAAAAGAAGTAAAAAGAGTCAAATTTGGTAATTCAAATATTGGACCAAAAGTTGATGATTTTTGGTTGGTAGGTCCTTTAAAGATTACTCCTATTCAAGAAGTAGAGTTTGCTAACAAACTTGCTCATCAAGAGCTACCATTCAAACAGCAAGTTCAAAAACAAGTTCAAGATATGCTATTAATAGATGAAGTAGATGGCAACAAGATTTATGCTAAGAGTGGTTGGGGAATGAATGTTACCCCTCAGGTAGGTTGGTTAACAGGTTGGGTAGAACAACCTAACGGGAAAAAAATAGCTTTTTCATTGAACATTGAGATGAAACCGAACATGCCCGGTTCGGTCCGTAATGAAATAGCTCTTAAATCATTAAAAAAATTAGGTATTATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42801","NCBI_taxonomy_name":"Acinetobacter lactucae","NCBI_taxonomy_id":"1785128"}}}},"ARO_accession":"3006126","ARO_id":"44588","ARO_name":"OXA-947","CARD_short_name":"OXA-947","ARO_description":"OXA-947 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46522":{"category_aro_accession":"3007733","category_aro_cvterm_id":"46522","category_aro_name":"OXA-679-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-679.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5232":{"model_id":"5232","model_name":"OXA-948","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7607":{"protein_sequence":{"accession":"WP_204376238.1","sequence":"MRTRLFPLLSISISIFLSACSSPFIAPKDILPISAIKLSQQTIGTYFDEAQTQGVIVIKDGQNIDSYGNDLTRANTQYVPASTFKMLNALIGLENNKATVDEVFKWDGKKRSYSMWEKDMNLGEAMKLSAVPVYQELAKRIGLDLMQKEVKRVKFGNSNIGTKVDDFWLVGPLKITPIQEVEFADKLAHQELPFKQQVQKQVQDMLLIDEVDGNKIYAKSGWGMNVTPQVGWLTGWVEQPNGKKIAFSLNIEMKPNMPGSVRNEIALKSLKHLGII"},"dna_sequence":{"accession":"NG_073476.1","fmin":"0","fmax":"831","strand":"+","sequence":"GTGCGAACACGTTTATTTCCTTTATTAAGTATATCTATTTCAATTTTTTTAAGTGCATGTTCCTCTCCATTTATCGCACCTAAAGACATCTTACCTATTTCTGCTATTAAGCTAAGTCAACAAACGATTGGCACATACTTTGATGAAGCTCAGACTCAAGGCGTTATTGTTATTAAAGACGGTCAAAATATTGATAGTTATGGTAATGATTTAACCAGAGCCAATACACAATATGTACCTGCATCAACTTTTAAGATGTTAAATGCTTTAATTGGTTTGGAAAACAATAAAGCTACAGTCGATGAAGTTTTTAAGTGGGATGGGAAAAAACGTTCATATTCTATGTGGGAAAAAGATATGAATTTGGGTGAAGCCATGAAGTTATCAGCGGTTCCTGTATATCAAGAACTTGCAAAACGGATAGGCTTGGATCTGATGCAAAAAGAAGTAAAAAGAGTCAAATTTGGTAATTCAAATATTGGGACAAAAGTTGATGATTTCTGGTTGGTAGGTCCATTAAAGATTACTCCAATTCAAGAAGTAGAGTTTGCTGACAAACTTGCTCATCAAGAACTACCATTCAAACAGCAAGTCCAAAAACAAGTTCAAGATATGCTGTTAATAGATGAAGTAGATGGCAACAAGATTTATGCTAAGAGTGGTTGGGGAATGAATGTTACCCCTCAGGTAGGTTGGTTAACAGGTTGGGTGGAACAACCTAACGGGAAAAAAATAGCTTTTTCATTGAACATTGAGATGAAACCAAACATGCCTGGTTCAGTCCGTAATGAAATAGCTCTTAAATCATTAAAACACTTAGGTATTATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3006127","ARO_id":"44589","ARO_name":"OXA-948","CARD_short_name":"OXA-948","ARO_description":"OXA-948 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46522":{"category_aro_accession":"3007733","category_aro_cvterm_id":"46522","category_aro_name":"OXA-679-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-679.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5233":{"model_id":"5233","model_name":"OXA-949","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7608":{"protein_sequence":{"accession":"WP_204376239.1","sequence":"MRKNLFPLSISISIFLSACSSPFIGPKDILPISTIKQSQQAIGSYFNEAQTQGVIVIKDGQNIDTYGNDLTRANTQYVPASTFKMLNALIGLENNKATVDEVFKWDGKKRSYSMWEKDMNLGEAMKLSAVPVYQELAKRIGLDLMQKEVKRVDFGNSNIGTKVDDFWLVGPLKITPIQEVEFADKLAYRELPFKLQVQKQVQDMLLIDEVDGNKIYAKSGWGMNVTPQVGWLTGWVEQPNGKKIAFSLNIEMKPNMPGSVRNEIALKSLKKLGII"},"dna_sequence":{"accession":"NG_073477.1","fmin":"0","fmax":"828","strand":"+","sequence":"GTGCGAAAAAATTTATTTCCTTTAAGTATATCTATTTCAATTTTTTTAAGTGCATGCTCCTCTCCATTTATTGGACCTAAAGATATTTTACCTATTTCTACTATTAAGCAAAGTCAACAAGCGATTGGCTCCTACTTTAATGAAGCTCAAACACAGGGTGTTATTGTTATTAAGGATGGTCAAAATATTGATACTTATGGTAATGATTTAACTAGAGCCAATACACAATATGTACCTGCGTCAACTTTTAAGATGTTAAATGCTCTAATTGGTTTGGAAAACAATAAAGCTACAGTCGATGAAGTTTTTAAATGGGATGGGAAAAAACGTTCATATTCTATGTGGGAAAAAGATATGAATTTGGGTGAAGCCATGAAGTTATCAGCTGTTCCTGTATATCAAGAACTCGCAAAACGGATAGGCTTGGATCTAATGCAAAAAGAAGTTAAACGAGTCGATTTTGGTAATTCAAATATTGGTACAAAAGTTGATGATTTCTGGTTGGTAGGTCCATTAAAGATTACTCCTATTCAAGAAGTAGAGTTTGCTGACAAACTTGCCTATCGAGAGCTACCATTCAAACTGCAAGTACAAAAACAAGTCCAGGATATGCTGTTGATAGATGAAGTAGATGGCAACAAAATTTATGCTAAGAGTGGTTGGGGAATGAATGTCACCCCTCAAGTAGGTTGGTTAACAGGTTGGGTGGAACAACCTAACGGGAAAAAAATAGCTTTTTCATTGAACATTGAGATGAAACCAAACATGCCTGGTTCGGTCCGTAATGAAATAGCTCTTAAATCATTAAAAAAATTAGGTATTATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42801","NCBI_taxonomy_name":"Acinetobacter lactucae","NCBI_taxonomy_id":"1785128"}}}},"ARO_accession":"3006128","ARO_id":"44590","ARO_name":"OXA-949","CARD_short_name":"OXA-949","ARO_description":"OXA-949 is a OXA beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46522":{"category_aro_accession":"3007733","category_aro_cvterm_id":"46522","category_aro_name":"OXA-679-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-679.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5234":{"model_id":"5234","model_name":"OXY-2-11","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7609":{"protein_sequence":{"accession":"WP_004111091.1","sequence":"MIKSSWRKIAMLAAAVPLLLASGALWASTDAIHQKLTDLEKRSGGRLGVALINTADNSQILYRGDERFAMCSTSKVMAAAAVLKQSESNKEVVNKRLEINAADLVVWSPITEKHLQSGMTLAELSAATLQYSDNTAMNLIIGYLGGPEKVTAFARSIGDATFRLDRTEPTLNTAIPGDERDTSTPLAMAESLRKLTLGNALGEQQRAQLVTWLKGNTTGGQSIRAGLPESWVVGDKTGAGDYGTTNDIAVIWPEDHAPLVLVTYFTQPQQDAKNRKEVLAAAAKIVTEGL"},"dna_sequence":{"accession":"NG_049848.1","fmin":"0","fmax":"873","strand":"+","sequence":"ATGATAAAAAGTTCGTGGCGTAAAATTGCAATGCTAGCCGCCGCCGTTCCGCTGCTGCTGGCGAGCGGCGCACTGTGGGCCAGTACCGATGCTATCCATCAGAAGCTGACAGATCTCGAGAAGCGTTCAGGCGGCAGGTTGGGCGTGGCGCTAATCAACACGGCAGATAATTCTCAAATCTTATATCGCGGCGACGAGCGTTTTGCCATGTGCAGCACCAGTAAAGTGATGGCCGCCGCCGCGGTATTAAAACAGAGCGAAAGCAATAAAGAGGTGGTAAATAAAAGGCTGGAGATTAACGCAGCCGATTTGGTGGTCTGGAGTCCGATTACCGAAAAACATCTCCAGAGCGGAATGACGCTGGCTGAGCTAAGCGCGGCGACGCTGCAATATAGCGACAATACGGCGATGAATCTGATCATCGGCTACCTTGGCGGGCCGGAAAAAGTCACCGCCTTCGCCCGCAGTATCGGCGATGCCACCTTTCGTCTCGATCGTACGGAGCCCACGCTGAATACCGCCATCCCGGGCGATGAGCGTGATACCAGCACGCCGCTGGCGATGGCTGAAAGCCTGCGCAAGCTGACGCTTGGCAATGCGCTGGGCGAACAGCAACGCGCCCAGTTAGTCACCTGGCTGAAAGGCAATACCACCGGCGGGCAAAGCATTCGCGCGGGCCTGCCTGAAAGCTGGGTGGTCGGAGATAAAACCGGCGCCGGAGATTACGGCACCACCAATGATATTGCGGTTATCTGGCCGGAAGATCACGCTCCGCTGGTATTAGTCACCTACTTTACCCAGCCGCAGCAGGATGCGAAAAACCGCAAAGAGGTGTTAGCCGCAGCGGCAAAAATCGTCACCGAAGGGCTTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3002406","ARO_id":"38806","ARO_name":"OXY-2-11","CARD_short_name":"OXY-2-11","ARO_description":"OXY-2-11 is a beta-lactamase. From the Pasteur Institute (Genopole) list of OXY beta-lactamases.","ARO_category":{"38788":{"category_aro_accession":"3002388","category_aro_cvterm_id":"38788","category_aro_name":"OXY beta-lactamase","category_aro_description":"OXY beta-lactamases are chromosomal class A beta-lactamases that are found in Klebsiella oxytoca. At constitutive low levels, OXY beta-lactamases confer resistance to aminopenicillins and carboxypenicillins. At high induced levels,  OXY beta-lactamases confer resistance to penicillins, cephalosporins and aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5235":{"model_id":"5235","model_name":"OXY-2-12","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7610":{"protein_sequence":{"accession":"WP_063864548.1","sequence":"MIKSSWRKIAMLAAAVPLLLASGALWASTDAIHQKLTDLEKRSGGRLGVALINTADNSQILYRGDERFAMCSTSKVMAAAAVLKQSESNKEVVNKRLEINAADLVVWSPITEKHLQSGMTLAELSAATLQYSDNTAMNLIIGYLGGPEKVTAFARSIGDATFRLDRTEPTLNTAIPGDERDTSTPLAMAESLRKLTLGDALGEQQRAQLVTWLKGNTTGGQSIRAGLPESWVVGDKTGAGDYGTTNDIAVIWPENHAPLVLVTYFTQPQQDAKNRKEVLAAAAKIVTEGL"},"dna_sequence":{"accession":"NG_049849.1","fmin":"0","fmax":"873","strand":"+","sequence":"ATGATAAAAAGTTCGTGGCGTAAAATTGCAATGCTAGCCGCCGCCGTTCCGCTGCTGCTGGCGAGCGGCGCACTGTGGGCCAGTACCGATGCTATCCATCAGAAGCTGACAGATCTCGAGAAGCGTTCAGGCGGCAGGTTGGGCGTGGCGCTAATCAACACGGCAGATAATTCTCAAATCTTATATCGCGGCGACGAGCGTTTTGCCATGTGCAGCACCAGTAAAGTGATGGCCGCCGCCGCGGTATTAAAACAGAGCGAAAGCAATAAAGAGGTGGTAAATAAAAGGCTGGAGATTAACGCAGCCGATTTGGTGGTCTGGAGTCCGATTACCGAAAAACATCTCCAGAGCGGAATGACGCTGGCTGAGCTAAGCGCGGCGACGCTGCAATATAGCGACAATACGGCGATGAATCTGATCATCGGCTACCTTGGCGGGCCGGAAAAAGTCACCGCCTTCGCCCGCAGTATCGGCGATGCCACCTTTCGTCTCGATCGTACGGAGCCCACGCTGAATACCGCCATCCCGGGCGATGAGCGTGATACCAGCACGCCGCTGGCGATGGCTGAAAGCCTGCGCAAGCTGACGCTTGGCGATGCGCTGGGCGAACAGCAACGCGCCCAGTTAGTCACCTGGCTGAAAGGCAATACCACCGGCGGGCAAAGCATTCGCGCGGGCCTGCCTGAAAGCTGGGTGGTCGGCGATAAAACCGGTGCCGGAGATTACGGCACCACCAATGATATTGCGGTTATCTGGCCGGAAAATCACGCTCCGCTGGTATTAGTCACCTACTTTACCCAGCCGCAGCAGGATGCGAAAAACCGCAAAGAGGTGTTAGCCGCAGCGGCAAAAATCGTGACCGAAGGGCTTTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3002407","ARO_id":"38807","ARO_name":"OXY-2-12","CARD_short_name":"OXY-2-12","ARO_description":"OXY-2-12 is a beta-lactamase. From the Pasteur Institute (Genopole) list of OXY beta-lactamases.","ARO_category":{"38788":{"category_aro_accession":"3002388","category_aro_cvterm_id":"38788","category_aro_name":"OXY beta-lactamase","category_aro_description":"OXY beta-lactamases are chromosomal class A beta-lactamases that are found in Klebsiella oxytoca. At constitutive low levels, OXY beta-lactamases confer resistance to aminopenicillins and carboxypenicillins. At high induced levels,  OXY beta-lactamases confer resistance to penicillins, cephalosporins and aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5236":{"model_id":"5236","model_name":"OXY-2-13","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7611":{"protein_sequence":{"accession":"WP_063864549.1","sequence":"MIKSSWRKIAMLAAAVPLLLASGALWASTDAIHQKLTDLEKRSGGRLGVALINTADNSQILYRGDERFAMCSTSKVMAAAAVLKQSESNKEVVNKRLEINAADLVVWSPITEKHLQSGMTLAELSAATLQYSDNTAMNLIIGHLGGPEKVTAFAHSIGDATFRLDRTEPTLNTAIPGDERDTSTPLAMAESLRKLTLGDALGEQQRAQLVTWLKGNTTGGQSIRAGLPESWVVGDKTGAGDYGTTNDIAVIWPEDHAPLVLVTYFTQPQQDAKNRKEVLAAAAKIVTEGL"},"dna_sequence":{"accession":"NG_049850.1","fmin":"0","fmax":"873","strand":"+","sequence":"ATGATAAAAAGTTCGTGGCGTAAAATTGCAATGCTAGCCGCCGCCGTTCCGCTGCTGCTGGCGAGCGGCGCACTGTGGGCCAGTACCGATGCTATCCATCAGAAGCTGACAGATCTCGAGAAGCGTTCAGGCGGCAGGTTGGGCGTGGCGCTAATCAACACGGCAGATAATTCTCAAATCTTATATCGCGGCGACGAGCGTTTTGCCATGTGCAGCACCAGTAAAGTGATGGCCGCCGCCGCGGTATTAAAACAGAGCGAAAGCAATAAAGAGGTGGTAAATAAAAGGCTGGAGATTAACGCAGCCGATTTGGTGGTCTGGAGTCCGATTACCGAAAAACATCTCCAGAGCGGAATGACGCTGGCTGAGCTAAGCGCGGCGACGCTGCAATATAGCGACAATACGGCGATGAATCTGATCATCGGCCACCTTGGCGGGCCGGAAAAAGTCACCGCCTTCGCCCACAGTATCGGCGATGCCACCTTTCGTCTCGATCGTACGGAGCCCACGCTGAATACCGCCATCCCGGGCGATGAGCGTGATACCAGCACGCCGCTGGCGATGGCTGAAAGCCTACGCAAGCTGACGCTTGGCGATGCGCTGGGCGAACAGCAACGCGCCCAGTTAGTCACCTGGCTGAAAGGCAATACCACCGGCGGGCAAAGCATTCGCGCGGGCCTGCCTGAAAGCTGGGTGGTCGGCGATAAAACCGGCGCCGGAGATTACGGCACCACCAATGATATTGCGGTTATCTGGCCGGAAGATCACGCTCCGCTGGTATTAGTCACCTACTTTACCCAGCCGCAGCAGGATGCGAAAAACCGCAAAGAGGTGTTAGCCGCAGCGGCAAAAATCGTGACCGAAGGGCTTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3002408","ARO_id":"38808","ARO_name":"OXY-2-13","CARD_short_name":"OXY-2-13","ARO_description":"OXY-2-13 is a beta-lactamase. From the Pasteur Institute (Genopole) list of OXY beta-lactamases.","ARO_category":{"38788":{"category_aro_accession":"3002388","category_aro_cvterm_id":"38788","category_aro_name":"OXY beta-lactamase","category_aro_description":"OXY beta-lactamases are chromosomal class A beta-lactamases that are found in Klebsiella oxytoca. At constitutive low levels, OXY beta-lactamases confer resistance to aminopenicillins and carboxypenicillins. At high induced levels,  OXY beta-lactamases confer resistance to penicillins, cephalosporins and aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5237":{"model_id":"5237","model_name":"OXY-2-14","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7612":{"protein_sequence":{"accession":"WP_063842752.1","sequence":"MIKSSWRKIAMLAAAVPLLLASGALWASTDAIHQKLTDLEKRSGGRLGVALINTADNSQILYRGDERFAMCSTSKVMAAAAVLKQSESNKEVVNKRLEINAADLVVWSPITEKHLQSGMTLAELSAATLQYSDNTAMNLIIGYLGGPEKVTAFARSIGDATFRLDRTEPTLNTAIPGDERDTSTPLAMAESLRKLTLGDALGEQQRAQLVTWLKGNTTGGQSIRAGLPESWVVGDKTGSGDYGTTNDIAVIWPEDHAPLVLVTYFTQPQQDAKNRKEVLAAAAKIVTEGL"},"dna_sequence":{"accession":"NG_047529.1","fmin":"94","fmax":"967","strand":"+","sequence":"ATGATAAAAAGTTCGTGGCGTAAAATTGCAATGCTAGCCGCCGCCGTTCCGCTGCTGCTGGCGAGCGGCGCACTGTGGGCCAGTACCGATGCTATCCATCAGAAGCTGACAGATCTCGAGAAGCGTTCAGGCGGCAGGTTGGGCGTGGCGCTAATCAACACGGCAGATAATTCTCAAATCTTATATCGCGGCGACGAGCGTTTTGCCATGTGCAGCACCAGTAAAGTGATGGCCGCCGCCGCGGTATTAAAACAGAGCGAAAGCAATAAAGAGGTGGTAAATAAAAGGCTGGAGATTAACGCAGCCGATTTGGTGGTCTGGAGCCCGATTACCGAAAAACATCTCCAGAGCGGAATGACGCTGGCTGAGCTAAGCGCGGCGACGCTGCAATATAGCGACAATACGGCGATGAATCTGATCATCGGCTACCTTGGCGGGCCGGAAAAAGTCACCGCCTTCGCCCGCAGTATCGGCGATGCCACCTTTCGTCTCGATCGTACGGAGCCCACGCTGAATACCGCCATCCCGGGCGATGAGCGTGATACCAGCACGCCGCTGGCGATGGCTGAAAGCCTGCGCAAGCTGACGCTTGGCGATGCGCTGGGCGAACAGCAACGCGCCCAGTTAGTCACCTGGCTGAAAGGCAATACCACCGGCGGGCAAAGCATTCGCGCGGGCCTGCCTGAAAGCTGGGTGGTCGGCGATAAAACCGGCTCCGGAGATTACGGCACCACCAATGATATTGCGGTTATCTGGCCGGAAGATCACGCTCCGCTGGTATTAGTCACCTACTTTACCCAGCCGCAGCAGGATGCGAAAAACCGCAAAGAGGTGTTAGCCGCAGCGGCAAAAATCGTGACCGAAGGGCTTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3006129","ARO_id":"44591","ARO_name":"OXY-2-14","CARD_short_name":"OXY-2-14","ARO_description":"OXY-2-14 is a OXY beta-lactamase.","ARO_category":{"38788":{"category_aro_accession":"3002388","category_aro_cvterm_id":"38788","category_aro_name":"OXY beta-lactamase","category_aro_description":"OXY beta-lactamases are chromosomal class A beta-lactamases that are found in Klebsiella oxytoca. At constitutive low levels, OXY beta-lactamases confer resistance to aminopenicillins and carboxypenicillins. At high induced levels,  OXY beta-lactamases confer resistance to penicillins, cephalosporins and aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5238":{"model_id":"5238","model_name":"OXY-2-15","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7613":{"protein_sequence":{"accession":"WP_063864550.1","sequence":"MIKSSWRKIAMLAAAVPLLLASGALWASTDAIHQKLTDLEKRSGGRLGVALINTADNSQILYRGDERFAMCSTSKVMAAAAVLKQSESNKEVVNKRLEINAADLVVWSPITEKHLQSGMTLAELSAATLQYSDNTAMNLIIGYLGGPEKVTAFARSIGDATFRLDRTEPNTAIPGDERDTSTPLAMAESLRKLTLGDALGEQQRAQLVTWLKGNTTGGQSIRAGLPESWVVGDKTGAGDYGTTNDIAVIWPEDHAPLILVTYFTQPQQDAKNRKEVLAAAAKIVTEGL"},"dna_sequence":{"accession":"NG_049851.1","fmin":"0","fmax":"867","strand":"+","sequence":"ATGATAAAAAGTTCGTGGCGTAAAATTGCAATGCTAGCCGCCGCCGTTCCGCTGCTGCTGGCGAGCGGCGCACTGTGGGCCAGTACCGATGCTATCCATCAGAAGCTGACAGATCTCGAGAAGCGTTCAGGCGGCAGGTTGGGCGTGGCGCTAATCAACACGGCAGATAATTCTCAAATCTTATATCGCGGCGACGAGCGTTTTGCCATGTGCAGCACCAGTAAAGTGATGGCCGCCGCCGCGGTATTAAAACAGAGCGAAAGCAATAAAGAGGTGGTAAATAAAAGGCTGGAGATTAACGCAGCCGATTTGGTGGTCTGGAGTCCGATTACCGAAAAACATCTCCAGAGCGGAATGACGCTGGCTGAGCTAAGCGCGGCGACGCTGCAATATAGCGACAATACGGCGATGAATCTGATCATCGGCTACCTTGGCGGGCCGGAAAAAGTCACCGCCTTCGCCCGCAGTATCGGCGATGCCACCTTTCGTCTCGATCGTACGGAGCCCAATACCGCCATCCCGGGCGATGAGCGTGATACCAGCACGCCGCTGGCGATGGCTGAAAGCCTGCGCAAGCTGACGCTTGGCGATGCGCTGGGCGAACAGCAACGCGCCCAGTTAGTCACCTGGCTGAAAGGCAATACCACCGGCGGGCAAAGCATTCGCGCGGGCCTGCCTGAAAGCTGGGTGGTCGGCGATAAAACCGGCGCCGGAGATTACGGCACCACCAATGATATTGCGGTTATCTGGCCGGAAGATCACGCTCCGCTGATATTAGTCACCTACTTTACCCAGCCGCAGCAGGATGCGAAAAACCGCAAAGAGGTGTTAGCCGCAGCGGCAAAAATCGTGACCGAAGGGCTTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3006130","ARO_id":"44592","ARO_name":"OXY-2-15","CARD_short_name":"OXY-2-15","ARO_description":"OXY-2-15 is a OXY beta-lactamase.","ARO_category":{"38788":{"category_aro_accession":"3002388","category_aro_cvterm_id":"38788","category_aro_name":"OXY beta-lactamase","category_aro_description":"OXY beta-lactamases are chromosomal class A beta-lactamases that are found in Klebsiella oxytoca. At constitutive low levels, OXY beta-lactamases confer resistance to aminopenicillins and carboxypenicillins. At high induced levels,  OXY beta-lactamases confer resistance to penicillins, cephalosporins and aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5239":{"model_id":"5239","model_name":"PAU-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"575"}},"model_sequences":{"sequence":{"7614":{"protein_sequence":{"accession":"WP_148044424.1","sequence":"MKRRNFSVGMAFSAFGFSAIFPKKSFALGEQGQMTAVFQQLEAKAQGRLGVHVIDTATGHEFGYRSDELFMMLSSFKLLASALVLARADRGEESLTRRIRYRKQDLVPWSPVTEAYADGEGLTLAQLCHATITTSDNTAGNLILASYGGPQALTQYARQLGDKITRLDRNEPDLNTRVEGGSLDTTSPRAMAMTMNKLLLGDALSPLSRNLLRQWLLENTTGGKRLKAGTPADWTVGDKTGTNKTDANDIGILLPPQGAPVLVTAYLADSTASSQIKDATLAEVGRLTSIGIR"},"dna_sequence":{"accession":"NG_065882.1","fmin":"30","fmax":"912","strand":"+","sequence":"ATGAAAAGACGCAACTTCTCCGTCGGGATGGCATTTTCTGCCTTTGGCTTCAGTGCGATTTTCCCCAAGAAAAGCTTTGCCTTGGGCGAGCAAGGACAGATGACTGCTGTGTTTCAGCAACTCGAGGCTAAAGCCCAAGGCCGGTTGGGCGTACATGTCATAGACACAGCGACTGGTCACGAATTTGGCTACCGCTCTGACGAACTTTTCATGATGCTCAGTTCGTTCAAGCTGCTGGCGAGTGCCTTGGTGCTGGCGCGCGCGGATCGTGGTGAAGAGTCGCTCACTCGGCGTATTCGTTACCGCAAGCAGGACTTGGTGCCTTGGTCGCCAGTGACAGAGGCATATGCGGATGGCGAGGGGTTGACTTTGGCCCAACTCTGTCACGCGACGATAACCACCAGCGACAACACAGCGGGCAATCTCATACTAGCCAGCTACGGTGGCCCTCAAGCTCTCACCCAGTATGCCCGCCAACTCGGTGACAAGATCACGAGGCTCGATCGGAACGAACCCGACCTCAACACCCGAGTCGAAGGAGGAAGCTTGGATACGACCTCACCGCGAGCCATGGCCATGACCATGAACAAGCTCCTCTTGGGCGATGCACTCTCACCCTTATCGCGGAATTTGCTCCGCCAGTGGCTGCTCGAAAACACGACCGGGGGAAAGCGCCTCAAGGCCGGAACCCCTGCTGATTGGACCGTTGGCGACAAGACCGGGACCAACAAGACAGATGCGAACGACATAGGAATATTGCTACCACCGCAAGGCGCACCGGTCCTTGTGACTGCTTACCTCGCTGACAGCACGGCAAGCAGCCAAATAAAAGATGCAACGCTTGCAGAGGTAGGTAGGCTCACCTCTATAGGCATACGATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006964","ARO_id":"45426","ARO_name":"PAU-1","CARD_short_name":"PAU-1","ARO_description":"PAU-1 is a PAU beta-lactamase.","ARO_category":{"43891":{"category_aro_accession":"3005431","category_aro_cvterm_id":"43891","category_aro_name":"PAU beta-lactamase","category_aro_description":"PAU beta-lactamases are class A beta-lactamases found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5240":{"model_id":"5240","model_name":"PDC-100","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7615":{"protein_sequence":{"accession":"WP_058176209.1","sequence":"MRDTRFPCLCGIAASTLLFAATPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDRVQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPITLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_049867.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCGCCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCATTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTGGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCGGGTACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCACCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006480","ARO_id":"44942","ARO_name":"PDC-100","CARD_short_name":"PDC-100","ARO_description":"PDC-100 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5241":{"model_id":"5241","model_name":"PDC-101","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7616":{"protein_sequence":{"accession":"WP_063864560.1","sequence":"MRDTRFPCLCGIAASTLLFAATPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_049868.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCGCCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAACTGTTCCCAGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATTCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006481","ARO_id":"44943","ARO_name":"PDC-101","CARD_short_name":"PDC-101","ARO_description":"PDC-101 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5242":{"model_id":"5242","model_name":"PDC-102","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7617":{"protein_sequence":{"accession":"WP_063864561.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDLAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_049869.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGACGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTGGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCTGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAACTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAACGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATTCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTACCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006482","ARO_id":"44944","ARO_name":"PDC-102","CARD_short_name":"PDC-102","ARO_description":"PDC-102 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5243":{"model_id":"5243","model_name":"PDC-103","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7618":{"protein_sequence":{"accession":"WP_031690214.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTLETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_049870.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCTGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCCCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCATGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006483","ARO_id":"44945","ARO_name":"PDC-103","CARD_short_name":"PDC-103","ARO_description":"PDC-103 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5244":{"model_id":"5244","model_name":"PDC-106","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7619":{"protein_sequence":{"accession":"WP_063864563.1","sequence":"MRDTRFSCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQTKVPLKR"},"dna_sequence":{"accession":"NG_049873.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCTCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCCGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACTCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATTCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGACCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006484","ARO_id":"44946","ARO_name":"PDC-106","CARD_short_name":"PDC-106","ARO_description":"PDC-106 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5245":{"model_id":"5245","model_name":"PDC-107","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7620":{"protein_sequence":{"accession":"WP_063864564.1","sequence":"MRDTRFSCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_049874.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCTCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCACTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006485","ARO_id":"44947","ARO_name":"PDC-107","CARD_short_name":"PDC-107","ARO_description":"PDC-107 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5246":{"model_id":"5246","model_name":"PDC-108","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7621":{"protein_sequence":{"accession":"WP_063864565.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQGLDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_049875.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGGGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006486","ARO_id":"44948","ARO_name":"PDC-108","CARD_short_name":"PDC-108","ARO_description":"PDC-108 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5247":{"model_id":"5247","model_name":"PDC-109","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7622":{"protein_sequence":{"accession":"WP_029610673.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDSISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_049876.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGTCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACAGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTTATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCCCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006487","ARO_id":"44949","ARO_name":"PDC-109","CARD_short_name":"PDC-109","ARO_description":"PDC-109 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5248":{"model_id":"5248","model_name":"PDC-110","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7623":{"protein_sequence":{"accession":"WP_063864566.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSCLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_049878.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGATGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACTCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCTGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006488","ARO_id":"44950","ARO_name":"PDC-110","CARD_short_name":"PDC-110","ARO_description":"PDC-110 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5249":{"model_id":"5249","model_name":"PDC-111","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7624":{"protein_sequence":{"accession":"WP_063864567.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLRRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_049879.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAAGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAGGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006489","ARO_id":"44951","ARO_name":"PDC-111","CARD_short_name":"PDC-111","ARO_description":"PDC-111 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5250":{"model_id":"5250","model_name":"PDC-112","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7625":{"protein_sequence":{"accession":"WP_063864568.1","sequence":"MRDTRFPCLCGIAASILLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFSDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_049880.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCATACTGCTGTTCGCCACCACCCCGGCCATTGCCGACGAGGCCCCGGCAGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCTCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAACTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAAGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006490","ARO_id":"44952","ARO_name":"PDC-112","CARD_short_name":"PDC-112","ARO_description":"PDC-112 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5251":{"model_id":"5251","model_name":"PDC-113","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7626":{"protein_sequence":{"accession":"WP_063864569.1","sequence":"MRDTRFPCLCGIAASTLLFATTPTIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRRYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_049881.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGACCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGTCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCGCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006491","ARO_id":"44953","ARO_name":"PDC-113","CARD_short_name":"PDC-113","ARO_description":"PDC-113 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5252":{"model_id":"5252","model_name":"PDC-114","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7627":{"protein_sequence":{"accession":"WP_061189306.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALTQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRAGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_055478.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGACCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGTTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGCCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006492","ARO_id":"44954","ARO_name":"PDC-114","CARD_short_name":"PDC-114","ARO_description":"PDC-114 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5253":{"model_id":"5253","model_name":"PDC-115","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7628":{"protein_sequence":{"accession":"WP_031692400.1","sequence":"MRDTRFPCLCGIAASTLLLATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERFMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_055479.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGCTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGTTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAAGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATTCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006493","ARO_id":"44955","ARO_name":"PDC-115","CARD_short_name":"PDC-115","ARO_description":"PDC-115 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5254":{"model_id":"5254","model_name":"PDC-116","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7629":{"protein_sequence":{"accession":"WP_061193023.1","sequence":"MRDTRFPCLCGIAASTLLFAATPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRAGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_055480.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCGCCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCATTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGCCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCTAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTATGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006494","ARO_id":"44956","ARO_name":"PDC-116","CARD_short_name":"PDC-116","ARO_description":"PDC-116 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5255":{"model_id":"5255","model_name":"PDC-12","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7630":{"protein_sequence":{"accession":"WP_009313329.1","sequence":"MRDTRFPCLCGIAASTLLFAATPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_049882.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCGCCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37066","NCBI_taxonomy_name":"Pseudomonas","NCBI_taxonomy_id":"286"}}}},"ARO_accession":"3006495","ARO_id":"44957","ARO_name":"PDC-12","CARD_short_name":"PDC-12","ARO_description":"PDC-12 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5256":{"model_id":"5256","model_name":"PDC-120","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7631":{"protein_sequence":{"accession":"WP_023089477.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_055484.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTAGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006496","ARO_id":"44958","ARO_name":"PDC-120","CARD_short_name":"PDC-120","ARO_description":"PDC-120 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5257":{"model_id":"5257","model_name":"PDC-121","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7632":{"protein_sequence":{"accession":"WP_023085632.1","sequence":"MRDTRFSCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_055485.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCTCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTAGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCACTGCAACCGCACAGGATCGCTAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37066","NCBI_taxonomy_name":"Pseudomonas","NCBI_taxonomy_id":"286"}}}},"ARO_accession":"3006497","ARO_id":"44959","ARO_name":"PDC-121","CARD_short_name":"PDC-121","ARO_description":"PDC-121 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5258":{"model_id":"5258","model_name":"PDC-122","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7633":{"protein_sequence":{"accession":"WP_023109643.1","sequence":"MRDTRFSCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRMQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_055486.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCTCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCATGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006498","ARO_id":"44960","ARO_name":"PDC-122","CARD_short_name":"PDC-122","ARO_description":"PDC-122 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5259":{"model_id":"5259","model_name":"PDC-123","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7634":{"protein_sequence":{"accession":"WP_049321692.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_055487.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37066","NCBI_taxonomy_name":"Pseudomonas","NCBI_taxonomy_id":"286"}}}},"ARO_accession":"3006499","ARO_id":"44961","ARO_name":"PDC-123","CARD_short_name":"PDC-123","ARO_description":"PDC-123 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5260":{"model_id":"5260","model_name":"PDC-124","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7635":{"protein_sequence":{"accession":"WP_049239252.1","sequence":"MRDTRFPCLCGIAASTLLFATTSAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_055488.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTTCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCTCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006500","ARO_id":"44962","ARO_name":"PDC-124","CARD_short_name":"PDC-124","ARO_description":"PDC-124 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5261":{"model_id":"5261","model_name":"PDC-125","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7636":{"protein_sequence":{"accession":"WP_053813381.1","sequence":"MRHATILNLCGLAASTLFFATTSAFATEAPAERLKALVDAAVQPVMKANDIPGLAVAITLKGEPHYFSYGVASKEDARKVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASRHWPALQGSRFDGISLLDLGTYTAGGLPLQFPDAVQKDPAQIRDYYRQWQPTYAPGSHRQYSNPSIGLFGYLAARSLGQPFERSMERQLFPALGLEHTFIRVPAAQQGLYAQGYGKDDRPLRVGPGPLDAEAYGLKSSAADLLRFVEANLHPERLEKPWAQALDATHRGYYKVGDMTQGLGWEAYDWPIDLRRLQAGNSAPMALQAHKVARLPAPQALDGQRLLNKTGSTNGFGAYLAFIPGRDVGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLVR"},"dna_sequence":{"accession":"NG_050589.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCCATGCGACAATCCTCAACCTGTGCGGCCTCGCCGCTTCCACCCTGTTCTTCGCGACAACATCGGCCTTCGCCACGGAGGCGCCGGCGGAGCGCCTGAAGGCTCTGGTGGACGCCGCCGTGCAACCGGTCATGAAGGCCAATGATATCCCGGGACTGGCCGTCGCCATCACTCTCAAGGGCGAACCGCATTACTTCAGTTATGGGGTGGCCTCGAAGGAGGACGCCCGCAAGGTGACCCCCGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTACGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCGGCACTGGCCCGCCCTGCAGGGCAGCCGCTTCGACGGTATCAGCCTGCTCGACCTCGGCACCTACACCGCTGGCGGCCTGCCGCTACAGTTCCCCGATGCGGTGCAGAAGGATCCGGCGCAGATCCGCGACTATTACCGCCAGTGGCAACCGACCTACGCCCCGGGCAGCCACCGCCAGTACTCCAACCCGAGCATCGGTCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCATTCGAGCGCAGCATGGAACGGCAGCTGTTCCCGGCGCTCGGCCTGGAGCACACCTTTATCCGGGTGCCCGCCGCGCAGCAGGGGCTGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTGCGGGTCGGACCCGGTCCGCTGGACGCCGAGGCCTACGGGCTGAAGTCCAGCGCTGCGGACCTGCTGCGCTTCGTCGAGGCCAACCTGCACCCCGAGCGCCTGGAGAAGCCCTGGGCGCAGGCCCTCGACGCCACCCATCGCGGCTACTACAAGGTGGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGATTGGCCGATCGACCTGAGGCGCCTGCAGGCGGGCAACTCGGCGCCGATGGCGCTGCAGGCGCACAAGGTCGCCAGGTTGCCGGCGCCGCAAGCCCTGGACGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGTTTCGGCGCCTACCTGGCGTTCATCCCGGGACGCGACGTCGGCCTGGTGATCCTGGCCAATCGCAACTACCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGTYTGGAACAGCAGGCCAAGGTACCGCTGGTGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006501","ARO_id":"44963","ARO_name":"PDC-125","CARD_short_name":"PDC-125","ARO_description":"PDC-125 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5262":{"model_id":"5262","model_name":"PDC-126","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7637":{"protein_sequence":{"accession":"WP_064483991.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTVTLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRAGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_050782.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGTCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAACTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGCCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006502","ARO_id":"44964","ARO_name":"PDC-126","CARD_short_name":"PDC-126","ARO_description":"PDC-126 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5263":{"model_id":"5263","model_name":"PDC-127","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7638":{"protein_sequence":{"accession":"WP_064483992.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDRAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_050783.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCGGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006503","ARO_id":"44965","ARO_name":"PDC-127","CARD_short_name":"PDC-127","ARO_description":"PDC-127 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5264":{"model_id":"5264","model_name":"PDC-128","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7639":{"protein_sequence":{"accession":"WP_064483993.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRITRLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_050784.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTAGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCACCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTATGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006504","ARO_id":"44966","ARO_name":"PDC-128","CARD_short_name":"PDC-128","ARO_description":"PDC-128 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5265":{"model_id":"5265","model_name":"PDC-129","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7640":{"protein_sequence":{"accession":"WP_064483994.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRGGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_050785.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGTCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGGCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006505","ARO_id":"44967","ARO_name":"PDC-129","CARD_short_name":"PDC-129","ARO_description":"PDC-129 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5266":{"model_id":"5266","model_name":"PDC-13","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7641":{"protein_sequence":{"accession":"WP_063864570.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRLWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPTAERVKIAYTILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_049883.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTTCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCTCTGGGCGCAGGCGCTTGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCACGGCCGAGCGGGTGAAGATCGCCTACACCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006506","ARO_id":"44968","ARO_name":"PDC-13","CARD_short_name":"PDC-13","ARO_description":"PDC-13 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5267":{"model_id":"5267","model_name":"PDC-130","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7642":{"protein_sequence":{"accession":"WP_064483995.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQGKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRAGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQTGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_050786.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGGCAAGATGCGTCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGCCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGACCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006507","ARO_id":"44969","ARO_name":"PDC-130","CARD_short_name":"PDC-130","ARO_description":"PDC-130 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5268":{"model_id":"5268","model_name":"PDC-131","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7643":{"protein_sequence":{"accession":"WP_064483996.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGETPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_050787.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGACCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAGCCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006508","ARO_id":"44970","ARO_name":"PDC-131","CARD_short_name":"PDC-131","ARO_description":"PDC-131 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5269":{"model_id":"5269","model_name":"PDC-132","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7644":{"protein_sequence":{"accession":"WP_064483997.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTSGFGAYVAFVPGRDLGLVILANRNYPIAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_050788.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGTCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAGCGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCATTGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006509","ARO_id":"44971","ARO_name":"PDC-132","CARD_short_name":"PDC-132","ARO_description":"PDC-132 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5270":{"model_id":"5270","model_name":"PDC-133","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7645":{"protein_sequence":{"accession":"WP_064483998.1","sequence":"MRDTRFPCLCGIAASTLLFAATPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERIMEQRLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRQWAQALDATHRGYYKVGDMTQGLGWEAYDWPIALKRLQAGNSTPMALQPHRVARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLAR"},"dna_sequence":{"accession":"NG_050789.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCGCCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTGGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCGTCGAAAGAGGACGGTCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAAGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTACACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGTCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAGCGGATCATGGAGCAGCGCCTGTTCCCGGCCCTGGGCCTCGAACAGACTCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTCCGGGTCGGCCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGACTGGACCGGCAGTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCGCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGGTCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGGCGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006510","ARO_id":"44972","ARO_name":"PDC-133","CARD_short_name":"PDC-133","ARO_description":"PDC-133 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5271":{"model_id":"5271","model_name":"PDC-134","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7646":{"protein_sequence":{"accession":"WP_064483999.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFSDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_050790.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGACGAGGCCCCGGCAGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCTCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAACTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAAGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATTCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTACCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006511","ARO_id":"44973","ARO_name":"PDC-134","CARD_short_name":"PDC-134","ARO_description":"PDC-134 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5272":{"model_id":"5272","model_name":"PDC-135","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7647":{"protein_sequence":{"accession":"WP_064484000.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTVTLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSFGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_050791.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGTCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCTTCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAACTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006512","ARO_id":"44974","ARO_name":"PDC-135","CARD_short_name":"PDC-135","ARO_description":"PDC-135 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5273":{"model_id":"5273","model_name":"PDC-136","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7648":{"protein_sequence":{"accession":"WP_064484001.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTSGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_050792.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTAGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAACTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTATGGCAAGGACGACCGCCCCCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCATGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAGCGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006513","ARO_id":"44975","ARO_name":"PDC-136","CARD_short_name":"PDC-136","ARO_description":"PDC-136 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5274":{"model_id":"5274","model_name":"PDC-137","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7649":{"protein_sequence":{"accession":"WP_064484002.1","sequence":"MRDTRFPCLCGIAASTLLLATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDSASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_050793.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGCTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACAGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAACAACTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCTTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006514","ARO_id":"44976","ARO_name":"PDC-137","CARD_short_name":"PDC-137","ARO_description":"PDC-137 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5275":{"model_id":"5275","model_name":"PDC-138","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7650":{"protein_sequence":{"accession":"WP_064484003.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQPKVPLKR"},"dna_sequence":{"accession":"NG_050794.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGCCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006515","ARO_id":"44977","ARO_name":"PDC-138","CARD_short_name":"PDC-138","ARO_description":"PDC-138 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5276":{"model_id":"5276","model_name":"PDC-139","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7651":{"protein_sequence":{"accession":"WP_064484004.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLTR"},"dna_sequence":{"accession":"NG_050795.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTTCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTTGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGACGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006516","ARO_id":"44978","ARO_name":"PDC-139","CARD_short_name":"PDC-139","ARO_description":"PDC-139 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5277":{"model_id":"5277","model_name":"PDC-140","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7652":{"protein_sequence":{"accession":"WP_064484005.1","sequence":"MRHATILNLCGLAASTLFFATTSAFATEAPAERLKALVDAAVQPVMKANDIPGLAVAITLKGEPHYFSYGVASKEDARKVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASRHWPALQGSRFDGISLLDLGTYTAGGLPLQFPDAVQKDPAQIRDYYRQWQPTYAPGSHRQYSNPSIGLFGYLAARSLGQPFERSMERQLFPALGLEHTFIRVPAAQQGLYAQGYGKDDHPLRVGPGPLDAEAYGLKSSAADLLRFVEANLHPERLEKPWAQALDATHRGYYKVGDMTQGLGWEAYDWPIDLRRLQAGNSAPMALQAHKVARLPAPQALDGQRLLNKTGSTNGFGAYLAFIPGRDVGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLVR"},"dna_sequence":{"accession":"NG_050796.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCCATGCGACAATCCTCAACCTGTGCGGCCTCGCCGCTTCCACCCTGTTCTTCGCGACAACATCGGCCTTCGCCACGGAGGCGCCGGCGGAGCGCCTGAAGGCTCTGGTGGACGCCGCCGTGCAACCGGTCATGAAGGCCAATGATATCCCGGGACTGGCCGTCGCCATCACTCTCAAGGGCGAACCGCATTACTTCAGTTATGGGGTGGCCTCGAAGGAGGACGCCCGCAAGGTGACCCCCGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTACGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCGGCACTGGCCCGCCCTGCAGGGCAGCCGCTTCGACGGTATCAGCCTGCTCGACCTCGGCACCTACACCGCTGGCGGCCTGCCGCTACAGTTCCCCGATGCGGTGCAGAAGGATCCGGCGCAGATCCGCGACTATTACCGCCAGTGGCAACCGACCTACGCCCCGGGCAGCCACCGCCAGTACTCCAACCCGAGCATCGGTCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCATTCGAGCGCAGCATGGAACGGCAGCTGTTCCCGGCGCTCGGCCTGGAGCACACCTTTATCCGGGTGCCCGCCGCGCAGCAGGGGCTGTACGCCCAGGGCTACGGCAAGGACGACCACCCGCTGCGGGTCGGACCCGGTCCGCTGGACGCCGAGGCCTACGGGCTGAAGTCCAGCGCTGCGGACCTGCTGCGCTTCGTCGAGGCCAACCTGCACCCCGAGCGCCTGGAGAAGCCCTGGGCGCAGGCCCTCGACGCCACCCATCGCGGCTACTACAAGGTGGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGATTGGCCGATCGACCTGAGGCGCCTGCAGGCGGGCAACTCGGCGCCGATGGCGCTGCAGGCGCACAAGGTCGCCAGGTTGCCGGCGCCGCAAGCCCTGGACGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGTTTCGGCGCCTACCTGGCGTTCATCCCGGGACGCGACGTCGGCCTGGTGATCCTGGCCAATCGCAACTACCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAACAGCAGGCCAAGGTACCACTGGTGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006517","ARO_id":"44979","ARO_name":"PDC-140","CARD_short_name":"PDC-140","ARO_description":"PDC-140 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5278":{"model_id":"5278","model_name":"PDC-141","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7653":{"protein_sequence":{"accession":"WP_064484006.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQGKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRRYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_050797.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGGCAAGATGCGTCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCGCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006518","ARO_id":"44980","ARO_name":"PDC-141","CARD_short_name":"PDC-141","ARO_description":"PDC-141 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5279":{"model_id":"5279","model_name":"PDC-142","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7654":{"protein_sequence":{"accession":"WP_064511493.1","sequence":"MRDTRFPCLCGIAASTLLFATTSAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_050815.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTTCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCTCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006519","ARO_id":"44981","ARO_name":"PDC-142","CARD_short_name":"PDC-142","ARO_description":"PDC-142 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5280":{"model_id":"5280","model_name":"PDC-143","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7655":{"protein_sequence":{"accession":"WP_064511494.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRAGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_050816.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGTCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGCCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCAATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAGCCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006520","ARO_id":"44982","ARO_name":"PDC-143","CARD_short_name":"PDC-143","ARO_description":"PDC-143 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5281":{"model_id":"5281","model_name":"PDC-144","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7656":{"protein_sequence":{"accession":"WP_064511495.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQRDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDGRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTSGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_050817.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGTCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAGGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGGCCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAGCGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006521","ARO_id":"44983","ARO_name":"PDC-144","CARD_short_name":"PDC-144","ARO_description":"PDC-144 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5282":{"model_id":"5282","model_name":"PDC-145","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7657":{"protein_sequence":{"accession":"WP_064511496.1","sequence":"MRDTRFPCLCGIAASTLLFAATPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRAGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQPKVPLKR"},"dna_sequence":{"accession":"NG_050818.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCGCCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGCCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGCCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006522","ARO_id":"44984","ARO_name":"PDC-145","CARD_short_name":"PDC-145","ARO_description":"PDC-145 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5283":{"model_id":"5283","model_name":"PDC-146","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7658":{"protein_sequence":{"accession":"WP_064511497.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQTGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_050819.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGACCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006523","ARO_id":"44985","ARO_name":"PDC-146","CARD_short_name":"PDC-146","ARO_description":"PDC-146 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5284":{"model_id":"5284","model_name":"PDC-147","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7659":{"protein_sequence":{"accession":"WP_064511498.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFKRLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_050820.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTAGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCAAACGGCTCATGGAGCAGCAACTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCCCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCATGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006524","ARO_id":"44986","ARO_name":"PDC-147","CARD_short_name":"PDC-147","ARO_description":"PDC-147 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5285":{"model_id":"5285","model_name":"PDC-148","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7660":{"protein_sequence":{"accession":"WP_064511499.1","sequence":"MRDTRFPCLCGIAASTLLFTTTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDDISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRRYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTYLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_050821.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCACCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGTCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGACATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCGCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCTACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006525","ARO_id":"44987","ARO_name":"PDC-148","CARD_short_name":"PDC-148","ARO_description":"PDC-148 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5286":{"model_id":"5286","model_name":"PDC-149","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7661":{"protein_sequence":{"accession":"WP_064511500.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRRYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDGRPLRAGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_050822.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGTCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCGCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGGCCGCCCGCTACGGGCCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006526","ARO_id":"44988","ARO_name":"PDC-149","CARD_short_name":"PDC-149","ARO_description":"PDC-149 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5287":{"model_id":"5287","model_name":"PDC-15","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7662":{"protein_sequence":{"accession":"WP_023114693.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRLWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_049885.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTTCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCTCTGGGCGCAGGCGCTTGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37066","NCBI_taxonomy_name":"Pseudomonas","NCBI_taxonomy_id":"286"}}}},"ARO_accession":"3006527","ARO_id":"44989","ARO_name":"PDC-15","CARD_short_name":"PDC-15","ARO_description":"PDC-15 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5288":{"model_id":"5288","model_name":"PDC-150","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7663":{"protein_sequence":{"accession":"WP_064511501.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPKAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_050823.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGTCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCATGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAAGGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006528","ARO_id":"44990","ARO_name":"PDC-150","CARD_short_name":"PDC-150","ARO_description":"PDC-150 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5289":{"model_id":"5289","model_name":"PDC-151","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7664":{"protein_sequence":{"accession":"WP_053816671.1","sequence":"MRHATILNLCGLAASTLFFATTSAFATEAPAERLKALVDAAVQPVMKANDIPGLAVAITLKGEPHYFSYGVASKEDARKVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASRHWPALQGSRFDGISLLDLGTYTAGGLPLQFPDVVQKDPAQIRDYYRQWQPTYAPGSHRQYSNPSIGLFGYLAARSLGQPFERSMERQLFPALGLEHTFIRVPTAQQGLYAQGYGKDDHPLRVGPGPLDAEAYGLKSSAADLLRFVEANLHPERLEKPWAQALDATHRGYYKVGDMTQGLGWEAYDWPIDLKRLQAGNSAPMALQAHKVARLPAPQALDGQRLLNKTGSTNGFGAYLAFIPGRDVGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLVR"},"dna_sequence":{"accession":"NG_050824.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCCATGCGACAATCCTCAACCTGTGCGGCCTCGCCGCTTCCACCCTGTTCTTCGCGACAACATCGGCCTTCGCCACGGAGGCGCCGGCGGAGCGCCTGAAGGCTCTGGTGGACGCCGCCGTGCAACCGGTCATGAAGGCCAATGATATCCCGGGACTGGCCGTCGCCATCACTCTCAAGGGCGAACCGCATTACTTCAGTTATGGGGTGGCCTCGAAGGAGGACGCCCGCAAGGTGACCCCCGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTACGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCGGCACTGGCCCGCCCTGCAGGGCAGCCGCTTCGACGGTATCAGCCTGCTCGACCTCGGCACCTACACCGCTGGCGGCCTGCCGCTACAGTTCCCCGATGTGGTGCAGAAGGATCCGGCGCAGATCCGCGACTATTACCGCCAGTGGCAACCGACCTACGCCCCGGGCAGCCACCGCCAGTACTCCAACCCGAGCATCGGTCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCATTCGAGCGCAGCATGGAACGGCAGCTGTTCCCGGCGCTCGGCCTGGAGCACACCTTTATCCGGGTGCCCACCGCGCAGCAGGGGCTGTACGCCCAGGGCTACGGCAAGGACGACCACCCGCTGCGGGTCGGACCCGGTCCGCTGGACGCCGAGGCCTACGGGCTGAAGTCCAGCGCTGCGGACCTGCTGCGCTTCGTCGAGGCCAACCTGCACCCCGAGCGCCTGGAGAAGCCCTGGGCGCAGGCCCTCGACGCCACCCATCGCGGCTACTACAAGGTGGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGATTGGCCGATCGACCTGAAGCGCCTGCAGGCGGGCAACTCGGCGCCGATGGCGCTGCAGGCGCACAAGGTCGCCAGGTTGCCGGCGCCGCAAGCCCTGGACGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGTTTCGGCGCCTACCTGGCGTTCATCCCGGGACGCGACGTCGGCCTGGTGATCCTGGCCAATCGCAACTACCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAACAGCAGGCCAAGGTACCGCTGGTGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006529","ARO_id":"44991","ARO_name":"PDC-151","CARD_short_name":"PDC-151","ARO_description":"PDC-151 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5290":{"model_id":"5290","model_name":"PDC-152","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7665":{"protein_sequence":{"accession":"WP_064511502.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTVTLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQCAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_050825.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGTCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAACTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTGCGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006530","ARO_id":"44992","ARO_name":"PDC-152","CARD_short_name":"PDC-152","ARO_description":"PDC-152 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5291":{"model_id":"5291","model_name":"PDC-153","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7666":{"protein_sequence":{"accession":"WP_064511503.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLIVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDRAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_050826.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGATCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCGGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006531","ARO_id":"44993","ARO_name":"PDC-153","CARD_short_name":"PDC-153","ARO_description":"PDC-153 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5292":{"model_id":"5292","model_name":"PDC-154","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7667":{"protein_sequence":{"accession":"WP_064511504.1","sequence":"MRDTRFPCLCGIAASTLLFAATPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPSPLDAESYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_050827.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCGCCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCATTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTGGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGTTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGTCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCAGCCCGCTGGATGCCGAAAGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006532","ARO_id":"44994","ARO_name":"PDC-154","CARD_short_name":"PDC-154","ARO_description":"PDC-154 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5293":{"model_id":"5293","model_name":"PDC-155","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7668":{"protein_sequence":{"accession":"WP_064511505.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRRYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLKQTHLDVPEAALAQYAQGYGKDDRPLRAGPGPLGAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTSMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_050828.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGTCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCGCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCAAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGCCGGTCCCGGCCCGCTGGGTGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGTCGATGGCGCTGCAACCGCACAGGATCGCTAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006533","ARO_id":"44995","ARO_name":"PDC-155","CARD_short_name":"PDC-155","ARO_description":"PDC-155 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5294":{"model_id":"5294","model_name":"PDC-156","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7669":{"protein_sequence":{"accession":"WP_064511506.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGRQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRAGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_050829.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGTCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGACAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCCCTACGGGCCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006534","ARO_id":"44996","ARO_name":"PDC-156","CARD_short_name":"PDC-156","ARO_description":"PDC-156 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5295":{"model_id":"5295","model_name":"PDC-157","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7670":{"protein_sequence":{"accession":"WP_064511507.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRRYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPTAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_050830.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGTCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCGCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCACTGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006535","ARO_id":"44997","ARO_name":"PDC-157","CARD_short_name":"PDC-157","ARO_description":"PDC-157 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5296":{"model_id":"5296","model_name":"PDC-158","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7671":{"protein_sequence":{"accession":"WP_064511508.1","sequence":"MRDTRFPCLCGIAASTLLFAATPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVSEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_050831.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCGCCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCATTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTGGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGTTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGTCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAGCCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006536","ARO_id":"44998","ARO_name":"PDC-158","CARD_short_name":"PDC-158","ARO_description":"PDC-158 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5297":{"model_id":"5297","model_name":"PDC-159","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7672":{"protein_sequence":{"accession":"WP_064511509.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNLSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_050832.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCTTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCTGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATTCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006537","ARO_id":"44999","ARO_name":"PDC-159","CARD_short_name":"PDC-159","ARO_description":"PDC-159 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5298":{"model_id":"5298","model_name":"PDC-16","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7673":{"protein_sequence":{"accession":"WP_019485213.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_049886.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGTCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCAATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAGCCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006538","ARO_id":"45000","ARO_name":"PDC-16","CARD_short_name":"PDC-16","ARO_description":"PDC-16 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5299":{"model_id":"5299","model_name":"PDC-160","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7674":{"protein_sequence":{"accession":"WP_064511510.1","sequence":"MRHATILNLCGLAASTLFFATTSAFATAAPAERLKALVDAAVQPVMKANDIPGLAVAITLKGEPHYFSYGVASKEDARKVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASRHWPALQGSRFDGISLLDLGTYSAGGLPLQFPDAVQKDPAQIRDYYRQWQPTYAPGSHRQYSNPSIGLFGYLAARSLGQPFERSMERQLFPALGLEHTFIRVPAAQQGLYAQGYGKDDRPLRVGPGSLDAEAYGLKSSAADLLRFVEANLHPERLEKPWAQALDATHRGYYKVGDMTQGLGWEAYDWPIDLKRLQAGNSAPMALQAHKVARLPAPQALDGQRLLNKTGSTNGFGAYLAFIPGRDVGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLVR"},"dna_sequence":{"accession":"NG_050833.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCCATGCAACAATCCTCAACCTGTGCGGCCTCGCCGCTTCCACCCTGTTCTTCGCGACAACATCGGCCTTCGCCACGGCGGCGCCGGCGGAGCGCCTGAAGGCTCTGGTAGACGCCGCCGTGCAACCGGTCATGAAGGCCAATGATATCCCGGGACTGGCCGTCGCCATCACCCTCAAGGGCGAACCGCATTACTTCAGTTATGGGGTGGCCTCGAAGGAGGACGCCCGCAAGGTGACCCCCGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTACGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCGGCACTGGCCCGCCCTGCAGGGCAGCCGCTTCGACGGTATCAGCCTGCTCGACCTCGGCACCTACAGCGCTGGCGGCCTGCCGCTACAGTTCCCCGATGCGGTGCAGAAGGATCCGGCGCAGATCCGCGACTACTACCGCCAGTGGCAACCGACCTACGCCCCGGGCAGCCACCGCCAGTACTCCAACCCGAGCATCGGTCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCATTCGAGCGCAGCATGGAACGGCAGCTGTTCCCGGCGCTCGGCCTGGAGCACACCTTTATCCGGGTGCCCGCCGCGCAGCAGGGGCTGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTGCGGGTCGGACCCGGTTCGCTGGACGCCGAGGCCTACGGGCTGAAGTCCAGCGCTGCGGACCTGCTGCGCTTCGTCGAGGCCAACCTGCACCCCGAGCGCCTGGAGAAGCCCTGGGCGCAGGCCCTCGACGCCACCCATCGCGGCTACTACAAGGTGGGCGACATGACCCAGGGCCTGGGTTGGGAAGCCTACGATTGGCCGATCGACCTGAAGCGCCTGCAGGCGGGCAACTCGGCGCCGATGGCGCTACAGGCGCACAAGGTCGCCAGGTTGCCGGCGCCGCAAGCCCTGGACGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGTTTCGGCGCCTACCTGGCGTTCATCCCGGGACGCGACGTCGGCCTGGTGATCCTGGCCAATCGCAACTACCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAACAGCAGGCCAAGGTACCGCTGGTGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006539","ARO_id":"45001","ARO_name":"PDC-160","CARD_short_name":"PDC-160","ARO_description":"PDC-160 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5300":{"model_id":"5300","model_name":"PDC-161","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7675":{"protein_sequence":{"accession":"WP_064511511.1","sequence":"MRDTRFPCLCGIAASTLLFATTSAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_050834.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTTCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCTCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACTCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006540","ARO_id":"45002","ARO_name":"PDC-161","CARD_short_name":"PDC-161","ARO_description":"PDC-161 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5301":{"model_id":"5301","model_name":"PDC-162","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7676":{"protein_sequence":{"accession":"WP_064511512.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRTWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_050835.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGACCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006541","ARO_id":"45003","ARO_name":"PDC-162","CARD_short_name":"PDC-162","ARO_description":"PDC-162 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5302":{"model_id":"5302","model_name":"PDC-163","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7677":{"protein_sequence":{"accession":"WP_064511513.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVVLANRNYPIAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_050836.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGATGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACTCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGGTCCTGGCCAACCGCAACTATCCCATTGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006542","ARO_id":"45004","ARO_name":"PDC-163","CARD_short_name":"PDC-163","ARO_description":"PDC-163 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5303":{"model_id":"5303","model_name":"PDC-164","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7678":{"protein_sequence":{"accession":"WP_064511514.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFTATLAGYALTQDKMRLDDRASEHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_050837.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGACCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCGAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006543","ARO_id":"45005","ARO_name":"PDC-164","CARD_short_name":"PDC-164","ARO_description":"PDC-164 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5304":{"model_id":"5304","model_name":"PDC-165","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7679":{"protein_sequence":{"accession":"WP_064511515.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDSISLLDLATYTAGGLPLKFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_050838.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGTCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACAGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGAAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTTATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCCCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006544","ARO_id":"45006","ARO_name":"PDC-165","CARD_short_name":"PDC-165","ARO_description":"PDC-165 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5305":{"model_id":"5305","model_name":"PDC-166","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7680":{"protein_sequence":{"accession":"WP_065102306.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTVTLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_050946.1","fmin":"0","fmax":"1188","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGTCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAACTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006545","ARO_id":"45007","ARO_name":"PDC-166","CARD_short_name":"PDC-166","ARO_description":"PDC-166 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5306":{"model_id":"5306","model_name":"PDC-167","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7681":{"protein_sequence":{"accession":"WP_065102311.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERIMEQRLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRQWAQALDATHRGYYKVGDMTQGLGWEAYDWPIALKRLQAGNSTPMALQPHRVARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLAR"},"dna_sequence":{"accession":"NG_050947.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTGGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGTTATGGGCTGGCGTCGAAAGAGGACGGTCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAAGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTACACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGTCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAGCGGATCATGGAGCAGCGCCTGTTCCCGGCCCTGGGCCTCGAACAGACTCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTCCGGGTCGGCCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGACTGGACCGGCAGTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCGCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGGTCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGGCGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006546","ARO_id":"45008","ARO_name":"PDC-167","CARD_short_name":"PDC-167","ARO_description":"PDC-167 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5307":{"model_id":"5307","model_name":"PDC-168","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7682":{"protein_sequence":{"accession":"WP_054379352.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRAGPGPLGAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_050980.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGCCGGTCCCGGCCCGCTGGGTGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006547","ARO_id":"45009","ARO_name":"PDC-168","CARD_short_name":"PDC-168","ARO_description":"PDC-168 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5308":{"model_id":"5308","model_name":"PDC-169","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7683":{"protein_sequence":{"accession":"WP_065159028.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTYLDVPEAALAQYAQGYGKDDRPLRAGPGPLGAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_050981.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTACTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCTACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGCCGGTCCCGGCCCGCTGGGTGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006548","ARO_id":"45010","ARO_name":"PDC-169","CARD_short_name":"PDC-169","ARO_description":"PDC-169 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5309":{"model_id":"5309","model_name":"PDC-17","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7684":{"protein_sequence":{"accession":"WP_063864571.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDDRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_049887.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGACCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGTCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCCCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCATGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006549","ARO_id":"45011","ARO_name":"PDC-17","CARD_short_name":"PDC-17","ARO_description":"PDC-17 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5310":{"model_id":"5310","model_name":"PDC-170","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7685":{"protein_sequence":{"accession":"WP_065159032.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRRYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPIALKRLQAGNSTPMALQPHRVARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLAR"},"dna_sequence":{"accession":"NG_050982.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGTCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTACTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCGCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGATGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACTCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCGCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGGTCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGGCGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006550","ARO_id":"45012","ARO_name":"PDC-170","CARD_short_name":"PDC-170","ARO_description":"PDC-170 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5311":{"model_id":"5311","model_name":"PDC-171","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7686":{"protein_sequence":{"accession":"WP_058180135.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGRQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_050983.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGTCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGACAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCCCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006551","ARO_id":"45013","ARO_name":"PDC-171","CARD_short_name":"PDC-171","ARO_description":"PDC-171 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5312":{"model_id":"5312","model_name":"PDC-172","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7687":{"protein_sequence":{"accession":"WP_049272244.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHHGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_051496.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCACGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006552","ARO_id":"45014","ARO_name":"PDC-172","CARD_short_name":"PDC-172","ARO_description":"PDC-172 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5313":{"model_id":"5313","model_name":"PDC-174","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7688":{"protein_sequence":{"accession":"WP_070142141.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLKFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_052625.1","fmin":"100","fmax":"1294","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGTCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGAAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006553","ARO_id":"45015","ARO_name":"PDC-174","CARD_short_name":"PDC-174","ARO_description":"PDC-174 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5314":{"model_id":"5314","model_name":"PDC-175","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7689":{"protein_sequence":{"accession":"WP_077248206.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRAGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRITRLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_052891.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGTCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTAGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGCCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCACCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006554","ARO_id":"45016","ARO_name":"PDC-175","CARD_short_name":"PDC-175","ARO_description":"PDC-175 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5315":{"model_id":"5315","model_name":"PDC-176","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7690":{"protein_sequence":{"accession":"WP_077248207.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTTGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_052892.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCACCGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006555","ARO_id":"45017","ARO_name":"PDC-176","CARD_short_name":"PDC-176","ARO_description":"PDC-176 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5316":{"model_id":"5316","model_name":"PDC-177","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7691":{"protein_sequence":{"accession":"WP_085562393.1","sequence":"MRDTRFPCLCGIAASTLLFAATPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVVANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_054679.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCGCCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTGGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTACAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGTCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGTTGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006556","ARO_id":"45018","ARO_name":"PDC-177","CARD_short_name":"PDC-177","ARO_description":"PDC-177 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5317":{"model_id":"5317","model_name":"PDC-178","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7692":{"protein_sequence":{"accession":"WP_085562394.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTVTLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLGAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_054680.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGTCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAACTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGGTGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006557","ARO_id":"45019","ARO_name":"PDC-178","CARD_short_name":"PDC-178","ARO_description":"PDC-178 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5318":{"model_id":"5318","model_name":"PDC-179","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7693":{"protein_sequence":{"accession":"WP_087587950.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_054965.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006558","ARO_id":"45020","ARO_name":"PDC-179","CARD_short_name":"PDC-179","ARO_description":"PDC-179 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5319":{"model_id":"5319","model_name":"PDC-18","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7694":{"protein_sequence":{"accession":"WP_063864572.1","sequence":"MRDTRFPCLCGIAASTLLFAATPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLTARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_049888.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCGCCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCATTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCACCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTATGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006559","ARO_id":"45021","ARO_name":"PDC-18","CARD_short_name":"PDC-18","ARO_description":"PDC-18 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5320":{"model_id":"5320","model_name":"PDC-180","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7695":{"protein_sequence":{"accession":"WP_087587951.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPNSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRAGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTSGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_054966.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTAGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCAACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGCCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAGCGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006560","ARO_id":"45022","ARO_name":"PDC-180","CARD_short_name":"PDC-180","ARO_description":"PDC-180 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5321":{"model_id":"5321","model_name":"PDC-181","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7696":{"protein_sequence":{"accession":"WP_087587952.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRAGPGPLDTEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_054967.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTAGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGCCGGTCCCGGCCCGCTGGATACCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006561","ARO_id":"45023","ARO_name":"PDC-181","CARD_short_name":"PDC-181","ARO_description":"PDC-181 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5322":{"model_id":"5322","model_name":"PDC-182","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7697":{"protein_sequence":{"accession":"WP_087587953.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSHFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRRYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_054968.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGTCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCACTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCGCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006562","ARO_id":"45024","ARO_name":"PDC-182","CARD_short_name":"PDC-182","ARO_description":"PDC-182 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5323":{"model_id":"5323","model_name":"PDC-184","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7698":{"protein_sequence":{"accession":"WP_061199990.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRRYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTYLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_054970.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGTCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCGCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCTACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTATGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006563","ARO_id":"45025","ARO_name":"PDC-184","CARD_short_name":"PDC-184","ARO_description":"PDC-184 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5324":{"model_id":"5324","model_name":"PDC-185","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7699":{"protein_sequence":{"accession":"WP_087587955.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRRYSNPSISLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRAGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_054971.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGTCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCGCTATTCCAACCCGAGCATCAGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGCCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006564","ARO_id":"45026","ARO_name":"PDC-185","CARD_short_name":"PDC-185","ARO_description":"PDC-185 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5325":{"model_id":"5325","model_name":"PDC-186","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7700":{"protein_sequence":{"accession":"WP_087587956.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_054972.1","fmin":"0","fmax":"1188","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGTCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCATGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006565","ARO_id":"45027","ARO_name":"PDC-186","CARD_short_name":"PDC-186","ARO_description":"PDC-186 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5326":{"model_id":"5326","model_name":"PDC-187","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7701":{"protein_sequence":{"accession":"WP_087587957.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQSLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_054973.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGAGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006566","ARO_id":"45028","ARO_name":"PDC-187","CARD_short_name":"PDC-187","ARO_description":"PDC-187 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5327":{"model_id":"5327","model_name":"PDC-188","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7702":{"protein_sequence":{"accession":"WP_087587958.1","sequence":"MRDTRFPCLCGIAASTLLLATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDSASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFLALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_054974.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGCTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACAGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAACTGTTCCTAGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCTTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006567","ARO_id":"45029","ARO_name":"PDC-188","CARD_short_name":"PDC-188","ARO_description":"PDC-188 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5328":{"model_id":"5328","model_name":"PDC-189","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7703":{"protein_sequence":{"accession":"WP_024915536.1","sequence":"MRDTRFPCLCGIAASTLLFTATPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERIMEQRLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRQWAQALDATHRGYYKVGDMTQGLGWEAYDWPIALKRLQAGNSTPMALQPHRVARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLAR"},"dna_sequence":{"accession":"NG_054975.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCACCGCCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTGGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGTTATGGGCTGGCGTCGAAAGAGGACGGTCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAAGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTACACCGCCGGCGGCTTGCCGCTTCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGTCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAGCGGATCATGGAGCAGCGCCTGTTCCCGGCCCTGGGCCTCGAACAGACTCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTCCGGGTCGGCCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGACTGGACCGGCAGTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCGCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGGTCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGGCGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006568","ARO_id":"45030","ARO_name":"PDC-189","CARD_short_name":"PDC-189","ARO_description":"PDC-189 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5329":{"model_id":"5329","model_name":"PDC-190","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7704":{"protein_sequence":{"accession":"WP_087587959.1","sequence":"MRDTRFPCLCGIAASTLLFAATPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASEHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDRAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRAGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_054976.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCGCCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCGAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCGGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGCCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATTCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006569","ARO_id":"45031","ARO_name":"PDC-190","CARD_short_name":"PDC-190","ARO_description":"PDC-190 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5330":{"model_id":"5330","model_name":"PDC-191","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7705":{"protein_sequence":{"accession":"WP_087587960.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQLPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_054977.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGCTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006570","ARO_id":"45032","ARO_name":"PDC-191","CARD_short_name":"PDC-191","ARO_description":"PDC-191 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5331":{"model_id":"5331","model_name":"PDC-192","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7706":{"protein_sequence":{"accession":"WP_004365741.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPEILFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_054978.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGATCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006571","ARO_id":"45033","ARO_name":"PDC-192","CARD_short_name":"PDC-192","ARO_description":"PDC-192 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5332":{"model_id":"5332","model_name":"PDC-193","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7707":{"protein_sequence":{"accession":"WP_087587961.1","sequence":"MRDTKFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_054979.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAAATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAACTGTTCCCAGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGATCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATTCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006572","ARO_id":"45034","ARO_name":"PDC-193","CARD_short_name":"PDC-193","ARO_description":"PDC-193 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5333":{"model_id":"5333","model_name":"PDC-194","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7708":{"protein_sequence":{"accession":"WP_087587962.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALTQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPIPLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_054980.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGACCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAATGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCCCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCACTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006573","ARO_id":"45035","ARO_name":"PDC-194","CARD_short_name":"PDC-194","ARO_description":"PDC-194 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5334":{"model_id":"5334","model_name":"PDC-195","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7709":{"protein_sequence":{"accession":"WP_025325152.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVVLANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_054981.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACTCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGGTCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006574","ARO_id":"45036","ARO_name":"PDC-195","CARD_short_name":"PDC-195","ARO_description":"PDC-195 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5335":{"model_id":"5335","model_name":"PDC-196","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7710":{"protein_sequence":{"accession":"WP_148044425.1","sequence":"MHDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_065883.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCACGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCATGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006575","ARO_id":"45037","ARO_name":"PDC-196","CARD_short_name":"PDC-196","ARO_description":"PDC-196 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5336":{"model_id":"5336","model_name":"PDC-197","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7711":{"protein_sequence":{"accession":"WP_057388025.1","sequence":"MRDTGFPCLCGIAASTLLFAATSAIAGEAPADRLKTLVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASLHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYTPGSQRLYSNPSIGLFGYLAARSLGQPFERIMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVNANLHPERLDKPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_054982.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCGGATTCCCCTGCCTGTGCGGCATCGCCGCCTCCACACTGCTGTTCGCCGCCACCTCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGACACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGATATTCCGGGCCTGGCCGTGGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCTTCGAAAGAGGACGGTCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGTGCCAGCCTGCACTGGCCGGCGCTGCAAGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAAGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACACGCCGGGCAGCCAGCGCCTCTACTCCAACCCGAGCATCGGTCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGATCATGGAGCAGCAACTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCTCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCAATGCCAACCTGCATCCGGAGCGCCTGGACAAGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCGGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGACTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATCCCAGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAATTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006576","ARO_id":"45038","ARO_name":"PDC-197","CARD_short_name":"PDC-197","ARO_description":"PDC-197 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5337":{"model_id":"5337","model_name":"PDC-198","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7712":{"protein_sequence":{"accession":"WP_087587963.1","sequence":"MRDTRFPCLFGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_054983.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTTCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCCCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006577","ARO_id":"45039","ARO_name":"PDC-198","CARD_short_name":"PDC-198","ARO_description":"PDC-198 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5338":{"model_id":"5338","model_name":"PDC-199","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7713":{"protein_sequence":{"accession":"WP_087587964.1","sequence":"MRDTRFSCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_054984.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCTCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006578","ARO_id":"45040","ARO_name":"PDC-199","CARD_short_name":"PDC-199","ARO_description":"PDC-199 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5339":{"model_id":"5339","model_name":"PDC-20","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7714":{"protein_sequence":{"accession":"WP_016263090.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRRYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_049892.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGTCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCGCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006579","ARO_id":"45041","ARO_name":"PDC-20","CARD_short_name":"PDC-20","ARO_description":"PDC-20 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5340":{"model_id":"5340","model_name":"PDC-200","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7715":{"protein_sequence":{"accession":"WP_087587965.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMAPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_054985.1","fmin":"0","fmax":"1188","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCCCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006580","ARO_id":"45042","ARO_name":"PDC-200","CARD_short_name":"PDC-200","ARO_description":"PDC-200 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5341":{"model_id":"5341","model_name":"PDC-202","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7716":{"protein_sequence":{"accession":"WP_087587967.1","sequence":"MRDTGFPCLCGIAASTLLFAATSAIAGEAPADRLKTLVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALVQDKMRLDDRASLHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYTPGSQRLYSNPSIGLFGYLAARSLGQPFERIMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDKPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_054987.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCGGATTCCCCTGCCTGTGCGGCATCGCCGCCTCCACACTGCTGTTCGCCGCCACCTCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGACACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGATATTCCGGGCCTGGCCGTGGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCTTCGAAAGAGGACGGTCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGTCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCTGCACTGGCCGGCGCTGCAAGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAAGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACACGCCGGGCAGCCAGCGCCTCTACTCCAACCCGAGCATCGGTCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGATCATGGAGCAGCAACTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAAGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCGGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGACTGCCCGCGCCCCAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATCCCAGGCCGCGACCTGGGCCTGGTGATCCTGGCCAATCGCAATTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006581","ARO_id":"45043","ARO_name":"PDC-202","CARD_short_name":"PDC-202","ARO_description":"PDC-202 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5342":{"model_id":"5342","model_name":"PDC-203","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7717":{"protein_sequence":{"accession":"WP_087587968.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYPPGSQRRYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_054988.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGTCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACCCGCCGGGCAGCCAGCGCCGCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006582","ARO_id":"45044","ARO_name":"PDC-203","CARD_short_name":"PDC-203","ARO_description":"PDC-203 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5343":{"model_id":"5343","model_name":"PDC-204","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7718":{"protein_sequence":{"accession":"WP_087587969.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQCAQGYGKDDRPLRVGPGPLGAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_054989.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGTCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTGCGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGGCGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006583","ARO_id":"45045","ARO_name":"PDC-204","CARD_short_name":"PDC-204","ARO_description":"PDC-204 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5344":{"model_id":"5344","model_name":"PDC-205","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7719":{"protein_sequence":{"accession":"WP_087587970.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRRYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTYLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTSGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_054990.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGTCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCGCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCTACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAGCGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006584","ARO_id":"45046","ARO_name":"PDC-205","CARD_short_name":"PDC-205","ARO_description":"PDC-205 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5345":{"model_id":"5345","model_name":"PDC-206","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7720":{"protein_sequence":{"accession":"WP_087587971.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGNGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_054991.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGTCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCAACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006585","ARO_id":"45047","ARO_name":"PDC-206","CARD_short_name":"PDC-206","ARO_description":"PDC-206 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5346":{"model_id":"5346","model_name":"PDC-208","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7721":{"protein_sequence":{"accession":"WP_087587972.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRAGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_054993.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCACGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGCCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006586","ARO_id":"45048","ARO_name":"PDC-208","CARD_short_name":"PDC-208","ARO_description":"PDC-208 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5347":{"model_id":"5347","model_name":"PDC-209","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7722":{"protein_sequence":{"accession":"WP_087587973.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALTQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_054994.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGACCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006587","ARO_id":"45049","ARO_name":"PDC-209","CARD_short_name":"PDC-209","ARO_description":"PDC-209 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5348":{"model_id":"5348","model_name":"PDC-210","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7723":{"protein_sequence":{"accession":"WP_087587974.1","sequence":"MRDTRFPCLYGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLRRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_054995.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTACGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAAGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAGGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006588","ARO_id":"45050","ARO_name":"PDC-210","CARD_short_name":"PDC-210","ARO_description":"PDC-210 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5349":{"model_id":"5349","model_name":"PDC-211","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7724":{"protein_sequence":{"accession":"WP_088245216.1","sequence":"MRDTRFPCLCGIAASTLLFAATPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASEHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDRAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_055273.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCGCCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCGAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCGGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCCGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006589","ARO_id":"45051","ARO_name":"PDC-211","CARD_short_name":"PDC-211","ARO_description":"PDC-211 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5350":{"model_id":"5350","model_name":"PDC-213","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7725":{"protein_sequence":{"accession":"WP_073647245.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLSAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_055276.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGACGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAACTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGTCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATTCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006590","ARO_id":"45052","ARO_name":"PDC-213","CARD_short_name":"PDC-213","ARO_description":"PDC-213 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5351":{"model_id":"5351","model_name":"PDC-214","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7726":{"protein_sequence":{"accession":"WP_088245219.1","sequence":"MRDTGFPCLCGIAASTLLFAATSAIAGEAPADRLKTLVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASLHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYTPGSQRLYSNPSIGLFGYLAARSLGQPFERIMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDKPWAQALNATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_055277.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCGGATTCCCCTGCCTGTGCGGCATCGCCGCCTCCACACTGCTGTTCGCCGCCACCTCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGACACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGATATTCCGGGCCTGGCCGTGGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCTTCGAAAGAGGACGGTCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCTGCACTGGCCGGCGCTGCAAGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAAGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACACGCCGGGCAGCCAGCGCCTCTACTCCAACCCGAGCATCGGTCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGATCATGGAGCAGCAACTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCTCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAAGCCCTGGGCGCAGGCGCTCAATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCGGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGACTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATCCCAGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAATTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006591","ARO_id":"45053","ARO_name":"PDC-214","CARD_short_name":"PDC-214","ARO_description":"PDC-214 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5352":{"model_id":"5352","model_name":"PDC-215","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7727":{"protein_sequence":{"accession":"WP_088245220.1","sequence":"MRDTRFPCLCGIAASTLLFAATPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRGGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQPKVPLKR"},"dna_sequence":{"accession":"NG_055278.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCGCCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGGCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGCCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006592","ARO_id":"45054","ARO_name":"PDC-215","CARD_short_name":"PDC-215","ARO_description":"PDC-215 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5353":{"model_id":"5353","model_name":"PDC-216","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7728":{"protein_sequence":{"accession":"WP_088245221.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGSLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_055279.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCTCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006593","ARO_id":"45055","ARO_name":"PDC-216","CARD_short_name":"PDC-216","ARO_description":"PDC-216 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5354":{"model_id":"5354","model_name":"PDC-217","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7729":{"protein_sequence":{"accession":"WP_088245222.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRAGPGPLGAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_055280.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGCCGGTCCCGGCCCGCTGGGTGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006594","ARO_id":"45056","ARO_name":"PDC-217","CARD_short_name":"PDC-217","ARO_description":"PDC-217 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5355":{"model_id":"5355","model_name":"PDC-218","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7730":{"protein_sequence":{"accession":"WP_088245223.1","sequence":"MRDTRFPCLCGIAASTLLFAATPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_055281.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCGCCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCATTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTGGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGTTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006595","ARO_id":"45057","ARO_name":"PDC-218","CARD_short_name":"PDC-218","ARO_description":"PDC-218 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5356":{"model_id":"5356","model_name":"PDC-219","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7731":{"protein_sequence":{"accession":"WP_088245224.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMAPQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_055282.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAACTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCCGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006596","ARO_id":"45058","ARO_name":"PDC-219","CARD_short_name":"PDC-219","ARO_description":"PDC-219 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5357":{"model_id":"5357","model_name":"PDC-21a","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7732":{"protein_sequence":{"accession":"WP_063864574.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASLHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRRYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_049893.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGTCTCGACGACCGCGCCAGCCTGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCGCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006597","ARO_id":"45059","ARO_name":"PDC-21a","CARD_short_name":"PDC-21a","ARO_description":"PDC-21a is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5358":{"model_id":"5358","model_name":"PDC-21b","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7733":{"protein_sequence":{"accession":"WP_063864575.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDHPLRAGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_049894.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCACCCGCTACGGGCCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006598","ARO_id":"45060","ARO_name":"PDC-21b","CARD_short_name":"PDC-21b","ARO_description":"PDC-21b is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5359":{"model_id":"5359","model_name":"PDC-22","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7734":{"protein_sequence":{"accession":"WP_023108311.1","sequence":"MRDTRFPCLCGIAASTLLLATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_049895.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGCTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAACTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATTCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37066","NCBI_taxonomy_name":"Pseudomonas","NCBI_taxonomy_id":"286"}}}},"ARO_accession":"3006599","ARO_id":"45061","ARO_name":"PDC-22","CARD_short_name":"PDC-22","ARO_description":"PDC-22 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5360":{"model_id":"5360","model_name":"PDC-220","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7735":{"protein_sequence":{"accession":"WP_088245218.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMAPQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_055275.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCTTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCCGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATTCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006600","ARO_id":"45062","ARO_name":"PDC-220","CARD_short_name":"PDC-220","ARO_description":"PDC-220 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5361":{"model_id":"5361","model_name":"PDC-221","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7736":{"protein_sequence":{"accession":"WP_100931731.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALTQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAKGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_056055.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGACCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTTCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCAAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006601","ARO_id":"45063","ARO_name":"PDC-221","CARD_short_name":"PDC-221","ARO_description":"PDC-221 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5362":{"model_id":"5362","model_name":"PDC-222","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7737":{"protein_sequence":{"accession":"WP_100931732.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFIATLAGYALTQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_056056.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCATCGCCACCCTCGCCGGCTATGCCCTGACCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTTCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006602","ARO_id":"45064","ARO_name":"PDC-222","CARD_short_name":"PDC-222","ARO_description":"PDC-222 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5363":{"model_id":"5363","model_name":"PDC-223","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7738":{"protein_sequence":{"accession":"WP_100931733.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALTQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_056057.1","fmin":"0","fmax":"1137","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGACCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTTCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006603","ARO_id":"45065","ARO_name":"PDC-223","CARD_short_name":"PDC-223","ARO_description":"PDC-223 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5364":{"model_id":"5364","model_name":"PDC-224","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7739":{"protein_sequence":{"accession":"WP_101244936.1","sequence":"MRDTGFPCLCGIAASTLLFAATSAIAGEAPADRLKTLVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDSRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASLHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYTPGSQRLYSNPSIGLFGYLAARSLGQPFERIMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAKGYGVKTSAADLLRFVDANLHPERLDKPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_056102.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCGGATTCCCCTGCCTGTGCGGCATCGCCGCCTCCACACTGCTGTTCGCCGCCACCTCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGACACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGATATTCCGGGCCTGGCCGTGGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCTTCGAAAGAGGACAGTCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCTGCACTGGCCGGCGCTGCAAGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAAGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACACGCCGGGCAGCCAGCGCCTCTACTCCAACCCGAGCATCGGTCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGATCATGGAGCAGCAACTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCTCTACGGGTCGGTCCCGGCCCGCTGGATGCCAAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAAGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCGGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGACTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATCCCAGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAATTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006604","ARO_id":"45066","ARO_name":"PDC-224","CARD_short_name":"PDC-224","ARO_description":"PDC-224 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5365":{"model_id":"5365","model_name":"PDC-226","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7740":{"protein_sequence":{"accession":"WP_061190338.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALTQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTSGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_056104.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGACCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTTCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAGCGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006605","ARO_id":"45067","ARO_name":"PDC-226","CARD_short_name":"PDC-226","ARO_description":"PDC-226 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5366":{"model_id":"5366","model_name":"PDC-227","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7741":{"protein_sequence":{"accession":"WP_104009856.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQLPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTSGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_056419.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGTCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGCTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCCCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAGCGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006606","ARO_id":"45068","ARO_name":"PDC-227","CARD_short_name":"PDC-227","ARO_description":"PDC-227 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5367":{"model_id":"5367","model_name":"PDC-228","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7742":{"protein_sequence":{"accession":"WP_104009857.1","sequence":"MRDTGFPCLCGIAASTLLFAATSAIAGEAPADRLKTLVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDSRRVTPETLFEIGSVSKTFIATLAGYALAQDKMRLDDRASLHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYTPGSQRLYSNLSIGLFGYLAARSLGQPFERIMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAKGYGVKTSAADLLRFVDANLHPERLDKPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_056420.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCGGATTCCCCTGCCTGTGCGGCATCGCCGCCTCCACACTGCTGTTCGCCGCCACCTCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGACACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGATATTCCGGGCCTGGCCGTGGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCTTCGAAAGAGGACAGTCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCATCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCTGCACTGGCCGGCGCTGCAAGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAAGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACACGCCGGGCAGCCAGCGCCTCTACTCCAACCTGAGCATCGGTCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGATCATGGAGCAGCAACTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCTCTACGGGTCGGTCCCGGCCCGCTGGATGCCAAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAAGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCGGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGACTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATCCCAGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAATTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006607","ARO_id":"45069","ARO_name":"PDC-228","CARD_short_name":"PDC-228","ARO_description":"PDC-228 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5368":{"model_id":"5368","model_name":"PDC-229","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7743":{"protein_sequence":{"accession":"WP_104009858.1","sequence":"MRDTRFPCLCGIAASTLLFAATPAIAGEAPADRLKALVDAAVQPAMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRAGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_056421.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCGCCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCATTGGTCGACGCCGCCGTACAACCGGCGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGCCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCTAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTATGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006608","ARO_id":"45070","ARO_name":"PDC-229","CARD_short_name":"PDC-229","ARO_description":"PDC-229 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5369":{"model_id":"5369","model_name":"PDC-230","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7744":{"protein_sequence":{"accession":"WP_104009859.1","sequence":"MRDTRFPCLCGIAASTLLFAATPAIAGEAPADRLKALVDAAVQPAMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRAGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_056422.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCGCCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCATTGGTCGACGCCGCCGTACAACCGGCGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGCCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCTAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTATGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006609","ARO_id":"45071","ARO_name":"PDC-230","CARD_short_name":"PDC-230","ARO_description":"PDC-230 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5370":{"model_id":"5370","model_name":"PDC-232","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7745":{"protein_sequence":{"accession":"WP_104009861.1","sequence":"MRDTRFPCLCGIAASTLLFAATPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRAGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPIAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_056424.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCGCCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCATTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGCCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCTAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCATTGCCGAGCGGGTGAAGATCGCCTATGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006610","ARO_id":"45072","ARO_name":"PDC-232","CARD_short_name":"PDC-232","ARO_description":"PDC-232 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5371":{"model_id":"5371","model_name":"PDC-233","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7746":{"protein_sequence":{"accession":"WP_104009862.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRAGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRLWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_056425.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTTCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGCCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCTCTGGGCGCAGGCGCTTGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006611","ARO_id":"45073","ARO_name":"PDC-233","CARD_short_name":"PDC-233","ARO_description":"PDC-233 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5372":{"model_id":"5372","model_name":"PDC-234","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7747":{"protein_sequence":{"accession":"WP_104009832.1","sequence":"MRDTRFPCLCGIAASTLLFAATPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTSGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_056389.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCGCCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCATTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCTAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAGCGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTATGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006612","ARO_id":"45074","ARO_name":"PDC-234","CARD_short_name":"PDC-234","ARO_description":"PDC-234 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5373":{"model_id":"5373","model_name":"PDC-235","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7748":{"protein_sequence":{"accession":"WP_104009833.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQLPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_056390.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCTTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGCTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATTCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006613","ARO_id":"45075","ARO_name":"PDC-235","CARD_short_name":"PDC-235","ARO_description":"PDC-235 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5374":{"model_id":"5374","model_name":"PDC-236","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7749":{"protein_sequence":{"accession":"WP_104009834.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQPKVPLKR"},"dna_sequence":{"accession":"NG_056391.1","fmin":"0","fmax":"1182","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGCCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006614","ARO_id":"45076","ARO_name":"PDC-236","CARD_short_name":"PDC-236","ARO_description":"PDC-236 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5375":{"model_id":"5375","model_name":"PDC-237","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7750":{"protein_sequence":{"accession":"WP_104009835.1","sequence":"MRDTRFPCLCGIAASTLLFAATPAIAGEAPADRLKALVDAAVQPAMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRAGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPIAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_056392.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCGCCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCATTGGTCGACGCCGCCGTACAACCGGCGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGCCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCTAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCATTGCCGAGCGGGTGAAGATCGCCTATGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006615","ARO_id":"45077","ARO_name":"PDC-237","CARD_short_name":"PDC-237","ARO_description":"PDC-237 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5376":{"model_id":"5376","model_name":"PDC-238","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7751":{"protein_sequence":{"accession":"WP_104009836.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALTQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTYLDVPEAALAQYAQGYGKDDRPLRAGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_056393.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGACCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCTACCTCGACGTGCCCGAGGCGGCGTTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGCCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCATACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006616","ARO_id":"45078","ARO_name":"PDC-238","CARD_short_name":"PDC-238","ARO_description":"PDC-238 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5377":{"model_id":"5377","model_name":"PDC-239","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7752":{"protein_sequence":{"accession":"WP_104009837.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVPISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_056394.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTACCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006617","ARO_id":"45079","ARO_name":"PDC-239","CARD_short_name":"PDC-239","ARO_description":"PDC-239 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5378":{"model_id":"5378","model_name":"PDC-24","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7753":{"protein_sequence":{"accession":"WP_023115067.1","sequence":"MRDTRFPCLCGIAASTLLFAATPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_049897.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCGCCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCATTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCTAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTATGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37066","NCBI_taxonomy_name":"Pseudomonas","NCBI_taxonomy_id":"286"}}}},"ARO_accession":"3006618","ARO_id":"45080","ARO_name":"PDC-24","CARD_short_name":"PDC-24","ARO_description":"PDC-24 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5379":{"model_id":"5379","model_name":"PDC-241","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7754":{"protein_sequence":{"accession":"WP_104009838.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQGKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDRAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPITLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_056396.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGGCAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCGGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCCGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCACCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCATACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006619","ARO_id":"45081","ARO_name":"PDC-241","CARD_short_name":"PDC-241","ARO_description":"PDC-241 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5380":{"model_id":"5380","model_name":"PDC-242","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7755":{"protein_sequence":{"accession":"WP_104009839.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALTQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRAGPGPLDAEGYGVKASAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_056397.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGACCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTTCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGCCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGGCCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006620","ARO_id":"45082","ARO_name":"PDC-242","CARD_short_name":"PDC-242","ARO_description":"PDC-242 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5381":{"model_id":"5381","model_name":"PDC-243","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7756":{"protein_sequence":{"accession":"WP_104009840.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFIATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRAGPGPLRAGPGPLDAEGYRVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_056398.1","fmin":"0","fmax":"1215","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCATCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGCCGGTCCCGGCCCGCTACGGGCCGGTCCCGGCCCGCTGGATGCCGAAGGCTACAGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006621","ARO_id":"45083","ARO_name":"PDC-243","CARD_short_name":"PDC-243","ARO_description":"PDC-243 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5382":{"model_id":"5382","model_name":"PDC-244","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7757":{"protein_sequence":{"accession":"WP_104009841.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_056399.1","fmin":"0","fmax":"1170","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006622","ARO_id":"45084","ARO_name":"PDC-244","CARD_short_name":"PDC-244","ARO_description":"PDC-244 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5383":{"model_id":"5383","model_name":"PDC-245","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7758":{"protein_sequence":{"accession":"WP_100831609.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTVTLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIDLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_056400.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGTCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGACCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAACTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006623","ARO_id":"45085","ARO_name":"PDC-245","CARD_short_name":"PDC-245","ARO_description":"PDC-245 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5384":{"model_id":"5384","model_name":"PDC-246","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7759":{"protein_sequence":{"accession":"WP_104009842.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRRYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRAGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTSGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_056401.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGTCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCGCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGCCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAGCGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006624","ARO_id":"45086","ARO_name":"PDC-246","CARD_short_name":"PDC-246","ARO_description":"PDC-246 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5385":{"model_id":"5385","model_name":"PDC-247","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7760":{"protein_sequence":{"accession":"WP_104009843.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALTQGKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRTGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTSGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_056402.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGACCCAGGGCAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGACCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAGCGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006625","ARO_id":"45087","ARO_name":"PDC-247","CARD_short_name":"PDC-247","ARO_description":"PDC-247 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5386":{"model_id":"5386","model_name":"PDC-248","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7761":{"protein_sequence":{"accession":"WP_104009844.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKASAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYHWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_056403.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGATGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGGCCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACTCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACCACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006626","ARO_id":"45088","ARO_name":"PDC-248","CARD_short_name":"PDC-248","ARO_description":"PDC-248 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5387":{"model_id":"5387","model_name":"PDC-249","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7762":{"protein_sequence":{"accession":"WP_104009845.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRGGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_056404.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGTCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGGCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCAATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAGCCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36778","NCBI_taxonomy_name":"Pseudomonas sp.","NCBI_taxonomy_id":"306"}}}},"ARO_accession":"3006627","ARO_id":"45089","ARO_name":"PDC-249","CARD_short_name":"PDC-249","ARO_description":"PDC-249 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5388":{"model_id":"5388","model_name":"PDC-25","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7763":{"protein_sequence":{"accession":"WP_063864576.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVSGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_049898.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCTCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006628","ARO_id":"45090","ARO_name":"PDC-25","CARD_short_name":"PDC-25","ARO_description":"PDC-25 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5389":{"model_id":"5389","model_name":"PDC-250","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7764":{"protein_sequence":{"accession":"WP_058174497.1","sequence":"MRHATILNLCGLAASTLFFATTSAFATEAPAERLKALVDAAVQPVMKANDIPGLAVAITLKGEPHYFSYGVASKEDARKVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASRHWPALQGSRFDGISLLDLGTYTAGGLPLQFPGAVQKDPAQIRDYYRQWQPTYAPGSHRQYSNPSIGLFGYLAARSLGQPFERSMERQLFPALGLEHTFIRVPAAQQGLYAQGYGKDDRPLRVGPGPLDAEAYGLKSSVADLLRFVEANLHPERLEKPWAQALDATHRGYYKVGDMTQGLGWEAYDWPIDLRRLQAGNSAPMALQAHKVARLPAPQALDGQRLLNKTGSTNGFGAYLAFIPGRDVGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLVR"},"dna_sequence":{"accession":"NG_057582.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCCATGCGACAATCCTCAACCTGTGCGGCCTCGCCGCTTCCACCCTGTTCTTCGCGACAACATCGGCCTTCGCCACGGAGGCGCCGGCGGAGCGCCTGAAGGCTCTGGTGGACGCCGCCGTGCAACCGGTCATGAAGGCCAATGATATCCCGGGACTGGCCGTCGCCATCACTCTCAAGGGCGAACCGCATTACTTCAGTTATGGGGTGGCCTCGAAGGAGGACGCCCGCAAGGTGACCCCCGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTACGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGTGCCAGCCGGCACTGGCCCGCCCTGCAGGGCAGCCGCTTCGACGGTATCAGCCTGCTCGACCTCGGCACCTACACCGCTGGCGGCCTGCCGCTACAGTTCCCCGGTGCGGTGCAGAAGGATCCGGCGCAGATCCGCGACTATTACCGCCAGTGGCAACCGACCTACGCCCCGGGCAGCCACCGCCAGTACTCCAACCCGAGCATCGGTCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCATTCGAGCGCAGCATGGAACGGCAGCTGTTCCCGGCGCTCGGCCTGGAGCACACCTTTATCCGGGTGCCCGCCGCGCAGCAGGGGCTGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTGCGGGTCGGACCCGGTCCGCTGGACGCCGAGGCCTACGGGCTGAAGTCCAGCGTTGCGGACCTGCTGCGCTTCGTCGAGGCCAACCTGCACCCCGAGCGCCTGGAGAAGCCCTGGGCGCAGGCCCTCGACGCCACCCATCGCGGCTACTACAAGGTGGGCGACATGACCCAGGGCCTGGGTTGGGAAGCCTACGATTGGCCGATCGACCTGAGGCGCCTGCAGGCGGGCAACTCGGCGCCGATGGCGCTGCAGGCGCACAAGGTCGCCAGGTTGCCGGCGCCGCAAGCCCTGGACGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGTTTCGGCGCCTACCTGGCGTTCATCCCGGGACGCGACGTCGGCCTGGTGATCCTGGCCAATCGCAACTACCCCAATGCCGAGCGGGTGAAGATCGCTTACGCCATCCTCAGCGGCCTGGAACAGCAGGCCAAGGTACCGCTGGTGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006629","ARO_id":"45091","ARO_name":"PDC-250","CARD_short_name":"PDC-250","ARO_description":"PDC-250 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5390":{"model_id":"5390","model_name":"PDC-251","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7765":{"protein_sequence":{"accession":"WP_109791185.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTVTLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNLSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_057583.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGTCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCTGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAACTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006630","ARO_id":"45092","ARO_name":"PDC-251","CARD_short_name":"PDC-251","ARO_description":"PDC-251 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5391":{"model_id":"5391","model_name":"PDC-252","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7766":{"protein_sequence":{"accession":"WP_109791186.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFAATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_057584.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCGCCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCACGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006631","ARO_id":"45093","ARO_name":"PDC-252","CARD_short_name":"PDC-252","ARO_description":"PDC-252 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5392":{"model_id":"5392","model_name":"PDC-253","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7767":{"protein_sequence":{"accession":"WP_109791187.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMAPQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQPKVPLKR"},"dna_sequence":{"accession":"NG_057585.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCCGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGCCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006632","ARO_id":"45094","ARO_name":"PDC-253","CARD_short_name":"PDC-253","ARO_description":"PDC-253 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5393":{"model_id":"5393","model_name":"PDC-254","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7768":{"protein_sequence":{"accession":"WP_109791188.1","sequence":"MRDTRFPCLCGIAASTLLFATTLAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRRYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_057586.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCTGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGTCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCGCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006633","ARO_id":"45095","ARO_name":"PDC-254","CARD_short_name":"PDC-254","ARO_description":"PDC-254 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5394":{"model_id":"5394","model_name":"PDC-256","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7769":{"protein_sequence":{"accession":"WP_109791190.1","sequence":"MRDTRFPCLCGIAASTLLFAATPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDLAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_057588.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCGCCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTGGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCTGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAACTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATTCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006634","ARO_id":"45096","ARO_name":"PDC-256","CARD_short_name":"PDC-256","ARO_description":"PDC-256 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5395":{"model_id":"5395","model_name":"PDC-259","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7770":{"protein_sequence":{"accession":"WP_109791193.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRRYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTYLDVPEAALAQYAQGYGKDDRPLRVSPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_057591.2","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGTCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCGCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCTACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCAGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006635","ARO_id":"45097","ARO_name":"PDC-259","CARD_short_name":"PDC-259","ARO_description":"PDC-259 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5396":{"model_id":"5396","model_name":"PDC-26","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7771":{"protein_sequence":{"accession":"WP_063864577.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKAYDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRRYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLNVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_049899.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCTATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGTCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCGCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCAACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006636","ARO_id":"45098","ARO_name":"PDC-26","CARD_short_name":"PDC-26","ARO_description":"PDC-26 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5397":{"model_id":"5397","model_name":"PDC-260","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7772":{"protein_sequence":{"accession":"WP_109791194.1","sequence":"MRDTRFSCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_057592.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCTCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006637","ARO_id":"45099","ARO_name":"PDC-260","CARD_short_name":"PDC-260","ARO_description":"PDC-260 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5398":{"model_id":"5398","model_name":"PDC-261","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7773":{"protein_sequence":{"accession":"WP_109791195.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDLASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRRYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_057593.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGTCTCGACGACCTCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCGCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006638","ARO_id":"45100","ARO_name":"PDC-261","CARD_short_name":"PDC-261","ARO_description":"PDC-261 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5399":{"model_id":"5399","model_name":"PDC-262","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7774":{"protein_sequence":{"accession":"WP_109791196.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPSPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTSGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_057594.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCAGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAGCGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006639","ARO_id":"45101","ARO_name":"PDC-262","CARD_short_name":"PDC-262","ARO_description":"PDC-262 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5400":{"model_id":"5400","model_name":"PDC-263","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7775":{"protein_sequence":{"accession":"WP_109791197.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQGKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRHYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTSGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_057595.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGGCAAGATGCGTCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCACTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAGCGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006640","ARO_id":"45102","ARO_name":"PDC-263","CARD_short_name":"PDC-263","ARO_description":"PDC-263 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5401":{"model_id":"5401","model_name":"PDC-265","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7776":{"protein_sequence":{"accession":"WP_109791199.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_057597.2","fmin":"0","fmax":"1173","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCTTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATTCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006641","ARO_id":"45103","ARO_name":"PDC-265","CARD_short_name":"PDC-265","ARO_description":"PDC-265 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5402":{"model_id":"5402","model_name":"PDC-266","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7777":{"protein_sequence":{"accession":"WP_109791200.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGINLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_057598.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAACCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAACTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006642","ARO_id":"45104","ARO_name":"PDC-266","CARD_short_name":"PDC-266","ARO_description":"PDC-266 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5403":{"model_id":"5403","model_name":"PDC-267","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7778":{"protein_sequence":{"accession":"WP_109791201.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFKRLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAKGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_057599.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTAGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCAAACGGCTCATGGAGCAGCAACTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCCCTACGGGTCGGTCCCGGCCCGCTGGATGCCAAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCATGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006643","ARO_id":"45105","ARO_name":"PDC-267","CARD_short_name":"PDC-267","ARO_description":"PDC-267 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5404":{"model_id":"5404","model_name":"PDC-268","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7779":{"protein_sequence":{"accession":"WP_109791202.1","sequence":"MRDTRFPCLCGIAASTLLFAATPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRGGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_057600.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCGCCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCATTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGGCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCTAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTATGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006644","ARO_id":"45106","ARO_name":"PDC-268","CARD_short_name":"PDC-268","ARO_description":"PDC-268 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5405":{"model_id":"5405","model_name":"PDC-270","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7780":{"protein_sequence":{"accession":"WP_109791203.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRRYSNPSIDLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLNVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMTLQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_057601.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGTCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCGCTATTCCAACCCGAGCATCGACCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCAACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGACGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006645","ARO_id":"45107","ARO_name":"PDC-270","CARD_short_name":"PDC-270","ARO_description":"PDC-270 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5406":{"model_id":"5406","model_name":"PDC-271","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7781":{"protein_sequence":{"accession":"WP_058157026.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTVTLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTKGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_057602.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGTCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAACTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAAAGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006646","ARO_id":"45108","ARO_name":"PDC-271","CARD_short_name":"PDC-271","ARO_description":"PDC-271 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5407":{"model_id":"5407","model_name":"PDC-273","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7782":{"protein_sequence":{"accession":"WP_109791205.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALTQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMTLQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_057604.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGACCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACTCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGACGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006647","ARO_id":"45109","ARO_name":"PDC-273","CARD_short_name":"PDC-273","ARO_description":"PDC-273 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5408":{"model_id":"5408","model_name":"PDC-274","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7783":{"protein_sequence":{"accession":"WP_109791206.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFLALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_057605.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGACGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAACTGTTCCTAGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATTCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006648","ARO_id":"45110","ARO_name":"PDC-274","CARD_short_name":"PDC-274","ARO_description":"PDC-274 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5409":{"model_id":"5409","model_name":"PDC-275","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7784":{"protein_sequence":{"accession":"WP_111672883.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADAAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTVTLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_060537.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGCGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGTCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAACTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006649","ARO_id":"45111","ARO_name":"PDC-275","CARD_short_name":"PDC-275","ARO_description":"PDC-275 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5410":{"model_id":"5410","model_name":"PDC-276","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7785":{"protein_sequence":{"accession":"WP_111672890.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQSYGKDDRPLRVGPGPLDAESYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_060546.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGTCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGAGCTACGGCAAGGACGACCGCCCCCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAAGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGATTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006650","ARO_id":"45112","ARO_name":"PDC-276","CARD_short_name":"PDC-276","ARO_description":"PDC-276 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5411":{"model_id":"5411","model_name":"PDC-277","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7786":{"protein_sequence":{"accession":"WP_111672891.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLKFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERIMEQRLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRQWAQALDATHRGYYKVGDMTQGLGWEAYDWPIALKRLQAGNSTPMALQPHRVARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLAR"},"dna_sequence":{"accession":"NG_060547.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTGGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGTTATGGGCTGGCGTCGAAAGAGGACGGTCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAAGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTACACCGCCGGCGGCTTGCCGCTGAAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGTCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAGCGGATCATGGAGCAGCGCCTGTTCCCGGCCCTGGGCCTCGAACAGACTCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTCCGGGTCGGCCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGACTGGACCGGCAGTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCGCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGGTCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGGCGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006651","ARO_id":"45113","ARO_name":"PDC-277","CARD_short_name":"PDC-277","ARO_description":"PDC-277 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5412":{"model_id":"5412","model_name":"PDC-278","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7787":{"protein_sequence":{"accession":"WP_070698497.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRRYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLNVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_060548.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGTCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCGCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCAACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006652","ARO_id":"45114","ARO_name":"PDC-278","CARD_short_name":"PDC-278","ARO_description":"PDC-278 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5413":{"model_id":"5413","model_name":"PDC-279","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7788":{"protein_sequence":{"accession":"WP_111672892.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKEEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALTQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_060549.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGAAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGACCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGTTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006653","ARO_id":"45115","ARO_name":"PDC-279","CARD_short_name":"PDC-279","ARO_description":"PDC-279 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5414":{"model_id":"5414","model_name":"PDC-280","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7789":{"protein_sequence":{"accession":"WP_111672893.1","sequence":"MRDTRFPCLCGIAASTLLLATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFTATLAGYALAQNKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDYRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_060550.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGCTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGAACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAACTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACTACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCTTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006654","ARO_id":"45116","ARO_name":"PDC-280","CARD_short_name":"PDC-280","ARO_description":"PDC-280 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5415":{"model_id":"5415","model_name":"PDC-281","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7790":{"protein_sequence":{"accession":"WP_111672894.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQLPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQPKVPLKR"},"dna_sequence":{"accession":"NG_060551.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGCTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGCCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006655","ARO_id":"45117","ARO_name":"PDC-281","CARD_short_name":"PDC-281","ARO_description":"PDC-281 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5416":{"model_id":"5416","model_name":"PDC-282","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7791":{"protein_sequence":{"accession":"WP_111672895.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALTQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRRYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTYLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_060552.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGACCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCGCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCTACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006656","ARO_id":"45118","ARO_name":"PDC-282","CARD_short_name":"PDC-282","ARO_description":"PDC-282 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5417":{"model_id":"5417","model_name":"PDC-283","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7792":{"protein_sequence":{"accession":"WP_111672896.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALTQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRRYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQAIDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_060553.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGACCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCGCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGATCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006657","ARO_id":"45119","ARO_name":"PDC-283","CARD_short_name":"PDC-283","ARO_description":"PDC-283 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5418":{"model_id":"5418","model_name":"PDC-286","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7793":{"protein_sequence":{"accession":"WP_016252988.1","sequence":"MRDTRFPCLCGIAASTLLFATPPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_060538.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCCCCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCTGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACTCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006658","ARO_id":"45120","ARO_name":"PDC-286","CARD_short_name":"PDC-286","ARO_description":"PDC-286 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5419":{"model_id":"5419","model_name":"PDC-287","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7794":{"protein_sequence":{"accession":"WP_111672898.1","sequence":"MRDTRFPSLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALTQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_060556.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCAGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGACCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTATGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006659","ARO_id":"45121","ARO_name":"PDC-287","CARD_short_name":"PDC-287","ARO_description":"PDC-287 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5420":{"model_id":"5420","model_name":"PDC-288","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7795":{"protein_sequence":{"accession":"WP_111672899.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADETPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_060557.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGACGAGACCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAACTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATTCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006660","ARO_id":"45122","ARO_name":"PDC-288","CARD_short_name":"PDC-288","ARO_description":"PDC-288 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5421":{"model_id":"5421","model_name":"PDC-289","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7796":{"protein_sequence":{"accession":"WP_111672900.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFTATLAGYALAQDKMHLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_060558.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCACCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006661","ARO_id":"45123","ARO_name":"PDC-289","CARD_short_name":"PDC-289","ARO_description":"PDC-289 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5422":{"model_id":"5422","model_name":"PDC-290","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7797":{"protein_sequence":{"accession":"WP_111672901.1","sequence":"MRDTRFPCLCGIAASTLLFAATPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEDYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_060559.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCGCCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAACTCTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGACTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006662","ARO_id":"45124","ARO_name":"PDC-290","CARD_short_name":"PDC-290","ARO_description":"PDC-290 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5423":{"model_id":"5423","model_name":"PDC-291","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7798":{"protein_sequence":{"accession":"WP_111672903.1","sequence":"MRDTRFPCLCGIAASTLLFAATPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_060561.1","fmin":"0","fmax":"1173","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCGCCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCATTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTATGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006663","ARO_id":"45125","ARO_name":"PDC-291","CARD_short_name":"PDC-291","ARO_description":"PDC-291 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5424":{"model_id":"5424","model_name":"PDC-294","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7799":{"protein_sequence":{"accession":"WP_111672884.1","sequence":"MRNTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNLSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRAGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_060539.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCAATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGTCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCTGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGCCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006664","ARO_id":"45126","ARO_name":"PDC-294","CARD_short_name":"PDC-294","ARO_description":"PDC-294 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5425":{"model_id":"5425","model_name":"PDC-295","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7800":{"protein_sequence":{"accession":"WP_111672885.1","sequence":"MRDTRFPCLCGIAASTLLFAATPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQCAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALKGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_060540.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCGCCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCATTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTGCGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCTAGGCTGCCCGCGCCACAGGCGCTGAAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTATGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006665","ARO_id":"45127","ARO_name":"PDC-295","CARD_short_name":"PDC-295","ARO_description":"PDC-295 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5426":{"model_id":"5426","model_name":"PDC-296","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7801":{"protein_sequence":{"accession":"WP_111672886.1","sequence":"MRDTRFPCLCGIAASTLLFAATPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTYLDVPEAALAQCAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_060541.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCGCCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCATTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCTACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTGCGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCTAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTATGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006666","ARO_id":"45128","ARO_name":"PDC-296","CARD_short_name":"PDC-296","ARO_description":"PDC-296 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5427":{"model_id":"5427","model_name":"PDC-297","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7802":{"protein_sequence":{"accession":"WP_111672887.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPPRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_060542.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGTCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCCACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006667","ARO_id":"45129","ARO_name":"PDC-297","CARD_short_name":"PDC-297","ARO_description":"PDC-297 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5428":{"model_id":"5428","model_name":"PDC-298","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7803":{"protein_sequence":{"accession":"WP_061193431.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSISLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRAGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_060543.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGTCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCAGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGCCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006668","ARO_id":"45130","ARO_name":"PDC-298","CARD_short_name":"PDC-298","ARO_description":"PDC-298 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5429":{"model_id":"5429","model_name":"PDC-299","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7804":{"protein_sequence":{"accession":"WP_111672888.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFKRLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRAGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_060544.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGTCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCAAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGCCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006669","ARO_id":"45131","ARO_name":"PDC-299","CARD_short_name":"PDC-299","ARO_description":"PDC-299 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5430":{"model_id":"5430","model_name":"PDC-30","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7805":{"protein_sequence":{"accession":"WP_003110141.1","sequence":"MRDTRFPCLCGIAASTLLFAATPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQPKVPLKR"},"dna_sequence":{"accession":"NG_049902.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCGCCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGCCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006670","ARO_id":"45132","ARO_name":"PDC-30","CARD_short_name":"PDC-30","ARO_description":"PDC-30 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5431":{"model_id":"5431","model_name":"PDC-300","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7806":{"protein_sequence":{"accession":"WP_111672889.1","sequence":"MRDTRFPCLCGIAASTLLFAATPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAKGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAHAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_060545.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCGCCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCATTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCAAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCCATGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006671","ARO_id":"45133","ARO_name":"PDC-300","CARD_short_name":"PDC-300","ARO_description":"PDC-300 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5432":{"model_id":"5432","model_name":"PDC-301","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7807":{"protein_sequence":{"accession":"WP_111672908.1","sequence":"MRDTRFPCLCGIAASTLLFATTPGIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALTQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_060566.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGGCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGACCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006672","ARO_id":"45134","ARO_name":"PDC-301","CARD_short_name":"PDC-301","ARO_description":"PDC-301 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5433":{"model_id":"5433","model_name":"PDC-302","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7808":{"protein_sequence":{"accession":"WP_111672909.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_060567.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGTCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCTGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACTCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006673","ARO_id":"45135","ARO_name":"PDC-302","CARD_short_name":"PDC-302","ARO_description":"PDC-302 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5434":{"model_id":"5434","model_name":"PDC-303","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7809":{"protein_sequence":{"accession":"WP_111672910.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYHWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_060568.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGATGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACTCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACCACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006674","ARO_id":"45136","ARO_name":"PDC-303","CARD_short_name":"PDC-303","ARO_description":"PDC-303 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5435":{"model_id":"5435","model_name":"PDC-304","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7810":{"protein_sequence":{"accession":"WP_116786834.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYTQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_061620.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCTTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACACCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATTCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006675","ARO_id":"45137","ARO_name":"PDC-304","CARD_short_name":"PDC-304","ARO_description":"PDC-304 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5436":{"model_id":"5436","model_name":"PDC-305","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7811":{"protein_sequence":{"accession":"WP_116786837.1","sequence":"MRDTRFPCLCGIAASTLLFAATPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPSPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_061624.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCGCCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCATTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCAGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCTAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTATGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006676","ARO_id":"45138","ARO_name":"PDC-305","CARD_short_name":"PDC-305","ARO_description":"PDC-305 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5437":{"model_id":"5437","model_name":"PDC-307","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7812":{"protein_sequence":{"accession":"WP_122630845.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRRYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTKGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_062258.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGTCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCGCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAAGGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006677","ARO_id":"45139","ARO_name":"PDC-307","CARD_short_name":"PDC-307","ARO_description":"PDC-307 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5438":{"model_id":"5438","model_name":"PDC-308","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7813":{"protein_sequence":{"accession":"WP_122630846.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPSPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_062259.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCAGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006678","ARO_id":"45140","ARO_name":"PDC-308","CARD_short_name":"PDC-308","ARO_description":"PDC-308 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5439":{"model_id":"5439","model_name":"PDC-309","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7814":{"protein_sequence":{"accession":"WP_122630847.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAKGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_062260.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCACGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCAAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006679","ARO_id":"45141","ARO_name":"PDC-309","CARD_short_name":"PDC-309","ARO_description":"PDC-309 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5440":{"model_id":"5440","model_name":"PDC-31","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7815":{"protein_sequence":{"accession":"WP_016562272.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_049903.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTAGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAACTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCCCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCATGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37066","NCBI_taxonomy_name":"Pseudomonas","NCBI_taxonomy_id":"286"}}}},"ARO_accession":"3006680","ARO_id":"45142","ARO_name":"PDC-31","CARD_short_name":"PDC-31","ARO_description":"PDC-31 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5441":{"model_id":"5441","model_name":"PDC-310","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7816":{"protein_sequence":{"accession":"WP_122630848.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLRALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQLPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_062261.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAGGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGCTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCATGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006681","ARO_id":"45143","ARO_name":"PDC-310","CARD_short_name":"PDC-310","ARO_description":"PDC-310 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5442":{"model_id":"5442","model_name":"PDC-311","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7817":{"protein_sequence":{"accession":"WP_122630849.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRAGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_062262.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGTCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGCCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006682","ARO_id":"45144","ARO_name":"PDC-311","CARD_short_name":"PDC-311","ARO_description":"PDC-311 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5443":{"model_id":"5443","model_name":"PDC-312","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7818":{"protein_sequence":{"accession":"WP_122630850.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLRALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_062263.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAGGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCATGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006683","ARO_id":"45145","ARO_name":"PDC-312","CARD_short_name":"PDC-312","ARO_description":"PDC-312 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5444":{"model_id":"5444","model_name":"PDC-314","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7819":{"protein_sequence":{"accession":"WP_122630852.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLNRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTSGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_062265.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGTCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGAACAGGCCATGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAGCGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006684","ARO_id":"45146","ARO_name":"PDC-314","CARD_short_name":"PDC-314","ARO_description":"PDC-314 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5445":{"model_id":"5445","model_name":"PDC-315","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7820":{"protein_sequence":{"accession":"WP_122630882.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLNAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_062302.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGGGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGTAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGATGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGAATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACTCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006685","ARO_id":"45147","ARO_name":"PDC-315","CARD_short_name":"PDC-315","ARO_description":"PDC-315 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5446":{"model_id":"5446","model_name":"PDC-316","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7821":{"protein_sequence":{"accession":"WP_122630883.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTVTLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQLPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQSKVPLKR"},"dna_sequence":{"accession":"NG_062303.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGTCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGCTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAACTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAAGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGAGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006686","ARO_id":"45148","ARO_name":"PDC-316","CARD_short_name":"PDC-316","ARO_description":"PDC-316 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5447":{"model_id":"5447","model_name":"PDC-317","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7822":{"protein_sequence":{"accession":"WP_128268280.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGTRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_063888.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCACCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCACGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006687","ARO_id":"45149","ARO_name":"PDC-317","CARD_short_name":"PDC-317","ARO_description":"PDC-317 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5448":{"model_id":"5448","model_name":"PDC-318","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7823":{"protein_sequence":{"accession":"WP_150823478.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_066525.1","fmin":"0","fmax":"1197","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGTCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCAATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACTCCGATGGCGCTGCAGCCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006688","ARO_id":"45150","ARO_name":"PDC-318","CARD_short_name":"PDC-318","ARO_description":"PDC-318 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5449":{"model_id":"5449","model_name":"PDC-319","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7824":{"protein_sequence":{"accession":"WP_134254706.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQLPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDGRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_066526.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGCTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGGCCGCCCCCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006689","ARO_id":"45151","ARO_name":"PDC-319","CARD_short_name":"PDC-319","ARO_description":"PDC-319 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5450":{"model_id":"5450","model_name":"PDC-32","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7825":{"protein_sequence":{"accession":"WP_063864579.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKEPLKR"},"dna_sequence":{"accession":"NG_049904.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCATTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTGGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGAGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006690","ARO_id":"45152","ARO_name":"PDC-32","CARD_short_name":"PDC-32","ARO_description":"PDC-32 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5451":{"model_id":"5451","model_name":"PDC-320","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7826":{"protein_sequence":{"accession":"WP_150823479.1","sequence":"MRDTRFPCLCGIAASTLLFAATPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_066527.1","fmin":"0","fmax":"1197","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCGCCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006691","ARO_id":"45153","ARO_name":"PDC-320","CARD_short_name":"PDC-320","ARO_description":"PDC-320 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5452":{"model_id":"5452","model_name":"PDC-321","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7827":{"protein_sequence":{"accession":"WP_150823480.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALTQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPRPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_066528.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGACCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTTCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCCGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006692","ARO_id":"45154","ARO_name":"PDC-321","CARD_short_name":"PDC-321","ARO_description":"PDC-321 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5453":{"model_id":"5453","model_name":"PDC-322","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7828":{"protein_sequence":{"accession":"WP_138403314.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIDLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_066529.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGATCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGACCTGTTCGGCTATCTCGCCGCACGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006693","ARO_id":"45155","ARO_name":"PDC-322","CARD_short_name":"PDC-322","ARO_description":"PDC-322 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5454":{"model_id":"5454","model_name":"PDC-325","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7829":{"protein_sequence":{"accession":"WP_150823483.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTVTLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAKGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_066532.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGTCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAACTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCAAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006694","ARO_id":"45156","ARO_name":"PDC-325","CARD_short_name":"PDC-325","ARO_description":"PDC-325 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5455":{"model_id":"5455","model_name":"PDC-326","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7830":{"protein_sequence":{"accession":"WP_150823484.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_066533.1","fmin":"0","fmax":"1173","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGTCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCAATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAGCCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006695","ARO_id":"45157","ARO_name":"PDC-326","CARD_short_name":"PDC-326","ARO_description":"PDC-326 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5456":{"model_id":"5456","model_name":"PDC-327","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7831":{"protein_sequence":{"accession":"WP_150823485.1","sequence":"MRDTGFPCLCGIAASTLLFAATSAIAGEAPADRLKTLVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASLHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYTPGSQRLYSNPSIGLFGYLAARSLGQPFERIMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAKSYGVKTSAADLLRFVDANLHPERLDKPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_066534.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCGGATTCCCCTGCCTGTGCGGCATCGCCGCCTCCACACTGCTGTTCGCCGCCACCTCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGACACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGATATTCCGGGCCTGGCCGTGGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCTTCGAAAGAGGACGGTCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCTGCACTGGCCGGCGCTGCAAGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAAGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACACGCCGGGCAGCCAGCGCCTCTACTCCAACCCGAGCATCGGTCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGATCATGGAGCAGCAACTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCAAAAGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAAGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCGGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGACTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATCCCAGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAATTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006696","ARO_id":"45158","ARO_name":"PDC-327","CARD_short_name":"PDC-327","ARO_description":"PDC-327 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5457":{"model_id":"5457","model_name":"PDC-328","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7832":{"protein_sequence":{"accession":"WP_150823486.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLNVPEAALAQYAQGYGKDDRPLRAGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_066535.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCACGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCAACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGCCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006697","ARO_id":"45159","ARO_name":"PDC-328","CARD_short_name":"PDC-328","ARO_description":"PDC-328 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5458":{"model_id":"5458","model_name":"PDC-329","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7833":{"protein_sequence":{"accession":"WP_150823487.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALTQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTYLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAGGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_066536.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGACCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCTACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGGAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCACTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006698","ARO_id":"45160","ARO_name":"PDC-329","CARD_short_name":"PDC-329","ARO_description":"PDC-329 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5459":{"model_id":"5459","model_name":"PDC-33","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7834":{"protein_sequence":{"accession":"WP_012074328.1","sequence":"MRHATILNLCGLAASTLFFATTSAFATEAPAERLKALVDAAVQPVMKANDIPGLAVAITLKGEPHYFSYGVASKEDARKVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASRHWPALQGSRFDGISLLDLGTYSAGGLPLQFPDAVQKDPAQIRDYYRQWQPTYAPGSHRQYSNPSIGLFGYLAARSLGQPFERSMERQLFPALGLEHTFIRVPAAQQGLYAQGYGKDDRPLRVGPGPLDAEAYGLKSSAADLLRFVEANLHPERLEKPWAQALDATHRGYYKVGDMTQGLGWEAYDWPIDLKRLQAGNSAPMALQAHKVARLPAPQALDGQRLLNKTGSTNGFGAYLAFIPGRDVGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLVR"},"dna_sequence":{"accession":"NG_049905.1","fmin":"100","fmax":"1294","strand":"+","sequence":"ATGCGCCATGCGACAATCCTCAACCTGTGCGGCCTCGCCGCTTCCACCCTGTTCTTCGCGACAACATCGGCCTTCGCCACGGAGGCGCCGGCGGAGCGCCTGAAGGCTCTGGTGGACGCCGCCGTGCAACCGGTCATGAAGGCCAATGATATCCCGGGACTGGCCGTCGCCATCACTCTCAAGGGCGAACCGCATTACTTCAGTTATGGGGTGGCCTCGAAGGAGGACGCCCGCAAGGTGACCCCCGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTACGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCGGCACTGGCCCGCCCTGCAGGGCAGCCGCTTCGACGGTATCAGCCTGCTCGACCTCGGCACCTACAGCGCTGGCGGCCTGCCGCTACAGTTCCCCGATGCGGTGCAGAAGGATCCGGCGCAGATCCGCGACTACTACCGCCAGTGGCAACCGACCTACGCCCCGGGCAGCCACCGCCAGTACTCCAACCCGAGCATCGGTCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCATTCGAGCGCAGCATGGAACGGCAGCTGTTCCCGGCGCTCGGCCTGGAGCACACCTTTATCCGGGTGCCCGCCGCGCAGCAGGGGCTGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTGCGGGTCGGACCCGGTCCGCTGGACGCCGAGGCCTACGGGCTGAAGTCCAGCGCTGCGGACCTGCTGCGCTTCGTCGAGGCCAACCTGCACCCCGAGCGCCTGGAGAAGCCCTGGGCGCAGGCCCTCGACGCCACCCATCGCGGCTACTACAAGGTGGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCGACCTGAAGCGCCTGCAGGCGGGCAACTCGGCGCCGATGGCGCTGCAGGCGCACAAGGTCGCCAGGTTGCCGGCGCCGCAAGCCCTGGACGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGTTTCGGCGCCTACCTGGCGTTCATCCCGGGACGCGACGTCGGCCTGGTGATCCTGGCCAATCGCAACTACCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAACAGCAGGCCAAGGTACCGCTGGTGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006699","ARO_id":"45161","ARO_name":"PDC-33","CARD_short_name":"PDC-33","ARO_description":"PDC-33 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5460":{"model_id":"5460","model_name":"PDC-330","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7835":{"protein_sequence":{"accession":"WP_150823488.1","sequence":"MRDTRFPCLCGIAASTLLFAATPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLKFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_066537.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCGCCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCATTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGAAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCTAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTATGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006700","ARO_id":"45162","ARO_name":"PDC-330","CARD_short_name":"PDC-330","ARO_description":"PDC-330 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5461":{"model_id":"5461","model_name":"PDC-331","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7836":{"protein_sequence":{"accession":"WP_150823489.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGNGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_066538.1","fmin":"0","fmax":"1167","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGTCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAACGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCATGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006701","ARO_id":"45163","ARO_name":"PDC-331","CARD_short_name":"PDC-331","ARO_description":"PDC-331 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5462":{"model_id":"5462","model_name":"PDC-332","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7837":{"protein_sequence":{"accession":"WP_150823490.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_066539.1","fmin":"0","fmax":"1167","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006702","ARO_id":"45164","ARO_name":"PDC-332","CARD_short_name":"PDC-332","ARO_description":"PDC-332 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5463":{"model_id":"5463","model_name":"PDC-333","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7838":{"protein_sequence":{"accession":"WP_140423325.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLTVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDRAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAHAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_065445.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGACCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCGGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCCACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006703","ARO_id":"45165","ARO_name":"PDC-333","CARD_short_name":"PDC-333","ARO_description":"PDC-333 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5464":{"model_id":"5464","model_name":"PDC-334","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7839":{"protein_sequence":{"accession":"WP_148044426.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFIATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_065886.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCATCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006704","ARO_id":"45166","ARO_name":"PDC-334","CARD_short_name":"PDC-334","ARO_description":"PDC-334 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5465":{"model_id":"5465","model_name":"PDC-335","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7840":{"protein_sequence":{"accession":"WP_148044427.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALTQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQLPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_065887.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGACCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGCTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGTTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006705","ARO_id":"45167","ARO_name":"PDC-335","CARD_short_name":"PDC-335","ARO_description":"PDC-335 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5466":{"model_id":"5466","model_name":"PDC-336","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7841":{"protein_sequence":{"accession":"WP_148044428.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAKGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_065888.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCATCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCAAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006706","ARO_id":"45168","ARO_name":"PDC-336","CARD_short_name":"PDC-336","ARO_description":"PDC-336 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5467":{"model_id":"5467","model_name":"PDC-338","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7842":{"protein_sequence":{"accession":"WP_148044430.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRRYSNPSIGLFGYLAARSLGQPFERVMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_065890.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGTCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCGCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGGTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006707","ARO_id":"45169","ARO_name":"PDC-338","CARD_short_name":"PDC-338","ARO_description":"PDC-338 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5468":{"model_id":"5468","model_name":"PDC-339","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7843":{"protein_sequence":{"accession":"WP_148044431.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAAAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_065891.1","fmin":"0","fmax":"1182","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCTTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATTCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006708","ARO_id":"45170","ARO_name":"PDC-339","CARD_short_name":"PDC-339","ARO_description":"PDC-339 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5469":{"model_id":"5469","model_name":"PDC-34","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7844":{"protein_sequence":{"accession":"WP_003137570.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLTVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDRAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_049906.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGACCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCGGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37066","NCBI_taxonomy_name":"Pseudomonas","NCBI_taxonomy_id":"286"}}}},"ARO_accession":"3006709","ARO_id":"45171","ARO_name":"PDC-34","CARD_short_name":"PDC-34","ARO_description":"PDC-34 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5470":{"model_id":"5470","model_name":"PDC-340","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7845":{"protein_sequence":{"accession":"WP_148044432.1","sequence":"MRDTRFSCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAKGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_065892.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCTCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTAGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCAAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCACTGCAACCGCACAGGATCGCTAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006710","ARO_id":"45172","ARO_name":"PDC-340","CARD_short_name":"PDC-340","ARO_description":"PDC-340 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5471":{"model_id":"5471","model_name":"PDC-341","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7846":{"protein_sequence":{"accession":"WP_148044433.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_065893.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAACTGTTCCCAGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006711","ARO_id":"45173","ARO_name":"PDC-341","CARD_short_name":"PDC-341","ARO_description":"PDC-341 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5472":{"model_id":"5472","model_name":"PDC-342","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7847":{"protein_sequence":{"accession":"WP_148044434.1","sequence":"MRHATILNLCGLAASTLFFATTSAFATEAPAERLKALVDAAVQPVMKANDIPGLAVAITLKGEPHYFSYGVASKEDARKVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASRHWPALQGSRFDGISLLDLGTYTAGGLPLQFPDAVQKDPAQIRDYYRQWQPTYAPGSHRQYSNPSIDLFGYLAARSLGQPFERSMERQLFPALGLEHTFIRVPAAQQGLYAQGYGKDDHPLRVGPGPLDAEAYGLKSSAADLLRFVEANLHPERLEKPWAQALDATHRGYYKVGDMTQGLGWEAYDWPIDLKRLQAGNSAPMALQAHKVARLPAPQALDGQRLLNKTGSTNGFGAYLAFIPGRDVGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLVR"},"dna_sequence":{"accession":"NG_065894.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCCATGCGACAATCCTCAACCTGTGTGGCCTCGCCGCTTCCACCCTGTTCTTCGCGACAACATCGGCCTTCGCCACGGAGGCGCCGGCGGAGCGCCTGAAGGCTCTGGTGGACGCCGCCGTGCAACCGGTCATGAAGGCCAATGATATCCCGGGACTGGCCGTCGCCATCACTCTCAAGGGCGAACCGCATTACTTCAGTTATGGGGTGGCCTCGAAGGAGGACGCCCGCAAGGTGACCCCCGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTACGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCGGCACTGGCCCGCCCTGCAGGGCAGCCGCTTCGACGGTATCAGCCTGCTCGACCTCGGCACCTACACCGCTGGCGGCCTGCCGCTACAGTTCCCCGATGCGGTGCAGAAGGATCCGGCGCAGATCCGCGACTATTACCGCCAGTGGCAACCGACCTACGCCCCGGGCAGCCACCGCCAGTACTCCAACCCGAGCATCGATCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCATTCGAGCGCAGCATGGAACGGCAGCTGTTCCCGGCGCTCGGCCTGGAGCACACCTTTATCCGGGTGCCCGCCGCGCAGCAGGGGCTGTACGCCCAGGGCTACGGCAAGGACGACCACCCGCTGCGGGTCGGACCCGGTCCGCTGGACGCCGAGGCCTACGGGCTGAAGTCCAGCGCTGCGGACCTGCTGCGCTTCGTCGAGGCCAACCTGCACCCCGAGCGCCTGGAGAAGCCCTGGGCGCAGGCCCTCGACGCCACCCATCGCGGCTACTACAAGGTGGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGATTGGCCGATCGACCTGAAGCGCCTGCAGGCGGGCAACTCGGCGCCGATGGCGCTGCAGGCGCACAAGGTCGCCAGGTTGCCGGCGCCGCAAGCCCTGGACGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGTTTCGGCGCCTACCTGGCGTTCATCCCGGGACGCGACGTCGGCCTGGTGATCCTGGCCAATCGCAACTACCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAACAGCAGGCCAAGGTACCGCTGGTGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006712","ARO_id":"45174","ARO_name":"PDC-342","CARD_short_name":"PDC-342","ARO_description":"PDC-342 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5473":{"model_id":"5473","model_name":"PDC-343","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7848":{"protein_sequence":{"accession":"WP_148044435.1","sequence":"MRHATILNLCGLAASTLFFATTSAFATEAPAERLKALVDAAVQPVMKANDIPGLAVAITLKGEPHYFSYGVASKEDARKVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASRHWPALQGSRFDGISLLDLGTYTAGGLPLQFPDAVQKDPAQIRDYYRQWQPTYAPGSHRQYSNPSIGLFGYLAARSLGQPFERSMERQLFPALGLEHTFIRVPAAQQGLYAQGYGKDDRPLRVGPGPLDAEAYGLKSSAADLLRFVEANLHPERLEKPWAQALDATHRGYYKVGDMTQGLGWEAYDWPIDLKRLQAGNSAPMALQAHKVARLPAPQALDGQRLLNKTGSTNGFGAYLAFIPGRDVGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLVR"},"dna_sequence":{"accession":"NG_065895.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCCATGCGACAATCCTCAACCTGTGCGGCCTCGCCGCTTCCACCCTGTTCTTCGCGACAACATCGGCCTTCGCCACGGAGGCGCCGGCGGAGCGCCTGAAGGCTCTGGTGGACGCCGCCGTGCAACCGGTCATGAAGGCCAATGATATCCCGGGACTGGCCGTCGCCATCACTCTCAAGGGCGAACCGCATTACTTCAGTTATGGGGTGGCCTCGAAGGAGGACGCCCGCAAGGTGACCCCCGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTACGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGTGCCAGCCGGCACTGGCCCGCCCTGCAGGGCAGCCGCTTCGACGGTATCAGCCTGCTCGACCTCGGCACCTACACCGCTGGCGGCCTGCCGCTACAGTTCCCCGATGCGGTGCAGAAGGATCCGGCGCAGATCCGCGACTATTACCGCCAGTGGCAACCGACCTACGCCCCGGGCAGCCACCGCCAGTACTCCAACCCGAGCATCGGTCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCATTCGAGCGCAGCATGGAACGGCAGCTGTTCCCGGCGCTCGGCCTGGAGCACACCTTTATCCGGGTGCCCGCCGCGCAGCAGGGGCTGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTGCGGGTCGGACCCGGTCCGCTGGACGCCGAGGCCTACGGGCTGAAGTCCAGCGCTGCGGACCTGCTGCGCTTCGTCGAGGCCAACCTGCACCCCGAGCGCCTGGAGAAGCCCTGGGCGCAGGCCCTCGACGCCACCCATCGCGGCTACTACAAGGTGGGCGACATGACCCAGGGCCTGGGTTGGGAAGCCTACGATTGGCCGATCGACCTGAAGCGCCTGCAGGCGGGCAACTCGGCGCCGATGGCGCTACAGGCGCACAAGGTCGCCAGGTTGCCGGCGCCGCAAGCCCTGGACGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGTTTCGGCGCCTACCTGGCGTTCATCCCGGGACGCGACGTCGGCCTGGTGATCCTGGCCAATCGCAACTACCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAACAGCAGGCCAAGGTACCGCTGGTGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006713","ARO_id":"45175","ARO_name":"PDC-343","CARD_short_name":"PDC-343","ARO_description":"PDC-343 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5474":{"model_id":"5474","model_name":"PDC-344","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7849":{"protein_sequence":{"accession":"WP_148044436.1","sequence":"MRHATILNLCGLAASTLFFATTSAFATEAPAERLKALVDAAVQPVMKANDIPGLAVAITLKGEPHYFSYGVASKEDARKVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASRHWPALQGSRFDGISLLDLGTYTAGGLPLQFPDAVQKDPAQIRDYYRQWQPTYAPGSHRQYSNPSIGLFGYLAARSLGQPFERSMERQLFPALGLEHTFIRVPAAQQGLYAQGYGKDDRPLRVGPGPLDAEAYGLKSSAVDLLRFVEANLHPERLEKPWAQALDATHRGYYKVGDMTQGLGWEAYDWPIDLKRLQAGNSAPMALQAHKVARLPAPQALDGQRLLNKTGSTNGFGAYLAFIPGRDVGLVILANRNYPNAERVKIAYAILSGLEQQAKIPLVR"},"dna_sequence":{"accession":"NG_065896.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCCATGCGACAATCCTCAACCTGTGCGGCCTCGCCGCTTCCACCCTGTTCTTCGCGACAACATCGGCCTTCGCCACGGAGGCGCCGGCGGAGCGCCTGAAGGCTCTGGTGGACGCCGCCGTGCAACCGGTCATGAAGGCCAATGATATCCCGGGACTGGCCGTCGCCATCACTCTCAAGGGCGAACCGCATTACTTCAGTTATGGGGTGGCCTCGAAGGAGGACGCCCGCAAGGTGACCCCCGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTACGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGTGCCAGCCGGCACTGGCCCGCCCTGCAGGGCAGCCGCTTCGACGGTATCAGCCTGCTCGACCTCGGCACCTACACCGCTGGCGGCCTGCCGCTACAGTTCCCCGATGCGGTGCAGAAGGATCCGGCGCAGATCCGCGACTATTACCGCCAGTGGCAACCGACCTACGCCCCGGGCAGCCACCGCCAGTACTCCAACCCGAGCATCGGTCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCATTCGAGCGCAGCATGGAACGGCAGCTGTTCCCGGCGCTCGGCCTGGAGCACACCTTTATCCGGGTGCCCGCCGCGCAGCAGGGGCTGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTGCGGGTCGGACCCGGTCCGCTGGACGCCGAGGCCTACGGGCTGAAGTCCAGCGCTGTGGACCTGCTGCGCTTCGTCGAGGCCAACCTGCACCCCGAGCGCCTGGAGAAGCCCTGGGCGCAGGCCCTCGACGCCACCCATCGCGGCTACTACAAGGTGGGCGACATGACCCAGGGCCTGGGTTGGGAAGCCTACGATTGGCCGATCGACCTGAAGCGCCTGCAGGCGGGCAACTCGGCGCCGATGGCGCTACAGGCGCACAAGGTCGCCAGGTTGCCGGCGCCGCAAGCCCTGGACGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGTTTCGGCGCCTACCTGGCGTTCATCCCGGGACGCGACGTCGGCCTGGTGATCCTGGCCAATCGCAACTACCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAACAGCAGGCCAAGATACCGCTGGTGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006714","ARO_id":"45176","ARO_name":"PDC-344","CARD_short_name":"PDC-344","ARO_description":"PDC-344 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5475":{"model_id":"5475","model_name":"PDC-345","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7850":{"protein_sequence":{"accession":"WP_148044437.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQLPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSFGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLQVGPGPLDAKGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTSGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_065897.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGCTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCTTCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACAGGTCGGTCCCGGCCCGCTGGATGCCAAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAGCGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006715","ARO_id":"45177","ARO_name":"PDC-345","CARD_short_name":"PDC-345","ARO_description":"PDC-345 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5476":{"model_id":"5476","model_name":"PDC-347","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7851":{"protein_sequence":{"accession":"WP_148044439.1","sequence":"MRDTRFPCLCGIAASTLLFATTSAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALTQGKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQCAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMTLQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_065899.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCTCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGACCCAGGGCAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTAGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGTTGGCGCAGTGCGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGACACTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006716","ARO_id":"45178","ARO_name":"PDC-347","CARD_short_name":"PDC-347","ARO_description":"PDC-347 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5477":{"model_id":"5477","model_name":"PDC-348","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7852":{"protein_sequence":{"accession":"WP_148044440.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_065900.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGTTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006717","ARO_id":"45179","ARO_name":"PDC-348","CARD_short_name":"PDC-348","ARO_description":"PDC-348 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5478":{"model_id":"5478","model_name":"PDC-349","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7853":{"protein_sequence":{"accession":"WP_148044441.1","sequence":"MRDTRFPCLCGIAASTLLFAATPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAESYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_065901.1","fmin":"0","fmax":"1197","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCGCCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCATTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGTCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAAGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCTAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTATGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006718","ARO_id":"45180","ARO_name":"PDC-349","CARD_short_name":"PDC-349","ARO_description":"PDC-349 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5479":{"model_id":"5479","model_name":"PDC-35","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7854":{"protein_sequence":{"accession":"WP_003093423.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTVTLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_049907.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGTCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAACTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37066","NCBI_taxonomy_name":"Pseudomonas","NCBI_taxonomy_id":"286"}}}},"ARO_accession":"3006719","ARO_id":"45181","ARO_name":"PDC-35","CARD_short_name":"PDC-35","ARO_description":"PDC-35 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5480":{"model_id":"5480","model_name":"PDC-350","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7855":{"protein_sequence":{"accession":"WP_148044442.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTVTLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_065902.1","fmin":"0","fmax":"1173","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGTCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAACTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006720","ARO_id":"45182","ARO_name":"PDC-350","CARD_short_name":"PDC-350","ARO_description":"PDC-350 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5481":{"model_id":"5481","model_name":"PDC-351","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7856":{"protein_sequence":{"accession":"WP_148044443.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALTQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRAGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTSGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_065903.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGACCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGCCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAGCGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006721","ARO_id":"45183","ARO_name":"PDC-351","CARD_short_name":"PDC-351","ARO_description":"PDC-351 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5482":{"model_id":"5482","model_name":"PDC-353","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7857":{"protein_sequence":{"accession":"WP_128550481.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRAGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_065905.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAACTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGCCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006722","ARO_id":"45184","ARO_name":"PDC-353","CARD_short_name":"PDC-353","ARO_description":"PDC-353 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5483":{"model_id":"5483","model_name":"PDC-354","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7858":{"protein_sequence":{"accession":"WP_148044445.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAVVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPDPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_065906.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGTCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCTTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGACCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATTCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006723","ARO_id":"45185","ARO_name":"PDC-354","CARD_short_name":"PDC-354","ARO_description":"PDC-354 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5484":{"model_id":"5484","model_name":"PDC-355","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7859":{"protein_sequence":{"accession":"WP_148044446.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQARIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_065907.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCAGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACGGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006724","ARO_id":"45186","ARO_name":"PDC-355","CARD_short_name":"PDC-355","ARO_description":"PDC-355 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5485":{"model_id":"5485","model_name":"PDC-356","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7860":{"protein_sequence":{"accession":"WP_148044447.1","sequence":"MRDTGFPCLCGIAASTLLFAATSAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERIMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPIPLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_065908.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCGGATTCCCCTGCCTGTGCGGCATCGCCGCCTCCACACTGCTGTTCGCCGCCACCTCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGATATTCCGGGCCTGGCCGTGGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCTTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAAGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGATCATGGAGCAGCAACTGTTCCCGGCGCTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTATGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGTGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCCCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGTTTCGGCGCCTATGTGGCGTTCATCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTACCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006725","ARO_id":"45187","ARO_name":"PDC-356","CARD_short_name":"PDC-356","ARO_description":"PDC-356 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5486":{"model_id":"5486","model_name":"PDC-357","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7861":{"protein_sequence":{"accession":"WP_148044448.1","sequence":"MRDTRFSCLCGIAASTLLFATTPAIAGEVPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_065909.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCTCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGTCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006726","ARO_id":"45188","ARO_name":"PDC-357","CARD_short_name":"PDC-357","ARO_description":"PDC-357 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5487":{"model_id":"5487","model_name":"PDC-358","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7862":{"protein_sequence":{"accession":"WP_148044449.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLNVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_065910.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGTCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCAACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCAATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAGCCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006727","ARO_id":"45189","ARO_name":"PDC-358","CARD_short_name":"PDC-358","ARO_description":"PDC-358 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5488":{"model_id":"5488","model_name":"PDC-359","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7863":{"protein_sequence":{"accession":"WP_148044450.1","sequence":"MRDTRFPCLCGIAASTLLFAATPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERFMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_065911.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCGCCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTGGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGTTCATGGAGCAGCAACTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAAGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATTCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTACCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006728","ARO_id":"45190","ARO_name":"PDC-359","CARD_short_name":"PDC-359","ARO_description":"PDC-359 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5489":{"model_id":"5489","model_name":"PDC-36","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7864":{"protein_sequence":{"accession":"WP_023100808.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_049908.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCATTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTGGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGTTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCATCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACTCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATTCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37066","NCBI_taxonomy_name":"Pseudomonas","NCBI_taxonomy_id":"286"}}}},"ARO_accession":"3006729","ARO_id":"45191","ARO_name":"PDC-36","CARD_short_name":"PDC-36","ARO_description":"PDC-36 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5490":{"model_id":"5490","model_name":"PDC-360","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7865":{"protein_sequence":{"accession":"WP_148044451.1","sequence":"MRDTRFPCLCGIAASTLLLATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFTATLAGYALAQNKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_065912.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGCTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGAACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAACTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006730","ARO_id":"45192","ARO_name":"PDC-360","CARD_short_name":"PDC-360","ARO_description":"PDC-360 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5491":{"model_id":"5491","model_name":"PDC-361","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7866":{"protein_sequence":{"accession":"WP_031638595.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRIYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_065913.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGACGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGTGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCATCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAACTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGTTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCACTGAAGCGCCTACAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGATCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATTCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006731","ARO_id":"45193","ARO_name":"PDC-361","CARD_short_name":"PDC-361","ARO_description":"PDC-361 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5492":{"model_id":"5492","model_name":"PDC-362","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7867":{"protein_sequence":{"accession":"WP_148044452.1","sequence":"MRDTRFPCLCGIAASTLLFAATPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGGMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_065914.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCGCCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCATTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGGCATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCTAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTATGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006732","ARO_id":"45194","ARO_name":"PDC-362","CARD_short_name":"PDC-362","ARO_description":"PDC-362 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5493":{"model_id":"5493","model_name":"PDC-363","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7868":{"protein_sequence":{"accession":"WP_148044453.1","sequence":"MRDTKFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_065915.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAAATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006733","ARO_id":"45195","ARO_name":"PDC-363","CARD_short_name":"PDC-363","ARO_description":"PDC-363 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5494":{"model_id":"5494","model_name":"PDC-364","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7869":{"protein_sequence":{"accession":"WP_121347819.1","sequence":"MRDTGFPCLCGIAASTLLFAATSAIAGEAPADRLKTLVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKSFTATLAGYALAQDKMRLDDRASLHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYTPGSQRLYSNPSIGLFGYLAARSLGQPFERIMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDKPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_065916.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCGGATTCCCCTGCCTGTGCGGCATCGCCGCCTCCACACTGCTGTTCGCCGCCACCTCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGACACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGATATTCCGGGCCTGGCCGTGGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCTTCGAAAGAGGACGGTCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGTCCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGTGCCAGCCTGCACTGGCCGGCGCTGCAAGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAAGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACACGCCGGGCAGCCAGCGCCTCTACTCCAACCCGAGCATCGGTCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGATCATGGAGCAGCAACTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAAGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCGGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGACTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATCCCAGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAATTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006734","ARO_id":"45196","ARO_name":"PDC-364","CARD_short_name":"PDC-364","ARO_description":"PDC-364 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5495":{"model_id":"5495","model_name":"PDC-365","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7870":{"protein_sequence":{"accession":"WP_148044454.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRNYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_065917.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCATTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTGGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGTTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCAACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCATCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006735","ARO_id":"45197","ARO_name":"PDC-365","CARD_short_name":"PDC-365","ARO_description":"PDC-365 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5496":{"model_id":"5496","model_name":"PDC-366","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7871":{"protein_sequence":{"accession":"WP_148044455.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALTQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVRKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_065918.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGACCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCGGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGTTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006736","ARO_id":"45198","ARO_name":"PDC-366","CARD_short_name":"PDC-366","ARO_description":"PDC-366 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5497":{"model_id":"5497","model_name":"PDC-367","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7872":{"protein_sequence":{"accession":"WP_121286063.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLRRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_065919.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCCCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAAGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAGGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006737","ARO_id":"45199","ARO_name":"PDC-367","CARD_short_name":"PDC-367","ARO_description":"PDC-367 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5498":{"model_id":"5498","model_name":"PDC-368","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7873":{"protein_sequence":{"accession":"WP_148044456.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLRFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_065920.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCGGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCACGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006738","ARO_id":"45200","ARO_name":"PDC-368","CARD_short_name":"PDC-368","ARO_description":"PDC-368 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5499":{"model_id":"5499","model_name":"PDC-369","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7874":{"protein_sequence":{"accession":"WP_148044457.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPGAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_065921.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTAGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGGGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTAAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006739","ARO_id":"45201","ARO_name":"PDC-369","CARD_short_name":"PDC-369","ARO_description":"PDC-369 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5500":{"model_id":"5500","model_name":"PDC-37","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7875":{"protein_sequence":{"accession":"WP_023092413.1","sequence":"MRDTRFSCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_049909.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCTCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCCGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACTCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATTCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37066","NCBI_taxonomy_name":"Pseudomonas","NCBI_taxonomy_id":"286"}}}},"ARO_accession":"3006740","ARO_id":"45202","ARO_name":"PDC-37","CARD_short_name":"PDC-37","ARO_description":"PDC-37 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5501":{"model_id":"5501","model_name":"PDC-370","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7876":{"protein_sequence":{"accession":"WP_148044458.1","sequence":"MRDTRFSCLCGIAASTLLFAATPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_065922.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCTCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCGCCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAGCCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006741","ARO_id":"45203","ARO_name":"PDC-370","CARD_short_name":"PDC-370","ARO_description":"PDC-370 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5502":{"model_id":"5502","model_name":"PDC-371","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7877":{"protein_sequence":{"accession":"WP_126118969.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_065923.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCTTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCATCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006742","ARO_id":"45204","ARO_name":"PDC-371","CARD_short_name":"PDC-371","ARO_description":"PDC-371 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5503":{"model_id":"5503","model_name":"PDC-372","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7878":{"protein_sequence":{"accession":"WP_148044459.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALPPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_065924.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGTCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCAATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCCGCCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006743","ARO_id":"45205","ARO_name":"PDC-372","CARD_short_name":"PDC-372","ARO_description":"PDC-372 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5504":{"model_id":"5504","model_name":"PDC-373","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7879":{"protein_sequence":{"accession":"WP_148044460.1","sequence":"MRDTRFSCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFIATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAKGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_065925.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCTCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCATCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCAAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006744","ARO_id":"45206","ARO_name":"PDC-373","CARD_short_name":"PDC-373","ARO_description":"PDC-373 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5505":{"model_id":"5505","model_name":"PDC-374","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7880":{"protein_sequence":{"accession":"WP_003454242.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALTQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKRAREGDGA"},"dna_sequence":{"accession":"NG_065926.1","fmin":"100","fmax":"1315","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGACCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACTCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCGCTCGCGAGGGCGACGGAGCGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006745","ARO_id":"45207","ARO_name":"PDC-374","CARD_short_name":"PDC-374","ARO_description":"PDC-374 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5506":{"model_id":"5506","model_name":"PDC-375","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7881":{"protein_sequence":{"accession":"WP_148044461.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALTQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLKFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_065927.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGACCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGAAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGTTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006746","ARO_id":"45208","ARO_name":"PDC-375","CARD_short_name":"PDC-375","ARO_description":"PDC-375 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5507":{"model_id":"5507","model_name":"PDC-377","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7882":{"protein_sequence":{"accession":"WP_148044463.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQCLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_065929.1","fmin":"0","fmax":"1197","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTAGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGTGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006747","ARO_id":"45209","ARO_name":"PDC-377","CARD_short_name":"PDC-377","ARO_description":"PDC-377 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5508":{"model_id":"5508","model_name":"PDC-378","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7883":{"protein_sequence":{"accession":"WP_148044464.1","sequence":"MRDTRFPCLCGIAASTLLFAATPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPIAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_065930.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCGCCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCATTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCTAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCATTGCCGAGCGGGTGAAGATCGCCTATGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006748","ARO_id":"45210","ARO_name":"PDC-378","CARD_short_name":"PDC-378","ARO_description":"PDC-378 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5509":{"model_id":"5509","model_name":"PDC-379","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7884":{"protein_sequence":{"accession":"WP_148044465.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_065931.1","fmin":"0","fmax":"1176","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGATGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACTCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006749","ARO_id":"45211","ARO_name":"PDC-379","CARD_short_name":"PDC-379","ARO_description":"PDC-379 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5510":{"model_id":"5510","model_name":"PDC-38","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7885":{"protein_sequence":{"accession":"WP_022580963.1","sequence":"MRDTRFSCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDRAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_049910.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCTCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCGGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006750","ARO_id":"45212","ARO_name":"PDC-38","CARD_short_name":"PDC-38","ARO_description":"PDC-38 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5511":{"model_id":"5511","model_name":"PDC-381","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7886":{"protein_sequence":{"accession":"WP_148044467.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIDLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVVLANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_065933.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGACCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGATGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACTCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGGTCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006751","ARO_id":"45213","ARO_name":"PDC-381","CARD_short_name":"PDC-381","ARO_description":"PDC-381 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5512":{"model_id":"5512","model_name":"PDC-382","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7887":{"protein_sequence":{"accession":"WP_148044468.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFIATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_065934.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCATCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006752","ARO_id":"45214","ARO_name":"PDC-382","CARD_short_name":"PDC-382","ARO_description":"PDC-382 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5513":{"model_id":"5513","model_name":"PDC-383","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7888":{"protein_sequence":{"accession":"WP_148044469.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGNMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_065935.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCAACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006753","ARO_id":"45215","ARO_name":"PDC-383","CARD_short_name":"PDC-383","ARO_description":"PDC-383 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5514":{"model_id":"5514","model_name":"PDC-385","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7889":{"protein_sequence":{"accession":"WP_150823492.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSEQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_066541.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGTTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGAGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006754","ARO_id":"45216","ARO_name":"PDC-385","CARD_short_name":"PDC-385","ARO_description":"PDC-385 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5515":{"model_id":"5515","model_name":"PDC-386","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7890":{"protein_sequence":{"accession":"WP_150823493.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPLKRLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_066542.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTAGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGCTCAAACGGCTCATGGAGCAGCAACTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCCCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCATGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006755","ARO_id":"45217","ARO_name":"PDC-386","CARD_short_name":"PDC-386","ARO_description":"PDC-386 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5516":{"model_id":"5516","model_name":"PDC-387","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7891":{"protein_sequence":{"accession":"WP_152315506.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLTVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFIATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDRAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_066756.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGACCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCATCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCGGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006756","ARO_id":"45218","ARO_name":"PDC-387","CARD_short_name":"PDC-387","ARO_description":"PDC-387 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5517":{"model_id":"5517","model_name":"PDC-388","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7892":{"protein_sequence":{"accession":"WP_152315507.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIVLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_066757.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTGGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGTCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAACTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAAGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006757","ARO_id":"45219","ARO_name":"PDC-388","CARD_short_name":"PDC-388","ARO_description":"PDC-388 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5518":{"model_id":"5518","model_name":"PDC-389","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7893":{"protein_sequence":{"accession":"WP_164461293.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQSYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_068029.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCTTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGAGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATTCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006758","ARO_id":"45220","ARO_name":"PDC-389","CARD_short_name":"PDC-389","ARO_description":"PDC-389 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5519":{"model_id":"5519","model_name":"PDC-39","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7894":{"protein_sequence":{"accession":"WP_023091031.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_049911.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGTCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006759","ARO_id":"45221","ARO_name":"PDC-39","CARD_short_name":"PDC-39","ARO_description":"PDC-39 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5520":{"model_id":"5520","model_name":"PDC-390","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7895":{"protein_sequence":{"accession":"WP_164461294.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDNRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTSGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_068030.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGTCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACAACCGCCCCCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCATGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAGCGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006760","ARO_id":"45222","ARO_name":"PDC-390","CARD_short_name":"PDC-390","ARO_description":"PDC-390 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5521":{"model_id":"5521","model_name":"PDC-391","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7896":{"protein_sequence":{"accession":"WP_164461295.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLTVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFIATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDRAQILDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_068031.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGACCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCATCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCGGGCACAGATCCTCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006761","ARO_id":"45223","ARO_name":"PDC-391","CARD_short_name":"PDC-391","ARO_description":"PDC-391 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5522":{"model_id":"5522","model_name":"PDC-392","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7897":{"protein_sequence":{"accession":"WP_164461296.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_068032.1","fmin":"0","fmax":"1173","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGATCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006762","ARO_id":"45224","ARO_name":"PDC-392","CARD_short_name":"PDC-392","ARO_description":"PDC-392 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5523":{"model_id":"5523","model_name":"PDC-394","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7898":{"protein_sequence":{"accession":"WP_164461298.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALTQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_068034.1","fmin":"0","fmax":"1188","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGACCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTTCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006763","ARO_id":"45225","ARO_name":"PDC-394","CARD_short_name":"PDC-394","ARO_description":"PDC-394 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5524":{"model_id":"5524","model_name":"PDC-395","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7899":{"protein_sequence":{"accession":"WP_164461299.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLTVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDRAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPIAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_068035.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGACCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCGGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCATTGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006764","ARO_id":"45226","ARO_name":"PDC-395","CARD_short_name":"PDC-395","ARO_description":"PDC-395 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5525":{"model_id":"5525","model_name":"PDC-396","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7900":{"protein_sequence":{"accession":"WP_164461300.1","sequence":"MRDTGFPCLCGIAASTLLFAATSAIAGEAPADRLKTLVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASLHWPALQGSRFDGISLLDLATYTAGGLPLQLPDSVQKDQAQIRDYYRQWQPTYTPGSQRLYSNPSIGLFGYLAARSLGQPFERIMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDKPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_068036.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCGGATTCCCCTGCCTGTGCGGCATCGCCGCCTCCACACTGCTGTTCGCCGCCACCTCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGACACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGATATTCCGGGCCTGGCCGTGGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCTTCGAAAGAGGACGGTCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCTGCACTGGCCGGCGCTGCAAGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGCTCCCCGACTCGGTGCAGAAAGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACACGCCGGGCAGCCAGCGCCTCTACTCCAACCCGAGCATCGGTCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGATCATGGAGCAGCAACTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCTCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAAGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCGGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGACTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATCCCAGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAATTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAACGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006765","ARO_id":"45227","ARO_name":"PDC-396","CARD_short_name":"PDC-396","ARO_description":"PDC-396 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5526":{"model_id":"5526","model_name":"PDC-397","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7901":{"protein_sequence":{"accession":"WP_164461301.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPIAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_068037.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCTTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATTCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCATTGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006766","ARO_id":"45228","ARO_name":"PDC-397","CARD_short_name":"PDC-397","ARO_description":"PDC-397 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5527":{"model_id":"5527","model_name":"PDC-398","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7902":{"protein_sequence":{"accession":"WP_168247885.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTVTLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPQRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_068186.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGTCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAACTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACAAAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006767","ARO_id":"45229","ARO_name":"PDC-398","CARD_short_name":"PDC-398","ARO_description":"PDC-398 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5528":{"model_id":"5528","model_name":"PDC-399","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7903":{"protein_sequence":{"accession":"WP_168247886.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALTQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLKQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAGGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_068187.1","fmin":"0","fmax":"1197","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGACCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCAAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGGAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCACTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006768","ARO_id":"45230","ARO_name":"PDC-399","CARD_short_name":"PDC-399","ARO_description":"PDC-399 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5529":{"model_id":"5529","model_name":"PDC-40","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7904":{"protein_sequence":{"accession":"WP_063864581.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRHYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_049913.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGTCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCACTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006769","ARO_id":"45231","ARO_name":"PDC-40","CARD_short_name":"PDC-40","ARO_description":"PDC-40 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5530":{"model_id":"5530","model_name":"PDC-400","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7905":{"protein_sequence":{"accession":"WP_168247887.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVEAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRRYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_068188.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGAAGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGTCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCGCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006770","ARO_id":"45232","ARO_name":"PDC-400","CARD_short_name":"PDC-400","ARO_description":"PDC-400 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5531":{"model_id":"5531","model_name":"PDC-401","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7906":{"protein_sequence":{"accession":"WP_168247888.1","sequence":"MRDTRFPCLCGIAASTLLFAATPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPIALKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_068189.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCGCCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTGGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGTTATGGGCTGGCGTCGAAAGAGGACGGTCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAAGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTACACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCGCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTAGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006771","ARO_id":"45233","ARO_name":"PDC-401","CARD_short_name":"PDC-401","ARO_description":"PDC-401 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5532":{"model_id":"5532","model_name":"PDC-402","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7907":{"protein_sequence":{"accession":"WP_134265631.1","sequence":"MRDTRFPCPCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_068190.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCCGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006772","ARO_id":"45234","ARO_name":"PDC-402","CARD_short_name":"PDC-402","ARO_description":"PDC-402 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5533":{"model_id":"5533","model_name":"PDC-403","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7908":{"protein_sequence":{"accession":"WP_168247889.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPSPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_068191.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCTTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCAGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATTCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006773","ARO_id":"45235","ARO_name":"PDC-403","CARD_short_name":"PDC-403","ARO_description":"PDC-403 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5534":{"model_id":"5534","model_name":"PDC-404","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7909":{"protein_sequence":{"accession":"WP_168247890.1","sequence":"MRDTRFPCLCGIAASTLLFAATPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLGAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_068192.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCGCCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCATTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTGGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGGTGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006774","ARO_id":"45236","ARO_name":"PDC-404","CARD_short_name":"PDC-404","ARO_description":"PDC-404 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5535":{"model_id":"5535","model_name":"PDC-405","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7910":{"protein_sequence":{"accession":"WP_168247891.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGMAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALTQDKMRLDDCASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAGGYWVKTSAADLLRFVDANLHPERLDRPWAQAIDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALDGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_068193.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCATGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGACCCAGGACAAGATGCGCCTCGACGACTGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGGAGGCTACTGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGATCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCACTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGATGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006775","ARO_id":"45237","ARO_name":"PDC-405","CARD_short_name":"PDC-405","ARO_description":"PDC-405 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5536":{"model_id":"5536","model_name":"PDC-406","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7911":{"protein_sequence":{"accession":"WP_168247892.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLHLPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_068194.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGTCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCACCTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCATGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006776","ARO_id":"45238","ARO_name":"PDC-406","CARD_short_name":"PDC-406","ARO_description":"PDC-406 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5537":{"model_id":"5537","model_name":"PDC-407","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7912":{"protein_sequence":{"accession":"WP_124187209.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_068195.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006777","ARO_id":"45239","ARO_name":"PDC-407","CARD_short_name":"PDC-407","ARO_description":"PDC-407 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5538":{"model_id":"5538","model_name":"PDC-408","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7913":{"protein_sequence":{"accession":"WP_134450540.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTVTLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQLPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_068196.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGTCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAACTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAACTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006778","ARO_id":"45240","ARO_name":"PDC-408","CARD_short_name":"PDC-408","ARO_description":"PDC-408 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5539":{"model_id":"5539","model_name":"PDC-409","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7914":{"protein_sequence":{"accession":"WP_168247893.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRRYSNPSIDLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_068197.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGTCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCGCTATTCCAACCCGAGCATCGACCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006779","ARO_id":"45241","ARO_name":"PDC-409","CARD_short_name":"PDC-409","ARO_description":"PDC-409 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5540":{"model_id":"5540","model_name":"PDC-410","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7915":{"protein_sequence":{"accession":"WP_168247894.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFKRLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRAGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTSGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_068198.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTAGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCAAACGGCTCATGGAGCAGCAACTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCCCTACGGGCCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCATGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAGCGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006780","ARO_id":"45242","ARO_name":"PDC-410","CARD_short_name":"PDC-410","ARO_description":"PDC-410 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5541":{"model_id":"5541","model_name":"PDC-411","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7916":{"protein_sequence":{"accession":"WP_168247895.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNLSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAKGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_068199.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCTGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCAAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006781","ARO_id":"45243","ARO_name":"PDC-411","CARD_short_name":"PDC-411","ARO_description":"PDC-411 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5542":{"model_id":"5542","model_name":"PDC-412","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7917":{"protein_sequence":{"accession":"WP_168247896.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAAHSLGQPFKRLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRAGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_068200.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTAGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCACAGCCTGGGCCAGCCGTTCAAACGGCTCATGGAGCAGCAACTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCCCTACGGGCCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCATGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006782","ARO_id":"45244","ARO_name":"PDC-412","CARD_short_name":"PDC-412","ARO_description":"PDC-412 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5543":{"model_id":"5543","model_name":"PDC-414","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7918":{"protein_sequence":{"accession":"WP_168247898.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRRYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYSKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_068202.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGTCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCGCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACAGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006783","ARO_id":"45245","ARO_name":"PDC-414","CARD_short_name":"PDC-414","ARO_description":"PDC-414 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5544":{"model_id":"5544","model_name":"PDC-415","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7919":{"protein_sequence":{"accession":"WP_168247899.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALTQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMGQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_068203.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGACCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGGGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGTTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006784","ARO_id":"45246","ARO_name":"PDC-415","CARD_short_name":"PDC-415","ARO_description":"PDC-415 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5545":{"model_id":"5545","model_name":"PDC-416","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7920":{"protein_sequence":{"accession":"WP_168247900.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVVFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_068204.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGTGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006785","ARO_id":"45247","ARO_name":"PDC-416","CARD_short_name":"PDC-416","ARO_description":"PDC-416 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5546":{"model_id":"5546","model_name":"PDC-417","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7921":{"protein_sequence":{"accession":"WP_168247901.1","sequence":"MRDTRFPCLCGIAASTLLFAATPAIAGEAPADRLKALVDAAVQPAMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTYLDVPEAALAQYAQGYGKDDRPLRAGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_068205.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCGCCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCATTGGTCGACGCCGCCGTACAACCGGCGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCTACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGCCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCTAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTATGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006786","ARO_id":"45248","ARO_name":"PDC-417","CARD_short_name":"PDC-417","ARO_description":"PDC-417 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5547":{"model_id":"5547","model_name":"PDC-418","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7922":{"protein_sequence":{"accession":"WP_168247902.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_068206.1","fmin":"0","fmax":"1137","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGATGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACTCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006787","ARO_id":"45249","ARO_name":"PDC-418","CARD_short_name":"PDC-418","ARO_description":"PDC-418 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5548":{"model_id":"5548","model_name":"PDC-419","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7923":{"protein_sequence":{"accession":"WP_168247903.1","sequence":"MRDTRFPCLCGIAASTLLFAATPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLKFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAKGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_068207.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCGCCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCATTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGAAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCAAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCTAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTATGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006788","ARO_id":"45250","ARO_name":"PDC-419","CARD_short_name":"PDC-419","ARO_description":"PDC-419 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5549":{"model_id":"5549","model_name":"PDC-42","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7924":{"protein_sequence":{"accession":"WP_063864582.1","sequence":"MRHATILNLCGLAASTLFFATTSAFATEAPAERLKALVDAAVQPVMKANDIPGLAVAITLKGEPHYFSYGVASKEDARKVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASRHWPALQGSRFDGISLLDLGTYSAGGLPLQFPDAVQKDPAQIRDYYRQWQPTYAPGSHRQYSNPSIGLFGYLAARSLGQPFERSMERQLFPALGLEHTFIRVPAAQQGLYAQGYGKDDRPLRVGPGPLDAEAYGLKSSAADLLRFVEANLHPERLEKPWAQALDATHRGYYKVGDMTQGLGWEAYDWPIDLRRLQAGNSAPMALQAHKVARLPAPQALDGQRLLNKTGSTNGFGAYLAFIPGRDVGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLVR"},"dna_sequence":{"accession":"NG_049915.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCCATGCGACAATCCTCAACCTGTGCGGCCTCGCCGCTTCCACCCTGTTCTTCGCGACAACATCGGCCTTCGCCACGGAGGCGCCGGCGGAGCGCCTGAAGGCTCTGGTGGACGCCGCCGTGCAACCGGTCATGAAGGCCAATGATATCCCGGGACTGGCCGTCGCCATCACTCTCAAGGGCGAACCGCATTACTTCAGTTATGGGGTGGCCTCGAAGGAGGACGCCCGCAAGGTGACCCCCGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTACGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCGGCACTGGCCCGCCCTGCAGGGCAGCCGCTTCGACGGTATCAGCCTGCTCGACCTCGGCACCTACAGCGCTGGCGGCCTGCCGCTACAGTTCCCCGATGCGGTGCAGAAGGATCCGGCGCAGATCCGCGACTATTACCGCCAGTGGCAACCGACCTACGCCCCGGGCAGCCACCGCCAGTACTCCAACCCGAGCATCGGTCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCATTCGAGCGCAGCATGGAACGGCAGCTGTTCCCGGCGCTCGGCCTGGAGCACACCTTTATCCGGGTGCCCGCCGCGCAGCAGGGGCTGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTGCGGGTCGGACCCGGTCCGCTGGACGCCGAGGCCTACGGGCTGAAGTCCAGCGCTGCGGACCTGCTGCGCTTCGTCGAGGCCAACCTGCACCCCGAGCGCCTGGAGAAGCCCTGGGCGCAGGCCCTCGACGCCACCCATCGCGGCTACTACAAGGTGGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGATTGGCCGATCGACCTGAGGCGCCTGCAGGCGGGCAACTCGGCGCCGATGGCGCTGCAGGCGCACAAGGTCGCCAGGTTGCCGGCGCCGCAAGCCCTGGACGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGTTTCGGCGCTTACCTGGCGTTCATCCCGGGACGCGACGTCGGCCTGGTGATCCTGGCCAATCGCAACTACCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAACAGCAGGCCAAGGTACCGCTGGTGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006789","ARO_id":"45251","ARO_name":"PDC-42","CARD_short_name":"PDC-42","ARO_description":"PDC-42 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5550":{"model_id":"5550","model_name":"PDC-420","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7925":{"protein_sequence":{"accession":"WP_168247904.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALTQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGSLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_068208.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGACCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTTCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCTCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006790","ARO_id":"45252","ARO_name":"PDC-420","CARD_short_name":"PDC-420","ARO_description":"PDC-420 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5551":{"model_id":"5551","model_name":"PDC-421","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7926":{"protein_sequence":{"accession":"WP_168247905.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAAVAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_068209.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGGTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006791","ARO_id":"45253","ARO_name":"PDC-421","CARD_short_name":"PDC-421","ARO_description":"PDC-421 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5552":{"model_id":"5552","model_name":"PDC-422","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7927":{"protein_sequence":{"accession":"WP_179284354.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRRYSNPSIDLFGYLAARSLGQPFERLMEQQVFPALGLEQTYLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_070188.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGTCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCGCTATTCCAACCCGAGCATCGACCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCTACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006792","ARO_id":"45254","ARO_name":"PDC-422","CARD_short_name":"PDC-422","ARO_description":"PDC-422 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5553":{"model_id":"5553","model_name":"PDC-423","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7928":{"protein_sequence":{"accession":"WP_134600670.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALTQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIDLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_070189.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGACCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGACCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGTTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006793","ARO_id":"45255","ARO_name":"PDC-423","CARD_short_name":"PDC-423","ARO_description":"PDC-423 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5554":{"model_id":"5554","model_name":"PDC-424","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7929":{"protein_sequence":{"accession":"WP_179284357.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRGGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_070190.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAACTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGGCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006794","ARO_id":"45256","ARO_name":"PDC-424","CARD_short_name":"PDC-424","ARO_description":"PDC-424 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5555":{"model_id":"5555","model_name":"PDC-425","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7930":{"protein_sequence":{"accession":"WP_179284360.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALTQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGRRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_070191.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGACCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTTCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCGGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006795","ARO_id":"45257","ARO_name":"PDC-425","CARD_short_name":"PDC-425","ARO_description":"PDC-425 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5556":{"model_id":"5556","model_name":"PDC-426","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7931":{"protein_sequence":{"accession":"WP_179284362.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALTQDKIRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_070192.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGACCCAGGACAAGATACGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006796","ARO_id":"45258","ARO_name":"PDC-426","CARD_short_name":"PDC-426","ARO_description":"PDC-426 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5557":{"model_id":"5557","model_name":"PDC-427","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7932":{"protein_sequence":{"accession":"WP_179284365.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQLPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_070193.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCATTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTGGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGTTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGCTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCATCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACTCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATTCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006797","ARO_id":"45259","ARO_name":"PDC-427","CARD_short_name":"PDC-427","ARO_description":"PDC-427 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5558":{"model_id":"5558","model_name":"PDC-428","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7933":{"protein_sequence":{"accession":"WP_179284368.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDVEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_070194.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGTCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006798","ARO_id":"45260","ARO_name":"PDC-428","CARD_short_name":"PDC-428","ARO_description":"PDC-428 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5559":{"model_id":"5559","model_name":"PDC-430","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7934":{"protein_sequence":{"accession":"WP_179284371.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQLQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_070196.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTTGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006799","ARO_id":"45261","ARO_name":"PDC-430","CARD_short_name":"PDC-430","ARO_description":"PDC-430 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5560":{"model_id":"5560","model_name":"PDC-431","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7935":{"protein_sequence":{"accession":"WP_023118898.1","sequence":"MRDTKFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_070197.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAAATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTAGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006800","ARO_id":"45262","ARO_name":"PDC-431","CARD_short_name":"PDC-431","ARO_description":"PDC-431 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5561":{"model_id":"5561","model_name":"PDC-432","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7936":{"protein_sequence":{"accession":"WP_179284372.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_070198.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCACTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACTTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006801","ARO_id":"45263","ARO_name":"PDC-432","CARD_short_name":"PDC-432","ARO_description":"PDC-432 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5562":{"model_id":"5562","model_name":"PDC-433","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7937":{"protein_sequence":{"accession":"WP_133452685.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALTQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGNMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_070199.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGACCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCAACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006802","ARO_id":"45264","ARO_name":"PDC-433","CARD_short_name":"PDC-433","ARO_description":"PDC-433 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5563":{"model_id":"5563","model_name":"PDC-434","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7938":{"protein_sequence":{"accession":"WP_179284373.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATPAGYALTQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_070200.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCCCGCCGGCTATGCCCTGACCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006803","ARO_id":"45265","ARO_name":"PDC-434","CARD_short_name":"PDC-434","ARO_description":"PDC-434 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5564":{"model_id":"5564","model_name":"PDC-435","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7939":{"protein_sequence":{"accession":"WP_179284374.1","sequence":"MRDTRFPYLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPKALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_070201.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTACCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTGGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCAAAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006804","ARO_id":"45266","ARO_name":"PDC-435","CARD_short_name":"PDC-435","ARO_description":"PDC-435 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5565":{"model_id":"5565","model_name":"PDC-436","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7940":{"protein_sequence":{"accession":"WP_179284375.1","sequence":"MRDTRFSCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLSGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_070202.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCTCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCTCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCCGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACTCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATTCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006805","ARO_id":"45267","ARO_name":"PDC-436","CARD_short_name":"PDC-436","ARO_description":"PDC-436 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5566":{"model_id":"5566","model_name":"PDC-437","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7941":{"protein_sequence":{"accession":"WP_179284376.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQLPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNLSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDHPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_070203.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGCTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCTGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCACCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006806","ARO_id":"45268","ARO_name":"PDC-437","CARD_short_name":"PDC-437","ARO_description":"PDC-437 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5567":{"model_id":"5567","model_name":"PDC-439","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7942":{"protein_sequence":{"accession":"WP_179284378.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_070205.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACTCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCTGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACTCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006807","ARO_id":"45269","ARO_name":"PDC-439","CARD_short_name":"PDC-439","ARO_description":"PDC-439 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5568":{"model_id":"5568","model_name":"PDC-440","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7943":{"protein_sequence":{"accession":"WP_179284379.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPVLQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_070206.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTAGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGTACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006808","ARO_id":"45270","ARO_name":"PDC-440","CARD_short_name":"PDC-440","ARO_description":"PDC-440 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5569":{"model_id":"5569","model_name":"PDC-441","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7944":{"protein_sequence":{"accession":"WP_179284380.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQCAQGYGKDDRPPRVGPGPLGAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_070207.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTGCGCCCAGGGCTACGGCAAGGACGACCGCCCGCCACGGGTCGGTCCCGGCCCGCTGGGTGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACTTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006809","ARO_id":"45271","ARO_name":"PDC-441","CARD_short_name":"PDC-441","ARO_description":"PDC-441 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5570":{"model_id":"5570","model_name":"PDC-442","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7945":{"protein_sequence":{"accession":"WP_049305288.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRRYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTSGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_070208.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGTCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCGCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAGCGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006810","ARO_id":"45272","ARO_name":"PDC-442","CARD_short_name":"PDC-442","ARO_description":"PDC-442 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5571":{"model_id":"5571","model_name":"PDC-443","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7946":{"protein_sequence":{"accession":"WP_132710363.1","sequence":"MRDTGFPCLCGIAASTLLFAATSAIAGEAPADRLKTLVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASLHWPALQGSRFDGISLIDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYTPGSQRLYSNPSIGLFGYLAARSLGQPFERIMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDKPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_070209.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCGGATTCCCCTGCCTGTGCGGCATCGCCGCCTCCACACTGCTGTTCGCCGCCACCTCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGACACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGATATTCCGGGCCTGGCCGTGGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCTTCGAAAGAGGACGGTCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCTGCACTGGCCGGCGCTGCAAGGCAGCCGCTTCGACGGCATCAGCCTGATCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAAGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACACGCCGGGCAGCCAGCGCCTCTACTCCAACCCGAGCATCGGTCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGATCATGGAGCAGCAACTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAAGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCGGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATACCAGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAATTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006811","ARO_id":"45273","ARO_name":"PDC-443","CARD_short_name":"PDC-443","ARO_description":"PDC-443 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5572":{"model_id":"5572","model_name":"PDC-444","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7947":{"protein_sequence":{"accession":"WP_179284381.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFKRLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDGRPLRAGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_070210.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCAAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGGCCGCCCGCTACGGGCCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006812","ARO_id":"45274","ARO_name":"PDC-444","CARD_short_name":"PDC-444","ARO_description":"PDC-444 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5573":{"model_id":"5573","model_name":"PDC-445","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7948":{"protein_sequence":{"accession":"WP_179284382.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQVGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_070211.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGTCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006813","ARO_id":"45275","ARO_name":"PDC-445","CARD_short_name":"PDC-445","ARO_description":"PDC-445 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5574":{"model_id":"5574","model_name":"PDC-446","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7949":{"protein_sequence":{"accession":"WP_179284383.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAKGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_070212.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGTCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCAAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006814","ARO_id":"45276","ARO_name":"PDC-446","CARD_short_name":"PDC-446","ARO_description":"PDC-446 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5575":{"model_id":"5575","model_name":"PDC-447","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7950":{"protein_sequence":{"accession":"WP_179284384.1","sequence":"MRDTRFSCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPITLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_070213.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCTCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCACCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006815","ARO_id":"45277","ARO_name":"PDC-447","CARD_short_name":"PDC-447","ARO_description":"PDC-447 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5576":{"model_id":"5576","model_name":"PDC-448","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7951":{"protein_sequence":{"accession":"WP_179284385.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFIATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAKGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_070214.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCATCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCAAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006816","ARO_id":"45278","ARO_name":"PDC-448","CARD_short_name":"PDC-448","ARO_description":"PDC-448 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5577":{"model_id":"5577","model_name":"PDC-450","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7952":{"protein_sequence":{"accession":"WP_179284387.1","sequence":"MRDTRFPCLCGIAASTLLFTATPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERIMEQRLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRAGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRQWAQALDATHRGYYKVGDMTQGLGWEAYDWPIALKRLQAGNSTPMALQPHRVARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLAR"},"dna_sequence":{"accession":"NG_070216.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCACCGCCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTGGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGTTATGGGCTGGCGTCGAAAGAGGACGGTCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAAGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTACACCGCCGGCGGCTTGCCGCTTCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGTCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAGCGGATCATGGAGCAGCGCCTGTTCCCGGCCCTGGGCCTCGAACAGACTCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTCCGGGCCGGCCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGACTGGACCGGCAGTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCGCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGGTCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGGCGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006817","ARO_id":"45279","ARO_name":"PDC-450","CARD_short_name":"PDC-450","ARO_description":"PDC-450 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5578":{"model_id":"5578","model_name":"PDC-451","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7953":{"protein_sequence":{"accession":"WP_179284388.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQDYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_070217.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCTTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGACTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATTCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006818","ARO_id":"45280","ARO_name":"PDC-451","CARD_short_name":"PDC-451","ARO_description":"PDC-451 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5579":{"model_id":"5579","model_name":"PDC-452","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7954":{"protein_sequence":{"accession":"WP_179284389.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNLSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_070218.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCTGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006819","ARO_id":"45281","ARO_name":"PDC-452","CARD_short_name":"PDC-452","ARO_description":"PDC-452 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5580":{"model_id":"5580","model_name":"PDC-453","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7955":{"protein_sequence":{"accession":"WP_179945705.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDRAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDMPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPITLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_070227.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGATGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCGGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACATGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCACCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006820","ARO_id":"45282","ARO_name":"PDC-453","CARD_short_name":"PDC-453","ARO_description":"PDC-453 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5581":{"model_id":"5581","model_name":"PDC-454","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7956":{"protein_sequence":{"accession":"WP_141563014.1","sequence":"MRDTRFPCLCGIAASTLLFATTSAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALTQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_070228.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCTCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGACCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGTTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCACTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006821","ARO_id":"45283","ARO_name":"PDC-454","CARD_short_name":"PDC-454","ARO_description":"PDC-454 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5582":{"model_id":"5582","model_name":"PDC-455","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7957":{"protein_sequence":{"accession":"WP_058135553.1","sequence":"MRHATILNLCGLAASTLFFATTSAFATEAPAERLKALVDAAVQPVMKANDIPGLAVAITLKGEPHYFSYGVASKEDARKVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASRHWPALQGSRFDGISLLDLGTYTAGGLPLQFPDAVQKDPAQIRDYYRQWQPTYAPGSHRQYSNPSIGLFGYLAARSLGQPFERSMERQLFPALGLEHTFIRVPTAQQGLYAQGYGKDDRPLRVGPGPLDAEAYGLKSSAADLLRFVEANLHPERLEKPWAQALDATHRGYYKVGDMTQGLGWEAYDWPIDLKRLQAGNSAPMALQAHKVARLPAPQALDGQRLLNKTGSTNGFGAYLAFIPGRDVGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLVR"},"dna_sequence":{"accession":"NG_070229.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCCATGCGACAATCCTCAACCTGTGCGGCCTCGCCGCTTCCACCCTGTTCTTCGCGACAACATCGGCCTTCGCCACGGAGGCGCCGGCGGAGCGCCTGAAGGCTCTGGTGGACGCCGCCGTGCAACCGGTCATGAAGGCCAATGATATCCCGGGACTGGCCGTCGCCATCACTCTCAAGGGCGAACCGCATTACTTCAGTTATGGGGTGGCCTCGAAGGAGGACGCCCGCAAGGTGACCCCCGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTACGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCGGCACTGGCCCGCCCTGCAGGGCAGCCGCTTCGACGGTATCAGCCTGCTCGACCTCGGCACCTACACCGCTGGCGGCCTGCCGCTACAGTTCCCCGATGCGGTGCAGAAGGATCCGGCGCAGATCCGCGACTATTACCGCCAGTGGCAACCGACCTACGCCCCGGGCAGCCACCGCCAGTACTCCAACCCGAGCATCGGTCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCATTCGAGCGCAGCATGGAACGGCAGCTGTTCCCGGCGCTCGGCCTGGAGCACACCTTTATCCGGGTGCCCACCGCGCAGCAGGGGCTGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTGCGGGTCGGACCCGGTCCGCTGGACGCCGAGGCCTACGGGCTGAAGTCCAGCGCTGCGGACCTGCTGCGCTTCGTCGAGGCCAACCTGCACCCCGAGCGCCTGGAGAAGCCCTGGGCGCAGGCCCTCGACGCCACCCATCGCGGCTACTACAAGGTGGGCGACATGACCCAGGGCCTGGGTTGGGAAGCCTACGATTGGCCGATCGACCTGAAGCGCCTGCAGGCGGGCAACTCGGCGCCGATGGCGCTGCAGGCGCACAAGGTCGCCAGGTTGCCGGCGCCGCAAGCCCTGGACGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGTTTCGGCGCTTACCTGGCGTTCATCCCGGGACGCGACGTCGGCCTGGTGATCCTGGCCAATCGCAACTACCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAACAGCAGGCCAAGGTACCGCTGGTGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006822","ARO_id":"45284","ARO_name":"PDC-455","CARD_short_name":"PDC-455","ARO_description":"PDC-455 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5583":{"model_id":"5583","model_name":"PDC-456","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7958":{"protein_sequence":{"accession":"WP_188331879.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLTVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDRAQIRDYYRQWQPTYAPGSQRLYSNLSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_070751.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGACCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCGGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCTGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006823","ARO_id":"45285","ARO_name":"PDC-456","CARD_short_name":"PDC-456","ARO_description":"PDC-456 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5584":{"model_id":"5584","model_name":"PDC-457","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7959":{"protein_sequence":{"accession":"WP_094954583.1","sequence":"MRDTRFPCLCGIAASTLLFAATPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQANVPLKR"},"dna_sequence":{"accession":"NG_070752.1","fmin":"100","fmax":"1294","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCGCCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCATTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTGGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAACGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006824","ARO_id":"45286","ARO_name":"PDC-457","CARD_short_name":"PDC-457","ARO_description":"PDC-457 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5585":{"model_id":"5585","model_name":"PDC-458","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7960":{"protein_sequence":{"accession":"WP_197749407.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPSPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_071216.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTAGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCCCTACGGGTCGGTCCCAGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006825","ARO_id":"45287","ARO_name":"PDC-458","CARD_short_name":"PDC-458","ARO_description":"PDC-458 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5586":{"model_id":"5586","model_name":"PDC-459","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7961":{"protein_sequence":{"accession":"WP_197749408.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLKFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNLSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRAGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_071217.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTAGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGAAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCTGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCCCTACGGGCCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006826","ARO_id":"45288","ARO_name":"PDC-459","CARD_short_name":"PDC-459","ARO_description":"PDC-459 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5587":{"model_id":"5587","model_name":"PDC-46","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7962":{"protein_sequence":{"accession":"WP_043083525.1","sequence":"MRDTRFSCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_049919.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCTCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGTTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCATCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAAGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006827","ARO_id":"45289","ARO_name":"PDC-46","CARD_short_name":"PDC-46","ARO_description":"PDC-46 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5588":{"model_id":"5588","model_name":"PDC-460","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7963":{"protein_sequence":{"accession":"WP_197749409.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRVSQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRAGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTSGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_071218.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTAGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGTCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCCCTACGGGCCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAGCGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006828","ARO_id":"45290","ARO_name":"PDC-460","CARD_short_name":"PDC-460","ARO_description":"PDC-460 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5589":{"model_id":"5589","model_name":"PDC-462","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7964":{"protein_sequence":{"accession":"WP_197749411.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRVSQHWPALQGSRFDGISLLDLATYTAGGLPLKFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRAGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTSGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_071220.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTAGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGTCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGAAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCCCTACGGGCCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAGCGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006829","ARO_id":"45291","ARO_name":"PDC-462","CARD_short_name":"PDC-462","ARO_description":"PDC-462 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5590":{"model_id":"5590","model_name":"PDC-463","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7965":{"protein_sequence":{"accession":"WP_197749412.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRVSQHWPALQGSRFDGISLLDLATYTAGGLPLKFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTYLDVPEAALAQYAQGYGKDDRPLRAGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_071221.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTAGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGTCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGAAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCTACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCCCTACGGGCCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006830","ARO_id":"45292","ARO_name":"PDC-463","CARD_short_name":"PDC-463","ARO_description":"PDC-463 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5591":{"model_id":"5591","model_name":"PDC-465","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7966":{"protein_sequence":{"accession":"WP_197749414.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPSPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDASHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_071223.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTAGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCCCTACGGGTCGGTCCCAGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCTCCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006831","ARO_id":"45293","ARO_name":"PDC-465","CARD_short_name":"PDC-465","ARO_description":"PDC-465 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5592":{"model_id":"5592","model_name":"PDC-466","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7967":{"protein_sequence":{"accession":"WP_197749415.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRVSQHWPALQGSRFDGISLLDLATYTAGGLPLKFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYDKDDRPLRAGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTSGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_071224.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTAGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGTCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGAAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGACAAGGACGACCGCCCCCTACGGGCCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAGCGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006832","ARO_id":"45294","ARO_name":"PDC-466","CARD_short_name":"PDC-466","ARO_description":"PDC-466 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5593":{"model_id":"5593","model_name":"PDC-467","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7968":{"protein_sequence":{"accession":"WP_204376240.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSAQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_073478.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCTTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGCGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATTCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006833","ARO_id":"45295","ARO_name":"PDC-467","CARD_short_name":"PDC-467","ARO_description":"PDC-467 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5594":{"model_id":"5594","model_name":"PDC-468","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7969":{"protein_sequence":{"accession":"WP_204376241.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIDLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_073479.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCTTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGACCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATTCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006834","ARO_id":"45296","ARO_name":"PDC-468","CARD_short_name":"PDC-468","ARO_description":"PDC-468 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5595":{"model_id":"5595","model_name":"PDC-469","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7970":{"protein_sequence":{"accession":"WP_204376242.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQLPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAKGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_073480.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCTTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGCTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCAAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATTCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006835","ARO_id":"45297","ARO_name":"PDC-469","CARD_short_name":"PDC-469","ARO_description":"PDC-469 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5596":{"model_id":"5596","model_name":"PDC-470","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7971":{"protein_sequence":{"accession":"WP_204376243.1","sequence":"MRDTRFSCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNRFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_073481.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCTCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGTTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCATCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAAGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACCGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006836","ARO_id":"45298","ARO_name":"PDC-470","CARD_short_name":"PDC-470","ARO_description":"PDC-470 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5597":{"model_id":"5597","model_name":"PDC-471","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7972":{"protein_sequence":{"accession":"WP_204376244.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMTLQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_073482.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGACGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006837","ARO_id":"45299","ARO_name":"PDC-471","CARD_short_name":"PDC-471","ARO_description":"PDC-471 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5598":{"model_id":"5598","model_name":"PDC-472","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7973":{"protein_sequence":{"accession":"WP_204376245.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAKGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_073483.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAACTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCAAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006838","ARO_id":"45300","ARO_name":"PDC-472","CARD_short_name":"PDC-472","ARO_description":"PDC-472 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5599":{"model_id":"5599","model_name":"PDC-473","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7974":{"protein_sequence":{"accession":"WP_204378708.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTVTLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_073489.1","fmin":"0","fmax":"1179","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGTCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAACTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006839","ARO_id":"45301","ARO_name":"PDC-473","CARD_short_name":"PDC-473","ARO_description":"PDC-473 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5600":{"model_id":"5600","model_name":"PDC-474","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7975":{"protein_sequence":{"accession":"WP_204378709.1","sequence":"MRDTRFSCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGRLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_073490.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCTCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTAGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCGGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCACTGCAACCGCACAGGATCGCTAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006840","ARO_id":"45302","ARO_name":"PDC-474","CARD_short_name":"PDC-474","ARO_description":"PDC-474 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5601":{"model_id":"5601","model_name":"PDC-475","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7976":{"protein_sequence":{"accession":"WP_204378710.1","sequence":"MRDTRFSCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFIATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_073491.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCTCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCATCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCCGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACTCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATTCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006841","ARO_id":"45303","ARO_name":"PDC-475","CARD_short_name":"PDC-475","ARO_description":"PDC-475 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5602":{"model_id":"5602","model_name":"PDC-476","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7977":{"protein_sequence":{"accession":"WP_204378711.1","sequence":"MRDTRFSCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMAPQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_073492.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCTCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCCGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006842","ARO_id":"45304","ARO_name":"PDC-476","CARD_short_name":"PDC-476","ARO_description":"PDC-476 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5603":{"model_id":"5603","model_name":"PDC-58","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7978":{"protein_sequence":{"accession":"WP_063864583.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGINLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_049932.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTAGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAACCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006843","ARO_id":"45305","ARO_name":"PDC-58","CARD_short_name":"PDC-58","ARO_description":"PDC-58 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5604":{"model_id":"5604","model_name":"PDC-60","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7979":{"protein_sequence":{"accession":"WP_043089496.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVVLANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_049935.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGATGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACTCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGGTCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006844","ARO_id":"45306","ARO_name":"PDC-60","CARD_short_name":"PDC-60","ARO_description":"PDC-60 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5605":{"model_id":"5605","model_name":"PDC-64","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7980":{"protein_sequence":{"accession":"WP_043104614.1","sequence":"MRDTRFPCLCGIAASILLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFSDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_049939.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCATACTGCTGTTCGCCACCACCCCGGCCATTGCCGACGAGGCCCCGGCAGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCTCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAACTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCTGAAGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGATATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATTCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTACCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006845","ARO_id":"45307","ARO_name":"PDC-64","CARD_short_name":"PDC-64","ARO_description":"PDC-64 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5606":{"model_id":"5606","model_name":"PDC-71","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7981":{"protein_sequence":{"accession":"WP_031630420.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDHPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_049947.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCACCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006846","ARO_id":"45308","ARO_name":"PDC-71","CARD_short_name":"PDC-71","ARO_description":"PDC-71 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5607":{"model_id":"5607","model_name":"PDC-94","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7982":{"protein_sequence":{"accession":"WP_063864586.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGEDDRPLRAGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_049951.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTATTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCGAGGACGACCGCCCGCTACGGGCCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006847","ARO_id":"45309","ARO_name":"PDC-94","CARD_short_name":"PDC-94","ARO_description":"PDC-94 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5608":{"model_id":"5608","model_name":"PDC-95","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7983":{"protein_sequence":{"accession":"WP_063864587.1","sequence":"MRDTRFPCLCGIAASTLLFAATPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFSDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_049952.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCGCCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCTCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAACTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAAGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATTCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTACCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006848","ARO_id":"45310","ARO_name":"PDC-95","CARD_short_name":"PDC-95","ARO_description":"PDC-95 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5609":{"model_id":"5609","model_name":"PDC-96","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7984":{"protein_sequence":{"accession":"WP_063864588.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNLSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_049953.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCTGAGCATCGGTCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCAATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAGCCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006849","ARO_id":"45311","ARO_name":"PDC-96","CARD_short_name":"PDC-96","ARO_description":"PDC-96 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5610":{"model_id":"5610","model_name":"PDC-97","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7985":{"protein_sequence":{"accession":"WP_061196139.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRAGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_049954.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGCCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006850","ARO_id":"45312","ARO_name":"PDC-97","CARD_short_name":"PDC-97","ARO_description":"PDC-97 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5611":{"model_id":"5611","model_name":"PDC-98","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7986":{"protein_sequence":{"accession":"WP_023913271.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALTQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRRYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"NG_049955.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGACCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCGCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006851","ARO_id":"45313","ARO_name":"PDC-98","CARD_short_name":"PDC-98","ARO_description":"PDC-98 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5612":{"model_id":"5612","model_name":"PDC-99","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"7987":{"protein_sequence":{"accession":"WP_063864589.1","sequence":"MRDTRFSCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTTTLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"NG_049956.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCTCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCACCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006852","ARO_id":"45314","ARO_name":"PDC-99","CARD_short_name":"PDC-99","ARO_description":"PDC-99 is a PDC beta-lactamase.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5613":{"model_id":"5613","model_name":"PER-10","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7988":{"protein_sequence":{"accession":"WP_001100752.1","sequence":"MNVIIKAVVTASTLLMVSFSSFETSAQSPLLKEQIESIVIGKKATVGVAVWGPDDLEPLLINPFEKFPMQSVFKLHLAMLVLHQVDQGKLDLNQTVIVNRAKVLQNTWAPIMKAYQGDEFSVPVQQLLQYSVSDSDNVACDLLFELVGGPAALHDYIQSMGIKETAVVANEAQMHADDQVQYQNWTSMKGAAEILKKFEQKTQLSETSQALLWKWMVETTTGPERLKGLLPAGTVVAHKTGTSGIKAGKTAATNDLGIILLPDGRPLLVAVFVKDSAESSRTNEAIIAQVAQTAYQFELKKLSALSPN"},"dna_sequence":{"accession":"NG_059319.1","fmin":"100","fmax":"1027","strand":"+","sequence":"ATGAATGTCATTATAAAAGCTGTAGTTACTGCCTCGACGCTACTGATGGTATCTTTTAGTTCATTCGAAACCTCAGCGCAATCCCCACTGTTAAAAGAGCAAATTGAATCCATAGTCATTGGAAAAAAAGCCACTGTAGGCGTTGCAGTGTGGGGGCCTGACGATCTGGAACCTTTACTGATTAATCCTTTTGAAAAATTCCCAATGCAAAGTGTATTTAAATTGCATTTAGCTATGTTGGTACTGCATCAGGTTGATCAGGGAAAGTTGGATTTAAATCAGACCGTTATCGTAAACAGGGCTAAGGTTTTACAGAATACCTGGGCTCCGATAATGAAAGCGTATCAGGGAGACGAGTTTAGTGTTCCAGTGCAGCAACTGCTGCAATACTCGGTCTCGGACAGCGATAACGTGGCCTGTGATTTGTTATTTGAACTGGTTGGTGGACCAGCTGCTTTGCATGACTATATCCAGTCTATGGGTATAAAGGAGACCGCTGTGGTCGCAAATGAAGCGCAGATGCACGCCGATGATCAGGTGCAGTATCAAAACTGGACCTCGATGAAAGGTGCTGCAGAGATCCTGAAAAAGTTTGAGCAAAAAACACAGCTGTCTGAAACCTCGCAGGCTTTGTTATGGAAGTGGATGGTCGAAACCACCACAGGACCAGAGCGGTTAAAAGGTTTGTTACCAGCTGGTACTGTGGTCGCACATAAAACTGGTACTTCGGGTATCAAAGCCGGAAAAACTGCGGCCACTAATGATTTAGGTATCATTCTGTTGCCTGATGGACGGCCCTTGCTGGTTGCTGTTTTTGTGAAAGACTCAGCCGAGTCAAGCCGAACCAATGAAGCTATCATTGCGCAGGTTGCTCAGACTGCGTATCAATTTGAATTGAAAAAGCTTTCTGCCCTAAGCCCAAATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006131","ARO_id":"44593","ARO_name":"PER-10","CARD_short_name":"PER-10","ARO_description":"PER-10 is a PER beta-lactamase.","ARO_category":{"36195":{"category_aro_accession":"3000056","category_aro_cvterm_id":"36195","category_aro_name":"PER beta-lactamase","category_aro_description":"PER beta-lactamases are plasmid-mediated extended spectrum beta-lactamases found in the Enterobacteriaceae family.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5614":{"model_id":"5614","model_name":"PER-11","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7989":{"protein_sequence":{"accession":"WP_104009831.1","sequence":"MNVIIKAVVTASTLLMVSFSSFETSAQSPLLKEQIESIVIGKKATVGVAVWGPDDLEPLLINPFEKFPMQSVFKLHLAMLVLHQVDQGKLDLNQTVIVNRAKVLQNTWAPIMKAYQGDEFSVPVQQLLQYSVSLSDNVACDLLFELVGGPAALHDYIQSMGIKETAVVANEAQMHADDQVQYQNWTSMKGAAEILKKFEQKTQLSETSQALLWKWMVETTTGPERLKGLLPAGTVVAHKTGTSGIKAGKTAATNDLGIILLPDGRPLLVAVFVKDSAESSRTNEAIIAQAAQTAYQFELKKLSALSPN"},"dna_sequence":{"accession":"NG_056387.1","fmin":"100","fmax":"1027","strand":"+","sequence":"ATGAATGTCATTATAAAAGCTGTAGTTACTGCCTCGACGCTACTGATGGTATCTTTTAGTTCATTCGAAACCTCAGCGCAATCCCCACTGTTAAAAGAGCAAATTGAATCCATAGTCATTGGAAAAAAAGCCACTGTAGGCGTTGCAGTGTGGGGGCCTGACGATCTGGAACCTTTACTGATTAATCCTTTTGAAAAATTCCCAATGCAAAGTGTATTTAAATTGCATTTAGCTATGTTGGTACTGCATCAGGTTGATCAGGGAAAGTTGGATTTAAATCAGACCGTTATCGTAAACAGGGCTAAGGTTTTACAGAATACCTGGGCTCCGATAATGAAAGCGTATCAGGGAGACGAGTTTAGTGTTCCAGTGCAGCAACTGCTGCAATACTCGGTCTCGCTCAGCGATAACGTGGCCTGTGATTTGTTATTTGAACTGGTTGGTGGACCAGCTGCTTTGCATGACTATATCCAGTCTATGGGTATAAAGGAGACCGCTGTGGTCGCAAATGAAGCGCAGATGCACGCCGATGATCAGGTGCAGTATCAAAACTGGACCTCGATGAAAGGTGCTGCAGAGATCCTGAAAAAGTTTGAGCAAAAAACACAGCTGTCTGAAACCTCGCAGGCTTTGTTATGGAAGTGGATGGTCGAAACCACCACAGGACCAGAGCGGTTAAAAGGTTTGTTACCAGCTGGTACTGTGGTCGCACATAAAACTGGTACTTCGGGTATCAAAGCCGGAAAAACTGCGGCCACTAATGATTTAGGTATCATTCTGTTGCCTGATGGACGGCCCTTGCTGGTTGCTGTTTTTGTGAAAGACTCAGCCGAGTCAAGCCGAACCAATGAAGCTATCATTGCGCAGGCTGCTCAGACTGCGTATCAATTTGAATTGAAAAAGCTTTCTGCCCTAAGCCCAAATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3006132","ARO_id":"44594","ARO_name":"PER-11","CARD_short_name":"PER-11","ARO_description":"PER-11 is a PER beta-lactamase.","ARO_category":{"36195":{"category_aro_accession":"3000056","category_aro_cvterm_id":"36195","category_aro_name":"PER beta-lactamase","category_aro_description":"PER beta-lactamases are plasmid-mediated extended spectrum beta-lactamases found in the Enterobacteriaceae family.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5615":{"model_id":"5615","model_name":"PER-12","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7990":{"protein_sequence":{"accession":"WP_096865225.1","sequence":"MNVIIKAVVTASTLLMVSFSSFETSAQSPLLKEQIESIVIGKKATVGVAVWGPDDLEPLLINPFEKFPMQSVFKLHLAMLVLHQVDQGKLDLNQTVIVNRAKVLQNTWSPMMEEHPGDEFTVAVQQLLQYSVSHSDNVACDLLFELVGGPAALDAYIRSIGVKETAVVANEAQMHADDQVQYQNWTSMKGAAEILKKFEQKTQLSETSQALLWKWMVETTTGPERLKGLLPAGTVVAHKTGTSGVRAGKTAATNDLGIILLPDGRPLLVAVFVKDSAESSRTNEAIIAQVAQAAYQFELKKLSALSPN"},"dna_sequence":{"accession":"NG_059335.1","fmin":"100","fmax":"1027","strand":"+","sequence":"ATGAATGTCATTATAAAAGCTGTAGTTACTGCCTCGACGCTACTGATGGTATCTTTTAGTTCATTCGAAACCTCTGCACAATCCCCACTGTTAAAAGAGCAAATTGAATCCATAGTCATTGGAAAAAAAGCCACTGTAGGCGTTGCAGTGTGGGGGCCTGACGATCTGGAACCTTTACTGATTAATCCTTTTGAAAAATTCCCAATGCAAAGTGTATTTAAATTGCATTTAGCTATGTTGGTACTGCATCAGGTTGATCAGGGAAAGTTGGATTTAAATCAGACCGTTATCGTAAACAGGGCTAAGGTTTTACAGAATACCTGGTCGCCCATGATGGAAGAGCATCCGGGCGATGAATTTACTGTTGCTGTGCAGCAGTTGTTGCAATATTCGGTGTCGCATAGTGACAACGTGGCTTGTGATTTGTTATTCGAACTGGTTGGAGGGCCTGCAGCCTTAGATGCCTACATCCGTTCTATAGGAGTGAAAGAGACGGCTGTGGTCGCAAATGAAGCGCAGATGCACGCCGATGATCAGGTGCAGTATCAAAACTGGACCTCGATGAAGGGGGCCGCAGAGATCCTGAAAAAGTTTGAGCAAAAAACACAGCTGTCTGAAACCTCGCAGGCTTTGTTATGGAAGTGGATGGTCGAAACCACCACAGGACCAGAGCGGTTAAAAGGTTTGTTACCAGCAGGTACTGTGGTCGCACATAAAACTGGTACTTCGGGTGTCAGAGCCGGGAAAACTGCGGCCACTAATGATTTAGGTATCATTCTGTTGCCTGATGGACGGCCCTTGCTGGTTGCTGTTTTTGTGAAAGACTCAGCCGAGTCAAGCCGAACCAATGAAGCTATCATTGCGCAGGTTGCTCAGGCTGCGTATCAATTTGAATTGAAAAAGCTTTCTGCCCTAAGCCCAAATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36944","NCBI_taxonomy_name":"Providencia rettgeri","NCBI_taxonomy_id":"587"}}}},"ARO_accession":"3006133","ARO_id":"44595","ARO_name":"PER-12","CARD_short_name":"PER-12","ARO_description":"PER-12 is a PER beta-lactamase.","ARO_category":{"36195":{"category_aro_accession":"3000056","category_aro_cvterm_id":"36195","category_aro_name":"PER beta-lactamase","category_aro_description":"PER beta-lactamases are plasmid-mediated extended spectrum beta-lactamases found in the Enterobacteriaceae family.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5616":{"model_id":"5616","model_name":"PER-13","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7991":{"protein_sequence":{"accession":"WP_136512105.1","sequence":"MNVIIKAVVTASTLLMVSFSSFETSAQSPLLKEQIESIVIGKKATVGVAVWGPDDLEPLLINPFEKFPMQSVFKLHLAMLVLHQVDQGKLDLNQTVIVNRAKVLQNTWAPIMKAYQGDEFSVPVQQLLQYSVSHSDNVACDLLFELVGGPAALHDYIQSMGIKETAVVANEAQMHADDQVQYQNWTSMKGAAEILKKFEQKTQLSETSQALLWKWMVETTSGPERLKGLLPAGTVVAHKTGTSGIKAGKTAATNDLGIILLPDGRPLLVAVFVKDSAESSRTNEAIIAQVAQTAYQFELKKLSALSPN"},"dna_sequence":{"accession":"NG_064782.1","fmin":"0","fmax":"927","strand":"+","sequence":"ATGAATGTCATTATAAAAGCTGTAGTTACTGCCTCGACGCTACTGATGGTATCTTTTAGTTCATTCGAAACCTCAGCGCAATCCCCACTGTTAAAAGAGCAAATTGAATCCATAGTCATTGGAAAAAAAGCCACTGTAGGCGTTGCAGTGTGGGGGCCTGACGATCTGGAACCTTTACTGATTAATCCTTTTGAAAAATTCCCAATGCAAAGTGTATTTAAATTGCATTTAGCTATGTTGGTACTGCATCAGGTTGATCAGGGAAAGTTGGATTTAAATCAGACCGTTATCGTAAACAGGGCTAAGGTTTTACAGAATACCTGGGCTCCGATAATGAAAGCGTATCAGGGAGACGAGTTTAGTGTTCCAGTGCAGCAACTGCTGCAATACTCGGTCTCGCACAGCGATAACGTGGCCTGTGATTTGTTATTTGAACTGGTTGGTGGACCAGCTGCTTTGCATGACTATATCCAGTCTATGGGTATAAAGGAGACCGCTGTGGTCGCAAATGAAGCGCAGATGCACGCCGATGATCAGGTGCAGTATCAAAACTGGACCTCGATGAAAGGTGCTGCAGAGATCCTGAAAAAGTTTGAGCAAAAAACACAGCTGTCTGAAACCTCGCAGGCTTTGTTATGGAAGTGGATGGTCGAAACCACCTCAGGACCAGAGCGGTTAAAAGGTTTGTTACCAGCTGGTACTGTGGTCGCACATAAAACTGGTACTTCGGGTATCAAAGCCGGAAAAACTGCGGCCACTAATGATTTAGGTATCATTCTGTTGCCTGATGGACGGCCCTTGCTGGTTGCTGTTTTTGTGAAAGACTCAGCCGAGTCAAGCCGAACCAATGAAGCTATCATTGCGCAGGTTGCTCAGACTGCGTATCAATTTGAATTGAAAAAGCTTTCTGCCCTAAGCCCAAATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006134","ARO_id":"44596","ARO_name":"PER-13","CARD_short_name":"PER-13","ARO_description":"PER-13 is a PER beta-lactamase.","ARO_category":{"36195":{"category_aro_accession":"3000056","category_aro_cvterm_id":"36195","category_aro_name":"PER beta-lactamase","category_aro_description":"PER beta-lactamases are plasmid-mediated extended spectrum beta-lactamases found in the Enterobacteriaceae family.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5617":{"model_id":"5617","model_name":"PER-14","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7992":{"protein_sequence":{"accession":"WP_156404659.1","sequence":"MNVITKCVFTASALLMLGLSSFVVSAQSPLLKEQIETIVTGKKATVGVAVWGPDDLEPLLLNPFEKFPMQSVFKLHLAMLVLHQVDQGKLDLNQSVTVNRAAVLQNTWSPMMKDHQGDEFTVAVQQLLQYSVSHTDNVACDLLFELVGGPQALHAYIQSLGVKEAAVVANEAQMHADDQVQYQNWTSMKAAAQVLQKFEQKKQLSETSQALLWKWMVETTTGPQRLKGLLPAGTIVAHKTGTSGVRAGKTAATNDAGVIMLPDGRPLLVAVFVKDSAESERTNEAIIAQVAQAAYQFELKKLSAVSPD"},"dna_sequence":{"accession":"NG_067159.1","fmin":"0","fmax":"927","strand":"+","sequence":"ATGAATGTCATCACAAAATGTGTTTTCACCGCTTCTGCTCTGCTGATGCTTGGCTTAAGTTCATTTGTAGTATCAGCCCAATCCCCTTTGTTAAAAGAGCAGATTGAAACCATAGTGACGGGTAAAAAGGCCACTGTAGGTGTAGCAGTGTGGGGGCCTGACGATCTGGAACCTTTGTTGCTGAATCCATTTGAAAAGTTTCCGATGCAAAGTGTGTTTAAACTGCATTTAGCTATGTTAGTTCTGCATCAGGTCGATCAGGGGAAACTGGATTTAAATCAGTCTGTTACTGTTAATCGTGCTGCAGTATTACAAAATACCTGGTCGCCAATGATGAAAGATCATCAGGGCGATGAATTTACTGTTGCAGTACAGCAGTTACTGCAGTATTCGGTGTCACACACCGACAATGTGGCCTGCGATTTGTTATTTGAACTGGTGGGCGGGCCGCAAGCTTTGCATGCTTATATCCAGTCTTTAGGCGTTAAAGAAGCTGCCGTGGTAGCAAATGAAGCGCAAATGCATGCGGATGATCAGGTGCAATATCAAAACTGGACGTCGATGAAAGCCGCAGCACAAGTTCTGCAAAAGTTTGAACAGAAAAAGCAGTTGTCTGAAACCTCTCAGGCCTTGTTATGGAAATGGATGGTTGAAACCACCACAGGACCACAGCGGTTAAAAGGCTTGTTACCTGCTGGTACTATAGTGGCGCATAAAACCGGTACTTCGGGCGTCAGAGCAGGAAAAACTGCGGCGACTAATGATGCGGGCGTCATTATGTTGCCTGATGGACGGCCTTTATTGGTGGCGGTATTTGTCAAGGATTCGGCTGAATCAGAACGAACCAATGAAGCTATTATTGCGCAGGTTGCGCAAGCGGCTTATCAGTTTGAGCTGAAAAAACTCTCTGCAGTGAGTCCGGATTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3006135","ARO_id":"44597","ARO_name":"PER-14","CARD_short_name":"PER-14","ARO_description":"PER-14 is a PER beta-lactamase.","ARO_category":{"36195":{"category_aro_accession":"3000056","category_aro_cvterm_id":"36195","category_aro_name":"PER beta-lactamase","category_aro_description":"PER beta-lactamases are plasmid-mediated extended spectrum beta-lactamases found in the Enterobacteriaceae family.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5618":{"model_id":"5618","model_name":"PER-15","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7993":{"protein_sequence":{"accession":"WP_168247906.1","sequence":"MNVIIKAVVTASTLLMVSFSSFETSAQSPLLKEQIESIVIGKKATVGVAVWGPDDLEPLLINPFEKFPMQSVFKLHLAMLVLHQVDQGKLDLNQTVIVNRAKVLQNTWAPIMKAYQGDEFSVPVQQLLQYSVSHSDNVACDLLFELVGAPAALHDYIQSMGIKETAVVANEAQMHADDQVQYQNWTSMKGAAEILKKFEQKTQLSETSQALLWKWMVETTTGPERLKGLLPAGTVVAHKTGTSGIKAGKTAATNDLGIILLPDGRPLLVAVFVKDSAESSRTNEAIIAQVAQTAYQFELKKLSALSPN"},"dna_sequence":{"accession":"NG_068210.1","fmin":"0","fmax":"927","strand":"+","sequence":"ATGAATGTCATTATAAAAGCTGTAGTTACTGCCTCGACGCTACTGATGGTATCTTTTAGTTCATTCGAAACCTCAGCGCAATCCCCACTGTTAAAAGAGCAAATTGAATCCATAGTCATTGGAAAAAAAGCCACTGTAGGCGTTGCAGTGTGGGGGCCTGACGATCTGGAACCTTTACTGATTAATCCTTTTGAAAAATTCCCAATGCAAAGTGTATTTAAATTGCATTTAGCTATGTTGGTACTGCATCAGGTTGATCAGGGAAAGTTGGATTTAAATCAGACCGTTATCGTAAACAGGGCTAAGGTTTTACAGAATACCTGGGCTCCGATAATGAAAGCGTATCAGGGAGACGAGTTTAGTGTTCCAGTGCAGCAACTGCTGCAATACTCGGTCTCGCACAGCGATAACGTGGCCTGTGATTTGTTATTTGAACTGGTTGGTGCACCAGCTGCTTTGCATGACTATATCCAGTCTATGGGTATAAAGGAGACCGCTGTGGTCGCAAATGAAGCGCAGATGCACGCCGATGATCAGGTGCAGTATCAAAACTGGACCTCGATGAAAGGTGCTGCAGAGATCCTGAAAAAGTTTGAGCAAAAAACACAGCTGTCTGAAACCTCGCAGGCTTTGTTATGGAAGTGGATGGTCGAAACCACCACAGGACCAGAGCGGTTAAAAGGTTTGTTACCAGCTGGTACTGTGGTCGCACATAAAACTGGTACTTCGGGTATCAAAGCCGGAAAAACTGCGGCCACTAATGATTTAGGTATCATTCTGTTGCCTGATGGACGGCCCTTGCTGGTTGCTGTTTTTGTGAAAGACTCAGCCGAGTCAAGCCGAACCAATGAAGCTATCATTGCGCAGGTTGCTCAGACTGCGTATCAATTTGAATTGAAAAAGCTTTCTGCCCTAAGCCCAAATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006136","ARO_id":"44598","ARO_name":"PER-15","CARD_short_name":"PER-15","ARO_description":"PER-15 is a PER beta-lactamase.","ARO_category":{"36195":{"category_aro_accession":"3000056","category_aro_cvterm_id":"36195","category_aro_name":"PER beta-lactamase","category_aro_description":"PER beta-lactamases are plasmid-mediated extended spectrum beta-lactamases found in the Enterobacteriaceae family.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5619":{"model_id":"5619","model_name":"PER-16","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7994":{"protein_sequence":{"accession":"WP_202089433.1","sequence":"MNVIIKAVVTASTLLMVSFSSFETSAQSPLLKEQIESIVIGKKATVGVAVWGPDDLEPLLINPFEKFPMQSVFKLHLAMLVLHQVDQGKLDLNQTVIVNRAKVLQNTWSPMMEEHPGDEFTVAVQQLLQYSVSHSDNVACDLLFELVGGPAALDAYIRSIGVKETAVVANEAQMHADDQVQYQNWTSMKGAAEILRKFEQKTQLSETSQALLWKWMVETTTGPERLKGLLPAGTVVAHKTGTSGVRAGKTAATNDLGIILLPDGRPLLVAVFVKDSAESSRTNEAIIAQVAQAAYQFELKKLSALSPN"},"dna_sequence":{"accession":"NG_073484.1","fmin":"0","fmax":"927","strand":"+","sequence":"ATGAATGTCATTATAAAAGCTGTAGTTACTGCCTCGACGCTACTGATGGTATCTTTTAGTTCATTCGAAACCTCAGCGCAATCCCCACTGTTAAAAGAGCAAATTGAATCCATAGTCATTGGAAAAAAAGCCACTGTAGGCGTTGCAGTGTGGGGGCCTGACGATCTGGAACCTTTACTGATTAATCCTTTTGAAAAATTCCCAATGCAAAGTGTATTTAAATTGCATTTAGCTATGTTGGTACTGCATCAGGTTGATCAGGGAAAGTTGGATTTAAATCAGACCGTTATCGTAAACAGGGCTAAGGTTTTACAGAATACCTGGTCGCCCATGATGGAAGAGCATCCGGGCGATGAATTTACTGTTGCTGTGCAGCAGTTGTTGCAATATTCGGTGTCGCATAGTGACAACGTGGCTTGTGATTTGTTATTCGAACTGGTTGGAGGGCCTGCAGCCTTAGATGCCTACATCCGTTCTATAGGAGTGAAAGAGACGGCTGTGGTCGCAAATGAAGCGCAGATGCACGCCGATGATCAGGTGCAGTATCAAAACTGGACCTCGATGAAAGGTGCTGCAGAGATCCTGAGAAAGTTTGAGCAAAAAACACAGCTGTCTGAAACCTCGCAGGCTTTGTTATGGAAGTGGATGGTCGAAACCACCACAGGACCAGAGCGGTTAAAAGGTTTGTTACCAGCTGGTACTGTGGTCGCACATAAAACTGGTACTTCGGGTGTCAGAGCCGGGAAAACTGCGGCCACTAATGATTTAGGTATCATTCTGTTGCCTGATGGACGGCCCTTGCTGGTTGCTGTTTTTGTGAAAGACTCAGCCGAGTCAAGCCGAACTAATGAAGCTATCATTGCGCAGGTTGCTCAGGCTGCGTATCAATTTGAATTGAAAAAGCTTTCTGCCCTAAGCCCAAATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3006137","ARO_id":"44599","ARO_name":"PER-16","CARD_short_name":"PER-16","ARO_description":"PER-16 is a PER beta-lactamase.","ARO_category":{"36195":{"category_aro_accession":"3000056","category_aro_cvterm_id":"36195","category_aro_name":"PER beta-lactamase","category_aro_description":"PER beta-lactamases are plasmid-mediated extended spectrum beta-lactamases found in the Enterobacteriaceae family.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5620":{"model_id":"5620","model_name":"PER-8","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7995":{"protein_sequence":{"accession":"WP_063864596.1","sequence":"MNVIIKAVVTASTLLMVSFSSFETSAQSPLLKEQIESIVIEKKATVGVAVWGPDDLEPLLINPFEKFPMQSVFKLHLAMLVLHQVDQGKLDLNQTVIVNRAKVLQNTWAPIMKAYQGDQFSVPVQQLLQYSVSHSDNVACDLLFELVGGPAALHDYIQSMGIKETAVVANEAQMHADDQVQYQNWTSMKGAAEILKKFEQKTQLSETSQALLWKWMVETTTGPERLKGLLPAGTVVAHKTGTSGVRAGKTAATNDLGIILLPDGRPLLVAVFVKDSAESSRTNEAIIAQVAQAAYQFELKKLSALSPN"},"dna_sequence":{"accession":"NG_049967.1","fmin":"100","fmax":"1027","strand":"+","sequence":"ATGAATGTCATTATAAAAGCTGTAGTTACTGCCTCGACGCTACTGATGGTATCTTTTAGTTCATTCGAAACCTCAGCGCAATCCCCACTGTTAAAAGAGCAAATTGAATCCATAGTCATTGAAAAAAAAGCCACTGTAGGCGTTGCAGTGTGGGGGCCTGACGATCTGGAACCTTTACTGATTAATCCTTTTGAAAAATTCCCAATGCAAAGTGTATTTAAATTGCATTTAGCTATGTTGGTACTGCATCAGGTTGATCAGGGAAAGTTGGATTTAAATCAGACCGTTATCGTAAACAGGGCTAAGGTTTTACAGAATACCTGGGCTCCGATAATGAAAGCGTATCAGGGAGACCAGTTTAGTGTTCCAGTGCAGCAACTGCTGCAATACTCGGTCTCGCACAGCGATAACGTGGCCTGTGATTTGTTATTTGAACTGGTTGGTGGACCAGCTGCTTTGCATGACTATATCCAGTCTATGGGTATAAAGGAGACCGCTGTGGTCGCAAATGAAGCGCAGATGCACGCCGATGATCAGGTGCAGTATCAAAACTGGACCTCGATGAAGGGGGCCGCAGAGATCCTGAAAAAGTTTGAGCAAAAAACACAGCTGTCTGAAACCTCGCAGGCTTTGTTATGGAAGTGGATGGTCGAAACCACCACAGGACCAGAGCGGTTAAAAGGTTTGTTACCAGCTGGTACTGTGGTCGCACATAAAACTGGTACTTCGGGTGTCAGAGCCGGGAAAACTGCGGCCACTAATGATTTAGGTATCATTCTGTTGCCTGATGGACGGCCCTTGCTGGTTGCTGTTTTTGTGAAAGACTCAGCCGAGTCAAGCCGAACCAATGAAGCTATCATTGCGCAGGTTGCTCAGGCTGCGTATCAATTTGAATTGAAAAAGCTTTCTGCCCTAAGCCCAAATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3003184","ARO_id":"39761","ARO_name":"PER-8","CARD_short_name":"PER-8","ARO_description":"PER-8 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36195":{"category_aro_accession":"3000056","category_aro_cvterm_id":"36195","category_aro_name":"PER beta-lactamase","category_aro_description":"PER beta-lactamases are plasmid-mediated extended spectrum beta-lactamases found in the Enterobacteriaceae family.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5621":{"model_id":"5621","model_name":"PER-9","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7996":{"protein_sequence":{"accession":"WP_063864597.1","sequence":"MNVIIKAVVTASTLLMVSFSSFETSAQSPLLKEQIESIVIGKKATVGVAVWGPDDLEPLLINPFEKFPMQSVFKLHLAMLVLHQVDQGKLDLNQTVIVNRAKVLQNTWAPIMKAYQGDEFSVPVQQLLLYSVSHSDNVACDLLFELVGGPAALHDYIQSMGIKETAVVANEAQMHADDQVQYQNWTSMKGAAEILKKFEQKTQLSETSQALLWKWMVETTTGPERLKGLLPAGTVVAHKTGTSGIKAGKTAATNDLGIILLPDGRPLLVAVFVKDSAESSRTNEAIIAQVAQTAYQFELKKLSALSPN"},"dna_sequence":{"accession":"NG_049968.1","fmin":"0","fmax":"927","strand":"+","sequence":"ATGAATGTCATTATAAAAGCTGTAGTTACTGCCTCGACGCTACTGATGGTATCTTTTAGTTCATTCGAAACCTCAGCGCAATCCCCACTGTTAAAAGAGCAAATTGAATCCATAGTCATTGGAAAAAAAGCCACTGTAGGCGTTGCAGTGTGGGGGCCTGACGATCTGGAACCTTTACTGATTAATCCTTTTGAAAAATTCCCAATGCAAAGTGTATTTAAATTGCATTTAGCTATGTTGGTACTGCATCAGGTTGATCAGGGAAAGTTGGATTTAAATCAGACCGTTATCGTAAACAGGGCTAAGGTTTTACAGAATACCTGGGCTCCGATAATGAAAGCGTATCAGGGAGACGAGTTTAGTGTTCCAGTGCAGCAACTGCTGCTATACTCGGTCTCGCACAGCGATAACGTGGCCTGTGATTTGTTATTTGAACTGGTTGGTGGACCAGCTGCTTTGCATGACTATATCCAGTCTATGGGTATAAAGGAGACCGCTGTGGTCGCAAATGAAGCGCAGATGCACGCCGATGATCAGGTGCAGTATCAAAACTGGACCTCGATGAAAGGTGCTGCAGAGATCCTGAAAAAGTTTGAGCAAAAAACACAGCTGTCTGAAACCTCGCAGGCTTTGTTATGGAAGTGGATGGTCGAAACCACCACAGGACCAGAGCGGTTAAAAGGTTTGTTACCAGCTGGTACTGTGGTCGCACATAAAACTGGTACTTCGGGTATCAAAGCCGGAAAAACTGCGGCCACTAATGATTTAGGTATCATTCTGTTGCCTGATGGACGGCCCTTGCTGGTTGCTGTTTTTGTGAAAGACTCAGCCGAGTCAAGCCGAACCAATGAAGCTATCATTGCGCAGGTTGCTCAGACTGCGTATCAATTTGAATTGAAAAAGCTTTCTGCCCTAAGCCCAAATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3006138","ARO_id":"44600","ARO_name":"PER-9","CARD_short_name":"PER-9","ARO_description":"PER-9 is a PER beta-lactamase.","ARO_category":{"36195":{"category_aro_accession":"3000056","category_aro_cvterm_id":"36195","category_aro_name":"PER beta-lactamase","category_aro_description":"PER beta-lactamases are plasmid-mediated extended spectrum beta-lactamases found in the Enterobacteriaceae family.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5622":{"model_id":"5622","model_name":"PFM-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7997":{"protein_sequence":{"accession":"WP_148044470.1","sequence":"MKVINILSAVSMFCITCQALANDINLTLTHFKGPLYIVEDKEYVQENSMVYIGAQDITIIGATWTPATAEKLEQEIRKISSLPIKEVINTNYHTDRAGGNAYWKKLGASIVSTQMTYDLEKTNWRGIVDFTRQGMEHYPVLEQSLPDQVYPGDFALQNGHVRALYLGASHTEDGIFVYFPEERVLYGNCILKEKLGNMTFANRSEYPKTLKKLQGLIRSGELSVEAIIAGHNSPIQSVELIDHYLNLLEHGEQ"},"dna_sequence":{"accession":"NG_065936.1","fmin":"0","fmax":"762","strand":"+","sequence":"ATGAAAGTTATCAATATCCTCTCAGCCGTCAGCATGTTCTGCATCACCTGCCAGGCACTCGCTAACGATATAAACCTTACTCTTACCCACTTCAAGGGCCCCCTCTACATCGTGGAAGACAAGGAGTATGTGCAGGAAAACTCAATGGTGTATATCGGTGCGCAAGACATCACAATTATCGGCGCAACCTGGACCCCCGCCACCGCTGAAAAGCTGGAGCAGGAAATCAGGAAAATCAGCTCCCTGCCCATCAAAGAGGTGATCAACACCAACTACCACACCGACCGTGCGGGAGGTAACGCTTATTGGAAGAAACTTGGCGCCAGTATTGTCTCAACTCAGATGACTTATGACCTGGAAAAAACCAATTGGCGCGGTATTGTCGACTTTACCCGGCAAGGCATGGAACACTATCCGGTCCTGGAACAAAGCCTGCCGGACCAGGTTTACCCGGGCGACTTCGCCTTGCAAAACGGTCATGTTCGAGCGCTGTATTTAGGCGCGTCTCACACCGAAGATGGGATTTTTGTGTACTTTCCAGAAGAACGTGTCTTGTATGGAAACTGCATCCTCAAGGAAAAGCTGGGTAACATGACGTTCGCCAATCGCAGCGAGTACCCGAAAACCCTAAAGAAATTGCAAGGGCTGATCCGCAGCGGTGAGTTGTCCGTTGAAGCGATTATCGCAGGACATAACTCACCGATACAAAGCGTTGAGTTGATTGACCATTATCTGAACCTGCTCGAACACGGCGAGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3006965","ARO_id":"45427","ARO_name":"PFM-1","CARD_short_name":"PFM-1","ARO_description":"PFM-1 is a PFM beta-lactamase.","ARO_category":{"43892":{"category_aro_accession":"3005432","category_aro_cvterm_id":"43892","category_aro_name":"PFM beta-lactamase","category_aro_description":"PFM beta-lactamases are class B2 beta-lactamases found in Pseudomonas fluorescens.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5623":{"model_id":"5623","model_name":"PFM-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7998":{"protein_sequence":{"accession":"WP_057012521.1","sequence":"MKLINILSAISLACITSQVFANQSDLTLIHFKGPLYIVEDKEYVQENSMVYIGEQHITVIGATWTPATAEKLEQEIRKISPLPIKEVINTNYHTDRAGGNAYWRKLGASIVSTQMTYDLEKSQWRSIVDFTRQGMEHYPVLEQSLPDQVYPGDFALQNGHVRALYLGASHTEDGIFVYFPEERVLYGNCILKEKLGNMTFANRSEYPKTLKKLQGLISSGELPVEAIIAGHNSPIQSVELIDHYLNLLEHGEQ"},"dna_sequence":{"accession":"NG_067160.1","fmin":"0","fmax":"762","strand":"+","sequence":"ATGAAGCTTATTAATATCCTGTCAGCCATCAGCCTGGCCTGCATCACCTCCCAGGTCTTCGCTAACCAGAGTGACTTGACCCTTATCCACTTCAAAGGCCCGCTCTACATCGTTGAAGACAAGGAGTATGTGCAGGAGAACTCAATGGTCTACATTGGCGAGCAACACATCACGGTTATCGGCGCAACCTGGACCCCCGCCACCGCTGAAAAGCTGGAGCAGGAAATCAGGAAAATCAGCCCCCTGCCCATCAAGGAGGTGATCAACACCAACTACCACACCGACCGTGCGGGAGGTAACGCCTACTGGAGGAAGCTCGGCGCCAGTATTGTCTCCACGCAGATGACTTATGACCTGGAAAAAAGCCAATGGCGCAGTATTGTCGACTTTACCCGGCAAGGGATGGAACACTATCCGGTCCTGGAACAAAGCCTGCCGGACCAGGTTTATCCGGGCGACTTCGCCTTGCAAAACGGTCATGTTCGAGCGCTGTATTTAGGCGCGTCTCACACCGAAGATGGGATTTTTGTGTACTTTCCAGAAGAACGTGTGTTGTATGGAAACTGCATCCTCAAGGAAAAGCTGGGGAACATGACGTTCGCCAATCGCAGCGAGTACCCGAAAACCCTGAAGAAATTGCAAGGGCTGATCAGCAGCGGTGAATTGCCCGTTGAAGCGATTATCGCAGGACATAACTCACCGATACAGAGCGTTGAGTTGATTGACCATTATCTGAACCTGCTCGAACACGGCGAGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3006966","ARO_id":"45428","ARO_name":"PFM-2","CARD_short_name":"PFM-2","ARO_description":"PFM-2 is a PFM beta-lactamase.","ARO_category":{"43892":{"category_aro_accession":"3005432","category_aro_cvterm_id":"43892","category_aro_name":"PFM beta-lactamase","category_aro_description":"PFM beta-lactamases are class B2 beta-lactamases found in Pseudomonas fluorescens.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5624":{"model_id":"5624","model_name":"PFM-3","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"7999":{"protein_sequence":{"accession":"WP_156404660.1","sequence":"MKLINILSAISLACITSQVFANQSDLTLTHFKGPLYVVEDKEYVQENSMVYVGAQHITVIGATWTPATAEKLEQEIRKISPLPIKEVINTNYHTDRAGGNAYWKKLGASIVSTQMTYDLEKSQWRSIVDFTRQGMEHYPVLEQSLPDQVYPGDFALQNGHVRALYLGASHTEDGIFVYFPEERVLYGNCILKEKLGNMTFANRSEYPKTLKKLQGLISSGELPVEAIIAGHNSPIQSVELIDHYLNLLEHGEQ"},"dna_sequence":{"accession":"NG_067161.1","fmin":"0","fmax":"762","strand":"+","sequence":"ATGAAGCTTATTAATATCCTGTCAGCCATCAGCCTGGCCTGCATCACCTCCCAGGTCTTCGCTAACCAGAGTGACTTGACCCTTACCCACTTCAAAGGCCCGCTCTACGTCGTTGAAGACAAGGAGTATGTGCAGGAGAACTCAATGGTCTACGTTGGCGCGCAACACATCACAGTTATCGGCGCAACCTGGACTCCCGCCACCGCTGAAAAGCTGGAGCAGGAAATCAGAAAAATCAGCCCCCTGCCCATCAAGGAGGTAATCAACACCAACTACCACACCGACCGTGCGGGAGGTAACGCCTACTGGAAGAAACTCGGCGCCAGTATTGTCTCCACACAGATGACCTATGACCTGGAAAAAAGCCAGTGGCGCAGTATTGTCGACTTTACCCGGCAAGGGATGGAACACTATCCGGTCCTTGAACAAAGCCTGCCGGACCAGGTTTATCCGGGCGACTTCGCCTTGCAAAACGGTCATGTTCGAGCGCTCTATTTAGGCGCGTCTCACACCGAAGATGGGATTTTTGTGTATTTTCCAGAAGAACGTGTCTTGTATGGAAACTGCATCCTCAAGGAAAAGCTGGGTAACATGACGTTCGCCAATCGCAGCGAGTACCCGAAAACCCTGAAGAAATTGCAAGGGCTTATCAGCAGCGGTGAGTTGCCCGTTGAAGCGATCATCGCAGGACATAACTCACCGATACAGAGCGTTGAGTTGATTGACCATTATCTGAACCTGCTCGAACACGGCGAGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36937","NCBI_taxonomy_name":"Pseudomonas fluorescens","NCBI_taxonomy_id":"294"}}}},"ARO_accession":"3006967","ARO_id":"45429","ARO_name":"PFM-3","CARD_short_name":"PFM-3","ARO_description":"PFM-3 is a PFM beta-lactamase.","ARO_category":{"43892":{"category_aro_accession":"3005432","category_aro_cvterm_id":"43892","category_aro_name":"PFM beta-lactamase","category_aro_description":"PFM beta-lactamases are class B2 beta-lactamases found in Pseudomonas fluorescens.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5625":{"model_id":"5625","model_name":"PLA-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"575"}},"model_sequences":{"sequence":{"8000":{"protein_sequence":{"accession":"WP_032699754.1","sequence":"MRQYRFALLPLLAALALPGWAHQATVTTVKQAESQLQGRVGYAELDLASGQLLAGYRSDERFPMMSTFKVLLCGAVLSRVDAGEEQLDRRIHYRQQDLVEYSPVTEKHLTDGLTVGELCAAAITLSDNTAANLLLTTLGGPQGLTSFLRHSGDQTSRLDRWETELNEARPGDVRDTTTPQAMARTLRNLLTGRVLSSASQQQLQRWMVEDKVAGPLLRSVLPAGWFIADKTGAGNRGSRGIIAALGPDGKAARIVVIYLTGTPATMDERNKQIAAIGATLIRHWSADENRP"},"dna_sequence":{"accession":"NG_049969.1","fmin":"100","fmax":"976","strand":"+","sequence":"ATGCGTCAATATCGATTCGCCCTTCTCCCATTGTTAGCCGCCCTGGCGCTCCCCGGTTGGGCGCATCAAGCTACGGTGACGACGGTTAAACAAGCCGAAAGCCAGCTTCAGGGCCGGGTCGGCTACGCCGAACTGGATTTAGCTTCCGGGCAACTGCTGGCCGGCTATCGTTCTGACGAACGGTTCCCGATGATGAGCACTTTTAAAGTTCTGCTCTGCGGCGCAGTCTTGTCGCGTGTCGATGCCGGTGAAGAACAGCTCGATCGCCGTATCCATTACCGGCAGCAGGATCTGGTGGAATATTCGCCGGTGACGGAAAAGCATCTTACCGATGGGCTCACCGTGGGCGAACTGTGCGCTGCCGCCATTACCCTGAGCGATAATACGGCGGCAAACCTGCTGTTGACCACTCTCGGCGGCCCGCAGGGGCTGACCAGCTTCCTGCGCCACAGCGGCGACCAGACTTCGCGGCTTGACCGTTGGGAAACGGAACTCAATGAAGCGCGGCCGGGCGACGTGCGAGATACCACGACTCCGCAAGCGATGGCCAGGACACTGCGAAATCTGTTGACCGGCCGCGTGCTTTCCAGCGCCTCGCAGCAGCAGTTGCAACGCTGGATGGTAGAGGACAAAGTTGCGGGGCCGCTGTTGCGATCGGTGCTGCCGGCGGGCTGGTTTATTGCCGATAAGACCGGAGCCGGCAATCGCGGCTCGCGCGGGATCATCGCTGCTCTCGGTCCGGACGGTAAAGCTGCGCGCATCGTGGTGATTTATTTGACCGGGACCCCCGCCACAATGGATGAACGCAATAAACAGATTGCGGCCATCGGCGCAACGCTGATCAGGCACTGGTCCGCAGACGAGAACAGACCCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41225","NCBI_taxonomy_name":"Raoultella planticola","NCBI_taxonomy_id":"575"}}}},"ARO_accession":"3006968","ARO_id":"45430","ARO_name":"PLA-1","CARD_short_name":"PLA-1","ARO_description":"PLA-1 is a PLA beta-lactamase.","ARO_category":{"43893":{"category_aro_accession":"3005433","category_aro_cvterm_id":"43893","category_aro_name":"PLA beta-lactamase","category_aro_description":"PLA beta-lactamases are class A beta-lactamase found in Raoultella planticola.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5626":{"model_id":"5626","model_name":"PLA-2a","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"575"}},"model_sequences":{"sequence":{"8001":{"protein_sequence":{"accession":"WP_047664983.1","sequence":"MRQYRFALLPLLAALALPGWAHQATVTTVKQAESQLQGRVGYAELDLASGQLLAGYRSDERFPMMSTFKVLLCGAVLSRVDAGEEQLDRRIHYRQQDLVEYSPVTEKHLTDGLTVGELCAAAITLSDNTAANLLLTTLGGPQGLTSFLRHSGDQTSRLDRWETELNEARPGDVRDTTTPQAMARTLRNLLTGRVLSSASQQQLQRWMVEDKVAGPLLRSVLPAGWFIADKTGAGNRGSRGIIAALGPDGKAARIVVIYLTGTPATMDERNKQIAAIGATLVTHWSADENRP"},"dna_sequence":{"accession":"NG_049970.1","fmin":"100","fmax":"976","strand":"+","sequence":"ATGCGTCAATATCGATTCGCCCTTCTCCCATTGTTAGCCGCCCTGGCGCTCCCCGGTTGGGCGCATCAAGCTACGGTGACGACGGTTAAACAAGCCGAAAGCCAGCTTCAGGGCCGGGTCGGCTACGCCGAACTGGATTTAGCTTCCGGGCAACTGCTGGCCGGCTATCGTTCTGACGAACGGTTCCCGATGATGAGCACTTTTAAAGTTCTGCTCTGCGGCGCAGTCTTGTCGCGTGTCGATGCCGGTGAAGAACAGCTCGATCGCCGTATCCATTACCGGCAGCAGGATCTGGTGGAATATTCGCCGGTGACGGAAAAGCATCTTACCGATGGGCTCACCGTGGGCGAACTGTGCGCTGCCGCCATTACCCTGAGCGATAATACGGCGGCAAACCTGCTGTTGACCACTCTCGGCGGCCCGCAGGGGCTGACCAGCTTCCTGCGCCACAGCGGCGACCAGACTTCGCGGCTTGACCGTTGGGAAACGGAACTCAATGAAGCGCGGCCGGGCGACGTGCGAGATACCACAACTCCGCAAGCGATGGCCAGGACACTGCGAAATCTGTTGACCGGTCGCGTGCTTTCCAGCGCCTCGCAGCAGCAGTTGCAACGCTGGATGGTAGAGGACAAAGTTGCGGGGCCGCTGTTGCGATCGGTGCTGCCGGCAGGCTGGTTTATTGCCGATAAGACCGGAGCCGGCAATCGCGGCTCGCGCGGGATCATCGCTGCTCTCGGGCCGGACGGTAAAGCTGCGCGCATCGTGGTGATTTATTTGACCGGGACCCCCGCCACAATGGATGAACGCAATAAACAGATTGCGGCCATCGGCGCAACGCTGGTCACGCACTGGTCCGCAGACGAGAACAGACCCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41225","NCBI_taxonomy_name":"Raoultella planticola","NCBI_taxonomy_id":"575"}}}},"ARO_accession":"3006969","ARO_id":"45431","ARO_name":"PLA-2a","CARD_short_name":"PLA-2a","ARO_description":"PLA-2a is a PLA beta-lactamase.","ARO_category":{"43893":{"category_aro_accession":"3005433","category_aro_cvterm_id":"43893","category_aro_name":"PLA beta-lactamase","category_aro_description":"PLA beta-lactamases are class A beta-lactamase found in Raoultella planticola.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5627":{"model_id":"5627","model_name":"PLA-3","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"575"}},"model_sequences":{"sequence":{"8002":{"protein_sequence":{"accession":"WP_032696109.1","sequence":"MRQYRFALLPLLAALALPGWAHQATVTTVKQAESQLQGRVGYAELDLASGQLLAGYRSDERFPMMSTFKVLLCGAVLSRVDAGEEQLDRRIHYRQQDLVEYSPVTEKHLTDGLTVGELCAAAITLSDNTAANLLLTTLGGPQGLTSFLRHSGDQTSRLDRWETELNEARPGDVRDTTTPQAMARTLRNLLTGRVLSSASQQQLQRWMVEDKVAGPLLRSVLPAGWFIADKTGAGNRGSRGIIAALGPDGKAARIVVIYLTGPPATMDERNKQIAAIGATLVTHWSADENRP"},"dna_sequence":{"accession":"NG_049971.1","fmin":"100","fmax":"976","strand":"+","sequence":"ATGCGTCAATATCGATTCGCCCTTCTCCCATTGTTAGCCGCCCTGGCGCTCCCCGGTTGGGCGCATCAAGCTACGGTGACAACGGTTAAACAAGCCGAAAGCCAGCTTCAGGGCCGGGTCGGCTACGCCGAACTGGATTTAGCTTCCGGGCAACTGCTGGCCGGCTATCGTTCTGACGAACGGTTCCCGATGATGAGCACTTTTAAAGTTCTGCTCTGCGGCGCAGTCTTGTCGCGTGTCGATGCCGGTGAAGAACAGCTCGATCGCCGTATCCATTACCGGCAGCAGGATCTGGTGGAATATTCGCCGGTGACGGAAAAGCATCTTACCGATGGGCTCACCGTGGGCGAACTGTGCGCTGCCGCCATTACCCTGAGCGATAATACGGCGGCAAACCTGCTGTTGACCACTCTCGGCGGCCCGCAGGGGCTGACCAGCTTCCTGCGCCACAGCGGCGACCAGACGTCGCGGCTTGACCGTTGGGAAACGGAACTCAATGAAGCGCGGCCGGGCGACGTGCGAGATACCACGACTCCGCAAGCGATGGCCAGGACACTGCGAAATCTGTTGACCGGTCGCGTGCTTTCCAGCGCCTCGCAGCAGCAGTTGCAACGCTGGATGGTAGAGGACAAAGTTGCGGGGCCGCTGTTGCGATCGGTGCTGCCGGCGGGCTGGTTTATTGCCGATAAGACCGGAGCCGGCAATCGCGGCTCGCGCGGGATCATCGCGGCTCTCGGTCCGGACGGTAAAGCTGCGCGCATCGTGGTGATTTATTTGACCGGGCCCCCCGCCACAATGGATGAACGCAATAAACAGATTGCGGCCATCGGCGCAACGCTGGTCACGCACTGGTCCGCAGACGAGAACAGACCCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41225","NCBI_taxonomy_name":"Raoultella planticola","NCBI_taxonomy_id":"575"}}}},"ARO_accession":"3006970","ARO_id":"45432","ARO_name":"PLA-3","CARD_short_name":"PLA-3","ARO_description":"PLA-3 is a PLA beta-lactamase.","ARO_category":{"43893":{"category_aro_accession":"3005433","category_aro_cvterm_id":"43893","category_aro_name":"PLA beta-lactamase","category_aro_description":"PLA beta-lactamases are class A beta-lactamase found in Raoultella planticola.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5628":{"model_id":"5628","model_name":"PLA-6","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"575"}},"model_sequences":{"sequence":{"8003":{"protein_sequence":{"accession":"WP_063864598.1","sequence":"MRQYRFALLPLLAALALPGWAHQATVTTVKQAESQLQGRVGYAELDLASGQLLAGYRSDERFPMMSTFKVLLCGAVLSRVDAGEEQLDRRIHYRQQDLVEYSPVTEKHLTDGLTVGELCAAAITLSDNTAANLLLTTLGGPQGLTSFLRHSGDQTSRLDRWETELNEARPGDVRDTTTPQAMARTLRNLLTGSVLSSASQQQLQRWMVEDKVAGPLLRSVLPAGWFIADKTGAGNRGSRGIIAALGPDGKAARIVVIYLTGTPATMDERNKQIAAIGATLIRHWSADENRP"},"dna_sequence":{"accession":"NG_049972.1","fmin":"100","fmax":"976","strand":"+","sequence":"ATGCGTCAATATCGATTCGCCCTTCTCCCATTGTTAGCCGCCCTGGCGCTCCCCGGTTGGGCGCATCAAGCTACGGTGACGACGGTTAAACAAGCCGAAAGCCAGCTTCAGGGTCGGGTCGGCTACGCCGAACTGGATTTAGCTTCCGGGCAACTGCTGGCCGGCTATCGTTCTGACGAACGGTTCCCGATGATGAGCACTTTTAAAGTTCTGCTCTGCGGCGCAGTCTTGTCGCGTGTCGATGCTGGTGAAGAACAGCTCGATCGCCGTATCCATTACCGGCAGCAGGATCTGGTGGAATATTCGCCGGTGACGGAAAAGCATCTTACCGATGGGCTCACCGTGGGCGAACTGTGCGCTGCCGCCATTACCCTGAGCGATAATACGGCGGCAAACCTGCTGTTGACCACTCTCGGCGGCCCGCAGGGGCTGACCAGCTTCCTGCGCCACAGCGGCGACCAGACTTCGCGGCTTGACCGTTGGGAAACGGAACTCAATGAAGCGCGGCCGGGCGACGTGCGAGATACCACGACTCCGCAAGCGATGGCCAGGACACTGCGAAATCTGTTGACCGGCAGCGTGCTTTCCAGCGCCTCGCAGCAGCAGTTGCAACGCTGGATGGTAGAGGACAAAGTTGCGGGGCCGCTGTTGCGATCGGTGCTGCCGGCAGGCTGGTTTATTGCCGATAAGACCGGAGCCGGCAATCGCGGCTCGCGCGGGATCATCGCGGCTCTCGGTCCGGACGGTAAAGCTGCGCGCATCGTGGTGATTTATTTGACCGGGACCCCCGCCACAATGGATGAACGCAATAAACAGATTGCGGCCATCGGCGCAACGCTGATCAGGCACTGGTCCGCAGACGAGAACAGACCCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41225","NCBI_taxonomy_name":"Raoultella planticola","NCBI_taxonomy_id":"575"}}}},"ARO_accession":"3006971","ARO_id":"45433","ARO_name":"PLA-6","CARD_short_name":"PLA-6","ARO_description":"PLA-6 is a PLA beta-lactamase.","ARO_category":{"43893":{"category_aro_accession":"3005433","category_aro_cvterm_id":"43893","category_aro_name":"PLA beta-lactamase","category_aro_description":"PLA beta-lactamases are class A beta-lactamase found in Raoultella planticola.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5629":{"model_id":"5629","model_name":"PLN-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"575"}},"model_sequences":{"sequence":{"8004":{"protein_sequence":{"accession":"WP_041884311.1","sequence":"MLKQSINTVVLLLFLTFSSLFACAQKVAEPTRNPPEWTQPYQPFRIAGNLYYVGTSDLASYLITTPKGHILINTGLSSSLSSIKANVKTLGFKFSDIKILLTTQAHFDHMGAMAAIKKLTGAKFMVDEKDAKVAADGGRSDYALGGHRSTYVPVKADRILHDKDKITLGGMELVMLHHPGHTQGSCSFLFNVKDESRVYSVLIANMPTIVTEKKFSEVTTYPGIAKDYAYTLNAMKKLKFDMWLSSHASQFGLLTKHKPGDAYNPAAFIDQKGYDSAIRDLEDKFLRKE"},"dna_sequence":{"accession":"NG_055471.1","fmin":"100","fmax":"970","strand":"+","sequence":"ATGCTTAAACAGAGTATCAACACGGTAGTACTACTCCTTTTTCTGACATTCAGTTCTTTGTTTGCCTGTGCTCAAAAAGTAGCAGAACCTACAAGAAATCCGCCAGAATGGACTCAGCCTTACCAGCCTTTCCGGATTGCAGGTAATTTATATTACGTGGGTACCAGTGATCTGGCCAGTTATCTGATTACAACCCCAAAAGGTCATATTCTGATCAATACTGGTCTTTCTTCATCTTTATCATCGATTAAAGCGAATGTAAAAACCCTGGGCTTCAAATTTAGCGATATCAAAATACTACTGACCACTCAGGCTCATTTTGACCACATGGGTGCAATGGCAGCTATCAAAAAACTGACTGGTGCTAAGTTTATGGTAGATGAAAAGGATGCGAAAGTTGCAGCAGATGGAGGAAGATCAGATTATGCCCTGGGTGGTCATAGAAGTACTTATGTACCGGTTAAGGCAGACCGTATTTTACATGATAAGGATAAGATAACCTTAGGTGGGATGGAGCTCGTTATGCTACATCATCCCGGTCATACCCAAGGTTCATGCAGTTTCCTGTTTAATGTCAAAGATGAAAGCAGAGTTTATAGCGTCCTGATAGCCAATATGCCAACAATTGTCACAGAAAAAAAGTTCTCCGAAGTAACGACCTATCCAGGCATTGCCAAAGATTATGCCTATACGCTGAATGCGATGAAAAAGCTGAAATTTGATATGTGGCTTTCCTCTCATGCCAGTCAGTTTGGACTGCTGACCAAACACAAGCCTGGTGATGCCTATAATCCTGCCGCATTTATTGATCAGAAGGGTTATGATTCAGCAATCCGAGATTTAGAAGATAAATTTCTCAGGAAAGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3006972","ARO_id":"45434","ARO_name":"PLN-1","CARD_short_name":"PLN-1","ARO_description":"PLN-1 is a PLN beta-lactamase.","ARO_category":{"43894":{"category_aro_accession":"3005434","category_aro_cvterm_id":"43894","category_aro_name":"PLN beta-lactamase","category_aro_description":"PLN beta-lactamases are class B3 beta-lactamases found in Pedobacter lusitanus.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5630":{"model_id":"5630","model_name":"PME-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"8005":{"protein_sequence":{"accession":"WP_063864599.1","sequence":"MFLYFTQIRAWPLAALLLFMLAACAGAPRAPDDATDTASDALAALELRNGGRLGVFALDAGSGRSLGWREDERFGMCSTFKLLLAATVLDAARQGRLDGTAPIHFSDDDLVPHSPVLREHLALGSSTLTAPELARATQLTSDNAAANLLIRKLGGPEAVTALWRASGDEVSRLDRLEPDMNLLPPGDLRDSTSPRAMAQHVARLFTSEMLVPEDRERLREWMVETGTGLARLRAATPPHWQAGDKTGSAIAPLMPNKTHDVAVFWPPGRAPVIVAAYYESDAHHAGRIRAQDEAVLAQVGRIAVAWAGD"},"dna_sequence":{"accession":"NG_049973.1","fmin":"100","fmax":"1030","strand":"+","sequence":"ATGTTCCTTTACTTCACACAGATCCGCGCATGGCCGCTGGCCGCATTGCTGCTGTTTATGCTGGCCGCATGCGCTGGCGCGCCGCGCGCTCCCGATGACGCAACCGATACCGCAAGCGATGCGCTGGCGGCACTGGAACTGCGCAACGGCGGGCGTCTGGGCGTGTTCGCGCTGGATGCCGGCAGTGGCCGCAGTCTGGGCTGGCGCGAAGACGAGCGCTTCGGCATGTGCTCGACATTCAAGCTGCTGCTGGCGGCCACGGTGCTGGATGCGGCACGGCAGGGCCGGCTCGACGGCACCGCACCGATCCACTTCAGCGATGACGATCTGGTGCCGCATTCACCGGTGCTGCGCGAACACTTGGCCCTCGGCAGCAGCACGCTGACCGCACCCGAACTGGCCCGCGCCACCCAGCTGACCAGCGACAACGCCGCCGCCAATCTGCTGATCCGCAAGTTGGGCGGGCCGGAAGCCGTCACCGCACTCTGGCGCGCCAGTGGCGATGAAGTGAGCCGGCTGGACCGGCTGGAGCCAGACATGAATCTGCTGCCGCCCGGCGACCTGCGCGACAGCACCTCGCCGCGCGCGATGGCGCAGCACGTGGCCCGTCTGTTCACCTCCGAGATGCTCGTACCCGAAGACCGTGAACGCCTGCGCGAATGGATGGTTGAAACCGGCACCGGCCTTGCCCGCCTGCGCGCCGCCACGCCACCGCACTGGCAGGCCGGCGACAAGACCGGTTCTGCAATCGCGCCGCTGATGCCGAACAAGACCCACGATGTCGCGGTGTTCTGGCCGCCGGGCCGGGCGCCGGTCATCGTCGCCGCGTATTACGAATCCGATGCCCACCATGCCGGCAGGATCCGCGCGCAGGACGAGGCCGTGCTGGCGCAGGTCGGGCGTATTGCGGTGGCCTGGGCGGGCGATTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006973","ARO_id":"45435","ARO_name":"PME-1","CARD_short_name":"PME-1","ARO_description":"PME-1 is a PME beta-lactamase.","ARO_category":{"43895":{"category_aro_accession":"3005435","category_aro_cvterm_id":"43895","category_aro_name":"PME beta-lactamase","category_aro_description":"PME beta-lactamases are class A beta-lactamases found in Gammaproteobacteria.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5631":{"model_id":"5631","model_name":"POM-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"8006":{"protein_sequence":{"accession":"WP_044403015.1","sequence":"MRTLTTLGLALLLAQPAVAAQAVLPQLQPYTAPAAWLTPVAPLRIADNTWHIGTASITALLVKTPEGAVLLDGGMPQVADHLLANMRELGVAPGDLKLILHSHAHIDHVGPLAAIKKATGAQLVSNAESAVLLQRGDSQDIHFGDDMVFAPVQVDRLVQDGETVELGGMTFTAHFTPGHTPGSLSWTWTDRRDGKPLRIAYSDSLSAPGYSLWMNPRFPKIAEAFRSGFAAVRALPCDLLITPHAEASGWDYTNAEHPNPSPMSCKAYADKAEAAFDAQLKKQRGG"},"dna_sequence":{"accession":"NG_049974.1","fmin":"100","fmax":"961","strand":"+","sequence":"GTGCGTACCCTGACCACCCTCGGCCTTGCCCTGCTGCTGGCCCAACCCGCCGTGGCCGCCCAGGCCGTCCTGCCGCAACTGCAGCCCTACACCGCCCCGGCCGCCTGGCTGACCCCGGTGGCACCGCTGCGCATCGCCGACAACACCTGGCACATCGGCACCGCCAGCATCACCGCGCTGCTGGTGAAGACGCCGGAAGGCGCCGTGCTGCTGGACGGCGGCATGCCCCAGGTGGCCGACCACCTGCTGGCCAACATGCGCGAGCTGGGTGTGGCGCCGGGCGACCTCAAGCTGATCCTGCACAGCCACGCCCACATCGATCACGTGGGCCCGCTGGCCGCCATCAAGAAGGCCACCGGCGCGCAACTGGTGAGCAACGCCGAATCGGCCGTGCTGCTGCAGCGCGGCGACAGCCAGGACATCCACTTCGGCGACGACATGGTCTTCGCCCCGGTGCAGGTGGACCGCCTGGTGCAGGACGGCGAAACCGTGGAGCTGGGCGGCATGACCTTCACCGCCCACTTCACCCCCGGGCACACCCCCGGCAGCCTGAGCTGGACCTGGACCGACCGCCGCGACGGCAAGCCCCTGCGCATCGCCTATAGCGACAGCCTGAGCGCCCCCGGCTACAGCCTGTGGATGAACCCGCGCTTCCCGAAGATCGCCGAGGCCTTCCGCAGCGGCTTCGCCGCCGTCCGCGCCCTGCCCTGCGACCTGCTGATCACCCCCCACGCCGAGGCTAGCGGCTGGGACTACACCAACGCCGAACACCCCAACCCGTCACCCATGAGCTGCAAGGCCTACGCCGACAAGGCCGAGGCCGCCTTCGACGCGCAACTGAAGAAGCAGCGCGGCGGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37066","NCBI_taxonomy_name":"Pseudomonas","NCBI_taxonomy_id":"286"}}}},"ARO_accession":"3006974","ARO_id":"45436","ARO_name":"POM-1","CARD_short_name":"POM-1","ARO_description":"POM-1 is a POM beta-lactamase.","ARO_category":{"43896":{"category_aro_accession":"3005436","category_aro_cvterm_id":"43896","category_aro_name":"POM beta-lactamase","category_aro_description":"POM beta-lactamases are class B3 beta-lactamases found in Pseudomonas otitidis.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5632":{"model_id":"5632","model_name":"POM-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"8007":{"protein_sequence":{"accession":"WP_140423326.1","sequence":"MRTLTTLGLALLLAQPAVAAQAVLPQLQPYTAPAAWLTPVAPLRIADNTWHIGTASITALLVKTPEGAVLLDGGMPQVADHLLANMRELGVAPGDLKLILHSHAHIDHVGPLAAIKKATGAQLVSNAESAVLLQRGDSQDIHFGDDMVFAPVQVDRLVQDGETVELGGMTFTAHFTPGHTPGSLSWTWTDRRDGKPLRIAYSDSLSAPGYSLWMNPRFPKIAEAFRSGFAAVRALPCDLLITPHAEASGWDYTNAEHPNPSPMSCKAYADKAEAAFDAQLKKQRSG"},"dna_sequence":{"accession":"NG_065446.1","fmin":"0","fmax":"861","strand":"+","sequence":"GTGCGTACCCTGACCACCCTCGGCCTTGCCCTGCTGCTGGCCCAACCCGCCGTGGCCGCCCAGGCCGTCCTGCCGCAACTGCAGCCCTACACCGCACCGGCCGCCTGGCTGACCCCGGTGGCACCGCTGCGCATCGCCGACAACACCTGGCACATCGGCACCGCCAGCATCACCGCGCTGCTGGTGAAGACGCCGGAAGGCGCCGTGCTGCTGGACGGCGGCATGCCCCAGGTGGCCGATCACCTGCTGGCCAACATGCGCGAGCTGGGTGTGGCGCCGGGCGACCTCAAGCTGATCCTGCACAGCCACGCCCACATCGATCACGTGGGCCCGCTGGCCGCCATCAAGAAGGCCACCGGCGCGCAACTGGTGAGCAACGCCGAATCGGCCGTGCTGCTGCAACGCGGCGACAGCCAGGACATCCACTTCGGCGACGACATGGTCTTCGCCCCGGTGCAGGTGGACCGCCTGGTGCAGGACGGCGAGACGGTGGAACTGGGCGGCATGACCTTCACCGCCCACTTCACCCCCGGGCACACCCCCGGCAGCCTGAGCTGGACCTGGACCGACCGCCGCGACGGCAAGCCCCTGCGCATCGCCTACAGCGACAGCCTGAGCGCCCCCGGCTACAGCCTGTGGATGAACCCGCGCTTCCCGAAGATCGCCGAAGCCTTCCGCAGCGGCTTCGCCGCCGTCCGCGCCCTGCCCTGCGACCTGCTGATCACCCCCCACGCCGAGGCCAGCGGCTGGGACTACACCAACGCCGAACACCCCAACCCGTCGCCCATGAGCTGCAAGGCCTACGCCGACAAGGCCGAGGCCGCCTTCGACGCGCAACTGAAGAAGCAGCGCAGCGGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3006975","ARO_id":"45437","ARO_name":"POM-2","CARD_short_name":"POM-2","ARO_description":"POM-2 is a POM beta-lactamase.","ARO_category":{"43896":{"category_aro_accession":"3005436","category_aro_cvterm_id":"43896","category_aro_name":"POM beta-lactamase","category_aro_description":"POM beta-lactamases are class B3 beta-lactamases found in Pseudomonas otitidis.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5633":{"model_id":"5633","model_name":"PST-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"475"}},"model_sequences":{"sequence":{"8008":{"protein_sequence":{"accession":"WP_043942497.1","sequence":"MKLLFAALFVVMFCGLARASDSLPELRIEKIAEGVYLHTSFQQVQGYGLVDANGLVVLDGQGAYIIDTPWSERDTAALVAWLQERNYQVKASVSTHFHDDRTAGIEYLNAISVPTYASARTNALLKQNGKALATETFDDAPLWLLEGKVEVFYPGAGHSVDNLVVWLPEQKLLNGGCFVRAAAAGTLGNTADAVVSEWAASAERLQRRYPDAQLVIPGHGVPGDVSLLEHTRKLALAATAKD"},"dna_sequence":{"accession":"NG_057439.1","fmin":"100","fmax":"829","strand":"+","sequence":"ATGAAATTATTGTTTGCGGCGCTATTTGTCGTGATGTTCTGCGGACTCGCTCGGGCTAGCGATTCGCTGCCGGAACTGCGGATCGAGAAGATCGCCGAGGGCGTTTATCTGCATACATCTTTCCAGCAAGTGCAAGGCTATGGCCTTGTCGATGCGAACGGTCTGGTGGTGCTGGACGGACAGGGCGCCTACATCATCGACACGCCCTGGTCGGAGCGCGACACAGCGGCGCTGGTGGCCTGGTTGCAGGAGCGCAACTATCAGGTCAAGGCCAGTGTTTCGACGCACTTTCATGACGACCGCACGGCGGGGATCGAGTATCTGAACGCTATCTCGGTACCGACCTATGCCTCGGCACGGACCAATGCGTTGCTGAAGCAGAACGGCAAGGCGCTGGCGACCGAGACATTCGACGATGCGCCTTTATGGCTGCTCGAGGGCAAGGTCGAGGTCTTCTATCCCGGTGCTGGGCATAGCGTGGATAACCTCGTCGTGTGGTTGCCGGAGCAGAAGCTGCTGAACGGCGGGTGTTTCGTTCGGGCTGCGGCGGCCGGCACGCTGGGTAACACCGCCGATGCGGTCGTCAGCGAGTGGGCCGCTTCGGCAGAAAGGCTGCAGCGTCGATATCCCGATGCGCAGCTCGTCATTCCGGGTCATGGTGTGCCGGGAGATGTTTCCTTGCTCGAACACACGCGAAAACTTGCCTTGGCGGCAACTGCGAAAGATTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36856","NCBI_taxonomy_name":"Pseudomonas stutzeri","NCBI_taxonomy_id":"316"}}}},"ARO_accession":"3006976","ARO_id":"45438","ARO_name":"PST-1","CARD_short_name":"PST-1","ARO_description":"PST-1 is a PST beta-lactamase.","ARO_category":{"43897":{"category_aro_accession":"3005437","category_aro_cvterm_id":"43897","category_aro_name":"PST beta-lactamase","category_aro_description":"PST bea-lactamases are class B1 beta-lactamases found in Pseudomonas stutzeri.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5634":{"model_id":"5634","model_name":"PST-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"475"}},"model_sequences":{"sequence":{"8009":{"protein_sequence":{"accession":"WP_150823494.1","sequence":"MKLLFAALFVVMFCGLARAGDSLPELRIEKIAEGVYLHTSFQQVQGYGLVDANGLVVLDGQGAYIIDTPWSERDTAALVAWLQERNYQVKASVSTHFHDDRTAGIEYLNAISVPTYASARTNALLKQNGKALATETFDDAPLWLLEGKVEVFYPGAGHSVDNLVVWLPEQKLLNGGCFVRAAAAGTLGNTADAVVSEWAASAERLQRRYPDAQLVIPGHGVPGDVSLLEHTRKLAVAATAKD"},"dna_sequence":{"accession":"NG_066543.1","fmin":"0","fmax":"729","strand":"+","sequence":"ATGAAATTATTGTTTGCGGCGCTATTTGTCGTGATGTTCTGCGGACTCGCTCGGGCTGGCGATTCGCTGCCGGAACTGCGGATCGAGAAGATCGCCGAGGGCGTTTATCTGCATACATCTTTCCAGCAAGTGCAAGGCTATGGCCTTGTCGATGCGAACGGTCTGGTGGTGCTGGACGGACAGGGCGCCTACATCATCGACACGCCCTGGTCGGAGCGCGACACAGCGGCGCTGGTGGCCTGGTTGCAGGAGCGCAACTATCAGGTCAAGGCCAGTGTTTCGACGCACTTTCATGACGACCGCACGGCGGGGATCGAGTATCTGAACGCTATCTCGGTACCGACCTATGCCTCGGCACGGACCAATGCGTTGCTGAAGCAGAACGGCAAGGCGCTGGCGACCGAGACATTCGACGATGCGCCTTTATGGCTGCTCGAGGGCAAGGTCGAGGTCTTCTATCCCGGTGCTGGGCATAGCGTGGATAACCTCGTCGTGTGGTTGCCGGAGCAGAAGCTGCTGAATGGCGGGTGTTTCGTTCGGGCTGCGGCTGCCGGCACGCTGGGTAACACCGCCGATGCGGTCGTCAGCGAGTGGGCCGCTTCGGCAGAAAGGCTGCAGCGTCGATATCCCGATGCGCAGCTCGTCATTCCGGGTCATGGCGTGCCGGGAGATGTTTCCTTGCTCGAACACACGCGAAAACTTGCCGTGGCGGCAACTGCGAAGGATTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37066","NCBI_taxonomy_name":"Pseudomonas","NCBI_taxonomy_id":"286"}}}},"ARO_accession":"3006977","ARO_id":"45439","ARO_name":"PST-2","CARD_short_name":"PST-2","ARO_description":"PST-2 is a PST beta-lactamase.","ARO_category":{"43897":{"category_aro_accession":"3005437","category_aro_cvterm_id":"43897","category_aro_name":"PST beta-lactamase","category_aro_description":"PST bea-lactamases are class B1 beta-lactamases found in Pseudomonas stutzeri.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5635":{"model_id":"5635","model_name":"PSV-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"575"}},"model_sequences":{"sequence":{"8010":{"protein_sequence":{"accession":"WP_075226241.1","sequence":"MLRFLEESCVPMRRFACALAFTLSLPLASEAGPLMDTVGQLETEVGGRIGVVLRHTGSDWAVEHREDERFPMASTFKALLCGAVLSRVDRGEESLDDLVTYKATELVSYSPVTKNHVASGMSVGQLCEATVTMSDNSAANLLLKRVDGPEGLTRFLRGLGDRVTRLDRNEPAMNEARRGDPRDTTSPSAVLKTLDRLLFEGVLLPSSRAQLQQWMVDDKVADVLIRKHLPKGWRIADKSGAGHNGSRGIISVIWPETGQPYLAAAYMTGSDASIKQRNAVIAEIGKAMIEEIKQR"},"dna_sequence":{"accession":"NG_052626.1","fmin":"100","fmax":"988","strand":"+","sequence":"ATGTTGCGTTTTTTAGAGGAAAGCTGCGTTCCTATGAGGCGGTTTGCATGTGCGTTGGCCTTCACGTTGAGCTTGCCCTTAGCCAGCGAGGCGGGGCCACTGATGGATACAGTCGGTCAGTTGGAGACTGAGGTTGGAGGGCGCATTGGTGTGGTGTTGCGCCATACCGGATCTGACTGGGCCGTTGAGCATCGGGAGGATGAGCGCTTTCCCATGGCCAGCACGTTCAAGGCACTGCTCTGCGGAGCCGTTTTAAGCCGTGTTGATCGCGGTGAAGAGAGCCTTGATGATCTTGTCACTTACAAAGCAACCGAGCTCGTCTCTTATTCTCCTGTCACCAAGAACCATGTGGCTTCTGGAATGAGTGTTGGCCAGCTGTGTGAAGCGACGGTCACCATGAGCGATAACAGTGCTGCAAACTTGCTTTTGAAACGCGTTGATGGGCCGGAAGGGCTGACCAGATTCTTACGTGGGCTTGGTGATCGGGTGACGCGTCTGGACCGGAATGAGCCAGCTATGAACGAAGCCAGGCGCGGAGATCCCCGTGATACTACTTCGCCTTCTGCTGTGCTCAAGACATTGGACAGGTTGCTGTTTGAGGGTGTGTTGCTTCCGTCTTCCCGCGCACAGCTGCAGCAATGGATGGTGGATGACAAAGTTGCGGATGTGTTGATCCGAAAGCATCTGCCGAAGGGCTGGCGCATTGCAGACAAGAGCGGTGCTGGTCACAATGGTTCGCGTGGGATTATCAGTGTTATCTGGCCGGAAACGGGACAGCCATATCTTGCAGCAGCCTATATGACGGGCAGTGATGCGAGTATTAAGCAGCGCAATGCGGTGATCGCTGAGATTGGGAAGGCGATGATTGAGGAGATTAAACAGCGTTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3006978","ARO_id":"45440","ARO_name":"PSV-1","CARD_short_name":"PSV-1","ARO_description":"PSV-1 is a PSV beta-lactamase.","ARO_category":{"43898":{"category_aro_accession":"3005438","category_aro_cvterm_id":"43898","category_aro_name":"PSV beta-lactamase","category_aro_description":"PSV beta-lactamases are class A beta-lactamases found in Pseudovibrio.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5636":{"model_id":"5636","model_name":"RAHN-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"8011":{"protein_sequence":{"accession":"WP_063864600.1","sequence":"MMKNTLRKTALMAAAVVPMLAFSAASWAQTATKMTSVQQQLTALEKESGGRLGVMLIDTADNSQIAYRADERFAMCSTSKFMAASAILKESEVKKNLLTQHVALKQSDLVNYNPITEKHLNDGMTIGELAAAALQYSDNAAMNKLIEHLGGPHKVTDYARTLGDKTFRLDRTEPTLNTAIPGDDRDTTSPRAMALSLQHATLGSALAEPQRAQLVEWMKGNTTGAMSIRAGLPATWVVGDKTGSGDYGTTNDIAVIWPENKAPLVLVTYFTQPEKDAKSRRDVLASAAKIVTQGY"},"dna_sequence":{"accession":"NG_049975.1","fmin":"100","fmax":"988","strand":"+","sequence":"ATGATGAAAAATACCCTGCGTAAAACAGCACTGATGGCGGCGGCTGTAGTGCCAATGCTCGCATTCAGTGCGGCGTCCTGGGCGCAAACAGCGACGAAAATGACGTCAGTTCAGCAACAGTTGACGGCGCTGGAAAAAGAAAGCGGCGGGCGTCTGGGCGTGATGCTGATTGATACGGCGGACAACTCGCAAATTGCTTATCGTGCGGATGAACGTTTTGCGATGTGCAGCACCAGTAAGTTCATGGCGGCTTCGGCGATCCTGAAAGAGAGTGAAGTTAAGAAGAATCTGCTTACTCAGCATGTTGCGCTGAAACAATCGGATCTGGTGAATTACAACCCGATTACCGAAAAGCATCTTAACGATGGCATGACGATTGGGGAGCTGGCCGCGGCGGCCTTGCAGTACAGTGATAACGCCGCCATGAATAAGCTTATCGAGCATCTCGGCGGGCCACATAAGGTCACGGATTATGCACGTACGCTGGGTGACAAAACGTTCCGTCTGGACCGCACCGAACCGACGCTGAACACCGCGATCCCGGGCGATGACCGTGATACCACGTCACCGCGTGCAATGGCCCTGAGCCTGCAACATGCCACGCTGGGCTCCGCGCTGGCTGAACCGCAGCGCGCGCAACTGGTGGAATGGATGAAGGGTAACACCACCGGCGCGATGAGCATCCGCGCAGGTTTACCGGCGACCTGGGTTGTTGGCGATAAAACCGGCAGCGGCGATTACGGCACCACCAATGATATCGCGGTGATCTGGCCGGAAAATAAAGCGCCGCTGGTGCTGGTGACGTATTTCACCCAACCAGAAAAAGATGCAAAATCCCGTCGTGATGTGCTGGCAAGTGCGGCGAAGATTGTGACGCAGGGTTATTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3006979","ARO_id":"45441","ARO_name":"RAHN-1","CARD_short_name":"RAHN-1","ARO_description":"RAHN-1 is a RAHN beta-lactamase.","ARO_category":{"43899":{"category_aro_accession":"3005439","category_aro_cvterm_id":"43899","category_aro_name":"RAHN beta-lactamase","category_aro_description":"RAHN beta-lactamases are class A beta-lactamases found in Rahnella aquatilis.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5637":{"model_id":"5637","model_name":"RAHN-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"8012":{"protein_sequence":{"accession":"WP_063864601.1","sequence":"MMKNTLRKTVLMAAAVVPMLAFSAVSWAQTATKMTSVQQQLTALEKESGGRLGVMLINTEDNSQIAYRADERFAMCSTSKFMAASAILKQSETQTELLNRRVSLTRSDLVNYNPITEKHLDTGMTVGELAAAALQYSDNTAMNKLIEQLGGPQKVTEYARTLGDKTFRLDRTEPTLNTAIPGDDRDTTSPRAMALSLQHVTLGSALAEPQRAQLVEWMKGNTTGAMSIRAGLPATWVVGDKTGSGDYGTTNDIAVIWPDNKAPLILITYFTQPQKDAKSRRDVLASAAKIVTPGY"},"dna_sequence":{"accession":"NG_049976.1","fmin":"100","fmax":"988","strand":"+","sequence":"ATGATGAAAAATACCCTGCGTAAAACTGTGCTGATGGCGGCGGCTGTAGTGCCAATGCTCGCATTCAGTGCGGTGTCATGGGCGCAAACGGCGACAAAAATGACGTCAGTTCAGCAACAGTTGACGGCGCTGGAAAAAGAAAGCGGCGGGCGTCTTGGTGTGATGCTGATTAATACTGAAGACAATTCCCAGATTGCTTACCGCGCTGATGAACGTTTTGCCATGTGCAGCACCAGCAAGTTCATGGCCGCGTCAGCCATTCTTAAACAGAGCGAAACGCAAACGGAGTTGCTGAACCGCCGCGTCAGCCTCACCAGATCTGATCTGGTAAATTATAACCCGATCACCGAAAAGCATCTCGATACCGGCATGACGGTAGGCGAACTGGCCGCCGCCGCCTTGCAGTACAGCGATAATACCGCCATGAATAAACTGATTGAGCAGCTTGGTGGCCCGCAGAAAGTCACGGAATACGCCCGTACGCTCGGCGATAAAACGTTCCGGCTGGACCGCACTGAACCAACGCTGAACACCGCCATTCCGGGGGATGACCGCGACACCACTTCACCGCGTGCGATGGCTCTGAGTCTGCAACACGTCACGCTGGGCAGCGCGCTGGCTGAACCACAACGCGCGCAACTGGTGGAATGGATGAAAGGCAACACGACCGGCGCGATGAGTATCCGTGCGGGGCTGCCTGCGACCTGGGTGGTCGGCGATAAAACCGGCAGCGGCGATTACGGCACAACCAATGATATTGCGGTGATCTGGCCGGATAATAAGGCACCACTGATCCTGATTACCTATTTCACCCAGCCGCAGAAAGACGCGAAATCCCGCCGCGATGTGCTGGCTTCTGCTGCGAAGATTGTGACGCCGGGTTATTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3006980","ARO_id":"45442","ARO_name":"RAHN-2","CARD_short_name":"RAHN-2","ARO_description":"RAHN-2 is a RAHN beta-lactamase.","ARO_category":{"43899":{"category_aro_accession":"3005439","category_aro_cvterm_id":"43899","category_aro_name":"RAHN beta-lactamase","category_aro_description":"RAHN beta-lactamases are class A beta-lactamases found in Rahnella aquatilis.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5638":{"model_id":"5638","model_name":"RSA2-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"8013":{"protein_sequence":{"accession":"WP_128268281.1","sequence":"MANTTICRLCAVSQAGLSLGETLIKGQVMSFLRSAAIFAAVLLPLSAHAADLDQTIEALENRLDARIGVAIHDTGTGKVWGHREDERFLMNSTIKVPLCAAVLSRSDVDLSEELPVRAEDILEYAPVTEQHVGGTMTVADLCFATIDQSDNTAANLLFGRLGGPESLTTFLRSIGDDLTRSDRLEPDLNIWSAGDPRDTTTPAAMVRTLEAMLTGDALTATAREQLADWMRPGGVTGALMRPSVPHNWDVADKSGSGSNTRNLIAMLTPPDGAPIFVSLSISEAEVDFATRNAALVELSAAVVRSLHAQN"},"dna_sequence":{"accession":"NG_063889.1","fmin":"0","fmax":"933","strand":"+","sequence":"ATGGCAAACACAACGATTTGTCGCCTGTGCGCCGTGTCGCAGGCTGGTCTATCCCTCGGCGAGACTCTTATAAAAGGACAAGTCATGTCATTCCTCCGCTCTGCTGCCATTTTCGCGGCAGTTCTGCTCCCGCTTTCGGCCCATGCGGCCGACCTTGACCAGACCATCGAGGCACTTGAGAACCGGCTAGATGCGCGTATTGGCGTCGCCATCCACGATACCGGAACCGGCAAGGTTTGGGGCCACCGCGAGGATGAGCGGTTCCTGATGAACAGCACCATCAAGGTGCCGCTTTGCGCGGCTGTCCTGTCTCGCAGTGATGTGGACCTTTCCGAAGAACTGCCCGTGCGCGCCGAAGACATCCTCGAATACGCGCCCGTCACCGAGCAACATGTCGGTGGAACGATGACGGTGGCCGATCTGTGCTTTGCGACGATCGACCAGAGTGACAACACCGCCGCGAACCTGCTGTTTGGTCGGCTGGGTGGACCGGAAAGCCTGACGACATTTCTGCGCAGCATCGGCGACGACCTGACCCGCTCGGACCGGCTCGAGCCGGATCTAAACATCTGGTCGGCCGGTGATCCGCGCGACACCACAACCCCCGCCGCCATGGTGCGCACGCTTGAGGCGATGCTGACAGGGGACGCGCTGACCGCCACTGCACGGGAGCAACTGGCCGACTGGATGCGACCGGGCGGGGTCACCGGCGCGCTCATGCGTCCTTCGGTGCCGCACAACTGGGATGTGGCCGACAAGTCAGGCAGCGGAAGCAACACTCGTAATCTGATCGCGATGCTGACGCCGCCTGATGGCGCACCGATCTTCGTCAGTCTCTCGATCTCCGAAGCCGAAGTCGATTTCGCCACGCGAAACGCTGCCTTGGTCGAACTTTCGGCGGCCGTGGTGAGGAGCTTGCACGCACAAAACTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36791","NCBI_taxonomy_name":"uncultured bacterium","NCBI_taxonomy_id":"77133"}}}},"ARO_accession":"3006981","ARO_id":"45443","ARO_name":"RSA2-1","CARD_short_name":"RSA2-1","ARO_description":"RSA2-1 is a RSA2 beta-lactamase.","ARO_category":{"43900":{"category_aro_accession":"3005440","category_aro_cvterm_id":"43900","category_aro_name":"RSA2 beta-lactamase","category_aro_description":"RSA2 beta-lactamases are class A beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5639":{"model_id":"5639","model_name":"RSD2-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8014":{"protein_sequence":{"accession":"WP_128268284.1","sequence":"MQTNLIYAMEENAQIKTLFEAADVNATFILYDLQKDTIVGYDKVRSEKRYLPASTFKIANSLIGLATGAVKTEDEPIPYNGPSNPFIAAWKEDMGLKKAIAMSNVPIYQELARRIGLTRMQKYLKDLHYGNESVGEHVDRFWLDGPLQISAVEQVLFLKGLVQETLPFSKNIQKDVKSILLIEKTNAYRLYGKTGYGKTGWQNAPEKGIGWFVGWIEKSEGTYIFAFNMDMTDMSDAPKRINLSKTCLTILGLLNSE"},"dna_sequence":{"accession":"NG_063892.1","fmin":"0","fmax":"774","strand":"+","sequence":"ATGCAAACGAACCTGATTTACGCAATGGAAGAGAATGCTCAGATTAAAACGCTCTTTGAAGCAGCAGATGTTAATGCCACCTTTATTCTTTATGACCTGCAAAAAGACACCATAGTTGGATATGATAAGGTAAGGTCGGAAAAAAGGTATCTCCCTGCATCGACTTTCAAAATTGCTAATTCTCTCATTGGCTTGGCAACAGGTGCCGTTAAAACGGAAGATGAACCAATACCTTACAATGGCCCCAGCAATCCGTTTATAGCGGCATGGAAGGAAGATATGGGCTTGAAAAAAGCTATTGCTATGTCCAATGTGCCTATTTATCAGGAGTTGGCCCGAAGAATTGGATTAACGAGGATGCAAAAGTATTTAAAAGATCTTCATTATGGCAATGAATCGGTGGGAGAACATGTAGATCGTTTTTGGCTGGATGGACCACTTCAAATCAGTGCTGTGGAACAAGTGCTGTTTCTAAAAGGGCTAGTCCAGGAAACGCTCCCTTTTTCAAAAAACATCCAAAAAGATGTCAAGAGTATTCTCCTAATTGAAAAAACCAATGCTTATAGACTGTATGGAAAAACAGGCTATGGAAAAACAGGCTGGCAAAATGCTCCCGAAAAAGGCATAGGATGGTTTGTAGGATGGATTGAAAAGTCAGAAGGAACATACATTTTTGCATTCAATATGGACATGACTGATATGTCTGATGCCCCAAAGCGTATAAATCTGAGCAAAACTTGTTTAACAATTTTGGGGCTTCTCAATAGCGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36791","NCBI_taxonomy_name":"uncultured bacterium","NCBI_taxonomy_id":"77133"}}}},"ARO_accession":"3006982","ARO_id":"45444","ARO_name":"RSD2-1","CARD_short_name":"RSD2-1","ARO_description":"RSD2-1 is a RSD2 beta-lactamase.","ARO_category":{"43901":{"category_aro_accession":"3005441","category_aro_cvterm_id":"43901","category_aro_name":"RSD2 beta-lactamase","category_aro_description":"RSD2 beta-lactamases are class D beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5640":{"model_id":"5640","model_name":"RSD2-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8015":{"protein_sequence":{"accession":"WP_128268285.1","sequence":"MQTNLIYAMEENAQIKTLFEAADVNATFILYDLQKDTIVGYDKVRSEKRYLPASTFKIANSLIGLATGAVKTVDEPIPYNGPSNPFIAAWKEDMGLKKAIAMSNVPIYQELARRIGLTRMQKYLKDLHYGNESVGEHVDRFWLDGPLQISAVEQVLFLKGLVQETLPFSKNIQKDVKSILLIEKTNAYRLYGKTGLQNAHEKGIGWFVGWIEKSEGTYIFAFNMDMTDMSDAPKRINLSKTCLTILGLLNSE"},"dna_sequence":{"accession":"NG_063893.1","fmin":"0","fmax":"759","strand":"+","sequence":"ATGCAAACGAACCTGATTTACGCAATGGAAGAGAATGCTCAGATTAAAACACTCTTTGAAGCAGCAGATGTTAATGCCACCTTTATTCTTTATGACCTGCAAAAAGACACCATAGTTGGATATGATAAGGTAAGGTCGGAAAAAAGGTATCTCCCTGCATCGACTTTCAAAATTGCTAATTCTCTCATTGGCTTGGCAACAGGTGCCGTTAAAACGGTAGATGAACCAATACCTTACAATGGCCCCAGCAATCCGTTTATAGCGGCATGGAAGGAAGATATGGGCTTGAAAAAAGCCATTGCTATGTCCAATGTGCCTATTTATCAGGAGTTGGCCCGAAGAATTGGATTAACGAGGATGCAAAAGTATTTAAAAGATCTTCATTATGGCAATGAATCGGTGGGAGAACATGTAGATCGTTTTTGGCTGGATGGACCACTTCAAATCAGTGCTGTGGAACAAGTGCTGTTTCTAAAAGGGCTAGTCCAGGAAACGCTCCCTTTTTCAAAAAACATCCAAAAAGATGTCAAGAGTATTCTCCTAATTGAAAAAACCAATGCTTATAGACTGTATGGAAAAACAGGCTTGCAAAATGCTCACGAAAAAGGCATAGGATGGTTTGTAGGATGGATTGAAAAGTCAGAAGGAACATACATTTTTGCATTCAATATGGACATGACTGATATGTCTGATGCCCCAAAGCGTATAAATCTGAGCAAAACTTGTTTAACAATTTTGGGGCTTCTCAATAGCGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36791","NCBI_taxonomy_name":"uncultured bacterium","NCBI_taxonomy_id":"77133"}}}},"ARO_accession":"3006983","ARO_id":"45445","ARO_name":"RSD2-2","CARD_short_name":"RSD2-2","ARO_description":"RSD2-2 is a RSD2 beta-lactamase.","ARO_category":{"43901":{"category_aro_accession":"3005441","category_aro_cvterm_id":"43901","category_aro_name":"RSD2 beta-lactamase","category_aro_description":"RSD2 beta-lactamases are class D beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5641":{"model_id":"5641","model_name":"RUB-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"575"}},"model_sequences":{"sequence":{"8016":{"protein_sequence":{"accession":"WP_072186106.1","sequence":"MKHFRLCLIPVLAAFSLPVFAHPATLDTIKDAESRLHGRVGYAELDLVSGKMMDSYRSDERFPMMSTFKVILCGAVLARVDAGQEQLDRRIRYRQNDLVEYSPVTEKHLAEGMNVGELCHAAITMSDNTAANLLISTLGGPSGLTAFLRKTGDSVSRLDRWETALNEALPGDERDTTTPESMARTLHNLLTGDALSAESRRQLMRWMEMDNVAGPLLRSVLPAGWFIADKTGAGERGSRGIVAALGPDGKPSRIVVIYLTGTKATMDERNKQIADIGAALINHW"},"dna_sequence":{"accession":"NG_054671.1","fmin":"0","fmax":"855","strand":"+","sequence":"ATGAAACATTTTCGTCTTTGCCTTATCCCCGTGCTTGCCGCATTTTCACTGCCGGTTTTTGCCCACCCGGCGACGCTGGATACCATTAAAGATGCTGAAAGCCGGCTCCACGGCCGAGTCGGCTATGCCGAGTTGGATCTCGTCAGCGGAAAAATGATGGATAGCTATCGCTCTGATGAACGCTTCCCCATGATGAGCACCTTTAAAGTTATTCTGTGCGGCGCGGTGTTAGCGCGGGTTGATGCCGGGCAGGAACAGCTTGATCGCCGTATCCGCTACCGTCAGAACGACCTGGTTGAGTACTCGCCGGTAACGGAGAAACATCTCGCAGAGGGGATGAACGTGGGGGAATTATGCCATGCCGCGATCACCATGAGCGATAACACGGCGGCAAACCTGTTGATCTCTACGCTCGGCGGGCCGTCGGGGCTGACCGCATTTTTGCGGAAAACGGGTGACTCGGTGAGCCGTCTCGACCGTTGGGAAACGGCGCTGAATGAAGCGTTGCCGGGTGACGAGCGTGATACCACCACGCCTGAGTCCATGGCGCGGACGCTGCATAATTTGTTAACGGGCGATGCCCTGAGCGCTGAGTCACGTCGGCAATTAATGCGCTGGATGGAAATGGATAACGTCGCCGGACCGCTTTTGCGTTCGGTGTTGCCGGCAGGGTGGTTTATTGCTGACAAAACCGGTGCGGGTGAGCGTGGTTCGCGTGGCATCGTGGCGGCGCTGGGGCCTGATGGTAAACCGTCGCGTATCGTCGTGATTTACCTGACGGGAACCAAGGCAACGATGGACGAGCGCAATAAGCAGATCGCCGATATCGGCGCTGCGCTGATAAATCACTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43824","NCBI_taxonomy_name":"Serratia rubidaea","NCBI_taxonomy_id":"61652"}}}},"ARO_accession":"3006984","ARO_id":"45446","ARO_name":"RUB-1","CARD_short_name":"RUB-1","ARO_description":"RUB-1 is a RUB beta-lactamase.","ARO_category":{"43902":{"category_aro_accession":"3005442","category_aro_cvterm_id":"43902","category_aro_name":"RUB beta-lactamase","category_aro_description":"RUB beta-lactamases are class A beta-lactamases found in Serratia rubidaea.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5642":{"model_id":"5642","model_name":"SFC-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"8017":{"protein_sequence":{"accession":"WP_024531321.1","sequence":"MSRTGRLSVFFSAIFPLLTLTNMAEAASQPPQVTVDKLKRLENDFGGRIGVYAIDTGSNKTFGYRANERFPLCSSFKGFLAAAVLSKSQQQEGLLNQRIRYDNRVMEPHSPVTEKQITTGMTVAELSAATLQYSDNGAANLLLEKLIGGPEGMTSFMRSIGDNVFRLDRWELELNSAIPGDDRDTSTPKAVAESMQKLAFGNVLGLTERHQLMDWFKGNTTGGARIRASVPANWVVGDKTGTCGVYGTANDYAVIWPVGHAPIVLAVYTSKPDKNSKHSDAVIADASRIVLESFNIDALRMATGKSIGF"},"dna_sequence":{"accession":"NG_049980.1","fmin":"81","fmax":"1011","strand":"+","sequence":"ATGTCACGCACCGGTCGACTGTCTGTATTTTTCTCTGCCATATTTCCCCTGTTGACTCTGACTAATATGGCGGAGGCGGCGTCCCAACCCCCACAAGTAACAGTGGATAAATTGAAAAGATTGGAAAATGATTTTGGAGGGCGAATTGGGGTTTATGCTATTGATACTGGCTCAAATAAAACTTTTGGTTATAGAGCTAACGAGCGTTTTCCTCTCTGTAGTTCATTTAAAGGCTTCCTTGCTGCGGCAGTATTATCGAAAAGCCAGCAGCAAGAGGGCTTACTGAACCAGCGAATTCGCTATGACAATCGAGTTATGGAGCCTCATTCTCCTGTGACTGAAAAACAGATTACGACCGGCATGACAGTTGCCGAGTTGTCTGCTGCCACTCTGCAGTACAGTGATAATGGAGCCGCCAACCTGTTGCTCGAAAAGCTTATTGGTGGCCCTGAAGGAATGACGTCGTTTATGCGTTCCATTGGTGACAATGTATTTCGTCTGGACCGATGGGAACTGGAGTTGAATTCCGCCATTCCTGGTGATGATAGAGATACATCAACACCCAAAGCTGTTGCAGAAAGTATGCAAAAGCTGGCATTTGGAAATGTGCTTGGATTAACGGAGCGCCACCAACTGATGGATTGGTTTAAAGGGAATACAACAGGAGGAGCAAGAATACGTGCAAGCGTACCTGCAAACTGGGTGGTTGGAGACAAAACGGGTACTTGTGGTGTCTATGGTACAGCCAACGATTATGCAGTGATCTGGCCTGTAGGGCATGCGCCAATTGTTCTGGCTGTCTATACATCAAAACCAGACAAAAATTCCAAACACAGCGATGCTGTTATAGCAGATGCATCGCGCATTGTTCTTGAAAGCTTTAATATTGACGCATTACGTATGGCTACAGGAAAGTCTATCGGCTTCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39675","NCBI_taxonomy_name":"Serratia fonticola","NCBI_taxonomy_id":"47917"}}}},"ARO_accession":"3006985","ARO_id":"45447","ARO_name":"SFC-1","CARD_short_name":"SFC-1","ARO_description":"SFC-1 is a SFC beta-lactamase.","ARO_category":{"43903":{"category_aro_accession":"3005443","category_aro_cvterm_id":"43903","category_aro_name":"SFC beta-lactamase","category_aro_description":"SFC beta-lactamases are class A beta-lactamases found in Serratia fonticola.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5643":{"model_id":"5643","model_name":"SFO-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"575"}},"model_sequences":{"sequence":{"8018":{"protein_sequence":{"accession":"WP_032489477.1","sequence":"MVKNTLRQTTLMVATVMPLLFGSAPLWAQSANAKANIQQQLSELEKNSGGRLGVALIDTADNSQILYRGDERFPMCSTSKVMAVSALLKQSEMDKNLLAKRMEIKQSDLVNYNPIAEKHLDTGMTLAELSAAAIQYSDNTAMNKILEHLGGPAKVTEYARTIGDKTFRLDRTEPTLNTAIPSDKRDTTSPLAMAKSLQTLTLGKALGEPQRAQLVEWMKGNTTGGASIRAGLPATWVVGDKTGSGDYGTTNDIAVIWPANHAPLVLVTYFTQPQQNAEARKDVLAAAAKIVTEGL"},"dna_sequence":{"accession":"NG_049982.1","fmin":"100","fmax":"988","strand":"+","sequence":"ATGGTTAAAAATACATTACGTCAAACCACCCTGATGGTCGCTACGGTTATGCCGCTGCTGTTCGGTAGCGCACCATTATGGGCTCAATCCGCTAATGCCAAAGCGAATATTCAGCAGCAACTGTCCGAGCTCGAGAAAAACTCCGGTGGCCGCCTTGGCGTGGCGCTGATCGATACCGCCGATAATTCGCAGATCCTGTATCGTGGGGATGAACGTTTTCCCATGTGTAGCACTAGCAAGGTGATGGCGGTGTCGGCGTTGTTAAAACAGAGCGAGATGGATAAAAATCTTTTGGCTAAGCGGATGGAAATCAAACAATCCGATCTGGTCAACTACAACCCGATCGCCGAAAAACACCTGGATACCGGGATGACCCTTGCAGAGCTCAGTGCCGCCGCCATCCAGTACAGTGACAACACGGCGATGAACAAGATCCTTGAGCATCTTGGCGGCCCGGCAAAAGTGACAGAGTATGCGCGTACTATTGGTGATAAAACCTTTCGTCTCGATCGTACCGAGCCTACTTTAAATACTGCCATTCCCAGCGATAAGCGTGACACTACCTCGCCGCTGGCGATGGCAAAAAGCCTGCAAACCCTAACTTTGGGCAAGGCGCTGGGTGAACCACAGCGTGCTCAACTGGTTGAATGGATGAAGGGGAACACTACCGGCGGAGCCAGCATTCGCGCAGGTCTGCCAGCCACGTGGGTGGTCGGTGATAAAACCGGCAGTGGTGATTACGGTACCACTAACGATATCGCCGTGATTTGGCCAGCGAACCACGCACCGTTGGTGTTGGTAACCTATTTCACTCAGCCACAGCAGAATGCAGAAGCCCGCAAAGACGTGTTGGCTGCTGCCGCTAAAATTGTCACCGAAGGGCTTTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3006986","ARO_id":"45448","ARO_name":"SFO-1","CARD_short_name":"SFO-1","ARO_description":"SFO-1 is a SFO beta-lactamase.","ARO_category":{"43904":{"category_aro_accession":"3005444","category_aro_cvterm_id":"43904","category_aro_name":"SFO beta-lactamase","category_aro_description":"SFO beta-lactamases are class A beta-lactamases found in Gammaproteobacteria.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5644":{"model_id":"5644","model_name":"SGM-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"8019":{"protein_sequence":{"accession":"WP_009821475.1","sequence":"MKIVTALGALALLAAPASAADRQKTPAQEPAPTGNLDNLMPAAPRYLVPQSALEQVRNPKEIEEETGGRLGVALVDRQGALLLGFNRDERFAMCSTFKAPLAAAVLTGADGGKFGLEGTIPFGKEDVLDYAPVVKKNLKRGRMSMEELARAAVEVSDNSAANLLLPMLGGPEGLTAFMRVHGDDVTRLDRTEPALNENAEGDPRDTTTPAAMAGLMARLFFRDLKAESADRLRAWFNASSTGDKRIKAGLPEGWTSGSKTGSCGTAYNDVALVKSPTGEEYILAIYLDRPTIDAKKAEAAIAEAARAALNFVGQARKSGLE"},"dna_sequence":{"accession":"NG_049983.1","fmin":"100","fmax":"1066","strand":"+","sequence":"ATGAAGATCGTCACCGCCCTTGGCGCCCTGGCGCTGCTCGCCGCGCCCGCCTCCGCCGCCGACCGTCAGAAGACCCCGGCGCAGGAGCCCGCGCCGACCGGCAATCTCGACAATCTCATGCCCGCCGCGCCGCGCTATCTGGTGCCGCAATCGGCGCTGGAGCAGGTCCGCAATCCCAAGGAGATTGAGGAGGAGACGGGCGGCCGCCTGGGCGTCGCGCTGGTCGACCGGCAGGGCGCGCTGCTCTTGGGCTTCAACCGTGACGAGCGGTTCGCCATGTGCTCGACCTTCAAGGCGCCGCTGGCCGCCGCCGTGCTGACCGGCGCGGATGGCGGCAAGTTCGGGCTGGAAGGGACCATCCCCTTCGGCAAGGAGGATGTGCTCGATTACGCGCCGGTGGTGAAGAAGAACCTCAAGCGCGGCCGCATGTCGATGGAGGAACTGGCGCGCGCGGCGGTGGAGGTCAGCGACAATAGCGCCGCCAATCTGCTGCTGCCGATGCTGGGCGGGCCGGAAGGGCTGACCGCCTTCATGCGCGTCCATGGCGATGACGTCACCCGGCTCGACCGCACTGAACCCGCGCTCAACGAAAATGCGGAAGGCGACCCGCGCGACACGACCACGCCCGCCGCCATGGCGGGCCTGATGGCGCGCCTCTTCTTCCGCGACCTGAAGGCGGAGAGCGCCGACCGCCTGCGCGCCTGGTTCAACGCCAGCAGCACCGGCGACAAGCGCATCAAGGCCGGCCTGCCAGAAGGCTGGACCTCGGGCAGCAAGACCGGCAGCTGCGGCACCGCCTATAATGACGTGGCGCTGGTCAAGTCCCCCACCGGCGAGGAATATATCCTCGCCATCTATCTCGACCGCCCAACCATCGACGCGAAGAAAGCCGAAGCCGCGATCGCCGAAGCCGCCCGCGCCGCGCTGAACTTCGTGGGGCAAGCGCGCAAGAGCGGCCTGGAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3006987","ARO_id":"45449","ARO_name":"SGM-1","CARD_short_name":"SGM-1","ARO_description":"SGM-1 is a SGM beta-lactamase.","ARO_category":{"43905":{"category_aro_accession":"3005445","category_aro_cvterm_id":"43905","category_aro_name":"SGM beta-lactamase","category_aro_description":"SGM beta-lactamases are class A beta-lactamases found in members of the Sphingobium genus.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5645":{"model_id":"5645","model_name":"SGM-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"8020":{"protein_sequence":{"accession":"WP_041385949.1","sequence":"MPRRLIFAALLLAAPAAAQQEAPRQSLLPPPPRYMVSESAMKSVRNPKEIETESGGRLGVALVDGKGALILGFNRDERFAMCSTFKAPLAAAVLAGAEGGKFGLEGQISFAKADLLDYAPVVRKNVKRGRMSMEELAAAAVEVSDNSAANLLLPMVGGPEGLTRFIRAHGDMVTRLDRNEPSLNENAEGDERDTTSPAAMAGLMGRLIFRDLAPESAGKLRGWLNASTTGANRIKAGLPKGWISGSKTGSCGTAYNDVALVKAPSGEEYILAIYLDRPTVDAKAAEAAIAETARAALDFVDKAQKTGLE"},"dna_sequence":{"accession":"NG_049984.2","fmin":"100","fmax":"1030","strand":"+","sequence":"TTGCCCAGGCGCCTGATATTCGCGGCCCTGCTGCTCGCCGCCCCGGCGGCCGCGCAGCAGGAAGCGCCGCGCCAGTCGCTGCTCCCGCCGCCGCCCCGCTATATGGTGAGCGAATCCGCCATGAAGTCGGTCCGCAATCCCAAGGAGATAGAGACGGAAAGCGGCGGCCGGCTGGGCGTGGCGCTGGTCGACGGCAAGGGCGCGCTGATCCTTGGTTTCAACCGGGACGAGCGTTTCGCCATGTGCTCGACCTTCAAGGCGCCGCTCGCCGCCGCCGTGCTGGCGGGCGCGGAAGGCGGCAAGTTCGGGCTGGAGGGGCAGATCAGCTTCGCCAAGGCCGATCTGCTGGACTATGCCCCGGTCGTCAGGAAGAATGTGAAGCGCGGCCGCATGTCGATGGAGGAACTCGCCGCCGCCGCCGTGGAGGTCAGCGACAACAGCGCGGCCAACCTGCTGCTGCCGATGGTCGGCGGGCCGGAGGGCCTGACCCGCTTCATCCGCGCCCATGGCGACATGGTGACGCGGCTCGACCGCAATGAGCCGTCTCTCAACGAGAATGCGGAGGGCGACGAGCGCGACACCACCAGCCCCGCCGCCATGGCCGGCCTGATGGGCCGCCTGATCTTCCGCGACCTCGCTCCGGAAAGCGCCGGAAAGCTGCGCGGCTGGCTCAATGCCAGCACCACCGGCGCCAACCGGATCAAGGCGGGCCTGCCCAAGGGCTGGATCTCCGGCAGCAAGACGGGAAGCTGCGGCACCGCCTATAATGACGTGGCGCTGGTGAAGGCCCCGTCGGGCGAGGAATATATCCTGGCCATCTATCTCGACCGCCCGACGGTCGACGCCAAGGCCGCCGAAGCCGCCATAGCCGAAACCGCCCGCGCCGCGCTGGATTTCGTGGATAAGGCGCAGAAGACCGGGCTGGAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3006988","ARO_id":"45450","ARO_name":"SGM-2","CARD_short_name":"SGM-2","ARO_description":"SGM-2 is a SGM beta-lactamase.","ARO_category":{"43905":{"category_aro_accession":"3005445","category_aro_cvterm_id":"43905","category_aro_name":"SGM beta-lactamase","category_aro_description":"SGM beta-lactamases are class A beta-lactamases found in members of the Sphingobium genus.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5646":{"model_id":"5646","model_name":"SGM-3","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"8021":{"protein_sequence":{"accession":"WP_007688792.1","sequence":"MPRRLIFAALLLAAPAAAQQEAPRPSLLPPPPRYMVSESAMRSVRNPKEIETESGGRLGVALVDGKGALILGFNRDERFAMCSTFKAPLAAAVLAGAEGGKFGLEGQISFAKADLLDYAPVVRKNVKRGRMSMEELAAAAVEVSDNSAANLLLPMVGGPEGLTRFIRAHDDMVTRLDRNEPSLNENAEGDERDTTSPAAMAGLMGRLIFRDLAPESAGKLRGWLNASTTGANRIKAGLPKGWTSGSKTGSCGTAYNDVALVKAPSGEEYILAIYLDRPTVDAKAAEAAIAETARAALDFVDKAQKTGLE"},"dna_sequence":{"accession":"NG_052647.1","fmin":"100","fmax":"1030","strand":"+","sequence":"TTGCCCAGGCGCCTGATATTCGCGGCCCTGCTGCTCGCCGCCCCGGCGGCCGCGCAGCAGGAAGCGCCGCGCCCGTCGCTGCTCCCGCCGCCGCCTCGCTATATGGTCAGCGAATCCGCCATGAGGTCGGTCCGCAATCCCAAGGAGATCGAGACCGAAAGCGGCGGCCGGCTGGGCGTGGCGCTGGTCGACGGCAAGGGCGCGCTGATCCTTGGTTTCAACCGGGACGAGCGTTTCGCCATGTGCTCGACCTTCAAGGCGCCGCTCGCCGCCGCCGTGCTGGCGGGCGCGGAAGGCGGCAAGTTCGGGCTGGAGGGGCAGATCAGCTTCGCCAAGGCCGATCTGCTGGACTATGCCCCGGTCGTCAGGAAGAATGTGAAGCGCGGCCGCATGTCGATGGAGGAACTCGCCGCCGCCGCCGTGGAAGTCAGCGACAACAGCGCGGCCAACCTGCTGCTGCCGATGGTCGGCGGGCCGGAGGGCCTGACCCGCTTCATCCGCGCCCATGATGACATGGTGACGCGGCTCGACCGCAATGAGCCGTCTCTCAACGAGAATGCGGAGGGCGACGAGCGCGACACCACCAGCCCCGCCGCCATGGCCGGCCTGATGGGCCGCCTGATCTTCCGCGACCTCGCTCCGGAAAGCGCCGGAAAGCTGCGCGGCTGGCTCAATGCCAGCACCACCGGCGCCAACCGGATCAAGGCGGGCCTGCCCAAGGGCTGGACCTCCGGCAGCAAGACGGGAAGCTGCGGCACCGCCTATAATGACGTGGCGCTGGTGAAGGCCCCGTCGGGCGAGGAATATATCCTGGCCATCTATCTCGACCGCCCGACGGTCGACGCCAAGGCCGCCGAAGCCGCCATAGCCGAAACCGCCCGCGCCGCGCTGGATTTCGTGGATAAGGCGCAGAAGACCGGGCTGGAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3006989","ARO_id":"45451","ARO_name":"SGM-3","CARD_short_name":"SGM-3","ARO_description":"SGM-3 is a SGM beta-lactamase.","ARO_category":{"43905":{"category_aro_accession":"3005445","category_aro_cvterm_id":"43905","category_aro_name":"SGM beta-lactamase","category_aro_description":"SGM beta-lactamases are class A beta-lactamases found in members of the Sphingobium genus.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5647":{"model_id":"5647","model_name":"SGM-4","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"8022":{"protein_sequence":{"accession":"WP_013846594.1","sequence":"MPRRLLLAALLLAGPASAQQEAPRQSLLPPPPRYMVSESAMKSVRNPKEIESESGGRLGVALVDSKGALILGFNRDERFAMCSTFKAPLAAAVLSGAEGNKFGLEGQIGFTKADLLDHAPVVKKNARRGRMSMEELAAAAVEVSDNSAANLLLPMIGGPEGFTRYVRAHGDNVTRLDRTEPALNENAEGDERDTTSPAAMAGLMRRLIFTDLKPESAARLRGWLNASTTGGNRIKAGLPKDWTSGSKTGTCGTAYNDVALVKAPSGEEYILAIYLDRPTVDAKAAEAAIAETARAALDFVGKAQKTGLE"},"dna_sequence":{"accession":"NG_049986.1","fmin":"100","fmax":"1030","strand":"+","sequence":"TTGCCCAGACGCCTGCTCCTTGCGGCCCTGCTGCTCGCCGGCCCGGCATCGGCGCAGCAGGAAGCGCCGCGTCAGTCGCTGCTGCCGCCGCCGCCCCGCTATATGGTGAGCGAATCCGCCATGAAGTCGGTCCGCAATCCCAAGGAGATCGAAAGCGAAAGCGGCGGTCGCCTGGGCGTGGCGCTGGTCGACAGCAAGGGCGCGCTGATCCTTGGCTTCAACCGCGACGAGCGTTTCGCCATGTGCTCGACCTTCAAGGCCCCGCTTGCCGCGGCCGTCCTGTCCGGCGCGGAAGGCAATAAATTCGGGCTGGAAGGCCAGATTGGCTTTACCAAGGCCGACCTGCTCGACCATGCGCCGGTGGTCAAGAAGAACGCCAGGCGCGGCCGCATGTCGATGGAGGAACTGGCCGCCGCCGCCGTGGAGGTCAGCGACAACAGTGCCGCCAACCTGCTGCTGCCGATGATCGGCGGCCCGGAAGGCTTCACCCGCTATGTTCGCGCCCATGGCGACAATGTGACGCGCCTCGACCGCACCGAACCGGCGCTCAACGAAAATGCCGAGGGCGACGAACGCGACACCACCAGCCCCGCCGCCATGGCCGGGTTGATGCGCCGCCTGATCTTCACCGATTTGAAGCCGGAAAGCGCCGCCAGACTGCGCGGCTGGCTGAACGCCAGCACCACGGGCGGCAACCGCATCAAGGCAGGACTGCCCAAAGACTGGACCTCCGGCAGCAAGACGGGGACATGCGGCACCGCCTATAATGACGTCGCGCTGGTGAAGGCGCCTTCGGGCGAGGAATATATACTCGCCATCTATCTCGACCGCCCCACGGTCGACGCCAAGGCCGCCGAAGCCGCCATAGCCGAAACCGCCCGCGCCGCGCTGGATTTCGTCGGCAAGGCGCAGAAGACGGGGCTGGAGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3006990","ARO_id":"45452","ARO_name":"SGM-4","CARD_short_name":"SGM-4","ARO_description":"SGM-4 is a SGM beta-lactamase.","ARO_category":{"43905":{"category_aro_accession":"3005445","category_aro_cvterm_id":"43905","category_aro_name":"SGM beta-lactamase","category_aro_description":"SGM beta-lactamases are class A beta-lactamases found in members of the Sphingobium genus.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5648":{"model_id":"5648","model_name":"SGM-5","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"8023":{"protein_sequence":{"accession":"WP_007708339.1","sequence":"MAVRKSLSFAALTACLLVAMPLSAAPKKKAPAKKAEDVPVLPTQLPPAPRYLVPQSALTSVRNPKEIEEETGGRMGIALVDRDGALILGFNRDDRFAMCSTFKAPLAAAVLIGAEGGKFGLDGEIPFTKDDILDYAPVVKKNRKRGRMSMAELAQAAVEVSDNSAANLLLPMLGGPEGLTAFMRAHGDKITRLDRNEPALNENIEGDGRDTTSPAAMAGLMSRLLFRDMQAADADRLRGWLNASTTGDKRIKAGLPEGWTSGSKTGSCGTAYNDVALVKAPSGEEYILAIYLDRPTVDQKAAEAAIAEAAHSALEFVSKAKKSGLD"},"dna_sequence":{"accession":"NG_049987.1","fmin":"100","fmax":"1081","strand":"+","sequence":"ATGGCCGTCCGCAAGTCCCTGTCCTTCGCGGCGCTGACCGCCTGCCTGCTTGTCGCCATGCCGCTGTCCGCCGCACCCAAGAAGAAGGCTCCCGCCAAGAAGGCTGAGGATGTGCCGGTCCTGCCGACACAGTTACCCCCGGCGCCCCGATATCTGGTGCCGCAATCGGCCCTGACCTCGGTCCGCAATCCAAAGGAAATCGAGGAGGAGACGGGCGGGCGCATGGGCATTGCGCTGGTCGACCGCGACGGCGCACTCATCCTTGGCTTCAATCGCGACGATCGCTTTGCCATGTGCTCGACCTTCAAGGCGCCGCTTGCCGCCGCCGTGCTGATCGGCGCGGAGGGCGGCAAATTTGGTCTGGATGGAGAGATCCCTTTCACCAAGGACGATATTCTCGATTACGCGCCTGTAGTGAAGAAGAACAGGAAGCGCGGACGCATGTCGATGGCCGAGTTGGCGCAGGCCGCAGTCGAAGTGAGCGACAACAGCGCCGCCAACCTGCTGCTGCCGATGCTGGGCGGTCCGGAAGGGCTGACTGCCTTCATGCGTGCCCATGGCGACAAGATTACCCGGCTCGATCGCAACGAACCGGCCCTTAACGAGAATATCGAGGGTGATGGGCGCGATACGACCAGTCCCGCCGCCATGGCCGGGCTGATGAGCCGGCTGCTGTTCCGGGACATGCAGGCGGCCGACGCTGACAGGCTGCGCGGCTGGCTCAATGCCAGCACCACCGGTGACAAGCGGATCAAGGCGGGCCTGCCCGAAGGCTGGACCTCGGGCAGCAAGACCGGCAGTTGCGGCACGGCCTATAATGACGTCGCGCTGGTAAAGGCGCCGAGCGGCGAGGAATATATATTGGCGATCTATCTCGATCGCCCGACCGTCGACCAGAAGGCAGCAGAGGCCGCGATCGCCGAAGCGGCCCATTCGGCGCTCGAATTTGTCAGCAAGGCGAAGAAGAGCGGACTGGACTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3006991","ARO_id":"45453","ARO_name":"SGM-5","CARD_short_name":"SGM-5","ARO_description":"SGM-5 is a SGM beta-lactamase.","ARO_category":{"43905":{"category_aro_accession":"3005445","category_aro_cvterm_id":"43905","category_aro_name":"SGM beta-lactamase","category_aro_description":"SGM beta-lactamases are class A beta-lactamases found in members of the Sphingobium genus.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5649":{"model_id":"5649","model_name":"SGM-6","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"8024":{"protein_sequence":{"accession":"WP_004207704.1","sequence":"MALRKSLSLAALTACLVVTLPLSAAPKKKAPAKKAEEVPTLPTLMPPAPRYLVPQSALTSVRNPKEIEEETGGRMGIALVDREGALILGFNRDDRFAMCSTFKAPLAAAVLIGAQGGKFGLEGEIPFTKDDILDYAPVVKKNKKRGRMSMAELAEAAVEVSDNSAANLLLPMLGGPEGLTSFIRAHGDKITRLDRIEPELNENVAGDPRDTTSPAAMAGLMGRLLFRDMQAADADRLRGWLNASTTGDKRIKAGLPEGWTSGSKTGSCGTAYNDVALVKSPAGEEYILAIYLDRPTVDDKKAEAAIAEAAHSALEFVSKAQKSGLD"},"dna_sequence":{"accession":"NG_049988.1","fmin":"100","fmax":"1081","strand":"+","sequence":"ATGGCGCTGCGCAAATCCCTGTCGCTGGCGGCGCTGACCGCCTGTCTCGTCGTGACCCTGCCGCTGTCGGCCGCGCCCAAGAAGAAGGCGCCGGCCAAGAAGGCCGAAGAGGTGCCGACCCTGCCGACATTGATGCCGCCCGCACCACGCTATCTGGTGCCGCAATCCGCGCTCACCTCCGTCCGCAATCCCAAGGAGATCGAGGAGGAAACGGGCGGGCGCATGGGCATCGCGCTGGTCGATCGCGAGGGCGCGCTGATCCTGGGCTTCAACCGCGATGATCGCTTTGCCATGTGCTCGACCTTCAAGGCGCCGCTGGCCGCCGCCGTGCTGATCGGCGCCCAGGGCGGCAAGTTCGGGCTGGAGGGGGAGATACCATTCACCAAGGACGATATTCTCGATTATGCGCCGGTGGTGAAGAAGAACAAGAAGCGCGGCCGCATGTCGATGGCCGAACTGGCCGAGGCGGCGGTCGAAGTGAGCGACAACAGCGCCGCCAACCTGTTGCTGCCGATGCTGGGCGGGCCGGAGGGGCTGACCTCCTTCATTCGTGCCCATGGCGACAAGATCACGCGGCTCGACCGTATCGAACCCGAGCTGAACGAGAATGTCGCCGGCGATCCCCGCGACACGACCAGTCCGGCGGCGATGGCCGGGCTGATGGGACGGTTGCTGTTCCGCGATATGCAGGCGGCCGATGCCGACAGGCTGCGCGGCTGGCTCAATGCCAGCACCACCGGCGACAAAAGGATCAAGGCGGGCCTGCCCGAAGGCTGGACGTCGGGCAGCAAGACCGGCAGCTGCGGCACCGCCTATAATGACGTCGCACTGGTGAAGTCGCCGGCGGGCGAGGAATATATATTGGCCATCTATCTCGACCGGCCGACCGTGGACGACAAGAAGGCCGAGGCGGCGATCGCCGAGGCCGCCCATTCGGCGCTGGAATTCGTCAGCAAGGCGCAGAAGAGCGGGCTGGACTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3006992","ARO_id":"45454","ARO_name":"SGM-6","CARD_short_name":"SGM-6","ARO_description":"SGM-6 is a SGM beta-lactamase.","ARO_category":{"43905":{"category_aro_accession":"3005445","category_aro_cvterm_id":"43905","category_aro_name":"SGM beta-lactamase","category_aro_description":"SGM beta-lactamases are class A beta-lactamases found in members of the Sphingobium genus.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5650":{"model_id":"5650","model_name":"SGM-7","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"8025":{"protein_sequence":{"accession":"WP_010337133.1","sequence":"MALRKSLSLAALTACLVVALPLSAAPKKKAPAKKVEEVPTLPTLLPPAPRYLVPQSALTSVRNPKEIEEETGGRMGIALVDREGALILGFNRDDRFAMCSTFKAPLAAAVLIGAQGGKFGLEGEIPFTKDDILDYAPVVKKNKKRGRMSMAELAAAAVEVSDNSAANLLLPMLGGPEGLTSFIRAHGDKITRLDRIEPDLNENIAGDPRDTTSPAAMAGLMGRLLFRDMAAADADRLRGWLNASTTGDKRIKAGLPEGWTSGSKTGSCGTAYNDVALVKSPAGEEYILAIYLDRPTVDDKKAEAAIAEAAHSALEFVSKAQKSGLN"},"dna_sequence":{"accession":"NG_050614.1","fmin":"100","fmax":"1081","strand":"+","sequence":"ATGGCGCTGCGCAAATCCCTCTCGCTCGCGGCGCTGACGGCCTGTCTGGTCGTGGCCTTGCCGTTGTCGGCCGCGCCCAAGAAGAAGGCGCCGGCCAAGAAGGTGGAAGAGGTGCCGACCCTGCCGACATTGTTGCCGCCGGCACCACGCTATCTGGTGCCGCAATCCGCGCTCACCTCCGTCCGCAATCCCAAGGAGATCGAGGAGGAGACCGGCGGGCGCATGGGCATCGCGCTGGTCGATCGCGAGGGTGCGCTGATCCTGGGTTTCAACCGCGATGATCGCTTTGCCATGTGCTCGACCTTCAAGGCGCCGCTGGCCGCCGCCGTGCTGATCGGCGCGCAGGGCGGCAAGTTCGGGCTGGAGGGGGAGATCCCCTTCACCAAGGACGATATTCTCGATTACGCGCCGGTCGTGAAGAAGAACAAGAAGCGTGGCCGCATGTCGATGGCCGAACTGGCCGCGGCGGCCGTGGAGGTCAGCGACAACAGTGCCGCCAACCTGTTGCTGCCGATGCTGGGCGGGCCGGAGGGGCTGACCTCCTTCATCCGCGCCCATGGCGACAAGATCACGCGGCTCGATCGCATCGAGCCGGACCTCAACGAGAATATTGCGGGCGATCCGCGCGACACGACCAGCCCGGCGGCGATGGCCGGGCTGATGGGGCGGCTGTTGTTCCGCGACATGGCAGCGGCCGATGCCGACAGGCTGCGCGGCTGGCTGAATGCCAGCACCACCGGCGACAAAAGGATCAAGGCTGGTCTGCCCGAAGGCTGGACCTCGGGCAGCAAGACCGGCAGCTGCGGTACCGCCTATAATGACGTCGCGCTGGTGAAGTCGCCGGCGGGCGAGGAATATATATTGGCCATCTATCTCGACCGGCCGACCGTGGACGACAAGAAGGCCGAGGCGGCGATCGCCGAAGCCGCCCATTCGGCGCTGGAGTTCGTCAGCAAGGCGCAGAAGAGCGGGCTGAACTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3006993","ARO_id":"45455","ARO_name":"SGM-7","CARD_short_name":"SGM-7","ARO_description":"SGM-7 is a SGM beta-lactamase.","ARO_category":{"43905":{"category_aro_accession":"3005445","category_aro_cvterm_id":"43905","category_aro_name":"SGM beta-lactamase","category_aro_description":"SGM beta-lactamases are class A beta-lactamases found in members of the Sphingobium genus.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5651":{"model_id":"5651","model_name":"SHN-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"475"}},"model_sequences":{"sequence":{"8026":{"protein_sequence":{"accession":"WP_011497575.1","sequence":"MRFILCLLLMVSSLTYAAQGPSKLKIVQLSDIVYQHTSLSDGDAYGVMAANGLIVIVGKQAYLIDTPWTEADTNTLIQWVTVKGLTIGGVIVTHFHQDSSGGLAVLNKLKINTYATTLTNQLLKANNREPASNEITSETFDLVPGVIQAYYPGAGHTQDNLVVWLAKSNLLFGGCLVQSFNNRKLLNIEDASIKDWPKSLQNVMVKYPNIDMVIPGHGQIGDVSLLELTQQLARKAL"},"dna_sequence":{"accession":"NG_059313.1","fmin":"100","fmax":"814","strand":"+","sequence":"ATGCGATTTATTCTGTGTCTATTGTTAATGGTATCCAGTCTCACTTATGCAGCTCAGGGGCCGTCAAAGCTCAAAATTGTGCAACTCTCCGATATTGTCTACCAGCATACCTCACTATCAGATGGTGACGCTTATGGCGTTATGGCTGCAAACGGCTTAATTGTTATCGTGGGCAAGCAAGCCTATTTGATTGACACCCCATGGACGGAAGCGGATACCAACACATTAATTCAATGGGTTACCGTTAAAGGCTTAACCATAGGTGGGGTCATAGTCACCCATTTTCATCAAGACTCCAGTGGCGGGCTTGCAGTATTAAATAAACTAAAAATAAATACCTATGCGACGACACTGACAAATCAATTGTTAAAAGCCAATAACCGTGAACCGGCAAGCAATGAAATCACTTCTGAGACCTTTGATCTAGTCCCAGGAGTGATCCAAGCTTATTACCCAGGTGCGGGTCATACCCAAGATAATCTTGTTGTCTGGTTAGCGAAATCTAATTTACTCTTTGGCGGTTGTTTAGTGCAGAGTTTTAACAATAGAAAACTGCTCAACATCGAAGATGCTTCAATTAAAGATTGGCCGAAATCATTGCAAAATGTCATGGTTAAATACCCAAACATAGATATGGTTATCCCAGGGCATGGCCAAATAGGGGACGTGAGTTTGTTAGAGCTAACCCAACAGCTTGCCAGAAAAGCCTTGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3006994","ARO_id":"45456","ARO_name":"SHN-1","CARD_short_name":"SHN-1","ARO_description":"SHN-1 is a SHN beta-lactamase.","ARO_category":{"43906":{"category_aro_accession":"3005446","category_aro_cvterm_id":"43906","category_aro_name":"SHN beta-lactamase","category_aro_description":"SHN beta-lactamases are class B1 beta-lactamases found in Shewanella denitrificans.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5652":{"model_id":"5652","model_name":"SHV-115","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"8027":{"protein_sequence":{"accession":"WP_156404661.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWHADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGKRGARGIVALLGPNNKAERIVVIYLRDTPASMAKRNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"NG_067162.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCACGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCAAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCAAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001164","ARO_id":"37544","ARO_name":"SHV-115","CARD_short_name":"SHV-115","ARO_description":"SHV-115 is an extended-spectrum beta-lactamase that has been found in clinical isolates.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5653":{"model_id":"5653","model_name":"SHV-116","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"8028":{"protein_sequence":{"accession":"WP_117062210.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWHADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"NG_068211.1","fmin":"100","fmax":"961","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCACGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001165","ARO_id":"37545","ARO_name":"SHV-116","CARD_short_name":"SHV-116","ARO_description":"SHV-116 is a beta-lactamase that has been found in clinical isolates.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5654":{"model_id":"5654","model_name":"SHV-132","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"8029":{"protein_sequence":{"accession":"WP_063864620.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMLSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"NG_050009.1","fmin":"100","fmax":"961","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGTTGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGGATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001341","ARO_id":"37741","ARO_name":"SHV-132","CARD_short_name":"SHV-132","ARO_description":"SHV-132 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5655":{"model_id":"5655","model_name":"SHV-146","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"8030":{"protein_sequence":{"accession":"WP_063864631.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGKRGARGIVALLGPNNKAERIVVIYLRDTPASMAKRNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"NG_050020.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACCCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCAAGCGGGGTGCGCGCGGCATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCAAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001346","ARO_id":"37746","ARO_name":"SHV-146","CARD_short_name":"SHV-146","ARO_description":"SHV-146 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5656":{"model_id":"5656","model_name":"SHV-171","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"8031":{"protein_sequence":{"accession":"WP_070984444.1","sequence":"MRFIRLCIIFLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"NG_068212.1","fmin":"100","fmax":"961","strand":"+","sequence":"ATGCGTTTTATTCGCCTGTGTATTATCTTCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACATCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGAGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATCGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3001355","ARO_id":"37755","ARO_name":"SHV-171","CARD_short_name":"SHV-171","ARO_description":"SHV-171 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5657":{"model_id":"5657","model_name":"SHV-190","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"8032":{"protein_sequence":{"accession":"WP_063864666.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALLEHWQR"},"dna_sequence":{"accession":"NG_050056.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTCACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAATGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGCATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTAGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGCTCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3003590","ARO_id":"40200","ARO_name":"SHV-190","CARD_short_name":"SHV-190","ARO_description":"SHV-190 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5658":{"model_id":"5658","model_name":"SHV-191","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"8033":{"protein_sequence":{"accession":"WP_063864667.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLVSGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIDDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"NG_050057.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGTCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACATCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGACGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3003591","ARO_id":"40201","ARO_name":"SHV-191","CARD_short_name":"SHV-191","ARO_description":"SHV-191 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5659":{"model_id":"5659","model_name":"SIM-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"8034":{"protein_sequence":{"accession":"WP_063864722.1","sequence":"MRTLLILCLFGTLNTAFAEEAQPDLKIEKIEEGIYLHTSFQEYKGFGIVKKQGLVVLDNHKAYLIDTPASAGDTEKLVNWLEKNDFTVNGSISTHFHDDSTAGIEWLNTKSIPTYASKLTNELLNKNGKTQAKHSFDKESFWLVKNKIEIFYPGPGHTQDNEVVWIPNKKILFGGCFIKPNGLGNLSDANLEAWPDSAKKMISKYSKAKLVIPSHSEIGDASLLKLTWEQAIKGLNESKSKPPLIN"},"dna_sequence":{"accession":"NG_050132.1","fmin":"0","fmax":"741","strand":"+","sequence":"ATGAGAACTTTATTGATTTTATGTTTATTCGGCACTTTAAATACCGCGTTTGCGGAAGAAGCCCAGCCAGATTTAAAAATTGAAAAAATAGAAGAAGGGATCTATCTTCATACATCTTTTCAAGAGTACAAGGGATTCGGCATCGTTAAAAAACAAGGCTTAGTAGTTCTTGACAATCACAAGGCATATCTCATCGACACTCCAGCTTCCGCAGGAGATACTGAAAAGCTAGTAAACTGGCTCGAAAAAAATGATTTCACTGTCAATGGAAGCATTTCAACACATTTCCACGACGACAGTACTGCTGGGATAGAGTGGCTTAATACAAAGTCCATCCCCACATATGCATCTAAATTGACAAATGAATTGCTAAATAAAAATGGCAAAACTCAAGCCAAGCACTCTTTTGATAAAGAGAGCTTTTGGTTGGTCAAAAATAAAATTGAAATTTTTTATCCAGGCCCAGGACACACTCAAGATAACGAAGTTGTCTGGATACCTAATAAAAAAATCCTATTCGGGGGCTGTTTTATAAAACCGAATGGCCTTGGCAATCTAAGTGACGCAAATTTGGAAGCTTGGCCAGACTCCGCAAAAAAAATGATATCAAAATACAGTAAGGCAAAACTTGTTATCCCAAGCCACAGTGAAATCGGAGACGCATCACTATTGAAACTCACATGGGAACAGGCCATTAAAGGTTTAAATGAAAGCAAATCAAAACCGCCGCTCATTAATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005494","ARO_id":"43956","ARO_name":"SIM-2","CARD_short_name":"SIM-2","ARO_description":"SIM-2 is a SIM beta-lactamase.","ARO_category":{"41370":{"category_aro_accession":"3004206","category_aro_cvterm_id":"41370","category_aro_name":"SIM beta-lactamase","category_aro_description":"SIM beta-lactamases are Class B beta-lactamases that are capable of hydrolyzing a wide variety of beta-lactams, including penicillins, narrow- to expanded-spectrum cephalosporins, and carbapenem. The SIM family of beta-lactamases appear to be transferable through integrons.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5660":{"model_id":"5660","model_name":"SPN79-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"8035":{"protein_sequence":{"accession":"WP_122630830.1","sequence":"MEEREMEMTKGSWMVAMAILGIAACAPAPAPQAATTRAVEVAGTPVIAPARADTLGDDIVIRHLAGRIWLHVTLSPDANRIPSNGLLVDEGDGVLLIDTAWDDEQTGRLAEWSLRRLGKPIRRSISTHFHDDRLGGIDTLRALGIDARALDLTVSKAREKGKASLPAIYMTVAQRARMDPAGFEVFHPGPGHSPDNIVVWFPAEGVLFGGCFVKGAESRDLGNLSDADVGRWPASVAAVLDRYPRASIVIPGHGAPGGLNLLSHTTALLAAPAHNGGG"},"dna_sequence":{"accession":"NG_062234.1","fmin":"0","fmax":"837","strand":"+","sequence":"ATGGAGGAACGGGAGATGGAGATGACGAAGGGCAGCTGGATGGTGGCCATGGCGATCCTGGGCATCGCCGCGTGCGCGCCCGCGCCGGCGCCGCAGGCCGCGACCACGCGGGCGGTCGAGGTGGCGGGGACGCCGGTGATCGCGCCGGCGAGGGCGGACACGCTGGGCGACGACATCGTGATCCGGCACCTGGCGGGGCGGATCTGGCTGCACGTGACGCTCTCCCCCGACGCGAACCGCATCCCCTCCAACGGCCTGCTGGTGGACGAGGGCGACGGCGTGCTCCTGATCGACACCGCGTGGGACGACGAGCAGACCGGCCGCCTGGCCGAGTGGAGCCTGCGCCGCCTGGGCAAGCCCATCCGCCGCTCCATCTCCACGCACTTCCACGACGACCGGCTGGGCGGCATCGACACGCTGCGGGCGCTCGGCATCGACGCCCGCGCGCTGGACCTGACAGTGTCGAAGGCGCGGGAGAAGGGGAAGGCGTCGCTGCCCGCCATCTACATGACGGTGGCGCAGCGCGCGCGGATGGACCCGGCGGGGTTCGAGGTCTTCCATCCCGGCCCGGGCCACTCGCCCGACAACATCGTCGTCTGGTTCCCGGCGGAGGGCGTGCTCTTCGGCGGCTGCTTCGTGAAGGGCGCCGAATCGCGCGACCTGGGCAACCTCTCCGACGCCGACGTGGGCCGCTGGCCCGCCTCCGTCGCCGCCGTCCTCGACCGCTATCCCCGCGCCTCCATCGTCATCCCCGGCCACGGCGCCCCCGGCGGGCTGAACCTGCTGTCGCACACTACCGCGCTCCTCGCCGCGCCGGCGCACAACGGTGGCGGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36791","NCBI_taxonomy_name":"uncultured bacterium","NCBI_taxonomy_id":"77133"}}}},"ARO_accession":"3006995","ARO_id":"45457","ARO_name":"SPN79-1","CARD_short_name":"SPN79-1","ARO_description":"SPN79-1 is a SPN79 beta-lactamase.","ARO_category":{"43907":{"category_aro_accession":"3005447","category_aro_cvterm_id":"43907","category_aro_name":"SPN79 beta-lactamase","category_aro_description":"SPN beta-lactamases are class B1 beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5661":{"model_id":"5661","model_name":"SPR-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"575"}},"model_sequences":{"sequence":{"8036":{"protein_sequence":{"accession":"WP_012145975.1","sequence":"MKKNLGYLTAMTVALCFGAQAQLNPAQPLSSAPPYSLFEQWAQPVAPFQMFPHVYYVGTRNLSSVLLSTPEGLILIDAALDASAPAIRAHIEALGFNIKDLRYILNSHARLDQAGGIARLQVWSGAKVVASAANAQQLALGGKQDFALGDALSFPPVKVDIIVGEGDSITLGDLKLTALMTPGHLPGATSWLTTLHQGGQSYRLVYADSLATPDYYLIDNKNYPSLVQDIRGSFARLAQQQADIFIVNKGTRFDLDNKMQRLQAGDLDAFVDRQGLQQYVQQSQQTFEAQLKQQQSKM"},"dna_sequence":{"accession":"NG_052102.1","fmin":"100","fmax":"997","strand":"+","sequence":"ATGAAAAAAAACCTTGGTTATCTGACGGCTATGACGGTTGCTCTGTGTTTCGGCGCTCAGGCGCAGCTTAATCCGGCACAGCCGTTGTCCAGTGCGCCGCCCTATTCGCTTTTTGAACAGTGGGCGCAGCCGGTCGCGCCATTTCAGATGTTCCCGCATGTTTATTACGTGGGCACCCGCAACCTATCGTCCGTGCTGCTGAGCACGCCGGAAGGACTGATTCTGATCGACGCCGCGCTGGACGCCAGCGCTCCGGCAATAAGAGCGCACATAGAGGCTTTGGGTTTTAACATCAAGGATCTGCGCTATATCCTCAATAGTCACGCGCGTCTCGATCAGGCGGGTGGCATTGCGCGTCTGCAAGTCTGGAGCGGGGCAAAAGTTGTCGCCAGCGCTGCCAATGCCCAACAGTTGGCGCTTGGCGGCAAACAGGATTTTGCTCTGGGAGATGCGCTGAGCTTCCCGCCGGTGAAGGTCGATATTATCGTCGGGGAGGGGGACAGCATTACCTTGGGCGACCTGAAATTAACGGCATTGATGACGCCAGGCCATTTGCCGGGGGCCACCTCGTGGCTGACCACGCTACATCAGGGAGGGCAAAGTTACCGACTGGTCTATGCTGATAGCCTGGCAACGCCGGACTACTATCTGATCGACAACAAAAACTACCCCAGTCTGGTGCAGGATATCCGTGGCAGTTTTGCTCGGTTGGCTCAGCAGCAGGCGGATATTTTTATCGTCAATAAGGGAACGCGCTTCGATCTGGATAATAAAATGCAACGCCTGCAGGCTGGCGATCTGGATGCGTTTGTCGATCGTCAGGGGTTGCAGCAATATGTGCAACAGTCACAACAGACATTTGAGGCGCAGTTAAAACAGCAACAAAGTAAAATGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3006996","ARO_id":"45458","ARO_name":"SPR-1","CARD_short_name":"SPR-1","ARO_description":"SPR-1 is a SPR beta-lactamase.","ARO_category":{"43908":{"category_aro_accession":"3005448","category_aro_cvterm_id":"43908","category_aro_name":"SPR beta-lactamase","category_aro_description":"SPR beta-lactamases are class B beta-lactamases found in Serratia proteamaculans.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5662":{"model_id":"5662","model_name":"SPS-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"8037":{"protein_sequence":{"accession":"WP_013255389.1","sequence":"MNLFRNYYNPIRNVMLIIFFVLTDLSLIAQTQPEYPVIRLNDELEVREILPNAFVITHKFPWGGNSLVVLIGEKYAVFVDTPYTPEATENVLDWINKQYGNRQFIEINTGYHVDNLGGNDALLHRNIPIIGSDKTVSLLRERGEATRQLTMGWLEGPGNEKFLKRHETIPYVGPSQIFQLTEGYHFTVGDEPIEVFFPGETHAPDNIVVYFPERKILFGGCMLRVGNGTGNRADANMDTWKSSVERLRDFDCVAVIPGHGIRFDPGVIENTISVLP"},"dna_sequence":{"accession":"NG_059316.1","fmin":"100","fmax":"931","strand":"+","sequence":"ATGAATCTTTTCAGGAATTACTATAATCCAATCCGTAATGTTATGTTAATTATTTTCTTTGTTCTAACTGACTTGTCGTTGATTGCGCAAACACAACCAGAATATCCTGTTATCAGATTAAATGACGAACTCGAAGTACGCGAAATTCTTCCCAATGCTTTTGTCATTACGCATAAATTCCCATGGGGGGGGAACTCGTTAGTTGTTTTGATCGGAGAAAAATATGCGGTCTTTGTCGACACTCCATATACTCCAGAGGCTACCGAGAACGTACTGGATTGGATAAATAAGCAATATGGTAATCGTCAATTCATTGAAATTAATACAGGTTACCATGTAGATAATCTTGGCGGAAACGATGCGCTTTTACACAGAAATATACCAATTATCGGTTCCGATAAAACTGTATCATTACTTCGTGAACGTGGGGAAGCCACTAGACAGCTAACAATGGGGTGGCTGGAAGGCCCGGGAAATGAAAAATTCTTGAAACGACATGAAACTATTCCCTATGTAGGACCATCGCAGATATTTCAATTAACGGAAGGGTATCATTTTACTGTGGGAGATGAACCAATTGAAGTTTTTTTCCCTGGGGAAACACATGCTCCTGATAACATAGTCGTGTATTTCCCAGAGCGAAAAATATTATTTGGTGGATGCATGTTGCGGGTAGGCAATGGAACTGGAAATAGAGCGGATGCAAACATGGATACATGGAAATCATCCGTGGAACGATTACGGGATTTCGATTGTGTTGCCGTAATTCCAGGACATGGAATTCGATTTGATCCTGGCGTAATTGAAAATACGATTTCTGTTTTGCCATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3006997","ARO_id":"45459","ARO_name":"SPS-1","CARD_short_name":"SPS-1","ARO_description":"SPS-1 is a SPS beta-lactamase.","ARO_category":{"43909":{"category_aro_accession":"3005449","category_aro_cvterm_id":"43909","category_aro_name":"SPS beta-lactamase","category_aro_description":"SPS beta-lactamases are class B1 beta lactamases found in Sediminispirochaeta smaragdinae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5663":{"model_id":"5663","model_name":"SPU-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"575"}},"model_sequences":{"sequence":{"8038":{"protein_sequence":{"accession":"WP_063864748.1","sequence":"MKKYFSFCLLGIFIFCFSQQNLKRDITKIIQGKNALVAVSVMNSKGKTEVNINGNKKVPMLSVFKFHIALAVLDLVDRGILDLEQNIFVKKSELLENTWSPIRDKYPNGNVNIPLREIIEHTVSQSDNNGCDILLRLIGGVDTVQKFIESKGIKDFAIKYNEEEMNKNGKSIYSNYTTANASSRLLQKFYNGEIISESSRDFLFRIMYETSTGADRLISLLPPDVIVAHKTGTSGIVSGIQAATNDVGIIILPDDEYYTISVFVINSKENTSTNEKIIADISKTVWDYYFQNK"},"dna_sequence":{"accession":"NG_050141.1","fmin":"0","fmax":"882","strand":"+","sequence":"ATGAAAAAATATTTTTCTTTTTGTCTTTTGGGGATTTTTATTTTTTGTTTTTCTCAACAAAATTTAAAAAGAGATATCACAAAGATTATACAAGGCAAGAATGCCCTTGTGGCGGTATCTGTGATGAACTCAAAAGGGAAAACAGAAGTAAATATTAACGGAAACAAAAAAGTTCCGATGCTTAGTGTGTTCAAATTTCACATTGCATTGGCAGTTTTGGATTTGGTGGACAGAGGTATTTTGGATTTGGAACAAAATATTTTTGTCAAGAAATCAGAACTTTTGGAGAATACTTGGAGCCCCATTCGTGATAAATATCCGAATGGCAATGTGAATATCCCTTTGAGAGAAATCATAGAACACACTGTTTCTCAGAGTGATAACAATGGTTGTGACATTCTGCTGAGGTTGATTGGAGGAGTTGATACTGTCCAGAAATTCATCGAGAGCAAGGGTATCAAAGATTTTGCGATAAAATACAATGAAGAAGAAATGAATAAGAATGGGAAATCCATCTACTCAAACTATACAACCGCAAACGCCTCCAGCAGGCTTCTGCAAAAATTTTATAATGGTGAGATAATTTCCGAGTCTTCCAGAGATTTTCTATTCAGAATCATGTATGAGACTTCTACTGGAGCAGACAGGCTCATATCCCTGCTTCCTCCAGATGTTATCGTTGCCCATAAAACAGGGACTTCTGGCATTGTATCTGGAATTCAGGCTGCTACCAATGATGTGGGAATCATCATTTTACCTGATGACGAATACTACACCATATCTGTTTTTGTGATAAATTCCAAAGAAAATACATCAACTAACGAAAAAATAATTGCTGATATATCAAAAACAGTGTGGGATTATTATTTTCAAAATAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3006998","ARO_id":"45460","ARO_name":"SPU-1","CARD_short_name":"SPU-1","ARO_description":"SPU-1 is a SPU beta-lactamase.","ARO_category":{"43910":{"category_aro_accession":"3005450","category_aro_cvterm_id":"43910","category_aro_name":"SPU beta-lactamase","category_aro_description":"SPU beta-lactamases are class A beta-lactamases found in Capnocytophaga sputigena.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5664":{"model_id":"5664","model_name":"SRT-3","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"725"}},"model_sequences":{"sequence":{"8039":{"protein_sequence":{"accession":"WP_033642964.1","sequence":"MTKMNRLAAALIAALILPTAHAAQQQDIDAVIQPLMKKYGVPGMAIAVSVDGKQQIYPYGVASKQTGKPITEQTLFEVGSLSKTFTATLAVYAQQQGKLSFSDPASHYLPELRGSAFDGVSLLNLATHTSGLPLFVPDDVTDNAQLMAYYRAWQPKHPAGSYRVYSNLGIGMLGMIAAKSLDRPFIQAMEQGMLPALGMSHTYIQVPAAQMANYAQGYNKDDKPVRVNPGPLDAESYGIKSNARDLIRYLDANLQQAKVAQPWREALAATHVGYYKAGVFTQDLMWENYPYPVKLSRLIEGNNAGMIMNGTPATAITPPQPELRAGWYNKTGSTGGFSTYAVFIPAKNIAVVMLANKWFPNDDRVEAAYRIVQALDKR"},"dna_sequence":{"accession":"NG_070754.1","fmin":"0","fmax":"1137","strand":"+","sequence":"ATGACGAAAATGAACCGCCTGGCGGCCGCGCTGATCGCCGCACTGATCTTGCCGACCGCGCACGCCGCGCAGCAGCAGGATATCGACGCCGTTATTCAGCCGCTGATGAAAAAATACGGCGTGCCGGGCATGGCGATCGCCGTATCGGTCGATGGCAAACAGCAGATTTACCCGTATGGCGTCGCCTCGAAACAGACCGGCAAACCGATCACCGAGCAGACGCTGTTCGAGGTGGGGTCGCTGAGCAAAACCTTCACCGCGACGCTGGCGGTCTATGCGCAGCAGCAGGGCAAGCTGTCGTTCAGCGATCCGGCCAGCCATTATCTGCCTGAGCTGCGCGGCAGCGCCTTCGACGGCGTCAGCCTGCTGAATCTGGCGACCCACACATCCGGCCTGCCGCTGTTCGTGCCGGACGACGTGACCGACAACGCCCAACTGATGGCTTACTACCGGGCCTGGCAGCCGAAGCACCCGGCGGGCAGCTACCGCGTCTATTCCAACCTCGGCATCGGCATGCTGGGCATGATCGCCGCCAAGAGCCTCGATCGGCCGTTTATCCAGGCCATGGAGCAGGGCATGCTGCCGGCGCTGGGCATGAGCCACACCTACATTCAGGTGCCGGCGGCGCAGATGGCCAACTATGCCCAGGGTTACAACAAGGACGATAAGCCGGTGCGCGTCAATCCCGGCCCGCTGGACGCCGAATCTTACGGCATCAAATCCAACGCCCGCGATCTGATTCGTTACCTGGACGCCAACCTGCAGCAGGCGAAGGTCGCGCAGCCGTGGCGCGAGGCGCTGGCCGCCACGCACGTCGGCTATTACAAAGCGGGCGTGTTCACGCAGGATCTGATGTGGGAGAACTACCCGTACCCGGTAAAACTGTCGCGGCTGATCGAGGGCAACAACGCCGGGATGATAATGAACGGCACGCCGGCCACCGCCATCACGCCGCCGCAGCCGGAGCTGCGCGCCGGTTGGTATAATAAAACCGGTTCGACCGGCGGTTTCTCCACCTACGCGGTGTTTATCCCGGCGAAAAATATCGCCGTGGTGATGCTGGCCAACAAATGGTTCCCGAACGACGATCGGGTCGAGGCGGCTTACCGCATCGTGCAAGCGCTGGATAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3006853","ARO_id":"45315","ARO_name":"SRT-3","CARD_short_name":"SRT-3","ARO_description":"SRT-3 is a SRT beta-lactamase.","ARO_category":{"36234":{"category_aro_accession":"3000095","category_aro_cvterm_id":"36234","category_aro_name":"SRT beta-lactamase","category_aro_description":"SRT beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5665":{"model_id":"5665","model_name":"SST-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"8040":{"protein_sequence":{"accession":"WP_063864750.1","sequence":"MTKMNRLAAALIAALILPTAHAAQQQDIDAVIQPLMKKYGVPGMAIAVSVDGKQQIYPYGVASKQTGKPITEQTLFEVGSLSKTFTATLAVYAQQQGKLSFNDPASRYLPELRGSAFDGVSLLNLATHTSGLPLFVPDDVTDNAQLMAYYRAWQPKHPAGSYRVYSNLGIGMLGMIAAKSLDQPFTQAMEQGMLPALGMRHTYVQVPAAQMANYAQGYNKDDKPVRVNPGPLDAESYGIKSNARDLIRYLDANLQQVKVAHAWREALTATHVGYYKAGAFTQDLMWENYPYPVKLSRLIEGNNAGMIMNGTPATAITPPQPELRAGWYNKTGSTGGFSTYAVFIPAKNIAVVMLANKWFPNDDRVEAAYRIVQALDKR"},"dna_sequence":{"accession":"NG_050144.1","fmin":"100","fmax":"1237","strand":"+","sequence":"ATGACGAAAATGAACCGCCTGGCGGCCGCGCTGATCGCCGCACTGATCTTGCCGACCGCGCACGCCGCGCAGCAGCAGGATATCGACGCCGTTATTCAGCCGCTGATGAAAAAATATGGCGTGCCGGGCATGGCGATCGCCGTGTCGGTCGACGGCAAACAGCAGATTTACCCGTATGGCGTCGCCTCGAAGCAGACCGGCAAACCGATCACCGAGCAGACGCTGTTCGAAGTGGGCTCGCTGAGCAAAACCTTCACCGCGACGCTGGCGGTCTATGCGCAGCAGCAGGGCAAGCTGTCGTTCAACGATCCGGCCAGCCGCTACCTGCCCGAGCTGCGCGGCAGCGCCTTCGACGGCGTCAGCCTGCTGAATCTGGCGACGCATACCTCCGGCCTGCCGCTGTTCGTGCCGGACGACGTGACCGACAACGCCCAACTGATGGCCTACTACCGGGCCTGGCAGCCGAAACATCCGGCGGGCAGCTACCGCGTCTATTCCAACCTCGGCATCGGCATGCTGGGCATGATCGCCGCCAAGAGCCTCGACCAGCCGTTTACCCAGGCGATGGAGCAGGGGATGCTGCCGGCGTTGGGCATGCGCCACACCTACGTTCAGGTGCCGGCGGCGCAGATGGCCAACTATGCGCAGGGCTACAACAAGGACGATAAGCCGGTGCGGGTCAATCCCGGCCCGCTGGACGCCGAGTCTTACGGCATCAAGTCCAACGCTCGCGATCTGATTCGCTATCTGGACGCCAACCTGCAGCAGGTGAAGGTCGCGCACGCGTGGCGCGAGGCGCTGACCGCGACGCACGTCGGTTATTACAAGGCGGGCGCGTTCACGCAGGATCTGATGTGGGAGAACTACCCGTACCCGGTGAAATTGTCTCGTTTGATCGAGGGCAACAACGCCGGGATGATCATGAACGGCACGCCGGCTACCGCCATCACGCCGCCGCAGCCGGAATTGCGCGCCGGCTGGTATAACAAAACCGGCTCTACCGGCGGTTTCTCCACCTACGCGGTGTTTATCCCGGCGAAGAATATCGCCGTGGTGATGCTGGCCAACAAATGGTTCCCGAACGACGATCGGGTCGAGGCGGCTTACCGCATCGTGCAAGCGTTGGATAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36783","NCBI_taxonomy_name":"Serratia marcescens","NCBI_taxonomy_id":"615"}}}},"ARO_accession":"3006999","ARO_id":"45461","ARO_name":"SST-1","CARD_short_name":"SST-1","ARO_description":"SST-1 is a SST beta-lactamase.","ARO_category":{"43911":{"category_aro_accession":"3005451","category_aro_cvterm_id":"43911","category_aro_name":"SST beta-lactamase","category_aro_description":"SST beta-lactamases are class C beta-lactamases found in Serratia marcescens.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5666":{"model_id":"5666","model_name":"STA-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8041":{"protein_sequence":{"accession":"WP_109545039.1","sequence":"MHPPLRPHPLWCSLRPATLALLLGVFGCRTSVPAPRPAAEPFTSITEDLRIQPLAPGVWRLVALSGEEWGHIPANGLVIAEGGGVLLVDPGWTEAQGERLLQWVEDTLKVPVHAGVATHFHADRTGGLRALQARGIPTHALALTAALTSQQDRPAPTHLFPGPAQQLGPVELFFPGPGHAPDNITVWHAASGILFGGCMVKDLKASSLGNLSDADLASWPRSVESLQARYPAARTVIPGHGEPGDTSLLAHTLELLRAGSR"},"dna_sequence":{"accession":"NG_057419.1","fmin":"100","fmax":"886","strand":"+","sequence":"ATGCATCCACCACTGCGTCCTCATCCCCTCTGGTGTTCACTGCGCCCCGCCACATTGGCCCTCCTCTTGGGAGTGTTCGGCTGCCGGACCAGTGTCCCGGCTCCGCGTCCTGCAGCGGAACCGTTCACTTCGATCACCGAGGACCTCCGCATCCAGCCCCTGGCACCGGGGGTCTGGCGCCTCGTGGCGCTCTCGGGCGAGGAATGGGGCCACATCCCCGCCAACGGGCTCGTCATCGCCGAGGGCGGCGGCGTGCTGCTCGTGGATCCGGGATGGACGGAAGCACAGGGTGAGCGGCTGCTCCAGTGGGTCGAAGACACCCTGAAGGTCCCCGTCCACGCGGGCGTGGCCACCCACTTCCATGCCGACCGGACGGGAGGTCTTCGCGCCCTTCAGGCACGCGGCATTCCCACCCATGCGCTCGCGCTCACCGCGGCGCTGACCTCACAGCAAGACCGCCCGGCTCCCACCCACCTCTTTCCAGGGCCCGCTCAACAGCTCGGCCCGGTGGAGCTGTTTTTTCCCGGACCTGGCCACGCTCCGGACAACATCACCGTGTGGCACGCCGCCAGCGGCATCCTCTTTGGAGGCTGCATGGTCAAGGACCTGAAGGCCTCGTCCCTGGGCAACCTCTCCGACGCGGACCTCGCCTCTTGGCCCAGGAGCGTGGAATCCCTCCAGGCGCGATATCCCGCTGCGCGCACCGTGATCCCCGGTCATGGTGAGCCCGGAGACACCTCGTTGCTCGCGCACACCTTGGAACTCCTTCGCGCGGGCTCACGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3007000","ARO_id":"45462","ARO_name":"STA-1","CARD_short_name":"STA-1","ARO_description":"STA-1 is a STA beta-lactamase.","ARO_category":{"43912":{"category_aro_accession":"3005452","category_aro_cvterm_id":"43912","category_aro_name":"STA beta-lactamase","category_aro_description":"STA beta-lactamases are class B1 beta-lactamases found in Stigmatella aurantiaca.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5668":{"model_id":"5668","model_name":"TEM-98","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8043":{"protein_sequence":{"accession":"WP_063865138.1","sequence":"MDPQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKLW"},"dna_sequence":{"accession":"NG_050307.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGGATCCTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCTTTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3006139","ARO_id":"44601","ARO_name":"TEM-98","CARD_short_name":"TEM-98","ARO_description":"TEM-98 is a TEM beta-lactamase.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5669":{"model_id":"5669","model_name":"TEM-99","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8044":{"protein_sequence":{"accession":"WP_063865144.1","sequence":"MDPQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSSGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKLW"},"dna_sequence":{"accession":"NG_050308.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGGATCCTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTAGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCTTTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3006140","ARO_id":"44602","ARO_name":"TEM-99","CARD_short_name":"TEM-99","ARO_description":"TEM-99 is a TEM beta-lactamase.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5670":{"model_id":"5670","model_name":"TER-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"8045":{"protein_sequence":{"accession":"WP_063865145.1","sequence":"MRHSLFAPILLLALFALPAWAHEATVNQVKAAERQLEARVGYAELDLASGRLLASYRPDERFPMMSTFKVPLCAAVLARVDAGEEKLDRRVRYRQQDLVEYSPVTEKHLADGMTVAELCAAAITLSDNTAANLLLASVGGTQGLTAFLRRSGDQTSRLDRWETELNEALPGDARDTTTPQAMAKTLHNLLTGSVLSAASRQQLRSWMVDDKVAGPLLRSTLPHGWFIADKTGAGNRGSRGIIAALGPDGQPARIVIIYLTGTEASMDERNRQIAEIGETLVKHW"},"dna_sequence":{"accession":"NG_050309.1","fmin":"100","fmax":"955","strand":"+","sequence":"ATGCGCCACTCTCTTTTTGCCCCGATCCTCCTGCTCGCCCTGTTCGCCCTGCCCGCCTGGGCGCATGAGGCGACGGTAAACCAGGTCAAAGCCGCTGAGCGCCAGCTCGAGGCCAGAGTAGGCTACGCGGAGCTGGATTTAGCCAGCGGACGGCTGCTGGCAAGCTATCGCCCCGACGAGCGTTTCCCGATGATGAGCACCTTTAAAGTGCCGCTCTGCGCGGCGGTACTGGCGCGCGTGGATGCCGGAGAGGAGAAGCTCGATCGCCGCGTCCGCTACCGTCAGCAGGATCTGGTTGAATACTCCCCGGTGACCGAAAAGCACCTCGCCGACGGCATGACGGTAGCCGAGCTGTGCGCTGCGGCAATCACCCTTAGCGATAACACCGCCGCTAATCTGCTGCTGGCGAGCGTCGGCGGCACGCAGGGGTTGACCGCCTTCCTGCGCCGCAGCGGAGACCAGACTTCGCGCCTCGACCGCTGGGAGACCGAGCTTAACGAGGCCCTGCCCGGCGACGCGCGTGATACCACCACGCCGCAGGCGATGGCCAAAACCTTGCACAATCTGCTCACCGGCAGCGTGCTTTCCGCCGCATCGCGACAGCAGCTGCGCAGCTGGATGGTTGACGATAAGGTTGCCGGCCCGCTGCTGCGCTCGACGCTGCCGCACGGCTGGTTTATCGCTGACAAAACCGGCGCGGGCAACCGCGGGTCGCGCGGTATTATCGCCGCCCTCGGCCCGGACGGGCAGCCCGCGCGTATCGTAATTATTTATTTAACCGGCACCGAGGCCTCAATGGATGAGCGGAACCGGCAGATTGCCGAGATTGGTGAGACGCTGGTTAAGCACTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39585","NCBI_taxonomy_name":"Raoultella terrigena","NCBI_taxonomy_id":"577"}}}},"ARO_accession":"3007001","ARO_id":"45463","ARO_name":"TER-1","CARD_short_name":"TER-1","ARO_description":"TER-1 is a TER beta-lactamase.","ARO_category":{"43913":{"category_aro_accession":"3005453","category_aro_cvterm_id":"43913","category_aro_name":"TER beta-lactamase","category_aro_description":"TER beta-lactamases are class A beta-lactamases found in Raoultella terrigena.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5671":{"model_id":"5671","model_name":"TER-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"8046":{"protein_sequence":{"accession":"WP_063865146.1","sequence":"MRHSLFAPILLLALFALPAWAHEATVNQVKAAERQLEARVGYAELDLASGRLLASYRPDERFPMMSTFKVPLCAAVLARVDAGEEKLDRRVRYRQQDLVEYSPVTEKHLADGMTVAELCAAAITLSDNTAANLLLASVGGPQGLTAFLRRSGDQTSRLDRWETELNEALPGDARDTTTPQAMAKTLRNLLTGSVLSAASRQQLRSWMVDDKVAGPLLRSALPHGWFIADKTGAGNRGSRGIIAALGPDGQPARIVIIYLTGTEASMDERNRQIAEIGETLVKHW"},"dna_sequence":{"accession":"NG_050310.1","fmin":"100","fmax":"955","strand":"+","sequence":"ATGCGCCACTCTCTTTTTGCCCCGATCCTCCTGCTCGCCCTGTTCGCCCTGCCCGCCTGGGCGCATGAGGCGACGGTAAACCAGGTCAAAGCCGCTGAGCGCCAGCTCGAGGCCAGAGTAGGCTACGCGGAGCTGGATTTAGCCAGCGGACGGCTGCTGGCAAGCTATCGCCCCGACGAGCGTTTCCCGATGATGAGCACCTTTAAAGTGCCGCTCTGCGCGGCGGTACTGGCGCGCGTGGATGCCGGAGAGGAGAAGCTCGATCGCCGCGTCCGCTACCGTCAGCAGGATCTGGTTGAATACTCCCCGGTGACCGAAAAGCACCTCGCCGACGGCATGACGGTAGCCGAGCTGTGCGCTGCGGCAATCACCCTTAGCGATAACACCGCCGCTAATCTGCTGCTGGCGAGCGTCGGCGGCCCGCAGGGGTTGACCGCCTTCCTGCGCCGCAGCGGAGACCAGACTTCGCGCCTCGACCGCTGGGAGACCGAGCTTAACGAGGCCCTGCCCGGCGACGCGCGTGATACCACCACGCCGCAGGCGATGGCCAAAACCTTGCGCAATCTGCTCACCGGCAGCGTGCTTTCCGCCGCATCGCGACAGCAGCTGCGCAGCTGGATGGTTGACGATAAGGTTGCCGGCCCGCTGCTGCGCTCGGCGCTGCCGCACGGCTGGTTTATCGCTGACAAAACCGGCGCGGGCAACCGCGGGTCGCGCGGTATTATCGCCGCCCTCGGCCCGGACGGGCAGCCCGCGCGCATCGTAATTATTTATTTAACCGGCACCGAGGCCTCAATGGATGAGCGGAACCGGCAGATTGCCGAGATTGGTGAGACGCTGGTTAAGCACTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39585","NCBI_taxonomy_name":"Raoultella terrigena","NCBI_taxonomy_id":"577"}}}},"ARO_accession":"3007007","ARO_id":"45469","ARO_name":"TER-2","CARD_short_name":"TER-2","ARO_description":"TER-2 is a TER beta-lactamase.","ARO_category":{"43913":{"category_aro_accession":"3005453","category_aro_cvterm_id":"43913","category_aro_name":"TER beta-lactamase","category_aro_description":"TER beta-lactamases are class A beta-lactamases found in Raoultella terrigena.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5672":{"model_id":"5672","model_name":"TTU-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"475"}},"model_sequences":{"sequence":{"8047":{"protein_sequence":{"accession":"WP_015818996.1","sequence":"MRVFLVIFILFIAGDLCAGEEMPGFSVEEIEKNVFLHGSYSQVNGFGLVSSNGLVVIENKKAFIVDTPWSEKDTINLVQWIEGRNLVLIGSISTHSHEDRTAGIKWLNAHSIPTYASALTNELLKKDDKEVATKSFEGAELMLADGLIEAYYPGGGHTIDNIVVWLPKSQILFGGCLVRSVDSTGLGYVGEADIKNWSSSVENVLSKYPEIKAVVPGHGKIGGLSLLTHTKKLAISALPKLSN"},"dna_sequence":{"accession":"NG_059314.1","fmin":"100","fmax":"832","strand":"+","sequence":"ATGAGAGTTTTTTTAGTAATATTCATACTATTTATTGCCGGGGATTTATGTGCCGGTGAGGAAATGCCAGGTTTTAGCGTTGAGGAAATTGAAAAGAATGTATTTCTACATGGGTCCTATAGTCAGGTAAACGGTTTTGGGTTGGTAAGCTCAAATGGGTTGGTGGTTATTGAGAATAAGAAAGCGTTTATTGTCGATACTCCTTGGTCGGAAAAAGATACCATTAATCTTGTTCAGTGGATTGAGGGTAGAAACTTAGTATTAATAGGGAGTATTTCCACTCATTCACATGAAGATAGAACCGCCGGAATTAAATGGCTTAATGCTCATTCGATTCCTACGTATGCCTCCGCCTTAACCAACGAGTTATTGAAAAAAGACGACAAAGAGGTTGCGACGAAGTCGTTCGAGGGGGCAGAGCTAATGTTAGCCGACGGCCTAATAGAAGCGTATTATCCCGGAGGTGGGCATACAATAGATAATATAGTGGTTTGGTTGCCAAAATCTCAAATATTATTTGGTGGTTGCCTTGTGCGGAGTGTAGATTCAACTGGACTTGGGTATGTAGGCGAAGCAGATATTAAAAACTGGTCTAGTTCCGTCGAGAACGTGCTGTCGAAGTATCCTGAGATTAAAGCGGTTGTTCCTGGTCATGGGAAGATAGGCGGGCTTTCACTATTGACTCATACTAAGAAGCTTGCTATCTCAGCTCTACCTAAGTTGTCAAATTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3007002","ARO_id":"45464","ARO_name":"TTU-1","CARD_short_name":"TTU-1","ARO_description":"TTU-1 is a TTU beta-lactamase.","ARO_category":{"43914":{"category_aro_accession":"3005454","category_aro_cvterm_id":"43914","category_aro_name":"TTU beta-lactamase","category_aro_description":"TTU beta-lactamases are class B1 beta-lactamases found in Teredinibacter turnerae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5673":{"model_id":"5673","model_name":"VEB-10","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"8048":{"protein_sequence":{"accession":"WP_063865150.1","sequence":"MKIVKRILLVLLSLFFTIVYSNAQTDNLTLKIENVLKAKNARIGVAIFNSNEKDTLKINNDFHFPMQSVMKFPIALAVLSEIDKGNLSFEQKIEITPQDLLPKMWSPIKEEFPNGTTLTIEQILNYTVSESDNIGCDILLKLIGGTDSVQKFLNANHFTDISIKANEEQMHKDWNTQYQNWATPTAMNKLLIDTYNNKNQLLSKKSYDFIWKIMRETTTGSNRLKGQLPKNTIVAHKTGTSGINNGIAAATNDVGVITLPNGQLIFISVFVAESKETSEINEKIISDIAKITWDYYLNK"},"dna_sequence":{"accession":"NG_050318.1","fmin":"0","fmax":"900","strand":"+","sequence":"ATGAAAATCGTAAAAAGGATATTATTAGTATTGTTAAGTTTATTTTTTACAATTGTGTATTCAAATGCTCAAACTGACAACTTAACTTTGAAAATTGAGAATGTTTTAAAGGCAAAAAATGCCAGAATAGGAGTAGCAATATTCAACAGCAATGAGAAGGATACTTTGAAGATTAATAACGACTTCCATTTCCCGATGCAAAGCGTTATGAAATTTCCGATTGCTTTAGCCGTTTTGTCTGAGATAGATAAAGGGAATCTTTCTTTTGAACAAAAAATAGAGATTACCCCTCAAGACCTTTTGCCTAAAATGTGGAGTCCGATTAAAGAGGAATTCCCTAATGGAACAACTTTGACGATTGAACAAATACTAAATTATACAGTATCAGAGAGCGACAATATTGGTTGTGATATTTTGCTAAAATTAATCGGAGGAACTGATTCTGTTCAAAAATTCTTGAATGCTAATCATTTCACTGATATTTCAATCAAAGCAAACGAAGAACAAATGCACAAGGATTGGAATACCCAATATCAAAATTGGGCAACCCCAACAGCGATGAACAAACTGTTAATAGATACTTATAATAATAAGAACCAATTACTTTCTAAAAAAAGTTATGATTTTATTTGGAAAATTATGAGAGAAACAACAACAGGAAGTAACCGATTAAAAGGACAATTACCAAAGAATACAATTGTTGCTCATAAAACAGGGACTTCCGGAATAAATAATGGAATTGCAGCAGCCACTAATGATGTTGGGGTAATTACTTTACCGAATGGACAATTAATTTTTATAAGCGTATTTGTTGCAGAGTCCAAAGAAACTTCGGAAATTAATGAAAAGATTATTTCAGACATTGCAAAAATAACGTGGGATTACTATTTGAATAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3003146","ARO_id":"39723","ARO_name":"VEB-10","CARD_short_name":"VEB-10","ARO_description":"VEB-10 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36182":{"category_aro_accession":"3000043","category_aro_cvterm_id":"36182","category_aro_name":"VEB beta-lactamase","category_aro_description":"VEB beta-lactamases or Vietnamese extended-spectrum beta-lactamases are class A beta-lactamases that confer high-level resistance to oxyimino cephalosporins and to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5674":{"model_id":"5674","model_name":"VEB-11","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"8049":{"protein_sequence":{"accession":"WP_063865151.1","sequence":"MKIVKRILLVLLSLFFTIVYSNAQTDNLTLKIENVLKEKNARIGVAIFNSNEKDTLKINNDFHFPMQSVMKFPIALAVLSEIDKGNLSFEQKIEITPQDLLPKTWSPIKEEFPNGTTLTIEQILNYTVSESDNIGCDILLKLIGGTDSVQKFLNANHFTDISIKANEEQMHKDWNTQYQNWATPTAMNKLLIDTYNNKNQLLSKKSYDFIWKIMRETTTGSNRLKGQLPKNTIVAHKTGTSGINNGIAAATNDVGVITLPNGQLIFISVFVAESKETSEINEKIISDIAKITWNYYLNK"},"dna_sequence":{"accession":"NG_050319.1","fmin":"0","fmax":"900","strand":"+","sequence":"ATGAAAATCGTAAAAAGGATATTATTAGTATTGTTAAGTTTATTTTTTACAATTGTGTATTCAAATGCTCAAACTGACAACTTAACTTTGAAAATTGAGAATGTTTTAAAGGAAAAAAATGCCAGAATAGGAGTAGCAATATTCAACAGCAATGAGAAGGATACTTTGAAGATTAATAACGACTTCCATTTCCCGATGCAAAGCGTTATGAAATTTCCGATTGCTTTAGCCGTTTTGTCTGAGATAGATAAAGGGAATCTTTCTTTTGAACAAAAAATAGAGATTACCCCTCAAGACCTTTTGCCTAAAACGTGGAGTCCGATTAAAGAGGAATTCCCTAATGGAACAACTTTGACGATTGAACAAATACTAAATTATACAGTATCAGAGAGCGACAATATTGGTTGTGATATTTTGCTAAAATTAATCGGAGGAACTGATTCTGTTCAAAAATTCTTGAATGCTAATCATTTCACTGATATTTCAATCAAAGCAAACGAAGAACAAATGCACAAGGATTGGAATACCCAATATCAAAATTGGGCAACCCCAACAGCGATGAACAAACTGTTAATAGATACTTATAATAATAAGAACCAATTACTTTCTAAAAAAAGTTATGATTTTATTTGGAAAATTATGAGAGAAACAACAACAGGAAGTAACCGATTAAAAGGACAATTACCAAAGAATACAATTGTTGCTCATAAAACAGGGACTTCCGGAATAAATAATGGAATTGCAGCAGCCACTAATGATGTTGGGGTAATTACTTTACCGAATGGACAATTAATTTTTATAAGCGTATTTGTTGCAGAGTCCAAAGAAACTTCGGAAATTAATGAAAAGATTATTTCAGACATTGCAAAAATAACGTGGAATTACTATTTGAATAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006208","ARO_id":"44670","ARO_name":"VEB-11","CARD_short_name":"VEB-11","ARO_description":"VEB-11 is a VEB beta-lactamase.","ARO_category":{"36182":{"category_aro_accession":"3000043","category_aro_cvterm_id":"36182","category_aro_name":"VEB beta-lactamase","category_aro_description":"VEB beta-lactamases or Vietnamese extended-spectrum beta-lactamases are class A beta-lactamases that confer high-level resistance to oxyimino cephalosporins and to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5675":{"model_id":"5675","model_name":"VEB-12","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"8050":{"protein_sequence":{"accession":"WP_063865152.1","sequence":"MKIVKRILLVLLSLFFTVEYSNAQTDNLTLKIENVLKAKNARIGVAIFNSNEKDTLKINNDFHFPMQSVMKFPIALAVLSEIDKGNLSFEQKIEITPQDLLPKTWSPIKEEFPNGTTLTIEQILNYTVSESDNIGCDILLKLIGGTDSVQKFLNANHFTDISIKANEEQMHKDWNTQYQNWATPTAMNKLLIDTYNNKNQLLSKKSYDFIWKIMRETTAGSNRLKGQLPKNTIVAHKTGTSGINNGIAAATNDVGVITLPNGQLIFISVFVAESKETSEINEKIISDIAKITWNYYLNK"},"dna_sequence":{"accession":"NG_050320.1","fmin":"0","fmax":"900","strand":"+","sequence":"ATGAAAATCGTAAAAAGGATATTATTAGTATTGTTAAGTTTATTTTTTACAGTTGAGTATTCAAATGCTCAAACTGACAACTTAACTTTGAAAATTGAGAATGTTTTAAAGGCAAAAAATGCCAGAATAGGAGTAGCAATATTCAACAGCAATGAGAAGGATACTTTGAAGATTAATAACGACTTCCATTTCCCGATGCAAAGCGTTATGAAATTTCCGATTGCTTTAGCCGTTTTGTCTGAGATAGATAAAGGGAATCTTTCTTTTGAACAAAAAATAGAGATTACCCCTCAAGACCTTTTGCCTAAAACGTGGAGTCCGATTAAAGAGGAATTCCCTAATGGAACAACTTTGACGATTGAACAAATACTAAATTATACAGTATCAGAGAGCGACAATATTGGTTGTGATATTTTGCTAAAATTAATCGGAGGAACTGATTCTGTTCAAAAATTCTTGAATGCTAATCATTTCACTGATATTTCAATCAAAGCAAACGAAGAACAAATGCACAAGGATTGGAATACCCAATATCAAAATTGGGCAACCCCAACAGCGATGAACAAACTGTTAATAGATACTTATAATAATAAGAACCAATTACTTTCTAAAAAAAGTTATGATTTTATTTGGAAAATTATGAGAGAAACAACAGCAGGAAGTAACCGATTAAAAGGACAATTACCAAAGAATACAATTGTTGCTCATAAAACAGGGACTTCCGGAATAAATAATGGAATTGCAGCAGCCACTAATGATGTTGGGGTAATTACTTTACCGAATGGACAATTAATTTTTATAAGCGTATTTGTTGCAGAGTCCAAAGAAACTTCGGAAATTAATGAAAAGATTATTTCAGACATTGCAAAAATAACGTGGAATTACTATTTGAATAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006209","ARO_id":"44671","ARO_name":"VEB-12","CARD_short_name":"VEB-12","ARO_description":"VEB-12 is a VEB beta-lactamase.","ARO_category":{"36182":{"category_aro_accession":"3000043","category_aro_cvterm_id":"36182","category_aro_name":"VEB beta-lactamase","category_aro_description":"VEB beta-lactamases or Vietnamese extended-spectrum beta-lactamases are class A beta-lactamases that confer high-level resistance to oxyimino cephalosporins and to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5676":{"model_id":"5676","model_name":"VEB-13","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"8051":{"protein_sequence":{"accession":"WP_063865153.1","sequence":"MKIVKRILLVLLSLFFTVVYSNAQTDNLTLKIENVLKAKNARIGVAIFNSNEKDTLKINNDFHFPMQSVMKFPIALAVLSEIDKGNLSFEQKIEITPQDLLPKTWSPIKEEFPNGTTLTIEQILNYTVSESDNIGCDILLKLIGGTDSVQKFLNANHFTDISIKANEEQMHKDWNTQYQNWATPTAMNKLLIDTYNNKNQLLSKKSYDFIWKIMRETTAGSNRLKGQLPKNTIVAHKTGTSGINNGIAAATNDVGVITLPNGQLIFISVFVAESKETSEINEKIISDIAKITWNYYLNK"},"dna_sequence":{"accession":"NG_050321.1","fmin":"0","fmax":"900","strand":"+","sequence":"ATGAAAATCGTAAAAAGGATATTATTAGTATTGTTAAGTTTATTTTTTACAGTTGTGTATTCAAATGCTCAAACTGACAACTTAACTTTGAAAATTGAGAATGTTTTAAAGGCAAAAAATGCCAGAATAGGAGTAGCAATATTCAACAGCAATGAGAAGGATACTTTGAAGATTAATAACGACTTCCATTTCCCGATGCAAAGCGTTATGAAATTTCCGATTGCTTTAGCCGTTTTGTCTGAGATAGATAAAGGGAATCTTTCTTTTGAACAAAAAATAGAGATTACCCCTCAAGACCTTTTGCCTAAAACGTGGAGTCCGATTAAAGAGGAATTCCCTAATGGAACAACTTTGACGATTGAACAAATACTAAATTATACAGTATCAGAGAGCGACAATATTGGTTGTGATATTTTGCTAAAATTAATCGGAGGAACTGATTCTGTTCAAAAATTCTTGAATGCTAATCATTTCACTGATATTTCAATCAAAGCAAACGAAGAACAAATGCACAAGGATTGGAATACCCAATATCAAAATTGGGCAACCCCAACAGCGATGAACAAACTGTTAATAGATACTTATAATAATAAGAACCAATTACTTTCTAAAAAAAGTTATGATTTTATTTGGAAAATTATGAGAGAAACAACAGCAGGAAGTAACCGATTAAAAGGACAATTACCAAAGAATACAATTGTTGCTCATAAAACAGGGACTTCCGGAATAAATAATGGAATTGCAGCAGCCACTAATGATGTTGGGGTAATTACTTTACCGAATGGACAATTAATTTTTATAAGCGTATTTGTTGCAGAGTCCAAAGAAACTTCGGAAATTAATGAAAAGATTATTTCAGACATTGCAAAAATAACGTGGAATTACTATTTGAATAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006210","ARO_id":"44672","ARO_name":"VEB-13","CARD_short_name":"VEB-13","ARO_description":"VEB-13 is a VEB beta-lactamase.","ARO_category":{"36182":{"category_aro_accession":"3000043","category_aro_cvterm_id":"36182","category_aro_name":"VEB beta-lactamase","category_aro_description":"VEB beta-lactamases or Vietnamese extended-spectrum beta-lactamases are class A beta-lactamases that confer high-level resistance to oxyimino cephalosporins and to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5677":{"model_id":"5677","model_name":"VEB-14","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"8052":{"protein_sequence":{"accession":"WP_063865154.1","sequence":"MKIVKRILLVLLSLFFTVVYSNAQTDNLTLKIENVLKAKNARIGVAIFNSNEKDTLKINNDFHFPMQSVMKFPIALAVLSEIDKGNLSFEQKIEITPQDLLPKTWSPIKEEFPNGTTLTIEQILNYTVSESDNIGCDILLKLIGGTDSVQKFLNANHFTDISIKANEEQMHKDWNTQYQNWATPTAMNKLLIDTYNNKNQLLSKKSYDFIWKIMRETTGSNRLKGQLPKNTIVAHKTGTSGINNGIAAATNDVGVITLPNGQLIFISVFVAESKETSEINEKIISDIAKITWNYYLNK"},"dna_sequence":{"accession":"NG_050322.1","fmin":"0","fmax":"897","strand":"+","sequence":"ATGAAAATCGTAAAAAGGATATTATTAGTATTGTTAAGTTTATTTTTTACAGTTGTGTATTCAAATGCTCAAACTGACAACTTAACTTTGAAAATTGAGAATGTTTTAAAGGCAAAAAATGCCAGAATAGGAGTAGCAATATTCAACAGCAATGAGAAGGATACTTTGAAGATTAATAACGACTTCCATTTCCCGATGCAAAGCGTTATGAAATTTCCGATTGCTTTAGCCGTTTTGTCTGAGATAGATAAAGGGAATCTTTCTTTTGAACAAAAAATAGAGATTACCCCTCAAGACCTTTTGCCTAAAACGTGGAGTCCGATTAAAGAGGAATTCCCTAATGGAACAACTTTGACGATTGAACAAATACTAAATTATACAGTATCAGAGAGCGACAATATTGGTTGTGATATTTTGCTAAAATTAATCGGAGGAACTGATTCTGTTCAAAAATTCTTGAATGCTAATCATTTCACTGATATTTCAATCAAAGCAAACGAAGAACAAATGCACAAGGATTGGAATACCCAATATCAAAATTGGGCAACCCCAACAGCGATGAACAAACTGTTAATAGATACTTATAATAATAAGAACCAATTACTTTCTAAAAAAAGTTATGATTTTATTTGGAAAATTATGAGAGAAACAACAGGAAGTAACCGATTAAAAGGACAATTACCAAAGAATACAATTGTTGCTCATAAAACAGGGACTTCCGGAATAAATAATGGAATTGCAGCAGCCACTAATGATGTTGGGGTAATTACTTTACCGAATGGACAATTAATTTTTATAAGCGTATTTGTTGCAGAGTCCAAAGAAACTTCGGAAATTAATGAAAAGATTATTTCAGACATTGCAAAAATAACGTGGAATTACTATTTGAATAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006211","ARO_id":"44673","ARO_name":"VEB-14","CARD_short_name":"VEB-14","ARO_description":"VEB-14 is a VEB beta-lactamase.","ARO_category":{"36182":{"category_aro_accession":"3000043","category_aro_cvterm_id":"36182","category_aro_name":"VEB beta-lactamase","category_aro_description":"VEB beta-lactamases or Vietnamese extended-spectrum beta-lactamases are class A beta-lactamases that confer high-level resistance to oxyimino cephalosporins and to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5678":{"model_id":"5678","model_name":"VEB-15","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"8053":{"protein_sequence":{"accession":"WP_063865155.1","sequence":"MKIVKRILLVLLSLFFTVVYSNAQTDNLTLKIENVLKAKNARIGVAIFNSNEKDTLKINNDFHFPMQSVMKFPIALAVLSEIDKGNLSFEQKIEITPQDLLPKMWSPIKEEFPNGTTLTIEQILNYTVSESDNIGCDILLKLIGGTDSVQKFLNANHFTDISIKANEEQMHKDWNTQYQNWATPTAMNKLLIDTYNNKNQLLSKKSYDFIWKIMRETTTGSNRLKGQLPKNTIVAHKTGTSGINNGIAAATNDVGVITLPNGQLIFISVFVAESKETSEINEKIISDIAKITWDYYLNK"},"dna_sequence":{"accession":"NG_050323.1","fmin":"0","fmax":"900","strand":"+","sequence":"ATGAAAATCGTAAAAAGGATATTATTAGTATTGTTAAGTTTATTTTTTACAGTTGTGTATTCAAATGCTCAAACTGACAACTTAACTTTGAAAATTGAGAATGTTTTAAAGGCAAAAAATGCCAGAATAGGAGTAGCAATATTCAACAGCAATGAGAAGGATACTTTGAAGATTAATAACGACTTCCATTTCCCGATGCAAAGCGTTATGAAATTTCCGATTGCTTTAGCCGTTTTGTCTGAGATAGATAAAGGGAATCTTTCTTTTGAACAAAAAATAGAGATTACCCCTCAAGACCTTTTGCCTAAAATGTGGAGTCCGATTAAAGAGGAATTCCCTAATGGAACAACTTTGACGATTGAACAAATACTAAATTATACAGTATCAGAGAGCGACAATATTGGTTGTGATATTTTGCTAAAATTAATCGGAGGAACTGATTCTGTTCAAAAATTCTTGAATGCTAATCATTTCACTGATATTTCAATCAAAGCAAACGAAGAACAAATGCACAAGGATTGGAATACCCAATATCAAAATTGGGCAACCCCAACAGCGATGAACAAACTGTTAATAGATACTTATAATAATAAGAACCAATTACTTTCTAAAAAAAGTTATGATTTTATTTGGAAAATTATGAGAGAAACAACAACAGGAAGTAACCGATTAAAAGGACAATTACCAAAGAATACAATTGTTGCTCATAAAACAGGGACTTCCGGAATAAATAATGGAATTGCAGCAGCCACTAATGATGTTGGGGTAATTACTTTACCGAATGGACAATTAATTTTTATAAGCGTATTTGTTGCAGAGTCCAAAGAAACTTCGGAAATTAATGAAAAGATTATTTCAGACATTGCAAAAATAACGTGGGATTACTATTTGAATAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3006212","ARO_id":"44674","ARO_name":"VEB-15","CARD_short_name":"VEB-15","ARO_description":"VEB-15 is a VEB beta-lactamase.","ARO_category":{"36182":{"category_aro_accession":"3000043","category_aro_cvterm_id":"36182","category_aro_name":"VEB beta-lactamase","category_aro_description":"VEB beta-lactamases or Vietnamese extended-spectrum beta-lactamases are class A beta-lactamases that confer high-level resistance to oxyimino cephalosporins and to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5679":{"model_id":"5679","model_name":"VEB-17","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"8054":{"protein_sequence":{"accession":"WP_063865157.1","sequence":"MKIVKRILLVLLSLFFTIAYSNAQTDNLTLKIENVLKAKNARIGVAIFNSNEKDTLKINNDFHYPMQSVMKFPIALAVLSEIDKGNLSFEQKIEITPQDLLPKMWSPIKEEFPNGTTLTIEQILNYTVSESDNIGCDILLKLIGGTDSVQKFLNANHFTDISIKANEEQMHKDWNTQYQNWATPTAMNKLLIDTYNNKNQLLSKKSYDFIWKIMRETTTGSNRLKGQLPKNTIVAHKTGTSGINNGIAAATNDVGVITLPNGQLIFISVFVAESKETSEINEKIISDIAKITWDYYLNK"},"dna_sequence":{"accession":"NG_050325.1","fmin":"0","fmax":"900","strand":"+","sequence":"ATGAAAATCGTAAAAAGGATATTATTAGTATTGTTAAGTTTATTTTTTACAATTGCGTATTCAAATGCTCAAACTGACAACTTAACTTTGAAAATTGAGAATGTTTTAAAGGCAAAAAATGCCAGAATAGGAGTAGCAATATTCAACAGCAATGAGAAGGATACTTTGAAGATTAATAACGACTTCCATTACCCGATGCAAAGCGTTATGAAATTTCCGATTGCTTTAGCCGTTTTGTCTGAGATAGATAAAGGGAATCTTTCTTTTGAACAAAAAATAGAGATTACCCCTCAAGACCTTTTGCCTAAAATGTGGAGTCCGATTAAAGAGGAATTCCCTAATGGAACAACTTTGACGATTGAACAAATACTAAATTATACAGTATCAGAGAGCGACAATATTGGTTGTGATATTTTGCTAAAATTAATCGGAGGAACTGATTCTGTTCAAAAATTCTTGAATGCTAATCATTTCACTGATATTTCAATCAAAGCAAACGAAGAACAAATGCACAAGGATTGGAATACCCAATATCAAAATTGGGCAACCCCAACAGCGATGAACAAACTGTTAATAGATACTTATAATAATAAGAACCAATTACTTTCTAAAAAAAGTTATGATTTTATTTGGAAAATTATGAGAGAAACAACAACAGGAAGTAACCGATTAAAAGGACAATTACCAAAGAATACAATTGTTGCTCATAAAACAGGGACTTCCGGAATAAATAATGGAATTGCAGCAGCCACTAATGATGTTGGGGTAATTACTTTACCGAATGGACAATTAATTTTTATAAGCGTATTTGTTGCAGAGTCCAAAGAAACTTCGGAAATTAATGAAAAGATTATTTCAGACATTGCAAAAATAACGTGGGATTACTATTTGAATAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3006213","ARO_id":"44675","ARO_name":"VEB-17","CARD_short_name":"VEB-17","ARO_description":"VEB-17 is a VEB beta-lactamase.","ARO_category":{"36182":{"category_aro_accession":"3000043","category_aro_cvterm_id":"36182","category_aro_name":"VEB beta-lactamase","category_aro_description":"VEB beta-lactamases or Vietnamese extended-spectrum beta-lactamases are class A beta-lactamases that confer high-level resistance to oxyimino cephalosporins and to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5680":{"model_id":"5680","model_name":"VEB-19","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"8055":{"protein_sequence":{"accession":"WP_094009812.1","sequence":"MKIVKRILLVLLSLFFTIVYSNAQTDNLTLKIENVLKAKNARIGVAIFNSNEKDTLKINNDFHFPMQSVMKFPIALAVLSEIDKGNLSFEQKIEITPQDLLPKTWSPIKEEFPNGTTLTIEQILNYTVSESDNIGCDILLKLIGGTDSVQKFLNANHFTDISIKANEEQMHKDWNTQYQNWATPTAMNKLLIDTYNNKNQLLSKKSYDFIWKIMRETTTGSNRLKGQLPKNTIVAHKTGTSGINNGIAAATNDVGVITLPNGQLIFISVFVAESKETSEINEKIISDIAKITWDYYLNK"},"dna_sequence":{"accession":"NG_055500.1","fmin":"0","fmax":"900","strand":"+","sequence":"ATGAAAATCGTAAAAAGGATATTATTAGTATTGTTAAGTTTATTTTTTACAATTGTGTATTCAAATGCTCAAACTGACAACTTAACTTTGAAAATTGAGAATGTTTTAAAGGCAAAAAATGCCAGAATAGGAGTAGCAATATTCAACAGCAATGAGAAGGATACTTTGAAGATTAATAACGACTTCCATTTCCCGATGCAAAGCGTTATGAAATTTCCGATTGCTTTAGCCGTTTTGTCTGAGATAGATAAAGGGAATCTTTCTTTTGAACAAAAAATAGAGATTACCCCTCAAGACCTTTTGCCTAAAACGTGGAGTCCGATTAAAGAGGAATTCCCTAATGGAACAACTTTGACGATTGAACAAATACTAAATTATACAGTATCAGAGAGCGACAATATTGGTTGTGATATTTTGCTAAAATTAATCGGAGGAACTGATTCTGTTCAAAAATTCTTGAATGCTAATCATTTCACTGATATTTCAATCAAAGCAAACGAAGAACAAATGCACAAGGATTGGAATACCCAATATCAAAATTGGGCAACCCCAACAGCGATGAACAAACTGTTAATAGATACTTATAATAATAAGAACCAATTACTTTCTAAAAAAAGTTATGATTTTATTTGGAAAATTATGAGAGAAACAACAACAGGAAGTAACCGATTAAAAGGACAATTACCAAAGAATACAATTGTTGCTCATAAAACAGGGACTTCCGGAATAAATAATGGAATTGCAGCAGCCACTAATGATGTTGGGGTAATTACTTTACCGAATGGACAATTAATTTTTATAAGCGTATTTGTTGCAGAGTCCAAAGAAACTTCGGAAATTAATGAAAAGATTATTTCAGACATTGCAAAAATAACGTGGGATTACTATTTGAATAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3006214","ARO_id":"44676","ARO_name":"VEB-19","CARD_short_name":"VEB-19","ARO_description":"VEB-19 is a VEB beta-lactamase.","ARO_category":{"36182":{"category_aro_accession":"3000043","category_aro_cvterm_id":"36182","category_aro_name":"VEB beta-lactamase","category_aro_description":"VEB beta-lactamases or Vietnamese extended-spectrum beta-lactamases are class A beta-lactamases that confer high-level resistance to oxyimino cephalosporins and to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5681":{"model_id":"5681","model_name":"VEB-20","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"8056":{"protein_sequence":{"accession":"WP_128268286.1","sequence":"MKIVKRILLVLLSLFFTVVYSNAQTDNLTLKIENVLKAKNARIGVAIFNSNEKDTLKINNDFHFPMQSVMKFPIALAVLSEIDKGNLSFEQKIEITPQDLLPKTWSPIKEEFPNGTTLTIEQILNYTVSESDNIGCDILLKLIGGTDSVQKFLNANHFTDISIKANEEQMHKDWNTQYQNWATPTAMNKLLIDTYNNKNQLLSKKSYDFIWKIMRETTTGSNRLKGQLPKNTIVAHRTGTSGINNGIAAATNDVGVITLPNGQLIFISVFVAESKETSEINEKIISDIAKITWNYYLNK"},"dna_sequence":{"accession":"NG_063894.1","fmin":"0","fmax":"900","strand":"+","sequence":"ATGAAAATCGTAAAAAGGATATTATTAGTATTGTTAAGTTTATTTTTTACAGTTGTGTATTCAAATGCTCAAACTGACAACTTAACTTTGAAAATTGAGAATGTTTTAAAGGCAAAAAATGCCAGAATAGGAGTAGCAATATTCAACAGCAATGAGAAGGATACTTTGAAGATTAATAACGACTTCCATTTCCCGATGCAAAGCGTTATGAAATTTCCGATTGCTTTAGCCGTTTTGTCTGAGATAGATAAAGGGAATCTTTCTTTTGAACAAAAAATAGAGATTACCCCTCAAGACCTTTTGCCTAAAACGTGGAGTCCGATTAAAGAGGAATTCCCTAATGGAACAACTTTGACGATTGAACAAATACTAAATTATACAGTATCAGAGAGCGACAATATTGGTTGTGATATTTTGCTAAAATTAATCGGAGGAACTGATTCTGTTCAAAAATTCTTGAATGCTAATCATTTCACTGATATTTCAATCAAAGCAAACGAAGAACAAATGCACAAGGATTGGAATACCCAATATCAAAATTGGGCAACCCCAACAGCGATGAACAAACTGTTAATAGATACTTATAATAATAAGAACCAATTACTTTCTAAAAAAAGTTATGATTTTATTTGGAAAATTATGAGAGAAACAACAACAGGAAGTAACCGATTAAAAGGACAATTACCAAAGAATACAATTGTTGCTCATAGAACAGGGACTTCCGGAATAAATAATGGAATTGCAGCAGCCACTAATGATGTTGGGGTAATTACTTTACCGAATGGACAATTAATTTTTATAAGCGTATTTGTTGCAGAGTCCAAAGAAACTTCGGAAATTAATGAAAAGATTATTTCAGACATTGCAAAAATAACGTGGAATTACTATTTGAATAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006215","ARO_id":"44677","ARO_name":"VEB-20","CARD_short_name":"VEB-20","ARO_description":"VEB-20 is a VEB beta-lactamase.","ARO_category":{"36182":{"category_aro_accession":"3000043","category_aro_cvterm_id":"36182","category_aro_name":"VEB beta-lactamase","category_aro_description":"VEB beta-lactamases or Vietnamese extended-spectrum beta-lactamases are class A beta-lactamases that confer high-level resistance to oxyimino cephalosporins and to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5682":{"model_id":"5682","model_name":"VEB-21","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"8057":{"protein_sequence":{"accession":"WP_044103626.1","sequence":"MKIVKRILLVLLSLFFTIEYSNAQTDNLTLKIENVLKAKNARIGVAIFNSNEKDTLKINNDFHFPMQSVMKFPIALAVLSEIDKGNLSFEQKIEITPQDLLPKTWSPIKEEFPNGTTLTIEQILNYTVSESDNIGCDILLKLIGGTDSVQKFLNANHFTDISIKANEEQMHKDWNTQYQNWATPTAMNKLLIDTYNNKNQLLSKKSYDFIWKIMRETTTGSNRLKGQLPKNTIVAHKTGTSGINNGITAATNDVGVITLPNGQLIFISVFVAESKETSEINEKIISDIAKITWNYYLNK"},"dna_sequence":{"accession":"NG_063895.1","fmin":"0","fmax":"900","strand":"+","sequence":"ATGAAAATCGTAAAAAGGATATTATTAGTATTGTTAAGTTTATTTTTTACAATTGAGTATTCAAATGCTCAAACTGACAACTTAACTTTGAAAATTGAGAATGTTTTAAAGGCAAAAAATGCCAGAATAGGAGTAGCAATATTCAACAGCAATGAGAAGGATACTTTGAAGATTAATAACGACTTCCATTTCCCGATGCAAAGCGTTATGAAATTTCCGATTGCTTTAGCCGTTTTGTCTGAGATAGATAAAGGGAATCTTTCTTTTGAACAAAAAATAGAGATTACCCCTCAAGACCTTTTGCCTAAAACGTGGAGTCCGATTAAAGAGGAATTCCCTAATGGAACAACTTTGACGATTGAACAAATACTAAATTATACAGTATCAGAGAGCGACAATATTGGTTGTGATATTTTGCTAAAATTAATCGGAGGAACTGATTCTGTTCAAAAATTCTTGAATGCTAATCATTTCACTGATATTTCAATCAAAGCAAACGAAGAACAAATGCACAAGGATTGGAATACCCAATATCAAAATTGGGCAACCCCAACAGCGATGAACAAACTGTTAATAGATACTTATAATAATAAGAACCAATTACTTTCTAAAAAAAGTTATGATTTTATTTGGAAAATTATGAGAGAAACAACAACAGGAAGTAACCGATTAAAAGGACAATTACCAAAGAATACAATTGTTGCTCATAAAACAGGGACTTCCGGAATAAATAATGGAATTACAGCAGCCACTAATGATGTTGGGGTAATTACTTTACCGAATGGACAATTAATTTTTATAAGCGTATTTGTTGCAGAGTCCAAAGAAACTTCGGAAATTAATGAAAAGATTATTTCAGACATTGCAAAAATAACGTGGAATTACTATTTGAATAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40550","NCBI_taxonomy_name":"Acinetobacter calcoaceticus\/baumannii complex","NCBI_taxonomy_id":"909768"}}}},"ARO_accession":"3006216","ARO_id":"44678","ARO_name":"VEB-21","CARD_short_name":"VEB-21","ARO_description":"VEB-21 is a VEB beta-lactamase.","ARO_category":{"36182":{"category_aro_accession":"3000043","category_aro_cvterm_id":"36182","category_aro_name":"VEB beta-lactamase","category_aro_description":"VEB beta-lactamases or Vietnamese extended-spectrum beta-lactamases are class A beta-lactamases that confer high-level resistance to oxyimino cephalosporins and to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5683":{"model_id":"5683","model_name":"VEB-22","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"8058":{"protein_sequence":{"accession":"WP_148044475.1","sequence":"MKIVKRILLVLLSLFFTTVYSNAQTDNLTLKIENVLKAKNARIGVAIFNSNEKDTLKINNDFHFPMQSVMKFPIALAVLSEIDKGNLSFEQKIEITPQDLLPKTWSPIKEEFPNGTTLTIEQILNYTVSESDNIGCDILLKLIGGTDSVQKFLNANHFTDISIKANEEQMHKDWNTQYQNWATPTAMNKLLIDTYNNKNQLLSKKSYDFIWKIMRETTTGSNRLKGQLPKNTIVAHKTGTSGINNGIAAATNDVGVITLPNGQLIFISVFVAESKETSEINEKIISDIAKITWNYYLNK"},"dna_sequence":{"accession":"NG_065941.1","fmin":"0","fmax":"900","strand":"+","sequence":"ATGAAAATCGTAAAAAGGATATTATTAGTATTGTTAAGTTTATTTTTTACAACTGTGTATTCAAATGCTCAAACTGACAACTTAACTTTGAAAATTGAGAATGTTTTAAAGGCAAAAAATGCCAGAATAGGAGTAGCAATATTCAACAGCAATGAGAAGGATACTTTGAAGATTAATAACGACTTCCATTTCCCGATGCAAAGCGTTATGAAATTTCCGATTGCTTTAGCCGTTTTGTCTGAGATAGATAAAGGGAATCTTTCTTTTGAACAAAAAATAGAGATTACCCCTCAAGACCTTTTGCCTAAAACGTGGAGTCCGATTAAAGAGGAATTCCCTAATGGAACAACTTTGACGATTGAACAAATACTAAATTATACAGTATCAGAGAGCGACAATATTGGTTGTGATATTTTGCTAAAATTAATCGGAGGAACTGATTCTGTTCAAAAATTCTTGAATGCTAATCATTTCACTGATATTTCAATCAAAGCAAACGAAGAACAAATGCACAAGGATTGGAATACCCAATATCAAAATTGGGCAACCCCAACAGCGATGAACAAACTGTTAATAGATACTTATAATAATAAGAACCAATTACTTTCTAAAAAAAGTTATGATTTTATTTGGAAAATTATGAGAGAAACAACAACAGGAAGTAACCGATTAAAAGGACAATTACCAAAGAATACAATTGTTGCTCATAAAACAGGGACTTCCGGAATAAATAATGGAATTGCAGCAGCCACTAATGATGTTGGGGTAATTACTTTACCGAATGGACAATTAATTTTTATAAGCGTATTTGTTGCAGAGTCCAAAGAAACTTCGGAAATTAATGAAAAGATTATTTCAGACATTGCAAAAATAACGTGGAATTACTATTTGAATAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3006217","ARO_id":"44679","ARO_name":"VEB-22","CARD_short_name":"VEB-22","ARO_description":"VEB-22 is a VEB beta-lactamase.","ARO_category":{"36182":{"category_aro_accession":"3000043","category_aro_cvterm_id":"36182","category_aro_name":"VEB beta-lactamase","category_aro_description":"VEB beta-lactamases or Vietnamese extended-spectrum beta-lactamases are class A beta-lactamases that confer high-level resistance to oxyimino cephalosporins and to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5684":{"model_id":"5684","model_name":"VEB-23","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"8059":{"protein_sequence":{"accession":"WP_156404662.1","sequence":"MKIVKRILLVLLSLFFTIEYSNAQTDNLTLKIENVLKAKNARIGVAIFNSNEKDTLKINNDFHFPMQSVMKFPIALAVLSEIDKGNLSFEQKIEITPQDLLPKTWSPIKEEFPNGTTLTIEQILNYTVSESDNIGCDILLKLIGGTDSVQKFLNANHFTDISIKANEEQMHKDWNTQYQNWATPTAMNKLLIDTYNNKNQLLSKKSYDFIWKIMRETTTGSNRLKGQLPKNTIVAHKTGTSGINNGIAAATNDVGVITLPNGQLIFISVFVAESKETSEINEKIISDIAKITWNYYLNK"},"dna_sequence":{"accession":"NG_067164.1","fmin":"0","fmax":"900","strand":"+","sequence":"ATGAAAATCGTAAAAAGGATATTATTAGTATTGTTAAGTTTATTTTTTACAATTGAGTATTCAAATGCTCAAACTGACAACTTAACTTTGAAAATTGAGAATGTTTTAAAGGCAAAAAATGCCAGAATAGGAGTAGCAATATTCAACAGCAATGAGAAGGATACTTTGAAGATTAATAACGACTTCCATTTCCCGATGCAAAGCGTTATGAAATTTCCGATTGCTTTAGCCGTTTTGTCTGAGATAGATAAAGGGAATCTTTCTTTTGAACAAAAAATAGAGATTACCCCTCAAGACCTTTTGCCTAAAACGTGGAGTCCGATTAAAGAGGAATTCCCTAATGGAACAACTTTGACGATTGAACAAATACTAAATTATACAGTATCAGAGAGCGACAATATTGGTTGTGATATTTTGCTAAAATTAATCGGAGGAACTGATTCTGTTCAAAAATTCTTGAATGCTAATCATTTCACTGATATTTCAATCAAAGCAAACGAAGAACAAATGCACAAGGATTGGAATACCCAATATCAAAATTGGGCAACCCCAACAGCGATGAACAAACTGTTAATAGATACTTATAATAATAAGAACCAATTACTTTCTAAAAAAAGTTATGATTTTATTTGGAAAATTATGAGAGAAACAACAACAGGAAGTAACCGATTAAAAGGACAATTACCAAAGAATACAATTGTTGCTCATAAAACAGGGACTTCCGGAATAAATAATGGAATTGCAGCAGCCACTAATGATGTTGGGGTAATTACTTTACCGAATGGACAATTAATTTTTATAAGCGTATTTGTTGCAGAGTCCAAAGAAACTTCGGAAATTAATGAAAAGATTATTTCAGACATTGCAAAAATAACGTGGAATTACTATTTGAATAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3006218","ARO_id":"44680","ARO_name":"VEB-23","CARD_short_name":"VEB-23","ARO_description":"VEB-23 is a VEB beta-lactamase.","ARO_category":{"36182":{"category_aro_accession":"3000043","category_aro_cvterm_id":"36182","category_aro_name":"VEB beta-lactamase","category_aro_description":"VEB beta-lactamases or Vietnamese extended-spectrum beta-lactamases are class A beta-lactamases that confer high-level resistance to oxyimino cephalosporins and to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5685":{"model_id":"5685","model_name":"VEB-24","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"8060":{"protein_sequence":{"accession":"WP_156404663.1","sequence":"MKIVKRILLVLLSLFFTVVYSNAQADNLTLKIENVLKAKNARIGVAIFNSNEKDTLKINNDFHYPMQSVMKFPIALAVLSEIDKGNLSFEQKIEITPQDLLPKMWSPIKEEFPNGTTLTIEQILNYTVSETDNIGCDILLKLIGGTDSVQKFLNANHFTDISIKANEEQMHKDWNTQYQNWATPTAMNKLLIDTYNNKNQLLSKKSYDFIWKIMRETTTGSNRLKGQLPKNTIVAHKTGTSGINNGITAATNDVGVITLPNGQLIFISVFVAESKETSEINEKIISDIAKITWDYYLNK"},"dna_sequence":{"accession":"NG_067165.1","fmin":"0","fmax":"900","strand":"+","sequence":"ATGAAAATCGTAAAAAGGATATTATTAGTATTGTTAAGTTTATTTTTTACAGTTGTGTATTCAAATGCTCAAGCTGACAACTTAACTTTGAAAATTGAGAATGTTTTAAAGGCAAAAAATGCCAGAATAGGAGTAGCAATATTCAACAGCAATGAGAAGGATACTTTGAAGATTAATAACGACTTCCATTACCCGATGCAAAGCGTTATGAAATTTCCGATTGCTTTAGCCGTTTTGTCTGAGATAGATAAAGGGAATCTTTCTTTTGAACAAAAAATAGAGATTACCCCTCAAGACCTTTTGCCTAAAATGTGGAGTCCGATTAAAGAGGAATTCCCTAATGGAACAACTTTGACGATTGAACAAATACTAAATTATACAGTATCAGAGACCGACAATATTGGTTGTGATATTTTGCTAAAATTAATCGGAGGAACTGATTCTGTTCAAAAATTCTTGAATGCTAATCATTTCACTGATATTTCAATCAAAGCAAACGAAGAACAAATGCACAAGGATTGGAATACCCAATATCAAAATTGGGCAACCCCAACAGCGATGAACAAACTGTTAATAGATACTTATAATAATAAGAACCAATTACTTTCTAAAAAAAGTTATGATTTTATTTGGAAAATTATGAGAGAAACAACAACAGGAAGTAACCGATTAAAAGGACAATTACCAAAGAATACAATTGTTGCTCATAAAACAGGGACTTCCGGAATAAATAATGGAATTACAGCAGCCACTAATGATGTTGGGGTAATTACTTTACCGAATGGACAATTAATTTTTATAAGCGTATTTGTTGCAGAGTCCAAAGAAACTTCGGAAATTAATGAAAAGATTATTTCAGACATTGCAAAAATAACGTGGGATTACTATTTGAATAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36944","NCBI_taxonomy_name":"Providencia rettgeri","NCBI_taxonomy_id":"587"}}}},"ARO_accession":"3006219","ARO_id":"44681","ARO_name":"VEB-24","CARD_short_name":"VEB-24","ARO_description":"VEB-24 is a VEB beta-lactamase.","ARO_category":{"36182":{"category_aro_accession":"3000043","category_aro_cvterm_id":"36182","category_aro_name":"VEB beta-lactamase","category_aro_description":"VEB beta-lactamases or Vietnamese extended-spectrum beta-lactamases are class A beta-lactamases that confer high-level resistance to oxyimino cephalosporins and to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5686":{"model_id":"5686","model_name":"VEB-25","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"8061":{"protein_sequence":{"accession":"WP_160164840.1","sequence":"MKIVKRILLVLLSLFFTIVYSNAQTDNLTLKIENVLKAKNARIGVAIFNSNEKDTLKINNDFHFPMQSVMKFPIALAVLSEIDKGNLSFEQKIEITPQDLLPKTWSPIKEEFPNGTTLTIEQILNYTVSESDNIGCDILLKLIGGTDSVQKFLNANHFTDISIKANEEQMHKDWNTQYQNWATPTAMNKLLIDTYNNKNQLLSKKSYDFIWKIMRETTTGSNRLKGQLPKNTIVAHRTGTSGINNGIAAATNDVGVITLPNGQLIFISVFVAESKETSEINEKIISDIAKITWNYYLNK"},"dna_sequence":{"accession":"NG_067227.1","fmin":"0","fmax":"900","strand":"+","sequence":"ATGAAAATCGTAAAAAGGATATTATTAGTATTGTTAAGTTTATTTTTTACAATTGTGTATTCAAATGCTCAAACTGACAACTTAACTTTGAAAATTGAGAATGTTTTAAAGGCAAAAAATGCCAGAATAGGAGTAGCAATATTCAACAGCAATGAGAAGGATACTTTGAAGATTAATAACGACTTCCATTTCCCGATGCAAAGCGTTATGAAATTTCCGATTGCTTTAGCCGTTTTGTCTGAGATAGATAAAGGGAATCTTTCTTTTGAACAAAAAATAGAGATTACCCCTCAAGACCTTTTGCCTAAAACGTGGAGTCCGATTAAAGAGGAATTCCCTAATGGAACAACTTTGACGATTGAACAAATACTAAATTATACAGTATCAGAGAGCGACAATATTGGTTGTGATATTTTGCTAAAATTAATCGGAGGAACTGATTCTGTTCAAAAATTCTTGAATGCTAATCATTTCACTGATATTTCAATCAAAGCAAACGAAGAACAAATGCACAAGGATTGGAATACCCAATATCAAAATTGGGCAACCCCAACAGCGATGAACAAACTGTTAATAGATACTTATAATAATAAGAACCAATTACTTTCTAAAAAAAGTTATGATTTTATTTGGAAAATTATGAGAGAAACAACAACAGGAAGTAACCGATTAAAAGGACAATTACCAAAGAATACAATTGTTGCTCATAGAACAGGGACTTCCGGAATAAATAATGGAATTGCAGCAGCCACTAATGATGTTGGGGTAATTACTTTACCGAATGGACAATTAATTTTTATAAGCGTATTTGTTGCAGAGTCCAAAGAAACTTCGGAAATTAATGAAAAGATTATTTCAGACATTGCAAAAATAACGTGGAATTACTATTTGAATAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39097","NCBI_taxonomy_name":"Klebsiella pneumoniae subsp. pneumoniae","NCBI_taxonomy_id":"72407"}}}},"ARO_accession":"3006220","ARO_id":"44682","ARO_name":"VEB-25","CARD_short_name":"VEB-25","ARO_description":"VEB-25 is a VEB beta-lactamase.","ARO_category":{"36182":{"category_aro_accession":"3000043","category_aro_cvterm_id":"36182","category_aro_name":"VEB beta-lactamase","category_aro_description":"VEB beta-lactamases or Vietnamese extended-spectrum beta-lactamases are class A beta-lactamases that confer high-level resistance to oxyimino cephalosporins and to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5687":{"model_id":"5687","model_name":"VEB-26","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"8062":{"protein_sequence":{"accession":"WP_179284393.1","sequence":"MKIVKRILLVLLSLFFTIVYSNAQTDNLTLKIENVLKAKNARIGVAIFNSNEKDTLKINNDFHFPMQSVMKFPIALAVLSEIDKGNLSFEQKIEITPQDLLPKTWSPIKEEFPNGTTLTIEQILNYTVSESDNIGCDILLKLIGGTDSVQKFLNANHFTDISIKANEEQMHKDWNAQYQNWATPTAMNKLLIDTYNNKNQLLSKKSYDFIWKIMRETTTGSNRLKGQLPKNTIVAHKTGTSGINNGIAAATNDVGVITLPNGQLIFISVFVAESKETSEINEKIISDIAKITWNYYLNK"},"dna_sequence":{"accession":"NG_070222.1","fmin":"0","fmax":"900","strand":"+","sequence":"ATGAAAATCGTAAAAAGGATATTATTAGTATTGTTAAGTTTATTTTTTACAATTGTGTATTCAAATGCTCAAACTGACAACTTAACTTTGAAAATTGAGAATGTTTTAAAGGCAAAAAATGCCAGAATAGGAGTAGCAATATTCAACAGCAATGAGAAGGATACTTTGAAGATTAATAACGACTTCCATTTCCCGATGCAAAGCGTTATGAAATTTCCGATTGCTTTAGCCGTTTTGTCTGAGATAGATAAAGGGAATCTTTCTTTTGAACAAAAAATAGAGATTACCCCTCAAGACCTTTTGCCTAAAACGTGGAGTCCGATTAAAGAGGAATTCCCTAATGGAACAACTTTGACGATTGAACAAATACTAAATTATACAGTATCAGAGAGCGACAATATTGGTTGTGATATTTTGCTAAAATTAATCGGAGGAACTGATTCTGTTCAAAAATTCTTGAATGCTAATCATTTCACTGATATTTCAATCAAAGCAAACGAAGAACAAATGCACAAGGATTGGAATGCCCAATATCAAAATTGGGCAACCCCAACAGCGATGAACAAACTGTTAATAGATACTTATAATAATAAGAACCAATTACTTTCTAAAAAAAGTTATGATTTTATTTGGAAAATTATGAGAGAAACAACAACAGGAAGTAACCGATTAAAAGGACAATTACCAAAGAATACAATTGTTGCTCATAAAACAGGGACTTCCGGAATAAATAATGGAATTGCAGCAGCCACTAATGATGTTGGGGTAATTACTTTACCGAATGGACAATTAATTTTTATAAGCGTATTTGTTGCAGAGTCCAAAGAAACTTCGGAAATTAATGAAAAGATTATTTCAGACATTGCAAAAATAACGTGGAATTACTATTTGAATAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36783","NCBI_taxonomy_name":"Serratia marcescens","NCBI_taxonomy_id":"615"}}}},"ARO_accession":"3006221","ARO_id":"44683","ARO_name":"VEB-26","CARD_short_name":"VEB-26","ARO_description":"VEB-26 is a VEB beta-lactamase.","ARO_category":{"36182":{"category_aro_accession":"3000043","category_aro_cvterm_id":"36182","category_aro_name":"VEB beta-lactamase","category_aro_description":"VEB beta-lactamases or Vietnamese extended-spectrum beta-lactamases are class A beta-lactamases that confer high-level resistance to oxyimino cephalosporins and to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5688":{"model_id":"5688","model_name":"VEB-27","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"8063":{"protein_sequence":{"accession":"WP_188331880.1","sequence":"MKIVKRILLVLLSLFFTVVYSNAQADNLTLKIENVLKAKNARIGVAIFNSNEKDTLKINNDFHFPMQSVMKFPIALAVLSEIDKGNLSFEQKIEITPQDLLPKMWSPIKEEFPNGTTLTIEQILNYTVSETDNIGCDILLKLIGGTDSVQKFLNANHFTDISIKANEEQMHKDWNTQYQNWATPTAMNKLLIDTYNNKNQLLSKKSYDFIWKIMRETTTGSNRLKGQLPKNTIVAHKTGTSGINNGITAATNDVGVITLPNGQLIFISVFVAESKETSEINEKIISDIAKITWNYYLNK"},"dna_sequence":{"accession":"NG_070755.1","fmin":"0","fmax":"900","strand":"+","sequence":"ATGAAAATCGTAAAAAGGATATTATTAGTATTGTTAAGTTTATTTTTTACAGTTGTGTATTCAAATGCTCAAGCTGACAACTTAACTTTGAAAATTGAGAATGTTTTAAAGGCAAAAAATGCCAGAATAGGAGTAGCAATATTCAACAGCAATGAGAAGGATACTTTGAAGATTAATAACGACTTCCATTTCCCGATGCAAAGCGTTATGAAATTTCCGATTGCTTTAGCCGTTTTGTCTGAGATAGATAAAGGGAATCTTTCTTTTGAACAAAAAATAGAGATTACCCCTCAAGACCTTTTGCCTAAAATGTGGAGTCCGATTAAAGAGGAATTCCCTAATGGAACAACTTTGACGATTGAACAAATACTAAATTATACAGTATCAGAGACCGACAATATTGGTTGTGATATTTTGCTAAAATTAATCGGAGGAACTGATTCTGTTCAAAAATTCTTGAATGCTAATCATTTCACTGATATTTCAATCAAAGCAAACGAAGAACAAATGCACAAGGATTGGAATACCCAATATCAAAATTGGGCAACCCCAACAGCGATGAACAAACTGTTAATAGATACTTATAATAATAAGAACCAATTACTTTCTAAAAAAAGTTATGATTTTATTTGGAAAATTATGAGAGAAACAACAACAGGAAGTAACCGATTAAAAGGACAATTACCAAAGAATACAATTGTTGCTCATAAAACAGGGACTTCCGGAATAAATAATGGAATTACAGCAGCCACTAATGATGTTGGGGTAATTACTTTACCGAATGGACAATTAATTTTTATAAGCGTATTTGTTGCAGAGTCCAAAGAAACTTCGGAAATTAATGAAAAGATTATTTCAGACATTGCAAAAATAACGTGGAATTACTATTTGAATAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36946","NCBI_taxonomy_name":"Providencia stuartii","NCBI_taxonomy_id":"588"}}}},"ARO_accession":"3006222","ARO_id":"44684","ARO_name":"VEB-27","CARD_short_name":"VEB-27","ARO_description":"VEB-27 is a VEB beta-lactamase.","ARO_category":{"36182":{"category_aro_accession":"3000043","category_aro_cvterm_id":"36182","category_aro_name":"VEB beta-lactamase","category_aro_description":"VEB beta-lactamases or Vietnamese extended-spectrum beta-lactamases are class A beta-lactamases that confer high-level resistance to oxyimino cephalosporins and to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5689":{"model_id":"5689","model_name":"VHH-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"8064":{"protein_sequence":{"accession":"WP_063865164.1","sequence":"MKKLFLLLGLLACSSATYAANLMKTSPRLKKHISGRIGVSVWDTQTDEHWDYRGDERFPMMSTFKTLACATMLSDMDNEKLDKNATAKVEERNMVVWSPVMDRMASQTTRIEHACEAAMLMSDNTAANIVLRSIGGPRGVTTFLRSIGDKATRLDRFEPRLNEANPGDKRDTTTPNAMVNTLHTLLEGDALSYESRIQLKIWMQDNKVSDSLMRSVLPKGWSIADRSGAGGFGSRGITAMIWKENHKPVYISIYITETDLSLQARDQVIAQVSQLILDEYNTI"},"dna_sequence":{"accession":"NG_050334.1","fmin":"100","fmax":"952","strand":"+","sequence":"ATGAAAAAGCTATTTCTGCTACTTGGATTGTTAGCCTGTTCGAGTGCAACGTACGCCGCAAACTTAATGAAAACATCTCCGCGATTGAAGAAGCATATTTCGGGTCGAATCGGTGTGTCTGTCTGGGATACTCAAACCGATGAACATTGGGACTATAGAGGCGACGAGCGCTTCCCGATGATGAGCACATTCAAAACGCTTGCATGTGCAACGATGCTTAGTGACATGGATAATGAAAAGCTCGATAAAAACGCCACTGCCAAAGTAGAAGAGCGCAATATGGTGGTTTGGTCACCAGTAATGGATCGTATGGCAAGTCAAACAACGCGTATTGAACATGCTTGTGAAGCCGCAATGCTGATGAGCGACAATACCGCAGCCAACATTGTTTTGCGTAGCATTGGGGGTCCACGCGGTGTCACTACGTTCTTGCGTTCTATCGGTGATAAAGCAACGCGCCTTGACCGTTTTGAACCAAGACTGAACGAGGCGAACCCGGGCGACAAGCGAGACACCACAACACCTAATGCCATGGTAAATACGCTGCATACGTTGTTAGAAGGTGATGCGCTATCCTACGAATCACGCATTCAATTAAAAATCTGGATGCAGGATAACAAAGTCTCTGATTCTTTGATGCGCTCTGTGTTACCAAAGGGTTGGTCGATTGCCGATCGTTCTGGCGCAGGTGGCTTTGGATCACGCGGTATCACAGCAATGATCTGGAAAGAGAATCATAAACCGGTCTACATCAGCATTTACATTACTGAAACCGATTTATCCTTGCAGGCGCGCGATCAGGTTATCGCTCAAGTGAGCCAGTTAATACTGGATGAGTACAATACTATTTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36785","NCBI_taxonomy_name":"Vibrio harveyi","NCBI_taxonomy_id":"669"}}}},"ARO_accession":"3007003","ARO_id":"45465","ARO_name":"VHH-1","CARD_short_name":"VHH-1","ARO_description":"VHH-1 is a VHH beta-lactamase.","ARO_category":{"43915":{"category_aro_accession":"3005455","category_aro_cvterm_id":"43915","category_aro_name":"VHH beta-lactamase","category_aro_description":"VHH beta-lactamases are class A beta-lactamases found in Vibrio harveyi.","category_aro_class_name":"AMR Gene Family"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5690":{"model_id":"5690","model_name":"VHW-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"8065":{"protein_sequence":{"accession":"WP_063865165.1","sequence":"MKKLFLLLGLLACSSATYAAKLNEDISAIEEHISGRIGVSVWDTQTDEHWDYRGDERFPMMSTFKTLACATMLSDMDNEKLDKNATAKVEERNMVVWSPVMDRMAGQTTRFEHACEAAMLMSDNSAAHIVLRSIWGVHAGGTSFLRSIGDKATRLDRFEPRLNEANPGDKRDTTTPNAMVNTLHTLLEGDALSYESRIQLKIWMQDNKVSDSLMRSVLPKGWSIADRSGAGGFGSRGITAMIWKENHKPVYISIYITETDLSLQARDQVIAQVSQLILDEVQYYLALAKY"},"dna_sequence":{"accession":"NG_050335.1","fmin":"100","fmax":"973","strand":"+","sequence":"ATGAAAAAGCTATTTCTGCTACTTGGATTGTTAGCCTGTTCGAGTGCAACGTACGCCGCCAAACTTAATGAAGACATCTCCGCGATTGAAGAGCATATTTCGGGTCGAATCGGTGTGTCTGTCTGGGATACTCAAACCGATGAACATTGGGACTATAGAGGCGACGAGCGCTTCCCGATGATGAGCACATTCAAAACGCTTGCATGTGCAACGATGCTTAGTGACATGGATAATGAAAAGCTCGATAAAAACGCCACTGCCAAAGTAGAAGAGCGCAATATGGTGGTTTGGTCACCAGTAATGGATCGTATGGCAGGTCAAACAACGCGTTTTGAACATGCTTGTGAAGCCGCAATGCTTATGAGCGACAATTCCGCAGCCCACATTGTTTTGCGTAGCATTTGGGGGGTCCACGCGGGGGGCACTTCGTTCTTGCGTTCTATCGGTGATAAAGCAACGCGCCTTGACCGTTTTGAACCAAGACTGAACGAGGCGAACCCGGGCGACAAGCGAGACACCACAACACCTAATGCCATGGTAAATACGCTGCATACGTTGTTAGAAGGTGATGCGCTATCCTACGAATCACGCATTCAATTAAAAATCTGGATGCAGGATAACAAAGTCTCTGATTCTTTGATGCGCTCTGTGTTACCAAAGGGTTGGTCGATTGCCGATCGTTCTGGCGCAGGTGGCTTTGGATCACGCGGTATCACAGCAATGATCTGGAAAGAGAATCATAAACCGGTCTACATCAGCATTTACATTACTGAAACCGATTTATCCTTGCAGGCGCGCGATCAGGTTATCGCTCAAGTGAGCCAGTTAATACTGGATGAAGTACAATACTATTTAGCGCTCGCTAAATACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36785","NCBI_taxonomy_name":"Vibrio harveyi","NCBI_taxonomy_id":"669"}}}},"ARO_accession":"3007004","ARO_id":"45466","ARO_name":"VHW-1","CARD_short_name":"VHW-1","ARO_description":"VHW-1 is a VHW beta-lactamase.","ARO_category":{"43916":{"category_aro_accession":"3005456","category_aro_cvterm_id":"43916","category_aro_name":"VHW beta-lactamase","category_aro_description":"VHW beta-lactamases are class A beta-lactamases found Vibrio harveyi.","category_aro_class_name":"AMR Gene Family"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5691":{"model_id":"5691","model_name":"VIM-40","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"8066":{"protein_sequence":{"accession":"WP_063865190.1","sequence":"MLKVISSLLVYMTASVMAVASPLAHSGEPSGEYPTVNEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLVEAEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSANVLYGGCAVHELSRTSAGNVADADLAEWPTSVERIQKHYPEAEVVIPGHGLPGGLDLLQHTANVVKAHKNRSVAE"},"dna_sequence":{"accession":"NG_050368.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGTTAAAAGTTATTAGTAGTTTATTGGTCTACATGACCGCGTCTGTCATGGCTGTCGCAAGTCCGTTAGCCCATTCCGGGGAGCCGAGTGGTGAGTATCCGACAGTCAACGAAATTCCGGTCGGAGAGGTCCGACTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCGGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAAAAGCAAATTGGACTTCCCGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGTCGAGGCAGAGGGGAACGAGATTCCCACGCATTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAGCTCTTCTATCCTGGTGCTGCGCATTCGACCGACAATCTGGTTGTATACGTCCCGTCAGCGAACGTGCTATACGGTGGTTGTGCCGTTCATGAGTTGTCACGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCGTTGAGCGGATTCAAAAACACTACCCGGAAGCAGAGGTCGTCATTCCCGGGCACGGTCTACCGGGCGGTCTAGACTTGCTCCAGCACACAGCGAACGTTGTCAAAGCACACAAAAATCGCTCAGTCGCCGAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3002310","ARO_id":"38710","ARO_name":"VIM-40","CARD_short_name":"VIM-40","ARO_description":"VIM-40 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5692":{"model_id":"5692","model_name":"VIM-41","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"8067":{"protein_sequence":{"accession":"WP_063865191.1","sequence":"MFKLLSKLLVYLTASIMAIASPLAFSVDSSGEYPTVSEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEVEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSASVLYGGCAIYELSRTSAGNVANADLAEWPTSIERIQQHYPEAQFVIPGHGLPGGLDLLKHTTNVVKAHTNRSVVE"},"dna_sequence":{"accession":"NG_050369.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGTTCAAACTTTTGAGTAAGTTATTGGTCTATTTGACCGCGTCTATCATGGCTATTGCGAGTCCGCTCGCTTTTTCCGTAGATTCTAGCGGTGAGTATCCGACAGTCAGCGAAATTCCGGTCGGGGAGGTCCGGCTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCAGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAGAAGCAAATTGGACTTCCTGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGTAGAGGGGAACGAGATTCCCACGCACTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAACTCTTCTATCCTGGTGCTGCGCATTCGACCGACAACTTAGTTGTGTACGTCCCGTCTGCGAGTGTGCTCTATGGTGGTTGTGCGATTTATGAGTTGTCACGCACGTCTGCGGGGAACGTGGCCAATGCCGATCTGGCTGAATGGCCCACCTCCATTGAGCGGATTCAACAACACTACCCGGAAGCACAGTTCGTCATTCCGGGGCACGGCCTGCCGGGCGGTCTAGACTTGCTCAAGCACACAACGAATGTTGTAAAAGCGCACACAAATCGCTCAGTCGTTGAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002311","ARO_id":"38711","ARO_name":"VIM-41","CARD_short_name":"VIM-41","ARO_description":"VIM-41 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5693":{"model_id":"5693","model_name":"VIM-44","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"8068":{"protein_sequence":{"accession":"WP_063865194.1","sequence":"MFKLLSKLLVYLTASIMAIASPLAFSVDSSGEYPTVSEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEVEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSASVLYGGCAIYELSRTSAGNVADADLAEWPTSIERIQQHYPEAQFVIPGHGLPGGLDLLKHTTNVVNAHTNRSVVE"},"dna_sequence":{"accession":"NG_050372.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGTTCAAACTTTTGAGTAAGTTATTGGTCTATTTGACCGCGTCTATCATGGCTATTGCGAGTCCGCTCGCTTTTTCCGTAGATTCTAGCGGTGAGTATCCGACAGTCAGCGAAATTCCGGTCGGGGAGGTCCGGCTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCAGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAGAAGCAAATTGGACTTCCTGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCGCCGTCGACACGCCGGCTAGCCGAGGTAGAGGGGAACGAGATTCCCACGCACTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAACTCTTCTATCCTGGTGCTGCGCATTCGACCGACAACTTAGTTGTGTACGTCCCGTCTGCGAGTGTGCTCTATGGTGGTTGTGCGATTTATGAGTTGTCACGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCATTGAGCGGATTCAACAACACTACCCGGAAGCACAGTTCGTCATTCCGGGGCACGGCCTGCCGGGCGGTCTAGACTTGCTCAAGCACACAACGAATGTTGTAAATGCGCACACAAATCGCTCAGTCGTTGAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3003660","ARO_id":"40270","ARO_name":"VIM-44","CARD_short_name":"VIM-44","ARO_description":"VIM-44 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5694":{"model_id":"5694","model_name":"VIM-45","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"8069":{"protein_sequence":{"accession":"WP_063865195.1","sequence":"MFKLLSKLLVYLTASIMAIASPLAFSVDSSGEYPIVSEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEVEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSASVLYGGCAIYELSRTSAGNVADADLAEWPTSIERIQQHYPEAQFVIPGHGLPGGLDLLKHTTNVVKAHTNRSVVE"},"dna_sequence":{"accession":"NG_050373.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGTTCAAACTTTTGAGTAAGTTATTGGTCTATTTGACCGCGTCTATCATGGCTATTGCGAGTCCGCTCGCTTTTTCCGTAGATTCTAGCGGTGAGTATCCGATAGTCAGCGAAATTCCGGTCGGGGAGGTCCGGCTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCAGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAGAAGCAAATTGGACTTCCTGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGTAGAGGGGAACGAGATTCCCACGCACTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAACTCTTCTATCCTGGTGCTGCGCATTCGACCGACAACTTAGTTGTGTACGTCCCGTCTGCGAGTGTGCTCTATGGTGGTTGTGCGATTTATGAGTTGTCACGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCATTGAGCGGATTCAACAACACTACCCGGAAGCACAGTTCGTCATTCCGGGGCACGGCCTGCCGGGCGGTCTAGACTTGCTCAAGCACACAACGAATGTTGTAAAAGCGCACACAAATCGCTCAGTCGTTGAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3003661","ARO_id":"40271","ARO_name":"VIM-45","CARD_short_name":"VIM-45","ARO_description":"VIM-45 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5695":{"model_id":"5695","model_name":"VIM-46","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"8070":{"protein_sequence":{"accession":"WP_063865196.1","sequence":"MFKFLSKLLVYLTASIMAIASPLAFSVDSSGEYPTASEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEVEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSASVLYGGCAIYELSRTSAGNVADADLAEWPTSIERIQQHYPEAQFVIPGHGLPGGLDLLKHTTNVVKAHTNRSVVE"},"dna_sequence":{"accession":"NG_050374.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGTTCAAATTTTTGAGTAAGTTATTGGTCTATTTGACCGCGTCTATCATGGCTATTGCGAGTCCGCTCGCTTTTTCCGTAGATTCTAGCGGTGAGTATCCGACAGCCAGCGAAATTCCGGTCGGGGAGGTCCGGCTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCAGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAGAAGCAAATTGGACTTCCTGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGTAGAGGGGAACGAGATTCCCACGCACTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAACTCTTCTATCCTGGTGCTGCGCATTCGACCGACAACTTAGTTGTGTACGTCCCGTCTGCGAGTGTGCTCTATGGTGGTTGTGCGATTTATGAGTTGTCACGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCATTGAGCGGATTCAACAACACTACCCGGAAGCACAGTTCGTCATTCCGGGGCACGGCCTGCCGGGCGGTCTAGACTTGCTCAAGCACACAACGAATGTTGTAAAAGCGCACACAAATCGCTCAGTCGTTGAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3003662","ARO_id":"40272","ARO_name":"VIM-46","CARD_short_name":"VIM-46","ARO_description":"VIM-46 is a beta-lactamase. Name originally from the historical Lahey list of beta-lactamases, some of which did not include sequence data.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5696":{"model_id":"5696","model_name":"VIM-47","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"8071":{"protein_sequence":{"accession":"WP_063865197.1","sequence":"MFKVVSSLLFYMTASLMAVASPLAHSGESRGEYPTVSEIPVGEVRLYQIDDGVWSHIATHTFDGVVYPSNGLIVRDGDELLLIDTAWGTKNTVALLAEIEKQIGLPVTRSVSTHFHDDRVGGVDALRAAGVATYASPSTRRLAEAEGNEVPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSANVLYGGCAVLELSRTSAGNVADADLAEWPGSVERIQQHYPEAEVVIPGHGLPGGLDLLQHTANVVKAHTNRSVAE"},"dna_sequence":{"accession":"NG_050375.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGTTCAAAGTTGTTAGTAGTTTATTGTTCTACATGACCGCCTCTCTAATGGCTGTAGCTAGTCCGTTAGCCCATTCCGGGGAGTCGAGAGGTGAGTATCCGACAGTCAGCGAAATTCCGGTCGGAGAAGTTCGGCTGTACCAGATTGACGATGGTGTTTGGTCGCATATCGCAACGCATACGTTTGATGGCGTGGTGTACCCGTCCAATGGTCTCATTGTCCGTGATGGCGATGAGTTGCTTTTGATTGATACAGCTTGGGGTACGAAAAACACAGTGGCCCTTCTCGCGGAGATTGAGAAGCAAATTGGACTTCCCGTAACGCGTTCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGAGTTGATGCCCTTAGGGCGGCTGGAGTGGCGACGTACGCATCGCCCTCGACACGCCGTCTAGCCGAGGCAGAGGGGAACGAGGTTCCCACACACTCTCTAGAAGGGCTCTCATCGAGTGGGGACGCAGTGCGTTTCGGTCCAGTAGAGCTCTTCTATCCTGGTGCTGCGCATTCGACCGACAATCTGGTTGTATACGTCCCGTCAGCGAACGTGCTATACGGTGGTTGTGCCGTTCTGGAATTGTCACGCACATCCGCGGGAAACGTGGCCGATGCCGACCTGGCTGAATGGCCCGGTTCCGTTGAGCGGATTCAACAACATTACCCAGAAGCAGAGGTGGTCATTCCCGGGCACGGTCTACCGGGCGGTCTAGACTTGCTCCAGCACACAGCGAACGTTGTCAAAGCACACACAAATCGCTCAGTCGCCGAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005495","ARO_id":"43957","ARO_name":"VIM-47","CARD_short_name":"VIM-47","ARO_description":"VIM-47 is a VIM beta-lactamase.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5697":{"model_id":"5697","model_name":"VIM-48","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"8072":{"protein_sequence":{"accession":"WP_136512106.1","sequence":"MFKFLSKLLVYLTASIMAIASPLAFSVDSSGEYPTVSEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEVEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSASVLYGGCAIYELSRTSAGNVADADLAEWPTSIERIQQHYPEAQFVIPGHGLPGGLDLLKHTTNVVKAHTNRSVVE"},"dna_sequence":{"accession":"NG_064783.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGTTCAAATTTTTGAGTAAGTTATTGGTCTATTTGACCGCGTCTATCATGGCTATTGCGAGTCCGCTCGCTTTTTCCGTAGATTCTAGCGGTGAGTATCCGACAGTCAGCGAAATTCCGGTCGGGGAGGTCCGGCTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCAGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAGAAGCAAATTGGACTTCCTGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGTAGAGGGGAACGAGATTCCCACGCACTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAACTCTTCTATCCTGGTGCTGCGCATTCGACCGACAACTTAGTTGTGTACGTCCCGTCTGCGAGTGTGCTCTATGGTGGTTGTGCGATTTATGAGTTGTCACGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCATTGAGCGGATTCAACAACACTACCCGGAAGCACAGTTCGTCATTCCGGGGCACGGCCTGCCGGGCGGTCTAGACTTGCTCAAGCACACAACGAATGTTGTAAAAGCGCACACAAATCGCTCAGTCGTTGAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3005496","ARO_id":"43958","ARO_name":"VIM-48","CARD_short_name":"VIM-48","ARO_description":"VIM-48 is a VIM beta-lactamase.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5698":{"model_id":"5698","model_name":"VIM-49","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"8073":{"protein_sequence":{"accession":"WP_063865198.1","sequence":"MLKVISSLLVYMTASVMAVASPLAHSGEPSGEYPTVNEIPVGEVRLYQIADGVWSHISTQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRKAGVATYASPSTRRLAEAEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSANVLYGGCAVLALSRTSAGNVADADLAEWPTSVERIQKHYPEAEVVIPGHGLPGGLDLLQHTANVVTAHKNRSVAE"},"dna_sequence":{"accession":"NG_050376.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGTTAAAAGTTATTAGTAGTTTATTGGTCTACATGACCGCGTCTGTCATGGCTGTAGCTAGTCCGTTAGCCCATTCCGGGGAGCCGAGTGGTGAGTATCCGACAGTCAACGAAATTCCGGTCGGAGAGGTCCGGCTTTACCAGATTGCTGATGGTGTTTGGTCGCATATCTCAACGCAGTCGTTTGATGGCGCGGTCTACCCATCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCCCTTCTCGCGGAGATTGAGAAGCAAATTGGACTTCCCGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGAAGGCTGGAGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGCAGAGGGGAACGAGATTCCCACGCACTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAGCTCTTCTATCCCGGTGCTGCGCATTCGACCGACAATCTGGTTGTATACGTCCCGTCAGCGAACGTGCTATACGGTGGTTGTGCCGTTCTTGCGTTGTCACGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCGTTGAGCGGATTCAAAAACACTACCCGGAAGCAGAGGTCGTCATTCCCGGGCACGGTCTACCGGGCGGTCTAGACTTGCTCCAGCACACAGCGAACGTTGTCACAGCACACAAAAATCGCTCAGTCGCCGAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005497","ARO_id":"43959","ARO_name":"VIM-49","CARD_short_name":"VIM-49","ARO_description":"VIM-49 is a VIM beta-lactamase.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5699":{"model_id":"5699","model_name":"VIM-50","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"8074":{"protein_sequence":{"accession":"WP_063865199.1","sequence":"MFKLLSKLLVYLTASIMAIASPLAFSVDSSGEYPTVSEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEVEGSEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSASVLYGGCAIYELSLTSAGNVADADLAEWPTSIERIQQHYPEAQFVIPGHGLPGGLDLLKHTTNVVKAHTNRSVVE"},"dna_sequence":{"accession":"NG_050378.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGTTCAAACTTTTGAGTAAGTTATTGGTCTATTTGACCGCGTCTATCATGGCTATTGCGAGTCCGCTCGCTTTTTCCGTAGATTCTAGCGGTGAGTATCCGACAGTCAGCGAAATTCCGGTCGGGGAGGTCCGGCTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCAGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAGAAGCAAATTGGACTTCCTGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGTAGAGGGGAGCGAGATTCCCACGCACTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAACTCTTCTATCCTGGTGCTGCGCATTCGACCGACAACTTAGTTGTGTACGTCCCGTCTGCGAGTGTGCTCTATGGTGGTTGTGCGATTTATGAGTTGTCACTCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCATTGAGCGGATTCAACAACACTACCCGGAAGCACAGTTCGTCATTCCGGGGCACGGCCTGCCGGGCGGTCTAGACTTGCTCAAGCACACAACGAATGTTGTAAAAGCGCACACAAATCGCTCAGTCGTTGAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005498","ARO_id":"43960","ARO_name":"VIM-50","CARD_short_name":"VIM-50","ARO_description":"VIM-50 is a VIM beta-lactamase.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5700":{"model_id":"5700","model_name":"VIM-51","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"8075":{"protein_sequence":{"accession":"WP_063865200.1","sequence":"MFKLLSKLLVYLTASIMAIASPLAFSVDSSGEYPTVSEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEVEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSASVLYGGCAIYELSRTSVGNVADADLAEWPTSIERIQQHYPEAQFVIPGHGLPGGLDLLKHTTNVVKAHTNRSVVE"},"dna_sequence":{"accession":"NG_050379.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGTTCAAACTTTTGAGTAAGTTATTGGTCTATTTGACCGCGTCTATCATGGCTATTGCGAGTCCGCTCGCTTTTTCCGTAGATTCTAGCGGTGAGTATCCGACAGTCAGCGAAATTCCGGTCGGGGAGGTCCGGCTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCAGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAGAAGCAAATTGGACTTCCTGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGTAGAGGGGAACGAGATTCCCACGCACTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAACTCTTCTATCCTGGTGCTGCGCATTCGACCGACAACTTAGTTGTGTACGTCCCGTCTGCGAGTGTGCTCTATGGTGGTTGTGCGATTTATGAGTTGTCACGCACGTCTGTGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCATTGAGCGGATTCAACAACACTACCCGGAAGCACAGTTCGTCATTCCGGGGCACGGCCTGCCGGGCGGTCTAGACTTGCTCAAGCACACAACGAATGTTGTAAAAGCGCACACAAATCGCTCAGTCGTTGAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3005499","ARO_id":"43961","ARO_name":"VIM-51","CARD_short_name":"VIM-51","ARO_description":"VIM-51 is a VIM beta-lactamase.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5701":{"model_id":"5701","model_name":"VIM-52","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"8076":{"protein_sequence":{"accession":"WP_094009807.1","sequence":"MLKVISSLLVYMTASVMAVASPLAHSGEPSGEYPTVNEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEAEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSANVLYGGCAVRELSSTSAGNVADADLAEWPTSVERIQKHYPEAEVVIPGHGLPGGLDLLQHTANVVKAHKNRSVAE"},"dna_sequence":{"accession":"NG_055489.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGTTAAAAGTTATTAGTAGTTTATTGGTCTACATGACCGCGTCTGTCATGGCTGTCGCAAGTCCGTTAGCCCATTCCGGGGAGCCGAGTGGTGAGTATCCGACAGTCAACGAAATTCCGGTCGGAGAGGTCCGACTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCGGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAAAAGCAAATTGGACTTCCCGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGCAGAGGGGAACGAGATTCCCACGCATTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAGCTCTTCTATCCTGGTGCTGCGCATTCGACCGACAATCTGGTTGTATACGTCCCGTCAGCGAACGTGCTATACGGTGGTTGTGCCGTTCGTGAGTTGTCAAGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCGTTGAGCGGATTCAAAAACACTACCCGGAAGCAGAGGTCGTCATTCCCGGGCACGGTCTACCGGGCGGTCTAGACTTGCTCCAGCACACAGCGAACGTTGTCAAAGCACACAAAAATCGCTCAGTCGCCGAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3005500","ARO_id":"43962","ARO_name":"VIM-52","CARD_short_name":"VIM-52","ARO_description":"VIM-52 is a VIM beta-lactamase.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5702":{"model_id":"5702","model_name":"VIM-53","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"8077":{"protein_sequence":{"accession":"WP_122630828.1","sequence":"MLKVISSLLVYLTASIMAIASPLAFSVDSSGEYPTVSEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEVEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSASVLYGGCAIYELSRTSAGNVADADLAEWPTSIERIQQHYPEAQFVIPGHGLPGGLDLLKHTTNVVKAHTNRSVAE"},"dna_sequence":{"accession":"NG_062231.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGTTAAAAGTTATTAGTAGTTTATTGGTCTATTTGACCGCGTCTATCATGGCTATTGCGAGTCCGCTCGCTTTTTCCGTAGATTCTAGCGGTGAGTATCCGACAGTCAGCGAAATTCCGGTCGGGGAGGTCCGGCTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCAGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAGAAGCAAATTGGACTTCCTGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGTAGAGGGGAACGAGATTCCCACGCACTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAACTCTTCTATCCTGGTGCTGCGCATTCGACCGACAACTTAGTTGTGTACGTCCCGTCTGCGAGTGTGCTCTATGGTGGTTGTGCGATTTATGAGTTGTCACGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCATTGAGCGGATTCAACAACACTACCCGGAAGCACAGTTCGTCATTCCGGGGCACGGCCTGCCGGGCGGTCTAGACTTGCTCAAGCACACAACGAATGTTGTAAAAGCGCACACAAATCGCTCAGTCGCCGAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005501","ARO_id":"43963","ARO_name":"VIM-53","CARD_short_name":"VIM-53","ARO_description":"VIM-53 is a VIM beta-lactamase.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5703":{"model_id":"5703","model_name":"VIM-54","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"8078":{"protein_sequence":{"accession":"WP_077064888.1","sequence":"MLKVISSLLVYMTASVMAVASPLAHSGEPSGEYPTVNEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEAEGSEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSANVLYGGCAVHELSRTSAGNVADADLAEWPTSVERIQKHYPEAEVVIPGHGLPGGLDLLQHTANVVKAHKNRSVAE"},"dna_sequence":{"accession":"NG_052864.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGTTAAAAGTTATTAGTAGTTTATTGGTCTACATGACCGCGTCTGTCATGGCTGTCGCAAGTCCGTTAGCCCATTCCGGGGAGCCGAGTGGTGAGTATCCGACAGTCAACGAAATTCCGGTCGGAGAGGTCCGACTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCGGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAAAAGCAAATTGGACTTCCCGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGCAGAGGGGAGCGAGATTCCCACGCATTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAGCTCTTCTATCCTGGTGCTGCGCATTCGACCGACAATCTGGTTGTATACGTCCCGTCAGCGAACGTGCTATACGGTGGTTGTGCCGTTCATGAGTTGTCACGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCGTTGAGCGGATTCAAAAACACTACCCGGAAGCAGAGGTCGTCATTCCCGGGCACGGTCTACCGGGCGGTCTAGACTTGCTCCAGCACACAGCGAACGTTGTCAAAGCACACAAAAATCGCTCAGTCGCCGAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36783","NCBI_taxonomy_name":"Serratia marcescens","NCBI_taxonomy_id":"615"}}}},"ARO_accession":"3005502","ARO_id":"43964","ARO_name":"VIM-54","CARD_short_name":"VIM-54","ARO_description":"VIM-54 is a VIM beta-lactamase.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5704":{"model_id":"5704","model_name":"VIM-55","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"8079":{"protein_sequence":{"accession":"WP_136512107.1","sequence":"MLKVISSLLVYMTASVMAVASPLAHSGEPSGEYPTVNEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEAEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSAKVLYGGCAVHELSRTSAGNVADADLAEWPTSVERIQKRYPEAEVVIPGHGLPGGLDLLQHTANVVKAHKNRSVAE"},"dna_sequence":{"accession":"NG_064784.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGTTAAAAGTTATTAGTAGTTTATTGGTCTACATGACCGCGTCTGTCATGGCTGTCGCAAGTCCGTTAGCCCATTCCGGGGAGCCGAGTGGTGAGTATCCGACAGTCAACGAAATTCCGGTCGGAGAGGTCCGACTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCGGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAAAAGCAAATTGGACTTCCCGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGCAGAGGGGAACGAGATTCCCACGCATTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAGCTCTTCTATCCTGGTGCTGCGCATTCGACCGACAATCTGGTTGTATACGTCCCGTCAGCGAAAGTGCTATACGGTGGTTGTGCCGTTCATGAGTTGTCACGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCGTTGAGCGGATTCAAAAACGCTACCCGGAAGCAGAGGTCGTCATTCCCGGGCACGGTCTACCGGGCGGTCTAGACTTGCTCCAGCACACAGCGAACGTTGTCAAAGCACACAAAAATCGCTCAGTCGCCGAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3005503","ARO_id":"43965","ARO_name":"VIM-55","CARD_short_name":"VIM-55","ARO_description":"VIM-55 is a VIM beta-lactamase.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5705":{"model_id":"5705","model_name":"VIM-56","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"8080":{"protein_sequence":{"accession":"WP_104009846.1","sequence":"MFTLLSKLLVYLTASIMAIASPLAFSVDSSGEYPTVSEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEVEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSASVLYGGCAIYELSRTSAGGVADADLAEWPTSIERIQQHYPEAQFVIPGHGLPGGLDLLKHTTNVVKAHTNRSVVE"},"dna_sequence":{"accession":"NG_056405.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGTTCACGCTTTTGAGTAAGTTATTGGTCTATTTGACCGCGTCTATCATGGCTATTGCGAGTCCGCTCGCTTTTTCCGTAGATTCTAGCGGTGAGTATCCGACAGTCAGCGAAATTCCGGTCGGGGAGGTCCGGCTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCAGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAGAAGCAAATTGGACTTCCTGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGTAGAGGGGAACGAGATTCCCACGCACTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAACTCTTCTATCCTGGTGCTGCGCATTCGACCGACAACTTAGTTGTGTACGTCCCGTCTGCGAGTGTGCTCTATGGTGGTTGTGCGATTTATGAGTTGTCACGCACGTCTGCGGGGGGCGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCATTGAGCGGATTCAACAACACTACCCGGAAGCACAGTTCGTCATTCCGGGGCACGGCCTGCCGGGCGGTCTAGACTTGCTCAAGCACACAACGAATGTTGTAAAAGCGCACACAAATCGCTCAGTCGTTGAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3005504","ARO_id":"43966","ARO_name":"VIM-56","CARD_short_name":"VIM-56","ARO_description":"VIM-56 is a VIM beta-lactamase.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5706":{"model_id":"5706","model_name":"VIM-57","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"8081":{"protein_sequence":{"accession":"WP_111672914.1","sequence":"MLKVISSLLVYMTASVMAVASPLAHSGEPSGEYPTVNEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEAEGNEIPTHSLEGLSSSGDAVRFGPVEIFYPGAAHSTDNLVVYVPSANVLYGGCAVHELSSTSAGNVADADLAEWPTSVERIQKHYPEAEVVIPGHGLPGGLDLLQHTANVVKAHKNRSVAE"},"dna_sequence":{"accession":"NG_060572.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGTTAAAAGTTATTAGTAGTTTATTGGTCTACATGACCGCGTCTGTCATGGCTGTCGCAAGTCCGTTAGCCCATTCCGGGGAGCCGAGTGGTGAGTATCCGACAGTCAACGAAATTCCGGTCGGAGAGGTCCGACTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCGGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAAAAGCAAATTGGACTTCCCGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGCAGAGGGGAACGAGATTCCCACGCATTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAGATCTTCTATCCTGGTGCTGCGCATTCGACCGACAATCTGGTTGTATACGTCCCGTCAGCGAACGTGCTATACGGTGGTTGTGCCGTTCATGAGTTGTCAAGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCGTTGAGCGGATTCAAAAACACTACCCGGAAGCAGAGGTCGTCATTCCCGGGCACGGTCTACCGGGCGGTCTAGACTTGCTCCAGCACACAGCGAACGTTGTCAAAGCACACAAAAATCGCTCAGTCGCCGAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3005505","ARO_id":"43967","ARO_name":"VIM-57","CARD_short_name":"VIM-57","ARO_description":"VIM-57 is a VIM beta-lactamase.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5707":{"model_id":"5707","model_name":"VIM-58","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"8082":{"protein_sequence":{"accession":"WP_111772163.1","sequence":"MFKFLSKLLVYLTASIMAIASPLAFSVDSSGEYPTVSEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEVEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSASVLYGGCAIYELSRTSAGGVADADLAEWPTSIERIQQHYPEAQFVIPGHGLPGGLDLLKHTTNVVKAHTNRSVVE"},"dna_sequence":{"accession":"NG_060588.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGTTCAAATTTTTGAGTAAGTTATTGGTCTATTTGACCGCGTCTATCATGGCTATTGCGAGTCCGCTCGCTTTTTCCGTAGATTCTAGCGGTGAGTATCCGACAGTCAGCGAAATTCCGGTCGGGGAGGTCCGGCTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCAGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAGAAGCAAATTGGACTTCCTGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGTAGAGGGGAACGAGATTCCCACGCACTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAACTCTTCTATCCTGGTGCTGCGCATTCGACCGACAACTTAGTTGTGTACGTCCCGTCTGCGAGTGTGCTCTATGGTGGTTGTGCGATTTATGAGTTGTCACGCACGTCTGCGGGGGGCGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCATTGAGCGGATTCAACAACACTACCCGGAAGCACAGTTCGTCATTCCGGGGCACGGCCTGCCGGGCGGTCTAGACTTGCTCAAGCACACAACGAATGTTGTAAAAGCGCACACAAATCGCTCAGTCGTTGAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3005506","ARO_id":"43968","ARO_name":"VIM-58","CARD_short_name":"VIM-58","ARO_description":"VIM-58 is a VIM beta-lactamase.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5708":{"model_id":"5708","model_name":"VIM-59","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"8083":{"protein_sequence":{"accession":"WP_114699283.1","sequence":"MLKVISSLLVYMTASVMAVASPLAHSGEPSGEYPTVNEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEAEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSANVLYGGCAVHELSSTSAGNVADADLAEWPTSVERIQKRYPEAEVVIPGHGLPGGLDLLQHTANVVKAHKNRSVAE"},"dna_sequence":{"accession":"NG_061412.1","fmin":"93","fmax":"894","strand":"+","sequence":"ATGTTAAAAGTTATTAGTAGTTTATTGGTCTACATGACCGCGTCTGTCATGGCTGTCGCAAGTCCGTTAGCCCATTCCGGGGAGCCGAGTGGTGAGTATCCGACAGTCAACGAAATTCCGGTCGGAGAGGTCCGACTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCGGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAAAAGCAAATTGGACTTCCCGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGCAGAGGGGAACGAGATTCCCACGCATTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAGCTCTTCTATCCTGGTGCTGCGCATTCGACCGACAATCTGGTTGTATACGTCCCGTCAGCGAACGTGCTATACGGTGGTTGTGCCGTTCATGAGTTGTCAAGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCGTTGAGCGGATTCAAAAACGCTACCCGGAAGCAGAGGTCGTCATTCCCGGGCACGGTCTACCGGGCGGTCTAGACTTGCTCCAGCACACAGCGAACGTTGTCAAAGCACACAAAAATCGCTCAGTCGCCGAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3005507","ARO_id":"43969","ARO_name":"VIM-59","CARD_short_name":"VIM-59","ARO_description":"VIM-59 is a VIM beta-lactamase.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5709":{"model_id":"5709","model_name":"VIM-60","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"8084":{"protein_sequence":{"accession":"WP_114699277.1","sequence":"MFKLLSKLLVYLTASIMAIASPLAFSVDSSGEYPTVSEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEVEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSASVLYGGCAIYELSLTSAGNVADADLAEWPTSIERIQQRYPEAQFVIPGHGLPGGLDLLKHTTNVVKAHTNRSVVE"},"dna_sequence":{"accession":"NG_061404.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGTTCAAACTTTTGAGTAAGTTATTGGTCTATTTGACCGCGTCTATCATGGCTATTGCGAGTCCGCTCGCTTTTTCCGTAGATTCTAGCGGTGAGTATCCGACAGTCAGCGAAATTCCGGTCGGGGAGGTCCGGCTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCAGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAGAAGCAAATTGGACTTCCTGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGTAGAGGGGAACGAGATTCCCACGCACTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAACTCTTCTATCCTGGTGCTGCGCATTCGACCGACAACTTAGTTGTGTACGTCCCGTCTGCGAGTGTGCTCTATGGTGGTTGTGCGATTTATGAGTTGTCACTCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCATTGAGCGGATTCAACAACGCTACCCGGAAGCACAGTTCGTCATTCCGGGGCACGGCCTGCCGGGCGGTCTAGACTTGCTCAAGCACACAACGAATGTTGTAAAAGCGCACACAAATCGCTCAGTCGTTGAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005508","ARO_id":"43970","ARO_name":"VIM-60","CARD_short_name":"VIM-60","ARO_description":"VIM-60 is a VIM beta-lactamase.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5710":{"model_id":"5710","model_name":"VIM-61","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"8085":{"protein_sequence":{"accession":"WP_123002103.1","sequence":"MFQIRSFLVGISAFVMAVLGSAAYSAQPGGEYPTVDDIPVGEVRLYKIGDGVWSHIATQKLGDTVYSSNGLIVRDADELLLIDTAWGAKNTVALLAEIEKQIGLPVTRSISTHFHDDRVGGVDVLRAAGVATYTSPLTRQLAEAAGNEVPAHSLKALSSSGDVVRFGPVEVFYPGAAHSGDNLVVYVPAVRVLFGGCAVHEASRESAGYVADANLAEWPATIKRIQQRYPEAEVVIPGHGLPGGLELLQHTTNVVKTHKVRPVAE"},"dna_sequence":{"accession":"NG_062359.1","fmin":"0","fmax":"798","strand":"+","sequence":"ATGTTTCAAATTCGCAGCTTTCTGGTTGGTATCAGTGCATTCGTCATGGCCGTACTTGGATCAGCAGCATATTCCGCACAGCCTGGCGGTGAATATCCGACAGTAGATGACATACCGGTAGGGGAAGTTCGGCTGTACAAGATTGGCGATGGCGTTTGGTCGCATATCGCAACTCAGAAACTCGGTGACACGGTGTACTCGTCTAATGGACTTATCGTCCGCGATGCTGATGAGTTGCTTCTTATTGATACAGCGTGGGGGGCGAAGAACACGGTAGCCCTTCTCGCGGAGATTGAAAAGCAAATTGGACTTCCAGTAACGCGCTCAATTTCTACGCACTTCCATGACGATCGAGTCGGTGGAGTTGATGTCCTCCGGGCGGCTGGAGTGGCAACGTACACCTCACCCTTGACACGCCAGCTGGCCGAAGCGGCGGGAAACGAGGTGCCTGCGCACTCTCTAAAAGCGCTCTCCTCTAGTGGAGATGTGGTGCGCTTCGGTCCCGTAGAGGTTTTCTATCCTGGTGCTGCGCATTCGGGCGACAATCTTGTGGTATACGTGCCGGCCGTGCGCGTACTGTTTGGTGGCTGTGCAGTTCATGAGGCGTCACGCGAATCCGCGGGTTATGTTGCCGATGCCAATTTGGCAGAATGGCCTGCTACCATTAAACGAATTCAACAGCGGTATCCGGAAGCAGAGGTCGTCATCCCCGGCCACGGTCTACCGGGCGGTCTGGAATTGCTCCAACACACAACTAACGTTGTCAAAACGCACAAAGTACGCCCGGTGGCCGAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005509","ARO_id":"43971","ARO_name":"VIM-61","CARD_short_name":"VIM-61","ARO_description":"VIM-61 is a VIM beta-lactamase.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5711":{"model_id":"5711","model_name":"VIM-62","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"8086":{"protein_sequence":{"accession":"WP_128268287.1","sequence":"MFKLLSKLLVYLTASIMAIASPLVFSVDSSGEYPTVSEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEVEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSASVLYGGCAIYELSRTSAGNVADADLAEWPTSIERIQQHYPEAQFVIPGHGLPGGLDLLKHTTNVVKAHTNRSVVE"},"dna_sequence":{"accession":"NG_063896.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGTTCAAACTTTTGAGTAAGTTATTGGTCTATTTGACCGCGTCTATCATGGCTATTGCGAGTCCGCTCGTTTTTTCCGTAGATTCTAGCGGTGAGTATCCGACAGTCAGCGAAATTCCGGTCGGGGAGGTCCGGCTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCAGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAGAAGCAAATTGGACTTCCTGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGTAGAGGGGAACGAGATTCCCACGCACTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAACTCTTCTATCCTGGTGCTGCGCATTCGACCGACAACTTAGTTGTGTACGTCCCGTCTGCGAGTGTGCTCTATGGTGGTTGTGCGATTTATGAGTTGTCACGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCATTGAGCGGATTCAACAACACTACCCGGAAGCACAGTTCGTCATTCCGGGGCACGGCCTGCCGGGCGGTCTAGACTTGCTCAAGCACACAACGAATGTTGTAAAAGCGCACACAAATCGCTCAGTCGTTGAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36803","NCBI_taxonomy_name":"Pseudomonas putida","NCBI_taxonomy_id":"303"}}}},"ARO_accession":"3005510","ARO_id":"43972","ARO_name":"VIM-62","CARD_short_name":"VIM-62","ARO_description":"VIM-62 is a VIM beta-lactamase.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5712":{"model_id":"5712","model_name":"VIM-63","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"8087":{"protein_sequence":{"accession":"WP_136512108.1","sequence":"MFKLLSKLLVYLTASIMAIASPLAFSVDSSGEYPTVSEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEVEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSASVLYGGCAIYELSRTSAGNVADADLAEWPTSIERLQQHYPEAQFVIPGHGLPGGLDLLKHTTNVVKAHTNRSVVE"},"dna_sequence":{"accession":"NG_064785.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGTTCAAACTTTTGAGTAAGTTATTGGTCTATTTGACCGCGTCTATCATGGCTATTGCGAGTCCGCTCGCTTTTTCCGTAGATTCTAGCGGTGAGTATCCGACAGTCAGCGAAATTCCGGTCGGGGAGGTCCGGCTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCAGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAGAAGCAAATTGGACTTCCTGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGTAGAGGGGAACGAGATTCCCACGCACTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAACTCTTCTATCCTGGTGCTGCGCATTCGACCGACAACTTAGTTGTGTACGTCCCGTCTGCGAGTGTGCTCTATGGTGGTTGTGCGATTTATGAGTTGTCACGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCATTGAGCGGCTTCAACAACACTACCCGGAAGCACAGTTCGTCATTCCGGGGCACGGCCTGCCGGGCGGTCTAGACTTGCTCAAGCACACAACGAATGTTGTAAAAGCGCACACAAATCGCTCAGTCGTTGAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005511","ARO_id":"43973","ARO_name":"VIM-63","CARD_short_name":"VIM-63","ARO_description":"VIM-63 is a VIM beta-lactamase.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35976":{"category_aro_accession":"0000059","category_aro_cvterm_id":"35976","category_aro_name":"cefepime","category_aro_description":"Cefepime (INN) is a fourth-generation cephalosporin antibiotic developed in 1994. It contains an aminothiazolyl group that decreases its affinity with beta-lactamases. Cefepime shows high binding affinity with penicillin-binding proteins and has an extended spectrum of activity against Gram-positive and Gram-negative bacteria, with greater activity against both Gram-negative and Gram-positive organisms than third-generation agents.","category_aro_class_name":"Antibiotic"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"35987":{"category_aro_accession":"0000070","category_aro_cvterm_id":"35987","category_aro_name":"ertapenem","category_aro_description":"Ertapenem is a carbapenem antibiotic and is highly resistant to beta-lactamases like other carbapenems. It inhibits bacterial cell wall synthesis.","category_aro_class_name":"Antibiotic"},"35990":{"category_aro_accession":"0000073","category_aro_cvterm_id":"35990","category_aro_name":"meropenem","category_aro_description":"Meropenem is an ultra-broad spectrum injectable antibiotic used to treat a wide variety of infections, including meningitis and pneumonia. It is a beta-lactam and belongs to the subgroup of carbapenem, similar to imipenem and ertapenem.","category_aro_class_name":"Antibiotic"},"36309":{"category_aro_accession":"3000170","category_aro_cvterm_id":"36309","category_aro_name":"imipenem","category_aro_description":"Imipenem is a broad-spectrum antibiotic and is usually taken with cilastatin, which prevents hydrolysis of imipenem by renal dehydropeptidase-I. It is resistant to hydrolysis by most other beta-lactamases. Notable exceptions are the KPC beta-lactamases and Ambler Class B enzymes.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"36989":{"category_aro_accession":"3000645","category_aro_cvterm_id":"36989","category_aro_name":"cefotaxime","category_aro_description":"Cefotaxime is a semisynthetic cephalosporin taken parenterally. It is resistant to most beta-lactamases and active against Gram-negative rods and cocci due to its aminothiazoyl and methoximino functional groups.","category_aro_class_name":"Antibiotic"},"40361":{"category_aro_accession":"3003707","category_aro_cvterm_id":"40361","category_aro_name":"faropenem","category_aro_description":"Faropenem is an orally active beta-lactam antibiotic belonging to the penem group.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5713":{"model_id":"5713","model_name":"VIM-64","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"8088":{"protein_sequence":{"accession":"WP_140423327.1","sequence":"MLKVISSLLVYMTASVMAVASPLAHSGEPSGEYPTVNEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEAEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSANVLYGGCAVHELSLTSAGNVADADLAEWPTSVERIQKHYPEAEVVIPGHGLPGGLDLLQHTANVVKAHKNRSVAE"},"dna_sequence":{"accession":"NG_065447.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGTTAAAAGTTATTAGTAGTTTATTGGTCTACATGACCGCGTCTGTCATGGCTGTCGCAAGTCCGTTAGCCCATTCCGGGGAGCCGAGTGGTGAGTATCCGACAGTCAACGAAATTCCGGTCGGAGAGGTCCGACTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCGGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAAAAGCAAATTGGACTTCCCGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGCAGAGGGGAACGAGATTCCCACGCATTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAGCTCTTCTATCCTGGTGCTGCGCATTCGACCGACAATCTGGTTGTATACGTCCCGTCAGCGAACGTGCTATACGGTGGTTGTGCCGTTCATGAGTTGTCACTCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCGTTGAGCGGATTCAAAAACACTACCCGGAAGCAGAGGTCGTCATTCCCGGGCACGGTCTACCGGGCGGTCTAGACTTGCTCCAGCACACAGCGAACGTTGTCAAAGCACACAAAAATCGCTCAGTCGCCGAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3005512","ARO_id":"43974","ARO_name":"VIM-64","CARD_short_name":"VIM-64","ARO_description":"VIM-64 is a VIM beta-lactamase.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5714":{"model_id":"5714","model_name":"VIM-65","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"8089":{"protein_sequence":{"accession":"WP_140423328.1","sequence":"MFKLLSKLLVYLTASIMAIASPLAFSVDSSGEYPTASEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEVEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSASVLYGGCAIYELSRTSVGNVADADLAEWPTSIERIQQHYPEAQFVIPGHGLPGGLDLLKHTTNVVKAHTNRSVVE"},"dna_sequence":{"accession":"NG_065448.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGTTCAAACTTTTGAGTAAGTTATTGGTCTATTTGACCGCGTCTATCATGGCTATTGCGAGTCCGCTCGCTTTTTCCGTAGATTCTAGCGGTGAGTATCCGACAGCCAGCGAAATTCCGGTCGGGGAGGTCCGGCTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCAGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAGAAGCAAATTGGACTTCCTGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGTAGAGGGGAACGAGATTCCCACGCACTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAACTCTTCTATCCTGGTGCTGCGCATTCGACCGACAACTTAGTTGTGTACGTCCCGTCTGCGAGTGTGCTCTATGGTGGTTGTGCGATTTATGAGTTGTCACGCACGTCTGTGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCATTGAGCGGATTCAACAACACTACCCGGAAGCACAGTTCGTCATTCCGGGGCACGGCCTGCCGGGCGGTCTAGACTTGCTCAAGCACACAACGAATGTTGTAAAAGCGCACACAAATCGCTCAGTCGTTGAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3005513","ARO_id":"43975","ARO_name":"VIM-65","CARD_short_name":"VIM-65","ARO_description":"VIM-65 is a VIM beta-lactamase.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5715":{"model_id":"5715","model_name":"VIM-66","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"8090":{"protein_sequence":{"accession":"WP_136512109.1","sequence":"MFKLLSKLLVYLTASIMAIASPLAFSVDSSGEYPTVSEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPLTRRLAEVEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSASVLYGGCAIYELSLTSAGNVADADLAEWPTSIERIQQRYPEAQFVIPGHGLPGGLDLLKHTTNVVKAHTNRSVVE"},"dna_sequence":{"accession":"NG_064786.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGTTCAAACTTTTGAGTAAGTTATTGGTCTATTTGACCGCGTCTATCATGGCTATTGCGAGTCCGCTCGCTTTTTCCGTAGATTCTAGCGGTGAGTATCCGACAGTCAGCGAAATTCCGGTCGGGGAGGTCCGGCTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCAGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAGAAGCAAATTGGACTTCCTGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTTGACACGCCGGCTAGCCGAGGTAGAGGGGAACGAGATTCCCACGCACTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAACTCTTCTATCCTGGTGCTGCGCATTCGACCGACAACTTAGTTGTGTACGTCCCGTCTGCGAGTGTGCTCTATGGTGGTTGTGCGATTTATGAGTTGTCACTCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCATTGAGCGGATTCAACAACGCTACCCGGAAGCACAGTTCGTCATTCCGGGGCACGGCCTGCCGGGCGGTCTAGACTTGCTCAAGCACACAACGAATGTTGTAAAAGCGCACACAAATCGCTCAGTCGTTGAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005514","ARO_id":"43976","ARO_name":"VIM-66","CARD_short_name":"VIM-66","ARO_description":"VIM-66 is a VIM beta-lactamase.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5716":{"model_id":"5716","model_name":"VIM-67","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"8091":{"protein_sequence":{"accession":"WP_142875125.1","sequence":"MFKLLSKLLVYLTASIMAIASPLAFSVDSSGEYPTASEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEVEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSASVLYGGCAIYELSRTSAGNVADADLAEWPTSIERIQQHYPEAQFVIPGHGLPGGLDLLKHTTNVVKAHTNRSVVE"},"dna_sequence":{"accession":"NG_065942.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGTTCAAACTTTTGAGTAAGTTATTGGTCTATTTGACCGCGTCTATCATGGCTATTGCGAGTCCGCTCGCTTTTTCCGTAGATTCTAGCGGTGAGTATCCGACAGCCAGCGAAATTCCGGTCGGGGAGGTCCGGCTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCAGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAGAAGCAAATTGGACTTCCTGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGTAGAGGGGAACGAGATTCCCACGCACTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAACTCTTCTATCCTGGTGCTGCGCATTCGACCGACAACTTAGTTGTGTACGTCCCGTCTGCGAGTGTGCTCTATGGTGGTTGTGCGATTTATGAGTTGTCACGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCATTGAGCGGATTCAACAACACTACCCGGAAGCACAGTTCGTCATTCCGGGGCACGGCCTGCCGGGCGGTCTAGACTTGCTCAAGCACACAACGAATGTTGTAAAAGCGCACACAAATCGCTCAGTCGTTGAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39098","NCBI_taxonomy_name":"Enterobacter hormaechei","NCBI_taxonomy_id":"158836"}}}},"ARO_accession":"3005515","ARO_id":"43977","ARO_name":"VIM-67","CARD_short_name":"VIM-67","ARO_description":"VIM-67 is a VIM beta-lactamase.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5717":{"model_id":"5717","model_name":"VIM-68","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"8092":{"protein_sequence":{"accession":"WP_148044476.1","sequence":"MLKVISSLLVYMTASVMAVASPLAHSGEPSGEYPTVNEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTVALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEAEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSANVLYGGCAVHELSSTSAGNVADADLAEWPTSVERIQKHYPEAEVVIPGHGLPGGLDLLQHTANVVKAHKNRSVAE"},"dna_sequence":{"accession":"NG_065943.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGTTAAAAGTTATTAGTAGTTTATTGGTCTACATGACCGCGTCTGTCATGGCTGTCGCAAGTCCGTTAGCCCATTCCGGGGAGCCGAGTGGTGAGTATCCGACAGTCAACGAAATTCCGGTCGGAGAGGTCCGACTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCGGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGTGGCACTTCTCGCGGAGATTGAAAAGCAAATTGGACTTCCCGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGCAGAGGGGAACGAGATTCCCACGCATTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAGCTCTTCTATCCTGGTGCTGCGCATTCGACCGACAATCTGGTTGTATACGTCCCGTCAGCGAACGTGCTATACGGTGGTTGTGCCGTTCATGAGTTGTCAAGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCGTTGAGCGGATTCAAAAACACTACCCGGAAGCAGAGGTCGTCATTCCCGGGCACGGTCTACCGGGCGGTCTAGACTTGCTCCAGCACACAGCGAACGTTGTCAAAGCACACAAAAATCGCTCAGTCGCCGAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36946","NCBI_taxonomy_name":"Providencia stuartii","NCBI_taxonomy_id":"588"}}}},"ARO_accession":"3005516","ARO_id":"43978","ARO_name":"VIM-68","CARD_short_name":"VIM-68","ARO_description":"VIM-68 is a VIM beta-lactamase.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5718":{"model_id":"5718","model_name":"VIM-69","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"8093":{"protein_sequence":{"accession":"WP_130202201.1","sequence":"MFQFRSFLVGISAFVMAVLGSAAYSAQPGGEYPTVDDIPVGEVRLYKIGDGVWSHIATQKLGDTVYSSNGLIVRDADELLLIDTAWGAKNTAALLAEIEKQIGLPVTRSISTHFHDDRVGGVDVLRAAGVATYASPLTRQLAEAAGNEVPTHSLKALSSSGDVVRFGPVEVFYPGAAHSGDNLVVYVPAVRVLFGGCAVHEASRESAGNVADANLAEWPATIKRIQQRYPEAEVVIPGHGLPGGLELLQHTTDVVKTHKVRPVAE"},"dna_sequence":{"accession":"NG_067166.1","fmin":"100","fmax":"898","strand":"+","sequence":"ATGTTTCAATTTCGCAGCTTTCTGGTTGGTATCAGTGCATTCGTCATGGCCGTACTTGGATCAGCAGCATATTCCGCGCAGCCTGGCGGTGAATATCCGACAGTAGATGACATACCGGTAGGGGAAGTTCGGCTGTACAAGATTGGCGATGGCGTTTGGTCGCATATCGCAACTCAGAAACTCGGTGACACGGTGTACTCGTCTAATGGGCTTATCGTCCGCGATGCTGATGAGTTGCTTCTTATAGATACAGCGTGGGGGGCGAAGAACACGGCAGCCCTTCTCGCGGAGATTGAAAAGCAAATTGGACTTCCAGTAACGCGCTCAATTTCTACGCACTTCCATGACGATCGAGTCGGTGGAGTTGATGTCCTCCGGGCGGCTGGAGTGGCAACGTACGCCTCACCCTTGACACGCCAGCTGGCCGAAGCGGCGGGAAACGAGGTGCCTACGCACTCTCTAAAAGCGCTCTCCTCTAGCGGAGATGTGGTGCGCTTCGGTCCCGTAGAGGTTTTCTATCCTGGTGCTGCGCATTCGGGCGACAATCTTGTGGTATACGTGCCGGCCGTGCGCGTACTGTTTGGTGGCTGTGCAGTTCATGAGGCGTCACGCGAATCCGCGGGTAATGTTGCCGATGCCAATTTGGCAGAATGGCCTGCTACCATTAAACGAATTCAACAGCGGTATCCGGAAGCAGAGGTCGTCATCCCCGGCCACGGTCTACCGGGCGGTCTGGAATTGCTCCAACACACAACTGACGTTGTCAAAACGCACAAAGTACGCCCGGTGGCCGAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005517","ARO_id":"43979","ARO_name":"VIM-69","CARD_short_name":"VIM-69","ARO_description":"VIM-69 is a VIM beta-lactamase.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5719":{"model_id":"5719","model_name":"VIM-70","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"8094":{"protein_sequence":{"accession":"WP_164461303.1","sequence":"MLKVISSLLVYMTASVMAVASPLAHSGEPSGEYPTVNEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEAEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSANVLYGGCAVHELSGTSAGNVADADLAEWPTSVERIQKHYPEAEVVIPGHGLPGGLDLLQHTANVVKAHKNRSVAE"},"dna_sequence":{"accession":"NG_068039.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGTTAAAAGTTATTAGTAGTTTATTGGTCTACATGACCGCGTCTGTCATGGCTGTCGCAAGTCCGTTAGCCCATTCCGGGGAGCCGAGTGGTGAGTATCCGACAGTCAACGAAATTCCGGTCGGAGAGGTCCGACTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCGGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAAAAGCAAATTGGACTTCCCGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGCAGAGGGGAACGAGATTCCCACGCATTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAGCTCTTCTATCCTGGTGCTGCGCATTCGACCGACAATCTGGTTGTATACGTCCCGTCAGCGAACGTGCTATACGGTGGTTGTGCCGTTCATGAGTTGTCAGGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCGTTGAGCGGATTCAAAAACACTACCCGGAAGCAGAGGTCGTCATTCCCGGGCACGGTCTACCGGGCGGTCTAGACTTGCTCCAGCACACAGCGAACGTTGTCAAAGCACACAAAAATCGCTCAGTCGCCGAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005518","ARO_id":"43980","ARO_name":"VIM-70","CARD_short_name":"VIM-70","ARO_description":"VIM-70 is a VIM beta-lactamase.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5720":{"model_id":"5720","model_name":"VIM-71","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"8095":{"protein_sequence":{"accession":"WP_179284394.1","sequence":"MSKVISRLLVYMTASVMAVASSLSHSGAPSGEYPTVNEIPVGEVRLFQIADSVWSHIATQSFNGTVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPITRAVSTHFHDDRVGGDDVLRAAGVATYASPLTRRLAEAEGNEIPTHSLEGLASSGDAVRFGPVELFYPGAAHSTDNIVVYVPSSNVLFGGCAVHELSRTSAGNVADADLAEWPTSLERIQERYPEAEVVIPGHGLPGTLDLLQHTANVVKAHKIRSVAE"},"dna_sequence":{"accession":"NG_070223.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGTCAAAAGTTATTAGTAGATTATTGGTCTACATGACCGCGTCCGTCATGGCTGTGGCTAGTTCGTTAAGCCATTCCGGGGCGCCGAGTGGTGAGTATCCGACAGTCAACGAAATTCCGGTCGGAGAGGTCCGGCTTTTCCAGATTGCCGATAGTGTTTGGTCGCATATCGCAACGCAGTCGTTTAATGGCACGGTCTACCCGTCCAATGGACTCATTGTCCGTGATGGTGATGAGTTGCTATTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCCCTTCTCGCGGAGATTGAGAAGCAAATTGGCCTTCCCATAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGATGATGTGCTTCGGGCGGCTGGGGTGGCCACGTACGCATCACCGTTGACACGCCGGCTAGCCGAGGCAGAGGGGAACGAGATTCCCACGCACTCTCTAGAAGGACTCGCATCGAGTGGGGACGCAGTGCGCTTCGGCCCAGTAGAGCTCTTCTATCCTGGTGCTGCGCATTCGACCGACAATATCGTTGTATACGTCCCGTCATCGAACGTGCTATTCGGTGGTTGTGCCGTTCATGAGTTGTCACGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCCTTGAGCGGATTCAAGAACGCTACCCGGAAGCAGAGGTCGTCATTCCCGGGCACGGTCTACCGGGCACTCTAGACTTACTCCAGCACACAGCGAACGTTGTCAAAGCACACAAAATTCGCTCAGTCGCCGAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43205","NCBI_taxonomy_name":"Vibrio alginolyticus","NCBI_taxonomy_id":"663"}}}},"ARO_accession":"3005519","ARO_id":"43981","ARO_name":"VIM-71","CARD_short_name":"VIM-71","ARO_description":"VIM-71 is a VIM beta-lactamase.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5721":{"model_id":"5721","model_name":"VIM-72","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"8096":{"protein_sequence":{"accession":"WP_188331881.1","sequence":"MFKLLSKLLVYLTASIMAIASPLAFSVDSSGEYPTVSEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEVEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSASVLYGGCAIYELSRTSAGTVADADLAEWPTSIERIQQHYPEAQFVIPGHGLPGGLDLLKHTTNVVKAHTNRSVVE"},"dna_sequence":{"accession":"NG_070756.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGTTCAAACTTTTGAGTAAGTTATTGGTCTATTTGACCGCGTCTATCATGGCTATTGCGAGTCCGCTCGCTTTTTCCGTAGATTCTAGCGGTGAGTATCCGACAGTCAGCGAAATTCCGGTCGGGGAGGTCCGGCTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCAGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAGAAGCAAATTGGACTTCCTGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGTAGAGGGGAACGAGATTCCCACGCACTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAACTCTTCTATCCTGGTGCTGCGCATTCGACCGACAACTTAGTTGTGTACGTCCCGTCTGCGAGTGTGCTCTATGGTGGTTGTGCGATTTATGAGTTGTCACGCACGTCTGCGGGGACCGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCATTGAGCGGATTCAACAACACTACCCGGAAGCACAGTTCGTCATTCCGGGGCACGGCCTGCCGGGCGGTCTAGACTTGCTCAAGCACACAACGAATGTTGTAAAAGCGCACACAAATCGCTCAGTCGTTGAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005520","ARO_id":"43982","ARO_name":"VIM-72","CARD_short_name":"VIM-72","ARO_description":"VIM-72 is a VIM beta-lactamase.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5722":{"model_id":"5722","model_name":"VIM-73","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"8097":{"protein_sequence":{"accession":"WP_188331882.1","sequence":"MFKLLSKLLVYLTASIMAIASPLAFSVDSSGEYPTVSEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEVEGNEISTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSASVLYGGCAIYELSRTSAGNVADADLAEWPTSIERIQQHYPEAQFVIPGHGLPGGLDLLKHTTNVVKAHTNRSVVE"},"dna_sequence":{"accession":"NG_070757.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGTTCAAACTTTTGAGTAAGTTATTGGTCTATTTGACCGCGTCTATCATGGCTATTGCGAGTCCGCTCGCTTTTTCCGTAGATTCTAGCGGTGAGTATCCGACAGTCAGCGAAATTCCGGTCGGGGAGGTCCGGCTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCAGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAGAAGCAAATTGGACTTCCTGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGTAGAGGGGAACGAGATTTCCACGCACTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAACTCTTCTATCCTGGTGCTGCGCATTCGACCGACAACTTAGTTGTGTACGTCCCGTCTGCGAGTGTGCTCTATGGTGGTTGTGCGATTTATGAGTTGTCACGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCATTGAGCGGATTCAACAACACTACCCGGAAGCACAGTTCGTCATTCCGGGGCACGGCCTGCCGGGCGGTCTAGACTTGCTCAAGCACACAACGAATGTTGTAAAAGCGCACACAAATCGCTCAGTCGTTGAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3005521","ARO_id":"43983","ARO_name":"VIM-73","CARD_short_name":"VIM-73","ARO_description":"VIM-73 is a VIM beta-lactamase.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5723":{"model_id":"5723","model_name":"YEM-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"475"}},"model_sequences":{"sequence":{"8098":{"protein_sequence":{"accession":"WP_004874166.1","sequence":"MLKTILQFFVLFTVTQGAYASKIALVKLSDNLYVVEDDYYYRENSMVYIGKDYITVIGATWTPDTAKELDAQIKKISKKPIAEVINTNYHTDRAGGNLYWKSIGAELISTKMTYNLMEKHWQDILETTRKGYDGFPDIPLVLPTKTFDNNFELQNGEIKAIYTGESHTPDGIFVYFPKEKTLYGNCIIKEKLGNLASANIKEYPKTLQKLKNLNLDIKTVVGGHDSPIHGSELIDSYKKLIEAANK"},"dna_sequence":{"accession":"NG_070759.1","fmin":"100","fmax":"841","strand":"+","sequence":"ATGTTAAAAACAATATTACAATTTTTTGTTTTATTCACTGTAACTCAAGGTGCTTATGCATCTAAAATAGCATTGGTAAAATTAAGTGATAATCTTTATGTTGTCGAGGACGACTATTATTACAGAGAAAACTCCATGGTTTACATTGGTAAAGACTATATTACCGTTATTGGTGCCACCTGGACACCGGATACAGCTAAAGAATTAGATGCGCAAATCAAAAAAATAAGTAAAAAACCCATCGCTGAAGTTATCAATACCAATTATCATACGGACAGGGCCGGTGGTAATTTATATTGGAAAAGTATTGGTGCTGAATTGATTTCTACCAAAATGACGTATAATTTAATGGAAAAACATTGGCAAGATATTCTTGAGACTACCCGTAAAGGGTACGATGGCTTCCCTGATATTCCCCTTGTTTTGCCGACAAAGACTTTTGATAATAACTTTGAACTACAAAATGGCGAGATAAAAGCTATCTACACAGGTGAATCTCATACTCCTGACGGAATATTTGTTTATTTTCCGAAGGAAAAAACCTTATATGGAAATTGCATAATTAAAGAGAAATTAGGTAATTTGGCCTCTGCTAATATAAAGGAGTACCCTAAGACCTTACAGAAACTTAAAAATTTAAATCTCGATATAAAGACAGTTGTCGGTGGTCATGACTCACCAATACATGGTTCCGAACTTATCGATAGCTATAAAAAACTAATCGAAGCCGCTAATAAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3007005","ARO_id":"45467","ARO_name":"YEM-1","CARD_short_name":"YEM-1","ARO_description":"YEM-1 is a YEM beta-lactamase.","ARO_category":{"43917":{"category_aro_accession":"3005457","category_aro_cvterm_id":"43917","category_aro_name":"YEM beta-lactamase","category_aro_description":"YEM beta-lactamases are class B2 beta-lactamases found in Yersinia mollaretii.","category_aro_class_name":"AMR Gene Family"},"36309":{"category_aro_accession":"3000170","category_aro_cvterm_id":"36309","category_aro_name":"imipenem","category_aro_description":"Imipenem is a broad-spectrum antibiotic and is usually taken with cilastatin, which prevents hydrolysis of imipenem by renal dehydropeptidase-I. It is resistant to hydrolysis by most other beta-lactamases. Notable exceptions are the KPC beta-lactamases and Ambler Class B enzymes.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5724":{"model_id":"5724","model_name":"ZOG-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"475"}},"model_sequences":{"sequence":{"8099":{"protein_sequence":{"accession":"WP_013992183.1","sequence":"MTYKSTVLLLFLITAFFSCKSQQPTLTYSSEDLKIIPLSKNSFVHISYLSTGDFGKVACNGLIYINQGQAVVFDTPTDNETSEELIHWITETKKQQIKAVVINHFHDDCLGGIEAFHELSIPSYASNTTIELAKKEGNPVPQIGFDTTNELTIGKQKIINRHFGEAHTKDNIVSYIPSEHLLFGGCALKSLNAAKGYLGDANTNEWGNTIKKIKAAYPDLKTAIPGHGEYGGSELLDYTISLFSTKQ"},"dna_sequence":{"accession":"NG_057434.1","fmin":"100","fmax":"844","strand":"+","sequence":"ATGACCTATAAATCAACCGTATTACTTTTGTTCTTGATTACGGCTTTCTTTTCCTGTAAGTCACAACAACCGACCTTAACTTACAGTAGCGAGGACTTAAAAATCATCCCGCTCTCCAAAAACAGCTTCGTCCATATCTCTTACCTATCGACCGGAGACTTTGGAAAAGTGGCCTGTAACGGACTTATCTACATAAACCAAGGCCAGGCCGTTGTTTTCGATACGCCCACCGACAACGAAACTTCCGAAGAGCTCATCCATTGGATAACCGAAACTAAAAAACAACAGATCAAGGCCGTGGTCATCAACCACTTTCACGACGACTGCCTTGGCGGGATCGAGGCCTTTCACGAACTAAGCATTCCCTCTTACGCTAGCAATACGACCATAGAACTTGCTAAAAAAGAAGGAAACCCGGTTCCACAAATTGGTTTTGACACCACCAACGAACTGACCATTGGGAAGCAAAAAATAATCAACCGTCATTTTGGCGAGGCCCATACCAAAGACAACATTGTAAGTTACATCCCTAGCGAGCACCTCCTTTTTGGCGGATGCGCCCTTAAATCGCTCAATGCCGCCAAAGGATACCTAGGCGATGCGAACACCAACGAATGGGGCAACACCATCAAAAAGATAAAAGCAGCCTATCCCGACCTTAAAACGGCCATTCCCGGACACGGGGAATACGGAGGCTCAGAATTACTGGATTATACCATTTCCCTTTTTAGCACGAAACAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3007006","ARO_id":"45468","ARO_name":"ZOG-1","CARD_short_name":"ZOG-1","ARO_description":"ZOG-1 is a ZOG beta-lactamase.","ARO_category":{"43918":{"category_aro_accession":"3005458","category_aro_cvterm_id":"43918","category_aro_name":"ZOG beta-lactamase","category_aro_description":"ZOG beta-lactamases are class B1 beta-lactamases found in Zobellia galactanivorans.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5726":{"model_id":"5726","model_name":"norC","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"8122":{"protein_sequence":{"accession":"AGP27106.1","sequence":"MNETYRGGNKLILGIVLGVITFWLFAQSLVNVVPNLQQSFGADMGTISIAVSLTALFSGMFVVGAGGLADKIGRVKMTNIGLLLSIIGSALIIITNLPALLILGRIIQGVSAACIMPSTLAIMKTYYEGAERQRALSYWSIGSWGGSGICSLFGGAVATTMGWRWIFIFSIIVAVLSMLLIKGTPETKSEVTNTHKFDVAGLIVLVVMLLSLNVVITKGAALGYTSLWFFGLIAIVIVAFFIFLNVEKKVDNPLIDFKLFENKPYTGATISNFLLNGVAGTLIVANTFVQQGLGYTALQAGYLSITYLIMVLLMIRVGEKLLQKMGSKRPMLLGTFIVIIGIALISLVFLPGIFYVISCVVGYLCFGLGLGIYATPSTDTAISNAPLDKVGVASGIYKMASSLGGAFGVAISGAVYAGAVAATSIHTGAMIALWVNVLMGIMAFIAILFAIPNDDKRVKDAK"},"dna_sequence":{"accession":"CP005288.1","fmin":"116946","fmax":"118335","strand":"+","sequence":"ATGAATGAAACGTATCGCGGGGGCAACAAGTTAATCTTAGGTATTGTATTAGGTGTTATTACATTTTGGTTGTTTGCACAATCACTTGTAAATGTTGTGCCAAATTTACAACAAAGTTTTGGTGCAGACATGGGAACAATTAGTATTGCGGTAAGTCTAACCGCACTATTTTCAGGCATGTTTGTTGTTGGAGCAGGCGGCCTAGCAGATAAAATTGGACGCGTGAAAATGACAAATATCGGCTTATTATTAAGTATTATTGGTTCAGCATTAATTATTATTACAAATTTACCAGCATTGCTAATTTTAGGCCGTATTATACAAGGCGTATCAGCAGCGTGTATTATGCCTTCCACATTGGCCATTATGAAAACTTATTATGAGGGTGCTGAACGTCAGCGTGCCTTAAGCTATTGGTCTATCGGTTCTTGGGGTGGAAGTGGTATCTGTTCACTCTTCGGTGGGGCAGTTGCGACAACTATGGGTTGGAGATGGATTTTCATCTTCTCAATCATCGTTGCCGTACTTTCAATGTTACTCATCAAAGGGACGCCTGAAACGAAATCAGAAGTTACCAATACACATAAATTTGACGTTGCAGGTCTAATTGTTCTAGTAGTTATGTTATTAAGTTTAAACGTTGTCATTACTAAAGGTGCAGCACTTGGTTATACATCATTATGGTTCTTTGGTTTGATTGCAATCGTAATTGTAGCATTCTTTATTTTCTTAAATGTTGAGAAAAAAGTAGATAATCCGCTTATTGATTTTAAATTATTTGAAAATAAACCATATACAGGTGCAACGATTTCGAACTTCTTATTAAACGGTGTTGCAGGTACATTAATTGTAGCGAATACATTCGTACAACAAGGTTTAGGTTATACAGCATTGCAGGCAGGATACTTATCAATCACTTATTTAATCATGGTGTTATTGATGATTAGAGTTGGTGAAAAATTATTACAAAAAATGGGTTCTAAGCGACCAATGTTATTAGGTACATTCATTGTGATCATTGGTATTGCACTTATTTCATTAGTATTCTTACCAGGCATATTTTATGTTATCAGTTGTGTCGTAGGATATTTATGTTTTGGACTAGGCTTAGGTATTTATGCAACACCTTCTACAGATACAGCTATTTCAAATGCACCGTTAGATAAAGTTGGCGTTGCTTCAGGTATTTATAAAATGGCTTCATCACTTGGTGGTGCATTCGGTGTCGCAATTAGTGGTGCAGTATATGCCGGTGCAGTTGCTGCAACGAGCATTCATACAGGTGCGATGATTGCACTTTGGGTTAACGTATTAATGGGAATCATGGCATTTATCGCAATTTTATTTGCGATTCCTAATGATGATAAACGTGTCAAAGATGCGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35508","NCBI_taxonomy_name":"Staphylococcus aureus","NCBI_taxonomy_id":"1280"}}}},"ARO_accession":"3007010","ARO_id":"45478","ARO_name":"norC","CARD_short_name":"norC","ARO_description":"NorC is a multidrug efflux pump in Staphylococcus aureus that confers resistance to fluoroquinolones and other structurally unrelated antibiotics like tetracycline. It shares 61% similarity with NorB, and is a structural homolog of Blt of Bacillus subtilis. Like NorA and NorB, NorC is regulated by mgrA, also known as NorR.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35963":{"category_aro_accession":"0000045","category_aro_cvterm_id":"35963","category_aro_name":"acriflavine","category_aro_description":"Acriflavine is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"43746":{"category_aro_accession":"3005386","category_aro_cvterm_id":"43746","category_aro_name":"disinfecting agents and antiseptics","category_aro_description":"Disinfectants that can also interact with antimicrobial resistance mechanisms, e.g. molecule efflux, and thus are the targets of disinfectant resistance.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"5879":{"model_id":"5879","model_name":"MCR-10.5","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"8605":{"protein_sequence":{"accession":"WP_242934127.1","sequence":"MPVLFRMRVIPLVLLLALVFAFLLNWPVLLHFYDILSRLEHVRAGFVISIPFVLVAALNFVFMPFSVRYLLKPFFALLLVTGSVVSYATLKYKVMFDQSMIENILETNPQEAHAYLNGSLVLWLVFMGILPAILLFLIKIEYADKWYKGVAHRLLSMLASLILIAGVAALYYQDYASVGRNNPTLNKEIIPANYAYSTFHYVKDTYFTTKMPFRTLGDDARRVTRNGKPTLMFLVIGETARSQNFSMNGYPRDTNAFTSKIDGVISFRNMRSCGTATAVSVPCMFSDMNRTDYDGKKAAGSENVLDIVQKTGVSLLWKENDGGCKGVCSRIPTVEINPGISKKLCDGKTCYDDVMLENLDTEIGKMAGDKLIAFHMIGSHGPTYYQRYPAVHRHFMPECARSDIENCTQEQLVNTYDNTIRHTDYVLAQMIEKLKQYSEQYNTVLLYVSDHGESLGESGLYLHGTPYKLAPDQQTHIPMQLWMSPGFIAAKNINAACLQHNAVNRTYSHDNLFASVLGLWDITTGAYLPESDLFRECRG"},"dna_sequence":{"accession":"OM638112.1","fmin":"0","fmax":"1620","strand":"-","sequence":"ATGCCCGTACTTTTCAGGATGAGGGTAATCCCCTTGGTTTTACTTCTGGCACTCGTTTTTGCATTCTTACTTAACTGGCCGGTGTTGCTGCATTTCTACGATATCCTGAGCCGTCTTGAACATGTGAGGGCGGGGTTCGTCATCTCCATTCCGTTTGTGCTGGTTGCAGCGCTTAACTTTGTGTTTATGCCCTTCTCGGTTCGCTACCTGCTCAAACCCTTCTTTGCCCTGTTGCTGGTCACCGGTTCGGTGGTGAGTTACGCCACACTGAAATATAAAGTGATGTTTGATCAGTCCATGATCGAAAATATACTGGAAACAAACCCACAGGAAGCGCATGCCTACCTGAATGGCTCACTGGTGCTGTGGCTGGTCTTCATGGGCATTCTTCCGGCTATCCTGTTGTTTTTGATTAAAATTGAATATGCAGACAAATGGTACAAAGGGGTTGCCCACCGGCTGCTTTCCATGCTCGCTTCGCTGATCCTGATTGCAGGTGTTGCCGCTCTGTATTACCAGGATTATGCTTCTGTCGGGCGCAATAACCCGACGCTGAACAAAGAAATTATCCCGGCAAACTATGCGTACAGCACTTTCCATTACGTGAAGGATACCTATTTTACGACGAAAATGCCTTTCCGGACGCTGGGGGATGATGCAAGGCGCGTTACCCGGAATGGTAAACCCACGCTGATGTTCCTGGTAATTGGCGAAACGGCACGGAGCCAGAATTTCTCCATGAACGGCTACCCGCGTGACACAAATGCCTTTACCAGCAAAATCGATGGCGTTATTTCGTTCAGGAATATGCGTTCCTGTGGCACGGCGACCGCAGTCTCGGTGCCCTGTATGTTCTCGGATATGAACCGGACGGATTACGATGGTAAAAAGGCTGCCGGCAGTGAAAATGTCCTCGACATCGTGCAGAAAACGGGGGTTTCGCTGTTGTGGAAAGAAAACGATGGCGGGTGTAAAGGCGTATGCAGCCGTATCCCGACTGTCGAAATTAATCCCGGTATCAGTAAAAAACTGTGTGACGGTAAAACCTGCTATGACGATGTTATGCTGGAAAACCTGGATACCGAAATCGGCAAAATGGCCGGAGACAAGCTGATCGCCTTCCATATGATTGGCAGCCATGGACCGACCTATTACCAGCGTTATCCGGCAGTGCATCGTCACTTCATGCCGGAATGTGCGCGCAGCGATATCGAAAACTGCACGCAGGAACAGCTGGTTAATACCTACGACAATACCATTCGCCACACCGACTATGTGTTAGCGCAGATGATTGAAAAGCTTAAGCAATACAGCGAACAGTACAACACCGTACTGCTGTATGTGTCCGATCACGGCGAATCTCTGGGAGAGAGCGGACTGTATCTGCACGGTACCCCCTACAAACTGGCACCGGATCAGCAGACGCACATCCCGATGCAGCTCTGGATGTCGCCAGGCTTCATTGCTGCTAAAAATATTAACGCCGCGTGTCTGCAGCATAATGCCGTTAACAGGACATATTCCCACGATAACCTTTTCGCGTCCGTACTGGGGCTCTGGGACATCACCACCGGGGCCTATCTTCCGGAAAGCGACCTGTTCCGCGAATGTCGTGGATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3007274","ARO_id":"46020","ARO_name":"MCR-10.5","CARD_short_name":"MCR-10.5","ARO_description":"An MCR-10-type colistin resistance gene variant.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5880":{"model_id":"5880","model_name":"MCR-10.3","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"8610":{"protein_sequence":{"accession":"MBO4158890.1","sequence":"MPVLFRMRVIPLVLLLALVFAFLLNWPVLLHFYDILSRLEHVRAGFVISIPFVLVAALNFVFMPFSVRYLLKPFFALLLVTGSVVSYATLKYKVMFDQSMIENILETNPQEAHAYLNGSLVLWLVFMGILPAILLFLIKIEYADKWYKGVAHRLLSMLASLILIAGVAALYYQDYASVGRNNPTLNKEIIPANYAYSTFHYVKDTYFTTKMPFRTLGDDARRVTRNGKPTLMFLVIGETARSQNFSMNGYPRDTNAFTSKIDGVISFRNMRSCGTATAVSVPCMFSDMNRTDYDGKKAAGSENVLDIVQKTGVSLLWKENDGGCKGVCSRIPTVEINPGISKKLCDGKTCYDDVMLENLDTEIGKMAGDKLIAFHMIGSHGPTYYQRYPAEHRHFMPECARSDIENCTQEQLVNTYDNTIRHTDYVLAQMIEKLKQYSEQYNTILLYVSDHGESLGESGLYLHGTPYKLAPDQQTHIPMQLWMSPGFIAAKNINAACLQHNAVNRTYSHDNLFASVLGLWDITTGAYLPESDLFRECRG"},"dna_sequence":{"accession":"JAGFWV010000051.1","fmin":"2206","fmax":"3826","strand":"-","sequence":"ATGCCCGTACTTTTCAGGATGAGGGTAATCCCCTTGGTTTTACTTCTGGCACTCGTTTTTGCATTCTTACTTAACTGGCCGGTGTTGCTGCATTTCTACGATATCCTGAGCCGTCTTGAACATGTGAGGGCGGGGTTCGTCATCTCCATTCCGTTTGTGCTGGTTGCAGCGCTTAACTTTGTGTTTATGCCCTTCTCGGTTCGCTACCTGCTCAAACCCTTCTTTGCCCTGTTGCTGGTCACCGGTTCGGTGGTGAGTTACGCCACACTGAAATATAAAGTGATGTTTGATCAGTCCATGATCGAAAATATACTGGAAACAAACCCACAGGAAGCGCATGCCTACCTGAATGGCTCACTGGTGCTGTGGCTGGTCTTCATGGGCATTCTTCCGGCTATCCTGTTGTTTTTGATTAAAATTGAATATGCAGACAAATGGTACAAAGGGGTTGCCCACCGGCTGCTTTCCATGCTCGCTTCGCTGATCCTGATTGCAGGTGTTGCCGCTCTGTATTACCAGGATTATGCTTCTGTCGGGCGCAATAACCCGACGCTGAACAAAGAAATTATCCCGGCAAACTATGCGTACAGCACTTTCCATTACGTGAAGGATACCTATTTTACGACGAAAATGCCTTTCCGGACGCTGGGGGATGATGCAAGGCGCGTTACCCGGAATGGTAAACCCACGCTGATGTTCCTGGTAATTGGCGAAACGGCACGGAGCCAGAATTTCTCCATGAACGGCTACCCGCGTGACACAAATGCCTTTACCAGCAAAATCGATGGCGTTATTTCGTTCAGGAATATGCGTTCCTGTGGCACGGCGACCGCAGTCTCGGTGCCCTGTATGTTCTCGGATATGAACCGGACAGATTACGATGGTAAAAAGGCTGCCGGCAGTGAAAATGTCCTCGACATCGTGCAGAAAACGGGGGTTTCGCTGTTGTGGAAAGAAAACGATGGCGGGTGTAAAGGCGTATGCAGCCGTATCCCGACTGTCGAAATTAATCCCGGTATCAGTAAAAAACTGTGTGACGGTAAAACCTGCTATGACGATGTTATGCTGGAAAACCTGGATACCGAAATCGGCAAAATGGCCGGAGACAAGCTGATCGCCTTCCATATGATTGGCAGCCATGGACCGACCTATTACCAGCGTTATCCGGCAGAGCATCGTCACTTCATGCCGGAATGTGCGCGCAGCGATATCGAAAACTGCACGCAGGAACAGCTGGTTAATACCTACGACAATACCATTCGCCACACCGACTATGTGTTAGCGCAGATGATTGAAAAGCTTAAGCAATACAGCGAACAGTACAACACCATACTGCTGTATGTGTCCGATCACGGCGAATCTCTGGGAGAGAGCGGACTGTATCTGCACGGTACCCCCTACAAACTGGCACCGGATCAGCAGACGCACATCCCGATGCAGCTCTGGATGTCGCCAGGCTTCATTGCTGCTAAAAATATTAACGCCGCGTGTCTGCAGCATAATGCCGTTAACAGGACATATTCCCACGATAACCTTTTCGCGTCCGTACTGGGGCTCTGGGACATCACCACCGGGGCCTATCTTCCGGAAAGCGACCTGTTCCGCGAATGTCGTGGATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39773","NCBI_taxonomy_name":"Enterobacter kobei","NCBI_taxonomy_id":"208224"}}}},"ARO_accession":"3007275","ARO_id":"46021","ARO_name":"MCR-10.3","CARD_short_name":"MCR-10.3","ARO_description":"An MCR-10-type colistin resistance gene variant.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5727":{"model_id":"5727","model_name":"mdeA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"200"}},"model_sequences":{"sequence":{"8123":{"protein_sequence":{"accession":"WP_002289367.1","sequence":"MTKHLQDFLITVIAGMGMLLSTLDTGIINVALSFLRGQFQTTTNIASFTITGYTLALAISILPLGVLSDKFGKLKISYLGFVLFGLSSLFCGFANSIGWLITGRIIQGMGAAALQATSAALITTLVSEDRKNSAISILGVMIGLGPVLGPSLGGILLSLNLWRFIFWINVPFALIVIICNHYLLTKVSEQTSEWTLDSLGTVLNASMLVCLLLGLSLLSKPHLLGISLILIIISFLIGIWFYRLECSKESALVNVKGLSENPRVLSYLFQTVAFGFASAMIFLLPPFIFEQLYHLGVGQTGFLVLGAPAGLVLFSRISGKINDGSKNKSFSHIGLGIIILSLIFLLLLTPSWPYLFLTLGLFIYGIGGGYFQPANMASIMLASPMKMQGSTGALQRMVQNIAISAGSAIGSTCLNLWSNNLLLATRIGWGITLVLVILSLKELTPFKMTNKTE"},"dna_sequence":{"accession":"NZ_CP044221.1","fmin":"1355942","fmax":"1357304","strand":"-","sequence":"ATGACGAAACATTTACAAGATTTTTTAATAACAGTTATCGCAGGTATGGGAATGTTATTATCCACCCTTGATACAGGTATTATCAATGTTGCATTATCCTTTTTGAGGGGACAATTTCAAACCACAACTAACATTGCCTCTTTTACAATAACTGGATATACTTTAGCATTAGCTATCTCTATCTTACCTTTAGGAGTATTAAGCGATAAATTTGGAAAGTTAAAGATTTCCTACTTAGGATTTGTACTTTTTGGACTGAGCTCCTTATTTTGTGGATTTGCTAATAGTATTGGCTGGCTCATTACTGGCCGGATTATTCAAGGAATGGGAGCGGCGGCTTTGCAAGCTACTTCAGCAGCTCTGATTACCACTTTAGTTTCCGAAGACCGCAAAAACAGTGCTATTAGTATTTTAGGAGTTATGATTGGCTTAGGACCTGTCCTCGGTCCTTCCTTAGGAGGCATACTACTTTCTTTAAATCTCTGGCGCTTTATTTTCTGGATTAATGTTCCCTTTGCTCTTATTGTCATCATTTGTAATCACTATCTCCTTACTAAAGTCTCCGAACAAACTAGTGAGTGGACATTAGATTCTCTTGGAACAGTTCTCAATGCTTCTATGTTGGTTTGTCTTCTCTTAGGACTATCCTTACTCAGTAAGCCTCACCTATTAGGTATCAGTCTTATTTTGATCATCATTAGTTTCTTGATCGGGATTTGGTTTTACCGTCTTGAATGCAGCAAAGAGAGTGCTCTTGTCAATGTCAAGGGGCTGAGCGAGAATCCTCGAGTACTTTCTTATCTTTTTCAAACGGTCGCTTTTGGTTTTGCCTCTGCAATGATATTCTTACTTCCACCCTTCATTTTTGAACAATTATATCATTTAGGAGTGGGGCAGACAGGCTTTCTTGTACTAGGAGCACCTGCAGGCCTGGTTCTTTTTTCAAGAATATCTGGTAAAATCAATGATGGCAGTAAAAATAAATCATTTAGCCATATTGGTTTGGGTATCATTATTTTATCCTTAATTTTCCTCCTACTTCTCACGCCTAGCTGGCCCTATTTATTCTTAACTTTAGGATTATTTATTTATGGTATTGGCGGAGGATACTTTCAGCCTGCTAATATGGCTAGTATTATGCTAGCTAGTCCTATGAAAATGCAAGGTAGCACAGGAGCATTGCAACGAATGGTACAAAACATTGCTATTTCAGCTGGTTCAGCCATTGGATCAACTTGCTTAAACCTTTGGTCAAATAATCTATTATTGGCTACCCGAATTGGCTGGGGAATTACACTCGTTCTAGTTATTCTCAGTTTAAAAGAACTAACACCATTTAAAATGACTAATAAAACAGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"45480","NCBI_taxonomy_name":"Streptococcus mutans","NCBI_taxonomy_id":"1309"}}}},"ARO_accession":"3007011","ARO_id":"45479","ARO_name":"mdeA","CARD_short_name":"mdeA","ARO_description":"mdeA is a multidrug efflux pump that confers resistance  in varying degrees to several unrelated antibiotics, including kanamycin, tetracycline, ampicillin, oxacillin, ciprofloxacin, nalidixic acid, acriflavine, and ethidium bromide.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35963":{"category_aro_accession":"0000045","category_aro_cvterm_id":"35963","category_aro_name":"acriflavine","category_aro_description":"Acriflavine is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"43746":{"category_aro_accession":"3005386","category_aro_cvterm_id":"43746","category_aro_name":"disinfecting agents and antiseptics","category_aro_description":"Disinfectants that can also interact with antimicrobial resistance mechanisms, e.g. molecule efflux, and thus are the targets of disinfectant resistance.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"5728":{"model_id":"5728","model_name":"sepA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"100"}},"model_sequences":{"sequence":{"8124":{"protein_sequence":{"accession":"WP_042355600.1","sequence":"MIVNFFKHKFYNLLTTMIVLFVFVLSGAIFLTFLGFGLYGLSRILIYFRLGDFTYNRNMYDNLLYYGSYIIFGYFIIFAVEHLMDYFRKMLPENAYFRGATFHLISYTVATTLFYFIIHLHYVYINIDFWVIMVIIGFLYVCKLQFYPESKNLNNRK"},"dna_sequence":{"accession":"NC_016941.1","fmin":"2187139","fmax":"2187613","strand":"-","sequence":"ATGATTGTGAACTTTTTCAAGCATAAATTTTATAATTTATTAACTACAATGATTGTTCTCTTTGTGTTTGTGTTGTCCGGTGCAATTTTTTTAACATTTCTAGGTTTTGGACTTTATGGTCTTAGCAGGATACTTATATACTTTAGGTTAGGTGATTTCACGTATAATAGAAATATGTATGATAATTTATTGTATTACGGTAGTTATATCATATTTGGTTATTTTATCATTTTTGCAGTCGAACATTTAATGGATTATTTTAGAAAGATGCTTCCTGAAAATGCATATTTTAGAGGAGCAACATTCCATTTAATATCTTATACGGTTGCTACTACATTATTTTATTTCATTATTCATTTACATTATGTGTATATTAATATTGATTTTTGGGTCATCATGGTAATCATAGGCTTTCTTTATGTATGTAAACTTCAATTTTACCCTGAAAGTAAAAATCTCAATAATAGAAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37074","NCBI_taxonomy_name":"Staphylococcus","NCBI_taxonomy_id":"1279"}}}},"ARO_accession":"3007012","ARO_id":"45481","ARO_name":"sepA","CARD_short_name":"sepA","ARO_description":"sepA is a multidrug efflux pump that confers resistance to disinfecting agents and dyes.","ARO_category":{"36004":{"category_aro_accession":"0010003","category_aro_cvterm_id":"36004","category_aro_name":"small multidrug resistance (SMR) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Small multidrug resistance (SMR) proteins are a relatively small family of transporters, restricted to prokaryotic cells. They are also the smallest multidrug transporters, with only four transmembrane alpha-helices and no significant extramembrane domain.","category_aro_class_name":"AMR Gene Family"},"35963":{"category_aro_accession":"0000045","category_aro_cvterm_id":"35963","category_aro_name":"acriflavine","category_aro_description":"Acriflavine is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish.","category_aro_class_name":"Antibiotic"},"43746":{"category_aro_accession":"3005386","category_aro_cvterm_id":"43746","category_aro_name":"disinfecting agents and antiseptics","category_aro_description":"Disinfectants that can also interact with antimicrobial resistance mechanisms, e.g. molecule efflux, and thus are the targets of disinfectant resistance.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"5729":{"model_id":"5729","model_name":"sdrM","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"200"}},"model_sequences":{"sequence":{"8125":{"protein_sequence":{"accession":"BAB43261.1","sequence":"MRLKSIITVIALILIMFMSAIESSIISLALPTIKQDLNAGNLISLIFTAYFIALVIANPIVGELLSRFKIIYVAIAGLLLFSIGSFMCGLSTNFTMLIISRVIQGFGSGVLMSLSQIVPKLAFEIPLRYKIMGIVGSVWGISSIIGPLLGGGILEFATWHWLFYINIPIAIIAIILVIWTFHFPEEETVAKSKFDTKGLTLFYVFIGLIMFALLNQQLLLLNFLSFILAIVVAMCLFKVEKHVSSPFLPVVEFNRSITLVFITDLLTAICLMGFNLYIPVYLQEQLGLSPLQSGLVIFPLSVAWITLNFNLHRIEAKLSRKVIYLLSFTLLLVSSIIISFGIKLPVLIAFVLILAGLSFGYIYTKDSVIVQEETSPLQMKKMMSFYGLTKNLGASIGSTIMGYLYAIQSGIFGPNLHNVLSAVAVISIGLIVLWVVFFKEQSSQSKE"},"dna_sequence":{"accession":"BA000018.3","fmin":"2239879","fmax":"2241223","strand":"-","sequence":"ATGCGATTAAAGTCAATCATAACTGTTATAGCTTTAATATTAATTATGTTTATGTCAGCGATTGAATCATCTATTATTTCGCTTGCATTACCTACAATTAAACAAGATTTAAATGCAGGAAATTTAATTTCATTAATTTTTACAGCGTATTTTATCGCATTAGTAATTGCCAATCCTATAGTGGGAGAATTACTTTCGAGATTTAAAATTATTTATGTGGCAATTGCAGGATTACTTTTATTTAGTATAGGTAGTTTTATGTGTGGTTTAAGTACTAATTTTACTATGCTAATTATATCACGCGTGATACAAGGTTTTGGATCAGGTGTATTGATGTCATTATCGCAAATTGTTCCAAAGTTAGCATTTGAAATTCCGTTACGATATAAAATTATGGGCATAGTTGGCAGTGTTTGGGGTATTTCGAGTATCATTGGACCGCTTCTAGGTGGTGGTATATTAGAATTTGCAACATGGCATTGGTTATTCTACATAAATATACCGATTGCGATCATTGCCATTATATTAGTTATATGGACATTTCATTTTCCAGAGGAAGAAACAGTTGCTAAATCAAAATTTGATACTAAAGGGCTCACGCTATTTTATGTATTTATTGGATTGATTATGTTTGCTTTATTAAACCAACAGCTATTACTTTTAAATTTCTTGAGTTTTATCTTAGCTATCGTTGTGGCAATGTGTTTATTTAAAGTAGAAAAACATGTTTCTTCACCATTTTTACCTGTGGTTGAATTTAATCGTTCGATTACTTTAGTTTTTATAACGGACCTTCTAACAGCTATTTGTTTAATGGGATTCAATTTATATATTCCAGTCTACCTTCAAGAACAACTAGGATTATCTCCATTGCAAAGTGGATTGGTTATTTTTCCTTTATCTGTAGCTTGGATTACATTGAATTTTAATTTACATCGAATTGAAGCAAAACTATCAAGGAAAGTTATTTACTTACTATCATTTACATTGTTACTAGTAAGTAGTATTATCATTTCATTTGGTATTAAATTGCCGGTACTTATAGCATTTGTGTTAATTTTGGCAGGATTAAGTTTTGGATATATTTATACGAAAGATAGTGTAATTGTCCAAGAGGAAACTAGCCCATTACAAATGAAGAAAATGATGTCATTTTATGGATTAACTAAAAATCTTGGGGCATCAATAGGTTCAACAATAATGGGATATCTTTATGCGATACAATCAGGAATCTTTGGTCCAAACTTACACAATGTGTTAAGTGCTGTTGCTGTAATTAGCATTGGGCTTATTGTTTTATGGGTCGTATTTTTTAAAGAACAGTCATCTCAATCAAAAGAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35514","NCBI_taxonomy_name":"Staphylococcus aureus subsp. aureus N315","NCBI_taxonomy_id":"158879"}}}},"ARO_accession":"3007013","ARO_id":"45482","ARO_name":"sdrM","CARD_short_name":"sdrM","ARO_description":"sdrM encodes an efflux pump that confers resistance to norfloxacin and ethidium bromide, making this a multidrug resistance gene.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"43746":{"category_aro_accession":"3005386","category_aro_cvterm_id":"43746","category_aro_name":"disinfecting agents and antiseptics","category_aro_description":"Disinfectants that can also interact with antimicrobial resistance mechanisms, e.g. molecule efflux, and thus are the targets of disinfectant resistance.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"5730":{"model_id":"5730","model_name":"qacJ","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"75"}},"model_sequences":{"sequence":{"8126":{"protein_sequence":{"accession":"CAD55144.1","sequence":"MPYLYLVIAIITEIIGTSFLKTAEGFTKLWPTLGTLISFGICFYFLSVTMKYLPLNVSYATWAGLGLVLTTIVSVVIFKESVNLISIFSIILIIIGVVLLNVFGSSH"},"dna_sequence":{"accession":"AJ512814.1","fmin":"1427","fmax":"1751","strand":"+","sequence":"ATGCCTTACTTATATTTAGTAATAGCGATTATAACTGAAATAATAGGAACTAGTTTCTTAAAAACAGCAGAAGGATTTACAAAACTTTGGCCAACATTAGGCACACTTATTTCATTCGGGATATGTTTCTATTTTTTAAGTGTAACTATGAAATATTTACCACTCAATGTATCTTATGCAACTTGGGCAGGGTTAGGACTAGTTCTTACAACAATAGTTTCAGTTGTAATTTTCAAAGAAAGCGTCAATTTAATTAGTATATTTTCAATAATCTTAATTATTATTGGTGTTGTGCTTCTTAACGTTTTTGGATCAAGTCATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35508","NCBI_taxonomy_name":"Staphylococcus aureus","NCBI_taxonomy_id":"1280"}}}},"ARO_accession":"3007014","ARO_id":"45483","ARO_name":"qacJ","CARD_short_name":"qacJ","ARO_description":"qacJ is a small multidrug resistance (SMR) efflux pump that confers resistance to quaternary ammonium compounds.","ARO_category":{"36004":{"category_aro_accession":"0010003","category_aro_cvterm_id":"36004","category_aro_name":"small multidrug resistance (SMR) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Small multidrug resistance (SMR) proteins are a relatively small family of transporters, restricted to prokaryotic cells. They are also the smallest multidrug transporters, with only four transmembrane alpha-helices and no significant extramembrane domain.","category_aro_class_name":"AMR Gene Family"},"40514":{"category_aro_accession":"3003823","category_aro_cvterm_id":"40514","category_aro_name":"benzalkonium chloride","category_aro_description":"Benzalkonium chloride is a type of cationic surfactant. It is an organic salt called a quaternary ammonium compound. It has three main categories of use: as a biocide, a cationic surfactant, and as a phase transfer agent.","category_aro_class_name":"Antibiotic"},"43746":{"category_aro_accession":"3005386","category_aro_cvterm_id":"43746","category_aro_name":"disinfecting agents and antiseptics","category_aro_description":"Disinfectants that can also interact with antimicrobial resistance mechanisms, e.g. molecule efflux, and thus are the targets of disinfectant resistance.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"5731":{"model_id":"5731","model_name":"qacG","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"75"}},"model_sequences":{"sequence":{"8127":{"protein_sequence":{"accession":"WP_015740450.1","sequence":"MHYLYLFISIATEIIGTSFLKTSEGFTKLWPTLGTLLSFGICFYFLSLTIKFLPLNITYATWAGLGLVLTTIISVIVFKENVNLISIISIGLIVIGVVLLNVFGESH"},"dna_sequence":{"accession":"NG_051904.1","fmin":"100","fmax":"424","strand":"+","sequence":"ATGCATTATTTATATTTATTTATCTCAATTGCAACAGAAATAATCGGAACTAGTTTTTTAAAAACATCAGAAGGTTTCACAAAGTTATGGCCAACATTAGGTACACTACTTTCGTTTGGAATTTGCTTTTATTTTTTAAGTTTAACAATAAAATTTTTGCCCTTAAATATAACTTACGCAACATGGGCAGGTCTAGGATTAGTATTAACAACAATAATCTCAGTTATCGTTTTTAAAGAAAATGTTAATTTAATTAGTATAATTTCTATTGGCTTAATTGTTATAGGTGTAGTGCTCTTAAATGTATTTGGAGAAAGCCATTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35506","NCBI_taxonomy_name":"Bacteria, Viruses, Fungi, and other genome sequence associated with antimicrobial resistance","NCBI_taxonomy_id":"2"}}}},"ARO_accession":"3007015","ARO_id":"45484","ARO_name":"qacG","CARD_short_name":"qacG","ARO_description":"qacG is a small multidrug resistance efflux pump that confers resistance to benzalkonium chloride and ethidium bromide.","ARO_category":{"36004":{"category_aro_accession":"0010003","category_aro_cvterm_id":"36004","category_aro_name":"small multidrug resistance (SMR) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Small multidrug resistance (SMR) proteins are a relatively small family of transporters, restricted to prokaryotic cells. They are also the smallest multidrug transporters, with only four transmembrane alpha-helices and no significant extramembrane domain.","category_aro_class_name":"AMR Gene Family"},"40514":{"category_aro_accession":"3003823","category_aro_cvterm_id":"40514","category_aro_name":"benzalkonium chloride","category_aro_description":"Benzalkonium chloride is a type of cationic surfactant. It is an organic salt called a quaternary ammonium compound. It has three main categories of use: as a biocide, a cationic surfactant, and as a phase transfer agent.","category_aro_class_name":"Antibiotic"},"43746":{"category_aro_accession":"3005386","category_aro_cvterm_id":"43746","category_aro_name":"disinfecting agents and antiseptics","category_aro_description":"Disinfectants that can also interact with antimicrobial resistance mechanisms, e.g. molecule efflux, and thus are the targets of disinfectant resistance.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"5732":{"model_id":"5732","model_name":"SHD-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"350"}},"model_sequences":{"sequence":{"8128":{"protein_sequence":{"accession":"WP_011495276.1","sequence":"MEFSRMMLNLVRKVFTTGPRVLSVVSLLSVNVLGINLAQAVTSEESVPKFSIEPLANNVYLHQSFQQTESFGLVGANGLVVINEGKAFIVDTPWSESDTAVLVDWIKEQGYQLVGSVSTHSHEDRTAGIGWLNAHSIPTFASELTNQILKESEKPLASHPFALPQASLFDGQLEAFYPGGGHALDNLVVWLPKSNILFGGCLVRSLDSTSLGYTGEAVLEQWPTSAMKVLAKFPDVELVVPGHGEPGDKQLLIHTKALAESGAKQASAK"},"dna_sequence":{"accession":"NG_077967.1","fmin":"100","fmax":"910","strand":"+","sequence":"ATGGAGTTTTCAAGAATGATGTTAAATCTAGTGCGCAAGGTGTTCACTACGGGGCCCAGAGTGCTCAGTGTTGTCAGCTTGCTAAGTGTTAACGTATTAGGCATAAACTTGGCACAGGCTGTGACTAGCGAGGAAAGCGTACCGAAATTTAGCATTGAGCCATTAGCCAATAATGTGTATTTGCACCAGTCCTTTCAACAGACTGAAAGTTTTGGCCTAGTCGGCGCCAATGGCTTAGTGGTGATTAATGAGGGAAAGGCCTTTATCGTCGATACCCCTTGGTCTGAAAGTGACACTGCGGTGCTGGTTGATTGGATTAAAGAACAAGGTTATCAATTGGTTGGCAGTGTATCAACTCACTCACATGAAGACAGAACAGCAGGCATAGGCTGGCTCAATGCTCACAGTATTCCGACATTTGCCTCTGAATTAACCAATCAGATTTTAAAAGAATCGGAAAAGCCGCTGGCAAGCCATCCTTTTGCACTGCCACAGGCGAGTTTGTTTGATGGCCAGCTGGAGGCATTTTATCCCGGTGGTGGGCATGCGCTAGATAATTTAGTGGTCTGGTTGCCTAAATCAAATATTCTCTTTGGCGGCTGTTTAGTTCGCAGCTTAGACTCAACAAGCCTAGGCTACACGGGAGAAGCGGTGTTAGAACAATGGCCGACATCTGCGATGAAAGTGCTCGCTAAATTCCCTGATGTAGAACTTGTGGTGCCAGGCCATGGTGAGCCTGGTGATAAACAGCTGTTAATTCACACAAAGGCTTTGGCCGAATCTGGGGCGAAGCAAGCGTCAGCTAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"45487","NCBI_taxonomy_name":"Shewanella denitrificans","NCBI_taxonomy_id":"192073"}}}},"ARO_accession":"3007017","ARO_id":"45486","ARO_name":"SHD-1","CARD_short_name":"SHD-1","ARO_description":"SHD-1 is a SHD beta-lactamase.","ARO_category":{"45485":{"category_aro_accession":"3007016","category_aro_cvterm_id":"45485","category_aro_name":"SHD beta-lactamase","category_aro_description":"SHD beta-lactamases are class B1 beta-lactamases found in Shewanella denitrificans.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5733":{"model_id":"5733","model_name":"fexB","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"520"}},"model_sequences":{"sequence":{"8130":{"protein_sequence":{"accession":"AEV23046.1","sequence":"MNHQNEKNIASNVLLISILGLSVLVGSVTADMVNPVLGVIGKELGGSEAQVSWVVSGVALVLSIAIPFYGRLSDFLNIKKLFTNGFLILTIGSLICIFAPNLIILVLGRMFQGAGMAAIPVLSIVIISKIYPPGQRGRILGIIAGCIGVGTAGGPIFGGVVGQLLGWQSLFWVTFVLGLIIVLGVQISMPKIESPDNNSHQNFDVLGGLLLGLTVGGFLLGITLSEMYGLISIQTTTSFSISMIALIVLIYRVINVKNPFIPPVILKNRLYVSSIFIVFLSMFAYVSMLVFIPLLVVEVNGLSTGQAGLILLSGGVAVAILSPIVGRLSDKVHPKILLLVGLIIMGLSSLYMSFVAGASPVLLSIGSLGIGIAFAFINSPVNNVAVLALPKEQVGVGTGLFQGAMYLGAGTGASLIGALLSMRHGVKASFNPFYTLTAPHYSDIFLTITCIVLVALIVTLNISSRDLKQ"},"dna_sequence":{"accession":"JN201336.1","fmin":"10636","fmax":"12046","strand":"-","sequence":"ATGAATCATCAAAATGAAAAAAATATAGCATCAAATGTGTTGTTAATTAGTATCTTAGGCTTGTCTGTTTTAGTGGGTTCAGTTACTGCAGATATGGTTAATCCTGTTCTCGGTGTGATTGGAAAAGAATTAGGTGGGTCTGAGGCGCAAGTTAGTTGGGTCGTAAGTGGTGTTGCCTTAGTTCTATCTATAGCAATTCCCTTTTATGGACGTTTATCTGATTTTTTAAATATTAAAAAACTCTTTACTAACGGATTTCTAATATTAACTATAGGAAGTTTAATATGTATATTCGCGCCCAATTTAATTATTTTAGTATTGGGTAGAATGTTTCAAGGAGCTGGCATGGCAGCCATACCTGTGCTATCTATTGTTATAATATCTAAAATTTATCCGCCTGGACAGAGAGGAAGAATTTTAGGTATTATTGCTGGTTGTATTGGCGTTGGCACTGCAGGAGGCCCAATATTTGGCGGCGTTGTAGGACAATTATTAGGTTGGCAATCATTATTTTGGGTCACTTTTGTTCTGGGTTTAATTATAGTTCTAGGTGTTCAAATATCAATGCCTAAAATAGAATCACCAGATAATAACAGTCATCAAAATTTTGATGTTTTAGGTGGACTATTATTAGGATTAACCGTAGGTGGTTTTTTACTTGGTATTACGCTTTCAGAAATGTATGGTTTGATTTCTATACAAACAACCACAAGTTTTTCTATATCTATGATAGCTTTAATAGTGTTAATATATCGCGTGATTAATGTTAAAAATCCTTTTATCCCTCCAGTTATATTGAAGAACCGTTTATATGTAAGCTCAATTTTCATTGTATTTCTTTCAATGTTTGCTTATGTCTCTATGCTTGTTTTTATTCCATTATTAGTTGTTGAGGTTAATGGGTTAAGTACTGGACAGGCAGGCTTAATATTACTTTCTGGTGGTGTCGCTGTTGCAATCCTTTCACCAATAGTGGGAAGATTATCTGACAAAGTGCATCCTAAAATACTATTATTAGTTGGACTAATTATTATGGGCTTATCTTCTTTATATATGAGCTTCGTAGCAGGCGCATCACCTGTATTATTATCTATCGGGAGTTTAGGGATAGGTATCGCTTTTGCATTTATTAACTCTCCAGTGAATAATGTTGCAGTACTTGCTTTACCTAAAGAACAAGTTGGTGTAGGTACGGGGTTGTTTCAAGGTGCAATGTATCTTGGGGCAGGAACAGGTGCCTCACTAATAGGGGCTTTATTGTCAATGAGACATGGGGTTAAAGCATCTTTTAATCCTTTTTATACTTTAACTGCCCCGCACTATTCTGATATATTTTTAACCATTACGTGCATCGTGTTAGTTGCTTTAATTGTTACTTTAAATATAAGTAGTAGGGATTTAAAGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36779","NCBI_taxonomy_name":"Enterococcus faecium","NCBI_taxonomy_id":"1352"}}}},"ARO_accession":"3007019","ARO_id":"45490","ARO_name":"fexB","CARD_short_name":"fexB","ARO_description":"FexB is a plasmid-encoded exporter gene which confers resistance to florfenicol. Originally identified in Enterococcus sp. isolated from swine by Liu et al. 2012.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"36600":{"category_aro_accession":"3000461","category_aro_cvterm_id":"36600","category_aro_name":"florfenicol","category_aro_description":"Florfenicol is a fluorine derivative of chloramphenicol, where the nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3) and the hydroxyl group (-OH), by a fluorine group (-F). The action mechanism is the same as chloramphenicol's, where the antibiotic binds to the 23S RNA of the 50S subunit of bacterial ribosomes to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"5736":{"model_id":"5736","model_name":"NDM-33","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"554"}},"model_sequences":{"sequence":{"8132":{"protein_sequence":{"accession":"UBU60937.1","sequence":"MELPNIMHPVAKLSTALAAALMLSGCMPGEIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGTVASNGLIVRDGGRVLLVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGLVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR"},"dna_sequence":{"accession":"MZ004933.1","fmin":"9952","fmax":"10765","strand":"-","sequence":"ATGGAATTGCCCAATATTATGCACCCGGTCGCGAAGCTGAGCACCGCATTAGCCGCTGCATTGATGCTGAGCGGGTGCATGCCCGGTGAAATCCGCCCGACGATTGGCCAGCAAATGGAAACTGGCGACCAACGGTTTGGCGATCTGGTTTTCCGCCAGCTCGCACCGAATGTCTGGCAGCACACTTCCTATCTCGACATGCCGGGTTTCGGGACAGTCGCTTCCAACGGTTTGATCGTCAGGGATGGCGGCCGCGTGCTGTTGGTCGATACCGCCTGGACCGATGACCAGACCGCCCAGATCCTCAACTGGATCAAGCAGGAGATCAACCTGCCGGTCGCGCTGGCGGTGGTGACTCACGCGCATCAGGACAAGATGGGCGGTATGGACGCGCTGCATGCGGCGGGGATTGCGACTTATGCCAATGCGTTGTCGAACCAGCTTGCCCCGCAAGAGGGGCTGGTTGCGGCGCAACACAGCCTGACTTTCGCCGCCAATGGCTGGGTCGAACCAGCAACCGCGCCCAACTTTGGCCCGCTCAAGGTATTTTACCCCGGCCCCGGCCACACCAGTGACAATATCACCGTTGGGATCGACGGCACCGACATCGCTTTTGGTGGCTGCCTGATCAAGGACAGCAAGGCCAAGTCGCTCGGCAATCTCGGTGATGCCGACACTGAGCACTACGCCGCGTCAGCGCGCGCGTTTGGTGCGGCGTTCCCCAAGGCCAGCATGATCGTGATGAGCCATTCCGCCCCCGATAGCCGCGCCGCAATCACTCATACGGCCCGCATGGCCGACAAGCTGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3007023","ARO_id":"45495","ARO_name":"NDM-33","CARD_short_name":"NDM-33","ARO_description":"NDM-33 confers resistance to all beta-lactam antibiotics except aztreonam. It was first identified in an E. coli strain isolated from hospital sewage. It differs from NDM-5 by a single amino acid substitution (A72T).","ARO_category":{"36196":{"category_aro_accession":"3000057","category_aro_cvterm_id":"36196","category_aro_name":"NDM beta-lactamase","category_aro_description":"NDM beta-lactamases or New Delhi metallo-beta-lactamases are class B beta-lactamases that confer resistance to a broad range of antibiotics including carbapenems, cephalosporins and penicillins.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2823":{"model_id":"2823","model_name":"Mycoplasmopsis fermentans 23S rRNA with mutation conferring resistance to macrolide antibiotics","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"41093","param_value":"5000"},"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"8308":"g2057a"},"Curated-R":{"8308":"g2057a"},"clinical":{"8308":"g2057a"}}},"model_sequences":{"sequence":{"4167":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"NC_021002.1","fmin":"901870","fmax":"904756","strand":"-","sequence":"CTTTTAAACCGATCGATTTATTAGTATTGGTCAGCTCAACGTATTACTACGCTTACACCTCCAACCTATCAACCTCATAGTCTATAAGGAATCTCAAGGGAATACTTATCTCTGAGGAGGCTTCCCACTTAGATGCTTTCAGCGGTTATCCTTTCCGTACTTAGCTACCCAGCTATGCTCCTGGCGGAACAACTGGAACACCAGTGGTACGTCCACTCCGGTCCTCTCGTACTAAGAGCGGCTCTCATCAATATTCCAACGCCCACATCAGATAGGGACCAAACTGTCTCACGACGTTTTGAACCCAGCTCGCGTACCGCTTTAATGGGCGAACAGCCCAACCCTTGGAACCGACTCCAGCTCCAGGATGCGATGAGCCGACATCGAGGTGCCAAACCTTGCCGTCGATGTGATCTCTTGGGCAAGATAAGCCTGTTATCCCCAGGGTAACTTTTATCCGTTGAGCGACTGCCATTCCACAATGTACAGCCGGATCACTAAGTCCTGCTTTCGCACCTGCTCGACTTGTAAGTCTCACAGTCAAGCACACTTCTACCTTTGCGCTCTACATACGGTTTCTGACCGTACTGAGTGTACCTTTGAACGCCTCCGTTACTCTTTAGGAGGCGACCGCCCCAGTCAAACTACCCGTCACGCACTGTCCACCCACCTGATGATGATGGCATGTTAGAAACTCAATATACCAAGGGTGGTATTTCAAGGATGACTCCACGAGAACTAGCGTCCTCGCTTCAAAGTCTCCCACCTATCCTACACATGTTAGACCAAGTTCCAATACGAAACTGTAGTAAAGCTCCATGGGGTCTTTTCGTCTTGATGCGGGTACCCAGCGTTTTCACTGGGACCATAATTTCACCGAGTCTAGTGTTGAGACAGTTGAGAGATCATTGCGCCTTTCGTGCAGGTCAGTATTTAGCCGACAAGGAATTTCGCTACCTTAGGACCGTTATAGTTACGGCCGCCGTTCACCCGGGCTTCATTTCAACGCTTCGCAAATGCTAACGCATCCACTTAACCTTCGGGCACTGGGCAGGCTTCACCCCCTATACATCACCTTGCGGTTTAGCAGAGAGCTGTGTTTTTGATAAACAGTTGCCCCTCATAATTTACTGTGGCCTAAGTGTTACCTTAGGCGCCCCTTCTTGCGAACTTACGGGGTCATTTTGCAGAGTTCCTTAACACTAGTTTTCTCGCTCGCCTTAGAATACTCATCTCGGGGACGTGTGTCCGTTCTCGGTACAGGTTTCCATAATATTAAGTTTAGAAGCTTTTCTTGGAAGTGTGGAATCATCTAATTCGGTTTGACCCTATGCATCACGCCTCCCGGTTATAGACTGCGGATTTGCCTACAGTCACCAGTGAACGCTTACCCCACAATCCAGTAAGTGGTAAGATTATCCTCCTCCGTCACTCCATCACTATTATAGAAAGTACAGGAATATTAACCTGTTGTCCATCGGCTACGCTTTTCAGCCTCGTCTTAGGTCCTGACTAACCCTGGGTGGACGAACCTTGCCCAGGAAACCTTCCCCAATAGGCGTCGTAGATTCTCACTACGAATCGTTACTCATACCGGCATTCTCACTTCCTAGCGCTCCACCAGTCCTCACGGTCTGACTTCATTGCCCTAGGAACGCTCCTCTAACGTAAATATAATTACCCGCGGCTTCGGTATCGTGTTTTAGTCCCGTTAAATTGTTGGCGCAAGGTCTCTTGACTAGTGAGCTATTACGCACTCTTTAAAAGGTGGCTGCTTCTGAGCCAACTTCCTAGTTGTTTATGAAACCTCACAACCTTTCTCACTTAACACGATTTTGGGACCTTAGCCGGCGATCTGGGTTGTTGCCCTCGCGAGCCGGGACGTTAGCACCCCGGTTCCGACTGCATAGCAATACATAGCGGTATTCGGAGTTTGATTATAGTCAGTACCCCTAGGCGAGGCCATTCCATATTCAGTGCTCTACCACCACTACTTAACACTACACGCTAGCCCTAAAGCTATTTCGAGGAGAACCAGCTATCTCCAAGTTCGATTGGAATTTCTCCACTATTCACAAGTCATCCGGGCACTTTTCAGCGTACTACGGTTCGGCCCTCCGCTTGGGGTTAGCCAAGTTTCAGCCTGCTCATGAATAGATCACATGGTTTCGGGTATATGACAACATACTAAGACGCCCTATTAAGACTCGATTTCTCTACGGCTCCGCTTTTTTCTGCTTAACCTCGCATGCTGTCATAACTCGCCGGTCCATACTGCAAGATGTACGCCATCACCCATAAACGGGCTCTGACTAATTGTAAGTAAGTGGTTTCAGAATCTATTTCACTCCCCTCTCGGGGTTCTTTTCACCTTTCCCTCACGGTACTAGTTCACTATCGGTGTCTGATTAGTATTTAGCCTTACCGGGTGGTCCCGGCAGATTCAGACAGGGTTCCACGTGCCCCGCCCTACTCAGGATACGATCAGAAGACTTAACAATTTCACATACGGGGGTATCACCCTCTATGCCGCTTCTTCCCAAAAGCTTCTGCTATCATTAAGTTTTGTAACTTCATGTAGATCGTCCTACAACCCCCATTGCTGGGTTTGGGCTCTTTCTCGTTCGCTCGCCGCTACTAAAGAAATCATTGTTTATTTTCTCTTCCTCTTGCTACTAAGATGTTTCAGTTCACAAGGTGTCTCACTCAAGTTCCTATGAATTCAGAACAAGGCAACTAGGCATTACCCTAGTTAGGTTTCCCCATTCGGAAATCCCCGTTTCATAGCATATTTCCGGCTCCACGAGGCTTATCGCAGGTAATCACGTCCTTCATCGACTTTCAGACCCAAGGCATCCACCACAAACTCTTCCTTATTTAAAAGTA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41329","NCBI_taxonomy_name":"Mycoplasmopsis fermentans PG18","NCBI_taxonomy_id":"496833"}}}},"ARO_accession":"3004177","ARO_id":"41328","ARO_name":"Mycoplasmopsis fermentans 23S rRNA with mutation conferring resistance to macrolide antibiotics","CARD_short_name":"Mfer_23S_MAC","ARO_description":"Point mutation in the 23S rRNA of Mycoplasmopsis fermentans shown to confer resistance to macrolide type antibiotics.","ARO_category":{"41251":{"category_aro_accession":"3004125","category_aro_cvterm_id":"41251","category_aro_name":"23S rRNA with mutation conferring resistance to macrolide antibiotics","category_aro_description":"Nucleotide point mutations in the 23S rRNA subunit may confer resistance to macrolide antibiotics.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35982":{"category_aro_accession":"0000065","category_aro_cvterm_id":"35982","category_aro_name":"clarithromycin","category_aro_description":"Clarithromycin is a methyl derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome and is used to treat pharyngitis, tonsillitis, acute maxillary sinusitis, acute bacterial exacerbation of chronic bronchitis, pneumonia (especially atypical pneumonias associated with Chlamydia pneumoniae or TWAR), and skin structure infections.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2891":{"model_id":"2891","model_name":"Alkalihalobacillus clausii chloramphenicol acetyltransferase","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"350"}},"model_sequences":{"sequence":{"4424":{"protein_sequence":{"accession":"AAQ63644.1","sequence":"MEILTLLIRDTMGSKRIFLNPYFQQQPTFSLTNEINITILMKNLKKKHYKLYPAFIFMVTKIVNAHREFRINFNSEGNLGYWTEICPLYTIFDNKSHTFSGIWSPNLTIFSEFHSKYENDAERYNGTRRLFPKKPIPDNPIPISMIPWSSFTAFNLNINNGGDFLLPIITGGKYSQVNDELFLPVSIQNASCLFVMATMQSVFINDLQNLVDESEDWIYLVVSDEWYY"},"dna_sequence":{"accession":"AY238971.1","fmin":"1054","fmax":"1741","strand":"+","sequence":"ATGGAAATTTTAACACTATTAATTCGTGATACCATGGGATCGAAAAGAATATTTTTGAACCCCTATTTCCAGCAGCAGCCAACATTCAGTCTGACGAATGAAATTAATATAACTATACTTATGAAGAACTTAAAGAAAAAGCATTATAAGTTATATCCTGCGTTTATTTTTATGGTGACAAAAATCGTGAACGCCCATAGAGAATTTAGAATAAATTTTAACTCAGAAGGAAATTTAGGTTACTGGACGGAGATTTGCCCACTCTATACCATTTTTGATAACAAATCACACACATTTTCTGGCATCTGGTCACCAAACTTAACTATTTTTTCTGAGTTTCATTCTAAATATGAAAATGATGCAGAAAGATACAATGGCACGAGGAGATTATTTCCAAAAAAACCAATACCAGATAACCCTATTCCGATTTCTATGATTCCTTGGAGTTCTTTTACAGCATTTAATCTAAATATAAATAATGGCGGAGATTTTCTCTTACCCATAATAACTGGAGGGAAGTATTCACAAGTAAATGATGAATTATTCCTGCCTGTCTCTATCCAAAATGCATCATGCCTATTTGTGATGGCTACCATGCAAAGTGTTTTTATCAATGACTTACAAAACCTTGTTGATGAAAGTGAAGACTGGATTTACCTGGTCGTTAGTGATGAATGGTATTATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36882","NCBI_taxonomy_name":"Alkalihalobacillus clausii","NCBI_taxonomy_id":"79880"}}}},"ARO_accession":"3004452","ARO_id":"41663","ARO_name":"Alkalihalobacillus clausii chloramphenicol acetyltransferase","CARD_short_name":"Acla_ACT_CHL","ARO_description":"A chloramphenicol resistance determinant described in Alkalihalobacillus clausii.","ARO_category":{"36261":{"category_aro_accession":"3000122","category_aro_cvterm_id":"36261","category_aro_name":"chloramphenicol acetyltransferase (CAT)","category_aro_description":"Inactivates chloramphenicol by addition of an acyl group. CAT is used to describe many variants of the chloramphenicol acetyltransferase gene in a range of organisms including Acinetobacter calcoaceticus, Agrobacterium tumefaciens, Alkalihalobacillus clausii, Bacillus subtilis, Campylobacter coli, Enterococcus faecalis, Enterococcus faecium, Lactococcus lactis, Listeria monocytogenes, Listonella anguillarum, Morganella morganii, Photobacterium damselae subsp. piscicida, Proteus mirabilis, Salmonella typhi, Serratia marcescens, Shigella flexneri, Staphylococcus aureus, Staphylococcus haemolyticus, Staphylococcus intermedius, Streptococcus agalactiae, Streptococcus suis and Streptomyces acrimycini.","category_aro_class_name":"AMR Gene Family"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1524":{"model_id":"1524","model_name":"Limosilactobacillus reuteri cat-TC","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"688":{"protein_sequence":{"accession":"AAB53259.1","sequence":"MNFNKIDLDNWKRKEIFNHYLNQQTTFSITTEIDISVLYRNIKQEGYKFYPAFIFLVTRVINSNTAFRTGYNSDGELGYWDKLEPLYTIFDGVSKTFSGIWTSVKNDFKEFYDLYLSDVEKYNGSGKLFPKTPIPENAFSLSIIPWTSFTGFNLNINNNSNYLLPIITAGKFINKGNSIYLPLSLQVHHSVCDGYHAGLFMNSIRNCQIGLMTGFYNIDKPTVLFTVGFLMSLTCPLI"},"dna_sequence":{"accession":"U75299.1","fmin":"0","fmax":"717","strand":"+","sequence":"ATGAACTTTAATAAAATTGATTTAGACAATTGGAAGAGAAAAGAGATATTTAATCATTATTTGAACCAACAAACGACTTTTAGTATAACCACAGAAATTGATATTAGTGTTTTATACCGAAACATAAAACAAGAAGGATATAAATTTTACCCTGCATTTATTTTCTTAGTGACAAGGGTGATAAACTCAAATACAGCTTTTAGAACTGGTTACAATAGCGACGGAGAGTTAGGTTATTGGGATAAGTTAGAGCCACTTTATACAATTTTTGATGGTGTATCTAAAACATTCTCTGGTATTTGGACTTCTGTAAAGAATGACTTCAAAGAGTTTTATGATTTATACCTTTCTGATGTAGAGAAATATAATGGTTCGGGGAAATTGTTTCCCAAAACACCTATACCTGAAAATGCTTTTTCTCTTTCTATTATTCCATGGACTTCATTTACTGGGTTTAACTTAAATATCAATAATAATAGTAATTACCTTCTACCCATTATTACAGCAGGAAAATTCATTAATAAAGGTAATTCAATATATTTACCGCTATCTTTACAGGTACATCATTCTGTTTGTGATGGTTATCATGCAGGATTGTTTATGAACTCTATCAGGAATTGTCAGATAGGCCTAATGACTGGCTTTTATAATATAGATAAGCCGACTGTACTTTTTACAGTCGGTTTTCTAATGTCACTAACCTGCCCGTTAATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36855","NCBI_taxonomy_name":"Limosilactobacillus reuteri","NCBI_taxonomy_id":"1598"}}}},"ARO_accession":"3002671","ARO_id":"39105","ARO_name":"Limosilactobacillus reuteri cat-TC","CARD_short_name":"Lreu_cat-TC","ARO_description":"cat-TC is a plasmid-encoded variant of the cat gene found in Limosilactobacillus reuteri.","ARO_category":{"36261":{"category_aro_accession":"3000122","category_aro_cvterm_id":"36261","category_aro_name":"chloramphenicol acetyltransferase (CAT)","category_aro_description":"Inactivates chloramphenicol by addition of an acyl group. CAT is used to describe many variants of the chloramphenicol acetyltransferase gene in a range of organisms including Acinetobacter calcoaceticus, Agrobacterium tumefaciens, Alkalihalobacillus clausii, Bacillus subtilis, Campylobacter coli, Enterococcus faecalis, Enterococcus faecium, Lactococcus lactis, Listeria monocytogenes, Listonella anguillarum, Morganella morganii, Photobacterium damselae subsp. piscicida, Proteus mirabilis, Salmonella typhi, Serratia marcescens, Shigella flexneri, Staphylococcus aureus, Staphylococcus haemolyticus, Staphylococcus intermedius, Streptococcus agalactiae, Streptococcus suis and Streptomyces acrimycini.","category_aro_class_name":"AMR Gene Family"},"36521":{"category_aro_accession":"3000382","category_aro_cvterm_id":"36521","category_aro_name":"azidamfenicol","category_aro_description":"Azidamfenicol is a water soluble derivative of chloramphenicol, sharing the same mode of action of inhibiting peptide synthesis by interacting with the 23S RNA of the 50S ribosomal subunit.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36595":{"category_aro_accession":"3000456","category_aro_cvterm_id":"36595","category_aro_name":"thiamphenicol","category_aro_description":"Derivative of Chloramphenicol. The nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3).","category_aro_class_name":"Antibiotic"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"89":{"model_id":"89","model_name":"vanY gene in vanA cluster","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"50"}},"model_sequences":{"sequence":{"3278":{"protein_sequence":{"accession":"AAA65958.1","sequence":"MKKLFFLLLLLFLIYLGYDYVNEALFSQEKVEFQNYDQNPKEHLENSGTSENTQEKTITEEQVYQGNLLLINSKYPVRQESVKSDIVNLSKHDELINGYGLLDSNIYMSKEIAQKFSEMVNDAVKGGVSHFIINSGYRDFDEQSVLYQEMGAEYALPAGYSEHNSGLSLDVGSSLTKMERAPEGKWIEENAWKYGFILRYPEDKTELTGIQYEPWHIRYVGLPHSAIMKEKNFVLEEYMDYLKEEKTISVSVNGEKYEIFYYPVTKNTTIHVPTNLRYEISGNNIDGVIVTVFPGSTHTNSRR"},"dna_sequence":{"accession":"M97297.1","fmin":"9051","fmax":"9963","strand":"+","sequence":"ATGAAGAAGTTGTTTTTTTTATTGTTATTGTTATTCTTAATATACTTAGGTTATGACTACGTTAATGAAGCACTGTTTTCTCAGGAAAAAGTCGAATTTCAAAATTATGATCAAAATCCCAAAGAACATTTAGAAAATAGTGGGACTTCTGAAAATACCCAAGAGAAAACAATTACAGAAGAACAGGTTTATCAAGGAAATCTGCTATTAATCAATAGTAAATATCCTGTTCGCCAAGAAAGTGTGAAGTCAGATATCGTGAATTTATCTAAACATGACGAATTAATAAATGGATACGGGTTGCTTGATAGTAATATTTATATGTCAAAAGAAATAGCACAAAAATTTTCAGAGATGGTCAATGATGCTGTAAAGGGTGGCGTTAGTCATTTTATTATTAATAGTGGCTATCGAGACTTTGATGAGCAAAGTGTGCTTTACCAAGAAATGGGGGCTGAGTATGCCTTACCAGCAGGTTATAGTGAGCATAATTCAGGTTTATCACTAGATGTAGGATCAAGCTTGACGAAAATGGAACGAGCCCCTGAAGGAAAGTGGATAGAAGAAAATGCTTGGAAATACGGGTTCATTTTACGTTATCCAGAGGACAAAACAGAGTTAACAGGAATTCAATATGAACCATGGCATATTCGCTATGTTGGTTTACCACATAGTGCGATTATGAAAGAAAAGAATTTCGTTCTCGAGGAATATATGGATTACCTAAAAGAAGAAAAAACCATTTCTGTTAGTGTAAATGGGGAAAAATATGAGATCTTTTATTATCCTGTTACTAAAAATACCACCATTCATGTGCCGACTAATCTTCGTTATGAGATATCAGGAAACAATATAGACGGTGTAATTGTGACAGTGTTTCCCGGATCAACACATACTAATTCAAGGAGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36779","NCBI_taxonomy_name":"Enterococcus faecium","NCBI_taxonomy_id":"1352"}}}},"ARO_accession":"3002955","ARO_id":"39389","ARO_name":"vanY gene in vanA cluster","CARD_short_name":"vanY_in_vanA_cl","ARO_description":"Also known as vanYA, is a vanY variant found in the vanA gene cluster.","ARO_category":{"36216":{"category_aro_accession":"3000077","category_aro_cvterm_id":"36216","category_aro_name":"vanY","category_aro_description":"VanY is a D,D-carboxypeptidase that cleaves removes the terminal D-Ala from peptidoglycan for the addition of D-Lactate. The D-Ala-D-Lac peptidoglycan subunits have reduced binding affinity with vancomycin compared to D-Ala-D-Ala.","category_aro_class_name":"AMR Gene Family"},"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"35948":{"category_aro_accession":"0000029","category_aro_cvterm_id":"35948","category_aro_name":"teicoplanin","category_aro_description":"Teicoplanin is a glycopeptide antibiotic used in the prophylaxis and treatment of serious infections caused by Gram-positive bacteria. Teicoplanin has a unique acyl-aliphatic chain, and binds to cell wall precursors to inhibit transglycosylation  and transpeptidation.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"97":{"model_id":"97","model_name":"vanXY gene in vanC cluster","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"125"}},"model_sequences":{"sequence":{"39":{"protein_sequence":{"accession":"AAF61331.1","sequence":"MNTLQLINKNHPLKKNQEPPHLVLAPFSDHDVYLQPEVAKQWERLVRATGLEKDIRLVDGYRTEKEQRRLWEYSLKENGLAYTKQFVALPGCSEHQIGLAIDVGLKKQEDDDLICPHFRDSAAADLFMQQMMNYGFILRYPEDKQEITGISYEPWHFRYVGLPHSQVITAQKWTLEEYHDYLAQTVRQFA"},"dna_sequence":{"accession":"AF162694.1","fmin":"2438","fmax":"3011","strand":"+","sequence":"ATGAACACATTACAATTGATCAATAAAAACCATCCATTGAAAAAAAATCAAGAGCCCCCGCACTTAGTGCTAGCTCCTTTTAGCGATCACGATGTTTACCTGCAGCCAGAAGTGGCAAAACAATGGGAACGACTCGTACGAGCAACCGGACTAGAAAAGGACATTCGTCTGGTAGATGGGTATCGTACGGAAAAAGAACAGCGACGCTTGTGGGAGTATTCTCTAAAAGAAAACGGGTTAGCTTATACCAAACAATTCGTTGCTTTGCCAGGTTGCAGTGAACATCAAATCGGTCTGGCCATTGATGTAGGACTAAAGAAACAAGAAGATGATGATCTTATCTGCCCTCATTTTCGAGATAGTGCTGCTGCTGATTTATTTATGCAGCAGATGATGAATTATGGCTTTATTCTACGCTATCCGGAAGATAAACAAGAGATCACCGGTATCAGTTATGAACCTTGGCATTTTCGTTATGTCGGGCTTCCCCATAGCCAAGTCATCACTGCCCAAAAATGGACTCTGGAAGAATACCATGATTACTTGGCTCAGACAGTGAGGCAGTTCGCATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36781","NCBI_taxonomy_name":"Enterococcus gallinarum","NCBI_taxonomy_id":"1353"}}}},"ARO_accession":"3002966","ARO_id":"39400","ARO_name":"vanXY gene in vanC cluster","CARD_short_name":"vanXY_in_vanC","ARO_description":"Also known as vanXYC, is a vanXY variant found in the vanC gene cluster.","ARO_category":{"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"36635":{"category_aro_accession":"3000496","category_aro_cvterm_id":"36635","category_aro_name":"vanXY","category_aro_description":"VanXY is a protein with both D,D-carboxypeptidase and D,D-dipeptidase activity, found in Enterococcus gallinarum. It cleaves and removes the terminal D-Ala of peptidoglycan subunits for the incorporation of D-Ser by VanC. D-Ala-D-Ser has low binding affinity with vancomycin.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"178":{"model_id":"178","model_name":"vanH gene in vanA cluster","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"200"}},"model_sequences":{"sequence":{"3279":{"protein_sequence":{"accession":"AAA65955.1","sequence":"MNNIGITVYGCEQDEADAFHALSPRFGVMATIINANVSESNAKSAPFNQCISVGHKSEISASILLALKRAGVKYISTRSIGCNHIDTTAAKRMGITVDNVAYSPDSVADYTMMLILMAVRNVKSIVRSVEKHDFRLDSDRGKVLSDMTVGVVGTGQIGKAVIERLRGFGCKVLAYSRSRSIEVNYVPFDELLQNSDIVTLHVPLNTDTHYIISHEQIQRMKQGAFLINTGRGPLVDTYELVKALENGKLGGAALDVLEGEEEFFYSDCTQKPIDNQFLLKLQRMPNVIITPHTAYYTEQALRDTVEKTIKNCLDFERRQEHE"},"dna_sequence":{"accession":"M97297.1","fmin":"6017","fmax":"6986","strand":"+","sequence":"ATGAATAACATCGGCATTACTGTTTATGGATGTGAGCAGGATGAGGCAGATGCATTCCATGCTCTTTCGCCTCGCTTTGGCGTTATGGCAACGATAATTAACGCCAACGTGTCGGAATCCAACGCCAAATCCGCGCCTTTCAATCAATGTATCAGTGTGGGACATAAATCAGAGATTTCCGCCTCTATTCTTCTTGCGCTGAAGAGAGCCGGTGTGAAATATATTTCTACCCGAAGCATCGGCTGCAATCATATAGATACAACTGCTGCTAAGAGAATGGGCATCACTGTCGACAATGTGGCGTACTCGCCGGATAGCGTTGCCGATTATACTATGATGCTAATTCTTATGGCAGTACGCAACGTAAAATCGATTGTGCGCTCTGTGGAAAAACATGATTTCAGGTTGGACAGCGACCGTGGCAAGGTACTCAGCGACATGACAGTTGGTGTGGTGGGAACGGGCCAGATAGGCAAAGCGGTTATTGAGCGGCTGCGAGGATTTGGATGTAAAGTGTTGGCTTATAGTCGCAGCCGAAGTATAGAGGTAAACTATGTACCGTTTGATGAGTTGCTGCAAAATAGCGATATCGTTACGCTTCATGTGCCGCTCAATACGGATACGCACTATATTATCAGCCACGAACAAATACAGAGAATGAAGCAAGGAGCATTTCTTATCAATACTGGGCGCGGTCCACTTGTAGATACCTATGAGTTGGTTAAAGCATTAGAAAACGGGAAACTGGGCGGTGCCGCATTGGATGTATTGGAAGGAGAGGAAGAGTTTTTCTACTCTGATTGCACCCAAAAACCAATTGATAATCAATTTTTACTTAAACTTCAAAGAATGCCTAACGTGATAATCACACCGCATACGGCCTATTATACCGAGCAAGCGTTGCGTGATACCGTTGAAAAAACCATTAAAAACTGTTTGGATTTTGAAAGGAGACAGGAGCATGAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36779","NCBI_taxonomy_name":"Enterococcus faecium","NCBI_taxonomy_id":"1352"}}}},"ARO_accession":"3002942","ARO_id":"39376","ARO_name":"vanH gene in vanA cluster","CARD_short_name":"vanH_in_vanA_cl","ARO_description":"Also known as vanHA, is a vanH variant in the vanA gene cluster.","ARO_category":{"36015":{"category_aro_accession":"3000006","category_aro_cvterm_id":"36015","category_aro_name":"vanH","category_aro_description":"VanH is a D-specific alpha-ketoacid dehydrogenase that synthesizes D-lactate. D-lactate is incorporated into the end of the peptidoglycan subunits, decreasing vancomycin binding affinity.","category_aro_class_name":"AMR Gene Family"},"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"35948":{"category_aro_accession":"0000029","category_aro_cvterm_id":"35948","category_aro_name":"teicoplanin","category_aro_description":"Teicoplanin is a glycopeptide antibiotic used in the prophylaxis and treatment of serious infections caused by Gram-positive bacteria. Teicoplanin has a unique acyl-aliphatic chain, and binds to cell wall precursors to inhibit transglycosylation  and transpeptidation.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"217":{"model_id":"217","model_name":"vanX gene in vanA cluster","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"200"}},"model_sequences":{"sequence":{"3281":{"protein_sequence":{"accession":"AAA65957.1","sequence":"MEIGFTFLDEIVHGVRWDAKYATWDNFTGKPVDGYEVNRIVGTYELAESLLKAKELAATQGYGLLLWDGYRPKRAVNCFMQWAAQPENNLTKESYYPNIDRTEMISKGYVASKSSHSRGSAIDLTLYRLDTGELVPMGSRFDFMDERSHHAANGISCNEAQNRRRLRSIMENSGFEAYSLEWWHYVLRDEPYPNSYFDFPVK"},"dna_sequence":{"accession":"M97297.1","fmin":"8015","fmax":"8624","strand":"+","sequence":"ATGGAAATAGGATTTACTTTTTTAGATGAAATAGTACACGGTGTTCGTTGGGACGCTAAATATGCCACTTGGGATAATTTCACCGGAAAACCGGTTGACGGTTATGAAGTAAATCGCATTGTAGGGACATACGAGTTGGCTGAATCGCTTTTGAAGGCAAAAGAACTGGCTGCTACCCAAGGGTACGGATTGCTTCTATGGGACGGTTACCGTCCTAAGCGTGCTGTAAACTGTTTTATGCAATGGGCTGCACAGCCGGAAAATAACCTGACAAAGGAAAGTTATTATCCCAATATTGACCGAACTGAGATGATTTCAAAAGGATACGTGGCTTCAAAATCAAGCCATAGCCGCGGCAGTGCCATTGATCTTACGCTTTATCGATTAGACACGGGTGAGCTTGTACCAATGGGGAGCCGATTTGATTTTATGGATGAACGCTCTCATCATGCGGCAAATGGAATATCATGCAATGAAGCGCAAAATCGCAGACGTTTGCGCTCCATCATGGAAAACAGTGGGTTTGAAGCATATAGCCTCGAATGGTGGCACTATGTATTAAGAGACGAACCATACCCCAATAGCTATTTTGATTTCCCCGTTAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36779","NCBI_taxonomy_name":"Enterococcus faecium","NCBI_taxonomy_id":"1352"}}}},"ARO_accession":"3002949","ARO_id":"39383","ARO_name":"vanX gene in vanA cluster","CARD_short_name":"vanX_in_vanA_cl","ARO_description":"Also known as vanXA, is a vanX variant found in the vanA gene cluster.","ARO_category":{"36020":{"category_aro_accession":"3000011","category_aro_cvterm_id":"36020","category_aro_name":"vanX","category_aro_description":"VanX is a D,D-dipeptidase that cleaves D-Ala-D-Ala but not D-Ala-D-Lac, ensuring that the latter dipeptide that has reduced binding affinity with vancomycin is used to synthesize peptidoglycan substrate.","category_aro_class_name":"AMR Gene Family"},"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"35948":{"category_aro_accession":"0000029","category_aro_cvterm_id":"35948","category_aro_name":"teicoplanin","category_aro_description":"Teicoplanin is a glycopeptide antibiotic used in the prophylaxis and treatment of serious infections caused by Gram-positive bacteria. Teicoplanin has a unique acyl-aliphatic chain, and binds to cell wall precursors to inhibit transglycosylation  and transpeptidation.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"332":{"model_id":"332","model_name":"R39","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"3308":{"protein_sequence":{"accession":"CAA37699.1","sequence":"MLFPTARRTGFAALAALALVPAAACSGSAAPAEAEPASAEVTAEDLSGEFERLESEFDARLGVYAVDTGTGEEVFHRADERFGYASTHKAFTAALVLGQNTPEELEEVVTYTEEDLVDYSPITEQHVDTGMTLLEVADAAVRHSDNTAANLLFEELGGPEGFEEDMRELGDDVISADRIETELNEVPPGETRDTSTPRAMAGSLEAFVLGDVLEEGPRDVLTEMLLNNTTGDELIRAGVPEDWRVGDKTGGGSHGSRNDIAVVWPPEDDPIVIAVMSTREQEDAEFDNALVSGATEVVVEALAP"},"dna_sequence":{"accession":"X53650.1","fmin":"320","fmax":"1235","strand":"+","sequence":"ATGTTGTTCCCCACGGCCCGCAGGACCGGGTTCGCGGCCCTGGCCGCGCTCGCGCTCGTCCCCGCCGCGGCCTGCTCCGGCTCCGCCGCGCCCGCCGAGGCGGAGCCGGCGAGCGCGGAGGTGACGGCCGAGGACCTCTCCGGTGAGTTCGAGCGGCTGGAATCGGAGTTCGACGCCCGTCTCGGGGTCTACGCGGTGGACACCGGGACCGGGGAGGAGGTCTTCCACCGCGCCGACGAGCGGTTCGGCTACGCCTCCACCCACAAGGCGTTCACGGCGGCCCTGGTCCTGGGGCAGAACACCCCCGAGGAGCTGGAGGAGGTCGTCACCTACACCGAAGAGGACCTGGTCGACTACTCCCCCATCACCGAGCAGCACGTCGACACGGGGATGACCCTGCTGGAGGTGGCCGACGCCGCCGTCCGCCACAGCGACAACACCGCCGCGAACCTGCTGTTCGAGGAGCTGGGCGGACCCGAGGGGTTCGAGGAGGACATGCGGGAGCTCGGCGACGACGTGATCTCGGCGGACCGGATCGAGACCGAGCTCAACGAGGTGCCGCCCGGCGAGACCCGGGACACGAGCACGCCGCGCGCCATGGCCGGGAGCCTGGAGGCGTTCGTGCTCGGTGACGTCCTGGAGGAGGGCCCGCGCGACGTGCTCACCGAGATGCTCCTCAACAACACGACCGGTGACGAGCTGATCCGGGCGGGGGTCCCCGAGGACTGGCGTGTCGGTGACAAGACCGGCGGCGGCAGCCACGGTTCGCGCAACGACATCGCCGTCGTCTGGCCCCCCGAGGACGACCCCATCGTCATCGCGGTCATGTCCACCCGTGAGCAGGAGGACGCCGAATTCGACAACGCCCTGGTCTCGGGGGCGACCGAGGTCGTCGTGGAGGCACTGGCCCCGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40175","NCBI_taxonomy_name":"Actinomadura sp. R39","NCBI_taxonomy_id":"72570"}}}},"ARO_accession":"3003565","ARO_id":"40174","ARO_name":"R39","CARD_short_name":"R39","ARO_description":"Class A beta-lactamase found in Actinomadura R39.","ARO_category":{"41362":{"category_aro_accession":"3004198","category_aro_cvterm_id":"41362","category_aro_name":"R39 beta-lactamase","category_aro_description":"R39 beta-lactamases are Class A beta-lactamases encoded in Actinomadura R39 with the ability to hydrolyze penicillins.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"499":{"model_id":"499","model_name":"vanS gene in vanB cluster","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"3454":{"protein_sequence":{"accession":"AAB05623.1","sequence":"MERKGIFIKVFSYTIIVLLLLVGVTATLFAQQFVSYFRAMEAQQTVKSYQPLVELIQNSDRLDMQEVAGLFHYNNQSFEFYIEDKEGSVLYATPNADTSNSVRPDFLYVVHRDDNISIVAQSKAGVGLLYQGLTIRGIVMIAIMVVFSLLCAYIFARQMTTPIKALADSANKMANLKEVPPPLERKDELGALAHDMHSMYIRLKETIARLEDEIAREHELEETQRYFFAAASHELKTPIAAVSVLLEGMLENIGDYKDHSKYLRECIKMMDRQGKTISEILELVSLNDGRIVPIAEPLDIGRTVAELLPDFQTLAEANNQRFVTDIPAGQIVLSDPKLIQKALSNVILNAVQNTPQGGEVRIWSEPGAEKYRLSVLNMGVHIDDTALSKLFIPFYRIDQARSRKSGRSGLGLAIVQKTLDAMSLQYALENTSDGVLFWLDLPPTSTL"},"dna_sequence":{"accession":"U35369.1","fmin":"839","fmax":"2183","strand":"+","sequence":"ATGGAAAGAAAAGGGATTTTCATTAAGGTTTTTTCCTATACGATCATTGTCCTGTTACTGCTTGTCGGTGTAACGGCAACACTGTTTGCACAGCAATTTGTGTCTTATTTCAGAGCGATGGAAGCACAGCAAACAGTAAAATCCTATCAGCCATTGGTGGAACTGATTCAGAATAGCGATAGGCTTGATATGCAAGAGGTGGCAGGGCTGTTTCACTACAATAACCAATCCTTTGAGTTTTATATTGAAGATAAAGAGGGAAGCGTACTCTATGCCACACCGAATGCCGATACATCAAATAGTGTTAGGCCCGACTTTCTTTATGTGGTACATAGAGATGATAATATTTCGATTGTTGCTCAAAGCAAGGCAGGTGTGGGATTGCTTTATCAAGGGCTGACAATTCGGGGAATTGTTATGATTGCGATAATGGTTGTATTCAGCCTTTTATGCGCGTATATCTTTGCGCGGCAAATGACAACGCCGATCAAAGCCTTAGCGGACAGTGCGAATAAAATGGCAAACCTGAAAGAAGTACCGCCGCCGCTGGAGCGAAAGGATGAGCTTGGCGCACTGGCTCACGACATGCATTCCATGTATATCAGGCTGAAAGAAACCATCGCAAGGCTGGAGGATGAAATCGCAAGGGAACATGAGTTGGAGGAAACACAGCGATATTTCTTTGCGGCAGCCTCTCATGAGTTAAAAACGCCCATCGCGGCTGTAAGCGTTCTGTTGGAGGGAATGCTTGAAAATATCGGTGACTACAAAGACCATTCTAAGTATCTGCGCGAATGCATCAAAATGATGGACAGGCAGGGCAAAACCATTTCCGAAATACTGGAGCTTGTCAGCCTGAACGATGGGAGAATCGTACCCATAGCCGAACCGCTGGACATAGGGCGCACGGTTGCCGAGCTGCTACCCGATTTTCAAACCTTGGCAGAGGCAAACAACCAGCGGTTCGTCACAGATATTCCAGCCGGACAAATTGTCCTGTCCGATCCGAAGCTGATCCAAAAGGCGCTATCCAATGTCATATTGAATGCGGTTCAGAACACGCCCCAGGGAGGTGAGGTACGGATATGGAGTGAGCCTGGGGCTGAAAAATACCGTCTTTCCGTTTTGAACATGGGCGTTCACATTGATGATACTGCACTTTCAAAGCTGTTCATCCCATTCTATCGCATTGATCAGGCGCGAAGCAGAAAAAGTGGGCGAAGCGGTTTGGGGCTTGCCATCGTACAAAAAACGCTGGATGCCATGAGCCTCCAATATGCGCTGGAAAACACCTCAGATGGCGTTTTGTTCTGGCTGGATTTACCGCCCACATCAACACTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35918","NCBI_taxonomy_name":"Enterococcus faecalis","NCBI_taxonomy_id":"1351"}}}},"ARO_accession":"3002932","ARO_id":"39366","ARO_name":"vanS gene in vanB cluster","CARD_short_name":"vanS_in_vanB_cl","ARO_description":"Also known as vanSB, is a vanS variant found in the vanB gene cluster.","ARO_category":{"36210":{"category_aro_accession":"3000071","category_aro_cvterm_id":"36210","category_aro_name":"vanS","category_aro_description":"VanS is similar to histidine protein kinases like EnvZ and acts as a response regulator by activating VanR. VanS is required for high level transcription of other van glycopeptide resistance genes.","category_aro_class_name":"AMR Gene Family"},"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"626":{"model_id":"626","model_name":"vanH gene in vanB cluster","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"200"}},"model_sequences":{"sequence":{"3452":{"protein_sequence":{"accession":"AAB05626.1","sequence":"MRKSMGITVFGCEQDEANAFRTLSPDFHIIPTLISDAISADNAKLAAGNQCISVGHKSEVSEATILALRKVGVKYISTRSIGCNHIDTTAAERMGISVGTVAYSPDSVADYALMLMLMAIRGAKSTIHAVAQQNFRLDCVRGKELRDMTVGVIGTGHIGQAVVKRLRGFGCRVLAYDNSRKIEADYVQLDELLKNSDIVTLHVPLCADTRHLIGQSEIGEMKQGAFLINTGRGALVDTGSLVEALGSGKLGGAALDVLEGEDQFVYTDCSQKVLDHPFLSQLLRMPNVIITPHTAYYTERVLRDTTEKTIRNCLNFERSLQHE"},"dna_sequence":{"accession":"U35369.1","fmin":"4006","fmax":"4978","strand":"+","sequence":"ATGAGAAAAAGTATGGGCATTACTGTTTTTGGATGCGAGCAGGATGAGGCAAATGCTTTCCGCACCTTATCACCAGATTTTCATATTATCCCTACGCTGATCAGTGATGCGATATCGGCAGACAACGCAAAATTGGCCGCTGGCAATCAATGCATTAGCGTAGGCCATAAGTCCGAGGTTTCCGAGGCGACAATTCTTGCGCTGAGAAAGGTCGGGGTAAAATACATTTCTACCCGCAGCATCGGCTGCAATCACATTGATACGACTGCCGCCGAGAGAATGGGGATCTCGGTTGGCACAGTTGCGTATTCGCCGGACAGCGTTGCGGATTATGCTTTGATGCTGATGCTGATGGCCATACGGGGTGCAAAGTCCACCATACACGCCGTGGCGCAACAAAATTTCAGACTGGATTGTGTCCGGGGGAAAGAGCTGCGGGATATGACTGTGGGAGTTATTGGAACCGGCCATATAGGGCAAGCGGTCGTCAAAAGGCTGCGGGGATTTGGATGCCGTGTGCTAGCCTATGATAACAGCCGAAAAATTGAGGCAGATTATGTCCAGCTTGATGAGCTTCTAAAAAACAGCGATATTGTTACGCTCCATGTGCCGCTTTGTGCGGATACCCGCCATCTGATCGGCCAGAGCGAAATCGGAGAGATGAAGCAAGGCGCATTTTTAATCAACACTGGGCGCGGGGCGCTTGTCGATACCGGGTCGCTGGTGGAGGCACTGGGAAGCGGAAAGCTGGGCGGTGCGGCACTGGATGTGTTGGAGGGCGAGGATCAGTTTGTTTATACCGACTGCTCGCAGAAAGTGCTTGACCATCCCTTTTTGTCGCAGCTCCTAAGGATGCCAAATGTGATCATCACACCCCATACGGCGTACTACACCGAGCGTGTGCTGCGAGATACCACAGAAAAAACAATCAGGAATTGTCTTAACTTTGAAAGGAGTTTACAGCATGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35918","NCBI_taxonomy_name":"Enterococcus faecalis","NCBI_taxonomy_id":"1351"}}}},"ARO_accession":"3002943","ARO_id":"39377","ARO_name":"vanH gene in vanB cluster","CARD_short_name":"vanH_in_vanB_cl","ARO_description":"Also known as vanHB, is a vanH variant in the vanB gene cluster.","ARO_category":{"36015":{"category_aro_accession":"3000006","category_aro_cvterm_id":"36015","category_aro_name":"vanH","category_aro_description":"VanH is a D-specific alpha-ketoacid dehydrogenase that synthesizes D-lactate. D-lactate is incorporated into the end of the peptidoglycan subunits, decreasing vancomycin binding affinity.","category_aro_class_name":"AMR Gene Family"},"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"691":{"model_id":"691","model_name":"vanR gene in vanE cluster","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"167":{"protein_sequence":{"accession":"AAL27445.1","sequence":"MAKILILDDEKEIVSLLSTLLSNEGYEVYEAMSGKESLEIIENNKIDLAILDVMLPDISGFDVLQSIREKQFFPVLMLTARGQDMDKITGLSMGADDYIVKPFNPFEVLARVKTQLRRYQTYNSQSIDETNEYAKNGLNISVNSRKVFLYDEEIKLTPIEFDILWYLCRNEGRVISSEELFEKVWKEDYLENNNTVMAHIAKIREKMHEKPRQPNIIKTVWGVGYTIEK"},"dna_sequence":{"accession":"FJ872411.1","fmin":"43513","fmax":"44203","strand":"+","sequence":"ATGGCTAAAATACTAATTTTAGATGATGAAAAAGAGATTGTAAGTCTTCTAAGTACGCTACTTTCTAACGAAGGATATGAGGTTTATGAGGCTATGTCAGGAAAAGAAAGCTTGGAGATTATAGAAAATAACAAGATCGATTTAGCCATACTAGATGTCATGCTTCCCGATATTTCCGGTTTTGATGTATTGCAAAGCATTAGAGAAAAACAATTTTTTCCTGTGTTGATGCTAACTGCTCGAGGTCAGGATATGGATAAAATTACTGGACTGTCTATGGGGGCAGATGACTATATTGTTAAGCCGTTCAATCCTTTTGAAGTGTTGGCTAGAGTGAAAACACAGCTACGTAGATATCAAACGTATAATTCTCAAAGTATAGATGAAACAAATGAATATGCAAAAAATGGATTAAATATATCTGTCAACAGTCGAAAAGTATTCTTATATGATGAAGAAATTAAATTAACGCCTATTGAATTTGATATCTTGTGGTATTTGTGTAGAAATGAAGGTCGCGTAATATCGTCAGAAGAGTTATTTGAAAAAGTCTGGAAAGAAGACTATCTAGAGAATAATAATACTGTTATGGCGCATATTGCTAAAATTAGAGAAAAGATGCATGAAAAGCCGAGACAGCCAAATATTATAAAAACGGTATGGGGAGTAGGTTATACAATTGAAAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35918","NCBI_taxonomy_name":"Enterococcus faecalis","NCBI_taxonomy_id":"1351"}}}},"ARO_accession":"3002924","ARO_id":"39358","ARO_name":"vanR gene in vanE cluster","CARD_short_name":"vanR_in_vanE_cl","ARO_description":"Also known as vanRE, is a vanR variant found in the vanE gene cluster.","ARO_category":{"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"36713":{"category_aro_accession":"3000574","category_aro_cvterm_id":"36713","category_aro_name":"vanR","category_aro_description":"VanR is a OmpR-family transcriptional activator in the VanSR regulatory system. When activated by VanS, it promotes cotranscription of VanA, VanH, and VanX.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"734":{"model_id":"734","model_name":"vanT gene in vanC cluster","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"200"}},"model_sequences":{"sequence":{"151":{"protein_sequence":{"accession":"AAD22403.1","sequence":"MKNKGIDQFRVIAAMMVVAIHCLPLHYLWPEGDILITLTIFRVAVPFFFMISGYYVFAELAVANSYPSRQRVFNFIKKQLKVYLLATLMFLPLALYSQTIGFDLPVGTLVQVLLVNGILYHLWYFPALITGSLLLTSLLIHVSFKKVFWLAAGLYLIGLGGDSWFGLIQQTPIEPFYTAVFHLLDGTRNGIFFTPLFLCLGVLVRKQSEKRSLSKTALFFLISLIGLLIESAYLHGFSIPKHDSMYLFLPVVLFFLFPLILRWHPHRTWKHPGQLSLWLYLLHPYTIAGTHFLSQKISILQNNLINYLVVLILTIGFICLFLRQKHSWFRHKQTTPVKRAVKEFSKTALLHNLQEIQRIISPKTKVMAVVKADAYGCGAKEVAPVLEQAGIDFFAVATIDEGIRLRKNAVKSPILVLGYTSPKRIKELRRYSLTQSIISEGHAVALSQRKVAIDCHLAIDTGMHRLGVTPTIDSILSIFDLPFLTISGVYSHLGSADRLNPDSMIRTQKQIACFDQILLELDQRQISYGITHLQSSYGILNYPDLNYDYVRPGILLTGSLSDTNEPTKQRVSLQPILTLKAQLITKRVVAKGEAIGYGQTAVANQETTVGVVSIGYCDGLPRSLSNQEFCLSYRGQSLPQIGLICMDMLLIDLSHCPTIPIESEIEILTDWSDTAEQVQTITNELICRIGPRVSARIK"},"dna_sequence":{"accession":"AF162694.1","fmin":"3007","fmax":"5104","strand":"+","sequence":"ATGAAAAATAAAGGAATCGATCAATTTCGTGTGATTGCAGCCATGATGGTGGTTGCGATCCATTGTCTTCCCCTTCACTATTTATGGCCAGAAGGCGATATCCTAATCACATTGACGATTTTTCGAGTAGCTGTTCCTTTCTTTTTTATGATCAGTGGTTACTATGTGTTTGCAGAACTTGCTGTGGCCAATAGTTATCCTTCGCGACAACGAGTATTCAACTTTATCAAAAAACAGCTAAAAGTCTATCTATTAGCCACACTAATGTTTTTACCATTAGCACTCTATAGTCAAACGATCGGCTTCGATCTACCAGTTGGAACATTAGTACAAGTACTTTTGGTCAATGGCATTCTTTATCATCTTTGGTACTTTCCGGCTTTGATTACTGGGAGCCTGCTCCTAACAAGTTTGCTGATACATGTCTCCTTCAAAAAAGTGTTCTGGCTTGCGGCTGGATTGTACCTGATTGGATTAGGTGGTGATAGTTGGTTTGGACTGATCCAACAGACACCAATCGAACCATTCTATACTGCTGTGTTCCACCTATTAGATGGTACCCGCAACGGTATTTTCTTTACACCATTGTTTTTGTGCTTAGGTGTGCTGGTCAGAAAACAATCAGAGAAAAGAAGTTTATCCAAAACAGCTCTCTTCTTTTTGATCAGTCTTATCGGATTGCTTATTGAGAGTGCGTACTTGCATGGGTTTTCTATACCTAAACATGACAGTATGTATCTCTTCTTGCCTGTTGTACTCTTTTTCTTATTTCCGCTGATCTTGCGCTGGCATCCCCACAGGACTTGGAAGCATCCAGGACAGCTATCTTTGTGGCTTTACCTTTTACATCCTTATACAATTGCCGGCACACACTTTTTGAGCCAAAAAATCAGCATTCTGCAAAACAATCTAATCAACTATTTGGTTGTTTTGATCTTGACGATTGGATTCATTTGCCTCTTTTTAAGACAAAAACACTCATGGTTTAGACACAAACAAACAACGCCCGTTAAAAGGGCCGTAAAAGAATTCTCAAAGACAGCCCTTTTGCATAATCTACAGGAGATCCAGCGGATCATCTCACCGAAAACAAAAGTGATGGCAGTCGTTAAAGCCGATGCCTACGGCTGTGGTGCCAAGGAAGTTGCTCCTGTTTTAGAACAAGCCGGAATTGATTTTTTTGCGGTGGCTACGATTGATGAAGGTATTCGATTGCGGAAAAATGCTGTCAAAAGCCCCATCTTGGTCTTGGGATATACCTCTCCAAAACGCATAAAAGAACTTCGTCGCTACTCATTGACCCAATCGATCATCAGCGAAGGTCATGCTGTAGCATTGTCACAAAGAAAAGTAGCGATTGACTGTCATTTAGCCATCGATACTGGGATGCATCGGTTAGGTGTAACACCGACTATCGATTCGATTCTTTCGATTTTCGATTTGCCCTTCTTGACGATCAGTGGTGTTTATTCTCATCTTGGTTCGGCAGATCGCTTAAATCCTGATAGTATGATTCGCACTCAGAAGCAGATTGCCTGCTTCGATCAGATTCTCCTAGAGTTGGATCAGAGACAGATTTCTTATGGTATCACACACTTACAAAGCAGTTATGGTATTTTGAATTATCCAGACTTAAACTATGATTATGTGCGTCCGGGGATTTTATTGACAGGATCCCTCAGTGATACGAACGAGCCTACAAAACAACGAGTAAGCTTACAGCCTATTCTGACCCTCAAAGCACAGTTGATCACTAAGCGAGTCGTTGCCAAAGGGGAAGCGATCGGTTATGGGCAAACCGCCGTCGCGAATCAAGAAACAACTGTTGGTGTTGTGAGCATCGGCTATTGTGACGGACTGCCCCGTTCTCTATCAAATCAAGAGTTTTGTCTTTCCTATCGCGGTCAGTCCTTGCCGCAGATCGGCTTGATCTGCATGGACATGCTTTTGATAGACTTGAGCCATTGTCCTACGATCCCAATTGAAAGTGAAATTGAAATTCTGACAGATTGGAGCGATACTGCCGAGCAAGTACAAACTATAACCAATGAGTTGATTTGTCGGATCGGTCCACGAGTCAGTGCTAGGATCAAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36781","NCBI_taxonomy_name":"Enterococcus gallinarum","NCBI_taxonomy_id":"1353"}}}},"ARO_accession":"3002970","ARO_id":"39404","ARO_name":"vanT gene in vanC cluster","CARD_short_name":"vanT_in_vanC_cl","ARO_description":"Also known as vanTC, is a vanT variant found in the vanC gene cluster.","ARO_category":{"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"36511":{"category_aro_accession":"3000372","category_aro_cvterm_id":"36511","category_aro_name":"vanT","category_aro_description":"VanT is a membrane bound serine racemase, converting L-serine to D-serine. It is associated with VanC, which incorporated D-serine into D-Ala-D-Ser terminal end of peptidoglycan subunits that have a decreased binding affinity with vancomycin. It was isolated from Enterococcus gallinarum.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"826":{"model_id":"826","model_name":"TolC","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"900"}},"model_sequences":{"sequence":{"563":{"protein_sequence":{"accession":"ACN32294.1","sequence":"MQMKKLLPILIGLSLSGFSSLSQAENLMQVYQQARLSNPELRKSAADRDAAFEKINEARSPLLPQLGLGADYTYSNGYRDANGINSNATSASLQLTQSIFDMSKWRALTLQEKAAGIQDVTYQTDQQTLILNTATAYFNVLNAIDVLSYTQAQKEAIYRQLDQTTQRFNVGLVAITDVQNARAQYDTVLANEVTARNNLDNAVEQLRQITGNYYPELAALNVENFKTDKPQPVNALLKEAEKRNLSLLQARLSQDLAREQIRQAQDGHLPTLDLTASTGISDTSYSGSKTRGAAGTQYDDSNMGQNKVGLSFSLPIYQGGMVNSQVKQAQYNFVGASEQLESAHRSVVQTVRSSFNNINASISSINAYKQAVVSAQSSLDAMEAGYSVGTRTIVDVLDATTTLYNAKQELANARYNYLINQLNIKSALGTLNEQDLLALNNALSKPVSTNPENVAPQTPEQNAIADGYAPDSPAPVVQQTSARTTTSNGHNPFRN"},"dna_sequence":{"accession":"FJ768952.1","fmin":"0","fmax":"1488","strand":"+","sequence":"ATGCAAATGAAGAAATTGCTCCCCATTCTTATCGGCCTGAGCCTTTCTGGGTTCAGTTCGTTGAGCCAGGCCGAGAACCTGATGCAAGTTTATCAGCAAGCACGCCTTAGTAACCCGGAATTGCGTAAGTCTGCCGCCGATCGTGATGCTGCCTTTGAAAAAATTAATGAAGCGCGCAGTCCATTACTGCCACAGCTAGGTTTAGGTGCAGATTACACCTATAGCAACGGCTACCGCGACGCGAACGGCATCAACTCTAACGCGACCAGTGCGTCCTTGCAGTTAACTCAATCCATTTTTGATATGTCGAAATGGCGTGCGTTAACGCTGCAGGAAAAAGCAGCAGGGATTCAGGACGTCACGTATCAGACCGATCAGCAAACCTTGATCCTCAACACCGCGACCGCTTATTTCAACGTGTTGAATGCTATTGACGTTCTTTCCTATACACAGGCACAAAAAGAAGCGATCTACCGTCAATTAGATCAAACCACCCAACGTTTTAACGTGGGCCTGGTAGCGATCACCGACGTGCAGAACGCCCGCGCACAGTACGATACCGTGCTGGCGAACGAAGTGACCGCACGTAATAACCTTGATAACGCGGTAGAGCAGCTGCGCCAGATCACCGGTAACTACTATCCGGAACTGGCTGCGCTGAATGTCGAAAACTTTAAAACCGACAAACCACAGCCGGTTAACGCGCTGCTGAAAGAAGCCGAAAAACGCAACCTGTCGCTGTTACAGGCACGCTTGAGCCAGGACCTGGCGCGCGAGCAAATTCGCCAGGCGCAGGATGGTCACTTACCGACTCTGGATTTAACGGCTTCTACCGGGATTTCTGACACCTCTTATAGCGGTTCGAAAACCCGTGGTGCCGCTGGTACCCAGTATGACGATAGCAATATGGGCCAGAACAAAGTTGGCCTGAGCTTCTCGCTGCCGATTTATCAGGGCGGAATGGTTAACTCGCAGGTGAAACAGGCACAGTACAACTTTGTCGGTGCCAGCGAGCAACTGGAAAGTGCCCATCGTAGCGTCGTGCAGACCGTGCGTTCCTCCTTCAACAACATTAATGCATCTATCAGTAGCATTAACGCCTACAAACAAGCCGTAGTTTCCGCTCAAAGCTCATTAGACGCGATGGAAGCGGGCTACTCGGTCGGTACGCGTACCATTGTTGATGTGTTGGATGCGACCACCACGTTGTACAACGCCAAGCAAGAGCTGGCGAATGCGCGTTATAACTACCTGATTAATCAGCTGAATATTAAGTCAGCTCTGGGTACGTTGAACGAGCAGGATCTGCTGGCACTGAACAATGCGCTGAGCAAACCGGTTTCCACTAATCCGGAAAACGTTGCACCGCAAACGCCGGAACAGAATGCTATTGCTGATGGTTATGCGCCTGATAGCCCGGCACCAGTCGTTCAGCAAACATCCGCACGCACTACCACCAGTAACGGTCATAACCCTTTCCGTAACTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3000237","ARO_id":"36376","ARO_name":"TolC","CARD_short_name":"TolC","ARO_description":"TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.","ARO_category":{"36002":{"category_aro_accession":"0010001","category_aro_cvterm_id":"36002","category_aro_name":"ATP-binding cassette (ABC) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding\/hydrolysis to transport substrates across cell membranes.","category_aro_class_name":"AMR Gene Family"},"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35930":{"category_aro_accession":"0000011","category_aro_cvterm_id":"35930","category_aro_name":"cloxacillin","category_aro_description":"Cloxacillin is a semisynthetic, isoxazolyl penicillin derivative in the beta-lactam class of antibiotics. It interferes with peptidogylcan synthesis and is commonly used for treating penicillin-resistant Staphylococcus aureus infections.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"35987":{"category_aro_accession":"0000070","category_aro_cvterm_id":"35987","category_aro_name":"ertapenem","category_aro_description":"Ertapenem is a carbapenem antibiotic and is highly resistant to beta-lactamases like other carbapenems. It inhibits bacterial cell wall synthesis.","category_aro_class_name":"Antibiotic"},"35995":{"category_aro_accession":"0000078","category_aro_cvterm_id":"35995","category_aro_name":"piperacillin","category_aro_description":"Piperacillin is an acetylureidopenicillin and has an extended spectrum of targets relative to other beta-lactam antibiotics. It inhibits cell wall synthesis in bacteria, and is usually taken with the beta-lactamase inhibitor tazobactam to overcome penicillin-resistant bacteria.","category_aro_class_name":"Antibiotic"},"36250":{"category_aro_accession":"3000111","category_aro_cvterm_id":"36250","category_aro_name":"novobiocin","category_aro_description":"Novobiocin is an aminocoumarin antibiotic produced by Streptomyces spheroides and Streptomyces niveus, and binds DNA gyrase subunit B inhibiting ATP-dependent DNA supercoiling.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36309":{"category_aro_accession":"3000170","category_aro_cvterm_id":"36309","category_aro_name":"imipenem","category_aro_description":"Imipenem is a broad-spectrum antibiotic and is usually taken with cilastatin, which prevents hydrolysis of imipenem by renal dehydropeptidase-I. It is resistant to hydrolysis by most other beta-lactamases. Notable exceptions are the KPC beta-lactamases and Ambler Class B enzymes.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36593":{"category_aro_accession":"3000454","category_aro_cvterm_id":"36593","category_aro_name":"polymyxin B","category_aro_description":"Polymyxin B is mixture of mostly polymyxins B1 and B2, mainly used for resistant gram-negative infections. They are polypeptides with cationic detergent action on cell membranes.","category_aro_class_name":"Antibiotic"},"36969":{"category_aro_accession":"3000625","category_aro_cvterm_id":"36969","category_aro_name":"polymyxin B1","category_aro_description":"Polymyxin B1 is in the family of polymyxin lipopeptides with a 6-methyloctanoic acid acyl group. These antibiotics disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36970":{"category_aro_accession":"3000626","category_aro_cvterm_id":"36970","category_aro_name":"polymyxin B2","category_aro_description":"Polymyxin B2 is in the family of polymyxin lipopeptides with a 6-methylheptanoic acid acyl group. These antibiotics disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36971":{"category_aro_accession":"3000627","category_aro_cvterm_id":"36971","category_aro_name":"polymyxin B3","category_aro_description":"Polymyxin B3 is in the family of polymyxin lipopeptides with an octanoic acid acyl group. These antibiotics disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36972":{"category_aro_accession":"3000628","category_aro_cvterm_id":"36972","category_aro_name":"polymyxin B4","category_aro_description":"Polymyxin B4 is in the family of polymyxin lipopeptides with a heptanoic acid acyl group. These antibiotics disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37084":{"category_aro_accession":"3000704","category_aro_cvterm_id":"37084","category_aro_name":"cefalotin","category_aro_description":"Cefalotin is a semisynthetic cephalosporin antibiotic activate against staphylococci. It is resistant to staphylococci beta-lactamases but hydrolyzed by enterobacterial beta-lactamases.","category_aro_class_name":"Antibiotic"},"37250":{"category_aro_accession":"3000870","category_aro_cvterm_id":"37250","category_aro_name":"triclosan","category_aro_description":"Triclosan is a common antibacterial agent added to many consumer products as a biocide.  It is an inhibitor of fatty acid biosynthesis by blocking enoyl-carrier protein reductase (FabI).","category_aro_class_name":"Antibiotic"},"40523":{"category_aro_accession":"3003832","category_aro_cvterm_id":"40523","category_aro_name":"ticarcillin","category_aro_description":"Ticarcillin is a carboxypenicillin used for the treatment of Gram-negative bacteria, particularly P. aeruginosa. Ticarcillin's antibiotic properties arise from its ability to prevent cross-linking of peptidoglycan during cell wall synthesis, when the bacteria try to divide, causing cell death.","category_aro_class_name":"Antibiotic"},"46133":{"category_aro_accession":"3007382","category_aro_cvterm_id":"46133","category_aro_name":"gentamicin","category_aro_description":"Gentamicin is a commonly used aminoglycoside antibiotic derived from members of the Micromonospora genus of bacteria. It acts by binding the 30S ribosomal subunit, thus inhibiting protein synthesis. Gentamicin is typically used to treat Gram-negative infections of the repiratory and urinary tract, as well as infections of the bone and soft tissue. It also exhibits considerable nephrotoxicity and ototoxicity. Gentamicin is administered as a mixture of gentamicin type C (which makes about around 80% of the complex) and types A, B, and X (distributed in the remaining 20% of the complex).","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36242":{"category_aro_accession":"3000103","category_aro_cvterm_id":"36242","category_aro_name":"aminocoumarin antibiotic","category_aro_description":"Aminocoumarin antibiotics bind DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling.","category_aro_class_name":"Drug Class"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"43746":{"category_aro_accession":"3005386","category_aro_cvterm_id":"43746","category_aro_name":"disinfecting agents and antiseptics","category_aro_description":"Disinfectants that can also interact with antimicrobial resistance mechanisms, e.g. molecule efflux, and thus are the targets of disinfectant resistance.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"995":{"model_id":"995","model_name":"MexG","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"260"}},"model_sequences":{"sequence":{"5202":{"protein_sequence":{"accession":"AAG07592.1","sequence":"MQRFIDNSLESNWLWLTARICLALMFVASGLAKLFDYQASLEEMRAAGLEPAWLFNIATAVTLLAGSALVLLDRKLWLGAGALAVFLLLTILIVHTFWSKTGVEAKLAMFFALEHIAVIGGLIATAIASAQRQRLRQDVSVAATYQKA"},"dna_sequence":{"accession":"AE004091.2","fmin":"4705955","fmax":"4706402","strand":"+","sequence":"ATGCAGCGCTTCATCGATAACTCGCTCGAAAGCAACTGGCTCTGGCTGACCGCCCGGATCTGCCTGGCCCTGATGTTCGTCGCCTCGGGACTGGCGAAGCTGTTCGACTATCAGGCCAGCCTGGAGGAAATGCGCGCCGCCGGCCTGGAGCCGGCCTGGCTGTTCAACATCGCCACCGCCGTGACCCTGCTGGCCGGCTCCGCGCTGGTCCTGCTGGACCGCAAGCTATGGCTCGGCGCCGGGGCGCTGGCGGTGTTCCTGCTGCTGACCATCCTCATCGTCCACACCTTCTGGAGCAAGACCGGCGTCGAAGCCAAGCTGGCGATGTTCTTCGCCCTCGAACACATCGCGGTGATCGGCGGCCTGATCGCCACGGCCATCGCCAGCGCGCAACGCCAGCGGCTGCGCCAGGACGTCTCCGTGGCCGCCACCTACCAGAAGGCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36804","NCBI_taxonomy_name":"Pseudomonas aeruginosa PAO1","NCBI_taxonomy_id":"208964"}}}},"ARO_accession":"3000806","ARO_id":"37186","ARO_name":"MexG","CARD_short_name":"MexG","ARO_description":"MexG is a membrane protein required for MexGHI-OpmD efflux activity.","ARO_category":{"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1036":{"model_id":"1036","model_name":"vanW gene in vanB cluster","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"50"}},"model_sequences":{"sequence":{"3455":{"protein_sequence":{"accession":"AAB05625.1","sequence":"MNRKRLTQRFPFLLPMRQAQRKICFYAGMRFDGCCYAQTIGEKTLPYLLFETDCALYNHNTGFDMIYQENKVFNLKLAAKTLNGLLIKPGETFSFWRLVRHADKDTPYKDGLTVANGKLTTMSGGGMCQMSNLLFWVFLHTPLTIIQRSGHVVKEFPEPNSDEIKGVDATISEGWIDLKVRNDTDCTYQIWVTLDDEKIIGQVFADKQPQALYKIANGSIQYVRESGGIYEYAKVERMQVALGTGEIIDCKLLYTNKCKICYPLPESVDIQEANQ"},"dna_sequence":{"accession":"U35369.1","fmin":"3182","fmax":"4010","strand":"+","sequence":"ATGAACAGAAAAAGATTGACACAGCGCTTCCCGTTCCTGCTTCCAATGAGACAAGCGCAGAGAAAAATATGCTTTTATGCGGGAATGAGATTTGACGGCTGTTGCTATGCACAGACGATAGGAGAAAAAACGCTTCCCTATTTGCTCTTTGAAACGGATTGTGCGTTATACAACCACAATACCGGATTTGACATGATATACCAAGAAAACAAGGTGTTCAACTTAAAGCTGGCGGCAAAGACCTTAAACGGCCTATTGATAAAACCGGGGGAAACCTTTTCTTTCTGGCGGCTGGTACGCCATGCGGACAAAGATACCCCCTATAAAGACGGCCTTACGGTGGCCAATGGTAAGCTCACCACCATGTCGGGCGGCGGTATGTGCCAGATGAGCAATTTACTATTTTGGGTGTTCCTGCATACGCCATTGACAATTATCCAGCGCAGCGGTCACGTAGTAAAGGAGTTTCCAGAGCCAAACAGTGACGAGATCAAAGGGGTGGATGCAACCATCTCAGAGGGCTGGATTGATTTAAAAGTGCGAAACGATACCGACTGCACCTACCAAATATGGGTGACCCTAGATGATGAGAAAATCATCGGTCAGGTGTTCGCCGACAAACAGCCTCAAGCATTATACAAAATTGCAAACGGCAGTATTCAGTATGTCCGTGAAAGTGGCGGGATTTATGAATATGCCAAGGTTGAACGGATGCAAGTTGCCTTAGGTACCGGGGAAATAATAGATTGCAAGCTGCTTTATACAAACAAATGCAAAATCTGCTATCCCCTCCCGGAAAGTGTGGATATTCAGGAGGCGAACCAATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35918","NCBI_taxonomy_name":"Enterococcus faecalis","NCBI_taxonomy_id":"1351"}}}},"ARO_accession":"3002964","ARO_id":"39398","ARO_name":"vanW gene in vanB cluster","CARD_short_name":"vanW_in_vanB_cl","ARO_description":"Also known as vanWB, is a vanW variant found in the vanB gene cluster.","ARO_category":{"36011":{"category_aro_accession":"3000002","category_aro_cvterm_id":"36011","category_aro_name":"vanW","category_aro_description":"vanW is an accessory gene, with unknown function, found on vancomycin resistance operons.","category_aro_class_name":"AMR Gene Family"},"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1144":{"model_id":"1144","model_name":"vgbB","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"4415":{"protein_sequence":{"accession":"AAC61670.1","sequence":"MNFYLEEFNLSIPDSGPYGITSSEDGKVWFTQHKANKISSLDQSGRIKEFEVPTPDAKVMCLIVSSLGDIWFTENGANKIGKLSKKGGFTEYPLPQPDSGPYGITEGLNGDIWFTQLNGDRIGKLTADGTIYEYDLPNKGSYPAFITLGSDNALWFTENQNNSIGRITNTGKLEEYPLPTNAAAPVGITSGNDGALWFVEIMGNKIGRITTTGEISEYDIPTPNARPHAITAGKNSEIWFTEWGANQIGRITNDKTIQEYQLQTENAEPHGITFGKDGSVWFALKCKIGKLNLNE"},"dna_sequence":{"accession":"AF015628.1","fmin":"398","fmax":"1286","strand":"+","sequence":"ATGAATTTTTATTTAGAGGAGTTTAACTTGTCTATTCCCGATTCAGGTCCATACGGTATAACTTCATCAGAAGACGGAAAGGTATGGTTCACACAACATAAGGCAAACAAAATCAGCAGTCTAGATCAGAGTGGTAGGATAAAAGAATTCGAAGTTCCTACCCCTGATGCTAAAGTGATGTGTTTAATTGTATCTTCACTTGGAGACATATGGTTTACAGAGAATGGTGCAAATAAAATCGGAAAGCTCTCAAAAAAAGGTGGCTTTACAGAATATCCATTGCCACAGCCGGATTCTGGTCCTTACGGAATAACGGAAGGTCTAAATGGCGATATATGGTTTACCCAATTGAATGGAGATCGTATAGGAAAGTTGACAGCTGATGGGACTATTTATGAATATGATTTGCCAAATAAGGGATCTTATCCTGCTTTTATTACTTTAGGTTCGGATAACGCACTTTGGTTCACGGAGAACCAAAATAATTCTATTGGAAGGATTACAAATACAGGGAAATTAGAAGAATATCCTCTACCAACAAATGCAGCGGCTCCAGTGGGTATCACTAGTGGTAACGATGGTGCACTCTGGTTTGTCGAAATTATGGGCAACAAAATAGGTCGAATCACTACAACTGGTGAGATTAGCGAATATGATATTCCAACTCCAAACGCACGTCCACACGCTATAACCGCGGGGAAAAATAGCGAAATATGGTTTACTGAATGGGGGGCAAATCAAATCGGCAGAATTACAAACGACAAAACAATTCAAGAATATCAACTTCAAACAGAAAATGCGGAACCTCATGGTATTACCTTTGGAAAAGATGGATCCGTATGGTTTGCATTAAAATGTAAAATTGGGAAGCTGAATTTGAACGAATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36766","NCBI_taxonomy_name":"Staphylococcus cohnii","NCBI_taxonomy_id":"29382"}}}},"ARO_accession":"3001308","ARO_id":"37707","ARO_name":"vgbB","CARD_short_name":"vgbB","ARO_description":"VgbB inactivates streptogramin B-type antibiotics by linearizing the lactone ring on the ester bond through an elimination mechanism, thus conferring resistance.","ARO_category":{"36515":{"category_aro_accession":"3000376","category_aro_cvterm_id":"36515","category_aro_name":"streptogramin vgb lyase","category_aro_description":"vgb (Virginiamycin B) lyase inactivates type B streptogramin antibiotics by linearizing the streptogramin lactone ring at the ester linkage through an elimination mechanism, thus conferring resistance to these compounds.","category_aro_class_name":"AMR Gene Family"},"36722":{"category_aro_accession":"3000583","category_aro_cvterm_id":"36722","category_aro_name":"pristinamycin IA","category_aro_description":"Pristinamycin IA is a type B streptogramin antibiotic produced by Streptomyces pristinaespiralis. It binds to the P site of the 50S subunit of the bacterial ribosome, preventing the extension of protein chains.","category_aro_class_name":"Antibiotic"},"36723":{"category_aro_accession":"3000584","category_aro_cvterm_id":"36723","category_aro_name":"quinupristin","category_aro_description":"Quinupristin is a type B streptogramin and a semisynthetic derivative of pristinamycin 1A. It is a component of the drug Synercid and interacts with the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"37019":{"category_aro_accession":"3000675","category_aro_cvterm_id":"37019","category_aro_name":"pristinamycin IB","category_aro_description":"Pristinamycin IB is a class B streptogramin similar to pristinamycin IA, the former containing a N-methyl-4-(methylamino)phenylalanine instead of a N-methyl-4-(dimethylamino)phenylalanine in its class A streptogramin counterpart (one less methyl group).","category_aro_class_name":"Antibiotic"},"37021":{"category_aro_accession":"3000677","category_aro_cvterm_id":"37021","category_aro_name":"virginiamycin S2","category_aro_description":"Virginiamycin S2 is a streptogramin B antibiotic.","category_aro_class_name":"Antibiotic"},"37022":{"category_aro_accession":"3000678","category_aro_cvterm_id":"37022","category_aro_name":"pristinamycin IC","category_aro_description":"Pristinamycin IC is a class B streptogramin derived from virginiamycin S1.","category_aro_class_name":"Antibiotic"},"37023":{"category_aro_accession":"3000679","category_aro_cvterm_id":"37023","category_aro_name":"vernamycin C","category_aro_description":"Vernamycin C is a streptogramin B antibiotic.","category_aro_class_name":"Antibiotic"},"37024":{"category_aro_accession":"3000680","category_aro_cvterm_id":"37024","category_aro_name":"patricin A","category_aro_description":"Patricin A is a streptogramin B antibiotic.","category_aro_class_name":"Antibiotic"},"37025":{"category_aro_accession":"3000681","category_aro_cvterm_id":"37025","category_aro_name":"patricin B","category_aro_description":"Patricin B is a streptogramin B antibiotic.","category_aro_class_name":"Antibiotic"},"37026":{"category_aro_accession":"3000682","category_aro_cvterm_id":"37026","category_aro_name":"ostreogrycin B3","category_aro_description":"Ostreogrycin B3 is a derivative of pristinamycin IA, with an additional 3-hydroxy group on its 4-oxopipecolic acid.","category_aro_class_name":"Antibiotic"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35967":{"category_aro_accession":"0000050","category_aro_cvterm_id":"35967","category_aro_name":"streptogramin B antibiotic","category_aro_description":"Streptogramin B antibiotics are are cyclic hepta- or hexa-depsipeptides.  Type B streptogramins block the peptide exit tunnel of the 50S bacterial ribosome. The general composition of group B streptogramins is 3-hydroxypicolinic acid-L-Thr-D-aminobutyric acid (or D-Ala)-L-Pro-L-Phe (or 4-N-,N-(dimethylamino)-L-Phe)-X-L-phenylglycine. Used alone, streptogramin B antibiotics are bacteriostatic, but is bactericidal when used with streptogramin A antibiotics.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1308":{"model_id":"1308","model_name":"vanT gene in vanE cluster","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"200"}},"model_sequences":{"sequence":{"180":{"protein_sequence":{"accession":"AAL27444.1","sequence":"MKHRANGIDLFRIFAATMVVAIHTFPFQSIAPFLDEVITLTVFRVAVPFFFMITGYFLLGRLSLNFSYNNNQRVKKYLYKIGMIYLYSILLYFPLSLLNGTISLKMNILLLLKVFIFDGTFYHLWYFPASIIGTILVTLLLRSIGFKLTVAFSTCLYLVGLGGDSWYGITNQVPLLNKLYTFIFSWSDYTRSGVFFTPVFLCLGIFAYRVSKKLTASKILNLLFYVFIIGMTFESIFLHRFTNVKHDSMYLLLPSCALILFLMLLNWQPKLKVKESADLTLLVYILHPLVIVIVHSISKYIPILKNSLLNFLLVVVCSFILAQLLLNLKRKLRVSKQKIPFERASKEISASAIHHNINEIRKIIPKNTNIMGVVKANAYGCGMVEVAYELEKIGISFFCVATIEEAIALRKSGNQGDILILGYTHPNRINDIKKYNLIQSIVSEEHGKVLNLKKIPIRCHLQVDTGMHRLGVTPNVTIIQQMYLFSNLKIEGIYSHLGSSDSLEQESIARTNTQIFLFNNILSDLEQMGISYGYTHIQSSYGILNYPELSFDFVRIGILCYGFLSDYNSPTKIPIDLQPIVKVKASLITERIVEAGEYVGYGLGAKVEKRTRIGVVSIGYADGIPRALSNAKLTLEFKGQSIKQIGNICMDMMLVDLSEVEDISLNDELIVLPNISKIADEEQTITNELLSRLGSRLGTELN"},"dna_sequence":{"accession":"FJ872411.1","fmin":"41336","fmax":"43445","strand":"+","sequence":"ATGAAGCATAGAGCTAACGGCATTGATCTATTTCGAATATTCGCTGCTACTATGGTTGTTGCTATCCATACATTCCCTTTTCAATCAATAGCACCTTTTTTAGACGAAGTCATAACGTTAACTGTGTTTCGGGTAGCTGTCCCTTTTTTCTTTATGATTACAGGATATTTTTTGTTAGGAAGATTGTCATTAAATTTTTCGTATAATAATAATCAGAGAGTGAAAAAATATCTATACAAAATTGGAATGATTTATTTATATTCTATTTTATTGTATTTCCCATTATCTTTACTAAATGGCACTATTTCATTAAAAATGAACATACTTTTACTTTTAAAGGTTTTCATTTTTGACGGTACCTTTTATCACCTATGGTACTTTCCAGCTAGTATAATTGGAACGATTTTAGTAACCCTACTGTTACGTAGTATAGGATTTAAATTAACAGTCGCATTTTCTACATGTCTATATCTAGTTGGACTTGGTGGAGACAGCTGGTACGGGATAACCAATCAAGTTCCATTGCTAAATAAACTGTATACATTTATTTTTAGTTGGTCGGACTATACGCGTTCAGGTGTTTTCTTTACGCCTGTGTTTCTTTGCCTAGGAATATTTGCCTATAGAGTATCTAAAAAGTTAACTGCATCAAAGATATTAAACTTGCTTTTTTATGTGTTTATCATAGGTATGACTTTTGAGAGTATATTTCTACACCGATTTACGAACGTCAAACACGATAGTATGTATCTCTTATTGCCTTCATGTGCATTAATTTTGTTTTTAATGTTATTAAACTGGCAACCAAAACTAAAGGTAAAAGAATCAGCCGATTTAACGTTACTGGTTTATATTCTCCATCCATTAGTTATTGTAATTGTCCATTCTATAAGTAAGTATATTCCGATATTAAAAAACAGTTTGCTAAATTTCTTGTTAGTAGTCGTGTGCAGCTTTATACTAGCTCAGCTTCTGTTAAACTTAAAAAGAAAGCTAAGAGTTAGTAAGCAAAAAATACCATTTGAACGTGCTAGTAAAGAAATATCAGCTAGTGCAATACACCATAATATTAATGAAATACGAAAGATAATTCCCAAAAATACAAATATTATGGGTGTTGTGAAGGCAAATGCGTATGGCTGTGGCATGGTAGAGGTAGCTTATGAATTAGAAAAAATCGGTATTTCATTTTTCTGCGTAGCTACTATAGAAGAAGCAATTGCTTTAAGGAAATCAGGAAACCAAGGGGATATTTTAATTTTAGGGTATACACATCCCAATCGCATTAATGATATAAAAAAATATAATTTGATTCAATCGATTGTAAGTGAAGAACATGGGAAAGTGTTGAATCTAAAAAAAATACCTATTCGTTGTCATTTACAGGTTGATACTGGGATGCATCGTTTAGGTGTTACACCGAACGTAACAATTATTCAGCAGATGTATCTTTTTTCCAATCTTAAGATTGAGGGGATATACTCACACTTAGGTTCTTCAGACTCATTAGAGCAAGAATCAATCGCTCGAACAAATACTCAAATTTTTTTATTCAATAATATACTAAGTGATTTGGAACAAATGGGTATTTCCTACGGTTATACTCATATCCAAAGCAGCTATGGTATTTTAAATTACCCAGAATTAAGCTTTGATTTTGTGAGAATAGGAATTCTCTGTTATGGATTTTTAAGTGACTATAATAGTCCGACTAAAATCCCTATAGATTTACAACCTATAGTAAAAGTAAAAGCCTCTTTGATTACAGAAAGAATTGTGGAGGCAGGTGAATATGTTGGCTATGGATTAGGCGCTAAAGTTGAAAAAAGAACAAGAATAGGTGTCGTTAGTATTGGGTATGCGGACGGTATACCAAGGGCATTATCCAATGCTAAACTTACGTTAGAGTTTAAAGGTCAATCAATAAAACAGATTGGGAATATTTGTATGGATATGATGCTTGTTGATCTGTCCGAAGTGGAAGATATTTCCTTGAATGATGAACTAATCGTGTTACCTAATATTAGTAAAATCGCTGATGAAGAACAAACAATTACCAATGAGCTATTGAGTCGATTAGGTTCGAGGTTAGGTACAGAGTTAAATTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35918","NCBI_taxonomy_name":"Enterococcus faecalis","NCBI_taxonomy_id":"1351"}}}},"ARO_accession":"3002971","ARO_id":"39405","ARO_name":"vanT gene in vanE cluster","CARD_short_name":"vanT_in_vanE_cl","ARO_description":"Also known as vanTE, is a vanT variant found in the vanE gene cluster.","ARO_category":{"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"36511":{"category_aro_accession":"3000372","category_aro_cvterm_id":"36511","category_aro_name":"vanT","category_aro_description":"VanT is a membrane bound serine racemase, converting L-serine to D-serine. It is associated with VanC, which incorporated D-serine into D-Ala-D-Ser terminal end of peptidoglycan subunits that have a decreased binding affinity with vancomycin. It was isolated from Enterococcus gallinarum.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1453":{"model_id":"1453","model_name":"vanY gene in vanD cluster","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"50"}},"model_sequences":{"sequence":{"338":{"protein_sequence":{"accession":"AAM09853.1","sequence":"MERQNNNENQYGRNRRKDKRKKLFFYRAACAMLGLLIVCVIFGAVYFLRESKDPVLPSKENTKTGKDYSFLADGQSEDESPISEPAISNRANAIDLNIIAANAIVMNKDTDALLYQKKRHGQNCAGQYSKDDYGVDRA"},"dna_sequence":{"accession":"AY082011.1","fmin":"3848","fmax":"4265","strand":"+","sequence":"GTGGAACGTCAAAATAACAATGAAAACCAGTATGGAAGGAATCGCAGAAAAGACAAAAGAAAAAAATTGTTTTTTTACAGAGCAGCATGTGCCATGCTCGGTCTGCTCATAGTCTGTGTAATTTTTGGAGCTGTGTATTTTCTCAGAGAGAGTAAAGATCCGGTTCTTCCATCCAAAGAAAATACAAAGACAGGCAAGGACTATTCATTTTTGGCCGACGGTCAGAGTGAGGATGAGTCTCCGATTTCGGAGCCAGCCATATCCAACCGGGCGAATGCGATTGACCTGAACATCATAGCAGCAAATGCCATTGTGATGAATAAAGACACCGATGCGTTATTGTATCAAAAAAAACGGCACGGACAGAATTGCGCCGGCCAGTACAGCAAAGATGATTACGGCGTTGACCGTGCTTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36779","NCBI_taxonomy_name":"Enterococcus faecium","NCBI_taxonomy_id":"1352"}}}},"ARO_accession":"3002957","ARO_id":"39391","ARO_name":"vanY gene in vanD cluster","CARD_short_name":"vanY_in_vanD_cl","ARO_description":"Also known as vanYD, is a vanY variant found in the vanD gene cluster.","ARO_category":{"36216":{"category_aro_accession":"3000077","category_aro_cvterm_id":"36216","category_aro_name":"vanY","category_aro_description":"VanY is a D,D-carboxypeptidase that cleaves removes the terminal D-Ala from peptidoglycan for the addition of D-Lactate. The D-Ala-D-Lac peptidoglycan subunits have reduced binding affinity with vancomycin compared to D-Ala-D-Ala.","category_aro_class_name":"AMR Gene Family"},"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"35948":{"category_aro_accession":"0000029","category_aro_cvterm_id":"35948","category_aro_name":"teicoplanin","category_aro_description":"Teicoplanin is a glycopeptide antibiotic used in the prophylaxis and treatment of serious infections caused by Gram-positive bacteria. Teicoplanin has a unique acyl-aliphatic chain, and binds to cell wall precursors to inhibit transglycosylation  and transpeptidation.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1594":{"model_id":"1594","model_name":"vgbA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"4416":{"protein_sequence":{"accession":"AAA98349.1","sequence":"MEFKLQELNLTNQDTGPYGITVSDKGKVWITQHKANMISCINLDGKITEYPLPTPDAKVMCLTISSDGEVWFTENAANKIGRITKKGIIKEYTLPNPDSAPYGITEGPNGDIWFTEMNGNRIGRITDDGKIREYELPNKGSYPSFITLGSDNALWFTENQNNAIGRITESGDITEFKIPTPASGPVGITKGNDDALWFVEIIGNKIGRITPLGEITEFKIPTPNARPHAITAGAGIDLWFTEWGANKIGRLTSNNIIEEYPIQIKSAEPHGICFDGETIWFAMECDKIGKLTLIKDNME"},"dna_sequence":{"accession":"M20129.1","fmin":"640","fmax":"1540","strand":"+","sequence":"ATGGAATTTAAATTACAAGAATTAAATCTTACTAACCAAGATACAGGACCATATGGTATAACCGTTTCAGATAAGGGGAAAGTTTGGATTACACAACATAAAGCAAATATGATAAGTTGCATCAATTTAGATGGAAAAATTACAGAGTACCCACTACCGACACCAGATGCAAAAGTCATGTGTTTAACTATATCCTCAGATGGGGAAGTTTGGTTTACTGAGAATGCAGCAAACAAAATAGGGAGGATTACAAAAAAAGGGATTATTAAGGAATATACATTGCCTAACCCAGATTCAGCACCCTACGGTATTACAGAAGGACCAAATGGAGATATATGGTTTACAGAAATGAATGGCAACCGTATTGGACGTATTACGGACGACGGTAAAATTCGTGAATACGAGCTGCCTAATAAAGGATCTTACCCTTCTTTTATCACTTTGGGTTCTGATAATGCCCTGTGGTTCACAGAAAATCAAAATAATGCTATTGGTAGAATTACAGAAAGTGGGGATATTACAGAGTTTAAAATTCCTACACCTGCATCAGGACCAGTTGGTATTACAAAGGGGAACGACGATGCTTTATGGTTTGTGGAAATTATCGGTAATAAGATAGGGCGAATAACTCCTCTGGGGGAAATTACCGAATTCAAAATTCCAACGCCAAACGCTCGACCTCATGCAATTACTGCTGGAGCAGGAATTGATTTATGGTTTACTGAATGGGGGGCTAATAAAATAGGAAGGCTGACAAGCAATAATATAATTGAGGAATACCCAATTCAAATCAAAAGTGCTGAACCACATGGCATTTGTTTCGATGGTGAAACAATTTGGTTTGCAATGGAGTGTGACAAGATAGGCAAATTAACTCTCATTAAGGATAATATGGAGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35508","NCBI_taxonomy_name":"Staphylococcus aureus","NCBI_taxonomy_id":"1280"}}}},"ARO_accession":"3001307","ARO_id":"37706","ARO_name":"vgbA","CARD_short_name":"vgbA","ARO_description":"vgbA inactivates streptogramin B-type antibiotics by linearizing the lactone ring on the ester bond using an elimination mechanism, thus conferring resistance to these compounds.","ARO_category":{"36515":{"category_aro_accession":"3000376","category_aro_cvterm_id":"36515","category_aro_name":"streptogramin vgb lyase","category_aro_description":"vgb (Virginiamycin B) lyase inactivates type B streptogramin antibiotics by linearizing the streptogramin lactone ring at the ester linkage through an elimination mechanism, thus conferring resistance to these compounds.","category_aro_class_name":"AMR Gene Family"},"36722":{"category_aro_accession":"3000583","category_aro_cvterm_id":"36722","category_aro_name":"pristinamycin IA","category_aro_description":"Pristinamycin IA is a type B streptogramin antibiotic produced by Streptomyces pristinaespiralis. It binds to the P site of the 50S subunit of the bacterial ribosome, preventing the extension of protein chains.","category_aro_class_name":"Antibiotic"},"36723":{"category_aro_accession":"3000584","category_aro_cvterm_id":"36723","category_aro_name":"quinupristin","category_aro_description":"Quinupristin is a type B streptogramin and a semisynthetic derivative of pristinamycin 1A. It is a component of the drug Synercid and interacts with the 50S subunit of the bacterial ribosome to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"37019":{"category_aro_accession":"3000675","category_aro_cvterm_id":"37019","category_aro_name":"pristinamycin IB","category_aro_description":"Pristinamycin IB is a class B streptogramin similar to pristinamycin IA, the former containing a N-methyl-4-(methylamino)phenylalanine instead of a N-methyl-4-(dimethylamino)phenylalanine in its class A streptogramin counterpart (one less methyl group).","category_aro_class_name":"Antibiotic"},"37021":{"category_aro_accession":"3000677","category_aro_cvterm_id":"37021","category_aro_name":"virginiamycin S2","category_aro_description":"Virginiamycin S2 is a streptogramin B antibiotic.","category_aro_class_name":"Antibiotic"},"37022":{"category_aro_accession":"3000678","category_aro_cvterm_id":"37022","category_aro_name":"pristinamycin IC","category_aro_description":"Pristinamycin IC is a class B streptogramin derived from virginiamycin S1.","category_aro_class_name":"Antibiotic"},"37023":{"category_aro_accession":"3000679","category_aro_cvterm_id":"37023","category_aro_name":"vernamycin C","category_aro_description":"Vernamycin C is a streptogramin B antibiotic.","category_aro_class_name":"Antibiotic"},"37024":{"category_aro_accession":"3000680","category_aro_cvterm_id":"37024","category_aro_name":"patricin A","category_aro_description":"Patricin A is a streptogramin B antibiotic.","category_aro_class_name":"Antibiotic"},"37025":{"category_aro_accession":"3000681","category_aro_cvterm_id":"37025","category_aro_name":"patricin B","category_aro_description":"Patricin B is a streptogramin B antibiotic.","category_aro_class_name":"Antibiotic"},"37026":{"category_aro_accession":"3000682","category_aro_cvterm_id":"37026","category_aro_name":"ostreogrycin B3","category_aro_description":"Ostreogrycin B3 is a derivative of pristinamycin IA, with an additional 3-hydroxy group on its 4-oxopipecolic acid.","category_aro_class_name":"Antibiotic"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35967":{"category_aro_accession":"0000050","category_aro_cvterm_id":"35967","category_aro_name":"streptogramin B antibiotic","category_aro_description":"Streptogramin B antibiotics are are cyclic hepta- or hexa-depsipeptides.  Type B streptogramins block the peptide exit tunnel of the 50S bacterial ribosome. The general composition of group B streptogramins is 3-hydroxypicolinic acid-L-Thr-D-aminobutyric acid (or D-Ala)-L-Pro-L-Phe (or 4-N-,N-(dimethylamino)-L-Phe)-X-L-phenylglycine. Used alone, streptogramin B antibiotics are bacteriostatic, but is bactericidal when used with streptogramin A antibiotics.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1647":{"model_id":"1647","model_name":"MexI","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1900"}},"model_sequences":{"sequence":{"5392":{"protein_sequence":{"accession":"AAG07594.1","sequence":"MTFTDLFVRRPVLALVVSTLILLLGLFSLGKLPIRQYPLLESSTITVTTEYPGASADLMQGFVTQPIAQAVSSVEGIDYLSSTSVQGRSVVTIRMLLNRDSTQAMTETMAKVNSVRYKLPERAYDSVIERSSGETTAVAYVGFSSKTLPIPALTDYLSRVVEPMFSSIDGVAKVQTFGGQRLAMRLWLDADRLAGRGLTASDVAEAIRRNNYQAAPGMVKGQYVLSNVRVNTDLTNVDDFREMVIRNDGNGLVRLRDVGTVELGAAATETSALMDGDPAVHLGLFPTPTGNPLVIVDGIRKLLPEIQKTLPPDVRVDLAYETSRFIQASIDEVVRTLVEALLIVVLVIYLCLGSLRSVLIPVATIPLSMLGAAALMLAFGFSVNLLTLLAMVLAIGLVVDDAIVVVENVHRHIEEGKSPVAAALIGAREVAGPVIAMTITLAAVYTPIGLMGGLTGALFREFALTLAGAVIVSGVVALTLSPVMSSLLLQAHQNEGRMGRAAEWFFGGLTRRYGQVLEFSLGHRWLTGGLALLVCISLPLLYSMPKRELAPTEDQAAVLTAIKAPQHANLDYVELFARKLDQVYTSIPETVSTWIINGTDGPAASFGGINLAAWEKRERDASAIQSELQGKVGDVEGSSIFAFQLAALPGSTGGLPVQMVLRSPQDYPVLYRTMEEIKQKARQSGLFVVVDSDLDYNNPVVQVRIDRAKANSLGIRMQDIGESLAVLVGENYVNRFGMEGRSYDVIPQSLRDQRFTPQALARQFVRTQDGNLVPLSTVVRVALQVEPNKLIQFDQQNAATLQAIPAPGVSMGQAVAFLDDVARGLPAGFSHDWQSDSRQYTQEGNTLVFAFLAALVVIYLVLAAQYESLADPLIILITVPLSICGALLPLALGYATMNIYTQIGLVTLIGLISKHGILMVEFANELQLHERLDRRAAILRAAQIRLRPVLMTTAAMVFGLVPLLFASGAGAASRFGLGVVIVSGMLVGTLFTLFVLPTVYTLLARNHAEVDKSPRSRQLAEADLLVNKA"},"dna_sequence":{"accession":"AE004091.2","fmin":"4707534","fmax":"4710624","strand":"+","sequence":"ATGACCTTTACCGACCTGTTCGTCCGCCGGCCGGTGCTGGCGCTGGTGGTCAGCACGCTGATCCTGCTGCTCGGCCTGTTCTCCCTGGGCAAGCTGCCGATCCGCCAGTACCCGCTGCTGGAAAGCTCGACCATCACCGTCACCACCGAGTACCCCGGCGCCTCCGCCGATCTCATGCAAGGCTTCGTCACCCAGCCGATCGCCCAGGCGGTGTCGTCGGTGGAGGGCATCGACTACCTTTCCTCGACCTCGGTGCAGGGGCGTAGCGTGGTGACCATCCGCATGCTGCTCAACCGCGATTCGACCCAGGCGATGACCGAGACCATGGCCAAGGTCAACTCGGTGCGCTACAAGCTGCCCGAGCGTGCCTACGACTCGGTGATCGAACGCTCTTCCGGCGAGACCACCGCGGTAGCCTACGTCGGCTTTTCCAGCAAGACCCTGCCGATCCCGGCGTTGACCGACTACCTGTCGCGGGTGGTCGAGCCGATGTTCTCTTCCATCGACGGCGTGGCCAAGGTCCAGACCTTTGGCGGCCAGCGCCTGGCCATGCGCCTCTGGCTCGACGCCGACCGCCTCGCCGGGCGCGGCCTGACCGCCTCCGACGTGGCCGAGGCGATCCGCCGCAACAACTACCAGGCGGCGCCGGGGATGGTGAAGGGGCAGTACGTGCTGTCCAACGTGCGGGTCAACACCGACCTGACCAACGTCGACGACTTCCGCGAGATGGTCATCCGCAACGATGGCAACGGCCTGGTGCGCCTGCGCGACGTCGGTACCGTCGAACTGGGCGCCGCGGCCACCGAGACCAGCGCACTGATGGACGGCGACCCGGCGGTGCACCTGGGGTTGTTCCCGACGCCCACCGGCAACCCGCTGGTGATCGTCGACGGCATCCGCAAGCTGCTGCCGGAGATCCAGAAGACCCTGCCGCCGGATGTCCGCGTCGACCTCGCCTACGAGACTTCGCGCTTCATCCAGGCCTCCATCGACGAGGTGGTGCGGACCCTGGTGGAAGCGCTGCTGATCGTGGTGCTGGTGATCTACCTCTGCCTCGGCTCGCTGCGCAGCGTGCTGATCCCGGTGGCGACCATTCCCCTGTCGATGCTCGGCGCCGCCGCGCTGATGCTGGCCTTCGGCTTCAGCGTCAACCTGCTGACCCTGCTGGCGATGGTGCTGGCCATCGGGCTGGTGGTGGACGACGCCATCGTGGTGGTGGAGAACGTCCACCGCCACATCGAGGAAGGCAAGTCGCCGGTGGCGGCGGCGCTGATCGGCGCCCGCGAAGTGGCCGGCCCGGTGATCGCCATGACCATCACCCTGGCCGCCGTGTACACCCCCATCGGCCTGATGGGCGGCCTCACCGGCGCGCTGTTCCGCGAGTTCGCCCTGACCCTGGCGGGCGCGGTGATCGTGTCCGGGGTGGTGGCGCTGACCCTGTCGCCGGTGATGAGTTCGCTGCTGCTCCAGGCGCACCAGAACGAGGGGCGCATGGGCCGCGCCGCCGAGTGGTTCTTCGGCGGCCTGACGCGGCGCTACGGGCAGGTCCTGGAGTTCTCCCTGGGCCACCGCTGGCTGACCGGCGGCCTGGCATTGCTGGTGTGCATCAGCCTGCCGCTGCTGTATTCGATGCCCAAGCGCGAACTGGCGCCGACCGAGGACCAGGCCGCGGTGCTCACCGCGATCAAGGCGCCGCAGCACGCCAACCTCGACTATGTCGAACTGTTCGCGCGCAAGCTCGACCAGGTCTACACCAGCATCCCGGAAACCGTGAGCACCTGGATCATCAACGGCACCGACGGACCGGCGGCGAGCTTCGGCGGGATCAACCTGGCGGCCTGGGAAAAACGCGAGCGCGACGCCTCGGCGATCCAGTCCGAGCTGCAAGGCAAGGTCGGCGATGTCGAGGGCAGCAGCATCTTCGCCTTCCAGTTGGCCGCCCTGCCCGGCTCCACCGGCGGCCTGCCGGTGCAGATGGTGCTGCGCAGCCCGCAGGACTATCCAGTGCTCTACCGGACCATGGAAGAGATCAAGCAGAAGGCCCGACAGAGCGGGCTGTTCGTGGTGGTCGACAGCGACCTCGACTACAACAACCCGGTGGTCCAGGTCCGCATCGACCGCGCCAAGGCCAACAGCCTGGGCATCCGCATGCAGGACATCGGCGAGTCGCTGGCGGTGCTGGTGGGCGAGAACTACGTCAACCGCTTCGGCATGGAGGGCCGCTCCTACGACGTGATCCCACAGAGCCTGCGCGACCAGCGTTTCACTCCGCAAGCGCTGGCACGACAGTTCGTGCGCACCCAGGACGGCAACCTGGTGCCGCTGTCGACGGTGGTCCGGGTGGCGCTTCAGGTCGAACCGAACAAGCTGATCCAGTTCGACCAGCAGAACGCCGCGACCCTCCAGGCGATCCCCGCGCCCGGCGTCTCCATGGGCCAGGCGGTGGCCTTCCTCGACGACGTGGCGCGCGGCCTGCCGGCCGGCTTCAGCCACGACTGGCAATCCGACTCGCGGCAATACACCCAGGAAGGCAACACCCTGGTGTTCGCCTTCCTCGCCGCCCTGGTGGTGATCTACCTGGTGCTCGCCGCGCAGTACGAGAGCCTGGCCGACCCGCTGATCATCCTGATCACCGTGCCGCTGTCGATCTGCGGCGCGCTGCTGCCGCTGGCGCTGGGCTACGCGACGATGAACATCTATACGCAGATCGGCCTGGTCACCCTGATCGGCCTGATCAGCAAGCACGGCATCCTCATGGTCGAGTTCGCCAACGAACTGCAACTCCACGAGCGCCTCGACCGCCGCGCGGCGATCCTGCGCGCCGCGCAGATCCGCCTGCGGCCGGTGCTGATGACCACCGCGGCAATGGTCTTCGGCCTGGTGCCGCTGCTCTTCGCCAGCGGCGCCGGCGCCGCCAGCCGCTTCGGCCTGGGCGTGGTGATCGTCTCCGGGATGCTGGTCGGCACCCTCTTCACCCTGTTCGTGCTGCCCACCGTCTATACCCTGCTGGCGCGCAACCACGCGGAAGTCGACAAGAGCCCGCGCAGCCGGCAACTGGCCGAGGCCGATCTGCTGGTGAACAAGGCATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36804","NCBI_taxonomy_name":"Pseudomonas aeruginosa PAO1","NCBI_taxonomy_id":"208964"}}}},"ARO_accession":"3000808","ARO_id":"37188","ARO_name":"MexI","CARD_short_name":"MexI","ARO_description":"MexI is the inner membrane transporter of the efflux complex MexGHI-OpmD.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35963":{"category_aro_accession":"0000045","category_aro_cvterm_id":"35963","category_aro_name":"acriflavine","category_aro_description":"Acriflavine is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"43746":{"category_aro_accession":"3005386","category_aro_cvterm_id":"43746","category_aro_name":"disinfecting agents and antiseptics","category_aro_description":"Disinfectants that can also interact with antimicrobial resistance mechanisms, e.g. molecule efflux, and thus are the targets of disinfectant resistance.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1669":{"model_id":"1669","model_name":"vanZ gene in vanF cluster","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"350"}},"model_sequences":{"sequence":{"566":{"protein_sequence":{"accession":"AAF36806.1","sequence":"MLTPLTVLYTYFCTIIFCIVFQIGFFFKALKNISIRHFLWVYVFLFYLALVYMMTGIGNVWVVGRYETLIRVSEINLLPFSSEGVTTYILNIILFMPLGFLLPTIWPQFRTIKNTACTGFFFSLAIELTQLLNHRITDIDDLLMNTLGAIIGYLLYRAFKMIYTRDEKKLDNKSSLVIKYEAIFYIVCSFIGMILLYYPFLLRKII"},"dna_sequence":{"accession":"AF155139.1","fmin":"4338","fmax":"4959","strand":"+","sequence":"ATGCTTACACCACTTACAGTTTTATATACTTATTTTTGTACTATTATTTTTTGTATTGTGTTTCAAATTGGATTTTTTTTTAAAGCGCTAAAAAATATATCTATTAGGCATTTTCTATGGGTGTATGTTTTTCTGTTCTACCTTGCGCTAGTGTATATGATGACGGGGATAGGGAATGTATGGGTAGTAGGAAGATATGAAACATTGATTCGTGTAAGTGAAATCAACTTACTTCCATTTTCTTCTGAAGGTGTTACTACGTATATTTTGAACATTATTCTGTTTATGCCGTTAGGTTTTTTATTGCCAACTATTTGGCCGCAGTTTAGAACAATTAAAAATACTGCATGTACTGGATTCTTTTTTTCATTGGCTATTGAGCTAACTCAATTGCTAAATCATAGAATTACAGATATTGATGATTTACTTATGAACACCCTGGGGGCGATTATTGGGTATTTATTATATAGAGCTTTTAAAATGATATATACAAGAGATGAAAAAAAGCTTGATAATAAATCTTCTCTAGTAATAAAATACGAGGCTATTTTTTATATAGTTTGCTCGTTTATAGGTATGATATTACTTTATTATCCATTTTTATTACGAAAAATTATTTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39542","NCBI_taxonomy_name":"Paenibacillus popilliae ATCC 14706","NCBI_taxonomy_id":"1212764"}}}},"ARO_accession":"3002963","ARO_id":"39397","ARO_name":"vanZ gene in vanF cluster","CARD_short_name":"vanZ_in_vanF_cl","ARO_description":"Also known as vanZF, is a vanZ variant found in the vanF gene cluster.","ARO_category":{"36255":{"category_aro_accession":"3000116","category_aro_cvterm_id":"36255","category_aro_name":"vanZ","category_aro_description":"VanZ is a teicoplanin resistance gene that is an accessory protein. VanZ prevents the incorporation of the terminal D-Ala into peptidoglycan subunits.","category_aro_class_name":"AMR Gene Family"},"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1812":{"model_id":"1812","model_name":"KHM-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"1557":{"protein_sequence":{"accession":"BAF91108.1","sequence":"MKIALVISFGLLLFTNMVCADDSLPELDIQKIEDGVYLYTAYEKIEGWGLVGSNGLVVLDNKNAYLIDTPISATDTEKLVKWIDAQGFTAKASISTHFHTDSTGGIAFLNSKSIPTYASKLTNQLLKNKGEEQATHSFGKNPYWLLKNKIEAFYPGAGHTPDNLVVWLPKQKILFGGCFVKPEGLGNLSHAVIAEWPASAEKLIARYSNATMVVPGHGKVGDASLLEKTRQRAVEALAAKK"},"dna_sequence":{"accession":"AB364006.1","fmin":"61","fmax":"787","strand":"+","sequence":"ATGAAAATAGCTCTTGTTATATCGTTTGGTCTGCTGTTGTTTACCAATATGGTATGCGCTGACGATTCATTACCAGAACTAGATATCCAAAAAATAGAAGACGGCGTTTATCTGTACACCGCTTACGAAAAAATCGAAGGCTGGGGGCTTGTTGGCTCTAACGGATTAGTCGTGCTTGATAACAAAAATGCTTATCTGATTGATACGCCCATTTCAGCCACAGATACTGAAAAATTAGTGAAGTGGATTGACGCGCAGGGCTTTACGGCCAAGGCAAGTATTTCTACCCATTTCCACACCGACAGTACAGGCGGTATTGCATTTCTCAACTCCAAGTCCATTCCAACCTATGCCTCCAAGCTAACTAACCAGCTGCTTAAAAATAAAGGCGAAGAGCAGGCTACGCATTCGTTCGGTAAGAATCCTTATTGGCTATTAAAAAATAAAATCGAAGCCTTTTATCCGGGTGCGGGTCACACACCTGATAATTTAGTAGTGTGGCTGCCGAAACAGAAAATTTTATTTGGTGGCTGTTTTGTCAAACCCGAAGGCCTTGGCAATCTTAGCCATGCGGTAATTGCAGAATGGCCAGCTTCCGCCGAAAAACTTATCGCCCGTTATAGCAATGCAACAATGGTAGTTCCCGGTCACGGAAAAGTTGGCGACGCATCGCTGCTGGAAAAAACCAGGCAGCGCGCAGTTGAAGCGCTTGCAGCTAAAAAGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3000847","ARO_id":"37227","ARO_name":"KHM-1","CARD_short_name":"KHM-1","ARO_description":"KHM-1 is a plasmid-mediated metallo-beta-lactamase found in Citrobacter freundii that confers resistance to all broad-spectrum beta-lactams, execpt for monobactams.","ARO_category":{"41371":{"category_aro_accession":"3004207","category_aro_cvterm_id":"41371","category_aro_name":"KHM beta-lactamase","category_aro_description":"KHM beta-lactamases are Class B beta-lactamases that can confer resistance to all classes of beta-lactams, except the monobactams.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1920":{"model_id":"1920","model_name":"vanS gene in vanF cluster","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"680":{"protein_sequence":{"accession":"AAR84673.1","sequence":"MGKILRGFRSKMIILLGLSMLLSSAITYLLFKVLQLYYYTSVDYGDTLAYFRKIIQNIGDFNVFLLLFILLSILFFFLLTKPYSAYFNEISKGIHYLAQGDFKHRVQILSNDEFSDIAQSINLASEKLEQAIERGDFSESSKEQLVVNLAHDLRTPLTSVLGYLDLILKDDNLTENQIRHYLTIAFTKSQRLERLIDELFEITRMNYGMLPIKKKQIDLSELLIQLKEELYPVFEKNDLIARMNITSPLSIMGDGELLARVFENLLINANRYGYEGQYVDINGFIDSEEVVIQVINYGDAIPPDELPHIFDMLFTGDKARTHQENSTGLGLFIAENIVEQHNGTITAESDLIRTIFEVRLPMADS"},"dna_sequence":{"accession":"AF155139.1","fmin":"2199","fmax":"3297","strand":"+","sequence":"ATGGGTAAAATACTACGAGGCTTTCGTTCAAAAATGATAATATTGTTAGGTTTAAGCATGTTGTTGTCTAGCGCCATAACATACCTACTCTTTAAAGTACTCCAATTGTATTATTATACAAGTGTTGATTATGGAGATACACTAGCTTATTTTCGCAAAATCATACAAAATATTGGAGACTTTAACGTCTTTTTACTGTTATTTATCTTGCTTTCGATATTATTTTTCTTTTTACTTACAAAACCCTATTCTGCCTATTTCAATGAAATTTCAAAAGGAATTCATTATCTCGCTCAGGGTGACTTTAAGCATCGAGTTCAAATATTGTCAAATGATGAATTTAGTGATATTGCACAAAGCATTAATCTGGCAAGTGAAAAATTGGAACAAGCCATAGAAAGGGGTGACTTTTCGGAAAGTAGTAAAGAGCAGTTAGTAGTAAATTTGGCTCATGATTTGCGCACACCTCTTACCTCTGTTTTAGGTTATTTAGATTTAATCCTTAAGGATGATAACTTGACTGAAAATCAGATCAGACATTATTTAACGATTGCCTTTACCAAATCTCAACGCTTAGAAAGGTTAATTGATGAATTATTTGAAATAACTAGGATGAATTATGGCATGTTACCAATTAAAAAGAAACAAATCGATTTAAGTGAGCTACTTATTCAATTGAAAGAAGAGTTGTATCCTGTCTTCGAGAAAAACGATTTGATAGCAAGAATGAATATTACTTCCCCTTTATCTATTATGGGTGATGGAGAGTTATTGGCACGTGTGTTTGAAAATCTTCTGATTAATGCAAATCGCTATGGGTATGAGGGGCAGTATGTAGATATCAACGGTTTTATTGATTCAGAGGAAGTCGTTATTCAAGTTATCAATTATGGGGATGCTATTCCTCCAGATGAACTGCCTCATATTTTTGATATGCTTTTTACTGGTGACAAAGCACGAACTCATCAAGAAAATAGTACAGGTCTCGGTTTATTCATTGCGGAGAATATTGTAGAGCAACACAATGGGACAATAACTGCCGAAAGTGATTTAATACGCACGATATTTGAAGTCCGATTACCAATGGCGGATTCCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39542","NCBI_taxonomy_name":"Paenibacillus popilliae ATCC 14706","NCBI_taxonomy_id":"1212764"}}}},"ARO_accession":"3002936","ARO_id":"39370","ARO_name":"vanS gene in vanF cluster","CARD_short_name":"vanS_in_vanF_cl","ARO_description":"Also known as vanSF, is a vanS variant found in the vanF gene cluster.","ARO_category":{"36210":{"category_aro_accession":"3000071","category_aro_cvterm_id":"36210","category_aro_name":"vanS","category_aro_description":"VanS is similar to histidine protein kinases like EnvZ and acts as a response regulator by activating VanR. VanS is required for high level transcription of other van glycopeptide resistance genes.","category_aro_class_name":"AMR Gene Family"},"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3":{"model_id":"3","model_name":"Escherichia coli ompF with mutation conferring resistance to beta-lactam antibiotics","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"2253":"G141D","2254":"G141E","2255":"R154A","2256":"R154D"},"Curated-R":{"2253":"G141D","2254":"G141E","2255":"R154A","2256":"R154D"},"clinical":{"2253":"G141D","2254":"G141E","2255":"R154A","2256":"R154D"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"650"}},"model_sequences":{"sequence":{"5413":{"protein_sequence":{"accession":"AAC74015.1","sequence":"MMKRNILAVIVPALLVAGTANAAEIYNKDGNKVDLYGKAVGLHYFSKGNGENSYGGNGDMTYARLGFKGETQINSDLTGYGQWEYNFQGNNSEGADAQTGNKTRLAFAGLKYADVGSFDYGRNYGVVYDALGYTDMLPEFGGDTAYSDDFFVGRVGGVATYRNSNFFGLVDGLNFAVQYLGKNERDTARRSNGDGVGGSISYEYEGFGIVGAYGAADRTNLQEAQPLGNGKKAEQWATGLKYDANNIYLAANYGETRNATPITNKFTNTSGFANKTQDVLLVAQYQFDFGLRPSIAYTKSKAKDVEGIGDVDLVNYFEVGATYYFNKNMSTYVDYIINQIDSDNKLGVGSDDTVAVGIVYQF"},"dna_sequence":{"accession":"U00096.3","fmin":"985893","fmax":"986982","strand":"-","sequence":"ATGATGAAGCGCAATATTCTGGCAGTGATCGTCCCTGCTCTGTTAGTAGCAGGTACTGCAAACGCTGCAGAAATCTATAACAAAGATGGCAACAAAGTAGATCTGTACGGTAAAGCTGTTGGTCTGCATTATTTTTCCAAGGGTAACGGTGAAAACAGTTACGGTGGCAATGGCGACATGACCTATGCCCGTCTTGGTTTTAAAGGGGAAACTCAAATCAATTCCGATCTGACCGGTTATGGTCAGTGGGAATATAACTTCCAGGGTAACAACTCTGAAGGCGCTGACGCTCAAACTGGTAACAAAACGCGTCTGGCATTCGCGGGTCTTAAATACGCTGACGTTGGTTCTTTCGATTACGGCCGTAACTACGGTGTGGTTTATGATGCACTGGGTTACACCGATATGCTGCCAGAATTTGGTGGTGATACTGCATACAGCGATGACTTCTTCGTTGGTCGTGTTGGCGGCGTTGCTACCTATCGTAACTCCAACTTCTTTGGTCTGGTTGATGGCCTGAACTTCGCTGTTCAGTACCTGGGTAAAAACGAGCGTGACACTGCACGCCGTTCTAACGGCGACGGTGTTGGCGGTTCTATCAGCTACGAATACGAAGGCTTTGGTATCGTTGGTGCTTATGGTGCAGCTGACCGTACCAACCTGCAAGAAGCTCAACCTCTTGGCAACGGTAAAAAAGCTGAACAGTGGGCTACTGGTCTGAAGTACGACGCGAACAACATCTACCTGGCAGCGAACTACGGTGAAACCCGTAACGCTACGCCGATCACTAATAAATTTACAAACACCAGCGGCTTCGCCAACAAAACGCAAGACGTTCTGTTAGTTGCGCAATACCAGTTCGATTTCGGTCTGCGTCCGTCCATCGCTTACACCAAATCTAAAGCGAAAGACGTAGAAGGTATCGGTGATGTTGATCTGGTGAACTACTTTGAAGTGGGCGCAACCTACTACTTCAACAAAAACATGTCCACCTATGTTGACTACATCATCAACCAGATCGATTCTGACAACAAACTGGGCGTAGGTTCAGACGACACCGTTGCTGTGGGTATCGTTTACCAGTTCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36849","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. MG1655","NCBI_taxonomy_id":"511145"}}}},"ARO_accession":"3003390","ARO_id":"39974","ARO_name":"Escherichia coli ompF with mutation conferring resistance to beta-lactam antibiotics","CARD_short_name":"Ecol_ompF_BLA","ARO_description":"The Escherichia coli ompF (oprF) is a nonspecific porin channel involved in the membrane translocation of small hydrophilic molecules, including and especially beta-lactam antibiotics. Mutations in ompF can decrease diffusion of antibiotics across the cellular membrane, thereby decreasing overall susceptibility through absence of porin function.","ARO_category":{"41445":{"category_aro_accession":"3004281","category_aro_cvterm_id":"41445","category_aro_name":"General Bacterial Porin with reduced permeability to beta-lactams","category_aro_description":"These are GBPs that are associated with decreased susceptibility to beta-lactams either through mutations in the porin protein, absence of the porin protein, or expression of the porin protein.","category_aro_class_name":"AMR Gene Family"},"35976":{"category_aro_accession":"0000059","category_aro_cvterm_id":"35976","category_aro_name":"cefepime","category_aro_description":"Cefepime (INN) is a fourth-generation cephalosporin antibiotic developed in 1994. It contains an aminothiazolyl group that decreases its affinity with beta-lactamases. Cefepime shows high binding affinity with penicillin-binding proteins and has an extended spectrum of activity against Gram-positive and Gram-negative bacteria, with greater activity against both Gram-negative and Gram-positive organisms than third-generation agents.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36383":{"category_aro_accession":"3000244","category_aro_cvterm_id":"36383","category_aro_name":"reduced permeability to antibiotic","category_aro_description":"Reduction in permeability to antibiotic, generally through reduced production of porins, can provide resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2148":{"model_id":"2148","model_name":"Ureaplasma urealyticum gyrB conferring resistance to fluoroquinolones","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"3048":"P462S","4638":"E502Q"},"Curated-R":{"3048":"P462S","4638":"E502Q"},"clinical":{"3048":"P462S","4638":"E502Q"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1200"}},"model_sequences":{"sequence":{"5887":{"protein_sequence":{"accession":"WP_004025678.1","sequence":"MNDSNKENKYTAESIKVLEGLEAVRKRPGMYIGSTQSEGLHHMIWEIVDNSIDEAMGGFATVVKVIIKKDGVIRVEDDGRGIPVGIHEKTGLSGVETVLTVLHAGGKFDNDSYKVSGGLHGVGASVVNALSKNFKVWVNKNYVQHYVEFINGGHAIEPLKIINDKDIKEKGTTIEFIPDFEIMEENEWDELKIMARLKQLAYLNKGVNIEFESEMTNRKEKWHYEGGLKEYIADLNAEKEPLFDAIVYGEEEKEVKVPGHNDQTYNIKCEVAFQYNNSYNNSTHSFCNNINTTEGGTHEEGFKLAITRLLNKYAIDKKYLKDTDDKITKEDVSEGLTAIISIKHPNPQYEGQTKKKLGNSEVRPYVNEITSIIFEKFLNENPEESKKIVAKVMQAAEARRRSHEAREATRRKSPFESNSLPGKLADCSNRDSSVTEIYIVEGDSAGGSAKTGREREFQAILPLRGKIINVEKAKIDKIFANEEIQNMITAFGAGIGPEFNIEKLRYSKIIIMTDADVDGSHIRILLLTFFYRYMLPLIQNGNVYIAQPPLYKVSYGKTIKYAYSDQELEKIKSTLLNTKYNIQRYKGLGEMNPDQLWETTMDPKNRLLLKVNIEDAAIADKTFSLLMGDDVTPRKEFIEKNAKYVKNIDA"},"dna_sequence":{"accession":"NC_011374.1","fmin":"104283","fmax":"106236","strand":"+","sequence":"ATGAACGATTCTAATAAAGAAAATAAATACACCGCTGAAAGTATTAAAGTACTTGAAGGATTAGAAGCGGTACGAAAACGTCCTGGTATGTATATTGGTTCAACTCAATCAGAAGGTTTGCACCATATGATTTGAGAAATTGTTGATAACTCAATCGATGAAGCAATGGGTGGTTTTGCAACAGTTGTTAAAGTTATTATAAAAAAAGATGGAGTAATACGAGTTGAAGATGATGGACGTGGAATTCCAGTTGGAATTCATGAAAAAACTGGTTTATCAGGTGTTGAAACTGTATTAACTGTGTTGCATGCTGGAGGTAAATTTGATAATGATAGTTACAAAGTCTCTGGTGGATTACATGGTGTTGGTGCATCTGTTGTTAATGCTTTAAGTAAAAACTTTAAAGTTTGAGTTAATAAAAATTATGTTCAACATTACGTTGAATTTATTAATGGTGGACATGCTATTGAACCATTAAAAATAATTAACGACAAAGATATCAAAGAAAAAGGAACAACAATTGAGTTTATTCCTGACTTTGAAATCATGGAAGAAAATGAATGAGATGAGCTAAAAATAATGGCTCGTTTAAAACAATTAGCTTACCTTAATAAAGGTGTTAATATCGAATTTGAATCAGAAATGACTAATCGTAAAGAAAAATGACATTACGAAGGTGGTTTAAAAGAGTATATAGCTGATTTAAACGCTGAAAAAGAACCATTATTTGATGCTATTGTTTACGGTGAAGAAGAAAAAGAAGTTAAAGTTCCAGGTCACAATGATCAAACTTATAACATTAAATGTGAAGTAGCATTTCAATACAATAATTCGTACAACAATTCAACACACTCATTCTGTAATAACATTAATACTACAGAAGGTGGAACACACGAAGAAGGTTTTAAATTAGCGATTACACGTTTATTAAACAAATATGCAATCGATAAAAAGTATTTAAAAGACACTGATGATAAAATCACTAAAGAAGACGTGAGCGAAGGGTTAACAGCGATTATTTCTATTAAGCACCCTAACCCTCAATATGAAGGTCAAACAAAGAAAAAATTAGGAAATAGTGAAGTTCGTCCTTATGTTAATGAAATTACTTCTATAATTTTCGAAAAATTCTTAAATGAAAATCCAGAAGAATCAAAAAAAATTGTTGCTAAAGTTATGCAAGCCGCTGAGGCACGTCGTCGTTCTCATGAAGCGCGTGAAGCTACAAGACGAAAATCACCATTTGAATCAAATTCATTACCAGGTAAATTAGCTGATTGTTCAAATCGTGATTCAAGTGTTACAGAAATTTATATTGTCGAAGGGGATTCAGCTGGTGGATCAGCAAAAACTGGTCGTGAACGTGAATTCCAAGCAATTTTACCATTGCGTGGAAAAATTATTAATGTTGAAAAAGCAAAAATTGACAAGATTTTCGCTAATGAAGAAATTCAAAACATGATTACTGCTTTTGGAGCAGGAATAGGGCCTGAATTTAATATTGAAAAATTAAGATATTCAAAAATTATTATTATGACCGATGCCGATGTCGATGGTAGCCATATTCGAATCTTGTTATTAACATTCTTTTATCGATACATGTTACCATTGATTCAAAATGGTAATGTTTATATTGCTCAACCACCACTTTATAAAGTGAGTTATGGTAAAACAATTAAATATGCATATTCTGATCAAGAATTAGAAAAAATTAAATCAACATTGTTGAATACAAAATATAACATTCAACGTTATAAAGGGTTAGGGGAGATGAATCCTGATCAATTATGAGAAACAACAATGGATCCTAAAAATCGTCTTTTATTAAAAGTTAATATTGAAGATGCGGCAATCGCTGATAAAACATTTTCTTTATTAATGGGTGATGATGTAACACCACGAAAAGAATTTATTGAAAAAAATGCAAAATATGTAAAGAATATTGATGCTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40302","NCBI_taxonomy_name":"Ureaplasma urealyticum","NCBI_taxonomy_id":"2130"}}}},"ARO_accession":"3003305","ARO_id":"39889","ARO_name":"Ureaplasma urealyticum gyrB conferring resistance to fluoroquinolones","CARD_short_name":"Uure_gyrB_FLO","ARO_description":"Point mutation in Ureaplasma urealyticum resulting in fluoroquinolone resistance.","ARO_category":{"37244":{"category_aro_accession":"3000864","category_aro_cvterm_id":"37244","category_aro_name":"fluoroquinolone resistant gyrB","category_aro_description":"Point mutations in DNA gyrase subunit B (gyrB) observed in Mycobacterium tuberculosis can result in resistance to fluoroquinolones.","category_aro_class_name":"AMR Gene Family"},"35942":{"category_aro_accession":"0000023","category_aro_cvterm_id":"35942","category_aro_name":"enoxacin","category_aro_description":"Enoxacin belongs to a group called fluoroquinolones. Its mode of action depends upon blocking bacterial DNA replication by binding itself to DNA gyrase and causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37004":{"category_aro_accession":"3000660","category_aro_cvterm_id":"37004","category_aro_name":"lomefloxacin","category_aro_description":"Lomefloxacin is a difluoropiperazinyl quinolone, sharing similar activities with other fluoroquinolones. It is used to treat urinary tract infections. Relative to other fluoroquinolones, it has a longer half life and has higher serum concentrations.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37007":{"category_aro_accession":"3000663","category_aro_cvterm_id":"37007","category_aro_name":"ofloxacin","category_aro_description":"Ofloxacin is a 6-fluoro, 7-piperazinyl quinolone with a methyl-substituted oxazine ring. It has a broad spectrum of activity including many enterobacteria and mycoplasma but most anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"37008":{"category_aro_accession":"3000664","category_aro_cvterm_id":"37008","category_aro_name":"trovafloxacin","category_aro_description":"Trovafloxacin is a trifluoroquinalone with a broad spectrum of activity that acts by inhibiting the uncoiling of supercoiled DNA. While potent against many Gram-positive and Gram-negative bacteria, it is less active against pseudomonads and Cl. difficile. It is usually taken as the prodrug trovafloxacin mesylate or alatrofloxacin mesylate for oral or intravenous administration, respectively.","category_aro_class_name":"Antibiotic"},"37009":{"category_aro_accession":"3000665","category_aro_cvterm_id":"37009","category_aro_name":"grepafloxacin","category_aro_description":"Grepafloxacin is a broad-spectrum antibacterial quinoline. It is no longer taken due to its high toxicity.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"37142":{"category_aro_accession":"3000762","category_aro_cvterm_id":"37142","category_aro_name":"pefloxacin","category_aro_description":"Pefloxacin is structurally and functionally similar to norfloxacin. It is poorly active against mycobacteria, while anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2086":{"model_id":"2086","model_name":"Escherichia coli 16S rRNA (rrnB) mutation conferring resistance to tetracycline","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"2900":"a964g","12977":"a1055g","12979":"g1053a","12978":"c1054t"},"Curated-R":{"2900":"a964g","12977":"a1055g","12979":"g1053a","12978":"c1054t"},"clinical":{"2900":"a964g","12977":"a1055g","12979":"g1053a","12978":"c1054t"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"41093","param_value":"2700"}},"model_sequences":{"sequence":{"3236":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"U00096.1","fmin":"4166658","fmax":"4168200","strand":"+","sequence":"AAATTGAAGAGTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAACGGTAACAGGAAGAAGCTTGCTTCTTTGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCGGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGGAGTAAAGTTAATACCTTTGCTCATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACGAAGACTGACGCTCAGGTGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGTCGACTTGGAGGTTGTGCCCTTGAGGCGTGGCTTCCGGAGCTAACGCGTTAAGTCGACCGCCTGGGGAGTACGGCCGCAAGGTTAAAACTCAAATGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGATGCAACGCGAAGAACCTTACCTGGTCTTGACATCCACGGAAGTTTTCAGAGATGAGAATGTGCCTTCGGGAACCGTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGAAATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCCTTTGTTGCCAGCGGTCCGGCCGGGAACTCAAAGGAGACTGCCAGTGATAAACTGGAGGAAGGTGGGGATGACGTCAAGTCATCATGGCCCTTACGACCAGGGCTACACACGTGCTACAATGGCGCATACAAAGAGAAGCGACCTCGCGAGAGCAAGCGGACCTCATAAAGTGCGTCGTAGTCCGGATTGGAGTCTGCAACTCGACTCCATGAAGTCGGAATCGCTAGTAATCGTGGATCAGAATGCCACGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACACCATGGGAGTGGGTTGCAAAAGAAGTAGGTAGCTTAACCTTCGGGAGGGCGCTTACCACTTTGTGATTCATGACTGGGGTGAAGTCGTAACAAGGTAACCGTAGGGGAACCTGCGGTTGGATCACCTCCTTA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36905","NCBI_taxonomy_name":"Escherichia coli str. K-12","NCBI_taxonomy_id":"83333"}}}},"ARO_accession":"3003411","ARO_id":"39995","ARO_name":"Escherichia coli 16S rRNA (rrnB) mutation conferring resistance to tetracycline","CARD_short_name":"Ecol_16S_TET","ARO_description":"Point mutations in the 3' major domain of the rrnB 16S rRNA gene of Escherichia coli can confer resistance to tetracycline.","ARO_category":{"40280":{"category_aro_accession":"3003669","category_aro_cvterm_id":"40280","category_aro_name":"16S rRNA with mutation conferring resistance to tetracycline derivatives","category_aro_description":"Point mutations in the bacterial 16S rRNA region shown clinically to confer resistance to tetracycline and tetracycline derivatives (polyketide antibiotics).","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2203":{"model_id":"2203","model_name":"MCR-1.1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"3390":{"protein_sequence":{"accession":"AKF16168.1","sequence":"MMQHTSVWYRRSVSPFVLVASVAVFLTATANLTFFDKISQTYPIADNLGFVLTIAVVLFGAMLLITTLLSSYRYVLKPVLILLLIMGAVTSYFTDTYGTVYDTTMLQNALQTDQAETKDLLNAAFIMRIIGLGVLPSLLVAFVKVDYPTWGKGLMRRLGLIVASLALILLPVVAFSSHYASFFRVHKPLRSYVNPIMPIYSVGKLASIEYKKASAPKDTIYHAKDAVQATKPDMRKPRLVVFVVGETARADHVSFNGYERDTFPQLAKIDGVTNFSNVTSCGTSTAYSVPCMFSYLGADEYDVDTAKYQENVLDTLDRLGVSILWRDNNSDSKGVMDKLPKAQFADYKSATNNAICNTNPYNECRDVGMLVGLDDFVAANNGKDMLIMLHQMGNHGPAYFKRYDEKFAKFTPVCEGNELAKCEHQSLINAYDNALLATDDFIAQSIQWLQTHSNAYDVSMLYVSDHGESLGENGVYLHGMPNAFAPKEQRSVPAFFWTDKQTGITPMATDTVLTHDAITPTLLKLFDVTADKVKDRTAFIR"},"dna_sequence":{"accession":"KP347127.1","fmin":"22412","fmax":"24038","strand":"+","sequence":"ATGATGCAGCATACTTCTGTGTGGTACCGACGCTCGGTCAGTCCGTTTGTTCTTGTGGCGAGTGTTGCCGTTTTCTTGACCGCGACCGCCAATCTTACCTTTTTTGATAAAATCAGCCAAACCTATCCCATCGCGGACAATCTCGGCTTTGTGCTGACGATCGCTGTCGTGCTCTTTGGCGCGATGCTACTGATCACCACGCTGTTATCATCGTATCGCTATGTGCTAAAGCCTGTGTTGATTTTGCTATTAATCATGGGCGCGGTGACCAGTTATTTTACTGACACTTATGGCACGGTCTATGATACGACCATGCTCCAAAATGCCCTACAGACCGACCAAGCCGAGACCAAGGATCTATTAAACGCAGCGTTTATCATGCGTATCATTGGTTTGGGTGTGCTACCAAGTTTGCTTGTGGCTTTTGTTAAGGTGGATTATCCGACTTGGGGCAAGGGTTTGATGCGCCGATTGGGCTTGATCGTGGCAAGTCTTGCGCTGATTTTACTGCCTGTGGTGGCGTTCAGCAGTCATTATGCCAGTTTCTTTCGCGTGCATAAGCCGCTGCGTAGCTATGTCAATCCGATCATGCCAATCTACTCGGTGGGTAAGCTTGCCAGTATTGAGTATAAAAAAGCCAGTGCGCCAAAAGATACCATTTATCACGCCAAAGACGCGGTACAAGCAACCAAGCCTGATATGCGTAAGCCACGCCTAGTGGTGTTCGTCGTCGGTGAGACGGCACGCGCCGATCATGTCAGCTTCAATGGCTATGAGCGCGATACTTTCCCACAGCTTGCCAAGATCGATGGCGTGACCAATTTTAGCAATGTCACATCGTGCGGCACATCGACGGCGTATTCTGTGCCGTGTATGTTCAGCTATCTGGGCGCGGATGAGTATGATGTCGATACCGCCAAATACCAAGAAAATGTGCTGGATACGCTGGATCGCTTGGGCGTAAGTATCTTGTGGCGTGATAATAATTCGGACTCAAAAGGCGTGATGGATAAGCTGCCAAAAGCGCAATTTGCCGATTATAAATCCGCGACCAACAACGCCATCTGCAACACCAATCCTTATAACGAATGCCGCGATGTCGGTATGCTCGTTGGCTTAGATGACTTTGTCGCTGCCAATAACGGCAAAGATATGCTGATCATGCTGCACCAAATGGGCAATCACGGGCCTGCGTATTTTAAGCGATATGATGAAAAGTTTGCCAAATTCACGCCAGTGTGTGAAGGTAATGAGCTTGCCAAGTGCGAACATCAGTCCTTGATCAATGCTTATGACAATGCCTTGCTTGCCACCGATGATTTCATCGCTCAAAGTATCCAGTGGCTGCAGACGCACAGCAATGCCTATGATGTCTCAATGCTGTATGTCAGCGATCATGGCGAAAGTCTGGGTGAGAACGGTGTCTATCTACATGGTATGCCAAATGCCTTTGCACCAAAAGAACAGCGCAGTGTGCCTGCATTTTTCTGGACGGATAAGCAAACTGGCATCACGCCAATGGCAACCGATACCGTCCTGACCCATGACGCGATCACGCCGACATTATTAAAGCTGTTTGATGTCACCGCGGACAAAGTCAAAGACCGCACCGCATTCATCCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3003689","ARO_id":"40335","ARO_name":"MCR-1.1","CARD_short_name":"MCR-1.1","ARO_description":"MCR-1 is a plasmid-borne phosphoethanolamine transferase that interferes with binding of colistin to the cell membrane via addition of phosphoethanolamine to lipid A, resulting reduction in negative charge of the cell membrane.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2215":{"model_id":"2215","model_name":"Pseudomonas aeruginosa gyrA and parC conferring resistance to fluoroquinolones","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"3986":"S80L"},"Curated-R":{"3986":"S80L"},"clinical":{"3986":"S80L"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1400"}},"model_sequences":{"sequence":{"3408":{"protein_sequence":{"accession":"BAA37152.1","sequence":"MSESLDLSLEGVERRSLAEFTEQAYLNYSMYVIMDRALPHIGDGLKPVQRRIVYAMSELGLDADSKHKKSARTVGDVLGKFHPHGDSACYEAMVLMAQPFSYRYPLVDGQGNWGAPDDPKSFAAMRYTEARLSRYSEVLLSELGQGTVDWVPNFDGTLDEPAVLPARLPNLLLNGTTGIAVGMATDVPPHNLREVASACVRLLDQPGATVAELCEHVPGPDFPTEAEIITPRADLQKVYETGRGSVRMRAVYRFEDGDIVIHALPHQVSGSKVLEQIAGQMQAKKLPMVADLRDESDHENPTRIVIIPRSNRVDVEELMTHLFATTDLETSYRVNLNIIGLDGKPAVKDLRQLLSEWLQFRIGTVRRRLQFRLDKVERRLHLLDGLLIAFLNLDEVIHIIRTEDQPKAVLMERFELSEVQADYILDTRLRQLARLEEMKIRGEQEELLKEQKRLQTLLGSEAKLKKLVREELIKDAETYGDDRRSPIVARAEARALSETELMPTEPVTVVLSEKGWVRCAKGHDIDAAGLSYKAGDGFKAAAPGRSNQYAVFIDSTGRSYSLPAHSLPSARGQGEPLSGRLTPPPGASFECVLLPDDDALFVIASDAGYGFVVKGEDLQAKNKAGKALLSLPNGSAVVAPRPVRDVEQDWLAAVTTEGRLLLFKVSDLPQLGKGKGNKIIGIPGERVASREEYLTDLAVLPAGATLVLQAGKRTLSLKGDDLEHYKGERGRRGNKLPRGFQRVDSLLVDIPPQD"},"dna_sequence":{"accession":"AB003428.1","fmin":"151","fmax":"2416","strand":"+","sequence":"ATGAGCGAATCCCTCGATCTGAGCCTGGAAGGGGTCGAACGCCGGTCGTTGGCCGAGTTCACCGAGCAGGCCTATCTGAACTATTCCATGTACGTGATCATGGACCGCGCCCTGCCGCATATCGGCGACGGCCTGAAACCGGTGCAGCGACGCATCGTCTACGCCATGAGCGAACTGGGGCTGGATGCCGATTCCAAGCACAAGAAGTCGGCGCGCACCGTCGGCGACGTGCTCGGCAAGTTCCACCCGCACGGCGACTCGGCCTGCTACGAGGCCATGGTGCTGATGGCGCAGCCGTTCTCCTATCGCTATCCGCTGGTGGACGGCCAGGGCAACTGGGGGGCTCCGGACGATCCCAAGTCCTTCGCCGCCATGCGTTATACCGAGGCGCGCCTGTCGCGCTATTCCGAGGTGCTGCTCAGCGAACTGGGCCAGGGTACCGTGGACTGGGTACCGAACTTCGACGGCACCCTCGACGAGCCGGCCGTGCTGCCGGCCCGCCTGCCCAACCTGCTGCTCAACGGCACCACCGGCATCGCGGTGGGCATGGCCACCGACGTGCCGCCGCACAACCTGCGGGAAGTCGCGTCGGCCTGCGTGCGCCTGCTCGACCAGCCGGGCGCGACGGTCGCCGAATTGTGCGAACACGTGCCGGGCCCGGACTTCCCCACCGAAGCCGAGATCATCACCCCGCGCGCCGACCTGCAGAAGGTCTACGAGACCGGCCGCGGTTCGGTGCGCATGCGCGCGGTGTACCGCTTCGAGGACGGCGATATCGTCATCCACGCCCTGCCGCACCAGGTGTCCGGTTCCAAGGTGCTGGAACAGATCGCCGGGCAGATGCAGGCCAAGAAGCTGCCGATGGTGGCCGACCTGCGCGACGAGTCGGACCACGAGAACCCGACCCGCATCGTCATCATCCCGCGTTCGAACCGGGTCGATGTCGAAGAGCTGATGACCCATCTGTTCGCCACCACCGACCTGGAGACCAGCTACCGGGTCAACCTGAACATCATCGGCCTCGACGGCAAGCCGGCAGTCAAGGACCTGCGCCAGTTGCTCTCGGAGTGGCTGCAGTTCCGCATCGGCACCGTGCGTCGACGCCTGCAGTTCCGCCTGGACAAGGTCGAGCGCCGCCTGCATCTGCTGGATGGCTTGCTGATCGCCTTCCTCAACCTCGACGAGGTGATCCACATCATCCGCACCGAGGACCAGCCCAAGGCGGTGCTGATGGAGCGCTTCGAACTCAGCGAGGTGCAGGCCGACTACATCCTCGACACCCGCCTGCGCCAGTTGGCACGCCTGGAAGAGATGAAGATCCGCGGCGAGCAGGAAGAGTTGCTGAAGGAGCAGAAGCGCCTGCAGACCCTGCTCGGCAGCGAGGCCAAGCTGAAGAAGCTGGTGCGCGAGGAGCTGATCAAGGACGCCGAGACCTACGGCGACGACCGCCGTTCGCCGATCGTCGCCCGCGCCGAGGCCCGCGCGCTGTCGGAAACCGAGCTGATGCCCACCGAACCGGTGACCGTGGTGCTCTCGGAAAAAGGCTGGGTGCGTTGCGCCAAGGGCCACGACATCGACGCCGCCGGCCTCTCCTACAAGGCCGGCGACGGCTTCAAGGCCGCCGCGCCGGGACGCTCGAACCAGTATGCGGTGTTCATCGACTCCACCGGGCGCAGCTACTCGCTGCCGGCCCACAGCCTGCCGTCCGCGCGAGGCCAGGGCGAGCCACTCAGCGGCCGGCTGACGCCGCCGCCGGGGGCCAGCTTCGAATGCGTGCTGCTGCCGGACGACGATGCGCTGTTCGTGATCGCTTCCGACGCCGGCTATGGTTTCGTGGTCAAGGGCGAGGACCTGCAGGCCAAGAACAAGGCCGGCAAGGCCCTGCTCAGCCTGCCCAACGGCTCCGCCGTGGTGGCGCCGCGCCCGGTGCGCGATGTGGAGCAGGATTGGCTGGCGGCCGTGACGACCGAGGGCCGTCTGCTATTGTTCAAGGTCTCCGACCTGCCGCAGCTCGGCAAGGGCAAGGGCAACAAGATCATCGGCATCCCCGGCGAACGCGTGGCCAGCCGCGAGGAATACCTCACCGACCTGGCTGTTCTGCCAGCCGGGGCGACGTTGGTCCTGCAGGCCGGAAAGCGTACCCTGTCGCTCAAGGGCGACGACCTGGAACACTACAAGGGGGAGCGAGGCCGGCGAGGCAACAAGCTGCCGCGCGGTTTCCAGCGCGTCGACAGCCTGCTGGTGGATATTCCGCCACAGGATTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3003702","ARO_id":"40355","ARO_name":"Pseudomonas aeruginosa gyrA and parC conferring resistance to fluoroquinolones","CARD_short_name":"Paer_ParC_FLO","ARO_description":"Point mutation in Pseudomonas aeruginosa parC resulting in fluoroquinolone resistance also requiring a gyrA mutation.","ARO_category":{"36913":{"category_aro_accession":"3000619","category_aro_cvterm_id":"36913","category_aro_name":"fluoroquinolone resistant parC","category_aro_description":"ParC is a subunit of topoisomerase IV, which decatenates and relaxes DNA to allow access to genes for transcription or translation. Point mutations in ParC prevent fluoroquinolone antibiotics from inhibiting DNA synthesis, and confer low-level resistance. Higher-level resistance results from both gyrA and parC mutations.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"37007":{"category_aro_accession":"3000663","category_aro_cvterm_id":"37007","category_aro_name":"ofloxacin","category_aro_description":"Ofloxacin is a 6-fluoro, 7-piperazinyl quinolone with a methyl-substituted oxazine ring. It has a broad spectrum of activity including many enterobacteria and mycoplasma but most anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"37142":{"category_aro_accession":"3000762","category_aro_cvterm_id":"37142","category_aro_name":"pefloxacin","category_aro_description":"Pefloxacin is structurally and functionally similar to norfloxacin. It is poorly active against mycobacteria, while anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3453":{"model_id":"3453","model_name":"OXA-289","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"530"}},"model_sequences":{"sequence":{"8311":{"protein_sequence":{"accession":"WP_081400730.1","sequence":"MPKILKHLSLCASVMIGLTLLGCQNFHAPTQSAVSKKHDQTEIASLFQHAQTVGVFVTYDGQTLQAYGNALSRSNTAYIPASTFKMLNALIGIQHHKTSPNEVFKWDGKKRAFASWEKDLTLAEAMQASAVPVYQELARRIGLELMANEVKRVGFGNAEIGTQVDDFWLVGPLKITPIEEVKFAYALANKQLEFDQSVQKQVKQMVFVDEVHGTKIYAKSGWGMDVTPQVGWWTGWIEQPNGQVIAFSLNLEINKPEHGDARKAIVYQALQQLKLLQKQ"},"dna_sequence":{"accession":"APRM01000005.1","fmin":"282563","fmax":"283403","strand":"-","sequence":"ATGCCAAAAATACTAAAACATCTTAGCCTTTGCGCATCTGTAATGATTGGACTGACCTTGCTTGGTTGTCAAAATTTTCACGCCCCAACTCAAAGCGCCGTGTCAAAAAAACACGATCAAACCGAGATCGCTTCTTTATTCCAACATGCTCAAACTGTTGGCGTATTTGTTACATATGATGGGCAAACACTTCAAGCATATGGCAATGCGTTGAGTCGATCGAATACGGCTTATATTCCAGCCTCAACCTTCAAGATGTTAAATGCTCTGATTGGGATACAGCATCACAAAACTTCACCAAACGAAGTGTTTAAATGGGATGGCAAAAAGCGTGCTTTTGCGAGCTGGGAAAAAGATTTAACTTTAGCCGAGGCGATGCAGGCATCAGCAGTGCCTGTTTATCAGGAATTGGCTCGGCGTATCGGGTTAGAGTTGATGGCGAACGAAGTAAAACGCGTTGGCTTTGGCAATGCCGAGATCGGAACGCAAGTCGATGATTTTTGGTTGGTTGGCCCGCTTAAGATTACCCCAATTGAAGAGGTTAAATTTGCTTATGCTTTGGCAAATAAGCAGCTTGAATTTGACCAATCTGTGCAAAAACAAGTGAAACAGATGGTCTTCGTTGATGAAGTTCATGGAACTAAGATTTATGCCAAAAGTGGTTGGGGGATGGATGTAACACCGCAAGTGGGTTGGTGGACGGGCTGGATTGAACAACCGAATGGACAGGTGATTGCATTTTCTTTAAATCTGGAAATAAATAAGCCTGAGCACGGTGATGCGCGTAAAGCGATTGTTTATCAAGCATTACAACAATTGAAATTGTTACAGAAGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"45611","NCBI_taxonomy_name":"Acinetobacter sp. NIPH 298","NCBI_taxonomy_id":"1217692"}}}},"ARO_accession":"3001744","ARO_id":"38144","ARO_name":"OXA-289","CARD_short_name":"OXA-289","ARO_description":"OXA-289 is a beta-lactamase found in Acinetobacter spp.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2223":{"model_id":"2223","model_name":"MexZ","model_type":"protein overexpression model","model_type_id":"41091","model_description":"Protein Overexpression Models (POM) are similar to Protein Variant Models (PVM) in that they include a protein reference sequence, a curated BLASTP bitscore cut-off, and mapped resistance variants. Whereas PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, reporting only those with curated mutations conferring AMR, POMs are restricted to regulatory proteins and report both wild-type sequences and\/or sequences with mutations leading to overexpression of efflux complexes. The former lead to efflux of antibiotics at basal levels, while the latter can confer clinical resistance. POMs include a protein reference sequence (often from wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Perfect RGI match is 100% identical to the wild-type reference protein sequence along its entire length, a Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value may or may not contain at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off may or may not contain at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"3168":"G195E","3173":"V44A","3174":"G46S","3175":"Q10Z"},"Curated-R":{"3168":"G195E","3173":"V44A","3174":"G46S","3175":"Q10Z"},"clinical":{"3168":"G195E","3173":"V44A","3174":"G46S","3175":"Q10Z"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"390"}},"model_sequences":{"sequence":{"5526":{"protein_sequence":{"accession":"AAG05408.1","sequence":"MARKTKEESQKTRDGILDAAERVFLEKGVGTTAMADLADAAGVSRGAVYGHYKNKIEVCLAMCDRAFGQIEVPDENARVPALDILLRAGMGFLRQCCEPGSVQRVLEILYLKCERSDENEPLLRRRELLEKQGQRFGLRQIRRAVERGELPARLDVELASIYLQSLWDGICGTLAWTERLRDDPWNRAERMFRAGLDSLRSSPYLLLADA"},"dna_sequence":{"accession":"AE004091.2","fmin":"2212676","fmax":"2213309","strand":"+","sequence":"GTGGCCAGGAAAACCAAAGAGGAATCCCAGAAAACCCGCGACGGCATACTCGATGCCGCCGAGCGGGTTTTCCTGGAAAAGGGCGTGGGCACCACTGCCATGGCCGACCTGGCGGACGCCGCCGGGGTTTCTCGCGGTGCGGTCTACGGCCACTACAAGAACAAGATCGAGGTCTGCCTGGCGATGTGCGACCGCGCCTTCGGCCAGATCGAGGTACCCGACGAAAACGCCAGGGTGCCGGCGCTGGATATCCTCCTGCGCGCCGGCATGGGCTTTCTCCGCCAGTGCTGCGAGCCCGGTTCGGTGCAGCGGGTGCTGGAGATCCTCTACCTCAAGTGCGAACGCAGCGACGAGAACGAGCCGCTGTTGCGCCGCCGCGAGCTGCTCGAGAAGCAGGGGCAACGCTTCGGCCTCCGGCAGATCCGCCGGGCGGTGGAACGCGGCGAACTGCCGGCGCGGCTGGACGTCGAGCTGGCCAGCATCTATCTGCAATCGCTCTGGGACGGCATCTGCGGCACCCTGGCCTGGACCGAGCGCCTGCGCGACGATCCCTGGAACCGCGCCGAACGCATGTTCCGCGCCGGCCTCGACAGCCTGCGCAGTTCTCCCTACCTGTTGCTGGCGGACGCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36804","NCBI_taxonomy_name":"Pseudomonas aeruginosa PAO1","NCBI_taxonomy_id":"208964"}}}},"ARO_accession":"3003709","ARO_id":"40363","ARO_name":"MexZ","CARD_short_name":"MexZ","ARO_description":"MexZ is a transcriptional regulator that downregulates the mexXY multidrug transporter operon, which confers to aminoglycoside resistance on Pseudomonas aeruginosa.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35933":{"category_aro_accession":"0000014","category_aro_cvterm_id":"35933","category_aro_name":"gentamicin C","category_aro_description":"Gentamicin C is a mixture of gentamicin C1, gentamicin C1a, and gentamicin C2 (these differ in substituents at position C6'). Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35963":{"category_aro_accession":"0000045","category_aro_cvterm_id":"35963","category_aro_name":"acriflavine","category_aro_description":"Acriflavine is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35990":{"category_aro_accession":"0000073","category_aro_cvterm_id":"35990","category_aro_name":"meropenem","category_aro_description":"Meropenem is an ultra-broad spectrum injectable antibiotic used to treat a wide variety of infections, including meningitis and pneumonia. It is a beta-lactam and belongs to the subgroup of carbapenem, similar to imipenem and ertapenem.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36998":{"category_aro_accession":"3000654","category_aro_cvterm_id":"36998","category_aro_name":"arbekacin","category_aro_description":"A synthetic derivative (1-N-(4-amino-2-hydroxybutyryl) of dibekacin used in Japan. It is active against methicillin-resistant Staph. aureus and shows synergy with ampicillin when treating gentamicin and vancomycin resistant enterocci.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37007":{"category_aro_accession":"3000663","category_aro_cvterm_id":"37007","category_aro_name":"ofloxacin","category_aro_description":"Ofloxacin is a 6-fluoro, 7-piperazinyl quinolone with a methyl-substituted oxazine ring. It has a broad spectrum of activity including many enterobacteria and mycoplasma but most anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"46133":{"category_aro_accession":"3007382","category_aro_cvterm_id":"46133","category_aro_name":"gentamicin","category_aro_description":"Gentamicin is a commonly used aminoglycoside antibiotic derived from members of the Micromonospora genus of bacteria. It acts by binding the 30S ribosomal subunit, thus inhibiting protein synthesis. Gentamicin is typically used to treat Gram-negative infections of the repiratory and urinary tract, as well as infections of the bone and soft tissue. It also exhibits considerable nephrotoxicity and ototoxicity. Gentamicin is administered as a mixture of gentamicin type C (which makes about around 80% of the complex) and types A, B, and X (distributed in the remaining 20% of the complex).","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"43746":{"category_aro_accession":"3005386","category_aro_cvterm_id":"43746","category_aro_name":"disinfecting agents and antiseptics","category_aro_description":"Disinfectants that can also interact with antimicrobial resistance mechanisms, e.g. molecule efflux, and thus are the targets of disinfectant resistance.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2269":{"model_id":"2269","model_name":"Escherichia coli nfsB with mutation conferring resistance to nitrofurantoin","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"40394":{"param_type":"nonsense mutation","param_description":"A sequence change where, compared to a reference sequence, one codon is replaced by a termination codon through a nucleotide substitution. These are described as a substitution of the wildtype codon to a termination codon. Format is given as [wild type AA][position][Ter], for example Q42Ter where Q42 is a wildtype amino acid replaced by a premature termination codon.","param_type_id":"40394","param_value":{"8196":"E137Ter","18534":"W94Ter"}},"snp":{"Curated-R":{"8196":"Q10Z","18531":"F84S","18532":"G192D","18533":"G192S","18534":"G192S"},"param_value":{"18531":"F84S","18532":"G192D","18533":"G192S"},"clinical":{"18531":"F84S","18532":"G192D","18533":"G192S"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"5250":{"protein_sequence":{"accession":"AAC73679.1","sequence":"MDIISVALKRHSTKAFDASKKLTPEQAEQIKTLLQYSPSSTNSQPWHFIVASTEEGKARVAKSAAGNYVFNERKMLDASHVVVFCAKTAMDDVWLKLVVDQEDADGRFATPEAKAANDKGRKFFADMHRKDLHDDAEWMAKQVYLNVGNFLLGVAALGLDAVPIEGFDAAILDAEFGLKEKGYTSLVVVPVGHHSVEDFNATLPKSRLPQNITLTEV"},"dna_sequence":{"accession":"U00096.3","fmin":"604770","fmax":"605424","strand":"-","sequence":"ATGGATATCATTTCTGTCGCCTTAAAGCGTCATTCCACTAAGGCATTTGATGCCAGCAAAAAACTTACCCCGGAACAGGCCGAGCAGATCAAAACGCTACTGCAATACAGCCCATCCAGCACCAACTCCCAGCCGTGGCATTTTATTGTTGCCAGCACGGAAGAAGGTAAAGCGCGTGTTGCCAAATCCGCTGCCGGTAATTACGTGTTCAACGAGCGTAAAATGCTTGATGCCTCGCACGTCGTGGTGTTCTGTGCAAAAACCGCGATGGACGATGTCTGGCTGAAGCTGGTTGTTGACCAGGAAGATGCCGATGGCCGCTTTGCCACGCCGGAAGCGAAAGCCGCGAACGATAAAGGTCGCAAGTTCTTCGCTGATATGCACCGTAAAGATCTGCATGATGATGCAGAGTGGATGGCAAAACAGGTTTATCTCAACGTCGGTAACTTCCTGCTCGGCGTGGCGGCTCTGGGTCTGGACGCGGTACCCATCGAAGGTTTTGACGCCGCCATCCTCGATGCAGAATTTGGTCTGAAAGAGAAAGGCTACACCAGTCTGGTGGTTGTTCCGGTAGGTCATCACAGCGTTGAAGATTTTAACGCTACGCTGCCGAAATCTCGTCTGCCGCAAAACATCACCTTAACCGAAGTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36849","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. MG1655","NCBI_taxonomy_id":"511145"}}}},"ARO_accession":"3003756","ARO_id":"40413","ARO_name":"Escherichia coli nfsB with mutation conferring resistance to nitrofurantoin","CARD_short_name":"Ecol_nfsB_NIT","ARO_description":"nfsB encodes the minor oxygen-insesitive nitroreductase in E. coli. The first step of resistance to nitrofurazone is mutation of nfsA, while the increased resistance associated with second step mutants is a consequence of nfsB mutation.","ARO_category":{"40412":{"category_aro_accession":"3003755","category_aro_cvterm_id":"40412","category_aro_name":"Antibiotic resistant nfsB","category_aro_description":"The nsfB gene encodes a minor oxygen-insensitive nitroreductase. NfsB reduces a broad range of nitroaromatic compounds including the antibiotics nitrofurazone and nitrofurantoin. NfsB is a flavin mononucleotide (FMN)-containing protein and uses both NADH and NADPH as a source of reducing equivalents. Mutations in nfsB lead to increased resistance to nitrofurazone and furazolidone in an nfsA mutant background.","category_aro_class_name":"AMR Gene Family"},"35992":{"category_aro_accession":"0000075","category_aro_cvterm_id":"35992","category_aro_name":"nitrofurantoin","category_aro_description":"Nitrofurantoin is an antibiotic used to treat urinary tract infections. It inhibits enzyme synthesis by inhibiting essential enzymes involved in the citric acid cycle, as well as those involved in DNA, RNA, and protein synthesis. It is marketed under the following brand names: Furadantin, Macrobid, Macrodantin, Nitro Macro and Urantoin.","category_aro_class_name":"Antibiotic"},"41240":{"category_aro_accession":"3004116","category_aro_cvterm_id":"41240","category_aro_name":"nitrofuran antibiotic","category_aro_description":"Nitrofurans are chemotherapeutic agents with antibacterial and antiprotozoal activity.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2278":{"model_id":"2278","model_name":"Bifidobacterium bifidum ileS conferring resistance to mupirocin","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"2200"}},"model_sequences":{"sequence":{"5227":{"protein_sequence":{"accession":"ADP36409.1","sequence":"MSETTNSHVYPKANEGGETASVAPNPSFPNMEETVLKYWDKDDTFNKSVERNPSGDHSQNEFVFFDGPPFANGLPHYGHLLTGYAKDVIPRYQTMKGRKVNRVFGWDTHGLPAELEAQKELGIDSVDQIEKMGIDKFNDACRASVLKYTHEWQDYVHRQARWVDFEHGYKTLNIPYMESVMWAFKQLYEKGLAYQGYRVLPYCPKDQTPLSAHELRMDADVYQDRQDTTVSVAVKLRDEEDAYAVFWTTTPWTVPTNFAIVVGADIDYVEVRPTQGKYAGKKFYFGKPLLSKYEKELGEDYEVVRELKGSEMAGWRYWPVFPYFAGDKAESEGNVPGPEGYQIFTADYVDTVEGTGLVHQAPYGEDDMNTLNAHGIKSTDVLDAGCRFTAQCPDYEGMYVFDANKPILRNLRNGDGPLAEIPAEHRAILFQEKSYVHSYPHCWRCATPLIYKPVSSWFVSVTKIKPRLLELNQQINWIPENVKDGQFGKWLANARDWSISRNRFWGSPIPVWVSDDPKYPRVDVYGSLEELKADFGDYPRDKDGNVNMHRPWIDNLTRVNPDDPTGKSHMHRISDVLDCWFESGSMSFAQFHYPFENKEKFEQHFPADYIVEYIGQTRGWFYLLHVMATALFDRPAFKNVICHGIVLGSDGQKMSKHLRNYPDVNGVFDKYGSDAMRWFLMSSPILRGGNLIVTAEGIRDTVRQVMLPVWSSYYFFTLYANAANGGAGFDARQLRADEVAGLPEMDRYLLARTRRLVERVEKSLDEFAISDACDAASDFIDVLTNWYIRNTRDRFWKEDVNAFNTLYTVLEVFMRVLAPLAPMESESVWRGLTGGESVHLADWPYVADEKTGEATELGRVLVDDPALVDAMEKVREIVSGALSLRKAAQIRVRQPLAKLTVVVEDVDAVKAYDEILKSELNIKDIEFCTMEDAGSQGLKIVHELKVNARAAGPRLGKQVQFAIKASKTGAWHVDAATGAPVVETPNGEVALEAGEYELINRVEEENAAEADASVSAALPTGGFVILDTVLTADLEAEGYARDVIRAVQDARKAADLDIADRIALVLTVPSANVADVERFRDLIAHETLATSFAVKEGAELGVEVAKA"},"dna_sequence":{"accession":"CP001840.1","fmin":"1610636","fmax":"1613960","strand":"-","sequence":"GTGAGCGAAACCACCAATTCCCACGTGTATCCCAAGGCGAACGAGGGCGGCGAGACCGCCAGCGTCGCGCCGAACCCGAGTTTCCCCAACATGGAGGAAACCGTCCTGAAGTATTGGGACAAGGACGACACCTTCAACAAGTCCGTTGAACGCAACCCTTCCGGCGACCATAGTCAGAACGAGTTCGTGTTCTTCGACGGCCCGCCGTTCGCGAACGGCCTGCCGCACTACGGCCACCTGCTGACCGGTTACGCGAAGGACGTGATCCCGCGCTACCAGACCATGAAGGGCCGCAAGGTCAACCGCGTGTTCGGCTGGGACACGCACGGTCTGCCCGCCGAGCTGGAGGCGCAGAAGGAGCTCGGCATCGACTCGGTCGACCAGATCGAGAAGATGGGCATCGACAAGTTCAATGACGCCTGCCGCGCCTCCGTCCTGAAGTACACGCACGAATGGCAGGATTACGTGCATCGTCAGGCCCGCTGGGTCGACTTCGAGCACGGGTACAAGACGCTGAACATCCCGTATATGGAGTCGGTGATGTGGGCGTTCAAGCAGCTGTACGAGAAGGGCCTGGCGTACCAGGGCTACCGCGTGCTGCCGTACTGCCCGAAGGATCAGACGCCGCTTTCGGCGCACGAGCTGCGCATGGACGCCGACGTGTATCAGGATCGTCAGGACACCACCGTGTCGGTGGCCGTGAAGCTGCGCGACGAGGAGGACGCCTACGCGGTCTTCTGGACCACCACGCCGTGGACCGTGCCCACTAACTTCGCGATCGTCGTCGGCGCTGACATCGACTATGTCGAGGTGCGCCCGACGCAGGGCAAGTACGCCGGCAAGAAGTTCTACTTCGGCAAGCCCCTGCTCTCCAAGTACGAGAAGGAGCTCGGCGAGGATTACGAGGTCGTGCGCGAGCTCAAGGGCTCCGAGATGGCCGGTTGGCGTTACTGGCCGGTGTTCCCGTACTTCGCTGGCGACAAAGCCGAGTCTGAGGGCAACGTGCCGGGGCCCGAAGGCTACCAAATCTTTACCGCGGACTACGTAGACACCGTCGAGGGTACCGGCCTGGTTCACCAGGCTCCCTATGGTGAGGACGATATGAACACGCTGAACGCGCACGGCATCAAGAGCACTGACGTGCTCGACGCCGGCTGCCGCTTCACCGCGCAGTGCCCCGATTACGAGGGCATGTACGTGTTCGACGCGAACAAGCCGATCCTGCGCAACCTGCGCAACGGAGACGGCCCGCTGGCCGAGATCCCGGCCGAGCATCGCGCGATCCTGTTCCAGGAGAAGAGCTATGTGCACTCCTACCCGCATTGCTGGCGTTGCGCCACGCCGCTGATCTACAAGCCTGTGAGCTCATGGTTCGTGTCGGTGACGAAGATCAAGCCGCGCCTGTTGGAGCTCAACCAGCAGATCAACTGGATTCCTGAGAATGTCAAGGATGGTCAGTTCGGTAAGTGGCTCGCCAACGCGCGCGACTGGTCGATCTCCCGCAACCGCTTCTGGGGTTCGCCGATCCCGGTGTGGGTGAGCGATGACCCGAAGTACCCGCGCGTCGACGTGTACGGTTCGTTGGAGGAGCTCAAGGCCGACTTCGGCGACTACCCGCGCGACAAGGACGGCAACGTCAACATGCACCGTCCGTGGATCGACAACCTCACGCGCGTCAACCCGGACGACCCGACCGGCAAGAGCCACATGCACCGTATCAGCGACGTGCTCGACTGCTGGTTCGAATCCGGTTCGATGTCGTTCGCGCAGTTCCACTACCCGTTCGAGAACAAGGAGAAGTTCGAGCAGCACTTCCCGGCCGACTACATTGTCGAATACATCGGCCAGACCCGCGGCTGGTTCTACCTGCTGCACGTGATGGCCACCGCGCTGTTCGACCGCCCGGCGTTCAAGAACGTGATCTGCCACGGCATCGTGCTCGGTTCCGACGGCCAGAAGATGTCGAAGCACCTGCGCAACTACCCGGACGTGAACGGCGTGTTCGACAAGTACGGTTCCGACGCCATGCGCTGGTTCCTTATGTCGTCGCCGATCCTGCGCGGCGGCAACCTCATTGTTACCGCTGAGGGCATCCGCGACACCGTGCGCCAGGTCATGCTGCCGGTGTGGAGCTCCTACTACTTCTTCACGCTGTATGCGAACGCGGCCAATGGCGGGGCCGGCTTCGACGCCCGTCAGCTGCGCGCGGACGAGGTGGCGGGTCTGCCTGAGATGGATCGTTACCTGCTGGCCCGCACCCGCAGGCTCGTAGAGCGTGTAGAGAAGTCGCTCGACGAGTTCGCGATTTCTGACGCGTGCGATGCGGCGAGTGACTTCATCGACGTGCTCACCAACTGGTACATCCGCAACACCCGTGATCGCTTCTGGAAGGAGGACGTGAATGCGTTCAACACGCTGTACACCGTGCTTGAGGTGTTCATGCGCGTTCTCGCGCCGCTCGCCCCGATGGAGTCCGAATCCGTGTGGCGTGGCCTGACCGGCGGCGAATCCGTGCATCTGGCCGATTGGCCGTACGTCGCGGACGAGAAGACCGGTGAGGCGACCGAGCTTGGCCGTGTGCTGGTCGACGACCCGGCACTGGTGGACGCGATGGAGAAGGTGCGCGAGATCGTCTCCGGCGCTCTGTCGTTGCGCAAGGCCGCCCAGATCCGTGTGCGCCAGCCGCTCGCCAAGCTCACCGTCGTGGTCGAGGATGTGGATGCCGTCAAGGCGTACGACGAAATTCTCAAGTCAGAGCTTAATATAAAGGATATTGAGTTCTGCACGATGGAGGATGCCGGTTCGCAGGGGCTGAAGATCGTGCACGAGCTGAAGGTCAACGCCCGCGCCGCCGGCCCGCGCCTCGGCAAGCAGGTCCAGTTCGCCATCAAGGCGTCCAAGACCGGTGCCTGGCATGTCGATGCCGCGACCGGTGCTCCGGTCGTCGAGACGCCGAACGGCGAGGTTGCGCTGGAGGCTGGCGAATACGAGCTAATCAACCGCGTGGAGGAGGAGAACGCCGCCGAGGCCGACGCTTCCGTGTCGGCCGCTCTGCCTACCGGCGGTTTCGTGATTCTCGATACCGTGCTGACCGCCGACCTGGAGGCCGAGGGCTACGCCCGCGACGTGATTCGCGCCGTGCAGGACGCCCGCAAGGCCGCCGACCTGGACATCGCCGATCGCATCGCCCTGGTGCTGACCGTGCCGTCCGCCAATGTGGCCGATGTCGAGCGGTTCCGCGATCTGATCGCCCATGAGACGCTGGCCACCTCCTTCGCGGTGAAGGAAGGTGCCGAGCTGGGCGTGGAGGTCGCCAAGGCGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40437","NCBI_taxonomy_name":"Bifidobacterium bifidum PRL2010","NCBI_taxonomy_id":"702459"}}}},"ARO_accession":"3003730","ARO_id":"40419","ARO_name":"Bifidobacterium bifidum ileS conferring resistance to mupirocin","CARD_short_name":"Bbif_ileS_MUP","ARO_description":"Bifidobacteria have an intrinsically resistant form of ileS (isoleucyl-tRNA synthetase) that confers resistance to mupirocin.","ARO_category":{"36585":{"category_aro_accession":"3000446","category_aro_cvterm_id":"36585","category_aro_name":"antibiotic-resistant isoleucyl-tRNA synthetase (ileS)","category_aro_description":"Mupirocin inhibits protein synthesis by interfering with isoleucyl-tRNA synthetase (ileS).  Mutations in ileS can confer low-level mupirocin resistance.","category_aro_class_name":"AMR Gene Family"},"36693":{"category_aro_accession":"3000554","category_aro_cvterm_id":"36693","category_aro_name":"mupirocin","category_aro_description":"Mupirocin, also known as pseudomonic acid, is a bacteriostatic polyketide antibiotic from Pseudomonas fluorescens used to treat S. aureus and MRSA. It inhibits Ile tRNA synthetase.","category_aro_class_name":"Antibiotic"},"45733":{"category_aro_accession":"3007151","category_aro_cvterm_id":"45733","category_aro_name":"mupirocin-like antibiotic","category_aro_description":"A group of antibiotics including mupirocin and similar mixtures (such as those including pseudomonic acid A).","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2254":{"model_id":"2254","model_name":"Staphylococcus aureus fusA with mutation conferring resistance to fusidic acid","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"40330":{"param_type":"multiple resistance variants","param_description":"A set of nucleotide or amino acid substitutions that are all required to confer resistance to an antibiotic drug or drug class, encoded as: [wild-type 1][position 1][mutation 1],[wild-type 2][position 2][mutation 2], etc. For example, D63Y,T142K.","param_type_id":"40330","param_value":{"3355":"A67T,P406L","3358":"H457Y,S416F","3374":"D189V,L430S","3375":"T387I,E449K","3388":"G452C,R659L","3365":"F652S,Y654N"}},"snp":{"Curated-R":{"3355":"G192S","3356":"H457Y","3357":"L461K","3358":"L461K","3367":"H457Q","3368":"M453I","3369":"P404L","3370":"A376V","3371":"F441Y","3372":"V90A","3373":"V90I","3374":"V90I","3375":"V90I","3377":"L461S","3379":"L461F","3360":"T436I","3361":"G452S","3362":"L456F","3364":"R464C","3366":"P406L","3380":"F88L","3381":"Q115L","3382":"P404Q","3383":"V407F","3384":"D434N","3385":"G451V","3386":"G452C","3387":"G452V","3388":"G452V","3389":"R464H","3390":"R464S","3391":"R464L","10274":"H457N","10275":"H457L","3365":"H457L"},"param_value":{"3356":"H457Y","3357":"L461K","3367":"H457Q","3368":"M453I","3369":"P404L","3370":"A376V","3371":"F441Y","3372":"V90A","3373":"V90I","3377":"L461S","3379":"L461F","3360":"T436I","3361":"G452S","3362":"L456F","3364":"R464C","3366":"P406L","3380":"F88L","3381":"Q115L","3382":"P404Q","3383":"V407F","3384":"D434N","3385":"G451V","3386":"G452C","3387":"G452V","3389":"R464H","3390":"R464S","3391":"R464L","10274":"H457N","10275":"H457L"},"clinical":{"3356":"H457Y","3357":"L461K","3367":"H457Q","3368":"M453I","3369":"P404L","3370":"A376V","3371":"F441Y","3372":"V90A","3373":"V90I","3377":"L461S","3379":"L461F","10274":"H457N","10275":"H457L"},"experimental":{"3360":"T436I","3361":"G452S","3362":"L456F","3364":"R464C","3366":"P406L","3380":"F88L","3381":"Q115L","3382":"P404Q","3383":"V407F","3384":"D434N","3385":"G451V","3386":"G452C","3387":"G452V","3389":"R464H","3390":"R464S","3391":"R464L"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1350"}},"model_sequences":{"sequence":{"3510":{"protein_sequence":{"accession":"CAG39573.1","sequence":"MAREFSLEKTRNIGIMAHIDAGKTTTTERILYYTGRIHKIGETHEGASQMDWMEQEQDRGITITSAATTAAWEGHRVNIIDTPGHVDFTVEVERSLRVLDGAVTVLDAQSGVEPQTETVWRQATTYGVPRIVFVNKMDKLGANFEYSVSTLHDRLQANAAPIQLPIGAEDEFEAIIDLVEMKCFKYTNDLGTEIEEIEIPEDHLDRAEEARASLIEAVAETSDELMEKYLGDEEISVSELKEAIRQATTNVEFYPVLCGTAFKNKGVQLMLDAVIDYLPSPLDVKPIIGHRASNPEEEVIAKADDSAEFAALAFKVMTDPYVGKLTFFRVYSGTMTSGSYVKNSTKGKRERVGRLLQMHANSRQEIDTVYSGDIAAAVGLKDTGTGDTLCGEKNDIILESMEFPEPVIHLSVEPKSKADQDKMTQALVKLQEEDPTFHAHTDEETGQVIIGGMGELHLDILVDRMKKEFNVECNVGAPMVSYRETFKSSAQVQGKFSRQSGGRGQYGDVHIEFTPNETGAGFEFENAIVGGVVPREYIPSVEAGLKDAMENGVLAGYPLIDVKAKLYDGSYHDVDSSEMAFKIAASLALKEAAKKCDPVILEPMMKVTIEMPEEYMGDIMGDVTSRRGRVDGMEPRGNAQVVNAYVPLSEMFGYATSLRSNTQGRGTYTMYFDHYAEVPKSIAEDIIKKNKGE"},"dna_sequence":{"accession":"BX571856.1","fmin":"599702","fmax":"601784","strand":"+","sequence":"ATGGCTAGAGAATTTTCATTAGAAAAAACTCGTAATATCGGTATCATGGCTCACATTGATGCTGGTAAAACGACTACGACTGAACGTATTCTTTATTACACTGGCCGTATCCACAAAATTGGTGAAACACATGAAGGTGCTTCACAAATGGACTGGATGGAGCAAGAACAAGACCGTGGTATTACTATCACATCTGCTGCAACAACAGCAGCTTGGGAAGGTCACCGTGTAAACATTATCGATACACCTGGACACGTAGACTTCACTGTAGAAGTTGAACGTTCATTACGTGTACTTGACGGAGCAGTTACAGTACTTGATGCACAATCAGGTGTTGAACCTCAAACTGAAACAGTTTGGCGTCAGGCTACAACTTATGGTGTTCCACGTATCGTATTTGTAAACAAAATGGACAAATTAGGTGCTAACTTCGAATACTCTGTAAGTACATTACATGATCGTTTACAAGCTAACGCTGCTCCAATCCAATTACCAATTGGTGCGGAAGACGAATTCGAAGCAATCATTGACTTAGTTGAAATGAAATGTTTCAAATATACAAATGATTTAGGTACTGAAATTGAAGAAATTGAAATTCCTGAAGACCACTTAGATAGAGCTGAAGAAGCTCGTGCTAGCTTAATCGAAGCAGTTGCAGAAACTAGCGACGAATTAATGGAAAAATATCTTGGTGACGAAGAAATTTCAGTTTCTGAATTAAAAGAAGCTATCCGCCAAGCTACTACTAACGTAGAATTCTACCCAGTACTTTGTGGTACAGCTTTCAAAAACAAAGGTGTTCAATTAATGCTTGACGCTGTAATTGATTACTTACCTTCACCACTAGACGTTAAACCAATTATTGGTCACCGTGCTAGCAACCCTGAAGAAGAAGTAATCGCGAAAGCAGACGATTCAGCTGAATTCGCTGCATTAGCGTTCAAAGTTATGACTGACCCTTATGTTGGTAAATTAACATTCTTCCGTGTGTACTCAGGTACAATGACATCTGGTTCATACGTTAAGAACTCTACTAAAGGTAAACGTGAACGTGTAGGTCGTTTATTACAAATGCACGCTAACTCACGTCAAGAAATCGATACTGTATACTCTGGAGATATCGCTGCTGCGGTAGGTCTTAAAGATACAGGTACTGGTGATACTTTATGTGGTGAGAAAAATGACATTATCTTGGAATCAATGGAATTCCCAGAGCCAGTTATTCACTTATCAGTAGAGCCAAAATCTAAAGCTGACCAAGATAAAATGACTCAAGCTTTAGTTAAATTACAAGAAGAAGACCCAACATTCCATGCACACACTGACGAAGAAACTGGACAAGTTATCATCGGTGGTATGGGTGAGCTTCACTTAGACATCTTAGTAGACCGTATGAAGAAAGAATTCAACGTTGAATGTAACGTAGGTGCTCCAATGGTTTCATATCGTGAAACATTCAAATCATCTGCACAAGTTCAAGGTAAATTCTCTCGTCAATCTGGTGGTCGTGGTCAATACGGTGATGTTCACATTGAATTCACACCAAACGAAACAGGCGCAGGTTTCGAATTCGAAAACGCTATCGTTGGTGGTGTAGTTCCTCGTGAATACATTCCATCAGTAGAAGCTGGTCTTAAAGATGCTATGGAAAATGGTGTCTTAGCAGGTTATCCATTAATTGATGTTAAAGCTAAATTATATGATGGTTCATACCATGATGTCGATTCATCTGAAATGGCCTTCAAAATTGCTGCATCATTAGCACTTAAAGAAGCTGCTAAAAAATGTGATCCTGTAATCTTAGAACCAATGATGAAAGTAACTATTGAAATGCCTGAAGAGTACATGGGTGATATCATGGGTGACGTAACATCTCGTCGTGGACGTGTTGATGGTATGGAACCTCGTGGTAATGCACAAGTTGTTAATGCTTATGTACCACTTTCAGAAATGTTCGGTTATGCAACATCATTACGTTCAAACACTCAAGGTCGCGGTACTTACACTATGTACTTCGATCACTATGCTGAAGTTCCAAAATCAATCGCTGAAGATATTATCAAGAAAAATAAAGGTGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35517","NCBI_taxonomy_name":"Staphylococcus aureus subsp. aureus MRSA252","NCBI_taxonomy_id":"282458"}}}},"ARO_accession":"3003735","ARO_id":"40390","ARO_name":"Staphylococcus aureus fusA with mutation conferring resistance to fusidic acid","CARD_short_name":"Saur_fusA_FA","ARO_description":"The mutations to this gene are involved in altering the translation elongation factor G (EF-G) in association with the ribosome to prevent fusidic acid from binding EF-G and preventing translation.","ARO_category":{"40389":{"category_aro_accession":"3003734","category_aro_cvterm_id":"40389","category_aro_name":"antibiotic resistant fusA","category_aro_description":"Antibiotic resistant fusA is caused by mutations to the elongation factor G (EF-G) and confers resistance to fusidic acid.","category_aro_class_name":"AMR Gene Family"},"37139":{"category_aro_accession":"3000759","category_aro_cvterm_id":"37139","category_aro_name":"fusidic acid","category_aro_description":"Fusidic acid is the only commercially available fusidane, a group of steroid-like antibiotics. It is most active against Gram-positive bacteria, and acts by inhibiting elongation factor G to  block protein synthesis.","category_aro_class_name":"Antibiotic"},"45735":{"category_aro_accession":"3007153","category_aro_cvterm_id":"45735","category_aro_name":"fusidane antibiotic","category_aro_description":"A group of antibiotics possessing steroid rings or steroid-like structures.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2256":{"model_id":"2256","model_name":"Staphylococcus aureus fusE with mutation conferring resistance to fusidic acid","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"3414":"Q140L"},"Curated-R":{"3414":"Q140L"},"clinical":{"3414":"Q140L"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"4642":{"protein_sequence":{"accession":"ADL24064.1","sequence":"MSRVGKKIIDIPSDVTVTFDGNHVTVKGPKGELSRTLNERMTFKQEENTIEVVRPSDSKEDRTNHGTTRALLNNMVQGVSQGYVKVLELVGVGYRAQMQGKDLILNVGYSHPVEIKAEENITFSVEKNTVVKVEGISKEQVGALASNIRSVRPPEPYKGKGIRYQGEYVRRKEGKTGK"},"dna_sequence":{"accession":"CP002114.2","fmin":"2306994","fmax":"2307531","strand":"-","sequence":"ATGAGTCGTGTTGGTAAGAAAATTATTGACATCCCTAGTGACGTAACAGTAACTTTTGATGGAAATCATGTAACTGTTAAAGGTCCTAAAGGTGAATTATCAAGAACTTTAAATGAAAGAATGACATTCAAACAAGAAGAAAACACAATTGAAGTTGTAAGACCATCTGATTCTAAAGAAGATAGAACAAACCATGGTACAACTCGTGCTTTATTAAACAATATGGTACAAGGTGTTTCTCAAGGATACGTAAAAGTACTTGAACTTGTTGGTGTAGGTTACCGTGCTCAAATGCAAGGTAAAGACTTAATCCTTAACGTTGGTTATTCTCACCCAGTAGAAATTAAAGCTGAAGAAAACATTACTTTCTCAGTTGAGAAAAACACAGTCGTTAAAGTTGAAGGTATTTCAAAAGAACAAGTTGGAGCATTAGCATCTAACATCCGTTCAGTAAGACCTCCAGAGCCTTACAAAGGTAAAGGTATTCGTTACCAAGGTGAATACGTTCGCCGTAAAGAAGGTAAAACTGGTAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40393","NCBI_taxonomy_name":"Staphylococcus aureus subsp. aureus JKD6159","NCBI_taxonomy_id":"869816"}}}},"ARO_accession":"3003737","ARO_id":"40392","ARO_name":"Staphylococcus aureus fusE with mutation conferring resistance to fusidic acid","CARD_short_name":"Saur_fusE_FA","ARO_description":"The mutations to the rplF gene encoding riboprotein L6 have been shown to cause fusidic acid resistance, demonstrating a potential secondary site of action of the antibiotic that is blocked through these mutations. Several types of mutations have been identified that cause resistance, including SNPs, frameshift mutations and early stop codons.","ARO_category":{"40391":{"category_aro_accession":"3003736","category_aro_cvterm_id":"40391","category_aro_name":"antibiotic resistant fusE","category_aro_description":"Antibiotic resistant fusE is caused by mutations in a region of the rplF gene encoding riboprotein L6, and confers resistance to fusidic acid.","category_aro_class_name":"AMR Gene Family"},"37139":{"category_aro_accession":"3000759","category_aro_cvterm_id":"37139","category_aro_name":"fusidic acid","category_aro_description":"Fusidic acid is the only commercially available fusidane, a group of steroid-like antibiotics. It is most active against Gram-positive bacteria, and acts by inhibiting elongation factor G to  block protein synthesis.","category_aro_class_name":"Antibiotic"},"45735":{"category_aro_accession":"3007153","category_aro_cvterm_id":"45735","category_aro_name":"fusidane antibiotic","category_aro_description":"A group of antibiotics possessing steroid rings or steroid-like structures.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2272":{"model_id":"2272","model_name":"Enterococcus faecalis cls with mutation conferring resistance to daptomycin","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"3603":"H215R","3582":"R267H","3581":"R218Q"},"Curated-R":{"3603":"H215R","3582":"R267H","3581":"R218Q","18556":"R218Q","18557":"R218Q"},"experimental":{"3603":"H215R","3582":"R267H","3581":"R218Q"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"900"},"41342":{"param_type":"deletion mutation from peptide sequence","param_description":"A peptide sequence change between the translation initiation (start) and termination (stop) codon where, compared to a reference sequence, one or more amino acids are deleted and therefore are not present. These represent in-frame deletions which do not result in frameshift variants and may include multiple amino acids. Format is given by [wildtype AA][position]del for a single peptide deletion or [wildtype AA][position]_[wildtype AA][position]del for a deleted peptide range, e.g. K527del or Q517_N518del.","param_type_id":"41342","param_value":{"18556":"N74_Q76del","18557":"K61del"}}},"model_sequences":{"sequence":{"3537":{"protein_sequence":{"accession":"AEA93051.1","sequence":"MILSVLTVIYFINAIIAGITILLKPRDVAAIWAWLLVLIALPVFGFFLYLFFGRGLTDKKKFYLQQSDLRELENFQNFQEESFELYSQKMPTEEQQQFTDFFSSLNRMPLTKKNDVEIFTDGTEKFNALMADIKKAQHSIHIEYYAFVTDHIGTKILNLLEEKAAEGVEVRLLYDAFGSKGTKVHHLNELKKNGGFVQTFITSQKALLKFRLNYHDHRKIVVIDGKVGYIGGFNVADQYAGTTKKFGYWRDTHLRIQGPATSLLQMRFLMDWNVSSPEKNRVAYQLDYFFKLEALVPEANTSIQMIASGPNSDREQIKLAFIKLITSAKKRVWIQTPYLVPDDSVLAALKVAAASGVDVKIMIPDKPDHPFIYRATQYYGRLLMKENIEILIYNGGFLHAKTMIMDDEVCTVGSANQDIRSYKLNFEANAVLYDKKIIDQLEAIFLEDRKKCTTMTPEVVRDMSKWLIFKQQISRLFSPIL"},"dna_sequence":{"accession":"CP002621.1","fmin":"376485","fmax":"377931","strand":"+","sequence":"TTGATTCTTAGCGTCTTAACAGTTATTTATTTTATTAATGCAATTATTGCGGGAATTACCATTTTGTTAAAACCTCGAGATGTAGCAGCAATTTGGGCATGGCTACTCGTACTGATTGCTCTACCCGTTTTTGGTTTTTTCTTATATTTATTCTTTGGTCGCGGTTTAACCGACAAAAAGAAATTTTATTTGCAACAAAGTGATTTGCGGGAATTAGAGAATTTTCAGAATTTCCAAGAAGAAAGTTTTGAACTTTATAGTCAAAAGATGCCGACGGAGGAGCAACAACAGTTTACAGACTTTTTTTCCTCGTTAAATAGGATGCCTCTGACTAAGAAAAATGATGTTGAAATTTTTACGGATGGTACGGAAAAATTCAATGCGTTGATGGCGGATATAAAAAAAGCTCAGCACTCCATTCATATTGAATATTATGCCTTTGTAACGGATCATATCGGTACCAAAATTTTGAACTTATTAGAAGAAAAGGCGGCTGAAGGGGTTGAAGTGCGGTTGCTTTACGATGCCTTTGGCTCAAAGGGCACCAAGGTTCATCATTTGAATGAATTGAAAAAAAACGGTGGTTTTGTCCAAACGTTTATTACTTCTCAAAAAGCACTTTTGAAGTTTCGTTTGAATTATCATGATCACCGGAAAATTGTTGTTATTGACGGAAAAGTAGGCTACATTGGCGGCTTTAATGTTGCCGATCAATATGCCGGAACGACTAAAAAGTTTGGCTATTGGCGGGATACACATTTACGGATTCAAGGGCCAGCAACCTCATTACTGCAAATGCGTTTTTTAATGGATTGGAACGTCTCTTCCCCCGAGAAAAATCGTGTGGCGTATCAATTGGATTATTTCTTTAAACTTGAAGCATTGGTGCCAGAGGCAAATACATCCATTCAGATGATTGCCAGTGGTCCTAACAGTGACCGTGAACAAATTAAATTGGCCTTTATTAAATTGATTACTTCTGCCAAGAAAAGAGTCTGGATTCAAACGCCGTATTTAGTTCCTGATGATAGTGTCTTGGCTGCTTTAAAGGTTGCTGCGGCTTCAGGAGTAGATGTTAAAATTATGATTCCAGATAAGCCCGACCATCCGTTTATTTATCGAGCAACACAGTATTACGGCCGCTTATTGATGAAAGAAAATATTGAAATTTTAATTTATAACGGTGGTTTCTTACATGCGAAAACAATGATTATGGATGATGAAGTCTGCACAGTTGGTTCAGCCAATCAAGATATCCGAAGTTACAAATTAAACTTTGAAGCAAATGCTGTGTTATATGATAAAAAAATCATTGATCAATTAGAAGCAATTTTCTTAGAAGATCGAAAAAAATGTACAACAATGACTCCAGAAGTTGTTCGTGACATGTCAAAATGGTTGATTTTTAAACAACAAATTTCACGATTATTTTCACCAATTCTTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40433","NCBI_taxonomy_name":"Enterococcus faecalis OG1RF","NCBI_taxonomy_id":"474186"}}}},"ARO_accession":"3003760","ARO_id":"40417","ARO_name":"Enterococcus faecalis cls with mutation conferring resistance to daptomycin","CARD_short_name":"Efae_cls_DAP","ARO_description":"Cardiolipin synthase (cls) is an inner membrane protein involved in membrane synthesis and phosopholipid metabolism, with mutations to the gene being capable of conferring daptomycin resistance.","ARO_category":{"39856":{"category_aro_accession":"3003272","category_aro_cvterm_id":"39856","category_aro_name":"daptomycin resistant cls","category_aro_description":"Cardiolipin synthetase catalyzes the formation of cardiolipin from two phosphatidylglycerol molecules. Cardiolipin is important in membrane translocation and permeabilization. Current known mutations on the enzyme confer resistance to daptomycin.","category_aro_class_name":"AMR Gene Family"},"35985":{"category_aro_accession":"0000068","category_aro_cvterm_id":"35985","category_aro_name":"daptomycin","category_aro_description":"Daptomycin is a novel lipopeptide antibiotic used in the treatment of certain infections caused by Gram-positive organisms. Daptomycin interferes with the bacterial cell membrane, reducing membrane potential and inhibiting cell wall synthesis.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2271":{"model_id":"2271","model_name":"Staphylococcus aureus mupB conferring resistance to mupirocin","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"2000"}},"model_sequences":{"sequence":{"3524":{"protein_sequence":{"accession":"AEY83581.1","sequence":"MENENIIEEQKILNFWKEENIFKKSIDNRKNDNPFVFYDGPPTANGLPHTGHVLGRVIKDLFARYKTMQGFYVERKAGWDTHGLPVELGVEKKLGIKDKNEIEKYGIEKFINECKNSVFMYEKQWREFSELIGYWVDMEKPYKTMDNTYIESIWYILSDFHKKGLLYKGHKVTPYCPSCETSLSSHEVAQGYKEVKDISVILKFPILDSDENFLVWTTTPWSLPGNIALAINAEEIYVKVNYDNEIFIIMESLLQSVFKDEDNIDIVSKHKGKEFVGKEYLAPFPNKSLMNNENSYKVLPADFVTNKDGTGIVHIAPAYGEDDYKLVQENNIPFINVIDSRGKYNQDSPIFKGELAKESDINIIKELTHLNLLFKKEKYEHSYPFCWRCDNPLIYYAMEGWFIKTTAYKNEIKENNQKIEWYPDHIKNGRFGNFLDNMIDWNIGRKRYWGTPLNIWKCSTCSHEFSPKSINDLIQHSIEDIPSDIELHRPYIDNVKCKCQNCGGDMCREEEVIDVWFDSGSMPFAQNHYPFSGPIQNSYPADFIAEGVDQTRGWFYSLLVISTIFKGEAPYKNALSLGHILDSNGQKMSKSKGNVIDPISMIKTYGADSLRWTLVSDSVPWTNKRFSENMVAQSKSRVIDTLKNIFNFYNMYQKIDNYDYTRDTPKQLNLLDNWAISRMNSVIKEVELHLEKYNPTNASRAIGEFINEISNWYIRRSRSRFWSSEMNEDKKSAYFTLRLILINTCKIIAPFTPFTSEEIHLNLTKKSVHLEDFPQAKEEYINLKLEEDMNKVLDIVEKSRSIRNNINIKTKQPLSNMYIYDNNNLDNEFLRKYKDIIKDEINVKKINIVSDLDNFLEYDVKPNFSTLGPKLGKDMKQFQILFKNIKKEEMNKLINDFDKLQKVFDSLGVTIEEKDFIISKIPKKGFSLSSNDSDRLIILDTNLTQELIREGFVRELIRVIQQLRKQQNFNIEERINVVIDIDSDGLLSIKNNINILKENVLINNLKFEKRETMKYFKINQKEIGIQLMSSFTN"},"dna_sequence":{"accession":"JQ231224.1","fmin":"90","fmax":"3192","strand":"+","sequence":"TTGGAAAACGAGAATATAATAGAAGAACAAAAAATCTTAAATTTTTGGAAAGAAGAAAACATTTTCAAAAAGAGTATTGATAATAGAAAAAATGATAATCCATTTGTTTTTTACGATGGTCCTCCAACTGCCAATGGCTTACCACATACAGGTCACGTGTTAGGAAGAGTAATAAAAGATTTATTTGCTCGATATAAGACAATGCAAGGATTTTATGTTGAAAGAAAAGCTGGGTGGGATACCCATGGACTACCTGTAGAACTTGGTGTTGAAAAAAAACTTGGAATTAAGGATAAAAATGAAATAGAAAAATATGGAATAGAAAAATTTATAAATGAATGTAAAAATAGTGTGTTTATGTATGAAAAACAGTGGAGAGAATTTAGTGAACTAATCGGATATTGGGTAGATATGGAAAAACCGTACAAAACAATGGATAATACGTATATAGAATCAATCTGGTATATATTGTCTGACTTTCATAAAAAAGGTCTTTTATACAAAGGGCATAAAGTTACCCCGTATTGTCCAAGCTGTGAAACTTCTTTAAGTTCTCATGAAGTAGCTCAGGGATATAAGGAAGTAAAAGATATCTCTGTAATCTTAAAATTTCCGATTTTAGACAGTGATGAGAATTTCTTAGTTTGGACGACAACTCCATGGAGCTTACCAGGTAATATAGCTTTAGCCATAAATGCTGAAGAAATATATGTTAAAGTTAATTATGATAATGAAATTTTTATTATCATGGAAAGTTTGTTGCAAAGTGTTTTTAAAGATGAAGACAATATAGATATAGTAAGTAAACATAAAGGAAAAGAATTTGTAGGAAAAGAATACCTCGCTCCTTTCCCTAACAAGTCTCTTATGAACAATGAAAACTCATATAAAGTTTTACCTGCTGATTTTGTTACAAATAAAGATGGTACGGGTATCGTCCATATTGCTCCGGCTTATGGGGAAGATGATTACAAATTAGTTCAAGAAAATAATATACCCTTTATTAATGTTATTGATTCTAGAGGAAAATATAATCAAGATTCTCCTATTTTTAAAGGAGAGCTAGCTAAAGAATCAGATATTAACATTATTAAAGAACTTACACATTTAAATCTACTTTTCAAAAAAGAAAAATATGAACATAGCTATCCTTTTTGTTGGAGATGTGATAATCCATTAATCTATTATGCAATGGAAGGTTGGTTTATAAAAACAACGGCTTATAAAAATGAAATAAAGGAAAACAATCAAAAAATAGAATGGTATCCAGACCATATTAAAAATGGAAGGTTTGGAAATTTCTTAGATAATATGATTGATTGGAATATTGGTAGAAAAAGATATTGGGGCACTCCACTAAATATATGGAAATGCTCCACGTGTTCCCATGAGTTTTCACCTAAAAGCATAAATGATCTAATACAACATTCCATTGAAGATATTCCTTCTGATATAGAATTACATCGACCTTATATAGATAATGTGAAATGTAAATGTCAAAATTGTGGTGGTGACATGTGTAGAGAAGAAGAAGTCATTGATGTATGGTTTGATAGTGGATCGATGCCTTTTGCACAAAATCACTATCCATTTAGTGGTCCCATTCAAAACTCATACCCAGCTGACTTTATAGCTGAAGGAGTTGATCAAACTAGAGGGTGGTTTTATAGCTTATTGGTGATTTCAACAATTTTCAAAGGGGAAGCACCTTATAAAAACGCATTGTCATTAGGACATATATTAGATTCCAATGGACAAAAAATGTCGAAAAGTAAAGGGAATGTTATAGATCCTATATCAATGATAAAAACTTATGGCGCTGATTCTTTAAGATGGACATTAGTTTCTGACAGCGTTCCTTGGACTAACAAAAGGTTTTCAGAAAATATGGTGGCACAATCAAAATCGAGAGTAATTGATACTTTAAAAAATATATTTAACTTCTATAATATGTATCAAAAAATTGATAATTATGACTATACTAGGGATACTCCTAAACAGCTGAATTTACTTGATAATTGGGCTATATCTCGAATGAATTCAGTTATAAAAGAGGTAGAGCTGCATTTAGAAAAATATAACCCTACAAATGCATCAAGAGCTATTGGGGAGTTTATCAATGAAATAAGTAATTGGTATATTAGAAGATCTAGAAGTCGATTTTGGAGTAGTGAAATGAATGAGGATAAAAAGAGTGCGTATTTTACTCTTAGACTTATTTTGATTAATACTTGTAAAATAATAGCTCCTTTCACCCCATTTACTAGCGAGGAAATACATCTAAATCTCACCAAAAAAAGTGTACACTTAGAAGATTTCCCTCAAGCCAAGGAAGAATATATAAATTTAAAACTAGAAGAAGATATGAATAAAGTTTTAGATATTGTCGAAAAATCTAGAAGCATAAGAAATAACATAAACATCAAAACAAAACAACCACTTTCAAACATGTATATATATGACAATAATAATCTTGATAATGAATTTCTAAGAAAATACAAAGACATCATTAAAGATGAAATAAATGTTAAAAAGATAAATATTGTTTCTGATTTAGACAATTTTTTAGAATATGATGTAAAACCGAACTTTTCAACTTTAGGCCCTAAATTAGGAAAAGATATGAAACAATTCCAAATTTTATTTAAAAATATTAAAAAAGAAGAAATGAATAAACTAATCAATGATTTCGATAAACTTCAAAAAGTTTTTGACTCTTTAGGTGTAACAATTGAGGAAAAGGATTTTATTATTAGTAAAATACCTAAAAAGGGATTCTCTCTTTCAAGCAATGACTCTGATCGTCTTATCATTTTAGACACTAATTTGACTCAAGAATTAATTCGCGAAGGGTTTGTCAGAGAATTAATTCGTGTTATTCAACAACTAAGAAAACAACAGAACTTTAATATTGAAGAACGTATAAATGTAGTAATAGACATAGATTCCGATGGTTTACTATCAATTAAAAATAATATCAATATATTGAAAGAAAATGTACTAATTAATAATCTAAAATTTGAGAAAAGAGAAACTATGAAATATTTTAAAATTAATCAGAAAGAAATTGGTATTCAGTTAATGTCTAGCTTTACAAATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35508","NCBI_taxonomy_name":"Staphylococcus aureus","NCBI_taxonomy_id":"1280"}}}},"ARO_accession":"3000510","ARO_id":"36649","ARO_name":"Staphylococcus aureus mupB conferring resistance to mupirocin","CARD_short_name":"Saur_mupB_MUP","ARO_description":"An alternative isoleucyl-tRNA synthetase conferring resistance to mupirocin.","ARO_category":{"36585":{"category_aro_accession":"3000446","category_aro_cvterm_id":"36585","category_aro_name":"antibiotic-resistant isoleucyl-tRNA synthetase (ileS)","category_aro_description":"Mupirocin inhibits protein synthesis by interfering with isoleucyl-tRNA synthetase (ileS).  Mutations in ileS can confer low-level mupirocin resistance.","category_aro_class_name":"AMR Gene Family"},"36693":{"category_aro_accession":"3000554","category_aro_cvterm_id":"36693","category_aro_name":"mupirocin","category_aro_description":"Mupirocin, also known as pseudomonic acid, is a bacteriostatic polyketide antibiotic from Pseudomonas fluorescens used to treat S. aureus and MRSA. It inhibits Ile tRNA synthetase.","category_aro_class_name":"Antibiotic"},"45733":{"category_aro_accession":"3007151","category_aro_cvterm_id":"45733","category_aro_name":"mupirocin-like antibiotic","category_aro_description":"A group of antibiotics including mupirocin and similar mixtures (such as those including pseudomonic acid A).","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2270":{"model_id":"2270","model_name":"Staphylococcus aureus mupA conferring resistance to mupirocin","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"2000"}},"model_sequences":{"sequence":{"3523":{"protein_sequence":{"accession":"CAA53189.1","sequence":"MTKKYLNTQNEISAFWNTQKIFKKSIDNRKGQESFVFYDGPPTANGLPHAGHVLGRVIKDLVARLKTMQGFYVERKAGWDTHGLPVELEVEKKIGIKGKQDIEKYGIENFINECKKSVFNYEKEWRDFSKDLGYWVDMDSPYITLENNYIESVWNILSTFHKKGLLYKGHKVTPYCTHDQTALSSHEVAQGYKNVKDLSAVVKFQLTNSKDTYFLSWTTTPWTLPANVALAINKDLNYSKIRVENEYYILATDLINSIITEKYEIIDTFSGSNLINLKYIPPFESDGLVNAYYVVDGEFVTNSEGTGIVHIAPAHGEDDYQLVLERDLDFLNVITREGVYNDRFPELVGNKAKNSDIEIIKLLSKKQLLYKKQKYEHNYPHCWRCGNPLIYYAMEGWFIKTTNFKNEIINNNNNIEWFPSHIKEGRMGNFLENMVDWNIGRNRYWGTPLNVWICNDCNHEYAPSSIKDLQNNSINKIDEDIELHRPYVDNITLSCPKCNGKMSRVEEVIDVWFDSGSMPFAQHHYPFDNQKIFNQHFPADFIAEGVDQTRGWFYSLLVISTILKGKSSYKRALSLGHILDSNGKKMSKSKGNVINPTELINKYGADSLRWALISDSAPWNNKRFSENIVAQTKSKFIDTLDNIYKFYNMYNKIDHYNPNNEITKSRNTLDNWALSRLNTLIKESNIYVNNYDFTSAARLINEYTNTISNWYIGDSRGRFWEQGISNDKKDAYNTLYEILTTLSRLVAPFVPFISEKIHYNLTGKSVHLQDYPQYKESFINQALEDEMHTVIKIVELSRQARKNADLKIKQPLSKMVIKPNSQLNLSFLPNYYSIIKDELNIKNIELTDNINDYITYELKLNFSSVGPKLGNKTKNIQTLIDSLSEYDKKSLIESNNFKSLSSDAELTKDDFIIKTLPKDSYQLSEDNDCVILLDKNLSPELIREGHARELIRLIQQLRKKKNLPINQRIDIYIGVTGELLESIKTNKNMFKENFVIKNIHLNVIDEYENTIHFNNKEIKISLLY"},"dna_sequence":{"accession":"X75439.1","fmin":"476","fmax":"3551","strand":"+","sequence":"TTGACAAAGAAATATTTAAACACCCAGAATGAAATATCAGCATTTTGGAATACTCAAAAGATATTTAAAAAATCAATTGACAATAGAAAAGGACAGGAAAGTTTTGTTTTTTATGACGGCCCCCCAACTGCAAATGGCCTTCCTCATGCTGGCCATGTTCTTGGAAGAGTAATCAAGGATTTAGTTGCAAGATTAAAAACTATGCAAGGTTTTTATGTAGAAAGAAAAGCAGGATGGGATACCCATGGCTTACCAGTTGAATTAGAGGTTGAAAAAAAAATTGGAATTAAAGGAAAACAAGACATTGAAAAGTATGGAATAGAAAATTTTATAAATGAATGTAAAAAAAGTGTATTTAATTATGAAAAAGAATGGCGGGATTTTTCTAAAGATTTAGGATACTGGGTTGACATGGACTCCCCCTATATAACTCTTGAGAATAATTATATTGAAAGTGTATGGAATATATTATCTACATTCCATAAAAAAGGACTATTATATAAGGGACATAAGGTGACTCCTTATTGTACACATGATCAAACCGCTTTAAGTTCTCATGAAGTAGCGCAAGGCTATAAAAACGTTAAAGATTTATCAGCTGTTGTTAAATTTCAACTTACAAATAGTAAAGATACTTATTTCTTAAGTTGGACTACCACTCCCTGGACTTTGCCTGCAAATGTAGCATTAGCTATAAATAAAGATCTTAATTATTCAAAAATTCGGGTAGAAAATGAGTATTATATCTTAGCTACAGATCTAATTAATTCTATAATAACTGAAAAATACGAAATTATTGATACCTTTTCAGGAAGTAATTTAATTAATTTAAAATACATTCCTCCTTTTGAAAGCGACGGTTTAGTTAATGCATATTACGTTGTTGATGGAGAATTTGTTACTAACTCAGAAGGAACTGGTATTGTTCATATAGCACCAGCTCATGGGGAAGATGACTACCAATTGGTTTTAGAGCGTGATTTGGATTTCTTAAATGTTATAACAAGAGAAGGAGTATATAATGATAGGTTCCCTGAATTAGTTGGTAATAAAGCTAAAAATAGTGATATAGAAATCATAAAATTATTATCCAAAAAACAACTTTTATATAAAAAACAAAAATATGAGCATAATTATCCTCATTGTTGGAGATGTGGTAATCCTTTGATATATTATGCGATGGAAGGTTGGTTTATTAAAACAACTAATTTTAAGAATGAAATTATTAACAATAATAATAATATAGAGTGGTTTCCTTCTCATATTAAGGAAGGGAGAATGGGAAATTTCTTAGAAAATATGGTTGATTGGAACATTGGTAGAAATAGATATTGGGGAACACCATTAAATGTATGGATTTGCAATGATTGTAATCACGAATACGCACCAAGTAGTATTAAGGATTTACAAAATAATTCCATCAATAAAATTGATGAAGATATTGAGTTGCATAGACCTTATGTTGATAATATCACTCTTAGTTGCCCTAAGTGTAATGGGAAAATGTCTCGAGTAGAAGAAGTAATCGATGTTTGGTTTGATAGCGGCTCTATGCCGTTTGCTCAGCATCATTATCCTTTTGATAACCAGAAAATTTTTAATCAACACTTTCCAGCTGATTTTATTGCAGAAGGAGTTGATCAAACGAGAGGCTGGTTTTACAGTTTACTAGTAATTTCTACTATTCTAAAAGGAAAATCTTCTTATAAACGTGCTTTATCTTTAGGACATATTCTAGACAGTAATGGTAAAAAAATGTCTAAAAGTAAAGGAAACGTTATTAATCCAACTGAATTAATTAATAAGTACGGAGCCGATTCTTTAAGATGGGCCTTAATTTCGGATAGTGCTCCATGGAATAACAAAAGATTCTCAGAAAATATAGTAGCTCAGACCAAATCGAAATTTATAGATACGCTTGATAATATTTATAAATTTTATAATATGTATAATAAAATAGATCACTATAATCCTAATAATGAAATTACAAAAAGTAGAAATACATTAGATAATTGGGCTCTTTCTCGCTTAAACACCTTAATAAAAGAAAGTAATATTTATGTAAATAATTACGATTTCACTTCCGCAGCCAGATTAATTAACGAATATACCAATACAATAAGTAATTGGTATATCGGAGATTCGAGAGGACGATTTTGGGAACAAGGAATTTCTAACGATAAAAAAGATGCGTACAATACGCTTTATGAAATTTTAACAACTTTATCAAGACTAGTGGCTCCATTTGTTCCATTTATATCTGAAAAAATCCATTATAATTTGACTGGAAAAAGTGTGCATTTACAAGATTATCCACAATATAAAGAAAGTTTTATTAATCAAGCATTGGAAGATGAAATGCATACCGTTATAAAAATTGTAGAATTATCTAGACAGGCTCGCAAAAATGCAGATTTAAAAATTAAGCAACCTTTATCGAAAATGGTGATTAAACCTAATAGTCAATTAAACTTAAGTTTTTTACCTAATTACTATTCAATAATAAAAGACGAATTAAATATAAAAAACATTGAATTAACTGATAATATTAATGACTATATTACCTATGAGCTTAAATTGAATTTTTCTTCTGTGGGACCAAAACTAGGGAACAAAACGAAAAATATTCAAACATTGATAGACTCCCTATCAGAGTATGATAAAAAAAGTTTAATTGAGTCTAATAACTTCAAAAGTTTATCTTCTGATGCTGAGTTAACTAAGGATGATTTTATAATTAAAACCTTACCTAAGGATAGTTATCAACTCAGTGAAGATAATGACTGCGTTATATTATTAGATAAAAATTTATCTCCTGAATTAATTCGCGAAGGACATGCTAGAGAGCTCATTAGATTAATTCAACAATTAAGAAAAAAGAAAAATTTACCAATAAATCAACGTATTGATATTTATATCGGTGTAACTGGGGAATTATTAGAATCAATAAAAACCAATAAAAATATGTTTAAAGAAAATTTCGTGATTAAAAATATACACTTAAATGTTATAGATGAATATGAAAATACTATTCATTTTAATAATAAAGAAATAAAAATTTCCTTATTATATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35508","NCBI_taxonomy_name":"Staphylococcus aureus","NCBI_taxonomy_id":"1280"}}}},"ARO_accession":"3000521","ARO_id":"36660","ARO_name":"Staphylococcus aureus mupA conferring resistance to mupirocin","CARD_short_name":"Saur_mupA_MUP","ARO_description":"An alternative isoleucyl-tRNA synthetase conferring resistance to mupirocin.","ARO_category":{"36585":{"category_aro_accession":"3000446","category_aro_cvterm_id":"36585","category_aro_name":"antibiotic-resistant isoleucyl-tRNA synthetase (ileS)","category_aro_description":"Mupirocin inhibits protein synthesis by interfering with isoleucyl-tRNA synthetase (ileS).  Mutations in ileS can confer low-level mupirocin resistance.","category_aro_class_name":"AMR Gene Family"},"36693":{"category_aro_accession":"3000554","category_aro_cvterm_id":"36693","category_aro_name":"mupirocin","category_aro_description":"Mupirocin, also known as pseudomonic acid, is a bacteriostatic polyketide antibiotic from Pseudomonas fluorescens used to treat S. aureus and MRSA. It inhibits Ile tRNA synthetase.","category_aro_class_name":"Antibiotic"},"45733":{"category_aro_accession":"3007151","category_aro_cvterm_id":"45733","category_aro_name":"mupirocin-like antibiotic","category_aro_description":"A group of antibiotics including mupirocin and similar mixtures (such as those including pseudomonic acid A).","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2080":{"model_id":"2080","model_name":"Escherichia coli 16S rRNA (rrsH) mutation conferring resistance to spectinomycin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"4818":"c1192t"},"Curated-R":{"4818":"c1192t"},"clinical":{"4818":"c1192t"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"41093","param_value":"2700"}},"model_sequences":{"sequence":{"3228":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"U00096.1","fmin":"223770","fmax":"225312","strand":"+","sequence":"AAATTGAAGAGTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAACGGTAACAGGAAGAAGCTTGCTTCTTTGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCGGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGGAGTAAAGTTAATACCTTTGCTCATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACGAAGACTGACGCTCAGGTGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGTCGACTTGGAGGTTGTGCCCTTGAGGCGTGGCTTCCGGAGCTAACGCGTTAAGTCGACCGCCTGGGGAGTACGGCCGCAAGGTTAAAACTCAAATGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGATGCAACGCGAAGAACCTTACCTGGTCTTGACATCCACAGAACTTTCCAGAGATGGATTGGTGCCTTCGGGAACTGTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGAAATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCTTTTGTTGCCAGCGGTCCGGCCGGGAACTCAAAGGAGACTGCCAGTGATAAACTGGAGGAAGGTGGGGATGACGTCAAGTCATCATGGCCCTTACGACCAGGGCTACACACGTGCTACAATGGCGCATACAAAGAGAAGCGACCTCGCGAGAGCAAGCGGACCTCATAAAGTGCGTCGTAGTCCGGATTGGAGTCTGCAACTCGACTCCATGAAGTCGGAATCGCTAGTAATCGTGGATCAGAATGCCACGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACACCATGGGAGTGGGTTGCAAAAGAAGTAGGTAGCTTAACCTTCGGGAGGGCGCTTACCACTTTGTGATTCATGACTGGGGTGAAGTCGTAACAAGGTAACCGTAGGGGAACCTGCGGTTGGATCACCTCCTTA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36905","NCBI_taxonomy_name":"Escherichia coli str. K-12","NCBI_taxonomy_id":"83333"}}}},"ARO_accession":"3003372","ARO_id":"39956","ARO_name":"Escherichia coli 16S rRNA (rrsH) mutation conferring resistance to spectinomycin","CARD_short_name":"Ecol_16rrsH_SPT","ARO_description":"Point mutations in the 3' major domain of the rrsH 16S rRNA gene of Escherichia coli can confer resistance to spectinomycin.","ARO_category":{"40277":{"category_aro_accession":"3003666","category_aro_cvterm_id":"40277","category_aro_name":"16s rRNA with mutation conferring resistance to aminoglycoside antibiotics","category_aro_description":"Point mutations in the 16S rRNA of bacteria can confer resistance to aminoglycosides.","category_aro_class_name":"AMR Gene Family"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2300":{"model_id":"2300","model_name":"Acinetobacter baumannii ampC beta-lactamase","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"3566":{"protein_sequence":{"accession":"ACJ42146.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNRSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWQPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGFYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"CP001182.1","fmin":"2873299","fmax":"2874451","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATCGCAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGCAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTGGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCATTTGGTTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCTGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTTAACCCACAGAAATATCCGGCTGATATTCAACGGGCAATTAATGAAACACATCAAGGGTTCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACATATGTAGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35531","NCBI_taxonomy_name":"Acinetobacter baumannii AB0057","NCBI_taxonomy_id":"480119"}}}},"ARO_accession":"3003796","ARO_id":"40481","ARO_name":"Acinetobacter baumannii ampC beta-lactamase","CARD_short_name":"Abau_ampC_BLA","ARO_description":"A class C beta-lactamase found in Acinetobacter baumannii that confers resistance to piperacillin and cefepime.","ARO_category":{"41396":{"category_aro_accession":"3004232","category_aro_cvterm_id":"41396","category_aro_name":"ampC-type beta-lactamase","category_aro_description":"AmpC beta-lactamases are clinically important class C beta-lactamase enzymes which confer resistance to cephalosporins and penicillin-like antibiotics. AmpC beta-lactamases are typically found in Enterobacteriaceae, and were described in Escherichia coli in 1940 as the first reported enzymatic deactivation of penicillin. The name AmpC connects these enzymes functionally across many species, however these enzymes are generally unnamed and not phylogenetically related.","category_aro_class_name":"AMR Gene Family"},"35976":{"category_aro_accession":"0000059","category_aro_cvterm_id":"35976","category_aro_name":"cefepime","category_aro_description":"Cefepime (INN) is a fourth-generation cephalosporin antibiotic developed in 1994. It contains an aminothiazolyl group that decreases its affinity with beta-lactamases. Cefepime shows high binding affinity with penicillin-binding proteins and has an extended spectrum of activity against Gram-positive and Gram-negative bacteria, with greater activity against both Gram-negative and Gram-positive organisms than third-generation agents.","category_aro_class_name":"Antibiotic"},"35995":{"category_aro_accession":"0000078","category_aro_cvterm_id":"35995","category_aro_name":"piperacillin","category_aro_description":"Piperacillin is an acetylureidopenicillin and has an extended spectrum of targets relative to other beta-lactam antibiotics. It inhibits cell wall synthesis in bacteria, and is usually taken with the beta-lactamase inhibitor tazobactam to overcome penicillin-resistant bacteria.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2304":{"model_id":"2304","model_name":"Staphylococcus aureus agrA with mutation conferring resistance to daptomycin","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"40394":{"param_type":"nonsense mutation","param_description":"A sequence change where, compared to a reference sequence, one codon is replaced by a termination codon through a nucleotide substitution. These are described as a substitution of the wildtype codon to a termination codon. Format is given as [wild type AA][position][Ter], for example Q42Ter where Q42 is a wildtype amino acid replaced by a premature termination codon.","param_type_id":"40394","param_value":{"3885":"Y100Ter"}},"snp":{"Curated-R":{"3885":"c1192t"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"3571":{"protein_sequence":{"accession":"CAG41107.1","sequence":"MKIFICEDDPKQRENMVTIIKNYIMIEEKPMEIALATDNPYEVLEQAKNMNDIGCYFLDIQLSTDINGIKLGSEIRKHDPVGNIIFVTSHSELTYLTFVYKVAAMDFIFKDDPAELRTRIIDCLETAHTRLQLLSKDNSVETIELKRGSNSVYVQYDDIMFFESSTKSHRLIAHLDNRQIEFYGNLKELSQLDDRFFRCHNSFVVNRHNIESIDSKERIVYFKNKEHCYASVRNVKKI"},"dna_sequence":{"accession":"BX571856.1","fmin":"2186109","fmax":"2186826","strand":"+","sequence":"ATGAAAATTTTCATTTGCGAAGACGATCCAAAACAAAGAGAAAACATGGTTACCATTATCAAAAATTATATAATGATAGAAGAAAAGCCTATGGAAATTGCCCTCGCAACTGATAATCCTTATGAGGTGCTTGAGCAAGCTAAAAATATGAATGACATAGGCTGTTACTTTTTAGATATTCAACTTTCAACTGATATTAATGGTATCAAATTAGGCAGTGAAATTCGTAAGCATGACCCAGTTGGTAACATTATTTTCGTTACGAGTCACAGTGAACTTACGTATTTAACATTTGTCTACAAAGTTGCAGCGATGGATTTTATTTTTAAAGATGATCCAGCAGAATTAAGAACTCGAATTATAGATTGTTTAGAAACTGCACATACACGCTTACAATTATTATCAAAAGATAATAGCGTTGAAACGATTGAGTTAAAACGTGGCAGTAATTCAGTGTATGTTCAATATGATGATATTATGTTTTTTGAATCATCAACAAAATCTCACAGACTCATTGCCCATTTAGATAACCGTCAAATTGAATTTTATGGTAATTTAAAAGAACTGAGTCAATTAGATGATCGTTTCTTCAGATGTCATAATAGCTTTGTCGTCAATCGTCATAATATCGAATCTATTGATTCGAAAGAGCGTATTGTTTATTTTAAAAATAAAGAACACTGCTATGCATCGGTGAGAAACGTTAAAAAAATATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35517","NCBI_taxonomy_name":"Staphylococcus aureus subsp. aureus MRSA252","NCBI_taxonomy_id":"282458"}}}},"ARO_accession":"3003803","ARO_id":"40488","ARO_name":"Staphylococcus aureus agrA with mutation conferring resistance to daptomycin","CARD_short_name":"Saur_agrA_DAP","ARO_description":"agrA is an autoinducer in a peptide-quorum two-component regulatory system whose mutations confer daptomycin resistance.","ARO_category":{"40489":{"category_aro_accession":"3003804","category_aro_cvterm_id":"40489","category_aro_name":"daptomycin resistant agrA","category_aro_description":"Mutations to the regulatory gene agrA confer daptomycin resistance.","category_aro_class_name":"AMR Gene Family"},"35985":{"category_aro_accession":"0000068","category_aro_cvterm_id":"35985","category_aro_name":"daptomycin","category_aro_description":"Daptomycin is a novel lipopeptide antibiotic used in the treatment of certain infections caused by Gram-positive organisms. Daptomycin interferes with the bacterial cell membrane, reducing membrane potential and inhibiting cell wall synthesis.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3330":{"model_id":"3330","model_name":"Mycoplasma genitalium gyrA mutation confers resistance to fluoroquinolones","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"8782":"M95I","8789":"G93C"},"Curated-R":{"8782":"M95I","8789":"G93C"},"clinical":{"8782":"M95I","8789":"G93C"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1400"}},"model_sequences":{"sequence":{"5402":{"protein_sequence":{"accession":"AAC71220.1","sequence":"MAKQQDQVDKIRENLDNSTVKSISLANELERSFMEYAMSVIVARALPDARDGLKPVHRRVLYGAYIGGMHHDRPFKKSARIVGDVMSKFHPHGDMAIYDTMSRMAQDFSLRYLLIDGHGNFGSIDGDRPAAQRYTEARLSKLAAELLKDIDKDTVDFIANYDGEEKEPTVLPAAFPNLLANGSSGIAVGMSTSIPSHNLSELIAGLIMLIDNPQCTFQELLTVIKGPDFPTGANIIYTKGIESYFETGKGNVVIRSKVEIEQLQTRSALVVTEIPYMVNKTTLIEKIVELVKAEEISGIADIRDESSREGIRLVIEVKRDTVPEVLLNQLFKSTRLQVRFPVNMLALVKGAPVLLNMKQALEVYLDHQIDVLVRKTKFVLNKQQERYHILSGLLIAALNIDEVVAIIKKSANNQEAINTLNTKFKLDEIQAKAVLDMRLRSLSVLEVNKLQTEQKELKDSIEFCKKVLADQKLQLKIIKEELQKINDQFGDERRSEILYDISEEIDDESLIKVENVVITMSTNGYLKRIGVDAYNLQHRGGVGVKGLTTYVDDSISQLLVCSTHSDLLFFTDKGKVYRIRAHQIPYGFRTNKGIPAVNLIKIEKDERICSLLSVNNYDDGYFFFCTKNGIVKRTSLNEFINILSNGKRAISFDDNDTLYSVIKTHGNDEIFIGSTNGFVVRFHENQLRVLSRTARGVFGISLNKGEFVNGLSTSSNGSLLLSVGQNGIGKLTSIDKYRLTKRNAKGVKTLRVTDRTGPVVTTTTVFGNEDLLMISSAGKIVRTSLQELSEQGKNTSGVKLIRLKDNERLERVTIFKEELEDKEMQLEDVGSKQITQ"},"dna_sequence":{"accession":"L43967.2","fmin":"4811","fmax":"7322","strand":"+","sequence":"ATGGCAAAGCAACAAGATCAAGTAGATAAGATTCGTGAAAACTTAGACAATTCAACTGTCAAAAGTATTTCATTAGCAAATGAACTTGAGCGTTCATTCATGGAATATGCTATGTCAGTTATTGTTGCTCGTGCTTTACCTGATGCTAGAGATGGACTTAAACCAGTTCATCGTCGTGTTCTTTATGGTGCTTATATTGGTGGCATGCACCATGATCGTCCTTTTAAAAAGTCTGCGAGGATTGTTGGTGATGTAATGAGTAAATTCCACCCTCATGGTGATATGGCAATATATGACACCATGTCAAGAATGGCTCAAGACTTTTCATTAAGATACCTTTTAATTGATGGTCATGGTAATTTTGGTTCTATAGATGGTGATAGACCTGCTGCACAACGTTATACAGAAGCAAGATTATCTAAACTTGCAGCAGAACTTTTAAAAGATATTGATAAAGATACAGTTGACTTTATTGCTAATTATGATGGTGAGGAAAAAGAACCAACTGTTCTACCAGCAGCTTTCCCTAACTTACTTGCAAATGGTTCTAGTGGGATTGCAGTTGGAATGTCAACATCTATTCCTTCCCATAATCTCTCTGAATTAATTGCGGGTTTAATCATGTTAATTGATAATCCTCAATGCACTTTTCAAGAATTATTAACTGTAATTAAAGGACCTGATTTTCCAACAGGAGCTAACATTATCTACACAAAAGGAATTGAAAGCTACTTTGAAACAGGTAAAGGCAATGTAGTAATTCGTTCTAAAGTTGAGATAGAACAATTGCAAACAAGAAGTGCATTAGTTGTAACTGAAATTCCTTACATGGTTAACAAAACTACCTTAATTGAAAAGATTGTAGAACTTGTTAAAGCTGAAGAGATTTCAGGAATTGCTGATATCCGTGATGAATCCTCTCGAGAAGGAATAAGGTTAGTGATTGAAGTAAAACGCGACACTGTACCTGAAGTTTTATTAAATCAACTTTTTAAATCAACAAGATTACAAGTACGCTTCCCTGTTAATATGCTTGCTTTAGTTAAAGGAGCTCCTGTACTTCTCAACATGAAACAAGCTTTGGAAGTATATCTTGATCATCAAATTGATGTTCTTGTTAGAAAAACAAAGTTTGTGCTTAATAAACAACAAGAACGTTATCACATTTTAAGCGGACTTTTAATTGCTGCTTTAAATATTGATGAGGTTGTTGCAATTATTAAAAAATCAGCAAATAACCAGGAAGCAATTAATACATTAAATACAAAGTTTAAGCTTGATGAAATTCAAGCTAAAGCAGTTCTTGACATGCGTTTAAGGAGCTTAAGCGTACTTGAAGTTAACAAACTTCAAACTGAACAAAAAGAGTTAAAAGATTCAATTGAATTTTGTAAGAAAGTGTTAGCTGATCAAAAATTACAGCTAAAAATAATCAAAGAGGAATTGCAAAAAATCAATGATCAGTTTGGTGATGAAAGAAGAAGTGAAATTCTCTATGATATCTCTGAGGAAATTGATGATGAATCATTGATAAAAGTTGAGAATGTAGTGATAACTATGTCTACAAATGGTTATCTAAAAAGGATTGGAGTTGATGCTTATAATCTTCAACATCGTGGTGGAGTTGGGGTTAAAGGGCTAACTACTTATGTTGATGATAGTATTAGTCAATTATTGGTCTGTTCAACTCACTCTGACTTATTATTTTTTACTGATAAGGGTAAGGTTTATAGAATTAGAGCTCATCAAATTCCCTATGGTTTTAGAACAAATAAAGGTATTCCCGCTGTTAACTTAATCAAAATTGAAAAGGATGAAAGAATTTGTTCATTGTTATCTGTTAATAACTATGATGATGGTTATTTCTTTTTCTGTACTAAAAATGGAATTGTTAAAAGAACGAGCTTGAATGAATTCATCAACATCTTAAGTAATGGTAAGCGGGCTATATCTTTTGATGATAATGACACTTTGTATTCAGTAATTAAAACCCACGGAAATGATGAGATTTTTATTGGTTCTACCAATGGATTTGTTGTTCGCTTCCATGAAAATCAACTCAGAGTTCTTTCAAGAACAGCAAGAGGTGTATTTGGTATCAGTTTAAATAAAGGAGAATTTGTTAATGGACTATCAACTTCAAGCAACGGTAGCTTACTTTTATCAGTCGGTCAAAATGGAATAGGTAAATTAACGAGCATAGATAAATATAGACTCACAAAACGTAATGCTAAGGGAGTTAAAACTCTAAGGGTTACTGATAGAACAGGCCCTGTTGTTACAACAACCACTGTTTTTGGTAATGAGGATCTTTTAATGATTTCCTCTGCTGGTAAAATTGTGCGTACCAGTTTACAAGAACTTTCAGAACAAGGTAAAAACACTTCTGGTGTTAAGTTAATTAGATTAAAAGATAATGAACGTTTAGAAAGAGTAACTATCTTTAAAGAAGAGTTAGAAGACAAAGAAATGCAACTAGAAGATGTTGGATCCAAACAAATTACGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42585","NCBI_taxonomy_name":"Mycoplasma genitalium G37","NCBI_taxonomy_id":"243273"}}}},"ARO_accession":"3004631","ARO_id":"42620","ARO_name":"Mycoplasma genitalium gyrA mutation confers resistance to fluoroquinolones","CARD_short_name":"Mgen_gyrA_FLO","ARO_description":"Mycoplasma Genitalium GyrA mutations confers resistance to fluoroquinolones such as Moxifloxacin.","ARO_category":{"39876":{"category_aro_accession":"3003292","category_aro_cvterm_id":"39876","category_aro_name":"fluoroquinolone resistant gyrA","category_aro_description":"DNA gyrase is responsible for DNA supercoiling and consists of two alpha and two beta subunits. GyrA point mutations confer resistance by preventing fluoroquinolone antibiotics from binding the alpha-subunit.","category_aro_class_name":"AMR Gene Family"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2375":{"model_id":"2375","model_name":"Rm3","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"3669":{"protein_sequence":{"accession":"AGU01679.2","sequence":"MSLTPPRALVLALLLASPGTQAQTPAPATPPTPGCEVCATWNADQAPFRLFGNTYYVGMKGLSSVLVTSPQGHVLIDGGLPESAPKIIANIGALGFRIEDVKLILNSHGHIDHAGGLAELQRRSNALVAASPSAALDLASGEVGPDDPQYHALPKYPPVKDMRLARDGGQFNVGPVYLTAHATPGHTPGGLSWTWQSCDGPRCLNMVYADSINAVSRPGFKFSASSEYPNALADLRHSFETLEKLPCDVLISAHPEASQLWQRLEASATGGSDAFVDPQACRAYVAAARTLLDSRLDQEKQQ"},"dna_sequence":{"accession":"KF485393.2","fmin":"6723","fmax":"7632","strand":"+","sequence":"ATGTCCCTCACACCACCACGCGCGCTGGTCCTGGCCCTGCTGCTGGCCAGCCCCGGCACCCAGGCGCAAACACCGGCTCCAGCCACACCGCCAACGCCGGGCTGCGAAGTCTGCGCCACCTGGAATGCCGACCAGGCACCGTTCCGCCTCTTCGGCAATACCTATTACGTGGGCATGAAAGGCCTCAGTTCCGTGCTGGTGACGTCGCCGCAGGGCCATGTGCTGATCGATGGCGGCTTGCCGGAATCGGCGCCCAAGATCATCGCCAATATCGGCGCGCTGGGCTTTCGCATAGAGGACGTCAAGCTGATCCTCAATTCGCACGGCCATATCGACCATGCGGGCGGCCTGGCCGAACTGCAGCGGCGCAGCAATGCCCTGGTGGCGGCCAGCCCGTCGGCCGCGCTGGACCTGGCGTCGGGCGAAGTGGGCCCGGACGACCCGCAATACCATGCGCTGCCCAAATATCCGCCCGTCAAGGACATGCGCCTGGCGCGCGACGGCGGCCAGTTCAATGTCGGCCCCGTCTACCTGACGGCGCATGCCACGCCAGGGCACACGCCCGGGGGCCTGAGCTGGACGTGGCAATCGTGCGACGGTCCCCGCTGCCTGAACATGGTCTACGCGGACAGCATCAACGCCGTCTCGCGCCCCGGTTTCAAGTTCAGCGCCAGCAGTGAGTATCCGAACGCCCTGGCGGACTTGCGCCACAGCTTCGAGACCCTGGAAAAACTGCCCTGCGACGTGCTCATTTCGGCGCATCCGGAGGCGTCGCAATTGTGGCAACGACTGGAAGCGAGCGCCACGGGCGGCAGCGATGCCTTCGTCGATCCGCAGGCCTGCCGCGCCTACGTGGCGGCGGCGCGCACCTTGCTCGACTCTCGTCTGGACCAGGAAAAACAGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36791","NCBI_taxonomy_name":"uncultured bacterium","NCBI_taxonomy_id":"77133"}}}},"ARO_accession":"3003894","ARO_id":"40596","ARO_name":"Rm3","CARD_short_name":"Rm3","ARO_description":"Rm3 is a class B3 metallo-beta-lactamase isolated from a metagenomic soil sample in Yorkshire, United Kingdom, shown to confer resistance to clinically used penicillins, cephalosporins, and carbapenems.","ARO_category":{"41389":{"category_aro_accession":"3004225","category_aro_cvterm_id":"41389","category_aro_name":"Rm3 family beta-lactamase","category_aro_description":"A family encompassing subclass B3 Rm3-like beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2405":{"model_id":"2405","model_name":"Neisseria gonorrhoeae parC conferring resistance to fluoroquinolones","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"4454":"S87R","4455":"E91G","13183":"S87N"},"Curated-R":{"4454":"S87R","4455":"E91G","13183":"S87N"},"clinical":{"4454":"S87R","4455":"E91G","13183":"S87N"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1400"}},"model_sequences":{"sequence":{"5461":{"protein_sequence":{"accession":"AAW89918.1","sequence":"MNTQPHASHTDSNTLMLGRYAERAYLEYAMSVVKGRALPEVSDGQKPVQRRILFAMRDMGLTAGAKPVKSARVVGEILGKYHPHGDSSAYEAMVRMAQDFTLRYPLIDGIGNFGSRDGDGAAAMRYTEARLTPIAELLLSEINQGTVDFMPNYDGAFDEPLHLPARLPMVLLNGASGIAVGMATEIPSHNLNEVTQAAIALLKKPTLETADLMQYIPAPDFAGGGQIITPADELRRIYETGKGSVRVRARYEIEKLARGQWRVIVTELPPNANSAKILAEIEEQTNPKPKAGKKQLNQDRLNTKKLMLDLIDRVRDESDGEHPVRLVFEPKSSRIDTDTFINTLMAQTSLEGNVSMNLVMMGLDNRPAQKNLKTILQEWLDFRVVTVTRRLKFRLNQVEKRLHILEGRLKVFLHIDEVIKVIRESDDPKADLMAVFGLTEIQAEDILEIRLRQLARLEGFKLEKELNELREEQGRLNIFLGDENEKRKLIIKEMQADMKQFGDARRTLVEEAGRAVLTQTAADEPITLILSEKGWIRSRAGHNLDLSQTAFKEGDRLKQTLEGRTVLPVVILDSSGRTYSIDAAEIPGGRGDGVPVSSLIELQNGAKPVAMLTGLPEQHYLLSSSGGYGFIAKLGDMVGRVKAGKVVMTADSGETVLPPVAVYASSFINPDCKIIAATSQNRALAFPIGELKIMAKGKGLQIIGLNAGESMTHTAVSSEPEILIESEGRRGAAHKDRLPVALIEAKRGKKGRLLPISGSLKQLSSPK"},"dna_sequence":{"accession":"AE004969.1","fmin":"1210523","fmax":"1212827","strand":"+","sequence":"ATGAATACGCAACCGCACGCTTCCCATACCGATTCCAACACGCTGATGCTCGGCCGATACGCCGAACGCGCCTATCTCGAATACGCCATGAGCGTGGTCAAAGGCCGCGCGCTGCCTGAAGTTTCAGACGGCCAAAAGCCCGTGCAGCGGCGCATTTTGTTTGCCATGCGCGATATGGGTTTGACGGCGGGGGCGAAGCCGGTGAAATCGGCGCGCGTGGTCGGCGAGATTTTGGGTAAATACCATCCGCACGGCGACAGTTCCGCCTATGAGGCGATGGTGCGCATGGCTCAGGATTTTACCTTGCGCTACCCCTTAATCGACGGCATCGGCAACTTCGGTTCGCGCGACGGCGACGGGGCGGCGGCGATGCGTTACACCGAAGCGCGGCTGACGCCGATTGCGGAATTGCTGTTGTCCGAAATCAATCAGGGGACGGTGGATTTTATGCCGAACTACGACGGCGCGTTTGACGAGCCGCTGCACCTTCCCGCCCGCTTGCCTATGGTGTTGCTCAACGGCGCGTCGGGCATCGCGGTGGGTATGGCGACCGAGATTCCGTCGCACAATTTGAACGAAGTCACGCAGGCGGCGATTGCACTGTTGAAGAAACCGACGCTGGAAACCGCCGACCTGATGCAATATATTCCTGCTCCCGATTTTGCCGGCGGCGGTCAAATCATCACGCCGGCGGACGAATTGCGCCGTATTTACGAAACCGGCAAGGGCAGCGTGCGCGTGCGTGCGCGTTATGAAATCGAGAAATTGGCGCGCGGACAGTGGCGCGTCATCGTAACCGAACTGCCGCCGAACGCCAACTCCGCCAAAATCCTTGCCGAAATCGAAGAGCAAACCAACCCGAAACCGAAAGCGGGTAAAAAGCAGCTCAACCAAGACCGGCTCAATACCAAAAAGCTGATGCTGGATTTAATCGACCGCGTGCGCGACGAGTCCGACGGCGAACATCCCGTGCGCCTTGTATTTGAACCGAAATCCAGCCGCATCGATACCGATACCTTCATCAACACGCTGATGGCGCAAACTTCGCTGGAAGGCAATGTGTCCATGAACTTGGTGATGATGGGTTTGGACAACCGCCCCGCGCAGAAAAACCTGAAAACGATTTTGCAGGAATGGCTGGATTTCCGCGTCGTTACCGTAACACGCCGTCTGAAATTCCGTTTAAACCAAGTGGAAAAACGGCTGCACATCCTCGAAGGCCGTCTGAAAGTCTTTCTGCACATCGACGAAGTGATTAAAGTCATCCGCGAATCGGACGACCCGAAAGCCGATTTGATGGCGGTGTTCGGGCTGACCGAAATCCAAGCCGAAGACATTTTGGAAATCCGCCTGCGTCAGCTGGCGCGTTTGGAAGGTTTCAAACTCGAAAAAGAATTGAACGAATTGCGCGAAGAACAAGGCCGTCTGAATATCTTTTTGGGCGACGAAAACGAAAAACGCAAGCTGATTATCAAAGAGATGCAGGCGGACATGAAGCAGTTCGGCGACGCGCGCCGCACGCTGGTGGAAGAGGCCGGACGCGCCGTGCTGACACAAACCGCCGCCGACGAACCCATCACGCTGATTTTGTCGGAAAAAGGCTGGATACGCAGCCGTGCCGGACATAATCTCGATTTGAGCCAAACCGCGTTCAAAGAAGGCGACCGCCTCAAACAAACCCTTGAAGGCCGCACTGTTTTACCCGTCGTCATCCTCGATTCATCGGGCAGAACCTACTCGATCGATGCCGCCGAAATCCCCGGCGGACGCGGCGACGGCGTACCGGTTTCCTCCTTAATCGAGTTGCAAAACGGCGCGAAACCCGTCGCGATGTTGACAGGATTGCCGGAACAACATTATTTATTATCAAGCAGCGGCGGCTACGGCTTTATCGCCAAGCTGGGCGATATGGTCGGACGCGTGAAAGCGGGCAAAGTGGTGATGACCGCAGACAGCGGCGAAACCGTCCTGCCGCCGGTTGCCGTCTATGCCTCCTCGTTCATCAACCCCGACTGCAAAATCATTGCAGCCACCAGTCAAAACCGCGCCCTCGCCTTCCCCATCGGCGAATTGAAAATTATGGCGAAAGGCAAAGGACTGCAAATCATCGGATTAAACGCCGGCGAATCGATGACGCATACCGCCGTTTCTTCCGAGCCGGAAATCCTGATTGAAAGCGAAGGCAGGCGCGGCGCGGCGCACAAAGACCGCCTCCCCGTCGCCCTGATTGAGGCAAAACGCGGCAAAAAAGGCAGACTGTTGCCCATATCGGGCAGCCTGAAACAGCTTTCTTCCCCCAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40638","NCBI_taxonomy_name":"Neisseria gonorrhoeae FA 1090","NCBI_taxonomy_id":"242231"}}}},"ARO_accession":"3003929","ARO_id":"40639","ARO_name":"Neisseria gonorrhoeae parC conferring resistance to fluoroquinolones","CARD_short_name":"Ngon_parC_FLO","ARO_description":"Point mutations in Neisseria gonorrhoeae parC protein that confer resistance to fluoroquinolone by reducing affinity to antibiotic binding site.","ARO_category":{"36913":{"category_aro_accession":"3000619","category_aro_cvterm_id":"36913","category_aro_name":"fluoroquinolone resistant parC","category_aro_description":"ParC is a subunit of topoisomerase IV, which decatenates and relaxes DNA to allow access to genes for transcription or translation. Point mutations in ParC prevent fluoroquinolone antibiotics from inhibiting DNA synthesis, and confer low-level resistance. Higher-level resistance results from both gyrA and parC mutations.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"40338":{"category_aro_accession":"3003690","category_aro_cvterm_id":"40338","category_aro_name":"sitafloxacin","category_aro_description":"Sitafloxacin is a fluoroquinolone active against multi-resistant Gram-positive and negative pathogens. Sitafloxacin shows inhibitory activity against DNA gyrase and topoisomerase IV, which blocks bacterial DNA replication, thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5881":{"model_id":"5881","model_name":"MCR-10.4","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"8609":{"protein_sequence":{"accession":"MBO4150342.1","sequence":"MPVLFRMRVIPLVLLLALVFAFLLNWPVLLHFYDILSRLEHVRAGFVISIPFVLVAALNFVFMPFSVRYLLKPFFALLLVTGSVVSYATLKYKVMFDQSMIENILETNPQEAHSYLNGSLVLWLVFMGILPAILLFLIKIEYADKWYKGVAHRLLSMLASLILIAGVAALYYQDYASVGRNNPTLNKEIIPANYAYSTFHYVKDTYFTTKMPFRTLGDDARRVTRNGKPTLMFLVIGETARSQNFSMNGYPRDTNAFTSKIDGVISFRNMRSCGTATAVSVPCMFSDMNRTDYDGKKAAGSENVLDIVQKTGVSLLWKENDGGCKGVCSRIPTVEINPGISKKLCDGKTCYDDVMLENLDTEIGKMAGDKLIAFHMIGSHGPTYYQRYPAEHRHFMPECARSDIENCTQEQLVNTYDNTIRHTDYVLAQMIEKLKQYSEQYNTVLLYVSDHGESLGESGLYLHGTPYKLAPDQQTHIPMQLWMSPGFIAAKNINAACLQHNAVNRTYSHDNLFASVLGLWDITTGAYLPESDLFRECRG"},"dna_sequence":{"accession":"JAGFWU010000059.1","fmin":"6396","fmax":"8016","strand":"-","sequence":"ATGCCCGTACTTTTCAGGATGAGGGTAATCCCCTTGGTTTTACTTCTGGCACTCGTTTTTGCATTCTTACTTAACTGGCCGGTGTTGCTGCATTTCTACGATATCCTGAGCCGTCTTGAACATGTGAGGGCGGGGTTCGTCATCTCCATTCCGTTTGTGCTGGTTGCAGCGCTTAACTTTGTGTTTATGCCCTTCTCGGTTCGCTACCTGCTCAAACCCTTCTTTGCCCTGTTGCTGGTCACCGGTTCGGTGGTGAGTTACGCCACACTGAAATATAAAGTGATGTTTGATCAGTCCATGATCGAAAATATACTGGAAACAAACCCACAGGAAGCGCATTCCTACCTGAATGGCTCACTGGTGCTGTGGCTGGTCTTCATGGGCATTCTTCCGGCTATCCTGTTGTTTTTGATTAAAATTGAATATGCAGACAAATGGTACAAAGGGGTTGCCCACCGGCTGCTTTCCATGCTCGCTTCGCTGATCCTGATTGCAGGTGTTGCCGCTCTGTATTACCAGGATTATGCTTCTGTCGGGCGCAATAACCCGACGCTGAACAAAGAAATTATCCCGGCAAACTATGCGTACAGCACTTTCCATTACGTGAAGGATACCTATTTTACGACGAAAATGCCTTTCCGGACGCTGGGGGATGATGCAAGGCGCGTTACCCGGAATGGTAAACCCACGCTGATGTTCCTGGTAATTGGCGAAACGGCACGGAGCCAGAATTTCTCCATGAACGGCTACCCGCGTGACACAAATGCCTTTACCAGCAAAATCGATGGCGTTATTTCGTTCAGGAATATGCGTTCCTGTGGCACGGCGACCGCAGTCTCGGTGCCCTGTATGTTCTCGGATATGAACCGGACGGATTACGATGGTAAAAAGGCTGCCGGCAGTGAAAATGTCCTCGACATCGTGCAGAAAACGGGGGTTTCGCTGTTGTGGAAAGAAAACGATGGCGGGTGTAAAGGCGTATGCAGCCGTATCCCGACTGTCGAAATTAATCCCGGTATCAGTAAAAAACTGTGTGACGGTAAAACCTGCTATGACGATGTTATGCTGGAAAACCTGGATACCGAAATCGGCAAAATGGCCGGAGACAAGCTGATCGCCTTCCATATGATTGGCAGCCATGGACCGACCTATTACCAGCGTTATCCGGCAGAGCATCGTCACTTCATGCCGGAATGTGCGCGCAGCGATATCGAAAACTGCACGCAGGAACAGCTGGTTAATACCTACGACAATACCATTCGCCACACCGACTATGTGTTAGCGCAGATGATTGAAAAGCTTAAGCAATACAGCGAACAGTACAACACCGTACTGCTGTATGTGTCCGATCACGGCGAATCTCTGGGAGAGAGCGGACTGTATCTGCACGGTACCCCCTACAAACTGGCACCGGATCAGCAGACGCACATCCCGATGCAGCTCTGGATGTCGCCAGGCTTCATTGCTGCTAAAAATATTAACGCCGCGTGTCTGCAGCATAATGCCGTTAACAGGACATATTCCCACGATAACCTTTTCGCGTCCGTACTGGGGCTCTGGGACATCACCACCGGGGCCTATCTTCCGGAAAGCGACCTGTTCCGCGAATGTCGTGGATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"45936","NCBI_taxonomy_name":"Enterobacter ludwigii","NCBI_taxonomy_id":"299767"}}}},"ARO_accession":"3007276","ARO_id":"46022","ARO_name":"MCR-10.4","CARD_short_name":"MCR-10.4","ARO_description":"An MCR-10-type colistin resistance gene variant.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5882":{"model_id":"5882","model_name":"MCR-10.2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"8612":{"protein_sequence":{"accession":"MBO4154571.1","sequence":"MPVLFRMRVIPLVLLLALVFAFLLNWPVLLHFYDILSRLEHVRAGFVISIPFVLVAALNFVFMPFSVRYLLKPFFALLLVTGSVVSYATLKYKVMFDQSMIENILETNPQEAHSYLNGSLVLWLVFMGILPAILLFLIKIEYTDKWYKGVAHRLLSMLASLILIAGVAALYYQDYASVGRNNPTLNKEIIPANYAYSTFHYVKDTYFTTKMPFRTLGDDARRVTRNGKPTLMFLVIGETARSQNFSMNGYPRDTNAFTSKIDGVISFRNMRSCGTATAVSVPCMFSDMNRTDYDGKKAAGSENVLDIVQKTGVSLLWKENDGGCKGVCSRIPTVEINPGISKKLCDGKTCYDDVMLENLDTEIGKMAGDKLIAFHMIGSHGPTYYQRYPAEHRHFMPECARSDIENCTQEQLVNTYDNTIRHTDYVLAQMIEKLKQYSEQYNTVLLYVSDHGESLGESGLYLHGTPYKLAPDQQTHIPMQLWMSPDFIAAKNINAACLQHNAVNRTYSHDNLFASVLGLWDITTGAYLPESDLFRECRG"},"dna_sequence":{"accession":"JAGFWW010000009.1","fmin":"24887","fmax":"26507","strand":"-","sequence":"ATGCCCGTACTTTTCAGGATGAGGGTAATCCCCCTGGTTTTACTTCTGGCACTCGTTTTTGCATTCTTACTTAACTGGCCGGTGTTGCTGCATTTCTACGATATCCTGAGCCGTCTTGAACATGTGAGGGCGGGGTTCGTCATCTCCATTCCGTTTGTGCTGGTTGCAGCGCTTAACTTTGTGTTTATGCCCTTCTCGGTTCGCTACCTGCTTAAACCCTTCTTTGCCCTGTTGCTGGTCACCGGTTCGGTGGTGAGTTACGCCACACTGAAATATAAAGTGATGTTTGATCAGTCCATGATCGAAAATATACTGGAAACAAACCCACAGGAAGCGCATTCCTACCTGAATGGCTCACTGGTGCTGTGGCTGGTCTTTATGGGCATTCTTCCGGCTATCCTGTTGTTTTTGATTAAAATTGAATATACAGACAAATGGTACAAAGGGGTTGCCCACCGGCTGCTTTCCATGCTCGCTTCGCTGATCCTGATTGCAGGTGTTGCCGCTCTGTATTACCAGGATTATGCTTCTGTCGGGCGCAATAACCCGACGCTGAACAAAGAAATTATCCCGGCAAACTATGCGTACAGCACTTTCCATTACGTGAAGGATACCTATTTTACGACGAAAATGCCTTTCCGGACGCTGGGGGATGATGCAAGGCGCGTTACCCGGAATGGTAAACCCACGCTGATGTTCCTGGTAATTGGCGAAACGGCACGGAGCCAGAATTTCTCCATGAACGGCTACCCGCGTGACACAAATGCCTTTACCAGCAAAATCGATGGCGTTATTTCGTTCAGGAATATGCGTTCCTGCGGCACGGCGACCGCAGTCTCGGTGCCCTGTATGTTCTCGGATATGAACCGGACGGATTACGATGGTAAAAAGGCTGCCGGCAGTGAAAATGTCCTCGACATTGTGCAGAAAACGGGGGTTTCGCTGTTGTGGAAAGAAAACGATGGCGGGTGTAAAGGCGTATGCAGCCGTATCCCGACTGTCGAAATTAATCCCGGTATCAGTAAAAAACTGTGTGACGGTAAAACCTGCTATGACGATGTTATGCTGGAAAACCTGGATACCGAAATCGGCAAAATGGCCGGAGACAAGCTGATCGCCTTCCATATGATTGGCAGCCATGGACCGACCTATTACCAGCGTTATCCGGCAGAGCATCGTCACTTCATGCCGGAATGTGCGCGCAGCGATATCGAAAACTGCACGCAGGAACAGCTGGTTAATACCTACGACAATACCATTCGCCACACCGACTATGTGTTAGCGCAGATGATTGAAAAGCTTAAGCAATACAGCGAACAGTACAACACCGTACTGCTGTATGTGTCCGATCACGGCGAATCTCTGGGAGAGAGCGGACTGTATCTGCACGGTACCCCCTACAAACTGGCACCGGATCAGCAGACGCACATCCCGATGCAGCTCTGGATGTCGCCAGACTTCATTGCTGCTAAAAATATTAACGCCGCGTGTCTGCAGCATAATGCCGTTAACAGGACATATTCCCACGATAACCTTTTCGCGTCCGTACTGGGGCTCTGGGACATCACCACCGGGGCCTATCTTCCGGAAAGCGACCTGTTCCGCGAATGTCGTGGATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39773","NCBI_taxonomy_name":"Enterobacter kobei","NCBI_taxonomy_id":"208224"}}}},"ARO_accession":"3007277","ARO_id":"46023","ARO_name":"MCR-10.2","CARD_short_name":"MCR-10.2","ARO_description":"An MCR-10-type colistin resistance gene variant.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2445":{"model_id":"2445","model_name":"Erm(44)v","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"5167":{"protein_sequence":{"accession":"CDL65151.1","sequence":"MNNKNPKNSQNFITSQKHINEILNETNIGIDDNIIEIGTGKGHFTKYMSNIARFITSIEIDKALYCNLKNDISLSTNIELVNKDILIYEFPKYKQYKVFGSIPYNISTEIVKKILYESNAEYNYLIVEFGFAKRIMDKKRALALLLLPKIDIEILKVIPNSYFHPKPKVDSALILLKQHKSLISKNDENAYHFFVYKWINKEYKQLFTKNQFNKALKHAKVQNINEISKEQFISIFHSYKLFN"},"dna_sequence":{"accession":"HG796218.2","fmin":"48616","fmax":"49348","strand":"+","sequence":"ATGAATAACAAAAATCCTAAAAACTCACAAAATTTTATAACATCTCAAAAGCATATTAACGAGATATTAAATGAAACAAACATAGGCATTGATGATAATATAATTGAAATTGGAACTGGAAAAGGACACTTTACAAAATACATGTCCAATATAGCTAGATTTATAACTAGTATAGAAATTGACAAGGCTTTATATTGTAATTTGAAAAATGATATTAGTTTGTCAACTAATATTGAATTAGTGAATAAAGATATACTGATATATGAGTTTCCTAAATACAAGCAGTATAAAGTTTTTGGTAGCATCCCATATAATATAAGTACTGAAATAGTCAAAAAAATCTTATATGAAAGTAATGCTGAATATAACTATCTTATTGTAGAATTCGGATTTGCTAAACGAATTATGGATAAAAAAAGAGCGTTAGCCTTATTACTTTTACCTAAAATTGATATTGAAATTTTAAAAGTAATTCCCAACTCTTATTTTCATCCTAAACCTAAAGTAGATTCAGCGTTAATCTTACTAAAGCAGCACAAATCTTTAATCTCAAAAAATGATGAAAATGCATATCATTTTTTTGTATATAAATGGATAAACAAAGAATATAAACAGCTATTTACAAAGAATCAGTTTAATAAAGCGTTAAAACATGCAAAGGTACAGAATATAAATGAAATATCAAAAGAACAATTTATATCAATTTTTCATAGTTATAAATTGTTTAATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36844","NCBI_taxonomy_name":"Staphylococcus xylosus","NCBI_taxonomy_id":"1288"}}}},"ARO_accession":"3003971","ARO_id":"40752","ARO_name":"Erm(44)v","CARD_short_name":"Erm(44)v","ARO_description":"Variant of Erm(44)v isolated from Staphylococcus saprophyticus, confers resistance to lincosamide and macrolide antibiotics but not streptogramins.","ARO_category":{"36699":{"category_aro_accession":"3000560","category_aro_cvterm_id":"36699","category_aro_name":"Erm 23S ribosomal RNA methyltransferase","category_aro_description":"Erm proteins are part of the RNA methyltransferase family and methylate A2058 (E. coli nomenclature) of the 23S ribosomal RNA conferring degrees of resistance to Macrolides, Lincosamides and Streptogramin b. This is called the MLSb phenotype.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2424":{"model_id":"2424","model_name":"YojI","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1050"}},"model_sequences":{"sequence":{"5261":{"protein_sequence":{"accession":"AAC75271.1","sequence":"MELLVLVWRQYRWPFISVMALSLASAALGIGLIAFINQRLIETADTSLLVLPEFLGLLLLLMAVTLGSQLALTTLGHHFVYRLRSEFIKRILDTHVERIEQLGSASLLAGLTSDVRNITIAFVRLPELVQGIILTIGSAAYLWMLSGKMLLVTAIWMAITIWGGFVLVARVYKHMATLRETEDKLYTDFQTVLEGRKELTLNRERAEYVFNNLYIPDAQEYRHHIIRADTFHLSAVNWSNIMMLGAIGLVFWMANSLGWADTNVAATYSLTLLFLRTPLLSAVGALPTLLTAQVAFNKLNKFALAPFKAEFPRPQAFPNWQTLELRNVTFAYQDNAFSVGPINLTIKRGELLFLIGGNGSGKSTLAMLLTGLYQPQSGEILLDGKPVSGEQPEDYRKLFSAVFTDVWLFDQLLGPEGKPANPQLVEKWLAQLKMAHKLELSNGRIVNLKLSKGQKKRVALLLALAEERDIILLDEWAADQDPHFRREFYQVLLPLMQEMGKTIFAISHDDHYFIHADRLLEMRNGQLSELTGEERDAASRDAVARTA"},"dna_sequence":{"accession":"U00096.3","fmin":"2306971","fmax":"2308615","strand":"-","sequence":"ATGGAACTTCTTGTACTTGTCTGGCGGCAGTATCGCTGGCCATTTATCAGTGTGATGGCGCTAAGCCTCGCCAGTGCGGCATTAGGCATTGGCTTAATTGCTTTTATCAATCAGCGCCTTATCGAAACGGCGGATACCAGTCTGCTGGTGTTGCCGGAGTTTCTGGGATTATTGCTGCTGTTGATGGCAGTCACTCTCGGATCGCAACTGGCGCTCACCACTTTGGGGCATCACTTCGTTTACCGACTGCGTAGTGAATTTATCAAGCGGATTCTGGATACTCACGTCGAGCGCATTGAACAACTCGGTAGCGCCTCGTTGCTGGCGGGGTTAACCAGCGATGTGCGCAATATCACCATTGCTTTTGTGCGTCTGCCGGAACTGGTGCAGGGGATCATTCTCACTATCGGTTCAGCGGCGTATCTGTGGATGCTGTCGGGCAAAATGTTGCTGGTAACGGCTATCTGGATGGCGATCACCATCTGGGGCGGTTTTGTGCTGGTGGCGCGGGTGTACAAACATATGGCGACCCTGCGTGAAACCGAAGACAAGCTGTACACGGATTTTCAAACTGTACTTGAAGGGCGCAAAGAGCTGACTCTGAACCGGGAACGCGCCGAGTATGTGTTTAACAACCTCTACATTCCTGATGCGCAAGAGTATCGCCACCATATTATTCGCGCAGACACCTTCCATCTTAGTGCCGTGAACTGGTCAAACATCATGATGCTGGGCGCAATCGGCCTGGTGTTCTGGATGGCGAACAGCCTCGGTTGGGCTGATACCAACGTTGCCGCGACCTATTCGTTGACGCTTTTATTCCTGCGTACGCCGCTGCTTTCGGCGGTTGGCGCATTGCCGACGCTGCTGACGGCGCAGGTGGCGTTTAACAAGCTGAACAAATTCGCGCTCGCGCCTTTCAAAGCAGAGTTTCCGCGCCCGCAGGCGTTTCCCAACTGGCAAACGCTGGAGCTGCGTAACGTGACGTTTGCTTATCAGGATAACGCGTTTTCCGTTGGTCCGATTAATCTCACCATCAAACGTGGCGAGCTGCTGTTTCTGATTGGCGGCAACGGTAGCGGAAAATCGACGCTGGCGATGTTGTTGACGGGCTTGTATCAGCCACAAAGCGGCGAAATCTTGCTGGATGGCAAACCTGTCAGCGGCGAACAACCGGAAGATTATCGCAAACTGTTTTCGGCAGTGTTTACCGATGTCTGGCTGTTTGATCAACTGCTGGGGCCGGAGGGTAAACCCGCTAACCCGCAACTGGTTGAGAAGTGGCTGGCGCAGCTGAAAATGGCTCATAAGCTTGAGTTAAGCAACGGGCGTATTGTTAACCTGAAGTTATCAAAAGGGCAGAAAAAACGCGTGGCGCTGTTGCTGGCGCTGGCAGAAGAACGCGATATTATCCTGCTGGATGAATGGGCGGCGGATCAGGATCCACACTTCCGTCGTGAGTTTTATCAGGTGTTGCTGCCGCTGATGCAGGAGATGGGTAAAACTATTTTCGCTATCAGTCATGATGATCATTACTTTATCCACGCCGACCGCCTGCTGGAAATGCGCAATGGGCAACTTAGCGAGCTGACGGGCGAAGAGCGCGATGCCGCTTCGCGTGATGCCGTTGCCCGGACGGCATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36849","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. MG1655","NCBI_taxonomy_id":"511145"}}}},"ARO_accession":"3003952","ARO_id":"40722","ARO_name":"YojI","CARD_short_name":"YojI","ARO_description":"YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules.  The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI.","ARO_category":{"36002":{"category_aro_accession":"0010001","category_aro_cvterm_id":"36002","category_aro_name":"ATP-binding cassette (ABC) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding\/hydrolysis to transport substrates across cell membranes.","category_aro_class_name":"AMR Gene Family"},"40721":{"category_aro_accession":"3003951","category_aro_cvterm_id":"40721","category_aro_name":"microcin J25","category_aro_description":"Microcin J25 is a peptide antibiotic that inhibits transcription by bacterial RNA polymerase. MccJ25 is produced by Escherichia coli strains that harbor a plasmid-borne antibiotic-synthesis and antibiotic-export cassette, consisting of a gene for MccJ25 precursor (a 58 residue linear peptide), two genes for factors that process MccJ25 precursor into MccJ25, and one gene for export of MccJ25.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2482":{"model_id":"2482","model_name":"Chlamydomonas reinhardtii 16S rRNA (rrnS) mutation conferring resistance to streptomycin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"4751":"a858c","4752":"a859g","4753":"a1123g","4754":"a1123c","4755":"g1125a","4750":"c856t","4749":"a474c","4748":"t14g"},"Curated-R":{"4751":"a858c","4752":"a859g","4753":"a1123g","4754":"a1123c","4755":"g1125a","4750":"c856t","4749":"a474c","4748":"t14g"},"clinical":{"4751":"a858c","4752":"a859g","4753":"a1123g","4754":"a1123c","4755":"g1125a","4750":"c856t","4749":"a474c","4748":"t14g"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"41093","param_value":"2500"}},"model_sequences":{"sequence":{"4108":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"NC_005353.1","fmin":"38549","fmax":"40023","strand":"+","sequence":"ATCCATGGAGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCATGCTTAACACATGCAAGTCGAACGAGCAAAGCAATTTGTGTAGTGGCGAACGGGTGCGTAACGCGTAAGAACCTACCTATCGGAGGGGGATAACATTGGGAAACTGTTGCTAATACCCCATACAGCTGAGGAGTGAAAGGTGAAAAACCGCCGATAGAGGGGCTTGCGTCTGATTAGCTAGTTGGTGGGGGTAACGGCCTCCCAAGGCCACGAGCAGTAGCTGGTCTGAGAGGATGATCAGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGAGGAATTTTTCGCAATGGGCGCAAGCGACGGAGCAATGCCGCGTGCAGGAAGAAGGCCTGTGGGTCGTAAACTGCTTTTCTCAGAGAAGAAGTTCTGACGGTATCTGAGGAATAAGCACCGGCTAACTCTGTGCCAGCAGCCGCGGTAATACAGAGGGTGCAAGCGTTGTCCGCAATGATTGGGCGTAAAGCGTCTGTAGGTGGCTCGTAAAGTCTAATGTCAAATACCAGGGCTCAACCTTGGACCGGCATTGGAGTACTCACGAGCTTGAGTACGGTAGGGGCAGAGGGAATTCCATGTGGAGCGGTGAAATGCGTAGAGATATGGAGGAACACCAGTGGCGAAGGCGCTCTGCTGGGCCGAAACTGACACTGAGAGACGAAAGCTGGGGGAGCGAATAGGATTAGATACCCTAGTAGTCCCAGCCGTAAACTATGGAGACTAAGTGCTGCCGCAAGCAGTGCTGTAGCTAACGCGTTAAGTCTCCCGCCTGGGGAGTATGCTCGCAAGAGTGAAACTCAAAGGAATTGACGGGACCGCACAAGCGGTGGATTATGTGGATTAATTCGATACAACGCGAAGAACCTTACCAGGGTTTGACATGTCAAGAACCTCTCAGAAATGGGAGGGTGCCCTAACGGACTTGAACACAGGTGGTGCATGGCTGTCGTCAGCTCGTGCTGTGAAGTGTATAGTTAAGTCTCATAACGAGCGCAACCCTCGTCTTTAGTTGCCATTTGGTTCTCTAAAGAGACTGCCAGTGTAAGCTGGAGGAAGGTGAGGATGACGTCAAGTCAGCATGCCCCTTACATCCTGGGCTTCACACGTAATACAATGGTTGGGACAATCAGAAGCGACTCGTGAGAGCTAGCGGCTCTGTTAAACCCAACCTCAGTTCGGATTGTAGGCTGCAACTCGCCTACATGAAGCCGGAATCGCTAGTAATCGCCAGTCAGCTATATGGCGGTGAATACGTTCCCGGGTCTTGTACACACCGCCCGTCACACCATGGAAGCTGGTTCTGCTCCAAGTCGTTACCCTAACCTTCGGGAGGGGGGCGCCTAAAGCAGGGCTAGTGACTAGGGTGAAGTCGTAACAAGGTAGGGCTACTGGAAGGTGGCCCTGGCTCACCTCCTTC","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40815","NCBI_taxonomy_name":"Chlamydomonas reinhardtii","NCBI_taxonomy_id":"3055"}}}},"ARO_accession":"3003978","ARO_id":"40814","ARO_name":"Chlamydomonas reinhardtii 16S rRNA (rrnS) mutation conferring resistance to streptomycin","CARD_short_name":"Crei_16rrnS_STR","ARO_description":"Point mutation in C. reinhardtii rrnS conferring resistance to streptomycin antibiotic.","ARO_category":{"40277":{"category_aro_accession":"3003666","category_aro_cvterm_id":"40277","category_aro_name":"16s rRNA with mutation conferring resistance to aminoglycoside antibiotics","category_aro_description":"Point mutations in the 16S rRNA of bacteria can confer resistance to aminoglycosides.","category_aro_class_name":"AMR Gene Family"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2518":{"model_id":"2518","model_name":"tetB(58)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"3854":{"protein_sequence":{"accession":"APB03215.1","sequence":"MSSSMIQPGTERQLKNRTSLGQTVRNSLTMAYRGLLKLRRTPEQLFDVTFQPIIFTLMFTYIFGGAISGDVASYLPVIIPGILVQTVITTSVVTGVQLREDMDKGVFDRFKSLPIARIAPLAGALLADTIRYTIATVLTFTMGYIMGYRPEGGLGYVALAGLVVILCSWAISWIFAFCGVIARSASGVQGISMIVLFPLTFLSNAFVPVDTMPGWLQWFVNMNPISHLVTAVRDLTNAGTVGWDLTISLVGAAVIVAIFAPITVRAYMRRT"},"dna_sequence":{"accession":"KX531045.1","fmin":"0","fmax":"816","strand":"+","sequence":"ATGAGCAGCTCCATGATTCAGCCTGGGACGGAACGTCAGCTTAAGAACCGCACGAGTTTGGGTCAGACGGTCCGAAATTCGTTGACGATGGCTTACCGCGGGCTGCTGAAGCTCCGGCGCACGCCCGAGCAGTTGTTTGACGTCACGTTTCAGCCCATTATTTTTACGCTGATGTTCACCTATATTTTTGGGGGCGCCATCTCGGGTGACGTGGCGAGTTATTTGCCCGTCATCATTCCCGGCATCCTCGTCCAGACCGTGATTACGACCTCCGTCGTCACAGGCGTTCAGCTGCGCGAGGATATGGATAAAGGCGTATTCGACCGATTCAAATCGCTGCCGATTGCACGCATCGCACCGCTGGCGGGTGCCCTGCTGGCAGACACGATTCGGTATACCATTGCGACAGTGCTTACCTTTACGATGGGATATATTATGGGGTATCGGCCCGAGGGCGGCTTGGGTTATGTTGCTCTTGCGGGGTTGGTCGTCATTTTGTGCTCATGGGCCATTAGCTGGATTTTTGCTTTCTGCGGCGTGATTGCAAGATCTGCCTCCGGCGTGCAGGGGATATCGATGATCGTGCTGTTTCCGCTCACGTTTCTCTCCAACGCGTTCGTGCCGGTGGATACGATGCCGGGCTGGCTGCAGTGGTTCGTCAATATGAATCCGATCTCGCATCTTGTGACAGCCGTTCGGGATCTCACCAACGCTGGCACCGTGGGCTGGGATCTCACGATATCCTTGGTTGGCGCCGCGGTTATCGTGGCGATCTTTGCTCCCATTACGGTTCGTGCGTACATGCGCCGCACTTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40862","NCBI_taxonomy_name":"Paenibacillus sp. LC231","NCBI_taxonomy_id":"1120679"}}}},"ARO_accession":"3003981","ARO_id":"40863","ARO_name":"tetB(58)","CARD_short_name":"tetB(58)","ARO_description":"Tetracycline resistant TetB(58) efflux pump found in Paenibacillus sp. LC231, a strain of Paenibacillus isolated from Lechuguilla Cave, NM, USA. Described by Pawlowski et al. 2016.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"3403":{"model_id":"3403","model_name":"Mycobacterium tuberculosis rpsA mutations conferring resistance to pyrazinamide","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"40494":{"param_type":"frameshift mutation","param_description":"A frameshift is a sequence change between the translation initiation (start) and termination (stop) codon where, compared to a reference sequence, translation shifts to another reading frame as caused by nucleotide insertions and deletions. In ARO, these are annotated at the protein level with the first changed most N-terminal wildtype amino acid position. Format is given as [wildtype AA][position]fs, e.g. S531fs where S531 is a frameshifted coordinate beginning with codon 531. Termination may also be denoted as: Ter[position]fs.","param_type_id":"40494","param_value":{"9722":"Ter482fs"}},"snp":{"ReSeqTB-High":{"9722":"t14g","9719":"A381V","9720":"A412V","9721":"A440T"},"param_value":{"9719":"A381V","9720":"A412V","9721":"A440T","8872":"D342N","8873":"D343N","8874":"A344P","8877":"S324F","8878":"E325K","8879":"G341R","8880":"D123A","8875":"I351F"},"clinical":{"9719":"A381V","9720":"A412V","9721":"A440T","8872":"D342N","8873":"D343N","8874":"A344P","8877":"S324F","8878":"E325K","8879":"G341R","8880":"D123A","8875":"I351F"},"Curated-R":{"8872":"D342N","8873":"D343N","8874":"A344P","8877":"S324F","8878":"E325K","8879":"G341R","8880":"D123A","8875":"I351F","18560":"I351F"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"930"},"41342":{"param_type":"deletion mutation from peptide sequence","param_description":"A peptide sequence change between the translation initiation (start) and termination (stop) codon where, compared to a reference sequence, one or more amino acids are deleted and therefore are not present. These represent in-frame deletions which do not result in frameshift variants and may include multiple amino acids. Format is given by [wildtype AA][position]del for a single peptide deletion or [wildtype AA][position]_[wildtype AA][position]del for a deleted peptide range, e.g. K527del or Q517_N518del.","param_type_id":"41342","param_value":{"18560":"A438del"}}},"model_sequences":{"sequence":{"8802":{"protein_sequence":{"accession":"NP_216146.1","sequence":"MPSPTVTSPQVAVNDIGSSEDFLAAIDKTIKYFNDGDIVEGTIVKVDRDEVLLDIGYKTEGVIPARELSIKHDVDPNEVVSVGDEVEALVLTKEDKEGRLILSKKRAQYERAWGTIEALKEKDEAVKGTVIEVVKGGLILDIGLRGFLPASLVEMRRVRDLQPYIGKEIEAKIIELDKNRNNVVLSRRAWLEQTQSEVRSEFLNNLQKGTIRKGVVSSIVNFGAFVDLGGVDGLVHVSELSWKHIDHPSEVVQVGDEVTVEVLDVDMDRERVSLSLKATQEDPWRHFARTHAIGQIVPGKVTKLVPFGAFVRVEEGIEGLVHISELAERHVEVPDQVVAVGDDAMVKVIDIDLERRRISLSLKQANEDYTEEFDPAKYGMADSYDEQGNYIFPEGFDAETNEWLEGFEKQRAEWEARYAEAERRHKMHTAQMEKFAAAEAAGRGADDQSSASSAPSEKTAGGSLASDAQLAALREKLAGSA"},"dna_sequence":{"accession":"NC_000962.3","fmin":"1833541","fmax":"1834987","strand":"+","sequence":"ATGCCGAGTCCCACCGTCACCTCGCCGCAAGTAGCCGTCAACGACATAGGCTCTAGCGAGGACTTTCTCGCCGCAATAGACAAAACGATCAAGTACTTCAACGATGGCGACATCGTCGAAGGCACCATCGTCAAAGTGGACCGGGACGAGGTGCTCCTCGACATCGGCTACAAGACCGAAGGCGTGATCCCCGCCCGCGAACTGTCCATCAAGCACGACGTCGACCCCAACGAGGTCGTTTCCGTCGGTGACGAGGTCGAAGCCCTGGTGCTCACCAAGGAGGACAAAGAGGGCCGGCTCATCCTCTCCAAGAAACGCGCGCAGTACGAGCGTGCCTGGGGCACCATCGAGGCGCTCAAGGAGAAGGACGAGGCCGTCAAGGGCACGGTCATCGAGGTCGTCAAGGGTGGCCTGATCCTCGACATCGGGCTGCGCGGTTTCCTGCCCGCCTCGCTGGTGGAGATGCGCCGGGTGCGCGACCTGCAGCCCTACATCGGCAAGGAGATCGAGGCCAAGATCATCGAGCTGGACAAGAACCGCAACAACGTGGTGCTGTCCCGTCGCGCCTGGCTGGAGCAGACCCAGTCCGAGGTGCGCAGCGAGTTCCTGAATAACTTGCAAAAAGGCACCATCCGAAAGGGTGTCGTGTCCTCGATCGTCAACTTCGGCGCGTTCGTCGATCTCGGCGGTGTGGACGGTCTGGTGCATGTCTCCGAGCTATCGTGGAAGCACATCGACCACCCGTCCGAGGTGGTCCAGGTTGGTGACGAGGTCACCGTCGAGGTGCTCGACGTCGACATGGACCGTGAGCGGGTTTCGTTGTCACTCAAGGCGACTCAGGAAGACCCGTGGCGGCACTTCGCCCGCACTCACGCGATCGGGCAGATCGTGCCGGGCAAGGTCACCAAGTTGGTTCCGTTCGGTGCATTCGTCCGCGTCGAGGAGGGTATCGAGGGCCTGGTGCACATCTCCGAGCTGGCCGAGCGTCACGTCGAGGTGCCCGATCAGGTGGTTGCCGTCGGCGACGACGCGATGGTCAAGGTCATCGACATCGACCTGGAGCGCCGTCGGATCTCGTTGTCGCTCAAGCAAGCCAATGAGGACTACACCGAGGAGTTCGACCCGGCGAAGTACGGCATGGCCGACAGTTACGACGAGCAGGGCAACTACATCTTCCCCGAGGGCTTCGATGCCGAAACCAACGAATGGCTTGAGGGATTCGAAAAGCAGCGCGCCGAATGGGAAGCTCGGTACGCCGAGGCCGAGCGCCGGCACAAGATGCACACCGCGCAGATGGAGAAGTTCGCCGCCGCCGAGGCGGCTGGACGCGGCGCGGACGATCAGTCGTCGGCCAGTAGCGCACCGTCGGAAAAGACCGCGGGTGGATCACTGGCCAGCGACGCCCAGCTGGCGGCCCTGCGGGAAAAACTCGCCGGCAGCGCTTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3004721","ARO_id":"42776","ARO_name":"Mycobacterium tuberculosis rpsA mutations conferring resistance to pyrazinamide","CARD_short_name":"Mtub_rpsA_PZA","ARO_description":"RpsA, the 30S ribosomal protein S1 of Mycobacterium tuberculosis, is involved in trans-translation and is targeted by pyrazinonic acid, the active form of the antibiotic pyrazinamide, which disrupts the initiation of mRNA translation. Mutations in the amino acid sequence of rpsA can confer resistance to pyrazinamide maintaining rpsA function.","ARO_category":{"42777":{"category_aro_accession":"3004722","category_aro_cvterm_id":"42777","category_aro_name":"pyrazinamide resistant rpsA","category_aro_description":"The 30S ribosomal protein S1 of Mycobacterium tuberculosis is required for mRNA translation initiation, playing a particular role in trans-translation. Mutations to rpsA prevent pyrazinoic acid, the active form of pyrazinamide catalyzed by pncA, from targeting RpsA to inhibit translation.","category_aro_class_name":"AMR Gene Family"},"39997":{"category_aro_accession":"3003413","category_aro_cvterm_id":"39997","category_aro_name":"pyrazinamide","category_aro_description":"Pyrazinamide is an antimycobacterial. It is highly specific and active only against Mycobacterium tuberculosis. This compound is a prodrug and needs to be activated inside the cell. It interferes with the bacterium's ability to synthesize new fatty acids, causing cell death.","category_aro_class_name":"Antibiotic"},"45737":{"category_aro_accession":"3007155","category_aro_cvterm_id":"45737","category_aro_name":"pyrazine antibiotic","category_aro_description":"A group of antibiotics derived from pyrazine.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2287":{"model_id":"2287","model_name":"Mycolicibacterium smegmatis ndh with mutation conferring resistance to isoniazid","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"3649":"I17T","3650":"T29P","3651":"H46P","3652":"G84D","3653":"L100P","3654":"A115T","3655":"Y122N","3656":"R145C","3657":"F170S","3658":"A187P","3659":"V246A","3660":"V272E","3661":"V300G","3663":"Y361H","3662":"Q335H"},"Curated-R":{"3649":"I17T","3650":"T29P","3651":"H46P","3652":"G84D","3653":"L100P","3654":"A115T","3655":"Y122N","3656":"R145C","3657":"F170S","3658":"A187P","3659":"V246A","3660":"V272E","3661":"V300G","3663":"Y361H","3662":"Q335H"},"experimental":{"3649":"I17T","3650":"T29P","3651":"H46P","3652":"G84D","3653":"L100P","3654":"A115T","3655":"Y122N","3656":"R145C","3657":"F170S","3658":"A187P","3659":"V246A","3660":"V272E","3661":"V300G","3663":"Y361H","3662":"Q335H"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"5368":{"protein_sequence":{"accession":"AIU22003.1","sequence":"MSHPGATASDRHKVVIIGSGFGGLTAAKTLKRADVDVKLIARTTHHLFQPLLYQVATGIISEGEIAPATRVILRKQKNAQVLLCDVTHIDLENKTVDSVLLGHTYSTPYDSLIIAAGAGQSYFGNDHFAEFAPGMKSIDDALELRGRILGAFEQAERSSDPVRRAKLLTFTVVGAGPTGVEMAGQIAELADQTLRGSFRHIDPTEARVILLDAAPAVLPPMGEKLGKKARARLEKMGVEVQLGAMVTDVDRNGITVKDSDGTIRRIESACKVWSAGVSASPLGKDLAEQSGVELDRAGRVKVQPDLTLPGHPNVFVVGDMAAVEGVPGVAQGAIQGGRYAAKIIKREVSGTSPKIRTPFEYFDKGSMATVSRFSAVAKVGPVEFAGFFAWLCWLVLHLVYLVGFKTKIVTLLSWGVTFLSTKRGQLTITEQQAYARTRIEELEEIAAAVQDTEKAAS"},"dna_sequence":{"accession":"CP009496.1","fmin":"3684057","fmax":"3685431","strand":"+","sequence":"ATGAGCCATCCCGGAGCTACGGCGTCGGATCGGCATAAAGTCGTCATCATCGGTTCGGGTTTCGGTGGTCTCACCGCTGCCAAGACCCTCAAGCGCGCTGACGTCGACGTCAAGCTAATCGCCCGTACCACGCACCACCTCTTCCAGCCGCTGCTCTACCAGGTGGCGACCGGCATCATCTCCGAGGGCGAGATCGCCCCGGCCACTCGAGTGATCCTCCGCAAGCAGAAGAACGCCCAGGTCCTTCTCTGCGATGTGACGCACATCGATCTGGAGAACAAGACCGTGGATTCGGTGCTGCTCGGTCACACCTACTCGACGCCCTACGACAGCCTCATCATCGCCGCGGGCGCGGGTCAGTCCTACTTCGGCAACGACCACTTCGCCGAGTTCGCACCCGGCATGAAGTCGATCGACGATGCGCTGGAGCTGCGCGGTCGCATCCTCGGCGCGTTCGAACAGGCCGAGCGCTCCAGCGACCCGGTGCGCCGCGCGAAGTTGCTGACGTTCACCGTCGTCGGCGCGGGCCCGACCGGCGTCGAGATGGCCGGACAGATCGCCGAATTGGCCGACCAGACTTTGCGGGGCAGCTTCCGCCACATCGATCCCACCGAGGCCCGGGTGATCCTGCTCGACGCCGCACCGGCCGTGCTACCGCCCATGGGCGAGAAGCTCGGCAAGAAGGCGCGGGCCCGTCTGGAGAAGATGGGCGTCGAGGTCCAGCTGGGTGCGATGGTCACCGACGTCGACCGCAACGGCATCACCGTCAAGGATTCCGACGGGACCATCCGTCGCATCGAGTCGGCGTGCAAGGTGTGGTCGGCCGGTGTGTCGGCCAGCCCTCTCGGCAAGGATCTCGCCGAGCAGTCGGGTGTCGAACTCGACCGCGCGGGCCGGGTCAAGGTACAGCCCGACCTGACGCTGCCCGGTCACCCGAACGTGTTCGTCGTGGGCGACATGGCGGCCGTCGAGGGCGTGCCCGGTGTGGCGCAGGGCGCCATCCAGGGTGGCCGCTACGCCGCGAAGATCATCAAGCGTGAGGTCAGTGGCACCAGCCCGAAGATCCGCACGCCGTTCGAGTACTTCGACAAGGGCTCGATGGCGACGGTGTCGCGGTTCTCCGCGGTGGCCAAGGTGGGTCCCGTCGAGTTCGCGGGCTTCTTCGCCTGGTTGTGCTGGCTCGTGCTGCACCTGGTGTACCTGGTCGGGTTCAAGACGAAGATCGTCACACTGCTGTCGTGGGGCGTGACGTTCCTGAGCACCAAGCGTGGTCAGCTCACCATCACCGAGCAGCAGGCCTATGCGCGAACCCGCATCGAGGAGCTCGAGGAGATCGCGGCGGCGGTGCAGGACACCGAGAAAGCCGCGTCCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36871","NCBI_taxonomy_name":"Mycolicibacterium smegmatis","NCBI_taxonomy_id":"1772"}}}},"ARO_accession":"3003778","ARO_id":"40460","ARO_name":"Mycolicibacterium smegmatis ndh with mutation conferring resistance to isoniazid","CARD_short_name":"Msme_ndh_INH","ARO_description":"Mutations in the Mycolicibacterium smegmatis ndh gene that results in increased resistance to isoniazid.","ARO_category":{"40053":{"category_aro_accession":"3003460","category_aro_cvterm_id":"40053","category_aro_name":"antibiotic resistant ndh","category_aro_description":"ndh is a NADH oxidase. It participates in antibiotic resistance by diminishing NADH oxidation and consequently causes an increase in NADH concentration and depletion of NAD+. This alteration of the NADH\/NAD+ ratio prevents the peroxidation reactions required for the activation of INH, as well as the displacement of the NADH-isonicotinic acyl complex from InhA enzyme binding site.","category_aro_class_name":"AMR Gene Family"},"36659":{"category_aro_accession":"3000520","category_aro_cvterm_id":"36659","category_aro_name":"isoniazid","category_aro_description":"Isoniazid is an organic compound that is the first-line anti tuberculosis medication in prevention and treatment. As a prodrug, it is activated by mycobacterial catalase-peroxidases such as M. tuberculosis KatG. Isoniazid inhibits mycolic acid synthesis, which prevents cell wall synthesis in mycobacteria.","category_aro_class_name":"Antibiotic"},"45734":{"category_aro_accession":"3007152","category_aro_cvterm_id":"45734","category_aro_name":"isoniazid-like antibiotic","category_aro_description":"A group of antibiotics containing isoniazid and its derivatives.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1745":{"model_id":"1745","model_name":"KPC-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"1032":{"protein_sequence":{"accession":"AAK70220.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"AY034847.1","fmin":"5","fmax":"887","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002312","ARO_id":"38712","ARO_name":"KPC-2","CARD_short_name":"KPC-2","ARO_description":"KPC-2 is a beta-lactamase found in Klebsiella pneumoniae and Pseudomonas aeruginosa.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2666":{"model_id":"2666","model_name":"Escherichia coli fabI mutations conferring resistance to isoniazid and triclosan","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"7383":"G93A","7384":"G93S","7385":"G93V","7386":"M159T","7387":"F203L","7388":"F203C","7389":"F203A","7390":"F203V"},"Curated-R":{"7383":"G93A","7384":"G93S","7385":"G93V","7386":"M159T","7387":"F203L","7388":"F203C","7389":"F203A","7390":"F203V"},"clinical":{"7383":"G93A","7384":"G93S","7385":"G93V","7386":"M159T","7387":"F203L","7388":"F203C","7389":"F203A","7390":"F203V"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"5254":{"protein_sequence":{"accession":"AAC74370.1","sequence":"MGFLSGKRILVTGVASKLSIAYGIAQAMHREGAELAFTYQNDKLKGRVEEFAAQLGSDIVLQCDVAEDASIDTMFAELGKVWPKFDGFVHSIGFAPGDQLDGDYVNAVTREGFKIAHDISSYSFVAMAKACRSMLNPGSALLTLSYLGAERAIPNYNVMGLAKASLEANVRYMANAMGPEGVRVNAISAGPIRTLAASGIKDFRKMLAHCEAVTPIRRTVTIEDVGNSAAFLCSDLSAGISGEVVHVDGGFSIAAMNELELK"},"dna_sequence":{"accession":"U00096.3","fmin":"1350250","fmax":"1351039","strand":"-","sequence":"ATGGGTTTTCTTTCCGGTAAGCGCATTCTGGTAACCGGTGTTGCCAGCAAACTATCCATCGCCTACGGTATCGCTCAGGCGATGCACCGCGAAGGAGCTGAACTGGCATTCACCTACCAGAACGACAAACTGAAAGGCCGCGTAGAAGAATTTGCCGCTCAATTGGGTTCTGACATCGTTCTGCAGTGCGATGTTGCAGAAGATGCCAGCATCGACACCATGTTCGCTGAACTGGGGAAAGTTTGGCCGAAATTTGACGGTTTCGTACACTCTATTGGTTTTGCACCTGGCGATCAGCTGGATGGTGACTATGTTAACGCCGTTACCCGTGAAGGCTTCAAAATTGCCCACGACATCAGCTCCTACAGCTTCGTTGCAATGGCAAAAGCTTGCCGCTCCATGCTGAATCCGGGTTCTGCCCTGCTGACCCTTTCCTACCTTGGCGCTGAGCGCGCTATCCCGAACTACAACGTTATGGGTCTGGCAAAAGCGTCTCTGGAAGCGAACGTGCGCTATATGGCGAACGCGATGGGTCCGGAAGGTGTGCGTGTTAACGCCATCTCTGCTGGTCCGATCCGTACTCTGGCGGCCTCCGGTATCAAAGACTTCCGCAAAATGCTGGCTCATTGCGAAGCCGTTACCCCGATTCGCCGTACCGTTACTATTGAAGATGTGGGTAACTCTGCGGCATTCCTGTGCTCCGATCTCTCTGCCGGTATCTCCGGTGAAGTGGTCCACGTTGACGGCGGTTTCAGCATTGCTGCAATGAACGAACTCGAACTGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36849","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. MG1655","NCBI_taxonomy_id":"511145"}}}},"ARO_accession":"3004045","ARO_id":"41097","ARO_name":"Escherichia coli fabI mutations conferring resistance to isoniazid and triclosan","CARD_short_name":"Ecol_fabI_MULT","ARO_description":"fabI is a enoyl-acyl carrier reductase used in lipid metabolism and fatty acid biosynthesis. The bacterial biocide Triclosan blocks the final reduction step in fatty acid elongation, inhibiting biosynthesis. Point mutations in fabI can confer resistance to Triclosan and Isoniazid.","ARO_category":{"41434":{"category_aro_accession":"3004270","category_aro_cvterm_id":"41434","category_aro_name":"antibiotic resistant fabI","category_aro_description":"fabI is a enoyl-acyl carrier reductase used in lipid metabolism and fatty acid biosynthesis. The bacterial biocide Triclosan blocks the final reduction step in fatty acid elongation, inhibiting biosynthesis. Point mutations in fabI can confer resistance to Triclosan and Isoniazid.","category_aro_class_name":"AMR Gene Family"},"37250":{"category_aro_accession":"3000870","category_aro_cvterm_id":"37250","category_aro_name":"triclosan","category_aro_description":"Triclosan is a common antibacterial agent added to many consumer products as a biocide.  It is an inhibitor of fatty acid biosynthesis by blocking enoyl-carrier protein reductase (FabI).","category_aro_class_name":"Antibiotic"},"43746":{"category_aro_accession":"3005386","category_aro_cvterm_id":"43746","category_aro_name":"disinfecting agents and antiseptics","category_aro_description":"Disinfectants that can also interact with antimicrobial resistance mechanisms, e.g. molecule efflux, and thus are the targets of disinfectant resistance.","category_aro_class_name":"Drug Class"},"45734":{"category_aro_accession":"3007152","category_aro_cvterm_id":"45734","category_aro_name":"isoniazid-like antibiotic","category_aro_description":"A group of antibiotics containing isoniazid and its derivatives.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2681":{"model_id":"2681","model_name":"Escherichia coli fabG mutations conferring resistance to triclosan","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"7530":"Y151V"},"Curated-R":{"7530":"Y151V"},"clinical":{"7530":"Y151V"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"5523":{"protein_sequence":{"accession":"AAC74177.1","sequence":"MNFEGKIALVTGASRGIGRAIAETLAARGAKVIGTATSENGAQAISDYLGANGKGLMLNVTDPASIESVLEKIRAEFGEVDILVNNAGITRDNLLMRMKDEEWNDIIETNLSSVFRLSKAVMRAMMKKRHGRIITIGSVVGTMGNGGQANYAAAKAGLIGFSKSLAREVASRGITVNVVAPGFIETDMTRALSDDQRAGILAQVPAGRLGGAQEIANAVAFLASDEAAYITGETLHVNGGMYMV"},"dna_sequence":{"accession":"U00096.3","fmin":"1150669","fmax":"1151404","strand":"+","sequence":"ATGAATTTTGAAGGAAAAATCGCACTGGTAACCGGTGCAAGCCGCGGAATTGGCCGCGCAATTGCTGAAACGCTCGCAGCCCGTGGCGCGAAAGTTATTGGCACTGCGACCAGTGAAAATGGCGCTCAGGCGATCAGTGATTATTTAGGTGCCAACGGCAAAGGTCTGATGTTGAATGTGACCGACCCGGCATCTATCGAATCTGTTCTGGAAAAAATTCGCGCAGAATTTGGTGAAGTGGATATCCTGGTCAATAATGCCGGTATCACTCGTGATAACCTGTTAATGCGAATGAAAGATGAAGAGTGGAACGATATTATCGAAACCAACCTTTCATCTGTTTTCCGTCTGTCAAAAGCGGTAATGCGCGCTATGATGAAAAAGCGTCATGGTCGTATTATCACTATCGGTTCTGTGGTTGGTACCATGGGAAATGGCGGTCAGGCCAACTACGCTGCGGCGAAAGCGGGCTTGATCGGCTTCAGTAAATCACTGGCGCGCGAAGTTGCGTCACGCGGTATTACTGTAAACGTTGTTGCTCCGGGCTTTATTGAAACGGACATGACACGTGCGCTGAGCGATGACCAGCGTGCGGGTATCCTGGCGCAGGTTCCTGCGGGTCGCCTCGGCGGCGCACAGGAAATCGCCAACGCGGTTGCATTCCTGGCATCCGACGAAGCAGCTTACATCACGGGTGAAACTTTGCATGTGAACGGCGGGATGTACATGGTCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36849","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. MG1655","NCBI_taxonomy_id":"511145"}}}},"ARO_accession":"3004049","ARO_id":"41114","ARO_name":"Escherichia coli fabG mutations conferring resistance to triclosan","CARD_short_name":"Ecol_fabG_TRC","ARO_description":"fabG is a 3-oxoacyl-acyl carrier protein reductase involved in lipid metabolism and fatty acid biosynthesis.The bacterial biocide Triclosan blocks the final reduction step in fatty acid elongation, inhibiting biosynthesis. Point mutations in fabG can confer resistance to Triclosan.","ARO_category":{"41448":{"category_aro_accession":"3004284","category_aro_cvterm_id":"41448","category_aro_name":"antibiotic resistant fabG","category_aro_description":"fabG is a 3-oxoacyl-acyl carrier protein reductase involved in lipid metabolism and fatty acid biosynthesis. The bacterial biocide Triclosan blocks the final reduction step in fatty acid elongation, inhibiting biosynthesis. Point mutations in fabG can confer resistance to Triclosan.","category_aro_class_name":"AMR Gene Family"},"37250":{"category_aro_accession":"3000870","category_aro_cvterm_id":"37250","category_aro_name":"triclosan","category_aro_description":"Triclosan is a common antibacterial agent added to many consumer products as a biocide.  It is an inhibitor of fatty acid biosynthesis by blocking enoyl-carrier protein reductase (FabI).","category_aro_class_name":"Antibiotic"},"43746":{"category_aro_accession":"3005386","category_aro_cvterm_id":"43746","category_aro_name":"disinfecting agents and antiseptics","category_aro_description":"Disinfectants that can also interact with antimicrobial resistance mechanisms, e.g. molecule efflux, and thus are the targets of disinfectant resistance.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2694":{"model_id":"2694","model_name":"MexCD-OprJ with type A NfxB mutation","model_type":"efflux pump system meta-model","model_type_id":"41112","model_description":"Efflux Pump System Meta-Models (EPS) are dedicated to efflux complexes and their regulators, such as AcrAB-TolC. Using the efflux pump components parameter, this model type simply includes a list of detection models for each component of the complex. This model type is still under development and not currently supported by the Resistance Gene Identifier (RGI) software.","model_param":{"41141":{"param_type":"efflux pump components","param_description":"Association of proteins within efflux protein complexes or regulatory networks are encoded by the efflux pump components parameter: model_id,model_id,model_id, etc.","param_type_id":"41141","param_value":{"7551":"2691,805,1523,704"}},"snp":{"Curated-R":{"7551":"Y151V"}}},"ARO_accession":"3004061","ARO_id":"41128","ARO_name":"MexCD-OprJ with type A NfxB mutation","CARD_short_name":"Paer_NfxBa_MULT","ARO_description":"MexCD\u2013OprJ with type A NfxB phenotype are four to eight times more resistant to ofloxacin, erythromycin, and new zwitterionic cephems, i.e., cefpirome, cefclidin, cefozopran, and cefoselis, than the parent strain, PAO1.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36250":{"category_aro_accession":"3000111","category_aro_cvterm_id":"36250","category_aro_name":"novobiocin","category_aro_description":"Novobiocin is an aminocoumarin antibiotic produced by Streptomyces spheroides and Streptomyces niveus, and binds DNA gyrase subunit B inhibiting ATP-dependent DNA supercoiling.","category_aro_class_name":"Antibiotic"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"37007":{"category_aro_accession":"3000663","category_aro_cvterm_id":"37007","category_aro_name":"ofloxacin","category_aro_description":"Ofloxacin is a 6-fluoro, 7-piperazinyl quinolone with a methyl-substituted oxazine ring. It has a broad spectrum of activity including many enterobacteria and mycoplasma but most anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36242":{"category_aro_accession":"3000103","category_aro_cvterm_id":"36242","category_aro_name":"aminocoumarin antibiotic","category_aro_description":"Aminocoumarin antibiotics bind DNA gyrase subunit B to inhibit ATP-dependent DNA supercoiling.","category_aro_class_name":"Drug Class"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"5943":{"model_id":"5943","model_name":"TEM-247","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"490"}},"model_sequences":{"sequence":{"8665":{"protein_sequence":{"accession":"UTS94241.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLFLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"ON651488.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTATTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"46213","NCBI_taxonomy_name":"Pseudomonas alloputida","NCBI_taxonomy_id":"1940621"}}}},"ARO_accession":"3007451","ARO_id":"46212","ARO_name":"TEM-247","CARD_short_name":"TEM-247","ARO_description":"TEM-247 is a TEM class A beta-lactamase.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2753":{"model_id":"2753","model_name":"HMB-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"8286":{"protein_sequence":{"accession":"AMY61250.1","sequence":"MKIHLWISLGLLLLTNIVLAEEPLPELEVKKIDEGVYLHTSYENYPSWGLVASHGLVFVDGKDAYIIDTPATVKDTEVLVQWINDQGFKPKASISTHFHDDSTIGIAYLNSKSIPTYASEQTNELLNKEVAAQATHSFKKNPYWLLKNKIEAFYPGAGHTPDNLVVWLPKQKILFGGCFVKPEGLGNLSHAVVSEWPASAEKLINRYSDAKIVVPGHGTMGDASLLEKTKQRALEAVAKKK"},"dna_sequence":{"accession":"KU961660.2","fmin":"2031","fmax":"2757","strand":"+","sequence":"ATGAAAATACATTTATGGATATCATTGGGTCTTTTGCTGCTGACAAACATCGTTCTTGCAGAAGAACCGCTACCCGAACTGGAAGTTAAAAAAATCGATGAGGGTGTTTATCTGCATACGTCCTATGAAAATTATCCAAGCTGGGGCTTGGTTGCATCCCACGGTTTGGTTTTTGTGGATGGTAAAGACGCTTACATTATTGATACACCCGCTACTGTTAAAGACACAGAAGTGTTAGTGCAATGGATTAACGATCAAGGCTTCAAACCCAAGGCCAGCATTTCTACGCACTTTCACGATGACAGCACCATCGGCATTGCCTACTTAAATTCCAAATCCATTCCGACCTACGCATCAGAACAAACTAATGAATTGCTTAATAAAGAAGTCGCTGCACAGGCAACGCATTCGTTTAAGAAAAATCCTTATTGGCTGTTAAAAAATAAAATCGAAGCTTTTTATCCGGGCGCTGGCCACACGCCTGACAATTTAGTGGTGTGGTTGCCGAAGCAGAAAATTCTATTCGGTGGCTGTTTTGTAAAACCCGAAGGGCTGGGAAATTTAAGCCATGCGGTAGTTTCTGAATGGCCTGCTTCTGCAGAAAAACTTATCAATCGCTATAGCGACGCAAAAATCGTAGTACCGGGTCATGGAACAATGGGCGATGCATCGCTGCTGGAAAAAACCAAACAGCGTGCGCTTGAGGCGGTTGCAAAGAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3004092","ARO_id":"41198","ARO_name":"HMB-1","CARD_short_name":"HMB-1","ARO_description":"Shotgun cloning of beta-lactam resistant P. aeruginosa NRZ-03096 yielded a clone producing a novel subclass B1 enzyme with only 74.3% identity to the next nearest relative, KHM-1. The novel MBL was named HMB-1 (for Hamburg MBL). HMB-1 gene was chromosomally located as part of a Tn 3 family transposon that was named Tn 6345, where expression of bla HMB-1 in E. coli TOP10 led to increased resistance to beta-lactams.","ARO_category":{"41373":{"category_aro_accession":"3004209","category_aro_cvterm_id":"41373","category_aro_name":"HMB beta-lactamase","category_aro_description":"First identified from a multi-drug resistant Pseudomonas aeruginosa clinical isolate in 2012, HMB type beta-lactamases can be encoded in transposons and hydrolyze carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2746":{"model_id":"2746","model_name":"AcrAD-TolC","model_type":"efflux pump system meta-model","model_type_id":"41112","model_description":"Efflux Pump System Meta-Models (EPS) are dedicated to efflux complexes and their regulators, such as AcrAB-TolC. Using the efflux pump components parameter, this model type simply includes a list of detection models for each component of the complex. This model type is still under development and not currently supported by the Resistance Gene Identifier (RGI) software.","model_param":{"41141":{"param_type":"efflux pump components","param_description":"Association of proteins within efflux protein complexes or regulatory networks are encoded by the efflux pump components parameter: model_id,model_id,model_id, etc.","param_type_id":"41141","param_value":{"7770":"2661,1427,826,1337,986,152,2764"}},"snp":{"Curated-R":{"7770":"Y151V"}}},"ARO_accession":"3004082","ARO_id":"41184","ARO_name":"AcrAD-TolC","CARD_short_name":"AcrAD-TolC","ARO_description":"AcrAD-TolC efflux pump system in E. coli from the resistance-nodulation-division family, was shown to participate in the efflux of aminoglycosides.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35924":{"category_aro_accession":"0000005","category_aro_cvterm_id":"35924","category_aro_name":"neomycin","category_aro_description":"Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"46133":{"category_aro_accession":"3007382","category_aro_cvterm_id":"46133","category_aro_name":"gentamicin","category_aro_description":"Gentamicin is a commonly used aminoglycoside antibiotic derived from members of the Micromonospora genus of bacteria. It acts by binding the 30S ribosomal subunit, thus inhibiting protein synthesis. Gentamicin is typically used to treat Gram-negative infections of the repiratory and urinary tract, as well as infections of the bone and soft tissue. It also exhibits considerable nephrotoxicity and ototoxicity. Gentamicin is administered as a mixture of gentamicin type C (which makes about around 80% of the complex) and types A, B, and X (distributed in the remaining 20% of the complex).","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2778":{"model_id":"2778","model_name":"MCR-2.1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"5514":{"protein_sequence":{"accession":"SBV31106.1","sequence":"MTSHHSWYRYSINPFVLMGLVALFLAATANLTFFEKAMAVYPVSDNLGFIISMAVAVMGAMLLIVVLLSYRYVLKPVLILLLIMGAVTSYFTDTYGTVYDTTMLQNAMQTDQAESKDLMNLAFFVRIIGLGVLPSVLVAVAKVNYPTWGKGLIQRAMTWGVSLVLLLVPIGLFSSQYASFFRVHKPVRFYINPITPIYSVGKLASIEYKKATAPTDTIYHAKDAVQTTKPSERKPRLVVFVVGETARADHVQFNGYGRETFPQLAKVDGLANFSQVTSCGTSTAYSVPCMFSYLGQDDYDVDTAKYQENVLDTLDRLGVGILWRDNNSDSKGVMDKLPATQYFDYKSATNNTICNTNPYNECRDVGMLVGLDDYVSANNGKDMLIMLHQMGNHGPAYFKRYDEQFAKFTPVCEGNELAKCEHQSLINAYDNALLATDDFIAKSIDWLKTHEANYDVAMLYVSDHGESLGENGVYLHGMPNAFAPKEQRAVPAFFWSNNTTFKPTASDTVLTHDAITPTLLKLFDVTAGKVKDRAAFIQ"},"dna_sequence":{"accession":"LT598652.1","fmin":"26778","fmax":"28395","strand":"+","sequence":"ATGACATCACATCACTCTTGGTATCGCTATTCTATCAATCCTTTTGTGCTGATGGGTTTGGTGGCGTTATTTTTGGCAGCGACAGCGAACCTGACATTTTTTGAAAAAGCGATGGCGGTCTATCCTGTATCGGATAACTTAGGCTTTATCATCTCAATGGCGGTGGCGGTGATGGGTGCTATGCTACTGATTGTCGTGCTGTTATCCTATCGCTATGTGCTAAAGCCTGTCCTGATTTTGCTACTGATTATGGGTGCGGTGACGAGCTATTTTACCGATACTTATGGCACGGTCTATGACACCACCATGCTCCAAAATGCCATGCAAACCGACCAAGCCGAGTCTAAGGACTTGATGAATTTGGCGTTTTTTGTGCGAATTATCGGGCTTGGCGTGTTGCCAAGTGTGTTGGTCGCAGTTGCCAAAGTCAATTATCCAACATGGGGCAAAGGTCTGATTCAGCGTGCGATGACATGGGGTGTCAGCCTTGTGCTGTTGCTTGTGCCGATTGGACTATTTAGCAGTCAGTATGCGAGTTTCTTTCGGGTGCATAAGCCAGTGCGTTTTTATATCAACCCGATTACGCCGATTTATTCGGTGGGTAAGCTTGCCAGTATCGAGTACAAAAAAGCCACTGCGCCAACAGACACCATCTATCATGCCAAAGACGCCGTGCAGACCACCAAGCCGAGCGAGCGTAAGCCACGCCTAGTGGTGTTCGTCGTCGGTGAGACGGCGCGTGCTGACCATGTGCAGTTCAATGGCTATGGCCGTGAGACTTTCCCGCAGCTTGCCAAAGTTGATGGCTTGGCGAATTTTAGCCAAGTGACATCGTGTGGCACATCGACGGCGTATTCTGTGCCGTGTATGTTCAGCTATTTGGGTCAAGATGACTATGATGTCGATACCGCCAAATACCAAGAAAATGTGCTAGATACGCTTGACCGCTTGGGTGTGGGTATCTTGTGGCGTGATAATAATTCAGACTCAAAAGGCGTGATGGATAAGCTACCTGCCACGCAGTATTTTGATTATAAATCAGCAACCAACAATACCATCTGTAACACCAATCCCTATAACGAATGCCGTGATGTCGGTATGCTTGTCGGGCTAGATGACTATGTCAGCGCCAATAATGGCAAAGATATGCTCATCATGCTACACCAAATGGGCAATCATGGGCCGGCGTACTTTAAGCGTTATGATGAGCAATTTGCCAAATTCACCCCCGTGTGCGAAGGCAACGAGCTTGCCAAATGCGAACACCAATCACTCATCAATGCCTATGACAATGCGCTACTTGCGACTGATGATTTTATCGCCAAAAGCATCGATTGGCTAAAAACGCATGAAGCGAACTACGATGTCGCCATGCTCTATGTCAGTGACCACGGCGAGAGCTTGGGCGAAAATGGTGTCTATCTGCATGGTATGCCAAATGCCTTTGCACCAAAAGAACAGCGAGCTGTGCCTGCGTTTTTTTGGTCAAATAATACGACATTCAAGCCAACTGCCAGCGATACTGTGCTGACGCATGATGCGATTACGCCAACACTGCTTAAGCTGTTTGATGTCACAGCGGGCAAGGTCAAAGACCGCGCGGCATTTATCCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3004110","ARO_id":"41231","ARO_name":"MCR-2.1","CARD_short_name":"MCR-2.1","ARO_description":"MCR-2 is a plasmid-borne phosphoethanolamine transferase that interferes with binding of colistin to the cell membrane via addition of phosphoethanolamine to lipid A, resulting in reduction of the negative charge of the cell membrane. Originally identified in a Belgian sample of Escherichia coli by Xavier et al, (2016).","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2789":{"model_id":"2789","model_name":"Escherichia coli mipA","model_type":"protein knockout model","model_type_id":"40354","model_description":"Protein Knockout Models (PKM) reflect resistance by the absence of a gene product, most often deletion of a gene involved in antibiotic import, such as Vibrio cholerae OmpT. Like Protein Homolog Models (PHMs), PKMs include a reference sequence and a bitscore cut-off for detection using BLASTP but instead are designed to only report lack of detection under Perfect or Strict criteria. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff. This model type is still under development and not currently supported by the Resistance Gene Identifier (RGI) software.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"5859":{"protein_sequence":{"accession":"NP_310518.1","sequence":"MTKLKLLALGVLIATSAGVAHAEGKFSLGAGVGVVEHPYKDYDTDVYPVPVINYEGDNFWFRGLGGGYYLWNDATDKLSITAYWSPLYFKAKDSGDHQMRHLDDRKSTMMAGLSYAHFTQYGYLRTTLAGDTLDNSNGIVWDMAWLYRYTNGGLTVTPGIGVQWNSENQNEYYYGVSRKESARSGLRGYNSNDSWSPYLELSASYNFLGDWSVYGTARYTRLSDEVTDSPIVDKSWTGLISTGITYKF"},"dna_sequence":{"accession":"NC_002695.2","fmin":"2467467","fmax":"2468214","strand":"-","sequence":"GTGACCAAACTCAAACTTCTGGCACTTGGAGTGCTTATCGCAACGTCTGCAGGCGTAGCGCACGCTGAAGGTAAATTTTCCCTGGGCGCAGGCGTAGGTGTCGTTGAACACCCATATAAAGATTACGATACCGATGTTTACCCAGTACCGGTAATCAACTATGAAGGCGATAACTTCTGGTTCCGTGGCTTAGGTGGTGGTTACTACCTGTGGAATGACGCAACGGATAAACTTTCAATTACCGCTTACTGGTCGCCGCTTTACTTCAAAGCTAAAGACAGTGGCGATCACCAAATGCGTCACCTGGATGACCGTAAGAGCACCATGATGGCTGGTCTGTCTTATGCTCACTTTACCCAGTACGGTTACCTGCGTACCACCCTGGCTGGCGATACCCTGGATAACAGCAACGGCATCGTCTGGGATATGGCCTGGTTGTATCGTTACACCAACGGTGGCCTGACCGTGACTCCGGGTATTGGTGTGCAGTGGAACAGCGAAAACCAGAACGAATACTATTATGGCGTATCGCGCAAAGAGTCCGCTCGCAGCGGTCTGCGTGGCTATAACTCGAACGACAGCTGGAGCCCTTACCTGGAGCTGAGCGCCAGCTACAACTTCCTCGGCGACTGGAGTGTTTACGGTACCGCGCGCTACACCCGTCTGTCTGATGAAGTTACTGACAGCCCGATTGTGGATAAATCCTGGACTGGCCTGATTTCTACCGGGATCACCTACAAATTCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36747","NCBI_taxonomy_name":"Escherichia coli O157:H7 str. Sakai","NCBI_taxonomy_id":"386585"}}}},"ARO_accession":"3004127","ARO_id":"41253","ARO_name":"Escherichia coli mipA","CARD_short_name":"Ecol_mipA","ARO_description":"MltA-interacting protein (mipA), is an antibiotic resistance-related outer membrane protein. Deletion of mipA increases kanamycin, nalidixic acid and streptomycin resistance.","ARO_category":{"41444":{"category_aro_accession":"3004280","category_aro_cvterm_id":"41444","category_aro_name":"MipA-interacting Protein","category_aro_description":"The MltA-interacting Protein (MipA) family consists mainly of homologs to MipA and OmpV proteins. Proteins of this family, are predicted to form a beta-barrel.","category_aro_class_name":"AMR Gene Family"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36383":{"category_aro_accession":"3000244","category_aro_cvterm_id":"36383","category_aro_name":"reduced permeability to antibiotic","category_aro_description":"Reduction in permeability to antibiotic, generally through reduced production of porins, can provide resistance.","category_aro_class_name":"Resistance Mechanism"},"40429":{"category_aro_accession":"3003764","category_aro_cvterm_id":"40429","category_aro_name":"resistance by absence","category_aro_description":"Mechanism of antibiotic resistance conferred by deletion of gene (usually a porin).","category_aro_class_name":"Resistance Mechanism"}}},"2795":{"model_id":"2795","model_name":"MCR-3.1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"4121":{"protein_sequence":{"accession":"ASF81896.1","sequence":"MPSLIKIKIVPLMFFLALYFAFMLNWRGVLHFYEILYKLEDFKFGFAISLPILLVAALNFVFVPFSIRYLIKPFFALLIALSAIVSYTMMKYRVLFDQNMIQNIFETNQNEALAYLSLPIIVWVTIAGFIPAILLFFVEIEYEEKWFKGILTRALSMFASLIVIAVIAALYYQDYVSVGRNNSNLQREIVPANFVNSTVKYVYNRYLAEPIPFTTLGDDAKRDTNQSKPTLMFLVVGETARGKNFSMNGYEKDTNPFTSKSGGVISFNDVRSCGTATAVSVPCMFSNMGRKEFDDNRARNSEGLLDVLQKTGISIFWKENDGGCKGVCDRVPNIEIEPKDHPKFCDKNTCYDEVVLQDLDSEIAQMKGDKLVGFHLIGSHGPTYYKRYPDAHRQFTPDCPRSDIENCTDEELTNTYDNTIRYTDFVIGEMIAKLKTYEDKYNTALLYVSDHGESLGALGLYLHGTPYQFAPDDQTRVPMQVWMSPGFTKEKGVDMACLQQKAADTRYSHDNIFSSVLGIWDVKTSVYEKGLDIFSQCRNVQ"},"dna_sequence":{"accession":"KY924928.1","fmin":"161133","fmax":"162759","strand":"+","sequence":"ATGCCTTCCCTTATAAAAATAAAAATTGTTCCGCTTATGTTCTTTTTGGCACTGTATTTTGCATTTATGCTGAACTGGCGTGGAGTTCTCCATTTTTACGAAATCCTTTACAAATTAGAAGATTTTAAGTTTGGTTTCGCCATTTCATTACCAATATTGCTTGTTGCAGCGCTTAACTTTGTATTTGTTCCATTTTCGATACGGTATTTAATAAAGCCTTTTTTTGCACTTCTTATCGCACTTAGTGCAATCGTTAGTTACACAATGATGAAGTATAGAGTCTTGTTTGATCAAAACATGATTCAGAATATTTTTGAAACCAATCAAAATGAGGCGTTAGCATATTTAAGCTTACCAATTATAGTATGGGTTACTATTGCTGGTTTTATCCCTGCCATTTTACTTTTCTTTGTTGAAATTGAATATGAGGAAAAATGGTTCAAAGGGATTCTAACTCGTGCCCTATCGATGTTTGCATCACTTATAGTGATTGCGGTTATTGCAGCACTATACTATCAAGATTATGTGTCAGTGGGGCGCAACAATTCAAACCTCCAGCGTGAGATTGTTCCAGCCAATTTCGTTAATAGTACCGTTAAATACGTTTACAATCGTTATCTTGCTGAACCAATCCCATTTACAACTTTAGGTGATGATGCAAAACGGGATACTAATCAAAGTAAGCCCACGTTGATGTTTCTGGTCGTTGGTGAAACCGCTCGTGGTAAAAATTTCTCGATGAATGGCTATGAGAAAGACACCAATCCATTTACCAGTAAATCTGGTGGCGTGATCTCCTTTAATGATGTTCGTTCGTGTGGGACTGCAACCGCTGTATCCGTCCCCTGCATGTTCTCCAATATGGGGAGAAAGGAGTTTGATGATAATCGCGCTCGCAATAGCGAGGGCCTGCTAGATGTGTTGCAAAAAACGGGGATCTCCATTTTTTGGAAGGAGAACGATGGAGGCTGCAAAGGCGTCTGCGACCGAGTACCTAACATCGAAATCGAACCAAAGGATCACCCTAAGTTCTGCGATAAAAACACATGCTATGACGAGGTTGTCCTTCAAGACCTCGATAGTGAAATTGCTCAAATGAAAGGGGATAAGCTGGTTGGCTTCCACCTGATAGGTAGCCATGGCCCAACCTACTACAAGCGCTACCCTGATGCTCATCGTCAGTTCACCCCTGACTGTCCACGCAGTGATATTGAAAACTGCACAGATGAAGAGCTCACCAACACCTATGACAACACCATCCGCTACACCGATTTCGTGATTGGAGAGATGATTGCCAAGTTGAAAACCTACGAAGATAAGTACAACACCGCGTTGCTCTACGTCTCCGATCATGGTGAATCACTGGGAGCATTAGGGCTTTACCTACACGGTACACCGTACCAGTTTGCACCGGATGATCAGACCCGTGTTCCTATGCAGGTGTGGATGTCACCTGGATTTACCAAAGAGAAAGGCGTTGATATGGCGTGTTTGCAGCAGAAAGCCGCTGATACTCGTTACTCACACGATAATATTTTCTCATCTGTATTGGGTATCTGGGACGTCAAAACATCAGTTTACGAAAAGGGTCTAGATATTTTCAGTCAATGTCGTAATGTTCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3004139","ARO_id":"41267","ARO_name":"MCR-3.1","CARD_short_name":"MCR-3.1","ARO_description":"MCR-3 is a plasmid-borne phosphoethanolamine transferase that interferes with binding of colistin to the cell membrane via addition of phosphoethanolamine to lipid A, resulting reduction in negative charge of the cell membrane. Originally described by Yin et al. 2017, from a porcine Escherichia coli plasmid pWJ1.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2818":{"model_id":"2818","model_name":"Streptomyces ambofaciens 23S rRNA with mutation conferring resistance to macrolide antibiotics","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"41093","param_value":"5000"},"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"7931":"a2305g"},"Curated-R":{"7931":"a2305g"},"clinical":{"7931":"a2305g"}}},"model_sequences":{"sequence":{"4163":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"NZ_CP012949.1","fmin":"4334992","fmax":"4338141","strand":"+","sequence":"ACAGTGGACGCGAGCATCTGTGGCCAAGTTTTTAAGGGCGCACGGTGGATGCCTTGGCACCAGGAACCGATGAAGGACGTGGGAGGCCACGATAGTCCCCGGGGAGCCGTCAACCAGGCTTTGATCCGGGGGTTTCCGAATGGGGAAACCCGGCAGTCGTCATGGGCTGTCACCCGCTGCTGAACACATAGGCAGTGTGGAGGGAACGCGGGGAAGTGAAACATCTCAGTACCCGCAGGAAGAGAAAACAACCGTGATTCCGGGAGTAGTGGCGAGCGAAACCGGATGAGGCCAAACCGTATACGTGTGAGACCCGGCAGGGGTTGCGTGTGCGGGGTTGTGGGATCTCTCTTTCACAGTCTGCCGGCTGTGAGGCGAGTCAGAAACCGTTGATGTAGGCGAAGGACATGCGAAAGGTCCGGCGTAGAGGGTAAGACCCCCGTAGTCGAAACATCAGCGGCTCGTTTGAGAGACACCCAAGTAGCACGGGGCCCGAGAAATCCCGTGTGAATCTGGCGGGACCACCCGCTAAGCCTAAATATTCCCTGGTGACCGATAGCGGATAGTACCGTGAGGGAATGGTGAAAAGTACCGCGGGAGCGGAGTGAAATAGTACCTGAAACCGTGTGCCTACAAGCCGTGGGAGCGTCGGACATCAAGCTTGCTTGGTGTCTCGTGACTGCGTGCCTTTTGAAGAATGAGCCTGCGAGTTTGCGGTGTGTTGCGAGGTTAACCCGAGTGGGGAAGCCGTAGCGAAAGCGAGTCCGAATAGGGCGTTTCAGTAGCACGCTCAAGACCCGAAGCGGAGTGATCTAGCCATGGGCAGGTTGAAGCGGAGGTAAGACTTCGTGGAGGACCGAACCCACCAGGGTTGAAAACCTGGGGGATGACCTGTGGTTAGGGGTGAAAGGCCAATCAAACTCCGTGATAGCTGGTTCTCCCCGAAATGCATTTAGGTGCAGCGTCGTGTGTTTCTTGCCGGAGGTAGAGCACTGGATAGGCGATGGGCCCTACCGGGTTACTGACCTTAGCCAAACTCCGAATGCCGGTAAGTGAGAGCGCGGCAGTGAGACTGTGGGGGATAAGCTCCATGGTCGAGAGGGAAACAGCCCAGAGCATCGACTAAGGCCCCTAAGCGTACGCTAAGTGGGAAAGGATGTGGAGTCGCACAGACAACCAGGAGGTTGGCTTAGAAGCAGCCACCCTTGAAAGAGTGCGTAATAGCTCACTGGTCTAGTGATTCCGCGCCGACAATGTAGCGGGGCTCAAGCGTACCGCCGAAGTCGTGTCATTCATACAATAGGGCCAACGCCTGTATGGATGGGTAGGGGAGCGTCGTGTGCCGGGTGAAGCAGCCGCGGAAGCGAGTTGTGGACGGTTCACGAGTGAGAATGCAGGCATGAGTAGCGATACAAACGTGAGAAACGTTTGCGCCGATTGACTAAGGGTTCCTGGGTCAAGCTGATCTGCCCAGGGTAAGTCGGGACCTAAGGCGAGGCCGACAGGCGTAGTCGATGGATAACCGGTTGATATTCCGGTACCCGCTGTGAAGCGTCAAACATCGAGCATCGTGATGCTAAGGCCGTGAAGCCGCCCTGATCTCTTCGGAGTTGAGGGGAGTGGTGGAGCCGCCGGACCAAGCGGTTAGTAGGTGAGTGATGGGGTGACGCAGGAAGGTAGTCCATCCCGGGCGGTGGTTGTCCCGGGGTAAGGGTGTAGGACGTCAGGTAGGTAAATCCGCCTGGCAATAGTCTGAGACCTGATGCCGAGCCGATTGTGGTGAAGTGGATGATCCTATGCTGTCGAGAAAAGCCTCTAGCGAGTTTCATGGCGGCCCGTACCCTAAACCGACTCAGGTGGTCAGGTAGAGAATACCGAGGCGTTCGGGTGAACTATGGTTAAGGAACTCGGCAAAATGCCCCCGTAACTTCGGGAGAAGGGGGGCCACACCTGGTGATGATCTTTACGGTCTGAGCTGGGGGTGGCCGCAGAGACCAGCGAGAAGCGACTGTTTACTAAAAACACAGGTCCGTGCGAAGCCGTAAGGCGATGTATACGGACTGACGCCTGCCCGGTGCTGGAACGTTAAGGGGACCGGTTAGCTCCATTTCGGTGGGGCGAAGCTGAGAACTTAAGCGCCAGTAAACGGCGGTGGTAACTATAACCATCCTAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCTGCACGAATGGCGTAACGACTTCTCGACTGTCTCAACCATAGGCCCGGTGAAATTGCACTACGAGTAAAGATGCTCGTTTCGCGCAGCAGGACGGAAAGACCCCGGGACCTTTACTACAGTTTGATATTGGTGTTCGGTTCGGCTTGTGTAGGATAGCTGGGAGACTTTGAAGCTCGCACGCCAGTGTGGGTGGAGTCGTCGTTGAAATACCAGTCTGGTCGTGCTGGATGTCTAACCTGGGTCCGTGATCCGGATCAGGGACAGTGTCTGATGGGTAGTTTAACTGGGGCGGTTGCCTCCTAAAGAGTAACGGAGGCGCCCAAAGGTTCCCTCAGCCTGGTTGGCAATCAGGTGTTGAGTGTAAGTGCACAAGGGAGCTTGACTGTGAGACCGACGGGTCGAGCAGGGACGAAAGTCGGGACTAGTGATCCGGCGGTGGCTTGTGGAAGCGCCGTCGCTCAACGGATAAAAGGTACCCCGGGGATAACAGGCTGATCTTCCCCAAGAGTCCATATCGACGGGATGGTTTGGCACCTCGATGTCGGCTCGTCGCATCCTGGGGCTGGAGTCGGTCCCAAGGGTTGGGCTGTTCGCCCATTAAAGCGGTACGCGAGCTGGGTTTAGAACGTCGTGAGACAGTTCGGTCCCTATCCGCTGTGCGCGTAGGAGTCTTGAGAAGGGCTGTCCCTAGTACGAGAGGACCGGGACGGACGAACCTCTGGTGTGCCAGTTGTCCTGCCAAGGGCATGGCTGGTTGGCTACGTTCGGGAGGGATAACCGCTGAAAGCATCTAAGCGGGAAGCCTGCTTCGAGATGAGGACTCCCACCCCCTTGAGGGGTTAAGGCTCCCAGTAGACGACTGGGTTGATAGGCCGGATCTGGAAGCACCGCAAGGTGTGGAGGTGACCGGTACTAATAGGCCGAGGGCTTGTCCTCAGTTG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36864","NCBI_taxonomy_name":"Streptomyces ambofaciens","NCBI_taxonomy_id":"1889"}}}},"ARO_accession":"3004171","ARO_id":"41322","ARO_name":"Streptomyces ambofaciens 23S rRNA with mutation conferring resistance to macrolide antibiotics","CARD_short_name":"Samb_23S_MAC","ARO_description":"Point mutation in the 23S rRNA of Streptomyces ambofaciens shown to confer resistance to macrolide type antibiotics.","ARO_category":{"41251":{"category_aro_accession":"3004125","category_aro_cvterm_id":"41251","category_aro_name":"23S rRNA with mutation conferring resistance to macrolide antibiotics","category_aro_description":"Nucleotide point mutations in the 23S rRNA subunit may confer resistance to macrolide antibiotics.","category_aro_class_name":"AMR Gene Family"},"36295":{"category_aro_accession":"3000156","category_aro_cvterm_id":"36295","category_aro_name":"spiramycin","category_aro_description":"Spiramycin is a 16-membered macrolide and is natural product produced by Streptomyces ambofaciens. It binds to the 50S subunit of bacterial ribosomes and inhibits peptidyl transfer activity to disrupt protein synthesis.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2848":{"model_id":"2848","model_name":"MCR-4.1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"4477":{"protein_sequence":{"accession":"ASR73329.1","sequence":"MISRFKTLSVNQFTFITALFYVAIFNLPLFGIVRKGIEKQPEVDPLFIASMPLFLTFALSFLFSIFTVKYLLKPFFIVLTLLSSSVFFAAYQYNVVFDYGMIENTFQTHPAEALMYVNLASITNLLLTGLLPSYLIYKADIHYQPFFKELLHKLAFMLLMFVGIGIVAFFYYQDYAAFVRNNSELRRYIVPTYFVSSASKYLNEHYLQTPMEYQQLGLDAKNASRNPNTKPNLLVVVVGETARSMSYQYYGYNKPTNAHTQNQGLIAFNDTSSCGTATAVSLPCMFSRMGRADYDPRRANAQDTVIDVLSHSGIKVQWFDNDSGCKGVCDQVENLTIDLKSDPKLCSGQYCFDQVLLNKLDKILAVAPSQDTVIFLHIIGSHGPTYYLRYPPEHRKFIPDCPRSDIQNCSQEELINTYDNTILYTDFILSEVVNKLKGKQDMFDTAMLYLSDHGESLGEKGMYLHGAPYSIAPKEQTSVPMLAWVSNDFSQDNQLNMTCVAQRAEQGGFSHDNLFDSLLGLMNVKTTVYQSQLDIFAPCRY"},"dna_sequence":{"accession":"MF543359.1","fmin":"5807","fmax":"7433","strand":"-","sequence":"GTGATTTCTAGATTTAAGACGTTATCGGTTAACCAATTCACTTTCATCACTGCGTTGTTTTATGTTGCCATTTTCAATCTACCGCTCTTTGGTATAGTGCGAAAAGGAATTGAAAAACAACCAGAAGTTGATCCCCTTTTCATCGCATCTATGCCGCTATTTTTAACATTTGCGCTGAGTTTTTTGTTTTCAATTTTTACCGTCAAATACCTGCTGAAGCCCTTTTTTATCGTATTGACGTTACTTTCCTCAAGTGTATTTTTTGCAGCCTATCAATACAATGTCGTGTTTGACTACGGCATGATAGAAAACACGTTTCAAACACATCCTGCTGAAGCATTGATGTATGTAAATCTTGCATCAATTACCAATCTACTGCTGACTGGGCTATTACCGTCATATCTTATTTATAAGGCCGATATTCATTATCAGCCCTTTTTTAAGGAGTTATTGCATAAATTAGCCTTTATGCTGCTAATGTTCGTTGGCATTGGGATAGTCGCCTTTTTTTACTATCAAGATTATGCTGCATTTGTTCGAAACAACAGTGAGTTAAGGCGTTACATTGTCCCTACCTATTTTGTCAGTAGTGCATCTAAATATCTCAATGAGCACTATTTGCAGACGCCCATGGAATACCAACAACTTGGCCTAGATGCGAAGAATGCCAGTCGTAACCCGAACACTAAACCTAACTTATTAGTGGTTGTTGTGGGTGAAACTGCGCGCTCAATGAGCTATCAATATTATGGATATAACAAGCCAACCAATGCTCATACCCAAAATCAGGGGCTGATTGCGTTTAACGATACTAGCTCATGCGGCACGGCCACGGCGGTGTCTCTACCCTGTATGTTTTCACGAATGGGGCGGGCAGACTATGATCCTCGCCGTGCTAATGCTCAAGACACAGTGATTGATGTGTTAAGTCATAGTGGTATAAAAGTACAGTGGTTTGATAATGATTCTGGCTGTAAAGGTGTGTGTGATCAGGTTGAAAATCTCACGATAGATTTGAAGAGTGATCCGAAGCTGTGTTCTGGCCAATATTGTTTTGACCAAGTATTGCTCAACAAATTAGATAAAATTCTGGCAGTAGCACCAAGTCAAGATACAGTAATTTTTTTGCATATCATTGGTAGTCATGGACCAACTTATTATCTTAGATACCCGCCAGAGCATCGTAAATTTATACCGGATTGTCCGCGCAGTGATATTCAAAATTGCAGTCAAGAAGAACTGATTAACACCTACGACAACACTATTCTATATACGGATTTTATTCTCAGTGAAGTGGTGAATAAATTAAAAGGTAAGCAGGATATGTTCGATACTGCAATGCTGTATCTCTCTGACCATGGTGAGTCTTTGGGTGAAAAGGGCATGTATTTACATGGTGCGCCCTATAGTATTGCACCGAAAGAACAAACTAGCGTACCAATGCTGGCTTGGGTATCTAATGACTTTAGCCAAGATAATCAGTTGAACATGACTTGTGTTGCACAGCGAGCAGAACAGGGCGGCTTTTCCCACGACAATTTGTTCGACAGTTTGCTAGGACTTATGAATGTAAAAACCACCGTCTATCAGAGCCAACTCGATATTTTTGCACCTTGCAGGTATTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41493","NCBI_taxonomy_name":"Salmonella sp.","NCBI_taxonomy_id":"599"}}}},"ARO_accession":"3004325","ARO_id":"41492","ARO_name":"MCR-4.1","CARD_short_name":"MCR-4.1","ARO_description":"MCR-4 is a plasmid-borne phosphoethanolamine transferase variant of MCR-1, isolated from Salmonella enterica serovar Typhimurium of porcine origin in Italy, Spain and Belgium through 2013 and 2015-2016. MCR-4 confers resistance to collistin via addition of a phosphoethanolamine group to lipid A, reducing the negative charge of the cell membrane. Described by Carattoli et al. 2017.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2849":{"model_id":"2849","model_name":"MCR-5.1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"5583":{"protein_sequence":{"accession":"ASK40551.1","sequence":"MRLSAFITFLKMRPQVRTEFLTLFISLVFTLLCNGVFWNALLAGRDSLTSGTWLMLLCTGLLITGLQWLLLLLVATRWSVKPLLILLAVMTPAAVYFMRNYGVYLDKAMLRNLMETDVREASELLQWRMLPYLLVAAVSVWWIARVRVLRTGWKQAVMMRSACLAGALAMISMGLWPVMDVLIPTLRENKPLRYLITPANYVISGIRVLTEQASSSADEAREVVAADAHRGPQEQGRRPRALVLVVGETVRAANWGLSGYERQTTPELAARDVINFSDVTSCGTDTATSLPCMFSLNGRRDYDERQIRRRESVLHVLNRSDVNILWRDNQSGCKGVCDGLPFENLSSAGHPTLCHGERCLDEILLEGLAEKITTSRSDMLIVLHMLGNHGPAYFQRYPASYRRWSPTCDTTDLASCSHEALVNTYDNAVLYTDHVLARTIDLLSGIRSHDTALLYVSDHGESLGEKGLYLHGIPYVIAPDEQIKVPMIWWQSSQVYADQACMQTHASRAPVSHDHLFHTLLGMFDVKTAAYTPELDLLATCRKGQPQ"},"dna_sequence":{"accession":"KY807920.1","fmin":"9895","fmax":"11539","strand":"-","sequence":"ATGCGGTTGTCTGCATTTATCACTTTCTTGAAAATGCGCCCGCAAGTGCGCACTGAATTTTTGACTCTGTTCATCAGCCTTGTGTTCACCCTGCTGTGCAATGGCGTGTTTTGGAATGCCCTTCTTGCTGGACGCGACTCCCTAACTTCTGGAACATGGCTAATGCTCCTTTGCACTGGGTTGCTGATCACCGGGCTGCAATGGTTGTTGCTCCTTCTGGTGGCCACGCGCTGGAGTGTCAAGCCACTACTGATTCTGCTTGCTGTCATGACGCCCGCCGCCGTTTATTTCATGCGCAACTACGGGGTTTATCTCGACAAGGCCATGCTGCGGAATCTGATGGAGACGGACGTCAGGGAAGCCAGTGAGCTGTTGCAATGGAGAATGCTGCCCTACTTGTTGGTTGCAGCCGTATCCGTGTGGTGGATTGCGAGAGTCAGGGTTTTACGAACGGGCTGGAAACAAGCGGTAATGATGCGCAGCGCTTGTCTGGCTGGCGCTCTCGCCATGATTTCCATGGGTCTGTGGCCAGTCATGGATGTGCTGATACCCACGCTTCGTGAAAACAAGCCGCTTCGCTATTTGATCACTCCTGCAAACTACGTCATCTCGGGCATTCGGGTTTTGACTGAACAGGCGTCATCGTCAGCAGACGAAGCAAGGGAAGTCGTTGCAGCCGATGCGCATCGAGGGCCTCAAGAACAAGGCCGCCGTCCTCGTGCTCTCGTACTGGTTGTCGGGGAAACCGTCAGGGCGGCTAATTGGGGGTTGAGCGGCTATGAACGACAAACCACCCCTGAGTTGGCCGCACGCGACGTGATCAATTTTTCCGATGTCACCAGTTGCGGGACGGATACGGCTACATCCCTTCCCTGCATGTTTTCCCTCAATGGTCGGCGCGACTACGACGAACGCCAGATTCGTCGGCGCGAGTCCGTGCTGCACGTTTTAAACCGTAGTGACGTCAACATTCTCTGGCGCGATAACCAGTCGGGCTGTAAAGGCGTCTGTGATGGACTGCCCTTTGAAAACCTGTCTTCGGCAGGCCATCCCACACTGTGCCATGGCGAGCGCTGCCTGGATGAAATTCTGCTCGAAGGGTTGGCCGAGAAGATAACAACAAGCCGCAGCGATATGCTGATCGTTCTGCATATGCTGGGCAATCACGGCCCAGCGTATTTCCAGCGCTATCCCGCAAGCTACCGACGCTGGTCGCCAACCTGCGACACCACCGATCTGGCCAGCTGTTCGCATGAAGCCTTGGTGAACACCTACGACAACGCCGTGCTTTACACCGATCATGTGCTTGCCCGTACCATTGACCTGCTGTCCGGCATCCGCTCACACGACACGGCGCTGCTGTACGTTTCCGATCATGGGGAATCGCTCGGCGAGAAAGGCCTGTATCTCCATGGCATACCTTACGTCATCGCGCCGGATGAGCAGATCAAGGTGCCGATGATCTGGTGGCAGTCGAGTCAGGTTTATGCCGACCAAGCCTGTATGCAAACTCATGCCTCTCGGGCACCGGTAAGTCACGATCACCTGTTTCACACCTTGCTCGGGATGTTCGACGTGAAAACCGCTGCCTACACGCCAGAGTTGGACCTTCTGGCAACATGCAGAAAAGGACAACCACAATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35704","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Paratyphi B","NCBI_taxonomy_id":"57045"}}}},"ARO_accession":"3004332","ARO_id":"41500","ARO_name":"MCR-5.1","CARD_short_name":"MCR-5.1","ARO_description":"MCR-5 is a transposon-associated phosphoethanolamine transferase gene, identified in Salmonella Paratyphi B dTa+ (d-tartrate fermenting Salmonella enterica subsp. enterica serovar Paratyphi B) isolates from food-producing animals. The isolates were collected between 2011 and 2013, and retrieved from the German National Reference Laboratory for Salmonella. MCR-5 confers resistance to collistin through the addition of a phosphoethanolamine group to lipid A, causing a reduction in negative charge of the cell membrane. Described by Borowiak et al, 2017.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3705":{"model_id":"3705","model_name":"Mycobacterium tuberculosis clpC1 with mutation conferring resistance to pyrazinamide","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"9636":"G258V"},"ReSeqTB-Minimal":{"9636":"G258V"},"clinical":{"9636":"G258V"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1600"}},"model_sequences":{"sequence":{"8823":{"protein_sequence":{"accession":"YP_177995.1","sequence":"MFERFTDRARRVVVLAQEEARMLNHNYIGTEHILLGLIHEGEGVAAKSLESLGISLEGVRSQVEEIIGQGQQAPSGHIPFTPRAKKVLELSLREALQLGHNYIGTEHILLGLIREGEGVAAQVLVKLGAELTRVRQQVIQLLSGYQGKEAAEAGTGGRGGESGSPSTSLVLDQFGRNLTAAAMEGKLDPVIGREKEIERVMQVLSRRTKNNPVLIGEPGVGKTAVVEGLAQAIVHGEVPETLKDKQLYTLDLGSLVAGSRYRGDFEERLKKVLKEINTRGDIILFIDELHTLVGAGAAEGAIDAASILKPKLARGELQTIGATTLDEYRKYIEKDAALERRFQPVQVGEPTVEHTIEILKGLRDRYEAHHRVSITDAAMVAAATLADRYINDRFLPDKAIDLIDEAGARMRIRRMTAPPDLREFDEKIAEARREKESAIDAQDFEKAASLRDREKTLVAQRAEREKQWRSGDLDVVAEVDDEQIAEVLGNWTGIPVFKLTEAETTRLLRMEEELHKRIIGQEDAVKAVSKAIRRTRAGLKDPKRPSGSFIFAGPSGVGKTELSKALANFLFGDDDALIQIDMGEFHDRFTASRLFGAPPGYVGYEEGGQLTEKVRRKPFSVVLFDEIEKAHQEIYNSLLQVLEDGRLTDGQGRTVDFKNTVLIFTSNLGTSDISKPVGLGFSKGGGENDYERMKQKVNDELKKHFRPEFLNRIDDIIVFHQLTREEIIRMVDLMISRVAGQLKSKDMALVLTDAAKALLAKRGFDPVLGARPLRRTIQREIEDQLSEKILFEEVGPGQVVTVDVDNWDGEGPGEDAVFTFTGTRKPPAEPDLAKAGAHSAGGPEPAAR"},"dna_sequence":{"accession":"NC_000962.3","fmin":"4038157","fmax":"4040704","strand":"-","sequence":"ATGTTCGAACGATTTACCGACCGTGCCCGCAGGGTCGTCGTCCTGGCTCAGGAAGAGGCCAGGATGCTCAACCACAACTACATCGGCACCGAGCACATTCTTTTAGGCCTGATCCATGAAGGGGAAGGCGTTGCCGCCAAGTCACTGGAGTCGTTGGGGATCTCGCTGGAAGGTGTGCGCAGTCAGGTCGAGGAGATCATCGGCCAGGGCCAGCAGGCGCCGTCTGGGCACATTCCGTTTACCCCCCGCGCCAAAAAGGTCCTCGAGCTGAGCTTGCGTGAAGCGCTGCAGCTTGGCCACAACTACATCGGGACCGAACACATTTTGCTGGGCCTCATCCGAGAGGGTGAAGGCGTGGCCGCCCAGGTGCTGGTCAAGCTGGGCGCCGAGCTGACCCGGGTGCGCCAGCAGGTGATCCAGCTGCTCTCCGGTTACCAAGGCAAGGAGGCCGCCGAAGCCGGCACCGGCGGCCGCGGGGGAGAGTCCGGCTCTCCGTCTACGTCCTTGGTGCTCGACCAGTTCGGCCGCAACCTCACGGCGGCGGCGATGGAAGGCAAACTGGACCCGGTCATCGGCCGCGAGAAGGAAATCGAGCGGGTCATGCAGGTGCTCTCTCGGCGCACCAAGAACAACCCGGTGCTGATCGGCGAGCCCGGCGTCGGCAAGACCGCGGTCGTCGAAGGACTGGCGCAGGCCATCGTGCACGGCGAGGTGCCCGAGACGCTCAAGGACAAGCAGCTCTACACGCTGGATCTGGGATCGCTGGTGGCGGGTAGCCGCTACCGCGGTGACTTCGAGGAACGCCTCAAGAAGGTGCTCAAGGAGATCAACACCCGCGGTGACATCATCCTGTTTATCGACGAGCTGCACACCTTGGTCGGTGCTGGAGCCGCCGAGGGCGCGATCGACGCCGCCTCGATCCTGAAACCGAAGCTCGCTCGCGGTGAACTGCAAACGATCGGCGCCACCACGCTCGACGAATACCGCAAGTACATCGAGAAGGACGCCGCGCTGGAGCGCCGCTTCCAGCCGGTGCAGGTGGGTGAGCCGACGGTGGAGCACACCATCGAGATCCTCAAGGGCCTGCGGGACCGGTACGAGGCGCACCACCGGGTGTCGATCACCGATGCGGCGATGGTGGCCGCCGCGACCCTGGCCGACCGCTACATCAACGACCGGTTCCTGCCCGACAAGGCGATCGACCTGATCGACGAGGCGGGTGCTCGGATGCGGATTCGTCGCATGACCGCACCGCCAGACCTACGCGAGTTCGATGAGAAGATCGCCGAGGCTCGTCGGGAGAAGGAATCGGCTATCGACGCCCAGGACTTCGAGAAGGCCGCCAGCCTGCGCGACCGGGAGAAGACACTGGTCGCACAGCGTGCTGAGCGCGAAAAGCAGTGGCGTTCAGGCGATCTTGACGTGGTCGCGGAGGTCGACGACGAGCAGATCGCCGAGGTGCTGGGCAACTGGACCGGTATCCCGGTGTTCAAGCTCACCGAGGCCGAGACCACCCGGCTGTTGCGGATGGAAGAAGAGCTGCACAAGCGGATCATCGGGCAAGAGGACGCCGTCAAGGCCGTTTCCAAGGCCATCCGGCGTACCCGGGCCGGGCTGAAAGACCCCAAGCGCCCGTCGGGCTCGTTCATCTTCGCCGGCCCGTCCGGTGTCGGTAAGACCGAACTGTCCAAGGCGCTGGCCAACTTCTTGTTCGGTGACGACGACGCGCTTATTCAGATTGACATGGGTGAATTCCACGACCGGTTCACCGCGTCGCGGCTATTCGGCGCGCCGCCCGGATACGTCGGCTACGAGGAGGGCGGCCAACTCACCGAGAAGGTGCGGCGCAAGCCGTTCTCGGTGGTGCTGTTCGACGAGATCGAGAAGGCGCATCAGGAGATCTACAACAGCCTGCTGCAGGTGCTCGAGGATGGCCGGCTCACCGACGGGCAGGGCCGCACGGTGGACTTCAAGAACACCGTGCTGATCTTTACGTCCAATCTGGGCACCTCCGACATCTCTAAGCCGGTCGGTCTGGGCTTTTCCAAGGGCGGCGGTGAGAACGACTACGAGCGGATGAAACAGAAGGTCAACGACGAGCTGAAGAAACACTTCCGCCCGGAGTTCCTCAACCGCATCGACGACATCATCGTCTTCCACCAGCTGACCCGCGAGGAGATCATCCGGATGGTCGACCTGATGATCAGCCGGGTCGCCGGCCAGCTCAAGAGCAAGGACATGGCGCTGGTGCTGACCGATGCGGCCAAGGCGCTGCTGGCCAAGCGTGGCTTCGACCCGGTGTTGGGGGCCCGCCCGTTGCGGCGCACCATCCAGCGTGAGATCGAAGATCAGCTCTCGGAGAAGATCCTCTTCGAGGAGGTCGGGCCGGGTCAGGTGGTCACCGTCGACGTGGACAACTGGGACGGTGAAGGTCCCGGCGAGGACGCGGTGTTCACCTTCACCGGTACCCGCAAGCCGCCGGCCGAGCCGGATCTGGCCAAGGCTGGAGCGCACAGCGCGGGCGGCCCGGAGCCGGCCGCGCGGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3004957","ARO_id":"43143","ARO_name":"Mycobacterium tuberculosis clpC1 with mutation conferring resistance to pyrazinamide","CARD_short_name":"Mtub_clpC1_PZA","ARO_description":"Mutations that occur in clpC1 that result in or contribute to antibiotic resistance to pyrazinamide.","ARO_category":{"43064":{"category_aro_accession":"3004878","category_aro_cvterm_id":"43064","category_aro_name":"pyrazinamide resistant clpC1","category_aro_description":"clpC1 is a subunit of the clp protease that is ATP-dependent. It functions to direct the clp protease to specific substrates. In the presence of ATP it hydrolyses proteins and may be involved in the degradation of denatured proteins.","category_aro_class_name":"AMR Gene Family"},"39997":{"category_aro_accession":"3003413","category_aro_cvterm_id":"39997","category_aro_name":"pyrazinamide","category_aro_description":"Pyrazinamide is an antimycobacterial. It is highly specific and active only against Mycobacterium tuberculosis. This compound is a prodrug and needs to be activated inside the cell. It interferes with the bacterium's ability to synthesize new fatty acids, causing cell death.","category_aro_class_name":"Antibiotic"},"45737":{"category_aro_accession":"3007155","category_aro_cvterm_id":"45737","category_aro_name":"pyrazine antibiotic","category_aro_description":"A group of antibiotics derived from pyrazine.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2914":{"model_id":"2914","model_name":"Bifidobacterium adolescentis rpoB mutants conferring resistance to rifampicin","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"2000"}},"model_sequences":{"sequence":{"5874":{"protein_sequence":{"accession":"WP_041777404.1","sequence":"MAEATTNTTTIIARADQHDIDLHKASDRVNFGSIREPIDVPYLLGVQTDSFDWLIGNERWQKRVQEDLENGTNTVPHTSGLDEVFQEISPIENFAQTMSLTFSDPYFEEPRHTVQECKEKDYTYSAPLYVNAEFENGDTGEIKSQTVFMGDFPLQTPHGTFIIGGTERVIVSQLVRSPGVYFDRSQDRTSDKEVFGAKIIPSRGAWLEFEIDKRDVLGVRVDRKRKQSAIVFLMAIGMTKDEIADAFKDYPLVMDALAKETVQTQDEALTDLYRKIRPADTPTPEAGKNLLDSFYFNTKRYDLARVGRYKINRKLGLEKDVNDRSLSREDIIATIKYLVTLHAGETKFPGKRDGQDVDLRVDVDDIDHFGNRRIRQVGELIQNQLRTGLSRMERVVRERMTTQDPEAITPQSLINIRPVNATIKEFFGTSQLSQFMDQNNPLAGVTNKRRLSALGPGGLSRDRASMEVRDVHPSHFGRMCPIESPEGPNIGLIGSLATFGRINPFGFIETPYRKVVNGHVTDEVEYMTADRDAEHVIAQANQELDENGNFVKKQALARVGEEEAVDVPVSSVDYMDVSPRQMVSVGASLIPFLEHDEGHRALMGTNMQRQAVPLIESERPLVGTGAEWRAAVDSGDVILAEKPGVVTYVSADIIRTMNDDGTTSSYKLAKFQRSNQTTCYNQVPLIHDGERVEAGTVLADGPATQKGEMALGKNLLIAFMPWNGYNYEDAVIISQRLVQDDTLSSIHIEEYEIDARETKLGAEEITRDLPNVGEDAVANLDERGIIRIGAEVEAGDILVGKVTPKGETELTPEERLLRAIFGEKSREVRDTSLRVPHGETGTVIAVKEITREDAEEDGDELPNGVNQMIRVYIAQHRKITQGDKLSGRHGNKGVISRILPEEDMPFLADGTPVDIMLNPLGVPSRMNLGQVLELHLGWIAHAGWDISLDPDAEAAWKKYVPQGAEKGAPGTPVATPVFDGVRPETIKGLLSCTLPDRDGNKLVGPDGKATLFDGRTGEPFPKPISVGYMYMLKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLHEMMTTKSDDVDGRVRVYGAIVKGENLPPAGIPESFKVLLKEMQSLSLNVEVLNADGVAIDMKEEDDDPSTSSDDLGFNIGARPDAAAKEDQVAEEPEFQ"},"dna_sequence":{"accession":"NC_008618.1","fmin":"1667063","fmax":"1670624","strand":"-","sequence":"TTGGCTGAGGCTACGACGAACACCACCACCATCATCGCACGCGCCGACCAGCATGATATTGATCTGCACAAGGCGTCGGACCGTGTGAATTTCGGCTCCATCCGCGAGCCCATTGATGTACCCTACCTGTTGGGTGTACAGACTGACAGCTTTGACTGGCTCATCGGCAACGAGCGCTGGCAGAAGCGAGTCCAGGAGGATCTGGAGAACGGCACCAACACCGTGCCCCACACCTCCGGTCTTGACGAGGTCTTCCAGGAGATCTCCCCGATCGAGAACTTCGCTCAGACCATGAGCCTGACCTTCTCCGATCCGTACTTCGAAGAACCGCGCCACACCGTGCAGGAATGCAAGGAGAAGGATTACACCTACTCCGCGCCGCTGTACGTGAACGCCGAATTCGAGAACGGCGACACCGGCGAAATCAAGTCCCAGACCGTGTTCATGGGCGATTTCCCGCTGCAGACCCCGCACGGCACCTTCATCATCGGTGGTACCGAGCGAGTGATCGTGTCCCAGCTCGTGCGTTCCCCGGGCGTGTACTTCGACCGTTCCCAGGACCGTACCTCCGATAAGGAAGTCTTCGGCGCGAAGATCATCCCGAGCCGTGGCGCATGGCTCGAGTTCGAGATCGACAAGCGCGACGTCCTCGGCGTGCGCGTGGACCGTAAGCGCAAGCAGTCCGCCATCGTGTTCCTCATGGCCATCGGCATGACCAAGGATGAAATTGCCGACGCCTTCAAGGACTACCCGCTGGTCATGGACGCTCTCGCCAAGGAGACCGTGCAGACCCAGGACGAGGCCCTGACCGACCTGTACCGCAAGATCCGTCCGGCCGACACCCCGACTCCGGAAGCCGGCAAGAACCTGCTGGACTCCTTCTACTTCAACACCAAGCGTTACGATCTGGCCCGCGTCGGCCGTTACAAGATCAACCGCAAGCTTGGTCTGGAAAAGGACGTCAACGACCGCAGCCTGTCCCGCGAGGACATCATCGCCACCATCAAGTACTTGGTCACCCTGCATGCGGGCGAGACCAAGTTCCCGGGCAAGCGCGACGGCCAGGACGTTGACCTGCGCGTGGACGTCGACGATATCGACCACTTCGGCAACCGTCGTATCCGCCAGGTCGGCGAGCTGATCCAGAACCAGCTGCGCACCGGTCTGAGCCGTATGGAGCGTGTGGTCCGCGAACGTATGACCACCCAGGATCCCGAGGCCATCACCCCGCAGTCCCTGATCAACATCCGTCCGGTGAACGCCACCATCAAGGAGTTCTTCGGAACCTCCCAGCTGTCCCAGTTCATGGATCAGAACAACCCGCTGGCTGGCGTGACCAACAAGCGTCGTCTGTCCGCTCTGGGCCCCGGTGGCCTGTCCCGCGACCGCGCCTCCATGGAAGTGCGAGACGTGCACCCGTCCCATTTCGGCCGTATGTGCCCGATCGAGTCTCCTGAAGGCCCGAACATCGGTCTGATCGGCTCCCTGGCAACCTTCGGTCGCATCAACCCGTTCGGTTTCATCGAGACCCCGTACCGCAAGGTCGTCAACGGCCACGTCACCGATGAAGTCGAGTACATGACCGCTGACCGCGATGCCGAGCACGTCATCGCCCAGGCCAACCAGGAGCTCGACGAGAACGGCAACTTCGTCAAGAAGCAGGCTCTTGCCCGAGTCGGCGAAGAGGAAGCGGTCGATGTGCCGGTCAGCTCCGTCGATTACATGGACGTCTCCCCGCGTCAGATGGTTTCCGTCGGCGCCTCCCTGATTCCGTTCCTGGAGCACGATGAGGGCCACCGAGCGCTGATGGGCACCAACATGCAGCGTCAGGCCGTGCCGCTGATCGAATCCGAGCGTCCGCTCGTGGGCACCGGCGCCGAATGGCGCGCCGCCGTCGATTCCGGCGACGTCATCCTGGCCGAGAAGCCGGGCGTGGTGACCTACGTGTCCGCCGACATCATCCGTACCATGAACGACGATGGCACCACCAGCTCCTACAAGCTGGCCAAATTCCAGCGTTCCAACCAGACCACCTGCTACAACCAGGTCCCGCTCATCCACGACGGTGAACGCGTGGAAGCCGGCACCGTGCTGGCCGATGGTCCGGCAACCCAGAAGGGCGAGATGGCACTGGGCAAGAACCTGCTCATCGCCTTCATGCCGTGGAACGGCTACAACTACGAGGATGCTGTGATCATCTCCCAGCGCCTTGTGCAGGACGACACCCTGAGCTCCATCCACATCGAGGAGTACGAGATCGATGCCCGTGAAACCAAGCTGGGCGCCGAAGAGATCACCCGCGACCTGCCGAACGTCGGCGAGGACGCGGTGGCCAACCTCGACGAGCGTGGCATCATCCGCATCGGCGCCGAAGTCGAAGCCGGCGACATCCTGGTCGGCAAGGTCACCCCGAAGGGCGAGACCGAGCTGACTCCGGAAGAGCGCCTGCTGCGCGCCATCTTCGGTGAGAAGAGCCGCGAAGTGCGTGACACCTCGCTGCGCGTGCCTCACGGCGAGACCGGCACCGTCATCGCGGTCAAGGAAATCACCCGCGAGGACGCCGAGGAAGACGGCGACGAACTGCCGAACGGCGTGAACCAGATGATTCGCGTCTACATCGCACAGCACCGTAAGATCACCCAGGGCGACAAGCTCTCCGGCCGTCACGGCAACAAGGGCGTCATCTCCCGCATCCTGCCGGAAGAGGACATGCCGTTCCTCGCCGACGGTACTCCGGTGGACATCATGCTGAACCCGCTGGGCGTGCCTTCTCGAATGAACCTTGGCCAGGTGCTGGAACTGCACCTCGGCTGGATCGCGCACGCTGGCTGGGACATCTCCCTGGATCCGGATGCCGAGGCCGCTTGGAAGAAGTACGTGCCGCAGGGCGCCGAAAAGGGCGCTCCGGGCACTCCGGTGGCCACCCCGGTGTTCGACGGCGTCCGTCCGGAAACCATCAAGGGCCTGCTCAGCTGCACCCTTCCGGACCGCGACGGCAACAAGCTCGTCGGCCCCGACGGCAAGGCGACCCTGTTCGACGGCCGTACCGGCGAACCGTTCCCGAAGCCGATCTCCGTGGGCTACATGTACATGCTGAAGCTGCACCACCTGGTCGACGACAAGATCCACGCCCGCTCCACCGGCCCGTACTCCATGATCACCCAGCAGCCGCTGGGCGGCAAGGCTCAGTTCGGTGGCCAGCGCTTCGGCGAGATGGAAGTGTGGGCCCTCGAGGCCTACGGTGCCGCCTACACGCTGCACGAAATGATGACCACCAAGTCCGATGACGTCGACGGCCGCGTGCGCGTCTACGGCGCCATCGTGAAGGGCGAGAACCTGCCGCCGGCAGGCATCCCGGAGTCCTTCAAGGTGCTGCTTAAGGAAATGCAGTCCCTGTCCCTGAATGTCGAAGTGCTCAACGCCGACGGCGTGGCTATCGACATGAAGGAAGAGGACGACGATCCGTCCACATCCTCCGATGATCTGGGCTTCAACATTGGTGCGCGTCCTGACGCTGCCGCCAAGGAAGATCAGGTTGCCGAGGAACCCGAATTCCAGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42564","NCBI_taxonomy_name":"Bifidobacterium adolescentis","NCBI_taxonomy_id":"1680"}}}},"ARO_accession":"3004480","ARO_id":"41743","ARO_name":"Bifidobacterium adolescentis rpoB mutants conferring resistance to rifampicin","CARD_short_name":"Bado_rpoB_RIF","ARO_description":"Bifidobacterium are antibiotic resistant probiotics are prescribed to upkeep the population beneficial bacteria in the gut microbiome. However, horizontal gene transfer among gut microbes could create harmful antibiotic-resistant pathogenic bacteria, such as Mycobacterium tuberculosis. Lokesh et al. analyzed Bifidobacterium antitubercular drug resistance and mutations in rpoB. They found that B. animalis, B. longum and B. adolescentis showed considerable resistance to pyrazinamide, isoniazid, and streptomycin, while B. adolescentis had mutations both in the rifampicin (RIF) pocket and in regions outside the pockets, and also showed considerable resistance to RIF.","ARO_category":{"36349":{"category_aro_accession":"3000210","category_aro_cvterm_id":"36349","category_aro_name":"rifamycin-resistant beta-subunit of RNA polymerase (rpoB)","category_aro_description":"Rifampin resistant RNA polymerases include amino acids substitutions which disrupt the affinity of rifampin for its binding site. These mutations are frequently concentrated in the rif I region of the beta-subunit and most often involve amino acids which make direct interactions with rifampin. However, mutations which also confer resistance can occur outside this region and may involve amino acids which do not directly make contact with rifampin.","category_aro_class_name":"AMR Gene Family"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3144":{"model_id":"3144","model_name":"MCR-8.1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"5002":{"protein_sequence":{"accession":"AVX52225.1","sequence":"MFKYLLSFKLNPVQRTWAAAFFFTTIGNIALWQTLWINVDVHNIHNLLFFASLPIFLFCFLSILLTPVMVIPYLCRPLLVVLILISACCSYFMMKYNILIDRSMVQNFFETNQAELTSYLSVPFLSTLFLLGIVPAIILALPSTDNKRGAFRIELWWLAHICIAVVLLAMVTMVFYKDYASLIRNNMQIKDQALPFNFVRNTNGYLKRKYQASSTILQSVGEDAVRPIYSNAPPKLVVVVVGETARAQNFQLNGYSRVTNPYLSRRHDVISFKNVSSCGTATAISLPCMFSRMSRNEYNEVRAASEENLLDILKRTGVEVLWRNNNNGGCKGICKRVPTDDMPAMKVIGECVNKDGTCFDEVLLNQLSSRINAMQGDALIVLHQMGSHGPTYFERYPSTSKVFSPTCDSNLIEKCSNKELVNTYDNTLVYTDRMLSKTIELLQRYSGMRDVAMIYLSDHGESLGESGIYLHGTPYIIAPNEQTHIPMFMWFSSSFAQHSKLNLECLTGNADKQYSHDNFYHSILGLFNVKTSVYKPELDMFTLCRQSDHTPLSSAVVREKTDGNG"},"dna_sequence":{"accession":"MG736312.1","fmin":"50454","fmax":"52152","strand":"-","sequence":"ATGTTCAAGTATCTTTTATCTTTCAAACTGAACCCGGTACAACGGACCTGGGCTGCAGCATTTTTTTTCACTACAATCGGCAACATAGCACTTTGGCAAACACTATGGATTAATGTAGATGTTCATAATATACATAATCTACTTTTTTTTGCCAGTCTGCCAATATTTCTTTTCTGCTTTCTAAGTATCTTACTTACACCAGTCATGGTTATTCCATATTTATGCAGGCCTCTACTTGTAGTTCTTATTCTAATCAGTGCCTGCTGTAGTTATTTCATGATGAAATACAACATATTAATTGACCGCAGCATGGTGCAAAACTTTTTTGAGACTAATCAGGCTGAATTAACATCATACTTATCCGTTCCTTTTCTTTCCACTCTATTTCTACTTGGCATTGTACCAGCAATTATCCTGGCGTTGCCTTCAACAGACAATAAGCGGGGAGCTTTTAGAATTGAATTGTGGTGGTTGGCGCATATTTGCATAGCTGTAGTCTTATTAGCCATGGTTACCATGGTGTTTTATAAGGATTACGCATCTCTCATACGAAACAATATGCAGATTAAAGACCAGGCTTTACCTTTTAACTTTGTGCGTAATACGAATGGTTACCTTAAAAGAAAATACCAGGCATCTTCAACAATTCTACAAAGCGTGGGGGAGGATGCTGTACGTCCAATATATTCAAATGCTCCACCGAAACTGGTGGTTGTCGTCGTGGGCGAAACCGCCAGAGCACAGAATTTCCAGCTGAATGGCTATTCGCGGGTAACCAACCCCTATCTTTCCAGACGACATGATGTTATCAGTTTCAAAAATGTGTCGTCATGCGGAACGGCTACCGCAATATCACTACCCTGCATGTTCTCGCGAATGTCACGTAACGAATACAATGAAGTCCGTGCCGCATCAGAAGAAAACTTGCTGGATATCCTTAAACGTACAGGTGTTGAGGTGCTATGGCGCAACAATAACAATGGTGGTTGTAAGGGAATCTGCAAGCGAGTACCCACAGATGATATGCCGGCAATGAAAGTAATTGGGGAATGTGTTAACAAAGATGGTACATGCTTTGATGAGGTGTTATTAAATCAACTCTCATCCCGAATTAATGCAATGCAGGGTGATGCGCTTATTGTTTTACATCAAATGGGCAGTCATGGACCAACATATTTTGAACGTTATCCGTCTACAAGTAAAGTCTTTAGCCCAACTTGCGACAGCAACCTGATCGAAAAATGCTCAAATAAAGAACTGGTCAATACATACGACAATACGCTAGTTTATACTGATCGTATGCTGAGCAAAACTATTGAACTGTTGCAACGTTATTCCGGGATGCGTGACGTTGCTATGATATATCTTTCTGATCATGGAGAATCGCTGGGGGAAAGCGGAATATATCTTCATGGCACACCATATATTATTGCCCCCAATGAACAAACACACATCCCGATGTTTATGTGGTTTTCGTCTTCATTCGCGCAGCATTCCAAATTAAATCTAGAATGCCTGACCGGTAATGCCGACAAACAATACAGTCATGATAATTTTTATCATTCAATACTTGGTCTCTTCAACGTAAAAACCAGTGTATATAAACCGGAGTTAGATATGTTTACTCTATGTCGACAATCTGACCACACACCACTGTCTTCCGCAGTTGTAAGAGAGAAAACAGATGGGAATGGTTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3004516","ARO_id":"42225","ARO_name":"MCR-8.1","CARD_short_name":"MCR-8.1","ARO_description":"A novel phosphoethanolamine transferase and mobile colistin resistance gene identified from carbapenem-resistant NDM-1-producing Klebsiella pneumoniae.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3739":{"model_id":"3739","model_name":"Mycobacterium tuberculosis fabG1 mutation conferring resistance to ethionamide","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"41339":{"param_type":"nucleotide substitution in promoter region","param_description":"A nucleotide sequence change where, compared to a reference sequence, one nucleotide is replaced by one other nucleotide in the promoter region of a gene. These substitutions are indicated as upstream of the reference sequence transcription initiation site. Format is given by [-][position][wildtype][>][mutation], e.g. -11t>c or -15g>Var where Var represents any possible substitution.","param_type_id":"41339","param_value":{"13397":"-15c>t","14766":"-15c>t","14768":"-16a>g","14770":"-8t>c","14772":"-8t>g","14774":"-8t>a","13198":"-15c>t","13200":"-8t>a","14764":"-17g>t"}},"snp":{"CRyPTIC-R":{"13397":"G258V","14217":"G258V"},"WHO-R":{"14766":"G258V","14768":"G258V","14770":"G258V","14772":"G258V","14774":"G258V","14764":"G258V"},"ReSeqTB-Minimal":{"13198":"G258V"},"ReSeqTB-High":{"13200":"G258V"}},"48039":{"param_type":"synonymous substitution for alternative promoter","param_description":"A synonymous or silent substitution in the coding DNA sequence of one gene which influences the promoter region of another gene. These substitutions do not change the amino acid sequence of a protein but may still influence the phenotype, including decreased susceptibility to antimicrobial compounds.","param_type_id":"48039","param_value":{"14217":"L203L"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"425"}},"model_sequences":{"sequence":{"8814":{"protein_sequence":{"accession":"NP_215999.1","sequence":"MTATATEGAKPPFVSRSVLVTGGNRGIGLAIAQRLAADGHKVAVTHRGSGAPKGLFGVECDVTDSDAVDRAFTAVEEHQGPVEVLVSNAGLSADAFLMRMTEEKFEKVINANLTGAFRVAQRASRSMQRNKFGRMIFIGSVSGSWGIGNQANYAASKAGVIGMARSIARELSKANVTANVVAPGYIDTDMTRALDERIQQGALQFIPAKRVGTPAEVAGVVSFLASEDASYISGAVIPVDGGMGMGH"},"dna_sequence":{"accession":"NC_000962.3","fmin":"1673439","fmax":"1674183","strand":"+","sequence":"GTGACTGCCACAGCCACTGAAGGGGCCAAACCCCCATTCGTATCCCGTTCAGTCCTGGTTACCGGAGGAAACCGGGGGATCGGGCTGGCGATCGCACAGCGGCTGGCTGCCGACGGCCACAAGGTGGCCGTCACCCACCGTGGATCCGGAGCGCCAAAGGGGCTGTTTGGCGTCGAATGTGACGTCACCGACAGCGACGCCGTCGATCGCGCCTTCACGGCGGTAGAAGAGCACCAGGGTCCGGTCGAGGTGCTGGTGTCCAACGCCGGCCTATCCGCGGACGCATTCCTCATGCGGATGACCGAGGAAAAGTTCGAGAAGGTCATCAACGCCAACCTCACCGGGGCGTTCCGGGTGGCTCAACGGGCATCGCGCAGCATGCAGCGCAACAAATTCGGTCGAATGATATTCATAGGTTCGGTCTCCGGCAGCTGGGGCATCGGCAACCAGGCCAACTACGCAGCCTCCAAGGCCGGAGTGATTGGCATGGCCCGCTCGATCGCCCGCGAGCTGTCGAAGGCAAACGTGACCGCGAATGTGGTGGCCCCGGGCTACATCGACACCGATATGACCCGCGCGCTGGATGAGCGGATTCAGCAGGGGGCGCTGCAATTTATCCCAGCGAAGCGGGTCGGCACCCCCGCCGAGGTCGCCGGGGTGGTCAGCTTCCTGGCTTCCGAGGATGCGAGCTATATCTCCGGTGCGGTCATCCCGGTCGACGGCGGCATGGGTATGGGCCACTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3004933","ARO_id":"43119","ARO_name":"Mycobacterium tuberculosis fabG1 mutation conferring resistance to ethionamide","CARD_short_name":"Mtub_fabG1_ETO","ARO_description":"Mutations that occur in Mycobacterium tuberculosis fabG1 resulting in or contributing to resistance in ethionamide.","ARO_category":{"43074":{"category_aro_accession":"3004888","category_aro_cvterm_id":"43074","category_aro_name":"ethionamide resistant fabG1","category_aro_description":"fabG1 is involved in the fatty acid synthesis pathway, acting in the first reduction step for mycolic acid. It is associated with ethionamide resistance.","category_aro_class_name":"AMR Gene Family"},"40067":{"category_aro_accession":"3003474","category_aro_cvterm_id":"40067","category_aro_name":"ethionamide","category_aro_description":"Ethionamide is a second-line antitubercular agent that inhibits mycolic acid synthesis.","category_aro_class_name":"Antibiotic"},"45738":{"category_aro_accession":"3007156","category_aro_cvterm_id":"45738","category_aro_name":"thioamide antibiotic","category_aro_description":"A group of antibiotics possessing the thioamide functional group.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3714":{"model_id":"3714","model_name":"Mycobacterium tuberculosis gpsI with mutations conferring resistance to pyrazinamide","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1400"},"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"13012":"C160G"},"ReSeqTB-Minimal":{"13012":"C160G"},"clinical":{"13012":"C160G"}}},"model_sequences":{"sequence":{"8819":{"protein_sequence":{"accession":"NP_217299.1","sequence":"MSAAEIDEGVFETTATIDNGSFGTRTIRFETGRLALQAAGAVVAYLDDDNMLLSATTASKNPKEHFDFFPLTVDVEERMYAAGRIPGSFFRREGRPSTDAILTCRLIDRPLRPSFVDGLRNEIQIVVTILSLDPGDLYDVLAINAASASTQLGGLPFSGPIGGVRVALIDGTWVGFPTVDQIERAVFDMVVAGRIVEGDVAIMMVEAEATENVVELVEGGAQAPTESVVAAGLEAAKPFIAALCTAQQELADAAGKSGKPTVDFPVFPDYGEDVYYSVSSVATDELAAALTIGGKAERDQRIDEIKTQVVQRLADTYEGREKEVGAALRALTKKLVRQRILTDHFRIDGRGITDIRALSAEVAVVPRAHGSALFERGETQILGVTTLDMIKMAQQIDSLGPETSKRYMHHYNFPPFSTGETGRVGSPKRREIGHGALAERALVPVLPSVEEFPYAIRQVSEALGSNGSTSMGSVCASTLALLNAGVPLKAPVAGIAMGLVSDDIQVEGAVDGVVERRFVTLTDILGAEDAFGDMDFKVAGTKDFVTALQLDTKLDGIPSQVLAGALEQAKDARLTILEVMAEAIDRPDEMSPYAPRVTTIKVPVDKIGEVIGPKGKVINAITEETGAQISIEDDGTVFVGATDGPSAQAAIDKINAIANPQLPTVGERFLGTVVKTTDFGAFVSLLPGRDGLVHISKLGKGKRIAKVEDVVNVGDKLRVEIADIDKRGKISLILVADEDSTAAATDAATVTS"},"dna_sequence":{"accession":"NC_000962.3","fmin":"3090338","fmax":"3092597","strand":"-","sequence":"ATGTCTGCCGCTGAAATTGACGAAGGCGTGTTCGAGACGACCGCCACCATCGACAACGGGAGCTTTGGCACCCGGACCATCCGCTTCGAGACCGGCCGATTGGCCTTGCAGGCCGCCGGCGCGGTGGTCGCCTACCTCGACGACGACAACATGCTGCTGTCGGCGACCACCGCCAGCAAGAACCCCAAAGAACACTTCGACTTCTTCCCCCTCACGGTCGACGTCGAGGAGCGCATGTATGCGGCCGGCCGCATCCCCGGTTCGTTCTTCCGTCGCGAGGGCCGACCCTCCACCGACGCGATCCTGACCTGCCGGCTCATCGACCGCCCGCTGCGCCCGTCGTTTGTCGACGGGCTGCGCAACGAGATCCAAATCGTGGTGACGATTCTCAGCCTGGATCCGGGCGATCTCTACGACGTATTGGCGATCAACGCGGCGTCGGCGTCCACCCAGCTGGGCGGTCTGCCGTTCTCCGGGCCCATCGGCGGTGTGCGGGTGGCGCTCATCGACGGCACCTGGGTCGGCTTCCCCACCGTCGACCAGATCGAGCGCGCCGTGTTCGACATGGTCGTGGCCGGCCGGATCGTCGAGGGTGATGTTGCCATCATGATGGTCGAAGCCGAGGCCACCGAAAACGTCGTCGAGCTCGTCGAAGGTGGTGCCCAAGCGCCGACGGAAAGCGTGGTGGCCGCGGGCCTGGAGGCGGCCAAGCCGTTTATCGCCGCGCTGTGCACCGCGCAGCAGGAGCTTGCCGATGCCGCTGGAAAGTCGGGCAAACCGACCGTCGACTTCCCGGTGTTCCCTGACTACGGCGAAGACGTGTACTACTCGGTGTCCTCGGTGGCCACCGACGAGTTGGCCGCCGCGTTGACCATCGGCGGTAAAGCCGAGCGCGACCAGCGCATCGACGAAATCAAGACCCAGGTTGTGCAGCGGCTCGCCGACACCTACGAGGGTCGCGAAAAGGAGGTCGGCGCCGCGTTGCGTGCCCTGACCAAAAAGCTGGTTCGGCAGCGCATCCTCACCGACCATTTCCGTATCGACGGCCGCGGCATCACCGACATTCGCGCATTGTCGGCCGAGGTGGCCGTGGTTCCGCGCGCGCACGGCAGCGCGCTGTTCGAACGCGGCGAAACCCAGATCCTGGGTGTGACCACACTCGACATGATCAAGATGGCCCAGCAGATCGACTCGTTGGGGCCGGAGACATCGAAGCGGTACATGCACCACTACAACTTCCCGCCGTTCTCCACCGGCGAGACCGGTCGGGTCGGTTCGCCCAAGCGGCGTGAGATCGGGCACGGCGCACTGGCCGAGCGGGCCCTGGTGCCGGTGTTGCCGAGCGTCGAGGAATTCCCGTATGCCATTCGCCAGGTGTCGGAGGCTCTGGGCTCCAACGGGTCGACCTCGATGGGGTCGGTGTGCGCGTCGACGCTGGCGCTGCTCAACGCCGGGGTGCCGCTCAAGGCGCCGGTGGCCGGCATCGCGATGGGCCTGGTCTCCGACGACATTCAAGTAGAAGGGGCGGTCGACGGCGTTGTGGAGCGTCGCTTCGTCACCCTCACCGACATCCTCGGCGCCGAAGACGCGTTCGGTGACATGGACTTCAAGGTCGCCGGGACCAAGGACTTCGTCACCGCGCTGCAGCTGGACACCAAGCTCGACGGGATCCCTTCGCAGGTGCTTGCCGGAGCACTCGAGCAGGCCAAGGACGCCCGCCTCACGATCTTGGAGGTGATGGCTGAGGCCATCGATAGACCCGACGAAATGAGTCCCTACGCCCCGCGGGTGACCACCATCAAGGTTCCGGTGGACAAGATCGGGGAGGTCATCGGACCCAAGGGCAAGGTCATCAACGCCATCACCGAGGAGACCGGCGCGCAGATCTCCATCGAAGACGACGGCACCGTGTTCGTCGGCGCCACCGACGGGCCATCGGCACAGGCCGCGATCGACAAGATCAACGCCATCGCCAACCCGCAGCTGCCGACGGTGGGCGAACGGTTCCTCGGAACCGTGGTCAAGACCACCGATTTCGGTGCCTTTGTATCGTTGCTGCCTGGCCGCGACGGTCTGGTGCACATTTCCAAACTCGGCAAGGGCAAGCGCATCGCGAAGGTCGAGGACGTTGTCAATGTCGGTGACAAGCTGCGGGTGGAGATCGCCGACATCGACAAACGGGGCAAGATCTCCCTGATCCTGGTCGCCGACGAGGACAGCACCGCCGCCGCTACCGATGCCGCGACGGTCACCAGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3004977","ARO_id":"43164","ARO_name":"Mycobacterium tuberculosis gpsI with mutations conferring resistance to pyrazinamide","CARD_short_name":"Mtub_gpsI_PZA","ARO_description":"Mutations in gpsI that can contribute to or confer resistance to pyrazinamide.","ARO_category":{"43066":{"category_aro_accession":"3004880","category_aro_cvterm_id":"43066","category_aro_name":"pyrazinamide resistant gpsI","category_aro_description":"gpsI codes for polyribonucleotide nucleotidyltransferase which is a protein involved in mRNA degradation. It catalyzes the phosphorolysis of single-stranded polyribonucleotides in the 3'- to 5'-direction.","category_aro_class_name":"AMR Gene Family"},"39997":{"category_aro_accession":"3003413","category_aro_cvterm_id":"39997","category_aro_name":"pyrazinamide","category_aro_description":"Pyrazinamide is an antimycobacterial. It is highly specific and active only against Mycobacterium tuberculosis. This compound is a prodrug and needs to be activated inside the cell. It interferes with the bacterium's ability to synthesize new fatty acids, causing cell death.","category_aro_class_name":"Antibiotic"},"45737":{"category_aro_accession":"3007155","category_aro_cvterm_id":"45737","category_aro_name":"pyrazine antibiotic","category_aro_description":"A group of antibiotics derived from pyrazine.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3296":{"model_id":"3296","model_name":"erm(45)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"5168":{"protein_sequence":{"accession":"CEJ95855.1","sequence":"MNQNIKFTQNFITNEKLLSNIMKQINIDENDIIYEVGTGKGHLTSKLAEKCKHVYSIELDKKLYELSSNKLQDNSRVTLINQDILQFNYPYRKKYKIVGNIPFNISTQIVKDAVFRSQASEMYFIVEEGFYKRMIDTRRTLSLQLQTQVYIQQLLPIPAGSFHPKPKVNCILIKLTRHISDIKDKHKKKYEFFISKWVNKEYSKLFTKNQYHQALKHARIKDLNKISYEQVLSVFESYILFNPRK"},"dna_sequence":{"accession":"LN680996.1","fmin":"12073","fmax":"12811","strand":"+","sequence":"ATGAATCAAAATATTAAGTTTACTCAAAATTTTATTACAAACGAAAAATTATTATCTAATATAATGAAACAAATAAATATAGATGAGAATGACATAATTTATGAGGTTGGAACTGGTAAAGGTCATCTGACCTCTAAATTAGCAGAAAAATGTAAGCATGTTTATTCAATAGAGTTAGATAAAAAATTATATGAACTTTCTTCGAATAAGTTACAAGATAATAGTAGAGTTACTCTAATCAATCAAGATATTTTACAATTCAATTATCCGTATAGAAAAAAATATAAGATAGTTGGTAACATACCATTCAATATAAGTACTCAAATCGTGAAAGATGCAGTATTTAGAAGCCAAGCTTCTGAGATGTATTTTATTGTAGAAGAAGGTTTCTACAAAAGAATGATAGATACTCGTAGAACTCTAAGTTTGCAACTACAAACACAGGTTTATATACAACAATTGTTACCTATACCTGCTGGAAGTTTTCACCCAAAGCCAAAAGTAAATTGTATTTTAATAAAACTTACAAGACACATATCAGATATAAAAGATAAACATAAGAAAAAATATGAGTTTTTTATATCAAAGTGGGTTAATAAAGAGTATTCAAAATTATTCACTAAAAATCAGTATCATCAAGCATTGAAACATGCAAGGATAAAAGACCTTAATAAAATAAGTTATGAACAAGTATTATCAGTTTTTGAAAGTTATATATTATTCAATCCACGAAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42526","NCBI_taxonomy_name":"Mammaliicoccus fleurettii","NCBI_taxonomy_id":"150056"}}}},"ARO_accession":"3004595","ARO_id":"42525","ARO_name":"erm(45)","CARD_short_name":"erm(45)","ARO_description":"Erm45 is an rRNA methylase that confers resistances to macrolide, lincosamide, and streptogramin B.","ARO_category":{"36699":{"category_aro_accession":"3000560","category_aro_cvterm_id":"36699","category_aro_name":"Erm 23S ribosomal RNA methyltransferase","category_aro_description":"Erm proteins are part of the RNA methyltransferase family and methylate A2058 (E. coli nomenclature) of the 23S ribosomal RNA conferring degrees of resistance to Macrolides, Lincosamides and Streptogramin b. This is called the MLSb phenotype.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"36722":{"category_aro_accession":"3000583","category_aro_cvterm_id":"36722","category_aro_name":"pristinamycin IA","category_aro_description":"Pristinamycin IA is a type B streptogramin antibiotic produced by Streptomyces pristinaespiralis. It binds to the P site of the 50S subunit of the bacterial ribosome, preventing the extension of protein chains.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35967":{"category_aro_accession":"0000050","category_aro_cvterm_id":"35967","category_aro_name":"streptogramin B antibiotic","category_aro_description":"Streptogramin B antibiotics are are cyclic hepta- or hexa-depsipeptides.  Type B streptogramins block the peptide exit tunnel of the 50S bacterial ribosome. The general composition of group B streptogramins is 3-hydroxypicolinic acid-L-Thr-D-aminobutyric acid (or D-Ala)-L-Pro-L-Phe (or 4-N-,N-(dimethylamino)-L-Phe)-X-L-phenylglycine. Used alone, streptogramin B antibiotics are bacteriostatic, but is bactericidal when used with streptogramin A antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5883":{"model_id":"5883","model_name":"MCR-3.17","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"8577":{"protein_sequence":{"accession":"WP_111273846.1","sequence":"MPYILKIKIVPFIFLLAFYFAFMLNWPGVLHFYDIIYKLEGFKLGFAISLPILLVAALNLVFIPFSVRYLVKPFFALLILLSTIVSYAMMKYRVLFDQNMIQNIFETNRNEAFAYLNFPILGWVTIVGFIPAILLFFVEVEYEDKWLNGVITRSLSMLASIIVITVIAALYYQDYVSVGRNNSNLQREIIPANFVNSTVKYVYNRYLAEPIPFTTLGDDAKRDTNQSKPTLMFLVVGETARGKNFSMNGYEKDTNPFTSNSGGVISFNDVRSCGTATAVSVPCMFSNMGRKEFDDNLARNSEGLLDVLQKTGISIFWKENDGGCKGVCDRVPNIEIKPKDYPKFCDKNTCYDEVVLQNLDSEIAQMKGDKLVGFHLIGSHGPTYYKRYPDAHRQFTPDCPRSDIENCTDEELTNTYDNTIRYTDFVIAEMIAKLKTYEDKYNTALLYVSDHGESLGAMGLYLHGTPYKFAPDDQTRVPMQVWMSPGFIKEKGMNMECLQKNAAANRYSHDNIFSSVLGIWDVKTAIYEQELDIFKQCRNN"},"dna_sequence":{"accession":"MH332767.1","fmin":"0","fmax":"1623","strand":"+","sequence":"ATGCCTTACATTTTGAAAATTAAAATTGTGCCATTTATTTTTTTGTTGGCCTTTTATTTCGCGTTCATGTTGAACTGGCCTGGTGTACTCCATTTCTATGATATCATCTATAAGTTGGAGGGTTTCAAACTTGGGTTTGCAATTTCTCTTCCAATTTTATTAGTTGCGGCATTGAACCTTGTTTTTATCCCATTTTCAGTTCGATATTTAGTTAAACCCTTTTTCGCTCTTCTAATCTTGCTGAGTACTATCGTAAGCTACGCCATGATGAAGTATCGGGTTCTGTTTGATCAAAACATGATTCAGAACATTTTTGAAACCAATCGCAATGAGGCGTTTGCATATTTAAACTTTCCAATCCTGGGTTGGGTTACTATTGTGGGGTTTATTCCTGCTATTTTACTTTTCTTTGTTGAAGTTGAATATGAGGATAAATGGCTTAACGGGGTTATAACTCGTTCCCTATCGATGCTTGCATCCATTATAGTGATTACTGTTATTGCAGCACTATACTATCAGGACTATGTTTCTGTAGGACGCAATAACTCAAATCTCCAGCGTGAAATTATTCCGGCCAATTTCGTTAATAGTACCGTTAAATATGTTTACAATCGTTATCTTGCTGAACCAATCCCATTTACAACTTTAGGTGATGATGCAAAACGGGATACTAATCAAAGTAAGCCCACGTTGATGTTCCTGGTCGTTGGTGAAACCGCTCGTGGTAAAAATTTCTCGATGAATGGCTATGAGAAAGACACCAACCCATTTACCAGTAACTCTGGTGGTGTGATCTCCTTTAATGATGTTCGTTCATGTGGGACTGCAACCGCTGTATCTGTCCCCTGCATGTTCTCCAATATGGGGAGAAAGGAGTTTGATGATAATCTCGCTCGTAATAGCGAGGGTTTGCTAGATGTATTGCAAAAAACGGGGATTTCCATTTTTTGGAAGGAGAACGATGGCGGCTGCAAAGGCGTCTGCGATCGAGTTCCTAACATAGAGATCAAGCCGAAGGATTACCCAAAGTTCTGTGATAAAAACACATGCTATGACGAGGTTGTCCTTCAAAACCTCGATAGTGAAATTGCCCAAATGAAAGGGGATAAGCTGGTTGGCTTCCACCTGATTGGTAGCCATGGCCCAACTTACTACAAGCGATATCCTGATGCTCATCGTCAGTTCACCCCTGACTGTCCACGCAGTGATATCGAAAACTGCACGGATGAAGAGCTTACCAACACCTATGACAACACCATCCGCTACACGGATTTCGTGATTGCAGAGATGATTGCCAAGTTGAAAACCTACGAAGATAAGTACAACACCGCGTTGCTCTACGTCTCCGATCACGGTGAATCACTGGGAGCTATGGGGCTTTACCTGCACGGTACACCATACAAATTTGCACCGGATGATCAGACCCGCGTACCTATGCAGGTGTGGATGTCACCTGGTTTCATCAAAGAAAAAGGCATGAATATGGAATGTTTGCAGAAAAATGCCGCAGCCAATCGCTATTCTCATGACAACATATTTTCTTCTGTCCTGGGAATATGGGATGTGAAGACGGCTATCTACGAACAAGAATTAGATATCTTTAAGCAATGTCGGAATAATTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37047","NCBI_taxonomy_name":"Aeromonas","NCBI_taxonomy_id":"642"}}}},"ARO_accession":"3007278","ARO_id":"46024","ARO_name":"MCR-3.17","CARD_short_name":"MCR-3.17","ARO_description":"An MCR-3-type colistin resistance gene variant.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3268":{"model_id":"3268","model_name":"Clostridioides difficile gyrB conferring resistance to fluoroquinolones","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"8669":"D426N","8670":"R447L","8671":"E466V","8672":"S416A","8673":"D426V","8675":"E466K","8814":"R377G","8815":"R389P","8816":"E399K","8818":"V423F","8819":"R457T","8820":"D465Y","8834":"S366A","8835":"S366V","8836":"S464T","8837":"I139R","8838":"V130I","8846":"K444F","8674":"R447K","8817":"D409N"},"Curated-R":{"8669":"D426N","8670":"R447L","8671":"E466V","8672":"S416A","8673":"D426V","8675":"E466K","8814":"R377G","8815":"R389P","8816":"E399K","8818":"V423F","8819":"R457T","8820":"D465Y","8834":"S366A","8835":"S366V","8836":"S464T","8837":"I139R","8838":"V130I","8846":"K444F","8674":"R447K","8817":"D409N"},"clinical":{"8669":"D426N","8670":"R447L","8671":"E466V","8672":"S416A","8673":"D426V","8675":"E466K","8814":"R377G","8815":"R389P","8816":"E399K","8818":"V423F","8819":"R457T","8820":"D465Y","8834":"S366A","8835":"S366V","8836":"S464T","8837":"I139R","8838":"V130I","8846":"K444F","8674":"R447K","8817":"D409N"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"5316":{"protein_sequence":{"accession":"ADK13120.1","sequence":"MMQEKKQTYDENQIQVLEGLEAVRKRPGMYIGSTSSRGLHHLVYEIVDNSIDEALAGYCDKINVIIHKDNSITVTDNGRGMPVGMHHKMKKPTVEVIMTILHAGGKFGGGGYKVSGGLHGVGASVVNALSEICEVEVKRESHIWRQVFKRGKVASGLDIIGDSEEHGTKIHFKPDAEIFDEIEYDYDTLAQRLRELAFLNKGIKIRLEDERDDKEEIFHYEGGIKSFVTYLNRNKQPIHKEPIYVEGKKDDYSVEIAIQYNDGYTENIFAFANNIDTVEGGTHLAGFKSALTRVFNDYAKKFGILKENDKNLSGEDIREGLTAVISVKLVDPQFEGQTKTKLGNSEVRGIVDSIMGESLNNFLQENPQVAKMILDKSLMASRAREAARKARELTRRKSILENTSLPGKLADCSSKDPSECEIYLVEGDSAGGSAKQGRNRKFQAILPLRGKIMNVEKQRLDKILGYEEIRAMITAFGAGIGKDFDVNKIRYNKIIIMTDADVDGAHIRTLLLTFFFRYMKELVEKCHVYIAQPPLYRVAKGKKEYYAYSDDELDVLLTEIGGKDSNVDIQRYKGLGEMDSEQLWDTTMNPETRTLIQVNVEDTMAADEIFTILMGDKVEPRRNFIQENAKKVVNLDI"},"dna_sequence":{"accession":"CP001666.1","fmin":"4516","fmax":"6430","strand":"+","sequence":"ATGATGCAAGAAAAAAAGCAAACTTATGATGAAAATCAAATACAAGTATTAGAAGGTCTTGAAGCTGTTAGAAAAAGACCTGGAATGTATATTGGAAGTACTAGTTCTAGGGGGCTTCATCATTTAGTGTATGAGATAGTTGATAATAGCATAGATGAGGCATTGGCAGGATATTGCGATAAAATAAATGTAATTATACATAAAGATAATTCTATAACAGTTACGGATAATGGTAGAGGAATGCCTGTTGGAATGCACCATAAAATGAAGAAACCAACTGTAGAAGTTATAATGACTATACTACATGCAGGAGGGAAATTTGGTGGTGGAGGATACAAAGTTTCCGGCGGACTTCATGGAGTTGGAGCATCAGTTGTAAATGCTTTATCTGAAATCTGTGAAGTTGAAGTAAAAAGAGAAAGCCATATATGGAGACAGGTATTTAAAAGAGGAAAAGTAGCAAGCGGACTTGACATAATAGGTGATAGTGAGGAGCACGGAACAAAAATTCACTTTAAACCAGATGCAGAAATATTTGATGAAATAGAATATGATTATGATACATTGGCTCAAAGGCTTAGAGAATTGGCATTTTTAAACAAGGGTATAAAAATAAGGTTAGAAGATGAGAGAGATGATAAAGAAGAAATATTTCACTATGAAGGTGGAATAAAGTCCTTTGTAACTTATCTTAATAGAAATAAACAACCAATTCATAAAGAGCCTATATACGTAGAAGGCAAAAAAGATGACTACTCTGTAGAAATTGCTATTCAATACAATGATGGGTATACTGAAAATATTTTTGCTTTTGCTAATAACATAGATACAGTAGAAGGTGGAACTCATTTAGCTGGATTTAAGTCAGCACTTACTAGAGTATTTAATGATTATGCAAAAAAATTTGGTATATTAAAAGAAAATGATAAGAACCTATCAGGAGAAGATATAAGGGAAGGCCTTACTGCAGTTATATCTGTAAAACTTGTAGACCCTCAATTTGAAGGCCAGACGAAAACAAAACTAGGAAATAGTGAAGTGCGTGGTATAGTTGACAGCATAATGGGAGAGTCCTTAAATAATTTTTTACAGGAAAATCCTCAAGTAGCAAAGATGATACTTGATAAATCACTTATGGCATCACGTGCTAGAGAAGCGGCAAGAAAAGCAAGAGAGCTTACAAGACGTAAATCTATACTTGAAAATACTTCTCTTCCAGGAAAATTAGCAGATTGTTCATCTAAAGATCCTTCTGAATGTGAAATATATTTAGTCGAGGGTGATTCTGCAGGTGGATCTGCAAAACAAGGTAGAAATAGAAAATTTCAAGCTATACTTCCGCTACGTGGTAAAATAATGAATGTTGAGAAACAAAGGCTTGACAAAATACTTGGCTATGAAGAAATAAGAGCTATGATAACGGCATTTGGAGCAGGTATAGGAAAAGACTTTGATGTAAATAAAATAAGATACAATAAAATAATAATAATGACAGATGCAGATGTAGATGGTGCGCACATAAGAACATTATTACTTACTTTTTTCTTCAGATATATGAAGGAACTTGTTGAAAAATGTCACGTTTATATAGCTCAACCACCTTTATATAGAGTAGCTAAAGGGAAGAAGGAATACTACGCATATTCAGATGATGAATTAGATGTATTGCTTACTGAAATAGGTGGGAAAGACAGTAATGTAGATATACAAAGATATAAAGGACTTGGAGAAATGGATTCAGAGCAACTTTGGGATACTACAATGAATCCTGAAACAAGGACTCTTATTCAAGTAAATGTAGAGGACACTATGGCTGCTGATGAAATCTTTACTATACTTATGGGTGACAAGGTAGAACCTCGTAGAAATTTTATACAAGAAAATGCTAAAAAAGTTGTAAACTTAGATATATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42599","NCBI_taxonomy_name":"Clostridium ljungdahlii DSM 13528","NCBI_taxonomy_id":"748727"}}}},"ARO_accession":"3004562","ARO_id":"42469","ARO_name":"Clostridioides difficile gyrB conferring resistance to fluoroquinolones","CARD_short_name":"Cdif_gyrB_FLO","ARO_description":"Point mutations in gyrB of Clostridioides difficile conferring resistance to fluoroquinolone antibiotics.","ARO_category":{"37244":{"category_aro_accession":"3000864","category_aro_cvterm_id":"37244","category_aro_name":"fluoroquinolone resistant gyrB","category_aro_description":"Point mutations in DNA gyrase subunit B (gyrB) observed in Mycobacterium tuberculosis can result in resistance to fluoroquinolones.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"45747":{"category_aro_accession":"3007165","category_aro_cvterm_id":"45747","category_aro_name":"gemifloxacin","category_aro_description":"Gemifloxacin is a broad-spectrum, fourth generation, oral fluoroquinolone antibiotic used in the treatment of various bacterial infections, primarily in the lungs. It has been discontinued for therapeutic use in the US over concerns of tendon and peripheral neuron toxicity, although it is still available for experimental application and elsewhere for therapeutic use. It is usually administered as a mesylate salt, gemifloxacin mesylate.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3749":{"model_id":"3749","model_name":"Neisseria gonorrhoeae mtrC with mutation conferring resistance to azithromycin","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"750"},"41339":{"param_type":"nucleotide substitution in promoter region","param_description":"A nucleotide sequence change where, compared to a reference sequence, one nucleotide is replaced by one other nucleotide in the promoter region of a gene. These substitutions are indicated as upstream of the reference sequence transcription initiation site. Format is given by [-][position][wildtype][>][mutation], e.g. -11t>c or -15g>Var where Var represents any possible substitution.","param_type_id":"41339","param_value":{"9861":"-120c>t"}},"snp":{"Curated-R":{"9861":"D409N"}}},"model_sequences":{"sequence":{"6036":{"protein_sequence":{"accession":"QIH19826.1","sequence":"MAFYASKAMRAAALAAAVALALSSCGKGGDAAQGGQPAGREAPAPVVGVVTVHPQTVALTVELPGRLESLRTADVRAQVGGIIQKRLFQEGSYVRAGQPLYQIDSSTYEAGLESARAQLATAQATLAKADADLARYKPLVSADAISKQEYDAAVTAKRSAEAGVKAAQAAIKSAGINLNRSRITAPISGFIGQSKVSEGTLLNAGDTTVLATIRQTNPMYVNVTQSASEVMKLRRQIAEGKLLAADGAIAVGIKFDDGTVYPEKGRLLFADPTVDESTGQITLRAAVSNDQNILMPGLYVRVLMDQVAADNAFIVPQQAVTRGAKDTVMIVNAQGGMEPREVTVAQQQGTNWIVTSGLKDGDKVVVEGISIAGMTGAKKVTPKEWAPSENQAAAPQAGVQTASEAKPASEAK"},"dna_sequence":{"accession":"CP043871.1","fmin":"1391526","fmax":"1392765","strand":"-","sequence":"ATGGCTTTTTATGCTTCTAAGGCGATGCGTGCGGCCGCGTTGGCTGCCGCCGTTGCATTGGCACTGTCGTCTTGCGGTAAAGGAGGAGACGCGGCGCAGGGCGGGCAGCCTGCGGGTCGGGAAGCCCCCGCGCCCGTCGTCGGCGTCGTAACCGTCCATCCGCAAACCGTCGCATTGACCGTCGAGTTGCCGGGGCGTTTGGAATCGCTGCGTACCGCCGATGTCCGCGCCCAAGTCGGCGGCATCATCCAAAAACGCCTGTTCCAAGAAGGCAGTTATGTCCGCGCCGGGCAGCCGCTGTATCAGATCGACAGTTCCACTTATGAAGCAGGTCTGGAAAGCGCGCGCGCGCAACTGGCAACGGCACAGGCAACGCTTGCCAAAGCGGATGCGGATTTGGCGCGTTACAAACCGCTGGTTTCCGCCGATGCCATCAGTAAACAAGAGTACGATGCTGCGGTAACGGCGAAACGTTCTGCCGAGGCGGGCGTTAAAGCGGCGCAGGCGGCGATCAAATCCGCCGGCATCAATCTGAACCGTTCGCGCATTACCGCGCCGATTTCGGGCTTTATCGGTCAGTCCAAAGTTTCCGAAGGTACGCTGTTGAATGCGGGCGATACAACTGTTTTAGCCACCATCCGCCAAACCAATCCGATGTATGTGAACGTTACCCAGTCTGCATCCGAAGTGATGAAACTGCGCCGGCAGATAGCCGAAGGCAAGCTGCTGGCGGCGGATGGTGCGATTGCGGTCGGCATCAAATTTGACGACGGTACGGTTTATCCTGAAAAAGGCCGCCTGCTGTTTGCTGATCCGACCGTTGACGAATCGACCGGTCAGATTACCTTGCGCGCCGCCGTATCGAACGATCAGAATATCCTGATGCCCGGCCTGTATGTGCGTGTGCTGATGGATCAGGTGGCGGCGGATAATGCATTCATCGTTCCACAGCAGGCGGTAACGCGCGGTGCGAAAGATACCGTGATGATTGTGAATGCCCAGGGCGGTATGGAACCCCGCGAGGTAACGGTCGCGCAACAGCAGGGTACGAATTGGATTGTTACGTCGGGTCTGAAGGACGGGGACAAGGTGGTTGTGGAAGGCATCAGTATCGCCGGTATGACGGGGGCGAAAAAGGTAACGCCTAAAGAATGGGCGCCGTCTGAAAATCAAGCTGCCGCCCCTCAAGCCGGCGTTCAGACGGCATCTGAAGCCAAACCTGCTTCTGAAGCGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36806","NCBI_taxonomy_name":"Neisseria gonorrhoeae","NCBI_taxonomy_id":"485"}}}},"ARO_accession":"3005004","ARO_id":"43192","ARO_name":"Neisseria gonorrhoeae mtrC with mutation conferring resistance to azithromycin","CARD_short_name":"Ngon_mtrC_AZM","ARO_description":"Mutation in the mtrC efflux pump of Neisseria gonorrhoea shown to confer resistance to azithromycin, a macrolide type antibiotic.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"3753":{"model_id":"3753","model_name":"TxR","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"6043":{"protein_sequence":{"accession":"AAK37618.1","sequence":"MKVQKCKATIHRRSLDADPLLPLIGNSTCISELRNKLKKYAQCDAEVLIQGETGVGKGMCARIIHELSSRHIYPFVEVNCGAIPSGLIASELFGHEKGAFTGAISDRIGFIQKANKGTLFLDEIGDMPPDLQIHLLHFLESKQIHKVGADKIIDVDCRVIAASHVDLKSEVIQGGFREDLFYRQNILPLTIPPLRKRGEDTVILSERFLEELSNGKVQSMSPEVKKKLLKHKWPGNVRELRNVIQRAIVMCEDNTLHIADLGLDNNERQLLPSVEQIDLDYLLKAIEDNKHNMSAAARNLGISRTTLYRLIKKYNLPI"},"dna_sequence":{"accession":"AF353562.1","fmin":"963","fmax":"1920","strand":"+","sequence":"ATGAAAGTGCAAAAATGCAAAGCTACGATACACAGACGTTCTTTGGATGCAGACCCATTACTTCCTCTTATTGGTAATAGCACTTGCATCAGTGAACTACGTAACAAACTCAAAAAATACGCGCAATGTGATGCGGAAGTACTCATCCAAGGCGAAACCGGGGTGGGCAAAGGTATGTGTGCTCGAATCATTCACGAACTTTCAAGTAGACATATATACCCATTTGTTGAAGTTAACTGCGGAGCGATTCCAAGCGGACTCATCGCATCAGAGCTCTTCGGTCATGAGAAAGGAGCATTTACGGGGGCGATTTCGGATCGAATCGGCTTCATTCAAAAAGCGAACAAAGGGACGCTATTTCTCGATGAAATCGGCGACATGCCGCCTGATCTACAAATTCATTTGCTGCATTTTTTGGAGAGTAAGCAAATCCATAAAGTTGGTGCAGACAAAATCATTGATGTGGATTGCCGCGTCATCGCAGCCAGCCATGTAGATTTAAAAAGTGAAGTAATACAAGGAGGATTCCGAGAGGATTTATTTTACCGACAAAACATACTACCACTCACTATCCCCCCACTTCGAAAGCGTGGTGAGGATACGGTCATATTGTCAGAGCGTTTTTTAGAAGAATTATCCAACGGAAAAGTTCAGAGTATGTCTCCGGAAGTGAAGAAAAAGCTACTGAAACATAAATGGCCCGGCAACGTGAGAGAGCTGCGCAATGTCATTCAAAGGGCGATTGTAATGTGTGAGGATAACACTCTTCACATCGCCGATCTCGGCTTGGACAATAACGAAAGACAGCTCCTTCCCTCTGTTGAACAAATTGACTTAGATTATTTGTTAAAAGCAATCGAAGACAACAAACACAACATGAGTGCGGCTGCGAGGAATTTAGGTATTTCTAGAACCACACTCTACCGTCTAATCAAGAAATATAACCTGCCCATCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36785","NCBI_taxonomy_name":"Vibrio harveyi","NCBI_taxonomy_id":"669"}}}},"ARO_accession":"3005008","ARO_id":"43196","ARO_name":"TxR","CARD_short_name":"TxR","ARO_description":"TxR is a putative transcription regulator that plays a role in conferring tetracycline resistance. It is required for proper functioning of Tet35.","ARO_category":{"36002":{"category_aro_accession":"0010001","category_aro_cvterm_id":"36002","category_aro_name":"ATP-binding cassette (ABC) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding\/hydrolysis to transport substrates across cell membranes.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"3895":{"model_id":"3895","model_name":"Mycobacterium tuberculosis ethA mutations conferring resistance to perchlozone","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1010"},"40394":{"param_type":"nonsense mutation","param_description":"A sequence change where, compared to a reference sequence, one codon is replaced by a termination codon through a nucleotide substitution. These are described as a substitution of the wildtype codon to a termination codon. Format is given as [wild type AA][position][Ter], for example Q42Ter where Q42 is a wildtype amino acid replaced by a premature termination codon.","param_type_id":"40394","param_value":{"18536":"L62Ter","18537":"L265Ter"}},"snp":{"Curated-R":{"18536":"D409N","18537":"D409N"}}},"model_sequences":{"sequence":{"8811":{"protein_sequence":{"accession":"NP_218371.1","sequence":"MTEHLDVVIVGAGISGVSAAWHLQDRCPTKSYAILEKRESMGGTWDLFRYPGIRSDSDMYTLGFRFRPWTGRQAIADGKPILEYVKSTAAMYGIDRHIRFHHKVISADWSTAENRWTVHIQSHGTLSALTCEFLFLCSGYYNYDEGYSPRFAGSEDFVGPIIHPQHWPEDLDYDAKNIVVIGSGATAVTLVPALADSGAKHVTMLQRSPTYIVSQPDRDGIAEKLNRWLPETMAYTAVRWKNVLRQAAVYSACQKWPRRMRKMFLSLIQRQLPEGYDVRKHFGPHYNPWDQRLCLVPNGDLFRAIRHGKVEVVTDTIERFTATGIRLNSGRELPADIIITATGLNLQLFGGATATIDGQQVDITTTMAYKGMMLSGIPNMAYTVGYTNASWTLKADLVSEFVCRLLNYMDDNGFDTVVVERPGSDVEERPFMEFTPGYVLRSLDELPKQGSRTPWRLNQNYLRDIRLIRRGKIDDEGLRFAKRPAPVGV"},"dna_sequence":{"accession":"NC_000962.3","fmin":"4326003","fmax":"4327473","strand":"-","sequence":"ATGACCGAGCACCTCGACGTTGTCATCGTGGGCGCTGGAATCTCCGGTGTCAGCGCGGCCTGGCACCTGCAGGACCGTTGCCCGACCAAGAGCTACGCCATCCTGGAAAAGCGGGAATCCATGGGCGGCACCTGGGATTTGTTCCGTTATCCCGGAATTCGCTCCGACTCCGACATGTACACGCTAGGTTTCCGATTCCGTCCCTGGACCGGACGGCAGGCGATCGCCGACGGCAAGCCCATCCTCGAGTACGTCAAGAGCACCGCGGCCATGTATGGAATCGACAGGCATATCCGGTTCCACCACAAGGTGATCAGTGCCGATTGGTCGACCGCGGAAAACCGCTGGACCGTTCACATCCAAAGCCACGGCACGCTCAGCGCCCTCACCTGCGAATTCCTCTTTCTGTGCAGCGGCTACTACAACTACGACGAGGGCTACTCGCCGAGATTCGCCGGCTCGGAGGATTTCGTCGGGCCGATCATCCATCCGCAGCACTGGCCCGAGGACCTCGACTACGACGCTAAGAACATCGTCGTGATCGGCAGTGGCGCAACGGCGGTCACGCTCGTGCCGGCGCTGGCGGACTCGGGCGCCAAGCACGTCACGATGCTGCAGCGCTCACCCACCTACATCGTGTCGCAGCCAGACCGGGACGGCATCGCCGAGAAGCTCAACCGCTGGCTGCCGGAGACCATGGCCTACACCGCGGTACGGTGGAAGAACGTGCTGCGCCAGGCGGCCGTGTACAGCGCCTGCCAGAAGTGGCCACGGCGCATGCGGAAGATGTTCCTGAGCCTGATCCAGCGCCAGCTACCCGAGGGGTACGACGTGCGAAAGCACTTCGGCCCGCACTACAACCCCTGGGACCAGCGATTGTGCTTGGTGCCCAACGGCGACCTGTTCCGGGCCATTCGTCACGGGAAGGTCGAGGTGGTGACCGACACCATTGAACGGTTCACCGCGACCGGAATCCGGCTGAACTCAGGTCGCGAACTGCCGGCTGACATCATCATTACCGCAACGGGGTTGAACCTGCAGCTTTTTGGTGGGGCGACGGCGACTATCGACGGACAACAAGTGGACATCACCACGACGATGGCCTACAAGGGCATGATGCTTTCCGGCATCCCCAACATGGCCTACACGGTTGGCTACACCAATGCCTCCTGGACGCTGAAGGCCGACCTGGTGTCGGAGTTTGTCTGTCGCTTGTTGAATTACATGGACGACAACGGTTTTGACACCGTGGTCGTCGAGCGACCGGGCTCAGATGTCGAAGAGCGGCCCTTCATGGAGTTCACCCCAGGTTACGTGCTGCGCTCGCTGGACGAGCTGCCCAAGCAGGGTTCGCGTACACCGTGGCGCCTGAATCAGAACTACCTACGTGACATCCGGCTCATCCGGCGCGGCAAGATCGACGACGAGGGTCTGCGGTTCGCCAAAAGGCCTGCCCCGGTGGGGGTTTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3005178","ARO_id":"43531","ARO_name":"Mycobacterium tuberculosis ethA mutations conferring resistance to perchlozone","CARD_short_name":"Mtub_ethA_PCL","ARO_description":"Mutations in ethA conferring resistance to perchlozone, a novel thiosemicarbazone.","ARO_category":{"43561":{"category_aro_accession":"3005205","category_aro_cvterm_id":"43561","category_aro_name":"perchlozone resistant ethA","category_aro_description":"Genetic variants of ethA from Mycobacterium spp. including tuberculosis, which confer resistance to the antibiotic perchlozone.","category_aro_class_name":"AMR Gene Family"},"43528":{"category_aro_accession":"3005175","category_aro_cvterm_id":"43528","category_aro_name":"perchlozone","category_aro_description":"Perchlozone is a novel thiosemicarbazone used for the treatment of multidrug-resistant tuberculosis. It is similar to thiacetazone with only a different side chain attached to the thiosemicarbazone moiety. Perchlozone is a prodrug that is activated by ethA and inhibits the HadABC complex.","category_aro_class_name":"Antibiotic"},"45743":{"category_aro_accession":"3007161","category_aro_cvterm_id":"45743","category_aro_name":"thiosemicarbazone antibiotic","category_aro_description":"A group of antibiotics derived from thiosemicarbazide (possessing the thiosemicarbazone functional group).","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5737":{"model_id":"5737","model_name":"salB","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"8291":{"protein_sequence":{"accession":"MBW0770001.1","sequence":"MLFLFEEKPLEIENKQLIKRLSFHIEDHEHLALIGVNGIGKSTLLHHIHKNELIDTAMMEQDLSKHDDIDVMDYVMSAYPKLVELRKDLSDIDSLNSYIELDGYNVENNIIIEGNKLGLSSTHFEQKIGTLSGGEQTKVSFLKVILSDAPLLLIDEPTNHMDKEMKVWLIKAFKSEQRAILFVSHDREFLNETPDAILELTKDGATRYSGHYDDYKNQKDIEIETEKLKYEKEQKEQKAIEESIKKYKEWYQRAAQKASVRSPYAQKQLSKLAKRFKSKEHQLNRKLEESKSDNPLEENKSFSIENNEFKSHYLVRFENVSFSYKSREIFKDTYFEIKRNQTVIIEGKNGSGKSTLIQLILGNLLPMSGAVKKHPDLDIGYFSQDFQNLNPNNSVLEEVMDIENMMITDARTILASFYFDKSRMNDKVRQLSMGEKCRLQFVKLYFSNPHILILDEPTNYFDISMQEKIIQLIQSFNGAVIIVSHDEIFKDEIRDQVWKIENCKLIHENVSINTPIDAESMKDELKILEQYTDERNKETDF"},"dna_sequence":{"accession":"JAHWBZ010000013.1","fmin":"187616","fmax":"189242","strand":"-","sequence":"ATGCTATTTTTATTTGAAGAAAAACCATTAGAAATTGAGAATAAACAGCTTATAAAACGTTTGTCATTTCATATCGAAGACCATGAGCATTTAGCCCTTATCGGTGTTAATGGTATTGGTAAATCTACGCTATTACATCATATTCATAAAAATGAATTGATTGATACAGCTATGATGGAACAAGATTTAAGTAAACATGATGATATTGATGTTATGGATTATGTCATGTCTGCATATCCAAAGTTAGTTGAATTGAGAAAAGATTTATCTGACATTGATTCTTTAAATAGTTATATAGAATTAGACGGATATAACGTTGAAAATAACATTATTATTGAAGGAAATAAATTAGGATTATCATCAACACATTTTGAGCAAAAGATAGGCACTTTAAGTGGTGGTGAGCAAACTAAAGTCTCATTTTTAAAAGTTATTTTATCAGATGCACCATTATTATTAATAGACGAACCAACTAACCATATGGATAAAGAGATGAAAGTGTGGTTAATAAAAGCTTTTAAATCAGAACAAAGAGCTATTCTATTCGTATCGCATGATAGAGAGTTTTTAAATGAAACACCAGATGCTATTTTAGAACTCACAAAAGATGGTGCAACTCGATATTCAGGTCATTATGATGATTATAAAAATCAAAAAGATATTGAAATTGAAACAGAAAAATTAAAATATGAAAAAGAACAGAAAGAACAAAAAGCAATAGAAGAAAGTATTAAGAAATACAAAGAATGGTATCAAAGGGCTGCTCAGAAAGCTTCTGTTCGTAGTCCATATGCTCAAAAACAATTAAGTAAATTAGCTAAAAGATTTAAATCAAAAGAACATCAGTTAAATCGTAAATTAGAAGAATCAAAATCTGATAATCCGTTAGAAGAAAATAAATCCTTTTCTATAGAAAATAATGAATTTAAATCACATTATTTAGTAAGATTCGAAAATGTTTCATTTTCATATAAGAGTCGTGAAATTTTTAAAGACACTTATTTTGAAATAAAGAGAAATCAAACTGTAATTATAGAAGGTAAAAATGGGTCCGGTAAATCTACATTGATACAATTAATTTTAGGTAACTTATTACCAATGAGTGGAGCTGTCAAAAAGCACCCAGACTTAGACATAGGATACTTCTCGCAAGATTTTCAAAATTTAAACCCAAACAACTCGGTATTAGAAGAAGTTATGGATATTGAGAATATGATGATAACAGACGCGAGGACTATTTTAGCGAGTTTTTATTTTGATAAGAGCAGGATGAATGATAAAGTTCGTCAGTTATCAATGGGAGAAAAGTGCAGGTTACAATTTGTAAAATTATATTTTTCTAACCCACACATCTTAATTTTAGATGAACCAACTAATTATTTTGATATTAGTATGCAAGAGAAAATCATACAATTAATCCAAAGTTTTAATGGTGCAGTAATTATTGTGTCGCATGATGAAATTTTTAAAGATGAAATAAGAGACCAAGTTTGGAAGATTGAAAACTGTAAGCTCATTCATGAAAATGTATCTATTAATACACCTATTGATGCTGAATCGATGAAGGATGAGTTAAAAATATTAGAGCAATATACAGATGAAAGAAATAAAGAAACAGACTTCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39555","NCBI_taxonomy_name":"Mammaliicoccus lentus","NCBI_taxonomy_id":"42858"}}}},"ARO_accession":"3007026","ARO_id":"45570","ARO_name":"salB","CARD_short_name":"salB","ARO_description":"salB is a ABC-F subfamily protein gene that confers resistance to lincosamides and class A streptogramins.","ARO_category":{"45589":{"category_aro_accession":"3007030","category_aro_cvterm_id":"45589","category_aro_name":"sal-type ABC-F protein","category_aro_description":"Sal proteins are a part of the ABC-F proteins, expressed in staphylococci that confer resistance to group A streptogramin, lincosamide, and pleuromutilin antibiotics through ribosomal protection.","category_aro_class_name":"AMR Gene Family"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"virginiamycin M1","category_aro_description":"Virginiamycin M1 is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37015":{"category_aro_accession":"3000671","category_aro_cvterm_id":"37015","category_aro_name":"tiamulin","category_aro_description":"Tiamulin is a pleuromutilin derivative currently used in veterinary medicine. It binds to the 23 rRNA of the 50S ribosomal subunit to inhibit protein translation.","category_aro_class_name":"Antibiotic"},"37713":{"category_aro_accession":"3001314","category_aro_cvterm_id":"37713","category_aro_name":"retapamulin","category_aro_description":"Retapamulin is a semi-synthetic pleuromutilin antibiotic approved for the treatment of skin infections.","category_aro_class_name":"Antibiotic"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35952":{"category_aro_accession":"0000034","category_aro_cvterm_id":"35952","category_aro_name":"streptogramin A antibiotic","category_aro_description":"Streptogramin A antibiotics are cyclic polyketide peptide hybrids that bind to the ribosomal peptidyl transfer centre. Structural variation arises from substituting a proline for its desaturated derivative and by its substitution for Ala or Cys. Used alone, streptogramin A antibiotics are bacteriostatic, but is bactericidal when used with streptogramin B antibiotics.","category_aro_class_name":"Drug Class"},"37014":{"category_aro_accession":"3000670","category_aro_cvterm_id":"37014","category_aro_name":"pleuromutilin antibiotic","category_aro_description":"Pleuromutilins are natural fungal products that target bacterial protein translation by binding the the 23S rRNA, blocking the ribosome P site at the 50S subunit. They are mostly used for agriculture and veterinary purposes.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5738":{"model_id":"5738","model_name":"salC","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"8292":{"protein_sequence":{"accession":"MBW0764195.1","sequence":"MLFLFEKKSLEIDNKLLIPSLTFIIEENEHLAIVGINGIGKSTLLNKIHHKENIETAMMEQDLTKYGTLNVMEYIMLTYPQLSSLRENLSDLDNINRYIELDGYEIEQNIIIEGKKLGLTERHFDQLISTLSGGEQTKVSFLKVKLDKARLLLIDEPTNHMDEEMKVWLTNAFKQEKRAILFVSHDKTFLNETPDAILELSSSGATKYSGQYDNYKQQKDLEYKTIKLQYEKQEKEQRAIEETIKKYKEWYQKASQKASVRNPYQQKQLSKLAKKFKSKEYQMNKKLEQTNLSDPEEEGKTFSMQHHAFKSHYLVKFKNVTFSYNEKPIFNDVSFHIKRNQNVIIEGQNGSGKSTLIKLILGQLTPDEGEVIVHPELEIGYFSQDFNNLNMKNTVLEEIMSIQEMKEAEARTILANYYFNENRINDVVANLSMGEKCRIQFVKLYFSNPHILILDEPTNYFDIEMQEKIIQLIQSFQGSTLIISHDKYFKEKLKDQIWTIKNLDLVHENLKIENPLNADSIKNQLNELEQYTDERNRETEF"},"dna_sequence":{"accession":"JAAQPD010000007.1","fmin":"115792","fmax":"117418","strand":"-","sequence":"ATGCTATTTTTATTTGAAAAAAAGTCTTTAGAGATTGACAATAAACTGCTCATACCTTCACTAACATTTATTATTGAAGAAAATGAACATTTGGCAATAGTCGGCATAAATGGTATCGGAAAATCTACACTTTTAAATAAAATCCATCATAAAGAAAATATTGAAACAGCAATGATGGAACAAGATTTAACTAAATATGGAACTTTAAATGTCATGGAGTATATTATGTTAACTTATCCACAATTATCATCGTTAAGAGAAAATCTAAGTGATTTGGATAATATAAATAGATATATTGAATTAGACGGTTACGAAATTGAGCAAAACATTATAATTGAAGGAAAAAAGTTAGGATTAACAGAAAGGCACTTTGATCAATTAATTTCTACTTTAAGTGGTGGTGAGCAAACAAAAGTTTCGTTTTTGAAAGTTAAATTAGATAAAGCACGATTATTATTAATTGATGAACCAACTAACCATATGGATGAAGAAATGAAAGTATGGTTAACTAATGCATTTAAACAAGAAAAACGTGCAATATTATTTGTTTCTCACGATAAGACTTTTTTAAATGAAACACCAGACGCAATTTTGGAACTGAGTAGTAGTGGTGCAACAAAATACTCAGGTCAGTATGACAATTACAAGCAACAAAAAGATTTAGAATATAAAACGATTAAGCTACAATACGAAAAACAAGAAAAAGAGCAACGAGCAATTGAAGAAACAATTAAAAAATATAAAGAATGGTATCAAAAAGCTTCACAAAAAGCTTCAGTAAGAAATCCTTATCAACAAAAACAACTTAGCAAGCTTGCGAAAAAGTTTAAATCGAAAGAATATCAAATGAATAAAAAACTTGAACAAACCAATTTATCAGATCCTGAAGAGGAAGGAAAAACATTTTCAATGCAACATCACGCCTTCAAATCTCATTATTTAGTTAAATTTAAAAATGTGACATTTTCATATAATGAAAAGCCTATTTTTAATGATGTCTCTTTTCATATTAAGCGAAATCAAAATGTTATCATTGAAGGTCAAAATGGCTCAGGTAAATCTACTTTGATCAAGTTGATACTAGGTCAACTGACACCTGATGAGGGAGAAGTAATCGTACATCCTGAATTAGAAATAGGTTATTTTTCACAAGATTTTAATAACTTAAATATGAAAAATACTGTGTTAGAAGAAATAATGTCTATTCAAGAAATGAAAGAAGCGGAAGCAAGAACAATTTTAGCGAATTATTATTTTAATGAAAATAGAATTAATGATGTTGTTGCCAATTTATCTATGGGTGAAAAATGTAGAATACAGTTTGTTAAATTGTATTTTTCAAATCCACATATACTCATATTAGATGAGCCAACTAACTATTTTGATATTGAAATGCAAGAAAAAATCATACAATTAATTCAATCTTTTCAAGGATCAACACTTATCATTTCACATGATAAATATTTTAAAGAAAAGCTTAAAGATCAAATTTGGACAATAAAGAATCTAGATTTGGTACATGAAAATCTTAAAATTGAGAATCCATTAAATGCTGATTCTATTAAAAATCAATTAAATGAATTAGAGCAATATACCGACGAAAGAAATAGAGAAACAGAGTTCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42526","NCBI_taxonomy_name":"Mammaliicoccus fleurettii","NCBI_taxonomy_id":"150056"}}}},"ARO_accession":"3007027","ARO_id":"45571","ARO_name":"salC","CARD_short_name":"salC","ARO_description":"salC is a ABC-F subfamily protein gene that confers resistance to lincosamides and class A streptogramins.","ARO_category":{"45589":{"category_aro_accession":"3007030","category_aro_cvterm_id":"45589","category_aro_name":"sal-type ABC-F protein","category_aro_description":"Sal proteins are a part of the ABC-F proteins, expressed in staphylococci that confer resistance to group A streptogramin, lincosamide, and pleuromutilin antibiotics through ribosomal protection.","category_aro_class_name":"AMR Gene Family"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"virginiamycin M1","category_aro_description":"Virginiamycin M1 is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37015":{"category_aro_accession":"3000671","category_aro_cvterm_id":"37015","category_aro_name":"tiamulin","category_aro_description":"Tiamulin is a pleuromutilin derivative currently used in veterinary medicine. It binds to the 23 rRNA of the 50S ribosomal subunit to inhibit protein translation.","category_aro_class_name":"Antibiotic"},"37713":{"category_aro_accession":"3001314","category_aro_cvterm_id":"37713","category_aro_name":"retapamulin","category_aro_description":"Retapamulin is a semi-synthetic pleuromutilin antibiotic approved for the treatment of skin infections.","category_aro_class_name":"Antibiotic"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35952":{"category_aro_accession":"0000034","category_aro_cvterm_id":"35952","category_aro_name":"streptogramin A antibiotic","category_aro_description":"Streptogramin A antibiotics are cyclic polyketide peptide hybrids that bind to the ribosomal peptidyl transfer centre. Structural variation arises from substituting a proline for its desaturated derivative and by its substitution for Ala or Cys. Used alone, streptogramin A antibiotics are bacteriostatic, but is bactericidal when used with streptogramin B antibiotics.","category_aro_class_name":"Drug Class"},"37014":{"category_aro_accession":"3000670","category_aro_cvterm_id":"37014","category_aro_name":"pleuromutilin antibiotic","category_aro_description":"Pleuromutilins are natural fungal products that target bacterial protein translation by binding the the 23S rRNA, blocking the ribosome P site at the 50S subunit. They are mostly used for agriculture and veterinary purposes.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5739":{"model_id":"5739","model_name":"salD","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"8293":{"protein_sequence":{"accession":"WP_082039181.1","sequence":"MSFYFTEKPFERFGKTLIEEVNLSVEPGEHIAIVGDNGVGKSTLLNAIYNKYNDSTYLMDQELSKYKNETAINYIMSWYPELLDIKLAMQTDYEKIGDYIELNGYEIEEQIILQAKQLNLEESDLDKQMGQLSGGQQTKVALVRAMISEKNLILLDEPTNHLDKQMIHIVVDYIKQAKQSILYVSHHRGFIDETATHIIEITPQATRKFTGNYSQYKSIIDVERETQKKVYEKKQKEIKALEATVDRVKNWHKTANQSASVRNPLEQKRLSKLAQKAKVKESQINQKLEKIKVQQPKSDDRHFHFENQDALNKKYLMQLYDFSITIDGKNIYQNANFEIKDNENIILTGPNGSGKSLLISIIKQSIIPDEGDIYITPSLKIAYFDQKNDNLNYDSTALTMLLNMEGMERSQAQTILASFGFDNQKINLPISQLSMGEKSRLQFVLLYFSNPHLLILDEPTNYFDIATQDLILQMLKQFAGQVMIVTHDEYLKSQITATHWTIKDKKLMNLTLSEKHSPNMVDDTLKLLDDYKSIDEFGHFETDN"},"dna_sequence":{"accession":"NZ_JAIEXG010000001.1","fmin":"252896","fmax":"254531","strand":"+","sequence":"ATGTCTTTTTATTTTACAGAAAAGCCATTTGAAAGGTTCGGCAAGACATTAATAGAAGAGGTTAATTTAAGTGTTGAACCAGGTGAACATATAGCAATTGTTGGTGATAACGGGGTAGGTAAATCAACATTACTCAATGCAATTTACAATAAATATAATGATTCAACGTATTTGATGGATCAAGAATTATCGAAGTATAAAAATGAAACGGCAATAAATTATATTATGTCGTGGTATCCAGAATTATTAGATATTAAACTTGCTATGCAAACTGATTATGAAAAAATTGGTGACTATATAGAACTTAATGGATATGAAATAGAAGAACAAATCATTTTACAAGCAAAGCAATTAAATTTAGAAGAGTCAGATTTAGATAAACAAATGGGGCAGTTAAGTGGCGGACAACAAACCAAAGTAGCATTAGTTCGAGCAATGATTTCAGAAAAAAATTTAATCTTGTTGGATGAACCAACAAATCACTTAGATAAACAAATGATTCATATTGTCGTGGATTATATAAAGCAAGCAAAGCAAAGTATATTATACGTGTCACATCATAGAGGATTTATCGACGAAACTGCAACGCACATTATTGAAATTACACCACAAGCTACAAGAAAATTTACTGGTAATTATAGTCAATATAAATCCATTATAGATGTTGAAAGAGAAACTCAAAAAAAGGTATACGAGAAAAAGCAAAAAGAAATAAAAGCTTTGGAAGCAACCGTAGATAGAGTTAAAAATTGGCATAAAACTGCGAATCAATCTGCAAGTGTTCGTAATCCGTTAGAGCAAAAGCGTTTGAGTAAATTAGCTCAAAAGGCAAAGGTTAAAGAATCACAAATAAATCAAAAACTTGAAAAGATTAAAGTCCAACAGCCTAAGTCGGATGATCGTCACTTCCATTTTGAGAATCAAGATGCGCTAAATAAAAAATATTTAATGCAATTATATGATTTTAGCATCACTATTGATGGTAAGAATATTTATCAAAATGCAAATTTCGAAATTAAAGATAATGAAAACATTATACTTACTGGCCCGAATGGTAGTGGCAAATCATTATTAATCTCAATTATCAAGCAGTCAATAATACCAGATGAGGGTGATATTTATATAACGCCTTCTCTAAAAATAGCTTATTTTGACCAAAAAAATGACAATTTAAATTATGACAGCACAGCATTAACAATGTTATTAAACATGGAGGGTATGGAACGTAGTCAAGCACAAACGATATTAGCGTCATTTGGATTTGATAACCAAAAAATAAACCTTCCAATTTCTCAATTATCTATGGGAGAGAAAAGTAGATTACAGTTTGTATTATTATATTTCTCAAATCCACATTTATTAATTCTCGACGAACCAACCAATTACTTCGATATTGCTACGCAAGATTTAATATTACAGATGCTAAAGCAATTTGCAGGACAAGTAATGATTGTGACGCATGATGAATACTTGAAATCTCAAATTACAGCGACACATTGGACAATTAAAGATAAAAAGTTAATGAATTTAACATTATCAGAGAAGCATTCACCCAATATGGTGGATGATACATTAAAATTATTAGATGATTATAAGTCGATAGATGAATTCGGACATTTTGAAACAGACAACTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"45587","NCBI_taxonomy_name":"Staphylococcus gallinarum","NCBI_taxonomy_id":"1293"}}}},"ARO_accession":"3007028","ARO_id":"45572","ARO_name":"salD","CARD_short_name":"salD","ARO_description":"salD is a ABC-F subfamily protein gene that confers resistance to lincosamides and class A streptogramins.","ARO_category":{"45589":{"category_aro_accession":"3007030","category_aro_cvterm_id":"45589","category_aro_name":"sal-type ABC-F protein","category_aro_description":"Sal proteins are a part of the ABC-F proteins, expressed in staphylococci that confer resistance to group A streptogramin, lincosamide, and pleuromutilin antibiotics through ribosomal protection.","category_aro_class_name":"AMR Gene Family"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"virginiamycin M1","category_aro_description":"Virginiamycin M1 is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37015":{"category_aro_accession":"3000671","category_aro_cvterm_id":"37015","category_aro_name":"tiamulin","category_aro_description":"Tiamulin is a pleuromutilin derivative currently used in veterinary medicine. It binds to the 23 rRNA of the 50S ribosomal subunit to inhibit protein translation.","category_aro_class_name":"Antibiotic"},"37713":{"category_aro_accession":"3001314","category_aro_cvterm_id":"37713","category_aro_name":"retapamulin","category_aro_description":"Retapamulin is a semi-synthetic pleuromutilin antibiotic approved for the treatment of skin infections.","category_aro_class_name":"Antibiotic"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35952":{"category_aro_accession":"0000034","category_aro_cvterm_id":"35952","category_aro_name":"streptogramin A antibiotic","category_aro_description":"Streptogramin A antibiotics are cyclic polyketide peptide hybrids that bind to the ribosomal peptidyl transfer centre. Structural variation arises from substituting a proline for its desaturated derivative and by its substitution for Ala or Cys. Used alone, streptogramin A antibiotics are bacteriostatic, but is bactericidal when used with streptogramin B antibiotics.","category_aro_class_name":"Drug Class"},"37014":{"category_aro_accession":"3000670","category_aro_cvterm_id":"37014","category_aro_name":"pleuromutilin antibiotic","category_aro_description":"Pleuromutilins are natural fungal products that target bacterial protein translation by binding the the 23S rRNA, blocking the ribosome P site at the 50S subunit. They are mostly used for agriculture and veterinary purposes.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5740":{"model_id":"5740","model_name":"salE","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"8294":{"protein_sequence":{"accession":"WP_096809342.1","sequence":"MSFYFAQKPFEMFGKTLIQSVDLQFEKGEHIAVIGNNGVGKTTLLKALNNKYKEDTYLMDQNMTTFGNMTGIDYVISLNTELFHLKQALMDNYEKVSDYIALNGYEFEQTIITKAKQMALTEADLDKPIKVLSGGQQTRLALLRAFISNKPLILLDEPTNHLDQEMIDQLINHIQQSKRTIIYVSHHRGFIDQTASHVIEITPESTRKFNGNYKQYKEIKDLESQTEQRIYNKQQKEIQDLERTIKRVQTWHHSAQQKASVRNPIEQKKLSKLAQRAKVKEKQLNQKLQEKHIQEPSKETKSYYFSHQTSLPKRFLIRFEDVSVNIDGQAIYKHAHFEMKQNENILLTGPNGSGKSLFIALIRQHLSPDEGIIEITPSLKIGYFDHTNNNLNEAESPLSMLLVRTNITRSQAQTLLASFNFDKDQIKKPIRYLSMGEKSRLQFVLLYFSGANLLVLDEPTNYFDIVTQDLILSMIQSFTGQVLIVTHDSYLQSQFKAVHWEIKNQQLYNVSLTHTRESNLDETLKLLGEYKFIDENGHFETDN"},"dna_sequence":{"accession":"NZ_CP017459.1","fmin":"1364720","fmax":"1366352","strand":"+","sequence":"ATGTCTTTTTATTTTGCCCAAAAACCTTTTGAAATGTTTGGAAAAACACTGATTCAGTCAGTGGATTTACAATTTGAAAAGGGTGAACATATTGCTGTGATTGGTAATAATGGCGTTGGGAAAACGACTTTATTAAAAGCATTAAATAATAAGTATAAAGAAGATACTTATTTGATGGACCAAAACATGACTACCTTTGGAAACATGACGGGGATAGACTATGTAATAAGCTTAAACACAGAATTGTTTCATTTAAAACAAGCGTTAATGGATAACTATGAAAAAGTTTCAGATTATATCGCTTTAAATGGCTATGAATTTGAACAAACCATTATAACTAAAGCGAAGCAAATGGCTCTAACGGAAGCAGATCTTGACAAACCAATTAAAGTATTAAGCGGCGGCCAACAAACTAGGCTTGCTTTATTGAGAGCATTTATTTCAAACAAACCATTGATATTGCTGGACGAACCAACCAATCATTTAGACCAAGAAATGATAGACCAATTGATTAACCATATACAACAATCAAAACGCACAATCATATATGTGTCGCATCATAGAGGATTTATAGATCAGACCGCGAGTCATGTTATAGAAATAACACCCGAAAGTACAAGAAAATTTAATGGCAATTATAAGCAATACAAAGAGATAAAAGATTTAGAAAGTCAAACAGAACAACGTATATATAATAAACAACAAAAAGAAATACAAGACCTCGAACGTACGATCAAACGCGTACAAACATGGCATCATTCTGCTCAGCAAAAAGCAAGTGTACGTAATCCGATTGAACAGAAAAAGTTGAGCAAATTAGCGCAAAGGGCAAAGGTGAAGGAAAAACAATTAAACCAAAAATTACAAGAAAAACATATTCAAGAACCGAGTAAAGAAACAAAGTCATATTACTTTAGTCATCAGACTAGCCTTCCTAAACGTTTCTTAATTCGTTTTGAAGATGTTAGCGTTAATATTGATGGACAAGCTATATATAAACACGCTCATTTTGAAATGAAACAAAATGAAAATATATTACTTACTGGTCCAAATGGAAGTGGTAAATCGCTTTTCATCGCTTTGATTAGACAGCATTTATCACCAGACGAAGGTATTATAGAGATTACGCCATCGTTAAAGATAGGTTACTTTGATCATACAAATAACAATCTAAATGAAGCAGAATCTCCATTATCAATGTTGTTAGTAAGAACTAACATAACGCGTAGCCAAGCGCAGACATTACTTGCTTCATTTAATTTTGATAAGGATCAAATCAAAAAACCAATTCGCTATTTGTCTATGGGGGAAAAAAGTCGTTTACAATTTGTATTATTATATTTTTCAGGTGCTAATTTATTAGTATTGGATGAGCCTACGAACTATTTTGATATTGTAACTCAAGATTTAATTTTAAGTATGATTCAAAGTTTTACCGGTCAAGTATTGATTGTTACACATGATTCATATTTACAATCTCAATTTAAAGCTGTACATTGGGAAATAAAAAATCAACAACTTTATAATGTATCTTTAACTCATACGCGTGAATCAAACTTAGATGAAACCCTTAAGTTACTAGGTGAATATAAATTTATAGATGAAAATGGTCATTTTGAAACAGACAACTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"45588","NCBI_taxonomy_name":"Staphylococcus nepalensis","NCBI_taxonomy_id":"214473"}}}},"ARO_accession":"3007029","ARO_id":"45573","ARO_name":"salE","CARD_short_name":"salE","ARO_description":"salE is a ABC-F subfamily protein gene that confers resistance to lincosamides and class A streptogramins.","ARO_category":{"45589":{"category_aro_accession":"3007030","category_aro_cvterm_id":"45589","category_aro_name":"sal-type ABC-F protein","category_aro_description":"Sal proteins are a part of the ABC-F proteins, expressed in staphylococci that confer resistance to group A streptogramin, lincosamide, and pleuromutilin antibiotics through ribosomal protection.","category_aro_class_name":"AMR Gene Family"},"37015":{"category_aro_accession":"3000671","category_aro_cvterm_id":"37015","category_aro_name":"tiamulin","category_aro_description":"Tiamulin is a pleuromutilin derivative currently used in veterinary medicine. It binds to the 23 rRNA of the 50S ribosomal subunit to inhibit protein translation.","category_aro_class_name":"Antibiotic"},"37713":{"category_aro_accession":"3001314","category_aro_cvterm_id":"37713","category_aro_name":"retapamulin","category_aro_description":"Retapamulin is a semi-synthetic pleuromutilin antibiotic approved for the treatment of skin infections.","category_aro_class_name":"Antibiotic"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35952":{"category_aro_accession":"0000034","category_aro_cvterm_id":"35952","category_aro_name":"streptogramin A antibiotic","category_aro_description":"Streptogramin A antibiotics are cyclic polyketide peptide hybrids that bind to the ribosomal peptidyl transfer centre. Structural variation arises from substituting a proline for its desaturated derivative and by its substitution for Ala or Cys. Used alone, streptogramin A antibiotics are bacteriostatic, but is bactericidal when used with streptogramin B antibiotics.","category_aro_class_name":"Drug Class"},"37014":{"category_aro_accession":"3000670","category_aro_cvterm_id":"37014","category_aro_name":"pleuromutilin antibiotic","category_aro_description":"Pleuromutilins are natural fungal products that target bacterial protein translation by binding the the 23S rRNA, blocking the ribosome P site at the 50S subunit. They are mostly used for agriculture and veterinary purposes.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"229":{"model_id":"229","model_name":"vanTm gene in vanL cluster","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"175"}},"model_sequences":{"sequence":{"301":{"protein_sequence":{"accession":"ABX54689.1","sequence":"MKKQNTGVNNFRLIAAAMVVAIHCFPFQTISKELDTLVTLTVFRIAVPFFFMVSGYYLLGPIPSSATNTYQINNYIKKQLKVYTFAIVLYLPLAFYSQSITLDMSIISFIKQLLFNGFFYHLWFFPAWVLGLLIVQFLLKRMNIQTVLFITFVAYLIGLGGDSWWGIVKQVPFFFRFYNAIFQLFGYTRNGLFYAPLFFALGAYLYKMNIKNFNSARNNYLLLLFSIEMILESYFLHLFNIPKHDSMYLFLPFVMTLVFIKIYNWSPKNNLLNSSQLSLGVYLIHPYIIAVIHSISIYVSIFTNSIINYLSVLLISYLTIRLILKRKEW"},"dna_sequence":{"accession":"EU250284.1","fmin":"2574","fmax":"3564","strand":"+","sequence":"ATGAAAAAACAAAATACGGGTGTAAATAATTTCCGTTTAATCGCTGCTGCCATGGTAGTAGCGATTCATTGCTTTCCATTTCAAACAATCAGTAAAGAACTAGATACATTGGTTACGCTAACTGTCTTTCGTATTGCCGTTCCTTTTTTCTTCATGGTTTCTGGGTACTACCTACTAGGTCCAATTCCAAGTTCAGCCACAAATACTTATCAAATTAATAACTATATAAAGAAACAGCTTAAAGTTTATACTTTCGCTATAGTTCTGTATCTACCTTTAGCGTTTTATAGTCAATCTATCACTTTGGATATGTCAATTATTAGTTTTATAAAACAACTACTTTTTAACGGTTTTTTTTACCATCTTTGGTTTTTCCCTGCATGGGTATTAGGATTATTAATTGTTCAATTTTTATTAAAAAGAATGAATATACAGACTGTATTGTTTATAACATTTGTGGCTTATTTAATAGGACTAGGAGGGGATAGTTGGTGGGGAATAGTTAAACAAGTTCCCTTTTTTTTCAGATTTTACAATGCTATATTTCAATTATTTGGTTATACACGAAATGGTCTATTTTATGCGCCGTTATTCTTTGCACTGGGAGCATATCTATACAAGATGAATATTAAAAACTTTAATTCCGCAAGAAATAACTATCTTTTACTGCTTTTTAGTATAGAAATGATTTTAGAAAGTTATTTCTTACATCTCTTTAACATTCCTAAACATGACAGTATGTATTTGTTTTTACCGTTTGTAATGACTTTGGTGTTTATCAAAATATACAATTGGTCACCAAAAAATAATTTATTGAACAGCTCTCAGCTATCTCTAGGAGTATATCTTATACATCCATATATCATCGCAGTAATTCACTCTATCTCAATTTACGTTTCTATTTTTACTAATAGCATAATTAATTATTTAAGTGTGCTATTGATAAGTTACCTAACTATAAGACTAATACTAAAAAGGAAGGAATGGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35918","NCBI_taxonomy_name":"Enterococcus faecalis","NCBI_taxonomy_id":"1351"}}}},"ARO_accession":"3002973","ARO_id":"39407","ARO_name":"vanTm gene in vanL cluster","CARD_short_name":"vanTm_in_vanL","ARO_description":"Also known as vanTmL, is a vanT variant found in the vanL gene cluster. vanTmL codes for the membrane-binding domain of vanTL.","ARO_category":{"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"36511":{"category_aro_accession":"3000372","category_aro_cvterm_id":"36511","category_aro_name":"vanT","category_aro_description":"VanT is a membrane bound serine racemase, converting L-serine to D-serine. It is associated with VanC, which incorporated D-serine into D-Ala-D-Ser terminal end of peptidoglycan subunits that have a decreased binding affinity with vancomycin. It was isolated from Enterococcus gallinarum.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"298":{"model_id":"298","model_name":"vanY gene in vanG cluster","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"50"}},"model_sequences":{"sequence":{"416":{"protein_sequence":{"accession":"ABA71729.1","sequence":"MNHMNMKHRRRKRRRNQSFLFTGILLLVVVSASSFLWYGFGNAAKKDSVIEEMPFTITQDGMQAKEEIKKTVLETSYGGKQQVAEENHGNTQNAGTDEAWNLMLVNRDNAIPDNYEVNLVEVEGGERVDERIYEPLMEMLNAAREENWGELPMVVSGYRTQEKQQSLYDEKIAKFKKEGYSDSEAVRQAEQWVAVPGHSEHQLGFAVDINGATYDVYLWLQENSYKYGFIFRYPGSKTDITGTAEEVWHYRYVGVEAATEMYENGLCLEEYLEKKQSEN"},"dna_sequence":{"accession":"DQ212986.1","fmin":"4222","fmax":"5062","strand":"+","sequence":"ATGAACCATATGAATATGAAACACAGACGCAGAAAACGCAGACGTAACCAATCTTTTTTGTTCACAGGAATTTTACTCTTAGTTGTAGTATCTGCAAGCAGTTTTTTATGGTACGGTTTTGGCAATGCGGCAAAAAAAGACAGTGTTATTGAAGAAATGCCATTTACCATTACACAGGACGGAATGCAGGCAAAGGAAGAAATAAAGAAAACGGTACTGGAAACTTCCTATGGCGGCAAACAGCAGGTAGCGGAAGAAAATCACGGCAATACACAAAATGCAGGGACAGACGAAGCGTGGAATTTAATGCTTGTCAACAGAGATAATGCGATTCCAGACAATTACGAAGTAAATCTGGTCGAAGTAGAGGGCGGGGAGCGTGTAGATGAGCGTATCTATGAACCTCTTATGGAAATGCTTAATGCGGCAAGGGAGGAAAACTGGGGCGAATTGCCGATGGTAGTATCTGGCTATCGGACGCAGGAAAAACAGCAGAGCCTTTATGATGAAAAGATTGCAAAGTTCAAAAAAGAGGGGTATTCAGACAGTGAAGCCGTAAGGCAGGCAGAACAATGGGTTGCAGTGCCAGGTCACAGTGAGCATCAGCTCGGTTTTGCAGTGGATATTAACGGGGCAACTTATGATGTTTATCTATGGTTGCAGGAAAACAGCTATAAATACGGCTTTATCTTCAGATATCCCGGCAGTAAAACGGATATTACCGGGACTGCTGAAGAAGTATGGCATTACCGTTATGTTGGAGTGGAAGCGGCAACTGAAATGTATGAAAATGGATTATGTCTTGAGGAATATCTTGAGAAAAAGCAATCAGAAAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35918","NCBI_taxonomy_name":"Enterococcus faecalis","NCBI_taxonomy_id":"1351"}}}},"ARO_accession":"3002959","ARO_id":"39393","ARO_name":"vanY gene in vanG cluster","CARD_short_name":"vanY_in_vanG_cl","ARO_description":"Also known as vanYG, is a vanY variant found in the vanG gene cluster.","ARO_category":{"36216":{"category_aro_accession":"3000077","category_aro_cvterm_id":"36216","category_aro_name":"vanY","category_aro_description":"VanY is a D,D-carboxypeptidase that cleaves removes the terminal D-Ala from peptidoglycan for the addition of D-Lactate. The D-Ala-D-Lac peptidoglycan subunits have reduced binding affinity with vancomycin compared to D-Ala-D-Ala.","category_aro_class_name":"AMR Gene Family"},"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"390":{"model_id":"390","model_name":"vanS gene in vanG cluster","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"706":{"protein_sequence":{"accession":"ABA71728.1","sequence":"MDSDYTQLQTKILIRTAVVLFGAFALISASLSLLSGHFSRAVVGILEIFYKDYEKALVVYTYVFRDNKEWFVMIAAFVSFLIVLRLYLKGFTKYFNEINRGINALKEESSEDVVLSSELAATEKTINTIKHTLEQQKTAALVAEQRKNDLVVYLAHDLKTPLTSVIGYLTLLRDEKQISDELREKYICISLEKAERLENLINEFFEITRFNLSNIILEYSVVNLTRMLEQLVFEFNPMLAEKKLNCVLKTMPNKMIRCDANKMQRVFDNLLRNAVNYSFENTEISITVTQNENMVHIKFVNHGNTIPKEKLERIFEQFYRLDTSRSTGNGGAGLGLAIAREIVMLHGGTITARSEDEKIEFEVTILSS"},"dna_sequence":{"accession":"DQ212986.1","fmin":"2979","fmax":"4086","strand":"+","sequence":"ATGGACAGTGACTATACACAGCTCCAGACAAAAATATTAATAAGGACAGCGGTTGTGCTATTCGGGGCGTTTGCTCTGATTTCCGCATCTCTTAGTTTATTAAGCGGGCATTTTTCAAGGGCTGTTGTGGGGATTTTGGAAATATTCTATAAAGATTATGAAAAGGCTTTGGTGGTATACACCTATGTGTTTCGGGACAATAAAGAATGGTTTGTGATGATAGCTGCATTTGTGTCGTTTCTAATTGTATTACGATTGTATCTGAAAGGCTTCACAAAGTATTTTAATGAAATAAACAGAGGTATTAATGCCTTGAAAGAGGAAAGTTCAGAAGATGTTGTATTATCTTCTGAGCTTGCGGCGACTGAAAAAACAATCAATACAATTAAGCATACCCTTGAACAGCAGAAAACTGCGGCGCTGGTTGCAGAGCAAAGGAAGAACGACCTTGTAGTGTATCTTGCTCATGATTTAAAGACTCCGCTTACATCTGTGATTGGATATTTGACATTGCTTAGGGACGAGAAGCAAATTTCAGATGAATTAAGGGAAAAGTATATATGTATTTCACTGGAAAAAGCAGAACGATTGGAAAATCTGATCAATGAATTTTTTGAGATTACACGTTTTAATCTTTCCAACATAATACTTGAATATAGTGTGGTAAATTTAACTCGTATGTTGGAGCAGTTGGTTTTTGAATTCAATCCAATGCTTGCGGAAAAAAAATTAAATTGTGTTCTTAAGACGATGCCGAATAAAATGATACGCTGCGACGCCAATAAAATGCAGAGGGTATTCGATAATTTATTGAGAAATGCAGTGAATTATAGTTTTGAGAATACAGAGATTTCTATTACAGTCACACAAAATGAAAATATGGTTCATATTAAATTTGTAAATCATGGAAATACAATTCCAAAAGAGAAACTGGAACGTATTTTTGAACAGTTTTATCGTCTGGATACTTCCAGAAGCACAGGGAATGGCGGCGCAGGCTTAGGGCTTGCTATTGCAAGGGAAATCGTAATGCTGCATGGAGGGACAATAACCGCCCGCAGTGAAGATGAAAAGATTGAATTTGAAGTGACGATTCTTTCATCGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35918","NCBI_taxonomy_name":"Enterococcus faecalis","NCBI_taxonomy_id":"1351"}}}},"ARO_accession":"3002937","ARO_id":"39371","ARO_name":"vanS gene in vanG cluster","CARD_short_name":"vanS_in_vanG_cl","ARO_description":"Also known as vanSG, is a vanS variant found in the vanG gene cluster.","ARO_category":{"36210":{"category_aro_accession":"3000071","category_aro_cvterm_id":"36210","category_aro_name":"vanS","category_aro_description":"VanS is similar to histidine protein kinases like EnvZ and acts as a response regulator by activating VanR. VanS is required for high level transcription of other van glycopeptide resistance genes.","category_aro_class_name":"AMR Gene Family"},"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"465":{"model_id":"465","model_name":"vanS gene in vanO cluster","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"650"}},"model_sequences":{"sequence":{"4550":{"protein_sequence":{"accession":"AHA41504.1","sequence":"MLAGVLLLAAVWVFLLRGRSTNFQFPALADFARVFDPSNFGPVVFVPAAILALGFLLVFGLVGGWILAGRMLAPLARITRAAREAGSGSLSYRIELEGRNDEFRELADAFDAMLARLEARDAAQQRFAANASHELRTPLAITQTLLDVARNDPNRDGGELDERLRAVNARAIELTEALLLLSRTDQRSFSREDVDLSLIAEEAAETLLPFAEKHGVSIETSGDIAPVIGSHALLLQLTTNLLHNAIVHNVPEHGSVQISTAIGSESVMLTVENTGDKLSPQLVSTLTEPFQRGTARTRGDDARVGLGLAIVKSITQAHDGSLTLSPRAAGGLSVAVRLPAAQRRP"},"dna_sequence":{"accession":"KF478993.1","fmin":"4909","fmax":"5947","strand":"-","sequence":"ATGCTCGCTGGTGTCTTGCTCCTTGCGGCGGTTTGGGTTTTCCTGCTGAGAGGGCGGTCCACGAATTTCCAATTCCCTGCTCTGGCCGACTTTGCCCGGGTCTTCGACCCGAGCAACTTCGGTCCCGTGGTGTTTGTCCCGGCAGCGATCTTGGCGCTCGGGTTCTTGCTGGTGTTCGGCCTTGTGGGTGGTTGGATTCTCGCGGGCCGAATGCTTGCCCCGTTGGCGCGCATTACGCGCGCCGCGCGGGAGGCGGGGAGTGGCTCGCTGTCGTACCGGATCGAACTGGAGGGACGCAACGACGAGTTCCGTGAACTTGCCGATGCCTTCGACGCCATGCTCGCACGGCTCGAAGCACGAGACGCCGCGCAGCAGCGATTCGCCGCCAACGCCTCCCACGAGTTGCGCACCCCGCTGGCGATCACACAAACCCTTCTCGATGTCGCCCGCAACGATCCGAACCGCGACGGCGGCGAGCTCGACGAACGCCTCCGCGCTGTCAACGCACGGGCGATCGAGCTCACCGAGGCATTGCTCCTGCTCAGCCGTACCGACCAACGGTCCTTCAGCCGAGAAGACGTCGATCTGTCGCTCATCGCGGAAGAAGCCGCCGAGACACTCCTCCCGTTCGCGGAGAAGCACGGCGTCAGCATCGAGACCTCCGGGGACATCGCGCCGGTCATCGGCTCACACGCACTCTTGCTGCAGTTGACTACGAACCTTCTGCACAATGCGATCGTCCACAATGTCCCCGAGCACGGCAGCGTGCAGATCAGCACCGCCATCGGCTCCGAGTCCGTCATGCTCACGGTCGAGAACACCGGCGACAAGCTCAGTCCACAGTTGGTCTCGACACTCACCGAGCCGTTTCAGCGCGGCACTGCTCGCACCCGCGGGGACGATGCGAGGGTGGGCCTTGGCCTGGCGATCGTCAAGAGCATCACGCAGGCACACGACGGATCCCTCACGCTCAGCCCCCGAGCTGCCGGCGGGCTCTCCGTAGCAGTGCGACTGCCCGCCGCTCAGCGACGACCGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36897","NCBI_taxonomy_name":"Rhodococcus hoagii","NCBI_taxonomy_id":"43767"}}}},"ARO_accession":"3002941","ARO_id":"39375","ARO_name":"vanS gene in vanO cluster","CARD_short_name":"vanS_in_vanO_cl","ARO_description":"Also known as vanSO, is a vanS variant found in the vanO gene cluster.","ARO_category":{"36210":{"category_aro_accession":"3000071","category_aro_cvterm_id":"36210","category_aro_name":"vanS","category_aro_description":"VanS is similar to histidine protein kinases like EnvZ and acts as a response regulator by activating VanR. VanS is required for high level transcription of other van glycopeptide resistance genes.","category_aro_class_name":"AMR Gene Family"},"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"518":{"model_id":"518","model_name":"vanXY gene in vanN cluster","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"125"}},"model_sequences":{"sequence":{"8149":{"protein_sequence":{"accession":"AEP40501.1","sequence":"MHNFYLQLVNQQHPWKSFNHSPQLVQATYAEEKILIDSKVNHQFNQLLETLQLTDRIMIVDGHRTVAEQKHLWNYSLNAHGVNYTKSYVASPGCSEHHTGLAIDLGLRKTEHDLIAPRFEGPEAELFLQHMKDYGFILRYPKNKQKITGIAYEPWHFRYVGTPHSQIIMDHGWTLEEYIEFLKHQIEAVS"},"dna_sequence":{"accession":"JF802084.2","fmin":"1592","fmax":"2165","strand":"+","sequence":"ATGCATAATTTTTATTTACAGCTTGTAAACCAACAACACCCTTGGAAATCATTTAATCATTCGCCACAGCTTGTTCAAGCGACCTATGCGGAAGAAAAGATTTTAATAGATTCCAAGGTTAACCATCAATTCAATCAGTTACTTGAAACACTACAATTAACTGATCGCATCATGATCGTTGATGGTCATCGAACGGTTGCTGAGCAAAAACATTTGTGGAACTATTCTTTAAACGCACATGGGGTGAATTATACAAAAAGTTATGTAGCATCTCCTGGCTGTAGTGAACATCATACGGGACTAGCAATTGATCTCGGTCTACGAAAGACAGAACATGATCTCATTGCGCCACGCTTCGAGGGACCAGAAGCCGAACTGTTTTTACAACATATGAAAGATTATGGATTTATTTTACGCTATCCTAAAAATAAGCAAAAAATTACAGGAATTGCTTATGAGCCTTGGCATTTTCGCTATGTAGGTACCCCTCATAGTCAAATCATCATGGACCACGGATGGACCTTAGAAGAGTATATTGAATTTTTAAAACATCAAATTGAGGCGGTCTCATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36779","NCBI_taxonomy_name":"Enterococcus faecium","NCBI_taxonomy_id":"1352"}}}},"ARO_accession":"3002969","ARO_id":"39403","ARO_name":"vanXY gene in vanN cluster","CARD_short_name":"vanXY_in_vanN","ARO_description":"Also known as vanXYN, is a vanXY variant found in the vanN gene cluster.","ARO_category":{"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"36635":{"category_aro_accession":"3000496","category_aro_cvterm_id":"36635","category_aro_name":"vanXY","category_aro_description":"VanXY is a protein with both D,D-carboxypeptidase and D,D-dipeptidase activity, found in Enterococcus gallinarum. It cleaves and removes the terminal D-Ala of peptidoglycan subunits for the incorporation of D-Ser by VanC. D-Ala-D-Ser has low binding affinity with vancomycin.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"744":{"model_id":"744","model_name":"vanS gene in vanL cluster","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"744":{"protein_sequence":{"accession":"ABX54692.1","sequence":"MKSKAETTTIKQILIKYLVTIGLSMLAYLVFLLTILIIMRNFVWDGTEPIYRVLHFFYRLFNFEGILIIGVILILFVVTLFFVMKIIGYLKQIIEATKQLLEKPEQRVKLSSGLFELQEEMNQLREKNNADNRAAKEAEKRKNDLIVYLAHDLRTPLTSVIGYLTLLKEEPEISVQTRAKYTNIALSKAFRLEELLSEFFDVTRFNLTNLTINEELVDLSVMLEQISYEFLPILEEKKLSWNLHVESNIKSLLDPGKMERVFDNLMRNAINYSFEDTIIDLSLEKKESQAIFKITNRTYTIPKEKLEKIFEPFYRMDTSRSSSTGGTGLGLPIVREIIEASKGTINVSSSNNEMTFIIYLPYID"},"dna_sequence":{"accession":"EU250284.1","fmin":"5415","fmax":"6510","strand":"+","sequence":"TTGAAAAGTAAGGCGGAAACTACAACTATAAAACAGATACTAATAAAATATTTAGTAACTATAGGTTTATCGATGCTTGCCTATTTAGTATTTCTTCTAACAATACTTATTATAATGAGAAATTTTGTATGGGACGGCACGGAGCCTATCTATCGTGTCTTGCACTTTTTTTATCGTCTTTTTAATTTTGAAGGGATATTGATTATCGGTGTGATACTTATCCTATTCGTTGTTACATTGTTTTTTGTTATGAAGATAATTGGCTATTTAAAACAAATCATCGAGGCGACGAAACAATTGCTTGAAAAACCAGAACAGCGTGTTAAGCTATCAAGTGGCCTGTTCGAATTACAAGAAGAAATGAACCAACTACGTGAAAAAAATAATGCTGACAATCGCGCAGCTAAAGAAGCGGAAAAGAGAAAAAACGATTTGATTGTTTATTTAGCTCATGATTTACGTACGCCATTAACTAGCGTAATTGGGTATTTAACGCTGTTAAAAGAAGAACCGGAAATATCGGTTCAAACTAGAGCTAAGTATACGAACATCGCTTTGAGTAAAGCTTTTCGCCTTGAAGAATTATTGAGTGAATTTTTTGATGTGACGAGATTTAATTTGACTAACTTAACAATAAATGAAGAACTAGTAGATTTAAGTGTGATGTTAGAGCAAATCAGCTACGAATTTTTACCTATTTTGGAAGAAAAAAAACTTTCTTGGAATCTACACGTCGAGAGTAATATAAAATCTCTTTTAGATCCAGGAAAAATGGAACGTGTTTTTGATAACTTGATGCGAAATGCTATTAATTATAGCTTTGAAGATACAATAATTGATTTAAGTTTAGAAAAAAAAGAATCTCAAGCTATTTTTAAAATTACAAATAGGACCTATACAATCCCAAAAGAAAAATTAGAAAAAATATTCGAACCGTTTTACCGAATGGACACATCTAGAAGTAGCAGTACAGGTGGAACTGGGCTTGGTCTACCGATTGTAAGGGAAATTATTGAAGCTTCCAAAGGAACTATAAACGTTAGTAGTAGCAATAATGAAATGACTTTTATAATCTATTTACCATACATAGATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35918","NCBI_taxonomy_name":"Enterococcus faecalis","NCBI_taxonomy_id":"1351"}}}},"ARO_accession":"3002938","ARO_id":"39372","ARO_name":"vanS gene in vanL cluster","CARD_short_name":"vanS_in_vanL_cl","ARO_description":"Also known as vanSL, is a vanS variant found in the vanL gene cluster.","ARO_category":{"36210":{"category_aro_accession":"3000071","category_aro_cvterm_id":"36210","category_aro_name":"vanS","category_aro_description":"VanS is similar to histidine protein kinases like EnvZ and acts as a response regulator by activating VanR. VanS is required for high level transcription of other van glycopeptide resistance genes.","category_aro_class_name":"AMR Gene Family"},"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"752":{"model_id":"752","model_name":"vanR gene in vanM cluster","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"337":{"protein_sequence":{"accession":"ACL82957.1","sequence":"MRRISILIAEDEEEIADLLAIHLEKEGYDVIKVHDGQEALHVIQAQSIDLIILDIMMPKMDGYEVTRQVRAQYNMPIIFLSAKTSDFDKVHGLVIGGDDYITKPFTPIELVARVNAQLRRSMKLNHPQADDKKSILEFGEIVISPDQRTVFLYGENIGLTPKEFDILYLLASHPKKVYSVENIFQQVWNDAYFGGGNTVMVHIRTLRKKLGEDKRKNKLIKTVWGVGYTFNG"},"dna_sequence":{"accession":"FJ349556.1","fmin":"981","fmax":"1680","strand":"+","sequence":"ATGAGACGTATATCGATTTTAATTGCTGAAGATGAAGAAGAAATTGCTGATTTGCTTGCCATTCACCTGGAAAAAGAAGGATATGACGTTATTAAAGTACATGACGGACAAGAAGCCCTCCATGTAATCCAGGCTCAATCAATTGATTTGATAATTTTAGATATTATGATGCCGAAAATGGATGGATATGAAGTAACCCGTCAAGTCCGTGCACAGTATAATATGCCAATCATTTTTTTAAGTGCGAAAACTTCTGATTTCGATAAGGTGCATGGTCTAGTGATTGGAGGGGATGATTATATAACAAAGCCATTTACCCCGATTGAATTGGTTGCTCGTGTGAACGCTCAATTGCGGCGCTCTATGAAGTTGAATCACCCCCAAGCAGATGATAAAAAATCTATCTTGGAGTTCGGTGAGATCGTGATTTCTCCTGATCAACGTACAGTTTTTCTTTATGGTGAAAACATCGGGTTAACGCCGAAAGAGTTTGATATTTTGTATTTATTAGCCAGTCATCCAAAGAAAGTTTATAGTGTCGAAAATATTTTCCAGCAAGTTTGGAATGATGCATACTTTGGAGGCGGTAATACGGTAATGGTGCATATTCGCACCTTGCGGAAAAAACTTGGAGAAGATAAGCGAAAAAATAAGTTAATCAAAACTGTGTGGGGAGTGGGGTATACGTTCAATGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36779","NCBI_taxonomy_name":"Enterococcus faecium","NCBI_taxonomy_id":"1352"}}}},"ARO_accession":"3002928","ARO_id":"39362","ARO_name":"vanR gene in vanM cluster","CARD_short_name":"vanR_in_vanM_cl","ARO_description":"Also known as vanRM, is a vanR variant found in the vanM gene cluster.","ARO_category":{"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"36713":{"category_aro_accession":"3000574","category_aro_cvterm_id":"36713","category_aro_name":"vanR","category_aro_description":"VanR is a OmpR-family transcriptional activator in the VanSR regulatory system. When activated by VanS, it promotes cotranscription of VanA, VanH, and VanX.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"35948":{"category_aro_accession":"0000029","category_aro_cvterm_id":"35948","category_aro_name":"teicoplanin","category_aro_description":"Teicoplanin is a glycopeptide antibiotic used in the prophylaxis and treatment of serious infections caused by Gram-positive bacteria. Teicoplanin has a unique acyl-aliphatic chain, and binds to cell wall precursors to inhibit transglycosylation  and transpeptidation.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"943":{"model_id":"943","model_name":"vanU gene in vanG cluster","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"100"}},"model_sequences":{"sequence":{"339":{"protein_sequence":{"accession":"ABA71726.1","sequence":"MRVSYNKLWKLLIDRDMKKGELREAVGVSKSTFAKLGKNENVSLTVLLAICEYLNCDFGDIIEALPETPDKERDS"},"dna_sequence":{"accession":"DQ212986.1","fmin":"2029","fmax":"2257","strand":"+","sequence":"ATGCGTGTTAGTTATAATAAGCTCTGGAAGCTTTTAATTGATAGGGACATGAAAAAAGGCGAGCTTCGTGAGGCTGTTGGAGTAAGTAAAAGCACATTTGCGAAATTGGGCAAGAATGAGAATGTTTCTTTGACTGTTTTGTTAGCAATATGTGAGTATTTGAATTGTGATTTTGGCGATATTATAGAAGCGTTGCCAGAAACCCCCGATAAGGAGCGTGACAGTTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35918","NCBI_taxonomy_name":"Enterococcus faecalis","NCBI_taxonomy_id":"1351"}}}},"ARO_accession":"3004253","ARO_id":"41417","ARO_name":"vanU gene in vanG cluster","CARD_short_name":"vanU_in_vanG_cl","ARO_description":"Also known as vanUG, is a vanG variant found in the vanG gene cluster.","ARO_category":{"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"36714":{"category_aro_accession":"3000575","category_aro_cvterm_id":"36714","category_aro_name":"vanU","category_aro_description":"VanU is a transcriptional activator of vancomycin resistance genes.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1033":{"model_id":"1033","model_name":"vanS gene in vanN cluster","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"78":{"protein_sequence":{"accession":"AEP40504.1","sequence":"MKNKLNDPLIKRILLRYVSTVLLAIGIYGGVLLLLLFLFRLRTWYGDEPFYLFLRTLYIRFNLIGLVSSGAFLLLLMITLVYIFKLIGYLNETITATKQLLEAPEQRIQLSTELFTVQEEMNQIRENNNQANRAAKVAEQRKNDLIVYLAHDLRTSLTSVIGYLTLLKEEPQISTELRAKYTDIALDKALRLEELIGEFFEVTQFNLTKLTINKEIVDLSIMLEQISYEFLPILNEKGLKWQLAIDKGIKAEVDPNKMGRVFDNLIRNAINYSFSNSTIHLSLEKNGQNLELKITNETHTLPEEKLTQIFEPFYRVDTSRSSSTGGTGLGLSIVKDIVEASGGRIHAQSSNNQMTFTLTLPISE"},"dna_sequence":{"accession":"JF802084.1","fmin":"5019","fmax":"6114","strand":"+","sequence":"TTGAAAAATAAGTTGAACGATCCTTTGATCAAAAGAATCTTACTAAGATATGTATCAACCGTTCTTCTTGCGATTGGCATTTATGGTGGAGTTTTATTGCTCCTTTTGTTTTTATTCCGTTTACGAACCTGGTATGGCGATGAACCCTTTTATTTATTTTTACGAACTTTGTATATCCGCTTCAATTTGATTGGCCTCGTCTCAAGTGGTGCGTTTCTTCTTTTGCTGATGATTACTCTCGTTTATATTTTCAAACTTATTGGCTACTTGAATGAAACTATTACGGCAACTAAACAATTATTGGAAGCACCTGAACAACGTATCCAACTATCGACCGAGCTATTCACAGTTCAAGAAGAAATGAATCAAATTAGAGAAAATAATAATCAAGCAAACCGTGCAGCGAAAGTAGCAGAACAACGAAAAAATGATCTGATTGTTTACTTAGCACATGATCTGCGTACATCATTAACTAGCGTGATCGGTTATTTGACGTTGTTAAAAGAAGAACCGCAGATCTCCACAGAATTACGAGCAAAATATACGGATATCGCCTTAGACAAAGCGTTACGTTTAGAAGAATTGATTGGTGAGTTTTTTGAAGTCACCCAATTCAATTTGACAAAGCTTACAATAAATAAAGAAATTGTGGATCTAAGTATTATGCTAGAGCAAATCAGCTATGAATTTTTACCAATTCTAAATGAAAAAGGACTTAAATGGCAATTAGCGATTGATAAAGGGATCAAAGCAGAAGTTGATCCAAACAAAATGGGACGAGTTTTTGACAATTTAATCCGTAATGCAATCAATTACAGTTTCTCAAACTCAACGATCCACCTAAGTCTAGAAAAAAATGGACAAAATTTAGAACTCAAAATCACAAACGAAACGCATACCTTACCAGAAGAAAAGCTTACGCAAATTTTCGAACCTTTTTATCGTGTCGATACTTCAAGGAGTAGCAGCACTGGTGGTACAGGACTTGGATTATCGATTGTAAAAGATATCGTGGAAGCATCCGGCGGAAGGATTCATGCTCAAAGTAGCAATAATCAAATGACATTTACGCTTACCTTGCCTATCAGTGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36779","NCBI_taxonomy_name":"Enterococcus faecium","NCBI_taxonomy_id":"1352"}}}},"ARO_accession":"3002940","ARO_id":"39374","ARO_name":"vanS gene in vanN cluster","CARD_short_name":"vanS_in_vanN_cl","ARO_description":"Also known as vanSN, is a vanS variant found in the vanN gene cluster.","ARO_category":{"36210":{"category_aro_accession":"3000071","category_aro_cvterm_id":"36210","category_aro_name":"vanS","category_aro_description":"VanS is similar to histidine protein kinases like EnvZ and acts as a response regulator by activating VanR. VanS is required for high level transcription of other van glycopeptide resistance genes.","category_aro_class_name":"AMR Gene Family"},"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1219":{"model_id":"1219","model_name":"vanR gene in vanN cluster","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"379":{"protein_sequence":{"accession":"AEP40503.1","sequence":"MDTIVIVDDEKEIANLMTTFLENEGFKVMTFYSGKEALDYIDQNGASLAILDVMLPDLDGFQILQHIRQTFFFPVLMLTAKGENLDKITGLTLGADDYITKPFNPLEVVARVKTQLRRTQRYDQPSHSQSDEEFTKEGLVLKKNSHQVFLFDQEVLITPLEFKILLYLFEHQGTVVSSETLFEEVWQEKYLDNNNTVMAHIARLREKLGEKPRKPKYIKTVWGVGYIIEK"},"dna_sequence":{"accession":"JF802084.1","fmin":"4337","fmax":"5030","strand":"+","sequence":"ATGGATACAATTGTAATCGTTGATGATGAGAAAGAAATTGCCAATTTAATGACGACCTTTCTAGAAAATGAAGGATTCAAGGTCATGACCTTTTATAGCGGAAAGGAAGCACTGGATTATATTGATCAAAACGGTGCTTCCTTGGCCATTTTGGATGTGATGTTACCTGATTTAGATGGCTTCCAAATATTACAACACATCCGTCAAACATTCTTTTTCCCCGTATTGATGTTGACCGCAAAAGGAGAAAACTTAGATAAAATCACCGGACTGACTCTAGGCGCAGATGACTACATTACGAAACCTTTCAACCCGCTGGAAGTCGTGGCGCGAGTAAAAACACAACTGCGACGTACTCAGCGTTACGATCAGCCTTCCCATAGTCAATCGGATGAAGAATTTACAAAGGAAGGTTTGGTACTGAAAAAAAACAGCCACCAAGTTTTCTTATTTGATCAAGAAGTGTTGATTACACCCTTGGAGTTTAAGATCCTGCTCTACCTATTTGAGCATCAAGGGACAGTAGTCTCTTCTGAAACATTATTTGAAGAAGTTTGGCAAGAAAAATATTTAGACAATAATAATACAGTAATGGCACATATTGCTCGTTTAAGAGAAAAATTAGGCGAAAAACCAAGAAAACCAAAATATATTAAAACAGTTTGGGGGGTAGGCTATATCATTGAAAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36779","NCBI_taxonomy_name":"Enterococcus faecium","NCBI_taxonomy_id":"1352"}}}},"ARO_accession":"3002929","ARO_id":"39363","ARO_name":"vanR gene in vanN cluster","CARD_short_name":"vanR_in_vanN_cl","ARO_description":"Also known as vanRN, is a vanR variant found in the vanN gene cluster.","ARO_category":{"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"36713":{"category_aro_accession":"3000574","category_aro_cvterm_id":"36713","category_aro_name":"vanR","category_aro_description":"VanR is a OmpR-family transcriptional activator in the VanSR regulatory system. When activated by VanS, it promotes cotranscription of VanA, VanH, and VanX.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1328":{"model_id":"1328","model_name":"vanS gene in vanM cluster","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"44":{"protein_sequence":{"accession":"ACL82958.1","sequence":"MAKMRSSFRTKIILLFAVSMLLAGMVTYLLFKGLQLYYHTMIHRGNPLAELRDFIESIGDFNFFFLLFILLSLSVFYILTKPYSAYFDEISTGIQYLALGDFKRRVNIQSNDEFGDIAQAINQASEKLEEAIQRGDFSENSKEQLVVNLAHDLRTPLTSVLGYLDLVLKDEKLTKEQVRHFLTIAFTKSQRLEKLIDELFEITRMNYGMLSIEKKPINLTDLLLQLKEELYPIFEKNGLTARMNTLPHLPVSADGEMLARVFENLLTNANRYGHDGQFVDINGFVDEEEVVVQVVNYGDSIPPNELPYLFDMFYTGDKARTHKEDSTGLGLFIAKNIVEQHNGTVTAESSLIRTVFEVRLPLESAPIDQV"},"dna_sequence":{"accession":"FJ349556.1","fmin":"1672","fmax":"2785","strand":"+","sequence":"ATGGCTAAAATGAGAAGCAGTTTTCGCACCAAAATCATCTTGTTATTTGCTGTAAGCATGCTTCTGGCTGGTATGGTAACTTACTTACTTTTTAAAGGACTACAGCTTTATTATCATACTATGATTCATCGTGGTAACCCATTAGCCGAACTTCGCGATTTCATAGAGAGTATTGGAGACTTTAACTTCTTTTTCCTATTATTTATCTTACTGTCGCTGTCGGTTTTCTATATACTCACTAAGCCCTATTCTGCTTATTTCGATGAAATATCAACCGGAATTCAATACCTCGCACTTGGCGACTTTAAACGCCGGGTTAATATCCAATCAAATGATGAATTTGGGGATATTGCTCAAGCTATTAATCAGGCAAGTGAAAAATTAGAAGAAGCCATACAAAGAGGTGATTTTTCAGAAAACAGCAAAGAACAATTAGTTGTAAATTTGGCTCATGATTTGCGTACGCCGCTAACTTCTGTTTTAGGTTATTTAGATTTAGTTCTTAAGGATGAGAAGTTGACAAAAGAACAAGTCAGGCATTTTTTAACGATCGCCTTTACGAAATCACAGCGTTTAGAAAAACTGATTGATGAATTATTCGAAATCACGAGAATGAACTATGGCATGCTATCAATTGAAAAAAAGCCAATTAATTTAACTGATCTGCTTCTTCAATTGAAAGAAGAATTGTATCCGATTTTCGAGAAAAACGGTTTGACCGCTCGAATGAATACACTGCCTCATTTACCTGTTTCGGCTGATGGAGAGATGTTGGCTCGAGTGTTTGAAAATCTGTTGACCAATGCCAATCGTTACGGACATGACGGTCAGTTTGTAGATATTAATGGGTTTGTTGATGAAGAAGAAGTGGTTGTTCAAGTTGTGAATTATGGAGATAGCATTCCTCCGAACGAACTTCCGTATCTTTTTGATATGTTCTATACCGGTGATAAAGCACGAACCCATAAAGAGGATAGCACTGGTCTTGGACTATTTATTGCGAAGAATATTGTGGAACAGCATAATGGAACGGTTACGGCTGAAAGCAGTCTAATACGTACGGTATTTGAAGTTCGTTTACCGCTGGAAAGTGCTCCTATTGACCAAGTTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36779","NCBI_taxonomy_name":"Enterococcus faecium","NCBI_taxonomy_id":"1352"}}}},"ARO_accession":"3002939","ARO_id":"39373","ARO_name":"vanS gene in vanM cluster","CARD_short_name":"vanS_in_vanM_cl","ARO_description":"Also known as vanSM, is a vanS variant found in the vanM gene cluster.","ARO_category":{"36210":{"category_aro_accession":"3000071","category_aro_cvterm_id":"36210","category_aro_name":"vanS","category_aro_description":"VanS is similar to histidine protein kinases like EnvZ and acts as a response regulator by activating VanR. VanS is required for high level transcription of other van glycopeptide resistance genes.","category_aro_class_name":"AMR Gene Family"},"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"35948":{"category_aro_accession":"0000029","category_aro_cvterm_id":"35948","category_aro_name":"teicoplanin","category_aro_description":"Teicoplanin is a glycopeptide antibiotic used in the prophylaxis and treatment of serious infections caused by Gram-positive bacteria. Teicoplanin has a unique acyl-aliphatic chain, and binds to cell wall precursors to inhibit transglycosylation  and transpeptidation.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1510":{"model_id":"1510","model_name":"vanTr gene in vanL cluster","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"200"}},"model_sequences":{"sequence":{"353":{"protein_sequence":{"accession":"ABX54690.1","sequence":"MVENKMRAYKEFYVESLLHNVQVIKKNIPKSTKIMAVVKANAYGINAVNVAIILEYIGIDFFAVATIDEAIALRKNGITSNILILGYTTPTKVDDLIHYELTQTIVSKEHAYFLNKTGKKIMCHLKVDTGMHRLGVEPTLEEICPIFNYPFLKIKGVYSHLGSADDLSEEGKQRTIKQISRYNTIIAELKRKRVDVGLTHLQSSYGILNYSELAYDYVRPGIILYGLLSNNDHNVKLHLDLQPVVAVKAQLISKKKIAPGEYIGYGTDTQLTSSKTIGVLSIGYADGIPRNLSNGEYCVVFEDKQIPQIGRICMDMMLVDLSNCSDIPLGVMVDVLPNIEEISQIQSTITNEIISCLGSRLGMEVK"},"dna_sequence":{"accession":"EU250284.1","fmin":"3557","fmax":"4658","strand":"+","sequence":"ATGGTAGAAAACAAAATGAGAGCCTACAAAGAATTCTATGTAGAATCATTGTTGCATAATGTACAAGTTATCAAAAAAAACATACCCAAGTCTACTAAAATAATGGCAGTAGTGAAAGCAAATGCCTATGGAATAAATGCAGTGAATGTAGCTATTATCTTAGAATATATAGGAATTGACTTTTTTGCAGTTGCTACTATAGATGAAGCTATTGCTTTAAGAAAAAATGGCATTACAAGTAATATTTTAATTTTAGGATACACTACACCAACCAAGGTAGATGATCTTATCCATTACGAACTTACCCAAACAATAGTAAGCAAAGAACACGCGTATTTTCTTAATAAAACAGGAAAGAAGATAATGTGTCATTTAAAAGTCGACACAGGGATGCATCGGTTAGGTGTTGAACCTACGTTAGAAGAAATCTGTCCTATTTTTAACTACCCTTTTTTAAAGATAAAGGGTGTTTATTCTCACTTGGGCTCAGCAGACGATTTATCTGAGGAAGGCAAACAACGAACTATAAAACAAATTAGCCGATACAATACCATTATTGCAGAATTAAAACGAAAACGTGTTGACGTAGGGCTAACCCATCTCCAAAGTAGTTATGGTATACTTAATTATTCTGAGTTAGCGTATGACTATGTTCGTCCTGGAATTATTTTATATGGGCTTTTAAGTAATAATGACCACAACGTCAAATTGCATTTGGATCTCCAGCCTGTAGTAGCGGTTAAAGCTCAGTTAATTTCAAAAAAAAAGATAGCTCCTGGTGAATATATTGGCTACGGTACAGATACACAATTAACTTCTTCCAAAACTATAGGGGTATTAAGCATTGGGTATGCTGACGGAATCCCTAGAAATTTATCAAATGGAGAATATTGTGTCGTGTTTGAAGATAAGCAAATCCCTCAAATTGGACGTATTTGTATGGACATGATGTTAGTAGATTTGTCAAATTGTTCAGATATCCCTTTAGGTGTAATGGTTGATGTATTACCTAATATTGAAGAAATATCTCAAATCCAAAGCACCATAACGAATGAAATAATAAGTTGTTTGGGTAGTCGCTTGGGGATGGAAGTAAAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35918","NCBI_taxonomy_name":"Enterococcus faecalis","NCBI_taxonomy_id":"1351"}}}},"ARO_accession":"3002974","ARO_id":"39408","ARO_name":"vanTr gene in vanL cluster","CARD_short_name":"vanTr_in_vanL","ARO_description":"Also known as vanTrL, is a vanT variant found in the vanL gene cluster. vanTrL codes for the racemase component of vanT.","ARO_category":{"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"36511":{"category_aro_accession":"3000372","category_aro_cvterm_id":"36511","category_aro_name":"vanT","category_aro_description":"VanT is a membrane bound serine racemase, converting L-serine to D-serine. It is associated with VanC, which incorporated D-serine into D-Ala-D-Ser terminal end of peptidoglycan subunits that have a decreased binding affinity with vancomycin. It was isolated from Enterococcus gallinarum.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1622":{"model_id":"1622","model_name":"vanW gene in vanG cluster","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"50"}},"model_sequences":{"sequence":{"535":{"protein_sequence":{"accession":"ABA71730.1","sequence":"MIEVYKLTQRKRLTQLFPFLLPLRKWQRKKYFYFKMKFDGNRYAKKTSEKLLPNTVFETSSLMLNENSGFDMKYQINKVHNLKLAAKTINKVIIEPKETFSFWQLVRWADRHEKYKDGLNLVNGKIVGSYGGGLCQLSNMLFWLFLHTPLVIVERHGHAVESFPSTTEDLPCGTDATINEGWLDLKLRNDTDNTFQIEISFDDNFMYGRILSQSSVNIEYTVFNSSVSYFKREEKVYQIASVCRTEKDKMTGSQTEKELYVNQCEIAYKLPDDVKIEERGV"},"dna_sequence":{"accession":"DQ212986.1","fmin":"5137","fmax":"5983","strand":"+","sequence":"GTGATTGAGGTGTATAAATTAACACAAAGAAAAAGACTAACGCAGTTGTTTCCTTTTTTGCTACCTCTCCGCAAATGGCAAAGAAAAAAATATTTTTATTTCAAAATGAAATTTGACGGCAATAGATACGCAAAAAAGACATCTGAGAAATTGTTACCAAACACAGTATTTGAAACATCATCACTTATGCTAAATGAAAATAGTGGATTTGATATGAAGTACCAAATCAATAAGGTACACAACCTAAAACTTGCCGCAAAAACAATCAATAAAGTGATTATTGAGCCGAAAGAAACATTTTCATTTTGGCAGCTTGTACGATGGGCAGACCGTCACGAGAAATATAAGGACGGATTAAATCTTGTTAATGGAAAGATTGTAGGCTCTTATGGCGGAGGTTTGTGTCAATTGAGTAATATGCTATTTTGGCTTTTTTTACACACGCCGCTTGTTATTGTCGAGCGACACGGACACGCAGTTGAGTCTTTCCCATCAACAACCGAAGATTTGCCCTGCGGTACTGATGCTACGATTAACGAAGGTTGGTTAGACCTAAAACTCCGTAACGACACGGACAATACTTTCCAGATTGAGATTAGTTTTGATGACAACTTTATGTATGGTCGAATTTTGTCGCAAAGCTCCGTAAATATTGAATATACGGTTTTTAATTCGTCTGTTTCCTATTTCAAGCGAGAGGAAAAAGTATATCAAATAGCTTCTGTTTGTCGTACAGAAAAAGACAAAATGACTGGTAGTCAGACGGAAAAAGAATTGTATGTCAACCAATGTGAAATAGCCTATAAGCTACCCGATGATGTAAAAATTGAAGAAAGAGGTGTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35918","NCBI_taxonomy_name":"Enterococcus faecalis","NCBI_taxonomy_id":"1351"}}}},"ARO_accession":"3002965","ARO_id":"39399","ARO_name":"vanW gene in vanG cluster","CARD_short_name":"vanW_in_vanG_cl","ARO_description":"Also known as vanWG, is a vanW variant found in the vanG gene cluster.","ARO_category":{"36011":{"category_aro_accession":"3000002","category_aro_cvterm_id":"36011","category_aro_name":"vanW","category_aro_description":"vanW is an accessory gene, with unknown function, found on vancomycin resistance operons.","category_aro_class_name":"AMR Gene Family"},"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1689":{"model_id":"1689","model_name":"vanR gene in vanO cluster","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"4685":{"protein_sequence":{"accession":"AHA41505.1","sequence":"MASMRVLVVEDERFMAEAIRDGLRLEAIAADIAGDGDTALDLLGVNAYDIAVLDRDIPGPSGDEIAQRIVASGGGIPILMLTAADRMDDKASGFELGADDYLTKPFELQELVLRLRALDRRRAHSRPPVREIAGLQLDPFRREVYRDGRYVALTRKQFAVLEVLVAAEGGVISAEELLERAWDENADPFTNAVRITVSTLRKRLGEPWLIATVPGVGYRIDTEPDARGGGDGG"},"dna_sequence":{"accession":"KF478993.1","fmin":"6002","fmax":"6704","strand":"-","sequence":"ATGGCGAGCATGCGTGTGTTGGTCGTCGAGGACGAGCGGTTCATGGCGGAAGCCATCCGCGATGGGCTGCGCCTGGAAGCGATCGCGGCCGACATCGCCGGTGATGGGGACACTGCCCTGGATCTGTTGGGCGTCAACGCCTACGACATCGCCGTCCTCGACCGTGATATCCCCGGCCCCTCCGGTGACGAGATCGCCCAGCGCATCGTCGCTTCCGGTGGCGGCATACCAATCCTGATGCTCACTGCCGCGGACCGGATGGACGACAAGGCCTCCGGGTTCGAGCTCGGTGCCGACGACTACCTCACCAAGCCTTTCGAGCTGCAGGAGCTCGTGCTCCGTCTCCGGGCCCTCGACCGCAGGCGCGCGCACAGCAGGCCGCCCGTGCGGGAGATCGCTGGTCTGCAGCTGGACCCGTTCCGTCGCGAGGTCTACCGGGACGGCCGGTACGTCGCGCTGACCCGGAAGCAGTTCGCGGTGCTCGAAGTTCTCGTCGCTGCCGAGGGCGGTGTGATCAGCGCCGAGGAGTTGCTGGAGCGGGCGTGGGACGAGAACGCCGATCCGTTCACGAATGCCGTGCGCATCACGGTCTCGACGTTGCGCAAGCGGCTCGGCGAACCGTGGCTGATCGCCACGGTGCCGGGGGTCGGGTACCGCATCGATACCGAACCGGACGCCAGAGGCGGGGGCGACGGTGGATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36897","NCBI_taxonomy_name":"Rhodococcus hoagii","NCBI_taxonomy_id":"43767"}}}},"ARO_accession":"3002930","ARO_id":"39364","ARO_name":"vanR gene in vanO cluster","CARD_short_name":"vanR_in_vanO_cl","ARO_description":"Also known as vanRO, is a vanR variant found in the vanO gene cluster.","ARO_category":{"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"36713":{"category_aro_accession":"3000574","category_aro_cvterm_id":"36713","category_aro_name":"vanR","category_aro_description":"VanR is a OmpR-family transcriptional activator in the VanSR regulatory system. When activated by VanS, it promotes cotranscription of VanA, VanH, and VanX.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1724":{"model_id":"1724","model_name":"vanH gene in vanM cluster","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"200"}},"model_sequences":{"sequence":{"534":{"protein_sequence":{"accession":"ACL82960.1","sequence":"MVLVMKDIGITIYGSEQDEADVFQEISSRFGVTPTIVSSPISETNVMLAPKNKCISVGHKSEIHKSILIALKESGVKYISTRSIGYNHIDMKAAEKMGIAVENVTYSPDSVADYTLMLILMAIRHTKSTLCSMEKHDFRLNSVRGKVLRDLTVGVLGTGHIGKAVIERLQGFGGHVLAYGNNKEATANYVSFNELLQKSDILTIHVPLSDDTYHMIGHEQIKAMKQGAFLINTARGGLIDTEVLVKALEDGKLGGAALDVLEGEEGLFYFDCTQKPINNQFLLKLQRMPNVTITPHTAYYSEKTLRDTVEKTVKNCLEFERRETHE"},"dna_sequence":{"accession":"FJ349556.1","fmin":"3883","fmax":"4864","strand":"+","sequence":"ATGGTCTTAGTAATGAAAGATATCGGCATTACCATTTATGGATCTGAGCAGGATGAGGCTGATGTGTTCCAGGAAATTTCATCTCGATTTGGCGTTACACCTACCATTGTAAGCTCTCCTATATCAGAAACCAACGTAATGTTAGCCCCTAAAAATAAGTGTATCAGCGTGGGGCACAAGTCTGAGATTCACAAATCTATCCTTATTGCATTGAAGGAATCCGGCGTCAAATATATCTCTACTCGAAGTATTGGTTACAATCATATAGATATGAAGGCAGCGGAAAAAATGGGTATTGCTGTCGAGAACGTCACTTATTCACCAGATAGTGTTGCCGATTATACATTGATGCTGATACTTATGGCAATACGCCATACGAAATCTACTTTGTGCTCTATGGAAAAACATGATTTCAGACTGAACAGCGTCCGTGGTAAAGTACTGCGTGACCTGACAGTAGGTGTACTGGGAACCGGTCATATAGGCAAAGCGGTTATTGAGCGACTACAGGGGTTTGGAGGTCACGTGTTGGCGTACGGCAACAACAAAGAGGCGACGGCAAATTATGTATCCTTCAATGAATTACTGCAAAAAAGTGACATTCTAACCATTCATGTACCCCTTAGCGATGACACATACCATATGATCGGTCACGAACAGATTAAAGCAATGAAACAGGGCGCCTTTCTTATTAATACTGCTCGAGGTGGACTTATAGATACCGAAGTTCTGGTTAAAGCACTGGAGGACGGAAAACTGGGGGGCGCCGCATTAGATGTATTAGAGGGAGAAGAAGGGCTTTTCTACTTTGATTGCACCCAAAAGCCAATTAACAATCAATTTTTGCTGAAACTTCAAAGGATGCCAAATGTGACAATCACACCGCATACGGCTTACTATAGCGAAAAAACGTTACGTGATACTGTTGAAAAAACAGTCAAGAACTGTTTGGAATTTGAGAGGAGAGAGACACATGAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36779","NCBI_taxonomy_name":"Enterococcus faecium","NCBI_taxonomy_id":"1352"}}}},"ARO_accession":"3002947","ARO_id":"39381","ARO_name":"vanH gene in vanM cluster","CARD_short_name":"vanH_in_vanM_cl","ARO_description":"Also known as vanHM, is a vanH variant in the vanM gene cluster.","ARO_category":{"36015":{"category_aro_accession":"3000006","category_aro_cvterm_id":"36015","category_aro_name":"vanH","category_aro_description":"VanH is a D-specific alpha-ketoacid dehydrogenase that synthesizes D-lactate. D-lactate is incorporated into the end of the peptidoglycan subunits, decreasing vancomycin binding affinity.","category_aro_class_name":"AMR Gene Family"},"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"35948":{"category_aro_accession":"0000029","category_aro_cvterm_id":"35948","category_aro_name":"teicoplanin","category_aro_description":"Teicoplanin is a glycopeptide antibiotic used in the prophylaxis and treatment of serious infections caused by Gram-positive bacteria. Teicoplanin has a unique acyl-aliphatic chain, and binds to cell wall precursors to inhibit transglycosylation  and transpeptidation.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1872":{"model_id":"1872","model_name":"vanXY gene in vanL cluster","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"125"}},"model_sequences":{"sequence":{"168":{"protein_sequence":{"accession":"ABX54688.1","sequence":"MDNDYKYYLQLVNKQYPWQINNGSKKMVRVPYTDKEIYLDAVVVEHLIQLIETIQLQEKIEIVDGYRTIDEQKELWEFSLKDRGKRYTHDYVAYPGCSEHHTGLALDIGLKKTAHDIIAPKFNGEEAKKFLEHMKDYGFILRYPPNKKKVTGIAYEPWHFRYVGVPHSQIITQQAWTLEEYIAFLHTVGEKVS"},"dna_sequence":{"accession":"EU250284.1","fmin":"1996","fmax":"2578","strand":"+","sequence":"ATGGATAACGATTACAAGTATTATTTACAATTAGTCAATAAGCAATATCCTTGGCAGATAAACAATGGTTCTAAAAAAATGGTAAGGGTGCCTTATACAGATAAAGAAATTTATTTAGATGCAGTTGTTGTTGAACATTTGATTCAGTTGATCGAAACTATTCAATTACAAGAGAAAATAGAAATAGTTGATGGTTACCGTACGATAGACGAACAAAAAGAATTATGGGAATTTTCTTTAAAAGATAGAGGGAAACGATATACTCATGATTATGTTGCCTATCCTGGGTGTAGTGAGCATCATACTGGACTTGCATTAGATATTGGTCTTAAAAAAACAGCACATGATATCATAGCACCAAAATTTAATGGAGAAGAGGCAAAAAAATTTTTAGAGCATATGAAAGATTACGGATTTATTTTAAGGTACCCTCCAAACAAAAAAAAGGTAACAGGGATTGCGTATGAACCGTGGCATTTTAGGTATGTTGGAGTTCCTCACAGCCAAATCATTACTCAGCAAGCTTGGACGCTGGAAGAATATATCGCTTTTTTACACACAGTAGGAGAAAAAGTTTCATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35918","NCBI_taxonomy_name":"Enterococcus faecalis","NCBI_taxonomy_id":"1351"}}}},"ARO_accession":"3002968","ARO_id":"39402","ARO_name":"vanXY gene in vanL cluster","CARD_short_name":"vanXY_in_vanL","ARO_description":"Also known as vanXYL, is a vanXY variant found in the vanL gene cluster.","ARO_category":{"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"36635":{"category_aro_accession":"3000496","category_aro_cvterm_id":"36635","category_aro_name":"vanXY","category_aro_description":"VanXY is a protein with both D,D-carboxypeptidase and D,D-dipeptidase activity, found in Enterococcus gallinarum. It cleaves and removes the terminal D-Ala of peptidoglycan subunits for the incorporation of D-Ser by VanC. D-Ala-D-Ser has low binding affinity with vancomycin.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1983":{"model_id":"1983","model_name":"vanT gene in vanN cluster","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"200"}},"model_sequences":{"sequence":{"259":{"protein_sequence":{"accession":"AEP40502.2","sequence":"MKNVNTGINQFRLIAAFMVVAIHCFPFQSFSKTLDILITLTLFRTAVPFFLMVTGFYLIGPIATKRGYPAYLKIKKFLKKQVKLYVLATLIYLPLAFYSGVITFKTSVIQFFQLIFFEGVLYHLWYFPALILGVLIVYCLLQRFTLRQVLLVTFLFYLLCLGGDSWWGLARQIPVLEKSYQGIFTLMIHTRNGLFFAPFFLTLGASFHQSEWNMRTSKAKYFLLIASLGMLVESYLLHSFSSPKHDSAYLFLPVVMFFLFPLILNWQPTRVIADASTISLGIYVLHPYVIAVVHTLAKKITILNNSLIYYLCVSLLTSLIILYVHSKKKKTTKNQATFVPRTKKVLSKQAVIHNLAQINQVIPKTTKIMAVIKANAYGTDDTEFARILEQQGVDFFAVATIDEGIRLRENGIKSKILILGYTPSIRIKELAHYTLIQTIVSKEHAYSLNQQKIPISCHLKIDTGMHRLGVEPVVQEVSSLYRLPYLNIQGIYSHLGSADDRSDKGMKRTRKQISIFDYLLHELELQKIDVGVTHLQSSYGILNYPELVYDYVRPGILLYGYLSEHNGDSKINLNLQPILDVQALLVSKKWVAAGEYLGYSLDTKLVSPKLIGIVSIGYADGVPRELSHNEFYLAYQGQNLPQIGRICMDMLLVDLTDSPEIKVESQISIFPELEQTANQTNTLTNEIISRLGNRFYTEWS"},"dna_sequence":{"accession":"JF802084.1","fmin":"2161","fmax":"4264","strand":"+","sequence":"ATGAAAAACGTAAATACCGGGATCAATCAATTTCGATTGATCGCTGCTTTCATGGTCGTTGCGATTCACTGTTTTCCTTTTCAGTCGTTTAGTAAAACTCTTGATATATTGATTACTTTGACACTCTTTCGAACTGCCGTACCTTTTTTCTTAATGGTCACAGGTTTTTATTTAATTGGACCGATTGCCACTAAGAGAGGCTATCCAGCCTATTTAAAGATAAAAAAATTTTTAAAAAAGCAAGTGAAGCTATATGTGCTTGCTACGCTCATTTATCTTCCACTAGCTTTTTATAGTGGTGTGATCACTTTCAAGACGAGTGTCATTCAATTTTTTCAACTCATCTTTTTCGAAGGAGTTCTTTACCACTTGTGGTATTTTCCAGCATTGATTTTAGGTGTTCTCATCGTTTACTGCTTATTACAGCGGTTCACGCTTCGACAAGTTTTATTAGTGACTTTTCTATTCTATTTACTATGTTTGGGCGGCGATAGCTGGTGGGGGTTAGCTAGACAAATTCCTGTGTTAGAAAAAAGTTATCAAGGGATATTTACGCTCATGATCCATACTCGAAATGGACTATTTTTTGCCCCTTTCTTTTTAACACTCGGTGCTTCGTTCCATCAATCAGAGTGGAACATGCGTACATCTAAAGCCAAGTATTTTTTGTTGATTGCTAGTTTAGGCATGCTAGTGGAAAGCTATTTGCTACACTCCTTTAGTTCACCAAAACATGATAGTGCATACCTATTCTTGCCTGTGGTGATGTTTTTTCTTTTTCCACTTATTTTGAACTGGCAGCCTACACGTGTCATTGCCGACGCTTCGACAATCAGTTTAGGTATTTATGTCCTTCATCCTTATGTCATTGCTGTTGTCCATACTTTAGCCAAAAAAATAACGATACTAAACAATAGTTTAATTTATTATCTCTGCGTTTCCCTTTTAACTAGTTTGATTATTCTTTATGTACACTCTAAGAAAAAGAAAACGACAAAAAATCAGGCTACGTTTGTCCCTAGAACAAAAAAAGTACTCTCTAAGCAAGCAGTTATCCATAATTTGGCACAAATCAATCAAGTGATTCCGAAAACAACGAAAATAATGGCTGTCATAAAAGCCAACGCTTATGGAACTGATGATACAGAATTTGCTCGAATCTTAGAACAACAAGGAGTTGATTTTTTTGCTGTCGCTACCATTGATGAAGGCATTCGTTTGCGAGAAAATGGAATTAAAAGCAAAATCTTAATTCTAGGCTATACACCATCGATACGAATAAAAGAATTAGCTCACTACACATTAATACAAACAATCGTTAGCAAAGAACATGCTTATTCATTAAATCAACAAAAGATACCTATTTCGTGCCATCTAAAAATTGATACTGGCATGCATCGTTTAGGTGTTGAGCCTGTGGTTCAGGAGGTTTCATCCTTATATCGATTACCCTACTTAAATATTCAAGGTATTTATTCTCATCTCGGTTCAGCTGATGATCGAAGTGACAAAGGAATGAAACGCACGAGAAAACAAATTTCGATTTTTGATTATTTATTACATGAACTAGAACTTCAAAAAATCGATGTCGGTGTTACGCATCTGCAAAGTAGCTATGGTATTTTGAATTATCCTGAACTGGTCTATGATTATGTTCGTCCTGGTATTCTTTTATACGGTTATTTAAGTGAACATAATGGAGATTCAAAAATCAACTTAAATTTGCAACCAATTTTAGATGTCCAAGCACTGCTCGTATCAAAAAAATGGGTTGCTGCTGGTGAATATCTTGGCTATAGCCTTGATACTAAACTAGTTTCTCCAAAGCTGATTGGTATCGTCAGCATCGGCTATGCAGACGGTGTTCCTAGAGAGTTATCTCACAATGAGTTTTATCTTGCTTATCAGGGACAAAATCTACCACAAATCGGACGAATTTGTATGGATATGCTATTAGTGGATTTGACTGATTCTCCAGAAATCAAAGTAGAGTCACAAATTAGTATCTTCCCAGAACTAGAACAAACTGCTAATCAAACGAATACATTGACTAACGAAATCATCAGTCGCTTAGGTAATCGTTTCTACACCGAATGGTCCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36779","NCBI_taxonomy_name":"Enterococcus faecium","NCBI_taxonomy_id":"1352"}}}},"ARO_accession":"3002975","ARO_id":"39409","ARO_name":"vanT gene in vanN cluster","CARD_short_name":"vanT_in_vanN_cl","ARO_description":"Also known as vanTN, is a vanT variant found in the vanN gene cluster.","ARO_category":{"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"36511":{"category_aro_accession":"3000372","category_aro_cvterm_id":"36511","category_aro_name":"vanT","category_aro_description":"VanT is a membrane bound serine racemase, converting L-serine to D-serine. It is associated with VanC, which incorporated D-serine into D-Ala-D-Ser terminal end of peptidoglycan subunits that have a decreased binding affinity with vancomycin. It was isolated from Enterococcus gallinarum.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2242":{"model_id":"2242","model_name":"vanW gene in vanI cluster","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"50"}},"model_sequences":{"sequence":{"5272":{"protein_sequence":{"accession":"BAE83690.1","sequence":"MLRRKPWVFLLVILFSQLSLSILLGATVTYGAGYAKAPEGLTVWEKDLGGMTKDEAYAVLAEVIPKAVVYDRTVYFLELNQTDQDLKDYLASQYIISTGNVITDAFEYLHRMSRTIPSPELLNQEEVLAQLRKFALDIDQPGKAAEAYYENGEIVIEEGSLGVRLDVDKSWEQLQQSIGMETVPLVTEVIVVHPTTAELEKVKDPLGDYTTYFNPSFHERVTNVRLAAEAINGLILPPGGEFSFNDTVGKREPERGYLPALMYMGNRVVTDDGGGICQDSTTLYQATKQARLEVLERYSHSLPVSYVPLGQDATVAYGALDFRFRNTTQGYLLLNAATGGNWIRVRIFGVADSEHPALDEPDGYPVKPREWSK"},"dna_sequence":{"accession":"AP008230.1","fmin":"2195400","fmax":"2196522","strand":"-","sequence":"ATGTTAAGAAGGAAACCATGGGTCTTTCTTTTGGTAATTTTATTTAGTCAGCTTAGCTTATCTATACTTTTGGGGGCTACGGTAACCTACGGTGCGGGTTATGCGAAGGCACCCGAGGGGTTGACGGTTTGGGAAAAAGATCTGGGTGGGATGACCAAGGATGAGGCCTATGCAGTCCTTGCCGAAGTAATCCCCAAGGCAGTCGTCTATGACCGGACGGTTTATTTCTTGGAGCTAAACCAAACCGATCAAGATCTAAAGGACTATCTGGCAAGTCAATACATCATTTCCACCGGAAATGTTATTACGGATGCCTTTGAGTACCTGCACAGAATGTCAAGGACTATCCCGTCTCCTGAGTTACTCAATCAGGAGGAAGTTCTTGCTCAGCTCCGCAAGTTCGCCCTGGATATCGATCAGCCGGGTAAGGCGGCTGAAGCCTATTATGAGAATGGCGAGATCGTCATCGAAGAGGGCAGTTTGGGAGTCAGACTTGATGTGGACAAATCATGGGAACAACTGCAGCAAAGCATAGGCATGGAGACGGTGCCGCTTGTTACGGAGGTCATAGTGGTTCACCCTACTACGGCCGAATTAGAGAAGGTCAAAGATCCCTTGGGGGATTACACCACCTATTTTAACCCTTCCTTTCATGAACGGGTTACCAATGTACGGCTTGCGGCTGAAGCGATCAATGGACTTATTCTTCCGCCGGGTGGTGAATTCTCCTTTAATGATACGGTGGGAAAACGTGAGCCTGAAAGAGGGTATTTGCCGGCTTTAATGTATATGGGCAATAGAGTTGTCACAGATGATGGCGGAGGGATTTGCCAGGATTCGACCACTCTTTATCAAGCGACCAAACAGGCCAGGCTGGAAGTGCTGGAAAGATACAGCCATTCTCTGCCGGTTTCCTATGTTCCGTTGGGGCAGGATGCTACGGTTGCTTATGGAGCGCTGGATTTCCGCTTTCGGAACACGACTCAGGGTTATTTGCTGCTTAATGCAGCTACAGGCGGCAATTGGATTCGGGTAAGAATTTTCGGTGTGGCCGATTCTGAACACCCTGCCCTTGACGAACCGGACGGTTATCCTGTAAAACCCAGAGAATGGTCAAAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42594","NCBI_taxonomy_name":"Desulfitobacterium hafniense Y51","NCBI_taxonomy_id":"138119"}}}},"ARO_accession":"3003724","ARO_id":"40380","ARO_name":"vanW gene in vanI cluster","CARD_short_name":"vanW_in_vanI_cl","ARO_description":"Also known as vanWI, is a vanW variant found in the vanI gene cluster.","ARO_category":{"36011":{"category_aro_accession":"3000002","category_aro_cvterm_id":"36011","category_aro_name":"vanW","category_aro_description":"vanW is an accessory gene, with unknown function, found on vancomycin resistance operons.","category_aro_class_name":"AMR Gene Family"},"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"35948":{"category_aro_accession":"0000029","category_aro_cvterm_id":"35948","category_aro_name":"teicoplanin","category_aro_description":"Teicoplanin is a glycopeptide antibiotic used in the prophylaxis and treatment of serious infections caused by Gram-positive bacteria. Teicoplanin has a unique acyl-aliphatic chain, and binds to cell wall precursors to inhibit transglycosylation  and transpeptidation.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2245":{"model_id":"2245","model_name":"vanK gene in vanI cluster","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"5268":{"protein_sequence":{"accession":"BAE85481.1","sequence":"MLNVDKISEETYYAFISQADLGNFMQYPSWAKVKTEWTSDLLGWFTPDNKLAGCGLILYRKMPCLNRYLAYCPRGPLIDWQSPNLREWFEPLVAYLRSKQVFSIKIDPPVVQAKWSAPTIKTFLGQAREQGSKGKVLRDLPPDEDYTTVQQVQQQLRQMGWRKQRGDTGFAATQPQYVYRLPLEGRSLEEVFAGFHTNWRRNVKKAERLGVKVRVGTEQDLPAFYELLKVTSERDHFKVRSFSYFSNLYRSLKAEAADRIALYLAEDEEELLAATLAVHSNAHSWYLYGASSNVKREKAPNHAIQWRMIQDAYQLKAYTYDFRGISPTLDESDPLFGLLRFKLGFGGEACEMISAWDYPLQPLLYRAFQLYLKRR"},"dna_sequence":{"accession":"AP008230.1","fmin":"4204949","fmax":"4206077","strand":"-","sequence":"ATGTTAAACGTTGACAAGATAAGTGAAGAAACCTATTATGCGTTCATTTCTCAAGCGGATCTAGGCAATTTTATGCAGTATCCTTCCTGGGCCAAGGTCAAAACTGAGTGGACCAGCGATTTATTGGGGTGGTTCACCCCGGACAATAAATTGGCAGGGTGTGGTTTGATCTTATACCGGAAAATGCCCTGCCTTAACCGGTACCTGGCGTATTGTCCCCGCGGTCCCCTTATTGACTGGCAGAGCCCCAACCTCAGGGAATGGTTCGAACCTCTTGTGGCTTATTTGAGAAGCAAGCAGGTTTTCAGTATCAAGATCGATCCTCCGGTGGTCCAGGCAAAATGGTCTGCCCCCACCATTAAAACGTTTTTAGGGCAAGCCCGTGAACAGGGCAGCAAAGGGAAAGTTTTGCGCGATTTGCCGCCGGACGAAGACTACACAACGGTCCAACAAGTGCAGCAGCAATTACGGCAAATGGGTTGGCGGAAGCAGCGGGGGGATACGGGTTTCGCTGCGACCCAGCCCCAATATGTTTACCGCCTGCCCTTAGAGGGGCGCAGCCTGGAGGAGGTCTTCGCCGGTTTTCATACCAACTGGAGGCGCAATGTTAAAAAGGCCGAGCGTTTGGGCGTCAAGGTCCGGGTCGGGACCGAACAGGATTTACCGGCTTTTTATGAGCTGCTGAAGGTAACTTCAGAACGGGATCACTTCAAGGTGCGCAGTTTCTCCTACTTTTCCAATCTGTACCGGTCCTTAAAGGCTGAAGCGGCAGACCGTATTGCTCTTTATCTGGCGGAAGATGAAGAGGAATTATTGGCTGCTACCTTAGCCGTCCATTCCAACGCCCACTCATGGTATCTTTACGGGGCCAGCAGCAATGTAAAACGGGAGAAGGCCCCGAATCATGCTATCCAGTGGCGGATGATTCAAGATGCTTATCAGCTTAAGGCCTACACCTATGATTTTAGAGGCATCAGCCCTACCCTGGATGAATCTGACCCCCTGTTTGGGTTGTTGAGATTTAAATTGGGCTTTGGAGGCGAGGCTTGTGAAATGATCAGTGCTTGGGACTACCCCCTGCAGCCTTTATTATACCGGGCTTTCCAGCTGTACTTAAAACGGCGGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42594","NCBI_taxonomy_name":"Desulfitobacterium hafniense Y51","NCBI_taxonomy_id":"138119"}}}},"ARO_accession":"3003727","ARO_id":"40384","ARO_name":"vanK gene in vanI cluster","CARD_short_name":"vanK_in_vanI_cl","ARO_description":"Also known as vanKI, is a peptidoglycan bridge formation protein also known as FemAB that is part of the vanI glycopeptide resistance gene cluster.","ARO_category":{"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"39349":{"category_aro_accession":"3002915","category_aro_cvterm_id":"39349","category_aro_name":"vanK","category_aro_description":"VanK is a member of the Fem family of enzymes that add the cross-bridge amino acids to the stem pentapeptide of cell wall precursors in Streptomyces coelicolor that confers inducible, high-level vancomycin resistance.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"35948":{"category_aro_accession":"0000029","category_aro_cvterm_id":"35948","category_aro_name":"teicoplanin","category_aro_description":"Teicoplanin is a glycopeptide antibiotic used in the prophylaxis and treatment of serious infections caused by Gram-positive bacteria. Teicoplanin has a unique acyl-aliphatic chain, and binds to cell wall precursors to inhibit transglycosylation  and transpeptidation.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5912":{"model_id":"5912","model_name":"QnrB80","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"8621":{"protein_sequence":{"accession":"AKO62872.1","sequence":"MALALVGEKIDRNRFTGEKIENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNASALDIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGTQVLGATFSGSDLSGGEFSTFDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDNYQASLLMERLGIAIIG"},"dna_sequence":{"accession":"KM985473.1","fmin":"0","fmax":"645","strand":"+","sequence":"ATGGCTCTGGCACTCGTTGGCGAAAAAATTGACAGAAACCGCTTCACCGGTGAGAAAATTGAAAATAGTACATTTTTTAACTGTGATTTTTCAGGTGCCGACCTGAGCGGCACTGAATTTATCGGCTGTCAGTTCTATGATCGTGAAAGCCAGAAAGGGTGCAATTTTAGTCGTGCGATGCTGAAAGATGCCATTTTTAAAAGCTGTGATTTATCCATGGCGGATTTTCGCAATGCCAGTGCGCTTGACATTGAAATTCGCCACTGCCGCGCACAAGGCGCAGATTTCCGCGGCGCAAGCTTTATGAATATGATCACCACGCGCACCTGGTTTTGTAGCGCATATATCACGAATACAAATCTAAGCTACGCCAATTTTTCGAAAGTCGTGCTGGAAAAGTGTGAGCTGTGGGAAAACCGTTGGATGGGTACCCAGGTACTGGGCGCGACGTTCAGTGGTTCAGATCTCTCCGGCGGCGAGTTTTCGACTTTCGACTGGCGAGCAGCAAACTTCACACATTGCGATCTGACCAATTCGGAGTTGGGTGACTTAGATATTCGGGGGGTTGATTTACAAGGCGTTAAGTTGGACAACTACCAGGCATCGTTGCTCATGGAACGTCTTGGCATCGCGATTATTGGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3003192","ARO_id":"39769","ARO_name":"QnrB80","CARD_short_name":"QnrB80","ARO_description":"QnrB80 is a fluoroquinolone resistance gene in Lahey's list of qnr genes.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5742":{"model_id":"5742","model_name":"Erm(52)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"8296":{"protein_sequence":{"accession":"QQM99828.1","sequence":"MKNLGYSQNFLVNKKLVERLISKSNIDVTDYVIEIGPGKGIITDVLSQHAGEVVAVEYDQELYNNLVRYHSHDNVTYIFGDFLKYKLPLNRRYKIFSNIPFQITADIIRKLTDDVNPPSDINIIIQREAAKKNCGIPLQKYEGFRAAIIKAQYKVEITHSFKRSDFFPSPNVDTVMLHMQLWDDRLSGDDLQNYKDLVAFFYTNIKGETAKERLSILFSNEQIKRLGKANRISLSNSYTLITAEQWMNIYYYSKIGLTDEKKKKFQDAYKKLQKMNKKLKKQNRTSLRKSSSNKKCRTRIDTSNGTKNR"},"dna_sequence":{"accession":"MW269959.1","fmin":"0","fmax":"930","strand":"+","sequence":"ATGAAAAATCTTGGATATTCACAAAATTTTTTGGTTAATAAAAAGTTGGTAGAACGTTTAATAAGCAAGTCAAATATTGATGTAACAGATTATGTTATTGAAATTGGTCCTGGAAAAGGGATAATAACAGATGTACTTTCTCAGCATGCTGGAGAGGTTGTTGCAGTTGAATATGATCAAGAATTATATAATAATTTAGTAAGATATCACAGTCATGATAATGTTACATATATATTTGGTGATTTTTTAAAATATAAGTTGCCTTTAAATCGCAGATATAAAATATTCTCCAATATTCCTTTTCAGATAACAGCGGATATTATTAGGAAATTAACAGACGATGTAAATCCACCATCAGATATAAATATCATAATTCAAAGAGAGGCAGCTAAAAAGAATTGCGGTATTCCATTACAAAAATATGAAGGTTTTCGTGCTGCTATAATAAAGGCACAATATAAGGTAGAAATTACACATAGTTTTAAAAGGAGCGATTTTTTTCCTTCGCCTAATGTTGATACAGTTATGCTTCATATGCAGTTATGGGATGATAGATTGAGTGGTGATGATCTTCAAAATTATAAAGATTTAGTGGCTTTTTTTTACACTAATATTAAAGGAGAGACTGCTAAAGAGAGACTTTCTATTTTATTTTCTAATGAGCAAATCAAAAGATTGGGAAAAGCCAATAGAATTAGTCTTTCAAATTCATATACGTTAATCACGGCCGAGCAGTGGATGAATATTTATTATTACTCCAAAATTGGATTGACAGATGAAAAGAAAAAAAAGTTTCAAGATGCATATAAAAAACTTCAAAAAATGAATAAAAAATTGAAAAAGCAAAACAGAACATCTTTACGAAAGTCTAGTAGCAATAAGAAATGTAGAACAAGGATTGATACTTCTAATGGTACAAAAAATAGATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36807","NCBI_taxonomy_name":"Clostridioides difficile","NCBI_taxonomy_id":"1496"}}}},"ARO_accession":"3007041","ARO_id":"45600","ARO_name":"Erm(52)","CARD_short_name":"Erm(52)","ARO_description":"Erm(52) is an Erm ribosomal RNA methyltransferase.","ARO_category":{"36699":{"category_aro_accession":"3000560","category_aro_cvterm_id":"36699","category_aro_name":"Erm 23S ribosomal RNA methyltransferase","category_aro_description":"Erm proteins are part of the RNA methyltransferase family and methylate A2058 (E. coli nomenclature) of the 23S ribosomal RNA conferring degrees of resistance to Macrolides, Lincosamides and Streptogramin b. This is called the MLSb phenotype.","category_aro_class_name":"AMR Gene Family"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5743":{"model_id":"5743","model_name":"msr(G)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"8297":{"protein_sequence":{"accession":"QNR09092.1","sequence":"MEQICFELENVEVTYLDKEVLKIERLAVHQFDRIGIVGKNGAGKSTLLKLLAGIIKPTTGKVNRLVENGYFEQLETPSVRDADPVLLGKLDVPKDSNQLSGGEQTRMKLAKLFTHYYEALLIDEPTTHLDQEGISFLLDELRYYYGALVLISHDRSVLDELVTTIWEVHEGKVRIYSGNYSDYMAQKKLEREQQSQAHEQFIKEKSRLEKAAQEKMKKAEKVAQAGRLSKKDANAKPDKSFMTKSKGTSQKAMQRAAKAIEQRMEKLQEVDAVKEDRQINFHQSRNLELHNKFPIMADRFTLQVDNKVLLNEVSFQMPLGKKIAISGKNGAGKSTLLHHIAINAPGLTISPKAKIGYFRQMSYQYTRDETVLEFLKNRSEYDERFLRSVLHSMLFVGTDILKSVKSLSGGEAIRLQLCQLFLGEYNILLLDEPTNFLDIYAIEALERFITAYKGTIIFVSHDRRFIDCVADCIYFIEDQQLKLRG"},"dna_sequence":{"accession":"CP046364.1","fmin":"33122","fmax":"34580","strand":"+","sequence":"ATGGAACAAATCTGTTTTGAATTAGAAAATGTAGAAGTGACATATCTAGATAAAGAGGTTTTAAAGATTGAAAGATTAGCTGTACACCAATTTGACCGTATCGGCATAGTCGGTAAAAATGGTGCAGGTAAAAGCACGTTACTAAAATTACTGGCGGGTATCATTAAGCCAACAACGGGAAAGGTGAATCGGCTTGTTGAGAATGGCTATTTTGAGCAACTTGAAACTCCATCAGTACGTGATGCTGATCCAGTGTTACTTGGAAAATTAGACGTACCAAAAGACTCTAATCAGCTAAGCGGTGGGGAACAAACAAGGATGAAACTCGCTAAATTGTTTACTCATTATTATGAAGCTTTATTAATTGATGAGCCGACTACTCACTTAGACCAAGAGGGGATTTCGTTTTTGCTCGATGAACTTAGGTATTACTATGGAGCGCTTGTATTAATTAGTCATGACCGTTCTGTATTAGATGAACTAGTTACGACAATTTGGGAAGTTCATGAAGGTAAGGTACGAATCTATTCAGGAAATTACAGCGACTACATGGCACAAAAGAAGTTAGAACGTGAACAGCAGAGTCAAGCACATGAACAGTTCATAAAAGAAAAGAGCAGGTTAGAAAAAGCAGCACAAGAAAAAATGAAGAAAGCTGAAAAAGTTGCACAAGCAGGTCGATTGTCAAAAAAAGATGCGAATGCAAAGCCGGATAAGTCCTTTATGACAAAATCCAAAGGTACGAGCCAAAAAGCTATGCAGCGTGCAGCAAAGGCCATTGAGCAACGAATGGAAAAACTTCAGGAAGTCGATGCTGTAAAAGAGGATAGGCAAATAAACTTCCATCAATCGAGAAATTTAGAGCTGCATAATAAATTTCCGATAATGGCAGACCGATTTACTCTTCAAGTGGATAACAAAGTATTATTAAATGAAGTAAGTTTTCAAATGCCGCTTGGTAAAAAAATTGCAATTTCGGGTAAAAATGGTGCTGGCAAAAGTACTTTACTCCACCATATTGCTATCAATGCGCCAGGTTTAACAATTTCACCAAAAGCAAAAATTGGATACTTTCGTCAAATGAGCTATCAATATACAAGGGATGAAACGGTATTGGAATTTCTGAAAAATCGTTCTGAATACGATGAGAGATTTTTACGAAGCGTTCTACATTCCATGTTGTTTGTCGGCACAGATATATTAAAAAGTGTAAAATCATTAAGTGGTGGTGAAGCGATTCGTCTACAATTATGTCAATTATTTTTAGGAGAGTATAATATTTTATTGTTAGATGAACCAACCAATTTTTTAGATATCTATGCTATTGAAGCGTTAGAAAGATTTATTACAGCATATAAAGGCACTATTATCTTCGTATCACATGATCGCAGGTTTATTGATTGTGTAGCAGATTGTATATATTTCATTGAAGATCAACAGCTAAAATTAAGGGGTTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43299","NCBI_taxonomy_name":"Macrococcus canis","NCBI_taxonomy_id":"1855823"}}}},"ARO_accession":"3007042","ARO_id":"45601","ARO_name":"msr(G)","CARD_short_name":"msr(G)","ARO_description":"msr(G) is a part of the msr subfamily of ABC-F ribosomal protection proteins.","ARO_category":{"41695":{"category_aro_accession":"3004471","category_aro_cvterm_id":"41695","category_aro_name":"msr-type ABC-F protein","category_aro_description":"msr-type ABC-F subfamily ribosomal protection proteins expression in Staphylococci species and confer resistance to erythromycin and streptogramin B antibiotics through antibiotic target protection mechanisms.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5744":{"model_id":"5744","model_name":"msr(I)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"8298":{"protein_sequence":{"accession":"QQA64075.1","sequence":"MEQICFELEKIEVTYLDKKVLEIDRLAVHQFDRIGIVGKNGVGKSTLLKLLAGHIQPTVGKVKRQVEYGYFEQVEGPKDISTDPKLLSQLHVDENSKGLSGGEQTRLKLAQLFTDYYESLLIDEPTTHLDQEGISFLIEELKYYYGALVLISHDRYVLDELVTTIWEVDDGKVKVYSGDYSEYIEQKKLERSKQTQAHEQFLKEKKRLEKAAEEKMKKAEKIAKSSAKSKDSKVKANRMFESKSKGTTQKALQRAAKAVEQRVKKLEVIDAPKKEQTIRFHQTNIILELHNKFPIMADQLTITVGNKILLNNVNFQFALGETIAITGKNGSGKSTLIHHILQREKGITISPKAVIGSYEQMGYQFKTDETVMDFMKNRSDYGESKIRSVLYAMSFTGNDLKKSVQKLSGGEATRLVLCQLFLGRYNVLILDEPTNFLDVFCIEALETFLKGYEGTVILISHDKTFLDRVADSEYVLENQNLKKNR"},"dna_sequence":{"accession":"CP065927.1","fmin":"1658157","fmax":"1659615","strand":"-","sequence":"ATGGAACAAATTTGTTTTGAATTAGAAAAAATTGAAGTAACTTATTTAGATAAAAAAGTATTAGAGATAGATCGTTTAGCAGTTCATCAATTTGATAGAATTGGTATTGTTGGAAAAAATGGTGTTGGTAAGAGTACTCTGCTAAAATTACTTGCAGGTCATATTCAACCTACAGTTGGAAAAGTAAAGCGTCAAGTAGAATATGGTTATTTTGAACAGGTAGAAGGTCCTAAAGATATATCAACAGATCCTAAGTTACTTAGCCAATTACATGTTGATGAGAATTCGAAAGGGCTAAGTGGTGGTGAACAAACAAGATTAAAACTTGCACAGTTATTTACGGACTATTATGAATCTTTATTAATTGATGAGCCAACTACACATTTGGACCAAGAAGGTATATCATTTTTAATAGAAGAGTTGAAATACTATTATGGGGCACTGGTATTAATAAGTCATGACCGATATGTTTTAGATGAACTTGTGACTACAATTTGGGAAGTTGATGATGGGAAAGTAAAAGTATATTCAGGAGATTACAGTGAATATATCGAGCAAAAGAAACTTGAAAGATCAAAACAAACTCAGGCTCATGAACAGTTCTTAAAGGAAAAAAAACGTTTAGAAAAAGCAGCAGAAGAAAAAATGAAAAAAGCAGAAAAAATTGCTAAATCTTCTGCTAAATCAAAAGACTCTAAAGTAAAAGCAAATCGTATGTTTGAATCAAAATCAAAGGGTACAACTCAAAAAGCGTTACAACGTGCTGCTAAGGCTGTTGAACAAAGAGTAAAAAAACTTGAAGTTATAGATGCGCCTAAAAAAGAACAAACTATCCGTTTTCATCAAACAAATATCATACTTGAGTTACATAACAAGTTTCCAATTATGGCTGATCAATTAACGATTACAGTAGGAAATAAGATACTTTTAAACAATGTTAACTTTCAATTTGCATTAGGTGAAACGATTGCTATTACTGGTAAAAATGGTTCTGGGAAATCAACATTAATTCACCACATATTACAACGTGAAAAAGGAATTACTATTTCTCCAAAGGCTGTTATAGGCTCTTATGAGCAGATGGGATATCAATTTAAAACTGATGAAACTGTAATGGACTTTATGAAAAATAGAAGCGATTATGGAGAAAGTAAAATACGTTCTGTACTATATGCTATGAGTTTTACTGGGAATGATTTAAAAAAGAGTGTTCAAAAATTAAGTGGTGGCGAGGCGACTCGTTTAGTCCTATGTCAATTATTTCTAGGAAGATACAACGTTTTGATTTTAGATGAACCTACTAACTTTTTAGATGTTTTTTGTATTGAAGCTTTAGAAACATTTTTAAAAGGCTATGAAGGAACAGTTATACTAATATCACATGATAAAACATTTTTAGATCGTGTAGCTGATAGTGAATACGTTCTAGAAAATCAGAACCTTAAAAAAAATAGATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36764","NCBI_taxonomy_name":"Streptococcus pyogenes","NCBI_taxonomy_id":"1314"}}}},"ARO_accession":"3007043","ARO_id":"45602","ARO_name":"msr(I)","CARD_short_name":"msr(I)","ARO_description":"msr(I) is part of the msr subfamily of ABC-F ribosomal protection proteins.","ARO_category":{"41695":{"category_aro_accession":"3004471","category_aro_cvterm_id":"41695","category_aro_name":"msr-type ABC-F protein","category_aro_description":"msr-type ABC-F subfamily ribosomal protection proteins expression in Staphylococci species and confer resistance to erythromycin and streptogramin B antibiotics through antibiotic target protection mechanisms.","category_aro_class_name":"AMR Gene Family"},"35944":{"category_aro_accession":"0000025","category_aro_cvterm_id":"35944","category_aro_name":"fosfomycin","category_aro_description":"Fosfomycin (also known as phosphomycin and phosphonomycin) is a broad-spectrum antibiotic produced by certain Streptomyces species. It is effective on gram positive and negative bacteria as it targets the cell wall, an essential feature shared by both bacteria. Its specific target is MurA (MurZ in E.coli), which attaches phosphoenolpyruvate (PEP) to UDP-N-acetylglucosamine, a step of commitment to cell wall synthesis. In the active site of MurA, the active cysteine molecule is alkylated which stops the catalytic reaction.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"45731":{"category_aro_accession":"3007149","category_aro_cvterm_id":"45731","category_aro_name":"phosphonic acid antibiotic","category_aro_description":"A group of antibiotics derived from phosphonic acids.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5746":{"model_id":"5746","model_name":"Erm(51)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"8300":{"protein_sequence":{"accession":"QKE44141.1","sequence":"MPTYRPNKGRHENGQNYLVNKSMIKKVVDLVPVSASVPVIEIGPGHGALTFPLQDRVLATGGSLTAVEIDPASVRWLEERLRPEVHLYEQDVLDFVLPDGPHVLVGNLPFHLTTAILRHVLHSPGWTHAVFLVQWEVARRRAGVGGATMMTAQWWPWFDFEQHGRIPSTHFRPRPTVDAGVLVMRRREEPLVNWSERARYASFVHAVFTGKGRGIADIVSRVVGRRRERRCAEVLREAGVPANALPKQLDAGQWATLFKAVGR"},"dna_sequence":{"accession":"MN928789.1","fmin":"0","fmax":"792","strand":"+","sequence":"ATGCCTACCTACAGGCCGAACAAGGGCCGTCACGAGAACGGCCAGAACTACCTCGTCAACAAGTCAATGATTAAGAAGGTCGTTGACCTTGTCCCTGTCAGTGCGTCCGTCCCGGTCATAGAGATCGGCCCGGGACACGGGGCGCTGACCTTTCCCCTCCAGGACCGTGTCCTGGCTACCGGTGGATCGTTGACCGCCGTCGAGATCGACCCGGCCTCCGTCCGGTGGCTGGAGGAGCGGCTGCGCCCGGAGGTTCACCTGTACGAGCAGGACGTCCTTGATTTTGTGCTGCCGGACGGCCCGCACGTCCTGGTGGGGAACCTGCCGTTTCACCTGACCACCGCGATCCTGCGGCACGTCCTTCACTCACCGGGGTGGACTCACGCGGTCTTCCTGGTGCAGTGGGAGGTCGCGCGTCGCCGCGCCGGCGTCGGTGGTGCCACGATGATGACAGCCCAGTGGTGGCCCTGGTTCGACTTCGAACAGCACGGGCGAATACCATCCACACATTTCCGTCCCCGCCCCACCGTCGACGCCGGTGTCCTGGTGATGCGTCGCCGGGAAGAGCCTCTCGTCAACTGGTCGGAGCGTGCGCGGTACGCGTCGTTCGTCCATGCCGTGTTCACCGGCAAGGGCCGAGGCATCGCCGACATCGTGTCCCGGGTCGTGGGGCGTCGGCGTGAACGACGGTGTGCTGAGGTCCTGCGTGAGGCCGGTGTTCCGGCAAACGCACTGCCGAAACAGTTGGACGCGGGGCAGTGGGCCACACTGTTTAAGGCCGTGGGGCGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36897","NCBI_taxonomy_name":"Rhodococcus hoagii","NCBI_taxonomy_id":"43767"}}}},"ARO_accession":"3007033","ARO_id":"45592","ARO_name":"Erm(51)","CARD_short_name":"Erm(51)","ARO_description":"Erm(51) is an Erm ribosomal RNA methyltransferase.","ARO_category":{"36699":{"category_aro_accession":"3000560","category_aro_cvterm_id":"36699","category_aro_name":"Erm 23S ribosomal RNA methyltransferase","category_aro_description":"Erm proteins are part of the RNA methyltransferase family and methylate A2058 (E. coli nomenclature) of the 23S ribosomal RNA conferring degrees of resistance to Macrolides, Lincosamides and Streptogramin b. This is called the MLSb phenotype.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35982":{"category_aro_accession":"0000065","category_aro_cvterm_id":"35982","category_aro_name":"clarithromycin","category_aro_description":"Clarithromycin is a methyl derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome and is used to treat pharyngitis, tonsillitis, acute maxillary sinusitis, acute bacterial exacerbation of chronic bronchitis, pneumonia (especially atypical pneumonias associated with Chlamydia pneumoniae or TWAR), and skin structure infections.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"37019":{"category_aro_accession":"3000675","category_aro_cvterm_id":"37019","category_aro_name":"pristinamycin IB","category_aro_description":"Pristinamycin IB is a class B streptogramin similar to pristinamycin IA, the former containing a N-methyl-4-(methylamino)phenylalanine instead of a N-methyl-4-(dimethylamino)phenylalanine in its class A streptogramin counterpart (one less methyl group).","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35967":{"category_aro_accession":"0000050","category_aro_cvterm_id":"35967","category_aro_name":"streptogramin B antibiotic","category_aro_description":"Streptogramin B antibiotics are are cyclic hepta- or hexa-depsipeptides.  Type B streptogramins block the peptide exit tunnel of the 50S bacterial ribosome. The general composition of group B streptogramins is 3-hydroxypicolinic acid-L-Thr-D-aminobutyric acid (or D-Ala)-L-Pro-L-Phe (or 4-N-,N-(dimethylamino)-L-Phe)-X-L-phenylglycine. Used alone, streptogramin B antibiotics are bacteriostatic, but is bactericidal when used with streptogramin A antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5749":{"model_id":"5749","model_name":"mreA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"8303":{"protein_sequence":{"accession":"AAB64408.1","sequence":"MMKIHYINDYKDIQAKEDCVLVLGYFDGLHLGHKALFDKAKKIATEKNLKIVVLTFNETPRLTFARFQPELLLHLTSPEKRSEKFQEYGVDELYLMNFTSHFSKVSSDLFIKKYIYGLRAKAAVVGFDYKFGHNRTSGDYLARNFKGPVYIIDEISEGGEKISSTRIRQLITEGNVEKANQLLGYEFSTCGMVVHGDARGRTIGFPTANLAPINRTYLPADGVYISNVLINGKYYRAMTSIGKNITFGGTELRLEANIFDFDGDIYGETIEIFWLKRIREMVKFNGIDDLVKQLKKDKEIALNWKKDSQTL"},"dna_sequence":{"accession":"U92073.1","fmin":"118","fmax":"1054","strand":"+","sequence":"ATCATGAAAATCCATTACATTAATGATTATAAAGATATTCAAGCTAAAGAAGATTGCGTCTTAGTTTTGGGCTATTTTGATGGCTTACATCTGGGACATAAAGCCCTCTTTGATAAAGCTAAAAAAATCGCGACCGAAAAAAATTTGAAAATTGTCGTCTTAACGTTTAATGAGACACCTCGTCTAACCTTCGCTCGCTTCCAACCTGAATTATTGCTACATCTTACCTCTCCAGAAAAACGTTCTGAAAAATTTCAAGAGTATGGCGTCGATGAGTTATATTTAATGAATTTTACCAGTCATTTTTCAAAAGTATCTTCTGACCTTTTTATTAAGAAATATATTTATGGTCTCAGAGCAAAAGCTGCTGTTGTCGGTTTTGATTATAAGTTCGGTCATAATCGTACCAGTGGTGATTATCTAGCGCGTAATTTCAAGGGACCAGTCTATATTATTGATGAAATTTCTGAAGGTGGTGAAAAAATCTCTTCTACACGTATTCGTCAATTGATTACAGAGGGTAATGTTGAGAAAGCTAACCAACTTTTGGGTTATGAGTTTTCAACCTGTGGCATGGTAGTACATGGAGATGCTAGAGGACGAACTATAGGGTTCCCAACTGCTAATCTAGCTCCTATTAATCGCACTTACTTACCTGCAGACGGTGTTTATATTTCCAATGTTCTGATTAATGGAAAATATTATAGAGCAATGACGAGCATTGGAAAAAATATCACTTTTGGTGGTACAGAACTTCGTTTAGAAGCTAATATCTTTGATTTTGATGGCGACATTTATGGAGAAACTATTGAAATTTTCTGGTTAAAAAGAATCAGAGAAATGGTAAAGTTTAATGGTATTGACGATCTTGTAAAACAACTTAAAAAAGATAAAGAAATTGCTTTAAATTGGAAAAAAGATAGTCAAACTCTTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36847","NCBI_taxonomy_name":"Streptococcus agalactiae","NCBI_taxonomy_id":"1311"}}}},"ARO_accession":"3007050","ARO_id":"45609","ARO_name":"mreA","CARD_short_name":"mreA","ARO_description":"mreA is a macrolide efflux pump.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"36295":{"category_aro_accession":"3000156","category_aro_cvterm_id":"36295","category_aro_name":"spiramycin","category_aro_description":"Spiramycin is a 16-membered macrolide and is natural product produced by Streptomyces ambofaciens. It binds to the 50S subunit of bacterial ribosomes and inhibits peptidyl transfer activity to disrupt protein synthesis.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"5751":{"model_id":"5751","model_name":"OXA-290","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"530"}},"model_sequences":{"sequence":{"8401":{"protein_sequence":{"accession":"ENU29139.1","sequence":"MIGLTLLGCQNLHAPTQSAVSKKHDQTEIASLFQHTQTVGVFVTYDGQTFQEYGNALSRSNTAYIPASTFKMLNALIGIQHHKSSPNEVFKWDGKKRAFASWEKDLTLAEAMQASAVPVYQELARRIGLELMANEVKRVGFGNTEIGTQVDDFWLVGPLKITPVDEVKFAYALANKQLAFDQSVQEQVKQMVFVDEVHGTKIYAKSGWGMDVTPQVGWWTGWIEQPNGQVIAFALNLEINKPEHGDARKAIVYQALQQLKLLQKQ"},"dna_sequence":{"accession":"APOK01000044.1","fmin":"289938","fmax":"290736","strand":"-","sequence":"ATGATTGGACTGACGTTGCTAGGTTGCCAAAATTTGCACGCCCCAACTCAAAGCGCCGTGTCAAAAAAACACGATCAAACCGAGATCGCTTCTTTATTCCAACATACTCAAACTGTTGGCGTATTTGTTACATATGATGGGCAAACATTTCAAGAATATGGCAATGCGTTGAGTCGATCGAATACGGCTTATATTCCAGCCTCAACCTTCAAGATGTTAAATGCTCTGATTGGGATACAGCATCACAAAAGTTCGCCCAACGAAGTGTTTAAATGGGATGGCAAAAAGCGTGCTTTTGCGAGCTGGGAAAAAGATTTAACTTTAGCCGAGGCGATGCAGGCATCAGCAGTGCCTGTTTATCAGGAATTGGCTCGGCGTATCGGGTTAGAGTTGATGGCGAACGAAGTAAAACGCGTTGGCTTTGGCAATACTGAGATCGGAACGCAAGTCGATGATTTTTGGTTGGTTGGCCCGCTTAAGATTACCCCCGTTGACGAAGTGAAATTTGCTTATGCTCTGGCAAATAAGCAGCTTGCATTTGACCAATCTGTGCAAGAACAAGTGAAACAGATGGTCTTCGTTGATGAAGTTCATGGAACTAAGATTTATGCCAAAAGTGGTTGGGGTATGGATGTAACACCGCAAGTGGGTTGGTGGACGGGCTGGATTGAACAACCGAATGGACAGGTGATTGCATTTGCTTTAAATCTGGAAATAAATAAGCCTGAGCACGGTGATGCGCGTAAAGCGATTGTTTATCAAGCATTACAACAATTGAAATTGTTACAGAAGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39511","NCBI_taxonomy_name":"Acinetobacter sp. CIP-A165","NCBI_taxonomy_id":"40373"}}}},"ARO_accession":"3001745","ARO_id":"38145","ARO_name":"OXA-290","CARD_short_name":"OXA-290","ARO_description":"OXA-290 is a beta-lactamase found in Acinetobacter spp.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5752":{"model_id":"5752","model_name":"Helicobacter pylori gyrA conferring resistance to fluoroquinolones","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"12352":"T87I","12353":"A88P","12354":"D91H","12358":"D99V","12362":"V172I","12365":"D34N","12369":"G85C","12541":"N87K","12542":"N87Y","12544":"D91G","12545":"D91N","12546":"D91Y","13165":"D87G","12543":"N87I"},"Curated-R":{"12352":"T87I","12353":"A88P","12354":"D91H","12358":"D99V","12362":"V172I","12365":"D34N","12367":"D34N","12368":"D34N","12369":"G85C","12541":"N87K","12542":"N87Y","12544":"D91G","12545":"D91N","12546":"D91Y","12898":"D91Y","12899":"D91Y","12900":"D91Y","12903":"D91Y","12906":"D91Y","12907":"D91Y","13165":"D87G","12364":"D87G","12543":"N87I","12901":"N87I"},"clinical":{"12352":"T87I","12353":"A88P","12354":"D91H","12358":"D99V","12362":"V172I","12365":"D34N","12369":"G85C","12541":"N87K","12542":"N87Y","12544":"D91G","12545":"D91N","12546":"D91Y","13165":"D87G","12543":"N87I"}},"40330":{"param_type":"multiple resistance variants","param_description":"A set of nucleotide or amino acid substitutions that are all required to confer resistance to an antibiotic drug or drug class, encoded as: [wild-type 1][position 1][mutation 1],[wild-type 2][position 2][mutation 2], etc. For example, D63Y,T142K.","param_type_id":"40330","param_value":{"12367":"D91G,D161N","12368":"D34Y,R140K","12898":"N87K,H57Y","12899":"D91N,V77A","12900":"D91N,A97V","12903":"S63P,D91N","12906":"D91N,R130K","12907":"S63P,R130K","12364":"R140K,D192N","12901":"D91Y,A97V"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1400"}},"model_sequences":{"sequence":{"8325":{"protein_sequence":{"accession":"WP_001153763.1","sequence":"MQDNSVNETKNIVEVGIDSSIEESYLAYSMSVIIGRALPDARDGLKPVHRRILYAMHELGLTSKVAYKKSARIVGDVIGKYHPHGDNAVYDALVRMAQDFSMRLELVDGQGNFGSIDGDNAAAMRYTEARMTKASEEILRDIDKDTIDFVPNYDDTLKEPDILPSRLPNLLVNGANGIAVGMATSIPPHRMDEIIDALVHVLENPNAGLDEILEFVKGPDFPTGGIIYGKAGIIEAYKTGRGRVKVRAKVHVEKTKNKEIIVLDEMPFQTNKAKLVEQISDLAREKQIEGISEVRDESDREGIRVVIELKRDAMSEIVLNHLYKLTTMETTFSIILLAIYNKEPKIFTLLELLHLFLNHRKTIIIRRTIFELEKAKARAHILEGYLIALDNIDEIVRLIKTSQSPEAAKNALMERFTLSEIQSKAILEMRLQRLTGLERDKIKEEYQNLLELIDDLNGILKSEDRLNGVVKTELLEVKEQFSSPRRTEIQESYENIDIEDLIANEPMVVSMSYKGYVKRVDLKAYEKQNRGGKGKLSGSTYEDDFIENFFVANTHDILLFITNKGQLYHLKVYKIPEASRIAMGKAIVNLISLAPDEKIMATLSTKDFSDERSLAFFTKNGVVKRTNLSEFESNRSCGIRAIVLDEGDELVSAKVVDKNAKHLLIASHLGIFIKFPLEEVREIGRTTRGVIGIKLNENDFVVGAVVISDDGNKLLSVSENGLGKQTLAEAYRGQSRGGKGVIGMKLTQKTGNLVGVISVDDENLDLMILTASAKMIRVSIKDIRETGRNASGVKLINTADKVMYVNSCPKEEEPENLETSSAQNLFE"},"dna_sequence":{"accession":"NC_000915.1","fmin":"752511","fmax":"754995","strand":"+","sequence":"ATGCAAGATAATTCAGTCAATGAAACAAAAAATATTGTAGAAGTGGGGATTGATTCTTCTATTGAAGAGAGCTATTTAGCTTATTCCATGAGCGTGATCATAGGGCGCGCTTTACCGGACGCTAGAGATGGCTTAAAGCCCGTGCATAGGCGTATTTTGTATGCGATGCATGAATTAGGCCTTACTTCAAAAGTCGCTTACAAAAAAAGCGCTAGGATCGTGGGTGATGTGATTGGTAAATACCACCCCCATGGCGATAATGCGGTTTATGATGCGCTAGTGAGAATGGCGCAAGATTTTTCCATGCGTTTGGAATTAGTGGATGGGCAGGGCAACTTTGGCTCTATTGATGGCGATAACGCCGCAGCGATGCGTTACACTGAAGCCAGAATGACTAAGGCGAGTGAAGAAATTTTAAGGGATATTGATAAAGACACCATTGATTTTGTGCCTAATTATGACGATACCTTAAAAGAGCCAGATATTTTACCAAGCCGTCTGCCTAACCTTTTAGTCAATGGGGCTAATGGGATCGCTGTGGGGATGGCGACTTCTATCCCCCCTCACAGGATGGATGAAATCATAGACGCTTTAGTGCATGTCTTAGAAAACCCTAACGCTGGATTAGATGAAATCTTAGAATTTGTCAAAGGGCCTGATTTTCCCACTGGTGGGATCATTTATGGCAAGGCGGGTATTATTGAAGCCTATAAAACGGGGCGAGGACGCGTGAAAGTGCGGGCCAAAGTGCATGTGGAAAAAACAAAAAATAAAGAAATCATCGTTTTAGATGAAATGCCTTTTCAAACCAATAAAGCCAAATTAGTGGAACAAATCAGCGATTTAGCGCGAGAAAAGCAAATTGAAGGCATTAGTGAAGTGCGCGATGAGAGCGATAGAGAGGGCATTAGAGTGGTGATTGAATTAAAAAGAGACGCGATGAGTGAAATTGTCTTAAACCACCTCTACAAACTCACCACTATGGAAACCACTTTTAGCATCATTTTACTCGCTATTTACAATAAAGAGCCTAAGATTTTCACGCTTTTAGAGTTGTTGCACCTTTTCTTAAACCACAGAAAAACCATTATTATAAGACGCACGATTTTTGAATTAGAAAAGGCTAAGGCCAGAGCGCATATTTTAGAGGGCTATTTGATCGCACTAGACAATATTGATGAAATCGTGCGACTCATTAAAACAAGCCAAAGCCCAGAAGCGGCTAAAAACGCCTTAATGGAGCGTTTCACTTTGAGCGAGATTCAAAGCAAGGCCATTTTAGAAATGCGTTTGCAACGCTTAACAGGCCTTGAAAGGGATAAGATCAAAGAAGAATACCAAAACTTGTTGGAGCTTATTGATGATCTCAATGGCATTTTAAAGAGCGAAGATCGCTTGAATGGAGTCGTCAAAACAGAGCTTTTAGAAGTCAAAGAGCAATTTTCTTCTCCAAGGCGCACTGAAATTCAAGAATCTTATGAAAATATTGACATAGAAGATTTGATCGCTAATGAGCCTATGGTAGTGAGCATGAGTTATAAAGGCTATGTGAAAAGAGTGGATTTAAAAGCTTATGAAAAGCAAAATCGTGGTGGTAAAGGCAAGCTTTCAGGCAGCACTTATGAAGACGATTTCATTGAAAACTTTTTTGTGGCTAACACGCATGATATTTTGCTCTTTATCACCAATAAGGGGCAATTGTATCATTTGAAAGTCTATAAAATCCCAGAAGCGAGCCGGATCGCTATGGGTAAAGCCATTGTAAATTTAATCTCGCTCGCTCCGGATGAAAAGATCATGGCGACTCTAAGCACCAAAGACTTTAGCGATGAACGCTCTTTGGCCTTCTTCACGAAAAATGGCGTGGTGAAGCGCACCAATTTGAGCGAATTTGAAAGCAACAGGAGTTGTGGTATCAGAGCGATTGTTTTAGATGAAGGCGATGAATTAGTGAGCGCAAAAGTTGTGGATAAAAACGCTAAGCATTTGCTCATCGCATCGCATTTGGGCATTTTCATTAAATTCCCTTTAGAAGAGGTGCGCGAGATCGGAAGAACTACTCGTGGGGTTATAGGCATCAAGCTGAATGAAAACGATTTTGTTGTCGGTGCGGTCGTTATTAGCGATGATGGCAACAAGCTTTTGAGCGTGAGTGAAAACGGGCTTGGCAAGCAAACTTTAGCCGAAGCGTATAGAGGGCAATCTCGTGGAGGTAAGGGGGTCATTGGCATGAAGCTCACTCAAAAAACCGGCAATCTAGTGGGCGTTATCAGCGTGGATGATGAAAATTTGGATTTGATGATCCTTACTGCAAGCGCAAAAATGATCAGAGTTTCTATTAAAGATATTAGAGAAACCGGAAGAAACGCTAGTGGGGTAAAGCTCATAAACACCGCCGATAAAGTCATGTATGTCAATTCTTGCCCTAAAGAAGAAGAGCCAGAAAATTTAGAAACCTCTTCGGCACAAAATTTGTTTGAGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36906","NCBI_taxonomy_name":"Helicobacter pylori","NCBI_taxonomy_id":"210"}}}},"ARO_accession":"3007052","ARO_id":"45612","ARO_name":"Helicobacter pylori gyrA conferring resistance to fluoroquinolones","CARD_short_name":"Hpyl_gyrA_FLO","ARO_description":"Point mutations in the quinolone resistance-determining regions of Helicobacter pylori observed to confer resistance to fluoroquinolone antibiotics.","ARO_category":{"39876":{"category_aro_accession":"3003292","category_aro_cvterm_id":"39876","category_aro_name":"fluoroquinolone resistant gyrA","category_aro_description":"DNA gyrase is responsible for DNA supercoiling and consists of two alpha and two beta subunits. GyrA point mutations confer resistance by preventing fluoroquinolone antibiotics from binding the alpha-subunit.","category_aro_class_name":"AMR Gene Family"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5753":{"model_id":"5753","model_name":"Helicobacter pylori gyrB conferring resistance to fluoroquinolones","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"40438":{"param_type":"co-dependent single resistance variant","param_description":"A set of nucleotide or amino acid substitutions in different genes that are all required to confer resistance to an antibiotic drug or drug class, encoded as: [cvterm_id gene 1],[SNP 1],[SNP 2],etc+[cvterm_id gene 2],[SNP 1],[SNP 2],etc. For example: 39879,A90V,M94V+40052,D472H. A nucleotide substitution resulting in a change from an amino acid codon to a stop codon is encoded as [wild type amino acid][position][Ter], for example Q42Ter.","param_type_id":"40438","param_value":{"12373":"45612,N87K+45613,F438S","12374":"45612,N87K,V199A+45613,D481E,R484K","12375":"45612,N87K,V199I+45613,D484K","12377":"45612,D91N+45613,D481E,D484K","12379":"45612,D91N,A129T+45613,S479G","12380":"45612,A129T+45613,S479G","12381":"45612,D91N+45613,R484K","12382":"45612,N87Y+45613,R484K","13239":"45612,D91G,V199I+45613,D481E","12376":"45612,D91N,V199I+45613,D481E,D484K"}},"snp":{"Curated-R":{"12373":"N87I","12374":"N87I","12375":"N87I","12377":"N87I","12378":"E463K","12379":"E463K","12380":"E463K","12381":"E463K","12382":"E463K","13239":"E463K","12376":"E463K"},"param_value":{"12378":"E463K"},"clinical":{"12378":"E463K"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1200"}},"model_sequences":{"sequence":{"8313":{"protein_sequence":{"accession":"WP_001182024.1","sequence":"MQNYQSHSIKVLKGLEGVRKRPGMYIGDTNVGGLHHMVYEVVDNAVDESMAGFCDTINITLTDEGSCIVEDNGRGIPVDIHPTEKIPACTVVLTILHAGGKFDNDTYKVSGGLHGVGVSVVNALSKRLIMTIKKEGQIYRQEFEKGIPTSELEIIGKTKSAKESGTTIEFFPDESVMEVVEFQAGILQKRFKEMAYLNDGLKISFKEEKTQLQETYFYEDGLKQFVKDSAKKELLTPIISFKSMDEETRTSIEVALAYADDYNENTLSFVNNIKTSEGGTHEAGFKMGLSKAILQYIGNNIKTKESRPISEDIKEGLIAVVSLKMSEPLFEGQTKSKLGSSYARALVSKLVYDKIHQFLEENPNEAKIIANKALLAAKAREASKKARELTRKKDNLSVGTLPGKLADCQSKDPLESEIFLVEGDSAGGSAKQGRDRVFQAILPLKGKILNVEKSHLSKILKSEEIKNMITAFGCGIQESFDIERLRYHKIIIMTDADVDGSHIQTLLMTFFYRYLRPLIEQGHVYIAQAPLYKYKKGKTEIYLKDSVALDHFLIEHGINSVDIEGIGKNDLMNLLKVARHYRYALLELEKRYNLLEILRFLIETKDALSLDMKVLEKSILEKLEGLNYQILRSFATEESLHLHTQTPKGLVEFNLDDNLFKEVLFEEANYTYQKLMEYNLDFLENKDILAFLEEVENHAKKGANIQRYKGLGEMNPNDLWETTMHKENRSLIKLKIEDLEKTDAVFSLCMGDEVEPRRAFIQAHAKDVKQLDV"},"dna_sequence":{"accession":"NC_000915.1","fmin":"527685","fmax":"530007","strand":"+","sequence":"ATGCAAAATTACCAGAGCCATAGTATTAAGGTTTTAAAAGGCTTAGAGGGGGTTAGGAAACGCCCTGGAATGTATATTGGTGATACCAATGTGGGTGGGTTGCACCACATGGTGTATGAAGTCGTGGATAACGCTGTAGATGAGAGCATGGCGGGTTTTTGCGATACGATTAATATCACTTTGACCGATGAGGGTTCATGCATCGTAGAAGATAACGGGCGAGGCATTCCTGTAGATATTCACCCCACGGAAAAAATCCCCGCTTGCACCGTGGTTTTAACGATTTTGCATGCGGGGGGCAAGTTTGATAACGATACTTATAAAGTTTCAGGCGGTTTGCATGGCGTGGGCGTTTCGGTTGTGAACGCTTTGAGCAAACGCTTGATTATGACCATTAAAAAAGAGGGTCAAATTTATCGCCAAGAGTTTGAAAAGGGTATTCCTACTAGCGAGCTTGAAATCATTGGCAAAACCAAAAGCGCTAAAGAAAGCGGCACGACTATTGAATTTTTCCCTGATGAAAGCGTGATGGAAGTCGTTGAATTTCAAGCGGGTATTTTACAAAAACGCTTTAAAGAAATGGCGTATCTTAACGATGGCTTAAAAATTTCTTTCAAAGAAGAAAAAACCCAACTGCAAGAGACTTATTTCTATGAAGACGGCTTGAAACAATTCGTTAAAGACAGCGCTAAAAAAGAATTGCTCACCCCCATTATTTCGTTTAAAAGCATGGATGAAGAAACGCGCACTTCTATAGAAGTCGCTCTAGCGTATGCTGATGATTATAATGAAAACACTTTAAGCTTTGTGAATAACATTAAAACTTCTGAAGGTGGCACGCATGAGGCGGGCTTTAAAATGGGCTTGTCTAAAGCAATTTTGCAATATATTGGCAATAATATTAAAACCAAAGAGTCACGCCCCATCTCTGAAGATATTAAAGAGGGGTTGATCGCTGTTGTGAGCTTGAAAATGAGCGAGCCTTTGTTTGAAGGGCAGACTAAATCCAAACTCGGCAGTTCGTATGCGCGCGCGTTGGTTTCAAAATTAGTCTATGATAAAATCCATCAATTTTTAGAAGAAAACCCTAACGAAGCCAAAATCATTGCCAATAAAGCCCTACTAGCTGCAAAAGCCAGAGAAGCCAGTAAGAAAGCCAGAGAGCTTACAAGGAAAAAAGATAATTTGAGTGTCGGCACTTTGCCTGGAAAATTAGCCGATTGCCAGAGTAAAGACCCCTTAGAGAGTGAAATCTTTTTAGTGGAGGGCGATAGTGCGGGCGGGAGCGCTAAACAAGGGCGCGATAGGGTTTTCCAAGCGATCTTGCCCCTAAAAGGTAAGATTTTAAATGTGGAAAAAAGCCATTTATCAAAAATCCTAAAATCAGAAGAAATTAAAAACATGATCACGGCTTTTGGGTGCGGCATTCAAGAGAGTTTTGATATAGAAAGATTGCGCTATCATAAAATCATTATCATGACCGATGCTGATGTGGATGGGAGCCATATCCAAACCTTGCTGATGACTTTTTTCTATCGTTATTTGCGCCCGCTGATTGAACAAGGGCATGTTTATATCGCTCAAGCCCCTCTTTACAAATACAAGAAGGGCAAGACAGAAATTTATCTTAAAGACAGCGTCGCTTTGGATCATTTTTTAATTGAGCATGGCATCAATTCGGTGGATATTGAAGGGATTGGCAAGAACGATTTGATGAACTTGTTAAAAGTGGCACGCCATTACCGCTATGCGCTTTTGGAATTAGAAAAACGCTACAATTTGCTAGAAATTTTACGCTTTCTCATTGAAACTAAGGACGCCTTAAGCCTTGATATGAAAGTTTTAGAAAAAAGCATTTTAGAAAAATTAGAGGGCTTGAATTATCAGATCTTACGCTCTTTTGCCACTGAAGAAAGCTTACATTTGCACACGCAAACCCCTAAAGGCTTGGTGGAATTTAACCTAGATGACAATCTCTTTAAAGAAGTGTTGTTTGAAGAAGCGAATTACACTTACCAAAAGCTTATGGAGTATAATTTAGACTTCTTAGAAAATAAGGATATTTTGGCGTTTTTAGAAGAAGTGGAAAATCACGCTAAAAAGGGAGCGAATATCCAGCGCTATAAGGGGCTAGGCGAGATGAACCCTAATGATTTGTGGGAAACGACCATGCATAAAGAAAACCGCAGCTTGATCAAACTCAAAATTGAAGATTTAGAAAAAACCGATGCAGTCTTTTCGCTTTGCATGGGCGATGAAGTAGAGCCTAGAAGAGCCTTTATCCAAGCGCATGCTAAAGATGTGAAACAACTAGATGTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36906","NCBI_taxonomy_name":"Helicobacter pylori","NCBI_taxonomy_id":"210"}}}},"ARO_accession":"3007053","ARO_id":"45613","ARO_name":"Helicobacter pylori gyrB conferring resistance to fluoroquinolones","CARD_short_name":"Hpyl_gyrB_FLO","ARO_description":"Point mutations in Helicobacter pylori conferring resistance to fluoroquinolone antibiotics.","ARO_category":{"37244":{"category_aro_accession":"3000864","category_aro_cvterm_id":"37244","category_aro_name":"fluoroquinolone resistant gyrB","category_aro_description":"Point mutations in DNA gyrase subunit B (gyrB) observed in Mycobacterium tuberculosis can result in resistance to fluoroquinolones.","category_aro_class_name":"AMR Gene Family"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5779":{"model_id":"5779","model_name":"nimD","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"150"}},"model_sequences":{"sequence":{"8454":{"protein_sequence":{"accession":"CAA54273.1","sequence":"MFREMPRKRQLLPTEESVAILERMTNGTLALHGDDGYPYAVPVSYVYADGKIYFHSAMQGPKVDAILRNDKVSFCVVEQDEVKPAEFTTYFRSVIVFGKARILTDENEKRNALNLLADKYSHGEAGMEAEMAKGFNHLLMIEITVEQMTGKEAIELTRGRNGCS"},"dna_sequence":{"accession":"X76949.1","fmin":"1548","fmax":"2043","strand":"+","sequence":"ATGTTTAGAGAAATGCCGCGTAAGCGGCAATTGTTGCCAACAGAAGAAAGCGTTGCCATTCTTGAACGGATGACAAACGGGACGTTGGCTCTTCATGGGGATGACGGCTATCCGTATGCCGTCCCTGTCAGTTATGTATATGCCGATGGCAAAATTTACTTCCACAGTGCCATGCAAGGGCCAAAAGTGGATGCCATCCTGCGGAATGACAAGGTCTCGTTCTGCGTAGTGGAGCAGGATGAGGTCAAGCCGGCCGAGTTTACCACCTATTTTCGGAGCGTGATAGTCTTTGGCAAGGCCCGCATACTGACCGACGAGAACGAAAAACGAAATGCCTTAAACCTGCTGGCCGACAAGTATTCGCATGGCGAAGCGGGCATGGAGGCTGAAATGGCCAAAGGGTTCAATCATTTGCTGATGATAGAAATCACAGTAGAGCAGATGACCGGAAAAGAAGCCATCGAACTGACAAGGGGAAGAAACGGATGTTCTTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35916","NCBI_taxonomy_name":"Bacteroides fragilis","NCBI_taxonomy_id":"817"}}}},"ARO_accession":"3007106","ARO_id":"45674","ARO_name":"nimD","CARD_short_name":"nimD","ARO_description":"nimD is a nitroimidazole reductase mainly found in Bacteroides fragilis that is associated with the deactivation of nitroimidazole antibiotics such as metronidazole. Minimum inhibitory concentrations observed in isolates vary greatly depending on species, strain, and nitroimidazole treatment.","ARO_category":{"45671":{"category_aro_accession":"3007103","category_aro_cvterm_id":"45671","category_aro_name":"nitroimidazole reductase","category_aro_description":"Nitroimidazole reductases are a group of enzymes that deactivate nitroimidazole antibiotics by reducing their nitro functional group to an amino group. These enzymes are associated with resistance to nitroimidazole derivatives in Bacteroides fragilis but have also been reported in a variety of anaerobic Gram-negative and Gram-positive genera. The minimum inhibitory concentrations for these enzymes vary greatly depending on species, strain, and precise nitroimidazole treatment used.","category_aro_class_name":"AMR Gene Family"},"37033":{"category_aro_accession":"3000689","category_aro_cvterm_id":"37033","category_aro_name":"metronidazole","category_aro_description":"Metronidazole is a nitroimidazole that is active against anaerobic bacteria and protozoa. It is not effective against aerobic bacteria. Nitroimidazoles act by oxidizing DNA causing strand breaks and cell death.","category_aro_class_name":"Antibiotic"},"41239":{"category_aro_accession":"3004115","category_aro_cvterm_id":"41239","category_aro_name":"nitroimidazole antibiotic","category_aro_description":"Nitroimidazoles are a group of drugs that have both antiprotozoal and antibacterial activity, classified with respect to the location of the nitro functional group.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5756":{"model_id":"5756","model_name":"Helicobacter pylori pbp3 conferring resistance to amoxicillin","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"12384":"A499V","12387":"D2N","12388":"A50S","12389":"F490Y","12390":"A541T","12385":"E536K","12987":"V374L"},"Curated-R":{"12384":"A499V","12387":"D2N","12388":"A50S","12389":"F490Y","12390":"A541T","12385":"E536K","12987":"V374L"},"clinical":{"12384":"A499V","12387":"D2N","12388":"A50S","12389":"F490Y","12390":"A541T","12385":"E536K","12987":"V374L"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"8371":{"protein_sequence":{"accession":"EJC52487.1","sequence":"MDNKNIDPNFNPERFLETQKYKGSITALIFLLLFFIFLMVAFKKAFFAQANMPNLVMSKQDTAARGTIYSQDNYSLAASQTLFKLGFDTRFLNPDKEDFFIDFLSIYSNIPKKSLKDAINTKGYIILAYDLTPNMAANIRDLNKKFLAFGVFQNFKDAHDKVWQKQGLNIEVSGVSRHYPYQNSLEPIIGYVQKQEEDKLTLTTGKKGVEKSQDHLLKAQQNGIRTGKRDVSFNFIQNHSYTEVERLDGYEVYLSIPLKLQREIETLLDKTKDKLKAKEILVGIINPKSGEILSLASSKRFNPNAIKTSDYESLNLSVAEKVFEPGSTIKPIVYSLLLDKNLINPKERIDLNHGYYQLGKYTIKDDFIPSKKAVVEDILIQSSNVGMIKISKNLNPEDFYNGLLGYGFSQKTGIDLSLEATGKIPPLSAFKREVLKGSVSYGYGLNATFLQLLRAYAVFSNEGKLTTPYLVQRETAPNGDIYIPSPKPTFQVISPKSARKMKETLIKVVRYGTGKNAQFEGLYIGGKTGTARVAKNGSYSAESYNSSFFGFAEDERQVFTIGVVILGSHGKEEYYASKIAAPIFKEITEILVRYNYLSPSIAIQNVLEKNRFKIK"},"dna_sequence":{"accession":"AKPU01000002.1","fmin":"217824","fmax":"219672","strand":"-","sequence":"ATGGATAATAAAAACATTGATCCCAACTTCAACCCAGAACGATTTTTAGAAACCCAAAAATACAAGGGCTCTATTACGGCTTTAATCTTTTTATTGCTTTTTTTTATTTTTTTAATGGTGGCTTTTAAAAAAGCTTTTTTTGCCCAAGCCAACATGCCTAATCTAGTGATGAGCAAACAAGACACTGCGGCTAGGGGGACTATCTATAGTCAAGACAACTACAGCCTAGCCGCTTCGCAAACCCTTTTCAAACTGGGCTTTGATACAAGGTTTTTAAACCCGGATAAAGAAGATTTTTTCATTGATTTCCTTTCTATTTATAGCAATATCCCTAAAAAGTCCTTAAAAGACGCCATCAATACGAAAGGCTATATTATTCTAGCCTATGATCTCACGCCCAATATGGCCGCTAACATTAGAGACTTGAATAAGAAATTTTTAGCCTTTGGGGTTTTTCAAAATTTCAAAGACGCGCACGATAAGGTGTGGCAAAAGCAAGGGCTAAACATTGAAGTGAGCGGCGTTTCCAGGCATTACCCTTATCAAAATAGCCTAGAGCCAATCATTGGCTATGTGCAAAAACAAGAAGAAGACAAGCTCACTTTAACTACCGGTAAAAAAGGCGTTGAAAAATCTCAAGATCACTTGCTTAAAGCCCAACAAAATGGCATAAGAACAGGCAAAAGAGATGTGAGTTTTAATTTTATTCAAAACCACTCTTACACAGAGGTTGAGCGCCTTGATGGCTATGAGGTGTATTTGAGCATTCCTTTAAAACTCCAAAGAGAAATTGAAACCCTATTGGATAAAACCAAAGACAAACTCAAGGCTAAAGAAATCCTAGTGGGTATCATTAACCCTAAAAGCGGGGAAATCTTATCGCTAGCTTCAAGCAAGCGCTTCAATCCTAACGCCATTAAAACCAGCGATTATGAAAGCTTGAATTTGAGCGTTGCCGAAAAGGTTTTTGAGCCAGGCAGCACGATCAAACCCATTGTTTATTCCTTGCTGTTAGACAAGAATTTGATCAACCCTAAAGAACGCATTGATTTAAACCATGGCTATTACCAATTAGGAAAATACACCATTAAAGACGACTTTATCCCTAGTAAAAAAGCCGTTGTGGAAGATATTTTGATCCAATCTAGCAATGTGGGCATGATAAAAATCAGCAAAAATCTCAACCCGGAGGATTTCTATAATGGGCTTTTAGGCTATGGATTTTCTCAAAAAACCGGCATTGATTTATCCTTAGAAGCCACAGGAAAGATCCCTCCTTTGTCCGCTTTCAAGCGTGAAGTGTTAAAGGGGAGCGTCTCTTATGGCTATGGGCTGAACGCGACTTTTTTGCAGCTTTTAAGGGCTTATGCGGTGTTTTCTAATGAAGGCAAATTGACTACCCCCTATTTAGTGCAACGAGAGACCGCCCCTAATGGCGATATTTACATCCCTAGCCCCAAACCCACTTTTCAAGTCATTAGCCCCAAAAGCGCCAGGAAAATGAAAGAAACCTTAATCAAAGTGGTGCGTTATGGCACAGGCAAAAACGCTCAATTTGAAGGGTTATACATAGGGGGCAAAACAGGCACGGCTAGGGTTGCTAAAAACGGGAGTTACAGCGCGGAATCCTACAACAGCTCTTTTTTTGGGTTCGCTGAAGATGAAAGGCAGGTTTTTACTATCGGCGTGGTTATCTTAGGCTCGCACGGCAAGGAAGAATATTATGCTAGCAAGATTGCAGCCCCTATTTTTAAAGAAATCACCGAAATTTTAGTGCGTTACAATTACCTATCGCCCTCTATTGCGATTCAAAACGTGCTCGAGAAAAACCGCTTTAAGATAAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"45618","NCBI_taxonomy_name":"Helicobacter pylori Hp P-30","NCBI_taxonomy_id":"992087"}}}},"ARO_accession":"3007057","ARO_id":"45617","ARO_name":"Helicobacter pylori pbp3 conferring resistance to amoxicillin","CARD_short_name":"Hpyl_pbp3_AMX","ARO_description":"Point mutations in Helicobacter pylori pbp3 observed to confer resistance to amoxicillin.","ARO_category":{"40661":{"category_aro_accession":"3003938","category_aro_cvterm_id":"40661","category_aro_name":"Penicillin-binding protein mutations conferring resistance to beta-lactam antibiotics","category_aro_description":"Mutations in PBP transpeptidases that change the affinity for penicillin thereby conferring resistance to penicillin antibiotics.","category_aro_class_name":"AMR Gene Family"},"35981":{"category_aro_accession":"0000064","category_aro_cvterm_id":"35981","category_aro_name":"amoxicillin","category_aro_description":"Amoxicillin is a moderate-spectrum, bacteriolytic, beta-lactam antibiotic used to treat bacterial infections caused by susceptible microorganisms. A derivative of penicillin, it has a wider range of treatment but remains relatively ineffective against Gram-negative bacteria. It is commonly taken with clavulanic acid, a beta-lactamase inhibitor. Like other beta-lactams, amoxicillin interferes with the synthesis of peptidoglycan.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5757":{"model_id":"5757","model_name":"Helicobacter pylori pbp2 mutants conferring resistance to amoxicillin","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"12413":"A296V","12414":"S494H","12415":"A541M","12416":"E572G","12417":"I259T"},"Curated-R":{"12413":"A296V","12414":"S494H","12415":"A541M","12416":"E572G","12417":"I259T"},"clinical":{"12413":"A296V","12414":"S494H","12415":"A541M","12416":"E572G","12417":"I259T"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"8370":{"protein_sequence":{"accession":"AAK17127.1","sequence":"MKNLRYKLLLFVFIGFWGLLVLNLFILSVKNQEYYEKLAERNMTKKEFLVPTRGDITDRNDEFLATNELVFGVFLPSRLKQKELLEKIEIIQKFFPNFSKETLLNNYQKENSLYNHNLIKVVGFIPYIAMQPLYAKLIQTQGIFALPLDKRYYPNNALASHVLGYVGVASLQDLKDDEENQYSQIVGKTGIEKEYNKLLQGKVGYKIMRVNALNQELATLEVVPPSTNNHLQLSLDKRLQKEADKLFENKRGAILVMNAENGELLVAGSYPEYNLNDFVGGISQDKWQKLQDDIYNPLLNRFANALYPPGSVVKMGVGLSFLENLHITENTTIPTPPFIEVGKRKFRDWKKTGHGNSNLYKAIRESVDVYFYKFGLEISIEKLSKTLREVGFGEKTGVDLPNEFVGIVPDNLWKLKRFNQDWRVGDTLITAIGQGSFLATPLQVLAYTGLIATGKLATPHFAINNKQPLKDPLNSFQKKKLQALRVGMYEVCNHKDGTAYHSTRGSKVTLACKTGTAQVVEIAQNIVNRMKEKDMEYFHRSHAWITAFLPYEKPKYAITILVEHGEGGSKLGGLLVKMSNKLYELGYL"},"dna_sequence":{"accession":"AF315504.1","fmin":"116","fmax":"1883","strand":"+","sequence":"ATGAAAAATCTTCGCTATAAGCTTTTGCTCTTTGTTTTTATAGGGTTTTGGGGGTTATTGGTTTTAAATTTATTTATTTTAAGCGTTAAAAATCAAGAATACTATGAAAAATTGGCCGAACGCAACATGACCAAAAAGGAATTTCTAGTCCCTACAAGGGGCGATATTACAGACAGAAATGATGAGTTTTTAGCCACTAACGAATTGGTGTTTGGCGTGTTTTTGCCTAGTAGACTGAAACAAAAAGAACTTTTGGAAAAAATTGAAATCATCCAAAAGTTTTTCCCTAACTTTTCCAAAGAAACGCTTTTAAACAATTACCAAAAAGAAAATTCGCTTTATAACCACAACCTCATTAAAGTGGTGGGATTCATTCCTTATATCGCCATGCAACCTCTTTATGCCAAACTCATCCAAACTCAAGGCATTTTTGCTCTTCCCTTAGACAAGCGCTACTACCCTAATAACGCTTTAGCTTCACATGTTTTAGGCTATGTGGGGGTGGCAAGCTTGCAAGATCTAAAAGACGATGAAGAAAATCAATACAGCCAGATTGTAGGCAAAACCGGCATTGAAAAAGAATATAACAAGCTTTTACAAGGCAAGGTGGGCTATAAAATCATGCGTGTCAATGCACTCAATCAAGAATTAGCCACTTTAGAAGTAGTGCCGCCAAGCACCAACAACCACTTGCAATTGAGTTTAGACAAACGCTTGCAAAAAGAAGCGGACAAGCTCTTTGAAAATAAGAGAGGGGCTATTTTAGTGATGAACGCAGAAAATGGGGAATTGCTCGTTGCAGGAAGTTACCCTGAATACAATTTGAACGATTTTGTAGGCGGGATCAGTCAAGACAAATGGCAAAAACTTCAAGATGATATTTATAACCCCTTATTAAACCGCTTCGCTAACGCTTTGTATCCGCCGGGATCTGTGGTTAAAATGGGCGTGGGCTTGAGCTTTTTAGAAAACCTTCATATCACAGAAAACACCACCATACCCACCCCGCCTTTTATTGAAGTGGGCAAGCGCAAATTCAGGGACTGGAAAAAAACAGGGCATGGCAATTCTAATTTGTATAAAGCGATTAGGGAGTCCGTGGATGTGTATTTTTATAAGTTTGGGCTTGAAATCTCTATAGAAAAACTCTCTAAAACCTTAAGAGAAGTGGGCTTTGGGGAAAAAACAGGCGTTGATTTGCCGAATGAATTTGTGGGGATTGTGCCGGATAATTTGTGGAAACTCAAACGATTCAATCAAGATTGGCGCGTTGGGGACACGCTCATTACTGCTATTGGGCAAGGCTCTTTTTTAGCCACGCCCTTACAAGTGCTAGCCTATACGGGACTCATTGCGACAGGCAAACTGGCAACGCCTCATTTTGCTATCAATAATAAACAGCCGCTCAAAGACCCCCTGAATAGTTTTCAAAAAAAGAAGCTCCAAGCCTTGCGCGTGGGCATGTATGAAGTGTGTAACCATAAAGACGGCACCGCTTATCATTCCACAAGGGGTTCTAAGGTTACTTTAGCGTGTAAAACCGGCACCGCGCAAGTCGTGGAAATCGCTCAAAACATCGTCAATCGCATGAAAGAAAAGGATATGGAGTATTTCCATCGATCCCATGCGTGGATTACCGCATTTTTGCCTTATGAAAAACCCAAATACGCTATCACTATTTTAGTAGAACATGGGGAAGGGGGGTCAAAACTAGGGGGCTTGTTAGTGAAAATGAGCAATAAACTCTATGAGCTTGGCTATCTTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36906","NCBI_taxonomy_name":"Helicobacter pylori","NCBI_taxonomy_id":"210"}}}},"ARO_accession":"3007058","ARO_id":"45619","ARO_name":"Helicobacter pylori pbp2 mutants conferring resistance to amoxicillin","CARD_short_name":"Hpyl_pbp2_AMX","ARO_description":"Point mutations in Helicobacter pylori pbp2 observed to confer resistance to amoxicillin.","ARO_category":{"40661":{"category_aro_accession":"3003938","category_aro_cvterm_id":"40661","category_aro_name":"Penicillin-binding protein mutations conferring resistance to beta-lactam antibiotics","category_aro_description":"Mutations in PBP transpeptidases that change the affinity for penicillin thereby conferring resistance to penicillin antibiotics.","category_aro_class_name":"AMR Gene Family"},"35981":{"category_aro_accession":"0000064","category_aro_cvterm_id":"35981","category_aro_name":"amoxicillin","category_aro_description":"Amoxicillin is a moderate-spectrum, bacteriolytic, beta-lactam antibiotic used to treat bacterial infections caused by susceptible microorganisms. A derivative of penicillin, it has a wider range of treatment but remains relatively ineffective against Gram-negative bacteria. It is commonly taken with clavulanic acid, a beta-lactamase inhibitor. Like other beta-lactams, amoxicillin interferes with the synthesis of peptidoglycan.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5758":{"model_id":"5758","model_name":"Helicobacter pylori pbp1 mutants conferring resistance to amoxicillin","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"40394":{"param_type":"nonsense mutation","param_description":"A sequence change where, compared to a reference sequence, one codon is replaced by a termination codon through a nucleotide substitution. These are described as a substitution of the wildtype codon to a termination codon. Format is given as [wild type AA][position][Ter], for example Q42Ter where Q42 is a wildtype amino acid replaced by a premature termination codon.","param_type_id":"40394","param_value":{"12510":"L610Ter"}},"snp":{"Curated-R":{"12510":"I259T","12418":"T556S","12419":"N562Y","12420":"T593A","12421":"S414R","12422":"G595S","12426":"S405N","12427":"A474T","12428":"T558S","12429":"N562H","12430":"S402G","12432":"N107R","12433":"A201V","12434":"V250I","12435":"S543T","12511":"V374L","12512":"S414N","12513":"I450V","12552":"T593S","12553":"T593G","12554":"T593K","13113":"R649K","13114":"R656P","13115":"R656H","12425":"F366L","18538":"F366L","18539":"F366L","18542":"F366L","18541":"F366L","18540":"F366L"},"param_value":{"12418":"T556S","12419":"N562Y","12420":"T593A","12421":"S414R","12422":"G595S","12426":"S405N","12427":"A474T","12428":"T558S","12429":"N562H","12430":"S402G","12432":"N107R","12433":"A201V","12434":"V250I","12435":"S543T","12511":"V374L","12512":"S414N","12513":"I450V","12552":"T593S","12553":"T593G","12554":"T593K","13113":"R649K","13114":"R656P","13115":"R656H","12425":"F366L"},"clinical":{"12418":"T556S","12419":"N562Y","12420":"T593A","12421":"S414R","12422":"G595S","12426":"S405N","12427":"A474T","12428":"T558S","12429":"N562H","12430":"S402G","12432":"N107R","12433":"A201V","12434":"V250I","12435":"S543T","12511":"V374L","12512":"S414N","12513":"I450V","12552":"T593S","12553":"T593G","12554":"T593K","13113":"R649K","13114":"R656P","13115":"R656H","12425":"F366L"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1300"},"41344":{"param_type":"insertion mutation from peptide sequence","param_description":"A peptide sequence change between the translation initiation (start) and termination (stop) codon where, compared to the reference sequence, one or more amino acids are inserted. These represent in-frame insertions which do not result in frameshift variants and where the insertion is not a duplication of a sequence immediately N-terminal (5'), and are denoted with wildtype flanking residues. Format is given by [wildtype AA position]_[wildtype AA position]ins[AA sequence], e.g. K464_D465insE or P46_A47insYS.","param_type_id":"41344","param_value":{"18538":"K464_D465insE","18539":"K464_D465insN","18542":"G595_V596insA","18541":"G595_V596insS","18540":"G595_V596insG"}}},"model_sequences":{"sequence":{"8369":{"protein_sequence":{"accession":"AAK17126.1","sequence":"MLKKIFYGFIVLFLIIVGLLAILIAQVWVTTDKDIAKIKDYRPGVASQILDRKGRLIANIYDKEFRFYARFEEIPPRFIESLLAVEDTLFFEHGGINLDAIMRAMIKNAKSGRYTEGGSTLTQQLVKNMVLTREKTLTRKLKEAIISIRIEKVLSKEEILERYLNQTFFGHGYYGVKTASLGYFKKPLDKLTLKEIAMLVALPRAPSFYDPTKNLEFSLSRANDILRRLYSLGWISSNELKSALNEVPIVYNQTSTQNIAPYVVDEVLKQLDQLDGLKTQGYIIKLTIDLDYQRLALESLRFGHQKILEKIAKEKPKTNASNEDEDNLNASMIVTDTSTGKILALVGGIDYKKSAFNRATQAKRQFGSAIKPFVYQIAFDNGYSTTSKIPDTARNFENGNYSKNSKQNHAWHPSNYSRKFLGLVTLQEALSHSLNLATINLSDQLGFEKIYQSLSDMGFKNLPKDLSIVLGSFAISPIEAAEKYSLFSNYGTMLKPMLIESITNQQNDVKTFTPMETKKITSKEQAFLTISVLMNAVENGTGSLAHIKGLEVAGKTGTSNNNIDAWFIGFTPTLQSVIWFGRDDNTPISKGATGGVVSAPVYSYFMRNILSIEPSLKRKFDVPKGLRKEIVDKIPYYSTPNSITPTPKRTDDSEERLLF"},"dna_sequence":{"accession":"AF315503.1","fmin":"77","fmax":"2057","strand":"+","sequence":"ATGCTAAAAAAGATTTTTTATGGTTTTATCGTTTTATTTTTGATTATCGTAGGGTTGTTAGCCATTCTTATCGCTCAAGTTTGGGTAACTACGGATAAGGATATTGCTAAAATTAAAGATTATCGCCCGGGCGTCGCTTCACAGATTTTAGACCGAAAAGGGCGTTTGATCGCTAATATCTATGATAAGGAATTTCGTTTTTATGCGCGTTTTGAAGAAATCCCCCCACGATTTATTGAAAGCCTTTTAGCGGTAGAAGACACCCTCTTTTTTGAACATGGGGGGATCAATTTAGACGCTATCATGCGCGCTATGATTAAAAACGCTAAAAGCGGTCGTTACACCGAGGGGGGTAGCACCCTAACCCAACAACTCGTTAAAAACATGGTGCTCACACGAGAAAAAACCCTAACCAGAAAACTCAAAGAAGCTATCATTTCCATACGCATTGAAAAAGTCTTAAGCAAAGAAGAAATTTTAGAGCGCTATTTGAACCAAACTTTTTTTGGGCATGGGTATTATGGCGTGAAAACCGCAAGTTTAGGGTATTTTAAAAAACCCCTTGACAAACTCACGCTTAAAGAAATCGCCATGTTAGTCGCCTTGCCTAGGGCTCCGAGTTTTTATGATCCTACCAAAAATTTAGAATTTTCACTTTCTAGGGCTAATGATATTTTAAGGCGGTTGTATTCTTTAGGCTGGATTTCTTCTAACGAGCTCAAATCCGCTCTCAATGAAGTGCCAATCGTCTATAACCAAACTTCCACGCAAAATATCGCTCCCTATGTCGTGGATGAAGTATTGAAGCAATTGGATCAATTAGACGGGTTAAAAACTCAAGGCTATATTATAAAGCTCACGATAGATTTGGATTACCAACGCTTAGCGTTAGAGTCCTTGCGTTTTGGGCATCAAAAAATCTTAGAAAAAATCGCTAAAGAAAAGCCAAAAACTAACGCGTCTAATGAAGATGAAGACAACTTGAACGCTAGCATGATAGTTACAGACACGAGCACCGGTAAGATTTTAGCTTTAGTGGGAGGGATTGATTATAAAAAAAGCGCTTTCAATCGCGCCACGCAAGCCAAACGGCAATTTGGGAGCGCGATCAAGCCTTTTGTGTATCAAATCGCTTTTGATAATGGCTATTCCACGACTTCTAAAATCCCTGATACCGCGCGAAACTTTGAAAATGGCAATTATAGTAAAAACAGCAAACAAAACCATGCATGGCACCCCAGCAATTATTCTCGCAAGTTTTTAGGGCTTGTAACCTTGCAAGAAGCTTTGAGCCATTCATTAAATCTAGCCACGATCAATTTAAGCGATCAGCTTGGCTTTGAAAAAATTTATCAATCTTTAAGCGATATGGGGTTTAAAAACCTCCCTAAAGACTTGTCTATTGTGTTAGGGAGCTTTGCTATCTCACCCATTGAAGCGGCTGAAAAGTATTCTTTATTTTCTAATTACGGCACTATGCTCAAACCCATGCTCATTGAAAGCATCACTAACCAACAAAACGATGTCAAAACTTTCACGCCTATGGAAACCAAAAAGATCACCTCCAAAGAACAGGCTTTTTTAACCATTTCAGTGCTGATGAATGCGGTAGAAAACGGCACAGGGAGTTTGGCTCACATTAAAGGTTTAGAAGTCGCCGGTAAAACCGGAACTTCTAACAACAATATTGACGCTTGGTTCATTGGCTTTACCCCCACCTTGCAAAGCGTGATCTGGTTTGGGAGGGACGATAACACGCCTATTAGCAAAGGAGCGACAGGAGGCGTTGTGAGCGCGCCTGTGTATTCGTATTTCATGCGTAATATTCTAAGCATTGAACCTTCTTTAAAAAGAAAGTTTGATGTCCCCAAAGGCTTGCGTAAAGAAATTGTGGATAAAATCCCCTACTATTCAACCCCCAATTCCATCACCCCCACCCCCAAAAGAACAGACGATAGCGAAGAACGCTTGTTGTTCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36906","NCBI_taxonomy_name":"Helicobacter pylori","NCBI_taxonomy_id":"210"}}}},"ARO_accession":"3007060","ARO_id":"45621","ARO_name":"Helicobacter pylori pbp1 mutants conferring resistance to amoxicillin","CARD_short_name":"Hpyl_pbp1_AMX","ARO_description":"Point mutations in Helicobacter pylori pbp1 observed to confer resistance to amoxicillin.","ARO_category":{"40661":{"category_aro_accession":"3003938","category_aro_cvterm_id":"40661","category_aro_name":"Penicillin-binding protein mutations conferring resistance to beta-lactam antibiotics","category_aro_description":"Mutations in PBP transpeptidases that change the affinity for penicillin thereby conferring resistance to penicillin antibiotics.","category_aro_class_name":"AMR Gene Family"},"35981":{"category_aro_accession":"0000064","category_aro_cvterm_id":"35981","category_aro_name":"amoxicillin","category_aro_description":"Amoxicillin is a moderate-spectrum, bacteriolytic, beta-lactam antibiotic used to treat bacterial infections caused by susceptible microorganisms. A derivative of penicillin, it has a wider range of treatment but remains relatively ineffective against Gram-negative bacteria. It is commonly taken with clavulanic acid, a beta-lactamase inhibitor. Like other beta-lactams, amoxicillin interferes with the synthesis of peptidoglycan.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5759":{"model_id":"5759","model_name":"Helicobacter pylori frxA mutation conferring resistance to metronidazole","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"40394":{"param_type":"nonsense mutation","param_description":"A sequence change where, compared to a reference sequence, one codon is replaced by a termination codon through a nucleotide substitution. These are described as a substitution of the wildtype codon to a termination codon. Format is given as [wild type AA][position][Ter], for example Q42Ter where Q42 is a wildtype amino acid replaced by a premature termination codon.","param_type_id":"40394","param_value":{"12437":"R86Ter","12455":"L39Ter","12462":"K105Ter","12463":"M149Ter","12464":"A192Ter","12461":"E199Ter"}},"snp":{"Curated-R":{"12437":"F366L","12455":"F366L","12462":"F366L","12463":"F366L","12464":"F366L","12439":"R3T","12451":"P41L","12452":"A15V","12468":"A16T","12469":"A32V","12470":"A85V","12471":"I44F","12472":"I117M","12473":"M126F","12474":"S43A","12475":"V7I","12476":"Y62D","12501":"A48G","12502":"G441A","12503":"C13A","12507":"A70G","12508":"K97E","12509":"V9I","12461":"V9I","12445":"V9I"},"param_value":{"12439":"R3T","12451":"P41L","12452":"A15V","12468":"A16T","12469":"A32V","12470":"A85V","12471":"I44F","12472":"I117M","12473":"M126F","12474":"S43A","12475":"V7I","12476":"Y62D","12501":"A48G","12502":"G441A","12503":"C13A","12507":"A70G","12508":"K97E","12509":"V9I"},"clinical":{"12439":"R3T","12451":"P41L","12452":"A15V","12468":"A16T","12469":"A32V","12470":"A85V","12471":"I44F","12472":"I117M","12473":"M126F","12474":"S43A","12475":"V7I","12476":"Y62D","12501":"A48G","12502":"G441A","12503":"C13A","12507":"A70G","12508":"K97E","12509":"V9I"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"420"},"40494":{"param_type":"frameshift mutation","param_description":"A frameshift is a sequence change between the translation initiation (start) and termination (stop) codon where, compared to a reference sequence, translation shifts to another reading frame as caused by nucleotide insertions and deletions. In ARO, these are annotated at the protein level with the first changed most N-terminal wildtype amino acid position. Format is given as [wildtype AA][position]fs, e.g. S531fs where S531 is a frameshifted coordinate beginning with codon 531. Termination may also be denoted as: Ter[position]fs.","param_type_id":"40494","param_value":{"12445":"R106fs"}}},"model_sequences":{"sequence":{"8317":{"protein_sequence":{"accession":"AAD07703.1","sequence":"MDREQVVALQHQRFAAKKYDPNRRISQKDWEALVEVGRLAPSSIGLEPWKMLLLKNERMKEDLKPMAWGALFGLEGASHFVIYLARKGVTYDSDYVKKVMHEVKKRDYDTNSRFAQIIKNFQENDMKLNSERSLFDWASKQTYIQMANMMMAAAMLGIDSCPIEGYDQEKVEAYLEEKGYLNTAEFGVSVMACFGYRNQEITPKTRWKTEVIYEVIE"},"dna_sequence":{"accession":"AE000511.1","fmin":"687927","fmax":"688581","strand":"+","sequence":"ATGGACAGAGAACAAGTGGTTGCTTTACAGCACCAACGATTTGCTGCAAAAAAATACGATCCTAATCGTCGTATTTCCCAAAAGGATTGGGAAGCTTTGGTTGAAGTGGGGAGATTAGCCCCTTCTTCAATCGGGCTTGAACCATGGAAAATGCTTTTATTGAAAAATGAACGCATGAAAGAAGATTTAAAACCGATGGCCTGGGGGGCGCTTTTTGGTTTGGAGGGAGCGAGCCATTTTGTCATTTATCTTGCGCGAAAAGGCGTTACTTATGACAGCGATTACGTTAAAAAAGTGATGCATGAGGTTAAAAAAAGGGATTATGACACTAATTCTAGGTTCGCTCAAATCATCAAAAATTTCCAAGAGAACGATATGAAACTCAATAGCGAACGATCTTTGTTTGATTGGGCTAGCAAGCAGACTTATATCCAAATGGCGAACATGATGATGGCAGCGGCCATGTTAGGGATTGATTCTTGCCCGATTGAAGGGTATGATCAAGAAAAAGTGGAGGCTTATTTAGAGGAAAAAGGCTATCTGAACACGGCGGAATTTGGCGTGTCGGTAATGGCTTGTTTTGGTTATCGTAACCAAGAAATCACCCCTAAAACCCGCTGGAAGACAGAAGTTATTTATGAAGTGATTGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36758","NCBI_taxonomy_name":"Helicobacter pylori 26695","NCBI_taxonomy_id":"85962"}}}},"ARO_accession":"3007059","ARO_id":"45620","ARO_name":"Helicobacter pylori frxA mutation conferring resistance to metronidazole","CARD_short_name":"Hpyl_fxrA_MTZ","ARO_description":"FrxA encodes an NADH-flavin oxidoreductase in Helicobacter pylori. Mutations in this gene confer resistance to nitrofuran antibiotics and metronidazole.","ARO_category":{"45616":{"category_aro_accession":"3007056","category_aro_cvterm_id":"45616","category_aro_name":"Antibiotic resistant Helicobacter pylori nitroreductase","category_aro_description":"Inactivation of the oxygen-insensitive NADPH nitroreductases in Helicobacter pylori play a role in metronidazole resistance.","category_aro_class_name":"AMR Gene Family"},"37033":{"category_aro_accession":"3000689","category_aro_cvterm_id":"37033","category_aro_name":"metronidazole","category_aro_description":"Metronidazole is a nitroimidazole that is active against anaerobic bacteria and protozoa. It is not effective against aerobic bacteria. Nitroimidazoles act by oxidizing DNA causing strand breaks and cell death.","category_aro_class_name":"Antibiotic"},"41239":{"category_aro_accession":"3004115","category_aro_cvterm_id":"41239","category_aro_name":"nitroimidazole antibiotic","category_aro_description":"Nitroimidazoles are a group of drugs that have both antiprotozoal and antibacterial activity, classified with respect to the location of the nitro functional group.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5761":{"model_id":"5761","model_name":"VAM-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"425"}},"model_sequences":{"sequence":{"8320":{"protein_sequence":{"accession":"QTJ60982.1","sequence":"MNFLIKNILLITLFVPFVTAANNTDTKTLEVKQLTDNIYQHISYKHVEPWGFIGASGLIVVDGDAAYLIDTPWTTKATNQLIEWIEDRGLVLKSAIVTHFHEDASGDLPLLNDLKVNTYATSLTNQLLKLNNKEISNTEISSNELKIFNGIATVYYPGPGHTEDNIVVWLPNEKLLFGGCFVKSLRNKSLGYTGDANIGEWSNSIQRVLQRYPDIVTVVPGHGQVGDVSLLLHTQKLASSDKTSDK"},"dna_sequence":{"accession":"MW827739.1","fmin":"0","fmax":"741","strand":"+","sequence":"ATGAATTTTCTGATAAAAAATATTCTGCTCATTACTCTTTTTGTTCCTTTTGTAACAGCAGCAAACAATACAGACACTAAAACGCTGGAGGTTAAACAATTAACCGATAATATCTATCAGCATATCTCATATAAACATGTTGAGCCTTGGGGGTTTATTGGCGCGTCTGGCTTAATTGTAGTCGATGGAGATGCGGCATACCTGATTGACACTCCTTGGACGACCAAAGCAACCAATCAACTTATTGAATGGATTGAAGATAGAGGTCTCGTACTAAAAAGCGCAATAGTAACTCACTTTCATGAAGATGCGAGTGGTGATTTACCACTTTTAAATGATTTAAAAGTTAACACTTATGCCACTTCACTCACTAATCAACTTCTTAAACTCAATAACAAAGAAATTTCGAATACTGAAATATCGAGCAATGAACTCAAAATTTTCAACGGCATTGCGACAGTGTATTATCCTGGCCCAGGCCATACTGAAGATAACATCGTTGTTTGGTTACCGAATGAAAAGCTATTATTTGGCGGTTGCTTTGTTAAAAGCCTCCGTAATAAAAGTCTAGGTTACACTGGAGATGCAAATATAGGCGAATGGTCGAACTCTATTCAAAGAGTGCTGCAACGCTATCCAGATATAGTCACTGTAGTGCCTGGGCATGGTCAGGTTGGAGACGTTAGTTTACTCCTTCATACACAAAAATTAGCATCATCCGATAAGACTTCTGACAAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43205","NCBI_taxonomy_name":"Vibrio alginolyticus","NCBI_taxonomy_id":"663"}}}},"ARO_accession":"3007062","ARO_id":"45623","ARO_name":"VAM-1","CARD_short_name":"VAM-1","ARO_description":"VAM-1 is a subclass B1 metallo-beta-lactamase, conferring resistance to beta-lactam antibiotics such as carbapenems and cephalosporins.","ARO_category":{"45626":{"category_aro_accession":"3007065","category_aro_cvterm_id":"45626","category_aro_name":"VAM beta-lactamase","category_aro_description":"VAM beta-lactamases are class B1 beta-lactamases found in Vibrio alginolyticus.","category_aro_class_name":"AMR Gene Family"},"35979":{"category_aro_accession":"0000062","category_aro_cvterm_id":"35979","category_aro_name":"ceftriaxone","category_aro_description":"Ceftriaxone is a third-generation cephalosporin antibiotic. The presence of an aminothiazolyl sidechain increases ceftriazone's resistance to beta-lactamases. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"36989":{"category_aro_accession":"3000645","category_aro_cvterm_id":"36989","category_aro_name":"cefotaxime","category_aro_description":"Cefotaxime is a semisynthetic cephalosporin taken parenterally. It is resistant to most beta-lactamases and active against Gram-negative rods and cocci due to its aminothiazoyl and methoximino functional groups.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5762":{"model_id":"5762","model_name":"Erm(50)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8322":{"protein_sequence":{"accession":"BBJ25230.1","sequence":"MPTYRPNKGRHENGQNYLVNEATIRRIVDLVPVNASVPVIEIGPGHGALTFPLQDRVLAAGGSLTAVEIDPASVRWLEKRLRPEVHLYEQDVLDFVLPDGPHVLVGNLPFHLTTAILRHVLHSPGWTHAVLLVQWEVARRRAGVGGATMMTAQWWPWVDFEQYGRVPSTHFRPRPTVDAGVLVIRRREEPLVDWSERARYASFVHDVFTGKGRGVADIVSRVVGRRRARRCAQVLREAGVPAHALPKQLDAGQWATLFTAVGC"},"dna_sequence":{"accession":"LC473083.1","fmin":"20056","fmax":"20848","strand":"-","sequence":"ATGCCTACCTACAGGCCGAACAAGGGCCGTCACGAGAACGGCCAGAACTACCTCGTCAATGAGGCGACGATCAGACGGATCGTCGACCTCGTCCCCGTCAACGCCTCCGTCCCGGTCATCGAGATCGGCCCGGGACACGGGGCGCTGACCTTTCCCCTTCAGGATCGTGTCTTGGCTGCCGGTGGATCGTTGACCGCCGTCGAGATCGACCCGGCCTCTGTCCGGTGGTTGGAGAAGCGGCTGCGCCCGGAGGTCCACCTGTACGAGCAGGATGTCCTTGATTTTGTGCTTCCGGACGGCCCGCACGTCCTGGTGGGGAACCTGCCGTTCCACCTGACCACCGCGATCCTGCGGCACGTCCTTCACTCACCGGGGTGGACCCACGCGGTGCTCCTGGTGCAGTGGGAGGTCGCGCGCCGCCGCGCCGGTGTCGGTGGTGCCACGATGATGACTGCCCAGTGGTGGCCGTGGGTCGACTTCGAACAGTACGGGCGGGTGCCGTCCACGCATTTCCGTCCCCGCCCCACCGTCGACGCCGGTGTCCTGGTGATACGTCGCCGGGAGGAACCTCTCGTGGACTGGTCGGAGCGTGCGCGGTACGCGTCCTTCGTCCATGACGTGTTCACCGGCAAGGGCCGTGGCGTCGCCGACATCGTGTCCCGGGTTGTGGGGCGTCGGCGTGCGCGACGGTGTGCCCAGGTCTTGCGTGAGGCCGGTGTTCCGGCACACGCACTGCCGAAACAGTTGGACGCGGGGCAGTGGGCCACACTGTTTACGGCCGTGGGGTGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40344","NCBI_taxonomy_name":"Cutibacterium acnes","NCBI_taxonomy_id":"1747"}}}},"ARO_accession":"3007032","ARO_id":"45591","ARO_name":"Erm(50)","CARD_short_name":"Erm(50)","ARO_description":"Erm(50) is an Erm ribosomal RNA methyltransferase.","ARO_category":{"36699":{"category_aro_accession":"3000560","category_aro_cvterm_id":"36699","category_aro_name":"Erm 23S ribosomal RNA methyltransferase","category_aro_description":"Erm proteins are part of the RNA methyltransferase family and methylate A2058 (E. coli nomenclature) of the 23S ribosomal RNA conferring degrees of resistance to Macrolides, Lincosamides and Streptogramin b. This is called the MLSb phenotype.","category_aro_class_name":"AMR Gene Family"},"35946":{"category_aro_accession":"0000027","category_aro_cvterm_id":"35946","category_aro_name":"roxithromycin","category_aro_description":"Roxithromycin is a semi-synthetic, 14-carbon ring macrolide antibiotic derived from erythromycin. It is used to treat respiratory tract, urinary and soft tissue infections. Roxithromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35982":{"category_aro_accession":"0000065","category_aro_cvterm_id":"35982","category_aro_name":"clarithromycin","category_aro_description":"Clarithromycin is a methyl derivative of erythromycin, sharing the 14-carbon macrolide ring. The antibiotic binds to the 50S subunit of the ribosome and is used to treat pharyngitis, tonsillitis, acute maxillary sinusitis, acute bacterial exacerbation of chronic bronchitis, pneumonia (especially atypical pneumonias associated with Chlamydia pneumoniae or TWAR), and skin structure infections.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"4069":{"model_id":"4069","model_name":"OXA-647","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"6442":{"protein_sequence":{"accession":"WP_140423315.1","sequence":"MKILILLPLLSCLGLTACSLPVSSLPSPSTSTQAIASLFDQAQSSGVLVIQRDQQVQVYGNDLNRANTEYVPASTFKMLNALIGLQHGKATTNEIFKWDGKKRSFTAWEKDMTLGQAMQASAVPVYQELARRIGLELMQQEVQRIQFGNQQIGQQVDNFWLVGPLKVTPKQEVQFVSALAREQLAFDPQVQQQVKAMLFLQERKAYRLYVKSGWGMDVEPQVGWLTGWVETPQAEIVAFSLNMQMQNGIDPAIRLEILQQALAELGLYPKDEG"},"dna_sequence":{"accession":"NG_065433.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGAAAATTTTGATTTTGCTGCCTTTACTTAGTTGCTTGGGCCTGACAGCATGTAGCCTACCCGTTTCATCTCTCCCATCTCCAAGCACTTCGACTCAAGCGATTGCCAGCTTATTTGATCAGGCGCAAAGCTCTGGTGTTTTAGTGATTCAGCGTGATCAACAAGTACAGGTCTATGGCAATGATTTAAATCGTGCAAATACCGAATATGTTCCCGCCTCTACTTTTAAAATGCTCAATGCTCTGATTGGCCTGCAACATGGCAAAGCCACAACCAATGAAATTTTTAAATGGGATGGCAAGAAACGCAGCTTTACCGCCTGGGAAAAAGACATGACTCTCGGCCAAGCCATGCAAGCTTCTGCGGTACCGGTCTATCAAGAACTGGCGCGTCGTATTGGTCTGGAATTAATGCAACAGGAAGTACAACGCATCCAATTTGGTAATCAGCAGATTGGTCAACAGGTCGATAACTTCTGGTTGGTAGGCCCTTTGAAAGTTACTCCAAAACAGGAAGTCCAATTTGTTTCTGCGTTGGCCCGAGAGCAACTGGCCTTTGATCCTCAAGTCCAGCAACAAGTCAAAGCCATGTTATTTTTACAGGAGCGGAAAGCTTATCGACTATATGTCAAATCCGGTTGGGGCATGGATGTGGAACCGCAAGTCGGCTGGCTCACCGGCTGGGTTGAAACACCGCAGGCTGAAATCGTGGCATTTTCACTCAATATGCAGATGCAAAATGGTATAGATCCGGCGATCCGCCTTGAAATTTTGCAGCAGGCTTTGGCCGAATTAGGGCTTTATCCAAAAGATGAAGGATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36948","NCBI_taxonomy_name":"Acinetobacter lwoffii","NCBI_taxonomy_id":"28090"}}}},"ARO_accession":"3005337","ARO_id":"43696","ARO_name":"OXA-647","CARD_short_name":"OXA-647","ARO_description":"OXA-647 is a beta-lactamase in the OXA-134 family of OXA beta-lactamases that confers resistance to ampicillin and cephalothin.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46489":{"category_aro_accession":"3007700","category_aro_cvterm_id":"46489","category_aro_name":"OXA-134-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-134.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5750":{"model_id":"5750","model_name":"Helicobacter pylori rpoB mutation conferring resistance to rifampicin","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"12306":"L525P","12307":"Q527K","12308":"Q527R","12309":"D530V","12310":"S545L","12311":"I586N","12313":"D530G","12314":"D530I","12315":"D530Y","12316":"D530L","12317":"D530F","12318":"H540Y","12319":"H540N","12320":"L525I","12321":"D530N","12322":"D530E","12323":"I2619V","12325":"T2537A","12326":"F2538L","12327":"I837V","12331":"A2414T","12332":"K2068R","12336":"V149F","12337":"V149Q","12338":"V149K","12339":"V149E","12340":"V149D","12341":"V149W","12342":"R701H","12383":"A2414V","12312":"I586L","12324":"V2592L","12333":"Q2079K"},"Curated-R":{"12306":"L525P","12307":"Q527K","12308":"Q527R","12309":"D530V","12310":"S545L","12311":"I586N","12313":"D530G","12314":"D530I","12315":"D530Y","12316":"D530L","12317":"D530F","12318":"H540Y","12319":"H540N","12320":"L525I","12321":"D530N","12322":"D530E","12323":"I2619V","12325":"T2537A","12326":"F2538L","12327":"I837V","12331":"A2414T","12332":"K2068R","12336":"V149F","12337":"V149Q","12338":"V149K","12339":"V149E","12340":"V149D","12341":"V149W","12342":"R701H","12383":"A2414V","12897":"A2414V","12312":"I586L","12324":"V2592L","12333":"Q2079K"},"clinical":{"12306":"L525P","12307":"Q527K","12308":"Q527R","12309":"D530V","12310":"S545L","12311":"I586N","12313":"D530G","12314":"D530I","12315":"D530Y","12316":"D530L","12317":"D530F","12318":"H540Y","12319":"H540N","12320":"L525I","12321":"D530N","12322":"D530E","12323":"I2619V","12325":"T2537A","12326":"F2538L","12327":"I837V","12331":"A2414T","12332":"K2068R","12336":"V149F","12337":"V149Q","12338":"V149K","12339":"V149E","12340":"V149D","12341":"V149W","12342":"R701H","12383":"A2414V","12312":"I586L","12324":"V2592L","12333":"Q2079K"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"3000"},"40330":{"param_type":"multiple resistance variants","param_description":"A set of nucleotide or amino acid substitutions that are all required to confer resistance to an antibiotic drug or drug class, encoded as: [wild-type 1][position 1][mutation 1],[wild-type 2][position 2][mutation 2], etc. For example, D63Y,T142K.","param_type_id":"40330","param_value":{"12897":"V148I,V149F"}}},"model_sequences":{"sequence":{"8304":{"protein_sequence":{"accession":"AAD08242.1","sequence":"MSKKIPLKNRLRADFTKTPTDLEVPNLLLLQRDSYDSFLYSKEGKESGIEKVFKSIFPIQDEHNRITLEYAGCEFGKSKYTVREAMERGITYSIPLKIKVRLILWEKDTKSGEKNGIKDIKEQSIFIREIPLMTERTSFIINGVERVVVNQLHRSPGVIFKEEESSTSLNKLIYTGQIIPDRGSWLYFEYDSKDVLYARINKRRKVPVTILFRAMDYQKQDIIKMFYPLVKVRYENDKYLIPFASLDANQRMEFDLKDPQGKVILLAGKKLTSRKIKELKENHLEWVEYPMDILLNRHLAEPVMVGKEVLLDMLTQLDKNKLEKIHDLGVQEFVIINDLALGHDASIIQSFSADSESLKLLKQTEKIDDENALAAIRIHKVMKPGDPVTTEVAKQFVKKLFFDPERYDLTMVGRMKMNHKLGLHVPDYITTLTHEDIITTVKYLMKIKNNQGKIDDRDHLGNRRIRAVGELLANELHSGLVKMQKTIKDKLTTMSGAFDSLMPHDLVNSKMITSTIMEFFMGGQLSQFMDQTNPLSEVTHKRRLSALGEGGLVKDRVGFEARDVHPTHYGRICPIETPEGQNIGLINTLSTFTRVNDLGFIEAPYKKVVDGKVVGETIYLTAIQEDSHIIAPASTPIDEEGNILGDLIETRVEGEIVLNEKSKVTLMDLSSSMLVGVAASLIPFLEHDDANRALMGTNMQRQAVPLLRSDAPIVGTGIEKIIARDSWGAIKANRAGVVEKIDSKNIYILGESKEEAYIDAYSLQKNLRTNQNTSFNQVPIVKVGDKVGAGQIIADGPSMDRGELALGKNVRVAFMPWNGYNFEDAIVVSECITKDDIFTSTHIYEKEVDARELKHGVEEFTADIPDVKEEALAHLDESGIVKVGTYVSAGMILVGKTSPKGEIKSTPEERLLRAIFGDKAGHVVNKSLYCPPSLEGTVIDVKVFTKKGYEKDARVLSAYEEEKAKLDMEHFDRLTMLNREELLRVSSLLSQAILEEPFSHNGKDYKEGDQIPKEEIASINRFTLASLVKKYSKEVQNHYEITKNNFLEQKKVLGEEHEEKLSILEKDDILPNGVIKKVKLYIATKRKLKVGDKMAGRHGNKGIVSNIVPVADMPYTADGEPVDIVLNPLGVPSRMNIGQILEMHLGLVGKEFGKQIARMLEDKTKDFAKELRAKMLEIANAINEKDPLTIHALENCSDEELLEYAKDWSKGVKMAIPVFEGISQEKFYKLFELAKIAMDGKMDLYDGRTGEKMRERVNVGYMYMIKLHHLVDEKVHARSTGPYSLVTHQPVGGKALFGGQRFGEMEVWALEAYGAAHTLKEMLTIKSDDIRGRENAYRAIAKGEQVGESEIPETFYVLTKELQSLALDINIFGDDVDEDGAPKPIVIKEDDRPKDFSSFQLTLASPEKIHSWSYGEVKKPETINYRTLKPERDGLFCMKIFGPTKDYECLCGKYKKPRFKDIGTCEKCGVAITHSKVRRFRMGHIELATPVAHIWYVNSLPSRIGTLLGVKMKDLERVLYYEAYIVKEPGEAAYDNEGTKLVMKYDILNEEQYQNISRRYEDRGFVAQMGGEAIKDLLEEIDLITLLQSLKEEVKDTNSDAKKKKLIKRLKVVESFLNSGNRPEWMMLTVLPVLPPDLRPLVALDGGKFAVSDVNELYRRVINRNQRLKRLMELGAPEIIVRNEKRMLQEAVDVLFDNGRSTNAVKGANKRPLKSLSEIIKGKQGRFRQNLLGKRVDFSGRSVIVVGPNLKMDECGLPKNMALELFKPHLLSKLEERGYATTLKQAKRMIEQKSNEVWECLQEITEGYPVLLNRAPTLHKQSIQAFHPKLIDGKAIQLHPLVCSAFNADFDGDQMAVHVPLSQEAIAECKVLMLSSMNILLPASGKAVAIPSQDMVLGLYYLSLEKSGVKGEHKLFSSVNEIITAIDTKELDIHAKIRVLDQGNIIATSAGRMIIKSILPDFIPTDLWNRPMKKKDIGVLVDYVHKVGGIGITATFLDNLKTLGFRYATKAGISISMEDIITPKDKQKMVEKAKVEVKKIQQQYDQGLLTDQERYNKIIDTWTEVNDKMSKEMMTAIAQDKEGFNSIYMMADSGARGSAAQIRQLSAMRGLMTKPDGSIIETPIISNFKEGLNVLEYFNSTHGARKGLADTALKTANAGYLTRKLIDVSQNVKVVSDDCGTHEGIEITDIAVGSELIEPLEERIFGRVLLEDVIDPITNEILLYADTLIDEEGAKKVVEAGIKSITIRTPVTCKAPKGVCAKCYGLNLGEGKMSYPGEAVGVVAAQSIGEPGTQLTLRTFHVGGTASRSQDEREIVASKEGFVRFYNLRTYTNKEGKNIIANRRNASILVVEPKIKAPFDGELRIETVYEEVVVSVKNGDQEAKFVLRRSDIVKPSELAGVGGKIEGKVYLPYASGHKVHKGGSIADIIQEGWNVPNRIPYASELLVKDNDPIAQDVYAKEKGVIKYYVLEANHLERTHGIKKGDMVSEKGLFAVIADDNGREAARHYIARGSEILIDDNSEVSTNSVISKPTTNTFKTIATWDPYNTPIIADFKGKVGFVDVIAGVTVAEKEDENTGITSLVVNDYIPSGYKPSLFLEGANGEEMRYFLEPKTSIAISDGSSVEQAEVLAKIPKATVKSRDITGGLPRVSELFEARKPKPKDVAILSEVDGIVSFGKPIRNKEHIIVTSKDGRSMDYFVDKGKQILVHADEFVHAGEAMTDGVISSHDILRISGEKELYKYIVSEVQQVYRRQGVSIADKHIEIIVSQMLRQVRILDSGDSKFIEGDLVSKKLFKEENARVIALKGEPAIAEPVLLGITRAAIGSDSIISAASFQETTKVLTEASIAMKKDFLEDLKENVVLGRMIPVGTGMYKNKKIVLRALEDNSKF"},"dna_sequence":{"accession":"AE000511.1","fmin":"1268376","fmax":"1277049","strand":"-","sequence":"ATGTCAAAAAAAATTCCCCTAAAAAACCGCTTGAGAGCTGATTTTACAAAAACCCCAACAGATTTAGAAGTCCCTAATTTATTATTATTACAACGAGACAGCTATGATTCTTTCTTGTATTCTAAAGAGGGTAAAGAGAGCGGGATTGAAAAGGTTTTTAAATCCATTTTCCCTATCCAAGATGAGCATAACCGCATCACTTTAGAATACGCGGGTTGCGAATTTGGCAAGTCTAAATACACCGTTAGAGAAGCGATGGAGAGGGGCATTACCTACTCTATCCCTCTCAAAATTAAGGTGCGCTTGATCTTGTGGGAAAAAGATACCAAGAGTGGCGAAAAGAACGGCATTAAGGATATTAAAGAACAAAGCATTTTCATTCGTGAGATCCCTTTGATGACAGAACGCACTTCATTTATTATTAATGGGGTGGAGCGCGTGGTGGTCAATCAACTCCACAGAAGCCCCGGTGTGATTTTCAAAGAAGAAGAGTCTAGCACTTCTTTAAACAAGCTCATTTACACAGGGCAAATCATTCCTGATAGGGGTTCGTGGTTGTATTTTGAATACGATTCTAAAGATGTTTTATACGCTCGTATCAATAAACGCCGTAAAGTGCCTGTTACCATTTTATTCAGGGCGATGGATTATCAAAAACAAGACATCATCAAAATGTTCTACCCGCTTGTTAAAGTGCGTTATGAAAACGATAAATATTTGATCCCGTTTGCTTCATTAGACGCCAATCAAAGAATGGAATTTGACTTGAAAGATCCTCAAGGCAAGGTTATTCTTTTAGCGGGTAAAAAGCTCACTTCAAGAAAGATTAAAGAGCTTAAAGAAAACCATTTAGAATGGGTGGAATACCCTATGGATATTTTACTCAATCGCCATTTAGCTGAGCCTGTTATGGTAGGGAAAGAAGTCTTATTGGACATGCTCACTCAGCTAGATAAAAACAAATTAGAAAAAATCCACGATTTAGGCGTGCAAGAATTTGTGATCATCAACGATCTGGCGTTAGGGCATGACGCTTCCATTATCCAATCTTTTTCAGCCGATTCTGAGTCTTTGAAATTACTCAAGCAAACCGAAAAAATTGATGATGAAAACGCTCTAGCGGCGATTCGTATCCATAAGGTTATGAAACCAGGCGATCCCGTTACGACTGAAGTGGCTAAGCAGTTTGTCAAAAAACTTTTCTTTGATCCAGAACGCTATGATTTGACCATGGTGGGCCGCATGAAAATGAATCACAAGTTAGGCTTGCATGTGCCTGATTACATTACGACTTTAACGCATGAAGATATTATCACCACCGTTAAATACCTCATGAAGATCAAAAACAATCAAGGCAAGATTGATGACAGGGACCACTTGGGCAATCGTAGGATTAGGGCGGTAGGGGAATTGTTGGCCAATGAATTGCATTCAGGTTTAGTGAAAATGCAAAAGACCATTAAAGACAAGCTCACTACCATGAGCGGGGCTTTTGATTCGCTCATGCCCCATGACTTGGTCAATTCTAAAATGATCACAAGCACCATCATGGAATTTTTCATGGGCGGTCAGCTCTCGCAATTTATGGATCAAACGAATCCCTTGAGTGAGGTTACGCACAAGCGCCGCCTTTCAGCGCTCGGCGAAGGGGGGTTGGTGAAAGACAGAGTGGGGTTTGAAGCCAGGGATGTGCACCCCACGCATTATGGCCGAATTTGTCCCATTGAGACCCCAGAAGGTCAAAATATCGGTCTGATCAACACCCTTTCCACTTTCACAAGAGTGAATGATTTAGGCTTTATTGAAGCCCCTTATAAAAAGGTTGTGGATGGCAAGGTCGTGGGTGAGACGATTTATTTGACCGCTATTCAAGAAGACAGCCACATCATCGCTCCCGCAAGCACCCCCATTGATGAAGAGGGGAATATTTTGGGCGATTTGATTGAAACGCGCGTGGAAGGCGAGATCGTTTTAAACGAAAAAAGCAAAGTAACCTTAATGGATTTAAGCTCTAGCATGCTAGTGGGGGTAGCCGCATCGCTCATTCCTTTCTTAGAGCATGATGACGCCAACCGTGCCTTAATGGGGACTAACATGCAGCGCCAAGCGGTGCCCTTATTAAGAAGCGACGCTCCCATTGTAGGCACGGGGATTGAAAAAATTATTGCTAGGGATTCTTGGGGAGCGATCAAAGCCAATCGCGCAGGCGTTGTAGAAAAAATTGATTCTAAAAATATTTATATTTTAGGCGAAAGCAAAGAAGAAGCCTATATTGATGCGTATTCTTTGCAAAAAAACTTGCGCACCAACCAAAACACCAGTTTCAATCAAGTCCCTATCGTTAAAGTGGGCGATAAAGTGGGAGCCGGGCAAATCATCGCTGATGGCCCTAGCATGGATAGAGGCGAGTTGGCGTTAGGGAAAAATGTGCGCGTGGCGTTCATGCCTTGGAATGGCTATAACTTTGAAGACGCGATCGTGGTGAGTGAGTGCATCACTAAAGATGATATTTTCACTTCCACCCACATTTATGAAAAAGAAGTGGATGCTAGGGAGCTTAAGCATGGTGTGGAAGAATTTACCGCTGATATTCCTGATGTGAAAGAAGAAGCGCTCGCTCATCTTGATGAAAGCGGGATCGTTAAAGTCGGTACTTATGTGAGCGCTGGCATGATTTTGGTGGGCAAAACTTCTCCTAAAGGCGAGATTAAAAGCACGCCTGAAGAGCGGCTTTTAAGGGCTATTTTTGGGGATAAAGCCGGGCATGTGGTCAATAAGAGTTTGTATTGCCCTCCCAGTTTGGAAGGCACGGTGATTGATGTGAAAGTCTTCACTAAAAAAGGCTATGAGAAAGACGCGCGAGTTTTGAGCGCGTATGAAGAAGAAAAAGCCAAGCTTGATATGGAGCATTTTGATCGCTTGACCATGCTCAATAGAGAAGAATTGTTGCGCGTTAGCTCGCTCCTTTCTCAAGCGATTTTAGAAGAGCCTTTCAGCCATAACGGCAAGGATTATAAAGAAGGCGATCAAATCCCTAAAGAAGAAATCGCTTCAATCAACCGCTTCACTTTGGCTAGTTTGGTCAAAAAGTATTCTAAAGAAGTGCAAAACCACTATGAAATCACTAAAAACAATTTCTTAGAGCAAAAGAAAGTTTTGGGCGAAGAGCATGAAGAAAAGCTTTCTATTTTAGAAAAAGATGATATTTTGCCTAATGGCGTGATCAAAAAAGTCAAGCTCTATATCGCTACAAAACGAAAGCTTAAAGTGGGCGATAAAATGGCAGGAAGGCATGGGAATAAAGGGATTGTGTCTAATATCGTGCCGGTTGCGGATATGCCTTATACCGCTGATGGCGAGCCTGTAGATATTGTTTTAAACCCTTTAGGCGTGCCAAGCCGCATGAATATCGGGCAGATTTTAGAAATGCATTTAGGCTTAGTGGGGAAAGAATTTGGGAAGCAAATCGCTCGCATGCTAGAGGATAAAACCAAAGATTTTGCCAAAGAATTGCGTGCTAAAATGCTAGAAATCGCTAACGCTATTAATGAAAAAGACCCCTTGACAATCCATGCGCTTGAGAATTGTTCTGATGAAGAGCTTTTGGAATACGCAAAAGATTGGAGCAAGGGCGTTAAGATGGCTATCCCTGTGTTTGAAGGCATCTCGCAAGAAAAATTTTATAAGCTATTTGAATTAGCTAAGATCGCTATGGATGGCAAAATGGATCTGTATGACGGACGCACAGGCGAGAAAATGAGGGAGCGCGTGAATGTGGGCTACATGTATATGATCAAACTCCACCATTTAGTGGATGAAAAAGTCCATGCCAGAAGCACAGGCCCTTATAGCTTAGTAACGCACCAGCCCGTGGGGGGTAAAGCGCTCTTTGGGGGTCAAAGGTTTGGGGAAATGGAAGTGTGGGCCTTGGAAGCTTATGGCGCAGCGCACACTCTAAAAGAAATGCTCACCATTAAATCCGATGATATTAGAGGCAGAGAGAACGCTTATAGGGCTATCGCTAAAGGTGAGCAAGTGGGCGAGAGTGAAATCCCTGAGACTTTCTATGTTTTGACTAAAGAATTGCAATCGCTCGCTTTGGATATTAATATTTTTGGGGACGATGTGGATGAGGATGGAGCACCTAAACCCATTGTCATTAAAGAAGATGACAGGCCTAAAGACTTTAGCTCTTTCCAGCTCACACTAGCTAGCCCTGAAAAAATCCATTCTTGGAGTTATGGGGAAGTTAAAAAGCCAGAAACGATCAATTATCGCACCCTAAAACCTGAACGAGACGGCTTGTTTTGCATGAAAATCTTTGGCCCCACTAAAGATTATGAATGCTTGTGCGGCAAATACAAAAAGCCTCGCTTCAAAGACATTGGCACATGCGAAAAATGCGGCGTGGCGATCACGCACTCCAAAGTCAGGCGTTTTAGAATGGGGCATATTGAATTGGCCACTCCTGTAGCGCATATCTGGTATGTTAATTCCTTGCCTAGCCGTATCGGCACGCTTTTAGGCGTTAAGATGAAAGACTTAGAGCGCGTGTTGTATTATGAAGCTTATATCGTTAAAGAACCAGGCGAAGCCGCTTATGACAATGAAGGCACTAAGCTTGTGATGAAATACGATATTTTGAATGAAGAGCAGTATCAAAATATCTCACGAAGATACGAAGACAGGGGCTTTGTAGCGCAAATGGGCGGTGAAGCGATCAAGGATTTGTTAGAAGAAATTGATTTGATCACCTTATTGCAGAGTTTGAAAGAAGAAGTGAAAGACACCAATTCTGATGCGAAAAAGAAAAAACTCATTAAGCGTTTGAAAGTGGTAGAAAGCTTTTTAAATTCTGGTAATAGGCCTGAATGGATGATGCTCACGGTTTTACCGGTATTGCCACCGGATTTAAGGCCTTTAGTCGCGCTAGATGGCGGGAAGTTTGCAGTCAGCGATGTGAATGAATTGTATCGTCGTGTCATCAATCGTAACCAACGCTTGAAACGCTTAATGGAGCTTGGAGCGCCAGAAATCATTGTGCGCAATGAAAAAAGGATGTTGCAAGAAGCCGTGGATGTGCTTTTTGATAACGGCCGCAGCACTAATGCGGTTAAAGGGGCTAACAAACGCCCTTTAAAATCGCTCAGTGAAATCATTAAAGGCAAGCAGGGGCGTTTCAGGCAAAACCTTTTAGGTAAGCGCGTGGATTTTTCAGGCAGAAGCGTGATTGTGGTTGGGCCTAATCTCAAAATGGATGAATGCGGGTTGCCTAAAAACATGGCGTTAGAACTCTTCAAACCGCATTTGTTATCCAAGCTTGAAGAGAGAGGCTATGCCACCACGCTCAAACAGGCTAAACGCATGATTGAGCAAAAAAGCAATGAAGTATGGGAGTGCTTGCAAGAAATCACAGAGGGGTATCCGGTGCTACTCAACCGCGCTCCTACCTTGCACAAGCAATCCATTCAAGCGTTCCATCCAAAGCTGATTGACGGCAAAGCGATCCAATTGCACCCGTTAGTGTGTTCAGCGTTCAACGCCGATTTTGACGGGGACCAAATGGCGGTGCATGTGCCTTTAAGCCAGGAAGCGATCGCTGAATGCAAGGTGCTGATGCTAAGCTCTATGAATATCCTTTTGCCTGCTAGCGGTAAGGCCGTAGCCATTCCTAGCCAAGATATGGTTTTAGGGCTTTATTATCTTTCTTTAGAAAAGAGCGGGGTCAAGGGCGAGCATAAGCTTTTTTCTAGCGTGAATGAAATCATCACCGCCATTGACACGAAAGAATTAGACATCCACGCAAAGATTAGGGTTTTAGATCAAGGGAATATTATCGCTACGAGTGCAGGGCGCATGATCATTAAGTCCATTTTGCCTGATTTTATCCCTACGGATTTGTGGAACAGACCCATGAAGAAAAAAGATATTGGCGTGCTTGTGGATTATGTGCATAAAGTTGGCGGTATCGGTATTACTGCAACCTTTTTGGATAATTTAAAAACGCTTGGCTTTAGGTATGCGACTAAGGCTGGTATTTCTATCTCTATGGAGGATATTATCACGCCAAAAGACAAGCAAAAAATGGTGGAAAAAGCCAAAGTAGAGGTTAAAAAAATCCAGCAACAATACGATCAAGGGCTGCTCACTGACCAAGAGCGTTACAATAAGATCATTGACACTTGGACTGAAGTCAATGACAAAATGAGTAAAGAAATGATGACCGCTATCGCGCAAGATAAAGAGGGCTTTAACTCTATTTATATGATGGCAGATAGCGGCGCAAGGGGTAGCGCGGCGCAAATCCGTCAGCTTTCAGCGATGAGGGGTCTTATGACAAAGCCGGACGGCAGTATCATTGAAACGCCCATTATTTCTAACTTTAAAGAGGGGTTGAATGTCTTAGAATACTTCAATTCCACGCATGGCGCTAGAAAGGGCTTAGCGGATACAGCGCTAAAAACAGCCAATGCGGGGTATTTGACCAGAAAGCTCATTGATGTTTCGCAAAATGTCAAGGTGGTGTCTGATGATTGCGGCACGCATGAAGGGATTGAAATCACGGATATTGCGGTGGGGAGTGAGCTGATTGAACCTTTAGAAGAGCGTATTTTTGGGCGCGTTTTATTAGAAGATGTGATCGATCCCATTACGAATGAAATCTTGCTTTATGCGGACACTTTGATTGATGAAGAGGGTGCTAAAAAGGTGGTTGAAGCCGGGATTAAATCCATTACGATCCGCACCCCAGTAACTTGTAAAGCGCCAAAGGGCGTGTGCGCGAAATGCTATGGCTTGAATTTGGGCGAAGGCAAGATGAGTTATCCGGGTGAAGCGGTGGGCGTGGTAGCCGCGCAATCTATTGGGGAGCCTGGAACGCAGCTCACTTTAAGGACTTTCCATGTGGGCGGGACAGCGAGCAGGAGTCAGGATGAGCGCGAAATCGTAGCGAGCAAAGAAGGTTTTGTGCGTTTTTACAACCTTAGGACTTACACGAATAAAGAGGGTAAAAACATTATCGCTAACCGCCGTAACGCTTCTATTTTAGTGGTAGAGCCTAAGATTAAAGCGCCTTTTGATGGGGAATTACGCATTGAAACGGTTTATGAAGAAGTCGTTGTGAGCGTGAAAAATGGCGATCAAGAAGCTAAATTTGTTTTAAGGAGAAGCGATATTGTCAAGCCAAGCGAATTAGCCGGCGTTGGCGGTAAGATTGAGGGGAAAGTGTATTTGCCTTATGCTAGTGGGCATAAGGTGCATAAGGGGGGAAGTATCGCTGATATTATCCAAGAGGGCTGGAATGTGCCTAATCGCATCCCTTATGCGAGCGAATTGCTAGTCAAGGATAATGACCCTATTGCGCAAGATGTGTATGCCAAAGAAAAAGGCGTAATCAAATACTATGTTTTAGAGGCTAACCATTTAGAGCGCACCCATGGGATCAAAAAGGGCGATATGGTGAGTGAAAAAGGCTTGTTTGCGGTGATAGCTGATGATAATGGTAGGGAAGCCGCTCGCCATTATATCGCTAGGGGTTCTGAGATCTTGATTGATGATAATAGTGAAGTGAGCACTAATAGCGTGATTTCTAAACCCACGACTAACACTTTCAAAACGATTGCCACATGGGATCCTTACAACACCCCTATCATTGCGGACTTTAAAGGTAAGGTGGGTTTTGTGGATGTTATCGCAGGGGTTACGGTCGCTGAAAAAGAAGACGAAAATACCGGTATCACAAGCTTAGTGGTGAATGATTACATTCCAAGCGGATACAAACCAAGCTTGTTTTTAGAGGGGGCTAATGGCGAAGAGATGCGTTATTTCCTAGAGCCAAAAACCTCTATCGCCATTAGCGATGGCTCTAGCGTGGAGCAAGCTGAAGTGTTAGCGAAAATCCCTAAAGCGACCGTTAAATCTAGGGATATTACCGGGGGTCTCCCAAGGGTTTCGGAACTCTTTGAAGCGAGAAAACCCAAGCCTAAAGATGTGGCGATCCTTTCTGAAGTTGATGGGATTGTGAGTTTTGGCAAACCCATTCGCAATAAAGAACACATCATCGTAACTTCTAAAGATGGCCGTTCCATGGATTATTTTGTGGATAAAGGCAAGCAAATTTTAGTGCATGCCGATGAATTTGTGCATGCGGGAGAAGCGATGACGGACGGAGTAATTTCAAGCCATGATATTTTAAGGATCAGTGGCGAAAAAGAGCTTTATAAATACATTGTGAGCGAAGTCCAGCAAGTGTATCGCAGGCAGGGGGTGAGCATTGCGGACAAGCACATTGAAATCATTGTTTCTCAAATGCTAAGACAGGTGCGTATTTTAGACAGCGGGGATAGCAAGTTTATTGAAGGGGATTTAGTCAGTAAAAAACTTTTCAAAGAAGAAAACGCTCGTGTGATCGCTTTAAAAGGCGAGCCAGCGATTGCTGAACCGGTGCTTTTAGGGATCACTAGAGCGGCTATTGGGAGCGATAGCATCATCTCAGCGGCCTCTTTCCAAGAAACGACTAAAGTTTTAACAGAAGCCAGTATCGCTATGAAAAAAGACTTTTTAGAGGATTTGAAAGAGAATGTGGTGTTGGGGAGGATGATCCCTGTGGGAACAGGCATGTATAAGAATAAAAAAATCGTGTTAAGAGCGCTTGAGGATAACTCTAAATTTTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36758","NCBI_taxonomy_name":"Helicobacter pylori 26695","NCBI_taxonomy_id":"85962"}}}},"ARO_accession":"3007051","ARO_id":"45610","ARO_name":"Helicobacter pylori rpoB mutation conferring resistance to rifampicin","CARD_short_name":"Hpyl_rpoB_RIF","ARO_description":"Rifampicin inhibits transcription by binding the beta subunit of RNA polymerase. Helicobacter pylori mutations associated with rifampicin resistance typically occur in the rifampicin resistance determining region of rpoB between codons 525 and 586.","ARO_category":{"36349":{"category_aro_accession":"3000210","category_aro_cvterm_id":"36349","category_aro_name":"rifamycin-resistant beta-subunit of RNA polymerase (rpoB)","category_aro_description":"Rifampin resistant RNA polymerases include amino acids substitutions which disrupt the affinity of rifampin for its binding site. These mutations are frequently concentrated in the rif I region of the beta-subunit and most often involve amino acids which make direct interactions with rifampin. However, mutations which also confer resistance can occur outside this region and may involve amino acids which do not directly make contact with rifampin.","category_aro_class_name":"AMR Gene Family"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5763":{"model_id":"5763","model_name":"Neisseria gonorrhoeae rpld","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"12558":"G70D"},"Curated-R":{"12558":"G70D"},"clinical":{"12558":"G70D"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"8334":{"protein_sequence":{"accession":"WP_003690088.1","sequence":"MELKVIDAKGQVSGSLSVSDALFAREYNEALVHQLVNAYLANARSGNRAQKTRAEVKHSTKKPWRQKGTGRARSGMTSSPLWRKGGRAFPNKPDENFTQKVNRKMYRAGMATILSQLARDERLFVIEALTAETPKTKVFAEQVKNLALEQVLFVTKRLDENVYLASRNLPNVLVLEAQQVDPYSLLRYKKVIITKDAVAQLEEQWV"},"dna_sequence":{"accession":"AE004969.1","fmin":"1805308","fmax":"1805929","strand":"-","sequence":"ATGGAATTGAAAGTAATTGACGCTAAAGGACAAGTTTCAGGCAGCCTGTCTGTTTCTGATGCTTTGTTCGCCCGCGAATACAATGAAGCGTTGGTTCACCAGCTGGTAAATGCCTACTTGGCAAACGCCCGCTCTGGTAACCGTGCTCAAAAAACCCGTGCCGAAGTAAAACACTCAACCAAAAAACCATGGCGTCAAAAAGGTACCGGCCGCGCCCGTTCCGGTATGACTTCTTCTCCGCTGTGGCGTAAAGGCGGTCGCGCGTTCCCGAACAAACCCGACGAAAACTTCACTCAAAAAGTAAACCGTAAAATGTACCGTGCCGGTATGGCGACTATCCTGTCCCAATTGGCGCGTGACGAGCGTTTGTTTGTGATTGAGGCGTTGACTGCCGAAACTCCCAAAACCAAAGTTTTTGCCGAACAAGTAAAAAATTTGGCTCTGGAGCAAGTGCTGTTTGTAACCAAACGGCTCGACGAGAATGTTTACTTGGCTTCACGCAACTTGCCAAACGTATTGGTTTTGGAAGCTCAACAAGTTGATCCTTACAGCTTGCTGCGTTATAAAAAAGTAATCATCACTAAAGATGCGGTTGCACAATTAGAGGAGCAATGGGTATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36806","NCBI_taxonomy_name":"Neisseria gonorrhoeae","NCBI_taxonomy_id":"485"}}}},"ARO_accession":"3004956","ARO_id":"43142","ARO_name":"Neisseria gonorrhoeae rpld","CARD_short_name":"Ngon_rpld","ARO_description":"rpld encodes for the 50S L4 ribosomal protein, is a macrolide resistance protein identified in Neisseria gonorrhoeae.","ARO_category":{"43188":{"category_aro_accession":"3005001","category_aro_cvterm_id":"43188","category_aro_name":"50S rRNA with mutation conferring resistance to macrolide antibiotics","category_aro_description":"Nucleotide point mutations in the 50S rRNA subunit (not in the 23s rRNA range) may confer resistance to macrolide antibiotics.","category_aro_class_name":"AMR Gene Family"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5765":{"model_id":"5765","model_name":"FosY","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"250"}},"model_sequences":{"sequence":{"8437":{"protein_sequence":{"accession":"QTE33800.1","sequence":"MLKSINHICFSVSNLNDSIHFYKNILRGELLVSGKTTAYLIVGGLWISLNEETDIPRDEIQFSYTHIAFSIEEDEFYEWYQRLKENNVNILEGRNRDVRDKMSIYFTDPDGHKLELHTGTLKDRLNYYKETKPHMTFYDE"},"dna_sequence":{"accession":"MN961674.1","fmin":"0","fmax":"423","strand":"+","sequence":"ATGCTAAAATCAATTAATCATATTTGCTTTTCAGTGAGTAACTTAAATGATTCAATACATTTCTATAAAAATATACTACGTGGAGAATTATTAGTAAGTGGAAAAACAACTGCTTATTTAATTGTGGGTGGCTTATGGATATCTTTAAATGAAGAAACAGATATTCCTAGAGATGAAATTCAGTTTTCATATACACATATTGCATTTAGTATTGAAGAAGATGAATTTTACGAATGGTATCAAAGATTAAAAGAAAATAACGTAAACATTTTAGAGGGGCGTAATAGAGATGTAAGAGATAAAATGTCTATTTACTTTACTGATCCTGATGGACATAAATTAGAATTGCATACTGGAACACTTAAAGATAGATTAAATTATTATAAAGAAACAAAACCACATATGACCTTTTATGATGAATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35508","NCBI_taxonomy_name":"Staphylococcus aureus","NCBI_taxonomy_id":"1280"}}}},"ARO_accession":"3007069","ARO_id":"45631","ARO_name":"FosY","CARD_short_name":"FosY","ARO_description":"A thiol transferase isolated in Staphylococcus aureus that leads to resistance of fosfomycin.","ARO_category":{"36272":{"category_aro_accession":"3000133","category_aro_cvterm_id":"36272","category_aro_name":"fosfomycin thiol transferase","category_aro_description":"Catalyzes the addition of a thiol group from a nucleophilic molecule to fosfomycin.","category_aro_class_name":"AMR Gene Family"},"35944":{"category_aro_accession":"0000025","category_aro_cvterm_id":"35944","category_aro_name":"fosfomycin","category_aro_description":"Fosfomycin (also known as phosphomycin and phosphonomycin) is a broad-spectrum antibiotic produced by certain Streptomyces species. It is effective on gram positive and negative bacteria as it targets the cell wall, an essential feature shared by both bacteria. Its specific target is MurA (MurZ in E.coli), which attaches phosphoenolpyruvate (PEP) to UDP-N-acetylglucosamine, a step of commitment to cell wall synthesis. In the active site of MurA, the active cysteine molecule is alkylated which stops the catalytic reaction.","category_aro_class_name":"Antibiotic"},"45731":{"category_aro_accession":"3007149","category_aro_cvterm_id":"45731","category_aro_name":"phosphonic acid antibiotic","category_aro_description":"A group of antibiotics derived from phosphonic acids.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5766":{"model_id":"5766","model_name":"MCR-1.33","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"8433":{"protein_sequence":{"accession":"UGY30527.1","sequence":"MMQHTSVWYRRSVSPFVLVASVAVFLTATANLTFFDKISQTYPIADNLGFVLTIAVVLFGAMLLITTLLSSYRYVLKPVLILLLIMGAVTSYFTDTYGTVYDTTMLQNALQTDQAETKDLLNAAFIMRIIGLGVLPSLLVAFVKVDYPTWGKGLMRRLGLIVASLALILLPVVAFSSHYASFFRVHKPLRSYVNPIMPIYSVGKLASIGYKKASAPKDTIYHAKDAVQATKPDMRKPRLVVFVVGETARADHVSFNGYERDTFPQLAKIDGVTNFSNVTSCGTSTAYSVPCMFSYLGADEYDVDTAKYQENVLDTLDRLGVSILWRDNNSDSKGVMDKLPKAQFADYKSATNNAICNTNPYNECRDVGMLVGLDDFVAANNGKDMLIMLHQMGNHGPAYFKRYDEKFAKFTPVCEGNELAKCEHQSLINAYDNALLATDDFIAQSIQWLQTHSNAYDVSMLYVSDHGESLGENGVYLHGMPNAFAPKEQRSVPAFFWTDKQTGITPMATDTVLTHDAITPTLLKLFDVTADKVKDRTAFIR"},"dna_sequence":{"accession":"OL624718.1","fmin":"0","fmax":"1626","strand":"+","sequence":"ATGATGCAGCATACTTCTGTGTGGTACCGACGCTCGGTCAGTCCGTTTGTTCTTGTGGCGAGTGTTGCCGTTTTCTTGACCGCGACCGCCAATCTTACCTTTTTTGATAAAATCAGCCAAACCTATCCCATCGCGGACAATCTCGGCTTTGTGCTGACGATCGCTGTCGTGCTCTTTGGCGCGATGCTACTGATCACCACGCTGTTATCATCGTATCGCTATGTGCTAAAGCCTGTGTTGATTTTGCTATTAATCATGGGCGCGGTGACCAGTTATTTTACTGACACTTATGGCACGGTCTATGATACGACCATGCTCCAAAATGCCCTACAGACCGACCAAGCCGAGACCAAGGATCTATTAAACGCAGCGTTTATCATGCGTATCATTGGTTTGGGTGTGCTACCAAGTTTGCTTGTGGCTTTTGTTAAGGTGGATTATCCGACTTGGGGCAAGGGTTTGATGCGCCGATTGGGCTTGATCGTGGCAAGTCTTGCGCTGATTTTACTGCCTGTGGTGGCGTTCAGCAGTCATTATGCCAGTTTCTTTCGCGTGCATAAGCCGCTGCGTAGCTATGTCAATCCGATCATGCCAATCTACTCGGTGGGTAAGCTTGCCAGTATTGGGTATAAAAAAGCCAGTGCGCCAAAAGATACCATTTATCACGCCAAAGACGCGGTACAAGCAACCAAGCCTGATATGCGTAAGCCACGCCTAGTGGTGTTCGTCGTCGGTGAGACGGCACGCGCCGATCATGTCAGCTTCAATGGCTATGAGCGCGATACTTTCCCACAGCTTGCCAAGATCGATGGCGTGACCAATTTTAGCAATGTCACATCGTGCGGCACATCGACGGCGTATTCTGTGCCGTGTATGTTCAGCTATCTGGGCGCGGATGAGTATGATGTCGATACCGCCAAATACCAAGAAAATGTGCTGGATACGCTGGATCGCTTGGGCGTAAGTATCTTGTGGCGTGATAATAATTCGGACTCAAAAGGCGTGATGGATAAGCTGCCAAAAGCGCAATTTGCCGATTATAAATCCGCGACCAACAACGCCATCTGCAACACCAATCCTTATAACGAATGCCGCGATGTCGGTATGCTCGTTGGCTTAGATGACTTTGTCGCTGCCAATAACGGCAAAGATATGCTGATCATGCTGCACCAAATGGGCAATCACGGGCCTGCGTATTTTAAGCGATATGATGAAAAGTTTGCCAAATTCACGCCAGTGTGTGAAGGTAATGAGCTTGCCAAGTGCGAACATCAGTCCTTGATCAATGCTTATGACAATGCCTTGCTTGCCACCGATGATTTCATCGCTCAAAGTATCCAGTGGCTGCAGACGCACAGCAATGCCTATGATGTCTCAATGCTGTATGTCAGCGATCATGGCGAAAGTCTGGGTGAGAACGGTGTCTATCTACATGGTATGCCAAATGCCTTTGCACCAAAAGAACAGCGCAGTGTGCCTGCATTTTTCTGGACGGATAAGCAAACTGGCATCACGCCAATGGCAACCGATACCGTCCTGACCCATGACGCGATCACGCCGACATTATTAAAGCTGTTTGATGTCACCGCGGACAAAGTCAAAGACCGCACCGCATTCATCCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3007070","ARO_id":"45632","ARO_name":"MCR-1.33","CARD_short_name":"MCR-1.33","ARO_description":"An MCR-1-type colistin resistance gene variant, first described in a multi-drug-resistant Escherichia coli isolate recovered from a urinary tract infection, and co-occurring with the carbapenemase NDM-5.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5767":{"model_id":"5767","model_name":"Bacillus subtilis rpoB mutants conferring resistance to rifampin","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"12589":"S487L","12590":"A478N","12591":"Q469K","12592":"Q469R","12593":"H482Y"},"Curated-R":{"12589":"S487L","12590":"A478N","12591":"Q469K","12592":"Q469R","12593":"H482Y"},"clinical":{"12589":"S487L","12590":"A478N","12591":"Q469K","12592":"Q469R","12593":"H482Y"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"2300"}},"model_sequences":{"sequence":{"8438":{"protein_sequence":{"accession":"CAB11883.2","sequence":"MTGQLVQYGRHRQRRSYARISEVLELPNLIEIQTSSYQWFLDEGLREMFQDISPIEDFTGNLSLEFIDYSLGEPKYPVEESKERDVTYSAPLRVKVRLINKETGEVKDQDVFMGDFPIMTDTGTFIINGAERVIVSQLVRSPSVYFSGKVDKNGKKGFTATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVLLRALGFGSDQEILDLIGENEYLRNTLDKDNTENSDKALLEIYERLRPGEPPTVENAKSLLDSRFFDPKRYDLANVGRYKINKKLHIKNRLFNQRLAETLVDPETGEILAEKGQILDRRTLDKVLPYLENGIGFRKLYPNGGVVEDEVTLQSIKIFAPTDQEGEQVINVIGNAYIEEEIKNITPADIISSISYFFNLLHGVGDTDDIDHLGNRRLRSVGELLQNQFRIGLSRMERVVRERMSIQDTNTITPQQLINIRPVIASIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALGPGGLTRERAGMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYAKVNRFGFIETPYRRVDPETGKVTGRIDYLTADEEDNYVVAQANARLDDEGAFIDDSIVARFRGENTVVSRNRVDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMQPEAPFVGTGMEYVSGKDSGAAVICKHPGIVERVEAKNVWVRRYEEVDGQKVKGNLDKYSLLKFVRSNQGTCYNQRPIVSVGDEVVKGEILADGPSMELGELALGRNVMVGFMTWDGYNYEDAIIMSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDDRGIIRIGAEVKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIIHDVKVFNREDGDELPPGVNQLVRVYIVQKRKISEGDKMAGRHGNKGVISKILPEEDMPYLPDGTPIDIMLNPLGVPSRMNIGQVLELHMGMAARYLGIHIASPVFDGAREEDVWETLEEAGMSRDAKTVLYDGRTGEPFDNRVSVGIMYMIKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTVKSDDVVGRVKTYEAIVKGDNVPEPGVPESFKVLIKELQSLGMDVKILSGDEEEIEMRDLEDEEDAKQADGLALSGDEEPEETASADVERDVVTKE"},"dna_sequence":{"accession":"AL009126.3","fmin":"121918","fmax":"125500","strand":"+","sequence":"TTGACAGGTCAACTAGTTCAGTATGGACGACACCGCCAGCGCAGAAGCTATGCTCGCATTAGCGAAGTGTTAGAATTACCAAATCTCATTGAAATTCAAACCTCTTCTTATCAGTGGTTTCTTGATGAGGGTCTTAGAGAGATGTTTCAAGACATATCACCAATTGAGGATTTCACTGGTAACCTCTCTCTTGAGTTCATTGATTATAGTTTAGGTGAGCCTAAATATCCTGTAGAGGAATCAAAAGAACGTGATGTGACTTACTCAGCTCCGCTAAGAGTGAAGGTTCGTTTAATTAACAAAGAAACTGGAGAGGTAAAAGACCAAGATGTCTTCATGGGTGATTTCCCTATTATGACAGATACAGGTACTTTTATCATTAACGGTGCGGAACGTGTTATCGTTTCCCAGCTTGTTCGGTCTCCAAGTGTATATTTCAGTGGTAAAGTAGACAAAAACGGTAAAAAAGGTTTTACCGCAACTGTCATTCCAAACCGTGGCGCATGGTTAGAATACGAAACTGATGCGAAAGATGTTGTTTATGTCCGCATTGATCGCACACGTAAGTTGCCGGTTACGGTTCTTTTGCGTGCTCTCGGCTTCGGCTCCGATCAAGAGATTCTTGATCTCATAGGAGAAAACGAATACCTGCGAAATACGCTTGATAAAGATAACACAGAAAACAGCGACAAAGCGTTGCTGGAAATTTACGAGCGTCTCCGTCCTGGAGAGCCGCCTACAGTAGAAAATGCGAAAAGCTTGCTTGATTCTCGTTTCTTTGATCCGAAACGATACGATCTTGCCAATGTAGGACGCTATAAAATTAATAAAAAACTTCATATTAAGAATCGCCTCTTCAATCAGAGACTTGCTGAAACGCTTGTTGATCCTGAAACAGGAGAAATCCTTGCTGAAAAAGGCCAGATTCTTGATAGAAGAACGCTTGATAAAGTACTGCCATACTTAGAAAACGGAATCGGTTTTAGAAAGCTGTATCCGAATGGCGGCGTTGTTGAAGATGAAGTGACTCTTCAATCAATTAAAATCTTTGCTCCGACTGATCAAGAAGGAGAACAGGTTATCAATGTAATCGGCAATGCTTACATCGAAGAAGAGATTAAAAACATCACGCCTGCTGATATTATTTCTTCAATCAGCTACTTCTTCAACCTGCTGCACGGAGTAGGCGACACAGATGATATCGATCATCTTGGAAACCGCCGTTTACGTTCTGTAGGCGAGCTTCTCCAGAACCAATTCCGTATCGGTTTAAGCCGTATGGAGCGTGTGGTTCGTGAGAGAATGTCAATTCAAGATACGAATACAATTACGCCTCAGCAGCTGATCAATATTCGTCCTGTTATTGCGTCCATTAAAGAGTTCTTTGGAAGCTCACAGCTTTCTCAATTCATGGATCAGACGAACCCGCTTGCTGAATTAACGCACAAGCGTCGTCTGTCAGCATTAGGACCGGGCGGATTGACACGTGAGCGTGCCGGAATGGAAGTGCGTGACGTTCACTACTCCCACTATGGCCGTATGTGTCCGATTGAAACGCCTGAGGGCCCGAACATCGGTTTGATCAACTCACTATCATCTTATGCAAAAGTAAACCGTTTTGGCTTTATTGAAACGCCATATCGCCGCGTTGACCCTGAAACAGGGAAGGTAACGGGCAGAATCGATTACTTAACTGCTGATGAAGAGGATAACTATGTTGTCGCTCAAGCGAATGCTCGTCTTGATGACGAAGGCGCCTTTATTGATGACAGCATCGTAGCTCGTTTCCGCGGGGAGAACACCGTTGTTTCCAGAAATCGTGTAGACTACATGGATGTATCGCCTAAGCAGGTTGTATCTGCTGCGACAGCATGTATCCCGTTCTTAGAAAACGATGACTCCAACCGTGCCCTCATGGGAGCGAACATGCAGCGTCAGGCTGTGCCTTTGATGCAGCCGGAAGCGCCATTTGTTGGAACTGGTATGGAATACGTATCAGGAAAAGACTCTGGTGCCGCTGTTATTTGTAAACACCCTGGTATCGTTGAACGCGTAGAAGCCAAAAACGTTTGGGTTCGCCGTTATGAAGAAGTAGACGGTCAAAAAGTAAAAGGAAACCTGGATAAATACAGCCTGCTGAAATTTGTCCGCTCTAACCAAGGTACGTGCTACAACCAGCGTCCGATCGTAAGTGTCGGCGATGAAGTGGTAAAAGGAGAAATCCTTGCTGACGGTCCTTCTATGGAGCTTGGTGAACTTGCACTTGGCCGTAACGTAATGGTCGGCTTCATGACGTGGGATGGCTACAACTATGAGGATGCCATCATCATGAGTGAACGCCTAGTGAAGGATGATGTTTATACATCTATCCACATTGAAGAATACGAATCAGAAGCACGTGATACGAAACTTGGACCTGAAGAAATCACTCGCGATATTCCAAACGTCGGTGAAGATGCGCTTCGCAATCTTGATGACCGCGGAATCATCCGTATTGGGGCAGAAGTAAAAGACGGAGATCTTCTTGTTGGTAAAGTAACGCCTAAAGGCGTAACTGAACTGACTGCCGAAGAACGCCTTCTTCACGCCATCTTTGGCGAGAAAGCCCGCGAGGTTCGTGATACTTCTCTTCGTGTGCCTCATGGCGGCGGCGGAATTATCCATGACGTTAAAGTCTTCAACCGTGAAGACGGAGACGAACTTCCTCCAGGTGTTAACCAGTTAGTACGCGTATATATCGTTCAGAAACGTAAGATTTCTGAAGGGGATAAAATGGCCGGTCGTCACGGTAACAAAGGTGTTATCTCTAAGATTCTTCCTGAAGAGGATATGCCTTACCTTCCTGACGGCACACCAATTGATATCATGCTTAACCCGCTGGGCGTACCATCACGTATGAACATCGGGCAGGTATTGGAACTTCACATGGGTATGGCCGCTCGTTACCTTGGCATTCACATTGCATCTCCTGTATTTGACGGAGCGCGAGAAGAGGATGTCTGGGAAACACTTGAAGAAGCCGGCATGTCTCGTGACGCCAAAACAGTGCTTTACGACGGACGTACTGGAGAGCCGTTTGATAACCGTGTATCTGTCGGTATCATGTACATGATCAAACTGGCTCACATGGTTGACGATAAACTTCATGCACGCTCTACAGGCCCTTACTCACTTGTTACGCAGCAGCCTCTTGGCGGTAAAGCGCAATTTGGCGGACAGCGTTTTGGTGAGATGGAGGTTTGGGCACTTGAAGCTTACGGTGCGGCTTACACTCTTCAAGAAATTCTGACTGTTAAGTCTGATGACGTGGTTGGACGTGTGAAAACATACGAAGCCATCGTTAAAGGCGACAATGTTCCTGAACCAGGTGTTCCGGAATCATTCAAAGTATTAATCAAAGAACTTCAAAGCTTAGGTATGGATGTCAAAATCCTTTCTGGTGATGAAGAAGAAATAGAAATGAGAGATTTAGAAGACGAAGAAGATGCGAAACAAGCTGACGGCCTGGCATTATCAGGTGATGAAGAGCCGGAAGAAACAGCATCTGCAGACGTTGAACGCGATGTAGTAACAAAAGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39579","NCBI_taxonomy_name":"Bacillus subtilis subsp. subtilis str. 168","NCBI_taxonomy_id":"224308"}}}},"ARO_accession":"3007073","ARO_id":"45635","ARO_name":"Bacillus subtilis rpoB mutants conferring resistance to rifampin","CARD_short_name":"Bsub_rpoB_RIF","ARO_description":"Point mutations that occur within the Bacillus subtilis rpoB gene resulting in resistance to rifampin.","ARO_category":{"36349":{"category_aro_accession":"3000210","category_aro_cvterm_id":"36349","category_aro_name":"rifamycin-resistant beta-subunit of RNA polymerase (rpoB)","category_aro_description":"Rifampin resistant RNA polymerases include amino acids substitutions which disrupt the affinity of rifampin for its binding site. These mutations are frequently concentrated in the rif I region of the beta-subunit and most often involve amino acids which make direct interactions with rifampin. However, mutations which also confer resistance can occur outside this region and may involve amino acids which do not directly make contact with rifampin.","category_aro_class_name":"AMR Gene Family"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5768":{"model_id":"5768","model_name":"cph","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"475"}},"model_sequences":{"sequence":{"8439":{"protein_sequence":{"accession":"AAA92037.1","sequence":"MTLSHLVDVVRRAHPDVDLEGAGVHSGQFHDVLIARDRVFRFPKTAGAAAELPGRVAVLTAVDAVELGVGVPVPLSEVRDGGPHGFLVLSRLHGTPLERGDATSPEVIDVVAAEFARVLRAMAGADVEKLRLVLPVADAGRWRGFAGRVRATLFPLMSEDGRARAERELAAAVAMDHVATGLVHGDLGGENVLWQQVEELPRLTGIVDWDEAKVGDPAEDLAAVGASYGPELVERVVALLGAGDLWPRIRAYQGTFALQQALAGAEDGDDEELEDGLTAYR"},"dna_sequence":{"accession":"U13078.1","fmin":"205","fmax":"1051","strand":"+","sequence":"ATGACCTTGTCCCACCTTGTTGACGTGGTTCGGCGTGCCCACCCGGATGTCGATCTTGAGGGTGCCGGTGTGCACTCCGGCCAGTTCCACGACGTGTTGATCGCGCGTGACCGGGTGTTCCGGTTTCCCAAGACGGCTGGCGCGGCGGCGGAGCTGCCGGGTCGGGTGGCGGTGCTGACGGCGGTCGACGCGGTGGAGCTGGGGGTGGGGGTGCCGGTTCCGCTGTCGGAGGTGCGGGACGGCGGTCCGCACGGGTTCCTGGTGCTCAGCCGGCTGCACGGCACGCCGTTGGAGCGGGGGGACGCGACGTCGCCCGAGGTGATCGACGTCGTGGCCGCCGAGTTCGCGCGGGTGTTGCGGGCGATGGCCGGCGCTGATGTGGAGAAGTTGCGGCTGGTGCTGCCGGTCGCCGACGCCGGGCGGTGGCGCGGGTTCGCCGGGCGGGTCCGGGCGACGCTGTTCCCGCTGATGTCGGAGGACGGCCGGGCGCGGGCCGAGCGCGAGTTGGCGGCGGCCGTGGCGATGGACCACGTCGCCACCGGGTTGGTGCACGGGGATCTCGGCGGGGAGAACGTGTTGTGGCAGCAGGTCGAGGAGCTGCCGCGGCTGACCGGGATCGTGGACTGGGACGAGGCCAAGGTGGGCGACCCGGCGGAGGACCTGGCGGCGGTGGGGGCCAGTTATGGGCCTGAGCTGGTGGAGCGGGTGGTCGCGCTGCTCGGGGCGGGGGACCTGTGGCCGCGGATCCGGGCTTACCAGGGGACGTTCGCGTTGCAGCAGGCGCTGGCGGGTGCCGAGGACGGCGACGACGAAGAACTGGAAGACGGCCTGACCGCCTACCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"45638","NCBI_taxonomy_name":"Saccharothrix mutabilis subsp. capreolus","NCBI_taxonomy_id":"66854"}}}},"ARO_accession":"3007075","ARO_id":"45637","ARO_name":"cph","CARD_short_name":"cph","ARO_description":"cph is a phosphotransferase that confers resistance to capreomycin.","ARO_category":{"45636":{"category_aro_accession":"3007074","category_aro_cvterm_id":"45636","category_aro_name":"capreomycin phosphotransferase","category_aro_description":"Capreomycin family of phosphotransferases confer resistance to capreomycin antibiotics.","category_aro_class_name":"AMR Gene Family"},"40875":{"category_aro_accession":"3003993","category_aro_cvterm_id":"40875","category_aro_name":"capreomycin","category_aro_description":"Capreomycin is an aminoglycoside antibiotic, capable of treating a large number of infections but in particular used for killing bacteria causing tuberculosis.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5748":{"model_id":"5748","model_name":"mef(J)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8302":{"protein_sequence":{"accession":"QQA64076.1","sequence":"MENNKWKQKFFAIYTGQFFSLLSSAAVQFGIIWWLTDKTGGSPLLLTLAGLAGFLPQALVGPFAGTITDRYSRKFLMISADMTVALGSLILFLILHFYEANIIFVILILALRSLATAFHMPAMQASIPLLAPEEALTKVAGWGQMVASVSNIVGPAVGMSILSVSSIKWVLLLDILGAVVASGILLFINIPKIQKTESVELTSFFVEMKEGYNALVNHPILLKLTILMTIVAVLYIPLGTYFPLMTRNHFGKGVVEAGTVEIAFAIGLIVGGSLLGIIGDKFEKVKTMAIGMLLMGLALFFSGLLSPSLFFIFIILSGLVGFSGPLFSAPFYAYIQTEIEPQLLGRIFSFVTSLSLLATPIGYALSGLLIEFTSVSILFSIIGVLVILSGLITLKVK"},"dna_sequence":{"accession":"CP065927.1","fmin":"1659728","fmax":"1660922","strand":"-","sequence":"ATGGAAAACAACAAATGGAAGCAGAAGTTTTTTGCAATATATACAGGACAATTCTTTTCACTATTAAGTAGTGCGGCCGTTCAATTTGGTATTATTTGGTGGCTAACTGATAAAACTGGTGGTTCACCATTGCTTCTAACACTAGCAGGACTTGCAGGTTTTTTACCACAAGCATTAGTAGGACCTTTTGCTGGCACGATTACAGACCGTTATTCACGGAAGTTTTTGATGATTTCAGCAGATATGACTGTTGCGTTAGGTAGTTTAATTTTATTTTTAATATTGCATTTCTATGAGGCTAATATCATTTTTGTAATTCTGATTTTAGCACTTAGATCATTAGCAACTGCTTTTCATATGCCAGCAATGCAAGCATCAATTCCTTTACTTGCCCCTGAAGAAGCATTGACAAAGGTCGCTGGTTGGGGGCAAATGGTAGCATCCGTTTCTAATATAGTAGGACCAGCTGTAGGGATGTCAATTCTTTCAGTGAGCTCAATTAAATGGGTACTACTTTTAGATATACTTGGAGCTGTAGTTGCAAGTGGGATTTTACTTTTTATAAATATACCTAAAATACAAAAAACTGAATCTGTTGAACTTACAAGTTTTTTTGTAGAAATGAAAGAAGGGTATAATGCCCTTGTTAATCATCCTATCTTGTTGAAACTTACAATACTTATGACAATCGTAGCAGTCCTATACATACCACTTGGAACTTACTTCCCACTTATGACAAGAAATCATTTTGGGAAAGGTGTTGTTGAAGCTGGTACAGTAGAGATTGCATTTGCTATCGGTTTAATAGTAGGCGGTTCATTGTTAGGTATAATAGGTGATAAATTTGAAAAAGTGAAGACAATGGCAATTGGAATGCTATTGATGGGACTGGCACTATTTTTCTCTGGTCTTCTCTCACCATCACTTTTCTTTATCTTTATAATTTTGTCCGGATTGGTTGGATTTTCAGGACCTTTATTTTCTGCACCATTCTATGCTTATATTCAAACTGAGATTGAGCCACAATTATTAGGAAGAATTTTCAGTTTTGTAACAAGTCTCTCACTTTTAGCCACGCCAATTGGATATGCATTATCTGGTTTACTAATTGAATTTACTAGTGTTTCTATATTGTTTTCAATCATTGGTGTATTAGTAATACTAAGTGGTCTTATTACTTTAAAAGTGAAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36764","NCBI_taxonomy_name":"Streptococcus pyogenes","NCBI_taxonomy_id":"1314"}}}},"ARO_accession":"3007049","ARO_id":"45608","ARO_name":"mef(J)","CARD_short_name":"mef(J)","ARO_description":"mef(J) is an mef efflux pump protein.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"5747":{"model_id":"5747","model_name":"mef(H)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"100"}},"model_sequences":{"sequence":{"8301":{"protein_sequence":{"accession":"QQM99829.1","sequence":"MGISLFLELPAIVSYWVVTVMCFVAMGVSTMFVVQIYTLVQTQTPPQLVGKIMATLVAVAMCGQPIGQMVYGILFDVFIQETWVVMFVASIASIMISIYSKRIFQKLEI"},"dna_sequence":{"accession":"MW269960.1","fmin":"0","fmax":"330","strand":"+","sequence":"ATGGGAATTTCGCTATTTTTAGAATTGCCTGCAATAGTTTCCTACTGGGTAGTTACAGTGATGTGCTTTGTGGCTATGGGTGTATCTACTATGTTTGTTGTTCAAATTTACACTCTTGTTCAGACACAAACACCACCGCAATTAGTAGGAAAGATAATGGCTACGCTGGTAGCAGTTGCTATGTGCGGTCAACCTATTGGACAAATGGTTTACGGTATTTTATTCGATGTATTTATACAAGAAACATGGGTTGTTATGTTTGTAGCTTCTATTGCTTCAATCATGATTTCAATATATTCAAAAAGAATTTTTCAAAAGTTAGAGATATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36807","NCBI_taxonomy_name":"Clostridioides difficile","NCBI_taxonomy_id":"1496"}}}},"ARO_accession":"3007047","ARO_id":"45606","ARO_name":"mef(H)","CARD_short_name":"mef(H)","ARO_description":"mef(H) is an mef efflux pump protein.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"3847":{"model_id":"3847","model_name":"lsaD","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"900"}},"model_sequences":{"sequence":{"6160":{"protein_sequence":{"accession":"AXF35727.1","sequence":"MSNIKINNLTFGYTDQLIFDNVNINIDDQWKLGLVGRNGRGKTTLLKILLGEVDVHLEIKTNKSFVYFPQTINDKDQLTLFVLQELADFEQWELERELTLMGVDLDTLWRPFNSLSGGEQTKTLLALLFLDEHNYPLIDEPTNHLDKASREKVAAYLSEKKGYILISHDRNFLNKTTDHTLAIERADLQVYAGNFAIYEEEKRLRDLTEKAQDDKLRKEIGRLKQTAREKEAWSRNLEATKSRKKRGFDSETKRVDKGFIGRKAANMMQKSKNLEKRMKEDIADKELLLKNWEEVPGLEMSVLESHQKRLLTVENLAAGFEDFLFEPVSFTLEQGQVLALTGENGRGKSSLMKVLTGEFTGRYVGTFELAHNLVISEVRQLADNRGFLNEFAKKENLELELFLNNLRKLGVERKVFEQKIENMSQGQQRKVELARALSQPAHIYLWDEPLNYLDVFNQEQIIQMIKRSKPSMLVIEHDQYFVDQVADAQIELIKSSV"},"dna_sequence":{"accession":"MH473150.1","fmin":"0","fmax":"1494","strand":"+","sequence":"ATGTCGAATATTAAAATAAATAATTTAACATTTGGTTATACCGATCAGCTTATTTTTGACAATGTAAATATCAATATTGATGACCAATGGAAGCTGGGATTGGTTGGCCGTAACGGGAGAGGGAAAACTACACTTTTAAAAATCCTTCTTGGAGAAGTGGATGTACATCTTGAAATTAAAACCAATAAGAGCTTTGTGTATTTTCCTCAGACGATTAATGATAAAGACCAGTTGACCTTATTTGTCTTGCAAGAGTTAGCTGACTTTGAGCAGTGGGAACTTGAGCGTGAATTGACACTAATGGGCGTAGATTTAGATACTTTATGGCGTCCTTTCAATAGTCTTTCTGGTGGAGAGCAAACAAAGACACTCTTAGCACTTTTATTCTTGGATGAGCATAATTATCCGCTCATCGATGAGCCAACCAATCATCTTGATAAAGCTTCACGTGAGAAAGTTGCAGCCTACTTGTCAGAAAAAAAGGGATATATTTTAATCTCACATGACCGTAATTTTCTCAATAAGACGACAGATCATACACTTGCGATAGAGCGTGCGGACTTACAAGTATATGCAGGTAATTTTGCTATCTACGAGGAGGAAAAAAGATTGCGAGATCTCACGGAAAAGGCACAAGATGATAAACTCAGGAAAGAAATCGGTAGATTGAAACAAACGGCGCGTGAAAAAGAAGCGTGGTCGCGTAACTTAGAAGCAACAAAATCCCGTAAGAAACGAGGTTTTGATTCGGAAACAAAACGTGTTGATAAAGGTTTTATTGGACGAAAAGCAGCAAATATGATGCAAAAGTCTAAAAATCTCGAAAAGCGCATGAAAGAGGATATCGCTGACAAGGAACTACTTCTAAAAAATTGGGAAGAAGTACCTGGATTGGAAATGAGTGTCTTAGAGAGTCATCAAAAACGCTTACTGACAGTGGAAAATTTAGCGGCTGGATTTGAAGACTTTCTTTTTGAACCTGTGTCTTTTACACTTGAACAAGGTCAGGTGCTTGCACTAACAGGAGAAAATGGTAGAGGAAAATCTTCTCTAATGAAAGTCCTCACAGGTGAATTTACTGGCCGTTATGTTGGAACATTTGAGTTGGCCCATAACTTGGTCATTTCCGAAGTAAGACAACTTGCAGATAATAGAGGGTTTCTGAACGAGTTTGCCAAAAAAGAAAACTTAGAATTAGAACTTTTTCTCAACAATTTGCGCAAATTAGGCGTAGAGCGCAAAGTTTTTGAGCAAAAAATCGAAAATATGAGTCAGGGACAGCAGCGTAAAGTCGAACTGGCCCGCGCCTTAAGTCAGCCGGCGCATATTTATCTTTGGGATGAACCCCTCAACTATCTTGATGTTTTTAATCAAGAACAAATTATTCAAATGATAAAGAGAAGCAAGCCTAGTATGCTTGTCATTGAGCACGATCAGTATTTTGTTGATCAAGTAGCAGATGCCCAAATCGAACTCATAAAAAGCAGCGTTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43338","NCBI_taxonomy_name":"Lactococcus garvieae","NCBI_taxonomy_id":"1363"}}}},"ARO_accession":"3005121","ARO_id":"43337","ARO_name":"lsaD","CARD_short_name":"lsaD","ARO_description":"The lsa(D) gene represents an ABC-F subfamily protein expressed in Lactococcus garvieae. It confers resistance to Streptogramins A, Pleuromutilins and Lincosamides.","ARO_category":{"41696":{"category_aro_accession":"3004472","category_aro_cvterm_id":"41696","category_aro_name":"lsa-type ABC-F protein","category_aro_description":"A subgroup of the ABC-F protein subfamily of ATP-binding cassette proteins. lsa-type ABC-F proteins confer resistance to streptogramin, lincosamide and pleuromutilin antibiotics through antibiotic target protection of the ribosome.","category_aro_class_name":"AMR Gene Family"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"virginiamycin M1","category_aro_description":"Virginiamycin M1 is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37015":{"category_aro_accession":"3000671","category_aro_cvterm_id":"37015","category_aro_name":"tiamulin","category_aro_description":"Tiamulin is a pleuromutilin derivative currently used in veterinary medicine. It binds to the 23 rRNA of the 50S ribosomal subunit to inhibit protein translation.","category_aro_class_name":"Antibiotic"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35952":{"category_aro_accession":"0000034","category_aro_cvterm_id":"35952","category_aro_name":"streptogramin A antibiotic","category_aro_description":"Streptogramin A antibiotics are cyclic polyketide peptide hybrids that bind to the ribosomal peptidyl transfer centre. Structural variation arises from substituting a proline for its desaturated derivative and by its substitution for Ala or Cys. Used alone, streptogramin A antibiotics are bacteriostatic, but is bactericidal when used with streptogramin B antibiotics.","category_aro_class_name":"Drug Class"},"37014":{"category_aro_accession":"3000670","category_aro_cvterm_id":"37014","category_aro_name":"pleuromutilin antibiotic","category_aro_description":"Pleuromutilins are natural fungal products that target bacterial protein translation by binding the the 23S rRNA, blocking the ribosome P site at the 50S subunit. They are mostly used for agriculture and veterinary purposes.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5769":{"model_id":"5769","model_name":"PRC-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"8440":{"protein_sequence":{"accession":"QTV22830.1","sequence":"MRHLYRPLFVALALLAASHAPAAPSLETQVDAAAKSMMQTHAIPGMAIAISHKGQSHFFEYGVASLENGQTVDRHTLFELGSISKLFTATLGAYAEARGTLNLSDNASQYLPALQGSAFDHISLLDLATYTSGGLPLQFPDTVSNERQMLDYYRNWQAVYPPGTQRLYSNPSIGLFGHLAAASLAKPFQQLMEKDLLPQLSMQESYVRIPTEQMEHYAWGYRDDKAVRVTPGALDAEAYGLKSTAADVLRFIDANLHPDQLPAPLRQAISATHRGYYQVGDMTQALGWERYAYPISLEKLQAGNSAEMALQPQTVARFAAPKPAEGDLLLNKTGSTNGFGAYILLLPARDTGLVILANRNYPNAERVRLALQLLDAIEP"},"dna_sequence":{"accession":"MW854031.1","fmin":"0","fmax":"1140","strand":"+","sequence":"ATGCGCCACCTGTACCGCCCTCTGTTCGTCGCCCTGGCGCTGCTGGCCGCCAGCCACGCGCCGGCCGCACCTTCACTGGAAACACAGGTGGACGCCGCTGCGAAGTCGATGATGCAGACCCATGCCATTCCCGGCATGGCCATCGCCATCAGCCACAAGGGGCAGTCGCATTTCTTCGAATACGGCGTCGCATCCCTTGAAAACGGCCAGACGGTGGATCGCCATACCCTTTTCGAGCTGGGCTCGATCAGCAAACTCTTCACCGCCACCCTCGGCGCCTACGCCGAAGCGCGCGGCACGCTGAACCTCAGTGACAACGCCAGCCAGTATCTGCCGGCCCTGCAGGGCAGCGCCTTCGATCACATCAGTTTGCTGGATCTGGCCACTTACACCTCGGGCGGCCTGCCACTGCAGTTCCCGGACACGGTCAGCAACGAACGGCAGATGCTCGATTACTACCGCAACTGGCAGGCGGTGTATCCGCCGGGTACGCAGCGGCTGTATTCCAACCCCAGCATCGGCCTGTTCGGCCACCTGGCAGCAGCCAGTCTGGCCAAGCCGTTTCAGCAGTTGATGGAGAAGGATCTGCTGCCGCAACTGAGCATGCAGGAAAGCTACGTCCGTATACCGACCGAGCAGATGGAGCACTATGCCTGGGGCTACCGCGACGACAAGGCGGTGCGCGTGACGCCCGGCGCGCTGGATGCCGAAGCCTACGGGTTGAAATCTACTGCCGCCGACGTGCTACGCTTCATCGACGCCAATCTGCACCCGGATCAACTACCCGCACCACTGCGCCAGGCGATCAGCGCAACACATCGTGGCTACTACCAGGTCGGCGACATGACTCAGGCGCTGGGCTGGGAGCGCTACGCCTACCCCATCAGCCTAGAAAAACTGCAGGCTGGCAACTCAGCAGAAATGGCGCTGCAACCGCAGACCGTGGCGCGTTTCGCTGCGCCCAAGCCTGCCGAAGGTGACCTGCTGCTGAACAAGACCGGCTCGACCAACGGCTTCGGCGCCTACATCCTACTGCTGCCGGCGCGCGATACCGGCCTGGTGATACTCGCCAACCGCAATTACCCCAATGCCGAACGCGTGCGCCTGGCCTTGCAATTGCTGGACGCGATCGAGCCGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"45649","NCBI_taxonomy_name":"Pseudomonas wenzhouensis","NCBI_taxonomy_id":"2906062"}}}},"ARO_accession":"3007085","ARO_id":"45648","ARO_name":"PRC-1","CARD_short_name":"PRC-1","ARO_description":"PRC-1 is a beta-lactamase that confers resistance to certain cephalosporins and penicillins.","ARO_category":{"45647":{"category_aro_accession":"3007084","category_aro_cvterm_id":"45647","category_aro_name":"PRC beta-lactamase","category_aro_description":"PRC beta-lactamases are class C beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35975":{"category_aro_accession":"0000058","category_aro_cvterm_id":"35975","category_aro_name":"cefazolin","category_aro_description":"Cefazolin, also known as cefazoline or cephazolin, is a first generation cephalosporin antibiotic. It is administered parenterally, and is active against a broad spectrum of bacteria.","category_aro_class_name":"Antibiotic"},"35979":{"category_aro_accession":"0000062","category_aro_cvterm_id":"35979","category_aro_name":"ceftriaxone","category_aro_description":"Ceftriaxone is a third-generation cephalosporin antibiotic. The presence of an aminothiazolyl sidechain increases ceftriazone's resistance to beta-lactamases. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"35981":{"category_aro_accession":"0000064","category_aro_cvterm_id":"35981","category_aro_name":"amoxicillin","category_aro_description":"Amoxicillin is a moderate-spectrum, bacteriolytic, beta-lactam antibiotic used to treat bacterial infections caused by susceptible microorganisms. A derivative of penicillin, it has a wider range of treatment but remains relatively ineffective against Gram-negative bacteria. It is commonly taken with clavulanic acid, a beta-lactamase inhibitor. Like other beta-lactams, amoxicillin interferes with the synthesis of peptidoglycan.","category_aro_class_name":"Antibiotic"},"36976":{"category_aro_accession":"3000632","category_aro_cvterm_id":"36976","category_aro_name":"benzylpenicillin","category_aro_description":"Benzylpenicillin, commonly referred to as penicillin G, is effective against both Gram-positive and Gram-negative bacteria. It is unstable in acid.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"36989":{"category_aro_accession":"3000645","category_aro_cvterm_id":"36989","category_aro_name":"cefotaxime","category_aro_description":"Cefotaxime is a semisynthetic cephalosporin taken parenterally. It is resistant to most beta-lactamases and active against Gram-negative rods and cocci due to its aminothiazoyl and methoximino functional groups.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5770":{"model_id":"5770","model_name":"KPC-90","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"8441":{"protein_sequence":{"accession":"QXT58056.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTYTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"MZ570431.1","fmin":"0","fmax":"888","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3007087","ARO_id":"45651","ARO_name":"KPC-90","CARD_short_name":"KPC-90","ARO_description":"KPC-90 is a KPC beta-lactamase.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5771":{"model_id":"5771","model_name":"KPC-83","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8442":{"protein_sequence":{"accession":"QRM14288.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFTKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"MW581775.1","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCACTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36936","NCBI_taxonomy_name":"Aeromonas caviae","NCBI_taxonomy_id":"648"}}}},"ARO_accession":"3007089","ARO_id":"45653","ARO_name":"KPC-83","CARD_short_name":"KPC-83","ARO_description":"KPC-83 is a KPC beta-lactamase.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5772":{"model_id":"5772","model_name":"FosM1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"250"}},"model_sequences":{"sequence":{"8445":{"protein_sequence":{"accession":"DAC85639.1","sequence":"MNIKGINHFLFSVSNLEESIKFYQSVFDAKLLVKGTSTAYFDLNGIWLALNEEIDIPRNEINQSYTHIAFSIEEGDFEKVYEKLKQLHVHILTGRERDVKDKKSIYFTDPDGHKFEFHTGTLQDRLAYYQQEKKHMEFFN"},"dna_sequence":{"accession":"BK012111.1","fmin":"0","fmax":"423","strand":"+","sequence":"GTGAATATAAAAGGCATTAATCACTTCTTATTTTCAGTATCCAATTTAGAGGAATCTATCAAATTTTATCAGAGTGTTTTTGATGCAAAGCTTTTAGTAAAAGGGACAAGCACGGCATATTTTGATTTGAATGGGATATGGCTTGCGCTAAATGAAGAAATAGATATTCCTCGAAATGAAATAAACCAATCCTATACACATATCGCTTTTTCAATAGAGGAAGGTGACTTTGAAAAAGTATATGAAAAATTAAAGCAATTACATGTACATATTCTTACAGGCCGCGAAAGAGATGTAAAAGATAAAAAGTCGATTTATTTTACCGATCCGGATGGGCATAAATTTGAATTCCATACAGGTACATTACAGGATCGATTGGCTTATTATCAACAGGAAAAAAAGCATATGGAGTTTTTTAATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"45662","NCBI_taxonomy_name":"Bacillus massiliigabonensis","NCBI_taxonomy_id":"1871011"}}}},"ARO_accession":"3007097","ARO_id":"45661","ARO_name":"FosM1","CARD_short_name":"FosM1","ARO_description":"FosM1 is a thiol transferase discovered in human gut microflora that leads to the resistance of fosfomycin.","ARO_category":{"36272":{"category_aro_accession":"3000133","category_aro_cvterm_id":"36272","category_aro_name":"fosfomycin thiol transferase","category_aro_description":"Catalyzes the addition of a thiol group from a nucleophilic molecule to fosfomycin.","category_aro_class_name":"AMR Gene Family"},"35944":{"category_aro_accession":"0000025","category_aro_cvterm_id":"35944","category_aro_name":"fosfomycin","category_aro_description":"Fosfomycin (also known as phosphomycin and phosphonomycin) is a broad-spectrum antibiotic produced by certain Streptomyces species. It is effective on gram positive and negative bacteria as it targets the cell wall, an essential feature shared by both bacteria. Its specific target is MurA (MurZ in E.coli), which attaches phosphoenolpyruvate (PEP) to UDP-N-acetylglucosamine, a step of commitment to cell wall synthesis. In the active site of MurA, the active cysteine molecule is alkylated which stops the catalytic reaction.","category_aro_class_name":"Antibiotic"},"45731":{"category_aro_accession":"3007149","category_aro_cvterm_id":"45731","category_aro_name":"phosphonic acid antibiotic","category_aro_description":"A group of antibiotics derived from phosphonic acids.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5773":{"model_id":"5773","model_name":"FosM2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"250"}},"model_sequences":{"sequence":{"8446":{"protein_sequence":{"accession":"DAC85640.1","sequence":"MIKGINHFLFSVSDLEKSIQFYQEVFEAKLLVKGKNTAYFDLNGLWLALNMEKDIPRNEIKQSYTHIAFSIEETAFDRMYDQLEKLGVNILTGRPRDEKDKKSIYFTDPDGHKFEFHTGTLQDRLNYYKQEKPYMDFYI"},"dna_sequence":{"accession":"BK012112.1","fmin":"0","fmax":"420","strand":"+","sequence":"TTGATAAAAGGAATAAACCATTTTCTATTTTCTGTTTCTGATTTGGAGAAATCGATCCAATTTTATCAAGAAGTCTTTGAGGCAAAATTATTGGTCAAAGGGAAAAATACAGCCTATTTTGATTTGAATGGTCTCTGGCTGGCGCTTAATATGGAAAAAGATATCCCTCGGAATGAAATAAAACAGTCCTATACACATATTGCCTTTTCCATAGAAGAAACTGCGTTTGACCGTATGTATGATCAATTAGAGAAATTAGGTGTTAACATCTTAACGGGTCGTCCCAGAGATGAAAAGGATAAAAAGTCCATTTATTTTACCGATCCTGATGGTCATAAGTTTGAATTTCATACCGGCACATTGCAAGATCGATTGAATTATTATAAACAGGAGAAGCCATATATGGATTTTTACATATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"45664","NCBI_taxonomy_name":"Gracilibacillus timonensis","NCBI_taxonomy_id":"1816696"}}}},"ARO_accession":"3007098","ARO_id":"45663","ARO_name":"FosM2","CARD_short_name":"FosM2","ARO_description":"FosM2 is a thiol transferase discovered in human gut microflora that leads to the resistance of fosfomycin.","ARO_category":{"36272":{"category_aro_accession":"3000133","category_aro_cvterm_id":"36272","category_aro_name":"fosfomycin thiol transferase","category_aro_description":"Catalyzes the addition of a thiol group from a nucleophilic molecule to fosfomycin.","category_aro_class_name":"AMR Gene Family"},"35944":{"category_aro_accession":"0000025","category_aro_cvterm_id":"35944","category_aro_name":"fosfomycin","category_aro_description":"Fosfomycin (also known as phosphomycin and phosphonomycin) is a broad-spectrum antibiotic produced by certain Streptomyces species. It is effective on gram positive and negative bacteria as it targets the cell wall, an essential feature shared by both bacteria. Its specific target is MurA (MurZ in E.coli), which attaches phosphoenolpyruvate (PEP) to UDP-N-acetylglucosamine, a step of commitment to cell wall synthesis. In the active site of MurA, the active cysteine molecule is alkylated which stops the catalytic reaction.","category_aro_class_name":"Antibiotic"},"45731":{"category_aro_accession":"3007149","category_aro_cvterm_id":"45731","category_aro_name":"phosphonic acid antibiotic","category_aro_description":"A group of antibiotics derived from phosphonic acids.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5774":{"model_id":"5774","model_name":"FosM3","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"250"}},"model_sequences":{"sequence":{"8447":{"protein_sequence":{"accession":"DAC85641.1","sequence":"MVKIKGLNHLLFSVSNLEESIEFYRNVFDAKLLVKGRSTAYFDVNGIWLALNEEKDIPRNEINQSYTHIAFSIEETEFDGIYHKLKELNVNILSGRPRDQKDKKSIYFTDLDGHKFEFHTGTLQDRLDYYKEEKKHMEFYNE"},"dna_sequence":{"accession":"BK012113.1","fmin":"0","fmax":"429","strand":"+","sequence":"ATGGTGAAGATAAAAGGTCTAAATCATTTATTATTTTCTGTGTCTAATTTAGAGGAATCAATAGAATTTTATAGAAATGTGTTTGATGCCAAGCTGTTAGTTAAAGGGAGAAGCACGGCCTATTTCGACGTAAATGGTATATGGCTTGCCCTTAATGAGGAAAAAGATATTCCTCGTAATGAAATTAACCAGTCATACACACATATAGCCTTTTCAATAGAAGAAACAGAGTTTGATGGAATATATCACAAGCTAAAAGAATTGAATGTAAACATCTTATCAGGTCGTCCAAGAGACCAGAAAGATAAAAAGTCTATTTACTTTACAGACCTGGATGGTCATAAGTTTGAGTTTCACACAGGTACTTTACAAGACAGGCTGGATTATTACAAAGAGGAAAAAAAACATATGGAGTTTTACAATGAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"45666","NCBI_taxonomy_name":"Bacillus phocaeensis","NCBI_taxonomy_id":"1720202"}}}},"ARO_accession":"3007099","ARO_id":"45665","ARO_name":"FosM3","CARD_short_name":"FosM3","ARO_description":"FosM3 is a thiol transferase discovered in human gut microflora that leads to the resistance of fosfomycin.","ARO_category":{"36272":{"category_aro_accession":"3000133","category_aro_cvterm_id":"36272","category_aro_name":"fosfomycin thiol transferase","category_aro_description":"Catalyzes the addition of a thiol group from a nucleophilic molecule to fosfomycin.","category_aro_class_name":"AMR Gene Family"},"35944":{"category_aro_accession":"0000025","category_aro_cvterm_id":"35944","category_aro_name":"fosfomycin","category_aro_description":"Fosfomycin (also known as phosphomycin and phosphonomycin) is a broad-spectrum antibiotic produced by certain Streptomyces species. It is effective on gram positive and negative bacteria as it targets the cell wall, an essential feature shared by both bacteria. Its specific target is MurA (MurZ in E.coli), which attaches phosphoenolpyruvate (PEP) to UDP-N-acetylglucosamine, a step of commitment to cell wall synthesis. In the active site of MurA, the active cysteine molecule is alkylated which stops the catalytic reaction.","category_aro_class_name":"Antibiotic"},"45731":{"category_aro_accession":"3007149","category_aro_cvterm_id":"45731","category_aro_name":"phosphonic acid antibiotic","category_aro_description":"A group of antibiotics derived from phosphonic acids.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5775":{"model_id":"5775","model_name":"BcIII","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"350"}},"model_sequences":{"sequence":{"8450":{"protein_sequence":{"accession":"EJR72097.1","sequence":"MFVLNKFFTNSHYKKIVPVVLLSCATLIGCSNSNTQSESTKQTNQTNQVKQENIGNHAFAKLEKEYNAKLGIYALDTSTNQTVAYHADDRFAFASTSKSLAVGALLRQNSIEALDERITYTREDLSNYNPITEMHVDTGMTLKELADASVRYSDSTAHNLILKKLGGPSAFEKILRKMGDTVTNSERFEPELNEVNPGETHDTSTPKAIAKTLQSFTLGTVLPSEKRELLVDWMKRNTTGNKLIRAGVPKGWEVADKTGAGSYGTRNDIAIIWPPNKKPIVLSILSNHDKEDAEYDDTLIADATKIVLETLKVTNK"},"dna_sequence":{"accession":"AHFI01000047.1","fmin":"24003","fmax":"24954","strand":"-","sequence":"ATGTTCGTTTTAAACAAGTTCTTTACCAATTCACATTACAAAAAAATTGTACCTGTCGTATTACTTTCATGCGCGACACTGATAGGGTGTTCTAATAGTAATACGCAATCAGAATCAACTAAACAAACAAATCAAACCAATCAAGTTAAGCAAGAAAATATAGGTAATCATGCTTTTGCTAAACTTGAAAAAGAATATAACGCTAAACTTGGTATTTACGCACTGGACACAAGTACGAATCAGACTGTTGCTTACCATGCAGATGATCGTTTTGCATTTGCCTCTACATCTAAATCATTAGCAGTGGGAGCTCTTTTACGTCAGAATTCAATAGAAGCTCTTGATGAAAGAATTACGTATACACGTGAAGACCTATCTAATTATAATCCAATTACTGAAATGCATGTGGATACAGGAATGACGTTAAAAGAACTTGCAGATGCTTCTGTTCGATATAGTGACAGTACGGCACATAATTTAATTCTTAAAAAGTTAGGTGGTCCATCCGCATTTGAAAAAATCTTGAGGAAAATGGGTGATACTGTTACTAACTCCGAGCGATTTGAACCTGAATTAAATGAAGTAAATCCAGGAGAAACACATGATACGAGTACACCAAAAGCAATCGCTAAGACGCTTCAATCTTTTACATTAGGAACTGTACTACCATCTGAGAAACGTGAACTGTTAGTAGATTGGATGAAGAGAAATACGACTGGGAATAAATTAATTCGTGCGGGTGTACCAAAAGGATGGGAAGTAGCTGATAAAACAGGTGCAGGATCTTATGGAACAAGGAATGATATCGCAATTATTTGGCCACCAAATAAAAAGCCGATTGTTCTTTCCATCCTTTCTAATCATGATAAAGAAGATGCAGAATACGATGATACACTTATTGCAGACGCTACGAAAATCGTGTTAGAAACTCTAAAAGTTACGAATAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"45669","NCBI_taxonomy_name":"Bacillus cereus VD166","NCBI_taxonomy_id":"1053240"}}}},"ARO_accession":"3007101","ARO_id":"45668","ARO_name":"BcIII","CARD_short_name":"BcIII","ARO_description":"Bacillus cereus beta-lactamase III is a class A beta-lactamase that breaks down a number of penicillins and cephalosporins in Bacillus cereus.","ARO_category":{"45667":{"category_aro_accession":"3007100","category_aro_cvterm_id":"45667","category_aro_name":"class A Bacillus cereus Bc beta-lactamase","category_aro_description":"Class A Bacillus cereus Bc beta-lactamases are enzymes that break down beta-lactam antibiotics, particularly penicillins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5776":{"model_id":"5776","model_name":"KPC-93","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"8451":{"protein_sequence":{"accession":"QYZ75849.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNNRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"MZ569034.1","fmin":"0","fmax":"897","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAACCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3007102","ARO_id":"45670","ARO_name":"KPC-93","CARD_short_name":"KPC-93","ARO_description":"KPC-93 is a KPC beta-lactamase.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5777":{"model_id":"5777","model_name":"nimA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"150"}},"model_sequences":{"sequence":{"8452":{"protein_sequence":{"accession":"CAA50581.1","sequence":"MFREMRRKRQLLPPEESLAILERMTGGTLALHGDNGYPYAVPVSYVYADGKIYFHGAVQGHKMDAIRQHPEVSFCVVEQDRIVPAEFTTYFRSVIVFGKARILTDEVEKRAALLRLAEKYSSGESGMQDEIDKGFDHLVMVEITVEHMTGKEAIQLVRRKGNNRWDAFPSKDVFIR"},"dna_sequence":{"accession":"X71444.1","fmin":"1613","fmax":"2144","strand":"+","sequence":"ATGTTCAGAGAAATGCGGCGCAAACGCCAGTTGTTGCCGCCCGAAGAAAGCTTGGCGATACTGGAGCGCATGACCGGCGGTACGCTTGCCCTTCATGGCGACAACGGATATCCGTATGCCGTCCCCGTGAGCTATGTGTATGCCGACGGGAAGATTTATTTTCACGGTGCCGTGCAAGGGCATAAGATGGATGCCATCAGGCAGCATCCCGAAGTCTCGTTTTGTGTGGTGGAGCAAGACCGGATAGTTCCTGCCGAGTTTACAACCTATTTCCGGAGTGTCATTGTCTTCGGTAAAGCCCGTATCCTGACCGATGAGGTCGAGAAGCGTGCCGCTCTGCTTCGGCTGGCAGAGAAGTATTCGTCCGGCGAGTCGGGTATGCAAGACGAGATAGACAAGGGATTCGACCATCTGGTAATGGTGGAGATAACCGTCGAGCACATGACAGGCAAGGAGGCTATACAGCTGGTGCGCAGAAAGGGAAATAACAGGTGGGACGCTTTTCCGTCAAAGGACGTTTTTATCAGATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39546","NCBI_taxonomy_name":"Phocaeicola vulgatus","NCBI_taxonomy_id":"821"}}}},"ARO_accession":"3007104","ARO_id":"45672","ARO_name":"nimA","CARD_short_name":"nimA","ARO_description":"nimA is a nitroimidazole reductase mainly found in Bacteroides fragilis that is associated with the deactivation of nitroimidazole antibiotics such as metronidazole. Minimum inhibitory concentrations observed in isolates vary greatly depending on species, strain, and nitroimidazole treatment.","ARO_category":{"45671":{"category_aro_accession":"3007103","category_aro_cvterm_id":"45671","category_aro_name":"nitroimidazole reductase","category_aro_description":"Nitroimidazole reductases are a group of enzymes that deactivate nitroimidazole antibiotics by reducing their nitro functional group to an amino group. These enzymes are associated with resistance to nitroimidazole derivatives in Bacteroides fragilis but have also been reported in a variety of anaerobic Gram-negative and Gram-positive genera. The minimum inhibitory concentrations for these enzymes vary greatly depending on species, strain, and precise nitroimidazole treatment used.","category_aro_class_name":"AMR Gene Family"},"37033":{"category_aro_accession":"3000689","category_aro_cvterm_id":"37033","category_aro_name":"metronidazole","category_aro_description":"Metronidazole is a nitroimidazole that is active against anaerobic bacteria and protozoa. It is not effective against aerobic bacteria. Nitroimidazoles act by oxidizing DNA causing strand breaks and cell death.","category_aro_class_name":"Antibiotic"},"41239":{"category_aro_accession":"3004115","category_aro_cvterm_id":"41239","category_aro_name":"nitroimidazole antibiotic","category_aro_description":"Nitroimidazoles are a group of drugs that have both antiprotozoal and antibacterial activity, classified with respect to the location of the nitro functional group.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5778":{"model_id":"5778","model_name":"nimC","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"150"}},"model_sequences":{"sequence":{"8453":{"protein_sequence":{"accession":"CAA54269.1","sequence":"MFRAMRPKRHELPTDESVGILKRMTNGTLALHGDGDYPYAVPVSYVYSDGRIYFHTATQGHKVDALMRNDKVSFCVVEQDDVKSAEFTTYFRSVIPFGRARILTDETENGAALQLLADKYSSGMPGLEAVIAKGFRHLLMVEIDIEHLTGKESIELVREKNDM"},"dna_sequence":{"accession":"X76948.1","fmin":"1638","fmax":"2130","strand":"+","sequence":"ATGTTCAGAGCGATGCGTCCGAAGCGGCACGAGTTGCCCACCGATGAGAGCGTAGGCATATTGAAGCGAATGACCAACGGCACGCTGGCCCTGCATGGCGATGGCGATTATCCGTATGCCGTGCCCGTCAGCTATGTGTACAGCGACGGGCGAATCTATTTCCACACGGCCACGCAAGGGCATAAGGTAGATGCCCTGATGCGGAACGACAAGGTATCGTTCTGCGTGGTGGAGCAAGATGACGTGAAATCTGCCGAGTTCACCACTTACTTCCGGAGCGTAATACCGTTCGGCAGGGCACGCATCCTGACGGACGAGACGGAGAACGGTGCCGCATTGCAGCTGCTTGCCGACAAATATTCGTCCGGTATGCCCGGTCTGGAGGCCGTGATAGCCAAAGGCTTCCGTCACCTGCTGATGGTGGAGATAGATATTGAGCACCTGACGGGCAAGGAATCTATCGAGCTGGTCAGGGAAAAGAATGACATGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39568","NCBI_taxonomy_name":"Bacteroides thetaiotaomicron","NCBI_taxonomy_id":"818"}}}},"ARO_accession":"3007105","ARO_id":"45673","ARO_name":"nimC","CARD_short_name":"nimC","ARO_description":"nimC is a nitroimidazole reductase mainly found in Bacteroides fragilis that is associated with the deactivation of nitroimidazole antibiotics such as metronidazole. Minimum inhibitory concentrations observed in isolates vary greatly depending on species, strain, and nitroimidazole treatment.","ARO_category":{"45671":{"category_aro_accession":"3007103","category_aro_cvterm_id":"45671","category_aro_name":"nitroimidazole reductase","category_aro_description":"Nitroimidazole reductases are a group of enzymes that deactivate nitroimidazole antibiotics by reducing their nitro functional group to an amino group. These enzymes are associated with resistance to nitroimidazole derivatives in Bacteroides fragilis but have also been reported in a variety of anaerobic Gram-negative and Gram-positive genera. The minimum inhibitory concentrations for these enzymes vary greatly depending on species, strain, and precise nitroimidazole treatment used.","category_aro_class_name":"AMR Gene Family"},"37033":{"category_aro_accession":"3000689","category_aro_cvterm_id":"37033","category_aro_name":"metronidazole","category_aro_description":"Metronidazole is a nitroimidazole that is active against anaerobic bacteria and protozoa. It is not effective against aerobic bacteria. Nitroimidazoles act by oxidizing DNA causing strand breaks and cell death.","category_aro_class_name":"Antibiotic"},"41239":{"category_aro_accession":"3004115","category_aro_cvterm_id":"41239","category_aro_name":"nitroimidazole antibiotic","category_aro_description":"Nitroimidazoles are a group of drugs that have both antiprotozoal and antibacterial activity, classified with respect to the location of the nitro functional group.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5780":{"model_id":"5780","model_name":"nimE","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"150"}},"model_sequences":{"sequence":{"8455":{"protein_sequence":{"accession":"QCQ47774.1","sequence":"MFREMRRKRQLLPQEESVAILEKMTNGTLALHGDNGYPYAVPLSYFYADGKIYFHCAKIGHKVDAIMQNNKVSFCVVEQDNIKPAEFTTYFRSVIVFGKAYILTDETEKRMAMTLLVNKYSFGEPGLSDEIAKSINHLLMVKIDIEHMTGKEAIDLVREKEKFCTSEKTS"},"dna_sequence":{"accession":"CP036548.1","fmin":"4326","fmax":"4839","strand":"+","sequence":"ATGTTCAGAGAAATGCGTCGTAAACGACAGTTGTTGCCACAAGAAGAGAGCGTGGCAATTCTTGAAAAAATGACAAACGGGACTTTAGCTCTCCACGGAGATAATGGCTATCCTTATGCCGTTCCTCTCAGTTATTTTTATGCTGATGGCAAAATCTATTTTCATTGCGCCAAGATAGGGCATAAGGTGGACGCTATTATGCAAAACAATAAAGTATCGTTTTGCGTTGTGGAACAAGACAATATTAAACCTGCCGAATTCACGACCTACTTTCGAAGTGTGATAGTCTTTGGAAAGGCCTATATTTTAACCGACGAAACAGAAAAACGTATGGCTATGACTTTGCTGGTGAATAAATATTCTTTCGGTGAGCCAGGTTTGTCTGATGAAATAGCCAAAAGCATCAACCATCTACTGATGGTAAAGATCGATATCGAACACATGACGGGCAAGGAGGCCATCGATTTGGTTAGAGAGAAAGAAAAGTTTTGTACTTCAGAGAAAACCTCTTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35916","NCBI_taxonomy_name":"Bacteroides fragilis","NCBI_taxonomy_id":"817"}}}},"ARO_accession":"3007107","ARO_id":"45675","ARO_name":"nimE","CARD_short_name":"nimE","ARO_description":"nimE is a nitroimidazole reductase mainly found in Bacteroides fragilis that is associated with the deactivation of nitroimidazole antibiotics such as metronidazole. Minimum inhibitory concentrations observed in isolates vary greatly depending on species, strain, and nitroimidazole treatment.","ARO_category":{"45671":{"category_aro_accession":"3007103","category_aro_cvterm_id":"45671","category_aro_name":"nitroimidazole reductase","category_aro_description":"Nitroimidazole reductases are a group of enzymes that deactivate nitroimidazole antibiotics by reducing their nitro functional group to an amino group. These enzymes are associated with resistance to nitroimidazole derivatives in Bacteroides fragilis but have also been reported in a variety of anaerobic Gram-negative and Gram-positive genera. The minimum inhibitory concentrations for these enzymes vary greatly depending on species, strain, and precise nitroimidazole treatment used.","category_aro_class_name":"AMR Gene Family"},"37033":{"category_aro_accession":"3000689","category_aro_cvterm_id":"37033","category_aro_name":"metronidazole","category_aro_description":"Metronidazole is a nitroimidazole that is active against anaerobic bacteria and protozoa. It is not effective against aerobic bacteria. Nitroimidazoles act by oxidizing DNA causing strand breaks and cell death.","category_aro_class_name":"Antibiotic"},"41239":{"category_aro_accession":"3004115","category_aro_cvterm_id":"41239","category_aro_name":"nitroimidazole antibiotic","category_aro_description":"Nitroimidazoles are a group of drugs that have both antiprotozoal and antibacterial activity, classified with respect to the location of the nitro functional group.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5916":{"model_id":"5916","model_name":"LnuH","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"8648":{"protein_sequence":{"accession":"WP_051021433.1","sequence":"MTQLQMINKTKSIAQQDENVSAVFMYGSFTKSEGDKYSDIEFYIFLKNKENFSSEKWVNQIHPVALYFTNEYGSEVAIFENMVRGEFHFLKTEEIEIIKSWDGIVAFSDFDQMNLIDKDGHLTKTLNQIKTKSPERITNENILWLSQSLLNVILTTSNLIKREEFAHAHHSLSNVQKYLLWLIRARTNKTQHWESPTKSLEKDIDTTWYFAYKTVTSDLNPKNIILAFENSLNLSEKLFDELNIEPKMKEILHEIRKNYR"},"dna_sequence":{"accession":"NC_020125.1","fmin":"1861440","fmax":"1862223","strand":"-","sequence":"ATGACGCAGTTACAAATGATTAACAAAACAAAATCTATAGCTCAACAAGACGAAAATGTTTCCGCTGTTTTTATGTATGGTTCATTTACTAAAAGCGAAGGAGATAAATATTCTGATATCGAATTTTACATCTTTTTAAAAAATAAAGAAAATTTCTCGTCGGAAAAATGGGTAAATCAAATTCATCCTGTGGCATTATATTTTACAAATGAATATGGAAGCGAAGTTGCTATTTTTGAGAATATGGTCAGAGGCGAATTTCATTTTTTAAAAACGGAGGAAATTGAAATTATCAAATCTTGGGACGGAATTGTTGCATTTAGCGATTTTGACCAAATGAACCTAATCGACAAAGACGGACATTTAACGAAAACACTAAATCAAATCAAAACGAAATCGCCCGAAAGAATAACAAATGAAAACATCTTGTGGTTAAGTCAATCATTACTGAATGTTATACTGACAACAAGCAACTTAATTAAGCGAGAAGAATTTGCTCATGCTCATCATAGTTTATCAAATGTTCAGAAATATTTGCTTTGGCTTATTAGAGCAAGAACAAACAAAACCCAACATTGGGAAAGTCCAACTAAAAGTCTTGAAAAGGATATTGATACGACTTGGTATTTTGCGTATAAAACAGTAACATCGGATTTAAATCCTAAAAATATAATTTTAGCTTTTGAAAACTCATTAAATTTATCGGAAAAACTATTTGACGAACTAAATATTGAACCAAAAATGAAAGAAATCCTACATGAAATAAGAAAAAACTACCGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"46175","NCBI_taxonomy_name":"Riemerella anatipestifer RA-CH-2","NCBI_taxonomy_id":"1271752"}}}},"ARO_accession":"3004600","ARO_id":"42533","ARO_name":"LnuH","CARD_short_name":"LnuH","ARO_description":"LnuH is a lincosamide nucleotidyltransferase transferase.","ARO_category":{"36360":{"category_aro_accession":"3000221","category_aro_cvterm_id":"36360","category_aro_name":"lincosamide nucleotidyltransferase (LNU)","category_aro_description":"Resistance to the lincosamide antibiotic by ATP-dependent modification of the 3' and\/or 4'-hydroxyl groups of the methylthiolincosamide sugar.","category_aro_class_name":"AMR Gene Family"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5781":{"model_id":"5781","model_name":"nimF","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"150"}},"model_sequences":{"sequence":{"8471":{"protein_sequence":{"accession":"CAD56147.1","sequence":"MFREMRRKRQQLSAEESIAILERMTNGVLALHGDEGYPYAVPVSYVYADGKIYFHSAMKGHKVDAIMRNERVSFCVVERDDVCPGEFTTYFRSVVLFGKTRILTEEAEKLAALSLLADKYSPGEPGKDAEIAKGFNLLMVEIAVEHMTGKE"},"dna_sequence":{"accession":"AJ515145.1","fmin":"0","fmax":"453","strand":"+","sequence":"ATGTTCAGAGAAATGCGGCGTAAGCGGCAGCAACTGTCTGCCGAAGAAAGTATTGCCATCCTTGAACGGATGACGAACGGAGTGCTGGCACTTCATGGGGATGAAGGTTATCCGTATGCCGTCCCTGTCAGTTATGTATATGCGGATGGGAAGATTTATTTCCACAGTGCCATGAAAGGCCATAAGGTGGATGCCATCATGCGGAATGAACGTGTTTCGTTCTGCGTAGTGGAACGGGACGATGTCTGTCCGGGCGAGTTCACCACCTACTTCAGGAGCGTGGTGCTCTTCGGCAAGACCCGTATTTTGACGGAAGAGGCCGAAAAGTTGGCGGCCTTGAGCTTGCTTGCCGACAAATATTCACCGGGAGAACCCGGTAAAGATGCCGAAATCGCCAAAGGGTTTAACCTGCTGATGGTGGAAATTGCAGTCGAGCACATGACAGGCAAGGAA","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39546","NCBI_taxonomy_name":"Phocaeicola vulgatus","NCBI_taxonomy_id":"821"}}}},"ARO_accession":"3007108","ARO_id":"45676","ARO_name":"nimF","CARD_short_name":"nimF","ARO_description":"nimF is a nitroimidazole reductase that shares significant identity with other nim genes which are associated with the deactivation of nitroimidazole antibiotics.","ARO_category":{"45671":{"category_aro_accession":"3007103","category_aro_cvterm_id":"45671","category_aro_name":"nitroimidazole reductase","category_aro_description":"Nitroimidazole reductases are a group of enzymes that deactivate nitroimidazole antibiotics by reducing their nitro functional group to an amino group. These enzymes are associated with resistance to nitroimidazole derivatives in Bacteroides fragilis but have also been reported in a variety of anaerobic Gram-negative and Gram-positive genera. The minimum inhibitory concentrations for these enzymes vary greatly depending on species, strain, and precise nitroimidazole treatment used.","category_aro_class_name":"AMR Gene Family"},"37033":{"category_aro_accession":"3000689","category_aro_cvterm_id":"37033","category_aro_name":"metronidazole","category_aro_description":"Metronidazole is a nitroimidazole that is active against anaerobic bacteria and protozoa. It is not effective against aerobic bacteria. Nitroimidazoles act by oxidizing DNA causing strand breaks and cell death.","category_aro_class_name":"Antibiotic"},"41239":{"category_aro_accession":"3004115","category_aro_cvterm_id":"41239","category_aro_name":"nitroimidazole antibiotic","category_aro_description":"Nitroimidazoles are a group of drugs that have both antiprotozoal and antibacterial activity, classified with respect to the location of the nitro functional group.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5782":{"model_id":"5782","model_name":"nimG","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"150"}},"model_sequences":{"sequence":{"8457":{"protein_sequence":{"accession":"OUQ50894.1","sequence":"MFREMRRKRQLLSTKESVAILERMTNGTLALHGDDGYPYAVPVSYVYADGKIYFHSAMKGHKVDAISRNDKISFCVVEQDDIKPSEFTTYFRSVIVFGKARILTDEGEKRVALGLLADKYSHGEAGMEAEIAKGFNHLLMVEITVEHMTGKESIELIKERNDCS"},"dna_sequence":{"accession":"NFLR01000029.1","fmin":"2830","fmax":"3325","strand":"-","sequence":"ATGTTTAGAGAAATGCGCCGTAAACGGCAATTATTGTCAACAAAAGAAAGCGTTGCCATCCTTGAAAGGATGACGAACGGGACATTGGCTCTTCACGGGGATGACGGTTACCCGTATGCCGTCCCTGTCAGTTATGTATATGCCGATGGCAAAATATACTTCCACAGTGCCATGAAAGGTCACAAAGTGGATGCCATTTCGCGGAATGACAAGATTTCGTTCTGCGTGGTGGAACAGGATGATATCAAGCCTTCTGAGTTTACCACTTACTTCCGGAGCGTGATAGTTTTTGGCAAGGCCCGCATATTGACGGATGAAGGCGAGAAACGTGTTGCTTTGGGTTTATTGGCAGACAAGTATTCGCATGGCGAAGCTGGCATGGAGGCTGAAATAGCTAAGGGATTCAACCATTTGTTGATGGTGGAAATTACAGTTGAGCATATGACAGGCAAGGAGTCCATAGAACTGATTAAAGAAAGAAATGACTGTTCTTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"45678","NCBI_taxonomy_name":"Alistipes sp. An116","NCBI_taxonomy_id":"1965546"}}}},"ARO_accession":"3007109","ARO_id":"45677","ARO_name":"nimG","CARD_short_name":"nimG","ARO_description":"nimG is a nitroimidazole reductase that shares significant identity with other nim genes which are associated with the deactivation of nitroimidazole antibiotics.","ARO_category":{"45671":{"category_aro_accession":"3007103","category_aro_cvterm_id":"45671","category_aro_name":"nitroimidazole reductase","category_aro_description":"Nitroimidazole reductases are a group of enzymes that deactivate nitroimidazole antibiotics by reducing their nitro functional group to an amino group. These enzymes are associated with resistance to nitroimidazole derivatives in Bacteroides fragilis but have also been reported in a variety of anaerobic Gram-negative and Gram-positive genera. The minimum inhibitory concentrations for these enzymes vary greatly depending on species, strain, and precise nitroimidazole treatment used.","category_aro_class_name":"AMR Gene Family"},"37033":{"category_aro_accession":"3000689","category_aro_cvterm_id":"37033","category_aro_name":"metronidazole","category_aro_description":"Metronidazole is a nitroimidazole that is active against anaerobic bacteria and protozoa. It is not effective against aerobic bacteria. Nitroimidazoles act by oxidizing DNA causing strand breaks and cell death.","category_aro_class_name":"Antibiotic"},"41239":{"category_aro_accession":"3004115","category_aro_cvterm_id":"41239","category_aro_name":"nitroimidazole antibiotic","category_aro_description":"Nitroimidazoles are a group of drugs that have both antiprotozoal and antibacterial activity, classified with respect to the location of the nitro functional group.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5783":{"model_id":"5783","model_name":"nimH","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"150"}},"model_sequences":{"sequence":{"8478":{"protein_sequence":{"accession":"ACR56004.1","sequence":"FREMRRKRQLLPTEESITILEKMTNGTLALHGDNGYPYAVPVSYVYADGKIYFHSAVKGHKVDAILRNNKVSFCVVEQDDVKPAEFTTYFRSVIAFGKARILADEGEKQLAFRLLADKYSHGEVGMEAEIAKGFNHLLMVEIMVEHMTGKE"},"dna_sequence":{"accession":"FJ969397.1","fmin":"2","fmax":"455","strand":"+","sequence":"TTCAGAGAAATGCGGCGTAAGCGGCAATTGTTGCCAACTGAGGAAAGCATCACTATCCTCGAAAAGATGACGAACGGAACGTTGGCTCTCCATGGGGACAACGGCTATCCGTATGCCGTCCCCGTCAGTTATGTATATGCAGATGGCAAGATATACTTCCACAGTGCCGTGAAAGGGCATAAAGTGGATGCCATCTTGCGAAACAATAAGGTCTCGTTCTGCGTGGTGGAGCAAGATGATGTCAAGCCTGCTGAATTTACCACTTACTTCCGAAGCGTGATAGCTTTCGGCAAAGCACGTATTCTGGCGGATGAGGGAGAAAAACAGCTTGCCTTTCGGCTATTGGCAGACAAGTATTCGCATGGTGAGGTCGGCATGGAAGCTGAAATAGCCAAAGGTTTCAATCATTTGCTGATGGTGGAAATCATGGTTGAGCACATGACAGGCAAGGAA","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35916","NCBI_taxonomy_name":"Bacteroides fragilis","NCBI_taxonomy_id":"817"}}}},"ARO_accession":"3007110","ARO_id":"45679","ARO_name":"nimH","CARD_short_name":"nimH","ARO_description":"nimH is a nitroimidazole reductase mainly found in Bacteroides fragilis that is associated with the deactivation of nitroimidazole antibiotics such as metronidazole. Minimum inhibitory concentrations observed in isolates vary greatly depending on species, strain, and nitroimidazole treatment.","ARO_category":{"45671":{"category_aro_accession":"3007103","category_aro_cvterm_id":"45671","category_aro_name":"nitroimidazole reductase","category_aro_description":"Nitroimidazole reductases are a group of enzymes that deactivate nitroimidazole antibiotics by reducing their nitro functional group to an amino group. These enzymes are associated with resistance to nitroimidazole derivatives in Bacteroides fragilis but have also been reported in a variety of anaerobic Gram-negative and Gram-positive genera. The minimum inhibitory concentrations for these enzymes vary greatly depending on species, strain, and precise nitroimidazole treatment used.","category_aro_class_name":"AMR Gene Family"},"37033":{"category_aro_accession":"3000689","category_aro_cvterm_id":"37033","category_aro_name":"metronidazole","category_aro_description":"Metronidazole is a nitroimidazole that is active against anaerobic bacteria and protozoa. It is not effective against aerobic bacteria. Nitroimidazoles act by oxidizing DNA causing strand breaks and cell death.","category_aro_class_name":"Antibiotic"},"41239":{"category_aro_accession":"3004115","category_aro_cvterm_id":"41239","category_aro_name":"nitroimidazole antibiotic","category_aro_description":"Nitroimidazoles are a group of drugs that have both antiprotozoal and antibacterial activity, classified with respect to the location of the nitro functional group.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5784":{"model_id":"5784","model_name":"nimI","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"150"}},"model_sequences":{"sequence":{"8459":{"protein_sequence":{"accession":"ERK40265.1","sequence":"MNRLDNMEFREMRRKRQQLSDAECVGILENATSGTLALQGDGGYPYAVPISYVHADGKLYFHSALKGHKVDAIRGCDKASFCVIEQDEVHGEEYTPYFRSVIAFGRIRILEDEAERMAAARLLGDRYHPHHEEALGRELAKSFSHMLVICLDIEHMTGKEAIELVRMKRQRA"},"dna_sequence":{"accession":"AWEY01000007.1","fmin":"190961","fmax":"191480","strand":"-","sequence":"ATGAATCGTTTGGACAATATGGAATTTAGAGAAATGCGGCGCAAACGCCAGCAACTTTCAGACGCGGAGTGCGTCGGAATCCTGGAGAACGCCACGTCGGGAACCCTTGCCCTGCAAGGGGATGGCGGCTATCCCTACGCCGTGCCTATCAGTTATGTCCACGCCGACGGCAAACTGTACTTCCACAGTGCTCTGAAAGGCCACAAAGTCGACGCCATCAGAGGCTGCGACAAGGCTTCGTTTTGCGTCATCGAGCAAGACGAGGTGCATGGCGAGGAGTACACGCCCTACTTCCGCAGCGTCATCGCTTTTGGACGAATCCGCATTCTTGAAGACGAAGCGGAGCGGATGGCGGCCGCCCGGCTGCTCGGCGACCGCTATCATCCCCATCATGAGGAAGCGCTCGGCAGGGAACTGGCCAAGAGTTTCAGCCACATGCTGGTCATCTGTCTCGACATCGAGCACATGACAGGCAAGGAAGCCATCGAGTTGGTGAGGATGAAGCGGCAGCGCGCATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"45681","NCBI_taxonomy_name":"Prevotella baroniae F0067","NCBI_taxonomy_id":"1115809"}}}},"ARO_accession":"3007111","ARO_id":"45680","ARO_name":"nimI","CARD_short_name":"nimI","ARO_description":"nimI is a nitroimidazole reductase discovered in the Prevotella baroniae that is associated with the deactivation of nitroimidazole antibiotics such as metronidazole. Although not found in Bacteroids fragilis, the source organism of most nim genes, nimI shares significant similarity with other nitroimidazole reductases. nimI is chromosomally encoded in P. baroniae, suggesting that it is intrinsic to this species.","ARO_category":{"45671":{"category_aro_accession":"3007103","category_aro_cvterm_id":"45671","category_aro_name":"nitroimidazole reductase","category_aro_description":"Nitroimidazole reductases are a group of enzymes that deactivate nitroimidazole antibiotics by reducing their nitro functional group to an amino group. These enzymes are associated with resistance to nitroimidazole derivatives in Bacteroides fragilis but have also been reported in a variety of anaerobic Gram-negative and Gram-positive genera. The minimum inhibitory concentrations for these enzymes vary greatly depending on species, strain, and precise nitroimidazole treatment used.","category_aro_class_name":"AMR Gene Family"},"37033":{"category_aro_accession":"3000689","category_aro_cvterm_id":"37033","category_aro_name":"metronidazole","category_aro_description":"Metronidazole is a nitroimidazole that is active against anaerobic bacteria and protozoa. It is not effective against aerobic bacteria. Nitroimidazoles act by oxidizing DNA causing strand breaks and cell death.","category_aro_class_name":"Antibiotic"},"41239":{"category_aro_accession":"3004115","category_aro_cvterm_id":"41239","category_aro_name":"nitroimidazole antibiotic","category_aro_description":"Nitroimidazoles are a group of drugs that have both antiprotozoal and antibacterial activity, classified with respect to the location of the nitro functional group.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5785":{"model_id":"5785","model_name":"nimJ","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"150"}},"model_sequences":{"sequence":{"8473":{"protein_sequence":{"accession":"AIM40056.1","sequence":"MNEFREMRRKRQQLSEEESIAILQKATAGTLALLGDNDYPYAVPISYVYADGRLYFHSALSGHKVDAIRKCDKASFCVIEQDEVHPEKYTTFFRSVIAFGRIHIIEDETEKLETARMLVNRYNPNQEEALQKELENGLSRMLMIRFDIEHLTGKEAIELVRRHQK"},"dna_sequence":{"accession":"KJ816753.1","fmin":"19294","fmax":"19792","strand":"-","sequence":"ATGAATGAATTTAGAGAAATGAGGCGCAAACGCCAACAGCTTTCAGAAGAAGAAAGCATTGCCATATTGCAAAAAGCTACGGCCGGCACTTTAGCATTACTTGGCGACAATGACTATCCCTATGCCGTCCCCATCAGCTATGTCTATGCCGATGGCAGATTATATTTCCATAGTGCACTGAGCGGTCATAAAGTCGATGCCATACGAAAGTGTGACAAGGCTTCGTTCTGTGTCATCGAACAGGATGAAGTGCATCCAGAGAAATACACCACTTTCTTTCGGAGTGTCATCGCATTTGGAAGAATCCATATCATTGAGGATGAAACTGAGAAACTGGAAACAGCCCGGATGCTTGTGAACAGATATAATCCCAACCAAGAGGAAGCCTTGCAGAAAGAGTTGGAGAATGGCCTGTCGCGGATGCTGATGATTCGTTTCGACATAGAGCATCTTACGGGAAAAGAAGCGATAGAATTAGTGAGAAGGCATCAAAAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35916","NCBI_taxonomy_name":"Bacteroides fragilis","NCBI_taxonomy_id":"817"}}}},"ARO_accession":"3007112","ARO_id":"45682","ARO_name":"nimJ","CARD_short_name":"nimJ","ARO_description":"nimJ is a nitroimidazole reductase mainly found in Bacteroides fragilis that is associated with the deactivation of nitroimidazole antibiotics such as metronidazole. Minimum inhibitory concentrations observed in isolates vary greatly depending on species, strain, and nitroimidazole treatment.","ARO_category":{"45671":{"category_aro_accession":"3007103","category_aro_cvterm_id":"45671","category_aro_name":"nitroimidazole reductase","category_aro_description":"Nitroimidazole reductases are a group of enzymes that deactivate nitroimidazole antibiotics by reducing their nitro functional group to an amino group. These enzymes are associated with resistance to nitroimidazole derivatives in Bacteroides fragilis but have also been reported in a variety of anaerobic Gram-negative and Gram-positive genera. The minimum inhibitory concentrations for these enzymes vary greatly depending on species, strain, and precise nitroimidazole treatment used.","category_aro_class_name":"AMR Gene Family"},"37033":{"category_aro_accession":"3000689","category_aro_cvterm_id":"37033","category_aro_name":"metronidazole","category_aro_description":"Metronidazole is a nitroimidazole that is active against anaerobic bacteria and protozoa. It is not effective against aerobic bacteria. Nitroimidazoles act by oxidizing DNA causing strand breaks and cell death.","category_aro_class_name":"Antibiotic"},"41239":{"category_aro_accession":"3004115","category_aro_cvterm_id":"41239","category_aro_name":"nitroimidazole antibiotic","category_aro_description":"Nitroimidazoles are a group of drugs that have both antiprotozoal and antibacterial activity, classified with respect to the location of the nitro functional group.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5786":{"model_id":"5786","model_name":"nimK","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"150"}},"model_sequences":{"sequence":{"8461":{"protein_sequence":{"accession":"AXA20009.1","sequence":"MFREMRRKRQQLSTEECIAILEKMTSGVLALNEEGGYPYAVPLSYVYSDNKIYFHSAIKGHKIELLEKNENVSFCVIFQDHIVPEEFTTYFQSVIVFGKARILLDEKEKMSALWKLGEKYSSGNAEALSAEISKGKNHLLIIEIAIEHMTGKESIELVRAKKSIKESK"},"dna_sequence":{"accession":"MG827401.1","fmin":"3868","fmax":"4375","strand":"-","sequence":"ATGTTCAGAGAAATGCGTCGCAAGCGACAACAGTTATCCACAGAAGAGTGCATTGCTATTCTTGAAAAAATGACTTCTGGTGTATTGGCTCTTAATGAAGAAGGCGGCTATCCTTATGCCGTTCCTTTAAGTTACGTATATTCGGATAATAAAATCTACTTTCACAGTGCCATAAAAGGACATAAGATAGAATTACTGGAAAAGAATGAAAACGTCTCTTTTTGCGTAATTTTTCAAGACCATATCGTTCCTGAAGAATTTACCACTTATTTCCAAAGTGTAATTGTATTTGGCAAAGCCCGTATTTTATTGGATGAGAAGGAAAAGATGTCAGCGTTGTGGAAATTAGGAGAAAAATATTCATCAGGTAACGCCGAAGCACTGTCTGCAGAGATAAGTAAAGGGAAGAACCATCTGCTTATTATTGAGATTGCTATCGAGCATATGACAGGAAAAGAATCTATAGAGTTGGTACGGGCCAAGAAATCGATAAAAGAGTCCAAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"45684","NCBI_taxonomy_name":"Prevotella bivia","NCBI_taxonomy_id":"28125"}}}},"ARO_accession":"3007113","ARO_id":"45683","ARO_name":"nimK","CARD_short_name":"nimK","ARO_description":"nimK is a nitroimidazole reductase mainly found in Bacteroides fragilis that is associated with the deactivation of nitroimidazole antibiotics such as metronidazole. Minimum inhibitory concentrations observed in isolates vary greatly depending on species, strain, and nitroimidazole treatment.","ARO_category":{"45671":{"category_aro_accession":"3007103","category_aro_cvterm_id":"45671","category_aro_name":"nitroimidazole reductase","category_aro_description":"Nitroimidazole reductases are a group of enzymes that deactivate nitroimidazole antibiotics by reducing their nitro functional group to an amino group. These enzymes are associated with resistance to nitroimidazole derivatives in Bacteroides fragilis but have also been reported in a variety of anaerobic Gram-negative and Gram-positive genera. The minimum inhibitory concentrations for these enzymes vary greatly depending on species, strain, and precise nitroimidazole treatment used.","category_aro_class_name":"AMR Gene Family"},"37033":{"category_aro_accession":"3000689","category_aro_cvterm_id":"37033","category_aro_name":"metronidazole","category_aro_description":"Metronidazole is a nitroimidazole that is active against anaerobic bacteria and protozoa. It is not effective against aerobic bacteria. Nitroimidazoles act by oxidizing DNA causing strand breaks and cell death.","category_aro_class_name":"Antibiotic"},"41239":{"category_aro_accession":"3004115","category_aro_cvterm_id":"41239","category_aro_name":"nitroimidazole antibiotic","category_aro_description":"Nitroimidazoles are a group of drugs that have both antiprotozoal and antibacterial activity, classified with respect to the location of the nitro functional group.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5787":{"model_id":"5787","model_name":"nimB","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"150"}},"model_sequences":{"sequence":{"8463":{"protein_sequence":{"accession":"CAA50578.1","sequence":"MFREMRRKRQLLPTEESVAILERMTNGTLALHGDDGYPYAVPISYVYADGKIYFHSAMKGHKVDAILQNDKVSFCVVEQDDIRPSEFTTYFRSVIVFGKAHILTDELEKRVALGLLADKYSYGEAGMEAEIAKGFNHLLIVKIAIEHITGKEAIELTKNRNDRP"},"dna_sequence":{"accession":"X71443.1","fmin":"793","fmax":"1288","strand":"+","sequence":"ATGTTTAGAGAAATGCGACGTAAGCGGCAATTATTGCCAACAGAAGAAAGCGTTGCCATCCTTGAAAGGATGACGAACGGAACATTGGCTCTTCATGGGGACGATGGTTACCCGTATGCCGTTCCCATCAGTTATGTATATGCTGATGGCAAAATATATTTCCATAGTGCCATGAAAGGTCATAAAGTGGATGCCATTTTGCAGAATGACAAGGTATCATTCTGCGTGGTAGAACAGGATGACATCAGACCGTCTGAGTTTACCACTTACTTTCGAAGTGTGATAGTCTTTGGCAAAGCCCACATATTGACGGATGAACTCGAAAAACGTGTTGCTTTGGGTTTATTGGCAGACAAGTATTCGTATGGCGAAGCTGGCATGGAGGCTGAAATAGCCAAAGGGTTCAATCATTTGTTAATAGTGAAAATTGCAATTGAGCATATTACAGGCAAGGAAGCCATAGAACTGACCAAAAATAGGAATGACCGTCCTTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35916","NCBI_taxonomy_name":"Bacteroides fragilis","NCBI_taxonomy_id":"817"}}}},"ARO_accession":"3004655","ARO_id":"42693","ARO_name":"nimB","CARD_short_name":"nimB","ARO_description":"nimB is a nitroimidazole reductase mainly found in Bacteroides fragilis that is associated with the deactivation of nitroimidazole antibiotics such as metronidazole. Minimum inhibitory concentrations observed in isolates vary greatly depending on species, strain, and nitroimidazole treatment.","ARO_category":{"45671":{"category_aro_accession":"3007103","category_aro_cvterm_id":"45671","category_aro_name":"nitroimidazole reductase","category_aro_description":"Nitroimidazole reductases are a group of enzymes that deactivate nitroimidazole antibiotics by reducing their nitro functional group to an amino group. These enzymes are associated with resistance to nitroimidazole derivatives in Bacteroides fragilis but have also been reported in a variety of anaerobic Gram-negative and Gram-positive genera. The minimum inhibitory concentrations for these enzymes vary greatly depending on species, strain, and precise nitroimidazole treatment used.","category_aro_class_name":"AMR Gene Family"},"37033":{"category_aro_accession":"3000689","category_aro_cvterm_id":"37033","category_aro_name":"metronidazole","category_aro_description":"Metronidazole is a nitroimidazole that is active against anaerobic bacteria and protozoa. It is not effective against aerobic bacteria. Nitroimidazoles act by oxidizing DNA causing strand breaks and cell death.","category_aro_class_name":"Antibiotic"},"41239":{"category_aro_accession":"3004115","category_aro_cvterm_id":"41239","category_aro_name":"nitroimidazole antibiotic","category_aro_description":"Nitroimidazoles are a group of drugs that have both antiprotozoal and antibacterial activity, classified with respect to the location of the nitro functional group.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5788":{"model_id":"5788","model_name":"crxA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"8464":{"protein_sequence":{"accession":"MBS5055441.1","sequence":"MKLRDFFLIILLLCWCDIYAHTIKVSDKLNLIQLNENVYIHTENDNNGIVYINGGKAVIVSTPENDEETNYLIDYIRNHLKSEIVACVVDRWHPDAMGGLNAIKKANIPSYANRLTQVIAKERMLPIPENGFDITLELTVGKSKLICHYLGEAHTKDGIVVWLPNEKILFGGNQVRAKGWYGNIGDANLREWSNTIARVKDLYGDAKIVIPGHGHYGGNELLDYTINLYRPTLWGKILKWNDVQVKPVFNNCGVIFELAESDSINEGKRFLKNATIYIQQKNKNRYLKIQSPMIRHDNEESQVLSSDKGRLQIYNITMNELIEDLYYKQLYISLEEQSVDALIILKEAIR"},"dna_sequence":{"accession":"JAGZKL010000021.1","fmin":"2570","fmax":"3623","strand":"+","sequence":"ATGAAATTAAGAGACTTCTTTTTAATTATACTTTTGTTATGTTGGTGTGATATTTATGCGCATACTATCAAGGTTAGTGATAAACTGAACTTGATTCAGCTGAATGAGAACGTTTATATTCATACTGAAAATGACAATAATGGTATTGTTTATATAAATGGTGGTAAGGCTGTAATTGTTTCAACTCCTGAAAACGATGAAGAAACTAACTATTTAATTGATTATATCAGGAATCACTTGAAAAGTGAAATTGTAGCTTGTGTCGTAGATAGATGGCACCCTGATGCAATGGGCGGATTAAATGCCATTAAAAAAGCTAATATACCATCTTATGCCAACAGACTTACTCAGGTAATAGCGAAAGAAAGAATGTTACCTATTCCGGAAAATGGGTTTGATATTACTTTGGAATTGACCGTTGGCAAAAGTAAGTTGATATGTCATTATTTAGGAGAGGCACATACGAAGGATGGGATTGTGGTGTGGCTACCAAACGAGAAGATTCTTTTTGGCGGTAATCAGGTACGTGCAAAAGGTTGGTATGGAAATATTGGTGACGCTAATTTACGGGAATGGTCTAATACAATTGCCCGTGTGAAAGATTTATATGGAGATGCAAAGATCGTGATACCTGGACATGGACATTATGGAGGAAATGAATTGTTGGACTATACAATAAATCTTTATAGACCGACTTTATGGGGTAAAATCTTGAAATGGAATGATGTACAGGTAAAACCGGTATTTAATAATTGTGGGGTAATATTTGAATTAGCAGAGTCTGATTCTATCAATGAGGGAAAAAGATTCTTGAAAAATGCGACAATTTATATTCAGCAGAAGAATAAAAACAGATATTTGAAGATTCAATCTCCAATGATTAGACATGATAATGAGGAGAGCCAGGTACTGTCATCTGATAAAGGTAGGTTGCAGATATATAATATAACAATGAATGAATTGATTGAAGATTTATACTATAAACAATTATATATATCTTTAGAAGAACAATCGGTTGATGCTTTAATCATTTTGAAAGAAGCTATAAGATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"45695","NCBI_taxonomy_name":"Bacteroides sp.","NCBI_taxonomy_id":"29523"}}}},"ARO_accession":"3007118","ARO_id":"45694","ARO_name":"crxA","CARD_short_name":"crxA","ARO_description":"crxA is a subclass B1 metallo-betal-lactamase from Bacteroides xylanisolvens that hydrolyzes carbapenems such as imipenem and meropenem.","ARO_category":{"45693":{"category_aro_accession":"3007117","category_aro_cvterm_id":"45693","category_aro_name":"subclass B1 Bacteroides xylanisolvens crx beta-lactamase","category_aro_description":"Subclass B1 Bacteroides xylanisolvens crx beta-lactamases are zinc metallo-beta-lactamases that hydrolyze carbapenems.","category_aro_class_name":"AMR Gene Family"},"35990":{"category_aro_accession":"0000073","category_aro_cvterm_id":"35990","category_aro_name":"meropenem","category_aro_description":"Meropenem is an ultra-broad spectrum injectable antibiotic used to treat a wide variety of infections, including meningitis and pneumonia. It is a beta-lactam and belongs to the subgroup of carbapenem, similar to imipenem and ertapenem.","category_aro_class_name":"Antibiotic"},"36309":{"category_aro_accession":"3000170","category_aro_cvterm_id":"36309","category_aro_name":"imipenem","category_aro_description":"Imipenem is a broad-spectrum antibiotic and is usually taken with cilastatin, which prevents hydrolysis of imipenem by renal dehydropeptidase-I. It is resistant to hydrolysis by most other beta-lactamases. Notable exceptions are the KPC beta-lactamases and Ambler Class B enzymes.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5789":{"model_id":"5789","model_name":"tet(O\/32\/O)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"900"}},"model_sequences":{"sequence":{"8465":{"protein_sequence":{"accession":"CAC41371.2","sequence":"MKIINLGILAHVDAGKTTLTESLLYTSGAIAELGSVDEGTTRTDTMNLERQRGITIQTAVTSFQWEDVKVNIIDTPGHMDFLTEAYRSLSVLDGAVLVISAKDGVQAQTRILFHALQKMNIPTIIFINKIDQNGIDLQRVYQSIKDKLTSDMIVMQEVSLSPKITMTDISDLDKWDMIISGSDELLERYVAEDSLDIQELQYEKCKRTRCCSLFPVYHGSAKDNLGTEKLIEAITETFITETDDIQSELCGYVFKVEYTERKKRLSYLRLYHGTLHLRDTLLLSKKEKIKITEMCIPSNGEIVPVDHACPGEIVILADDTLKLNDILGNEKLLPHKTRIDNPMPLLRTTVEPQKPEQREALLNALTEIADTDPLLHFDIDTVTHEIILSFLGKVQLEVICSLLEEKYHVGVAMKEPSVIYLERPLRKAEYTIHIEVPPNPFWASVGLSIEPLPIGSGVQYESRVSLGYLNQSFQNAVMEGVLYGCEQGLYGWKVTDCKICFEYGLYYSPVSTPADFRLLSPIVLEQALKKAGTELLEPYLHFEIYAPQEYLSRAYHDAPRYCADIVSTQIKNDEVILKGEIPARCIQEYRNDLTYFTNGQGVCLTELKGYQPAIGKFICQPRRPNSRIDKVRHMFHKLA"},"dna_sequence":{"accession":"AJ295238.3","fmin":"163","fmax":"2083","strand":"+","sequence":"ATGAAAATAATTAACTTAGGCATTCTGGCTCACGTTGACGCAGGAAAGACAACATTAACGGAAAGTTTATTGTATACCAGTGGTGCAATTGCAGAACTAGGGAGCGTAGATGAAGGCACAACAAGGACAGATACAATGAATTTGGAGCGTCAAAGGGGAATCACTATCCAGACAGCAGTGACATCTTTTCAGTGGGAGGATGTAAAAGTCAACATTATAGATACGCCAGGCCATATGGATTTTTTAACCGAAGCATACCGCTCTTTATCTGTCCTTGACGGAGCTGTTTTAGTCATTTCGGCAAAAGACGGCGTACAGGCACAGACGCGTATATTATTCCATGCGCTTCAGAAAATGAACATTCCGACAATTATCTTTATAAATAAGATAGACCAAAATGGAATCGACCTACAGCGTGTTTACCAAAGCATTAAAGACAAACTTACCAGTGATATGATTGTCATGCAGGAGGTTTCCCTGTCGCCAAAGATAACCATGACCGATATTTCTGATTTGGACAAATGGGATATGATTATTTCCGGAAGCGATGAACTATTAGAACGATATGTTGCAGAGGATTCTTTGGATATACAGGAATTACAATATGAAAAGTGCAAAAGAACCAGATGCTGCTCTTTGTTTCCTGTTTATCATGGGAGTGCAAAAGACAATTTAGGAACAGAAAAACTGATTGAAGCGATTACAGAAACTTTCATTACAGAAACAGACGATATTCAGTCTGAATTATGTGGATATGTTTTTAAGGTTGAGTATACAGAGCGGAAAAAACGGCTTTCTTATTTACGCCTGTATCATGGGACGCTCCATTTACGGGATACCCTGCTGCTGTCAAAAAAGGAAAAAATAAAGATTACAGAAATGTGTATTCCGTCAAATGGTGAAATCGTCCCGGTTGACCATGCCTGTCCGGGAGAAATTGTTATTTTAGCTGATGATACTTTGAAACTGAACGACATTCTGGGAAATGAAAAACTCCTGCCTCACAAAACACGGATTGATAATCCCATGCCATTACTTCGGACAACGGTAGAGCCGCAAAAGCCGGAGCAAAGGGAAGCCCTGTTAAATGCCCTCACAGAGATTGCTGATACAGACCCTCTTTTGCATTTTGACATTGATACTGTTACACATGAGATTATATTATCTTTTTTGGGAAAAGTACAGTTAGAAGTTATTTGTTCGCTATTAGAAGAAAAATATCATGTGGGCGTGGCTATGAAAGAGCCTTCGGTTATTTATCTGGAAAGACCGCTTAGAAAAGCAGAATATACCATCCACATAGAAGTCCCGCCAAATCCTTTCTGGGCTTCTGTCGGGTTGTCCATAGAGCCGCTCCCTATTGGAAGCGGAGTGCAGTATGAAAGCAGAGTTTCACTTGGATATTTAAATCAATCGTTCCAAAATGCGGTTATGGAGGGGGTTCTTTATGGCTGCGAGCAGGGGCTGTATGGATGGAAAGTGACAGACTGTAAAATCTGTTTTGAATATGGATTGTATTATAGTCCTGTAAGTACCCCCGCAGACTTTCGGCTGCTTTCCCCTATCGTATTGGAGCAGGCTTTAAAAAAAGCAGGGACAGAACTATTAGAGCCATATCTCCACTTTGAAATTTATGCACCGCAGGAATATCTCTCACGGGCGTATCATGATGCTCCAAGGTATTGTGCAGATATTGTAAGTACTCAGATAAAGAATGACGAGGTCATTCTGAAAGGAGAAATCCCTGCTAGATGTATTCAAGAATACAGGAACGATTTAACTTATTTCACAAATGGGCAGGGAGTCTGCTTGACAGAGTTAAAAGGATACCAGCCAGCTATTGGTAAATTTATTTGCCAACCCCGCCGCCCGAATAGCCGTATAGATAAGGTTCGGCATATGTTCCACAAGTTAGCTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36797","NCBI_taxonomy_name":"Clostridiaceae bacterium K10","NCBI_taxonomy_id":"185309"}}}},"ARO_accession":"3007119","ARO_id":"45696","ARO_name":"tet(O\/32\/O)","CARD_short_name":"tet(O\/32\/O)","ARO_description":"Tet(O\/32\/O) is a mosaic tetracycline resistance gene and ribosomal protection protein.","ARO_category":{"35921":{"category_aro_accession":"0000002","category_aro_cvterm_id":"35921","category_aro_name":"tetracycline-resistant ribosomal protection protein","category_aro_description":"A family of proteins known to bind to the 30S ribosomal subunit. This interaction prevents tetracycline and tetracycline derivatives from inhibiting ribosomal function. Thus, these proteins confer elevated resistance to tetracycline derivatives as a ribosomal protection protein.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5790":{"model_id":"5790","model_name":"tet(O\/M\/O)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"875"}},"model_sequences":{"sequence":{"8466":{"protein_sequence":{"accession":"AAR29485.1","sequence":"MKIINLGILAHVDAGKTTLTESLLYTSGAIAELGSVDEGTTRTDTMNLERQRGITIQTAVTSFQWEDVKVNIIDTPGHMDFLAEVYRSLSVLDGAVLLVSAKDGIQAQTRILFHALQIMKIPTIFFINKIDQEGIDLPMVYREMKAKLSSEIIVKQKVGQHPHINVTDNDDMEQWDAVIMGNDELLEKYMSGKPFKMSELEQEENRRFQNGTLFPVYHGSAKNNLGIRQLIEVIASKFYSSTPEGQSELCGQVFKIEYSEERQRLAYVRLYGGILHLRDSVRISEKEKIKITEMYTSINGELCKIDKAYSGEIVILQNEFLKLNSVLGDTKLLPQRERIENPLPMLQTTVEPSKPQQREMLLDALLEISDSDPLLQYYVDTTTHEIILSFLGNVQMEVICAILEEKYHVEAEIKEPTVIYMERPLRKAEYTIHIEVPPNPFWASVGLSIEPLPIGSGVQYESRVSLGYLNQSFQNAVMEGVLYGCEQGLYGWKVTDCKICFEYGLYYSPVSTPADFRLLSPIVLEQALKKAGTELLEPYLHFEIYAPQEYLSRAYHDAPRYCADIVSTQIKNDEVILKGEIPARCIQEYRNDLTCFTNGQGVCLTELKGYQPAIGKFICQPRRPNSRIDKVRHMFHKLA"},"dna_sequence":{"accession":"AY394560.1","fmin":"0","fmax":"1920","strand":"+","sequence":"ATGAAAATAATTAACTTAGGCATTCTGGCTCACGTTGACGCAGGAAAGACAACATTAACGGAAAGTTTATTGTATACCAGTGGTGCAATTGCAGAACTAGGGAGCGTAGATGAAGGCACAACAAGGACAGATACAATGAATTTGGAGCGTCAAAGGGGAATCACTATCCAGACAGCAGTGACATCTTTTCAGTGGGAGGATGTAAAAGTCAACATTATAGATACGCCAGGCCATATGGATTTTTTGGCGGAAGTATACCGTTCTTTATCCGTATTAGACGGAGCAGTATTATTAGTTTCTGCAAAGGATGGCATACAGGCACAGACCCGTATACTGTTTCATGCACTACAGATAATGAAGATTCCGACAATTTTTTTCATCAATAAAATTGACCAAGAGGGGATTGATTTGCCAATGGTATATCGGGAAATGAAAGCAAAGCTTTCTTCGGAAATTATAGTGAAGCAAAAGGTTGGGCAGCATCCCCATATAAATGTAACGGACAATGACGATATGGAACAGTGGGATGCGGTAATTATGGGAAACGATGAACTATTAGAGAAATATATGTCAGGGAAACCGTTTAAAATGTCAGAACTGGAACAGGAAGAAAACAGGAGATTCCAAAACGGAACGTTATTTCCCGTTTATCACGGAAGCGCTAAAAACAATCTGGGGATTCGGCAGCTTATAGAAGTAATTGCCAGTAAATTTTATTCATCAACGCCTGAAGGTCAATCTGAACTATGCGGGCAGGTTTTTAAGATTGAATATTCGGAAGAAAGACAACGTCTTGCATATGTACGCCTTTATGGCGGAATCCTGCATTTGCGGGATTCGGTTAGAATATCGGAAAAGGAAAAAATAAAAATTACAGAAATGTATACTTCAATAAATGGTGAATTATGTAAAATTGATAAGGCTTATTCCGGGGAAATTGTTATTTTGCAAAATGAGTTTTTGAAGCTAAATAGTGTTCTTGGAGATACAAAGCTATTGCCACAGAGAGAGAGAATTGAAAATCCTCTCCCTATGCTCCAAACAACTGTTGAACCGAGCAAACCTCAACAAAGGGAAATGTTACTTGATGCACTTTTAGAAATCTCCGACAGTGACCCGCTTCTACAATATTATGTGGATACTACAACGCATGAGATTATACTTTCTTTTTTGGGGAATGTGCAGATGGAAGTCATTTGTGCCATCCTTGAGGAAAAATATCATGTGGAGGCAGAAATAAAAGAGCCTACTGTTATATATATGGAAAGACCGCTTAGAAAAGCAGAATATACCATCCACATAGAAGTCCCGCCAAATCCTTTCTGGGCTTCTGTCGGGTTGTCCATAGAGCCGCTCCCTATTGGAAGCGGAGTGCAGTATGAAAGCAGAGTTTCACTTGGATATTTAAATCAATCGTTCCAAAATGCGGTTATGGAGGGGGTTCTTTATGGCTGCGAGCAGGGGCTGTATGGATGGAAAGTGACAGACTGTAAAATCTGTTTTGAATATGGATTGTATTATAGTCCTGTAAGTACCCCCGCAGACTTTCGGCTGCTTTCCCCTATCGTATTGGAGCAGGCTTTAAAAAAAGCAGGGACAGAACTATTAGAGCCATATCTCCACTTTGAAATTTATGCACCGCAGGAATATCTCTCACGGGCGTATCATGATGCTCCAAGGTATTGTGCAGATATTGTAAGTACTCAGATAAAGAATGACGAGGTCATTCTGAAAGGAGAAATCCCTGCTAGATGTATTCAAGAATACAGGAACGATTTAACTTGTTTCACAAATGGGCAGGGAGTCTGCTTGACAGAGTTAAAAGGATACCAGCCAGCTATTGGTAAATTTATTTGCCAACCCCGCCGCCCGAATAGCCGTATAGATAAGGTTCGGCATATGTTCCACAAGTTAGCTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36835","NCBI_taxonomy_name":"Campylobacter coli","NCBI_taxonomy_id":"195"}}}},"ARO_accession":"3007120","ARO_id":"45697","ARO_name":"tet(O\/M\/O)","CARD_short_name":"tet(O\/M\/O)","ARO_description":"Tet(O\/M\/O) is a mosaic tetracycline resistance gene and ribosomal protection protein.","ARO_category":{"35921":{"category_aro_accession":"0000002","category_aro_cvterm_id":"35921","category_aro_name":"tetracycline-resistant ribosomal protection protein","category_aro_description":"A family of proteins known to bind to the 30S ribosomal subunit. This interaction prevents tetracycline and tetracycline derivatives from inhibiting ribosomal function. Thus, these proteins confer elevated resistance to tetracycline derivatives as a ribosomal protection protein.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5791":{"model_id":"5791","model_name":"tet(O\/W)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"900"}},"model_sequences":{"sequence":{"8467":{"protein_sequence":{"accession":"AAR29969.1","sequence":"MKIINLGILAHVDAGKTTLTESLLYTSGAIAELGSVDEGTTRTDTMNLERQRGITIQTAVTSFQWEDVKVNIIDTPGHMDFLAEVYRSLAVLDGAILVISAKDGVQAQTRILFHALRKMNIPTVIFINKIDQAGVDLQSVVQSVRDKLSADIIIKQTVSLSPEIVLEENTDIEAWDAVIENNDALLEKYIAGEPISQEKLAREEQRRVQEASLFPVYHGSAKKGLGIQPLMDAVTGLFQPIGEQGSATLCGSVFKVEYTDCGQRRVYLRLYSGTLRLRDTVALAGREKLKITEMRIPSKGEIVRTDTAYPGEIVILPSDSVRLNDVLGDQTRLPRKRWREAPLPMLRTTIAPKTAAQRERLLDALTQLADTDPLLRCEVDSITHEIILSFLGRVQLEVVSALLSEKYKIETVVKEPTVIYMERPLKAASHTIHIEVPPNPFWASIGLSVTPLPLGSGVQYESRVSLGYLNQSFQNAVRDGIRYGLEQGLFGWNVTDCKICFEYGLYYSPVSTPADFRSLAPIVLEQALKESGTQLLEPYLSFTLYAPQEYLSRAYHDAPKYCATIETAQVKKDEVVFTGEIPARCIQAYRTDLAFYTNGQSVCLTELKGYQAAVGQPVIQPRRPNNRLDKVRHMFQKVM"},"dna_sequence":{"accession":"AY485122.1","fmin":"0","fmax":"1920","strand":"+","sequence":"ATGAAAATAATTAACTTAGGCATTCTGGCTCACGTTGACGCAGGAAAGACAACATTAACGGAAAGTTTATTGTATACCAGTGGTGCAATTGCAGAACTAGGGAGCGTAGATGAAGGCACAACAAGGACAGATACAATGAATTTGGAGCGTCAAAGGGGAATCACTATCCAGACAGCAGTGACATCTTTTCAGTGGGAGGATGTAAAAGTCAACATTATAGATACGCCAGGCCATATGGATTTTTTGGCGGAGGTGTACCGCTCTTTGGCTGTTTTAGATGGGGCCATCTTGGTGATCTCCGCGAAAGATGGCGTGCAGGCCCAGACCCGTATTCTGTTCCATGCCCTGCGGAAAATGAACATTCCCACCGTTATCTTTATCAACAAGATCGACCAGGCTGGCGTTGATTTGCAGAGCGTGGTTCAGTCTGTTCGGGATAAGCTCTCCGCCGATATTATCATCAAGCAGACGGTGTCGCTGTCCCCGGAAATAGTCCTGGAGGAAAATACCGACATAGAAGCATGGGATGCGGTCATCGAAAATAACGATGCATTATTGGAAAAGTATATCGCAGGAGAACCAATCAGCCAGGAAAAACTTGCGCGGGAGGAACAGCGGCGGGTTCAAGAAGCCTCCCTGTTTCCGGTCTATCATGGCAGCGCCAAAAAGGGCCTTGGCATTCAACCGTTGATGGATGCGGTGACAGGACTGTTCCAACCGATTGGGGAACAGGGGAGCGCCACCCTATGCGGCAGCGTTTTCAAGGTTGAGTACACCGATTGCGGCCAGCGGCGTGTCTATCTGCGGCTATACAGCGGAACGCTGCGCCTGCGGGATACGGTGGCCCTGGCCGGGAGAGAAAAGCTGAAAATCACAGAGATGCGTATTCCATCCAAAGGGGAAATTGTTCGGACAGACACCGCTTATCCGGGCGAAATTGTTATCCTTCCCAGCGACAGCGTGAGGTTAAACGATGTATTAGGGGATCAAACCCGGCTCCCTCGTAAAAGGTGGCGCGAGGCCCCCCTCCCCATGCTGCGGACGACGATTGCGCCGAAAACGGCAGCGCAAAGAGAACGGCTGCTGGACGCTCTTACGCAACTTGCGGATACTGACCCGCTTTTGCGCTGCGAAGTGGATTCCATCACCCATGAGATCATTCTTTCTTTTTTGGGCCGGGTGCAGTTGGAGGTCGTTTCCGCTTTGCTGTCGGAAAAATACAAGATTGAAACAGTGGTAAAGGAACCCACCGTCATTTATATGGAGCGGCCGCTCAAAGCAGCCAGCCACACCATCCATATCGAGGTGCCGCCCAACCCGTTTTGGGCATCTATCGGACTGTCTGTTACACCACTCCCGCTTGGCTCCGGCGTACAATACGAGAGCCGGGTTTCGCTGGGATACTTGAACCAGAGTTTTCAAAACGCTGTCAGGGATGGTATCCGTTACGGGCTGGAGCAGGGCTTGTTCGGCTGGAACGTAACGGACTGTAAGATTTGCTTTGAATACGGGCTTTATTACAGTCCAGTCAGCACGCCGGCGGACTTCCGCTCATTGGCCCCGATTGTATTGGAACAGGCATTGAAGGAATCGGGGACGCAGCTGCTGGAACCTTATCTCTCCTTCACCCTCTATGCGCCCCAGGAATACCTTTCCAGGGCTTATCATGATGCACCGAAATACTGTGCCACCATCGAAACGGCCCAGGTAAAAAAGGATGAAGTTGTCTTTACTGGCGAGATTCCCGCCCGCTGTATACAGGCATACCGTACTGATCTGGCCTTTTACACCAACGGGCAGAGCGTATGCCTTACAGAGCTAAAAGGGTATCAGGCCGCTGTCGGCCAGCCGGTCATCCAGCCCCGCCGTCCAAACAACCGCCTGGACAAGGTGCGCCATATGTTTCAGAAGGTAATGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36809","NCBI_taxonomy_name":"Megasphaera elsdenii","NCBI_taxonomy_id":"907"}}}},"ARO_accession":"3007121","ARO_id":"45698","ARO_name":"tet(O\/W)","CARD_short_name":"tet(O\/W)","ARO_description":"Tet(O\/W) is a mosaic tetracycline resistance gene and ribosomal protection protein.","ARO_category":{"35921":{"category_aro_accession":"0000002","category_aro_cvterm_id":"35921","category_aro_name":"tetracycline-resistant ribosomal protection protein","category_aro_description":"A family of proteins known to bind to the 30S ribosomal subunit. This interaction prevents tetracycline and tetracycline derivatives from inhibiting ribosomal function. Thus, these proteins confer elevated resistance to tetracycline derivatives as a ribosomal protection protein.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5792":{"model_id":"5792","model_name":"tet(O\/W\/32\/O)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"900"}},"model_sequences":{"sequence":{"8468":{"protein_sequence":{"accession":"ABF69686.1","sequence":"MKIINLGILAHVDAGKTTLTESLLYTSGAIAELGSVDEGTTRTDTMNLERQRGITIQTAVTSFQWEDVKVNIIDTPGHMDFLAEVYRSLAVLDGAILVISAKDGVQAQTRILFHALRKMNIPTVIFINKIDQAGVDLQSVVQSVRDKLSADIIIKQTVSLSPEIVLEENTDIEAWDAVIENNDKLLEKYIAGEPISREKLVREEQRRVQDASLFPVYYGSAKKGLGIQPLMDAVTGLFQPIGEQGSAALCGSVFKVEYTDCGQRRVYLRLYSGTLRLRDTVALAGREKLKITEMRIPSKGEIVRTDTAYPGEIVILADDTLKLNDILGNEKLLPHKTRIDNPMPLLRTTVEPQKPEQREALLNALAEIADTDPLLHFDIDTVTHEIMLSFLGKVQLEVICSLLEEKYHVGVAMKEPSVIYLERPLRKAEYTIHIEVPPNPFWASIGLSVTPLPLGSGVQYESRVSLGYLNQSFQNAVRDGIRYGLEQGLYGWKVTDCKICFEYGLYYSPVSTPADFRLLSPIVLEQALKKAGTELLEPYLHFEIYAPQEYLSRAYHDAPRYCADIVSTQIKNDEVILKGEIPARCIQEYRNDLTNFTNGQGVCLTELKGYQPAIGKFICQPRRPNSRIDKVRHMFHKLA"},"dna_sequence":{"accession":"DQ525023.1","fmin":"28","fmax":"1948","strand":"+","sequence":"ATGAAAATAATTAACTTAGGCATTCTGGCTCACGTTGACGCAGGAAAGACAACATTAACGGAAAGTTTATTGTATACCAGTGGTGCAATTGCAGAACTAGGGAGCGTAGATGAAGGCACAACAAGGACAGATACAATGAATTTGGAGCGTCAAAGGGGAATCACTATCCAGACAGCAGTGACATCTTTTCAGTGGGAGGATGTAAAAGTCAACATTATAGATACGCCAGGCCATATGGATTTTTTGGCGGAGGTGTACCGCTCTTTGGCTGTTTTAGATGGGGCCATCTTGGTGATCTCCGCTAAAGATGGCGTGCAGGCCCAGACCCGTATTCTGTTCCATGCCCTGCGGAAAATGAACATTCCCACCGTTATCTTTATCAACAAGATCGACCAGGCTGGCGTTGATTTGCAGAGCGTGGTTCAGTCTGTTCGGGATAAGCTCTCCGCCGATATTATCATCAAGCAGACGGTGTCACTGTCCCCGGAAATAGTCCTGGAGGAAAATACCGACATAGAAGCATGGGATGCGGTCATCGAAAATAACGATAAATTATTGGAAAAGTATATCGCAGGAGAACCAATCAGCCGGGAAAAACTTGTGCGGGAGGAACAGCGGCGGGTTCAAGACGCCTCCCTGTTCCCGGTCTATTATGGCAGCGCCAAAAAGGGCCTTGGCATTCAACCGTTGATGGATGCGGTGACAGGGCTGTTCCAACCGATTGGGGAACAGGGGAGCGCCGCCCTATGCGGCAGCGTTTTCAAGGTGGAGTATACAGATTGCGGCCAGCGGCGTGTCTATCTACGGCTATACAGCGGAACGCTGCGCCTGCGGGATACGGTGGCCCTGGCCGGGAGAGAAAAGCTGAAAATCACAGAGATGCGTATTCCATCCAAAGGGGAAATTGTTCGGACAGACACCGCTTATCCGGGAGAAATTGTTATTTTAGCTGATGATACTTTGAAACTGAACGACATTCTAGGAAATGAAAAACTCCTGCCTCATAAAACACGGATTGATAATCCCATGCCATTACTTCGGACAACGGTAGAGCCGCAAAAGCCGGAGCAAAGGGAAGCCCTGTTAAATGCCCTCGCAGAGATTGCTGATACAGACCCTCTTTTGCATTTTGACATTGATACTGTTACACATGAGATTATGTTATCTTTTTTGGGAAAAGTACAGTTAGAAGTTATTTGTTCGCTATTAGAAGAAAAATATCATGTGGGCGTGGCTATGAAAGAGCCTTCGGTTATTTATCTGGAAAGACCGCTTAGAAAAGCAGAATATACCATCCACATAGAAGTCCCGCCCAACCCGTTTTGGGCATCCATCGGACTGTCTGTTACACCACTCCCGCTTGGCTCCGGTGTACAATACGAGAGCCGGGTTTCGCTGGGATACTTGAACCAGAGTTTTCAAAACGCTGTCAGGGATGGTATCCGTTACGGGCTGGAGCAGGGGCTGTATGGATGGAAAGTGACAGACTGTAAAATCTGTTTTGAATATGGATTGTATTATAGTCCTGTAAGTACCCCCGCAGACTTTCGGCTGCTTTCCCCTATCGTATTGGAGCAGGCTTTAAAAAAAGCAGGGACAGAACTATTAGAGCCATATCTCCACTTTGAAATTTATGCACCGCAGGAATATCTCTCACGGGCGTATCATGATGCTCCAAGGTATTGTGCAGATATTGTAAGTACTCAGATAAAGAATGACGAGGTCATTCTGAAAGGAGAAATCCCTGCTAGATGTATTCAAGAATACAGGAACGATTTAACTAATTTCACAAATGGGCAGGGAGTCTGCTTGACAGAGTTAAAAGGATACCAGCCAGCTATTGGTAAATTTATTTGCCAACCCCGCCGCCCGAATAGCCGTATAGATAAGGTTCGGCATATGTTCCACAAGTTAGCTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42569","NCBI_taxonomy_name":"Lactobacillus johnsonii","NCBI_taxonomy_id":"33959"}}}},"ARO_accession":"3007122","ARO_id":"45699","ARO_name":"tet(O\/W\/32\/O)","CARD_short_name":"tet(O\/W\/32\/O)","ARO_description":"Tet(O\/W\/32\/O) is a mosaic tetracycline resistance gene and ribosomal protection protein.","ARO_category":{"35921":{"category_aro_accession":"0000002","category_aro_cvterm_id":"35921","category_aro_name":"tetracycline-resistant ribosomal protection protein","category_aro_description":"A family of proteins known to bind to the 30S ribosomal subunit. This interaction prevents tetracycline and tetracycline derivatives from inhibiting ribosomal function. Thus, these proteins confer elevated resistance to tetracycline derivatives as a ribosomal protection protein.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5793":{"model_id":"5793","model_name":"tet(O\/W\/O)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"900"}},"model_sequences":{"sequence":{"8469":{"protein_sequence":{"accession":"AAO42740.1","sequence":"MKIINLGILAHVDAGKTTLTESLLYTSGAIAELGSVDEGTTRTDTMNLERQRGITIQTAVTSFQWEDVKVNIIDTPGHMDFLAEVYRSLAVLDGAILVISAKDGVQAQTRILFHALRKMNIPTVIFINKIDQAGVDLQSVVQSVRDKLSADIIIKQTVSLSPEIVLEENTDIEAWDAVIENNDALLEKYIAGEPISQEKLAREEQRRVQEASLFPVYHGSAKKGLGIQPLMDAVTGLFQPIGEQGSATLCGSVFKVEYTDCGQRRVYLRLYSGTLRLRDTVALAGREKLKITEMRIPSKGEIVRTDTAYPGEIVILPSDSVRLNDVLGDQTRLPRKRWREAPLPMLRTTIAPKTAAQRERLLDALTQLADTDPLLRCEVDSITHEIILSFLGRVQLEVVSALLSEKYKIETVVKEPTVIYMERPLKAASHTIHIEVPPNPFWASIGLSVTPLPLGSGVQYESRVSLGYLNQSFQNAVRDGIRYGLEQGLFGWNVTDCKICFEYGLYYSPVSTPADFRSLAPIVLEQALKESGTQLLEPYLSFTLYAPQEYLSRAYHDAPRYCADIVSTQIKNDEVILKGEIPARCIQEYRNDLTYFTNGQGVCLTELKGYQPAIGKFICQPRRPNSRIDKVRHMFHKLA"},"dna_sequence":{"accession":"AY196920.1","fmin":"0","fmax":"1920","strand":"+","sequence":"ATGAAAATAATTAACTTAGGCATTCTGGCTCACGTTGACGCAGGAAAGACAACATTAACGGAAAGTTTATTGTATACCAGTGGTGCAATTGCAGAACTAGGGAGCGTAGATGAAGGCACAACAAGGACAGATACAATGAATTTGGAGCGTCAAAGGGGAATCACTATCCAGACAGCAGTGACATCTTTTCAGTGGGAGGATGTAAAAGTCAACATTATAGATACGCCAGGCCATATGGATTTTTTGGCGGAGGTGTACCGCTCTTTGGCTGTTTTAGATGGGGCCATCTTGGTGATCTCCGCGAAAGATGGCGTGCAGGCCCAGACCCGTATTCTGTTCCATGCCCTGCGGAAAATGAACATTCCCACCGTTATCTTTATCAACAAGATCGACCAGGCTGGCGTTGATTTGCAGAGCGTGGTTCAGTCTGTTCGGGATAAGCTCTCCGCCGATATTATCATCAAGCAGACGGTGTCGCTGTCCCCGGAAATAGTCCTGGAGGAAAATACCGACATAGAAGCATGGGATGCGGTCATCGAAAATAACGATGCATTATTGGAAAAGTATATCGCAGGAGAACCAATCAGCCAGGAAAAACTTGCGCGGGAGGAACAGCGGCGGGTTCAAGAAGCCTCCCTGTTTCCGGTCTATCATGGCAGCGCCAAAAAGGGCCTTGGCATTCAACCGTTGATGGATGCGGTGACAGGACTGTTCCAACCGATTGGGGAACAGGGGAGCGCCACCCTATGCGGCAGCGTTTTCAAGGTTGAGTACACCGATTGCGGCCAGCGGCGTGTCTATCTGCGGCTATACAGCGGAACGCTGCGCCTGCGGGATACGGTGGCCCTGGCCGGGAGAGAAAAGCTGAAAATCACAGAGATGCGTATTCCATCCAAAGGGGAAATTGTTCGGACAGACACCGCTTATCCGGGCGAAATTGTTATCCTTCCCAGCGACAGCGTGAGGTTAAACGATGTATTAGGGGATCAAACCCGGCTCCCTCGTAAAAGGTGGCGCGAGGCCCCCCTCCCCATGCTGCGGACGACGATTGCGCCGAAAACGGCAGCGCAAAGAGAACGGCTGCTGGACGCTCTTACGCAACTTGCGGATACTGACCCGCTTTTGCGCTGCGAAGTGGATTCCATCACCCATGAGATCATTCTTTCTTTTTTGGGCCGGGTGCAGTTGGAGGTCGTTTCCGCTTTGCTGTCGGAAAAATACAAGATTGAAACAGTGGTAAAGGAACCCACCGTCATTTATATGGAGCGGCCGCTCAAAGCAGCCAGCCACACCATCCATATCGAGGTGCCGCCCAACCCGTTTTGGGCATCTATCGGACTGTCTGTTACACCACTCCCGCTTGGCTCCGGCGTACAATACGAGAGCCGGGTTTCGCTGGGATACTTGAACCAGAGTTTTCAAAACGCTGTCAGGGATGGTATCCGTTACGGGCTGGAGCAGGGCTTGTTCGGCTGGAACGTAACGGACTGTAAGATTTGCTTTGAATACGGGCTTTATTACAGTCCAGTCAGCACGCCGGCGGACTTCCGCTCATTGGCCCCGATTGTATTGGAACAGGCATTGAAGGAATCGGGGACGCAGCTGCTGGAACCTTATCTCTCCTTCACCCTCTATGCACCGCAGGAATATCTCTCACGGGCGTATCATGATGCTCCAAGGTATTGTGCAGATATTGTAAGTACTCAGATAAAGAATGACGAGGTCATTCTGAAAGGAGAAATCCCTGCTAGATGTATTCAAGAATACAGGAACGATTTAACTTATTTCACAAATGGGCAGGGAGTCTGCTTGACAGAGTTAAAAGGATACCAGCCAGCTATTGGTAAATTTATTTGCCAACCCCGCCGCCCGAATAGCCGTATAGATAAGGTTCGGCATATGTTCCACAAGTTAGCTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36809","NCBI_taxonomy_name":"Megasphaera elsdenii","NCBI_taxonomy_id":"907"}}}},"ARO_accession":"3007123","ARO_id":"45700","ARO_name":"tet(O\/W\/O)","CARD_short_name":"tet(O\/W\/O)","ARO_description":"Tet(O\/W\/O) is a mosaic tetracycline resistance gene and ribosomal protection protein.","ARO_category":{"35921":{"category_aro_accession":"0000002","category_aro_cvterm_id":"35921","category_aro_name":"tetracycline-resistant ribosomal protection protein","category_aro_description":"A family of proteins known to bind to the 30S ribosomal subunit. This interaction prevents tetracycline and tetracycline derivatives from inhibiting ribosomal function. Thus, these proteins confer elevated resistance to tetracycline derivatives as a ribosomal protection protein.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5794":{"model_id":"5794","model_name":"tet(W\/32\/O)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"875"}},"model_sequences":{"sequence":{"8470":{"protein_sequence":{"accession":"AAL09826.1","sequence":"MNIINIGILAHVDAGKTTLTESLLYASGTISEPGSVEKGTTRTDTMFLERQRGITIQTAVTSFQWHSCKVNIVDTPGHMDFLAEVYRSLAVLDGAILVLSARDGVQAQTRVLFHALRKLNIPTIIFINKIDQVDIDLEGVYQSVRDKLSADIIIKQTVSLSPEIVLEENTDIEAWDAVIENNDGLLEKYIAGEPISREELAREEQRRVQAASLFPVYHGSAKNGLGIQRLMDAVIGLFQPTKEQGRTALCGSVFKVEYTDCGQRLVYLRLYSGTLRLRDTVALAGREKLKITEMRIPSKGEIVRTDTAHKGEIVILPSDSLRLNDILGDKTQLPREMWSDAPFSMLRTTITPKTAEQRDRLLDALTQIADTDPLLCYEVDSITQEIILSFLGRVQLEVVSALLAEKYKIETAVKEPTVIYLERPLKVASHTIHIEVPPNPFWASIGLSVTPLPLGSGVQYESRVSLGYLNQSFQNAVMDGIRYGLEQGLCGWNVTDCKICFEYGLYYSPVSTPADFRSLAPIVLELALKESGTQLLEPYLSFTLYAPQEYLSRAYHDAPKYCATIETAQIKKDEVVFTGEIPARCIQAYRTDLASYTNGRSVCLTELKGYQAAVGQPVIQPRRPNSRLDRVRHMFQKVM"},"dna_sequence":{"accession":"AY049983.2","fmin":"8308","fmax":"10228","strand":"+","sequence":"ATGAACATTATCAATATCGGGATTCTTGCCCATGTAGATGCGGGCAAGACGACACTGACAGAAAGCCTGCTGTATGCCAGCGGAACCATTTCAGAGCCGGGGAGCGTCGAAAAAGGGACAACGAGAACGGACACTATGTTTTTGGAGCGGCAGCGTGGAATTACCATTCAAACGGCAGTCACTTCTTTCCAGTGGCACAGTTGTAAAGTCAACATTGTGGATACTCCCGGCCACATGGATTTCTTGGCAGAGGTATACCGCTCTCTGGCCGTTTTGGACGGGGCCATCTTGGTGCTCTCCGCTAGAGATGGCGTACAGGCCCAGACCCGAGTTCTGTTCCATGCCCTACGGAAATTGAACATCCCCACCATTATCTTTATCAACAAGATCGACCAGGTTGACATTGATTTGGAGGGCGTATATCAGTCTGTTCGGGATAAGCTCTCCGCCGATATTATCATCAAGCAGACGGTATCGCTGTCCCCGGAAATAGTTCTGGAGGAAAATACCGACATAGAAGCATGGGATGCGGTCATCGAAAATAACGATGGATTATTGGAAAAGTATATCGCAGGAGAGCCAATCAGCCGGGAAGAACTTGCGCGGGAGGAACAGCGGCGGGTTCAAGCCGCTTCCCTGTTCCCAGTCTATCATGGTAGCGCCAAAAACGGCCTTGGCATTCAACGGTTGATGGATGCGGTGATAGGGCTGTTCCAACCGACCAAGGAACAGGGGCGCACCGCCCTGTGCGGCAGCGTTTTCAAGGTGGAGTATACAGATTGCGGCCAGAGGCTTGTCTATCTGCGGCTATACAGCGGAACGCTGCGTCTGCGGGATACGGTGGCCCTGGCCGGGAGAGAAAAGCTGAAAATCACAGAGATGCGTATTCCATCCAAAGGGGAGATTGTTCGGACAGATACCGCCCATAAGGGCGAAATTGTCATCCTTCCCAGCGACAGTTTGAGATTAAACGATATATTGGGGGACAAAACCCAACTTCCTCGTGAAATGTGGAGTGATGCTCCCTTCTCTATGCTGCGGACAACGATTACGCCAAAAACGGCAGAGCAAAGAGATCGGTTGCTGGACGCTCTTACGCAAATTGCGGATACTGACCCGCTTTTGTGCTACGAGGTGGATTCCATCACCCAAGAGATCATTCTTTCTTTTTTGGGCCGGGTGCAGTTGGAGGTTGTTTCCGCTTTGCTGGCGGAAAAGTATAAGATTGAAACAGCGGTGAAGGAACCCACCGTCATTTATTTAGAGCGGCCGCTCAAAGTGGCCAGCCACACCATCCATATCGAGGTGCCGCCCAACCCGTTTTGGGCATCCATCGGACTGTCTGTTACGCCGCTCCCGCTTGGCTCCGGTGTACAATACGAGAGCCGGGTTTCCCTGGGATACTTGAACCAGAGTTTTCAAAACGCTGTCATGGATGGTATCCGTTACGGTCTGGAGCAAGGCTTGTGTGGCTGGAACGTAACGGACTGTAAGATTTGCTTTGAATACGGGCTTTATTATAGCCCGGTCAGCACGCCGGCGGACTTTCGCTCATTGGCCCCGATTGTATTGGAACTGGCATTAAAGGAATCAGGGACACAGTTGCTGGAACCTTATCTCTCCTTCACCCTCTATGCGCCCCAGGAATACCTTTCCAGGGCTTATCATGATGCGCCGAAATATTGTGCCACCATCGAAACGGCCCAGATAAAAAAGGATGAAGTTGTCTTTACTGGCGAGATTCCCGCCCGTTGCATACAGGCATACCGTACTGATTTGGCCTCTTACACCAATGGGCGGAGCGTGTGCCTGACGGAACTGAAAGGGTATCAGGCCGCTGTCGGCCAGCCGGTCATCCAGCCCCGCCGTCCAAACAGCCGCCTGGACAGGGTGCGCCATATGTTTCAGAAGGTAATGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43836","NCBI_taxonomy_name":"Trueperella pyogenes","NCBI_taxonomy_id":"1661"}}}},"ARO_accession":"3007124","ARO_id":"45701","ARO_name":"tet(W\/32\/O)","CARD_short_name":"tet(W\/32\/O)","ARO_description":"Tet(W\/32\/O) is a mosaic tetracycline resistance gene and ribosomal protection protein.","ARO_category":{"35921":{"category_aro_accession":"0000002","category_aro_cvterm_id":"35921","category_aro_name":"tetracycline-resistant ribosomal protection protein","category_aro_description":"A family of proteins known to bind to the 30S ribosomal subunit. This interaction prevents tetracycline and tetracycline derivatives from inhibiting ribosomal function. Thus, these proteins confer elevated resistance to tetracycline derivatives as a ribosomal protection protein.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3308":{"model_id":"3308","model_name":"tet(47)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"5415":{"protein_sequence":{"accession":"AKQ05891.1","sequence":"MRCHFRCNLALPLLVFLNLSRAIKDYQTMSSINNILVIGAGIAGPSVCYWLKRFGFSPVLIEKSANLRKGGHALDVRGVAIDLVKRMGIYEKIGNRRTQVEFGRYMDTQGNILHEEKGERFCYREGEDVEITRGDLVEILIDAIEGVPCYLNQSIDSIKQRDGDVAVRFKDGKIEYYDLIIGADGLHSTTRRMVFDKDEYQLTNLGAYFSVFSIPNYLNLNHTEIQFEANQKLISMTSDKNPKMAEVAFMFRVQNVLNNRRDENEQKRFLRDTFQGFGWETSKILELMSDSDDFYFDSVSQVKMKSWTKGRVALLGDAGYCASPISGQGNNLALVGAYVLAGELKQASDNYHQAFNRYNELLHPFIEANQKLGVLVNESFLVQDEVSKEVAEERSNKIMEEVKIVSNMISLPDYE"},"dna_sequence":{"accession":"KR857681.1","fmin":"0","fmax":"1248","strand":"+","sequence":"ATGCGCTGTCATTTCCGATGTAATCTCGCGCTGCCGCTTCTTGTATTCCTCAATCTTAGTAGAGCAATAAAGGATTATCAAACAATGTCTTCTATAAATAATATTCTTGTAATAGGAGCTGGAATTGCTGGACCCTCAGTCTGCTATTGGTTAAAAAGATTTGGTTTTTCTCCCGTTTTAATTGAAAAGTCTGCCAATTTACGAAAAGGAGGGCATGCACTGGATGTTCGAGGTGTTGCAATCGACCTCGTCAAAAGAATGGGCATCTACGAAAAAATAGGCAATAGGCGCACTCAGGTGGAATTTGGACGATACATGGACACTCAAGGCAATATCTTGCATGAAGAAAAGGGTGAAAGATTTTGCTATAGAGAAGGTGAGGATGTTGAAATTACCCGCGGTGATTTAGTTGAGATATTGATAGATGCCATTGAAGGCGTTCCCTGCTATCTCAATCAATCGATTGACAGCATTAAACAGAGGGATGGCGATGTAGCCGTTCGATTTAAAGATGGCAAGATCGAGTATTACGATCTGATTATTGGCGCTGACGGCTTGCATTCAACAACAAGACGCATGGTTTTTGATAAAGATGAATATCAATTAACTAACCTTGGGGCGTACTTTAGCGTTTTTAGTATTCCAAATTATCTCAATTTGAATCACACCGAAATCCAGTTCGAGGCCAATCAAAAACTGATATCTATGACTAGCGACAAGAATCCTAAAATGGCTGAAGTCGCATTCATGTTCCGTGTACAGAATGTCTTGAATAATAGGCGCGATGAAAATGAGCAAAAGAGATTCCTACGCGACACTTTTCAAGGTTTTGGTTGGGAAACGTCGAAAATACTTGAACTGATGTCAGATAGTGATGATTTTTATTTTGATTCAGTCTCCCAAGTGAAAATGAAGTCATGGACTAAGGGTCGAGTTGCCTTATTGGGCGACGCGGGTTACTGCGCATCCCCAATATCTGGTCAAGGTAATAATCTGGCACTAGTTGGTGCTTATGTTTTGGCGGGAGAACTAAAACAGGCAAGCGACAATTATCACCAAGCATTTAATCGTTATAATGAATTGTTACATCCATTCATTGAAGCCAATCAAAAATTGGGAGTCTTGGTTAACGAGTCGTTTCTCGTTCAGGATGAAGTCTCAAAGGAAGTTGCGGAAGAACGATCAAATAAGATAATGGAAGAAGTAAAAATCGTCTCGAATATGATTTCGTTACCGGATTATGAATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36791","NCBI_taxonomy_name":"uncultured bacterium","NCBI_taxonomy_id":"77133"}}}},"ARO_accession":"3004613","ARO_id":"42577","ARO_name":"tet(47)","CARD_short_name":"tet(47)","ARO_description":"A tetracycline inactivating enzyme. A flavoenzyme capable of degrading tetracycline antibiotics.","ARO_category":{"36176":{"category_aro_accession":"3000036","category_aro_cvterm_id":"36176","category_aro_name":"tetracycline inactivation enzyme","category_aro_description":"Enzymes or other gene products which hydroxylate tetracycline and other tetracycline derivatives. Hydroxylation inactivates tetracycline-like antibiotics, thus conferring resistance to these compounds.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"37012":{"category_aro_accession":"3000668","category_aro_cvterm_id":"37012","category_aro_name":"oxytetracycline","category_aro_description":"Oxytetracycline is a derivative of tetracycline with a 5-hydroxyl group. Its activity is similar to other tetracyclines.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3401":{"model_id":"3401","model_name":"tet(X3)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"760"}},"model_sequences":{"sequence":{"5596":{"protein_sequence":{"accession":"QBQ85438.1","sequence":"MTMRIDTDKQMNLLSDKNVAIIGGGPVGLTMAKLLQQNGIDVSVYERDNDREARIFGGTLDLHKGSGQEAMKKAGLLQTYYDLALPMGVNIADEKGNILSTKNVKPENRFDNPEINRNDLRAILLNSLENDTVIWDRKLVMLEPGKKKWTLTFENKPSETADLVILANGGMSKIRSFVTDTQVEETGTFNIQADILQPEINCPGFFQLCNGNRLMAGHQGILLFANPNNNGALYLGISFKTPDEWKNKIPLDFQDRNSVADFLLKRFSKWSEVYKQLIRSVSTFQCLPTRKFPLNNDWKSNRPLPITMIGDAAHLMSPFAGQGVNTGLLDALILSENLTNGEFTSIENAIENYEQQMFVYAKDTQDESTENETEMFSPNFSFQKLLNL"},"dna_sequence":{"accession":"MK134375.1","fmin":"6173","fmax":"7340","strand":"+","sequence":"ATGACAATGCGAATAGATACAGACAAACAAATGAATTTACTTAGTGATAAGAACGTTGCAATAATTGGTGGTGGACCCGTTGGACTGACTATGGCAAAATTATTACAGCAAAACGGCATAGACGTTTCAGTTTACGAAAGAGACAACGACCGAGAGGCAAGAATTTTTGGTGGAACCCTTGACCTACACAAAGGTTCAGGTCAGGAAGCAATGAAAAAAGCGGGATTGTTACAAACTTATTATGACTTAGCCTTACCAATGGGTGTAAATATTGCTGATGAAAAAGGCAATATTTTATCCACAAAAAATGTAAAGCCCGAAAATCGATTTGACAATCCTGAAATAAACAGAAATGACTTAAGGGCTATCTTGTTGAATAGTTTAGAAAACGACACGGTTATTTGGGATAGAAAACTTGTTATGCTTGAACCTGGTAAGAAGAAGTGGACACTAACTTTTGAGAATAAACCGAGTGAAACAGCAGATTTGGTTATTCTTGCCAATGGTGGAATGTCGAAAATAAGGAGCTTTGTTACCGACACGCAAGTTGAAGAAACCGGTACTTTCAACATCCAAGCTGATATTCTTCAACCGGAAATAAACTGTCCCGGATTTTTTCAGCTATGCAACGGCAACCGATTAATGGCGGGACATCAGGGCATTTTATTGTTTGCCAATCCCAATAATAATGGTGCATTGTATTTAGGAATTAGTTTTAAAACGCCCGATGAATGGAAAAATAAAATTCCCTTAGATTTTCAGGACAGAAACAGCGTTGCCGATTTTTTATTGAAAAGATTTTCCAAATGGAGTGAAGTTTACAAACAATTAATACGTTCGGTATCAACATTTCAATGCTTGCCCACAAGGAAATTTCCTTTGAACAATGATTGGAAAAGTAACCGTCCATTACCCATAACAATGATTGGCGATGCTGCTCATTTGATGTCGCCTTTTGCAGGACAGGGTGTAAATACGGGATTATTGGATGCTTTGATATTGTCTGAAAACCTTACAAACGGAGAATTTACAAGTATTGAAAATGCCATCGAAAACTACGAACAACAAATGTTTGTTTATGCAAAAGATACGCAGGACGAATCGACAGAAAACGAAACCGAAATGTTTAGTCCCAATTTTTCGTTTCAAAAATTATTGAATCTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3004719","ARO_id":"42774","ARO_name":"tet(X3)","CARD_short_name":"tet(X3)","ARO_description":"A tetracyline resistance gene located on an approximately 300-kb plasmid, designated p47AB. It inactivates all tetracyclines, including tigecycline, eravacycline, and omadacycline.Adjacent to insertion sequence ISVsa3 on the conjugative plasmid.","ARO_category":{"36176":{"category_aro_accession":"3000036","category_aro_cvterm_id":"36176","category_aro_name":"tetracycline inactivation enzyme","category_aro_description":"Enzymes or other gene products which hydroxylate tetracycline and other tetracycline derivatives. Hydroxylation inactivates tetracycline-like antibiotics, thus conferring resistance to these compounds.","category_aro_class_name":"AMR Gene Family"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3797":{"model_id":"3797","model_name":"tet(X6)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"6092":{"protein_sequence":{"accession":"QIM09823.1","sequence":"MTLLKHKKITIIGAGPVGLTMARLLQQNGVDITVYERDKDQDARIFGGTLDLHRDSGQEAMKRAGLLQTYYDLALPMGVNIVDEKGNILTTKNVRPENRFDNPEINRNDLRTILLNSLQNDTVIWDRKLVTLEPDKEKWILTFEDKSSETADLVIIANGGMSKVRKFVTDTEVEETGTFNIQADIHQPEVNCPGFFQLCNGNRLMAAHQGNLLFANPNNNGALHFGISFKTPDEWKSKTRVDFQDRNSVVDFLLKKFSDWDERYKELIRLTSSFVGLATRIFPLDKSWKSKRPLPITMIGDAAHLMPPFAGQGVNSGLMDALILSDNLTNGKFNSIEEAIENYEQQMFAYGREAQAESIINETEMFSLDFSFQKLMNL"},"dna_sequence":{"accession":"MN507533.1","fmin":"36121","fmax":"37258","strand":"+","sequence":"ATGACTTTACTAAAACATAAAAAAATTACAATAATTGGTGCCGGGCCTGTTGGATTAACAATGGCGAGATTGTTACAGCAAAACGGCGTGGACATTACAGTTTACGAGAGAGACAAAGACCAAGATGCAAGGATTTTTGGTGGGACACTTGATCTGCACAGGGATTCGGGACAGGAAGCAATGAAAAGAGCGGGATTGTTACAAACTTATTATGACTTAGCTTTACCAATGGGTGTAAATATTGTTGATGAAAAGGGCAATATTTTAACCACAAAAAATGTAAGACCCGAAAATCGTTTTGACAATCCTGAAATAAACAGAAATGACTTAAGGACTATCCTATTAAATAGTTTACAAAATGATACCGTCATTTGGGATAGAAAACTTGTTACCCTTGAACCTGATAAGGAGAAGTGGATACTAACTTTTGAGGATAAATCGAGTGAAACAGCAGATCTGGTTATTATTGCCAATGGTGGAATGTCTAAAGTAAGAAAATTTGTTACCGACACGGAAGTTGAAGAAACAGGTACTTTCAATATACAAGCCGATATTCATCAACCGGAGGTGAACTGTCCTGGATTTTTTCAGCTTTGCAATGGAAACCGGCTAATGGCTGCTCATCAAGGTAATTTATTATTTGCGAATCCTAATAATAATGGTGCATTGCATTTTGGAATAAGTTTTAAAACACCTGATGAATGGAAAAGCAAAACGCGGGTAGATTTTCAAGACAGAAATAGTGTCGTTGATTTTCTCCTGAAAAAATTTTCCGATTGGGACGAACGCTACAAAGAACTGATTCGTTTGACATCATCTTTTGTAGGGTTAGCGACACGAATATTTCCCTTAGATAAGTCTTGGAAAAGTAAGCGTCCATTACCCATAACGATGATTGGAGATGCTGCTCATTTGATGCCTCCTTTTGCAGGACAAGGCGTAAACAGTGGGTTGATGGATGCCTTGATATTGTCGGATAATCTGACCAATGGGAAATTTAACAGCATTGAAGAGGCTATTGAAAATTATGAACAGCAAATGTTTGCTTATGGAAGAGAAGCACAGGCAGAATCAATAATAAACGAAACGGAAATGTTCAGCCTCGACTTTTCTTTCCAAAAACTAATGAATCTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43258","NCBI_taxonomy_name":"Proteus genomosp. 6","NCBI_taxonomy_id":"1311820"}}}},"ARO_accession":"3005056","ARO_id":"43257","ARO_name":"tet(X6)","CARD_short_name":"tet(X6)","ARO_description":"Tet(X6) is a tetracycline inactivating enzyme. It is a tet(X) variant.","ARO_category":{"36176":{"category_aro_accession":"3000036","category_aro_cvterm_id":"36176","category_aro_name":"tetracycline inactivation enzyme","category_aro_description":"Enzymes or other gene products which hydroxylate tetracycline and other tetracycline derivatives. Hydroxylation inactivates tetracycline-like antibiotics, thus conferring resistance to these compounds.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36291":{"category_aro_accession":"3000152","category_aro_cvterm_id":"36291","category_aro_name":"minocycline","category_aro_description":"Minocycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"37012":{"category_aro_accession":"3000668","category_aro_cvterm_id":"37012","category_aro_name":"oxytetracycline","category_aro_description":"Oxytetracycline is a derivative of tetracycline with a 5-hydroxyl group. Its activity is similar to other tetracyclines.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3888":{"model_id":"3888","model_name":"tet(X1)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"650"}},"model_sequences":{"sequence":{"6215":{"protein_sequence":{"accession":"CAC47933.1","sequence":"MANLLQQNGIDITVYERDENPKARVWGGTLDLHKNSGQEAMKKVGLLQTYYDLALPMGVNFADEKGNIIATRNPTLENKFDNPEINRNALRKMLLGSLKNDTVVWDRKSIGLEQENGKWLLHFENKPTALADFIIVSNGGMSKIRNFVSDNEVEETGTFIIQGDIPEPETNCPEFYKLCNNNRLMTAHQGNLLVANPFNNGMLTYGVIFKKPEEWNNGKGLDFKPTKSVSEFLTNRFSNWSNEYKELIRSTTFFVGLTIKIFPLDKKPWKSNRPLPITLIGDTAHLMPPFAGQGVNIGLMDALILSENLTNGKFGTIQSAIDDYEQRMFVYATEAQADSTKNEIEMRNPSFTFQQLMNV"},"dna_sequence":{"accession":"AJ311171.1","fmin":"12109","fmax":"13189","strand":"-","sequence":"ATGGCAAACTTGTTACAACAAAACGGTATTGACATTACCGTTTACGAAAGAGATGAAAACCCAAAAGCACGAGTTTGGGGCGGAACGCTTGACCTTCACAAAAATTCAGGACAAGAAGCAATGAAAAAAGTAGGATTGTTGCAAACCTACTATGATTTGGCGCTACCTATGGGCGTAAACTTTGCTGATGAGAAGGGTAACATTATAGCAACAAGAAACCCGACACTCGAAAATAAGTTTGACAACCCCGAAATAAATAGAAACGCGTTGCGAAAAATGTTGCTTGGCAGCTTGAAAAATGACACAGTTGTTTGGGATAGAAAATCTATTGGGCTTGAACAAGAAAACGGAAAATGGCTGCTACATTTTGAAAATAAGCCAACTGCATTGGCCGACTTTATTATTGTTTCCAATGGTGGAATGTCTAAAATAAGAAATTTTGTTTCAGATAATGAAGTCGAAGAAACAGGTACTTTTATTATTCAGGGCGACATTCCTGAACCAGAAACGAACTGCCCTGAATTTTATAAGTTGTGCAACAACAATAGACTAATGACCGCACATCAAGGGAATTTATTAGTTGCGAATCCATTTAACAACGGAATGTTAACTTACGGTGTCATTTTCAAAAAGCCTGAAGAATGGAATAATGGAAAAGGATTAGATTTTAAGCCCACAAAAAGCGTTTCCGAGTTCTTGACAAACAGGTTTTCAAATTGGAGCAATGAATACAAGGAGTTAATTCGTTCAACAACTTTTTTCGTTGGTTTAACAATAAAAATATTTCCGCTAGACAAAAAGCCTTGGAAGAGTAATCGTCCGTTACCCATAACTTTAATTGGCGACACAGCTCACCTAATGCCACCTTTTGCAGGGCAGGGCGTAAACATTGGACTAATGGACGCTTTGATTTTGTCAGAAAATCTTACAAACGGGAAATTTGGAACGATACAAAGTGCTATTGATGACTATGAACAACGAATGTTTGTTTACGCAACAGAAGCACAAGCGGACTCGACAAAGAATGAAATAGAAATGCGAAATCCGAGCTTTACTTTTCAACAGCTAATGAATGTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39568","NCBI_taxonomy_name":"Bacteroides thetaiotaomicron","NCBI_taxonomy_id":"818"}}}},"ARO_accession":"3005166","ARO_id":"43518","ARO_name":"tet(X1)","CARD_short_name":"tet(X1)","ARO_description":"Tetracycline resistance gene tet(X) ortholog described by Fang et al. 2020.","ARO_category":{"36176":{"category_aro_accession":"3000036","category_aro_cvterm_id":"36176","category_aro_name":"tetracycline inactivation enzyme","category_aro_description":"Enzymes or other gene products which hydroxylate tetracycline and other tetracycline derivatives. Hydroxylation inactivates tetracycline-like antibiotics, thus conferring resistance to these compounds.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36291":{"category_aro_accession":"3000152","category_aro_cvterm_id":"36291","category_aro_name":"minocycline","category_aro_description":"Minocycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"37012":{"category_aro_accession":"3000668","category_aro_cvterm_id":"37012","category_aro_name":"oxytetracycline","category_aro_description":"Oxytetracycline is a derivative of tetracycline with a 5-hydroxyl group. Its activity is similar to other tetracyclines.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5795":{"model_id":"5795","model_name":"ROB-11","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"8477":{"protein_sequence":{"accession":"QSX93372.1","sequence":"MLNKLKIGTLLLLTLTACSPNSVHSVTSNPQPASAPVQQSATQATFQQTLANLEQQYQARIGVYVWDTETGHSLSYRADERFAYASTFKALLAGAVLQSLPEKDLNRTISYSQKDLVSYSPETQKYVGKGMTIAQLCEAAVRFSDNSATNLLLKELGGVEQYQRILRQLGDNVTHANRLEPDLNQAKPNDIRDTSTPKQMAMNLNAYLLGNTLTESQKTILWNWLDNNATGNPLIRAATPTSWKVYDKSGAGKYGVRNDIAVVRIPNRKPIVMAIMSTQFTEEAKFNNKLVEDAAKQVFHTLQLN"},"dna_sequence":{"accession":"MW735840.1","fmin":"0","fmax":"918","strand":"+","sequence":"ATGTTAAATAAGTTAAAAATCGGCACATTATTATTGCTGACATTAACGGCTTGTTCGCCCAATTCTGTTCATTCGGTAACGTCTAATCCGCAGCCTGCTAGTGCGCCTGTGCAACAATCAGCCACACAAGCCACCTTTCAACAGACTTTGGCGAATTTGGAACAGCAGTATCAAGCCCGAATTGGCGTTTATGTATGGGATACAGAAACGGGACATTCTTTGTCTTATCGTGCAGATGAACGCTTTGCTTATGCGTCCACTTTCAAGGCGTTGTTGGCTGGGGCGGTGTTGCAATCGCTGCCTGAAAAAGATTTAAATCGTACCATTTCATATAGCCAAAAAGATTTGGTTAGTTATTCTCCCGAAACCCAAAAATACGTTGGCAAAGGCATGACGATTGCCCAATTATGTGAAGCAGCCGTGCGGTTTAGCGACAACAGCGCGACCAATTTGCTGCTCAAAGAATTGGGTGGCGTGGAACAATATCAACGTATTTTGCGACAATTAGGCGATAACGTAACCCATGCCAATCGGCTAGAACCCGATTTAAATCAAGCCAAACCCAACGATATTCGTGATACGAGTACACCCAAACAAATGGCGATGAATTTAAATGCGTATTTATTGGGCAACACATTAACCGAATCGCAAAAAACGATTTTGTGGAATTGGTTGGACAATAACGCAACAGGCAATCCATTGATTCGCGCTGCTACGCCAACATCGTGGAAAGTGTACGATAAAAGCGGGGCGGGTAAATATGGTGTACGCAATGATATTGCGGTGGTTCGCATACCAAATCGCAAACCGATTGTGATGGCAATCATGAGTACGCAATTTACCGAAGAAGCCAAATTCAACAATAAATTAGTAGAAGATGCAGCAAAGCAAGTATTTCATACTTTACAGCTCAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36867","NCBI_taxonomy_name":"Pasteurella multocida","NCBI_taxonomy_id":"747"}}}},"ARO_accession":"3007125","ARO_id":"45705","ARO_name":"ROB-11","CARD_short_name":"ROB-11","ARO_description":"ROB-11 is a class A beta-lactamase from the blaROB AMR gene family.","ARO_category":{"39428":{"category_aro_accession":"3002994","category_aro_cvterm_id":"39428","category_aro_name":"ROB beta-lactamase","category_aro_description":"ROB beta-lactamases are a class A beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5796":{"model_id":"5796","model_name":"ROB-12","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"8475":{"protein_sequence":{"accession":"QSX93374.1","sequence":"MLNKLKIGTLLLLTLLLLTLTACSPNSVHSVTSNPQPASAPVQQSATQATFQQTLANLEQQYQARIGVYVWDTETGHSLSYRADERFAYASTFKALLAGAVLQSLPEKDLNRTISYSQKDLVSYSPETQKYVGKGMTIAQLCEAAVRFSDNSATNLLLKELGGVEQYQRILRQLGDNVTHANRLEPDLNQAKPNDIRDTSTPKQMAMNLNAYLLGNTLTESQKTILWNWLDNNATGNPLIRAATPTSWKVYDKSGAGKYGVRNDIAVVRIPNRKPIVMAIMSTQFTEEAKFNNKLVEDAAKQVFHTLQLN"},"dna_sequence":{"accession":"MW735842.1","fmin":"0","fmax":"933","strand":"+","sequence":"ATGTTAAATAAGTTAAAAATCGGCACATTATTATTGCTGACATTATTATTGCTGACATTAACGGCTTGTTCGCCCAATTCTGTTCATTCGGTAACGTCTAATCCGCAGCCTGCTAGTGCGCCTGTGCAACAATCAGCCACACAAGCCACCTTTCAACAGACTTTGGCGAATTTGGAACAGCAGTATCAAGCCCGAATTGGCGTTTATGTATGGGATACAGAAACGGGACATTCTTTGTCTTATCGTGCAGATGAACGCTTTGCTTATGCGTCCACTTTCAAGGCGTTGTTGGCTGGGGCGGTGTTGCAATCGCTGCCTGAAAAAGATTTAAATCGTACCATTTCATATAGCCAAAAAGATTTGGTTAGTTATTCTCCCGAAACCCAAAAATACGTTGGCAAAGGCATGACGATTGCCCAATTATGTGAAGCAGCCGTGCGGTTTAGCGACAACAGCGCGACCAATTTGCTGCTCAAAGAATTGGGTGGCGTGGAACAATATCAACGTATTTTGCGACAATTAGGCGATAACGTAACCCATGCCAATCGGCTAGAACCCGATTTAAATCAAGCCAAACCCAACGATATTCGTGATACGAGTACACCCAAACAAATGGCGATGAATTTAAATGCGTATTTATTGGGCAACACATTAACCGAATCGCAAAAAACGATTTTGTGGAATTGGTTGGACAATAACGCAACAGGCAATCCATTGATTCGCGCTGCTACGCCAACATCGTGGAAAGTGTACGATAAAAGCGGGGCGGGTAAATATGGTGTACGCAATGATATTGCGGTGGTTCGCATACCAAATCGCAAACCGATTGTGATGGCAATCATGAGTACGCAATTTACCGAAGAAGCCAAATTCAACAATAAATTAGTAGAAGATGCAGCAAAGCAAGTATTTCATACTTTACAGCTCAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36867","NCBI_taxonomy_name":"Pasteurella multocida","NCBI_taxonomy_id":"747"}}}},"ARO_accession":"3007126","ARO_id":"45706","ARO_name":"ROB-12","CARD_short_name":"ROB-12","ARO_description":"ROB-12 is a class A beta-lactamase from the blaROB AMR gene family.","ARO_category":{"39428":{"category_aro_accession":"3002994","category_aro_cvterm_id":"39428","category_aro_name":"ROB beta-lactamase","category_aro_description":"ROB beta-lactamases are a class A beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3808":{"model_id":"3808","model_name":"ROB-13","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"620"}},"model_sequences":{"sequence":{"6103":{"protein_sequence":{"accession":"AGH37381.1","sequence":"MFNKLKIGTLLLLTLTACSLNSVHSVTSNPQPASAPVQQSATQATFQQTLANLEQQYQARIGVYVWDTETGHSLSYRADERFAYASTFKALLAGAVLQSLPEKDLNRTISYSQKDLVSYSPETQKYVGKGMTIAQLCEAAVRFSDNSATNLLLKELGGVEQYQRILRQLGDNVTHTNRLEPDLNQAKPNDIRDTSTPKQMAMNLNAYLLGNTLTESQKTILWNWLDNNATGNPLIRAATPTSWKVYDKSGAGKYGVRNDIAVVRIPNRKPIVMAIMSTQFTEEAKFNNKLVEDAAKQVFHTLQLN"},"dna_sequence":{"accession":"CP003745.1","fmin":"87300","fmax":"88218","strand":"-","sequence":"ATGTTTAATAAGTTAAAAATCGGCACATTATTATTGCTGACATTAACGGCTTGTTCGCTCAATTCTGTTCATTCGGTAACGTCTAATCCGCAGCCTGCTAGTGCGCCTGTGCAACAATCAGCCACACAAGCCACCTTTCAACAGACTTTGGCGAATTTGGAACAGCAGTATCAAGCCCGAATTGGCGTTTATGTATGGGATACAGAAACGGGACATTCTTTGTCTTATCGTGCAGATGAACGCTTTGCTTATGCGTCCACTTTCAAGGCGTTGTTGGCTGGGGCGGTGTTGCAATCGCTGCCTGAAAAAGATTTAAATCGTACCATTTCATATAGCCAAAAAGATTTGGTTAGTTATTCTCCCGAAACCCAAAAATACGTTGGCAAAGGCATGACGATTGCCCAATTATGTGAAGCAGCCGTGCGGTTTAGCGACAACAGCGCGACCAATTTGCTGCTCAAAGAATTGGGTGGCGTGGAACAATATCAACGTATTTTGCGACAATTAGGCGATAACGTAACCCATACCAATCGGCTAGAACCCGATTTAAATCAAGCCAAACCCAACGATATTCGTGATACGAGTACACCCAAACAAATGGCGATGAATTTAAATGCGTATTTATTGGGCAACACATTAACCGAATCGCAAAAAACGATTTTGTGGAATTGGTTGGACAATAACGCAACAGGCAATCCATTGATTCGCGCTGCTACGCCAACATCGTGGAAAGTGTACGATAAAAGCGGGGCGGGTAAATATGGTGTACGCAATGATATTGCGGTGGTTCGCATACCAAATCGCAAACCGATTGTGATGGCAATCATGAGTACGCAATTTACCGAAGAAGCCAAATTCAACAATAAATTAGTAGAAGATGCAGCAAAGCAAGTATTTCATACTTTACAGCTCAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43277","NCBI_taxonomy_name":"Bibersteinia trehalosi USDA-ARS-USMARC-192","NCBI_taxonomy_id":"1171377"}}}},"ARO_accession":"3005072","ARO_id":"43276","ARO_name":"ROB-13","CARD_short_name":"ROB-13","ARO_description":"ROB-13 is a beta-lactamase from the blaROB AMR gene family. It was found in Bibersteinia trehalosi.","ARO_category":{"39428":{"category_aro_accession":"3002994","category_aro_cvterm_id":"39428","category_aro_name":"ROB beta-lactamase","category_aro_description":"ROB beta-lactamases are a class A beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1273":{"model_id":"1273","model_name":"Streptomyces rimosus otr(A)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"660":{"protein_sequence":{"accession":"CAA37477.1","sequence":"MNKLNLGILAHVDAGKTSLTERLLHRTGVIDEVGSVDAGTTTTDSMELERQRGITIRSAVATFVLDDLKVNLIDTPGHSDFISEVERALGVLDGAVLVVSAVEGVQPQTRILMRTLRRLGIPTLVFVNKIDRGGARPDGVLREIRDRLTPAAVALSAVADAGTPRARAIALGPDTDPDFAVRVGELLADHDDAFLTAYLDEEHVLTEKEYAEELAAQTARGLVHPVYFGSALTGEGLDHLVHGIRELLPSVHASQDAPLRATVFKVDRGARGEAVAYLRLVSGTLGTRDSVTLHRVDHTGRVTEHAGRITALRVFEHGSATSETRATAGDIAQAWGLKDVRVGDRAGHLDGPPPRNFFAPPSLETVIRPERPEEAGRLHAALRMLDEQDPSIDLRQDEENAAGAVVRLYGEVQKEILGSTLAESFGVRVRFDPTRTVCIEKPVGTGEALIELDTRTHNYFWGAPWVCASDRPSPARAITFRLAVELGSLPLAFHKAIEETVHTTLRHGLYGWQVTDCAVTLTRTGVRSPVSAADDFRKANARLVLMDALGRAGTEVHEPVSSFELEVPAARLSPVLAKLAELGATPGVPTAEGDVFRLEGTMPTSLVHDFNQRVPGLTQGEGVFLAEHRGYRPAVGQPPVRPRPEGPNPLNRDEYILHVLKRV"},"dna_sequence":{"accession":"X53401.1","fmin":"0","fmax":"1992","strand":"+","sequence":"ATGAACAAGCTGAATCTGGGCATCCTGGCCCACGTTGACGCCGGCAAGACCAGCCTCACCGAGCGCCTGCTGCACCGCACCGGTGTGATCGACGAGGTCGGCAGCGTGGACGCCGGCACCACGACGACCGACTCGATGGAGCTGGAGCGGCAGCGCGGCATCACCATCCGGTCCGCCGTGGCCACGTTCGTCCTGGACGATCTCAAGGTCAACCTCATCGACACCCCGGGCCACTCCGACTTCATCTCCGAGGTCGAGCGGGCGCTCGGGGTGCTCGACGGCGCGGTCCTGGTGGTCTCGGCCGTCGAGGGCGTCCAGCCGCAGACCCGCATCCTGATGCGGACCCTGCGCAGGCTGGGCATTCCCACGCTGGTCTTCGTCAACAAGATCGACCGGGGCGGCGCGCGTCCCGACGGTGTGCTGCGGGAGATCCGCGACCGGCTCACCCCCGCCGCGGTGGCACTGTCCGCCGTGGCGGACGCCGGCACGCCGCGGGCCCGCGCGATCGCGCTCGGCCCGGACACCGACCCGGACTTCGCCGTCCGGGTCGGTGAGCTGCTGGCCGACCACGACGACGCGTTCCTCACCGCCTACCTGGACGAGGAACACGTACTGACCGAGAAGGAGTACGCGGAGGAACTGGCCGCGCAGACCGCGCGCGGTCTGGTGCACCCGGTGTACTTCGGGTCCGCGCTGACCGGCGAGGGCCTGGACCATCTGGTGCACGGCATCCGGGAGTTGCTGCCGTCCGTGCACGCGTCGCAGGACGCGCCGCTGCGGGCCACCGTGTTCAAGGTGGACCGTGGCGCGCGCGGCGAGGCCGTCGCGTACCTGCGGCTGGTCTCCGGCACGCTGGGCACCCGCGATTCGGTGACGCTGCACCGCGTCGACCACACCGGCCGGGTCACCGAGCACGCCGGACGCATCACCGCGCTGCGGGTCTTCGAGCACGGGTCGGCCACCAGCGAGACCCGGGCGACCGCCGGGGACATCGCGCAGGCGTGGGGCCTGAAGGACGTACGGGTCGGTGACCGGGCCGGGCACCTCGACGGTCCCCCGCCGCGCAACTTCTTCGCGCCGCCCAGCCTGGAGACCGTGATCAGGCCGGAGCGCCCGGAGGAAGCGGGACGGCTGCACGCCGCGCTGCGCATGCTGGACGAGCAGGACCCCTCGATCGACCTGCGGCAGGACGAGGAGAACGCGGCCGGCGCGGTGGTCCGCCTCTACGGGGAGGTGCAGAAGGAGATCCTCGGCAGCACGCTCGCGGAGTCCTTCGGCGTACGGGTGCGCTTCGACCCGACCCGTACGGTCTGCATCGAAAAGCCCGTGGGGACCGGCGAGGCGCTGATCGAGCTGGACACGCGGACGCACAACTACTTCTGGGGCGCACCGTGGGTCTGCGCGTCGGACCGGCCGAGCCCGGCGCGGGCGATCACGTTCCGTTTGGCGGTGGAACTGGGCTCGCTCCCCCTGGCCTTCCACAAGGCCATCGAGGAGACGGTGCACACCACCCTGCGGCACGGTCTGTACGGCTGGCAGGTCACCGACTGCGCCGTCACCCTGACCCGTACCGGCGTTCGCAGTCCGGTCAGCGCGGCCGACGACTTCCGCAAGGCCAACGCGCGCTTGGTCCTGATGGACGCGCTCGGCAGGGCCGGTACGGAGGTGCACGAGCCGGTCAGCTCCTTCGAACTGGAGGTGCCCGCCGCCCGGCTCAGCCCGGTACTTGCGAAACTCGCGGAACTGGGCGCGACGCCCGGTGTGCCCACGGCCGAGGGGGACGTCTTCCGCCTGGAGGGCACGATGCCGACCAGCCTCGTGCACGACTTCAACCAGCGGGTTCCCGGACTGACCCAGGGCGAGGGCGTGTTCCTGGCCGAGCACCGGGGCTACCGGCCCGCCGTCGGACAGCCGCCCGTGCGGCCGCGGCCCGAGGGGCCCAACCCGCTCAACCGCGACGAGTACATCCTGCACGTGCTCAAGCGCGTGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36773","NCBI_taxonomy_name":"Streptomyces rimosus","NCBI_taxonomy_id":"1927"}}}},"ARO_accession":"3002891","ARO_id":"39325","ARO_name":"Streptomyces rimosus otr(A)","CARD_short_name":"otr(A)S.rim","ARO_description":"Streptomyces rimosus otr(A) is an oxytetracycline resistance ribosomal protection protein found in Streptomyces rimosus.","ARO_category":{"35921":{"category_aro_accession":"0000002","category_aro_cvterm_id":"35921","category_aro_name":"tetracycline-resistant ribosomal protection protein","category_aro_description":"A family of proteins known to bind to the 30S ribosomal subunit. This interaction prevents tetracycline and tetracycline derivatives from inhibiting ribosomal function. Thus, these proteins confer elevated resistance to tetracycline derivatives as a ribosomal protection protein.","category_aro_class_name":"AMR Gene Family"},"37012":{"category_aro_accession":"3000668","category_aro_cvterm_id":"37012","category_aro_name":"oxytetracycline","category_aro_description":"Oxytetracycline is a derivative of tetracycline with a 5-hydroxyl group. Its activity is similar to other tetracyclines.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5797":{"model_id":"5797","model_name":"Streptomyces lividans otr(A)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"8476":{"protein_sequence":{"accession":"AAA26830.1","sequence":"MRTLNIGILAHVDAGKTSLTERLLFDHGAVDRLGSVDAGDTRTVDGGIERRRGITIRSAVAAFTVGDTRVNLIDTPGHSDFVAEVERALEVLDGAVLLLSAVEGVQARTRVLMRALRRLRLPTIVFVNKIDRAGARTDGLLGDVRRLLTPHVAPLTEVADAGTPRARVTRRPPDGRTAEALAEVDTEVLAALVDGPEPTGEDVARALAARTADGSFHPLYHGSALGGQGVAELVEGLLGLIPAATPGTSGGTSGGTEPRGTVFAVRPGPAGERTAYLRLYGGEVHPRRRLTFLRRESDGRTTEVSGRVTRLDVVGGDATLTAGNIAALTVPGGLRVGDRLGGPTDRAPQFAPPTLQTLVRARHPEQAAPLRSALLALADQDPLLHARPAASGATALLLYGEVQMEVLAATLAEDFGIEAEFTPGRVRFLERPAGTDEAAEEMPWLDRTRYFATIGLRVEPGPRGSGGAFGYETELGALPRAFHQAVEETVHDTLRTGLTGAAVTDYRVTLIRSGFSSPLSTAADFRGLTPLVLRRALARAGTVLHEPYQAFEAEVPADTLAAVTALLASLGADFTGTTGGDPAWIVTGELPARRVREAELRLPGLTHGEAVWSSRPCEDRPLKAGNSGPGTGVGGHSGE"},"dna_sequence":{"accession":"M74049.1","fmin":"342","fmax":"2262","strand":"+","sequence":"ATGCGCACCCTGAACATCGGCATTCTGGCCCACGTCGACGCGGGTAAGACCAGCCTGACCGAACGGCTCCTGTTCGACCACGGCGCCGTCGACCGGCTCGGCAGCGTCGACGCCGGCGACACCCGTACGGTCGACGGCGGTATCGAGCGCCGCCGCGGCATCACCATCCGCTCCGCCGTCGCCGCCTTCACCGTCGGCGACACGCGCGTCAACCTGATCGACACCCCGGGACACTCCGACTTCGTCGCGGAGGTCGAGCGGGCCCTGGAAGTGCTCGACGGGGCGGTGCTGCTGCTGTCCGCCGTCGAGGGCGTCCAGGCGCGGACCCGCGTCCTGATGCGCGCGCTGCGGCGGCTGCGGCTGCCCACGATCGTGTTCGTCAACAAGATCGACCGGGCCGGCGCGCGCACCGACGGCCTCCTCGGTGACGTCCGGCGCCTGCTGACGCCGCACGTCGCGCCGCTGACCGAGGTGGCGGACGCCGGTACCCCGCGCGCCCGGGTCACCCGCCGCCCGCCGGACGGGCGGACCGCGGAGGCCCTCGCCGAGGTCGACACGGAGGTCCTGGCCGCGCTGGTCGACGGCCCCGAGCCGACCGGGGAGGACGTGGCCCGCGCCCTCGCCGCCCGTACCGCCGACGGCTCGTTCCACCCGCTGTACCACGGCTCCGCGCTCGGCGGACAGGGCGTCGCGGAGCTGGTCGAGGGCCTGCTCGGCCTGATCCCGGCCGCCACGCCGGGCACGTCCGGCGGCACGTCCGGCGGCACGGAACCGCGCGGCACGGTCTTCGCCGTGCGCCCCGGACCCGCCGGCGAGCGCACCGCGTACCTCAGGCTGTACGGCGGCGAGGTGCACCCGCGCCGGCGGCTCACCTTCCTGCGGCGCGAGTCCGACGGGCGGACCACCGAGGTCTCCGGCCGGGTGACCCGCCTCGACGTCGTCGGCGGCGACGCCACGCTCACCGCCGGGAACATCGCCGCGCTCACCGTTCCCGGGGGCCTGCGCGTCGGCGACCGGCTCGGCGGACCGACCGACCGTGCACCGCAGTTCGCGCCACCGACCCTGCAGACGCTGGTCCGGGCCCGGCACCCGGAGCAGGCGGCGCCGCTGCGCTCCGCCCTGCTGGCGCTGGCCGACCAGGACCCGCTGCTGCACGCCCGACCGGCGGCGTCCGGCGCCACCGCCCTGCTCCTGTACGGCGAGGTCCAGATGGAGGTGCTCGCGGCGACACTGGCCGAGGACTTCGGGATCGAGGCGGAGTTCACGCCGGGCCGCGTCCGGTTCCTGGAGCGTCCGGCGGGCACCGACGAGGCCGCGGAGGAGATGCCGTGGCTCGACCGCACCCGGTACTTCGCGACGATCGGGCTGCGCGTCGAACCGGGTCCGCGCGGCTCCGGCGGGGCCTTCGGGTACGAGACGGAGCTCGGCGCGCTCCCCCGGGCCTTCCACCAGGCCGTCGAGGAGACCGTCCACGACACGCTGCGGACCGGGCTCACCGGTGCGGCGGTCACCGACTACCGGGTCACGCTGATCCGCTCCGGCTTCAGCTCGCCGCTCAGCACGGCCGCCGACTTCCGCGGGCTGACACCGCTCGTGCTGCGCCGTGCCCTCGCCCGCGCGGGGACCGTGCTCCACGAGCCGTACCAGGCCTTCGAGGCGGAGGTCCCGGCGGACACGCTGGCCGCCGTGACGGCCCTGCTGGCCTCGCTGGGCGCGGACTTCACCGGAACGACGGGGGGCGACCCGGCCTGGATCGTCACCGGCGAGCTGCCGGCCCGGCGGGTGCGGGAGGCCGAGCTGCGGCTGCCGGGGCTGACGCACGGGGAGGCGGTCTGGTCCTCCCGCCCTTGCGAGGACCGACCGCTGAAGGCCGGAAACTCTGGGCCTGGCACGGGAGTTGGCGGGCATTCGGGTGAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39551","NCBI_taxonomy_name":"Streptomyces lividans 1326","NCBI_taxonomy_id":"1200984"}}}},"ARO_accession":"3007127","ARO_id":"45707","ARO_name":"Streptomyces lividans otr(A)","CARD_short_name":"otr(A)S.liv","ARO_description":"Streptomyces lividans otr(A) is an oxytetracycline resistance ribosomal protection protein found in Streptomyces lividans.","ARO_category":{"35921":{"category_aro_accession":"0000002","category_aro_cvterm_id":"35921","category_aro_name":"tetracycline-resistant ribosomal protection protein","category_aro_description":"A family of proteins known to bind to the 30S ribosomal subunit. This interaction prevents tetracycline and tetracycline derivatives from inhibiting ribosomal function. Thus, these proteins confer elevated resistance to tetracycline derivatives as a ribosomal protection protein.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5798":{"model_id":"5798","model_name":"mcr-10.1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"8479":{"protein_sequence":{"accession":"QDO66747.1","sequence":"MPVLFRMRVIPLVLLLALVFAFLLNWPVLLHFYDILSRLEHVRAGFVISIPFVLVAALNFVFMPFSVRYLLKPFFALLLVTGSVVSYATLKYKVMFDQSMIENILETNPQEAHAYLNGSLVLWLVFMGILPAILLFLIKIEYADKWYKGVAHRLLSMLASLILIAGVAALYYQDYASVGRNNPTLNKEIIPANYAYSTFHYVKDTYFTTKMPFRTLGDDARRVTRNGKPTLMFLVIGETARSQNFSMNGYPRDTNAFTSKIDGVISFRNMRSCGTATAVSVPCMFSDMNRTDYDGKKAAGSENVLDIVQKTGVSLLWKENDGGCKGVCSRIPTVEINPGISKKLCDGKTCYDDVMLENLDTEIGKMAGDKLIAFHMIGSHGPTYYQRYPAEHRHFMPECARSDIENCTQEQLVNTYDNTIRHTDYVLAQMIEKLKQYSEQYNTVLLYVSDHGESLGESGLYLHGTPYKLAPDQQTHIPMQLWMSPGFIAAKNINAACLQHNAVNRTYSHDNLFASVLGLWDITTGAYLPESDLFRECRG"},"dna_sequence":{"accession":"MN179494.1","fmin":"0","fmax":"1620","strand":"+","sequence":"ATGCCCGTACTTTTCAGGATGAGGGTAATCCCCTTGGTTTTACTTCTGGCACTCGTTTTTGCATTCTTACTTAACTGGCCGGTGTTGCTGCATTTCTACGATATCCTGAGCCGTCTTGAACATGTGAGGGCGGGGTTCGTCATCTCCATTCCGTTTGTGCTGGTTGCAGCGCTTAACTTTGTGTTTATGCCCTTCTCGGTTCGCTACCTGCTCAAACCCTTCTTTGCCCTGTTGCTGGTCACCGGTTCGGTGGTGAGTTACGCCACACTGAAATATAAAGTGATGTTTGATCAGTCCATGATCGAAAATATACTGGAAACAAACCCACAGGAAGCGCATGCCTACCTGAATGGCTCACTGGTGCTGTGGCTGGTCTTCATGGGCATTCTTCCGGCTATCCTGTTGTTTTTGATTAAAATTGAATATGCAGACAAATGGTACAAAGGGGTTGCCCACCGGCTGCTTTCCATGCTCGCTTCGCTGATCCTGATTGCAGGTGTTGCCGCTCTGTATTACCAGGATTATGCTTCTGTCGGGCGCAATAACCCGACGCTGAACAAAGAAATTATCCCGGCAAACTATGCGTACAGCACTTTCCATTACGTGAAGGATACCTATTTTACGACGAAAATGCCTTTCCGGACGCTGGGGGATGATGCAAGGCGCGTTACCCGGAATGGTAAACCCACGCTGATGTTCCTGGTAATTGGCGAAACGGCACGGAGCCAGAATTTCTCCATGAACGGCTACCCGCGTGACACAAATGCCTTTACCAGCAAAATCGATGGCGTTATTTCGTTCAGGAATATGCGTTCCTGTGGCACGGCGACCGCAGTCTCGGTGCCCTGTATGTTCTCGGATATGAACCGGACGGATTACGATGGTAAAAAGGCTGCCGGCAGTGAAAATGTCCTCGACATCGTGCAGAAAACGGGGGTTTCGCTGTTGTGGAAAGAAAACGATGGCGGGTGTAAAGGCGTATGCAGCCGTATCCCGACTGTCGAAATTAATCCCGGTATCAGTAAAAAACTGTGTGACGGTAAAACCTGCTATGACGATGTTATGCTGGAAAACCTGGATACCGAAATCGGCAAAATGGCCGGAGACAAGCTGATCGCCTTCCATATGATTGGCAGCCATGGACCGACCTATTACCAGCGTTATCCGGCAGAGCATCGTCACTTCATGCCGGAATGTGCGCGCAGCGATATCGAAAACTGCACGCAGGAACAGCTGGTTAATACCTACGACAATACCATTCGCCACACCGACTATGTGTTAGCGCAGATGATTGAAAAGCTTAAGCAATACAGCGAACAGTACAACACCGTACTGCTGTATGTGTCCGATCACGGCGAATCTCTGGGAGAGAGCGGACTGTATCTGCACGGTACCCCCTACAAACTGGCACCGGATCAGCAGACGCACATCCCGATGCAGCTCTGGATGTCGCCAGGCTTCATTGCTGCTAAAAATATTAACGCCGCGTGTCTGCAGCATAATGCCGTTAACAGGACATATTCCCACGATAACCTTTTCGCGTCCGTACTGGGGCTCTGGGACATCACCACCGGGGCCTATCTTCCGGAAAGCGACCTGTTCCGCGAATGTCGTGGATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43769","NCBI_taxonomy_name":"Enterobacter roggenkampii","NCBI_taxonomy_id":"1812935"}}}},"ARO_accession":"3007137","ARO_id":"45718","ARO_name":"mcr-10.1","CARD_short_name":"mcr-10.1","ARO_description":"An MCR-10-type colistin resistance gene variant.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5799":{"model_id":"5799","model_name":"MAB","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"8480":{"protein_sequence":{"accession":"ALP44181.1","sequence":"MISRRALLVGGVSAVGVVAAGCSRNGNRRPAPDELASLEKDFGGRIGVYALDTGSGDTVGHRADERFLMCSTVKTFIVSAILRRRLSEPGLLDQRIQYTQSDVLEWAPITSQHVSTGMTVSELCDATLRYSDNTGANLLITQLGGPKETEKFVRSLGDNVTRMDRTEVQLNIPDGDLDTSTPQQLVANLRRLVLDEGLDSRGRDLLTDWLKRNTTGDQSIRAAVPAGWTVADKTGGGFKGETNDIAVIWPPGRAPIVMAVLTVPEDPTSTKGKPTIAAATRIVLRAFGA"},"dna_sequence":{"accession":"KT159981.2","fmin":"248","fmax":"1118","strand":"+","sequence":"ATGATCTCTCGTCGCGCACTTCTTGTCGGTGGGGTATCGGCGGTCGGTGTGGTGGCTGCCGGTTGTTCGCGCAACGGCAACCGTCGGCCCGCGCCGGACGAACTCGCCTCGCTGGAAAAGGATTTCGGCGGCCGCATCGGTGTCTACGCGTTGGACACCGGGTCGGGTGACACGGTCGGCCACCGCGCCGATGAACGCTTTCTGATGTGCTCGACGGTCAAGACCTTCATCGTCTCGGCCATCCTGCGCCGGAGACTGAGCGAACCGGGCCTGTTGGACCAGCGAATTCAGTACACGCAATCCGACGTTCTGGAATGGGCGCCGATCACCTCGCAACACGTGTCCACCGGAATGACCGTCTCGGAACTGTGTGATGCGACGCTCCGCTATAGCGACAACACCGGTGCCAACCTGCTGATCACCCAACTCGGCGGCCCGAAGGAGACAGAGAAGTTCGTCCGAAGCCTGGGCGACAACGTCACTCGCATGGACCGCACGGAGGTACAGCTGAACATCCCCGACGGCGATCTGGATACCTCGACCCCGCAGCAGCTGGTGGCCAATCTGCGCCGACTGGTCCTCGACGAAGGGCTGGATTCACGGGGACGGGATCTGCTGACCGATTGGTTGAAGCGAAATACCACCGGCGACCAGTCCATTCGGGCAGCAGTTCCCGCCGGGTGGACGGTCGCAGACAAGACCGGCGGCGGCTTCAAGGGTGAAACCAACGACATCGCGGTGATCTGGCCCCCGGGCCGTGCACCCATCGTGATGGCGGTACTCACCGTCCCGGAGGACCCCACATCCACCAAAGGTAAGCCGACGATTGCCGCGGCCACCCGAATCGTGCTGCGGGCCTTCGGCGCTTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36888","NCBI_taxonomy_name":"Mycobacteroides abscessus","NCBI_taxonomy_id":"36809"}}}},"ARO_accession":"3007180","ARO_id":"45919","ARO_name":"MAB","CARD_short_name":"MAB","ARO_description":"MAB is a broad-spectrum class A beta-lactamase produced by Mycobacterium abscessus that has been shown to hydrolyze a large number of beta-lactam antibiotics.","ARO_category":{"45918":{"category_aro_accession":"3007179","category_aro_cvterm_id":"45918","category_aro_name":"class A Mycobacterium abscessus beta-lactamase","category_aro_description":"Class A beta-lactamse from M. abscessus.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"35980":{"category_aro_accession":"0000063","category_aro_cvterm_id":"35980","category_aro_name":"cefuroxime","category_aro_description":"Cefuroxime is a second-generation cephalosporin antibiotic with increased stability with beta-lactamases than first-generation cephalosporins. Cefuroxime is active against Gram-positive organisms but less active against methicillin-resistant strains.","category_aro_class_name":"Antibiotic"},"35981":{"category_aro_accession":"0000064","category_aro_cvterm_id":"35981","category_aro_name":"amoxicillin","category_aro_description":"Amoxicillin is a moderate-spectrum, bacteriolytic, beta-lactam antibiotic used to treat bacterial infections caused by susceptible microorganisms. A derivative of penicillin, it has a wider range of treatment but remains relatively ineffective against Gram-negative bacteria. It is commonly taken with clavulanic acid, a beta-lactamase inhibitor. Like other beta-lactams, amoxicillin interferes with the synthesis of peptidoglycan.","category_aro_class_name":"Antibiotic"},"37084":{"category_aro_accession":"3000704","category_aro_cvterm_id":"37084","category_aro_name":"cefalotin","category_aro_description":"Cefalotin is a semisynthetic cephalosporin antibiotic activate against staphylococci. It is resistant to staphylococci beta-lactamases but hydrolyzed by enterobacterial beta-lactamases.","category_aro_class_name":"Antibiotic"},"40523":{"category_aro_accession":"3003832","category_aro_cvterm_id":"40523","category_aro_name":"ticarcillin","category_aro_description":"Ticarcillin is a carboxypenicillin used for the treatment of Gram-negative bacteria, particularly P. aeruginosa. Ticarcillin's antibiotic properties arise from its ability to prevent cross-linking of peptidoglycan during cell wall synthesis, when the bacteria try to divide, causing cell death.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5884":{"model_id":"5884","model_name":"MCR-1.15","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"8578":{"protein_sequence":{"accession":"WP_116786830.1","sequence":"MQHTSVWYRRSVSPFVLVASVAVFLTATANLTFFDKISQTYPIADNLGFVLTIAVVLFGAMLLITTLLSSYRYVLKPVLILLLIMGAVTSYFTDTYGTVYDTTMLQNALQTDQAETKDLLNAAFIMRIIGLGVLPSLLVAFVKVDYPTWGKGLMRRLGLIVASLALILLPVVAFSSHYASFFRVHKPLRSYVNPIMPIYSVGKLASIEYKKASAPKDTIYHAKDAVQATKPDMRKPRLVVFVVGETARADHVSFNGYERDTFPQLAKIDGVTNFSNVKSCGTSTAYSVPCMFSYLGADEYDVDTAKYQENVLDTLDRLGVSILWRDNNSDSKGVMDKLPKAQFADYKSATNNAICNTNPYNECRDVGMLVGLDDFVAANNGKDMLIMLHQMGNHGPAYFKRYDEKFAKFTPVCEGNELAKCEHQSLINAYDNALLATDDFIAQSIQWLQTHSNAYDVSMLYVSDHGESLGENGVYLHGMPNAFAPKEQRSVPAFFWTDKQTGITPMATDTVLTHDAITPTLLKLFDVTADKVKDRTAFIR"},"dna_sequence":{"accession":"MG763897.1","fmin":"528","fmax":"2151","strand":"+","sequence":"ATGCAGCATACTTCTGTGTGGTACCGACGCTCGGTCAGTCCGTTTGTTCTTGTGGCGAGTGTTGCCGTTTTCTTGACCGCGACCGCCAATCTTACCTTTTTTGATAAAATCAGCCAAACCTATCCCATCGCGGACAATCTCGGCTTTGTGCTGACGATCGCTGTCGTGCTCTTTGGCGCGATGCTACTGATCACCACGCTGTTATCATCGTATCGCTATGTGCTAAAGCCTGTGTTGATTTTGCTATTAATCATGGGCGCGGTGACCAGTTATTTTACTGACACTTATGGCACGGTCTATGATACGACCATGCTCCAAAATGCCCTACAGACCGACCAAGCCGAGACCAAGGATCTATTAAACGCAGCGTTTATCATGCGTATCATTGGTTTGGGTGTGCTACCAAGTTTGCTTGTGGCTTTTGTTAAGGTGGATTATCCGACTTGGGGCAAGGGTTTGATGCGCCGATTGGGCTTGATCGTGGCAAGTCTTGCGCTGATTTTACTGCCTGTGGTGGCGTTCAGCAGTCATTATGCCAGTTTCTTTCGCGTGCATAAGCCGCTGCGTAGCTATGTCAATCCGATCATGCCAATCTACTCGGTGGGTAAGCTTGCCAGTATTGAGTATAAAAAAGCCAGTGCGCCAAAAGATACCATTTATCACGCCAAAGACGCGGTACAAGCAACCAAGCCTGATATGCGTAAGCCACGCCTAGTGGTGTTCGTCGTCGGTGAGACGGCACGCGCCGATCATGTCAGCTTCAATGGCTATGAGCGCGATACTTTCCCACAGCTTGCCAAGATCGATGGCGTGACCAATTTTAGCAATGTCAAATCGTGCGGCACATCGACGGCGTATTCTGTGCCGTGTATGTTCAGCTATCTGGGCGCGGATGAGTATGATGTCGATACCGCCAAATACCAAGAAAATGTGCTGGATACGCTGGATCGCTTGGGCGTAAGTATCTTGTGGCGTGATAATAATTCGGACTCAAAAGGCGTGATGGATAAGCTGCCAAAAGCGCAATTTGCCGATTATAAATCCGCGACCAACAACGCCATCTGCAACACCAATCCTTATAACGAATGCCGCGATGTCGGTATGCTCGTTGGCTTAGATGACTTTGTCGCTGCCAATAACGGCAAAGATATGCTGATCATGCTGCACCAAATGGGCAATCACGGGCCTGCGTATTTTAAGCGATATGATGAAAAGTTTGCCAAATTCACGCCAGTGTGTGAAGGTAATGAGCTTGCCAAGTGCGAACATCAGTCCTTGATCAATGCTTATGACAATGCCTTGCTTGCCACCGATGATTTCATCGCTCAAAGTATCCAGTGGCTGCAGACGCACAGCAATGCCTATGATGTCTCAATGCTGTATGTCAGCGATCATGGCGAAAGTCTGGGTGAGAACGGTGTCTATCTACATGGTATGCCAAATGCCTTTGCACCAAAAGAACAGCGCAGTGTGCCTGCATTTTTCTGGACGGATAAGCAAACTGGCATCACGCCAATGGCAACCGATACCGTCCTGACCCATGACGCGATCACGCCGACATTATTAAAGCTGTTTGATGTCACCGCGGACAAAGTCAAAGACCGCACCGCATTCATCCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3007279","ARO_id":"46025","ARO_name":"MCR-1.15","CARD_short_name":"MCR-1.15","ARO_description":"An MCR-1-type colistin resistance gene variant.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5885":{"model_id":"5885","model_name":"MCR-1.26","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"8579":{"protein_sequence":{"accession":"WP_034169413.1","sequence":"MQHTSVWYRRSVSPFVLVASVAVFLTATANLTFFDKISQTYPIADNLGFVLTIAVVLFGAMLLITTLLSSYRYVLKPVLILLLIMGAVTSYFTDTYGTVYDTTMLQNALQTDQAETKDLLNAAFIMRIIGLGVLPSLLVAFVKVDYPTWGKGLMRRLGLIVASLALILLPVVAFSSHYASFFRVHKPLRSYVNPIMPIYSVGKLASIEYKKASAPKDTIYHAKDAVQATKPDMRKPRLVVFVVGETARADHVSFNGYERDTFPQLAKIDGVTNFSNVTSCGTSTAYSVPCMFSYLGADEYDVDTAKYQENVLDTLDRLGVSILWRDNNSDSKGVMDKLPKAQFADYKSATNNAICNTNPYNECRDVGMLVGLDDFVAANNGKDMLIMLHQMGNHGPAYFKRYDEKFAKFTPVCEGNELAKCEHQSLINAYDNALLATDDFIAQSIQWLQTHSNAYDVSMLYVSDHGESLGENGVYLHGMPNAFAPKEQRSVPAFFWTDKQTGITPMATDTVLTHDAITPTLLKLFDVTADKVKDRTAFIR"},"dna_sequence":{"accession":"JAAGSA010000042.1","fmin":"3573","fmax":"5196","strand":"+","sequence":"ATGCAGCATACTTCTGTGTGGTACCGACGCTCGGTCAGTCCGTTTGTTCTTGTGGCGAGTGTTGCCGTTTTCTTGACCGCGACCGCCAATCTTACCTTTTTTGATAAAATCAGCCAAACCTATCCCATCGCGGACAATCTCGGCTTTGTGCTGACGATCGCTGTCGTGCTCTTTGGCGCGATGCTACTGATCACCACGCTGTTATCATCGTATCGCTATGTGCTAAAGCCTGTGTTGATTTTGCTATTAATCATGGGCGCGGTGACCAGTTATTTTACTGACACTTATGGCACGGTCTATGATACGACCATGCTCCAAAATGCCCTACAGACCGACCAAGCCGAGACCAAGGATCTATTAAACGCAGCGTTTATCATGCGTATCATTGGTTTGGGTGTGCTACCAAGTTTGCTTGTGGCTTTTGTTAAGGTGGATTATCCGACTTGGGGCAAGGGTTTGATGCGCCGATTGGGCTTGATCGTGGCAAGTCTTGCGCTGATTTTACTGCCTGTGGTGGCGTTCAGCAGTCATTATGCCAGTTTCTTTCGCGTGCATAAGCCGCTGCGTAGCTATGTCAATCCGATCATGCCAATCTACTCGGTGGGTAAGCTTGCCAGTATTGAGTATAAAAAAGCCAGTGCGCCAAAAGATACCATTTATCACGCCAAAGACGCGGTACAAGCAACCAAGCCTGATATGCGTAAGCCACGCCTAGTGGTGTTCGTCGTCGGTGAGACGGCACGCGCCGATCATGTCAGCTTCAATGGCTATGAGCGCGATACTTTCCCACAGCTTGCCAAGATCGATGGCGTGACCAATTTTAGCAATGTCACATCGTGCGGCACATCGACGGCGTATTCTGTGCCGTGTATGTTCAGCTATCTGGGCGCGGATGAGTATGATGTCGATACCGCCAAATACCAAGAAAATGTGCTGGATACGCTGGATCGCTTGGGCGTAAGTATCTTGTGGCGTGATAATAATTCGGACTCAAAAGGCGTGATGGATAAGCTGCCAAAAGCGCAATTTGCCGATTATAAATCCGCGACCAACAACGCCATCTGCAACACCAATCCTTATAACGAATGCCGCGATGTCGGTATGCTCGTTGGCTTAGATGACTTTGTCGCTGCCAATAACGGCAAAGATATGCTGATCATGCTGCACCAAATGGGCAATCACGGGCCTGCGTATTTTAAGCGATATGATGAAAAGTTTGCCAAATTCACGCCAGTGTGTGAAGGTAATGAGCTTGCCAAGTGCGAACATCAGTCCTTGATCAATGCTTATGACAATGCCTTGCTTGCCACCGATGATTTCATCGCTCAAAGTATCCAGTGGCTGCAGACGCACAGCAATGCCTATGATGTCTCAATGCTGTATGTCAGCGATCATGGCGAAAGTCTGGGTGAGAACGGTGTCTATCTACATGGTATGCCAAATGCCTTTGCACCAAAAGAACAGCGCAGTGTGCCTGCATTTTTCTGGACGGATAAGCAAACTGGCATCACGCCAATGGCAACCGATACCGTCCTGACCCATGACGCGATCACGCCGACATTATTAAAGCTGTTTGATGTCACCGCGGACAAAGTCAAAGACCGCACCGCATTCATCCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3007280","ARO_id":"46026","ARO_name":"MCR-1.26","CARD_short_name":"MCR-1.26","ARO_description":"An MCR-1-type colistin resistance gene variant.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5886":{"model_id":"5886","model_name":"MCR-5.4","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"8613":{"protein_sequence":{"accession":"QCT85452.1","sequence":"MRLSAFITFLKMRPQVRTEFLTLFISLVFTLLCNGVFWNALLAGRDSLTSGTWLMLLCTGLLITGLQWLLLLLVATRWSVKPLLILLAVMTPAAVYFMRNYGVYFDKAMLRNLMETDVREASELLQWRMLPYLLVAAVSVWWIARVRVLRTGWKQAVMMRSACLAGALAMISMGLWPVMDVLIPTLRENKPLRYLITPANYVISGIRVLTEQASSSADEAREVVAADAHRGPQEQGRRPRALVLVVGETVRAANWGLSGYERQTTPELAARDVINFSDVTSCGTDTATSLPCMFSLNGRRDYDERQIRRRESVLHVLNRSDVNILWRDNQSGCKGVCDGLPFENLSSAGHPTLCHGERCLDEILLEGLAEKITTSRSDMLIVLHMLGNHGPAYFQRYPASYRRWSPTCDTTDLASCSHEALVNTYDNAVLYTDHVLARTIDLLSGIRSHDTALLYVSDHGESLGEKGLYLHGIPYVIAPDEQIKVPMIWWQSSQVYADQACMQTHASRAPVSHDHLFHTLLGMFDVKTAAYTPELDLLATCRKGQPQ"},"dna_sequence":{"accession":"MK965519.1","fmin":"5046","fmax":"6690","strand":"-","sequence":"ATGCGGTTGTCTGCATTTATCACTTTCTTGAAAATGCGCCCGCAAGTGCGCACTGAATTTTTGACTCTGTTCATCAGCCTTGTGTTCACCCTGCTGTGCAATGGCGTGTTTTGGAATGCCCTTCTTGCTGGACGCGACTCCCTAACTTCTGGAACATGGCTAATGCTCCTTTGCACTGGGTTGCTGATCACCGGGCTGCAATGGTTGTTGCTCCTTCTGGTGGCCACGCGCTGGAGTGTCAAGCCACTACTGATTCTGCTTGCTGTCATGACGCCCGCCGCCGTTTATTTCATGCGCAACTACGGGGTTTATTTCGACAAGGCCATGCTGCGGAATCTGATGGAGACGGACGTCAGGGAAGCCAGTGAGCTGTTGCAATGGAGAATGCTGCCCTACTTGTTGGTTGCAGCCGTATCCGTGTGGTGGATTGCGAGAGTCAGGGTTTTACGAACGGGCTGGAAACAAGCGGTAATGATGCGCAGCGCTTGTCTGGCTGGCGCTCTCGCCATGATTTCCATGGGTCTGTGGCCAGTCATGGATGTGCTGATACCCACGCTTCGTGAAAACAAGCCGCTTCGCTATTTGATCACTCCTGCAAACTACGTCATCTCGGGCATTCGGGTTTTGACTGAACAGGCGTCATCGTCAGCAGACGAAGCAAGGGAAGTCGTTGCAGCCGATGCGCATCGAGGGCCTCAAGAACAAGGCCGCCGTCCTCGTGCTCTCGTACTGGTTGTCGGGGAAACCGTCAGGGCGGCTAATTGGGGGTTGAGCGGCTATGAACGACAAACCACCCCTGAGTTGGCCGCACGCGACGTGATCAATTTTTCCGATGTCACCAGTTGCGGGACGGATACGGCTACATCCCTTCCCTGCATGTTTTCCCTCAATGGTCGGCGCGACTACGACGAACGCCAGATTCGTCGGCGCGAGTCCGTGCTGCACGTTTTAAACCGTAGTGACGTCAACATTCTCTGGCGCGATAACCAGTCGGGCTGTAAAGGCGTCTGTGATGGACTGCCCTTTGAAAACCTGTCTTCGGCAGGCCATCCCACACTGTGCCATGGCGAGCGCTGCCTGGATGAAATTCTGCTCGAAGGGTTGGCCGAGAAGATAACAACAAGCCGCAGCGATATGCTGATCGTTCTGCATATGCTGGGCAATCACGGCCCAGCGTATTTCCAGCGCTATCCCGCAAGCTACCGACGCTGGTCGCCAACCTGCGACACCACCGATCTGGCCAGCTGTTCGCATGAAGCCTTGGTGAACACCTACGACAACGCCGTGCTTTACACCGATCATGTGCTTGCCCGTACCATTGACCTGCTGTCCGGCATCCGCTCACACGACACGGCGCTGCTGTACGTTTCCGATCATGGGGAATCGCTCGGCGAGAAAGGCCTGTATCTCCATGGCATACCTTACGTCATCGCGCCGGATGAGCAGATCAAGGTGCCGATGATCTGGTGGCAGTCGAGTCAGGTTTATGCCGACCAAGCCTGTATGCAAACTCATGCCTCTCGGGCACCGGTAAGTCACGATCACCTGTTTCACACCTTGCTCGGGATGTTCGACGTGAAAACCGCTGCCTACACGCCAGAGTTGGACCTTCTGGCAACATGCAGAAAAGGACAACCACAATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"46170","NCBI_taxonomy_name":"hospital metagenome","NCBI_taxonomy_id":"1755691"}}}},"ARO_accession":"3007281","ARO_id":"46027","ARO_name":"MCR-5.4","CARD_short_name":"MCR-5.4","ARO_description":"An MCR-5-type colistin resistance gene variant.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5800":{"model_id":"5800","model_name":"blaC","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8481":{"protein_sequence":{"accession":"CCP44842.1","sequence":"MRNRGFGRRELLVAMAMLVSVTGCARHASGARPASTTLPAGADLADRFAELERRYDARLGVYVPATGTTAAIEYRADERFAFCSTFKAPLVAAVLHQNPLTHLDKLITYTSDDIRSISPVAQQHVQTGMTIGQLCDAAIRYSDGTAANLLLADLGGPGGGTAAFTGYLRSLGDTVSRLDAEEPELNRDPPGDERDTTTPHAIALVLQQLVLGNALPPDKRALLTDWMARNTTGAKRIRAGFPADWKVIDKTGTGDYGRANDIAVVWSPTGVPYVVAVMSDRAGGGYDAEPREALLAEAATCVAGVLA"},"dna_sequence":{"accession":"AL123456.3","fmin":"2325885","fmax":"2326809","strand":"-","sequence":"ATGCGCAACAGAGGATTCGGTCGTCGCGAACTGCTGGTAGCGATGGCAATGCTGGTTTCCGTGACGGGGTGTGCACGGCATGCGAGCGGGGCCCGTCCGGCATCGACAACCTTGCCGGCCGGAGCGGATCTGGCGGATCGCTTCGCCGAGCTGGAGCGCAGATACGATGCCCGGCTTGGGGTGTATGTGCCCGCCACCGGCACCACCGCCGCGATCGAATACCGCGCCGATGAGCGGTTCGCATTCTGCTCCACGTTCAAGGCGCCGCTCGTGGCGGCGGTGCTGCACCAAAACCCGCTCACGCATCTGGACAAACTGATCACCTACACCAGTGACGACATTCGGTCGATCTCCCCGGTGGCCCAACAACACGTTCAGACCGGGATGACGATCGGGCAGCTTTGCGATGCGGCGATACGCTATAGCGACGGCACCGCCGCCAACCTGTTGCTGGCCGATCTTGGCGGTCCCGGGGGCGGCACCGCGGCATTTACCGGCTACCTCCGCAGCTTGGGTGACACCGTGAGCCGGTTGGACGCCGAGGAACCGGAGTTGAACCGCGATCCGCCCGGGGACGAACGGGATACCACAACACCGCACGCCATCGCCCTGGTGTTGCAGCAGCTTGTTCTCGGCAACGCGTTGCCGCCCGACAAGCGGGCACTGCTCACCGATTGGATGGCGCGCAACACCACCGGAGCCAAGCGGATCCGAGCGGGCTTTCCCGCCGATTGGAAGGTGATCGACAAGACCGGGACCGGTGACTACGGACGAGCAAACGACATCGCGGTCGTGTGGTCACCGACCGGCGTGCCCTACGTGGTGGCCGTCATGTCCGATCGTGCCGGCGGCGGGTATGACGCCGAGCCCCGTGAGGCGCTGCTCGCCGAGGCGGCGACGTGCGTTGCCGGTGTGCTTGCATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3007182","ARO_id":"45921","ARO_name":"blaC","CARD_short_name":"blaC","ARO_description":"blaC is a broad-spectrum class A beta-lactamase coded in the chromosome of Mycobacterium tuberculosis. It has been shown to hydrolyze a large number of beta-lactam antibiotics and is a major obstacle in the treatment of tuberculosis with such drugs.","ARO_category":{"45920":{"category_aro_accession":"3007181","category_aro_cvterm_id":"45920","category_aro_name":"class A Mycobacterium tuberculosis bla beta-lactamase","category_aro_description":"Class A beta-lactamase from M. tuberculosis.","category_aro_class_name":"AMR Gene Family"},"35927":{"category_aro_accession":"0000008","category_aro_cvterm_id":"35927","category_aro_name":"cefoxitin","category_aro_description":"Cefoxitin is a cephamycin antibiotic often grouped with the second generation cephalosporins. Cefoxitin is bactericidal and acts by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. Cefoxitin's 7-alpha-methoxy group and 3' leaving group make it a poor substrate for most beta-lactamases.","category_aro_class_name":"Antibiotic"},"35981":{"category_aro_accession":"0000064","category_aro_cvterm_id":"35981","category_aro_name":"amoxicillin","category_aro_description":"Amoxicillin is a moderate-spectrum, bacteriolytic, beta-lactam antibiotic used to treat bacterial infections caused by susceptible microorganisms. A derivative of penicillin, it has a wider range of treatment but remains relatively ineffective against Gram-negative bacteria. It is commonly taken with clavulanic acid, a beta-lactamase inhibitor. Like other beta-lactams, amoxicillin interferes with the synthesis of peptidoglycan.","category_aro_class_name":"Antibiotic"},"37084":{"category_aro_accession":"3000704","category_aro_cvterm_id":"37084","category_aro_name":"cefalotin","category_aro_description":"Cefalotin is a semisynthetic cephalosporin antibiotic activate against staphylococci. It is resistant to staphylococci beta-lactamases but hydrolyzed by enterobacterial beta-lactamases.","category_aro_class_name":"Antibiotic"},"40522":{"category_aro_accession":"3003831","category_aro_cvterm_id":"40522","category_aro_name":"temocillin","category_aro_description":"Temocillin is a beta-lactamase resistant carboxypenicillin. It is primarily used for the treatment of multiple drug resistant, Gram-negative bacteria, specifically Enterobacteriaceae.","category_aro_class_name":"Antibiotic"},"40523":{"category_aro_accession":"3003832","category_aro_cvterm_id":"40523","category_aro_name":"ticarcillin","category_aro_description":"Ticarcillin is a carboxypenicillin used for the treatment of Gram-negative bacteria, particularly P. aeruginosa. Ticarcillin's antibiotic properties arise from its ability to prevent cross-linking of peptidoglycan during cell wall synthesis, when the bacteria try to divide, causing cell death.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5801":{"model_id":"5801","model_name":"Mycobacterium tuberculosis Rv1258c mutations confer resistance to ethambutol and capreomycin","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"12644":"T297P","12645":"I328T"},"Curated-R":{"12644":"T297P","12645":"I328T"},"clinical":{"12644":"T297P","12645":"I328T"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"8790":{"protein_sequence":{"accession":"NP_215774.1","sequence":"MRNSNRGPAFLILFATLMAAAGDGVSIVAFPWLVLQREGSAGQASIVASATMLPLLFATLVAGTAVDYFGRRRVSMVADALSGAAVAGVPLVAWGYGGDAVNVLVLAVLAALAAAFGPAGMTARDSMLPEAAARAGWSLDRINGAYEAILNLAFIVGPAIGGLMIATVGGITTMWITATAFGLSILAIAALQLEGAGKPHHTSRPQGLVSGIAEGLRFVWNLRVLRTLGMIDLTVTALYLPMESVLFPKYFTDHQQPVQLGWALMAIAGGGLVGALGYAVLAIRVPRRVTMSTAVLTLGLASMVIAFLPPLPVIMVLCAVVGLVYGPIQPIYNYVIQTRAAQHLRGRVVGVMTSLAYAAGPLGLLLAGPLTDAAGLHATFLALALPIVCTGLVAIRLPALRELDLAPQADIDRPVGSAQ"},"dna_sequence":{"accession":"NC_000962.3","fmin":"1406080","fmax":"1407340","strand":"-","sequence":"ATGAGAAACAGCAACCGCGGCCCGGCATTCCTGATCCTGTTCGCAACGCTGATGGCGGCCGCGGGTGATGGCGTCTCGATAGTCGCGTTTCCGTGGCTGGTGTTGCAGCGCGAGGGCAGCGCTGGGCAGGCCTCGATCGTGGCCAGTGCGACCATGCTGCCGCTGTTGTTCGCCACGCTGGTCGCCGGCACCGCGGTCGACTACTTCGGGCGTCGCCGGGTGTCGATGGTGGCCGATGCGCTGTCGGGTGCGGCGGTGGCCGGCGTCCCCCTGGTGGCGTGGGGGTACGGCGGCGACGCGGTCAACGTGCTGGTGCTGGCCGTATTGGCCGCCCTGGCGGCCGCCTTCGGCCCGGCAGGCATGACGGCTCGTGACTCGATGCTGCCCGAGGCCGCCGCTCGGGCAGGCTGGTCGTTGGACCGCATCAACGGCGCCTACGAGGCGATCCTCAACCTGGCCTTTATTGTCGGCCCGGCCATCGGTGGCTTGATGATCGCGACGGTTGGCGGCATCACCACAATGTGGATTACCGCGACGGCATTCGGGTTGTCCATCCTCGCGATTGCCGCCCTGCAACTCGAGGGTGCCGGCAAGCCGCACCACACCTCGCGGCCCCAAGGGTTGGTATCCGGGATCGCCGAGGGGCTGCGCTTCGTCTGGAACCTGCGGGTATTGCGCACCCTCGGGATGATTGACCTGACCGTCACCGCGCTGTATCTGCCGATGGAGAGCGTGCTGTTCCCGAAATACTTCACCGACCACCAGCAACCGGTGCAGCTGGGTTGGGCGTTGATGGCGATCGCCGGCGGCGGCCTGGTGGGAGCGCTGGGGTATGCCGTGTTGGCTATCCGCGTTCCCCGTCGCGTGACCATGTCGACCGCGGTTCTTACCCTGGGTTTGGCATCGATGGTCATCGCGTTCCTGCCGCCACTGCCGGTCATCATGGTGTTGTGCGCGGTGGTCGGCCTGGTGTACGGACCCATCCAGCCGATCTATAACTACGTGATACAGACGCGGGCAGCACAGCATCTGCGCGGCCGGGTAGTCGGGGTGATGACGTCGCTGGCCTACGCCGCCGGCCCGTTGGGTCTGTTGCTGGCCGGTCCACTGACCGACGCCGCTGGACTGCATGCCACGTTTCTCGCGTTGGCACTGCCCATCGTGTGCACCGGGCTGGTCGCGATCCGGCTGCCCGCGCTGCGCGAACTGGATCTGGCGCCCCAAGCGGACATCGATCGGCCCGTAGGATCGGCTCAGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3007185","ARO_id":"45924","ARO_name":"Mycobacterium tuberculosis Rv1258c mutations confer resistance to ethambutol and capreomycin","CARD_short_name":"Mtub_tap_EMCM","ARO_description":"Mutations in the M. tuberculosis efflux pump Rv1258c (Tap) conferring resistance to multiple ethambutol and capreomycin.","ARO_category":{"45923":{"category_aro_accession":"3007184","category_aro_cvterm_id":"45923","category_aro_name":"multidrug resistant Rv1258c","category_aro_description":"Mutations in the Rv1258c efflux pump contributing to resistance to multiple antibiotics.","category_aro_class_name":"AMR Gene Family"},"36636":{"category_aro_accession":"3000497","category_aro_cvterm_id":"36636","category_aro_name":"ethambutol","category_aro_description":"Ethambutol is an antimycobacterial drug prescribed to treat tuberculosis. It is usually given in combination with other tuberculosis drugs, such as isoniazid, rifampicin, and pyrazinamide. Ethambutol inhibits arabinosyl biosynthesis, disrupting mycobacterial cell wall formation.","category_aro_class_name":"Antibiotic"},"40875":{"category_aro_accession":"3003993","category_aro_cvterm_id":"40875","category_aro_name":"capreomycin","category_aro_description":"Capreomycin is an aminoglycoside antibiotic, capable of treating a large number of infections but in particular used for killing bacteria causing tuberculosis.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36666":{"category_aro_accession":"3000527","category_aro_cvterm_id":"36666","category_aro_name":"polyamine antibiotic","category_aro_description":"Polyamine antibiotics are organic compounds having two or more primary amino groups.","category_aro_class_name":"Drug Class"},"45734":{"category_aro_accession":"3007152","category_aro_cvterm_id":"45734","category_aro_name":"isoniazid-like antibiotic","category_aro_description":"A group of antibiotics containing isoniazid and its derivatives.","category_aro_class_name":"Drug Class"},"45737":{"category_aro_accession":"3007155","category_aro_cvterm_id":"45737","category_aro_name":"pyrazine antibiotic","category_aro_description":"A group of antibiotics derived from pyrazine.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5802":{"model_id":"5802","model_name":"Mycobacterium tuberculosis Rv1258c mutations confer resistance to pyrazinamide, isoniazid, and streptomycin","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"},"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"12648":"S292L","12649":"V219A"},"Curated-R":{"12648":"S292L","12649":"V219A"},"clinical":{"12648":"S292L","12649":"V219A"}}},"model_sequences":{"sequence":{"8788":{"protein_sequence":{"accession":"NP_215774.1","sequence":"MRNSNRGPAFLILFATLMAAAGDGVSIVAFPWLVLQREGSAGQASIVASATMLPLLFATLVAGTAVDYFGRRRVSMVADALSGAAVAGVPLVAWGYGGDAVNVLVLAVLAALAAAFGPAGMTARDSMLPEAAARAGWSLDRINGAYEAILNLAFIVGPAIGGLMIATVGGITTMWITATAFGLSILAIAALQLEGAGKPHHTSRPQGLVSGIAEGLRFVWNLRVLRTLGMIDLTVTALYLPMESVLFPKYFTDHQQPVQLGWALMAIAGGGLVGALGYAVLAIRVPRRVTMSTAVLTLGLASMVIAFLPPLPVIMVLCAVVGLVYGPIQPIYNYVIQTRAAQHLRGRVVGVMTSLAYAAGPLGLLLAGPLTDAAGLHATFLALALPIVCTGLVAIRLPALRELDLAPQADIDRPVGSAQ"},"dna_sequence":{"accession":"NC_000962.3","fmin":"1406080","fmax":"1407340","strand":"-","sequence":"ATGAGAAACAGCAACCGCGGCCCGGCATTCCTGATCCTGTTCGCAACGCTGATGGCGGCCGCGGGTGATGGCGTCTCGATAGTCGCGTTTCCGTGGCTGGTGTTGCAGCGCGAGGGCAGCGCTGGGCAGGCCTCGATCGTGGCCAGTGCGACCATGCTGCCGCTGTTGTTCGCCACGCTGGTCGCCGGCACCGCGGTCGACTACTTCGGGCGTCGCCGGGTGTCGATGGTGGCCGATGCGCTGTCGGGTGCGGCGGTGGCCGGCGTCCCCCTGGTGGCGTGGGGGTACGGCGGCGACGCGGTCAACGTGCTGGTGCTGGCCGTATTGGCCGCCCTGGCGGCCGCCTTCGGCCCGGCAGGCATGACGGCTCGTGACTCGATGCTGCCCGAGGCCGCCGCTCGGGCAGGCTGGTCGTTGGACCGCATCAACGGCGCCTACGAGGCGATCCTCAACCTGGCCTTTATTGTCGGCCCGGCCATCGGTGGCTTGATGATCGCGACGGTTGGCGGCATCACCACAATGTGGATTACCGCGACGGCATTCGGGTTGTCCATCCTCGCGATTGCCGCCCTGCAACTCGAGGGTGCCGGCAAGCCGCACCACACCTCGCGGCCCCAAGGGTTGGTATCCGGGATCGCCGAGGGGCTGCGCTTCGTCTGGAACCTGCGGGTATTGCGCACCCTCGGGATGATTGACCTGACCGTCACCGCGCTGTATCTGCCGATGGAGAGCGTGCTGTTCCCGAAATACTTCACCGACCACCAGCAACCGGTGCAGCTGGGTTGGGCGTTGATGGCGATCGCCGGCGGCGGCCTGGTGGGAGCGCTGGGGTATGCCGTGTTGGCTATCCGCGTTCCCCGTCGCGTGACCATGTCGACCGCGGTTCTTACCCTGGGTTTGGCATCGATGGTCATCGCGTTCCTGCCGCCACTGCCGGTCATCATGGTGTTGTGCGCGGTGGTCGGCCTGGTGTACGGACCCATCCAGCCGATCTATAACTACGTGATACAGACGCGGGCAGCACAGCATCTGCGCGGCCGGGTAGTCGGGGTGATGACGTCGCTGGCCTACGCCGCCGGCCCGTTGGGTCTGTTGCTGGCCGGTCCACTGACCGACGCCGCTGGACTGCATGCCACGTTTCTCGCGTTGGCACTGCCCATCGTGTGCACCGGGCTGGTCGCGATCCGGCTGCCCGCGCTGCGCGAACTGGATCTGGCGCCCCAAGCGGACATCGATCGGCCCGTAGGATCGGCTCAGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3007186","ARO_id":"45925","ARO_name":"Mycobacterium tuberculosis Rv1258c mutations confer resistance to pyrazinamide, isoniazid, and streptomycin","CARD_short_name":"Mtub_tap_MULT","ARO_description":"Mutations in the M. tuberculosis efflux pump Rv1258c (Tap) conferring resistance to pyrazinamide, isoniazid, and streptomycin.","ARO_category":{"45923":{"category_aro_accession":"3007184","category_aro_cvterm_id":"45923","category_aro_name":"multidrug resistant Rv1258c","category_aro_description":"Mutations in the Rv1258c efflux pump contributing to resistance to multiple antibiotics.","category_aro_class_name":"AMR Gene Family"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36659":{"category_aro_accession":"3000520","category_aro_cvterm_id":"36659","category_aro_name":"isoniazid","category_aro_description":"Isoniazid is an organic compound that is the first-line anti tuberculosis medication in prevention and treatment. As a prodrug, it is activated by mycobacterial catalase-peroxidases such as M. tuberculosis KatG. Isoniazid inhibits mycolic acid synthesis, which prevents cell wall synthesis in mycobacteria.","category_aro_class_name":"Antibiotic"},"39997":{"category_aro_accession":"3003413","category_aro_cvterm_id":"39997","category_aro_name":"pyrazinamide","category_aro_description":"Pyrazinamide is an antimycobacterial. It is highly specific and active only against Mycobacterium tuberculosis. This compound is a prodrug and needs to be activated inside the cell. It interferes with the bacterium's ability to synthesize new fatty acids, causing cell death.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36666":{"category_aro_accession":"3000527","category_aro_cvterm_id":"36666","category_aro_name":"polyamine antibiotic","category_aro_description":"Polyamine antibiotics are organic compounds having two or more primary amino groups.","category_aro_class_name":"Drug Class"},"45734":{"category_aro_accession":"3007152","category_aro_cvterm_id":"45734","category_aro_name":"isoniazid-like antibiotic","category_aro_description":"A group of antibiotics containing isoniazid and its derivatives.","category_aro_class_name":"Drug Class"},"45737":{"category_aro_accession":"3007155","category_aro_cvterm_id":"45737","category_aro_name":"pyrazine antibiotic","category_aro_description":"A group of antibiotics derived from pyrazine.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3710":{"model_id":"3710","model_name":"Mycobacterium tuberculosis Rv1258c mutations confer resistance to streptomycin","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"40494":{"param_type":"frameshift mutation","param_description":"A frameshift is a sequence change between the translation initiation (start) and termination (stop) codon where, compared to a reference sequence, translation shifts to another reading frame as caused by nucleotide insertions and deletions. In ARO, these are annotated at the protein level with the first changed most N-terminal wildtype amino acid position. Format is given as [wildtype AA][position]fs, e.g. S531fs where S531 is a frameshifted coordinate beginning with codon 531. Termination may also be denoted as: Ter[position]fs.","param_type_id":"40494","param_value":{"9851":"E194fs"}},"snp":{"ReSeqTB-Minimal":{"9851":"V219A"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"8787":{"protein_sequence":{"accession":"NP_215774.1","sequence":"MRNSNRGPAFLILFATLMAAAGDGVSIVAFPWLVLQREGSAGQASIVASATMLPLLFATLVAGTAVDYFGRRRVSMVADALSGAAVAGVPLVAWGYGGDAVNVLVLAVLAALAAAFGPAGMTARDSMLPEAAARAGWSLDRINGAYEAILNLAFIVGPAIGGLMIATVGGITTMWITATAFGLSILAIAALQLEGAGKPHHTSRPQGLVSGIAEGLRFVWNLRVLRTLGMIDLTVTALYLPMESVLFPKYFTDHQQPVQLGWALMAIAGGGLVGALGYAVLAIRVPRRVTMSTAVLTLGLASMVIAFLPPLPVIMVLCAVVGLVYGPIQPIYNYVIQTRAAQHLRGRVVGVMTSLAYAAGPLGLLLAGPLTDAAGLHATFLALALPIVCTGLVAIRLPALRELDLAPQADIDRPVGSAQ"},"dna_sequence":{"accession":"NC_000962.3","fmin":"1406080","fmax":"1407340","strand":"-","sequence":"ATGAGAAACAGCAACCGCGGCCCGGCATTCCTGATCCTGTTCGCAACGCTGATGGCGGCCGCGGGTGATGGCGTCTCGATAGTCGCGTTTCCGTGGCTGGTGTTGCAGCGCGAGGGCAGCGCTGGGCAGGCCTCGATCGTGGCCAGTGCGACCATGCTGCCGCTGTTGTTCGCCACGCTGGTCGCCGGCACCGCGGTCGACTACTTCGGGCGTCGCCGGGTGTCGATGGTGGCCGATGCGCTGTCGGGTGCGGCGGTGGCCGGCGTCCCCCTGGTGGCGTGGGGGTACGGCGGCGACGCGGTCAACGTGCTGGTGCTGGCCGTATTGGCCGCCCTGGCGGCCGCCTTCGGCCCGGCAGGCATGACGGCTCGTGACTCGATGCTGCCCGAGGCCGCCGCTCGGGCAGGCTGGTCGTTGGACCGCATCAACGGCGCCTACGAGGCGATCCTCAACCTGGCCTTTATTGTCGGCCCGGCCATCGGTGGCTTGATGATCGCGACGGTTGGCGGCATCACCACAATGTGGATTACCGCGACGGCATTCGGGTTGTCCATCCTCGCGATTGCCGCCCTGCAACTCGAGGGTGCCGGCAAGCCGCACCACACCTCGCGGCCCCAAGGGTTGGTATCCGGGATCGCCGAGGGGCTGCGCTTCGTCTGGAACCTGCGGGTATTGCGCACCCTCGGGATGATTGACCTGACCGTCACCGCGCTGTATCTGCCGATGGAGAGCGTGCTGTTCCCGAAATACTTCACCGACCACCAGCAACCGGTGCAGCTGGGTTGGGCGTTGATGGCGATCGCCGGCGGCGGCCTGGTGGGAGCGCTGGGGTATGCCGTGTTGGCTATCCGCGTTCCCCGTCGCGTGACCATGTCGACCGCGGTTCTTACCCTGGGTTTGGCATCGATGGTCATCGCGTTCCTGCCGCCACTGCCGGTCATCATGGTGTTGTGCGCGGTGGTCGGCCTGGTGTACGGACCCATCCAGCCGATCTATAACTACGTGATACAGACGCGGGCAGCACAGCATCTGCGCGGCCGGGTAGTCGGGGTGATGACGTCGCTGGCCTACGCCGCCGGCCCGTTGGGTCTGTTGCTGGCCGGTCCACTGACCGACGCCGCTGGACTGCATGCCACGTTTCTCGCGTTGGCACTGCCCATCGTGTGCACCGGGCTGGTCGCGATCCGGCTGCCCGCGCTGCGCGAACTGGATCTGGCGCCCCAAGCGGACATCGATCGGCCCGTAGGATCGGCTCAGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3004971","ARO_id":"43157","ARO_name":"Mycobacterium tuberculosis Rv1258c mutations confer resistance to streptomycin","CARD_short_name":"Mtub_tap_STR","ARO_description":"Mutations in the Rv1258c (Tap) gene that can contribute to or confer resistance to streptomycin.","ARO_category":{"43156":{"category_aro_accession":"3004970","category_aro_cvterm_id":"43156","category_aro_name":"streptomycin resistant Rv1258c","category_aro_description":"An efflux pump in mycobacterium that contributes to intrinsic antibiotic resistance. The pump uses the electrochemical gradient as a source of energy.","category_aro_class_name":"AMR Gene Family"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5755":{"model_id":"5755","model_name":"Helicobacter pylori rdxA mutation conferring resistance to metronidazole","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"40394":{"param_type":"nonsense mutation","param_description":"A sequence change where, compared to a reference sequence, one codon is replaced by a termination codon through a nucleotide substitution. These are described as a substitution of the wildtype codon to a termination codon. Format is given as [wild type AA][position][Ter], for example Q42Ter where Q42 is a wildtype amino acid replaced by a premature termination codon.","param_type_id":"40394","param_value":{"12411":"Q50Ter","12412":"Q5Ter","12438":"N73Ter","12482":"A50Ter","13116":"D59Ter"}},"snp":{"Curated-R":{"12411":"V219A","12412":"V219A","12438":"V219A","12482":"V219A","13116":"V219A","12386":"R16C","12392":"R16H","12393":"C19Y","12394":"T31E","12395":"R90K","12396":"H97T","12397":"S108A","12398":"A118T","12399":"A118S","12400":"G189C","12402":"P106S","12404":"A68E","12405":"A67V","12408":"A1G","12436":"A1G","12444":"C148Y","12446":"G189S","12479":"G189S","12480":"G189S","12481":"G189S","12483":"G189S","12484":"G189S","12496":"G47A","12497":"T184G","12498":"G60A","12499":"C273T","12500":"C49T","12504":"D59N","12505":"L210V","12506":"H97Y","12478":"H97Y","13117":"D59S","12401":"K64N","12485":"K64N"},"param_value":{"12386":"R16C","12392":"R16H","12393":"C19Y","12394":"T31E","12395":"R90K","12396":"H97T","12397":"S108A","12398":"A118T","12399":"A118S","12400":"G189C","12402":"P106S","12404":"A68E","12405":"A67V","12408":"A1G","12444":"C148Y","12446":"G189S","12496":"G47A","12497":"T184G","12498":"G60A","12499":"C273T","12500":"C49T","12504":"D59N","12505":"L210V","12506":"H97Y","13117":"D59S","12401":"K64N"},"clinical":{"12386":"R16C","12392":"R16H","12393":"C19Y","12394":"T31E","12395":"R90K","12396":"H97T","12397":"S108A","12398":"A118T","12399":"A118S","12400":"G189C","12402":"P106S","12404":"A68E","12405":"A67V","12408":"A1G","12444":"C148Y","12446":"G189S","12496":"G47A","12497":"T184G","12498":"G60A","12499":"C273T","12500":"C49T","12504":"D59N","12505":"L210V","12506":"H97Y","13117":"D59S","12401":"K64N"}},"40494":{"param_type":"frameshift mutation","param_description":"A frameshift is a sequence change between the translation initiation (start) and termination (stop) codon where, compared to a reference sequence, translation shifts to another reading frame as caused by nucleotide insertions and deletions. In ARO, these are annotated at the protein level with the first changed most N-terminal wildtype amino acid position. Format is given as [wildtype AA][position]fs, e.g. S531fs where S531 is a frameshifted coordinate beginning with codon 531. Termination may also be denoted as: Ter[position]fs.","param_type_id":"40494","param_value":{"12436":"L13fs","12479":"T38fs","12480":"G112fs","12481":"A190fs","12483":"A96fs","12484":"T62fs","12478":"C18fs","12485":"T162fs"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"8315":{"protein_sequence":{"accession":"WP_000670110.1","sequence":"MKFLDQEKRRQLLNERHSCKMFDSHYEFSSTELEEIAEIARLSPSSYNTQPWHFVMVTDKDLKKQIAAHSYFNEEMIKSASALMVVCSLRPSELLPHGHYMQNLYPESYKVRVIPSFAQMLGVRFNHSMQRLESYILEQCYIAVGQICMGVSLMGLDSCIIGGFDPLKVGEVLEERINKPKIACLIALGKRVAEASQKSRKSKVDAITWL"},"dna_sequence":{"accession":"NC_000915.1","fmin":"1013552","fmax":"1014185","strand":"-","sequence":"ATGAAATTTTTGGATCAAGAAAAAAGAAGACAATTATTAAACGAGCGCCATTCTTGCAAGATGTTTGATAGCCATTATGAGTTTTCTAGCACAGAATTAGAAGAAATCGCTGAAATCGCCAGGCTATCGCCAAGCTCTTACAACACGCAGCCATGGCATTTTGTGATGGTTACTGATAAGGATTTAAAAAAACAAATTGCAGCGCACAGCTATTTCAATGAAGAGATGATTAAAAGCGCTTCAGCGTTAATGGTGGTATGCTCTTTAAGACCCAGCGAGTTGTTACCACACGGCCACTACATGCAAAATCTCTATCCGGAGTCTTATAAAGTTAGAGTGATCCCCTCTTTTGCTCAAATGCTTGGCGTGAGATTCAACCACAGCATGCAAAGATTAGAAAGCTATATTTTAGAGCAATGCTATATCGCTGTGGGGCAAATTTGCATGGGCGTGAGCTTAATGGGATTGGATAGTTGCATTATTGGAGGCTTTGATCCTTTAAAGGTGGGCGAAGTTTTAGAAGAGCGTATCAATAAGCCTAAAATCGCATGCTTGATCGCTTTGGGCAAGAGGGTGGCAGAAGCGAGTCAAAAATCAAGAAAATCAAAAGTTGATGCGATTACTTGGTTGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36906","NCBI_taxonomy_name":"Helicobacter pylori","NCBI_taxonomy_id":"210"}}}},"ARO_accession":"3007055","ARO_id":"45615","ARO_name":"Helicobacter pylori rdxA mutation conferring resistance to metronidazole","CARD_short_name":"Hpyl_rdxA_MTZ","ARO_description":"The rdxA gene in Helicobacter pylori encodes an NADPH nitroreductase. Mutations in this gene are associated with metronidazole resistance.","ARO_category":{"45616":{"category_aro_accession":"3007056","category_aro_cvterm_id":"45616","category_aro_name":"Antibiotic resistant Helicobacter pylori nitroreductase","category_aro_description":"Inactivation of the oxygen-insensitive NADPH nitroreductases in Helicobacter pylori play a role in metronidazole resistance.","category_aro_class_name":"AMR Gene Family"},"37033":{"category_aro_accession":"3000689","category_aro_cvterm_id":"37033","category_aro_name":"metronidazole","category_aro_description":"Metronidazole is a nitroimidazole that is active against anaerobic bacteria and protozoa. It is not effective against aerobic bacteria. Nitroimidazoles act by oxidizing DNA causing strand breaks and cell death.","category_aro_class_name":"Antibiotic"},"41239":{"category_aro_accession":"3004115","category_aro_cvterm_id":"41239","category_aro_name":"nitroimidazole antibiotic","category_aro_description":"Nitroimidazoles are a group of drugs that have both antiprotozoal and antibacterial activity, classified with respect to the location of the nitro functional group.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5804":{"model_id":"5804","model_name":"vanH gene in vanP cluster","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"200"}},"model_sequences":{"sequence":{"8484":{"protein_sequence":{"accession":"MBY8651254.1","sequence":"MREIAVLGSSEEEKKIFKKYASAYQVTLRFYENIEQVCKEGRQSLLSISHAEDMSENNLKRLHQAGVEYISTRSIGLNHIDMAAAKRLDMQVNNVAYSPESVAEHTVMLMLMALRNMKNTEKNVEQYDYRLPKKRFRELRELTVGVVGTGRIGQTVIGLLRGFGCRIICYDTYQVEGLDYVSYEELLAESDIITYHIPLTEESLHMLNQDNIRLVKPGAYIVNTARGALIDNEALIAALESGQLAGAALDVVENEESFFYKKCKNVGQELALLSRMKNVVLTPHSAFYTSQALEDVVENSIKNCLEYKEEAVYA"},"dna_sequence":{"accession":"JAINTN010000010.1","fmin":"17893","fmax":"18838","strand":"-","sequence":"ATGAGAGAAATTGCCGTTTTGGGAAGTAGTGAAGAAGAGAAGAAAATCTTTAAGAAATATGCTTCTGCATATCAGGTTACACTTCGCTTTTATGAGAATATAGAGCAGGTTTGTAAGGAAGGCAGACAAAGCCTTTTAAGTATCAGTCATGCAGAGGATATGTCAGAAAACAATTTGAAAAGACTGCATCAGGCAGGAGTAGAGTATATTTCAACAAGAAGCATTGGTCTGAATCATATTGATATGGCAGCAGCAAAGCGTCTGGATATGCAGGTAAACAATGTAGCATATTCGCCGGAAAGTGTGGCAGAACATACCGTTATGCTGATGTTAATGGCACTTCGCAATATGAAGAATACGGAGAAGAATGTCGAGCAGTATGATTACCGTCTTCCAAAGAAGCGATTCCGTGAATTGCGGGAGCTGACAGTAGGTGTTGTCGGAACCGGAAGAATCGGACAGACCGTTATCGGACTGTTACGAGGGTTTGGCTGCAGGATTATCTGCTACGATACCTATCAGGTAGAGGGACTTGATTATGTTTCTTACGAAGAACTCTTAGCAGAGAGTGACATTATTACTTATCATATCCCTTTGACAGAAGAAAGCCTTCATATGTTGAATCAGGATAACATAAGACTTGTCAAACCGGGTGCCTATATCGTTAATACGGCAAGAGGCGCTTTGATTGACAATGAAGCATTGATTGCCGCATTAGAGAGTGGCCAGCTTGCCGGTGCAGCACTTGATGTGGTAGAAAATGAGGAGTCGTTCTTTTATAAGAAATGCAAGAATGTAGGACAGGAGCTGGCTCTTCTTAGCAGAATGAAAAACGTTGTCCTTACACCACACAGTGCCTTCTATACCAGTCAGGCATTAGAAGACGTAGTAGAAAACAGCATTAAAAATTGTTTAGAATATAAGGAGGAAGCAGTATATGCGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36779","NCBI_taxonomy_name":"Enterococcus faecium","NCBI_taxonomy_id":"1352"}}}},"ARO_accession":"3007188","ARO_id":"45927","ARO_name":"vanH gene in vanP cluster","CARD_short_name":"vanH_in_vanP_cl","ARO_description":"vanH variant in the vanP cluster.","ARO_category":{"36015":{"category_aro_accession":"3000006","category_aro_cvterm_id":"36015","category_aro_name":"vanH","category_aro_description":"VanH is a D-specific alpha-ketoacid dehydrogenase that synthesizes D-lactate. D-lactate is incorporated into the end of the peptidoglycan subunits, decreasing vancomycin binding affinity.","category_aro_class_name":"AMR Gene Family"},"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"35948":{"category_aro_accession":"0000029","category_aro_cvterm_id":"35948","category_aro_name":"teicoplanin","category_aro_description":"Teicoplanin is a glycopeptide antibiotic used in the prophylaxis and treatment of serious infections caused by Gram-positive bacteria. Teicoplanin has a unique acyl-aliphatic chain, and binds to cell wall precursors to inhibit transglycosylation  and transpeptidation.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5805":{"model_id":"5805","model_name":"vanP","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"350"}},"model_sequences":{"sequence":{"8485":{"protein_sequence":{"accession":"MBY8651253.1","sequence":"MRKVLVLFGGCSEEHDISVKSATEVYHYIDKQKYDVTYVGITKDGRWRKVNSPKEPLEESKTMAILSPDTGKKGILLIEENTYTLQEIDVIFPVMHGKMGEDGQLQGIMELSGIPYVGCDIESSVIAMDKSLANMVADRAGILVPWFMAKNDVKEFDADILPYPVFVKPARSGSSFGISKVENREQFADAVKEALQYDSKILVEEAIQGQEVACAIMGRGEELLTGEVDMVQVKNGFFRIHQEKNPEGGSENAVITVPAPLDMPATERIKKEAKKIYKALGCKGLARVDMFLTKEGRIVLNEVNTLPGMTCYSRYPAMMKAAGIEFTDMVERLIEEALGANA"},"dna_sequence":{"accession":"JAINTN010000010.1","fmin":"16872","fmax":"17901","strand":"-","sequence":"ATGCGTAAAGTATTAGTATTATTTGGAGGATGTTCAGAGGAGCACGATATTTCCGTAAAATCAGCAACAGAGGTTTATCATTACATTGATAAGCAGAAATATGACGTGACATATGTAGGAATTACAAAGGATGGCAGATGGAGAAAGGTAAACAGTCCGAAGGAGCCATTAGAGGAAAGCAAGACGATGGCAATTCTATCACCGGATACAGGAAAGAAAGGCATCTTATTAATAGAAGAGAATACATATACTTTACAGGAAATCGATGTGATTTTTCCGGTGATGCATGGAAAGATGGGTGAAGACGGTCAGCTTCAGGGAATTATGGAACTGTCTGGAATTCCTTATGTTGGATGCGATATTGAATCCTCCGTAATCGCCATGGATAAGTCACTTGCCAATATGGTAGCCGACAGAGCAGGGATTTTGGTGCCTTGGTTTATGGCAAAAAATGATGTCAAAGAATTTGATGCAGACATTCTTCCTTATCCGGTATTTGTAAAGCCGGCAAGATCCGGCTCATCCTTTGGTATCAGCAAGGTAGAGAACCGCGAGCAGTTTGCTGATGCCGTAAAGGAAGCATTGCAATATGACAGTAAGATATTAGTTGAGGAAGCCATTCAGGGACAGGAAGTAGCCTGTGCCATTATGGGAAGAGGAGAGGAGTTACTGACAGGGGAAGTCGATATGGTACAGGTGAAAAATGGATTTTTCCGTATTCATCAGGAGAAAAATCCGGAGGGCGGTTCAGAAAATGCAGTGATTACGGTACCGGCTCCACTTGATATGCCTGCAACAGAGCGTATCAAAAAGGAAGCGAAAAAAATCTATAAAGCGCTTGGCTGTAAAGGTCTTGCCCGTGTGGATATGTTCCTGACAAAAGAGGGACGAATTGTATTAAATGAAGTCAATACCCTTCCGGGAATGACCTGTTACAGCCGTTATCCGGCAATGATGAAGGCAGCAGGAATTGAATTTACCGATATGGTGGAACGTCTGATAGAAGAAGCTTTGGGTGCTAATGCATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36779","NCBI_taxonomy_name":"Enterococcus faecium","NCBI_taxonomy_id":"1352"}}}},"ARO_accession":"3007189","ARO_id":"45928","ARO_name":"vanP","CARD_short_name":"vanP","ARO_description":"vanP is a D-Ala-D-Ala ligase homolog that synthesizes D-Ala-D-Lac, an alternative substrate for peptidoglycan synthesis that reduces vancomycin binding affinity. It is associated with both vancomycin and teicoplanin resistance.","ARO_category":{"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"39340":{"category_aro_accession":"3002906","category_aro_cvterm_id":"39340","category_aro_name":"Van ligase","category_aro_description":"Van ligases synthesize alternative substrates for peptidoglycan synthesis that reduce vancomycin binding affinity.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"35948":{"category_aro_accession":"0000029","category_aro_cvterm_id":"35948","category_aro_name":"teicoplanin","category_aro_description":"Teicoplanin is a glycopeptide antibiotic used in the prophylaxis and treatment of serious infections caused by Gram-positive bacteria. Teicoplanin has a unique acyl-aliphatic chain, and binds to cell wall precursors to inhibit transglycosylation  and transpeptidation.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5806":{"model_id":"5806","model_name":"vanX gene in vanP cluster","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"200"}},"model_sequences":{"sequence":{"8487":{"protein_sequence":{"accession":"MBY8651252.1","sequence":"MKSEFVYLDEVIPGVRWDAKYATWDNFMGMPVNGYQVNRVVGTVEMADALKEVSKLAKEKGVGLLLWDGYRPVRAVSHFMEWVKKSKDESRKAKHYPHIDKKTMIEEGYIAEYSGHSRGSTIDLTLYDLESKKLLDMGGDFDLMDEISHYAAEGITKEEKENRKLLRDLMVKCGFVPYENEWWHYSLKDEPYPDTYFDFVIE"},"dna_sequence":{"accession":"JAINTN010000010.1","fmin":"16154","fmax":"16763","strand":"-","sequence":"ATGAAATCAGAATTTGTTTATTTGGATGAAGTAATACCGGGAGTAAGATGGGATGCAAAATATGCTACTTGGGATAATTTTATGGGAATGCCTGTTAATGGTTATCAGGTCAATCGTGTTGTAGGTACAGTTGAGATGGCAGATGCCTTAAAGGAGGTCAGTAAGCTTGCAAAGGAAAAGGGCGTTGGTTTACTTTTGTGGGATGGATACCGTCCTGTCCGTGCGGTTTCCCACTTTATGGAATGGGTAAAAAAGAGTAAAGATGAAAGCCGTAAGGCGAAGCATTATCCACATATTGATAAAAAGACGATGATAGAGGAAGGCTACATTGCAGAGTATTCCGGTCACAGCAGGGGAAGTACGATTGATTTGACACTGTATGATTTGGAAAGCAAAAAGCTTCTGGACATGGGTGGGGATTTTGATTTGATGGACGAAATCTCCCACTATGCGGCAGAGGGGATTACCAAGGAAGAGAAGGAGAATCGTAAATTACTTCGGGATTTGATGGTCAAATGCGGATTTGTTCCATATGAAAATGAATGGTGGCATTATTCGTTAAAAGACGAGCCATATCCGGATACATATTTTGACTTTGTCATTGAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36779","NCBI_taxonomy_name":"Enterococcus faecium","NCBI_taxonomy_id":"1352"}}}},"ARO_accession":"3007190","ARO_id":"45929","ARO_name":"vanX gene in vanP cluster","CARD_short_name":"vanX_in_vanP_cl","ARO_description":"vanX variant in the vanP cluster.","ARO_category":{"36020":{"category_aro_accession":"3000011","category_aro_cvterm_id":"36020","category_aro_name":"vanX","category_aro_description":"VanX is a D,D-dipeptidase that cleaves D-Ala-D-Ala but not D-Ala-D-Lac, ensuring that the latter dipeptide that has reduced binding affinity with vancomycin is used to synthesize peptidoglycan substrate.","category_aro_class_name":"AMR Gene Family"},"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"35948":{"category_aro_accession":"0000029","category_aro_cvterm_id":"35948","category_aro_name":"teicoplanin","category_aro_description":"Teicoplanin is a glycopeptide antibiotic used in the prophylaxis and treatment of serious infections caused by Gram-positive bacteria. Teicoplanin has a unique acyl-aliphatic chain, and binds to cell wall precursors to inhibit transglycosylation  and transpeptidation.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5807":{"model_id":"5807","model_name":"vanR gene in vanP cluster","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"8489":{"protein_sequence":{"accession":"MBY8651251.1","sequence":"MNNSQKNILIVDDEEEIADLLEVYLKNEGYQVFKYYSGQGVLECIEHEDIHLALLDVMLPDTDGFSLCRKIREKWFFPIIMLTAKVEETDKIMGITLGADDYITKPFNPLEVLARVKGQLRRADVYNVSLGNEEEASKENVFQIRGLEINENNHTCFLYGEEISLTPIEFNILLCLCKHLGEVVSSEELFETVWGEKYMDSNNTVFSHVARIREKMHEEARKPKFIKTVWGVGYKIEKS"},"dna_sequence":{"accession":"JAINTN010000010.1","fmin":"15360","fmax":"16080","strand":"-","sequence":"ATGAATAATAGTCAGAAAAACATACTTATTGTAGATGATGAAGAAGAAATCGCAGACTTATTAGAAGTATATTTAAAAAATGAAGGATATCAGGTTTTTAAATATTATAGCGGGCAGGGGGTTTTAGAGTGCATCGAGCATGAAGACATTCACCTTGCCCTGTTAGATGTTATGCTGCCGGATACGGATGGATTCAGTCTGTGCAGAAAGATTCGGGAGAAATGGTTCTTTCCGATTATCATGTTGACAGCAAAGGTAGAGGAAACCGATAAGATTATGGGCATCACGTTAGGAGCCGACGATTACATAACCAAACCATTTAATCCATTAGAGGTATTGGCAAGAGTGAAAGGTCAGCTTAGACGTGCCGATGTCTATAATGTTTCACTGGGAAATGAAGAAGAAGCTTCCAAAGAAAATGTATTTCAGATTCGTGGTCTGGAAATCAATGAAAACAATCATACCTGTTTTTTATATGGTGAAGAGATTTCTCTGACGCCGATAGAGTTTAATATTCTGCTGTGCCTTTGCAAGCATTTAGGAGAAGTTGTTTCATCAGAAGAGTTATTCGAAACGGTGTGGGGGGAGAAATACATGGATAGTAACAATACTGTTTTTTCTCATGTCGCCCGCATTCGTGAAAAGATGCATGAAGAGGCAAGGAAACCAAAATTCATTAAAACTGTCTGGGGTGTCGGTTACAAGATAGAGAAATCATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36779","NCBI_taxonomy_name":"Enterococcus faecium","NCBI_taxonomy_id":"1352"}}}},"ARO_accession":"3007191","ARO_id":"45930","ARO_name":"vanR gene in vanP cluster","CARD_short_name":"vanR_in_vanP_cl","ARO_description":"vanR variant in the vanP cluster.","ARO_category":{"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"36713":{"category_aro_accession":"3000574","category_aro_cvterm_id":"36713","category_aro_name":"vanR","category_aro_description":"VanR is a OmpR-family transcriptional activator in the VanSR regulatory system. When activated by VanS, it promotes cotranscription of VanA, VanH, and VanX.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"35948":{"category_aro_accession":"0000029","category_aro_cvterm_id":"35948","category_aro_name":"teicoplanin","category_aro_description":"Teicoplanin is a glycopeptide antibiotic used in the prophylaxis and treatment of serious infections caused by Gram-positive bacteria. Teicoplanin has a unique acyl-aliphatic chain, and binds to cell wall precursors to inhibit transglycosylation  and transpeptidation.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5808":{"model_id":"5808","model_name":"vanS gene in vanP cluster","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"8490":{"protein_sequence":{"accession":"MBY8651250.1","sequence":"MNKRLKKSISRYFFIRFLQGLCCMSFFLVFALGISYLWCSERVWYEGEVSYFIVHILHEYWYVLFLGLMIIGCIVIAMINIRCIAQGISDIMQAVRDVNEENEVQIELPDYLADAQAQLTDIKNHVEWNKKTAQEAVQRKNDLIMYLAHDLKTPLTSTIGYLTLLHDEKEISKEVRDKYMGIALKKSLRLEELLNEFFEIARFNFSTMVLEKGNVNMSVMVEQLLYEFKPLFDKKGLTYTIDLEKDVNVYCDVEKMERVFDNLLKNIVNYSYENTEIAITLKANGEQGMLFVIRNHGKTIPKEKCERIFEQFYRLDGSRGTKTGGSGLGLAVVKEIVELHEGTVTCESENEEICFRITI"},"dna_sequence":{"accession":"JAINTN010000010.1","fmin":"14253","fmax":"15333","strand":"-","sequence":"ATGAATAAGAGACTTAAAAAGAGTATTTCGCGCTACTTTTTTATCCGTTTTTTGCAGGGATTATGTTGTATGTCCTTTTTTTTAGTTTTTGCGTTGGGTATATCTTATTTGTGGTGCTCCGAAAGGGTATGGTACGAAGGAGAAGTCAGTTACTTTATTGTACATATTTTGCATGAATACTGGTATGTCCTGTTTTTGGGACTTATGATTATTGGATGTATTGTGATTGCCATGATAAATATAAGATGTATTGCACAGGGAATCAGTGACATTATGCAGGCAGTCCGTGATGTAAATGAAGAGAATGAGGTACAAATCGAACTTCCGGATTATCTGGCAGACGCACAGGCTCAGTTAACAGATATCAAAAATCATGTCGAGTGGAATAAAAAGACAGCACAGGAAGCCGTACAGAGAAAAAATGATCTGATTATGTATCTGGCACACGATTTAAAGACACCGCTTACTTCTACGATTGGTTATCTGACACTGCTTCATGATGAAAAAGAGATTTCTAAAGAAGTCCGTGACAAATATATGGGAATTGCATTAAAAAAATCCTTGCGTTTAGAAGAACTTTTGAATGAATTCTTTGAAATTGCCCGTTTTAATTTTTCTACTATGGTACTGGAAAAAGGAAATGTCAATATGTCAGTGATGGTGGAACAGCTTTTGTATGAGTTTAAGCCGTTATTTGATAAGAAAGGTCTGACCTATACCATAGATTTGGAAAAAGATGTCAATGTCTACTGTGATGTAGAGAAGATGGAGCGTGTGTTTGATAATTTGCTTAAAAATATAGTAAATTACAGTTATGAAAATACAGAGATTGCGATAACCCTAAAAGCAAATGGGGAACAGGGTATGCTTTTTGTAATTCGAAATCATGGTAAAACCATTCCAAAAGAAAAATGTGAACGCATTTTTGAACAGTTCTATCGTCTGGATGGTTCCCGTGGAACAAAGACAGGAGGTTCCGGGCTTGGTCTTGCCGTTGTAAAGGAAATCGTAGAGCTTCATGAAGGAACGGTAACCTGTGAAAGTGAAAATGAAGAAATCTGCTTTCGTATTACCATATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36779","NCBI_taxonomy_name":"Enterococcus faecium","NCBI_taxonomy_id":"1352"}}}},"ARO_accession":"3007192","ARO_id":"45931","ARO_name":"vanS gene in vanP cluster","CARD_short_name":"vanS_in_vanP_cl","ARO_description":"vanS variant in the vanP cluster.","ARO_category":{"36210":{"category_aro_accession":"3000071","category_aro_cvterm_id":"36210","category_aro_name":"vanS","category_aro_description":"VanS is similar to histidine protein kinases like EnvZ and acts as a response regulator by activating VanR. VanS is required for high level transcription of other van glycopeptide resistance genes.","category_aro_class_name":"AMR Gene Family"},"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"35948":{"category_aro_accession":"0000029","category_aro_cvterm_id":"35948","category_aro_name":"teicoplanin","category_aro_description":"Teicoplanin is a glycopeptide antibiotic used in the prophylaxis and treatment of serious infections caused by Gram-positive bacteria. Teicoplanin has a unique acyl-aliphatic chain, and binds to cell wall precursors to inhibit transglycosylation  and transpeptidation.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1814":{"model_id":"1814","model_name":"AAC(6')-Ie-APH(2'')-Ia bifunctional protein","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"900"}},"model_sequences":{"sequence":{"5296":{"protein_sequence":{"accession":"AAA88548.1","sequence":"MNIVENEICIRTLIDDDFPLMLKWLTDERVLEFYGGRDKKYTLESLKKHYTEPWEDEVFRVIIEYNNVPIGYGQIYKMYDELYTDYHYPKTDEIVYGMDQFIGEPNYWSKGIGTRYIKLIFEFLKKERNANAVILDPHKNNPRAIRAYQKSGFRIIEDLPEHELHEGKKEDCYLMEYRYDDNATNVKAMKYLIEHYFDNFKVDSIEIIGSGYDSVAYLVNNEYIFKTKFSTNKKKGYAKEKAIYNFLNTNLETNVKIPNIEYSYISDELSILGYKEIKGTFLTPEIYSTMSEEEQNLLKRDIASFLRQMHGLDYTDISECTIDNKQNVLEEYILLRETIYNDLTDIEKDYIESFMERLNATTVFEGKKCLCHNDFSCNHLLLDGNNRLTGIIDFGDSGIIDEYCDFIYLLEDSEEEIGTNFGEDILRMYGNIDIEKAKEYQDIVEEYYPIETIVYGIKNIKQEFIENGRKEIYKRTYKD"},"dna_sequence":{"accession":"GU565967.1","fmin":"24979","fmax":"26419","strand":"-","sequence":"ATGAATATAGTTGAAAATGAAATATGTATAAGAACTTTAATAGATGATGATTTTCCTTTGATGTTAAAATGGTTAACTGATGAAAGAGTATTAGAATTTTATGGTGGTAGAGATAAAAAATATACATTAGAATCATTAAAAAAACATTATACAGAGCCTTGGGAAGATGAAGTTTTTAGAGTAATTATTGAATATAACAATGTTCCTATTGGATATGGACAAATATATAAAATGTATGATGAGTTATATACTGATTATCATTATCCAAAAACTGATGAGATAGTCTATGGTATGGATCAATTTATAGGAGAGCCAAATTATTGGAGTAAAGGAATTGGTACAAGATATATTAAATTGATTTTTGAATTTTTGAAAAAAGAAAGAAATGCTAATGCAGTTATTTTAGACCCTCATAAAAATAATCCAAGAGCAATAAGGGCATACCAAAAATCTGGTTTTAGAATTATTGAAGATTTGCCAGAACATGAATTACACGAGGGCAAAAAAGAAGATTGTTATTTAATGGAATATAGATATGATGATAATGCCACAAATGTTAAGGCAATGAAATATTTAATTGAGCATTACTTTGATAATTTCAAAGTAGATAGTATTGAAATAATCGGTAGTGGTTATGATAGTGTGGCATATTTAGTTAATAATGAATACATTTTTAAAACAAAATTTAGTACTAATAAGAAAAAAGGTTATGCAAAAGAAAAAGCAATATATAATTTTTTAAATACAAATTTAGAAACTAATGTAAAAATTCCTAATATTGAATATTCGTATATTAGTGATGAATTATCTATACTAGGTTATAAAGAAATTAAAGGAACTTTTTTAACACCAGAAATTTATTCTACTATGTCAGAAGAAGAACAAAATTTGTTAAAACGAGATATTGCCAGTTTTTTAAGACAAATGCACGGTTTAGATTATACAGATATTAGTGAATGTACTATTGATAATAAACAAAATGTATTAGAAGAGTATATATTGTTGCGTGAAACTATTTATAATGATTTAACTGATATAGAAAAAGATTATATAGAAAGTTTTATGGAAAGACTAAATGCAACAACAGTTTTTGAGGGTAAAAAGTGTTTATGCCATAATGATTTTAGTTGTAATCATCTATTGTTAGATGGCAATAATAGATTAACTGGAATAATTGATTTTGGAGATTCTGGAATTATAGATGAATATTGTGATTTTATATACTTACTTGAAGATAGTGAAGAAGAAATAGGAACAAATTTTGGAGAAGATATATTAAGAATGTATGGAAATATAGATATTGAGAAAGCAAAAGAATATCAAGATATAGTTGAAGAATATTATCCTATTGAAACTATTGTTTATGGAATTAAAAATATTAAACAGGAATTTATCGAAAATGGTAGAAAAGAAATTTATAAAAGGACTTATAAAGATTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35508","NCBI_taxonomy_name":"Staphylococcus aureus","NCBI_taxonomy_id":"1280"}}}},"ARO_accession":"3002597","ARO_id":"38997","ARO_name":"AAC(6')-Ie-APH(2'')-Ia bifunctional protein","CARD_short_name":"AAC6_Ie_APH2_Ia","ARO_description":"AAC(6')-Ie-APH(2'')-Ia is an aminoglycoside acetyltransferase encoded by plasmids and transposons in S. aureus, E. faecalis, E. faecium and Staphylococcus warneri.","ARO_category":{"46171":{"category_aro_accession":"3007419","category_aro_cvterm_id":"46171","category_aro_name":"aminoglycoside bifunctional resistance protein","category_aro_description":"Bifunctional aminoglycoside-inactivating enzymes composed of two separate functional domains. These proteins possess activity from both enzyme components, thereby conferring resistance to the combination of antibiotics from both domains, and may include acetylation, phosphorylation or nucleotidylation activity.","category_aro_class_name":"AMR Gene Family"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"40942":{"category_aro_accession":"3004015","category_aro_cvterm_id":"40942","category_aro_name":"gentamicin A","category_aro_description":"Gentamicin A is part of a complex of broad spectrum aminoglycoside antibiotics. Gentamicin inhibits protein synthesis, resulting in bacterial cell death.","category_aro_class_name":"Antibiotic"},"46128":{"category_aro_accession":"3007378","category_aro_cvterm_id":"46128","category_aro_name":"2'-N-ethylnetilmicin","category_aro_description":"2'-N-ethylnetilmicin is an aminoglycoside antibiotic and a derivative of netilmicin.","category_aro_class_name":"Antibiotic"},"46129":{"category_aro_accession":"3007379","category_aro_cvterm_id":"46129","category_aro_name":"5-episisomicin","category_aro_description":"5-episosomicin is a semisynthetic aminoglycoside antibiotic similar to sisomicin.","category_aro_class_name":"Antibiotic"},"46133":{"category_aro_accession":"3007382","category_aro_cvterm_id":"46133","category_aro_name":"gentamicin","category_aro_description":"Gentamicin is a commonly used aminoglycoside antibiotic derived from members of the Micromonospora genus of bacteria. It acts by binding the 30S ribosomal subunit, thus inhibiting protein synthesis. Gentamicin is typically used to treat Gram-negative infections of the repiratory and urinary tract, as well as infections of the bone and soft tissue. It also exhibits considerable nephrotoxicity and ototoxicity. Gentamicin is administered as a mixture of gentamicin type C (which makes about around 80% of the complex) and types A, B, and X (distributed in the remaining 20% of the complex).","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5809":{"model_id":"5809","model_name":"glycopeptide resistance gene cluster vanP","model_type":"gene cluster meta-model","model_type_id":"40298","model_description":"Gene Cluster Meta-Models (GCM) are used to curate spatial clusters of individual genes within operons, such as for glycopeptide resistance gene clusters. The individual genes will have their own individual detection models (e.g. PHM, PVM, POM, etc.) while the GCM checks to see if all the component genes of the cluster have a Strict or Perfect hit and are ordered correctly within an operon. GCMs are encoded using the gene order parameter. This model type is still under development and not currently supported by the Resistance Gene Identifier (RGI) software.","model_param":{"40297":{"param_type":"gene order","param_description":"Spatial clusters of genes are encoded using the gene order parameter: [gene type]:[cvterm_id],[gene type]:[cvterm_id], etc. The gene type designations are: R = regulatory, C = core, A = accessory.","param_type_id":"40297","param_value":{"12653":"C:45927,C:45928,C:45929,R:45930,R:45931"}},"snp":{"Curated-R":{"12653":"K64N"}}},"ARO_accession":"3007187","ARO_id":"45926","ARO_name":"glycopeptide resistance gene cluster vanP","CARD_short_name":"vanP_cluster","ARO_description":"This cluster confers resistance to both vancomycin and teicoplanin by allowing restructuring of peptidoglycan precursors to end in D-Ala-D-Lac. Resistance is acquired after multiple treatments with sub-minimum inhibitory concentrations of vancomycin. Gene orientation: vanHPXRS.","ARO_category":{"36373":{"category_aro_accession":"3000234","category_aro_cvterm_id":"36373","category_aro_name":"glycopeptide resistance gene cluster","category_aro_description":"Genes that when expressed confer resistance to vancomycin and teicoplanin type antibiotics.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"35948":{"category_aro_accession":"0000029","category_aro_cvterm_id":"35948","category_aro_name":"teicoplanin","category_aro_description":"Teicoplanin is a glycopeptide antibiotic used in the prophylaxis and treatment of serious infections caused by Gram-positive bacteria. Teicoplanin has a unique acyl-aliphatic chain, and binds to cell wall precursors to inhibit transglycosylation  and transpeptidation.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2092":{"model_id":"2092","model_name":"Enterobacter aerogenes acrR with mutation conferring multidrug antibiotic resistance","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"2992":"R45C"},"Curated-R":{"2992":"R45C","7538":"R45C"},"clinical":{"2992":"R45C"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"410"},"40494":{"param_type":"frameshift mutation","param_description":"A frameshift is a sequence change between the translation initiation (start) and termination (stop) codon where, compared to a reference sequence, translation shifts to another reading frame as caused by nucleotide insertions and deletions. In ARO, these are annotated at the protein level with the first changed most N-terminal wildtype amino acid position. Format is given as [wildtype AA][position]fs, e.g. S531fs where S531 is a frameshifted coordinate beginning with codon 531. Termination may also be denoted as: Ter[position]fs.","param_type_id":"40494","param_value":{"7538":"A47fs"}}},"model_sequences":{"sequence":{"4661":{"protein_sequence":{"accession":"CAC35723.1","sequence":"MARKTKQQALETRQLILDVALRLFSQQGVSSTSLAAIAKAAGVTRGAIYWHFKNKSDLFNEIWSLSDASISDLEVEYRAKFPNDPLSVVREILVYILEATVVEERRRLMMEIIFHKCEFVGEMAVVQQAQRSLWLESYDRIEQTLKDCITAQQLPANLLTRRAAILMRSYLSGLMENWLFAPESFNLHAEARAYVDALIEMYQTCPSLRSSSEVMA"},"dna_sequence":{"accession":"AJ306389.1","fmin":"636","fmax":"1287","strand":"-","sequence":"ATGGCACGAAAAACCAAACAACAGGCACTTGAAACCCGGCAACTGATTCTTGACGTCGCCCTGCGATTGTTTTCGCAGCAAGGGGTATCATCTACCTCGTTGGCCGCGATTGCAAAAGCTGCTGGAGTGACCAGGGGCGCTATATACTGGCATTTCAAAAACAAATCCGATCTGTTTAATGAAATATGGAGTCTTTCTGACGCCAGCATTAGCGATCTCGAAGTTGAGTATCGGGCAAAATTCCCTAACGATCCACTGTCAGTTGTTCGCGAAATACTGGTTTATATCCTCGAAGCGACGGTAGTAGAGGAGCGTAGGCGCCTGATGATGGAAATCATCTTCCATAAATGCGAATTTGTCGGAGAAATGGCCGTTGTCCAACAAGCGCAGCGCAGTTTATGGCTTGAAAGCTACGATCGTATTGAGCAAACATTAAAAGATTGTATCACTGCTCAACAATTACCTGCGAATTTACTCACTCGCCGTGCGGCAATTCTGATGCGCAGTTATCTTTCCGGATTAATGGAAAACTGGCTCTTTGCACCAGAGAGTTTTAACCTTCATGCGGAAGCCCGTGCTTATGTCGATGCGCTGATTGAGATGTATCAGACCTGCCCGTCGCTACGAAGTTCGTCTGAGGTCATGGCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36770","NCBI_taxonomy_name":"Klebsiella aerogenes","NCBI_taxonomy_id":"548"}}}},"ARO_accession":"3003374","ARO_id":"39958","ARO_name":"Enterobacter aerogenes acrR with mutation conferring multidrug antibiotic resistance","CARD_short_name":"Kaer_acrR_MULT","ARO_description":"AcrR is a repressor of the AcrAB-TolC multidrug efflux complex. AcrR mutations result in high level antibiotic resistance.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35963":{"category_aro_accession":"0000045","category_aro_cvterm_id":"35963","category_aro_name":"acriflavine","category_aro_description":"Acriflavine is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37084":{"category_aro_accession":"3000704","category_aro_cvterm_id":"37084","category_aro_name":"cefalotin","category_aro_description":"Cefalotin is a semisynthetic cephalosporin antibiotic activate against staphylococci. It is resistant to staphylococci beta-lactamases but hydrolyzed by enterobacterial beta-lactamases.","category_aro_class_name":"Antibiotic"},"37250":{"category_aro_accession":"3000870","category_aro_cvterm_id":"37250","category_aro_name":"triclosan","category_aro_description":"Triclosan is a common antibacterial agent added to many consumer products as a biocide.  It is an inhibitor of fatty acid biosynthesis by blocking enoyl-carrier protein reductase (FabI).","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"43746":{"category_aro_accession":"3005386","category_aro_cvterm_id":"43746","category_aro_name":"disinfecting agents and antiseptics","category_aro_description":"Disinfectants that can also interact with antimicrobial resistance mechanisms, e.g. molecule efflux, and thus are the targets of disinfectant resistance.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"5811":{"model_id":"5811","model_name":"KPC-123","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8524":{"protein_sequence":{"accession":"UNN26644.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTYTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEADDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"ON012820.1","fmin":"0","fmax":"909","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36934","NCBI_taxonomy_name":"Citrobacter koseri","NCBI_taxonomy_id":"545"}}}},"ARO_accession":"3007196","ARO_id":"45938","ARO_name":"KPC-123","CARD_short_name":"KPC-123","ARO_description":"KPC-123 is a KPC beta-lactamase.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35976":{"category_aro_accession":"0000059","category_aro_cvterm_id":"35976","category_aro_name":"cefepime","category_aro_description":"Cefepime (INN) is a fourth-generation cephalosporin antibiotic developed in 1994. It contains an aminothiazolyl group that decreases its affinity with beta-lactamases. Cefepime shows high binding affinity with penicillin-binding proteins and has an extended spectrum of activity against Gram-positive and Gram-negative bacteria, with greater activity against both Gram-negative and Gram-positive organisms than third-generation agents.","category_aro_class_name":"Antibiotic"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36989":{"category_aro_accession":"3000645","category_aro_cvterm_id":"36989","category_aro_name":"cefotaxime","category_aro_description":"Cefotaxime is a semisynthetic cephalosporin taken parenterally. It is resistant to most beta-lactamases and active against Gram-negative rods and cocci due to its aminothiazoyl and methoximino functional groups.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5812":{"model_id":"5812","model_name":"PAM-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"8493":{"protein_sequence":{"accession":"BAO01151.1","sequence":"MRFLASLALPLFAANLAVAAPKPLPQLEAYEGLQAWLVPVEPLRISDHVWQIGTASISALLVKTDAGAVLIDGGMPQVADHLLANMKKLGVQPQDLRLILHSHAHIDHVGPLAAIKRATGAVLVSNAESAVLLQRGGADDIHFGSGMLFAPLTPERLVQDGEAVTLGDTTFTVHFTPGHTPGSMSWTWTDTQDGKPLRIAYADSLSAPGYQLRDNARYPHLVDAFRASFAAVRALPCDLLLTPHAEGSGWDYTNAEKPHPAPVSCKAYADKAEQKLDQMLAEQAKSR"},"dna_sequence":{"accession":"AB858498.1","fmin":"0","fmax":"864","strand":"+","sequence":"ATGCGTTTCCTCGCCAGCCTCGCGCTGCCCCTGTTCGCCGCCAACCTGGCGGTCGCCGCCCCCAAGCCCCTGCCGCAGCTGGAGGCCTATGAAGGGCTGCAAGCCTGGCTGGTGCCGGTGGAACCGCTGCGCATCAGCGACCACGTCTGGCAGATCGGCACCGCCAGCATCAGCGCCCTGCTGGTGAAAACCGACGCCGGCGCGGTGCTCATCGACGGCGGCATGCCCCAGGTGGCCGACCACCTGCTGGCCAATATGAAGAAGCTCGGCGTGCAGCCCCAGGACCTGCGCCTGATCCTCCACAGCCACGCCCACATCGACCACGTCGGCCCGCTGGCGGCGATCAAGCGCGCCACCGGCGCTGTGCTGGTGAGCAACGCCGAATCCGCCGTGCTGCTGCAACGCGGCGGCGCCGACGACATCCACTTCGGCAGCGGCATGCTCTTCGCCCCGCTGACGCCCGAGCGCCTGGTGCAGGACGGCGAGGCGGTGACCCTGGGCGACACCACCTTCACCGTGCATTTCACCCCGGGCCACACCCCGGGCAGCATGAGCTGGACCTGGACCGACACCCAGGACGGCAAGCCCCTGCGCATCGCCTACGCCGACAGCCTCAGCGCGCCGGGCTACCAACTGCGCGACAACGCCCGCTACCCCCACCTGGTCGACGCCTTCCGTGCCAGCTTCGCCGCCGTCCGCGCCCTGCCCTGCGACCTGCTGCTGACACCCCACGCCGAAGGCAGCGGCTGGGACTACACCAACGCCGAAAAGCCGCACCCGGCCCCGGTGAGCTGCAAGGCCTATGCGGACAAAGCCGAGCAGAAGCTCGACCAGATGCTCGCCGAGCAGGCAAAGTCGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"45942","NCBI_taxonomy_name":"Pseudomonas alcaligenes","NCBI_taxonomy_id":"43263"}}}},"ARO_accession":"3007199","ARO_id":"45941","ARO_name":"PAM-1","CARD_short_name":"PAM-1","ARO_description":"PAM-1 is a member of the PAM family of subclass B3 metallo-beta-lactamases found in members of the Psuedomonas genus.","ARO_category":{"45940":{"category_aro_accession":"3007198","category_aro_cvterm_id":"45940","category_aro_name":"PAM beta-lactamase","category_aro_description":"A family of subclass B3 metallo-beta-lactamases discovered in Pseudomonas alcaligenes and found in other members of the Pseudomonas genus. PAM beta-lactamases hydrolyze cephalosporins and carbenems.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36984":{"category_aro_accession":"3000640","category_aro_cvterm_id":"36984","category_aro_name":"doripenem","category_aro_description":"Doripenem is a carbapenem with a broad range of activity against Gram-positive and Gram-negative bacteria, and along with meropenem, it is the most active beta-lactam antibiotic against Pseudomonas aeruginosa. It inhibits bacterial cell wall synthesis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5813":{"model_id":"5813","model_name":"PAM-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"8525":{"protein_sequence":{"accession":"GJN52392.1","sequence":"MRLLASLALPLFAANLAVAAPAQLPQLEAYKGLDAWLVPVEPLRISDHVWQIGTASISALLVKTDAGAVLIDGGMPQVADHLLANMKKLGVAPQDVRLILHSHAHIDHVGPLAAIKRATGAMLVSNAESAVLLQRGGANDIHFGSGMLFEPIQTDRLVQDGEAVTLGDTTFTVHFTPGHTPGSMSWTWADTRDGKPLRIAYSDSLSAPGYQLRHNARYPHLVEAFRASFAAVRALPCDLLLTPHAEGSGWDYANAARPHPQPVSCKAYADKAEANLDKMLAEQANKR"},"dna_sequence":{"accession":"BQKM01000003.1","fmin":"545052","fmax":"545916","strand":"+","sequence":"ATGCGTTTGCTCGCCAGCCTCGCGCTGCCCCTGTTCGCCGCCAACCTGGCGGTCGCCGCCCCCGCCCAGCTGCCCCAGCTGGAGGCCTACAAGGGCCTCGACGCCTGGCTGGTGCCGGTGGAGCCCCTGCGCATCAGCGACCACGTGTGGCAGATCGGCACCGCCAGCATCAGCGCCCTGCTGGTGAAGACCGACGCCGGCGCGGTGCTCATTGACGGCGGCATGCCCCAGGTGGCCGACCACCTGCTGGCCAACATGAAGAAGCTCGGCGTGGCCCCGCAGGATGTGCGCCTGATCCTCCACAGCCACGCCCACATCGACCACGTCGGCCCGCTGGCGGCAATCAAGCGCGCCACCGGCGCCATGCTGGTGAGCAACGCCGAATCCGCCGTGCTGCTGCAGCGCGGCGGCGCCAACGACATCCACTTCGGCAGCGGCATGCTCTTCGAACCGATCCAGACCGACCGCCTGGTGCAGGACGGCGAGGCCGTGACCCTGGGCGACACCACCTTCACCGTGCACTTCACCCCGGGGCACACGCCCGGCAGCATGAGCTGGACCTGGGCCGACACCCGGGACGGCAAGCCCCTGCGCATCGCCTACAGCGACAGCCTCAGCGCGCCGGGCTACCAGCTGCGCCACAACGCCCGCTACCCGCACCTCGTGGAAGCCTTCCGCGCAAGCTTCGCCGCCGTCCGCGCCCTGCCCTGCGACCTGCTGCTCACGCCCCACGCCGAAGGCAGCGGCTGGGACTACGCCAACGCCGCCAGGCCGCACCCGCAGCCGGTCAGCTGCAAGGCCTACGCGGACAAGGCCGAGGCGAATCTCGACAAGATGCTCGCCGAGCAGGCGAACAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"45944","NCBI_taxonomy_name":"Pseudomonas tohonis","NCBI_taxonomy_id":"2725477"}}}},"ARO_accession":"3007200","ARO_id":"45943","ARO_name":"PAM-2","CARD_short_name":"PAM-2","ARO_description":"PAM-2 is a member of the PAM family of subclass B3 metallo-beta-lactamases found in members of the Pseudomonas genus.","ARO_category":{"45940":{"category_aro_accession":"3007198","category_aro_cvterm_id":"45940","category_aro_name":"PAM beta-lactamase","category_aro_description":"A family of subclass B3 metallo-beta-lactamases discovered in Pseudomonas alcaligenes and found in other members of the Pseudomonas genus. PAM beta-lactamases hydrolyze cephalosporins and carbenems.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5814":{"model_id":"5814","model_name":"PAM-3","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"8507":{"protein_sequence":{"accession":"GJN50066.1","sequence":"MRLLASLALPLFAANLAVAAPAQLPQLEAYKGLDAWLVPVEPLRISDHVWQIGTASISALLVKTDAGAVLIDGGMPQVADHLLANMKKLGVAPQDVRLILHSHAHIDHVGPLAAIKRATGAALVSNAESAVLLQRGGADDIHFGSGMLFEPIQTDRLVQDGEAVTLGDTTFTVHFTPGHTPGSMSWTWTDTQDGKPLRIAYSDSLSAPGYQLRHNARYPHLVDAFRESFAAVRALPCDLLLTPHAEGSGWDYANAARPHPQPVSCKAYADKAEANLDKMLAEQANKR"},"dna_sequence":{"accession":"BQKL01000042.1","fmin":"20312","fmax":"21176","strand":"+","sequence":"ATGCGTTTGCTCGCCAGCCTCGCGCTGCCCCTGTTCGCCGCCAACCTGGCGGTCGCCGCCCCCGCCCAGCTGCCCCAGCTGGAGGCCTACAAGGGCCTCGACGCCTGGCTGGTGCCGGTGGAGCCCCTGCGCATCAGCGACCACGTCTGGCAGATCGGCACCGCCAGCATCAGCGCCCTGCTGGTGAAGACCGACGCCGGCGCGGTGCTCATCGATGGGGGCATGCCCCAGGTGGCCGACCACCTGCTGGCCAACATGAAGAAGCTCGGCGTGGCCCCGCAGGATGTGCGCCTGATCCTCCACAGCCACGCGCACATCGACCATGTCGGCCCGCTGGCGGCGATCAAGCGCGCCACCGGCGCCGCGCTGGTGAGCAACGCCGAATCCGCCGTGCTGCTGCAACGCGGCGGCGCCGACGACATCCACTTCGGCAGCGGCATGCTCTTCGAACCGATCCAGACCGACCGCCTGGTGCAGGACGGCGAGGCCGTGACCCTGGGCGACACCACCTTCACCGTGCACTTCACCCCGGGGCACACGCCCGGCAGCATGAGCTGGACCTGGACCGACACCCAGGACGGCAAGCCCCTGCGCATCGCCTACAGCGACAGCCTCAGCGCGCCGGGCTACCAGCTGCGCCACAACGCCCGCTACCCGCACCTTGTGGACGCCTTCCGCGAAAGCTTCGCCGCCGTCCGCGCCCTGCCCTGCGACCTGCTGCTCACGCCCCACGCCGAAGGCAGCGGCTGGGACTACGCCAACGCCGCCAGGCCGCATCCGCAGCCGGTCAGCTGCAAGGCCTACGCGGACAAGGCCGAGGCGAATCTCGACAAGATGCTCGCCGAGCAGGCGAACAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"45944","NCBI_taxonomy_name":"Pseudomonas tohonis","NCBI_taxonomy_id":"2725477"}}}},"ARO_accession":"3007201","ARO_id":"45945","ARO_name":"PAM-3","CARD_short_name":"PAM-3","ARO_description":"PAM-3 is a member of the PAM family of subclass B3 metallo-beta-lactamases found in members of the Pseudomonas genus.","ARO_category":{"45940":{"category_aro_accession":"3007198","category_aro_cvterm_id":"45940","category_aro_name":"PAM beta-lactamase","category_aro_description":"A family of subclass B3 metallo-beta-lactamases discovered in Pseudomonas alcaligenes and found in other members of the Pseudomonas genus. PAM beta-lactamases hydrolyze cephalosporins and carbenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3658":{"model_id":"3658","model_name":"NDM-16a","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"5930":{"protein_sequence":{"accession":"AKZ20823.1","sequence":"MELPNIMHPVAKLSTALAAALMLSGCMPGEIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTAHMADKLR"},"dna_sequence":{"accession":"KP862821.1","fmin":"0","fmax":"813","strand":"+","sequence":"ATGGAATTGCCCAATATTATGCACCCGGTCGCGAAGCTGAGCACCGCATTAGCCGCTGCATTGATGCTGAGCGGGTGCATGCCCGGTGAAATCCGCCCGACGATTGGCCAGCAAATGGAAACTGGCGACCAACGGTTTGGCGATCTGGTTTTCCGCCAGCTCGCACCGAATGTCTGGCAGCACACTTCCTATCTCGACATGCCGGGTTTCGGGGCAGTCGCTTCCAACGGTTTGATCGTCAGGGATGGCGGCCGCGTGCTGGTGGTCGATACCGCCTGGACCGATGACCAGACCGCCCAGATCCTCAACTGGATCAAGCAGGAGATCAACCTGCCGGTCGCGCTGGCGGTGGTGACTCACGCGCATCAGGACAAGATGGGCGGTATGGACGCGCTGCATGCGGCGGGGATTGCGACTTATGCCAATGCGTTGTCGAACCAGCTTGCCCCGCAAGAGGGGATGGTTGCGGCGCAACACAGCCTGACTTTCGCCGCCAATGGCTGGGTCGAACCAGCAACCGCGCCCAACTTTGGCCCGCTCAAGGTATTTTACCCCGGCCCCGGCCACACCAGTGACAATATCACCGTTGGGATCGACGGCACCGACATCGCTTTTGGTGGCTGCCTGATCAAGGACAGCAAGGCCAAGTCGCTCGGCAATCTCGGTGATGCCGACACTGAGCACTACGCCGCGTCAGCGCGCGCGTTTGGTGCGGCGTTCCCCAAGGCCAGCATGATCGTGATGAGCCATTCCGCCCCCGATAGCCGCGCCGCAATCACTCATACGGCCCACATGGCCGACAAGCTGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3003664","ARO_id":"40274","ARO_name":"NDM-16a","CARD_short_name":"NDM-16a","ARO_description":"New Delhi class B metallo-beta-lactamase-16a variant of NDM-1.","ARO_category":{"36196":{"category_aro_accession":"3000057","category_aro_cvterm_id":"36196","category_aro_name":"NDM beta-lactamase","category_aro_description":"NDM beta-lactamases or New Delhi metallo-beta-lactamases are class B beta-lactamases that confer resistance to a broad range of antibiotics including carbapenems, cephalosporins and penicillins.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5815":{"model_id":"5815","model_name":"NDM-16b","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8506":{"protein_sequence":{"accession":"BCO01847.1","sequence":"MELPNIMHPVAKLSTALAAALMLSGCMPGEIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLLVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGLVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASVRAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR"},"dna_sequence":{"accession":"AP024206.1","fmin":"9811","fmax":"10624","strand":"-","sequence":"ATGGAATTGCCCAATATTATGCACCCGGTCGCGAAGCTGAGCACCGCATTAGCCGCTGCATTGATGCTGAGCGGGTGCATGCCCGGTGAAATCCGCCCGACGATTGGCCAGCAAATGGAAACTGGCGACCAACGGTTTGGCGATCTGGTTTTCCGCCAGCTCGCACCGAATGTCTGGCAGCACACTTCCTATCTCGACATGCCGGGTTTCGGGGCAGTCGCTTCCAACGGTTTGATCGTCAGGGATGGCGGCCGCGTGCTGTTGGTCGATACCGCCTGGACCGATGACCAGACCGCCCAGATCCTCAACTGGATCAAGCAGGAGATCAACCTGCCGGTCGCGCTGGCGGTGGTGACTCACGCGCATCAGGACAAGATGGGCGGTATGGACGCGCTGCATGCGGCGGGGATTGCGACTTATGCCAATGCGTTGTCGAACCAGCTTGCCCCGCAAGAGGGGCTGGTTGCGGCGCAACACAGCCTGACTTTCGCCGCCAATGGCTGGGTCGAACCAGCAACCGCGCCCAACTTTGGCCCGCTCAAGGTATTTTACCCCGGCCCCGGCCACACCAGTGACAATATCACCGTTGGGATCGACGGCACCGACATCGCTTTTGGTGGCTGCCTGATCAAGGACAGCAAGGCCAAGTCGCTCGGCAATCTCGGTGATGCCGACACTGAGCACTACGCCGCGTCAGTGCGCGCGTTTGGTGCGGCGTTCCCCAAGGCCAGCATGATCGTGATGAGCCATTCCGCCCCCGATAGCCGCGCCGCAATCACTCATACGGCCCGCATGGCCGACAAGCTGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3007202","ARO_id":"45946","ARO_name":"NDM-16b","CARD_short_name":"NDM-16b","ARO_description":"New Delhi class B metallo-beta-lactamase 16b variant.","ARO_category":{"36196":{"category_aro_accession":"3000057","category_aro_cvterm_id":"36196","category_aro_name":"NDM beta-lactamase","category_aro_description":"NDM beta-lactamases or New Delhi metallo-beta-lactamases are class B beta-lactamases that confer resistance to a broad range of antibiotics including carbapenems, cephalosporins and penicillins.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5817":{"model_id":"5817","model_name":"AAC(6')-Iap","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"200"}},"model_sequences":{"sequence":{"8509":{"protein_sequence":{"accession":"BCD41405.1","sequence":"MSGCAATIRQATPADAAAWSQLRVGLWPDADDPLEELAQSLADPEGAVFLACAADGEAVGFAEVRLRHDYVNGTGSSPVGFLEGWYVTPQWQGRAVGRALLAEVQAWTRDAGCSELASDSRLEDLEAHAAHRACGFVETERVVYFRMPLDAVTRG"},"dna_sequence":{"accession":"LC536747.1","fmin":"0","fmax":"468","strand":"+","sequence":"GTGAGCGGCTGCGCTGCCACGATCCGCCAGGCCACACCGGCCGATGCCGCTGCATGGTCGCAGCTGCGCGTGGGCCTGTGGCCCGACGCCGATGATCCACTGGAGGAGCTGGCGCAGTCGCTGGCCGATCCGGAAGGTGCGGTGTTCCTGGCGTGCGCGGCTGATGGTGAGGCGGTCGGTTTCGCTGAGGTACGCCTGCGCCACGACTATGTGAACGGCACCGGTTCCTCGCCGGTCGGGTTCCTGGAAGGCTGGTATGTAACGCCGCAGTGGCAGGGCCGCGCTGTCGGCCGTGCCCTGCTGGCGGAAGTGCAGGCGTGGACGCGGGACGCGGGCTGCAGCGAGCTGGCCTCGGACAGCCGCCTGGAGGACTTAGAGGCGCACGCGGCACACCGCGCCTGTGGCTTTGTAGAGACCGAGCGGGTGGTCTATTTCCGCATGCCGCTGGACGCGGTCACGCGGGGGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37076","NCBI_taxonomy_name":"Stenotrophomonas maltophilia","NCBI_taxonomy_id":"40324"}}}},"ARO_accession":"3007204","ARO_id":"45948","ARO_name":"AAC(6')-Iap","CARD_short_name":"AAC(6')-Iap","ARO_description":"AAC(6')-Iap is an aminoglycoside acetyltransferase that confers resistance to a number of aminoglycoside antibiotics.","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"A category of aminoglycoside N-acetyltransferase enzymes with modification regiospecificity based at the 6'-amino group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics through acetylation of the 6-amino group of the compound.","category_aro_class_name":"AMR Gene Family"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"46128":{"category_aro_accession":"3007378","category_aro_cvterm_id":"46128","category_aro_name":"2'-N-ethylnetilmicin","category_aro_description":"2'-N-ethylnetilmicin is an aminoglycoside antibiotic and a derivative of netilmicin.","category_aro_class_name":"Antibiotic"},"46129":{"category_aro_accession":"3007379","category_aro_cvterm_id":"46129","category_aro_name":"5-episisomicin","category_aro_description":"5-episosomicin is a semisynthetic aminoglycoside antibiotic similar to sisomicin.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5818":{"model_id":"5818","model_name":"KBL-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"8510":{"protein_sequence":{"accession":"BCL63355.1","sequence":"MRLTFPFAAAVSILFALPLHAETVAEAARALEAELGGRIGVVLRAPEDDPLAVWRGDEAFPMASTFKVPLCGAVLARIDAGEEQAARILPVETAALVEWSPVTEQQAGRGMSIADLCHATITMSDNTAANLLLDTVGGPAGLTAFLRDIGDATTRLDRTEPALNEALPEDMRDTTTPAAMADTLELLLFSELLSPEARAQLESWMRQDAVADDLLRASLPEGWMIGDKTGAGGNGSRSIIAVLRGPAGEPWLATVYMTQTGGDMDKRNAAIARIGAAMIGEIQARR"},"dna_sequence":{"accession":"LC579778.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTCTTACATTTCCCTTCGCGGCGGCGGTTTCGATCCTGTTCGCGCTTCCCCTCCATGCCGAAACCGTGGCCGAAGCCGCCCGCGCGCTCGAGGCCGAACTCGGCGGCCGGATCGGTGTCGTTCTGCGCGCTCCCGAAGACGATCCTTTGGCGGTCTGGCGCGGCGACGAAGCCTTTCCCATGGCCAGCACCTTCAAGGTGCCGCTTTGCGGCGCGGTCCTTGCGCGGATCGATGCGGGCGAAGAGCAAGCGGCGCGGATCCTGCCGGTCGAAACCGCCGCTCTGGTCGAATGGTCGCCGGTCACCGAACAGCAGGCGGGCCGCGGGATGAGCATTGCCGATCTCTGCCATGCCACGATCACCATGAGCGACAATACCGCCGCCAATCTTCTGCTCGACACGGTCGGCGGGCCTGCCGGTCTGACCGCTTTCCTGCGCGATATCGGCGATGCGACGACGCGGCTCGACCGCACCGAACCGGCGCTGAACGAGGCCCTGCCCGAGGATATGCGCGACACGACGACGCCGGCGGCGATGGCCGACACGCTGGAGCTTCTGCTGTTTTCCGAACTCCTCTCGCCCGAGGCGCGGGCGCAGCTTGAAAGCTGGATGCGGCAGGATGCCGTCGCCGACGACCTGCTGCGCGCGAGCCTGCCCGAGGGCTGGATGATCGGCGACAAGACCGGCGCGGGCGGCAACGGTTCGCGCTCGATCATCGCCGTCCTTCGGGGACCGGCGGGCGAGCCTTGGCTGGCGACCGTCTACATGACGCAAACCGGCGGGGATATGGACAAGCGCAACGCGGCCATTGCCCGCATCGGCGCGGCCATGATCGGCGAAATCCAAGCAAGGCGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37076","NCBI_taxonomy_name":"Stenotrophomonas maltophilia","NCBI_taxonomy_id":"40324"}}}},"ARO_accession":"3007206","ARO_id":"45950","ARO_name":"KBL-1","CARD_short_name":"KBL-1","ARO_description":"KBL-1 is a KBL class A beta-lactamase that confers resistance to a number of penicillin antibiotics.","ARO_category":{"45949":{"category_aro_accession":"3007205","category_aro_cvterm_id":"45949","category_aro_name":"KBL beta-lactamase","category_aro_description":"Kathmandu beta-lactamases are a group of class A beta-lactamases that hydrolyze penicillin antibiotics.","category_aro_class_name":"AMR Gene Family"},"35981":{"category_aro_accession":"0000064","category_aro_cvterm_id":"35981","category_aro_name":"amoxicillin","category_aro_description":"Amoxicillin is a moderate-spectrum, bacteriolytic, beta-lactam antibiotic used to treat bacterial infections caused by susceptible microorganisms. A derivative of penicillin, it has a wider range of treatment but remains relatively ineffective against Gram-negative bacteria. It is commonly taken with clavulanic acid, a beta-lactamase inhibitor. Like other beta-lactams, amoxicillin interferes with the synthesis of peptidoglycan.","category_aro_class_name":"Antibiotic"},"35995":{"category_aro_accession":"0000078","category_aro_cvterm_id":"35995","category_aro_name":"piperacillin","category_aro_description":"Piperacillin is an acetylureidopenicillin and has an extended spectrum of targets relative to other beta-lactam antibiotics. It inhibits cell wall synthesis in bacteria, and is usually taken with the beta-lactamase inhibitor tazobactam to overcome penicillin-resistant bacteria.","category_aro_class_name":"Antibiotic"},"36976":{"category_aro_accession":"3000632","category_aro_cvterm_id":"36976","category_aro_name":"benzylpenicillin","category_aro_description":"Benzylpenicillin, commonly referred to as penicillin G, is effective against both Gram-positive and Gram-negative bacteria. It is unstable in acid.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5820":{"model_id":"5820","model_name":"Streptomyces venezuelae rox","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"8512":{"protein_sequence":{"accession":"APE19944.1","sequence":"MFDVIVVGGGPTGLMLAGELRLHGVRVLVLEKETEPTRQSRAQGLHVRSIEVMAQRGLLERFLERGHTVAVGGFFAGLATSWPERLDTAHSYVLAVPQVITEQLLAEHATALGAEIRRGRALVGLRQDEDGVTVDLADGEQLRARYVVGCDGGRSTVRKLLGVAFPGEPSRVETLLGEMEMTASQEELTSVMTEVRKTQQRFGAMPLGDGVFRVVVPAEGVAEDRTASPTLDEFKQQLRAHAGTDFGVHSPRWLSRFGDATRQAERYRVDRVFLAGDAAHIHPPTGGQGLNLGIQDAFNLGWKLAAEVDGWAPEGLLDTYHAERHPVATEVLDNTRAQIQLMSTEPGPQAVRRLMAELVEFENVNRYLIEKITAISVRYDVGEGHELLGRRMRDLALKHGRLYERMHEGRGLLLDQTGRLSVAGWEDRVDHVVEVSEELDVPAVLLRPDGHVVWAGEDQQELLTRMPAWFGAATAG"},"dna_sequence":{"accession":"CP018074.1","fmin":"518413","fmax":"519844","strand":"+","sequence":"ATGTTTGACGTGATCGTTGTCGGTGGCGGTCCGACCGGCTTGATGCTGGCCGGCGAACTGCGGCTGCACGGCGTGCGCGTACTCGTGCTGGAGAAGGAGACGGAGCCGACGCGGCAGTCCCGCGCGCAGGGGCTGCACGTCCGCAGCATCGAGGTGATGGCCCAGCGCGGGCTCCTGGAGCGCTTCCTCGAACGCGGGCACACGGTCGCGGTCGGCGGCTTCTTCGCCGGTCTGGCGACCTCGTGGCCCGAGCGGCTGGACACCGCGCACTCGTACGTCCTCGCCGTCCCGCAGGTGATCACCGAGCAGCTGCTGGCCGAGCACGCCACCGCACTCGGAGCCGAGATCCGACGCGGCCGGGCACTGGTCGGTCTCCGCCAGGACGAGGACGGCGTGACGGTCGACCTGGCCGACGGCGAACAGCTGCGCGCACGGTACGTCGTCGGCTGCGACGGCGGCCGCAGCACGGTGCGCAAGCTGCTCGGCGTGGCGTTCCCCGGCGAGCCGTCCAGGGTCGAGACCCTGCTCGGCGAGATGGAGATGACCGCCTCCCAGGAGGAGTTGACCTCCGTCATGACCGAGGTCCGCAAGACCCAGCAGCGATTCGGCGCGATGCCCCTGGGGGACGGGGTCTTCCGCGTCGTCGTCCCCGCCGAGGGCGTCGCCGAGGACCGGACGGCCTCCCCGACCCTCGACGAGTTCAAGCAGCAGCTGCGGGCCCACGCCGGGACGGACTTCGGCGTGCACTCGCCCCGGTGGCTCTCCCGCTTCGGCGACGCCACCCGACAGGCCGAGCGCTACCGGGTCGACCGGGTGTTCCTCGCTGGCGACGCGGCGCACATCCACCCGCCGACCGGCGGGCAGGGCCTCAACCTCGGCATCCAGGACGCGTTCAACCTCGGCTGGAAGCTGGCCGCCGAGGTCGACGGCTGGGCGCCGGAGGGACTCCTCGACACGTACCACGCCGAGCGGCACCCGGTGGCCACCGAGGTCCTGGACAACACCCGCGCGCAGATCCAGCTGATGTCGACGGAGCCGGGGCCGCAGGCGGTCCGCCGGCTCATGGCGGAACTCGTGGAGTTCGAGAACGTCAACCGGTACCTGATCGAGAAGATCACGGCGATCTCGGTCCGTTACGACGTCGGCGAGGGCCACGAGCTGCTCGGCCGCCGGATGCGGGACCTCGCGCTCAAGCACGGCCGGCTCTACGAGCGGATGCACGAGGGCCGTGGACTGCTGCTCGACCAGACCGGCCGGCTCTCGGTCGCCGGGTGGGAGGACCGGGTCGACCACGTCGTCGAGGTCAGCGAGGAACTGGACGTGCCCGCGGTGCTGCTGCGTCCCGACGGCCACGTCGTGTGGGCGGGCGAGGACCAGCAGGAGCTGCTCACCCGGATGCCCGCGTGGTTCGGCGCCGCCACGGCCGGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36873","NCBI_taxonomy_name":"Streptomyces venezuelae","NCBI_taxonomy_id":"54571"}}}},"ARO_accession":"3007209","ARO_id":"45953","ARO_name":"Streptomyces venezuelae rox","CARD_short_name":"Sven_rox","ARO_description":"Streptomyces venezuelae rox is a class A flavoprotein monooxygenase that confers resistance to rifamycin antibiotics. It acts by oxygenating the naphthyl group of the antibiotic, leading to a ring opening event and linearization of the molecule.","ARO_category":{"36584":{"category_aro_accession":"3000445","category_aro_cvterm_id":"36584","category_aro_name":"rifampin monooxygenase","category_aro_description":"Enzyme responsible for the decolorization of rifampin by monoxygenation.","category_aro_class_name":"AMR Gene Family"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36656":{"category_aro_accession":"3000517","category_aro_cvterm_id":"36656","category_aro_name":"rifaximin","category_aro_description":"Rifaximin is a semi-synthetic rifamycin used to treat traveller's diarrhea. Rifaximin inhibits RNA synthesis by binding to the beta subunit of bacterial RNA polymerase.","category_aro_class_name":"Antibiotic"},"36673":{"category_aro_accession":"3000534","category_aro_cvterm_id":"36673","category_aro_name":"rifapentine","category_aro_description":"Rifapentine is a semisynthetic rifamycin that inhibits DNA-dependent RNA synthesis. It is often used in the treatment of tuberculosis and leprosy.","category_aro_class_name":"Antibiotic"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5821":{"model_id":"5821","model_name":"Nocardia farcinica rox","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"8513":{"protein_sequence":{"accession":"BAD58386.1","sequence":"MIDVIIAGGGPTGLMLAGELRLHGVRTVVLEKEPTPNQHSRSRGLHARSIEVMDQRGLLERFLAHGEQFRVGGFFAGLAAEWPADLDTAHSYVLAIPQVVTERLLTEHATELGAEIRRGCEVAGLDQDADGVTAELADGTRLRARYLVGCDGGRSTVRRLLGVDFPGEPTRVETLLADVRIDVPVETLTAVVAEVRKTQLRFGAVPAGDGFFRLIVPAQGLSADRAAPTLDELKRCLHATAGTDFGVHSPRWLSRFGDATRLAERYRTGRVLLAGDAAHIHPPTGGQGLNLGIQDAFNLGWKLAAAIGGWAPPDLLDSYHDERHPVAAEVLDNTRAQMTLLSLDPGPRAVRRLMAELVEFPDVNRHLIEKITAIAVRYDLGDGHDLVGRRLRDIPLTEGRLYERMRGGRGLLLDRTGRLSVSGWSDRVDHLADPGAALDVPAALLRPDGHVAWVGEDQDDLLAHLPRWFGAAT"},"dna_sequence":{"accession":"AP006618.1","fmin":"3747376","fmax":"3748798","strand":"+","sequence":"GTGATCGATGTGATCATCGCGGGTGGCGGACCGACCGGCTTGATGCTGGCCGGCGAACTGCGCCTGCACGGTGTGCGCACGGTGGTACTGGAGAAGGAGCCCACCCCGAACCAGCACTCCCGCAGTCGGGGCCTGCACGCGCGCAGCATCGAGGTGATGGACCAGCGCGGGCTGCTGGAGCGGTTCCTCGCGCACGGCGAGCAGTTCCGGGTCGGCGGGTTCTTCGCCGGGCTGGCCGCCGAATGGCCCGCCGACCTGGACACCGCGCACTCCTACGTGCTCGCGATTCCCCAGGTCGTCACCGAGCGCCTGCTCACCGAGCACGCCACCGAACTCGGCGCCGAGATCCGCCGCGGCTGCGAAGTGGCCGGGTTGGATCAGGACGCGGACGGGGTGACCGCCGAGCTGGCCGACGGCACGCGGTTGCGCGCCCGGTACCTGGTCGGCTGCGACGGCGGACGCTCGACCGTGCGCCGTCTGCTCGGGGTCGACTTCCCCGGCGAACCCACCCGGGTCGAGACGTTGCTGGCCGACGTGCGGATCGACGTGCCGGTCGAGACACTGACCGCGGTGGTCGCCGAGGTGCGCAAGACCCAACTGCGATTCGGGGCCGTCCCGGCCGGCGACGGGTTCTTCCGGCTGATCGTGCCCGCGCAGGGCCTGTCCGCGGACCGCGCCGCACCCACCCTCGACGAGCTGAAGCGATGCCTGCACGCGACGGCGGGCACCGATTTCGGCGTGCACTCCCCGCGCTGGCTGTCCCGCTTCGGCGACGCCACCCGGCTCGCCGAGCGCTACCGCACCGGGCGGGTGCTGCTGGCGGGCGACGCCGCCCACATCCATCCGCCGACCGGCGGCCAGGGCCTCAATCTGGGCATCCAGGACGCCTTCAACCTCGGCTGGAAGCTCGCCGCCGCGATCGGCGGCTGGGCGCCGCCGGACCTGCTGGACAGCTACCACGACGAACGCCATCCGGTCGCCGCCGAGGTGCTGGACAACACCCGCGCCCAGATGACGCTGCTCTCCCTCGACCCCGGCCCGCGCGCGGTGCGCAGACTGATGGCGGAGCTGGTCGAATTCCCCGACGTGAACCGGCACCTGATCGAGAAGATCACCGCGATCGCCGTCCGCTACGACCTCGGCGACGGCCACGACCTGGTCGGTCGACGGCTGCGCGACATCCCGCTCACCGAAGGCCGCCTCTACGAGCGGATGCGCGGCGGCCGCGGGCTGCTGCTCGACCGGACCGGGCGGCTGTCGGTATCGGGCTGGTCCGACCGCGTCGACCACCTCGCCGACCCGGGCGCGGCGCTCGACGTCCCGGCGGCGCTGCTGCGCCCGGACGGGCACGTCGCGTGGGTGGGCGAGGACCAGGACGATCTGCTCGCCCACCTGCCCCGCTGGTTCGGCGCCGCCACCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41346","NCBI_taxonomy_name":"Nocardia farcinica IFM 10152","NCBI_taxonomy_id":"247156"}}}},"ARO_accession":"3007210","ARO_id":"45954","ARO_name":"Nocardia farcinica rox","CARD_short_name":"Nfar_rox","ARO_description":"Nocardia farcinica rox is a rifampin monooxygenase that inactivates rifampin.","ARO_category":{"36584":{"category_aro_accession":"3000445","category_aro_cvterm_id":"36584","category_aro_name":"rifampin monooxygenase","category_aro_description":"Enzyme responsible for the decolorization of rifampin by monoxygenation.","category_aro_class_name":"AMR Gene Family"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5832":{"model_id":"5832","model_name":"MCR-8.3","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"8526":{"protein_sequence":{"accession":"WP_150823497.1","sequence":"MFKYLLSFKLNPVQRTWAAAFFFTTIGNIALWQTLWINVDVHNIHNLLFFASLPIFLFCFLSILLTPVMVIPYLCRPLLVVLILISACCSYFMMKYNILIDRSMVQNFFETNQAELTSYLSVPFLSTLFLLGIVPAIILALPSTDNKRGAFRIELWWLAHICIAVVLLAMVTMVFYKDYASLIRNNMQIKDQALPFNFVRNTNGYLKRKYQASSTILQSVGEDAVRPIYSNAPPKLVVVVVGETARAQNFQLNGYSRVTNPYLSRRHDVISFKNVSSCGTATAISLPCMFSRMSRNEYNEVRAASEENLLDILKRTGVEVLWRNNNNGGCKGICKRVPTDDMPAMKVIGECVNKDGTCFDEVLLNQLSSRINAMQGDALIVLHQMGSHGPKYFERYPSTSKVFSPTCDSNLIEKCSNKELVNTYDNTLVYTDRMLSKTIELLQRYSGMRDVAMIYLSDHGESLGESGIYLHGTPYIIAPNEQTHIPMFMWFSSSFAQHSKLNLECLTGNADKQYSHDNFYHSILGLFNVKTSVYKPELDMFTLCRQSDHTPLSSAVVREKTDGNG"},"dna_sequence":{"accession":"MH598530.1","fmin":"0","fmax":"1698","strand":"+","sequence":"ATGTTCAAGTATCTTTTATCTTTCAAACTGAACCCGGTACAACGGACCTGGGCTGCAGCATTTTTTTTCACTACAATCGGCAACATAGCACTTTGGCAAACACTATGGATTAATGTAGATGTTCATAATATACATAATCTACTTTTTTTTGCCAGTCTGCCAATATTTCTTTTCTGCTTTCTAAGTATCTTACTTACACCAGTCATGGTTATTCCATATTTATGCAGGCCTCTACTTGTAGTTCTTATTCTAATCAGTGCCTGCTGTAGTTATTTCATGATGAAATACAACATATTAATTGACCGCAGCATGGTGCAAAACTTTTTTGAGACTAATCAGGCTGAATTAACATCATACTTATCCGTTCCTTTTCTTTCCACTCTATTTCTACTTGGCATTGTACCAGCAATTATCCTGGCGTTGCCTTCAACAGACAATAAGCGGGGAGCTTTTAGAATTGAATTGTGGTGGTTGGCGCATATTTGCATAGCTGTAGTCTTATTAGCCATGGTTACCATGGTGTTTTATAAGGATTACGCATCTCTCATACGAAACAATATGCAGATTAAAGACCAGGCTTTACCTTTTAACTTTGTGCGTAATACGAATGGTTACCTTAAAAGAAAATACCAGGCATCTTCAACAATTCTACAAAGCGTGGGGGAGGATGCTGTACGTCCAATATATTCAAATGCTCCACCGAAACTGGTGGTTGTCGTCGTGGGCGAAACCGCCAGAGCACAGAATTTCCAGCTGAATGGCTATTCGCGGGTAACCAACCCCTATCTTTCCAGACGACATGATGTTATCAGTTTCAAAAATGTGTCGTCATGCGGAACGGCTACCGCAATATCACTACCCTGCATGTTCTCGCGAATGTCACGTAACGAATACAATGAAGTCCGTGCCGCATCAGAAGAAAACTTGCTGGATATCCTTAAACGTACAGGTGTTGAGGTGCTATGGCGCAACAATAACAATGGTGGTTGTAAGGGAATCTGCAAGCGAGTACCCACAGATGATATGCCGGCAATGAAAGTAATTGGGGAATGTGTTAACAAAGATGGTACATGCTTTGATGAGGTGTTATTAAATCAACTCTCATCCCGAATTAATGCAATGCAGGGTGATGCGCTTATTGTTTTACATCAAATGGGCAGTCATGGACCAAAATATTTTGAACGTTATCCGTCTACAAGTAAAGTCTTTAGCCCAACTTGCGACAGCAACCTGATCGAAAAATGCTCAAATAAAGAACTGGTCAATACATACGACAATACGCTAGTTTATACTGATCGTATGCTGAGCAAAACTATTGAACTGTTGCAACGTTATTCCGGGATGCGTGACGTTGCTATGATATATCTTTCTGATCATGGAGAATCGCTGGGGGAAAGCGGAATATATCTTCATGGCACACCATATATTATTGCCCCCAATGAACAAACACACATCCCGATGTTTATGTGGTTTTCGTCTTCATTCGCGCAGCATTCCAAATTAAATCTAGAATGCCTGACCGGTAATGCCGACAAACAATACAGTCATGATAATTTTTATCATTCAATACTTGGTCTCTTCAACGTAAAAACCAGTGTATATAAACCGGAGTTAGATATGTTTACTCTATGTCGACAATCTGACCACACACCACTGTCTTCCGCAGTTGTAAGAGAGAAAACAGATGGGAATGGTTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3007227","ARO_id":"45973","ARO_name":"MCR-8.3","CARD_short_name":"MCR-8.3","ARO_description":"An MCR-8-type colistin resistance gene variant.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5816":{"model_id":"5816","model_name":"Klebsiella pneumoniae mutant PhoQ conferring resistance to colistin","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"12717":"V24G"},"Curated-R":{"12717":"V24G"},"clinical":{"12717":"V24G"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"850"}},"model_sequences":{"sequence":{"8508":{"protein_sequence":{"accession":"QWW12915.1","sequence":"MKGLLRHIFPLSLRVRFLLATAGVVLVLSLAYGMVALVGYSVSFDKTTFRLLRGESNLFYMLARWENGAIDVDIPENLNMESPTVTLIYDEQGKLLWAQRDVPWLAKRIQPEWLKRNGFHEIEADVDSSSMLLRNNHEIQEQLDAIREQGDDSEMTHSVAINLYPATSKMPQLSIVVVDTIPVELKRSYMVWSWFVYVLAANLLLVIPLLWVAAWWSLRPIESLAKEVRELEEHHREKLNPNTTRELTRLVSNLNRLVRSERERYDKYRTTLTDLTHSLKTPLAVMQSTLRSLRGEKISVDEAEPVMLEQISRISQQIGYYLHRASMRSGGTLLSRELHPIAPLLDSLTSALNKVYQRKGVNISLDISPEITFVGEQNDFMEVMGNVLDNACKYCLEFVEVSVRQTTDSHLHILVEDDGPGIPQSQRRAVFDRGQRADTLRPGQGVGLSVAREIVEQYDGEIIAGESLLGGACMEVVFGRQQMEDKQS"},"dna_sequence":{"accession":"CP052761.1","fmin":"3075931","fmax":"3077398","strand":"+","sequence":"ATGAAGGGACTGTTGCGGCATATCTTCCCGCTGTCATTACGGGTTCGCTTCCTGCTGGCGACCGCCGGGGTGGTGCTGGTGCTCTCCCTGGCCTACGGCATGGTGGCCCTGGTGGGCTATAGCGTTAGCTTCGATAAAACCACCTTTCGCCTGCTGCGCGGCGAGAGCAATCTCTTTTATATGCTGGCGAGATGGGAAAACGGCGCTATTGACGTCGATATCCCGGAAAACCTGAATATGGAAAGCCCGACGGTGACCCTTATCTACGATGAGCAGGGCAAACTGCTGTGGGCGCAGCGTGATGTTCCATGGCTGGCGAAACGCATTCAACCGGAATGGCTGAAACGCAATGGCTTCCATGAGATTGAAGCCGATGTCGACAGCAGCAGTATGCTGTTGCGCAATAACCATGAGATTCAGGAACAGCTGGACGCTATCCGCGAACAGGGCGACGACTCTGAGATGACCCACTCGGTGGCGATCAACCTCTACCCGGCCACCAGCAAAATGCCTCAGCTCAGCATTGTGGTGGTCGACACCATTCCGGTGGAGCTCAAGCGCAGTTATATGGTGTGGAGCTGGTTTGTCTATGTGCTGGCCGCCAACCTGCTGCTGGTGATCCCCCTGCTGTGGGTCGCCGCCTGGTGGAGCCTGCGGCCCATTGAGTCGCTGGCCAAAGAGGTGCGCGAACTGGAGGAACATCACCGCGAAAAGCTCAATCCCAACACCACTCGCGAGCTGACCCGGCTGGTCAGCAACCTCAACCGCCTGGTTCGCAGCGAGCGCGAACGCTATGACAAATACCGCACTACCCTCACCGATCTCACTCACAGTCTGAAAACGCCGCTGGCGGTGATGCAGAGTACACTGCGCTCGCTGCGCGGCGAGAAGATCAGCGTCGACGAGGCGGAGCCGGTGATGCTGGAGCAGATAAGCCGCATCTCGCAGCAGATTGGTTATTACCTGCATCGCGCCAGCATGCGCAGCGGCGGCACCCTCTTGAGCCGGGAATTACACCCGATTGCCCCCCTGCTTGACAGCCTGACTTCCGCTCTCAACAAGGTCTATCAGCGCAAAGGGGTCAATATCTCGCTCGACATCTCGCCGGAGATCACTTTTGTCGGCGAGCAGAACGATTTTATGGAAGTGATGGGTAACGTTCTTGATAACGCCTGTAAGTATTGCCTGGAGTTCGTGGAAGTTTCCGTGCGCCAGACCACCGACAGCCATCTGCACATCCTGGTGGAAGACGATGGGCCGGGGATCCCGCAGAGCCAGCGCCGGGCCGTTTTCGACCGCGGCCAGCGGGCTGATACCCTGCGTCCCGGCCAGGGGGTAGGGCTCTCCGTTGCGCGTGAAATTGTCGAACAATATGATGGAGAGATCATCGCCGGGGAAAGCCTGCTCGGCGGCGCCTGCATGGAGGTGGTGTTTGGCCGCCAGCAGATGGAAGATAAACAGAGTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3007203","ARO_id":"45947","ARO_name":"Klebsiella pneumoniae mutant PhoQ conferring resistance to colistin","CARD_short_name":"Kpne_PhoQ_CST","ARO_description":"Mutations in Klebsiella pneumoniae PhoQ of the two-component PhoPQ regulatory system conferring resistance to colistin.","ARO_category":{"36002":{"category_aro_accession":"0010001","category_aro_cvterm_id":"36002","category_aro_name":"ATP-binding cassette (ABC) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding\/hydrolysis to transport substrates across cell membranes.","category_aro_class_name":"AMR Gene Family"},"41433":{"category_aro_accession":"3004269","category_aro_cvterm_id":"41433","category_aro_name":"pmr phosphoethanolamine transferase","category_aro_description":"This family of phosphoethanolamine transferase catalyze the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine to lipid A, which impedes the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"46471":{"category_aro_accession":"3007684","category_aro_cvterm_id":"46471","category_aro_name":"transmembrane protein conferring colistin resistance","category_aro_description":"Mutations in mgrB transmembrane proteins can confer resistance to the antibiotic colistin.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"36593":{"category_aro_accession":"3000454","category_aro_cvterm_id":"36593","category_aro_name":"polymyxin B","category_aro_description":"Polymyxin B is mixture of mostly polymyxins B1 and B2, mainly used for resistant gram-negative infections. They are polypeptides with cationic detergent action on cell membranes.","category_aro_class_name":"Antibiotic"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"},"40429":{"category_aro_accession":"3003764","category_aro_cvterm_id":"40429","category_aro_name":"resistance by absence","category_aro_description":"Mechanism of antibiotic resistance conferred by deletion of gene (usually a porin).","category_aro_class_name":"Resistance Mechanism"}}},"5819":{"model_id":"5819","model_name":"HelR","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"8511":{"protein_sequence":{"accession":"CCA59315.1","sequence":"MRVLSSVDQLDGTSAFDLPDRLSAKTDPALIAADERHFSAIAKSLAETITELSDRLDATRKAPGGVGREAMDRDAEIHRLTGRLRTLRRFGLDLCLGRIVTADDAEPVYVGRLGLTDSTGRRLLVDWRSPAAEPFFAATHADPMGLTSRRRYRWTGGRVSDYWDEVFTADGLEEHAALDDQSAFIASLGSSRSPQMRDVLATIQADQDAIIRAGSRGTLVVDGGPGTGKTVVALHRSAHLLYADPRLGHRRGGVLFVGPHQPYLAYVADVLPSLGEEGVRTCTVRDLVAEGAGAAVERDAEVARLKSSADMVRAIEAAVRFYEEPPTQRMTVSTDWADVRLTADDWAEAFDAPEAGTPHNEAREQIWEELGSILLGKLGDEVPEEEFRRALRQDEELAGALHGAWPLLEAADLVGDLWSVPAYLRKCAPWLDREDVAKLQRADAQAWTVSDLPLLDAARQRLGDPEAARRRRRQQATVAAERARMADVIADVLAADDDGEGAVTMLRGQDLKDTLVDEAALTGVEPDLLAGPFAHIVVDEAQELSDAEWQMLLLRCPSRSFTIVGDRAQARHGFTESWEERLARVGLDRITVASLSINYRTPEEVMAEAEPAIRAALPDANVPTSVRSSGVPVLRGPVEELDTIVDEWLAANADGTACVIGAPRFRPGPRVRSLTPSLSKGLEFDLVVLVDPEDFGGGIEGAVDRYVAMTRATKQLVILTSS"},"dna_sequence":{"accession":"FR845719.1","fmin":"6559170","fmax":"6561339","strand":"-","sequence":"GTGCGTGTGCTTTCGTCGGTGGACCAGTTGGACGGCACCAGTGCGTTCGACCTTCCCGACCGCCTCTCCGCCAAGACCGACCCGGCGCTGATCGCCGCGGACGAGCGGCACTTCTCGGCCATCGCGAAGAGCCTCGCGGAGACGATCACCGAGCTGTCCGACCGGCTGGACGCCACGCGCAAGGCGCCCGGCGGGGTCGGCCGGGAGGCGATGGACCGCGACGCGGAGATCCACCGCCTGACCGGCAGGCTGCGCACCCTCCGCCGCTTCGGCCTCGACCTGTGCCTCGGGCGCATCGTGACGGCGGACGACGCGGAGCCGGTGTACGTCGGGCGCCTCGGGCTCACCGACAGCACCGGGCGCCGCCTCCTCGTCGACTGGCGCTCCCCCGCGGCCGAGCCGTTCTTCGCGGCCACCCACGCCGACCCGATGGGGCTGACGAGCCGCCGCAGGTACCGCTGGACCGGGGGCCGCGTCAGTGACTACTGGGACGAGGTGTTCACCGCCGACGGTCTCGAGGAGCACGCGGCACTGGACGACCAGTCGGCGTTCATCGCCAGCCTGGGCAGCAGCCGTTCGCCGCAGATGCGCGATGTGCTCGCCACCATCCAGGCCGACCAGGACGCCATCATCCGCGCCGGGTCCCGCGGCACCCTCGTCGTCGACGGCGGACCGGGCACGGGCAAGACCGTCGTCGCCCTGCACCGCTCCGCGCACCTGCTGTACGCGGACCCGCGCCTCGGACACCGGCGGGGCGGGGTCCTCTTCGTCGGCCCGCACCAGCCCTACCTGGCGTACGTCGCCGACGTCCTGCCCAGCCTCGGCGAGGAGGGCGTGCGGACCTGCACCGTGCGGGACCTCGTCGCCGAGGGCGCCGGAGCGGCCGTCGAGCGGGACGCGGAGGTGGCCCGGCTGAAGTCGTCGGCCGACATGGTGCGGGCCATCGAGGCGGCCGTGCGGTTCTACGAGGAGCCGCCGACCCAGCGGATGACGGTGTCGACGGACTGGGCCGACGTGCGGCTGACCGCCGACGACTGGGCCGAGGCGTTCGACGCGCCGGAGGCCGGCACGCCGCACAACGAGGCGCGTGAGCAGATCTGGGAGGAGCTGGGCTCGATCCTCCTGGGCAAGCTCGGCGACGAGGTCCCCGAGGAGGAGTTCCGGCGGGCGCTGCGGCAGGACGAGGAGCTGGCGGGGGCCCTGCACGGGGCGTGGCCGCTCCTGGAGGCGGCCGACCTGGTGGGCGACCTGTGGTCGGTCCCCGCGTACCTGCGCAAGTGCGCGCCGTGGCTGGACCGCGAGGACGTGGCGAAGCTCCAGCGCGCGGACGCGCAGGCCTGGACGGTGTCCGACCTGCCGCTCCTGGACGCGGCGCGGCAGCGGCTCGGCGACCCGGAGGCGGCGCGGCGCAGGCGCCGGCAGCAGGCCACCGTCGCCGCCGAGCGCGCGCGCATGGCCGACGTCATCGCGGACGTGCTCGCGGCGGACGACGACGGCGAGGGCGCGGTGACGATGCTGCGCGGCCAGGACCTCAAGGACACGCTGGTCGACGAGGCGGCGCTGACGGGTGTCGAACCGGACCTGCTCGCCGGGCCGTTCGCGCACATCGTCGTGGACGAGGCGCAGGAGCTGTCGGACGCCGAGTGGCAGATGCTGCTGCTGCGCTGCCCGTCCCGGAGCTTCACCATCGTCGGCGACCGCGCGCAGGCCAGGCACGGCTTCACCGAGTCGTGGGAGGAGCGGCTCGCCCGGGTCGGCCTCGACCGGATCACGGTGGCGTCGCTGAGCATCAACTACCGCACGCCGGAAGAGGTCATGGCGGAGGCCGAGCCGGCGATCCGGGCCGCGCTGCCCGACGCGAACGTGCCGACGTCGGTCCGCAGCAGCGGTGTCCCGGTGCTCCGCGGTCCGGTGGAGGAGCTGGACACGATCGTCGACGAGTGGCTGGCCGCCAACGCCGACGGGACCGCCTGTGTCATCGGCGCGCCCCGGTTCCGGCCGGGGCCGCGGGTGCGGTCGCTGACCCCGTCGCTGTCGAAGGGCCTGGAGTTCGACCTGGTCGTGCTCGTGGACCCGGAGGACTTCGGCGGGGGCATCGAGGGAGCGGTCGACCGCTATGTGGCGATGACCCGCGCGACGAAGCAGCTCGTGATCCTCACCAGCTCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36896","NCBI_taxonomy_name":"Streptomyces venezuelae ATCC 10712","NCBI_taxonomy_id":"953739"}}}},"ARO_accession":"3007208","ARO_id":"45952","ARO_name":"HelR","CARD_short_name":"HelR","ARO_description":"HelR is a helicase-like protein that confers resistance to rifamycins by displacing them from the RNA polymerase complex. The protein forces the antibiotic away from the polymerase by binding in its place. It then ejects itself from the complex, allowing the polymerase to resume normal function.","ARO_category":{"45951":{"category_aro_accession":"3007207","category_aro_cvterm_id":"45951","category_aro_name":"helicase-like RNA polymerase protection protein","category_aro_description":"Helicase-like proteins that confer resistance to antibiotics such as rifamycins by preventing or disrupting their binding to RNA polymerase.","category_aro_class_name":"AMR Gene Family"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36656":{"category_aro_accession":"3000517","category_aro_cvterm_id":"36656","category_aro_name":"rifaximin","category_aro_description":"Rifaximin is a semi-synthetic rifamycin used to treat traveller's diarrhea. Rifaximin inhibits RNA synthesis by binding to the beta subunit of bacterial RNA polymerase.","category_aro_class_name":"Antibiotic"},"36669":{"category_aro_accession":"3000530","category_aro_cvterm_id":"36669","category_aro_name":"rifabutin","category_aro_description":"Rifabutin is a semisynthetic rifamycin used in tuberculosis therapy. It inhibits DNA-dependent RNA synthesis.","category_aro_class_name":"Antibiotic"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5822":{"model_id":"5822","model_name":"NDM-34","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8514":{"protein_sequence":{"accession":"QVU28093.1","sequence":"MELPNIMHPVAKLSTALAAALMLSGCMPGEIRPTIGQQMETGDQRFGDMVFRQIAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLLVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR"},"dna_sequence":{"accession":"MZ254705.1","fmin":"0","fmax":"813","strand":"+","sequence":"ATGGAATTGCCCAATATTATGCACCCGGTCGCGAAGCTGAGCACCGCATTAGCCGCTGCATTGATGCTGAGCGGGTGCATGCCCGGTGAAATCCGCCCGACGATTGGCCAGCAAATGGAAACTGGCGACCAACGGTTTGGCGATATGGTTTTCCGCCAGATCGCACCGAATGTCTGGCAGCACACTTCCTATCTCGACATGCCGGGTTTCGGGGCAGTCGCTTCCAACGGTTTGATCGTCAGGGATGGCGGCCGCGTGCTGTTGGTCGATACCGCCTGGACCGATGACCAGACCGCCCAGATCCTCAACTGGATCAAGCAGGAGATCAACCTGCCGGTCGCGCTGGCGGTGGTGACTCACGCGCATCAGGACAAGATGGGCGGTATGGACGCGCTGCATGCGGCGGGGATTGCGACTTATGCCAATGCGTTGTCGAACCAGCTTGCCCCGCAAGAGGGGATGGTTGCGGCGCAACACAGCCTGACTTTCGCCGCCAATGGCTGGGTCGAACCAGCAACCGCGCCCAACTTTGGCCCGCTCAAGGTATTTTACCCCGGCCCCGGCCACACCAGTGACAATATCACCGTTGGGATCGACGGCACCGACATCGCTTTTGGTGGCTGCCTGATCAAGGACAGCAAGGCCAAGTCGCTCGGCAATCTCGGTGATGCCGACACTGAGCACTACGCCGCGTCAGCGCGCGCGTTTGGTGCGGCGTTCCCCAAGGCCAGCATGATCGTGATGAGCCATTCCGCCCCCGATAGCCGCGCCGCAATCACTCATACGGCCCGCATGGCCGACAAGCTGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39615","NCBI_taxonomy_name":"Vibrio parahaemolyticus","NCBI_taxonomy_id":"670"}}}},"ARO_accession":"3007211","ARO_id":"45955","ARO_name":"NDM-34","CARD_short_name":"NDM-34","ARO_description":"NDM-34 is a NDM beta-lactamase.","ARO_category":{"36196":{"category_aro_accession":"3000057","category_aro_cvterm_id":"36196","category_aro_name":"NDM beta-lactamase","category_aro_description":"NDM beta-lactamases or New Delhi metallo-beta-lactamases are class B beta-lactamases that confer resistance to a broad range of antibiotics including carbapenems, cephalosporins and penicillins.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5823":{"model_id":"5823","model_name":"NDM-35","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8515":{"protein_sequence":{"accession":"QVU28098.1","sequence":"MELPNIMHPVAKLSTALAAALMLSGCMPGEIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGDRVLLVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGLVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR"},"dna_sequence":{"accession":"MZ265788.1","fmin":"0","fmax":"813","strand":"+","sequence":"ATGGAATTGCCCAATATTATGCACCCGGTCGCGAAGCTGAGCACCGCATTAGCCGCTGCATTGATGCTGAGCGGGTGCATGCCCGGTGAAATCCGCCCGACGATTGGCCAGCAAATGGAAACTGGCGACCAACGGTTTGGCGATCTGGTTTTCCGCCAGCTCGCACCGAATGTCTGGCAGCACACTTCCTATCTCGACATGCCGGGTTTCGGGGCAGTCGCTTCCAACGGTTTGATCGTCAGGGATGGCGACCGCGTGCTGTTGGTCGATACCGCCTGGACCGATGACCAGACCGCCCAGATCCTCAACTGGATCAAGCAGGAGATCAACCTGCCGGTCGCGCTGGCGGTGGTGACTCACGCGCATCAGGACAAGATGGGCGGTATGGACGCGCTGCATGCGGCGGGGATTGCGACTTATGCCAATGCGTTGTCGAACCAGCTTGCCCCGCAAGAGGGGCTGGTTGCGGCGCAACACAGCCTGACTTTCGCCGCCAATGGCTGGGTCGAACCAGCAACCGCGCCCAACTTTGGCCCGCTCAAGGTATTTTACCCCGGCCCCGGCCACACCAGTGACAATATCACCGTTGGGATCGACGGCACCGACATCGCTTTTGGTGGCTGCCTGATCAAGGACAGCAAGGCCAAGTCGCTCGGCAATCTCGGTGATGCCGACACTGAGCACTACGCCGCGTCAGCGCGCGCGTTTGGTGCGGCGTTCCCCAAGGCCAGCATGATCGTGATGAGCCATTCCGCCCCCGATAGCCGCGCCGCAATCACTCATACGGCCCGCATGGCCGACAAGCTGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3007212","ARO_id":"45956","ARO_name":"NDM-35","CARD_short_name":"NDM-35","ARO_description":"NDM-35 is a NDM beta-lactamase.","ARO_category":{"36196":{"category_aro_accession":"3000057","category_aro_cvterm_id":"36196","category_aro_name":"NDM beta-lactamase","category_aro_description":"NDM beta-lactamases or New Delhi metallo-beta-lactamases are class B beta-lactamases that confer resistance to a broad range of antibiotics including carbapenems, cephalosporins and penicillins.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5824":{"model_id":"5824","model_name":"NDM-36","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8516":{"protein_sequence":{"accession":"MBT0799486.1","sequence":"MELPNIMHPVAKLSTALAAALMLSGCMPGEIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLLVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGLVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASVRAFGAAFPKASMIVMSHSAPDSRAAITYTARMADKLR"},"dna_sequence":{"accession":"JAHAWL010000074.1","fmin":"271","fmax":"1084","strand":"+","sequence":"ATGGAATTGCCCAATATTATGCACCCGGTCGCGAAGCTGAGCACCGCATTAGCCGCTGCATTGATGCTGAGCGGGTGCATGCCCGGTGAAATCCGCCCGACGATTGGCCAGCAAATGGAAACTGGCGACCAACGGTTTGGCGATCTGGTTTTCCGCCAGCTCGCACCGAATGTCTGGCAGCACACTTCCTATCTCGACATGCCGGGTTTCGGGGCAGTCGCTTCCAACGGTTTGATCGTCAGGGATGGCGGCCGCGTGCTGTTGGTCGATACCGCCTGGACCGATGACCAGACCGCCCAGATCCTCAACTGGATCAAGCAGGAGATCAACCTGCCGGTCGCGCTGGCGGTGGTGACTCACGCGCATCAGGACAAGATGGGCGGTATGGACGCGCTGCATGCGGCGGGGATTGCGACTTATGCCAATGCGTTGTCGAACCAGCTTGCCCCGCAAGAGGGGCTGGTTGCGGCGCAACACAGCCTGACTTTCGCCGCCAATGGCTGGGTCGAACCAGCAACCGCGCCCAACTTTGGCCCGCTCAAGGTATTTTACCCCGGCCCCGGCCACACCAGTGACAATATCACCGTTGGGATCGACGGCACCGACATCGCTTTTGGTGGCTGCCTGATCAAGGACAGCAAGGCCAAGTCGCTCGGCAATCTCGGTGATGCCGACACTGAGCACTACGCCGCGTCAGTGCGCGCGTTTGGTGCGGCGTTCCCCAAGGCCAGCATGATCGTGATGAGCCATTCCGCCCCCGATAGCCGCGCCGCAATCACTTATACGGCCCGCATGGCCGACAAGCTGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3007213","ARO_id":"45957","ARO_name":"NDM-36","CARD_short_name":"NDM-36","ARO_description":"NDM-36 is a NDM beta-lactamase.","ARO_category":{"36196":{"category_aro_accession":"3000057","category_aro_cvterm_id":"36196","category_aro_name":"NDM beta-lactamase","category_aro_description":"NDM beta-lactamases or New Delhi metallo-beta-lactamases are class B beta-lactamases that confer resistance to a broad range of antibiotics including carbapenems, cephalosporins and penicillins.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5825":{"model_id":"5825","model_name":"NDM-37","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8517":{"protein_sequence":{"accession":"ULB43298.1","sequence":"MELPNIMHPVAKLSTALAAALMLSGCMPGEIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLLVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGLVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITYTARMADKLR"},"dna_sequence":{"accession":"CP091926.1","fmin":"98948","fmax":"99761","strand":"+","sequence":"ATGGAATTGCCCAATATTATGCACCCGGTCGCGAAGCTGAGCACCGCATTAGCCGCTGCATTGATGCTGAGCGGGTGCATGCCCGGTGAAATCCGCCCGACGATTGGCCAGCAAATGGAAACTGGCGACCAACGGTTTGGCGATCTGGTTTTCCGCCAGCTCGCACCGAATGTCTGGCAGCACACTTCCTATCTCGACATGCCGGGTTTCGGGGCAGTCGCTTCCAACGGTTTGATCGTCAGGGATGGCGGCCGCGTGCTGTTGGTCGATACCGCCTGGACCGATGACCAGACCGCCCAGATCCTCAACTGGATCAAGCAGGAGATCAACCTGCCGGTCGCGCTGGCGGTGGTGACTCACGCGCATCAGGACAAGATGGGCGGTATGGACGCGCTGCATGCGGCGGGGATTGCGACTTATGCCAATGCGTTGTCGAACCAGCTTGCCCCGCAAGAGGGGCTGGTTGCGGCGCAACACAGCCTGACTTTCGCCGCCAATGGCTGGGTCGAACCAGCAACCGCGCCCAACTTTGGCCCGCTCAAGGTATTTTACCCCGGCCCCGGCCACACCAGTGACAATATCACCGTTGGGATCGACGGCACCGACATCGCTTTTGGTGGCTGCCTGATCAAGGACAGCAAGGCCAAGTCGCTCGGCAATCTCGGTGATGCCGACACTGAGCACTACGCCGCGTCAGCGCGCGCGTTTGGTGCGGCGTTCCCCAAGGCCAGCATGATCGTGATGAGCCATTCCGCCCCCGATAGCCGCGCCGCAATCACTTATACGGCCCGCATGGCCGACAAGCTGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3007214","ARO_id":"45958","ARO_name":"NDM-37","CARD_short_name":"NDM-37","ARO_description":"NDM-37 is a NDM beta-lactamase.","ARO_category":{"36196":{"category_aro_accession":"3000057","category_aro_cvterm_id":"36196","category_aro_name":"NDM beta-lactamase","category_aro_description":"NDM beta-lactamases or New Delhi metallo-beta-lactamases are class B beta-lactamases that confer resistance to a broad range of antibiotics including carbapenems, cephalosporins and penicillins.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5826":{"model_id":"5826","model_name":"NDM-38","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8518":{"protein_sequence":{"accession":"QWO25674.1","sequence":"MELPNIMHPVAKLSTALAAALMLSGCVPGEIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR"},"dna_sequence":{"accession":"MZ359766.1","fmin":"0","fmax":"813","strand":"+","sequence":"ATGGAATTGCCCAATATTATGCACCCGGTCGCGAAGCTGAGCACCGCATTAGCCGCTGCATTGATGCTGAGCGGGTGCGTGCCCGGTGAAATCCGCCCGACGATTGGCCAGCAAATGGAAACTGGCGACCAACGGTTTGGCGATCTGGTTTTCCGCCAGCTCGCACCGAATGTCTGGCAGCACACTTCCTATCTCGACATGCCGGGTTTCGGGGCAGTCGCTTCCAACGGTTTGATCGTCAGGGATGGCGGCCGCGTGCTGGTGGTCGATACCGCCTGGACCGATGACCAGACCGCCCAGATCCTCAACTGGATCAAGCAGGAGATCAACCTGCCGGTCGCGCTGGCGGTGGTGACTCACGCGCATCAGGACAAGATGGGCGGTATGGACGCGCTGCATGCGGCGGGGATTGCGACTTATGCCAATGCGTTGTCGAACCAGCTTGCCCCGCAAGAGGGGATGGTTGCGGCGCAACACAGCCTGACTTTCGCCGCCAATGGCTGGGTCGAACCAGCAACCGCGCCCAACTTTGGCCCGCTCAAGGTATTTTACCCCGGCCCCGGCCACACCAGTGACAATATCACCGTTGGGATCGACGGCACCGACATCGCTTTTGGTGGCTGCCTGATCAAGGACAGCAAGGCCAAGTCGCTCGGCAATCTCGGTGATGCCGACACTGAGCACTACGCCGCGTCAGCGCGCGCGTTTGGTGCGGCGTTCCCCAAGGCCAGCATGATCGTGATGAGCCATTCCGCCCCCGATAGCCGCGCCGCAATCACTCATACGGCCCGCATGGCCGACAAGCTGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36944","NCBI_taxonomy_name":"Providencia rettgeri","NCBI_taxonomy_id":"587"}}}},"ARO_accession":"3007215","ARO_id":"45959","ARO_name":"NDM-38","CARD_short_name":"NDM-38","ARO_description":"NDM-38 is a NDM beta-lactamase.","ARO_category":{"36196":{"category_aro_accession":"3000057","category_aro_cvterm_id":"36196","category_aro_name":"NDM beta-lactamase","category_aro_description":"NDM beta-lactamases or New Delhi metallo-beta-lactamases are class B beta-lactamases that confer resistance to a broad range of antibiotics including carbapenems, cephalosporins and penicillins.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5827":{"model_id":"5827","model_name":"NDM-39","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8519":{"protein_sequence":{"accession":"QYZ89892.1","sequence":"MELLNIMHPVAKLSTALAAALMLSGCMPGEIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLLVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGLVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR"},"dna_sequence":{"accession":"MZ748325.1","fmin":"0","fmax":"813","strand":"+","sequence":"ATGGAATTGCTCAATATTATGCACCCGGTCGCGAAGCTGAGCACCGCATTAGCCGCTGCATTGATGCTGAGCGGGTGCATGCCCGGTGAAATCCGCCCGACGATTGGCCAGCAAATGGAAACTGGCGACCAACGGTTTGGCGATCTGGTTTTCCGCCAGCTCGCACCGAATGTCTGGCAGCACACTTCCTATCTCGACATGCCGGGTTTCGGGGCAGTCGCTTCCAACGGTTTGATCGTCAGGGATGGCGGCCGCGTGCTGTTGGTCGATACCGCCTGGACCGATGACCAGACCGCCCAGATCCTCAACTGGATCAAGCAGGAGATCAACCTGCCGGTCGCGCTGGCGGTGGTGACTCACGCGCATCAGGACAAGATGGGCGGTATGGACGCGCTGCATGCGGCGGGGATTGCGACTTATGCCAATGCGTTGTCGAACCAGCTTGCCCCGCAAGAGGGGCTGGTTGCGGCGCAACACAGCCTGACTTTCGCCGCCAATGGCTGGGTCGAACCAGCAACCGCGCCCAACTTTGGCCCGCTCAAGGTATTTTACCCCGGCCCCGGCCACACCAGTGACAATATCACCGTTGGGATCGACGGCACCGACATCGCTTTTGGTGGCTGCCTGATCAAGGACAGCAAGGCCAAGTCGCTCGGCAATCTCGGTGATGCCGACACTGAGCACTACGCCGCGTCAGCGCGCGCGTTTGGTGCGGCGTTCCCCAAGGCCAGCATGATCGTGATGAGCCATTCCGCCCCCGATAGCCGCGCCGCAATCACTCATACGGCCCGCATGGCCGACAAGCTGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3007216","ARO_id":"45960","ARO_name":"NDM-39","CARD_short_name":"NDM-39","ARO_description":"NDM-39 is a NDM beta-lactamase.","ARO_category":{"36196":{"category_aro_accession":"3000057","category_aro_cvterm_id":"36196","category_aro_name":"NDM beta-lactamase","category_aro_description":"NDM beta-lactamases or New Delhi metallo-beta-lactamases are class B beta-lactamases that confer resistance to a broad range of antibiotics including carbapenems, cephalosporins and penicillins.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5828":{"model_id":"5828","model_name":"NDM-40","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8520":{"protein_sequence":{"accession":"QYZ89893.1","sequence":"MELRNIMHPVAKLSTALAAALMLSGCMPGEIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR"},"dna_sequence":{"accession":"MZ748326.1","fmin":"0","fmax":"813","strand":"+","sequence":"ATGGAATTGCGCAATATTATGCACCCGGTCGCGAAGCTGAGCACCGCATTAGCCGCTGCATTGATGCTGAGCGGGTGCATGCCCGGTGAAATCCGCCCGACGATTGGCCAGCAAATGGAAACTGGCGACCAACGGTTTGGCGATCTGGTTTTCCGCCAGCTCGCACCGAATGTCTGGCAGCACACTTCCTATCTCGACATGCCGGGTTTCGGGGCAGTCGCTTCCAACGGTTTGATCGTCAGGGATGGCGGCCGCGTGCTGGTGGTCGATACCGCCTGGACCGATGACCAGACCGCCCAGATCCTCAACTGGATCAAGCAGGAGATCAACCTGCCGGTCGCGCTGGCGGTGGTGACTCACGCGCATCAGGACAAGATGGGCGGTATGGACGCGCTGCATGCGGCGGGGATTGCGACTTATGCCAATGCGTTGTCGAACCAGCTTGCCCCGCAAGAGGGGATGGTTGCGGCGCAACACAGCCTGACTTTCGCCGCCAATGGCTGGGTCGAACCAGCAACCGCGCCCAACTTTGGCCCGCTCAAGGTATTTTACCCCGGCCCCGGCCACACCAGTGACAATATCACCGTTGGGATCGACGGCACCGACATCGCTTTTGGTGGCTGCCTGATCAAGGACAGCAAGGCCAAGTCGCTCGGCAATCTCGGTGATGCCGACACTGAGCACTACGCCGCGTCAGCGCGCGCGTTTGGTGCGGCGTTCCCCAAGGCCAGCATGATCGTGATGAGCCATTCCGCCCCCGATAGCCGCGCCGCAATCACTCATACGGCCCGCATGGCCGACAAGCTGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3007217","ARO_id":"45961","ARO_name":"NDM-40","CARD_short_name":"NDM-40","ARO_description":"NDM-40 is a NDM beta-lactamase.","ARO_category":{"36196":{"category_aro_accession":"3000057","category_aro_cvterm_id":"36196","category_aro_name":"NDM beta-lactamase","category_aro_description":"NDM beta-lactamases or New Delhi metallo-beta-lactamases are class B beta-lactamases that confer resistance to a broad range of antibiotics including carbapenems, cephalosporins and penicillins.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5829":{"model_id":"5829","model_name":"NDM-41","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8521":{"protein_sequence":{"accession":"UAX43328.1","sequence":"MELPNIMHPVAKVSTALAAALMLSGCMPGEIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLLVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGLVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR"},"dna_sequence":{"accession":"MZ913436.1","fmin":"0","fmax":"813","strand":"+","sequence":"ATGGAATTGCCCAATATTATGCACCCGGTCGCGAAGGTGAGCACCGCATTAGCCGCTGCATTGATGCTGAGCGGGTGCATGCCCGGTGAAATCCGCCCGACGATTGGCCAGCAAATGGAAACTGGCGACCAACGGTTTGGCGATCTGGTTTTCCGCCAGCTCGCACCGAATGTCTGGCAGCACACTTCCTATCTCGACATGCCGGGTTTCGGGGCAGTCGCTTCCAACGGTTTGATCGTCAGGGATGGCGGCCGCGTGCTGTTGGTCGATACCGCCTGGACCGATGACCAGACCGCCCAGATCCTCAACTGGATCAAGCAGGAGATCAACCTGCCGGTCGCGCTGGCGGTGGTGACTCACGCGCATCAGGACAAGATGGGCGGTATGGACGCGCTGCATGCGGCGGGGATTGCGACTTATGCCAATGCGTTGTCGAACCAGCTTGCCCCGCAAGAGGGGCTGGTTGCGGCGCAACACAGCCTGACTTTCGCCGCCAATGGCTGGGTCGAACCAGCAACCGCGCCCAACTTTGGCCCGCTCAAGGTATTTTACCCCGGCCCCGGCCACACCAGTGACAATATCACCGTTGGGATCGACGGCACCGACATCGCTTTTGGTGGCTGCCTGATCAAGGACAGCAAGGCCAAGTCGCTCGGCAATCTCGGTGATGCCGACACTGAGCACTACGCCGCGTCAGCGCGCGCGTTTGGTGCGGCGTTCCCCAAGGCCAGCATGATCGTGATGAGCCATTCCGCCCCCGATAGCCGCGCCGCAATCACTCATACGGCCCGCATGGCCGACAAGCTGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3007218","ARO_id":"45962","ARO_name":"NDM-41","CARD_short_name":"NDM-41","ARO_description":"NDM-41 is a NDM beta-lactamase.","ARO_category":{"36196":{"category_aro_accession":"3000057","category_aro_cvterm_id":"36196","category_aro_name":"NDM beta-lactamase","category_aro_description":"NDM beta-lactamases or New Delhi metallo-beta-lactamases are class B beta-lactamases that confer resistance to a broad range of antibiotics including carbapenems, cephalosporins and penicillins.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5830":{"model_id":"5830","model_name":"NDM-42","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8522":{"protein_sequence":{"accession":"UOU25745.1","sequence":"MELPNIMHPVAKLSTALAAALMLSGCMLGEIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR"},"dna_sequence":{"accession":"ON205946.1","fmin":"20","fmax":"833","strand":"+","sequence":"ATGGAATTGCCCAATATTATGCACCCGGTCGCGAAGCTGAGCACCGCATTAGCCGCTGCATTGATGCTGAGCGGGTGCATGCTCGGTGAAATCCGCCCGACGATTGGCCAGCAAATGGAAACTGGCGACCAACGGTTTGGCGATCTGGTTTTCCGCCAGCTCGCACCGAATGTCTGGCAGCACACTTCCTATCTCGACATGCCGGGTTTCGGGGCAGTCGCTTCCAACGGTTTGATCGTCAGGGATGGCGGCCGCGTGCTGGTGGTCGATACCGCCTGGACCGATGACCAGACCGCCCAGATCCTCAACTGGATCAAGCAGGAGATCAACCTGCCGGTCGCGCTGGCGGTGGTGACTCACGCGCATCAGGACAAGATGGGCGGTATGGACGCGCTGCATGCGGCGGGGATTGCGACTTATGCCAATGCGTTGTCGAACCAGCTTGCCCCGCAAGAGGGGATGGTTGCGGCGCAACACAGCCTGACTTTCGCCGCCAATGGCTGGGTCGAACCAGCAACCGCGCCCAACTTTGGCCCGCTCAAGGTATTTTACCCCGGCCCCGGCCACACCAGTGACAATATCACCGTTGGGATCGACGGCACCGACATCGCTTTTGGTGGCTGCCTGATCAAGGACAGCAAGGCCAAGTCGCTCGGCAATCTCGGTGATGCCGACACTGAGCACTACGCCGCGTCAGCGCGCGCGTTTGGTGCGGCGTTCCCCAAGGCCAGCATGATCGTGATGAGCCATTCCGCCCCCGATAGCCGCGCCGCAATCACTCATACGGCCCGCATGGCCGACAAGCTGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3007219","ARO_id":"45963","ARO_name":"NDM-42","CARD_short_name":"NDM-42","ARO_description":"NDM-42 is a NDM beta-lactamase.","ARO_category":{"36196":{"category_aro_accession":"3000057","category_aro_cvterm_id":"36196","category_aro_name":"NDM beta-lactamase","category_aro_description":"NDM beta-lactamases or New Delhi metallo-beta-lactamases are class B beta-lactamases that confer resistance to a broad range of antibiotics including carbapenems, cephalosporins and penicillins.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5831":{"model_id":"5831","model_name":"NDM-43","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8523":{"protein_sequence":{"accession":"UTQ48691.1","sequence":"MELPNIMHPVAKLSTALAAALMLSGCMPGEIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPNSRAAITHTARMANKLR"},"dna_sequence":{"accession":"ON954084.1","fmin":"0","fmax":"813","strand":"+","sequence":"ATGGAATTGCCCAATATTATGCACCCGGTCGCGAAGCTGAGCACCGCATTAGCCGCTGCATTGATGCTGAGCGGGTGCATGCCCGGTGAAATCCGCCCGACGATTGGCCAGCAAATGGAAACTGGCGACCAACGGTTTGGCGATCTGGTTTTCCGCCAGCTCGCACCGAATGTCTGGCAGCACACTTCCTATCTCGACATGCCGGGTTTCGGGGCAGTCGCTTCCAACGGTTTGATCGTCAGGGATGGCGGCCGCGTGCTGGTGGTCGATACCGCCTGGACCGATGACCAGACCGCCCAGATCCTCAACTGGATCAAGCAGGAGATCAACCTGCCGGTCGCGCTGGCGGTGGTGACTCACGCGCATCAGGACAAGATGGGCGGTATGGACGCGCTGCATGCGGCGGGGATTGCGACTTATGCCAATGCGTTGTCGAACCAGCTTGCCCCGCAAGAGGGGATGGTTGCGGCGCAACACAGCCTGACTTTCGCCGCCAATGGCTGGGTCGAACCAGCAACCGCGCCCAACTTTGGCCCGCTCAAGGTATTTTACCCCGGCCCCGGCCACACCAGTGACAATATCACCGTTGGGATCGACGGCACCGACATCGCTTTTGGTGGCTGCCTGATCAAGGACAGCAAGGCCAAGTCGCTCGGCAATCTCGGTGATGCCGACACTGAGCACTACGCCGCGTCAGCGCGCGCGTTTGGTGCGGCGTTCCCCAAGGCCAGCATGATCGTGATGAGCCATTCCGCCCCCAATAGCCGCGCCGCAATCACTCATACGGCCCGCATGGCCAACAAGCTGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3007220","ARO_id":"45964","ARO_name":"NDM-43","CARD_short_name":"NDM-43","ARO_description":"NDM-43 is a NDM beta-lactamase.","ARO_category":{"36196":{"category_aro_accession":"3000057","category_aro_cvterm_id":"36196","category_aro_name":"NDM beta-lactamase","category_aro_description":"NDM beta-lactamases or New Delhi metallo-beta-lactamases are class B beta-lactamases that confer resistance to a broad range of antibiotics including carbapenems, cephalosporins and penicillins.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5833":{"model_id":"5833","model_name":"MCR-8.4","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"8527":{"protein_sequence":{"accession":"WP_118860654.1","sequence":"MFKYLLSFKLNPVQRTWAAAFFFTTIGNIALWQTLWINVDVHNIHNLLFFASLPIFLFCFLSILLTPVMVIPYLCRPLLVVLILISACCSYFMMKYNILIDRSMVQNFFETNQAELTSYLSVPFLSTLFLLGIVPAIILALPSTDNKRGAFRIELWWLAHICIAVVLLAMVTMVFYKDYASLIRNNMQIKDQALPFNFVRNTNGYLKRKYQASSTILQSVGEDAVRPIYSNAPPKLVVVVVGETARAQNFQLNGYSRVTNPYLSRRHDVISFKNVSSCGTATAISLPCMFSRMSRNEYNEVRAASEENLLDILKRTGVEVLWRNNNNGGCKGICKRVPTDDMPAMKVIGECVNKDGTCFDEVLLNQLSSRINAMQGDALIVLHQMGSHGPTYFERYPSTSKVFRPTCDSNLIEKCSNKELVNTYDNTLVYTDRMLSKTIELLQRYSGMRDVAMIYLSDHGESLGESGIYLHGTPYIIAPNEQTHIPMFMWFSSSFAQHSKLNLECLTGNADKQYSHDNFYHSILGLFNVKTSVYKPELDMFTLCRQSDHTPLSSAVVREKTDGNG"},"dna_sequence":{"accession":"MH791448.1","fmin":"0","fmax":"1698","strand":"+","sequence":"ATGTTCAAGTATCTTTTATCTTTCAAACTGAACCCGGTACAACGGACCTGGGCTGCAGCATTTTTTTTCACTACAATCGGCAACATAGCACTTTGGCAAACACTATGGATTAATGTAGATGTTCATAATATACATAATCTACTTTTTTTTGCCAGTCTGCCAATATTTCTTTTCTGCTTTCTAAGTATCTTACTTACACCAGTCATGGTTATTCCATATTTATGCAGGCCTCTACTTGTAGTTCTTATTCTAATCAGTGCCTGCTGTAGTTATTTCATGATGAAATACAACATATTAATTGACCGCAGCATGGTGCAAAACTTTTTTGAGACTAATCAGGCTGAATTAACATCATACTTATCCGTTCCTTTTCTTTCCACTCTATTTCTACTTGGCATTGTACCAGCAATTATCCTGGCGTTGCCTTCAACAGACAATAAGCGGGGAGCTTTTAGAATTGAATTGTGGTGGTTGGCGCATATTTGCATAGCTGTAGTCTTATTAGCCATGGTTACCATGGTGTTTTATAAGGATTACGCATCTCTCATACGAAACAATATGCAGATTAAAGACCAGGCTTTACCTTTTAACTTTGTGCGTAATACGAATGGTTACCTTAAAAGAAAATACCAGGCATCTTCAACAATTCTACAAAGCGTGGGGGAGGATGCTGTACGTCCAATATATTCAAATGCTCCACCGAAACTGGTGGTTGTCGTCGTGGGCGAAACCGCCAGAGCACAGAATTTCCAGCTGAATGGCTATTCGCGGGTAACCAACCCCTATCTTTCCAGACGACATGATGTTATCAGTTTCAAAAATGTGTCGTCATGCGGAACGGCTACCGCAATATCACTACCCTGCATGTTCTCGCGAATGTCACGTAACGAATACAATGAAGTCCGTGCCGCATCAGAAGAAAACTTGCTGGATATCCTTAAACGTACAGGTGTTGAGGTGCTATGGCGCAACAATAACAATGGTGGTTGTAAGGGAATCTGCAAGCGAGTACCCACAGATGATATGCCGGCAATGAAAGTAATTGGGGAATGTGTTAACAAAGATGGTACATGCTTTGATGAGGTGTTATTAAATCAACTCTCATCCCGAATTAATGCAATGCAGGGTGATGCGCTTATTGTTTTACATCAAATGGGCAGTCATGGACCAACATATTTTGAACGTTATCCGTCTACAAGTAAAGTCTTTCGCCCAACTTGCGACAGCAACCTGATCGAAAAATGCTCAAATAAAGAACTGGTCAATACATACGACAATACGCTAGTTTATACTGATCGTATGCTGAGCAAAACTATTGAACTGTTGCAACGTTATTCCGGGATGCGTGACGTTGCTATGATATATCTTTCTGATCATGGAGAATCGCTGGGGGAAAGCGGAATATATCTTCATGGCACACCATATATTATTGCCCCCAATGAACAAACACACATCCCGATGTTTATGTGGTTTTCGTCTTCATTCGCGCAGCATTCCAAATTAAATCTAGAATGCCTGACCGGTAATGCCGACAAACAATACAGTCATGATAATTTTTATCATTCAATACTTGGTCTCTTCAACGTAAAAACCAGTGTATATAAACCGGAGTTAGATATGTTTACTCTATGTCGACAATCTGACCACACACCACTGTCTTCCGCAGTTGTAAGAGAGAAAACAGATGGGAATGGTTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"45686","NCBI_taxonomy_name":"Raoultella ornithinolytica","NCBI_taxonomy_id":"54291"}}}},"ARO_accession":"3007228","ARO_id":"45974","ARO_name":"MCR-8.4","CARD_short_name":"MCR-8.4","ARO_description":"An MCR-8-type colistin resistance gene variant.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5834":{"model_id":"5834","model_name":"MCR-8.2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"8603":{"protein_sequence":{"accession":"QIF88262.1","sequence":"MFKYLLSFKLNPVQRTWAAAFFFTTIGNIALWQTLWINVDVHNIHNLLFFVSLPIFLFCFLSILLTPVMVIPYLCRPLLVVLILISACCSYFMMKYNILIDRSMVQNFFETNQAELTSYLSVPFLSTLFLLGIVPAIILALPSTDNKRGAFRIELWWLAHICIAVVLLAMVTMVFYKDYASLIRNNMQIKDQALPFNFVRNTNGYLKRKYQASSTILQSVGEDAVRPIYSNSPPKLVVVVVGETARAQNFQLNGYSRVTNPYLSRRHDVISFKNVSSCGTATAISLPCMFSRMSRNEYNEVRAASEENLLDILKRTGVEVLWRNNNNGGCKGICKRVPTDDMPAMKVIGECVNKDGTCFDEVLLYQLSSRINAMQGDALIVLHQMGSHGPTYFERYPSTSKVFSPTCDSNLIEKCSNKELVNTYDNTLVYTDRMLSKTIELLQRYSGMRDVAMIYLSDHGESLGESGIYLHGTPYIIAPKEQTHIPMFMWFSSSFAQHSKLNLECLTGNADKQYSHDNFYHSILGLFNVKTSVYKPELDMFTLCRQSDHTPLSSAVVREKTDGNG"},"dna_sequence":{"accession":"CP047337.1","fmin":"174843","fmax":"176541","strand":"+","sequence":"ATGTTCAAGTATCTTTTATCTTTCAAACTGAACCCGGTACAACGGACCTGGGCTGCAGCATTTTTTTTCACTACAATCGGCAACATAGCACTTTGGCAAACACTATGGATTAATGTAGATGTTCATAATATACATAATCTACTTTTTTTTGTCAGTCTGCCAATATTTCTTTTCTGCTTTCTAAGTATCTTACTTACACCAGTCATGGTTATTCCATATTTATGCAGGCCTCTACTTGTAGTTCTTATTCTAATCAGTGCCTGCTGTAGTTATTTCATGATGAAATACAACATATTAATTGACCGCAGCATGGTGCAAAACTTTTTTGAGACTAATCAGGCTGAATTAACATCATACTTATCCGTTCCTTTTCTTTCCACTCTATTTCTACTTGGCATTGTACCAGCAATTATCCTGGCGTTGCCTTCAACAGACAATAAGCGGGGAGCTTTTAGAATTGAATTGTGGTGGTTGGCGCATATTTGCATAGCTGTAGTCTTATTAGCCATGGTTACCATGGTGTTTTATAAGGATTACGCATCTCTCATACGAAACAATATGCAGATTAAAGACCAAGCTTTACCTTTTAACTTTGTGCGTAATACGAATGGTTACCTTAAAAGAAAATACCAGGCATCTTCAACAATTCTACAAAGCGTGGGGGAGGATGCTGTACGTCCAATATATTCAAATTCTCCACCGAAACTGGTGGTTGTCGTCGTGGGCGAAACCGCCAGAGCACAGAATTTCCAGCTGAATGGCTATTCGCGGGTAACCAACCCCTATCTTTCCAGACGACATGATGTTATCAGTTTCAAAAATGTGTCGTCATGCGGAACGGCTACCGCAATATCACTACCCTGCATGTTCTCGCGAATGTCACGTAACGAATACAATGAAGTCCGTGCCGCATCAGAAGAAAACTTGCTGGATATCCTTAAACGTACAGGTGTTGAGGTGCTATGGCGCAACAATAACAATGGTGGTTGTAAGGGAATCTGCAAGCGAGTACCCACAGATGATATGCCGGCAATGAAAGTAATTGGGGAATGTGTTAACAAAGATGGTACATGCTTTGATGAGGTGTTATTATATCAACTCTCATCCCGAATTAATGCAATGCAGGGTGATGCGCTTATTGTTTTACATCAAATGGGCAGTCATGGACCAACATATTTTGAACGTTATCCGTCTACAAGTAAAGTCTTTAGCCCAACTTGCGACAGCAACCTGATCGAAAAATGCTCAAATAAAGAACTGGTCAATACATACGACAATACGCTAGTTTATACTGATCGTATGCTGAGCAAAACTATTGAACTGTTGCAACGTTATTCCGGGATGCGTGACGTTGCTATGATATATCTTTCTGATCATGGAGAATCGCTGGGGGAAAGCGGAATATATCTTCATGGCACACCATATATTATTGCCCCCAAGGAACAAACACACATCCCGATGTTTATGTGGTTTTCGTCTTCATTCGCGCAGCATTCCAAATTAAATCTAGAATGCCTGACCGGTAATGCCGACAAACAATACAGTCATGATAATTTTTATCATTCAATACTTGGTCTCTTCAACGTAAAAACCAGTGTATATAAACCGGAGTTAGATATGTTTACTCTATGTCGACAATCTGACCACACACCACTGTCTTCCGCAGTTGTAAGAGAGAAAACAGATGGGAATGGTTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3007229","ARO_id":"45975","ARO_name":"MCR-8.2","CARD_short_name":"MCR-8.2","ARO_description":"An MCR-8-type colistin resistance gene variant.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5835":{"model_id":"5835","model_name":"MCR-1.34","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"8529":{"protein_sequence":{"accession":"WP_231236808.1","sequence":"MIQHTSVWYRRSVSPFVLVASVAVFLTATANLTFFDKISQTYPIADNLGFVLTIAVVLFGAMLLITTLLSSYRYVLKPVLILLLIMGAVTSYFTDTYGTVYDTTMLQNALQTDQAETKDLLNAAFIMRIIGLGVLPSLLVAFVKVDYPTWGKGLMRRLGLIVASLALILLPVVAFSSHYASFFRVHKPLRSYVNPIMPIYSVGKLASIEYKKASAPKDTIYHAKDAVQATKPDMRKPRLVVFVVGETARADHVSFNGYERDTFPQLAKIDGVTNFSNVTSCGTSTAYSVPCMFSYLGADEYDVDTAKYQENVLDTLDRLGVSILWRDNNSDSKGVMDKLPKAQFADYKSATNNAICNTNPYNECRDVGMLVGLDDFVAANNGKDMLIMLHQMGNHGPAYFKRYDEKFAKFTPVCEGNELAKCEHQSLINAYDNALLATDDFIAQSIQWLQTHSNAYDVSMLYVSDHGESLGENGVYLHGMPNAFAPKEQRSVPAFFWTDKQTGITPMATDTVLTHDAITPTLLKLFDVTADKVKDRTAFIR"},"dna_sequence":{"accession":"MZ450868.1","fmin":"0","fmax":"1626","strand":"+","sequence":"ATGATACAGCATACTTCTGTGTGGTACCGACGCTCGGTCAGTCCGTTTGTTCTTGTGGCGAGTGTTGCCGTTTTCTTGACCGCGACCGCCAATCTTACCTTTTTTGATAAAATCAGCCAAACCTATCCCATCGCGGACAATCTCGGCTTTGTGCTGACGATCGCTGTCGTGCTCTTTGGCGCGATGCTACTGATCACCACGCTGTTATCATCGTATCGCTATGTGCTAAAGCCTGTGTTGATTTTGCTATTAATCATGGGCGCGGTGACCAGTTATTTTACTGACACTTATGGCACGGTCTATGATACGACCATGCTCCAAAATGCCCTACAGACCGACCAAGCCGAGACCAAGGATCTATTAAACGCAGCGTTTATCATGCGTATCATTGGTTTGGGTGTGCTACCAAGTTTGCTTGTGGCTTTTGTTAAGGTGGATTATCCGACTTGGGGCAAGGGTTTGATGCGCCGATTGGGCTTGATCGTGGCAAGTCTTGCGCTGATTTTACTGCCTGTGGTGGCGTTCAGCAGTCATTATGCCAGTTTCTTTCGCGTGCATAAGCCGCTGCGTAGCTATGTCAATCCGATCATGCCAATCTACTCGGTGGGTAAGCTTGCCAGTATTGAGTATAAAAAAGCCAGTGCGCCAAAAGATACCATTTATCACGCCAAAGACGCGGTACAAGCAACCAAGCCTGATATGCGTAAGCCACGCCTAGTGGTGTTCGTCGTCGGTGAGACGGCACGCGCCGATCATGTCAGCTTCAATGGCTATGAGCGCGATACTTTCCCACAGCTTGCCAAGATCGATGGCGTGACCAATTTTAGCAATGTCACATCGTGCGGCACATCGACGGCGTATTCTGTGCCGTGTATGTTCAGCTATCTGGGCGCGGATGAGTATGATGTCGATACCGCCAAATACCAAGAAAATGTGCTGGATACGCTGGATCGCTTGGGCGTAAGTATCTTGTGGCGTGATAATAATTCGGACTCAAAAGGCGTGATGGATAAGCTGCCAAAAGCGCAATTTGCCGATTATAAATCCGCGACCAACAACGCCATCTGCAACACCAATCCTTATAACGAATGCCGCGATGTCGGTATGCTCGTTGGCTTAGATGACTTTGTCGCTGCCAATAACGGCAAAGATATGCTGATCATGCTGCACCAAATGGGCAATCACGGGCCTGCGTATTTTAAGCGATATGATGAAAAGTTTGCCAAATTCACGCCAGTGTGTGAAGGTAATGAGCTTGCCAAGTGCGAACATCAGTCCTTGATCAATGCTTATGACAATGCCTTGCTTGCCACCGATGATTTCATCGCTCAAAGTATCCAGTGGCTGCAGACGCACAGCAATGCCTATGATGTCTCAATGCTGTATGTCAGCGATCATGGCGAAAGTCTGGGTGAGAACGGTGTCTATCTACATGGTATGCCAAATGCCTTTGCACCAAAAGAACAGCGCAGTGTGCCTGCATTTTTCTGGACGGATAAGCAAACTGGCATCACGCCAATGGCAACCGATACCGTCCTGACCCATGACGCGATCACGCCGACATTATTAAAGCTGTTTGATGTCACCGCGGACAAAGTCAAAGACCGCACCGCATTCATCCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3007230","ARO_id":"45976","ARO_name":"MCR-1.34","CARD_short_name":"MCR-1.34","ARO_description":"An MCR-1-type colistin resistance gene variant.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5836":{"model_id":"5836","model_name":"MCR-4.6","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"8530":{"protein_sequence":{"accession":"AXI82465.1","sequence":"MISRFKTLSVNQFTFITALFYVAIFNLPLFGIVRKGIEKQPEVDPLFIASMPLFLTFALSFLFSIFTVKYLLKPFFIVLTLLSSSVFFAAYQYNVVFDYGMIENTFQTHPAEALMYVNLASITNLLLTGLLPSYLIYKADIHYQPFFKELLHKLAFMLLMFVGIGIVAFFYYQDYAAFVRNNSELRRYIVPTYFVSSASKYLNEHYLQTPMEYQQLGLDAKNASRNPNTKPNLLVFVVGETARSMSYQYYGYNKPTNAHTQNQGLIAFNDTSSCGTATAVSLPCMFSRMGRADYDPRRANAQDTVIDVLSHSGIKVQWFDNDSGCKGVCDQVENLTIDLKSDPKLCSGQYCFDQVLLNKLDKILAVAPSQDTVIFLHIIGSHGPTYYLRYPPEHRKFIPDCPRSDIQNCSQEELINTYDNTILYTDFILSEVVNKLKGKQDMFDTAMLYLSDHGESLGEKGMYLHGAPYSIAPKEQTSVPMLAWVSNDFSQDNQLNMTCVAQRAEQGGFSHDNLFDSLLGLMNVKTTVYQSQLDIFAPCRY"},"dna_sequence":{"accession":"MH423812.1","fmin":"0","fmax":"1626","strand":"+","sequence":"GTGATTTCTAGATTTAAGACGTTATCGGTTAACCAATTCACTTTCATCACTGCGTTGTTTTATGTTGCCATTTTCAATCTACCGCTCTTTGGTATAGTGCGAAAAGGAATTGAAAAACAACCAGAAGTTGATCCCCTTTTCATCGCATCTATGCCGCTATTTTTAACATTTGCGCTGAGTTTTTTGTTTTCAATTTTTACCGTCAAATACCTGCTGAAGCCCTTTTTTATCGTATTGACGTTACTTTCCTCAAGTGTATTTTTTGCAGCCTATCAATACAATGTCGTGTTTGACTACGGCATGATAGAAAACACGTTTCAAACACATCCTGCTGAAGCATTGATGTATGTAAATCTTGCATCAATTACCAATCTACTGCTGACTGGGCTATTACCGTCATATCTTATTTATAAGGCCGATATTCATTATCAGCCCTTTTTTAAGGAGTTATTGCATAAATTAGCCTTTATGCTGCTAATGTTCGTTGGCATTGGGATAGTCGCCTTTTTTTACTATCAAGATTATGCTGCATTTGTTCGAAACAACAGTGAGTTAAGGCGTTACATTGTCCCTACCTATTTTGTCAGTAGTGCATCTAAATATCTCAATGAGCACTATTTGCAGACGCCCATGGAATACCAACAACTTGGCCTAGATGCGAAGAATGCCAGTCGTAACCCGAACACTAAACCTAACTTATTAGTGTTTGTTGTGGGTGAAACTGCGCGCTCAATGAGCTATCAATATTATGGATATAACAAGCCAACCAATGCTCATACCCAAAATCAGGGGCTGATTGCGTTTAACGATACTAGCTCATGCGGCACGGCCACGGCGGTGTCTCTACCCTGTATGTTTTCACGAATGGGGCGGGCAGACTATGATCCTCGCCGTGCTAATGCTCAAGACACAGTGATTGATGTGTTAAGTCATAGTGGTATAAAAGTACAGTGGTTTGATAATGATTCTGGCTGTAAAGGTGTGTGTGATCAGGTTGAAAATCTCACGATAGATTTGAAGAGTGATCCGAAGCTGTGTTCTGGCCAATATTGTTTTGACCAAGTATTGCTCAACAAATTAGATAAAATTCTGGCAGTAGCACCAAGTCAAGATACAGTAATTTTTTTGCATATCATTGGTAGTCATGGACCAACTTATTATCTTAGATACCCGCCAGAGCATCGTAAATTTATACCGGATTGTCCGCGCAGTGATATTCAAAATTGCAGTCAAGAAGAACTGATTAACACCTACGACAACACTATTCTATATACGGATTTTATTCTCAGTGAAGTGGTGAATAAATTAAAAGGTAAGCAGGATATGTTCGATACTGCAATGCTGTATCTCTCTGACCATGGTGAGTCTTTGGGTGAAAAGGGCATGTATTTACATGGTGCGCCCTATAGTATTGCACCGAAAGAACAAACTAGCGTACCAATGCTGGCTTGGGTATCTAATGACTTTAGCCAAGATAATCAGTTGAACATGACTTGTGTTGCACAGCGAGCAGAACAGGGCGGCTTTTCCCACGACAATTTGTTCGACAGTTTGCTAGGACTTATGAATGTAAAAACCACCGTCTATCAGAGCCAACTCGATATTTTTGCACCTTGCAGGTATTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35810","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Kedougou","NCBI_taxonomy_id":"358771"}}}},"ARO_accession":"3007231","ARO_id":"45977","ARO_name":"MCR-4.6","CARD_short_name":"MCR-4.6","ARO_description":"An MCR-4-type colistin resistance gene variant.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5837":{"model_id":"5837","model_name":"MCR-1.27","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"8604":{"protein_sequence":{"accession":"WP_163397051.1","sequence":"MMQHTSVWCRRSVSPFVLVASVAVFLTATANLTFFDKISQTYPIADNLGFVLTIAVVLFGAMLLITTLLSSYRYVLKPVLILLLIMGAVTSYFTDTYGTVYDTTMLQNALQTDQAETKDLLNAAFIMRIIGLGVLPSLLVAFVKVDYPTWGKGLMRRLGLIVASLALILLPVVAFSSHYASFFRVHKPLRSYVNPIMPIYSVGKLASIEYKKASAPKDTIYHAKDAVQATKPDMRKPRLVVFVVGETARADHVSFNGYERDTFPQLAKIDGVTNFSNVTSCGTSTAYSVPCMFSYLGADEYDVDTAKYQENVLDTLDRLGVSILWRDNNSDSKGVMDKLPKAQFADYKSATNNAICNTNPYNECRDVGMLVGLDDFVAANNGKDMLIMLHQMGNHGPAYFKRYDEKFAKFTPVCEGNELAKCEHQSLINAYDNALLATDDFIAQSIQWLQTHSNAYDVSMLYVSDHGESLGENGVYLHGMPNAFAPKEQRSVPAFFWTDKQTGITPMATDTVLTHDAITPTLLKLFDVTADKVKDRTAFIR"},"dna_sequence":{"accession":"JAAGSB010000042.1","fmin":"27546","fmax":"29172","strand":"-","sequence":"ATGATGCAGCATACTTCTGTGTGGTGCCGACGCTCGGTCAGTCCGTTTGTTCTTGTGGCGAGTGTTGCCGTTTTCTTGACCGCGACCGCCAATCTTACCTTTTTTGATAAAATCAGCCAAACCTATCCCATCGCGGACAATCTCGGCTTTGTGCTGACGATCGCTGTCGTGCTCTTTGGCGCGATGCTACTGATCACCACGCTGTTATCATCGTATCGCTATGTGCTAAAGCCTGTGTTGATTTTGCTATTAATCATGGGCGCGGTGACCAGTTATTTTACTGACACTTATGGCACGGTCTATGATACGACCATGCTCCAAAATGCCCTACAGACCGACCAAGCCGAGACCAAGGATCTATTAAACGCAGCGTTTATCATGCGTATCATTGGTTTGGGTGTGCTACCAAGTTTGCTTGTGGCTTTTGTTAAGGTGGATTATCCGACTTGGGGCAAGGGTTTGATGCGCCGATTGGGCTTGATCGTGGCAAGTCTTGCGCTGATTTTACTGCCTGTGGTGGCGTTCAGCAGTCATTATGCCAGTTTCTTTCGCGTGCATAAGCCGCTGCGTAGCTATGTCAATCCGATCATGCCAATCTACTCGGTGGGTAAGCTTGCCAGTATTGAGTATAAAAAAGCCAGTGCGCCAAAAGATACCATTTATCACGCCAAAGACGCGGTACAAGCAACCAAGCCTGATATGCGTAAGCCACGCCTAGTGGTGTTCGTCGTCGGTGAGACGGCACGCGCCGATCATGTCAGCTTCAATGGCTATGAGCGCGATACTTTCCCACAGCTTGCCAAGATCGATGGCGTGACCAATTTTAGCAATGTCACATCGTGCGGCACATCGACGGCGTATTCTGTGCCGTGTATGTTCAGCTATCTGGGCGCGGATGAGTATGATGTCGATACCGCCAAATACCAAGAAAATGTGCTGGATACGCTGGATCGCTTGGGCGTAAGTATCTTGTGGCGTGATAATAATTCGGACTCAAAAGGCGTGATGGATAAGCTGCCAAAAGCGCAATTTGCCGATTATAAATCCGCGACCAACAACGCCATCTGCAACACCAATCCTTATAACGAATGCCGCGATGTCGGTATGCTCGTTGGCTTAGATGACTTTGTCGCTGCCAATAACGGCAAAGATATGCTGATCATGCTGCACCAAATGGGCAATCACGGGCCTGCGTATTTTAAGCGATATGATGAAAAGTTTGCCAAATTCACGCCAGTGTGTGAAGGTAATGAGCTTGCCAAGTGCGAACATCAGTCCTTGATCAATGCTTATGACAATGCCTTGCTTGCCACCGATGATTTCATCGCTCAAAGTATCCAGTGGCTGCAGACGCACAGCAATGCCTATGATGTCTCAATGCTGTATGTCAGCGATCATGGCGAAAGTCTGGGTGAGAACGGTGTCTATCTACATGGTATGCCAAATGCCTTTGCACCAAAAGAACAGCGCAGTGTGCCTGCATTTTTCTGGACGGATAAGCAAACTGGCATCACGCCAATGGCAACCGATACCGTCCTGACCCATGACGCGATCACGCCGACATTATTAAAGCTGTTTGATGTCACCGCGGACAAAGTCAAAGACCGCACCGCATTCATCCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3007232","ARO_id":"45978","ARO_name":"MCR-1.27","CARD_short_name":"MCR-1.27","ARO_description":"An MCR-1-type colistin resistance gene variant.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5838":{"model_id":"5838","model_name":"MCR-1.18","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"8532":{"protein_sequence":{"accession":"WP_106743337.1","sequence":"MMQHTSVWDRRSVSPFVLVASVAVFLTATANLTFFDKISQTYPIADNLGFVLTIAVVLFGAMLLITTLLSSYRYVLKPVLILLLIMGAVTSYFTDTYGTVYDTTMLQNALQTDQAETKDLLNAAFIMRIIGLGVLPSLLVAFVKVDYPTWGKGLMRRLGLIVASLALILLPVVAFSSHYASFFRVHKPLRSYVNPIMPIYSVGKLASIEYKKASAPKDTIYHAKDAVQATKPDMRKPRLVVFVVGETARADHVSFNGYERDTFPQLAKIDGVTNFSNVTSCGTSTAYSVPCMFSYLGADEYDVDTAKYQENVLDTLDRLGVSILWRDNNSDSKGVMDKLPKAQFADYKSATNNAICNTNPYNECRDVGMLVGLDDFVAANNGKDMLIMLHQMGNHGPAYFKRYDEKFAKFTPVCEGNELAKCEHQSLINAYDNALLATDDFIAQSIQWLQTHSNAYDVSMLYVSDHGESLGENGVYLHGMPNAFAPKEQRSVPAFFWTDKQTGITPMATDTVLTHDAITPTLLKLFDVTADKVKDRTAFIR"},"dna_sequence":{"accession":"PGLM01000025.1","fmin":"10887","fmax":"12513","strand":"+","sequence":"ATGATGCAGCATACTTCTGTGTGGGACCGACGCTCGGTCAGTCCGTTTGTTCTTGTGGCGAGTGTTGCCGTTTTCTTGACCGCGACCGCCAATCTTACCTTTTTTGATAAAATCAGCCAAACCTATCCCATCGCGGACAATCTCGGCTTTGTGCTGACGATCGCTGTCGTGCTCTTTGGCGCGATGCTACTGATCACCACGCTGTTATCATCGTATCGCTATGTGCTAAAGCCTGTGTTGATTTTGCTATTAATCATGGGCGCGGTGACCAGTTATTTTACTGACACTTATGGCACGGTCTATGATACGACCATGCTCCAAAATGCCCTACAGACCGACCAAGCCGAGACCAAGGATCTATTAAACGCAGCGTTTATCATGCGTATCATTGGTTTGGGTGTGCTACCAAGTTTGCTTGTGGCTTTTGTTAAGGTGGATTATCCGACTTGGGGCAAGGGTTTGATGCGCCGATTGGGCTTGATCGTGGCAAGTCTTGCGCTGATTTTACTGCCTGTGGTGGCGTTCAGCAGTCATTATGCCAGTTTCTTTCGCGTGCATAAGCCGCTGCGTAGCTATGTCAATCCGATCATGCCAATCTACTCGGTGGGTAAGCTTGCCAGTATTGAGTATAAAAAAGCCAGTGCGCCAAAAGATACCATTTATCACGCCAAAGACGCGGTACAAGCAACCAAGCCTGATATGCGTAAGCCACGCCTAGTGGTGTTCGTCGTCGGTGAGACGGCACGCGCCGATCATGTCAGCTTCAATGGCTATGAGCGCGATACTTTCCCACAGCTTGCCAAGATCGATGGCGTGACCAATTTTAGCAATGTCACATCGTGCGGCACATCGACGGCGTATTCTGTGCCGTGTATGTTCAGCTATCTGGGCGCGGATGAGTATGATGTCGATACCGCCAAATACCAAGAAAATGTGCTGGATACGCTGGATCGCTTGGGCGTAAGTATCTTGTGGCGTGATAATAATTCGGACTCAAAAGGCGTGATGGATAAGCTGCCAAAAGCGCAATTTGCCGATTATAAATCCGCGACCAACAACGCCATCTGCAACACCAATCCTTATAACGAATGCCGCGATGTCGGTATGCTCGTTGGCTTAGATGACTTTGTCGCTGCCAATAACGGCAAAGATATGCTGATCATGCTGCACCAAATGGGCAATCACGGGCCTGCGTATTTTAAGCGATATGATGAAAAGTTTGCCAAATTCACGCCAGTGTGTGAAGGTAATGAGCTTGCCAAGTGCGAACATCAGTCCTTGATCAATGCTTATGACAATGCCTTGCTTGCCACCGATGATTTCATCGCTCAAAGTATCCAGTGGCTGCAGACGCACAGCAATGCCTATGATGTCTCAATGCTGTATGTCAGCGATCATGGCGAAAGTCTGGGTGAGAACGGTGTCTATCTACATGGTATGCCAAATGCCTTTGCACCAAAAGAACAGCGCAGTGTGCCTGCATTTTTCTGGACGGATAAGCAAACTGGCATCACGCCAATGGCAACCGATACCGTCCTGACCCATGACGCGATCACGCCGACATTATTAAAGCTGTTTGATGTCACCGCGGACAAAGTCAAAGACCGCACCGCATTCATCCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3007233","ARO_id":"45979","ARO_name":"MCR-1.18","CARD_short_name":"MCR-1.18","ARO_description":"An MCR-1-type colistin resistance gene variant.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5839":{"model_id":"5839","model_name":"MCR-1.23","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"8533":{"protein_sequence":{"accession":"WP_160164897.1","sequence":"MMQHTSVWYRRSVIPFVLVASVAVFLTATANLTFFDKISQTYPIADNLGFVMTIAVLLFGPMLLITTMLSSHRYVLKTVLILLLIMDAVTNYFTDTYGTVYDTTMLQNALQTDQAETKDLLNAAFIMRIIGLGVLPSLLVAFVKVDYPTWGKGLMRRLGLIVASLALILLPVVAFSSHYASFFRVHKPLRSYVNPIMPIYSVGKLASIEYKKASAPKDTIYHAKDAVQATKPDMRKPRLVVFVVGETARADHVSFNGYERDTFPQLAKIDGVTNFSNVTSCGTSTAYSVPCMFSYLGADEYDVDTAKYQENVLDTLDRLGVSILWRDNNSDSKGVMDKLPKAQFADYKSATNNAICNTNPYNECRDVGMLVGLDDFVAANNGKDMLIMLHQMGNHGPAYFKRYDEKFAKFTPVCEGNELAKCEHQSLINAYDNALLATDDFIAQSIQWLQTHSNAYDVSMLYVSDHGESLGENGVYLHGMPNAFAPKEQRSVPAFFWTDKQTGITPMATDTVLTHDAITPTLLKLFDVTADKVKDRTAFIR"},"dna_sequence":{"accession":"MN873697.1","fmin":"0","fmax":"1626","strand":"+","sequence":"ATGATGCAGCATACTTCTGTGTGGTACCGACGCTCGGTCATTCCGTTTGTTCTTGTGGCGAGTGTTGCCGTTTTCTTGACCGCGACCGCCAATCTTACCTTTTTTGATAAAATCAGCCAAACCTATCCCATCGCGGACAATCTCGGCTTTGTGATGACAATCGCTGTCTTGCTCTTTGGTCCGATGCTACTGATCACCACGATGTTATCATCGCATCGCTATGTGCTAAAGACTGTGTTGATTTTGCTCTTAATCATGGACGCGGTGACCAATTATTTTACTGACACTTATGGCACGGTCTATGATACGACCATGCTCCAAAATGCCCTACAGACCGACCAAGCCGAGACCAAGGATCTATTAAACGCAGCGTTTATCATGCGTATCATTGGTTTGGGTGTGCTACCAAGTTTGCTNGTGGCTTTTGTTAAGGTGGATTATCCGACTTGGGGCAAGGGTTTGATGCGCCGATTGGGCTTGATCGTGGCAAGTCTTGCGCTGATTTTACTGCCTGTGGTGGCGTTCAGCAGTCATTATGCCAGTTTCTTTCGCGTGCATAAGCCGCTGCGTAGCTATGTCAATCCGATCATGCCAATCTACTCGGTGGGTAAGCTTGCCAGTATTGAGTATAAAAAAGCCAGTGCGCCAAAAGATACCATTTATCACGCCAAAGACGCGGTACAAGCAACCAAGCCTGATATGCGTAAGCCACGCCTAGTGGTGTTCGTCGTCGGTGAGACGGCACGCGCCGATCATGTCAGCTTCAATGGCTATGAGCGCGATACTTTCCCACAGCTTGCCAAGATCGATGGCGTGACCAATTTTAGCAATGTCACATCGTGCGGCACATCGACGGCGTATTCTGTGCCGTGTATGTTCAGCTATCTGGGCGCGGATGAGTATGATGTCGATACCGCCAAATACCAAGAAAATGTGCTGGATACGCTGGATCGCTTGGGCGTAAGTATCTTGTGGCGTGATAATAATTCGGACTCAAAAGGCGTGATGGATAAGCTGCCAAAAGCGCAATTTGCCGATTATAAATCCGCGACCAACAACGCCATCTGCAACACCAATCCTTATAACGAATGCCGCGATGTCGGTATGCTCGTTGGCTTAGATGACTTTGTCGCTGCCAATAACGGCAAAGATATGCTGATCATGCTGCACCAAATGGGCAATCACGGGCCTGCGTATTTTAAGCGATATGATGAAAAGTTTGCCAAATTCACGCCAGTGTGTGAAGGTAATGAGCTTGCCAAGTGCGAACATCAGTCCTTGATCAATGCTTATGACAATGCCTTGCTTGCCACCGATGATTTCATCGCTCAAAGTATCCAGTGGCTGCAGACGCACAGCAATGCCTATGATGTCTCAATGCTGTATGTCAGCGATCATGGCGAAAGTCTGGGTGAGAACGGTGTCTATCTACATGGTATGCCAAATGCCTTTGCACCAAAAGAACAGCGCAGTGTGCCTGCATTTTTCTGGACGGATAAGCAAACTGGCATCACGCCAATGGCAACCGATACCGTCCTGACCCATGACGCGATCACGCCGACATTATTAAAGCTGTTTGATGTCACCGCGGACAAAGTCAAAGACCGCACCGCATTCATCCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35672","NCBI_taxonomy_name":"Salmonella enterica","NCBI_taxonomy_id":"28901"}}}},"ARO_accession":"3007234","ARO_id":"45980","ARO_name":"MCR-1.23","CARD_short_name":"MCR-1.23","ARO_description":"An MCR-1-type colistin resistance gene variant.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5840":{"model_id":"5840","model_name":"MCR-1.20","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"8534":{"protein_sequence":{"accession":"WP_140423329.1","sequence":"MMQHTSVWYRRSVSPFVLVASVAVFLTATANLTFFDKISQTYPIADNLGFVLTIAVVLFGALLLITTLLSSYRYVLKPVLILLLIMGAVTSYFTDTYGTVYDTTMLQNALQTDQAETKDLLNAAFIMRIIGLGVLPSLLVAFVKVDYPTWGKGLMRRLGLIVASLALILLPVVAFSSHYASFFRVHKPLRSYVNPIMPIYSVGKLASIEYKKASAPKDTIYHAKDAVQATKPDMRKPRLVVFVVGETARADHVSFNGYERDTFPQLAKIDGVTNFSNVTSCGTSTAYSVPCMFSYLGADEYDVDTAKYQENVLDTLDRLGVSILWRDNNSDSKGVMDKLPKAQFADYKSATNNAICNTNPYNECRDVGMLVGLDDFVAANNGKDMLIMLHQMGNHGPAYFKRYDEKFAKFTPVCEGNELAKCEHQSLINAYDNALLATDDFIAQSIQWLQTHSNAYDVSMLYVSDHGESLGENGVYLHGMPNAFAPKEQRSVPAFFWTDKQTGITPMATDTVLTHDAITPTLLKLFDVTADKVKDRTAFIR"},"dna_sequence":{"accession":"LS398440.1","fmin":"0","fmax":"1626","strand":"+","sequence":"ATGATGCAGCATACTTCTGTGTGGTACCGACGCTCGGTCAGTCCGTTTGTTCTTGTGGCGAGTGTTGCCGTTTTCTTGACCGCGACCGCCAATCTTACCTTTTTTGATAAAATCAGCCAAACCTATCCCATCGCGGACAATCTCGGCTTTGTGCTGACGATCGCTGTCGTGCTCTTTGGCGCGCTGCTACTGATCACCACGCTGTTATCATCGTATCGCTATGTGCTAAAGCCTGTGTTGATTTTGCTATTAATCATGGGCGCGGTGACCAGTTATTTTACTGACACTTATGGCACGGTCTATGATACGACCATGCTCCAAAATGCCCTACAGACCGACCAAGCCGAGACCAAGGATCTATTAAACGCAGCGTTTATCATGCGTATCATTGGTTTGGGTGTGCTACCAAGTTTGCTTGTGGCTTTTGTTAAGGTGGATTATCCGACTTGGGGCAAGGGTTTGATGCGCCGATTGGGCTTGATCGTGGCAAGTCTTGCGCTGATTTTACTGCCTGTGGTGGCGTTCAGCAGTCATTATGCCAGTTTCTTTCGCGTGCATAAGCCGCTGCGTAGCTATGTCAATCCGATCATGCCAATCTACTCGGTGGGTAAGCTTGCCAGTATTGAGTATAAAAAAGCCAGTGCGCCAAAAGATACCATTTATCACGCCAAAGACGCGGTACAAGCAACCAAGCCTGATATGCGTAAGCCACGCCTAGTGGTGTTCGTCGTCGGTGAGACGGCACGCGCCGATCATGTCAGCTTCAATGGCTATGAGCGCGATACTTTCCCACAGCTTGCCAAGATCGATGGCGTGACCAATTTTAGCAATGTCACATCGTGCGGCACATCGACGGCGTATTCTGTGCCGTGTATGTTCAGCTATCTGGGCGCGGATGAGTATGATGTCGATACCGCCAAATACCAAGAAAATGTGCTGGATACGCTGGATCGCTTGGGCGTAAGTATCTTGTGGCGTGATAATAATTCGGACTCAAAAGGCGTGATGGATAAGCTGCCAAAAGCGCAATTTGCCGATTATAAATCCGCGACCAACAACGCCATCTGCAACACCAATCCTTATAACGAATGCCGCGATGTCGGTATGCTCGTTGGCTTAGATGACTTTGTCGCTGCCAATAACGGCAAAGATATGCTGATCATGCTGCACCAAATGGGCAATCACGGGCCTGCGTATTTTAAGCGATATGATGAAAAGTTTGCCAAATTCACGCCAGTGTGTGAAGGTAATGAGCTTGCCAAGTGCGAACATCAGTCCTTGATCAATGCTTATGACAATGCCTTGCTTGCCACCGATGATTTCATCGCTCAAAGTATCCAGTGGCTGCAGACGCACAGCAATGCCTATGATGTCTCAATGCTGTATGTCAGCGATCATGGCGAAAGTCTGGGTGAGAACGGTGTCTATCTACATGGTATGCCAAATGCCTTTGCACCAAAAGAACAGCGCAGTGTGCCTGCATTTTTCTGGACGGATAAGCAAACTGGCATCACGCCAATGGCAACCGATACCGTCCTGACCCATGACGCGATCACGCCGACATTATTAAAGCTGTTTGATGTCACCGCGGACAAAGTCAAAGACCGCACCGCATTCATCCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3007235","ARO_id":"45981","ARO_name":"MCR-1.20","CARD_short_name":"MCR-1.20","ARO_description":"An MCR-1-type colistin resistance gene variant.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5841":{"model_id":"5841","model_name":"MCR-1.28","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"8535":{"protein_sequence":{"accession":"WP_181464119.1","sequence":"MMQHTSVWYRRSVSPFVLVASVAVFLTATANLTFFDKISQTYPIADNLGFVLTIAVVLFGAMLLITTLLSSYRYVLKPVLILLLIMGAVTSYFTDTYGTVYDTTMLQNALQTDQAETKDLLNAAFIMRIIGLGVLPSLLVAFVKVDYPTWGKGLMRRLGLIVASLALILLPVVAFSSHYASFFRVHKPLRSYVNPIMPIYSVGKLASIEYKKANAPKDTIYHAKDAVQATKPDMRKPRLVVFVVGETARADHVSFNGYERDTFPQLAKIDGVTNFSNVTSCGTSTAYSVPCMFSYLGADEYDVDTAKYQENVLDTLDRLGVSILWRDNNSDSKGVMDKLPKAQFADYKSATNNAICNTNPYNECRDVGMLVGLDDFVAANNGKDMLIMLHQMGNHGPAYFKRYDEKFAKFTPVCEGNELAKCEHQSLINAYDNALLATDDFIAQSIQWLQTHSNAYDVSMLYVSDHGESLGENGVYLHGMPNAFAPKEQRSVPAFFWTDKQTGITPMATDTVLTHDAITPTLLKLFDVTADKVKDRTAFIR"},"dna_sequence":{"accession":"MT770924.1","fmin":"0","fmax":"1626","strand":"+","sequence":"ATGATGCAGCATACTTCTGTGTGGTACCGACGCTCGGTCAGTCCGTTTGTTCTTGTGGCGAGTGTTGCCGTTTTCTTGACCGCGACCGCCAATCTTACCTTTTTTGATAAAATCAGCCAAACCTATCCCATCGCGGACAATCTCGGCTTTGTGCTGACGATCGCTGTCGTGCTCTTTGGCGCGATGCTACTGATCACCACGCTGTTATCATCGTATCGCTATGTGCTAAAGCCTGTGTTGATTTTGCTATTAATCATGGGCGCGGTGACCAGTTATTTTACTGACACTTATGGCACGGTCTATGATACGACCATGCTCCAAAATGCCCTACAGACCGACCAAGCCGAGACCAAGGATCTATTAAACGCAGCGTTTATCATGCGTATCATTGGTTTGGGTGTGCTACCAAGTTTGCTTGTGGCTTTTGTTAAGGTGGATTATCCGACTTGGGGCAAGGGTTTGATGCGCCGATTGGGCTTGATCGTGGCAAGTCTTGCGCTGATTTTACTGCCTGTGGTGGCGTTCAGCAGTCATTATGCCAGTTTCTTTCGCGTGCATAAGCCGCTGCGTAGCTATGTCAATCCGATCATGCCAATCTACTCGGTGGGTAAGCTTGCCAGTATTGAGTATAAAAAAGCCAATGCGCCAAAAGATACCATTTATCACGCCAAAGACGCGGTACAAGCAACCAAGCCTGATATGCGTAAGCCACGCCTAGTGGTGTTCGTCGTCGGTGAGACGGCACGCGCCGATCATGTCAGCTTCAATGGCTATGAGCGCGATACTTTCCCACAGCTTGCCAAGATCGATGGCGTGACCAATTTTAGCAATGTCACATCGTGCGGCACATCGACGGCGTATTCTGTGCCGTGTATGTTCAGCTATCTGGGCGCGGATGAGTATGATGTCGATACCGCCAAATACCAAGAAAATGTGCTGGATACGCTGGATCGCTTGGGCGTAAGTATCTTGTGGCGTGATAATAATTCGGACTCAAAAGGCGTGATGGATAAGCTGCCAAAAGCGCAATTTGCCGATTATAAATCCGCGACCAACAACGCCATCTGCAACACCAATCCTTATAACGAATGCCGCGATGTCGGTATGCTCGTTGGCTTAGATGACTTTGTCGCTGCCAATAACGGCAAAGATATGCTGATCATGCTGCACCAAATGGGCAATCACGGGCCTGCGTATTTTAAGCGATATGATGAAAAGTTTGCCAAATTCACGCCAGTGTGTGAAGGTAATGAGCTTGCCAAGTGCGAACATCAGTCCTTGATCAATGCTTATGACAATGCCTTGCTTGCCACCGATGATTTCATCGCTCAAAGTATCCAGTGGCTGCAGACGCACAGCAATGCCTATGATGTCTCAATGCTGTATGTCAGCGATCATGGCGAAAGTCTGGGTGAGAACGGTGTCTATCTACATGGTATGCCAAATGCCTTTGCACCAAAAGAACAGCGCAGTGTGCCTGCATTTTTCTGGACGGATAAGCAAACTGGCATCACGCCAATGGCAACCGATACCGTCCTGACCCATGACGCGATCACGCCGACATTATTAAAGCTGTTTGATGTCACCGCGGACAAAGTCAAAGACCGCACCGCATTCATCCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3007236","ARO_id":"45982","ARO_name":"MCR-1.28","CARD_short_name":"MCR-1.28","ARO_description":"An MCR-1-type colistin resistance gene variant.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5842":{"model_id":"5842","model_name":"MCR-1.21","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"8536":{"protein_sequence":{"accession":"WP_140423330.1","sequence":"MMQHTSVWYRRSVSPFVLVASVAVFLTATANLTFFDKISQTYPIADNLGFVLTIAVVLFGAMLLITTLLSSYRYVLKPVLILLLIMGAVTSYFTDTYGTVYDTTMLQNALQTDQAETKDLLNAAFIMRIIGLGVLPSLLVAFVKVDYPTWGKGLMRRLGLIVASLALILLPVVAFSSHYASFFRVHKPLRSYVNPIMPIYSVGKLASIEYKKASAPKDTIYHAKDAVQATKPDMRKPRLVVFVVGETARADHVSFNGYERDTFPQLAKIDGVTNFSNVTSCGTSTAYSVPCMFSYLGADEYDVDTAKYQENVLDTLDRLGVSILWRDNNSDSKGVMDKLPKAQFADYKSATNNAICNTNPYNECRDVGMLVGLDDFVAANNGKDMLIMLHQMGNHGPAYFKRYDEKFAKFTSVCEGNELAKCEHQSLINAYDNALLATDDFIAQSIQWLQTHSNAYDVSMLYVSDHGESLGENGVYLHGMPNAFAPKEQRSVPAFFWTDKQTGITPMATDTVLTHDAITPTLLKLFDVTADKVKDRTAFIR"},"dna_sequence":{"accession":"MK965883.1","fmin":"0","fmax":"1626","strand":"+","sequence":"ATGATGCAGCATACTTCTGTGTGGTACCGACGCTCGGTCAGTCCGTTTGTTCTTGTGGCGAGTGTTGCCGTTTTCTTGACCGCGACCGCCAATCTTACCTTTTTTGATAAAATCAGCCAAACCTATCCCATCGCGGACAATCTCGGCTTTGTGCTGACGATCGCTGTCGTGCTCTTTGGCGCGATGCTACTGATCACCACGCTGTTATCATCGTATCGCTATGTGCTAAAGCCTGTGTTGATTTTGCTATTAATCATGGGCGCGGTGACCAGTTATTTTACTGACACTTATGGCACGGTCTATGATACGACCATGCTCCAAAATGCCCTACAGACCGACCAAGCCGAGACCAAGGATCTATTAAACGCAGCGTTTATCATGCGTATCATTGGTTTGGGTGTGCTACCAAGTTTGCTTGTGGCTTTTGTTAAGGTGGATTATCCGACTTGGGGCAAGGGTTTGATGCGCCGATTGGGCTTGATCGTGGCAAGTCTTGCGCTGATTTTACTGCCTGTGGTGGCGTTCAGCAGTCATTATGCCAGTTTCTTTCGCGTGCATAAGCCGCTGCGTAGCTATGTCAATCCGATCATGCCAATCTACTCGGTGGGTAAGCTTGCCAGTATTGAGTATAAAAAAGCCAGTGCGCCAAAAGATACCATTTATCACGCCAAAGACGCGGTACAAGCAACCAAGCCTGATATGCGTAAGCCACGCCTAGTGGTGTTCGTCGTCGGTGAGACGGCACGCGCCGATCATGTCAGCTTCAATGGCTATGAGCGCGATACTTTCCCACAGCTTGCCAAGATCGATGGCGTGACCAATTTTAGCAATGTCACATCGTGCGGCACATCGACGGCGTATTCTGTGCCGTGTATGTTCAGCTATCTGGGCGCGGATGAGTATGATGTCGATACCGCCAAATACCAAGAAAATGTGCTGGATACGCTGGATCGCTTGGGCGTAAGTATCTTGTGGCGTGATAATAATTCGGACTCAAAAGGCGTGATGGATAAGCTGCCAAAAGCGCAATTTGCCGATTATAAATCCGCGACCAACAACGCCATCTGCAACACCAATCCTTATAACGAATGCCGCGATGTCGGTATGCTCGTTGGCTTAGATGACTTTGTCGCTGCCAATAACGGCAAAGATATGCTGATCATGCTGCACCAAATGGGCAATCACGGGCCTGCGTATTTTAAGCGATATGATGAAAAGTTTGCCAAATTCACGTCAGTGTGTGAAGGTAATGAGCTTGCCAAGTGCGAACATCAGTCCTTGATCAATGCTTATGACAATGCCTTGCTTGCCACCGATGATTTCATCGCTCAAAGTATCCAGTGGCTGCAGACGCACAGCAATGCCTATGATGTCTCAATGCTGTATGTCAGCGATCATGGCGAAAGTCTGGGTGAGAACGGTGTCTATCTACATGGTATGCCAAATGCCTTTGCACCAAAAGAACAGCGCAGTGTGCCTGCATTTTTCTGGACGGATAAGCAAACTGGCATCACGCCAATGGCAACCGATACCGTCCTGACCCATGACGCGATCACGCCGACATTATTAAAGCTGTTTGATGTCACCGCGGACAAAGTCAAAGACCGCACCGCATTCATCCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3007237","ARO_id":"45983","ARO_name":"MCR-1.21","CARD_short_name":"MCR-1.21","ARO_description":"An MCR-1-type colistin resistance gene variant.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5843":{"model_id":"5843","model_name":"MCR-1.16","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"8537":{"protein_sequence":{"accession":"WP_136512110.1","sequence":"MMQHTSVWYRRSVSPFVLVASVAVFLTATANLTFFDKISQTYPIADNLGFVLTIAVVLFGAMLLITTLLSSYRYVLKPVLILLLIMGAVTSYFTDTYGTVYDTTMLQNALQTDQAETKDLLNAAFIMRIIGLGVLPSLLVAFVKVDYPTWGKGLMRRLGLIVASLALILLPVVAFSSHYASFFRVHKPLRSYVNPIMPIYSVGKLASIEYKKASAPKDTIYHAKDAVQATKPDMRKPRLVVFVVGETARADHVSFNGYERDTFPQLAKIDGVTNFSNVTSCGTSTAYSVPCMFSYLGADEYDVDTAKYQENVLDTLDSLGVSILWRDNNSDSKGVMDKLPKAQFADYKSATNNAICNTNPYNECRDVGMLVGLDDFVAANNGKDMLIMLHQMGNHGPAYFKRYDEKFAKFTPVCEGNELAKCEHQSLINAYDNALLATDDFIAQSIQWLQTHSNAYDVSMLYVSDHGESLGENGVYLHGMPNAFAPKEQRSVPAFFWTDKQTGITPMATDTVLTHDAITPTLLKLFDVTADKVKDRTAFIR"},"dna_sequence":{"accession":"MK568462.1","fmin":"0","fmax":"1626","strand":"+","sequence":"ATGATGCAGCATACTTCTGTGTGGTACCGACGCTCGGTCAGTCCGTTTGTTCTTGTGGCGAGTGTTGCCGTTTTCTTGACCGCGACCGCCAATCTTACCTTTTTTGATAAAATCAGCCAAACCTATCCCATCGCGGACAATCTCGGCTTTGTGCTGACGATCGCTGTCGTGCTCTTTGGCGCGATGCTACTGATCACCACGCTGTTATCATCGTATCGCTATGTGCTAAAGCCTGTGTTGATTTTGCTATTAATCATGGGCGCGGTGACCAGTTATTTTACTGACACTTATGGCACGGTCTATGATACGACCATGCTCCAAAATGCCCTACAGACCGACCAAGCCGAGACCAAGGATCTATTAAACGCAGCGTTTATCATGCGTATCATTGGTTTGGGTGTGCTACCAAGTTTGCTTGTGGCTTTTGTTAAGGTGGATTATCCGACTTGGGGCAAGGGTTTGATGCGCCGATTGGGCTTGATCGTGGCAAGTCTTGCGCTGATTTTACTGCCTGTGGTGGCGTTCAGCAGTCATTATGCCAGTTTCTTTCGCGTGCATAAGCCGCTGCGTAGCTATGTCAATCCGATCATGCCAATCTACTCGGTGGGTAAGCTTGCCAGTATTGAGTATAAAAAAGCCAGTGCGCCAAAAGATACCATTTATCACGCCAAAGACGCGGTACAAGCAACCAAGCCTGATATGCGTAAGCCACGCCTAGTGGTGTTCGTCGTCGGTGAGACGGCACGCGCCGATCATGTCAGCTTCAATGGCTATGAGCGCGATACTTTCCCACAGCTTGCCAAGATCGATGGCGTGACCAATTTTAGCAATGTCACATCGTGCGGCACATCGACGGCGTATTCTGTGCCGTGTATGTTCAGCTATCTGGGCGCGGATGAGTATGATGTCGATACCGCCAAATACCAAGAAAATGTGCTGGATACGCTGGATAGCTTGGGCGTAAGTATCTTGTGGCGTGATAATAATTCGGACTCAAAAGGCGTGATGGATAAGCTGCCAAAAGCGCAATTTGCCGATTATAAATCCGCGACCAACAACGCCATCTGCAACACCAATCCTTATAACGAATGCCGCGATGTCGGTATGCTCGTTGGCTTAGATGACTTTGTCGCTGCCAATAACGGCAAAGATATGCTGATCATGCTGCACCAAATGGGCAATCACGGGCCTGCGTATTTTAAGCGATATGATGAAAAGTTTGCCAAATTCACGCCAGTGTGTGAAGGTAATGAGCTTGCCAAGTGCGAACATCAGTCCTTGATCAATGCTTATGACAATGCCTTGCTTGCCACCGATGATTTCATCGCTCAAAGTATCCAGTGGCTGCAGACGCACAGCAATGCCTATGATGTCTCAATGCTGTATGTCAGCGATCATGGCGAAAGTCTGGGTGAGAACGGTGTCTATCTACATGGTATGCCAAATGCCTTTGCACCAAAAGAACAGCGCAGTGTGCCTGCATTTTTCTGGACGGATAAGCAAACTGGCATCACGCCAATGGCAACCGATACCGTCCTGACCCATGACGCGATCACGCCGACATTATTAAAGCTGTTTGATGTCACCGCGGACAAAGTCAAAGACCGCACCGCATTCATCCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3007238","ARO_id":"45984","ARO_name":"MCR-1.16","CARD_short_name":"MCR-1.16","ARO_description":"An MCR-1-type colistin resistance gene variant.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5844":{"model_id":"5844","model_name":"MCR-1.22","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"8538":{"protein_sequence":{"accession":"WP_148044477.1","sequence":"MMQHTSVWYRRSVSPFVLVASVAVFLTATANLTFFDKISQTYPIADNLGFVLTIAVVLFGAMLLITTLLSSYRYVLKPVLILLLIMGAVTSYFTDTYGTVYDTTMLQNALQTDQAETKDLLNAAFIMRIIGLGVLPSLLVAFVKVDYPTWGKGLMRRLGLIVASLALILLPVVAFSSHYASFFRVHKPLRSYVNPIMPIYSVGKLASIEYKKASAPKDTIYHAKDAVQATKPDMRKPRLVVFVVGETARADHVSFNGYERDTFPQLAKIDGVTNFSNVTSCGTSTAYSVPCMFSYLGADEYDVDTAKYQENVLDTLDRLGVSILWRDNNSDSKGVMDKLPKAQFADYKSATNNAICNTNPYNECRDVGMLVGLDDFVAANNGKDMLIMLHQMGNHGPAYFKRYDEKFAKFTPVCEGNELAKCEHQFLINAYDNALLATDDFIAQSIQWLQTHSNAYDVSMLYVSDHGESLGENGVYLHGMPNAFAPKEQRSVPAFFWTDKQTGITPMATDTVLTHDAITPTLLKLFDVTADKVKDRTAFIR"},"dna_sequence":{"accession":"MN017134.1","fmin":"0","fmax":"1626","strand":"+","sequence":"ATGATGCAGCATACTTCTGTGTGGTACCGACGCTCGGTCAGTCCGTTTGTTCTTGTGGCGAGTGTTGCCGTTTTCTTGACCGCGACCGCCAATCTTACCTTTTTTGATAAAATCAGCCAAACCTATCCCATCGCGGACAATCTCGGCTTTGTGCTGACGATCGCTGTCGTGCTCTTTGGCGCGATGCTACTGATCACCACGCTGTTATCATCGTATCGCTATGTGCTAAAGCCTGTGTTGATTTTGCTATTAATCATGGGCGCGGTGACCAGTTATTTTACTGACACTTATGGCACGGTCTATGATACGACCATGCTCCAAAATGCCCTACAGACCGACCAAGCCGAGACCAAGGATCTATTAAACGCAGCGTTTATCATGCGTATCATTGGTTTGGGTGTGCTACCAAGTTTGCTTGTGGCTTTTGTTAAGGTGGATTATCCGACTTGGGGCAAGGGTTTGATGCGCCGATTGGGCTTGATCGTGGCAAGTCTTGCGCTGATTTTACTGCCTGTGGTGGCGTTCAGCAGTCATTATGCCAGTTTCTTTCGCGTGCATAAGCCGCTGCGTAGCTATGTCAATCCGATCATGCCAATCTACTCGGTGGGTAAGCTTGCCAGTATTGAGTATAAAAAAGCCAGTGCGCCAAAAGATACCATTTATCACGCCAAAGACGCGGTACAAGCAACCAAGCCTGATATGCGTAAGCCACGCCTAGTGGTGTTCGTCGTCGGTGAGACGGCACGCGCCGATCATGTCAGCTTCAATGGCTATGAGCGCGATACTTTCCCACAGCTTGCCAAGATCGATGGCGTGACCAATTTTAGCAATGTCACATCGTGCGGCACATCGACGGCGTATTCTGTGCCGTGTATGTTCAGCTATCTGGGCGCGGATGAGTATGATGTCGATACCGCCAAATACCAAGAAAATGTGCTGGATACGCTGGATCGCTTGGGCGTAAGTATCTTGTGGCGTGATAATAATTCGGACTCAAAAGGCGTGATGGATAAGCTGCCAAAAGCGCAATTTGCCGATTATAAATCCGCGACCAACAACGCCATCTGCAACACCAATCCTTATAACGAATGCCGCGATGTCGGTATGCTCGTTGGCTTAGATGACTTTGTCGCTGCCAATAACGGCAAAGATATGCTGATCATGCTGCACCAAATGGGCAATCACGGGCCTGCGTATTTTAAGCGATATGATGAAAAGTTTGCCAAATTCACGCCAGTGTGTGAAGGTAATGAGCTTGCCAAGTGCGAACATCAGTTCTTGATCAATGCTTATGACAATGCCTTGCTTGCCACCGATGATTTCATCGCTCAAAGTATCCAGTGGCTGCAGACGCACAGCAATGCCTATGATGTCTCAATGCTGTATGTCAGCGATCATGGCGAAAGTCTGGGTGAGAACGGTGTCTATCTACATGGTATGCCAAATGCCTTTGCACCAAAAGAACAGCGCAGTGTGCCTGCATTTTTCTGGACGGATAAGCAAACTGGCATCACGCCAATGGCAACCGATACCGTCCTGACCCATGACGCGATCACGCCGACATTATTAAAGCTGTTTGATGTCACCGCGGACAAAGTCAAAGACCGCACCGCATTCATCCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3007239","ARO_id":"45985","ARO_name":"MCR-1.22","CARD_short_name":"MCR-1.22","ARO_description":"An MCR-1-type colistin resistance gene variant.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5845":{"model_id":"5845","model_name":"MCR-1.19","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"8539":{"protein_sequence":{"accession":"WP_129336087.1","sequence":"MMQHTSVWYRRSVSPFVLVASVAVFLTATANLTFFDKISQTYPIADNLGFVLTIAVVLFGAMLLITTLLSSYRYVLKPVLILLLIMGAVTSYFTDTYGTVYDTTMLQNALQTDQAETKDLLNAAFIMRIIGLGVLPSLLVAFVKVDYPTWGKGLMRRLGLIVASLALILLPVVAFSSHYASFFRVHKPLRSYVNPIMPIYSVGKLASIEYKKASAPKDTIYHAKDAVQATKPDMRKPRLVVFVVGETARADHVSFNGYERDTFPQLAKIDGVTNFSNVTSCGTSTAYSVPCMFSYLGADEYDVDTAKYQENVLDTLDRLGVSILWRDNNSDSKGVMDKLPKAQFADYKSATNNAICNTNPYNECRDVGMLVGLDDFVAANNGKDMLIMLHQMGNHGPAYFKRYDEKFAKFTPVCEGNELAKCEHQSLINAYDNALLATDDFIAQSIQWLQTHSNAYDVSMLYVSDHGESLGENGVYLHGMPNAFAPKEQRSVPAFFWTDKQTGITPMATDTILTHDAITPTLLKLFDVTADKVKDRTAFIR"},"dna_sequence":{"accession":"MK490674.1","fmin":"0","fmax":"1626","strand":"+","sequence":"ATGATGCAGCATACTTCTGTGTGGTACCGACGCTCGGTCAGTCCGTTTGTTCTTGTGGCGAGTGTTGCCGTTTTCTTGACCGCGACCGCCAATCTTACCTTTTTTGATAAAATCAGCCAAACCTATCCCATCGCGGACAATCTCGGCTTTGTGCTGACGATCGCTGTCGTGCTCTTTGGCGCGATGCTACTGATCACCACGCTGTTATCATCGTATCGCTATGTGCTAAAGCCTGTGTTGATTTTGCTATTAATCATGGGCGCGGTGACCAGTTATTTTACTGACACTTATGGCACGGTCTATGATACGACCATGCTCCAAAATGCCCTACAGACCGACCAAGCCGAGACCAAGGATCTATTAAACGCAGCGTTTATCATGCGTATCATTGGTTTGGGTGTGCTACCAAGTTTGCTTGTGGCTTTTGTTAAGGTGGATTATCCGACTTGGGGCAAGGGTTTGATGCGCCGATTGGGCTTGATCGTGGCAAGTCTTGCGCTGATTTTACTGCCTGTGGTGGCGTTCAGCAGTCATTATGCCAGTTTCTTTCGCGTGCATAAGCCGCTGCGTAGCTATGTCAATCCGATCATGCCAATCTACTCGGTGGGTAAGCTTGCCAGTATTGAGTATAAAAAAGCCAGTGCGCCAAAAGATACCATTTATCACGCCAAAGACGCGGTACAAGCAACCAAGCCTGATATGCGTAAGCCACGCCTAGTGGTGTTCGTCGTCGGTGAGACGGCACGCGCCGATCATGTCAGCTTCAATGGCTATGAGCGCGATACTTTCCCACAGCTTGCCAAGATCGATGGCGTGACCAATTTTAGCAATGTCACATCGTGCGGCACATCGACGGCGTATTCTGTGCCGTGTATGTTCAGCTATCTGGGCGCGGATGAGTATGATGTCGATACCGCCAAATACCAAGAAAATGTGCTGGATACGCTGGATCGCTTGGGCGTAAGTATCTTGTGGCGTGATAATAATTCGGACTCAAAAGGCGTGATGGATAAGCTGCCAAAAGCGCAATTTGCCGATTATAAATCCGCGACCAACAACGCCATCTGCAACACCAATCCTTATAACGAATGCCGCGATGTCGGTATGCTCGTTGGCTTAGATGACTTTGTCGCTGCCAATAACGGCAAAGATATGCTGATCATGCTGCACCAAATGGGCAATCACGGGCCTGCGTATTTTAAGCGATATGATGAAAAGTTTGCCAAATTCACGCCAGTGTGTGAAGGTAATGAGCTTGCCAAGTGCGAACATCAGTCCTTGATCAATGCTTATGACAATGCCTTGCTTGCCACCGATGATTTCATCGCTCAAAGTATCCAGTGGCTGCAGACGCACAGCAATGCCTATGATGTCTCAATGCTGTATGTCAGCGATCATGGCGAAAGTCTGGGTGAGAACGGTGTCTATCTACATGGTATGCCAAATGCCTTTGCACCAAAAGAACAGCGCAGTGTGCCTGCATTTTTCTGGACGGATAAGCAAACTGGCATCACGCCAATGGCAACCGATACCATCCTGACCCATGACGCGATCACGCCGACATTATTAAAGCTGTTTGATGTCACCGCGGACAAAGTCAAAGACCGCACCGCATTCATCCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35672","NCBI_taxonomy_name":"Salmonella enterica","NCBI_taxonomy_id":"28901"}}}},"ARO_accession":"3007240","ARO_id":"45986","ARO_name":"MCR-1.19","CARD_short_name":"MCR-1.19","ARO_description":"An MCR-1-type colistin resistance gene variant.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5846":{"model_id":"5846","model_name":"MCR-1.29","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"8540":{"protein_sequence":{"accession":"WP_188331884.1","sequence":"MMQHTSVWYRRSVSPFVLVASVAVFLTATANLTFFDKISQTYPIADNLGFVLTIAVVLFGAMLLITTLLSSYRYVLKPVLILLLIMGAVTSYFTDTYGTVYDTTMLQNALQTDQAETKDLLNAAFIMRIIGLGVLPSLLVAFVKVDYPTWGKGLMRRLGLIVASLALILLPVVAFSSHYASFFRVHKPLRSYVNPIMPIYSVGKLASIEYKKASAPKDTIYHAKDAVQATKPDMRKPRLVVFVVGETARADHVSFNGYERDTFPQLAKIDGVTNFSNVTSCGTSTAYSVPCMFSYLGADEYDVDTAKYQENVLDTLDRLGVSILWRDNNSDSKGVMDKLPKAQFADYKSATNNAICNTNPYNECRDVGMLVGLDDFVAANNGKDMLIMLHQMGNHGSAYFKRYDEKFAKFTPVCEGNELAKCEHQSLINAYDNALLATDDFIAQSIQWLQTHSNAYDVSMLYVSDHGESLGENGVYLHGMPNAFAPKEQRSVPAFFWTDKQTGITPMATDTVLTHDAITPTLLKLFDVTADKVKDRTAFIR"},"dna_sequence":{"accession":"MT731964.1","fmin":"0","fmax":"1626","strand":"+","sequence":"ATGATGCAGCATACTTCTGTGTGGTACCGACGCTCGGTCAGTCCGTTTGTTCTTGTGGCGAGTGTTGCCGTTTTCTTGACCGCGACCGCCAATCTTACCTTTTTTGATAAAATCAGCCAAACCTATCCCATCGCGGACAATCTCGGCTTTGTGCTGACGATCGCTGTCGTGCTCTTTGGCGCGATGCTACTGATCACCACGCTGTTATCATCGTATCGCTATGTGCTAAAGCCTGTGTTGATTTTGCTATTAATCATGGGCGCGGTGACCAGTTATTTTACTGACACTTATGGCACGGTCTATGATACGACCATGCTCCAAAATGCCCTACAGACCGACCAAGCCGAGACCAAGGATCTATTAAACGCAGCGTTTATCATGCGTATCATTGGTTTGGGTGTGCTACCAAGTTTGCTTGTGGCTTTTGTTAAGGTGGATTATCCGACTTGGGGCAAGGGTTTGATGCGCCGATTGGGCTTGATCGTGGCAAGTCTTGCGCTGATTTTACTGCCTGTGGTGGCGTTCAGCAGTCATTATGCCAGTTTCTTTCGCGTGCATAAGCCGCTGCGTAGCTATGTCAATCCGATCATGCCAATCTACTCGGTGGGTAAGCTTGCCAGTATTGAGTATAAAAAAGCCAGTGCGCCAAAAGATACCATTTATCACGCCAAAGACGCGGTACAAGCAACCAAGCCTGATATGCGTAAGCCACGCCTAGTGGTGTTCGTCGTCGGTGAGACGGCACGCGCCGATCATGTCAGCTTCAATGGCTATGAGCGCGATACTTTCCCACAGCTTGCCAAGATCGATGGCGTGACCAATTTTAGCAATGTCACATCGTGCGGCACATCGACGGCGTATTCTGTGCCGTGTATGTTCAGCTATCTGGGCGCGGATGAGTATGATGTCGATACCGCCAAATACCAAGAAAATGTGCTGGATACGCTGGATCGCTTGGGCGTAAGTATCTTGTGGCGTGATAATAATTCGGACTCAAAAGGCGTGATGGATAAGCTGCCAAAAGCGCAATTTGCCGATTATAAATCCGCGACCAACAACGCCATCTGCAACACCAATCCTTATAACGAATGCCGCGATGTCGGTATGCTCGTTGGCTTAGATGACTTTGTCGCTGCCAATAACGGCAAAGATATGCTGATCATGCTGCACCAAATGGGCAATCACGGGTCTGCGTATTTTAAGCGATATGATGAAAAGTTTGCCAAATTCACGCCAGTGTGTGAAGGTAATGAGCTTGCCAAGTGCGAACATCAGTCCTTGATCAATGCTTATGACAATGCCTTGCTTGCCACCGATGATTTCATCGCTCAAAGTATCCAGTGGCTGCAGACGCACAGCAATGCCTATGATGTCTCAATGCTGTATGTCAGCGATCATGGCGAAAGTCTGGGTGAGAACGGTGTCTATCTACATGGTATGCCAAATGCCTTTGCACCAAAAGAACAGCGCAGTGTGCCTGCATTTTTCTGGACGGATAAGCAAACTGGCATCACGCCAATGGCAACCGATACCGTCCTGACCCATGACGCGATCACGCCGACATTATTAAAGCTGTTTGATGTCACCGCGGACAAAGTCAAAGACCGCACCGCATTCATCCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36791","NCBI_taxonomy_name":"uncultured bacterium","NCBI_taxonomy_id":"77133"}}}},"ARO_accession":"3007241","ARO_id":"45987","ARO_name":"MCR-1.29","CARD_short_name":"MCR-1.29","ARO_description":"An MCR-1-type colistin resistance gene variant.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5847":{"model_id":"5847","model_name":"MCR-1.30","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"8541":{"protein_sequence":{"accession":"WP_188331885.1","sequence":"MMQHTSVWYRRSVSPFVLVASVAVFLTATANLTFFDKISQTYPIADNLGFVLTIAVVLFGAMLLITTLLSSYRYVLKPVLILLLIMGAVTSYFTDTYGTVYDTTMLQNALQTDQAETKDLLNAAFIMRIIGLGVLPSLLVAFVKVDYPTWGKGLMRRLGLIVASLALILLPVVAFSSHYASFFRVHKPLRSYVNPIMPIYSVGKLASIEYKKASAPKDTIYHAKDAVQATKPDMRKPRLVVFVVGETARADHVSFNGYERDTFPQLAKIDGVTNFSNVTSCGTSTAYSVPCMFSYLGADEYDVDTAKYQENVLDTLDRLGVSILWRDNNSDSKGVMDKLPKAQFADYKSATNNAICNTNPYNECRDVGMLVGLDDFVAANNGKDMLIMLHQMGNHGPAYFKRYDEKFAKFTPVCEGNELAKCEHQSLINAYDNALLATDDFIAQSIQWLQTHSNAYDVSMLYVSDHGESLGENDVYLHGMPNAFAPKEQRSVPAFFWTDKQTGITPMATDTVLTHDAITPTLLKLFDVTADKVKDRTAFIR"},"dna_sequence":{"accession":"MT731965.1","fmin":"0","fmax":"1626","strand":"+","sequence":"ATGATGCAGCATACTTCTGTGTGGTACCGACGCTCGGTCAGTCCGTTTGTTCTTGTGGCGAGTGTTGCCGTTTTCTTGACCGCGACCGCCAATCTTACCTTTTTTGATAAAATCAGCCAAACCTATCCCATCGCGGACAATCTCGGCTTTGTGCTGACGATCGCTGTCGTGCTCTTTGGCGCGATGCTACTGATCACCACGCTGTTATCATCGTATCGCTATGTGCTAAAGCCTGTGTTGATTTTGCTATTAATCATGGGCGCGGTGACCAGTTATTTTACTGACACTTATGGCACGGTCTATGATACGACCATGCTCCAAAATGCCCTACAGACCGACCAAGCCGAGACCAAGGATCTATTAAACGCAGCGTTTATCATGCGTATCATTGGTTTGGGTGTGCTACCAAGTTTGCTTGTGGCTTTTGTTAAGGTGGATTATCCGACTTGGGGCAAGGGTTTGATGCGCCGATTGGGCTTGATCGTGGCAAGTCTTGCGCTGATTTTACTGCCTGTGGTGGCGTTCAGCAGTCATTATGCCAGTTTCTTTCGCGTGCATAAGCCGCTGCGTAGCTATGTCAATCCGATCATGCCAATCTACTCGGTGGGTAAGCTTGCCAGTATTGAGTATAAAAAAGCCAGTGCGCCAAAAGATACCATTTATCACGCCAAAGACGCGGTACAAGCAACCAAGCCTGATATGCGTAAGCCACGCCTAGTGGTGTTCGTCGTCGGTGAGACGGCACGCGCCGATCATGTCAGCTTCAATGGCTATGAGCGCGATACTTTCCCACAGCTTGCCAAGATCGATGGCGTGACCAATTTTAGCAATGTCACATCGTGCGGCACATCGACGGCGTATTCTGTGCCGTGTATGTTCAGCTATCTGGGCGCGGATGAGTATGATGTCGATACCGCCAAATACCAAGAAAATGTGCTGGATACGCTGGATCGCTTGGGCGTAAGTATCTTGTGGCGTGATAATAATTCGGACTCAAAAGGCGTGATGGATAAGCTGCCAAAAGCGCAATTTGCCGATTATAAATCCGCGACCAACAACGCCATCTGCAACACCAATCCTTATAACGAATGCCGCGATGTCGGTATGCTCGTTGGCTTAGATGACTTTGTCGCTGCCAATAACGGCAAAGATATGCTGATCATGCTGCACCAAATGGGCAATCACGGGCCTGCGTATTTTAAGCGATATGATGAAAAGTTTGCCAAATTCACGCCAGTGTGTGAAGGTAATGAGCTTGCCAAGTGCGAACATCAGTCCTTGATCAATGCTTATGACAATGCCTTGCTTGCCACCGATGATTTCATCGCTCAAAGTATCCAGTGGCTGCAGACGCACAGCAATGCCTATGATGTCTCAATGCTGTATGTCAGCGATCATGGCGAAAGTCTGGGTGAGAACGATGTCTATCTACATGGTATGCCAAATGCCTTTGCACCAAAAGAACAGCGCAGTGTGCCTGCATTTTTCTGGACGGATAAGCAAACTGGCATCACGCCAATGGCAACCGATACCGTCCTGACCCATGACGCGATCACGCCGACATTATTAAAGCTGTTTGATGTCACCGCGGACAAAGTCAAAGACCGCACCGCATTCATCCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36791","NCBI_taxonomy_name":"uncultured bacterium","NCBI_taxonomy_id":"77133"}}}},"ARO_accession":"3007242","ARO_id":"45988","ARO_name":"MCR-1.30","CARD_short_name":"MCR-1.30","ARO_description":"An MCR-1-type colistin resistance gene variant.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5848":{"model_id":"5848","model_name":"MCR-1.24","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"8542":{"protein_sequence":{"accession":"WP_160164898.1","sequence":"MMQHTSVWYRRSVSPFVLVASVAVFLTATANLTFFDKISQTYPIADNLGFVLTIAVVLFGAMLLITTLLSSYRYVLKPVLILLLIMGAVTSYFTDTYGTVYDTTMLQNALQTDQAETKDLLNAAFIMRIIGLGVLPSLLVAFVKVDYPTWGKGLMRRLGLIVASLAPILLPVVAFSSQYSSFFRVHKPPCSYVNPIMPIYSVGKLASTEYKKASAPKDSIYHAKDAVQATKPDMCKPRVVVFVVGETARADHVSFNGYERDTFPQLAKIDGVTNFSNVTSCGTSTAYFVPCMFSYLGADEYDVDTAKYQENVLDTLDRLGVSILWRDNNSDSKGVMDKLPKAQFADYKSATNNAICNTNPYNECRDVGMLVGLDDFVAANNGKDMLIMLHQMGNHGPAYFKRYDEKFAKFTPVCEGNELAKCEHQSLINAYDNALLATDDFIAQSIQWLQTHSNAYDVSMLYVSDHGESLGENGVYLHGMPNAFAPKEQRSVPAFFWTDKQTGITPMATDTVLTHDAITPTLLKLFDVTADKVKDRTAFIR"},"dna_sequence":{"accession":"MN879257.1","fmin":"0","fmax":"1626","strand":"+","sequence":"ATGATGCAGCATACTTCTGTGTGGTACCGACGCTCGGTCAGTCCGTTTGTTCTTGTGGCGAGTGTTGCCGTTTTCTTGACCGCGACCGCCAATCTTACCTTTTTTGATAAAATCAGCCAAACCTATCCCATCGCGGACAATCTCGGCTTTGTGCTGACGATCGCTGTCGTGCTCTTTGGCGCGATGCTACTGATCACCACGCTGTTATCATCGTATCGCTATGTGCTAAAGCCTGTGTTGATTTTGCTATTAATCATGGGCGCGGTGACCAGTTATTTTACTGACACTTATGGCACGGTCTATGATACGACCATGCTCCAAAATGCCCTACAGACCGACCAAGCCGAGACCAAGGATCTATTAAACGCAGCGTTTATCATGCGTATCATTGGTTTGGGTGTGCTACCAAGTTTGCTTGTGGCTTTTGTTAAGGTGGATTATCCGACTTGGGGCAAGGGTTTGATGCGCCGATTGGGCTTGATCGTGGCAAGTCTTGCGCCGATTTTACTGCCTGTGGTGGCGTTCAGCAGTCAGTATTCCAGTTTCTTTCGCGTGCATAAGCCGCCATGTAGCTATGTCAATCCGATCATGCCAATCTACTCGGTGGGTAAGCTGGCCAGTACTGAGTATAAAAAAGCCAGTGCGCCAAAAGATTCCATTTATCACGCCAAAGACGCGGTACAAGCAACCAAGCCTGATATGTGTAAGCCACGCGTAGTGGTGTTCGTCGTCGGTGAGACGGCACGCGCCGATCACGTCAGCTTCAATGGCTATGAGCGCGATACTTTCCCACAGCTTGCCAAGATCGATGGCGTGACCAATTTTAGCAATGTCACATCGTGCGGCACATCGACGGCGTATTTTGTGCCGTGTATGTTCAGCTATCTGGGCGCGGATGAGTATGATGTCGATACCGCCAAATACCAAGAAAATGTGCTGGATACGCTGGATCGCTTGGGCGTAAGTATCTTGTGGCGTGATAATAATTCGGACTCAAAAGGCGTGATGGATAAGCTGCCAAAAGCGCAATTTGCCGATTATAAATCCGCGACCAACAACGCCATCTGCAACACCAATCCTTATAACGAATGCCGCGATGTCGGTATGCTCGTTGGCTTAGATGACTTTGTCGCTGCCAATAACGGCAAAGATATGCTGATCATGCTGCACCAAATGGGCAATCACGGGCCTGCGTATTTTAAGCGATATGATGAAAAGTTTGCCAAATTCACGCCAGTGTGTGAAGGTAATGAGCTTGCCAAGTGCGAACATCAGTCCTTGATCAATGCTTATGACAATGCCTTGCTTGCCACCGATGATTTCATCGCTCAAAGTATCCAGTGGCTGCAGACGCACAGCAATGCCTATGATGTCTCAATGCTGTATGTCAGCGATCATGGCGAAAGTCTGGGTGAGAACGGTGTCTATCTACATGGTATGCCAAATGCCTTTGCACCAAAAGAACAGCGCAGTGTGCCTGCATTTTTCTGGACGGATAAGCAAACTGGCATCACGCCAATGGCAACCGATACCGTCCTGACCCATGACGCGATCACGCCGACATTATTAAAGCTGTTTGATGTCACCGCGGACAAAGTCAAAGACCGCACCGCATTCATCCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3007243","ARO_id":"45989","ARO_name":"MCR-1.24","CARD_short_name":"MCR-1.24","ARO_description":"An MCR-1-type colistin resistance gene variant.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5849":{"model_id":"5849","model_name":"MCR-1.17","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"8543":{"protein_sequence":{"accession":"WP_136512111.1","sequence":"MMQHTSVWYRRSVSPFVLVASVAVFLTATANLTFFDKISQTYPIADNLGFVLTIAVVLFGAMLLITTLLSSYRYVLKPVLILLLIMGAVTSYFTDTYGTVYDTTMLQNALQTDQAETKDLLNAAFIMRIIGLGVLPTLLVAFVKVDYPTWGKGLMRRLGLIVASLALILLPVVAFSSHYASFFRVHKPLRSYVNPIMPIYSVGKLASIEYKKASAPKDTIYHAKDAVQATKPDMRKPRLVVFVVGETARADHVSFNGYERDTFPQLAKIDGVTNFSNVTSCGTSTAYSVPCMFSYLGADEYDVDTAKYQENVLDTLDRLGVSILWRDNNSDSKGVMDKLPKAQFADYKSATNNAICNTNPYNECRDVGMLVGLDDFVAANNGKDMLIMLHQMGNHGPAYFKRYDEKFAKFTPVCEGNELAKCEHQSLINAYDNALLATDDFIAQSIQWLQTHSNAYDVSMLYVSDHGESLGENGVYLHGMPNAFAPKEQRSVPAFFWTDKQTGITPMATDTVLTHDAITPTLLKLFDVTADKVKDRTAFIR"},"dna_sequence":{"accession":"MK568463.1","fmin":"0","fmax":"1626","strand":"+","sequence":"ATGATGCAGCATACTTCTGTGTGGTACCGACGCTCGGTCAGTCCGTTTGTTCTTGTGGCGAGTGTTGCCGTTTTCTTGACCGCGACCGCCAATCTTACCTTTTTTGATAAAATCAGCCAAACCTATCCCATCGCGGACAATCTCGGCTTTGTGCTGACGATCGCTGTCGTGCTCTTTGGCGCGATGCTACTGATCACCACGCTGTTATCATCGTATCGCTATGTGCTAAAGCCTGTGTTGATTTTGCTATTAATCATGGGCGCGGTGACCAGTTATTTTACTGACACTTATGGCACGGTCTATGATACGACCATGCTCCAAAATGCCCTACAGACCGACCAAGCCGAGACCAAGGATCTATTAAACGCAGCGTTTATCATGCGTATCATTGGTTTGGGTGTGCTACCAACTTTGCTTGTGGCTTTTGTTAAGGTGGATTATCCGACTTGGGGCAAGGGTTTGATGCGCCGATTGGGCTTGATCGTGGCAAGTCTTGCGCTGATTTTACTGCCTGTGGTGGCGTTCAGCAGTCATTATGCCAGTTTCTTTCGCGTGCATAAGCCGCTGCGTAGCTATGTCAATCCGATCATGCCAATCTACTCGGTGGGTAAGCTTGCCAGTATTGAGTATAAAAAAGCCAGTGCGCCAAAAGATACCATTTATCACGCCAAAGACGCGGTACAAGCAACCAAGCCTGATATGCGTAAGCCACGCCTAGTGGTGTTCGTCGTCGGTGAGACGGCACGCGCCGATCATGTCAGCTTCAATGGCTATGAGCGCGATACTTTCCCACAGCTTGCCAAGATCGATGGCGTGACCAATTTTAGCAATGTCACATCGTGCGGCACATCGACGGCGTATTCTGTGCCGTGTATGTTCAGCTATCTGGGCGCGGATGAGTATGATGTCGATACCGCCAAATACCAAGAAAATGTGCTGGATACGCTGGATCGCTTGGGCGTAAGTATCTTGTGGCGTGATAATAATTCGGACTCAAAAGGCGTGATGGATAAGCTGCCAAAAGCGCAATTTGCCGATTATAAATCCGCGACCAACAACGCCATCTGCAACACCAATCCTTATAACGAATGCCGCGATGTCGGTATGCTCGTTGGCTTAGATGACTTTGTCGCTGCCAATAACGGCAAAGATATGCTGATCATGCTGCACCAAATGGGCAATCACGGGCCTGCGTATTTTAAGCGATATGATGAAAAGTTTGCCAAATTCACGCCAGTGTGTGAAGGTAATGAGCTTGCCAAGTGCGAACATCAGTCCTTGATCAATGCTTATGACAATGCCTTGCTTGCCACCGATGATTTCATCGCTCAAAGTATCCAGTGGCTGCAGACGCACAGCAATGCCTATGATGTCTCAATGCTGTATGTCAGCGATCATGGCGAAAGTCTGGGTGAGAACGGTGTCTATCTACATGGTATGCCAAATGCCTTTGCACCAAAAGAACAGCGCAGTGTGCCTGCATTTTTCTGGACGGATAAGCAAACTGGCATCACGCCAATGGCAACCGATACCGTCCTGACCCATGACGCGATCACGCCGACATTATTAAAGCTGTTTGATGTCACCGCGGACAAAGTCAAAGACCGCACCGCATTCATCCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3007244","ARO_id":"45990","ARO_name":"MCR-1.17","CARD_short_name":"MCR-1.17","ARO_description":"An MCR-1-type colistin resistance gene variant.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5850":{"model_id":"5850","model_name":"MCR-1.31","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"8544":{"protein_sequence":{"accession":"WP_213994614.1","sequence":"MMQHTSVWYRRSVSPFVLVASVAVFLTATANLTFFDKISQTYPIADNLGFVLTIAVVLFGAMLLITTLLSSYRYVLKPVLILLLIMGAVTSYFTDTYGTVYDTTMLQNALQTDQAETKDLLNAVFIMRIIGLGVLPSLLVAFVKVDYPTWGKGLMRRLGLIVASLALILLPVVAFSSHYASFFRVHKPLRSYVNPIMPIYSVGKLASIEYKKASAPKDTIYHAKDAVQATKPDMRKPRLVVFVVGETARADHVSFNGYERDTFPQLAKIDGVTNFSNVTSCGTSTAYSVPCMFSYLGADEYDVDTAKYQENVLDTLDRLGVSILWRDNNSDSKGVMDKLPKAQFADYKSATNNAICNTNPYNECRDVGMLVGLDDFVAANNGKDMLIMLHQMGNHGPAYFKRYDEKFAKFTPVCEGNELAKCEHQSLINAYDNALLATDDFIAQSIQWLQTHSNAYDVSMLYVSDHGESLGENGVYLHGMPNAFAPKEQRSVPAFFWTDKQTGITPMATDTVLTHDAITPTLLKLFDVTADKVKDRTAFIR"},"dna_sequence":{"accession":"MW940640.1","fmin":"0","fmax":"1626","strand":"+","sequence":"ATGATGCAGCATACTTCTGTGTGGTACCGACGCTCGGTCAGTCCGTTTGTTCTTGTGGCGAGTGTTGCCGTTTTCTTGACCGCGACCGCCAATCTTACCTTTTTTGATAAAATCAGCCAAACCTATCCCATCGCGGACAATCTCGGCTTTGTGCTGACGATCGCTGTCGTGCTCTTTGGCGCGATGCTACTGATCACCACGCTGTTATCATCGTATCGCTATGTGCTAAAGCCTGTGTTGATTTTGCTATTAATCATGGGCGCGGTGACCAGTTATTTTACTGACACTTATGGCACGGTCTATGATACGACCATGCTCCAAAATGCCCTACAGACCGACCAAGCCGAGACCAAGGATCTATTAAACGCAGTGTTTATCATGCGTATCATTGGTTTGGGTGTGCTACCAAGTTTGCTTGTGGCTTTTGTTAAGGTGGATTATCCGACTTGGGGCAAGGGTTTGATGCGCCGATTGGGCTTGATCGTGGCAAGTCTTGCGCTGATTTTACTGCCTGTGGTGGCGTTCAGCAGTCATTATGCCAGTTTCTTTCGCGTGCATAAGCCGCTGCGTAGCTATGTCAATCCGATCATGCCAATCTACTCGGTGGGTAAGCTTGCCAGTATTGAGTATAAAAAAGCCAGTGCGCCAAAAGATACCATTTATCACGCCAAAGACGCGGTACAAGCAACCAAGCCTGATATGCGTAAGCCACGCCTAGTGGTGTTCGTCGTCGGTGAGACGGCACGCGCCGATCATGTCAGCTTCAATGGCTATGAGCGCGATACTTTCCCACAGCTTGCCAAGATCGATGGCGTGACCAATTTTAGCAATGTCACATCGTGCGGCACATCGACGGCGTATTCTGTGCCGTGTATGTTCAGCTATCTGGGCGCGGATGAGTATGATGTCGATACCGCCAAATACCAAGAAAATGTGCTGGATACGCTGGATCGCTTGGGCGTAAGTATCTTGTGGCGTGATAATAATTCGGACTCAAAAGGCGTGATGGATAAGCTGCCAAAAGCGCAATTTGCCGATTATAAATCCGCGACCAACAACGCCATCTGCAACACCAATCCTTATAACGAATGCCGCGATGTCGGTATGCTCGTTGGCTTAGATGACTTTGTCGCTGCCAATAACGGCAAAGATATGCTGATCATGCTGCACCAAATGGGCAATCACGGGCCTGCGTATTTTAAGCGATATGATGAAAAGTTTGCCAAATTCACGCCAGTGTGTGAAGGTAATGAGCTTGCCAAGTGCGAACATCAGTCCTTGATCAATGCTTATGACAATGCCTTGCTTGCCACCGATGATTTCATCGCTCAAAGTATCCAGTGGCTGCAGACGCACAGCAATGCCTATGATGTCTCAATGCTGTATGTCAGCGATCATGGCGAAAGTCTGGGTGAGAACGGTGTCTATCTACATGGTATGCCAAATGCCTTTGCACCAAAAGAACAGCGCAGTGTGCCTGCATTTTTCTGGACGGATAAGCAAACTGGCATCACGCCAATGGCAACCGATACCGTCCTGACCCATGACGCGATCACGCCGACATTATTAAAGCTGTTTGATGTCACCGCGGACAAAGTCAAAGACCGCACCGCATTCATCCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3007245","ARO_id":"45991","ARO_name":"MCR-1.31","CARD_short_name":"MCR-1.31","ARO_description":"An MCR-1-type colistin resistance gene variant.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5851":{"model_id":"5851","model_name":"MCR-1.14","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"8545":{"protein_sequence":{"accession":"WP_109545052.1","sequence":"MMQHTSVWYRRSVSPFVLVASVAVFLTATANLTFFDKVSQTYPIADNLGFVLTIAVVLFGAMLLITTLLSSYRYVLKPVLILLLIMGAVTSYFTDTYGTVYDTTMLQNALQTDQAETKDLLNAAFIMRIIGLGVLPSLLVAFVKVDYPTWGKGLMRRLGLIVASLALILLPVVAFSSHYASFFRVHKPLRSYVNPIIPIYSVGKLASIEYKKASAPKDTIYHAKDAVQATKPDMRKPRLVVFVVGETARADHVSFNGYERDTFPQLAKIDGVTNFSNVTSCGTSTAYSVPCMFSYLGADEYDVDTAKYQENVLDTLDRLGVSILWRDNNSDSKGVMDKLPKAQFADYKSATNNAICNTNPYNECRDVGMLVGLDDFVAANNGKDMLIMLHQMGNHGPAYFKRYDEKFAKFTPVCEGNELAKCEHQSLINAYDNALLATDDFIAQSIQWLQTHSNAYDVSMLYVSDHGESLGENGVYLHGMPNAFAPKEQRSVPAFFWTDKQTGITPMATDTVLTHDAITPTLLKLFDVTADKVKDRTAFIR"},"dna_sequence":{"accession":"KX443408.2","fmin":"7322","fmax":"8948","strand":"+","sequence":"ATGATGCAGCATACTTCTGTGTGGTACCGACGCTCGGTCAGTCCGTTTGTTCTTGTGGCGAGTGTTGCCGTTTTCTTGACCGCGACCGCCAATCTTACCTTTTTTGATAAGGTCAGCCAAACCTATCCCATCGCGGACAATCTCGGCTTTGTGCTGACGATCGCTGTCGTGCTCTTTGGCGCGATGCTACTGATCACCACGCTGTTATCATCGTATCGCTATGTGCTAAAGCCTGTGTTGATTTTGCTATTAATCATGGGCGCGGTGACCAGTTATTTTACTGACACTTATGGCACGGTCTATGATACGACCATGCTCCAAAATGCCCTACAGACCGACCAAGCCGAGACCAAGGATCTATTAAACGCAGCGTTTATCATGCGTATCATTGGTTTGGGTGTGCTACCAAGTTTGCTTGTGGCTTTTGTTAAGGTGGATTATCCGACTTGGGGCAAGGGTTTGATGCGCCGATTGGGCTTGATCGTGGCAAGTCTTGCGCTGATTTTACTGCCTGTGGTGGCGTTCAGCAGTCATTATGCCAGTTTCTTTCGCGTGCATAAGCCGCTGCGTAGCTATGTCAATCCGATCATACCAATCTACTCGGTGGGTAAGCTTGCCAGTATTGAGTATAAAAAAGCCAGTGCGCCAAAAGATACCATTTATCACGCCAAAGACGCGGTACAAGCAACCAAGCCTGATATGCGTAAGCCACGCCTAGTGGTGTTCGTCGTCGGTGAGACGGCACGCGCCGATCATGTCAGCTTCAATGGCTATGAGCGCGATACTTTCCCACAGCTTGCCAAGATCGATGGCGTGACCAATTTTAGCAATGTCACATCGTGCGGCACATCGACGGCGTATTCTGTGCCGTGTATGTTCAGCTATCTGGGCGCGGATGAGTATGATGTCGATACCGCCAAATACCAAGAAAATGTGCTGGATACGCTGGATCGCTTGGGCGTAAGTATCTTGTGGCGTGATAATAATTCGGACTCAAAAGGCGTGATGGATAAGCTGCCAAAAGCGCAATTTGCCGATTATAAATCCGCGACCAACAACGCCATCTGCAACACCAATCCTTATAACGAATGCCGCGATGTCGGTATGCTCGTTGGCTTAGATGACTTTGTCGCTGCCAATAACGGCAAAGATATGCTGATCATGCTGCACCAAATGGGCAATCACGGGCCTGCGTATTTTAAGCGATATGATGAAAAGTTTGCCAAATTCACGCCAGTGTGTGAAGGTAATGAGCTTGCCAAGTGCGAACATCAGTCCTTGATCAATGCTTATGACAATGCCTTGCTTGCCACCGATGATTTCATCGCTCAAAGTATCCAGTGGCTGCAGACGCACAGCAATGCCTATGATGTCTCAATGCTGTATGTCAGCGATCATGGCGAAAGTCTGGGTGAGAACGGTGTCTATCTACATGGTATGCCAAATGCCTTTGCACCAAAAGAACAGCGCAGTGTGCCTGCATTTTTCTGGACGGATAAGCAAACTGGCATCACGCCAATGGCAACCGATACCGTCCTGACCCATGACGCGATCACGCCGACATTATTAAAGCTGTTTGATGTCACCGCGGACAAAGTCAAAGACCGCACCGCATTCATCCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3007246","ARO_id":"45992","ARO_name":"MCR-1.14","CARD_short_name":"MCR-1.14","ARO_description":"An MCR-1-type colistin resistance gene variant.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5852":{"model_id":"5852","model_name":"MCR-1.25","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"8546":{"protein_sequence":{"accession":"WP_160164899.1","sequence":"MMQHTSVWYRRSVTPFVLVASVAVFLTATANLTFFDKISQTYPIADNLGFVLTIAVVLFGAMLLITTLLSSYRYVLKPVLILLLIMGAVTSYFTDTYGTVYDTTMLQNALQTDQAETKDLLNAAFIMRIIGLGVLPSLLVAFVKVDYPTWGKGLMRRLGLIVASLALILLPVVAFSSHYASFFRVHKPVRSYVNPIMPIYSVGKLASIEYKKASAPKDTIYHAKDAVQATKPDMRKPRLVVFVVGETARADHVSFNGYERDTFPQLAKIDGVTNFSNVTSCGTSTAYSVPCMFSYLGADEYDVDTAKYQENVLDTLDRLGVSILWRDNNSDSKGVMDKLPKAQFADYKSATNNAICNTNPYNECRDVGMLVGLDDFVAANNGKDMLIMLHQMGNHGPAYFKRYDEKFAKFTPVCEGNELAKCEHQSLINAYDNALLATDDFIAQSIQWLQTHSNAYDVSMLYVSDHGESLGENGVYLHGMPNAFAPKEQRSVPAFFWTDKQTGITPMATDTVLTHDAITPTLLKLFDVTADKVKDRTAFIR"},"dna_sequence":{"accession":"MN879259.1","fmin":"0","fmax":"1626","strand":"+","sequence":"ATGATGCAGCATACTTCTGTGTGGTACCGACGCTCGGTCACTCCGTTTGTTCTTGTGGCGAGTGTTGCCGTTTTCTTGACCGCGACCGCCAATCTTACCTTTTTTGATAAAATCAGCCAAACCTATCCCATCGCGGACAATCTCGGCTTTGTGCTGACGATCGCTGTCGTGCTCTTTGGCGCGATGCTACTGATCACCACGCTGTTATCATCGTATCGCTATGTGCTAAAGCCTGTGTTGATTTTGCTATTAATCATGGGCGCGGTGACCAGTTATTTTACTGACACTTATGGCACGGTCTATGATACGACCATGCTCCAAAATGCCCTACAGACCGACCAAGCCGAGACCAAGGATCTATTAAACGCAGCGTTTATCATGCGTATCATTGGTTTGGGTGTGCTACCAAGTTTGCTTGTGGCTTTTGTTAAGGTGGATTATCCGACTTGGGGCAAGGGTTTGATGCGCCGATTGGGCTTGATCGTGGCAAGTCTTGCGCTGATTTTACTGCCTGTGGTGGCGTTCAGCAGTCATTATGCCAGTTTCTTTCGCGTGCATAAGCCGGTGCGTAGCTATGTCAATCCGATCATGCCAATCTACTCGGTGGGTAAGCTTGCCAGTATTGAGTATAAAAAAGCCAGTGCGCCAAAAGATACCATTTATCACGCCAAAGACGCGGTACAAGCAACCAAGCCTGATATGCGTAAGCCACGCCTAGTGGTGTTCGTCGTCGGTGAGACGGCACGCGCCGATCATGTCAGCTTCAATGGCTATGAGCGCGATACTTTCCCACAGCTTGCCAAGATCGATGGCGTGACCAATTTTAGCAATGTCACATCGTGCGGCACATCGACGGCGTATTCTGTGCCGTGTATGTTCAGCTATCTGGGCGCGGATGAGTATGATGTCGATACCGCCAAATACCAAGAAAATGTGCTGGATACGCTGGATCGCTTGGGCGTAAGTATCTTGTGGCGTGATAATAATTCGGACTCAAAAGGCGTGATGGATAAGCTGCCAAAAGCGCAATTTGCCGATTATAAATCCGCGACCAACAACGCCATCTGCAACACCAATCCTTATAACGAATGCCGCGATGTCGGTATGCTCGTTGGCTTAGATGACTTTGTCGCTGCCAATAACGGCAAAGATATGCTGATCATGCTGCACCAAATGGGCAATCACGGGCCTGCGTATTTTAAGCGATATGATGAAAAGTTTGCCAAATTCACGCCAGTGTGTGAAGGTAATGAGCTTGCCAAGTGCGAACATCAGTCCTTGATCAATGCTTATGACAATGCCTTGCTTGCCACCGATGATTTCATCGCTCAAAGTATCCAGTGGCTGCAGACGCACAGCAATGCCTATGATGTCTCAATGCTGTATGTCAGCGATCATGGCGAAAGTCTGGGTGAGAACGGTGTCTATCTACATGGTATGCCAAATGCCTTTGCACCAAAAGAACAGCGCAGTGTGCCTGCATTTTTCTGGACGGATAAGCAAACTGGCATCACGCCAATGGCAACCGATACCGTCCTGACCCATGACGCGATCACGCCGACATTATTAAAGCTGTTTGATGTCACCGCGGACAAAGTCAAAGACCGCACCGCATTCATCCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3007247","ARO_id":"45993","ARO_name":"MCR-1.25","CARD_short_name":"MCR-1.25","ARO_description":"An MCR-1-type colistin resistance gene variant.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5853":{"model_id":"5853","model_name":"MCR-3.33","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"8547":{"protein_sequence":{"accession":"WP_188331892.1","sequence":"MPSLIKIKIVPLIFFLALYFAFMLNWRGVLHFYEILYKLEDFKFGFAISLPILLVAALNFAFVPFSIRYLVKPFFALLIALSAIVSYTMMKYRVLFDQNMIQNIFETNQNEALAYLSLPIIGWVTIAGFIPAILLFFVEIEYEEKWFKGILTRVLSMFASLIVIAVIAALYYQDYVSVGRNNSNLQREIVPANFVNSTVKYVYNRYLAEPIPFTTLGDDAKRDTNKSKPTLMFLVVGETARGKNFSMNGYEKDTNPFTSKSGGVISFNDVRSCGTATAVSVPCMFSNMGRKEFDDNLARNSEGLLDVLQKTGVSIFWKENDGGCKGVCDRVPNIEVKPKDYPKFCDKNTCYDEVVLQDLDSEIAQMKGDKLVGFHLIGSHGPTYYKRYPDAHRQFTPDCPRSDIENCTDEELTNTYDNTIRYTDFVIAEMIAKLKTYEDKYNTALLYVSDHGESLGAMGLYLHGTPYKFAPDDQTRVPMQVWMSPGFIKEKGMNMECLQKNAAANRYSHDNIFSSVLGIWDVKTAIYEQELDIFKQCRNN"},"dna_sequence":{"accession":"MT791039.1","fmin":"0","fmax":"1623","strand":"+","sequence":"ATGCCTTCCCTTATAAAAATAAAAATTGTGCCGCTCATATTTTTTTTGGCACTGTATTTTGCATTTATGCTGAACTGGCGTGGAGTTCTCCATTTTTACGAAATTCTTTACAAATTAGAAGATTTTAAATTTGGTTTCGCCATTTCATTACCAATATTGCTTGTTGCAGCGCTTAATTTTGCATTTGTTCCATTTTCGATACGGTATTTAGTAAAGCCTTTTTTTGCACTTCTTATCGCACTTAGCGCAATCGTTAGTTACACAATGATGAAGTATAGAGTCTTGTTTGATCAAAACATGATTCAGAATATTTTTGAAACCAATCAAAATGAGGCATTAGCATATTTAAGTTTGCCAATTATAGGATGGGTTACTATTGCTGGCTTTATCCCTGCCATTTTACTTTTCTTTGTTGAAATTGAATATGAGGAAAAATGGTTTAAAGGAATTCTAACTCGCGTCCTATCGATGTTTGCATCCCTTATAGTGATTGCGGTTATTGCAGCACTATACTATCAAGATTATGTTTCAGTGGGGCGCAACAATTCAAACCTCCAGCGTGAAATTGTTCCGGCCAATTTTGTTAATAGTACCGTTAAATATGTTTATAATCGTTATCTTGCAGAACCAATCCCATTTACTACTTTAGGTGATGATGCAAAACGGGATACTAATAAAAGTAAGCCCACGTTGATGTTCCTGGTCGTTGGTGAAACTGCTCGTGGTAAAAATTTCTCGATGAATGGCTATGAGAAAGATACCAACCCATTTACCAGTAAATCTGGTGGTGTGATCTCCTTTAATGATGTTCGTTCGTGTGGGACAGCAACCGCTGTATCTGTCCCCTGCATGTTCTCCAATATGGGGAGAAAGGAGTTTGATGATAATCTCGCTCGTAATAGCGAGGGTTTGTTAGATGTGTTGCAGAAAACGGGGGTCTCCATTTTTTGGAAGGAGAACGATGGCGGCTGCAAAGGCGTCTGCGACCGAGTACCTAACATCGAGGTCAAACCGAAGGATTACCCAAAGTTCTGCGATAAAAACACATGCTATGACGAGGTTGTCCTTCAAGACCTCGATAGTGAAATTGCTCAAATGAAAGGGGATAAGCTGGTTGGCTTCCACCTGATAGGTAGCCATGGCCCAACCTACTACAAACGCTACCCTGATGCTCATCGTCAGTTCACCCCTGATTGTCCACGCAGTGATATCGAAAACTGCACGGATGAAGAGCTCACCAACACCTATGACAACACCATCCGCTACACCGATTTCGTGATTGCAGAGATGATTGCCAAGTTGAAAACCTACGAAGATAAGTACAACACCGCATTGCTCTACGTCTCCGATCACGGTGAATCACTGGGAGCTATGGGGCTTTACCTGCACGGTACACCGTACAAGTTTGCACCGGATGATCAGACCCGCGTACCTATGCAGGTGTGGATGTCACCTGGTTTCATCAAAGAAAAAGGCATGAATATGGAATGTTTGCAGAAAAATGCCGCAGCCAATCGCTATTCTCATGACAACATATTTTCTTCTGTCCTGGGAATATGGGATGTGAAGACAGCTATCTACGAACAAGAATTAGATATCTTTAAGCAATGTCGGAATAATTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42604","NCBI_taxonomy_name":"Aeromonas jandaei","NCBI_taxonomy_id":"650"}}}},"ARO_accession":"3007248","ARO_id":"45994","ARO_name":"MCR-3.33","CARD_short_name":"MCR-3.33","ARO_description":"An MCR-3-type colistin resistance gene variant.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5854":{"model_id":"5854","model_name":"MCR-3.14","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"8548":{"protein_sequence":{"accession":"WP_111273843.1","sequence":"MPSLIKIKIVPLIFFLALYFAFMLNWRGVLHFYEILYKLEDFKFGFAISLPILLVAALNFVFVLFSIRYLVKPFFALLIALSAIVSYTMMKYRVLFDQNMIQNIFETNQNEALAYLSLPIIGWVTIAGFIPAILLFFVEIEYEKKWFKGIITRALSMFASLIVIAVIAALYYQDYVSVGRNNSNLQREIVPANFVNSTVKYVYNRYLAEPIPFTTLGDDAKRDTNQSKPTLMFLVVGETARGKNFSMNGYEKDTNPFTSKSGGVISFNDVRSCGTATAVSVPCMFSNMGRKEFDDNLARNSEGLLDVLQKTGVSIFWKENDGGCKGVCDRVPNIEIKPKDYPKFCDKNTCYDEVVLQELDSEIAQMKGDKLVGFHLIGSHGPTYYKRYPDAHRQFTPDCPRSDIENCTDEELTNTYDNTIRYTDFVIGEMIAKLKTYEDKYNTALLYVSDHGESLGALGLYLHGTPYKFAPDDQTRVPMQVWMSPGFIKEKGMNMECLQKNAAANRYSHDNIFSSVLGIWDVKTAIYEQELDIFKQCRNN"},"dna_sequence":{"accession":"MH332764.1","fmin":"0","fmax":"1623","strand":"+","sequence":"ATGCCTTCCCTTATAAAAATAAAAATTGTTCCGCTTATATTTTTTTTGGCACTGTATTTTGCATTTATGCTGAACTGGCGTGGAGTTCTCCATTTTTACGAAATCCTTTACAAATTAGAAGATTTTAAGTTTGGTTTCGCCATTTCATTACCAATATTGCTTGTTGCAGCGCTTAACTTTGTATTTGTTCTATTTTCGATACGGTATTTAGTAAAGCCTTTTTTTGCACTTCTGATCGCACTTAGTGCAATCGTTAGTTACACAATGATGAAGTATAGAGTCTTGTTTGATCAAAACATGATTCAGAATATTTTTGAAACCAATCAAAATGAGGCCTTAGCATATTTAAGCTTACCAATTATAGGATGGGTTACTATTGCTGGCTTTATCCCTGCCATTTTACTTTTCTTTGTTGAAATTGAATATGAGAAAAAATGGTTCAAAGGGATTATAACTCGTGCCCTATCGATGTTTGCATCACTTATAGTGATTGCGGTTATTGCAGCACTATACTATCAAGATTATGTGTCAGTGGGGCGCAACAATTCAAACCTCCAGCGTGAGATTGTTCCAGCCAATTTCGTTAATAGTACCGTTAAATACGTTTACAATCGTTATCTTGCTGAACCAATCCCATTTACAACTTTAGGTGATGATGCAAAACGGGATACTAATCAAAGTAAGCCCACGTTGATGTTTCTGGTCGTTGGTGAAACCGCTCGTGGTAAAAATTTCTCGATGAATGGCTATGAGAAAGATACCAACCCATTCACAAGTAAGTCTGGTGGTGTGATCTCCTTTAATGATGTTCGTTCGTGTGGGACTGCAACCGCTGTATCTGTCCCCTGCATGTTTTCCAATATGGGGAGAAAGGAGTTTGATGATAATCTCGCTCGTAATAGCGAGGGTTTGTTAGATGTGTTGCAGAAAACGGGGGTCTCCATTTTTTGGAAGGAGAACGATGGCGGCTGCAAAGGCGTCTGCGACCGAGTTCCTAACATCGAGATCAAACCGAAGGATTACCCAAAGTTCTGCGATAAAAACACATGCTATGACGAGGTTGTCCTTCAAGAGCTCGACAGTGAAATTGCTCAAATGAAAGGGGATAAGCTGGTTGGCTTCCACCTGATAGGTAGCCATGGCCCAACCTACTACAAGCGCTACCCTGATGCTCATCGTCAGTTCACCCCTGACTGTCCACGCAGTGATATTGAAAACTGCACAGATGAAGAGCTCACCAACACCTATGACAACACCATCCGCTACACCGATTTCGTGATTGGAGAGATGATTGCCAAGTTGAAAACCTACGAAGATAAGTACAACACCGCGTTGCTCTACGTCTCCGATCATGGTGAATCACTGGGAGCATTAGGGCTTTACCTACACGGTACACCGTACAAGTTTGCACCGGATGATCAGACCCGTGTTCCTATGCAGGTGTGGATGTCACCTGGTTTCATCAAAGAAAAAGGCATGAATATGGAATGTTTGCAGAAAAATGCCGCAGCCAATCGCTATTCTCATGACAACATATTTTCTTCTGTCCTGGGAATATGGGATGTGAAGACGGCTATCTACGAACAAGAATTAGATATCTTTAAGCAATGCCGGAATAATTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"45937","NCBI_taxonomy_name":"Aeromonas bivalvium","NCBI_taxonomy_id":"440079"}}}},"ARO_accession":"3007249","ARO_id":"45995","ARO_name":"MCR-3.14","CARD_short_name":"MCR-3.14","ARO_description":"An MCR-3-type colistin resistance gene variant.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5855":{"model_id":"5855","model_name":"MCR-3.37","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"8549":{"protein_sequence":{"accession":"WP_188331896.1","sequence":"MPSLIKIKIVPLIFFLALYFAFMLNWRGVLHFYEILYKLEDFKFGFAISLPILLVAALNFVFVPFSIRYLIKPFFALLIALSAIVSYTMMKYRVLFDQNMIQNIFETNQNEALAYLSLPIIGWVTIAGFIPAILLFFVEIEYEEKWFKGILTRALSMFASLIVIAVIAALYYQDYVSVGRNNSNLQREIVPANFVNSTVKYVYNRYLAEPIPFITLGDDAKRDTNQSKPTLMFLVVGETARGKNFSMNGYEKDTNPFTSKSGGVISFNDVRSCGTATAVSVPCMFSNMGRKEFDDNLARNSEGLLDVLQKTGVSIFWKENDGGCKGVCDRVPNIEIKPKDYPKFCNKNTCYDEVVLQDLDSEIAQMKGDKLVGFHLIGSHGPTYYKRYPDAHRQFTPDCPRSDIENCTDEELTNTYDNTIRYTDFVIAEMIAKLKTYEDKYNTALLYVSDHGESLGAMGLYLHGTPYKFAPDDQTRVPMQVWMSPGFIKEKGMNMECLQKNAAANRYSHDNIFSSVLGIWDVKTAIYEQELDIFKQCRNN"},"dna_sequence":{"accession":"MT809047.1","fmin":"0","fmax":"1623","strand":"+","sequence":"ATGCCTTCCCTTATAAAAATAAAAATTGTTCCGCTTATATTTTTTTTGGCACTGTATTTTGCATTTATGCTGAACTGGCGTGGCGTTCTCCATTTTTACGAAATCCTTTACAAATTAGAAGATTTTAAGTTTGGTTTCGCCATTTCATTACCAATATTGCTTGTTGCAGCGCTTAACTTTGTATTTGTTCCATTTTCGATACGGTATTTAATAAAGCCTTTTTTTGCACTTCTTATCGCACTTAGTGCAATCGTTAGTTACACAATGATGAAGTATAGAGTCTTGTTTGATCAAAACATGATTCAAAATATTTTTGAAACCAATCAAAATGAGGCGTTAGCATATTTAAGCTTACCAATTATAGGATGGGTTACTATTGCTGGCTTTATCCCTGCCATTTTACTTTTCTTTGTTGAAATTGAATATGAGGAAAAATGGTTCAAAGGGATTCTAACTCGTGCCCTATCGATGTTTGCATCACTTATAGTGATTGCGGTTATTGCAGCACTATACTATCAAGATTATGTGTCAGTGGGGCGCAACAATTCAAACCTCCAGCGTGAAATTGTTCCAGCCAATTTCGTTAATAGTACCGTTAAATACGTTTACAATCGTTATCTTGCTGAACCAATCCCATTTATAACTTTAGGTGATGATGCAAAACGGGATACTAATCAAAGTAAGCCCACGTTGATGTTTCTGGTCGTTGGTGAAACCGCTCGTGGTAAAAATTTCTCGATGAATGGCTATGAGAAAGACACCAATCCATTTACCAGTAAATCTGGTGGCGTGATCTCCTTTAATGATGTTCGTTCGTGTGGGACTGCAACCGCTGTATCTGTCCCCTGCATGTTCTCCAATATGGGGAGAAAGGAGTTTGATGATAATCTCGCTCGTAATAGCGAGGGCTTGTTAGATGTGTTGCAGAAAACGGGGGTCTCCATTTTTTGGAAGGAGAACGATGGCGGTTGCAAAGGCGTCTGCGACCGAGTTCCTAACATCGAGATCAAACCGAAGGATTACCCAAAGTTCTGCAATAAAAACACATGCTATGACGAGGTTGTCCTTCAAGACCTCGACAGTGAAATTGCTCAAATGAAAGGGGATAAGCTGGTTGGCTTCCACCTGATAGGTAGCCATGGCCCAACCTACTACAAACGCTACCCTGATGCTCATCGTCAGTTCACTCCTGACTGTCCACGCAGTGATATTGAAAACTGCACAGATGAAGAGCTCACCAACACCTATGACAACACCATCCGCTACACCGATTTCGTGATTGCAGAGATGATTGCCAAGTTGAAAACCTACGAAGATAAGTACAACACCGCGTTGCTCTACGTCTCCGATCACGGTGAATCACTGGGAGCTATGGGGCTTTACCTGCACGGTACACCATACAAATTTGCACCGGATGATCAGACCCGCGTACCTATGCAGGTGTGGATGTCACCTGGTTTCATCAAAGAAAAAGGCATGAATATGGAATGTTTGCAGAAAAATGCCGCAGCCAATCGCTATTCTCATGACAACATATTTTCTTCTGTCCTGGGAATATGGGATGTGAAGACGGCTATCTACGAACAAGAATTAGATATCTTTAAGCAATGTCGGAATAATTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39677","NCBI_taxonomy_name":"Aeromonas veronii","NCBI_taxonomy_id":"654"}}}},"ARO_accession":"3007250","ARO_id":"45996","ARO_name":"MCR-3.37","CARD_short_name":"MCR-3.37","ARO_description":"An MCR-3-type colistin resistance gene variant.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5856":{"model_id":"5856","model_name":"MCR-3.38","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"8550":{"protein_sequence":{"accession":"WP_039039919.1","sequence":"MPSLIKIKIVPLIFFLALYFAFMLNWRGVLHFYEILYKLEDFKFGFAISLPILLVAALNFVFVPFSIRYLVKPFFALLIALSAIVSYTMMKYRVLFDQNMIQNIFETNQNEALAYLSLTIIGWVTIAGFIPAILLFFVEIEYEEKWFKGILTRVLSMFASLIVIAVIAALYYQDYVSVGRNNSNLQREIVPANFVNSTVKYVYNRYFAEPIPFTTLGDDAKRDTNKSKPTLMFLVVGETARGKNFSMNGYEKDTNPFTSKSGGLISFNDVRSCGTATAVSVPCMFSNMGRKEFDDNLARNSEGLLDVLQKTGVSIFWKENDGGCKGVCDRVPNIEIKPKDHPKFCDKNTCYDEVVLQDLDSEIAQMKGDKLVGFHLIGSHGPTYYKRYPDAHRQFTPDCPRIDIENCTDEELTNTYDNTIRYTDFVIAEMIAKLKTYEDKYNTALLYVSDHGESLGAMGLYLHGTPYKFAPDDQTRVPMQIWMSPGFIKEKGMNMECLQKNATTNRYSHDNIFSSVLGIWDVKTAIYEQELDIFKQCRNN"},"dna_sequence":{"accession":"MT787344.1","fmin":"0","fmax":"1623","strand":"+","sequence":"ATGCCTTCCCTTATAAAAATAAAAATTGTGCCGCTCATATTTTTTTTGGCACTGTATTTTGCATTTATGCTGAACTGGCGTGGAGTTCTCCATTTTTACGAAATTCTTTACAAATTAGAAGACTTTAAATTTGGTTTCGCCATTTCATTACCAATATTGCTTGTTGCAGCGCTTAACTTTGTATTTGTTCCATTTTCGATACGGTATTTAGTAAAGCCTTTTTTTGCACTTCTTATCGCACTTAGCGCAATCGTTAGTTACACAATGATGAAGTATAGAGTCTTGTTTGATCAAAACATGATTCAGAATATTTTTGAAACCAATCAAAATGAGGCATTAGCATATTTAAGCTTGACAATTATAGGATGGGTTACTATTGCTGGCTTTATCCCTGCCATTTTACTTTTCTTTGTTGAAATTGAATATGAGGAAAAATGGTTTAAAGGGATTCTAACTCGCGTCCTATCGATGTTTGCATCCCTTATAGTGATTGCGGTTATTGCAGCACTATACTATCAAGATTATGTTTCAGTGGGGCGCAACAATTCAAACCTCCAGCGTGAAATTGTTCCGGCCAATTTTGTTAATAGTACCGTTAAATATGTTTATAATCGTTATTTTGCAGAACCAATCCCATTTACTACTTTAGGTGATGATGCAAAACGGGATACTAATAAAAGTAAGCCCACGTTGATGTTCCTGGTCGTTGGTGAAACGGCTCGTGGTAAAAATTTCTCGATGAATGGCTATGAGAAAGATACCAACCCATTTACCAGTAAATCTGGTGGTCTGATCTCCTTTAATGATGTTCGTTCGTGTGGGACAGCAACCGCTGTATCTGTCCCCTGCATGTTCTCCAATATGGGGAGAAAGGAGTTTGATGATAATCTCGCTCGTAATAGCGAGGGTTTGTTAGATGTGTTGCAGAAAACGGGGGTCTCCATTTTTTGGAAGGAGAACGATGGCGGCTGCAAAGGCGTCTGCGACCGAGTACCTAACATCGAGATCAAACCGAAGGATCACCCAAAGTTCTGCGATAAAAACACATGCTATGACGAGGTTGTCCTTCAAGACCTCGATAGTGAAATTGCTCAAATGAAAGGGGATAAGCTGGTTGGCTTCCACCTGATAGGTAGCCATGGCCCAACCTACTACAAACGCTACCCTGATGCTCATCGTCAGTTCACCCCTGATTGTCCACGCATTGATATCGAAAACTGCACGGATGAAGAGCTCACCAACACCTATGACAACACCATCCGCTACACCGATTTCGTGATTGCAGAGATGATTGCCAAATTGAAAACCTACGAAGATAAGTACAACACCGCGTTGCTCTACGTCTCTGATCACGGTGAATCACTGGGAGCTATGGGGCTTTACCTGCACGGTACACCGTACAAGTTTGCACCGGATGATCAGACCCGCGTACCTATGCAGATCTGGATGTCACCAGGTTTCATCAAAGAAAAAGGCATGAATATGGAATGTTTGCAGAAAAATGCCACAACCAATCGCTATTCTCATGACAACATATTTTCTTCTGTCCTGGGGATATGGGATGTGAAGACAGCTATCTACGAACAAGAATTAGATATCTTTAAGCAATGTCGGAATAATTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36936","NCBI_taxonomy_name":"Aeromonas caviae","NCBI_taxonomy_id":"648"}}}},"ARO_accession":"3007251","ARO_id":"45997","ARO_name":"MCR-3.38","CARD_short_name":"MCR-3.38","ARO_description":"An MCR-3-type colistin resistance gene variant.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5857":{"model_id":"5857","model_name":"MCR-3.15","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"8551":{"protein_sequence":{"accession":"WP_111273844.1","sequence":"MPSLIKIKIVPLIFFLALYFAFMLNWRGVLHFYEILYKLEDFKFGFAISLPILLVAALNFVFVPFSIRYLVKPFFALLIALSAIVSYTMMKYRVLFDQNMIQNIFETNQNEALAYLSLTIIGWVTIAGFIPAILLFFVEIEYEEKWFKGILTRVLSMFASLIVIAVIAALYYQDYVSVGRNNSNLQREIVPANFVNSTVKYVYNRYFAEPIPFTTLGDDAKRDTNKSKPTLMFLVVGETARGKNFSMNGYEKDTNPFTSKSGGVISFNDVRSCGTATAVSVPCMFSNMGRKEFDDNLARNSEGLLDVLQKTGVSIFWKENDGGCKGVCDRVPNIEIKPKDHPKFCDKNTCYDEVVLQDLDSEIAQMKGDKLVGFHLIGSHGPTYYKRYPDAHRQFTPDCPRIDIENCTDEELTNTYDNTIRYTDLVIAEMIAKLKNYEDKYNTALLYVSDHGESLGAMGLYLHGTPYKFAPDDQTRVPMQIWMSPGFIKEKGMNMECLQKNATTNRYSHDNIFSSVLGIWDVKTAIYEQELDIFKQCRNN"},"dna_sequence":{"accession":"MH332765.1","fmin":"0","fmax":"1623","strand":"+","sequence":"ATGCCTTCCCTTATAAAAATAAAAATTGTGCCGCTCATATTTTTTTTGGCACTGTATTTTGCATTTATGCTGAACTGGCGTGGAGTTCTCCATTTTTACGAAATTCTTTACAAATTAGAAGACTTTAAATTTGGTTTCGCCATTTCATTACCAATATTGCTTGTTGCAGCGCTTAACTTTGTATTTGTTCCATTTTCGATACGGTATTTAGTAAAGCCTTTTTTTGCACTTCTTATCGCACTTAGCGCAATCGTTAGTTACACAATGATGAAGTATAGAGTCTTGTTTGATCAAAACATGATTCAGAATATTTTTGAAACCAATCAAAATGAGGCATTAGCATATTTAAGCTTGACAATTATAGGATGGGTTACTATTGCTGGCTTTATCCCTGCCATTTTACTTTTCTTTGTTGAAATTGAATATGAGGAAAAATGGTTTAAAGGGATTCTAACTCGCGTCCTATCGATGTTTGCATCCCTTATAGTGATTGCGGTTATTGCAGCACTATACTATCAAGATTATGTTTCAGTGGGGCGCAACAATTCAAACCTCCAGCGTGAAATTGTTCCGGCCAATTTTGTTAATAGTACCGTTAAATATGTTTATAATCGTTATTTTGCAGAACCAATCCCATTTACTACTTTAGGTGATGATGCAAAACGGGATACTAATAAAAGTAAGCCCACGTTGATGTTCCTGGTCGTTGGTGAAACGGCTCGTGGTAAAAATTTCTCGATGAATGGCTATGAGAAAGATACCAACCCATTTACCAGTAAATCTGGTGGTGTGATCTCCTTTAATGATGTTCGTTCGTGTGGGACAGCAACCGCTGTATCTGTCCCCTGCATGTTCTCCAATATGGGGAGAAAGGAGTTTGATGATAATCTCGCTCGTAATAGCGAGGGTTTGTTAGATGTGTTGCAGAAAACGGGGGTCTCCATTTTTTGGAAGGAGAACGATGGCGGCTGCAAAGGCGTCTGCGACCGAGTACCTAACATCGAGATCAAACCGAAGGATCACCCAAAGTTCTGCGATAAAAACACATGCTATGACGAGGTTGTCCTTCAAGACCTCGATAGTGAAATTGCTCAAATGAAAGGGGATAAGCTGGTTGGCTTCCACCTGATAGGTAGCCATGGCCCAACCTACTACAAACGCTACCCTGATGCTCATCGTCAGTTCACCCCTGATTGTCCACGCATTGATATCGAAAACTGCACGGATGAAGAGCTCACCAACACCTATGACAACACCATCCGCTACACCGATTTAGTGATTGCAGAGATGATTGCCAAATTGAAAAACTACGAAGATAAGTACAACACCGCGTTGCTCTACGTCTCTGATCACGGTGAATCACTGGGAGCTATGGGGCTTTACCTGCACGGTACACCGTACAAGTTTGCACCGGATGATCAGACCCGCGTACCTATGCAGATCTGGATGTCACCAGGTTTCATCAAAGAAAAAGGCATGAATATGGAATGTTTGCAGAAAAATGCCACAACCAATCGCTATTCTCATGACAACATATTTTCTTCTGTCCTGGGGATATGGGATGTGAAGACAGCTATCTACGAACAAGAATTAGATATCTTTAAGCAATGTCGGAATAATTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39526","NCBI_taxonomy_name":"Aeromonas media","NCBI_taxonomy_id":"651"}}}},"ARO_accession":"3007252","ARO_id":"45998","ARO_name":"MCR-3.15","CARD_short_name":"MCR-3.15","ARO_description":"An MCR-3-type colistin resistance gene variant.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5858":{"model_id":"5858","model_name":"MCR-3.27","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"8552":{"protein_sequence":{"accession":"WP_017778762.1","sequence":"MPSLIKIKIVPLIFFLALYFAFMLNWRGVLHFYEILYKLEDFKFGFAISLPILLVAALNFVFVPFSIRYLVKPFFALLIALSAIVSYTMMKYRVLFDQNMIQNIFETNQNEALAYLSLTIIGWVTIAGFIPAILLFFVEIEYEEKWFKGILTRVLSMFASLIVIAVIAALYYQDYVSVGRNNSNLQREIVPANFVNSTVKYVYNRYFAEPIPFTTLGDDAKRDTNKSKPTLMFLVVGETARGKNFSMNGYEKDTNPFTSKSGGVISFNDVRSCGTATAVSVPCMFSNMGRKEFDDNLARNSEGLLDVLQKTGVSIFWKENDGGCKGVCDRVPNIEIKPKDHPKFCDKNTCYDEVVLQDLDSEIAQMKGDKLVGFHLIGSHGPTYYKRYPDAHRQFTPDCPRIDIENCTDEELTNTYDNTIRYTDLVIAEMIAKLKTYEDKYNTALLYVSDHGESLGAMGLYLHGTPYKFAPDDQTRVPMQIWMSPGFIKEKGMNMECLQKNATTNRYSHDNIFSSVLGIWDVKTAIYEQELDIFKQCRNN"},"dna_sequence":{"accession":"MH131694.1","fmin":"0","fmax":"1623","strand":"+","sequence":"ATGCCTTCCCTTATAAAAATAAAAATTGTGCCGCTCATATTTTTTTTGGCACTGTATTTTGCATTTATGCTGAACTGGCGTGGAGTTCTCCATTTTTACGAAATTCTTTACAAATTAGAAGACTTTAAATTTGGTTTCGCCATTTCATTACCAATATTGCTTGTTGCAGCGCTTAACTTTGTATTTGTTCCATTTTCGATACGGTATTTAGTAAAGCCTTTTTTTGCACTTCTTATCGCACTTAGCGCAATCGTTAGTTACACAATGATGAAGTATAGAGTCTTGTTTGATCAAAACATGATTCAGAATATTTTTGAAACCAATCAAAATGAGGCATTAGCATATTTAAGCTTGACAATTATAGGATGGGTTACTATTGCTGGCTTTATCCCTGCCATTTTACTTTTCTTTGTTGAAATTGAATATGAGGAAAAATGGTTTAAAGGGATTCTAACTCGCGTCCTATCGATGTTTGCATCCCTTATAGTGATTGCGGTTATTGCAGCACTATACTATCAAGATTATGTTTCAGTGGGGCGCAACAATTCAAACCTCCAGCGTGAAATTGTTCCGGCCAATTTTGTTAATAGTACCGTTAAATATGTTTATAATCGTTATTTTGCAGAACCAATCCCATTTACTACTTTAGGTGATGATGCAAAACGGGATACTAATAAAAGTAAGCCCACGTTGATGTTCCTGGTCGTTGGTGAAACGGCTCGTGGTAAAAATTTCTCGATGAATGGCTATGAGAAAGATACCAACCCATTTACCAGTAAATCTGGTGGTGTGATCTCCTTTAATGATGTTCGTTCGTGTGGGACAGCAACCGCTGTATCTGTCCCCTGCATGTTCTCCAATATGGGGAGAAAGGAGTTTGATGATAATCTCGCTCGTAATAGCGAGGGTTTGTTAGATGTGTTGCAGAAAACGGGGGTCTCCATTTTTTGGAAGGAGAACGATGGCGGCTGCAAAGGCGTCTGCGACCGAGTACCTAACATCGAGATCAAACCGAAGGATCACCCAAAGTTCTGCGATAAAAACACATGCTATGACGAGGTTGTCCTTCAAGACCTCGATAGTGAAATTGCTCAAATGAAAGGGGATAAGCTGGTTGGCTTCCACCTGATAGGTAGCCATGGCCCAACCTACTACAAACGCTACCCTGATGCTCATCGTCAGTTCACCCCTGATTGTCCACGCATTGATATCGAAAACTGCACGGATGAAGAGCTCACCAACACCTATGACAACACCATCCGCTACACCGATTTAGTGATTGCAGAGATGATTGCCAAATTGAAAACCTACGAAGATAAGTACAACACCGCGTTGCTCTACGTCTCTGATCACGGTGAATCACTGGGAGCTATGGGGCTTTACCTGCACGGTACACCGTACAAGTTTGCACCGGATGATCAGACCCGCGTACCTATGCAGATCTGGATGTCACCAGGTTTCATCAAAGAAAAAGGCATGAATATGGAATGTTTGCAGAAAAATGCCACAACCAATCGCTATTCTCATGACAACATATTTTCTTCTGTCCTGGGGATATGGGATGTGAAGACAGCTATCTACGAACAAGAATTAGATATCTTTAAGCAATGTCGGAATAATTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37047","NCBI_taxonomy_name":"Aeromonas","NCBI_taxonomy_id":"642"}}}},"ARO_accession":"3007253","ARO_id":"45999","ARO_name":"MCR-3.27","CARD_short_name":"MCR-3.27","ARO_description":"An MCR-3-type colistin resistance gene variant.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5859":{"model_id":"5859","model_name":"MCR-3.32","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"8553":{"protein_sequence":{"accession":"WP_188331891.1","sequence":"MPSLIKIKIVPLIFFWALYFAFMLNWRGVLHFYEILYKLEDFKFGFAISLPILLVAALNFVFVPFSIRYLVKPFFALLIALSAIVSYTMMKYRVLFDQNMIQNIFETNQNEALAYLSLPIIGWVTIAGFIPAILLFFVEIEYEKKWFKGIITRALSMFTSLIVIAVIAALYYQDYVSVGRNNSNLQREIVPANFVNSTIKYVYNRYLAEPIPFTTLGDDAKRDTNQSKPTLMFLVVGETARGKNFSMNGYEKDTNPFTSKSGGVISFNDVRSCGTATAVSVPCMFSNMGRKEFDDNLARNSEGLLDVLQKTGVSIFWKENDGGCKGVCDRVSNIEIKPKDYPKFCDKNTCYDEVVLQDLDSEIAQMKGDKLVGFHLIGSHGPTYYKRYPDAHRQFTPDCPRSDIENCTDEELTNTYDNTIRYTDFVIAEMIAKLKTYEDKYNTALLYVSDHGESLGALGLYLHGTPYKFAPDDQTRVPMQVWMSPGFIKEKGMNMECLQKNATANRYSHDNIFSSVLGIWDVKTAIYEQELDIFKQCRNN"},"dna_sequence":{"accession":"MT757847.1","fmin":"0","fmax":"1623","strand":"+","sequence":"ATGCCTTCCCTTATAAAAATAAAAATTGTTCCGCTTATATTTTTTTGGGCACTGTATTTTGCATTTATGCTGAACTGGCGTGGAGTTCTCCATTTTTACGAAATCCTTTACAAATTAGAAGATTTTAAGTTTGGTTTCGCCATTTCATTACCAATATTGCTTGTTGCAGCGCTTAACTTTGTATTTGTTCCATTTTCGATACGGTATTTAGTAAAGCCTTTTTTTGCACTTCTGATCGCACTTAGTGCAATCGTTAGTTACACAATGATGAAGTATAGAGTCTTGTTTGATCAAAACATGATTCAGAATATTTTTGAAACCAATCAAAATGAGGCCTTAGCATATTTAAGCTTACCAATTATAGGATGGGTTACTATTGCTGGCTTTATCCCTGCCATTTTACTTTTCTTTGTTGAAATTGAATATGAGAAAAAATGGTTCAAAGGGATTATAACTCGTGCCCTATCGATGTTTACATCACTTATAGTGATTGCGGTTATTGCAGCACTATACTATCAAGATTATGTGTCAGTGGGGCGAAACAATTCAAACCTCCAGCGTGAAATTGTTCCAGCCAATTTCGTTAATAGTACCATTAAATACGTTTACAATCGTTATCTTGCTGAACCAATCCCATTTACAACTTTAGGTGATGATGCAAAACGGGATACTAATCAAAGTAAGCCCACGTTGATGTTTCTGGTTGTTGGTGAAACCGCTCGTGGTAAAAATTTCTCGATGAATGGCTATGAGAAAGACACCAATCCATTTACCAGTAAATCTGGTGGCGTGATCTCCTTTAATGATGTTCGTTCGTGTGGGACTGCAACCGCTGTATCTGTCCCCTGCATGTTCTCCAATATGGGGAGAAAGGAGTTTGATGACAATCTCGCTCGTAATAGCGAGGGCTTGTTAGATGTGTTGCAGAAAACGGGGGTTTCCATTTTTTGGAAGGAGAACGATGGCGGTTGCAAAGGCGTCTGCGACCGAGTTTCTAACATCGAGATCAAACCGAAGGATTACCCAAAGTTCTGCGATAAAAACACATGCTATGACGAGGTTGTCCTTCAAGACCTCGATAGTGAAATTGCTCAAATGAAAGGGGATAAGCTGGTTGGCTTCCACCTGATAGGTAGCCATGGCCCAACCTACTACAAACGCTACCCTGATGCTCATCGTCAGTTCACTCCTGACTGTCCACGCAGTGATATTGAAAACTGCACAGATGAAGAGCTCACCAACACCTATGACAACACCATCCGCTACACCGATTTCGTGATTGCAGAGATGATTGCCAAGTTGAAAACCTACGAAGATAAGTACAACACCGCGTTGCTCTACGTCTCCGATCATGGTGAATCACTGGGAGCATTAGGGCTTTACCTGCACGGTACACCGTACAAGTTTGCACCGGATGATCAGACCCGTGTTCCTATGCAGGTGTGGATGTCACCTGGTTTCATCAAAGAAAAAGGCATGAATATGGAATGTTTGCAGAAAAATGCCACAGCCAATCGCTATTCTCATGACAACATATTTTCTTCTGTCCTGGGAATATGGGATGTGAAGACGGCTATCTACGAACAAGAATTAGATATCTTTAAGCAATGTCGGAATAATTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36791","NCBI_taxonomy_name":"uncultured bacterium","NCBI_taxonomy_id":"77133"}}}},"ARO_accession":"3007254","ARO_id":"46000","ARO_name":"MCR-3.32","CARD_short_name":"MCR-3.32","ARO_description":"An MCR-3-type colistin resistance gene variant.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5860":{"model_id":"5860","model_name":"MCR-3.31","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"8554":{"protein_sequence":{"accession":"WP_188331890.1","sequence":"MPSLIKIKIVPLIFFWALYFAFMLNWRVVLHFYEILYKLEDFKFGFAISLPILLVAALNFVFVPFSIRYLVKPFFALLIALSAIVSYTMMKYRVLFDQNMIQNIFETNQNEALAYLSLPIIGWVTIAGFIPAILLFFVEIEYEKKWFKGIITRALSMFTSLIVIAVIAALYYQDYVSVGRNNSNLQREIVPANFVNSTIKYVYNRYLAEPIPFTTLGDDAKRDTNQSKPTLMFLVVGETARGKNFSMNGYEKDTNPFTSKSGGVISFNDVRSCGTATAVSVPCMFSNMGRKEFDDNLARNSEGLLDVLQKTGVSIFWKENDGGCKGVCDRVSNIEIKPKDYPKFCDKNTCYDEVVLQDLDSEIAQMKGDKLVGFHLIGSHGPTYYKRYPDAHRQFTPDCPRSDIENCTDEELTNTYDNTIRYTDFVIAEMIAKLKTYEDKYNTALLYVSDHGESLGALGLYLHGTPYKFAPNDQTRVPMQVWMSPGFIKEKGMNMECLQKNAAANRYSHDNIFSSVLGIWDVKTAIYEQELDIFKQCRNN"},"dna_sequence":{"accession":"MT757846.1","fmin":"0","fmax":"1623","strand":"+","sequence":"ATGCCTTCCCTTATAAAAATAAAAATTGTTCCGCTTATATTTTTTTGGGCACTGTATTTTGCATTTATGCTGAACTGGCGTGTAGTTCTCCATTTTTACGAAATCCTTTACAAATTAGAAGATTTTAAGTTTGGTTTCGCCATTTCATTACCAATATTGCTTGTTGCAGCGCTTAACTTTGTATTTGTTCCATTTTCGATACGGTATTTAGTAAAGCCTTTTTTTGCACTTCTGATCGCACTTAGTGCAATCGTTAGTTACACAATGATGAAGTATAGAGTCTTGTTTGATCAAAACATGATTCAGAATATTTTTGAAACCAATCAAAATGAGGCCTTAGCATATTTAAGCTTGCCAATTATAGGATGGGTTACTATTGCTGGCTTTATCCCTGCCATTTTACTTTTCTTTGTTGAAATTGAATATGAGAAAAAATGGTTCAAAGGGATTATAACTCGTGCCCTATCGATGTTTACATCACTTATAGTGATTGCGGTTATTGCAGCACTATACTATCAAGATTATGTGTCAGTGGGGCGAAACAATTCAAACCTCCAGCGTGAAATTGTTCCAGCCAATTTCGTTAATAGTACCATTAAATACGTTTACAATCGTTATCTTGCTGAACCAATCCCATTTACAACTTTAGGTGATGATGCAAAACGGGATACTAATCAAAGTAAGCCCACGTTGATGTTTCTGGTCGTTGGTGAAACCGCTCGTGGTAAAAATTTCTCGATGAATGGCTATGAGAAAGACACCAATCCATTTACCAGTAAATCTGGTGGCGTGATCTCCTTTAATGATGTTCGTTCGTGTGGGACTGCAACCGCTGTATCTGTCCCCTGCATGTTCTCCAATATGGGGAGAAAGGAGTTTGATGACAATCTCGCTCGTAATAGCGAGGGCTTGTTAGATGTGTTGCAGAAAACGGGGGTTTCCATTTTTTGGAAGGAGAACGATGGCGGTTGCAAAGGCGTCTGCGACCGAGTTTCTAACATCGAGATCAAACCGAAGGATTACCCAAAGTTCTGCGATAAAAACACATGCTATGACGAGGTTGTCCTTCAAGACCTCGATAGTGAAATTGCTCAAATGAAAGGGGATAAGCTGGTTGGCTTCCACCTGATAGGTAGCCATGGCCCAACCTACTACAAACGCTACCCTGATGCTCATCGTCAGTTCACTCCTGACTGTCCACGCAGTGATATTGAAAACTGCACAGATGAAGAGCTCACCAACACCTATGACAACACCATCCGCTACACCGATTTCGTGATTGCAGAGATGATTGCCAAGTTGAAAACCTACGAAGATAAGTACAACACCGCGTTGCTCTACGTCTCCGATCATGGTGAATCACTGGGAGCATTAGGGCTTTACCTGCACGGTACACCGTACAAGTTTGCACCGAATGATCAGACCCGTGTTCCTATGCAGGTGTGGATGTCACCTGGTTTCATCAAAGAAAAAGGCATGAATATGGAATGTTTGCAGAAAAATGCCGCAGCCAATCGCTATTCTCATGACAACATATTTTCTTCTGTCCTGGGAATATGGGATGTGAAGACGGCTATCTACGAACAAGAATTAGATATCTTTAAGCAATGTCGGAATAATTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36791","NCBI_taxonomy_name":"uncultured bacterium","NCBI_taxonomy_id":"77133"}}}},"ARO_accession":"3007255","ARO_id":"46001","ARO_name":"MCR-3.31","CARD_short_name":"MCR-3.31","ARO_description":"An MCR-3-type colistin resistance gene variant.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5861":{"model_id":"5861","model_name":"MCR-3.23","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"8555":{"protein_sequence":{"accession":"WP_094313523.1","sequence":"MPSLIKIKIVPLMFFLALYFAFMLNWRGVLHFYEILYKLEDFKFGFAISLPILLVAALNFVFVPFSIRYLIKPFFALLIALSAIVSYTMMKYRVLFDQNMIKNIFETNQNEALAYLSLPIIVWVTIAGFIPAILLFFVEIEYEEKWFKGILTRALSMFASLIVIAVIAALYYQDYVSVGRNNSNLQREIVPANFVNSTVKYVYNRYLAEPIPFTTLGDDAKRDTNQSKPTLMFLVVGETARGKNFSMNGYEKDTNPFTSKSGGVISFNDVRSCGTATAVSVPCMFSNMGRKEFDDNRARNSEGLLDVLQKTGISIFWKENDGGCKGVCDRVPNIEIEPKDHPKFCDKNTCYDEVVLQDLDSEIAQMKGDKLVGFHLIGSHGPTYYKRYPDAHRQFTPDCPRSDIENCTDEELTNTYDNTIRYTDFVIGEMIAKLKTYEDKYNTALLYVSDHGESLGALGLYLHGTPYQFAPDDQTRVPMQVWMSPGFTKEKGVDMACLQQKAADTRYSHDNIFSSVLGIWDVKTSVYEKGLDIFSQCRNVQ"},"dna_sequence":{"accession":"NQCZ01000032.1","fmin":"2791","fmax":"4417","strand":"+","sequence":"ATGCCTTCCCTTATAAAAATAAAAATTGTTCCGCTTATGTTCTTTTTGGCACTGTATTTTGCATTTATGCTGAACTGGCGTGGAGTTCTCCATTTTTACGAAATCCTTTACAAATTAGAAGATTTTAAGTTTGGTTTCGCCATTTCATTACCAATATTGCTTGTTGCAGCGCTTAACTTTGTATTTGTTCCATTTTCGATACGGTATTTAATAAAGCCTTTTTTTGCACTTCTTATCGCACTTAGTGCAATCGTTAGTTACACAATGATGAAGTATAGAGTCTTGTTTGATCAAAACATGATTAAGAATATTTTTGAAACCAATCAAAATGAGGCGTTAGCATATTTAAGCTTACCAATTATAGTATGGGTTACTATTGCTGGTTTTATCCCTGCCATTTTACTTTTCTTTGTTGAAATTGAATATGAGGAAAAATGGTTCAAAGGGATTCTAACTCGTGCCCTATCGATGTTTGCATCACTTATAGTGATTGCGGTTATTGCAGCACTATACTATCAAGATTATGTGTCAGTGGGGCGCAACAATTCAAACCTCCAGCGTGAGATTGTTCCAGCCAATTTCGTTAATAGTACCGTTAAATACGTTTACAATCGTTATCTTGCTGAACCAATCCCATTTACAACTTTAGGTGATGATGCAAAACGGGATACTAATCAAAGTAAGCCCACGTTGATGTTTCTGGTCGTTGGTGAAACCGCTCGTGGTAAAAATTTCTCGATGAATGGCTATGAGAAAGACACCAATCCATTTACCAGTAAATCTGGTGGCGTGATCTCCTTTAATGATGTTCGTTCGTGTGGGACTGCAACCGCTGTATCCGTCCCCTGCATGTTCTCCAATATGGGGAGAAAGGAGTTTGATGATAATCGCGCTCGCAATAGCGAGGGCCTGCTAGATGTGTTGCAAAAAACGGGGATCTCCATTTTTTGGAAGGAGAACGATGGAGGCTGCAAAGGCGTCTGCGACCGAGTACCTAACATCGAAATCGAACCAAAGGATCACCCTAAGTTCTGCGATAAAAACACATGCTATGACGAGGTTGTCCTTCAAGACCTCGATAGTGAAATTGCTCAAATGAAAGGGGATAAGCTGGTTGGCTTCCACCTGATAGGTAGCCATGGCCCAACCTACTACAAGCGCTACCCTGATGCTCATCGTCAGTTCACCCCTGACTGTCCACGCAGTGATATTGAAAACTGCACAGATGAAGAGCTCACCAACACCTATGACAACACCATCCGCTACACCGATTTCGTGATTGGAGAGATGATTGCCAAGTTGAAAACCTACGAAGATAAGTACAACACCGCGTTGCTCTACGTCTCCGATCATGGTGAATCACTGGGAGCATTAGGGCTTTACCTACACGGTACACCGTACCAGTTTGCACCGGATGATCAGACCCGTGTTCCTATGCAGGTGTGGATGTCACCTGGATTTACCAAAGAGAAAGGCGTTGATATGGCGTGTTTGCAGCAGAAAGCCGCTGATACTCGTTACTCACACGATAATATTTTCTCATCTGTATTGGGTATCTGGGACGTCAAAACATCAGTTTACGAAAAGGGTCTAGATATTTTCAGTCAATGTCGTAATGTTCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3007256","ARO_id":"46002","ARO_name":"MCR-3.23","CARD_short_name":"MCR-3.23","ARO_description":"An MCR-3-type colistin resistance gene variant.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5862":{"model_id":"5862","model_name":"MCR-3.36","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"8556":{"protein_sequence":{"accession":"WP_188331895.1","sequence":"MPSLIKIKIVPLMFFLALYFAFMLNWRGVLHFYEILYKLEDFKFGFAISLPILLVAALNFVFVPFSIRYLIKPFFALLIALSAIVSYTMMKYRVLFDQNMIQNIFETNQNEALAYLSLPIIGWVTIAGFIPAILLFFVEIEYEEKWFKGILTRALSMFASLIVIAVIAALYYQDYVSVGRNNSNLQREIVPANFVNSTVKYVYNRYLAEPIPFTTLGDDAKRDTNQSKPTLMFLVVGETARGKNFSMNGYEKDTNPFTSKSGGVISFNDVRSCGTATAVSVPCMFSNMGRKEFDDNLARNSEGLLDVLQKTGVSIFWKENDGGCKGVCDRVPNIEIKPKDYPKFCDKNTCYDEVVLQDLDSEIAQMKGDKLVGFHLIGSHGPTYYKRYPDAHRQFTPDCPRSDIENCTDEELTNTYDNTIRYTDFVIAEMIAKLKTYEDKYNTALLYVSDHGESLGAMGLYLHGTPYKFAPDDQTRVPMQVWMSPGFIKEKGMNMECLQKNAAANRYSHDNIFSSVLGIWDVKTAIYEQELDIFKQCRNN"},"dna_sequence":{"accession":"MT809045.1","fmin":"0","fmax":"1623","strand":"+","sequence":"ATGCCTTCCCTTATAAAAATAAAAATTGTTCCGCTTATGTTTTTTTTGGCACTGTATTTTGCATTTATGCTGAACTGGCGTGGAGTTCTCCATTTTTACGAAATCCTTTACAAATTAGAAGATTTTAAGTTTGGTTTCGCCATTTCATTACCAATATTGCTTGTTGCAGCGCTTAACTTTGTATTTGTTCCATTTTCGATACGGTATTTAATAAAGCCTTTTTTTGCACTTCTTATCGCACTTAGTGCAATCGTTAGTTACACAATGATGAAGTATAGAGTCTTGTTTGATCAAAACATGATTCAGAATATTTTTGAAACCAATCAAAATGAGGCGTTAGCATATTTAAGCTTACCAATTATAGGATGGGTTACTATTGCTGGCTTTATCCCTGCCATTTTACTTTTCTTTGTTGAAATTGAATATGAGGAAAAATGGTTCAAAGGGATTCTAACTCGTGCCCTATCGATGTTTGCATCACTTATAGTGATTGCGGTTATTGCAGCACTATACTATCAAGATTATGTGTCAGTGGGGCGCAACAATTCAAACCTCCAGCGTGAAATTGTTCCAGCCAATTTCGTTAATAGTACCGTTAAATACGTTTACAATCGTTATCTTGCTGAACCAATCCCATTTACAACTTTAGGTGATGATGCAAAACGGGATACTAATCAAAGTAAGCCCACGTTGATGTTTCTGGTCGTTGGTGAAACCGCTCGCGGTAAAAATTTCTCGATGAATGGCTATGAGAAAGACACCAATCCATTTACCAGTAAATCTGGTGGCGTGATCTCCTTTAATGATGTTCGTTCGTGTGGGACTGCAACCGCTGTATCTGTCCCCTGCATGTTCTCCAATATGGGGAGAAAGGAGTTTGATGATAATCTCGCTCGTAATAGCGAGGGTTTGTTAGATGTGTTGCAGAAAACGGGGGTCTCCATTTTTTGGAAGGAGAACGATGGCGGCTGCAAAGGCGTCTGCGACCGAGTTCCTAACATCGAGATCAAACCGAAGGATTACCCAAAGTTCTGCGATAAAAACACATGCTATGACGAGGTTGTCCTTCAAGACCTCGATAGTGAAATTGCTCAAATGAAAGGGGATAAGCTGGTTGGCTTCCACCTGATAGGTAGCCATGGCCCAACCTACTACAAACGCTACCCTGATGCTCATCGTCAGTTCACCCCTGATTGTCCACGCAGTGATATCGAAAACTGCACGGATGAAGAGCTCACCAACACCTATGACAACACCATCCGCTACACCGATTTCGTGATTGCAGAGATGATTGCCAAGTTGAAAACCTACGAAGATAAGTACAACACCGCATTGCTCTACGTCTCCGATCACGGTGAATCACTGGGAGCTATGGGGCTTTACCTGCACGGTACACCGTACAAGTTTGCACCGGATGATCAGACCCGCGTACCTATGCAGGTGTGGATGTCACCTGGTTTCATCAAAGAAAAAGGCATGAATATGGAATGTTTGCAGAAAAATGCCGCAGCCAATCGCTATTCTCATGACAACATATTTTCTTCTGTCCTGGGAATATGGGATGTGAAGACAGCTATCTACGAACAAGAATTAGATATCTTTAAGCAATGTCGGAATAATTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42604","NCBI_taxonomy_name":"Aeromonas jandaei","NCBI_taxonomy_id":"650"}}}},"ARO_accession":"3007257","ARO_id":"46003","ARO_name":"MCR-3.36","CARD_short_name":"MCR-3.36","ARO_description":"An MCR-3-type colistin resistance gene variant.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5863":{"model_id":"5863","model_name":"MCR-3.25","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"8557":{"protein_sequence":{"accession":"WP_103252528.1","sequence":"MPSLIKIKIVPLMFFLALYFAFMLNWRGVLHFYEILYKLEDFKFGFAISLPILLVAALNFVFVPFSIRYLIKPFFALLIALSAIVSYTMMKYRVLFDQNMIQNIFETNQNEALAYLSLPIIGWVTIAGFIPAILLFFVEIEYEEKWFKGILTRALSMFASLIVIAVIAALYYQDYVSVGRNNSNLQREIVPANFVNSTVKYVYNRYLAEPIPFTTLGDDAKRDTNQSKPTLMFLVVGETARGKNFSMNGYEKDTNPFTSKSGGVISFNDVRSCGTATAVSVPCMFSNMGRKEFDDNLARNSEGLLDVLQKTGVSIFWKENDGGCKGVCDRVPNIEIKPKDYPKFCDKNTCYDEVVLQELDSEIAQMKGDKLVGFHLIGSHGPTYYKRYPDAHRQFTPDCPRSDIENCTDEELTNTYDNTIRYTDFVIGEMIAKLKTYEDKYNTALLYVSDHGESLGALGLYLHGTPYKFAPDDQTRVPMQVWMSPGFITEKGMNMECLQKNAAANRYSHDNIFSSVLGIWDVKTAIYEQELDIFKQCRNN"},"dna_sequence":{"accession":"PPTE01000085.1","fmin":"602","fmax":"2225","strand":"+","sequence":"ATGCCTTCCCTTATAAAAATAAAAATTGTTCCGCTTATGTTCTTTTTGGCACTGTATTTTGCATTTATGCTGAACTGGCGTGGAGTTCTCCATTTTTACGAAATCCTTTACAAATTAGAAGATTTTAAGTTTGGTTTCGCCATTTCATTACCAATATTGCTTGTTGCAGCGCTTAACTTTGTATTTGTTCCATTTTCGATACGGTATTTAATAAAGCCTTTTTTTGCACTTCTTATCGCACTTAGTGCAATCGTTAGTTACACAATGATGAAGTATAGAGTCTTGTTTGATCAAAACATGATTCAGAATATTTTTGAAACCAATCAAAATGAGGCGTTAGCATATTTAAGCTTACCAATTATAGGATGGGTTACTATTGCTGGTTTTATCCCTGCCATTTTACTTTTCTTTGTTGAAATTGAATATGAGGAAAAATGGTTCAAAGGGATTCTAACTCGTGCCCTATCGATGTTTGCATCACTTATAGTGATTGCGGTTATTGCAGCACTATACTATCAAGATTATGTGTCAGTGGGGCGCAACAATTCAAACCTCCAGCGTGAGATTGTTCCAGCCAATTTCGTTAATAGTACCGTTAAATACGTTTACAATCGTTATCTTGCTGAACCAATCCCATTTACAACTTTAGGTGATGATGCAAAACGGGATACTAATCAAAGTAAGCCCACGTTGATGTTTCTGGTCGTTGGTGAAACCGCTCGTGGTAAAAATTTCTCGATGAATGGCTATGAGAAAGACACCAATCCATTTACCAGTAAATCTGGTGGCGTGATCTCCTTTAATGATGTTCGTTCGTGTGGGACTGCAACCGCTGTATCTGTCCCCTGCATGTTTTCCAATATGGGGAGAAAGGAGTTTGATGATAATCTCGCTCGTAATAGCGAGGGTTTGTTAGATGTGTTGCAGAAAACGGGGGTCTCCATTTTTTGGAAGGAGAACGATGGCGGCTGCAAAGGCGTCTGCGACCGAGTTCCTAACATCGAGATCAAACCGAAGGATTACCCAAAGTTCTGCGATAAAAACACATGCTATGACGAGGTTGTCCTTCAAGAGCTCGACAGTGAAATTGCTCAAATGAAAGGGGATAAGCTGGTTGGCTTCCACCTGATAGGTAGCCATGGCCCAACCTACTACAAGCGCTACCCTGATGCTCATCGTCAGTTCACCCCTGACTGTCCACGCAGTGATATTGAAAACTGCACAGATGAAGAGCTCACCAACACCTATGACAACACCATCCGCTACACCGATTTCGTGATTGGAGAGATGATTGCCAAGTTGAAAACCTACGAAGATAAGTACAACACCGCGTTGCTCTACGTCTCCGATCATGGTGAATCACTGGGAGCATTAGGGCTTTACCTACACGGTACACCGTACAAGTTTGCACCGGATGATCAGACCCGTGTTCCTATGCAGGTGTGGATGTCACCTGGTTTCATCACAGAAAAAGGCATGAATATGGAATGTTTGCAGAAAAATGCCGCAGCCAATCGCTATTCTCATGACAACATATTTTCTTCTGTCCTGGGAATATGGGATGTGAAGACGGCTATCTACGAACAAGAATTAGATATCTTTAAGCAATGTCGGAATAATTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39677","NCBI_taxonomy_name":"Aeromonas veronii","NCBI_taxonomy_id":"654"}}}},"ARO_accession":"3007258","ARO_id":"46004","ARO_name":"MCR-3.25","CARD_short_name":"MCR-3.25","ARO_description":"An MCR-3-type colistin resistance gene variant.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5864":{"model_id":"5864","model_name":"MCR-3.22","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"8558":{"protein_sequence":{"accession":"WP_094308975.1","sequence":"MPSLIKIKIVPLMFFLALYFAFMLNWRGVLHFYEILYKLEDFKFGFAISLPILLVAALNFVFVPFSIRYLIKPFFALLIALSAIVSYTMMKYRVLFDQNMIQNIFETNQNEALAYLSLPIIVWVTIAGFIPAILLFFVEIEYEEKWFKGILTRALSMFASLIVIAVIAALYYQDYVSVGRNNSNLQREIVPANFVNSTVKYVYNRYLAEPIPFTTLGDDAKRDTNQSKPTLMFLVVGETARGKNFSMNGYEKDTNPFTSKSGGVISFNDVRSCGTATAVSVPCMFSNMGRKEFDDDRARNSEGLLDVLQKTGISIFWKENDGGCKGVCDRVPNIEIEPKDHPKFCDKNTCYDEVVLQDLDSEIAQMKGDKLVVFHLIGSHGPTYYKRYPDAHRQFTPDCPRSDIENCTDEELTNTYDNTIRYTDFVIGEMIAKLKTYEDKYNTALLYVSDHGESLGALGLYLHGTPYQFAPDDQTRVPMQVWMSPGFTKEKGVDMACLQQKAADTRYSHDNIFSSVLGIWDVKTSVYEKGLDIFSQCRNVQ"},"dna_sequence":{"accession":"NQCT02000005.1","fmin":"57","fmax":"1683","strand":"+","sequence":"ATGCCTTCCCTTATAAAAATAAAAATTGTTCCGCTTATGTTCTTTTTGGCACTGTATTTTGCATTTATGCTGAACTGGCGTGGAGTTCTCCATTTTTACGAAATCCTTTACAAATTAGAAGATTTTAAGTTTGGTTTCGCCATTTCATTACCAATATTGCTTGTTGCAGCGCTTAACTTTGTATTTGTTCCATTTTCGATACGGTATTTAATAAAGCCTTTTTTTGCACTTCTTATCGCACTTAGTGCAATCGTTAGTTACACAATGATGAAGTATAGAGTCTTGTTTGATCAAAACATGATTCAGAATATTTTTGAAACCAATCAAAATGAGGCGTTAGCATATTTAAGCTTACCAATTATAGTATGGGTTACTATTGCTGGTTTTATCCCTGCCATTTTACTTTTCTTTGTTGAAATTGAATATGAGGAAAAATGGTTCAAAGGGATTCTAACTCGTGCCCTATCGATGTTTGCATCACTTATAGTGATTGCGGTTATTGCAGCACTATACTATCAAGATTATGTGTCAGTGGGGCGCAACAATTCAAACCTCCAGCGTGAGATTGTTCCAGCCAATTTCGTTAATAGTACCGTTAAATACGTTTACAATCGTTATCTTGCTGAACCAATCCCATTTACAACTTTAGGTGATGATGCAAAACGGGATACTAATCAAAGTAAGCCCACGTTGATGTTTCTGGTCGTTGGTGAAACCGCTCGTGGTAAAAATTTCTCGATGAATGGCTATGAGAAAGACACCAATCCATTTACCAGTAAATCTGGTGGCGTGATCTCCTTTAATGATGTTCGTTCGTGTGGGACTGCAACCGCTGTATCCGTCCCCTGCATGTTCTCCAATATGGGGAGAAAGGAGTTTGATGATGATCGCGCTCGCAATAGCGAGGGCCTGCTAGATGTGTTGCAAAAAACGGGGATCTCCATTTTTTGGAAGGAGAACGATGGAGGCTGCAAAGGCGTCTGCGACCGAGTACCTAACATCGAAATCGAACCAAAGGATCACCCTAAGTTCTGCGATAAAAACACATGCTATGACGAGGTTGTCCTTCAAGACCTCGATAGTGAAATTGCTCAAATGAAAGGGGATAAGCTGGTTGTCTTCCACCTGATAGGTAGCCATGGCCCAACCTACTACAAGCGCTACCCTGATGCTCATCGTCAGTTCACCCCTGACTGTCCACGCAGTGATATTGAAAACTGCACAGATGAAGAGCTCACCAACACCTATGACAACACCATCCGCTACACCGATTTCGTGATTGGAGAGATGATTGCCAAGTTGAAAACCTACGAAGATAAGTACAACACCGCGTTGCTCTACGTCTCCGATCATGGTGAATCACTGGGAGCATTAGGGCTTTACCTACACGGTACACCGTACCAGTTTGCACCGGATGATCAGACCCGTGTTCCTATGCAGGTGTGGATGTCACCTGGATTTACCAAAGAGAAAGGCGTTGATATGGCGTGTTTGCAGCAGAAAGCCGCTGATACTCGTTACTCACACGATAATATTTTCTCATCTGTATTGGGTATCTGGGACGTCAAAACATCAGTTTACGAAAAGGGTCTAGATATTTTCAGTCAATGTCGTAATGTTCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37059","NCBI_taxonomy_name":"Klebsiella","NCBI_taxonomy_id":"570"}}}},"ARO_accession":"3007259","ARO_id":"46005","ARO_name":"MCR-3.22","CARD_short_name":"MCR-3.22","ARO_description":"An MCR-3-type colistin resistance gene variant.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5865":{"model_id":"5865","model_name":"MCR-3.16","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"8559":{"protein_sequence":{"accession":"WP_111273845.1","sequence":"MPSLIKIKIVPLMFFLALYFAFMLNWRGVLHFYEILYKLEDFKFGFAISLPILLVAALNFVFVPFSIRYLIKPFFALLIALSAIVSYTMMKYRVLFDQNMIQNIFETNQNEALAYLSLPIIVWVTIAGFIPAILLFFVEIEYEEKWFKGILTRALSMFASLIVIAVIAALYYQDYVSVGRNNSNLQREIVPANFVNSTVKYVYNRYLAEPIPFTTLGDDAKRDTNQSKPTLMFLVVGETARGKNFSMNGYEKDTNPFTSKSGGVISFNDVRSCGTATAVSVPCMFSNMGRKEFDDNLARNSEGLLDVLQKTGVSIFWKENDGGCKGVCDRVPNIEIKPKDYPKFCDKNTCYDEVVLQELDSEIAQMKGDKLVGFHLIGSHGPTYYKRYPDAHRQFTPDCPRSDIENCTDEELTNTYDNTIRYTDFVIAEMIAKLKTYEDKYNTALLYVSDHGESLGALGLYLHGTPYKFAPDDQTRVPMQVWMSPGFIKEKGMNMECLQKNAAANRYSHDNIFSSVLGIWDVKTAIYEQELDIFKQCRNN"},"dna_sequence":{"accession":"MH332766.1","fmin":"0","fmax":"1623","strand":"+","sequence":"ATGCCTTCCCTTATAAAAATAAAAATTGTTCCGCTTATGTTCTTTTTGGCACTGTATTTTGCATTTATGCTGAACTGGCGTGGAGTTCTCCATTTTTACGAAATCCTTTACAAATTAGAAGATTTTAAGTTTGGTTTCGCCATTTCATTACCAATATTGCTTGTTGCAGCGCTTAACTTTGTATTTGTTCCATTTTCGATACGGTATTTAATAAAGCCTTTTTTTGCACTTCTTATCGCACTTAGTGCAATCGTTAGTTACACAATGATGAAGTATAGAGTCTTGTTTGATCAAAACATGATTCAGAATATTTTTGAAACCAATCAAAATGAGGCGTTAGCATATTTAAGCTTACCAATAATAGTATGGGTTACTATTGCTGGTTTTATCCCTGCCATTTTACTTTTCTTTGTTGAAATTGAATATGAGGAAAAATGGTTCAAAGGGATTCTAACTCGTGCCCTATCGATGTTTGCATCACTTATAGTGATTGCGGTTATTGCAGCACTATACTATCAAGATTATGTGTCAGTGGGGCGCAACAATTCAAACCTCCAGCGTGAGATTGTTCCAGCCAATTTCGTTAATAGTACCGTTAAATACGTTTACAATCGTTATCTTGCTGAACCAATCCCATTTACAACTTTAGGTGATGATGCAAAACGGGATACTAATCAAAGTAAGCCCACGTTGATGTTTCTGGTCGTTGGTGAAACCGCTCGTGGTAAAAATTTCTCGATGAATGGCTATGAGAAAGACACCAATCCATTTACCAGTAAATCTGGTGGCGTGATCTCCTTTAATGATGTTCGTTCGTGTGGGACTGCAACCGCTGTATCTGTCCCCTGCATGTTTTCCAATATGGGGAGAAAGGAGTTTGATGATAATCTCGCTCGTAATAGCGAGGGTTTGTTAGATGTGTTGCAGAAAACGGGGGTCTCCATTTTTTGGAAGGAGAACGATGGCGGCTGCAAAGGCGTCTGCGACCGAGTTCCTAACATCGAGATCAAACCGAAGGATTACCCAAAGTTCTGCGATAAAAACACATGCTATGACGAGGTTGTCCTTCAAGAGCTCGACAGTGAAATTGCTCAAATGAAAGGGGATAAGCTGGTTGGCTTCCACCTGATAGGTAGCCATGGCCCAACCTACTACAAACGCTACCCTGATGCTCATCGTCAGTTCACTCCTGACTGTCCACGCAGTGATATTGAAAACTGCACAGATGAAGAGCTCACCAACACCTATGACAACACCATCCGCTACACCGATTTCGTGATTGCAGAGATGATTGCCAAGTTGAAAACCTACGAAGATAAGTACAACACCGCGTTGCTCTACGTCTCCGATCATGGTGAATCACTGGGAGCATTAGGGCTTTACCTGCACGGTACACCGTACAAGTTTGCACCGGATGATCAGACCCGTGTTCCTATGCAGGTGTGGATGTCACCTGGTTTCATCAAAGAAAAAGGCATGAATATGGAATGTTTGCAGAAAAATGCCGCAGCCAATCGCTATTCTCATGACAACATATTTTCTTCTGTCCTGGGAATATGGGATGTGAAGACGGCTATCTACGAACAAGAATTAGATATCTTTAAGCAATGTCGGAATAATTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37047","NCBI_taxonomy_name":"Aeromonas","NCBI_taxonomy_id":"642"}}}},"ARO_accession":"3007260","ARO_id":"46006","ARO_name":"MCR-3.16","CARD_short_name":"MCR-3.16","ARO_description":"An MCR-3-type colistin resistance gene variant.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5866":{"model_id":"5866","model_name":"MCR-3.26","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"8560":{"protein_sequence":{"accession":"WP_140423331.1","sequence":"MPSLIKIKIVPLMFFLALYFAFMLNWRGVLHFYEILYKLEDFKFGFAISLPILLVAALNFVFVPFSIRYLIKPFFALLIALSAIVSYTMMKYRVLFDQNMIQNIFETNQNEALAYLSLPIIVWVTIAGFIPAILLFFVEIEYEEKWFKGILTRALSMFASLIVIAVIAALYYQDYVSVGRNNSNLQREIVPANFVNSTVKYVYNRYLAEPIPFTTLGDDAKRDTNQSKPTLMFLVVGETARGKNFSMNGYEKDTNPFTSKSGGVISFNDVRSCGTATAVSVPCMFSNMGRKEFDDDRARNSEGLLDVLQKTGISIFWKENDGGCKGVCDRVPNIEIEPKDHPKFCDKNTCYDEVVLQDLDSEIAQMKGDKLVGFHLIGSHGPTYYKRYPDAHRQFTPDCPRSDIENCTDEELTNTYDNTIRYTDFVIGEMIAKLKTYEDKYNTALLYVSDHGESLGALGLYLHGTPYQFAPDDQTRVPMQVWMSPGFTKEKGVDMACLQQKAADTRYSHDNIFSSVLGIWDVKTSVYEKGLDIFSQCRNVQ"},"dna_sequence":{"accession":"MH371139.1","fmin":"0","fmax":"1626","strand":"+","sequence":"ATGCCTTCCCTTATAAAAATAAAAATTGTTCCGCTTATGTTCTTTTTGGCACTGTATTTTGCATTTATGCTGAACTGGCGTGGAGTTCTCCATTTTTACGAAATCCTTTACAAATTAGAAGATTTTAAGTTTGGTTTCGCCATTTCATTACCAATATTGCTTGTTGCAGCGCTTAACTTTGTATTTGTTCCATTTTCGATACGGTATTTAATAAAGCCTTTTTTTGCACTTCTTATCGCACTTAGTGCAATCGTTAGTTACACAATGATGAAGTATAGAGTCTTGTTTGATCAAAACATGATTCAGAATATTTTTGAAACCAATCAAAATGAGGCGTTAGCATATTTAAGCTTACCAATTATAGTATGGGTTACTATTGCTGGTTTTATCCCTGCCATTTTACTTTTCTTTGTTGAAATTGAATATGAGGAAAAATGGTTCAAAGGGATTCTAACTCGTGCCCTATCGATGTTTGCATCACTTATAGTGATTGCGGTTATTGCAGCACTATACTATCAAGATTATGTGTCAGTGGGGCGCAACAATTCAAACCTCCAGCGTGAGATTGTTCCAGCCAATTTCGTTAATAGTACCGTTAAATACGTTTACAATCGTTATCTTGCTGAACCAATCCCATTTACAACTTTAGGTGATGATGCAAAACGGGATACTAATCAAAGTAAGCCCACGTTGATGTTTCTGGTCGTTGGTGAAACCGCTCGTGGTAAAAATTTCTCGATGAATGGCTATGAGAAAGACACCAATCCATTTACCAGTAAATCTGGTGGCGTGATCTCCTTTAATGATGTTCGTTCGTGTGGGACTGCAACCGCTGTATCCGTCCCCTGCATGTTCTCCAATATGGGGAGAAAGGAGTTTGATGATGATCGCGCTCGCAATAGCGAGGGCCTGCTAGATGTGTTGCAAAAAACGGGGATCTCCATTTTTTGGAAGGAGAACGATGGAGGCTGCAAAGGCGTCTGCGACCGAGTACCTAACATCGAAATCGAACCAAAGGATCACCCTAAGTTCTGCGATAAAAACACATGCTATGACGAGGTTGTCCTTCAAGACCTCGATAGTGAAATTGCTCAAATGAAAGGGGATAAGCTGGTTGGCTTCCACCTGATAGGTAGCCATGGCCCAACCTACTACAAGCGCTACCCTGATGCTCATCGTCAGTTCACCCCTGACTGTCCACGCAGTGATATTGAAAACTGCACAGATGAAGAGCTCACCAACACCTATGACAACACCATCCGCTACACCGATTTCGTGATTGGAGAGATGATTGCCAAGTTGAAAACCTACGAAGATAAGTACAACACCGCGTTGCTCTACGTCTCCGATCATGGTGAATCACTGGGAGCATTAGGGCTTTACCTACACGGTACACCGTACCAGTTTGCACCGGATGATCAGACCCGTGTTCCTATGCAGGTGTGGATGTCACCTGGATTTACCAAAGAGAAAGGCGTTGATATGGCGTGTTTGCAGCAGAAAGCCGCTGATACTCGTTACTCACACGATAATATTTTCTCATCTGTATTGGGTATCTGGGACGTCAAAACATCAGTTTACGAAAAGGGTCTAGATATTTTCAGTCAATGTCGTAATGTTCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3007261","ARO_id":"46007","ARO_name":"MCR-3.26","CARD_short_name":"MCR-3.26","ARO_description":"An MCR-3-type colistin resistance gene variant.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5867":{"model_id":"5867","model_name":"MCR-3.21","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"8561":{"protein_sequence":{"accession":"AWY10763.1","sequence":"MPSLIKIKIVPLMFFLALYFAFMLNWRGVLHFYEILYKLEDFKFGFAISLPILLVAALNFVFVPFSIRYLIKPFFALLIALSAIVSYTMMKYRVLFDQNMIQNIFETNQNEALAYLSLPIIVWVTIAGFIPAILLFFVEIEYEEKWFKGILTRALSMFASLIVIAVIAALYYQDYVSVGRNNSNLQREIVPANFVNSTVKYVYNRYLAEPIPFTTLGDDAKRDTNQSKPTLMFLVVGETARGKNFSMNGYEKDTNPFTSKSGGVISFNDVRSCGTATAVSVPCMFSNMGRKEFDDDRARNSEGLLDVLQKTGISIFWKENDGGCKGVCDRVPNIEIEPKDHPKFCDKNTCYDEVVLQDLDSEIAQMKGDKLVGFHLIGSHGPTYYKRYPDAHRQFTPDCPRSDIENCTDEELTNTYDNTIRYTDFVIGEMIAKLKTYEDKYNTALLYVSDHGESLGALGLYLHGTPYKFAPDDQTRVPMQVWMSPGFTKEKGVDMACLQQKAADTRYSHDNIFSSVLGIWDVKTSVYEKGLDIFSQCRNVQ"},"dna_sequence":{"accession":"MH423812.1","fmin":"0","fmax":"1626","strand":"+","sequence":"ATGCCTTCCCTTATAAAAATAAAAATTGTTCCGCTTATGTTCTTTTTGGCACTGTATTTTGCATTTATGCTGAACTGGCGTGGAGTTCTCCATTTTTACGAAATCCTTTACAAATTAGAAGATTTTAAGTTTGGTTTCGCCATTTCATTACCAATATTGCTTGTTGCAGCGCTTAACTTTGTATTTGTTCCATTTTCGATACGGTATTTAATAAAGCCTTTTTTTGCACTTCTTATCGCACTTAGTGCAATCGTTAGTTACACAATGATGAAGTATAGAGTCTTGTTTGATCAAAACATGATTCAGAATATTTTTGAAACCAATCAAAATGAGGCGTTAGCATATTTAAGCTTACCAATTATAGTATGGGTTACTATTGCTGGTTTTATCCCTGCCATTTTACTTTTCTTTGTTGAAATTGAATATGAGGAAAAATGGTTCAAAGGGATTCTAACTCGTGCCCTATCGATGTTTGCATCACTTATAGTGATTGCGGTTATTGCAGCACTATACTATCAAGATTATGTGTCAGTGGGGCGCAACAATTCAAACCTCCAGCGTGAGATTGTTCCAGCCAATTTCGTTAATAGTACCGTTAAATACGTTTACAATCGTTATCTTGCTGAACCAATCCCATTTACAACTTTAGGTGATGATGCAAAACGGGATACTAATCAAAGTAAGCCCACGTTGATGTTTCTGGTCGTTGGTGAAACCGCTCGTGGTAAAAATTTCTCGATGAATGGCTATGAGAAAGACACCAATCCATTTACCAGTAAATCTGGTGGCGTGATCTCCTTTAATGATGTTCGTTCGTGTGGGACTGCAACCGCTGTATCCGTCCCCTGCATGTTCTCCAATATGGGGAGAAAGGAGTTTGATGATGATCGCGCTCGCAATAGCGAGGGCCTGCTAGATGTGTTGCAAAAAACGGGGATCTCCATTTTTTGGAAGGAGAACGATGGAGGCTGCAAAGGCGTCTGCGACCGAGTACCTAACATCGAAATCGAACCAAAGGATCACCCTAAGTTCTGCGATAAAAACACATGCTATGACGAGGTTGTCCTTCAAGACCTCGATAGTGAAATTGCTCAAATGAAAGGGGATAAGCTGGTTGGCTTCCACCTGATAGGTAGCCATGGCCCAACCTACTACAAGCGCTACCCTGATGCTCATCGTCAGTTCACCCCTGACTGTCCACGCAGTGATATTGAAAACTGCACAGATGAAGAGCTCACCAACACCTATGACAACACCATCCGCTACACCGATTTCGTGATTGGAGAGATGATTGCCAAGTTGAAAACCTACGAAGATAAGTACAACACCGCGTTGCTCTACGTCTCCGATCATGGTGAATCACTGGGAGCATTAGGGCTTTACCTACACGGTACACCGTACAAGTTTGCACCGGATGATCAGACCCGTGTTCCTATGCAGGTGTGGATGTCACCTGGATTTACCAAAGAGAAAGGCGTTGATATGGCGTGTTTGCAGCAGAAAGCCGCTGATACTCGTTACTCACACGATAATATTTTCTCATCTGTATTGGGTATCTGGGACGTCAAAACATCAGTTTACGAAAAGGGTCTAGATATTTTCAGTCAATGTCGTAATGTTCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3007262","ARO_id":"46008","ARO_name":"MCR-3.21","CARD_short_name":"MCR-3.21","ARO_description":"An MCR-3-type colistin resistance gene variant.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5868":{"model_id":"5868","model_name":"MCR-3.18","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"8562":{"protein_sequence":{"accession":"WP_111273847.1","sequence":"MPSLIKIKIVPLMFFLALYFAFMLNWRGVLHFYEILYKLEDFKFGFAISLPILLVAALNFVFVPFSIRYLIKPFFALLIALSAIVSYTMMKYRVLFDQNMIQNIFETNQNEALAYLSLPIIVWVTIAGFIPAILLFFVEIEYEEKWFKGILTRALSMFASLIVIAVIAALYYQDYVSVGRNNSNLQREIVPANFVNSTVKYVYNRYLAEPIPFTTLGDDAKRDTNQSKPTLMFLVVGETARGKNFSMNGYEKDTNPFTSKSGGVISFNDVRSCGTATAVSVPCMFSNMGRKEFDDNLARNSEGLLDVLQKTGVSIFWKENDGGCKGVCDRVPNIEIKPKDYPKFCDKNTCYDEVVLQELDSEIAQMKGDKLVGFHLIGSHGPTYYKRYPDAHRQFTPDCPSSDIENCTDEELTNTYDNTIRYTDFVIAEMIAKLKTYEDKYNTALLYVSDHGESLGALGLYLHGTPYKFAPDDQTRVPMQVWMSPGFIKEKGMNMECLQKNAAANRYSHDNIFSSVLGIWDVKTAIYEQELDIFKQCRNN"},"dna_sequence":{"accession":"MH332768.1","fmin":"0","fmax":"1623","strand":"+","sequence":"ATGCCTTCCCTTATAAAAATAAAAATTGTTCCGCTTATGTTCTTTTTGGCACTGTATTTTGCATTTATGCTGAACTGGCGTGGAGTTCTCCATTTTTACGAAATCCTTTACAAATTAGAAGATTTTAAGTTTGGTTTCGCCATTTCATTACCAATATTGCTTGTTGCAGCGCTTAACTTTGTATTTGTTCCATTTTCGATACGGTATTTAATAAAGCCTTTTTTTGCACTTCTTATCGCACTTAGTGCAATCGTTAGTTACACAATGATGAAGTATAGAGTCTTGTTTGATCAAAACATGATTCAGAATATTTTTGAAACCAATCAAAATGAGGCGTTAGCATATTTAAGCTTACCAATTATAGTATGGGTTACTATTGCTGGTTTTATCCCTGCCATTTTACTTTTCTTTGTTGAAATTGAATATGAGGAAAAATGGTTCAAAGGGATTCTAACTCGTGCCCTATCGATGTTTGCATCACTTATAGTGATTGCGGTTATTGCAGCACTATACTATCAAGATTATGTGTCAGTGGGGCGCAACAATTCAAACCTCCAGCGTGAGATTGTTCCAGCCAATTTCGTTAATAGTACCGTTAAATACGTTTACAATCGTTATCTTGCTGAACCAATCCCATTTACAACTTTAGGTGATGATGCAAAACGGGATACTAATCAAAGTAAGCCCACGTTGATGTTTCTGGTCGTTGGTGAAACCGCTCGTGGTAAAAATTTCTCGATGAATGGCTATGAGAAAGACACCAATCCATTTACCAGTAAATCTGGTGGCGTGATCTCCTTTAATGATGTTCGTTCGTGTGGGACTGCAACCGCTGTATCTGTCCCCTGCATGTTTTCCAATATGGGGAGAAAGGAGTTTGATGATAATCTCGCTCGTAATAGCGAGGGTTTGTTAGATGTGTTGCAGAAAACGGGGGTCTCCATTTTTTGGAAGGAGAACGATGGCGGCTGCAAAGGCGTCTGCGACCGAGTTCCTAACATCGAGATCAAACCGAAGGATTACCCAAAGTTCTGCGATAAAAACACATGCTATGACGAGGTTGTCCTTCAAGAGCTCGACAGTGAAATTGCTCAAATGAAAGGGGATAAGCTGGTTGGCTTCCACCTGATAGGTAGCCATGGCCCAACCTACTACAAACGCTACCCTGATGCTCATCGTCAGTTCACTCCTGACTGTCCAAGCAGTGATATTGAAAACTGCACAGATGAAGAGCTCACCAACACCTATGACAACACCATCCGCTACACCGATTTCGTGATTGCAGAGATGATTGCCAAGTTGAAAACCTACGAAGATAAGTACAACACCGCGTTGCTCTACGTCTCCGATCATGGTGAATCACTGGGAGCATTAGGGCTTTACCTGCACGGTACACCGTACAAGTTTGCACCGGATGATCAGACCCGTGTTCCTATGCAGGTGTGGATGTCACCTGGTTTCATCAAAGAAAAAGGCATGAATATGGAATGTTTGCAGAAAAATGCCGCAGCCAATCGCTATTCTCATGACAACATATTTTCTTCTGTCCTGGGAATATGGGATGTGAAGACGGCTATCTACGAACAAGAATTAGATATCTTTAAGCAATGTCGGAATAATTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36936","NCBI_taxonomy_name":"Aeromonas caviae","NCBI_taxonomy_id":"648"}}}},"ARO_accession":"3007263","ARO_id":"46009","ARO_name":"MCR-3.18","CARD_short_name":"MCR-3.18","ARO_description":"An MCR-3-type colistin resistance gene variant.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5869":{"model_id":"5869","model_name":"MCR-3.40","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"8563":{"protein_sequence":{"accession":"WP_188331897.1","sequence":"MPSLIKIKIVPLMFFLALYFAFMLNWRGVLHFYEILYKLEDFKFGFAISLPILLVAALNFVFVPFSIRYLIKPFFALLIALSAIVSYTMMKYRVLFDQNMIQNIFETNQNEALAYLSLPIIVWVTIAGFIPAILLFFVEIEYEEKWFKGILTRALSMFASLIVIAVIAALYYQDYVSVGRNNSNLQREIVPANFVNSTVKYVYNRYLAEPIPFTTLGDDAKRDTNQSKPTLMFLVVGETARGKNFSMNGYEKDTNPFTSKSGGVISFNDVRSCGTATAVSVPCMFSNMGRKEFDDNRARNSEGLLDVLQKTGISIFWKENDGGCKGVCDRVPNIEIEPKDHPKFCDKNTCYDEVVLQDLDSEIAQMKGDKLVGFHLIGSHGPTYYKRYPDAHRQFTPDCPRSDIENCTDEELTNTYDNTIRYTDFVIGEMIAKLKTYEDKYNTALLYVSDHGESLGALGLYLHGTPYTFAPDDQTRVPMQVWMSPGFTKEKGVDMACLQQKAADTRYSHDNIFSSVLGIWDVKTSVYEKGLDIFSQCRNVQ"},"dna_sequence":{"accession":"MT872722.1","fmin":"0","fmax":"1626","strand":"+","sequence":"ATGCCTTCCCTTATAAAAATAAAAATTGTTCCGCTTATGTTCTTTTTGGCACTGTATTTTGCATTTATGCTGAACTGGCGTGGAGTTCTCCATTTTTACGAAATCCTTTACAAATTAGAAGATTTTAAGTTTGGTTTCGCCATTTCATTACCAATATTGCTTGTTGCAGCGCTTAACTTTGTATTTGTTCCATTTTCGATACGGTATTTAATAAAGCCTTTTTTTGCACTTCTTATCGCACTTAGTGCAATCGTTAGTTACACAATGATGAAGTATAGAGTCTTGTTTGATCAAAACATGATTCAGAATATTTTTGAAACCAATCAAAATGAGGCGTTAGCATATTTAAGCTTACCAATTATAGTATGGGTTACTATTGCTGGTTTTATCCCTGCCATTTTACTTTTCTTTGTTGAAATTGAATATGAGGAAAAATGGTTCAAAGGGATTCTAACTCGTGCCCTATCGATGTTTGCATCACTTATAGTGATTGCGGTTATTGCAGCACTATACTATCAAGATTATGTGTCAGTGGGGCGCAACAATTCAAACCTCCAGCGTGAGATTGTTCCAGCCAATTTCGTTAATAGTACCGTTAAATACGTTTACAATCGTTATCTTGCTGAACCAATCCCATTTACAACTTTAGGTGATGATGCAAAACGGGATACTAATCAAAGTAAGCCCACGTTGATGTTTCTGGTCGTTGGTGAAACCGCTCGTGGTAAAAATTTCTCGATGAATGGCTATGAGAAAGACACCAATCCATTTACCAGTAAATCTGGTGGCGTGATCTCCTTTAATGATGTTCGTTCGTGTGGGACTGCAACCGCTGTATCCGTCCCCTGCATGTTCTCCAATATGGGGAGAAAGGAGTTTGATGATAATCGCGCTCGCAATAGCGAGGGCCTGCTAGATGTGTTGCAAAAAACGGGGATCTCCATTTTTTGGAAGGAGAACGATGGAGGCTGCAAAGGCGTCTGCGACCGAGTACCTAACATCGAAATCGAACCAAAGGATCACCCTAAGTTCTGCGATAAAAACACATGCTATGACGAGGTTGTCCTTCAAGACCTCGATAGTGAAATTGCTCAAATGAAAGGGGATAAGCTGGTTGGCTTCCACCTGATAGGTAGCCATGGCCCAACCTACTACAAGCGCTACCCTGATGCTCATCGTCAGTTCACCCCTGACTGTCCACGCAGTGATATTGAAAACTGCACAGATGAAGAGCTCACCAACACCTATGACAACACCATCCGCTACACCGATTTCGTGATTGGAGAGATGATTGCCAAGTTGAAAACCTACGAAGATAAGTACAACACCGCGTTGCTCTACGTCTCCGATCATGGTGAATCACTGGGAGCATTAGGGCTTTACCTACACGGTACACCGTACACGTTTGCACCGGATGATCAGACCCGTGTTCCTATGCAGGTGTGGATGTCACCTGGATTTACCAAAGAGAAAGGCGTTGATATGGCGTGTTTGCAGCAGAAAGCCGCTGATACTCGTTACTCACACGATAATATTTTCTCATCTGTATTGGGTATCTGGGACGTCAAAACATCAGTTTACGAAAAGGGTCTAGATATTTTCAGTCAATGTCGTAATGTTCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3007264","ARO_id":"46010","ARO_name":"MCR-3.40","CARD_short_name":"MCR-3.40","ARO_description":"An MCR-3-type colistin resistance gene variant.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5870":{"model_id":"5870","model_name":"MCR-3.24","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"8564":{"protein_sequence":{"accession":"WP_094321595.1","sequence":"MPSLIKIKIVPLMFFLALYFAFMLNWRGVLHFYEILYKLEDFKFGFAISLPILLVAALNFVFVPFSIRYLIKPFFALLIALSAIVSYTMMKYRVLFDQNMIQNIFETNQNEALAYLSLPIIVWVTIAGFIPAILLFFVEIEYEEKWFKGILTRALSMFASLIVIAVIAALYYQDYVSVGRNNSNLQREIVPANFVNSTVKYVYNRYLAEPIPFTTLGDDAKRDTNQSKPTLMFLVVGETARGKNFSMNGYEKDTNPFTSKSGGVISFNDVRSCGTATAVSVPCMFSNMGRKEFDDNRARNSEGLLDVLQKTGISIFWKENDGGCKGVCDRVPNIEIEPKDHPKFCDKNTCYDEVVLQDLDSEIAQMKGDKLVGFHLIGSHGPTYYKRYPDAHRQFTPDCPRSDIENCTDEELTNTYDNTIRYTDFVIGEMIAKLKTYEDKYNTALLYVSDHGESLGALGLYLHGTPYNFAPDDQTRVPMQVWMSPGFTKEKGVDMACLQQKAADTRYSHDNIFSSVLGIWDVKTSVYEKGLDIFSQCRNVQ"},"dna_sequence":{"accession":"NQCB01000188.1","fmin":"5572","fmax":"7198","strand":"+","sequence":"ATGCCTTCCCTTATAAAAATAAAAATTGTTCCGCTTATGTTCTTTTTGGCACTGTATTTTGCATTTATGCTGAACTGGCGTGGAGTTCTCCATTTTTACGAAATCCTTTACAAATTAGAAGATTTTAAGTTTGGTTTCGCCATTTCATTACCAATATTGCTTGTTGCAGCGCTTAACTTTGTATTTGTTCCATTTTCGATACGGTATTTAATAAAGCCTTTTTTTGCACTTCTTATCGCACTTAGTGCAATCGTTAGTTACACAATGATGAAGTATAGAGTCTTGTTTGATCAAAACATGATTCAGAATATTTTTGAAACCAATCAAAATGAGGCGTTAGCATATTTAAGCTTACCAATTATAGTATGGGTTACTATTGCTGGTTTTATCCCTGCCATTTTACTTTTCTTTGTTGAAATTGAATATGAGGAAAAATGGTTCAAAGGGATTCTAACTCGTGCCCTATCGATGTTTGCATCACTTATAGTGATTGCGGTTATTGCAGCACTATACTATCAAGATTATGTGTCAGTGGGGCGCAACAATTCAAACCTCCAGCGTGAGATTGTTCCAGCCAATTTCGTTAATAGTACCGTTAAATACGTTTACAATCGTTATCTTGCTGAACCAATCCCATTTACAACTTTAGGTGATGATGCAAAACGGGATACTAATCAAAGTAAGCCCACGTTGATGTTTCTGGTCGTTGGTGAAACCGCTCGTGGTAAAAATTTCTCGATGAATGGCTATGAGAAAGACACCAATCCATTTACCAGTAAATCTGGTGGCGTGATCTCCTTTAATGATGTTCGTTCGTGTGGGACTGCAACCGCTGTATCCGTCCCCTGCATGTTCTCCAATATGGGGAGAAAGGAGTTTGATGATAATCGCGCTCGCAATAGCGAGGGCCTGCTAGATGTGTTGCAAAAAACGGGGATCTCCATTTTTTGGAAGGAGAACGATGGAGGCTGCAAAGGCGTCTGCGACCGAGTACCTAACATCGAAATCGAACCAAAGGATCACCCTAAGTTCTGCGATAAAAACACATGCTATGACGAGGTTGTCCTTCAAGACCTCGATAGTGAAATTGCTCAAATGAAAGGGGATAAGCTGGTTGGCTTCCACCTGATAGGTAGCCATGGCCCAACCTACTACAAGCGCTACCCTGATGCTCATCGTCAGTTCACCCCTGACTGTCCACGCAGTGATATTGAAAACTGCACAGATGAAGAGCTCACCAACACCTATGACAACACCATCCGCTACACCGATTTCGTGATTGGAGAGATGATTGCCAAGTTGAAAACCTACGAAGATAAGTACAACACCGCGTTGCTCTACGTCTCCGATCATGGTGAATCACTGGGAGCATTAGGGCTTTACCTACACGGTACACCGTACAACTTTGCACCGGATGATCAGACCCGTGTTCCTATGCAGGTGTGGATGTCACCTGGATTTACCAAAGAGAAAGGCGTTGATATGGCGTGTTTGCAGCAGAAAGCCGCTGATACTCGTTACTCACACGATAATATTTTCTCATCTGTATTGGGTATCTGGGACGTCAAAACATCAGTTTACGAAAAGGGTCTAGATATTTTCAGTCAATGTCGTAATGTTCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3007265","ARO_id":"46011","ARO_name":"MCR-3.24","CARD_short_name":"MCR-3.24","ARO_description":"An MCR-3-type colistin resistance gene variant.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5871":{"model_id":"5871","model_name":"MCR-3.20","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"8751":{"protein_sequence":{"accession":"BCG06510.1","sequence":"MFDQNMIQNIFETNQNEALAYLSLPIIVWVTIAGFIPAILLFFVEIEYEEKWFKGILTRALSMFASLIVIAVIAALYYQDYVSVGRNNSNLQREIVPANFVNSTVKYVYNRYLAEPIPFTTLGDDAKRDTNQSKPTLMFLVVGETARGKNFSMNGYEKDTNPFTSKSGGVISFNDVRSCGTATAVSVPCMFSNMGRKEFDENRARNSEGLLDVLQKTGISIFWKENDGGCKGVCDRVPNIEIEPKDHPKFCDKNTCYDEVVLQDLDSEIAQMKGDKLVGFHLIGSHGPTYYKRYPDAHRQFTPDCPRSDIENCTDEELTNTYDNTIRYTDFVIGEMIAKLKTYEDKYNTALLYVSDHGESLGALGLYLHGTPYQFAPDDQTRVPMQVWMSPGFTKEKGVDMACLQQKAADTRYSHDNIFSSVLGIWDVKTSVYEKGLDIFSQCRNVQ"},"dna_sequence":{"accession":"LC549806.1","fmin":"4172","fmax":"5516","strand":"+","sequence":"TTGTTTGATCAAAACATGATTCAGAATATTTTTGAAACCAATCAAAATGAGGCGTTAGCATATTTAAGCTTACCAATTATAGTATGGGTTACTATTGCTGGTTTTATCCCTGCCATTTTACTTTTCTTTGTTGAAATTGAATATGAGGAAAAATGGTTCAAAGGGATTCTAACTCGTGCCCTATCGATGTTTGCATCACTTATAGTGATTGCGGTTATTGCAGCACTATACTATCAAGATTATGTGTCAGTGGGGCGCAACAATTCAAACCTCCAGCGTGAGATTGTTCCAGCCAATTTCGTTAATAGTACCGTTAAATACGTTTACAATCGTTATCTTGCTGAACCAATCCCATTTACAACTTTAGGTGATGATGCAAAACGGGATACTAATCAAAGTAAGCCCACGTTGATGTTTCTGGTCGTTGGTGAAACCGCTCGTGGTAAAAATTTCTCGATGAATGGCTATGAGAAAGACACCAATCCATTTACCAGTAAATCTGGTGGCGTGATCTCCTTTAATGATGTTCGTTCGTGTGGGACTGCAACCGCTGTATCCGTCCCCTGCATGTTCTCCAATATGGGGAGAAAGGAGTTTGATGAAAATCGCGCTCGCAATAGCGAGGGCCTGCTAGATGTGTTGCAAAAAACGGGGATCTCCATTTTTTGGAAGGAGAACGATGGAGGCTGCAAAGGCGTCTGCGACCGAGTACCTAACATCGAAATCGAACCAAAGGATCACCCTAAGTTCTGCGATAAAAACACATGCTATGACGAGGTTGTCCTTCAAGACCTCGATAGTGAAATTGCTCAAATGAAAGGGGATAAGCTGGTTGGCTTCCACCTGATAGGTAGCCATGGCCCAACCTACTACAAGCGCTACCCTGATGCTCATCGTCAGTTCACCCCTGACTGTCCACGCAGTGATATTGAAAACTGCACAGATGAAGAGCTCACCAACACCTATGACAACACCATCCGCTACACCGATTTCGTGATTGGAGAGATGATTGCCAAGTTGAAAACCTACGAAGATAAGTACAACACCGCGTTGCTCTACGTCTCCGATCATGGTGAATCACTGGGAGCATTAGGGCTTTACCTACACGGTACACCGTACCAGTTTGCACCGGATGATCAGACCCGTGTTCCTATGCAGGTGTGGATGTCACCTGGATTTACCAAAGAGAAAGGCGTTGATATGGCGTGTTTGCAGCAGAAAGCCGCTGATACTCGTTACTCACACGATAATATTTTCTCATCTGTATTGGGTATCTGGGACGTCAAAACATCAGTTTACGAAAAGGGTCTAGATATTTTCAGTCAATGTCGTAATGTTCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3007266","ARO_id":"46012","ARO_name":"MCR-3.20","CARD_short_name":"MCR-3.20","ARO_description":"An MCR-3-type colistin resistance gene variant.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5872":{"model_id":"5872","model_name":"MCR-3.35","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"8566":{"protein_sequence":{"accession":"WP_188331894.1","sequence":"MPSLIKIKIVPLMFFLALYFAFMLNWRGVLHFYEILYKLEDFKFGFAISLPILLVAALNFVFVPFSIRYLVKPFFALLIALSAIVSYTMMKYRVLFDQNMIQNIFETNQNEALAYLNLPIIGWVTIAGFIPAILLFFVDIEYEEKWFKGILTRALSMFASLIVIAVIAALYYQDYVSVGRNNSNLQREIVPANFVNSTVKYVYNRYLAEPIPFTTLGDDAKRDTNQSKPTLMFLVVGETARGKNFSMNGYEKDTNPFTSKSGGVISFNDVRSCGTATAVSVPCMFSNMGRKEFDDNLARNSEGLLDVLQKTGVSIFWKENDGGCKGVCDRVPNIEIKPKDYPKFCDKNTCYDEVVLQDLDSEIAQMKGDKLVGFHLIGSHGPTYYKRYPDAHRQFTPDCPRSDIENCTDEELTNTYDNTIRYTDFVIAEMIAKLKTYEDKYNTALLYVSDHGESLGAMGLYLHGTPYKFAPDDQTRVPMQVWMSPGFIKEKGMNMECLQKNAAANRYSHDNIFSSVLGIWDVKTAIYEQKLDIFKQCRNN"},"dna_sequence":{"accession":"MT809044.1","fmin":"0","fmax":"1623","strand":"+","sequence":"ATGCCTTCCCTTATAAAAATAAAAATTGTTCCGCTTATGTTTTTTTTGGCACTGTATTTTGCATTTATGCTGAACTGGCGTGGAGTTCTCCATTTTTACGAAATCCTTTACAAATTAGAAGATTTTAAGTTTGGTTTCGCCATTTCATTACCAATATTGCTTGTTGCAGCGCTTAACTTTGTATTTGTTCCATTTTCGATACGGTATTTAGTAAAGCCTTTTTTTGCACTTCTGATCGCACTTAGTGCAATCGTTAGTTACACAATGATGAAGTATAGAGTCTTGTTTGATCAAAACATGATTCAGAATATTTTTGAAACCAATCAAAATGAGGCGTTAGCATATTTAAACTTACCAATTATAGGATGGGTTACTATTGCTGGTTTTATCCCTGCCATTTTACTTTTCTTTGTTGATATTGAATATGAGGAAAAATGGTTCAAAGGGATTCTAACTCGTGCCCTATCGATGTTTGCATCACTTATAGTGATTGCTGTTATTGCAGCACTATACTATCAAGATTATGTGTCAGTGGGGCGCAACAATTCAAACCTCCAGCGTGAAATTGTTCCAGCCAATTTTGTTAATAGTACCGTTAAATACGTTTACAATCGTTATCTTGCTGAACCAATCCCATTTACAACTTTAGGTGATGATGCAAAACGGGATACTAATCAAAGTAAGCCCACGTTGATGTTTCTGGTCGTTGGTGAAACCGCTCGTGGTAAAAATTTCTCGATGAATGGCTATGAGAAAGACACCAATCCATTTACCAGTAAATCTGGTGGCGTGATCTCCTTTAATGATGTTCGTTCGTGTGGGACTGCAACCGCTGTATCTGTCCCTTGCATGTTCTCCAATATGGGGAGAAAGGAGTTTGATGACAATCTCGCTCGTAATAGCGAGGGCTTGTTAGATGTGTTGCAGAAAACGGGGGTCTCCATTTTTTGGAAGGAGAACGATGGCGGTTGCAAAGGCGTCTGCGACCGAGTTCCTAACATCGAGATCAAACCGAAGGATTACCCAAAGTTCTGCGATAAAAACACATGCTATGACGAGGTTGTCCTTCAAGACCTCGACAGTGAAATTGCTCAAATGAAAGGGGATAAGCTGGTTGGCTTCCACCTGATAGGTAGCCATGGCCCAACCTACTACAAACGCTACCCTGATGCTCATCGTCAGTTCACTCCTGACTGTCCACGCAGTGATATTGAAAACTGCACAGATGAAGAGCTCACCAACACCTATGACAACACCATCCGCTACACCGATTTCGTGATTGCAGAGATGATTGCCAAGTTGAAAACCTACGAAGATAAGTACAACACCGCGTTGCTCTACGTCTCCGATCACGGTGAATCACTGGGAGCTATGGGGCTTTACCTGCACGGTACACCGTACAAGTTTGCACCGGATGATCAGACCCGCGTACCTATGCAGGTGTGGATGTCACCTGGTTTCATCAAAGAAAAAGGCATGAATATGGAATGTTTGCAGAAAAATGCCGCAGCCAATCGCTATTCTCATGACAACATATTTTCTTCTGTCCTGGGAATATGGGATGTGAAGACGGCTATCTACGAACAAAAATTAGATATCTTTAAGCAATGTCGGAATAATTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42604","NCBI_taxonomy_name":"Aeromonas jandaei","NCBI_taxonomy_id":"650"}}}},"ARO_accession":"3007267","ARO_id":"46013","ARO_name":"MCR-3.35","CARD_short_name":"MCR-3.35","ARO_description":"An MCR-3-type colistin resistance gene variant.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5873":{"model_id":"5873","model_name":"MCR-3.34","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"8567":{"protein_sequence":{"accession":"WP_188331893.1","sequence":"MPSLIKIKIVPLMFFLALYFAFMLNWRGVLHFYEILYKLEDFKFGFAISLPILLVAALNFVFVPFSIRYLVKPFFALLIALSAIVSYTMMKYRVLFDQNMIQNIFETNQNEALAYLNLPIIGWVTIAGFIPAILLFFVDIEYEEKWFKGILTRALSMFASLIVIAVIAALYYQDYVSVGRNNSNLQREIVPANFVNSTVKYVYNRYLAEPIPFTTLGDDAKRDTNQSKPTLMFLVVGETARGKNFSMNGYEKDTNPFTSKSGGVISFNDVRSCGTATAVSVPCMFSNMGRKEFDDNLARNSEGLLDVLQKTGVSIFWKENDGGCKGVCDRVPNIEIKPKDYPKFCDKNTCYDEVVLQDLDSEIAQMKGDKLVGFHLIGSHGPTYYKRYPDAHRQFTPDCPRSDIENCTDEELTNTYDNTIRYTDFVIAEMITKLKTYEDKYNTALLYVSDHGESLGAMGLYLHGTPYKFAPDDQTRVPMQVWMSPGFIKEKGMNMECLQKNAAANRYSHDNIFSSVLGIWDVKTAIYEQKLDIFKQCRNN"},"dna_sequence":{"accession":"MT791040.1","fmin":"0","fmax":"1623","strand":"+","sequence":"ATGCCTTCCCTTATAAAAATAAAAATTGTTCCGCTTATGTTTTTTTTGGCACTGTATTTTGCATTTATGCTGAACTGGCGTGGAGTTCTCCATTTTTACGAAATCCTTTACAAATTAGAAGATTTTAAGTTTGGTTTCGCCATTTCATTACCAATATTGCTTGTTGCAGCGCTTAACTTTGTATTTGTTCCATTTTCGATACGGTATTTAGTAAAGCCTTTTTTTGCACTTCTGATCGCACTTAGTGCAATCGTTAGTTACACAATGATGAAGTATAGAGTCTTGTTTGATCAAAACATGATTCAGAATATTTTTGAAACCAATCAAAATGAGGCGTTAGCATATTTAAACTTACCAATTATAGGATGGGTTACTATTGCTGGTTTTATCCCTGCCATTTTACTTTTCTTTGTTGATATTGAATATGAGGAAAAATGGTTCAAAGGGATTCTAACTCGTGCCCTATCGATGTTTGCATCACTTATAGTGATTGCGGTTATTGCAGCACTATACTATCAAGATTATGTGTCAGTGGGGCGAAACAATTCAAACCTCCAGCGTGAAATTGTTCCAGCCAATTTCGTTAATAGTACCGTTAAATACGTTTATAATCGTTATCTTGCTGAGCCAATCCCATTTACAACTTTAGGTGATGATGCAAAACGGGATACTAATCAAAGTAAGCCCACGTTGATGTTTCTGGTCGTTGGTGAAACCGCTCGTGGTAAAAATTTCTCGATGAATGGCTATGAGAAAGACACCAATCCATTTACCAGTAAATCTGGTGGCGTGATCTCCTTTAATGATGTTCGTTCGTGTGGGACTGCAACTGCTGTATCTGTCCCCTGCATGTTCTCCAATATGGGGAGAAAGGAGTTTGATGACAATCTCGCCCGTAATAGCGAGGGCTTGTTAGATGTGTTGCAGAAAACGGGGGTCTCCATTTTTTGGAAGGAGAACGATGGCGGTTGCAAAGGCGTCTGCGACCGAGTTCCTAACATCGAGATCAAACCGAAGGATTACCCAAAGTTCTGCGATAAAAACACATGCTATGACGAGGTTGTCCTTCAAGACCTCGACAGTGAAATTGCTCAAATGAAAGGGGATAAGCTGGTTGGCTTCCACCTGATAGGTAGCCATGGCCCAACCTACTACAAACGCTACCCTGATGCTCATCGTCAGTTCACTCCTGACTGTCCACGCAGTGATATTGAAAACTGCACAGATGAAGAGCTCACCAACACCTATGACAACACCATCCGCTACACCGATTTCGTGATTGCAGAGATGATTACCAAGTTGAAAACCTACGAAGATAAGTACAACACCGCGTTGCTCTACGTCTCCGATCACGGTGAATCACTGGGAGCTATGGGGCTTTACCTGCACGGTACACCATACAAGTTTGCACCGGATGATCAGACCCGCGTACCTATGCAGGTGTGGATGTCACCTGGTTTCATCAAAGAAAAAGGCATGAATATGGAATGTTTGCAGAAAAATGCCGCAGCCAATCGCTATTCTCATGACAACATATTTTCTTCTGTCCTGGGAATATGGGATGTGAAGACGGCTATCTACGAACAAAAATTAGATATCTTTAAGCAATGTCGGAATAATTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42604","NCBI_taxonomy_name":"Aeromonas jandaei","NCBI_taxonomy_id":"650"}}}},"ARO_accession":"3007268","ARO_id":"46014","ARO_name":"MCR-3.34","CARD_short_name":"MCR-3.34","ARO_description":"An MCR-3-type colistin resistance gene variant.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5874":{"model_id":"5874","model_name":"MCR-3.13","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"8568":{"protein_sequence":{"accession":"WP_111273842.1","sequence":"MPSLIKIKIVPLMFFLALYFAFMLNWRGVLHFYEILYKLEDFKFGFAVSLPILLVAALNFVFVPFSIRYLIKPFFALLIALSAIVSYTMMKYRVLFDQNMIQNIFETNQNEALAYLSLPIIGWVTIAGFIPAILLFFVEIEYEEKWFKGILTRALSMFASLIVIAVIAALYYQDYVSVGRNNSNLQREIVPANFVNSTVKYVYNRYLAEPIPFTTLGDDAKRDTNQSKPTLMFLVVGETARGKNFSMNGYEKDTNPFTSKSGGVISFNDVRSCGTATAVSVPCMFSNMGRKEFDDNLARNSEGLLDVLQKTGVSIFWKENDGGCKGVCDRVPNIEIKPKDYPKFCDKNTCYDEVVLQELNSEIAQMKGDKLVGFHLIGSHGPTYYKRYPDAHRQFTPDCPRSDIENCTDEELTNTYDNTIRYTDFVIAEMIAKLKTYEDKYNTALLYVSDHGESLGALGLYLHGTPYKFAPDDQTRVPMQVWMSPGFIKEKGMNMECLQKNAAANRYSHDNIFSSVLGIWDVKTAIYEQELDIFKQCRNN"},"dna_sequence":{"accession":"MH332763.1","fmin":"0","fmax":"1623","strand":"+","sequence":"ATGCCTTCCCTTATAAAAATAAAAATTGTTCCGCTTATGTTCTTTTTGGCACTGTATTTTGCATTTATGCTGAACTGGCGTGGAGTTCTCCATTTTTACGAAATCCTTTACAAATTAGAAGATTTTAAGTTTGGTTTCGCCGTTTCATTACCAATATTGCTTGTTGCAGCGCTTAACTTTGTATTTGTTCCATTTTCGATACGGTATTTAATAAAGCCTTTTTTTGCACTTCTTATCGCACTTAGTGCAATCGTTAGTTACACAATGATGAAGTATAGAGTCTTGTTTGATCAAAACATGATTCAGAATATTTTTGAAACCAATCAAAATGAGGCGTTAGCATATTTAAGCTTACCAATTATAGGATGGGTTACTATTGCTGGTTTTATCCCTGCCATTTTACTTTTCTTTGTTGAAATTGAATATGAGGAAAAATGGTTCAAAGGGATTCTAACTCGTGCCCTATCGATGTTTGCATCACTTATAGTGATTGCGGTTATTGCAGCACTATACTATCAAGATTATGTGTCAGTGGGGCGCAACAATTCAAACCTCCAGCGTGAGATTGTTCCAGCCAATTTCGTTAATAGTACCGTTAAATACGTTTACAATCGTTATCTTGCTGAACCAATCCCATTTACAACTTTAGGTGATGATGCAAAACGGGATACTAATCAAAGTAAGCCCACGTTGATGTTTCTGGTCGTTGGTGAAACCGCTCGTGGTAAAAATTTCTCGATGAATGGCTATGAGAAAGACACCAATCCATTTACCAGTAAATCTGGTGGCGTGATCTCCTTTAATGATGTTCGTTCGTGTGGGACTGCAACCGCTGTATCTGTCCCCTGCATGTTTTCCAATATGGGGAGAAAGGAGTTTGATGATAATCTCGCTCGTAATAGCGAGGGTTTGTTAGATGTGTTGCAGAAAACGGGGGTCTCCATTTTTTGGAAGGAGAACGATGGCGGCTGCAAAGGCGTCTGCGACCGAGTTCCTAACATCGAGATCAAACCGAAGGATTACCCAAAGTTCTGCGATAAAAACACATGCTATGACGAGGTTGTCCTTCAAGAGCTCAACAGTGAAATTGCTCAAATGAAAGGGGATAAGCTGGTTGGCTTCCACCTGATAGGTAGCCATGGCCCAACCTACTACAAACGCTACCCTGATGCTCATCGTCAGTTCACTCCTGACTGTCCACGCAGTGATATTGAAAACTGCACAGATGAAGAGCTCACCAACACCTATGACAACACCATCCGCTACACCGATTTCGTGATTGCAGAGATGATTGCCAAGTTGAAAACCTACGAAGATAAGTACAACACCGCGTTGCTCTACGTCTCCGATCATGGTGAATCACTGGGAGCATTAGGGCTTTACCTGCACGGTACACCGTACAAGTTTGCACCGGATGATCAGACCCGTGTTCCTATGCAGGTGTGGATGTCACCTGGTTTCATCAAAGAAAAAGGCATGAATATGGAATGTTTGCAGAAAAATGCCGCAGCCAATCGCTATTCTCATGACAACATATTTTCTTCTGTCCTGGGAATATGGGATGTGAAGACGGCTATCTACGAACAAGAATTAGATATCTTTAAGCAATGTCGGAATAATTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36936","NCBI_taxonomy_name":"Aeromonas caviae","NCBI_taxonomy_id":"648"}}}},"ARO_accession":"3007269","ARO_id":"46015","ARO_name":"MCR-3.13","CARD_short_name":"MCR-3.13","ARO_description":"An MCR-3-type colistin resistance gene variant.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5875":{"model_id":"5875","model_name":"MCR-3.28","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"8569":{"protein_sequence":{"accession":"WP_150823496.1","sequence":"MPSLIKIKIVPLMFFLALYFAFVLNWRGVLHFYEILYKLEDFKFGFAISLPILLVAALNFVFVPFSIRYLIKPFFALLIALSAIVSYTMMKYRVLFDQNMIQNIFETNQNEALAYLSLPIIVWVTIAGFIPAILLFFVEIEYEEKWFKGILTRALSMFASLIVIAVIAALYYQDYVSVGRNNSNLQREIVPANFVNSTVKYVYNRYLAEPIPFTTLGDDAKRDTNQSKPTLMFLVVGETARGKNFSMNGYEKDTNPFTSKSGGVISFNDVRSCGTATAVSVPCMFSNMGRKEFDDNRARNSEGLLDVLQKTGISIFWKENDGGCKGVCDRVPNIEIEPKDHPKFCDKNTCYDEVVLQDLDSEIAQMKGDKLVGFHLIGSHGPTYYKRYPDAHRQFTPDCPRSDIENCTDEELTNTYDNTIRYTDFVIGEMIAKLKTYEDKYNTALLYVSDHGESLGELGLYLHGTPYQFAPDDQTRVPMQVWMSPGFTKEKGVDMACLQQKAADTRYSHDNIFSSVLGIWDVKTSVYEKGLDIFSQCRNVQ"},"dna_sequence":{"accession":"MH522717.1","fmin":"0","fmax":"1626","strand":"+","sequence":"ATGCCTTCCCTTATAAAAATAAAAATTGTTCCGCTTATGTTCTTTTTGGCACTGTATTTTGCATTTGTGCTGAACTGGCGTGGAGTTCTCCATTTTTACGAAATCCTTTACAAATTAGAAGATTTTAAGTTTGGTTTCGCCATTTCATTACCAATATTGCTTGTTGCAGCGCTTAACTTTGTATTTGTTCCATTTTCGATACGGTATTTAATAAAGCCTTTTTTTGCACTTCTTATCGCACTTAGTGCAATCGTTAGTTACACAATGATGAAGTATAGAGTCTTGTTTGATCAAAACATGATTCAGAATATTTTTGAAACCAATCAAAATGAGGCGTTAGCATATTTAAGCTTACCAATTATAGTATGGGTTACTATTGCTGGTTTTATCCCTGCCATTTTACTTTTCTTTGTTGAAATTGAATATGAGGAAAAATGGTTCAAAGGGATTCTAACTCGTGCCCTATCGATGTTTGCATCACTTATAGTGATTGCGGTTATTGCAGCACTATACTATCAAGATTATGTGTCAGTGGGGCGCAACAATTCAAACCTCCAGCGTGAGATTGTTCCAGCCAATTTCGTTAATAGTACCGTTAAATACGTTTACAATCGTTATCTTGCTGAACCAATCCCATTTACAACTTTAGGTGATGATGCAAAACGGGATACTAATCAAAGTAAGCCCACGTTGATGTTTCTGGTCGTTGGTGAAACCGCTCGTGGTAAAAATTTCTCGATGAATGGCTATGAGAAAGACACCAATCCATTTACCAGTAAATCTGGTGGCGTGATCTCCTTTAATGATGTTCGTTCGTGTGGGACTGCAACCGCTGTATCCGTCCCCTGCATGTTCTCCAATATGGGGAGAAAGGAGTTTGATGATAATCGCGCTCGCAATAGCGAGGGCCTGCTAGATGTGTTGCAAAAAACGGGGATCTCCATTTTTTGGAAGGAGAACGATGGAGGCTGCAAAGGCGTCTGCGACCGAGTACCTAACATCGAAATCGAACCAAAGGATCACCCTAAGTTCTGCGATAAAAACACATGCTATGACGAGGTTGTCCTTCAAGACCTCGATAGTGAAATTGCTCAAATGAAAGGGGATAAGCTGGTTGGCTTCCACCTGATAGGTAGCCATGGCCCAACCTACTACAAGCGCTACCCTGATGCTCATCGTCAGTTCACCCCTGACTGTCCACGCAGTGATATTGAAAACTGCACAGATGAAGAGCTCACCAACACCTATGACAACACCATCCGCTACACCGATTTCGTGATTGGAGAGATGATTGCCAAGTTGAAAACCTACGAAGATAAGTACAACACCGCGTTGCTCTACGTCTCCGATCATGGTGAATCACTGGGAGAATTAGGGCTTTACCTACACGGTACACCGTACCAGTTTGCACCGGATGATCAGACCCGTGTTCCTATGCAGGTGTGGATGTCACCTGGATTTACCAAAGAGAAAGGCGTTGATATGGCGTGTTTGCAGCAGAAAGCCGCTGATACTCGTTACTCACACGATAATATTTTCTCATCTGTATTGGGTATCTGGGACGTCAAAACATCAGTTTACGAAAAGGGTCTAGATATTTTCAGTCAATGTCGTAATGTTCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3007270","ARO_id":"46016","ARO_name":"MCR-3.28","CARD_short_name":"MCR-3.28","ARO_description":"An MCR-3-type colistin resistance gene variant.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5876":{"model_id":"5876","model_name":"MCR-3.39","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"8570":{"protein_sequence":{"accession":"UUD58346.1","sequence":"MPSLIKIKIVPLMFFLALYFAFVLNWRGVLHFYEILYKLEDFKFGFAISLPILLVAALNFVFVPFSIRYLIKPFFALLIALSAIVSYTMMKYRVLFDQNMIQNIFETNQNEALAYLSLPIIVWVTIAGFIPAILLFFVEIEYEEKWFKGILTRALSMFASLIVIAVIAALYYQDYVSVGRNNSNLQREIVPANFVNSTVKYVYNRYLAEPIPFTTLGDDAKRDTNQSKPTLMFLVVGETARGKNFSMNGYEKDTNPFTSKSGGVISFNDVRSCGTATAVSVPCMFSNMGRKEFDDNRARNSEGLLDVLQKTGISIFWKENDGGCKGVCDRVPNIEIEPKDHPKFCDKNTCYDEVVLQDLDSEIAQMKGDKLVGFHLIGSHGPTYYKRYPDAHRQFTPDCPRSDIENCTDEELTNTYDNTIRYTDFVIGEMIAKLKTYEDKYNTALLYVSDHGESLGALGLYLHGTPYQFAPDDQTRVPMQVWMSPGFIKEKGVDMACLQQKAADTRYSHDNIFSSVLGIWDVKTSVYEKGLDIFSQCRNVQ"},"dna_sequence":{"accession":"CP075741.1","fmin":"74095","fmax":"75721","strand":"+","sequence":"ATGCCTTCCCTTATAAAAATAAAAATTGTTCCGCTTATGTTCTTTTTGGCACTGTATTTTGCATTTGTGCTGAACTGGCGTGGAGTTCTCCATTTTTACGAAATCCTTTACAAATTAGAAGATTTTAAGTTTGGTTTCGCCATTTCATTACCAATATTGCTTGTTGCAGCGCTTAACTTTGTATTTGTTCCATTTTCGATACGGTATTTAATAAAGCCTTTTTTTGCACTTCTTATCGCACTTAGTGCAATCGTTAGTTACACAATGATGAAGTATAGAGTCTTGTTTGATCAAAACATGATTCAGAATATTTTTGAAACCAATCAAAATGAGGCGTTAGCATATTTAAGCTTACCAATTATAGTATGGGTTACTATTGCTGGTTTTATCCCTGCCATTTTACTTTTCTTTGTTGAAATTGAATATGAGGAAAAATGGTTCAAAGGGATTCTAACTCGTGCCCTATCGATGTTTGCATCACTTATAGTGATTGCGGTTATTGCAGCACTATACTATCAAGATTATGTGTCAGTGGGGCGCAACAATTCAAACCTCCAGCGTGAGATTGTTCCAGCCAATTTCGTTAATAGTACCGTTAAATACGTTTACAATCGTTATCTTGCTGAACCAATCCCATTTACAACTTTAGGTGATGATGCAAAACGGGATACTAATCAAAGTAAGCCCACGTTGATGTTTCTGGTCGTTGGTGAAACCGCTCGTGGTAAAAATTTCTCGATGAATGGCTATGAGAAAGACACCAATCCATTTACCAGTAAATCTGGTGGCGTGATCTCCTTTAATGATGTTCGTTCGTGTGGGACTGCAACCGCTGTATCCGTCCCCTGCATGTTCTCCAATATGGGGAGAAAGGAGTTTGATGATAATCGCGCTCGCAATAGCGAGGGCCTGCTAGATGTGTTGCAAAAAACGGGGATCTCCATTTTTTGGAAGGAGAACGATGGAGGCTGCAAAGGCGTCTGCGACCGAGTACCTAACATCGAAATCGAACCAAAGGATCACCCTAAGTTCTGCGATAAAAACACATGCTATGACGAGGTTGTCCTTCAAGACCTCGATAGTGAAATTGCTCAAATGAAAGGGGATAAGCTGGTTGGCTTCCACCTGATAGGTAGCCATGGCCCAACCTACTACAAGCGCTACCCTGATGCTCATCGTCAGTTCACCCCTGACTGTCCACGCAGTGATATTGAAAACTGCACAGATGAAGAGCTCACCAACACCTATGACAACACCATCCGCTACACCGATTTCGTGATTGGAGAGATGATTGCCAAGTTGAAAACCTACGAAGATAAGTACAACACCGCGTTGCTCTACGTCTCCGATCATGGTGAATCACTGGGAGCATTAGGGCTTTACCTACACGGTACACCGTACCAGTTTGCACCGGATGATCAGACCCGTGTTCCTATGCAGGTGTGGATGTCACCTGGATTTATCAAAGAGAAAGGCGTTGATATGGCGTGTTTGCAGCAGAAAGCCGCTGATACTCGTTACTCACACGATAATATTTTCTCATCTGTATTGGGTATCTGGGACGTCAAAACATCAGTTTACGAAAAGGGTCTAGATATTTTCAGTCAATGTCGTAATGTTCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3007271","ARO_id":"46017","ARO_name":"MCR-3.39","CARD_short_name":"MCR-3.39","ARO_description":"An MCR-3-type colistin resistance gene variant.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5877":{"model_id":"5877","model_name":"MCR-3.29","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"8571":{"protein_sequence":{"accession":"WP_136512112.1","sequence":"MPSLIKIKIVPLMFFLALYFAFVLNWRGVLHFYEILYKLEDFKFGFAISLPILLVAALNFVFVPFSIRYLIKPFFALLIALSAIVSYTMMKYRVLFDQNMIQNIFETNQNEALAYLSLPIIVWVTIAGFIPAILLFFVEIEYEEKWFKGILTRALSMFASLIVIAVIAALYYQDYVSVGRNNSNLQREIVPANFVNSTVKYVYNRYLAEPIPFTTLGDDAKRDTNQSKPTLMFLVVGETARGKNFSMNGYEKDTNPFTSKSGGVISFNDVRSCGTATAVSVPCMFSNMGRKEFDDNRARNSEGLLDVLQKTGISIFWKENDGGCKGVCDRVPNIEIEPKDHPKFCDKNTCYDEVVLQDLDSEIAQMKGDKLVVFHLIGSHGPTYYKRYPDAHRQFTPDCPRSDIENCTDEELTNTYDNTIRYTDFVIGEMIAKLKTYEDKYNTALLYVSDHGESLGALGLYLHGTPYQFAPDDQTRVPMQVWMSPGFTKEKGVDMACLQQKAADTRYSHDNIFSSVLGIWDVKTSVYEKGLDIFSQCRNVQ"},"dna_sequence":{"accession":"MK521074.1","fmin":"0","fmax":"1626","strand":"+","sequence":"ATGCCTTCCCTTATAAAAATAAAAATTGTTCCGCTTATGTTCTTTTTGGCACTGTATTTTGCATTTGTGCTGAACTGGCGTGGAGTTCTCCATTTTTACGAAATCCTTTACAAATTAGAAGATTTTAAGTTTGGTTTCGCCATTTCATTACCAATATTGCTTGTTGCAGCGCTTAACTTTGTATTTGTTCCATTTTCGATACGGTATTTAATAAAGCCTTTTTTTGCACTTCTTATCGCACTTAGTGCAATCGTTAGTTACACAATGATGAAGTATAGAGTCTTGTTTGATCAAAACATGATTCAGAATATTTTTGAAACCAATCAAAATGAGGCGTTAGCATATTTAAGCTTACCAATTATAGTATGGGTTACTATTGCTGGTTTTATCCCTGCCATTTTACTTTTCTTTGTTGAAATTGAATATGAGGAAAAATGGTTCAAAGGGATTCTAACTCGTGCCCTATCGATGTTTGCATCACTTATAGTGATTGCGGTTATTGCAGCACTATACTATCAAGATTATGTGTCAGTGGGGCGCAACAATTCAAACCTCCAGCGTGAGATTGTTCCAGCCAATTTCGTTAATAGTACCGTTAAATACGTTTACAATCGTTATCTTGCTGAACCAATCCCATTTACAACTTTAGGTGATGATGCAAAACGGGATACTAATCAAAGTAAGCCCACGTTGATGTTTCTGGTCGTTGGTGAAACCGCTCGTGGTAAAAATTTCTCGATGAATGGCTATGAGAAAGACACCAATCCATTTACCAGTAAATCTGGTGGCGTGATCTCCTTTAATGATGTTCGTTCGTGTGGGACTGCAACCGCTGTATCCGTCCCCTGCATGTTCTCCAATATGGGGAGAAAGGAGTTTGATGATAATCGCGCTCGCAATAGCGAGGGCCTGCTAGATGTGTTGCAAAAAACGGGGATCTCCATTTTTTGGAAGGAGAACGATGGAGGCTGCAAAGGCGTCTGCGACCGAGTACCTAACATCGAAATCGAACCAAAGGATCACCCTAAGTTCTGCGATAAAAACACATGCTATGACGAGGTTGTCCTTCAAGACCTCGATAGTGAAATTGCTCAAATGAAAGGGGATAAGCTGGTTGTCTTCCACCTGATAGGTAGCCATGGCCCAACCTACTACAAGCGCTACCCTGATGCTCATCGTCAGTTCACCCCTGACTGTCCACGCAGTGATATTGAAAACTGCACAGATGAAGAGCTCACCAACACCTATGACAACACCATCCGCTACACCGATTTCGTGATTGGAGAGATGATTGCCAAGTTGAAAACCTACGAAGATAAGTACAACACCGCGTTGCTCTACGTCTCCGATCATGGTGAATCACTGGGAGCATTAGGGCTTTACCTACACGGTACACCGTACCAGTTTGCACCGGATGATCAGACCCGTGTTCCTATGCAGGTGTGGATGTCACCTGGATTTACCAAAGAGAAAGGCGTTGATATGGCGTGTTTGCAGCAGAAAGCCGCTGATACTCGTTACTCACACGATAATATTTTCTCATCTGTATTGGGTATCTGGGACGTCAAAACATCAGTTTACGAAAAGGGTCTAGATATTTTCAGTCAATGTCGTAATGTTCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3007272","ARO_id":"46018","ARO_name":"MCR-3.29","CARD_short_name":"MCR-3.29","ARO_description":"An MCR-3-type colistin resistance gene variant.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5878":{"model_id":"5878","model_name":"MCR-3.19","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"8572":{"protein_sequence":{"accession":"AWM63467.1","sequence":"MPSLIKIKIVPLMFFLALYFAFVLNWRGVLHFYEILYKLEDFKFGFAISLPILLVAALNFVFVPFSIRYLIKPFFALLIALSAIVSYTMMKYRVLFDQNMIQNIFETNQNEALAYLSLPIIVWVTIAGFIPAILLFFVEIEYEEKWFKGILTRALSMFASLIVIAVIAALYYQDYVSVGRNNSNLQREIVPANFVNSTVKYVYNRYLAEPIPFTTLGDDAKRDTNQSKPTLMFLVVGETARGKNFSMNGYEKDTNPFTSKSGGVISFNDVRSCGTATAVSVPCMFSNMGRKEFDDNRARNSEGLLDVLQKTGISIFWKENDGGCKGVCDRVPNIEIEPKDHPKFCDKNTCYDEVVLQDLDSEIAQMKGDKLVGFHLIGSHGPTYYKRYPDAHRQFTPDCPRSDIENCTDEELTNTYDNTIRYTDFVIGEMIAKLKTYEDKYNTALLYVSDHGESLGALGLYLHGTPYQFAPDDQTRVPMQVWMSPGFTKEKGVDMACLQQKAADTRYSHDNIFSSVLGIWDVKTSVYEKGLDIFSQCRNVQ"},"dna_sequence":{"accession":"MH043626.1","fmin":"47490","fmax":"49116","strand":"+","sequence":"ATGCCTTCCCTTATAAAAATAAAAATTGTTCCGCTTATGTTCTTTTTGGCACTGTATTTTGCATTTGTGCTGAACTGGCGTGGAGTTCTCCATTTTTACGAAATCCTTTACAAATTAGAAGATTTTAAGTTTGGTTTCGCCATTTCATTACCAATATTGCTTGTTGCAGCGCTTAACTTTGTATTTGTTCCATTTTCGATACGGTATTTAATAAAGCCTTTTTTTGCACTTCTTATCGCACTTAGTGCAATCGTTAGTTACACAATGATGAAGTATAGAGTCTTGTTTGATCAAAACATGATTCAGAATATTTTTGAAACCAATCAAAATGAGGCGTTAGCATATTTAAGCTTACCAATTATAGTATGGGTTACTATTGCTGGTTTTATCCCTGCCATTTTACTTTTCTTTGTTGAAATTGAATATGAGGAAAAATGGTTCAAAGGGATTCTAACTCGTGCCCTATCGATGTTTGCATCACTTATAGTGATTGCGGTTATTGCAGCACTATACTATCAAGATTATGTGTCAGTGGGGCGCAACAATTCAAACCTCCAGCGTGAGATTGTTCCAGCCAATTTCGTTAATAGTACCGTTAAATACGTTTACAATCGTTATCTTGCTGAACCAATCCCATTTACAACTTTAGGTGATGATGCAAAACGGGATACTAATCAAAGTAAGCCCACGTTGATGTTTCTGGTCGTTGGTGAAACCGCTCGTGGTAAAAATTTCTCGATGAATGGCTATGAGAAAGACACCAATCCATTTACCAGTAAATCTGGTGGCGTGATCTCCTTTAATGATGTTCGTTCGTGTGGGACTGCAACCGCTGTATCCGTCCCCTGCATGTTCTCCAATATGGGGAGAAAGGAGTTTGATGATAATCGCGCTCGCAATAGCGAGGGCCTGCTAGATGTGTTGCAAAAAACGGGGATCTCCATTTTTTGGAAGGAGAACGATGGAGGCTGCAAAGGCGTCTGCGACCGAGTACCTAACATCGAAATCGAACCAAAGGATCACCCTAAGTTCTGCGATAAAAACACATGCTATGACGAGGTTGTCCTTCAAGACCTCGATAGTGAAATTGCTCAAATGAAAGGGGATAAGCTGGTTGGCTTCCACCTGATAGGTAGCCATGGCCCAACCTACTACAAGCGCTACCCTGATGCTCATCGTCAGTTCACCCCTGACTGTCCACGCAGTGATATTGAAAACTGCACAGATGAAGAGCTCACCAACACCTATGACAACACCATCCGCTACACCGATTTCGTGATTGGAGAGATGATTGCCAAGTTGAAAACCTACGAAGATAAGTACAACACCGCGTTGCTCTACGTCTCCGATCATGGTGAATCACTGGGAGCATTAGGGCTTTACCTACACGGTACACCGTACCAGTTTGCACCGGATGATCAGACCCGTGTTCCTATGCAGGTGTGGATGTCACCTGGATTTACCAAAGAGAAAGGCGTTGATATGGCGTGTTTGCAGCAGAAAGCCGCTGATACTCGTTACTCACACGATAATATTTTCTCATCTGTATTGGGTATCTGGGACGTCAAAACATCAGTTTACGAAAAGGGTCTAGATATTTTCAGTCAATGTCGTAATGTTCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3007273","ARO_id":"46019","ARO_name":"MCR-3.19","CARD_short_name":"MCR-3.19","ARO_description":"An MCR-3-type colistin resistance gene variant.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5887":{"model_id":"5887","model_name":"MCR-5.3","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"8614":{"protein_sequence":{"accession":"AXF93714.1","sequence":"MRLSAFITFLKMRPQVRTEFLTLFISLVFTLLCNGVFWNALLAGRDSLTSGTWLMLLCTGLLITGLQWLLLLLVATRWSVKPLLILLAVMTPAAVYFMRNYGVYLDKAMLRNLMETDVREASELLQWRMLPYLLVAAVSVWWIARVRVLRTGWKQAVMMRSACLAGALAMISMGLWPVMDVLIPTLRENKPLRYLITPANYVISGIRVLTEQASSSADEAREVVAADAHRGPQEQGRRPRALVLVVGETVRAANWGLSGYERQTTPELAARDVINFSDVTSCGTDTATSLPCMFSLNGRRDYDERQIRRRESVLHVLNRSDVNILWRDNQSGCKGVCDGLPFENLSSAGHPTLCHGERCLDEILLEGLAEKITTSRSDMLIVLHMLGNHGPAYFQRYPASYRRWSPTCDTTDLSSCSHEALVNTYDNAVLYTDHVLARTIDLLSGIRSHDTALLYVSDHGESLGEKGLYLHGIPYVIAPDEQIKVPMIWWQSSQVYADQACMQTHASRAPVSHDHLFHTLLGMFDVKTAAYTPELDLLATCRKGQPQ"},"dna_sequence":{"accession":"MH062179.1","fmin":"0","fmax":"1644","strand":"-","sequence":"ATGCGGTTGTCTGCATTTATCACTTTCTTGAAAATGCGCCCGCAAGTGCGCACTGAATTTTTGACTCTGTTCATCAGCCTTGTGTTCACCCTGCTGTGCAATGGCGTGTTTTGGAATGCCCTTCTTGCTGGACGCGACTCCCTAACTTCTGGAACATGGCTAATGCTCCTTTGCACTGGGTTGCTGATCACCGGGCTGCAATGGTTGTTGCTCCTTCTGGTGGCCACGCGCTGGAGTGTCAAGCCACTACTGATTCTGCTTGCTGTCATGACGCCCGCCGCCGTTTATTTCATGCGCAACTACGGGGTTTATCTCGACAAGGCCATGCTGCGGAATCTGATGGAGACGGACGTCAGGGAAGCCAGTGAGCTGTTGCAATGGAGAATGCTGCCCTACTTGTTGGTTGCAGCCGTATCCGTGTGGTGGATTGCGAGAGTCAGGGTTTTACGAACGGGCTGGAAACAAGCGGTAATGATGCGCAGCGCTTGTCTGGCTGGCGCTCTCGCCATGATTTCCATGGGTCTGTGGCCAGTCATGGATGTGCTGATACCCACGCTTCGTGAAAACAAGCCGCTTCGCTATTTGATCACTCCTGCAAACTACGTCATCTCGGGCATTCGGGTTTTGACTGAACAGGCGTCATCGTCAGCAGACGAAGCAAGGGAAGTCGTTGCAGCCGATGCGCATCGAGGGCCTCAAGAACAAGGCCGCCGTCCTCGTGCTCTCGTACTGGTTGTCGGGGAAACCGTCAGGGCGGCTAATTGGGGGTTGAGCGGCTATGAACGACAAACCACCCCTGAGTTGGCCGCACGCGACGTGATCAATTTTTCCGATGTCACCAGTTGCGGGACGGATACGGCTACATCCCTTCCCTGCATGTTTTCCCTCAATGGTCGGCGCGACTACGACGAACGCCAGATTCGTCGGCGCGAGTCCGTGCTGCACGTTTTAAACCGTAGTGACGTCAACATTCTCTGGCGCGATAACCAGTCGGGCTGTAAAGGCGTCTGTGATGGACTGCCCTTTGAAAACCTGTCTTCGGCAGGCCATCCCACACTGTGCCATGGCGAGCGCTGCCTGGATGAAATTCTGCTCGAAGGGTTGGCCGAGAAGATAACAACAAGCCGCAGCGATATGCTGATCGTTCTGCATATGCTGGGCAATCACGGCCCAGCGTATTTCCAGCGCTATCCCGCAAGCTACCGACGCTGGTCGCCAACCTGCGACACCACCGATCTGTCCAGCTGTTCGCATGAAGCCTTGGTGAACACCTACGACAACGCCGTGCTTTACACCGATCATGTGCTTGCCCGTACCATTGACCTGCTGTCCGGCATCCGCTCACACGACACGGCGCTGCTGTACGTTTCCGATCATGGGGAATCGCTCGGCGAGAAAGGCCTGTATCTCCATGGCATACCTTACGTCATCGCGCCGGATGAGCAGATCAAGGTGCCGATGATCTGGTGGCAGTCGAGTCAGGTTTATGCCGACCAAGCCTGTATGCAAACTCATGCCTCTCGGGCACCGGTAAGTCACGATCACCTGTTTCACACCTTGCTCGGGATGTTCGACGTGAAAACCGCTGCCTACACGCCAGAGTTGGACCTTCTGGCAACATGCAGAAAAGGACAACCACAATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3007282","ARO_id":"46028","ARO_name":"MCR-5.3","CARD_short_name":"MCR-5.3","ARO_description":"An MCR-5-type colistin resistance gene variant.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5888":{"model_id":"5888","model_name":"MCR-2.4","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"8582":{"protein_sequence":{"accession":"WP_188331886.1","sequence":"MTSHHSWYRYSINPFVLMGLVALFLAATANLTFFEKAMAVYPVSDNLGFIISMAVALMGAMLLIVVLFSYRYVLKPVLILLLMMGAVTSYFTDTYGTVYDTTMLQNALQTDQAESKDLMNLAFFVRIIGLGVLPSIVVAWVKVDYPTWGKGLIQRAMTWGVSLVLLLVPIGLFSSQYASFFRVHKPVRFYINPITPIYSVGKLASIEYKKATAPKDTIYHAKDAVQTTKPSERKPRLVVFVVGETVRADHVQFNGYSRETFPQLAKVDGLANFSQVTSCGTSTAYSVPCMFSYLGQDDYDVDTAKYQENVLDTLDRLGVDILWRDNNSDSKGVMDKLPATQYFDYKSATNNTICNTNPYNECRDVGMLVGLDDYVSANNGKDMLIMLHQMGNHGPAYFKRYDEQFAKFTPVCEGNELAKCEHQSLINAYDNALLATDDFIAKSIDWLKTHEANYDVAMLYVSDHGESLGENGVYLHGMPNAFAPKEQRAVPAFFWSNNTSFKPTASDTALTHDAITPTLLKLFDVTAGKVKDRTAFIQ"},"dna_sequence":{"accession":"MT757845.1","fmin":"0","fmax":"1617","strand":"+","sequence":"ATGACATCACATCACTCTTGGTATCGCTACTCCATCAATCCTTTTGTACTGATGGGTTTGGTGGCGTTATTTTTGGCGGCAACAGCGAACCTGACATTTTTTGAAAAAGCGATGGCGGTCTATCCTGTATCGGATAACTTAGGCTTTATCATCTCAATGGCGGTTGCACTGATGGGTGCTATGCTATTGATTGTCGTTCTGTTTTCCTATCGTTATGTGCTCAAGCCTGTGCTGATTTTGCTTTTGATGATGGGTGCGGTAACCAGTTATTTTACCGATACTTATGGCACAGTCTATGATACGACCATGCTACAAAATGCCCTGCAAACCGACCAAGCTGAGTCCAAGGACTTGATGAATTTGGCGTTTTTTGTGCGGATTATTGGGCTTGGTGTTTTGCCGAGCATAGTGGTGGCGTGGGTCAAGGTGGATTATCCAACATGGGGCAAAGGCCTGATTCAGCGTGCGATGACGTGGGGTGTCAGCCTTGTGCTGTTGCTTGTGCCGATTGGGTTATTTAGCAGTCAGTATGCGAGTTTCTTTCGGGTGCATAAGCCAGTGCGTTTTTATATCAACCCGATTACGCCGATTTATTCGGTGGGTAAGCTTGCCAGTATCGAGTACAAAAAAGCCACTGCGCCAAAAGACACCATCTATCATGCCAAAGATGCCGTGCAGACCACCAAGCCGAGCGAGCGTAAGCCACGCCTAGTGGTGTTCGTCGTCGGTGAGACGGTGCGCGCTGACCATGTGCAGTTCAATGGCTATAGCCGTGAGACTTTCCCGCAGCTTGCCAAAGTTGATGGCTTGGCGAACTTTAGCCAAGTGACATCGTGTGGCACATCGACGGCGTATTCTGTGCCGTGTATGTTCAGCTATCTGGGTCAAGATGACTATGATGTCGATACCGCCAAATACCAAGAAAATGTCCTAGATACGCTTGACCGCTTGGGCGTGGATATCTTGTGGCGTGATAATAATTCAGACTCAAAAGGCGTGATGGATAAGCTGCCTGCCACGCAGTATTTTGATTATAAATCAGCGACCAACAACACCATCTGCAACACCAATCCCTATAACGAATGTCGTGATGTCGGTATGCTTGTTGGGCTAGACGACTATGTCAGCGCCAATAATGGCAAAGATATGCTTATCATGCTACACCAAATGGGCAATCATGGGCCGGCGTACTTTAAGCGTTATGATGAGCAATTTGCCAAATTCACCCCTGTGTGCGAAGGCAATGAGCTTGCCAAATGCGAACATCAATCGCTCATCAATGCCTATGATAATGCACTACTTGCCACCGATGATTTTATCGCCAAAAGTATCGATTGGCTAAAAACACATGAAGCAAACTACGATGTCGCCATGCTCTATGTCAGCGACCACGGCGAGAGCTTGGGCGAAAATGGTGTCTATTTGCATGGTATGCCAAATGCCTTTGCACCAAAAGAACAGCGTGCCGTACCTGCGTTTTTTTGGTCAAATAATACATCGTTCAAGCCAACTGCCAGCGATACTGCATTGACCCATGATGCAATTACGCCGACACTGCTTAAGCTGTTTGATGTCACAGCGGGCAAGGTCAAAGACCGCACGGCATTTATCCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36791","NCBI_taxonomy_name":"uncultured bacterium","NCBI_taxonomy_id":"77133"}}}},"ARO_accession":"3007283","ARO_id":"46029","ARO_name":"MCR-2.4","CARD_short_name":"MCR-2.4","ARO_description":"An MCR-2-type colistin resistance gene variant.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5889":{"model_id":"5889","model_name":"MCR-2.3","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"8639":{"protein_sequence":{"accession":"HCJ5800995.1","sequence":"MTSHHSWYRYSINPFVLMGLVALFLAATANLTFFEKAMAVYPVSDNLGFIISMAVAVMGAMLLIVVLLSYRYVLKPVLILLLIMGAVTSYFTDTYGTVYDTTMLQNAMQTDQAESKDLMNLAFFVRIIGLGVLPSLLVAVAKVGYPTWGKSLIQRAMTWGVSLVLLLVPIGLFSSQYASFFRVHKPVRFYINPITPIYSVGKLASIEYKKATAPTDTIYHAKDAVQTTKPSERKPRLVVFVVGETARADHVQFNGYSRETFPQLAKVDGLANFSQVTSCGTSTAYSVPCMFSYLGQDDYDVDTAKYQENVLDTLDRLGVGILWRDNNSDSKGVMDKLPATQYFDYKSATNNTICNTNPYNECRDVGMLVGLDDYVSANNGKDMLIMLHQMGNHGPAYFKRYDEQFTKFTPVCEGNELAKCEHQSLINAYDNALLATDDFIAKSIDWLKTHEANYDVAMLYVSDHGESLGENGVYLHGMPNAFAPKEQRAVPVFFWSNNTTFKPTASDTALTHDAITPTLLKLFDVTADKVKDRTAFIQ"},"dna_sequence":{"accession":"DAILHT010000102.1","fmin":"1367","fmax":"2984","strand":"+","sequence":"ATGACATCACATCACTCTTGGTATCGCTATTCTATCAATCCCTTTGTGCTGATGGGTTTGGTGGCGTTATTTTTGGCAGCGACAGCGAACCTGACATTTTTTGAAAAAGCGATGGCGGTCTATCCTGTATCGGATAACTTAGGCTTTATCATCTCAATGGCGGTGGCGGTGATGGGTGCTATGCTATTGATTGTTGTGCTATTATCCTATCGCTATGTGCTAAAGCCTGTGCTGATTTTGCTGCTTATCATGGGTGCGGTGACGAGCTATTTTACCGATACTTATGGCACGGTCTATGACACCACCATGCTCCAAAATGCCATGCAAACCGACCAAGCCGAGTCTAAAGACTTGATGAATTTGGCGTTTTTTGTGCGGATTATCGGGCTTGGCGTGTTGCCAAGTCTATTGGTCGCAGTTGCCAAAGTGGGTTATCCAACATGGGGCAAAAGCCTGATTCAGCGTGCGATGACGTGGGGTGTCAGCCTTGTGTTGTTGCTTGTGCCGATTGGGTTATTTAGCAGTCAGTATGCGAGTTTCTTTCGGGTGCATAAGCCAGTGCGTTTTTATATCAACCCGATTACGCCGATTTATTCGGTGGGTAAGCTTGCCAGTATCGAGTACAAAAAAGCCACTGCACCAACAGACACCATCTATCATGCCAAAGATGCCGTGCAGACCACCAAGCCTAGCGAGCGTAAGCCCCGTCTAGTGGTGTTCGTCGTCGGTGAGACGGCGCGTGCTGACCATGTGCAGTTCAATGGCTATAGCCGTGAGACTTTCCCGCAGCTTGCCAAAGTTGATGGCTTGGCGAACTTTAGCCAAGTGACATCGTGTGGCACATCGACGGCGTATTCTGTGCCGTGTATGTTCAGCTATTTGGGTCAAGATGACTATGATGTCGATACCGCCAAATACCAAGAAAATGTGCTAGATACGCTTGACCGCTTGGGCGTGGGTATCTTGTGGCGTGATAATAATTCAGACTCAAAAGGCGTGATGGATAAGCTACCTGCTACGCAGTATTTTGATTATAAATCAGCGACCAACAACACCATCTGTAACACCAACCCTTATAATGAATGTCGTGATGTCGGTATGCTTGTTGGGCTTGATGACTATGTCAGCGCCAATAATGGCAAAGATATGCTCATCATGCTACACCAAATGGGCAATCATGGGCCGGCGTACTTTAAGCGTTATGATGAGCAATTTACCAAATTCACCCCTGTGTGCGAAGGCAACGAGCTTGCCAAATGCGAACATCAATCGCTCATCAATGCCTATGATAATGCACTGCTTGCCACCGATGATTTTATCGCCAAAAGTATCGATTGGCTAAAAACACATGAAGCAAACTACGATGTCGCCATGCTCTATGTCAGCGACCACGGCGAGAGCTTGGGCGAAAATGGTGTCTATCTGCATGGTATGCCAAATGCCTTTGCACCAAAAGAACAACGAGCCGTACCTGTGTTTTTTTGGTCAAATAATACGACATTCAAGCCAACTGCCAGCGATACTGCATTGACCCATGATGCGATTACGCCGACATTGCTTAAGCTGTTTGATGTCACAGCTGATAAGGTCAAAGACCGCACGGCATTTATCCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3007284","ARO_id":"46030","ARO_name":"MCR-2.3","CARD_short_name":"MCR-2.3","ARO_description":"An MCR-2-type colistin resistance gene variant.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5890":{"model_id":"5890","model_name":"MCR-2.8","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"8584":{"protein_sequence":{"accession":"WP_219860731.1","sequence":"MTSHHSWYRYSINPFVLMGLVALFLAATANLTFFEKAMAVYPVSDNLGFIISMAVAVMGAMLLIVVLLSYRYVLKPVLILLLIMGAVTSYFTDTYGTVYDTTMLQNAMQTDQAESKDLMNLAFFVRIIGLGVLPSVLVAVAKVNYPTWGKGLIQRAMTWGVSLVLLLVPIGLFSSQYASFFRVHKPVRFYINPITPIYSVGKLASIEYKKATAPTDTIYHAKDAVQTTKPSERKPRLVVFVVGETARADHVQFNGYGRETFPQLAKVDGLANFSQVTSCGTSTAYSVPCMFSYLGQDDYDVDTAKYQENVLDTLDRLGVGILWRDNNSDSKGVMDKLPATQYFDYKSATNNTICNTNPYNECRDVGMLVGLDDYVSANNGKDMLIMLHQTGNHGPAYFKRYDEQFAKFTPVCEGNELAKCEHQSLINAYDNALLATDDFIAKSIDWLKTHEANYDVAMLYVSDHGESLGENGVYLHGMPNAFAPKEQRAVPAFFWSNNTTFKPTASDTVLTHDAITPTLLKLFDVTAGKVKDRAAFIQ"},"dna_sequence":{"accession":"MZ520325.1","fmin":"0","fmax":"1617","strand":"+","sequence":"ATGACATCACATCACTCTTGGTATCGCTATTCTATCAATCCTTTTGTGCTGATGGGTTTGGTGGCGTTATTTTTGGCAGCGACAGCGAACCTGACATTTTTTGAAAAAGCGATGGCGGTCTATCCTGTATCGGATAACTTAGGCTTTATCATCTCAATGGCGGTGGCGGTGATGGGTGCTATGCTACTGATTGTCGTGCTGTTATCCTATCGCTATGTGCTAAAGCCTGTCCTGATTTTGCTACTGATTATGGGTGCGGTGACGAGCTATTTTACCGATACTTATGGCACGGTCTATGACACCACCATGCTCCAAAATGCCATGCAAACCGACCAAGCCGAGTCTAAGGACTTGATGAATTTGGCGTTTTTTGTGCGAATTATCGGGCTTGGCGTGTTGCCAAGTGTGTTGGTCGCAGTTGCCAAAGTCAATTATCCAACATGGGGCAAAGGTCTGATTCAGCGTGCGATGACATGGGGTGTCAGCCTTGTGCTGTTGCTTGTGCCGATTGGACTATTTAGCAGTCAGTATGCGAGTTTCTTTCGGGTGCATAAGCCAGTGCGTTTTTATATCAACCCGATTACGCCGATTTATTCGGTGGGTAAGCTTGCCAGTATCGAGTACAAAAAAGCCACTGCGCCAACAGACACCATCTATCATGCCAAAGACGCCGTGCAGACCACCAAGCCGAGCGAGCGTAAGCCACGCCTAGTGGTGTTCGTCGTCGGTGAGACGGCGCGTGCTGACCATGTGCAGTTCAATGGCTATGGCCGTGAGACTTTCCCGCAGCTTGCCAAAGTTGATGGCTTGGCGAATTTTAGCCAAGTGACATCGTGTGGCACATCGACGGCGTATTCTGTGCCGTGTATGTTCAGCTATTTGGGTCAAGATGACTATGATGTCGATACCGCCAAATACCAAGAAAATGTGCTAGATACGCTTGACCGCTTGGGTGTGGGTATCTTGTGGCGTGATAATAATTCAGACTCAAAAGGCGTGATGGATAAGCTACCTGCCACGCAGTATTTTGATTATAAATCAGCAACCAACAATACCATCTGTAACACCAATCCCTATAACGAATGCCGTGATGTCGGTATGCTTGTCGGGCTAGATGACTATGTCAGCGCCAATAATGGCAAAGATATGCTCATCATGCTACACCAAACGGGCAATCATGGGCCGGCGTACTTTAAGCGTTATGATGAGCAATTTGCCAAATTCACCCCCGTGTGCGAAGGCAACGAGCTTGCCAAATGCGAACACCAATCACTCATCAATGCCTATGACAATGCGCTACTTGCGACTGATGATTTTATCGCCAAAAGCATCGATTGGCTAAAAACGCATGAAGCGAACTACGATGTCGCCATGCTCTATGTCAGTGACCACGGCGAGAGCTTGGGCGAAAATGGTGTCTATCTGCATGGTATGCCAAATGCCTTTGCACCAAAAGAACAGCGAGCTGTGCCTGCGTTTTTTTGGTCAAATAATACGACATTCAAGCCAACTGCCAGCGATACTGTGCTGACGCATGATGCGATTACGCCAACACTGCTTAAGCTGTTTGATGTCACAGCGGGCAAGGTCAAAGACCGCGCGGCATTTATCCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3007285","ARO_id":"46031","ARO_name":"MCR-2.8","CARD_short_name":"MCR-2.8","ARO_description":"An MCR-2-type colistin resistance gene variant.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5891":{"model_id":"5891","model_name":"MCR-2.5","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"8585":{"protein_sequence":{"accession":"WP_188331887.1","sequence":"MTSQHSWYRYSINPFVLMGLVAFFLAATANLTFFEKAMAVYPVSDNLGFIVSMAVALMGAMLLIVVLLSYRYVLKPVLILLLIMGAVTSYFTDTYGTVYDTTMLQNAMQTDQAESKDLMNLAFFVRIIGLGVLPSLLVAVAKVNYPTWGKSLIQRAMTWGVSLVLLLVPIGLFSSQYASFFRVHKPVRFYINPITPIYSVGKLASIEYKKATAPTDTIYHAKDAVQTTKPSERKPRLVVFVVGETARADHVQFNGYGRETFPQLAKVDGLANFSQVTSCGTSTAYSVPCMFSYLGQDDYDVDTAKYQENVLDTLDRLGVGILWRDNNSDSKGVMDKLPATQYFDYKSATNNTICNTNPYNECRDVGMLVGLDDYVSTNNGKDMLIMLHQMGNHGPAYFKRYDEQFAKFTPVCEGNELAKCEHQSLINAYDNALLATDDFIAKSIDWLKTHEANYDVAMLYVSDHGESLGENGVYLHGMPNAFAPKEQRAVPAFFWSNNTTFKPTASDTVLTHDAITPTLLKLFDVTAGKVKDRTAFIQ"},"dna_sequence":{"accession":"MT757842.1","fmin":"0","fmax":"1617","strand":"+","sequence":"ATGACATCACAGCACTCTTGGTATCGCTACTCCATCAATCCTTTTGTACTGATGGGTTTGGTGGCGTTTTTTTTGGCAGCGACAGCGAACCTGACATTTTTTGAAAAAGCGATGGCGGTCTATCCTGTATCGGATAACTTAGGCTTTATCGTCTCAATGGCGGTTGCGCTGATGGGTGCTATGCTATTGATTGTCGTGCTATTATCCTATCGCTATGTGCTAAAGCCTGTCCTGATTTTGCTACTGATTATGGGTGCGGTGACGAGCTATTTTACCGATACTTATGGCACGGTCTATGATACCACCATGCTCCAAAATGCCATGCAAACCGACCAAGCCGAGTCTAAAGACTTGATGAATTTGGCGTTTTTTGTGCGGATTATCGGGCTTGGTGTGTTGCCAAGTCTATTGGTCGCAGTTGCCAAAGTTAATTATCCAACATGGGGCAAAAGCCTGATTCAGCGTGCGATGACGTGGGGTGTCAGCCTTGTGCTGTTGCTTGTGCCGATTGGACTATTTAGCAGTCAGTATGCGAGTTTCTTTCGGGTGCATAAGCCAGTGCGTTTTTATATCAATCCGATTACGCCGATTTATTCGGTGGGTAAGCTTGCCAGTATCGAGTACAAAAAAGCCACTGCGCCGACAGACACCATCTATCATGCCAAAGATGCCGTGCAGACCACCAAGCCTAGCGAGCGTAAGCCACGCCTAGTGGTGTTCGTCGTCGGTGAGACGGCTCGTGCTGACCATGTGCAGTTCAATGGCTATGGCCGTGAGACTTTCCCACAGCTTGCTAAGGTCGATGGCTTGGCGAATTTTAGCCAAGTGACATCGTGTGGCACATCGACGGCGTATTCTGTGCCGTGTATGTTCAGCTATCTGGGTCAAGATGACTATGATGTCGATACCGCCAAATACCAAGAAAATGTGCTAGATACGCTTGACCGCTTGGGCGTGGGTATCTTGTGGCGTGATAATAATTCAGACTCAAAAGGCGTGATGGATAAGCTACCTGCCACGCAGTATTTTGATTATAAATCAGCAACCAACAACACCATCTGTAACACCAACCCTTATAATGAATGTCGTGATGTCGGTATGCTTGTTGGGCTAGATGACTATGTCAGCACCAATAATGGTAAAGATATGCTCATCATGCTACACCAAATGGGCAATCATGGGCCGGCGTACTTTAAGCGTTATGATGAGCAATTTGCCAAATTCACCCCCGTGTGCGAAGGCAACGAGCTTGCCAAATGCGAACATCAATCGCTCATCAATGCCTATGATAATGCGCTACTTGCCACCGATGATTTTATCGCCAAAAGTATCGATTGGCTAAAAACACATGAAGCAAACTACGATGTCGCCATGCTCTATGTCAGCGACCACGGCGAGAGTTTGGGCGAGAATGGCGTCTATTTGCATGGTATGCCAAATGCCTTTGCACCAAAAGAACAGCGAGCCGTGCCTGCGTTTTTTTGGTCAAATAATACGACATTCAAGCCAACTGCCAGCGACACTGTGCTGACGCATGATGCGATTACGCCAACACTGCTTAAGCTGTTTGATGTCACAGCGGGCAAGGTCAAAGACCGCACGGCATTTATCCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36791","NCBI_taxonomy_name":"uncultured bacterium","NCBI_taxonomy_id":"77133"}}}},"ARO_accession":"3007286","ARO_id":"46032","ARO_name":"MCR-2.5","CARD_short_name":"MCR-2.5","ARO_description":"An MCR-2-type colistin resistance gene variant.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5892":{"model_id":"5892","model_name":"MCR-2.7","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"8586":{"protein_sequence":{"accession":"WP_188331889.1","sequence":"MTSQHSWYRYSINPFVLMGLVAFFLAATANLTFFEKAMAVYPVSDNLGFIVSMAVALMGAMLLIVVLLSYRYVLKPVLILLLIMGAVTSYFTDTYGTVYDTTMLQNAMQTDQAESKDLMNLAFFVRIIGLGVLPSVLVAVAKVNYPTWGKGLIQRAMTWGVSLVLLLVPIGLFSSQYASFFRVHKPVRFYINPITPIYSVGKLASIEYKKATAPTDTIYHAKDAVQTTKPSERKPRLVVFVVGETARADHVQFNGYGRETFPQLAKVDGLANFSQVTSCGTSTAYSVPCMFSYLGQDDYDVDTAKYQENVLDTLDRLGVGILWRDNNSDSKGVMDKLPATQYFDYKSATNNTICSTNPYNECRDVGMLVGLDDYVSANNGKDMLIMLHQMGNHGPAYFKRYDEQFAKFTPVCEGNELAKCEHQSLINAYDNALLATDDFIAKSIDWLKTHEANYDVAMLYVSDHGESLGENGVYLHGMPNAFAPKEQRAVPAFFWSNNTSFKPTASDTVLTHDAITPTLLKLFDVTADKVKDRTAFIQ"},"dna_sequence":{"accession":"MT757843.1","fmin":"0","fmax":"1617","strand":"+","sequence":"ATGACATCACAGCACTCTTGGTATCGCTACTCCATCAATCCTTTTGTACTGATGGGTTTGGTGGCGTTTTTTTTGGCAGCGACAGCGAACCTGACATTTTTTGAAAAAGCGATGGCGGTCTATCCTGTATCGGATAACTTAGGCTTTATCGTCTCAATGGCGGTTGCGCTGATGGGTGCTATGCTATTGATTGTCGTGCTATTATCCTATCGCTATGTGCTAAAGCCTGTCCTGATTTTGCTACTGATTATGGGTGCGGTGACGAGCTATTTTACCGATACTTATGGCACGGTCTATGATACCACCATGCTCCAAAATGCCATGCAAACCGACCAAGCCGAGTCTAAAGACTTGATGAATTTGGCGTTTTTTGTGCGGATTATCGGGCTTGGTGTGTTGCCAAGTGTGTTGGTCGCAGTTGCCAAAGTCAATTATCCAACATGGGGCAAAGGCCTGATTCAGCGTGCGATGACGTGGGGTGTCAGCCTTGTGCTGTTGCTTGTGCCGATTGGACTATTTAGCAGTCAGTATGCGAGTTTCTTTCGGGTGCATAAGCCAGTGCGTTTTTATATTAACCCGATTACGCCGATTTATTCGGTGGGTAAGCTTGCCAGTATCGAGTACAAAAAAGCCACTGCGCCAACAGACACTATCTATCATGCCAAAGATGCCGTGCAGACCACCAAGCCGAGCGAGCGTAAGCCACGCCTAGTGGTGTTCGTCGTCGGTGAGACGGCTCGTGCTGACCATGTGCAGTTCAATGGCTATGGCCGCGAGACTTTCCCACAGCTTGCCAAAGTTGACGGCTTGGCGAACTTTAGCCAAGTGACATCGTGTGGCACATCGACGGCGTATTCTGTGCCGTGTATGTTTAGCTATCTGGGTCAAGATGACTATGATGTCGATACCGCCAAATACCAAGAAAATGTGCTGGATACGCTTGACCGCTTGGGCGTGGGCATCTTGTGGCGTGATAATAATTCAGACTCAAAAGGTGTGATGGATAAGCTACCTGCCACGCAGTATTTTGATTATAAATCAGCGACCAACAACACCATCTGTAGCACCAACCCCTATAATGAATGTCGTGATGTCGGTATGCTTGTCGGGCTAGATGACTATGTCAGCGCCAATAATGGCAAAGATATGCTCATCATGCTACACCAAATGGGCAATCATGGGCCGGCGTACTTTAAGCGTTATGATGAGCAATTTGCCAAATTCACCCCTGTGTGCGAAGGCAACGAGCTTGCCAAATGCGAACATCAATCGCTCATCAATGCCTATGATAATGCGCTACTTGCCACCGATGATTTTATCGCCAAAAGTATCGATTGGCTAAAAACACATGAAGCGAACTACGATGTCGCCATGCTGTATGTCAGCGACCACGGCGAGAGCTTGGGTGAGAATGGCGTCTATCTGCATGGTATGCCAAATGCCTTTGCACCAAAAGAACAGCGAGCCGTGCCTGCGTTTTTTTGGTCAAATAATACATCGTTCAAGCCAACTGCCAGCGATACTGTGCTGACTCATGATGCGATTACGCCGACACTGCTTAAGCTGTTTGATGTCACAGCCGACAAGGTCAAAGACCGCACGGCATTTATCCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36791","NCBI_taxonomy_name":"uncultured bacterium","NCBI_taxonomy_id":"77133"}}}},"ARO_accession":"3007287","ARO_id":"46033","ARO_name":"MCR-2.7","CARD_short_name":"MCR-2.7","ARO_description":"An MCR-2-type colistin resistance gene variant.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5893":{"model_id":"5893","model_name":"MCR-2.6","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"8587":{"protein_sequence":{"accession":"WP_188331888.1","sequence":"MTSQHSWYRYSINPFVLMGLVALFLAATANLAFFEKAMAVYPVSDNLGFIISMAVALMGAMLLIVVLLSYRYVLKPVLILLLIMGAVTSYFTDTYGTVYDTTMLQNAMQTDQAESKDLMNLAFFVRIIGLGVLPSVLVAVAKVNYPTWGKGLIQRAMTWGVSLALLLVPIGLFSSQYASFFRVHKPVRFYINPITPIYSVGKLASIEYKKATAPTDTIYHAKDAVQTTKPSERKPRLVVFVVGETARADHVQFNGYGRETFPQLAKVDGLANFSQVTSCGTSTAYSVPCMFSYLGQDDYDVDTAKYQENVLDTLDRLGVGILWRDNNSDSKGVMDKLPATQYFDYKSATNNTICNTNPYNECRDVGMLVGLDDYVSANNGKDMLIMLHQMGNHGPAYFKRYDEQFAKFTPVCEGNELAKCEHQSLINAYDNALLATDDFIAKSIDWLKTHEANYDVAMLYVSDHGESLGENGVYLHGMPNAFAPKEQRAVPAFFWSNNTTFKPTASDTALTHDAITPTLLKLFDVTADKVKDRTAFIQ"},"dna_sequence":{"accession":"MT757844.1","fmin":"0","fmax":"1617","strand":"+","sequence":"ATGACATCACAGCACTCTTGGTATCGCTACTCCATCAATCCCTTTGTACTGATGGGTTTGGTGGCGTTATTTTTGGCAGCGACAGCGAACCTGGCATTTTTTGAAAAAGCGATGGCGGTCTATCCTGTATCGGATAACTTAGGCTTTATCATCTCAATGGCGGTTGCACTGATGGGTGCTATGCTATTGATTGTCGTGCTGTTATCCTATCGCTATGTGCTAAAGCCTGTGCTGATTTTGCTACTGATTATGGGTGCAGTGACGAGCTATTTTACCGATACTTATGGCACGGTCTATGACACCACCATGCTCCAAAATGCCATGCAAACCGACCAAGCCGAGTCTAAGGACTTGATGAATTTGGCGTTTTTTGTGCGGATTATCGGGCTTGGTGTGTTGCCAAGTGTGTTGGTCGCAGTTGCCAAAGTCAATTATCCAACATGGGGCAAAGGCCTGATTCAGCGTGCGATGACGTGGGGTGTCAGCCTTGCGCTGTTGCTTGTGCCGATTGGGCTATTTAGCAGCCAGTATGCGAGTTTCTTTCGTGTGCATAAGCCAGTGCGTTTTTATATCAACCCGATTACGCCGATTTATTCGGTGGGCAAGCTTGCCAGTATCGAGTACAAAAAAGCCACTGCACCAACAGACACCATCTATCATGCCAAAGATGCCGTACAGACCACCAAGCCTAGCGAGCGTAAGCCCCGTCTAGTGGTGTTCGTCGTCGGTGAGACGGCGCGTGCTGACCATGTGCAGTTCAATGGCTATGGCCGTGAGACTTTCCCACAGCTTGCTAAAGTTGATGGCTTGGCGAACTTTAGCCAAGTGACATCGTGTGGCACATCGACAGCGTATTCTGTGCCGTGTATGTTTAGCTATTTGGGTCAAGATGACTATGATGTCGATACCGCCAAATACCAAGAAAATGTGCTAGATACGCTTGACCGCTTGGGCGTGGGTATCTTGTGGCGTGATAATAATTCAGACTCAAAAGGTGTGATGGATAAGCTACCTGCCACGCAGTATTTTGATTATAAATCAGCGACCAACAACACCATCTGTAACACCAATCCTTATAACGAATGTCGTGATGTTGGTATGCTTGTCGGGCTAGATGACTATGTCAGCGCCAATAATGGCAAAGATATGCTCATCATGCTACACCAAATGGGCAATCATGGGCCGGCGTACTTTAAGCGTTATGATGAGCAATTTGCCAAATTCACCCCTGTGTGCGAAGGCAACGAGCTTGCCAAATGCGAACATCAATCGCTCATCAATGCCTATGATAATGCGCTACTTGCCACCGATGATTTTATCGCCAAAAGTATCGATTGGCTAAAAACACATGAAGCGAACTATGATGTCGCCATGCTCTATGTCAGCGACCACGGCGAGAGCTTGGGTGAGAATGGCGTCTATTTGCACGGTATGCCAAATGCCTTTGCGCCAAAAGAACAGCGAGCCGTACCTGCATTTTTTTGGTCAAATAATACGACATTTAAGCCAACTGCCAGCGATACTGCATTGACCCATGATGCGATTACGCCGACACTGCTTAAGCTGTTTGATGTCACAGCCGACAAGGTCAAAGACCGCACGGCATTTATCCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36791","NCBI_taxonomy_name":"uncultured bacterium","NCBI_taxonomy_id":"77133"}}}},"ARO_accession":"3007288","ARO_id":"46034","ARO_name":"MCR-2.6","CARD_short_name":"MCR-2.6","ARO_description":"An MCR-2-type colistin resistance gene variant.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5894":{"model_id":"5894","model_name":"MCR-1.32","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"8588":{"protein_sequence":{"accession":"WP_213994615.1","sequence":"MVQHTSVWYRRSVGPFVLVASVAVFLTATANLTFFDKISQTYPIADNLGFVLTIAVVLFGAMLLITTLLSSYRYVLKPVLILLLIMGAVTSYFTDTYGTVYDTTMLQNALQTDQAETKDLLNAAFIMRIIGLGVLPSLLVAFVKVDYPTWGKGLMRRLGLIVASLALILLPVVAFSSHYASFFRVHKPLRSYVNPIMPIYSVGKLASIEYKKASAPKDTIYHAKDAVQATKPDMRKPRLVVFVVGETARADHVSFNGYERDTFPQLAKIDGVTNFSNVTSCGTSTAYSVPCMFSYLGADEYDVDTAKYQENVLDTLDRLGVSILWRDNNSDSKGVMDKLPKAQFADYKSATNNAICNTNPYNECRDVGMLVGLDDFVAANNGKDMLIMLHQMGNHGPAYFKRYDEKFAKFTPVCEGNELAKCEHQSLINAYDNALLATDDFIAQSIQWLQTHSNAYDVSMLYVSDHGESLGENGVYLHGMPNAFAPKEQRSVPAFFWTDKQTGITPMATDTVLTHDAITPTLLKLFDVTADKVKDRTAFIR"},"dna_sequence":{"accession":"MF084991.1","fmin":"0","fmax":"1626","strand":"+","sequence":"ATGGTGCAGCATACTTCTGTGTGGTACCGACGCTCGGTCGGTCCGTTTGTTCTTGTGGCGAGTGTTGCCGTTTTCTTGACCGCGACCGCCAATCTTACCTTTTTTGATAAAATCAGCCAAACCTATCCCATCGCGGACAATCTCGGCTTTGTGCTGACGATCGCTGTCGTGCTCTTTGGCGCGATGCTACTGATCACCACGCTGTTATCATCGTATCGCTATGTGCTAAAGCCTGTGTTGATTTTGCTATTAATCATGGGCGCGGTGACCAGTTATTTTACTGACACTTATGGCACGGTCTATGATACGACCATGCTCCAAAATGCCCTACAGACCGACCAAGCCGAGACCAAGGATCTATTAAACGCAGCGTTTATCATGCGTATCATTGGTTTGGGTGTGCTACCAAGTTTGCTTGTGGCTTTTGTTAAGGTGGATTATCCGACTTGGGGCAAGGGTTTGATGCGCCGATTGGGCTTGATCGTGGCAAGTCTTGCGCTGATTTTACTGCCTGTGGTGGCGTTCAGCAGTCATTATGCCAGTTTCTTTCGCGTGCATAAGCCGCTGCGTAGCTATGTCAATCCGATCATGCCAATCTACTCGGTGGGTAAGCTTGCCAGTATTGAGTATAAAAAAGCCAGTGCGCCAAAAGATACCATTTATCACGCCAAAGACGCGGTACAAGCAACCAAGCCTGATATGCGTAAGCCACGCCTAGTGGTGTTCGTCGTCGGTGAGACGGCACGCGCCGATCATGTCAGCTTCAATGGCTATGAGCGCGATACTTTCCCACAGCTTGCCAAGATCGATGGCGTGACCAATTTTAGCAATGTCACATCGTGCGGCACATCGACGGCGTATTCTGTGCCGTGTATGTTCAGCTATCTGGGCGCGGATGAGTATGATGTCGATACCGCCAAATACCAAGAAAATGTGCTGGATACGCTGGATCGCTTGGGCGTAAGTATCTTGTGGCGTGATAATAATTCGGACTCAAAAGGCGTGATGGATAAGCTGCCAAAAGCGCAATTTGCCGATTATAAATCCGCGACCAACAACGCCATCTGCAACACCAATCCTTATAACGAATGCCGCGATGTCGGTATGCTCGTTGGCTTAGATGACTTTGTCGCTGCCAATAACGGCAAAGATATGCTGATCATGCTGCACCAAATGGGCAATCACGGGCCTGCGTATTTTAAGCGATATGATGAAAAGTTTGCCAAATTCACGCCAGTGTGTGAAGGTAATGAGCTTGCCAAGTGCGAACATCAGTCCTTGATCAATGCTTATGACAATGCCTTGCTTGCCACCGATGATTTCATCGCTCAAAGTATCCAGTGGCTGCAGACGCACAGCAATGCCTATGATGTCTCAATGCTGTATGTCAGCGATCATGGCGAAAGTCTGGGTGAGAACGGTGTCTATCTACATGGTATGCCAAATGCCTTTGCACCAAAAGAACAGCGCAGTGTGCCTGCATTTTTCTGGACGGATAAGCAAACTGGCATCACGCCAATGGCAACCGATACCGTCCTGACCCATGACGCGATCACGCCGACATTATTAAAGCTGTTTGATGTCACCGCGGACAAAGTCAAAGACCGCACCGCATTCATCCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3007289","ARO_id":"46035","ARO_name":"MCR-1.32","CARD_short_name":"MCR-1.32","ARO_description":"An MCR-1-type colistin resistance gene variant.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5895":{"model_id":"5895","model_name":"FosXCC","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"150"}},"model_sequences":{"sequence":{"8589":{"protein_sequence":{"accession":"AIF29598.1","sequence":"MGVGKLIYGISHITFIVKDLDKATKFFKEIFEAKEIYSSEDKKFSISKEKFFLINDLWIAVMEGEEMEKSYNHIAFKIDESDYEMYLKRIENLGLEIKAGRKRVIGEGNSIYFYDYDNHLFELHTGTLETRLLRYQKEPTD"},"dna_sequence":{"accession":"KC876749.1","fmin":"4708","fmax":"5134","strand":"+","sequence":"TTGGGGGTGGGAAAGTTGATATATGGAATTAGTCATATTACTTTTATTGTCAAAGACCTAGATAAAGCCACAAAATTTTTTAAAGAAATTTTTGAAGCCAAAGAAATTTATTCAAGCGAAGACAAAAAGTTTTCTATATCCAAAGAAAAATTTTTCTTGATAAACGACCTTTGGATTGCAGTTATGGAAGGAGAGGAAATGGAAAAAAGCTATAATCATATAGCATTTAAAATAGATGAATCGGATTATGAAATGTACCTTAAGAGAATAGAAAACCTTGGTTTAGAGATAAAAGCTGGGAGAAAAAGGGTTATAGGAGAGGGGAATTCAATATATTTTTATGACTATGATAATCATCTTTTCGAACTCCACACTGGAACATTGGAAACAAGACTTCTTCGCTACCAAAAAGAACCAACAGATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36835","NCBI_taxonomy_name":"Campylobacter coli","NCBI_taxonomy_id":"195"}}}},"ARO_accession":"3003208","ARO_id":"39792","ARO_name":"FosXCC","CARD_short_name":"FosXCC","ARO_description":"fosXCC is a fosfomycin resistance gene that modifies MurA isolated from Campylobacter species. It is highly resistant to fosfomycin.","ARO_category":{"36272":{"category_aro_accession":"3000133","category_aro_cvterm_id":"36272","category_aro_name":"fosfomycin thiol transferase","category_aro_description":"Catalyzes the addition of a thiol group from a nucleophilic molecule to fosfomycin.","category_aro_class_name":"AMR Gene Family"},"35944":{"category_aro_accession":"0000025","category_aro_cvterm_id":"35944","category_aro_name":"fosfomycin","category_aro_description":"Fosfomycin (also known as phosphomycin and phosphonomycin) is a broad-spectrum antibiotic produced by certain Streptomyces species. It is effective on gram positive and negative bacteria as it targets the cell wall, an essential feature shared by both bacteria. Its specific target is MurA (MurZ in E.coli), which attaches phosphoenolpyruvate (PEP) to UDP-N-acetylglucosamine, a step of commitment to cell wall synthesis. In the active site of MurA, the active cysteine molecule is alkylated which stops the catalytic reaction.","category_aro_class_name":"Antibiotic"},"45731":{"category_aro_accession":"3007149","category_aro_cvterm_id":"45731","category_aro_name":"phosphonic acid antibiotic","category_aro_description":"A group of antibiotics derived from phosphonic acids.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5896":{"model_id":"5896","model_name":"FosG","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"175"}},"model_sequences":{"sequence":{"8590":{"protein_sequence":{"accession":"RTB44598.1","sequence":"MLRGLNHITIAVSDLGRSLAFYTDIVGMLAHVRWDNGAYLSLGGVWFCLSCDKVMPSKDYSHIALDISEDDFASFLEKLRRADVTEWKQNSSEGYSVYFLDPDGNKLEAHSGSLQSRLSSLKDKPYPGLVWL"},"dna_sequence":{"accession":"RWWU01000174.1","fmin":"102811","fmax":"103210","strand":"-","sequence":"GTGCTCCGAGGATTGAACCACATCACCATCGCTGTAAGCGATTTAGGCCGTTCTCTCGCCTTTTATACTGATATCGTCGGTATGCTCGCTCACGTACGCTGGGATAACGGTGCTTACCTTAGTCTAGGCGGTGTTTGGTTTTGTCTTTCCTGTGACAAGGTGATGCCAAGTAAGGATTATTCTCATATTGCCTTAGATATTTCAGAAGATGACTTTGCATCATTTTTGGAGAAACTGAGGAGAGCCGATGTCACTGAGTGGAAACAAAATTCAAGTGAAGGCTATTCGGTGTATTTCTTAGATCCTGATGGAAATAAACTAGAAGCGCATAGCGGCTCGTTACAATCTCGTTTAAGTTCTTTAAAAGACAAACCTTATCCGGGCTTAGTATGGCTTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3007368","ARO_id":"46115","ARO_name":"FosG","CARD_short_name":"FosG","ARO_description":"FosG is a glutathione transferase that confers resistance to fosfomycin.","ARO_category":{"36272":{"category_aro_accession":"3000133","category_aro_cvterm_id":"36272","category_aro_name":"fosfomycin thiol transferase","category_aro_description":"Catalyzes the addition of a thiol group from a nucleophilic molecule to fosfomycin.","category_aro_class_name":"AMR Gene Family"},"35944":{"category_aro_accession":"0000025","category_aro_cvterm_id":"35944","category_aro_name":"fosfomycin","category_aro_description":"Fosfomycin (also known as phosphomycin and phosphonomycin) is a broad-spectrum antibiotic produced by certain Streptomyces species. It is effective on gram positive and negative bacteria as it targets the cell wall, an essential feature shared by both bacteria. Its specific target is MurA (MurZ in E.coli), which attaches phosphoenolpyruvate (PEP) to UDP-N-acetylglucosamine, a step of commitment to cell wall synthesis. In the active site of MurA, the active cysteine molecule is alkylated which stops the catalytic reaction.","category_aro_class_name":"Antibiotic"},"45731":{"category_aro_accession":"3007149","category_aro_cvterm_id":"45731","category_aro_name":"phosphonic acid antibiotic","category_aro_description":"A group of antibiotics derived from phosphonic acids.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5897":{"model_id":"5897","model_name":"FosH","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"100"}},"model_sequences":{"sequence":{"8591":{"protein_sequence":{"accession":"ADF48907.1","sequence":"MGILGISHLTFVVRDVERTARLVCEGLGAEEVYDSKAKNFSLSREKFFLLGGVWLAFMEGVPSERSYRHVAFEVTEEEIARYEASLRNLGVEVREPRPRVAGEGLSLYFYDYDNNLFELHAGTLAQRLERYTQ"},"dna_sequence":{"accession":"GU966683.1","fmin":"970","fmax":"1372","strand":"+","sequence":"ATGGGAATTCTTGGCATTAGTCATCTGACATTCGTGGTCCGCGATGTAGAGCGCACTGCGAGACTGGTCTGCGAAGGACTTGGGGCGGAAGAGGTATACGACAGCAAAGCCAAAAACTTTTCGCTGTCACGAGAGAAGTTTTTTCTCTTGGGCGGCGTATGGCTTGCTTTCATGGAAGGAGTGCCATCGGAGCGGTCCTATCGGCACGTCGCTTTTGAAGTGACCGAAGAGGAAATTGCAAGATATGAGGCTAGCCTTAGAAACCTCGGTGTGGAAGTCAGAGAGCCGCGGCCAAGAGTGGCTGGAGAGGGGCTGTCACTGTATTTCTACGACTATGACAACAACTTATTCGAGCTACATGCGGGAACACTGGCGCAACGACTTGAAAGGTATACGCAATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3007369","ARO_id":"46116","ARO_name":"FosH","CARD_short_name":"FosH","ARO_description":"FosH is a hydrolase that confers resistance to fosfomycin.","ARO_category":{"36272":{"category_aro_accession":"3000133","category_aro_cvterm_id":"36272","category_aro_name":"fosfomycin thiol transferase","category_aro_description":"Catalyzes the addition of a thiol group from a nucleophilic molecule to fosfomycin.","category_aro_class_name":"AMR Gene Family"},"35944":{"category_aro_accession":"0000025","category_aro_cvterm_id":"35944","category_aro_name":"fosfomycin","category_aro_description":"Fosfomycin (also known as phosphomycin and phosphonomycin) is a broad-spectrum antibiotic produced by certain Streptomyces species. It is effective on gram positive and negative bacteria as it targets the cell wall, an essential feature shared by both bacteria. Its specific target is MurA (MurZ in E.coli), which attaches phosphoenolpyruvate (PEP) to UDP-N-acetylglucosamine, a step of commitment to cell wall synthesis. In the active site of MurA, the active cysteine molecule is alkylated which stops the catalytic reaction.","category_aro_class_name":"Antibiotic"},"45731":{"category_aro_accession":"3007149","category_aro_cvterm_id":"45731","category_aro_name":"phosphonic acid antibiotic","category_aro_description":"A group of antibiotics derived from phosphonic acids.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5898":{"model_id":"5898","model_name":"FosI","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"100"}},"model_sequences":{"sequence":{"8592":{"protein_sequence":{"accession":"AFJ38137.1","sequence":"MKGISHITFIVRDLNRMAALLCEGLGAREVYDSSNQNFSLSREKFFVLGSTWLAAMEGEPPAERSYQHVAFAVSETDLPAYQARLEALGVEIRPPRSRVDGEGLSLYFYDFDNHLFELHSGTLEQRLVRYQAGR"},"dna_sequence":{"accession":"CP003505.2","fmin":"17007","fmax":"17412","strand":"-","sequence":"ATGAAAGGCATCAGCCACATCACATTCATCGTCCGCGACCTGAATCGTATGGCCGCACTTCTCTGTGAGGGACTGGGTGCGCGTGAGGTGTATGACAGCTCAAACCAGAACTTCTCGTTGTCCCGCGAAAAGTTCTTTGTGCTTGGTAGTACGTGGCTAGCTGCAATGGAAGGTGAACCGCCCGCCGAGCGTTCATATCAGCATGTTGCCTTTGCGGTGAGTGAGACGGACTTGCCTGCGTATCAAGCCAGACTTGAGGCACTCGGCGTTGAGATTCGGCCACCGCGTAGCCGTGTTGACGGTGAGGGTCTCTCCCTGTACTTCTACGACTTTGACAATCATTTATTTGAACTTCATTCAGGTACTTTAGAGCAGCGCCTTGTCCGGTATCAGGCGGGGCGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"46118","NCBI_taxonomy_name":"Mycobacteroides abscessus subsp. bolletii F1725","NCBI_taxonomy_id":"1168066"}}}},"ARO_accession":"3007370","ARO_id":"46117","ARO_name":"FosI","CARD_short_name":"FosI","ARO_description":"FosI is a fosfomycin resistance gene.","ARO_category":{"36272":{"category_aro_accession":"3000133","category_aro_cvterm_id":"36272","category_aro_name":"fosfomycin thiol transferase","category_aro_description":"Catalyzes the addition of a thiol group from a nucleophilic molecule to fosfomycin.","category_aro_class_name":"AMR Gene Family"},"35944":{"category_aro_accession":"0000025","category_aro_cvterm_id":"35944","category_aro_name":"fosfomycin","category_aro_description":"Fosfomycin (also known as phosphomycin and phosphonomycin) is a broad-spectrum antibiotic produced by certain Streptomyces species. It is effective on gram positive and negative bacteria as it targets the cell wall, an essential feature shared by both bacteria. Its specific target is MurA (MurZ in E.coli), which attaches phosphoenolpyruvate (PEP) to UDP-N-acetylglucosamine, a step of commitment to cell wall synthesis. In the active site of MurA, the active cysteine molecule is alkylated which stops the catalytic reaction.","category_aro_class_name":"Antibiotic"},"45731":{"category_aro_accession":"3007149","category_aro_cvterm_id":"45731","category_aro_name":"phosphonic acid antibiotic","category_aro_description":"A group of antibiotics derived from phosphonic acids.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5899":{"model_id":"5899","model_name":"FosA8","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"100"}},"model_sequences":{"sequence":{"8593":{"protein_sequence":{"accession":"QEI22965.1","sequence":"MLNALNHLTLAVSNLPASITFWRDLLGLRLHAEWHTGAYLTCGDLWLCLSYDETRTFIPPQNSDYTHYAFSVEPEHFDAVAQKLKDAGVTVWKENKSEGASFYFLDPDGHKLELHVGDLAARLAACREKPYAGMVFTSDEA"},"dna_sequence":{"accession":"MN150127.1","fmin":"0","fmax":"426","strand":"+","sequence":"ATGCTTAACGCCCTTAACCATCTGACCCTTGCTGTCAGCAACTTGCCTGCCAGCATCACTTTCTGGCGCGATCTTCTTGGCCTGCGCCTGCACGCCGAATGGCACACCGGAGCTTACCTTACCTGTGGCGATCTCTGGCTCTGCCTGTCTTATGACGAGACGCGGACATTCATCCCACCACAGAACAGCGATTACACCCACTACGCCTTTTCTGTTGAACCGGAACACTTTGACGCCGTCGCGCAAAAGCTCAAAGACGCTGGCGTAACGGTCTGGAAAGAGAACAAAAGCGAAGGGGCGTCGTTCTATTTTCTCGACCCGGACGGGCACAAACTGGAACTGCATGTGGGCGATCTGGCCGCGCGTCTGGCGGCGTGTCGGGAGAAGCCTTACGCGGGAATGGTTTTTACGTCAGATGAAGCGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3007371","ARO_id":"46119","ARO_name":"FosA8","CARD_short_name":"FosA8","ARO_description":"FosA8 is a plasmid-located fosfomycin resistance gene.","ARO_category":{"36272":{"category_aro_accession":"3000133","category_aro_cvterm_id":"36272","category_aro_name":"fosfomycin thiol transferase","category_aro_description":"Catalyzes the addition of a thiol group from a nucleophilic molecule to fosfomycin.","category_aro_class_name":"AMR Gene Family"},"35944":{"category_aro_accession":"0000025","category_aro_cvterm_id":"35944","category_aro_name":"fosfomycin","category_aro_description":"Fosfomycin (also known as phosphomycin and phosphonomycin) is a broad-spectrum antibiotic produced by certain Streptomyces species. It is effective on gram positive and negative bacteria as it targets the cell wall, an essential feature shared by both bacteria. Its specific target is MurA (MurZ in E.coli), which attaches phosphoenolpyruvate (PEP) to UDP-N-acetylglucosamine, a step of commitment to cell wall synthesis. In the active site of MurA, the active cysteine molecule is alkylated which stops the catalytic reaction.","category_aro_class_name":"Antibiotic"},"45731":{"category_aro_accession":"3007149","category_aro_cvterm_id":"45731","category_aro_name":"phosphonic acid antibiotic","category_aro_description":"A group of antibiotics derived from phosphonic acids.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5900":{"model_id":"5900","model_name":"FosBx1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"150"}},"model_sequences":{"sequence":{"8594":{"protein_sequence":{"accession":"QLF01382.1","sequence":"MLRGINHICFSVSNLENSIMFYEKVLEGELLVKGRKLAYFNICGVWIALNEETHIPRNEIHQSYTHIAFSVEKEDFKCLIQRLEENDVHILQGRERDVRDCESIYFVDPDGHKFEFHSGTLQDRLNYYRDEKPHMTFY"},"dna_sequence":{"accession":"CP043966.1","fmin":"1915971","fmax":"1916388","strand":"+","sequence":"TTGTTAAGGGGAATCAATCATATTTGTTTTTCGGTATCTAATTTAGAAAACTCTATTATGTTTTATGAAAAAGTATTAGAAGGAGAATTATTAGTTAAAGGAAGAAAATTGGCTTATTTTAACATATGTGGAGTATGGATAGCGCTTAATGAAGAGACGCATATTCCGAGAAATGAGATTCATCAATCTTATACGCACATTGCATTTTCTGTTGAAAAAGAAGACTTTAAATGTCTAATACAGCGATTAGAAGAAAATGATGTTCATATTTTACAAGGAAGAGAACGTGATGTAAGAGATTGCGAATCTATATACTTTGTTGATCCTGACGGTCATAAATTTGAGTTTCACTCAGGGACACTGCAAGACCGTTTAAATTATTATAGAGATGAGAAACCTCATATGACATTTTATTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36751","NCBI_taxonomy_name":"Bacillus cereus","NCBI_taxonomy_id":"1396"}}}},"ARO_accession":"3007372","ARO_id":"46120","ARO_name":"FosBx1","CARD_short_name":"FosBx1","ARO_description":"FosBx1 is a fosfomycin resistance gene.","ARO_category":{"36272":{"category_aro_accession":"3000133","category_aro_cvterm_id":"36272","category_aro_name":"fosfomycin thiol transferase","category_aro_description":"Catalyzes the addition of a thiol group from a nucleophilic molecule to fosfomycin.","category_aro_class_name":"AMR Gene Family"},"35944":{"category_aro_accession":"0000025","category_aro_cvterm_id":"35944","category_aro_name":"fosfomycin","category_aro_description":"Fosfomycin (also known as phosphomycin and phosphonomycin) is a broad-spectrum antibiotic produced by certain Streptomyces species. It is effective on gram positive and negative bacteria as it targets the cell wall, an essential feature shared by both bacteria. Its specific target is MurA (MurZ in E.coli), which attaches phosphoenolpyruvate (PEP) to UDP-N-acetylglucosamine, a step of commitment to cell wall synthesis. In the active site of MurA, the active cysteine molecule is alkylated which stops the catalytic reaction.","category_aro_class_name":"Antibiotic"},"45731":{"category_aro_accession":"3007149","category_aro_cvterm_id":"45731","category_aro_name":"phosphonic acid antibiotic","category_aro_description":"A group of antibiotics derived from phosphonic acids.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5901":{"model_id":"5901","model_name":"PJM-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"11350":{"protein_sequence":{"accession":"WP_213603971.1","sequence":"MTLRSTLLSALVALALPSAALASDATTAKACADDAGWNDPATPLKVYGNTWYVGTCGISALLVTSDEGHILVDAATPQAGPQILANIRALGFKPEDVRAIVFSHEHFDHAGSLAELQQATGAPVYARAPAVATLKRGASDRSDPQHEVLDPFAPVQQVVVLDDDGVVRVGPLALQVVSTPGHTPGGTSWTWRSCEGDDCRQMVYADSLTAISDDVYRYSDDAAHPGYVAAFRETLARVAALECDILVTPHPSASQLWSRIGPRADRPLVDTSACRTYAQTATQRLDKRLADEASKPPVPAP"},"dna_sequence":{"accession":"NG_080789.1","fmin":"100","fmax":"1006","strand":"+","sequence":"ATGACGCTCCGCTCCACCCTGCTTTCCGCTCTGGTCGCGCTCGCGCTTCCCTCCGCCGCGCTCGCTTCCGACGCGACCACGGCCAAAGCCTGCGCCGACGATGCCGGCTGGAACGATCCCGCCACGCCGCTGAAGGTCTACGGCAACACCTGGTACGTCGGCACGTGCGGCATCAGCGCCTTGCTGGTGACCTCCGATGAAGGCCACATCCTGGTCGACGCCGCCACGCCGCAGGCCGGCCCGCAGATCCTCGCCAATATCCGCGCCCTCGGCTTCAAGCCGGAGGATGTGCGTGCCATCGTGTTCTCGCACGAGCACTTCGACCATGCCGGCAGCCTGGCCGAGTTGCAGCAGGCCACGGGCGCGCCTGTGTATGCGCGTGCGCCTGCCGTTGCCACGCTCAAGCGCGGCGCCAGCGATCGCAGCGATCCGCAGCATGAGGTACTCGATCCGTTCGCGCCGGTCCAGCAGGTGGTCGTACTCGACGACGACGGCGTGGTGCGTGTCGGTCCGCTCGCCCTGCAGGTCGTTTCCACGCCGGGACACACGCCCGGCGGCACCAGCTGGACCTGGCGCTCGTGCGAGGGCGACGACTGCCGGCAGATGGTCTACGCCGACAGCCTGACCGCGATCTCCGACGACGTGTACCGCTACAGCGACGATGCGGCGCACCCTGGTTACGTGGCGGCATTCCGCGAGACGCTGGCGCGGGTCGCGGCACTCGAGTGCGACATCCTGGTGACGCCACATCCGTCGGCCAGCCAACTCTGGTCCCGCATCGGTCCTCGCGCCGACCGCCCGCTGGTCGACACCAGCGCCTGCCGCACCTATGCACAGACCGCGACGCAGCGGCTGGACAAGCGGCTCGCGGACGAAGCGTCGAAGCCCCCCGTGCCTGCGCCTTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"46123","NCBI_taxonomy_name":"Pseudoxanthomonas japonensis","NCBI_taxonomy_id":"69284"}}}},"ARO_accession":"3007374","ARO_id":"46122","ARO_name":"PJM-1","CARD_short_name":"PJM-1","ARO_description":"PJM-1 is a chromosomally-encoded subclass B3 metallo-beta-lactamase found in P. japonensis confering resistance to a range of antibiotics including ampicillin, cefalotin, and cefoxitin.","ARO_category":{"46121":{"category_aro_accession":"3007373","category_aro_cvterm_id":"46121","category_aro_name":"PJM beta-lactamase","category_aro_description":"A family of subclass B3 metallo-beta-lactamases with activity against a range of beta-lactam antibiotics.","category_aro_class_name":"AMR Gene Family"},"35927":{"category_aro_accession":"0000008","category_aro_cvterm_id":"35927","category_aro_name":"cefoxitin","category_aro_description":"Cefoxitin is a cephamycin antibiotic often grouped with the second generation cephalosporins. Cefoxitin is bactericidal and acts by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. Cefoxitin's 7-alpha-methoxy group and 3' leaving group make it a poor substrate for most beta-lactamases.","category_aro_class_name":"Antibiotic"},"36309":{"category_aro_accession":"3000170","category_aro_cvterm_id":"36309","category_aro_name":"imipenem","category_aro_description":"Imipenem is a broad-spectrum antibiotic and is usually taken with cilastatin, which prevents hydrolysis of imipenem by renal dehydropeptidase-I. It is resistant to hydrolysis by most other beta-lactamases. Notable exceptions are the KPC beta-lactamases and Ambler Class B enzymes.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"36989":{"category_aro_accession":"3000645","category_aro_cvterm_id":"36989","category_aro_name":"cefotaxime","category_aro_description":"Cefotaxime is a semisynthetic cephalosporin taken parenterally. It is resistant to most beta-lactamases and active against Gram-negative rods and cocci due to its aminothiazoyl and methoximino functional groups.","category_aro_class_name":"Antibiotic"},"37084":{"category_aro_accession":"3000704","category_aro_cvterm_id":"37084","category_aro_name":"cefalotin","category_aro_description":"Cefalotin is a semisynthetic cephalosporin antibiotic activate against staphylococci. It is resistant to staphylococci beta-lactamases but hydrolyzed by enterobacterial beta-lactamases.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5902":{"model_id":"5902","model_name":"KPC-87","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"475"}},"model_sequences":{"sequence":{"8596":{"protein_sequence":{"accession":"QUR41143.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYAANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"MZ067230.1","fmin":"0","fmax":"879","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGCGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3007375","ARO_id":"46125","ARO_name":"KPC-87","CARD_short_name":"KPC-87","ARO_description":"KPC-87 is a chromosome-encoded carbapenemase found in Klebsiella pneumonia.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35990":{"category_aro_accession":"0000073","category_aro_cvterm_id":"35990","category_aro_name":"meropenem","category_aro_description":"Meropenem is an ultra-broad spectrum injectable antibiotic used to treat a wide variety of infections, including meningitis and pneumonia. It is a beta-lactam and belongs to the subgroup of carbapenem, similar to imipenem and ertapenem.","category_aro_class_name":"Antibiotic"},"36309":{"category_aro_accession":"3000170","category_aro_cvterm_id":"36309","category_aro_name":"imipenem","category_aro_description":"Imipenem is a broad-spectrum antibiotic and is usually taken with cilastatin, which prevents hydrolysis of imipenem by renal dehydropeptidase-I. It is resistant to hydrolysis by most other beta-lactamases. Notable exceptions are the KPC beta-lactamases and Ambler Class B enzymes.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5903":{"model_id":"5903","model_name":"KPC-86","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8638":{"protein_sequence":{"accession":"QUR41142.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARGTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"MZ067229.1","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGGTACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3007381","ARO_id":"46131","ARO_name":"KPC-86","CARD_short_name":"KPC-86","ARO_description":"KPC-86 is a chromosome-encoded carbapenemase found in Klebsiella pneumonia.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5904":{"model_id":"5904","model_name":"KPC-95","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"475"}},"model_sequences":{"sequence":{"8599":{"protein_sequence":{"accession":"QYE52347.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSTIPGDARYTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKYSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"MZ646141.1","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCACCATCCCAGGCGATGCGCGCTATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGTACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3007383","ARO_id":"46134","ARO_name":"KPC-95","CARD_short_name":"KPC-95","ARO_description":"KPC-95 is a chromosome-encoded carbapenemase found in Klebsiella pneumonia.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5905":{"model_id":"5905","model_name":"ANT(9)-Ib","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"8601":{"protein_sequence":{"accession":"AAA16527.1","sequence":"MRRIYLNTYEQINKVKKILRKHLKNNLIGTYMFGSGVESGLKPNSDLDFLVVVSEPLTDQSKEILIQKIRPISKKIGDKSNLRYIELTIIIQQEMVPWNHPPKQEFIYGEWLQELYEQGYIPQKELNSDLTIMLYQAKRKNKRIYGNYDLEELLPDIPFSDVRRAIMDSSEELIDNYQDDETNSILTLCRMILTMDTGKIIPKDIAGNAVAESSPLEHRERILLAVRSYLGENIEWTNENVNLTINYLNNRLKKL"},"dna_sequence":{"accession":"M69221.1","fmin":"270","fmax":"1038","strand":"+","sequence":"GTGAGGAGGATATATTTGAATACATACGAACAAATTAATAAAGTGAAAAAAATACTTCGGAAACATTTAAAAAATAACCTTATTGGTACTTACATGTTTGGATCAGGAGTTGAGAGTGGACTAAAACCAAATAGTGATCTTGACTTTTTAGTCGTCGTATCTGAACCATTGACAGATCAAAGTAAAGAAATACTTATACAAAAAATTAGACCTATTTCAAAAAAAATAGGAGATAAAAGCAACTTACGATATATTGAATTAACAATTATTATTCAGCAAGAAATGGTACCGTGGAATCATCCTCCCAAACAAGAATTTATTTATGGAGAATGGTTACAAGAGCTTTATGAACAAGGATACATTCCTCAGAAGGAATTAAATTCAGATTTAACCATAATGCTTTACCAAGCAAAACGAAAAAATAAAAGAATATACGGAAATTATGACTTAGAGGAATTACTACCTGATATTCCATTTTCTGATGTGAGAAGAGCCATTATGGATTCGTCAGAGGAATTAATAGATAATTATCAGGATGATGAAACCAACTCTATATTAACTTTATGCCGTATGATTTTAACTATGGACACGGGTAAAATCATACCAAAAGATATTGCGGGAAATGCAGTGGCTGAATCTTCTCCATTAGAACATAGGGAGAGAATTTTGTTAGCAGTTCGTAGTTATCTTGGAGAGAATATTGAATGGACTAATGAAAATGTAAATTTAACTATAAACTATTTAAATAACAGATTAAAAAAATTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35918","NCBI_taxonomy_name":"Enterococcus faecalis","NCBI_taxonomy_id":"1351"}}}},"ARO_accession":"3007401","ARO_id":"46152","ARO_name":"ANT(9)-Ib","CARD_short_name":"ANT(9)-Ib","ARO_description":"A plasmid-borne ANT(9)-I variant identified from Enterococcus faecalis. ANT(9)-Ib confers resistance to spectinomycin through enzymatic inactivation.","ARO_category":{"36367":{"category_aro_accession":"3000228","category_aro_cvterm_id":"36367","category_aro_name":"ANT(9)","category_aro_description":"A category of aminoglycoside O-nucleotidyltransferase enzymes with modification regiospecificity based at the 9-hydroxyl group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics, specifically streptomycin, by transfer of an AMP group from an ATP substrate to the 9-hydroxyl group of the compound.","category_aro_class_name":"AMR Gene Family"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5906":{"model_id":"5906","model_name":"KPC-94","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"475"}},"model_sequences":{"sequence":{"8602":{"protein_sequence":{"accession":"QYE52346.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELEHSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKYSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"MZ646140.1","fmin":"0","fmax":"879","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGTACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3007402","ARO_id":"46153","ARO_name":"KPC-94","CARD_short_name":"KPC-94","ARO_description":"KPC-94 is a mutated carbapenemase allele found in Klebsiella pneumoniae.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"35990":{"category_aro_accession":"0000073","category_aro_cvterm_id":"35990","category_aro_name":"meropenem","category_aro_description":"Meropenem is an ultra-broad spectrum injectable antibiotic used to treat a wide variety of infections, including meningitis and pneumonia. It is a beta-lactam and belongs to the subgroup of carbapenem, similar to imipenem and ertapenem.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5734":{"model_id":"5734","model_name":"PFM-4","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"515"}},"model_sequences":{"sequence":{"8131":{"protein_sequence":{"accession":"MBU4627809.1","sequence":"MKLINILSVISLACITSQVFANKSDLTLTHFKGPLYIVEDKEYVQENSMVYVGEQHITVIGATWTPATAEKLEQEIRKISPLPIKEVINTNYHTDRAGGNAYWKKLGASIVSTQMTYDLEKSQWRSIVDFTRQGMEHYPILEQSLPDQVYPGNFDLQNGHVRALYLGASHTEDGIFVYFPEERVLYGNCILKEKLGNMTFANRSEYPKTLKKLQGLIRSGELPVEAIIAGHNSPIQNVELIDHYLTLLEHGEQ"},"dna_sequence":{"accession":"JACOMR010000005.1","fmin":"4634","fmax":"5396","strand":"+","sequence":"ATGAAGCTTATTAATATTCTGTCAGTCATCAGCCTGGCCTGCATTACCTCCCAGGTCTTCGCTAACAAGAGTGACTTGACCCTTACCCACTTCAAAGGCCCGCTCTACATCGTTGAAGACAAGGAATATGTGCAGGAGAACTCAATGGTCTACGTTGGCGAGCAACACATCACGGTTATTGGCGCAACCTGGACCCCAGCCACCGCTGAAAAGCTTGAGCAGGAAATCAGGAAAATCAGCCCCCTGCCCATCAAGGAGGTGATCAATACCAACTACCACACCGACCGCGCGGGAGGTAACGCCTACTGGAAGAAGCTCGGCGCCAGTATTGTCTCAACGCAGATGACCTATGACCTGGAAAAAAGCCAGTGGCGCAGTATTGTCGACTTTACCCGGCAAGGGATGGAGCACTATCCAATCCTGGAACAAAGCCTGCCAGACCAGGTATACCCGGGCAACTTCGACTTGCAAAACGGCCATGTTAGAGCACTGTATTTAGGCGCGTCTCACACCGAAGATGGGATTTTTGTGTACTTTCCAGAAGAGCGTGTGTTGTATGGAAACTGCATTCTCAAGGAAAAGCTGGGTAACATGACATTCGCGAATCGCAGCGAGTACCCGAAAACCCTGAAGAAATTGCAAGGGCTGATCCGCAGTGGTGAATTGCCCGTTGAAGCGATTATCGCAGGGCATAACTCACCGATACAGAACGTTGAGTTGATTGACCATTATCTGACCCTGCTTGAACACGGCGAGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"45494","NCBI_taxonomy_name":"Pseudomonas sp. BF61","NCBI_taxonomy_id":"2741068"}}}},"ARO_accession":"3007021","ARO_id":"45492","ARO_name":"PFM-4","CARD_short_name":"PFM-4","ARO_description":"PFM-4 (BioF) is a class B2 metallo-beta-lactamase first identified in Pseudomonas. It belongs to the PFM-like beta-lactamase gene family. It confers resistance to carbapenems and some cephalosporins.","ARO_category":{"43892":{"category_aro_accession":"3005432","category_aro_cvterm_id":"43892","category_aro_name":"PFM beta-lactamase","category_aro_description":"PFM beta-lactamases are class B2 beta-lactamases found in Pseudomonas fluorescens.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"639":{"model_id":"639","model_name":"AAC(3)-IVa","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"3715":{"protein_sequence":{"accession":"ABB43029.1","sequence":"MQYEWRKAELIGQLLNLGVTPGGVLLVHSSFRSVRPLEDGPLGLIEALRAALGPGGTLVMPSWSGLDDEPFDPATSPVTPDLGVVSDTFWRLPNVKRSAHPFAFAAAGPQAEQIISDPLPLPPHSPASPVARVHELDGQVLLLGVGHDANTTLHLAELMAKVPYGVPRHCTILQDGKLVRVDYLENDHCCERFALADRWLKEKSLQKEGPVGHAFARLIRSRDIVATALGQLGRDPLIFLHPPEAGCEECDAARQSIG"},"dna_sequence":{"accession":"DQ241380.1","fmin":"0","fmax":"777","strand":"+","sequence":"GTGCAATACGAATGGCGAAAAGCCGAGCTCATCGGTCAGCTTCTCAACCTTGGGGTTACCCCCGGCGGTGTGCTGCTGGTCCACAGCTCCTTCCGTAGCGTCCGGCCCCTCGAAGATGGGCCACTTGGACTGATCGAGGCCCTGCGTGCTGCGCTGGGTCCGGGAGGGACGCTCGTCATGCCCTCGTGGTCAGGTCTGGACGACGAGCCGTTCGATCCTGCCACGTCGCCCGTTACACCGGACCTTGGAGTTGTCTCTGACACATTCTGGCGCCTGCCAAATGTAAAGCGCAGCGCCCATCCATTTGCCTTTGCGGCAGCGGGGCCACAGGCAGAGCAGATCATCTCTGATCCATTGCCCCTGCCACCTCACTCGCCTGCAAGCCCGGTCGCCCGTGTCCATGAACTCGATGGGCAGGTACTTCTCCTCGGCGTGGGACACGATGCCAACACGACGCTGCATCTTGCCGAGTTGATGGCAAAGGTTCCCTATGGGGTGCCGAGACACTGCACCATTCTTCAGGATGGCAAGTTGGTACGCGTCGATTATCTCGAGAATGACCACTGCTGTGAGCGCTTTGCCTTGGCGGACAGGTGGCTCAAGGAGAAGAGCCTTCAGAAGGAAGGTCCAGTCGGTCATGCCTTTGCTCGGTTGATCCGCTCCCGCGACATTGTGGCGACAGCCCTGGGTCAACTGGGCCGAGATCCGTTGATCTTCCTGCATCCGCCAGAGGCGGGATGCGAAGAATGCGATGCCGCTCGCCAGTCGATTGGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002539","ARO_id":"38939","ARO_name":"AAC(3)-IVa","CARD_short_name":"AAC(3)-IVa","ARO_description":"AAC(3)-IV is a plasmid-encoded aminoglycoside acetyltransferase in E. coli, C. jejuni and P. stutzeri.","ARO_category":{"36461":{"category_aro_accession":"3000322","category_aro_cvterm_id":"36461","category_aro_name":"AAC(3)","category_aro_description":"A category of aminoglycoside N-acetyltransferase enzymes with modification regiospecificity based at the 3-amino group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics through acetylation of the 3-amino group of the compound.","category_aro_class_name":"AMR Gene Family"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35955":{"category_aro_accession":"0000037","category_aro_cvterm_id":"35955","category_aro_name":"apramycin","category_aro_description":"Apramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections in animals. Apramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"46127":{"category_aro_accession":"3007377","category_aro_cvterm_id":"46127","category_aro_name":"6'-N-ethylnetilmicin","category_aro_description":"6'-N-ethylnetilmicin is an aminoglycoside antibiotic and a derivative of netilmicin.","category_aro_class_name":"Antibiotic"},"46128":{"category_aro_accession":"3007378","category_aro_cvterm_id":"46128","category_aro_name":"2'-N-ethylnetilmicin","category_aro_description":"2'-N-ethylnetilmicin is an aminoglycoside antibiotic and a derivative of netilmicin.","category_aro_class_name":"Antibiotic"},"46133":{"category_aro_accession":"3007382","category_aro_cvterm_id":"46133","category_aro_name":"gentamicin","category_aro_description":"Gentamicin is a commonly used aminoglycoside antibiotic derived from members of the Micromonospora genus of bacteria. It acts by binding the 30S ribosomal subunit, thus inhibiting protein synthesis. Gentamicin is typically used to treat Gram-negative infections of the repiratory and urinary tract, as well as infections of the bone and soft tissue. It also exhibits considerable nephrotoxicity and ototoxicity. Gentamicin is administered as a mixture of gentamicin type C (which makes about around 80% of the complex) and types A, B, and X (distributed in the remaining 20% of the complex).","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5907":{"model_id":"5907","model_name":"QnrAS","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"8616":{"protein_sequence":{"accession":"CAQ79275.1","sequence":"MAKYNEIFDNVDFSKQDLRESYFEGCKFYRCDFNRTNLRDSRFVDCVFIEQGAIEGCHFDYSDLRDASFKRCRLTMSNFKGANCFGVEFRECDLKGANFVQASFVNQISHQMYFCSAYITGCNLSYANFERLCIEKCDLFENKWNGANLQGASFKGSDLSRGAFSEDSWGQFRMQDANLCHCELDGLDPRRIDLTGVKICAWQQEQLLEPLGLVVLPD"},"dna_sequence":{"accession":"FM178379.1","fmin":"1699483","fmax":"1700140","strand":"-","sequence":"ATGGCTAAATATAATGAAATATTCGATAACGTGGATTTTTCGAAACAAGATTTAAGAGAATCCTATTTTGAAGGGTGTAAGTTTTATCGATGTGATTTCAATCGAACCAATCTGAGAGACTCCCGATTTGTTGATTGTGTTTTTATCGAACAGGGGGCAATTGAAGGTTGTCATTTTGATTACAGTGACTTAAGGGACGCATCATTTAAACGCTGTCGCTTAACCATGTCTAATTTTAAAGGCGCAAATTGCTTTGGTGTCGAATTTAGAGAGTGTGATTTAAAAGGAGCTAATTTTGTTCAAGCCAGTTTTGTTAATCAAATAAGTCATCAAATGTATTTCTGCTCTGCTTATATTACGGGGTGTAATTTGTCTTATGCGAATTTTGAACGCCTATGTATCGAGAAATGTGACTTGTTTGAGAACAAATGGAACGGAGCTAATTTACAAGGGGCATCTTTTAAGGGTTCGGACCTTTCTCGTGGCGCATTCTCTGAAGACTCGTGGGGTCAATTTAGAATGCAAGATGCAAACTTATGTCATTGTGAATTGGATGGTTTAGATCCCCGTAGAATTGATTTAACCGGTGTTAAGATCTGTGCATGGCAACAAGAGCAATTATTAGAGCCATTAGGATTAGTGGTACTGCCTGACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"46173","NCBI_taxonomy_name":"Aliivibrio salmonicida LFI1238","NCBI_taxonomy_id":"316275"}}}},"ARO_accession":"3004668","ARO_id":"42715","ARO_name":"QnrAS","CARD_short_name":"QnrAS","ARO_description":"Located on the chromosome of Aliivibrio salmonicida. Provides low-level resistance to quinolones.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5908":{"model_id":"5908","model_name":"QnrB39","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"8617":{"protein_sequence":{"accession":"EFE09657.1","sequence":"MTLALVGEKIDRNRFTGVKVENSTFFNCDFSGTDLSGTEFIGCQFYDRESQKGCNFSRAILKDAIFKSCDLSMADFRNASALGIEIRHCRAQGSDFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGTQVLGATFSGSDLSGGEFSSFDWRAANFTHCDLTNSELGDLDVRGVDLQGVKLDSYQASLILERLGIAVIG"},"dna_sequence":{"accession":"ABWL02000005.1","fmin":"133565","fmax":"134210","strand":"-","sequence":"ATGACTCTGGCGTTGGTTGGCGAAAAAATTGACAGAAACAGGTTCACCGGTGTGAAAGTTGAAAATAGCACGTTTTTCAACTGTGATTTTTCGGGTACCGACCTTAGCGGCACTGAATTTATTGGCTGCCAGTTTTATGATCGAGAGAGCCAGAAAGGGTGTAATTTTAGTCGCGCTATCCTGAAAGATGCCATTTTCAAAAGCTGTGATTTATCCATGGCGGATTTCAGAAATGCCAGCGCGCTGGGAATCGAGATTCGCCACTGCCGCGCGCAAGGTTCGGATTTTCGCGGTGCCAGTTTTATGAATATGATCACCACCCGCACCTGGTTTTGCAGCGCTTATATCACCAATACAAACTTAAGCTACGCCAACTTTTCGAAAGTCGTACTGGAAAAGTGCGAGCTGTGGGAAAACCGTTGGATGGGTACTCAGGTACTGGGGGCGACGTTCAGTGGTTCAGATCTTTCCGGCGGCGAGTTTTCGTCGTTCGACTGGCGGGCCGCGAACTTTACGCACTGTGACCTGACCAACTCGGAGCTGGGTGATTTAGACGTCCGTGGGGTGGATTTACAAGGCGTTAAACTGGACAGCTACCAGGCGTCTTTGATCCTGGAGCGTCTTGGCATCGCTGTCATTGGTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39643","NCBI_taxonomy_name":"Citrobacter youngae ATCC 29220","NCBI_taxonomy_id":"500640"}}}},"ARO_accession":"3002754","ARO_id":"39188","ARO_name":"QnrB39","CARD_short_name":"QnrB39","ARO_description":"QnrB39 is a chromosome-mediated quinolone resistance protein found in Citrobacter youngae.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5909":{"model_id":"5909","model_name":"QnrB75","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"8618":{"protein_sequence":{"accession":"AKI82195.1","sequence":"MALALVGEKIDRNRFTGEKIENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGGKFSRAMLKDAIFKSCDLSMADFRNSSALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGAQVLGATFSGSDLSGGEFSTFDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDNYQASLLMERLGIAVIG"},"dna_sequence":{"accession":"KP207591.1","fmin":"2075","fmax":"2720","strand":"-","sequence":"ATGGCTCTGGCACTCGTTGGCGAAAAAATTGACAGAAACCGTTTCACCGGTGAGAAAATTGAAAATAGTACATTTTTTAACTGTGATTTTTCAGGTGCCGACCTGAGCGGCACTGAATTTATCGGCTGTCAGTTCTATGATCGTGAAAGCCAGAAAGGGGGCAAATTTAGTCGTGCGATGCTGAAAGATGCCATTTTTAAAAGCTGTGATTTATCCATGGCGGATTTTCGCAATTCCAGTGCGCTGGGCATTGAAATTCGCCACTGCCGCGCACAAGGCGCAGATTTCCGCGGCGCAAGCTTTATGAATATGATCACCACGCGCACCTGGTTTTGTAGCGCATATATCACGAATACCAATCTAAGCTACGCCAATTTTTCGAAAGTCGTGTTGGAAAAGTGTGAGCTGTGGGAAAACCGTTGGATGGGTGCCCAGGTACTGGGCGCGACGTTCAGTGGTTCGGATCTCTCCGGCGGCGAGTTTTCGACTTTCGACTGGCGAGCAGCAAACTTCACACATTGCGATCTGACCAATTCGGAGTTGGGTGACTTAGATATTCGGGGCGTTGATTTACAAGGCGTTAAGCTGGACAACTACCAGGCGTCGTTGCTCATGGAGCGGCTTGGCATCGCGGTGATTGGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3003187","ARO_id":"39764","ARO_name":"QnrB75","CARD_short_name":"QnrB75","ARO_description":"QnrB75 is a fluoroquinolone resistance gene in Lahey's list of qnr genes.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5910":{"model_id":"5910","model_name":"QnrB77","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"8619":{"protein_sequence":{"accession":"AKO62869.1","sequence":"MALALVGEKIDRNRFTGEKIENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNSSALGIEIRHCRAQGTDFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGAQVLGATFSGSDLSGGEFSTFDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDNYQASLLMERLGIAVIG"},"dna_sequence":{"accession":"KM985470.1","fmin":"0","fmax":"645","strand":"+","sequence":"ATGGCTCTGGCACTCGTTGGCGAAAAAATTGACAGAAACCGTTTCACCGGTGAGAAAATTGAAAATAGTACATTTTTTAACTGTGATTTTTCAGGTGCCGACCTGAGCGGCACTGAATTTATCGGCTGTCAGTTCTATGATCGTGAAAGCCAGAAAGGGTGCAATTTTAGTCGTGCGATGCTGAAAGATGCCATTTTTAAAAGCTGTGATTTATCCATGGCGGATTTTCGCAATTCCAGTGCGCTGGGCATTGAAATTCGCCACTGCCGCGCACAAGGCACAGATTTCCGCGGCGCAAGCTTTATGAATATGATCACCACGCGCACCTGGTTTTGTAGCGCATATATCACGAATACCAATCTAAGCTACGCCAATTTTTCGAAAGTCGTGTTGGAAAAGTGTGAGCTGTGGGAAAACCGTTGGATGGGTGCCCAGGTACTGGGCGCGACGTTCAGTGGTTCAGATCTCTCCGGCGGCGAGTTTTCGACTTTCGACTGGCGAGCAGCGAACTTCACACATTGCGATCTGACCAATTCGGAGTTGGGTGACTTAGATATTCGGGGCGTTGATTTACAAGGCGTTAAGCTGGACAACTACCAGGCGTCGTTGCTCATGGAGCGGCTTGGCATCGCGGTGATTGGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3003189","ARO_id":"39766","ARO_name":"QnrB77","CARD_short_name":"QnrB77","ARO_description":"QnrB77 is a fluoroquinolone resistance gene in Lahey's list of qnr genes.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5911":{"model_id":"5911","model_name":"QnrB78","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"8620":{"protein_sequence":{"accession":"AKO62870.1","sequence":"MALALVGEKIDRNRFTGEKIENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNASALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGAQVLGATFSGSDLSGGEFSTFDWRAANFTHCDLTNSELGDLDIRSVDLQGVKLDNYQASLLMERLGIAIIG"},"dna_sequence":{"accession":"KM985471.1","fmin":"0","fmax":"645","strand":"+","sequence":"ATGGCTCTGGCACTCGTTGGCGAAAAAATTGACAGAAACCGTTTCACCGGTGAGAAAATTGAAAATAGTACATTTTTTAACTGTGATTTTTCAGGTGCCGACCTAAGTGGTACTGAATTTATCGGCTGTCAGTTCTATGATCGTGAAAGCCAGAAAGGGTGCAATTTTAGTCGTGCAATGCTGAAAGATGCCATTTTTAAAAGCTGTGATTTATCCATGGCGGATTTTCGCAATGCCAGTGCGCTGGGCATTGAAATTCGCCACTGCCGCGCACAAGGCGCAGATTTCCGCGGCGCAAGCTTTATGAATATGATCACTACACGCACCTGGTTTTGCAGCGCATATATCACTAACACAAATCTAAGCTACGCCAATTTTTCGAAAGTCGTGCTGGAAAAGTGTGAGCTGTGGGAAAACCGTTGGATGGGTGCCCAGGTACTGGGCGCGACGTTCAGTGGTTCAGATCTCTCCGGCGGCGAGTTTTCGACTTTCGACTGGCGAGCAGCAAACTTCACACATTGCGATCTGACCAATTCGGAGTTGGGTGACTTAGATATTCGGAGCGTTGATTTACAAGGCGTTAAGTTGGACAACTACCAGGCATCGTTGCTCATGGAACGTCTTGGCATCGCGATTATTGGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3003190","ARO_id":"39767","ARO_name":"QnrB78","CARD_short_name":"QnrB78","ARO_description":"QnrB78 is a fluoroquinolone resistance gene in Lahey's list of qnr genes.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5917":{"model_id":"5917","model_name":"Mrx","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"8632":{"protein_sequence":{"accession":"AAS13767.1","sequence":"MSERRYSPLATLFAATFLFRIGNAVAALALPWFVLSHTKSAAWAGATAASSVIATIIGAWVGGGLVDRFGRAPVALISGVVGGVAMASIPLLDAVGALSNTGLIACVVLGAAFDAPGMAAQDSELPKLGHVAGLSVERVSSLKAVIGNVAILGGPALGGAAIGLLGAAPTLGLTAFCSVLAGLLGAWVLPARAARTMTTTATLSMRAGVAFLWSEPLLRPLFGIVMIFVGIVGANGSVIMPALFVDAGRQVAELGLFSSMMGAGGLLGIAIHASVGARISAQNWLAVAFCGSAVGSLLLSQLPGVPVLMLLGALVGLLTGSVSPILNAAIYNRTPPELLGRVLGTVSAVMLSASPMVMLAAGAFVDLAGPLPGLVVSAVFAGLVALLSLRLQFATMAAAATASAPTHTEGEH"},"dna_sequence":{"accession":"AY522923.1","fmin":"7744","fmax":"8983","strand":"-","sequence":"ATGAGCGAACGTCGATATAGCCCGCTCGCGACGCTGTTCGCGGCGACCTTTCTCTTCCGGATCGGCAACGCGGTGGCGGCCCTCGCGCTTCCATGGTTCGTCCTGTCTCATACAAAGAGCGCGGCCTGGGCGGGCGCCACGGCCGCTAGCAGCGTCATCGCGACCATCATCGGCGCGTGGGTTGGTGGTGGCCTCGTCGATCGGTTCGGGCGCGCGCCCGTCGCATTGATCTCGGGTGTGGTGGGCGGCGTGGCCATGGCGAGCATCCCACTGCTCGATGCCGTTGGCGCCCTCTCGAACACTGGGCTGATCGCTTGCGTGGTGCTCGGTGCCGCGTTCGACGCACCCGGTATGGCCGCGCAGGACAGTGAGCTGCCCAAACTCGGCCACGTCGCCGGGCTCTCCGTTGAGCGCGTCTCGTCACTGAAAGCGGTGATCGGGAACGTCGCGATTCTAGGTGGCCCGGCCCTTGGGGGGGCCGCAATCGGCCTGCTTGGCGCTGCGCCAACGCTCGGGCTGACGGCGTTCTGCTCCGTCCTTGCAGGTCTGCTCGGCGCGTGGGTGCTTCCCGCGCGTGCCGCTCGGACGATGACCACGACGGCGACTCTCTCCATGCGCGCCGGCGTCGCTTTTCTCTGGAGCGAACCCCTGCTGCGCCCTCTCTTTGGTATAGTGATGATCTTCGTGGGCATCGTTGGCGCCAACGGCAGCGTCATCATGCCTGCGCTGTTTGTAGATGCAGGACGCCAAGTAGCAGAGCTCGGGCTGTTCTCCTCAATGATGGGGGCTGGTGGTCTCCTTGGCATTGCCATTCATGCGTCGGTCGGCGCCCGGATATCAGCGCAGAACTGGCTGGCGGTGGCATTTTGTGGCTCTGCGGTGGGCTCGCTTCTGCTTTCACAGTTGCCAGGCGTGCCGGTGCTGATGTTGTTGGGCGCGCTCGTGGGACTGCTGACCGGCTCAGTCTCTCCCATTCTCAACGCTGCCATCTACAACCGCACGCCGCCAGAACTTCTCGGCCGGGTACTCGGCACGGTCTCGGCGGTGATGCTGTCAGCCTCGCCCATGGTTATGCTTGCGGCCGGCGCGTTTGTCGACCTTGCTGGTCCGCTCCCTGGCCTCGTTGTATCGGCCGTGTTTGCGGGGCTCGTGGCTCTACTCTCGCTCCGTCTTCAATTTGCTACAATGGCGGCGGCAGCCACAGCCTCCGCCCCAACCCATACAGAAGGTGAACACTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36810","NCBI_taxonomy_name":"Aeromonas hydrophila","NCBI_taxonomy_id":"644"}}}},"ARO_accession":"3003839","ARO_id":"40531","ARO_name":"Mrx","CARD_short_name":"Mrx","ARO_description":"Mrx is part of the macrolide inactivation gene cluster in Aeromonas hydrophila.","ARO_category":{"36472":{"category_aro_accession":"3000333","category_aro_cvterm_id":"36472","category_aro_name":"macrolide phosphotransferase (MPH)","category_aro_description":"Macrolide phosphotransferases (MPH) are enzymes encoded by macrolide phosphotransferase genes (mph genes). These enzymes phosphorylate macrolides in GTP dependent manner at 2'-OH of desosamine sugar thereby inactivating them. Characterized MPH's are differentiated based on their substrate specificity.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"36284":{"category_aro_accession":"3000145","category_aro_cvterm_id":"36284","category_aro_name":"tylosin","category_aro_description":"Tylosin is a 16-membered macrolide, naturally produced by Streptomyces fradiae. It interacts with the bacterial ribosome 50S subunit to inhibit protein synthesis.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5918":{"model_id":"5918","model_name":"kdpD","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1500"}},"model_sequences":{"sequence":{"8633":{"protein_sequence":{"accession":"CYF42523.1","sequence":"MSNTESLNIGKKRGSLTIYIGYSPGVGKTFEMLSNAIELFQSNIDIKIGYIEPHQRDETNALAEQLPKIATNFTKHGSHHFQYLDVDRIIKESPTIVLIDELAHTNISRDRHEKRYMDIEEILNHGIDVHTTLNIQHIESLSSQIELMTGVHVKERVPDYFIMSADVLEVVDISPEQLIKRLKAGKVYKKDRLDVAFSNFFTYTHLSELRTLTLRTVADLMSDKEKVRHNHKTSLKPHIAVAISGSIYNEAVIKEAFHIAQKEHAKFTAIYIDVFEKNRQYKDSQKQVHQHLMLAKSLGAKVKVVYSQTVALGLDEWCKNQDVTKLIIGQHIRNKWRDFFNTPLIDHLMSFEHSYKIEIVPIKQIPVELKMNKSPYRPKGKRFAIDMLKMILIQIICVMMGLWIYQLDKHESSTIILMIFLIGIILLSIWTRSYIIGFLAAIINVFVFNYFFTEPRYTFEVYRFDYPITFIVSILTSILTSALLKQIKFQYSITKKQLYRTDLLFQFNDSIKQTYTVENLLINAGYQINQLLQQSITVYVINQSKVIKTIPLQNHIDNTTQQHEQALSWVIKNERQAGATTDTFPGINKWLIPIGTSPIKGILAIDYQSSQVINPYDASILESMLNELSLAVENVSLLKQTRESMLQAERQLTHSNFLRSISHDIRTPLTTIMGNLDILVSHSKDMSIIEKEQLLVHSFQESQYLYLLVTNILSLTKLQSSNVQIKLQPYLVSELVEEIDMILERRHLKKRITVSSSVDLQFIHIDSKLILQALFNLIENAVKHTSTDTKINLSIRYASDEQIEFAVIDEGPGISLEEQQKIFEPFYTGSNKYFKDNQKESMGLGLYLVQTILHKHQSNLQYKPNQPHGSIFYFNIDTDFNEGDI"},"dna_sequence":{"accession":"FHDU01000010.1","fmin":"53978","fmax":"56636","strand":"-","sequence":"ATGTCAAACACTGAATCGCTAAACATAGGAAAAAAGCGTGGATCTTTAACAATTTACATCGGTTACAGTCCAGGTGTTGGTAAAACATTTGAGATGCTTTCAAATGCCATTGAACTATTTCAAAGTAACATTGATATTAAAATAGGATATATTGAACCGCATCAACGTGATGAAACAAATGCATTAGCTGAACAATTACCTAAAATCGCAACCAATTTTACTAAACATGGTAGTCATCATTTTCAATATTTAGATGTCGACCGCATAATCAAAGAATCGCCGACAATAGTACTTATCGATGAGTTAGCACATACGAACATTTCTAGAGATCGTCATGAGAAACGATATATGGATATTGAAGAAATTTTAAATCATGGTATCGATGTTCATACTACTTTGAACATTCAACATATCGAAAGTTTAAGTAGTCAAATTGAACTGATGACCGGTGTACATGTTAAAGAACGTGTACCCGACTATTTCATAATGAGCGCCGATGTATTAGAAGTCGTAGATATCTCACCTGAACAATTAATTAAGCGCTTAAAAGCTGGCAAGGTATATAAAAAGGATAGGCTAGATGTAGCATTTAGTAATTTCTTTACGTATACCCACCTAAGCGAACTGCGTACATTGACGTTAAGAACAGTTGCCGACTTGATGAGTGATAAAGAAAAAGTCCGACACAATCATAAAACGTCACTCAAACCTCATATTGCTGTGGCAATTAGTGGGAGCATTTATAATGAAGCAGTAATTAAAGAGGCATTCCATATTGCTCAAAAAGAACATGCAAAATTCACTGCTATTTATATAGATGTATTCGAAAAGAACAGGCAATATAAAGATAGTCAAAAGCAAGTGCATCAACATCTCATGCTTGCAAAATCTTTAGGAGCAAAAGTGAAAGTAGTTTATAGCCAAACCGTTGCATTAGGATTAGACGAATGGTGTAAAAATCAAGATGTAACCAAATTAATTATCGGACAACATATTAGAAATAAGTGGCGAGACTTTTTCAATACACCTTTAATTGACCATTTAATGTCCTTTGAACATAGCTATAAAATCGAAATCGTTCCAATCAAACAAATACCTGTTGAATTGAAAATGAACAAATCACCCTATCGTCCTAAAGGCAAACGTTTCGCCATAGATATGTTAAAAATGATTTTGATTCAAATAATTTGTGTAATGATGGGACTGTGGATTTATCAACTTGATAAGCATGAGTCTAGTACGATTATTTTAATGATTTTTCTCATCGGCATCATTTTATTATCCATTTGGACGCGGTCCTACATCATTGGCTTTTTAGCAGCAATTATTAACGTATTTGTTTTTAATTATTTTTTTACGGAACCTAGATATACATTTGAAGTATACCGCTTTGACTATCCTATTACATTTATCGTTAGCATTTTAACAAGTATTTTAACGAGTGCTTTATTAAAACAAATTAAATTCCAATACTCCATTACTAAAAAGCAACTTTATCGTACAGATTTATTATTTCAATTTAATGATTCGATTAAACAAACTTATACAGTTGAAAACTTACTAATAAATGCTGGATACCAAATTAATCAATTATTGCAACAATCAATTACTGTATACGTTATCAATCAATCGAAAGTAATTAAAACAATACCATTGCAAAACCATATCGATAATACGACTCAACAGCATGAACAAGCATTAAGCTGGGTAATTAAAAATGAAAGACAAGCTGGTGCAACAACAGATACATTTCCAGGCATTAATAAATGGTTGATACCAATTGGCACATCTCCGATTAAAGGCATTCTAGCCATTGATTACCAAAGTTCTCAAGTGATTAATCCATATGATGCATCAATATTAGAATCAATGTTAAATGAACTTTCTCTCGCCGTTGAAAATGTGTCGTTACTTAAACAAACGAGAGAATCCATGTTACAGGCTGAACGTCAACTGACACATTCAAATTTTTTAAGATCAATTTCGCATGACATACGTACACCGTTAACAACAATTATGGGAAATTTAGATATTTTAGTATCACATAGTAAAGATATGTCTATCATAGAAAAAGAACAATTACTTGTGCATAGTTTTCAAGAAAGTCAGTATTTATATCTATTAGTGACAAATATTTTATCATTAACAAAATTACAGTCATCAAATGTTCAGATAAAATTGCAACCTTATCTCGTTAGTGAATTAGTAGAAGAAATCGATATGATTCTAGAACGTCGCCATTTAAAAAAGCGTATAACTGTATCATCCTCAGTAGATTTACAGTTTATACACATTGACAGTAAGTTGATTTTACAAGCTTTATTCAATTTGATTGAAAATGCAGTTAAACACACTTCTACTGACACCAAAATCAATTTATCTATTCGTTATGCTAGCGATGAACAAATCGAATTTGCCGTTATAGACGAAGGACCTGGAATTAGTTTAGAAGAACAACAAAAGATATTCGAGCCTTTTTACACAGGATCAAATAAATATTTTAAAGATAACCAAAAAGAAAGCATGGGACTAGGCTTATATTTAGTACAGACTATCCTACACAAACATCAATCAAACTTACAATATAAACCGAACCAACCACACGGCAGTATATTCTATTTCAATATAGATACAGACTTTAATGAAGGAGACATATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35508","NCBI_taxonomy_name":"Staphylococcus aureus","NCBI_taxonomy_id":"1280"}}}},"ARO_accession":"3004047","ARO_id":"41099","ARO_name":"kdpD","CARD_short_name":"kdpD","ARO_description":"kdpD is a component of the two-component regulatory system, kdpDE. This system is involved in potassium transport and homeostasis, and has been implicated in virulence factor regulation along with kdpE.","ARO_category":{"41098":{"category_aro_accession":"3004046","category_aro_cvterm_id":"41098","category_aro_name":"kdpDE","category_aro_description":"kdpDE is a two-component regulatory system in Escherichia coli, well studied for its role in potassium transport and homeostasis. kdpE is also implicated in virulence loci regulation and overexpression of kdpE is shown to confer resistance to aminoglycoside antibiotics.","category_aro_class_name":"AMR Gene Family"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"5919":{"model_id":"5919","model_name":"QnrB76","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"8634":{"protein_sequence":{"accession":"BBW41109.1","sequence":"MTPLLYKKTGTNMALALVGEKIDRNRFTGEKIENSTFFNCDFSGADLSGTEFIGCQFYDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNASALGIEIRHCRAQGADFRGASFMNMITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGAQVLGATFSGSDLSGGEFSTFDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDNYQASLLMERLGIAIIG"},"dna_sequence":{"accession":"AP022513.1","fmin":"2715236","fmax":"2715917","strand":"+","sequence":"ATGACGCCATTACTGTATAAAAAAACAGGTACAAATATGGCTCTGGCACTCGTTGGCGAAAAAATTGACAGAAACCGCTTCACCGGTGAGAAAATTGAAAATAGTACATTTTTTAACTGTGATTTTTCAGGTGCCGACCTGAGTGGCACTGAATTTATCGGCTGTCAGTTCTATGATCGTGAAAGCCAGAAAGGGTGCAATTTTAGTCGTGCAATGCTGAAAGATGCCATTTTTAAAAGCTGTGATTTATCCATGGCGGATTTTCGCAATGCCAGTGCGCTGGGCATTGAAATTCGCCACTGCCGCGCACAAGGCGCAGATTTCCGCGGCGCAAGCTTTATGAATATGATCACTACACGCACCTGGTTTTGCAGCGCATATATCACTAACACAAATCTAAGCTACGCCAATTTTTCGAAAGTCGTGCTGGAAAAGTGTGAGCTGTGGGAAAACCGTTGGATGGGTGCCCAGGTACTGGGCGCGACGTTCAGTGGTTCAGATCTCTCCGGCGGCGAGTTTTCGACTTTCGACTGGCGAGCAGCAAACTTCACACATTGCGATCTGACCAATTCGGAGTTGGGTGACTTAGATATTCGGGGCGTTGATTTACAAGGCGTTAAGTTGGACAACTACCAGGCATCGTTGCTCATGGAACGTCTTGGCATCGCGATTATTGGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43754","NCBI_taxonomy_name":"Citrobacter portucalensis","NCBI_taxonomy_id":"1639133"}}}},"ARO_accession":"3003188","ARO_id":"39765","ARO_name":"QnrB76","CARD_short_name":"QnrB76","ARO_description":"QnrB76 is a fluoroquinolone resistance gene in Lahey's list of qnr genes.","ARO_category":{"36558":{"category_aro_accession":"3000419","category_aro_cvterm_id":"36558","category_aro_name":"quinolone resistance protein (qnr)","category_aro_description":"Qnr proteins are pentapeptide repeat proteins that mimic DNA and protect the cell from the activity of fluoroquinolone antibiotics.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"37003":{"category_aro_accession":"3000659","category_aro_cvterm_id":"37003","category_aro_name":"gatifloxacin","category_aro_description":"Gatifloxacin is an 8-methoxy, 7-piperazinyl, 6-fluoroquinolone that can be taken orally or by intravenous administration. It is active against most Gram-positive and Gram-negative bacteria, but inactive against non-fermenting Gram-negative rods including Pseudomonas aeruginosa.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5921":{"model_id":"5921","model_name":"leuO","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8636":{"protein_sequence":{"accession":"VWQ00850.1","sequence":"MPEVQTDHPETAELSKPQLRMVDLNLLTVFDAVMQEQNITRAAHALGMSQPAVSNAVARLKVMFNDELFVRYGRGIQPTARAFQLFGSVRQALQLVQNELPGSGFEPASSERVFHLCVCSPLDSILTSQIYNHIEQIAPNIHVMFKSSLNQNTEHQLRYQETEFVISYEDFHRPEFTSVPLFKDEMVLVASKNHPTIKGPLLKHDVYNEQHAAVSLDRFASFSQTWYDTVDKQASIAYQGMAMMSVLSVVSQTHLVAIAPRWLAEEFAESLELQVLPLPLKQNSRTCYLSWHEAAGRDKGHQWMEEQLVSICKR"},"dna_sequence":{"accession":"LR730402.1","fmin":"740042","fmax":"740987","strand":"+","sequence":"ATGCCAGAGGTACAAACAGATCATCCAGAGACGGCGGAGTTAAGCAAGCCACAGCTACGCATGGTCGATCTCAACTTATTAACCGTTTTCGATGCCGTGATGCAGGAGCAAAACATCACCCGTGCCGCTCATGCTCTGGGAATGTCGCAACCTGCGGTCAGTAACGCTGTTGCACGCCTGAAGGTGATGTTTAATGACGAGCTTTTTGTTCGTTATGGCCGTGGTATTCAACCGACTGCTCGCGCATTTCAACTTTTTGGCTCAGTTCGTCAGGCATTGCAACTAGTACAAAATGAATTGCCTGGTTCAGGTTTTGAACCCGCGAGCAGTGAACGTGTATTTCATCTTTGTGTTTGCAGCCCGTTAGACAGCATTCTGACCTCGCAGATTTATAATCACATTGAGCAGATTGCGCCAAATATACATGTTATGTTCAAGTCTTCATTAAATCAGAACACTGAACATCAGCTGCGTTATCAGGAAACGGAGTTTGTGATTAGTTATGAAGACTTCCATCGCCCTGAATTTACCAGTGTGCCATTATTTAAAGATGAAATGGTGTTGGTAGCCAGCAAAAATCATCCAACAATTAAAGGCCCGTTACTGAAGCATGATGTTTATAACGAACAACACGCTGCGGTTTCGCTCGATCGTTTCGCATCATTTAGTCAAACCTGGTATGACACGGTAGATAAGCAAGCCAGTATCGCGTATCAGGGCATGGCAATGATGAGCGTACTTAGCGTGGTGTCGCAAACGCATCTGGTCGCTATTGCGCCGCGTTGGTTGGCTGAAGAGTTCGCTGAATCCTTAGAGTTACAGGTATTACCGCTGCCGTTAAAACAAAACAGCAGAACCTGTTATCTCTCCTGGCATGAAGCTGCCGGGCGCGATAAAGGCCATCAGTGGATGGAAGAGCAATTAGTCTCAATTTGCAAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3003843","ARO_id":"40537","ARO_name":"leuO","CARD_short_name":"leuO","ARO_description":"leuO, a LysR family transcription factor, exists in a wide variety of bacteria of the family Enterobacteriaceae and is involved in the regulation of as yet unidentified genes affecting the stress response and pathogenesis expression. LeuO is also an activator of the MdtNOP efflux pump.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35963":{"category_aro_accession":"0000045","category_aro_cvterm_id":"35963","category_aro_name":"acriflavine","category_aro_description":"Acriflavine is a topical antiseptic. It has the form of an orange or brown powder. It may be harmful in the eyes or if inhaled. Acriflavine is also used as treatment for external fungal infections of aquarium fish.","category_aro_class_name":"Antibiotic"},"35965":{"category_aro_accession":"0000047","category_aro_cvterm_id":"35965","category_aro_name":"puromycin","category_aro_description":"Puromycin is an aminonucleoside antibiotic, derived from Streptomyces alboniger, that causes premature chain termination during ribosomal protein translation.","category_aro_class_name":"Antibiotic"},"36174":{"category_aro_accession":"3000034","category_aro_cvterm_id":"36174","category_aro_name":"nucleoside antibiotic","category_aro_description":"Nucleoside antibiotics are made of modified nucleosides and nucleotides with wide-ranging activities and means of antibacterial effects. This drug class includes aminonucleoside antibiotics, which contain an amino group.","category_aro_class_name":"Drug Class"},"43746":{"category_aro_accession":"3005386","category_aro_cvterm_id":"43746","category_aro_name":"disinfecting agents and antiseptics","category_aro_description":"Disinfectants that can also interact with antimicrobial resistance mechanisms, e.g. molecule efflux, and thus are the targets of disinfectant resistance.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"922":{"model_id":"922","model_name":"AAC(6')-30\/AAC(6')-Ib' bifunctional protein","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"8193":{"protein_sequence":{"accession":"CAE48335.2","sequence":"MTFLIRPVEQSDAESWERLRNLLWEGDDHKSEITQFFNGEVEEPNEVLLAVTEENDAIAHIELSLRYDIDGLTGIKTGYIEGLFVEERHRAAGVVLKLLRAAEFWARDQGCLAFASDRDDRVIIYARYTGAPPNNSLGITKYSIVTNSNDSVTLRLMTEHDLAMLYEWLNRSHIVEWWGGEEARPTLADVQEQYLPSVLAQESVTPYIAMLNGEPIGYAQSYVALGSGDGWWEEETDPGVRGIDQSLANASQLGKGLGTKLVRALVELLFNDPEVTKIQTDPSPSNLRAIRCYEKAGFERQGTVTTPDGPAVYMVQTRQAFERTRSVA"},"dna_sequence":{"accession":"AJ584652.2","fmin":"1926","fmax":"2913","strand":"+","sequence":"ATGACATTCCTGATCCGACCCGTAGAACAAAGTGACGCTGAATCTTGGGAGCGCTTACGCAACCTTTTGTGGGAGGGCGACGACCACAAAAGCGAGATCACACAATTCTTCAACGGCGAAGTAGAAGAACCCAATGAAGTGTTGCTTGCCGTAACCGAAGAAAATGATGCAATAGCGCACATCGAGCTATCGTTGAGGTATGACATTGATGGCTTGACGGGCATCAAGACCGGTTACATCGAAGGCCTTTTTGTAGAGGAGCGGCACCGTGCCGCAGGTGTAGTCCTCAAGCTATTGCGAGCCGCAGAGTTCTGGGCAAGAGATCAAGGATGTCTGGCGTTTGCCTCAGACAGGGATGATCGTGTCATCATCTATGCTCGCTACACGGGAGCGCCACCTAACAATTCATTAGGCATCACAAAGTACAGCATCGTGACCAACAGCAACGATTCCGTCACACTGCGCCTCATGACTGAGCATGACCTTGCGATGCTCTATGAGTGGCTAAATCGATCTCATATCGTCGAGTGGTGGGGCGGAGAAGAAGCACGCCCGACACTTGCTGACGTACAGGAACAGTACTTGCCAAGCGTTTTAGCGCAAGAGTCCGTCACTCCATACATTGCAATGCTGAATGGAGAGCCGATTGGGTATGCCCAGTCGTACGTTGCTCTTGGAAGCGGGGACGGATGGTGGGAAGAAGAAACCGATCCAGGAGTACGCGGAATAGACCAGTCACTGGCGAATGCATCACAACTGGGCAAAGGCTTGGGAACCAAGCTGGTTCGAGCTCTGGTTGAGTTGCTGTTCAATGATCCCGAGGTCACCAAGATCCAAACGGACCCGTCGCCGAGCAACTTGCGAGCGATCCGATGCTACGAGAAAGCGGGGTTTGAGAGGCAAGGTACCGTAACCACCCCAGATGGTCCAGCCGTGTACATGGTTCAAACACGCCAGGCATTCGAGCGAACACGCAGTGTTGCCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002599","ARO_id":"38999","ARO_name":"AAC(6')-30\/AAC(6')-Ib' bifunctional protein","CARD_short_name":"AAC6_30_AAC6_Ib","ARO_description":"AAC(6')-30\/AAC(6')-Ib' is an integron-encoded aminoglycoside acetyltransferase in P. aeruginosa.","ARO_category":{"46171":{"category_aro_accession":"3007419","category_aro_cvterm_id":"46171","category_aro_name":"aminoglycoside bifunctional resistance protein","category_aro_description":"Bifunctional aminoglycoside-inactivating enzymes composed of two separate functional domains. These proteins possess activity from both enzyme components, thereby conferring resistance to the combination of antibiotics from both domains, and may include acetylation, phosphorylation or nucleotidylation activity.","category_aro_class_name":"AMR Gene Family"},"40942":{"category_aro_accession":"3004015","category_aro_cvterm_id":"40942","category_aro_name":"gentamicin A","category_aro_description":"Gentamicin A is part of a complex of broad spectrum aminoglycoside antibiotics. Gentamicin inhibits protein synthesis, resulting in bacterial cell death.","category_aro_class_name":"Antibiotic"},"46133":{"category_aro_accession":"3007382","category_aro_cvterm_id":"46133","category_aro_name":"gentamicin","category_aro_description":"Gentamicin is a commonly used aminoglycoside antibiotic derived from members of the Micromonospora genus of bacteria. It acts by binding the 30S ribosomal subunit, thus inhibiting protein synthesis. Gentamicin is typically used to treat Gram-negative infections of the repiratory and urinary tract, as well as infections of the bone and soft tissue. It also exhibits considerable nephrotoxicity and ototoxicity. Gentamicin is administered as a mixture of gentamicin type C (which makes about around 80% of the complex) and types A, B, and X (distributed in the remaining 20% of the complex).","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"924":{"model_id":"924","model_name":"AAC(6')-I33","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"362":{"protein_sequence":{"accession":"AEZ05106.1","sequence":"MAYEFCEIGESNEYIILAARILTKSFLDIGNNSWPDMKSATKEVEECIEKPNICLGIHENEKLLGWIGLRPMYKLTWELHPLVISTQYQNKGIGRLLINELEKKAKQIGIIGIVLGTDDEYFKTSLSAVDLYGENILDEIRTIKNIKNHPYEFYQKCGYSIVGVIPDANGKRKPDIWMWKKIND"},"dna_sequence":{"accession":"JN596280.1","fmin":"1202","fmax":"1757","strand":"+","sequence":"ATGGCGTATGAGTTCTGCGAAATAGGTGAATCAAACGAATATATTATTCTGGCGGCTAGAATCTTAACGAAATCATTCCTAGATATCGGTAATAATTCCTGGCCTGACATGAAAAGTGCTACTAAAGAAGTTGAAGAATGCATTGAGAAGCCAAACATATGTCTTGGAATACATGAAAATGAAAAATTGCTTGGATGGATTGGCCTTAGGCCCATGTACAAATTAACATGGGAATTACATCCCTTGGTAATAAGTACTCAATATCAGAATAAAGGTATTGGAAGACTTTTAATAAATGAATTAGAAAAAAAAGCAAAGCAAATTGGAATAATTGGAATAGTATTGGGAACTGACGATGAATACTTTAAAACTTCATTATCAGCTGTTGATCTTTACGGCGAAAATATTCTTGATGAGATAAGGACTATTAAAAACATAAAAAATCATCCGTACGAATTCTATCAAAAATGTGGGTATTCCATTGTCGGAGTAATACCCGATGCAAATGGAAAAAGGAAGCCAGATATTTGGATGTGGAAGAAGATAAATGATTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002587","ARO_id":"38987","ARO_name":"AAC(6')-I33","CARD_short_name":"AAC(6')-I33","ARO_description":"AAC(6')-I33 is an integron-encoded aminoglycoside acetyltransferase in P. aeruginosa.","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"A category of aminoglycoside N-acetyltransferase enzymes with modification regiospecificity based at the 6'-amino group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics through acetylation of the 6-amino group of the compound.","category_aro_class_name":"AMR Gene Family"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"339":{"model_id":"339","model_name":"ANT(3'')-II-AAC(6')-IId bifunctional protein","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"900"}},"model_sequences":{"sequence":{"8182":{"protein_sequence":{"accession":"AAL51021.2","sequence":"MSNAVPAEISVQLSLALNAIERHLESTLLAVHLYGSALDGGLKPYSDIDLLVTVAAQLDETVRQALVVDLLEISASPGQSEALRALEVTIVVHGDVVPWRYPARRELQFGEWQRKDILAGIFEPATTDVDLAILLTKVRQHSLALAGSAAEDFFNPVPEGDLFKALSDTLKLWNSQPDWEGDERNVVLTLSRIWYSAATGKIAPKDIVANWAIERLPDQHKPVLLEARQAYLGRGEDCLASRADQLAAFVHFVKHEATKLLGAMPVMSKTKLGITKYSIVTNSNDSVTLRLMTEHDLAMLYEWLNRSHIVEWWGGEEARPTLADVQEQYLPSVLAQESVTPYIAMLNGEPIGYAQSYVALGSGDGWWEEETDPGVRGIDQSLANASQLGKGLGTKLVRALVELLFNDPEVTKIQTDPSPSNLRAIRCYEKAGFERQGTVTTPDGPAVYMVQTRQAFERTRSDA"},"dna_sequence":{"accession":"AF453998.2","fmin":"3554","fmax":"4946","strand":"+","sequence":"ATGAGTAACGCAGTACCCGCCGAGATTTCGGTACAGCTATCACTGGCTCTCAACGCCATCGAGCGTCATCTGGAATCAACGTTGCTGGCCGTGCATTTGTACGGCTCTGCACTGGACGGTGGCCTGAAGCCATACAGTGATATTGATTTGCTGGTTACTGTGGCTGCACAGCTCGATGAGACTGTCCGACAAGCCCTGGTCGTAGATCTCTTGGAAATTTCTGCCTCCCCTGGCCAAAGTGAGGCTCTCCGCGCCTTGGAAGTTACCATCGTCGTGCATGGTGATGTTGTCCCTTGGCGTTATCCGGCCAGACGGGAACTGCAATTCGGGGAGTGGCAGCGTAAAGACATTCTTGCGGGCATCTTCGAGCCCGCCACAACCGATGTTGATCTGGCTATTCTGCTAACTAAAGTAAGGCAGCATAGCCTTGCATTGGCAGGTTCGGCCGCAGAGGATTTCTTTAACCCAGTTCCGGAAGGCGATCTATTCAAGGCATTGAGCGACACTCTGAAACTATGGAATTCGCAGCCGGATTGGGAAGGCGATGAGCGGAATGTAGTGCTTACCTTGTCTCGCATTTGGTACAGCGCAGCAACCGGCAAGATCGCACCGAAGGATATCGTTGCCAACTGGGCAATTGAGCGTCTGCCAGATCAACATAAGCCCGTACTGCTTGAAGCCCGGCAGGCTTATCTTGGACGAGGAGAAGATTGCTTGGCCTCACGCGCGGATCAGTTGGCGGCGTTCGTTCACTTCGTGAAACATGAAGCCACTAAATTGCTTGGTGCCATGCCAGTGATGTCTAAAACAAAGTTAGGCATCACAAAGTACAGCATCGTGACCAACAGCAACGATTCCGTCACACTGCGCCTCATGACTGAGCATGACCTTGCGATGCTCTATGAGTGGCTAAATCGATCTCATATCGTCGAGTGGTGGGGCGGAGAAGAAGCACGCCCGACACTTGCTGACGTACAGGAACAGTACTTGCCAAGCGTTTTAGCGCAAGAGTCCGTCACTCCATACATTGCAATGCTGAATGGAGAGCCGATTGGGTATGCCCAGTCGTACGTTGCTCTTGGAAGCGGGGACGGATGGTGGGAAGAAGAAACCGATCCAGGAGTACGCGGAATAGACCAGTCACTGGCGAATGCATCACAACTGGGCAAAGGCTTGGGAACCAAGCTGGTTCGAGCTCTGGTTGAGTTGCTGTTCAATGATCCCGAGGTCACCAAGATCCAAACGGACCCGTCGCCGAGCAACTTGCGAGCGATCCGATGCTACGAGAAAGCGGGGTTTGAGAGGCAAGGTACCGTAACCACCCCAGATGGTCCAGCCGTGTACATGGTTCAAACACGCCAGGCATTCGAGCGAACACGCAGTGATGCCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36783","NCBI_taxonomy_name":"Serratia marcescens","NCBI_taxonomy_id":"615"}}}},"ARO_accession":"3002598","ARO_id":"38998","ARO_name":"ANT(3'')-II-AAC(6')-IId bifunctional protein","CARD_short_name":"ANT3II_ANT6II","ARO_description":"ANT(3'')-II-AAC(6')-IId is an integron-encoded aminoglycoside acetyltransferase in S. marcescens.","ARO_category":{"46171":{"category_aro_accession":"3007419","category_aro_cvterm_id":"46171","category_aro_name":"aminoglycoside bifunctional resistance protein","category_aro_description":"Bifunctional aminoglycoside-inactivating enzymes composed of two separate functional domains. These proteins possess activity from both enzyme components, thereby conferring resistance to the combination of antibiotics from both domains, and may include acetylation, phosphorylation or nucleotidylation activity.","category_aro_class_name":"AMR Gene Family"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"40942":{"category_aro_accession":"3004015","category_aro_cvterm_id":"40942","category_aro_name":"gentamicin A","category_aro_description":"Gentamicin A is part of a complex of broad spectrum aminoglycoside antibiotics. Gentamicin inhibits protein synthesis, resulting in bacterial cell death.","category_aro_class_name":"Antibiotic"},"46128":{"category_aro_accession":"3007378","category_aro_cvterm_id":"46128","category_aro_name":"2'-N-ethylnetilmicin","category_aro_description":"2'-N-ethylnetilmicin is an aminoglycoside antibiotic and a derivative of netilmicin.","category_aro_class_name":"Antibiotic"},"46129":{"category_aro_accession":"3007379","category_aro_cvterm_id":"46129","category_aro_name":"5-episisomicin","category_aro_description":"5-episosomicin is a semisynthetic aminoglycoside antibiotic similar to sisomicin.","category_aro_class_name":"Antibiotic"},"46133":{"category_aro_accession":"3007382","category_aro_cvterm_id":"46133","category_aro_name":"gentamicin","category_aro_description":"Gentamicin is a commonly used aminoglycoside antibiotic derived from members of the Micromonospora genus of bacteria. It acts by binding the 30S ribosomal subunit, thus inhibiting protein synthesis. Gentamicin is typically used to treat Gram-negative infections of the repiratory and urinary tract, as well as infections of the bone and soft tissue. It also exhibits considerable nephrotoxicity and ototoxicity. Gentamicin is administered as a mixture of gentamicin type C (which makes about around 80% of the complex) and types A, B, and X (distributed in the remaining 20% of the complex).","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2751":{"model_id":"2751","model_name":"APH(3')-IXa","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"4068":{"protein_sequence":{"accession":"ENV34035.1","sequence":"MINDMKISLPQSLKSFIGNQPLQKDKVGQSPSDVYSFTKNNEKYYLKTTELIYAQTTYSIIREAKILDWLDGKLNVPELVLMDTDHENEYMISKAVPAKPLQDFTGKSDQFFIDIYTDALAQLQSISIKNCPFISNKKFRLAEAEFFIENGLLDELDDDEKDLKLWSSYQNFAEFLDDLKQQNFQEEYVFSHGDLTDSNVFLSHDAQIYFLDVGRAGIADRFVDIAFIERSLREDCSEDAALQFLNHLAEDDSFKRNYFLKLDELN"},"dna_sequence":{"accession":"APPN01000061.1","fmin":"80497","fmax":"81298","strand":"+","sequence":"ATGATCAATGATATGAAAATTTCACTTCCGCAAAGTCTTAAAAGTTTTATTGGAAATCAACCATTACAAAAAGATAAAGTGGGACAATCCCCTTCTGATGTGTATTCTTTTACCAAAAATAATGAAAAATACTATTTAAAAACCACTGAGCTAATTTATGCTCAAACAACTTATAGTATCATACGTGAAGCAAAAATACTCGACTGGCTAGATGGAAAGCTCAATGTTCCAGAGCTAGTTTTAATGGATACCGACCATGAAAATGAGTACATGATCAGCAAGGCAGTCCCCGCAAAACCCTTACAAGATTTCACAGGAAAAAGTGATCAATTTTTCATAGATATTTATACAGATGCTTTGGCACAATTACAGTCTATTTCAATAAAAAACTGTCCATTTATATCCAATAAAAAATTTCGATTAGCTGAGGCGGAATTCTTTATTGAAAATGGCTTACTTGATGAATTGGATGATGATGAAAAAGATCTAAAGCTTTGGTCCAGTTATCAAAATTTTGCTGAATTCTTAGATGATCTAAAACAGCAAAATTTCCAAGAAGAATATGTATTTAGTCATGGTGACCTAACCGACAGCAATGTATTTTTAAGTCATGATGCACAAATCTACTTTTTAGATGTCGGACGTGCTGGTATCGCAGATCGATTTGTAGATATTGCCTTTATTGAACGTAGTCTACGAGAAGATTGCTCTGAGGATGCTGCACTTCAATTTTTAAATCATTTAGCAGAAGACGATTCTTTTAAACGGAATTATTTTCTAAAATTGGATGAGTTAAATTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41193","NCBI_taxonomy_name":"Acinetobacter gerneri DSM 14967 = CIP 107464 = MTCC 9824","NCBI_taxonomy_id":"1120926"}}}},"ARO_accession":"3004087","ARO_id":"41192","ARO_name":"APH(3')-IXa","CARD_short_name":"APH(3')-IXa","ARO_description":"APH(3')-IXa is an aminoglycoside phosphoryltransferase that acts on the 3-OH target of aminoglycosides.","ARO_category":{"36265":{"category_aro_accession":"3000126","category_aro_cvterm_id":"36265","category_aro_name":"APH(3')","category_aro_description":"A category of aminoglycoside O-phosphotransferase enzymes with modification regiospecificity based at the 3'-hydroxyl group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics, specifically kanamycin and neomycin, by the ATP-dependent phosphorylation of the 3'-hydroxyl group of the compound.","category_aro_class_name":"AMR Gene Family"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5923":{"model_id":"5923","model_name":"Klebsiella pneumoniae lamB with mutations conferring resistance to ceftazidime-avibactam","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"12832":"R374L","12833":"R374S","12834":"R134P","12835":"R33H"},"Curated-R":{"12832":"R374L","12833":"R374S","12834":"R134P","12835":"R33H"},"clinical":{"12832":"R374L","12833":"R374S","12834":"R134P","12835":"R33H"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"8640":{"protein_sequence":{"accession":"WAH47136.1","sequence":"MMITLRKLPLAVAVAAGVMSAQALAVDFHGYARSGIGWTGSGGEQQCFKATGAQSKYRLGNECETYAELKLGQELWKEGDKSFYFDTNVAYSVNQEDDWESTSPAFREANIQGKNLIDWLPGSTLWAGKRFYQRHDVHMIDFYYWDISGPGAGLENVDLGFGKLSLAATRNSESGGSYTFSSDDTKKYAAKTANDVFDIRLAGLETNPGGVLELGVDYGRANPQDDYRLEDGASKDGWMWTGEHTQSIWGGFNKFVVQYATDAMTSWNSGHSQGTSIDNNGSMIRVLDHGAMDFNDDWGLMYVAMYQDVDLDSKNGSTWYTVGVRPMYKWTPIMSTQLEIGYDNVKSQRTSENNNQYKITLAQQWQAGNSVWSRPAIRIFATYAKWDENWGYSNTSGLQTKDSSGSGAFTSSRGDDSEVTFGAQMEVWW"},"dna_sequence":{"accession":"CP109607.1","fmin":"4992596","fmax":"4993886","strand":"-","sequence":"ATGATGATTACTCTGCGCAAACTTCCTCTGGCGGTCGCCGTCGCAGCAGGCGTGATGTCTGCTCAGGCGCTGGCTGTCGATTTCCATGGCTACGCGCGTTCCGGCATTGGCTGGACCGGCAGCGGCGGCGAGCAACAGTGCTTCAAAGCAACCGGCGCTCAAAGTAAATACCGTCTTGGTAACGAATGTGAAACCTATGCGGAACTGAAGCTGGGCCAGGAGCTGTGGAAGGAAGGGGATAAGAGTTTTTATTTCGATACTAACGTTGCCTATTCCGTGAATCAGGAAGATGACTGGGAAAGCACCTCTCCGGCGTTCCGTGAAGCCAACATCCAGGGTAAAAACCTGATCGACTGGCTGCCGGGCTCCACGCTGTGGGCGGGTAAACGCTTCTATCAGCGTCATGACGTTCACATGATCGACTTCTACTACTGGGATATCTCCGGCCCGGGTGCAGGTCTGGAAAACGTTGACCTTGGCTTCGGTAAGCTCTCTCTGGCCGCTACCCGTAACTCAGAAAGCGGCGGCTCTTATACTTTCTCCAGCGATGACACCAAAAAATATGCTGCGAAAACTGCCAACGACGTCTTTGATATCCGTCTGGCGGGTCTGGAAACCAACCCGGGCGGCGTGCTGGAGTTAGGGGTCGATTACGGCCGTGCTAACCCGCAGGATGACTATCGCCTGGAAGACGGCGCGTCGAAAGACGGCTGGATGTGGACCGGTGAACATACTCAGTCTATCTGGGGCGGCTTCAACAAGTTTGTGGTTCAGTACGCCACTGACGCAATGACCTCCTGGAACAGCGGCCACTCTCAGGGGACCAGCATCGATAACAACGGCAGCATGATCCGCGTTCTGGATCACGGCGCGATGGACTTCAACGATGACTGGGGCCTGATGTACGTGGCAATGTACCAGGACGTGGATCTGGACAGCAAGAACGGTTCTACCTGGTACACCGTGGGTGTCCGTCCGATGTACAAATGGACGCCGATCATGAGCACCCAGCTGGAAATCGGTTACGACAACGTGAAATCCCAGCGTACCAGCGAAAACAACAACCAGTACAAAATTACTCTGGCTCAACAGTGGCAGGCAGGCAACAGCGTCTGGTCTCGTCCGGCTATCCGTATCTTCGCAACCTACGCGAAGTGGGATGAAAACTGGGGCTACAGCAACACCTCCGGTCTGCAGACGAAAGACAGCAGCGGAAGCGGCGCTTTCACCTCCAGCCGCGGTGACGACAGCGAAGTTACCTTCGGTGCCCAGATGGAAGTGTGGTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3007420","ARO_id":"46176","ARO_name":"Klebsiella pneumoniae lamB with mutations conferring resistance to ceftazidime-avibactam","CARD_short_name":"Kpne_lamB_CZA","ARO_description":"LamB is a maltoporin that negatively regulates antibiotic resistance. Knockout strains of lamB are shown to exhibit higher levels of resistance than wild-type strains. Mutations in the lamB gene of Klebsiella are associated with resistance to ceftazidime-avibactam.","ARO_category":{"41443":{"category_aro_accession":"3004279","category_aro_cvterm_id":"41443","category_aro_name":"Sugar Porin (SP)","category_aro_description":"Members of the Sugar Porin family tend to facilitate the transport of maltodextrins and other sugars across the outer membrane of Gram-negative bacteria. These porins form a homotrimeric structure.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36383":{"category_aro_accession":"3000244","category_aro_cvterm_id":"36383","category_aro_name":"reduced permeability to antibiotic","category_aro_description":"Reduction in permeability to antibiotic, generally through reduced production of porins, can provide resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5924":{"model_id":"5924","model_name":"Klebsiella pneumoniae PBP3 mutants conferring resistance to ceftazidime-avibactam","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"12836":"L367Q"},"Curated-R":{"12836":"L367Q"},"clinical":{"12836":"L367Q"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1100"}},"model_sequences":{"sequence":{"8643":{"protein_sequence":{"accession":"CDO16001.1","sequence":"MKAAPKTPKAKRQEEQANFISWRFALLCGCILLALAFLLGRVAWLQVISPDMLVRQGDMRSLRVQEVSTARGMITDRSGRPLAVSVPVKAIWADPKELHDAGGVTLDTRWKALADALNMPLDQLATRINTNPRMRFIYLARQVNPDMADYIKKLKLPGIHLREESRRYYPSGEVTAHLIGFTNVDSQGIEGVEKSFDKWLTGQPGERIVRKDRYGRVIEDISSTDSQAAHNLALSIDERLQALVYRELNNAVAFNKAESGSAVLVDVNTGEVLAMANSPSYNPNNFAGTAKDTMRNRAITDVFEPGSTVKPMVVMTALQRGIVNENTVLNTVPYRINGHEIKDVARYSELTLTGVLQKSSNVGVSKLALAMPSSVLVDTYSRFGLGKATNLGLVGERSGLYPQKQRWSDIERATFSFGYGLMVTPLQLARVYATIGSYGIYRPLSITKVDPPVPGERVFPESLVRTVVHMMESVALPGGGGVKAAIKGYRIAIKTGTAKKVGPDGRYINKYIAYTAGVAPASHPRFALVVVINDPQAGKYYGGAVSAPVFGAIMGGVLRTMNIEPDALATGEKSEFVINQGEGTGGRS"},"dna_sequence":{"accession":"FO834906.1","fmin":"4514344","fmax":"4516111","strand":"-","sequence":"ATGAAAGCAGCGCCAAAAACGCCTAAAGCAAAACGTCAGGAAGAACAGGCCAACTTTATCAGTTGGCGTTTTGCGTTGCTGTGCGGCTGTATTCTGCTGGCGCTGGCTTTTCTGCTGGGTCGCGTCGCCTGGCTACAGGTGATCAGCCCCGATATGCTGGTGCGCCAGGGCGATATGCGTTCTTTGCGCGTACAGGAAGTGTCCACCGCGCGCGGGATGATTACCGATCGCTCCGGACGTCCGCTGGCGGTCAGCGTGCCGGTGAAGGCTATCTGGGCCGACCCGAAAGAGCTCCATGACGCCGGTGGGGTTACCCTGGATACGCGCTGGAAAGCGCTGGCGGATGCCCTCAATATGCCGCTGGATCAGCTGGCGACGCGCATCAATACCAATCCGCGGATGCGGTTTATCTATCTGGCGCGTCAGGTTAATCCTGACATGGCCGATTACATCAAGAAGCTGAAGCTGCCGGGCATTCATCTGCGCGAAGAATCCCGTCGTTACTACCCTTCCGGGGAAGTAACCGCTCACCTCATCGGCTTTACCAACGTCGATAGCCAGGGGATTGAAGGGGTTGAGAAAAGCTTTGATAAATGGCTTACCGGTCAGCCGGGCGAGCGTATCGTACGTAAAGACCGCTATGGCCGGGTAATTGAAGACATCTCTTCTACCGATAGCCAGGCAGCGCACAACCTGGCGCTGAGTATCGACGAACGCCTGCAGGCGCTGGTCTATCGCGAGCTGAACAACGCCGTGGCCTTTAACAAAGCCGAGTCGGGCAGCGCCGTGTTAGTGGATGTTAACACCGGTGAAGTGCTGGCGATGGCCAACAGCCCATCCTATAACCCGAACAACTTCGCCGGTACGGCAAAAGACACCATGCGTAACCGTGCGATTACCGACGTGTTTGAGCCGGGTTCGACGGTGAAACCGATGGTGGTCATGACGGCGCTGCAGCGCGGTATCGTCAACGAAAATACCGTGCTCAATACCGTGCCTTATCGAATTAACGGCCACGAAATCAAAGACGTGGCGCGCTACAGCGAATTGACCCTGACCGGGGTGCTACAGAAGTCGAGTAACGTCGGTGTTTCTAAGCTGGCGTTAGCGATGCCGTCCTCAGTGTTAGTAGATACTTACTCACGTTTTGGGCTTGGAAAGGCGACCAATTTGGGGTTGGTCGGAGAACGCAGTGGCTTATATCCTCAAAAACAACGGTGGTCTGACATAGAGAGGGCCACCTTTTCTTTCGGCTATGGGCTAATGGTAACCCCGTTACAGTTAGCGCGAGTCTACGCAACGATTGGCAGCTATGGCATCTATCGCCCGTTGTCGATTACCAAGGTTGATCCTCCGGTTCCGGGCGAGCGCGTCTTCCCGGAATCACTCGTTCGTACCGTCGTTCATATGATGGAAAGCGTGGCGCTGCCCGGCGGCGGCGGTGTGAAAGCGGCGATCAAAGGCTATCGCATCGCGATTAAAACCGGTACGGCGAAAAAAGTGGGGCCGGATGGCCGCTATATCAACAAATATATTGCTTACACCGCAGGCGTTGCGCCCGCCAGCCATCCGCGCTTCGCGCTGGTGGTGGTGATCAACGACCCGCAGGCAGGTAAATACTACGGTGGCGCCGTTTCCGCGCCGGTCTTCGGTGCCATCATGGGCGGCGTATTGCGCACCATGAACATCGAGCCGGATGCGCTGGCAACGGGCGAAAAAAGTGAATTTGTAATTAATCAAGGCGAGGGAACAGGTGGCAGATCGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3007421","ARO_id":"46177","ARO_name":"Klebsiella pneumoniae PBP3 mutants conferring resistance to ceftazidime-avibactam","CARD_short_name":"Kpne_PBP3_BLA","ARO_description":"Mutant PBP3 in Klebsiella pneumoniae conferring resistance to ceftazidime-avibactam.","ARO_category":{"40661":{"category_aro_accession":"3003938","category_aro_cvterm_id":"40661","category_aro_name":"Penicillin-binding protein mutations conferring resistance to beta-lactam antibiotics","category_aro_description":"Mutations in PBP transpeptidases that change the affinity for penicillin thereby conferring resistance to penicillin antibiotics.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5926":{"model_id":"5926","model_name":"ThfT","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"8645":{"protein_sequence":{"accession":"QCK45398.1","sequence":"MSPIFNGPKMSVQRLVSIAMLIALTLVISKFSIPVIPQQLVISFAFIGNTMIGMIAGPIWAFISLALVDVTDNLASGSGNFIIWWTLMEAVQGLLYGFFFYRKPLSTANKKDWLYVSLATIIIMLFGTFIFTPLLIQIYFHVPFWAQYAAGRWFKVFEIPLRVVITMLLVPALQRIPEIKKLNQA"},"dna_sequence":{"accession":"CP035438.1","fmin":"631752","fmax":"632310","strand":"-","sequence":"ATGTCACCTATTTTTAATGGACCAAAAATGTCCGTTCAACGTCTTGTCTCTATCGCTATGCTAATTGCCCTAACCCTAGTCATTAGCAAATTTTCAATACCAGTTATTCCGCAACAATTGGTTATTAGTTTTGCCTTTATCGGTAATACCATGATTGGCATGATTGCTGGTCCAATTTGGGCTTTTATTTCCCTAGCCCTAGTTGATGTGACTGATAACCTAGCCAGTGGGTCAGGTAATTTCATCATTTGGTGGACCCTAATGGAGGCTGTTCAGGGGCTCTTGTATGGTTTTTTCTTCTACCGGAAACCACTGTCAACAGCCAATAAAAAAGACTGGCTTTATGTTAGCCTAGCAACAATTATCATCATGTTGTTTGGAACCTTCATCTTTACACCTCTTTTGATTCAAATCTACTTCCATGTCCCATTTTGGGCTCAATATGCAGCAGGAAGATGGTTTAAAGTCTTTGAAATCCCTCTTCGGGTCGTTATCACCATGTTATTAGTGCCAGCCCTTCAAAGAATACCTGAAATCAAAAAATTAAATCAAGCCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36764","NCBI_taxonomy_name":"Streptococcus pyogenes","NCBI_taxonomy_id":"1314"}}}},"ARO_accession":"3007427","ARO_id":"46183","ARO_name":"ThfT","CARD_short_name":"ThfT","ARO_description":"ThfT is an ECF transporter S component that expands the substrate profile of endogenous ECF transporters to include folate biosynthesis end products. It confers resistance to the folate synthesis inhibitor sulfamethoxazole by allowing uptake of host folate.","ARO_category":{"46182":{"category_aro_accession":"3007426","category_aro_cvterm_id":"46182","category_aro_name":"ECF transporter S component","category_aro_description":"ECF transporter S component genes involved in host nutrient uptake.","category_aro_class_name":"AMR Gene Family"},"36468":{"category_aro_accession":"3000329","category_aro_cvterm_id":"36468","category_aro_name":"sulfamethoxazole","category_aro_description":"Sulfamethoxazole is a sulfonamide antibiotic usually taken with trimethoprim, a diaminopyrimidine antibiotic. Sulfamethoxazole inhibits dihydropteroate synthase, essential to tetrahydrofolic acid biosynthesis. This pathway generates compounds used in the synthesis of many amino acids and nucleotides.","category_aro_class_name":"Antibiotic"},"36421":{"category_aro_accession":"3000282","category_aro_cvterm_id":"36421","category_aro_name":"sulfonamide antibiotic","category_aro_description":"Sulfonamides are broad spectrum, synthetic antibiotics that contain the sulfonamide group. Sulfonamides inhibit dihydropteroate synthase, which catalyzes the conversion of p-aminobenzoic acid to dihydropteroic acid as part of the tetrahydrofolic acid biosynthetic pathway. Tetrahydrofolic acid is essential for folate synthesis, a precursor of many nucleotides and amino acids. Many sulfamides are taken with trimethoprim, an inhibitor of dihydrofolate reductase, also disturbing the trihydrofolic acid synthesis pathway.","category_aro_class_name":"Drug Class"},"46180":{"category_aro_accession":"3007424","category_aro_cvterm_id":"46180","category_aro_name":"resistance by host-dependent nutrient acquisition","category_aro_description":"Resistance via uptake of host nutrients to bypass antibiotic mechanism.","category_aro_class_name":"Resistance Mechanism"}}},"5927":{"model_id":"5927","model_name":"almF","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"125"}},"model_sequences":{"sequence":{"8646":{"protein_sequence":{"accession":"PNM48229.1","sequence":"MKQAIENILIERLQTSIEGISSILTNKFFDEFDSFSFIDIVAKVESQFSAQINLFDMPLTMESSVNEVIDWLVSEVGE"},"dna_sequence":{"accession":"LOSL02000001.1","fmin":"267459","fmax":"267696","strand":"-","sequence":"ATGAAACAAGCCATTGAAAATATTCTTATTGAGCGATTACAAACCAGTATTGAGGGTATTTCATCGATACTCACCAATAAATTTTTCGATGAGTTTGATTCCTTCTCTTTCATCGATATTGTCGCCAAAGTAGAAAGCCAGTTTTCGGCACAAATTAATCTATTTGATATGCCATTAACCATGGAATCGTCAGTCAATGAAGTCATTGATTGGTTAGTGAGCGAAGTAGGGGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36789","NCBI_taxonomy_name":"Vibrio cholerae","NCBI_taxonomy_id":"666"}}}},"ARO_accession":"3007431","ARO_id":"46187","ARO_name":"almF","CARD_short_name":"almF","ARO_description":"almF is a glycine carrier protein associated with the almEFG operon in Vibrio cholerae. It is activated by almE and carries the glycyl molecule later added to lipid A by almG.","ARO_category":{"46184":{"category_aro_accession":"3007428","category_aro_cvterm_id":"46184","category_aro_name":"polymyxin resistance operon","category_aro_description":"Operon or gene clusters confering resistance to polymyxin antibiotics.","category_aro_class_name":"AMR Gene Family"},"46186":{"category_aro_accession":"3007430","category_aro_cvterm_id":"46186","category_aro_name":"alm glycyl carrier protein","category_aro_description":"Glycyl carrier proteins associated with polymixin resistance operons.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5928":{"model_id":"5928","model_name":"almE","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"8647":{"protein_sequence":{"accession":"MCO7070877.1","sequence":"MPYNSATDLLQREGYGVVHNQFINKMAMCCETRHSILAAIQANRHAPALWVKQKTYTYQEMTDMALSLSDYWHLQGVQRVAILSVRDLAAYSAIWASYLGGMTYIPLNARATTEQIQETLIATQCDSIMVDAQQLSRLSSLLDTCIDRLHIYALPDVDMEPLRQQYPQHTFHTVQITEQDVELLVAKYHLDNEHEYAYIMQTSGSTGKPKRIAVSYSNLHCYISQIDKLFPLNAQDRVGQYSDLTFDLSVHDIFYSLISGACLYVVPELAKLSPAEFIRHHQLTVWLSVPTVIELALQRQTLTPHSLPSLRLSFFCGQALLHDLAEQWQQATQQPVINLYGPTECTIAITYHRFVAHSGMASVPIGRAFEEECLAIINEQGELMRFESAPEGYRGELLLSGKQLVNGYLNDPLNTQSAFFQHEGRIWYRSGDIVTKSNGVLIHLGRRDHQVKIAGQRVELEEIETVVRRVTQAHSVAIVPWPLSESGYASGTVAFVDTHTQWQPDLWLSQCKQQLNPTFVPKRWYAIEQLPRNANGKTDIKALQQQLASQTYETSH"},"dna_sequence":{"accession":"JAKJWK010000010.1","fmin":"102683","fmax":"104354","strand":"-","sequence":"ATGCCATACAATTCTGCGACAGATTTGTTACAGAGAGAGGGTTATGGTGTCGTGCATAACCAATTTATCAATAAAATGGCGATGTGCTGCGAGACAAGACACTCTATTTTGGCGGCCATTCAGGCTAACCGACATGCCCCTGCATTATGGGTTAAACAGAAAACCTACACCTATCAAGAGATGACCGATATGGCACTCTCATTGAGTGACTATTGGCATTTACAGGGCGTGCAGCGAGTTGCGATCCTTTCGGTACGCGATCTCGCGGCTTATTCTGCGATTTGGGCGAGCTATTTGGGCGGTATGACTTATATTCCGCTCAATGCGCGAGCAACAACAGAACAGATCCAAGAGACGCTGATCGCGACACAATGTGATTCCATCATGGTAGACGCGCAGCAATTGAGTCGTTTGTCCTCCTTACTAGATACTTGCATTGACCGATTACACATTTATGCGCTGCCTGATGTGGATATGGAACCGTTACGTCAGCAATATCCTCAGCACACTTTTCACACAGTGCAAATAACCGAACAAGATGTGGAATTACTGGTAGCGAAATACCATTTAGACAATGAACATGAGTACGCTTATATCATGCAAACCTCAGGTTCGACTGGTAAACCCAAACGTATTGCGGTCAGCTACAGTAATTTGCATTGCTATATCAGTCAAATTGACAAACTATTTCCACTCAATGCGCAAGATCGAGTGGGGCAATATTCTGATTTGACTTTTGATCTTTCGGTACATGATATTTTTTACAGTTTGATCTCTGGTGCTTGTTTATATGTTGTGCCTGAATTAGCGAAATTAAGTCCAGCGGAATTTATTCGTCACCATCAATTAACGGTATGGCTTTCTGTGCCTACTGTTATTGAGTTGGCCCTACAAAGACAAACCTTAACCCCACACAGTTTACCTTCTCTGCGACTGAGTTTTTTCTGCGGACAAGCCTTGCTGCATGATTTAGCCGAACAATGGCAACAGGCCACCCAGCAGCCGGTGATCAATCTGTATGGTCCAACAGAGTGCACGATTGCTATTACCTATCATCGATTTGTCGCCCATTCAGGTATGGCATCGGTGCCGATTGGCCGTGCTTTTGAAGAGGAGTGTTTAGCCATCATCAACGAACAAGGTGAATTGATGCGCTTTGAATCTGCACCCGAGGGGTATCGCGGAGAATTACTTCTGTCGGGCAAACAATTAGTCAATGGTTATCTGAATGATCCGCTGAATACGCAAAGTGCCTTTTTCCAGCACGAAGGGCGTATTTGGTATCGTTCAGGTGACATTGTCACTAAATCAAATGGCGTGCTGATTCATCTTGGGCGTCGCGATCACCAAGTGAAAATTGCCGGACAACGGGTGGAATTAGAAGAGATTGAAACCGTTGTTCGCCGCGTGACTCAAGCGCACAGCGTGGCGATAGTGCCTTGGCCTTTAAGTGAGTCGGGCTATGCCAGCGGCACGGTGGCGTTTGTGGATACCCATACCCAATGGCAACCAGATCTGTGGTTGAGCCAATGCAAACAACAATTAAATCCAACTTTTGTGCCTAAGCGTTGGTATGCCATTGAACAATTACCAAGAAATGCCAATGGCAAAACCGATATTAAAGCTTTACAACAACAATTAGCGAGTCAGACATATGAAACAAGCCATTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36789","NCBI_taxonomy_name":"Vibrio cholerae","NCBI_taxonomy_id":"666"}}}},"ARO_accession":"3007433","ARO_id":"46189","ARO_name":"almE","CARD_short_name":"almE","ARO_description":"almE is a glycyltransferase found in Vibrio cholerae that transfers glycine to the carrier protein almF. almE is part of the almEFG polymyxin resistance operon.","ARO_category":{"46184":{"category_aro_accession":"3007428","category_aro_cvterm_id":"46184","category_aro_name":"polymyxin resistance operon","category_aro_description":"Operon or gene clusters confering resistance to polymyxin antibiotics.","category_aro_class_name":"AMR Gene Family"},"46188":{"category_aro_accession":"3007432","category_aro_cvterm_id":"46188","category_aro_name":"alm glycyltransferase","category_aro_description":"Glycyl transferase associated with polymyxin resistance operons not interacting with lipid A.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5914":{"model_id":"5914","model_name":"cfrE","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"650"}},"model_sequences":{"sequence":{"8623":{"protein_sequence":{"accession":"RHO92765.1","sequence":"MIYSKYEVMKRCISGMNFPDYRYEQLIKMIFAQHIPDFHSMYMLPERLRSNLAETFGTSVCGLVPVTHRASGQADKVLFQLKDGNCVETVNLHYKKGWESFCVSSQCGCGFGCKFCATGAIGHKRNMTADEITDQILYFYLAGHQINSVSFMGMGEPFANPNLFDALKILTNPSLFGLSQRRITISTIGMIPGIKRLTRDFPQVNLAFSLHSPFEKQRSELMPINQTYPLHKVMDALDAHVANTKRRLFLAYIMLGGINDSAEHAKALAHLILSRGALSYLYHVDLIPYNATDKTARKFTASNHEAIKNFSDILHSNRISVAIRMQFGSDIGAGCGQLYADERD"},"dna_sequence":{"accession":"QUDP01000003.1","fmin":"16034","fmax":"17069","strand":"-","sequence":"ATGATTTATTCAAAATATGAGGTTATGAAGCGATGTATATCGGGAATGAATTTTCCGGATTATCGCTATGAGCAATTGATAAAGATGATTTTTGCACAGCATATTCCTGACTTTCATTCCATGTATATGCTGCCGGAAAGACTAAGATCAAATTTGGCGGAAACTTTTGGGACCTCTGTCTGCGGCCTTGTTCCAGTTACACATCGGGCATCGGGCCAGGCAGATAAGGTGCTTTTTCAATTAAAGGATGGAAACTGCGTCGAAACGGTGAACCTGCATTACAAAAAAGGATGGGAATCTTTTTGCGTCTCATCTCAATGCGGCTGTGGGTTTGGCTGCAAATTCTGCGCAACAGGTGCTATCGGACACAAACGCAATATGACCGCTGATGAAATAACAGATCAAATTCTGTATTTTTATCTTGCAGGGCATCAAATCAATAGTGTTTCTTTTATGGGAATGGGCGAGCCGTTTGCGAATCCCAATTTATTTGACGCATTAAAAATCCTGACAAACCCGTCTTTGTTCGGATTAAGCCAGCGACGCATTACCATATCGACGATTGGAATGATTCCCGGGATAAAACGGCTGACCCGTGATTTTCCGCAGGTGAATTTAGCTTTTTCGCTGCACTCGCCTTTTGAAAAGCAACGTTCGGAATTGATGCCGATCAATCAAACTTATCCGCTCCATAAAGTAATGGATGCGTTGGATGCGCACGTTGCAAATACCAAAAGGCGCTTGTTCCTGGCTTATATTATGCTGGGCGGAATAAATGATTCGGCAGAGCATGCGAAAGCGTTAGCGCACCTTATTTTGAGCCGGGGAGCGTTGTCCTATCTATATCATGTTGATCTTATCCCATATAACGCAACAGATAAGACGGCGCGAAAATTTACCGCTTCAAATCACGAAGCCATTAAAAACTTCAGTGATATTTTACATTCCAACCGTATCAGCGTGGCTATCAGAATGCAGTTCGGTTCTGATATCGGCGCCGGGTGCGGGCAGTTGTATGCTGATGAAAGGGATTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"46174","NCBI_taxonomy_name":"Clostridium sp. AF37-7","NCBI_taxonomy_id":"2293017"}}}},"ARO_accession":"3005023","ARO_id":"43214","ARO_name":"cfrE","CARD_short_name":"cfrE","ARO_description":"The gene cfr(E) is a cfr-like gene found in Clostridioides difficile isolate DF11. It confers resistance to antibiotics targeting to the 23s rRNA through hypermethylation of nucleotide A2503.","ARO_category":{"36341":{"category_aro_accession":"3000202","category_aro_cvterm_id":"36341","category_aro_name":"Cfr 23S ribosomal RNA methyltransferase","category_aro_description":"Cfr genes produce enzymes which catalyze the methylation of the 23S rRNA subunit at position 8 of adenine-2503. Methylation of 23S rRNA at this site confers resistance to some classes of antibiotics, including streptogramins, chloramphenicols, florfenicols, linezolids and clindamycin.","category_aro_class_name":"AMR Gene Family"},"36595":{"category_aro_accession":"3000456","category_aro_cvterm_id":"36595","category_aro_name":"thiamphenicol","category_aro_description":"Derivative of Chloramphenicol. The nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3).","category_aro_class_name":"Antibiotic"},"37015":{"category_aro_accession":"3000671","category_aro_cvterm_id":"37015","category_aro_name":"tiamulin","category_aro_description":"Tiamulin is a pleuromutilin derivative currently used in veterinary medicine. It binds to the 23 rRNA of the 50S ribosomal subunit to inhibit protein translation.","category_aro_class_name":"Antibiotic"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"36218":{"category_aro_accession":"3000079","category_aro_cvterm_id":"36218","category_aro_name":"oxazolidinone antibiotic","category_aro_description":"Oxazolidinones are a class of synthetic antibiotics discovered the the 1980's.  They inhibit protein synthesis by binding to domain V of the 23S rRNA of the 50S subunit of bacterial ribosomes.  Linezolid is the only member of this class currently in clinical use.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"37014":{"category_aro_accession":"3000670","category_aro_cvterm_id":"37014","category_aro_name":"pleuromutilin antibiotic","category_aro_description":"Pleuromutilins are natural fungal products that target bacterial protein translation by binding the the 23S rRNA, blocking the ribosome P site at the 50S subunit. They are mostly used for agriculture and veterinary purposes.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5975":{"model_id":"5975","model_name":"APH(9)-Ic","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"8697":{"protein_sequence":{"accession":"WCI13726.1","sequence":"MSFASAQHLGEVLQQSYGITPTAVVPRPVGADANASVYRVDARHGQWWLKCRTYQVAPAVWDSLHWMRGTLGIDEIVAPWPALTGGASVQRWGLQFTLFPYVEGQSGFEAALSRTQWKRLGEVLRRLHGAQLPAELQQALPIVRLETAALETVGQWLAGEGLAAAKDGLGRAFVSVWDQQHARIAALHAQARELLAALQDAPVDLHLCHTDLHAGNLLMGNDGGLHLIDWDGLSLAPRERDLMFIGAAVGGRWGRENPLGFEEGYGSDRGDPRWIAWYRHWRILQDLIEFQQVLLGSDGEDRSPQLRRQSLHYLGEQFAPGNVFDAAERVYRALDQVPGRCQHRPG"},"dna_sequence":{"accession":"ON693243.1","fmin":"0","fmax":"1041","strand":"+","sequence":"ATGTCATTCGCTTCGGCGCAGCATCTCGGCGAAGTCCTGCAACAATCCTATGGCATCACCCCCACCGCCGTGGTGCCACGCCCGGTGGGCGCCGACGCCAATGCCAGCGTGTATCGCGTCGATGCGCGGCACGGGCAGTGGTGGTTGAAATGCCGTACCTACCAGGTCGCCCCAGCGGTGTGGGACAGCCTGCATTGGATGCGCGGCACGCTGGGTATCGATGAGATCGTCGCGCCGTGGCCGGCGTTGACCGGTGGTGCGTCTGTGCAGCGCTGGGGATTGCAGTTCACCCTGTTCCCGTATGTGGAAGGCCAGTCCGGATTCGAGGCGGCGTTGAGCCGCACGCAGTGGAAACGGCTGGGGGAGGTGCTGCGGCGCCTGCATGGCGCGCAGTTGCCAGCGGAACTGCAGCAGGCACTGCCGATCGTACGGCTGGAAACCGCGGCGCTGGAGACCGTCGGGCAATGGTTGGCCGGCGAGGGCCTGGCGGCCGCGAAGGACGGGCTGGGCCGCGCATTCGTTTCGGTATGGGACCAGCAGCATGCGCGCATCGCGGCGCTGCATGCGCAGGCACGGGAGCTGCTAGCGGCGTTGCAGGACGCGCCGGTAGACCTGCATCTGTGCCACACCGATCTGCATGCCGGCAACCTGCTGATGGGCAATGACGGGGGCCTGCACCTGATCGATTGGGATGGTCTGTCGCTGGCCCCGCGCGAGCGTGACCTGATGTTCATCGGTGCCGCTGTTGGCGGGCGCTGGGGTCGCGAGAATCCACTGGGGTTCGAGGAGGGCTACGGCAGCGATCGCGGTGACCCGCGCTGGATCGCCTGGTACCGGCACTGGCGCATTCTGCAGGACCTGATCGAGTTCCAGCAGGTGCTGCTGGGCAGTGACGGGGAGGACCGATCGCCGCAGTTGCGCCGGCAGTCACTGCACTACCTGGGGGAGCAGTTCGCACCGGGCAATGTGTTCGATGCGGCGGAGCGGGTATATCGCGCGCTGGATCAGGTTCCAGGCCGTTGCCAGCATCGCCCCGGGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37076","NCBI_taxonomy_name":"Stenotrophomonas maltophilia","NCBI_taxonomy_id":"40324"}}}},"ARO_accession":"3007539","ARO_id":"46310","ARO_name":"APH(9)-Ic","CARD_short_name":"APH(9)-Ic","ARO_description":"APH(9)-Ic is a chromosomal-encoded aminoglycoside phosphotransferase in S. maltophilia.","ARO_category":{"36292":{"category_aro_accession":"3000153","category_aro_cvterm_id":"36292","category_aro_name":"APH(9)","category_aro_description":"A category of aminoglycoside O-phosphotransferase enzymes with modification regiospecificity based at the 9-hydroxyl group of the respective antibiotic. These enzymes are characterized by enzymatic antibiotic inactivation, specifically of spectinomycin, by the ATP-dependent phosphorylation of the 9-hydroxyl group of the compound.","category_aro_class_name":"AMR Gene Family"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5972":{"model_id":"5972","model_name":"Mycobacterium tuberculosis 16S rRNA (rrnS) mutation conferring resistance to amikacin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"13255":"a1401g","13330":"g1484t","13075":"c462t","13076":"a514c","13077":"c1402t"},"CRyPTIC-R":{"13255":"a1401g","13330":"g1484t"},"clinical":{"13255":"a1401g","13330":"g1484t","13074":"g1484t","13075":"c462t","13076":"a514c","13077":"c1402t","13072":"a1401g"},"Curated-R":{"13074":"g1484t","13075":"c462t","13076":"a514c","13077":"c1402t","13072":"a1401g"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"41093","param_value":"2700"}},"model_sequences":{"sequence":{"8695":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"NC_000962.3","fmin":"1471845","fmax":"1473382","strand":"+","sequence":"TTTTGTTTGGAGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGGAAAGGTCTCTTCGGAGATACTCGAGTGGCGAACGGGTGAGTAACACGTGGGTGATCTGCCCTGCACTTCGGGATAAGCCTGGGAAACTGGGTCTAATACCGGATAGGACCACGGGATGCATGTCTTGTGGTGGAAAGCGCTTTAGCGGTGTGGGATGAGCCCGCGGCCTATCAGCTTGTTGGTGGGGTGACGGCCTACCAAGGCGACGACGGGTAGCCGGCCTGAGAGGGTGTCCGGCCACACTGGGACTGAGATACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCGACGCCGCGTGGGGGATGACGGCCTTCGGGTTGTAAACCTCTTTCACCATCGACGAAGGTCCGGGTTCTCTCGGATTGACGGTAGGTGGAGAAGAAGCACCGGCCAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGTGCGAGCGTTGTCCGGAATTACTGGGCGTAAAGAGCTCGTAGGTGGTTTGTCGCGTTGTTCGTGAAATCTCACGGCTTAACTGTGAGCGTGCGGGCGATACGGGCAGACTAGAGTACTGCAGGGGAGACTGGAATTCCTGGTGTAGCGGTGGAATGCGCAGATATCAGGAGGAACACCGGTGGCGAAGGCGGGTCTCTGGGCAGTAACTGACGCTGAGGAGCGAAAGCGTGGGGAGCGAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGGTGGGTACTAGGTGTGGGTTTCCTTCCTTGGGATCCGTGCCGTAGCTAACGCATTAAGTACCCCGCCTGGGGAGTACGGCCGCAAGGCTAAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGCGGAGCATGTGGATTAATTCGATGCAACGCGAAGAACCTTACCTGGGTTTGACATGCACAGGACGCGTCTAGAGATAGGCGTTCCCTTGTGGCCTGTGTGCAGGTGGTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTCTCATGTTGCCAGCACGTAATGGTGGGGACTCGTGAGAGACTGCCGGGGTCAACTCGGAGGAAGGTGGGGATGACGTCAAGTCATCATGCCCCTTATGTCCAGGGCTTCACACATGCTACAATGGCCGGTACAAAGGGCTGCGATGCCGCGAGGTTAAGCGAATCCTTAAAAGCCGGTCTCAGTTCGGATCGGGGTCTGCAACTCGACCCCGTGAAGTCGGAGTCGCTAGTAATCGCAGATCAGCAACGCTGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACGTCATGAAAGTCGGTAACACCCGAAGCCAGTGGCCTAACCCTCGGGAGGGAGCTGTCGAAGGTGGGATCGGCGATTGGGACGAAGTCGTAACAAGGTAGCCGTACCGGAAGGTGCGGCTGGATCACCTCCTTTCT","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3007536","ARO_id":"46307","ARO_name":"Mycobacterium tuberculosis 16S rRNA (rrnS) mutation conferring resistance to amikacin","CARD_short_name":"Mtub_16rrnS_AMK","ARO_description":"Point mutation in M. tuberculosis rrnS conferring resistance to amikacin antibiotic.","ARO_category":{"40277":{"category_aro_accession":"3003666","category_aro_cvterm_id":"40277","category_aro_name":"16s rRNA with mutation conferring resistance to aminoglycoside antibiotics","category_aro_description":"Point mutations in the 16S rRNA of bacteria can confer resistance to aminoglycosides.","category_aro_class_name":"AMR Gene Family"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5974":{"model_id":"5974","model_name":"Mycobacterium tuberculosis 16S rRNA (rrnS) mutation conferring resistance to kanamycin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"13257":"a1401g","13080":"g1484t","13082":"a514c","13083":"c1402t","13081":"c462t"},"CRyPTIC-R":{"13257":"a1401g"},"clinical":{"13257":"a1401g","13078":"a1401g","13080":"g1484t","13082":"a514c","13083":"c1402t","13081":"c462t"},"Curated-R":{"13078":"a1401g","13080":"g1484t","13082":"a514c","13083":"c1402t","13081":"c462t"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"41093","param_value":"2700"}},"model_sequences":{"sequence":{"8696":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"NC_000962.3","fmin":"1471845","fmax":"1473382","strand":"+","sequence":"TTTTGTTTGGAGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGGAAAGGTCTCTTCGGAGATACTCGAGTGGCGAACGGGTGAGTAACACGTGGGTGATCTGCCCTGCACTTCGGGATAAGCCTGGGAAACTGGGTCTAATACCGGATAGGACCACGGGATGCATGTCTTGTGGTGGAAAGCGCTTTAGCGGTGTGGGATGAGCCCGCGGCCTATCAGCTTGTTGGTGGGGTGACGGCCTACCAAGGCGACGACGGGTAGCCGGCCTGAGAGGGTGTCCGGCCACACTGGGACTGAGATACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCGACGCCGCGTGGGGGATGACGGCCTTCGGGTTGTAAACCTCTTTCACCATCGACGAAGGTCCGGGTTCTCTCGGATTGACGGTAGGTGGAGAAGAAGCACCGGCCAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGTGCGAGCGTTGTCCGGAATTACTGGGCGTAAAGAGCTCGTAGGTGGTTTGTCGCGTTGTTCGTGAAATCTCACGGCTTAACTGTGAGCGTGCGGGCGATACGGGCAGACTAGAGTACTGCAGGGGAGACTGGAATTCCTGGTGTAGCGGTGGAATGCGCAGATATCAGGAGGAACACCGGTGGCGAAGGCGGGTCTCTGGGCAGTAACTGACGCTGAGGAGCGAAAGCGTGGGGAGCGAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGGTGGGTACTAGGTGTGGGTTTCCTTCCTTGGGATCCGTGCCGTAGCTAACGCATTAAGTACCCCGCCTGGGGAGTACGGCCGCAAGGCTAAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGCGGAGCATGTGGATTAATTCGATGCAACGCGAAGAACCTTACCTGGGTTTGACATGCACAGGACGCGTCTAGAGATAGGCGTTCCCTTGTGGCCTGTGTGCAGGTGGTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTCTCATGTTGCCAGCACGTAATGGTGGGGACTCGTGAGAGACTGCCGGGGTCAACTCGGAGGAAGGTGGGGATGACGTCAAGTCATCATGCCCCTTATGTCCAGGGCTTCACACATGCTACAATGGCCGGTACAAAGGGCTGCGATGCCGCGAGGTTAAGCGAATCCTTAAAAGCCGGTCTCAGTTCGGATCGGGGTCTGCAACTCGACCCCGTGAAGTCGGAGTCGCTAGTAATCGCAGATCAGCAACGCTGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACGTCATGAAAGTCGGTAACACCCGAAGCCAGTGGCCTAACCCTCGGGAGGGAGCTGTCGAAGGTGGGATCGGCGATTGGGACGAAGTCGTAACAAGGTAGCCGTACCGGAAGGTGCGGCTGGATCACCTCCTTTCT","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3007537","ARO_id":"46308","ARO_name":"Mycobacterium tuberculosis 16S rRNA (rrnS) mutation conferring resistance to kanamycin","CARD_short_name":"Mtub_16rrnS_KAN","ARO_description":"Point mutation in M. tuberculosis rrnS conferring resistance to kanamycin antibiotic.","ARO_category":{"40277":{"category_aro_accession":"3003666","category_aro_cvterm_id":"40277","category_aro_name":"16s rRNA with mutation conferring resistance to aminoglycoside antibiotics","category_aro_description":"Point mutations in the 16S rRNA of bacteria can confer resistance to aminoglycosides.","category_aro_class_name":"AMR Gene Family"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"6038":{"model_id":"6038","model_name":"VIM-77","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8858":{"protein_sequence":{"accession":"WP_231869637.1","sequence":"MFKLLSKLLVYLTASIMAIASPLAFSVDSSGEYPTVSEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEVEGDEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSASVLYGGCAIYELSRTSAGNVADADLAEWPTSIERIQQHYPEAQFVIPGHGLPGGLDLLKHTTNVVKAHTNRSVVE"},"dna_sequence":{"accession":"NG_078035.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGTTCAAACTTTTGAGTAAGTTATTGGTCTATTTGACCGCGTCTATCATGGCTATTGCGAGTCCGCTCGCTTTTTCCGTAGATTCTAGCGGTGAGTATCCGACAGTCAGCGAAATTCCGGTCGGGGAGGTCCGGCTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCAGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAGAAGCAAATTGGACTTCCTGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGTAGAGGGGGACGAGATTCCCACGCACTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAACTCTTCTATCCTGGTGCTGCGCATTCGACCGACAACTTAGTTGTGTACGTCCCGTCTGCGAGTGTGCTCTATGGTGGTTGTGCGATTTATGAGTTGTCACGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCATTGAGCGGATTCAACAACACTACCCGGAAGCACAGTTCGTCATTCCGGGGCACGGCCTGCCGGGCGGTCTAGACTTGCTCAAGCACACAACGAATGTTGTAAAAGCGCACACAAATCGCTCAGTCGTTGAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"46601","NCBI_taxonomy_name":"Pseudomonas shirazica","NCBI_taxonomy_id":"1940636"}}}},"ARO_accession":"3007814","ARO_id":"46600","ARO_name":"VIM-77","CARD_short_name":"VIM-77","ARO_description":"VIM-77 is a subclass B1 carbapenem-hydrolyzing metallo-beta-lactamase.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"6040":{"model_id":"6040","model_name":"VIM-79","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8860":{"protein_sequence":{"accession":"UBL87558.1","sequence":"MLKVISSLLVYMTASVMAVASPLAHSGEPSGEYPTVNEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEAEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSANVLFGGCAVHELSRTSAGNVADADLAEWPTSVERIQKHYPEAEVVIPGHGLPGGLDLLQHTANVVKAHKNRSVAE"},"dna_sequence":{"accession":"OK217280.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGTTAAAAGTTATTAGTAGTTTATTGGTCTACATGACCGCGTCTGTCATGGCTGTCGCAAGTCCGTTAGCCCATTCCGGGGAGCCGAGTGGTGAGTATCCGACAGTCAACGAAATTCCGGTCGGAGAGGTCCGACTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCGGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAAAAGCAAATTGGACTTCCCGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGCAGAGGGGAACGAGATTCCCACGCATTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAGCTCTTCTATCCTGGTGCTGCGCATTCGACCGACAATCTGGTTGTATACGTCCCGTCAGCGAACGTGCTATTCGGTGGTTGTGCCGTTCATGAGTTGTCACGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCGTTGAGCGGATTCAAAAACACTACCCGGAAGCAGAGGTCGTCATTCCCGGGCACGGTCTACCGGGCGGTCTAGACTTGCTCCAGCACACAGCGAACGTTGTCAAAGCACACAAAAATCGCTCAGTCGCCGAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3007816","ARO_id":"46603","ARO_name":"VIM-79","CARD_short_name":"VIM-79","ARO_description":"VIM-79 is a subclass B1 carbapenem-hydrolyzing metallo-beta-lactamase.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"6042":{"model_id":"6042","model_name":"VIM-81","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8862":{"protein_sequence":{"accession":"UNZ81762.1","sequence":"MFKLLSKLLVYLTASIMAIASPLAFSVDSSGEHPTVSEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEVEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSASVLYGGCAIYELSRTSAGNVADADLAEWPTSIERIQQHYPEAQFVIPGHGLPGGLDLLKHTTNVVKAHTNRSVVE"},"dna_sequence":{"accession":"ON059758.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGTTCAAACTTTTGAGTAAGTTATTGGTCTATTTGACCGCGTCTATCATGGCTATTGCGAGTCCGCTCGCTTTTTCCGTAGATTCTAGCGGTGAGCATCCGACAGTCAGCGAAATTCCGGTCGGGGAGGTCCGGCTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCAGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAGAAGCAAATTGGACTTCCTGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGTAGAGGGGAACGAGATTCCCACGCACTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAACTCTTCTATCCTGGTGCTGCGCATTCGACCGACAACTTAGTTGTGTACGTCCCGTCTGCGAGTGTGCTCTATGGTGGTTGTGCGATTTATGAGTTGTCACGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCATTGAGCGGATTCAACAACACTACCCGGAAGCACAGTTCGTCATTCCGGGGCACGGCCTGCCGGGCGGTCTAGACTTGCTCAAGCACACAACGAATGTTGTAAAAGCGCACACAAATCGCTCAGTCGTTGAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3007818","ARO_id":"46605","ARO_name":"VIM-81","CARD_short_name":"VIM-81","ARO_description":"VIM-81 is a subclass B1 carbapenem-hydrolyzing metallo-beta-lactamase.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5929":{"model_id":"5929","model_name":"almEFG","model_type":"gene cluster meta-model","model_type_id":"40298","model_description":"Gene Cluster Meta-Models (GCM) are used to curate spatial clusters of individual genes within operons, such as for glycopeptide resistance gene clusters. The individual genes will have their own individual detection models (e.g. PHM, PVM, POM, etc.) while the GCM checks to see if all the component genes of the cluster have a Strict or Perfect hit and are ordered correctly within an operon. GCMs are encoded using the gene order parameter. This model type is still under development and not currently supported by the Resistance Gene Identifier (RGI) software.","model_param":{"40297":{"param_type":"gene order","param_description":"Spatial clusters of genes are encoded using the gene order parameter: [gene type]:[cvterm_id],[gene type]:[cvterm_id], etc. The gene type designations are: R = regulatory, C = core, A = accessory.","param_type_id":"40297","param_value":{"12842":"C:46189,C:46187,C:41538"}},"snp":{"Curated-R":{"12842":"c462t"}}},"ARO_accession":"3007434","ARO_id":"46190","ARO_name":"almEFG","CARD_short_name":"almEFG","ARO_description":"The almEFG operon is responsible for glycylation of lipid A as a mechanism of colistin resistance in Vibrio cholerae. Its mechanism involves transfer of a glycyl molecule to the carrier protein almF by almE followed by glycylation of lipid A by almG.","ARO_category":{"46184":{"category_aro_accession":"3007428","category_aro_cvterm_id":"46184","category_aro_name":"polymyxin resistance operon","category_aro_description":"Operon or gene clusters confering resistance to polymyxin antibiotics.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5962":{"model_id":"5962","model_name":"tet(62)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"8684":{"protein_sequence":{"accession":"QIQ10744.1","sequence":"MSISLSLINYGEAMQTEARINKSLAIVLSVIVLDAMGLGLVMPVLPELLRGLVPGGQVTGHYGMLLAVYALMQVFFAPLLGRLSDRYGRRPVLIMSLAGAAIDYAVMAAAPVLWVIYIGRMIAGITGATGAVAASAIADTMPSNQRARWFGYMGACYGAGMIAGPAIGGLAGSLSVHAPFIAAAVLNGTGFLLAYLFLKETRPAGSQPAVSETFSLREFLLPVSFLKGMTALALVFFIIQLVGQLPATLWVIYTEDRFAWDTTMVGFSLAAFGAVHTVFQAFVTGPLSARFGERRTLIIGMAADACGFLALAMITQSWMILPVLLLLATGGVGMPALQAMLSGAAGEDEQGSLQGTLTSLTNLSSIIGPLGFSAFYAITAVAWNGWVWIGGAALYCISFAILRRSS"},"dna_sequence":{"accession":"MN340018.1","fmin":"32306","fmax":"33527","strand":"+","sequence":"ATGTCCATTTCCTTATCATTGATAAATTATGGTGAAGCTATGCAGACGGAAGCACGGATCAATAAATCTCTGGCCATTGTGCTCAGTGTCATTGTGCTGGATGCAATGGGGCTCGGGCTTGTGATGCCGGTTCTGCCGGAGTTGTTGCGCGGACTGGTGCCAGGCGGACAGGTAACAGGGCATTATGGTATGTTGCTGGCTGTCTATGCGCTGATGCAGGTGTTCTTTGCGCCGCTGCTAGGGCGATTGTCAGATCGCTATGGCCGCCGTCCGGTGCTGATTATGTCGCTTGCCGGTGCAGCAATTGACTATGCCGTCATGGCAGCAGCACCGGTGCTCTGGGTGATTTATATCGGCCGCATGATTGCCGGTATTACCGGAGCGACAGGTGCGGTTGCGGCATCGGCGATTGCCGATACGATGCCGTCAAACCAGCGGGCGCGCTGGTTCGGTTATATGGGCGCCTGTTACGGTGCCGGAATGATTGCGGGGCCTGCGATCGGCGGGCTGGCAGGCAGCCTGTCTGTGCACGCCCCCTTTATCGCGGCTGCTGTACTGAACGGAACCGGTTTTCTGCTGGCTTATCTTTTTCTCAAAGAGACACGTCCGGCAGGTTCGCAGCCGGCAGTTTCAGAAACATTCAGTTTGCGTGAGTTTCTGTTGCCGGTCAGCTTTCTCAAAGGGATGACCGCACTTGCGCTGGTGTTTTTCATTATCCAGCTGGTGGGGCAGCTTCCTGCAACATTGTGGGTGATCTATACGGAAGATCGTTTCGCGTGGGACACAACCATGGTCGGCTTTTCACTGGCGGCTTTCGGTGCCGTGCATACCGTGTTTCAGGCTTTTGTGACCGGCCCGCTCTCAGCCCGTTTTGGTGAGCGCCGCACATTGATCATCGGCATGGCTGCCGATGCCTGCGGTTTTCTGGCGCTGGCCATGATCACGCAAAGCTGGATGATACTGCCGGTACTATTGCTGCTGGCAACCGGCGGTGTCGGCATGCCCGCATTGCAGGCAATGTTGTCTGGGGCTGCCGGAGAGGATGAGCAGGGGAGTTTGCAGGGCACACTGACCAGCCTGACGAACCTGAGTTCGATTATCGGGCCCCTTGGTTTCTCGGCTTTCTACGCAATAACCGCAGTTGCATGGAATGGCTGGGTGTGGATTGGCGGTGCTGCGCTTTATTGCATCAGCTTCGCGATCCTGCGCCGGTCTTCATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36791","NCBI_taxonomy_name":"uncultured bacterium","NCBI_taxonomy_id":"77133"}}}},"ARO_accession":"3007492","ARO_id":"46260","ARO_name":"tet(62)","CARD_short_name":"tet(62)","ARO_description":"A novel tetA-type efflux pump.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"3340":{"model_id":"3340","model_name":"AAC(6')-I-43","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"330"}},"model_sequences":{"sequence":{"5464":{"protein_sequence":{"accession":"AEA07977.1","sequence":"MIYNIINIADSEKNKEDAARILYSAFRGKGKDAWPTLDSAREEIAECIASPNICLGITLDDRLVGWGGLRPMYETTWELHPLVIDPDYQGNGLGRLLLSKIESTATTNRIIGIMLGTDDETLSTSLSMTDIDESNIFQEIKNIINIKNHPFEFYKKCGYIIVGIVPNANGYRKPDIWMWKNLEKKSG"},"dna_sequence":{"accession":"HQ247816.1","fmin":"638","fmax":"1202","strand":"+","sequence":"ATGATTTATAACATAATTAACATTGCTGATTCTGAAAAGAACAAGGAAGACGCTGCACGAATTCTATATTCTGCATTTCGCGGAAAGGGAAAAGATGCTTGGCCTACATTAGATTCAGCTCGTGAAGAAATAGCAGAGTGCATAGCAAGTCCTAATATTTGCTTGGGCATAACCTTAGATGATCGCTTAGTAGGGTGGGGCGGACTTCGTCCCATGTATGAAACCACATGGGAATTGCATCCCTTAGTAATAGATCCTGATTATCAAGGTAATGGATTAGGAAGACTGCTCCTATCAAAGATTGAGAGCACTGCAACCACAAATAGAATAATTGGTATAATGCTTGGAACAGATGATGAGACATTGAGTACAAGTCTTTCAATGACTGATATAGATGAGTCTAATATTTTCCAAGAGATAAAAAATATAATTAATATAAAGAATCATCCATTTGAATTTTATAAAAAATGCGGGTACATCATTGTCGGTATAGTACCTAACGCAAATGGGTATAGAAAACCTGACATTTGGATGTGGAAGAATCTAGAAAAGAAAAGTGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3004641","ARO_id":"42650","ARO_name":"AAC(6')-I-43","CARD_short_name":"AAC(6')-I-43","ARO_description":"AAC(6')-I-43 (aacA43) is an aminoglycoside acetyltransferase encoded by integrons found in Klebsiella pneumoniae, Escherichia coli, and Enterobacter cloaecae.","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"A category of aminoglycoside N-acetyltransferase enzymes with modification regiospecificity based at the 6'-amino group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics through acetylation of the 6-amino group of the compound.","category_aro_class_name":"AMR Gene Family"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5963":{"model_id":"5963","model_name":"tet(63)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"800"}},"model_sequences":{"sequence":{"8685":{"protein_sequence":{"accession":"QJR33972.1","sequence":"MNYINNKIKSLSYNILFWLCILSFFSVLNEMVLNVSLPDIAISFNTSPAITNWVNTAYMLTFSIGTAVYGKLSDQVSIKKLLILGIILSCLGSLIGFFGHKHFLILILGRLIQGIGSAAFPSLVMVVVSRNITKAKQGKAFGFIGSIVALGEGIGPSIGGVVTHYIHWSYLLIIPIFTLITIPFLNKIMEPGESQKGDLDILGILLMSISIISFMLFTTSYKWFYLITFVIFFIIFIKHIVKVTHPFIDPALRKNPSFIFGLISGALIFATVAGFISMVPYMMKALYHINAATIGNNVILPGTISVIIFGYIGGYLVDKKGALFVFVIGSLFISISFLVIAFFVELNLWVTTISFIFVMGGLSFTKTVISTIVSSSLSHEEVGSGMSLLNFTSFLSEGTGIIIMGGLLSTQFLNYNFLSEFITFSTNLYSNILIGCTIIIALCCLLTFILFNRTVKQHT"},"dna_sequence":{"accession":"CP053076.1","fmin":"16644","fmax":"18024","strand":"-","sequence":"TTGAACTATATAAACAATAAAATTAAAAGCTTAAGTTATAATATTTTATTTTGGCTCTGTATTCTTTCATTTTTTAGCGTATTAAATGAAATGGTTTTAAACGTTTCACTTCCTGATATAGCTATTTCTTTTAATACTTCACCTGCTATTACTAATTGGGTTAATACTGCCTACATGCTAACTTTTTCAATTGGTACAGCAGTATACGGCAAATTATCTGATCAAGTAAGCATTAAAAAACTACTTATTTTAGGGATTATTTTAAGTTGCTTAGGCTCATTAATTGGATTTTTTGGTCATAAACATTTTTTAATTTTAATTTTAGGTAGGTTAATACAAGGAATAGGTTCTGCTGCGTTTCCTTCTCTTGTTATGGTTGTCGTATCACGTAATATAACTAAAGCAAAACAAGGGAAGGCATTTGGATTTATAGGATCAATTGTTGCATTGGGTGAAGGAATAGGGCCTTCAATAGGAGGCGTTGTAACTCATTATATTCATTGGTCATATTTACTTATAATACCTATTTTCACATTAATAACCATTCCTTTTCTTAATAAAATCATGGAACCTGGCGAATCTCAAAAAGGAGATTTAGATATATTAGGGATCCTTTTAATGTCTATAAGTATCATAAGCTTTATGTTATTTACAACAAGTTACAAATGGTTTTATTTAATAACCTTTGTTATTTTCTTTATCATTTTTATTAAACATATTGTAAAAGTTACCCATCCTTTTATTGACCCAGCTTTGCGGAAGAACCCATCATTTATTTTTGGATTGATTTCAGGAGCTCTTATATTTGCTACTGTAGCCGGATTTATCTCAATGGTTCCTTATATGATGAAAGCTCTTTACCATATAAACGCCGCGACAATTGGGAACAATGTTATTCTTCCTGGTACTATAAGTGTTATTATATTTGGATATATTGGTGGATACTTAGTAGATAAAAAAGGTGCTTTGTTTGTCTTTGTTATAGGTTCGCTATTTATATCTATTAGTTTTCTTGTTATTGCATTTTTTGTTGAATTAAATTTGTGGGTAACAACCATCTCTTTCATTTTTGTCATGGGAGGACTTTCATTTACAAAAACTGTTATATCAACGATAGTTTCTAGTAGCCTTTCTCATGAAGAAGTCGGTTCTGGTATGAGCTTATTAAATTTTACTAGTTTTTTATCAGAAGGCACAGGCATTATAATAATGGGCGGATTACTATCAACACAATTTTTAAATTATAATTTCCTTTCAGAATTCATTACTTTTTCCACCAACCTTTACAGTAATATCCTTATTGGTTGTACAATTATAATTGCACTTTGTTGTTTGTTAACATTTATATTATTTAATCGTACAGTAAAACAACACACTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35508","NCBI_taxonomy_name":"Staphylococcus aureus","NCBI_taxonomy_id":"1280"}}}},"ARO_accession":"3007493","ARO_id":"46261","ARO_name":"tet(63)","CARD_short_name":"tet(63)","ARO_description":"A tetracycline efflux MFS Transporter from Staphylococcus aureus.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35986":{"category_aro_accession":"0000069","category_aro_cvterm_id":"35986","category_aro_name":"doxycycline","category_aro_description":"Doxycycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"5964":{"model_id":"5964","model_name":"tet(64)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"675"}},"model_sequences":{"sequence":{"8686":{"protein_sequence":{"accession":"WP_124470450.1","sequence":"MNPSMIAILTTVVLDAIGVGLVMPILPGLLRTLAGAGGADTHYGMLLALYALAQFLCAPVLGALSDRFGRRPVLLASLAGAALDYLLMAYAPTLAWLYAGRLIAGITGANVAVATAYVTDVTAEPDRARRFGQLGAAMGIGFIAGPVLGGLLGAWHLRAPFAAAALLNALNLALVWRSLPESRPPAARAGRATVSLNAFASLRRLRGGPALVPLIGVYVIVALVSQAPATLWILYGQAHFGWSTPVAGLSLAGYGACHALAQAFAIGPLIARLGERRALALGLAGDALGLVVIAFANAAWVPFALLPLFAAGGMTLPALQAMLARQVDDARQGELQGTLASVASLIGVAGPLVVTAAYAATRDAWPGLVWAAAALLYLLVPPLLAHARPARESPAA"},"dna_sequence":{"accession":"NG_071182.1","fmin":"100","fmax":"1291","strand":"+","sequence":"TTGAATCCTTCCATGATTGCCATCCTGACGACCGTCGTGCTTGACGCGATCGGCGTCGGGCTCGTGATGCCGATCCTGCCCGGGCTGCTGCGCACCCTCGCCGGCGCGGGCGGCGCCGACACGCACTACGGCATGCTGCTCGCGCTGTACGCGCTGGCGCAGTTCCTGTGCGCCCCCGTCCTTGGCGCGCTGAGCGACCGCTTCGGCCGCCGGCCCGTGCTGCTCGCGTCGCTCGCGGGCGCCGCGCTCGACTACCTGCTGATGGCGTATGCGCCGACGCTCGCGTGGCTCTATGCCGGGCGGCTGATCGCGGGCATCACGGGCGCGAACGTCGCGGTCGCGACCGCGTACGTCACCGACGTGACCGCGGAACCCGATCGCGCGCGCCGTTTCGGTCAATTGGGCGCCGCGATGGGGATCGGCTTCATCGCCGGCCCGGTGCTCGGCGGCCTGCTCGGCGCGTGGCATCTGCGCGCGCCGTTCGCCGCCGCGGCGCTGCTCAATGCGCTCAATCTCGCACTCGTCTGGCGGAGCCTGCCGGAATCGCGGCCGCCGGCCGCGCGCGCCGGCCGCGCCACGGTGAGCCTCAACGCGTTCGCGAGCCTGCGGCGGCTGCGCGGCGGCCCGGCGCTCGTCCCGCTGATCGGCGTCTACGTGATCGTGGCGCTGGTGTCGCAGGCGCCCGCGACGCTGTGGATCCTGTACGGACAGGCGCATTTCGGCTGGTCGACGCCGGTCGCGGGCCTGTCGCTCGCCGGCTACGGCGCGTGCCACGCGCTCGCGCAGGCGTTCGCGATCGGGCCGCTGATCGCGCGGCTCGGTGAGCGTCGCGCGCTCGCGCTGGGCCTCGCCGGCGACGCGCTCGGCCTCGTGGTCATCGCGTTCGCCAACGCGGCCTGGGTGCCGTTCGCGCTATTGCCGCTGTTCGCGGCGGGCGGCATGACGCTGCCGGCGCTGCAGGCGATGCTCGCGCGCCAGGTCGACGATGCCCGGCAGGGCGAGCTGCAGGGCACGCTCGCGAGCGTCGCGAGCCTGATCGGCGTCGCCGGGCCGCTCGTCGTCACCGCGGCCTATGCGGCAACCCGCGACGCGTGGCCCGGGCTCGTCTGGGCCGCGGCCGCGTTGCTCTACCTGCTGGTGCCGCCGCTGCTGGCCCACGCGCGGCCGGCGCGAGAAAGTCCGGCCGCGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"46263","NCBI_taxonomy_name":"Burkholderia ubonensis","NCBI_taxonomy_id":"101571"}}}},"ARO_accession":"3007494","ARO_id":"46262","ARO_name":"tet(64)","CARD_short_name":"tet(64)","ARO_description":"A tetracycline efflux MFS Transporter from Burkholderia ubonensis.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35986":{"category_aro_accession":"0000069","category_aro_cvterm_id":"35986","category_aro_name":"doxycycline","category_aro_description":"Doxycycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"5965":{"model_id":"5965","model_name":"Shigella flexneri acrA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"8687":{"protein_sequence":{"accession":"NP_706356.2","sequence":"MNKNRGFTPLAVVLMLSGSLALTGCDDKQAQQGGQQMPAVGVVTVKTEPLQITTELPGRTSAYRIAEVRPQVSGIILKRNFKEGSDIEAGVSLYQIDPATYQATYDSAKGDLAKAQAAANIAQLTVNRYQKLLGTQYISKQGYDQALADAQQANAAVTAAKAAVETARINLAYTKVTSPISGRIGKSNVTEGALVQNGQATVLATVQQLDPIYVDVTQSSNDFLRLKQELANGTLKQENGKAKVSLITSDGIKFPQDGTLEFSDVTVDQTTGSITLRAIFPNPDHTLLPGMFVRARLEEGLNPNAILVPQQGVTRTPRGDATVLVVGADDKVETRPIVASQAIGDKWLVTEGLKAGDRVVISGLQKVRPGVQVKAQEVTADNNQQAASGAQPEQSKS"},"dna_sequence":{"accession":"NC_004337.2","fmin":"420956","fmax":"422150","strand":"-","sequence":"ATGAACAAAAACAGAGGGTTTACGCCTCTGGCGGTCGTTCTGATGCTCTCAGGCAGCTTAGCCCTAACAGGATGTGACGACAAACAGGCCCAACAAGGTGGCCAGCAGATGCCCGCCGTTGGCGTAGTAACAGTCAAAACTGAACCTCTGCAGATCACAACCGAGCTTCCAGGTCGCACCAGTGCCTACCGGATCGCAGAAGTTCGTCCTCAAGTTAGCGGGATTATCCTGAAGCGTAATTTCAAAGAAGGTAGCGACATCGAAGCTGGTGTCTCTCTCTATCAGATTGATCCTGCGACCTATCAGGCGACATACGACAGTGCGAAAGGTGATCTGGCGAAAGCCCAGGCTGCAGCCAATATCGCGCAATTGACGGTGAATCGTTATCAGAAACTGCTCGGTACTCAGTACATCAGTAAGCAAGGGTACGATCAGGCTCTGGCTGATGCGCAACAGGCGAATGCTGCGGTAACTGCGGCGAAAGCTGCCGTTGAAACTGCGCGGATCAATCTGGCTTACACCAAAGTCACCTCTCCGATTAGCGGTCGCATTGGTAAGTCGAACGTGACGGAAGGCGCATTGGTACAGAACGGTCAGGCGACTGTGCTGGCAACCGTGCAGCAACTTGATCCGATCTACGTTGATGTGACCCAGTCCAGCAACGACTTCCTTCGCCTGAAACAGGAACTGGCGAATGGCACGCTGAAACAAGAGAACGGCAAAGCCAAAGTGTCGCTGATCACCAGTGACGGCATTAAGTTCCCGCAGGACGGTACGCTGGAATTCTCTGACGTTACCGTTGATCAGACCACTGGGTCTATCACCCTACGCGCTATCTTCCCGAACCCGGATCACACTCTGCTGCCGGGTATGTTCGTGCGCGCACGTCTGGAAGAAGGGCTTAATCCAAACGCTATTTTAGTCCCGCAACAGGGCGTAACCCGTACGCCGCGTGGTGATGCCACCGTACTGGTAGTTGGCGCGGATGACAAAGTGGAAACCCGTCCGATCGTTGCAAGCCAGGCTATTGGCGATAAGTGGCTGGTGACAGAAGGTCTGAAAGCAGGCGATCGCGTAGTAATAAGTGGGCTGCAGAAAGTGCGTCCTGGTGTCCAGGTAAAAGCACAAGAAGTTACCGCTGATAATAACCAGCAAGCCGCAAGCGGTGCTCAGCCTGAACAGTCCAAGTCTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40665","NCBI_taxonomy_name":"Shigella flexneri 2a str. 301","NCBI_taxonomy_id":"198214"}}}},"ARO_accession":"3007509","ARO_id":"46278","ARO_name":"Shigella flexneri acrA","CARD_short_name":"Sfle_acrA","ARO_description":"AcrA is a subunit of the AcrAB multidrug efflux system found in Shigella flexneri, which is encoded by the acrRAB operon.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"37084":{"category_aro_accession":"3000704","category_aro_cvterm_id":"37084","category_aro_name":"cefalotin","category_aro_description":"Cefalotin is a semisynthetic cephalosporin antibiotic activate against staphylococci. It is resistant to staphylococci beta-lactamases but hydrolyzed by enterobacterial beta-lactamases.","category_aro_class_name":"Antibiotic"},"37250":{"category_aro_accession":"3000870","category_aro_cvterm_id":"37250","category_aro_name":"triclosan","category_aro_description":"Triclosan is a common antibacterial agent added to many consumer products as a biocide.  It is an inhibitor of fatty acid biosynthesis by blocking enoyl-carrier protein reductase (FabI).","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"43746":{"category_aro_accession":"3005386","category_aro_cvterm_id":"43746","category_aro_name":"disinfecting agents and antiseptics","category_aro_description":"Disinfectants that can also interact with antimicrobial resistance mechanisms, e.g. molecule efflux, and thus are the targets of disinfectant resistance.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"5930":{"model_id":"5930","model_name":"KPC-96","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8656":{"protein_sequence":{"accession":"UAY85936.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVNGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"OK086970.1","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGAATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3007436","ARO_id":"46194","ARO_name":"KPC-96","CARD_short_name":"KPC-96","ARO_description":"KPC-96 is a KPC beta-lactamase.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5931":{"model_id":"5931","model_name":"EBR-5","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"350"}},"model_sequences":{"sequence":{"8655":{"protein_sequence":{"accession":"UWX67704.1","sequence":"MKKVFSFVTLIGTFAFGQIKPIQIDSINSHLYVYQTFNSFQGIDYNANGMFLITDKGIILFDVPWQKSQYQTMNDLVLEKYHLPVIAVFVTHSHEDRAGDLSFYNELNIPTYASSFTNSILKKEGKATSKFEIELGKTYRFGKEKFVIEYFGQGHTADNLVVWFPKYKVLNGGCLIKGADAKNLGYIGEANVTEWPKTVQKLVTKHPKINQVIPGHDNWKANGHIENTFKLLEK"},"dna_sequence":{"accession":"CP104209.1","fmin":"786782","fmax":"787487","strand":"-","sequence":"ATGAAAAAAGTATTTTCTTTTGTCACATTGATTGGAACGTTTGCATTTGGTCAAATAAAACCGATTCAAATAGATTCTATTAATTCTCATCTTTACGTTTATCAAACATTTAATTCATTTCAAGGCATTGATTATAATGCGAATGGAATGTTTTTGATCACTGATAAAGGAATTATTTTGTTTGACGTGCCTTGGCAAAAATCTCAGTATCAAACAATGAATGATCTTGTATTAGAGAAATATCATTTACCAGTTATTGCTGTTTTTGTCACACATTCACACGAAGATAGAGCAGGGGATTTAAGCTTTTACAATGAATTAAATATCCCAACATACGCTTCATCTTTCACTAATTCTATTTTAAAAAAGGAAGGAAAAGCAACTTCGAAATTTGAAATAGAATTAGGTAAAACCTATAGATTTGGTAAAGAAAAATTTGTCATCGAATATTTTGGACAAGGTCATACAGCGGATAATCTTGTGGTTTGGTTTCCGAAATATAAGGTTTTGAATGGAGGTTGTTTGATCAAAGGAGCAGATGCAAAAAATTTAGGTTATATTGGTGAAGCTAATGTTACTGAATGGCCAAAAACAGTTCAGAAATTAGTAACGAAACATCCAAAAATTAACCAAGTTATTCCAGGTCATGATAATTGGAAAGCAAATGGGCATATAGAAAATACGTTTAAACTTTTAGAAAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"46203","NCBI_taxonomy_name":"Empedobacter stercoris","NCBI_taxonomy_id":"1628248"}}}},"ARO_accession":"3007437","ARO_id":"46195","ARO_name":"EBR-5","CARD_short_name":"EBR-5","ARO_description":"EBR-5 is an EBR beta-lactamase.","ARO_category":{"41368":{"category_aro_accession":"3004204","category_aro_cvterm_id":"41368","category_aro_name":"EBR beta-lactamase","category_aro_description":"EBR beta-lactamases are Class B beta-lactamases first isolated from Empedobacter brevis and are able to hydrolyze penicillins, cephalosporins, and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"35980":{"category_aro_accession":"0000063","category_aro_cvterm_id":"35980","category_aro_name":"cefuroxime","category_aro_description":"Cefuroxime is a second-generation cephalosporin antibiotic with increased stability with beta-lactamases than first-generation cephalosporins. Cefuroxime is active against Gram-positive organisms but less active against methicillin-resistant strains.","category_aro_class_name":"Antibiotic"},"35995":{"category_aro_accession":"0000078","category_aro_cvterm_id":"35995","category_aro_name":"piperacillin","category_aro_description":"Piperacillin is an acetylureidopenicillin and has an extended spectrum of targets relative to other beta-lactam antibiotics. It inhibits cell wall synthesis in bacteria, and is usually taken with the beta-lactamase inhibitor tazobactam to overcome penicillin-resistant bacteria.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"37084":{"category_aro_accession":"3000704","category_aro_cvterm_id":"37084","category_aro_name":"cefalotin","category_aro_description":"Cefalotin is a semisynthetic cephalosporin antibiotic activate against staphylococci. It is resistant to staphylococci beta-lactamases but hydrolyzed by enterobacterial beta-lactamases.","category_aro_class_name":"Antibiotic"},"40933":{"category_aro_accession":"3004006","category_aro_cvterm_id":"40933","category_aro_name":"ceftiofur","category_aro_description":"Ceftiofur is a third-generation broad spectrum cephalosporin and beta-lactam antibiotic predominantly used in veterinary medicine. It causes cell lysis by disrupting peptidoglycan cross-linkage and cell wall formation by binding to PBPs.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5932":{"model_id":"5932","model_name":"LAQ-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"8654":{"protein_sequence":{"accession":"QXM27670.1","sequence":"MKKSLCAVLLLTASCSALAAPQTEKQIADTVNRIMTPLMKEQAIPGMAVAVIYQGKTHYFVYGKADIAANQPVTQHTLFELGSVSKTFTGVLGGEAIARGEIRLDDPASKYWPALTGKQWKGITLLHLATYTAGGLPLQVPDEVTDQAALLHFYQNWQPQWTPGAKRLYANASIGLFGMLAVKPSGMDFEQAMTSRVFQPLELNHTWINVPAAEEKHYAWGYRDGKPVHVSPGMLDAESYGVKTTIEDMASWVRANMNPAGVKDEMLKQGIELAQSRYWRIGEMYQGLGWEMLNWPVKAKTVVDGSDNKIALASLTAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFIPEKNIGIVMLANKSYPNPARVDAAYRILDTLK"},"dna_sequence":{"accession":"MZ497396.1","fmin":"2000","fmax":"3143","strand":"+","sequence":"ATGAAAAAATCCCTTTGCGCCGTGCTGCTGCTCACCGCTTCATGCTCTGCGCTTGCCGCGCCTCAAACTGAAAAACAGATCGCTGATACCGTCAATCGCATCATGACCCCGCTCATGAAAGAACAGGCGATTCCGGGCATGGCCGTCGCCGTGATTTATCAAGGAAAGACGCACTATTTTGTCTACGGCAAAGCAGATATCGCCGCGAATCAGCCCGTCACTCAGCACACCTTGTTTGAGCTGGGCTCCGTGAGCAAAACCTTTACCGGCGTTCTGGGCGGCGAAGCCATCGCACGCGGTGAAATCAGGCTTGACGATCCCGCCAGCAAATACTGGCCTGCGCTGACGGGTAAACAATGGAAAGGCATTACTCTGCTGCATCTGGCTACTTACACCGCAGGCGGTTTGCCGCTGCAAGTGCCGGATGAGGTAACCGATCAGGCGGCGCTTCTGCATTTCTACCAAAACTGGCAACCGCAGTGGACGCCGGGCGCAAAACGCCTGTACGCCAACGCCAGTATCGGTTTATTCGGCATGCTGGCGGTCAAGCCATCAGGGATGGATTTTGAACAGGCAATGACCTCACGCGTGTTCCAGCCGCTGGAACTCAATCACACCTGGATTAACGTCCCGGCAGCAGAGGAGAAGCATTACGCCTGGGGCTATCGTGACGGTAAACCGGTGCACGTTTCGCCCGGCATGCTTGATGCGGAATCTTACGGCGTCAAAACGACCATTGAAGATATGGCGAGCTGGGTTCGGGCCAATATGAATCCTGCGGGCGTTAAAGATGAAATGCTTAAGCAAGGAATCGAACTGGCACAGTCACGTTACTGGCGTATCGGGGAGATGTATCAGGGCTTAGGCTGGGAAATGCTGAACTGGCCGGTGAAAGCAAAAACCGTCGTCGACGGCAGCGATAACAAAATCGCACTGGCATCGCTGACGGCCGTCGAAGTGAATCCTCCCGCGCCCGCAGTTAAAGCCTCGTGGGTGCACAAGACGGGTTCAACCGGCGGATTTGGGAGCTACGTCGCCTTTATTCCTGAAAAGAACATCGGCATCGTGATGCTGGCGAATAAAAGCTATCCTAACCCTGCGCGTGTCGATGCGGCGTATCGTATCCTGGACACGTTGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"46202","NCBI_taxonomy_name":"Lelliottia amnigena","NCBI_taxonomy_id":"61646"}}}},"ARO_accession":"3007438","ARO_id":"46196","ARO_name":"LAQ-1","CARD_short_name":"LAQ-1","ARO_description":"LAQ-1 beta lactamase is a class C beta lactamase.","ARO_category":{"46199":{"category_aro_accession":"3007441","category_aro_cvterm_id":"46199","category_aro_name":"LAQ beta lactamase","category_aro_description":"LAQ is a class C beta lactamase.","category_aro_class_name":"AMR Gene Family"},"35927":{"category_aro_accession":"0000008","category_aro_cvterm_id":"35927","category_aro_name":"cefoxitin","category_aro_description":"Cefoxitin is a cephamycin antibiotic often grouped with the second generation cephalosporins. Cefoxitin is bactericidal and acts by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. Cefoxitin's 7-alpha-methoxy group and 3' leaving group make it a poor substrate for most beta-lactamases.","category_aro_class_name":"Antibiotic"},"35975":{"category_aro_accession":"0000058","category_aro_cvterm_id":"35975","category_aro_name":"cefazolin","category_aro_description":"Cefazolin, also known as cefazoline or cephazolin, is a first generation cephalosporin antibiotic. It is administered parenterally, and is active against a broad spectrum of bacteria.","category_aro_class_name":"Antibiotic"},"35976":{"category_aro_accession":"0000059","category_aro_cvterm_id":"35976","category_aro_name":"cefepime","category_aro_description":"Cefepime (INN) is a fourth-generation cephalosporin antibiotic developed in 1994. It contains an aminothiazolyl group that decreases its affinity with beta-lactamases. Cefepime shows high binding affinity with penicillin-binding proteins and has an extended spectrum of activity against Gram-positive and Gram-negative bacteria, with greater activity against both Gram-negative and Gram-positive organisms than third-generation agents.","category_aro_class_name":"Antibiotic"},"36976":{"category_aro_accession":"3000632","category_aro_cvterm_id":"36976","category_aro_name":"benzylpenicillin","category_aro_description":"Benzylpenicillin, commonly referred to as penicillin G, is effective against both Gram-positive and Gram-negative bacteria. It is unstable in acid.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5933":{"model_id":"5933","model_name":"WUS-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"440"}},"model_sequences":{"sequence":{"8652":{"protein_sequence":{"accession":"UPP01678.1","sequence":"MRQFLYTIALLTCSFIAHAQSERLKIEKLNDKMYVYTTYQEFNGVQYSSNALYVVTDDGVLLIDTPWDKEQYEPLVNHIKQAHNKEIKWVITTHFHEDRSGGLDYFNKAGAQTYTFVQTNEMLKERNEPQAQHTFDKERHFTFGNDKLTVYFLGEGHTKDNTVVWFPQEKILYGGCLIKSAEATSIGNIADANVNAWPKTIKAVKRKFKKVKSIIPGHDQWNLSGHIENTERILEEYHRDNLNKNN"},"dna_sequence":{"accession":"OL872181.1","fmin":"0","fmax":"741","strand":"+","sequence":"ATGCGTCAATTTCTTTACACTATCGCCTTGCTAACATGCTCATTTATTGCACATGCCCAATCCGAAAGACTAAAGATCGAAAAGTTAAATGACAAAATGTATGTCTACACTACCTATCAAGAGTTTAATGGTGTACAATACTCCTCTAACGCCTTATATGTAGTAACTGACGATGGAGTATTGCTCATCGACACCCCTTGGGATAAAGAGCAATATGAACCTTTAGTAAATCACATCAAGCAAGCACACAACAAAGAGATTAAATGGGTAATCACTACCCACTTTCACGAAGATCGATCGGGAGGGTTAGATTACTTTAATAAAGCTGGAGCTCAAACGTATACCTTTGTACAAACTAATGAGATGCTAAAAGAGCGCAATGAACCTCAAGCACAACACACTTTTGATAAAGAAAGACACTTTACCTTCGGCAATGATAAACTAACGGTTTATTTCTTAGGTGAAGGTCACACAAAAGACAATACTGTCGTGTGGTTTCCACAAGAAAAAATACTGTATGGAGGTTGTCTGATTAAGAGTGCTGAAGCTACAAGTATTGGAAATATAGCGGATGCAAATGTAAATGCCTGGCCTAAAACCATTAAAGCGGTAAAACGCAAATTTAAAAAGGTGAAATCTATCATCCCAGGACACGATCAATGGAATCTGTCAGGACATATAGAGAATACCGAGCGTATCTTAGAGGAATACCATCGAGATAATTTAAATAAAAACAATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"46201","NCBI_taxonomy_name":"Myroides albus","NCBI_taxonomy_id":"2562892"}}}},"ARO_accession":"3007435","ARO_id":"46193","ARO_name":"WUS-1","CARD_short_name":"WUS-1","ARO_description":"WUS-1 is a WUS beta-lactamase.","ARO_category":{"46198":{"category_aro_accession":"3007440","category_aro_cvterm_id":"46198","category_aro_name":"WUS beta-lactamase","category_aro_description":"WUS is a family of the metallo-beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35961":{"category_aro_accession":"0000043","category_aro_cvterm_id":"35961","category_aro_name":"carbenicillin","category_aro_description":"Carbenicillin is a semi-synthetic antibiotic belonging to the carboxypenicillin subgroup of the penicillins. It has gram-negative coverage which includes Pseudomonas aeruginosa but limited gram-positive coverage. The carboxypenicillins are susceptible to degradation by beta-lactamase enzymes. Carbenicillin antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Antibiotic"},"36309":{"category_aro_accession":"3000170","category_aro_cvterm_id":"36309","category_aro_name":"imipenem","category_aro_description":"Imipenem is a broad-spectrum antibiotic and is usually taken with cilastatin, which prevents hydrolysis of imipenem by renal dehydropeptidase-I. It is resistant to hydrolysis by most other beta-lactamases. Notable exceptions are the KPC beta-lactamases and Ambler Class B enzymes.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5934":{"model_id":"5934","model_name":"SSA","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"8653":{"protein_sequence":{"accession":"CBI71171.1","sequence":"MKRIFPAYILLTAFLLACSSNATTQNANQSNKPAAAQEAKADDKQNRELQKQIEQIASAARGRVGVHAVVLETGESVSLDEQGRFPMQSVYKFPIGMAVLAQVDAGKLKLDERVRVEKSEYVREGMHSPLRDKNPNEAEVSVRELLRLAVSESDGTASDVLFRLAGGSEAITRYLSDLKVTEIIVADTEKEIGQDWDTQYRNWASPKGAVMLLRAFHEGRGLSAESRALLLKLMTDTPTGPKRLKGLLPKGTVVAHKTGTSGANASGISAATNDIGIVTLPNGRHLAIAVFVSDSPADLTTREGVIAKVAKAAWDQWGK"},"dna_sequence":{"accession":"FN640464.1","fmin":"1522","fmax":"2482","strand":"-","sequence":"ATGAAAAGAATATTTCCGGCTTACATTCTGCTTACAGCTTTCCTACTGGCCTGCTCCAGCAACGCCACGACTCAAAATGCTAATCAATCAAACAAGCCCGCCGCTGCTCAGGAAGCAAAGGCGGATGATAAGCAGAACCGCGAGCTGCAAAAACAGATAGAGCAGATAGCTTCAGCGGCACGCGGGCGCGTGGGCGTTCATGCGGTCGTGCTGGAAACGGGTGAATCCGTCTCCCTGGATGAGCAGGGCCGATTTCCTATGCAGAGCGTTTATAAGTTCCCGATTGGCATGGCTGTACTCGCGCAAGTAGATGCCGGAAAGCTAAAGCTTGACGAGCGCGTGCGCGTTGAAAAGAGCGAATACGTTAGAGAGGGCATGCACAGCCCCTTGCGAGACAAAAATCCGAACGAAGCTGAGGTGAGCGTGCGCGAGTTGCTGCGATTAGCTGTCTCTGAATCGGACGGTACGGCGAGCGATGTGCTGTTCAGACTGGCGGGCGGCAGCGAAGCAATCACCAGATACCTCAGCGACCTTAAGGTCACAGAGATTATCGTAGCCGACACGGAGAAAGAGATAGGGCAGGACTGGGACACTCAGTATCGCAACTGGGCTTCGCCCAAGGGAGCAGTTATGCTTCTACGCGCATTCCATGAGGGGCGCGGGCTCTCCGCAGAGAGCAGGGCGCTCTTGCTGAAATTGATGACTGACACCCCTACCGGACCGAAAAGGCTGAAAGGACTTTTGCCTAAGGGCACAGTCGTCGCGCACAAGACCGGAACATCTGGAGCAAACGCTAGCGGCATCAGCGCCGCGACCAACGATATAGGAATAGTGACGCTGCCGAACGGTCGCCATCTGGCCATAGCCGTTTTCGTTTCCGATTCTCCGGCCGATCTAACCACGCGCGAGGGCGTGATTGCCAAAGTCGCTAAGGCTGCGTGGGACCAGTGGGGAAAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36791","NCBI_taxonomy_name":"uncultured bacterium","NCBI_taxonomy_id":"77133"}}}},"ARO_accession":"3007442","ARO_id":"46200","ARO_name":"SSA","CARD_short_name":"SSA","ARO_description":"SSA is an SSA beta lactamase.","ARO_category":{"46197":{"category_aro_accession":"3007439","category_aro_cvterm_id":"46197","category_aro_name":"SSA beta-lactamase","category_aro_description":"SSA beta-lactamases are a family of Class A beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35927":{"category_aro_accession":"0000008","category_aro_cvterm_id":"35927","category_aro_name":"cefoxitin","category_aro_description":"Cefoxitin is a cephamycin antibiotic often grouped with the second generation cephalosporins. Cefoxitin is bactericidal and acts by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. Cefoxitin's 7-alpha-methoxy group and 3' leaving group make it a poor substrate for most beta-lactamases.","category_aro_class_name":"Antibiotic"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"35981":{"category_aro_accession":"0000064","category_aro_cvterm_id":"35981","category_aro_name":"amoxicillin","category_aro_description":"Amoxicillin is a moderate-spectrum, bacteriolytic, beta-lactam antibiotic used to treat bacterial infections caused by susceptible microorganisms. A derivative of penicillin, it has a wider range of treatment but remains relatively ineffective against Gram-negative bacteria. It is commonly taken with clavulanic acid, a beta-lactamase inhibitor. Like other beta-lactams, amoxicillin interferes with the synthesis of peptidoglycan.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5935":{"model_id":"5935","model_name":"NDM-44","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8657":{"protein_sequence":{"accession":"UVJ50740.1","sequence":"MELPNIMHPVAKLSTALAAALMLSGCMPGEIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMANKLR"},"dna_sequence":{"accession":"OP288001.1","fmin":"0","fmax":"813","strand":"+","sequence":"ATGGAATTGCCCAATATTATGCACCCGGTCGCGAAGCTGAGCACCGCATTAGCCGCTGCATTGATGCTGAGCGGGTGCATGCCCGGTGAAATCCGCCCGACGATTGGCCAGCAAATGGAAACTGGCGACCAACGGTTTGGCGATCTGGTTTTCCGCCAGCTCGCACCGAATGTCTGGCAGCACACTTCCTATCTCGACATGCCGGGTTTCGGGGCAGTCGCTTCCAACGGTTTGATCGTCAGGGATGGCGGCCGCGTGCTGGTGGTCGATACCGCCTGGACCGATGACCAGACCGCCCAGATCCTCAACTGGATCAAGCAGGAGATCAACCTGCCGGTCGCGCTGGCGGTGGTGACTCACGCGCATCAGGACAAGATGGGCGGTATGGACGCGCTGCATGCGGCGGGGATTGCGACTTATGCCAATGCGTTGTCGAACCAGCTTGCCCCGCAAGAGGGGATGGTTGCGGCGCAACACAGCCTGACTTTCGCCGCCAATGGCTGGGTCGAACCAGCAACCGCGCCCAACTTTGGCCCGCTCAAGGTATTTTACCCCGGCCCCGGCCACACCAGTGACAATATCACCGTTGGGATCGACGGCACCGACATCGCTTTTGGTGGCTGCCTGATCAAGGACAGCAAGGCCAAGTCGCTCGGCAATCTCGGTGATGCCGACACTGAGCACTACGCCGCGTCAGCGCGCGCGTTTGGTGCGGCGTTCCCCAAGGCCAGCATGATCGTGATGAGCCATTCCGCCCCCGATAGCCGCGCCGCAATCACTCATACGGCCCGCATGGCCAACAAGCTGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3007443","ARO_id":"46204","ARO_name":"NDM-44","CARD_short_name":"NDM-44","ARO_description":"NDM-44 is a subclass B1 NDM metallo-beta-lactamase.","ARO_category":{"36196":{"category_aro_accession":"3000057","category_aro_cvterm_id":"36196","category_aro_name":"NDM beta-lactamase","category_aro_description":"NDM beta-lactamases or New Delhi metallo-beta-lactamases are class B beta-lactamases that confer resistance to a broad range of antibiotics including carbapenems, cephalosporins and penicillins.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5936":{"model_id":"5936","model_name":"NDM-45","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8659":{"protein_sequence":{"accession":"UZC76856.1","sequence":"MELPNIMHPVAKLSTALAAALMLSGCMPGEIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLLVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMAALHAAGIATYANALSNQLAPQEGLVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR"},"dna_sequence":{"accession":"OP696898.1","fmin":"0","fmax":"813","strand":"+","sequence":"ATGGAATTGCCCAATATTATGCACCCGGTCGCGAAGCTGAGCACCGCATTAGCCGCTGCATTGATGCTGAGCGGGTGCATGCCCGGTGAAATCCGCCCGACGATTGGCCAGCAAATGGAAACTGGCGACCAACGGTTTGGCGATCTGGTTTTCCGCCAGCTCGCACCGAATGTCTGGCAGCACACTTCCTATCTCGACATGCCGGGTTTCGGGGCAGTCGCTTCCAACGGTTTGATCGTCAGGGATGGCGGCCGCGTGCTGTTGGTCGATACCGCCTGGACCGATGACCAGACCGCCCAGATCCTCAACTGGATCAAGCAGGAGATCAACCTGCCGGTCGCGCTGGCGGTGGTGACTCACGCGCATCAGGACAAGATGGGCGGTATGGCCGCGCTGCATGCGGCGGGGATTGCGACTTATGCCAATGCGTTGTCGAACCAGCTTGCCCCGCAAGAGGGGCTGGTTGCGGCGCAACACAGCCTGACTTTCGCCGCCAATGGCTGGGTCGAACCAGCAACCGCGCCCAACTTTGGCCCGCTCAAGGTATTTTACCCCGGCCCCGGCCACACCAGTGACAATATCACCGTTGGGATCGACGGCACCGACATCGCTTTTGGTGGCTGCCTGATCAAGGACAGCAAGGCCAAGTCGCTCGGCAATCTCGGTGATGCCGACACTGAGCACTACGCCGCGTCAGCGCGCGCGTTTGGTGCGGCGTTCCCCAAGGCCAGCATGATCGTGATGAGCCATTCCGCCCCCGATAGCCGCGCCGCAATCACTCATACGGCCCGCATGGCCGACAAGCTGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3007444","ARO_id":"46205","ARO_name":"NDM-45","CARD_short_name":"NDM-45","ARO_description":"NDM-45 is a NDM class B metallo beta-lactamase.","ARO_category":{"36196":{"category_aro_accession":"3000057","category_aro_cvterm_id":"36196","category_aro_name":"NDM beta-lactamase","category_aro_description":"NDM beta-lactamases or New Delhi metallo-beta-lactamases are class B beta-lactamases that confer resistance to a broad range of antibiotics including carbapenems, cephalosporins and penicillins.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5937":{"model_id":"5937","model_name":"KPC-100","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"480"}},"model_sequences":{"sequence":{"8658":{"protein_sequence":{"accession":"URC16703.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGMANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"ON521726.1","fmin":"31","fmax":"913","strand":"-","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCATGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3007446","ARO_id":"46207","ARO_name":"KPC-100","CARD_short_name":"KPC-100","ARO_description":"KPC-100 is an inhibitor-resistant carbapenem-hydrolyzing KPC beta-lactamase.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5938":{"model_id":"5938","model_name":"NDM-46","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8660":{"protein_sequence":{"accession":"UZC76857.1","sequence":"MELPNIMHPVAKLSTALVAALMLSGCMPGEIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLLVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGLVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR"},"dna_sequence":{"accession":"OP696899.1","fmin":"0","fmax":"813","strand":"+","sequence":"ATGGAATTGCCCAATATTATGCACCCGGTCGCGAAGCTGAGCACCGCATTAGTCGCTGCATTGATGCTGAGCGGGTGCATGCCCGGTGAAATCCGCCCGACGATTGGCCAGCAAATGGAAACTGGCGACCAACGGTTTGGCGATCTGGTTTTCCGCCAGCTCGCACCGAATGTCTGGCAGCACACTTCCTATCTCGACATGCCGGGTTTCGGGGCAGTCGCTTCCAACGGTTTGATCGTCAGGGATGGCGGCCGCGTGCTGTTGGTCGATACCGCCTGGACCGATGACCAGACCGCCCAGATCCTCAACTGGATCAAGCAGGAGATCAACCTGCCGGTCGCGCTGGCGGTGGTGACTCACGCGCATCAGGACAAGATGGGCGGTATGGACGCGCTGCATGCGGCGGGGATTGCGACTTATGCCAATGCGTTGTCGAACCAGCTTGCCCCGCAAGAGGGGCTGGTTGCGGCGCAACACAGCCTGACTTTCGCCGCCAATGGCTGGGTCGAACCAGCAACCGCGCCCAACTTTGGCCCGCTCAAGGTATTTTACCCCGGCCCCGGCCACACCAGTGACAATATCACCGTTGGGATCGACGGCACCGACATCGCTTTTGGTGGCTGCCTGATCAAGGACAGCAAGGCCAAGTCGCTCGGCAATCTCGGTGATGCCGACACTGAGCACTACGCCGCGTCAGCGCGCGCGTTTGGTGCGGCGTTCCCCAAGGCCAGCATGATCGTGATGAGCCATTCCGCCCCCGATAGCCGCGCCGCAATCACTCATACGGCCCGCATGGCCGACAAGCTGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3007445","ARO_id":"46206","ARO_name":"NDM-46","CARD_short_name":"NDM-46","ARO_description":"NDM-46 is an NDM metallo-beta-lactamase.","ARO_category":{"36196":{"category_aro_accession":"3000057","category_aro_cvterm_id":"36196","category_aro_name":"NDM beta-lactamase","category_aro_description":"NDM beta-lactamases or New Delhi metallo-beta-lactamases are class B beta-lactamases that confer resistance to a broad range of antibiotics including carbapenems, cephalosporins and penicillins.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5939":{"model_id":"5939","model_name":"NDM-47","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8662":{"protein_sequence":{"accession":"UZC76858.1","sequence":"MELPNIMHPVAKLSTALAAALMLSGCMPGEIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPLEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR"},"dna_sequence":{"accession":"OP696900.1","fmin":"0","fmax":"813","strand":"+","sequence":"ATGGAATTGCCCAATATTATGCACCCGGTCGCGAAGCTGAGCACCGCATTAGCCGCTGCATTGATGCTGAGCGGGTGCATGCCCGGTGAAATCCGCCCGACGATTGGCCAGCAAATGGAAACTGGCGACCAACGGTTTGGCGATCTGGTTTTCCGCCAGCTCGCACCGAATGTCTGGCAGCACACTTCCTATCTCGACATGCCGGGTTTCGGGGCAGTCGCTTCCAACGGTTTGATCGTCAGGGATGGCGGCCGCGTGCTGGTGGTCGATACCGCCTGGACCGATGACCAGACCGCCCAGATCCTCAACTGGATCAAGCAGGAGATCAACCTGCCGGTCGCGCTGGCGGTGGTGACTCACGCGCATCAGGACAAGATGGGCGGTATGGACGCGCTGCATGCGGCGGGGATTGCGACTTATGCCAATGCGTTGTCGAACCAGCTTGCCCCGCTAGAGGGGATGGTTGCGGCGCAACACAGCCTGACTTTCGCCGCCAATGGCTGGGTCGAACCAGCAACCGCGCCCAACTTTGGCCCGCTCAAGGTATTTTACCCCGGCCCCGGCCACACCAGTGACAATATCACCGTTGGGATCGACGGCACCGACATCGCTTTTGGTGGCTGCCTGATCAAGGACAGCAAGGCCAAGTCGCTCGGCAATCTCGGTGATGCCGACACTGAGCACTACGCCGCGTCAGCGCGCGCGTTTGGTGCGGCGTTCCCCAAGGCCAGCATGATCGTGATGAGCCATTCCGCCCCCGATAGCCGCGCCGCAATCACTCATACGGCCCGCATGGCCGACAAGCTGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3007447","ARO_id":"46208","ARO_name":"NDM-47","CARD_short_name":"NDM-47","ARO_description":"NDM-47 is a NDM metallo-beta-lactamase.","ARO_category":{"36196":{"category_aro_accession":"3000057","category_aro_cvterm_id":"36196","category_aro_name":"NDM beta-lactamase","category_aro_description":"NDM beta-lactamases or New Delhi metallo-beta-lactamases are class B beta-lactamases that confer resistance to a broad range of antibiotics including carbapenems, cephalosporins and penicillins.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5941":{"model_id":"5941","model_name":"KPC-97","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8663":{"protein_sequence":{"accession":"UAY85937.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVNSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"OK086971.1","fmin":"0","fmax":"897","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCAACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3007449","ARO_id":"46210","ARO_name":"KPC-97","CARD_short_name":"KPC-97","ARO_description":"KPC-97 is a KPC class A beta-lactamase.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5942":{"model_id":"5942","model_name":"KPC-98","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8664":{"protein_sequence":{"accession":"UAZ57792.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDHWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKYSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"MZ893466.1","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCACTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGTACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3007450","ARO_id":"46211","ARO_name":"KPC-98","CARD_short_name":"KPC-98","ARO_description":"KPC-98 is a KPC beta-lactamase.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5940":{"model_id":"5940","model_name":"TEM-246","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"475"}},"model_sequences":{"sequence":{"8661":{"protein_sequence":{"accession":"ULU82601.1","sequence":"MSIQHFRVALIPFFAAFCLHVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAWQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"OM617738.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCATGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCTGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36806","NCBI_taxonomy_name":"Neisseria gonorrhoeae","NCBI_taxonomy_id":"485"}}}},"ARO_accession":"3007448","ARO_id":"46209","ARO_name":"TEM-246","CARD_short_name":"TEM-246","ARO_description":"TEM-246 is a class A TEM beta-lactamase found in Neisseria gonorrhoeae.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5944":{"model_id":"5944","model_name":"TEM-244","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8666":{"protein_sequence":{"accession":"QWY17601.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPATLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"MZ026156.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGCAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3007453","ARO_id":"46215","ARO_name":"TEM-244","CARD_short_name":"TEM-244","ARO_description":"TEM-244 is a TEM beta-lactamase.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5945":{"model_id":"5945","model_name":"KPC-99","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"498"}},"model_sequences":{"sequence":{"8667":{"protein_sequence":{"accession":"UBJ91320.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDSWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"OK086803.1","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACAGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3007452","ARO_id":"46214","ARO_name":"KPC-99","CARD_short_name":"KPC-99","ARO_description":"KPC-99 is a KPC class A beta-lactamase.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5946":{"model_id":"5946","model_name":"TEM-245","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"475"}},"model_sequences":{"sequence":{"8668":{"protein_sequence":{"accession":"ULU82600.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWESELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"OM617737.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAATCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36806","NCBI_taxonomy_name":"Neisseria gonorrhoeae","NCBI_taxonomy_id":"485"}}}},"ARO_accession":"3007454","ARO_id":"46216","ARO_name":"TEM-245","CARD_short_name":"TEM-245","ARO_description":"TEM-245 is a TEM class A beta-lactamase.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5947":{"model_id":"5947","model_name":"dfrL","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"200"}},"model_sequences":{"sequence":{"8669":{"protein_sequence":{"accession":"CAC8536249.1","sequence":"MGENIEGRCCQELRKPYMTFVWAEDSNGLIGSSGDLPWNLPLDMKHFKNVTMDDVVVMGRKTYESIPVRPLKNRINIVLTNNKSYVADGAIVCHSKEDVLNYLKENKIEKPIHVIGGISAFEMFKDEVNILHRTIIDETFEGDTYMPEIDYKYFRCIDIADGVVDEKNKYPHRFLVYERKKFIDLMDYGGLLE"},"dna_sequence":{"accession":"CAIIKR010000012.1","fmin":"2869","fmax":"3451","strand":"+","sequence":"ATGGGTGAGAATATAGAAGGTCGATGTTGTCAGGAGTTGAGGAAGCCGTATATGACTTTTGTTTGGGCTGAAGATAGTAATGGCTTAATTGGAAGTTCAGGTGATCTGCCTTGGAATTTACCATTAGATATGAAGCATTTTAAAAACGTAACGATGGATGACGTCGTGGTTATGGGAAGAAAAACATACGAAAGTATCCCAGTACGTCCGCTGAAAAATCGTATCAATATCGTTTTAACAAACAATAAATCCTATGTAGCTGATGGTGCTATTGTGTGTCATAGTAAAGAAGATGTGTTAAATTATTTAAAGGAAAACAAGATTGAAAAACCGATTCATGTCATTGGGGGAATCTCAGCTTTTGAGATGTTCAAAGACGAGGTAAACATCTTGCATCGAACAATTATCGATGAAACCTTTGAAGGTGACACGTACATGCCTGAAATTGACTATAAATATTTTCGTTGTATCGATATAGCAGACGGAGTTGTCGATGAAAAGAATAAATACCCTCATCGATTCTTAGTCTACGAACGCAAGAAATTTATCGACCTTATGGATTATGGTGGATTATTGGAATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35508","NCBI_taxonomy_name":"Staphylococcus aureus","NCBI_taxonomy_id":"1280"}}}},"ARO_accession":"3007456","ARO_id":"46219","ARO_name":"dfrL","CARD_short_name":"dfrL","ARO_description":"dfrL is a gene encoding a trimethoprim-resistant dihydrofolate reductase (DHFR) identified in Staphylococcus aureus.","ARO_category":{"37617":{"category_aro_accession":"3001218","category_aro_cvterm_id":"37617","category_aro_name":"trimethoprim resistant dihydrofolate reductase dfr","category_aro_description":"Alternative dihydropteroate synthase dfr present on plasmids produces alternate proteins that are less sensitive to trimethoprim from inhibiting its role in folate synthesis, thus conferring trimethoprim resistance.","category_aro_class_name":"AMR Gene Family"},"35958":{"category_aro_accession":"0000040","category_aro_cvterm_id":"35958","category_aro_name":"streptomycin","category_aro_description":"Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36476":{"category_aro_accession":"3000337","category_aro_cvterm_id":"36476","category_aro_name":"iclaprim","category_aro_description":"Iclaprim is a bactericidal compound that inhibits dihydrofolate reductase. It is used against clinically important Gram-positive pathogens, including methicillin-sensitive Staphylococcus aureus and methicillin-resistant S. aureus.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5948":{"model_id":"5948","model_name":"EstT","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"8670":{"protein_sequence":{"accession":"UXD71803.1","sequence":"MKKKLLWILILGLIIISCKQRKTEMKEKIIKTNGIELCTESFGNKKNPAILLVAGATVSMLYWDTEFCQQLSEKGFFVIRYDNRDVGKSTNYEPGSTPYDIVDLTNDAISILDGYKIDKAHFVGISLGGLISQIASIKFADRVNSLTLMSSGPWGDSDPTIPEMDTSILDFHSKAGTVNWTNEDSVVNYLIQGAELMSGKKQFDKQRSEKLIRAEFNRANNYISMFNHAASQGGGGEEYWNRLNEIKQPTLIIHGTDDKIWHYKNAGFLLEKIKGSNLITLEGTGHELHVDDWKSIIDGIEKHIND"},"dna_sequence":{"accession":"CP094932.1","fmin":"14993","fmax":"15914","strand":"+","sequence":"ATGAAAAAAAAACTACTTTGGATATTAATTTTAGGACTGATAATAATCAGTTGCAAACAAAGGAAAACAGAAATGAAAGAGAAAATAATTAAAACAAACGGCATTGAACTCTGTACGGAAAGTTTTGGAAATAAGAAAAATCCAGCAATCCTTTTGGTAGCAGGTGCAACCGTATCAATGCTGTATTGGGACACTGAATTTTGCCAACAATTATCTGAAAAAGGATTTTTTGTTATTCGTTACGACAACAGAGATGTAGGAAAATCCACTAATTATGAACCAGGTTCTACTCCATACGATATTGTTGACTTAACTAATGACGCTATTTCAATATTGGATGGCTACAAGATTGACAAAGCACATTTTGTGGGGATTTCTTTGGGCGGACTAATTTCTCAAATAGCATCAATAAAGTTTGCCGACAGAGTTAACTCCTTAACTCTTATGTCATCAGGCCCTTGGGGAGACTCAGACCCAACTATACCTGAAATGGACACGAGTATTTTAGATTTCCATAGTAAAGCAGGTACAGTCAATTGGACAAATGAAGACAGTGTGGTAAACTATTTAATTCAGGGTGCAGAATTAATGAGTGGCAAGAAACAATTTGACAAACAAAGAAGTGAAAAACTGATAAGAGCTGAGTTCAATAGAGCCAACAATTATATAAGTATGTTCAATCACGCTGCATCGCAAGGTGGTGGTGGTGAAGAATATTGGAACAGATTAAACGAAATCAAACAACCCACCTTAATTATCCACGGAACAGACGACAAAATTTGGCATTATAAGAATGCAGGTTTTTTACTAGAAAAAATAAAAGGTTCAAATCTAATCACCCTTGAAGGTACAGGACACGAATTACACGTTGATGATTGGAAATCAATAATTGATGGAATAGAAAAACACATAAATGACTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"46223","NCBI_taxonomy_name":"Sphingobacterium faecium","NCBI_taxonomy_id":"34087"}}}},"ARO_accession":"3007459","ARO_id":"46222","ARO_name":"EstT","CARD_short_name":"EstT","ARO_description":"EstT is a gene encoding for a serine-dependent macrolide alpha\/beta-hydrolase.","ARO_category":{"36459":{"category_aro_accession":"3000320","category_aro_cvterm_id":"36459","category_aro_name":"macrolide esterase","category_aro_description":"Hydrolytic enzymes that cleave the macrocycle lactone ring of macrolide antibiotics.","category_aro_class_name":"AMR Gene Family"},"46238":{"category_aro_accession":"3007472","category_aro_cvterm_id":"46238","category_aro_name":"tilmicosin","category_aro_description":"Tilmicosin is a macrolide antibiotic used for livestock and poultry synthesized from tylomycin. It is mainly used to treat common bacterial infections and diseases caused by mycoplasma infection in livestock and poultry breeding. Tilmicosin has broad-spectrum antibacterial properties and has a strong inhibitory effect on most Gram positive and negative bacteria.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5950":{"model_id":"5950","model_name":"IMP-96","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"380"}},"model_sequences":{"sequence":{"8672":{"protein_sequence":{"accession":"WP_186931965.1","sequence":"MKKLFVLCVCFLCSITAAGAALPDLKIEKLEEGVYVHTSFEEVNGWGVVSKHGLVVLVNTDAYLIDTPFTATDTEKLVNWFVERGYKIKGTISSHFHSDSTGGIEWLNSQSIPTYASELTNELLKKDGKVQAKNSFSGVSYWLVKNKIEVFYPGPGHTQDNVVVWLPEKKILFGGCFVKPDGLGNLGDANLEAWPKSAKILMSKYGKAKLVVSGHSEIGDASLLKRTWEQAVKGLNESKKPSQPSN"},"dna_sequence":{"accession":"NG_080776.1","fmin":"0","fmax":"741","strand":"+","sequence":"ATGAAGAAATTATTTGTTTTATGTGTATGCTTCCTTTGTAGCATTACTGCCGCAGGAGCGGCTTTGCCTGATTTAAAAATCGAGAAGCTTGAAGAAGGTGTTTATGTTCATACATCGTTCGAAGAAGTTAACGGTTGGGGTGTTGTTTCTAAACACGGTTTGGTGGTTCTTGTAAACACTGACGCCTATCTGATTGACACTCCATTTACTGCTACAGATACTGAAAAGTTAGTCAATTGGTTTGTGGAGCGCGGCTATAAAATCAAAGGCACTATTTCCTCACATTTCCATAGCGACAGCACAGGGGGAATAGAGTGGCTTAATTCTCAATCTATTCCCACGTATGCATCTGAATTAACAAATGAACTTCTTAAAAAAGACGGTAAGGTGCAAGCTAAAAACTCATTTAGCGGAGTTAGTTATTGGCTAGTTAAAAATAAAATTGAAGTTTTTTATCCCGGCCCGGGGCACACTCAAGATAACGTAGTGGTTTGGTTACCTGAAAAGAAAATTTTATTCGGTGGTTGTTTTGTTAAACCGGACGGTCTTGGTAATTTGGGTGACGCAAATTTAGAAGCTTGGCCAAAGTCCGCCAAAATATTAATGTCTAAATATGGTAAAGCAAAACTGGTTGTTTCAGGTCATAGTGAAATTGGGGACGCATCACTCTTGAAACGTACATGGGAACAGGCTGTTAAAGGGCTAAATGAAAGTAAAAAACCATCACAGCCAAGTAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"46226","NCBI_taxonomy_name":"Stenotrophomonas sp.","NCBI_taxonomy_id":"69392"}}}},"ARO_accession":"3007461","ARO_id":"46225","ARO_name":"IMP-96","CARD_short_name":"IMP-96","ARO_description":"IMP-96 is an IMP beta-lactamase.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5951":{"model_id":"5951","model_name":"IMP-92","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"350"}},"model_sequences":{"sequence":{"8673":{"protein_sequence":{"accession":"WP_240067720.1","sequence":"MKKIFVLFVFLFCSITAAGESLPDIKIEKLDEDVYVHTSFEKITGWGVITKHGLVVLVNTDAYIIDTPFTAKDTEKLVRWFVGRGYKIKGSISSHFHSDSAGGIEWLNSQSIPTYASKLTNELLKKNGNAQAVNSFSGVSYWLVKHKIEVFYPGPGHTQDNVVVWLPEKKILFGGCFIKPDGLGYLGDANLEAWPKSAETLMSKYGNAKLVVSSHSEIGGASLLKRTWEQAVKGLKESKNHHSPK"},"dna_sequence":{"accession":"NG_079227.1","fmin":"0","fmax":"738","strand":"+","sequence":"ATGAAAAAAATATTTGTGTTATTTGTATTTTTGTTTTGCAGTATTACTGCCGCCGGAGAGTCTTTGCCTGATATAAAAATTGAGAAACTTGACGAAGATGTTTATGTTCATACTTCTTTTGAAAAGATAACCGGCTGGGGTGTTATTACTAAACACGGCTTGGTGGTTCTTGTAAATACTGATGCCTATATAATTGACACTCCATTTACAGCTAAAGATACTGAAAAATTAGTCCGCTGGTTTGTGGGGCGTGGTTATAAAATCAAAGGCAGTATTTCCTCACATTTTCATAGCGATAGCGCAGGTGGAATTGAGTGGCTTAATTCTCAATCTATCCCCACATATGCATCTAAATTAACAAATGAGCTTCTTAAAAAGAACGGTAATGCGCAAGCCGTAAACTCATTTAGTGGCGTTAGCTATTGGCTAGTTAAACATAAAATTGAAGTTTTCTATCCAGGACCAGGGCACACTCAGGATAATGTAGTGGTTTGGTTGCCTGAAAAGAAAATTTTATTTGGCGGTTGTTTTATTAAGCCGGACGGTCTTGGTTATTTGGGAGACGCAAATCTAGAAGCATGGCCTAAGTCCGCAGAAACATTAATGTCTAAGTATGGTAATGCAAAACTGGTTGTTTCGAGTCATAGTGAAATTGGGGGCGCATCACTATTGAAGCGCACTTGGGAGCAGGCTGTTAAGGGGCTAAAAGAAAGTAAAAACCATCACAGCCCCAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3007462","ARO_id":"46227","ARO_name":"IMP-92","CARD_short_name":"IMP-92","ARO_description":"IMP-92 is an IMP beta-lactamase.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5952":{"model_id":"5952","model_name":"IMP-93","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"375"}},"model_sequences":{"sequence":{"8674":{"protein_sequence":{"accession":"WP_234855925.1","sequence":"MKKLFVLCIFLFCSITAAGESLPDLKIEKLEDGVYVHTSFEEVNGWGVFAKHGLVFLVNTDAYLIDTPFAAKDTEKLVNWFVERGYKIKGSISSHFHSDSSGGIEWLNSQSIPTYASELTNELLKKNGKVQAKNSFSGVSYWLLKNKIEIFYPGPGHTQDNVVVWLPEKKILFGGCFVKPYGLGNLDDANVEAWPHSAEILMSRYGNAKLVVPSHSDVGDASLLKLTWEQAVKGLKESKKPSQPSN"},"dna_sequence":{"accession":"NG_079228.1","fmin":"100","fmax":"841","strand":"+","sequence":"ATGAAAAAATTATTTGTTTTATGTATCTTTTTGTTTTGTAGCATTACTGCCGCAGGAGAGTCTTTGCCTGATTTAAAAATTGAGAAGCTTGAAGACGGTGTTTATGTTCATACATCGTTTGAAGAAGTTAACGGTTGGGGTGTTTTTGCTAAACACGGTTTGGTGTTTCTTGTAAACACAGACGCCTATCTGATTGACACTCCATTTGCTGCTAAAGACACTGAAAAGTTAGTAAATTGGTTTGTGGAGCGCGGTTATAAAATAAAAGGCAGTATTTCCTCACATTTTCATAGCGACAGCTCGGGTGGAATAGAATGGCTTAACTCTCAATCTATTCCCACGTATGCATCTGAATTAACAAACGAACTTCTTAAAAAGAACGGTAAGGTGCAAGCTAAAAACTCATTTAGCGGAGTTAGTTATTGGCTACTTAAAAATAAAATTGAAATTTTTTATCCGGGCCCTGGGCACACTCAAGATAACGTAGTGGTTTGGTTGCCTGAAAAGAAAATTTTATTTGGTGGGTGTTTTGTTAAACCGTACGGTCTTGGAAATCTCGATGATGCAAATGTTGAAGCGTGGCCACATTCTGCTGAAATATTAATGTCTAGGTATGGTAATGCAAAACTGGTTGTTCCAAGCCATAGTGACGTCGGAGATGCGTCGCTCTTGAAGCTTACATGGGAGCAGGCTGTTAAAGGGCTAAAAGAAAGTAAAAAACCATCACAGCCAAGTAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3007463","ARO_id":"46228","ARO_name":"IMP-93","CARD_short_name":"IMP-93","ARO_description":"IMP-93 is an IMP beta-lactamase.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5953":{"model_id":"5953","model_name":"IMP-94","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"360"}},"model_sequences":{"sequence":{"8675":{"protein_sequence":{"accession":"WP_240067721.1","sequence":"MSKLFIFFMFLFCSITAAAESLPDLKIERLDEGVYVHTSFEEVNGWGVVPKHGLVVLVNTEAYLIDTPFTAKDTEKLVTWFVGRGYKIKGSISSHFHSDSTGGIEWLNSQSIPTYASELTNELLKKDGKVQAKNSFGGVSYWLVKNKIEVFYPGPGHTPDNVVVWLPENRVLFGGCFVKPYGLGNLGDANLEAWPKSAKLLMSKYGKAKLVVPSHSEVGDASLLKRTLEHAVKGLNESKKPSKPSN"},"dna_sequence":{"accession":"NG_079229.1","fmin":"0","fmax":"741","strand":"+","sequence":"ATGAGCAAGTTATTTATATTCTTTATGTTTTTGTTTTGTAGCATTACTGCCGCAGCAGAGTCTTTGCCAGATTTAAAAATTGAGAGGCTTGATGAAGGCGTTTATGTTCATACTTCGTTTGAAGAAGTTAACGGTTGGGGTGTTGTTCCTAAACACGGCTTGGTGGTTCTTGTAAATACTGAGGCCTATCTGATTGACACTCCATTTACGGCTAAAGATACTGAAAAGTTAGTCACTTGGTTTGTGGGACGCGGCTATAAAATAAAAGGCAGTATTTCCTCTCATTTTCATAGCGACAGCACGGGCGGAATAGAGTGGCTTAATTCTCAATCTATCCCCACGTATGCATCTGAATTAACAAATGAACTTCTTAAAAAAGACGGTAAGGTACAAGCTAAAAATTCATTTGGCGGAGTTAGCTATTGGCTAGTTAAGAATAAGATTGAAGTTTTTTATCCTGGTCCAGGGCACACTCCAGATAACGTAGTGGTTTGGCTACCTGAAAATAGAGTTTTGTTCGGTGGTTGTTTTGTTAAACCGTACGGTCTTGGTAATTTGGGTGACGCAAATTTAGAAGCTTGGCCAAAGTCCGCCAAATTATTAATGTCCAAATATGGTAAGGCAAAACTGGTTGTTCCAAGTCACAGTGAAGTTGGAGACGCATCACTCTTGAAGCGAACATTAGAACATGCGGTTAAAGGGTTAAATGAAAGTAAAAAACCATCAAAACCAAGTAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36941","NCBI_taxonomy_name":"Achromobacter xylosoxidans","NCBI_taxonomy_id":"85698"}}}},"ARO_accession":"3007464","ARO_id":"46229","ARO_name":"IMP-94","CARD_short_name":"IMP-94","ARO_description":"IMP-94 is an IMP beta-lactamase.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5954":{"model_id":"5954","model_name":"IMP-95","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"360"}},"model_sequences":{"sequence":{"8676":{"protein_sequence":{"accession":"WP_242934067.1","sequence":"MKKLFVLCVCFFCSITAAGAALPDLKIEKLEEGVFVHTSYEEVKGWGVVTKHGLVVLIGADAYLIDTPFTAKDTEKLVNWFVERGYKIKGTVSSHFHSDSTGGIEWLNSQSIPTYASELTNELLKKDGKVQAKNSFDGVSYWLAKDKIEVFYPGPGHTQDNVVVWLPEKEILFGGCFVKPHGLGNLGDANLEAWPESAKILMEKYGKAKLVVSGHSETGDATHLKRTWEQAVKGLKESKKTLQPSN"},"dna_sequence":{"accession":"NG_079887.1","fmin":"0","fmax":"741","strand":"+","sequence":"ATGAAGAAATTATTTGTTTTATGTGTATGCTTCTTTTGTAGCATTACTGCCGCAGGAGCGGCTTTACCTGATTTAAAAATCGAGAAGCTTGAAGAAGGTGTTTTTGTTCATACATCGTATGAAGAAGTTAAAGGTTGGGGTGTTGTTACTAAACACGGTTTGGTGGTTCTCATAGGCGCTGACGCCTATCTGATTGATACTCCATTTACTGCTAAAGATACTGAAAAGTTAGTCAATTGGTTTGTGGAGCGCGGCTATAAAATAAAAGGCACTGTTTCCTCACATTTCCATAGCGACAGTACGGGGGGAATAGAGTGGCTTAACTCTCAGTCTATCCCCACGTATGCGTCTGAATTAACGAATGAACTTCTGAAAAAAGACGGTAAGGTTCAAGCCAAAAACTCATTTGACGGGGTTAGTTATTGGCTGGCGAAAGATAAAATAGAAGTGTTTTATCCTGGCCCTGGCCACACTCAAGACAACGTAGTAGTTTGGCTGCCTGAAAAGGAAATATTATTTGGCGGTTGCTTTGTTAAGCCTCACGGCCTTGGTAATTTGGGTGACGCAAATTTAGAGGCTTGGCCAGAGTCCGCCAAAATATTGATGGAAAAATATGGTAAAGCAAAGCTGGTTGTTTCAGGTCATAGCGAAACCGGAGACGCGACACACTTGAAGCGTACCTGGGAGCAGGCTGTTAAAGGACTTAAAGAAAGTAAAAAGACATTGCAGCCAAGCAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3007465","ARO_id":"46230","ARO_name":"IMP-95","CARD_short_name":"IMP-95","ARO_description":"IMP-95 is an IMP beta-lactamase.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5955":{"model_id":"5955","model_name":"IND-17","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"350"}},"model_sequences":{"sequence":{"8677":{"protein_sequence":{"accession":"QAT79362.1","sequence":"MRKSIRFLIISVLFLSQFVNAQVRDFVIEPPIKPNLYIYKTFGVFGGREYSTNAMYLVTKKGVVLFDVPWQKTQYQSLMDTIKKRHNLPIIAVFATHSHDDRAGDLSFYNNKGIKTYATVKTNELLKKEGKATSSEITKTGKPYRIGGEEFVVDFLGEGHTADNVVVWFPKYNILDGGCLVKSRNATDLGYTGEANVKQWPLTMAKLKSKYPGATMVVPGHDEWKGGGHVEHTLELLNENKK"},"dna_sequence":{"accession":"MK401904.1","fmin":"0","fmax":"729","strand":"+","sequence":"ATGAGAAAAAGTATTCGATTTTTAATTATTTCCGTTTTATTTTTAAGTCAGTTTGTTAATGCTCAGGTAAGAGATTTTGTGATCGAACCTCCCATTAAACCCAATCTGTATATTTACAAAACTTTTGGTGTATTTGGAGGCAGAGAATATTCTACCAATGCGATGTATCTAGTTACCAAAAAAGGAGTCGTTCTCTTTGATGTGCCTTGGCAGAAAACGCAATATCAAAGCCTGATGGATACTATAAAAAAACGCCATAACCTACCGATTATTGCTGTATTTGCAACACATTCGCATGATGATAGAGCGGGAGATTTAAGTTTTTACAATAATAAAGGAATTAAAACTTACGCAACTGTAAAAACCAATGAGCTATTGAAGAAAGAAGGAAAAGCTACATCAAGTGAGATCACAAAAACAGGAAAGCCTTATCGTATAGGAGGAGAAGAGTTTGTTGTAGATTTTCTTGGAGAAGGGCACACTGCAGATAATGTCGTGGTATGGTTTCCAAAATACAATATATTGGATGGTGGATGTCTTGTAAAAAGCAGAAATGCAACAGACTTGGGCTATACTGGTGAAGCCAATGTAAAGCAGTGGCCTTTGACAATGGCTAAACTAAAATCTAAATACCCTGGAGCAACGATGGTTGTTCCCGGACATGACGAATGGAAAGGTGGAGGTCATGTAGAACATACACTGGAACTTCTAAATGAAAATAAAAAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"46236","NCBI_taxonomy_name":"Chryseobacterium sp.","NCBI_taxonomy_id":"1871047"}}}},"ARO_accession":"3007470","ARO_id":"46235","ARO_name":"IND-17","CARD_short_name":"IND-17","ARO_description":"IND-17 is an IND beta-lactamase and confers resistance to ampicillin, nitrocefin, cefazolin, cefuroxime, ceftazidime, imipenem, meropenem in Chryseobacterium spp.","ARO_category":{"36199":{"category_aro_accession":"3000060","category_aro_cvterm_id":"36199","category_aro_name":"IND beta-lactamase","category_aro_description":"IND beta-lactamases are class B carbapenem-hydrolyzing beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5949":{"model_id":"5949","model_name":"IMP-91","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"375"}},"model_sequences":{"sequence":{"8671":{"protein_sequence":{"accession":"WP_079387329.1","sequence":"MKKLFVLCVFFFCNIAVAEESLPDLKIEKLEEGVYVHTSFEEAKGWSVVTKHGLVVLVKNDAYLIDTPITAKDTEKLVNWFVERGYKIKGSISTHFHGDSTAGIEWLNSQSIPTYASELTNELLKKDNKVQAKHSFNGVSYSLIKNKIEVFYPGPGHTQDNVVVWLPEKKILFGGCFVKPDGLGYLGDANLEAWPKSAKILMSKYGKAKLVVSSHSDIGDVSLLKRTWEQAVKGLNESKKSSQPSD"},"dna_sequence":{"accession":"NG_076634.1","fmin":"100","fmax":"841","strand":"+","sequence":"ATGAAAAAATTATTTGTTTTATGTGTATTCTTCTTCTGCAACATTGCAGTTGCAGAAGAATCTTTGCCTGATTTAAAAATTGAGAAGCTTGAAGAAGGCGTTTATGTTCATACTTCGTTTGAAGAAGCTAAAGGTTGGAGTGTGGTCACTAAACACGGTTTGGTGGTTCTTGTGAAAAATGACGCCTATCTGATTGATACTCCAATTACTGCTAAAGATACTGAAAAATTAGTCAATTGGTTTGTTGAGCGGGGCTATAAAATCAAAGGCAGTATTTCCACACATTTCCATGGTGACAGTACGGCTGGAATAGAGTGGCTTAATTCTCAATCTATCCCCACATATGCTTCTGAATTAACAAATGAACTTCTTAAAAAAGACAATAAGGTACAAGCTAAACACTCTTTTAATGGGGTTAGTTATTCACTAATTAAAAACAAAATTGAAGTTTTTTATCCAGGCCCAGGGCACACTCAAGATAACGTAGTGGTTTGGTTACCTGAAAAGAAAATTTTATTCGGTGGTTGCTTTGTTAAACCGGACGGTCTTGGCTATTTGGGGGACGCAAATTTAGAAGCTTGGCCAAAGTCCGCTAAAATATTAATGTCTAAATATGGTAAAGCAAAACTAGTTGTGTCGAGTCATAGTGATATTGGAGATGTATCACTCTTGAAACGTACATGGGAGCAGGCTGTTAAAGGGCTGAATGAAAGTAAAAAATCATCACAGCCAAGCGACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3007460","ARO_id":"46224","ARO_name":"IMP-91","CARD_short_name":"IMP-91","ARO_description":"IMP-91 is an IMP beta-lactamase.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3338":{"model_id":"3338","model_name":"AAC(6')-I-48","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"5449":{"protein_sequence":{"accession":"BAN78519.1","sequence":"MSKLGPTKPAPSMANTPVGNVVPCKTPDHPGWLELRLQLWPDGSTEEFLPEMAAACAEPDRFGQFLFLSPGGLAEGLVEVALRTDYVNGTESSPVAFLEGVFVVPASRGLGIARALVAAAEGWARDRGCTEFASDAEVSNVGSHAMHAALGFVETERVVFFRKVVAP"},"dna_sequence":{"accession":"AB472901.2","fmin":"1185","fmax":"1689","strand":"+","sequence":"ATGAGCAAGTTAGGTCCCACTAAACCTGCACCGAGCATGGCGAACACTCCGGTTGGAAACGTCGTGCCATGCAAGACGCCAGATCACCCTGGCTGGCTTGAGTTGCGCCTGCAGCTGTGGCCAGATGGCTCAACCGAGGAGTTCCTTCCCGAGATGGCTGCGGCCTGCGCTGAACCCGACCGCTTCGGCCAGTTTTTGTTCCTGTCGCCGGGCGGCTTGGCGGAGGGCCTGGTCGAGGTGGCGCTTCGCACGGACTACGTCAACGGCACCGAAAGCTCGCCAGTCGCCTTTCTCGAAGGCGTCTTCGTGGTGCCAGCGAGTCGAGGCCTTGGCATCGCCAGAGCGCTGGTGGCTGCGGCGGAAGGCTGGGCTAGAGATCGTGGCTGCACTGAGTTCGCCTCGGACGCCGAGGTCAGCAACGTTGGTAGTCACGCCATGCACGCCGCTCTTGGTTTCGTCGAAACTGAGCGCGTCGTGTTCTTCCGTAAGGTCGTGGCACCGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3004638","ARO_id":"42632","ARO_name":"AAC(6')-I-48","CARD_short_name":"AAC(6')-I-48","ARO_description":"AAC(6')-I-48 (AAC(6')-Iag) is an aminoglycoside acetyltransferase encoded by integrons in Pseudomonas aeruginosa.","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"A category of aminoglycoside N-acetyltransferase enzymes with modification regiospecificity based at the 6'-amino group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics through acetylation of the 6-amino group of the compound.","category_aro_class_name":"AMR Gene Family"},"35926":{"category_aro_accession":"0000007","category_aro_cvterm_id":"35926","category_aro_name":"dibekacin","category_aro_description":"Dibekacin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Dibekacin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35956":{"category_aro_accession":"0000038","category_aro_cvterm_id":"35956","category_aro_name":"netilmicin","category_aro_description":"Netilmicin is a member of the aminoglycoside family of antibiotics. These antibiotics have the ability to kill a wide variety of bacteria by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. Netilmicin is not absorbed from the gut and is therefore only given by injection or infusion. It is only used in the treatment of serious infections particularly those resistant to gentamicin.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"46128":{"category_aro_accession":"3007378","category_aro_cvterm_id":"46128","category_aro_name":"2'-N-ethylnetilmicin","category_aro_description":"2'-N-ethylnetilmicin is an aminoglycoside antibiotic and a derivative of netilmicin.","category_aro_class_name":"Antibiotic"},"46129":{"category_aro_accession":"3007379","category_aro_cvterm_id":"46129","category_aro_name":"5-episisomicin","category_aro_description":"5-episosomicin is a semisynthetic aminoglycoside antibiotic similar to sisomicin.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5957":{"model_id":"5957","model_name":"RAD-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"475"}},"model_sequences":{"sequence":{"8679":{"protein_sequence":{"accession":"UWS41116.1","sequence":"MKTKIVGTVILIFIEFISCHHNKSKNNWKSFFKDNNVNGTFVLKKLNSNETLIYNQERSDKKYTPASTFKILNSMIALQVLSVTDVNDTIQWDGIDRGYESWNKDQTMKSALPISCVWFYQELARRTGQKEMQKWLTKSNYGNKKIGSKIDKFWLDGTLAISANEQIVFLEKLINNKLPFDKNIQESVKKIMITDSTEHYIIHSKTGWGNNIGWNIGYIETKNNIWIFALNMDMNDIKMADIRKKITYNILKDQKIIQ"},"dna_sequence":{"accession":"CP104076.1","fmin":"214174","fmax":"214951","strand":"-","sequence":"ATGAAAACAAAAATAGTAGGCACAGTTATTTTGATTTTTATAGAATTCATTAGTTGCCATCACAATAAGAGTAAAAATAATTGGAAGTCTTTTTTTAAAGATAATAATGTAAACGGGACATTTGTACTAAAAAAGTTAAATTCAAATGAAACTCTAATTTACAATCAAGAGAGAAGTGATAAAAAATATACACCTGCTTCCACCTTTAAAATTCTAAACTCTATGATTGCATTACAGGTATTGTCTGTTACAGATGTAAATGACACAATTCAATGGGACGGAATAGACCGAGGATATGAATCTTGGAATAAAGATCAAACCATGAAATCCGCATTGCCTATTTCATGTGTATGGTTTTACCAAGAATTGGCTCGTAGAACGGGACAAAAAGAAATGCAAAAATGGCTTACAAAATCAAACTATGGGAATAAGAAAATTGGGAGTAAAATTGACAAATTTTGGCTTGATGGTACTCTTGCTATTTCGGCAAATGAACAAATTGTTTTTCTTGAAAAACTCATAAATAATAAATTACCATTTGATAAAAACATTCAAGAGAGCGTAAAAAAAATAATGATTACAGACTCTACAGAACATTATATCATTCACTCAAAAACAGGCTGGGGAAACAATATAGGCTGGAATATAGGTTATATAGAAACAAAAAATAATATTTGGATTTTTGCATTGAATATGGATATGAATGACATAAAAATGGCAGATATAAGAAAAAAAATAACTTATAACATTTTAAAAGATCAAAAAATAATTCAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36951","NCBI_taxonomy_name":"Riemerella anatipestifer","NCBI_taxonomy_id":"34085"}}}},"ARO_accession":"3007483","ARO_id":"46250","ARO_name":"RAD-1","CARD_short_name":"RAD-1","ARO_description":"RAD-1 is a class D RAD beta-lactamase found in Riemerella anatipestifer.","ARO_category":{"46249":{"category_aro_accession":"3007482","category_aro_cvterm_id":"46249","category_aro_name":"RAD beta-lactamase","category_aro_description":"RAD beta-lactamases are a class D beta-lactamase first identified in Riemerella anatipestifer.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5958":{"model_id":"5958","model_name":"dfrB10","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"150"}},"model_sequences":{"sequence":{"8680":{"protein_sequence":{"accession":"ALZ46148.1","sequence":"MDQSSNEVSTPVAGQFALPLRATFGLGDRVRKKSGAAWQGQVVGWYCTKLTPEGYAVESESHPGSVQIYPVAALERVA"},"dna_sequence":{"accession":"KU130294.1","fmin":"208177","fmax":"208414","strand":"-","sequence":"ATGGATCAAAGTAGCAATGAAGTCAGCACTCCAGTTGCTGGCCAGTTTGCGCTCCCATTGCGCGCCACGTTTGGCCTGGGAGATCGCGTACGCAAGAAATCTGGCGCCGCTTGGCAAGGTCAAGTTGTCGGCTGGTACTGCACAAAACTGACCCCTGAAGGCTATGCAGTCGAGTCCGAGTCTCACCCAGGCTCAGTACAGATTTATCCTGTGGCTGCGCTTGAACGCGTGGCCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36803","NCBI_taxonomy_name":"Pseudomonas putida","NCBI_taxonomy_id":"303"}}}},"ARO_accession":"3007489","ARO_id":"46256","ARO_name":"dfrB10","CARD_short_name":"dfrB10","ARO_description":"A dihydrofolate reductase and trimethoprim resistance gene found on a mega-plasmid (0.4 Mb) from a Pseudomonas putida strain.","ARO_category":{"37617":{"category_aro_accession":"3001218","category_aro_cvterm_id":"37617","category_aro_name":"trimethoprim resistant dihydrofolate reductase dfr","category_aro_description":"Alternative dihydropteroate synthase dfr present on plasmids produces alternate proteins that are less sensitive to trimethoprim from inhibiting its role in folate synthesis, thus conferring trimethoprim resistance.","category_aro_class_name":"AMR Gene Family"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5959":{"model_id":"5959","model_name":"dfrB11","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"150"}},"model_sequences":{"sequence":{"8681":{"protein_sequence":{"accession":"PKO69073.1","sequence":"MDQSSKEVGTPVVGQFALPSHATFGLGDRVRKKSGAAWQGQVVGWYCTKLTPEGYAVESESHPGSVQIYPVNALERVA"},"dna_sequence":{"accession":"PHCQ01000010.1","fmin":"114139","fmax":"114376","strand":"-","sequence":"ATGGATCAAAGTAGTAAAGAGGTTGGCACTCCCGTTGTTGGCCAGTTTGCACTCCCGTCGCACGCCACGTTTGGCCTTGGAGACCGCGTTCGCAAGAAATCGGGCGCCGCTTGGCAGGGTCAAGTTGTGGGCTGGTATTGCACAAAGCTGACCCCTGAAGGCTATGCCGTCGAGTCCGAGTCTCACCCAGGCTCGGTACAAATTTATCCAGTGAATGCGCTTGAACGCGTGGCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"46258","NCBI_taxonomy_name":"Betaproteobacteria bacterium HGW-Betaproteobacteria-16","NCBI_taxonomy_id":"2013707"}}}},"ARO_accession":"3007490","ARO_id":"46257","ARO_name":"dfrB11","CARD_short_name":"dfrB11","ARO_description":"A dihydrofolate reductase and trimethoprim resistance gene found in a groundwater sample at the Horonobe Underground Research laboratory in Japan in 2017, in a Betaproteobacteria sequence.","ARO_category":{"37617":{"category_aro_accession":"3001218","category_aro_cvterm_id":"37617","category_aro_name":"trimethoprim resistant dihydrofolate reductase dfr","category_aro_description":"Alternative dihydropteroate synthase dfr present on plasmids produces alternate proteins that are less sensitive to trimethoprim from inhibiting its role in folate synthesis, thus conferring trimethoprim resistance.","category_aro_class_name":"AMR Gene Family"},"36327":{"category_aro_accession":"3000188","category_aro_cvterm_id":"36327","category_aro_name":"trimethoprim","category_aro_description":"Trimethoprim is a synthetic 5-(3,4,5- trimethoxybenzyl) pyrimidine inhibitor of dihydrofolate reductase, inhibiting synthesis of tetrahydrofolic acid. Tetrahydrofolic acid is an essential precursor in the de novo synthesis of the DNA nucleotide thymidine. Trimethoprim is a bacteriostatic antibiotic mainly used in the prophylaxis and treatment of urinary tract infections in combination with sulfamethoxazole, a sulfonamide antibiotic.","category_aro_class_name":"Antibiotic"},"36310":{"category_aro_accession":"3000171","category_aro_cvterm_id":"36310","category_aro_name":"diaminopyrimidine antibiotic","category_aro_description":"Diaminopyrimidines are a class of organic compounds containing a pyrimidine ring substituted by two amine groups.  They are inhibitors of dihydrofolate reductase, an enzyme critical for DNA synthesis.","category_aro_class_name":"Drug Class"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5960":{"model_id":"5960","model_name":"Mycobacterium abscessus atpE with mutation conferring resistance to bedaquiline","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"12938":"A64P","12937":"D29A"},"Curated-R":{"12938":"A64P","12937":"D29A"},"clinical":{"12938":"A64P","12937":"D29A"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"100"}},"model_sequences":{"sequence":{"8682":{"protein_sequence":{"accession":"ABC24999.1","sequence":"MADPTIVAGALIGGGLIMAGGAIGAGIGDGIAGNALISGVARQPEAQGRLFTPFFITVGLVEAAYFINLAFMALFVFATPGAS"},"dna_sequence":{"accession":"DQ306899.1","fmin":"91","fmax":"343","strand":"+","sequence":"ATGGCGGACCCCACAATTGTTGCTGGTGCCCTCATCGGTGGTGGGTTGATCATGGCCGGAGGCGCCATCGGTGCCGGTATCGGTGACGGTATCGCCGGTAACGCTCTGATCTCCGGTGTGGCTCGTCAGCCCGAGGCTCAGGGCCGGCTGTTCACCCCGTTCTTCATCACCGTCGGTCTGGTTGAGGCTGCGTACTTCATCAACCTGGCCTTCATGGCGTTGTTCGTCTTCGCGACTCCCGGCGCCAGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36888","NCBI_taxonomy_name":"Mycobacteroides abscessus","NCBI_taxonomy_id":"36809"}}}},"ARO_accession":"3007476","ARO_id":"46243","ARO_name":"Mycobacterium abscessus atpE with mutation conferring resistance to bedaquiline","CARD_short_name":"Mabs_atpE_BDQ","ARO_description":"Mutations to the ATPase subunit C atpE gene, which is involved with the production of ATP, confer resistance to bedaquiline by altering the antibiotic's target.","ARO_category":{"46244":{"category_aro_accession":"3007477","category_aro_cvterm_id":"46244","category_aro_name":"antibiotic resistant ATP synthase","category_aro_description":"ATP synthase enzymes, specifically subunit C, resistant to diarylquinolone antibiotics including Bedaquiline. Mutations in ATP synthase confer antibiotic resistance by disrupting binding and blocking of ATP synthase reactions by Bedaquiline.","category_aro_class_name":"AMR Gene Family"},"41933":{"category_aro_accession":"3004492","category_aro_cvterm_id":"41933","category_aro_name":"bedaquiline","category_aro_description":"A diarylquinoline antibiotic drug sold under the brand name Sirturo, used to treat infection from Mycobacterium spp., particularly multidrug-resistant tuberculosis. Bedaquiline disrupts ATP synthase by proton pump blockage, inhibiting ATP synthesis.","category_aro_class_name":"Antibiotic"},"41932":{"category_aro_accession":"3004491","category_aro_cvterm_id":"41932","category_aro_name":"diarylquinoline antibiotic","category_aro_description":"A class of antibiotics used to treat specifically Mycobacterium tuberculosis infection; therefore, referred to as an antimycobacterial. Diarylquinoline antibiotics inhibit ATP synthesis in tuberculosis cells by disruption of mycobacterial ATP synthase.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5961":{"model_id":"5961","model_name":"Pseudomonas aeruginosa ampR with mutation conferring resistance to aztreonam","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"12939":"D135N","12940":"D135G"},"Curated-R":{"12939":"D135N","12940":"D135G"},"clinical":{"12939":"D135N","12940":"D135G"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8683":{"protein_sequence":{"accession":"P24734.3","sequence":"MVRPHLPLNALRAFEASARHLSFTRAAIELCVTQAAVSHQVKSLEERLGVALFKRLPRGLMLTHEGESLLPVLCDSFDRIAGLLERFEGGHYRDVLTVGAVGTFTVGWLLPRLEDFQARHPFIDLRLSTHNNRVDIAAEGLDYAIRFGGGAWHGTEALALFEAPLTVLCCPEVAAQLHSPADLLQHTLLRSYRADEWPLWFQAAGLPAHAPLTRSIVFDTSLAMLEAARQGVGVALAPAAMFARQLASESIRRPFATEVSTGSYWLTRLQSRGETSAMLAFRGWLLEMAAVEARGR"},"dna_sequence":{"accession":"AE004091.2","fmin":"4592989","fmax":"4593880","strand":"-","sequence":"TTGGTTCGACCCCATTTGCCGCTGAACGCCCTGCGCGCCTTCGAAGCTTCGGCCCGGCACCTGAGCTTCACCCGCGCGGCCATCGAGCTGTGCGTGACCCAGGCGGCGGTCAGCCACCAGGTGAAGAGCCTCGAGGAGCGTCTCGGCGTGGCCCTGTTCAAGCGTCTGCCGCGCGGCCTCATGCTGACCCACGAGGGCGAGAGCCTGCTGCCGGTGCTGTGTGACTCCTTCGACCGCATCGCCGGCCTGCTGGAACGTTTCGAGGGTGGCCACTACCGGGACGTGCTCACCGTCGGCGCGGTCGGAACCTTCACGGTCGGTTGGCTGCTGCCGCGGCTGGAGGACTTCCAGGCGCGCCATCCCTTCATCGATCTGCGCCTGTCCACCCACAACAACCGCGTCGACATCGCCGCCGAGGGGCTCGACTACGCGATCCGCTTCGGCGGCGGCGCCTGGCACGGCACCGAGGCGCTGGCGTTGTTCGAGGCGCCGCTGACGGTGCTCTGCTGCCCGGAGGTCGCCGCCCAGTTGCACAGTCCCGCCGACCTGCTGCAGCACACCCTGCTGCGCTCCTACCGCGCCGACGAGTGGCCGCTGTGGTTCCAGGCGGCCGGACTGCCGGCGCACGCGCCACTGACCCGGAGCATCGTCTTCGACACCTCGCTGGCCATGCTCGAGGCGGCCCGCCAGGGTGTCGGCGTGGCCCTGGCGCCGGCGGCGATGTTTGCCCGGCAACTGGCCAGCGAGAGCATCCGGCGTCCGTTCGCCACCGAAGTGAGTACCGGCAGCTACTGGCTGACGCGCTTGCAGTCGCGGGGGGAGACCAGCGCGATGCTGGCGTTCCGGGGGTGGTTGCTGGAGATGGCTGCCGTTGAGGCGCGGGGGAGATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36804","NCBI_taxonomy_name":"Pseudomonas aeruginosa PAO1","NCBI_taxonomy_id":"208964"}}}},"ARO_accession":"3007491","ARO_id":"46259","ARO_name":"Pseudomonas aeruginosa ampR with mutation conferring resistance to aztreonam","CARD_short_name":"Paer_ampR_ATM","ARO_description":"ampR is a regulatory gene that plays an essential role in regulating antibiotic resistance in P. aeruginosa. Mutation in ampR leads to its loss of control over blaPDC-16, allowing overexpression of blaPDC-16 and further resistance to aztreonam.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"46581":{"category_aro_accession":"3007797","category_aro_cvterm_id":"46581","category_aro_name":"ampR transcriptional regulator with mutation conferring resistance to monobactam antibiotics","category_aro_description":"ampR is a LysR-type transcriptional regulator for beta-lactamase-encoding gene expression. Mutations in ampR of certain organisms have been shown to confer resistance to antibiotics due to beta-lactamase overexpression.","category_aro_class_name":"AMR Gene Family"},"36689":{"category_aro_accession":"3000550","category_aro_cvterm_id":"36689","category_aro_name":"aztreonam","category_aro_description":"Aztreonam was the first monobactam discovered, and is greatly effective against Gram-negative bacteria while inactive against Gram-positive bacteria. Artreonam is a poor substrate for beta-lactamases, and may even act as an inhibitor. In Gram-negative bacteria, Aztreonam interferes with filamentation, inhibiting cell division and leading to cell death.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5967":{"model_id":"5967","model_name":"ANT(9)-Ic","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"8689":{"protein_sequence":{"accession":"QWQ57435.1","sequence":"MDRNHAAIPEEAAKALIVLQECLGSSLQALYLHGSAVNGGLRPNSDVDLLAVCDRNPAPETSALLVDRLMQISGRHPVAPGMPRCLEVMLFLRQDLAASRYPARCAFIYGEWLRDEFEAGIVPQAHTDPEYTLVLAQAGQEAISLVGPTREHLLPSVPQGDVRRAIADALPALIGNLAGDERNVLLTLARMWYTLETGTFVPKDAAAEWALPLVSPETAAALALAQAAYRGAAVDDWQSHPLLAGQAAEELAHQVRLLF"},"dna_sequence":{"accession":"MZ241296.1","fmin":"267","fmax":"1047","strand":"+","sequence":"ATGGATAGAAATCACGCAGCAATCCCCGAAGAAGCGGCAAAGGCCCTGATCGTCCTGCAGGAATGCCTGGGGTCATCCTTGCAGGCCCTATATCTGCATGGCTCCGCCGTGAATGGCGGCCTTCGCCCCAACAGCGACGTCGACCTGCTGGCGGTCTGTGACCGGAATCCGGCACCTGAAACCAGTGCGCTTCTCGTTGATCGGCTGATGCAGATATCGGGCCGGCACCCGGTCGCCCCGGGAATGCCCCGATGCCTGGAGGTGATGCTCTTTCTGCGGCAGGACCTCGCCGCATCTCGCTATCCTGCGCGGTGCGCCTTCATCTATGGAGAATGGCTGCGTGACGAATTCGAGGCCGGGATCGTGCCGCAGGCCCATACCGACCCTGAATATACACTGGTGCTCGCGCAAGCCGGCCAAGAAGCAATAAGCCTTGTCGGCCCCACGCGGGAGCATCTTCTGCCGTCCGTGCCGCAAGGAGACGTGCGACGGGCGATTGCCGATGCCTTGCCTGCCCTTATCGGCAACCTTGCAGGCGATGAGCGCAATGTCCTGCTGACGCTGGCGCGGATGTGGTACACGCTCGAAACCGGAACATTCGTGCCGAAGGACGCCGCCGCCGAATGGGCGCTGCCCCTTGTTTCCCCCGAAACCGCAGCAGCCCTTGCGCTCGCGCAGGCGGCCTATCGGGGCGCGGCTGTCGACGACTGGCAAAGCCATCCCCTGCTCGCAGGGCAGGCGGCTGAGGAACTGGCACATCAGGTGCGGCTGCTTTTCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"45773","NCBI_taxonomy_name":"Brucella intermedia","NCBI_taxonomy_id":"94625"}}}},"ARO_accession":"3007515","ARO_id":"46284","ARO_name":"ANT(9)-Ic","CARD_short_name":"ANT(9)-Ic","ARO_description":"ANT(9)-Ic encodes an intrinsic, chromosomal aminoglycoside nucleotidyltransferase in Brucella intermedia.","ARO_category":{"36367":{"category_aro_accession":"3000228","category_aro_cvterm_id":"36367","category_aro_name":"ANT(9)","category_aro_description":"A category of aminoglycoside O-nucleotidyltransferase enzymes with modification regiospecificity based at the 9-hydroxyl group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics, specifically streptomycin, by transfer of an AMP group from an ATP substrate to the 9-hydroxyl group of the compound.","category_aro_class_name":"AMR Gene Family"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3943":{"model_id":"3943","model_name":"MCR-3.41","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"6306":{"protein_sequence":{"accession":"MBA2799562.1","sequence":"MPSLIKIKIVPLMFFLALYFAFMLNWRGVLHFYEILYKLEDFKFGFAISLPILLVAALNFVFVPFSIRYLIKPFFALLIALSAIVSYTMMKYRVLFDQNMIQNIFETNQNEALAYLSLPIIGWVTIAGFIPAILLFFVEIEYEEKWFKGILTRTLSMFASLIVIAVIAALYYQDYVSVGRNNSNLQREIVPANFVNSTVKYVYNRYLAEPIPFTTLGDDAKRDTNQSKPTLMFLVVGETARGKNFSMNGYEKDTNPFTSKSGGVISFNDVRSCGTATAVSVPCMFSNMGRKEFDDNLARNSEGLLDVLQKTGVSIFWKENDGGCKGVCDRVPNIEIKPKDYPKFCDKNTCYDEVVLQELDSEIAQMKGDKLVGFHLIGSHGPTYYKRYPDAHRQFTPDCPRSDIENCTDEELTNTYDNTIRYTDFVIGEMIAKLKTYEDKYNTALLYVSDHGESLGALGLYLHGTPYKFAPDDQTRVPMQVWMSPGFITEKGMNMECLQKNAAANRYSHDNIFSSVLGIWDVKTAIYEQELDIFKQCRNN"},"dna_sequence":{"accession":"JACEGL010000001.1","fmin":"3105355","fmax":"3106978","strand":"-","sequence":"ATGCCTTCCCTTATAAAAATAAAAATTGTTCCGCTTATGTTCTTTTTGGCACTGTATTTTGCATTTATGCTGAACTGGCGTGGAGTTCTCCATTTTTACGAAATCCTTTACAAATTAGAAGATTTTAAGTTTGGTTTCGCCATTTCATTACCAATATTGCTTGTTGCAGCGCTTAACTTTGTATTTGTTCCATTTTCGATACGGTATTTAATAAAGCCTTTTTTTGCACTTCTTATCGCACTTAGTGCAATCGTTAGTTACACAATGATGAAGTATAGAGTCTTGTTTGATCAAAACATGATTCAGAATATTTTTGAAACCAATCAAAATGAGGCGTTAGCATATTTAAGCTTACCAATTATAGGATGGGTTACTATTGCTGGTTTTATCCCTGCCATTTTACTTTTCTTTGTTGAAATTGAATATGAGGAAAAATGGTTCAAAGGGATTCTAACTCGTACCCTATCGATGTTTGCATCACTTATAGTGATTGCGGTTATTGCAGCACTATACTATCAAGATTATGTGTCAGTGGGGCGCAACAATTCAAACCTCCAGCGTGAGATTGTTCCAGCCAATTTCGTTAATAGTACCGTTAAATACGTTTACAATCGTTATCTTGCTGAACCAATCCCATTTACAACTTTAGGTGATGATGCAAAACGGGATACTAATCAAAGTAAGCCCACGTTGATGTTTCTGGTCGTTGGTGAAACCGCTCGTGGTAAAAATTTCTCGATGAATGGCTATGAGAAAGACACCAATCCATTTACCAGTAAATCTGGTGGCGTGATCTCCTTTAATGATGTTCGTTCGTGTGGGACTGCAACCGCTGTATCTGTCCCCTGCATGTTTTCCAATATGGGGAGAAAGGAGTTTGATGATAATCTCGCTCGTAATAGCGAGGGTTTGTTAGATGTGTTGCAGAAAACGGGGGTCTCCATTTTTTGGAAGGAGAACGATGGCGGCTGCAAAGGCGTCTGCGACCGAGTTCCTAACATCGAGATCAAACCGAAGGATTACCCAAAGTTCTGCGATAAAAACACATGCTATGACGAGGTTGTCCTTCAAGAGCTCGACAGTGAAATTGCTCAAATGAAAGGGGATAAGCTGGTTGGCTTCCACCTGATAGGTAGCCATGGCCCAACCTACTACAAGCGCTACCCTGATGCTCATCGTCAGTTCACCCCTGACTGTCCACGCAGTGATATTGAAAACTGCACAGATGAAGAGCTCACCAACACCTATGACAACACCATCCGCTACACCGATTTCGTGATTGGAGAGATGATTGCCAAGTTGAAAACCTACGAAGATAAGTACAACACCGCGTTGCTCTACGTCTCCGATCATGGTGAATCACTGGGAGCATTAGGGCTTTACCTACACGGTACACCGTACAAGTTTGCACCGGATGATCAGACCCGTGTTCCTATGCAGGTGTGGATGTCACCTGGTTTCATCACAGAAAAAGGCATGAATATGGAATGTTTGCAGAAAAATGCCGCAGCCAATCGCTATTCTCATGACAACATATTTTCTTCTGTCCTGGGAATATGGGATGTGAAGACGGCTATCTACGAACAAGAATTAGATATCTTTAAGCAATGTCGGAATAATTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39677","NCBI_taxonomy_name":"Aeromonas veronii","NCBI_taxonomy_id":"654"}}}},"ARO_accession":"3005221","ARO_id":"43577","ARO_name":"MCR-3.41","CARD_short_name":"MCR-3.41","ARO_description":"Novel mcr-3.41 gene identified in an Aeromonas veronii C198 isolate from a patient with Septicemia in Thailand by Hatrongjit et. al.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2262":{"model_id":"2262","model_name":"mef(C)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"4640":{"protein_sequence":{"accession":"BAL43360.1","sequence":"MENRKWFKTYMFIWAGQFASMLTSYAVQFAIVIWLSLEYKSAEVLAYAGIAAMLPQALIGLIAGVYVDRLNRKYVMIFSDAFIALCALLLLVILQNENVNLIWIYILLGLRSVGNAFHAPALQAIAPLIVPQNELIKVAGINQVLHSVCRIGGPAIGTLAIAYLPISKVLYLDLIGALLAILSLVMVKIPNVVAKSKSSAHSIATEFSEGFQTVSKNKGLRYLFLYAMAITFVIMPAAIMFPLLTTGHFAGGKWEIGIVEVVWGGGMLIGGVILSIFKLKGSKVVAVNVMYVLLGLTFILSGVLPASWFVGFVMVTAIGGISLSVFNGCFTAIVQTEVSPEKLGRVFSLYYSLAVLPSVIGLLFTGLIAEVIGVNITFIISGCLAILVGILSFSTRNLMQLGKIKNI"},"dna_sequence":{"accession":"AB571865.1","fmin":"144312","fmax":"145536","strand":"-","sequence":"ATGGAAAACCGTAAATGGTTTAAGACCTATATGTTTATATGGGCTGGACAGTTTGCTTCAATGCTTACAAGTTATGCTGTTCAGTTTGCTATTGTTATATGGCTTAGTCTGGAGTACAAGTCAGCCGAAGTTTTAGCCTACGCAGGAATAGCAGCTATGTTGCCTCAAGCATTGATAGGCTTAATAGCAGGTGTATATGTTGACCGTCTCAATCGTAAATATGTAATGATTTTTTCGGATGCTTTTATAGCTCTCTGTGCCCTTTTGTTACTCGTCATTTTACAAAATGAAAATGTTAATCTTATATGGATATACATTTTATTGGGTTTACGCTCTGTTGGTAATGCTTTTCACGCTCCGGCACTACAGGCAATTGCTCCGCTGATTGTACCCCAAAATGAATTGATAAAGGTAGCAGGAATTAATCAGGTGTTACATTCGGTTTGCAGGATTGGTGGTCCTGCCATTGGCACATTAGCCATTGCTTATCTTCCTATTTCAAAAGTATTGTACTTGGATTTGATTGGAGCATTGCTGGCTATTCTTTCACTCGTGATGGTGAAAATTCCCAATGTGGTTGCGAAGTCAAAATCGTCTGCACATTCTATTGCTACAGAATTTTCGGAAGGGTTTCAGACTGTTTCAAAAAACAAAGGTTTGCGTTATCTTTTTCTTTATGCAATGGCGATAACCTTTGTTATAATGCCAGCTGCCATTATGTTTCCGTTGCTCACAACAGGGCATTTTGCAGGAGGAAAATGGGAGATAGGAATTGTAGAAGTGGTTTGGGGCGGAGGTATGCTTATTGGCGGTGTCATCCTGAGTATTTTCAAATTGAAAGGCTCAAAAGTAGTCGCAGTCAATGTTATGTATGTATTATTGGGACTTACATTTATTTTGAGTGGTGTATTACCTGCAAGTTGGTTTGTAGGATTTGTGATGGTAACAGCCATTGGCGGTATCAGCCTGTCTGTTTTCAATGGCTGTTTTACAGCAATTGTACAAACAGAGGTAAGTCCTGAAAAATTAGGACGTGTATTTTCACTTTATTATAGTTTGGCAGTTTTGCCAAGTGTAATCGGTTTATTATTCACAGGCCTGATTGCAGAAGTTATTGGTGTAAACATTACGTTTATCATAAGCGGTTGTTTGGCAATCCTTGTGGGTATTCTTTCGTTTAGCACTCGCAACTTAATGCAATTAGGTAAAATCAAAAATATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40398","NCBI_taxonomy_name":"Photobacterium damselae subsp. damselae","NCBI_taxonomy_id":"85581"}}}},"ARO_accession":"3003745","ARO_id":"40401","ARO_name":"mef(C)","CARD_short_name":"mef(C)","ARO_description":"mef(C) is a macrolide efflux gene isolated from a plasmid in Photobacterium damselae.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"37012":{"category_aro_accession":"3000668","category_aro_cvterm_id":"37012","category_aro_name":"oxytetracycline","category_aro_description":"Oxytetracycline is a derivative of tetracycline with a 5-hydroxyl group. Its activity is similar to other tetracyclines.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"1401":{"model_id":"1401","model_name":"mef(E)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"5490":{"protein_sequence":{"accession":"AAK99775.1","sequence":"MKIDKKNEAFLIVSRGISRIGDIMFDFANNTFLAGLNPTSLSLVAVYQSLESVIGVLFNLFGGVIADSFKRKKIIIVANILCGIACIILSFISQEQWMVFAIVITNIILAFMSAFSGPSYKAFTKEIVKKDSISQLNSLLEITSTIIKVTIPMVAILLYKLLGIHGVLLLDGFSFLIAASLISFIVPVNDEVVTKDKMTIGGVLNDLKIGFKYIYSHKTIFMIIILSAFVNFFLAAYNLLLPYSNQMFGEISDGLYGVFLTAEAIGGFIGAILSGVINKTLSSKRLMVFLSCSGLMLMLSTPLYFLFQNFIILAFSPALFSLFISIFNIQFFSIVQREVDTEFLGRVFGIIFTVAILFMPVGSGFFSVVLNPNNTFNLFIIGVSITILSLIFSTLLKRYDKNS"},"dna_sequence":{"accession":"AE007317.1","fmin":"953382","fmax":"954594","strand":"+","sequence":"TTGAAAATAGATAAAAAAAACGAGGCTTTCCTTATTGTAAGTAGAGGCATATCTCGAATTGGAGATATTATGTTTGACTTTGCGAATAATACCTTTCTTGCAGGATTAAATCCAACATCTTTATCATTGGTTGCAGTATATCAGTCACTAGAAAGTGTGATAGGTGTTCTTTTTAATTTATTTGGTGGAGTCATTGCAGATAGTTTCAAGCGGAAAAAAATTATTATTGTTGCAAATATCTTATGTGGTATTGCTTGTATAATTCTTTCATTCATATCACAAGAGCAGTGGATGGTCTTTGCAATTGTCATCACTAATATTATCTTGGCATTTATGAGTGCTTTTTCTGGACCGTCCTATAAAGCATTTACAAAAGAAATTGTAAAAAAGGATAGTATATCACAACTTAATTCATTGCTAGAGATAACAAGTACTATAATTAAAGTAACAATACCAATGGTAGCAATTTTATTATATAAGCTACTTGGGATACATGGTGTTTTACTATTGGATGGATTCTCATTTCTAATTGCTGCATCACTGATTTCCTTTATTGTACCCGTTAATGACGAAGTGGTCACAAAGGATAAAATGACAATAGGAGGAGTTTTAAATGACTTAAAAATAGGGTTTAAGTATATTTATAGTCATAAGACAATATTTATGATTATTATTCTCTCTGCTTTTGTTAATTTTTTTCTAGCAGCTTATAATTTATTGTTACCTTATAGTAATCAAATGTTTGGAGAAATTTCAGATGGGCTTTATGGTGTTTTTCTAACTGCGGAAGCAATTGGAGGATTTATTGGAGCGATATTAAGTGGTGTTATAAATAAAACCTTGTCAAGCAAACGTTTAATGGTCTTCTTATCATGTTCAGGATTGATGTTAATGCTATCAACGCCACTCTATTTTTTGTTTCAAAACTTCATTATTCTAGCCTTTTCTCCGGCATTATTTAGTCTATTTATTTCTATTTTTAATATTCAATTTTTCTCTATTGTTCAAAGAGAAGTTGATACTGAGTTTCTCGGTAGAGTCTTTGGAATCATCTTTACGGTAGCTATTCTTTTTATGCCAGTTGGGTCTGGATTTTTCTCAGTAGTTTTAAATCCTAACAATACTTTTAATCTTTTTATTATTGGTGTATCTATTACGATATTATCGCTAATATTCAGCACGCTATTGAAGAGGTATGATAAAAATAGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39596","NCBI_taxonomy_name":"Streptococcus pneumoniae R6","NCBI_taxonomy_id":"171101"}}}},"ARO_accession":"3000614","ARO_id":"36908","ARO_name":"mef(E)","CARD_short_name":"mef(E)","ARO_description":"mef(E) is a proton motive efflux pump in Streptococcus pneumoniae that confers resistance to macrolides. It is found on the same operon as mefA and the ABC-efflux pump mel.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"5745":{"model_id":"5745","model_name":"mef(F)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8299":{"protein_sequence":{"accession":"QNR09091.1","sequence":"MNNMNWKRKFIAIFTGQFFSLLSSAAVQFSIIWWLTDTSGGSPLILTLAGLAGFMPQALLGPFAGTITDRYSRKVIMIIADMTVALGSLALFVSMYFYDPSIILVIIVLIVRSLATAFHMPAMQASIPLIAPKEHLTKVSGWGQTVASISNIVGPAAGMSLLAISSVEWVLLLDVFGAVIASSILLFIHIPNVQSSETVDSSSFISDMKEGYHALVKHPVLLRLTVTITIVSVLYIPLGTYFPLMTRNHFEKGVVEAGIIEIVFAVGLIFGGILMGIFGDRFEKLKLIVSGMILMGIALFISGTLPSTLFYGFIVMAGLVGLSGPLFSAPFYALIQTEIEPHLLGRVFSFVGSLALLATPLGYAFAGVLIHLTNVAVLFLITGILIVLNAVIVRKAK"},"dna_sequence":{"accession":"CP046364.1","fmin":"31811","fmax":"33005","strand":"+","sequence":"ATGAATAATATGAATTGGAAACGGAAATTTATTGCGATTTTTACAGGGCAGTTCTTTTCACTATTAAGCAGTGCTGCTGTTCAATTTAGTATCATTTGGTGGTTAACAGATACATCAGGAGGTTCTCCACTGATTTTAACATTAGCAGGACTGGCTGGATTTATGCCACAAGCATTGTTAGGTCCTTTTGCAGGAACTATTACTGATCGTTATTCACGAAAAGTGATTATGATAATTGCAGATATGACGGTTGCACTTGGAAGTTTAGCTTTATTTGTATCAATGTATTTTTATGATCCGAGTATTATATTGGTGATAATTGTATTGATCGTTCGTTCATTAGCAACTGCATTCCATATGCCGGCTATGCAAGCGTCTATTCCACTAATAGCCCCAAAAGAGCATTTGACAAAAGTTTCTGGATGGGGACAGACAGTGGCTTCTATATCAAATATTGTTGGTCCAGCAGCGGGGATGTCATTACTAGCGATAAGCTCCGTTGAGTGGGTTCTATTACTAGATGTCTTTGGGGCAGTAATTGCTAGTAGTATTTTGCTATTTATTCACATTCCAAATGTACAGAGTTCAGAAACTGTTGATTCTTCTAGTTTTATCAGCGATATGAAAGAAGGATATCATGCACTTGTAAAACATCCTGTTTTATTAAGGTTAACAGTCACGATTACGATTGTTTCGGTGCTGTATATTCCGCTAGGCACTTACTTTCCGCTTATGACACGAAATCATTTCGAGAAGGGCGTAGTTGAAGCTGGAATAATCGAAATTGTTTTTGCTGTTGGCCTCATCTTTGGTGGTATATTAATGGGGATTTTCGGAGATCGATTTGAAAAATTGAAACTCATTGTTAGCGGAATGATACTGATGGGGATTGCCTTATTCATTTCTGGCACACTTCCATCAACTTTATTCTATGGATTTATCGTAATGGCTGGTCTAGTGGGATTGTCTGGTCCATTATTTTCAGCTCCGTTTTATGCTCTTATCCAAACCGAAATTGAACCTCATTTACTTGGGAGAGTGTTTAGTTTTGTTGGAAGTTTGGCATTACTTGCAACACCGTTGGGTTACGCATTTGCTGGGGTTCTGATCCACTTAACAAATGTGGCCGTATTATTTTTGATTACAGGTATATTAATTGTATTAAATGCTGTTATCGTAAGGAAAGCAAAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43299","NCBI_taxonomy_name":"Macrococcus canis","NCBI_taxonomy_id":"1855823"}}}},"ARO_accession":"3007044","ARO_id":"45603","ARO_name":"mef(F)","CARD_short_name":"mef(F)","ARO_description":"mef(F) is an mef efflux pump protein.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"36297":{"category_aro_accession":"3000158","category_aro_cvterm_id":"36297","category_aro_name":"azithromycin","category_aro_description":"Azithromycin is a 15-membered macrolide and falls under the subclass of azalide. Like other macrolides, azithromycin binds bacterial ribosomes to inhibit protein synthesis. The nitrogen substitution at the C-9a position prevents its degradation.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"5969":{"model_id":"5969","model_name":"Bacillus subtilis rpsE mutations conferring resistance to spectinomycin","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"13022":"C85G","13023":"A77T","13025":"G64C","13026":"G83C","13027":"G83A","13028":"C88G","13029":"G83T","13030":"G73T","13031":"A67G","13032":"G89C"},"Curated-R":{"13022":"C85G","13023":"A77T","13025":"G64C","13026":"G83C","13027":"G83A","13028":"C88G","13029":"G83T","13030":"G73T","13031":"A67G","13024":"A67G","13032":"G89C"},"clinical":{"13022":"C85G","13023":"A77T","13025":"G64C","13026":"G83C","13027":"G83A","13028":"C88G","13029":"G83T","13030":"G73T","13031":"A67G","13032":"G89C"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"300"},"40330":{"param_type":"multiple resistance variants","param_description":"A set of nucleotide or amino acid substitutions that are all required to confer resistance to an antibiotic drug or drug class, encoded as: [wild-type 1][position 1][mutation 1],[wild-type 2][position 2][mutation 2], etc. For example, D63Y,T142K.","param_type_id":"40330","param_value":{"13024":"G82T,G86T"}}},"model_sequences":{"sequence":{"8692":{"protein_sequence":{"accession":"NP_388014.1","sequence":"MRRIDPSKLELEERLVTVNRVAKVVKGGRRFRFAALVVVGDKNGHVGFGTGKAQEVPEAIRKAVEDAKKNLIEVPMVGTTIPHEIIGRFGAGNILLKPASEGTGVIAGGPVRAVLELAGVADILSKSLGSNTPINMIRATLQGLSELKRAEDVAKLRGKSVEELLG"},"dna_sequence":{"accession":"NC_000964.3","fmin":"143360","fmax":"143861","strand":"+","sequence":"ATGCGTCGTATTGACCCAAGCAAATTAGAGTTAGAAGAACGCTTAGTTACGGTTAACCGCGTAGCGAAAGTTGTTAAAGGTGGTCGTCGTTTCCGCTTCGCAGCTCTAGTCGTTGTCGGTGACAAAAACGGACACGTAGGATTCGGTACTGGTAAAGCACAAGAAGTACCAGAAGCGATTCGCAAAGCTGTTGAAGATGCGAAAAAGAATTTGATTGAAGTACCAATGGTTGGAACTACAATTCCACACGAAATCATCGGACGTTTCGGTGCAGGTAACATCTTGTTAAAACCTGCTTCTGAAGGTACTGGAGTTATCGCTGGAGGCCCTGTACGTGCGGTACTTGAGCTAGCTGGTGTAGCTGATATCCTTTCTAAGTCTTTAGGTTCTAACACACCGATCAACATGATTCGTGCAACACTTCAAGGTTTAAGTGAACTTAAACGTGCTGAAGACGTTGCGAAGCTTCGTGGAAAATCTGTAGAAGAACTGTTAGGATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39579","NCBI_taxonomy_name":"Bacillus subtilis subsp. subtilis str. 168","NCBI_taxonomy_id":"224308"}}}},"ARO_accession":"3007527","ARO_id":"46298","ARO_name":"Bacillus subtilis rpsE mutations conferring resistance to spectinomycin","CARD_short_name":"Bsub_rpsE_SPT","ARO_description":"Amino acid substitutions in ribosomal protein S5, rpsE, is associated with resistance to spectinomycin (SpcR).","ARO_category":{"46297":{"category_aro_accession":"3007526","category_aro_cvterm_id":"46297","category_aro_name":"spectinomycin resistant rpsE","category_aro_description":"Amino acid substitutions in ribosomal protein S5, the product of the rpsE gene, is associated with resistance to spectinomycin (SpcR). This protein is located on the 30S subunit and interacts with 16S rRNA and other proteins.","category_aro_class_name":"AMR Gene Family"},"35957":{"category_aro_accession":"0000039","category_aro_cvterm_id":"35957","category_aro_name":"spectinomycin","category_aro_description":"Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation.","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5970":{"model_id":"5970","model_name":"Streptococcus pyogenes PBP2x conferring resistance to beta-lactam antibiotics","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"13036":"T553K","13037":"P601L","13038":"M593T"},"Curated-R":{"13036":"T553K","13037":"P601L","13038":"M593T"},"clinical":{"13036":"T553K","13037":"P601L","13038":"M593T"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1500"}},"model_sequences":{"sequence":{"8693":{"protein_sequence":{"accession":"QTH61293.1","sequence":"MKKWQKYVLDYVVRDRRTPVENRVRVGQNMMLLTIFIFFIFIINFMIIIGTDQKFGVSLSEGAKKVYQETVTIQAKRGTIYDRNGTAIAVDSTTYSIYAILDKSFVSASDEKLYVQPSQYETVADILKKHLGMKKTDVIKQLKRKGLFQVSFGPSGSGISYSTMSTIQKAMEDAKIKGIAFTTSPGRMYPNGTFASEFIGLASLTEDKKTGVKSLVGKTGLEASFDKILSGQDGVITYQKDRNGTTLLGTGKTVKKAIDGKDIYTTLSEPIQTFLETQMDVFQAKSNGQLASATLVNAKTGEILATTQRPTYNADTLKGLENTNYKWYSALHQGNFEPGSTMKVMTLAAAIDDKVFNPNETFSNANGLTIADATIQDWSINEGISTGQYMNYAQGFAFSSNVGMTKLEQKMGNAKWMNYLTKFRFGFPTRFGLKDEDAGIFPSDNIVTQAMSAFGQGISVTQIQMLRAFTAISNNGEMLEPQFISQIYDPNTASFRTANKEIVGKPVSKKAASETRQYMIGVGTDPEFGTLYSKTFGPIIKVGDLPVAVKSGTAQIGSEDGSGYQDGGLTNYVYSVVAMVPADKPDFLMYVTMTKPQHFGPLFWQDVVNPVLEEAYLMQDTLTKPVVSDANRQTTYKLPNFVGKNPGETSSELRRNLVQPVVLGTGSKIKKVSHQPGQTLTENQQVLILSDRFVEVPDMYGWTKSNVKTFAKWTGIDISFKGTDSGRVMKQSVDVGKSLKKIKKMTITLGD"},"dna_sequence":{"accession":"CP072112.1","fmin":"1373040","fmax":"1375296","strand":"-","sequence":"ATGAAAAAATGGCAAAAATATGTTTTAGATTATGTTGTGCGCGATAGGAGAACTCCAGTCGAAAATCGCGTTCGAGTTGGACAAAATATGATGCTCTTAACTATCTTTATTTTCTTTATTTTCATTATTAATTTCATGATTATTATTGGAACAGATCAAAAGTTTGGAGTTAGTTTGTCAGAAGGGGCGAAGAAGGTTTATCAAGAAACCGTTACGATCCAAGCTAAGCGTGGGACCATTTATGATCGAAATGGTACAGCTATTGCAGTGGATTCTACGACTTATAGCATATACGCAATTTTGGATAAATCATTTGTCTCGGCTTCAGATGAAAAGTTATATGTACAACCTTCTCAGTATGAAACAGTAGCTGATATTTTAAAAAAGCATCTGGGAATGAAAAAAACAGATGTAATTAAACAGCTTAAGCGTAAAGGACTTTTCCAAGTCTCGTTTGGACCGTCAGGGTCTGGCATTTCATATAGTACTATGTCTACTATTCAAAAGGCTATGGAAGATGCCAAAATCAAGGGAATTGCTTTCACAACTAGTCCTGGTCGTATGTATCCAAATGGGACATTTGCTTCAGAATTTATAGGCCTAGCATCTCTAACAGAAGATAAAAAGACAGGTGTTAAGAGTTTAGTTGGAAAAACAGGTTTAGAAGCTTCTTTTGATAAAATTTTATCAGGTCAAGATGGTGTTATTACTTATCAAAAAGATCGAAATGGGACCACACTCTTGGGTACAGGTAAGACTGTCAAGAAAGCTATTGATGGCAAAGATATTTACACAACGCTATCTGAGCCTATCCAGACCTTCTTAGAAACCCAGATGGATGTTTTTCAAGCCAAATCAAATGGTCAGTTGGCCAGTGCAACACTTGTTAATGCTAAAACTGGTGAAATTTTGGCAACAACACAACGCCCCACTTATAATGCTGATACTCTGAAAGGACTTGAAAATACGAACTACAAATGGTACAGTGCACTTCATCAAGGAAATTTTGAACCAGGTTCAACCATGAAAGTGATGACTCTGGCAGCGGCTATTGATGATAAAGTTTTCAACCCAAACGAAACCTTTAGCAATGCTAATGGTTTGACAATTGCAGATGCTACTATTCAAGACTGGTCTATTAACGAAGGCATTTCCACAGGACAGTACATGAATTATGCACAAGGATTTGCCTTCTCAAGTAACGTTGGGATGACTAAACTTGAACAAAAAATGGGTAATGCAAAATGGATGAATTATTTGACGAAGTTCCGCTTTGGTTTTCCTACTCGTTTTGGTTTAAAAGATGAAGACGCAGGTATATTTCCTTCTGATAATATCGTGACTCAAGCTATGAGCGCTTTTGGTCAAGGGATTTCTGTAACCCAGATTCAAATGCTTAGAGCCTTTACTGCTATTTCTAATAATGGTGAGATGTTAGAGCCACAATTTATCAGTCAAATTTATGATCCTAACACAGCAAGTTTTAGAACGGCAAATAAAGAAATTGTTGGAAAACCTGTATCAAAAAAAGCCGCTAGTGAAACAAGACAATACATGATTGGTGTAGGAACAGACCCTGAGTTTGGAACACTCTATTCAAAAACATTTGGACCAATTATTAAAGTGGGTGATTTACCTGTTGCTGTTAAATCAGGAACAGCACAAATTGGTTCAGAAGATGGAAGTGGTTATCAAGATGGTGGATTGACTAACTATGTCTATTCGGTTGTGGCAATGGTGCCAGCTGATAAACCAGACTTTTTGATGTATGTTACTATGACTAAACCACAACATTTTGGTCCCCTTTTTTGGCAAGATGTGGTTAACCCAGTATTGGAAGAAGCATACTTAATGCAAGATACACTAACTAAGCCAGTAGTATCAGATGCTAATCGTCAAACAACTTATAAATTACCAAACTTTGTAGGAAAGAATCCTGGTGAGACATCAAGCGAGTTGCGTCGAAATCTTGTCCAGCCAGTTGTCCTTGGTACTGGCAGCAAGATCAAAAAAGTATCGCATCAGCCCGGTCAAACGTTAACAGAAAACCAACAAGTTCTCATATTATCAGACCGTTTTGTGGAGGTACCAGACATGTATGGCTGGACAAAATCCAATGTTAAAACCTTTGCTAAATGGACTGGGATAGACATCAGCTTTAAAGGAACAGATTCTGGTCGTGTTATGAAACAAAGTGTTGATGTTGGTAAGTCCTTGAAAAAAATAAAAAAAATGACCATTACTTTAGGAGATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36764","NCBI_taxonomy_name":"Streptococcus pyogenes","NCBI_taxonomy_id":"1314"}}}},"ARO_accession":"3007531","ARO_id":"46302","ARO_name":"Streptococcus pyogenes PBP2x conferring resistance to beta-lactam antibiotics","CARD_short_name":"Spyo_PBP2x_BLA","ARO_description":"PBP2x is a penicillin-binding protein and beta-lactam resistance enzyme. Mutations can cause resistance to some beta-lactam antibiotics.","ARO_category":{"40661":{"category_aro_accession":"3003938","category_aro_cvterm_id":"40661","category_aro_name":"Penicillin-binding protein mutations conferring resistance to beta-lactam antibiotics","category_aro_description":"Mutations in PBP transpeptidases that change the affinity for penicillin thereby conferring resistance to penicillin antibiotics.","category_aro_class_name":"AMR Gene Family"},"35981":{"category_aro_accession":"0000064","category_aro_cvterm_id":"35981","category_aro_name":"amoxicillin","category_aro_description":"Amoxicillin is a moderate-spectrum, bacteriolytic, beta-lactam antibiotic used to treat bacterial infections caused by susceptible microorganisms. A derivative of penicillin, it has a wider range of treatment but remains relatively ineffective against Gram-negative bacteria. It is commonly taken with clavulanic acid, a beta-lactamase inhibitor. Like other beta-lactams, amoxicillin interferes with the synthesis of peptidoglycan.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"36989":{"category_aro_accession":"3000645","category_aro_cvterm_id":"36989","category_aro_name":"cefotaxime","category_aro_description":"Cefotaxime is a semisynthetic cephalosporin taken parenterally. It is resistant to most beta-lactamases and active against Gram-negative rods and cocci due to its aminothiazoyl and methoximino functional groups.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5971":{"model_id":"5971","model_name":"MCR-4.7","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1100"}},"model_sequences":{"sequence":{"8694":{"protein_sequence":{"accession":"WP_223106954.1","sequence":"MISRFKTLSVNQFTFITALFYVAIFNLPLFGIVRKGIEKQPEVDPLFIASMPLFLTFALSFLFSIFTVKYLLKPFFIVLTLLSSSVFFAAYQYNVVFDYGMIENTFQTHPAEALMYVNLASITNLLLTGLLPSYLIYKADIHYQPFFKELLHKLAFMLLMFVGIGIVAFFYYQDYAAFGRNNSELRRYIVPTYFVSSASKYLNEHYLQTPMEYQQLGLDAKNASRNPNTKPNLLVFVVGETARSMSYQYYGYNKPTNAHTQNQGLIAFNDTSSCGTATAVSLPCMFSRMGRADYDPRRANAQDTVIDVLSHSGIKVQWFDNDSGCKGVCDRVENLTIDLKSDPKLCSGQYCFDQVLLNKLDKILAVAPSQDTVIFLHIIGSHGPTYYLRYPPEHRKFIPDCPRSDIQNCSQEELINTYDNTILYTDFILSEVVNKLKGKQDMFDTAMLYLSDHGESLGEKGMYLHGAPYSIAPKEQTSVPMLAWISNDFSQDNQLNMTCVAQRAEQGGFSHDNLFDSLLGLMNVKTTVYQSQLDIFAPCRY"},"dna_sequence":{"accession":"NG_088453.1","fmin":"100","fmax":"1726","strand":"+","sequence":"GTGATTTCTAGATTTAAGACGTTATCGGTTAACCAATTCACTTTCATCACTGCGTTGTTTTATGTTGCCATTTTCAATCTACCGCTCTTTGGTATAGTGCGAAAAGGAATTGAAAAACAACCAGAAGTTGATCCCCTTTTCATCGCATCTATGCCGCTATTTTTAACATTTGCGCTGAGTTTTTTGTTTTCAATTTTTACCGTCAAATACCTGCTGAAGCCCTTTTTTATCGTATTGACGTTACTTTCCTCAAGTGTATTTTTTGCAGCCTATCAATACAATGTCGTGTTTGACTACGGCATGATAGAAAACACGTTTCAAACACATCCTGCTGAAGCATTGATGTATGTAAATCTTGCATCAATTACCAATCTACTGCTGACTGGGCTATTACCGTCATATCTTATTTATAAGGCCGATATTCATTATCAGCCCTTTTTTAAGGAGTTATTGCATAAATTAGCCTTTATGCTGCTAATGTTCGTTGGCATTGGGATAGTCGCCTTTTTTTACTATCAAGATTATGCTGCATTTGGTCGAAACAACAGTGAGTTAAGGCGTTACATTGTCCCTACCTATTTTGTCAGTAGTGCATCTAAATATCTCAATGAGCACTATTTGCAGACGCCCATGGAATACCAACAACTTGGCCTAGATGCGAAGAATGCCAGTCGTAACCCGAACACTAAACCTAACTTATTAGTGTTTGTTGTGGGTGAAACTGCGCGCTCAATGAGCTATCAATATTATGGATATAACAAGCCAACCAATGCTCATACCCAAAATCAGGGGCTGATTGCGTTTAACGATACTAGCTCATGCGGCACGGCCACGGCGGTGTCTCTACCCTGTATGTTTTCACGAATGGGGCGGGCAGACTATGATCCTCGCCGTGCTAATGCTCAAGACACAGTGATTGATGTGTTAAGTCATAGTGGTATAAAAGTACAGTGGTTTGATAATGATTCTGGCTGTAAAGGTGTGTGTGATCGGGTTGAAAATCTCACGATAGATTTGAAGAGTGATCCGAAGCTGTGTTCTGGCCAATATTGTTTTGACCAAGTATTGCTCAACAAATTAGATAAAATTCTGGCAGTAGCACCAAGTCAAGATACAGTAATTTTTTTGCATATCATTGGTAGTCATGGACCAACTTATTATCTTAGATACCCGCCAGAGCATCGTAAATTTATACCGGATTGTCCGCGCAGTGATATTCAAAATTGCAGTCAAGAAGAACTGATTAACACCTACGACAACACTATTCTATATACGGATTTTATTCTCAGTGAAGTGGTGAATAAATTAAAAGGTAAGCAGGATATGTTCGATACTGCAATGCTGTATCTCTCTGACCATGGTGAGTCTTTGGGTGAAAAGGGCATGTATTTACATGGTGCGCCCTATAGTATTGCACCGAAAGAACAAACTAGCGTACCAATGCTGGCTTGGATATCTAATGACTTTAGCCAAGATAATCAGTTGAACATGACTTGTGTTGCACAGCGAGCAGAACAGGGCGGCTTTTCCCACGACAATTTGTTCGACAGTTTGCTAGGACTTATGAATGTAAAAACCACCGTCTATCAGAGCCAACTCGATATTTTTGCACCTTGCAGGTATTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3007533","ARO_id":"46304","ARO_name":"MCR-4.7","CARD_short_name":"MCR-4.7","ARO_description":"An MCR-4-type colistin resistance gene variant.","ARO_category":{"41432":{"category_aro_accession":"3004268","category_aro_cvterm_id":"41432","category_aro_name":"MCR phosphoethanolamine transferase","category_aro_description":"A group of mobile colistin resistance genes encode the MCR family of phosphoethanolamine transferases, which catalyze the addition of phosphoethanolamine onto lipid A, thus interfering with the binding of colistin to the cell membrane.","category_aro_class_name":"AMR Gene Family"},"36966":{"category_aro_accession":"3000622","category_aro_cvterm_id":"36966","category_aro_name":"colistin A","category_aro_description":"Colistin A, or polymyxin E1, has a 6-octanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36968":{"category_aro_accession":"3000624","category_aro_cvterm_id":"36968","category_aro_name":"colistin B","category_aro_description":"Colistin B, or polymyxin E2, has a 6-heptanoic acid lipid tail. Polymyxins disrupt the cell membrane of Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"36192":{"category_aro_accession":"3000053","category_aro_cvterm_id":"36192","category_aro_name":"peptide antibiotic","category_aro_description":"Peptide antibiotics have a wide range of antibacterial mechanisms, depending on the amino acids that make up the antibiotic, although most act to disrupt the cell membrane in some manner. Subclasses of peptide antibiotics can include additional sidechains of other types, such as lipids in the case of the lipopeptide antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5976":{"model_id":"5976","model_name":"Erysipelothrix rhusiopathiae gyrA with mutation conferring resistance to enrofloxacin","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"13087":"T86I","13088":"T86K"},"Curated-R":{"13087":"T86I","13088":"T86K"},"clinical":{"13087":"T86I","13088":"T86K"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1600"}},"model_sequences":{"sequence":{"8698":{"protein_sequence":{"accession":"VEH83056.1","sequence":"MEDNTQSYDKIKQRNISEEMKKSFVSYAMSVIVSRALPDVRDGLKPVHRRILYAMNDLGMTSDKPYKKSARIVGEVIGKYHPHGDTAVYDSMVRMAQEFSYRYMLIDGHGNFGSIDGDGAAAMRYTEARMSKISMELIRDINKNTVDFIDNYDGEEREPVVLPSRFPNVLVNGGTGIAVGMATNIPPHNLGEVIDATIALIDNPDITIKELMEDYIFGPDFPTGALLLGRSGIKSAFETGRGSVVMRAKVDIEEMKNGKPRIIISEIPYQVNKATLVEKIATLVRDKEIDGITDLRDESNREGIRIVVELRREVQAEVVLNQLYRLTALQSSFGVNMLALVNGRPELLNLLQVLSHYRDHQIEIVTRRTQFELKKAEDRAHILQGLMIALDHIDEVISIIRSSKDDPEAITRLNEAFDLTEIQSKAVLDMQLRRLTGLQRDKVENEFNELTILIVDLKDILANHDRLLTIIKDELIEIKTKFGDDRRSEIVEADIDMLDEDLIPVEDIVVTMTMNGYIKRTTVDSFNTQNRGGKGVRGISTYDEDTVDQFIAMSTHDYLLLFTNLGKVYRIRGFNVPSSSRTSKGIPVVNLLNLTEGETVKTLVKVAKDDESKYAFFVTKQGIVKRVEVQEFESIRQNGKIAITLREDDELVGVRMTNGDNEIIIGGSNGKAVRFDENEVRSMGRTASGVIGFNVDEGEVVGIATDREGQYILAVTEKGYGKRTDIAEYRRTKRGAKGVKTVNITEKNGNLVSLRAVNGDEEALIISNEGTVIRTEISNIGIYGRSTIGVRLINVGETDSVSQVAILQPTVEEPDEEQTTDQVEPVNEKEIEIAE"},"dna_sequence":{"accession":"LR134439.1","fmin":"77539","fmax":"80047","strand":"-","sequence":"ATGGAAGATAATACACAGAGTTATGACAAAATAAAACAACGTAATATTTCTGAAGAAATGAAAAAATCATTCGTCTCCTATGCCATGTCGGTTATTGTTTCACGTGCGTTGCCAGATGTGCGTGATGGTTTGAAACCAGTTCACCGCCGTATTTTATATGCGATGAATGATCTTGGTATGACAAGTGATAAACCTTATAAAAAATCTGCTCGTATTGTTGGTGAAGTAATTGGTAAGTATCACCCTCATGGTGATACAGCTGTTTATGATTCAATGGTACGTATGGCACAAGAATTTTCATATCGATATATGTTGATTGATGGTCACGGTAACTTCGGATCAATCGATGGAGATGGTGCGGCTGCGATGCGTTATACAGAAGCGCGTATGTCTAAAATCTCAATGGAATTAATTCGTGATATCAATAAGAATACTGTAGATTTTATTGATAACTATGATGGTGAAGAGCGTGAACCCGTTGTACTACCATCGCGTTTCCCTAATGTTCTTGTTAATGGTGGTACTGGGATTGCGGTTGGTATGGCAACAAATATTCCTCCTCATAATCTTGGAGAAGTAATTGATGCAACGATTGCATTAATCGATAACCCAGATATAACAATCAAAGAACTAATGGAAGATTATATTTTTGGTCCTGATTTTCCAACAGGGGCACTTTTACTTGGACGTAGTGGAATCAAGTCAGCGTTTGAAACAGGACGAGGTTCTGTAGTTATGCGGGCAAAAGTGGATATCGAAGAAATGAAGAATGGTAAACCACGAATTATTATTTCCGAAATCCCATATCAAGTTAATAAAGCTACTTTAGTAGAAAAAATCGCAACACTTGTTCGTGATAAAGAAATTGATGGAATCACAGACCTAAGAGATGAATCAAACCGTGAAGGAATTCGTATTGTAGTAGAACTACGAAGAGAAGTTCAAGCGGAAGTTGTATTAAACCAACTTTATCGTCTTACAGCACTCCAATCATCGTTTGGGGTGAATATGTTAGCACTTGTTAATGGAAGACCTGAGTTATTAAATCTATTACAAGTATTAAGTCACTATCGTGATCATCAAATTGAAATTGTTACACGTAGAACACAATTTGAATTGAAAAAAGCAGAAGATCGCGCACATATCCTACAAGGACTTATGATTGCACTTGATCATATTGATGAAGTTATTTCAATCATACGTTCATCCAAGGATGATCCAGAAGCGATTACTCGACTCAATGAAGCGTTTGATTTAACAGAAATTCAATCTAAAGCAGTATTAGATATGCAATTGCGTCGTTTGACCGGATTGCAACGTGATAAAGTTGAGAATGAATTCAATGAATTAACTATTCTAATTGTTGATTTAAAAGATATTTTAGCGAACCACGACCGATTGCTTACAATCATTAAAGATGAATTAATCGAAATCAAAACAAAATTTGGTGATGATCGTCGTTCTGAAATTGTAGAAGCTGATATTGATATGTTAGATGAAGACTTAATTCCAGTTGAAGATATTGTTGTTACGATGACAATGAATGGATATATCAAACGTACCACAGTTGATTCATTCAATACACAAAATCGCGGTGGAAAAGGTGTACGCGGTATTAGTACATACGATGAAGACACCGTTGATCAATTTATAGCGATGTCGACACATGATTATCTATTACTCTTTACAAACCTCGGAAAAGTTTACCGTATTCGCGGATTTAATGTACCGTCATCAAGCCGTACATCAAAAGGAATACCAGTTGTTAACTTATTAAACCTTACAGAAGGTGAAACCGTTAAAACGCTCGTTAAAGTTGCGAAAGATGACGAATCAAAATATGCATTCTTCGTTACAAAACAAGGTATTGTGAAACGTGTTGAAGTTCAAGAGTTTGAATCAATACGCCAAAACGGTAAAATTGCGATTACACTTCGTGAAGATGACGAACTCGTAGGTGTTCGCATGACAAACGGAGATAATGAAATCATTATCGGAGGAAGCAACGGTAAGGCCGTTCGATTCGATGAAAATGAAGTCCGTTCTATGGGACGTACAGCATCAGGTGTTATTGGATTTAATGTTGATGAAGGTGAAGTAGTAGGAATTGCTACTGACCGTGAAGGTCAATATATCCTAGCTGTAACCGAAAAAGGTTACGGTAAGCGTACTGACATCGCGGAATACCGACGCACCAAACGTGGGGCTAAGGGCGTTAAAACAGTAAACATTACTGAGAAGAATGGTAACCTTGTCTCACTTCGTGCAGTTAACGGTGATGAGGAAGCATTAATCATCTCTAATGAAGGAACTGTTATTCGTACAGAAATCAGTAACATCGGAATTTATGGACGATCAACGATTGGTGTTCGTTTGATTAACGTTGGTGAAACAGATTCTGTGTCGCAAGTTGCGATTCTTCAACCTACAGTTGAGGAACCAGATGAAGAACAAACAACAGATCAAGTAGAACCTGTTAATGAAAAAGAAATAGAAATTGCAGAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43311","NCBI_taxonomy_name":"Erysipelothrix rhusiopathiae","NCBI_taxonomy_id":"1648"}}}},"ARO_accession":"3007544","ARO_id":"46315","ARO_name":"Erysipelothrix rhusiopathiae gyrA with mutation conferring resistance to enrofloxacin","CARD_short_name":"Erhu_gyrA_ENR","ARO_description":"Sequence analysis of the gyrA gene showed that resistance of E. rhusiopathiae strains to enrofloxacin is due to a mutation at position 257.","ARO_category":{"39876":{"category_aro_accession":"3003292","category_aro_cvterm_id":"39876","category_aro_name":"fluoroquinolone resistant gyrA","category_aro_description":"DNA gyrase is responsible for DNA supercoiling and consists of two alpha and two beta subunits. GyrA point mutations confer resistance by preventing fluoroquinolone antibiotics from binding the alpha-subunit.","category_aro_class_name":"AMR Gene Family"},"45604":{"category_aro_accession":"3007045","category_aro_cvterm_id":"45604","category_aro_name":"enrofloxacin","category_aro_description":"Enrofloxacin is a broad-spectrum fluoroquinolone antibiotic. It is used in veterinary medicine predominately for dogs and cats but is sometimes used for other animals.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5977":{"model_id":"5977","model_name":"OXA-1038","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8699":{"protein_sequence":{"accession":"UBJ91323.1","sequence":"MRVLALSAVFLVASIIGMPAVAKEWQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGQTRDIATWNRDHNLITAMKYSVVPVYQEFARQIGEARMSKMLHAFDYGNEDISGNVDTFWLDGGIRISAIEQISFLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYSTRIEPKIGWWVGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP"},"dna_sequence":{"accession":"OK180617.1","fmin":"0","fmax":"798","strand":"+","sequence":"ATGCGTGTATTAGCCTTATCGGCTGTGTTTTTGGTGGCATCGATTATCGGAATGCCTGCGGTAGCAAAGGAATGGCAAGAAAACAAAAGTTGGAATGCTCACTTTACTGAACATAAATCACAGGGCGTAGTTGTGCTCTGGAATGAGAATAAGCAGCAAGGATTTACCAATAATCTTAAACGGGCGAACCAAGCATTTTTACCCGCATCTACCTTTAAAATTCCCAATAGCTTGATCGCCCTCGATTTGGGCGTGGTTAAGGATGAACACCAAGTCTTTAAGTGGGATGGACAGACGCGCGATATCGCCACTTGGAATCGCGATCATAATCTAATCACCGCGATGAAATATTCGGTTGTGCCTGTTTATCAAGAATTTGCCCGCCAAATTGGCGAGGCACGTATGAGCAAGATGCTACATGCTTTCGATTATGGTAATGAGGACATTTCGGGCAATGTAGATACTTTTTGGCTTGATGGTGGTATTCGAATTTCGGCCATTGAGCAAATCAGCTTTTTAAGAAAGCTGTATCACAATAAGTTACACGTATCGGAGCGCAGTCAGCGCATCGTGAAACAAGCCATGCTGACCGAAGCCAATGGCGACTATATTATTCGGGCTAAAACTGGATACTCGACTAGAATCGAACCTAAGATTGGCTGGTGGGTCGGTTGGGTTGAACTTGATGATAATGTGTGGTTTTTTGCGATGAATATGGATATGCCCACATCGGATGGTTTAGGGCTGCGCCAAGCCATCACAAAAGAAGTGCTCAAACAGGAAAAAATTATTCCCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39674","NCBI_taxonomy_name":"Shewanella xiamenensis","NCBI_taxonomy_id":"332186"}}}},"ARO_accession":"3007561","ARO_id":"46334","ARO_name":"OXA-1038","CARD_short_name":"OXA-1038","ARO_description":"The blaOXA-48-like enzyme demonstrated significant hydrolysis activity against meropenem, and the classical beta-lactamase inhibitor had no significant inhibitory effect. This is a novel OXA carbapenemases in S. xiamenensis.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46510":{"category_aro_accession":"3007721","category_aro_cvterm_id":"46510","category_aro_name":"OXA-48-like beta-lactamase","category_aro_description":"OXA-48-type beta-lactamases are now routinely encountered in bacterial infections caused by carbapenam-resistant Enterobacterales. OXA-48-like proteins confer resistance to penicillin (which is efficiently hydrolyzed) and carbapenam antibiotics (which is more slowly broken down). The spectrum of activity of these variants varies, with some hydrolyzing expanded-spectrum oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35990":{"category_aro_accession":"0000073","category_aro_cvterm_id":"35990","category_aro_name":"meropenem","category_aro_description":"Meropenem is an ultra-broad spectrum injectable antibiotic used to treat a wide variety of infections, including meningitis and pneumonia. It is a beta-lactam and belongs to the subgroup of carbapenem, similar to imipenem and ertapenem.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5978":{"model_id":"5978","model_name":"OXA-1039","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8700":{"protein_sequence":{"accession":"UBJ91324.1","sequence":"MRVLALSAVFLVASIIGMPAVAKEWQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGQTRDIATWNRDHNLITAMKYSVVPVYQEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISATEQITFLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYSTRIEPKIGWWVGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP"},"dna_sequence":{"accession":"OK180618.1","fmin":"0","fmax":"798","strand":"+","sequence":"ATGCGTGTATTAGCCTTATCGGCTGTGTTTTTGGTGGCATCGATTATCGGAATGCCTGCGGTAGCAAAGGAATGGCAAGAAAACAAAAGTTGGAATGCTCACTTTACTGAACATAAATCACAGGGCGTAGTTGTGCTCTGGAATGAGAATAAGCAGCAAGGATTTACCAATAATCTTAAACGGGCGAACCAAGCATTTTTACCCGCATCTACCTTTAAAATTCCCAATAGCTTGATCGCCCTCGATTTGGGCGTGGTTAAGGATGAACACCAAGTCTTTAAGTGGGATGGACAGACGCGCGATATCGCCACTTGGAATCGCGATCATAATCTAATCACCGCGATGAAATATTCAGTTGTGCCTGTTTATCAAGAATTTGCCCGCCAAATTGGCGAGGCACGTATGAGCAAGATGCTACATGCTTTCGATTATGGTAATGAGGACATTTCGGGCAATGTAGACAGTTTCTGGCTCGATGGTGGTATTCGAATTTCGGCCACTGAGCAAATCACCTTTTTAAGAAAGCTGTATCACAATAAGTTACACGTATCGGAGCGCAGCCAGCGTATTGTCAAACAAGCCATGCTGACCGAAGCCAATGGCGACTATATTATTCGGGCTAAAACGGGATACTCGACTAGAATCGAACCTAAGATTGGCTGGTGGGTCGGTTGGGTTGAACTTGATGATAATGTGTGGTTTTTTGCGATGAATATGGATATGCCCACATCGGATGGTTTAGGGCTGCGCCAAGCCATCACAAAAGAAGTGCTCAAACAGGAAAAAATTATTCCCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39674","NCBI_taxonomy_name":"Shewanella xiamenensis","NCBI_taxonomy_id":"332186"}}}},"ARO_accession":"3007562","ARO_id":"46335","ARO_name":"OXA-1039","CARD_short_name":"OXA-1039","ARO_description":"The blaOXA-48-like enzyme demonstrated significant hydrolysis activity against meropenem, and the classical beta-lactamase inhibitor had no significant inhibitory effect. This is a novel OXA carbapenemases in S. xiamenensis.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46510":{"category_aro_accession":"3007721","category_aro_cvterm_id":"46510","category_aro_name":"OXA-48-like beta-lactamase","category_aro_description":"OXA-48-type beta-lactamases are now routinely encountered in bacterial infections caused by carbapenam-resistant Enterobacterales. OXA-48-like proteins confer resistance to penicillin (which is efficiently hydrolyzed) and carbapenam antibiotics (which is more slowly broken down). The spectrum of activity of these variants varies, with some hydrolyzing expanded-spectrum oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35990":{"category_aro_accession":"0000073","category_aro_cvterm_id":"35990","category_aro_name":"meropenem","category_aro_description":"Meropenem is an ultra-broad spectrum injectable antibiotic used to treat a wide variety of infections, including meningitis and pneumonia. It is a beta-lactam and belongs to the subgroup of carbapenem, similar to imipenem and ertapenem.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5979":{"model_id":"5979","model_name":"FRI-11","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"8701":{"protein_sequence":{"accession":"UAN43462.1","sequence":"MFFLRKSASTFIFLLCLPLNSFASQESNSVEQMRELETSFGGRIGVYILNTKNGKEFSYRQDERFPLCSSFKAFLAASVLKKTQEKSVSLDDMMEYSGRVMEKHSPVSEKYRKTGASVRTLAKAAIQYSDNGASNLLMERYIGGPEGLTAFMRSTGDTDFRLDRWELELNSAIPGDERDTSTPKAVAMSLKNIAFGSVLDAKNKSLLQEWLKGNTTGNARIRAAVPDKWDVGDKTGTCGFYGTANDVAILWPDANSPAVMAVYTTRPNQNDKHDEAVIKNAAKIAINAVYGSYK"},"dna_sequence":{"accession":"CP074152.1","fmin":"56484","fmax":"57369","strand":"-","sequence":"ATGTTTTTTTTAAGAAAAAGTGCAAGTACATTTATTTTTTTGCTCTGTCTTCCATTGAACTCATTCGCCTCTCAGGAAAGTAATAGTGTTGAGCAAATGAGGGAATTGGAAACTTCTTTTGGGGGGCGGATAGGTGTTTATATTTTAAACACAAAAAATGGGAAAGAATTTTCCTACAGACAAGATGAGAGATTTCCTTTATGTAGTTCATTTAAGGCATTCCTAGCTGCATCCGTATTAAAAAAAACTCAGGAGAAATCTGTTTCTCTTGATGATATGATGGAATATTCTGGACGTGTTATGGAAAAGCATTCTCCTGTGTCAGAAAAATACCGCAAAACAGGAGCAAGCGTGCGGACTTTGGCCAAGGCAGCAATTCAGTATAGTGACAATGGAGCTTCTAATCTATTAATGGAAAGATACATAGGAGGTCCTGAGGGTTTGACTGCATTTATGCGGTCAACGGGAGACACTGACTTCAGGCTTGATCGTTGGGAATTAGAATTAAACTCAGCTATTCCAGGCGATGAACGAGATACTTCAACTCCAAAAGCAGTGGCAATGAGCCTTAAAAATATTGCTTTTGGTTCAGTACTCGATGCTAAAAATAAATCATTGCTGCAGGAATGGCTTAAAGGCAACACTACTGGTAATGCGCGAATTAGAGCTGCGGTTCCAGATAAGTGGGATGTTGGCGATAAAACAGGCACCTGTGGTTTTTATGGTACAGCCAATGATGTTGCTATTTTATGGCCAGACGCTAATTCACCTGCAGTTATGGCTGTCTACACAACACGTCCTAATCAAAACGACAAACATGACGAAGCAGTAATTAAAAATGCTGCAAAAATAGCTATAAATGCAGTGTATGGAAGTTATAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"46406","NCBI_taxonomy_name":"Enterobacter sp. JBIWA008","NCBI_taxonomy_id":"2831892"}}}},"ARO_accession":"3007632","ARO_id":"46405","ARO_name":"FRI-11","CARD_short_name":"FRI-11","ARO_description":"FRI-11 is a FRI-type carbapenem-hydrolyzing class A beta-lactamase.","ARO_category":{"42915":{"category_aro_accession":"3004796","category_aro_cvterm_id":"42915","category_aro_name":"FRI beta-lactamase","category_aro_description":"FRI is a carbapenem-Hydrolyzing Class A beta-Lactamase from Enterobacter cloacae.","category_aro_class_name":"AMR Gene Family"},"35987":{"category_aro_accession":"0000070","category_aro_cvterm_id":"35987","category_aro_name":"ertapenem","category_aro_description":"Ertapenem is a carbapenem antibiotic and is highly resistant to beta-lactamases like other carbapenems. It inhibits bacterial cell wall synthesis.","category_aro_class_name":"Antibiotic"},"35990":{"category_aro_accession":"0000073","category_aro_cvterm_id":"35990","category_aro_name":"meropenem","category_aro_description":"Meropenem is an ultra-broad spectrum injectable antibiotic used to treat a wide variety of infections, including meningitis and pneumonia. It is a beta-lactam and belongs to the subgroup of carbapenem, similar to imipenem and ertapenem.","category_aro_class_name":"Antibiotic"},"36309":{"category_aro_accession":"3000170","category_aro_cvterm_id":"36309","category_aro_name":"imipenem","category_aro_description":"Imipenem is a broad-spectrum antibiotic and is usually taken with cilastatin, which prevents hydrolysis of imipenem by renal dehydropeptidase-I. It is resistant to hydrolysis by most other beta-lactamases. Notable exceptions are the KPC beta-lactamases and Ambler Class B enzymes.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5980":{"model_id":"5980","model_name":"KPC-125","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"8702":{"protein_sequence":{"accession":"WP_248496376.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARATSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKYSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"NG_080778.1","fmin":"100","fmax":"982","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGCTACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGTACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3007633","ARO_id":"46407","ARO_name":"KPC-125","CARD_short_name":"KPC-125","ARO_description":"KPC-125 is a KPC-type class A beta-lactamase. KPC-125 is a variant of KPC-3, differing by a D179A polymorphism within the omega-loop region.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5981":{"model_id":"5981","model_name":"CAE-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"575"}},"model_sequences":{"sequence":{"8703":{"protein_sequence":{"accession":"QXW20276.1","sequence":"MIQRRQFSLGLAWTAIGSLAGCAAGPSAAAKTERHWSHAMAQIEQDAQGRLGVAMLDTGSGLALGWRQDERFAMCSTFKLPLAAWVLALVDQGRERLDARVQYSEAELVEYSPVSGPKAGARGGLTVGELCAATVSLSDNSAANVLLARHGGPAALTAWLRSQGDSITRLDRNEPSLNEATVGDERDTTTPLAMLHTMQRLVLGNSLSPSSRATLQRWLIETSTGDQRLRAGAPGWKVGDKTGTSGSSGTANDIGVLWPPAGGAPVLVSCYLTQSTARPEQRDAAIAQVARAVLAARQYQAQ"},"dna_sequence":{"accession":"CP079746.1","fmin":"15693","fmax":"16602","strand":"+","sequence":"ATGATACAAAGAAGACAGTTTTCCTTGGGTTTGGCATGGACCGCCATCGGGTCTCTGGCCGGATGCGCCGCAGGCCCCAGTGCTGCGGCGAAAACCGAGCGCCACTGGTCCCACGCCATGGCGCAAATTGAACAGGACGCGCAAGGCCGCCTGGGTGTGGCAATGCTGGACACAGGCAGTGGCCTGGCACTGGGGTGGAGACAGGACGAACGCTTTGCCATGTGCAGCACTTTCAAGCTCCCCTTGGCGGCCTGGGTGCTGGCACTGGTCGACCAAGGTCGTGAGCGCTTGGACGCACGCGTGCAGTACTCCGAGGCGGAGCTGGTGGAGTATTCCCCCGTCAGCGGCCCGAAAGCGGGTGCACGGGGCGGGCTGACCGTGGGCGAGCTGTGCGCCGCGACAGTGAGCCTGAGCGACAACTCCGCAGCCAACGTGCTGCTTGCACGCCATGGCGGCCCCGCTGCGCTGACGGCTTGGCTGCGCTCGCAAGGGGACTCCATCACACGACTGGATCGCAATGAGCCCTCATTAAACGAAGCCACCGTGGGCGATGAGCGCGACACCACCACACCACTTGCCATGCTTCATACCATGCAACGGCTGGTCCTGGGCAATTCACTGTCACCCTCATCACGCGCAACGCTACAACGCTGGCTGATCGAGACCAGCACGGGGGACCAACGCCTGCGGGCAGGCGCACCAGGTTGGAAAGTGGGCGACAAGACGGGCACCTCTGGCAGCAGTGGCACCGCGAACGACATTGGGGTGCTGTGGCCACCGGCAGGCGGCGCCCCGGTACTGGTGAGTTGCTACCTCACACAGTCCACAGCCCGCCCCGAGCAGCGCGATGCCGCCATCGCCCAGGTCGCCCGCGCTGTGTTGGCGGCGCGACAGTATCAGGCGCAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"46410","NCBI_taxonomy_name":"Comamonas aquatica","NCBI_taxonomy_id":"225991"}}}},"ARO_accession":"3007635","ARO_id":"46409","ARO_name":"CAE-1","CARD_short_name":"CAE-1","ARO_description":"CAE-1 is a CAE beta-lactamase and confers resistance to ampicillin, piperacillin, cefazolin, cefuroxime, and ceftriaxone, and elevates the MIC of ampicillin-sulbactam two-fold in Escherichia coli DH5alpha, suggesting that CAE-1 functions as a broad-spectrum beta-lactamase.","ARO_category":{"46408":{"category_aro_accession":"3007634","category_aro_cvterm_id":"46408","category_aro_name":"CAE beta-lactamase","category_aro_description":"CAE beta-lactamases are a novel class A serine beta-lactamase family first isolated from Comamonas aquatica.","category_aro_class_name":"AMR Gene Family"},"35975":{"category_aro_accession":"0000058","category_aro_cvterm_id":"35975","category_aro_name":"cefazolin","category_aro_description":"Cefazolin, also known as cefazoline or cephazolin, is a first generation cephalosporin antibiotic. It is administered parenterally, and is active against a broad spectrum of bacteria.","category_aro_class_name":"Antibiotic"},"35979":{"category_aro_accession":"0000062","category_aro_cvterm_id":"35979","category_aro_name":"ceftriaxone","category_aro_description":"Ceftriaxone is a third-generation cephalosporin antibiotic. The presence of an aminothiazolyl sidechain increases ceftriazone's resistance to beta-lactamases. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"35980":{"category_aro_accession":"0000063","category_aro_cvterm_id":"35980","category_aro_name":"cefuroxime","category_aro_description":"Cefuroxime is a second-generation cephalosporin antibiotic with increased stability with beta-lactamases than first-generation cephalosporins. Cefuroxime is active against Gram-positive organisms but less active against methicillin-resistant strains.","category_aro_class_name":"Antibiotic"},"35995":{"category_aro_accession":"0000078","category_aro_cvterm_id":"35995","category_aro_name":"piperacillin","category_aro_description":"Piperacillin is an acetylureidopenicillin and has an extended spectrum of targets relative to other beta-lactam antibiotics. It inhibits cell wall synthesis in bacteria, and is usually taken with the beta-lactamase inhibitor tazobactam to overcome penicillin-resistant bacteria.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"763":{"model_id":"763","model_name":"catA1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"400"}},"model_sequences":{"sequence":{"482":{"protein_sequence":{"accession":"CAA23899.1","sequence":"MEKKITGYTTVDISQWHRKEHFEAFQSVAQCTYNQTVQLDITAFLKTVKKNKHKFYPAFIHILARLMNAHPEFRMAMKDGELVIWDSVHPCYTVFHEQTETFSSLWSEYHDDFRQFLHIYSQDVACYGENLAYFPKGFIENMFFVSANPWVSFTSFDLNVANMDNFFAPVFTMGKYYTQGDKVLMPLAIQVHHAVCDGFHVGRMLNELQQYCDEWQGGA"},"dna_sequence":{"accession":"V00622.1","fmin":"243","fmax":"903","strand":"+","sequence":"ATGGAGAAAAAAATCACTGGATATACCACCGTTGATATATCCCAATGGCATCGTAAAGAACATTTTGAGGCATTTCAGTCAGTTGCTCAATGTACCTATAACCAGACCGTTCAGCTGGATATTACGGCCTTTTTAAAGACCGTAAAGAAAAATAAGCACAAGTTTTATCCGGCCTTTATTCACATTCTTGCCCGCCTGATGAATGCTCATCCGGAATTCCGTATGGCAATGAAAGACGGTGAGCTGGTGATATGGGATAGTGTTCACCCTTGTTACACCGTTTTCCATGAGCAAACTGAAACGTTTTCATCGCTCTGGAGTGAATACCACGACGATTTCCGGCAGTTTCTACACATATATTCGCAAGATGTGGCGTGTTACGGTGAAAACCTGGCCTATTTCCCTAAAGGGTTTATTGAGAATATGTTTTTCGTCTCAGCCAATCCCTGGGTGAGTTTCACCAGTTTTGATTTAAACGTGGCCAATATGGACAACTTCTTCGCCCCCGTTTTCACCATGGGCAAATATTATACGCAAGGCGACAAGGTGCTGATGCCGCTGGCGATTCAGGTTCATCATGCCGTCTGTGATGGCTTCCATGTCGGCAGAATGCTTAATGAATTACAACAGTACTGCGATGAGTGGCAGGGCGGGGCGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3002683","ARO_id":"39117","ARO_name":"catA1","CARD_short_name":"catA1","ARO_description":"catA1 (formerly in CARD as catI) is a chromosome and transposon-encoded variant of the cat gene found in Escherichia coli and Acinetobacter baumannii.","ARO_category":{"36261":{"category_aro_accession":"3000122","category_aro_cvterm_id":"36261","category_aro_name":"chloramphenicol acetyltransferase (CAT)","category_aro_description":"Inactivates chloramphenicol by addition of an acyl group. CAT is used to describe many variants of the chloramphenicol acetyltransferase gene in a range of organisms including Acinetobacter calcoaceticus, Agrobacterium tumefaciens, Alkalihalobacillus clausii, Bacillus subtilis, Campylobacter coli, Enterococcus faecalis, Enterococcus faecium, Lactococcus lactis, Listeria monocytogenes, Listonella anguillarum, Morganella morganii, Photobacterium damselae subsp. piscicida, Proteus mirabilis, Salmonella typhi, Serratia marcescens, Shigella flexneri, Staphylococcus aureus, Staphylococcus haemolyticus, Staphylococcus intermedius, Streptococcus agalactiae, Streptococcus suis and Streptomyces acrimycini.","category_aro_class_name":"AMR Gene Family"},"36521":{"category_aro_accession":"3000382","category_aro_cvterm_id":"36521","category_aro_name":"azidamfenicol","category_aro_description":"Azidamfenicol is a water soluble derivative of chloramphenicol, sharing the same mode of action of inhibiting peptide synthesis by interacting with the 23S RNA of the 50S ribosomal subunit.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36595":{"category_aro_accession":"3000456","category_aro_cvterm_id":"36595","category_aro_name":"thiamphenicol","category_aro_description":"Derivative of Chloramphenicol. The nitro group (-NO2) is substituted by a sulfomethyl group (-SO2CH3).","category_aro_class_name":"Antibiotic"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5982":{"model_id":"5982","model_name":"Clostridioides difficile cplR","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1000"}},"model_sequences":{"sequence":{"8704":{"protein_sequence":{"accession":"AJP12342.1","sequence":"MLLVKVENLKKYYADKLILDIDKLEILENDKIGLVGSNGQGKTTLLKAILGEIEIDEGYTYLTESYSYISQSENNIETCGHSKEKSLLNAPDKFEEHLSGGEKVKLKIADALSNKKNIIIADEPTSNLDKKSIGVLEDMFKRHEGALLLISHDRRFLDELCTTILELEDGKLKAYKGNYTDYLMQKDEEVKRADFEYQEYVKEKKRLEKALLYKKALSDGIRKTPKRMGNSEARLHKMGGQTNKKKLDSNVKAIKSRIDKLEVKNKPKVSKEMNIKIQDGMEIISKNLVEVKDMTLKLENKLLLDNVSFKIKRGKKIALLGDNGCGKSTLIKEILADKNDNIKINNKVKVGYFDQNQSLLDEEKSVLYNTKVNSSFDESFIRINLSLFGFKGDDVYKKVKVLSGGEKVKIALCKIILEDNNFLVFDEPTNYLDIKSMEALEKALINTDKTMLIVSHDRVFVSHICNYIIEIKDAKIREFDCNYDEYTISRNKKTPSRENQIKKENLLVLENRLTTVISMLSIEKDNLKKELYESEYNELLKQINKLKNSF"},"dna_sequence":{"accession":"CP010905.2","fmin":"2984766","fmax":"2986419","strand":"-","sequence":"ATGTTGTTAGTAAAAGTAGAAAATTTAAAGAAATATTATGCAGATAAATTAATTTTGGATATAGATAAACTTGAAATATTAGAAAATGACAAAATAGGTCTAGTTGGTTCAAATGGTCAAGGAAAAACAACATTATTAAAAGCAATATTGGGAGAAATAGAAATTGATGAAGGATATACTTACCTTACAGAAAGCTATTCTTATATAAGTCAGAGTGAAAATAATATTGAAACATGTGGTCATAGTAAGGAGAAGAGTCTTTTAAATGCTCCAGATAAATTTGAAGAACACTTATCAGGAGGGGAAAAGGTTAAGTTAAAAATAGCAGATGCGCTGAGTAATAAGAAAAATATCATAATAGCTGATGAGCCAACTTCAAACTTAGATAAAAAAAGCATTGGGGTTTTGGAAGATATGTTTAAAAGGCATGAGGGAGCATTATTATTAATATCTCATGATAGACGTTTTCTGGATGAGTTATGTACAACTATATTAGAACTAGAAGATGGAAAACTAAAAGCTTACAAAGGCAATTACACTGATTATTTAATGCAAAAAGATGAAGAAGTAAAAAGAGCTGATTTTGAGTATCAAGAATATGTTAAAGAGAAAAAAAGGCTTGAAAAAGCTCTTTTATATAAAAAAGCTTTAAGTGATGGCATAAGAAAAACACCAAAAAGAATGGGTAATTCAGAAGCTAGGTTGCACAAAATGGGTGGTCAGACTAATAAGAAAAAGTTGGACTCAAATGTGAAGGCTATAAAAAGCAGAATTGATAAACTTGAGGTAAAGAATAAACCTAAAGTTTCTAAAGAAATGAACATTAAGATTCAAGATGGTATGGAGATAATTAGCAAAAATCTAGTAGAGGTAAAAGATATGACTCTAAAGTTAGAAAATAAGCTCCTGTTAGATAATGTTTCCTTTAAGATAAAAAGAGGTAAAAAGATAGCATTATTAGGTGATAATGGGTGTGGAAAAAGTACTCTGATAAAAGAAATATTGGCTGATAAAAATGACAATATAAAAATAAATAACAAGGTAAAAGTAGGTTATTTTGACCAAAATCAAAGTTTATTAGATGAGGAAAAGAGTGTTCTATACAATACTAAAGTTAATAGTTCATTTGATGAATCTTTTATAAGGATAAACTTAAGCCTATTTGGGTTTAAAGGTGATGATGTCTACAAAAAAGTAAAAGTACTTAGTGGTGGAGAAAAGGTAAAAATAGCACTATGTAAAATAATATTGGAAGATAATAATTTTTTAGTATTTGATGAACCAACAAATTACTTAGATATAAAATCTATGGAAGCACTGGAAAAGGCACTGATAAATACTGATAAAACTATGCTTATAGTGTCTCATGATAGAGTATTTGTATCACATATTTGTAACTATATTATAGAGATAAAAGATGCTAAAATAAGGGAGTTTGATTGTAATTATGACGAATATACAATTAGCAGAAATAAAAAAACTCCTAGTAGAGAAAACCAAATCAAAAAAGAAAATCTTCTAGTATTAGAAAATAGACTTACAACTGTTATATCTATGTTATCTATAGAAAAAGATAATCTAAAAAAAGAATTGTATGAATCAGAATATAATGAATTACTAAAACAAATCAATAAATTAAAAAATAGCTTTTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"37603","NCBI_taxonomy_name":"Clostridioides difficile 630","NCBI_taxonomy_id":"272563"}}}},"ARO_accession":"3007637","ARO_id":"46412","ARO_name":"Clostridioides difficile cplR","CARD_short_name":"cplR","ARO_description":"CplR is an ABC-F ATPase ribosomal protection protein from Clostridioides difficile which confers resistance to pleuromutilins and lincosamides. Its resistance to these antibiotics increases in synergy with erythromcyin resistance methylases (e.g., ermB).","ARO_category":{"45630":{"category_aro_accession":"3007068","category_aro_cvterm_id":"45630","category_aro_name":"Miscellaneous ABC-F subfamily ATP-binding cassette ribosomal protection proteins","category_aro_description":"ABC-F subfamily ATP-binding cassette ribosomal protection proteins of unknown, unclear or miscellaneous classification which nevertheless confer resistance to antibiotics through ribosomal protection and not through antibiotic efflux. These proteins should be further reviewed to elucidate associated genes, their function, origin and classification.","category_aro_class_name":"AMR Gene Family"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"virginiamycin M1","category_aro_description":"Virginiamycin M1 is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"46411":{"category_aro_accession":"3007636","category_aro_cvterm_id":"46411","category_aro_name":"iboxamycin","category_aro_description":"Iboxamycin is a fully synthetic lincosamide antibiotic. Like other lincosamides, it selectively targets the bacterial ribosome and prevents elongation of the peptide chain. Iboxamycin has been shown to  be effective against bacterial strains otherwise resistant to licosamide antibiotics.","category_aro_class_name":"Antibiotic"},"46414":{"category_aro_accession":"3007639","category_aro_cvterm_id":"46414","category_aro_name":"A201A","category_aro_description":"A201A is a nucleoside antibiotic. It inhibits translation by binding to the peptidyl transferase center on the large ribosomal subunit. This prevents the binding of aminoacyl-tRNA to the A-site.","category_aro_class_name":"Antibiotic"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35952":{"category_aro_accession":"0000034","category_aro_cvterm_id":"35952","category_aro_name":"streptogramin A antibiotic","category_aro_description":"Streptogramin A antibiotics are cyclic polyketide peptide hybrids that bind to the ribosomal peptidyl transfer centre. Structural variation arises from substituting a proline for its desaturated derivative and by its substitution for Ala or Cys. Used alone, streptogramin A antibiotics are bacteriostatic, but is bactericidal when used with streptogramin B antibiotics.","category_aro_class_name":"Drug Class"},"36174":{"category_aro_accession":"3000034","category_aro_cvterm_id":"36174","category_aro_name":"nucleoside antibiotic","category_aro_description":"Nucleoside antibiotics are made of modified nucleosides and nucleotides with wide-ranging activities and means of antibacterial effects. This drug class includes aminonucleoside antibiotics, which contain an amino group.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5983":{"model_id":"5983","model_name":"Clostridium perfringes cplR","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"950"}},"model_sequences":{"sequence":{"8705":{"protein_sequence":{"accession":"BAB80490.1","sequence":"MTFYDYIYSPVIYRRDFFMSLARLNKVKKYYGDKLILDIDKLEILDEDRIGLVGVNGAGKTTLIKSLLGQIPIDEGNVSLTKSFAYISQSENSNEETLNNNFKNVFNAPFEYHEFLSGGEKVKFKIAKALGENKHLIIADEPTANLDENSIETLENMLKNYNGALLLVSHDRRFLDSLCNTIIEIEDGKIKTYKGNFSKYLELKTLERQRAEIEYNSYINEKKHLENAILNKRNLKDSLRKTPKRMGNSEARLHKMGPQRAKKNLDNNIKALRSRIDHLDIKEKPKTIKEIKIRVQDNLKIASKNLIEAKDFTLFAGNKLLLKDIKFKIKNGKKVALIGDNGCGKSTLLKNIISKEDNIKVLDNVVIGYFDQSQKILKDDESILKNILKDCSYDENFVRINLDGFGFKGDDVFKKVSSLSGGEKVKIALCKILLSDNNLIILDEPTNYLDIKSMESLETALINCNKTLIVVSHDRNFISNVCDYILEIDNNLIHEFSGTYDEYIKFKKKPKLDDKERANKDSLLLLENRLSNVISLLSIEPDNNKKSLLENEYYNLLKELKNLRKRLS"},"dna_sequence":{"accession":"BA000016.3","fmin":"967228","fmax":"968935","strand":"-","sequence":"TTGACTTTTTATGACTATATATACTCTCCTGTAATTTATAGGAGGGATTTTTTTATGTCTTTAGCAAGATTAAATAAAGTAAAAAAATATTATGGAGATAAATTAATTCTAGATATAGATAAACTAGAAATTTTAGATGAAGATAGAATCGGATTAGTTGGAGTTAATGGTGCTGGTAAAACTACACTTATTAAATCTTTATTAGGTCAAATTCCTATTGATGAAGGAAATGTATCTCTAACTAAAAGCTTTGCTTATATAAGTCAAAGTGAAAATTCTAATGAAGAAACTTTAAATAATAATTTTAAGAATGTATTCAATGCTCCTTTTGAATACCATGAGTTTTTATCAGGTGGAGAAAAGGTTAAATTTAAAATAGCTAAAGCTCTAGGTGAAAATAAACATTTAATTATTGCTGATGAGCCTACTGCTAATTTAGATGAAAACAGCATTGAAACTCTTGAAAACATGCTAAAAAACTATAATGGTGCATTACTTCTAGTATCACATGATAGAAGATTTCTAGATTCATTATGTAACACTATTATTGAAATTGAAGATGGAAAAATAAAAACTTATAAAGGAAATTTCTCTAAATATCTAGAGCTAAAAACTTTAGAGAGGCAAAGAGCTGAAATTGAGTATAATTCTTATATAAATGAAAAAAAGCATCTTGAAAATGCTATCCTTAATAAGCGAAACTTAAAAGATAGTCTTCGAAAAACACCTAAAAGAATGGGTAATTCTGAAGCTAGATTACACAAAATGGGGCCTCAAAGAGCAAAGAAAAATCTAGATAATAATATAAAGGCCTTAAGAAGTAGAATTGATCATCTTGACATTAAGGAAAAGCCTAAAACAATAAAAGAGATTAAAATTAGAGTTCAAGATAATTTAAAAATAGCTTCTAAAAATCTTATAGAAGCTAAAGATTTCACATTATTTGCAGGTAATAAGCTTCTACTTAAAGATATTAAATTTAAAATAAAGAATGGTAAGAAAGTAGCACTTATTGGTGATAATGGTTGTGGTAAAAGTACATTGCTAAAAAATATTATTTCAAAAGAAGACAATATAAAAGTTTTAGATAATGTTGTTATAGGCTACTTTGATCAATCTCAAAAGATATTAAAAGATGATGAATCAATACTAAAAAATATTCTTAAAGATTGTTCTTATGATGAAAATTTTGTGAGAATAAATCTAGATGGTTTTGGTTTTAAAGGAGATGATGTATTTAAGAAAGTCTCTTCCTTAAGTGGTGGTGAAAAAGTAAAAATAGCACTTTGTAAAATATTATTATCTGATAATAACTTAATAATATTGGACGAACCTACAAACTATCTTGACATAAAATCTATGGAATCTCTAGAGACTGCATTGATTAATTGTAATAAAACATTAATTGTAGTTTCTCATGATAGAAACTTTATTTCTAATGTATGCGATTATATTTTAGAGATAGATAACAATTTAATTCATGAATTTTCTGGCACCTATGATGAATATATAAAATTTAAGAAAAAACCTAAGTTAGATGATAAAGAAAGAGCTAATAAAGATAGTCTTCTTCTCTTAGAAAACAGACTTTCTAATGTAATATCGCTCCTTTCAATAGAACCTGACAACAATAAAAAAAGTTTATTAGAAAATGAATATTATAATTTACTTAAAGAATTAAAAAACTTAAGAAAAAGATTAAGTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"46420","NCBI_taxonomy_name":"Clostridium perfringens str. 13","NCBI_taxonomy_id":"195102"}}}},"ARO_accession":"3007644","ARO_id":"46419","ARO_name":"Clostridium perfringes cplR","CARD_short_name":"Cper_cplR","ARO_description":"CplR is an ABC-F ATPase ribosomal protection protein from Clostridium perfringes which confers resistance to pleuromutilins and lincosamides.","ARO_category":{"45630":{"category_aro_accession":"3007068","category_aro_cvterm_id":"45630","category_aro_name":"Miscellaneous ABC-F subfamily ATP-binding cassette ribosomal protection proteins","category_aro_description":"ABC-F subfamily ATP-binding cassette ribosomal protection proteins of unknown, unclear or miscellaneous classification which nevertheless confer resistance to antibiotics through ribosomal protection and not through antibiotic efflux. These proteins should be further reviewed to elucidate associated genes, their function, origin and classification.","category_aro_class_name":"AMR Gene Family"},"35964":{"category_aro_accession":"0000046","category_aro_cvterm_id":"35964","category_aro_name":"lincomycin","category_aro_description":"Lincomycin is a lincosamide antibiotic that comes from the actinomyces Streptomyces lincolnensis. It binds to the 23s portion of the 50S subunit of bacterial ribosomes and inhibit early elongation of peptide chain by inhibiting transpeptidase reaction.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"37013":{"category_aro_accession":"3000669","category_aro_cvterm_id":"37013","category_aro_name":"virginiamycin M1","category_aro_description":"Virginiamycin M1 is a streptogramin A antibiotic.","category_aro_class_name":"Antibiotic"},"37713":{"category_aro_accession":"3001314","category_aro_cvterm_id":"37713","category_aro_name":"retapamulin","category_aro_description":"Retapamulin is a semi-synthetic pleuromutilin antibiotic approved for the treatment of skin infections.","category_aro_class_name":"Antibiotic"},"46411":{"category_aro_accession":"3007636","category_aro_cvterm_id":"46411","category_aro_name":"iboxamycin","category_aro_description":"Iboxamycin is a fully synthetic lincosamide antibiotic. Like other lincosamides, it selectively targets the bacterial ribosome and prevents elongation of the peptide chain. Iboxamycin has been shown to  be effective against bacterial strains otherwise resistant to licosamide antibiotics.","category_aro_class_name":"Antibiotic"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35952":{"category_aro_accession":"0000034","category_aro_cvterm_id":"35952","category_aro_name":"streptogramin A antibiotic","category_aro_description":"Streptogramin A antibiotics are cyclic polyketide peptide hybrids that bind to the ribosomal peptidyl transfer centre. Structural variation arises from substituting a proline for its desaturated derivative and by its substitution for Ala or Cys. Used alone, streptogramin A antibiotics are bacteriostatic, but is bactericidal when used with streptogramin B antibiotics.","category_aro_class_name":"Drug Class"},"37014":{"category_aro_accession":"3000670","category_aro_cvterm_id":"37014","category_aro_name":"pleuromutilin antibiotic","category_aro_description":"Pleuromutilins are natural fungal products that target bacterial protein translation by binding the the 23S rRNA, blocking the ribosome P site at the 50S subunit. They are mostly used for agriculture and veterinary purposes.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5984":{"model_id":"5984","model_name":"Clostridium sporogenes cplR","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1040"}},"model_sequences":{"sequence":{"8706":{"protein_sequence":{"accession":"AKC61310.1","sequence":"MVSIKLDKVKKYYEDKLILDIDNLEIKENSRIGIVGENGAGKTTLIKVILGELDIDEGKVFFHANYSYISQSENYTGSCNDGRIKSILGAPDNYNEFLSGGEKVKISINQALSSNSNFLIADEPTANLDTNTIKSIEKLISEYKGGLLLVSHDRDFLNNLCDNILEIENGKVKLYKCGYSKYLKLKAKEREVEKREYEEYITEKKRLEKAMMVKKNQQDSIRKAPKRMGNSEARLHKMGDQKSKKHLDGNIKSLKSRINHLEVKEKPISSKDIKIKITEGNKIPSKTVIEVKNLDLYIGDKLLIKDGNFKIKNGKKAAIIGENGCGKTTLIKEILKRDTENIRLSKYISIGYFDQNQDILDKDKTILDNIKSTSSYDESFMRIQLAGFGFKGDTIYKNVSILSGGEKVKVALSKIILSDTNTLILDEPTNYLDIKSIEALENALINTDKTIVMISHDRSFISSICNYIIEIKDTKLNCFSGTYTAFTEERVNYETKKQDNHSEREKKEKLLILENRLSKIISEISFEKDLIVKEKLNEEYIKLLNDIKLLKK"},"dna_sequence":{"accession":"CP009225.1","fmin":"653878","fmax":"655537","strand":"-","sequence":"ATGGTATCAATAAAATTAGATAAAGTAAAAAAATATTATGAAGATAAATTAATTTTAGATATAGACAATTTAGAAATAAAAGAAAATAGTAGAATCGGAATTGTTGGAGAAAATGGAGCTGGTAAAACAACTCTTATTAAAGTTATTTTAGGTGAACTAGATATTGATGAGGGAAAAGTATTTTTTCATGCTAATTATTCATATATAAGCCAAAGTGAAAACTATACTGGTTCCTGCAATGATGGCAGAATCAAGAGTATATTAGGTGCACCAGATAATTATAATGAATTTTTATCCGGTGGAGAAAAGGTGAAAATTAGTATTAATCAAGCCCTTAGTTCTAATAGCAATTTTCTTATAGCAGATGAGCCAACAGCTAATCTTGACACTAATACTATAAAAAGCATTGAAAAACTTATAAGTGAATATAAAGGAGGACTTTTATTAGTTTCTCATGATAGAGATTTTTTAAATAATCTTTGTGATAATATATTAGAAATAGAAAATGGAAAAGTTAAATTATATAAGTGTGGTTATTCAAAATATCTTAAACTAAAAGCTAAAGAAAGAGAAGTTGAAAAAAGAGAATATGAAGAATATATAACTGAAAAAAAGCGACTTGAAAAGGCTATGATGGTAAAAAAAAATCAACAAGATTCTATTAGAAAAGCACCTAAAAGAATGGGAAATTCGGAAGCAAGACTTCATAAAATGGGAGATCAGAAATCAAAAAAACACTTAGATGGAAATATAAAATCTTTAAAAAGTAGAATTAATCATCTTGAAGTGAAAGAAAAACCTATTTCTAGCAAAGATATTAAGATAAAAATTACTGAAGGTAATAAAATACCTTCTAAAACAGTAATAGAAGTAAAAAATTTAGATTTATATATAGGTGATAAACTTCTTATAAAAGATGGAAATTTCAAAATAAAAAACGGTAAAAAAGCAGCTATTATTGGTGAAAATGGCTGTGGTAAAACAACTTTAATAAAAGAAATATTAAAAAGAGATACAGAAAACATTAGATTATCAAAGTATATTTCTATAGGATATTTTGATCAAAATCAAGACATTTTAGATAAAGACAAAACAATATTAGATAATATAAAATCAACTAGTTCTTATGATGAAAGCTTTATGAGAATACAATTAGCTGGATTTGGGTTTAAAGGAGACACTATATACAAAAATGTTTCTATATTAAGTGGAGGAGAAAAAGTTAAAGTTGCACTTTCCAAAATAATTTTAAGTGATACTAATACTTTGATTTTAGATGAACCTACCAATTATTTAGATATAAAATCTATTGAAGCTTTAGAAAATGCACTTATTAATACAGACAAAACAATTGTAATGATATCTCATGATAGATCTTTTATTTCTAGTATATGTAATTATATAATTGAAATAAAAGATACTAAACTAAATTGTTTTTCGGGTACTTATACTGCTTTCACTGAAGAAAGAGTAAACTATGAAACTAAAAAACAGGATAACCATAGTGAGCGTGAAAAGAAGGAAAAATTATTAATCTTAGAAAATAGACTTTCAAAAATAATTTCAGAAATATCTTTTGAGAAAGATTTGATAGTTAAAGAGAAGTTAAATGAGGAATATATTAAATTATTAAACGACATCAAATTATTAAAAAAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43756","NCBI_taxonomy_name":"Clostridium sporogenes","NCBI_taxonomy_id":"1509"}}}},"ARO_accession":"3007645","ARO_id":"46421","ARO_name":"Clostridium sporogenes cplR","CARD_short_name":"Cspo_cplR","ARO_description":"CplR is an ABC-F ATPase ribosomal protection protein from Clostridium sporogenes which confers resistance to pleuromutilins and lincosamides.","ARO_category":{"45630":{"category_aro_accession":"3007068","category_aro_cvterm_id":"45630","category_aro_name":"Miscellaneous ABC-F subfamily ATP-binding cassette ribosomal protection proteins","category_aro_description":"ABC-F subfamily ATP-binding cassette ribosomal protection proteins of unknown, unclear or miscellaneous classification which nevertheless confer resistance to antibiotics through ribosomal protection and not through antibiotic efflux. These proteins should be further reviewed to elucidate associated genes, their function, origin and classification.","category_aro_class_name":"AMR Gene Family"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"37713":{"category_aro_accession":"3001314","category_aro_cvterm_id":"37713","category_aro_name":"retapamulin","category_aro_description":"Retapamulin is a semi-synthetic pleuromutilin antibiotic approved for the treatment of skin infections.","category_aro_class_name":"Antibiotic"},"46411":{"category_aro_accession":"3007636","category_aro_cvterm_id":"46411","category_aro_name":"iboxamycin","category_aro_description":"Iboxamycin is a fully synthetic lincosamide antibiotic. Like other lincosamides, it selectively targets the bacterial ribosome and prevents elongation of the peptide chain. Iboxamycin has been shown to  be effective against bacterial strains otherwise resistant to licosamide antibiotics.","category_aro_class_name":"Antibiotic"},"46413":{"category_aro_accession":"3007638","category_aro_cvterm_id":"46413","category_aro_name":"hygromycin A","category_aro_description":"Hygromycin A is an antibiotic produced by Streptomyces hygroscopicus. It inhibits translation by binding to the peptidyl transferase center on the large ribosomal subunit. This prevents the binding of aminoacyl-tRNA to the A-site. Not to confused with Hygromycin B, which is structurally distinct.","category_aro_class_name":"Antibiotic"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"36012":{"category_aro_accession":"3000003","category_aro_cvterm_id":"36012","category_aro_name":"antibiotic without defined classification","category_aro_description":"These compounds are antibiotics of unique structure or origin, without a defined classification.","category_aro_class_name":"Drug Class"},"37014":{"category_aro_accession":"3000670","category_aro_cvterm_id":"37014","category_aro_name":"pleuromutilin antibiotic","category_aro_description":"Pleuromutilins are natural fungal products that target bacterial protein translation by binding the the 23S rRNA, blocking the ribosome P site at the 50S subunit. They are mostly used for agriculture and veterinary purposes.","category_aro_class_name":"Drug Class"},"35999":{"category_aro_accession":"0001003","category_aro_cvterm_id":"35999","category_aro_name":"antibiotic target protection","category_aro_description":"Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5986":{"model_id":"5986","model_name":"PSZ-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"8707":{"protein_sequence":{"accession":"WGF22896.1","sequence":"MKLISQTLIATALTSACSMAFATTADVQATVDRAIKPLMQQQSIPGMAVAVVIKGQPHYFTWGMADVKQQRPVTQDTLFELGSVSKTFTGVLGGVAVNKGEIALSDAASKYWPALNTPQWRDTTLLQLATYTAGGLPLQVPDAVTDEKALANFYQQWQPQWTPGSTRQYANSSIGLFGWLATKPSGLTFEQAMQQRVFTPLQLKHTFITVPDAAKNAYAWGYREGKPVRVSPGMLDAEAYGVKSSVKDMARWMQANMDPQQVNDKPLQQALDFAQTRFYRTDALYQGLGWEMLDWPAQAEMAVKGADNKVALGPQPVRDAESHPRVSASWVHKTGATGGFGAYVAFIPEKQVGIVILANKNYPNTERVKAAMQILKALQ"},"dna_sequence":{"accession":"OQ725878.1","fmin":"202","fmax":"1342","strand":"+","sequence":"GTGAAATTGATTTCTCAAACATTGATAGCAACAGCGCTGACCTCGGCGTGCTCCATGGCGTTTGCCACCACGGCAGATGTGCAAGCAACCGTTGATCGGGCGATCAAACCGCTAATGCAGCAGCAATCGATTCCCGGCATGGCGGTAGCGGTGGTGATTAAAGGCCAGCCGCACTATTTCACCTGGGGCATGGCGGATGTCAAACAGCAGCGCCCGGTCACCCAAGACACGCTGTTTGAGCTGGGTTCGGTGAGTAAAACCTTCACCGGCGTGCTAGGTGGCGTCGCGGTGAATAAAGGCGAGATCGCGCTGAGCGATGCTGCCAGCAAATATTGGCCGGCACTGAATACGCCGCAGTGGCGCGACACCACGCTGCTGCAGCTGGCGACTTACACCGCTGGCGGCTTGCCGCTGCAGGTGCCCGATGCCGTGACCGATGAAAAGGCGCTGGCGAACTTCTATCAACAATGGCAACCACAATGGACGCCGGGCAGCACGCGTCAATATGCCAACAGCAGCATCGGCTTATTTGGCTGGCTGGCGACGAAACCCAGCGGGCTTACTTTTGAACAGGCAATGCAGCAGCGCGTATTCACGCCATTGCAGCTCAAGCACACCTTTATCACCGTGCCTGACGCCGCGAAAAACGCTTACGCATGGGGCTACCGCGAAGGCAAACCGGTGCGCGTGTCGCCGGGCATGCTGGATGCTGAAGCCTATGGCGTGAAGTCGTCGGTTAAAGATATGGCGCGCTGGATGCAGGCCAATATGGATCCGCAGCAGGTTAACGATAAGCCGCTGCAGCAGGCGCTGGATTTCGCGCAAACGCGTTTCTATCGCACCGATGCGCTCTATCAAGGTTTGGGGTGGGAGATGCTGGATTGGCCCGCTCAGGCGGAGATGGCGGTGAAGGGCGCGGATAACAAGGTGGCGCTTGGGCCGCAGCCGGTGCGGGATGCCGAATCACATCCGCGTGTCAGCGCGTCGTGGGTGCATAAGACCGGCGCAACCGGTGGGTTCGGTGCTTATGTCGCCTTCATCCCGGAGAAGCAGGTCGGCATTGTGATATTGGCAAACAAAAATTATCCCAATACCGAGCGGGTTAAAGCCGCGATGCAGATTCTGAAAGCGTTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"46425","NCBI_taxonomy_name":"Pantoea sp.","NCBI_taxonomy_id":"69393"}}}},"ARO_accession":"3007648","ARO_id":"46424","ARO_name":"PSZ-1","CARD_short_name":"PSZ-1","ARO_description":"PSZ-1 is a PSZ beta-lactamase found in Pantoea endophytica. The gene showed resistance to penicillins and several first-, second-and third-generation cephalosporins as well as aztreonam.","ARO_category":{"46423":{"category_aro_accession":"3007647","category_aro_cvterm_id":"46423","category_aro_name":"PSZ beta-lactamase","category_aro_description":"PSZ beta-lactamases are a novel AmpC enzyme gene family, which was found on a strain of Pantoea endophytica isolated from a rabbit in a livestock farm in China. It shows resistance to penicillins and several cephalosporins, and shares the highest amino acid similarity with the function-characterized AmpC enzyme ERH-1.","category_aro_class_name":"AMR Gene Family"},"35927":{"category_aro_accession":"0000008","category_aro_cvterm_id":"35927","category_aro_name":"cefoxitin","category_aro_description":"Cefoxitin is a cephamycin antibiotic often grouped with the second generation cephalosporins. Cefoxitin is bactericidal and acts by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. Cefoxitin's 7-alpha-methoxy group and 3' leaving group make it a poor substrate for most beta-lactamases.","category_aro_class_name":"Antibiotic"},"35975":{"category_aro_accession":"0000058","category_aro_cvterm_id":"35975","category_aro_name":"cefazolin","category_aro_description":"Cefazolin, also known as cefazoline or cephazolin, is a first generation cephalosporin antibiotic. It is administered parenterally, and is active against a broad spectrum of bacteria.","category_aro_class_name":"Antibiotic"},"35981":{"category_aro_accession":"0000064","category_aro_cvterm_id":"35981","category_aro_name":"amoxicillin","category_aro_description":"Amoxicillin is a moderate-spectrum, bacteriolytic, beta-lactam antibiotic used to treat bacterial infections caused by susceptible microorganisms. A derivative of penicillin, it has a wider range of treatment but remains relatively ineffective against Gram-negative bacteria. It is commonly taken with clavulanic acid, a beta-lactamase inhibitor. Like other beta-lactams, amoxicillin interferes with the synthesis of peptidoglycan.","category_aro_class_name":"Antibiotic"},"36976":{"category_aro_accession":"3000632","category_aro_cvterm_id":"36976","category_aro_name":"benzylpenicillin","category_aro_description":"Benzylpenicillin, commonly referred to as penicillin G, is effective against both Gram-positive and Gram-negative bacteria. It is unstable in acid.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"37084":{"category_aro_accession":"3000704","category_aro_cvterm_id":"37084","category_aro_name":"cefalotin","category_aro_description":"Cefalotin is a semisynthetic cephalosporin antibiotic activate against staphylococci. It is resistant to staphylococci beta-lactamases but hydrolyzed by enterobacterial beta-lactamases.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5987":{"model_id":"5987","model_name":"CDA-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"8708":{"protein_sequence":{"accession":"AID52933.1","sequence":"MKKSLCLTLLLAASCSTFAAPKQLTAQQIEKIVNRTISPLLKEQAIPGMAVAVIYKGYPLYFTWGKADVQHNEPVTRQTLFELGSVSKTFTGVLGGDTLARGEISLSDPAQKYWPELTGSQWKGITLLQLATYTAGGLPLQVPDEVTDSASLLNFYQSWQPQWAPGSKRLYANASIGLFGALMVKPSGMGFEQAMTTRVLEPLKLAHTWITVPPAEESHYAWGYRNDKAVRVSPGMLDAEAYGVKSSIEDMAHWVQANMVPERVEDQNLQQGIKLAQSRYWRIGSMYQGLGWEMLNWPLKGKVIIDGSDNKVALAPQTAVAIDPPAPLVKASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPERVKAAYAILEALQ"},"dna_sequence":{"accession":"KJ650399.1","fmin":"0","fmax":"1149","strand":"+","sequence":"ATGAAAAAATCCCTCTGCCTGACGCTGCTGCTCGCCGCCTCATGCTCTACTTTTGCCGCGCCAAAGCAGCTTACCGCGCAGCAGATCGAAAAAATCGTTAATCGCACGATTTCGCCGCTGCTGAAAGAGCAGGCGATCCCGGGTATGGCAGTCGCCGTTATCTATAAAGGCTACCCGCTGTATTTCACCTGGGGCAAAGCCGACGTGCAGCATAACGAACCGGTAACCCGGCAAACTCTGTTCGAGCTTGGTTCTGTAAGTAAAACATTTACCGGCGTGCTGGGCGGGGATACGCTGGCTCGCGGCGAGATAAGCCTTAGCGATCCGGCGCAAAAATATTGGCCAGAGCTAACCGGCAGCCAGTGGAAAGGAATAACGCTATTGCAACTGGCAACCTATACAGCAGGCGGGTTGCCGCTACAGGTGCCTGATGAAGTTACCGACAGCGCCTCGCTGCTCAACTTTTACCAGTCATGGCAGCCGCAGTGGGCACCAGGCAGCAAAAGGCTCTATGCCAACGCCAGCATTGGGTTGTTTGGGGCGTTGATGGTTAAGCCTTCAGGAATGGGCTTCGAGCAGGCGATGACAACGCGAGTGCTGGAACCATTGAAGCTGGCTCATACCTGGATAACCGTTCCTCCCGCTGAAGAGAGCCATTACGCCTGGGGCTACCGCAACGACAAAGCGGTACGCGTTTCACCGGGCATGCTGGATGCAGAAGCCTACGGCGTTAAGTCCAGCATCGAAGATATGGCGCACTGGGTGCAGGCGAATATGGTGCCGGAGCGGGTGGAAGACCAAAATCTGCAACAGGGGATCAAACTTGCTCAGTCTCGCTACTGGCGGATTGGCAGCATGTATCAGGGTCTGGGCTGGGAAATGCTGAACTGGCCGCTGAAGGGCAAAGTGATTATCGACGGCAGCGATAATAAAGTCGCCCTTGCCCCGCAGACCGCGGTCGCTATTGACCCACCGGCCCCGCTAGTGAAGGCATCCTGGGTACACAAAACTGGCTCAACCGGCGGCTTCGGTAGCTATGTGGCCTTTATTCCCGAAAAGCAGTTGGGCATCGTGATGCTGGCGAACAAAAGCTACCCGAATCCTGAGCGGGTAAAAGCCGCCTACGCTATTCTCGAAGCGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"46428","NCBI_taxonomy_name":"Cedecea davisae","NCBI_taxonomy_id":"158484"}}}},"ARO_accession":"3007650","ARO_id":"46427","ARO_name":"CDA-1","CARD_short_name":"CDA-1","ARO_description":"CDA-1 was recovered from a urine sample and is intermediate or resistant to third-generation cephalosporins and carbapenems. Susceptibility testing, isoelectric focusing, and analysis of outer membrane proteins showed that AmpC beta-lactamase expression combined with porin deficiency accounted for the carbapenem resistance.","ARO_category":{"35996":{"category_aro_accession":"0000079","category_aro_cvterm_id":"35996","category_aro_name":"clavulanic acid","category_aro_description":"Clavulanic acid is a beta-lactamase inhibitor (marketed by GlaxoSmithKline, formerly Beecham) combined with penicillin group antibiotics to overcome certain types of antibiotic resistance. It is used to overcome resistance in bacteria that secrete beta-lactamase, which otherwise inactivates most penicillins.","category_aro_class_name":"Adjuvant"},"46426":{"category_aro_accession":"3007649","category_aro_cvterm_id":"46426","category_aro_name":"CDA beta-lactamase","category_aro_description":"A CDA beta-lactamase was identified as a novel class C enzyme that was phylogenetically and biochemically close to the chromosome-borne beta-lactamases of the genera Enterobacter and Citrobacter.","category_aro_class_name":"AMR Gene Family"},"35927":{"category_aro_accession":"0000008","category_aro_cvterm_id":"35927","category_aro_name":"cefoxitin","category_aro_description":"Cefoxitin is a cephamycin antibiotic often grouped with the second generation cephalosporins. Cefoxitin is bactericidal and acts by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. Cefoxitin's 7-alpha-methoxy group and 3' leaving group make it a poor substrate for most beta-lactamases.","category_aro_class_name":"Antibiotic"},"37084":{"category_aro_accession":"3000704","category_aro_cvterm_id":"37084","category_aro_name":"cefalotin","category_aro_description":"Cefalotin is a semisynthetic cephalosporin antibiotic activate against staphylococci. It is resistant to staphylococci beta-lactamases but hydrolyzed by enterobacterial beta-lactamases.","category_aro_class_name":"Antibiotic"},"40523":{"category_aro_accession":"3003832","category_aro_cvterm_id":"40523","category_aro_name":"ticarcillin","category_aro_description":"Ticarcillin is a carboxypenicillin used for the treatment of Gram-negative bacteria, particularly P. aeruginosa. Ticarcillin's antibiotic properties arise from its ability to prevent cross-linking of peptidoglycan during cell wall synthesis, when the bacteria try to divide, causing cell death.","category_aro_class_name":"Antibiotic"},"41256":{"category_aro_accession":"3004129","category_aro_cvterm_id":"41256","category_aro_name":"cephaloridine","category_aro_description":"Cephaloridine is a semisynthetic, broad-spectrum, first-generation cephalosporin with antibacterial activity. Cephaloridine binds to and inactivates penicillin-binding proteins (PBPs) located on the inner membrane of the bacterial cell wall. PBPs are enzymes involved in the terminal stages of assembling the bacterial cell wall and in reshaping the cell wall during growth and division. Inactivation of PBPs interferes with the cross-linkage of peptidoglycan chains necessary for bacterial cell wall strength and rigidity. This results in the weakening of the bacterial cell wall and causes cell lysis.","category_aro_class_name":"Antibiotic"},"40955":{"category_aro_accession":"3004023","category_aro_cvterm_id":"40955","category_aro_name":"ticarcillin-clavulanic acid","category_aro_description":"An antibiotic cocktail containing the beta-lactam antibiotic ticarcillin and the beta-lactamase inhibitor clavulanic acid (clavulanate).","category_aro_class_name":"Antibiotic+Adjuvant"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5988":{"model_id":"5988","model_name":"erm(56)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"450"}},"model_sequences":{"sequence":{"8709":{"protein_sequence":{"accession":"WGG63489.1","sequence":"MSAYSRGRHENGQNFLTDSRVIASLLERVGSTSGPLIEIGPGQGALTHPLSCTGRSLTAVEIDPALAGALRRELDDAVTVINEDFLRYRLPAHPHVIVGNIPFHITTSILRRLLRAPGWTDAVLLMQWEVARRRAGVGASTMMTAQWAPWFTFELGERVSREAFTPRPSVDGGVLHIRRRPKMLVPVGKRKAFQALVHAVYTGKGRGIVDIVTQAKIFPSRQAARKWAERSGVHSHQLPSDLSVAQMVSLFESRGAVPPRRRKQRK"},"dna_sequence":{"accession":"OQ326498.1","fmin":"486","fmax":"1287","strand":"+","sequence":"ATGTCTGCATATTCTCGTGGTCGTCACGAAAACGGCCAGAACTTTCTCACTGACTCCCGCGTTATCGCCTCTCTCTTGGAGCGTGTGGGAAGCACTAGCGGCCCCTTGATTGAGATTGGTCCCGGCCAAGGAGCGCTGACTCATCCGTTGTCTTGTACGGGACGATCTCTCACAGCTGTTGAAATTGACCCCGCGCTGGCAGGTGCGCTGCGGCGGGAACTTGACGATGCTGTGACTGTCATCAACGAAGATTTTCTGAGATACCGTCTGCCAGCCCACCCTCATGTGATTGTTGGTAACATCCCGTTTCATATCACCACATCCATCTTGCGGCGCCTTCTTCGCGCCCCAGGCTGGACCGACGCTGTGCTGCTTATGCAGTGGGAGGTTGCCCGCCGACGTGCTGGCGTCGGTGCGTCAACCATGATGACCGCCCAGTGGGCTCCGTGGTTCACTTTTGAGCTTGGAGAACGTGTTAGCCGGGAGGCGTTTACCCCTCGTCCTAGTGTGGATGGTGGCGTTTTGCACATCCGACGCCGTCCTAAAATGTTGGTACCAGTTGGAAAGCGAAAGGCGTTCCAAGCTCTAGTGCACGCCGTCTATACGGGGAAGGGTCGTGGGATCGTCGATATCGTCACCCAAGCGAAGATATTTCCCTCTCGACAGGCGGCGCGGAAATGGGCCGAGCGGTCCGGTGTGCATTCGCATCAGCTGCCCTCTGACCTGTCTGTTGCTCAGATGGTCAGCCTCTTCGAAAGCCGTGGGGCAGTTCCGCCGCGACGCCGCAAACAGAGGAAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43836","NCBI_taxonomy_name":"Trueperella pyogenes","NCBI_taxonomy_id":"1661"}}}},"ARO_accession":"3007654","ARO_id":"46432","ARO_name":"erm(56)","CARD_short_name":"erm(56)","ARO_description":"Erm(56) is an Erm ribosomal RNA methyltransferase. Expression of the cloned erm(56) confers resistance to MLSB in T. pyogenes and Escherichia coli.","ARO_category":{"36699":{"category_aro_accession":"3000560","category_aro_cvterm_id":"36699","category_aro_name":"Erm 23S ribosomal RNA methyltransferase","category_aro_description":"Erm proteins are part of the RNA methyltransferase family and methylate A2058 (E. coli nomenclature) of the 23S ribosomal RNA conferring degrees of resistance to Macrolides, Lincosamides and Streptogramin b. This is called the MLSb phenotype.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35983":{"category_aro_accession":"0000066","category_aro_cvterm_id":"35983","category_aro_name":"clindamycin","category_aro_description":"Clindamycin is a lincosamide antibiotic that blocks A-site aminoacyl-tRNA binding. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria.","category_aro_class_name":"Antibiotic"},"36722":{"category_aro_accession":"3000583","category_aro_cvterm_id":"36722","category_aro_name":"pristinamycin IA","category_aro_description":"Pristinamycin IA is a type B streptogramin antibiotic produced by Streptomyces pristinaespiralis. It binds to the P site of the 50S subunit of the bacterial ribosome, preventing the extension of protein chains.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35936":{"category_aro_accession":"0000017","category_aro_cvterm_id":"35936","category_aro_name":"lincosamide antibiotic","category_aro_description":"Lincosamides (e.g. lincomycin, clindamycin) are a class of drugs which bind to the 23s portion of the 50S subunit of bacterial ribosomes. This interaction inhibits early elongation of peptide chains by inhibiting the transpeptidase reaction, acting similarly to macrolides.","category_aro_class_name":"Drug Class"},"35945":{"category_aro_accession":"0000026","category_aro_cvterm_id":"35945","category_aro_name":"streptogramin antibiotic","category_aro_description":"Streptogramin antibiotics are natural products produced by various members of the Streptomyces genus. These antibiotics bind to the P site of the 50S subunit of bacterial ribosomes to inhibit protein synthesis. The family consists of two subgroups, type A and type B, which are simultaneously produced by the same bacterial species in a ratio of roughly 70:30.","category_aro_class_name":"Drug Class"},"35967":{"category_aro_accession":"0000050","category_aro_cvterm_id":"35967","category_aro_name":"streptogramin B antibiotic","category_aro_description":"Streptogramin B antibiotics are are cyclic hepta- or hexa-depsipeptides.  Type B streptogramins block the peptide exit tunnel of the 50S bacterial ribosome. The general composition of group B streptogramins is 3-hydroxypicolinic acid-L-Thr-D-aminobutyric acid (or D-Ala)-L-Pro-L-Phe (or 4-N-,N-(dimethylamino)-L-Phe)-X-L-phenylglycine. Used alone, streptogramin B antibiotics are bacteriostatic, but is bactericidal when used with streptogramin A antibiotics.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"6065":{"model_id":"6065","model_name":"VRA-F","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"13250":"K84E"},"Curated-R":{"13250":"K84E"},"clinical":{"13250":"K84E"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8888":{"protein_sequence":{"accession":"WP_323056190.1","sequence":"MAILEVKQLTKIYGTKKMAQEVLRDINMSIEEGEFIAIMGPSGSGKTTLLNVLSSIDYISQGSITLKGKKLEKLSNKELSDIREHDIGFIFQEYNLLHTLTVKENIMLPLTVQKLDKEHMLNRYEKVAEALNILDISDKYPSELSGGQRQRTSAARAFITLPSIIFADEPTGALDSKSTQDLLKRLTRMNEAFKSTIIMVTHDPVAASYANRVVMLKDGQIFTELYQGDDDKHTFFKEIIRVQSVLGGVNYDL"},"dna_sequence":{"accession":"NZ_JAYEPV010000001.1","fmin":"691066","fmax":"691828","strand":"-","sequence":"GTGGCAATTTTAGAAGTAAAACAATTAACAAAAATATATGGAACTAAAAAAATGGCACAAGAAGTGTTGCGAGATATCAATATGTCTATTGAAGAAGGCGAGTTTATTGCTATTATGGGTCCCTCTGGATCTGGGAAAACGACATTATTAAATGTTTTAAGTTCAATTGATTATATTTCACAAGGTTCTATTACATTAAAAGGAAAAAAATTAGAAAAGCTTTCAAACAAGGAATTATCTGATATACGCGAGCATGATATTGGTTTTATTTTTCAAGAGTATAATTTACTGCATACATTGACTGTTAAAGAAAACATAATGTTACCACTAACGGTTCAGAAGTTAGATAAAGAACATATGTTAAATCGTTATGAAAAAGTAGCAGAAGCATTAAATATATTGGATATTAGTGATAAATACCCTTCTGAATTGTCTGGTGGACAAAGACAACGAACATCTGCTGCAAGAGCGTTTATTACATTACCTTCTATTATATTTGCTGACGAACCAACAGGTGCACTGGATTCTAAAAGTACTCAAGATTTATTAAAACGATTAACAAGAATGAATGAAGCATTTAAGTCTACAATTATTATGGTAACGCATGATCCTGTTGCAGCAAGTTATGCCAATCGAGTAGTGATGCTAAAAGATGGTCAAATTTTCACTGAATTATACCAAGGGGATGACGATAAACATACCTTTTTCAAAGAAATAATACGTGTACAAAGTGTTTTAGGTGGCGTTAATTATGACCTTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35508","NCBI_taxonomy_name":"Staphylococcus aureus","NCBI_taxonomy_id":"1280"}}}},"ARO_accession":"3007843","ARO_id":"46632","ARO_name":"VRA-F","CARD_short_name":"VRA-F","ARO_description":"VRA-F is an ABC transporter ATP-binding protein, or ATP-binding cassette.","ARO_category":{"36002":{"category_aro_accession":"0010001","category_aro_cvterm_id":"36002","category_aro_name":"ATP-binding cassette (ABC) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. ATP-binding cassette (ABC) transporters are present in all cells of all organisms and use the energy of ATP binding\/hydrolysis to transport substrates across cell membranes.","category_aro_class_name":"AMR Gene Family"},"35947":{"category_aro_accession":"0000028","category_aro_cvterm_id":"35947","category_aro_name":"vancomycin","category_aro_description":"Vancomycin is a glycopeptide antibiotic used in the prophylaxis and treatment of infections caused by Gram-positive bacteria. Vancomycin inhibits the synthesis of peptidoglycan, the major component of the cell wall of gram-positive bacteria. Its mechanism of action is unusual in that it acts by binding precursors of peptidoglycan, rather than by interacting with an enzyme.","category_aro_class_name":"Antibiotic"},"36220":{"category_aro_accession":"3000081","category_aro_cvterm_id":"36220","category_aro_name":"glycopeptide antibiotic","category_aro_description":"Glycopeptide antibiotics are natural products produced non-ribosomally by Actinomycetales bacteria. With the exception of bleomycins, they act by binding the terminal D-Ala-D-Ala in peptidoglycan precursors of the growing bacterial cell wall and are generally active against Gram-positive bacteria.  This inhibits transglycosylation leading to cell death due to osmotic stress.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"6067":{"model_id":"6067","model_name":"SIE-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"8890":{"protein_sequence":{"accession":"APL95059.1","sequence":"MIATMTIAASLAISPAAAATGPEPEAMAAMDRAGGARASDDPLTRPMAVERAKEWLAPLPPERVFGNSYLVGFAGLSVALIDTGAGLVLIDGALPQAAPMILSNVRKLGFDPRDIKFILSTEPHYDHAGGIAALARDTGATVVASRRGAEGLRAGAHAKDDPQFDYGGAWPAVSRLRVMKDGEVLRIGRASITAHATPGHTMGSMTWSWNACEGKRCKAIVFASSLNPVSADRYRFTAPSSAPIVKGFEASYRRMGALKCDILISAHPDNAGAGRYGSGSGACRSYAERSRRLLAKRLAEERRETSK"},"dna_sequence":{"accession":"CP013070.1","fmin":"2379245","fmax":"2380169","strand":"-","sequence":"ATGATCGCAACGATGACAATCGCCGCGTCGCTGGCCATCAGCCCGGCGGCGGCAGCGACAGGGCCGGAGCCGGAAGCCATGGCGGCCATGGACCGGGCGGGCGGCGCCCGCGCCTCCGATGACCCTCTGACCCGGCCGATGGCGGTCGAAAGAGCCAAGGAATGGCTTGCGCCCCTGCCGCCCGAAAGGGTTTTCGGCAACAGCTATCTGGTCGGCTTCGCGGGTCTCAGCGTCGCCTTGATCGACACGGGTGCGGGCCTGGTGCTGATCGACGGCGCGCTTCCGCAGGCGGCGCCGATGATCCTCAGCAATGTTCGCAAGCTGGGCTTCGACCCCAGAGACATCAAATTTATTCTGAGTACCGAGCCGCATTATGATCATGCTGGCGGGATCGCCGCCCTGGCGCGCGACACCGGCGCCACCGTGGTGGCCAGCCGGCGCGGCGCGGAGGGCCTGCGGGCAGGCGCGCATGCGAAGGACGATCCGCAATTCGACTATGGCGGCGCCTGGCCGGCGGTGTCGCGGCTGCGCGTCATGAAGGACGGAGAGGTTCTGAGGATCGGCCGCGCATCCATCACCGCGCATGCGACGCCGGGCCACACGATGGGCAGCATGACATGGAGCTGGAACGCCTGCGAGGGCAAGAGGTGCAAGGCGATCGTCTTCGCCTCCAGCCTCAATCCGGTGTCGGCCGACCGTTACCGTTTCACCGCGCCTTCCAGCGCGCCGATCGTCAAGGGCTTCGAAGCCAGCTACAGGCGCATGGGCGCTTTGAAGTGCGACATTTTGATCTCCGCGCATCCCGACAATGCGGGCGCGGGGCGGTATGGCAGTGGATCCGGGGCCTGCCGGTCCTATGCGGAACGTTCGCGCCGCCTGCTCGCGAAGCGGTTGGCCGAGGAGCGGCGAGAGACGTCGAAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"46636","NCBI_taxonomy_name":"Sphingobium indicum B90A","NCBI_taxonomy_id":"861109"}}}},"ARO_accession":"3007846","ARO_id":"46635","ARO_name":"SIE-1","CARD_short_name":"SIE-1","ARO_description":"SIE-1 is SIE beta-lactamase gene family variant.","ARO_category":{"46634":{"category_aro_accession":"3007845","category_aro_cvterm_id":"46634","category_aro_name":"SIE beta-lactamase","category_aro_description":"SIE is a subclass B3 metallo-beta-lactamase with enzymatic activity against cephalosporins and carbapanems, first identified from Sphingobium indicum.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5989":{"model_id":"5989","model_name":"putative nickel\/cobalt transporter","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"8710":{"protein_sequence":{"accession":"NP_217372.1","sequence":"MASSQLDRQRSRSAKMNRALTAAEWWRLGLMFAVIVALHLVGWLTVTLLVEPARLSLGGKAFGIGVGLTAYTLGLRHAFDADHIAAIDNTTRKLMSDGHRPLAVGFFFSLGHSTVVFGLAVMLVTGLKAIVGPVENDSSTLHHYTGLIGTSISGAFLYLIGILNVIVLVGIVRVFAHLRRGDYDEAELEQQLDNRGLLIRFLGRFTKSLTKSWHMYPVGFLFGLGFDTATEIALLVLAGTSAAAGLPWYAILCLPVLFAAGMCLLDTIDGSFMNFAYGWAFSSPVRKIYYNITVTGLSVAVALLIGSVELLGLIANQLGWQGPFWDWLGGLDLNTVGFVVVAMFALTWAIALLVWHYGRVEERWTPAPDRTT"},"dna_sequence":{"accession":"NC_000962.3","fmin":"3166683","fmax":"3167802","strand":"+","sequence":"ATGGCCAGCAGCCAGCTCGACAGGCAGAGGTCGCGGTCGGCCAAAATGAACCGCGCTCTGACAGCAGCAGAATGGTGGCGTCTGGGCCTGATGTTCGCGGTGATCGTCGCCTTGCATCTGGTTGGCTGGCTCACCGTGACGCTCTTGGTGGAGCCCGCGCGGCTCAGCTTGGGCGGCAAGGCATTCGGCATCGGCGTCGGGCTGACGGCGTACACGCTGGGCTTACGGCACGCGTTCGACGCCGACCACATCGCCGCCATCGACAACACCACCCGCAAGCTGATGAGCGACGGACACCGACCCCTTGCCGTCGGGTTCTTCTTTTCACTGGGCCACTCCACGGTGGTCTTCGGGCTGGCGGTAATGCTGGTGACCGGACTCAAGGCTATCGTCGGACCGGTCGAGAACGACTCCTCGACGCTGCATCACTACACAGGCTTGATCGGTACCAGCATTTCCGGCGCGTTCCTGTATTTGATCGGCATCCTCAACGTCATCGTCCTGGTCGGCATCGTGCGTGTCTTCGCCCACCTGCGCCGCGGCGACTACGACGAAGCCGAACTCGAACAGCAGTTGGACAACCGCGGACTGCTCATCCGGTTCCTCGGCCGCTTCACCAAGTCACTCACCAAGTCCTGGCATATGTACCCGGTCGGATTTTTGTTCGGTCTCGGGTTCGACACCGCCACCGAGATCGCGCTGTTGGTGCTGGCGGGAACCAGTGCCGCGGCCGGCCTGCCCTGGTATGCCATCCTGTGCCTGCCCGTCTTGTTCGCCGCCGGCATGTGTCTGCTGGACACCATCGACGGTTCGTTCATGAATTTCGCGTACGGCTGGGCCTTCTCCAGCCCCGTGCGCAAGATCTACTACAACATCACCGTCACCGGACTGTCGGTGGCAGTCGCACTGTTGATTGGCAGCGTTGAGCTGCTGGGCCTGATCGCCAACCAGTTGGGTTGGCAGGGCCCGTTCTGGGACTGGCTTGGCGGCCTCGACCTCAACACCGTCGGCTTCGTCGTCGTCGCGATGTTCGCGCTCACCTGGGCCATTGCCCTGCTGGTCTGGCACTACGGCCGCGTTGAAGAGCGGTGGACCCCGGCGCCCGACCGCACAACTTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3007659","ARO_id":"46437","ARO_name":"putative nickel\/cobalt transporter","CARD_short_name":"Rv2856","ARO_description":"Ectopic expression of NiCoT in Escherichia coli CS109 resulted in the increase of intracellular nickel uptake with enhanced tolerance towards several antibiotics when NiCoT was overexpressed in E. coli and Mycobacterium smegmatis. The presence of a sub-inhibitory dose of nickel resulted in the manifestation of low-level tolerance towards these drugs.","ARO_category":{"46435":{"category_aro_accession":"3007657","category_aro_cvterm_id":"46435","category_aro_name":"metal transporters with antibiotic efflux","category_aro_description":"Efflux pumps also regulate the level of metal ions in the cytoplasm but are toxic when in excess. Metals often act as a facilitator in the proliferation and persistence of antibiotic resistance. Therefore, metal contamination in natural environments could have an important role in maintaining and promoting antibiotic resistance. The presence of metals co-selects for antibiotic resistance and leads to the development of cross-resistance. Micro-organisms adopt various mechanisms that may confer resistance against more than one antimicrobial, of which multidrug efflux systems are the most common.","category_aro_class_name":"AMR Gene Family"},"36659":{"category_aro_accession":"3000520","category_aro_cvterm_id":"36659","category_aro_name":"isoniazid","category_aro_description":"Isoniazid is an organic compound that is the first-line anti tuberculosis medication in prevention and treatment. As a prodrug, it is activated by mycobacterial catalase-peroxidases such as M. tuberculosis KatG. Isoniazid inhibits mycolic acid synthesis, which prevents cell wall synthesis in mycobacteria.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"37006":{"category_aro_accession":"3000662","category_aro_cvterm_id":"37006","category_aro_name":"norfloxacin","category_aro_description":"Norfloxacin is a 6-fluoro, 7-piperazinyl quinolone with a wide range of activity against Gram-negative bacteria. It is inactive against most anaerobes.","category_aro_class_name":"Antibiotic"},"37007":{"category_aro_accession":"3000663","category_aro_cvterm_id":"37007","category_aro_name":"ofloxacin","category_aro_description":"Ofloxacin is a 6-fluoro, 7-piperazinyl quinolone with a methyl-substituted oxazine ring. It has a broad spectrum of activity including many enterobacteria and mycoplasma but most anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"37010":{"category_aro_accession":"3000666","category_aro_cvterm_id":"37010","category_aro_name":"sparfloxacin","category_aro_description":"Sparfloxacin is a dimethylpiperazinyl difluoroquinolone that acts by inhibiting DNA gyrase. It is active against aerobic Gram-positive and Gram-negative bacteria, as well as some mycobacteria. It has moderate activity against some anaerobes.","category_aro_class_name":"Antibiotic"},"46133":{"category_aro_accession":"3007382","category_aro_cvterm_id":"46133","category_aro_name":"gentamicin","category_aro_description":"Gentamicin is a commonly used aminoglycoside antibiotic derived from members of the Micromonospora genus of bacteria. It acts by binding the 30S ribosomal subunit, thus inhibiting protein synthesis. Gentamicin is typically used to treat Gram-negative infections of the repiratory and urinary tract, as well as infections of the bone and soft tissue. It also exhibits considerable nephrotoxicity and ototoxicity. Gentamicin is administered as a mixture of gentamicin type C (which makes about around 80% of the complex) and types A, B, and X (distributed in the remaining 20% of the complex).","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"45734":{"category_aro_accession":"3007152","category_aro_cvterm_id":"45734","category_aro_name":"isoniazid-like antibiotic","category_aro_description":"A group of antibiotics containing isoniazid and its derivatives.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"6000":{"model_id":"6000","model_name":"Mycobacterium tuberculosis ddn mutation conferring resistance to nitroimidazole antibiotics","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"15418":"M1Var","15420":"L49P"},"WHO-R":{"15418":"M1Var","15419":"M1Var","15423":"M1Var","15424":"M1Var","15420":"L49P"},"clinical":{"15418":"M1Var","15420":"L49P"},"Curated-R":{"13131":"M1Var"}},"40394":{"param_type":"nonsense mutation","param_description":"A sequence change where, compared to a reference sequence, one codon is replaced by a termination codon through a nucleotide substitution. These are described as a substitution of the wildtype codon to a termination codon. Format is given as [wild type AA][position][Ter], for example Q42Ter where Q42 is a wildtype amino acid replaced by a premature termination codon.","param_type_id":"40394","param_value":{"15419":"W20Ter","15423":"W88Ter","15424":"W139Ter","13131":"W20Ter"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"275"}},"model_sequences":{"sequence":{"8721":{"protein_sequence":{"accession":"NP_218064.1","sequence":"MPKSPPRFLNSPLSDFFIKWMSRINTWMYRRNDGEGLGGTFQKIPVALLTTTGRKTGQPRVNPLYFLRDGGRVIVAASKGGAEKNPMWYLNLKANPKVQVQIKKEVLDLTARDATDEERAEYWPQLVTMYPSYQDYQSWTDRTIPIVVCEP"},"dna_sequence":{"accession":"NC_000962.3","fmin":"3986843","fmax":"3987299","strand":"+","sequence":"ATGCCGAAATCACCGCCGCGGTTTCTGAATTCGCCGCTCAGCGACTTCTTTATCAAGTGGATGTCACGGATTAATACCTGGATGTACCGCCGCAACGACGGGGAGGGTCTGGGCGGCACCTTCCAGAAGATTCCGGTCGCGCTGCTGACCACCACCGGCCGCAAGACCGGCCAGCCGCGGGTCAACCCGCTCTACTTCCTGCGCGACGGTGGGCGGGTCATTGTCGCGGCCTCCAAGGGCGGCGCGGAGAAGAACCCGATGTGGTACCTCAACCTCAAGGCCAACCCCAAGGTTCAGGTACAGATCAAAAAGGAAGTGCTGGACCTTACCGCGCGGGACGCGACCGACGAGGAGCGCGCCGAATATTGGCCACAGTTGGTCACGATGTACCCAAGTTATCAGGACTACCAGTCCTGGACCGACCGCACGATCCCGATCGTGGTTTGCGAACCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3007661","ARO_id":"46441","ARO_name":"Mycobacterium tuberculosis ddn mutation conferring resistance to nitroimidazole antibiotics","CARD_short_name":"Mtub_ddn_MULT","ARO_description":"ddn is a protein-coding gene involved in the bioreductive activation of bicyclic 4-nitroimidazole prodrugs such as PA-824 and delamanid developed for anti-tuberculosis therapy against both replicating and persistent bacteria.","ARO_category":{"46434":{"category_aro_accession":"3007656","category_aro_cvterm_id":"46434","category_aro_name":"antibiotic resistant Mycobacterium tuberculosis nitroreductase","category_aro_description":"Inactivation of the F420-dependent anti-oxidant mechanism that protects M.tuberculosis against oxidative stress and bactericidal agents plays a role in antibiotic resistance.","category_aro_class_name":"AMR Gene Family"},"41931":{"category_aro_accession":"3004490","category_aro_cvterm_id":"41931","category_aro_name":"delamanid","category_aro_description":"A novel nitroimidazole antibiotic for treating Mycobacterium tuberculosis infection. Delamanid inhibits bacterial cell wall growth by mycolic acid synthesis disruption and is particularly effective in combination therapies against multidrug-resistant tuberculosis.","category_aro_class_name":"Antibiotic"},"46306":{"category_aro_accession":"3007535","category_aro_cvterm_id":"46306","category_aro_name":"pretomanid","category_aro_description":"Pretomanid is an antibiotic medication used for the treatment of multi-drug-resistant tuberculosis affecting the lungs.","category_aro_class_name":"Antibiotic"},"41239":{"category_aro_accession":"3004115","category_aro_cvterm_id":"41239","category_aro_name":"nitroimidazole antibiotic","category_aro_description":"Nitroimidazoles are a group of drugs that have both antiprotozoal and antibacterial activity, classified with respect to the location of the nitro functional group.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"6001":{"model_id":"6001","model_name":"Rv1877","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1300"}},"model_sequences":{"sequence":{"8722":{"protein_sequence":{"accession":"NP_216393.1","sequence":"MAGPTAPTTAPTAIRAGGPLLSPVRRNIIFTALVFGVLVAATGQTIVVPALPTIVAELGSTVDQSWAVTSYLLGGTVVVVVAGKLGDLLGRNRVLLGSVVVFVVGSVLCGLSQTMTMLAISRALQGVGAGAISVTAYALAAEVVPLRDRGRYQGVLGAVFGVNTVTGPLLGGWLTDYLSWRWAFWINVPVSIAVLTVAATAVPALARPPKPVIDYLGILVIAVATTALIMATSWGGTTYAWGSATIVGLLIGAAVALGFFVWLEGRAAAAILPPRLFGSPVFAVCCVLSFVVGFAMLGALTFVPIYLGYVDGASATASGLRTLPMVIGLLIASTGTGVLVGRTGRYKIFPVAGMALMAVAFLLMSQMDEWTPPLLQSLYLVVLGAGIGLSMQVLVLIVQNTSSFEDLGVATSGVTFFRVVGASFGTATFGALFVNFLDRRLGSALTSGAVPVPAVPSPAVLHQLPQSMAAPIVRAYAESLTQVFLCAVSVTVVGFILALLLREVPLTDIHDDADDLGDGFGVPRAESPEDVLEIAVRRMLPNGVRLRDIATQPGCGLGVAELWALLRIYQYQRLFEAVRLTDIGRHLHVPYQVFEPVFDRLVQTGYAARDGDILTLTPSGHRQVDSLAVLIRQWLLDHLAVAPGLKRQPDHQFEAALQHVTDAVLVQRDWYEDLGDLSESRQLAATT"},"dna_sequence":{"accession":"NC_000962.3","fmin":"2125903","fmax":"2127967","strand":"+","sequence":"ATGGCGGGCCCCACAGCACCGACCACTGCCCCCACCGCAATCCGAGCCGGTGGCCCGCTGCTCAGTCCGGTGCGACGCAACATTATTTTCACCGCACTTGTGTTCGGGGTGCTGGTCGCTGCGACCGGCCAAACCATCGTTGTGCCCGCATTGCCGACGATCGTCGCCGAGCTGGGCAGCACCGTTGACCAGTCGTGGGCGGTCACCAGCTATCTGCTGGGGGGAACTGTCGTGGTTGTGGTGGCTGGCAAGCTCGGTGATCTGCTCGGCCGCAACAGGGTGCTGCTAGGCTCCGTCGTGGTCTTCGTCGTTGGCTCTGTGCTGTGCGGGTTATCGCAGACGATGACCATGCTGGCGATCTCTCGCGCACTGCAGGGCGTCGGTGCCGGTGCGATTTCCGTCACCGCCTACGCGCTGGCCGCTGAGGTGGTCCCACTGCGGGACCGTGGCCGCTACCAGGGCGTCTTAGGTGCGGTGTTCGGTGTCAACACGGTCACCGGTCCGCTGCTGGGGGGCTGGCTCACCGACTATCTGAGCTGGCGGTGGGCGTTTTGGATCAACGTGCCGGTTTCGATCGCGGTGCTGACAGTGGCGGCAACCGCCGTCCCTGCGTTGGCCCGACCGCCCAAACCGGTCATCGACTACCTTGGGATCCTGGTCATCGCTGTGGCCACGACCGCTTTGATCATGGCCACAAGTTGGGGCGGAACCACCTACGCCTGGGGCTCAGCGACCATTGTCGGGCTGTTGATCGGGGCCGCAGTGGCGCTGGGTTTCTTCGTGTGGCTGGAGGGCCGCGCCGCTGCGGCCATCCTGCCGCCCAGGCTGTTTGGCAGCCCAGTATTTGCCGTGTGCTGCGTCCTGTCCTTCGTGGTCGGATTCGCGATGCTGGGTGCACTGACCTTCGTACCGATCTATCTGGGGTACGTGGACGGCGCGTCGGCGACCGCGTCAGGTCTGCGCACGTTGCCGATGGTGATCGGCCTGCTGATCGCCTCGACCGGGACGGGTGTCCTGGTCGGCCGGACGGGCCGCTACAAGATCTTCCCGGTCGCGGGGATGGCGCTGATGGCGGTTGCGTTCCTGCTGATGTCGCAGATGGACGAGTGGACGCCACCGCTGCTGCAATCGCTGTACCTGGTCGTCCTAGGTGCCGGCATCGGATTGTCCATGCAGGTGCTCGTTCTCATCGTGCAGAACACGTCGTCTTTCGAAGACCTCGGCGTCGCAACATCGGGTGTGACCTTCTTCCGGGTGGTCGGCGCCTCGTTTGGTACCGCAACATTCGGTGCGTTGTTCGTAAACTTCCTGGACCGAAGACTCGGTTCCGCGCTGACGTCGGGCGCCGTGCCTGTCCCGGCAGTGCCATCTCCGGCTGTCTTGCATCAGCTGCCCCAGAGCATGGCCGCCCCGATCGTGCGGGCATATGCCGAGTCGCTCACCCAGGTGTTCCTTTGCGCGGTCTCGGTCACGGTGGTCGGTTTCATCCTGGCGCTGTTGCTGCGAGAGGTACCGCTCACCGACATCCACGATGACGCCGACGACCTCGGCGACGGGTTCGGTGTGCCCAGAGCCGAATCGCCGGAGGATGTGTTGGAAATCGCGGTTCGGCGTATGCTGCCGAACGGGGTGCGACTGCGCGATATTGCGACACAACCCGGTTGCGGACTCGGCGTCGCCGAGCTGTGGGCCCTTCTGCGGATCTATCAATACCAGCGGCTGTTCGAGGCAGTACGGCTGACCGATATCGGTAGACACCTGCACGTGCCCTATCAGGTCTTTGAACCCGTCTTCGACCGTCTGGTCCAGACCGGCTACGCGGCACGCGACGGCGACATCTTGACGCTAACCCCGTCCGGGCACCGTCAGGTCGACTCCCTCGCAGTTTTGATCCGTCAGTGGCTGCTCGACCACTTGGCCGTGGCGCCCGGCTTGAAGCGACAGCCAGACCACCAATTCGAAGCCGCTCTGCAGCACGTCACCGACGCGGTGCTCGTTCAACGAGACTGGTATGAAGATCTGGGCGACCTGTCGGAATCACGCCAACTCGCGGCTACAACGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3007662","ARO_id":"46442","ARO_name":"Rv1877","CARD_short_name":"Rv1877","ARO_description":"Rv1877, a putative Major Facilitator Superfamily efflux pump from M. tuberculosis actively effluxes fluoroquinolones ofloxacin and levofloxacin.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"37007":{"category_aro_accession":"3000663","category_aro_cvterm_id":"37007","category_aro_name":"ofloxacin","category_aro_description":"Ofloxacin is a 6-fluoro, 7-piperazinyl quinolone with a methyl-substituted oxazine ring. It has a broad spectrum of activity including many enterobacteria and mycoplasma but most anaerobes are resistant.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"6037":{"model_id":"6037","model_name":"VIM-76","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8857":{"protein_sequence":{"accession":"BDA82255.1","sequence":"MFKLLSKLLVYLTASIMAIASPLAFSVDSSGEYPTVSEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAELEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSASVLYGGCAIYELSLTSAGNVADADLAEWPTSIERIQQRYPEAQFVIPGHGLPGGLDLLKHTTNVVKAHTNRSVVE"},"dna_sequence":{"accession":"LC648428.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGTTCAAACTTTTGAGTAAGTTATTGGTCTATTTGACCGCGTCTATCATGGCTATTGCGAGTCCGCTCGCTTTTTCCGTAGATTCTAGCGGTGAGTATCCGACAGTCAGCGAAATTCCGGTCGGGGAGGTCCGGCTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCAGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAGAAGCAAATTGGACTTCCTGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGCTAGAGGGGAACGAGATTCCCACGCACTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAACTCTTCTATCCTGGTGCTGCGCATTCGACCGACAACTTAGTTGTGTACGTCCCGTCTGCGAGTGTGCTCTATGGTGGTTGTGCGATTTATGAGTTGTCACTCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCATTGAGCGGATTCAACAACGCTACCCGGAAGCACAGTTCGTCATTCCGGGGCACGGCCTGCCGGGCGGTCTAGACTTGCTCAAGCACACAACGAATGTTGTAAAAGCGCACACAAATCGCTCAGTCGTTGAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3007813","ARO_id":"46599","ARO_name":"VIM-76","CARD_short_name":"VIM-76","ARO_description":"VIM-76 is a subclass B1 carbapenem-hydrolyzing metallo-beta-lactamase.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"6039":{"model_id":"6039","model_name":"VIM-78","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8859":{"protein_sequence":{"accession":"UBK22127.1","sequence":"MLKVISSLLVYMTASVMAVASPLAHSGEPSGEYPTVNEIPVGEVRLYQIADGVWSHIATRSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEAEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSANVLYGGCAVHELSRTSAGNVADADLAEWPTSVERIQKHYPEAEVVIPGHGLPGGLDLLQHTANVVKAHKNRSVAE"},"dna_sequence":{"accession":"OK180983.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGTTAAAAGTTATTAGTAGTTTATTGGTCTACATGACCGCGTCTGTCATGGCTGTCGCAAGTCCGTTAGCCCATTCCGGGGAGCCGAGTGGTGAGTATCCGACAGTCAACGAAATTCCGGTCGGAGAGGTCCGACTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCGGTCGTTTGATGGCGCGGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAAAAGCAAATTGGACTTCCCGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGCAGAGGGGAACGAGATTCCCACGCATTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAGCTCTTCTATCCTGGTGCTGCGCATTCGACCGACAATCTGGTTGTATACGTCCCGTCAGCGAACGTGCTATACGGTGGTTGTGCCGTTCATGAGTTGTCACGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCGTTGAGCGGATTCAAAAACACTACCCGGAAGCAGAGGTCGTCATTCCCGGGCACGGTCTACCGGGCGGTCTAGACTTGCTCCAGCACACAGCGAACGTTGTCAAAGCACACAAAAATCGCTCAGTCGCCGAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3007815","ARO_id":"46602","ARO_name":"VIM-78","CARD_short_name":"VIM-78","ARO_description":"VIM-78 is a subclass B1 carbapenem-hydrolyzing metallo-beta-lactamase.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"6041":{"model_id":"6041","model_name":"VIM-80","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8861":{"protein_sequence":{"accession":"MBC9045152.1","sequence":"MFKLLSKLLVYLTASIMAIASPLAFSVDSSGEYPTVSEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEVEGNEITHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSASVLYGGCAIYELSRTSAGNVADADLAEWPTSIERIQQHYPEAQFVIPGHGLPGGLDLLKHTTNVVKAHTNRSVVE"},"dna_sequence":{"accession":"JACTAE010000183.1","fmin":"98","fmax":"896","strand":"-","sequence":"ATGTTCAAACTTTTGAGTAAGTTATTGGTCTATTTGACCGCGTCTATCATGGCTATTGCGAGTCCGCTCGCTTTTTCCGTAGATTCTAGCGGTGAGTATCCGACAGTCAGCGAAATTCCGGTCGGGGAGGTCCGGCTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCAGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAGAAGCAAATTGGACTTCCTGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGTAGAGGGGAACGAGATTACGCACTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAACTCTTCTATCCTGGTGCTGCGCATTCGACCGACAACTTAGTTGTGTACGTCCCGTCTGCGAGTGTGCTCTATGGTGGTTGTGCGATTTATGAGTTGTCACGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCATTGAGCGGATTCAACAACACTACCCGGAAGCACAGTTCGTCATTCCGGGGCACGGCCTGCCGGGCGGTCTAGACTTGCTCAAGCACACAACGAATGTTGTAAAAGCGCACACAAATCGCTCAGTCGTTGAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3007817","ARO_id":"46604","ARO_name":"VIM-80","CARD_short_name":"VIM-80","ARO_description":"VIM-80 is a subclass B1 carbapenem-hydrolyzing metallo-beta-lactamase.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"6043":{"model_id":"6043","model_name":"VIM-82","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8863":{"protein_sequence":{"accession":"WP_238839790.1","sequence":"MFKLLSKLLVYLTASIMAIASPLAFSVDSSGEYPTVSEIPVGEVRLYQIADGVWSHIATRSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEVEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSASVLYGGCAIYELSRTSAGTVADADLAEWPTSIERIQQHYPEAQFVIPGHGLPGGLDLLKHTTNVVKAHTNRSVVE"},"dna_sequence":{"accession":"NG_088450.1","fmin":"100","fmax":"901","strand":"+","sequence":"ATGTTCAAACTTTTGAGTAAGTTATTGGTCTATTTGACCGCGTCTATCATGGCTATTGCGAGTCCGCTCGCTTTTTCCGTAGATTCTAGCGGTGAGTATCCGACAGTCAGCGAAATTCCGGTCGGGGAGGTCCGGCTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCGGTCGTTTGATGGCGCAGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAGAAGCAAATTGGACTTCCTGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGTAGAGGGGAACGAGATTCCCACGCACTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAACTCTTCTATCCTGGTGCTGCGCATTCGACCGACAACTTAGTTGTGTACGTCCCGTCTGCGAGTGTGCTCTATGGTGGTTGTGCGATTTATGAGTTGTCACGCACGTCTGCGGGGACCGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCATTGAGCGGATTCAACAACACTACCCGGAAGCACAGTTCGTCATTCCGGGGCACGGCCTGCCGGGCGGTCTAGACTTGCTCAAGCACACAACGAATGTTGTAAAAGCGCACACAAATCGCTCAGTCGTTGAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3007819","ARO_id":"46606","ARO_name":"VIM-82","CARD_short_name":"VIM-82","ARO_description":"VIM-82 is a subclass B1 carbapenem-hydrolyzing metallo-beta-lactamase.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"6044":{"model_id":"6044","model_name":"VIM-83","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8864":{"protein_sequence":{"accession":"UWI53403.1","sequence":"MLKVISSLLVYMTASVMAVASPLAHSGEPSGEYPTVNEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEAKGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSANVLYGGCAVHELSSTSAGNVADADLAEWPTSVERIQKHYPEAEVVIPGHGLPGGLDLLQHTANVVKAHKNRSVAE"},"dna_sequence":{"accession":"OP353772.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGTTAAAAGTTATTAGTAGTTTATTGGTCTACATGACCGCGTCTGTCATGGCTGTCGCAAGTCCGTTAGCCCATTCCGGGGAGCCGAGTGGTGAGTATCCGACAGTCAACGAAATTCCGGTCGGAGAGGTCCGACTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCGGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAAAAGCAAATTGGACTTCCCGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGCAAAGGGGAACGAGATTCCCACGCATTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAGCTCTTCTATCCTGGTGCTGCGCATTCGACCGACAATCTGGTTGTATACGTCCCGTCAGCGAACGTGCTATACGGTGGTTGTGCCGTTCATGAGTTGTCAAGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCGTTGAGCGGATTCAAAAACACTACCCGGAAGCAGAGGTCGTCATTCCCGGGCACGGTCTACCGGGCGGTCTAGACTTGCTCCAGCACACAGCGAACGTTGTCAAAGCACACAAAAATCGCTCAGTCGCCGAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3007820","ARO_id":"46607","ARO_name":"VIM-83","CARD_short_name":"VIM-83","ARO_description":"VIM-83 is a subclass B1 carbapenem-hydrolyzing metallo-beta-lactamase.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"6045":{"model_id":"6045","model_name":"VIM-84","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8865":{"protein_sequence":{"accession":"UWQ12890.1","sequence":"MFKLLSKLLVYLTASIMAIASPLAFSVDSSGEYPTVSEIPVGEVRLYQIADGVWSHIATRSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEVEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSASVLYGGCAIYELSLTSAGNVADADLAEWPTSIERIQQHYPEAQFVIPGHGLPGGLDLLKHTTNVVKAHTNRSVVE"},"dna_sequence":{"accession":"ON688661.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGTTCAAACTTTTGAGTAAGTTATTGGTCTATTTGACCGCGTCTATCATGGCTATTGCGAGTCCGCTCGCTTTTTCCGTAGATTCTAGCGGTGAGTATCCGACAGTCAGCGAAATTCCGGTCGGGGAGGTCCGGCTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCGGTCGTTTGATGGCGCAGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAGAAGCAAATTGGACTTCCTGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGTAGAGGGGAACGAGATTCCCACGCACTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAACTCTTCTATCCTGGTGCTGCGCATTCGACCGACAACTTAGTTGTGTACGTCCCGTCTGCGAGTGTGCTCTATGGTGGTTGTGCGATTTATGAGTTGTCACTCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCATTGAGCGGATTCAACAACACTACCCGGAAGCACAGTTCGTCATTCCGGGGCACGGCCTGCCGGGCGGTCTAGACTTGCTCAAGCACACAACGAATGTTGTAAAAGCGCACACAAATCGCTCAGTCGTTGAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3007821","ARO_id":"46608","ARO_name":"VIM-84","CARD_short_name":"VIM-84","ARO_description":"VIM-84 is a subclass B1 carbapenem-hydrolyzing metallo-beta-lactamase.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"6002":{"model_id":"6002","model_name":"aadT","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"900"}},"model_sequences":{"sequence":{"8732":{"protein_sequence":{"accession":"AMD83542.1","sequence":"MKATNLDPKRWWILLAVVLAFLPIVIDMTVLHVAVPSLTQSLSATSNQVLWIIDIYPLLMAGLLVPMGTLADRVGNRKILLIGLVIFGIASVLAAFSQTASMLIAARALLALGGAMIMPCVLGIIRRTFEDSRERAIALGIWGTIGSAGAAIGPLIGGGLLEYFWWGSVFLINVPIMLVVAPMCYFLLSRKEAITPGHWAFGQALLLIVGLISFVYALKAGLGGKQSLLIVLPLVVLSIGLLTIFVRKQLNSPQPMLDLSLFSRPAILAGIIMAMVAAGALAGVELTLAMELQYVIRLTPLQAGLFMVPIMVAAAIGGPIAGFLSNKFGLRLVATMSLILAAIALVSLSYSDFHHPGIIVPFILASIGLTLSIGLTASSIAIMGSVPAEKGGAAGSLESTGYELGTGLGITLFGVFMAYIFGSHLQVPSDLTAVLAEKARLSIGDTYLVASQLPVEQGTALINAGKIAFSSAHVNLLLTAGIIIGILSIVVFFMLAKYRDENSL"},"dna_sequence":{"accession":"KT852971.1","fmin":"29104","fmax":"30619","strand":"+","sequence":"ATGAAAGCTACCAATCTTGATCCGAAACGCTGGTGGATATTGCTCGCTGTCGTGCTTGCATTTCTGCCGATTGTGATTGATATGACTGTACTGCATGTTGCGGTTCCCTCATTAACCCAATCGCTGAGTGCCACAAGTAACCAAGTCTTATGGATTATTGATATTTATCCATTACTTATGGCTGGACTTTTAGTTCCGATGGGAACTTTGGCTGATCGTGTCGGCAATCGTAAGATTCTGCTGATTGGCTTGGTTATATTTGGAATTGCCTCAGTCCTTGCGGCATTTTCCCAAACGGCTTCTATGCTGATTGCCGCACGTGCTTTATTAGCATTAGGCGGTGCCATGATTATGCCCTGTGTATTGGGTATTATTCGCAGAACCTTCGAAGACAGTCGCGAACGTGCCATTGCGCTGGGTATTTGGGGCACAATCGGATCAGCCGGTGCCGCCATTGGACCGCTCATTGGTGGGGGATTGTTAGAATATTTCTGGTGGGGTTCAGTTTTCCTGATTAACGTCCCAATCATGCTGGTTGTCGCACCAATGTGCTATTTCTTATTGTCCCGAAAAGAAGCTATAACCCCTGGACATTGGGCATTTGGTCAAGCGCTATTGCTGATTGTCGGTTTGATTTCGTTTGTATATGCACTAAAAGCAGGCTTAGGCGGTAAACAGTCGTTGTTGATTGTCTTGCCTTTGGTCGTTTTATCTATCGGCTTATTAACCATATTTGTACGCAAACAGCTGAATTCTCCTCAGCCGATGCTAGATCTTTCGCTATTTTCACGTCCTGCTATTTTAGCCGGCATTATTATGGCAATGGTTGCTGCAGGCGCTTTGGCAGGGGTTGAGTTAACTTTGGCAATGGAGCTGCAATATGTCATTCGTTTAACACCGCTGCAAGCCGGTCTTTTTATGGTTCCGATTATGGTTGCGGCCGCTATTGGCGGGCCTATTGCTGGTTTTTTATCCAATAAATTTGGACTCCGTCTGGTTGCGACCATGTCATTAATATTGGCAGCAATTGCGTTGGTCAGTTTGAGTTATTCAGATTTTCATCATCCGGGAATCATCGTTCCCTTTATTTTAGCTTCGATTGGATTAACACTGAGTATTGGTTTAACAGCTTCATCCATTGCGATCATGGGCTCAGTACCTGCAGAAAAGGGCGGTGCGGCAGGTTCACTTGAAAGTACAGGTTATGAACTGGGTACAGGACTAGGTATTACTTTATTTGGTGTTTTCATGGCCTATATATTTGGCAGTCATCTTCAAGTGCCGTCAGATTTAACTGCTGTTTTAGCAGAAAAAGCCAGACTTTCGATTGGTGATACCTATTTAGTGGCGAGCCAGTTACCCGTTGAACAAGGTACAGCATTGATTAACGCAGGTAAAATTGCCTTCAGTTCAGCTCATGTTAATTTATTATTAACAGCAGGGATTATCATCGGGATACTCTCCATTGTGGTATTTTTTATGCTAGCTAAATATCGAGATGAGAATTCATTGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3007669","ARO_id":"46449","ARO_name":"aadT","CARD_short_name":"aadT","ARO_description":"The AadT pump is a novel multidrug efflux pump from the proton antiporter 2 (DHA2) family and was discovered in Acinetobacter multidrug resistance plasmids. The presence of AadT decreased bacterial susceptibility to antibiotics (erythromycin and tetracycline), biocides (chlorhexidine), and dyes (ethidium bromide and DAPI) and was able to mediate ethidium transport.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"45598":{"category_aro_accession":"3007039","category_aro_cvterm_id":"45598","category_aro_name":"chlorhexidine","category_aro_description":"Chlorhexidine is a disinfectant and antiseptic that is used for skin disinfection, including mouthwashes (chlorhexidine gluconate).","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"43746":{"category_aro_accession":"3005386","category_aro_cvterm_id":"43746","category_aro_name":"disinfecting agents and antiseptics","category_aro_description":"Disinfectants that can also interact with antimicrobial resistance mechanisms, e.g. molecule efflux, and thus are the targets of disinfectant resistance.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"6003":{"model_id":"6003","model_name":"Clostridioides difficile nimB","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"250"}},"model_sequences":{"sequence":{"8724":{"protein_sequence":{"accession":"CBE03766.1","sequence":"MFKEMRLKKREMTKEDTVEVLKNGEFGTFSTISENGYPYGVAVNYVYFNDSIYFHCARNGHKLDNISKNNKVSFLVVANESVIPDKFSTTYSSAIVFGKACTVENEEKKNALVEIIKKYSKGFFEEGMKYIEKDMNLTTVVKIEIDHISGKASRI"},"dna_sequence":{"accession":"FN545816.1","fmin":"1547473","fmax":"1547941","strand":"-","sequence":"ATGTTTAAAGAAATGAGATTGAAAAAAAGAGAAATGACAAAAGAAGATACTGTTGAAGTATTAAAAAATGGTGAATTTGGTACTTTTTCCACTATATCTGAAAATGGTTATCCTTATGGAGTTGCTGTAAATTATGTATACTTTAATGATTCTATTTACTTTCATTGTGCAAGAAATGGACATAAGTTAGATAATATATCGAAAAACAACAAAGTTTCTTTTTTAGTAGTTGCTAATGAAAGTGTTATTCCAGATAAATTTAGTACTACTTATTCTAGTGCTATAGTTTTTGGAAAAGCTTGCACTGTAGAAAATGAAGAAAAGAAAAATGCTCTTGTAGAAATAATAAAAAAATATTCTAAAGGATTCTTTGAAGAAGGCATGAAGTACATAGAGAAGGATATGAACTTAACAACTGTTGTTAAAATAGAAATTGACCATATTTCTGGTAAAGCTTCACGTATATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"46452","NCBI_taxonomy_name":"Clostridioides difficile R20291","NCBI_taxonomy_id":"645463"}}}},"ARO_accession":"3007671","ARO_id":"46451","ARO_name":"Clostridioides difficile nimB","CARD_short_name":"CdnimB","ARO_description":"Clostridioides difficile nimB is a heme-dependent flavin enzyme that degrades nitroimidazoles to amines lacking antimicrobial activity. NimB expression alone is not sufficient for nitroimidazole resistance. Constitutive transcription of nimB, which is driven by a mutation in the promoter PnimBG, is a mechanism of clinically-relevant heme-dependent metronidazole resistance in C. difficile.","ARO_category":{"45671":{"category_aro_accession":"3007103","category_aro_cvterm_id":"45671","category_aro_name":"nitroimidazole reductase","category_aro_description":"Nitroimidazole reductases are a group of enzymes that deactivate nitroimidazole antibiotics by reducing their nitro functional group to an amino group. These enzymes are associated with resistance to nitroimidazole derivatives in Bacteroides fragilis but have also been reported in a variety of anaerobic Gram-negative and Gram-positive genera. The minimum inhibitory concentrations for these enzymes vary greatly depending on species, strain, and precise nitroimidazole treatment used.","category_aro_class_name":"AMR Gene Family"},"37033":{"category_aro_accession":"3000689","category_aro_cvterm_id":"37033","category_aro_name":"metronidazole","category_aro_description":"Metronidazole is a nitroimidazole that is active against anaerobic bacteria and protozoa. It is not effective against aerobic bacteria. Nitroimidazoles act by oxidizing DNA causing strand breaks and cell death.","category_aro_class_name":"Antibiotic"},"41239":{"category_aro_accession":"3004115","category_aro_cvterm_id":"41239","category_aro_name":"nitroimidazole antibiotic","category_aro_description":"Nitroimidazoles are a group of drugs that have both antiprotozoal and antibacterial activity, classified with respect to the location of the nitro functional group.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2884":{"model_id":"2884","model_name":"RSA1-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"4271":{"protein_sequence":{"accession":"AUW34365.1","sequence":"MGMQLARSTILTVLLCLPIAVTATTKEEIQKIERQRNLTVGIALVDDGGTLLFGHRETQRFAMCSTFKLPLAAATLKQIESGKWSAAERLSYSAGQLDAYAPAAKRYLPTGYITVAEANQASVQLSDNTAANLLLDKLGGPSQLTSMFRSLGDSVSRLDRREPDLNTNVSGDPRDTTTPGAMARIVAKLVYGNYLSTAGREQLQRLLIGNNTGDSRIRAGIASGWTTGDKTGSCPNGGRNDAAFLVSPDGRRFALTVYLNAPSLDDKARNEVVATVARLAVESIR"},"dna_sequence":{"accession":"MG739510.1","fmin":"0","fmax":"858","strand":"+","sequence":"ATGGGAATGCAACTAGCTAGGTCGACGATCCTCACTGTTTTGCTCTGTCTGCCGATTGCTGTAACGGCTACGACTAAGGAGGAGATCCAAAAGATTGAGCGTCAGCGCAACCTCACGGTTGGCATCGCTCTTGTAGACGACGGGGGAACACTCCTGTTCGGTCATCGCGAAACGCAGCGCTTCGCCATGTGCTCGACATTTAAGTTGCCGCTGGCGGCTGCAACGCTTAAGCAAATCGAGAGCGGAAAGTGGTCTGCCGCCGAGCGGCTGAGCTATAGCGCTGGCCAATTAGATGCCTACGCGCCAGCTGCCAAGAGATATCTACCTACAGGCTACATCACGGTAGCTGAGGCTAACCAAGCCTCGGTCCAGCTCAGCGATAATACTGCTGCCAACTTGCTGCTTGACAAACTCGGAGGGCCATCGCAGCTCACATCCATGTTTCGCTCCCTCGGCGATTCCGTGAGTCGCCTGGATAGAAGAGAACCCGATTTGAACACCAACGTTTCGGGTGACCCGCGCGACACGACTACGCCGGGCGCGATGGCACGCATTGTCGCAAAGCTGGTATATGGAAACTATCTAAGTACAGCAGGCCGAGAGCAATTGCAGCGGCTTCTCATTGGCAATAACACAGGCGACTCGAGGATTCGCGCTGGAATCGCATCTGGCTGGACGACTGGCGACAAAACGGGTTCCTGCCCCAATGGCGGACGAAATGACGCTGCGTTCCTGGTAAGCCCTGATGGCCGCAGATTTGCGCTGACAGTGTACCTGAACGCCCCATCGCTTGACGACAAGGCACGGAACGAGGTGGTCGCTACGGTAGCTCGCTTGGCGGTTGAGAGTATCCGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36791","NCBI_taxonomy_name":"uncultured bacterium","NCBI_taxonomy_id":"77133"}}}},"ARO_accession":"3004444","ARO_id":"41637","ARO_name":"RSA1-1","CARD_short_name":"RSA1-1","ARO_description":"RSA1-1 is a class A beta-lactamase resistance enzyme identified from a functional metagenomic study of contaminated river sediments.","ARO_category":{"41636":{"category_aro_accession":"3004443","category_aro_cvterm_id":"41636","category_aro_name":"RSA beta-lactamase","category_aro_description":"A family of class A beta-lactamase enzymes, RSA beta-lactamases show carbapenemase and cephalosporinase activity.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"6005":{"model_id":"6005","model_name":"IreK","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1400"}},"model_sequences":{"sequence":{"8733":{"protein_sequence":{"accession":"WKR28567.1","sequence":"MIEIGKKLNGRYHIIGSIGSGGMANVYLAHDLILDRDVAVKVLRFDFQNDQAAIRRFQREALAATELVHPNIVSVYDVGEEDGLQYLVMEYVKGMDLKRYIQTHFPITYSTVVDITQQILSAVAMAHEHRIIHRDLKPQNILIDEHGTVKITDFGIAIALSETSITQTNTMLGSVHYLSPEQARGSMATNQSDIYAVGIILYEMLTGNVPFDGESAVTIALKHFQEEIPSVKMFDPGIPQSLENVVRHATAKDPSDRYKTANEMAEDLYTSLSASRLNEPAWEPTALLGETKVLTPIPEDIAEPEETTPVEVPEDIADDILAEQPPKKNRKKLWIGLAIAALIALAIGGLAFAMSGGKDVEVPDVTNETKADASQALQSAGLKVDSETKKIPDDKIEEGKVVKTDPEAKSSVKKGRSVTLYISSGTEKIEMADYTNESYESAVEALKKLGFSEDQITTKKEYSDSVSTDSIIKQKPAAGKKVDPKKDKVTLTVSEGPEAVTLPSYAGYSYENAVIALKQLGISDSQITRVDQASDTVEPGLVITQDPAPGGTVTPKNGQVTLYVSKGSDKVTLSDYSGISYDNAVSRLIALGIPESQIKRVDEESDKVEKDTVISQEPASGTAVDPKNDTITLHVSKGSDSVTVPDISGYSPKAAEDSINNAGLKINEQGLSGSGDGQVVERTSPSAGSKVKKGDAVTVYYSKANDSKSTTSESSTSN"},"dna_sequence":{"accession":"CP124778.1","fmin":"2492204","fmax":"2494361","strand":"+","sequence":"ATGATAGAAATCGGCAAGAAGCTGAATGGTCGATATCACATTATTGGCAGCATCGGAAGCGGCGGCATGGCCAACGTCTATTTAGCACACGATTTAATTTTAGACCGAGACGTTGCAGTAAAAGTCTTGCGCTTTGACTTCCAAAACGATCAAGCCGCCATCCGACGTTTTCAGCGTGAAGCACTAGCCGCAACTGAGCTGGTTCACCCGAATATCGTCAGTGTGTACGATGTAGGCGAAGAAGATGGACTACAATATTTAGTCATGGAATATGTGAAAGGAATGGACTTGAAACGTTACATCCAAACGCATTTCCCAATTACTTATTCCACAGTTGTGGATATTACGCAACAAATTTTATCTGCTGTCGCAATGGCACATGAACATAGAATTATTCACCGGGATTTAAAACCGCAAAACATTCTGATTGACGAACACGGCACAGTCAAAATTACTGACTTTGGGATTGCGATTGCTTTGTCAGAAACGTCAATTACGCAAACGAACACAATGTTAGGTTCGGTGCATTACTTATCGCCAGAACAAGCGCGCGGAAGCATGGCGACTAACCAATCAGATATTTACGCTGTGGGAATTATTCTCTATGAAATGCTAACAGGGAATGTACCTTTTGATGGTGAATCAGCCGTAACGATTGCCTTAAAACATTTTCAAGAAGAAATTCCTTCTGTCAAAATGTTTGATCCAGGGATTCCTCAATCATTGGAAAATGTGGTTCGTCATGCAACCGCAAAAGACCCAAGCGATCGCTACAAAACAGCGAATGAGATGGCAGAAGACTTATACACGTCCTTGTCAGCCAGTCGTTTAAACGAACCTGCGTGGGAACCAACGGCTTTATTAGGAGAAACGAAAGTATTAACTCCGATTCCCGAAGACATCGCTGAACCGGAAGAGACAACGCCTGTCGAAGTCCCAGAAGATATCGCAGATGACATTTTAGCTGAACAACCACCGAAGAAAAACCGTAAAAAATTGTGGATTGGCTTAGCAATTGCGGCATTAATTGCTTTAGCAATAGGTGGCTTAGCCTTTGCAATGTCGGGTGGTAAAGACGTTGAAGTTCCTGATGTTACAAACGAAACGAAAGCGGACGCTTCACAAGCGCTACAAAGTGCCGGGCTGAAAGTCGATAGTGAAACCAAAAAAATTCCCGATGATAAGATTGAAGAAGGCAAGGTGGTCAAAACAGACCCCGAAGCAAAATCATCTGTGAAAAAAGGCCGATCTGTTACTTTATACATCAGCTCTGGAACAGAAAAAATTGAGATGGCCGATTATACAAATGAATCGTATGAATCTGCTGTCGAAGCCTTGAAAAAACTAGGGTTTTCAGAAGATCAAATTACAACGAAAAAAGAATACAGTGATTCTGTGTCTACGGATAGCATTATTAAACAAAAACCAGCTGCAGGTAAAAAAGTTGATCCGAAAAAAGACAAAGTCACTTTAACGGTCAGTGAAGGACCAGAAGCGGTTACTTTGCCTAGTTACGCCGGTTATTCTTACGAAAATGCAGTAATTGCACTGAAACAATTAGGCATTTCTGACTCTCAAATTACGCGTGTCGACCAAGCAAGCGATACGGTAGAACCAGGTTTAGTCATTACGCAAGACCCCGCACCAGGTGGGACCGTGACACCTAAAAATGGCCAAGTGACGTTATATGTAAGTAAAGGTAGCGACAAAGTGACACTTTCTGATTATAGCGGAATTTCTTACGATAATGCGGTAAGTCGCTTAATTGCTTTAGGTATCCCAGAATCTCAAATTAAACGAGTGGACGAAGAAAGCGACAAAGTTGAAAAAGATACCGTGATTAGTCAAGAACCAGCTTCTGGTACCGCTGTTGATCCGAAAAATGACACGATTACTTTACATGTCAGCAAAGGCAGTGACTCAGTAACTGTTCCTGATATTTCAGGTTATTCGCCAAAAGCTGCAGAAGACAGCATCAATAATGCTGGCCTTAAAATCAATGAACAAGGATTATCTGGCTCTGGCGATGGCCAAGTCGTTGAACGAACTAGCCCATCCGCTGGCAGCAAAGTCAAAAAAGGCGACGCTGTTACGGTTTATTATTCAAAAGCAAATGATTCAAAAAGCACCACTAGTGAAAGTAGTACGAGTAATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35918","NCBI_taxonomy_name":"Enterococcus faecalis","NCBI_taxonomy_id":"1351"}}}},"ARO_accession":"3007678","ARO_id":"46460","ARO_name":"IreK","CARD_short_name":"IreK","ARO_description":"E. faecalis IreK maintains cell wall integrity, possibly by regulating peptidoglycan biosynthesis and metabolism. Antibiotic-induced cell wall stress leads to activation of IreK-mediated phosphorylation signaling pathways to mitigate and repair the damage. Absence of IreK leads to cell envelope defects and increased susceptibility to a variety of cephalosporins, including ceftriaxone. Increased IreK phosphorylation in response to ceftriaxone treatment has been shown to correlate with antimicrobial resistance.","ARO_category":{"46469":{"category_aro_accession":"3007683","category_aro_cvterm_id":"46469","category_aro_name":"Serine\/threonine kinases","category_aro_description":"The eukaryotic-type Ser\/Thr kinase (STKs) IreK (intrinsic resistance of enterococci kinase) belongs to a family of transmembrane kinases defined by the presence of multiple extracellular PASTA (penicillin-binding protein and serine\/threonine kinase associated) domains. In prokaryotes, STKs modulate cellular functions such as growth, differentiation, and secondary metabolism. When the external environment changes, prokaryotes rely on signal transduction systems, including STKs that quickly sense these changes and alter gene expression to induce the appropriate metabolic changes.","category_aro_class_name":"AMR Gene Family"},"35979":{"category_aro_accession":"0000062","category_aro_cvterm_id":"35979","category_aro_name":"ceftriaxone","category_aro_description":"Ceftriaxone is a third-generation cephalosporin antibiotic. The presence of an aminothiazolyl sidechain increases ceftriazone's resistance to beta-lactamases. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36383":{"category_aro_accession":"3000244","category_aro_cvterm_id":"36383","category_aro_name":"reduced permeability to antibiotic","category_aro_description":"Reduction in permeability to antibiotic, generally through reduced production of porins, can provide resistance.","category_aro_class_name":"Resistance Mechanism"}}},"6006":{"model_id":"6006","model_name":"OXA-481","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8734":{"protein_sequence":{"accession":"AKF41838.1","sequence":"MNKYFTCYVVASLFLSGCTVQHNLINETPSQIVQGHNQVIHQYFDEKNTSGVLVIQTDKKINLYGNALSRANTEYVPASTFKMLNALIGLENQKTDINEIFKWKGEKRSFTAWEKDMTLGEAMKLSAVPVYQELARRIGLDLMQKEVKRIGFGNAEIGQQVDNFWLVGPLKVTPIQEVEFVSQLAHTQLPFSEKVQANVKNMLLLEESNGYKIFGKTGWAMDIKPQVGWLTGWVEQPDGKIVAFALNMEMRSEMPASIRNELLMNSLKQ"},"dna_sequence":{"accession":"KP264123.1","fmin":"89","fmax":"896","strand":"+","sequence":"ATGAATAAATATTTTACTTGCTATGTGGTTGCTTCTCTTTTTCTTTCTGGTTGTACGGTTCAGCATAATTTAATAAATGAAACCCCGAGTCAGATTGTTCAAGGACATAATCAGGTGATTCATCAATACTTTGATGAAAAAAACACCTCAGGTGTGCTGGTTATTCAAACAGATAAAAAAATTAATCTATATGGTAATGCTCTAAGCCGCGCAAATACAGAATATGTGCCAGCCTCTACATTTAAAATGTTGAATGCCCTGATCGGATTGGAGAACCAGAAAACGGATATTAATGAAATATTTAAATGGAAGGGCGAGAAAAGGTCATTTACCGCTTGGGAAAAAGACATGACACTAGGAGAAGCCATGAAGCTTTCTGCAGTCCCAGTCTATCAGGAACTTGCGCGACGTATCGGTCTTGATCTCATGCAAAAAGAAGTAAAACGTATTGGTTTCGGTAATGCTGAAATTGGACAGCAGGTTGATAATTTCTGGTTGGTAGGACCATTAAAGGTTACGCCTATTCAAGAGGTAGAGTTTGTTTCCCAATTAGCACATACACAGCTTCCATTTAGTGAAAAAGTGCAGGCTAATGTAAAAAATATGCTTCTTTTAGAAGAGAGTAATGGCTACAAAATTTTTGGAAAGACTGGTTGGGCAATGGATATAAAACCACAAGTGGGCTGGTTGACCGGCTGGGTTGAGCAGCCAGATGGAAAAATTGTCGCTTTTGCATTAAATATGGAAATGCGGTCAGAAATGCCGGCATCTATACGTAATGAATTATTGATGAATTCATTAAAACAG","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3003638","ARO_id":"40248","ARO_name":"OXA-481","CARD_short_name":"OXA-481","ARO_description":"OXA-481 is a carbapenem-hydrolyzing class D beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"6007":{"model_id":"6007","model_name":"TEM-103","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8735":{"protein_sequence":{"accession":"EAC0197234.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDELNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AAAGNS010000063.1","fmin":"144","fmax":"1005","strand":"-","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACTAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35673","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Panama","NCBI_taxonomy_id":"29472"}}}},"ARO_accession":"3000966","ARO_id":"37346","ARO_name":"TEM-103","CARD_short_name":"TEM-103","ARO_description":"TEM-103 is an inhibitor-resistant beta-lactamase that has been found in E. coli.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35981":{"category_aro_accession":"0000064","category_aro_cvterm_id":"35981","category_aro_name":"amoxicillin","category_aro_description":"Amoxicillin is a moderate-spectrum, bacteriolytic, beta-lactam antibiotic used to treat bacterial infections caused by susceptible microorganisms. A derivative of penicillin, it has a wider range of treatment but remains relatively ineffective against Gram-negative bacteria. It is commonly taken with clavulanic acid, a beta-lactamase inhibitor. Like other beta-lactams, amoxicillin interferes with the synthesis of peptidoglycan.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"6008":{"model_id":"6008","model_name":"TEM-61","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8736":{"protein_sequence":{"accession":"BCD58813.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDKLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDHWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGKRGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"LC542923.1","fmin":"2479","fmax":"3340","strand":"-","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATAAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATCATTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTAAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36783","NCBI_taxonomy_name":"Serratia marcescens","NCBI_taxonomy_id":"615"}}}},"ARO_accession":"3000930","ARO_id":"37310","ARO_name":"TEM-61","CARD_short_name":"TEM-61","ARO_description":"TEM-61 is an extended-spectrum beta-lactamase that has been found in clinical isolates.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36689":{"category_aro_accession":"3000550","category_aro_cvterm_id":"36689","category_aro_name":"aztreonam","category_aro_description":"Aztreonam was the first monobactam discovered, and is greatly effective against Gram-negative bacteria while inactive against Gram-positive bacteria. Artreonam is a poor substrate for beta-lactamases, and may even act as an inhibitor. In Gram-negative bacteria, Aztreonam interferes with filamentation, inhibiting cell division and leading to cell death.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"36989":{"category_aro_accession":"3000645","category_aro_cvterm_id":"36989","category_aro_name":"cefotaxime","category_aro_description":"Cefotaxime is a semisynthetic cephalosporin taken parenterally. It is resistant to most beta-lactamases and active against Gram-negative rods and cocci due to its aminothiazoyl and methoximino functional groups.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"6009":{"model_id":"6009","model_name":"OKP-B-14","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"525"}},"model_sequences":{"sequence":{"8737":{"protein_sequence":{"accession":"ABL75154.1","sequence":"CLISLIAALPLAVFASPQPLEQIKISESQLAGRVGYVEMDLASGRTLAAWRASERFPLMSTFKVLLCGAVLARVDAGDEQLDRRIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAGNLLLKSVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDVRDTTTPASMATTLRKLLTTPSLSARSQQLLLQWMVDDRVAGPLIRAVLPAGWFIADKTGAGERGSRGIVALLGPDGKAERIVVIYLRDTAATMAERNQQIAGIGAALI"},"dna_sequence":{"accession":"DQ995288.1","fmin":"2","fmax":"827","strand":"+","sequence":"TGCCTTATCTCCCTGATTGCCGCCCTGCCACTGGCGGTATTCGCCAGCCCTCAGCCGCTTGAGCAGATTAAAATCAGCGAAAGTCAGCTGGCGGGCCGGGTGGGCTATGTTGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCAGTGAGCGCTTTCCGCTGATGAGCACCTTTAAAGTGCTGCTCTGCGGCGCGGTGCTGGCCCGGGTGGATGCCGGCGACGAACAGCTGGATCGGCGGATCCACTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGCCGACGGGATGACCGTTGGCGAACTCTGCGCCGCCGCCATCACCATGAGCGACAACAGCGCCGGCAATCTGCTGTTGAAGAGCGTCGGCGGCCCTGCGGGATTGACCGCTTTTCTGCGCCAGATCGGTGACAACGTCACCCGTCTTGACCGCTGGGAAACGGAACTCAATGAGGCGCTTCCCGGCGACGTGCGCGACACCACCACCCCGGCCAGCATGGCCACCACCCTGCGCAAGTTGCTAACCACCCCCTCTCTGAGCGCCCGTTCGCAGCAGCTGCTGCTGCAGTGGATGGTTGACGACCGGGTGGCCGGCCCGTTGATCCGCGCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAAACCGGGGCCGGTGAGCGGGGCTCACGCGGCATTGTCGCCCTGCTCGGCCCGGACGGCAAAGCGGAGCGTATCGTGGTGATCTATCTACGGGATACCGCGGCGACCATGGCCGAACGTAACCAGCAGATCGCCGGGATAGGCGCGGCGCTGATC","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3002447","ARO_id":"38847","ARO_name":"OKP-B-14","CARD_short_name":"OKP-B-14","ARO_description":"OKP-B-14 is a beta-lactamase found in Klebsiella pneumoniae.","ARO_category":{"38817":{"category_aro_accession":"3002417","category_aro_cvterm_id":"38817","category_aro_name":"OKP beta-lactamase","category_aro_description":"OKP beta-lactamases are chromosomal class A beta-lactamase that confer resistance to penicillins and early cephalosporins in Klebsiella pneumoniae. OKP beta-lactamases can be subdivided into two groups: OKP-A and OKP-B which diverge by about 4.2%.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"6010":{"model_id":"6010","model_name":"OXA-105","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8738":{"protein_sequence":{"accession":"WP_265760908.1","sequence":"MNKYFTCYVFASLFLSGCTVQHNLINETPSQIAQGHNQVIHQYFDEKNTSGVLVIQTDKKINLYGNALSRANTEYVPASTFKMLNALIGLENQKTDINEIFKWKGEKRSFTAWEKDMTLGEAMKLSAVPVYQELARRIGLDLMQKEVKRIGFGNAEIGQQVDNFWLVGPLKVTPIQEVEFVSQLAHTQLPFSEKVQANVKNMLLLEESNGYKIFGKTGWAMDIKPQAGWLTGWVEQPDGKIVAFALNMEMRSEMPASIRNELLMKSLKQLNII"},"dna_sequence":{"accession":"JANRFO010000004.1","fmin":"57304","fmax":"58126","strand":"+","sequence":"ATGAATAAATATTTTACTTGCTATGTGTTTGCCTCTCTTTTTCTTTCTGGTTGTACGGTTCAGCATAATTTAATAAATGAAACCCCGAGTCAGATTGCTCAAGGACATAATCAGGTGATTCATCAATACTTTGATGAAAAAAACACCTCAGGTGTGCTGGTTATTCAAACAGATAAAAAAATTAATCTGTATGGTAATGCTCTAAGCCGCGCAAATACAGAATATGTGCCAGCCTCTACATTTAAAATGTTGAATGCCCTGATCGGATTGGAGAACCAGAAAACGGATATTAATGAAATATTTAAATGGAAGGGCGAGAAAAGGTCATTTACCGCTTGGGAAAAAGACATGACACTAGGAGAAGCCATGAAGCTTTCCGCAGTCCCAGTCTATCAGGAACTTGCGCGACGTATCGGTCTTGATCTCATGCAAAAAGAAGTAAAACGTATTGGTTTCGGTAATGCTGAAATTGGACAGCAGGTTGATAATTTCTGGTTGGTAGGGCCATTAAAGGTTACGCCTATTCAAGAGGTAGAGTTTGTTTCTCAATTGGCGCATACACAGCTTCCATTTAGTGAAAAAGTGCAGGCTAATGTAAAAAATATGCTTCTTTTAGAAGAGAGTAATGGCTACAAAATTTTTGGAAAGACTGGTTGGGCAATGGATATAAAACCACAAGCGGGCTGGTTGACCGGCTGGGTTGAGCAGCCAGATGGAAAAATTGTCGCTTTTGCATTAAATATGGAAATGCGGTCAGAAATGCCGGCATCTATACGTAATGAATTATTGATGAAATCATTAAAACAGCTGAATATTATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39672","NCBI_taxonomy_name":"Acinetobacter radioresistens","NCBI_taxonomy_id":"40216"}}}},"ARO_accession":"3001708","ARO_id":"38108","ARO_name":"OXA-105","CARD_short_name":"OXA-105","ARO_description":"OXA-105 is a beta-lactamase found in Acinetobacter spp.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"6004":{"model_id":"6004","model_name":"Mycobacterium tuberculosis Rv0678 with mutation conferring resistance to bedaquiline","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"40394":{"param_type":"nonsense mutation","param_description":"A sequence change where, compared to a reference sequence, one codon is replaced by a termination codon through a nucleotide substitution. These are described as a substitution of the wildtype codon to a termination codon. Format is given as [wild type AA][position][Ter], for example Q42Ter where Q42 is a wildtype amino acid replaced by a premature termination codon.","param_type_id":"40394","param_value":{"14494":"W42Ter","14559":"Y92Ter","14583":"E113Ter","14585":"Q115Ter","14594":"R132Ter","14595":"R134Ter","14598":"E138Ter","14604":"Y145Ter","14608":"E147Ter","14611":"R156Ter","14615":"Y157Ter","14470":"Q22Ter","14487":"R38Ter","14517":"S53Ter","14545":"Q76Ter"}},"snp":{"WHO-R":{"14494":"L49P","14559":"L49P","14583":"L49P","14585":"L49P","14594":"L49P","14595":"L49P","14598":"L49P","14604":"L49P","14608":"L49P","14611":"L49P","14615":"L49P","14470":"L49P","14487":"L49P","14477":"L32S","14485":"A36V","14495":"C46R","14530":"I67S","14535":"N70D","14588":"L117R","14591":"G121R","14606":"M146T","14517":"M146T","14545":"M146T"},"param_value":{"14477":"L32S","14485":"A36V","14495":"C46R","14530":"I67S","14535":"N70D","14588":"L117R","14591":"G121R","14606":"M146T","13141":"T33A"},"clinical":{"14477":"L32S","14485":"A36V","14495":"C46R","14530":"I67S","14535":"N70D","14588":"L117R","14591":"G121R","14606":"M146T","13141":"T33A"},"Curated-R":{"13141":"T33A"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"8727":{"protein_sequence":{"accession":"NP_215192.1","sequence":"MSVNDGVDQMGAEPDIMEFVEQMGGYFESRSLTRLAGRLLGWLLVCDPERQSSEELATALAASSGGISTNARMLIQFGFIERLAVAGDRRTYFRLRPNAFAAGERERIRAMAELQDLADVGLRALGDAPPQRSRRLREMRDLLAYMENVVSDALGRYSQRTGEDD"},"dna_sequence":{"accession":"NC_000962.3","fmin":"778989","fmax":"779487","strand":"+","sequence":"GTGAGCGTCAACGACGGGGTCGATCAGATGGGCGCCGAGCCCGACATCATGGAATTCGTCGAACAGATGGGCGGCTATTTCGAGTCCAGGAGTTTGACTCGGTTGGCGGGTCGATTGTTGGGCTGGCTGCTGGTGTGTGATCCCGAGCGGCAGTCCTCGGAGGAACTGGCGACGGCGCTGGCGGCCAGCAGCGGGGGGATCAGCACCAATGCCCGGATGCTGATCCAATTTGGGTTCATTGAGCGGCTCGCGGTCGCCGGGGATCGGCGCACCTATTTCCGGTTGCGGCCCAACGCTTTCGCGGCTGGCGAGCGTGAACGCATCCGGGCAATGGCCGAACTGCAGGACCTGGCTGACGTGGGGCTGAGGGCGCTGGGCGACGCCCCGCCGCAGCGAAGCCGACGGCTGCGGGAGATGCGGGATCTGTTGGCATATATGGAGAACGTCGTCTCCGACGCCCTGGGGCGATACAGCCAGCGAACCGGAGAGGACGACTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3007674","ARO_id":"46455","ARO_name":"Mycobacterium tuberculosis Rv0678 with mutation conferring resistance to bedaquiline","CARD_short_name":"Mtub_Rv0678_BDQ","ARO_description":"Rv0678 encodes a transcription factor which negatively regulates the expression of the mmpS5\/L5 efflux pump. Loss-of-function mutations in rv0678 are a common mechanism of resistance.","ARO_category":{"46454":{"category_aro_accession":"3007673","category_aro_cvterm_id":"46454","category_aro_name":"bedaquiline resistant Rv0678","category_aro_description":"Loss-of-function mutations in the Mycobacterium Rv0678 gene associated with bedaquiline resistance.","category_aro_class_name":"AMR Gene Family"},"41933":{"category_aro_accession":"3004492","category_aro_cvterm_id":"41933","category_aro_name":"bedaquiline","category_aro_description":"A diarylquinoline antibiotic drug sold under the brand name Sirturo, used to treat infection from Mycobacterium spp., particularly multidrug-resistant tuberculosis. Bedaquiline disrupts ATP synthase by proton pump blockage, inhibiting ATP synthesis.","category_aro_class_name":"Antibiotic"},"41932":{"category_aro_accession":"3004491","category_aro_cvterm_id":"41932","category_aro_name":"diarylquinoline antibiotic","category_aro_description":"A class of antibiotics used to treat specifically Mycobacterium tuberculosis infection; therefore, referred to as an antimycobacterial. Diarylquinoline antibiotics inhibit ATP synthesis in tuberculosis cells by disruption of mycobacterial ATP synthase.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"6012":{"model_id":"6012","model_name":"Mycobacterium tuberculosis Rv2535c with mutation conferring resistance to bedaquiline","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"13152":"L44P"},"Curated-R":{"13152":"L44P","13154":"L44P","13202":"L44P"},"clinical":{"13152":"L44P"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"},"40494":{"param_type":"frameshift mutation","param_description":"A frameshift is a sequence change between the translation initiation (start) and termination (stop) codon where, compared to a reference sequence, translation shifts to another reading frame as caused by nucleotide insertions and deletions. In ARO, these are annotated at the protein level with the first changed most N-terminal wildtype amino acid position. Format is given as [wildtype AA][position]fs, e.g. S531fs where S531 is a frameshifted coordinate beginning with codon 531. Termination may also be denoted as: Ter[position]fs.","param_type_id":"40494","param_value":{"13154":"R271fs","13202":"A15fs"}}},"model_sequences":{"sequence":{"8741":{"protein_sequence":{"accession":"NP_217051.1","sequence":"MTHSQRRDKLKAQIAASGLDAMLISDLINVRYLSGFSGSNGALLVFADERDAVLATDGRYRTQAASQAPDLEVAIERAVGRYLAGRAGEAGVGKLGFESHVVTVDGLDALAGALEGKNTELVRASGTVESLREVKDAGELALLRLACEAADAALTDLVARGGLRPGRTERQVSRELEALMLDHGADAVSFETIVAAGANSAIPHHRPTDAVLQVGDFVKIDFGALVAGYHSDMTRTFVLGKAADWQLEIYQLVAEAQQAGRQALLPGAELRGVDAAARQLIADAGYGEHFGHGLGHGVGLQIHEAPGIGVTSAGTLLAGSVVTVEPGVYLPGRGGVRIEDTLVVAGGTPKMPETAGQTPELLTRFPKELAIL"},"dna_sequence":{"accession":"NC_000962.3","fmin":"2859299","fmax":"2860418","strand":"-","sequence":"GTGACACATTCCCAGCGTCGAGACAAGCTGAAAGCACAAATCGCTGCCTCCGGGTTGGATGCGATGCTGATCAGCGACCTGATAAACGTGCGATATCTATCAGGCTTCAGCGGGTCCAACGGCGCATTGCTGGTGTTCGCCGATGAGCGCGATGCCGTGTTGGCCACCGACGGCCGGTACCGCACTCAGGCCGCCTCGCAAGCGCCCGACCTCGAAGTGGCTATCGAGCGCGCGGTCGGGCGCTACCTGGCCGGCCGGGCCGGCGAGGCCGGCGTGGGAAAGCTGGGCTTCGAGAGCCACGTGGTCACGGTGGACGGCCTGGACGCCTTGGCGGGCGCGCTGGAGGGCAAGAACACCGAGTTGGTGCGGGCATCCGGAACTGTGGAGTCACTGCGCGAGGTTAAAGACGCCGGCGAGCTGGCGCTGCTGCGACTAGCCTGCGAAGCAGCCGATGCCGCGCTGACCGACTTGGTGGCCCGCGGCGGCCTGCGGCCGGGCCGAACCGAACGGCAGGTGAGCCGCGAGCTGGAGGCCCTGATGCTCGATCATGGCGCTGACGCGGTGTCATTCGAGACGATCGTGGCTGCCGGGGCCAATTCGGCGATCCCGCACCACCGGCCGACCGACGCGGTGCTGCAGGTCGGCGATTTCGTGAAGATCGACTTCGGCGCCCTGGTCGCCGGGTACCACTCCGATATGACCCGCACCTTCGTGTTGGGCAAGGCCGCCGACTGGCAGCTAGAGATCTATCAGCTGGTGGCCGAGGCGCAACAGGCCGGTCGGCAGGCGTTGCTGCCGGGTGCCGAGCTGCGGGGGGTGGACGCTGCAGCGCGCCAGCTGATCGCCGACGCCGGCTACGGCGAGCACTTCGGTCACGGACTGGGACACGGTGTTGGCCTGCAGATACATGAAGCGCCGGGCATCGGGGTCACATCCGCCGGTACACTACTGGCGGGCTCCGTGGTGACCGTGGAGCCCGGTGTCTATTTACCCGGCCGCGGCGGTGTCCGCATCGAGGACACATTGGTAGTGGCTGGCGGGACGCCGAAAATGCCTGAAACCGCCGGGCAGACCCCGGAATTGTTGACCCGGTTCCCCAAAGAACTGGCCATTCTGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3007692","ARO_id":"46479","ARO_name":"Mycobacterium tuberculosis Rv2535c with mutation conferring resistance to bedaquiline","CARD_short_name":"Mtub_Rv2535_BDQ","ARO_description":"These pepQ\/Rv2535c mutations increase efflux through the mmpL5-mmpS5 (Rv0676c-Rv0677c) transporter, such as preventing degradation of MmpL5, which leads to reduced susceptibility to bedaquiline and clofazimine.","ARO_category":{"46478":{"category_aro_accession":"3007691","category_aro_cvterm_id":"46478","category_aro_name":"bedaquiline resistant Rv2535c","category_aro_description":"Loss-of-function mutations in Rv2535c are a common mechanism of resistance.","category_aro_class_name":"AMR Gene Family"},"40939":{"category_aro_accession":"3004012","category_aro_cvterm_id":"40939","category_aro_name":"clofazimine","category_aro_description":"Clofazimine is a fluoroquinolone-class phenazine dye used for the treatment of leprosy. Clofazimine binds to DNA and disrupts bacterial DNA gyrase, thereby causing double-stranded DNA breaks, and subsequent cell death.","category_aro_class_name":"Antibiotic"},"41933":{"category_aro_accession":"3004492","category_aro_cvterm_id":"41933","category_aro_name":"bedaquiline","category_aro_description":"A diarylquinoline antibiotic drug sold under the brand name Sirturo, used to treat infection from Mycobacterium spp., particularly multidrug-resistant tuberculosis. Bedaquiline disrupts ATP synthase by proton pump blockage, inhibiting ATP synthesis.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"41932":{"category_aro_accession":"3004491","category_aro_cvterm_id":"41932","category_aro_name":"diarylquinoline antibiotic","category_aro_description":"A class of antibiotics used to treat specifically Mycobacterium tuberculosis infection; therefore, referred to as an antimycobacterial. Diarylquinoline antibiotics inhibit ATP synthesis in tuberculosis cells by disruption of mycobacterial ATP synthase.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"6013":{"model_id":"6013","model_name":"AMZ-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"775"}},"model_sequences":{"sequence":{"8742":{"protein_sequence":{"accession":"WHL54874.1","sequence":"MHPRRHFCAGLLAVGLFAAVSAPAAGRSELPYIDSVVNEAARAVIRQHDIAGMVIAVTHQGRQRFYTYGVESLQTRRAVNRDTIFEVGSISKTFTVTLAAYAQAKGLLQLTDSPARFLPELAGTEFAKLSLLNLATHTTGGFPLQVPDEVRDNAQLMQYLKAWKPEHAPGTYRSYANPSIGMLGVVAAVSLKQPFAQAMEKDLFPKLGLSSTFIDVPAAKASRYAQGYNKQGAPVRVNPGVLAAEAYGVKTSARDLLRFVEASMDMDVLDKDIRRAIADTHVGYYQVGAMTQDMVWEQFPYPVPLDSLLTANAGTLNSQSHPAQALQPPLAPQAQTWINKTGSTNGFGAYVAFVPARKLGIVILANRNYPNDARVRLAAEILGAVEKQPMAPAGAR"},"dna_sequence":{"accession":"OQ948417.1","fmin":"0","fmax":"1191","strand":"+","sequence":"ATGCATCCCCGTAGACACTTTTGCGCCGGCCTCCTTGCCGTTGGGCTTTTTGCCGCCGTGTCAGCGCCCGCCGCGGGACGCTCCGAGCTGCCCTACATCGACAGCGTCGTGAACGAGGCGGCCCGCGCGGTTATCCGCCAGCACGACATCGCGGGCATGGTGATAGCCGTGACGCACCAAGGCCGCCAGCGTTTCTACACCTATGGCGTCGAATCATTGCAGACGCGGCGCGCCGTCAATCGGGACACGATCTTTGAAGTGGGCTCGATCAGCAAGACCTTCACCGTGACGCTTGCCGCGTATGCGCAGGCGAAGGGCTTGTTGCAGTTGACCGACAGTCCGGCGCGTTTTTTGCCCGAGCTGGCCGGCACTGAATTCGCCAAACTGTCCTTGCTGAACCTGGCGACGCACACGACGGGCGGTTTTCCGTTGCAGGTGCCTGACGAGGTGCGCGACAACGCGCAATTGATGCAATACCTGAAGGCCTGGAAGCCGGAGCATGCGCCCGGCACGTATCGCTCGTATGCCAATCCCAGCATTGGCATGCTGGGCGTCGTGGCGGCTGTCAGCTTGAAGCAGCCGTTTGCCCAGGCGATGGAAAAGGACCTTTTTCCGAAGCTGGGGCTGTCCAGCACGTTCATCGACGTGCCCGCCGCCAAGGCGTCGCGCTACGCGCAGGGCTACAACAAGCAGGGCGCGCCGGTGCGCGTGAATCCAGGCGTGCTGGCAGCCGAGGCCTATGGCGTGAAAACCAGCGCGCGCGACCTGCTGCGCTTCGTCGAGGCCAGCATGGACATGGACGTGCTGGACAAGGACATCCGCCGCGCCATTGCGGACACCCACGTGGGCTATTACCAGGTGGGCGCAATGACGCAGGACATGGTGTGGGAGCAGTTCCCGTATCCCGTGCCGCTGGATTCGCTGCTGACGGCCAACGCCGGCACGCTGAACAGCCAGAGCCATCCGGCCCAGGCGCTGCAGCCGCCGCTGGCGCCGCAGGCCCAGACCTGGATCAACAAGACGGGGTCCACCAACGGCTTCGGGGCCTACGTGGCGTTTGTGCCCGCGCGCAAGCTCGGCATCGTCATTCTGGCCAACCGCAATTACCCGAACGACGCGCGCGTGCGTCTGGCGGCGGAAATTCTGGGGGCGGTGGAGAAGCAGCCTATGGCGCCCGCCGGCGCGCGTTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"46482","NCBI_taxonomy_name":"Achromobacter mucicolens","NCBI_taxonomy_id":"1389922"}}}},"ARO_accession":"3007694","ARO_id":"46481","ARO_name":"AMZ-1","CARD_short_name":"AMZ-1","ARO_description":"Achromobacter mucicolens Y3, isolated from a goose on a farm in Wenzhou, showed resistance to multiple antibiotics, including penicillins and cephalosporins. AMZ-1 showed resistance to amoxicillin, penicillin G, ampicillin, cephalothin and cefoxitin, and the resistance activity could be inhibited by beta-lactamase inhibitors.","ARO_category":{"46480":{"category_aro_accession":"3007693","category_aro_cvterm_id":"46480","category_aro_name":"AMZ beta-lactamase","category_aro_description":"The AMZ genes showed resistance against some beta-lactam antibiotics, including amoxicillin and cephalothin, and the beta-lactamase AMZ-1 exhibited a similar substrate spectrum response. Similar to other AmpC beta-lactamases, AMZ-1 is strongly inhibited by avibactam but much less strongly inhibited by tazobactam.","category_aro_class_name":"AMR Gene Family"},"35927":{"category_aro_accession":"0000008","category_aro_cvterm_id":"35927","category_aro_name":"cefoxitin","category_aro_description":"Cefoxitin is a cephamycin antibiotic often grouped with the second generation cephalosporins. Cefoxitin is bactericidal and acts by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. Cefoxitin's 7-alpha-methoxy group and 3' leaving group make it a poor substrate for most beta-lactamases.","category_aro_class_name":"Antibiotic"},"35981":{"category_aro_accession":"0000064","category_aro_cvterm_id":"35981","category_aro_name":"amoxicillin","category_aro_description":"Amoxicillin is a moderate-spectrum, bacteriolytic, beta-lactam antibiotic used to treat bacterial infections caused by susceptible microorganisms. A derivative of penicillin, it has a wider range of treatment but remains relatively ineffective against Gram-negative bacteria. It is commonly taken with clavulanic acid, a beta-lactamase inhibitor. Like other beta-lactams, amoxicillin interferes with the synthesis of peptidoglycan.","category_aro_class_name":"Antibiotic"},"36976":{"category_aro_accession":"3000632","category_aro_cvterm_id":"36976","category_aro_name":"benzylpenicillin","category_aro_description":"Benzylpenicillin, commonly referred to as penicillin G, is effective against both Gram-positive and Gram-negative bacteria. It is unstable in acid.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"37084":{"category_aro_accession":"3000704","category_aro_cvterm_id":"37084","category_aro_name":"cefalotin","category_aro_description":"Cefalotin is a semisynthetic cephalosporin antibiotic activate against staphylococci. It is resistant to staphylococci beta-lactamases but hydrolyzed by enterobacterial beta-lactamases.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"6014":{"model_id":"6014","model_name":"CMY-185","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"700"}},"model_sequences":{"sequence":{"8743":{"protein_sequence":{"accession":"WCB91330.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTEGGLPLKIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHSSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPYPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"OQ297612.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGAAGGCGGCCTACCGCTGAAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACAGTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTTACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3007695","ARO_id":"46483","ARO_name":"CMY-185","CARD_short_name":"CMY-185","ARO_description":"We identified ceftazidime\/avibactam resistance in E. coli associated with a novel CMY variant. Unlike other AmpC enzymes, CMY-185 appears to require an additional substitution on top of N346Y to confer ceftazidime\/avibactam resistance.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"6068":{"model_id":"6068","model_name":"NWM-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"8891":{"protein_sequence":{"accession":"QXM27671.1","sequence":"MEPALFDRLTLAASVAALAGCSAGLASSESAAKIEDAQHSSDIVRFANECEDWDDWDKPAKPFQIHAKTYYVGTCGIAAILIEGEDGLVLIDTGTEPGSRQVEANIAALGHSVSDIDAILTSHEHFDHVGGLARLQALSGATVHTSAAALPVLRTGKDDPRDPQAGLHPPMAPVGGTIRALGDGEIVEIGGARIKALATPGHTLGAMSWEWESCDAAGCVTIVLADSLSAVSADGYKFNEHPEYVAMFRKGIARMAETTCDILLTPHPSASDMIARAKTGTFEGGMTCSEYADSKTKALDERLAKEAADE"},"dna_sequence":{"accession":"MZ497415.1","fmin":"0","fmax":"933","strand":"+","sequence":"ATGGAGCCAGCTTTGTTCGATAGACTTACTCTTGCCGCCAGCGTCGCTGCGCTCGCCGGGTGCAGCGCCGGATTGGCATCCAGCGAAAGCGCCGCGAAGATCGAGGACGCGCAGCATTCGAGCGACATCGTCCGCTTCGCCAACGAATGCGAGGACTGGGACGATTGGGACAAGCCGGCCAAGCCCTTCCAGATCCATGCGAAGACCTATTACGTCGGCACCTGCGGGATTGCGGCGATCCTGATCGAGGGCGAGGATGGTCTGGTCCTGATCGACACGGGGACCGAGCCGGGGTCACGGCAGGTCGAGGCCAATATCGCCGCGTTGGGTCATTCCGTTTCCGACATCGATGCCATTCTCACTAGCCACGAGCACTTCGACCACGTCGGCGGTCTTGCGCGGCTGCAAGCGTTAAGCGGGGCGACGGTCCACACGAGCGCTGCCGCCCTGCCCGTTCTGCGCACCGGCAAGGACGACCCCCGCGATCCGCAGGCGGGGCTGCACCCTCCGATGGCTCCGGTCGGGGGAACGATACGCGCGCTGGGCGACGGCGAGATCGTGGAGATCGGCGGAGCGCGCATCAAGGCGCTGGCCACGCCGGGGCACACGCTCGGCGCGATGAGTTGGGAATGGGAAAGCTGCGACGCCGCAGGATGCGTTACCATCGTCCTTGCCGACAGCCTTTCCGCTGTCAGCGCGGACGGATACAAGTTCAACGAGCACCCCGAATACGTCGCCATGTTTCGCAAGGGCATCGCACGTATGGCGGAGACGACGTGCGACATCCTGCTGACCCCGCACCCTTCCGCCAGCGACATGATCGCGCGCGCCAAGACCGGCACTTTCGAAGGCGGCATGACCTGCTCCGAATATGCCGACAGCAAGACGAAAGCGCTGGACGAGCGGCTGGCCAAGGAAGCAGCGGACGAATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3007848","ARO_id":"46638","ARO_name":"NWM-1","CARD_short_name":"NWM-1","ARO_description":"NWM-1 is a NWM beta-lactamase gene family variant.","ARO_category":{"46637":{"category_aro_accession":"3007847","category_aro_cvterm_id":"46637","category_aro_name":"NWM beta-lactamase","category_aro_description":"NWM is a subclass B3 metallo beta-lactamase with enzymatic activity against carbapenems, first identified in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"6015":{"model_id":"6015","model_name":"Salmonella gallinarum folP with mutation conferring resistance to sulfonamides","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"13158":"R171P"},"Curated-R":{"13158":"R171P"},"clinical":{"13158":"R171P"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8745":{"protein_sequence":{"accession":"WMC40549.1","sequence":"MKLFAQGATLDLTHPHVMGILNVTPDSFSDGGAHNTLIEAVKHANLMVNAGATIIDVGGESTRPGAAEVSVEEELDRVIPVLEAIAQRFEVWISVDTSKPEVIREATRAGAHIINDVRSLSEPGALEAAAETGLPVSLMHMQGNPKTMQEAPKYDDVFAEVNRYFIEQIARCEKAGIAKEKLLLDPGFGFGKNLSHNYTLLARLGEFHHFNLPLLVGMSRKTMVGQLLNVGPSDRLNGSLACAVIAAMQGAQIIRVHDVKETVEAMRVVEATLSAKGNKRYE"},"dna_sequence":{"accession":"CP100648.1","fmin":"613398","fmax":"614247","strand":"+","sequence":"ATGAAACTCTTCGCTCAGGGCGCCACGCTCGATCTCACTCATCCGCATGTTATGGGTATCCTGAACGTAACGCCGGATTCGTTCTCCGACGGCGGCGCGCATAACACGCTGATTGAGGCGGTGAAACATGCGAATTTAATGGTGAATGCCGGTGCGACAATTATTGATGTGGGGGGGGAATCAACGCGACCAGGCGCGGCGGAAGTGAGCGTGGAAGAAGAGCTGGATCGCGTTATTCCGGTACTGGAAGCAATCGCGCAACGTTTTGAAGTGTGGATTTCTGTGGATACCTCTAAGCCCGAGGTGATCCGTGAAGCGACAAGGGCGGGCGCGCATATTATCAATGATGTCCGTTCGCTCTCCGAGCCCGGCGCGTTGGAAGCGGCAGCGGAAACCGGCTTGCCGGTCAGTCTTATGCACATGCAGGGCAACCCCAAAACCATGCAGGAGGCGCCGAAATATGACGATGTCTTTGCCGAGGTGAATCGCTACTTTATTGAGCAAATAGCACGTTGTGAGAAGGCCGGCATCGCAAAAGAGAAATTGTTGCTCGACCCCGGATTCGGTTTCGGTAAAAATCTCTCTCACAATTATACCTTACTGGCGCGACTGGGTGAGTTTCATCATTTTAACCTGCCGCTGCTGGTGGGCATGTCACGTAAAACGATGGTTGGTCAGTTACTTAACGTGGGACCATCAGACCGTCTGAACGGCAGCCTTGCGTGCGCGGTAATTGCCGCGATGCAGGGCGCGCAGATCATTCGCGTCCATGACGTCAAAGAAACCGTAGAGGCGATGCGGGTGGTAGAAGCCACTCTGTCTGCAAAGGGAAACAAACGCTATGAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35654","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Gallinarum","NCBI_taxonomy_id":"594"}}}},"ARO_accession":"3007749","ARO_id":"46529","ARO_name":"Salmonella gallinarum folP with mutation conferring resistance to sulfonamides","CARD_short_name":"Sgal_folP_SLF","ARO_description":"Point mutations in Salmonella gallinarum dihydropteroate synthase folP altered the stability of the protein, thus conferring sulfonamide resistance.","ARO_category":{"39999":{"category_aro_accession":"3003415","category_aro_cvterm_id":"39999","category_aro_name":"sulfonamide resistant dihydropteroate synthase folP","category_aro_description":"Point mutations in dihydropteroate synthase folP prevent sulfonamide antibiotics from inhibiting its role in folate synthesis, thus conferring sulfonamide resistance.","category_aro_class_name":"AMR Gene Family"},"36468":{"category_aro_accession":"3000329","category_aro_cvterm_id":"36468","category_aro_name":"sulfamethoxazole","category_aro_description":"Sulfamethoxazole is a sulfonamide antibiotic usually taken with trimethoprim, a diaminopyrimidine antibiotic. Sulfamethoxazole inhibits dihydropteroate synthase, essential to tetrahydrofolic acid biosynthesis. This pathway generates compounds used in the synthesis of many amino acids and nucleotides.","category_aro_class_name":"Antibiotic"},"36421":{"category_aro_accession":"3000282","category_aro_cvterm_id":"36421","category_aro_name":"sulfonamide antibiotic","category_aro_description":"Sulfonamides are broad spectrum, synthetic antibiotics that contain the sulfonamide group. Sulfonamides inhibit dihydropteroate synthase, which catalyzes the conversion of p-aminobenzoic acid to dihydropteroic acid as part of the tetrahydrofolic acid biosynthetic pathway. Tetrahydrofolic acid is essential for folate synthesis, a precursor of many nucleotides and amino acids. Many sulfamides are taken with trimethoprim, an inhibitor of dihydrofolate reductase, also disturbing the trihydrofolic acid synthesis pathway.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"6016":{"model_id":"6016","model_name":"Salmonella isangi gyrA conferring resistance to fluoroquinolones","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"13161":"S83F","13160":"D87N"},"Curated-R":{"13161":"S83F","13160":"D87N"},"clinical":{"13161":"S83F","13160":"D87N"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1300"}},"model_sequences":{"sequence":{"8746":{"protein_sequence":{"accession":"WP_001281271.1","sequence":"MSDLAREITPVNIEEELKSSYLDYAMSVIVGRALPDVRDGLKPVHRRVLYAMNVLGNDWNKAYKKSARVVGDVIGKYHPHGDSAVYDTIVRMAQPFSLRYMLVDGQGNFGSIDGDSAAAMRYTEIRLAKIAHELMADLEKETVDFVDNYDGTEKIPDVMPTKIPNLLVNGSSGIAVGMATNIPPHNLTEVINGCLAYIDNEDISIEGLMEHIPGPDFPTAAIINGRRGIEEAYRTGRGKVYIRARAEVEADAKTGRETIIVHEIPYQVNKARLIEKIAELVKDKRVEGISALRDESDKDGMRIVIEVKRDAVGEVVLNNLYSQTQLQVSFGINMVALHHGQPKIMNLKDIISAFVRHRREVVTRRTIFELRKARDRAHILEALAIALANIDPIIELIRRAPTPAEAKAALISRPWDLGNVAAMLERAGDDAARPEWLEPEFGVRDGQYYLTEQQAQAILDLRLQKLTGLEHEKLLDEYKELLEQIAELLHILGSADRLMEVIREEMELIRDQFGDERRTEITANSADINIEDLISQEDVVVTLSHQGYVKYQPLTDYEAQRRGGKGKSAARIKEEDFIDRLLVANTHDTILCFSSRGRLYWMKVYQLPEASRGARGRPIVNLLPLEANERITAILPVREYEEGVNVFMATASGTVKKTALTEFSRPRSAGIIAVNLNDGDELIGVDLTSGSDEVMLFSAAGKVVRFKEDAVRAMGRTATGVRGIKLAGDDKVVSLIIPRGEGAILTVTQNGYGKRTAADEYPTKSRATQGVISIKVTERNGSVVGAVQVDDCDQIMMITDAGTLVRTRVSEISVVGRNTQGVILIRTAEDENVVGLQRVAEPVDDEELDAIDGSVAEGDEDIAPEAESDDDVADDADE"},"dna_sequence":{"accession":"NZ_JARETA010000011.1","fmin":"134188","fmax":"136825","strand":"+","sequence":"ATGAGCGACCTTGCGAGAGAAATTACACCGGTCAACATTGAGGAGGAGCTGAAGAGCTCCTATCTGGATTATGCGATGTCGGTCATTGTTGGCCGTGCGCTGCCGGATGTCCGAGATGGCCTGAAGCCGGTACACCGTCGCGTACTTTACGCCATGAACGTATTGGGCAATGACTGGAACAAAGCCTATAAAAAATCTGCCCGTGTCGTTGGTGACGTAATCGGTAAATACCATCCCCACGGCGATTCCGCAGTGTATGACACCATCGTTCGTATGGCGCAGCCATTCTCGCTGCGTTACATGCTGGTGGATGGTCAGGGTAACTTCGGTTCTATTGACGGCGACTCCGCGGCGGCAATGCGTTATACGGAGATCCGTCTGGCGAAAATCGCCCACGAACTGATGGCCGATCTCGAAAAAGAGACGGTGGATTTCGTGGATAACTATGACGGTACGGAAAAAATTCCGGACGTCATGCCGACCAAAATTCCGAATCTGCTGGTGAACGGTTCTTCCGGTATCGCAGTAGGTATGGCGACGAATATCCCGCCGCACAACCTGACGGAAGTGATTAACGGCTGCCTGGCGTATATCGACAACGAAGACATCAGCATTGAAGGGCTGATGGAACATATTCCGGGGCCGGACTTCCCGACCGCCGCGATCATCAACGGTCGTCGTGGTATCGAAGAAGCCTACCGTACCGGTCGTGGCAAAGTGTACATTCGCGCCCGCGCGGAAGTTGAAGCTGACGCGAAAACGGGCCGTGAAACCATCATCGTCCATGAAATTCCCTATCAGGTGAACAAAGCGCGCCTGATCGAGAAAATCGCCGAGCTGGTGAAAGATAAACGCGTGGAAGGCATCAGCGCGCTGCGTGACGAATCCGACAAAGACGGGATGCGCATCGTGATTGAAGTGAAACGCGATGCGGTGGGCGAGGTGGTGCTTAATAATCTCTACTCCCAGACCCAGCTACAGGTTTCCTTCGGTATTAACATGGTGGCGCTGCATCACGGCCAGCCGAAGATCATGAACCTGAAAGACATCATTTCAGCGTTCGTGCGCCACCGCCGTGAAGTGGTGACGCGTCGGACTATTTTTGAACTGCGTAAAGCCCGTGACCGCGCGCATATCCTTGAAGCTCTGGCGATTGCGCTGGCTAACATCGACCCGATTATCGAACTGATTCGCCGCGCGCCAACGCCGGCAGAAGCAAAAGCGGCGCTGATTTCGCGTCCGTGGGATCTGGGCAACGTTGCTGCGATGCTGGAGCGCGCTGGTGATGACGCTGCGCGTCCGGAATGGCTGGAGCCAGAATTTGGCGTGCGTGACGGTCAGTATTACCTGACTGAGCAGCAGGCGCAGGCGATTCTGGATCTGCGTTTGCAGAAACTGACCGGCCTGGAGCATGAAAAACTGCTCGACGAATACAAAGAGTTGCTGGAGCAGATTGCTGAACTGCTGCACATTCTGGGCAGCGCCGATCGCCTGATGGAAGTGATCCGCGAAGAGATGGAGTTAATTCGCGATCAGTTCGGCGATGAGCGTCGTACCGAAATCACCGCCAACAGCGCCGATATTAATATCGAAGATCTGATTAGCCAGGAAGATGTTGTCGTGACGCTGTCTCACCAGGGTTACGTCAAATATCAACCGCTGACGGATTACGAAGCGCAACGTCGTGGTGGGAAAGGTAAATCTGCCGCGCGTATTAAAGAAGAAGACTTTATCGACCGTCTGCTGGTGGCCAACACCCATGACACCATCCTCTGCTTCTCCAGCCGGGGCCGTCTGTACTGGATGAAGGTCTATCAGTTGCCGGAAGCCAGCCGTGGCGCGCGCGGTCGTCCGATCGTTAACCTGCTGCCGCTGGAAGCCAACGAACGTATCACCGCGATTCTGCCGGTTCGTGAATACGAAGAGGGCGTCAACGTATTTATGGCGACCGCCAGCGGTACCGTGAAGAAAACGGCGCTGACCGAATTCAGCCGTCCGCGTTCCGCCGGTATTATCGCGGTGAACCTCAACGACGGCGACGAGCTGATTGGCGTTGACCTGACTTCTGGTTCTGACGAAGTCATGCTGTTCTCGGCCGCGGGTAAAGTGGTGCGCTTCAAAGAAGACGCCGTCCGTGCGATGGGGCGTACCGCGACCGGTGTGCGCGGTATTAAGCTGGCGGGAGACGATAAAGTCGTCTCTCTGATCATCCCACGCGGCGAAGGCGCTATTCTGACCGTAACGCAAAACGGCTACGGGAAGCGTACCGCAGCGGACGAGTACCCGACCAAGTCTCGTGCGACGCAGGGCGTTATCTCTATCAAAGTGACCGAGCGCAACGGTTCCGTTGTCGGTGCGGTACAGGTAGACGATTGCGACCAGATCATGATGATCACGGATGCCGGTACTCTGGTGCGTACCCGAGTGTCTGAGATCAGCGTAGTGGGACGTAATACCCAGGGCGTTATCCTTATCCGCACGGCGGAAGACGAAAACGTGGTGGGTCTGCAACGCGTTGCTGAACCGGTAGATGACGAAGAACTCGACGCTATCGACGGCAGCGTGGCGGAAGGGGATGAGGATATCGCCCCGGAAGCGGAAAGCGATGACGACGTTGCGGATGACGCTGACGAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"46532","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Isangi","NCBI_taxonomy_id":"1386015"}}}},"ARO_accession":"3007751","ARO_id":"46531","ARO_name":"Salmonella isangi gyrA conferring resistance to fluoroquinolones","CARD_short_name":"Sisa_gyrA_FLO","ARO_description":"Point mutations in Salmonella gyrA that confer resistance to ciprofloxacin and nalidixic acid which are fluoroquinolone antibiotics.","ARO_category":{"39876":{"category_aro_accession":"3003292","category_aro_cvterm_id":"39876","category_aro_name":"fluoroquinolone resistant gyrA","category_aro_description":"DNA gyrase is responsible for DNA supercoiling and consists of two alpha and two beta subunits. GyrA point mutations confer resistance by preventing fluoroquinolone antibiotics from binding the alpha-subunit.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"6017":{"model_id":"6017","model_name":"Salmonella isangi gyrB conferring resistance to fluoroquinolones","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"13162":"S464F"},"Curated-R":{"13162":"S464F"},"clinical":{"13162":"S464F"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1300"}},"model_sequences":{"sequence":{"8747":{"protein_sequence":{"accession":"WP_000072047.1","sequence":"MSNSYDSSSIKVLKGLDAVRKRPGMYIGDTDDGTGLHHMVFEVVDNAIDEALAGHCKDIVVTIHADNSVSVTDDGRGIPTGIHPEEGVSAAEVIMTVLHAGGKFDDNSYKVSGGLHGVGVSVVNALSQKLELVIQRDGKIHRQIYEHGVPQAPLAVTGDTDKTGTMVRFWPSHETFTNVTEFEYEILAKRLRELSFLNSGVSIRLRDKRDGKEDHFHYEGGIKAFVEYLNKNKTPIHPNIFYFSTEKDGIGVEVALQWNDGFQENIYCFTNNIPQRDGGTHLAGFRAAMTRTLNAYMDKEGYSKKAKVSATGDDAREGLIAVVSVKVPDPKFSSQTKDKLVSSEVKSAVEQQMNELLSEYLLENPSDAKIVVGKIIDAARAREAARRAREMTRRKGALDLAGLPGKLADCQERDPALSELYLVEGDSAGGSAKQGRNRKNQAILPLKGKILNVEKARFDKMLSSQEVATLITALGCGIGRDEYNPDKLRYHSIIIMTDADVDGSHIRTLLLTFFYRQMPEIVERGHVYIAQPPLYKVKKGKQEQYIKDDEAMDQYQISIALDGATLHANAHAPALSGEALEKLVSEYNATQKMIGRMERRFPKALLKELVYQPTLTEADLSDEQTVTRWVNALITELNEKEQHGSQWKFDVHTNTEQNLFEPIVRVRTHGVDTDYPLDHEFVTGAEYRRICTLGEKLRGLIEEDAFIERGERRQPVTSFEQALEWLVKESRRGLAIQRYKGLGEMNPDQLWETTMDPESRRMLRVTVKDAIAADQLFTTLMGDAVEPRRAFIEENALKAANIDI"},"dna_sequence":{"accession":"NZ_JARETA010000016.1","fmin":"58093","fmax":"60508","strand":"+","sequence":"ATGTCGAATTCTTATGACTCCTCCAGTATCAAAGTCCTGAAAGGGCTGGATGCGGTGCGTAAGCGCCCGGGTATGTATATCGGCGACACGGATGACGGCACCGGTCTGCACCACATGGTATTCGAGGTGGTAGATAACGCTATCGACGAAGCGCTCGCAGGTCACTGTAAAGATATCGTCGTGACTATTCACGCCGATAACTCCGTGTCCGTAACGGATGATGGCCGTGGCATTCCGACCGGGATTCACCCGGAAGAAGGCGTCTCAGCGGCGGAAGTGATCATGACCGTTCTGCACGCGGGCGGTAAATTTGACGATAACTCCTATAAAGTCTCTGGTGGTCTGCACGGCGTGGGCGTCTCGGTAGTCAACGCTCTGTCGCAAAAACTGGAACTGGTTATCCAGCGAGATGGCAAAATTCACCGTCAGATCTACGAGCACGGCGTGCCGCAGGCACCCCTGGCCGTCACTGGCGATACCGATAAAACCGGCACGATGGTACGTTTCTGGCCGAGCCACGAAACCTTCACTAACGTCACTGAATTTGAATATGAGATCCTGGCGAAACGCCTGCGTGAACTGTCATTCCTGAACTCTGGCGTTTCCATCCGTCTGCGCGACAAGCGTGACGGCAAAGAAGATCATTTCCACTACGAAGGCGGCATCAAGGCGTTTGTTGAATATCTCAACAAAAACAAAACGCCGATCCACCCGAATATCTTCTACTTCTCCACCGAAAAAGACGGTATCGGCGTGGAAGTAGCGCTGCAGTGGAACGACGGTTTCCAGGAAAACATCTACTGCTTTACCAACAACATTCCGCAGCGCGACGGCGGTACCCACCTGGCAGGCTTCCGTGCGGCGATGACCCGTACGCTGAACGCCTATATGGACAAAGAAGGTTACAGCAAAAAAGCTAAAGTCAGCGCTACCGGCGATGATGCCCGTGAAGGTCTGATTGCGGTGGTTTCCGTAAAAGTACCGGACCCGAAATTCTCCTCACAGACCAAAGATAAGCTGGTCTCTTCCGAGGTGAAATCGGCGGTGGAACAGCAGATGAACGAACTGCTGAGCGAATACCTGCTGGAAAACCCATCTGACGCGAAAATTGTCGTCGGCAAAATTATCGACGCCGCGCGTGCGCGTGAAGCGGCGCGTCGCGCCCGTGAAATGACCCGTCGTAAAGGCGCGCTGGATTTAGCCGGTCTGCCGGGCAAACTGGCGGACTGTCAGGAACGCGACCCGGCGCTGTCCGAACTGTACCTGGTGGAAGGGGACTCCGCGGGCGGCTCTGCGAAGCAGGGGCGTAACCGCAAGAACCAGGCGATTCTGCCGCTGAAAGGTAAAATCCTTAACGTTGAGAAAGCGCGCTTCGACAAGATGCTTTCCTCCCAGGAAGTGGCGACGCTGATCACCGCGCTGGGCTGCGGTATCGGTCGCGACGAGTACAACCCGGACAAGCTGCGCTATCACAGCATCATCATCATGACCGATGCGGACGTCGACGGCTCGCACATCCGTACGCTGCTGTTGACCTTCTTCTATCGTCAGATGCCGGAAATCGTCGAGCGCGGCCACGTCTACATTGCCCAGCCGCCGCTGTACAAAGTCAAGAAAGGCAAGCAGGAACAGTACATCAAAGACGACGAAGCGATGGATCAGTACCAGATTTCCATCGCGCTTGACGGTGCGACTCTGCACGCGAACGCTCATGCGCCAGCGCTATCCGGCGAAGCGTTAGAAAAACTGGTCTCTGAATATAACGCCACGCAGAAAATGATTGGTCGTATGGAGCGTCGCTTCCCGAAAGCGCTGCTCAAAGAGCTGGTGTATCAGCCAACTCTGACCGAAGCCGATCTTTCTGATGAGCAGACTGTAACGCGCTGGGTGAATGCGCTGATTACCGAGCTGAACGAGAAAGAGCAGCACGGCAGTCAGTGGAAGTTCGATGTTCATACTAATACGGAACAGAATCTGTTCGAGCCTATCGTTCGCGTGCGTACGCATGGTGTGGATACCGATTATCCGTTGGATCACGAGTTTGTGACCGGCGCGGAATATCGTCGTATCTGCACGCTGGGCGAGAAGCTGCGCGGTCTGATTGAAGAGGACGCGTTTATCGAACGCGGCGAGCGTCGCCAGCCGGTAACCAGCTTCGAGCAGGCGCTGGAGTGGCTGGTGAAAGAATCACGTCGCGGTCTGGCTATCCAGCGTTATAAAGGTCTGGGTGAAATGAACCCGGATCAGCTGTGGGAAACCACCATGGACCCGGAAAGCCGCCGTATGCTGCGCGTGACCGTCAAAGATGCGATTGCTGCCGACCAGCTGTTCACTACGCTGATGGGTGATGCCGTTGAGCCGCGTCGTGCCTTTATCGAAGAGAACGCCCTGAAAGCGGCGAATATCGATATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"46532","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Isangi","NCBI_taxonomy_id":"1386015"}}}},"ARO_accession":"3007752","ARO_id":"46533","ARO_name":"Salmonella isangi gyrB conferring resistance to fluoroquinolones","CARD_short_name":"Sisa_gyrB_FLO","ARO_description":"Point mutation in Salmonella isangi resulting in fluoroquinolone resistance.","ARO_category":{"37244":{"category_aro_accession":"3000864","category_aro_cvterm_id":"37244","category_aro_name":"fluoroquinolone resistant gyrB","category_aro_description":"Point mutations in DNA gyrase subunit B (gyrB) observed in Mycobacterium tuberculosis can result in resistance to fluoroquinolones.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"37005":{"category_aro_accession":"3000661","category_aro_cvterm_id":"37005","category_aro_name":"nalidixic acid","category_aro_description":"Nalidixic acid is a quinolone derivative of naphthyridine active against many enterobacteria, but ineffective against Ps aeruginosa, Gram-positive bacteria, and anaerobes. Acquired resistance is common in nalidixic acid treatments.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"6011":{"model_id":"6011","model_name":"MdtQ","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"900"}},"model_sequences":{"sequence":{"8739":{"protein_sequence":{"accession":"WMY66391.1","sequence":"MKLILNKSVLAALPLAIALAGCAPSHEVANPPQQQIPASHVSMDLPAAVKNGWPQTDWWKDYHDPQLNNLIQRALANAPDMQIAEQRIRLAEAQARMSQANLGPEMDFSADIERQRMSAEGLMGPFATDTDGNTGPWYTNGTFGLTAGWDLDLWGKNRALVKARIGELKAQVAEQAQTRELLSGSVARLYWQWQTEAAIKAVLQQVKNEQNNIVTVDKALYQRGITNSAEGAENDINVSKTDQQLADVTGTMKEIEARLMALTNSQSQSLNLKPASLPTVSAQLPDTLGYELLARRPDLQVAHWYIEASLSEVDAAKAAFYPDINLMAFLQQDALHLSDLFRHSAQQMGVTAGLTLPIFDSGRLNANLDIASAQNSLSIAQYNKAVVDAVNQVAKTASQVETLMAKSQQQQQVEKDAQRVVDLAQARMAAGILPGSRVSMAKLPALQERITALRLHGQWIDASIQLTSALGGGYHQTVK"},"dna_sequence":{"accession":"CP133868.1","fmin":"5051597","fmax":"5053037","strand":"-","sequence":"ATGAAATTGATATTAAATAAAAGCGTGCTGGCGGCATTGCCCCTGGCCATCGCGCTGGCTGGCTGCGCGCCATCTCATGAGGTTGCTAATCCGCCGCAGCAGCAAATTCCAGCCTCCCATGTTTCCATGGATCTCCCTGCCGCCGTGAAAAATGGCTGGCCGCAGACTGACTGGTGGAAAGATTACCATGACCCACAGCTTAATAATCTGATTCAGCGAGCGTTGGCCAACGCGCCGGATATGCAGATTGCCGAACAGCGCATCAGGCTTGCCGAAGCGCAGGCGCGAATGTCGCAGGCGAATCTTGGCCCGGAGATGGATTTCTCCGCCGATATTGAACGCCAGCGCATGTCGGCCGAAGGCCTGATGGGACCGTTTGCTACCGACACCGACGGCAATACCGGCCCGTGGTACACCAACGGTACCTTTGGCCTGACCGCCGGTTGGGATCTCGATCTGTGGGGAAAAAACCGTGCGCTGGTGAAAGCGCGTATCGGCGAGCTGAAAGCCCAGGTTGCTGAACAGGCCCAGACCCGTGAGCTGCTCTCCGGCAGCGTGGCGCGTCTGTACTGGCAGTGGCAGACGGAAGCGGCGATCAAAGCGGTGCTGCAGCAGGTGAAAAACGAGCAAAATAATATCGTGACGGTCGACAAGGCCCTGTATCAGCGCGGGATCACTAACTCCGCCGAAGGGGCGGAGAACGATATTAACGTCAGCAAAACCGACCAGCAGCTGGCGGACGTGACGGGCACGATGAAAGAGATTGAAGCGCGGCTGATGGCCCTGACCAACAGCCAGAGCCAGTCGCTAAACCTCAAACCCGCCAGCCTGCCAACGGTCAGCGCGCAGCTGCCAGATACCCTCGGCTATGAGCTGCTGGCGCGCCGCCCGGATCTGCAGGTCGCCCACTGGTATATTGAGGCGTCCCTGAGCGAAGTGGACGCGGCGAAAGCGGCGTTTTATCCGGACATCAATCTGATGGCGTTCCTGCAGCAGGATGCCCTGCACTTAAGCGATCTTTTCCGCCATTCGGCGCAGCAGATGGGCGTTACTGCCGGGTTGACGCTGCCGATCTTTGACAGCGGCCGCCTTAACGCCAACCTGGATATCGCCAGCGCGCAGAATAGCCTGTCGATCGCCCAGTACAACAAAGCGGTGGTGGATGCCGTTAACCAGGTGGCGAAAACCGCCAGCCAGGTCGAAACATTAATGGCCAAAAGCCAGCAGCAGCAGCAGGTTGAAAAAGACGCTCAACGGGTAGTAGATCTGGCGCAGGCCCGAATGGCGGCGGGGATCTTACCTGGCTCCAGAGTCAGTATGGCGAAGCTCCCGGCGCTGCAGGAGCGGATCACCGCATTGCGCCTGCACGGCCAGTGGATTGACGCTAGCATTCAACTGACCTCGGCCCTCGGCGGCGGCTACCACCAGACGGTGAAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3007682","ARO_id":"46464","ARO_name":"MdtQ","CARD_short_name":"MdtQ","ARO_description":"MdtQ is a putative multidrug resistance outer membrane protein found in carbapenem-resistant Klebsiella pneumoniae.","ARO_category":{"41442":{"category_aro_accession":"3004278","category_aro_cvterm_id":"41442","category_aro_name":"Outer Membrane Porin (Opr)","category_aro_description":"The Opr family consists of porins in Pseudomonas species, and other Gram-negative bacteria, that exhibit a variety of substrate selectivities.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36383":{"category_aro_accession":"3000244","category_aro_cvterm_id":"36383","category_aro_name":"reduced permeability to antibiotic","category_aro_description":"Reduction in permeability to antibiotic, generally through reduced production of porins, can provide resistance.","category_aro_class_name":"Resistance Mechanism"}}},"6019":{"model_id":"6019","model_name":"Treponema pallidum 23S rRNA with mutation conferring resistance to erythromycin","model_type":"rRNA gene variant model","model_type_id":"40295","model_description":"Ribosomal RNA (rRNA) Gene Variant Models (RVM) are similar to Protein Variant Models (PVM), i.e. detect  sequences based on their similarity to a curated reference sequence and secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles, except RVMs are designed to detect AMR acquired via mutation of genes encoding ribosomal RNAs (rRNA). RVMs include a rRNA reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTN bit-score above the curated BLASTN cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTN bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"13171":"a2100g","13172":"a2101g"},"Curated-R":{"13171":"a2100g","13172":"a2101g"},"clinical":{"13171":"a2100g","13172":"a2101g"}},"blastn_bit_score":{"param_type":"BLASTN bit-score","param_description":"The BLASTN bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a nucleotide reference sequence, e.g. the rRNA gene variant model. The BLASTN bit-score parameter is a curated value determined from BLASTN analysis of the canonical nucleotide reference sequence of a specific AMR-associated gene against the database of CARD reference sequences. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"41093","param_value":"4000"}},"model_sequences":{"sequence":{"8750":{"protein_sequence":{"accession":"","sequence":""},"dna_sequence":{"accession":"NR_076156.1","fmin":"0","fmax":"2947","strand":"+","sequence":"GCGAATAGTGGTTTACGGTGGATGTCTTGGAGTTGTCAGGCGATGAAGGTCGTGATAAGCTGCGAAAAGCCTCGGGGAGGAGCACATGTCCTGTGATCCGGGGATGACCGAATGGGGTAACCCGACAGGGTAAAGCCTTGTCATTGCCTTCCTGAATGAATAGGGAGGGTAAGGCGAAACTGGGTGAACTGAACCATCTAAGTAACTTGGGAAAAGAAATCAAGAGAGATTCCGAAAGTAGTGGCGAGCGAAATTGGAGGAGCCTAAACCTGTGTCTAACAGGGGTTGTAGGGCCGCGCGGGCTTGCGTTCGGTGGGTGAAATAATCCGGCCTATAGCAGAAAGGTTTTGGGAAAGCCTGACAGAGAGGGTGAAATCCCCGTATGCGGAATGGGGCGGACCTGCTGGTGCGGTACCTGAGTACGGCGGGACACGAGGAATCCTGTCGGAATCTGGGTCGACCACGATCTAAGGCTAAATACTCGACAACTACCGATAGTGGACAAGTACCGTGAGGGAAAGATGAAAAGAACCCCGGTGAGGGGAGTGAAATAGAACCTGAAACCGTAAACCAACAAGATGTTACAGCCTGTGAGGGTGGTAGCGTGCCTTTTGTAGAATGAGCCTGCGAGTTACGGTGTGCAGCAAGGTTAAGGGATAGGAGTCCTGGAGCCGGAGGGAAACCGAGTCTTAAAAGGGCGTGGTGAGTTGTACGTCGTAGACCCGAAGCCAGGGTGATCTAGTTATGAGCAGGTTGAAACAGGGGTGAAGCCTTGTGGAGGACCGAACTATAATCTGTTAAAAAAGGTATGGATGACTTGTGACTAGGAGTGAAAGGCTAAACAAACCTGGAGATAGCTGGTTCTCCCCGAAATGCCTTTAGGGACAGCCTTATACAAAACTGTCGGAGGTAAAGCACTGGATGGGCTAGGGGGTTTCATCGCCTACCAAACCCAATCAAACTCTGAATGCCGGCAGTCAACGTGTGGGAGTGAGACTGCGTGCGACAAGGTTCGTAGTCGAGAGGGAAACAGCCCAGACCGTCAGCTAAGGTCCCGAAATACCGCTTGAGTGTGAAATGAAGTGTGGGTACCTGGACAGCCAGGAGGTTGGCTTAGAAGCAGCCATTCCTTGAAAGAGTGCGTAATAGCTCACTGGTCGAGTACGCATGCGCAGATAATGTATCGGGGCTAAGCGGTATACCGAAGCTACGGGTCTTGCATTTTTGGTGCAAGGCGGTAGGGGAGCATTCCATGTACTGATGAAGGAATATCCGGGAGGAGTTCTGGAGGGGATGGAAGAGAGAATGCAGGTATAAGTACACGAAAAGGAGGGTGAGATTCCTTCCCGCCGAAAACCTAAGGTTTCCTGGGTGAAGGTCATCTGCTCAGGGTAAGTCGGCCCCTAAGGCGAGGACGAGGGTCGTAGTCGATGGGAATCCGGTTTATATTCCGGAACCTCTTGCAATTTCGATGGCAGGACGCGTGAGGTGAAGCCCGGCCAAAGATTGGTAGTTTTGGTCTAAGTATCCGAGCCGTTTTAAGAGCGATAGGCAAATCCGTCGTTCGAGGTAAGGTGCGAGTGCGACTGGAGCGATGAGCGAAGGGAAGCAGGTGTAGTCATGGCGACGGGAAATACTGTCTAAGGTTAGGTTGCAAGAGACCGTACCGCAAACCGACACAGGTAGGTAGGATGAGTAATCTAAGGCGCTCGAGAGAACTCGCGTCAAGGAACTCGGCAAAATACACACGTAACCTCGGGAGAAGTGTGACCCTTGCCTTTGGTGAGGGTGGCAGAAAGCAGGTCCAGGCGACTGTTTATCAAAAACATAGCCATCTGCAAATCAGTAATGAGACGTATAGGTGGTGACACCTGCCCGGTGCTGGAAGGTTAAGAGGAGAGGTTCGTGGTAACACAACGCTTTGAATTGAAGCCCCAGTAAACGGCGGCCGTAACTATAACGGTCCTAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCCGCACGAATGGTGTAACGACTCTGGACACTGTCTCGACGCGAGACTCGGTGAAATTTATGTACCGGTAAAGAAGCCGGTTACCCATAGTTAGACGGAAAGACCCCGTGAACCTTCACCGTAGCTTACTATTGGAACTTGGTTTACCATGTGTAGTATAGGTGGGAGACAGAGAAGCTTGGCCGTCAGGTTAGGCGGAGTCAACAGTGAAATACCACCCTTGGTACGTCAGGTTTCTAACCTTTGGCCGTGGATCCGGCAAAGGGACCGTGGTAGGTGGGCGGTTTGACTGGGGCGGTCGCCTCCTAAAAGGTAACGGAGGTGCGCGAAGGTCTCCTCACACCGGTTGGAAATCGGTGCGCGAGTGTAAAGGCACAAGGAGGCTTAACTGCGAGACCGACAGGTCGAGCAGATACGAAAGTAGGTCTTAGTGATCTGGCGGTAGCGTGTGGAAGCGCCGTCACTTAACGGATAAAAGGTACTCCGGGGATAACAGGCTGATTTTCCCCAAGAGTTCACATCGACGGGAAAGTTTGGCACCTCGATGTCGGCTCATCGCATCCTGGGGCTGAAGCAGGTCCCAAGGGTTTGGCTGTTCGCCAATTAAAGCGGTACGTGAGCTGGGTTCAGAACGTCGCGAGACAGTTCGGTCCCTATCTGCTATGGGCGTTGGATATGTGAGAGGAGCTGCTTTTAGTACGAGAGGACCGAAGTGGACGAACCTCTGGTGTACCAGTTATCCTGCCAAGGGTACGTGCTGGGTAGCTATGTTCGGAAGGGATAACCGCTGAAGGCATCTAAGTGGGAAGCCCGCCTCAAGATTACATATCCCTGAAGGTTGACCTTCCTGAAGACTCCTTGCACACTACAAGGTCGATAGGCTGGAGGTCTACGTACCGTAAGGTATTAAGCCGACCAGTACTAATAAGTCGTGAGGCTTGACCAT","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"46542","NCBI_taxonomy_name":"Treponema pallidum subsp. pallidum","NCBI_taxonomy_id":"161"}}}},"ARO_accession":"3007759","ARO_id":"46541","ARO_name":"Treponema pallidum 23S rRNA with mutation conferring resistance to erythromycin","CARD_short_name":"Tpal_23S_ERY","ARO_description":"Point mutations in 23S rRNA of Treponema pallidum subsp. pallidum (T. pallidum), the noncultivable agent of syphilis, shown clinically to confer resistance to erythromycin, a macrolide antibiotic.","ARO_category":{"41251":{"category_aro_accession":"3004125","category_aro_cvterm_id":"41251","category_aro_name":"23S rRNA with mutation conferring resistance to macrolide antibiotics","category_aro_description":"Nucleotide point mutations in the 23S rRNA subunit may confer resistance to macrolide antibiotics.","category_aro_class_name":"AMR Gene Family"},"35925":{"category_aro_accession":"0000006","category_aro_cvterm_id":"35925","category_aro_name":"erythromycin","category_aro_description":"Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure\/function processes critical for life or replication are inhibited.","category_aro_class_name":"Antibiotic"},"35919":{"category_aro_accession":"0000000","category_aro_cvterm_id":"35919","category_aro_name":"macrolide antibiotic","category_aro_description":"Macrolides are a group of drugs (typically antibiotics) that have a large macrocyclic lactone ring of 12-16 carbons to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides bind to the 50S-subunit of bacterial ribosomes, inhibiting the synthesis of vital proteins.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"6020":{"model_id":"6020","model_name":"aac(6')-Ib-cr10","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"350"}},"model_sequences":{"sequence":{"8755":{"protein_sequence":{"accession":"WP_124042715.1","sequence":"MTNSNDSVTLRLMTEHDLAMLYEWLNRSHIVEWWGGEEARPTLADVQEQYLPSVLAQESVTPYIAMLNGEPMGYAQSYVALGSGDGRWEEETDPGVRGIDQLLANASQLGKGLGTKLVRALVELLFNDPEVTKIQTDPSPSNLRAIRCYEKAGFERQGTVTTPYGPAVYMVQTRQAFERTRSDA"},"dna_sequence":{"accession":"NG_067968.1","fmin":"100","fmax":"655","strand":"+","sequence":"GTGACCAACAGCAACGATTCCGTCACACTGCGCCTCATGACTGAGCATGACCTTGCGATGCTCTATGAGTGGCTAAATCGATCTCATATCGTCGAGTGGTGGGGCGGAGAAGAAGCACGCCCGACACTTGCTGACGTACAGGAACAGTACTTGCCAAGCGTTTTAGCGCAAGAGTCCGTCACTCCATACATTGCAATGCTGAATGGAGAGCCGATGGGGTATGCCCAGTCGTACGTTGCTCTTGGAAGCGGGGACGGACGGTGGGAAGAAGAAACCGATCCAGGAGTACGCGGAATAGACCAGTTACTGGCGAATGCATCACAACTGGGCAAAGGCTTGGGAACCAAGCTGGTTCGAGCTCTGGTTGAGTTGCTGTTCAATGATCCCGAGGTCACCAAGATCCAAACGGACCCGTCGCCGAGCAACTTGCGAGCGATCCGATGCTACGAGAAAGCGGGGTTTGAGAGGCAAGGTACCGTAACCACCCCATATGGTCCAGCCGTGTACATGGTTCAAACACGCCAGGCATTCGAGCGAACACGCAGTGATGCCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3007770","ARO_id":"46553","ARO_name":"aac(6')-Ib-cr10","CARD_short_name":"aac(6')-Ib-cr10","ARO_description":"A fluoroquinolone-acetylating aminoglycoside acetyltransferase variant, identified from Escherichia coli. These variants confers resistance to both aminoglycoside and fluoroquinolone antibiotics.","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"A category of aminoglycoside N-acetyltransferase enzymes with modification regiospecificity based at the 6'-amino group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics through acetylation of the 6-amino group of the compound.","category_aro_class_name":"AMR Gene Family"},"43328":{"category_aro_accession":"3005113","category_aro_cvterm_id":"43328","category_aro_name":"AAC(6')-Ib-cr","category_aro_description":"A subfamily of aminoglycoside 6'-N-acetyltransferases, AAC(6'), which doubly confer resistance to aminoglycoside and fluoroquinolone antibiotics through fluoroquinolone-acetylating activity.","category_aro_class_name":"AMR Gene Family"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"6021":{"model_id":"6021","model_name":"aac(6')-Ib-cr11","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"350"}},"model_sequences":{"sequence":{"8756":{"protein_sequence":{"accession":"WP_159241551.1","sequence":"MTNSNDSVTLRLMTEHDLAMLYEWLNRSHIVEWWGGEEARPTLADVQEQYLPSVLAQESVTPYIAMLNGEPIGYAQSYVALGSGDGRWEEETDPGVRGIDQLLANASQLGKGLGTKLVRALVELLFNDSEVTKIQTDPSPSNLRAIRCYEKAGFERQGTVTTPYGPAVYMVQTRQAFERTRSDA"},"dna_sequence":{"accession":"NG_067969.1","fmin":"100","fmax":"655","strand":"+","sequence":"GTGACCAACAGCAACGATTCCGTCACACTGCGCCTCATGACTGAGCATGACCTTGCGATGCTCTATGAGTGGCTAAATCGATCTCATATCGTCGAGTGGTGGGGCGGAGAAGAAGCACGCCCGACACTTGCTGACGTACAGGAACAGTACTTGCCAAGCGTTTTAGCGCAAGAGTCCGTCACTCCATACATTGCAATGCTGAATGGAGAGCCGATTGGGTATGCCCAGTCGTACGTTGCTCTTGGAAGCGGGGACGGACGGTGGGAAGAAGAAACCGATCCAGGAGTACGCGGAATAGACCAGTTACTGGCGAATGCATCACAACTGGGCAAAGGCTTGGGAACCAAGCTGGTTCGAGCTCTGGTTGAGTTGCTGTTCAATGATTCCGAGGTCACCAAGATCCAAACGGACCCGTCGCCGAGCAACTTGCGAGCGATCCGATGCTACGAGAAAGCGGGGTTTGAGAGGCAAGGTACCGTAACCACCCCATATGGTCCAGCCGTGTACATGGTTCAAACACGCCAGGCATTCGAGCGAACACGCAGTGATGCCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3007771","ARO_id":"46554","ARO_name":"aac(6')-Ib-cr11","CARD_short_name":"aac(6')-Ib-cr11","ARO_description":"A fluoroquinolone-acetylating aminoglycoside acetyltransferase variant identified from Proteus mirabilis. These proteins confer resistance to both fluoroquinolone and aminoglycoside antibiotics.","ARO_category":{"36484":{"category_aro_accession":"3000345","category_aro_cvterm_id":"36484","category_aro_name":"AAC(6')","category_aro_description":"A category of aminoglycoside N-acetyltransferase enzymes with modification regiospecificity based at the 6'-amino group of the respective antibiotic. These enzymes inactivate aminoglycoside antibiotics through acetylation of the 6-amino group of the compound.","category_aro_class_name":"AMR Gene Family"},"43328":{"category_aro_accession":"3005113","category_aro_cvterm_id":"43328","category_aro_name":"AAC(6')-Ib-cr","category_aro_description":"A subfamily of aminoglycoside 6'-N-acetyltransferases, AAC(6'), which doubly confer resistance to aminoglycoside and fluoroquinolone antibiotics through fluoroquinolone-acetylating activity.","category_aro_class_name":"AMR Gene Family"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"6022":{"model_id":"6022","model_name":"Vibrio vulnificus rpoB mutants conferring resistance to rifampin","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"13175":"S522L"},"Curated-R":{"13175":"S522L"},"clinical":{"13175":"S522L"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"2500"}},"model_sequences":{"sequence":{"8757":{"protein_sequence":{"accession":"WP_011079201.1","sequence":"MVYSYTEKKRIRKDFGTRPQVLDIPYLLSIQLDSFDKFIEQDPEGQYGLEAAFRSVFPIQSYNGNSELQYVSYRLGEPVFDVKECQIRGVTYSKPLRVKLRLVIFDKDAPAGTVKDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNARIIPYRGSWLDFEFDPKDNLYVRIDRRRKLPSTIILRALGKSTEEILDTFFEKVNFEVKDQTLMMELVPDRLRGETATFDIEANGTVYVEKGRRVTARHIRQLEKEGVDQIEVPVEYIVGKVSSKDYINEATGEIIVAANQEISLEALAKLSQAGHKQLEVLFTNDLDHGPFMSETLRIDSSVDRISALVEIYRMMRPGEPPTKEAAEALFESLFFSEERYDLSTVGRMKFNSSIGRDDAEEQGTLDETDIIEVMKKLIAIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGDLDAVMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINSLSAFARCNEYGFLETPYRRVVDGVVTDEVDYLSAIEEGQFVIAQANAKLNEDGTFADELITARQKGESGLHPREHVDYMDVATNQVVSIAASLIPFLEHDDANRALMGANMQRQAVPTLKAEKPLVGTGIERNVAVDSGVTSVAKRGGIIQSVDASRIVVKVNEEELIPGEAGIDIYNLTKYTRSNQNTCINQRPCVMPGEPVLRGDVLADGPSTDLGELALGQNMRIAFMPWNGYNFEDSILVSERVVQEDRFTTIHIQELTCVARDTKLGSEEITADIPNVGESALSKLDESGIVYIGAEVKGGDILVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRVPNSVSGTIIDVQVFTRDGVEKDKRALEIEQMQLKEAKKDLTEEFQILEGGLLNRVKAVLLSGGYSEAKLDTTDRKKWLELTLEDDALQTQLEQLAEQYDELKADFDKKFETKRRKITQGDDLAPGVLKIVKVYLAVKRRIQPGDKMAGRHGNKGVISKINPVEDMPYDEKGQPVDIVLNPLGVPSRMNIGQILEVHLGLAAKGIGDKINQMVKEQQELAKFREFLQKVYDLGETRQKVDIASLSDEEVRTLIGNLRGGLPIATPVFDGASEASIKELLKLGGLPESGQLTLFDGRTGDAFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTKMYKNIVDGNHAMEPGMPESFNVLLKEIRSLGINIELEDEQ"},"dna_sequence":{"accession":"NC_004459.3","fmin":"1187563","fmax":"1191592","strand":"+","sequence":"ATGGTTTACTCTTATACCGAGAAAAAGCGCATCCGTAAGGACTTTGGTACTCGTCCACAAGTTTTGGACATTCCATACCTGCTATCGATCCAGCTCGATTCGTTCGATAAATTTATCGAACAGGATCCTGAAGGACAGTACGGTCTTGAGGCTGCTTTCCGTTCTGTATTCCCTATTCAGAGCTACAATGGTAATTCTGAGCTGCAATACGTTAGCTACCGTCTTGGTGAGCCAGTTTTTGATGTTAAAGAATGTCAAATCCGTGGTGTAACTTATTCAAAACCACTTCGCGTAAAGCTACGCCTAGTTATTTTTGATAAAGACGCGCCTGCAGGCACTGTAAAAGACATTAAAGAACAAGAAGTCTACATGGGTGAAATTCCACTCATGACAGACAATGGTACCTTTGTGATTAACGGTACCGAGAGGGTTATCGTATCTCAGCTACATCGAAGCCCAGGTGTGTTCTTCGACAGCGACAAAGGTAAGACTCACTCTTCTGGTAAAGTTCTGTACAACGCGCGTATCATTCCTTACCGTGGTTCATGGCTTGATTTTGAGTTTGATCCTAAGGACAACCTGTACGTACGTATCGACCGTCGTCGTAAGCTACCATCAACCATCATTCTTCGTGCACTAGGTAAGAGCACTGAAGAGATCTTGGATACTTTCTTCGAAAAAGTGAATTTCGAAGTGAAAGACCAGACGCTAATGATGGAGTTGGTACCAGATCGCCTACGTGGTGAAACGGCAACGTTTGATATCGAAGCAAACGGCACTGTCTATGTAGAGAAAGGTCGTCGTGTTACGGCACGCCACATCCGTCAACTTGAAAAAGAAGGCGTTGATCAGATCGAAGTACCGGTTGAGTACATCGTAGGCAAAGTGTCGTCAAAAGATTACATCAATGAAGCGACTGGCGAGATCATCGTTGCAGCGAACCAGGAAATCAGCCTTGAAGCATTGGCTAAGCTATCTCAAGCTGGCCACAAGCAGCTAGAAGTCCTGTTTACAAACGATCTAGACCATGGTCCATTCATGTCAGAAACACTACGCATCGACAGCTCTGTTGATCGTATTTCTGCACTGGTAGAAATCTACCGCATGATGCGCCCTGGTGAGCCACCAACGAAAGAAGCTGCTGAAGCTCTATTCGAAAGCTTGTTCTTCTCTGAAGAGCGTTATGACCTATCGACTGTTGGTCGTATGAAGTTCAACAGCTCCATTGGCCGTGATGATGCAGAAGAGCAAGGCACACTTGATGAAACTGACATCATCGAAGTGATGAAGAAGCTGATCGCTATCCGTAACGGTAAAGGCGAAGTGGACGATATCGACCACCTAGGTAACCGCCGTATCCGTTCTGTTGGTGAAATGGCTGAAAACCAATTCCGTGTTGGTCTAGTACGTGTTGAACGTGCAGTGAAAGAACGTCTGAGCCTAGGCGATCTTGACGCAGTGATGCCACAAGACTTGATCAATGCGAAGCCAATTTCTGCGGCAGTAAAAGAGTTCTTTGGCTCTTCTCAGCTGTCTCAGTTTATGGACCAAAACAACCCGCTATCAGAAGTCACGCACAAGCGTCGTATTTCTGCATTGGGTCCTGGTGGTCTTACTCGTGAGCGTGCTGGTTTCGAAGTTCGAGACGTACACGTAACTCACTACGGCCGCCTATGTCCGATCGAAACGCCTGAAGGTCCAAACATCGGTCTGATCAACTCTCTATCAGCATTTGCACGTTGTAACGAGTACGGCTTCCTAGAGACGCCATACCGTCGTGTTGTTGATGGTGTTGTGACAGACGAAGTGGATTACCTATCAGCGATCGAAGAAGGTCAATTTGTTATCGCTCAGGCGAACGCGAAGCTGAACGAAGATGGTACTTTCGCTGATGAGCTTATCACTGCTCGTCAAAAAGGCGAATCTGGTCTGCACCCACGTGAACATGTTGATTACATGGACGTTGCAACCAACCAGGTCGTATCTATCGCAGCATCGCTAATCCCGTTCCTAGAACACGACGATGCTAACCGCGCTCTAATGGGTGCGAACATGCAACGTCAGGCGGTTCCTACTCTGAAAGCAGAGAAACCACTTGTAGGTACAGGTATTGAGCGTAACGTAGCGGTTGACTCTGGTGTAACGTCGGTTGCTAAACGCGGCGGTATTATCCAGTCAGTTGACGCATCTCGTATCGTGGTGAAGGTTAATGAAGAAGAGTTGATTCCTGGCGAAGCTGGTATCGATATCTACAACCTAACCAAATACACTCGTTCTAACCAAAACACTTGTATCAACCAACGTCCATGTGTGATGCCGGGTGAACCAGTGCTACGTGGTGATGTGCTTGCTGATGGTCCTTCAACAGACCTAGGTGAACTTGCACTTGGTCAGAACATGCGTATCGCGTTCATGCCTTGGAACGGTTACAACTTCGAAGACTCGATCTTAGTATCTGAGCGCGTAGTTCAAGAAGACCGCTTCACGACTATCCACATTCAAGAACTGACTTGTGTGGCGCGTGATACCAAGCTGGGTTCGGAAGAAATCACAGCGGATATTCCAAACGTAGGTGAATCTGCTCTGTCTAAATTAGACGAGTCAGGTATTGTTTACATCGGTGCTGAAGTGAAGGGTGGCGACATCCTAGTTGGTAAAGTAACGCCAAAAGGTGAAACTCAGCTAACGCCTGAAGAGAAGCTACTACGTGCAATCTTTGGTGAAAAAGCATCTGACGTTAAAGATACGTCACTACGTGTACCAAACTCTGTTTCAGGTACCATCATCGACGTTCAAGTTTTCACTCGCGATGGCGTAGAGAAAGACAAGCGTGCGCTTGAAATTGAACAGATGCAGCTGAAAGAAGCGAAGAAAGACCTTACTGAAGAATTCCAGATTCTGGAAGGCGGTCTTCTAAACCGTGTTAAAGCGGTTCTTCTATCAGGTGGTTACTCTGAAGCGAAGCTAGATACAACTGATCGTAAGAAGTGGCTAGAACTGACTCTTGAAGACGACGCACTGCAAACTCAGCTTGAGCAACTTGCAGAGCAGTACGACGAGCTAAAAGCAGACTTCGATAAGAAGTTTGAAACCAAGCGTCGTAAGATCACTCAAGGTGATGACCTAGCGCCTGGCGTACTGAAGATCGTTAAAGTTTACCTAGCGGTGAAACGTCGTATCCAGCCTGGTGATAAGATGGCGGGTCGTCACGGTAACAAGGGTGTAATCTCTAAGATCAACCCTGTTGAAGACATGCCATACGATGAGAAAGGTCAGCCTGTAGACATCGTACTTAACCCATTGGGTGTACCTTCGCGTATGAACATCGGTCAGATCCTAGAAGTACACTTGGGTCTAGCAGCGAAAGGTATTGGTGACAAGATCAACCAGATGGTGAAAGAGCAGCAAGAACTCGCGAAATTCCGTGAATTCCTGCAAAAAGTTTATGATCTAGGCGAAACTCGCCAGAAAGTAGACATTGCTTCTCTGTCTGATGAAGAAGTTCGTACTCTGATTGGCAACCTACGTGGTGGCTTACCGATTGCGACTCCAGTATTTGACGGTGCGTCTGAAGCATCAATCAAAGAGCTACTGAAACTTGGCGGTCTGCCAGAGTCCGGTCAGCTAACTCTGTTTGATGGTCGCACAGGTGATGCGTTTGAGCGTCCTGTAACCGTAGGTTACATGTACATGCTGAAACTGAACCACCTTGTAGATGACAAGATGCACGCACGTTCTACTGGCTCGTACAGTCTGGTAACTCAGCAACCACTAGGTGGTAAAGCTCAGTTCGGTGGTCAGCGTTTCGGTGAGATGGAAGTATGGGCACTAGAAGCATACGGTGCTGCTTACACGCTACAAGAAATGCTAACGGTTAAGTCGGATGACGTTAACGGCCGTACTAAGATGTACAAAAACATCGTAGATGGTAACCACGCGATGGAACCAGGCATGCCTGAATCGTTCAACGTACTGTTGAAAGAGATCCGCTCGCTAGGTATCAACATCGAGCTAGAAGACGAACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"46578","NCBI_taxonomy_name":"Vibrio vulnificus CMCP6","NCBI_taxonomy_id":"216895"}}}},"ARO_accession":"3007794","ARO_id":"46577","ARO_name":"Vibrio vulnificus rpoB mutants conferring resistance to rifampin","CARD_short_name":"Vvul_rpoB_RIF","ARO_description":"Point mutations that occur within the Vibrio vulnificus rpoB gene resulting in resistance to rifampin.","ARO_category":{"36349":{"category_aro_accession":"3000210","category_aro_cvterm_id":"36349","category_aro_name":"rifamycin-resistant beta-subunit of RNA polymerase (rpoB)","category_aro_description":"Rifampin resistant RNA polymerases include amino acids substitutions which disrupt the affinity of rifampin for its binding site. These mutations are frequently concentrated in the rif I region of the beta-subunit and most often involve amino acids which make direct interactions with rifampin. However, mutations which also confer resistance can occur outside this region and may involve amino acids which do not directly make contact with rifampin.","category_aro_class_name":"AMR Gene Family"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"6023":{"model_id":"6023","model_name":"OXA-410","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"8758":{"protein_sequence":{"accession":"HCT5551642.1","sequence":"MNIKALLLITSAIFISACSPYIVSANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATATEVFKWDGQKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"DAKAKM010000001.1","fmin":"279004","fmax":"279829","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGTCTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCGCTACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGTTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACCTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3001601","ARO_id":"38001","ARO_name":"OXA-410","CARD_short_name":"OXA-410","ARO_description":"OXA-410 is an OXA-51-like beta-lactamase.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"355":{"model_id":"355","model_name":"TEM-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"1951":{"protein_sequence":{"accession":"CAD09800.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"AL513383.1","fmin":"161910","fmax":"162771","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35776","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Typhi str. CT18","NCBI_taxonomy_id":"220341"}}}},"ARO_accession":"3000873","ARO_id":"37253","ARO_name":"TEM-1","CARD_short_name":"TEM-1","ARO_description":"TEM-1 is a broad-spectrum beta-lactamase found in many Gram-negative bacteria. Confers resistance to penicillins and first generation cephalosphorins.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"35975":{"category_aro_accession":"0000058","category_aro_cvterm_id":"35975","category_aro_name":"cefazolin","category_aro_description":"Cefazolin, also known as cefazoline or cephazolin, is a first generation cephalosporin antibiotic. It is administered parenterally, and is active against a broad spectrum of bacteria.","category_aro_class_name":"Antibiotic"},"35981":{"category_aro_accession":"0000064","category_aro_cvterm_id":"35981","category_aro_name":"amoxicillin","category_aro_description":"Amoxicillin is a moderate-spectrum, bacteriolytic, beta-lactam antibiotic used to treat bacterial infections caused by susceptible microorganisms. A derivative of penicillin, it has a wider range of treatment but remains relatively ineffective against Gram-negative bacteria. It is commonly taken with clavulanic acid, a beta-lactamase inhibitor. Like other beta-lactams, amoxicillin interferes with the synthesis of peptidoglycan.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"37084":{"category_aro_accession":"3000704","category_aro_cvterm_id":"37084","category_aro_name":"cefalotin","category_aro_description":"Cefalotin is a semisynthetic cephalosporin antibiotic activate against staphylococci. It is resistant to staphylococci beta-lactamases but hydrolyzed by enterobacterial beta-lactamases.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"6024":{"model_id":"6024","model_name":"Mycobacterium tuberculosis iniA mutations conferring resistance to isoniazid","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1240"},"40494":{"param_type":"frameshift mutation","param_description":"A frameshift is a sequence change between the translation initiation (start) and termination (stop) codon where, compared to a reference sequence, translation shifts to another reading frame as caused by nucleotide insertions and deletions. In ARO, these are annotated at the protein level with the first changed most N-terminal wildtype amino acid position. Format is given as [wildtype AA][position]fs, e.g. S531fs where S531 is a frameshifted coordinate beginning with codon 531. Termination may also be denoted as: Ter[position]fs.","param_type_id":"40494","param_value":{"13190":"P94fs"}},"snp":{"Curated-R":{"13190":"S522L"}}},"model_sequences":{"sequence":{"8845":{"protein_sequence":{"accession":"NP_214856.1","sequence":"MVPAGLCAYRDLRRKRARKWGDTVTQPDDPRRVGVIVELIDHTIAIAKLNERGDLVQRLTRARQRITDPQVRVVIAGLLKQGKSQLLNSLLNLPAARVGDDEATVVITVVSYSAQPSARLVLAAGPDGTTAAVDIPVDDISTDVRRAPHAGGREVLRVEVGAPSPLLRGGLAFIDTPGVGGLGQPHLSATLGLLPEADAVLVVSDTSQEFTEPEMWFVRQAHQICPVGAVVATKTDLYPRWREIVNANAAHLQRARVPMPIIAVSSLLRSHAVTLNDKELNEESNFPAIVKFLSEQVLSRATERVRAGVLGEIRSATEQLAVSLGSELSVVNDPNLRDRLASDLERRKREAQQAVQQTALWQQVLGDGFNDLTADVDHDLRTRFRTVTEDAERQIDSCDPTAHWAEIGNDVENAIATAVGDNFVWAYQRSEALADDVARSFADAGLDSVLSAELSPHVMGTDFGRLKALGRMESKPLRRGHKMIIGMRGSYGGVVMIGMLSSVVGLGLFNPLSVGAGLILGRMAYKEDKQNRLLRVRSEAKANVRRFVDDISFVVSKQSRDRLKMIQRLLRDHYREIAEEITRSLTESLQATIAAAQVAETERDNRIRELQRQLGILSQVNDNLAGLEPTLTPRASLGRA"},"dna_sequence":{"accession":"NC_000962.3","fmin":"410837","fmax":"412760","strand":"+","sequence":"ATGGTCCCCGCCGGTTTGTGCGCATACCGTGATCTGAGGCGTAAACGAGCGAGAAAGTGGGGCGACACGGTGACCCAGCCCGATGACCCACGTCGGGTCGGTGTGATCGTCGAACTGATCGATCACACTATCGCCATCGCCAAACTGAACGAGCGTGGTGATCTAGTACAGCGGTTGACGCGGGCTCGCCAGCGGATCACCGACCCGCAGGTCCGTGTGGTGATCGCCGGGCTGCTCAAACAGGGCAAGAGTCAATTGCTCAATTCGTTGCTCAACCTGCCCGCGGCGCGAGTAGGCGATGACGAGGCCACCGTGGTGATCACCGTCGTAAGCTACAGCGCCCAACCGTCGGCCCGGCTTGTGCTGGCCGCCGGGCCCGACGGGACAACCGCAGCGGTTGACATTCCCGTCGATGACATCAGCACCGATGTGCGTCGGGCTCCGCACGCCGGTGGCCGCGAGGTGTTGCGGGTCGAGGTCGGCGCGCCCAGCCCGCTGCTGCGGGGCGGGCTGGCGTTTATCGATACTCCGGGTGTGGGCGGCCTCGGACAGCCCCACCTGTCGGCGACGCTGGGGCTGCTACCCGAGGCCGATGCCGTCTTGGTGGTCAGCGACACCAGCCAGGAATTCACCGAACCCGAGATGTGGTTCGTGCGGCAGGCCCACCAGATCTGTCCGGTCGGGGCGGTCGTGGCCACCAAGACCGACCTGTATCCGCGCTGGCGGGAGATCGTCAATGCCAATGCAGCACATCTGCAGCGGGCCCGGGTTCCGATGCCGATCATCGCAGTCTCATCACTGTTGCGCAGCCACGCGGTCACGCTTAACGACAAAGAGCTCAACGAAGAGTCCAACTTTCCGGCGATCGTCAAGTTTCTCAGCGAGCAGGTGCTTTCCCGCGCGACGGAGCGAGTGCGTGCTGGGGTACTCGGCGAAATACGTTCGGCAACAGAGCAATTGGCGGTGTCTCTAGGTTCCGAACTATCGGTGGTCAACGACCCGAACCTCCGTGACCGACTTGCTTCGGATTTGGAGCGGCGCAAACGGGAAGCCCAGCAGGCGGTGCAACAGACAGCGCTGTGGCAGCAGGTGCTGGGCGACGGGTTCAACGACCTGACTGCTGACGTGGACCACGACCTACGAACCCGCTTCCGCACCGTCACCGAAGACGCCGAGCGCCAGATCGACTCCTGTGACCCGACTGCGCATTGGGCCGAGATTGGCAACGACGTCGAGAATGCGATCGCCACAGCGGTCGGCGACAACTTCGTGTGGGCATACCAGCGTTCCGAAGCGTTGGCCGACGACGTCGCTCGCTCCTTTGCCGACGCGGGGTTGGACTCGGTCCTGTCAGCAGAGCTGAGCCCCCACGTCATGGGCACCGACTTCGGCCGGCTCAAAGCGCTGGGCCGGATGGAATCGAAACCGCTGCGCCGGGGCCATAAAATGATTATCGGCATGCGGGGTTCCTATGGCGGCGTGGTCATGATTGGCATGCTGTCGTCGGTGGTCGGACTTGGGTTGTTCAACCCGCTATCGGTGGGGGCCGGGTTGATCCTCGGCCGGATGGCATATAAAGAGGACAAACAAAACCGGTTGCTGCGGGTGCGCAGCGAGGCCAAGGCCAATGTGCGGCGCTTCGTCGACGACATTTCGTTCGTCGTCAGCAAACAATCACGGGATCGGCTCAAGATGATCCAGCGTCTGCTGCGCGACCACTACCGCGAGATCGCCGAAGAGATCACCCGGTCGCTCACCGAGTCCCTGCAGGCGACCATCGCGGCGGCGCAGGTGGCGGAAACCGAGCGGGACAATCGAATTCGGGAACTTCAGCGGCAATTGGGTATCCTGAGCCAGGTCAACGACAACCTTGCCGGCTTGGAGCCAACCTTGACGCCCCGGGCGAGCTTGGGACGAGCGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3007798","ARO_id":"46582","ARO_name":"Mycobacterium tuberculosis iniA mutations conferring resistance to isoniazid","CARD_short_name":"Mtub_iniA_INH","ARO_description":"Known mutations in Mycobacterium tuberculosis iniA which confer resistance to isoniazid.","ARO_category":{"46583":{"category_aro_accession":"3007799","category_aro_cvterm_id":"46583","category_aro_name":"isoniazid resistant iniA","category_aro_description":"Mutations that occurs on the iniA genes resulting in the resistance to isoniazid.","category_aro_class_name":"AMR Gene Family"},"36659":{"category_aro_accession":"3000520","category_aro_cvterm_id":"36659","category_aro_name":"isoniazid","category_aro_description":"Isoniazid is an organic compound that is the first-line anti tuberculosis medication in prevention and treatment. As a prodrug, it is activated by mycobacterial catalase-peroxidases such as M. tuberculosis KatG. Isoniazid inhibits mycolic acid synthesis, which prevents cell wall synthesis in mycobacteria.","category_aro_class_name":"Antibiotic"},"45734":{"category_aro_accession":"3007152","category_aro_cvterm_id":"45734","category_aro_name":"isoniazid-like antibiotic","category_aro_description":"A group of antibiotics containing isoniazid and its derivatives.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"6025":{"model_id":"6025","model_name":"RATA-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"8762":{"protein_sequence":{"accession":"WFS34552.1","sequence":"MNRLLQLTVLLLLLVTSCKTQSDKTDLLRNKIEQILSDKNAVVGVSIIGNNGKDTLSLHGDRRFPMQSVFKFHIALAVLSEIDKGKLSLDQKIEIRKDELLPEDFWSPLRDENPNGGIFTIERLIQYSVSHSDNTACDVLIRLIGTPKTVEEYIKKSGINDIQITFNEEDMQSKWENMFQNWTTPKAASQTLKLFYDNKNNLLSKSSYDFFWKTNKETTTGNNRIKGQLPEGTVVAHKTGSSGTNKETGITAAVNNIGIVFLPNGEHFIISVFVSESKENFDMNEKIIADIAKATYDFYTATEK"},"dna_sequence":{"accession":"CP121209.1","fmin":"1982452","fmax":"1983367","strand":"+","sequence":"ATGAATAGACTTCTTCAATTAACAGTTTTGCTTTTATTACTCGTAACAAGTTGTAAAACACAATCCGACAAGACCGACTTGCTTAGGAATAAAATTGAGCAAATATTATCCGACAAAAATGCAGTAGTTGGAGTTTCAATAATTGGGAACAATGGGAAAGACACACTTTCGCTACACGGAGACAGGCGATTCCCTATGCAAAGTGTATTTAAGTTCCATATAGCATTAGCTGTATTGTCGGAAATTGACAAGGGGAAACTTTCATTAGACCAGAAAATTGAGATTCGAAAAGATGAACTTTTACCAGAAGATTTTTGGAGTCCACTTAGAGACGAAAATCCTAATGGCGGAATCTTTACTATTGAAAGACTAATTCAATATTCTGTCTCACACAGCGACAATACTGCTTGCGATGTATTAATACGACTAATTGGAACACCTAAAACGGTTGAAGAGTATATTAAGAAAAGTGGCATAAATGATATACAGATTACATTCAACGAAGAAGATATGCAGTCAAAGTGGGAAAATATGTTTCAGAATTGGACTACACCGAAAGCGGCAAGCCAAACGCTTAAATTATTTTATGACAATAAAAACAACTTGCTTTCAAAAAGCAGTTATGACTTTTTTTGGAAGACAAATAAAGAGACCACAACCGGTAATAACCGAATTAAGGGACAATTACCCGAAGGGACAGTTGTTGCTCATAAAACAGGTTCGTCTGGAACAAACAAAGAAACAGGAATTACTGCCGCTGTAAACAATATAGGAATTGTTTTTTTACCGAATGGCGAACACTTTATCATCAGTGTTTTTGTAAGTGAATCAAAAGAAAATTTTGACATGAATGAAAAAATTATAGCGGACATTGCAAAAGCAACCTATGACTTTTACACAGCAACGGAAAAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36951","NCBI_taxonomy_name":"Riemerella anatipestifer","NCBI_taxonomy_id":"34085"}}}},"ARO_accession":"3007801","ARO_id":"46586","ARO_name":"RATA-1","CARD_short_name":"RATA-1","ARO_description":"RATA-1 is a class A RATA-family carbapenemase.","ARO_category":{"46585":{"category_aro_accession":"3007800","category_aro_cvterm_id":"46585","category_aro_name":"RATA beta-lactamase","category_aro_description":"RATA is a family of class A carbapenemases identified from the chromosome of Riemerella anatipestifer.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"6026":{"model_id":"6026","model_name":"RATA-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"8763":{"protein_sequence":{"accession":"WFS32678.1","sequence":"MNRLFQLTVLLLLFVTSCKTPSYKTDLLRNKIEQILSDKNAVVGVSIIGNNGKDTLSLNGDKRFPMQSVFKFHIALAVLSEIDKGKLSLDQKIEISKDELLPEDFWSPLRDENPNGGTFTIERLIQYSVSHSDNTACDVLIRLIGTPKTVEEYIKKSGINDIQITYNEEQMQAKWENMFQNWTTPKAASQTLKLFYENKSNLLSQSSYDFFWKTNKETTTGKNRIRGQLPEGTVVAHKTGWSGTNKETGITAAVNNIGIVFLPNGEYFIISVFVSESKEDFDTNEKIIADIAKATYDFYTTTEK"},"dna_sequence":{"accession":"CP121210.1","fmin":"1997284","fmax":"1998199","strand":"+","sequence":"ATGAATAGACTTTTTCAATTGACAGTTTTACTATTATTATTCGTTACAAGTTGTAAAACTCCCTCCTACAAGACAGACTTACTGCGAAATAAAATTGAGCAAATATTATCCGACAAAAACGCAGTAGTTGGAGTTTCAATAATTGGTAACAATGGAAAAGACACACTTTCGCTAAACGGAGACAAGCGATTTCCTATGCAAAGCGTATTTAAGTTCCACATAGCATTAGCTGTATTATCGGAAATTGACAAAGGAAAACTTTCCTTAGACCAAAAAATTGAGATTAGCAAAGATGAACTTTTACCGGAAGATTTTTGGAGCCCTCTTAGAGACGAAAACCCTAATGGTGGAACTTTTACTATTGAAAGACTAATTCAATATTCCGTTTCTCATAGCGACAATACTGCTTGTGATGTTTTAATACGGCTAATAGGAACACCTAAAACGGTTGAAGAATACATTAAAAAAAGTGGCATAAATGATATACAAATCACTTATAACGAAGAACAAATGCAGGCTAAGTGGGAAAATATGTTTCAGAATTGGACTACACCAAAAGCAGCAAGCCAAACTCTTAAATTATTTTATGAGAATAAAAGCAATTTGCTTTCACAAAGTAGTTATGACTTTTTTTGGAAAACGAATAAAGAGACAACAACTGGTAAAAACCGTATAAGGGGGCAATTGCCAGAAGGAACAGTTGTTGCTCACAAGACAGGTTGGTCAGGGACAAACAAAGAAACAGGAATTACTGCCGCAGTTAACAATATTGGTATCGTTTTTTTACCTAATGGCGAATACTTTATCATAAGTGTATTTGTAAGTGAATCAAAAGAAGATTTTGACACAAATGAAAAAATTATAGCAGACATTGCAAAAGCAACTTATGACTTTTACACAACAACTGAAAAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36951","NCBI_taxonomy_name":"Riemerella anatipestifer","NCBI_taxonomy_id":"34085"}}}},"ARO_accession":"3007802","ARO_id":"46587","ARO_name":"RATA-2","CARD_short_name":"RATA-2","ARO_description":"RATA-2 is a class A RATA-family carbapenemase.","ARO_category":{"46585":{"category_aro_accession":"3007800","category_aro_cvterm_id":"46585","category_aro_name":"RATA beta-lactamase","category_aro_description":"RATA is a family of class A carbapenemases identified from the chromosome of Riemerella anatipestifer.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2404":{"model_id":"2404","model_name":"Neisseria gonorrhoeae gyrA with mutations conferring resistance to fluoroquinolones","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"4449":"S91F","4450":"D95G","4451":"D95N","13182":"D95Y"},"Curated-R":{"4449":"S91F","4450":"D95G","4451":"D95N","13182":"D95Y"},"clinical":{"4449":"S91F","4450":"D95G","4451":"D95N","13182":"D95Y"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1500"}},"model_sequences":{"sequence":{"5269":{"protein_sequence":{"accession":"AAW89357.1","sequence":"MTDATIRHDHKFALETLPVSLEDEMRKSYLDYAMSVIVGRALPDVRDGLKPVHRRVLYAMHELKNNWNAAYKKSARIVGDVIGKYHPHGDSAVYDTIVRMAQNFAMRYVLIDGQGNFGSVDGLAAAAMRYTEIRMAKISHEMLADIEEETVNFGPNYDGSEHEPLVLPTRFPTLLVNGSSGIAVGMATNIPPHNLTDTINACLRLLDEPKTEIDELIDIIQAPDFPTGATIYGLGGVREGYKTGRGRVVIRGKTHIEPIGKNGEREAIVIDEIPYQVNKAKLVEKIGDLVREKTLEGISELRDESDKSGMRVVIELKRNENAEVVLNQLYKLTPLQDSFGINMVVLVDGQPRLLNLKQILSEFLRHRREVVTRRTLFRLKKARHEGHIAEGKAVALSNIDEIIKLIKESPNAAEAKEKLLARPWRSSLVEEMLTRSGLDLEMMRPEGLAANIGLKKQGYYLSEIQADAILRMSLRNLTGLDQKEIIESYKNLMGKIIDFVDILSKPERITQIIRDELEEIKTNYGDERRSEINPFGGDIADEDLIPQREMVVTLTHGGYIKTQPTTDYQAQRRGGRGKQAAATKDEDFIETLFVANTHDYLMCFTNLGKCHWIKVYKLPEGGRNSRGRPINNVIQLEEGEKVSAILAVREFPEDQYVFFATAQGMVKKVQLSAFKNVRAQGIKAIALKEGDYLVGAAQTGGADDIMLFSNLGKAIRFNEYWEKSGNDEAEDADIETEISDDLEDETADNENTLPSGKNGVRPSGRGSGGLRGMRLPADGKIVSLITFAPETEESGLQVLTATANGYGKRTPIADYSRKNKGGQGSIAINTGERNGDLVAATLVGETDDLMLITSGGVLIRTKVEQIRETGRAAAGVKLINLDEGETLVSLERVAEDESELSGASVISNVTEPEAEN"},"dna_sequence":{"accession":"AE004969.1","fmin":"618438","fmax":"621189","strand":"-","sequence":"ATGACCGACGCAACCATCCGCCACGACCACAAATTCGCCCTCGAAACCCTGCCCGTCAGCCTTGAAGACGAAATGCGCAAAAGCTATCTCGACTACGCCATGAGCGTCATTGTCGGGCGCGCGCTGCCGGACGTTCGCGACGGCCTAAAGCCGGTGCACCGGCGCGTACTGTACGCGATGCACGAGCTGAAAAATAACTGGAATGCCGCCTACAAAAAATCGGCGCGCATCGTCGGCGACGTCATCGGTAAATACCACCCCCACGGCGATTCCGCAGTTTACGACACCATCGTCCGTATGGCGCAAAATTTCGCTATGCGTTATGTGCTGATAGACGGACAGGGCAACTTCGGATCGGTGGACGGGCTTGCCGCCGCAGCCATGCGCTATACCGAAATCCGCATGGCGAAAATCTCACATGAAATGCTGGCAGACATTGAGGAAGAAACCGTTAATTTCGGCCCGAACTACGACGGTAGCGAACACGAGCCGCTTGTACTGCCGACCCGTTTCCCCACACTGCTCGTCAACGGCTCGTCCGGTATCGCCGTCGGTATGGCGACCAACATCCCGCCGCACAACCTCACCGACACCATCAACGCCTGTCTGCGTCTTTTGGACGAACCCAAAACCGAAATCGACGAACTGATCGACATTATCCAAGCCCCCGACTTCCCGACCGGGGCAACCATCTACGGCTTGGGCGGCGTGCGCGAAGGCTATAAAACAGGCCGCGGCCGCGTCGTTATACGCGGTAAGACCCATATCGAACCCATAGGCAAAAACGGCGAACGCGAAGCCATCGTTATCGACGAAATCCCCTATCAGGTCAACAAAGCCAAGTTGGTCGAGAAAATCGGCGATTTGGTTCGGGAAAAAACGCTGGAAGGCATTTCCGAGCTCCGCGACGAATCCGACAAATCCGGGATGCGCGTCGTTATCGAGCTGAAACGCAACGAAAATGCCGAAGTCGTCTTAAACCAACTCTACAAACTGACTCCGCTGCAAGACAGTTTCGGCATCAATATGGTTGTTTTGGTCGACGGACAACCGCGCCTGTTAAACCTGAAACAGATTCTCTCCGAATTCCTGCGCCACCGCCGCGAAGTCGTTACCCGACGTACGCTTTTCCGGCTGAAGAAGGCACGCCATGAAGGGCATATCGCCGAAGGCAAAGCCGTCGCACTGTCCAATATCGATGAAATCATCAAGCTCATCAAAGAATCGCCCAACGCGGCCGAGGCCAAAGAAAAACTGCTTGCGCGCCCTTGGCGCAGCAGCCTCGTTGAAGAAATGCTGACGCGTTCCGGTCTGGATTTGGAAATGATGCGTCCGGAAGGATTGGCTGCAAACATTGGTCTGAAAAAACAAGGTTATTACCTGAGCGAGATTCAGGCAGATGCTATTTTACGCATGAGCCTGCGAAACCTGACCGGCCTCGATCAGAAAGAAATTATCGAAAGCTACAAAAACCTGATGGGTAAAATCATCGACTTTGTGGATATCCTCTCCAAACCCGAACGCATTACCCAAATCATCCGTGACGAACTGGAAGAAATCAAAACCAACTATGGCGACGAACGCCGCAGCGAAATCAACCCGTTCGGCGGCGACATTGCCGATGAAGACCTGATTCCGCAACGCGAAATGGTCGTGACCCTGACCCACGGCGGCTATATAAAAACCCAGCCGACCACCGACTATCAGGCTCAGCGTCGCGGCGGGCGCGGCAAACAGGCGGCTGCCACCAAAGACGAAGACTTTATCGAAACCCTGTTTGTTGCCAACACGCATGACTATTTGATGTGTTTTACCAACCTCGGCAAGTGCCACTGGATTAAGGTTTACAAACTGCCCGAAGGCGGACGCAACAGCCGCGGCCGTCCGATTAACAACGTCATCCAGCTGGAAGAAGGCGAAAAAGTCAGCGCGATTCTGGCAGTACGCGAGTTTCCCGAAGACCAATACGTCTTCTTCGCCACCGCGCAGGGAATGGTGAAAAAAGTCCAACTTTCCGCCTTTAAAAACGTCCGCGCCCAAGGCATTAAAGCCATCGCACTCAAAGAAGGCGACTACCTCGTCGGCGCTGCGCAAACAGGCGGTGCGGACGACATTATGTTGTTCTCCAACTTGGGCAAAGCCATCCGCTTCAACGAATACTGGGAAAAATCCGGCAACGACGAAGCGGAAGATGCCGACATCGAAACCGAGATTTCAGACGACCTCGAAGACGAAACCGCCGACAACGAAAACACCCTGCCAAGCGGCAAAAACGGCGTGCGTCCGTCCGGTCGCGGCAGCGGCGGTTTGCGCGGTATGCGCCTGCCTGCCGACGGCAAAATCGTCAGCCTGATTACCTTCGCCCCTGAAACCGAAGAAAGCGGTTTGCAAGTTTTAACCGCCACCGCCAACGGATACGGAAAACGCACCCCGATTGCCGATTACAGCCGCAAAAACAAAGGCGGGCAAGGCAGTATTGCCATTAACACCGGCGAGCGCAACGGCGATTTGGTCGCCGCAACCTTGGTCGGCGAAACCGACGATTTGATGCTGATTACCAGCGGCGGCGTGCTTATCCGTACCAAAGTCGAACAAATCCGCGAAACCGGCCGCGCCGCAGCAGGCGTGAAACTGATTAACTTGGACGAAGGCGAAACCTTGGTATCGCTGGAACGTGTTGCCGAAGACGAATCCGAACTCTCCGGCGCTTCTGTAATTTCCAATGTAACCGAACCGGAAGCCGAGAACTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40638","NCBI_taxonomy_name":"Neisseria gonorrhoeae FA 1090","NCBI_taxonomy_id":"242231"}}}},"ARO_accession":"3003928","ARO_id":"40637","ARO_name":"Neisseria gonorrhoeae gyrA with mutations conferring resistance to fluoroquinolones","CARD_short_name":"Ngon_gyrA_FLO","ARO_description":"Point mutation in Neisseria gonorrhoeae DNA gyrase subunit A. Decreases affinity between fluoroquinolone antibiotic molecule and gyrA, thereby conferring resistance to fluoroquinolone.","ARO_category":{"39876":{"category_aro_accession":"3003292","category_aro_cvterm_id":"39876","category_aro_name":"fluoroquinolone resistant gyrA","category_aro_description":"DNA gyrase is responsible for DNA supercoiling and consists of two alpha and two beta subunits. GyrA point mutations confer resistance by preventing fluoroquinolone antibiotics from binding the alpha-subunit.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"40338":{"category_aro_accession":"3003690","category_aro_cvterm_id":"40338","category_aro_name":"sitafloxacin","category_aro_description":"Sitafloxacin is a fluoroquinolone active against multi-resistant Gram-positive and negative pathogens. Sitafloxacin shows inhibitory activity against DNA gyrase and topoisomerase IV, which blocks bacterial DNA replication, thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"6027":{"model_id":"6027","model_name":"CARB-56","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8847":{"protein_sequence":{"accession":"QVO43826.1","sequence":"MKKLFLLAGLMVCSTLSYASQLNEDISLLEQQTSSRIGVSVWDTQADERWDYRGDERFPLMSTFKTLACAKMLSDMDSGKLSKNATAKVDERSIVVWSPVMDKLAGQNTRIEHACEAAMLMSDNTAANLVLNEIGGPKAVTMFLRTIGDKATRLDRIEPRLNEATPGDSRDTTTPNAILNTLRTLIEGETLSYESRVQLKIWMQDNKVSDSLMRSVLPTGWSIADRSGAGGHGSRGINAIIWKENHRPVYISIYVTETELSLQARDQLVAQISQLILQKYKDN"},"dna_sequence":{"accession":"MZ092819.1","fmin":"0","fmax":"852","strand":"+","sequence":"ATGAAAAAGTTATTTTTGTTGGCTGGGCTAATGGTTTGCTCAACCCTAAGTTACGCGTCCCAACTGAATGAGGACATTTCTCTCCTCGAGCAACAAACCTCAAGCAGAATTGGGGTGTCAGTTTGGGATACCCAAGCAGACGAGCGTTGGGATTACCGTGGCGATGAACGCTTCCCACTCATGAGCACATTCAAAACCCTAGCTTGTGCCAAAATGCTAAGTGATATGGACAGCGGTAAGCTAAGTAAAAATGCGACCGCAAAAGTCGATGAGCGCAGTATCGTTGTATGGTCTCCAGTGATGGATAAGCTCGCAGGCCAAAACACACGCATAGAGCACGCGTGTGAAGCCGCTATGTTAATGAGTGATAATACTGCAGCCAACTTGGTATTAAATGAAATTGGCGGCCCTAAAGCCGTAACAATGTTTCTGCGAACAATTGGAGATAAAGCAACGCGCCTAGACAGAATAGAACCTCGCTTGAACGAAGCCACACCAGGCGACAGCCGCGATACAACCACACCTAACGCCATACTAAACACTCTGCGAACCTTGATCGAAGGCGAAACGTTGTCTTATGAGTCTCGTGTACAATTAAAAATCTGGATGCAAGACAACAAAGTTTCAGACTCGTTAATGCGTTCTGTATTACCAACAGGTTGGTCTATTGCAGACCGTTCTGGTGCGGGTGGTCATGGTTCGCGTGGCATTAACGCGATTATATGGAAGGAAAATCATCGACCTGTTTACATTAGTATTTATGTCACAGAAACCGAGCTCTCACTTCAAGCTAGGGACCAGCTCGTTGCGCAGATAAGTCAGTTGATTTTACAAAAGTACAAAGACAATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43205","NCBI_taxonomy_name":"Vibrio alginolyticus","NCBI_taxonomy_id":"663"}}}},"ARO_accession":"3007803","ARO_id":"46589","ARO_name":"CARB-56","CARD_short_name":"CARB-56","ARO_description":"CARB-56 is a class A CARB-17-like beta-lactamase identified from Vibrio alginolyticus.","ARO_category":{"36230":{"category_aro_accession":"3000091","category_aro_cvterm_id":"36230","category_aro_name":"CARB beta-lactamase","category_aro_description":"CARB beta-lactamases are class A lactamases that can hydrolyze carbenicillin. Many of the PSE beta-lactamases have been renamed as CARB-lactamases with the notable exception of PSE-2 which is now OXA-10.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"6028":{"model_id":"6028","model_name":"VIM-74","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8848":{"protein_sequence":{"accession":"QTG68659.1","sequence":"MFKLLSKLLVYLTASIMAIASPLAFSVDSSGEYPTVSEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEVEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSAGVLYGGCAIYELSRTSAGNVADADLAEWPTSIERIQQHYPEAQFVIPGHGLPGGLDLLKHTTNVVKAHTNRSVVE"},"dna_sequence":{"accession":"MW811442.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGTTCAAACTTTTGAGTAAGTTATTGGTCTATTTGACCGCGTCTATCATGGCTATTGCGAGTCCGCTCGCTTTTTCCGTAGATTCTAGCGGTGAGTATCCGACAGTCAGCGAAATTCCGGTCGGGGAGGTCCGGCTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCAGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAGAAGCAAATTGGACTTCCTGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGTAGAGGGGAACGAGATTCCCACGCACTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAACTCTTCTATCCTGGTGCTGCGCATTCGACCGACAACTTAGTTGTGTACGTCCCGTCTGCGGGTGTGCTCTATGGTGGTTGTGCGATTTATGAGTTGTCACGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCATTGAGCGGATTCAACAACACTACCCGGAAGCACAGTTCGTCATTCCGGGGCACGGCCTGCCGGGCGGTCTAGACTTGCTCAAGCACACAACGAATGTTGTAAAAGCGCACACAAATCGCTCAGTCGTTGAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3007804","ARO_id":"46590","ARO_name":"VIM-74","CARD_short_name":"VIM-74","ARO_description":"VIM-74 is a subclass B1 carbapenem-hydrolyzing metallo-beta-lactamase.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"6036":{"model_id":"6036","model_name":"VIM-75","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8856":{"protein_sequence":{"accession":"QYZ89894.1","sequence":"MLKVISSLLVYMTASVMAVASPLAHSGEPSGEYPTVNEIPVGEVRLYQIADGVWSHIATRSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEAEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSANVLYGGCAVHELSSTSAGNVADADLAEWPTSVERIQKHYPEAEVVIPGHGLPGGLDLLQHTANVVKAHKNRSVAE"},"dna_sequence":{"accession":"MZ748327.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGTTAAAAGTTATTAGTAGTTTATTGGTCTACATGACCGCGTCTGTCATGGCTGTCGCAAGTCCGTTAGCCCATTCCGGGGAGCCGAGTGGTGAGTATCCGACAGTCAACGAAATTCCGGTCGGAGAGGTCCGACTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCGGTCGTTTGATGGCGCGGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAAAAGCAAATTGGACTTCCCGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGCAGAGGGGAACGAGATTCCCACGCATTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAGCTCTTCTATCCTGGTGCTGCGCATTCGACCGACAATCTGGTTGTATACGTCCCGTCAGCGAACGTGCTATACGGTGGTTGTGCCGTTCATGAGTTGTCAAGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCGTTGAGCGGATTCAAAAACACTACCCGGAAGCAGAGGTCGTCATTCCCGGGCACGGTCTACCGGGCGGTCTAGACTTGCTCCAGCACACAGCGAACGTTGTCAAAGCACACAAAAATCGCTCAGTCGCCGAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3007812","ARO_id":"46598","ARO_name":"VIM-75","CARD_short_name":"VIM-75","ARO_description":"VIM-75 is a subclass B1 carbapenem-hydrolyzing metallo-beta-lactamase.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"6046":{"model_id":"6046","model_name":"VIM-85","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8866":{"protein_sequence":{"accession":"UWQ12891.1","sequence":"MFKLLSKLLVYLTASIMAIASPLAFSVDSSGEYPTVSEIPVGEVRLYQIADGVWSHIATRSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHNDRVGGVDVLRAAGVATYASPSTRRLAEVEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSASVLYGGCAIYELSLTSAGNVADADLAEWPTSIERIQQHYPEAQFVIPGHGLPGGLDLLKHTTNVVKAHTNRSVVE"},"dna_sequence":{"accession":"ON688662.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGTTCAAACTTTTGAGTAAGTTATTGGTCTATTTGACCGCGTCTATCATGGCTATTGCGAGTCCGCTCGCTTTTTCCGTAGATTCTAGCGGTGAGTATCCGACAGTCAGCGAAATTCCGGTCGGGGAGGTCCGGCTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCGGTCGTTTGATGGCGCAGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAGAAGCAAATTGGACTTCCTGTAACGCGTGCAGTCTCCACGCACTTTCATAACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGTAGAGGGGAACGAGATTCCCACGCACTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAACTCTTCTATCCTGGTGCTGCGCATTCGACCGACAACTTAGTTGTGTACGTCCCGTCTGCGAGTGTGCTCTATGGTGGTTGTGCGATTTATGAGTTGTCACTCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCATTGAGCGGATTCAACAACACTACCCGGAAGCACAGTTCGTCATTCCGGGGCACGGCCTGCCGGGCGGTCTAGACTTGCTCAAGCACACAACGAATGTTGTAAAAGCGCACACAAATCGCTCAGTCGTTGAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3007822","ARO_id":"46609","ARO_name":"VIM-85","CARD_short_name":"VIM-85","ARO_description":"VIM-85 is a subclass B1 carbapenem-hydrolyzing metallo-beta-lactamase.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"6047":{"model_id":"6047","model_name":"VIM-86","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8867":{"protein_sequence":{"accession":"WAU52774.1","sequence":"MLKVISSLLVYMTASVMAVASPLAHSGEPSGEYPTVNEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEAEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSAKVLYGGCAVHELSSTSAGNVADADLAEWPTSVERIQKHYPEAEVVIPGHGLPGGLDLLQHTANVVKAHKNRSVAE"},"dna_sequence":{"accession":"OP998371.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGTTAAAAGTTATTAGTAGTTTATTGGTCTACATGACCGCGTCTGTCATGGCTGTCGCAAGTCCGTTAGCCCATTCCGGGGAGCCGAGTGGTGAGTATCCGACAGTCAACGAAATTCCGGTCGGAGAGGTCCGACTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCGGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAAAAGCAAATTGGACTTCCCGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGCAGAGGGGAACGAGATTCCCACGCATTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAGCTCTTCTATCCTGGTGCTGCGCATTCGACCGACAATCTGGTTGTATACGTCCCGTCAGCGAAAGTGCTATACGGTGGTTGTGCCGTTCATGAGTTGTCAAGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCGTTGAGCGGATTCAAAAACACTACCCGGAAGCAGAGGTCGTCATTCCCGGGCACGGTCTACCGGGCGGTCTAGACTTGCTCCAGCACACAGCGAACGTTGTCAAAGCACACAAAAATCGCTCAGTCGCCGAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36946","NCBI_taxonomy_name":"Providencia stuartii","NCBI_taxonomy_id":"588"}}}},"ARO_accession":"3007823","ARO_id":"46610","ARO_name":"VIM-86","CARD_short_name":"VIM-86","ARO_description":"VIM-86 is a subclass B1 carbapenem-hydrolyzing metallo-beta-lactamase.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"6048":{"model_id":"6048","model_name":"VIM-87","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8868":{"protein_sequence":{"accession":"EME7055635.1","sequence":"MFKLLSKLLVYLTTSIMAIASPLAFSVDSSGEYPTVSEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEVEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSASVLYGGCAIYELSRTSAGNVADADLAEWPTSIERIQQHYPEAQFVIPGHGLPGGLDLLKHTTNVVKAHTNRSVVE"},"dna_sequence":{"accession":"ABPYXB010000003.1","fmin":"211323","fmax":"212124","strand":"-","sequence":"ATGTTCAAACTTTTGAGTAAGTTATTGGTCTATTTGACCACATCTATCATGGCTATTGCGAGTCCGCTCGCTTTTTCCGTAGATTCTAGCGGTGAGTATCCGACAGTCAGCGAAATTCCGGTCGGGGAGGTCCGGCTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCAGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAGAAGCAAATTGGACTTCCTGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGTAGAGGGGAACGAGATTCCCACGCACTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAACTCTTCTATCCTGGTGCTGCGCATTCGACCGACAACTTAGTTGTGTACGTCCCGTCTGCGAGTGTGCTCTATGGTGGTTGTGCGATTTATGAGTTGTCACGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCATTGAGCGGATTCAACAACACTACCCGGAAGCACAGTTCGTCATTCCGGGGCACGGCCTGCCGGGCGGTCTAGACTTGCTCAAGCACACAACGAATGTTGTAAAAGCGCACACAAATCGCTCAGTCGTTGAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3007824","ARO_id":"46611","ARO_name":"VIM-87","CARD_short_name":"VIM-87","ARO_description":"VIM-87 is a subclass B1 carbapenem-hydrolyzing metallo-beta-lactamase.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"6049":{"model_id":"6049","model_name":"GES-47","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"575"}},"model_sequences":{"sequence":{"8869":{"protein_sequence":{"accession":"BCT36862.1","sequence":"MRFIHALLLAGIAHSAYASEKLTFKTDLEKLEREKAAQIGVAIVDPQGEIVAGHRTAQRFAMCSTFKFPLAALVFERIDSGTERGDRKLSYGPDMIVEWSPATERFLASGYMTVLEAAQAAVQLSDNGATNLLLREIGGPAAMTQYFRKIGDSVSRLDRKEPEMSDNTPGDLRDTTTPIAMARTVAKVLYGGALTSTSTHTIERWLIGNQTGDATLRAGFPKDWVVGEKTGTCANGGRNDIGFFKAQERDYAVAVYTTAPKLSAVERDELVASVGQVITQLILSTDK"},"dna_sequence":{"accession":"LC612389.1","fmin":"0","fmax":"864","strand":"+","sequence":"ATGCGCTTCATTCACGCACTATTACTGGCAGGGATCGCTCACTCTGCATATGCGTCGGAAAAATTAACCTTCAAGACCGATCTTGAGAAGCTAGAGCGCGAAAAAGCAGCTCAGATCGGTGTTGCGATCGTCGATCCCCAAGGAGAGATCGTCGCGGGCCACCGAACGGCGCAGCGCTTTGCAATGTGCTCAACGTTCAAGTTTCCGCTAGCCGCGCTGGTCTTTGAAAGAATTGACTCAGGCACCGAGCGGGGGGATCGAAAACTTTCATATGGGCCGGACATGATCGTCGAATGGTCTCCTGCCACGGAGCGGTTTCTAGCATCGGGATACATGACGGTTCTCGAGGCAGCGCAAGCTGCGGTGCAGCTTAGCGACAATGGGGCTACTAACCTCTTACTGAGAGAAATTGGCGGACCTGCTGCAATGACGCAGTATTTTCGTAAAATTGGCGACTCTGTGAGTCGGCTAGACCGGAAAGAGCCGGAGATGAGCGACAACACACCTGGCGACCTCAGAGATACAACTACGCCTATTGCTATGGCACGTACTGTGGCTAAAGTCCTCTATGGCGGCGCACTGACGTCCACCTCGACCCACACCATTGAGAGGTGGCTGATCGGAAACCAAACGGGAGACGCGACACTACGAGCGGGTTTTCCTAAAGATTGGGTTGTTGGAGAGAAAACTGGTACCTGCGCCAACGGGGGCCGGAACGACATTGGTTTTTTTAAAGCCCAGGAGAGAGATTACGCTGTAGCGGTGTATACAACGGCCCCGAAACTATCGGCCGTAGAACGTGACGAATTAGTTGCCTCTGTCGGTCAAGTTATTACACAACTCATCCTGAGCACGGACAAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43788","NCBI_taxonomy_name":"Klebsiella michiganensis","NCBI_taxonomy_id":"1134687"}}}},"ARO_accession":"3007825","ARO_id":"46612","ARO_name":"GES-47","CARD_short_name":"GES-47","ARO_description":"GES-47 is a class A carbapenem-hydrolyzing GES-like beta-lactamase.","ARO_category":{"36205":{"category_aro_accession":"3000066","category_aro_cvterm_id":"36205","category_aro_name":"GES beta-lactamase","category_aro_description":"GES beta-lactamases or Guiana extended-spectrum beta-lactamases are related to the other plasmid-located class A beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"6050":{"model_id":"6050","model_name":"GES-48","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"575"}},"model_sequences":{"sequence":{"8870":{"protein_sequence":{"accession":"BCT36863.1","sequence":"MRFIHALLLAGIAHSAYSSEKLTFKTDLEKLEREKAAQIGVAIVDPQGEIVAGHRTAQRFAMCSTFKFPLAALVFERIDSGTERGDRKLSYGPDMIVEWSPATERFLASGHMTVLEAAQAAVQLSDNGATNLLLREIGGPAAMTQYFRKIGDSVSRLDRKEPEMSDNTPGDLRDTTTPIAMARTVAKVLYGGALTSTSTHTIERWLIGNQTGDATLRAGFPKDWVVGEKTGTCANGGRNDIGFFKAQERDYAVAVYTTAPKLSAVERDELVASVGQVITQLILSTDK"},"dna_sequence":{"accession":"LC612390.1","fmin":"0","fmax":"864","strand":"+","sequence":"ATGCGCTTCATTCACGCACTATTACTGGCAGGGATCGCTCACTCTGCATATTCGTCGGAAAAATTAACCTTCAAGACCGATCTTGAGAAGCTAGAGCGCGAAAAAGCAGCTCAGATCGGTGTTGCGATCGTCGATCCCCAAGGAGAGATCGTCGCGGGCCACCGAACGGCGCAGCGCTTTGCAATGTGCTCAACGTTCAAGTTTCCGCTAGCCGCGCTGGTCTTTGAAAGAATTGACTCAGGCACCGAGCGGGGGGATCGAAAACTTTCATATGGGCCGGACATGATCGTCGAATGGTCTCCTGCCACGGAGCGGTTTCTAGCATCGGGACACATGACGGTTCTCGAGGCAGCGCAAGCTGCGGTGCAGCTTAGCGACAATGGGGCTACTAACCTCTTACTGAGAGAAATTGGCGGACCTGCTGCAATGACGCAGTATTTTCGTAAAATTGGCGACTCTGTGAGTCGGCTAGACCGGAAAGAGCCGGAGATGAGCGACAACACACCTGGCGACCTCAGAGATACAACTACGCCTATTGCTATGGCACGTACTGTGGCTAAAGTCCTCTATGGCGGCGCACTGACGTCCACCTCGACCCACACCATTGAGAGGTGGCTGATCGGAAACCAAACGGGAGACGCGACACTACGAGCGGGTTTTCCTAAAGATTGGGTTGTTGGAGAGAAAACTGGTACCTGCGCCAACGGGGGCCGGAACGACATTGGTTTTTTTAAAGCCCAGGAGAGAGATTACGCTGTAGCGGTGTATACAACGGCCCCGAAACTATCGGCCGTAGAACGTGACGAATTAGTTGCCTCTGTCGGTCAAGTTATTACACAACTCATCCTGAGCACGGACAAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36936","NCBI_taxonomy_name":"Aeromonas caviae","NCBI_taxonomy_id":"648"}}}},"ARO_accession":"3007826","ARO_id":"46613","ARO_name":"GES-48","CARD_short_name":"GES-48","ARO_description":"GES-48 is a class A carbapenem-hydrolyzing GES-like beta-lactamase.","ARO_category":{"36205":{"category_aro_accession":"3000066","category_aro_cvterm_id":"36205","category_aro_name":"GES beta-lactamase","category_aro_description":"GES beta-lactamases or Guiana extended-spectrum beta-lactamases are related to the other plasmid-located class A beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"6051":{"model_id":"6051","model_name":"GES-49","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"575"}},"model_sequences":{"sequence":{"8871":{"protein_sequence":{"accession":"BCY26593.1","sequence":"MRFIHVLLLAGIAHSAYASEKLTFKTDLEKLEREKAAQIGVAIVDPQGEIVAGHRMAQRFAMCSTFKFPLAALVFERIDSGTERGDRKLSYGPDMIVKWSPATERFLASGHMTVLEAAQAAVQLSDNGATNLLLREIGGPAAMTQYFRKIGDSVSRLDRKEPEMSDNTPGDLRDTTTPIAMARTVAKVLYGGALTSTSTHTIERWLIGNQTGDATLRAGFPKDWVVGEKTGTCANGGRNDIGFFKAQERDYAVAVYTTAPKLSAVERDELVASVGQVITQLILSTDK"},"dna_sequence":{"accession":"LC637995.1","fmin":"0","fmax":"864","strand":"+","sequence":"ATGCGCTTCATTCACGTACTATTACTGGCAGGGATCGCTCACTCTGCATATGCGTCGGAAAAATTAACCTTCAAGACCGATCTTGAGAAGCTAGAGCGCGAAAAAGCAGCTCAGATCGGTGTTGCGATCGTCGATCCCCAAGGAGAGATCGTCGCGGGCCACCGAATGGCGCAGCGTTTTGCAATGTGCTCAACGTTCAAGTTTCCGCTAGCCGCGCTGGTCTTTGAAAGAATTGACTCAGGCACCGAGCGGGGGGATCGAAAACTTTCATATGGGCCGGACATGATCGTCAAATGGTCTCCTGCCACGGAGCGGTTTCTAGCATCGGGACACATGACGGTTCTCGAGGCAGCGCAAGCTGCGGTGCAGCTTAGCGACAATGGGGCTACTAACCTCTTACTGAGAGAAATTGGCGGACCTGCTGCAATGACGCAGTATTTTCGTAAAATTGGCGACTCTGTGAGTCGGCTAGACCGGAAAGAGCCGGAGATGAGCGACAACACACCTGGCGACCTCAGAGATACAACTACGCCTATTGCTATGGCACGTACTGTGGCTAAAGTCCTCTATGGCGGCGCACTGACGTCCACCTCGACCCACACCATTGAGAGGTGGCTGATCGGAAACCAAACGGGAGACGCGACACTACGAGCGGGTTTTCCTAAAGATTGGGTTGTTGGAGAGAAAACTGGTACCTGCGCCAACGGGGGCCGGAACGACATTGGTTTTTTTAAAGCCCAGGAGAGAGATTACGCTGTAGCGGTGTATACAACGGCCCCGAAACTATCGGCCGTAGAACGTGACGAATTAGTTGCCTCTGTCGGTCAAGTTATTACACAACTCATCCTGAGCACGGACAAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39671","NCBI_taxonomy_name":"Aeromonas veronii bv. veronii","NCBI_taxonomy_id":"197701"}}}},"ARO_accession":"3007827","ARO_id":"46614","ARO_name":"GES-49","CARD_short_name":"GES-49","ARO_description":"GES_49 is a class A  carbapenem-hydrolyzing GES-like beta-lactamase.","ARO_category":{"36205":{"category_aro_accession":"3000066","category_aro_cvterm_id":"36205","category_aro_name":"GES beta-lactamase","category_aro_description":"GES beta-lactamases or Guiana extended-spectrum beta-lactamases are related to the other plasmid-located class A beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"6052":{"model_id":"6052","model_name":"GES-50","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"575"}},"model_sequences":{"sequence":{"8872":{"protein_sequence":{"accession":"BDB58072.1","sequence":"MRFIHTLLLAGIAHSAYASEKLTFKTDLEKLEREKAAQIGVAIVDPQGEIVAGHRTAQRFAMCSTFKFPLAALVFERIDSGTERGDRKLSYGPDMIVEWSPATERFLASGHMTVLEAAQAAVQLSDNGATNLLLREIGGPAAMTQYFRKIGDSVSRLDRKEPEMSDNTPGDLRDTTTPIAMARTVAKVLYGGALTSTSTHTIERWLIGNQTGDATLRAGFPKDWVVGEKTGTCANGGRNDIGFFKAQERDYAVAVYTTAPKLSAVERDELVASVGQVITQLILSTDK"},"dna_sequence":{"accession":"LC654878.1","fmin":"0","fmax":"864","strand":"+","sequence":"ATGCGCTTCATTCACACACTATTACTGGCAGGGATCGCTCACTCTGCATATGCGTCGGAAAAATTAACCTTCAAGACCGATCTTGAGAAGCTAGAGCGCGAAAAAGCAGCTCAGATCGGTGTTGCGATCGTCGATCCCCAAGGAGAGATCGTCGCGGGCCACCGAACGGCGCAGCGCTTTGCAATGTGCTCAACGTTCAAGTTTCCGCTAGCCGCGCTGGTCTTTGAAAGAATTGACTCAGGCACCGAGCGGGGGGATCGAAAACTTTCATATGGGCCGGACATGATCGTCGAATGGTCTCCTGCCACGGAGCGGTTTCTAGCATCGGGACACATGACGGTTCTCGAGGCAGCGCAAGCTGCGGTGCAGCTTAGCGACAATGGGGCTACTAACCTCTTACTGAGAGAAATTGGCGGACCTGCTGCAATGACGCAGTATTTTCGTAAAATTGGCGACTCTGTGAGTCGGCTAGACCGGAAAGAGCCGGAGATGAGCGACAACACACCTGGCGACCTCAGAGATACAACTACGCCTATTGCTATGGCACGTACTGTGGCTAAAGTCCTCTATGGCGGCGCACTGACGTCCACCTCGACCCACACCATTGAGAGGTGGCTGATCGGAAACCAAACGGGAGACGCGACACTACGAGCGGGTTTTCCTAAAGATTGGGTTGTTGGAGAGAAAACTGGTACCTGCGCCAACGGGGGCCGGAACGACATTGGTTTTTTTAAAGCCCAGGAGAGAGATTACGCTGTAGCGGTGTATACAACGGCCCCGAAACTATCGGCCGTAGAACGTGACGAATTAGTTGCCTCTGTCGGTCAAGTTATTACACAACTCATCCTGAGCACGGACAAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43788","NCBI_taxonomy_name":"Klebsiella michiganensis","NCBI_taxonomy_id":"1134687"}}}},"ARO_accession":"3007828","ARO_id":"46615","ARO_name":"GES-50","CARD_short_name":"GES-50","ARO_description":"GES-50 is a class A carbapenem-hydrolyzing GES-like beta-lactamase.","ARO_category":{"36205":{"category_aro_accession":"3000066","category_aro_cvterm_id":"36205","category_aro_name":"GES beta-lactamase","category_aro_description":"GES beta-lactamases or Guiana extended-spectrum beta-lactamases are related to the other plasmid-located class A beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"6053":{"model_id":"6053","model_name":"GES-51","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"575"}},"model_sequences":{"sequence":{"8873":{"protein_sequence":{"accession":"BDB58073.1","sequence":"MRFIHVLLLAGIAHSAYASEKLTFKTDLEKLEREKAAQIGVAIVDPQGEIVAGHRMAQRFAMCSTFKFPLAALVFERIDSGTERGDRKLSYGPDMIVEWSPATERFLASGHMTVLEAAQAAVQLSDNGATNLLLREIGGPAAMTQYFRKIGDSVSRLDRKEPEMSDNTPGDLRDTTTPIAMARTVAKVLYGGALTSTSTHTIERWLIGNQTGDATLRAGFPKDWVVGEKTGTCANGGRNDIGFFKAQERDYAVAVYTTAPKLSAVERDELVASVGQVITQLILSTDK"},"dna_sequence":{"accession":"LC654879.1","fmin":"0","fmax":"864","strand":"+","sequence":"ATGCGCTTCATTCACGTACTATTACTGGCAGGGATCGCTCACTCTGCATATGCGTCGGAAAAATTAACCTTCAAGACCGATCTTGAGAAGCTAGAGCGCGAAAAAGCAGCTCAGATCGGTGTTGCGATCGTCGATCCCCAAGGAGAGATCGTCGCGGGCCACCGAATGGCGCAGCGTTTTGCAATGTGCTCAACGTTCAAGTTTCCGCTAGCCGCGCTGGTCTTTGAAAGAATTGACTCAGGCACCGAGCGGGGGGATCGAAAACTTTCATATGGGCCGGACATGATCGTCGAATGGTCTCCTGCCACGGAGCGGTTTCTAGCATCGGGACACATGACGGTTCTCGAGGCAGCGCAAGCTGCGGTGCAGCTTAGCGACAATGGGGCTACTAACCTCTTACTGAGAGAAATTGGCGGACCTGCTGCAATGACGCAGTATTTTCGTAAAATTGGCGACTCTGTGAGTCGGCTAGACCGGAAAGAGCCGGAGATGAGCGACAACACACCTGGCGACCTCAGAGATACAACTACGCCTATTGCTATGGCACGTACTGTGGCTAAAGTCCTCTATGGCGGCGCACTGACGTCCACCTCGACCCACACCATTGAGAGGTGGCTGATCGGAAACCAAACGGGAGACGCGACACTACGAGCGGGTTTTCCTAAAGATTGGGTTGTTGGAGAGAAAACTGGTACCTGCGCCAACGGGGGCCGGAACGACATTGGTTTTTTTAAAGCCCAGGAGAGAGATTACGCTGTAGCGGTGTATACAACGGCCCCGAAACTATCGGCCGTAGAACGTGACGAATTAGTTGCCTCTGTCGGTCAAGTTATTACACAACTCATCCTGAGCACGGACAAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43754","NCBI_taxonomy_name":"Citrobacter portucalensis","NCBI_taxonomy_id":"1639133"}}}},"ARO_accession":"3007829","ARO_id":"46616","ARO_name":"GES-51","CARD_short_name":"GES-51","ARO_description":"GES-51 is a class A carbapenem-hydrolyzing GES-like beta-lactamase.","ARO_category":{"36205":{"category_aro_accession":"3000066","category_aro_cvterm_id":"36205","category_aro_name":"GES beta-lactamase","category_aro_description":"GES beta-lactamases or Guiana extended-spectrum beta-lactamases are related to the other plasmid-located class A beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"6054":{"model_id":"6054","model_name":"GES-52","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"575"}},"model_sequences":{"sequence":{"8874":{"protein_sequence":{"accession":"UOM32505.1","sequence":"MRFIHALLLAGIAHSAYASEKLTFKTDLEKLEREKAAQIGVAIVDPQGEIVAGHRMAQRFAMCSTFKFPLAALVFERIDSGTERGDRKLSYGPDMIVKWSPATERFLASGHMTVLEAAQAAVQLSDNGATNLLLREIGGPAAMTQYFRKIGDSVSRLDRKEPEMGDNTPGDLRDTTTPIAMARTVAKVLYGGALTSTSTHTIERWLIGNQTGDATLRAGFPKDWVVGEKTGTCANGGQNDIGFFKAQERDYAVAVYTTAPKLSAVERDELVASVGQVITQLILSTDK"},"dna_sequence":{"accession":"ON166564.1","fmin":"0","fmax":"864","strand":"+","sequence":"ATGCGCTTCATTCACGCACTATTACTGGCAGGGATCGCTCACTCTGCATATGCGTCGGAAAAATTAACCTTCAAGACCGATCTTGAGAAGCTAGAGCGCGAAAAAGCAGCTCAGATCGGTGTTGCGATCGTCGATCCCCAAGGAGAGATCGTCGCGGGCCACCGAATGGCGCAGCGTTTTGCAATGTGCTCAACGTTCAAGTTTCCGCTAGCCGCGCTGGTCTTTGAAAGAATTGACTCAGGCACCGAGCGGGGGGATCGAAAACTTTCATATGGGCCGGACATGATCGTCAAATGGTCTCCTGCCACGGAGCGGTTTCTAGCATCGGGACACATGACGGTTCTCGAGGCAGCGCAAGCTGCGGTGCAGCTTAGCGACAATGGGGCTACTAACCTCTTACTGAGAGAAATTGGCGGACCTGCTGCAATGACGCAGTATTTTCGTAAAATTGGCGACTCTGTGAGTCGGCTAGACCGGAAAGAGCCGGAGATGGGCGACAACACACCTGGCGACCTCAGAGATACAACTACGCCTATTGCTATGGCACGTACTGTGGCTAAAGTCCTCTATGGCGGCGCACTGACGTCCACCTCGACCCACACCATTGAGAGGTGGCTGATCGGAAACCAAACGGGAGACGCGACACTACGAGCGGGTTTTCCTAAAGATTGGGTTGTTGGAGAGAAAACTGGTACCTGCGCCAACGGGGGCCAGAACGACATTGGTTTTTTTAAAGCCCAGGAGAGAGATTACGCTGTAGCGGTGTATACAACGGCCCCGAAACTATCGGCCGTAGAACGTGACGAATTAGTTGCCTCTGTCGGTCAAGTTATTACACAACTCATCCTGAGCACGGACAAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3007830","ARO_id":"46617","ARO_name":"GES-52","CARD_short_name":"GES-52","ARO_description":"GES-52 is a class A GES-like extended-spectrum beta-lactamase.","ARO_category":{"36205":{"category_aro_accession":"3000066","category_aro_cvterm_id":"36205","category_aro_name":"GES beta-lactamase","category_aro_description":"GES beta-lactamases or Guiana extended-spectrum beta-lactamases are related to the other plasmid-located class A beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"6055":{"model_id":"6055","model_name":"GES-53","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"575"}},"model_sequences":{"sequence":{"8875":{"protein_sequence":{"accession":"UQM94989.1","sequence":"MRFIHALLLAGIAHSAYASEKLTFKTDLEKLEREKAAQIGVAIVDPQGEIVAGHRMAQRFAMCSTFKFPLAALVFERIDSGTERGDRKLSYGPDMIVKWSPATERFLASGHMTVLEAAQAAVQLSDNGATNLLLREIGGPAAMTQYFRKIGDSVSRLDRKEPEMSDNTPGDLRDTTTPIAMARTVAKVLYGGALTSTSTHTIERWLIGNQTGDATLRAGFPKDWVVGEKTGTCANGGQNDIGFFKAQERDYAVAVYTTAPKLSAVERDELVASVGQVITQLILSTDK"},"dna_sequence":{"accession":"ON418962.1","fmin":"0","fmax":"864","strand":"+","sequence":"ATGCGCTTCATTCACGCACTATTACTGGCAGGGATCGCTCACTCTGCATATGCGTCGGAAAAATTAACCTTCAAGACCGATCTTGAGAAGCTAGAGCGCGAAAAAGCAGCTCAGATCGGTGTTGCGATCGTCGATCCCCAAGGAGAGATCGTCGCGGGCCACCGAATGGCGCAGCGTTTTGCAATGTGCTCAACGTTCAAGTTTCCGCTAGCCGCGCTGGTCTTTGAAAGAATTGACTCAGGCACCGAGCGGGGGGATCGAAAACTTTCATATGGGCCGGACATGATCGTCAAATGGTCTCCTGCCACGGAGCGGTTTCTAGCATCGGGACACATGACGGTTCTCGAGGCAGCGCAAGCTGCGGTGCAGCTTAGCGACAATGGGGCTACTAACCTCTTACTGAGAGAAATTGGCGGACCTGCTGCAATGACGCAGTATTTTCGTAAAATTGGCGACTCTGTGAGTCGGCTAGACCGGAAAGAGCCGGAGATGAGCGACAACACACCTGGCGACCTCAGAGATACAACTACGCCTATTGCTATGGCACGTACTGTGGCTAAAGTCCTCTATGGCGGCGCACTGACGTCCACCTCGACCCACACCATTGAGAGGTGGCTGATCGGAAACCAAACGGGAGACGCGACACTACGAGCGGGTTTTCCTAAAGATTGGGTTGTTGGAGAGAAAACTGGTACCTGCGCCAACGGGGGCCAGAACGACATTGGTTTTTTTAAAGCCCAGGAGAGAGATTACGCTGTAGCGGTGTATACAACGGCCCCGAAACTATCGGCCGTAGAACGTGACGAATTAGTTGCCTCTGTCGGTCAAGTTATTACACAACTCATCCTGAGCACGGACAAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3007831","ARO_id":"46618","ARO_name":"GES-53","CARD_short_name":"GES-53","ARO_description":"GES-53 is a class A carbapenem-hydrolyzing GES-like beta-lactamase.","ARO_category":{"36205":{"category_aro_accession":"3000066","category_aro_cvterm_id":"36205","category_aro_name":"GES beta-lactamase","category_aro_description":"GES beta-lactamases or Guiana extended-spectrum beta-lactamases are related to the other plasmid-located class A beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"6056":{"model_id":"6056","model_name":"GES-54","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"575"}},"model_sequences":{"sequence":{"8876":{"protein_sequence":{"accession":"BDI54505.1","sequence":"MRFIHALLLAGIAHSAYASEKLTFKTDLEKLEREKAAQIGVAIVDPQGEIVAGHRTAQRFAMCSTFKFPLAALVFERIDSGTERGDRKLSYGPDMIVKWSPAMERFLASGHMTVLEAAQAAVQLSDNGATNLLLREIGGPAAMTQYFRKIGDSVSRLDRKEPEMSDNTPGDLRDTTTPIAMARTVAKVLYGGALTSTSTHTIERWLIGNQTGDATLRAGFPKDWVVGEKTGTCANGGRNDIGFFKAQERDYAVAVYTTAPKLSAVERDELVASVGQVITQLILSTDK"},"dna_sequence":{"accession":"LC709174.1","fmin":"0","fmax":"864","strand":"+","sequence":"ATGCGCTTCATTCACGCACTATTACTGGCAGGGATCGCTCACTCTGCATATGCGTCGGAAAAATTAACCTTCAAGACCGATCTTGAGAAGCTAGAGCGCGAAAAAGCAGCTCAGATCGGTGTTGCGATCGTCGATCCCCAAGGAGAGATCGTCGCGGGCCACCGAACGGCGCAGCGCTTTGCAATGTGCTCAACGTTCAAGTTTCCGCTAGCCGCGCTGGTCTTTGAAAGAATTGACTCAGGCACCGAGCGGGGGGATCGAAAACTTTCATATGGGCCGGACATGATCGTCAAATGGTCTCCTGCCATGGAGCGGTTTCTAGCATCGGGACACATGACGGTTCTCGAGGCAGCGCAAGCTGCGGTGCAGCTTAGCGACAATGGGGCTACTAACCTCTTACTGAGAGAAATTGGCGGACCTGCTGCAATGACGCAGTATTTTCGTAAAATTGGCGACTCTGTGAGTCGGCTAGACCGGAAAGAGCCGGAGATGAGCGACAACACACCTGGCGACCTCAGAGATACAACTACGCCTATTGCTATGGCACGTACTGTGGCTAAAGTCCTCTATGGCGGCGCACTGACGTCCACCTCGACCCACACCATTGAGAGGTGGCTGATCGGAAACCAAACGGGAGACGCGACACTACGAGCGGGTTTTCCTAAAGATTGGGTTGTTGGAGAGAAAACTGGTACCTGCGCCAACGGGGGCCGGAACGACATTGGTTTTTTTAAAGCCCAGGAGAGAGATTACGCTGTAGCGGTGTATACAACGGCCCCGAAACTATCGGCCGTAGAACGTGACGAATTAGTTGCCTCTGTCGGTCAAGTTATTACACAACTCATCCTGAGCACGGACAAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39773","NCBI_taxonomy_name":"Enterobacter kobei","NCBI_taxonomy_id":"208224"}}}},"ARO_accession":"3007832","ARO_id":"46619","ARO_name":"GES-54","CARD_short_name":"GES-54","ARO_description":"GES-54 is a class A carbapenem-hydrolyzing GES-like beta-lactamase.","ARO_category":{"36205":{"category_aro_accession":"3000066","category_aro_cvterm_id":"36205","category_aro_name":"GES beta-lactamase","category_aro_description":"GES beta-lactamases or Guiana extended-spectrum beta-lactamases are related to the other plasmid-located class A beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"6057":{"model_id":"6057","model_name":"GES-55","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"575"}},"model_sequences":{"sequence":{"8877":{"protein_sequence":{"accession":"UUF81220.1","sequence":"MRFIHALLLAGIAHSAYASEKLTFKTDLEKLEREKAAQIGVAIVDPQGEIVAGHRMAQRFAMCSTFKFPLAALVFERIDSGTERGDRKLSYGPDMIVKWSPATERFLASGHMTVLEAAQAAVQLSDNGATNLLLREIGGPAAMTQYFRKIGDSVSRLDRKESEMSDNTPGDLRDTTTPIAMARTVAKVLYGGALTSTSTHTIERWLIGNQTGDATLRAGFPKDWVVGEKTGTCANGGRNDIGFFKAQERDYAVAVYTTAPKLSAVERDELVASVGQVITQLILSTDK"},"dna_sequence":{"accession":"ON714048.1","fmin":"0","fmax":"864","strand":"+","sequence":"ATGCGCTTCATTCACGCACTATTACTGGCAGGGATCGCTCACTCTGCATATGCGTCGGAAAAATTAACCTTCAAGACCGATCTTGAGAAGCTAGAGCGCGAAAAAGCAGCTCAGATCGGTGTTGCGATCGTCGATCCCCAAGGAGAGATCGTCGCGGGCCACCGAATGGCGCAGCGTTTTGCAATGTGCTCAACGTTCAAGTTTCCGCTAGCCGCGCTGGTCTTTGAAAGAATTGACTCAGGCACCGAGCGGGGGGATCGAAAACTTTCATATGGGCCGGACATGATCGTCAAATGGTCTCCTGCCACGGAGCGGTTTCTAGCATCGGGACACATGACGGTTCTCGAGGCAGCGCAAGCTGCGGTGCAGCTTAGCGACAATGGGGCTACTAACCTCTTACTGAGAGAAATTGGCGGACCTGCTGCAATGACGCAGTATTTTCGTAAAATTGGCGACTCTGTGAGTCGGCTAGACCGGAAAGAGTCGGAGATGAGCGACAACACACCTGGCGACCTCAGAGATACAACTACGCCTATTGCTATGGCACGTACTGTGGCTAAAGTCCTCTATGGCGGCGCACTGACGTCCACCTCGACCCACACCATTGAGAGGTGGCTGATCGGAAACCAAACGGGAGACGCGACACTACGAGCGGGTTTTCCTAAAGATTGGGTTGTTGGAGAGAAAACTGGTACCTGCGCCAACGGGGGCCGGAACGACATTGGTTTTTTTAAAGCCCAGGAGAGAGATTACGCTGTAGCGGTGTATACAACGGCCCCGAAACTATCGGCCGTAGAACGTGACGAATTAGTTGCCTCTGTCGGTCAAGTTATTACACAACTCATCCTGAGCACGGACAAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36783","NCBI_taxonomy_name":"Serratia marcescens","NCBI_taxonomy_id":"615"}}}},"ARO_accession":"3007833","ARO_id":"46620","ARO_name":"GES-55","CARD_short_name":"GES-55","ARO_description":"GES is a class A GES-like beta-lactamase.","ARO_category":{"36205":{"category_aro_accession":"3000066","category_aro_cvterm_id":"36205","category_aro_name":"GES beta-lactamase","category_aro_description":"GES beta-lactamases or Guiana extended-spectrum beta-lactamases are related to the other plasmid-located class A beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"6058":{"model_id":"6058","model_name":"GES-56","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"575"}},"model_sequences":{"sequence":{"8878":{"protein_sequence":{"accession":"UUT09019.1","sequence":"MRFIHALLLAGIAHSAYASEKLTFKTDLEKLEREKAAQIGVAIVDPQGEIVAGHRMAQRFAMCSTFKFPLAALVFERIDSGTERGDRKLSYGPDMIVEWSPATERFLASGHMTVLEAAQAAVQLSDNGAANLLLREIGGPAAMTQYFRKIGDSVSRLDRKEPEMGDNTPGDLRDTTTPIAMARTVAKVLYGGALTSTSTHTIERWLIGNQTGDATLRAGFPKDWVVGEKTGTCANGARNDIGFFKAQERDYAVAVYTTAPKLSAVERDELVASVGQVITQLILSTDK"},"dna_sequence":{"accession":"OP158701.1","fmin":"0","fmax":"864","strand":"+","sequence":"ATGCGCTTCATTCACGCACTATTACTGGCAGGGATCGCTCACTCTGCATATGCGTCGGAAAAATTAACCTTCAAGACCGATCTTGAGAAGCTAGAGCGCGAAAAAGCAGCTCAGATCGGTGTTGCGATCGTCGATCCCCAAGGAGAGATCGTCGCGGGCCACCGAATGGCGCAGCGTTTTGCAATGTGCTCAACGTTCAAGTTTCCGCTAGCCGCGCTGGTCTTTGAAAGAATTGACTCAGGCACCGAGCGGGGGGATCGAAAACTTTCATATGGGCCGGACATGATCGTCGAATGGTCTCCTGCCACGGAGCGGTTTCTAGCATCGGGACACATGACGGTTCTCGAGGCAGCGCAAGCTGCGGTGCAGCTTAGCGACAATGGGGCTGCTAACCTCTTACTGAGAGAAATTGGCGGACCTGCTGCAATGACGCAGTATTTTCGTAAAATTGGCGACTCTGTGAGTCGGCTAGACCGGAAAGAGCCGGAGATGGGCGACAACACACCTGGCGACCTCAGAGATACAACTACGCCTATTGCTATGGCACGTACTGTGGCTAAAGTCCTCTATGGCGGCGCACTGACGTCCACCTCGACCCACACCATTGAGAGGTGGCTGATCGGAAACCAAACGGGAGACGCGACACTACGAGCGGGTTTTCCTAAAGATTGGGTTGTTGGAGAGAAAACTGGTACCTGCGCCAACGGGGCCCGGAACGACATTGGTTTTTTTAAAGCCCAGGAGAGAGATTACGCTGTAGCGGTGTATACAACGGCCCCGAAACTATCGGCCGTAGAACGTGACGAATTAGTTGCCTCTGTCGGTCAAGTTATTACACAACTCATCCTGAGCACGGACAAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3007834","ARO_id":"46621","ARO_name":"GES-56","CARD_short_name":"GES-56","ARO_description":"GES-56 is a class A GES-like beta-lactamase.","ARO_category":{"36205":{"category_aro_accession":"3000066","category_aro_cvterm_id":"36205","category_aro_name":"GES beta-lactamase","category_aro_description":"GES beta-lactamases or Guiana extended-spectrum beta-lactamases are related to the other plasmid-located class A beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"6059":{"model_id":"6059","model_name":"GES-57","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"575"}},"model_sequences":{"sequence":{"8886":{"protein_sequence":{"accession":"UYS49421.1","sequence":"MRFIHALLLAGIAHSAYASENLTFKTDLEKLEREKAAQIGVAIVDPQGEIVAGHRMAQRFAMCSTFKFPLAALVFERIDSGTERGDRKLSYGPDMIVEWSPATERFLASGHMTVLEAAQAAVQLSDNGATNLLLREIGGPAAMTQYFRKIGDSVSRLDRNEPEMGDNTPGDLRDTTTPIAMARTVAKVLYGGALTSTSTHTIERWLIGNQTGDATLRAGFPKDWVVGEKTGTCANGGRNDIGFFKAQERDYAVAVYTTAPKLSAVERDELVASVGQVITQLILSTDK"},"dna_sequence":{"accession":"OP716785.1","fmin":"34","fmax":"898","strand":"+","sequence":"ATGCGCTTCATTCACGCACTATTACTGGCAGGGATCGCTCACTCTGCATATGCGTCGGAAAACTTAACCTTCAAGACCGATCTTGAGAAGCTAGAGCGCGAAAAAGCAGCTCAGATCGGTGTTGCGATCGTCGATCCCCAAGGAGAGATCGTCGCGGGCCACCGAATGGCGCAGCGTTTTGCAATGTGCTCAACGTTCAAGTTTCCGCTAGCCGCGCTGGTCTTTGAAAGAATTGACTCAGGCACCGAGCGGGGGGATCGAAAACTTTCATATGGGCCGGACATGATCGTCGAATGGTCTCCTGCCACGGAGCGGTTTCTAGCATCGGGACACATGACGGTTCTCGAGGCAGCGCAAGCTGCGGTGCAGCTTAGCGACAATGGGGCTACTAACCTCTTACTGAGAGAAATTGGCGGACCTGCTGCAATGACGCAGTATTTTCGTAAAATTGGCGACTCTGTGAGTCGGCTAGACCGGAATGAGCCGGAGATGGGCGACAACACACCTGGCGACCTCAGAGATACAACTACGCCTATTGCTATGGCACGTACTGTGGCTAAAGTCCTCTATGGCGGCGCACTGACGTCCACCTCGACCCACACCATTGAGAGGTGGCTGATCGGAAACCAAACGGGAGACGCGACACTACGAGCGGGTTTTCCTAAAGATTGGGTTGTTGGAGAGAAAACTGGTACCTGCGCCAACGGGGGCCGGAACGACATTGGTTTTTTTAAAGCCCAGGAGAGAGATTACGCTGTAGCGGTGTATACAACGGCCCCGAAACTATCGGCCGTAGAACGTGACGAATTAGTTGCCTCTGTCGGTCAAGTTATTACACAACTCATCCTGAGCACGGACAAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3007835","ARO_id":"46622","ARO_name":"GES-57","CARD_short_name":"GES-57","ARO_description":"GES-57 is a class A GES-like beta-lactamase.","ARO_category":{"36205":{"category_aro_accession":"3000066","category_aro_cvterm_id":"36205","category_aro_name":"GES beta-lactamase","category_aro_description":"GES beta-lactamases or Guiana extended-spectrum beta-lactamases are related to the other plasmid-located class A beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"6060":{"model_id":"6060","model_name":"CARB-57","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"575"}},"model_sequences":{"sequence":{"8880":{"protein_sequence":{"accession":"QVO43827.1","sequence":"MKKLFLLAGLMVCSTLSYASQLNEDISLIEQQTSSRIGVSVWDTQTDERWDYRGDERFPLMSTFKTLACATMLSDMDSGKLSKNATAKVDERSIVVWSPVMDKLAGQNTRVEHACEAAMLMSDNTAANLVLNEIGGPKAVTMFLRTIGDKATRLDRLEPRLNEATPGDNRDTTTPNAMVNTLRTLIEGETLSYESRVQLKIWMQDNKVSDSLMRSVLPTGWSIADRSGAGGHGSRGINAIIWKENHRPVYISIYVTETELSLQARDQLIAQISQLILQKYKDN"},"dna_sequence":{"accession":"MZ092820.1","fmin":"0","fmax":"852","strand":"+","sequence":"ATGAAAAAGTTATTTTTGTTGGCTGGGCTAATGGTTTGCTCAACCCTAAGTTACGCTTCCCAACTGAATGAAGACATTTCTCTCATCGAACAACAAACCTCAAGCAGAATTGGAGTCTCGGTTTGGGATACGCAAACCGATGAGCGCTGGGATTACCGTGGCGATGAACGCTTCCCACTCATGAGCACATTCAAAACCTTGGCTTGCGCCACAATGCTAAGTGATATGGACAGCGGTAAGCTAAGTAAAAATGCGACCGCGAAAGTCGATGAGCGCAGCATCGTTGTGTGGTCTCCAGTGATGGACAAACTCGCAGGCCAAAACACACGCGTAGAACACGCTTGTGAAGCCGCGATGTTGATGAGTGATAATACTGCTGCCAACTTAGTATTGAATGAAATCGGCGGTCCTAAGGCCGTGACAATGTTTCTGCGAACTATTGGTGATAAAGCGACGCGCCTAGATAGATTAGAACCACGTTTGAACGAAGCGACACCGGGAGACAACCGCGACACAACCACACCTAACGCCATGGTAAACACTCTGCGAACCTTGATTGAAGGAGAAACGTTGTCTTACGAGTCTCGCGTACAATTAAAAATCTGGATGCAGGACAACAAGGTTTCAGACTCGTTAATGCGTTCAGTATTACCAACAGGTTGGTCTATCGCCGACCGCTCTGGTGCGGGTGGTCACGGTTCGCGTGGTATTAACGCAATCATATGGAAGGAAAACCATCGTCCTGTTTACATTAGTATCTATGTCACAGAAACCGAGCTATCACTTCAAGCCAGAGACCAGCTCATCGCGCAAATCAGTCAGTTGATTTTACAGAAATACAAAGATAATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"46624","NCBI_taxonomy_name":"Vibrio diabolicus","NCBI_taxonomy_id":"50719"}}}},"ARO_accession":"3007836","ARO_id":"46623","ARO_name":"CARB-57","CARD_short_name":"CARB-57","ARO_description":"CARB-57 is a class A carbenicillin-hydrolyzing CARB-like beta-lactamase.","ARO_category":{"36230":{"category_aro_accession":"3000091","category_aro_cvterm_id":"36230","category_aro_name":"CARB beta-lactamase","category_aro_description":"CARB beta-lactamases are class A lactamases that can hydrolyze carbenicillin. Many of the PSE beta-lactamases have been renamed as CARB-lactamases with the notable exception of PSE-2 which is now OXA-10.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"6061":{"model_id":"6061","model_name":"CARB-58","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"8881":{"protein_sequence":{"accession":"QYJ63007.1","sequence":"MLWSSNDVTQQGSRPKTKLAILWSLMLLYKMCDNQNYGVTYMKLLLAFSLLIPSVVFASSSKFQQVEQDVKAIEVSLSARIGVSVLDTQNGEYWDYNGNQRFPLTSTFKTIACAKLLYDAEQGKVNPNSTVEIKKADLVTYSPVIEKQVGQAITLDDACFATMTTSDNTAANIILSAVGGPKGVTDFLRQIGDKETRLDRIEPDLNEGKLGDLRDTTTPKAIASTLNKFLFGSALSEMNQKKLESWMVNNQVTGNLLRSVLPAGWNIADRSGAGGFGARSITAVVWSEHQAPIIVSIYLAQTQASMAERNDAIVKIGHSIFDVYTSQSR"},"dna_sequence":{"accession":"MT990446.1","fmin":"54","fmax":"1044","strand":"+","sequence":"ATGTTATGGAGCAGCAACGATGTTACGCAGCAGGGCAGTCGCCCTAAAACAAAGTTAGCCATATTATGGAGCCTCATGCTTTTATATAAAATGTGTGACAATCAAAATTATGGGGTTACTTACATGAAGCTTTTATTGGCATTTTCGCTTTTAATACCATCCGTGGTTTTTGCAAGTAGTTCAAAGTTTCAGCAAGTTGAACAAGACGTTAAGGCAATTGAAGTTTCTCTTTCTGCTCGTATAGGTGTTTCCGTTCTTGATACTCAAAATGGAGAATATTGGGATTACAATGGCAATCAGCGCTTCCCGTTAACAAGTACTTTTAAAACAATAGCTTGCGCTAAATTACTATATGATGCTGAGCAAGGAAAAGTTAATCCCAATAGTACAGTCGAGATTAAGAAAGCAGATCTTGTGACCTATTCCCCTGTAATAGAAAAGCAAGTAGGGCAGGCAATCACACTCGATGATGCGTGCTTCGCAACTATGACTACAAGTGATAATACTGCGGCAAATATCATCCTAAGTGCTGTAGGTGGCCCCAAAGGCGTTACTGATTTTTTAAGACAAATTGGGGACAAAGAGACTCGTCTAGACCGTATTGAGCCTGATTTAAATGAAGGTAAGCTCGGTGATTTGAGGGATACGACAACTCCTAAGGCAATAGCCAGTACTTTGAATAAATTTTTATTTGGTTCCGCGCTATCTGAAATGAACCAGAAAAAATTAGAGTCTTGGATGGTGAACAATCAAGTCACTGGTAATTTACTACGTTCAGTATTGCCGGCGGGATGGAACATTGCGGATCGCTCAGGTGCTGGCGGATTTGGTGCTCGGAGTATTACAGCAGTTGTGTGGAGTGAGCATCAAGCCCCAATTATTGTGAGCATCTATCTAGCTCAAACACAGGCTTCAATGGCAGAGCGAAATGATGCGATTGTTAAAATTGGTCATTCAATTTTTGACGTTTATACATCACAGTCGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35805","NCBI_taxonomy_name":"Salmonella enterica subsp. enterica serovar Schwarzengrund","NCBI_taxonomy_id":"340190"}}}},"ARO_accession":"3007837","ARO_id":"46625","ARO_name":"CARB-58","CARD_short_name":"CARB-58","ARO_description":"CARB-58 is a PSE family class A carbenicillin-hydrolyzing CARB-like beta-lactamase.","ARO_category":{"36230":{"category_aro_accession":"3000091","category_aro_cvterm_id":"36230","category_aro_name":"CARB beta-lactamase","category_aro_description":"CARB beta-lactamases are class A lactamases that can hydrolyze carbenicillin. Many of the PSE beta-lactamases have been renamed as CARB-lactamases with the notable exception of PSE-2 which is now OXA-10.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"6062":{"model_id":"6062","model_name":"tet(65)","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"575"}},"model_sequences":{"sequence":{"8885":{"protein_sequence":{"accession":"WPF67354.1","sequence":"MLTTASLDAVGLGLVLPILPALLGQVGSAASTIPMHVGLLTALYAVMQFLCAPVLGRLSDRFGRRRVLLASLAGATVDYLILALTSTLWVFYVARAVAGITGATNAVTATVIADVTPPAERAKRYGWLGACYGGGMIAGPVIGGLFGGFSPHLPFLVAALLTAVNLTLSLSMLHETRPDLPIKSQESASTSAPFRLQAIQGVVPLIAAFGLVQLIGQAPGSTWVLFTQQRLDWSPVEVGISLSLFGLVQVLVQAVLTGRVVTRLGETRTIYLGIVADASGLIGLAFVTGSWAMMPILAALGVGGITVPALQTLLSQRTPEQHQGRLQGHLASLNSLTSILGPIAFTTIFALSQIDADGTLWFCAAALYIPCAILVTRNARSSG"},"dna_sequence":{"accession":"CP123906.1","fmin":"34168","fmax":"35320","strand":"-","sequence":"GTGCTCACTACCGCCAGCCTCGACGCCGTGGGGCTAGGCCTGGTTCTCCCGATCCTGCCCGCACTACTGGGTCAGGTCGGCTCGGCCGCAAGCACTATCCCCATGCATGTCGGATTGCTTACCGCGCTCTACGCGGTAATGCAGTTCCTTTGCGCTCCGGTACTGGGCAGACTGTCCGATCGCTTCGGCCGCCGTCGAGTACTGTTGGCTTCCTTGGCCGGCGCGACTGTCGACTATCTCATTCTGGCCTTGACTTCGACCCTCTGGGTCTTCTACGTAGCACGGGCTGTCGCGGGCATCACCGGGGCAACAAATGCCGTGACCGCCACCGTGATCGCCGACGTCACCCCACCCGCAGAGCGGGCCAAGCGATACGGATGGCTCGGGGCGTGCTACGGCGGAGGAATGATCGCCGGCCCCGTAATCGGCGGTCTCTTCGGTGGCTTCTCACCCCATTTGCCGTTCCTCGTAGCTGCTCTCCTGACGGCGGTGAATCTCACTCTCAGCTTGAGCATGCTGCACGAGACAAGACCAGATCTCCCAATCAAGTCACAGGAGTCAGCATCGACGTCTGCGCCTTTTCGACTCCAAGCTATCCAGGGGGTGGTGCCCCTCATTGCGGCTTTCGGCCTCGTACAGCTCATCGGCCAGGCCCCCGGCTCGACGTGGGTTCTGTTCACGCAACAACGTCTCGACTGGAGCCCCGTCGAAGTCGGGATTTCCTTGTCCCTCTTCGGTCTGGTGCAGGTGCTTGTTCAGGCCGTCCTCACCGGACGGGTCGTGACGCGACTCGGCGAAACTAGAACGATCTATCTCGGCATTGTCGCCGACGCGTCGGGTCTCATAGGTCTCGCATTCGTCACCGGCTCCTGGGCGATGATGCCCATCCTCGCAGCACTCGGAGTCGGAGGTATCACGGTCCCGGCCCTGCAGACACTGCTCTCCCAACGTACTCCCGAGCAGCACCAAGGCCGGCTGCAAGGCCACCTCGCTAGCCTCAACAGCCTCACATCAATCCTCGGGCCTATTGCCTTCACGACGATCTTCGCCCTGAGTCAGATAGACGCCGATGGCACTCTATGGTTCTGCGCCGCTGCGCTCTACATTCCTTGTGCGATCCTCGTCACAAGGAACGCAAGATCCTCTGGGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"46627","NCBI_taxonomy_name":"Corynebacterium sp. 22KM0430","NCBI_taxonomy_id":"2989735"}}}},"ARO_accession":"3007838","ARO_id":"46626","ARO_name":"tet(65)","CARD_short_name":"tet(65)","ARO_description":"tet(65) is a tetracycline efflux gene identified from a Corynebacterium oculi plasmid.","ARO_category":{"36003":{"category_aro_accession":"0010002","category_aro_cvterm_id":"36003","category_aro_name":"major facilitator superfamily (MFS) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient.","category_aro_class_name":"AMR Gene Family"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"6063":{"model_id":"6063","model_name":"CIM-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"475"}},"model_sequences":{"sequence":{"8883":{"protein_sequence":{"accession":"WP_123865086.1","sequence":"MKSVSQILLLSLFLFFLNCNTKKPSHVPKVVFKTDNLTVIQLSDHVYQHISYLNTDSFGRVPCNGMVVKQGDETVILDTPSDDKSSADLISWIKNNLNAGVNAVVATHFHNDCLGGLKEFDKNKIPSYASKKTIGLAQKNNANIPQHSFDNDLTLKVGSTNVFVKYFGEGHTKDNVVAYFPDERIMFGGCLIKEIGAGKGYLGDANVKDWSATVAKIKKHYPDVKIIIPGHGDTGGIKLLDYTIALFKDES"},"dna_sequence":{"accession":"NZ_CP033828.1","fmin":"721258","fmax":"722014","strand":"+","sequence":"ATGAAGTCCGTATCCCAAATACTATTACTTTCCCTGTTTTTATTTTTTTTGAATTGCAATACCAAGAAACCTTCACATGTGCCTAAGGTAGTCTTTAAAACCGATAACCTCACCGTTATTCAGTTGTCCGATCATGTGTACCAGCATATTTCTTACCTGAATACAGACTCTTTTGGCCGGGTACCCTGCAACGGAATGGTTGTAAAGCAGGGAGATGAAACCGTAATATTAGATACTCCTTCTGATGACAAAAGTTCAGCAGACCTTATTTCCTGGATTAAAAATAATCTGAATGCAGGTGTTAATGCTGTCGTTGCTACTCATTTTCACAATGACTGCTTGGGCGGTCTTAAAGAATTTGATAAAAATAAGATCCCTTCCTATGCCAGTAAGAAAACAATCGGTCTTGCTCAAAAGAATAATGCAAATATTCCACAGCATAGTTTTGACAATGATCTGACATTAAAAGTCGGGAGTACGAATGTTTTTGTGAAATATTTCGGTGAAGGCCATACAAAAGATAATGTAGTAGCCTACTTTCCTGATGAACGGATTATGTTTGGAGGTTGTTTGATCAAAGAAATAGGAGCAGGCAAAGGCTACTTAGGAGATGCTAATGTAAAAGACTGGTCAGCTACCGTGGCCAAGATAAAAAAACATTATCCTGATGTGAAAATTATCATCCCGGGTCATGGTGATACAGGAGGAATAAAACTACTGGATTATACGATTGCCCTTTTCAAGGATGAATCATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36916","NCBI_taxonomy_name":"Chryseobacterium indologenes","NCBI_taxonomy_id":"253"}}}},"ARO_accession":"3007840","ARO_id":"46629","ARO_name":"CIM-1","CARD_short_name":"CIM-1","ARO_description":"CIM-1 is a CIM-like carbapenem-hydrolyzing metallo-beta-lactamase identified from Chryseobacterium indologenes.","ARO_category":{"46628":{"category_aro_accession":"3007839","category_aro_cvterm_id":"46628","category_aro_name":"CIM beta-lactamase","category_aro_description":"CIM (C. indologenes MBL) are a family of subclass B1 metallo-beta-lactamases originally identified from Chryseobacterium indologenes, and which exhibit carbapenem-hydrolyzing activity.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"6066":{"model_id":"6066","model_name":"KPC-135","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8889":{"protein_sequence":{"accession":"WP_262697131.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"NG_088397.1","fmin":"3","fmax":"924","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3007844","ARO_id":"46633","ARO_name":"KPC-135","CARD_short_name":"KPC-135","ARO_description":"KPC-135 is a KPC-type class A beta-lactamase. KPC-125 is a variant of KPC-44, differing by a 6 basepair deletion.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"6070":{"model_id":"6070","model_name":"Mycobacterium tuberculosis Rv0678 with mutation conferring resistance to clofazimine","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"40394":{"param_type":"nonsense mutation","param_description":"A sequence change where, compared to a reference sequence, one codon is replaced by a termination codon through a nucleotide substitution. These are described as a substitution of the wildtype codon to a termination codon. Format is given as [wild type AA][position][Ter], for example Q42Ter where Q42 is a wildtype amino acid replaced by a premature termination codon.","param_type_id":"40394","param_value":{"14546":"Q76Ter","14584":"E113Ter","14586":"Q115Ter","14599":"E138Ter","14605":"Y145Ter","14612":"R156Ter","14471":"Q22Ter","14488":"R38Ter"}},"snp":{"WHO-R":{"14546":"D95Y","14584":"D95Y","14586":"D95Y","14599":"D95Y","14605":"D95Y","14612":"D95Y","14471":"D95Y","14478":"L32S","14486":"A36V","14488":"A36V","14496":"C46R","14531":"I67S","14536":"N70D","14589":"L117R","14592":"G121R","14607":"M146T"},"param_value":{"14478":"L32S","14486":"A36V","14496":"C46R","14531":"I67S","14536":"N70D","14589":"L117R","14592":"G121R","14607":"M146T"},"clinical":{"14478":"L32S","14486":"A36V","14496":"C46R","14531":"I67S","14536":"N70D","14589":"L117R","14592":"G121R","14607":"M146T"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"300"}},"model_sequences":{"sequence":{"8893":{"protein_sequence":{"accession":"NP_215192.1","sequence":"MSVNDGVDQMGAEPDIMEFVEQMGGYFESRSLTRLAGRLLGWLLVCDPERQSSEELATALAASSGGISTNARMLIQFGFIERLAVAGDRRTYFRLRPNAFAAGERERIRAMAELQDLADVGLRALGDAPPQRSRRLREMRDLLAYMENVVSDALGRYSQRTGEDD"},"dna_sequence":{"accession":"NC_000962.3","fmin":"778989","fmax":"779487","strand":"+","sequence":"GTGAGCGTCAACGACGGGGTCGATCAGATGGGCGCCGAGCCCGACATCATGGAATTCGTCGAACAGATGGGCGGCTATTTCGAGTCCAGGAGTTTGACTCGGTTGGCGGGTCGATTGTTGGGCTGGCTGCTGGTGTGTGATCCCGAGCGGCAGTCCTCGGAGGAACTGGCGACGGCGCTGGCGGCCAGCAGCGGGGGGATCAGCACCAATGCCCGGATGCTGATCCAATTTGGGTTCATTGAGCGGCTCGCGGTCGCCGGGGATCGGCGCACCTATTTCCGGTTGCGGCCCAACGCTTTCGCGGCTGGCGAGCGTGAACGCATCCGGGCAATGGCCGAACTGCAGGACCTGGCTGACGTGGGGCTGAGGGCGCTGGGCGACGCCCCGCCGCAGCGAAGCCGACGGCTGCGGGAGATGCGGGATCTGTTGGCATATATGGAGAACGTCGTCTCCGACGCCCTGGGGCGATACAGCCAGCGAACCGGAGAGGACGACTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3007852","ARO_id":"46642","ARO_name":"Mycobacterium tuberculosis Rv0678 with mutation conferring resistance to clofazimine","CARD_short_name":"Mtub_Rv0678_CFZ","ARO_description":"Genetic variants of the transcription factor Rv0678, which regulates expression of the mmpS5\/L5 efflux pump, that are associated with resistance to clofazimine antibiotics.","ARO_category":{"46643":{"category_aro_accession":"3007853","category_aro_cvterm_id":"46643","category_aro_name":"clofazimine resistant Rv0678","category_aro_description":"Loss-of-function mutations in the Mycobacterium Rv0678 gene associated with clofazimine resistance.","category_aro_class_name":"AMR Gene Family"},"40939":{"category_aro_accession":"3004012","category_aro_cvterm_id":"40939","category_aro_name":"clofazimine","category_aro_description":"Clofazimine is a fluoroquinolone-class phenazine dye used for the treatment of leprosy. Clofazimine binds to DNA and disrupts bacterial DNA gyrase, thereby causing double-stranded DNA breaks, and subsequent cell death.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"6071":{"model_id":"6071","model_name":"Mycobacterium tuberculosis atpE with mutation conferring resistance to bedaquiline","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"14624":"D28G","14625":"D28A","14626":"D28V","14627":"E61D","14628":"A63P","14629":"I66M"},"WHO-R":{"14624":"D28G","14625":"D28A","14626":"D28V","14627":"E61D","14628":"A63P","14629":"I66M"},"clinical":{"14624":"D28G","14625":"D28A","14626":"D28V","14627":"E61D","14628":"A63P","14629":"I66M"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"100"}},"model_sequences":{"sequence":{"8894":{"protein_sequence":{"accession":"NP_215821.1","sequence":"MDPTIAAGALIGGGLIMAGGAIGAGIGDGVAGNALISGVARQPEAQGRLFTPFFITVGLVEAAYFINLAFMALFVFATPVK"},"dna_sequence":{"accession":"NC_000962.3","fmin":"1461044","fmax":"1461290","strand":"+","sequence":"ATGGACCCCACTATCGCTGCCGGCGCCCTCATCGGCGGTGGACTGATCATGGCCGGTGGCGCCATCGGCGCCGGTATCGGTGACGGTGTCGCCGGTAACGCGCTTATCTCCGGTGTCGCCCGGCAACCCGAGGCGCAAGGGCGGCTGTTCACACCGTTCTTCATCACCGTCGGTTTGGTTGAGGCGGCATACTTCATCAACCTGGCGTTTATGGCGCTGTTCGTCTTCGCTACACCCGTCAAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3007854","ARO_id":"46644","ARO_name":"Mycobacterium tuberculosis atpE with mutation conferring resistance to bedaquiline","CARD_short_name":"Mtub_atpE_BDQ","ARO_description":"Genetic variants of ATPase subunit C atpE with mutations associated with resistance to bedaquiline antibiotics.","ARO_category":{"46244":{"category_aro_accession":"3007477","category_aro_cvterm_id":"46244","category_aro_name":"antibiotic resistant ATP synthase","category_aro_description":"ATP synthase enzymes, specifically subunit C, resistant to diarylquinolone antibiotics including Bedaquiline. Mutations in ATP synthase confer antibiotic resistance by disrupting binding and blocking of ATP synthase reactions by Bedaquiline.","category_aro_class_name":"AMR Gene Family"},"41933":{"category_aro_accession":"3004492","category_aro_cvterm_id":"41933","category_aro_name":"bedaquiline","category_aro_description":"A diarylquinoline antibiotic drug sold under the brand name Sirturo, used to treat infection from Mycobacterium spp., particularly multidrug-resistant tuberculosis. Bedaquiline disrupts ATP synthase by proton pump blockage, inhibiting ATP synthesis.","category_aro_class_name":"Antibiotic"},"41932":{"category_aro_accession":"3004491","category_aro_cvterm_id":"41932","category_aro_name":"diarylquinoline antibiotic","category_aro_description":"A class of antibiotics used to treat specifically Mycobacterium tuberculosis infection; therefore, referred to as an antimycobacterial. Diarylquinoline antibiotics inhibit ATP synthesis in tuberculosis cells by disruption of mycobacterial ATP synthase.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"6072":{"model_id":"6072","model_name":"KPC-134","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"8895":{"protein_sequence":{"accession":"UVJ69199.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARATSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDNRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"OP293349.1","fmin":"5","fmax":"911","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGCTACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAACCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3007857","ARO_id":"46647","ARO_name":"KPC-134","CARD_short_name":"KPC-134","ARO_description":"KPC-134 is an inhibitor-resistant KPC-2 variant which confers resistance to ceftazidime-avibactam.","ARO_category":{"36727":{"category_aro_accession":"3000588","category_aro_cvterm_id":"36727","category_aro_name":"avibactam","category_aro_description":"Serine beta-lactamase inhibitor targeting class A, class C, and some class D enzymes.","category_aro_class_name":"Adjuvant"},"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"45634":{"category_aro_accession":"3007072","category_aro_cvterm_id":"45634","category_aro_name":"ceftazidime-avibactam","category_aro_description":"An antibiotic-adjuvant admixture of the beta-lactam antibiotic ceftazidime and the non-beta-lactam beta-lactamase inhibitor avibactam.","category_aro_class_name":"Antibiotic+Adjuvant"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"6074":{"model_id":"6074","model_name":"BIM-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"8897":{"protein_sequence":{"accession":"ANY85569.1","sequence":"MRISLALCLLSILNFAVAEEVLPEIKVEKLEEGIYLHTSYLEYQGNIYEKHGLVVIDDRKAYIIDTPVLAIDTERLVKWFEERNFTIGASFSTHFHSDSSGGIEWLNKNSIPTYASELTNELLKKDGKAQAKNSFNAVSFWLVKNKIEVFYPGPGHTQDNEVVWIPSKKILFGGCFVKPDGLGYLGDANLEAWPNSARKLMSKYSNAKLVIPSHSEIGNASLLKRTWEQAVKGLNDSKKTSQLSK"},"dna_sequence":{"accession":"CP016446.1","fmin":"14508","fmax":"15246","strand":"-","sequence":"ATGAGAATATCGTTAGCTTTATGCTTGCTTAGTATTTTAAATTTTGCTGTTGCAGAAGAGGTATTGCCAGAAATAAAAGTTGAAAAGCTAGAAGAAGGAATCTATCTTCACACATCTTATCTAGAGTATCAGGGAAATATTTATGAAAAACATGGGTTGGTAGTTATTGATGATCGTAAGGCATATATAATTGATACGCCAGTTTTGGCTATAGATACTGAGCGGCTAGTAAAGTGGTTTGAAGAGCGTAACTTTACTATAGGGGCTAGTTTCTCAACACATTTTCATAGTGACAGTTCCGGCGGCATAGAATGGCTAAATAAAAATTCTATTCCTACATATGCATCTGAATTAACAAATGAACTTCTAAAAAAAGACGGCAAGGCGCAAGCTAAAAACTCTTTTAATGCAGTTAGTTTTTGGCTAGTTAAAAACAAAATTGAAGTTTTTTATCCGGGGCCAGGGCATACACAGGATAACGAGGTCGTGTGGATACCTAGTAAGAAAATATTATTCGGTGGTTGTTTTGTTAAGCCAGACGGTCTTGGGTATTTGGGTGACGCAAATTTAGAAGCTTGGCCAAATTCTGCTAGAAAGTTAATGTCTAAATATAGCAACGCAAAACTGGTTATTCCAAGCCATAGTGAAATAGGAAATGCATCACTCTTGAAGCGTACATGGGAGCAGGCTGTTAAAGGGCTAAATGACAGTAAAAAAACATCACAGCTCAGCAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36803","NCBI_taxonomy_name":"Pseudomonas putida","NCBI_taxonomy_id":"303"}}}},"ARO_accession":"3007859","ARO_id":"46649","ARO_name":"BIM-1","CARD_short_name":"BIM-1","ARO_description":"BIM-1 is an ambler molecular class B beta-lactamase. It confers resistance to carbapenems and cephalosporins.","ARO_category":{"46648":{"category_aro_accession":"3007858","category_aro_cvterm_id":"46648","category_aro_name":"BIM beta-lactamase","category_aro_description":"BIM is a family of ambler molecular class B beta-lactamases from Pseudomonas putida. It confers resistance to carbapenems and cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"6073":{"model_id":"6073","model_name":"CHM-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"475"}},"model_sequences":{"sequence":{"8896":{"protein_sequence":{"accession":"QAT79363.1","sequence":"MKTTLTHIVAIVFSFVIISCGSQHKDHFKAKEVYTSPHLVITQISEHSFIHTSFKQTNDFGNVPCNGLVVKNNNETIVFDTPINDKSSEELIQWINGTLHAKINAVIPTHFHDDSSGGLQAFHNHHIPSYAYSKTIELAKENKFVIPENSFNDSLVLKVGNEKTITRFFGEGHTKDNVVGYFPGEHILFGGCLLKELDAGKGYLGDANVAAWSNTVEKVKKEYPDVKIVVPGHGEYGNGKLLDYTITLFKTQ"},"dna_sequence":{"accession":"MK401906.1","fmin":"0","fmax":"759","strand":"+","sequence":"ATGAAAACTACCCTTACCCATATAGTCGCTATAGTATTTTCTTTCGTCATCATAAGCTGTGGCTCTCAACATAAAGACCATTTTAAAGCAAAAGAAGTGTATACATCTCCCCATCTGGTTATTACCCAGATTTCTGAACATTCTTTTATCCATACTTCTTTTAAACAAACAAATGATTTTGGTAATGTTCCCTGCAACGGACTTGTTGTAAAAAATAATAATGAAACCATTGTTTTCGACACCCCCATTAATGACAAAAGTTCAGAAGAACTGATACAATGGATCAATGGAACACTTCATGCAAAAATAAATGCCGTTATTCCGACCCATTTCCATGATGACAGTTCAGGAGGATTGCAGGCATTTCATAATCATCATATTCCTTCCTATGCCTATTCCAAAACCATTGAATTAGCCAAAGAAAACAAGTTTGTAATTCCTGAAAACAGTTTTAATGATTCGCTGGTTTTAAAAGTTGGCAATGAAAAAACTATCACGAGGTTTTTCGGTGAAGGTCATACCAAAGATAATGTGGTAGGGTATTTCCCTGGTGAACATATATTGTTTGGAGGCTGTTTATTAAAAGAGCTTGATGCAGGTAAAGGATATCTGGGAGATGCTAATGTGGCAGCATGGTCCAATACAGTTGAAAAAGTGAAAAAAGAATATCCTGATGTGAAAATTGTGGTTCCGGGACATGGAGAATATGGGAATGGAAAACTACTGGACTATACCATTACATTATTTAAAACTCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"46236","NCBI_taxonomy_name":"Chryseobacterium sp.","NCBI_taxonomy_id":"1871047"}}}},"ARO_accession":"3007855","ARO_id":"46645","ARO_name":"CHM-1","CARD_short_name":"CHM-1","ARO_description":"CHM is a subclass B1 metallo B-lactamase with enzymatic activity against cephalosporins and carbapenems, first identified in the Chryseobacterium spp. functional gene library.","ARO_category":{"46646":{"category_aro_accession":"3007856","category_aro_cvterm_id":"46646","category_aro_name":"CHM beta-lactamase","category_aro_description":"CHM is a subclass B1 metallo B-lactamase with enzymatic activity against cephalosporins and carbapenems, first identified in the Chryseobacterium spp. functional gene library.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"6075":{"model_id":"6075","model_name":"DYB-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"475"}},"model_sequences":{"sequence":{"8903":{"protein_sequence":{"accession":"BES62776.2","sequence":"MLKKFLLMIQVFCVATISAQSKTEKTEIADDIEILKLSDNLYLHRSFLETQSWGKVGANGLILIKNNEALLIDTPWNNEQTERLDKWISNSLHATIKTVIPTHWHEDRMGGLAYLQSKGVKSYANEQTIELAKTKNLPIPDTGFKDSIDINFQGFDLKLYYPGGGHTTDNIIVWIPSEDILFGGCFIKDLQSSNLGNLADADVAAWPQSIKWVLTKFPDIKTVVPGHGNMGGYNLLTHTLKLINEHNTVR"},"dna_sequence":{"accession":"AP028867.1","fmin":"3823966","fmax":"3824719","strand":"-","sequence":"ATGCTAAAAAAATTCCTACTCATGATACAGGTATTCTGTGTCGCAACAATCTCGGCTCAATCTAAAACTGAAAAAACCGAGATTGCAGATGATATCGAAATTCTGAAATTATCAGACAACCTTTACCTTCACAGAAGTTTTCTCGAAACCCAAAGCTGGGGTAAAGTAGGAGCAAACGGATTGATTCTCATAAAGAACAACGAAGCATTGCTTATTGATACTCCGTGGAACAATGAACAAACCGAAAGACTCGATAAATGGATATCAAACTCTTTACATGCAACCATTAAAACAGTAATACCTACCCATTGGCACGAAGACCGCATGGGCGGCTTAGCTTACCTTCAGTCGAAAGGAGTAAAATCTTATGCTAATGAGCAGACGATAGAACTAGCCAAAACTAAAAACCTTCCTATACCCGACACCGGATTTAAAGATTCAATCGACATCAATTTTCAGGGATTCGATCTCAAACTATATTATCCGGGAGGAGGACATACTACTGACAATATAATTGTATGGATTCCGTCCGAAGATATCCTTTTCGGAGGGTGTTTTATCAAGGACTTGCAATCATCCAATCTGGGAAATCTTGCCGATGCCGATGTTGCAGCATGGCCACAATCGATAAAATGGGTTCTAACCAAGTTTCCTGATATTAAGACTGTTGTTCCCGGACACGGTAACATGGGAGGATACAACCTCTTGACCCATACATTAAAGCTTATTAATGAACATAATACGGTCAGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"46652","NCBI_taxonomy_name":"Dysgonomonas capnocytophagoides","NCBI_taxonomy_id":"45254"}}}},"ARO_accession":"3007861","ARO_id":"46651","ARO_name":"DYB-1","CARD_short_name":"DYB-1","ARO_description":"DYB-1 is a subclass B1 metallo-beta-lactamases identified from Dysgonomonas capnocytophagoides. DYB-1 is associated with resistance to meropenem and ceftazidime.","ARO_category":{"46650":{"category_aro_accession":"3007860","category_aro_cvterm_id":"46650","category_aro_name":"DYB beta-lactamase","category_aro_description":"DYB is a family of subclass B1 metallo-beta-lactamases identified from Dysgonomonas capnocytophagoides. These enzymes confer resistance to beta-lactam antibiotics, including carbapenems.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"35990":{"category_aro_accession":"0000073","category_aro_cvterm_id":"35990","category_aro_name":"meropenem","category_aro_description":"Meropenem is an ultra-broad spectrum injectable antibiotic used to treat a wide variety of infections, including meningitis and pneumonia. It is a beta-lactam and belongs to the subgroup of carbapenem, similar to imipenem and ertapenem.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7301":{"model_id":"7301","model_name":"ACT-100","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10128":{"protein_sequence":{"accession":"UHK14157.1","sequence":"MKTKSLCCALMLSTSCSVLAAPMSEKQLSDVVERTVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQHWQPQWKPGTTRLYANASIGLFGALAVKPSGMSFEQAMTKRVFKPLKLDHTWINVPKEEEAHYAWGYRDGKATHVSPGMLDAKAYGVKTNVQDMASWVKANMNPDALPDSTLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVEAKTVVEGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKELGIVMLANKSYPNPARVEAAYRILSALQ"},"dna_sequence":{"accession":"OL794654.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGAAGACAAAATCCCTTTGCTGTGCCCTGATGCTCAGCACCTCCTGCTCTGTTCTCGCCGCGCCGATGTCAGAGAAACAGCTGTCTGACGTGGTGGAACGTACCGTTACCCCCCTGATGAAAGCGCAAGCCATTCCGGGCATGGCGGTAGCGGTGATTTATCAGGGTCAGCCGCACTACTTTACCTTCGGAAAGGCCGATGTTGCGGCGAACAAACCTGTCACCCCGCAAACCCTGTTTGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTATTAGGTGGCGATGCGATTGCGCGCGGAGAAATATCGCTGGGCGACCCCGTGACAAAGTACTGGCCCGAGCTAACAGGCAAGCAGTGGCAGGGTATTCGCATGTTGGATCTGGCGACCTACACCGCGGGTGGCCTGCCGCTACAGGTGCCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGTTTCTATCAACACTGGCAACCGCAGTGGAAACCAGGCACAACGCGTCTTTATGCGAACGCCAGCATCGGGCTTTTTGGCGCCCTCGCGGTTAAACCCTCCGGTATGAGCTTTGAACAGGCCATGACGAAGCGGGTCTTCAAGCCACTCAAACTGGACCATACATGGATTAACGTTCCGAAAGAAGAAGAGGCGCATTACGCCTGGGGATACCGTGACGGTAAAGCAACCCACGTTTCACCGGGAATGCTGGATGCCAAAGCGTATGGTGTCAAAACCAACGTCCAGGATATGGCGAGCTGGGTGAAGGCCAACATGAACCCTGACGCCCTTCCGGATTCAACGTTGAAACAGGGTATTGCCCTGGCACAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCGGTAGAAGCCAAAACCGTCGTGGAGGGCAGCGATAACAAGGTGGCTCTTGCACCGTTACCGGTGGCAGAAGTGAACCCTCCAGCTCCGCCAGTAAAAGCATCATGGGTACATAAAACAGGCTCGACGGGTGGATTCGGCAGCTATGTCGCATTTATTCCTGAGAAGGAACTCGGCATTGTTATGCTGGCGAACAAGAGCTACCCGAACCCGGCGCGCGTGGAAGCGGCATACCGTATTCTGAGCGCTCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3007883","ARO_id":"46675","ARO_name":"ACT-100","CARD_short_name":"ACT-100","ARO_description":"Cephalosporin-hydrolyzing class C beta-lactamase ACT-100.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7302":{"model_id":"7302","model_name":"ACT-101","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10129":{"protein_sequence":{"accession":"UHK14158.1","sequence":"MKTKSLCCALLLSTSCSVLAAPMSEKQLSDVVERTVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQHWQPQWKPGTTRLYANASIGLFGALAVKPSGMSFEQAMTKRVFKPLKLDHTWINVPKEEEAHYAWGYRDGKAIHVSPGMLDAEAYGVKTNIQDMASWLKANMNPDALPDSTLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVEAKTVVEGSDNKVALAPLPVAEVNPPAPPVKASWIHKTGSTGGFGSYVAFIPEKELGIVMLANKSYPNPARVEAAYRILSALQ"},"dna_sequence":{"accession":"OL794655.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGAAGACAAAATCCCTTTGCTGTGCCCTGCTGCTCAGCACCTCCTGCTCTGTTCTCGCCGCGCCGATGTCAGAGAAACAGCTGTCTGACGTGGTGGAACGTACCGTTACCCCCCTGATGAAAGCGCAAGCCATTCCGGGCATGGCGGTAGCGGTGATTTATCAGGGTCAGCCGCACTACTTTACCTTCGGAAAGGCCGATGTTGCGGCGAACAAACCTGTCACCCCGCAAACCCTGTTTGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTATTAGGTGGCGATGCGATTGCGCGCGGAGAAATATCGCTGGGCGACCCCGTGACAAAGTACTGGCCCGAGCTAACAGGCAAGCAGTGGCAGGGTATTCGCATGTTGGATCTGGCGACCTACACCGCGGGTGGCCTGCCGCTACAGGTGCCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGTTTCTATCAACACTGGCAACCGCAGTGGAAACCAGGCACAACGCGTCTTTATGCGAACGCCAGCATCGGGCTTTTTGGCGCCCTCGCGGTTAAACCCTCCGGTATGAGCTTTGAACAGGCCATGACGAAGCGGGTCTTCAAGCCACTCAAACTGGACCATACATGGATTAACGTTCCGAAAGAAGAAGAGGCGCATTACGCCTGGGGATACCGTGATGGTAAAGCAATCCACGTTTCACCGGGAATGCTGGATGCCGAAGCGTATGGTGTCAAAACCAACATCCAGGATATGGCGAGCTGGCTGAAGGCCAACATGAACCCTGACGCCCTTCCGGATTCAACGTTGAAACAGGGTATTGCCCTGGCACAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCGGTAGAGGCCAAAACCGTCGTGGAGGGCAGCGATAACAAGGTGGCTCTTGCACCGTTACCGGTGGCAGAAGTGAACCCTCCAGCTCCGCCAGTAAAAGCATCATGGATACATAAAACAGGCTCGACGGGTGGATTCGGCAGCTATGTCGCATTTATTCCTGAAAAGGAACTCGGCATTGTTATGCTGGCGAACAAGAGCTACCCGAACCCGGCGCGCGTGGAAGCGGCATACCGTATTCTGAGCGCTCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3007884","ARO_id":"46676","ARO_name":"ACT-101","CARD_short_name":"ACT-101","ARO_description":"Cephalosporin-hydrolyzing class C beta-lactamase ACT-101.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7303":{"model_id":"7303","model_name":"ACT-102","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10130":{"protein_sequence":{"accession":"UHK14159.1","sequence":"MKTKSLCCALLLSTSCSVLAAPMSEKQLSDVVERTVTPLMKAQAIPGMAVAVIYQGHPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQHWQPQWKPGATRLYANASIGLFGALAVKPSGMSFEQAMTKRVFKPLKLDHTWINVPKEEEAHYAWGYRDGKAIHVSPGMLDAEAYGVKTNIQDMASWVKANMNPDALPNSTLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVEAQTVVEGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKELGIVMLANKSYPNPARVEAAYRILSALQ"},"dna_sequence":{"accession":"OL794656.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGAAGACAAAATCCCTTTGCTGTGCCCTGCTGCTCAGCACCTCCTGCTCTGTTCTCGCCGCGCCGATGTCAGAGAAACAGCTGTCTGACGTGGTGGAACGTACCGTTACCCCCCTGATGAAAGCGCAAGCCATTCCGGGCATGGCGGTGGCGGTGATTTATCAGGGTCATCCGCACTACTTTACCTTCGGAAAGGCCGATGTTGCGGCGAACAAACCTGTCACCCCGCAAACCCTGTTTGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTATTAGGTGGCGATGCGATTGCGCGCGGAGAAATATCGCTGGGCGACCCCGTGACAAAGTACTGGCCCGAGCTAACAGGCAAGCAGTGGCAGGGTATTCGCATGTTGGATCTGGCGACCTACACCGCGGGTGGCCTGCCGCTACAGGTGCCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGTTTCTATCAACACTGGCAACCGCAGTGGAAACCAGGCGCAACGCGTCTTTATGCGAACGCCAGCATCGGGCTTTTTGGCGCCCTCGCGGTTAAACCCTCCGGTATGAGCTTTGAACAGGCCATGACGAAGCGGGTCTTCAAGCCACTCAAACTGGACCATACATGGATTAACGTTCCGAAAGAAGAAGAGGCGCATTACGCCTGGGGATACCGTGACGGTAAAGCAATCCACGTTTCACCGGGAATGCTGGATGCCGAAGCGTATGGTGTCAAAACCAACATCCAGGATATGGCGAGCTGGGTGAAGGCCAACATGAACCCTGACGCCCTTCCGAATTCAACGTTGAAACAGGGTATTGCCCTGGCACAGTCTCGCTACTGGCGCGTGGGTGCCATGTACCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCGGTAGAAGCCCAAACCGTCGTGGAGGGCAGCGATAACAAGGTGGCTCTTGCACCGTTACCGGTGGCAGAAGTGAACCCTCCAGCTCCGCCAGTAAAAGCATCATGGGTACATAAAACAGGCTCGACGGGTGGATTCGGCAGCTATGTCGCATTTATTCCTGAAAAGGAACTCGGCATTGTTATGCTGGCGAACAAGAGCTACCCGAACCCGGCGCGCGTGGAAGCGGCATACCGTATTCTGAGCGCTCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3007885","ARO_id":"46677","ARO_name":"ACT-102","CARD_short_name":"ACT-102","ARO_description":"Cephalosporin-hydrolyzing class C beta-lactamase ACT-102.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7304":{"model_id":"7304","model_name":"ACT-103","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10131":{"protein_sequence":{"accession":"UHK14163.1","sequence":"MKTKSLFCALLLSTSCSVLAAPMSEKQLSDVVERTVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQHWQPQWKPGTTRLYANASIGLFGALAVKPSGMSFEQAMTKRVFKPLKLDHTWINVPKEEEAHYAWGYRDGKAIHVSPGMLDAEAYGVKTNIQDMASWLKANMNPDALPDSTLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVEAKTVVEGSDNKVALAPLPVAEVNPPVPPVKASWVHKTGSTGGFGSYVAFIPEKELGIVMLANKSYPNPARVEAAYRILSALQ"},"dna_sequence":{"accession":"OL794660.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGAAGACAAAATCCCTTTTCTGTGCCCTGCTGCTCAGCACCTCCTGCTCTGTTCTCGCCGCGCCGATGTCAGAGAAACAGCTGTCTGACGTGGTGGAACGTACCGTTACCCCCCTGATGAAAGCGCAAGCCATTCCGGGCATGGCGGTAGCGGTGATTTATCAGGGTCAGCCGCACTACTTTACCTTCGGAAAGGCCGATGTTGCTGCGAACAAACCTGTCACCCCGCAAACCCTGTTTGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTATTAGGTGGCGATGCGATTGCGCGCGGAGAAATATCGCTGGGCGACCCCGTGACAAAGTACTGGCCCGAGCTAACAGGCAAGCAGTGGCAGGGTATTCGCATGTTGGATCTGGCGACCTACACCGCGGGTGGCCTGCCGCTACAGGTGCCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGTTTCTATCAACACTGGCAACCTCAGTGGAAACCAGGCACAACGCGTCTTTATGCGAACGCCAGCATCGGGCTTTTTGGCGCCCTCGCGGTTAAACCCTCCGGTATGAGCTTTGAACAGGCCATGACGAAGCGGGTCTTCAAGCCACTCAAACTGGACCATACATGGATTAACGTTCCGAAAGAAGAAGAGGCGCATTACGCCTGGGGATACCGTGATGGTAAAGCAATCCACGTTTCACCGGGAATGCTGGATGCCGAAGCGTATGGTGTCAAAACCAACATCCAGGATATGGCGAGCTGGCTGAAGGCCAACATGAACCCTGACGCCCTTCCGGATTCAACGTTGAAACAGGGTATTGCCCTGGCACAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCGGTAGAAGCCAAAACCGTCGTGGAGGGCAGCGATAACAAGGTGGCTCTTGCACCGTTACCGGTGGCAGAAGTGAACCCTCCAGTTCCGCCAGTAAAAGCATCATGGGTACATAAAACAGGCTCGACGGGTGGATTCGGCAGCTATGTCGCATTTATTCCTGAAAAGGAACTCGGCATTGTTATGCTGGCGAACAAGAGCTACCCGAACCCGGCGCGCGTGGAAGCGGCATACCGTATTCTGAGCGCTCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3007886","ARO_id":"46678","ARO_name":"ACT-103","CARD_short_name":"ACT-103","ARO_description":"Cephalosporin-hydrolyzing class C beta-lactamase ACT-103.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7305":{"model_id":"7305","model_name":"ACT-104","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10132":{"protein_sequence":{"accession":"UHK14164.1","sequence":"MKTKSLCCALLLSTSCSVLAAPMSEKQLSDVVERTVTPLMKAQAIPGMAVAVIYQGHPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQDWQPQWKPGTTRLYANASIGLFGALAVKPSGMSFEQAMTKRVFKPLKLDHTWINVPKEDEAHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVQDMASWVKANMNPAALPDSTLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVEAKTVVEGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKKLGIVMLANKSYPNPARVEAAYRILSALQ"},"dna_sequence":{"accession":"OL794661.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGAAGACAAAATCCCTTTGCTGCGCCCTGCTGCTCAGCACCTCCTGCTCTGTTCTCGCCGCACCGATGTCAGAGAAACAGCTGTCTGACGTGGTGGAACGTACCGTTACCCCCCTGATGAAGGCGCAAGCCATTCCGGGCATGGCGGTGGCGGTGATTTATCAGGGTCATCCGCACTACTTTACCTTCGGAAAGGCCGATGTTGCGGCGAACAAACCTGTCACCCCGCAAACCCTGTTTGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTATTAGGTGGCGATGCGATTGCGCGCGGAGAAATATCGCTGGGCGACCCCGTGACAAAGTACTGGCCCGAGCTAACAGGCAAGCAGTGGCAGGGTATTCGCATGTTGGATCTGGCGACCTACACCGCGGGTGGCCTGCCGCTACAGGTGCCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGTTTCTATCAAGACTGGCAACCGCAGTGGAAACCAGGCACAACGCGTCTTTATGCGAACGCCAGCATCGGGCTTTTTGGCGCCCTCGCGGTTAAACCCTCCGGTATGAGCTTTGAACAGGCCATGACGAAGCGGGTCTTCAAGCCGCTCAAACTGGACCATACATGGATTAACGTTCCGAAAGAAGACGAGGCGCATTACGCCTGGGGATACCGTGATGGTAAAGCGGTCCACGTTTCACCGGGAATGTTGGATGCCGAAGCGTATGGTGTCAAAACCAACGTCCAGGATATGGCGAGCTGGGTGAAGGCCAACATGAACCCTGCCGCCCTTCCGGATTCAACGTTGAAACAGGGTATTGCCCTGGCACAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCGGTAGAAGCCAAAACCGTCGTGGAGGGCAGCGATAACAAGGTGGCTCTTGCACCGTTACCGGTGGCAGAAGTGAACCCTCCAGCTCCGCCAGTAAAAGCATCATGGGTACATAAAACAGGCTCGACGGGTGGATTCGGCAGCTATGTCGCATTTATTCCTGAAAAGAAACTCGGCATTGTTATGCTGGCGAACAAGAGCTACCCGAACCCGGCGCGCGTGGAAGCGGCATACCGTATTCTGAGCGCTCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3007887","ARO_id":"46679","ARO_name":"ACT-104","CARD_short_name":"ACT-104","ARO_description":"Cephalosporin-hydrolyzing class C beta-lactamase ACT-104.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7306":{"model_id":"7306","model_name":"ACT-105","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10133":{"protein_sequence":{"accession":"UMO60338.1","sequence":"MMMTKSLCCALLLSTSCSVLATPMSEKQLAEVVERTVTPLMKAQAIPGMAVAVIYEGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIVRGEISLGDPVTKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMSYEQAITTRVFKPLKLDHTWINVPKAEEAHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVQDMASWVMVNMKPDSLQDNSLRKGLTLAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVEGSDNKVALAPLPAREVNPPAPPVNASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILSAL"},"dna_sequence":{"accession":"OM575023.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGATGACTAAATCCCTTTGCTGCGCCCTGCTGCTCAGCACCTCCTGCTCGGTATTGGCTACCCCGATGTCAGAAAAACAGCTGGCTGAGGTGGTGGAACGGACCGTTACGCCGCTGATGAAAGCGCAGGCCATTCCGGGTATGGCGGTGGCGGTGATTTATGAGGGTCAGCCGCACTACTTCACCTTCGGTAAAGCCGATGTTGCGGCGAACAAACCTGTCACTCCACAAACCTTGTTCGAACTGGGTTCTATAAGTAAAACCTTCACCGGCGTACTCGGTGGCGATGCCATTGTTCGCGGTGAAATATCGCTGGGCGATCCGGTGACAAAATACTGGCCTGAGCTAACAGGCAAGCAGTGGCAGGGGATCCGCATGCTGGATCTGGCAACCTATACCGCAGGAGGTTTGCCGTTACAGGTACCGGATGAGGTCACGGATAACGCCTCTCTGTTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCGGGCACCACGCGTCTTTACGCCAATGCCAGCATCGGTCTTTTTGGCGCGCTGGCGGTCAAACCTTCCGGCATGAGCTATGAGCAGGCCATAACGACGCGGGTCTTTAAGCCGCTCAAGCTGGACCATACGTGGATTAACGTTCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGATACCGCGACGGTAAAGCGGTACACGTTTCGCCAGGAATGCTGGACGCTGAAGCCTATGGCGTAAAAACCAACGTGCAGGATATGGCAAGCTGGGTGATGGTCAACATGAAGCCGGACTCCCTTCAGGATAATTCACTCAGGAAAGGCCTTACCCTGGCGCAGTCTCGCTACTGGCGCGTGGGGGCCATGTATCAGGGGTTAGGCTGGGAAATGCTTAACTGGCCGGTCGATGCCAAAACCGTGGTTGAAGGTAGCGACAATAAGGTTGCACTGGCACCGCTGCCTGCGAGAGAAGTGAATCCACCAGCGCCCCCGGTCAACGCATCCTGGGTCCATAAAACAGGCTCTACCGGCGGGTTTGGCAGCTACGTGGCATTTATTCCTGAAAAGCAGCTCGGTATTGTGATGCTGGCAAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCGTATTTTGAGCGCGCTGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36926","NCBI_taxonomy_name":"Enterobacter asburiae","NCBI_taxonomy_id":"61645"}}}},"ARO_accession":"3007888","ARO_id":"46680","ARO_name":"ACT-105","CARD_short_name":"ACT-105","ARO_description":"Cephalosporin-hydrolyzing class C beta-lactamase ACT-105.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7307":{"model_id":"7307","model_name":"ACT-106","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10134":{"protein_sequence":{"accession":"ULU82602.1","sequence":"MMKKSLCCALLLGLSCSALAAPVSEKQLAEVVANTVTPLMKAQSVPGMAVAVIYQGKPHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDDASLLRFYQHWQPQWKPGTTRLYANASIGLFGALAVKPSGMRYEQAMTERVFKPLALHHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPEKVADAPLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVVEGSDSKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKRIGIVMLANTSYPNPARVEAAYHILEALQ"},"dna_sequence":{"accession":"OM617739.1","fmin":"0","fmax":"1146","strand":"-","sequence":"ATGATGAAAAAATCCCTTTGCTGCGCCCTGCTGCTGGGCCTCTCTTGCTCTGCTCTCGCCGCGCCAGTGTCAGAAAAACAGCTGGCGGAGGTGGTCGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCTGTTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGAAAACCGCACTATTACACGTTTGGCAAGGCCGATATCGCGGCGAATAAACCCGTTACGCCTCAGACCCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGCGTTTTAGGTGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCTGAGCTGACGGGCAAGCAGTGGCAAGGGATTCGAATGCTGGATCTCGCCACCTACACCGCAGGCGGTCTGCCGCTACAGGTGCCCGATGAGGTGACGGATGACGCCTCCCTGCTGCGCTTCTATCAACACTGGCAGCCACAGTGGAAGCCAGGCACAACGCGCCTTTATGCCAACGCCAGCATCGGCCTGTTTGGTGCGCTGGCGGTTAAGCCTTCCGGCATGCGCTACGAGCAGGCGATGACCGAGCGAGTATTCAAACCGCTGGCGCTGCATCACACCTGGATTAACGTGCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGAATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCGGAGAAGGTTGCCGATGCCCCACTTAAGCAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGGTCGAAGGCAGCGACAGTAAGGTAGCGCTGGCGCCGTTGCCCGTGGCAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGCTCTACTGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCGGATCGGTATTGTGATGCTCGCGAATACAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCGAGGCGTTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3007889","ARO_id":"46681","ARO_name":"ACT-106","CARD_short_name":"ACT-106","ARO_description":"Cephalosporin-hydrolyzing class C beta-lactamase ACT-106.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7308":{"model_id":"7308","model_name":"ACT-107","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10135":{"protein_sequence":{"accession":"UNN26045.1","sequence":"MIKKSLCCALLLGMSYSGFTAQLSEKQLAEAVERTVTPLMKAHAIPGMAVAVIYQGQPHCFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPATKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDDVTDTASLLRFYQTWQPQWKPGTTRLYANASIGLFGALAVKPSGMSFEQAMTERVFKPLKLNHTWINVPKSEAQHYAWGYREGKPVHVSPGMLDAEAYGVKTNVQDMAAWVMANMAPENVAEASLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVDAKTLVDGSDNNVALAPLPAREVSPPAPPVKASWVHKTGSTGGFGSYVAFIPEKELGIVMLANKSYPNPARVEAAYRILDALQ"},"dna_sequence":{"accession":"OM967044.1","fmin":"2","fmax":"1148","strand":"+","sequence":"ATGATCAAAAAATCCCTTTGCTGCGCCCTGCTGCTCGGCATGTCATATTCCGGCTTTACCGCTCAGCTGTCAGAAAAACAGTTAGCTGAGGCGGTTGAACGTACCGTTACTCCGCTGATGAAGGCACACGCTATTCCGGGCATGGCGGTTGCCGTGATTTACCAGGGCCAGCCGCACTGTTTCACCTTCGGCAAAGCCGATGTCGCCGCGAATAAACCCGTCACGCCGCAAACCCTGTTCGAGCTGGGCTCCATCAGTAAAACGTTCACCGGCGTGCTGGGCGGTGATGCCATTGCCCGCGGCGAGATTTCGCTGGGCGATCCGGCAACGAAATACTGGCCTGAACTGACGGGCAAGCAGTGGCAGGGCATTCGAATGCTGGATCTGGCGACCTACACTGCGGGAGGTCTGCCGCTGCAGGTACCTGATGACGTGACGGACACCGCGTCGCTTCTGCGCTTTTACCAGACCTGGCAGCCGCAGTGGAAACCGGGCACCACGCGACTGTATGCCAACGCCAGCATCGGCCTGTTTGGCGCGCTGGCGGTTAAGCCTTCCGGCATGAGCTTTGAGCAGGCCATGACGGAACGCGTCTTTAAACCATTGAAGCTGAATCATACCTGGATTAACGTCCCGAAAAGCGAAGCGCAGCACTACGCATGGGGCTACCGGGAGGGGAAACCGGTCCACGTCTCACCAGGAATGCTGGACGCCGAAGCCTACGGCGTGAAAACCAACGTGCAGGATATGGCAGCCTGGGTGATGGCCAACATGGCACCGGAGAACGTTGCTGAAGCGTCACTTAAACAAGGTATTGCGCTGGCGCAGTCGCGCTACTGGCGCGTGGGTGCCATGTATCAAGGGTTAGGCTGGGAAATGCTTAACTGGCCGGTCGATGCCAAAACGCTGGTCGATGGCAGTGATAATAACGTTGCGCTGGCGCCGCTGCCTGCGAGAGAAGTGAGCCCTCCAGCTCCACCGGTCAAAGCATCGTGGGTACACAAAACGGGTTCAACCGGCGGGTTTGGCAGCTACGTGGCCTTCATCCCGGAGAAAGAGCTTGGCATCGTGATGCTGGCGAACAAGAGCTATCCGAACCCGGCGCGGGTTGAGGCGGCATACCGTATCCTCGACGCGCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"47907","NCBI_taxonomy_name":"Enterobacter huaxiensis","NCBI_taxonomy_id":"2494702"}}}},"ARO_accession":"3007890","ARO_id":"46682","ARO_name":"ACT-107","CARD_short_name":"ACT-107","ARO_description":"Cephalosporin-hydrolyzing class C beta-lactamase ACT-107.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7309":{"model_id":"7309","model_name":"ACT-108","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10136":{"protein_sequence":{"accession":"UQM99653.1","sequence":"MMKKSLCCALLLGLSCSALAAPVSEKQLAEVVANTVTPLMKAQSVPGMAVAVIYQGKPHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDDASLLRFYQHWQPQWKPGTTRLYANASIGLFGALAVKPSGMRYEQAMTERVFKPLALHHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPEKVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEVNTVVEGSDSKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQVGIVMLANKSYPNPARVEAAYHILEALQ"},"dna_sequence":{"accession":"OL445411.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCCCTTTGCTGCGCCCTGCTGCTGGGCCTCTCTTGCTCTGCTCTCGCCGCGCCAGTATCAGAAAAACAGCTGGCGGAGGTGGTCGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCTGTTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGAAAACCGCACTATTACACGTTTGGCAAGGCCGATATCGCGGCGAATAAACCCGTTACGCCTCAGACCCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGCGTTTTAGGTGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCTGAGCTGACGGGCAAGCAGTGGCAAGGGATTCGAATGCTGGATCTCGCCACCTACACCGCAGGCGGTCTGCCGCTACAGGTGCCCGATGAGGTGACGGATGACGCCTCCCTGCTGCGCTTCTATCAACACTGGCAGCCACAGTGGAAGCCAGGCACAACGCGCCTTTATGCCAACGCCAGCATCGGCCTGTTTGGTGCGCTGGCGGTTAAGCCTTCCGGCATGCGCTACGAGCAGGCGATGACCGAGCGAGTATTCAAACCGCTGGCGCTGCATCACACCTGGATTAACGTGCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGAATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCGGAGAAGGTTGCCGATGCCTCACTTAAGCAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGTCAACACGGTGGTCGAAGGCAGCGACAGTAAGGTAGCGCTGGCGCCGTTACCCGTGGCAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGTTCTACTGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGGTCGGTATTGTAATGCTCGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCGAGGCGCTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3007891","ARO_id":"46683","ARO_name":"ACT-108","CARD_short_name":"ACT-108","ARO_description":"Cephalosporin-hydrolyzing class C beta-lactamase ACT-108.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7310":{"model_id":"7310","model_name":"ACT-109","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10137":{"protein_sequence":{"accession":"UTT87806.1","sequence":"MMKKSLCCALLLSTSCAALAAPMSETQLAKVVERTVTPLMKAQSIPGMAVAVIYQGQPHYFTFGKADVAANTPVTAQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPELTGKQWQGVRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQSWQPQWAPGTTRLYANASIGLFGALAVKPSGMRFEQAMTERVLKPLNLNHTWINVPKAEEQHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVKDMASWVVANMAPDGVQDASLKQGMVLAQSRYWRTGSMYQGLGWEMLNWPVEAKTVVEGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKELGIIMLANKSYPNPERVEAAYRILSALQ"},"dna_sequence":{"accession":"OP022995.1","fmin":"0","fmax":"1146","strand":"-","sequence":"ATGATGAAAAAATCCCTGTGCTGCGCCCTGCTGCTCAGCACCTCCTGCGCTGCATTAGCCGCACCTATGTCAGAAACACAGCTGGCGAAGGTCGTGGAACGTACCGTTACGCCCCTGATGAAAGCGCAGTCTATTCCGGGTATGGCGGTCGCCGTGATTTATCAGGGCCAGCCGCACTACTTCACCTTCGGCAAGGCCGATGTCGCAGCGAACACACCCGTCACTGCACAAACGCTGTTTGAGCTGGGCTCAATCAGCAAAACCTTCACCGGCGTTCTGGGTGGCGATGCTATTGCTCGCGGTGAAATTTCGCTGGGCGATCCGGTGACCAAATACTGGCCTGAGCTGACCGGCAAACAGTGGCAGGGCGTTCGCATGCTGGACCTGGCAACCTATACTGCCGGTGGCCTGCCGTTACAGGTGCCCGATGAGGTTACCGATAATGCCTCGCTGCTGCGTTTTTACCAGTCCTGGCAACCACAGTGGGCGCCAGGCACCACGCGTCTTTATGCAAATGCCAGCATCGGTCTGTTTGGGGCTCTGGCGGTGAAACCTTCTGGCATGCGCTTTGAGCAGGCGATGACGGAGCGGGTCCTGAAGCCGCTTAACCTGAACCATACGTGGATTAACGTTCCGAAGGCAGAAGAACAGCATTACGCCTGGGGTTATCGTGACGGTAAAGCGGTTCACGTTTCGCCGGGCATGCTCGACGCTGAAGCGTATGGCGTGAAAACCAACGTTAAGGATATGGCGAGCTGGGTGGTGGCTAACATGGCCCCCGATGGCGTACAGGATGCCTCACTGAAGCAGGGCATGGTGCTTGCACAGTCTCGCTACTGGCGCACAGGCTCGATGTACCAGGGCCTGGGCTGGGAGATGCTCAACTGGCCGGTAGAAGCCAAAACCGTGGTGGAGGGCAGCGACAACAAGGTAGCGCTTGCACCGTTGCCCGTGGCAGAAGTGAACCCTCCTGCTCCACCGGTAAAAGCGTCATGGGTACATAAAACAGGCTCGACGGGCGGATTTGGCAGCTACGTGGCATTTATTCCTGAGAAGGAACTCGGCATCATTATGCTGGCGAACAAGAGCTATCCGAACCCGGAACGCGTGGAAGCGGCATACCGTATTCTGAGCGCTCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"45936","NCBI_taxonomy_name":"Enterobacter ludwigii","NCBI_taxonomy_id":"299767"}}}},"ARO_accession":"3007892","ARO_id":"46684","ARO_name":"ACT-109","CARD_short_name":"ACT-109","ARO_description":"Cephalosporin-hydrolyzing class C beta-lactamase ACT-109.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7311":{"model_id":"7311","model_name":"ACT-110","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10138":{"protein_sequence":{"accession":"BDT38917.1","sequence":"MKTKSLCCALLLSTSCSVLAAPMSEKQLSDVVERTVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQHWQPQWKPGTTRLYANASIGLFGALAVKPSGMSFEQAMTKRVFKPLKLDHTWINVPKEEEAHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVQDIASWVKANMNPAALPDSTLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVEAKTVVEGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKELGIVMLANKSYPNPARVEAAFRILSALQ"},"dna_sequence":{"accession":"LC733682.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGAAGACAAAATCCCTTTGCTGTGCCCTGCTGCTCAGCACCTCCTGCTCTGTTCTCGCCGCGCCGATGTCAGAGAAACAGCTGTCTGACGTGGTGGAACGTACCGTTACCCCCCTGATGAAAGCGCAAGCCATTCCGGGCATGGCGGTAGCGGTGATTTATCAGGGTCAGCCGCACTACTTTACCTTCGGAAAGGCCGATGTTGCTGCGAACAAACCTGTCACCCCGCAAACCCTGTTTGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTATTAGGTGGCGATGCGATTGCGCGCGGAGAAATATCGCTGGGCGACCCCGTGACAAAGTACTGGCCCGAGCTAACAGGCAAGCAGTGGCAGGGTATTCGCATGTTGGATCTGGCGACCTACACCGCGGGTGGCCTGCCGCTACAGGTGCCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGTTTCTATCAACACTGGCAACCGCAGTGGAAACCAGGCACAACGCGTCTTTATGCGAACGCCAGCATCGGGCTTTTTGGCGCCCTCGCGGTTAAACCCTCCGGTATGAGCTTTGAACAGGCCATGACGAAGCGGGTCTTCAAGCCACTCAAACTGGACCATACATGGATTAACGTTCCGAAAGAAGAAGAGGCGCATTACGCCTGGGGATACCGTGATGGTAAAGCGGTCCACGTTTCACCGGGAATGCTGGATGCCGAAGCGTATGGTGTCAAAACCAACGTCCAGGATATAGCGAGCTGGGTGAAGGCCAACATGAACCCTGCCGCCCTTCCGGATTCAACGCTGAAACAGGGTATTGCCCTGGCACAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCGGTAGAAGCCAAAACCGTCGTGGAGGGCAGCGATAACAAGGTGGCTCTTGCACCGTTACCGGTGGCAGAAGTGAACCCTCCAGCTCCGCCAGTAAAAGCATCATGGGTACATAAAACAGGCTCGACGGGTGGATTTGGCAGCTATGTCGCATTTATTCCTGAGAAGGAACTCGGCATTGTTATGCTGGCGAACAAGAGCTACCCGAACCCGGCGCGCGTGGAAGCGGCATTCCGTATTCTGAGCGCTCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39773","NCBI_taxonomy_name":"Enterobacter kobei","NCBI_taxonomy_id":"208224"}}}},"ARO_accession":"3007893","ARO_id":"46685","ARO_name":"ACT-110","CARD_short_name":"ACT-110","ARO_description":"Cephalosporin-hydrolyzing class C beta-lactamase ACT-110.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7312":{"model_id":"7312","model_name":"ACT-111","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10139":{"protein_sequence":{"accession":"RTM78732.1","sequence":"MMKKTLSCALLLSVASAAFAAPMSEKQLAEVVERTVTPLMNAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEITLGDPVTKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDTASLLRFYQNWQPKWKPGTTRLYANTSIGLFGALAVKPSGMSYEQAMTTRVFKPLKLDHTWINVPKAEEAHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVQDMASWVMVNMMPDSLQDSPLKHGIALAQSRYWRVGAMYQGLGWEMLNWPVDAQTVVGGSDNKVALAPLPAREVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILDALQ"},"dna_sequence":{"accession":"RXSJ01000003.1","fmin":"17151","fmax":"18297","strand":"-","sequence":"ATGATGAAAAAAACCCTAAGCTGTGCCCTGCTGCTCAGCGTTGCCAGCGCTGCATTCGCCGCACCGATGTCCGAAAAACAGCTGGCTGAGGTGGTGGAACGCACCGTTACGCCGCTGATGAACGCGCAGGCCATTCCGGGTATGGCGGTGGCGGTGATTTATCAGGGTCAGCCGCACTACTTTACCTTCGGTAAAGCTGATGTTGCAGCGAACAAACCCGTCACCCCGCAAACCTTGTTCGAGCTGGGTTCGATAAGTAAAACCTTCACCGGCGTATTGGGTGGTGATGCGATTGCGCGCGGTGAAATAACGCTGGGCGATCCGGTGACCAAATACTGGCCTGAGCTCACGGGCAAGCAGTGGCAGGGCATTCGCATGCTGGATCTGGCAACCTACACCGCAGGCGGTCTGCCGTTGCAGGTGCCGGATGAGGTCACGGATACCGCCTCCCTGCTGCGCTTTTATCAAAACTGGCAGCCAAAGTGGAAGCCGGGCACCACGCGTCTTTACGCTAACACCAGCATCGGTCTTTTTGGCGCGCTGGCGGTCAAACCCTCCGGCATGAGCTATGAGCAGGCCATGACGACGCGGGTCTTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTCCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGATACCGTGACGGTAAAGCGGTCCACGTTTCGCCAGGGATGCTGGACGCGGAAGCCTATGGCGTAAAAACCAACGTGCAGGATATGGCAAGCTGGGTGATGGTCAACATGATGCCGGACTCCCTTCAGGATTCCCCACTTAAACACGGTATTGCCCTGGCACAGTCTCGCTACTGGCGCGTGGGAGCCATGTATCAAGGATTGGGCTGGGAAATGCTGAACTGGCCGGTCGACGCCCAAACGGTAGTCGGGGGCAGCGACAATAAGGTGGCGCTGGCGCCGTTGCCTGCAAGAGAAGTGAATCCACCGGCACCACCGGTTAAGGCCTCCTGGGTCCATAAAACGGGCTCTACCGGCGGATTTGGCAGCTACGTGGCATTTATTCCTGAAAAGCAGCTCGGCATTGTGATGCTGGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCGTATACTCGACGCGCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"47909","NCBI_taxonomy_name":"Enterobacter quasiroggenkampii","NCBI_taxonomy_id":"2497436"}}}},"ARO_accession":"3007894","ARO_id":"46686","ARO_name":"ACT-111","CARD_short_name":"ACT-111","ARO_description":"Cephalosporin-hydrolyzing class C beta-lactamase ACT-111.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7313":{"model_id":"7313","model_name":"ACT-112","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10140":{"protein_sequence":{"accession":"WEG44939.1","sequence":"MMKKSLCCALLLSTSCAALAAPLSETQLAKVVERTVTPLMKAQSIPGMAVAVIYQGQPHYFTFGKADVAANTPVTAQTLFELGSISKTFTGVLGGDAIARGEMSLGDPVTKYWPELTGKQWQGVRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQYWQPQWAPGTTRLYANASIGLFGALAVKPSGMRFEQAMTERVLKPLNLNHTWINVPKAEEQHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVKDMASWVVANMAPDGVQDASLKQGMVLAQSRYWRTGSMYQGLGWEMLNWPVEAKTVVEGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKELGIVMLANKSYPNPARVEAAYRILSALQ"},"dna_sequence":{"accession":"OQ592375.1","fmin":"3","fmax":"1149","strand":"+","sequence":"ATGATGAAAAAATCCCTGTGCTGCGCTCTGCTGCTCAGCACCTCCTGCGCTGCATTAGCCGCACCTCTGTCAGAAACACAGCTGGCGAAGGTCGTGGAACGTACCGTTACGCCCCTGATGAAAGCGCAGTCTATTCCGGGTATGGCGGTCGCCGTGATCTATCAGGGCCAGCCGCACTACTTCACCTTCGGTAAGGCCGATGTCGCCGCGAACACACCCGTCACTGCACAAACGCTGTTTGAGCTGGGCTCAATCAGCAAAACCTTCACCGGCGTTCTGGGTGGCGATGCTATTGCTCGCGGTGAAATGTCGCTGGGCGATCCGGTGACCAAATACTGGCCTGAGCTGACCGGCAAACAGTGGCAGGGCGTTCGCATGCTGGACCTGGCAACCTATACTGCCGGTGGCCTGCCGTTACAGGTGCCCGATGAGGTTACCGATAATGCCTCGCTGCTGCGTTTTTACCAGTACTGGCAACCACAGTGGGCGCCAGGCACCACGCGTCTTTATGCGAATGCCAGCATCGGTCTGTTTGGGGCTCTGGCGGTGAAACCTTCTGGCATGCGCTTTGAGCAGGCGATGACGGAGCGGGTCCTGAAGCCGCTTAACCTGAACCATACGTGGATTAACGTTCCGAAGGCAGAAGAACAGCATTACGCCTGGGGTTATCGTGACGGTAAAGCGGTTCACGTTTCGCCGGGCATGCTCGATGCCGAAGCATATGGCGTGAAAACCAACGTGAAGGATATGGCGAGCTGGGTGGTGGCTAACATGGCCCCCGATGGGGTACAGGATGCCTCACTGAAGCAGGGCATGGTGCTTGCACAGTCTCGCTACTGGCGCACAGGCTCGATGTACCAGGGCCTGGGCTGGGAGATGCTCAACTGGCCGGTAGAAGCCAAAACCGTGGTGGAGGGCAGCGACAACAAAGTAGCGCTTGCACCGTTGCCCGTGGCAGAAGTGAACCCTCCTGCACCACCGGTAAAAGCGTCATGGGTACATAAAACAGGCTCGACGGGCGGATTTGGCAGCTACGTGGCATTTATTCCTGAGAAGGAACTCGGCATCGTTATGCTGGCGAACAAGAGCTACCCGAACCCGGCACGCGTGGAAGCGGCATACCGTATTCTGAGCGCTCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"45936","NCBI_taxonomy_name":"Enterobacter ludwigii","NCBI_taxonomy_id":"299767"}}}},"ARO_accession":"3007895","ARO_id":"46687","ARO_name":"ACT-112","CARD_short_name":"ACT-112","ARO_description":"Cephalosporin-hydrolyzing class C beta-lactamase ACT-112.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7314":{"model_id":"7314","model_name":"ACT-113","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10141":{"protein_sequence":{"accession":"WEG44940.1","sequence":"MMKKSLCCALLLGISCSALATPVSEKQLAEVVANTVTPLMKAQSVPGMAVAVIYQGKPHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALVVKPSGMPYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPENVADASLKQGIALAQSRYWRIGSMYQGLGWEMLKWPVEANTVVEGSDSKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANTSYPNPARVEAAYHILEALQ"},"dna_sequence":{"accession":"OQ592376.1","fmin":"3","fmax":"1149","strand":"+","sequence":"ATGATGAAAAAATCCCTTTGCTGCGCCCTGCTGCTCGGCATCTCTTGCTCTGCTCTCGCCACGCCAGTGTCAGAAAAACAGCTGGCGGAGGTGGTCGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCTGTTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGAAAACCGCACTATTACACGTTTGGCAAGGCCGATATCGCGGCGAATAAACCCGTTACGCCTCAGACCCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGCGTGTTAGGTGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTGACGGGCAAGCAGTGGCAGGGTATTCGTATGCTGGATCTCGCCACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGTGCGCTGGTGGTCAAACCTTCTGGCATGCCCTATGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTGCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGTATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCGGAGAACGTTGCTGATGCCTCACTTAAGCAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAAATGGCCCGTGGAGGCCAACACGGTGGTCGAGGGCAGCGACAGTAAGGTAGCGCTGGCGCCGTTGCCCGTGGCAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGCTCTACTGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATACAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCGAGGCGCTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3007896","ARO_id":"46688","ARO_name":"ACT-113","CARD_short_name":"ACT-113","ARO_description":"Cephalosporin-hydrolyzing class C beta-lactamase ACT-113.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7315":{"model_id":"7315","model_name":"ACT-115","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10142":{"protein_sequence":{"accession":"AXQ35263.1","sequence":"MMKKSLCCALLLGLSCSALAAPVSEKQLAEVVANTVTPLMKAQSVPGMAVAVIYQGKPHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMPYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPEKVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVVEGSDSKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANKSYPNPARVEAAYHILKALQ"},"dna_sequence":{"accession":"CP031726.1","fmin":"3150070","fmax":"3151216","strand":"-","sequence":"ATGATGAAAAAATCCCTTTGCTGCGCCCTGCTGCTGGGCCTCTCTTGCTCTGCTCTCGCCGCGCCAGTGTCAGAAAAACAGCTGGCGGAGGTGGTCGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCTGTTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGAAAACCGCACTATTACACGTTTGGCAAGGCCGATATCGCGGCGAATAAACCCGTTACGCCTCAGACCCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGCGTTTTAGGTGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTGACGGGCAAGCAGTGGCAGGGTATTCGTATGCTGGATCTCGCCACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTCAAACCTTCTGGCATGCCCTATGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTTCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGAATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCGGAGAAGGTTGCCGATGCCTCACTTAAGCAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGGTCGAAGGCAGCGACAGTAAGGTAGCGCTGGCGCCATTACCCGTGGCAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGTTCTACTGGCGGATTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCAAGGCGCTTCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39098","NCBI_taxonomy_name":"Enterobacter hormaechei","NCBI_taxonomy_id":"158836"}}}},"ARO_accession":"3007897","ARO_id":"46689","ARO_name":"ACT-115","CARD_short_name":"ACT-115","ARO_description":"Cephalosporin-hydrolyzing class C beta-lactamase ACT-115.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7316":{"model_id":"7316","model_name":"ACT-116","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10143":{"protein_sequence":{"accession":"WEY36194.1","sequence":"MMTKSLCCALLLSTSCSVLAAPMSEKQLAEVVERTVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMSYEQAITTRVFKPLKLDHTWINVPKAEEAHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVQDMASWVMVNMKPDSLQDSSLRKGITLAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVEGSDNKVALAPLPAREVNPPAPPVNASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILDALQ"},"dna_sequence":{"accession":"OQ642076.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGACTAAATCCCTTTGCTGCGCCCTGCTGCTCAGCACCTCCTGCTCGGTATTGGCTGCCCCGATGTCAGAAAAACAGCTGGCTGAGGTGGTGGAACGTACCGTTACGCCGCTGATGAAAGCGCAGGCCATTCCGGGTATGGCGGTGGCGGTGATTTATCAGGGTCAGCCGCACTACTTTACCTTCGGTAAAGCCGATGTTGCGGCGAACAAACCTGTCACCCCACAAACCTTATTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGCGTACTCGGCGGCGATGCCATTGCTCGCGGTGAAATATCGCTGGGCGATCCGGTGACAAAATACTGGCCTGAGCTGACAGGCAAGCAGTGGCAGGGGATCCGAATGCTGGATCTGGCAACCTATACCGCAGGTGGTTTGCCGTTACAGGTACCGGATGAGGTCACGGATAACGCCTCTCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCGGGCACCACGCGTCTTTATGCCAACGCCAGCATCGGTCTTTTTGGCGCGCTGGCGGTCAAACCTTCCGGCATGAGCTATGAGCAGGCCATAACGACGCGGGTCTTTAAGCCGCTCAAGCTGGACCATACATGGATTAACGTTCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGATACCGCGACGGTAAGGCGGTACACGTTTCGCCAGGCATGCTGGACGCTGAAGCCTATGGCGTAAAAACCAACGTGCAGGATATGGCAAGCTGGGTAATGGTCAACATGAAGCCGGACTCGCTTCAGGATAGTTCACTCAGGAAAGGCATTACCCTGGCGCAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAGGGTTTAGGCTGGGAAATGCTTAACTGGCCGGTCGATGCAAAAACCGTGGTTGAAGGTAGCGACAATAAGGTGGCGCTGGCACCGCTGCCTGCGAGAGAAGTGAATCCACCGGCGCCCCCGGTCAACGCATCCTGGGTCCATAAAACCGGCTCTACCGGCGGGTTTGGCAGCTACGTGGCATTTATTCCTGAAAAGCAGCTCGGCATTGTGATGCTGGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCGTATCCTCGACGCGCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3007898","ARO_id":"46690","ARO_name":"ACT-116","CARD_short_name":"ACT-116","ARO_description":"Cephalosporin-hydrolyzing class C beta-lactamase ACT-116.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7317":{"model_id":"7317","model_name":"ACT-117","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10144":{"protein_sequence":{"accession":"WEY36195.1","sequence":"MMKKSLCCALLLSTSCAALAAPMSETQLAKVVERTVTPLMKAQSIPGMAVAVIYQGQPHYFTFGKADVAANTPVTAQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPELTGKQWQGVRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQSWQPQWAPGTTRLYANASIGLFGALAVKPSGMRFEQAMTERVLKPLNLNHTWINVPKSEEQHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVKDMASWVVANMAPDGIQDASLKQGMVLAQSRYWRTGSMYQGLGWEMLNWPVEAKTVVEGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKELGIVMLANKSYPNPARVEAAYRILSALQ"},"dna_sequence":{"accession":"OQ642077.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCCCTGTGCTGCGCCCTGCTGCTCAGCACCTCCTGCGCTGCATTAGCCGCACCTATGTCAGAAACACAACTGGCGAAGGTCGTGGAACGTACCGTTACGCCCCTGATGAAAGCGCAGTCTATTCCGGGTATGGCGGTCGCCGTGATCTATCAGGGCCAGCCGCACTACTTCACCTTCGGCAAGGCCGATGTCGCCGCGAACACACCCGTCACTGCACAAACGCTGTTTGAGCTGGGCTCAATCAGCAAAACTTTCACCGGCGTTCTGGGTGGCGATGCTATTGCTCGCGGTGAAATTTCGCTGGGCGATCCGGTGACCAAATACTGGCCTGAGCTGACCGGCAAACAGTGGCAGGGCGTTCGCATGCTGGACCTGGCAACCTATACTGCCGGTGGCCTGCCGTTACAGGTGCCCGATGAGGTTACCGATAATGCCTCGCTGCTACGTTTTTACCAGTCCTGGCAACCACAGTGGGCGCCAGGCACCACGCGTCTTTATGCAAATGCCAGCATCGGTCTGTTTGGGGCTCTGGCGGTGAAACCTTCTGGCATGCGCTTTGAGCAGGCGATGACAGAGCGGGTCCTGAAGCCGCTTAACCTGAACCATACGTGGATTAACGTTCCGAAGTCAGAAGAACAGCATTACGCCTGGGGTTATCGTGACGGTAAAGCGGTTCACGTTTCGCCGGGCATGCTCGACGCCGAAGCGTATGGCGTGAAAACCAACGTGAAGGATATGGCGAGCTGGGTGGTGGCTAACATGGCCCCCGATGGCATACAGGATGCCTCACTGAAGCAGGGCATGGTGCTTGCACAGTCTCGCTACTGGCGCACAGGCTCGATGTACCAGGGCCTGGGCTGGGAGATGCTCAACTGGCCGGTAGAAGCCAAAACCGTGGTGGAGGGCAGCGACAACAAGGTGGCGCTTGCACCGTTGCCCGTGGCAGAAGTGAACCCTCCGGCTCCACCGGTAAAAGCGTCATGGGTACATAAAACAGGCTCGACGGGCGGATTTGGCAGCTACGTGGCATTTATCCCTGAGAAGGAACTCGGCATTGTTATGCTGGCGAACAAGAGCTACCCGAACCCGGCACGCGTGGAAGCGGCATACCGTATTCTGAGCGCTCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3007899","ARO_id":"46691","ARO_name":"ACT-117","CARD_short_name":"ACT-117","ARO_description":"Cephalosporin-hydrolyzing class C beta-lactamase ACT-117.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7318":{"model_id":"7318","model_name":"ACT-118","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10145":{"protein_sequence":{"accession":"WEY36196.1","sequence":"MIKKSLCCALLLGVSCSSIAASMTEKQLADVVEKSITPLMKAQSIPGMAIAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAVARGEISLGDPVIKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDSASLQRFYQTWQPQWKPGTTRLYANASIGLFGALAVKPSGMGFEQAMTTRVFKPLGLDHTWINVPKAEEAHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVQDMASWVVANMAPDNVQDASLKQGITLAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVEGSDNKVALAPLPAREVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILDALQ"},"dna_sequence":{"accession":"OQ642078.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATCAAAAAATCCCTTTGCTGCGCCCTGCTGCTCGGCGTGTCATGCTCCAGCATTGCTGCGTCGATGACAGAAAAACAGCTGGCTGACGTGGTGGAAAAAAGCATTACCCCCCTGATGAAAGCGCAGTCCATTCCGGGCATGGCGATTGCCGTGATCTACCAGGGCCAGCCGCACTATTTTACTTTTGGTAAAGCCGATGTTGCAGCGAACAAACCTGTTACCCCACAAACCCTGTTCGAACTAGGTTCTATCAGTAAAACTTTCACCGGCGTATTGGGCGGCGATGCTGTTGCCCGCGGTGAGATATCGCTGGGCGATCCGGTTATAAAGTACTGGCCTGAGCTGACGGGCAAGCAGTGGCAGGGGATTCGCATGCTGGATCTGGCGACCTATACCGCGGGAGGGTTACCGCTCCAGGTGCCGGATGAGGTGACAGACAGCGCGTCGCTGCAGCGCTTTTACCAGACATGGCAGCCGCAGTGGAAACCTGGCACCACGCGATTGTATGCGAACGCCAGCATCGGTCTGTTTGGCGCACTGGCGGTTAAACCTTCCGGCATGGGCTTTGAACAGGCCATGACGACGCGGGTCTTTAAACCGCTCGGGCTCGACCATACGTGGATCAACGTTCCGAAAGCAGAAGAGGCACATTACGCCTGGGGATACCGTGACGGTAAAGCGGTCCACGTGTCACCGGGGATGCTGGATGCCGAAGCCTACGGCGTGAAAACCAACGTGCAGGATATGGCGAGCTGGGTGGTGGCCAATATGGCTCCGGATAACGTTCAGGACGCATCGCTGAAGCAAGGCATTACGCTGGCGCAGTCGCGCTACTGGCGCGTGGGGGCCATGTATCAGGGATTAGGCTGGGAAATGCTTAACTGGCCGGTCGATGCCAAAACCGTGGTTGAAGGTAGCGACAACAAGGTCGCGCTGGCCCCCCTGCCTGCGAGAGAAGTGAATCCTCCGGCACCTCCGGTAAAAGCCTCATGGGTGCACAAAACCGGCTCCACCGGCGGATTCGGCAGCTATGTGGCCTTTATCCCGGAGAAGCAGCTTGGCATCGTGATGCTGGCGAACAAGAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCGTATCCTCGACGCGCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3007900","ARO_id":"46692","ARO_name":"ACT-118","CARD_short_name":"ACT-118","ARO_description":"Cephalosporin-hydrolyzing class C beta-lactamase ACT-118.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7319":{"model_id":"7319","model_name":"ACT-119","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10146":{"protein_sequence":{"accession":"WEY36198.1","sequence":"MMKKSLCCALLLGISCSALAAPVSDKQLAQVVADTITPLMKAQSIPGMAVAVIYQGKPHYYTFGKADVAANKPVTPDTLFELGSISKTFTGVLGGDAVARGEISLGDPVTKYWPELTGTQWQGIRMLDLATYTTGGLPLQVPDEVTDDASLLRFCQRWQPQWKPGTTRLYANASIGLFGALAVKPSGMRYEQAMTERVFKPLALHHTWINVPEAEEKNYAWGYRDGKAVHVSPGMLDAEAYGVKTNVQDMAGWVMANMAPEKVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEAKTVVEGSDGKVALAALPAVEVIPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANKSYPNPARVDAGYRILSALK"},"dna_sequence":{"accession":"OQ642080.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCCCTTTGCTGCGCCCTGCTGCTCGGCATTTCTTGCTCTGCTCTGGCCGCGCCGGTGTCGGATAAACAGCTGGCGCAGGTGGTCGCGGATACGATTACGCCGCTGATGAAAGCCCAGTCCATTCCCGGCATGGCGGTGGCCGTTATTTATCAGGGTAAACCGCACTACTACACCTTCGGCAAAGCCGACGTCGCGGCCAACAAACCGGTCACCCCAGATACCCTGTTCGAGCTGGGCTCTATAAGTAAAACCTTCACCGGGGTATTGGGTGGGGATGCTGTCGCTCGCGGTGAAATTTCGCTGGGCGATCCGGTGACCAAATACTGGCCTGAGCTGACAGGCACGCAGTGGCAGGGCATTCGGATGCTGGATCTGGCGACCTACACCACCGGCGGTTTGCCGCTACAGGTACCGGATGAGGTGACGGATGACGCCTCCCTGCTGCGCTTCTGTCAACGGTGGCAGCCGCAGTGGAAGCCGGGCACAACGCGTCTTTATGCAAACGCCAGCATCGGCCTGTTCGGGGCGCTGGCGGTTAAACCTTCCGGCATGCGTTACGAGCAGGCAATGACCGAGCGGGTATTTAAACCGCTGGCGCTGCATCACACCTGGATTAACGTTCCAGAAGCGGAAGAGAAAAATTACGCCTGGGGCTACCGTGACGGTAAAGCCGTTCACGTTTCGCCGGGAATGCTGGACGCGGAAGCCTATGGCGTCAAAACCAACGTGCAGGATATGGCTGGCTGGGTGATGGCAAACATGGCACCGGAGAAGGTCGCTGACGCCTCACTTAAGCAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGGATAGGTTCAATGTACCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCGGTGGAGGCCAAAACGGTGGTCGAGGGGAGTGACGGCAAGGTGGCGCTGGCCGCCTTGCCGGCGGTCGAGGTAATTCCTCCGGCACCGCCTGTAAAAGCCTCCTGGGTGCACAAAACCGGATCGACTGGCGGGTTCGGCAGCTACGTGGCCTTTATTCCGGAAAAACAGATCGGCATCGTGATGCTGGCGAATAAAAGTTACCCCAACCCGGCGCGCGTTGACGCGGGTTATCGTATTTTGAGCGCGCTGAAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3007901","ARO_id":"46693","ARO_name":"ACT-119","CARD_short_name":"ACT-119","ARO_description":"Cephalosporin-hydrolyzing class C beta-lactamase ACT-119.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7320":{"model_id":"7320","model_name":"ACT-120","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10147":{"protein_sequence":{"accession":"WLO97150.1","sequence":"MMKKSLCCALLLSTSCSVFAAPMSDKQLADVVERTITPLMKAQAIPGMAVAVIYQDQPHYFTFGIADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLTDPATKYWPELSGKQWQGIRLLDLATYTAGGLPLQVPDEVTDNASMLRFYQNWQPQWKRGTTRLYANSSIGLFGALAVKPSDMSYAQAMTQRVFKPLALHHTWINVPKAEEEHYAWGYRDGKPVHVSPGALDAEAYGVKSNVQDMASWVMTNMAPENIADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVDAKTVVDGSGNKVALAPLPAVEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANKSYPNPVRVEAAYHILDALQ"},"dna_sequence":{"accession":"OR398187.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCCCTTTGCTGTGCCCTGCTGCTCAGCACCTCTTGCTCTGTGTTCGCCGCGCCAATGTCAGATAAACAGCTGGCTGACGTGGTGGAACGTACCATTACGCCGTTGATGAAAGCCCAGGCCATTCCAGGAATGGCGGTTGCAGTGATTTATCAGGATCAGCCGCACTACTTTACCTTCGGCATTGCTGATGTCGCGGCGAACAAACCTGTCACCCCGCAAACCTTATTTGAGCTGGGCTCTATTAGTAAAACCTTCACCGGCGTTTTAGGTGGGGATGCCATTGCTCGCGGTGAGATTTCACTCACCGATCCGGCCACAAAATACTGGCCAGAATTGTCGGGCAAACAGTGGCAGGGGATTCGCCTGCTCGATCTGGCGACCTATACCGCTGGCGGTCTGCCCTTGCAGGTACCGGACGAGGTTACGGATAACGCCTCTATGCTGCGCTTCTATCAAAACTGGCAGCCACAGTGGAAGCGAGGCACCACGCGCCTTTATGCGAATTCCAGCATTGGTCTTTTTGGTGCACTGGCGGTTAAACCTTCCGACATGAGCTATGCGCAGGCCATGACGCAGCGAGTGTTTAAACCGCTGGCGCTGCATCACACCTGGATTAACGTTCCGAAAGCTGAAGAGGAGCATTACGCCTGGGGCTACCGCGATGGCAAACCGGTACACGTTTCGCCAGGCGCGCTGGACGCTGAAGCCTATGGCGTGAAAAGCAACGTGCAAGATATGGCGAGCTGGGTGATGACAAATATGGCGCCGGAGAACATTGCTGATGCGTCACTTAAGCAAGGGATCGCGCTGGCACAGTCTCGTTACTGGCGCATCGGATCCATGTATCAGGGGCTGGGCTGGGAGATGCTCAACTGGCCAGTAGACGCCAAAACTGTAGTCGACGGTAGCGGCAATAAAGTGGCATTAGCACCGCTGCCAGCGGTAGAAGTGAACCCTCCGGCGCCGCCTGTAAAAGCATCATGGGTACATAAAACCGGGTCGACGGGTGGGTTTGGCAGCTACGTGGCATTTATTCCTGAAAAGCAGATCGGTATTGTAATGCTCGCGAATAAAAGCTATCCGAACCCGGTACGCGTTGAGGCGGCATACCATATCCTCGACGCGCTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39098","NCBI_taxonomy_name":"Enterobacter hormaechei","NCBI_taxonomy_id":"158836"}}}},"ARO_accession":"3007902","ARO_id":"46694","ARO_name":"ACT-120","CARD_short_name":"ACT-120","ARO_description":"Cephalosporin-hydrolyzing class C beta-lactamase ACT-120.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7321":{"model_id":"7321","model_name":"ACT-121","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10148":{"protein_sequence":{"accession":"WLO97151.1","sequence":"MMKKSLCCALLLSTSCSVFAAPMSDKQLADVVERTITPLMKAQAIPGMAVAVIYQDQPHYFTFGIADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLTDPATKYWPELSGKQWQGIRLLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANSSIGLFGALAVKPSDMSYAQAMTQRVFKPLALHHTWINVPKAEEEHYAWGYRDGKPVHVSPGALDAEAYGVKSNVQDMASWVMTNMAPENVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVDAKTVVDGSGNKVALAPLPAVEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANKSYPNPVRVEAAYHILDALQ"},"dna_sequence":{"accession":"OR398188.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCCCTTTGCTGTGCCCTGCTGCTCAGCACCTCTTGCTCTGTGTTCGCCGCGCCAATGTCAGATAAACAGCTGGCTGACGTGGTGGAACGTACCATTACGCCGTTGATGAAAGCCCAGGCCATTCCAGGAATGGCGGTTGCAGTGATTTATCAGGATCAGCCGCACTACTTTACCTTCGGCATTGCTGATGTCGCGGCGAACAAACCTGTCACCCCGCAAACCTTATTTGAGCTAGGCTCTATTAGTAAAACCTTCACCGGCGTTTTAGGTGGGGATGCCATTGCTCGCGGTGAGATTTCACTCACCGATCCGGCCACAAAATACTGGCCAGAATTGTCGGGCAAACAGTGGCAGGGGATTCGCCTGCTCGATCTGGCGACCTATACCGCTGGCGGTCTGCCCTTGCAGGTACCGGACGAGGTTACGGATAATGCCTCTCTGCTGCGCTTCTATCAAAACTGGCAGCCACAGTGGAAGCCAGGCACCACGCGCCTTTATGCGAATTCCAGCATTGGTCTTTTTGGTGCACTGGCGGTTAAACCTTCCGACATGAGCTATGCGCAGGCCATGACGCAGCGAGTGTTTAAACCGCTGGCGCTACATCACACCTGGATTAACGTTCCGAAAGCTGAAGAGGAGCATTACGCCTGGGGCTACCGCGATGGCAAACCGGTACACGTTTCGCCAGGCGCGCTGGACGCTGAAGCCTATGGCGTGAAAAGCAACGTGCAAGATATGGCGAGCTGGGTGATGACAAATATGGCGCCGGAGAACGTTGCTGATGCGTCACTTAAGCAAGGGATCGCGCTGGCACAGTCTCGTTACTGGCGCATCGGATCCATGTATCAGGGGCTGGGCTGGGAGATGCTCAACTGGCCAGTAGACGCCAAAACTGTAGTCGACGGTAGCGGCAATAAAGTGGCACTGGCACCGCTGCCAGCGGTAGAAGTGAACCCTCCGGCGCCGCCTGTAAAAGCATCATGGGTACATAAAACCGGGTCGACGGGTGGGTTTGGCAGCTACGTGGCATTTATTCCTGAAAAGCAGATCGGTATTGTAATGCTCGCGAATAAAAGCTATCCGAACCCGGTACGCGTCGAGGCGGCATACCATATCCTCGACGCGCTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39098","NCBI_taxonomy_name":"Enterobacter hormaechei","NCBI_taxonomy_id":"158836"}}}},"ARO_accession":"3007903","ARO_id":"46695","ARO_name":"ACT-121","CARD_short_name":"ACT-121","ARO_description":"Cephalosporin-hydrolyzing class C beta-lactamase ACT-121.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7322":{"model_id":"7322","model_name":"ACT-122","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10149":{"protein_sequence":{"accession":"WLO97152.1","sequence":"MMKKSLCCALLLGISCSALATPVSEKQLAEMVANTVTPLMKAQSVPGMAVAVIYQGKPHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMPYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPEKVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVVEGSDSKVALAPLPVVEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANTSYPNPARVEAAYHILEALQ"},"dna_sequence":{"accession":"OR398189.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCCCTTTGCTGCGCCCTGCTGCTCGGCATCTCTTGCTCTGCTCTCGCCACGCCAGTGTCAGAAAAACAGCTGGCGGAGATGGTAGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCTGTTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGAAAACCGCACTATTACACGTTTGGCAAGGCCGATATCGCGGCGAATAAACCCGTTACGCCTCAGACCCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGCGTTTTAGGTGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTGACGGGCAAGCAGTGGCAGGGTATTCGTATGCTGGATCTCGCCACCTACACCGCTGGCGGTCTGCCGCTACAGGTACCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTCAAACCTTCTGGCATGCCCTATGAGCAAGCCATGACGACACGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTGCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGTATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCGGAGAAGGTTGCTGATGCCTCACTTAAGCAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGGTCGAGGGCAGCGACAGTAAGGTAGCGCTGGCGCCGTTGCCCGTGGTAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGCTCTACTGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATACAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCGAGGCGCTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39098","NCBI_taxonomy_name":"Enterobacter hormaechei","NCBI_taxonomy_id":"158836"}}}},"ARO_accession":"3007904","ARO_id":"46696","ARO_name":"ACT-122","CARD_short_name":"ACT-122","ARO_description":"Cephalosporin-hydrolyzing class C beta-lactamase ACT-122.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7323":{"model_id":"7323","model_name":"ACT-123","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10150":{"protein_sequence":{"accession":"WLO97153.1","sequence":"MMKKSLCCALLLGISCSALATPVSEKQLAEVVANTVTPLMKAQSVPGMAVAVIYQGKPHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTHLYANASIGLFGALAVKPSGMPYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPENVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVVEGSDSKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANTSYPNPARVEAAYHILEALQ"},"dna_sequence":{"accession":"OR398190.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCCCTTTGCTGCGCCCTGCTGCTCGGCATCTCTTGCTCTGCTCTCGCCACGCCAGTGTCAGAAAAACAGCTGGCGGAGGTGGTAGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCTGTTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGAAAACCGCACTATTACACGTTTGGCAAGGCCGATATCGCGGCGAATAAACCCGTTACGCCTCAGACCCTGTTCGAGCTAGGTTCTATAAGTAAAACCTTCACCGGCGTGTTAGGTGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTGACGGGCAAGCAGTGGCAGGGTATTCGTATGCTGGATCTCGCCACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCATCTTTACGCCAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTCAAACCTTCTGGCATGCCCTATGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTGCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGTATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCACCGGAGAACGTTGCTGATGCCTCACTTAAACAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGGTCGAGGGCAGCGACAGTAAGGTAGCGCTGGCGCCGTTGCCCGTGGCAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGCTCTACTGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATACAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCGAGGCGCTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39098","NCBI_taxonomy_name":"Enterobacter hormaechei","NCBI_taxonomy_id":"158836"}}}},"ARO_accession":"3007905","ARO_id":"46697","ARO_name":"ACT-123","CARD_short_name":"ACT-123","ARO_description":"Cephalosporin-hydrolyzing class C beta-lactamase ACT-123.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7324":{"model_id":"7324","model_name":"ACT-124","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10151":{"protein_sequence":{"accession":"WLO97154.1","sequence":"MMKKSLCCAVLLGISCSALAAPVSQKQLAEVVTNTITPLMKAQSVPGMAVAVIYQGKPHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARSEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPNEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMPYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMVNMAPEKVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEAKTVVEGSDSKVALAALPAVEINPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANKSYPNPARVEAAYHILEALQ"},"dna_sequence":{"accession":"OR398191.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCCCTTTGCTGCGCCGTGCTGCTCGGCATCTCTTGCTCTGCTCTCGCCGCGCCCGTATCACAAAAACAGCTGGCGGAGGTGGTCACGAATACGATTACCCCGCTGATGAAAGCCCAGTCTGTTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGAAAACCGCACTATTATACGTTTGGCAAGGCCGATATCGCGGCGAATAAACCCGTTACGCCTCAGACTCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGCGTTTTAGGTGGGGATGCCATTGCTCGCAGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTGACGGGCAAGCAGTGGCAGGGTATTCGTATGCTGGATCTCGCAACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGAATGAGGTCACGGATAACGCCTCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTCAAACCTTCTGGCATGCCCTATGAGCAAGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTGCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGTATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGTAAACATGGCGCCGGAGAAGGTTGCTGATGCCTCACTTAAGCAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTACCAGGGGCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCAAAAACGGTGGTCGAGGGCAGCGACAGTAAGGTGGCGCTGGCCGCCTTGCCTGCGGTCGAAATAAATCCTCCGGCTCCGCCTGTAAAAGCCTCCTGGGTGCACAAAACCGGGTCGACGGGCGGGTTCGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGCATCGTGATGCTCGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCGAGGCGCTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39098","NCBI_taxonomy_name":"Enterobacter hormaechei","NCBI_taxonomy_id":"158836"}}}},"ARO_accession":"3007906","ARO_id":"46698","ARO_name":"ACT-124","CARD_short_name":"ACT-124","ARO_description":"Cephalosporin-hydrolyzing class C beta-lactamase ACT-124.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7325":{"model_id":"7325","model_name":"ACT-131","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10152":{"protein_sequence":{"accession":"KUQ42458.1","sequence":"MMKKSLCCALLLSTSCAALAAPLSETQLAKVVERTVTPLMKAQSIPGMAVAVIYQGQPHYFTFGKADVAANTPVTAQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPELTGKQWQGVRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQSWQPQWAPGTTRLYANASIGLFGALAVKPSGMRFEQAMTERVLKPLNLNHTWINVPKSEEPHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVKDMASWVVANMAPDGVQDASLKQGMVLAQSRYWRTGSMYQGLGWEMLNWPVEAKTVVEGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKELGIVMLANKSYPNPARVEAAYRILSALQ"},"dna_sequence":{"accession":"LRCI01000124.1","fmin":"14945","fmax":"16091","strand":"-","sequence":"ATGATGAAAAAATCCCTGTGCTGCGCCCTGCTGCTCAGCACCTCCTGCGCTGCATTAGCCGCACCTCTGTCAGAAACACAGCTGGCGAAGGTCGTGGAACGTACCGTTACGCCCCTGATGAAAGCGCAGTCTATTCCGGGTATGGCGGTCGCCGTGATCTATCAGGGCCAGCCGCACTACTTCACCTTCGGCAAGGCCGATGTCGCAGCGAACACACCCGTCACTGCACAAACGCTGTTTGAGCTGGGCTCAATCAGCAAAACCTTCACCGGCGTTCTGGGTGGCGATGCTATTGCTCGCGGTGAAATTTCGCTGGGCGATCCGGTGACCAAATACTGGCCTGAGCTGACCGGCAAACAGTGGCAGGGCGTTCGCATGCTGGACCTGGCAACCTATACTGCCGGTGGCCTGCCGTTACAGGTGCCCGATGAGGTTACCGATAATGCCTCGCTGCTGCGTTTTTACCAGTCCTGGCAACCACAGTGGGCGCCAGGCACCACGCGTCTTTATGCAAATGCCAGCATCGGTCTGTTTGGGGCTCTGGCGGTGAAACCTTCTGGCATGCGCTTTGAGCAGGCGATGACGGAGCGGGTCCTGAAGCCGCTTAACCTGAACCATACGTGGATTAACGTTCCGAAGTCAGAAGAACCGCATTACGCCTGGGGTTATCGTGACGGTAAAGCGGTTCACGTTTCGCCCGGCATGCTCGATGCCGAAGCATATGGCGTGAAAACCAACGTGAAGGATATGGCGAGCTGGGTGGTGGCTAACATGGCCCCCGATGGGGTACAGGATGCCTCACTGAAGCAGGGCATGGTGCTTGCACAGTCTCGCTACTGGCGCACAGGCTCGATGTACCAGGGCCTGGGCTGGGAGATGCTCAACTGGCCGGTAGAAGCCAAAACCGTGGTGGAGGGCAGCGACAACAAGGTAGCACTTGCACCGTTGCCCGTGGCAGAAGTGAACCCTCCTGCTCCACCGGTAAAAGCGTCATGGGTGCATAAAACAGGCTCGACGGGCGGATTTGGCAGCTACGTGGCATTTATTCCTGAGAAGGAACTCGGCATCGTTATGCTGGCGAACAAGAGCTACCCGAACCCGGCACGCGTGGAAGCGGCATACCGTATTCTGAGCGCTCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"45936","NCBI_taxonomy_name":"Enterobacter ludwigii","NCBI_taxonomy_id":"299767"}}}},"ARO_accession":"3007907","ARO_id":"46699","ARO_name":"ACT-131","CARD_short_name":"ACT-131","ARO_description":"Cephalosporin-hydrolyzing class C beta-lactamase ACT-131.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7326":{"model_id":"7326","model_name":"ACT-140","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10153":{"protein_sequence":{"accession":"HDR2669832.1","sequence":"MMKKFLCCALLLSTSCSVLAAPMSEKQLADMVERNVTPLMKAQGIPGMAVAVIYQGQPHYFTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPDLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANSSIGLFGALAVKPSGMSYEQAMTTRVLKPLKLDHTWINVPKAEETHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVQDIASWVMANMAPDALQDTSLKQGITLAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVGGSDNKVALAPLPAREVSPPVPPVKASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILDALQ"},"dna_sequence":{"accession":"DAOHVV010000003.1","fmin":"383117","fmax":"384263","strand":"+","sequence":"ATGATGAAAAAATTCCTTTGCTGCGCCCTGCTGCTCAGCACATCCTGCTCTGTACTCGCCGCGCCGATGTCGGAAAAACAGCTGGCTGACATGGTAGAACGTAACGTTACGCCCCTGATGAAAGCGCAGGGTATTCCAGGCATGGCGGTGGCCGTGATTTATCAGGGCCAGCCACACTACTTTACCTTTGGAAAGGCCGATATCGCGGCGAACAAACCCGTCACCCCGCAAACCCTGTTCGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTGCTGGGGGGCGATGCTATTGCCCGCGGCGAAATTTCGCTGGGCGATCCGGTAACCAAATATTGGCCTGATCTGACCGGCAAGCAGTGGCAAGGGATTCGCATGCTGGATCTGGCAACCTACACCGCCGGTGGCCTGCCTTTACAGGTGCCCGATGAGGTCACAGATAACGCATCCCTGCTGCGCTTCTATCAAAACTGGCAGCCTCAGTGGAAGCCGGGCACAACGCGTCTTTACGCCAACTCCAGCATCGGTCTTTTTGGCGCGCTGGCGGTCAAACCTTCCGGCATGAGCTATGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGATCATACCTGGATTAACGTTCCGAAAGCGGAGGAGACGCATTACGCCTGGGGATATCGTGACGGTAAAGCGGTCCACGTTTCACCGGGCATGCTGGACGCAGAGGCATATGGCGTGAAAACCAACGTGCAGGATATAGCGAGCTGGGTGATGGCCAATATGGCCCCTGACGCACTGCAGGATACGTCCCTGAAGCAAGGCATTACGCTGGCGCAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAGGGGTTAGGTTGGGAGATGCTTAACTGGCCGGTCGATGCCAAAACCGTCGTCGGAGGCAGTGATAACAAGGTGGCGCTGGCACCGTTGCCTGCGAGAGAAGTGAGTCCACCCGTTCCCCCGGTTAAGGCCTCATGGGTGCACAAAACGGGCTCAACCGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGCTCGGCATTGTGATGCTGGCAAATAAAAGCTACCCGAACCCGGCGCGAGTTGAGGCGGCATACCGTATCCTCGACGCGCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"47906","NCBI_taxonomy_name":"Enterobacter bugandensis","NCBI_taxonomy_id":"881260"}}}},"ARO_accession":"3007908","ARO_id":"46700","ARO_name":"ACT-140","CARD_short_name":"ACT-140","ARO_description":"Cephalosporin-hydrolyzing class C beta-lactamase ACT-140.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7327":{"model_id":"7327","model_name":"ACT-141","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10154":{"protein_sequence":{"accession":"KTJ22338.1","sequence":"MMKKSLCCALLLGLSCSALAAPVSEKQLAEVVANTVTPLMKAQSVPGMAVAVIYQGKSHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDALARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMPYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPEKVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVVEGSDSKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANKSYPNPARVEAAYHILEALQ"},"dna_sequence":{"accession":"LPPY01000058.1","fmin":"457269","fmax":"458415","strand":"+","sequence":"ATGATGAAAAAATCCCTTTGCTGCGCCCTGCTGCTGGGCCTCTCTTGCTCTGCTCTCGCCGCGCCAGTGTCAGAAAAACAGCTGGCGGAGGTGGTCGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCTGTTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGAAAATCGCACTATTACACGTTTGGCAAGGCCGATATCGCGGCGAATAAACCCGTTACGCCTCAGACCCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGCGTTTTAGGTGGGGATGCCCTTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTGACGGGCAAGCAGTGGCAGGGTATTCGTATGCTGGATCTCGCCACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTCAAACCTTCTGGCATGCCCTATGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTTCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGAATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCGGAGAAGGTTGCCGATGCCTCACTTAAGCAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGGTCGAAGGCAGCGACAGTAAGGTAGCGCTGGCGCCGTTACCCGTGGCAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGTTCTACTGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCGAGGCGCTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39098","NCBI_taxonomy_name":"Enterobacter hormaechei","NCBI_taxonomy_id":"158836"}}}},"ARO_accession":"3007909","ARO_id":"46701","ARO_name":"ACT-141","CARD_short_name":"ACT-141","ARO_description":"Cephalosporin-hydrolyzing class C beta-lactamase ACT-141.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7328":{"model_id":"7328","model_name":"ACT-142","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10155":{"protein_sequence":{"accession":"EMC7919385.1","sequence":"MKTKSLCCALLLSTSCSVLAAPMSEKQLSDVVERTVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVAKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQHWQPQWKPGTTRLYANASIGLFGALAVKPSGMSFEQAMTKRVFKPLKLDHTWINVPKEEEAYYAWGYRDGKAVHVSPGMLDAEAYGVKTNVQDMASWVKANMNPAALPDSTLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVEAKTVVEGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKELGIVMLANKSYPNPARVEAAYRILSALQ"},"dna_sequence":{"accession":"ABPSFX010000064.1","fmin":"13703","fmax":"14849","strand":"+","sequence":"ATGAAGACAAAATCCCTTTGCTGTGCCCTGCTGCTCAGCACCTCCTGCTCTGTTCTCGCCGCGCCGATGTCAGAGAAACAGCTGTCTGACGTGGTGGAACGTACCGTTACCCCCCTGATGAAAGCGCAAGCCATTCCGGGCATGGCGGTAGCGGTGATTTATCAGGGTCAGCCGCACTACTTTACCTTCGGAAAGGCCGATGTTGCGGCGAACAAACCTGTCACCCCGCAAACCCTGTTTGAGCTGGGCTCTATAAGTAAAACCTTCACTGGCGTATTAGGTGGCGATGCGATTGCGCGCGGAGAAATATCGCTGGGCGACCCCGTGGCAAAGTACTGGCCCGAGCTAACAGGCAAGCAGTGGCAGGGTATTCGCATGTTGGATCTGGCGACCTACACCGCGGGTGGCCTGCCGCTACAGGTGCCGGATGAGGTCACGGATAACGCCTCCCTACTGCGCTTCTATCAACACTGGCAACCGCAGTGGAAACCAGGCACAACGCGTCTTTATGCGAACGCCAGCATCGGGCTTTTTGGCGCCCTCGCGGTTAAACCCTCCGGTATGAGCTTTGAACAGGCCATGACGAAGCGGGTCTTCAAGCCACTCAAACTGGACCATACATGGATTAACGTTCCGAAAGAAGAAGAGGCGTATTACGCCTGGGGATACCGTGATGGTAAAGCGGTCCACGTTTCACCGGGAATGTTGGATGCCGAAGCGTATGGTGTCAAAACCAACGTCCAGGATATGGCGAGCTGGGTGAAGGCCAACATGAACCCTGCCGCTCTTCCGGATTCAACGCTGAAACAGGGTATTGCCCTGGCACAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCGGTAGAAGCCAAAACCGTCGTGGAGGGCAGCGATAACAAGGTGGCTCTTGCACCGTTACCGGTGGCAGAAGTGAACCCTCCAGCTCCGCCAGTAAAAGCATCATGGGTACATAAAACAGGCTCGACGGGTGGATTCGGCAGCTATGTCGCATTTATTCCTGAGAAGGAACTCGGCATTGTTATGCTGGCGAACAAGAGCTACCCGAACCCGGCGCGCGTGGAAGCGGCATACCGTATTCTGAGCGCTCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39773","NCBI_taxonomy_name":"Enterobacter kobei","NCBI_taxonomy_id":"208224"}}}},"ARO_accession":"3007910","ARO_id":"46702","ARO_name":"ACT-142","CARD_short_name":"ACT-142","ARO_description":"Cephalosporin-hydrolyzing class C beta-lactamase ACT-142.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7329":{"model_id":"7329","model_name":"ACT-143","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10156":{"protein_sequence":{"accession":"AMZ75637.1","sequence":"MKTKSLCCALLLSTSCSVLAAPMSEKQLSDVVERTVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVTANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNTSLLRFYQHWQPQWKPGTTRLYANASIGLFGALAVKPSGMNFEQAMTKRVFKPLKLDHTWINVPKEEEAHYAWGYRDGKAIHVSPGMLDAEAYGVKTNIQDMASWLKANMNPDALSDSTLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVEAKTVVEGSDNKVALAPLLVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKELGIVMLANKSYPNPARVEAAYRILSALQ"},"dna_sequence":{"accession":"CP015227.1","fmin":"191990","fmax":"193136","strand":"+","sequence":"ATGAAGACAAAATCCCTTTGCTGTGCCCTGCTGCTCAGCACCTCCTGCTCTGTTCTCGCCGCGCCGATGTCAGAGAAACAGCTGTCTGACGTGGTGGAACGTACCGTTACCCCCCTGATGAAAGCGCAAGCCATTCCGGGCATGGCGGTGGCGGTGATTTATCAGGGTCAGCCGCACTACTTTACCTTCGGAAAGGCCGATGTTACGGCGAACAAACCTGTCACCCCGCAAACCCTGTTTGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTATTAGGTGGCGATGCGATTGCGCGCGGAGAAATATCGCTGGGCGACCCCGTGACAAAGTACTGGCCCGAGCTAACAGGCAAGCAGTGGCAGGGTATTCGCATGTTGGATCTGGCGACCTACACCGCGGGTGGCCTGCCGCTACAGGTGCCGGATGAGGTCACGGATAACACCTCCCTGCTGCGTTTCTATCAACACTGGCAACCGCAGTGGAAACCAGGCACAACGCGTCTTTATGCGAACGCCAGCATCGGGCTTTTTGGCGCCCTCGCGGTTAAACCCTCCGGTATGAACTTTGAACAGGCCATGACGAAGCGGGTCTTCAAGCCACTCAAACTGGACCATACATGGATTAACGTTCCGAAAGAAGAAGAGGCGCATTACGCCTGGGGATACCGTGATGGTAAAGCAATCCACGTTTCACCGGGAATGCTGGATGCCGAAGCGTATGGTGTCAAAACCAACATCCAGGATATGGCGAGCTGGCTGAAGGCCAACATGAACCCTGACGCCCTTTCGGATTCAACGTTGAAACAGGGTATTGCCCTGGCACAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCGGTAGAAGCCAAAACCGTCGTGGAGGGCAGCGATAACAAGGTGGCTCTTGCACCGTTACTGGTGGCAGAAGTGAACCCTCCAGCTCCGCCAGTAAAAGCATCATGGGTACATAAAACAGGCTCGACGGGTGGATTCGGCAGCTATGTCGCATTTATTCCTGAAAAGGAACTCGGCATTGTTATGCTGGCGAACAAGAGCTACCCGAACCCGGCGCGCGTGGAAGCGGCATACCGTATTCTGAGCGCTCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"47911","NCBI_taxonomy_name":"Enterobacter sp.","NCBI_taxonomy_id":"42895"}}}},"ARO_accession":"3007911","ARO_id":"46703","ARO_name":"ACT-143","CARD_short_name":"ACT-143","ARO_description":"Cephalosporin-hydrolyzing class C beta-lactamase ACT-143.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7330":{"model_id":"7330","model_name":"ACT-144","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10157":{"protein_sequence":{"accession":"EJK8937280.1","sequence":"MMKKSLCCALLLGLSCSALAAPVSEKQLAEVVANTVTPLMKAQSVPGMAVAVIYQGKPHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDDASLLRFYQHWQPQWKPGTTRLYANASIGLFGALAVKPSGMRYEQAMTERVFKPLALHHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPEKVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVVEGSDSKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANKSYPNPARVEAAYHILKALQ"},"dna_sequence":{"accession":"ABGYLI010000008.1","fmin":"45899","fmax":"47045","strand":"-","sequence":"ATGATGAAAAAATCCCTTTGCTGCGCCCTGCTGCTGGGCCTCTCTTGCTCTGCTCTCGCCGCGCCAGTGTCAGAAAAACAGCTGGCGGAGGTGGTCGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCTGTTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGAAAACCGCACTATTACACGTTTGGCAAGGCCGATATCGCGGCGAATAAACCCGTTACGCCTCAGACCCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGCGTTTTAGGTGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCTGAGCTGACGGGCAAGCAGTGGCAAGGGATTCGAATGCTGGATCTCGCCACCTACACCGCAGGCGGTCTGCCGCTACAGGTGCCCGATGAGGTGACGGATGACGCCTCCCTGCTGCGCTTCTATCAACACTGGCAGCCGCAGTGGAAGCCAGGCACAACGCGCCTTTATGCCAACGCCAGCATCGGCCTGTTTGGTGCGCTGGCGGTTAAGCCTTCCGGCATGCGCTACGAGCAGGCGATGACCGAGCGAGTATTCAAACCGCTGGCGCTGCATCACACCTGGATTAACGTGCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGAATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCGGAGAAGGTTGCCGATGCCTCACTTAAGCAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGGTCGAAGGCAGCGACAGTAAGGTAGCGCTGGCGCCATTACCCGTGGCAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGTTCTACTGGCGGATTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCAAGGCGCTTCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39098","NCBI_taxonomy_name":"Enterobacter hormaechei","NCBI_taxonomy_id":"158836"}}}},"ARO_accession":"3007912","ARO_id":"46704","ARO_name":"ACT-144","CARD_short_name":"ACT-144","ARO_description":"Cephalosporin-hydrolyzing class C beta-lactamase ACT-144.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7331":{"model_id":"7331","model_name":"ACT-145","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10158":{"protein_sequence":{"accession":"AUM01997.1","sequence":"MMTKSLCCALLLSTSCSVLAAPMSEKQLAEVVERTVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMSYEQAITTRVFKPLKLDHTWINVPKAEEPHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVQDMANWVMVNMKPDSLQDSSLRKGITLAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVEGSDNKVALAPLPAREVNPPAPPVNASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILDALQ"},"dna_sequence":{"accession":"CP020817.3","fmin":"405091","fmax":"406237","strand":"-","sequence":"ATGATGACTAAATCCCTTTGCTGCGCCCTGCTGCTCAGCACCTCCTGCTCGGTATTGGCTGCCCCGATGTCAGAAAAACAGCTGGCTGAGGTGGTGGAACGTACCGTTACGCCGCTGATGAAAGCGCAGGCCATTCCGGGTATGGCGGTGGCGGTGATTTATCAGGGTCAGCCGCACTACTTTACCTTCGGTAAAGCCGATGTTGCGGCGAACAAACCTGTCACCCCACAAACCTTATTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGCGTGCTGGGCGGCGATGCCATTGCTCGGGGTGAAATATCGCTGGGCGATCCGGTGACAAAATACTGGCCTGAGCTGACAGGCAAGCAGTGGCAGGGGATCCGCATGCTGGATCTGGCAACCTATACCGCAGGAGGTTTGCCGTTACAGGTACCGGATGAGGTCACGGATAACGCCTCTCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCGGGCACCACGCGTCTTTATGCCAACGCCAGCATCGGTCTTTTTGGCGCGCTGGCGGTCAAACCTTCCGGCATGAGCTATGAGCAGGCCATAACGACGCGGGTCTTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTTCCGAAAGCGGAAGAGCCGCATTACGCCTGGGGATACCGCGACGGTAAAGCGGTACACGTTTCGCCAGGCATGCTGGACGCTGAAGCCTATGGCGTAAAAACCAACGTGCAGGATATGGCAAACTGGGTGATGGTCAACATGAAGCCGGACTCGCTTCAGGATAGTTCACTCAGGAAAGGCATTACCCTGGCGCAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAGGGGTTAGGCTGGGAAATGCTTAACTGGCCGGTCGATGCCAAAACCGTGGTTGAAGGTAGCGACAATAAGGTGGCGCTGGCACCGTTGCCTGCGAGAGAAGTGAATCCACCGGCGCCCCCGGTCAACGCATCCTGGGTCCATAAAACAGGCTCTACCGGCGGGTTTGGCAGCTACGTGGCATTTATTCCCGAAAAGCAGCTCGGCATTGTGATGCTGGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCGTATCCTCGACGCGCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"47911","NCBI_taxonomy_name":"Enterobacter sp.","NCBI_taxonomy_id":"42895"}}}},"ARO_accession":"3007913","ARO_id":"46705","ARO_name":"ACT-145","CARD_short_name":"ACT-145","ARO_description":"Cephalosporin-hydrolyzing class C beta-lactamase ACT-145.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7332":{"model_id":"7332","model_name":"ACT-146","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10159":{"protein_sequence":{"accession":"EMN8661052.1","sequence":"MMKKFLCCALLLSTSCSVLAAPMSEKQLADVVERNVTPLMKAQGIPGMAVAVIYQGQPHYFTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPDLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANSSIGLFGALAVKPSGMSYEQAMTTRVFKPLKLDHTWINVPKAEETHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVQDMASWVMANMAPDALQDSSLKQGITLAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVGGSDNKVALAPLPAREVSPPVPPVKASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILDALQ"},"dna_sequence":{"accession":"ABMQTZ020000010.1","fmin":"130659","fmax":"131805","strand":"+","sequence":"ATGATGAAAAAATTCCTTTGCTGCGCCCTGCTGCTCAGCACATCCTGCTCTGTACTCGCCGCGCCGATGTCGGAAAAACAGCTGGCTGACGTGGTAGAACGCAACGTTACGCCCCTGATGAAAGCGCAGGGTATTCCAGGCATGGCGGTGGCCGTGATTTATCAGGGCCAGCCACATTACTTTACCTTTGGAAAGGCCGATATCGCGGCGAACAAACCCGTCACCCCGCAAACCCTGTTCGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTGCTGGGGGGCGATGCTATTGCCCGCGGCGAAATTTCGCTGGGCGATCCGGTAACCAAATATTGGCCTGATCTGACCGGCAAGCAGTGGCAAGGGATTCGCATGCTGGATCTGGCAACCTACACCGCCGGTGGCCTGCCTTTACAGGTGCCCGATGAGGTCACAGATAACGCTTCCCTGCTGCGCTTCTATCAAAACTGGCAGCCTCAGTGGAAGCCGGGCACAACGCGTCTTTACGCCAACTCCAGCATCGGTCTTTTTGGCGCGCTGGCGGTCAAACCTTCCGGCATGAGCTATGAGCAGGCCATGACGACGCGGGTCTTTAAGCCGCTCAAGCTGGATCATACCTGGATAAACGTCCCGAAAGCGGAGGAGACGCATTACGCCTGGGGATATCGTGACGGTAAAGCGGTCCACGTTTCACCGGGCATGCTGGACGCAGAGGCATATGGCGTGAAAACCAACGTGCAGGATATGGCGAGCTGGGTGATGGCCAATATGGCCCCTGACGCACTGCAGGATTCGTCCCTGAAGCAAGGCATTACGCTGGCGCAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAGGGGTTAGGTTGGGAGATGCTTAACTGGCCGGTCGATGCCAAAACCGTCGTCGGAGGCAGTGATAACAAGGTGGCGCTGGCACCGTTGCCTGCGAGAGAAGTGAGTCCACCCGTTCCCCCGGTTAAGGCCTCATGGGTGCACAAAACGGGCTCCACCGGCGGGTTTGGCAGCTATGTGGCCTTTATTCCTGAAAAGCAGCTCGGCATTGTGATGCTGGCGAATAAAAGCTATCCGAACCCGGCGCGAGTTGAGGCGGCATACCGTATCCTCGACGCGCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"47906","NCBI_taxonomy_name":"Enterobacter bugandensis","NCBI_taxonomy_id":"881260"}}}},"ARO_accession":"3007914","ARO_id":"46706","ARO_name":"ACT-146","CARD_short_name":"ACT-146","ARO_description":"Cephalosporin-hydrolyzing class C beta-lactamase ACT-146.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7333":{"model_id":"7333","model_name":"ACT-148","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10160":{"protein_sequence":{"accession":"CZY90887.1","sequence":"MMKKSLCCALLLGISCSALATPVSEKQLAEVVANTVTPLMKAQSVPGMAVAVIYQGKPHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMPYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPENVADASLKQGIALAQSRYWRTGSMYQGLGWEMLNWPVEANTVVEGSDSKVALAPLPVVEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANTSYPNPARVEAAYHILEALQ"},"dna_sequence":{"accession":"FKAD01000003.1","fmin":"468418","fmax":"469564","strand":"+","sequence":"ATGATGAAAAAATCCCTTTGCTGCGCCCTGCTGCTCGGCATCTCTTGCTCTGCTCTCGCCACGCCAGTGTCAGAAAAACAGCTGGCGGAGGTGGTAGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCTGTTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGAAAACCGCACTATTACACGTTTGGCAAGGCCGATATCGCGGCGAATAAACCCGTTACGCCTCAGACCCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGCGTTTTAGGTGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTGACGGGCAAGCAGTGGCAGGGTATTCGTATGCTGGATCTCGCCACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTCAAACCTTCTGGCATGCCCTATGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTGCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGTATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCGGAGAACGTTGCTGATGCCTCACTTAAGCAGGGCATCGCGCTGGCACAGTCGCGCTACTGGCGTACCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGGTCGAGGGCAGCGACAGTAAGGTAGCGCTGGCGCCGTTGCCCGTGGTAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGCTCTACTGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATACAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCGAGGCGCTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39098","NCBI_taxonomy_name":"Enterobacter hormaechei","NCBI_taxonomy_id":"158836"}}}},"ARO_accession":"3007915","ARO_id":"46707","ARO_name":"ACT-148","CARD_short_name":"ACT-148","ARO_description":"Cephalosporin-hydrolyzing class C beta-lactamase ACT-148.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7334":{"model_id":"7334","model_name":"ACT-150","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10161":{"protein_sequence":{"accession":"UKB65296.1","sequence":"MKTKSLCCALLLSTSCSVLAAPMSEKQLSDVVERTVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTSVLGGDAIARGEISLDDPVTKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQHWQPQWKPGTTRLYANASIGLFGALAVKPSGMSFEQAMTKRVFKPLKLDHTWINVPKEEEAHYAWGYRDGKATHVSPGMLDAEAYGVKTNVQDMASWVKANMNPDALPDSTLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVEAKTVVEGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKELGIVMLANKSYPNPARVEAAYRILSALQ"},"dna_sequence":{"accession":"CP091481.1","fmin":"380303","fmax":"381449","strand":"-","sequence":"ATGAAGACAAAATCCCTTTGCTGTGCCCTGCTGCTCAGTACCTCCTGCTCTGTTCTCGCCGCGCCGATGTCAGAGAAACAGCTGTCTGACGTGGTGGAACGTACCGTAACCCCCCTGATGAAAGCGCAAGCCATTCCGGGCATGGCGGTAGCGGTGATTTATCAGGGTCAGCCGCACTACTTTACCTTCGGAAAGGCCGATGTTGCGGCGAACAAACCTGTCACCCCGCAAACCCTGTTTGAGCTGGGCTCTATAAGTAAAACCTTCACCAGCGTATTAGGTGGCGATGCGATTGCGCGCGGAGAAATATCGCTGGACGACCCCGTGACAAAGTACTGGCCCGAGTTAACAGGCAAGCAGTGGCAGGGTATTCGCATGTTGGATCTGGCGACCTACACCGCGGGTGGCCTGCCGCTACAGGTGCCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGTTTCTATCAACACTGGCAACCGCAGTGGAAACCAGGCACAACGCGTCTTTATGCGAACGCCAGCATCGGGCTTTTTGGCGCCCTCGCGGTTAAACCCTCCGGTATGAGCTTTGAACAGGCCATGACGAAGCGGGTCTTCAAGCCACTCAAACTGGACCATACATGGATTAACGTTCCGAAAGAAGAAGAGGCGCATTACGCCTGGGGATACCGTGACGGTAAAGCAACCCACGTTTCACCGGGAATGCTGGATGCCGAAGCGTATGGTGTCAAAACCAACGTCCAGGATATGGCGAGCTGGGTGAAGGCCAACATGAACCCTGACGCCCTTCCGGATTCAACGTTGAAACAGGGTATTGCCCTGGCACAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCGGTAGAAGCCAAAACCGTCGTGGAGGGCAGCGATAACAAGGTGGCTCTTGCACCGTTACCGGTGGCAGAAGTGAACCCTCCAGCTCCGCCAGTAAAAGCATCATGGGTACATAAAACAGGCTCGACGGGTGGATTCGGCAGCTATGTCGCATTTATTCCTGAAAAGGAACTCGGCATTGTTATGCTGGCGAACAAGAGCTACCCGAACCCGGCGCGCGTGGAAGCGGCATACCGTATTCTGAGCGCTCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3007916","ARO_id":"46708","ARO_name":"ACT-150","CARD_short_name":"ACT-150","ARO_description":"Cephalosporin-hydrolyzing class C beta-lactamase ACT-150.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7335":{"model_id":"7335","model_name":"ACT-151","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10162":{"protein_sequence":{"accession":"MBW7688613.1","sequence":"MMKKSLCCALLLGLSCSALAAPVSEKQLAEVVANTVTPLMKAQSVPGMAVAVIYQGKSHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMPYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPEKVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVVEGSDSKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYHILEALQ"},"dna_sequence":{"accession":"JAHZRO010000014.1","fmin":"19385","fmax":"20531","strand":"-","sequence":"ATGATGAAAAAATCCCTTTGCTGCGCCCTGCTGCTGGGCCTCTCTTGCTCTGCTCTCGCCGCGCCAGTATCAGAAAAACAGCTGGCGGAGGTGGTCGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCTGTTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGAAAATCGCACTATTACACGTTTGGCAAGGCCGATATCGCGGCGAATAAACCCGTTACGCCTCAGACCCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGCGTTTTAGGTGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTGACGGGCAAGCAGTGGCAGGGTATTCGTATGCTGGATCTCGCCACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTCAAACCTTCTGGCATGCCCTATGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTTCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGAATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCGGAGAAGGTTGCCGATGCCTCACTTAAGCAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGGTCGAAGGCAGCGACAGTAAGGTAGCGCTGGCGCCGTTACCCGTGGCAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGTTCTACCGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGCTCGGTATTGTGATGCTCGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCGAGGCGCTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39098","NCBI_taxonomy_name":"Enterobacter hormaechei","NCBI_taxonomy_id":"158836"}}}},"ARO_accession":"3007917","ARO_id":"46709","ARO_name":"ACT-151","CARD_short_name":"ACT-151","ARO_description":"Cephalosporin-hydrolyzing class C beta-lactamase ACT-151.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7336":{"model_id":"7336","model_name":"ACT-153","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10163":{"protein_sequence":{"accession":"WRT49607.1","sequence":"MMKKFLCCALLLSTSCSVLAAPMSEKQLADVVERNVTPLMKAQGIPGMAVAVIYQGQPHYFTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPDLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANSSIGLFGALAVKPSGMNYEQAMTTRVFKPLKLDHTWINVPKAEETHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVQDMASWVMANMAPDALQDTSLKQGITLAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVGGSDNKVALAPLPAREVSPPVPPVKASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILDALQ"},"dna_sequence":{"accession":"CP141897.1","fmin":"2650701","fmax":"2651847","strand":"+","sequence":"ATGATGAAAAAATTCCTTTGCTGCGCCCTGCTGCTCAGCACATCCTGCTCTGTACTCGCCGCGCCGATGTCGGAAAAACAGCTGGCTGACGTGGTAGAACGTAACGTTACGCCCCTGATGAAAGCGCAGGGTATTCCAGGCATGGCGGTGGCCGTGATTTATCAGGGCCAGCCACACTACTTTACCTTTGGAAAGGCCGATATCGCGGCGAACAAACCCGTCACCCCGCAAACCCTGTTCGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTGCTGGGGGGCGATGCTATTGCCCGCGGCGAAATTTCGCTGGGCGATCCGGTAACCAAATATTGGCCTGATCTGACCGGCAAGCAGTGGCAAGGGATTCGCATGCTGGATCTGGCAACCTACACCGCCGGTGGCCTGCCTTTACAGGTGCCCGATGAGGTTACAGATAACGCTTCCCTGCTGCGCTTCTATCAAAACTGGCAGCCTCAGTGGAAGCCGGGCACAACGCGTCTTTACGCCAACTCCAGCATCGGTCTTTTTGGCGCGCTGGCGGTCAAACCTTCCGGCATGAACTATGAGCAGGCCATGACGACGCGGGTCTTTAAGCCGCTCAAGCTGGATCATACCTGGATTAACGTTCCGAAAGCGGAGGAGACGCATTACGCCTGGGGATATCGTGACGGTAAAGCGGTCCACGTTTCACCGGGCATGCTGGACGCAGAGGCATATGGCGTGAAAACCAACGTGCAGGATATGGCGAGCTGGGTGATGGCCAATATGGCCCCTGACGCGCTGCAGGATACGTCCCTGAAGCAAGGCATTACGCTGGCGCAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAGGGGTTAGGTTGGGAGATGCTTAACTGGCCGGTCGATGCCAAAACCGTCGTCGGAGGCAGTGATAACAAGGTGGCGCTGGCACCGTTGCCTGCGAGAGAAGTGAGTCCACCCGTTCCCCCGGTTAAGGCCTCATGGGTGCACAAAACGGGCTCCACCGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGCTCGGCATTGTGATGCTGGCGAATAAAAGCTATCCGAACCCGGCGCGAGTTGAGGCGGCATACCGTATCCTCGACGCGCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"47906","NCBI_taxonomy_name":"Enterobacter bugandensis","NCBI_taxonomy_id":"881260"}}}},"ARO_accession":"3007918","ARO_id":"46710","ARO_name":"ACT-153","CARD_short_name":"ACT-153","ARO_description":"Cephalosporin-hydrolyzing class C beta-lactamase ACT-153.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7337":{"model_id":"7337","model_name":"ACT-154","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10164":{"protein_sequence":{"accession":"UOY66714.1","sequence":"MKTKSLCCALLLSTSCSVLAAPMSEKQLSDVVERTVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVAKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQHWQPQWKPGTTRLYANASIGLFGALAVKPSGMSFEQAMTKRVFKPLKLDHTWINVPKEEEAHYAWGYRDGKAIHVSPGMLDAEAYGVKTNVQDMASWLKANMNPDALSDSTLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVEAKTLVEGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKGLGIVMLANKSYPNPARVEAAYRILSALQ"},"dna_sequence":{"accession":"CP083828.1","fmin":"381787","fmax":"382933","strand":"-","sequence":"ATGAAGACAAAATCCCTTTGCTGTGCCCTGCTGCTCAGCACCTCCTGCTCTGTTCTCGCCGCGCCGATGTCAGAGAAACAGCTGTCTGACGTGGTGGAACGTACCGTTACCCCCCTGATGAAAGCGCAAGCCATTCCGGGCATGGCGGTAGCGGTGATTTATCAGGGTCAGCCGCACTACTTTACCTTCGGAAAGGCCGATGTTGCGGCGAACAAACCTGTCACCCCGCAAACCCTGTTTGAGCTGGGCTCTATAAGTAAAACCTTCACTGGCGTATTAGGTGGCGATGCGATTGCGCGCGGAGAAATATCGCTGGGCGACCCCGTGGCAAAGTACTGGCCCGAGCTAACAGGCAAGCAGTGGCAGGGTATTCGCATGTTGGATCTGGCGACCTACACCGCGGGTGGCCTGCCGCTACAGGTGCCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGCTTCTATCAACACTGGCAACCGCAGTGGAAACCAGGCACAACGCGTCTTTATGCGAACGCCAGCATCGGGCTTTTTGGCGCCCTCGCGGTTAAACCCTCCGGCATGAGCTTTGAACAGGCCATGACGAAGCGGGTCTTCAAGCCACTCAAACTGGACCATACATGGATTAACGTTCCGAAAGAAGAAGAGGCGCATTACGCCTGGGGATACCGTGATGGTAAAGCAATCCACGTTTCACCGGGAATGCTGGATGCCGAAGCGTATGGTGTCAAAACCAACGTCCAGGATATGGCGAGCTGGCTGAAGGCCAACATGAACCCTGACGCCCTTTCGGATTCAACGTTGAAACAGGGTATTGCCCTGGCACAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCGGTAGAAGCCAAAACCCTCGTGGAGGGCAGCGATAACAAGGTGGCTCTTGCACCGTTACCGGTGGCAGAAGTGAACCCTCCAGCTCCGCCAGTAAAAGCATCATGGGTACATAAAACAGGCTCGACGGGTGGATTCGGCAGCTATGTCGCATTTATTCCTGAAAAGGGACTCGGCATTGTTATGCTGGCGAACAAGAGCTACCCGAACCCGGCGCGCGTGGAAGCGGCATACCGTATTCTGAGCGCTCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39773","NCBI_taxonomy_name":"Enterobacter kobei","NCBI_taxonomy_id":"208224"}}}},"ARO_accession":"3007919","ARO_id":"46711","ARO_name":"ACT-154","CARD_short_name":"ACT-154","ARO_description":"Cephalosporin-hydrolyzing class C beta-lactamase ACT-154.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7338":{"model_id":"7338","model_name":"ACT-155","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10165":{"protein_sequence":{"accession":"UJA58935.1","sequence":"MMKKSLCCALLLGLSCSALAAPVSEKQLAEVVANTVTPLMKAQSVPGMAVAVIYQGKSHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMPYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGTLDAQAYGVKTNVQDMANWVMANMAPEKVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVVEGSDSKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANKSYPNPARVEAAYHILKALQ"},"dna_sequence":{"accession":"CP090909.1","fmin":"3158864","fmax":"3160010","strand":"-","sequence":"ATGATGAAAAAATCCCTTTGCTGCGCCCTGCTGCTGGGCCTCTCTTGCTCTGCTCTCGCCGCGCCAGTGTCAGAAAAACAGCTGGCGGAGGTGGTCGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCTGTTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGAAAATCGCACTATTACACGTTTGGCAAGGCCGATATCGCGGCGAATAAACCCGTTACGCCTCAGACCCTGTTCGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTTTTAGGTGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTGACGGGCAAGCAGTGGCAGGGTATTCGTATGCTGGATCTCGCCACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTCAAACCTTCTGGCATGCCCTATGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTTCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGAACGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCGGAGAAGGTTGCCGATGCCTCACTTAAGCAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGGTCGAAGGCAGCGACAGTAAGGTAGCGCTGGCGCCGTTACCCGTGGCAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGTTCTACTGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCAAGGCGCTTCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39098","NCBI_taxonomy_name":"Enterobacter hormaechei","NCBI_taxonomy_id":"158836"}}}},"ARO_accession":"3007920","ARO_id":"46712","ARO_name":"ACT-155","CARD_short_name":"ACT-155","ARO_description":"Cephalosporin-hydrolyzing class C beta-lactamase ACT-155.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7339":{"model_id":"7339","model_name":"ACT-156","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10166":{"protein_sequence":{"accession":"MBW8248988.1","sequence":"MIKKSLCCALLLGVSCSSIAASMTEKQLADVVEKNITPLMKAQSIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTQYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDSASLLRFYQTWQPQWKPGTTRLYANASIGLFGALAVKPSGMGFEQAMTKRVFKPLGLDHTWINVPKAEEAHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVQDMASWVVANMAPDNVQDASLKQGITLAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVEGSDNKVALAPLPAREVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVDAAYRILDALQ"},"dna_sequence":{"accession":"JAHZUV010000006.1","fmin":"207634","fmax":"208780","strand":"+","sequence":"ATGATCAAAAAATCCCTTTGCTGCGCCCTGCTGCTCGGCGTGTCATGTTCCAGCATTGCTGCGTCGATGACAGAAAAACAGCTGGCTGACGTGGTGGAAAAAAACATTACCCCCCTGATGAAAGCGCAGTCCATTCCGGGCATGGCGGTTGCCGTGATCTACCAGGGCCAGCCGCACTATTTTACTTTTGGTAAAGCCGATGTTGCCGCGAACAAACCTGTTACCCCACAAACCCTGTTCGAACTGGGTTCTATCAGTAAAACTTTCACCGGCGTATTGGGCGGCGATGCCATTGCCCGCGGTGAAATATCGCTGGGCGATCCGGTGACCCAATACTGGCCTGAGCTGACGGGCAAGCAGTGGCAGGGGATTCGCATGCTGGATCTGGCGACCTATACCGCGGGAGGGTTACCGCTTCAGGTGCCGGACGAGGTGACCGACAGCGCGTCGCTGCTTCGCTTTTACCAGACATGGCAGCCGCAGTGGAAACCGGGCACCACGCGACTGTACGCGAACGCCAGCATCGGTCTGTTTGGCGCACTGGCGGTTAAACCTTCCGGCATGGGCTTTGAACAGGCCATGACGAAGCGGGTCTTTAAACCGCTCGGGCTCGACCATACGTGGATCAACGTTCCGAAAGCAGAAGAGGCACATTACGCCTGGGGATACCGTGACGGTAAAGCGGTCCACGTGTCACCGGGGATGCTGGACGCCGAAGCCTACGGCGTGAAAACCAACGTGCAGGATATGGCGAGCTGGGTGGTGGCCAATATGGCACCGGATAACGTTCAGGATGCATCCCTGAAGCAAGGCATTACGCTGGCACAGTCGCGCTACTGGCGCGTAGGGGCCATGTATCAAGGATTAGGCTGGGAAATGCTTAACTGGCCGGTCGATGCCAAAACCGTGGTTGAAGGTAGCGACAACAAGGTCGCGCTGGCCCCCCTGCCTGCGAGAGAAGTGAATCCTCCGGCGCCTCCGGTAAAAGCCTCATGGGTGCACAAAACCGGCTCCACCGGCGGATTCGGCAGCTATGTGGCCTTTATCCCTGAGAAACAGCTTGGCATCGTGATGCTGGCGAACAAGAGCTATCCGAACCCGGCACGCGTTGATGCGGCATACCGTATCCTCGACGCGCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"47908","NCBI_taxonomy_name":"Enterobacter mori","NCBI_taxonomy_id":"539813"}}}},"ARO_accession":"3007921","ARO_id":"46713","ARO_name":"ACT-156","CARD_short_name":"ACT-156","ARO_description":"Cephalosporin-hydrolyzing class C beta-lactamase ACT-156.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7340":{"model_id":"7340","model_name":"ACT-157","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10167":{"protein_sequence":{"accession":"WYI22699.1","sequence":"MMKKSLCCALLLGLSCSALAAPVSEKQLAEVVANTVTPLMKAQSVPGMAVAVIYQGKSHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMPYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPEKIADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVVEGSDSKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANKSYPNPARVEAAYHILEALQ"},"dna_sequence":{"accession":"CP149841.1","fmin":"420086","fmax":"421232","strand":"-","sequence":"ATGATGAAAAAATCCCTTTGCTGCGCCCTGCTGCTGGGCCTCTCTTGCTCTGCTCTCGCCGCGCCAGTGTCAGAAAAACAGCTGGCGGAGGTGGTCGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCTGTTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGAAAATCGCACTATTACACGTTTGGCAAGGCCGATATCGCGGCGAATAAACCCGTTACGCCTCAGACCCTGTTCGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTTTTAGGTGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTGACGGGCAAGCAGTGGCAGGGTATTCGTATGCTGGATCTCGCCACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTCAAACCTTCTGGCATGCCCTATGAGCAGGCCATGACGACGCGGGTCCTGAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTTCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGAATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCGGAGAAGATTGCCGATGCCTCACTTAAGCAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGGTCGAAGGCAGCGACAGTAAGGTAGCGCTGGCGCCGTTACCCGTGGCAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGTTCTACTGGCGGATTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCGAGGCGCTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39098","NCBI_taxonomy_name":"Enterobacter hormaechei","NCBI_taxonomy_id":"158836"}}}},"ARO_accession":"3007922","ARO_id":"46714","ARO_name":"ACT-157","CARD_short_name":"ACT-157","ARO_description":"Cephalosporin-hydrolyzing class C beta-lactamase ACT-157.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7341":{"model_id":"7341","model_name":"ACT-158","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10168":{"protein_sequence":{"accession":"MCC4544499.1","sequence":"MMKKSLCCALLLGLSCSALAAPVSEKQLAEVVANTVTPLMKAQSVPGMAVAVIYQGKPHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAITRGEISLDDPVTRYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDDASLLRFYQHWQPQWKPGTTRLYANASIGLFGALAVKPSGMRYEQAMTERVFKPLALHHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPEKVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVVEGSDSKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANKSYPNPARVEAAYHILEALQ"},"dna_sequence":{"accession":"JAJGSG010000001.1","fmin":"4450700","fmax":"4451846","strand":"+","sequence":"ATGATGAAAAAATCCCTTTGCTGCGCCCTGCTGCTGGGCCTCTCTTGCTCTGCTCTCGCCGCGCCAGTGTCAGAAAAACAGCTGGCGGAGGTGGTCGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCTGTTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGAAAACCGCACTATTACACGTTTGGCAAGGCCGATATCGCGGCGAATAAACCCGTTACGCCTCAGACCCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGCGTTTTAGGTGGGGATGCCATTACTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCTGAGCTGACGGGCAAGCAGTGGCAAGGGATTCGAATGCTGGATCTCGCCACCTACACCGCAGGCGGTCTGCCGCTACAGGTGCCCGATGAGGTGACGGATGACGCCTCCCTGCTGCGCTTCTATCAACACTGGCAGCCACAGTGGAAGCCAGGCACAACGCGCCTTTATGCCAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTTAAGCCTTCCGGCATGCGCTACGAGCAGGCGATGACCGAGCGAGTATTCAAACCGCTGGCGCTGCATCACACCTGGATTAACGTGCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGAATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCGGAGAAGGTTGCCGATGCCTCACTTAAGCAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGGTCGAAGGCAGCGACAGTAAGGTAGCGCTGGCGCCGTTACCCGTGGCAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGTTCTACCGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCGAGGCGCTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39098","NCBI_taxonomy_name":"Enterobacter hormaechei","NCBI_taxonomy_id":"158836"}}}},"ARO_accession":"3007923","ARO_id":"46715","ARO_name":"ACT-158","CARD_short_name":"ACT-158","ARO_description":"Cephalosporin-hydrolyzing class C beta-lactamase ACT-158.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7342":{"model_id":"7342","model_name":"ACT-159","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10169":{"protein_sequence":{"accession":"MCE1398600.1","sequence":"MMTKSLCCALLLSTSCSVLAAPMSEKQLADVVERTVTPLMKAQAIPGMAVAVIYQGQPRYFTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALATKPSGMGYEQAMTTRVFKPLKLDHTWINVPKAEEAHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVQDMASWVMANMAPGALQDTSLKQGITLAQSRYWRVGAMYQGLGWEMLNWPVDVKTVVGGSDNKVALAPLPAREVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILDAMQ"},"dna_sequence":{"accession":"JAJSXK010000010.1","fmin":"18801","fmax":"19947","strand":"-","sequence":"ATGATGACAAAATCCCTTTGCTGCGCCCTGCTGCTCAGCACCTCCTGCTCGGTATTAGCTGCCCCGATGTCAGAAAAACAGCTGGCTGACGTGGTGGAACGTACCGTTACGCCGCTGATGAAAGCGCAAGCCATTCCTGGCATGGCGGTGGCCGTGATTTATCAGGGCCAGCCACGCTACTTTACCTTCGGAAAAGCCGACATCGCGGCGAACAAGCCCGTCACCCCGCAAACCCTGTTCGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTGCTGGGAGGCGATGCCATTGCCCGCGGCGAAATATCGCTGGGCGATCCGGTAACCAAATATTGGCCTGAACTGACAGGCAAGCAGTGGCAGGGAATTCGCATGCTGGATCTGGCAACCTATACAGCAGGAGGTCTGCCGTTACAGGTACCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGCTTCTATCAAAACTGGCAGCCGCAGTGGAAGCCGGGCACCACGCGTCTTTATGCTAATGCCAGCATCGGTTTGTTTGGCGCGCTGGCGACCAAACCTTCCGGCATGGGCTATGAGCAGGCCATGACGACGCGGGTCTTTAAGCCGCTCAAGCTCGACCATACCTGGATTAACGTTCCGAAAGCGGAGGAGGCGCATTACGCCTGGGGATATCGTGACGGTAAAGCAGTCCACGTTTCACCGGGCATGCTGGACGCAGAGGCGTATGGCGTGAAAACCAACGTGCAGGATATGGCAAGCTGGGTGATGGCCAACATGGCCCCTGGCGCGCTGCAGGATACGTCCCTGAAGCAAGGCATTACGCTGGCGCAGTCCCGCTACTGGCGCGTGGGTGCTATGTATCAGGGGCTGGGCTGGGAGATGCTCAACTGGCCGGTCGATGTAAAAACCGTTGTCGGAGGCAGCGATAACAAGGTTGCCCTGGCACCGTTGCCCGCGAGAGAAGTGAATCCTCCGGCGCCTCCGGTAAAAGCCTCATGGGTGCATAAAACCGGCTCAACCGGCGGGTTTGGCAGCTACGTGGCATTTATTCCTGAAAAGCAGCTCGGCATTGTGATGCTGGCAAATAAAAGCTATCCGAACCCGGCGCGAGTTGAGGCGGCATACCGTATTCTTGACGCGATGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3007924","ARO_id":"46716","ARO_name":"ACT-159","CARD_short_name":"ACT-159","ARO_description":"Cephalosporin-hydrolyzing class C beta-lactamase ACT-159.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7343":{"model_id":"7343","model_name":"ACT-160","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10170":{"protein_sequence":{"accession":"MCK6739931.1","sequence":"MMKKFLCCALLLSTSCSVLAAPMSEKQLAAVVERNVTPLMKAQGIPGMAVAVIYQGQPHYFTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPDLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANSSIGLFGALAVKPSGMSYEQAMTTRVFKPLKLDHTWINVPKAEETHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVQDMASWVMANMAPDALQDTSLKQGITLAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVGGSDNKVALAPLPAREVSPPVPPVKASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILDALQ"},"dna_sequence":{"accession":"JAKMOE010000004.1","fmin":"493276","fmax":"494422","strand":"+","sequence":"ATGATGAAAAAATTCCTTTGCTGCGCCCTGCTGCTCAGCACATCCTGCTCTGTACTCGCCGCGCCGATGTCGGAAAAACAGCTGGCTGCCGTGGTAGAACGTAACGTTACGCCCCTGATGAAAGCGCAGGGTATTCCAGGCATGGCGGTGGCCGTGATTTATCAGGGCCAGCCACACTACTTTACCTTTGGAAAGGCCGATATCGCGGCGAACAAACCCGTCACCCCGCAAACCCTGTTCGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTGCTGGGGGGCGATGCTATTGCCCGCGGCGAAATTTCGCTGGGCGATCCGGTAACCAAATATTGGCCTGATCTGACCGGCAAGCAGTGGCAAGGGATTCGCATGCTGGATCTGGCAACCTACACCGCCGGTGGCCTGCCTTTACAGGTGCCCGATGAGGTCACAGATAACGCATCCCTGCTGCGCTTCTATCAAAACTGGCAGCCTCAGTGGAAGCCGGGCACAACGCGTCTTTACGCCAACTCCAGCATCGGTCTTTTTGGCGCGCTGGCGGTCAAACCTTCCGGCATGAGCTATGAGCAGGCCATGACGACGCGGGTCTTTAAGCCGCTCAAGCTGGATCATACCTGGATAAACGTCCCGAAAGCGGAGGAGACGCATTACGCCTGGGGATATCGTGACGGTAAAGCGGTCCACGTTTCACCGGGCATGCTGGACGCAGAGGCATATGGCGTGAAAACCAACGTGCAGGATATGGCGAGCTGGGTGATGGCCAATATGGCCCCTGACGCGCTGCAGGATACGTCCCTGAAGCAAGGCATTACGCTGGCGCAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAGGGGTTAGGTTGGGAGATGCTTAACTGGCCGGTCGATGCCAAAACCGTCGTCGGAGGCAGTGATAACAAGGTGGCGCTGGCACCGTTGCCTGCGAGAGAAGTGAGTCCACCCGTTCCCCCGGTTAAGGCCTCATGGGTGCACAAAACGGGCTCCACCGGCGGGTTTGGCAGCTATGTGGCCTTTATTCCTGAAAAGCAGCTCGGCATTGTGATGCTGGCGAATAAAAGCTATCCGAACCCGGCGCGAGTTGAGGCGGCATACCGTATCCTCGACGCGCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"47906","NCBI_taxonomy_name":"Enterobacter bugandensis","NCBI_taxonomy_id":"881260"}}}},"ARO_accession":"3007925","ARO_id":"46717","ARO_name":"ACT-160","CARD_short_name":"ACT-160","ARO_description":"Cephalosporin-hydrolyzing class C beta-lactamase ACT-160.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7344":{"model_id":"7344","model_name":"ACT-161","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10171":{"protein_sequence":{"accession":"MCO4185007.1","sequence":"MKTKSLCCALLLSTSCSVLAAPMSEKQLSDVVERTVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVAAKKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQHWQPQWKPGTTRLYANASIGLFGALAVKPSGMSFEQAMTKRVFKPLKLDHTWINVPKEEEAYYAWGYRDGKAVHVSPGMLDAEAYGVKTNVQDMASWVKANMNPAALPDSTLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVEAKTVVEGSDNKVALAPLPVAEVPPPAPPVKASWVHKTGSTGGFGSYVAFIPEKELGIVMLANKSYPNPARVEVAYRILSALQ"},"dna_sequence":{"accession":"JAIOHD010000008.1","fmin":"144977","fmax":"146123","strand":"+","sequence":"ATGAAGACAAAATCCCTTTGCTGTGCCCTGCTGCTCAGCACCTCCTGCTCTGTTCTCGCCGCGCCGATGTCAGAGAAACAGCTGTCTGACGTGGTGGAACGTACCGTTACCCCCCTGATGAAAGCGCAAGCCATTCCGGGCATGGCGGTAGCGGTGATTTATCAGGGTCAGCCGCACTACTTTACCTTCGGAAAGGCCGATGTTGCGGCGAAAAAACCTGTCACCCCGCAAACCCTGTTTGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTATTAGGTGGCGATGCGATTGCGCGCGGAGAAATATCGCTGGGCGACCCCGTGACAAAGTACTGGCCCGAGCTAACAGGCAAGCAGTGGCAGGGTATTCGCATGTTGGATCTGGCGACCTACACCGCGGGTGGCCTGCCGCTACAGGTGCCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGCTTCTATCAACACTGGCAACCGCAGTGGAAACCAGGCACAACGCGTCTTTATGCGAACGCCAGCATCGGGCTTTTTGGCGCCCTCGCGGTTAAACCCTCCGGTATGAGCTTTGAACAGGCCATGACGAAGCGGGTCTTCAAGCCACTCAAACTGGACCATACATGGATTAACGTTCCGAAAGAAGAAGAGGCGTATTACGCCTGGGGATACCGTGATGGTAAAGCGGTCCACGTTTCACCGGGAATGTTGGATGCCGAAGCGTATGGTGTCAAAACCAACGTCCAGGATATGGCGAGCTGGGTGAAGGCCAACATGAACCCTGCCGCTCTTCCGGATTCAACGCTGAAACAGGGTATTGCCCTGGCACAGTCTCGCTACTGGCGCGTGGGTGCCATGTACCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCGGTAGAAGCCAAAACCGTGGTGGAGGGCAGCGATAACAAGGTGGCTCTTGCACCGTTACCGGTGGCTGAAGTGCCCCCCCCAGCTCCGCCAGTAAAAGCGTCATGGGTACATAAAACAGGCTCGACGGGCGGATTTGGCAGCTATGTCGCATTTATTCCTGAGAAGGAACTCGGCATTGTTATGCTGGCGAACAAGAGCTACCCGAACCCGGCGCGCGTGGAAGTGGCATACCGTATTCTGAGCGCTCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39773","NCBI_taxonomy_name":"Enterobacter kobei","NCBI_taxonomy_id":"208224"}}}},"ARO_accession":"3007926","ARO_id":"46718","ARO_name":"ACT-161","CARD_short_name":"ACT-161","ARO_description":"Cephalosporin-hydrolyzing class C beta-lactamase ACT-161.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7345":{"model_id":"7345","model_name":"ACT-162","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10172":{"protein_sequence":{"accession":"MCS4603851.1","sequence":"MKTKSLCCALLLSTSCSVLAAPMSEKQLSDVVERTVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVAAKKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQHWQPQWKPGTTRLYANASIGLFGALAVKPSGMSFEQAMTKRVFKPLKLDHTWINVPKEEEAYYAWGYRDGKAVHVSPGMLDAEAYGVKTNVQDMASWVKANMNPAALPDSTLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVEAKTVVEGSDNKVALAPLPVAEVPPPAPPVKASWVHKTGSTGGFGSYVAFIPEKELGIVMLANKSYPNPARVEAAYRILSALQ"},"dna_sequence":{"accession":"JAHWRE010000025.1","fmin":"16929","fmax":"18075","strand":"-","sequence":"ATGAAGACAAAATCCCTTTGCTGTGCCCTGCTGCTCAGCACCTCCTGCTCTGTTCTCGCCGCGCCGATGTCAGAGAAACAGCTGTCTGACGTGGTGGAACGTACCGTTACCCCCCTGATGAAAGCGCAAGCCATTCCGGGCATGGCGGTAGCGGTGATTTATCAGGGTCAGCCGCACTACTTTACCTTCGGAAAGGCCGATGTTGCGGCGAAAAAACCTGTCACCCCGCAAACCCTGTTTGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTATTAGGTGGCGATGCGATTGCGCGCGGAGAAATATCGCTGGGCGACCCCGTGACAAAGTACTGGCCCGAGCTAACAGGCAAGCAGTGGCAGGGTATTCGCATGTTGGATCTGGCGACCTACACCGCGGGTGGCCTGCCGCTACAGGTGCCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGCTTCTATCAACACTGGCAACCGCAGTGGAAACCAGGCACAACGCGTCTTTATGCGAACGCCAGCATCGGGCTTTTTGGCGCCCTCGCGGTTAAACCCTCCGGTATGAGCTTTGAACAGGCCATGACGAAGCGGGTCTTCAAGCCACTCAAACTGGACCATACATGGATTAACGTTCCGAAAGAAGAAGAGGCGTATTACGCCTGGGGATACCGTGATGGTAAAGCGGTCCACGTTTCACCGGGAATGTTGGATGCCGAAGCGTATGGTGTCAAAACCAACGTCCAGGATATGGCGAGCTGGGTGAAGGCCAACATGAACCCTGCCGCTCTTCCGGATTCAACGCTGAAACAGGGTATTGCCCTGGCACAGTCTCGCTACTGGCGCGTGGGTGCCATGTACCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCGGTAGAAGCCAAAACCGTGGTGGAGGGCAGCGATAACAAGGTGGCTCTTGCACCGTTACCGGTGGCTGAAGTGCCCCCCCCAGCTCCGCCAGTAAAAGCGTCATGGGTACATAAAACAGGCTCGACGGGCGGATTTGGCAGCTATGTCGCATTTATTCCTGAGAAGGAACTCGGCATTGTTATGCTGGCGAACAAGAGCTACCCGAACCCGGCGCGCGTGGAAGCGGCATACCGTATTCTGAGCGCTCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39773","NCBI_taxonomy_name":"Enterobacter kobei","NCBI_taxonomy_id":"208224"}}}},"ARO_accession":"3007927","ARO_id":"46719","ARO_name":"ACT-162","CARD_short_name":"ACT-162","ARO_description":"Cephalosporin-hydrolyzing class C beta-lactamase ACT-162.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7346":{"model_id":"7346","model_name":"ACT-165","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10173":{"protein_sequence":{"accession":"MEG5635058.1","sequence":"MMKKFLCCALLLSTSCSVLAAPMSEKQLADVVERNVTPLMKAQGIPGMAVAVIYQGQPHYFTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPDLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANSSIGLFGALAVKPSGMSYEQAMTTRVFKPLKLDHTWINIPKAEETHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVQDMASWVMVNMAPDALQDTSLKQGITLAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVGGSDNKVALAPLPAREVNPPVPPVKASWVHKTGSTGGFGSYAAFIPEKQLGIVMLANKSYPNPARVEAAYRILDALQ"},"dna_sequence":{"accession":"JAXROJ010000007.1","fmin":"195157","fmax":"196303","strand":"+","sequence":"ATGATGAAAAAATTCCTTTGCTGCGCCCTGCTGCTCAGCACATCCTGCTCTGTACTCGCCGCGCCGATGTCGGAAAAACAGCTGGCTGACGTGGTAGAACGCAACGTTACGCCCCTGATGAAAGCGCAGGGTATTCCAGGCATGGCGGTAGCCGTGATTTATCAGGGCCAGCCACACTACTTTACCTTTGGAAAGGCCGATATCGCGGCGAACAAACCCGTCACCCCGCAAACCTTGTTCGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTGCTGGGGGGCGATGCTATTGCCCGCGGCGAAATTTCGCTGGGCGATCCGGTAACCAAATATTGGCCTGATCTGACCGGCAAGCAGTGGCAAGGGATTCGCATGCTGGATCTGGCAACCTACACCGCCGGTGGCCTGCCTTTACAGGTGCCCGATGAGGTCACAGATAACGCATCCCTGCTGCGCTTCTATCAAAACTGGCAGCCTCAGTGGAAGCCGGGCACAACGCGTCTTTACGCCAACTCCAGCATCGGTCTTTTTGGCGCGCTGGCGGTCAAACCTTCCGGCATGAGCTATGAGCAGGCCATGACGACGCGGGTCTTTAAGCCGCTCAAGCTGGATCATACCTGGATTAACATCCCGAAAGCGGAGGAGACGCATTACGCCTGGGGATATCGTGACGGTAAAGCGGTCCACGTTTCACCGGGCATGCTGGACGCAGAGGCATATGGCGTGAAAACCAACGTGCAGGATATGGCGAGCTGGGTGATGGTCAATATGGCCCCTGACGCACTGCAGGATACGTCCCTGAAGCAAGGCATTACGCTGGCGCAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAGGGGTTAGGTTGGGAGATGCTTAACTGGCCGGTCGATGCCAAAACCGTCGTCGGAGGCAGTGATAACAAGGTGGCGCTGGCACCGTTGCCTGCGAGAGAAGTGAATCCACCCGTTCCTCCGGTTAAGGCCTCATGGGTGCACAAAACGGGCTCCACCGGCGGGTTTGGCAGCTACGCGGCCTTTATTCCTGAAAAGCAGCTCGGCATTGTGATGCTGGCGAATAAAAGCTATCCGAACCCGGCGCGAGTTGAGGCGGCATACCGTATCCTCGACGCGCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"47906","NCBI_taxonomy_name":"Enterobacter bugandensis","NCBI_taxonomy_id":"881260"}}}},"ARO_accession":"3007928","ARO_id":"46720","ARO_name":"ACT-165","CARD_short_name":"ACT-165","ARO_description":"Cephalosporin-hydrolyzing class C beta-lactamase ACT-165.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7347":{"model_id":"7347","model_name":"ACT-166","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10174":{"protein_sequence":{"accession":"MEG5532466.1","sequence":"MMKKSLCCALLLSTSCAALAAPLSETQLAKVVERTVTPLMKAQSIPGMAVAVIYQGQPHYFTFGKADVAANTPVTAQTLFELGSISKTFTGVLGGDAIARGEMSLGDPVTKYWPELTGKQWQGVRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQSWQPQWAPGTTRLYANASIGLFGALAVKPSGMRFEQAMTERVLKPLNLNHTWINVPKSEEQHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVKDMASWVVANMAPDGIQDASLKQGMVLAQSRYWRTGSMYQGLGWEMLNWPVEAKTVVEGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKELGIVMLANKSYPNPARVEAAYRILSALQ"},"dna_sequence":{"accession":"JAXRNI010000004.1","fmin":"14773","fmax":"15919","strand":"-","sequence":"ATGATGAAAAAATCCCTGTGCTGCGCCCTGCTGCTCAGCACTTCCTGCGCTGCATTAGCCGCACCTCTGTCAGAAACACAGCTGGCAAAGGTCGTGGAACGTACCGTTACGCCCCTGATGAAAGCGCAGTCTATTCCGGGTATGGCGGTCGCCGTGATCTATCAGGGCCAGCCGCACTACTTCACCTTCGGCAAGGCCGATGTCGCAGCGAACACACCCGTCACTGCACAAACGCTGTTTGAGCTGGGCTCAATCAGCAAAACCTTCACCGGCGTTCTGGGTGGCGATGCTATTGCTCGCGGTGAAATGTCGCTGGGCGATCCGGTGACTAAATACTGGCCTGAGCTGACCGGCAAACAGTGGCAGGGCGTTCGCATGCTGGACCTGGCAACCTATACTGCCGGTGGCCTGCCGTTACAGGTGCCCGATGAGGTTACCGATAATGCCTCGCTGCTGCGTTTTTACCAGTCCTGGCAACCACAGTGGGCGCCAGGCACCACGCGTCTTTATGCAAATGCCAGCATCGGTCTGTTTGGGGCTCTGGCGGTGAAACCTTCTGGCATGCGCTTTGAGCAGGCGATGACAGAGCGGGTCCTGAAGCCGCTTAACCTGAACCATACGTGGATTAACGTTCCGAAGTCAGAAGAACAGCATTACGCCTGGGGTTATCGTGACGGTAAAGCGGTTCACGTTTCGCCGGGCATGCTCGACGCCGAAGCGTATGGCGTGAAAACCAACGTGAAGGATATGGCGAGCTGGGTGGTGGCTAACATGGCCCCCGATGGCATACAGGATGCCTCACTGAAGCAGGGCATGGTGCTTGCACAGTCTCGCTACTGGCGCACAGGCTCGATGTACCAAGGCCTGGGCTGGGAGATGCTCAACTGGCCGGTAGAAGCCAAAACCGTGGTGGAGGGCAGCGACAACAAGGTAGCGCTTGCACCGTTGCCCGTGGCAGAAGTGAACCCTCCGGCTCCACCGGTAAAAGCGTCATGGGTACATAAAACAGGCTCGACGGGCGGATTTGGCAGCTACGTGGCATTTATCCCTGAGAAGGAACTCGGCATTGTTATGCTGGCGAACAAGAGCTACCCGAACCCGGCACGCGTGGAAGCGGCATACCGTATTCTGAGCGCTCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"45936","NCBI_taxonomy_name":"Enterobacter ludwigii","NCBI_taxonomy_id":"299767"}}}},"ARO_accession":"3007929","ARO_id":"46721","ARO_name":"ACT-166","CARD_short_name":"ACT-166","ARO_description":"Cephalosporin-hydrolyzing class C beta-lactamase ACT-166.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7348":{"model_id":"7348","model_name":"ACT-167","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10175":{"protein_sequence":{"accession":"XAJ73541.1","sequence":"MMTKSLCYALLLSTSCSVLAAPMSEKQLAEVVERTVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVADNASLLRFYQNWQPQWKPGTTRLYANTSIGLFGALAVKPSGMSYEQAITTRVFKPLRLDHTWINVPKAEEAHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVQDMASWVMVNMKPDSLHDNSLRQGIALAQSRYWRVGAMYQGLGWEMLNWPVDARTVVEGSDNKVALAPLPAREVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILDALQ"},"dna_sequence":{"accession":"PP740475.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGACAAAATCCCTTTGCTACGCCCTGCTGCTCAGCACCTCCTGCTCAGTATTGGCTGCCCCGATGTCAGAAAAACAGCTGGCTGAAGTGGTGGAACGGACTGTTACGCCGCTGATGAAAGCGCAGGCCATTCCGGGTATGGCGGTGGCGGTGATTTATCAGGGTCAGCCGCACTACTTTACCTTCGGTAAAGCCGATGTTGCGGCAAACAAGCCTGTCACCCCACAAACCTTGTTCGAACTGGGTTCTATAAGTAAAACCTTCACCGGTGTACTGGGTGGCGATGCGATTGCTCGCGGTGAAATATCGCTGGGCGACCCGGTGACCAAATACTGGCCTGAGCTGACAGGCAAGCAGTGGCAGGGGATCCGCATGCTGGATCTGGCAACCTATACCGCAGGGGGTCTGCCGTTACAGGTACCGGATGAGGTCGCGGATAACGCCTCTCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCGGGCACCACGCGTCTTTACGCCAATACCAGCATCGGCCTTTTTGGCGCGCTGGCGGTCAAACCTTCCGGCATGAGCTATGAGCAGGCCATAACGACGCGGGTCTTTAAGCCGCTCAGGCTGGACCATACCTGGATTAACGTTCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGATACCGTGACGGTAAAGCGGTACACGTTTCGCCAGGCATGCTCGACGCGGAAGCCTATGGCGTAAAAACCAACGTGCAGGATATGGCAAGCTGGGTAATGGTCAACATGAAGCCGGACTCCCTTCATGATAATTCACTCAGGCAAGGCATTGCCCTGGCGCAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAGGGTTTAGGCTGGGAAATGCTTAACTGGCCGGTCGATGCCAGAACCGTGGTTGAAGGTAGCGACAATAAGGTGGCGCTGGCACCGCTGCCCGCGAGAGAAGTGAATCCACCAGCGCCTCCGGTAAAAGCCTCATGGGTGCACAAAACCGGCTCAACCGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGCTCGGCATTGTGATGCTGGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCGTATCCTCGACGCGCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"47911","NCBI_taxonomy_name":"Enterobacter sp.","NCBI_taxonomy_id":"42895"}}}},"ARO_accession":"3007930","ARO_id":"46722","ARO_name":"ACT-167","CARD_short_name":"ACT-167","ARO_description":"Cephalosporin-hydrolyzing class C beta-lactamase ACT-167.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7349":{"model_id":"7349","model_name":"ACT-168","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10176":{"protein_sequence":{"accession":"XAJ73542.1","sequence":"MMKKNLSCALLLSVASAAFAAPMSEKQLAEVVERTVTPLMNAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEITLGDPVTKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDTASLLRFYQNWQPKWKPGTTRLYANTSIGLFGALAVKPSGMSYEQAMTTRVFKPLKLDHTWINVPKAEEAHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVQDMASWVMVNMMPDSLQDSPLKHGIALAQSRYWRVGSMYQGLGWEMLNWPVDAQTVVGGSDNKVALAPLPAREVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILDALQ"},"dna_sequence":{"accession":"PP740476.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAAAACCTAAGCTGTGCCCTGCTGCTCAGCGTTGCCAGCGCTGCATTCGCCGCACCGATGTCCGAAAAACAGCTGGCTGAGGTGGTGGAACGTACCGTTACGCCGCTGATGAACGCGCAGGCCATTCCGGGTATGGCGGTGGCGGTGATTTATCAGGGTCAGCCGCACTACTTTACCTTCGGTAAAGCTGATGTTGCAGCGAACAAACCCGTCACCCCGCAAACCTTGTTCGAGCTGGGTTCGATAAGTAAAACCTTCACCGGCGTATTGGGTGGCGATGCGATTGCGCGCGGTGAAATAACGCTGGGCGATCCGGTGACCAAATACTGGCCTGAGCTCACGGGCAAGCAGTGGCAGGGCATTCGCATGCTGGATCTGGCAACCTATACCGCAGGCGGCCTGCCGTTGCAGGTGCCGGATGAGGTCACGGATACCGCCTCCCTGCTGCGCTTTTATCAAAACTGGCAGCCAAAGTGGAAGCCGGGCACCACGCGTCTTTACGCTAACACCAGCATCGGTCTTTTTGGCGCGCTGGCGGTCAAACCCTCCGGCATGAGCTATGAGCAGGCCATGACGACGCGGGTATTTAAGCCGCTCAAGCTGGACCATACATGGATTAACGTCCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGATACCGTGACGGTAAAGCGGTCCACGTTTCGCCAGGGATGCTGGACGCGGAAGCCTATGGCGTAAAAACCAACGTGCAGGATATGGCAAGCTGGGTGATGGTCAATATGATGCCGGACTCCCTTCAGGATTCCCCACTTAAACACGGTATTGCCCTGGCACAGTCTCGCTACTGGCGCGTGGGATCCATGTATCAAGGATTGGGCTGGGAAATGCTGAACTGGCCGGTCGACGCCCAAACGGTGGTCGGGGGCAGCGACAATAAGGTGGCGCTGGCGCCGTTGCCTGCAAGAGAAGTGAATCCACCGGCACCACCGGTTAAGGCCTCCTGGGTCCATAAAACGGGCTCTACCGGCGGATTTGGCAGCTACGTGGCATTTATTCCTGAAAAGCAGCTCGGCATTGTGATGCTGGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCGTATCCTCGACGCGCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"47909","NCBI_taxonomy_name":"Enterobacter quasiroggenkampii","NCBI_taxonomy_id":"2497436"}}}},"ARO_accession":"3007931","ARO_id":"46723","ARO_name":"ACT-168","CARD_short_name":"ACT-168","ARO_description":"Cephalosporin-hydrolyzing class C beta-lactamase ACT-168.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7350":{"model_id":"7350","model_name":"ACT-169","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10177":{"protein_sequence":{"accession":"XAJ73543.1","sequence":"MKTKSLCCALMLSTSCSVLAAPMSEKQLSDVVERTVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQHWQPQWKPGTTRLYANASIGLFGALAVKPSGMSFEQAMTKRVFKPLKLDHTWINVPKEEEAHYAWGYRDGKATHVSPGMLDAEAYGVKTNVQDMASWVKANMNPDALPDSTLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVEAKTFVEGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKELGIVMLANKSYPNPARVEAAYRILSALQ"},"dna_sequence":{"accession":"PP740477.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGAAGACAAAATCCCTTTGCTGTGCCCTGATGCTCAGCACCTCCTGCTCTGTTCTCGCCGCGCCGATGTCAGAGAAACAGCTGTCTGACGTGGTGGAACGTACCGTTACCCCCCTGATGAAAGCGCAAGCCATTCCGGGCATGGCGGTAGCGGTGATTTATCAGGGTCAGCCGCACTACTTTACCTTCGGAAAGGCCGATGTTGCGGCGAACAAACCTGTCACCCCGCAAACCCTGTTTGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTATTAGGTGGCGATGCGATTGCGCGCGGAGAAATATCGCTGGGCGACCCCGTGACAAAGTACTGGCCCGAGCTAACAGGCAAGCAGTGGCAGGGTATTCGCATGTTGGATCTGGCGACCTACACCGCGGGTGGCCTGCCGCTACAGGTGCCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGTTTCTATCAACACTGGCAACCGCAGTGGAAACCAGGCACAACGCGTCTTTATGCGAACGCCAGCATCGGGCTTTTTGGCGCCCTCGCGGTTAAACCCTCCGGTATGAGCTTTGAACAGGCCATGACGAAGCGGGTCTTCAAGCCACTCAAACTGGACCATACATGGATTAACGTTCCGAAAGAAGAAGAGGCGCATTACGCCTGGGGATACCGTGACGGTAAAGCAACCCACGTTTCACCGGGAATGCTGGATGCCGAAGCGTATGGTGTCAAAACCAACGTCCAGGATATGGCGAGCTGGGTGAAGGCCAACATGAACCCTGACGCCCTTCCGGATTCAACGTTGAAACAGGGTATTGCCCTGGCACAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCGGTAGAAGCCAAAACCTTCGTGGAGGGCAGCGATAACAAGGTGGCTCTTGCACCGTTACCGGTGGCAGAAGTGAACCCTCCAGCTCCGCCAGTAAAAGCATCATGGGTACATAAAACAGGCTCGACGGGTGGATTCGGCAGCTATGTCGCATTTATTCCTGAGAAGGAACTCGGCATTGTTATGCTGGCGAACAAGAGCTACCCGAACCCGGCGCGCGTGGAAGCGGCATACCGTATTCTGAGCGCTCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39773","NCBI_taxonomy_name":"Enterobacter kobei","NCBI_taxonomy_id":"208224"}}}},"ARO_accession":"3007932","ARO_id":"46724","ARO_name":"ACT-169","CARD_short_name":"ACT-169","ARO_description":"Cephalosporin-hydrolyzing class C beta-lactamase ACT-169.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7351":{"model_id":"7351","model_name":"ACT-170","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10178":{"protein_sequence":{"accession":"XAJ73544.1","sequence":"MMKKFLCCALLLNTSCSVLAAPMSEKQLADVVERNVTPLMKAQGIPGMAVAVIYQGQPHYFTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAISRGEISMGDPVTKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANSSIGLFGALAVKPSGMSYEQAMTARVFKPLKLDHTWINVPKAEETHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVQDMASWVMANMAPDALQDTSLKQGITLAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVGGSDNKVALAPLPAREVNPPVPLVKASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILDALQ"},"dna_sequence":{"accession":"PP740478.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATTCCTTTGCTGCGCCCTGCTGCTCAACACATCCTGCTCTGTACTCGCCGCGCCGATGTCGGAAAAACAGCTGGCTGACGTGGTAGAACGCAACGTTACGCCCCTGATGAAAGCGCAGGGTATTCCAGGCATGGCGGTGGCCGTGATTTATCAGGGCCAGCCACACTACTTTACCTTTGGAAAGGCCGATATCGCGGCGAACAAACCCGTCACCCCGCAAACCCTGTTCGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTGCTGGGGGGCGATGCTATTTCCCGCGGCGAAATTTCGATGGGCGATCCGGTAACTAAATATTGGCCTGAACTGACCGGCAAGCAGTGGCAAGGGATTCGCATGCTGGATCTGGCAACCTACACCGCCGGTGGCCTGCCTTTACAGGTGCCCGATGAGGTTACAGATAACGCATCCCTGCTGCGCTTCTATCAAAACTGGCAGCCTCAGTGGAAGCCGGGCACAACGCGTCTTTACGCCAACTCCAGCATCGGTCTTTTTGGCGCGCTGGCGGTCAAACCTTCCGGCATGAGCTATGAGCAGGCCATGACGGCGCGGGTCTTTAAGCCGCTCAAGCTGGATCATACCTGGATTAACGTTCCGAAAGCGGAGGAGACGCATTACGCCTGGGGATATCGTGACGGTAAAGCGGTCCACGTTTCACCGGGCATGCTGGACGCAGAGGCATATGGCGTGAAAACCAACGTGCAGGATATGGCGAGCTGGGTGATGGCCAACATGGCCCCTGACGCGCTGCAGGATACGTCCCTGAAGCAAGGCATTACGCTGGCGCAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAGGGGTTAGGTTGGGAGATGCTTAACTGGCCGGTCGATGCCAAAACCGTCGTCGGAGGCAGTGATAACAAGGTGGCGCTGGCACCGTTGCCTGCGAGAGAAGTGAATCCACCCGTTCCCCTGGTTAAGGCCTCATGGGTGCACAAAACGGGCTCCACCGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGCTCGGCATTGTGATGCTGGCGAATAAAAGCTATCCGAACCCGGCGCGAGTTGAGGCGGCATACCGTATCCTCGACGCGCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"47906","NCBI_taxonomy_name":"Enterobacter bugandensis","NCBI_taxonomy_id":"881260"}}}},"ARO_accession":"3007933","ARO_id":"46725","ARO_name":"ACT-170","CARD_short_name":"ACT-170","ARO_description":"Cephalosporin-hydrolyzing class C beta-lactamase ACT-170.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7352":{"model_id":"7352","model_name":"ACT-171","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10179":{"protein_sequence":{"accession":"XAJ73545.1","sequence":"MMKKSLCCALLLGISCSALATPVSEKQLAEVVANTVTPLMKAQSVPGMAVAVIYQGKPHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMPYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDARAYGVKTNVQDMANWVMANMAPENVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVVEGSDSKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANTSYPNPARVEAAYHILEALQ"},"dna_sequence":{"accession":"PP740479.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCCCTTTGCTGCGCCCTGCTGCTCGGCATCTCTTGCTCTGCTCTCGCCACGCCAGTGTCAGAAAAACAGCTGGCGGAGGTGGTAGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCTGTTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGAAAACCGCACTATTACACGTTTGGCAAGGCCGATATCGCGGCGAATAAACCCGTTACGCCTCAGACCCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGCGTGTTAGGTGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTGACGGGCAAGCAGTGGCAGGGTATTCGTATGCTGGATCTCGCCACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTCAAACCTTCTGGCATGCCCTATGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTGCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGTATGCTGGATGCACGAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCACCGGAGAACGTTGCTGATGCCTCACTTAAACAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGGTCGAGGGCAGCGACAGTAAGGTAGCGCTGGCGCCGTTGCCCGTGGCAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGCTCTACTGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATACAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCGAGGCGCTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39098","NCBI_taxonomy_name":"Enterobacter hormaechei","NCBI_taxonomy_id":"158836"}}}},"ARO_accession":"3007934","ARO_id":"46726","ARO_name":"ACT-171","CARD_short_name":"ACT-171","ARO_description":"Cephalosporin-hydrolyzing class C beta-lactamase ACT-171.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7353":{"model_id":"7353","model_name":"ACT-172","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10180":{"protein_sequence":{"accession":"XAJ73546.1","sequence":"MMKKFLCCALLLSTSCSVLAAPMSEKQLADVVERNVTPLMKAQGIPGMAVAVIYQGQPHYFTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPDLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANSSIGLFGALAVKPSGMSYEQAMTTRVLKPLKLDHTWINVPKAEETHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVQDMASWVMANMAPDALQDTSLKQGITLAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVGGSDNKVALAPLPAREVNPPVPPVKASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILDALQ"},"dna_sequence":{"accession":"PP740480.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATTCCTTTGCTGCGCCCTGCTGCTCAGCACATCCTGCTCTGTACTCGCCGCGCCGATGTCGGAAAAACAGCTGGCTGACGTGGTAGAACGCAACGTTACGCCCCTGATGAAAGCGCAGGGTATTCCAGGCATGGCGGTGGCCGTGATTTATCAGGGCCAGCCACACTACTTTACCTTTGGAAAGGCCGATATCGCGGCGAACAAACCCGTCACCCCGCAAACCCTGTTCGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTGCTGGGGGGCGATGCTATTGCCCGCGGCGAAATTTCGCTGGGCGATCCGGTAACCAAATATTGGCCTGATCTGACCGGCAAGCAGTGGCAAGGGATTCGCATGCTGGATCTGGCAACCTACACCGCCGGTGGCCTGCCTTTACAGGTGCCCGATGAGGTCACAGATAACGCTTCCCTGCTGCGCTTCTATCAAAACTGGCAGCCTCAGTGGAAGCCGGGCACAACGCGTCTTTACGCCAACTCCAGCATCGGTCTTTTTGGCGCGCTGGCGGTCAAACCTTCCGGCATGAGCTATGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGATCATACCTGGATTAACGTTCCGAAAGCGGAGGAGACGCATTACGCCTGGGGATATCGTGACGGTAAAGCGGTCCACGTTTCACCGGGCATGCTGGACGCAGAGGCATATGGCGTGAAAACCAACGTGCAGGATATGGCGAGCTGGGTGATGGCCAATATGGCCCCTGACGCACTGCAGGATACGTCCCTGAAGCAAGGCATTACGCTGGCGCAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAGGGGTTAGGTTGGGAGATGCTTAACTGGCCGGTCGATGCCAAAACCGTCGTCGGAGGCAGTGATAACAAGGTGGCGCTGGCACCGTTGCCTGCGAGAGAAGTGAATCCACCCGTTCCCCCGGTTAAGGCCTCATGGGTGCACAAAACGGGCTCCACCGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGCTCGGCATTGTGATGCTGGCGAATAAAAGCTATCCGAACCCGGCGCGAGTTGAGGCGGCATACCGTATCCTCGACGCGCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"47906","NCBI_taxonomy_name":"Enterobacter bugandensis","NCBI_taxonomy_id":"881260"}}}},"ARO_accession":"3007935","ARO_id":"46727","ARO_name":"ACT-172","CARD_short_name":"ACT-172","ARO_description":"Cephalosporin-hydrolyzing class C beta-lactamase ACT-172.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7354":{"model_id":"7354","model_name":"ACT-173","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10181":{"protein_sequence":{"accession":"XAJ73547.1","sequence":"MMTKSLSCALLLSVASSAFAAPMSEKQLAEVVERTVTPLMNAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNAALLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMSYEQAITTRVFKPLKLDHTWINVPKTEEAHYAWGYSDGKAVHVSPGMLDAEAYGVKTNVQDMASWVMVNMKPDSLQDSSLRKGIALAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVEGSDNKVALAPLPAREVNPPAPPVNASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVDAAYRILSAL"},"dna_sequence":{"accession":"PP740481.1","fmin":"0","fmax":"1143","strand":"+","sequence":"ATGATGACAAAATCCCTAAGCTGTGCCCTGCTGCTCAGCGTTGCCAGCTCTGCATTCGCCGCACCGATGTCCGAAAAACAGCTGGCTGAGGTGGTGGAACGTACCGTTACGCCGTTGATGAATGCGCAGGCCATCCCGGGTATGGCGGTGGCGGTGATTTATCAGGGTCAGCCGCACTACTTTACCTTCGGTAAAGCCGATGTTGCGGCAAACAAACCCGTTACCCCACAAACCTTGTTCGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTATTGGGTGGCGATGCCATTGCTCGCGGTGAAATATCGCTCGGCGATCCGGTGACAAAATACTGGCCTGAGCTGACGGGCAAACAGTGGCAGGGCATTCGCATGCTGGATCTGGCAACCTATACCGCAGGCGGTCTGCCGTTACAGGTACCGGATGAAGTCACGGATAACGCCGCTCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCGGGCACCACGCGTCTTTACGCCAATGCCAGCATCGGTCTTTTTGGCGCGCTGGCGGTCAAACCTTCCGGCATGAGCTATGAGCAGGCCATAACGACGCGGGTCTTTAAGCCACTCAAGCTGGACCATACCTGGATTAACGTTCCGAAAACGGAAGAGGCGCATTACGCCTGGGGATACAGCGACGGTAAAGCGGTCCACGTTTCGCCAGGAATGCTGGATGCGGAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCAAGCTGGGTGATGGTCAACATGAAGCCGGACTCGCTTCAGGATAGTTCACTCAGGAAAGGCATTGCCCTGGCGCAGTCTCGCTACTGGCGCGTGGGGGCCATGTATCAGGGGTTAGGCTGGGAAATGCTTAACTGGCCGGTCGATGCCAAAACCGTGGTTGAAGGCAGCGACAATAAGGTGGCGCTGGCACCGTTGCCTGCGAGAGAAGTGAATCCACCGGCGCCCCCGGTCAACGCGTCCTGGGTCCATAAAACAGGCTCTACCGGTGGGTTTGGCAGCTACGTGGCATTTATTCCTGAAAAACAGCTCGGCATTGTAATGCTGGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGATGCGGCATACCGTATTTTGAGCGCGCTGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"47911","NCBI_taxonomy_name":"Enterobacter sp.","NCBI_taxonomy_id":"42895"}}}},"ARO_accession":"3007936","ARO_id":"46728","ARO_name":"ACT-173","CARD_short_name":"ACT-173","ARO_description":"Cephalosporin-hydrolyzing class C beta-lactamase ACT-173.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7355":{"model_id":"7355","model_name":"ACT-174","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10182":{"protein_sequence":{"accession":"XAJ73548.1","sequence":"MMKKSLCCALLLGISCSALATPVSEKQLAEVVANTVTPLMKAQSVPGMAVAVIYQGKPHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQSIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMPYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPENVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVVEGSDSKVALAPLPVVEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANTSYPNPARVEAAYYILEALQ"},"dna_sequence":{"accession":"PP740482.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCCCTTTGCTGCGCCCTGCTGCTCGGCATCTCTTGCTCTGCTCTCGCCACGCCAGTGTCAGAAAAACAGCTGGCGGAGGTGGTCGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCTGTTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGAAAACCGCACTATTACACGTTTGGCAAGGCCGATATCGCGGCGAATAAACCCGTTACGCCTCAGACCCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGCGTTTTAGGTGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTGACGGGCAAGCAGTGGCAGAGTATTCGTATGCTGGATCTCGCCACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTCAAACCTTCTGGCATGCCCTATGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTGCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGTATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCGGAGAACGTTGCTGATGCCTCACTTAAGCAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGGTCGAGGGCAGCGACAGTAAGGTAGCGCTGGCGCCGTTGCCCGTGGTAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGCTCTACTGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATACAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACTATATCCTCGAGGCGCTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39098","NCBI_taxonomy_name":"Enterobacter hormaechei","NCBI_taxonomy_id":"158836"}}}},"ARO_accession":"3007937","ARO_id":"46729","ARO_name":"ACT-174","CARD_short_name":"ACT-174","ARO_description":"Cephalosporin-hydrolyzing class C beta-lactamase ACT-174.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7356":{"model_id":"7356","model_name":"ACT-175","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10183":{"protein_sequence":{"accession":"XAJ73549.1","sequence":"MMKKFLCCALLLSTSCSVLAAPMSEKQLADVVERNVTPLMKAQGIPGMAVAVIYQGQPHYFTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPDLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANSSIGLFGALAVKPSSMSYEQAMTTRVFKPLKLDHTWINVPKAEETHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVQDMASWVMANMAPDALQDTSLKQGITLAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVGGSDNKVALAPLPAREVSPPVPLVKASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILDALQ"},"dna_sequence":{"accession":"PP740483.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATTCCTTTGCTGCGCCCTGCTGCTCAGCACATCCTGCTCTGTACTCGCCGCGCCGATGTCGGAAAAACAGCTGGCTGACGTGGTAGAACGCAACGTTACGCCCCTGATGAAAGCGCAGGGTATTCCAGGCATGGCGGTGGCCGTGATTTATCAGGGCCAGCCACATTACTTTACCTTTGGAAAGGCCGATATCGCGGCGAACAAACCCGTCACCCCGCAAACCCTGTTCGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTGCTGGGGGGCGATGCTATTGCCCGCGGCGAAATTTCGCTGGGCGATCCGGTAACCAAATATTGGCCTGATCTGACCGGCAAGCAGTGGCAAGGGATTCGCATGCTGGATCTGGCAACCTACACCGCCGGTGGCCTGCCTTTACAGGTGCCCGATGAGGTCACAGATAACGCATCCCTGCTGCGCTTCTATCAAAACTGGCAGCCTCAGTGGAAGCCGGGCACAACGCGTCTTTACGCCAACTCCAGCATCGGTCTTTTTGGCGCGCTGGCGGTCAAACCTTCCAGCATGAGCTATGAGCAGGCCATGACGACGCGGGTCTTTAAGCCGCTCAAGCTGGATCATACCTGGATTAACGTTCCGAAAGCGGAGGAGACGCATTACGCCTGGGGATATCGTGACGGTAAAGCGGTCCACGTTTCACCGGGCATGCTGGATGCAGAGGCATATGGCGTGAAAACCAACGTGCAGGATATGGCGAGCTGGGTGATGGCCAATATGGCCCCTGACGCACTGCAGGATACGTCCCTGAAGCAAGGCATTACGCTGGCGCAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAGGGGTTAGGTTGGGAGATGCTTAACTGGCCGGTCGATGCCAAAACAGTCGTCGGAGGCAGTGATAACAAGGTGGCGCTGGCACCGTTGCCTGCGAGAGAAGTGAGTCCACCCGTTCCCTTGGTTAAGGCCTCATGGGTGCACAAAACGGGCTCCACCGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGCTCGGCATTGTGATGCTGGCGAATAAAAGCTATCCGAACCCGGCGCGAGTTGAGGCGGCATACCGTATCCTCGACGCGCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"47906","NCBI_taxonomy_name":"Enterobacter bugandensis","NCBI_taxonomy_id":"881260"}}}},"ARO_accession":"3007938","ARO_id":"46730","ARO_name":"ACT-175","CARD_short_name":"ACT-175","ARO_description":"Cephalosporin-hydrolyzing class C beta-lactamase ACT-175.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7357":{"model_id":"7357","model_name":"ACT-176","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10184":{"protein_sequence":{"accession":"XAJ73550.1","sequence":"MMKKSLCCALLLSVACSAFAAPMSEKQLAKVVERAVTPLMNAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTRYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDDVTDNASLLRFYQNWQPQWKPGTARLYANASIGLFGALAVKPSGMSFEEAMTKRVFKPLRLDHTWINVPKAEEAHYAWGYRDGKAVHVSPGMLDAEAYGIKTNVKDMASWVVANMAPDALQDSSLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVGGSDNKVALAPLPAREVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVETAYRILDALQ"},"dna_sequence":{"accession":"PP740484.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCCCTATGTTGTGCCCTGCTGCTCAGCGTTGCCTGCTCTGCCTTCGCCGCCCCCATGTCAGAAAAACAGCTGGCTAAGGTGGTGGAGCGTGCCGTTACGCCGCTGATGAACGCGCAGGCCATTCCGGGTATGGCGGTGGCGGTAATTTATCAGGGTCAGCCGCACTACTTTACCTTTGGTAAAGCGGATGTCGCGGCGAATAAACCTGTTACGCCTCAAACCTTGTTCGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTATTGGGTGGCGATGCCATTGCTCGCGGTGAAATCTCACTGGGCGATCCAGTGACAAGGTACTGGCCTGAGCTGACAGGAAAACAGTGGCAGGGCATTCGCATGCTGGATCTGGCAACCTATACCGCAGGGGGGTTGCCGTTACAGGTACCGGATGACGTCACTGACAACGCCTCTCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCGGGCACCGCGCGTCTTTATGCCAACGCCAGCATCGGTCTTTTTGGTGCTCTCGCGGTTAAACCCTCCGGCATGAGTTTTGAAGAGGCCATGACGAAGCGGGTCTTTAAGCCGCTCAGGCTCGACCATACGTGGATTAACGTACCAAAAGCGGAAGAGGCGCATTACGCCTGGGGATACCGTGACGGTAAAGCGGTACACGTTTCTCCAGGGATGCTGGACGCTGAAGCCTATGGCATAAAAACCAACGTGAAAGATATGGCGAGCTGGGTGGTGGCAAACATGGCCCCCGATGCCCTTCAGGATAGCTCTCTCAAACAAGGGATAGCCCTGGCACAGTCCCGCTACTGGCGCGTGGGTGCCATGTATCAGGGGTTAGGCTGGGAAATGCTGAACTGGCCGGTCGATGCCAAAACCGTGGTCGGGGGCAGCGACAATAAGGTGGCGCTGGCGCCGTTGCCTGCCAGAGAAGTCAATCCCCCGGCACCGCCGGTTAAGGCCTCCTGGGTACACAAAACGGGTTCAACCGGTGGGTTTGGGAGCTACGTGGCATTTATTCCTGAAAAACAGCTCGGCATTGTGATGCTGGCGAATAAAAGCTATCCGAATCCGGCACGCGTTGAGACGGCATACCGTATCCTCGACGCGCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"47910","NCBI_taxonomy_name":"Enterobacter sichuanensis","NCBI_taxonomy_id":"2071710"}}}},"ARO_accession":"3007939","ARO_id":"46731","ARO_name":"ACT-176","CARD_short_name":"ACT-176","ARO_description":"Cephalosporin-hydrolyzing class C beta-lactamase ACT-176.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7358":{"model_id":"7358","model_name":"ACT-177","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10185":{"protein_sequence":{"accession":"XAJ73551.1","sequence":"MMTKSLCCALLLSTSCSVLATPMSEKQLAEVVERTVTPLMKAQAIPGMAVAVIYEGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMSYEQAITTRVFKPLKLDHTWINVPKADEAHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVQDMASWVMVNMKPDSLQDNSLRQGIALAQSRYWRVGAMYQGLGWEMLNWPVDARTVVEGSDNKAALAPLPAREVNPPAPPVNASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILSAL"},"dna_sequence":{"accession":"PP740485.1","fmin":"0","fmax":"1143","strand":"+","sequence":"ATGATGACTAAATCCCTTTGCTGCGCCCTGCTGCTCAGCACCTCCTGCTCGGTATTGGCTACCCCGATGTCAGAAAAACAGCTGGCTGAGGTGGTGGAACGGACCGTTACGCCGCTGATGAAAGCGCAGGCCATTCCGGGTATGGCGGTGGCGGTGATTTATGAGGGTCAGCCGCACTACTTCACCTTCGGTAAAGCCGATGTTGCGGCGAACAAACCTGTCACTCCACAAACCTTGTTCGAACTGGGTTCTATAAGTAAAACCTTCACCGGCGTACTCGGTGGCGATGCCATTGCTCGCGGTGAAATATCGCTGGGCGATCCGGTGACAAAATACTGGCCTGAGCTGACAGGCAAGCAGTGGCAGGGGATCCGCATGCTGGATCTGGCAACCTATACCGCAGGAGGTTTGCCGTTACAGGTACCGGATGAGGTCACGGATAACGCCTCTCTGTTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCGGGCACCACGCGTCTTTACGCCAATGCCAGCATCGGTCTTTTTGGCGCGCTGGCGGTCAAACCTTCCGGCATGAGCTATGAGCAGGCCATAACGACGCGGGTCTTTAAGCCGCTCAAGCTGGACCATACGTGGATTAACGTTCCGAAAGCGGACGAGGCGCATTACGCCTGGGGATACCGCGACGGTAAAGCGGTACACGTTTCGCCAGGAATGCTGGACGCTGAAGCCTATGGCGTAAAAACCAACGTGCAGGATATGGCAAGCTGGGTGATGGTCAACATGAAGCCGGACTCCCTTCAGGATAATTCACTCAGGCAAGGCATTGCCCTGGCGCAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAGGGGTTAGGCTGGGAAATGCTTAACTGGCCGGTCGATGCCAGAACCGTGGTTGAAGGTAGCGACAATAAGGCGGCACTGGCACCGCTGCCTGCGAGAGAAGTGAATCCACCGGCGCCCCCGGTCAACGCGTCCTGGGTCCATAAAACAGGCTCTACCGGCGGGTTTGGCAGCTACGTAGCATTTATTCCTGAAAAGCAGCTCGGCATTGTGATGCTGGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCGTATTTTGAGCGCGCTGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36926","NCBI_taxonomy_name":"Enterobacter asburiae","NCBI_taxonomy_id":"61645"}}}},"ARO_accession":"3007940","ARO_id":"46732","ARO_name":"ACT-177","CARD_short_name":"ACT-177","ARO_description":"Cephalosporin-hydrolyzing class C beta-lactamase ACT-177.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7359":{"model_id":"7359","model_name":"ACT-178","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10186":{"protein_sequence":{"accession":"XAJ73552.1","sequence":"MMKKSLCCALLLGISCSALATPVSEKQLAEVVANTVTPLMKAQSVPGMAVAVIYQGKPHYYTFGKADIAANKPVTPQTLFELGSISKTFTAVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGDLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMPYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPENVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVVEGSDSKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANTSYPNPARVEAAYHILEALQ"},"dna_sequence":{"accession":"PP740486.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCCCTTTGCTGCGCCCTGCTGCTCGGCATCTCTTGCTCTGCTCTCGCCACGCCAGTGTCAGAAAAACAGCTGGCGGAGGTGGTCGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCTGTTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGAAAACCGCACTATTACACGTTTGGCAAGGCCGATATCGCGGCGAATAAACCCGTTACGCCTCAGACCCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGCCGTTTTAGGTGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTGACGGGCAAGCAGTGGCAGGGTATTCGTATGCTGGATCTCGCCACCTACACCGCTGGCGACCTGCCGCTACAGGTACCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTCAAACCTTCTGGCATGCCCTATGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTGCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGTATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCGGAGAACGTTGCTGATGCCTCACTTAAGCAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGGTCGAGGGCAGCGACAGTAAGGTAGCACTGGCGCCGTTGCCCGTGGCAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGCTCTACTGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATACAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCGAGGCGCTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39098","NCBI_taxonomy_name":"Enterobacter hormaechei","NCBI_taxonomy_id":"158836"}}}},"ARO_accession":"3007941","ARO_id":"46733","ARO_name":"ACT-178","CARD_short_name":"ACT-178","ARO_description":"Cephalosporin-hydrolyzing class C beta-lactamase ACT-178.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7360":{"model_id":"7360","model_name":"ACT-179","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10187":{"protein_sequence":{"accession":"XAJ73553.1","sequence":"MMKKSLCCALLLGISCSALATPVSEKQLAEVVANTVTPLMKAQSVPGMAVAVIYQGKPHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMPYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPENVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVVEGSDSKVALAPLPVAEVNPPAPSVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANTSYPNLARVEAAYHILEALQ"},"dna_sequence":{"accession":"PP740487.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCCCTTTGCTGCGCCCTGCTGCTCGGCATCTCTTGCTCTGCTCTCGCCACGCCAGTGTCAGAAAAACAGCTGGCGGAGGTGGTAGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCTGTTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGAAAACCGCACTATTACACGTTTGGCAAGGCCGATATCGCGGCGAATAAACCCGTTACGCCTCAGACCCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGCGTGTTAGGTGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTGACGGGCAAGCAGTGGCAGGGTATTCGTATGCTGGATCTCGCCACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTCAAACCTTCTGGCATGCCCTATGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTGCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGTATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCACCGGAGAACGTTGCTGATGCCTCACTTAAACAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGGTCGAGGGCAGCGACAGTAAGGTAGCGCTGGCGCCGTTGCCCGTGGCAGAAGTGAATCCACCGGCTCCCTCGGTCAAAGCGTCCTGGGTCCATAAAACGGGCTCTACTGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATACAAGCTATCCGAACCTGGCACGCGTTGAGGCGGCATACCATATCCTCGAGGCGCTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39098","NCBI_taxonomy_name":"Enterobacter hormaechei","NCBI_taxonomy_id":"158836"}}}},"ARO_accession":"3007942","ARO_id":"46734","ARO_name":"ACT-179","CARD_short_name":"ACT-179","ARO_description":"Cephalosporin-hydrolyzing class C beta-lactamase ACT-179.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7361":{"model_id":"7361","model_name":"ACT-180","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10188":{"protein_sequence":{"accession":"XAJ73554.1","sequence":"MMKKSLSCALLLSVACSAFAAPMSEKQLAKVVERAVTPLMNAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTRYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDDVTDNASLLRFYQNWQPQWKPGTARLYANASIGLFGALAVKPSGMSFEEAMTKRVFKPLRLDHTWINVPKAEEAHYAWGYRDGKAVHVSPGMLDAEAYGIKTNVKDMASWVVANMAPDALQDSSLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVGGSDNKVALAPLPAREVNPPVPPVKASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVETAYRILDALQ"},"dna_sequence":{"accession":"PP740488.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCCCTAAGTTGTGCCCTGCTGCTCAGCGTTGCCTGCTCTGCCTTCGCCGCCCCCATGTCAGAAAAACAGCTGGCTAAGGTGGTGGAGCGTGCCGTTACGCCGCTGATGAACGCGCAGGCCATTCCGGGTATGGCGGTGGCGGTAATTTATCAGGGTCAGCCGCACTACTTTACCTTTGGTAAAGCGGATGTCGCGGCGAATAAACCTGTTACGCCTCAAACCTTGTTCGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTATTGGGTGGCGATGCGATTGCTCGCGGTGAAATCTCACTGGGTGATCCAGTGACAAGGTACTGGCCTGAACTGACAGGAAAACAGTGGCAGGGCATTCGCATGCTGGATCTGGCAACCTATACCGCAGGGGGGTTGCCGTTACAGGTACCGGATGACGTCACTGATAACGCCTCTCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCGGGCACCGCGCGTCTTTATGCCAACGCCAGCATCGGTCTTTTTGGTGCTCTCGCGGTTAAACCCTCCGGCATGAGTTTTGAAGAGGCCATGACGAAGCGGGTCTTTAAGCCGCTCAGGCTCGACCATACGTGGATTAACGTACCAAAAGCGGAAGAGGCGCATTACGCCTGGGGATACCGTGACGGTAAAGCGGTACACGTTTCTCCAGGGATGCTGGACGCTGAAGCCTATGGCATAAAAACCAACGTGAAAGATATGGCGAGCTGGGTGGTGGCAAACATGGCCCCCGATGCCCTTCAGGATAGCTCTCTCAAACAAGGGATAGCCCTGGCACAGTCCCGCTACTGGCGCGTGGGTGCCATGTATCAGGGGTTAGGCTGGGAAATGCTGAACTGGCCGGTCGATGCCAAAACCGTGGTCGGGGGCAGCGACAATAAGGTGGCGCTGGCGCCGTTGCCTGCCAGAGAAGTCAATCCCCCGGTACCGCCGGTTAAGGCCTCCTGGGTACACAAAACGGGTTCAACCGGTGGGTTTGGGAGCTACGTGGCATTTATTCCTGAAAAACAGCTCGGCATTGTGATGCTGGCGAATAAAAGCTATCCGAATCCGGCACGCGTTGAGACGGCATACCGTATCCTCGACGCGCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"47910","NCBI_taxonomy_name":"Enterobacter sichuanensis","NCBI_taxonomy_id":"2071710"}}}},"ARO_accession":"3007943","ARO_id":"46735","ARO_name":"ACT-180","CARD_short_name":"ACT-180","ARO_description":"Cephalosporin-hydrolyzing class C beta-lactamase ACT-180.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7362":{"model_id":"7362","model_name":"ACT-181","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10189":{"protein_sequence":{"accession":"XAJ73555.1","sequence":"MKTKSLCCALLLSTSCSVLAAPMSEKQLSDVVERTVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTSVLGGDAIARGEISLDDPVTKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQHWQPQWKPGTTRLYADASIGLFGALAVKPSGMSFEQAMTKRVFKPLKLDHTWINVPKEEEAHYAWGYRDGKATHVSPGMLDAEAYGVKTNVQDMASWVKANMNPDALPDSTLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVEAKTVVEGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKELGIVMLANKSYPNPARVEAAYRILSALQ"},"dna_sequence":{"accession":"PP740489.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGAAGACAAAATCCCTTTGCTGTGCCCTGCTGCTCAGTACCTCCTGCTCTGTTCTCGCCGCGCCGATGTCAGAGAAACAGCTGTCTGACGTGGTGGAACGTACCGTAACCCCCCTGATGAAAGCGCAAGCCATTCCGGGCATGGCGGTAGCGGTGATTTATCAGGGTCAGCCGCACTACTTTACCTTCGGAAAGGCCGATGTTGCGGCGAACAAACCTGTCACCCCGCAAACCCTGTTTGAGCTGGGCTCTATAAGTAAAACCTTCACCAGCGTATTAGGTGGCGATGCGATTGCGCGCGGAGAAATATCGCTGGACGACCCCGTGACAAAGTACTGGCCCGAGTTAACAGGCAAGCAGTGGCAGGGTATTCGCATGTTGGATCTGGCGACCTACACCGCGGGTGGCCTGCCGCTACAGGTGCCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGTTTCTATCAACACTGGCAACCGCAGTGGAAACCAGGCACAACGCGTCTTTATGCGGACGCCAGCATCGGGCTTTTTGGCGCCCTCGCGGTTAAACCCTCCGGTATGAGCTTTGAACAGGCCATGACGAAGCGGGTCTTCAAGCCACTCAAACTGGACCATACATGGATTAACGTTCCGAAAGAAGAAGAGGCGCATTACGCCTGGGGATACCGTGACGGTAAAGCAACCCACGTTTCACCGGGAATGCTGGATGCCGAAGCGTATGGTGTCAAAACCAACGTCCAGGATATGGCGAGCTGGGTGAAGGCCAACATGAACCCTGACGCCCTTCCGGATTCAACGTTGAAACAGGGTATTGCCCTGGCACAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCGGTAGAAGCCAAAACCGTCGTGGAGGGCAGCGATAACAAGGTGGCTCTTGCACCGTTACCGGTGGCAGAAGTGAACCCTCCAGCTCCGCCAGTAAAAGCATCATGGGTACATAAAACAGGCTCGACGGGTGGATTCGGCAGCTATGTCGCATTTATTCCTGAAAAGGAACTCGGCATTGTTATGCTGGCGAACAAGAGCTACCCGAACCCGGCGCGCGTGGAAGCGGCATACCGTATTCTGAGCGCTCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39773","NCBI_taxonomy_name":"Enterobacter kobei","NCBI_taxonomy_id":"208224"}}}},"ARO_accession":"3007944","ARO_id":"46736","ARO_name":"ACT-181","CARD_short_name":"ACT-181","ARO_description":"Cephalosporin-hydrolyzing class C beta-lactamase ACT-181.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7363":{"model_id":"7363","model_name":"ACT-182","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10190":{"protein_sequence":{"accession":"XAJ73556.1","sequence":"MMTKSLCCALLLSTSCSVLAAPMSEKQLAEMVERTVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMSYEQAITTRVFKPLKLDHTWINVPKAEEAHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVKDMASWVMVNMKPDSLQDSSLRKGITLAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVEGSDNKVALAPLPAREVNPPAPPVNASWVHKTGSTGGFGSYVAFIPEKQLGIVLLANKSYPNPARVEAAYRILDALQ"},"dna_sequence":{"accession":"PP740490.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGACTAAATCCCTTTGCTGCGCCCTGCTGCTCAGCACATCCTGCTCGGTATTGGCTGCACCGATGTCAGAAAAACAGCTGGCTGAGATGGTGGAACGTACCGTTACGCCGCTGATGAAAGCGCAGGCCATTCCGGGTATGGCGGTGGCGGTGATTTATCAGGGTCAGCCGCACTACTTTACCTTCGGTAAAGCCGATGTCGCGGCGAATAAACCTGTCACTCCACAAACCTTATTCGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTACTGGGCGGCGATGCCATTGCTCGCGGTGAAATATCGCTGGGCGATCCGGTGACAAAATACTGGCCTGAGCTGACAGGCAAGCAGTGGCAGGGGATCCGCATGCTGGATCTGGCAACCTATACCGCAGGAGGTTTGCCGTTACAGGTACCGGATGAGGTCACGGATAACGCCTCTCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCGGGCACCACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGCGCGCTGGCGGTCAAACCTTCCGGTATGAGCTATGAGCAGGCCATAACGACGCGGGTCTTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTTCCCAAAGCGGAAGAGGCGCATTACGCCTGGGGATACCGCGACGGTAAGGCGGTACACGTTTCGCCAGGAATGCTGGACGCTGAAGCCTATGGCGTAAAAACCAACGTGAAGGATATGGCAAGCTGGGTGATGGTCAATATGAAGCCGGACTCGCTTCAGGATAGTTCACTCAGGAAAGGCATTACCCTGGCGCAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAGGGGTTAGGCTGGGAAATGCTTAACTGGCCGGTCGATGCAAAAACCGTGGTTGAAGGTAGCGACAATAAGGTGGCGCTGGCACCGTTGCCTGCGAGAGAAGTGAATCCACCGGCGCCCCCGGTCAATGCGTCCTGGGTCCATAAAACAGGCTCTACCGGCGGGTTTGGCAGCTACGTGGCATTTATTCCTGAAAAGCAGCTCGGCATTGTGTTGCTGGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCGTATCCTCGACGCGCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36926","NCBI_taxonomy_name":"Enterobacter asburiae","NCBI_taxonomy_id":"61645"}}}},"ARO_accession":"3007945","ARO_id":"46737","ARO_name":"ACT-182","CARD_short_name":"ACT-182","ARO_description":"Cephalosporin-hydrolyzing class C beta-lactamase ACT-182.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7364":{"model_id":"7364","model_name":"ACT-183","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10191":{"protein_sequence":{"accession":"XAJ73557.1","sequence":"MMKKSLCCALLLGISCSALATPVSEKQLAEVVANTVTPLMKAQSVPGMAVAVIYQGKPHYYTFGKADIAVNKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMPYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPENVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVVEGSDSKVALAPLPVVEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANTSYPNPARVEAAYHILEALQ"},"dna_sequence":{"accession":"PP740491.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCCCTTTGCTGCGCCCTGCTGCTCGGCATCTCTTGCTCTGCTCTCGCCACGCCAGTGTCAGAAAAACAGCTGGCGGAGGTGGTCGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCTGTTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGAAAACCGCACTATTACACGTTTGGCAAGGCCGATATCGCGGTGAATAAACCCGTTACGCCTCAGACCCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGCGTTTTAGGTGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTGACGGGCAAGCAGTGGCAGGGTATTCGTATGCTGGATCTCGCCACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTCAAACCTTCTGGCATGCCCTATGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTGCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGTATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCGGAGAACGTTGCTGATGCCTCACTTAAGCAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGGTCGAGGGCAGCGACAGTAAGGTAGCGCTGGCGCCGTTGCCCGTGGTAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGCTCTACTGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATACAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCGAGGCGCTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39098","NCBI_taxonomy_name":"Enterobacter hormaechei","NCBI_taxonomy_id":"158836"}}}},"ARO_accession":"3007946","ARO_id":"46738","ARO_name":"ACT-183","CARD_short_name":"ACT-183","ARO_description":"Cephalosporin-hydrolyzing class C beta-lactamase ACT-183.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7365":{"model_id":"7365","model_name":"ACT-184","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10192":{"protein_sequence":{"accession":"XAJ73558.1","sequence":"MMKKSLCCALLLGLSCSVLAAPVSEKQLAEVVANTVTPLMKAQSVPGMAVAVIYQGKSHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMPYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPEKVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVVEGSDSKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANKSYPNPARVEAAYHILEALQ"},"dna_sequence":{"accession":"PP740492.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCCCTTTGCTGCGCCCTGCTGCTGGGCCTCTCTTGCTCTGTTCTCGCCGCGCCAGTGTCAGAAAAACAGCTGGCGGAGGTGGTCGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCTGTTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGAAAATCGCACTATTACACGTTTGGCAAGGCCGATATCGCGGCGAATAAACCCGTTACGCCTCAGACCCTGTTCGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTTTTAGGTGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTGACGGGCAAGCAGTGGCAGGGTATTCGTATGCTGGATCTCGCCACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTCAAACCTTCTGGCATGCCCTATGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTTCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGAATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCGGAGAAGGTTGCCGATGCCTCACTTAAGCAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGGTCGAAGGCAGCGACAGTAAGGTAGCGCTGGCGCCGTTACCCGTGGCTGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGTTCTACTGGCGGATTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCGAGGCGCTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39098","NCBI_taxonomy_name":"Enterobacter hormaechei","NCBI_taxonomy_id":"158836"}}}},"ARO_accession":"3007947","ARO_id":"46739","ARO_name":"ACT-184","CARD_short_name":"ACT-184","ARO_description":"Cephalosporin-hydrolyzing class C beta-lactamase ACT-184.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7366":{"model_id":"7366","model_name":"ACT-185","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10193":{"protein_sequence":{"accession":"XAJ73559.1","sequence":"MKTKSLCCALLLSTSCSVLAAPMSEKQLSDVVERTVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQDWQPQWKPGTTRLYANASIGLFGALAVKPSGMSFEQAMTKRVFKPLKLDHTWINVPKEDEAHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVQDMASWVKANMNPAALPDSTLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVEAKTVVEGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKELGIVMLANKSYPNPARVEVAYRILSALQ"},"dna_sequence":{"accession":"PP740493.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGAAGACAAAATCCCTTTGCTGTGCCCTGCTGCTCAGCACCTCCTGCTCTGTTCTCGCCGCGCCGATGTCAGAGAAACAGCTGTCTGACGTGGTGGAACGTACCGTTACCCCCCTGATGAAAGCGCAAGCCATTCCGGGCATGGCGGTAGCGGTGATTTATCAGGGTCAGCCGCACTACTTTACCTTCGGAAAGGCCGATGTTGCGGCGAACAAACCTGTCACCCCGCAAACCCTGTTTGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTATTAGGTGGCGATGCGATTGCGCGCGGAGAAATATCGCTGGGCGACCCCGTGACAAAGTACTGGCCCGAGCTAACAGGCAAGCAGTGGCAGGGTATTCGCATGTTAGATCTGGCGACCTACACCGCGGGTGGCCTGCCGCTACAGGTGCCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGTTTCTATCAAGACTGGCAACCGCAGTGGAAACCAGGCACAACGCGTCTTTATGCGAACGCCAGCATCGGGCTTTTTGGCGCCCTCGCGGTTAAACCCTCCGGTATGAGCTTTGAACAGGCCATGACGAAGCGGGTCTTCAAGCCGCTCAAACTGGACCATACATGGATTAACGTTCCGAAAGAAGACGAGGCGCATTACGCCTGGGGATACCGTGATGGTAAAGCGGTCCACGTTTCACCGGGAATGTTGGATGCCGAAGCGTATGGTGTCAAAACCAACGTCCAGGATATGGCGAGCTGGGTGAAGGCCAACATGAACCCTGCCGCCCTTCCGGATTCAACGTTGAAACAGGGTATTGCCCTGGCACAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCGGTAGAAGCCAAAACCGTCGTGGAGGGCAGCGATAACAAGGTGGCTCTTGCACCGTTACCGGTGGCAGAAGTGAACCCTCCAGCTCCGCCAGTAAAAGCATCATGGGTACATAAAACAGGCTCGACGGGTGGATTCGGCAGCTATGTCGCATTTATTCCTGAGAAGGAACTCGGCATTGTTATGCTGGCGAACAAGAGCTACCCGAACCCGGCGCGCGTGGAAGTGGCATACCGTATTCTGAGCGCTCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39773","NCBI_taxonomy_name":"Enterobacter kobei","NCBI_taxonomy_id":"208224"}}}},"ARO_accession":"3007948","ARO_id":"46740","ARO_name":"ACT-185","CARD_short_name":"ACT-185","ARO_description":"Cephalosporin-hydrolyzing class C beta-lactamase ACT-185.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7367":{"model_id":"7367","model_name":"ACT-186","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10194":{"protein_sequence":{"accession":"XAJ73560.1","sequence":"MMKKSLCCALLLGISCSALATPVSEKQLAEVVANTVTPLMKAQSVPGMAVAVIYQGKPHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMPYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPEKVADASLKQGIALAQSRYWHIGSMYQGLGWEMLNWPVEANTVVEGSDSKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANTSYPNPARVEAAYHILEALQ"},"dna_sequence":{"accession":"PP740494.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCCCTTTGCTGCGCCCTGCTGCTCGGCATCTCTTGCTCTGCTCTCGCCACGCCAGTGTCAGAAAAACAGCTGGCGGAGGTGGTCGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCTGTTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGAAAACCGCACTATTACACGTTTGGCAAGGCCGATATCGCGGCGAATAAACCCGTTACGCCTCAGACCCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGCGTTTTAGGTGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTGACGGGCAAGCAGTGGCAGGGTATTCGTATGCTGGATCTCGCCACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTCAAACCTTCTGGCATGCCCTATGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTGCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGTATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCGGAGAAGGTTGCTGATGCCTCACTTAAGCAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCATATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGGTCGAGGGCAGCGACAGTAAGGTAGCGCTGGCACCGTTGCCCGTGGCAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGCTCTACTGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATACAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCGAGGCGCTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39098","NCBI_taxonomy_name":"Enterobacter hormaechei","NCBI_taxonomy_id":"158836"}}}},"ARO_accession":"3007949","ARO_id":"46741","ARO_name":"ACT-186","CARD_short_name":"ACT-186","ARO_description":"Cephalosporin-hydrolyzing class C beta-lactamase ACT-186.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7368":{"model_id":"7368","model_name":"ACT-187","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10195":{"protein_sequence":{"accession":"XAJ73561.1","sequence":"MMKKTLSCALLLSVASAAFAAPMSEKQLAEVVERTVTPLMNAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEIALGDPVTKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTNTASLLRFYQNWQPKWKPGTTRLYANTSIGLFGALAVKPSGMSYEQAMTTRVFKPLKLDHTWINVPKAEEAHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVQDMASWVMVNMMPDSLQDSPLKHGIALAQSRYWRVGAMYQGLGWEMLNWPVDAQTVVGGSDNKEALAPLPAREVNPPAPLVKASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILDALQ"},"dna_sequence":{"accession":"PP740495.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAGAAAACCCTAAGCTGTGCCCTGCTGCTCAGCGTTGCCAGCGCTGCATTCGCCGCACCGATGTCCGAAAAACAGCTGGCTGAGGTGGTGGAACGCACCGTTACGCCGCTGATGAACGCGCAGGCCATTCCGGGTATGGCGGTGGCGGTGATTTATCAGGGTCAGCCGCACTACTTTACCTTCGGTAAAGCTGATGTTGCAGCGAACAAACCTGTCACCCCGCAAACCTTGTTCGAGCTGGGTTCGATAAGTAAAACCTTCACCGGCGTATTGGGTGGCGATGCGATTGCGCGCGGTGAAATAGCGCTGGGCGATCCGGTGACCAAATACTGGCCTGAGCTCACGGGCAAGCAGTGGCAGGGCATTCGCATGCTGGATCTGGCAACCTATACCGCAGGCGGTCTGCCGTTGCAGGTGCCGGATGAGGTCACGAATACCGCCTCCCTGCTGCGCTTTTATCAAAACTGGCAGCCAAAGTGGAAGCCGGGCACCACGCGGCTTTACGCTAACACCAGCATCGGTCTTTTTGGCGCGCTGGCGGTCAAACCCTCCGGCATGAGCTATGAGCAGGCCATGACGACGCGGGTCTTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTCCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGATACCGTGACGGTAAAGCGGTCCACGTTTCGCCAGGGATGCTGGACGCGGAAGCCTATGGCGTAAAAACCAACGTGCAGGATATGGCAAGCTGGGTGATGGTCAACATGATGCCGGACTCCCTTCAGGATTCCCCACTTAAGCACGGTATTGCCCTGGCACAGTCTCGCTACTGGCGCGTGGGAGCCATGTATCAAGGATTGGGCTGGGAAATGCTGAACTGGCCGGTCGACGCCCAAACGGTGGTCGGGGGCAGCGACAATAAGGAGGCGCTGGCGCCGTTGCCTGCAAGAGAAGTGAATCCACCGGCACCACTGGTTAAGGCCTCCTGGGTCCATAAAACGGGCTCTACCGGCGGATTTGGCAGCTACGTGGCATTTATTCCTGAAAAGCAGCTCGGCATTGTGATGCTGGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCGTATCCTCGACGCGCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"47909","NCBI_taxonomy_name":"Enterobacter quasiroggenkampii","NCBI_taxonomy_id":"2497436"}}}},"ARO_accession":"3007950","ARO_id":"46742","ARO_name":"ACT-187","CARD_short_name":"ACT-187","ARO_description":"Cephalosporin-hydrolyzing class C beta-lactamase ACT-187.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7369":{"model_id":"7369","model_name":"ACT-188","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10196":{"protein_sequence":{"accession":"XAJ73562.1","sequence":"MMKKFLCCALLLSTSCSVLAAPMSEKQLADVVERNVTPLMKAQGIPGMAVAVIYQGQPHYFTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANSSIGLFGALAVKPSGMSYEQAMTTRVFKPLKLDHTWINVPKAEETHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVQDMASWVMANMAPDALQDTSLKQGITLAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVGGSDNKVALAPLPAREVNPPVAPVKASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILDALQ"},"dna_sequence":{"accession":"PP740496.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATTCCTTTGCTGCGCCCTGCTGCTCAGCACATCCTGCTCTGTACTCGCCGCGCCGATGTCGGAAAAACAGCTGGCTGACGTGGTAGAACGCAACGTTACGCCCCTGATGAAAGCGCAGGGTATTCCAGGCATGGCGGTGGCCGTGATTTATCAGGGCCAGCCACACTACTTTACCTTTGGAAAGGCCGATATCGCGGCGAACAAACCCGTCACCCCGCAAACCCTGTTCGAACTGGGCTCTATAAGTAAAACCTTCACCGGCGTGCTGGGGGGCGATGCTATTGCCCGCGGCGAAATTTCGCTGGGCGATCCGGTAACTAAATATTGGCCTGAACTGACCGGCAAGCAGTGGCAAGGGATTCGCATGCTGGATCTGGCAACCTACACCGCCGGTGGCCTGCCTTTACAGGTGCCCGATGAGGTTACAGATAACGCATCCCTGCTGCGCTTCTATCAAAACTGGCAGCCTCAGTGGAAGCCGGGCACAACGCGTCTATACGCCAACTCCAGCATCGGTCTTTTTGGCGCGCTGGCGGTCAAACCTTCCGGCATGAGCTATGAGCAGGCCATGACGACGCGGGTCTTTAAGCCGCTCAAGCTGGATCATACCTGGATTAACGTTCCGAAAGCGGAGGAGACGCATTACGCCTGGGGATATCGTGACGGTAAAGCGGTCCACGTTTCACCGGGCATGCTGGACGCAGAGGCATATGGCGTGAAAACCAACGTGCAGGATATGGCGAGCTGGGTGATGGCCAACATGGCCCCTGACGCGCTGCAGGATACGTCCCTGAAGCAAGGCATTACGCTGGCGCAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAGGGGTTAGGTTGGGAGATGCTTAACTGGCCGGTTGATGCCAAAACCGTCGTCGGAGGCAGTGATAACAAGGTGGCGCTGGCACCGTTGCCTGCGAGAGAAGTGAATCCACCCGTTGCCCCGGTTAAGGCCTCATGGGTGCACAAAACGGGCTCCACCGGCGGGTTTGGCAGCTATGTGGCCTTTATTCCTGAAAAGCAGCTCGGCATTGTGATGCTGGCGAATAAAAGCTATCCGAACCCGGCGCGAGTTGAGGCGGCATACCGTATCCTCGACGCGCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"47906","NCBI_taxonomy_name":"Enterobacter bugandensis","NCBI_taxonomy_id":"881260"}}}},"ARO_accession":"3007951","ARO_id":"46743","ARO_name":"ACT-188","CARD_short_name":"ACT-188","ARO_description":"Cephalosporin-hydrolyzing class C beta-lactamase ACT-188.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7370":{"model_id":"7370","model_name":"ACT-189","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10197":{"protein_sequence":{"accession":"XAJ73563.1","sequence":"MMKKSLCCALLLGISCSALAAPVSEKQLAEVVANTVTPLMKAQSVPGMAVAVIYQGKPHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMPYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPEKVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVVEGSDSKVALAPLPVAEVNPPAPPVKASWIHKTGSTGGFGSYVAFIPEKQIGIVMLANTSYPNPARVEAAYHILEALQ"},"dna_sequence":{"accession":"PP740497.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCCCTTTGCTGCGCCCTGCTGCTCGGCATCTCCTGCTCTGCTCTCGCCGCGCCAGTATCGGAAAAACAGCTGGCGGAGGTGGTCGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCTGTTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGAAAACCGCACTATTACACGTTTGGCAAGGCCGATATCGCGGCGAATAAACCCGTTACGCCTCAGACCCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGCGTTTTAGGTGGGGATGCCATTGCGCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTGACGGGCAAGCAGTGGCAGGGTATTCGTATGCTGGATCTCGCCACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGCTTTTATCAAAACTGGCAGCCACAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGCGCGCTGGCGGTCAAACCTTCCGGCATGCCCTATGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTGCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGTATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCGGAGAAGGTTGCCGATGCCTCACTTAAGCAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAAATGCTCAACTGGCCCGTGGAGGCCAACACGGTGGTCGAAGGCAGCGACAGTAAGGTGGCGCTGGCGCCGTTGCCCGTGGCAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGATCCATAAAACGGGTTCTACTGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATACAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCGAGGCGTTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39098","NCBI_taxonomy_name":"Enterobacter hormaechei","NCBI_taxonomy_id":"158836"}}}},"ARO_accession":"3007952","ARO_id":"46744","ARO_name":"ACT-189","CARD_short_name":"ACT-189","ARO_description":"Cephalosporin-hydrolyzing class C beta-lactamase ACT-189.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7371":{"model_id":"7371","model_name":"ACT-190","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10198":{"protein_sequence":{"accession":"XAJ73564.1","sequence":"MKTKSLFCALLLSTSCSVLAAPMSEKQLSDVVERTVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWLELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQHWQPQWKPGTTRLYANASIGLFGALAVKPSGMSFEQAMTKRVFKPLKLDHTWINVPKEEEAHYAWGYRDGKAIHVSPGMLDAEAYGVKTNIQDMASWLKANMNPDALPDSTLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVEAKTVVEGSDNKVALAPLPVAEVNPPVPPVKASWVHKTGSTGGFGSYVAFIPEKELGIVMLANKSYPNPARVEAAYRILSALQ"},"dna_sequence":{"accession":"PP740498.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGAAGACAAAATCCCTTTTCTGTGCCCTGCTGCTCAGCACCTCCTGCTCTGTTCTCGCCGCGCCGATGTCAGAGAAACAGCTGTCTGACGTGGTGGAACGTACCGTTACCCCCCTGATGAAAGCGCAAGCCATTCCGGGCATGGCGGTAGCGGTGATTTATCAGGGTCAGCCGCACTACTTTACCTTCGGAAAGGCCGATGTTGCTGCGAACAAACCTGTCACCCCGCAAACCCTGTTTGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTATTAGGTGGCGATGCGATTGCGCGCGGAGAAATATCGCTGGGCGACCCCGTGACAAAGTACTGGCTCGAGCTAACAGGCAAGCAGTGGCAGGGTATTCGCATGTTGGATCTGGCGACCTACACCGCGGGTGGCCTGCCGCTACAGGTGCCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGTTTCTATCAACACTGGCAACCTCAGTGGAAACCAGGCACAACGCGTCTTTATGCGAACGCCAGCATCGGGCTTTTTGGCGCCCTCGCGGTTAAACCCTCCGGTATGAGCTTTGAACAGGCCATGACGAAGCGGGTCTTCAAGCCACTCAAACTGGACCATACATGGATTAACGTTCCGAAAGAAGAAGAGGCGCATTACGCCTGGGGATACCGTGATGGTAAAGCAATCCACGTTTCACCGGGAATGCTGGATGCCGAAGCGTATGGTGTCAAAACCAACATCCAGGATATGGCGAGCTGGCTGAAGGCCAACATGAACCCTGACGCCCTTCCGGATTCAACGTTGAAACAGGGTATTGCCCTGGCACAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCGGTAGAAGCCAAAACCGTCGTGGAGGGCAGCGATAACAAGGTGGCTCTTGCACCGTTACCGGTGGCAGAAGTGAACCCTCCAGTTCCGCCAGTAAAAGCATCATGGGTACATAAAACAGGCTCGACGGGTGGATTCGGCAGCTATGTCGCATTTATTCCTGAAAAGGAACTCGGCATTGTTATGCTGGCGAACAAGAGCTACCCGAACCCGGCGCGCGTGGAAGCGGCATACCGTATTCTGAGCGCTCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39773","NCBI_taxonomy_name":"Enterobacter kobei","NCBI_taxonomy_id":"208224"}}}},"ARO_accession":"3007953","ARO_id":"46745","ARO_name":"ACT-190","CARD_short_name":"ACT-190","ARO_description":"Cephalosporin-hydrolyzing class C beta-lactamase ACT-190.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7372":{"model_id":"7372","model_name":"ACT-191","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10199":{"protein_sequence":{"accession":"XAJ73565.1","sequence":"MMKKSLCCALLLGISCSALATPVSEKQLAEVVANTVTPLMKAQSVPGMAVAVIYQGKPHYYTFGKADIAANKPVTPQTLFEPGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMPYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPENVADASLKQGIALAQSRYWRTGSMYQGLGWEMLNWPVEANTVVEGSDSKVALAPLPVVEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANTSYPNPARVEAAYHILEALQ"},"dna_sequence":{"accession":"PP740499.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCCCTTTGCTGCGCCCTGCTGCTCGGCATCTCTTGCTCTGCTCTCGCCACGCCAGTGTCAGAAAAACAGCTGGCGGAGGTGGTAGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCTGTTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGAAAACCGCACTATTACACGTTTGGCAAGGCCGATATCGCGGCGAATAAACCCGTTACGCCTCAGACCCTGTTCGAGCCGGGTTCTATAAGTAAAACCTTCACCGGCGTTTTAGGTGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTGACGGGCAAGCAGTGGCAGGGTATTCGTATGCTGGATCTCGCCACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTCAAACCTTCTGGCATGCCCTATGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTGCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGTATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCGGAGAACGTTGCTGATGCCTCACTTAAGCAGGGCATCGCGCTGGCACAGTCGCGCTACTGGCGTACCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGGTCGAGGGCAGCGACAGTAAGGTAGCGCTGGCGCCGTTGCCCGTGGTAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGCTCTACTGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATACAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCGAGGCGCTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39098","NCBI_taxonomy_name":"Enterobacter hormaechei","NCBI_taxonomy_id":"158836"}}}},"ARO_accession":"3007954","ARO_id":"46746","ARO_name":"ACT-191","CARD_short_name":"ACT-191","ARO_description":"Cephalosporin-hydrolyzing class C beta-lactamase ACT-191.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7373":{"model_id":"7373","model_name":"ACT-192","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10200":{"protein_sequence":{"accession":"XAJ73566.1","sequence":"MMKKSLCCALLLGISCSALAAPVSEKQLAEVVANTITPLMKAQSIPGMAVAVIYQGKPHYYTFGKADIAASKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNAALLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMGYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDDKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPENVADASLKQGISLAQSRYWRIGSMYQGLGWEMLNWPVEANTVIDGSDSKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANKSYPNPARVEAAYHILDALQ"},"dna_sequence":{"accession":"PP740500.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCTCTTTGCTGCGCCCTGCTGCTCGGCATCTCTTGCTCTGCTCTCGCCGCGCCAGTGTCAGAAAAACAGCTGGCGGAGGTGGTCGCGAATACGATTACCCCGCTGATGAAAGCCCAGTCGATTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGTAAACCGCACTATTATACGTTTGGCAAAGCCGATATCGCGGCCAGCAAACCCGTTACGCCTCAGACTCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGGGTTTTAGGAGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTGACGGGCAAGCAGTGGCAGGGGATTCGTATGCTGGATCTCGCAACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAATGCCGCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGTATCGGTCTTTTTGGCGCGCTGGCGGTCAAACCTTCCGGCATGGGCTATGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTTCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGATAAAGCGGTGCGCGTTTCGCCGGGAATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCGGAGAACGTTGCTGATGCCTCACTTAAGCAGGGCATCTCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGATCGACGGCAGCGACAGTAAGGTGGCGCTGGCACCGCTGCCCGTGGCAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGCTCTACTGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCGACGCGCTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39098","NCBI_taxonomy_name":"Enterobacter hormaechei","NCBI_taxonomy_id":"158836"}}}},"ARO_accession":"3007955","ARO_id":"46747","ARO_name":"ACT-192","CARD_short_name":"ACT-192","ARO_description":"Cephalosporin-hydrolyzing class C beta-lactamase ACT-192.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7374":{"model_id":"7374","model_name":"ACT-193","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10201":{"protein_sequence":{"accession":"XAJ73567.1","sequence":"MMKKSLSCALLLSVACSAFAAPMSEKQLAKVVERAVTPLMNAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTRYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDDVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMSFEEAMTKRVFKPLRLDHTWINVPKAEEAHYAWGYRDGKAVHVSPGMLDAEAYGIKTNVKDMASWVVANMAPDALQDSSLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVGGSDNKVALAPLPAREVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVETAYRILDALQ"},"dna_sequence":{"accession":"PP740501.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCCCTAAGTTGTGCCCTGCTGCTCAGCGTTGCCTGCTCTGCCTTCGCCGCCCCCATGTCAGAAAAACAGCTGGCTAAGGTGGTGGAGCGTGCCGTTACGCCGCTGATGAACGCGCAGGCCATTCCGGGTATGGCGGTGGCGGTAATTTATCAGGGTCAGCCGCACTACTTTACCTTTGGTAAAGCGGATGTCGCGGCGAATAAACCTGTTACGCCTCAAACCTTGTTCGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTATTGGGTGGCGATGCGATTGCTCGCGGTGAAATCTCACTGGGCGATCCAGTGACAAGGTACTGGCCTGAGCTGACAGGAAAACAGTGGCAGGGCATTCGCATGCTGGATCTGGCAACCTATACCGCAGGTGGGTTGCCGTTACAGGTACCGGATGACGTCACTGATAACGCCTCTCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAATGGAAGCCGGGCACCACGCGTCTTTATGCCAACGCCAGTATCGGTCTTTTTGGTGCTCTCGCGGTTAAACCCTCCGGCATGAGTTTTGAAGAGGCCATGACGAAGCGGGTCTTTAAGCCGCTCAGGCTCGACCATACGTGGATTAACGTACCAAAAGCGGAAGAGGCGCATTACGCCTGGGGATACCGTGACGGTAAAGCGGTACACGTTTCTCCAGGGATGCTGGACGCTGAAGCCTATGGCATAAAAACCAACGTGAAAGATATGGCGAGCTGGGTGGTGGCAAACATGGCCCCCGATGCCCTTCAGGATAGCTCTCTCAAACAAGGGATAGCCCTGGCACAGTCCCGCTACTGGCGCGTGGGTGCCATGTATCAGGGGTTAGGCTGGGAAATGCTGAACTGGCCGGTCGATGCCAAAACCGTGGTCGGGGGCAGCGACAATAAGGTGGCGCTGGCACCGTTGCCTGCAAGAGAAGTCAATCCCCCGGCACCGCCGGTTAAGGCCTCCTGGGTTCACAAAACGGGTTCTACCGGTGGGTTTGGGAGCTACGTGGCATTTATTCCTGAAAAACAGCTCGGCATTGTGATGCTGGCGAATAAAAGTTATCCGAATCCGGCACGCGTTGAGACGGCATACCGTATCCTCGACGCGCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"47910","NCBI_taxonomy_name":"Enterobacter sichuanensis","NCBI_taxonomy_id":"2071710"}}}},"ARO_accession":"3007956","ARO_id":"46748","ARO_name":"ACT-193","CARD_short_name":"ACT-193","ARO_description":"Cephalosporin-hydrolyzing class C beta-lactamase ACT-193.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7375":{"model_id":"7375","model_name":"ACT-194","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10202":{"protein_sequence":{"accession":"XAJ73568.1","sequence":"MMKKSLCCALLLGISCSALATPVSEKQLAEVVANTVTPLMKAQSVPGMAVAVIYQGKPHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMPYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPENVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVKANTVVEGSDSKVALAPLPVVEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANTSYPNPARVEAAYHILEALQ"},"dna_sequence":{"accession":"PP740502.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCCCTTTGCTGCGCCCTGCTGCTCGGCATCTCTTGCTCTGCTCTCGCCACGCCAGTGTCAGAAAAACAGCTGGCGGAGGTGGTCGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCTGTTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGAAAACCGCACTATTACACGTTTGGCAAGGCCGATATCGCGGCGAATAAACCCGTTACGCCTCAGACCCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGCGTTTTAGGTGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTGACGGGCAAGCAGTGGCAGGGTATTCGTATGCTGGATCTCGCCACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTCAAACCTTCTGGCATGCCCTATGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTGCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGTATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCAAACTGGGTCATGGCAAACATGGCGCCGGAGAACGTTGCTGATGCCTCACTTAAGCAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGAAGGCCAACACGGTGGTCGAGGGCAGCGACAGTAAGGTAGCGCTGGCGCCGTTGCCCGTGGTAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGCTCTACTGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATACAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCGAGGCGCTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39098","NCBI_taxonomy_name":"Enterobacter hormaechei","NCBI_taxonomy_id":"158836"}}}},"ARO_accession":"3007957","ARO_id":"46749","ARO_name":"ACT-194","CARD_short_name":"ACT-194","ARO_description":"Cephalosporin-hydrolyzing class C beta-lactamase ACT-194.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7376":{"model_id":"7376","model_name":"ACT-85","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10203":{"protein_sequence":{"accession":"MRN75760.1","sequence":"MMKKSLCCALLLGISCSALATPVSEKQLAEVVANTVTPLMKAQSVPGMAVAVIYQGKPHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMPYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMVNMAPEKVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVVEGSDSKVAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANTSYPNPARVEAAYHILEALQ"},"dna_sequence":{"accession":"WJXX01000007.1","fmin":"19311","fmax":"20451","strand":"-","sequence":"ATGATGAAAAAATCCCTTTGCTGCGCCCTGCTGCTCGGCATCTCTTGCTCTGCTCTCGCCACGCCAGTGTCAGAAAAACAGCTGGCGGAGGTGGTCGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCTGTTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGAAAACCGCACTATTACACGTTTGGCAAGGCCGATATCGCGGCGAATAAACCCGTTACGCCTCAGACCCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGCGTTTTAGGTGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTGACGGGCAAGCAGTGGCAGGGTATTCGTATGCTGGATCTCGCCACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTCAAACCTTCTGGCATGCCCTATGAGCAAGCCATGACGACACGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTGCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGTATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGTAAACATGGCGCCGGAGAAGGTTGCTGATGCCTCACTTAAGCAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGGTCGAGGGCAGCGACAGTAAGGTAGCGCCGTTGCCCGTGGCAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGCTCTACTGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATACAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCGAGGCGCTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39098","NCBI_taxonomy_name":"Enterobacter hormaechei","NCBI_taxonomy_id":"158836"}}}},"ARO_accession":"3007958","ARO_id":"46750","ARO_name":"ACT-85","CARD_short_name":"ACT-85","ARO_description":"Ceftazidime-hydrolyzing class C beta-lactamase ACT-85.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7377":{"model_id":"7377","model_name":"ACT-86","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10204":{"protein_sequence":{"accession":"MPV43777.1","sequence":"MMKKSLCCALLLGISCSALATPVSEKQLAEVVANTVTPLMKAQSVPGMAVAVIYQGKPHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMPYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPENVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVVEGSDSKVAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANTSYPNPARVEAAYHILEALQ"},"dna_sequence":{"accession":"WHOQ01000125.1","fmin":"30718","fmax":"31858","strand":"-","sequence":"ATGATGAAAAAATCCCTTTGCTGCGCCCTGCTGCTCGGCATCTCTTGCTCTGCTCTCGCCACGCCAGTGTCAGAAAAACAGCTGGCGGAGGTGGTCGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCTGTTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGAAAACCGCACTATTACACGTTTGGCAAGGCCGATATCGCGGCGAATAAACCCGTTACGCCTCAGACCCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGCGTTTTAGGTGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTGACGGGCAAGCAGTGGCAGGGTATTCGTATGCTGGATCTCGCCACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTCAAACCTTCTGGCATGCCCTATGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTGCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGATGGTAAAGCGGTGCGTGTTTCGCCGGGTATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCGGAGAACGTTGCTGATGCCTCACTTAAGCAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGGTCGAGGGCAGCGACAGTAAGGTAGCGCCGTTGCCCGTGGCAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGCTCTACTGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATACAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCGAGGCGCTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39098","NCBI_taxonomy_name":"Enterobacter hormaechei","NCBI_taxonomy_id":"158836"}}}},"ARO_accession":"3007959","ARO_id":"46751","ARO_name":"ACT-86","CARD_short_name":"ACT-86","ARO_description":"Ceftazidime-hydrolyzing class C beta-lactamase ACT-86.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7378":{"model_id":"7378","model_name":"ACT-88","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10205":{"protein_sequence":{"accession":"QTV32571.1","sequence":"MMKKSLCCALLLSTSCAALAAPLSETQLAKVVERTVTPLMKAQSIPGMAVAVIYQGQPHYFTFGKADVAANTPVTAQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPELTGKQWQGVRMLDLATYTAGGLPLQVPDEVTDNASLLHFYQSWQPQWAPGTMRLYANASIGLFGALAVKPSGMRFEQAMTERVLKPLNLNHTWINVPKAEEQHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVKDMASWVMANMAPDGVQDTSLKQGMVFAQSRYWRTGSMYQGLGWEMLNWPVEAKTVVEGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKELGIVMLANKSYPNPARVEAAYRILSALQ"},"dna_sequence":{"accession":"MW887657.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCCCTGTGCTGCGCCCTGCTGCTCAGCACCTCCTGCGCTGCATTAGCCGCACCTCTGTCAGAAACACAGCTGGCGAAGGTCGTGGAACGTACCGTTACGCCCCTGATGAAAGCGCAGTCTATTCCGGGTATGGCGGTCGCCGTGATCTATCAGGGCCAGCCGCACTACTTCACCTTCGGCAAGGCCGATGTCGCCGCGAATACACCCGTCACTGCACAAACGCTGTTTGAGCTGGGCTCAATCAGTAAAACCTTCACCGGCGTTCTGGGTGGCGATGCTATTGCTCGCGGTGAAATTTCGCTGGGCGATCCGGTGACCAAATACTGGCCTGAGCTGACCGGCAAACAGTGGCAGGGCGTTCGCATGCTGGATCTGGCAACCTATACTGCCGGTGGCCTGCCGTTACAGGTGCCCGATGAGGTTACCGATAATGCCTCGCTGCTGCATTTTTACCAGTCCTGGCAACCACAGTGGGCGCCAGGCACCATGCGTCTTTATGCGAATGCCAGCATCGGTCTGTTTGGGGCTCTGGCAGTGAAACCTTCTGGCATGCGCTTTGAGCAGGCGATGACGGAGCGGGTCCTGAAGCCGCTTAACCTGAACCATACGTGGATTAACGTTCCGAAGGCAGAAGAACAGCATTACGCCTGGGGTTATCGTGACGGTAAAGCGGTTCACGTTTCGCCGGGCATGCTCGACGCCGAAGCGTATGGCGTGAAAACCAACGTGAAGGATATGGCGAGCTGGGTGATGGCTAACATGGCCCCCGATGGGGTACAGGATACCTCACTGAAGCAGGGCATGGTGTTTGCACAGTCTCGCTACTGGCGCACAGGCTCGATGTACCAGGGCCTGGGCTGGGAGATGCTCAACTGGCCGGTAGAAGCCAAAACCGTGGTGGAGGGCAGCGACAACAAGGTAGCGCTTGCACCGTTGCCCGTGGCAGAAGTGAACCCTCCTGCTCCACCGGTAAAAGCGTCATGGGTACATAAAACAGGCTCGACGGGCGGATTTGGCAGCTACGTGGCATTTATCCCTGAGAAGGAACTCGGCATTGTTATGCTGGCGAACAAGAGCTACCCGAACCCGGCGCGCGTGGAAGCGGCATACCGTATTCTGAGCGCTCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"45936","NCBI_taxonomy_name":"Enterobacter ludwigii","NCBI_taxonomy_id":"299767"}}}},"ARO_accession":"3007960","ARO_id":"46752","ARO_name":"ACT-88","CARD_short_name":"ACT-88","ARO_description":"Cephalosporin-hydrolyzing class C beta-lactamase ACT-88.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7379":{"model_id":"7379","model_name":"ACT-89","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10206":{"protein_sequence":{"accession":"QUR41147.1","sequence":"MMRKSLCCALLLGISCSALATPVSEKQLAEVVANTITPLMKAQSVPGMAVAVIYQGKPHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDAVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMPYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPENVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVVEGSDSKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANTSYPNPARVEAAYHILEALQ"},"dna_sequence":{"accession":"MZ067484.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAGAAAATCCCTTTGCTGCGCCCTGCTGCTCGGCATCTCTTGCTCTGCTCTCGCCACGCCAGTGTCAGAAAAACAGCTGGCGGAGGTGGTCGCGAATACGATTACCCCGCTGATGAAAGCCCAGTCTGTTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGAAAACCGCACTATTACACATTTGGCAAGGCCGATATCGCGGCGAATAAACCCGTTACGCCTCAGACCCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGCGTTTTAGGTGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATGCGGTGACCAGATACTGGCCACAGCTGACGGGCAAGCAGTGGCAGGGTATTCGTATGCTGGATCTCGCCACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTCAAACCTTCTGGCATGCCCTATGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTGCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGTATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCGGAGAACGTTGCTGATGCCTCACTTAAGCAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGGTCGAGGGCAGCGACAGTAAGGTAGCACTGGCGCCGTTGCCCGTGGCAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGCTCTACTGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATACAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCGAGGCGCTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39098","NCBI_taxonomy_name":"Enterobacter hormaechei","NCBI_taxonomy_id":"158836"}}}},"ARO_accession":"3007961","ARO_id":"46753","ARO_name":"ACT-89","CARD_short_name":"ACT-89","ARO_description":"Cephalosporin-hydrolyzing class C beta-lactamase ACT-89.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7380":{"model_id":"7380","model_name":"ACT-90","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10207":{"protein_sequence":{"accession":"ESM21743.1","sequence":"MMKKSLCCALLLGISCSALAAPVSEKQLAEVVANTVTPLMKAQSIPGMAVAVIYQGKPHYYTFGKADTAASKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNAALLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMGYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPENVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVIEGSDSKVALAPLPVAEVNPPAPPVEASWVHKMGSTGGFGSYVAFIPEKQIGIVMLANKSYPNPARVEAAYHILDALQ"},"dna_sequence":{"accession":"AYIM01000001.1","fmin":"557504","fmax":"558650","strand":"-","sequence":"ATGATGAAAAAATCTCTTTGCTGCGCCCTGCTGCTCGGCATCTCTTGCTCTGCTCTCGCCGCGCCAGTGTCAGAAAAACAGCTGGCGGAGGTGGTCGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCGATTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGTAAACCGCACTATTACACGTTTGGCAAAGCCGATACCGCGGCCAGCAAACCCGTTACGCCTCAGACTCTGTTCGAGCTGGGCTCTATAAGTAAAACCTTCACCGGGGTTTTAGGAGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTGACGGGCAAGCAGTGGCAGGGGATTCGTATGCTGGATCTCGCAACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAATGCCGCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGTATCGGTCTTTTTGGCGCGCTGGCGGTCAAACCTTCCGGCATGGGCTATGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTTCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGAATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCGGAGAACGTTGCTGATGCCTCACTTAAGCAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGATCGAGGGCAGCGACAGTAAGGTGGCGCTGGCACCGCTTCCCGTGGCAGAAGTGAATCCACCGGCTCCCCCGGTCGAAGCGTCCTGGGTCCATAAAATGGGCTCTACTGGCGGGTTTGGCAGTTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCGACGCGCTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39098","NCBI_taxonomy_name":"Enterobacter hormaechei","NCBI_taxonomy_id":"158836"}}}},"ARO_accession":"3007962","ARO_id":"46754","ARO_name":"ACT-90","CARD_short_name":"ACT-90","ARO_description":"Cephalosporin-hydrolyzing class C beta-lactamase ACT-90.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7381":{"model_id":"7381","model_name":"ACT-91","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10208":{"protein_sequence":{"accession":"UEG31054.1","sequence":"MMTKSLSCALLLSVASSAFAAPMSEKQLAEVVERTVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVAANKAVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMSYEQAITTRVFKPLKLDHTWINVPKTEEAHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVQDMASWVMVNMKPDSLPDTSLRQGIALAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVKGSDNKVALAPLTAREVNPPAPPVNASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILDALQ"},"dna_sequence":{"accession":"OL351615.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGACAAAATCCCTAAGCTGTGCCCTGCTGCTCAGCGTTGCCAGCTCTGCATTCGCCGCACCGATGTCCGAAAAACAGCTGGCTGAGGTGGTGGAACGTACCGTTACGCCGCTGATGAAAGCGCAGGCCATCCCGGGCATGGCGGTGGCGGTGATTTATCAGGGTCAGCCGCACTACTTTACCTTCGGTAAAGCCGATGTTGCGGCAAACAAAGCTGTCACCCCACAAACCTTGTTCGAACTGGGTTCTATAAGTAAAACCTTCACCGGCGTATTGGGTGGCGATGCCATTGCTCGCGGTGAAATATCGCTGGGCGATCCGGTGACAAAATACTGGCCTGAGCTGACAGGCAAGCAGTGGCAGGGGATCCGCATGCTGGATCTGGCAACCTATACCGCAGGCGGTCTGCCGTTACAGGTACCGGATGAGGTCACGGATAACGCCTCTCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCGGGCACCACGCGTCTTTACGCCAATGCCAGCATCGGTCTTTTTGGCGCGCTGGCGGTCAAACCTTCCGGCATGAGCTATGAGCAGGCCATAACGACGCGGGTCTTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTTCCGAAAACGGAAGAGGCGCATTACGCCTGGGGATACCGCGACGGTAAAGCGGTCCACGTTTCGCCAGGAATGCTGGATGCAGAAGCCTATGGCGTAAAAACCAACGTGCAGGATATGGCAAGCTGGGTGATGGTTAATATGAAGCCAGACTCCCTCCCGGATACTTCACTCAGGCAAGGCATTGCCCTGGCGCAGTCTCGCTACTGGCGCGTGGGGGCCATGTATCAAGGGTTAGGTTGGGAAATGCTTAACTGGCCGGTCGATGCCAAAACCGTGGTTAAAGGTAGCGACAATAAGGTAGCGCTGGCACCGCTGACCGCGAGAGAAGTGAATCCGCCGGCACCGCCGGTCAACGCGTCCTGGGTCCATAAAACAGGCTCAACCGGCGGGTTTGGCAGCTACGTGGCATTTATTCCTGAAAAACAGCTCGGCATTGTGATGCTGGCGAATAAAAGCTATCCGAACCCTGCCCGCGTTGAGGCGGCATACCGTATCCTCGACGCGCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3007963","ARO_id":"46755","ARO_name":"ACT-91","CARD_short_name":"ACT-91","ARO_description":"Cephalosporin-hydrolyzing class C beta-lactamase ACT-91.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7382":{"model_id":"7382","model_name":"ACT-92","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10209":{"protein_sequence":{"accession":"UEG31055.1","sequence":"MMTKSLCCALLLSTSCSVLAAPMSEKQLAEVVERTVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMSYEQAITTRVFKPLKLDHTWINVPKAEEAHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVQDMANWVIVNMKPDSLQDSSLRKGITLAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVEGSDNKVALAPLPAREVNPPAPPVNASWVHKTDSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILDALQ"},"dna_sequence":{"accession":"OL351616.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGACTAAATCCCTTTGCTGCGCCCTGCTGCTCAGCACCTCCTGCTCGGTATTGGCTGCACCGATGTCAGAAAAACAGCTGGCTGAGGTGGTGGAACGTACCGTTACGCCGCTGATGAAAGCGCAGGCCATTCCGGGTATGGCAGTGGCGGTGATTTATCAGGGTCAGCCGCACTACTTTACCTTCGGTAAAGCCGATGTTGCGGCGAATAAACCTGTCACCCCACAAACCTTATTCGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTACTGGGCGGCGATGCCATTGCTCGGGGTGAAATATCGCTGGGCGATCCGGTGACCAAATACTGGCCTGAACTGACAGGCAAGCAGTGGCAGGGGATCCGCATGCTGGATCTGGCAACCTATACCGCAGGAGGTTTGCCGTTACAGGTACCGGATGAGGTCACGGATAACGCCTCTCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCGGGCACCACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGCGCGCTGGCGGTCAAACCTTCCGGCATGAGCTATGAGCAGGCCATAACGACGCGGGTCTTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTTCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGATACCGCGACGGTAAAGCGGTACACGTTTCGCCAGGCATGCTGGACGCTGAAGCCTATGGCGTAAAAACCAACGTGCAGGATATGGCAAACTGGGTGATAGTCAACATGAAGCCGGACTCGCTTCAGGATAGTTCACTCAGGAAAGGCATTACCCTGGCGCAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAGGGGTTAGGCTGGGAAATGCTTAACTGGCCGGTCGATGCCAAAACCGTGGTTGAAGGTAGCGACAATAAGGTGGCGCTGGCACCGTTGCCTGCGAGAGAAGTGAATCCACCGGCGCCCCCGGTCAACGCATCCTGGGTCCATAAAACAGACTCTACCGGCGGGTTTGGCAGCTACGTGGCATTTATTCCCGAAAAGCAGCTCGGCATTGTGATGCTGGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCGTATCCTCGACGCGCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3007964","ARO_id":"46756","ARO_name":"ACT-92","CARD_short_name":"ACT-92","ARO_description":"Cephalosporin-hydrolyzing class C beta-lactamase ACT-92.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7383":{"model_id":"7383","model_name":"ACT-93","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10210":{"protein_sequence":{"accession":"UEG31057.1","sequence":"MMTKSLCCALLLSTSCSVLAAPMSEKQLAEVVERTVTPLMKAQVIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMSYEQTITTRVFKPLKLDHTWINVPKAEEAHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVQDMASWVMVNMKPDSLQDSSLRKGLTLAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVEGSDNKVALAPLPAREVNPPAPPVNASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILDALQ"},"dna_sequence":{"accession":"OL351618.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGACTAAATCCCTTTGCTGCGCCCTGCTGCTCAGCACCTCCTGCTCGGTATTGGCTGCCCCGATGTCAGAAAAACAGCTGGCTGAGGTGGTGGAACGTACCGTTACGCCGCTGATGAAAGCTCAGGTCATTCCGGGTATGGCGGTGGCGGTGATTTATCAGGGTCAGCCGCACTACTTTACCTTCGGTAAAGCCGATGTCGCGGCGAATAAACCCGTCACCCCACAAACCTTATTCGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTACTGGGCGGCGATGCCATTGCTCGGGGTGAAATATCGCTGGGCGATCCGGTGACCAAATACTGGCCTGAGCTGACAGGCAAGCAGTGGCAGGGGATCCGCATGCTGGATCTGGCAACCTATACCGCAGGAGGTTTGCCGTTACAGGTACCGGATGAGGTCACGGATAACGCCTCTCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCGGGCACCACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGCGCGCTGGCGGTCAAACCTTCCGGCATGAGCTATGAGCAGACCATAACGACGCGGGTCTTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTTCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGATACCGCGACGGTAAGGCGGTACACGTTTCGCCAGGAATGCTGGACGCTGAAGCCTATGGCGTAAAAACCAACGTGCAGGATATGGCAAGCTGGGTGATGGTCAACATGAAGCCGGACTCGCTTCAGGATAGTTCACTCAGGAAAGGCCTTACCCTGGCGCAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAGGGGTTAGGCTGGGAAATGCTTAACTGGCCGGTCGATGCCAAAACCGTGGTTGAAGGTAGCGACAATAAGGTGGCGCTGGCACCGTTGCCTGCGAGAGAAGTGAATCCACCGGCGCCCCCGGTCAACGCATCCTGGGTCCATAAAACCGGCTCTACCGGCGGGTTTGGCAGCTACGTGGCGTTTATTCCCGAAAAGCAGCTCGGCATTGTGATGCTGGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCGTATCCTCGACGCGCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3007965","ARO_id":"46757","ARO_name":"ACT-93","CARD_short_name":"ACT-93","ARO_description":"Cephalosporin-hydrolyzing class C beta-lactamase ACT-93.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7384":{"model_id":"7384","model_name":"ACT-94","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10211":{"protein_sequence":{"accession":"UEG31058.1","sequence":"MMKKSLCCALLLGVSCSALATPVSEKQLAEVVANTVTPLMKAQSVPGMAVAVIYQGKPHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKSGTTRLYANASIGLFGALAVKPSGMPYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPENVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVVEGSDSKVALAPLPVVEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANTSYPNPARVEAAYHILEALQ"},"dna_sequence":{"accession":"OL351619.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCCCTTTGCTGCGCCCTGCTGCTCGGCGTCTCTTGCTCTGCTCTCGCCACGCCAGTGTCAGAAAAACAGCTGGCGGAGGTGGTCGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCTGTTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGAAAACCGCACTATTACACGTTTGGCAAGGCCGATATCGCGGCGAATAAACCCGTTACGCCTCAGACCCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGCGTGTTAGGTGGAGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTGACGGGCAAGCAGTGGCAGGGTATTCGTATGCTGGATCTCGCCACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGTCTGGCACAACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTCAAACCTTCTGGCATGCCCTATGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTGCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGTTTCGCCGGGTATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCGCCGGAGAACGTTGCTGATGCCTCACTTAAGCAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGGTCGAGGGCAGCGACAGTAAGGTAGCGCTGGCGCCGTTGCCCGTGGTAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGCTCTACTGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATACAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCGAGGCGCTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3007966","ARO_id":"46758","ARO_name":"ACT-94","CARD_short_name":"ACT-94","ARO_description":"Cephalosporin-hydrolyzing class C beta-lactamase ACT-94.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7385":{"model_id":"7385","model_name":"ACT-95","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10212":{"protein_sequence":{"accession":"UHK14138.1","sequence":"MKTKSLCCALLLSTSCSVLAAPMSEKQLSDVVERTVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQHWQPQWKPGTTRLYANASIGLFGALAVKPSGMSFEQAMTKRVFKPLKLDHTWINVPKEEEAHYAWGYRDGKAIHVSPGMLDAEAYGVKTNIQDMASWLKANMNPDALSDSTLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVEAKTVVEGSDNKVALAPLPVAEVNPPVPPVKASWVHKTGSTGGFGSYVAFIPEKELGIVMLANKSYPNPARVEAAYRILSALQ"},"dna_sequence":{"accession":"OL794635.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGAAGACAAAATCCCTTTGCTGTGCCCTGCTGCTCAGCACCTCCTGCTCTGTTCTCGCCGCGCCGATGTCAGAGAAACAGCTGTCTGACGTGGTGGAACGTACCGTTACCCCCCTGATGAAAGCGCAAGCCATTCCGGGCATGGCGGTAGCGGTGATTTATCAGGGTCAGCCGCACTACTTTACCTTCGGAAAGGCCGATGTTGCGGCGAACAAACCTGTCACCCCGCAAACCCTGTTTGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTATTAGGTGGCGATGCGATTGCGCGCGGAGAAATATCGCTGGGCGACCCCGTGACAAAGTACTGGCCCGAGCTAACAGGCAAGCAGTGGCAGGGTATTCGCATGTTGGATCTGGCGACCTACACCGCGGGTGGCCTGCCGCTACAGGTGCCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGTTTCTATCAACACTGGCAACCGCAGTGGAAACCAGGCACAACGCGTCTTTATGCGAACGCCAGCATCGGGCTTTTTGGCGCCCTCGCGGTTAAACCCTCCGGTATGAGCTTTGAACAGGCCATGACGAAGCGGGTCTTCAAGCCACTCAAACTGGACCATACATGGATTAACGTTCCGAAAGAAGAAGAGGCGCATTACGCCTGGGGATACCGTGATGGTAAAGCAATCCACGTTTCACCGGGAATGCTGGATGCCGAAGCGTATGGTGTCAAAACCAACATCCAGGATATGGCGAGCTGGCTGAAGGCCAACATGAACCCTGACGCCCTTTCGGATTCAACGTTGAAACAGGGTATTGCCCTGGCACAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCGGTAGAAGCCAAAACCGTCGTGGAGGGCAGCGATAACAAGGTGGCTCTTGCACCGTTACCGGTGGCAGAAGTGAACCCTCCAGTTCCGCCAGTAAAAGCATCATGGGTACATAAAACAGGCTCGACGGGTGGATTCGGCAGCTATGTCGCATTTATTCCTGAAAAGGAACTCGGCATTGTTATGCTGGCGAACAAGAGCTACCCGAACCCGGCGCGCGTGGAAGCGGCATACCGTATTCTGAGCGCTCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3007967","ARO_id":"46759","ARO_name":"ACT-95","CARD_short_name":"ACT-95","ARO_description":"Cephalosporin-hydrolyzing class C beta-lactamase ACT-95.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7386":{"model_id":"7386","model_name":"ACT-96","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10213":{"protein_sequence":{"accession":"UHK14141.1","sequence":"MKTKSLCCALMLSTSCSVLAAPMSEKQLSDVVERTVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQHWQPQWKPGTTRLYANASIGLFGALAVKPSGMNFEQAMTKRVFKPLKLDHTWINVPKEEEAHYAWGYRDGKAIHVSPGMLDAEAYGVKTNIQDMASWLKANMNPDALSDSTLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVEAKTVVEGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKELGIVMLANKSYPNPARVEAAFRILSALQ"},"dna_sequence":{"accession":"OL794638.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGAAGACAAAATCCCTTTGCTGTGCCCTGATGCTCAGCACCTCCTGCTCTGTTCTCGCCGCGCCGATGTCAGAGAAACAGCTGTCTGACGTGGTGGAACGTACCGTTACCCCCCTGATGAAAGCGCAAGCCATTCCGGGCATGGCGGTAGCGGTGATTTATCAGGGTCAGCCGCACTACTTTACCTTCGGAAAGGCCGATGTTGCGGCGAACAAACCTGTCACCCCGCAAACCCTGTTTGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTATTAGGTGGCGATGCGATTGCGCGCGGAGAAATATCGCTGGGCGACCCCGTGACAAAGTACTGGCCCGAGCTAACAGGCAAGCAGTGGCAGGGTATTCGCATGTTGGATCTGGCGACCTACACCGCGGGTGGCCTGCCGCTACAGGTGCCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGTTTCTATCAACACTGGCAACCGCAGTGGAAACCAGGCACAACGCGTCTTTATGCGAACGCCAGCATCGGGCTTTTTGGCGCCCTCGCGGTTAAACCCTCCGGTATGAACTTTGAACAGGCCATGACGAAGCGGGTCTTCAAGCCACTCAAACTGGACCATACATGGATTAACGTTCCGAAAGAAGAAGAGGCGCATTACGCCTGGGGATACCGTGATGGTAAAGCAATCCACGTTTCACCGGGAATGCTGGATGCCGAAGCGTATGGTGTCAAAACCAACATCCAGGATATGGCGAGCTGGCTGAAGGCCAACATGAACCCTGACGCCCTTTCGGATTCAACGTTGAAACAGGGTATTGCCCTGGCACAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCGGTAGAAGCCAAAACCGTCGTGGAGGGCAGCGATAACAAGGTGGCTCTTGCACCGTTACCGGTGGCAGAAGTGAACCCTCCAGCTCCGCCAGTAAAAGCATCATGGGTACATAAAACAGGCTCGACGGGCGGATTTGGCAGCTATGTCGCATTTATTCCTGAGAAGGAACTCGGCATTGTTATGCTGGCGAACAAGAGCTACCCGAACCCGGCGCGCGTGGAAGCGGCATTCCGTATTCTGAGCGCTCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3007968","ARO_id":"46760","ARO_name":"ACT-96","CARD_short_name":"ACT-96","ARO_description":"Cephalosporin-hydrolyzing class C beta-lactamase ACT-96.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7387":{"model_id":"7387","model_name":"ACT-97","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10214":{"protein_sequence":{"accession":"UHK14144.1","sequence":"MKTKSLCCALMLSTSCSVLAAPMSEKQLSNVVERTVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQHWQPQWKPGTTRLYANASIGLFGALAVKPSGMSFEQAMTKRVFKPLKLDHTWINVPKEEEAHYAWGYRDGKATHVSPGMLDAEAYGVKTNVQDMASWVKANMNPDALPDSTLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVEAKTVVEGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKELGIVMLANKSYPNPARVEAAYRILSALQ"},"dna_sequence":{"accession":"OL794641.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGAAGACAAAATCCCTTTGCTGTGCCCTGATGCTCAGCACCTCCTGCTCTGTTCTCGCCGCGCCGATGTCAGAGAAACAGCTGTCTAACGTGGTGGAACGTACCGTTACCCCCCTGATGAAAGCGCAAGCCATTCCGGGCATGGCGGTAGCGGTGATTTATCAGGGTCAGCCGCACTACTTTACCTTCGGAAAGGCCGATGTTGCGGCGAACAAACCTGTCACCCCGCAAACCCTGTTTGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTATTAGGTGGCGATGCGATTGCGCGCGGAGAAATATCGCTGGGCGACCCCGTGACAAAGTACTGGCCCGAGCTAACAGGCAAGCAGTGGCAGGGTATTCGCATGTTGGATCTGGCGACCTACACCGCGGGTGGCCTGCCGCTACAGGTGCCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGTTTCTATCAACACTGGCAACCGCAGTGGAAACCAGGCACAACGCGTCTTTATGCGAACGCCAGCATCGGGCTTTTTGGCGCCCTCGCGGTTAAACCCTCCGGTATGAGCTTTGAACAGGCCATGACGAAGCGGGTCTTCAAGCCACTCAAACTGGACCATACATGGATTAACGTTCCGAAAGAAGAAGAGGCGCATTACGCCTGGGGATACCGTGACGGTAAAGCAACCCACGTTTCACCGGGAATGCTGGATGCCGAAGCGTATGGTGTCAAAACCAACGTCCAGGATATGGCGAGCTGGGTGAAGGCCAACATGAACCCTGACGCCCTTCCGGATTCAACGTTGAAACAGGGTATTGCCCTGGCACAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCGGTAGAAGCCAAAACCGTCGTGGAGGGCAGCGATAACAAGGTGGCTCTTGCACCGTTACCGGTGGCAGAAGTGAACCCTCCAGCTCCGCCAGTAAAAGCATCATGGGTACATAAAACAGGCTCGACGGGTGGATTCGGCAGCTATGTCGCATTTATTCCTGAGAAGGAACTCGGCATTGTTATGCTGGCGAACAAGAGCTACCCGAACCCGGCGCGCGTGGAAGCGGCATACCGTATTCTGAGCGCTCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3007969","ARO_id":"46761","ARO_name":"ACT-97","CARD_short_name":"ACT-97","ARO_description":"Cephalosporin-hydrolyzing class C beta-lactamase ACT-97.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7388":{"model_id":"7388","model_name":"ACT-98","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10215":{"protein_sequence":{"accession":"UHK14151.1","sequence":"MKTKSLCCALLLSTSCSVLAAPMSEKQLSDVVERTVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQHWQPQWKPGTTRLYANASIGLFGALAVKPSGMSFEQAMTKRVFKPLKLDHTWINVPKEDEAHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVQDMASWVKANMNPAALPDSTLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVEAKTVVEGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKKLGIVMLANKSYPNPARVEAAYRILSALQ"},"dna_sequence":{"accession":"OL794648.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGAAGACAAAATCTCTTTGCTGTGCCCTGCTGCTCAGCACCTCTTGCTCTGTTCTCGCCGCGCCGATGTCAGAGAAACAGCTGTCTGACGTGGTGGAACGTACCGTTACCCCCCTGATGAAAGCGCAAGCCATTCCGGGCATGGCGGTAGCGGTGATTTATCAGGGTCAGCCGCACTACTTTACCTTCGGAAAGGCCGATGTTGCGGCGAACAAACCTGTCACCCCGCAAACCCTGTTTGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTATTAGGTGGCGATGCGATTGCGCGCGGAGAAATATCGCTGGGCGACCCCGTGACAAAGTACTGGCCCGAGCTAACAGGCAAGCAGTGGCAGGGTATTCGCATGTTGGATCTGGCGACCTACACCGCGGGTGGCCTGCCGCTACAGGTGCCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGTTTCTATCAACACTGGCAACCGCAGTGGAAACCAGGCACAACGCGTCTTTATGCGAACGCCAGCATCGGGCTTTTTGGCGCCCTCGCGGTTAAACCCTCCGGTATGAGCTTTGAACAGGCCATGACGAAGCGGGTCTTCAAGCCGCTCAAACTGGACCATACATGGATTAACGTTCCGAAAGAAGACGAGGCGCATTACGCCTGGGGATACCGTGATGGTAAAGCGGTCCACGTTTCACCGGGAATGTTGGATGCCGAAGCGTATGGTGTCAAAACCAACGTCCAGGATATGGCGAGCTGGGTGAAGGCCAACATGAACCCTGCCGCCCTTCCGGATTCAACGTTGAAACAGGGTATTGCCCTGGCACAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCGGTAGAAGCCAAAACCGTCGTGGAGGGCAGCGATAACAAGGTGGCTCTTGCACCGTTACCGGTGGCAGAAGTGAACCCTCCAGCTCCGCCAGTAAAAGCATCATGGGTACATAAAACAGGCTCGACGGGTGGATTCGGCAGCTATGTCGCATTTATTCCTGAAAAGAAACTCGGCATTGTTATGCTGGCGAACAAGAGCTACCCGAACCCGGCGCGCGTGGAAGCGGCATACCGTATTCTGAGCGCTCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3007970","ARO_id":"46762","ARO_name":"ACT-98","CARD_short_name":"ACT-98","ARO_description":"Cephalosporin-hydrolyzing class C beta-lactamase ACT-98.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7389":{"model_id":"7389","model_name":"ACT-99","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10216":{"protein_sequence":{"accession":"UHK14152.1","sequence":"MKTKSLCSALLLSTSCSVLAAPMSEKQLSDVVERTVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVAKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQHWQPQWKPGTTRLYANASIGLFGALAVKPSGMSFEQAMTKRVFKPLKLDHTWINVPKEEEAYYAWGYRDGKAVHVSPGMLDAEAYGVKTNVQDMASWVKANMNPAALPDSTLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVESKTVVEGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKELGIVMLANKSYPNPARVEAAYRILSALQ"},"dna_sequence":{"accession":"OL794649.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGAAGACAAAATCCCTTTGCAGTGCCCTGCTGCTCAGCACCTCCTGCTCTGTTCTCGCCGCGCCGATGTCAGAGAAACAGCTGTCTGACGTGGTGGAACGTACCGTTACCCCCCTGATGAAAGCGCAAGCCATTCCGGGCATGGCGGTAGCGGTGATTTATCAGGGTCAGCCGCACTACTTTACCTTCGGAAAGGCCGATGTTGCGGCGAACAAACCTGTCACCCCGCAAACCCTGTTTGAGCTGGGCTCTATAAGTAAAACCTTCACTGGCGTATTAGGTGGCGATGCGATTGCGCGCGGAGAAATATCGCTGGGCGACCCCGTGGCAAAGTACTGGCCCGAGCTAACAGGCAAGCAGTGGCAGGGTATTCGCATGTTGGATCTGGCGACCTACACCGCGGGTGGCCTGCCGCTACAGGTGCCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGCTTCTATCAACACTGGCAACCGCAGTGGAAACCAGGCACAACGCGTCTTTATGCGAACGCCAGCATCGGGCTTTTTGGCGCCCTCGCGGTTAAACCCTCCGGTATGAGCTTTGAACAGGCCATGACGAAGCGGGTCTTCAAGCCACTCAAACTGGACCATACATGGATTAACGTTCCGAAAGAAGAAGAGGCGTATTACGCCTGGGGATACCGTGATGGTAAAGCGGTCCACGTTTCACCGGGAATGTTGGATGCCGAAGCGTATGGTGTCAAAACCAACGTCCAGGATATGGCGAGCTGGGTGAAGGCCAACATGAACCCTGCCGCTCTTCCGGATTCAACGCTGAAACAGGGTATTGCCCTGGCACAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCGGTAGAATCCAAAACCGTCGTGGAGGGCAGCGATAACAAGGTGGCTCTTGCACCGTTACCGGTGGCAGAAGTGAACCCTCCAGCTCCGCCAGTAAAAGCATCATGGGTACATAAAACAGGCTCGACGGGTGGATTCGGCAGCTATGTCGCATTTATTCCTGAGAAGGAACTCGGCATTGTTATGCTGGCGAACAAGAGCTACCCGAACCCGGCGCGCGTGGAAGCGGCATACCGTATTCTGAGCGCTCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3007971","ARO_id":"46763","ARO_name":"ACT-99","CARD_short_name":"ACT-99","ARO_description":"Cephalosporin-hydrolyzing class C beta-lactamase ACT-99.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7390":{"model_id":"7390","model_name":"ACT-GC1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10217":{"protein_sequence":{"accession":"BAA07922.1","sequence":"MMKKSLCCALLLGISCSALATPVSEKQLAEVVANTVTPLMKAQSVPGMAVAVIYQGKPHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDPVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMPYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPENVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVVEGSDSKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANTSYPNPARVEAAYHILEALQ"},"dna_sequence":{"accession":"D44479.1","fmin":"389","fmax":"1544","strand":"+","sequence":"ATGATGAAAAAATCCCTTTGCTGCGCCCTGCTGCTCGGCATCTCTTGCTCTGCTCTCGCCACGCCAGTGTCAGAAAAACAGCTGGCGGAGGTGGTAGCGAATACGGTTACCCCGCTGATGAAAGCCCAGTCTGTTCCAGGCATGGCGGTGGCCGTTATTTATCAGGGAAAACCGCACTATTACACGTTTGGCAAGGCCGATATCGCGGCGAATAAACCCGTTACGCCTCAGACCCTGTTCGAGCTGGGTTCTATAAGTAAAACCTTCACCGGCGTGTTAGGTGGGGATGCCATTGCTCGCGGTGAAATTTCGCTGGACGATCCGGTGACCAGATACTGGCCACAGCTGACGGGCAAGCAGTGGCAGGGTATTCGTATGCTGGATCTCGCCACCTACACCGCTGGCGGCCTGCCGCTACAGGTACCGGATGAGGTCACGGATAACGCCTCCCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCTGGCACAACGCGTCTTTACGCCAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTCAAACCTTCTGGCATGCCCTATGAGCAGGCCATGACGACGCGGGTCCTTAAGCCGCTCAAGCTGGACCATACCTGGATTAACGTGCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGCTATCGTGACGGTAAAGCGGTGCGCGCGGTGCGCGTTTCGCCGGGTATGCTGGATGCACAAGCCTATGGCGTGAAAACCAACGTGCAGGATATGGCGAACTGGGTCATGGCAAACATGGCACCGGAGAACGTTGCTGATGCCTCACTTAAACAGGGCATCGCGCTGGCGCAGTCGCGCTACTGGCGTATCGGGTCAATGTATCAGGGTCTGGGCTGGGAGATGCTCAACTGGCCCGTGGAGGCCAACACGGTGGTCGAGGGCAGCGACAGTAAGGTAGCGCTGGCGCCGTTGCCCGTGGCAGAAGTGAATCCACCGGCTCCCCCGGTCAAAGCGTCCTGGGTCCATAAAACGGGCTCTACTGGCGGGTTTGGCAGCTACGTGGCCTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATACAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCATATCCTCGAGGCGCTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3007972","ARO_id":"46764","ARO_name":"ACT-GC1","CARD_short_name":"ACT-GC1","ARO_description":"Extended spectrum class C beta-lactamase ACT-GC1.","ARO_category":{"36211":{"category_aro_accession":"3000072","category_aro_cvterm_id":"36211","category_aro_name":"ACT beta-lactamase","category_aro_description":"ACT beta-lactamases, also known as AmpC beta-lactamases, are cephalosporinases that cannot be inhibited by clavulanate. These enzymes are encoded by genes located on the chromosome and can be induced by the presence of beta-lactam antibiotics. However recently, these genes have been found on plasmids and expressed at high constitutive levels in Escherichia coli and Klebsiella pneumoniae.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7391":{"model_id":"7391","model_name":"ADC-257","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10218":{"protein_sequence":{"accession":"QVU28095.1","sequence":"MQFKKISCLLLSPLFIFSTSIYADNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTSIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWQPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVAKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLKFIHANLNPQKYPTDIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKE"},"dna_sequence":{"accession":"MZ224611.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCAATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGACAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCATTATTAGAAAAATATGATGTGCCGGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAACACATCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGCAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTAGCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGCTTAAGTTTATTCATGCCAATCTGAACCCACAGAAATATCCGACAGATATTCAACGTGCAATTAATGAAACACATCAAGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCAACGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAACGCATTAAGGCAGCGTATGCAGTTTTAAATGCAATAAAGGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3007973","ARO_id":"46765","ARO_name":"ADC-257","CARD_short_name":"ADC-257","ARO_description":"Extended-spectrum class C beta-lactamase ADC-257.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7392":{"model_id":"7392","model_name":"ADC-258","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10219":{"protein_sequence":{"accession":"QVU28094.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGFYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"MZ224612.1","fmin":"0","fmax":"1167","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACCCCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCATTATTAGAAAAATATGATGTGCCGGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAGCTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTCCCAGATGAAGTACAAACAGATCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTGTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCCCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTTAACCCACAGAAATATCCGGCAGATATTCAACGGGCAATTAATGAAACACATCAAGGGTTCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACATATGTAGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3007974","ARO_id":"46766","ARO_name":"ADC-258","CARD_short_name":"ADC-258","ARO_description":"Extended-spectrum class C beta-lactamase ADC-258.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7393":{"model_id":"7393","model_name":"ADC-259","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10220":{"protein_sequence":{"accession":"UBX38689.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWQPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPSPLDAPAYGVKSTLPDMLSFIHANLTPQKYPTDIQRAINETHQGFYQVGTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTTGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"OK340849.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCATTATTAGAAAAATATGATGTACCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAGCTAAAAAATACACCGATTGATCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGCAACCTCGCTTTACAATTTCCAGATGAAGTACAAACAGATCAACAAGTTTTAACTTTTTTCAAAGACTGGCAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTGGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCAGCCCACTTGATGCCCCAGCATACGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTTACCCCACAGAAATATCCGACAGATATTCAACGGGCAATTAATGAAACACATCAAGGGTTCTATCAAGTCGGCACCATGTATCAGGCACTTGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCACCGGTTTCGGAACATATGTGGTCTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3007975","ARO_id":"46767","ARO_name":"ADC-259","CARD_short_name":"ADC-259","ARO_description":"Extended-spectrum class C beta-lactamase ADC-259.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7394":{"model_id":"7394","model_name":"ADC-260","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10221":{"protein_sequence":{"accession":"UCZ39549.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVKTDQQVLTFFKDWKPKNSIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGSLGAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNRFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"OK396701.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAGTATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAATTTCCAGATGAAGTAAAAACAGATCAGCAAGTTTTAACATTTTTTAAAGACTGGAAACCTAAAAACTCAATCGGTGAATATCGACAATATTCAAACCCAAGCATTGGTTTATTTGGAAAAGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCTCACTCGGTGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTAAATCCACAAAAATATCCAGCAGATATTCAACGGGCAATTAATGAAACACATCAGGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACCGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3007976","ARO_id":"46768","ARO_name":"ADC-260","CARD_short_name":"ADC-260","ARO_description":"Extended-spectrum class C beta-lactamase ADC-260.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7395":{"model_id":"7395","model_name":"ADC-261","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10222":{"protein_sequence":{"accession":"UGW32408.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVKTDQQVLTFFKDWKPKNSIGEYQQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYSVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTTGFGTYVVFIPKENIGLVMLTNKRIPIEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"OL774887.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAGTATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAATTTCCAGATGAAGTAAAAACAGATCAGCAAGTTTTAACATTTTTTAAAGACTGGAAACCTAAAAACTCAATCGGTGAATATCAACAATATTCAAACCCAAGCATTGGTTTATTTGGAAAAGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATAGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTAAATCCACAAAAATATCCAGCAGATATTCAACGGGCAATTAATGAAACACATCAGGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTACCGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAATTGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3007977","ARO_id":"46769","ARO_name":"ADC-261","CARD_short_name":"ADC-261","ARO_description":"Cefepime-hydrolyzing class C beta-lactamase ADC-261.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7396":{"model_id":"7396","model_name":"ADC-262","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10223":{"protein_sequence":{"accession":"UHO07582.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIYANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLSAIKK"},"dna_sequence":{"accession":"OL901271.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCGGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCTTATTTGGAAAAGTTGTTGCTTTGTCTATGAATAAACCTTTCGATCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAGGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCCACCTTACCGGATATGTTGAGTTTTATTTATGCCAACCTTAACCCACAGAAATATCCGGCAGATATTCAACGTGCAATTAATGAAACACATCAGGGTCGCTATCAAGTAAATACCATGTATCAAGCGCTTGGTTGGGAAGAGTTTTCTTATCCAGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACGTATGTGGTCTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAACAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAGTGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3007978","ARO_id":"46770","ARO_name":"ADC-262","CARD_short_name":"ADC-262","ARO_description":"Extended-spectrum class C beta-lactamase ADC-262.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7397":{"model_id":"7397","model_name":"ADC-263","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10224":{"protein_sequence":{"accession":"UHO07583.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTLFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYSVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPAMLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTTGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"OL901272.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAGCTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTCCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTGTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATAGCGTCAAATCAACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTAAATCCACAAAAATATCCGGCAGATATTCAACGTGCAATTAATGAAACACATCAGGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAATGTTACAAACTTTACTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCACCGGTTTCGGAACGTATGTGGTGTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCGTATGCAGTTTTAAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3007979","ARO_id":"46771","ARO_name":"ADC-263","CARD_short_name":"ADC-263","ARO_description":"Extended-spectrum class C beta-lactamase ADC-263.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7398":{"model_id":"7398","model_name":"ADC-264","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10225":{"protein_sequence":{"accession":"UHO07591.1","sequence":"MRFIKISCLLLPSLFIFNTSIYAGNTPKEQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEIYYGLRSVQDKKVVNGSTIFELGSVSKLFTAKAGGYAKTKGKISFEDTPGKYWKELKNTPIDQVNLLQLATYTSGNLGLQFPDEVQTDQQVLTFFKEWKPKNQIGEYRQYSNPSIGLFGKIVGLSMNQPFSQVLEKTIFPSLHLKNSYVNVPKIQMQNYAFGYNQENQPIRVTPGPLDAPAYGVKSTLPDMLSFIDANLNPQKYPADIRRAIDETHKGFYQIGTMYQALGWEEFSYPAPLQTLLDSNSEQIVMKSNKVTAISKEPSIKIFHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"OL901280.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTATAAAAATTTCCTGCTTACTTTTACCGTCTCTTTTTATTTTTAATACCTCAATTTATGCGGGCAATACACCAAAAGAGCAAGAAATTAAAAAACTGGTTGATCAAAACTTTAAACCTTTATTAGAAAAATATGATGTGCCCGGTATGGCGGTGGGCGTTATTCAAAATAATAAAAAGTATGAAATCTATTATGGTTTAAGATCCGTTCAAGATAAAAAAGTTGTAAATGGTAGTACTATTTTTGAGCTAGGTTCAGTCAGTAAATTATTTACTGCGAAGGCAGGCGGCTATGCAAAAACAAAAGGAAAAATCTCTTTTGAAGACACCCCAGGAAAATACTGGAAAGAACTAAAAAACACGCCTATTGATCAGGTCAATCTACTTCAACTTGCTACATATACGAGTGGCAACCTTGGCTTACAATTCCCAGATGAAGTACAAACAGACCAGCAAGTTTTAACTTTTTTCAAAGAATGGAAACCTAAAAATCAAATCGGTGAATATCGGCAATATTCAAACCCAAGTATTGGCTTATTTGGAAAAATTGTAGGCTTATCGATGAATCAGCCTTTTAGTCAGGTTTTAGAAAAGACAATTTTTCCGTCTCTTCACTTAAAAAATAGCTATGTAAATGTGCCTAAAATTCAGATGCAAAACTATGCATTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTACCCCAGGCCCACTCGATGCCCCTGCCTACGGGGTTAAATCTACATTACCAGACATGCTTAGCTTTATTGATGCCAATCTAAATCCACAAAAATATCCAGCAGATATTCGACGCGCAATTGATGAGACTCATAAAGGTTTTTATCAAATCGGCACCATGTATCAAGCATTAGGTTGGGAAGAATTTTCTTATCCAGCCCCTTTACAAACTTTATTAGACAGTAACTCTGAACAAATTGTGATGAAATCTAATAAAGTGACTGCCATTTCCAAAGAACCTTCAATCAAAATATTCCATAAAACGGGTTCAACTAATGGATTTGGAACTTATGTTGTGTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGCATTCCAAATGAAGAACGTATTAAAGCGGCTTACGCTGTATTGAATGCGATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39094","NCBI_taxonomy_name":"Acinetobacter calcoaceticus","NCBI_taxonomy_id":"471"}}}},"ARO_accession":"3007980","ARO_id":"46772","ARO_name":"ADC-264","CARD_short_name":"ADC-264","ARO_description":"Extended-spectrum class C beta-lactamase ADC-264.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7399":{"model_id":"7399","model_name":"ADC-265","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10226":{"protein_sequence":{"accession":"ULU82599.1","sequence":"MRFKKISCLLLPPLFIFSTSIYAGNTPKEQEVKKLIDQNFKPLLDKYDVPGMAVGVIQNNKKYEIYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKAKGKISFNDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKTKNAIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPPLHLKNSYVNVPKTQMQNYAYGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLTFINANLNPQKYPKDIQHAINETHQGFYQVGTMYQALGWEEFSYPAPLQTLLDSNSEQIVMKPNKVTAISKEPSVKMFHKTGSTNGFGSYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"OM572561.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGCCTACTTTTACCGCCTCTTTTTATTTTTAGTACCTCAATTTATGCGGGAAACACCCCCAAAGAACAAGAAGTTAAAAAACTGATAGATCAAAATTTTAAGCCTTTATTAGATAAATATGATGTGCCTGGTATGGCCGTGGGGGTCATTCAAAATAATAAAAAATATGAAATATATTATGGCCTACAATCTGTTCAGGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAACTAGGTTCGGTCAGTAAATTATTTACCGCTACAGCTGGTGGATATGCAAAAGCAAAAGGAAAAATCTCTTTTAATGACACACCCGGAAAATATTGGAAAGAACTAAAAAACACACCGATTGACCAAGTTAATCTTCTTCAACTTGCGACGTATACAAGTGGCAACCTTGCTTTGCAATTTCCAGATGAAGTTCAAACAGACCAACAAGTTTTAACTTTTTTCAAAGATTGGAAAACTAAAAACGCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCTTATTTGGAAAAGTTGTGGCTTTGTCTATGAATAAACCTTTTGACCAAGTCTTAGAAAAAACAATTTTTCCACCTCTCCATTTAAAAAATAGCTATGTAAACGTACCTAAAACTCAAATGCAAAATTATGCATATGGCTATAATCAAGAAAATCAGCCGATCCGAGTTAACCCTGGCCCGCTAGATGCCCCTGCGTACGGCGTTAAATCGACACTACCAGATATGCTGACTTTTATTAATGCCAACCTCAACCCACAGAAATATCCGAAAGATATTCAACATGCAATTAATGAAACACATCAAGGTTTCTATCAAGTCGGTACGATGTATCAAGCATTGGGTTGGGAAGAATTTTCTTATCCAGCGCCTTTACAAACTTTATTAGACAGTAATTCAGAGCAAATCGTGATGAAGCCTAATAAAGTGACTGCCATTTCCAAAGAACCTTCAGTTAAGATGTTCCACAAAACTGGCTCAACAAATGGCTTTGGATCTTATGTGGTGTTTATTCCAAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAACGCATTAAGGCAGCGTATGCAGTATTAAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3007981","ARO_id":"46773","ARO_name":"ADC-265","CARD_short_name":"ADC-265","ARO_description":"Extended-spectrum class C beta-lactamase ADC-265.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7400":{"model_id":"7400","model_name":"ADC-266","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10227":{"protein_sequence":{"accession":"UOU25744.1","sequence":"MRFKKISYLLLPSLFIFNTSIYAGNTSKDQEIKQLVDQNFKPLLEKYNVPGMAVGIIQNNKKYEAYYGLQSVQDKKAVNSNTIFELGSVSKLFTATAGAYAKNTGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGEIVGLSMKQPFSQVLEKTIFPDLGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPANIQRAINETHQGRYQVNSMYQALGWEEFAYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKDNIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"ON191578.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTACTTACTTTTACCTTCTCTTTTTATTTTTAATACCTCAATTTATGCGGGCAATACTTCTAAAGACCAAGAAATTAAACAATTGGTAGATCAAAATTTTAAACCCTTATTAGAAAAATATAATGTACCGGGTATGGCGGTAGGTATTATTCAAAACAATAAAAAATATGAAGCGTATTATGGTCTACAATCCGTTCAAGATAAAAAAGCTGTAAATAGCAATACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACTGCGACGGCAGGTGCTTATGCAAAAAATACAGGAAAAATCTCTTTTGATGATACACCGGGCAAATACTGGAAAGAGTTAAAAAACACTCCAATTGATCAGGTCAATTTACTTCAACTTGCCACCTATACAAGTGGTAACCTCGCTTTGCAATTCCCAGATGAAGTACAAACAGATCAACAGGTTTTAACTTTTTTTAAAGATTGGAAACCTAAAAACCCAATCGGTGAATATAGACAATATTCAAACCCAAGTATTGGCCTATTTGGGGAAATAGTTGGTTTATCAATGAAGCAGCCTTTTAGTCAGGTCTTGGAAAAAACGATTTTTCCGGACCTTGGCTTAAAACATAGCTATGTCAATGTGCCTAAAACTCAGATGCAAAACTATGCATTTGGTTATAACCAAGAAAATCAGCCAATTCGAGTTAACCCTGGCCCACTCGATGCCCCAGCATACGGCGTCAAATCGACCCTACCCGACATGCTGAGCTTTATTCATGCCAACCTGAATCCACAGAAATATCCGGCAAATATTCAACGTGCAATTAATGAGACACATCAAGGTCGCTATCAAGTAAATAGCATGTATCAGGCACTCGGTTGGGAAGAGTTTGCTTATCCAGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAACCTTCAGTTAAGATGTACCACAAAACTGGTTCAACCAATGGTTTCGGAACCTATGTCGTATTTATTCCTAAAGACAATATTGGTTTAGTCATGTTAACCAATAAACGCATTCCAAATGAAGAACGCATTAAGGCAGCTTATGCTGTGCTAAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36949","NCBI_taxonomy_name":"Acinetobacter nosocomialis","NCBI_taxonomy_id":"106654"}}}},"ARO_accession":"3007982","ARO_id":"46774","ARO_name":"ADC-266","CARD_short_name":"ADC-266","ARO_description":"Extended-spectrum class C beta-lactamase ADC-266.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7401":{"model_id":"7401","model_name":"ADC-267","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10228":{"protein_sequence":{"accession":"UTQ48801.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNRSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWQPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGFYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTSGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLDAIKK"},"dna_sequence":{"accession":"ON960904.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATCGCAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGCAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTGGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCATTTGGTTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCTGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTTAACCCACAGAAATATCCGGCTGATATTCAACGGGCAATTAATGAAACACATCAAGGGTTCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCAGCGGTTTCGGAACATATGTAGTGTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGGATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3007983","ARO_id":"46775","ARO_name":"ADC-267","CARD_short_name":"ADC-267","ARO_description":"Extended-spectrum class C beta-lactamase ADC-267.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7402":{"model_id":"7402","model_name":"ADC-268","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10229":{"protein_sequence":{"accession":"UTS94213.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVKTDQQVLTFFKDWKPKNSIGEYQQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYSVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTTGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"ON651460.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAGTATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAATTTCCAGATGAAGTAAAAACAGATCAGCAAGTTTTAACATTTTTTAAAGACTGGAAACCTAAAAACTCAATCGGTGAATATCAACAATATTCAAACCCAAGCATTGGTTTATTTGGAAAAGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATAGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTAAATCCACAAAAATATCCAGCAGATATTCAACGGGCAATTAATGAAACACATCAGGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTACCGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3007984","ARO_id":"46776","ARO_name":"ADC-268","CARD_short_name":"ADC-268","ARO_description":"Extended-spectrum class C beta-lactamase ADC-268.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7403":{"model_id":"7403","model_name":"ADC-269","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10230":{"protein_sequence":{"accession":"UTS94214.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWQPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQALEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIYANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLSAIKK"},"dna_sequence":{"accession":"ON651461.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGATCAACAAGTTTTAACTTTTTTCAAAGACTGGCAACCTAAAAACCCAATCGGTGAATATAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGCCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAGGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCCACCTTACCGGATATGTTGAGTTTTATTTATGCCAACCTTAACCCACAGAAATATCCGGCAGATATTCAACGTGCAATTAATGAAACACATCAGGGTCGCTATCAAGTAAATACCATGTATCAAGCGCTTGGTTGGGAAGAGTTTTCTTATCCAGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACGTATGTGGTCTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAACAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAGTGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3007985","ARO_id":"46777","ARO_name":"ADC-269","CARD_short_name":"ADC-269","ARO_description":"Extended-spectrum class C beta-lactamase ADC-269.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7404":{"model_id":"7404","model_name":"ADC-270","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10231":{"protein_sequence":{"accession":"UTS94215.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTMFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPKDIQRAINETHQGFYQVNTMYQALGWEDFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"ON651462.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCTGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACTGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTCCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATGTTTCCGGCTCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGCTGAGTTTTATTCATGCCAACCTCAACCCACAGAAATATCCGAAAGATATTCAACGTGCAATTAATGAAACACATCAAGGGTTCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGATTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCAACGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3007986","ARO_id":"46778","ARO_name":"ADC-270","CARD_short_name":"ADC-270","ARO_description":"Extended-spectrum class C beta-lactamase ADC-270.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7405":{"model_id":"7405","model_name":"ADC-271","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10232":{"protein_sequence":{"accession":"UTS94216.1","sequence":"MRFKKISCLLFSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTMFPALGLKHSYVNVAKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGFYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"ON651463.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTCTCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCTTATTTGGAAAAGTTGTTGCTTTGTCTATGAATAAACCTTTCGATCAAGTCTTAGAAAAAACAATGTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTGGCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTTAACCCACAGAAATATCCGGCTGATATTCAAAGGGCAATTAATGAAACACATCAAGGGTTCTATCAAGTAAATACCATGTATCAAGCGCTTGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACGTATGTGGTCTTTATTCCTAAAGAAAATATTGGATTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGTATTAAGGCAGCGTATGCAGTTTTAAATGCAATAAAAAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3007987","ARO_id":"46779","ARO_name":"ADC-271","CARD_short_name":"ADC-271","ARO_description":"Extended-spectrum class C beta-lactamase ADC-271.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7406":{"model_id":"7406","model_name":"ADC-272","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10233":{"protein_sequence":{"accession":"UTS94217.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNNSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPTDIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"ON651464.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAACAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATACGGCGTCAAATCCACCTTACCGGATATGTTAAGTTTTATTCATGCCAACCTTAACCCACAGAAATATCCGACAGATATTCAACGGGCAATTAATGAAACACATCAAGGTCGCTATCAAGTAAATACCATGTATCAAGCGCTTGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAGCCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACATATGTAGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3007988","ARO_id":"46780","ARO_name":"ADC-272","CARD_short_name":"ADC-272","ARO_description":"Extended-spectrum class C beta-lactamase ADC-272.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7407":{"model_id":"7407","model_name":"ADC-273","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10234":{"protein_sequence":{"accession":"UTS94218.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFNPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"ON651465.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAATCCGTTATTAGAAAAATATGATGTGCCGGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACTGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTCCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCTTATTTGGAAAAGTTGTTGCTTTGTCTATGAATAAACCTTTCGATCAAGTCTTAGAAAAAACAATTTTTCCGGCTCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCTGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTTAACCCACAGAAATATCCGGCTGATATTCAAAGGGCAATTAATGAAACACATCAAGGTCGCTATCAAGTAAATACCATGTATCAAGCGCTTGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAGCCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACATATGTAGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3007989","ARO_id":"46781","ARO_name":"ADC-273","CARD_short_name":"ADC-273","ARO_description":"Extended-spectrum class C beta-lactamase ADC-273.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7408":{"model_id":"7408","model_name":"ADC-274","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10235":{"protein_sequence":{"accession":"UTS94219.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGAYAKNKGKISFDDKPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPTDIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"ON651466.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCATTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGCTTATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATAAGCCTGGTAAATATTGGAAAGAGCTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTCCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAGGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCCACCTTACCGGATATGTTGAGTTTTATTCATGCCAACCTTAACCCACAGAAATATCCGACAGATATTCAACGGGCAATTAATGAAACACATCAAGGTCGCTATCAAGTAAATACCATGTATCAAGCGCTTGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAGCCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACATATGTAGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3007990","ARO_id":"46782","ARO_name":"ADC-274","CARD_short_name":"ADC-274","ARO_description":"Extended-spectrum class C beta-lactamase ADC-274.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7409":{"model_id":"7409","model_name":"ADC-275","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10236":{"protein_sequence":{"accession":"UTS94220.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPNDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKVLKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGFYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"ON651467.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACCCCAAATGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCATTATTAGAAAAATATGATGTGCCGGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGTGCTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGTCCACTCGATGCCCCAGCATACGGCGTCAAATCCACCTTACCGGATATGTTGAGTTTTATTCATGCCAACCTCAACCCACAGAAATATCCGGCAGATATTCAACGGGCAATTAATGAAACACATCAAGGGTTCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCAACGGTTTCGGAACATATGTGGTCTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3007991","ARO_id":"46783","ARO_name":"ADC-275","CARD_short_name":"ADC-275","ARO_description":"Extended-spectrum class C beta-lactamase ADC-275.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7410":{"model_id":"7410","model_name":"ADC-276","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10237":{"protein_sequence":{"accession":"UTS94221.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNRSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWQPKNPIGEYIQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRANPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGFYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTTGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLDAIKK"},"dna_sequence":{"accession":"ON651468.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATCGCAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGCAACCTAAAAACCCAATCGGTGAATACATACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTGGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCATTTGGTTATAACCAAGAAAATCAGCCGATTCGAGCTAACCCCGGCCCACTCGATGCCCCTGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTTAACCCACAGAAATATCCGGCTGATATTCAACGGGCAATTAATGAAACACATCAAGGGTTCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCACCGGTTTCGGAACATATGTAGTGTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGGATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3007992","ARO_id":"46784","ARO_name":"ADC-276","CARD_short_name":"ADC-276","ARO_description":"Extended-spectrum class C beta-lactamase ADC-276.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7411":{"model_id":"7411","model_name":"ADC-277","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10238":{"protein_sequence":{"accession":"UTS94222.1","sequence":"MRFKKISCLLLSPLFIFSTSIYADNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPINQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKFVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPTDIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLSGDCSKFCVST"},"dna_sequence":{"accession":"ON651469.1","fmin":"0","fmax":"1170","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGACAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTAGGTTCTGTTAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAGCTAAAAAATACACCGATTAACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTCCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGTTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATACGGCGTCAAATCCACCTTACCGGATATGTTAAGTTTTATTCATGCCAACCTTAACCCACAGAAATATCCGACAGATATTCAACGGGCAATTAATGAAACACATCAAGGTCGCTATCAAGTAAATACCATGTATCAAGCGCTTGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCAACGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAGTGGGGACTGTTCTAAATTTTGTGTAAGTACTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3007993","ARO_id":"46785","ARO_name":"ADC-277","CARD_short_name":"ADC-277","ARO_description":"Extended-spectrum class C beta-lactamase ADC-277.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7412":{"model_id":"7412","model_name":"ADC-278","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10239":{"protein_sequence":{"accession":"UTS94223.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNEKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIYANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLSAIKK"},"dna_sequence":{"accession":"ON651470.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATGAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGATCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCTTATTTGGAAAAGTTGTTGCTTTGTCTATGAATAAACCTTTCGATCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCCACCTTACCGGATATGTTGAGTTTTATTTATGCCAACCTTAACCCACAGAAATATCCGGCAGATATTCAACGTGCAATTAATGAAACACATCAGGGTCGCTATCAAGTAAATACCATGTATCAAGCGCTTGGTTGGGAAGAGTTTTCTTATCCAGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACGTATGTGGTCTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGTATTAAGGCAGCTTATGCTGTGCTGAGTGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3007994","ARO_id":"46786","ARO_name":"ADC-278","CARD_short_name":"ADC-278","ARO_description":"Extended-spectrum class C beta-lactamase ADC-278.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7413":{"model_id":"7413","model_name":"ADC-279","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10240":{"protein_sequence":{"accession":"UTS94224.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANFNSQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"ON651471.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCGGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCTTATTTGGAAAAGTTGTTGCTTTGTCTATGAATAAACCTTTCGATCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACTTCAACTCACAGAAATATCCGGCTGATATTCAACGGGCAATTAATGAAACACATCAAGGTCGCTATCAAGTAAATACCATGTATCAAGCGCTTGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAGCCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACATATGTAGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3007995","ARO_id":"46787","ARO_name":"ADC-279","CARD_short_name":"ADC-279","ARO_description":"Extended-spectrum class C beta-lactamase ADC-279.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7414":{"model_id":"7414","model_name":"ADC-280","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10241":{"protein_sequence":{"accession":"UTS94225.1","sequence":"MRFKKISCLLLSPLFIFSTSIYADNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDKPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDILSFIHANLNPQKYPTDIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"ON651472.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGACAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCATTATTAGAAAAATATGATGTGCCGGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATAAGCCTGGTAAATATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCTTATTTGGAAAAGTTGTTGCTTTGTCTATGAATAAACCTTTCGATCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAGGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATACGGCGTCAAATCCACCTTACCGGATATTTTGAGTTTTATTCATGCCAACCTTAACCCACAGAAATATCCGACAGATATTCAACGGGCAATTAATGAAACACATCAAGGTCGCTATCAAGTAAATACCATGTATCAAGCGCTTGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAGCCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACATATGTGGTCTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCGTATGCAGTTTTAAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3007996","ARO_id":"46788","ARO_name":"ADC-280","CARD_short_name":"ADC-280","ARO_description":"Extended-spectrum class C beta-lactamase ADC-280.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7415":{"model_id":"7415","model_name":"ADC-281","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10242":{"protein_sequence":{"accession":"UTS94249.1","sequence":"MQFKKISCLLLPPLFIFSSSIYAGNTPKEQEIKKLVDQNFKPLLEKYDVPGMAVGIIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKTKGTISFNDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVKTDQQVLTFFKEWKPKNSIGEYRQYSNPSIGLFGKVVALSMNKPFDQILEKTIFPDLGLKHSYINVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFINANLNPQKYPADIQRAINETHKGFCQVGTMYQALGWEEFSYPAPLQTLLDSNSEQIVMKPNKVTAISKEPSVKMFHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"ON651496.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCAATTTAAAAAAATTTCTTGCTTACTTTTACCTCCTCTTTTTATTTTTAGTAGCTCAATTTATGCGGGTAATACACCAAAAGAGCAAGAGATCAAAAAACTGGTTGATCAAAATTTTAAGCCTTTATTAGAAAAATATGATGTGCCCGGTATGGCTGTGGGCATTATTCAAAATAACAAAAAGTATGAAATGTATTATGGTCTACAATCCGTTCAAGATAAAAAAGCCGTTAATAGCAGTACTATTTTTGAGCTAGGTTCGGTCAGTAAATTATTTACCGCTACAGCAGGCGGATATGCCAAAACAAAAGGAACAATCTCTTTTAATGACACGCCCGGAAAATATTGGAAAGAACTAAAAAATACACCGATTGATCAAGTGAATTTACTTCAACTTGCGACATATACCAGTGGCAACCTTGCCTTGCAATTTCCAGATGAAGTAAAAACAGATCAGCAAGTTTTAACGTTTTTCAAAGAATGGAAACCTAAAAACTCAATCGGTGAATATAGACAATATTCAAATCCAAGCATTGGTTTATTTGGAAAAGTTGTTGCTTTGTCTATGAATAAACCTTTCGACCAAATCTTGGAAAAAACCATTTTTCCAGATCTTGGCTTAAAACATAGCTATATAAATGTGCCTAAAACTCAAATGCAAAACTATGCATTTGGCTATAACCAAGAAAATCAGCCGATTCGCGTTAATCCTGGTCCACTCGATGCACCAGCATACGGCGTTAAATCTACCCTACCGGATATGCTGAGTTTTATTAATGCCAACCTAAATCCACAAAAATATCCAGCAGATATTCAACGTGCAATTAATGAAACACATAAAGGTTTCTGCCAAGTGGGTACGATGTATCAAGCACTAGGTTGGGAAGAGTTTTCTTATCCAGCACCTTTACAAACTTTATTAGACAGTAATTCAGAACAAATCGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAACCTTCCGTTAAGATGTTCCACAAAACTGGATCGACTAACGGTTTTGGAACATATGTCGTGTTCATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACTAATAAACGTATTCCCAATGAAGAACGCATTAAAGCAGCTTATGCTGTGTTAAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42801","NCBI_taxonomy_name":"Acinetobacter lactucae","NCBI_taxonomy_id":"1785128"}}}},"ARO_accession":"3007997","ARO_id":"46789","ARO_name":"ADC-281","CARD_short_name":"ADC-281","ARO_description":"Extended-spectrum class C beta-lactamase ADC-281.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7416":{"model_id":"7416","model_name":"ADC-282","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10243":{"protein_sequence":{"accession":"UTS94250.1","sequence":"MRFKKISCLLLPPLFIISTSIYAGNTPKEQEVKKLVDQNFKPLLDKYDVPGMAVGVIQNNKKYEIYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKAKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKTKNAIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPPLHLKNSYVNVPKTQMQNYAYGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLTFINANLNPQKYPKDIQRAISETHQGFYQVGTMYQALGWEEFSYPAPLQTLLDSNSEQIVMKPNKVTAISKEPSVKMFHKTGSTNGFGSYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"ON651497.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGCTTACTTTTACCGCCTCTTTTTATTATTAGTACCTCAATTTATGCGGGCAATACACCAAAAGAACAAGAAGTTAAAAAACTGGTAGATCAAAATTTTAAGCCTTTATTAGATAAATATGATGTGCCTGGTATGGCCGTGGGGGTCATTCAAAATAATAAAAAATATGAAATATATTATGGCCTACAATCCGTTCAGGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAACTAGGTTCGGTCAGTAAATTATTTACCGCTACAGCTGGTGGATATGCAAAAGCAAAAGGAAAAATCTCTTTTGATGACACACCCGGAAAATATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAATCTTCTTCAACTTGCGACGTATACAAGTGGCAATCTCGCCTTACAATTTCCAGATGAAGTTCAAACAGACCAACAAGTTTTAACTTTTTTCAAAGATTGGAAAACTAAAAACGCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCTTATTTGGAAAAGTTGTGGCTTTGTCTATGAATAAACCTTTTGACCAAGTCTTAGAAAAAACAATTTTTCCACCTCTCCATTTAAAAAATAGCTATGTAAATGTACCCAAAACTCAAATGCAAAATTATGCATATGGCTATAACCAAGAAAATCAGCCGATCCGAGTTAACCCTGGCCCGCTAGATGCTCCAGCATACGGCGTTAAATCGACACTACCAGATATGCTGACTTTTATTAATGCCAACCTCAACCCACAGAAATATCCGAAAGATATTCAACGTGCAATTAGTGAAACACATCAAGGTTTCTATCAAGTCGGTACGATGTATCAAGCATTGGGTTGGGAAGAATTTTCTTATCCAGCACCTTTACAAACTTTATTAGACAGTAATTCAGAGCAAATCGTGATGAAGCCTAATAAAGTGACTGCCATTTCCAAAGAACCTTCAGTTAAGATGTTCCACAAAACTGGCTCAACAAATGGCTTTGGATCTTATGTGGTGTTTATTCCAAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAACGCATTAAGGCAGCGTATGCAGTATTAAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3007998","ARO_id":"46790","ARO_name":"ADC-282","CARD_short_name":"ADC-282","ARO_description":"Extended-spectrum class C beta-lactamase ADC-282.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7417":{"model_id":"7417","model_name":"ADC-283","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10244":{"protein_sequence":{"accession":"UUM03672.1","sequence":"MRFKKISCLLLSPLFIFSTSIYADNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDKPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWQPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"OP131856.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGACAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCGTTATTAGAAAAATATGATGTGCCGGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATAAGCCTGGTAAATATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAATTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGCAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCAACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTAAATCCACAAAAATATCCGGCAGATATTCAACGTGCAATTAATGAAACACATCAGGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCTGTTAAGATGTACCATAAAACTGGCTCAACCAACGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3007999","ARO_id":"46791","ARO_name":"ADC-283","CARD_short_name":"ADC-283","ARO_description":"Extended-spectrum class C beta-lactamase ADC-283.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7418":{"model_id":"7418","model_name":"ADC-284","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10245":{"protein_sequence":{"accession":"UVU92350.1","sequence":"MRFKKISCLLLPPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWQPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQALEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIYANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYMVFIPKENIGLVMLTNKRIPNEERIKAAYAVLSAIKK"},"dna_sequence":{"accession":"OP297826.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGCTTACTTTTACCTCCTCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGATCAACAAGTTTTAACTTTTTTCAAAGACTGGCAACCTAAAAACCCAATCGGTGAATATAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGCCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAGGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCCACCTTACCGGATATGTTGAGTTTTATTTATGCCAACCTTAACCCACAGAAATATCCGGCAGATATTCAACGTGCAATTAATGAAACACATCAGGGTCGCTATCAAGTAAATACCATGTATCAAGCGCTTGGTTGGGAAGAGTTTTCTTATCCAGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACGTATATGGTCTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAACAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAGTGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008000","ARO_id":"46792","ARO_name":"ADC-284","CARD_short_name":"ADC-284","ARO_description":"Extended-spectrum class C beta-lactamase ADC-284.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7419":{"model_id":"7419","model_name":"ADC-285","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10246":{"protein_sequence":{"accession":"UVU92353.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDREIKKLVDQNFKPLLDKYDVPGMAVGVIQNNKKYETYYGLQSVQDKKAVSSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPGLGLKHSYVNVPKNQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLKFINANLNPQKYPADIQRAINETHKGFYQVGTMYQALGWEEFSYPAPLQTLLDSNSEQTVMKPNKVTAISKEPSVKMFHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"OP297829.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCGAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCTTTATTAGATAAATATGATGTGCCGGGTATGGCCGTGGGCGTTATTCAGAATAATAAAAAATATGAAACGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAGTAGCAGTACCATTTTTGAACTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCAACGTATACAAGTGGTAACCTTGCCTTGCAGTTCCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAATCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAAGTTGTGGCATTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGGCCTTGGCTTAAAACATAGCTACGTAAATGTACCGAAGAACCAGATGCAAAACTATGCTTTTGGCTATAATCAAGAAAATCAGCCAATTCGTGTTAACCCTGGTCCGCTAGATGCTCCAGCATACGGCGTCAAATCGACACTACCCGATATGCTTAAGTTTATTAATGCCAACCTAAATCCACAAAAATATCCAGCAGATATTCAACGTGCAATTAATGAAACACATAAAGGTTTCTATCAAGTCGGCACCATGTATCAAGCATTAGGTTGGGAAGAATTTTCTTATCCAGCGCCTTTACAAACTTTATTAGACAGTAATTCAGAACAAACTGTGATGAAGCCTAATAAAGTGACTGCTATTTCAAAAGAACCTTCAGTTAAGATGTTCCACAAAACTGGCTCAACCAATGGTTTCGGAACATATGTCGTGTTCATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAACGCATTAAAGCAGCGTATGCAGTATTAAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3008001","ARO_id":"46793","ARO_name":"ADC-285","CARD_short_name":"ADC-285","ARO_description":"Extended-spectrum class C beta-lactamase ADC-285.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7420":{"model_id":"7420","model_name":"ADC-286","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10247":{"protein_sequence":{"accession":"UZF98454.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDREIKKLVDQNFKPLLDKYDVPGMAVGVIQNNKKYETYYGLQSVQDKKSVSSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTSGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKEWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPGLGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFINANINPQKYPADIQRAINETHQGFYQVGTMYQALGWEEFSYPAPLQTLLDSNSEQIVMKPNKVTAISKEPSIKMFHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"OP745003.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCGAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCTTTATTAGATAAATATGATGTGCCGGGTATGGCCGTGGGCGTTATTCAGAATAATAAAAAATATGAAACGTATTATGGTCTTCAATCTGTTCAAGATAAAAAATCCGTAAGTAGCAGTACCATTTTTGAACTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGTCTGGTAAATATTGGAAAGAACTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCAACGTATACAAGTGGTAACCTTGCCTTGCAGTTCCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGAATGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAAGTTGTTGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGGCCTTGGCTTAAAACATAGCTATGTAAATGTACCGAAGACCCAGATGCAAAACTATGCTTTTGGCTATAATCAAGAAAATCAGCCAATTCGTGTTAACCCCGGTCCGCTAGATGCTCCAGCATACGGTGTTAAATCGACCTTACCTGATATGCTGAGTTTCATTAATGCCAATATAAATCCACAAAAATATCCAGCAGATATTCAACGTGCAATTAATGAAACACATCAAGGTTTCTATCAAGTCGGCACCATGTATCAGGCACTTGGTTGGGAAGAATTTTCTTATCCAGCGCCTTTACAAACTTTATTAGACAGTAATTCAGAACAAATTGTAATGAAGCCTAATAAAGTGACTGCCATTTCCAAAGAACCTTCAATTAAGATGTTCCACAAAACTGGTTCGACTAACGGTTTTGGAACATATGTCGTGTTCATTCCTAAAGAAAATATTGGCTTAGTCATGTTGACCAATAAACGTATTCCGAATGAAGAACGCATTAAAGCAGCTTATGCTGTGTTAAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3008002","ARO_id":"46794","ARO_name":"ADC-286","CARD_short_name":"ADC-286","ARO_description":"Extended-spectrum class C beta-lactamase ADC-286.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7421":{"model_id":"7421","model_name":"ADC-287","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10248":{"protein_sequence":{"accession":"UZF98456.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDREIKKLVDQNFKPLLDKYDVPGMAVGVIQNNKKYETYYGLQSVQDKKSVSSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKEWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPGLGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFINANINPQKYPADIQRAINETHQGFYQVGTMYQALGWEEFSYPAPLQTLLDSNSEQIVMKPNKVTAISKEPSIKMFHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"OP745005.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCGAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCTTTATTAGATAAATATGATGTGCCGGGTATGGCCGTGGGCGTTATTCAGAATAATAAAAAATATGAAACGTATTATGGTCTTCAATCTGTTCAAGATAAAAAATCCGTAAGTAGCAGTACCATTTTTGAACTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCAACGTATACAAGTGGTAACCTTGCCTTGCAGTTCCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGAATGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAAGTTGTTGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGGCCTTGGCTTAAAACATAGCTATGTAAATGTACCGAAGACCCAGATGCAAAACTATGCTTTTGGCTATAATCAAGAAAATCAGCCAATTCGTGTTAACCCCGGTCCGCTAGATGCTCCAGCATACGGTGTTAAATCGACCTTACCTGATATGCTGAGTTTCATTAATGCCAATATAAATCCACAAAAATATCCAGCAGATATTCAACGTGCAATTAATGAAACACATCAAGGTTTCTATCAAGTCGGCACCATGTATCAGGCACTTGGTTGGGAAGAATTTTCTTATCCAGCGCCTTTACAAACTTTATTAGACAGTAATTCAGAACAAATTGTGATGAAGCCTAATAAAGTGACTGCCATTTCCAAAGAACCTTCAATTAAGATGTTCCACAAAACTGGTTCGACTAACGGTTTTGGAACATATGTCGTGTTCATTCCTAAAGAAAATATTGGCTTAGTCATGTTGACCAATAAACGTATTCCGAATGAAGAACGCATTAAAGCAGCTTATGCTGTGTTAAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3008003","ARO_id":"46795","ARO_name":"ADC-287","CARD_short_name":"ADC-287","ARO_description":"Extended-spectrum class C beta-lactamase ADC-287.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7422":{"model_id":"7422","model_name":"ADC-288","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10249":{"protein_sequence":{"accession":"UZF98458.1","sequence":"MRFNKISCLLLPPLFIFSTSIYADNTPKDQEIKKLVDQNFKPLLDKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNNSTIFELGSVSKLFTATAGGYAKTKGTISFKDTPGKYWKELKNTPIDQVNLLQLGTYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNSIGEYRQYSNPSIGLFGKIVALSMNKPFDQVLEKTIFPNLSLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPKDIQRAINETHQGFYQVGTMYQALGWEEFSYPAPLQTLLDSNSEQIVMKPNKVTAISKEPSVKMFHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"OP745007.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAACAAAATTTCTTGCTTACTTTTACCTCCTCTTTTTATTTTTAGTACCTCAATTTATGCGGACAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCTTTATTAGATAAATATGATGTGCCGGGTATGGCCGTGGGTGTTATTCAGAATAATAAAAAGTATGAAATGTATTATGGTCTACAATCTGTTCAAGATAAAAAAGCCGTAAATAATAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCTACAGCAGGTGGATATGCCAAAACAAAAGGGACAATCTCTTTTAAAGACACACCTGGAAAATATTGGAAAGAGCTAAAAAATACACCGATTGACCAGGTTAACTTACTTCAACTTGGTACCTATACAAGTGGCAACCTTGCTTTGCAATTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACTCAATCGGTGAATATAGACAATATTCAAATCCTAGTATTGGCCTATTTGGAAAGATTGTAGCTTTGTCTATGAATAAACCTTTTGATCAAGTCTTAGAAAAAACAATTTTTCCAAATCTGAGCTTAAAACATAGCTATGTAAATGTTCCTAAAACTCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCAATTCGTGTTAACCCTGGTCCGCTAGATGCACCTGCGTACGGCGTCAAATCGACACTACCAGACATGCTGAGTTTTATTCATGCCAACCTCAACCCACAGAAATATCCGAAAGATATTCAACGTGCAATTAATGAAACACATCAAGGTTTCTATCAAGTCGGCACCATGTATCAGGCTCTTGGTTGGGAAGAATTTTCTTATCCAGCGCCTTTACAAACTTTATTAGACAGTAATTCAGAACAAATTGTGATGAAGCCTAATAAAGTGACTGCCATTTCAAAAGAACCTTCAGTTAAGATGTTCCACAAAACTGGTTCAACCAATGGTTTCGGAACTTATGTCGTGTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTGACCAATAAACGTATTCCAAATGAAGAACGCATCAAGGCAGCGTATGCGGTGTTAAATGCAATAAAAAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3008004","ARO_id":"46796","ARO_name":"ADC-288","CARD_short_name":"ADC-288","ARO_description":"Extended-spectrum class C beta-lactamase ADC-288.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7423":{"model_id":"7423","model_name":"ADC-289","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10250":{"protein_sequence":{"accession":"UZQ18804.1","sequence":"MRFKKISYLLLPSLFIFNTSIYAGNTSKDQEIKQLVDQNFKPLLEKYNVPGMAVGIIQNNKKYETYYGLQSVQDKKAVNSNTIFELGSVSKLFTATAGAYAKNTGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLTLQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGEIVGLSMKQPFSQVLEKTIFPDLGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPANIQRAINETHQGRYQVNSMYQALGWEEFAYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKDNIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"OP806904.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTACTTACTTTTACCTTCTCTTTTTATTTTTAATACCTCAATTTATGCGGGCAATACTTCTAAAGACCAAGAAATTAAACAATTGGTAGATCAAAATTTTAAGCCCTTATTAGAAAAATATAATGTGCCGGGTATGGCGGTAGGTATTATTCAAAACAATAAAAAATATGAAACGTATTATGGCCTACAATCCGTTCAAGATAAAAAAGCTGTAAATAGCAATACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACTGCAACGGCAGGTGCTTATGCAAAAAATACAGGAAAAATCTCTTTTGATGATACGCCGGGCAAATACTGGAAAGAGTTAAAAAACACCCCAATTGATCAGGTCAATTTACTTCAACTTGCCACCTATACAAGTGGTAACCTCACCTTGCAATTCCCAGATGAAGTACAAACAGATCAACAGGTTTTAACTTTTTTTAAAGATTGGAAACCTAAAAACCCAATCGGTGAATATAGACAATATTCAAACCCAAGTATTGGCCTATTTGGGGAAATAGTTGGTTTATCAATGAAGCAGCCTTTTAGTCAGGTCTTGGAAAAAACGATTTTTCCGGACCTTGGCTTAAAACATAGCTATGTCAATGTGCCTAAAACTCAGATGCAAAACTATGCATTTGGCTATAACCAAGAAAATCAGCCAATTCGAGTTAACCCTGGCCCACTCGATGCCCCAGCATACGGCGTCAAATCGACCCTACCCGACATGCTGAGCTTTATTCATGCCAACCTGAACCCACAGAAATATCCGGCAAATATTCAACGTGCAATTAATGAGACACATCAAGGTCGCTATCAAGTAAATAGCATGTATCAGGCACTCGGTTGGGAAGAGTTTGCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAACCTTCAGTTAAGATGTACCACAAAACTGGTTCAACCAATGGTTTCGGAACCTATGTCGTATTTATTCCTAAAGACAATATTGGTTTAGTCATGTTAACCAATAAACGCATTCCAAATGAAGAACGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36949","NCBI_taxonomy_name":"Acinetobacter nosocomialis","NCBI_taxonomy_id":"106654"}}}},"ARO_accession":"3008005","ARO_id":"46797","ARO_name":"ADC-289","CARD_short_name":"ADC-289","ARO_description":"Extended-spectrum class C beta-lactamase ADC-289.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7424":{"model_id":"7424","model_name":"ADC-290","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10251":{"protein_sequence":{"accession":"UZQ18805.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGAYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVKTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"OP806905.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGCTTATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAGCTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTCCCAGATGAAGTAAAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGTGTCAAATCGACACTACCCGACATGCTGAGTTTTATTCATGCCAACCTCAACCCACAGAAATATCCGGCTGATATTCAACGGGCAATTAATGAAACACATCAAGGTCGCTATCAAGTAAATACCATGTACCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCCACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACGTATGTGGTCTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGTATTAAGGCAGCGTATGCAGTTTTAAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008006","ARO_id":"46798","ARO_name":"ADC-290","CARD_short_name":"ADC-290","ARO_description":"Extended-spectrum class C beta-lactamase ADC-290.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7425":{"model_id":"7425","model_name":"ADC-291","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10252":{"protein_sequence":{"accession":"WDE35083.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGIAVGVIQNNKKYEMYYGLQSVQDKKAVNSSSIFELGSVSKLFTATAGAYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVTPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPTDIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"OQ408539.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCGTTATTAGAAAAATATGATGTGCCGGGTATAGCTGTGGGTGTTATCCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTAGCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGCTTATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTACCCCCGGCCCACTCGATGCCCCAGCATACGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTTAACCCACAGAAATATCCGACAGATATTCAACGGGCAATTAATGAAACACATCAAGGTCGCTATCAAGTAAATACCATGTATCAAGCGCTTGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAGCCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACATATGTAGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008007","ARO_id":"46799","ARO_name":"ADC-291","CARD_short_name":"ADC-291","ARO_description":"Extended-spectrum class C beta-lactamase ADC-291.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7426":{"model_id":"7426","model_name":"ADC-292","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10253":{"protein_sequence":{"accession":"MDE4038918.1","sequence":"MRFKKISCLLLPPLFIFNTSIYAGNTPKEQEIKKLVDQNFKPLLEKYDVPGMAVGIIQNNKKYETYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVKTDQQVLTFFKEWKPKNSIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLENTVFPELGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLKFINANLNPQKYPKDIQRAINETHQGFYQVGTMYQALGWEEFSYPAPLQTLLDSNSEQIVMKPNKVTTISKEPSVKMFHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"JARCHN010000001.1","fmin":"691817","fmax":"692969","strand":"-","sequence":"ATGCGATTTAAAAAAATTTCTTGCTTACTTTTACCCCCTCTTTTTATTTTTAATACCTCAATTTATGCAGGGAATACACCAAAAGAGCAAGAAATTAAGAAACTGGTTGATCAAAATTTTAAACCGTTATTAGAAAAATATGATGTGCCTGGGATGGCTGTTGGCATCATCCAAAATAATAAAAAGTATGAAACATATTACGGCCTACAATCCGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAACTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCAACGTATACAAGTGGTAACCTTGCCTTGCAATTTCCAGATGAGGTAAAAACAGATCAGCAAGTTTTAACATTTTTCAAAGAATGGAAACCTAAAAACTCAATCGGTGAATATCGACAATATTCAAATCCAAGCATTGGTTTATTTGGAAAAGTTGTTGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAACACAGTTTTTCCAGAGCTTGGCTTAAAACATAGTTATGTGAATGTACCTAAAACTCAGATGCAAAACTATGCATTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAATCCTGGTCCACTCGATGCACCAGCATACGGCGTTAAATCTACCCTACCCGATATGCTTAAGTTTATTAATGCCAACCTAAATCCACAAAAATATCCGAAAGATATTCAACGTGCAATTAATGAAACACATCAAGGTTTCTATCAAGTCGGCACCATGTATCAGGCACTTGGTTGGGAAGAATTTTCTTATCCAGCGCCTTTACAAACTTTATTAGACAGTAATTCAGAGCAAATCGTGATGAAGCCTAATAAAGTGACTACAATTTCCAAAGAACCTTCAGTTAAGATGTTCCACAAAACTGGCTCAACAAATGGCTTTGGAACTTATGTGGTGTTTATTCCAAAAGAAAATATTGGCTTAGTCATGTTGACCAATAAACGTATTCCAAATGAAGAACGCATTAAGGCAGCTTATGCCGTGTTAAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3008008","ARO_id":"46800","ARO_name":"ADC-292","CARD_short_name":"ADC-292","ARO_description":"Extended-spectrum class C beta-lactamase ADC-292.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7427":{"model_id":"7427","model_name":"ADC-293","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10254":{"protein_sequence":{"accession":"WEG44937.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVKTDQQVLTFFKDWKPKNSIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYSVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPDKVTAISKEPSVKMYHKTGSTTGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"OQ592373.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAGTATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAATTTCCAGATGAAGTAAAAACAGATCAGCAAGTTTTAACATTTTTTAAAGACTGGAAACCTAAAAACTCAATCGGTGAATATCGACAATATTCAAACCCAAGCATTGGTTTATTTGGAAAAGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATAGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTAAATCCACAAAAATATCCAGCAGATATTCAACGGGCAATTAATGAAACACATCAGGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTGATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTACCGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008009","ARO_id":"46801","ARO_name":"ADC-293","CARD_short_name":"ADC-293","ARO_description":"Extended-spectrum class C beta-lactamase ADC-293.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7428":{"model_id":"7428","model_name":"ADC-294","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10255":{"protein_sequence":{"accession":"WEG44938.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALKFPDEVKTDQQVLTFFKDWKPKNSIGEYLQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYSVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTTGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"OQ592374.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAGTATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGAAATTTCCAGATGAAGTAAAAACAGATCAGCAAGTTTTAACATTTTTTAAAGACTGGAAACCTAAAAACTCAATCGGTGAATATCTACAATATTCAAACCCAAGCATTGGTTTATTTGGAAAAGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATAGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTAAATCCACAAAAATATCCAGCAGATATTCAACGGGCAATTAATGAAACACATCAGGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTACCGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008010","ARO_id":"46802","ARO_name":"ADC-294","CARD_short_name":"ADC-294","ARO_description":"Extended-spectrum class C beta-lactamase ADC-294.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7429":{"model_id":"7429","model_name":"ADC-295","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10256":{"protein_sequence":{"accession":"EKU38981.1","sequence":"MRFKKISCLLLPSLFIFNTSIYADNTPKEQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKNYEMYYGLQSVQDKKAVNGNTIFELGSVSKLFTATAGGYAKTKGKISFEDTPGKYWKELKNTPIDRVTLLQLATYTSGNLALQFPDEVQTDQQVLTFFKEWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPDLGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFVNANLNPQKYPADIQRAINETHKGFYQVGTMHQALGWEEFSYPAPLQTLLDSNSEQIVMKPNKVTAISKEPSVKIYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"AMSS01000044.1","fmin":"132747","fmax":"133899","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCCTGCTTACTTTTACCTTCTCTTTTCATTTTTAATACCTCAATTTATGCAGACAATACACCCAAAGAGCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCGTTATTAGAAAAATATGATGTGCCTGGCATGGCCGTGGGAGTTATCCAAAATAATAAAAACTATGAAATGTATTATGGCCTGCAATCGGTTCAAGATAAAAAAGCCGTAAATGGCAATACCATTTTCGAGCTAGGTTCAGTGAGTAAATTATTTACCGCCACAGCAGGTGGATATGCAAAAACAAAAGGAAAAATCTCTTTTGAAGACACACCCGGAAAGTATTGGAAAGAATTAAAAAACACACCAATTGACCGAGTTACCCTACTTCAGCTTGCGACGTATACGAGTGGCAACCTTGCGCTACAATTCCCAGATGAAGTCCAAACAGATCAGCAAGTTTTAACTTTTTTCAAAGAATGGAAACCTAAAAACCCAATCGGTGAATATCGACAATATTCAAATCCCAGCATTGGTCTATTTGGCAAAGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACCATTTTTCCAGATCTTGGCTTAAAACATAGCTATGTAAATGTGCCTAAGACTCAAATGCAAAACTATGCATTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTAGATGCGCCTGCGTACGGCGTTAAATCGACCTTACCTGATATGCTGAGTTTCGTTAATGCCAATCTAAATCCACAAAAATATCCGGCTGATATTCAACGCGCAATTAATGAGACACATAAAGGTTTCTATCAAGTAGGTACGATGCATCAAGCATTAGGTTGGGAAGAGTTCTCTTATCCAGCACCTTTACAGACTTTATTAGACAGTAATTCAGAGCAAATCGTGATGAAGCCTAATAAAGTCACTGCCATTTCCAAAGAACCTTCAGTTAAGATTTACCACAAAACTGGTTCAACCAATGGCTTTGGAACGTATGTCGTGTTTATTCCTAAAGAGAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCCAATGAAGAACGCATTAAAGCAGCTTACGCAGTGTTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36837","NCBI_taxonomy_name":"Acinetobacter sp.","NCBI_taxonomy_id":"472"}}}},"ARO_accession":"3008011","ARO_id":"46803","ARO_name":"ADC-295","CARD_short_name":"ADC-295","ARO_description":"Extended-spectrum class C beta-lactamase ADC-295.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7430":{"model_id":"7430","model_name":"ADC-302","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10257":{"protein_sequence":{"accession":"MDC5490025.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEIYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKVLKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPTDIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"JAOXAU010000001.1","fmin":"328180","fmax":"329332","strand":"-","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCATTATTAGAAAAATATGATGTGCCGGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATATATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGTGCTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATACGGCGTCAAATCCACCTTACCGGATATGTTGAGTTTTATTCATGCCAACCTTAACCCACAGAAATATCCGACAGATATTCAACGGGCAATTAATGAAACACATCAAGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCGTATGCAGTTTTAAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008012","ARO_id":"46804","ARO_name":"ADC-302","CARD_short_name":"ADC-302","ARO_description":"Extended-spectrum class C beta-lactamase ADC-302.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7431":{"model_id":"7431","model_name":"ADC-303","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10258":{"protein_sequence":{"accession":"MDC5131430.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVAKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLSAIKK"},"dna_sequence":{"accession":"JAOWYO010000004.1","fmin":"7515","fmax":"8667","strand":"-","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGCAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCTTATTTGGAAAAGTTGTTGCTTTGTCTATGAATAAACCTTTCGATCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTAGCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTTAACCCACAGAAATATCCGGCTGATATTCAAAGGGCAATTAATGAAACACATCAAGGTCGCTATCAAGTAAATACCATGTATCAAGCGCTTGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCAACGGTTTCGGAACATATGTCGTGTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAGTGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008013","ARO_id":"46805","ARO_name":"ADC-303","CARD_short_name":"ADC-303","ARO_description":"Extended-spectrum class C beta-lactamase ADC-303.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7432":{"model_id":"7432","model_name":"ADC-304","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10259":{"protein_sequence":{"accession":"MDC5177796.1","sequence":"MRFKKISCLLLSPLFIFSTSIYADNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"JANJCG010000001.1","fmin":"149346","fmax":"150498","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGACAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCATTATTAGAAAAATATGATGTGCCGGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAGCTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTCCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATACGGCGTCAAATCAACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTAAATCCACAAAAATATCCGGCAGATATTCAACGTGCAATTAATGAAACACATCAGGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTACTAGACAGTAATTCAGAACAGATTGTAATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCAACGGTTTCGGAACGTATGTGGTGTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCGTATGCAGTTTTAAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008014","ARO_id":"46806","ARO_name":"ADC-304","CARD_short_name":"ADC-304","ARO_description":"Extended-spectrum class C beta-lactamase ADC-304.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7433":{"model_id":"7433","model_name":"ADC-305","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10260":{"protein_sequence":{"accession":"MDC5206348.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWQPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANFNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"JAOWYW010000001.1","fmin":"351957","fmax":"353109","strand":"-","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCGGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGCAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCTTATTTGGAAAAGTTGTTGCTTTGTCTATGAATAAACCTTTCGATCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACTTCAACCCACAGAAATATCCGGCTGATATTCAACGGGCAATTAATGAAACACATCAAGGTCGCTATCAAGTAAATACCATGTATCAAGCGCTTGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAGCCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACATATGTAGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCGTATGCAGTTTTAAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008015","ARO_id":"46807","ARO_name":"ADC-305","CARD_short_name":"ADC-305","ARO_description":"Extended-spectrum class C beta-lactamase ADC-305.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7434":{"model_id":"7434","model_name":"ADC-306","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10261":{"protein_sequence":{"accession":"MDC5547987.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALDLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIYANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPTTLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLSAIKK"},"dna_sequence":{"accession":"JANJEG010000001.1","fmin":"150295","fmax":"151447","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCGGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAGCTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTCCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGACTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCTGGCCCACTCGATGCCCCAGCATACGGCGTCAAATCCACCTTACCGGATATGTTGAGTTTTATTTATGCCAACCTTAACCCACAGAAATATCCGGCTGATATTCAACGGGCAATTAATGAAACACATCAAGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGACAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCAACGGTTTCGGAACGTATGTGGTGTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAGTGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008016","ARO_id":"46808","ARO_name":"ADC-306","CARD_short_name":"ADC-306","ARO_description":"Extended-spectrum class C beta-lactamase ADC-306.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7435":{"model_id":"7435","model_name":"ADC-307","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10262":{"protein_sequence":{"accession":"MDC5515369.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVTKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPTDIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"JANJEC010000002.1","fmin":"31691","fmax":"32843","strand":"-","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCGGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTAACTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATACGGCGTCAAATCCACCTTACCGGATATGTTAAGTTTTATTCATGCCAACCTTAACCCACAGAAATATCCGACAGATATTCAACGGGCAATTAATGAAACACATCAAGGTCGCTATCAAGTAAATACCATGTATCAAGCGCTTGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAGCCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACATATGTAGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008017","ARO_id":"46809","ARO_name":"ADC-307","CARD_short_name":"ADC-307","ARO_description":"Extended-spectrum class C beta-lactamase ADC-307.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7436":{"model_id":"7436","model_name":"ADC-308","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10263":{"protein_sequence":{"accession":"MDC5119581.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVKTDQQVLTFFKDWKPKNSIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGHYQVNTMYQALGWEEFSYPAMLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYTVLNAIKK"},"dna_sequence":{"accession":"JANJCP010000016.1","fmin":"22911","fmax":"24063","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAGTATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAATTTCCAGATGAAGTAAAAACAGATCAGCAAGTTTTAACATTTTTTAAAGACTGGAAACCTAAAAACTCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACTCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATACGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTTAACCCACAGAAATATCCGGCAGATATTCAACGGGCAATTAATGAAACACATCAGGGTCACTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAATGTTACAAACTTTACTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACGTATGTGGTGTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCGTATACAGTTTTAAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008018","ARO_id":"46810","ARO_name":"ADC-308","CARD_short_name":"ADC-308","ARO_description":"Extended-spectrum class C beta-lactamase ADC-308.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7437":{"model_id":"7437","model_name":"ADC-309","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10264":{"protein_sequence":{"accession":"MDC4862281.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDKPGKYWKELKNTPIDQVNLLQLATYISGNLALQFPDEVQTDQQVLTFFKVWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPAPLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"JANJBJ010000001.1","fmin":"336390","fmax":"337542","strand":"-","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATAAGCCTGGTAAATATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATATAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGTCTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTGGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACTCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGTCCACTCGATGCCCCAGCATACGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTTAACCCACAGAAATATCCGGCAGATATTCAACGGGCAATTAATGAAACACATCAAGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCAGCACCTTTACAAACTTTATTAGACAGTAATTCAGAACAAATTGTGATGAAGCCTAATAAAGTGACTGCTATTTCAAAAGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCAACGGTTTCGGAACGTATGTGGTGTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCGTATGCAGTTTTAAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008019","ARO_id":"46811","ARO_name":"ADC-309","CARD_short_name":"ADC-309","ARO_description":"Extended-spectrum class C beta-lactamase ADC-309.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7438":{"model_id":"7438","model_name":"ADC-310","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10265":{"protein_sequence":{"accession":"MDC5062159.1","sequence":"MRFKKISCLLLSPLFIFNTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKVLKNTPIDQVNLLQLATYTSSNLALQFPDEVQTDQQVLTFFKDWQPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPTDIQRAINETHQGFYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKE"},"dna_sequence":{"accession":"JANJCA010000001.1","fmin":"295799","fmax":"296951","strand":"-","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAATACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCGTTATTAGAAAAATATGATGTACCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGTGCTAAAAAATACACCGATTGATCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTAGCAACCTCGCTTTACAATTTCCAGATGAAGTACAAACAGATCAACAAGTTTTAACTTTTTTCAAAGACTGGCAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTGGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTTGATGCCCCAGCATACGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTTAACCCACAGAAATATCCGACAGATATTCAACGGGCAATTAATGAAACACATCAAGGGTTCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTACTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCAACGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAACGCATTAAGGCAGCGTATGCAGTTTTAAATGCAATAAAGGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008020","ARO_id":"46812","ARO_name":"ADC-310","CARD_short_name":"ADC-310","ARO_description":"Extended-spectrum class C beta-lactamase ADC-310.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7439":{"model_id":"7439","model_name":"ADC-311","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10266":{"protein_sequence":{"accession":"MDC5482482.1","sequence":"MRFKKISCLLLSPLFIVSTSIYADNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGIIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDKPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGHYQVNTMYQALGWEEFSYPAMLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYTVLNAIKK"},"dna_sequence":{"accession":"JANJDX010000001.1","fmin":"343159","fmax":"344311","strand":"-","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTGTTAGTACCTCAATTTATGCGGACAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCGTTATTAGAAAAATATGATGTGCCGGGTATGGCTGTGGGTATTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGACAAGCCTGGTAAATATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCTTATTTGGAAAAGTTGTTGCTTTGTCTATGAATAAACCTTTCGATCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACTCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATACGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTTAACCCACAGAAATATCCGGCAGATATTCAACGGGCAATTAATGAAACACATCAGGGTCACTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAATGTTACAAACTTTACTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACGTATGTGGTGTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCGTATACAGTTTTAAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008021","ARO_id":"46813","ARO_name":"ADC-311","CARD_short_name":"ADC-311","ARO_description":"Extended-spectrum class C beta-lactamase ADC-311.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7440":{"model_id":"7440","model_name":"ADC-312","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10267":{"protein_sequence":{"accession":"MDC5528210.1","sequence":"MRFKKISCLLLSPLFIFSTSIYADNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGFYQLETMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"JANJED010000023.1","fmin":"49212","fmax":"50364","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGACAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTAGGTTCTGTTAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAGCTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGCTGAGTTTTATTCATGCCAACCTCAACCCACAGAAATATCCGGCAGATATTCAACGGGCAATTAATGAAACACATCAAGGGTTCTATCAATTAGAAACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGATAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCAACGGTTTCGGAACATATGTAGTGTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008022","ARO_id":"46814","ARO_name":"ADC-312","CARD_short_name":"ADC-312","ARO_description":"Extended-spectrum class C beta-lactamase ADC-312.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7441":{"model_id":"7441","model_name":"ADC-313","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10268":{"protein_sequence":{"accession":"MDC4557711.1","sequence":"MRFKKISCLLLSPLFIFSISIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKVLKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPEKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"JANIZI010000005.1","fmin":"165437","fmax":"166589","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTATCTCAATTTATGCGGGCAATACCCCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCATTATTAGAAAAATATGATGTGCCGGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGTGCTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCCACCTTACCGGATATGCTGAGTTTTATTCATGCCAACCTTAACCCAGAGAAATATCCGGCTGATATTCAAAGGGCAATTAATGAAACACATCAAGGTCGCTATCAAGTAAATACCATGTATCAAGCGCTTGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCAACGGTTTCGGAACGTATGTGGTGTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCGTATGCAGTTTTAAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008023","ARO_id":"46815","ARO_name":"ADC-313","CARD_short_name":"ADC-313","ARO_description":"Extended-spectrum class C beta-lactamase ADC-313.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7442":{"model_id":"7442","model_name":"ADC-314","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10269":{"protein_sequence":{"accession":"MDC5248995.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGAYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVKTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKSFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLKFIHANLNPQKYPADIQRAINETHQGFYQLETMYQALGWEEFSYPAPLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"JANJCW010000001.1","fmin":"341818","fmax":"342970","strand":"-","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGCTTATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAGCTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTCCCAGATGAAGTAAAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTAGCTTTGTCTATGAATAAATCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGTGTCAAATCGACACTACCCGATATGCTTAAGTTTATTCATGCCAACCTCAACCCACAGAAATATCCGGCAGATATTCAACGGGCAATTAATGAAACACATCAAGGGTTCTATCAATTAGAAACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCAGCACCTTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACGTATGTGGTGTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008024","ARO_id":"46816","ARO_name":"ADC-314","CARD_short_name":"ADC-314","ARO_description":"Extended-spectrum class C beta-lactamase ADC-314.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7443":{"model_id":"7443","model_name":"ADC-315","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10270":{"protein_sequence":{"accession":"MDC5406861.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWQPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVAKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLKFIHANLNPQKYPTDIQRAINETHQGHYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"JAOWZW010000001.1","fmin":"155565","fmax":"156717","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCGGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGCAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTGGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTAGCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCTGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGCTTAAGTTTATTCATGCCAATCTGAACCCACAGAAATATCCGACAGATATTCAACGTGCAATTAATGAAACACATCAGGGTCACTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACGTATGTGGTGTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008025","ARO_id":"46817","ARO_name":"ADC-315","CARD_short_name":"ADC-315","ARO_description":"Extended-spectrum class C beta-lactamase ADC-315.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7444":{"model_id":"7444","model_name":"ADC-316","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10271":{"protein_sequence":{"accession":"MDC4596988.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYVVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKGLKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWQPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNRENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPTDIQRAINETHQGFYQLNTMYQALSWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"JANIZP010000005.1","fmin":"2854","fmax":"4006","strand":"-","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACCCCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCGTTATTAGAAAAATATGTTGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGGGCTAAAAAATACACCGATTGATCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGCAACCTCGCTTTACAATTTCCAGATGAAGTACAAACAGATCAACAAGTTTTAACTTTTTTCAAAGACTGGCAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTGGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCGAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGCTGAGTTTTATTCATGCCAACCTCAACCCACAGAAATATCCGACAGATATTCAACGGGCAATTAATGAAACACATCAAGGGTTCTATCAACTAAATACCATGTATCAGGCACTCAGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCAACGGTTTCGGAACATATGTGGTCTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008026","ARO_id":"46818","ARO_name":"ADC-316","CARD_short_name":"ADC-316","ARO_description":"Extended-spectrum class C beta-lactamase ADC-316.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7445":{"model_id":"7445","model_name":"ADC-317","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10272":{"protein_sequence":{"accession":"MDC4589794.1","sequence":"MRFKKISCLILSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVAKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGFYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"JANIZQ010000004.1","fmin":"166469","fmax":"167621","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTAATTTTATCCCCTCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCATTATTAGAAAAATATGATGTGCCGGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCTTATTTGGAAAAGTTGTTGCTTTGTCTATGAATAAACCTTTCGATCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTAGCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTTAACCCACAGAAATATCCGGCTGATATTCAAAGGGCAATTAATGAAACACATCAAGGGTTCTATCAAGTAAATACCATGTATCAAGCGCTTGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCAAATAAAGTGACTGCTATTTCAAAAGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCAACGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGATTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCAGTTTTAAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008027","ARO_id":"46819","ARO_name":"ADC-317","CARD_short_name":"ADC-317","ARO_description":"Extended-spectrum class C beta-lactamase ADC-317.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7446":{"model_id":"7446","model_name":"ADC-318","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10273":{"protein_sequence":{"accession":"MDC4897557.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDKPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFNQVLEKTIFPALGLKHSYVNIPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIYANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPTTLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLSAIKK"},"dna_sequence":{"accession":"JANJBO010000013.1","fmin":"94441","fmax":"95593","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATAAGCCTGGTAAATATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAAGTTGTTGCTTTGTCTATGAATAAACCTTTCAACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATATACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAATCCTGGTCCACTCGATGCCCCAGCATACGGCGTCAAATCCACCTTACCGGATATGTTGAGTTTTATTTATGCCAACCTTAACCCACAGAAATATCCGGCTGATATTCAACGGGCAATTAATGAAACACATCAAGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGACAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCAACGGTTTCGGAACGTATGTGGTGTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAGTGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008028","ARO_id":"46820","ARO_name":"ADC-318","CARD_short_name":"ADC-318","ARO_description":"Extended-spectrum class C beta-lactamase ADC-318.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7447":{"model_id":"7447","model_name":"ADC-319","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10274":{"protein_sequence":{"accession":"MDC4364731.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGIIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQCRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"JAOWUQ010000001.1","fmin":"152291","fmax":"153443","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCGTTATTAGAAAAATATGATGTGCCGGGTATGGCTGTGGGTATTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCCAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTAAATCCACAAAAATATCCAGCAGATATTCAACGGGCAATTAATGAAACACATCAGTGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCAACGGTTTCGGAACATATGTAGTGTTTATACCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008029","ARO_id":"46821","ARO_name":"ADC-319","CARD_short_name":"ADC-319","ARO_description":"Extended-spectrum class C beta-lactamase ADC-319.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7448":{"model_id":"7448","model_name":"ADC-320","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10275":{"protein_sequence":{"accession":"MDC5360473.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDKSGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGFYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"JAOWZM010000001.1","fmin":"327036","fmax":"328188","strand":"-","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATCTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATAAGTCTGGTAAATATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAATTTACTTCAACTCGCGACGTATACAAGTGGCAACCTCGCTTTACAATTTCCAGATGAAGTACAAACAGATCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCTTATTTGGAAAAGTTGTTGCTTTGTCTATGAATAAACCTTTCGATCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATACGGCGTCAAATCCACCTTACCGGATATGTTGAGTTTTATTCATGCCAACCTCAACCCACAGAAATATCCGGCAGATATTCAACGGGCAATTAATGAAACACATCAAGGGTTCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCAACGGTTTCGGAACATATGTGGTCTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008030","ARO_id":"46822","ARO_name":"ADC-320","CARD_short_name":"ADC-320","ARO_description":"Extended-spectrum class C beta-lactamase ADC-320.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7449":{"model_id":"7449","model_name":"ADC-321","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10276":{"protein_sequence":{"accession":"MDC4513545.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNSIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPELGLKYSYVNVPKTQIQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLKFINANLNPQKYPADIQRAINETHQGFYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"JAOWVC010000002.1","fmin":"31566","fmax":"32718","strand":"-","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGATGATACGCCTGGTAAATATTGGAAAGAACTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACTCAATCGGTGAATATCGACAATATTCAAACCCAAGCATTGGTTTATTTGGAAAAGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACTATTTTTCCAGAGCTTGGCTTAAAATATAGTTATGTAAATGTGCCTAAAACTCAGATACAAAACTATGCATTTGGTTATAACCAAGAAAATCAGCCGATTCGAGTTAATCCTGGTCCACTCGATGCACCAGCATACGGCGTTAAATCTACCTTACCTGATATGCTTAAGTTTATTAATGCCAACCTAAACCCACAAAAATATCCAGCAGATATTCAACGGGCAATTAATGAAACACATCAAGGGTTCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCAACGGTTTCGGAACATATGTGGTCTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCGTATGCAGTTTTAAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008031","ARO_id":"46823","ARO_name":"ADC-321","CARD_short_name":"ADC-321","ARO_description":"Extended-spectrum class C beta-lactamase ADC-321.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7450":{"model_id":"7450","model_name":"ADC-322","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10277":{"protein_sequence":{"accession":"MDC4290945.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSITIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKSFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPANIQRAINETHQGRYQVNSMYQALGWEEFAYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKDNIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"JANIXO010000004.1","fmin":"7457","fmax":"8609","strand":"-","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTACGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCATTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCTTATTTGGAAAAGTTGTTGCTTTGTCTATGAATAAATCTTTCGATCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCATTTGGCTATAACCAAGAAAATCAGCCAATTCGAGTTAACCCTGGCCCACTCGATGCCCCAGCATACGGCGTCAAATCGACCCTACCCGACATGCTGAGCTTTATTCATGCCAACCTGAACCCACAGAAATATCCGGCAAATATTCAACGTGCAATTAATGAGACACATCAAGGTCGCTATCAAGTAAATAGCATGTATCAGGCACTCGGTTGGGAAGAGTTTGCTTATCCGGCAACGTTACAGACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAACCTTCAGTTAAGATGTACCACAAAACTGGTTCAACAAATGGTTTCGGAACCTATGTCGTATTTATTCCTAAAGACAATATTGGTTTAGTCATGTTAACCAATAAACGCATTCCAAATGAAGAACGCATTAAGGCAGCTTATGCTGTGCTAAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008032","ARO_id":"46824","ARO_name":"ADC-322","CARD_short_name":"ADC-322","ARO_description":"Extended-spectrum class C beta-lactamase ADC-322.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7451":{"model_id":"7451","model_name":"ADC-323","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10278":{"protein_sequence":{"accession":"MDC4357889.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKVLKNTPIDQVNLLQLAAYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGFYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"JANIXZ010000001.1","fmin":"356426","fmax":"357578","strand":"-","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACCCCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCATTATTAGAAAAATATGATGTGCCGGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGTGCTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGGCGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATACGGCGTCAAATCCACCTTACCGGATATGTTGAGTTTTATTCATGCCAACCTCAACCCACAGAAATATCCGGCAGATATTCAACGGGCAATTAATGAAACACATCAAGGGTTCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCAACGGTTTCGGAACATATGTGGTCTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008033","ARO_id":"46825","ARO_name":"ADC-323","CARD_short_name":"ADC-323","ARO_description":"Extended-spectrum class C beta-lactamase ADC-323.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7452":{"model_id":"7452","model_name":"ADC-324","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10279":{"protein_sequence":{"accession":"MDC5633961.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDKPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLNFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFINANLNPQKYPTDIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"JAOYRN010000002.1","fmin":"16794","fmax":"17946","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTACGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATAAGCCTGGTAAATATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAAATTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCTTATTTGGAAAAGTTGTTGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACTCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATACGGCGTCAAATCCACCTTACCGGATATGTTGAGTTTTATTAATGCCAACCTTAACCCACAAAAATATCCGACAGATATTCAACGGGCAATTAATGAAACACATCAAGGTCGCTATCAAGTAAATACCATGTATCAAGCGCTTGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCAACGGTTTCGGAACATATGTGGTCTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCGTATGCAGTTTTAAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008034","ARO_id":"46826","ARO_name":"ADC-324","CARD_short_name":"ADC-324","ARO_description":"Extended-spectrum class C beta-lactamase ADC-324.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7453":{"model_id":"7453","model_name":"ADC-325","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10280":{"protein_sequence":{"accession":"MDC4671831.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWQPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNRENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPTDIQRAINETHQGFYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLSAIKK"},"dna_sequence":{"accession":"JANIZX010000006.1","fmin":"38472","fmax":"39624","strand":"-","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAGTATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGCAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTGGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCGAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGCTGAGTTTTATTCATGCCAACCTCAACCCACAGAAATATCCGACAGATATTCAACGGGCAATTAATGAAACACATCAAGGGTTCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCAACGGTTTCGGAACATATGTGGTCTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAGTGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008035","ARO_id":"46827","ARO_name":"ADC-325","CARD_short_name":"ADC-325","ARO_description":"Extended-spectrum class C beta-lactamase ADC-325.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7454":{"model_id":"7454","model_name":"ADC-326","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10281":{"protein_sequence":{"accession":"MDC5297294.1","sequence":"MRFKKNSCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGIIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDKPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDTPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"JAOXAC010000001.1","fmin":"1143371","fmax":"1144523","strand":"+","sequence":"ATGCGATTTAAAAAAAATTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCGTTATTAGAAAAATATGATGTGCCGGGTATGGCTGTGGGTATTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGACAAGCCTGGTAAATATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATACCCCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTAAATCCACAAAAATATCCAGCAGATATTCAACGGGCAATTAATGAAACACATCAGGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCAACGGTTTCGGAACATATGTAGTGTTTATACCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008036","ARO_id":"46828","ARO_name":"ADC-326","CARD_short_name":"ADC-326","ARO_description":"Extended-spectrum class C beta-lactamase ADC-326.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7455":{"model_id":"7455","model_name":"ADC-327","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10282":{"protein_sequence":{"accession":"MDC4416129.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVAKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"JANIYJ010000001.1","fmin":"544772","fmax":"545924","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCATTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCTTATTTGGAAAAGTTGTTGCTTTGTCTATGAATAAACCTTTCGATCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTAGCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTTAACCCACAGAAATATCCGGCTGATATTCAAAGGGCAATTAATGAAACACATCAAGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCAACGGTTTCGGAACATATGTCGTGTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCGTATGCAGTTTTAAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008037","ARO_id":"46829","ARO_name":"ADC-327","CARD_short_name":"ADC-327","ARO_description":"Extended-spectrum class C beta-lactamase ADC-327.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7456":{"model_id":"7456","model_name":"ADC-328","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10283":{"protein_sequence":{"accession":"MDC4995114.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWQPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVAKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPTDIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLSAIKK"},"dna_sequence":{"accession":"JAOWXP010000001.1","fmin":"164166","fmax":"165318","strand":"-","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCATTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGCAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTGGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTAGCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCGACACTACCTGACATGCTGAGTTTTATTCATGCCAATCTGAACCCACAGAAATATCCGACAGATATTCAACGTGCAATTAATGAAACACATCAAGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCAACGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAGTGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008038","ARO_id":"46830","ARO_name":"ADC-328","CARD_short_name":"ADC-328","ARO_description":"Extended-spectrum class C beta-lactamase ADC-328.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7457":{"model_id":"7457","model_name":"ADC-329","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10284":{"protein_sequence":{"accession":"MDC5109664.1","sequence":"MRFKKISCLLLSPLFIFSTSIYADNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPINQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"JANJCJ010000001.1","fmin":"350346","fmax":"351498","strand":"-","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGACAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTAGGTTCTGTTAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAGCTAAAAAATACACCGATTAACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTCCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCTTATTTGGAAAAGTTGTTGCTTTGTCTATGAATAAACCTTTCGATCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTAAATCCACAAAAATATCCAGCAGATATTCAACGGGCAATTAATGAAACACATCAGGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCAACGGTTTCGGAACATATGTAGTGTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008039","ARO_id":"46831","ARO_name":"ADC-329","CARD_short_name":"ADC-329","ARO_description":"Extended-spectrum class C beta-lactamase ADC-329.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7458":{"model_id":"7458","model_name":"ADC-330","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10285":{"protein_sequence":{"accession":"MDC5665782.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDHTPDKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWQPKNPIGEYRQYSNPSIALFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIYANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLSAIKK"},"dna_sequence":{"accession":"JAOVSX010000002.1","fmin":"284110","fmax":"285262","strand":"-","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACCATACGCCTGATAAATATTGGAAAGAACTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGATCAACAAGTTTTAACTTTTTTCAAAGACTGGCAACCTAAAAACCCAATCGGTGAATATAGACAATATTCAAATCCAAGTATTGCCCTATTTGGAAAGGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAGGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCCACCTTACCGGATATGTTGAGTTTTATTTATGCCAACCTTAACCCACAGAAATATCCGGCAGATATTCAACGTGCAATTAATGAAACACATCAGGGTCGCTATCAAGTAAATACCATGTATCAAGCGCTTGGTTGGGAAGAGTTTTCTTATCCAGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACGTATGTGGTCTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAACAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAGTGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008040","ARO_id":"46832","ARO_name":"ADC-330","CARD_short_name":"ADC-330","ARO_description":"Extended-spectrum class C beta-lactamase ADC-330.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7459":{"model_id":"7459","model_name":"ADC-331","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10286":{"protein_sequence":{"accession":"MDC4333491.1","sequence":"MRFKKISCLLLSPLFIFSISIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKVLKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPTDIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLSAIKK"},"dna_sequence":{"accession":"JAOWUO010000003.1","fmin":"7548","fmax":"8700","strand":"-","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTATCTCAATTTATGCGGGCAATACCCCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCATTATTAGAAAAATATGATGTGCCGGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGTGCTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATACGGCGTCAAATCCACCTTACCGGATATGTTGAGTTTTATTCATGCCAACCTTAACCCACAGAAATATCCGACAGATATTCAACGGGCAATTAATGAAACACATCAAGGTCGCTATCAAGTAAATACCATGTATCAAGCGCTTGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAGCCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACATATGTAGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAGTGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008041","ARO_id":"46833","ARO_name":"ADC-331","CARD_short_name":"ADC-331","ARO_description":"Extended-spectrum class C beta-lactamase ADC-331.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7460":{"model_id":"7460","model_name":"ADC-332","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10287":{"protein_sequence":{"accession":"MDC5390807.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYNVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGAYAKNKGKISFDDTSGKYWKVLKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPTDIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"JANJDG010000058.1","fmin":"18817","fmax":"19969","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCGTTATTAGAAAAATATAATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGCTTATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGTCTGGTAAATATTGGAAAGTGCTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATACGGCGTCAAATCCACCTTACCGGATATGTTGAGTTTTATTCATGCCAACCTTAACCCACAAAAATATCCGACAGATATTCAACGGGCAATTAATGAAACACATCAAGGTCGCTATCAAGTAAATACCATGTATCAAGCGCTTGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAGCCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACATATGTAGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008042","ARO_id":"46834","ARO_name":"ADC-332","CARD_short_name":"ADC-332","ARO_description":"Extended-spectrum class C beta-lactamase ADC-332.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7461":{"model_id":"7461","model_name":"ADC-333","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10288":{"protein_sequence":{"accession":"MDC4787251.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDKPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYSADIQRAINETHQGRYQINTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLSAIKK"},"dna_sequence":{"accession":"JANJAT010000001.1","fmin":"146309","fmax":"147461","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATAAGCCTGGTAAATATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAAGTTGTTGCTTTGTCTATGAATAAACCTTTCGATCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAGGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATACGGCGTCAAATCCACCTTACCGGATATGTTGAGTTTTATTCATGCCAATCTGAACCCACAAAAATATTCGGCAGATATTCAACGTGCAATTAATGAAACACATCAGGGTCGCTATCAAATAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAGCCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCAACGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAGTGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008043","ARO_id":"46835","ARO_name":"ADC-333","CARD_short_name":"ADC-333","ARO_description":"Extended-spectrum class C beta-lactamase ADC-333.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7462":{"model_id":"7462","model_name":"ADC-334","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10289":{"protein_sequence":{"accession":"WIU89416.1","sequence":"MRFKKISYLLLPSLFIFNTSIYAGNTSKDQEIKQLVDQNFKPLLEKYNVPGMAVGIIQNNKKYETYYGLQSVQDKKAVNSNTIFELGSVSKLFTATAGAYAKNTGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLTLQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGEIVGLSMKQPFSQVLEKTIFPDLGLKHSYINVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPANIQRAINETHQGRYQVNSMYQALGWEEFAYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"OR102459.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTACTTACTTTTACCTTCTCTTTTTATTTTTAATACCTCAATTTATGCGGGCAATACTTCTAAAGACCAAGAAATTAAACAATTGGTAGATCAAAATTTTAAACCCTTATTAGAAAAATATAATGTACCGGGTATGGCGGTAGGTATTATTCAAAACAATAAAAAATATGAAACGTATTATGGCCTACAATCCGTTCAAGATAAAAAAGCTGTAAATAGCAATACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACTGCAACGGCAGGTGCTTATGCAAAAAATACAGGAAAAATCTCTTTTGATGATACGCCGGGCAAATACTGGAAAGAGTTAAAAAACACCCCAATTGATCAGGTCAATTTACTTCAACTTGCCACCTATACAAGTGGTAACCTCACCTTGCAATTCCCAGATGAAGTACAAACAGATCAACAGGTTTTAACTTTTTTTAAAGATTGGAAACCTAAAAACCCAATCGGTGAATATAGACAATATTCAAACCCAAGTATTGGCCTATTTGGGGAAATAGTTGGTTTATCAATGAAACAGCCTTTTAGTCAGGTCTTGGAAAAAACGATTTTTCCGGACCTTGGCTTAAAACATAGCTATATCAATGTGCCTAAAACTCAGATGCAAAACTATGCATTTGGCTATAACCAAGAAAATCAGCCAATTCGAGTTAACCCTGGTCCACTCGATGCCCCAGCATACGGCGTCAAATCGACCCTACCCGACATGCTGAGCTTTATTCATGCCAACCTGAACCCACAGAAATATCCGGCAAATATTCAACGTGCAATTAATGAGACACATCAAGGTCGCTATCAAGTAAATAGCATGTATCAGGCACTCGGTTGGGAAGAGTTTGCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAACCTTCAGTTAAGATGTACCACAAAACTGGTTCAACCAATGGTTTCGGAACCTATGTCGTATTTATACCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGCATTCCAAATGAAGAACGCATTAAAGCAGCTTATGCTGTGCTAAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36949","NCBI_taxonomy_name":"Acinetobacter nosocomialis","NCBI_taxonomy_id":"106654"}}}},"ARO_accession":"3008044","ARO_id":"46836","ARO_name":"ADC-334","CARD_short_name":"ADC-334","ARO_description":"Extended-spectrum class C beta-lactamase ADC-334.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7463":{"model_id":"7463","model_name":"ADC-335","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10290":{"protein_sequence":{"accession":"WIU89417.1","sequence":"MRLKKISYLLLPSLVILNTSIYAGNTAKDQQIKQLVDQNFKPLLEKYNVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGAYAKNKGKISFEDKPSKYWKELKNTPIDQVNLLQLATYTNGNLALQFPDEVQTDQQVLTFFKDWKSKNPIGEYRQYSNPSIGLFGKVVSLSMNQPFSQVLEKTIFPDLGLKHSYVNVPKTQMQHYAFGYNQQNQPIRVNPGPLDGPAYGVKSTLPDMLGFVHANLNPQQYPADIQRAINETHQGFYQVGTMYQALGWEEFSYPATLQTLLDSNSDQIVMKPNKVTAISKEPSVKMFHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"OR102460.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGACTTAAAAAAATTTCTTACTTACTTTTACCTTCTCTTGTTATTTTGAATACTTCAATTTATGCAGGTAATACTGCTAAAGACCAACAAATTAAACAACTTGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATAATGTGCCGGGTATGGCGGTAGGCGTTATTCAAAACAATAAAAAATATGAAATGTATTATGGCCTTCAATCTGTTCAAGATAAAAAAGCTGTAAATAGCAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAACTTTTTACTGCTACAGCAGGTGCTTATGCTAAGAATAAGGGAAAAATCTCTTTTGAAGATAAACCAAGTAAATACTGGAAAGAGCTAAAAAACACTCCGATTGATCAGGTCAATTTACTTCAACTTGCTACTTATACCAATGGTAATCTTGCGCTACAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAGTCTAAAAATCCAATTGGTGAATATAGACAATATTCCAACCCAAGTATTGGCCTATTTGGAAAAGTTGTAAGCTTATCGATGAATCAACCTTTTAGTCAGGTTTTAGAAAAAACAATTTTTCCAGACCTTGGCTTAAAACATAGTTATGTCAATGTGCCTAAAACTCAAATGCAACATTATGCTTTTGGCTATAACCAACAAAATCAGCCGATTCGAGTTAACCCTGGCCCCTTAGATGGCCCAGCTTACGGCGTCAAATCGACACTTCCAGACATGTTGGGGTTTGTTCATGCCAACCTGAACCCGCAGCAATATCCAGCTGATATTCAACGTGCAATTAATGAGACACATCAAGGTTTCTATCAAGTAGGTACCATGTATCAGGCGCTTGGTTGGGAAGAGTTTTCTTACCCTGCAACCTTACAAACTTTATTAGACAGTAATTCTGACCAGATTGTGATGAAGCCTAATAAAGTGACTGCTATTTCTAAAGAACCTTCAGTTAAAATGTTTCACAAAACTGGTTCAACCAATGGCTTCGGAACATACGTCGTATTTATTCCTAAAGAGAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAACGAAGAACGCATTAAGGCGGCTTATGCTGTGCTAAATGCGATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"47900","NCBI_taxonomy_name":"Acinetobacter seifertii","NCBI_taxonomy_id":"1530123"}}}},"ARO_accession":"3008045","ARO_id":"46837","ARO_name":"ADC-335","CARD_short_name":"ADC-335","ARO_description":"Extended-spectrum class C beta-lactamase ADC-335.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7464":{"model_id":"7464","model_name":"ADC-336","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10291":{"protein_sequence":{"accession":"WKB14824.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTSIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWQPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVAKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLKFIHANLNPQKYPTDIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTTGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKE"},"dna_sequence":{"accession":"OR232962.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAACACATCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGCAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTGGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTAGCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGCTTAAGTTTATTCATGCCAATCTGAACCCACAGAAATATCCGACAGATATTCAACGTGCAATTAATGAAACACATCAAGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCACCGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAACGCATTAAGGCAGCGTATGCAGTTTTAAATGCAATAAAGGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008046","ARO_id":"46838","ARO_name":"ADC-336","CARD_short_name":"ADC-336","ARO_description":"Extended-spectrum class C beta-lactamase ADC-336.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7465":{"model_id":"7465","model_name":"ADC-337","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10292":{"protein_sequence":{"accession":"WKB14825.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVKTDQQVLTFFKDWKPKNSIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYSVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTTTGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"OR232963.1","fmin":"0","fmax":"1155","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAGTATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAATTTCCAGATGAAGTAAAAACAGATCAGCAAGTTTTAACATTTTTTAAAGACTGGAAACCTAAAAACTCAATCGGTGAATATCGACAATATTCAAACCCAAGCATTGGTTTATTTGGAAAAGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATAGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTAAATCCACAAAAATATCCAGCAGATATTCAACGGGCAATTAATGAAACACATCAGGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACAACTACCGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008047","ARO_id":"46839","ARO_name":"ADC-337","CARD_short_name":"ADC-337","ARO_description":"Extended-spectrum class C beta-lactamase ADC-337.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7466":{"model_id":"7466","model_name":"ADC-338","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10293":{"protein_sequence":{"accession":"WLF01974.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDKPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWQPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVAKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"OR367331.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCGTTATTAGAAAAATATGATGTGCCGGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGACAAGCCTGGTAAATATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAATTTACTTCAACTCGCGACGTATACAAGTGGCAACCTCGCTTTACAATTTCCAGATGAAGTACAAACAGATCAACAAGTTTTAACTTTTTTCAAAGACTGGCAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTGGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTAGCTAAGACCCAGATGCAAAACTATGCATTTGGTTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTTAACCCACAGAAATATCCGGCTGATATTCAAAGGGCAATTAATGAAACACATCAGGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAACCTTCTGTTAAGATGTACCATAAAACTGGCTCAACCAACGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008048","ARO_id":"46840","ARO_name":"ADC-338","CARD_short_name":"ADC-338","ARO_description":"Extended-spectrum class C beta-lactamase ADC-338.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7467":{"model_id":"7467","model_name":"ADC-339","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10294":{"protein_sequence":{"accession":"WLF01975.1","sequence":"MRFKKISCLLLSPLFIFSTSIYADNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGFYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"OR367332.1","fmin":"0","fmax":"1167","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGACAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCATTATTAGAAAAATATGATGTGCCGGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAGCTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTCCCAGATGAAGTACAAACAGATCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTGTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCCCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTTAACCCACAGAAATATCCGGCAGATATTCAACGGGCAATTAATGAAACACATCAAGGGTTCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACATATGTAGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008049","ARO_id":"46841","ARO_name":"ADC-339","CARD_short_name":"ADC-339","ARO_description":"Extended-spectrum class C beta-lactamase ADC-339.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7468":{"model_id":"7468","model_name":"ADC-340","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10295":{"protein_sequence":{"accession":"WLF01976.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNEKYEMYEMYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKIQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIYANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLSAIKK"},"dna_sequence":{"accession":"OR367333.1","fmin":"0","fmax":"1170","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATGAAAAGTATGAAATGTATGAAATGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGATCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCTTATTTGGAAAAGTTGTTGCTTTGTCTATGAATAAACCTTTCGATCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGATCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCCACCTTACCGGATATGTTGAGTTTTATTTATGCCAACCTTAACCCACAGAAATATCCGGCAGATATTCAACGTGCAATTAATGAAACACATCAGGGTCGCTATCAAGTAAATACCATGTATCAAGCGCTTGGTTGGGAAGAGTTTTCTTATCCAGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACGTATGTGGTCTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGTATTAAGGCAGCTTATGCTGTGCTGAGTGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008050","ARO_id":"46842","ARO_name":"ADC-340","CARD_short_name":"ADC-340","ARO_description":"Extended-spectrum class C beta-lactamase ADC-340.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7469":{"model_id":"7469","model_name":"ADC-341","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10296":{"protein_sequence":{"accession":"WLF01977.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFIATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNLGLLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGFYQVNTMYQALGWEEFSYPATLQTLLDSSSEQIVMKPNKVTAISKEPSVKMYHKTGSTTGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"OR367334.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACCCCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCGTTATTAGAAAAATATGATGTGCCGGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTATCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAGCTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTCCCAGATGAAGTACAAACAGATCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTGTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCTCGGCTTACTCGATGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTTAACCCACAGAAATATCCGGCAGATATTCAACGGGCAATTAATGAAACACATCAAGGGTTCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAGTTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTACCGGTTTCGGAACATATGTAGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008051","ARO_id":"46843","ARO_name":"ADC-341","CARD_short_name":"ADC-341","ARO_description":"Extended-spectrum class C beta-lactamase ADC-341.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7470":{"model_id":"7470","model_name":"ADC-342","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10297":{"protein_sequence":{"accession":"WLF01978.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKVLKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGFYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVSAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"OR367335.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACCCCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCATTATTAGAAAAATATGATGTGCCGGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGTGCTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGTCCACTCGATGCCCCAGCATACGGCGTCAAATCCACCTTACCGGATATGTTGAGTTTTATTCATGCCAACCTCAACCCACAGAAATATCCGGCAGATATTCAACGGGCAATTAATGAAACACATCAAGGGTTCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGTCTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACGTATGTGGTGTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008052","ARO_id":"46844","ARO_name":"ADC-342","CARD_short_name":"ADC-342","ARO_description":"Extended-spectrum class C beta-lactamase ADC-342.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7471":{"model_id":"7471","model_name":"ADC-343","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10298":{"protein_sequence":{"accession":"BER91151.1","sequence":"MRFNKISCLLLSPLFIFNTSIYAGNPSKEQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNSIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPDLGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFINANLNPQKYPADIQRAINETHQGFYQVGTMYQALGWEEFSYPAPLQTLLDSNSEQIVMKPNKVTAISKEPSVKMFHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"LC777322.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAACAAGATTTCTTGCTTACTTTTATCTCCTCTTTTTATTTTTAATACATCAATTTATGCGGGCAATCCATCAAAAGAACAAGAAATTAAAAAACTGGTAGATCAGAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCTGTAAATAGCAGTACCATTTTTGAGCTAGGTTCAGTTAGTAAATTATTTACCGCAACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCAACGTATACAAGTGGTAACCTTGCCTTGCAGTTCCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACTCAATCGGTGAATATAGACAATATTCAAATCCAAGCATTGGTTTATTTGGAAAAGTTGTGGCATTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCAGATCTTGGCTTAAAACATAGCTATGTAAATGTTCCTAAAACTCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCAATTCGTGTTAACCCTGGTCCGCTAGATGCTCCAGCATATGGGGTTAAATCGACGCTACCAGATATGCTGAGTTTTATTAATGCCAACCTAAATCCACAAAAATATCCAGCAGATATTCAACGTGCAATTAATGAAACACATCAAGGTTTCTATCAAGTCGGCACCATGTATCAGGCACTTGGTTGGGAAGAATTTTCTTATCCAGCGCCTTTACAAACTTTATTAGACAGTAATTCAGAACAAATTGTGATGAAGCCTAATAAAGTGACTGCCATTTCCAAAGAACCTTCAGTTAAGATGTTCCACAAAACTGGTTCGACCAACGGTTTTGGAACATATGTCGTGTTCATTCCTAAAGAAAATATTGGCTTAGTCATGTTGACCAATAAACGTATTCCGAATGAAGAACGCATTAAAGCAGCGTATGCCGTGTTAAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3008053","ARO_id":"46845","ARO_name":"ADC-343","CARD_short_name":"ADC-343","ARO_description":"Extended-spectrum class C beta-lactamase ADC-343.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7472":{"model_id":"7472","model_name":"ADC-344","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10299":{"protein_sequence":{"accession":"WOW71214.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFRKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFINANLNPQKYPTDIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSSSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"OR754316.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCTCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAGTATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTAGAAAGGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATACGGCGTCAAATCCACCTTACCGGATATGTTGAGTTTTATTAATGCCAACCTTAACCCACAAAAATATCCGACAGATATTCAACGGGCAATTAATGAAACACATCAAGGTCGCTATCAAGTAAATACCATGTATCAAGCGCTTGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAGTTCAGAACAGATTGTGATGAAGCCTAATAAAGTGACTGCTATTTCAAAAGAGCCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACATATGTAGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008054","ARO_id":"46846","ARO_name":"ADC-344","CARD_short_name":"ADC-344","ARO_description":"Extended-spectrum class C beta-lactamase ADC-344.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7473":{"model_id":"7473","model_name":"ADC-345","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10300":{"protein_sequence":{"accession":"WOW71215.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWQPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYSVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPAMLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTTGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"OR754317.1","fmin":"39","fmax":"1191","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCATTATTAGAAAAATATGATGTACCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAGCTAAAAAATACACCGATTGATCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGCAACCTCGCTTTACAATTTCCAGATGAAGTACAAACAGATCAACAAGTTTTAACTTTTTTCAAAGACTGGCAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTGGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATAGCGTCAAATCAACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTAAATCCACAAAAATATCCGGCAGATATTCAACGTGCAATTAATGAAACACATCAGGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAATGTTACAAACTTTACTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCACCGGTTTCGGAACGTATGTGGTGTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCGTATGCAGTTTTAAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008055","ARO_id":"46847","ARO_name":"ADC-345","CARD_short_name":"ADC-345","ARO_description":"Extended-spectrum class C beta-lactamase ADC-345.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7474":{"model_id":"7474","model_name":"ADC-346","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10301":{"protein_sequence":{"accession":"BEV74606.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWQPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLSAIKK"},"dna_sequence":{"accession":"LC794503.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGATCAACAAGTTTTAACTTTTTTCAAAGACTGGCAACCTAAAAACCCAATCGGTGAATATAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATACGGTGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTTAACCCACAGAAATATCCGGCAGATATTCAACGTGCAATTAATGAAACACATCAGGGTCGCTATCAAGTAAATACCATGTATCAAGCGCTTGGTTGGGAAGAGTTTTCTTATCCAGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACGTATGTGGTCTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGTATTAAGGCAGCTTATGCTGTGCTGAGTGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008056","ARO_id":"46848","ARO_name":"ADC-346","CARD_short_name":"ADC-346","ARO_description":"Extended-spectrum class C beta-lactamase ADC-346.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7475":{"model_id":"7475","model_name":"ADC-347","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10302":{"protein_sequence":{"accession":"WVW91698.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGAYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLSAIKK"},"dna_sequence":{"accession":"PP328945.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCATTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGCTTATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAGCTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTAAATCCACAAAAATATCCAGCAGATATTCAACGGGCAATTAATGAAACACATCAGGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCAACGGTTTCGGAACATATGTAGTGTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAGTGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008057","ARO_id":"46849","ARO_name":"ADC-347","CARD_short_name":"ADC-347","ARO_description":"Extended-spectrum class C beta-lactamase ADC-347.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7476":{"model_id":"7476","model_name":"ADC-348","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10303":{"protein_sequence":{"accession":"WVW91699.1","sequence":"MRFKKISCLLLSPLFIFSTSIYADNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTSIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWQPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVAKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLKFIHANLNPQKYPTDIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKE"},"dna_sequence":{"accession":"PP328946.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGACAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAACACATCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTTCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGCAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTGGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTAGCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGCTTAAGTTTATTCATGCCAATCTGAACCCACAGAAATATCCGACAGATATTCAACGTGCAATTAATGAAACACATCAAGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCAACGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAACGCATTAAGGCAGCGTATGCAGTTTTAAATGCAATAAAGGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008058","ARO_id":"46850","ARO_name":"ADC-348","CARD_short_name":"ADC-348","ARO_description":"Extended-spectrum class C beta-lactamase ADC-348.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7477":{"model_id":"7477","model_name":"ADC-349","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10304":{"protein_sequence":{"accession":"WVW91700.1","sequence":"MRFKKISCLLLSPLFIFSTSIYADNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGFYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTTGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"PP328947.1","fmin":"0","fmax":"1167","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGACAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAGCTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTCCCAGATGAAGTACAAACAGATCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTGTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCCCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTTAACCCACAGAAATATCCGGCAGATATTCAACGGGCAATTAATGAAACACATCAAGGGTTCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTACCGGTTTCGGAACATATGTAGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008059","ARO_id":"46851","ARO_name":"ADC-349","CARD_short_name":"ADC-349","ARO_description":"Extended-spectrum class C beta-lactamase ADC-349.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7478":{"model_id":"7478","model_name":"ADC-350","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10305":{"protein_sequence":{"accession":"WVW91701.1","sequence":"MRFKKISYLLLPSLFIFNTSIYAGNTSKDQEIKQLVDQNFKPLLEKYNVPGMAVGVIQNNKKYETYYGLQSVQDKKAVNSNTIFELGSVSKLFTATAGAYAKNTGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGEIVGLSMKQPFSQVLEKTIFPDLGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPANIQRAINETHQGRYQVNSMYQALGWEEFAYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"PP328948.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGTTTTAAAAAAATTTCTTACTTACTTTTACCTTCTCTTTTTATTTTTAATACCTCAATTTATGCGGGCAATACTTCTAAAGACCAAGAAATTAAACAATTGGTAGATCAAAATTTTAAACCCTTATTAGAAAAATATAATGTGCCGGGTATGGCGGTAGGTGTTATTCAAAACAATAAAAAATATGAAACGTATTATGGTCTACAATCCGTTCAAGATAAAAAAGCTGTAAATAGCAATACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACTGCGACGGCAGGTGCTTATGCAAAAAATACAGGAAAAATTTCTTTTGATGATACGCCGGGCAAATACTGGAAAGAGTTAAAAAACACCCCAATTGATCAGGTCAATTTACTTCAACTTGCCACCTATACAAGTGGTAACCTCGCTTTGCAATTCCCAGATGAAGTACAAACAGATCAACAGGTTTTAACTTTTTTTAAAGATTGGAAACCTAAAAACCCAATCGGTGAATATAGACAATATTCAAACCCAAGTATTGGCCTATTTGGGGAAATAGTTGGTTTATCAATGAAGCAGCCTTTTAGTCAGGTCTTGGAAAAAACGATTTTTCCGGACCTTGGCTTAAAACATAGCTATGTCAATGTGCCTAAAACTCAGATGCAAAACTATGCATTTGGTTATAACCAAGAAAATCAGCCAATTCGAGTTAACCCTGGCCCACTCGATGCCCCAGCATACGGCGTCAAATCGACCCTACCCGATATGCTGAGCTTTATTCATGCCAACCTGAATCCACAGAAATATCCGGCAAATATTCAACGTGCAATTAATGAGACACATCAAGGTCGCTATCAAGTAAATAGCATGTATCAGGCACTCGGTTGGGAAGAGTTTGCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAACCTTCAGTTAAGATGTACCACAAAACTGGTTCAACTAATGGTTTCGGAACCTATGTCGTATTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGCATTCCAAATGAAGAACGCATTAAAGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36949","NCBI_taxonomy_name":"Acinetobacter nosocomialis","NCBI_taxonomy_id":"106654"}}}},"ARO_accession":"3008060","ARO_id":"46852","ARO_name":"ADC-350","CARD_short_name":"ADC-350","ARO_description":"Extended-spectrum class C beta-lactamase ADC-350.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7479":{"model_id":"7479","model_name":"ADC-351","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10306":{"protein_sequence":{"accession":"WVW91702.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDREIKKLVDQNFKPLLDKYDVPGMAVGVIQNNKKYETYYGLQSVQDKKSVISSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKEWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPGLGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFINANINPQKYPADIQRAINETHQGFYQVGTMYQALGWEEFSYPAPLQTLLDSNSEQIVMKPNKVTAISKEPSIKMFHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"PP328949.1","fmin":"0","fmax":"1155","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCGAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCTTTATTAGATAAATATGATGTGCCGGGTATGGCCGTGGGCGTTATTCAGAATAATAAAAAATATGAAACGTATTATGGTCTTCAATCTGTTCAAGATAAAAAATCCGTAATAAGTAGCAGTACCATTTTTGAACTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATTTCTTTTGACGATACGCCTGGTAAATATTGGAAAGAACTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCAACGTATACAAGTGGTAACCTTGCCTTGCAGTTCCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGAATGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAAGTTGTTGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGGCCTTGGCTTAAAACATAGCTATGTAAATGTACCGAAGACCCAGATGCAAAACTATGCTTTTGGCTATAATCAAGAAAATCAGCCAATTCGTGTTAACCCCGGTCCGCTAGATGCTCCAGCATACGGTGTTAAATCGACCTTACCTGATATGCTGAGTTTCATTAATGCCAATATAAATCCACAAAAATATCCAGCAGATATTCAACGTGCAATTAATGAAACACATCAAGGTTTCTATCAAGTCGGCACCATGTATCAGGCACTTGGTTGGGAAGAATTTTCTTATCCAGCGCCTTTACAAACTTTATTAGACAGTAATTCAGAACAAATTGTGATGAAGCCTAATAAAGTGACTGCCATTTCCAAAGAACCTTCAATTAAGATGTTCCACAAAACTGGTTCGACTAACGGTTTTGGAACATATGTCGTGTTCATTCCTAAAGAAAATATTGGCTTAGTCATGTTGACCAATAAACGTATTCCGAATGAAGAACGCATTAAAGCAGCTTATGCTGTGTTAAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3008061","ARO_id":"46853","ARO_name":"ADC-351","CARD_short_name":"ADC-351","ARO_description":"Extended-spectrum class C beta-lactamase ADC-351.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7480":{"model_id":"7480","model_name":"ADC-352","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10307":{"protein_sequence":{"accession":"WVW91703.1","sequence":"MRFKKISCLLLSPLFIFSTSIYASNTPKDQEIKKLVDQNFKPLLDKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVSSSTIFELGSVSKLFTATAGGYAKNKGKISFNDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNSIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPDLGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFINANLNPQKYPKDIQRAINETHKGFYQVGTMYQALGWEEFSYPAPLQTLLDSNSEQTVMKPNKVTAISKEPLVKMFHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"PP328950.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGCTTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGAGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCTTTATTAGATAAATATGATGTGCCGGGTATGGCCGTGGGTGTTATTCAGAATAATAAAAAGTATGAAATGTATTATGGTCTACAATCTGTTCAAGATAAAAAAGCCGTAAGTAGCAGTACCATTTTTGAACTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTAATGACACACCTGGAAAATATTGGAAAGAACTAAAAAACACACCGATTGACCAAGTTAACTTACTTCAACTCGCAACGTATACAAGTGGTAACCTTGCCTTGCAGTTCCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACTCAATCGGTGAATATAGACAATATTCAAATCCAAGCATTGGTTTATTTGGAAAAGTTGTGGCATTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCAGATCTTGGCTTAAAACATAGCTATGTAAATGTTCCTAAAACTCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCAATTCGTGTTAACCCTGGTCCGCTAGATGCTCCAGCATATGGGGTTAAATCGACGCTACCAGATATGCTAAGTTTTATTAATGCCAACCTCAACCCACAGAAATATCCGAAAGATATTCAACGTGCAATTAATGAAACACATAAAGGTTTCTATCAAGTCGGCACCATGTATCAAGCATTAGGTTGGGAAGAATTTTCTTATCCAGCGCCTTTACAAACTTTATTAGACAGTAATTCAGAACAAACTGTGATGAAGCCTAATAAAGTGACTGCTATTTCAAAAGAACCTTTAGTTAAGATGTTCCACAAAACTGGCTCAACCAATGGTTTCGGAACATATGTCGTGTTCATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAACGCATTAAAGCAGCGTATGCAGTATTAAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3008062","ARO_id":"46854","ARO_name":"ADC-352","CARD_short_name":"ADC-352","ARO_description":"Extended-spectrum class C beta-lactamase ADC-352.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7481":{"model_id":"7481","model_name":"ADC-353","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10308":{"protein_sequence":{"accession":"WVW91704.1","sequence":"MQFKKISCLLLPPLFIFSSSIYAGNTPKEQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSNTIFELGSVSKLFTATAGGYAKTKGTISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVKTDQQVLTFFKEWKSKNSIGEYRQYSNPSIGLFGKVVALSMNNPFDQVLEKTIFPDLGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFINANLNPQKYPADIQRAINETHKGFYQVGTMYQALGWEEFSYPAPLQTLLDSNSEQIVMKPNKVTAISKEPSVKMFHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"PP328951.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCAATTTAAAAAAATTTCTTGCTTACTTTTACCACCTCTTTTTATTTTTAGTAGCTCAATTTATGCGGGTAATACACCAAAAGAGCAAGAGATCAAAAAACTGGTTGATCAAAATTTTAAGCCTTTATTAGAAAAATATGATGTGCCCGGTATGGCTGTGGGCGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTACAATCCGTTCAAGATAAAAAAGCCGTTAATAGCAATACCATTTTTGAGCTAGGCTCGGTCAGTAAATTATTTACCGCTACAGCAGGCGGATATGCCAAAACGAAAGGAACAATCTCTTTTGATGACACGCCCGGAAAATATTGGAAAGAACTAAAAAATACACCGATAGATCAAGTGAATTTACTTCAACTTGCGACATATACCAGTGGCAACCTTGCCTTGCAATTTCCAGATGAAGTAAAAACAGATCAGCAAGTTTTAACGTTTTTCAAAGAATGGAAATCTAAAAACTCAATCGGTGAATATCGACAATATTCAAACCCAAGCATTGGTTTATTTGGAAAAGTTGTTGCTTTGTCTATGAATAACCCTTTCGACCAAGTCTTGGAAAAAACCATTTTTCCAGATCTTGGCTTAAAACATAGCTATGTAAATGTGCCTAAAACTCAAATGCAAAACTATGCATTTGGCTATAACCAAGAAAATCAGCCGATTCGCGTTAATCCAGGTCCACTCGATGCACCAGCATACGGCGTTAAATCTACCCTACCGGATATGCTGAGTTTTATTAATGCCAACCTAAATCCACAAAAATATCCAGCAGATATTCAACGTGCAATTAATGAAACACATAAAGGTTTCTACCAAGTGGGTACGATGTATCAAGCACTTGGTTGGGAAGAGTTTTCTTATCCAGCACCTTTACAAACTTTATTAGACAGTAATTCAGAACAAATCGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAACCTTCCGTTAAGATGTTCCACAAAACTGGATCGACTAACGGTTTTGGAACATATGTCGTGTTCATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACTAATAAACGTATTCCCAATGAAGAACGCATTAAAGCAGCTTATGCTGTGTTAAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36837","NCBI_taxonomy_name":"Acinetobacter sp.","NCBI_taxonomy_id":"472"}}}},"ARO_accession":"3008063","ARO_id":"46855","ARO_name":"ADC-353","CARD_short_name":"ADC-353","ARO_description":"Extended-spectrum class C beta-lactamase ADC-353.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7482":{"model_id":"7482","model_name":"ADC-354","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10309":{"protein_sequence":{"accession":"XGB73521.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFEDKPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWQPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLSPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLSAIKK"},"dna_sequence":{"accession":"PQ203893.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGAAGATAAGCCTGGTAAATATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAATTTACTTCAACTCGCGACGTATACAAGTGGCAACCTCGCTTTACAATTTCCAGATGAAGTACAAACAGATCAACAAGTTTTAACTTTTTTCAAAGACTGGCAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAGGTTGTGGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCATTTGGTTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTTAGCCCACAGAAATATCCGGCTGATATTCAAAGGGCAATTAATGAAACACATCAAGGTCGCTATCAAGTAAATACCATGTATCAAGCGCTTGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACCAACGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAGTGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008064","ARO_id":"46856","ARO_name":"ADC-354","CARD_short_name":"ADC-354","ARO_description":"Extended-spectrum class C beta-lactamase ADC-354.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7483":{"model_id":"7483","model_name":"ADC-355","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10310":{"protein_sequence":{"accession":"XGB73522.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVKTDQQVLTFFKDWKPKNSIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYSVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTFLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTTGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"PQ203894.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAGTATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAATTTCCAGATGAAGTAAAAACAGATCAGCAAGTTTTAACATTTTTTAAAGACTGGAAACCTAAAAACTCAATCGGTGAATATCGACAATATTCAAACCCAAGCATTGGTTTATTTGGAAAAGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATAGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTAAATCCACAAAAATATCCAGCAGATATTCAACGGGCAATTAATGAAACACATCAGGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGATGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTCTTAGACAGTAATTCAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTACCGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008065","ARO_id":"46857","ARO_name":"ADC-355","CARD_short_name":"ADC-355","ARO_description":"Extended-spectrum class C beta-lactamase ADC-355.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7484":{"model_id":"7484","model_name":"ADC-356","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10311":{"protein_sequence":{"accession":"XGB73523.1","sequence":"MRFKKISCLLLSPLFIFSTSIYADNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTTGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLKFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPTPLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"PQ203895.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCTCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGACAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTAGGTTCTGTTAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGACTGGTAAATATTGGAAAGAGCTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAGTTCCCAGATGAAGTACAAACAGACCAACAAGTTTTAACTTTTTTCAAAGACTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCTTATTTGGAAAAGTTGTTGCTTTGTCTATGAATAAACCTTTCGATCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACTCAAATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATACGGCGTCAAATCGACACTACCCGACATGCTTAAGTTTATTCATGCCAATCTGAACCCACAGAAATATCCGGCAGATATTCAACGGGCAATTAATGAAACACATCAAGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGACACCTTTACAAACTTTATTAGACAGTAATTCAGAACAAATTGTGATGAAGCCTAATAAAGTGACTGCTATTTCAAAAGAGCCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTAACGGTTTCGGAACATATGTAGTGTTTATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008066","ARO_id":"46858","ARO_name":"ADC-356","CARD_short_name":"ADC-356","ARO_description":"Extended-spectrum class C beta-lactamase ADC-356.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7485":{"model_id":"7485","model_name":"ADC-357","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10312":{"protein_sequence":{"accession":"XGB73524.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEIYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKTKGTISFKDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGKVVALSMNKPFNQVLEKTIFPGLSLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLKFINANLNPQKYPADIQRAINETHQGFYQVGTMHQALGWEEFSYPAPLQTLLDSNSEQIVMKPNKVTAISKEPSVKMFHKTGSTNGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"PQ203896.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAATTTTAAACCGTTATTAGAAAAATATGATGTGCCGGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATTTATTATGGTCTACAATCCGTTCAAGATAAAAAAGCCGTAAATAGCAGTACCATTTTTGAGCTCGGTTCAGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAACAAAAGGAACAATCTCTTTTAAAGACACACCCGGAAAATATTGGAAAGAGCTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTTGCTACCTATACAAGTGGCAACCTTGCTTTGCAATTTCCAGATGAAGTACAAACAGATCAACAAGTTTTAACTTTTTTCAAAGATTGGAAACCTAAAAACCCAATCGGTGAATACAGACAATATTCAAATCCAAGTATTGGCCTATTTGGAAAAGTTGTTGCTTTGTCTATGAATAAACCTTTCAACCAAGTCTTAGAAAAAACAATTTTTCCGGGCCTTAGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAATCAAGAAAATCAGCCAATTCGTGTTAACCCTGGTCCGCTAGATGCTCCAGCATACGGCGTTAAATCGACACTACCAGACATGCTTAAGTTTATTAATGCCAACCTAAATCCACAAAAATATCCAGCAGATATTCAACGTGCAATTAATGAAACACATCAAGGTTTCTATCAAGTCGGCACCATGCATCAAGCACTTGGTTGGGAAGAATTTTCTTATCCAGCGCCTTTACAAACTTTATTAGACAGTAATTCAGAACAAATTGTGATGAAGCCTAATAAAGTGACTGCCATTTCCAAAGAACCTTCAGTTAAGATGTTCCACAAAACTGGTTCGACCAACGGTTTTGGAACATATGTCGTGTTCATTCCTAAAGAAAATATTGGCTTAGTCATGTTAACTAATAAACGTATTCCGAATGAAGAACGCATTAAAGCAGCTTATGCCGTGTTAAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3008067","ARO_id":"46859","ARO_name":"ADC-357","CARD_short_name":"ADC-357","ARO_description":"Extended-spectrum class C beta-lactamase ADC-357.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7486":{"model_id":"7486","model_name":"ADC-358","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10313":{"protein_sequence":{"accession":"XGB73525.1","sequence":"MRFKKISYLLLPSLFIFNTSIYAGNTSKDQEIKQLVDQNFKPLLEKYNVPGMAVGIIQNNKKYEAYYGLQSVQDKKAVNSNTIFELGSVSKLFTATAGAYAKNTGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVQTDQQVLTFFKDWKPKNPIGEYRQYSNPSIGLFGEIVGLSMKQPFSQVLEKTIFPNLGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPANIQRAINETHQGRYQVNSMYQALGWEEFAYPATLQTLLDSNSEQVVMKPNKVTAISKEPSVKMYHKTGSTNGFGTYVLFIPKDNIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"PQ203897.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTACTTACTTTTACCTTCTCTTTTTATTTTTAATACCTCAATTTATGCGGGCAATACTTCTAAAGACCAAGAAATTAAACAATTGGTAGATCAAAATTTTAAACCCTTATTAGAAAAATATAATGTACCGGGTATGGCGGTAGGTATTATTCAAAACAATAAAAAATATGAAGCGTATTATGGTCTACAATCCGTTCAAGATAAAAAAGCTGTAAATAGCAATACCATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACTGCGACGGCAGGTGCTTATGCAAAAAATACAGGAAAAATCTCTTTTGATGATACACCGGGCAAATACTGGAAAGAGTTAAAAAACACTCCAATTGATCAGGTCAATTTACTTCAACTTGCCACCTATACAAGTGGTAACCTCGCTTTGCAATTCCCAGATGAAGTACAAACAGATCAACAGGTTTTAACTTTTTTTAAAGATTGGAAACCTAAAAACCCAATCGGTGAATATAGACAATATTCAAACCCAAGTATTGGCCTATTTGGGGAAATAGTTGGTTTATCAATGAAGCAGCCTTTTAGTCAGGTCTTGGAAAAAACGATTTTTCCGAACCTTGGCTTAAAACATAGCTATGTCAATGTGCCTAAAACTCAGATGCAAAACTATGCATTTGGCTATAACCAAGAAAATCAGCCAATTCGAGTTAACCCTGGCCCACTCGATGCCCCAGCATACGGCGTCAAATCGACCCTACCCGACATGCTGAGCTTTATTCATGCCAACCTGAACCCACAGAAATATCCGGCAAATATTCAACGTGCAATTAATGAGACACATCAAGGTCGCTATCAAGTAAATAGCATGTATCAGGCACTCGGTTGGGAAGAGTTTGCTTATCCGGCAACGTTACAAACTTTATTAGACAGTAATTCAGAACAGGTTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAAGAACCTTCAGTTAAGATGTACCACAAAACTGGTTCAACAAATGGTTTCGGAACCTATGTCTTATTTATTCCTAAAGACAATATTGGTTTAGTCATGTTAACCAATAAACGCATTCCAAATGAAGAACGCATTAAGGCAGCTTATGCTGTGCTAAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36949","NCBI_taxonomy_name":"Acinetobacter nosocomialis","NCBI_taxonomy_id":"106654"}}}},"ARO_accession":"3008068","ARO_id":"46860","ARO_name":"ADC-358","CARD_short_name":"ADC-358","ARO_description":"Extended-spectrum class C beta-lactamase ADC-358.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7487":{"model_id":"7487","model_name":"ADC-359","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10314":{"protein_sequence":{"accession":"XHE66941.1","sequence":"MRFKKISCLLLSPLFIFSTSIYAGNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVKTDQQVLTFFKDWKPKNSIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSTEQIVMKPNKVTAISKEPSVKMYHKTGSTTGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK"},"dna_sequence":{"accession":"PQ323407.1","fmin":"0","fmax":"1149","strand":"+","sequence":"ATGCGATTTAAAAAAATTTCTTGTCTACTTTTATCCCCGCTTTTTATTTTTAGTACCTCAATTTATGCGGGCAATACACCAAAAGACCAAGAAATTAAAAAACTGGTAGATCAAAACTTTAAACCGTTATTAGAAAAATATGATGTGCCAGGTATGGCTGTGGGTGTTATTCAAAATAATAAAAAGTATGAAATGTATTATGGTCTTCAATCTGTTCAAGATAAAAAAGCCGTAAATAGCAGTACTATTTTTGAGCTAGGTTCTGTCAGTAAATTATTTACCGCGACAGCAGGTGGATATGCAAAAAATAAAGGAAAAATCTCTTTTGACGATACGCCTGGTAAGTATTGGAAAGAACTAAAAAATACACCGATTGACCAAGTTAACTTACTTCAACTCGCGACGTATACAAGTGGTAACCTTGCCTTGCAATTTCCAGATGAAGTAAAAACAGATCAGCAAGTTTTAACATTTTTTAAAGACTGGAAACCTAAAAACTCAATCGGTGAATATCGACAATATTCAAACCCAAGCATTGGTTTATTTGGAAAAGTTGTAGCTTTGTCTATGAATAAACCTTTCGACCAAGTCTTAGAAAAAACAATTTTTCCGGCCCTTGGCTTAAAACATAGCTATGTAAATGTACCTAAGACCCAGATGCAAAACTATGCTTTTGGCTATAACCAAGAAAATCAGCCGATTCGAGTTAACCCCGGCCCACTCGATGCCCCAGCATATGGCGTCAAATCGACACTACCCGACATGTTGAGTTTTATTCATGCCAACCTAAATCCACAAAAATATCCAGCAGATATTCAACGGGCAATTAATGAAACACATCAGGGTCGCTATCAAGTAAATACCATGTATCAGGCACTCGGTTGGGAAGAGTTTTCTTATCCGGCAACGTTACAAACTTTATTAGACAGTACAGAACAGATTGTGATGAAACCTAATAAAGTGACTGCTATTTCAAAGGAACCTTCAGTTAAGATGTACCATAAAACTGGCTCAACTACCGGTTTCGGAACATATGTGGTGTTTATTCCTAAAGAAAATATTGGTTTAGTCATGTTAACCAATAAACGTATTCCAAATGAAGAGCGCATTAAGGCAGCTTATGCTGTGCTGAATGCAATAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008069","ARO_id":"46861","ARO_name":"ADC-359","CARD_short_name":"ADC-359","ARO_description":"Class C beta-lactamase ADC-359.","ARO_category":{"43920":{"category_aro_accession":"3005460","category_aro_cvterm_id":"43920","category_aro_name":"ADC beta-lactamases pending classification for carbapenemase activity","category_aro_description":"ADC beta-lactamases with undetermined carbapenemase activity.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7488":{"model_id":"7488","model_name":"AFM-3","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10315":{"protein_sequence":{"accession":"QTH36338.1","sequence":"MITKSNIARIGLSLALAMALPGCIPGEIRPSIGEQVDKGDQRFGDLVFRQLAPNVWQHTSFMDVPGFGAVSSNGLIVKDGERVLLVDTAWTDDQTSQILNWIKQEINLPVALAVVTHAHQDKMGGMGALHAEAIPTYANALSNQLAPQEGMTAAQHSLTFAANGWVDPATAPNFGPLRVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTERYAASARAFGAAFPKANTIAMSHSAPDSRAAITHTARMADKLR"},"dna_sequence":{"accession":"MW811438.1","fmin":"0","fmax":"804","strand":"+","sequence":"ATGATTACGAAATCGAACATCGCGCGGATTGGCTTGTCGCTGGCTTTGGCCATGGCGCTGCCCGGCTGCATCCCCGGCGAGATCCGCCCGTCGATTGGTGAGCAGGTGGATAAGGGTGACCAGCGCTTCGGCGATCTGGTGTTCCGCCAGCTGGCGCCCAATGTGTGGCAACATACCTCGTTCATGGATGTGCCGGGCTTTGGCGCGGTTTCTTCCAACGGGCTGATCGTCAAGGATGGCGAACGGGTGCTGTTGGTCGATACCGCCTGGACCGATGATCAGACCAGCCAGATCCTCAACTGGATTAAGCAAGAGATCAATCTGCCGGTGGCGCTGGCGGTGGTCACCCACGCGCATCAGGACAAGATGGGCGGGATGGGCGCGCTGCACGCGGAGGCAATCCCCACTTACGCCAATGCCTTGTCGAACCAGCTTGCCCCGCAAGAGGGGATGACGGCGGCGCAGCACAGCCTGACCTTCGCCGCCAACGGCTGGGTCGACCCGGCGACCGCGCCCAATTTCGGGCCGCTCAGGGTGTTCTATCCCGGCCCCGGCCACACCAGTGACAATATCACCGTCGGGATCGATGGCACCGACATCGCCTTTGGCGGCTGCCTGATCAAAGACAGCAAGGCCAAGTCGCTCGGCAATCTCGGCGATGCCGACACCGAACGCTATGCCGCCTCGGCGCGCGCATTTGGTGCGGCTTTTCCGAAGGCGAACACGATTGCGATGAGCCATTCCGCGCCTGACAGCCGCGCCGCGATCACCCACACCGCGCGGATGGCCGACAAGCTGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008070","ARO_id":"46862","ARO_name":"AFM-3","CARD_short_name":"AFM-3","ARO_description":"Subclass B1 metallo-beta-lactamase AFM-3.","ARO_category":{"43848":{"category_aro_accession":"3005388","category_aro_cvterm_id":"43848","category_aro_name":"AFM beta-lactamase","category_aro_description":"AFM beta-lactamases are class B1 beta-lactamases found in proteobacteria like Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7489":{"model_id":"7489","model_name":"AFM-4","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10316":{"protein_sequence":{"accession":"UIC51886.1","sequence":"MITKSNIARIGLLLALAMALPGCIPGEIRPSIGEQVDKGDQRFGDLVFRQLAPNVWQHTSFMDVPGFGAVSSNGLIVKDGERVLLVDTAWTDDQTSQILNWIKQEINLPVALAVVTHAHQDKMGGMGALHAEAIPTYANALSNQLAPQEGMTAAQHSLTFAANGWVDPATAPNFGPLRVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTERYAASARAFGAAFPKANTIAMSHSAPDSRAAITHTARMADKLR"},"dna_sequence":{"accession":"OM049002.1","fmin":"0","fmax":"804","strand":"+","sequence":"ATGATTACGAAATCGAACATCGCGCGGATTGGCTTGCTGCTGGCTTTGGCCATGGCGCTGCCCGGCTGCATCCCCGGCGAGATCCGCCCGTCGATTGGTGAGCAGGTGGATAAGGGTGACCAGCGCTTCGGCGATCTGGTGTTCCGCCAGCTGGCGCCCAATGTGTGGCAACATACCTCGTTCATGGATGTGCCGGGCTTTGGCGCGGTTTCTTCCAACGGGCTGATCGTCAAGGATGGCGAACGGGTGCTGTTGGTCGATACCGCCTGGACCGATGATCAGACCAGCCAGATCCTCAACTGGATTAAGCAAGAGATCAATCTGCCGGTGGCGCTGGCGGTGGTCACCCACGCGCATCAGGACAAGATGGGCGGGATGGGCGCGCTGCACGCGGAGGCAATCCCCACTTACGCCAATGCCTTGTCGAACCAGCTTGCCCCGCAAGAGGGGATGACGGCGGCGCAGCACAGCCTGACCTTCGCCGCCAACGGCTGGGTCGACCCGGCGACCGCGCCCAATTTCGGGCCGCTCAGGGTGTTCTATCCCGGCCCCGGCCACACCAGTGACAATATCACCGTCGGGATCGATGGCACCGACATCGCCTTTGGCGGCTGCCTGATCAAAGACAGCAAGGCCAAGTCGCTCGGCAATCTCGGCGATGCCGACACCGAACGCTATGCCGCCTCGGCGCGCGCATTTGGTGCGGCTTTTCCGAAGGCGAACACGATTGCGATGAGCCATTCCGCGCCTGACAGCCGCGCCGCGATCACCCACACCGCGCGGATGGCCGACAAGCTGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008071","ARO_id":"46863","ARO_name":"AFM-4","CARD_short_name":"AFM-4","ARO_description":"Subclass B1 metallo-beta-lactamase AFM-4.","ARO_category":{"43848":{"category_aro_accession":"3005388","category_aro_cvterm_id":"43848","category_aro_name":"AFM beta-lactamase","category_aro_description":"AFM beta-lactamases are class B1 beta-lactamases found in proteobacteria like Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7490":{"model_id":"7490","model_name":"AFM-5","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10317":{"protein_sequence":{"accession":"BFO05841.1","sequence":"MIVNQNLVRMGLPLVLAIALPGCIPGEIRPSIGEQVDKGDQRFGDLVFRQLAPNVWQHTSFMDVPGFGAVSSNGLIVKDGERVLLVDTAWTDDQTSQILNWIKQEVNLPVALAVVTHAHQDKMGGMGALHAAAIPTYANALSNQLAPQEGMTAAQHSLTFAANGWVDPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTERYAASARAFGAAFPKASMIVMSHSAPEGRAAITHTARMADQLR"},"dna_sequence":{"accession":"AP035765.1","fmin":"4610545","fmax":"4611349","strand":"-","sequence":"ATGATTGTGAATCAGAATTTGGTGCGGATGGGCTTGCCGCTGGTGTTGGCGATTGCGCTTCCGGGTTGCATCCCCGGTGAAATCCGCCCGTCGATTGGTGAGCAGGTGGATAAGGGTGACCAGCGATTTGGCGATCTGGTGTTCCGCCAACTCGCGCCCAATGTGTGGCAACATACCTCGTTCATGGATGTACCGGGCTTTGGCGCGGTTTCTTCCAACGGGCTGATCGTCAAGGACGGCGAGCGGGTGCTGCTGGTCGATACCGCTTGGACCGATGACCAGACCAGTCAGATCCTCAACTGGATCAAGCAGGAGGTCAATCTGCCGGTGGCGCTGGCGGTGGTGACCCATGCGCATCAGGACAAGATGGGCGGGATGGGCGCGTTGCACGCGGCGGCGATCCCGACTTATGCCAATGCGCTGTCGAACCAGCTCGCGCCGCAAGAGGGGATGACGGCGGCGCAGCATAGCCTAACCTTCGCCGCCAACGGCTGGGTCGACCCGGCGACCGCGCCCAACTTTGGCCCGCTCAAGGTATTTTACCCCGGCCCGGGCCACACCAGCGACAATATCACCGTCGGGATCGATGGCACCGACATCGCCTTTGGTGGCTGCCTGATTAAAGACAGCAAGGCCAAGTCGCTCGGCAATCTCGGCGATGCGGATACCGAACGCTATGCCGCCTCGGCGCGCGCATTTGGCGCAGCTTTCCCCAAGGCCAGCATGATCGTGATGAGCCATTCCGCGCCAGAGGGACGTGCCGCGATCACCCACACCGCGCGGATGGCCGACCAGCTGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"47923","NCBI_taxonomy_name":"Pseudomonas guariconensis","NCBI_taxonomy_id":"1288410"}}}},"ARO_accession":"3008072","ARO_id":"46864","ARO_name":"AFM-5","CARD_short_name":"AFM-5","ARO_description":"Subclass B1 metallo-beta-lactamase AFM-5.","ARO_category":{"43848":{"category_aro_accession":"3005388","category_aro_cvterm_id":"43848","category_aro_name":"AFM beta-lactamase","category_aro_description":"AFM beta-lactamases are class B1 beta-lactamases found in proteobacteria like Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7491":{"model_id":"7491","model_name":"AIM-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10318":{"protein_sequence":{"accession":"UBK05373.1","sequence":"MKRRFTLLGSVVALALSSTALASDAPASRGCADDAGWNDPAMPLKVYGNTWYVGTCGISALLVTSDAGHILVDAATPQAGPQILANIRALGFRPEDVRAIVFSHEHFDHAGSLAELQKATGAPVYARAPAVDTLKRGLPDRTDPQFEVAEPVAPVANIVTLADDGVVSVGPLALTAVASPGPTPGGTSWTWRSCEGDDCRQMVYADSLTAISDDVFRYSDDAAHPGYLAAFRNTLARVAALDCDILVTPHPSASGLWNRIGPRAAAPLMDTTACRRYAQGARQRLEKRLAEEAATSPSSGARP"},"dna_sequence":{"accession":"OK067203.1","fmin":"245","fmax":"1157","strand":"+","sequence":"ATGAAACGTCGCTTCACCCTGCTGGGCAGCGTAGTCGCCCTCGCCCTCTCATCCACAGCCCTCGCCTCCGATGCGCCCGCCTCCAGGGGCTGCGCCGACGATGCCGGCTGGAACGATCCGGCAATGCCCCTGAAGGTGTACGGAAACACCTGGTACGTTGGCACCTGCGGCATCAGTGCGCTGCTGGTCACTTCCGACGCGGGCCATATCCTGGTCGATGCCGCCACGCCGCAGGCGGGCCCGCAGATCCTGGCCAACATCCGCGCACTCGGTTTCAGGCCGGAGGACGTACGGGCCATCGTGTTCTCGCACGAGCATTTCGACCATGCCGGCAGCCTCGCAGAACTGCAGAAGGCCACGGGCGCACCGGTGTATGCGCGCGCGCCCGCGGTCGACACGTTGAAGCGCGGCCTGCCGGACCGCACCGACCCGCAATTCGAGGTGGCCGAACCCGTCGCGCCGGTCGCCAACATCGTCACCCTGGCCGACGACGGCGTGGTGAGCGTCGGCCCGCTGGCCCTGACGGCGGTCGCCTCGCCTGGCCCCACCCCGGGTGGCACCAGTTGGACCTGGCGCTCCTGCGAAGGCGACGACTGTCGCCAGATGGTCTACGCCGACAGCCTGACGGCGATCTCGGACGACGTCTTCCGCTACAGCGACGACGCCGCGCATCCCGGCTACCTGGCGGCATTCCGCAACACCCTCGCACGGGTCGCAGCGCTCGACTGCGACATCCTGGTCACCCCGCACCCCTCGGCCAGCGGCCTGTGGAACCGGATCGGCCCGAGGGCCGCCGCACCGCTGATGGACACCACCGCCTGCCGCCGCTACGCGCAGGGCGCGAGGCAGCGGCTGGAGAAGCGCCTGGCCGAGGAAGCCGCCACCTCCCCCTCCAGCGGCGCGCGGCCGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36791","NCBI_taxonomy_name":"uncultured bacterium","NCBI_taxonomy_id":"77133"}}}},"ARO_accession":"3008073","ARO_id":"46865","ARO_name":"AIM-2","CARD_short_name":"AIM-2","ARO_description":"Subclass B3 metallo-beta-lactamase AIM-2.","ARO_category":{"41380":{"category_aro_accession":"3004216","category_aro_cvterm_id":"41380","category_aro_name":"AIM beta-lactamase","category_aro_description":"A subclass B3 family of beta-lactamases that confer resistance to a range of beta-lactam antibiotics including penams, cephamycins, and cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7492":{"model_id":"7492","model_name":"ASU1-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10319":{"protein_sequence":{"accession":"QWJ89340.1","sequence":"MKKVILLTALFITACGGDVATTSNNSTAVATPEPYVEQTPGPRQSADAELERQFAEIAKEVEGKVGVAAVVLETGQNAAFNGDERFAMQSVYKVPISMAVMKQIDAGKYQPNQEIEIKKEDFVAAGQRSPLRDSFPNGTKVPLWHLIEYAVSQSDGTASDVLLRLAGGPAEVQKYITEIGITDMAVKNTEKELGTDVKIQYDNYSTPNAAVKLLAELKSGVSIDRERSKLIRDFMNESPTGPNRLRGLLPEAAYVAHKTGTSGTRNGVTAATNDIGIINLPNGKFLLIAVFVGDSPADEKARDAVIAKMAKAAWDKWGA"},"dna_sequence":{"accession":"MZ126682.1","fmin":"0","fmax":"960","strand":"+","sequence":"ATGAAAAAAGTCATCCTTTTAACAGCATTGTTCATTACAGCGTGCGGCGGCGATGTCGCGACGACCAGTAATAATTCGACTGCCGTTGCCACACCGGAGCCCTATGTTGAGCAGACGCCGGGTCCGCGACAATCTGCTGACGCCGAGCTTGAACGGCAGTTTGCCGAGATCGCAAAAGAGGTCGAGGGCAAGGTCGGCGTGGCGGCCGTCGTACTGGAAACGGGACAGAACGCGGCTTTTAATGGCGATGAGCGTTTCGCGATGCAAAGCGTTTACAAGGTACCCATCTCGATGGCCGTGATGAAACAGATCGACGCGGGCAAATATCAGCCGAACCAGGAGATCGAGATCAAGAAGGAAGATTTTGTCGCGGCGGGACAGCGGTCGCCCCTGCGGGACAGTTTTCCGAACGGGACAAAGGTACCGCTCTGGCATCTGATCGAATATGCGGTCTCGCAAAGCGACGGAACGGCCAGCGACGTGCTGCTGCGATTGGCCGGCGGGCCCGCGGAAGTCCAGAAATATATCACCGAGATCGGCATTACAGATATGGCGGTCAAGAACACCGAGAAGGAACTCGGGACGGACGTAAAGATCCAGTATGACAATTACTCGACGCCGAATGCGGCCGTTAAGCTGCTGGCAGAATTGAAAAGCGGCGTCTCGATCGACCGTGAACGGTCAAAGCTGATCCGCGATTTTATGAACGAATCGCCGACCGGCCCAAACCGGCTGCGCGGTCTGCTGCCCGAGGCGGCGTATGTTGCACACAAGACCGGAACTTCCGGCACCCGAAATGGTGTAACGGCCGCGACCAACGACATCGGCATAATAAATCTGCCGAACGGAAAGTTTCTGCTGATCGCTGTTTTTGTCGGAGACTCGCCGGCTGACGAAAAGGCCCGCGACGCCGTGATAGCCAAAATGGCAAAAGCGGCGTGGGACAAGTGGGGCGCTTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36791","NCBI_taxonomy_name":"uncultured bacterium","NCBI_taxonomy_id":"77133"}}}},"ARO_accession":"3008074","ARO_id":"46866","ARO_name":"ASU1-1","CARD_short_name":"ASU1-1","ARO_description":"Class A beta-lactamase ASU1-1.","ARO_category":{"46654":{"category_aro_accession":"3007863","category_aro_cvterm_id":"46654","category_aro_name":"ASU1 beta-lactamase","category_aro_description":"ASU1 is a family of class A beta-lactamase enzymes shown to confer resistance to beta-lactam and cephalosporin antibiotics through enzymatic inactivation.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7493":{"model_id":"7493","model_name":"AXC-6","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10320":{"protein_sequence":{"accession":"QUR41148.1","sequence":"MLTRRTFIALAVLAGGMPALARATTDKKTRWTRDSLATFQQALAKLEAASRGRLGVALLDVGSGQAAGYRADERFLMLSSFKTLSAAYVLARADRGEDQLSRRIPITDADVQEYSPVTRLHVGPRGMTLAELCEATITTSDNAAVNLMHKSYGGPQALTRYLRGLGDTVTRHDRYEPELNRPHPSEPQDTTTPQAMARTLDTLLFGDALKPQSRQQLQSWLLANTTGGKRLRAGMPADWKIGEKTGTYSKVGCNDAGFAQPPGAAPIIIAAYLETTAVPMEERDRCIAEVGRLVAALG"},"dna_sequence":{"accession":"MZ025964.1","fmin":"0","fmax":"897","strand":"+","sequence":"TTGCTGACAAGAAGAACCTTCATCGCCTTGGCCGTGCTGGCCGGCGGGATGCCCGCCCTGGCGCGCGCCACGACGGATAAGAAAACTCGATGGACGCGCGACAGTCTCGCGACATTCCAACAGGCCCTGGCCAAGCTGGAGGCGGCCAGCCGTGGCCGGCTGGGCGTGGCCCTGCTCGACGTGGGCAGCGGGCAGGCCGCCGGCTATCGCGCCGACGAACGTTTCCTGATGCTCAGTTCCTTCAAGACGCTGTCAGCGGCCTATGTGCTGGCGCGGGCCGACCGTGGCGAGGATCAGCTGTCGCGCCGCATCCCGATCACCGATGCCGATGTGCAGGAGTATTCGCCGGTCACGCGGCTGCATGTCGGGCCGCGAGGAATGACCTTGGCCGAACTCTGTGAAGCGACGATCACCACCAGCGACAACGCGGCGGTCAACCTCATGCACAAGAGCTATGGCGGCCCGCAGGCCCTGACCCGCTACCTGCGCGGCCTGGGCGATACCGTCACGCGTCATGATCGTTATGAACCCGAACTGAACCGCCCGCATCCGAGCGAGCCGCAAGACACCACCACTCCGCAGGCCATGGCGCGCACGCTGGACACGCTGTTGTTCGGCGACGCGCTCAAGCCGCAATCGCGGCAGCAACTGCAATCCTGGCTGCTGGCCAACACGACGGGTGGCAAGCGCCTGCGCGCCGGCATGCCGGCGGATTGGAAAATCGGCGAGAAGACCGGCACCTATTCGAAGGTGGGCTGCAACGACGCCGGCTTTGCGCAGCCGCCGGGCGCGGCGCCGATCATCATCGCGGCCTATCTGGAAACCACCGCGGTGCCGATGGAGGAGCGCGACCGCTGCATCGCCGAAGTCGGCAGGCTGGTGGCGGCATTGGGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39091","NCBI_taxonomy_name":"Achromobacter ruhlandii","NCBI_taxonomy_id":"72557"}}}},"ARO_accession":"3008075","ARO_id":"46867","ARO_name":"AXC-6","CARD_short_name":"AXC-6","ARO_description":"Carbapenem-hydrolyzing class A beta-lactamase AXC-6.","ARO_category":{"43853":{"category_aro_accession":"3005393","category_aro_cvterm_id":"43853","category_aro_name":"AXC beta-lactamase","category_aro_description":"AXC beta-lactamases are class A beta-lactamase found in the Anaeromyxobacter genus.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7494":{"model_id":"7494","model_name":"AXC-7","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10321":{"protein_sequence":{"accession":"UGN25768.1","sequence":"MLTRRTFIASAVLAGWIPALAHARTDKKTRWTRESLVAFQQGLAQVEAASRGRLGVALLDVGSGQAAGYRADERFLMLSSFKTLSAAYVLARADRGEDQLSRRIPITDADVREYSPVTRLHVGPRGMTLAELCEATITTSDNAAVNLMHKSYGGPQALTRYLRSLGDTVTRHDRYEPELNRPHPSEPQDTTTPQAMARTLDTLLFGDALKPQSRQQLQSWLLANTTGGKRLRAGMPADWKIGEKTGTYSKVGCNDAGFAQPPGAAPIIIAAYLETTAVPMEERDRCIAEVGRLVAALG"},"dna_sequence":{"accession":"OL516042.1","fmin":"0","fmax":"897","strand":"+","sequence":"TTGCTGACCCGAAGAACCTTCATTGCCTCGGCCGTGCTGGCCGGTTGGATTCCTGCCCTTGCACACGCCCGCACGGATAAGAAAACTCGATGGACGCGCGAAAGTCTCGTGGCGTTCCAACAAGGCCTTGCCCAAGTGGAGGCCGCCAGCCGCGGACGGCTGGGAGTGGCCCTGCTGGACGTGGGCAGTGGGCAAGCCGCCGGCTATCGCGCCGACGAACGCTTCCTGATGCTCAGCTCCTTCAAGACGCTGTCCGCGGCCTACGTGCTGGCGCGGGCCGACCGTGGCGAGGACCAGCTGTCGCGCCGCATCCCGATCACCGACGCCGATGTCCGGGAGTATTCGCCGGTCACGCGGCTGCATGTCGGGCCGCGGGGAATGACGCTGGCCGAACTCTGTGAAGCGACGATCACCACCAGCGACAACGCGGCGGTCAACCTCATGCACAAGAGCTATGGCGGCCCGCAAGCCCTGACCCGCTACCTGCGCAGCCTGGGCGATACCGTCACGCGCCACGATCGCTACGAACCCGAATTGAACCGCCCGCACCCGAGCGAACCGCAGGACACCACCACCCCGCAGGCCATGGCGCGCACGCTGGATACGCTACTGTTCGGCGACGCGCTCAAGCCGCAATCGCGGCAGCAACTGCAATCCTGGCTGCTGGCCAACACGACGGGCGGCAAGCGCCTGCGCGCCGGCATGCCGGCGGATTGGAAGATCGGCGAGAAGACAGGCACCTATTCGAAGGTGGGCTGCAACGACGCCGGCTTCGCGCAACCGCCCGGCGCGGCGCCGATCATCATCGCGGCCTATCTGGAAACCACCGCGGTGCCGATGGAGGAGCGCGACCGCTGCATCGCCGAGGTCGGCAGGCTGGTGGCGGCATTGGGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36941","NCBI_taxonomy_name":"Achromobacter xylosoxidans","NCBI_taxonomy_id":"85698"}}}},"ARO_accession":"3008076","ARO_id":"46868","ARO_name":"AXC-7","CARD_short_name":"AXC-7","ARO_description":"Carbapenem-hydrolyzing class A beta-lactamase AXC-7.","ARO_category":{"43853":{"category_aro_accession":"3005393","category_aro_cvterm_id":"43853","category_aro_name":"AXC beta-lactamase","category_aro_description":"AXC beta-lactamases are class A beta-lactamase found in the Anaeromyxobacter genus.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7495":{"model_id":"7495","model_name":"AXC-8","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10322":{"protein_sequence":{"accession":"BFR50331.1","sequence":"MLTRRTFIASAVLAGGMPALAHARTDKKTRWTRDNLATFQQALAKLEAASRGRLGVALLDVGSGQAAGYRADERFLMLSSFKTLSAAYVLARADRGEDQLSRRIPITDADVQEYSPVTRLHVGPRGMTLAELCEATITTSDNAAVNLMHKSYGGPQALTRYLRGLGDTVTRHDRYEPELNRPHPSEPQDTTTPRAMARTLDTLLFGDALKPQSRQQLQSWLLANTTGGKRLRAGMPADWKIGEKTGTYSKVGCNDAGFAQPPGAAPIIIAAYLETTAVPMEERDRCIAEVGRLVAALG"},"dna_sequence":{"accession":"LC834166.1","fmin":"0","fmax":"897","strand":"+","sequence":"ATGCTGACAAGAAGAACCTTCATCGCCTCGGCCGTGCTGGCCGGCGGGATGCCCGCCCTGGCGCACGCCAGGACGGATAAGAAAACTCGATGGACTCGCGACAACCTCGCGACATTCCAACAGGCCCTGGCCAAGCTGGAGGCGGCCAGCCGTGGCCGGCTGGGCGTGGCCCTGCTCGACGTGGGCAGCGGGCAGGCCGCCGGCTATCGCGCCGACGAACGTTTTTTGATGCTCAGTTCCTTCAAGACGCTGTCGGCGGCCTATGTGCTGGCGCGGGCCGACCGTGGCGAGGATCAGCTGTCGCGCCGCATCCCGATCACCGATGCCGATGTGCAGGAGTATTCGCCGGTCACGCGGCTGCATGTCGGGCCGCGAGGAATGACCTTGGCCGAACTCTGTGAAGCGACGATCACCACCAGCGACAACGCGGCGGTCAACCTCATGCACAAGAGCTATGGCGGCCCGCAGGCCCTGACCCGCTACCTGCGCGGCCTGGGCGATACCGTCACGCGCCATGATCGTTATGAACCCGAACTGAACCGCCCGCATCCGAGCGAGCCGCAAGACACCACCACCCCGCGGGCCATGGCGCGCACGCTGGACACGCTATTGTTCGGCGACGCGCTCAAGCCGCAATCGCGGCAGCAACTGCAATCCTGGCTGCTGGCCAACACGACGGGCGGCAAGCGCCTGCGCGCCGGCATGCCGGCGGATTGGAAAATCGGCGAGAAGACCGGCACCTATTCGAAGGTGGGCTGCAACGACGCCGGCTTTGCGCAGCCGCCGGGCGCGGCGCCGATCATCATCGCGGCCTATCTGGAAACCACCGCGGTGCCGATGGAGGAGCGCGACCGCTGCATCGCCGAGGTCGGCAGGCTGGTGGCGGCATTGGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39091","NCBI_taxonomy_name":"Achromobacter ruhlandii","NCBI_taxonomy_id":"72557"}}}},"ARO_accession":"3008077","ARO_id":"46869","ARO_name":"AXC-8","CARD_short_name":"AXC-8","ARO_description":"Carbapenem-hydrolyzing class A beta-lactamase AXC-8.","ARO_category":{"43853":{"category_aro_accession":"3005393","category_aro_cvterm_id":"43853","category_aro_name":"AXC beta-lactamase","category_aro_description":"AXC beta-lactamases are class A beta-lactamase found in the Anaeromyxobacter genus.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7496":{"model_id":"7496","model_name":"B3SU1-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10323":{"protein_sequence":{"accession":"QWJ89341.1","sequence":"MSARLLFAPLLIALLAGCATPLSGPAVTDAEPGQRAWAQSCEAMDEWDKPGPPFRIYGSTYYVGTCGITALLIAGPEGHTLIDTGTDKGAEVVLANIHALGFEPRDVKTILMSHEHFDHVGGMARLQDATGAAVVTTPAAAAVLRSGKPGGGDPQAASGHPDFPPVTGIIEELHDDRARKFGGTEFRPMFTPGHTPGAMSWSWRACEGEGCKSIVYVDSLNPISADGYRFSDHPELVAAFRKGIAAIAAADCDIVIAPHPVAVQWRDRLLGERALIDRDGCRAFAATASERLDKRLAREAAGG"},"dna_sequence":{"accession":"MZ126683.1","fmin":"0","fmax":"912","strand":"+","sequence":"ATGTCCGCTAGATTGCTCTTTGCACCGCTGCTTATCGCCCTTCTAGCCGGATGCGCCACACCGCTTTCCGGGCCGGCCGTCACCGATGCCGAGCCCGGCCAGCGCGCCTGGGCGCAAAGCTGCGAAGCGATGGACGAGTGGGACAAGCCCGGGCCGCCGTTCCGCATCTACGGAAGCACCTATTATGTCGGCACCTGCGGCATCACCGCGTTGCTGATCGCCGGCCCGGAAGGCCACACGCTGATCGACACCGGGACCGACAAGGGCGCCGAAGTCGTGCTCGCCAACATCCATGCGCTCGGATTCGAGCCGCGCGATGTGAAAACGATCCTGATGAGCCACGAACATTTCGATCATGTCGGCGGCATGGCGCGGTTGCAGGACGCAACAGGCGCCGCAGTGGTGACGACGCCCGCCGCCGCGGCAGTGCTCCGCAGCGGCAAACCGGGAGGCGGCGACCCCCAGGCGGCCTCGGGCCACCCTGACTTTCCGCCGGTCACCGGCATCATCGAAGAGCTGCACGACGATCGCGCGCGCAAGTTCGGCGGGACTGAATTTCGCCCCATGTTCACCCCGGGCCACACGCCCGGCGCGATGAGCTGGAGCTGGCGCGCGTGCGAAGGAGAGGGGTGCAAATCGATCGTCTATGTCGACAGTCTCAATCCGATCAGCGCCGATGGTTATCGCTTCTCCGATCACCCCGAATTAGTCGCCGCCTTCCGCAAGGGCATCGCCGCGATCGCCGCCGCGGATTGCGACATCGTCATCGCGCCGCATCCCGTCGCCGTGCAATGGCGAGACCGGTTGCTGGGTGAGCGTGCGCTGATCGACCGCGACGGGTGCCGCGCCTTCGCGGCTACAGCGAGCGAGCGGCTCGATAAACGGCTCGCCAGGGAGGCCGCCGGTGGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36791","NCBI_taxonomy_name":"uncultured bacterium","NCBI_taxonomy_id":"77133"}}}},"ARO_accession":"3008078","ARO_id":"46870","ARO_name":"B3SU1-1","CARD_short_name":"B3SU1-1","ARO_description":"Subclass B3 metallo-beta-lactamase B3SU1-1.","ARO_category":{"46655":{"category_aro_accession":"3007864","category_aro_cvterm_id":"46655","category_aro_name":"B3SU1 beta-lactamase","category_aro_description":"B3SU1 is a family of subclass B3 metallo-beta-lactamase enzymes which confer resistance to beta-lactam and cephalosporin antibiotics through enzymatic inactivation.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7497":{"model_id":"7497","model_name":"B3SU2-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10324":{"protein_sequence":{"accession":"QWJ89342.1","sequence":"MRKGRLLISIVLISVWLGVTGSFNYLKAQANDWTEPFPPFKIAGNLYYVGSKGLANYLITTPKGHILINSDLEENVPLIRASVEKLGFKFTDIKVLLISHAHWDHNAASDTIKKLTGAKYMVMEPDVSVVESGGKTDFQYGNDPTTLYKPTKVDRVLHDGEEVKLGGTTLVAHLTPGHTKGCTTWTLKVEEGGKKYNVVIVGSPNVNPGFRLVNNTAYPKIAEDYQKTFDVLKSLKCDIFLGAHGNYFGLEMKYPRFKDEGISVFVDPVGYKNYVEEREQAFKKELAKQKSGQ"},"dna_sequence":{"accession":"MZ126684.1","fmin":"0","fmax":"882","strand":"+","sequence":"ATGCGAAAAGGTAGGTTGTTAATTTCGATTGTCCTTATCAGTGTCTGGCTCGGTGTCACAGGGTCGTTCAATTACTTGAAGGCTCAAGCGAATGATTGGACTGAACCGTTTCCCCCGTTCAAGATCGCTGGGAATCTCTACTACGTGGGAAGTAAAGGTCTTGCGAACTACCTCATCACGACTCCCAAAGGCCACATCTTAATCAACAGCGATCTCGAAGAGAACGTCCCACTCATCCGCGCAAGCGTTGAGAAGCTGGGCTTCAAATTCACTGACATCAAGGTCCTGCTTATCAGTCATGCGCATTGGGATCACAATGCAGCCAGCGACACGATTAAGAAACTGACTGGTGCGAAGTACATGGTGATGGAGCCAGATGTGTCGGTCGTCGAGTCGGGAGGGAAGACCGACTTCCAGTATGGCAATGACCCGACAACACTCTATAAGCCTACGAAGGTCGACCGGGTACTGCACGATGGCGAGGAGGTAAAGTTGGGAGGAACTACCCTCGTAGCGCATCTGACTCCAGGCCACACAAAGGGGTGCACCACGTGGACGTTGAAGGTTGAGGAGGGCGGAAAGAAGTACAACGTCGTCATCGTTGGAAGTCCTAACGTGAATCCCGGTTTTCGACTTGTGAATAACACGGCCTATCCGAAGATTGCCGAGGATTATCAAAAGACATTCGACGTGCTGAAGTCGTTGAAGTGCGACATCTTCCTAGGTGCTCATGGGAATTACTTTGGTCTTGAGATGAAATACCCGCGTTTCAAGGATGAAGGAATTAGCGTCTTCGTGGACCCGGTTGGTTACAAGAATTACGTAGAGGAAAGAGAACAGGCGTTTAAGAAGGAACTTGCAAAACAAAAAAGTGGACAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36791","NCBI_taxonomy_name":"uncultured bacterium","NCBI_taxonomy_id":"77133"}}}},"ARO_accession":"3008079","ARO_id":"46871","ARO_name":"B3SU2-1","CARD_short_name":"B3SU2-1","ARO_description":"Subclass B3 metallo-beta-lactamase B3SU2-1.","ARO_category":{"46656":{"category_aro_accession":"3007865","category_aro_cvterm_id":"46656","category_aro_name":"B3SU2 beta-lactamase","category_aro_description":"B3SU2 is a family of subclass B3 metallo-beta-lactamases which confer resistance to beta-lactam and cephalosporin antibiotics through enzymatic inactivation.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7498":{"model_id":"7498","model_name":"BIC-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10325":{"protein_sequence":{"accession":"WKD79667.1","sequence":"MARPSKLALSFSILLPFLPFTSFAETWPQGDIARQKIVKLEKDFGGRIGVSAIDTGANRTFDFRADERFPLCSSFKGFLAGAVLSHSQQQEGLLEKRIDYKNRVMEPHSPISAQHSSTGMTVAQLAAAALQYSDNGATNLLLENVLGGPAGMTTFMRTLGDTTFRLDRWELELNSAIPGDDRDTSTPHAIARSLQKIALGEALQTAPRQQLVDWLIGNTTGGARIRAGVPVDWVVGDKTGTCGVYGTANDYAVIWPKTSAPIVLAIYTAKPNKEDKHSDAVIAEVTRAVLESFE"},"dna_sequence":{"accession":"OR143113.1","fmin":"120","fmax":"1005","strand":"+","sequence":"ATGGCACGCCCTTCTAAACTAGCTTTATCATTTTCTATTCTGTTGCCTTTTTTACCCTTCACCAGCTTCGCTGAAACCTGGCCACAGGGCGATATCGCCCGACAAAAAATCGTAAAGCTGGAAAAGGATTTCGGTGGGCGGATTGGAGTATCTGCCATCGATACGGGCGCCAATCGAACTTTTGACTTTCGAGCGGACGAACGTTTCCCTTTATGCAGCTCCTTTAAGGGCTTTTTGGCTGGCGCCGTGCTCTCCCACAGCCAACAGCAGGAAGGCTTACTGGAGAAACGTATCGACTATAAAAATCGGGTGATGGAACCTCACTCTCCCATCAGCGCACAACATAGTTCGACGGGTATGACCGTGGCGCAATTAGCGGCAGCGGCGCTGCAGTACAGCGACAACGGCGCGACAAATTTGCTTCTGGAAAACGTTCTGGGCGGGCCCGCCGGGATGACGACCTTCATGAGGACCTTAGGCGATACAACGTTTCGCTTGGATCGATGGGAACTCGAACTCAATAGCGCCATTCCGGGCGACGATCGAGATACCTCGACCCCCCACGCCATAGCCCGCAGCTTGCAAAAAATAGCGTTGGGTGAGGCGTTGCAAACCGCACCGCGTCAGCAGCTGGTTGATTGGCTCATCGGAAATACGACAGGTGGGGCGCGGATCCGGGCAGGCGTCCCTGTCGATTGGGTTGTAGGGGATAAAACGGGCACGTGCGGTGTGTACGGCACCGCCAATGATTATGCCGTCATATGGCCAAAAACATCCGCCCCGATTGTCTTGGCGATTTACACCGCAAAACCGAACAAGGAGGACAAACATAGCGATGCCGTTATTGCCGAAGTGACCCGTGCCGTTCTGGAAAGCTTTGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36937","NCBI_taxonomy_name":"Pseudomonas fluorescens","NCBI_taxonomy_id":"294"}}}},"ARO_accession":"3008080","ARO_id":"46872","ARO_name":"BIC-2","CARD_short_name":"BIC-2","ARO_description":"Carbapenem-hydrolyzing class A beta-lactamase BIC-2.","ARO_category":{"42864":{"category_aro_accession":"3004752","category_aro_cvterm_id":"42864","category_aro_name":"BIC Beta-lactamase","category_aro_description":"BIC is a class A beta-lactamase conferring resistance to carbapenem.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7499":{"model_id":"7499","model_name":"BMHC-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10326":{"protein_sequence":{"accession":"UZX27393.1","sequence":"MKIKTLNTLLLLFISFFISNCNSQKNVSFQPKVVYKSKNLIITQISKNAFEHTSFLQTESFGNVPCNGLIVRKNKETIVFDTPTNDLSSEELIKWINQELHSKINAIIPTHFHDDCLGGLKAFHNHKIPSYSYTKTIELAKMNNYEIPKNGFNDSIILKVGNENISAKYFGEGHTKDNIIGYFPSENIMFGGCLIKELGASKGYLGDANISTWSNTVEKVKKEYPDVKIIIPGHGEFGNSKLLDYTINLFKAE"},"dna_sequence":{"accession":"CP110126.1","fmin":"1785411","fmax":"1786173","strand":"+","sequence":"ATGAAAATTAAGACATTAAATACTTTACTATTATTATTCATTTCGTTTTTTATATCGAACTGTAACTCGCAGAAAAACGTTTCATTTCAACCCAAAGTTGTTTATAAATCTAAAAATTTAATAATAACACAGATTTCTAAAAACGCATTTGAGCATACCTCGTTTTTACAAACAGAAAGTTTCGGAAATGTTCCTTGCAATGGTTTAATTGTGAGAAAGAATAAAGAAACAATAGTATTTGATACACCAACAAATGATCTGAGTTCTGAAGAACTAATAAAATGGATAAATCAAGAACTTCATTCCAAAATTAATGCGATAATTCCAACACATTTCCATGATGATTGTTTGGGAGGACTAAAAGCATTTCATAATCACAAAATCCCTTCTTATTCATACACTAAAACCATAGAATTAGCCAAAATGAATAATTATGAAATTCCAAAAAATGGATTTAATGATTCCATAATTCTAAAAGTTGGTAACGAAAATATTAGTGCAAAATATTTTGGAGAAGGTCATACAAAAGATAATATTATTGGTTACTTTCCAAGTGAAAATATAATGTTTGGTGGTTGTCTAATAAAAGAACTTGGAGCAAGCAAAGGATATTTAGGTGATGCAAATATTTCAACTTGGTCAAATACAGTAGAAAAAGTGAAAAAAGAATATCCGGATGTAAAAATAATAATTCCAGGACATGGAGAATTTGGAAATAGTAAATTATTAGATTACACAATTAACTTGTTTAAAGCTGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36951","NCBI_taxonomy_name":"Riemerella anatipestifer","NCBI_taxonomy_id":"34085"}}}},"ARO_accession":"3008081","ARO_id":"46873","ARO_name":"BMHC-1","CARD_short_name":"BMHC-1","ARO_description":"Subclass B1 metallo-beta-lactamase BMHC-1.","ARO_category":{"46657":{"category_aro_accession":"3007866","category_aro_cvterm_id":"46657","category_aro_name":"BMHC beta-lactamase","category_aro_description":"BMHC is a family of subclass B1 metallo-beta-lactamase enzymes which confer resistance to carbapenem antibiotics through enzymatic inactivation.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7500":{"model_id":"7500","model_name":"BOR-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10327":{"protein_sequence":{"accession":"CAE32545.1","sequence":"MNRRGFGAGMLAALGAACMPPWARAGMRRAARPADAAAQAQRQLALLEQRHGVRLGVQVHDRDSDRAFSHRADERFPMCSTFKLLAAGAVLARADRGDDSLRRLIRYGAADIVAYSPVTGPRQAEGMTLEQLCEAAVTRSDNTAGNLLLSTLGGPPGLTAYARGLGDRMTRLDRIETALNEARPGDPRDTTTPAAMAGNLQRLLLGDALQSASRQRLADWLLASQTGDTRLRAGLPAGWRIGDKTGAGGHGTNNDIGVIWPRDGAPVLISAYLTQSSASREAQNAVLAEVGRIAAHAVAAWRLGS"},"dna_sequence":{"accession":"BX640443.1","fmin":"107141","fmax":"108059","strand":"+","sequence":"ATGAATCGACGTGGATTCGGGGCCGGCATGCTGGCGGCCCTGGGGGCGGCGTGCATGCCGCCATGGGCGCGCGCCGGCATGCGGCGCGCGGCGCGGCCGGCCGATGCGGCGGCGCAAGCGCAGCGCCAGCTTGCGCTGCTGGAGCAGCGGCATGGCGTGCGCCTGGGCGTCCAGGTGCACGATCGCGACAGCGATCGCGCGTTCAGCCATCGGGCCGACGAACGCTTTCCGATGTGCAGTACCTTCAAGCTGCTGGCCGCCGGCGCCGTATTGGCGCGCGCAGACCGCGGCGACGATAGCCTGCGGCGCCTGATCCGCTACGGCGCGGCGGACATCGTGGCGTATTCGCCGGTCACCGGGCCGCGCCAGGCCGAGGGCATGACGCTGGAGCAATTGTGCGAGGCGGCCGTCACGCGCAGCGACAACACCGCGGGCAACCTGCTGCTGTCGACGCTGGGCGGCCCGCCCGGGTTGACCGCCTACGCGCGCGGCCTGGGCGACCGGATGACGCGGCTCGACCGCATCGAGACCGCGCTCAACGAGGCCAGGCCAGGCGATCCGCGCGATACCACCACGCCGGCCGCCATGGCCGGCAACCTGCAGCGCCTGTTGCTGGGCGATGCCTTGCAGTCGGCTTCGCGCCAGCGGCTGGCCGATTGGTTGCTGGCCAGCCAGACCGGCGATACGCGCCTGCGCGCCGGCCTTCCCGCGGGCTGGCGTATCGGCGACAAGACGGGCGCGGGCGGCCATGGCACCAACAACGATATCGGCGTCATCTGGCCGCGCGATGGCGCGCCGGTGCTGATCTCGGCCTATCTCACCCAGTCCAGCGCCTCGCGCGAGGCGCAGAATGCTGTGCTGGCAGAAGTGGGTCGCATCGCCGCCCATGCGGTGGCGGCGTGGCGGCTTGGCAGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36800","NCBI_taxonomy_name":"Bordetella bronchiseptica","NCBI_taxonomy_id":"518"}}}},"ARO_accession":"3008082","ARO_id":"46874","ARO_name":"BOR-1","CARD_short_name":"BOR-1","ARO_description":"Class A beta-lactamase BOR-1.","ARO_category":{"46658":{"category_aro_accession":"3007867","category_aro_cvterm_id":"46658","category_aro_name":"BOR beta-lactamase","category_aro_description":"BOR is a family of class A beta-lactamase enzymes which confer resistance to beta-lactam antibiotics through enzymatic inactivation.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7501":{"model_id":"7501","model_name":"CAM-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10328":{"protein_sequence":{"accession":"MCD9185600.1","sequence":"MKLTAIILFLLAFSPGVFGQMSDALKITPLVGDFYIFTTYQTYKDAKVPANGMYVVTAEGVVLIDTPWDETQLQPLLNYIKEKHNKDVVMSVSTHFHEDRTNGIEFLKTKGVKTYTTRKTDELSQKKGYERAEFLLEKDTEFKLGQYKFQTFYPGEGHAPDNIVVWFPNEKILYGGCFIKSTEADDIGNLSDANINEWSNSIMKVQKKFKNPKFVIPGHDGWASTKSLKHTLKLIREFRGKTAQKK"},"dna_sequence":{"accession":"JAJQRF010000001.1","fmin":"996229","fmax":"996970","strand":"+","sequence":"ATGAAATTAACTGCAATTATTTTATTTTTACTCGCTTTTTCGCCCGGCGTTTTCGGACAAATGAGCGACGCGCTGAAAATTACTCCGCTCGTGGGCGATTTTTATATTTTTACGACTTATCAAACCTACAAAGACGCGAAAGTTCCTGCCAACGGGATGTATGTCGTGACCGCCGAAGGCGTTGTCCTGATCGACACGCCGTGGGATGAAACTCAGCTTCAGCCGCTTCTGAATTACATCAAGGAAAAGCATAACAAGGATGTCGTGATGAGCGTTTCGACGCATTTTCACGAAGACCGCACGAACGGCATCGAGTTTTTGAAAACGAAGGGCGTGAAAACCTACACGACCAGAAAAACCGACGAACTTTCGCAGAAAAAAGGCTACGAGCGCGCCGAATTTTTGCTTGAAAAAGATACGGAATTCAAACTCGGACAATACAAATTTCAGACCTTTTATCCCGGCGAAGGTCACGCGCCCGACAACATCGTGGTCTGGTTTCCGAACGAAAAAATTCTTTACGGCGGCTGTTTCATAAAAAGCACCGAAGCCGACGACATCGGAAATTTGTCCGACGCAAACATCAACGAATGGTCAAATTCGATTATGAAAGTGCAGAAAAAATTCAAGAATCCGAAATTCGTAATTCCCGGTCACGACGGCTGGGCAAGCACGAAATCTTTGAAACACACTTTGAAACTTATTCGGGAATTCAGGGGAAAAACTGCACAAAAGAAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"47919","NCBI_taxonomy_name":"Pyrinomonadaceae","NCBI_taxonomy_id":"2048906"}}}},"ARO_accession":"3008083","ARO_id":"46875","ARO_name":"CAM-2","CARD_short_name":"CAM-2","ARO_description":"Subclass B1 metallo-beta-lactamase CAM-2.","ARO_category":{"42464":{"category_aro_accession":"3004558","category_aro_cvterm_id":"42464","category_aro_name":"CAM beta-lactamase","category_aro_description":"CAM (Central Alberta Metallo) beta-lactamases are class B metallo-beta-lactamases and carbapenemases found to confer resistance to broad spectrum antibiotics in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7502":{"model_id":"7502","model_name":"CME-3","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10329":{"protein_sequence":{"accession":"UFK32676.1","sequence":"MKRISIIFLFFSLFVFSQHSKPELLEKINTITKGKKATVAVSVLGIENDFQFSNANGNLKMPMLSVFKFHIALAVLNQVDKGNLTLDQKILIKKSDLLENTWSPLREKYPDGNVELPLSEIITYTVAQSDNNGCDILLRLIGGTKTVQKLMDVNGIKNFQIKYNEEEMHKNDVKTLYANYTTTASMVKTLKAFYKGMFLSKRSTIFLMDIMTKTNTGMSKLPGLLPKVRMARKTGSSGKMKNGLTIAENDSGIVTLANGKHYAIAVFVKDSMESEEVNCGMIAQVSKIVWDALNKKNKP"},"dna_sequence":{"accession":"OL542677.1","fmin":"0","fmax":"900","strand":"+","sequence":"ATGAAAAGAATTAGTATTATTTTTCTGTTTTTCTCCCTTTTTGTTTTTTCTCAACATTCAAAACCTGAACTACTAGAGAAAATAAACACAATTACAAAAGGTAAAAAAGCCACAGTAGCTGTTTCTGTTTTGGGGATAGAAAATGATTTTCAGTTTAGTAACGCCAATGGTAATTTGAAAATGCCGATGCTGAGTGTTTTTAAATTTCATATTGCATTGGCGGTTCTAAATCAGGTAGACAAAGGTAACCTTACCTTGGATCAGAAAATACTGATTAAAAAATCGGATCTATTAGAAAATACATGGTCACCACTTCGTGAGAAGTATCCGGATGGAAATGTAGAACTTCCTTTAAGCGAAATTATTACTTATACCGTAGCCCAAAGTGACAACAACGGATGCGACATACTATTAAGGCTAATTGGCGGGACTAAAACTGTTCAGAAATTAATGGATGTGAATGGTATAAAAAACTTTCAGATAAAATATAATGAGGAAGAAATGCATAAAAATGATGTAAAAACTCTTTATGCAAATTACACGACCACAGCATCTATGGTAAAAACTCTGAAAGCGTTCTATAAAGGAATGTTTTTATCAAAAAGATCCACAATTTTTCTAATGGATATTATGACTAAAACCAATACCGGAATGTCAAAGCTTCCGGGCTTGCTGCCAAAAGTTAGAATGGCCAGAAAAACAGGTTCTTCGGGTAAAATGAAAAACGGATTAACGATTGCTGAGAACGATTCAGGAATTGTAACTTTAGCAAATGGTAAACATTATGCAATTGCAGTATTTGTAAAGGACTCTATGGAAAGTGAGGAAGTCAATTGTGGAATGATTGCCCAGGTCTCGAAAATTGTCTGGGATGCTTTAAATAAAAAAAATAAACCCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41081","NCBI_taxonomy_name":"Elizabethkingia anophelis","NCBI_taxonomy_id":"1117645"}}}},"ARO_accession":"3008084","ARO_id":"46876","ARO_name":"CME-3","CARD_short_name":"CME-3","ARO_description":"Extended-spectrum class A beta-lactamase CME-3.","ARO_category":{"42889":{"category_aro_accession":"3004774","category_aro_cvterm_id":"42889","category_aro_name":"CME beta-lactamase","category_aro_description":"CME is a class A beta-lactamase gene family belonging to Chryseobacterium meningosepticum.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7503":{"model_id":"7503","model_name":"CMH-10","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10330":{"protein_sequence":{"accession":"VAC93856.1","sequence":"MMKKSLSCALLLSVACSAFAAPMSEKQLADVVERTVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSVSKTFTGVLGGDAIARKEISLADPVTKYWPELTGKQWQGIRLLDLATYTAGGLPLQVPDDVTDNASLLRFYQSWQPKWAPGTTRLYANTSIGLFGSLAVKPSGMRFEQAMAERVFKPLKLNHTWINVPHAEEPHYAWGYREGKAVHVSPGMLDAEAYGVKSNVKDMASWVMANMAPETLPPSTLQQGIALAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVDGSDNKVALVPLPVAEVNPPAPPVKGSWVHKTGSTGGFGSYVAFIPEKQIGIVMLANKSYPNPVRVETAYRILDALQ"},"dna_sequence":{"accession":"UNTK01000039.1","fmin":"12291","fmax":"13437","strand":"+","sequence":"ATGATGAAAAAATCCCTAAGCTGCGCCCTGCTGCTCAGCGTTGCTTGCTCTGCTTTTGCCGCGCCGATGTCAGAAAAACAGCTGGCTGACGTCGTGGAACGTACCGTTACGCCCCTGATGAAGGCGCAGGCCATACCCGGAATGGCCGTGGCCGTCATTTATCAGGGCCAGCCACACTATTTCACTTTCGGTAAAGCAGACGTCGCGGCGAATAAGCCCGTCACGCCGCAAACCTTATTTGAACTGGGCTCCGTCAGTAAAACCTTCACTGGCGTGCTGGGTGGCGATGCCATTGCCCGCAAAGAGATTTCGCTGGCCGACCCGGTCACGAAATACTGGCCTGAATTGACGGGCAAGCAGTGGCAAGGCATTCGCCTGCTCGACCTGGCAACCTATACCGCAGGGGGATTGCCGTTGCAGGTACCGGATGATGTCACCGATAACGCCTCTCTGCTGCGTTTCTACCAGTCCTGGCAGCCAAAGTGGGCCCCGGGTACCACGCGTCTGTACGCCAACACCAGCATCGGTTTGTTTGGCTCACTGGCCGTTAAACCGTCCGGCATGCGCTTCGAGCAGGCCATGGCGGAGCGGGTCTTTAAGCCCCTGAAACTCAACCATACGTGGATAAACGTTCCACACGCTGAAGAGCCGCACTACGCATGGGGTTATCGTGAGGGAAAAGCGGTCCACGTTTCGCCTGGTATGCTGGATGCAGAAGCCTATGGCGTGAAATCTAACGTCAAAGATATGGCGAGCTGGGTGATGGCCAATATGGCACCTGAGACACTCCCGCCGTCCACTCTGCAGCAGGGTATTGCGCTGGCGCAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAAGGGTTAGGCTGGGAGATGCTCAACTGGCCGGTCGACGCCAAAACCGTGGTGGATGGCAGCGACAATAAGGTCGCACTGGTGCCGTTGCCGGTCGCAGAAGTGAATCCTCCGGCTCCGCCAGTAAAAGGCTCCTGGGTGCATAAAACGGGCTCTACGGGTGGGTTTGGCAGCTACGTGGCATTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCAAATAAAAGCTATCCGAATCCGGTACGGGTGGAAACGGCTTACCGTATCCTCGACGCGCTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3008085","ARO_id":"46877","ARO_name":"CMH-10","CARD_short_name":"CMH-10","ARO_description":"Class C beta-lactamase CMH-10.","ARO_category":{"42891":{"category_aro_accession":"3004776","category_aro_cvterm_id":"42891","category_aro_name":"CMH beta-lactamase","category_aro_description":"CMH is a class C beta-lactamase gene family belonging to Enterobacter cloacae.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7504":{"model_id":"7504","model_name":"CMH-11","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10331":{"protein_sequence":{"accession":"WFP34008.1","sequence":"MMKKSLSCALLLSVACSAFAAPMSEKQLADVVERTVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSVSKTFTGVLGGDAIARKEISLADPVTKYWPELTGKQWQGIRLLDLATYTAGGLPLQVPDDVTDNASLLRFYQSWQPKWAPGTTRLYANTSIGLFGSLAVKPSGMRFEQAMVERVFKPLKLTHTWINVPHAEEPHYAWGYREGKAVHVSPGMLDAEAYGVKSNVKDMASWLMANMAPETLPQSTLQQGIALAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVDGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANKSYPNPVRVETAYRILETLQ"},"dna_sequence":{"accession":"OQ709070.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCCCTAAGCTGCGCCCTGCTGCTCAGCGTTGCCTGCTCTGCTTTTGCCGCGCCGATGTCAGAAAAACAGCTGGCTGACGTCGTGGAACGTACAGTTACGCCCCTGATGAAGGCGCAGGCCATACCCGGAATGGCCGTGGCCGTCATTTATCAGGGCCAGCCACACTATTTTACTTTCGGTAAAGCAGACGTCGCGGCGAATAAGCCCGTCACGCCGCAAACCTTATTTGAGCTGGGCTCCGTCAGCAAAACCTTCACCGGCGTGCTGGGTGGCGATGCCATTGCCCGCAAAGAGATTTCGCTGGCCGACCCGGTCACGAAATATTGGCCTGAATTGACGGGCAAGCAGTGGCAAGGCATTCGCCTGCTCGACCTGGCAACCTATACCGCAGGCGGATTGCCGTTGCAGGTGCCGGATGATGTCACCGATAATGCCTCTCTGCTGCGTTTCTACCAGTCCTGGCAGCCAAAGTGGGCCCCGGGTACCACGCGTCTGTACGCCAACACCAGCATCGGCCTGTTTGGCTCACTGGCCGTTAAACCTTCCGGCATGCGCTTCGAGCAGGCCATGGTGGAGCGGGTCTTTAAGCCCCTGAAACTCACCCATACATGGATAAACGTTCCACACGCTGAAGAGCCGCACTACGCATGGGGTTATCGTGAGGGAAAAGCGGTCCACGTTTCGCCTGGTATGCTGGATGCAGAAGCCTATGGCGTGAAATCTAACGTCAAAGATATGGCGAGCTGGTTGATGGCCAATATGGCACCTGAGACACTCCCGCAGTCCACTCTGCAGCAGGGGATTGCGCTGGCGCAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAAGGGTTAGGCTGGGAGATGCTCAACTGGCCGGTCGACGCCAAAACCGTGGTGGATGGCAGCGATAATAAGGTTGCACTGGCGCCGTTGCCGGTCGCAGAAGTGAATCCTCCGGCTCCGCCAGTAAAAGCCTCCTGGGTGCATAAAACGGGCTCTACGGGTGGGTTTGGCAGCTACGTGGCGTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCAAATAAAAGCTATCCGAACCCGGTACGGGTGGAAACGGCTTACCGTATTCTCGAGACGCTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3008086","ARO_id":"46878","ARO_name":"CMH-11","CARD_short_name":"CMH-11","ARO_description":"Class C beta-lactamase CMH-11.","ARO_category":{"42891":{"category_aro_accession":"3004776","category_aro_cvterm_id":"42891","category_aro_name":"CMH beta-lactamase","category_aro_description":"CMH is a class C beta-lactamase gene family belonging to Enterobacter cloacae.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7505":{"model_id":"7505","model_name":"CMH-12","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10332":{"protein_sequence":{"accession":"WFP34010.1","sequence":"MMKKSLSCALLLSVACSAFAAPMSEKQLADVVERTVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSVSKTFTGVLGGDAIARKEISLADPVTKYWPELTGKQWQGIRLLDLATYTAGGLPLQVPDDVTDNASLLRFYQSWQPKWAPGTTRLYANTSIGLFGSLAVKPSGMRFEQAMAERVFKPLKLNHTWINVPHAEEPHYAWGYREGKAVHVSPGMLDAEAYGVKSNVKDMASWVMANMAPETLPQPTLKQGIALAQSRYWRVSAMYQGLGWEMLNWPVDVKTVVDGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANKSYPTPVRVETAYRILETLQ"},"dna_sequence":{"accession":"OQ709072.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCCCTAAGCTGCGCCCTGCTGCTCAGCGTTGCCTGCTCTGCTTTTGCCGCGCCGATGTCAGAAAAACAACTGGCTGACGTCGTGGAACGTACCGTTACGCCCCTGATGAAGGCGCAGGCCATACCCGGTATGGCCGTGGCCGTCATTTATCAGGGCCAGCCACACTATTTTACTTTCGGTAAAGCAGACGTTGCGGCGAATAAGCCCGTCACGCCGCAAACCTTATTTGAGCTGGGCTCCGTCAGCAAAACCTTCACCGGCGTGCTGGGTGGCGATGCCATTGCCCGCAAAGAGATTTCGCTGGCCGACCCGGTCACGAAATATTGGCCTGAATTGACGGGCAAGCAGTGGCAAGGCATTCGCCTGCTAGACCTGGCAACCTATACCGCAGGCGGATTGCCGTTGCAGGTACCGGATGATGTCACCGATAACGCCTCTCTGCTGCGTTTCTACCAGTCCTGGCAGCCAAAGTGGGCCCCGGGTACCACGCGTCTGTACGCCAACACCAGCATCGGCCTGTTTGGCTCACTGGCCGTTAAACCGTCCGGCATGCGCTTCGAGCAGGCCATGGCGGAGCGGGTCTTTAAGCCCCTGAAACTCAACCATACGTGGATAAACGTTCCACACGCTGAAGAGCCGCACTACGCATGGGGTTATCGTGAGGGAAAAGCGGTCCACGTTTCGCCTGGTATGCTGGATGCAGAAGCCTATGGCGTGAAATCTAACGTCAAAGATATGGCGAGCTGGGTGATGGCCAATATGGCACCTGAGACACTCCCGCAGCCCACTCTGAAGCAGGGTATTGCGCTGGCGCAGTCTCGCTACTGGCGCGTGAGTGCCATGTATCAAGGGTTAGGCTGGGAGATGCTCAACTGGCCGGTCGACGTCAAAACCGTGGTGGATGGCAGCGACAATAAGGTTGCACTGGCGCCGTTGCCGGTCGCAGAAGTGAATCCTCCGGCTCCGCCAGTAAAAGCCTCCTGGGTGCATAAAACGGGCTCTACGGGTGGGTTTGGCAGCTACGTGGCGTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCAAATAAAAGCTATCCGACCCCGGTACGGGTGGAAACGGCTTACCGTATTCTCGAGACGCTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3008087","ARO_id":"46879","ARO_name":"CMH-12","CARD_short_name":"CMH-12","ARO_description":"Class C beta-lactamase CMH-12.","ARO_category":{"42891":{"category_aro_accession":"3004776","category_aro_cvterm_id":"42891","category_aro_name":"CMH beta-lactamase","category_aro_description":"CMH is a class C beta-lactamase gene family belonging to Enterobacter cloacae.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7506":{"model_id":"7506","model_name":"CMH-13","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10333":{"protein_sequence":{"accession":"WLO97156.1","sequence":"MMKKSLSCALLLSVACSAFAAPMSEKQLADVVERTVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSVSKTFTGVLGGDAIARKEISLADPVTKYWPELTGKQWQGIRLLDLATYTAGGLPLQVPDDVTDNASLLSFYQSWQPKWAPGTTRLYANTSIGLFGSLAVKPSGMRFEQAMAERVFKPLKLNHTWINVPHAEEPHYAWGYREGKAVHVSPGMLDAEAYGVKSNVKDMASWVMANMAPETLPQSTLQQGIALAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVDGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANKSYPNPVRVETAYRILETLQ"},"dna_sequence":{"accession":"OR398193.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCCCTAAGCTGCGCCCTGCTGCTCAGCGTTGCCTGCTCTGCTTTTGCCGCGCCGATGTCAGAAAAACAGCTGGCTGACGTCGTGGAACGTACCGTTACGCCCCTGATGAAGGCGCAGGCCATACCCGGAATGGCCGTGGCCGTCATTTATCAGGGCCAGCCACACTATTTTACTTTCGGTAAAGCAGACGTCGCGGCGAATAAGCCCGTCACGCCGCAAACCTTATTTGAGCTGGGCTCCGTCAGCAAAACCTTCACCGGCGTGCTGGGTGGCGATGCCATTGCCCGCAAAGAGATTTCGCTGGCCGACCCGGTCACGAAATATTGGCCTGAATTGACGGGCAAGCAGTGGCAAGGCATTCGCCTGCTCGACCTGGCAACCTATACCGCAGGCGGATTGCCGTTGCAGGTACCGGATGATGTCACCGATAACGCCTCTCTGCTGAGTTTCTACCAGTCCTGGCAGCCAAAATGGGCCCCGGGTACCACGCGTCTGTACGCCAACACCAGCATCGGCCTGTTTGGCTCACTGGCCGTTAAACCGTCCGGCATGCGCTTCGAGCAGGCCATGGCGGAGCGGGTCTTTAAGCCCCTGAAACTCAACCATACGTGGATAAACGTTCCACACGCTGAAGAGCCCCACTACGCATGGGGTTATCGTGAGGGAAAAGCGGTCCACGTTTCGCCTGGTATGCTGGATGCAGAAGCCTATGGTGTGAAATCTAACGTCAAAGATATGGCGAGCTGGGTGATGGCCAATATGGCACCTGAGACACTCCCGCAGTCCACTCTGCAGCAGGGTATTGCGCTGGCGCAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAAGGGTTAGGCTGGGAGATGCTCAACTGGCCGGTCGATGCCAAAACCGTGGTGGATGGCAGCGACAATAAGGTCGCACTGGCGCCGTTGCCGGTCGCAGAAGTGAATCCTCCGGCTCCGCCAGTAAAAGCCTCCTGGGTGCATAAAACGGGCTCTACGGGTGGGTTTGGCAGCTACGTGGCGTTTATTCCTGAAAAGCAGATCGGTATTGTAATGCTCGCAAATAAAAGTTATCCGAACCCGGTACGGGTGGAAACGGCTTACCGTATTCTCGAGACGCTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3008088","ARO_id":"46880","ARO_name":"CMH-13","CARD_short_name":"CMH-13","ARO_description":"Class C beta-lactamase CMH-13.","ARO_category":{"42891":{"category_aro_accession":"3004776","category_aro_cvterm_id":"42891","category_aro_name":"CMH beta-lactamase","category_aro_description":"CMH is a class C beta-lactamase gene family belonging to Enterobacter cloacae.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7507":{"model_id":"7507","model_name":"CMH-14","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10334":{"protein_sequence":{"accession":"HAS1186197.1","sequence":"MMKKSLSCALLLSVACSAFAAPMSEKQLADVVERTVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSVSKTFTGVLGGDAIARKEISLADPVTKYWPELTGKQWQGIRLLDLATYTAGGLPLQVPDDVTDNASLLRFYQSWQPKWAPGTTRLYANTSIGLFGSLAVKPSGMRFEQAMAERVFKPLKLNHTWINVPHAEEPHYAWGYREGKAVHVSPGMLDAEAYGVKSNVKDMASWVMANMAPETLPPSTLQQGIALAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVDGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANKSYPNPVRVETAYRILDALQ"},"dna_sequence":{"accession":"DACOLN010000081.1","fmin":"11888","fmax":"13034","strand":"+","sequence":"ATGATGAAAAAATCCCTAAGCTGCGCCCTGCTGCTCAGCGTTGCTTGCTCTGCTTTTGCCGCGCCGATGTCAGAAAAACAGCTGGCTGACGTCGTGGAACGTACCGTTACGCCCCTGATGAAGGCGCAGGCCATACCCGGAATGGCCGTGGCCGTCATTTATCAGGGCCAGCCACACTATTTTACTTTCGGTAAAGCAGACGTCGCGGCGAATAAGCCCGTCACGCCGCAAACCTTATTTGAACTGGGCTCCGTCAGTAAAACCTTCACTGGCGTGCTGGGTGGCGATGCCATTGCCCGCAAAGAGATTTCGCTGGCCGACCCGGTCACGAAATACTGGCCTGAATTGACGGGCAAGCAGTGGCAAGGCATTCGCCTGCTCGACCTGGCAACCTATACCGCAGGCGGATTGCCGTTGCAGGTACCTGATGATGTCACCGATAACGCCTCTCTGCTGCGTTTCTACCAGTCCTGGCAGCCAAAGTGGGCCCCGGGTACCACGCGTCTGTACGCCAACACCAGCATCGGTTTGTTTGGCTCACTGGCCGTTAAACCGTCCGGCATGCGCTTCGAGCAGGCCATGGCGGAGCGGGTCTTTAAGCCCCTGAAACTCAACCATACGTGGATAAACGTTCCACACGCTGAAGAGCCGCACTACGCATGGGGTTATCGTGAGGGAAAAGCGGTCCACGTTTCGCCTGGTATGCTGGATGCAGAAGCCTATGGCGTGAAATCTAACGTCAAAGATATGGCGAGCTGGGTGATGGCCAATATGGCACCTGAGACACTCCCGCCGTCCACTCTGCAGCAGGGTATTGCGCTGGCGCAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAAGGGTTAGGCTGGGAGATGCTCAACTGGCCGGTCGACGCCAAAACCGTGGTGGATGGCAGCGACAATAAGGTCGCACTGGCGCCGTTGCCGGTCGCAGAAGTGAATCCTCCGGCTCCGCCAGTAAAAGCCTCCTGGGTGCATAAAACGGGCTCTACGGGTGGGTTTGGCAGCTACGTGGCGTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCAAATAAAAGCTATCCGAACCCGGTACGGGTGGAAACGGCTTACCGTATCCTCGACGCGCTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3008089","ARO_id":"46881","ARO_name":"CMH-14","CARD_short_name":"CMH-14","ARO_description":"Class C beta-lactamase CMH-14.","ARO_category":{"42891":{"category_aro_accession":"3004776","category_aro_cvterm_id":"42891","category_aro_name":"CMH beta-lactamase","category_aro_description":"CMH is a class C beta-lactamase gene family belonging to Enterobacter cloacae.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7508":{"model_id":"7508","model_name":"CMH-15","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10335":{"protein_sequence":{"accession":"TYR27460.1","sequence":"MMKKSLSCALLLSVACSAFAAPMSEKQLADVVERTVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSVSKTFTGVLGGDAIARKEISLADPVTKYWPELTGKQWQGIRLLDLATYTAGGLPLQVPDDVTDNASLLRFYQSWQPKWAPGTTRLYANTSIGLFGSLAVKPSGMRFEQAMAERVFKPLKLNHTWINVPHAEEPHYAWGYREGKAVHVSPGMLDAEAYGVKSNVKDMASWVMANMAPETLPQSTLQQGIALAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVDGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANKSYPNPVRVETAYRILETLQ"},"dna_sequence":{"accession":"VSZU01000030.1","fmin":"55768","fmax":"56914","strand":"+","sequence":"ATGATGAAAAAATCCCTAAGCTGCGCCCTGCTGCTCAGCGTTGCTTGCTCTGCTTTTGCCGCGCCGATGTCAGAAAAACAGCTGGCTGACGTCGTGGAACGTACCGTTACGCCCCTGATGAAGGCGCAGGCCATACCCGGAATGGCCGTGGCCGTCATTTATCAGGGCCAGCCACACTATTTTACTTTCGGTAAAGCAGACGTCGCGGCGAATAAGCCCGTCACGCCGCAAACCTTATTTGAGCTGGGCTCCGTCAGCAAAACCTTCACCGGCGTGCTGGGTGGCGATGCCATTGCCCGCAAAGAGATTTCGCTGGCCGACCCGGTCACGAAATATTGGCCTGAATTGACGGGCAAGCAGTGGCAAGGCATTCGCCTGCTCGACCTGGCAACCTATACCGCAGGCGGATTGCCGTTGCAGGTACCGGATGATGTCACCGATAACGCCTCTCTGCTGCGTTTCTACCAGTCCTGGCAGCCAAAGTGGGCCCCGGGTACCACGCGTCTGTACGCCAACACCAGCATCGGTTTGTTTGGCTCACTGGCTGTGAAACCGTCCGGCATGCGCTTCGAGCAGGCCATGGCGGAGCGGGTCTTTAAGCCCCTGAAACTTAACCATACGTGGATAAACGTTCCACACGCTGAAGAGCCGCACTACGCATGGGGTTATCGTGAGGGAAAAGCGGTCCACGTTTCGCCTGGTATGCTGGATGCAGAAGCCTATGGCGTGAAATCTAACGTCAAAGATATGGCGAGCTGGGTGATGGCCAATATGGCACCTGAGACACTCCCGCAGTCCACTCTGCAGCAGGGTATTGCGCTGGCGCAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAAGGGTTAGGCTGGGAGATGCTCAACTGGCCGGTCGACGCCAAAACCGTGGTGGATGGCAGCGACAATAAGGTCGCACTGGCGCCGTTGCCGGTCGCAGAAGTGAATCCTCCGGCTCCGCCAGTAAAAGCCTCCTGGGTGCATAAAACGGGCTCTACGGGTGGGTTTGGCAGCTACGTGGCGTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCAAATAAAAGCTATCCGAACCCGGTACGGGTGGAAACGGCTTACCGTATTCTCGAGACGCTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3008090","ARO_id":"46882","ARO_name":"CMH-15","CARD_short_name":"CMH-15","ARO_description":"Class C beta-lactamase CMH-15.","ARO_category":{"42891":{"category_aro_accession":"3004776","category_aro_cvterm_id":"42891","category_aro_name":"CMH beta-lactamase","category_aro_description":"CMH is a class C beta-lactamase gene family belonging to Enterobacter cloacae.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7509":{"model_id":"7509","model_name":"CMH-16","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10336":{"protein_sequence":{"accession":"KJX09314.1","sequence":"MMKKSLSCALLLSVACSAFAAPMSEKQLADVVERTVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSVSKTFTGVLGGDAIARKEISLADPVTKYWPELTGKQWQGIRLLDLATYTAGGLPLQVPDDVTDNASLLRFYQSWQPKWAPGTTRLYANTSIGLFGSLAVKPSGMRFEQAMAERVFKPLKLNHTWINVPHAEEPHYAWGYREGKAVHVSPGMLDAEAYGVKSNVKDMASWVMANMAPETLPPSTLQQGIALAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVDGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANKSYPNPVRVETAYRILETLQ"},"dna_sequence":{"accession":"JZKU01000015.1","fmin":"12026","fmax":"13172","strand":"+","sequence":"ATGATGAAAAAATCCCTAAGCTGCGCGCTGCTGCTCAGCGTTGCCTGCTCTGCTTTTGCCGCGCCGATGTCAGAAAAACAGCTGGCAGACGTCGTGGAACGTACCGTTACGCCCCTGATGAAGGCGCAGGCCATACCCGGTATGGCCGTGGCCGTCATTTATCAGGGCCAGCCACACTATTTTACTTTCGGTAAAGCAGACGTCGCGGCGAATAAGCCCGTCACGCCGCAAACCTTATTTGAACTGGGCTCCGTCAGTAAAACCTTCACTGGCGTGCTGGGTGGCGATGCCATTGCCCGCAAAGAGATTTCGCTGGCCGACCCGGTCACGAAATACTGGCCTGAATTGACGGGCAAGCAGTGGCAAGGCATTCGCCTGCTCGACCTGGCAACCTATACCGCAGGCGGATTGCCGTTGCAGGTACCGGATGATGTCACCGATAACGCCTCTCTGCTGCGTTTCTACCAGTCCTGGCAGCCAAAGTGGGCCCCGGGTACCACGCGTCTGTACGCCAACACCAGCATCGGTTTGTTTGGCTCACTGGCCGTTAAACCGTCCGGCATGCGCTTCGAGCAGGCCATGGCGGAGCGGGTCTTTAAGCCCCTGAAACTCAACCATACGTGGATAAACGTTCCACACGCTGAAGAGCCGCACTACGCATGGGGTTATCGTGAGGGAAAAGCGGTCCACGTTTCGCCTGGTATGCTGGATGCAGAAGCCTATGGCGTGAAATCTAACGTCAAAGATATGGCGAGCTGGGTGATGGCCAATATGGCACCTGAGACACTCCCGCCGTCCACTCTGCAGCAGGGTATTGCGCTGGCGCAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAAGGGTTAGGCTGGGAGATGCTCAACTGGCCGGTCGACGCCAAAACCGTAGTGGATGGCAGCGACAATAAGGTCGCACTGGCGCCGTTGCCGGTCGCAGAAGTGAATCCTCCGGCTCCGCCAGTAAAAGCCTCCTGGGTGCATAAAACGGGCTCTACGGGTGGGTTTGGCAGCTACGTGGCGTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCAAATAAAAGCTATCCGAACCCGGTACGGGTGGAAACGGCTTACCGTATTCTCGAGACGCTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3008091","ARO_id":"46883","ARO_name":"CMH-16","CARD_short_name":"CMH-16","ARO_description":"Class C beta-lactamase CMH-16.","ARO_category":{"42891":{"category_aro_accession":"3004776","category_aro_cvterm_id":"42891","category_aro_name":"CMH beta-lactamase","category_aro_description":"CMH is a class C beta-lactamase gene family belonging to Enterobacter cloacae.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7510":{"model_id":"7510","model_name":"CMH-17","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10337":{"protein_sequence":{"accession":"HCM9257039.1","sequence":"MMKKSLSCALLLSVACSAFAAPMSEKQLANVVERNVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSVSKTFTGVLGGDAIARKEISLADPVTKYWPELTGKQWQGIRLLDLATYTAGGLPLQVPDAVTDNASLLRFYQSWQPKWAPGTTRLYANTSIGLFGSLAVKPSGMRFEEAMTERVFKPLKLNHTWINIPHAEEPHYAWGYREGKAVHVSPGLLDAEAYGVKSNVKDMASWVMANMAPDTIQQPALKQGIALAQSRYWRVGAMYQGLGWEMLNWPVEAKTVVDGSDNKVALAPLPAAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANKSYPNPLRVETAYRILDTLQ"},"dna_sequence":{"accession":"DAJEDZ010000031.1","fmin":"12001","fmax":"13147","strand":"+","sequence":"ATGATGAAAAAATCCCTAAGCTGTGCACTGTTGCTCAGCGTTGCCTGCTCTGCCTTTGCCGCGCCAATGTCAGAAAAACAGCTGGCTAACGTCGTGGAACGTAACGTTACGCCCCTGATGAAAGCGCAGGCCATACCCGGTATGGCCGTGGCTGTCATTTATCAGGGTCAGCCGCACTATTTTACTTTTGGTAAAGCAGACGTCGCAGCGAATAAGCCTGTCACACCGCAAACCTTATTTGAGCTGGGCTCCGTCAGCAAAACTTTCACCGGGGTGCTGGGTGGCGATGCCATTGCCCGCAAAGAGATTTCGCTGGCCGACCCGGTCACGAAATATTGGCCTGAATTGACGGGCAAGCAGTGGCAGGGCATTCGCCTGCTCGATCTGGCAACTTATACCGCAGGTGGATTGCCGTTGCAGGTACCGGATGCTGTCACCGATAACGCCTCTCTGCTGCGTTTCTACCAGTCCTGGCAGCCAAAGTGGGCCCCGGGTACTACGCGTCTGTACGCCAACACCAGCATCGGTTTGTTTGGCTCACTGGCGGTTAAACCTTCCGGCATGCGCTTTGAGGAGGCCATGACGGAGCGGGTCTTTAAGCCCCTGAAACTCAATCATACGTGGATAAACATTCCACACGCTGAAGAGCCGCATTACGCATGGGGTTATCGTGAGGGTAAAGCGGTCCACGTTTCGCCGGGTCTGCTGGATGCAGAAGCCTATGGCGTGAAATCTAACGTCAAAGATATGGCGAGCTGGGTGATGGCCAATATGGCACCGGACACAATCCAGCAGCCCGCTCTGAAGCAGGGTATTGCGCTGGCTCAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAAGGGTTAGGCTGGGAGATGCTCAACTGGCCGGTGGAGGCCAAAACCGTGGTGGATGGCAGCGACAATAAGGTTGCACTGGCGCCGTTACCGGCAGCAGAAGTGAATCCTCCGGCTCCGCCTGTGAAAGCCTCATGGGTGCATAAAACGGGCTCTACGGGGGGGTTTGGCAGCTACGTGGCGTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATAAAAGCTATCCGAACCCGCTACGGGTGGAAACGGCTTACCGTATCCTCGACACGCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3008092","ARO_id":"46884","ARO_name":"CMH-17","CARD_short_name":"CMH-17","ARO_description":"Class C beta-lactamase CMH-17.","ARO_category":{"42891":{"category_aro_accession":"3004776","category_aro_cvterm_id":"42891","category_aro_name":"CMH beta-lactamase","category_aro_description":"CMH is a class C beta-lactamase gene family belonging to Enterobacter cloacae.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7511":{"model_id":"7511","model_name":"CMH-18","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10338":{"protein_sequence":{"accession":"HBB4753723.1","sequence":"MMKKSLSCALLLSVACSAFAAPMSEKQLADVVERTVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSVSKTFTGVLGGDAIARKEISLADPVTKYWPELTGKQWQGIRLLDLATYTAGGLPLQVPDDVTDNASLLRFYQSWQPKWAPGTTRLYANTSIGLFGSLAVKPSGMCFEQAMAERVFKPLKLNHTWINVPHAEEPHYAWGYREGKAVHVSPGMLDAEAYGVKSNVKDMASWVMANMAPETLPQSTLQQGIALAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVDGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANKSYPNPVRVETAYRILDALQ"},"dna_sequence":{"accession":"DADVEM010000069.1","fmin":"12010","fmax":"13156","strand":"+","sequence":"ATGATGAAAAAATCCCTAAGCTGCGCCCTGCTGCTCAGCGTTGCTTGCTCTGCTTTTGCCGCGCCGATGTCAGAAAAACAGCTGGCTGACGTCGTGGAACGTACCGTTACGCCCCTGATGAAGGCGCAGGCCATACCCGGAATGGCCGTGGCCGTCATTTATCAGGGCCAGCCACACTATTTTACTTTCGGTAAAGCAGACGTTGCGGCGAATAAGCCCGTCACGCCGCAAACCTTATTTGAGCTGGGCTCCGTCAGCAAAACCTTCACCGGCGTGCTGGGTGGCGATGCCATTGCCCGCAAAGAGATTTCGCTGGCCGACCCGGTCACGAAATATTGGCCTGAATTGACGGGCAAGCAGTGGCAAGGCATTCGCCTGCTAGACCTGGCAACCTATACCGCAGGCGGATTGCCGTTGCAGGTACCGGATGATGTCACCGATAACGCCTCTCTGCTGCGTTTCTACCAGTCCTGGCAGCCAAAGTGGGCCCCGGGTACCACGCGTCTGTACGCCAACACCAGCATCGGTTTGTTTGGCTCACTGGCCGTTAAACCGTCCGGCATGTGCTTCGAGCAGGCCATGGCGGAGCGGGTCTTTAAGCCCCTGAAACTCAACCATACGTGGATAAACGTTCCACACGCTGAAGAACCGCACTACGCATGGGGTTATCGTGAGGGAAAAGCGGTCCACGTTTCGCCTGGTATGCTGGATGCAGAAGCCTATGGCGTGAAATCTAACGTCAAAGATATGGCGAGTTGGGTGATGGCCAATATGGCACCTGAGACACTCCCGCAGTCCACTCTGCAGCAGGGTATTGCGCTGGCGCAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAAGGGTTAGGCTGGGAGATGCTCAACTGGCCGGTCGATGCCAAAACCGTGGTGGATGGCAGCGATAATAAGGTCGCACTGGCGCCGTTGCCGGTCGCAGAAGTGAATCCTCCGGCTCCGCCAGTAAAAGCCTCCTGGGTGCATAAAACGGGCTCTACGGGTGGGTTTGGCAGCTACGTGGCGTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCAAATAAAAGCTATCCGAACCCGGTACGGGTGGAAACGGCTTACCGTATCCTCGACGCGCTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3008093","ARO_id":"46885","ARO_name":"CMH-18","CARD_short_name":"CMH-18","ARO_description":"Class C beta-lactamase CMH-18.","ARO_category":{"42891":{"category_aro_accession":"3004776","category_aro_cvterm_id":"42891","category_aro_name":"CMH beta-lactamase","category_aro_description":"CMH is a class C beta-lactamase gene family belonging to Enterobacter cloacae.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7512":{"model_id":"7512","model_name":"CMH-19","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10339":{"protein_sequence":{"accession":"AVL16970.1","sequence":"MMKKSLSCALLLSVACSAFAAPMSEKQLADVVERTVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSVSKTFTGVLGGDAIARKEISLADPVTKYWPDLTGKQWQGIRLLDLATYTAGGLPLQVPDDVTDNASLLRFYQSWQPKWAPGTTRLYANTSIGLFGSLAVKPSGMRFEQAMAERVFKPLKLNHTWINVPHAEEPHYAWGYREGKAVHVSPGMLDAEAYGVKSNVKDMASWVMANMAPETLPPSTLQQGIALAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVDGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANKSYPNPVRVETAYRILDALH"},"dna_sequence":{"accession":"CP020089.1","fmin":"475586","fmax":"476732","strand":"-","sequence":"ATGATGAAAAAATCCCTAAGCTGCGCCCTGCTGCTCAGCGTTGCCTGCTCTGCTTTTGCCGCGCCGATGTCAGAAAAACAGCTGGCTGACGTCGTGGAACGTACCGTTACGCCCCTGATGAAGGCGCAGGCCATACCCGGTATGGCCGTGGCCGTCATTTATCAGGGCCAGCCACACTATTTTACTTTCGGTAAAGCAGACGTTGCGGCGAATAAGCCCGTCACGCCGCAAACCTTATTTGAGCTGGGCTCCGTCAGCAAAACCTTCACCGGCGTGCTGGGTGGCGATGCCATTGCCCGCAAAGAGATTTCGCTGGCCGACCCGGTCACGAAATATTGGCCTGATTTGACGGGCAAGCAGTGGCAAGGCATTCGCCTGCTCGACCTGGCAACCTATACCGCAGGCGGATTGCCGTTGCAGGTACCGGATGATGTCACCGATAACGCCTCTCTGCTGCGTTTCTACCAGTCCTGGCAGCCAAAGTGGGCACCGGGTACCACGCGTCTGTACGCCAACACCAGCATCGGTTTGTTTGGCTCACTGGCCGTTAAACCTTCCGGCATGCGCTTCGAGCAGGCCATGGCGGAGCGGGTCTTTAAGCCCCTGAAACTCAACCATACGTGGATAAACGTTCCACACGCTGAAGAGCCGCACTACGCATGGGGTTATCGTGAGGGAAAAGCGGTCCACGTTTCGCCTGGTATGCTGGATGCAGAAGCCTATGGCGTGAAATCTAACGTCAAAGATATGGCGAGCTGGGTGATGGCCAATATGGCACCTGAGACACTCCCGCCGTCCACTCTGCAGCAGGGTATTGCGCTGGCGCAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAAGGGTTAGGCTGGGAGATGCTCAACTGGCCGGTCGATGCCAAAACCGTGGTGGATGGCAGCGATAATAAGGTTGCACTGGCGCCGTTGCCGGTCGCAGAAGTGAATCCTCCGGCTCCGCCAGTAAAAGCCTCCTGGGTGCATAAAACGGGCTCTACGGGTGGGTTTGGCAGCTACGTGGCGTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCAAATAAAAGCTATCCGAACCCGGTACGGGTGGAAACGGCTTACCGTATCCTCGACGCGCTACACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3008094","ARO_id":"46886","ARO_name":"CMH-19","CARD_short_name":"CMH-19","ARO_description":"Class C beta-lactamase CMH-19.","ARO_category":{"42891":{"category_aro_accession":"3004776","category_aro_cvterm_id":"42891","category_aro_name":"CMH beta-lactamase","category_aro_description":"CMH is a class C beta-lactamase gene family belonging to Enterobacter cloacae.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7513":{"model_id":"7513","model_name":"CMH-20","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10340":{"protein_sequence":{"accession":"CZX96154.1","sequence":"MMKKSLSCALLLSVACSAFAAPMSEKQLADVVERTVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSVSKTFTGVLGGDAIARKEISLADPVTKYWPELTGKQWQGIRLLDLATYTAGGLPLQVPDAVTDNASLLRFYQSWQPKWAPGTTRLYANTSIGLFGSLAVKLSGMRFEQAMAERVFKPLKLNHTWINVPHAEESHYAWGYREGKAVHVSPGMLDAEAYGVKSNVKDMASWVMANMAPETLPQSTLQQGIALAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVDGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANKSYPNPVRVETAYRILETLQ"},"dna_sequence":{"accession":"FJYH01000022.1","fmin":"17564","fmax":"18710","strand":"-","sequence":"ATGATGAAAAAATCCCTAAGCTGCGCCCTGCTGCTCAGCGTTGCCTGCTCTGCTTTTGCCGCGCCGATGTCAGAAAAACAGCTGGCTGACGTCGTGGAACGTACCGTTACGCCCCTGATGAAGGCGCAGGCCATACCCGGTATGGCCGTGGCCGTCATTTATCAGGGCCAGCCACACTATTTTACTTTCGGTAAAGCAGACGTTGCGGCGAATAAGCCCGTCACGCCGCAAACCTTATTTGAGCTGGGCTCCGTCAGTAAAACCTTCACTGGCGTGCTGGGTGGCGATGCCATTGCCCGCAAAGAGATTTCGCTGGCCGACCCGGTCACAAAATATTGGCCTGAATTGACGGGCAAGCAGTGGCAAGGCATTCGCCTGCTAGACCTGGCAACCTATACCGCAGGCGGATTGCCGTTGCAGGTACCGGATGCTGTCACCGATAACGCCTCTCTGCTGCGTTTCTACCAGTCCTGGCAGCCAAAGTGGGCCCCGGGTACCACGCGTCTGTACGCCAACACCAGCATCGGTTTGTTTGGCTCACTGGCTGTGAAACTGTCCGGCATGCGCTTCGAGCAGGCCATGGCGGAGCGGGTCTTTAAGCCCCTGAAACTCAACCATACGTGGATAAACGTTCCACACGCTGAAGAGTCGCACTACGCATGGGGTTATCGTGAGGGAAAAGCGGTCCACGTTTCGCCTGGTATGCTGGATGCAGAAGCCTATGGCGTGAAATCTAACGTCAAAGATATGGCGAGCTGGGTGATGGCCAATATGGCACCTGAGACACTCCCGCAGTCCACTCTGCAGCAGGGTATTGCGCTGGCGCAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAAGGGTTAGGCTGGGAGATGCTCAACTGGCCGGTCGATGCCAAAACCGTGGTGGATGGCAGCGATAATAAGGTTGCACTGGCGCCGTTGCCGGTCGCAGAAGTGAATCCTCCGGCTCCGCCAGTAAAAGCCTCCTGGGTGCATAAAACGGGCTCTACGGGTGGGTTTGGCAGCTACGTGGCGTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCAAATAAAAGCTATCCGAACCCGGTACGGGTGGAAACGGCTTACCGTATTCTCGAGACGCTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3008095","ARO_id":"46887","ARO_name":"CMH-20","CARD_short_name":"CMH-20","ARO_description":"Class C beta-lactamase CMH-20.","ARO_category":{"42891":{"category_aro_accession":"3004776","category_aro_cvterm_id":"42891","category_aro_name":"CMH beta-lactamase","category_aro_description":"CMH is a class C beta-lactamase gene family belonging to Enterobacter cloacae.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7514":{"model_id":"7514","model_name":"CMH-21","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10341":{"protein_sequence":{"accession":"ELV2836914.1","sequence":"MMKKSLSCALLLSVACSAFAAPMSEKQLADVVERTVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSVSKTFTGVLGGDAIARKEISLADPVTKYWPELTGKQWQGIRLLDLATYTAGGLPLQVPDDVTDNASLLRFYQSWQPKWAPGTTRLYANTSIGLFGSLAVKPSGMRFEQAMAERVFKPLKLNHTWINVPHAEEPHYAWGYREGKAVHVSPGMLDAEAYGVKSNVKDMASWVMANMAPEALPQSTLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVDVKTVVDGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANKSYPNPVRVETAYRILDALQ"},"dna_sequence":{"accession":"ABOSQX010000067.1","fmin":"10030","fmax":"11176","strand":"+","sequence":"ATGATGAAAAAATCCCTAAGCTGCGCCCTGCTGCTCAGCGTTGCTTGCTCTGCTTTTGCCGCGCCGATGTCAGAAAAACAGCTGGCTGACGTCGTGGAACGTACCGTTACGCCCCTGATGAAGGCGCAGGCCATACCCGGAATGGCCGTGGCCGTCATTTATCAGGGCCAGCCACACTATTTTACTTTCGGTAAAGCAGACGTTGCGGCGAATAAGCCCGTCACGCCGCAAACCTTATTTGAGCTGGGCTCCGTCAGTAAAACCTTCACTGGCGTGCTGGGTGGCGATGCCATTGCCCGCAAAGAGATTTCGCTGGCCGACCCGGTCACGAAATACTGGCCTGAATTGACGGGCAAGCAGTGGCAAGGCATTCGCCTGCTCGACCTGGCAACCTATACCGCAGGCGGATTGCCGTTGCAGGTACCGGATGATGTCACCGATAACGCCTCTCTGCTGCGTTTCTACCAGTCCTGGCAGCCAAAGTGGGCCCCGGGTACCACGCGTCTGTACGCCAACACCAGCATCGGTTTGTTTGGCTCACTGGCCGTTAAACCGTCCGGCATGCGCTTCGAGCAGGCCATGGCGGAGCGGGTCTTTAAGCCCCTGAAACTCAACCATACGTGGATAAACGTTCCACACGCTGAAGAGCCGCACTACGCATGGGGTTATCGTGAGGGAAAAGCGGTCCACGTTTCGCCTGGTATGCTGGATGCAGAAGCCTATGGCGTGAAATCTAACGTCAAAGATATGGCGAGCTGGGTGATGGCCAATATGGCACCTGAGGCACTCCCGCAGTCCACTCTGAAGCAGGGTATTGCTCTGGCGCAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAAGGGTTAGGCTGGGAGATGCTCAACTGGCCGGTCGACGTCAAAACCGTGGTGGATGGCAGCGATAATAAGGTTGCACTGGCGCCGTTGCCGGTCGCAGAAGTGAATCCTCCGGCTCCGCCAGTAAAAGCCTCCTGGGTGCATAAAACGGGCTCTACGGGTGGGTTTGGCAGCTACGTGGCGTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCAAATAAAAGCTATCCGAACCCGGTACGGGTGGAAACGGCTTACCGTATCCTCGACGCGCTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3008096","ARO_id":"46888","ARO_name":"CMH-21","CARD_short_name":"CMH-21","ARO_description":"Class C beta-lactamase CMH-21.","ARO_category":{"42891":{"category_aro_accession":"3004776","category_aro_cvterm_id":"42891","category_aro_name":"CMH beta-lactamase","category_aro_description":"CMH is a class C beta-lactamase gene family belonging to Enterobacter cloacae.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7515":{"model_id":"7515","model_name":"CMH-24","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10342":{"protein_sequence":{"accession":"UOZ00392.1","sequence":"MMKKSLSCALLLSVACSAFAAPMSEKQLADVVERTVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSVSKTFTGVLGGDAIARKEISLADPVTKYWPELTGKQWQGIRLLDLATYTAGGLPLQVPDDVTDNASLLRFYQSWQPKWAPGTTRLYANTSIGLFGSLAVKPSGMRFEQAMVERVFKPLKLNHTWINVPHAEEPHYAWGYREGKAVHVSPGMLDAEAYGVKSNVKDMASWLMANMAPETLPQSTLQQGIALAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVDGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANKSYPNPVRVETAYRILETLQ"},"dna_sequence":{"accession":"CP083821.1","fmin":"433961","fmax":"435107","strand":"-","sequence":"ATGATGAAAAAATCCCTAAGCTGCGCCCTGCTGCTCAGCGTTGCCTGCTCTGCTTTTGCCGCGCCGATGTCAGAAAAACAGCTGGCTGACGTCGTGGAACGTACAGTTACGCCCCTGATGAAGGCGCAGGCCATACCCGGAATGGCCGTGGCCGTCATTTATCAGGGCCAGCCACACTATTTTACTTTCGGTAAAGCAGACGTCGCGGCGAATAAGCCCGTCACGCCGCAAACCTTATTTGAGCTGGGCTCCGTCAGCAAAACCTTCACCGGCGTGCTGGGTGGCGATGCCATTGCCCGCAAAGAGATTTCGCTGGCCGACCCGGTCACGAAATATTGGCCTGAATTGACGGGCAAGCAGTGGCAAGGCATTCGCCTGCTCGACCTGGCAACCTATACCGCAGGCGGATTGCCGTTGCAGGTGCCGGATGATGTCACCGATAATGCCTCTCTGCTGCGTTTCTACCAGTCCTGGCAGCCAAAGTGGGCCCCGGGTACCACGCGTCTGTACGCCAACACCAGCATCGGCCTGTTTGGCTCACTGGCCGTTAAACCTTCCGGCATGCGCTTCGAGCAGGCCATGGTGGAGCGGGTCTTTAAGCCCCTGAAACTCAACCATACATGGATAAACGTTCCACACGCTGAAGAGCCGCACTACGCATGGGGTTATCGTGAGGGAAAAGCGGTCCACGTTTCGCCTGGTATGCTGGATGCAGAAGCCTATGGCGTGAAATCTAACGTCAAAGATATGGCGAGCTGGTTGATGGCCAATATGGCACCTGAGACACTCCCGCAGTCCACTCTGCAGCAGGGGATTGCGCTGGCGCAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAAGGGTTAGGCTGGGAGATGCTCAACTGGCCGGTCGACGCCAAAACCGTGGTGGATGGCAGCGATAATAAGGTTGCACTGGCGCCGTTGCCGGTCGCAGAAGTGAATCCTCCGGCTCCGCCAGTAAAAGCCTCCTGGGTGCATAAAACGGGCTCTACGGGTGGGTTTGGCAGCTACGTGGCGTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCAAATAAAAGCTATCCGAACCCGGTACGGGTGGAAACGGCTTACCGTATTCTCGAGACGCTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3008097","ARO_id":"46889","ARO_name":"CMH-24","CARD_short_name":"CMH-24","ARO_description":"Class C beta-lactamase CMH-24.","ARO_category":{"42891":{"category_aro_accession":"3004776","category_aro_cvterm_id":"42891","category_aro_name":"CMH beta-lactamase","category_aro_description":"CMH is a class C beta-lactamase gene family belonging to Enterobacter cloacae.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7516":{"model_id":"7516","model_name":"CMH-25","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10343":{"protein_sequence":{"accession":"MDQ7216156.1","sequence":"MMKKSLSCALLFSVASSAFAAPMSEKQLADVVERTVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSVSKTFTGVLGGDAIARKEISLADPVTKYWPELTGKQWQGIRLLDLATYTAGGLPLQVPDDVTDNASLLRFYQSWQPKWAPGTTRLYANTSIGLFGSLAVKPSGMRFEQAMAERVFKPLKLNHTWINVPHAEEPHYAWGYREGKAVHVSPGMLDAEAYGVKSNVKDMASWVMANMAPETLPQPTLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVDVKTVVDGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANKSYPNPVRVETAYRILETLQ"},"dna_sequence":{"accession":"JAVGVQ010000056.1","fmin":"17355","fmax":"18501","strand":"-","sequence":"ATGATGAAAAAATCCCTAAGCTGCGCGCTGCTGTTCAGCGTTGCCAGCTCTGCTTTTGCCGCGCCGATGTCAGAAAAACAGCTGGCAGACGTCGTGGAACGTACCGTTACGCCCCTGATGAAGGCGCAGGCCATACCCGGTATGGCCGTGGCCGTCATTTATCAGGGCCAGCCACACTATTTTACTTTCGGTAAAGCAGACGTCGCGGCGAATAAGCCCGTCACGCCGCAAACCTTATTTGAGCTGGGCTCCGTCAGCAAAACCTTCACCGGCGTGCTGGGTGGCGATGCCATCGCCCGCAAAGAGATTTCACTGGCCGACCCGGTCACGAAATATTGGCCAGAATTGACGGGCAAGCAGTGGCAAGGCATTCGCCTGCTCGACCTGGCAACCTATACCGCAGGCGGATTGCCGTTGCAGGTACCGGATGATGTCACCGATAACGCCTCTCTGCTGCGTTTCTACCAGTCCTGGCAGCCAAAGTGGGCCCCGGGTACCACGCGTCTGTACGCCAACACCAGCATCGGCCTGTTTGGCTCACTGGCCGTTAAACCTTCCGGCATGCGCTTCGAGCAGGCCATGGCGGAGCGGGTCTTTAAGCCCCTGAAACTCAACCATACGTGGATAAACGTTCCACACGCTGAAGAGCCGCACTACGCATGGGGTTATCGTGAGGGAAAAGCGGTCCACGTTTCGCCTGGTATGCTGGATGCAGAAGCCTATGGCGTGAAATCTAACGTCAAAGATATGGCGAGCTGGGTGATGGCCAATATGGCACCTGAGACACTCCCGCAGCCCACTCTGAAGCAGGGTATTGCGCTGGCGCAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAAGGGTTAGGCTGGGAGATGCTCAACTGGCCGGTCGACGTCAAAACCGTGGTGGATGGCAGCGACAATAAGGTCGCACTGGCGCCGTTGCCGGTCGCAGAAGTGAATCCTCCGGCTCCGCCAGTAAAAGCCTCCTGGGTGCATAAAACGGGCTCTACGGGTGGGTTTGGCAGCTACGTGGCGTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCAAATAAAAGCTATCCGAACCCGGTACGGGTGGAAACGGCTTACCGTATTCTCGAGACGCTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3008098","ARO_id":"46890","ARO_name":"CMH-25","CARD_short_name":"CMH-25","ARO_description":"Class C beta-lactamase CMH-25.","ARO_category":{"42891":{"category_aro_accession":"3004776","category_aro_cvterm_id":"42891","category_aro_name":"CMH beta-lactamase","category_aro_description":"CMH is a class C beta-lactamase gene family belonging to Enterobacter cloacae.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7520":{"model_id":"7520","model_name":"CMH-29","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10347":{"protein_sequence":{"accession":"XAJ73535.1","sequence":"MMKKSLSCALLLSVACSAFAAPMSEKQLADVVERTITPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSVSKTFTGVLGGDAIARKEISLADPVTKYWPELTGKQWQGIRLLDLATYTAGGLPLQVPDDVTDNVSLLRFYQSWQPEWAPGTTRLYANTSIGLFGSLAVKPSGMRFEQAMAERVFKPLKLNHTWINVPHAEEPHYAWGYREGKAVHVSPGMLDAEAYGVKSNVKDMASWVMANMAPETLPQSTLQQGIALAQSRYWRVGAMYQGLGWEMLNWPVDVKTVVDGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANKSYPNPVRVETAYRILDALQ"},"dna_sequence":{"accession":"PP740469.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCCCTAAGCTGCGCGCTGTTGCTCAGCGTTGCCTGCTCTGCTTTTGCCGCGCCGATGTCAGAAAAACAGCTGGCTGACGTCGTGGAACGTACCATTACGCCCCTGATGAAGGCGCAGGCCATACCCGGAATGGCGGTGGCCGTCATTTATCAGGGCCAGCCACACTATTTTACTTTCGGTAAAGCAGACGTCGCGGCGAATAAGCCCGTCACGCCGCAAACCTTATTTGAGCTGGGCTCCGTCAGCAAAACCTTCACCGGCGTGCTGGGTGGCGATGCCATTGCCCGCAAAGAGATTTCACTGGCCGACCCAGTCACGAAATATTGGCCTGAATTGACGGGCAAGCAGTGGCAAGGCATTCGCCTGCTCGACCTGGCAACCTATACCGCAGGCGGATTGCCGTTGCAGGTACCGGATGATGTCACCGATAACGTCTCTCTGCTGCGTTTCTACCAGTCCTGGCAGCCAGAGTGGGCTCCGGGTACCACGCGTCTGTACGCCAACACCAGCATCGGCCTGTTTGGCTCACTGGCCGTTAAACCGTCCGGCATGCGCTTCGAGCAGGCCATGGCGGAGCGGGTCTTTAAGCCCCTGAAACTCAACCATACGTGGATAAACGTTCCACACGCTGAAGAGCCGCACTACGCATGGGGTTATCGTGAGGGAAAAGCGGTCCACGTTTCGCCTGGTATGCTGGATGCAGAAGCCTATGGCGTGAAATCTAACGTCAAAGATATGGCGAGCTGGGTGATGGCCAATATGGCACCTGAGACACTCCCGCAGTCCACTCTGCAGCAGGGTATTGCGCTGGCGCAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAAGGGTTAGGCTGGGAGATGCTCAACTGGCCGGTCGACGTCAAAACCGTGGTGGATGGCAGCGACAATAAGGTCGCACTGGCGCCGTTGCCGGTCGCAGAAGTGAATCCTCCGGCTCCGCCAGTAAAAGCCTCCTGGGTGCATAAAACGGGCTCTACGGGTGGGTTTGGCAGCTACGTGGCGTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCAAATAAAAGCTATCCGAACCCGGTACGGGTGGAAACGGCTTACCGTATCCTCGACGCGCTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3008102","ARO_id":"46894","ARO_name":"CMH-29","CARD_short_name":"CMH-29","ARO_description":"Class C beta-lactamase CMH-29.","ARO_category":{"42891":{"category_aro_accession":"3004776","category_aro_cvterm_id":"42891","category_aro_name":"CMH beta-lactamase","category_aro_description":"CMH is a class C beta-lactamase gene family belonging to Enterobacter cloacae.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7521":{"model_id":"7521","model_name":"CMH-30","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10348":{"protein_sequence":{"accession":"XAJ73536.1","sequence":"MMKKSLSCALLLSVACSAFAAPMSEKQLADVVERTVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSVSKTFTGVLGGDAIARKEISLADPVTKYWPELTGKQWQGIRLLDLATYTAGGLPLQVPDDVTDNASLLRFYQSWQPKWAPGTTRLYANTSIGLFGSLAVKPSGMRFEQAMAERVFKPLKLNHTWINVPHAEEPHYAWGYREGKAVHVSPGMLDAEAYGVKSNVKDMASWVMANMAPEALPQSTLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVDVKTVVDGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANKSYPNPVRVETAYRILDALH"},"dna_sequence":{"accession":"PP740470.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCCCTAAGCTGCGCCCTGCTGCTCAGCGTTGCTTGCTCTGCTTTTGCCGCGCCGATGTCAGAAAAACAGCTGGCTGACGTCGTGGAACGTACCGTTACGCCCCTGATGAAGGCGCAGGCCATACCCGGAATGGCCGTGGCCGTCATTTATCAGGGCCAGCCACACTATTTTACTTTCGGTAAAGCAGACGTTGCGGCGAATAAGCCCGTCACGCCGCAAACCTTATTTGAGCTGGGCTCCGTCAGTAAAACCTTCACTGGCGTGCTGGGTGGCGATGCCATTGCCCGCAAAGAGATTTCGCTGGCCGACCCGGTCACGAAATACTGGCCTGAATTGACGGGCAAGCAGTGGCAAGGCATTCGCCTGCTCGACCTGGCAACCTATACCGCAGGCGGATTGCCGTTGCAGGTACCGGATGATGTCACCGATAACGCCTCTCTGCTGCGTTTCTACCAGTCCTGGCAGCCAAAGTGGGCCCCGGGTACCACGCGTCTGTACGCCAACACCAGCATCGGTTTGTTTGGCTCACTGGCCGTTAAACCGTCCGGCATGCGCTTCGAGCAGGCCATGGCGGAGCGGGTCTTTAAGCCCCTGAAACTCAACCATACGTGGATAAACGTTCCACACGCTGAAGAGCCGCACTACGCATGGGGTTATCGTGAGGGAAAAGCGGTCCACGTTTCGCCTGGTATGCTGGATGCAGAAGCCTATGGCGTGAAATCTAACGTCAAAGATATGGCGAGCTGGGTGATGGCCAATATGGCACCTGAGGCACTCCCGCAGTCCACTCTGAAGCAGGGTATTGCTCTGGCGCAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAAGGGTTAGGCTGGGAGATGCTCAACTGGCCGGTCGACGTCAAAACCGTGGTGGATGGCAGCGATAATAAGGTTGCACTGGCGCCGTTGCCGGTCGCAGAAGTGAATCCTCCGGCTCCGCCAGTAAAAGCCTCCTGGGTGCATAAAACGGGCTCTACGGGTGGGTTTGGCAGCTACGTGGCGTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCAAATAAAAGCTATCCGAACCCGGTACGGGTGGAAACGGCTTACCGTATCCTCGACGCGCTACATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3008103","ARO_id":"46895","ARO_name":"CMH-30","CARD_short_name":"CMH-30","ARO_description":"Class C beta-lactamase CMH-30.","ARO_category":{"42891":{"category_aro_accession":"3004776","category_aro_cvterm_id":"42891","category_aro_name":"CMH beta-lactamase","category_aro_description":"CMH is a class C beta-lactamase gene family belonging to Enterobacter cloacae.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7522":{"model_id":"7522","model_name":"CMH-31","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10349":{"protein_sequence":{"accession":"XAJ73537.1","sequence":"MMKKSLSCALLLSVACSAFAAPMSEKQLADVVERTVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSVSKTFTGVLGGDAIARKEISLADPVTKYWPELTGKQWQGIRLLDLATYTAGGLPLQVPDDVTDNASLLRFYQSWQPKWAPGTTRLYANTSIGLFGSLAVKPSGMRFEQAMAERVFKPLKLNHTWINVPHAEEPHYAWGYREGKAVHVSPGMLDAEAYGVKSNVKDMASWVMANMAPETLPQPTLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVDGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANKSYPNPVRVETAYRILETLQ"},"dna_sequence":{"accession":"PP740471.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCCCTAAGCTGCGCGCTGCTGCTCAGCGTTGCCTGCTCTGCTTTTGCCGCGCCGATGTCAGAAAAACAGCTGGCAGACGTCGTGGAACGTACCGTTACGCCCCTGATGAAGGCGCAGGCCATACCCGGTATGGCCGTGGCCGTCATTTATCAGGGCCAGCCACACTATTTTACTTTCGGTAAAGCAGACGTTGCGGCGAATAAGCCCGTCACGCCGCAAACCTTATTTGAGCTGGGCTCCGTCAGCAAAACCTTCACCGGCGTGCTGGGTGGCGATGCCATTGCCCGCAAAGAGATTTCGCTGGCCGACCCGGTCACGAAATATTGGCCTGAATTGACGGGCAAGCAGTGGCAAGGCATTCGCCTGCTAGACCTGGCAACCTATACCGCAGGCGGATTGCCGTTGCAGGTACCGGATGATGTCACCGATAACGCCTCTCTGCTGCGTTTCTACCAGTCCTGGCAGCCAAAGTGGGCCCCGGGTACCACGCGTCTGTACGCCAACACCAGCATCGGCCTGTTTGGCTCACTGGCCGTTAAACCGTCCGGCATGCGCTTCGAGCAGGCCATGGCGGAGCGGGTCTTTAAGCCCCTGAAACTCAACCATACGTGGATAAACGTTCCACACGCTGAAGAGCCGCACTACGCATGGGGTTATCGTGAGGGAAAAGCGGTCCACGTTTCGCCTGGTATGCTGGATGCAGAAGCCTATGGCGTGAAATCTAACGTCAAAGATATGGCGAGCTGGGTGATGGCCAATATGGCACCTGAGACACTCCCGCAGCCCACTCTGAAGCAGGGTATTGCGCTGGCGCAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAAGGGTTAGGCTGGGAGATGCTCAACTGGCCGGTCGACGCCAAAACCGTGGTGGATGGCAGCGATAATAAGGTTGCACTGGCGCCGTTGCCGGTCGCAGAAGTGAATCCTCCGGCTCCGCCAGTAAAAGCCTCCTGGGTGCATAAAACGGGCTCTACGGGTGGGTTTGGCAGCTACGTGGCGTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCAAATAAAAGTTATCCGAACCCGGTACGGGTGGAAACGGCTTACCGTATTCTCGAGACGCTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3008104","ARO_id":"46896","ARO_name":"CMH-31","CARD_short_name":"CMH-31","ARO_description":"Class C beta-lactamase CMH-31.","ARO_category":{"42891":{"category_aro_accession":"3004776","category_aro_cvterm_id":"42891","category_aro_name":"CMH beta-lactamase","category_aro_description":"CMH is a class C beta-lactamase gene family belonging to Enterobacter cloacae.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7523":{"model_id":"7523","model_name":"CMH-32","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10350":{"protein_sequence":{"accession":"XAJ73538.1","sequence":"MMKKSLSCALLLSVACSAFAAPMSEKQLANAVERNVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSVSKTFTGVLGGDAIARKEISLADPVTKYWPELTGKQWQGIRLLDLATYTAGGLPLQVPDAVTDNASLLRFYQSWQPKWAPGTTRLYANTSIGLFGSLAVKPSGMHFEEAMTERVFKPLKLNHTWINIPHAEEPHYAWGYREGKAVHVSPGLLDAEAYGVKSNVKDMASWVMANMAPDTIQQPSLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVEAKTVVDGSDNKVALAPLPAAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANKSYPNPLRVETAYRILDTLQ"},"dna_sequence":{"accession":"PP740472.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCCCTAAGCTGTGCCCTGTTGCTCAGCGTTGCCTGCTCTGCCTTTGCCGCGCCAATGTCAGAAAAACAGCTGGCTAACGCCGTGGAACGTAACGTTACGCCCCTGATGAAAGCGCAGGCCATACCCGGTATGGCCGTGGCTGTCATTTATCAGGGTCAGCCGCACTATTTTACTTTTGGTAAAGCAGACGTTGCAGCGAATAAGCCTGTCACACCGCAAACCTTATTTGAGCTGGGCTCCGTCAGCAAAACTTTCACCGGCGTGCTGGGTGGCGATGCCATTGCCCGCAAAGAGATCTCGCTGGCCGACCCGGTCACGAAATATTGGCCTGAATTGACGGGCAAGCAGTGGCAGGGCATTCGCCTGCTCGATCTGGCAACCTATACCGCAGGTGGATTGCCGTTGCAGGTGCCGGATGCTGTCACCGATAACGCCTCTCTGCTGCGTTTCTACCAGTCCTGGCAGCCAAAGTGGGCCCCGGGTACTACGCGTCTGTACGCCAACACCAGCATCGGTTTGTTTGGCTCACTGGCGGTTAAACCTTCCGGCATGCACTTTGAGGAGGCCATGACGGAGCGGGTCTTTAAGCCCCTGAAACTCAACCATACGTGGATAAACATTCCACACGCTGAAGAGCCGCATTACGCATGGGGTTATCGTGAGGGTAAAGCGGTCCACGTTTCGCCGGGTCTGCTGGATGCAGAAGCCTATGGCGTGAAATCTAACGTCAAAGATATGGCGAGCTGGGTGATGGCCAATATGGCACCGGACACAATCCAGCAGCCCTCTCTGAAGCAGGGTATTGCGCTGGCGCAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAAGGGTTAGGCTGGGAGATGCTCAACTGGCCGGTGGAGGCCAAAACAGTAGTGGATGGCAGCGACAATAAGGTTGCACTGGCGCCGTTACCGGCAGCAGAAGTGAATCCTCCGGCTCCGCCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCTACGGGGGGGTTTGGCAGCTACGTGGCGTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATAAAAGCTATCCGAACCCGCTACGGGTGGAAACGGCTTACCGTATCCTCGACACGCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3008105","ARO_id":"46897","ARO_name":"CMH-32","CARD_short_name":"CMH-32","ARO_description":"Class C beta-lactamase CMH-32.","ARO_category":{"42891":{"category_aro_accession":"3004776","category_aro_cvterm_id":"42891","category_aro_name":"CMH beta-lactamase","category_aro_description":"CMH is a class C beta-lactamase gene family belonging to Enterobacter cloacae.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7524":{"model_id":"7524","model_name":"CMH-33","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10351":{"protein_sequence":{"accession":"XAJ73539.1","sequence":"MMKKSLSCALLLSVACSAFAAPMSEKQLADVVERTVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVAVNKPVTPQTLFELGSVSKTFTGVLGGDAIARKEISLADPVTKYWPELTGNQWQGIRLLDLATYTAGGLPLQVPDDVTDNASLLRFYQSWQPKWAPGTTRLYANTSIGLFGSLAVKPSGMRFEQAMAERVFKPLKLNHTWINVPHAEEPHYAWGYREGKAVHVSPGMLDAEAYGVKSNVKDMASWVMANMAPETLPQSTLQQGITLAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVDGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANKSYPNPVRVETAYRILDALQ"},"dna_sequence":{"accession":"PP740473.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCCCTAAGCTGCGCCCTGCTGCTCAGCGTTGCTTGCTCTGCTTTTGCCGCGCCGATGTCAGAAAAACAGCTGGCTGACGTCGTGGAACGTACCGTTACGCCCCTGATGAAGGCGCAGGCCATACCTGGTATGGCCGTGGCCGTCATTTATCAGGGCCAGCCACACTATTTTACTTTCGGTAAAGCAGACGTCGCGGTGAATAAGCCCGTCACGCCGCAAACCTTATTTGAACTGGGCTCCGTCAGTAAAACCTTCACTGGCGTGCTGGGTGGCGATGCCATTGCCCGCAAAGAGATTTCGCTGGCCGACCCGGTCACGAAATACTGGCCTGAATTGACGGGCAATCAGTGGCAAGGCATTCGCCTGCTCGACCTGGCAACCTATACCGCAGGCGGATTGCCGTTGCAGGTACCGGATGATGTCACCGATAACGCCTCTCTGCTGCGTTTCTACCAGTCCTGGCAGCCAAAGTGGGCCCCGGGTACCACGCGTCTGTACGCCAACACCAGCATCGGTTTGTTTGGCTCACTGGCCGTTAAACCGTCCGGCATGCGCTTCGAGCAGGCCATGGCGGAGCGGGTCTTTAAGCCCCTGAAACTCAACCATACGTGGATAAACGTTCCACACGCTGAAGAGCCGCACTACGCATGGGGTTATCGTGAGGGAAAAGCGGTCCACGTTTCGCCTGGTATGCTGGATGCAGAAGCCTATGGCGTGAAATCTAACGTCAAAGATATGGCGAGCTGGGTGATGGCCAATATGGCACCTGAGACACTCCCGCAGTCCACTCTGCAGCAGGGTATTACGCTGGCGCAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAAGGGTTAGGCTGGGAGATGCTCAACTGGCCGGTCGACGCCAAAACCGTGGTGGATGGCAGCGACAATAAGGTCGCACTGGCGCCGTTGCCGGTCGCAGAAGTGAATCCTCCGGCTCCGCCAGTAAAAGCCTCCTGGGTGCATAAAACGGGCTCTACGGGTGGGTTTGGCAGCTACGTGGCGTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCAAATAAAAGCTATCCGAACCCGGTACGGGTGGAAACGGCTTACCGTATCCTCGACGCGCTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3008106","ARO_id":"46898","ARO_name":"CMH-33","CARD_short_name":"CMH-33","ARO_description":"Class C beta-lactamase CMH-33.","ARO_category":{"42891":{"category_aro_accession":"3004776","category_aro_cvterm_id":"42891","category_aro_name":"CMH beta-lactamase","category_aro_description":"CMH is a class C beta-lactamase gene family belonging to Enterobacter cloacae.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7525":{"model_id":"7525","model_name":"CMH-34","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10352":{"protein_sequence":{"accession":"XAJ73540.1","sequence":"MMKKSLSCALLLSVACSAFAAPMSEKQLANVVERNVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSVSKTFTGVLGGDAIARKEISLADPVTKYWPELTGKQWQGIRLLDLATYTAGGLPLQVPDAVTDNASLLRFYQSWQPKWAPGTTRLYANTSIGLFGSLAVKPSGMRFEEAMTERVFKPLKLNHTWINIPHAEEPHYAWGYREGKAVHVSPGMLDAEAYGVKSNVKDMASWVMANMAPETIQQPALKQGIALAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVDGSDNKVALAPLPAAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANKSYPNPLRVETAYRILDTLQ"},"dna_sequence":{"accession":"PP740474.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCCCTAAGCTGTGCCCTGTTGCTCAGCGTTGCCTGCTCTGCCTTTGCCGCGCCAATGTCAGAAAAACAGCTGGCTAACGTCGTGGAACGTAACGTTACGCCCCTGATGAAAGCGCAGGCCATACCCGGTATGGCCGTGGCTGTCATTTATCAGGGTCAGCCGCACTATTTTACTTTTGGTAAAGCAGACGTCGCAGCGAATAAACCTGTCACACCGCAAACCTTATTTGAGCTGGGCTCCGTCAGCAAAACTTTCACCGGCGTGCTGGGTGGCGATGCCATTGCCCGCAAAGAGATCTCGCTGGCCGACCCGGTCACGAAATATTGGCCTGAATTGACGGGCAAGCAGTGGCAGGGCATTCGCCTGCTCGATCTGGCAACCTATACCGCAGGTGGATTGCCGTTGCAGGTACCGGATGCTGTCACCGATAACGCCTCTCTGCTGCGTTTCTACCAGTCCTGGCAGCCAAAGTGGGCCCCGGGTACTACGCGTCTGTACGCCAACACCAGCATCGGTTTGTTTGGCTCACTGGCGGTTAAACCTTCCGGCATGCGCTTTGAGGAGGCCATGACGGAGCGGGTCTTTAAGCCCCTGAAACTCAATCATACGTGGATAAACATTCCACACGCTGAAGAGCCGCATTACGCATGGGGTTATCGTGAGGGTAAAGCGGTCCACGTTTCGCCGGGTATGCTGGATGCAGAAGCCTATGGCGTGAAATCTAACGTCAAAGATATGGCGAGCTGGGTGATGGCCAATATGGCACCGGAGACAATCCAGCAGCCCGCTCTGAAGCAGGGTATTGCGCTGGCGCAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAAGGGTTAGGCTGGGAGATGCTCAACTGGCCGGTCGACGCCAAAACCGTGGTGGATGGCAGCGACAATAAGGTTGCACTGGCGCCGTTACCGGCAGCAGAAGTGAATCCTCCGGCTCCGCCTGTGAAAGCCTCATGGGTGCATAAAACGGGCTCTACGGGGGGGTTTGGCAGCTACGTGGCGTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCGAATAAAAGCTATCCGAACCCGCTACGGGTGGAAACGGCTTACCGTATCCTCGACACGCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3008107","ARO_id":"46899","ARO_name":"CMH-34","CARD_short_name":"CMH-34","ARO_description":"Class C beta-lactamase CMH-34.","ARO_category":{"42891":{"category_aro_accession":"3004776","category_aro_cvterm_id":"42891","category_aro_name":"CMH beta-lactamase","category_aro_description":"CMH is a class C beta-lactamase gene family belonging to Enterobacter cloacae.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7526":{"model_id":"7526","model_name":"CMH-7","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10353":{"protein_sequence":{"accession":"UBJ91318.1","sequence":"MMKKSLSCALLLSVACSAFAAPMSKKQLADVVERTVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSVSKTFTGVLGGDAIARKEISLADPVTKYWPELTGKQWQSIRLLDLATYTAGGLPLQVPDDVTDNVSLLRFYQSWQPKWAPGTTRLYANTSIGLFGSLAVKPSGMRFEQAMAERVFKPLKLNHTWINVPHAEEPHYAWGYREGKAVHVSPGMLDAEAYGVKSNVKDMASWVMANMAPETLSQSTLQQGIALAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVDGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANKSYPNPVRVETAYRILETLQ"},"dna_sequence":{"accession":"OK160063.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCCCTAAGCTGCGCGCTGCTGCTCAGCGTTGCCTGCTCTGCTTTTGCCGCGCCGATGTCAAAAAAACAGCTGGCTGACGTCGTGGAACGTACCGTTACGCCCCTGATGAAGGCGCAGGCCATACCCGGAATGGCCGTGGCCGTCATTTATCAGGGCCAGCCACACTATTTTACTTTCGGTAAAGCAGACGTCGCGGCGAATAAGCCCGTCACGCCGCAAACCTTATTTGAGCTGGGCTCCGTCAGCAAAACCTTCACCGGCGTGCTGGGTGGCGATGCCATTGCCCGCAAAGAGATTTCGCTGGCCGACCCGGTCACGAAATATTGGCCTGAATTGACGGGCAAGCAGTGGCAAAGCATTCGCCTGCTAGACCTGGCAACCTATACCGCAGGCGGATTGCCGTTGCAGGTACCGGATGATGTCACCGATAACGTCTCTCTGCTGCGTTTCTACCAGTCCTGGCAGCCAAAGTGGGCCCCGGGTACCACGCGTCTGTACGCCAACACCAGCATCGGTTTGTTTGGCTCACTGGCCGTCAAACCGTCCGGCATGCGCTTCGAGCAGGCCATGGCGGAGCGGGTCTTTAAGCCCCTGAAACTCAACCATACGTGGATAAACGTTCCACACGCTGAAGAGCCGCACTACGCATGGGGTTATCGTGAGGGAAAAGCGGTCCACGTTTCGCCTGGTATGCTGGATGCAGAAGCCTATGGCGTGAAATCTAACGTCAAAGATATGGCGAGCTGGGTGATGGCCAATATGGCACCTGAGACACTCTCGCAGTCCACTCTGCAGCAGGGTATTGCGCTGGCGCAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAAGGGTTAGGCTGGGAGATGCTCAACTGGCCGGTCGACGCCAAAACCGTGGTGGATGGCAGCGACAATAAGGTCGCACTGGCGCCGTTGCCGGTCGCAGAAGTGAATCCTCCGGCTCCGCCAGTAAAAGCCTCCTGGGTGCATAAAACGGGCTCTACGGGTGGGTTTGGCAGCTACGTGGCGTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCAAATAAAAGCTATCCGAACCCGGTACGGGTGGAAACGGCTTACCGTATTCTCGAGACGCTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3008108","ARO_id":"46900","ARO_name":"CMH-7","CARD_short_name":"CMH-7","ARO_description":"Class C beta-lactamase CMH-7.","ARO_category":{"42891":{"category_aro_accession":"3004776","category_aro_cvterm_id":"42891","category_aro_name":"CMH beta-lactamase","category_aro_description":"CMH is a class C beta-lactamase gene family belonging to Enterobacter cloacae.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7527":{"model_id":"7527","model_name":"CMH-8","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10354":{"protein_sequence":{"accession":"BDS51132.1","sequence":"MMKKSLSCALLLSVACSAFAAPMSEKQLADVVERTVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSVSKTFTGVLGGDAIARKEISLADPVTKYWPELTGKQWQGIRLLDLATYTAGGLPLQVPDDVTDNASLLRFYQSWQPKWAPGTTRLYANTSIGLFGSLAVKPSGMRFEQAMVERVFKPLKLNHTWINVPHAEEPHYAWGYREGKAVHVSPGMLDAEAYGVKSNVKDMASWLMANMAPETLPQSTLQQGIALAQSRYWRVGAMYQGLGWEMLNWPVDVKTVVDGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANKSYPNPVRVETAYRILETLQ"},"dna_sequence":{"accession":"LC732562.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCCCTAAGCTGCGCCCTGCTGCTCAGCGTTGCTTGCTCTGCTTTTGCCGCGCCGATGTCAGAAAAACAGCTGGCTGACGTCGTGGAACGTACCGTTACGCCCCTGATGAAGGCGCAGGCCATACCCGGAATGGCCGTGGCCGTCATTTATCAGGGCCAGCCACACTATTTTACTTTCGGTAAAGCAGACGTCGCGGCGAATAAGCCCGTCACGCCGCAAACCTTATTTGAACTGGGCTCCGTCAGTAAAACCTTCACCGGCGTGCTGGGTGGCGATGCCATTGCCCGCAAAGAGATTTCGCTGGCCGACCCGGTCACGAAATACTGGCCTGAATTGACGGGCAAGCAGTGGCAAGGCATTCGCCTGCTCGACCTGGCAACCTATACCGCAGGCGGATTGCCGTTGCAGGTGCCGGATGATGTCACCGATAATGCCTCTCTGCTGCGTTTCTACCAGTCCTGGCAGCCAAAGTGGGCCCCGGGTACCACGCGTCTGTACGCCAACACCAGCATCGGCCTGTTTGGCTCACTGGCCGTTAAACCTTCCGGCATGCGCTTCGAGCAGGCCATGGTGGAGCGGGTCTTTAAGCCCCTGAAACTCAACCATACATGGATAAACGTTCCACACGCTGAAGAGCCGCACTACGCATGGGGTTATCGTGAGGGAAAAGCGGTCCACGTTTCGCCTGGTATGCTGGATGCAGAAGCCTATGGCGTGAAATCTAACGTCAAAGATATGGCGAGCTGGTTGATGGCCAATATGGCACCTGAGACACTCCCGCAGTCCACTCTGCAGCAGGGTATTGCGCTGGCGCAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAAGGGTTAGGCTGGGAGATGCTCAACTGGCCGGTCGACGTCAAAACCGTGGTGGATGGCAGCGATAATAAGGTTGCACTGGCGCCGTTGCCGGTCGCAGAAGTGAATCCTCCGGCTCCGCCAGTAAAAGCCTCCTGGGTGCATAAAACGGGCTCTACGGGTGGGTTTGGCAGCTACGTGGCGTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCAAATAAAAGCTATCCGAACCCGGTACGGGTGGAAACGGCTTACCGTATTCTCGAGACGCTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3008109","ARO_id":"46901","ARO_name":"CMH-8","CARD_short_name":"CMH-8","ARO_description":"Class C beta-lactamase CMH-8.","ARO_category":{"42891":{"category_aro_accession":"3004776","category_aro_cvterm_id":"42891","category_aro_name":"CMH beta-lactamase","category_aro_description":"CMH is a class C beta-lactamase gene family belonging to Enterobacter cloacae.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7528":{"model_id":"7528","model_name":"CMH-9","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10355":{"protein_sequence":{"accession":"EMN0879540.1","sequence":"MMKKSLSCALLLSVACSAFAAPMSEKQLADVVERTVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSVSKTFTGVLGGDAIARKEISLADPVTKYWPELTGKQWQGIRLLDLATYTAGGLPLQVPDNVTDNASLLRFYQSWQPKWAPGTTRLYANTSIGLFGSLAVKPSGMRFEQAMAERVFKPLKLNHTWINVPHAEESHYAWGYREGKAVHVSPGMLDAEAYGVKSNVKDMASWVMANMAPETLPPSTLQQGIALAQSRYWRVGAMYQGLGWEMLNWPVDVKTVVDGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANKSYPNPVRVETAYRILETLQ"},"dna_sequence":{"accession":"ABFHGH030000056.1","fmin":"17692","fmax":"18838","strand":"-","sequence":"ATGATGAAAAAATCCCTAAGCTGCGCCCTGCTGCTCAGCGTTGCTTGCTCTGCTTTTGCCGCGCCGATGTCAGAAAAACAGCTGGCTGACGTCGTGGAACGTACCGTTACGCCCCTGATGAAGGCGCAGGCCATACCCGGTATGGCCGTGGCCGTCATTTATCAGGGCCAGCCACACTATTTTACTTTCGGTAAAGCAGACGTCGCGGCGAATAAGCCCGTCACGCCGCAAACCTTATTTGAACTGGGCTCCGTCAGTAAAACCTTTACTGGCGTGCTGGGTGGCGATGCCATTGCCCGCAAAGAGATTTCTCTGGCCGACCCGGTCACGAAATATTGGCCTGAATTGACGGGCAAGCAGTGGCAAGGCATTCGCCTGCTAGACCTGGCAACCTATACCGCAGGCGGATTGCCGTTGCAGGTACCGGATAATGTCACCGATAACGCCTCTCTGCTGCGTTTCTACCAGTCCTGGCAGCCAAAGTGGGCCCCGGGTACCACGCGTCTGTACGCCAACACCAGCATCGGTTTGTTTGGCTCACTGGCCGTTAAACCGTCCGGCATGCGCTTCGAGCAGGCCATGGCGGAGCGGGTCTTTAAGCCCCTGAAACTCAACCATACGTGGATAAACGTTCCACACGCTGAAGAGTCGCACTACGCATGGGGTTATCGTGAGGGAAAAGCGGTTCACGTTTCGCCTGGTATGCTGGATGCAGAAGCCTATGGCGTGAAATCTAACGTCAAAGATATGGCGAGCTGGGTGATGGCCAATATGGCACCTGAGACACTCCCGCCGTCCACTCTGCAGCAGGGTATTGCGCTGGCGCAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAAGGGTTAGGCTGGGAGATGCTCAACTGGCCGGTCGACGTCAAAACCGTGGTGGATGGCAGCGACAATAAGGTCGCACTGGCGCCGTTGCCGGTCGCAGAAGTGAATCCTCCGGCTCCGCCAGTAAAAGCCTCCTGGGTGCATAAAACGGGCTCTACGGGTGGGTTTGGCAGCTACGTGGCGTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCAAATAAAAGCTATCCGAACCCGGTACGGGTGGAAACGGCTTACCGTATTCTCGAGACGCTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3008110","ARO_id":"46902","ARO_name":"CMH-9","CARD_short_name":"CMH-9","ARO_description":"Class C beta-lactamase CMH-9.","ARO_category":{"42891":{"category_aro_accession":"3004776","category_aro_cvterm_id":"42891","category_aro_name":"CMH beta-lactamase","category_aro_description":"CMH is a class C beta-lactamase gene family belonging to Enterobacter cloacae.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7529":{"model_id":"7529","model_name":"CMY-172","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10356":{"protein_sequence":{"accession":"QLH93380.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSLAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPIPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"MT752965.1","fmin":"0","fmax":"1137","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCTTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTATCCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008111","ARO_id":"46903","ARO_name":"CMY-172","CARD_short_name":"CMY-172","ARO_description":"Inhibitor-resistant extended-spectrum class C beta-lactamase CMY-172.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7530":{"model_id":"7530","model_name":"CMY-175","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10357":{"protein_sequence":{"accession":"QVO43829.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGISLLHLATYTAGGLPLQIPDDVTDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQQLKLAHTWITVPQNEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"MZ092822.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCAGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTACGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACAATTAAAACTGGCGCATACCTGGATTACAGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43754","NCBI_taxonomy_name":"Citrobacter portucalensis","NCBI_taxonomy_id":"1639133"}}}},"ARO_accession":"3008112","ARO_id":"46904","ARO_name":"CMY-175","CARD_short_name":"CMY-175","ARO_description":"Class C beta-lactamase CMY-175.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7531":{"model_id":"7531","model_name":"CMY-176","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10358":{"protein_sequence":{"accession":"QVO43830.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHSVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGISLLHLATYTAGGLPLQIPDDVTDKAALLRFYQNWQPQWAPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKAVHVSPGQLDAEAYGVKSSVIDMARWVQVNMDASRVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFIPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"MZ092823.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCATTCTCCACGTTTGCCGCCGCCAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACTCAGTCACGCAGCAAACTCTGTTTGAGCTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCAGCCTGCTGCACTTAGCCACCTACACGGCAGGCGGCCTGCCGCTGCAGATCCCCGATGACGTTACGGATAAAGCCGCATTACTGCGTTTTTATCAAAACTGGCAGCCGCAATGGGCCCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACAGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGGCTGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGTGTTATTGATATGGCCCGCTGGGTTCAGGTCAACATGGACGCCAGCCGCGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGTAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCGGCAGTGAAAGCCTCATGGGTGCATAAAACGGGATCCACTGGAGGATTTGGCAGCTACGTAGCCTTCATTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43754","NCBI_taxonomy_name":"Citrobacter portucalensis","NCBI_taxonomy_id":"1639133"}}}},"ARO_accession":"3008113","ARO_id":"46905","ARO_name":"CMY-176","CARD_short_name":"CMY-176","ARO_description":"Class C beta-lactamase CMY-176.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7532":{"model_id":"7532","model_name":"CMY-177","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10359":{"protein_sequence":{"accession":"UBL87560.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHVSPGRLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGRYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"OK217282.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACGACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGATACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3008114","ARO_id":"46906","ARO_name":"CMY-177","CARD_short_name":"CMY-177","ARO_description":"Class C beta-lactamase CMY-177.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7533":{"model_id":"7533","model_name":"CMY-178","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10360":{"protein_sequence":{"accession":"UDF87831.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFTGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSLAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPIPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"OK554431.1","fmin":"0","fmax":"1137","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTACCGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCTTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTATCCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3008115","ARO_id":"46907","ARO_name":"CMY-178","CARD_short_name":"CMY-178","ARO_description":"Class C beta-lactamase CMY-178.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7534":{"model_id":"7534","model_name":"CMY-179","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10361":{"protein_sequence":{"accession":"UGN21642.1","sequence":"MMKKSICCALLLTASFSTFAASKTEQHIADIVNRTITPLMQEQAIPGMAVAIIYQGKPYYFTWGKADIANNRPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTQYWPELTGKQWRGISMLHLATYTAGGLPLQIPDDVTDKAALLRFYQNWQPQWAPGAKRLYANSSIGLFGALAVKPSGMSYEEALTRRVLQPLKLAHTWITVPQSEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSSVVDMTRWVQANMDASQVKEKTLQQGIELAQSRYWRIGDMYQGLGWEMLNWPVKADSIISGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKKLGIVMLANKSYPNPARVEAAWRILEKLQ"},"dna_sequence":{"accession":"OL606718.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCAATATGCTGCGCGTTGCTGCTGACAGCCTCTTTCTCAACGTTTGCCGCGTCAAAAACAGAACAACACATTGCCGATATCGTCAATCGCACCATCACACCGCTGATGCAAGAACAGGCTATTCCGGGTATGGCCGTGGCGATTATCTACCAGGGGAAACCGTATTACTTTACCTGGGGTAAAGCCGATATCGCCAATAACCGTCCCGTTACTCAGCAAACACTGTTTGAACTTGGCTCGGTCAGTAAGACGTTCAACGGCGTGTTGGGTGGCGATGCTATCGCCCGCGGCGAAATCAAGCTCAGCGATCCGGTCACGCAATACTGGCCAGAATTGACGGGCAAACAATGGCGGGGTATCAGCATGCTGCACTTAGCCACCTATACGGCGGGTGGTCTGCCGCTTCAGATCCCCGACGACGTTACGGATAAAGCCGCATTACTGCGCTTTTATCAAAACTGGCAGCCGCAATGGGCTCCAGGTGCTAAACGTCTCTATGCTAACTCCAGTATTGGCCTGTTTGGCGCACTAGCGGTGAAACCTTCAGGGATGAGCTATGAAGAGGCGCTAACCAGACGCGTCCTGCAGCCTTTAAAACTGGCGCATACCTGGATTACGGTTCCACAGAGCGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGAAAGCCAGTGCATGTTTCCCCCGGACAACTTGATGCCGAAGCCTATGGCGTGAAATCCAGCGTCGTCGATATGACTCGTTGGGTTCAGGCCAACATGGACGCCAGCCAGGTTAAGGAGAAAACGCTCCAGCAGGGCATTGAGCTTGCGCAATCACGTTACTGGCGTATTGGCGATATGTATCAGGGACTGGGCTGGGAGATGCTTAACTGGCCGGTGAAAGCCGACTCGATAATCAGCGGTAGCGACAGCAAAGTAGCGCTGGCAGCACTTCCCGCCGTTGAGGTAAATCCGCCAGCCCCGGCCGTGAAAGCCTCATGGGTGCATAAAACAGGGTCTACTGGCGGATTTGGCAGCTACGTTGCCTTCGTGCCAGAAAAAAAACTTGGCATCGTGATGCTGGCAAACAAAAGCTACCCTAACCCGGCTCGCGTAGAGGCCGCCTGGCGCATCCTGGAAAAGTTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"47904","NCBI_taxonomy_name":"Citrobacter meridianamericanus","NCBI_taxonomy_id":"2894201"}}}},"ARO_accession":"3008116","ARO_id":"46908","ARO_name":"CMY-179","CARD_short_name":"CMY-179","ARO_description":"Class C beta-lactamase CMY-179.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7535":{"model_id":"7535","model_name":"CMY-180","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10362":{"protein_sequence":{"accession":"UQM99654.1","sequence":"MMKKSICCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAIIYEEKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWRGISLLHLATYTAGGLPLQIPDDVTDKAALLRFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQSEQKNYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIELAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPARVEAAWRILEKLQ"},"dna_sequence":{"accession":"OL445412.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGATATGCTGCGCGCTGCTGCTGACAGCCTCTTTCTCCACGTTTGCTGCCGCAAAAACAGAACAACAAATTGCCGATATCGTTAACCGCACCATCACACCACTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTGGCGATTATCTACGAGGAGAAACCTTATTACTTTACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGACGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCGGGGTATCAGCCTGCTGCACTTAGCCACCTATACAGCGGGTGGCCTGCCGCTGCAGATCCCCGATGACGTTACGGATAAAGCCGCATTACTGCGCTTTTATCAAAACTGGCAACCACAATGGACTCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGTGCGCTGGCGGTGAAACCTTCAGGTATGAGCTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAAAGCGAACAAAAAAATTATGCCTGGGGCTATCGCGAAGGGAAGCCTGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATCGATATGGCCCGCTGGGTTCAGGCCAACATGGACGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAAGGCATTGAGCTTGCGCAGTCTCGCTACTGGCGTATTGGTGATATGTACCAAGGATTAGGCTGGGAGATGCTGAACTGGCCGTTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCAGCACCTGCCGTGAAAGCCTCATGGGTGCATAAAACGGGATCCACAGGTGGATTTGGCAGCTACGTTGCCTTCGTTCCAGAAAAAAACCTTGGCATAGTGATGCTGGCAAACAAAAGCTATCCTAACCCGGCTCGCGTAGAGGCGGCCTGGCGCATTCTTGAAAAACTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3008117","ARO_id":"46909","ARO_name":"CMY-180","CARD_short_name":"CMY-180","ARO_description":"Class C beta-lactamase CMY-180.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7536":{"model_id":"7536","model_name":"CMY-181","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10363":{"protein_sequence":{"accession":"UUG60967.1","sequence":"MMKKSICCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAIIYEGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWRGISLLHLATYTAGGLPLQIPDDITDKAALLRFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQSEQKNYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIELAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPARVEAAWRILEKLQ"},"dna_sequence":{"accession":"OP081530.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGATATGCTGCGCACTGCTGCTGACAGCCTCTTTCTCCACGTTTGCTGCCGCAAAAACAGAACAACAAATTGCCGATATCGTTAACCGCACCATCACACCACTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTGGCGATTATCTACGAGGGGAAACCTTATTACTTTACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGACGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCGGGGTATCAGCCTGCTGCACTTAGCCACCTATACAGCGGGTGGCCTGCCGCTGCAGATCCCCGATGACATTACGGATAAAGCCGCATTACTGCGCTTTTATCAAAACTGGCAACCACAATGGACTCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGTGCGCTGGCGGTGAAACCTTCAGGTATGAGCTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAAAGCGAACAAAAAAATTATGCCTGGGGCTATCGCGAAGGGAAGCCTGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATCGATATGGCCCGCTGGGTTCAGGCCAACATGGACGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGAGCTTGCGCAGTCTCGCTACTGGCGTATTGGTGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCAGCACCTGCCGTGAAAGCCTCATGGGTGCATAAAACAGGATCCACAGGCGGATTTGGCAGCTACGTTGCTTTCGTTCCAGAAAAAAACCTTGGCATCGTAATGTTGGCAAACAAAAGCTACCCCAACCCGGCTCGCGTCGAGGCGGCCTGGCGCATTCTTGAAAAACTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3008118","ARO_id":"46910","ARO_name":"CMY-181","CARD_short_name":"CMY-181","ARO_description":"Class C beta-lactamase CMY-181.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7537":{"model_id":"7537","model_name":"CMY-182","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10364":{"protein_sequence":{"accession":"BDT38919.1","sequence":"MMKKSICCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAIIYQGKPYYFTWGKADIANNRPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKFSDPVTQYWPELTGKQWQGISLLHLATYTAGGLPLQVPDDVTNKAALLRFYQSWQPQWAPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTKRVLHPLKLAHTWITVPQSEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMTRWVQANMDASQVQEKTLQQGIELAQSRYWRIGDMYQGLGWEMLNWPVKADSIISGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"LC733684.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGATATGCTGCGCGCTGCTGCTGACAGCTTCTTTCTCCACGTTTGCCGCCGCAAAAACAGAACAACAAATTGCCGATATCGTTAACCGCACCATCACACCGCTGATGCAGGAGCAGGCAATTCCGGGCATGGCCGTTGCGATTATCTATCAGGGGAAACCTTATTACTTTACCTGGGGTAAAGCCGATATCGCCAATAACCGTCCAGTCACGCAACAAACGCTGTTTGAACTCGGATCGGTCAGTAAAACGTTCAACGGTGTGCTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGTTCAGCGATCCGGTCACGCAGTACTGGCCTGAACTGACTGGTAAGCAGTGGCAGGGTATCAGCCTGCTGCACTTAGCCACCTACACGGCAGGCGGCCTGCCGCTTCAGGTTCCGGACGACGTTACGAATAAAGCCGCGTTACTACGCTTTTATCAAAGCTGGCAGCCGCAATGGGCCCCAGGCGCTAAACGTCTTTATGCTAACTCCAGCATTGGTCTGTTTGGCGCCCTGGCGGTGAAACCCTCAGGCATGAGCTACGAAGAGGCGATGACCAAACGCGTCCTGCACCCCTTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAGCGAACAAAAAGATTATGCCTGGGGTTATCGCGAAGGAAAGCCAGTGCATGTATCCCCTGGGCAACTTGATGCCGAAGCCTACGGGGTGAAATCGAGCGTTATCGATATGACCCGTTGGGTTCAGGCCAACATGGACGCCAGCCAGGTTCAGGAGAAAACGCTCCAGCAGGGCATCGAGCTTGCGCAGTCACGTTACTGGCGTATTGGCGATATGTACCAGGGCCTGGGCTGGGAGATGCTGAACTGGCCGGTGAAGGCCGACTCGATAATTAGCGGTAGCGACAGCAAAGTGGCACTGGCAGCGCTTCCTGCCGTTGAGGTAAACCCGCCCGCGCCTGCCGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGCGGATTCGGCAGCTACGTTGCGTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAGAGCTACCCAAACCCTGTTCGCGTCGAGGCCGCCTGGCGCATTCTTGAAAAACTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39584","NCBI_taxonomy_name":"Citrobacter braakii","NCBI_taxonomy_id":"57706"}}}},"ARO_accession":"3008119","ARO_id":"46911","ARO_name":"CMY-182","CARD_short_name":"CMY-182","ARO_description":"Class C beta-lactamase CMY-182.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7538":{"model_id":"7538","model_name":"CMY-183","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10365":{"protein_sequence":{"accession":"BDT38920.1","sequence":"MMKKSLCCALLLTAPFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADITNNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGISLLHLATYTAGGLPLQIPDDVTDKAALLRFYQNWQPQWAPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKAVHVSPGQLDAEAYGVKSSVIDMARWVQVNMDASRVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"LC733685.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCCCTTTCTCCACGTTTGCCGCCGCCAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCACCAATAACCACCCAGTCACGCAGCAAACTCTGTTTGAGCTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGTGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCAGCCTGCTGCACTTAGCCACCTACACGGCAGGCGGCCTGCCGCTGCAGATCCCCGATGACGTTACGGATAAAGCCGCATTACTGCGTTTTTATCAAAACTGGCAGCCGCAATGGGCCCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACAGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGGCTGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGTCAACATGGACGCCAGCCGCGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCAATCATCAACGGTAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCTGCCCCCGCTGTGAAAGCCTCATGGGTGCATAAAACGGGATCCACTGGAGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43754","NCBI_taxonomy_name":"Citrobacter portucalensis","NCBI_taxonomy_id":"1639133"}}}},"ARO_accession":"3008120","ARO_id":"46912","ARO_name":"CMY-183","CARD_short_name":"CMY-183","ARO_description":"Class C beta-lactamase CMY-183.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7539":{"model_id":"7539","model_name":"CMY-184","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10366":{"protein_sequence":{"accession":"WAK12379.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYSNSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYARGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQEGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"OP950674.1","fmin":"63","fmax":"1209","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACTCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCAGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGGAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3008121","ARO_id":"46913","ARO_name":"CMY-184","CARD_short_name":"CMY-184","ARO_description":"Class C beta-lactamase CMY-184.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7540":{"model_id":"7540","model_name":"CMY-186","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10367":{"protein_sequence":{"accession":"MDI2051974.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYSNSSIGLFVALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYARGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"JASAUU010000053.1","fmin":"658","fmax":"1804","strand":"-","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACTCTAACTCCAGCATTGGTCTGTTTGTCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCAGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008122","ARO_id":"46914","ARO_name":"CMY-186","CARD_short_name":"CMY-186","ARO_description":"Class C beta-lactamase CMY-186.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7541":{"model_id":"7541","model_name":"CMY-188","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10368":{"protein_sequence":{"accession":"WNH41907.1","sequence":"MMKKSICCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAIIYEGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWRGISLLHLATYTAGGLPLQIPDDITDKAALLRFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQSEQKNYAWGYREGKPVHVSPGQLDAKAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIELAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPVPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"OR562100.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGATATGCTGCGCACTGCTGCTGACAGCCTCTTTCTCCACGTTTGCTGCCGCAAAAACAGAACAACAAATTGCCGATATCGTTAACCGCACCATCACACCACTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTGGCGATTATCTACGAGGGGAAACCTTATTACTTTACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGACGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCGGGGTATCAGCCTGCTGCACTTAGCCACCTATACAGCGGGTGGCCTGCCGCTGCAGATCCCCGATGACATTACGGATAAAGCCGCATTACTGCGCTTTTATCAAAACTGGCAACCACAATGGACTCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGTGCGCTAGCGGTGAAACCTTCAGGTATGAGCTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAAAGCGAACAAAAAAACTATGCCTGGGGCTATCGCGAAGGGAAGCCTGTGCACGTTTCTCCGGGACAACTTGACGCCAAAGCCTATGGCGTGAAATCCAGCGTTATCGATATGGCCCGCTGGGTTCAGGCCAACATGGACGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGAGCTTGCGCAGTCTCGCTACTGGCGTATTGGTGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCAGTACCTGCCGTGAAAGCCTCATGGGTGCATAAAACGGGATCCACAGGTGGATTTGGCAGCTACGTTGCCTTCGTTCCAGAAAAAAACCTTGGCATAGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGCGTCGAGGCGGCCTGGCGCATTCTTGAAAAACTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3008123","ARO_id":"46915","ARO_name":"CMY-188","CARD_short_name":"CMY-188","ARO_description":"Class C beta-lactamase CMY-188.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7542":{"model_id":"7542","model_name":"CMY-189","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10369":{"protein_sequence":{"accession":"BAA02494.1","sequence":"MMKKSICCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAIIYEGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWRGISLLHLATYTAGGLPLQIPDDITDKAALLRFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQSEQKNYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIELAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPVPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"D13207.1","fmin":"142","fmax":"1288","strand":"+","sequence":"ATGATGAAAAAATCGATATGCTGCGCACTGCTGCTGACAGCCTCTTTCTCCACGTTTGCTGCCGCAAAAACAGAACAACAAATTGCCGATATCGTTAACCGCACCATCACACCACTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTGGCGATTATCTACGAGGGGAAACCTTATTACTTTACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGGTCGGTCAGTAAGACGTTTAACGGCGTGTTGGGCGGCGACGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCGGGGTATCAGCCTGCTGCACTTAGCCACCTATACAGCGGGTGGCCTGCCGCTGCAGATCCCCGATGACATTACGGATAAAGCCGCATTACTGCGCTTTTATCAAAACTGGCAACCACAATGGACTCCGGGCGCTAAGCGTCTTTACGCTAACTCCAGCATTGGTCTGTTTGGTGCGCTAGCGGTGAAACCTTCAGGTATGAGCTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAAAGCGAACAAAAAAACTATGCCTGGGGCTATCGCGAAGGGAAGCCTGTGCACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATCGATATGGCCCGCTGGGTTCAGGCCAACATGGACGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGAGCTTGCGCAGTCTCGCTACTGGCGTATTGGTGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCAGTACCTGCCGTGAAAGCCTCATGGGTGCATAAAACGGGATCCACAGGTGGATTTGGCAGCTACGTTGCCTTCGTTCCAGAAAAAAACCTTGGCATAGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGCGTCGAGGCGGCCTGGCGCATTCTTGAAAAACTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3008124","ARO_id":"46916","ARO_name":"CMY-189","CARD_short_name":"CMY-189","ARO_description":"Class C beta-lactamase CMY-189.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7543":{"model_id":"7543","model_name":"CMY-190","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10370":{"protein_sequence":{"accession":"WPR17911.1","sequence":"MMKKSLCCALLLAASFSTFAASKTEQHIADIVNRTITPLMKEQAIPGMAVAVIYQGKPYYFTWGKADIANNRPITQNTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTQYWPELTGKQWQGISLLHLATYTAGGLPLQIPDEVTDKTALLHFYQNWQPQWAPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTTRVLQPLKLAHTWITVPQSEQKDYAWGYRDGKPVHISPGQLDAEAYGVKSSIMDMARWVQANMDASHVQEKTLQQGIELAQSRYWRIGEMYQGLGWEMLNWPVKADTIINGSDSKIALSALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFIPEKNLGIVMLANKSYPNPARVDAAWRILEKLQ"},"dna_sequence":{"accession":"OR896917.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCGCTGCTGCTGGCCGCCTCTTTCTCCACGTTTGCCGCCTCGAAGACAGAACAACACATTGCCGATATCGTTAACCGCACCATCACACCGCTGATGAAAGAACAGGCCATTCCGGGTATGGCCGTGGCCGTTATCTACCAAGGAAAACCGTATTACTTTACCTGGGGTAAAGCTGATATCGCCAATAATCGTCCGATCACACAGAACACACTGTTTGAACTCGGTTCAGTCAGTAAGACCTTCAATGGCGTGCTGGGCGGCGATGCGATCGCCCGCGGCGAAATCAAGCTCAGCGATCCGGTCACGCAATACTGGCCTGAGCTGACGGGTAAGCAGTGGCAGGGTATCAGCCTGCTGCACTTAGCGACCTACACGGCAGGCGGCCTGCCGCTTCAGATCCCCGACGAGGTGACGGATAAAACCGCATTGCTGCACTTTTATCAAAACTGGCAACCTCAGTGGGCTCCGGGCGCTAAACGTCTCTATGCTAACTCCAGCATTGGTCTGTTTGGCGCACTGGCAGTGAAACCTTCGGGCATGAGCTACGAAGAGGCGATGACCACCCGCGTCCTGCAACCCTTAAAACTGGCACATACATGGATAACGGTTCCACAGAGCGAACAAAAAGACTATGCATGGGGCTATCGCGATGGCAAGCCTGTACATATTTCGCCGGGCCAGCTTGATGCCGAGGCGTATGGTGTGAAATCCAGCATTATGGATATGGCACGCTGGGTTCAGGCCAATATGGACGCCAGCCACGTGCAGGAGAAAACCCTGCAGCAAGGCATCGAGCTCGCGCAGTCACGTTACTGGCGCATTGGTGAGATGTACCAGGGCTTAGGCTGGGAAATGCTGAACTGGCCGGTAAAAGCAGACACGATTATCAACGGCAGCGACAGTAAAATCGCTCTGTCGGCGCTTCCGGCCGTTGAGGTAAACCCACCAGCCCCCGCAGTAAAAGCCTCCTGGGTACATAAAACAGGTTCGACTGGCGGATTTGGTAGTTATGTGGCTTTTATTCCGGAGAAAAATCTGGGCATCGTGATGCTGGCCAATAAAAGCTACCCGAATCCTGCTCGCGTCGACGCGGCCTGGCGCATCCTTGAAAAACTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41220","NCBI_taxonomy_name":"Citrobacter youngae","NCBI_taxonomy_id":"133448"}}}},"ARO_accession":"3008125","ARO_id":"46917","ARO_name":"CMY-190","CARD_short_name":"CMY-190","ARO_description":"Class C beta-lactamase CMY-190.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7544":{"model_id":"7544","model_name":"CMY-191","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10371":{"protein_sequence":{"accession":"WZE64858.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHSSPGQLDTEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"PP575761.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACAGTTCTCCGGGACAACTTGACACCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3008126","ARO_id":"46918","ARO_name":"CMY-191","CARD_short_name":"CMY-191","ARO_description":"Class C beta-lactamase CMY-191.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7519":{"model_id":"7519","model_name":"CMH-28","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11354":{"protein_sequence":{"accession":"XAJ73534.1","sequence":"MMKKSLSCALLLSVACSAFAAPMSEKQLADVVERTVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSVSKTFTGVLGGDAIARKEISLADPVTKYWPELTGKQWQGIRLLDLATYTAGGLPLQVPDDVTDNASLLRFYQSWQPKWVPGTTRLYANTSIGLFGSLAVKPSGMRFEQAMAERVFKPLKLNHTWINVPHAEEPHYAWGYREGKAIHVSPGMLDAEAYGVKSNVKDMASWVMANMAPETLPQSTLQQGIALAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVDGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANKSYPNPVRVETAYRILETLQ"},"dna_sequence":{"accession":"PP740468.1","fmin":"0","fmax":"1143","strand":"+","sequence":"ATGATGAAAAAATCCCTAAGCTGCGCCCTGCTGCTCAGCGTTGCTTGCTCTGCTTTTGCCGCGCCGATGTCAGAAAAACAGCTGGCTGACGTCGTGGAACGTACCGTTACGCCCCTGATGAAGGCGCAGGCCATACCCGGAATGGCCGTGGCCGTCATTTATCAGGGCCAGCCACACTATTTCACTTTCGGTAAAGCAGACGTCGCGGCGAATAAGCCCGTCACGCCGCAAACCTTATTTGAACTGGGCTCCGTCAGTAAAACCTTCACTGGCGTGCTGGGTGGCGATGCCATTGCCCGCAAAGAGATTTCGCTGGCCGACCCGGTCACGAAATACTGGCCTGAATTGACGGGCAAGCAGTGGCAAGGCATTCGCCTGCTCGACCTGGCAACCTATACCGCAGGCGGATTGCCGTTGCAGGTACCGGATGATGTCACCGATAACGCCTCTCTGCTGCGTTTCTACCAGTCCTGGCAGCCAAAGTGGGTCCCGGGTACCACGCGTCTGTACGCCAACACCAGCATCGGTTTGTTTGGCTCACTGGCCGTTAAACCGTCCGGCATGCGCTTCGAGCAGGCCATGGCGGAGCGGGTCTTTAAGCCCCTGAAACTCAACCATACGTGGATAAACGTTCCACACGCTGAAGAGCCGCACTACGCATGGGGTTATCGTGAGGGAAAAGCGATTCACGTTTCGCCTGGTATGCTGGATGCAGAAGCCTATGGCGTGAAATCTAACGTCAAAGATATGGCGAGCTGGGTGATGGCCAATATGGCACCTGAGACACTCCCGCAGTCCACTCTGCAGCAGGGTATTGCGCTAGCGCAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAAGGGTTAGGCTGGGAGATGCTCAACTGGCCGGTCGACGCCAAAACCGTGGTGGATGGCAGCGACAATAAGGTCGCACTGGCGCCGTTGCCGGTCGCAGAAGTGAATCCTCCGGCTCCGCCAGTAAAAGCCTCCTGGGTGCATAAAACGGGCTCTACGGGTGGGTTTGGCAGCTACGTGGCGTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCAAATAAAAGCTATCCGAACCCGGTACGGGTGGAAACGGCTTACCGTATTCTCGAGACGCTACAG","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3008101","ARO_id":"46893","ARO_name":"CMH-28","CARD_short_name":"CMH-28","ARO_description":"Class C beta-lactamase CMH-28.","ARO_category":{"42891":{"category_aro_accession":"3004776","category_aro_cvterm_id":"42891","category_aro_name":"CMH beta-lactamase","category_aro_description":"CMH is a class C beta-lactamase gene family belonging to Enterobacter cloacae.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7518":{"model_id":"7518","model_name":"CMH-27","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11353":{"protein_sequence":{"accession":"XAJ73533.1","sequence":"MMKKSLSCALLLSVACSAFAAPMSEKQLADVVERTVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSVSKTFTGVLGGDAIARKEISLADPVTKYWPELKGKQWQGIRLLDLATYTAGGLPLQVPDDVTDNASLLRFYQSWQPKWAPGTTRLYANTSIGLFGSLAVKPSGMRFEQAMAERVFKPLKLNHTWINVPHAEEPHYAWGYREGKAVHVSPGMLDAEAYGVKSNVKDMASWVMANMAPETLPPSTLQQGIALAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVDGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANKSYSNPVRVETAYRILDALQ"},"dna_sequence":{"accession":"PP740467.1","fmin":"0","fmax":"1143","strand":"+","sequence":"ATGATGAAAAAATCCCTAAGCTGCGCCCTGCTGCTCAGCGTTGCCTGCTCTGCTTTTGCCGCGCCGATGTCAGAAAAACAGCTGGCTGACGTCGTGGAACGTACCGTTACGCCCCTGATGAAGGCGCAGGCCATACCCGGAATGGCCGTGGCCGTCATTTATCAGGGCCAGCCACACTATTTTACTTTCGGTAAAGCAGACGTCGCGGCGAATAAGCCCGTCACGCCGCAAACCTTATTTGAGCTGGGCTCCGTCAGTAAAACCTTCACTGGCGTGCTGGGTGGCGATGCCATTGCCCGCAAAGAAATTTCGCTGGCCGACCCGGTCACGAAATATTGGCCGGAATTGAAGGGCAAGCAGTGGCAAGGCATTCGCCTGCTCGACCTGGCAACCTATACCGCAGGCGGATTGCCGTTGCAGGTACCGGATGATGTCACCGATAACGCCTCTCTGCTGCGTTTCTACCAGTCCTGGCAGCCAAAGTGGGCCCCGGGTACCACGCGTCTGTACGCCAACACCAGCATCGGTTTGTTTGGCTCACTGGCCGTTAAACCGTCCGGCATGCGCTTCGAGCAGGCCATGGCGGAGCGGGTCTTTAAGCCCCTGAAACTCAACCATACGTGGATAAACGTTCCACACGCTGAAGAGCCGCACTACGCATGGGGTTATCGTGAGGGAAAAGCGGTCCACGTTTCGCCTGGTATGCTGGATGCAGAAGCCTATGGCGTGAAATCTAACGTCAAAGATATGGCGAGCTGGGTGATGGCCAATATGGCACCTGAGACACTCCCGCCGTCCACTCTGCAGCAGGGTATTGCGCTGGCGCAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAAGGGTTAGGCTGGGAGATGCTCAACTGGCCGGTCGACGCCAAAACCGTGGTGGATGGCAGCGACAATAAGGTCGCACTGGCGCCGTTGCCGGTCGCAGAAGTGAATCCTCCGGCTCCGCCAGTAAAAGCCTCCTGGGTGCATAAAACGGGCTCTACGGGTGGATTTGGCAGCTACGTGGCGTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCAAATAAAAGCTATTCGAACCCGGTACGGGTGGAAACGGCTTACCGTATCCTCGACGCGCTACAG","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3008100","ARO_id":"46892","ARO_name":"CMH-27","CARD_short_name":"CMH-27","ARO_description":"Class C beta-lactamase CMH-27.","ARO_category":{"42891":{"category_aro_accession":"3004776","category_aro_cvterm_id":"42891","category_aro_name":"CMH beta-lactamase","category_aro_description":"CMH is a class C beta-lactamase gene family belonging to Enterobacter cloacae.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7545":{"model_id":"7545","model_name":"CMY-192","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10372":{"protein_sequence":{"accession":"WZW61258.1","sequence":"MMKKSLCCSSAAALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSLAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPIPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"PP693800.1","fmin":"0","fmax":"1149","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCAGCTCTGCTGCAGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCTTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTATCCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3008127","ARO_id":"46919","ARO_name":"CMY-192","CARD_short_name":"CMY-192","ARO_description":"Class C beta-lactamase CMY-192.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7546":{"model_id":"7546","model_name":"CMY-194","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10373":{"protein_sequence":{"accession":"XHJ89679.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYARGYREGKPVHVSPGQLDAEAYGVKSSVIDMARRVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"PQ374838.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCAGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCAGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36946","NCBI_taxonomy_name":"Providencia stuartii","NCBI_taxonomy_id":"588"}}}},"ARO_accession":"3008128","ARO_id":"46920","ARO_name":"CMY-194","CARD_short_name":"CMY-194","ARO_description":"Class C beta-lactamase CMY-194.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7547":{"model_id":"7547","model_name":"CMY-195","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10374":{"protein_sequence":{"accession":"XHO32879.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHSSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPDPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"PQ394536.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACAGTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTGACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3008129","ARO_id":"46921","ARO_name":"CMY-195","CARD_short_name":"CMY-195","ARO_description":"Class C beta-lactamase CMY-195.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7548":{"model_id":"7548","model_name":"CMY-196","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10375":{"protein_sequence":{"accession":"XHO32880.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHSSPGQFDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"PQ394537.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACAGTTCTCCGGGACAATTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3008130","ARO_id":"46922","ARO_name":"CMY-196","CARD_short_name":"CMY-196","ARO_description":"Class C beta-lactamase CMY-196.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7549":{"model_id":"7549","model_name":"CMY-197","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10376":{"protein_sequence":{"accession":"XHO32881.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPRQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHSSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"PQ394538.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCGGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACAGTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3008131","ARO_id":"46923","ARO_name":"CMY-197","CARD_short_name":"CMY-197","ARO_description":"Class C beta-lactamase CMY-197.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7550":{"model_id":"7550","model_name":"CMY-198","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10377":{"protein_sequence":{"accession":"XHO32882.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPELTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHVSPGQLDTEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"PQ394539.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACACCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3008132","ARO_id":"46924","ARO_name":"CMY-198","CARD_short_name":"CMY-198","ARO_description":"Class C beta-lactamase CMY-198.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7551":{"model_id":"7551","model_name":"CMY-199","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10378":{"protein_sequence":{"accession":"XHO32883.1","sequence":"MMKKSLCCALLLTASFSTFAAAKTEQQIADIVNRTITPLMQEQAIPGMAVAVIYQGKPYYFTWGKADIANNHPVTQQTLFELGSVSKTFNGVLGGDAIARGEIKLSDPVTKYWPKLTGKQWQGIRLLHLATYTAGGLPLQIPDDVRDKAALLHFYQNWQPQWTPGAKRLYANSSIGLFGALAVKPSGMSYEEAMTRRVLQPLKLAHTWITVPQNEQKDYAWGYREGKPVHVSPGQLDAEAYGVKSSVIDMARWVQANMDASHVQEKTLQQGIALAQSRYWRIGDMYQGLGWEMLNWPLKADSIINGSDSKVALAALPAVEVNPPAPAVKASWVHKTGSTGGFGSYVAFVPEKNLGIVMLANKSYPNPVRVEAAWRILEKLQ"},"dna_sequence":{"accession":"PQ394540.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGAAAAAATCGTTATGCTGCGCTCTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAACAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAGGAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAACCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCAGTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTTAACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTCAGCGATCCGGTCACGAAATACTGGCCAAAACTGACAGGCAAACAGTGGCAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTACCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCATTTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTTTACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCCTCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCATTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAAGATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCGGGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGATATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAGAAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGTATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCGCTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTGGCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAAGCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTACGTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAACAAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTTGAAAAGCTGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3008133","ARO_id":"46925","ARO_name":"CMY-199","CARD_short_name":"CMY-199","ARO_description":"Class C beta-lactamase CMY-199.","ARO_category":{"36208":{"category_aro_accession":"3000069","category_aro_cvterm_id":"36208","category_aro_name":"CMY beta-lactamase","category_aro_description":"CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7552":{"model_id":"7552","model_name":"CTX-M-243","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10379":{"protein_sequence":{"accession":"QPO25386.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYSPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAENRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"MW345818.1","fmin":"610","fmax":"1486","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAGTCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAGCTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCACAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTAGGTGATAAGACCGGCAGCGGCGACTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAACCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3008134","ARO_id":"46926","ARO_name":"CTX-M-243","CARD_short_name":"CTX-M-243","ARO_description":"Extended-spectrum class A beta-lactamase CTX-M-243.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7553":{"model_id":"7553","model_name":"CTX-M-245","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10380":{"protein_sequence":{"accession":"QSL96845.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTPPQPKAESRRDVLASAAKIFTDGL"},"dna_sequence":{"accession":"MN928785.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCCGCCTCAACCTAAGGCAGAGAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCTTCACCGACGGGTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36783","NCBI_taxonomy_name":"Serratia marcescens","NCBI_taxonomy_id":"615"}}}},"ARO_accession":"3008135","ARO_id":"46927","ARO_name":"CTX-M-245","CARD_short_name":"CTX-M-245","ARO_description":"Extended-spectrum class A beta-lactamase CTX-M-245.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7554":{"model_id":"7554","model_name":"CTX-M-246","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10381":{"protein_sequence":{"accession":"QVO43831.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTVDVQQKLAELEQQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLTELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDDTFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVAWMKGNTTGAASIQAGLPASWVVGDKTGSGDYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"MZ092824.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGTGGACGTACAGCAAAAACTTGCCGAATTAGAGCAGCAGTCGGGAGGAAGGCTGGGTGTGGCATTGATTAACACGGCGGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTCGAGATCAAAAAATCTGACCTGGTTAACTATAATCCGATTGCGGAAAAACACGTCAATGGGACGATGTCACTGACTGAGCTCAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGACACGTTCCGTCTCGACCGCACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACACTGCGTAATCTGACGCTGGGTAAAGCATTGGGTGACAGCCAACGGGCGCAGCTGGTGGCGTGGATGAAAGGCAATACTACCGGTGCCGCGAGTATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGACTATGGTACCACCAACGATATCGCGGTGATTTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCCCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"47917","NCBI_taxonomy_name":"Kluyvera intermedia","NCBI_taxonomy_id":"61648"}}}},"ARO_accession":"3008136","ARO_id":"46928","ARO_name":"CTX-M-246","CARD_short_name":"CTX-M-246","ARO_description":"Extended-spectrum class A beta-lactamase CTX-M-246.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7555":{"model_id":"7555","model_name":"CTX-M-247","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10382":{"protein_sequence":{"accession":"QWS81802.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAVAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYGDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAERRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"MZ379780.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGTCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACGGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGACTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGCGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008137","ARO_id":"46929","ARO_name":"CTX-M-247","CARD_short_name":"CTX-M-247","ARO_description":"Extended-spectrum class A beta-lactamase CTX-M-247.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7556":{"model_id":"7556","model_name":"CTX-M-248","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10383":{"protein_sequence":{"accession":"QWS81803.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAVAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTESTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAERRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"MZ379781.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGTCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAATCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGACTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGCGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008138","ARO_id":"46930","ARO_name":"CTX-M-248","CARD_short_name":"CTX-M-248","ARO_description":"Extended-spectrum class A beta-lactamase CTX-M-248.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7557":{"model_id":"7557","model_name":"CTX-M-249","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10384":{"protein_sequence":{"accession":"QWS81804.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAVAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYGDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTESTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAERRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"MZ379782.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGTCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACGGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAATCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGACTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGCGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008139","ARO_id":"46931","ARO_name":"CTX-M-249","CARD_short_name":"CTX-M-249","ARO_description":"Extended-spectrum class A beta-lactamase CTX-M-249.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7558":{"model_id":"7558","model_name":"CTX-M-251","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10385":{"protein_sequence":{"accession":"UBL87559.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNMAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGDYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"OK217281.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACATGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGACTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3008140","ARO_id":"46932","ARO_name":"CTX-M-251","CARD_short_name":"CTX-M-251","ARO_description":"Extended-spectrum class A beta-lactamase CTX-M-251.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7559":{"model_id":"7559","model_name":"CTX-M-252","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10386":{"protein_sequence":{"accession":"UHC46370.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSVVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAVAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAERRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"OL884447.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGTGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGTCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGACTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGCGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3008141","ARO_id":"46933","ARO_name":"CTX-M-252","CARD_short_name":"CTX-M-252","ARO_description":"Extended-spectrum class A beta-lactamase CTX-M-252.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7560":{"model_id":"7560","model_name":"CTX-M-253","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10387":{"protein_sequence":{"accession":"BDD95705.1","sequence":"MMTQSIRRSMLTVMATLPLLFSSATLHAQANSVQQQLEALEKSSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAVAAVLKQSESDKHLLNQRVEIKKSDLVNYNPIAEKHVNGTMTLAELGAAALQYSDNTAMNKLIAHLGGPDKVTAFARSLGDETFRLDRTEPTLNTAIPGDPRDTTTPLAMAQTLKNLTLGKALAETQRAQLVTWLKGNTTGSASIRAGLPKSWVVGDKTGSGDYGTTNDIAVIWPENHAPLVLVTYFTQPEQKAESRRDILAAAAKIVTHGF"},"dna_sequence":{"accession":"LC670768.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGATGACTCAGAGCATTCGCCGCTCAATGTTAACGGTGATGGCGACGCTACCCCTGCTATTTAGCAGCGCAACGCTGCATGCGCAGGCGAACAGCGTGCAACAGCAGCTGGAAGCCCTGGAGAAAAGTTCGGGAGGTCGGCTTGGCGTTGCGCTGATTAACACCGCCGATAATTCGCAGATTCTCTACCGTGCCGATGAACGTTTTGCGATGTGCAGTACCAGTAAGGTGATGGCGGTCGCGGCGGTGCTTAAACAGAGCGAGAGCGATAAGCACCTGCTAAATCAGCGCGTTGAAATCAAGAAGAGCGACCTGGTTAACTACAATCCCATTGCGGAGAAACACGTTAACGGCACGATGACGCTGGCTGAGCTTGGCGCAGCGGCGCTGCAGTATAGCGACAATACTGCCATGAATAAGCTGATTGCCCATCTGGGTGGTCCCGATAAAGTGACGGCGTTTGCTCGCTCGTTGGGTGATGAGACCTTCCGTCTGGACAGAACCGAGCCCACGCTCAATACCGCCATTCCAGGCGACCCGCGTGATACCACCACGCCGCTCGCGATGGCGCAGACCCTGAAAAATCTGACGCTGGGTAAAGCGCTGGCGGAAACTCAGCGGGCACAGTTGGTGACGTGGCTTAAGGGCAATACTACCGGTAGCGCGAGCATTCGGGCGGGTCTGCCGAAATCATGGGTAGTGGGCGATAAAACCGGCAGCGGAGATTATGGCACCACCAACGATATCGCGGTTATCTGGCCGGAAAACCACGCACCGCTGGTTCTGGTGACCTACTTTACCCAACCGGAGCAGAAGGCGGAAAGCCGTCGGGATATTCTGGCTGCGGCGGCGAAAATCGTAACCCACGGTTTCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36944","NCBI_taxonomy_name":"Providencia rettgeri","NCBI_taxonomy_id":"587"}}}},"ARO_accession":"3008142","ARO_id":"46934","ARO_name":"CTX-M-253","CARD_short_name":"CTX-M-253","ARO_description":"Extended-spectrum class A beta-lactamase CTX-M-253.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7561":{"model_id":"7561","model_name":"CTX-M-254","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10388":{"protein_sequence":{"accession":"UTS94240.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMSSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"ON651487.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGAGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3008143","ARO_id":"46935","ARO_name":"CTX-M-254","CARD_short_name":"CTX-M-254","ARO_description":"Extended-spectrum class A beta-lactamase CTX-M-254.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7562":{"model_id":"7562","model_name":"CTX-M-255","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10389":{"protein_sequence":{"accession":"UTH78367.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTSSGGYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"ON876322.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCAGCAGCGGCGGCTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3008144","ARO_id":"46936","ARO_name":"CTX-M-255","CARD_short_name":"CTX-M-255","ARO_description":"Inhibitor-resistant class A beta-lactamase CTX-M-255.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7563":{"model_id":"7563","model_name":"CTX-M-256","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10390":{"protein_sequence":{"accession":"UUF82537.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGQASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"OP081688.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCAGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39098","NCBI_taxonomy_name":"Enterobacter hormaechei","NCBI_taxonomy_id":"158836"}}}},"ARO_accession":"3008145","ARO_id":"46937","ARO_name":"CTX-M-256","CARD_short_name":"CTX-M-256","ARO_description":"Extended-spectrum class A beta-lactamase CTX-M-256.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7564":{"model_id":"7564","model_name":"CTX-M-257","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10391":{"protein_sequence":{"accession":"UVW30758.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRYTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGDYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"OP297846.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTTATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGACTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39098","NCBI_taxonomy_name":"Enterobacter hormaechei","NCBI_taxonomy_id":"158836"}}}},"ARO_accession":"3008146","ARO_id":"46938","ARO_name":"CTX-M-257","CARD_short_name":"CTX-M-257","ARO_description":"Extended-spectrum class A beta-lactamase CTX-M-257.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7565":{"model_id":"7565","model_name":"CTX-M-258","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10392":{"protein_sequence":{"accession":"UXG78560.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVTLINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"OP346113.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGACATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39098","NCBI_taxonomy_name":"Enterobacter hormaechei","NCBI_taxonomy_id":"158836"}}}},"ARO_accession":"3008147","ARO_id":"46939","ARO_name":"CTX-M-258","CARD_short_name":"CTX-M-258","ARO_description":"Extended-spectrum class A beta-lactamase CTX-M-258.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7566":{"model_id":"7566","model_name":"CTX-M-259","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10393":{"protein_sequence":{"accession":"UXY93308.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVAGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"OP572233.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGCGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008148","ARO_id":"46940","ARO_name":"CTX-M-259","CARD_short_name":"CTX-M-259","ARO_description":"Extended-spectrum class A beta-lactamase CTX-M-259.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7568":{"model_id":"7568","model_name":"CTX-M-261","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10395":{"protein_sequence":{"accession":"WHM00223.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAVAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGGYGTTNDIAMIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"OQ942222.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGTGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGATGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35672","NCBI_taxonomy_name":"Salmonella enterica","NCBI_taxonomy_id":"28901"}}}},"ARO_accession":"3008150","ARO_id":"46942","ARO_name":"CTX-M-261","CARD_short_name":"CTX-M-261","ARO_description":"Extended-spectrum class A beta-lactamase CTX-M-261.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7569":{"model_id":"7569","model_name":"CTX-M-262","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10396":{"protein_sequence":{"accession":"WHL55054.1","sequence":"MVKKSLRQFTLKATATVTLLLGSVPLYAQTADVQQKLAELERPSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"OQ135098.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGAAGGCGACGGCCACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCCGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3008151","ARO_id":"46943","ARO_name":"CTX-M-262","CARD_short_name":"CTX-M-262","ARO_description":"Extended-spectrum class A beta-lactamase CTX-M-262.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7570":{"model_id":"7570","model_name":"CTX-M-263","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10397":{"protein_sequence":{"accession":"WHL55055.1","sequence":"MVKKSLRQFTLKATAPVTLLLRRVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"OQ135099.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGAAGGCGACGGCACCCGTCACGCTGTTGTTACGACGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3008152","ARO_id":"46944","ARO_name":"CTX-M-263","CARD_short_name":"CTX-M-263","ARO_description":"Extended-spectrum class A beta-lactamase CTX-M-263.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7571":{"model_id":"7571","model_name":"CTX-M-264","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10398":{"protein_sequence":{"accession":"WHL55056.1","sequence":"MVKKSLRQFTLKATAPVTLLLGCVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDVVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAVPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESPRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"OQ135100.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGAAGGCGACGGCACCCGTCACGCTGTTGTTAGGATGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACGTTGTTAACTATAATCCGATAGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCGCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCGTTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTAATTCTGGTCACTTACTTCACCCAGCCTCAACCAAAGGCAGAAAGCCCTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3008153","ARO_id":"46945","ARO_name":"CTX-M-264","CARD_short_name":"CTX-M-264","ARO_description":"Extended-spectrum class A beta-lactamase CTX-M-264.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7572":{"model_id":"7572","model_name":"CTX-M-265","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10399":{"protein_sequence":{"accession":"WHL55057.1","sequence":"MVKKSLRQFTLKATAPVTLLLGCVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAVPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESPRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"OQ135101.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGAAGGCGACGGCACCCGTCACGCTGTTGTTAGGATGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATAGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCGTTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTAATTCTGGTCACTTACTTCACCCAGCCTCAACCAAAGGCAGAAAGCCCTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3008154","ARO_id":"46946","ARO_name":"CTX-M-265","CARD_short_name":"CTX-M-265","ARO_description":"Extended-spectrum class A beta-lactamase CTX-M-265.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7573":{"model_id":"7573","model_name":"CTX-M-266","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10400":{"protein_sequence":{"accession":"WKB12816.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKADSRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"OR224962.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGACAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008155","ARO_id":"46947","ARO_name":"CTX-M-266","CARD_short_name":"CTX-M-266","ARO_description":"Extended-spectrum class A beta-lactamase CTX-M-266.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7574":{"model_id":"7574","model_name":"CTX-M-267","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10401":{"protein_sequence":{"accession":"MDO7764851.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAVAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAEHRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"JAUPMU010000029.1","fmin":"822","fmax":"1698","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGTCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGACTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGCACCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3008156","ARO_id":"46948","ARO_name":"CTX-M-267","CARD_short_name":"CTX-M-267","ARO_description":"Extended-spectrum class A beta-lactamase CTX-M-267.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7575":{"model_id":"7575","model_name":"CTX-M-268","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10402":{"protein_sequence":{"accession":"WNH41474.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAGSRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"OR350836.1","fmin":"63","fmax":"939","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGGAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3008157","ARO_id":"46949","ARO_name":"CTX-M-268","CARD_short_name":"CTX-M-268","ARO_description":"Extended-spectrum class A beta-lactamase CTX-M-268.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7576":{"model_id":"7576","model_name":"CTX-M-269","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10403":{"protein_sequence":{"accession":"BET03970.1","sequence":"MVTKRVQRMMFAAVACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAVAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQHAERRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"LC779874.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGTGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGTCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGACTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGCACGCAGAGCGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3008158","ARO_id":"46950","ARO_name":"CTX-M-269","CARD_short_name":"CTX-M-269","ARO_description":"Extended-spectrum class A beta-lactamase CTX-M-269.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7577":{"model_id":"7577","model_name":"CTX-M-270","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10404":{"protein_sequence":{"accession":"WPW57311.1","sequence":"MMTQSIRRSMLTVMATLPLLFSSATLHAQTNSVQQQLEALEKSSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKQSESDKHLLNQRVEIKKSDLVNYNPIAEKHVNGTMTLAELGAAALQYSDNTAMNKLIAHLGGPDKVTAFARSLGDETFRLDRTEPTLNTAIPGDPRDTTTPLAMAQTLKNLTLGKALAETQRAQLVTWLKGNTTGSASIQAGLPKSWVVGDKTGSGDYGTTNDIAIIWPENHAPLVLVTYFTQPEQKAESRRYVLAAAAKIVTHGF"},"dna_sequence":{"accession":"OR921132.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGATGACTCAGAGCATTCGCCGCTCAATGTTAACGGTGATGGCGACGCTACCCCTGCTATTTAGCAGCGCAACGCTGCACGCGCAGACGAACAGCGTGCAACAGCAGCTGGAAGCCCTGGAGAAGAGTTCGGGAGGTCGGCTTGGCGTTGCGCTGATTAACACCGCCGATAATTCGCAGATTCTCTACCGTGCCGATGAACGTTTTGCGATGTGCAGTACCAGTAAGGTGATGGCGGCCGCGGCGGTGCTTAAACAGAGCGAGAGCGATAAGCACCTGCTAAATCAGCGCGTTGAAATCAAGAAGAGCGACCTGGTTAACTACAATCCCATTGCTGAGAAACACGTTAACGGCACGATGACGCTGGCTGAGCTTGGCGCAGCGGCGCTGCAGTATAGCGACAATACTGCCATGAATAAGCTGATTGCCCATCTGGGTGGGCCCGATAAAGTGACGGCGTTTGCTCGCTCGTTGGGTGATGAGACCTTCCGTCTGGACAGAACCGAGCCCACGCTCAATACCGCCATTCCAGGCGACCCGCGTGATACCACCACGCCGCTCGCGATGGCGCAGACCCTGAAAAATCTGACGCTGGGTAAAGCGCTGGCGGAAACTCAGCGGGCACAGTTGGTGACGTGGCTTAAGGGCAATACTACCGGTAGCGCGAGCATTCAGGCGGGTCTGCCGAAATCATGGGTAGTGGGCGATAAAACCGGCAGCGGAGATTATGGCACCACCAACGATATCGCGATTATCTGGCCGGAAAACCACGCACCGCTGGTTCTGGTGACCTACTTTACCCAACCGGAGCAGAAGGCGGAAAGCCGTCGGTATGTTCTGGCTGCGGCGGCGAAAATCGTAACCCACGGTTTCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36928","NCBI_taxonomy_name":"Kluyvera ascorbata","NCBI_taxonomy_id":"51288"}}}},"ARO_accession":"3008159","ARO_id":"46951","ARO_name":"CTX-M-270","CARD_short_name":"CTX-M-270","ARO_description":"Extended-spectrum class A beta-lactamase CTX-M-270.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7578":{"model_id":"7578","model_name":"CTX-M-271","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10405":{"protein_sequence":{"accession":"ENH5532102.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTATPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"ABTDWX010000102.1","fmin":"497","fmax":"1373","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCACTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36870","NCBI_taxonomy_name":"Shigella flexneri","NCBI_taxonomy_id":"623"}}}},"ARO_accession":"3008160","ARO_id":"46952","ARO_name":"CTX-M-271","CARD_short_name":"CTX-M-271","ARO_description":"Extended-spectrum class A beta-lactamase CTX-M-271.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7579":{"model_id":"7579","model_name":"CTX-M-272","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10406":{"protein_sequence":{"accession":"BFR97113.1","sequence":"MMTQSIRRSMLTVMATLPLLFSSATLHAQAYSVQQQLEALEKSSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKQSESDKHLLNQRVEIKKSDLVNYNPIAEKHVNGTMTLAELGAAALQYSDNTAMNKLIAHLGGPDKVTAFARSLGDETFRLDRTEPTLNTAIPGDPRDTTTPLAMAQTLKNLTLGKALAETQRAQLVTWLKGNTTGSASIRAGLPKSWVVGDKTGSGDYGTTNDIAVIWPENHAPLVLVTYFTQPEQKAESRRDILAAAAKIVTHGF"},"dna_sequence":{"accession":"LC841927.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGATGACTCAGAGCATTCGCCGCTCAATGTTAACGGTGATGGCGACGCTACCCCTGCTATTTAGCAGCGCAACGCTGCATGCGCAGGCGTACAGCGTGCAACAGCAGCTGGAAGCCCTGGAGAAAAGTTCGGGAGGTCGGCTTGGCGTTGCGCTGATTAACACCGCCGATAATTCGCAGATTCTCTACCGTGCCGATGAACGTTTTGCGATGTGCAGTACCAGTAAGGTGATGGCGGCCGCGGCGGTGCTTAAACAGAGCGAGAGCGATAAGCACCTGCTAAATCAGCGCGTTGAAATCAAGAAGAGCGACCTGGTTAACTACAATCCCATTGCGGAGAAACACGTTAACGGCACGATGACGCTGGCTGAGCTTGGCGCAGCGGCGCTGCAGTATAGCGACAATACTGCCATGAATAAGCTGATTGCCCATCTGGGTGGTCCCGATAAAGTGACGGCGTTTGCTCGCTCGTTGGGTGATGAGACCTTCCGTCTGGACAGAACCGAGCCCACGCTCAATACCGCCATTCCAGGCGACCCGCGTGATACCACCACGCCGCTCGCGATGGCGCAGACCCTGAAAAATCTGACGCTGGGTAAAGCGCTGGCGGAAACTCAGCGGGCACAGTTGGTGACGTGGCTTAAGGGCAATACTACCGGTAGCGCGAGCATTCGGGCGGGTCTGCCGAAATCATGGGTAGTGGGCGATAAAACCGGCAGCGGAGATTATGGCACCACCAACGATATCGCGGTTATCTGGCCGGAAAACCACGCACCGCTGGTTCTGGTGACCTACTTTACCCAACCGGAGCAGAAGGCGGAAAGCCGTCGGGATATTCTGGCTGCGGCGGCGAAAATCGTAACCCACGGTTTCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008161","ARO_id":"46953","ARO_name":"CTX-M-272","CARD_short_name":"CTX-M-272","ARO_description":"Extended-spectrum class A beta-lactamase CTX-M-272.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7580":{"model_id":"7580","model_name":"CTX-M-273","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10407":{"protein_sequence":{"accession":"XHE66952.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTESTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"PQ324802.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGTCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008162","ARO_id":"46954","ARO_name":"CTX-M-273","CARD_short_name":"CTX-M-273","ARO_description":"Extended-spectrum class A beta-lactamase CTX-M-273.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7581":{"model_id":"7581","model_name":"CTX-M-274","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10408":{"protein_sequence":{"accession":"XHO32884.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDRTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"PQ394541.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAGAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3008163","ARO_id":"46955","ARO_name":"CTX-M-274","CARD_short_name":"CTX-M-274","ARO_description":"Extended-spectrum class A beta-lactamase CTX-M-274.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7582":{"model_id":"7582","model_name":"CTX-M-275","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10409":{"protein_sequence":{"accession":"XHO32885.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASASKIVTDGL"},"dna_sequence":{"accession":"PQ394542.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGTCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3008164","ARO_id":"46956","ARO_name":"CTX-M-275","CARD_short_name":"CTX-M-275","ARO_description":"Extended-spectrum class A beta-lactamase CTX-M-275.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7583":{"model_id":"7583","model_name":"CTX-M-276","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10410":{"protein_sequence":{"accession":"XHO32886.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPNLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPMLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGGYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"PQ394543.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGATGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3008165","ARO_id":"46957","ARO_name":"CTX-M-276","CARD_short_name":"CTX-M-276","ARO_description":"Extended-spectrum class A beta-lactamase CTX-M-276.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7584":{"model_id":"7584","model_name":"CTX-M-277","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10411":{"protein_sequence":{"accession":"XHO32887.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGEERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGGYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"PQ394544.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGAGGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGCGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGGCTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3008166","ARO_id":"46958","ARO_name":"CTX-M-277","CARD_short_name":"CTX-M-277","ARO_description":"Extended-spectrum class A beta-lactamase CTX-M-277.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7585":{"model_id":"7585","model_name":"CTX-M-278","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10412":{"protein_sequence":{"accession":"XHO32888.1","sequence":"MVTKRVQRMMFAAAACIPLLLGSAPLYAQTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSVAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTVGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL"},"dna_sequence":{"accession":"PQ394545.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTGACAAAGAGAGTGCAACGGATGATGTTCGCGGCGGCGGCGTGCATTCCGCTGCTGCTGGGCAGCGCGCCGCTTTATGCGCAGACGAGTGCGGTGCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGAGGGCGGCTGGGCGTCGCGCTCATCGATACCGCAGATAATACGCAGGTGCTTTATCGCGGTGATGAACGCTTTCCAATGTGCAGTACCAGTAAAGTTATGGCGGCCGCGGCGGTGCTTAAGCAGAGTGAAACGCAAAAGCAGCTGCTTAATCAGCCTGTCGAGATCAAGCCTGCCGATCTGGTTAACTACAATCCGATTGCCGAAAAACACGTCAACGGCACAATGACGCTGGCAGAACTGAGCGTGGCCGCGTTGCAGTACAGCGACAATACCGCCATGAACAAATTGATTGCCCAGCTCGGTGGCCCGGGAGGCGTGACGGCTTTTGCCCGCGCGATCGGCGATGAGACGTTTCGTCTGGATCGCACTGAACCTACGCTGAATACCGCCATTCCCGGCGACCCGAGAGACACCACCACGCCGCGGGCGATGGCGCAGACGTTGCGTCAGCTTACGCTGGGTCATGCGCTGGGCGAAACCCAGCGGGCGCAGTTGGTGACGTGGCTCAAAGGCAATACGACCGGCGCAGCCAGCATTCGGGCCGGCTTACCGACGTCGTGGACTGTGGGTGATAAGACCGGCAGCGGCGACTACGGCACCACCAATGATATTGCGGTGATCTGGCCGCAGGGTCGTGCGCCGCTGGTTCTGGTGACCTATTTTACCCAGCCGCAACAGAACGCAGAGAGCCGCCGCGATGTGCTGGCTTCAGCGGCGAGAATCATCGCCGAAGGGCTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3008167","ARO_id":"46959","ARO_name":"CTX-M-278","CARD_short_name":"CTX-M-278","ARO_description":"Extended-spectrum class A beta-lactamase CTX-M-278.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7586":{"model_id":"7586","model_name":"DHA-30","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10413":{"protein_sequence":{"accession":"BEK76843.1","sequence":"MTKSLSATLVSALLAFSAPGLSAADNVAAVVDSTIKPLMAQQDIPGMAVAVSVKGKPYYFNYGFADVQAKQPVTENTLFELGSVSKTFTGVLGAVSVAKKETSLNDPAVKYQPELTQPQWKGITLLDLATYTAGGLPLQVPEAVKSSEDLLHFYQQWQPSWQPGKMRLYANSSIGLFGALTATAAGMPYEQLLTARILAPLGLSHTFITVPESAQSQYAYGYKNNQPVRVTGGPLDAESYGVKSASKDMLRWAEINMSPSRAGNADLEMAMYLAQTRYYKTAAINQGLGWEMYDWPQQKDMIINGVTNEVALQPHPVTDNQVQPYNRASWVHKTGATTGFGAYVAFIPEKQVAIVILANKNYPNTERVKAAQAILSALE"},"dna_sequence":{"accession":"LC773167.1","fmin":"0","fmax":"1140","strand":"+","sequence":"ATGACAAAATCTTTATCTGCAACACTGGTTTCCGCCCTGCTGGCCTTTTCTGCCCCGGGGCTCTCTGCCGCTGATAATGTCGCGGCAGTCGTCGACAGCACCATTAAACCGCTGATGGCACAGCAGGATATCCCCGGGATGGCGGTTGCTGTCTCCGTAAAGGGAAAACCGTATTACTTCAACTATGGTTTTGCGGATGTGCAGGCAAAACAGCCGGTCACTGAAAATACACTATTTGAACTCGGATCTGTAAGTAAAACTTTCACAGGTGTGCTGGGTGCGGTTTCCGTGGCGAAAAAAGAGACATCGCTGAATGACCCGGCAGTCAAATACCAGCCTGAACTGACACAGCCGCAGTGGAAAGGGATCACCTTACTGGATCTGGCGACCTATACCGCAGGCGGGCTGCCGTTACAGGTGCCGGAAGCGGTGAAAAGCAGTGAGGATCTGCTGCATTTCTATCAGCAGTGGCAGCCGTCATGGCAACCGGGAAAGATGCGTCTGTATGCGAACAGCAGTATCGGCCTGTTCGGCGCGCTGACCGCGACAGCGGCGGGAATGCCTTATGAGCAGCTGCTGACCGCACGTATCCTGGCGCCGCTGGGGTTATCACATACCTTTATTACTGTACCGGAAAGTGCGCAAAGTCAGTATGCATACGGTTATAAAAACAATCAGCCGGTACGGGTGACGGGGGGACCGCTCGATGCGGAATCTTACGGGGTAAAATCCGCCTCAAAAGATATGCTGCGCTGGGCAGAAATCAATATGTCGCCGTCACGGGCGGGCAATGCGGATCTGGAAATGGCGATGTATCTCGCACAGACCCGTTACTATAAAACGGCGGCAATCAACCAGGGACTGGGCTGGGAGATGTATGACTGGCCGCAGCAGAAAGATATGATCATTAACGGCGTGACCAATGAAGTGGCATTGCAGCCGCATCCGGTAACGGATAATCAGGTTCAGCCGTATAACCGCGCTTCCTGGGTACATAAAACAGGAGCAACAACCGGTTTCGGTGCTTATGTGGCCTTTATTCCGGAAAAACAGGTGGCGATTGTGATTCTGGCAAATAAAAACTACCCGAATACCGAAAGAGTCAAAGCCGCACAGGCTATTTTGAGTGCACTGGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36917","NCBI_taxonomy_name":"Morganella morganii","NCBI_taxonomy_id":"582"}}}},"ARO_accession":"3008168","ARO_id":"46960","ARO_name":"DHA-30","CARD_short_name":"DHA-30","ARO_description":"Class C beta-lactamase DHA-30.","ARO_category":{"36207":{"category_aro_accession":"3000068","category_aro_cvterm_id":"36207","category_aro_name":"DHA beta-lactamase","category_aro_description":"DHA beta-lactamases are plasmid-mediated AmpC \u03b2-lactamases that confer resistance to cephamycins and oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7587":{"model_id":"7587","model_name":"DHA-31","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10414":{"protein_sequence":{"accession":"WLO97155.1","sequence":"MTKSVSATLISALLAFSAPGFSAADNVAAVVDSTIKPLMAQQDIPGMAVAVSVKGKPYYFNYGFADVQAKQPVTENTLFELGSVSKTFTGVLGAVSVAKKETALNDPAAKYQPELALPQWKGITLLDLATYTAGGLPLQVPDAVKSRADLLNFYQQWQPSWKPGDMRLYANSSIGLFGALTANAAGMPYEQLLTARILAPLGLSHTFITVPESVQSRYAYGYKNKKPVRVSPGQLDAESYGVKSASKDMLRWAEMNMEPSRAGNADLEMAMYLAQTRYYKTAAINQGLGWEMYDSPQQKDMIINGVTNEVALQPHPVTDNQVQPYNRASWVHKTGATTGFGAYVAFIPEKQVAIVILANKNYPNTERVKAAQAILSALE"},"dna_sequence":{"accession":"OR398192.1","fmin":"0","fmax":"1140","strand":"+","sequence":"ATGACAAAATCTGTATCTGCAACACTGATTTCTGCCCTGCTGGCGTTTTCCGCCCCGGGGTTTTCTGCCGCTGATAATGTCGCAGCGGTGGTGGACAGCACTATTAAACCGCTGATGGCACAGCAGGATATTCCCGGGATGGCGGTTGCCGTATCCGTAAAGGGCAAGCCCTATTATTTTAACTATGGTTTTGCCGATGTTCAGGCAAAACAGCCGGTCACTGAAAATACACTATTTGAGCTCGGATCTGTAAGTAAAACTTTCACAGGTGTGCTGGGTGCGGTTTCTGTGGCGAAAAAAGAGACGGCGCTGAATGATCCGGCGGCAAAATATCAGCCGGAGCTGGCTCTGCCGCAGTGGAAGGGGATCACGCTGCTGGATCTGGCCACCTATACCGCAGGCGGGCTGCCGTTACAGGTACCGGATGCGGTGAAAAGCCGTGCGGATCTGCTGAATTTCTATCAGCAGTGGCAGCCATCATGGAAACCGGGCGATATGCGTCTGTATGCAAACAGCAGTATCGGCCTGTTTGGTGCTCTGACCGCCAATGCGGCGGGGATGCCGTATGAGCAGTTGCTGACCGCGCGGATCCTGGCACCGCTGGGATTATCTCACACCTTTATTACCGTGCCGGAAAGTGTGCAAAGCCGGTATGCGTACGGCTATAAAAACAAAAAACCGGTCCGCGTGTCGCCGGGACAGCTTGATGCGGAATCTTACGGCGTGAAATCCGCCTCAAAAGATATGCTGCGCTGGGCGGAAATGAATATGGAGCCGTCACGGGCCGGTAATGCGGATCTGGAAATGGCAATGTATCTCGCCCAGACCCGCTACTATAAAACCGCCGCGATTAACCAGGGGCTGGGCTGGGAAATGTATGACTCGCCGCAGCAGAAAGATATGATCATTAACGGTGTGACCAACGAGGTCGCATTGCAGCCGCATCCGGTAACAGACAACCAGGTTCAGCCGTATAACCGTGCTTCCTGGGTGCATAAAACGGGGGCAACAACTGGTTTCGGCGCCTATGTGGCCTTTATTCCGGAAAAACAGGTGGCGATTGTGATTCTGGCGAATAAAAACTACCCGAATACCGAAAGAGTCAAAGCTGCACAGGCTATTTTGAGTGCACTGGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36917","NCBI_taxonomy_name":"Morganella morganii","NCBI_taxonomy_id":"582"}}}},"ARO_accession":"3008169","ARO_id":"46961","ARO_name":"DHA-31","CARD_short_name":"DHA-31","ARO_description":"Class C beta-lactamase DHA-31.","ARO_category":{"36207":{"category_aro_accession":"3000068","category_aro_cvterm_id":"36207","category_aro_name":"DHA beta-lactamase","category_aro_description":"DHA beta-lactamases are plasmid-mediated AmpC \u03b2-lactamases that confer resistance to cephamycins and oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7588":{"model_id":"7588","model_name":"DHA-32","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10415":{"protein_sequence":{"accession":"WLY62595.1","sequence":"MTKSVSATLISALLAFSAPGFSAADNVAAVVDSTIKPLMAQQDIPGMAVAVSVKGKPYYFNYGFADVQAKQPVTENTLFELGSVSKTFTGVLGAVSVAKKETALNDPAAKYQPELALPQWKGITLLDLATYTAGGLPLQVPDAVKSRADLLNFYQQWQPSWKPGDMRLYANSSIGLFGALTANAAGMPYEQLLTARILAPLGLSHTFITVPESVQSRYAYGYKNKKPVRVSPGQLDAESYGVKSASKDMLRWAEMNMEPSRAGNADLEMAMYLAQTRYYKTAAINQGLGWEMYDWPQQKDMIINGVTNEVALQPHPVTDNQVQPYNRASWVHKTGATTGFGAYVAFIPEKQVAIVILANKNYPNTERVKAAQAILSALE"},"dna_sequence":{"accession":"OR438753.1","fmin":"0","fmax":"1140","strand":"+","sequence":"ATGACAAAATCTGTATCTGCAACACTGATTTCTGCCCTGCTGGCGTTTTCCGCCCCGGGGTTTTCTGCCGCTGATAATGTCGCAGCGGTGGTGGACAGCACTATTAAACCGCTGATGGCACAGCAGGATATTCCCGGGATGGCGGTTGCCGTATCCGTAAAGGGCAAGCCCTATTATTTTAACTATGGTTTTGCCGATGTTCAGGCAAAACAGCCGGTCACTGAAAATACACTATTTGAGCTCGGATCTGTAAGTAAAACTTTCACAGGTGTGCTGGGTGCGGTTTCTGTGGCGAAAAAAGAGACGGCGCTGAATGATCCGGCGGCAAAATATCAGCCGGAGCTGGCTCTGCCGCAGTGGAAGGGGATCACGCTGCTGGATCTGGCCACCTATACCGCAGGCGGGCTGCCGTTACAGGTACCGGATGCGGTGAAAAGCCGTGCGGATCTGCTGAATTTCTATCAGCAGTGGCAGCCATCATGGAAACCGGGCGATATGCGTCTGTATGCAAACAGCAGTATCGGCCTGTTTGGTGCTCTGACCGCCAATGCGGCGGGGATGCCGTATGAGCAGTTGCTGACCGCGCGGATCCTGGCACCGCTGGGATTATCTCACACCTTTATTACCGTGCCGGAAAGTGTGCAAAGCCGGTATGCGTACGGCTATAAAAACAAAAAACCGGTCCGCGTGTCGCCGGGACAGCTTGATGCGGAATCTTACGGCGTGAAATCCGCCTCAAAAGATATGCTGCGCTGGGCGGAAATGAATATGGAGCCGTCACGGGCCGGTAATGCGGATCTGGAAATGGCAATGTATCTCGCCCAGACCCGCTACTATAAAACCGCCGCGATTAACCAGGGGCTGGGCTGGGAAATGTATGACTGGCCGCAGCAGAAAGATATGATCATTAACGGTGTGACCAACGAGGTCGCATTGCAGCCGCATCCGGTAACAGACAACCAGGTTCAGCCGTATAACCGTGCTTCCTGGGTGCATAAAACGGGGGCAACAACTGGTTTCGGCGCCTATGTGGCCTTTATTCCGGAAAAACAGGTGGCGATTGTGATTCTGGCGAATAAAAACTACCCGAATACCGAAAGAGTCAAAGCTGCACAGGCTATTTTGAGTGCACTGGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36917","NCBI_taxonomy_name":"Morganella morganii","NCBI_taxonomy_id":"582"}}}},"ARO_accession":"3008170","ARO_id":"46962","ARO_name":"DHA-32","CARD_short_name":"DHA-32","ARO_description":"Class C beta-lactamase DHA-32.","ARO_category":{"36207":{"category_aro_accession":"3000068","category_aro_cvterm_id":"36207","category_aro_name":"DHA beta-lactamase","category_aro_description":"DHA beta-lactamases are plasmid-mediated AmpC \u03b2-lactamases that confer resistance to cephamycins and oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7589":{"model_id":"7589","model_name":"DHA-33","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10416":{"protein_sequence":{"accession":"WOL30716.1","sequence":"MKKSLSATLISALLAFSAPGFSAADNVAAVVDSTIKPLMAQQDIPGMAVAVSVKGKPYYFNYGFADIQAKQPVTENTLFELGSVSKTFTGVLGAVSVAKKEMALNDPAAKYQPELALPQWKGITLLDLATYTAGGLPLQVPDAVKSRADLLNFYQQWQPSRKPGDMRLYANSSIGLFGALTANAAGMPYEQLLTARILAPLGLSHTFITVPESAQSQYAYGYKNKKPVRVSPGQLDAKSYGVKSASKDMLRWAEMNMEPSRAGNADLEMAMYLAQTRYYKTAAINQGLGWEMYDWPQQKDMIINGVTNEVALQPHPVTDNQVQPYNRASWVHKTGATTGFGAYVAFIPEKQVAIVILANKNYPNTERVKAAQAILSALE"},"dna_sequence":{"accession":"OR715113.1","fmin":"0","fmax":"1140","strand":"+","sequence":"ATGAAAAAATCGTTATCTGCAACACTGATTTCCGCTCTGCTGGCGTTTTCCGCCCCGGGGTTTTCTGCCGCTGATAATGTCGCGGCGGTGGTGGACAGCACCATTAAACCGCTGATGGCACAGCAGGATATTCCCGGGATGGCGGTTGCCGTCTCCGTAAAGGGTAAGCCCTATTATTTCAATTATGGTTTTGCCGATATTCAGGCAAAACAGCCGGTCACTGAAAATACACTATTTGAGCTCGGATCTGTAAGTAAAACTTTCACAGGTGTGCTGGGTGCGGTTTCTGTGGCGAAAAAAGAGATGGCGCTGAATGATCCGGCGGCAAAATACCAGCCGGAGCTGGCTCTGCCGCAGTGGAAGGGGATCACATTGCTGGATCTGGCTACCTATACCGCAGGCGGACTGCCGTTACAGGTGCCGGATGCGGTAAAAAGCCGTGCGGATCTGCTGAATTTCTATCAGCAGTGGCAGCCGTCCCGGAAACCGGGCGATATGCGTCTGTATGCAAACAGCAGTATCGGCCTGTTTGGTGCTCTGACCGCAAACGCGGCGGGGATGCCGTATGAGCAGTTGCTGACTGCACGGATCCTGGCACCGCTGGGGTTATCTCACACCTTTATTACTGTGCCGGAAAGTGCGCAAAGCCAGTATGCGTACGGTTATAAAAACAAAAAACCGGTCCGCGTGTCGCCGGGACAGCTTGATGCGAAATCTTACGGCGTGAAATCCGCCTCAAAAGATATGCTGCGCTGGGCGGAAATGAATATGGAGCCGTCACGGGCCGGTAATGCGGATCTGGAAATGGCAATGTATCTCGCCCAGACCCGCTACTATAAAACCGCCGCGATTAACCAGGGGCTGGGCTGGGAAATGTATGACTGGCCGCAGCAGAAAGATATGATCATTAACGGTGTGACCAACGAGGTCGCATTGCAGCCGCATCCGGTAACAGACAACCAGGTTCAGCCGTATAACCGTGCTTCCTGGGTGCATAAAACGGGCGCAACAACTGGTTTCGGCGCCTATGTCGCCTTTATTCCGGAAAAACAGGTGGCGATTGTGATTCTGGCGAATAAAAACTACCCGAATACCGAAAGAGTCAAAGCTGCACAGGCTATTTTGAGTGCACTGGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3008171","ARO_id":"46963","ARO_name":"DHA-33","CARD_short_name":"DHA-33","ARO_description":"Class C beta-lactamase DHA-33.","ARO_category":{"36207":{"category_aro_accession":"3000068","category_aro_cvterm_id":"36207","category_aro_name":"DHA beta-lactamase","category_aro_description":"DHA beta-lactamases are plasmid-mediated AmpC \u03b2-lactamases that confer resistance to cephamycins and oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7590":{"model_id":"7590","model_name":"DHA-34","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10417":{"protein_sequence":{"accession":"XHO32889.1","sequence":"MKKSLSATLISALLAFSAPGFSAADNVAAVVDSTIKPLMAQQDIPGMAVAVSVKGKPYYFNYGFADIQAKQPVTENTLFELGSVSKTFTGVLGAVSVAKKEMALNDPAAKYQPELALPQWKGITLLDLATYTAGGLPLQVPDAVKSRADLLNFYQQWQPSRKPGDMRLYANSSIGLFGALTANAAGMPYEQLLTARILAPLGLSHTFITVPESAQSQYAYGYKNKKPVRVSPGQIDAESYGVKSASKDMLRWAEMNMEPSRAGNADLEMAMYLAQTRYYKTAAINQGLGWEMYDWPQQKDMIINGVTNEVALQPHPVTDNQVQPYNRASWVHKTGATTGFGAYVAFIPEKQVAIVILANKNYPNTERVKAAQAILSALE"},"dna_sequence":{"accession":"PQ394546.1","fmin":"0","fmax":"1140","strand":"+","sequence":"ATGAAAAAATCGTTATCTGCAACACTGATTTCCGCTCTGCTGGCGTTTTCCGCCCCGGGGTTTTCTGCCGCTGATAATGTCGCGGCGGTGGTGGACAGCACCATTAAACCGCTGATGGCACAGCAGGATATTCCCGGGATGGCGGTTGCCGTCTCCGTAAAGGGTAAGCCCTATTATTTCAATTATGGTTTTGCCGATATTCAGGCAAAACAGCCGGTCACTGAAAATACACTATTTGAGCTCGGATCTGTAAGTAAAACTTTCACAGGTGTGCTGGGTGCGGTTTCTGTGGCGAAAAAAGAGATGGCGCTGAATGATCCGGCGGCAAAATACCAGCCGGAGCTGGCTCTGCCGCAGTGGAAGGGGATCACATTGCTGGATCTGGCTACCTATACCGCAGGCGGACTGCCGTTACAGGTGCCGGATGCGGTAAAAAGCCGTGCGGATCTGCTGAATTTCTATCAGCAGTGGCAGCCGTCCCGGAAACCGGGCGATATGCGTCTGTATGCAAACAGCAGTATCGGCCTGTTTGGTGCTCTGACCGCAAACGCGGCGGGGATGCCGTATGAGCAGTTGCTGACTGCACGGATCCTGGCACCGCTGGGGTTATCTCACACCTTTATTACTGTGCCGGAAAGTGCGCAAAGCCAGTATGCGTACGGTTATAAAAACAAAAAACCGGTCCGCGTGTCGCCGGGACAGATTGATGCGGAATCTTACGGCGTGAAATCCGCCTCAAAAGATATGCTGCGCTGGGCGGAAATGAATATGGAGCCGTCACGGGCCGGTAATGCGGATCTGGAAATGGCAATGTATCTCGCCCAGACCCGCTACTATAAAACCGCCGCGATTAACCAGGGGCTGGGCTGGGAAATGTATGACTGGCCGCAGCAGAAAGATATGATCATTAACGGTGTGACCAACGAGGTCGCATTGCAGCCGCATCCGGTAACAGACAACCAGGTTCAGCCGTATAACCGTGCTTCCTGGGTGCATAAAACGGGCGCAACAACTGGTTTCGGCGCCTATGTCGCCTTTATTCCGGAAAAACAGGTGGCGATTGTGATTCTGGCGAATAAAAACTACCCGAATACCGAAAGAGTCAAAGCTGCACAGGCTATTTTGAGTGCACTGGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3008172","ARO_id":"46964","ARO_name":"DHA-34","CARD_short_name":"DHA-34","ARO_description":"Class C beta-lactamase DHA-34.","ARO_category":{"36207":{"category_aro_accession":"3000068","category_aro_cvterm_id":"36207","category_aro_name":"DHA beta-lactamase","category_aro_description":"DHA beta-lactamases are plasmid-mediated AmpC \u03b2-lactamases that confer resistance to cephamycins and oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7591":{"model_id":"7591","model_name":"FONA-10","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10418":{"protein_sequence":{"accession":"USH09259.1","sequence":"MVKNTLRQTTLMVATVMPLLFGSAPLWAQPANAKANIQQQLSELEKSSGGRLGVALIDTADNSQILYRGDERFPMCSTSKVMAVSALLKQSETDKNLLAKRMEIKQSDLVNYNPIAEKHLDTGMTLAEFSAATIQYSDNTAMNKILEHLGGPAKVTEFARTIGDKTFRLDRTEPTLNTAIPGDKRDTTSPLAMAKSLQNLTLGKALGEPQRAQLVEWMKGNTTGGASIRAGLPTTWVVGDKTGSGDYGTTNDIAVIWPANHAPLVLVTYFTQPQQNAEARKDVLAAAAKIVTEGL"},"dna_sequence":{"accession":"ON713462.1","fmin":"0","fmax":"888","strand":"+","sequence":"ATGGTTAAAAATACATTACGTCAAACCACCCTGATGGTGGCTACGGTTATGCCGTTGTTGTTCGGTAGCGCACCGTTATGGGCGCAACCCGCTAATGCCAAGGCGAATATTCAGCAGCAACTGTCTGAACTGGAGAAAAGCTCCGGTGGACGCTTGGGTGTGGCGCTGATCGATACCGCCGATAATTCGCAGATCCTGTATCGCGGGGATGAACGTTTTCCCATGTGCAGCACCAGCAAGGTGATGGCAGTGTCGGCGTTGTTAAAACAGAGCGAGACGGATAAAAATCTTTTGGCTAAGCGGATGGAGATCAAGCAATCCGATCTGGTCAACTACAACCCGATCGCCGAAAAACACCTGGATACCGGGATGACCCTGGCCGAGTTCAGCGCCGCCACCATCCAGTACAGTGACAACACGGCGATGAACAAGATCCTTGAGCATCTTGGCGGCCCGGCAAAAGTGACAGAATTTGCGCGTACTATTGGCGATAAAACCTTCCGCCTCGATCGTACCGAACCCACTTTAAATACCGCCATTCCAGGTGATAAGCGTGATACCACCTCACCGCTGGCGATGGCAAAAAGCCTGCAAAACCTGACCTTGGGCAAAGCGCTGGGTGAACCACAGCGTGCTCAACTGGTTGAATGGATGAAGGGGAATACTACCGGCGGAGCCAGCATTCGCGCAGGTCTGCCAACTACATGGGTGGTTGGGGATAAAACCGGCAGCGGTGATTACGGTACCACTAACGATATCGCCGTAATTTGGCCAGCGAACCACGCACCGTTGGTATTAGTAACCTATTTCACGCAACCACAGCAGAATGCCGAAGCTCGCAAAGACGTGTTGGCTGCGGCTGCTAAAATTGTTACCGAAGGTCTTTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39675","NCBI_taxonomy_name":"Serratia fonticola","NCBI_taxonomy_id":"47917"}}}},"ARO_accession":"3008173","ARO_id":"46965","ARO_name":"FONA-10","CARD_short_name":"FONA-10","ARO_description":"Class A beta-lactamase FONA-10.","ARO_category":{"42905":{"category_aro_accession":"3004787","category_aro_cvterm_id":"42905","category_aro_name":"FONA beta-lactamase","category_aro_description":"FONA is a class A beta-lactamase gene family found in Serratia fonticola.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7592":{"model_id":"7592","model_name":"FONA-11","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10419":{"protein_sequence":{"accession":"USH09260.1","sequence":"MVRNTLRQTTLMVATVMPLLFGSAPLWAQPANAKANIQQQLSELEKNSGGRLGVALIDTADNSQILYRGDERFPMCSTSKVMAVSALLKQSETDKNLLAKRMEIKQSDLVNYNPIAEKHLDTGMTLAEFSAATIQYSDNTAMNKILEHLGGPAKVTEFARTIGDKTFRLDRTEPTLNTAIPGDKRDTTSPQAMAKSLQNLTLGKALGEPQRAQLVEWMKGNTTGGASIRAGLPTTWVVGDKTGSGDYGTTNDIAVIWPANHAPLVLVTYFTQPQQNAEARKDVLAAAAKIVTAGL"},"dna_sequence":{"accession":"ON713463.1","fmin":"0","fmax":"888","strand":"+","sequence":"ATGGTTAGAAATACATTACGTCAAACCACCCTGATGGTCGCTACGGTTATGCCGTTGCTGTTCGGTAGCGCACCGTTATGGGCGCAACCCGCTAATGCCAAGGCCAATATTCAGCAGCAACTGTCTGAACTGGAGAAAAACTCCGGTGGCCGCCTGGGCGTGGCGCTGATCGATACCGCCGATAATTCGCAGATCCTGTATCGTGGGGATGAACGTTTTCCCATGTGCAGCACCAGCAAGGTGATGGCAGTGTCGGCGTTGTTAAAACAGAGCGAGACGGATAAAAATCTTTTGGCTAAGCGGATGGAGATCAAACAATCCGATCTGGTCAACTACAACCCGATCGCCGAAAAACATCTGGATACCGGGATGACCCTGGCCGAGTTCAGCGCCGCCACTATCCAGTACAGTGACAACACGGCGATGAACAAGATCCTTGAGCATCTTGGCGGCCCGGCAAAAGTGACAGAATTTGCGCGTACTATCGGCGATAAAACCTTCCGTCTCGATCGTACCGAACCCACTTTAAATACCGCCATCCCGGGTGATAAGCGTGACACCACCTCGCCGCAGGCGATGGCAAAAAGCCTGCAAAACCTGACCTTGGGCAAAGCGCTGGGTGAACCACAGCGTGCTCAACTGGTTGAATGGATGAAGGGGAATACTACCGGCGGAGCCAGCATTCGCGCAGGTCTGCCAACCACGTGGGTGGTCGGTGATAAAACCGGCAGCGGTGATTACGGTACCACTAACGATATCGCCGTGATTTGGCCAGCTAACCACGCACCGTTGGTATTGGTGACCTATTTCACGCAGCCACAGCAGAATGCCGAAGCCCGCAAAGACGTGTTGGCTGCGGCTGCTAAAATTGTCACCGCAGGACTTTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39675","NCBI_taxonomy_name":"Serratia fonticola","NCBI_taxonomy_id":"47917"}}}},"ARO_accession":"3008174","ARO_id":"46966","ARO_name":"FONA-11","CARD_short_name":"FONA-11","ARO_description":"Class A beta-lactamase FONA-11.","ARO_category":{"42905":{"category_aro_accession":"3004787","category_aro_cvterm_id":"42905","category_aro_name":"FONA beta-lactamase","category_aro_description":"FONA is a class A beta-lactamase gene family found in Serratia fonticola.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7593":{"model_id":"7593","model_name":"FONA-12","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10420":{"protein_sequence":{"accession":"USH09261.1","sequence":"MVRNTLRQTTLMVATVMPLLFGSAPLWAQPANAKANIQQQLSELEKNSGGRLGVALIDTADNSQILYRGDERFPMCSTSKVMAVSALLKQSETDKNLLAKRMEIKQSDLVNYNPIAEKHLDTGMTLAEFSAATIQYSDNTAMNKILEHLGGPAKVTEFARTIGDKTFRLDRTEPTLNTAIPGDKRDTTSPQAMAKSLQNLTLGKALAEPQRAQLVEWMKGNTTGGASIRAGLPTTWVVGDKTGSGDYGTTNDIAVIWPANHAPLVLVTYFTQPQQNAEARKDVLAAAAKIVTAGL"},"dna_sequence":{"accession":"ON713464.1","fmin":"0","fmax":"888","strand":"+","sequence":"ATGGTTAGAAATACATTACGTCAAACCACCCTGATGGTCGCTACGGTTATGCCGTTGCTGTTCGGTAGCGCACCATTATGGGCGCAACCCGCTAATGCCAAGGCCAATATTCAGCAGCAACTGTCTGAACTGGAGAAAAACTCCGGTGGCCGCCTGGGCGTGGCGCTGATCGATACCGCCGATAATTCGCAGATCCTGTATCGTGGGGATGAACGTTTTCCCATGTGCAGCACCAGCAAGGTGATGGCAGTGTCGGCGTTGTTAAAACAGAGCGAGACGGATAAAAATCTTTTGGCTAAGCGGATGGAGATCAAACAATCCGATCTGGTCAACTACAACCCGATCGCCGAAAAACACCTGGATACCGGGATGACCCTGGCCGAGTTCAGTGCCGCCACTATCCAGTACAGTGACAACACGGCGATGAACAAGATCCTTGAGCATCTTGGCGGCCCGGCAAAAGTGACAGAATTTGCGCGTACTATCGGCGATAAAACCTTCCGTCTCGATCGTACCGAACCCACTTTAAATACCGCCATCCCGGGTGATAAGCGTGACACCACCTCGCCGCAGGCGATGGCAAAAAGCCTGCAAAACCTGACCTTGGGCAAAGCGCTTGCTGAACCACAGCGTGCTCAACTGGTTGAATGGATGAAGGGGAATACTACCGGCGGAGCCAGCATTCGCGCAGGTCTGCCAACCACGTGGGTGGTCGGTGATAAAACCGGCAGCGGTGATTACGGTACCACTAACGATATCGCCGTGATTTGGCCAGCTAACCACGCACCGTTGGTGTTGGTGACCTATTTCACGCAGCCACAGCAGAATGCCGAAGCCCGCAAAGACGTGTTGGCTGCGGCTGCTAAAATTGTCACCGCAGGACTTTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39675","NCBI_taxonomy_name":"Serratia fonticola","NCBI_taxonomy_id":"47917"}}}},"ARO_accession":"3008175","ARO_id":"46967","ARO_name":"FONA-12","CARD_short_name":"FONA-12","ARO_description":"Class A beta-lactamase FONA-12.","ARO_category":{"42905":{"category_aro_accession":"3004787","category_aro_cvterm_id":"42905","category_aro_name":"FONA beta-lactamase","category_aro_description":"FONA is a class A beta-lactamase gene family found in Serratia fonticola.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7594":{"model_id":"7594","model_name":"FONA-13","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10421":{"protein_sequence":{"accession":"USH09262.1","sequence":"MVRNTLRQTTLMVATVMPLLFGSAPLWAQPANAKANIQQQLSELEKNSGGRLGVALIDTADNSQILYRGDERFPMCSTSKVMAVSALLKQSETDKNLLAKRMEIKQSDLVNYNPVAEKHLDTGMTLAEFSAATIQYSDNTAMNKILEHLGGPAKVTEFARTIGDKTFRLDRTEPTLNTAIPGDKRDTTSPQAMAKSLQNLTLGKALGEPQRAQLVEWMKGNTTGGASIRAGLPTTWVVGDKTGSGDYGTTNDIAVIWPANHAPLVLVTYFTQPQQNAEARKDVLAAAAKIVTAGL"},"dna_sequence":{"accession":"ON713465.1","fmin":"0","fmax":"888","strand":"+","sequence":"ATGGTTAGAAATACATTACGTCAAACCACCCTGATGGTCGCTACGGTTATGCCGTTGCTGTTCGGTAGCGCACCGTTATGGGCGCAACCCGCTAATGCCAAGGCCAATATTCAGCAGCAACTGTCTGAACTGGAGAAAAACTCCGGTGGCCGCCTGGGCGTGGCGCTGATCGATACCGCCGATAATTCGCAGATCCTGTATCGTGGGGATGAACGTTTTCCCATGTGCAGCACCAGCAAGGTGATGGCAGTGTCGGCGTTGTTAAAACAGAGCGAGACGGATAAAAATCTTTTGGCTAAGCGGATGGAGATCAAACAATCCGATCTGGTCAACTACAACCCGGTCGCCGAAAAACATCTGGATACCGGGATGACCCTGGCCGAGTTCAGCGCCGCCACTATCCAGTACAGTGACAACACGGCGATGAACAAGATCCTTGAGCATCTTGGCGGCCCGGCAAAAGTGACAGAATTTGCGCGTACTATCGGCGATAAAACCTTCCGTCTCGATCGTACCGAACCCACTTTAAATACCGCCATCCCGGGTGATAAGCGTGACACCACCTCGCCGCAGGCGATGGCAAAAAGCCTGCAAAACCTGACCTTGGGCAAAGCGCTGGGTGAACCACAGCGTGCTCAACTGGTTGAATGGATGAAGGGGAATACTACCGGCGGAGCCAGCATTCGCGCAGGTCTGCCAACCACGTGGGTGGTCGGTGATAAAACCGGCAGCGGTGATTACGGTACCACTAACGATATCGCCGTGATTTGGCCAGCTAACCACGCACCGTTGGTGTTGGTGACCTATTTCACGCAGCCACAGCAGAATGCCGAAGCCCGCAAAGACGTGTTGGCTGCGGCTGCTAAAATTGTCACCGCAGGACTTTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39675","NCBI_taxonomy_name":"Serratia fonticola","NCBI_taxonomy_id":"47917"}}}},"ARO_accession":"3008176","ARO_id":"46968","ARO_name":"FONA-13","CARD_short_name":"FONA-13","ARO_description":"Class A beta-lactamase FONA-13.","ARO_category":{"42905":{"category_aro_accession":"3004787","category_aro_cvterm_id":"42905","category_aro_name":"FONA beta-lactamase","category_aro_description":"FONA is a class A beta-lactamase gene family found in Serratia fonticola.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7595":{"model_id":"7595","model_name":"FONA-7","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10422":{"protein_sequence":{"accession":"QGF22214.1","sequence":"MVKNTLRQTTLMVATVMPLLFGSAPLWAQSANAKANIQQQLSELEKNSGGRLGVALIDTADNSQILYRADERFPMCSTSKVMAVSALLKQSETDKNLLAKRMEIKQSDLVNYNPIAEKHLDTGMTLAEFSAATIQYSDNTAMNKILEHLGGPAKVTEFARTIGDKTFRLDRTEPTLNTAIPGDKRDTTSPLAMAKSLQNLTLGKALGEPQRAQLVEWMKGNTTGGASIRAGLPITWVVGDKTGSGDYGTTNDIAVIWPANHAPLVLVTYFTQPQQNAEARKDVLAAAAKIVTEGL"},"dna_sequence":{"accession":"MN634199.1","fmin":"0","fmax":"888","strand":"+","sequence":"ATGGTTAAAAATACATTACGTCAAACCACCCTGATGGTCGCTACGGTTATGCCGTTGCTGTTCGGTAGCGCACCGCTATGGGCGCAATCCGCTAATGCCAAGGCGAATATTCAGCAGCAACTGTCTGAACTGGAGAAAAACTCCGGTGGCCGCCTGGGCGTGGCGCTGATCGATACCGCTGATAATTCGCAGATCCTGTATCGCGCGGATGAACGTTTTCCCATGTGCAGCACCAGCAAGGTGATGGCGGTGTCGGCGTTGTTAAAACAGAGCGAGACGGATAAAAATCTTTTGGCTAAGCGGATGGAGATCAAGCAATCCGATCTGGTCAACTACAACCCGATCGCCGAAAAACACCTGGATACCGGGATGACCTTGGCCGAGTTCAGCGCCGCCACTATCCAGTACAGTGACAACACGGCGATGAACAAGATCCTTGAGCATCTTGGCGGCCCGGCAAAGGTTACAGAGTTTGCGCGTACTATTGGCGATAAAACCTTCCGTCTCGATCGTACCGAACCCACTTTAAATACCGCTATTCCGGGTGATAAGCGCGATACCACCTCGCCGCTGGCGATGGCAAAAAGCCTGCAAAACCTGACCTTGGGCAAAGCGCTTGGTGAACCACAGCGTGCTCAACTGGTTGAATGGATGAAGGGGAACACTACTGGCGGAGCCAGCATTCGTGCAGGTCTGCCAATTACATGGGTGGTTGGGGATAAAACCGGTAGCGGTGATTACGGTACCACTAACGATATCGCCGTGATTTGGCCAGCTAACCACGCACCGTTGGTATTAGTAACCTATTTCACGCAGCCACAGCAGAATGCCGAAGCTCGTAAAGATGTGTTGGCTGCGGCTGCTAAAATTGTCACCGAAGGACTTTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39675","NCBI_taxonomy_name":"Serratia fonticola","NCBI_taxonomy_id":"47917"}}}},"ARO_accession":"3008177","ARO_id":"46969","ARO_name":"FONA-7","CARD_short_name":"FONA-7","ARO_description":"Class A beta-lactamase FONA-7.","ARO_category":{"42905":{"category_aro_accession":"3004787","category_aro_cvterm_id":"42905","category_aro_name":"FONA beta-lactamase","category_aro_description":"FONA is a class A beta-lactamase gene family found in Serratia fonticola.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7596":{"model_id":"7596","model_name":"FONA-8","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10423":{"protein_sequence":{"accession":"USH09257.1","sequence":"MVKNTLRQTTLMVATVMPLLFGSAPLWAQSANAKANIQQQLSELEKNSGGRLGVALIDTADNSQILYRADERFPMCSTSKVMAVSALLKQSETDKNLLAKRMEIKQSDLVNYNPIAEKHLDTGMTLAEFSAATIQYSDNTAMNKILEHLGGPAKVTEFARTIGDKTFRLDRTEPTLNTAIPGDKRDTTSPLAMAKSLQNLTLGKALGEPQRAQLVEWMKGNTTGGASIRAGLPTTWVVGDKTGSGDYGTTNDIAVIWPANHAPLVLVTYFTQPQQNAEARKDVLAAAAKIVTEGL"},"dna_sequence":{"accession":"ON713460.1","fmin":"0","fmax":"888","strand":"+","sequence":"ATGGTTAAAAATACATTACGTCAAACCACCCTGATGGTCGCTACGGTTATGCCGTTGCTGTTCGGTAGCGCACCGCTATGGGCGCAATCCGCTAATGCCAAGGCGAATATTCAGCAGCAACTGTCTGAACTGGAGAAAAACTCCGGTGGCCGCCTGGGCGTGGCGCTGATCGATACCGCTGATAATTCGCAGATCCTGTATCGCGCGGATGAACGTTTTCCCATGTGCAGCACCAGCAAGGTGATGGCGGTGTCGGCGTTGTTAAAACAGAGCGAGACGGATAAAAATCTTTTGGCTAAGCGGATGGAGATCAAGCAATCCGATCTGGTCAACTACAACCCGATCGCCGAAAAACACCTGGATACCGGGATGACCTTGGCCGAGTTCAGCGCCGCCACTATCCAGTACAGTGACAACACGGCGATGAACAAGATCCTTGAGCATCTTGGCGGCCCGGCAAAGGTTACAGAGTTTGCGCGTACTATTGGCGATAAAACCTTCCGTCTCGATCGTACCGAACCCACTTTAAATACCGCTATTCCGGGTGATAAGCGCGATACCACCTCGCCGCTGGCGATGGCAAAAAGCCTGCAAAACCTGACCTTGGGCAAAGCGCTTGGTGAACCACAGCGTGCTCAACTGGTTGAATGGATGAAGGGGAACACTACCGGCGGAGCCAGCATTCGTGCAGGTCTGCCAACTACATGGGTGGTTGGGGATAAAACCGGTAGCGGTGATTACGGTACCACTAATGATATCGCCGTGATTTGGCCAGCTAACCACGCACCGTTGGTATTAGTAACCTATTTCACGCAGCCACAGCAGAATGCCGAAGCTCGTAAAGACGTGTTGGCTGCGGCTGCTAAAATTGTCACCGAAGGACTTTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39675","NCBI_taxonomy_name":"Serratia fonticola","NCBI_taxonomy_id":"47917"}}}},"ARO_accession":"3008178","ARO_id":"46970","ARO_name":"FONA-8","CARD_short_name":"FONA-8","ARO_description":"Class A beta-lactamase FONA-8.","ARO_category":{"42905":{"category_aro_accession":"3004787","category_aro_cvterm_id":"42905","category_aro_name":"FONA beta-lactamase","category_aro_description":"FONA is a class A beta-lactamase gene family found in Serratia fonticola.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7597":{"model_id":"7597","model_name":"FONA-9","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10424":{"protein_sequence":{"accession":"USH09258.1","sequence":"MVKNTLRQTTLMVATVMPLLFGSAPLWAQSANAKANIQQQLSELEKNSGGRLGVALIDTADNSQILYRADERFPMCSTSKVMAVSALLKQSEKDKNLLAKRMEIKQSDLVNYNPIAEKHLDTGMTLAEFSAATIQYSDNTAMNKILEHLGGPAKVTEFARTIGDKTFRLDRTEPTLNTAIPGDKRDTTSPLAMAKSLQNLTLGKALGEPQRAQLVEWMKGNTTGGASIRAGLPTTWVVGDKTGSGDYGTTNDIAVIWPANHAPLVLVTYFTQPQQNAEARKDVLAAAAKIVTEGL"},"dna_sequence":{"accession":"ON713461.1","fmin":"0","fmax":"888","strand":"+","sequence":"ATGGTTAAAAATACATTACGTCAAACCACCCTGATGGTCGCTACGGTTATGCCGTTGCTGTTCGGTAGCGCACCGCTATGGGCGCAATCCGCTAATGCCAAGGCGAATATTCAGCAGCAACTGTCTGAACTGGAGAAAAACTCCGGTGGCCGCCTGGGCGTGGCGCTGATCGATACCGCTGATAATTCGCAGATCCTGTATCGCGCGGATGAACGTTTTCCCATGTGCAGCACCAGCAAGGTGATGGCGGTGTCGGCGTTGTTAAAACAGAGCGAGAAGGATAAAAATCTTTTGGCTAAGCGGATGGAGATCAAGCAATCCGATCTGGTCAACTACAACCCGATCGCCGAAAAACACCTGGATACCGGGATGACCTTGGCCGAGTTCAGCGCCGCCACTATTCAGTACAGTGACAACACGGCGATGAACAAGATCCTTGAGCATCTTGGCGGCCCGGCAAAGGTTACAGAGTTTGCGCGTACTATTGGCGATAAAACCTTCCGTCTCGATCGTACCGAACCCACTTTAAATACCGCTATTCCGGGTGATAAGCGCGATACCACCTCGCCGCTGGCGATGGCAAAAAGCCTGCAAAACCTGACCTTGGGCAAAGCGCTTGGTGAACCACAGCGTGCTCAACTGGTTGAATGGATGAAGGGGAACACTACCGGCGGAGCCAGCATTCGTGCAGGTCTGCCAACTACATGGGTGGTTGGGGATAAAACCGGTAGCGGTGATTACGGTACCACTAACGATATCGCCGTGATTTGGCCAGCTAACCACGCACCGTTGGTATTAGTAACCTATTTCACGCAGCCACAGCAGAATGCCGAAGCTCGTAAAGACGTGTTGGCTGCGGCTGCTAAAATTGTCACCGAAGGACTTTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39675","NCBI_taxonomy_name":"Serratia fonticola","NCBI_taxonomy_id":"47917"}}}},"ARO_accession":"3008179","ARO_id":"46971","ARO_name":"FONA-9","CARD_short_name":"FONA-9","ARO_description":"Class A beta-lactamase FONA-9.","ARO_category":{"42905":{"category_aro_accession":"3004787","category_aro_cvterm_id":"42905","category_aro_name":"FONA beta-lactamase","category_aro_description":"FONA is a class A beta-lactamase gene family found in Serratia fonticola.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7598":{"model_id":"7598","model_name":"FOX-18","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10425":{"protein_sequence":{"accession":"QVO43832.1","sequence":"MQQLCAFALLTLGSLLLAPCTYASEEAPLTATVDGIIQPMLKEYRIPGMAVAVLKDGKAHYFNYGVANREIGQRVNEQTLFEIGSVSKTLTATLGAYAAVKGGVELDDKVSQHAPWLKGSTFDGVTMAEIATYSAGGLPLQFPDEVDSNDKMRTYYRSWSPVYPAGTHRQYSNPSIGLFGHLAANSLGQPFEQLMSQTLLPKLGLHHTYIQVPESAMVNYAYGYSKEDKPVRVTPGVLAAEAYGIKTGSADLLKFVEANMGYQGDAAVKSAIALTHTGFYSVGEMTQGLGWESYAYPVTEPVLLAGNSPAVSFQANPVKRFAVPKAMGEQRLYNKTGSTGGFGAYVAFVPARGIAIVMLANRNYPIEARVKAAHAILSQLAE"},"dna_sequence":{"accession":"MZ092825.1","fmin":"0","fmax":"1149","strand":"+","sequence":"ATGCAACAACTATGTGCGTTCGCGCTACTGACGCTAGGTAGCCTGCTGCTAGCCCCTTGTACTTATGCCAGCGAGGAGGCCCCGCTGACCGCCACAGTGGACGGCATTATCCAGCCGATGCTCAAGGAGTATCGGATCCCGGGGATGGCGGTCGCCGTACTGAAAGATGGCAAGGCCCACTATTTCAACTATGGGGTTGCCAACCGGGAGATTGGCCAGCGGGTCAATGAGCAGACCCTGTTCGAGATCGGTTCGGTCAGCAAGACCCTGACCGCGACCCTTGGCGCCTATGCCGCGGTCAAGGGGGGGGTTGAGCTGGATGACAAGGTGAGCCAGCACGCCCCCTGGCTCAAAGGTTCCACCTTTGATGGTGTGACCATGGCCGAGATTGCCACCTACAGTGCGGGTGGTTTGCCGTTGCAGTTCCCCGATGAGGTAGATTCGAATGACAAGATGCGCACTTACTATCGGAGCTGGTCACCGGTTTATCCGGCGGGGACCCATCGCCAGTATTCCAACCCCAGCATAGGCCTGTTTGGTCACCTGGCCGCAAATAGTCTGGGCCAGCCATTTGAGCAACTGATGAGCCAGACCCTGCTGCCCAAGCTGGGTTTGCACCACACCTATATCCAGGTGCCGGAGTCGGCCATGGTGAACTATGCCTACGGCTATTCGAAGGAAGATAAGCCCGTCCGGGTCACTCCGGGCGTGCTGGCGGCCGAGGCTTACGGGATCAAGACCGGCTCGGCGGATCTGCTGAAGTTTGTCGAGGCCAACATGGGGTATCAGGGAGATGCCGCGGTAAAAAGCGCAATCGCGCTGACCCACACAGGTTTCTACTCGGTGGGAGAAATGACCCAGGGATTAGGATGGGAGAGTTACGCCTATCCGGTGACCGAGCCGGTGCTGCTGGCGGGCAACTCACCAGCGGTGAGCTTCCAGGCCAATCCGGTTAAGCGCTTTGCGGTGCCCAAAGCGATGGGTGAGCAGCGGCTCTATAACAAGACGGGCTCGACCGGCGGCTTTGGCGCCTATGTGGCGTTCGTGCCCGCCAGAGGGATAGCCATCGTCATGCTGGCCAATCGCAACTATCCCATCGAGGCCAGGGTGAAGGCGGCTCACGCCATCCTGAGTCAGTTGGCGGAGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36947","NCBI_taxonomy_name":"Aeromonas allosaccharophila","NCBI_taxonomy_id":"656"}}}},"ARO_accession":"3008180","ARO_id":"46972","ARO_name":"FOX-18","CARD_short_name":"FOX-18","ARO_description":"Cephalosporin-hydrolyzing class C beta-lactamase FOX-18.","ARO_category":{"36206":{"category_aro_accession":"3000067","category_aro_cvterm_id":"36206","category_aro_name":"FOX beta-lactamase","category_aro_description":"FOX beta-lactamases are plasmid-encoded AmpC-type beta-lactamase which conferred resistance to broad-spectrum cephalosporins and cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7599":{"model_id":"7599","model_name":"FOX-19","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10426":{"protein_sequence":{"accession":"QVO43833.1","sequence":"MQQRRALALLTLGSLLLTPCTYARGEAPLTATVDGAIQPMLKEYRIPGMAVAVLKDGKAHYFNYGVANRESGQRVSEQTLFEIGSVSKTLTATLGAYAAVKGGFELDDKVSQHAPWLKGSAFDGVTMAELATYSAGGLPLQFPDEVDLNDKMRTYYRHWSPVYPAGTHRLYSNPSIGLFGHLAANSLGQPFEQLMGQTLLPKLGLHHTYIQVPESAMVNYAYGYSKEDKPVRVTPGVLAAEAYGIKTGSADLLKFAEANMGYQGDAAVKSAIALTHTGFYSVGDMTQGLGWESYAYPLTELALLVGNSPAVSLKANPITRFAAPKAMGEQRLYNKTGSTGGFGAYVAFVPARGIAIVMLANRNYPIEARVKAAHAILSQLAE"},"dna_sequence":{"accession":"MZ092826.1","fmin":"0","fmax":"1149","strand":"+","sequence":"ATGCAACAACGACGTGCGCTCGCGCTACTGACGCTGGGTAGCCTGCTGCTAACCCCTTGTACTTATGCCCGTGGGGAGGCCCCGCTGACCGCCACTGTGGATGGCGCCATCCAGCCGATGCTCAAGGAGTATCGGATCCCGGGGATGGCGGTCGCCGTACTGAAAGATGGCAAGGCCCACTATTTCAACTATGGGGTTGCCAACCGCGAGAGTGGCCAGCGCGTCAGCGAGCAGACCCTGTTCGAGATTGGCTCGGTCAGCAAAACCCTGACCGCGACCCTCGGTGCCTATGCCGCAGTCAAGGGGGGCTTTGAGCTGGATGACAAGGTGAGCCAGCACGCCCCCTGGCTCAAAGGTTCCGCTTTCGATGGTGTGACCATGGCCGAGCTTGCCACCTACAGTGCGGGTGGTTTGCCGCTGCAGTTCCCCGATGAGGTAGATTTGAATGACAAGATGCGCACTTACTATCGGCACTGGTCACCGGTTTATCCGGCGGGGACTCATCGCCTGTATTCCAACCCCAGCATCGGCCTGTTTGGTCACCTGGCCGCAAATAGTCTGGGCCAGCCATTTGAGCAACTGATGGGCCAGACACTGCTGCCCAAACTGGGTTTGCACCACACCTATATCCAGGTGCCGGAGTCGGCCATGGTGAACTATGCCTACGGCTATTCGAAGGAAGATAAGCCCGTCCGGGTCACTCCGGGCGTGCTGGCGGCCGAGGCTTACGGGATCAAGACCGGCTCGGCGGATCTGCTGAAGTTTGCCGAGGCCAATATGGGGTATCAGGGAGATGCCGCGGTAAAAAGCGCGATCGCGCTGACCCACACCGGTTTCTACTCGGTGGGAGACATGACTCAGGGACTGGGCTGGGAGAGTTACGCCTATCCGTTGACCGAGCTGGCGCTGTTGGTAGGCAACTCGCCTGCGGTGAGCCTCAAGGCCAATCCGATCACGCGTTTTGCCGCGCCCAAAGCGATGGGCGAGCAGCGGCTCTATAACAAGACGGGCTCGACTGGCGGCTTTGGCGCCTATGTGGCGTTCGTGCCCGCCAGAGGGATCGCCATCGTCATGCTGGCCAATCGCAACTATCCCATCGAGGCCAGGGTGAAGGCGGCTCACGCCATCCTGAGTCAGTTGGCCGAGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36947","NCBI_taxonomy_name":"Aeromonas allosaccharophila","NCBI_taxonomy_id":"656"}}}},"ARO_accession":"3008181","ARO_id":"46973","ARO_name":"FOX-19","CARD_short_name":"FOX-19","ARO_description":"Cephalosporin-hydrolyzing class C beta-lactamase FOX-19.","ARO_category":{"36206":{"category_aro_accession":"3000067","category_aro_cvterm_id":"36206","category_aro_name":"FOX beta-lactamase","category_aro_description":"FOX beta-lactamases are plasmid-encoded AmpC-type beta-lactamase which conferred resistance to broad-spectrum cephalosporins and cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7600":{"model_id":"7600","model_name":"FOX-20","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10427":{"protein_sequence":{"accession":"UVW30757.1","sequence":"MQQRRALALLTLGSLLLTPCTYARGEAPLTATVDGAIQPMLKEYRIPGMAVAVLKDGKAHYFNYGVANRESGQHVSEQTLFEIGSVSKTLTATLGAYAAVKGGFELDDKVSQHAPWLKGSAFDGVTMAELATYSAGGLPLQFPDEVDLNDKMQTYYRSWSPVYPAGTHRQYSNLSIGLFGHLAANSLGQPFEQLMSQTLLPKLGLHHTYIQVPESAMANYAYGYSKEDKPIRVTPGVLAAEAYGIKTGSADLLKFTEANMGYQGDATVKSAIALTHTGFYSVGEMTQGLGWESYAYPVTEQALLAGNSPAVSFQANPVTRFAVPKAMGEQRLYNKTGSTGGFGAYVAFVPARGIAIVMLANRNYPIEARVKAAHAILSQLAE"},"dna_sequence":{"accession":"OP297845.1","fmin":"0","fmax":"1149","strand":"+","sequence":"ATGCAACAACGACGTGCGCTCGCGCTACTGACGCTGGGTAGCCTGCTGCTAACCCCTTGTACTTATGCCCGTGGGGAGGCCCCGCTGACCGCCACTGTGGATGGCGCCATCCAGCCGATGCTCAAGGAGTATCGGATCCCGGGGATGGCGGTCGCCGTACTGAAAGATGGCAAGGCCCACTATTTCAACTATGGGGTGGCCAACCGCGAGAGTGGTCAGCACGTCAGCGAGCAGACTCTGTTCGAGATTGGCTCGGTCAGCAAGACCCTGACCGCGACCCTTGGCGCCTATGCCGCAGTCAAGGGGGGCTTTGAGCTGGATGACAAGGTGAGCCAGCACGCCCCCTGGCTCAAAGGTTCCGCCTTTGATGGTGTGACCATGGCCGAGCTTGCCACCTACAGTGCGGGTGGTTTGCCGCTGCAGTTCCCCGATGAGGTAGATTTGAATGACAAGATGCAAACTTACTATCGGAGCTGGTCACCGGTTTATCCGGCGGGGACTCATCGCCAGTATTCCAACCTCAGCATAGGCCTGTTTGGTCACCTGGCCGCAAATAGTCTGGGCCAGCCATTTGAGCAACTGATGAGCCAGACCCTGCTGCCCAAACTGGGTTTGCACCACACCTATATCCAGGTGCCGGAGTCGGCCATGGCGAACTATGCCTACGGCTATTCGAAGGAAGATAAGCCTATCCGGGTCACTCCGGGCGTGCTGGCTGCCGAGGCTTACGGGATCAAGACCGGCTCGGCGGATCTGCTGAAGTTTACCGAGGCCAACATGGGGTATCAGGGAGATGCCACGGTAAAAAGCGCGATCGCGCTGACCCACACCGGTTTCTACTCGGTGGGAGAAATGACCCAAGGACTGGGCTGGGAGAGCTACGCCTATCCGGTGACCGAGCAGGCGTTGCTGGCGGGCAACTCCCCGGCGGTGAGCTTCCAGGCCAATCCGGTTACGCGCTTTGCGGTGCCCAAAGCGATGGGTGAGCAGCGGCTCTATAACAAAACGGGCTCGACCGGCGGCTTTGGCGCCTATGTGGCGTTCGTGCCCGCCAGAGGGATCGCCATCGTCATGCTGGCCAATCGCAACTATCCCATCGAGGCCAGGGTGAAGGCAGCTCACGCCATCCTGAGTCAGTTGGCCGAGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39098","NCBI_taxonomy_name":"Enterobacter hormaechei","NCBI_taxonomy_id":"158836"}}}},"ARO_accession":"3008182","ARO_id":"46974","ARO_name":"FOX-20","CARD_short_name":"FOX-20","ARO_description":"Cephalosporin-hydrolyzing class C beta-lactamase FOX-20.","ARO_category":{"36206":{"category_aro_accession":"3000067","category_aro_cvterm_id":"36206","category_aro_name":"FOX beta-lactamase","category_aro_description":"FOX beta-lactamases are plasmid-encoded AmpC-type beta-lactamase which conferred resistance to broad-spectrum cephalosporins and cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7601":{"model_id":"7601","model_name":"FOX-21","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10428":{"protein_sequence":{"accession":"BDT38924.1","sequence":"MQQRRALALLTLGSLLLAPCTYASGGAPLTAAVDGIIQPMLKEYRIPGMAVAVLKDGKAHYFNYGVANRESGQRVSEQTLFEIGSVSKTLTATLGAYAAVKGGFELDDKVSQHAPWLKGSAFDGVTMAELATYSAGGLPLQFPDKVDSNDKMRTYYLSWSPVYPAGTHRQYANTSIGLFGYLAASSLGPPFEQLMSQTLLPKLGLHHTYIQVPESAMVNYAYGYSKEDKPIRVTPGVLAAEAYGIKTGSADLLKFVEANMGYQGDAAVKSAIALTHTGFYSVGEMTQGLGWESYAYPVTEQTLLAGNSPAVSLQANPVTRFAVPKAMGEQRLYNKTGSTGGFGAYVAFVPARGIAIVMLANRNYPIEARVTAAHAILSQLAE"},"dna_sequence":{"accession":"LC733689.1","fmin":"0","fmax":"1149","strand":"+","sequence":"ATGCAACAACGACGTGCGCTCGCGCTACTGACGCTGGGTAGCCTGCTGCTAGCCCCTTGTACTTATGCCAGCGGGGGGGCTCCGCTGACCGCCGCTGTGGACGGCATTATCCAGCCGATGCTCAAGGAGTATCGGATCCCGGGGATGGCGGTCGCCGTGCTGAAAGATGGCAAGGCCCACTATTTCAACTATGGGGTTGCCAACCGCGAGAGTGGCCAGCGCGTCAGCGAGCAGACGCTGTTCGAGATTGGCTCGGTCAGCAAGACCCTGACCGCGACCCTCGGTGCCTATGCCGCAGTCAAGGGGGGCTTTGAGCTGGATGACAAGGTGAGCCAGCACGCCCCTTGGCTCAAAGGTTCCGCTTTCGATGGTGTGACCATGGCCGAGCTTGCCACCTACAGTGCGGGTGGTTTGCCGCTGCAGTTCCCCGATAAGGTGGATTCGAATGACAAGATGCGCACTTACTATCTGAGCTGGTCACCGGTTTATCCGGCGGGGACCCATCGTCAGTACGCCAATACCAGCATCGGTCTGTTCGGCTATCTGGCTGCCAGCTCCCTGGGCCCGCCATTTGAGCAACTGATGAGCCAGACCCTGCTGCCCAAGCTGGGTTTGCACCACACCTATATCCAGGTGCCGGAGTCGGCCATGGTGAACTATGCCTACGGCTATTCGAAGGAAGATAAGCCCATCCGGGTCACTCCGGGCGTGCTGGCGGCCGAGGCTTACGGGATCAAGACCGGCTCGGCGGATCTGCTGAAGTTTGTCGAGGCAAACATGGGGTATCAGGGAGATGCCGCGGTAAAAAGCGCGATCGCGCTGACCCACACCGGTTTCTACTCTGTAGGGGAAATGACCCAGGGGCTGGGCTGGGAGAGTTACGCCTATCCGGTGACCGAGCAGACATTGCTGGCGGGCAACTCACCAGCGGTGAGCCTCCAGGCCAATCCGGTTACGCGCTTTGCGGTGCCCAAAGCGATGGGCGAGCAGCGGCTCTATAACAAGACGGGCTCGACCGGCGGCTTTGGCGCCTATGTGGCGTTCGTGCCCGCCAGAGGGATCGCCATCGTCATGCTGGCCAATCGCAACTATCCCATCGAGGCCAGGGTGACGGCGGCTCACGCCATCCTGAGTCAGTTGGCCGAGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36947","NCBI_taxonomy_name":"Aeromonas allosaccharophila","NCBI_taxonomy_id":"656"}}}},"ARO_accession":"3008183","ARO_id":"46975","ARO_name":"FOX-21","CARD_short_name":"FOX-21","ARO_description":"Cephalosporin-hydrolyzing class C beta-lactamase FOX-21.","ARO_category":{"36206":{"category_aro_accession":"3000067","category_aro_cvterm_id":"36206","category_aro_name":"FOX beta-lactamase","category_aro_description":"FOX beta-lactamases are plasmid-encoded AmpC-type beta-lactamase which conferred resistance to broad-spectrum cephalosporins and cephamycins.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7602":{"model_id":"7602","model_name":"FRI-12","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10429":{"protein_sequence":{"accession":"UUM03679.1","sequence":"MFLRKKKASYLSFLLCLSFISFNSFATQGNNGVAKIKELETAFGGRIGVYLLNTENGKEFSYRQDERFPLCSSFKVFLAASVLKRTQSKSISLDDSVEYVGRVMEKHSPVSEKYREKGASVQTLAMAAIQYSDNGASNLLMERYIGGPEGLTAFMRSTGDTDFRLDRWELELNSAIPGDKRDTSTPKAVAMSLKNIAFGSILNAKNKALLQDWLKGNTTGNARVRAAVPDKWVVGDKTGTCGFYGTANDVAILWPDTNSPAVIAVYTTRPNQNDKHDEAVIKNAAKIAIDSVYGSYK"},"dna_sequence":{"accession":"OP142442.1","fmin":"0","fmax":"894","strand":"+","sequence":"ATGTTTCTTCGCAAAAAAAAAGCAAGCTACCTGTCTTTTCTGCTCTGCCTTTCTTTTATTTCATTTAACTCGTTTGCCACTCAGGGAAATAATGGTGTGGCTAAAATTAAGGAACTGGAAACTGCTTTCGGTGGGCGGATAGGTGTTTATCTTTTAAACACAGAAAATGGGAAAGAGTTTTCCTACAGACAGGATGAGAGATTTCCTTTGTGCAGTTCATTTAAGGTGTTTCTCGCTGCATCGGTGTTAAAAAGAACCCAGAGCAAATCTATTTCTCTTGATGATTCGGTGGAATATGTCGGTCGTGTTATGGAAAAGCATTCTCCTGTATCAGAAAAATATCGTGAAAAGGGAGCAAGCGTGCAGACTTTGGCTATGGCAGCAATTCAGTATAGTGACAATGGAGCTTCTAACCTGTTAATGGAAAGATACATCGGAGGTCCTGAAGGTTTGACTGCATTTATGCGGTCGACGGGAGATACTGACTTCAGGCTTGATCGCTGGGAATTAGAATTAAACTCAGCTATTCCAGGCGATAAACGTGACACATCCACTCCGAAAGCAGTAGCAATGAGCCTTAAAAATATTGCATTTGGTTCGATACTTAATGCTAAAAATAAAGCCTTACTGCAGGATTGGCTTAAAGGCAACACTACTGGTAATGCGCGAGTCAGAGCAGCTGTTCCAGATAAATGGGTTGTTGGCGATAAAACAGGTACCTGTGGTTTCTATGGTACAGCTAATGATGTTGCTATTTTATGGCCAGACACCAATTCACCTGCTGTTATCGCTGTGTATACAACGCGCCCCAATCAAAACGACAAGCATGATGAAGCAGTGATTAAAAATGCTGCAAAAATAGCTATAGATTCGGTATATGGAAGTTATAAATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36926","NCBI_taxonomy_name":"Enterobacter asburiae","NCBI_taxonomy_id":"61645"}}}},"ARO_accession":"3008184","ARO_id":"46976","ARO_name":"FRI-12","CARD_short_name":"FRI-12","ARO_description":"Carbapenem-hydrolyzing class A beta-lactamase FRI-12.","ARO_category":{"42915":{"category_aro_accession":"3004796","category_aro_cvterm_id":"42915","category_aro_name":"FRI beta-lactamase","category_aro_description":"FRI is a carbapenem-Hydrolyzing Class A beta-Lactamase from Enterobacter cloacae.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7603":{"model_id":"7603","model_name":"GES-58","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10430":{"protein_sequence":{"accession":"BED98385.1","sequence":"MRFIHALLLVGIAHSAYASEKLTFKTDLEKLERKKAAQIGVAIVDPQGEIVAGHRMAQRFAMCSTFKFPLAALVFERIDSGTERGDRKLSYGPDMIVEWSPATERFLASGHMTVLEAAQAAVQLSDNGATNLLLREIGGPAAMTQYFRKIGDSVSRLDRKEPEMSDNTPGDLRDTTTPIAMARTVAKVLYGGALTSTSTHTIERWLIGNQTGDATLRAGFPKDWVVGEKTGTCANGGRNDIGFFKAQERDYAVAVYTTAPKLSAVERDELVASVGQVITQLILSTDK"},"dna_sequence":{"accession":"LC763412.1","fmin":"0","fmax":"864","strand":"+","sequence":"ATGCGCTTCATTCACGCACTATTACTGGTAGGGATCGCTCACTCTGCATATGCGTCGGAAAAATTAACCTTCAAGACCGATCTTGAGAAGCTAGAGCGCAAAAAAGCAGCTCAGATCGGTGTTGCGATCGTCGATCCCCAAGGAGAGATCGTCGCGGGCCACCGAATGGCGCAGCGTTTTGCAATGTGCTCAACGTTCAAGTTTCCGCTAGCCGCGCTGGTCTTTGAAAGAATTGACTCAGGCACCGAGCGGGGGGATCGAAAACTTTCATATGGGCCGGACATGATCGTCGAATGGTCTCCTGCCACGGAGCGGTTTCTAGCATCGGGACACATGACGGTTCTCGAGGCAGCGCAAGCTGCGGTGCAGCTTAGCGACAATGGGGCTACTAACCTCTTACTGAGAGAAATTGGCGGACCTGCTGCAATGACGCAGTATTTTCGTAAAATTGGCGACTCTGTGAGTCGGCTAGACCGGAAAGAGCCGGAGATGAGCGACAACACACCTGGCGACCTCAGAGATACAACTACGCCTATTGCTATGGCACGTACTGTGGCTAAAGTCCTCTATGGCGGCGCACTGACGTCCACCTCGACCCACACCATTGAGAGGTGGCTGATCGGAAACCAAACGGGAGACGCGACACTACGAGCGGGTTTTCCTAAAGATTGGGTTGTTGGAGAGAAAACTGGTACCTGCGCCAACGGGGGCCGGAACGACATTGGTTTTTTTAAAGCCCAGGAGAGAGATTACGCTGTAGCGGTGTATACAACGGCCCCGAAACTATCGGCCGTAGAACGTGACGAATTAGTTGCCTCTGTCGGTCAAGTTATTACACAACTCATCCTGAGCACGGACAAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36926","NCBI_taxonomy_name":"Enterobacter asburiae","NCBI_taxonomy_id":"61645"}}}},"ARO_accession":"3008185","ARO_id":"46977","ARO_name":"GES-58","CARD_short_name":"GES-58","ARO_description":"Class A beta-lactamase GES-58.","ARO_category":{"36205":{"category_aro_accession":"3000066","category_aro_cvterm_id":"36205","category_aro_name":"GES beta-lactamase","category_aro_description":"GES beta-lactamases or Guiana extended-spectrum beta-lactamases are related to the other plasmid-located class A beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7604":{"model_id":"7604","model_name":"GES-59","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10431":{"protein_sequence":{"accession":"WGG88839.1","sequence":"MRFIHALFLAGIAHSASASENLTFRTDLEKLEREKAAEIGVAIVDPQGQIVAGHRIEQRFAMCSTFKFPLAALVFERIDSGTERGDRKLSYGRDMIVEWSPAAERFLASGHMTVLEAAQAAVQLSDNGATNLLLREIGGPAAMTQYFRKIGDSVSRLDRKEPEMNDNTPGDLRDTTTPIAMARTVAKVLYGGALTPTSTHTIERWLIGNQTGDATLRAGFPKDWVIGEKTGTCANGGRNDIGFFKAQDRDYAVAVYTTAPKLSAEQRDELVASVGQVITQLILSTDK"},"dna_sequence":{"accession":"OQ813783.1","fmin":"0","fmax":"864","strand":"+","sequence":"ATGCGCTTTATTCACGCACTATTCCTGGCAGGGATCGCTCACTCTGCATCTGCGTCGGAAAACTTAACCTTCAGGACCGATCTTGAGAAGCTAGAGCGCGAGAAAGCAGCTGAGATCGGTGTTGCGATCGTCGATCCCCAAGGACAGATCGTCGCGGGCCACCGAATCGAGCAGCGTTTTGCAATGTGCTCTACGTTCAAGTTTCCGCTAGCCGCGCTGGTCTTTGAAAGAATTGACTCAGGCACCGAGCGGGGGGATCGAAAACTTTCGTACGGGCGGGACATGATCGTCGAATGGTCTCCTGCCGCGGAGCGGTTTCTCGCATCGGGACATATGACGGTTCTCGAGGCAGCGCAAGCGGCGGTGCAGCTCAGCGACAATGGGGCTACTAACCTCTTACTGAGAGAAATTGGCGGACCTGCTGCAATGACGCAGTATTTTCGTAAAATTGGCGACTCTGTGAGTCGGCTAGACCGGAAAGAGCCGGAGATGAACGACAACACACCTGGCGACCTCAGAGATACAACCACGCCTATTGCTATGGCACGTACTGTGGCTAAAGTCCTCTATGGCGGCGCACTGACGCCCACCTCGACCCACACAATTGAGAGGTGGCTGATCGGAAACCAAACGGGAGACGCGACATTACGAGCGGGTTTTCCTAAAGATTGGGTTATTGGAGAGAAAACCGGCACCTGCGCCAACGGGGGCCGGAACGACATTGGGTTTTTTAAAGCCCAGGACAGAGATTACGCTGTAGCGGTGTATACAACGGCCCCGAAACTATCGGCCGAACAACGTGACGAATTAGTTGCCTCTGTCGGTCAAGTTATTACGCAACTCATCCTAAGTACGGACAAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008186","ARO_id":"46978","ARO_name":"GES-59","CARD_short_name":"GES-59","ARO_description":"Class A beta-lactamase GES-59.","ARO_category":{"36205":{"category_aro_accession":"3000066","category_aro_cvterm_id":"36205","category_aro_name":"GES beta-lactamase","category_aro_description":"GES beta-lactamases or Guiana extended-spectrum beta-lactamases are related to the other plasmid-located class A beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7605":{"model_id":"7605","model_name":"GES-60","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10432":{"protein_sequence":{"accession":"WZW61385.1","sequence":"MRFIHALLLAGIAHSAYASEKLTFKTDLEKLEREKAAQIGVAIVDPQGEIVAGHRMAQRFAMCSTFKFPLAALVFERIDSGTERGDRKLSYGPDMIVEWSPATERFLASGHMTVLEAAQAAVQLSDNGATKLLLREIGGPAAMTQYFRKIGDSVSRLDRKEPEMSDNTPGDLRDTTTPIAMARTVAKVLYGGALTSTSTHTIERWLIGNQTGDATLRAGFPKDWVVGEKTGTCANGGRNDIGFFKAQERDYAVAVYTTAPKLSAVERDELVASVGQVITQLILSTDK"},"dna_sequence":{"accession":"PP695362.1","fmin":"0","fmax":"864","strand":"+","sequence":"ATGCGCTTCATTCACGCACTATTACTGGCAGGGATCGCTCACTCTGCATATGCGTCGGAAAAATTAACCTTCAAGACCGATCTTGAGAAGCTAGAGCGCGAAAAAGCAGCTCAGATCGGTGTTGCGATCGTCGATCCCCAAGGAGAGATCGTCGCGGGCCACCGAATGGCGCAGCGTTTTGCAATGTGCTCAACGTTCAAGTTTCCGCTAGCCGCGCTGGTCTTTGAAAGAATTGACTCAGGCACCGAGCGGGGGGATCGAAAACTTTCATATGGGCCGGACATGATCGTCGAATGGTCTCCTGCCACGGAGCGGTTTCTAGCATCGGGACACATGACGGTTCTCGAGGCAGCGCAAGCTGCGGTGCAGCTTAGCGACAATGGGGCTACTAAGCTCTTACTGAGAGAAATTGGCGGACCTGCTGCAATGACGCAGTATTTTCGTAAAATTGGCGACTCTGTGAGTCGGCTAGACCGGAAAGAGCCGGAGATGAGCGACAACACACCTGGCGACCTCAGAGATACAACTACGCCTATTGCTATGGCACGTACTGTGGCTAAAGTCCTCTATGGCGGCGCACTGACGTCCACCTCGACCCACACCATTGAGAGGTGGCTGATCGGAAACCAAACGGGAGACGCGACACTACGAGCGGGTTTTCCTAAAGATTGGGTTGTTGGAGAGAAAACTGGTACCTGCGCCAACGGGGGCCGGAACGACATTGGTTTTTTTAAAGCCCAGGAGAGAGATTACGCTGTAGCGGTGTATACAACGGCCCCGAAACTATCGGCCGTAGAACGTGACGAATTAGTTGCCTCTGTCGGTCAAGTTATTACACAACTCATCCTGAGCACGGACAAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008187","ARO_id":"46979","ARO_name":"GES-60","CARD_short_name":"GES-60","ARO_description":"Extended-spectrum class A beta-lactamase GES-60.","ARO_category":{"36205":{"category_aro_accession":"3000066","category_aro_cvterm_id":"36205","category_aro_name":"GES beta-lactamase","category_aro_description":"GES beta-lactamases or Guiana extended-spectrum beta-lactamases are related to the other plasmid-located class A beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7606":{"model_id":"7606","model_name":"GES-61","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10433":{"protein_sequence":{"accession":"MEA9429459.1","sequence":"MRFIHALLLAGIAHSAYASEKLTFKTDLEKLEREKAAEIGVAIVDPQGEIVAGHRMAQRFAMCSTFKFPLAALVFERIDSGTERGDRKLSYGPDMIVKWSPATERFLASGHMTVLEAAQAAVQLSDNGATNLLLREIGGPAAMTQYFRKIGDSVSRLDRKEPEMSDNTPGDLRDTTTPIAMARTVAKVLYGGALTSTSTHTIERWLIGNQTGDATLRAGFPKDWVVGEKTGTCANGGRNDIGFFKAQERDYAVAVYTTAPKLSAVERDELVASVGQVITQLILSTDK"},"dna_sequence":{"accession":"JAYGON010000276.1","fmin":"64","fmax":"928","strand":"-","sequence":"ATGCGCTTCATTCACGCACTATTACTGGCAGGGATCGCTCACTCTGCATATGCGTCGGAAAAATTAACCTTCAAGACCGATCTTGAGAAGCTAGAGCGCGAAAAAGCAGCTGAGATCGGTGTTGCGATCGTCGATCCCCAAGGAGAGATCGTCGCGGGCCACCGAATGGCGCAGCGTTTTGCAATGTGCTCAACGTTCAAGTTTCCGCTAGCCGCGCTGGTCTTTGAAAGAATTGACTCAGGCACCGAGCGGGGGGATCGAAAACTTTCATATGGGCCGGACATGATCGTCAAATGGTCTCCTGCCACGGAGCGGTTTCTAGCATCGGGACACATGACGGTTCTCGAGGCAGCGCAAGCTGCGGTGCAGCTTAGCGACAATGGGGCTACTAACCTCTTACTGAGAGAAATTGGCGGACCTGCTGCAATGACGCAGTATTTTCGTAAAATTGGCGACTCTGTGAGTCGGCTAGACCGGAAAGAGCCGGAGATGAGCGACAACACACCTGGCGACCTCAGAGATACAACTACGCCTATTGCTATGGCACGTACTGTGGCTAAAGTCCTCTATGGCGGCGCACTGACGTCCACCTCGACCCACACCATTGAGAGGTGGCTGATCGGAAACCAAACGGGAGACGCGACACTACGAGCGGGTTTTCCTAAAGATTGGGTTGTTGGAGAGAAAACTGGTACCTGCGCCAACGGGGGCCGGAACGACATTGGTTTTTTTAAAGCCCAGGAGAGAGATTACGCTGTAGCGGTGTATACAACGGCCCCGAAACTATCGGCCGTAGAACGTGACGAATTAGTTGCCTCTGTCGGTCAAGTTATTACACAACTCATCCTGAGCACGGACAAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36936","NCBI_taxonomy_name":"Aeromonas caviae","NCBI_taxonomy_id":"648"}}}},"ARO_accession":"3008188","ARO_id":"46980","ARO_name":"GES-61","CARD_short_name":"GES-61","ARO_description":"Class A beta-lactamase GES-61.","ARO_category":{"36205":{"category_aro_accession":"3000066","category_aro_cvterm_id":"36205","category_aro_name":"GES beta-lactamase","category_aro_description":"GES beta-lactamases or Guiana extended-spectrum beta-lactamases are related to the other plasmid-located class A beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7607":{"model_id":"7607","model_name":"GES-62","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10434":{"protein_sequence":{"accession":"XFH17877.1","sequence":"MRFIHALLLAGIAHSAYASEKLTFKTDLEKLEREKAAQIGVAIVDPQGEIVAGHRMAQRFAMCSTFKFPLAALVFERIDSGTERGDRKLSYGPDMIVEWSPATERFLASGHMTVLEAAQAAVQLSDNGAANLLLREIGGPAAMTQYFRKIGDSVSRLDRKEPEMSDNTPGDLRDTTTPIAMARTVAKVLYGGALTSTSTHTIERWLIGNQTGDATLRAGFPKDWVVGEKTGTCANGGRNDIGFFKAQERDYAVAVYTTAPKLSAVERDELVASVGQVITQLILSTDK"},"dna_sequence":{"accession":"PQ117759.1","fmin":"0","fmax":"864","strand":"+","sequence":"ATGCGCTTCATTCACGCACTATTACTGGCAGGGATCGCTCACTCTGCATATGCGTCGGAAAAATTAACCTTCAAGACCGATCTTGAGAAGCTAGAGCGCGAAAAAGCAGCTCAGATCGGTGTTGCGATCGTCGATCCCCAAGGAGAGATCGTCGCGGGCCACCGAATGGCGCAGCGTTTTGCAATGTGCTCAACGTTCAAGTTTCCGCTAGCCGCGCTGGTCTTTGAAAGAATTGACTCAGGCACCGAGCGGGGGGATCGAAAACTTTCATATGGGCCGGACATGATCGTCGAATGGTCTCCTGCCACGGAGCGGTTTCTAGCATCGGGACACATGACGGTTCTCGAGGCAGCGCAAGCTGCGGTGCAGCTTAGCGACAATGGGGCTGCTAACCTCTTACTGAGAGAAATTGGCGGACCTGCTGCAATGACGCAGTATTTTCGTAAAATTGGCGACTCTGTGAGTCGGCTAGACCGGAAAGAGCCGGAGATGAGCGACAACACACCTGGCGACCTCAGAGATACAACTACGCCTATTGCTATGGCACGTACTGTGGCTAAAGTCCTCTATGGCGGCGCACTGACGTCCACCTCGACCCACACCATTGAGAGGTGGCTGATCGGAAACCAAACGGGAGACGCGACACTACGAGCGGGTTTTCCTAAAGATTGGGTTGTTGGAGAGAAAACTGGTACCTGCGCCAACGGGGGCCGGAACGACATTGGTTTTTTTAAAGCCCAGGAGAGAGATTACGCTGTAGCGGTGTATACAACGGCCCCGAAACTATCGGCCGTAGAACGTGACGAATTAGTTGCCTCTGTCGGTCAAGTTATTACACAACTCATCCTGAGCACGGACAAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008189","ARO_id":"46981","ARO_name":"GES-62","CARD_short_name":"GES-62","ARO_description":"Class A beta-lactamase GES-62.","ARO_category":{"36205":{"category_aro_accession":"3000066","category_aro_cvterm_id":"36205","category_aro_name":"GES beta-lactamase","category_aro_description":"GES beta-lactamases or Guiana extended-spectrum beta-lactamases are related to the other plasmid-located class A beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7608":{"model_id":"7608","model_name":"GES-65","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10435":{"protein_sequence":{"accession":"XHO32890.1","sequence":"MRFIHALLLAGIAHSAYASEKLTFKTDLEKLEREKAAQIGVAIVDPQGEIVAGHRMAQRFAMCSTFKFPLAALVFERIDSGTERGDRKLSYGPDMIVEWSPATERFLASGHMTVLEAAQAAVQLSDNGATNLLLREIGGPAAMTQYFRKIGDSVSRLDWKEPEMSDNTPGDLRDTTTPIAMARTVAKVLYGGALTSTSTHTIERWLIGNQTGDATLRAGFPKDWVVGEKTGTCANGGRNDIGFFKAQERDYAVAVYTTAPKLSAVERDELVASVGQVITQLILSTDK"},"dna_sequence":{"accession":"PQ394547.1","fmin":"0","fmax":"864","strand":"+","sequence":"ATGCGCTTCATTCACGCACTATTACTGGCAGGGATCGCTCACTCTGCATATGCGTCGGAAAAATTAACCTTCAAGACCGATCTTGAGAAGCTAGAGCGCGAAAAAGCAGCTCAGATCGGTGTTGCGATCGTCGATCCCCAAGGAGAGATCGTCGCGGGCCACCGAATGGCGCAGCGTTTTGCAATGTGCTCAACGTTCAAGTTTCCGCTAGCCGCGCTGGTCTTTGAAAGAATTGACTCAGGCACCGAGCGGGGGGATCGAAAACTTTCATATGGGCCGGACATGATCGTCGAATGGTCTCCTGCCACGGAGCGGTTTCTAGCATCGGGACACATGACGGTTCTCGAGGCAGCGCAAGCTGCGGTGCAGCTTAGCGACAATGGGGCTACTAACCTCTTACTGAGAGAAATTGGCGGACCTGCTGCAATGACGCAGTATTTTCGTAAAATTGGCGACTCTGTGAGTCGGCTAGACTGGAAAGAGCCGGAGATGAGCGACAACACACCTGGCGACCTCAGAGATACAACTACGCCTATTGCTATGGCACGTACTGTGGCTAAAGTCCTCTATGGCGGCGCACTGACGTCCACCTCGACCCACACCATTGAGAGGTGGCTGATCGGAAACCAAACGGGAGACGCGACACTACGAGCGGGTTTTCCTAAAGATTGGGTTGTTGGAGAGAAAACTGGTACCTGCGCCAACGGGGGCCGGAACGACATTGGTTTTTTTAAAGCCCAGGAGAGAGATTACGCTGTAGCGGTGTATACAACGGCCCCGAAACTATCGGCCGTAGAACGTGACGAATTAGTTGCCTCTGTCGGTCAAGTTATTACACAACTCATCCTGAGCACGGACAAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008190","ARO_id":"46982","ARO_name":"GES-65","CARD_short_name":"GES-65","ARO_description":"Class A beta-lactamase GES-65.","ARO_category":{"36205":{"category_aro_accession":"3000066","category_aro_cvterm_id":"36205","category_aro_name":"GES beta-lactamase","category_aro_description":"GES beta-lactamases or Guiana extended-spectrum beta-lactamases are related to the other plasmid-located class A beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7609":{"model_id":"7609","model_name":"GES-66","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10436":{"protein_sequence":{"accession":"MEX5467441.1","sequence":"MRFIHALLLAGIAHSAYASEKLTFKTDLEKLEREKAAQIGVAIVDPQGEIVAGHRMAQRFAMCSTFKFPLAALVFERIDSGTERGDRKLSYGPDMIVEWSPATKRFLASGHMTVLEAAQAAVQLSDNGATNLLLREIGGPAAMTQYFRKIGDSVSRLDRKEPEMSDNTPGDLRDTTTPIAMARTVAKVLYGGALTSTSTHTIERWLIGNQTGDATLRAGFPKDWVVGEKTGTCANGGRNDIGFFKAQERDYAVAVYTTAPKLSAVERDELVASVGQVITQLILSTDK"},"dna_sequence":{"accession":"JBFSES010000053.1","fmin":"184","fmax":"1048","strand":"-","sequence":"ATGCGCTTCATTCACGCACTATTACTGGCAGGGATCGCTCACTCTGCATATGCGTCGGAAAAATTAACCTTCAAGACCGATCTTGAGAAGCTAGAGCGCGAAAAAGCAGCTCAGATCGGTGTTGCGATCGTCGATCCCCAAGGAGAGATCGTCGCGGGCCACCGAATGGCGCAGCGTTTTGCAATGTGCTCAACGTTCAAGTTTCCGCTAGCCGCGCTGGTCTTTGAAAGAATTGACTCAGGCACCGAGCGGGGGGATCGAAAACTTTCATATGGGCCGGACATGATCGTCGAATGGTCTCCTGCCACGAAGCGGTTTCTAGCATCGGGACACATGACGGTTCTCGAGGCAGCGCAAGCTGCGGTGCAGCTTAGCGACAATGGGGCTACTAACCTCTTACTGAGAGAAATTGGCGGACCTGCTGCAATGACGCAGTATTTTCGTAAAATTGGCGACTCTGTGAGTCGGCTAGACCGGAAAGAGCCGGAGATGAGCGACAACACACCTGGCGACCTCAGAGATACAACTACGCCTATTGCTATGGCACGTACTGTGGCTAAAGTCCTCTATGGCGGCGCACTGACGTCCACCTCGACCCACACCATTGAGAGGTGGCTGATCGGAAACCAAACGGGAGACGCGACACTACGAGCGGGTTTTCCTAAAGATTGGGTTGTTGGAGAGAAAACTGGTACCTGCGCCAACGGGGGCCGGAACGACATTGGTTTTTTTAAAGCCCAGGAGAGAGATTACGCTGTAGCGGTGTATACAACGGCCCCGAAACTATCGGCCGTAGAACGTGACGAATTAGTTGCCTCTGTCGGTCAAGTTATTACACAACTCATCCTGAGCACGGACAAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008191","ARO_id":"46983","ARO_name":"GES-66","CARD_short_name":"GES-66","ARO_description":"Carbapenem-hydrolyzing class A beta-lactamase GES-66.","ARO_category":{"36205":{"category_aro_accession":"3000066","category_aro_cvterm_id":"36205","category_aro_name":"GES beta-lactamase","category_aro_description":"GES beta-lactamases or Guiana extended-spectrum beta-lactamases are related to the other plasmid-located class A beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7610":{"model_id":"7610","model_name":"GIM-3","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10437":{"protein_sequence":{"accession":"BDR24829.1","sequence":"MKNVLISLLVFIAFSASAQNDKALEIRQIEKGVYLHTSFKHVEGYGLVDSNGLIVLDGNQAYIIDTPWSEEDTRLLLSWIADRGYEVAASISTHFHEDRTAGIKLLNSKSIPTYTSELTKALLLREGKPAPAYYFKGNEFTLGNGIIELYYPGPGHTEDNIVAWLPKSQILFGGCLMRSHEWESLGNVSDASISSWGDSIKNIKSKDYAIQTIVPGHGKLGKSDMLDHTIDLAESASNKLMQPTAEASAD"},"dna_sequence":{"accession":"LC727552.1","fmin":"0","fmax":"753","strand":"+","sequence":"ATGAAAAATGTATTAATATCTTTGTTGGTATTTATAGCGTTCTCTGCTTCGGCTCAAAATGACAAAGCGCTTGAAATTAGACAAATAGAAAAAGGGGTATATCTTCATACATCCTTCAAGCATGTTGAAGGCTATGGGTTAGTCGATTCAAATGGATTAATAGTTTTAGATGGCAACCAAGCCTATATCATCGATACACCTTGGTCTGAAGAAGATACCCGGCTTCTGCTGTCTTGGATAGCTGACAGGGGGTATGAGGTTGCGGCCAGTATTTCAACTCATTTTCATGAGGATAGAACTGCTGGTATCAAATTGCTCAATTCGAAGTCAATTCCTACTTACACATCAGAGTTAACGAAAGCGCTTCTTTTGCGCGAAGGAAAGCCTGCTCCAGCTTATTACTTTAAAGGCAATGAGTTCACGTTAGGAAACGGGATTATAGAGTTATATTATCCCGGCCCCGGGCACACAGAGGATAATATTGTCGCTTGGTTGCCAAAAAGCCAAATATTATTTGGTGGTTGTCTCATGAGAAGTCATGAGTGGGAAAGCTTGGGTAATGTAAGTGATGCCTCAATTAGCTCTTGGGGAGACTCCATTAAAAATATAAAGTCGAAAGATTATGCCATCCAAACAATCGTTCCGGGACATGGCAAACTAGGCAAGTCAGATATGTTAGATCACACCATTGATCTAGCTGAGTCGGCTTCTAACAAATTAATGCAGCCGACCGCTGAGGCGTCGGCTGATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36783","NCBI_taxonomy_name":"Serratia marcescens","NCBI_taxonomy_id":"615"}}}},"ARO_accession":"3008192","ARO_id":"46984","ARO_name":"GIM-3","CARD_short_name":"GIM-3","ARO_description":"Subclass B1 metallo-beta-lactamase GIM-3.","ARO_category":{"39772":{"category_aro_accession":"3003195","category_aro_cvterm_id":"39772","category_aro_name":"GIM beta-lactamase","category_aro_description":"GIM beta-lactamase enzymes isolated from Pseudomonas aeruginosa, and found to confer broad-spectrum resistance to beta-lactam antibiotics.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7611":{"model_id":"7611","model_name":"GMA-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10438":{"protein_sequence":{"accession":"AHJ00703.1","sequence":"MKKSILLSSCLFISFLSTASTLNDSLYSIEQRTLGRIGVSVLDSTDQQWHYKGNERFPMMSTFKTLACAKMLQDSDRDILDISTMAPVKSDELIAWSPITKNMVGSSITIENACEATMKTSDNTAANIVLKHIGGPQGVTAFLRLIGDKVTQLDRFEPELNQAKADDLRDTTTPNAMNKTLYHILFEDVLAQNSKKQLKEWMQGNTVSDSLLRSVLPKGWSIADRSGAGANGSRGITAAIWTDEREPLIISIYLTQTNLSMPERNQVINEIGKAIFEEYAVK"},"dna_sequence":{"accession":"CP007004.1","fmin":"2973951","fmax":"2974800","strand":"+","sequence":"ATGAAAAAATCAATCTTACTTTCGAGCTGTTTGTTCATTTCTTTTTTATCGACCGCTTCAACATTGAACGACTCGCTCTATTCTATAGAACAACGCACCTTGGGACGCATAGGTGTATCAGTTTTAGATTCAACGGATCAACAATGGCACTATAAAGGGAATGAAAGGTTCCCTATGATGAGTACATTCAAGACATTAGCATGTGCAAAAATGCTACAGGACTCTGATAGAGACATTTTAGATATAAGTACAATGGCGCCAGTAAAATCCGATGAACTAATCGCTTGGTCACCAATAACAAAAAACATGGTTGGCAGTTCAATTACCATTGAAAATGCTTGTGAAGCTACGATGAAGACTAGTGATAATACTGCTGCAAACATAGTCTTAAAGCACATCGGAGGCCCACAGGGTGTCACTGCTTTTCTACGTTTGATCGGAGATAAAGTAACTCAATTAGATCGTTTTGAACCTGAACTAAACCAAGCCAAAGCTGATGACCTACGTGATACAACGACGCCAAATGCGATGAATAAGACCCTATATCATATTTTATTCGAAGATGTATTAGCTCAAAATTCAAAAAAACAACTTAAGGAATGGATGCAAGGGAACACTGTTTCCGATTCTTTACTCCGTTCTGTTTTACCAAAAGGGTGGTCTATTGCAGATCGTTCTGGTGCGGGAGCTAACGGTTCGCGCGGTATTACAGCAGCAATTTGGACTGACGAGCGCGAGCCATTAATCATTAGCATCTACCTGACACAAACCAACCTTTCTATGCCAGAACGTAATCAAGTTATTAATGAAATTGGTAAGGCTATTTTCGAAGAGTATGCTGTCAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39615","NCBI_taxonomy_name":"Vibrio parahaemolyticus","NCBI_taxonomy_id":"670"}}}},"ARO_accession":"3008193","ARO_id":"46985","ARO_name":"GMA-1","CARD_short_name":"GMA-1","ARO_description":"GMA family class A beta-lactamase GMA-1.","ARO_category":{"46659":{"category_aro_accession":"3007868","category_aro_cvterm_id":"46659","category_aro_name":"GMA beta-lactamase","category_aro_description":"GMA is a family of class A beta-lactamases which confer resistance to beta-lactam antibiotics through enzymatic inactivation.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7612":{"model_id":"7612","model_name":"GMA-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10439":{"protein_sequence":{"accession":"KAB0300971.1","sequence":"MKKSILLSSCLFISFLSTASTLNDSIYSIEQRTLGRIGVSVLDSTDQRWHYKGNERFPMMSTFKTLACAKMLQDSDRDILDISTMAPVKSDELIAWSPITKNMVGSLITIENACEATMKTSDNTAANIVLKHIGGPQGVTAFLRLTGDKVTQLDRFEPELNQAKADDLRDTTTPNAMNKTLHHILFEDVLAQNSKKQLKEWMQGNTVSDSLLRSVLPQGWSIADRSGAGANGSRGITAAIWTDEREPLIISIYLTQTNLSMPERNQVINEIGKAIFEEYAVK"},"dna_sequence":{"accession":"VXDD01000003.1","fmin":"611061","fmax":"611910","strand":"+","sequence":"ATGAAAAAATCAATCTTACTTTCGAGCTGTTTGTTCATTTCTTTTTTATCGACCGCTTCAACATTGAACGACTCGATCTATTCTATAGAACAACGCACCTTGGGACGCATAGGTGTATCAGTTTTAGATTCCACGGATCAACGATGGCACTATAAAGGGAATGAAAGGTTCCCTATGATGAGTACATTTAAGACATTAGCATGTGCAAAAATGCTACAAGACTCTGATAGAGACATTTTAGATATAAGTACAATGGCGCCAGTAAAATCCGATGAACTAATCGCTTGGTCACCAATAACAAAAAACATGGTTGGCAGTTTAATTACCATTGAAAATGCTTGTGAAGCTACGATGAAGACTAGTGATAATACTGCTGCAAACATAGTCTTAAAGCACATCGGAGGCCCACAGGGTGTCACTGCTTTTCTACGTTTGACCGGAGATAAAGTAACTCAATTAGATCGTTTTGAACCTGAACTAAACCAAGCCAAAGCTGATGACCTACGTGATACAACGACGCCAAATGCGATGAATAAGACCCTACATCATATTTTATTCGAAGATGTATTAGCTCAAAATTCAAAAAAACAACTTAAGGAATGGATGCAAGGGAACACTGTTTCCGATTCTTTACTCCGTTCTGTTTTACCACAAGGATGGTCTATTGCAGATCGTTCTGGTGCAGGTGCTAACGGTTCGCGTGGTATTACAGCTGCAATTTGGACTGACGAGCGCGAGCCATTAATCATTAGCATCTACCTGACACAAACCAACCTTTCTATGCCAGAACGTAATCAAGTTATTAATGAAATTGGTAAGGCTATTTTCGAAGAGTATGCTGTAAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"47933","NCBI_taxonomy_name":"Vibrio fortis","NCBI_taxonomy_id":"212667"}}}},"ARO_accession":"3008194","ARO_id":"46986","ARO_name":"GMA-2","CARD_short_name":"GMA-2","ARO_description":"GMA family class A beta-lactamase GMA-2.","ARO_category":{"46659":{"category_aro_accession":"3007868","category_aro_cvterm_id":"46659","category_aro_name":"GMA beta-lactamase","category_aro_description":"GMA is a family of class A beta-lactamases which confer resistance to beta-lactam antibiotics through enzymatic inactivation.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7613":{"model_id":"7613","model_name":"GOB-17","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10440":{"protein_sequence":{"accession":"AAW82619.1","sequence":"MRNFAILFFLLITFSWKAQVVKEPENTNEEWSRSYEPFRIAGNLYYVGTYDLASYLIVTDKGNILINTGLAGSLPMIKENIKKLGFNYKDIKILLLTQAHYDHTGALKDLQTETGAKFYADSADADVLKTGGKSDYEMGKYGATFKPIKPDILLKDQDKIKLGNTTLTLLHHPGHTKGSCSFIFETKDENRNYKVLIANMPSVIVDRKFSEIKDYPNIQADYAYTFKAMKKLDFDLWVASHASQFDLHTKHKEGDPYNPQVFMDKANYFAFLNSLETDYLEKIKNDSQKK"},"dna_sequence":{"accession":"AY899332.1","fmin":"0","fmax":"873","strand":"+","sequence":"ATGAGAAACTTTGCAATTTTATTTTTTTTACTGATCACTTTCAGCTGGAAAGCACAGGTTGTTAAAGAACCGGAAAATACAAATGAAGAATGGTCCCGATCATATGAGCCATTCAGAATTGCGGGTAACTTATACTATGTAGGAACTTACGATCTGGCTTCTTATTTAATAGTTACCGATAAAGGAAATATTCTCATTAATACAGGATTGGCAGGTTCTCTTCCTATGATAAAAGAGAATATTAAAAAACTGGGATTCAATTATAAAGACATTAAAATTCTGCTTTTAACCCAGGCGCATTATGATCATACAGGTGCATTAAAAGATTTGCAAACAGAAACAGGTGCGAAATTTTATGCAGACAGTGCTGATGCTGATGTATTGAAAACGGGCGGTAAATCCGATTATGAAATGGGGAAATACGGGGCAACCTTTAAGCCGATTAAGCCTGATATCCTGTTGAAAGATCAGGATAAAATAAAACTGGGGAATACAACCTTAACTTTACTTCATCATCCGGGGCACACAAAAGGTTCATGCAGTTTTATATTTGAAACAAAGGATGAAAACAGAAATTACAAAGTGCTGATAGCCAATATGCCATCGGTTATAGTTGACCGTAAGTTTTCCGAAATAAAAGATTACCCTAATATTCAGGCCGATTATGCTTATACATTTAAAGCCATGAAAAAACTGGATTTTGATCTTTGGGTCGCTTCACATGCAAGTCAGTTTGATTTACATACAAAACATAAAGAGGGAGACCCTTATAACCCACAGGTATTTATGGATAAGGCCAATTATTTTGCATTCCTCAATAGCCTGGAAACAGATTATCTGGAAAAAATTAAAAACGACTCACAAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36960","NCBI_taxonomy_name":"Elizabethkingia meningoseptica","NCBI_taxonomy_id":"238"}}}},"ARO_accession":"3008195","ARO_id":"46987","ARO_name":"GOB-17","CARD_short_name":"GOB-17","ARO_description":"Subclass B3 metallo-beta-lactamase GOB-17.","ARO_category":{"41376":{"category_aro_accession":"3004212","category_aro_cvterm_id":"41376","category_aro_name":"GOB beta-lactamase","category_aro_description":"The GOB family of beta-lactamases have been discovered in the Elizabethkingia meningoseptica and are classified as subclass B3 beta-lactamase. They confer resistance to cephalosporins, penicillins, and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7614":{"model_id":"7614","model_name":"GOB-47","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10441":{"protein_sequence":{"accession":"MVW92531.1","sequence":"MRNFAILFFLLITFSWKAQVVKEPENTNEEWSRSYQPFRIAGNLYYVGTYDLASYLIVTDKGNILINTGLAGSLPMIKENIKKLGFNYKDIKILLLTQAHYDHTGALKDLQTETGAKFYADSADADVLKTGGKSDYEMGKYGATFKPIKPDILLKDQDKIKLGNTTLTLLHHPGHTKGSCSFIFETKDENRNYKVLIANMPSVIVDRKFSEIKDYPNIQADYAYTFKAMKKLDFDLWVASHASQFDLHTKHKEGDPYNPQVFMDKANYFAFLNSLETDYLEKIKNDSQKK"},"dna_sequence":{"accession":"SYWC01000004.1","fmin":"300193","fmax":"301066","strand":"+","sequence":"ATGAGAAACTTTGCAATTTTATTTTTTTTACTGATCACTTTCAGCTGGAAAGCTCAGGTTGTTAAAGAACCGGAAAATACAAATGAAGAATGGTCCCGATCATATCAGCCATTCAGAATTGCAGGTAACTTATATTATGTGGGAACTTACGATCTGGCTTCTTATTTAATAGTTACCGATAAAGGAAATATTCTCATTAATACAGGATTGGCTGGTTCTCTTCCTATGATAAAAGAGAATATTAAAAAACTGGGATTCAATTATAAAGACATTAAAATTCTGCTTTTAACCCAGGCGCATTATGATCATACAGGTGCATTAAAAGATTTGCAAACAGAAACAGGTGCGAAATTTTATGCAGACAGTGCTGATGCTGATGTATTGAAAACGGGCGGTAAATCCGATTATGAAATGGGGAAATACGGGGCAACCTTTAAGCCGATTAAGCCTGATATCCTGTTGAAAGATCAGGATAAAATAAAACTGGGGAATACAACCTTAACTTTACTTCATCATCCGGGGCACACAAAAGGTTCATGCAGTTTTATATTTGAAACAAAGGATGAAAACAGAAATTATAAAGTGCTGATAGCCAATATGCCATCGGTTATAGTTGACCGTAAGTTTTCCGAAATAAAAGATTACCCTAATATTCAGGCCGATTATGCTTATACATTTAAAGCCATGAAAAAACTGGATTTTGATCTTTGGGTCGCTTCACATGCAAGTCAGTTTGATTTACATACAAAACATAAAGAGGGAGACCCTTATAACCCACAGGTATTTATGGATAAGGCCAATTATTTTGCATTCCTCAATAGCCTGGAAACAGATTATCTGGAAAAAATTAAAAACGACTCACAAAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36960","NCBI_taxonomy_name":"Elizabethkingia meningoseptica","NCBI_taxonomy_id":"238"}}}},"ARO_accession":"3008196","ARO_id":"46988","ARO_name":"GOB-47","CARD_short_name":"GOB-47","ARO_description":"Subclass B3 metallo-beta-lactamase GOB-47.","ARO_category":{"41376":{"category_aro_accession":"3004212","category_aro_cvterm_id":"41376","category_aro_name":"GOB beta-lactamase","category_aro_description":"The GOB family of beta-lactamases have been discovered in the Elizabethkingia meningoseptica and are classified as subclass B3 beta-lactamase. They confer resistance to cephalosporins, penicillins, and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7615":{"model_id":"7615","model_name":"GOB-52","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10442":{"protein_sequence":{"accession":"BBQ04269.1","sequence":"MRNFATLFFMFVCLGLNAQVVKEPENMPKEWNQTYEPFRIAGNLYYVGTYDLASYLIVTDKGNILINTGTAESLPIIKANIQKLGFNYKDIKILLLTQAHYDHTGALQDLKTETAAKFYADKADADVLRTGGNSDYEIGKYGVTFKPVTPDKTLKDQDKIKLGNTILTLLHHPGHTKGSCSFIFETKDEKRKYRVLIANMPSVIVDKKFSEVTAYPNIQSDYAYTFKAMKNLDFDLWVASHASQFDLHEKRKEGDPYNPQLFMDKQSYFQNLNDLEKSYLDKIKKDSQDK"},"dna_sequence":{"accession":"LC511769.1","fmin":"0","fmax":"873","strand":"+","sequence":"ATGAGAAATTTTGCTACACTGTTTTTCATGTTCGTTTGCTTGGGCTTGAATGCTCAGGTAGTAAAAGAACCTGAAAATATGCCCAAAGAATGGAACCAGACTTATGAACCCTTCAGAATTGCAGGTAATTTATATTACGTAGGAACCTATGATTTGGCTTCTTACCTTATTGTGACAGACAAAGGCAATATTCTCATTAATACAGGAACGGCAGAATCGCTTCCAATAATAAAAGCAAATATCCAAAAGCTCGGGTTTAATTATAAAGACATTAAGATCTTGCTGCTTACTCAGGCTCACTACGACCATACAGGTGCATTACAAGATCTTAAAACAGAAACCGCTGCAAAATTCTATGCCGATAAAGCAGATGCTGATGTCCTGAGAACAGGGGGAAATTCCGATTATGAAATTGGAAAATATGGTGTGACATTTAAACCTGTTACTCCGGATAAAACATTGAAAGATCAGGATAAAATAAAACTGGGAAATACAATCCTGACTTTGCTTCATCATCCGGGACATACAAAAGGTTCCTGTAGTTTTATTTTTGAAACAAAAGACGAGAAGAGAAAATATAGAGTTTTGATAGCTAATATGCCCTCCGTTATTGTTGATAAGAAATTTTCTGAAGTTACCGCATATCCAAATATTCAGTCCGATTATGCATATACTTTCAAAGCAATGAAGAATCTAGATTTTGACCTTTGGGTGGCATCACATGCAAGTCAGTTCGATCTGCATGAAAAACGTAAAGAAGGAGATCCGTACAATCCGCAATTGTTTATGGATAAGCAAAGCTATTTCCAAAACCTTAATGATTTGGAAAAAAGCTATCTCGACAAAATAAAAAAAGATTCACAAGATAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41081","NCBI_taxonomy_name":"Elizabethkingia anophelis","NCBI_taxonomy_id":"1117645"}}}},"ARO_accession":"3008197","ARO_id":"46989","ARO_name":"GOB-52","CARD_short_name":"GOB-52","ARO_description":"Subclass B3 metallo-beta-lactamase GOB-52.","ARO_category":{"41376":{"category_aro_accession":"3004212","category_aro_cvterm_id":"41376","category_aro_name":"GOB beta-lactamase","category_aro_description":"The GOB family of beta-lactamases have been discovered in the Elizabethkingia meningoseptica and are classified as subclass B3 beta-lactamase. They confer resistance to cephalosporins, penicillins, and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7616":{"model_id":"7616","model_name":"GOB-53","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10443":{"protein_sequence":{"accession":"UTS94243.1","sequence":"MRNFATLFFMFICLGLNAQVVKEPENMPKEWNQAYEPFRIAGNLYYVGTYDLASYLIVTDKGNILINTGTAESLPIIKANIQKLGFNYKDIKILLLTQAHYDHTGALQDFKTETAAKFYADKADADVLRTGGESDYEMGKYGVTFKPVTPDKTLKDQDKIKLGNTTLTLLHHPGHTKGSCSFIFETKDEKRKYRVLIANMPSVIVDKKFSEVTAYPNIQSDYAYTFGVMKKLDFDIWVASHASQFDLHEKRKEGDPYNPQLFMDKQSYFQNLNDLEKSYLDKIKKDSQDK"},"dna_sequence":{"accession":"ON651490.1","fmin":"0","fmax":"873","strand":"+","sequence":"ATGAGAAATTTTGCTACACTGTTTTTCATGTTCATTTGCTTGGGCTTGAATGCTCAGGTAGTAAAAGAACCTGAAAATATGCCCAAAGAATGGAACCAGGCTTATGAACCATTCAGAATTGCAGGTAATTTATATTACGTAGGAACCTATGATTTGGCTTCTTACCTTATTGTGACAGACAAAGGCAATATTCTCATTAATACAGGAACGGCAGAATCGCTTCCAATAATAAAAGCAAATATCCAAAAGCTCGGGTTTAATTATAAAGACATTAAGATCTTGCTGCTTACTCAGGCTCACTACGACCATACAGGTGCATTACAGGATTTTAAAACAGAAACCGCCGCAAAATTCTATGCCGATAAAGCAGATGCTGATGTCCTGAGAACAGGGGGGGAGTCCGATTATGAAATGGGAAAATATGGTGTGACATTTAAACCTGTTACTCCGGATAAAACATTGAAAGATCAGGATAAAATAAAACTGGGAAATACAACCCTGACTTTGCTTCATCATCCCGGACATACAAAAGGTTCCTGTAGTTTTATTTTTGAAACAAAAGACGAGAAGAGAAAATATAGAGTTTTGATAGCTAATATGCCCTCCGTTATTGTTGATAAGAAATTTTCTGAAGTTACCGCATATCCAAATATTCAGTCCGATTATGCTTATACCTTTGGTGTTATGAAAAAGCTGGATTTTGATATTTGGGTGGCCTCCCATGCAAGTCAGTTCGATCTCCATGAAAAACGTAAAGAAGGAGATCCGTACAATCCGCAATTGTTTATGGATAAGCAAAGCTATTTCCAAAACCTTAATGATTTGGAAAAAAGCTATCTCGACAAAATAAAAAAAGATTCACAAGATAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41081","NCBI_taxonomy_name":"Elizabethkingia anophelis","NCBI_taxonomy_id":"1117645"}}}},"ARO_accession":"3008198","ARO_id":"46990","ARO_name":"GOB-53","CARD_short_name":"GOB-53","ARO_description":"Subclass B3 metallo-beta-lactamase GOB-53.","ARO_category":{"41376":{"category_aro_accession":"3004212","category_aro_cvterm_id":"41376","category_aro_name":"GOB beta-lactamase","category_aro_description":"The GOB family of beta-lactamases have been discovered in the Elizabethkingia meningoseptica and are classified as subclass B3 beta-lactamase. They confer resistance to cephalosporins, penicillins, and carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7617":{"model_id":"7617","model_name":"HBL-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10444":{"protein_sequence":{"accession":"UNG16571.1","sequence":"MDRRTFGAGVLAWLGASAAGLPALAGVRDSLPAASDDAQRQLARLEAREGGRLGVSLLDVQSGYAIAYRADERFALCSTFKLLAVGAVLTRVARGEDDLSRPMRLSAADIVDYSPVTQQRLNEGMTLGQLCEAALLWGDNTAANLLLSTIGGPPGVTAYARALGDGATRLDRLETALNEARPGDERDTTTPAAMLGNLRQLVLGDALPAPERERLRDWLMQCRTGQQRLRAGLPAGWSLGHRTGAGGHGTCNDIGVAWPTPTTPVVISVYLTESPLDLPGRERVLAEAARILAHALASARLHAG"},"dna_sequence":{"accession":"OM212391.1","fmin":"0","fmax":"915","strand":"+","sequence":"ATGGACAGAAGAACGTTTGGCGCGGGTGTGCTGGCCTGGCTGGGCGCTTCGGCGGCGGGGCTGCCCGCCCTGGCCGGAGTGCGCGACAGCCTGCCCGCGGCCAGTGACGACGCGCAGCGCCAGCTGGCGCGCCTGGAGGCGCGCGAGGGCGGGCGCCTGGGCGTGAGCCTGCTCGATGTGCAAAGCGGCTACGCCATCGCCTACCGGGCCGATGAGCGCTTCGCCCTGTGCAGCACCTTCAAGCTTCTTGCCGTCGGCGCCGTGCTCACCCGCGTGGCCCGCGGCGAGGATGACCTGTCCCGGCCGATGCGCCTGAGCGCGGCCGACATCGTGGACTATTCACCGGTGACCCAGCAGCGGCTCAACGAGGGCATGACGCTGGGCCAGCTGTGCGAGGCGGCCCTGCTGTGGGGCGACAACACGGCGGCCAACCTCTTGCTGTCCACCATCGGCGGGCCGCCGGGCGTCACGGCCTATGCCCGCGCCCTGGGCGATGGCGCGACCCGGCTGGACCGTCTCGAGACCGCCTTGAACGAAGCCCGGCCCGGCGACGAGCGCGACACCACCACGCCGGCGGCCATGCTGGGCAACCTGAGGCAGCTGGTGCTGGGCGATGCCCTGCCGGCGCCCGAGCGCGAGCGCCTGCGCGACTGGCTGATGCAATGCCGCACGGGGCAGCAGCGGCTGCGCGCCGGCCTGCCCGCCGGCTGGTCCCTCGGCCATCGCACCGGCGCTGGCGGCCATGGCACCTGCAATGACATCGGCGTGGCCTGGCCCACGCCCACCACGCCGGTGGTGATCTCCGTCTATCTGACCGAATCGCCGCTGGATCTGCCCGGACGCGAACGGGTGCTGGCCGAGGCCGCGCGCATCCTGGCGCACGCCCTGGCGTCCGCCCGCCTGCACGCCGGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"45761","NCBI_taxonomy_name":"Bordetella hinzii","NCBI_taxonomy_id":"103855"}}}},"ARO_accession":"3008199","ARO_id":"46991","ARO_name":"HBL-1","CARD_short_name":"HBL-1","ARO_description":"Class A beta-lactamase HBL-1.","ARO_category":{"46660":{"category_aro_accession":"3007869","category_aro_cvterm_id":"46660","category_aro_name":"HBL beta-lactamase","category_aro_description":"HBL is a family of class A beta-lactamases which enzymatically inactivate beta-lactam antibiotics.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7618":{"model_id":"7618","model_name":"HER-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10445":{"protein_sequence":{"accession":"AAL26797.1","sequence":"MKKITPLFVIAFLTLIALLAPAQASVTPDMTDFLRQQEQRLHARIGMAVVNAQGETVFGYRQDERFPLTSTFKTLACAALLERLQKNGGSLDEQVTIPPDALLDYAPVTKNYLAPATISLRMLCAAAVSYSDNTAGNRILTYLGGPDAVTQFMRGIGDHVTRLDRTEPTLNEATPGDARDTSSPQKMAAGLQKILTSPPLISANRATLAQWMRDDKVGDALLRAALPKGWAIADKTGAGGYGSRAIIAAVYPPERPPFYVAIFITQTEASMKMANETIAEIGKQLFAGQP"},"dna_sequence":{"accession":"AF311385.1","fmin":"0","fmax":"873","strand":"+","sequence":"ATGAAAAAAATCACCCCGCTCTTTGTCATCGCATTTCTGACTCTGATCGCGTTACTGGCCCCGGCGCAGGCCTCCGTCACGCCAGATATGACGGACTTTTTACGCCAGCAGGAGCAACGGCTTCACGCCAGAATTGGCATGGCGGTTGTCAACGCGCAAGGCGAAACGGTGTTCGGTTATCGGCAGGACGAGCGTTTCCCGCTGACCAGCACCTTTAAAACCCTGGCCTGCGCCGCGTTGCTTGAGCGGTTGCAGAAAAACGGCGGTTCGCTGGATGAACAGGTGACTATTCCGCCAGACGCCTTGCTGGACTATGCGCCAGTGACTAAAAACTACCTCGCCCCTGCCACCATCTCTTTACGCATGCTGTGCGCGGCGGCGGTGAGCTACAGCGACAACACGGCGGGCAACCGCATTCTGACTTACCTTGGCGGCCCTGATGCCGTCACGCAGTTTATGCGCGGGATCGGCGACCATGTGACCCGTCTGGATCGAACGGAGCCCACGCTGAATGAAGCCACGCCAGGCGATGCGCGCGATACCTCTTCGCCGCAGAAGATGGCGGCAGGGCTGCAAAAAATCCTCACCTCCCCTCCCCTGATATCGGCTAACCGGGCGACGCTGGCGCAGTGGATGCGTGACGATAAAGTGGGAGATGCGCTGCTACGCGCCGCGCTGCCGAAAGGCTGGGCAATTGCCGATAAAACCGGGGCGGGCGGCTACGGCTCGCGGGCGATTATCGCGGCGGTCTATCCGCCGGAACGCCCGCCGTTTTATGTCGCGATTTTTATTACGCAAACGGAAGCCTCGATGAAAATGGCAAATGAAACCATTGCTGAAATCGGCAAGCAGTTGTTTGCCGGGCAGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41643","NCBI_taxonomy_name":"Atlantibacter hermannii","NCBI_taxonomy_id":"565"}}}},"ARO_accession":"3008200","ARO_id":"46992","ARO_name":"HER-1","CARD_short_name":"HER-1","ARO_description":"Penicillin-hydrolyzing class A beta-lactamase HER-1.","ARO_category":{"46661":{"category_aro_accession":"3007870","category_aro_cvterm_id":"46661","category_aro_name":"HER beta-lactamase","category_aro_description":"HER is a family of class A beta-lactamases which enzymatically inactivation penam-type beta-lactam antibiotics.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7619":{"model_id":"7619","model_name":"HER-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10446":{"protein_sequence":{"accession":"AAL26995.1","sequence":"MKKITPLFAIAFLTLIALLAPAQASVTPDMTDFLRQQEQRLHARIGMAVVNAQGETVFGYRQDERFPLTSTFKTLACAALLERLQKNGGSLDEQVTIPPDALLDYAPVTKNYLAPATISLRMLCAAAVSYSDNTAGNRILTYLGGPDAVTQFMRGIGDHVTRVDRTEPTLNEATPGDARDTSSPQKMAAGLQKILTAPPLTPANRAVLAQWMRDDKVGDALLRAALPKGWAIADKTGAGGYGSRAIIAAVYPPERPPFYVAIFITQTEASMKMANETIAEIGKQLFAGQP"},"dna_sequence":{"accession":"AF398334.1","fmin":"0","fmax":"873","strand":"+","sequence":"ATGAAAAAAATCACCCCGCTCTTTGCCATCGCATTTCTGACCCTGATCGCGTTACTGGCTCCGGCACAGGCCTCCGTCACGCCAGACATGACGGACTTTTTACGCCAGCAAGAGCAACGGCTTCACGCCAGAATTGGCATGGCGGTTGTCAACGCACAAGGCGAAACGGTGTTCGGTTATCGGCAGGACGAGCGTTTCCCGCTGACCAGCACCTTTAAAACCCTGGCCTGCGCCGCGTTGCTTGAGCGATTGCAGAAAAACGGCGGTTCGCTGGATGAACAGGTGACTATTCCGCCAGACGCGTTGCTGGACTATGCGCCAGTGACTAAAAACTACCTCGCCCCTGCCACCATCTCCTTACGCATGTTGTGCGCAGCGGCGGTGAGCTACAGCGACAACACGGCGGGCAACCGCATTCTGACTTACCTTGGCGGCCCGGATGCCGTCACGCAGTTTATGCGCGGGATCGGCGACCATGTGACCCGTGTGGATCGAACGGAGCCCACGCTGAATGAAGCCACGCCAGGCGATGCGCGCGATACCTCTTCGCCGCAAAAGATGGCGGCAGGGCTGCAAAAAATCCTCACCGCCCCTCCCCTGACGCCGGCTAACCGGGCGGTGCTGGCGCAGTGGATGCGTGACGATAAAGTGGGAGATGCGCTGCTACGCGCCGCGCTGCCGAAAGGCTGGGCAATTGCCGATAAAACCGGGGCGGGCGGCTACGGCTCGCGGGCGATTATCGCGGCGGTCTATCCGCCGGAACGCCCGCCGTTTTATGTCGCGATTTTTATTACGCAAACGGAAGCCTCGATGAAAATGGCAAATGAAACCATTGCTGAAATCGGCAAGCAGTTGTTTGCCGGGCAGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41643","NCBI_taxonomy_name":"Atlantibacter hermannii","NCBI_taxonomy_id":"565"}}}},"ARO_accession":"3008201","ARO_id":"46993","ARO_name":"HER-2","CARD_short_name":"HER-2","ARO_description":"Class A beta-lactamase HER-2.","ARO_category":{"46661":{"category_aro_accession":"3007870","category_aro_cvterm_id":"46661","category_aro_name":"HER beta-lactamase","category_aro_description":"HER is a family of class A beta-lactamases which enzymatically inactivation penam-type beta-lactam antibiotics.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7620":{"model_id":"7620","model_name":"HER-3","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10447":{"protein_sequence":{"accession":"AAL26996.1","sequence":"MKKITPLFAIAFLTLIALLAPAQASVTPDMTDFLRQQEQRLHARIGMAVVNAQGETVFGYRQDERFPLTSTFKTLACAALLERLQKNGGSLDEQVTIPPDALLDYAPVTKNYLAPATISLRMLCAAAVSYSDNTAGNRILTYLGGPDAVTQFMRGIGDHVTRLDRTEPTLNEATPGDARDTSSPQKMAAGLQKILTAPPLTPANRAVLAQWMRDDKVGDALLRAALPKGWAIADKTGAGGYGSRAIIAAVYPPERPPFYVAIFITQTEASMKMANETIAEIGKQLFAGQP"},"dna_sequence":{"accession":"AF398335.1","fmin":"0","fmax":"873","strand":"+","sequence":"ATGAAAAAAATCACCCCGCTCTTTGCCATCGCATTTCTGACCCTGATCGCGTTACTGGCTCCGGCACAGGCCTCCGTCACGCCAGACATGACGGACTTTTTACGCCAGCAAGAGCAACGGCTTCACGCCAGAATTGGCATGGCGGTTGTCAACGCACAAGGCGAAACGGTGTTCGGTTATCGGCAGGACGAGCGTTTCCCGCTGACCAGCACCTTTAAAACCCTGGCCTGCGCCGCGTTGCTTGAGCGATTGCAGAAAAACGGCGGTTCGCTGGATGAACAGGTGACTATTCCGCCAGACGCGTTGCTGGACTATGCGCCAGTGACTAAAAACTACCTCGCCCCTGCCACCATCTCCTTACGCATGTTGTGCGCAGCGGCGGTGAGCTACAGCGACAACACGGCGGGCAACCGCATTCTGACTTACCTTGGCGGCCCGGATGCCGTCACGCAGTTTATGCGCGGGATCGGCGACCATGTGACCCGTCTGGATCGAACGGAGCCCACGCTGAATGAAGCCACGCCAGGCGATGCGCGCGATACCTCTTCGCCGCAGAAGATGGCGGCAGGGCTGCAAAAAATCCTCACCGCCCCTCCCCTGACGCCGGCTAACCGGGCGGTGCTGGCGCAGTGGATGCGTGACGATAAAGTGGGAGATGCGCTGCTACGCGCCGCGCTGCCGAAAGGCTGGGCAATTGCCGATAAAACCGGGGCGGGCGGCTACGGCTCGCGGGCGATTATCGCGGCGGTCTATCCGCCGGAACGCCCGCCGTTTTATGTCGCGATTTTTATTACGCAAACGGAAGCCTCGATGAAAATGGCAAATGAAACCATTGCTGAAATCGGCAAGCAGTTGTTTGCCGGGCAGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41643","NCBI_taxonomy_name":"Atlantibacter hermannii","NCBI_taxonomy_id":"565"}}}},"ARO_accession":"3008202","ARO_id":"46994","ARO_name":"HER-3","CARD_short_name":"HER-3","ARO_description":"Class A beta-lactamase HER-3.","ARO_category":{"46661":{"category_aro_accession":"3007870","category_aro_cvterm_id":"46661","category_aro_name":"HER beta-lactamase","category_aro_description":"HER is a family of class A beta-lactamases which enzymatically inactivation penam-type beta-lactam antibiotics.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7621":{"model_id":"7621","model_name":"HER-4","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10448":{"protein_sequence":{"accession":"CAD60968.1","sequence":"MKKITPLFVIAFLTLIALLAPAQASVTPDMTDFLRQQEQRLHARIGMAVVNAQGETVFGYRQDERFPLTSTFKTLACAALLERLQKNGGSLDEQVTIPPDALLDYAPVTKNYLAPATISLRMLCAAAVSYSDNTAGNRILTYLAGPDAVTQFMRGIGDHVTRLDRTEPTLNEATPGDARDTSSPQKMAAGLQKILTSPPLISANRATLAQWMRDDKVGDALLRAALPKGWAIADKTGAGGYGSRAIIAAVYPPERPPFYVAIFITQTEASMKMANETTAEIGKQLFAGQP"},"dna_sequence":{"accession":"AJ536088.1","fmin":"0","fmax":"873","strand":"+","sequence":"ATGAAAAAAATCACCCCGCTCTTTGTCATCGCATTTCTGACTCTGATCGCGTTACTGGCCCCGGCGCAGGCCTCCGTCACGCCAGATATGACGGACTTTTTACGCCAGCAGGAGCAACGGCTTCACGCCAGAATTGGCATGGCGGTTGTCAACGCGCAAGGCGAAACGGTGTTCGGTTATCGGCAGGACGAGCGTTTCCCGCTGACCAGCACCTTTAAAACCCTGGCCTGCGCCGCGTTGCTTGAGCGGTTGCAGAAAAACGGCGGTTCGCTGGATGAACAGGTGACTATTCCGCCAGACGCCTTGCTGGACTATGCGCCAGTGACTAAAAACTACCTCGCCCCTGCCACCATCTCTTTACGCATGCTGTGCGCGGCGGCGGTGAGCTACAGCGACAACACGGCGGGCAACCGCATTCTGACTTACCTTGCCGGCCCTGATGCCGTCACGCAGTTTATGCGCGGGATCGGCGACCATGTGACCCGTCTGGATCGAACGGAGCCCACGCTGAATGAAGCCACGCCAGGCGATGCGCGCGATACCTCTTCGCCGCAGAAGATGGCGGCAGGGCTGCAAAAAATCCTCACCTCCCCTCCCCTGATATCGGCTAACCGGGCGACGCTGGCGCAGTGGATGCGTGACGATAAAGTGGGAGATGCGCTGCTACGCGCCGCGCTGCCGAAAGGCTGGGCAATTGCCGATAAAACCGGGGCGGGCGGCTACGGCTCGCGGGCGATTATCGCGGCGGTCTATCCGCCGGAACGCCCGCCGTTTTATGTCGCGATTTTTATTACGCAAACGGAAGCCTCGATGAAAATGGCAAATGAAACCACTGCTGAAATCGGCAAGCAGTTGTTTGCCGGGCAGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41643","NCBI_taxonomy_name":"Atlantibacter hermannii","NCBI_taxonomy_id":"565"}}}},"ARO_accession":"3008203","ARO_id":"46995","ARO_name":"HER-4","CARD_short_name":"HER-4","ARO_description":"Class A beta-lactamase HER-4.","ARO_category":{"46661":{"category_aro_accession":"3007870","category_aro_cvterm_id":"46661","category_aro_name":"HER beta-lactamase","category_aro_description":"HER is a family of class A beta-lactamases which enzymatically inactivation penam-type beta-lactam antibiotics.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7622":{"model_id":"7622","model_name":"HER-5","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10449":{"protein_sequence":{"accession":"CAD60969.1","sequence":"MKKITPLFAIAFLTLIALLAPAQASVTPDMTDFLRQQEQRLHARIGMAVVNAQGETVFGYRQDERFPLTSTFKTLACAALLERLQKNGGSLDEQVTIPPDALLDYAPVTKNYLAPATISLRMLCAAAVSYSDNTAGNRILTYLGGPDAVTQFMRGIGEHVTRLDRTEPTLNEATPGDARDTSSPQKMAAGLQKILTAPPLTPANRATLAQWMRDDKVGDALLRAALPKGWAIADKTGAGGYGSRAIIAAVYPPERPPFYVAIFITQTEASMKMANETIAEIGKQLFAGQP"},"dna_sequence":{"accession":"AJ536089.1","fmin":"0","fmax":"873","strand":"+","sequence":"ATGAAAAAAATCACCCCGCTCTTTGCCATCGCATTTCTGACCCTGATCGCGTTACTGGCCCCGGCGCAGGCCTCCGTCACGCCAGATATGACGGACTTTTTACGCCAGCAGGAGCAACGGCTTCACGCCAGAATTGGCATGGCGGTTGTCAACGCGCAAGGCGAAACGGTGTTCGGTTATCGGCAGGACGAGCGTTTCCCGCTGACCAGCACCTTTAAAACCCTGGCCTGCGCCGCGTTGCTTGAGCGATTGCAGAAAAACGGCGGTTCGCTGGATGAACAGGTGACTATTCCGCCAGACGCCTTGCTGGACTATGCGCCAGTGACTAAAAACTACCTCGCCCCTGCCACCATCTCCTTACGCATGTTGTGCGCAGCGGCGGTGAGCTACAGCGACAACACGGCGGGCAACCGCATTCTGACTTACCTTGGCGGCCCGGATGCCGTCACGCAGTTTATGCGCGGGATCGGCGAACATGTGACCCGTCTGGATCGAACGGAGCCCACGCTGAATGAAGCCACGCCAGGCGATGCGCGCGATACCTCTTCGCCGCAGAAGATGGCGGCAGGGCTGCAAAAAATCCTCACCGCCCCTCCCCTGACACCGGCTAACCGGGCGACGCTGGCGCAGTGGATGCGTGACGATAAAGTGGGAGATGCGCTGCTACGCGCCGCGCTGCCGAAAGGCTGGGCAATTGCCGATAAAACCGGGGCGGGCGGCTACGGCTCGCGGGCGATTATCGCGGCGGTCTATCCGCCGGAACGCCCGCCGTTTTATGTCGCGATTTTTATTACGCAAACGGAAGCCTCGATGAAAATGGCAAATGAAACCATTGCTGAAATCGGCAAGCAGTTGTTTGCCGGGCAGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41643","NCBI_taxonomy_name":"Atlantibacter hermannii","NCBI_taxonomy_id":"565"}}}},"ARO_accession":"3008204","ARO_id":"46996","ARO_name":"HER-5","CARD_short_name":"HER-5","ARO_description":"Class A beta-lactamase HER-5.","ARO_category":{"46661":{"category_aro_accession":"3007870","category_aro_cvterm_id":"46661","category_aro_name":"HER beta-lactamase","category_aro_description":"HER is a family of class A beta-lactamases which enzymatically inactivation penam-type beta-lactam antibiotics.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7623":{"model_id":"7623","model_name":"HER-6","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10450":{"protein_sequence":{"accession":"CAD60970.1","sequence":"MKKITPLFAIAFLTLIALLAPAQASVTPDMTDFLRQQEQRLHARIGMAVVNAQGETVFGYRQDERFPLTSTFKTLACAALLERLQKNGGSLDEQVTIPPDALLDYAPVTKNYLAPATISLRMLCAAAVSYSDNTAGNRILTYLGGPDAVTQFMRGIGDHVTRLDRTEPTLNEATPGDARDTSSPQKMAAGLQKILTAPPLTPANRATLAQWMRDDKVGDALLRAALPKGWAIADKTGAGGYGSRAIIAAVYPPERPPFYVAIFITQTEASMKMANEAIAAIGKQLFAGQP"},"dna_sequence":{"accession":"AJ536090.1","fmin":"0","fmax":"873","strand":"+","sequence":"ATGAAAAAAATCACCCCGCTCTTCGCCATCGCATTTCTAACCCTGATCGCGTTACTGGCTCCGGCACAGGCCTCCGTCACGCCAGATATGACGGACTTTTTACGCCAGCAGGAGCAACGGCTTCACGCCAGAATTGGCATGGCGGTTGTCAACGCGCAAGGCGAAACGGTGTTCGGTTATCGGCAGGACGAGCGTTTCCCGCTGACCAGCACCTTTAAAACCCTGGCCTGCGCCGCGTTGCTTGAGCGGTTGCAGAAAAACGGCGGTTCGCTGGATGAACAGGTGACTATTCCGCCAGACGCCTTGCTGGACTATGCGCCAGTGACTAAAAACTACCTCGCCCCTGCCACCATCTCCTTACGCATGTTGTGCGCAGCGGCGGTGAGCTACAGCGACAACACGGCGGGCAACCGCATTCTGACTTACCTTGGCGGCCCGGATGCCGTCACGCAGTTTATGCGCGGGATCGGCGACCATGTGACCCGTCTGGATCGAACGGAGCCCACGCTGAATGAAGCCACGCCAGGCGATGCGCGCGATACCTCTTCGCCGCAGAAGATGGCGGCAGGGCTGCAAAAAATCCTCACCGCCCCGCCCCTGACGCCGGCTAACCGGGCGACGCTGGCGCAATGGATGCGTGACGATAAAGTGGGAGATGCGCTGCTACGCGCCGCGCTGCCGAAAGGCTGGGCGATTGCCGATAAAACCGGGGCGGGCGGCTACGGCTCGCGGGCGATTATCGCGGCGGTCTATCCGCCGGAACGCCCGCCGTTTTATGTCGCGATTTTTATTACGCAAACCGAAGCCTCAATGAAAATGGCAAATGAAGCCATTGCTGCAATCGGCAAGCAGTTGTTTGCCGGGCAGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41643","NCBI_taxonomy_name":"Atlantibacter hermannii","NCBI_taxonomy_id":"565"}}}},"ARO_accession":"3008205","ARO_id":"46997","ARO_name":"HER-6","CARD_short_name":"HER-6","ARO_description":"Class A beta-lactamase HER-6.","ARO_category":{"46661":{"category_aro_accession":"3007870","category_aro_cvterm_id":"46661","category_aro_name":"HER beta-lactamase","category_aro_description":"HER is a family of class A beta-lactamases which enzymatically inactivation penam-type beta-lactam antibiotics.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7624":{"model_id":"7624","model_name":"HER-8","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10451":{"protein_sequence":{"accession":"CAD60972.1","sequence":"MKKITPLFAIAFLTLIALLAPAQASVTPDMTDFLRQQEQRLHARIGMAVVNAQGETVFGYRQDERFPLTSTFKTLACAALLERLQKNGGSLDEQVTIPPDALLDYAPVTKNYLAPATISLRMLCAAAVSYSDNTAGNRILTYLGGPDAVTQFMRGIGDPVTRLDRTEPTLNEATPGDARDTSSPQKMAAGLQKILTAPPLTPANRAVLAQWMRDDKVGDALLRAALPKGWAIADKTGAGGYGSRAIIAAVYPPERPPFYVAIFITQTEASMKMANEAIPAIGKQLFAGQP"},"dna_sequence":{"accession":"AJ536092.1","fmin":"0","fmax":"873","strand":"+","sequence":"ATGAAAAAAATCACCCCGCTCTTTGCCATCGCATTTCTGACCCTGATCGCGTTACTGGCTCCGGCACAGGCCTCCGTCACGCCAGACATGACGGACTTTTTACGCCAGCAGGAGCAACGGCTTCACGCCAGAATTGGCATGGCGGTTGTCAACGCGCAAGGCGAAACGGTGTTCGGTTATCGGCAGGACGAGCGTTTCCCGCTGACCAGCACCTTTAAAACCCTGGCCTGCGCCGCGTTGCTTGAGCGGTTGCAGAAAAACGGCGGTTCGCTGGATGAACAGGTGACTATTCCGCCAGACGCCTTGCTGGACTATGCGCCAGTGACTAAAAACTACCTCGCCCCTGCCACCATCTCTTTACGCATGCTGTGCGCGGCGGCGGTGAGCTACAGCGACAACACGGCGGGCAACCGCATTCTGACTTACCTTGGCGGCCCGGATGCCGTCACGCAGTTTATGCGCGGGATCGGCGACCCTGTGACCCGTCTGGATCGGACGGAGCCCACGCTGAATGAAGCCACGCCAGGCGATGCGCGCGATACCTCTTCGCCGCAGAAGATGGCGGCAGGGCTGCAAAAAATCCTCACCGCCCCTCCCCTGACGCCGGCTAACCGGGCGGTGCTGGCGCAGTGGATGCGTGACGATAAAGTGGGAGATGCGCTGCTACGCGCCGCGCTGCCGAAAGGCTGGGCAATTGCCGATAAAACCGGGGCGGGCGGCTACGGCTCGCGGGCGATTATCGCGGCGGTCTATCCGCCGGAACGCCCGCCGTTTTATGTCGCGATTTTTATTACGCAAACGGAAGCCTCAATGAAAATGGCAAATGAAGCCATTCCCGCAATCGGCAAGCAGTTGTTTGCCGGGCAGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41643","NCBI_taxonomy_name":"Atlantibacter hermannii","NCBI_taxonomy_id":"565"}}}},"ARO_accession":"3008206","ARO_id":"46998","ARO_name":"HER-8","CARD_short_name":"HER-8","ARO_description":"Class A beta-lactamase HER-8.","ARO_category":{"46661":{"category_aro_accession":"3007870","category_aro_cvterm_id":"46661","category_aro_name":"HER beta-lactamase","category_aro_description":"HER is a family of class A beta-lactamases which enzymatically inactivation penam-type beta-lactam antibiotics.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7625":{"model_id":"7625","model_name":"HMB-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10452":{"protein_sequence":{"accession":"KYO71936.1","sequence":"MKRFLTLCAALFATVAFAEDPLPELEVKKIDEGVYLYTSYENYPSWGLVASNGLVFVDGKDAYIIDTPATVKDTEVLVQWINDQGFKPKASISTHFHDDSTIGIAYLNSKSIPTYASEQTNELLNKEGAAQATHSFKKNPYWLLKNKIEAFYPGAGHTPDNLVVWLPKQKILFGGCFVKPHGLGNLSHAVVSEWPASAEKLINRYSDAKIVVPGHGTMGDASLLEKTKQHALEAVAKKK"},"dna_sequence":{"accession":"LOHH01000059.1","fmin":"823","fmax":"1543","strand":"-","sequence":"ATGAAACGATTTTTAACGCTCTGTGCTGCATTGTTTGCAACTGTTGCATTCGCAGAAGATCCGCTACCCGAACTGGAAGTTAAAAAAATCGATGAGGGAGTTTATTTGTACACATCCTATGAAAATTACCCAAGCTGGGGTTTGGTTGCATCCAACGGTTTGGTTTTTGTGGATGGTAAAGACGCTTACATTATTGATACGCCCGCCACCGTCAAAGACACAGAAGTGTTGGTGCAATGGATTAACGATCAAGGCTTTAAACCCAAAGCCAGCATCTCGACGCACTTTCATGATGACAGCACCATCGGCATTGCCTACTTGAATTCCAAATCCATTCCGACCTACGCATCAGAGCAAACCAATGAATTGCTTAATAAAGAAGGCGCTGCACAGGCAACGCATTCGTTTAAGAAAAATCCTTATTGGCTGTTAAAAAATAAAATCGAAGCTTTTTATCCGGGTGCTGGCCACACGCCGGACAATTTAGTGGTGTGGTTGCCGAAGCAGAAAATCCTATTCGGCGGCTGTTTTGTAAAACCCCACGGATTGGGAAATTTAAGCCATGCGGTAGTTTCTGAATGGCCTGCTTCTGCAGAAAAACTTATCAATCGCTATAGCGACGCAAAAATCGTAGTACCGGGTCATGGAACAATGGGCGATGCATCGCTGCTGGAAAAAACCAAACAGCATGCGCTTGAGGCGGTTGCAAAGAAGAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008207","ARO_id":"46999","ARO_name":"HMB-2","CARD_short_name":"HMB-2","ARO_description":"Subclass B1 metallo-beta-lactamase HMB-2.","ARO_category":{"41373":{"category_aro_accession":"3004209","category_aro_cvterm_id":"41373","category_aro_name":"HMB beta-lactamase","category_aro_description":"First identified from a multi-drug resistant Pseudomonas aeruginosa clinical isolate in 2012, HMB type beta-lactamases can be encoded in transposons and hydrolyze carbapenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7626":{"model_id":"7626","model_name":"IMI-10","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10453":{"protein_sequence":{"accession":"MDX7665057.1","sequence":"MSLNVKPSRIAILFSSCLVSISFFSQANTKGIDEIKNLETDFNGRIGVYALDTGSGKSFSYKANERFPLCSSFKGFLAAAVLKGSQDNQLNLNQIVNYNTRSLEFHSPITTKYKDNGMSLGDMAAAALQYSDNGATNIILERYIGGPEGMTKFMRSIGDKDFRLDRWELDLNTAIPGDERDTSTPAAVAKSLKTLALGNILNEREKETYQTWLKGNTTGAARIRASVPSDWVVGDKTGSCGAYGTANDYAVVWPKNRAPLIISVYTTKNEKEAKHEDKVIAEASRIAIDNLK"},"dna_sequence":{"accession":"JAXAFB010000014.1","fmin":"4243","fmax":"5122","strand":"-","sequence":"ATGTCACTTAATGTAAAACCAAGTAGAATAGCCATCTTGTTTAGCTCTTGTTTAGTTTCAATATCATTTTTCTCACAGGCCAATACAAAGGGAATCGATGAGATTAAAAACCTTGAAACAGATTTCAATGGTAGAATTGGTGTCTACGCTTTAGACACTGGCTCAGGTAAATCATTTTCGTACAAAGCAAATGAACGATTTCCATTATGTAGTTCTTTCAAAGGTTTTTTAGCTGCTGCTGTATTAAAAGGCTCTCAAGATAATCAACTAAATCTTAATCAGATCGTGAATTATAATACAAGAAGTTTAGAGTTCCATTCACCCATCACAACTAAATATAAAGATAATGGAATGTCATTAGGTGATATGGCTGCTGCCGCTTTACAATATAGCGACAATGGTGCTACTAATATTATTCTTGAACGATATATCGGTGGTCCTGAGGGTATGACTAAATTCATGCGGTCGATTGGAGATAAAGATTTTAGACTCGATCGTTGGGAGTTAGATCTAAACACAGCAATTCCTGGCGATGAACGTGACACATCTACACCTGCAGCAGTAGCTAAGAGCCTGAAAACCCTTGCTCTGGGTAACATACTTAATGAGCGTGAAAAGGAAACCTATCAGACATGGTTAAAGGGTAACACAACCGGTGCAGCGCGTATTCGTGCTAGCGTACCAAGCGATTGGGTAGTTGGCGATAAAACTGGTAGTTGCGGAGCATACGGTACGGCAAATGATTATGCGGTAGTCTGGCCAAAGAACCGAGCTCCTCTTATAATTTCTGTATACACTACAAAAAACGAAAAAGAAGCCAAGCATGAGGATAAAGTAATCGCAGAAGCTTCAAGAATCGCAATTGATAACCTTAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36926","NCBI_taxonomy_name":"Enterobacter asburiae","NCBI_taxonomy_id":"61645"}}}},"ARO_accession":"3008208","ARO_id":"47000","ARO_name":"IMI-10","CARD_short_name":"IMI-10","ARO_description":"Carbapenem-hydrolyzing class A beta-lactamase IMI-10.","ARO_category":{"36027":{"category_aro_accession":"3000018","category_aro_cvterm_id":"36027","category_aro_name":"IMI beta-lactamase","category_aro_description":"IMI beta-lactamases are a group of TEM-1-like beta-lactamase that are known to hydrolyze imipenem. IMI beta-lactamases are inhibited by clavulanic acid and tazobactam.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7627":{"model_id":"7627","model_name":"IMI-22","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10454":{"protein_sequence":{"accession":"UAN29788.1","sequence":"MLFNSKPSRISILLSSFLISISFSSQVNASGIDEIKKLETDFNGRIGVYALDTGSGKSFSYKANERFPLCSSFKGFLAAAVLKGSQDNQLNINQVVNYNTRSLEFHSPITTKYKENGMSLGDMAAAALQYSDNAATNIILERYIGGPEGMTKFMRSIGDKDFRLDRWELDLNTAIPGDERDTSTPAAVAKSLKNLALGNILNDHEKEIYQTWLKGNTTGAARIRASVPNDWVVGDKTGSCGAYGTANDYAVVWPKNRAPLIISVYTTKNEKEAKHNDKLIAETSRIAIKNLK"},"dna_sequence":{"accession":"CP074169.1","fmin":"25551","fmax":"26430","strand":"-","sequence":"ATGTTATTTAATTCGAAGCCAAGTAGAATATCCATCCTGTTAAGCTCTTTTTTGATTTCAATATCATTTTCCTCACAGGTCAATGCAAGTGGCATTGATGAGATTAAGAAACTTGAAACAGATTTCAATGGGAGGATTGGTGTGTATGCCTTAGATACCGGCTCTGGTAAATCATTTTCATACAAAGCGAATGAACGATTTCCTCTGTGTAGTTCTTTCAAAGGTTTTTTGGCTGCTGCTGTATTAAAGGGCTCTCAAGATAACCAACTTAATATTAATCAGGTTGTAAATTACAATACAAGAAGTTTAGAATTCCATTCCCCCATTACAACTAAATATAAAGAAAATGGAATGTCTTTAGGTGATATGGCTGCTGCTGCATTACAATATAGCGACAACGCTGCTACTAATATTATCCTTGAACGTTATATTGGTGGCCCTGAGGGCATGACTAAATTCATGCGGTCGATTGGAGATAAAGATTTTAGACTTGATCGTTGGGAGTTAGATCTTAACACAGCTATTCCTGGCGATGAACGTGACACATCCACACCCGCAGCAGTTGCTAAAAGTTTAAAAAACCTTGCTCTAGGTAATATACTTAACGACCATGAAAAGGAAATCTATCAGACATGGTTAAAGGGTAACACAACTGGCGCAGCGCGTATTCGTGCTAGCGTGCCAAACGATTGGGTAGTTGGCGATAAAACCGGTAGTTGCGGAGCATACGGTACGGCAAATGATTATGCTGTAGTCTGGCCAAAGAACAGGGCTCCTCTTATCATTTCTGTGTACACTACAAAAAATGAAAAAGAAGCCAAGCATAACGATAAGTTAATTGCAGAAACTTCAAGAATTGCAATTAAAAACCTTAAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"47930","NCBI_taxonomy_name":"Serratia ureilytica","NCBI_taxonomy_id":"300181"}}}},"ARO_accession":"3008209","ARO_id":"47001","ARO_name":"IMI-22","CARD_short_name":"IMI-22","ARO_description":"Carbapenem-hydrolyzing class A beta-lactamase IMI-22.","ARO_category":{"36027":{"category_aro_accession":"3000018","category_aro_cvterm_id":"36027","category_aro_name":"IMI beta-lactamase","category_aro_description":"IMI beta-lactamases are a group of TEM-1-like beta-lactamase that are known to hydrolyze imipenem. IMI beta-lactamases are inhibited by clavulanic acid and tazobactam.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7628":{"model_id":"7628","model_name":"IMI-23","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10455":{"protein_sequence":{"accession":"UAN29726.1","sequence":"MLLNTKPSIIAILLSYFLIPISFFSQANASGIDEIKKLETDFNGRIGVYALDTGSGKSFSYKANERFPLCSAFKGFLAAAVLKGSQDNQLNINQIVNYNARSLEFHSPITTKYKENGMSLGDMAAAALQYSDNGATNIILERYIGGPEGMTKFMRSIGDKDFRLDRWELDLNTAIPGDERDTSTPAAVAKSLKTLALGNILNSHEREIYQTWLKGNTTGAARIRASVPSDWVVGDKTGSCGAYGTANDYAVVWPKNRAPLIISVYTAKNEKEAKHNDKVIAETSRIAIKNLK"},"dna_sequence":{"accession":"CP074169.1","fmin":"56762","fmax":"57641","strand":"-","sequence":"ATGTTATTGAATACGAAGCCAAGTATAATAGCCATCCTGTTAAGCTATTTTTTAATTCCAATATCATTTTTCTCACAGGCCAATGCAAGTGGCATTGATGAGATTAAGAAACTTGAAACAGATTTCAATGGGAGGATTGGTGTATATGCCTTAGATACCGGCTCTGGTAAATCATTTTCATACAAAGCGAATGAACGATTTCCTCTGTGTAGTGCTTTCAAAGGTTTTTTAGCTGCTGCTGTATTAAAGGGCTCTCAAGATAACCAACTTAATATTAATCAAATTGTAAATTACAATGCAAGAAGTTTAGAATTCCATTCCCCCATTACAACTAAATATAAAGAAAATGGAATGTCTTTAGGTGATATGGCTGCTGCTGCATTACAATATAGCGACAACGGTGCTACTAATATTATCCTTGAACGTTATATTGGTGGTCCTGAGGGTATGACTAAATTCATGCGGTCGATTGGAGATAAAGATTTTAGACTTGATCGTTGGGAGTTAGATCTTAACACAGCTATTCCTGGCGATGAACGCGACACATCCACACCCGCAGCAGTTGCTAAAAGTTTAAAAACCCTTGCTCTAGGTAATATACTTAACAGCCATGAAAGGGAAATCTATCAGACATGGTTAAAGGGTAACACAACTGGCGCAGCGCGTATTCGTGCTAGCGTGCCAAGCGATTGGGTAGTTGGCGATAAAACCGGTAGTTGCGGAGCATACGGTACGGCAAATGATTATGCTGTAGTCTGGCCAAAGAACAGGGCTCCTCTTATCATTTCCGTGTACACTGCAAAAAATGAAAAAGAAGCCAAGCATAACGATAAGGTAATTGCAGAAACTTCAAGAATTGCAATTAAAAACCTTAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"47930","NCBI_taxonomy_name":"Serratia ureilytica","NCBI_taxonomy_id":"300181"}}}},"ARO_accession":"3008210","ARO_id":"47002","ARO_name":"IMI-23","CARD_short_name":"IMI-23","ARO_description":"Carbapenem-hydrolyzing class A beta-lactamase IMI-23.","ARO_category":{"36027":{"category_aro_accession":"3000018","category_aro_cvterm_id":"36027","category_aro_name":"IMI beta-lactamase","category_aro_description":"IMI beta-lactamases are a group of TEM-1-like beta-lactamase that are known to hydrolyze imipenem. IMI beta-lactamases are inhibited by clavulanic acid and tazobactam.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7629":{"model_id":"7629","model_name":"IMI-24","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10456":{"protein_sequence":{"accession":"ULG04426.1","sequence":"MSINEKKSKSAVFFSFFLIPISFYSQADTNAMDEIKKLETGFGGRVGVYALDTGSGKSFSYRANERFPLCSSFKGFLAAAVLKGSQDNQLNINEIVNYNKKNLEPHSPITQKYKENGMSLGDMAAAALQYSDNGAANIILERYIGGPEGMTNFMRSIGDEDFRLDRWELALNTAIPGDERDTSTPAAVGKSLKNLALGNILNDHEKETYQTWLKGNTTGAARIRASVPSDWVVGDKTGTCGAYGTANDYAVVWPKNRAPLIISVYTTKSEKEAKHDEKVIEEASRIAITHLK"},"dna_sequence":{"accession":"OM525830.1","fmin":"0","fmax":"879","strand":"+","sequence":"ATGTCAATTAATGAAAAAAAAAGTAAGTCAGCTGTCTTTTTTAGCTTTTTTTTAATCCCTATATCATTTTATTCACAGGCTGATACAAATGCCATGGATGAGATTAAGAAACTGGAAACAGGTTTCGGTGGCAGGGTTGGCGTCTACGCTTTAGACACTGGCTCTGGTAAATCATTTTCATACAGAGCGAATGAACGATTTCCTCTTTGTAGTTCTTTTAAAGGTTTTTTAGCCGCTGCTGTATTAAAGGGCTCGCAGGATAATCAACTGAATATTAATGAGATTGTAAATTATAATAAAAAAAATTTAGAACCCCACTCCCCTATTACGCAAAAATATAAAGAAAACGGAATGTCTCTAGGTGATATGGCTGCTGCCGCTTTACAATATAGCGACAATGGTGCTGCTAATATTATTCTTGAGCGTTATATCGGTGGTCCTGAAGGTATGACTAATTTCATGCGGTCTATTGGAGATGAAGACTTTAGACTCGATCGTTGGGAGTTAGCTCTAAATACAGCTATTCCTGGCGATGAACGTGACACTTCAACACCCGCAGCTGTAGGTAAAAGTTTAAAAAACCTTGCTCTGGGCAATATACTTAACGATCATGAAAAGGAAACATATCAGACATGGTTAAAGGGTAACACAACCGGCGCAGCGCGTATTCGTGCTAGCGTACCAAGCGACTGGGTCGTTGGCGATAAAACCGGTACTTGTGGAGCATACGGTACTGCAAATGATTATGCGGTTGTCTGGCCAAAAAACAGGGCTCCTCTTATCATTTCTGTGTACACTACAAAAAGTGAAAAAGAAGCAAAGCATGACGAGAAGGTAATCGAAGAAGCTTCAAGAATTGCAATTACACACCTTAAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36926","NCBI_taxonomy_name":"Enterobacter asburiae","NCBI_taxonomy_id":"61645"}}}},"ARO_accession":"3008211","ARO_id":"47003","ARO_name":"IMI-24","CARD_short_name":"IMI-24","ARO_description":"Carbapenem-hydrolyzing class A beta-lactamase IMI-24.","ARO_category":{"36027":{"category_aro_accession":"3000018","category_aro_cvterm_id":"36027","category_aro_name":"IMI beta-lactamase","category_aro_description":"IMI beta-lactamases are a group of TEM-1-like beta-lactamase that are known to hydrolyze imipenem. IMI beta-lactamases are inhibited by clavulanic acid and tazobactam.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7630":{"model_id":"7630","model_name":"IMI-25","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10457":{"protein_sequence":{"accession":"WVW91583.1","sequence":"MSINVKKSKSAVFFSFFLIPISFYSQADTNAMDEIKKLETGFGGRVGVYALDTGSGKSFSYRANERFPLCSSFKGFLAAAVLKGSQDNQLNINEIVNYNKRSLEPHSPITQKYKENGMSLGDMAAAALQYSDNGAANIILERYIGGPEGMTNFMRSIGDEDFRLDRWELALNTAIPGDERDTSTPAAVGKSLKNLALGNILNDHEKETYQTWLKGNTTGAARIRASVPSDWVVGDKTGTCGAYGTANDYAVVWPKNRAPLIISVYTTKSEKEAKHDEKVIEEASRIAITHLK"},"dna_sequence":{"accession":"PP296989.1","fmin":"0","fmax":"879","strand":"+","sequence":"ATGTCAATTAATGTAAAAAAAAGTAAATCAGCTGTCTTTTTTAGCTTTTTTTTAATCCCTATATCATTCTATTCACAGGCTGATACAAATGCCATGGATGAGATTAAGAAACTGGAAACAGGTTTCGGTGGCAGGGTTGGCGTCTACGCTTTAGACACTGGCTCTGGTAAATCATTTTCATACAGAGCGAATGAACGATTTCCTCTTTGTAGTTCTTTTAAAGGTTTTTTAGCCGCTGCTGTATTAAAGGGCTCGCAGGATAATCAGCTGAATATTAATGAGATTGTAAATTATAATAAAAGAAGTTTAGAACCCCACTCCCCTATTACGCAAAAATATAAAGAAAACGGAATGTCTCTAGGTGATATGGCTGCTGCCGCTTTACAATATAGCGACAATGGTGCTGCTAATATTATTCTTGAGCGTTATATCGGTGGTCCTGAAGGTATGACTAATTTCATGCGGTCTATTGGAGATGAAGACTTTAGACTCGATCGTTGGGAGTTAGCTCTAAATACAGCTATTCCTGGCGATGAACGTGACACTTCAACACCCGCAGCTGTAGGTAAAAGTTTAAAAAACCTTGCTCTGGGCAATATACTTAACGATCATGAAAAGGAAACATATCAGACATGGTTAAAGGGTAACACAACCGGCGCAGCGCGTATTCGTGCTAGCGTACCAAGCGACTGGGTCGTTGGCGATAAAACCGGTACTTGTGGAGCATACGGTACTGCAAATGATTATGCGGTTGTCTGGCCAAAAAACAGGGCTCCTCTTATCATTTCTGTGTACACTACAAAAAGTGAAAAAGAAGCAAAGCATGACGAGAAGGTAATCGAAGAAGCTTCAAGAATTGCAATTACACACCTTAAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3008212","ARO_id":"47004","ARO_name":"IMI-25","CARD_short_name":"IMI-25","ARO_description":"Carbapenem-hydrolyzing class A beta-lactamase IMI-25.","ARO_category":{"36027":{"category_aro_accession":"3000018","category_aro_cvterm_id":"36027","category_aro_name":"IMI beta-lactamase","category_aro_description":"IMI beta-lactamases are a group of TEM-1-like beta-lactamase that are known to hydrolyze imipenem. IMI beta-lactamases are inhibited by clavulanic acid and tazobactam.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7631":{"model_id":"7631","model_name":"IMI-26","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10458":{"protein_sequence":{"accession":"WVW91584.1","sequence":"MSLNLKPSRIAILFSSFLVSISFFSQANTKGIDEIKNLETDFNGRIGVYALDTGSGKSFSYKANERFPLCSSFKGFLAAAVLKGSQDNQLNLNQIVNYNTRSLEFYSPITTKYKDNGMSLGDMAAAALQYSDNGATNIILERYIGGPEGMTKFMRSIGDKDFRLDRWELDLNTAIPGDERDTSTPAAVAKSLKTLALGNILNEREKETYQTWLKGNTTGAARIRASVPSDWVVGDKTGSCGAYGTANDYAVVWPKNRAPLIISVYTTKNEKEAKHEDKVIAEASRIAIDNLK"},"dna_sequence":{"accession":"PP296990.1","fmin":"0","fmax":"879","strand":"+","sequence":"ATGTCACTTAATTTAAAACCAAGTAGAATAGCCATCTTGTTTAGCTCTTTTTTAGTTTCAATATCATTTTTCTCACAGGCCAATACAAAGGGAATCGATGAGATTAAAAACCTTGAAACAGATTTCAATGGTAGAATTGGTGTCTACGCTTTAGACACTGGCTCAGGTAAATCATTTTCGTACAAAGCAAATGAACGATTTCCATTATGTAGTTCTTTCAAAGGTTTTTTAGCTGCTGCTGTATTAAAAGGCTCTCAAGATAATCAACTAAATCTTAATCAGATCGTGAATTATAATACAAGAAGTTTAGAGTTCTATTCACCCATCACAACTAAATATAAAGATAATGGAATGTCATTAGGTGATATGGCTGCTGCCGCTTTACAATATAGCGACAATGGTGCTACTAATATTATTCTTGAACGATATATCGGTGGTCCTGAGGGTATGACTAAATTCATGCGGTCGATTGGAGATAAAGATTTTAGACTCGATCGTTGGGAGTTAGATCTAAACACAGCAATTCCTGGCGATGAACGTGACACATCTACACCTGCAGCAGTAGCTAAGAGCCTGAAAACCCTTGCTCTGGGTAACATACTTAATGAGCGTGAAAAGGAAACCTATCAGACATGGTTAAAGGGTAACACAACCGGTGCAGCGCGTATTCGTGCTAGCGTACCAAGCGATTGGGTAGTTGGCGATAAAACTGGTAGTTGCGGAGCATACGGTACGGCAAATGATTATGCGGTAGTCTGGCCAAAGAACCGAGCTCCTCTTATAATTTCTGTATACACTACAAAAAACGAAAAAGAAGCCAAGCATGAGGATAAAGTAATCGCAGAAGCTTCAAGAATCGCAATTGATAACCTTAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3008213","ARO_id":"47005","ARO_name":"IMI-26","CARD_short_name":"IMI-26","ARO_description":"Carbapenem-hydrolyzing class A beta-lactamase IMI-26.","ARO_category":{"36027":{"category_aro_accession":"3000018","category_aro_cvterm_id":"36027","category_aro_name":"IMI beta-lactamase","category_aro_description":"IMI beta-lactamases are a group of TEM-1-like beta-lactamase that are known to hydrolyze imipenem. IMI beta-lactamases are inhibited by clavulanic acid and tazobactam.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7632":{"model_id":"7632","model_name":"IMI-27","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10459":{"protein_sequence":{"accession":"WVW91582.1","sequence":"MSFNVKSSGIAIFFSSCLISTAFFSQANTNGTDEINKLEKDFNGRIGVYALDTGSGKSFSYRANERFPLCSSFKGFLAAAVLKSFQDNQLNIYQIVNYNTRNLEFHSPITTRYKENGMTLGDMAAAALQYSDNGATNIILERYIGGPEGMTKFMRSIGDDYFRLDRWELDLNTAIPGDERDTSTPAAVAKSLKNLALGNILNEDEKQTYQTWLKGNTTGAARIRASVPTDWEVGDKTGSCGAYGTANDYAIVWPKNRAPLIISVYTTKSEKEAKHDDKVIAEASRIAIRNLK"},"dna_sequence":{"accession":"PP296988.1","fmin":"0","fmax":"879","strand":"+","sequence":"ATGTCGTTTAATGTAAAATCGAGTGGTATAGCAATCTTCTTTAGCTCTTGTTTAATTTCAACAGCATTTTTTTCACAGGCCAATACAAATGGAACCGATGAGATTAATAAACTTGAAAAAGACTTCAATGGAAGGATTGGTGTCTACGCTTTAGATACAGGCTCTGGTAAATCATTTTCATACAGAGCGAATGAGCGATTTCCTCTGTGTAGTTCTTTTAAAGGTTTCTTAGCTGCCGCTGTACTAAAGAGCTTTCAAGATAATCAACTTAATATTTATCAGATTGTAAATTACAATACAAGGAATTTAGAATTCCATTCACCCATTACAACAAGATATAAAGAAAATGGAATGACTCTAGGCGATATGGCTGCCGCCGCGTTACAATATAGCGACAATGGTGCTACTAATATTATTCTTGAACGTTATATCGGTGGTCCTGAAGGTATGACTAAGTTCATGCGGTCGATTGGAGATGATTATTTTAGACTAGACCGTTGGGAATTAGATCTAAACACAGCTATTCCAGGCGATGAACGTGACACATCCACTCCGGCAGCAGTAGCTAAAAGTTTAAAAAACCTTGCTTTGGGCAATATACTTAATGAAGATGAAAAGCAAACATATCAGACATGGTTAAAGGGTAATACAACCGGCGCAGCGCGTATTCGTGCTAGCGTACCAACAGATTGGGAAGTTGGCGATAAAACCGGTAGTTGTGGAGCATACGGTACAGCAAATGATTATGCTATTGTCTGGCCAAAGAACAGGGCTCCTCTTATTATTTCTGTATACACTACTAAAAGTGAAAAAGAAGCCAAGCATGATGATAAGGTAATCGCAGAAGCTTCAAGGATTGCAATTAGAAACCTTAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3008214","ARO_id":"47006","ARO_name":"IMI-27","CARD_short_name":"IMI-27","ARO_description":"Carbapenem-hydrolyzing class A beta-lactamase IMI-27.","ARO_category":{"36027":{"category_aro_accession":"3000018","category_aro_cvterm_id":"36027","category_aro_name":"IMI beta-lactamase","category_aro_description":"IMI beta-lactamases are a group of TEM-1-like beta-lactamase that are known to hydrolyze imipenem. IMI beta-lactamases are inhibited by clavulanic acid and tazobactam.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7633":{"model_id":"7633","model_name":"IMP-100","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10460":{"protein_sequence":{"accession":"WHO54936.1","sequence":"MKKLFVLCIFLFCSITAAGESLPDLKIEKLEEGVYIHTSFEEVNGWGVFNKHGLVVLVDTDAYLIDTPFTAKDTEKLVNWFVERGYKIKGSISSHFHSDSTGGIEWLNSQSIPTYASELTNELLKKNGKVQAKNSFSGVSYWLVKNKIEIFYPGPGHTQDNVVVWLPENKILFGGCFVKPDGLGNLDDANLEAWPKSAKILMSKYGKAKLVVSSHSEIGNASLLKLTWEQAVKGLKESKKPSLPSN"},"dna_sequence":{"accession":"OR004774.1","fmin":"0","fmax":"741","strand":"+","sequence":"ATGAAAAAATTATTTGTTTTATGCATATTTTTGTTTTGTAGCATTACTGCCGCAGGAGAGTCTTTGCCTGATTTAAAAATTGAAAAACTTGAAGAAGGCGTTTATATTCATACATCGTTTGAAGAAGTTAACGGTTGGGGTGTTTTTAATAAACACGGTTTGGTGGTTCTTGTAGATACTGACGCCTATCTGATTGACACTCCATTTACTGCTAAAGATACTGAAAAGTTAGTCAATTGGTTTGTGGAGCGCGGCTATAAAATCAAAGGCAGTATTTCCTCACATTTCCATAGCGACAGCACGGGCGGAATAGAGTGGCTTAATTCTCAATCTATTCCCACGTATGCATCTGAATTAACAAATGAACTTCTTAAAAAGAACGGTAAGGTGCAAGCTAAAAACTCATTTAGCGGAGTTAGTTATTGGCTAGTTAAAAATAAAATTGAAATTTTTTATCCCGGTCCGGGGCACACTCAAGATAACGTAGTGGTTTGGCTACCTGAAAACAAAATTTTATTCGGTGGTTGTTTTGTTAAACCGGACGGTCTTGGTAATTTGGATGACGCAAATTTAGAAGCTTGGCCAAAGTCCGCCAAAATCTTAATGTCTAAATATGGTAAAGCAAAGTTGGTTGTTTCAAGTCATAGTGAAATTGGGAACGCATCACTCTTGAAACTTACTTGGGAGCAGGCTGTTAAAGGGCTAAAAGAAAGTAAAAAACCATCACTGCCAAGTAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008215","ARO_id":"47007","ARO_name":"IMP-100","CARD_short_name":"IMP-100","ARO_description":"Subclass B1 metallo-beta-lactamase IMP-100.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7634":{"model_id":"7634","model_name":"IMP-101","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10461":{"protein_sequence":{"accession":"WIF03690.1","sequence":"MSKLFVFFMFLFCSITAAAESLPDLKIEKLDEGVYVHTSFEEVNGWGVVPKHGLVVLVNTEAYLIDTPFTAKDTEKLVTWFVERGYKIKGSISSHFHSDSTGGIEWLNSQSIPTYASELTNELLKKDGKVQAKNSFSGASYWLVKKKIEVFYPGPGHTPDNVVVWLPENRVLFGGCFVKPYGLGNLGDANLEAWPKSAKLLMSKYGKAKLVVPSHSEVGDASLLKRTLEQAVKGLNESKKPSKPSN"},"dna_sequence":{"accession":"OR063824.1","fmin":"0","fmax":"741","strand":"+","sequence":"ATGAGCAAGTTATTTGTATTCTTTATGTTTTTGTTTTGTAGCATTACTGCCGCAGCAGAGTCTTTGCCAGATTTAAAAATTGAGAAGCTTGACGAAGGCGTTTATGTTCATACTTCGTTTGAAGAAGTTAACGGTTGGGGTGTTGTTCCTAAACACGGCTTGGTGGTTCTTGTAAATACTGAGGCCTATCTGATTGACACTCCATTTACGGCTAAAGATACTGAAAAGTTAGTCACTTGGTTTGTGGAACGCGGCTATAAAATAAAAGGCAGTATTTCCTCTCATTTTCATAGCGACAGCACGGGCGGAATAGAGTGGCTTAATTCTCAATCTATCCCCACGTATGCATCTGAATTAACAAATGAACTTCTTAAAAAAGACGGTAAAGTACAAGCTAAAAATTCATTTAGCGGAGCTAGCTATTGGCTAGTTAAGAAAAAGATTGAAGTTTTTTATCCTGGTCCAGGGCACACTCCAGATAACGTAGTGGTTTGGCTACCTGAAAATAGAGTTTTGTTCGGTGGTTGTTTTGTTAAACCGTACGGTCTAGGTAATTTGGGTGACGCAAATTTAGAAGCTTGGCCAAAGTCCGCCAAATTATTAATGTCCAAATATGGTAAGGCAAAACTGGTAGTTCCAAGTCACAGTGAAGTTGGAGACGCATCACTCTTGAAACGTACATTAGAACAGGCGGTTAAAGGGTTAAACGAAAGTAAAAAACCATCAAAACCAAGTAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"45942","NCBI_taxonomy_name":"Pseudomonas alcaligenes","NCBI_taxonomy_id":"43263"}}}},"ARO_accession":"3008216","ARO_id":"47008","ARO_name":"IMP-101","CARD_short_name":"IMP-101","ARO_description":"Subclass B1 metallo-beta-lactamase IMP-101.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7635":{"model_id":"7635","model_name":"IMP-102","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10462":{"protein_sequence":{"accession":"WLF01979.1","sequence":"MSKLFIFFMFLFCSITAAAESLPDLKIERLDEGVYVHTSFEEVNGWGVVPKHGLVVLVNTDAYLIDTPFTAKDTEKLVTWFVGRGYKIKGSISSHFHSDSTGGIEWLNSQSIPTYASELTNELLKKDGKVQAKNSFGGVSYWLVKNKIEVFYPGPGHTPDNVVVWLPENRVLFGGCFVKPYGLGNLGDANLEAWPKSAKLLMSKYGKAKLVVPSHSEVGDASLLKRTLEHAVKGLNESKKPSKPSN"},"dna_sequence":{"accession":"OR367336.1","fmin":"0","fmax":"741","strand":"+","sequence":"ATGAGCAAGTTATTTATATTCTTTATGTTTTTGTTTTGTAGCATTACTGCCGCAGCAGAGTCTTTGCCAGATTTAAAAATTGAGAGGCTTGATGAAGGCGTTTATGTTCATACTTCGTTTGAAGAAGTTAACGGTTGGGGTGTTGTTCCTAAACACGGCTTGGTGGTTCTTGTAAATACTGATGCCTATCTGATTGACACTCCATTTACGGCTAAAGATACTGAAAAGTTAGTCACTTGGTTTGTGGGACGCGGCTATAAAATAAAAGGCAGTATTTCCTCTCATTTTCATAGCGACAGCACGGGCGGAATAGAGTGGCTTAATTCTCAATCTATCCCCACGTATGCATCTGAATTAACAAATGAACTTCTTAAAAAAGACGGTAAGGTACAAGCTAAAAATTCATTTGGCGGAGTTAGCTATTGGCTAGTTAAGAATAAGATTGAAGTTTTTTATCCTGGTCCAGGGCACACTCCAGATAACGTAGTGGTTTGGCTACCTGAAAATAGAGTTTTGTTCGGTGGTTGTTTTGTTAAACCGTACGGTCTTGGTAATTTGGGTGACGCAAATTTAGAAGCTTGGCCAAAGTCCGCCAAATTATTAATGTCCAAATATGGTAAGGCAAAACTGGTTGTTCCAAGTCACAGTGAAGTTGGAGACGCATCACTCTTGAAGCGAACATTAGAACATGCGGTTAAAGGGTTAAATGAAAGTAAAAAACCATCAAAACCAAGTAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"47922","NCBI_taxonomy_name":"Pseudomonas asiatica","NCBI_taxonomy_id":"2219225"}}}},"ARO_accession":"3008217","ARO_id":"47009","ARO_name":"IMP-102","CARD_short_name":"IMP-102","ARO_description":"Subclass B1 metallo-beta-lactamase IMP-102.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7636":{"model_id":"7636","model_name":"IMP-104","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10463":{"protein_sequence":{"accession":"XGD01539.1","sequence":"MSKLSVFFIFLFCSIATAAESLPDLKIEKLDEGVYVHTSFEEVNGWGVVPKHGLVVLVNAEAYLIDTPFTAKDTEKLVTWFVERGYKIKGSISSHFHSDSTGGIEWLNSRSIPTYASELTNELLKKDGKVQATSSFSGVNYWLVKNKIEVFYPGPGHTPDNVVVWLPERKILFGGCFIKPYGLGNLGDANIEAWPKSAKLLKSKYGKAKLVVPSHSEVGDASLLKLTLEQAVKGLNESKKPSKPSN"},"dna_sequence":{"accession":"PQ218333.1","fmin":"0","fmax":"741","strand":"+","sequence":"ATGAGCAAGTTATCTGTATTCTTTATATTTTTGTTTTGCAGCATTGCTACCGCAGCAGAGTCTTTGCCAGATTTAAAAATTGAAAAGCTTGATGAAGGCGTTTATGTTCATACTTCGTTTGAAGAAGTTAACGGGTGGGGCGTTGTTCCTAAACATGGTTTGGTGGTTCTTGTAAATGCTGAGGCTTATCTAATTGACACTCCATTTACGGCTAAAGATACTGAAAAGTTAGTCACTTGGTTTGTGGAGCGTGGCTATAAAATAAAAGGCAGTATTTCCTCTCATTTTCATAGCGACAGCACGGGCGGAATAGAGTGGCTTAATTCTCGATCTATCCCCACGTATGCATCTGAATTAACAAATGAACTGCTTAAAAAAGACGGTAAGGTTCAAGCCACAAGTTCATTTAGCGGAGTTAACTATTGGCTAGTTAAAAATAAAATTGAAGTTTTTTATCCAGGCCCGGGACACACTCCAGATAACGTAGTGGTTTGGCTGCCTGAAAGGAAAATATTATTCGGTGGTTGTTTTATTAAACCGTACGGTTTAGGCAATTTGGGTGACGCAAATATAGAAGCTTGGCCAAAGTCCGCCAAATTATTAAAGTCCAAATATGGTAAGGCAAAACTGGTTGTTCCAAGTCACAGTGAAGTTGGAGACGCATCACTCTTGAAACTTACATTAGAGCAGGCGGTTAAAGGATTAAACGAAAGTAAAAAACCATCAAAACCAAGCAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"46213","NCBI_taxonomy_name":"Pseudomonas alloputida","NCBI_taxonomy_id":"1940621"}}}},"ARO_accession":"3008218","ARO_id":"47010","ARO_name":"IMP-104","CARD_short_name":"IMP-104","ARO_description":"Subclass B1 metallo-beta-lactamase IMP-104.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7637":{"model_id":"7637","model_name":"IMP-105","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10464":{"protein_sequence":{"accession":"XHO32891.1","sequence":"MKKLFVLCVFFFCNIAVAEESLPDLKIEKLEEGVYVHTSFEEVKGWTKHGLVVLVKNDAYLIDTPITAKDTEKLVNWFVERGYKIKGSISTHFHGDSTAGIEWLNSQSIPTYASELTNELLKKDNKVQAKHSFNGVSYSLIKNKIEVFYPGPGHTQDNVVVWLPEKKILFGGCFVKPDGLGYLGDANLEAWPKSAKILMSKYGKAKLVVSSHSDIGDVSLLKRTWEQAVKGLNESKKSSQPSD"},"dna_sequence":{"accession":"PQ394548.1","fmin":"0","fmax":"732","strand":"+","sequence":"ATGAAAAAATTATTTGTTTTATGTGTATTCTTCTTCTGCAACATTGCAGTTGCAGAAGAATCTTTGCCTGATTTAAAAATTGAGAAGCTTGAAGAAGGCGTTTATGTTCATACTTCGTTTGAAGAAGTTAAAGGTTGGACTAAACACGGTTTGGTGGTTCTTGTGAAAAATGACGCCTATCTGATTGATACTCCAATTACTGCTAAAGATACTGAAAAATTAGTCAATTGGTTTGTTGAGCGGGGCTATAAAATCAAAGGCAGTATTTCCACACATTTCCATGGTGACAGTACGGCTGGAATAGAGTGGCTTAATTCTCAATCTATCCCCACATATGCTTCTGAATTAACAAATGAACTTCTTAAAAAAGACAATAAGGTACAAGCTAAACACTCTTTTAATGGGGTTAGTTATTCACTAATTAAAAACAAAATTGAAGTTTTTTATCCAGGCCCAGGGCACACTCAAGATAACGTAGTGGTTTGGTTACCTGAAAAGAAAATTTTATTCGGTGGTTGCTTTGTTAAACCGGACGGTCTTGGCTATTTGGGGGACGCAAATTTAGAAGCTTGGCCAAAGTCCGCTAAAATATTAATGTCTAAATATGGTAAAGCAAAACTAGTTGTGTCGAGTCATAGTGATATTGGAGATGTATCACTCTTGAAACGTACATGGGAGCAGGCTGTTAAAGGGCTGAATGAAAGTAAAAAATCATCACAGCCAAGCGACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008219","ARO_id":"47011","ARO_name":"IMP-105","CARD_short_name":"IMP-105","ARO_description":"Subclass B1 metallo-beta-lactamase IMP-105.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7638":{"model_id":"7638","model_name":"IMP-86","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10465":{"protein_sequence":{"accession":"QIZ64888.1","sequence":"MKKLFVLCVFFFCNIAVAEESLPDLKIEKLEEGVYVHTSFEEAKGWGVVTKHGLVVLVKNDAYLIDTPVTAKDTEKLVNWFVERGYKIKGSISTHFHGDSTAGIEWLNSQSIPTYASELTNELLKKDNKVQAKHSFNGVSYSLIKNKIEVFYPGPGHTQDNVVVWLPEKKILFGGCFVKPDGLGYLGDANLEAWPKSAKILMSKYGKAKLVVSSHSDIGDVSLLKRTWEQAVKGLNESKKSSQPSD"},"dna_sequence":{"accession":"MT241520.1","fmin":"0","fmax":"741","strand":"+","sequence":"ATGAAAAAATTATTTGTTTTATGTGTATTCTTCTTCTGCAACATTGCAGTTGCAGAAGAATCTTTGCCTGATTTAAAAATTGAGAAGCTTGAAGAAGGCGTTTATGTTCATACTTCGTTTGAAGAAGCTAAAGGTTGGGGTGTGGTCACTAAACACGGTTTGGTGGTTCTTGTGAAAAATGACGCCTATCTGATTGATACTCCAGTTACTGCTAAAGATACTGAAAAATTAGTCAATTGGTTTGTTGAGCGGGGCTATAAAATCAAAGGCAGTATTTCCACACATTTCCATGGTGACAGTACGGCTGGAATAGAGTGGCTTAATTCTCAATCTATCCCCACATATGCTTCTGAATTAACAAATGAACTTCTTAAAAAAGACAATAAGGTACAAGCTAAACACTCTTTTAATGGGGTTAGTTATTCACTAATTAAAAACAAAATTGAAGTTTTTTATCCAGGCCCAGGGCACACTCAAGATAACGTAGTGGTTTGGTTACCTGAAAAGAAAATTTTATTCGGTGGTTGCTTTGTTAAACCGGACGGTCTTGGCTATTTGGGGGACGCAAATTTAGAAGCTTGGCCAAAGTCCGCTAAAATATTAATGTCTAAATATGGTAAAGCAAAACTAGTTGTGTCGAGTCATAGTGATATTGGAGATGTATCACTCTTGAAACGTACATGGGAGCAGGCTGTTAAAGGGCTGAATGAAAGTAAAAAATCATCACAGCCAAGCGACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008220","ARO_id":"47012","ARO_name":"IMP-86","CARD_short_name":"IMP-86","ARO_description":"Subclass B1 metallo-beta-lactamase IMP-86.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7639":{"model_id":"7639","model_name":"IMP-87","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10466":{"protein_sequence":{"accession":"QIZ64889.1","sequence":"MKKLFVLCVFFFCNIAVAEESLPDLKIEKLEEGVYVHTSFEEAKGWGVVTKHGLVVLVKNDAYLIDTPITAKDTEKLVNWFVERGYKIKGSISTHFHGDSTAGIEWLNSQSIPTYASELTNELLKKDNKVQAKHSFNGVSYSLIKNKIEVFYPGPGHTQDNVVVWLPEKKILFGGCFVKPDGLGYLGDANLEAWPKSAKILMSKYGKAKLVVSSHSDIGDVSLLKRTWEQAVKGLNESKKSSQPSD"},"dna_sequence":{"accession":"MT241521.1","fmin":"0","fmax":"741","strand":"+","sequence":"ATGAAAAAATTATTTGTTTTATGTGTATTCTTCTTCTGCAACATTGCAGTTGCAGAAGAATCTTTGCCTGATTTAAAAATTGAGAAGCTTGAAGAAGGCGTTTATGTTCATACTTCGTTTGAAGAAGCTAAAGGTTGGGGTGTGGTCACTAAACACGGTTTGGTGGTTCTTGTGAAAAATGACGCCTATCTGATTGATACTCCAATTACTGCTAAAGATACTGAAAAATTAGTCAATTGGTTTGTTGAGCGGGGCTATAAAATCAAAGGCAGTATTTCCACACATTTCCATGGTGACAGTACGGCTGGAATAGAGTGGCTTAATTCTCAATCTATCCCCACATATGCTTCTGAATTAACAAATGAACTTCTTAAAAAAGACAATAAGGTACAAGCTAAACACTCTTTTAATGGGGTTAGTTATTCACTAATTAAAAACAAAATTGAAGTTTTTTATCCAGGCCCAGGGCACACTCAAGATAACGTAGTGGTTTGGTTACCTGAAAAGAAAATTTTATTCGGTGGTTGCTTTGTTAAACCGGACGGTCTTGGCTATTTGGGGGACGCAAATTTAGAAGCTTGGCCAAAGTCCGCTAAAATATTAATGTCTAAATATGGTAAAGCAAAACTAGTTGTGTCGAGTCATAGTGATATTGGAGATGTATCACTCTTGAAACGTACATGGGAGCAGGCTGTTAAAGGGCTGAATGAAAGTAAAAAATCATCACAGCCAAGCGACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008221","ARO_id":"47013","ARO_name":"IMP-87","CARD_short_name":"IMP-87","ARO_description":"Subclass B1 metallo-beta-lactamase IMP-87.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7640":{"model_id":"7640","model_name":"IMP-90","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10467":{"protein_sequence":{"accession":"QTG68658.1","sequence":"MKKLFVLCIFLFLSITASGEVLPDLKIEKLEEGVYLHTSFEEVSGWGVVTKHGLVVLVNNDAYLIDTPSTTKDTEKLVAWFVERGFTIKGSVSSHFHSDSTGGIEWLNSQSIPTYASELTNELLKKNGKVQATNSFSGVSYWLVKNKIEIFYPGPGHTQDNVVVWLPENKILFGGCFVKPDGLGNLDDANLKAWPKSAKILMSKYGKAKLVVSSHSEIGNASLLKLTWEQAVKGLKESKQPLLPSN"},"dna_sequence":{"accession":"MW811441.1","fmin":"0","fmax":"741","strand":"+","sequence":"ATGAAAAAATTATTTGTTTTATGCATTTTTTTGTTTTTAAGTATTACTGCCTCAGGTGAGGTTTTGCCTGATTTGAAAATTGAGAAGCTTGAAGAGGGTGTTTATCTTCATACATCTTTTGAAGAGGTTAGCGGTTGGGGTGTTGTTACTAAACACGGTTTGGTAGTTCTTGTAAATAATGACGCCTATCTAATTGACACTCCATCTACAACTAAAGATACTGAAAAATTAGTTGCTTGGTTTGTAGAGCGCGGCTTTACAATAAAGGGAAGTGTTTCCTCACATTTTCATAGCGACAGCACGGGTGGAATAGAGTGGCTTAATTCTCAATCTATTCCCACGTATGCATCTGAGTTAACAAATGAACTTCTGAAAAAGAACGGTAAGGTGCAAGCTACAAACTCATTTAGCGGGGTTAGTTATTGGCTAGTTAAAAATAAAATTGAAATTTTTTATCCCGGCCCGGGACACACTCAAGATAACGTAGTGGTTTGGCTACCTGAAAACAAAATTTTATTCGGTGGTTGTTTTGTTAAACCGGACGGTCTTGGTAATTTGGATGACGCAAATTTAAAAGCTTGGCCAAAGTCCGCAAAAATATTAATGTCTAAATATGGTAAAGCAAAGTTAGTTGTTTCAAGTCATAGTGAAATTGGGAACGCATCACTCTTGAAACTTACTTGGGAGCAGGCTGTTAAAGGGCTAAAAGAAAGTAAACAACCATTACTACCAAGTAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008222","ARO_id":"47014","ARO_name":"IMP-90","CARD_short_name":"IMP-90","ARO_description":"Subclass B1 metallo-beta-lactamase IMP-90.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7641":{"model_id":"7641","model_name":"IMP-97","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10468":{"protein_sequence":{"accession":"BDR24828.1","sequence":"MSKLSVFFIFLFCSIATAAESLPDLKIEKLDEGVYVHTSFEEVNGWGVVPKHGLVVLVNAEAYLIDTPFTAKDTEKLVTWFVERGYKIKGSISSHFHSDSTGGIEWLNSRSIPTYASELTNELLKKDGKVQAKNSFSGVNYWLVKNKIEVFYPGPGHTPDNVVVWLPERKILFGGCFIKPYGLGNLGDANIEAWPKSAKLLKSKYGKAKLVVPSHSEVGDASLLKLTLEQAVKGLNESKKPSKPSN"},"dna_sequence":{"accession":"LC727551.1","fmin":"0","fmax":"741","strand":"+","sequence":"ATGAGCAAGTTATCTGTATTCTTTATATTTTTGTTTTGCAGCATTGCTACCGCAGCAGAGTCTTTGCCAGATTTAAAAATTGAAAAGCTTGATGAAGGCGTTTATGTTCATACTTCGTTTGAAGAAGTTAACGGGTGGGGCGTTGTTCCTAAACATGGTTTGGTGGTTCTTGTAAATGCTGAGGCTTACCTAATTGACACTCCATTTACGGCTAAAGATACTGAAAAGTTAGTCACTTGGTTTGTGGAGCGTGGCTATAAAATAAAAGGCAGCATTTCCTCTCATTTTCATAGCGACAGCACGGGCGGAATAGAGTGGCTTAATTCTCGATCTATCCCCACGTATGCATCTGAATTAACAAATGAACTGCTTAAAAAAGACGGTAAGGTTCAAGCCAAAAATTCATTTAGCGGAGTTAACTATTGGCTAGTTAAAAATAAAATTGAAGTTTTTTATCCAGGCCCGGGACACACTCCAGATAACGTAGTGGTTTGGTTGCCTGAAAGGAAAATATTATTCGGTGGTTGTTTTATTAAACCGTACGGTTTAGGCAATTTGGGTGACGCAAATATAGAAGCTTGGCCAAAGTCCGCCAAATTATTAAAGTCCAAATATGGTAAGGCAAAACTGGTTGTTCCAAGTCACAGTGAAGTTGGAGACGCATCACTCTTGAAACTTACATTAGAGCAGGCGGTTAAAGGGTTAAACGAAAGTAAAAAACCATCAAAACCAAGCAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3008223","ARO_id":"47015","ARO_name":"IMP-97","CARD_short_name":"IMP-97","ARO_description":"Subclass B1 metallo-beta-lactamase IMP-97.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7642":{"model_id":"7642","model_name":"IMP-98","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10469":{"protein_sequence":{"accession":"BDU49371.1","sequence":"MSKLSVFFIFLFCSIATAAESLPDLKIEKLDEGVYVHTSFEEVNGWGVVPKHGLVVLVNAEAYLIDTPFTAKDTEKLVTWFVERGYKIKGSISSHFHSDSTGGIEWLNSRSIPTYASELTNELLKKDGKVQATNSFSGVNYWLVKNKIEVFYPGPGHTPDNVVVWLPERKILFGGCFIKPYGLGNLGDANIEAWPKSAKLLKSKYGKAKLVVSSHSEVGDASLLKLTLEQAVKGLNESKKPSKPSN"},"dna_sequence":{"accession":"LC740578.1","fmin":"14","fmax":"755","strand":"+","sequence":"ATGAGCAAGTTATCTGTATTCTTTATATTTTTGTTTTGCAGCATTGCTACCGCAGCAGAGTCTTTGCCAGATTTAAAAATTGAAAAGCTTGATGAAGGCGTTTATGTTCATACTTCGTTTGAAGAAGTTAACGGGTGGGGCGTTGTTCCTAAACATGGTTTGGTGGTTCTTGTAAATGCTGAGGCTTATCTAATTGACACTCCATTTACGGCTAAAGATACTGAAAAGTTAGTCACTTGGTTTGTGGAGCGTGGCTATAAAATAAAAGGCAGTATTTCCTCTCATTTTCATAGCGACAGCACGGGCGGAATAGAGTGGCTTAATTCTCGATCTATCCCCACGTATGCATCTGAATTAACAAATGAACTGCTTAAAAAAGACGGTAAGGTTCAAGCCACAAATTCATTTAGCGGAGTTAACTATTGGCTAGTTAAAAATAAAATTGAAGTTTTTTATCCAGGCCCGGGACACACTCCAGATAACGTAGTGGTTTGGCTGCCTGAAAGGAAAATATTATTCGGTGGTTGTTTTATTAAACCGTACGGTTTAGGCAATTTGGGTGACGCAAATATAGAAGCTTGGCCAAAGTCCGCCAAATTATTAAAGTCCAAATATGGTAAGGCAAAACTGGTTGTTTCAAGTCACAGTGAAGTTGGAGACGCATCACTCTTGAAACTTACATTAGAGCAGGCGGTTAAAGGATTAAACGAAAGTAAAAAACCATCAAAACCAAGCAACTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008224","ARO_id":"47016","ARO_name":"IMP-98","CARD_short_name":"IMP-98","ARO_description":"Subclass B1 metallo-beta-lactamase IMP-98.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7643":{"model_id":"7643","model_name":"IMP-99","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10470":{"protein_sequence":{"accession":"WEG44269.1","sequence":"MKKLFVLCVFFLCNIAAADDSLPDLKIEKLEKGVYVHTSFEEVKGWGVVTKHGLVVLVKNDAYLIDTPSTAKDTEKLVNWFIEHGYRIKGSISTHFHGDSTAGIEWLNSQSISTYASELTNELLKKDNKVQATNSFSGVSYSLIKNKIEVFYPGPGHTQDNVVVWLPEKKILFGGCFVKPDGLGNLGDANLEAWPKSAKILMSKYGKAKLVVSSHSEIGNASLLQRTWEQAVKGLNESKKPLQPSS"},"dna_sequence":{"accession":"OQ533023.1","fmin":"0","fmax":"741","strand":"+","sequence":"ATGAAAAAATTATTTGTTTTATGTGTATTCTTCCTTTGCAACATTGCTGCTGCAGATGATTCTTTGCCTGATTTAAAAATTGAGAAGCTTGAAAAAGGCGTTTATGTTCATACTTCGTTTGAAGAAGTTAAAGGTTGGGGTGTAGTCACAAAACACGGTTTAGTGGTTCTTGTAAAGAATGATGCTTATCTGATAGATACTCCAAGTACCGCTAAAGATACTGAAAAATTAGTTAATTGGTTTATTGAGCACGGCTATAGAATCAAAGGCAGTATTTCCACACATTTCCATGGCGACAGTACGGCTGGAATAGAGTGGCTTAATTCTCAATCTATCTCCACGTATGCCTCTGAATTAACAAATGAACTTCTAAAAAAAGACAATAAGGTGCAAGCTACAAATTCTTTTAGTGGAGTTAGTTATTCACTTATCAAAAACAAAATTGAAGTTTTCTATCCAGGTCCAGGACACACTCAAGATAACGTAGTGGTTTGGTTACCTGAAAAGAAAATTTTATTCGGTGGTTGCTTTGTTAAACCGGACGGTCTTGGAAATTTAGGGGATGCAAATTTAGAAGCTTGGCCAAAGTCCGCTAAAATATTAATGTCTAAATATGGTAAAGCAAAACTGGTTGTTTCAAGTCATAGTGAAATTGGAAACGCATCACTCTTGCAACGCACATGGGAGCAGGCTGTTAAAGGGTTAAATGAAAGTAAAAAACCGTTACAGCCAAGTAGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008225","ARO_id":"47017","ARO_name":"IMP-99","CARD_short_name":"IMP-99","ARO_description":"Subclass B1 metallo-beta-lactamase IMP-99.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7644":{"model_id":"7644","model_name":"IND-18","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10471":{"protein_sequence":{"accession":"WDE35088.1","sequence":"MKRNIQFFIISMLLSPFATAQTTQVRDFVIEPQIQPNFYIYKTFGVFGGKEYSTNAVYLVTKKGVVLFDVPWQKTQYQSLLDTIQKRHNLPVIAVFATHSHEDRAGDLSFYNKKGIKTYATAKTNELLKKDGKATSTELIKTGKPYRIGGEEFIVDFLGEGHTADNVVVWFPKYKILDGGCLVKSKAAVDLGYTGEANVAQWPQTMTKLKYKYSQATLIIPGHDEWKGGGHVEHTLDLLHNK"},"dna_sequence":{"accession":"ON650755.1","fmin":"0","fmax":"729","strand":"+","sequence":"ATGAAAAGAAACATTCAGTTTTTTATTATTTCGATGTTGCTAAGTCCATTCGCAACGGCTCAAACCACTCAGGTAAGAGATTTTGTCATTGAACCACAGATTCAGCCCAATTTTTATATTTATAAAACTTTCGGAGTATTCGGAGGAAAAGAATATTCTACCAATGCTGTTTATCTGGTGACCAAAAAAGGGGTTGTCTTATTCGATGTCCCTTGGCAGAAAACACAGTATCAAAGTCTTTTGGATACTATTCAGAAAAGACATAACCTTCCTGTTATTGCGGTATTTGCAACTCATTCGCATGAAGACAGAGCCGGAGATTTAAGCTTTTATAATAAGAAAGGGATCAAAACCTACGCTACAGCTAAAACCAATGAGCTTTTGAAGAAGGATGGAAAAGCAACTTCTACTGAACTTATTAAAACAGGAAAACCTTATCGTATTGGTGGAGAAGAATTTATAGTAGACTTTCTTGGGGAAGGACATACTGCCGATAATGTAGTGGTATGGTTTCCCAAATATAAAATACTGGACGGAGGATGTCTTGTCAAGAGCAAAGCAGCTGTTGATCTTGGGTATACGGGAGAAGCCAATGTTGCCCAATGGCCTCAAACCATGACAAAACTTAAATACAAATATTCACAGGCAACTTTGATTATCCCCGGACACGATGAATGGAAAGGAGGCGGGCACGTAGAACATACACTTGACCTCCTGCATAACAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36916","NCBI_taxonomy_name":"Chryseobacterium indologenes","NCBI_taxonomy_id":"253"}}}},"ARO_accession":"3008226","ARO_id":"47018","ARO_name":"IND-18","CARD_short_name":"IND-18","ARO_description":"Subclass B1 metallo-beta-lactamase IND-18.","ARO_category":{"36199":{"category_aro_accession":"3000060","category_aro_cvterm_id":"36199","category_aro_name":"IND beta-lactamase","category_aro_description":"IND beta-lactamases are class B carbapenem-hydrolyzing beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7645":{"model_id":"7645","model_name":"IND-19","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10472":{"protein_sequence":{"accession":"WDE35087.1","sequence":"MKKSIQLLMMSMFLSPLINAQVKDFVIEPPVKPKLYLYKSFGVFGGKEYSANAVYLTTKKGVVLFDVPWQKEQYQTLMDTIQKRHHLPVIAVFATHSHDDRAGDLSFYNQKGIKTYATAKTNELLKKDGKATSTEIIKTGKPYKIGGEEFMVDFLGEGHTVDNVVVWFPKYKVLDGGCLVKSRTATDLGYTGEANVKQWPETMRKLKTKYAQATLVIPGHDEWKGGGHVQHTLDLLDKNKKPE"},"dna_sequence":{"accession":"ON650754.1","fmin":"0","fmax":"732","strand":"+","sequence":"ATGAAAAAAAGTATTCAGCTTTTGATGATGTCAATGTTTTTAAGCCCATTGATCAATGCCCAGGTTAAAGATTTTGTAATTGAGCCGCCTGTTAAACCCAAACTGTATCTTTATAAAAGTTTCGGAGTTTTCGGGGGTAAAGAATATTCTGCCAATGCTGTATATCTTACCACTAAGAAAGGAGTTGTCTTATTTGATGTCCCATGGCAAAAGGAACAATATCAAACCCTTATGGACACCATACAAAAGCGTCATCACCTTCCTGTAATTGCTGTATTTGCCACCCACTCTCATGATGACAGAGCGGGCGATCTAAGCTTTTACAATCAAAAAGGAATTAAAACATATGCGACCGCCAAGACCAATGAACTGTTGAAAAAAGACGGAAAAGCAACCTCAACCGAAATTATAAAAACAGGAAAACCTTACAAAATTGGTGGTGAAGAATTTATGGTAGACTTTCTTGGAGAAGGACATACAGTTGATAATGTTGTCGTATGGTTTCCCAAATATAAAGTACTGGACGGAGGATGTCTTGTAAAAAGCAGGACAGCCACTGACCTGGGATATACCGGTGAAGCAAATGTAAAACAATGGCCGGAAACCATGCGAAAACTAAAAACGAAATATGCTCAGGCCACTCTGGTAATCCCGGGACACGACGAATGGAAAGGCGGTGGCCATGTACAGCATACTCTGGATCTTCTGGATAAGAATAAAAAGCCGGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36916","NCBI_taxonomy_name":"Chryseobacterium indologenes","NCBI_taxonomy_id":"253"}}}},"ARO_accession":"3008227","ARO_id":"47019","ARO_name":"IND-19","CARD_short_name":"IND-19","ARO_description":"Subclass B1 metallo-beta-lactamase IND-19.","ARO_category":{"36199":{"category_aro_accession":"3000060","category_aro_cvterm_id":"36199","category_aro_name":"IND beta-lactamase","category_aro_description":"IND beta-lactamases are class B carbapenem-hydrolyzing beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7646":{"model_id":"7646","model_name":"KHM-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10473":{"protein_sequence":{"accession":"WEY36412.1","sequence":"MKAFLAAILFLLSNITFAEDPLPELEIKKIEEGVYLYTAYEKIEGWGLVGSNGLVVLDNKDAYLIDTPISATDTEKLVKWIDAQGFTAKASISTHFHSDSTGGIAFLNSKSIPTYASKQTNKLLKNKGEAQATHSFTKNPFWLVNKKIEVFFPGAGHTSDNVVVWMPEQKILFGGCFVKPDGLGNLSHAVIEEWPASAEKLIARYGTAKLVVPGHGKVGDASFLEKTKQRALEALAAKK"},"dna_sequence":{"accession":"OQ646729.1","fmin":"0","fmax":"720","strand":"+","sequence":"ATGAAAGCGTTTCTAGCAGCAATTTTATTTCTTTTATCAAACATCACTTTTGCTGAAGACCCTTTACCCGAGCTGGAAATTAAAAAAATCGAAGAGGGCGTTTATCTGTACACCGCTTACGAAAAAATTGAAGGCTGGGGGCTTGTTGGCTCTAACGGATTAGTCGTGCTTGATAACAAAGATGCTTACCTGATTGATACACCCATTTCAGCAACAGACACTGAAAAATTAGTGAAATGGATTGACGCGCAGGGCTTTACCGCTAAGGCAAGTATTTCCACACATTTCCATAGCGACAGTACCGGTGGCATAGCATTTCTCAACTCAAAGTCCATTCCAACTTATGCCTCCAAGCAAACTAACAAATTGCTTAAAAATAAAGGCGAAGCACAAGCCACCCATTCATTTACGAAAAATCCCTTTTGGTTGGTCAATAAAAAAATAGAAGTGTTTTTCCCCGGCGCTGGCCACACTTCAGATAATGTCGTGGTGTGGATGCCAGAACAGAAAATTCTATTCGGCGGCTGTTTTGTCAAACCTGACGGTCTCGGCAATCTTAGCCACGCAGTAATAGAAGAATGGCCTGCGTCCGCTGAAAAACTTATCGCACGCTACGGCACGGCAAAACTGGTGGTGCCAGGGCACGGCAAGGTTGGTGATGCTTCGTTCTTGGAAAAAACCAAACAGCGAGCACTTGAAGCGCTTGCAGCGAAAAAGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"47925","NCBI_taxonomy_name":"Pseudomonas mosselii","NCBI_taxonomy_id":"78327"}}}},"ARO_accession":"3008228","ARO_id":"47020","ARO_name":"KHM-2","CARD_short_name":"KHM-2","ARO_description":"Subclass B1 metallo-beta-lactamase KHM-2.","ARO_category":{"41371":{"category_aro_accession":"3004207","category_aro_cvterm_id":"41371","category_aro_name":"KHM beta-lactamase","category_aro_description":"KHM beta-lactamases are Class B beta-lactamases that can confer resistance to all classes of beta-lactams, except the monobactams.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7647":{"model_id":"7647","model_name":"KLUC-6","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10474":{"protein_sequence":{"accession":"BDS51134.1","sequence":"MVKKSLRQFALLAATVFPLLAGSVSLQAQTLSVEQKLAALEQRSGGRLGVALIDTADGSQILYRGDERFAMCSTSKVMAAAAVLKQSESQHDLLNQRIEIKKGDLTNYNPIAEKHVGGSMSLSDLSAAALQYSDNVAMNKLIAQLGGPQGVTAFARKIGDETFRLDRTEPTLNTAIPGDPRDTTSPRAMAQTLRNLTLGKALGDAQRAQLVTWMKGNTTGTASIQAGLPASWVVGDKTGSGDYGTTNDIAVIWPKDRAPLVLVTYFTQPQPEAESRRDVLASAAKIVTEGL"},"dna_sequence":{"accession":"LC732564.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGGTTAAAAAATCATTACGCCAGTTTGCGCTGTTGGCCGCGACGGTTTTTCCGCTGCTGGCAGGCAGCGTATCGCTACAGGCACAAACGCTGAGCGTAGAGCAGAAACTTGCGGCTTTAGAGCAGCGTTCAGGGGGACGGCTTGGGGTCGCGTTGATAGATACTGCGGATGGTTCGCAAATTCTCTATCGTGGCGATGAGCGTTTCGCGATGTGTAGTACCAGCAAAGTGATGGCCGCTGCCGCGGTGCTAAAGCAAAGTGAAAGTCAGCACGATCTTTTAAATCAGCGCATTGAGATCAAAAAGGGTGACCTGACTAACTATAACCCGATTGCGGAAAAACATGTCGGTGGGTCGATGTCGTTGTCTGATCTCAGCGCCGCGGCCTTGCAGTACAGCGATAACGTGGCGATGAATAAGCTTATCGCTCAACTGGGTGGCCCGCAGGGGGTTACCGCGTTTGCCCGTAAGATTGGGGATGAGACGTTTCGTCTCGATCGCACGGAACCGACGCTGAACACTGCAATTCCCGGCGATCCACGCGATACCACATCACCACGGGCTATGGCACAAACGCTGCGCAACCTGACGCTGGGAAAAGCGCTTGGTGACGCTCAAAGGGCGCAGTTGGTGACCTGGATGAAAGGGAATACGACTGGAACGGCCAGTATTCAGGCTGGACTACCGGCTTCGTGGGTGGTGGGCGATAAAACCGGCAGCGGTGATTACGGCACCACCAACGACATTGCAGTGATTTGGCCGAAAGATCGTGCACCATTGGTTTTGGTTACCTACTTCACGCAGCCTCAGCCTGAGGCGGAAAGCCGTCGTGATGTATTAGCCTCTGCGGCGAAAATCGTCACTGAGGGATTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"47916","NCBI_taxonomy_name":"Kluyvera cryocrescens","NCBI_taxonomy_id":"580"}}}},"ARO_accession":"3008229","ARO_id":"47021","ARO_name":"KLUC-6","CARD_short_name":"KLUC-6","ARO_description":"Extended-spectrum class A beta-lactamase KLUC-6.","ARO_category":{"43877":{"category_aro_accession":"3005417","category_aro_cvterm_id":"43877","category_aro_name":"KLUC beta-lactamase","category_aro_description":"KLUC beta-lactamases are class A beta-lactamases found in Kluyvera cryocrescens, Escherichia coli and Enterobacteriaceae.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7648":{"model_id":"7648","model_name":"KLUG-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10475":{"protein_sequence":{"accession":"AAN73274.1","sequence":"MMRHRVKRVMLMTTTCISLLLGSAPLYAQANDVQQKLAALEKSSGGRLGVALIDTADNAQTLYRADERFAMCSTSKVMAAAAVLKQSETQKKVLSQKVEIKSSDLINYNPITEKHVNGTMTLAELSAAALQYSDNTAMNKLIAHLGGPDKVTAFARAIGDNTFRLDRTEPTLNTAIPGDPRDTTTPLAMAQTLRNLTLGSALGETQRAQLVTWLKGNTTGAASIQAGLPTSWVVGDKTGSGDYGTTNDIAVIWPEGRAPLILVTYFTQPEQKAESRRDVLAAAAKIVTDGN"},"dna_sequence":{"accession":"AF501233.1","fmin":"533","fmax":"1409","strand":"+","sequence":"ATGATGAGACATCGCGTTAAGCGGGTAATGCTAATGACAACGACCTGTATTTCGCTGTTGCTGGGGAGTGCGCCGCTGTATGCGCAGGCGAACGACGTTCAGCAAAAGCTGGCGGCGCTGGAGAAAAGCAGCGGGGGGCGGTTGGGAGTGGCGCTGATTGACACCGCCGATAACGCACAGACGCTCTACCGCGCCGATGAGCGCTTTGCCATGTGCAGCACCAGTAAGGTGATGGCGGCAGCGGCGGTGCTCAAGCAAAGTGAAACGCAAAAGAAGGTGTTGAGTCAGAAGGTTGAGATTAAATCTTCAGACCTGATTAACTACAATCCCATCACTGAAAAACACGTCAACGGCACGATGACGCTGGCGGAATTGAGCGCCGCGGCGTTGCAGTACAGCGACAATACGGCCATGAACAAACTGATTGCCCATCTTGGGGGGCCGGATAAAGTGACGGCGTTTGCCCGTGCGATTGGGGATAACACCTTCCGGCTCGATCGTACTGAGCCGACGCTCAACACCGCGATCCCCGGCGACCCGCGCGATACCACCACGCCATTAGCGATGGCGCAGACGCTTCGCAATCTGACGTTGGGCAGTGCCTTAGGTGAAACTCAGCGTGCGCAACTGGTGACGTGGCTGAAAGGCAATACCACCGGCGCTGCCAGCATTCAGGCTGGGCTACCCACATCGTGGGTTGTCGGGGATAAAACCGGCAGCGGTGATTATGGTACGACGAATGACATCGCCGTTATCTGGCCGGAAGGGCGTGCGCCGCTTATTCTGGTCACTTACTTCACCCAACCGGAGCAGAAGGCAGAAAGTCGTCGTGACGTACTCGCTGCTGCCGCGAAAATCGTCACTGACGGTAATTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36929","NCBI_taxonomy_name":"Kluyvera georgiana","NCBI_taxonomy_id":"73098"}}}},"ARO_accession":"3008230","ARO_id":"47022","ARO_name":"KLUG-1","CARD_short_name":"KLUG-1","ARO_description":"CTX-M family extended-spectrum class A beta-lactamase KLUG-1.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7649":{"model_id":"7649","model_name":"KPC-101","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10476":{"protein_sequence":{"accession":"UBJ91322.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"OK086805.1","fmin":"0","fmax":"888","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008231","ARO_id":"47023","ARO_name":"KPC-101","CARD_short_name":"KPC-101","ARO_description":"Inhibitor-resistant carbapenem-hydrolyzing class A beta-lactamase KPC-101.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7650":{"model_id":"7650","model_name":"KPC-102","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10477":{"protein_sequence":{"accession":"UDU33959.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARYTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVDGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"OK652013.1","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCTATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGGATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008232","ARO_id":"47024","ARO_name":"KPC-102","CARD_short_name":"KPC-102","ARO_description":"Carbapenem-hydrolyzing class A beta-lactamase KPC-102.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7651":{"model_id":"7651","model_name":"KPC-103","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10478":{"protein_sequence":{"accession":"UFK32670.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"OL445423.1","fmin":"0","fmax":"918","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008233","ARO_id":"47025","ARO_name":"KPC-103","CARD_short_name":"KPC-103","ARO_description":"Class A beta-lactamase KPC-103.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7652":{"model_id":"7652","model_name":"KPC-104","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10479":{"protein_sequence":{"accession":"UFK32671.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTYTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"OL445424.1","fmin":"0","fmax":"906","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008234","ARO_id":"47026","ARO_name":"KPC-104","CARD_short_name":"KPC-104","ARO_description":"Class A beta-lactamase KPC-104.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7653":{"model_id":"7653","model_name":"KPC-105","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10480":{"protein_sequence":{"accession":"UFK32673.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELEQNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"OL445426.1","fmin":"0","fmax":"927","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCAGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008235","ARO_id":"47027","ARO_name":"KPC-105","CARD_short_name":"KPC-105","ARO_description":"Class A beta-lactamase KPC-105.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7654":{"model_id":"7654","model_name":"KPC-106","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10481":{"protein_sequence":{"accession":"UFK32675.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTYTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"OL445428.1","fmin":"0","fmax":"900","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008236","ARO_id":"47028","ARO_name":"KPC-106","CARD_short_name":"KPC-106","ARO_description":"Class A beta-lactamase KPC-106.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7655":{"model_id":"7655","model_name":"KPC-107","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10482":{"protein_sequence":{"accession":"UFK32672.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"OL445425.1","fmin":"0","fmax":"966","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008237","ARO_id":"47029","ARO_name":"KPC-107","CARD_short_name":"KPC-107","ARO_description":"Class A beta-lactamase KPC-107.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7656":{"model_id":"7656","model_name":"KPC-108","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10483":{"protein_sequence":{"accession":"UFK32674.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTENTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"OL445427.1","fmin":"0","fmax":"957","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008238","ARO_id":"47030","ARO_name":"KPC-108","CARD_short_name":"KPC-108","ARO_description":"Class A beta-lactamase KPC-108.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7657":{"model_id":"7657","model_name":"KPC-109","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10484":{"protein_sequence":{"accession":"UGY69815.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKYNKDDKYSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"OL744263.1","fmin":"0","fmax":"900","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGTACAACAAGGATGACAAGTACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008239","ARO_id":"47031","ARO_name":"KPC-109","CARD_short_name":"KPC-109","ARO_description":"Inhibitor-resistant carbapenem-hydrolyzing class A beta-lactamase KPC-109.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7658":{"model_id":"7658","model_name":"KPC-110","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10485":{"protein_sequence":{"accession":"UIH96895.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGRSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARYTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKYSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"CP100313.1","fmin":"37210","fmax":"38092","strand":"-","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCCGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCTATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGTACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008240","ARO_id":"47032","ARO_name":"KPC-110","CARD_short_name":"KPC-110","ARO_description":"Inhibitor-resistant class A beta-lactamase KPC-110.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7659":{"model_id":"7659","model_name":"KPC-111","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10486":{"protein_sequence":{"accession":"UIX50813.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAILGDARYTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKYSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"OL744330.1","fmin":"12172","fmax":"13054","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCTAGGCGATGCGCGCTATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGTACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008241","ARO_id":"47033","ARO_name":"KPC-111","CARD_short_name":"KPC-111","ARO_description":"Inhibitor-resistant class A beta-lactamase KPC-111.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7660":{"model_id":"7660","model_name":"KPC-112","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10487":{"protein_sequence":{"accession":"UIY90578.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"OM177660.1","fmin":"5","fmax":"875","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008242","ARO_id":"47034","ARO_name":"KPC-112","CARD_short_name":"KPC-112","ARO_description":"Inhibitor-resistant extended-spectrum class A beta-lactamase KPC-112.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7661":{"model_id":"7661","model_name":"KPC-113","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10488":{"protein_sequence":{"accession":"ULU82276.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRGAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"OM728506.1","fmin":"0","fmax":"885","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008243","ARO_id":"47035","ARO_name":"KPC-113","CARD_short_name":"KPC-113","ARO_description":"Inhibitor-resistant carbapenem-hydrolyzing class A beta-lactamase KPC-113.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7662":{"model_id":"7662","model_name":"KPC-114","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10489":{"protein_sequence":{"accession":"ULU82277.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"OM728507.1","fmin":"0","fmax":"888","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008244","ARO_id":"47036","ARO_name":"KPC-114","CARD_short_name":"KPC-114","ARO_description":"Inhibitor-resistant carbapenem-hydrolyzing class A beta-lactamase KPC-114.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7663":{"model_id":"7663","model_name":"KPC-115","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10490":{"protein_sequence":{"accession":"ULU82668.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELEPAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKYSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"OM714909.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGTACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008245","ARO_id":"47037","ARO_name":"KPC-115","CARD_short_name":"KPC-115","ARO_description":"Inhibitor-resistant class A beta-lactamase KPC-115.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7664":{"model_id":"7664","model_name":"KPC-116","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10491":{"protein_sequence":{"accession":"ULU82669.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNFAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"OM729575.1","fmin":"0","fmax":"882","strand":"-","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTTCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008246","ARO_id":"47038","ARO_name":"KPC-116","CARD_short_name":"KPC-116","ARO_description":"Carbapenem-hydrolyzing class A beta-lactamase KPC-116.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7665":{"model_id":"7665","model_name":"KPC-117","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10492":{"protein_sequence":{"accession":"UNN26047.1","sequence":"MSRCPIFRRFLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"OM933711.1","fmin":"0","fmax":"894","strand":"-","sequence":"ATGTCGCGATGCCCTATTTTCAGGCGTTTTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008247","ARO_id":"47039","ARO_name":"KPC-117","CARD_short_name":"KPC-117","ARO_description":"Inhibitor-resistant carbapenem-hydrolyzing class A beta-lactamase KPC-117.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7666":{"model_id":"7666","model_name":"KPC-118","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10493":{"protein_sequence":{"accession":"UNN26048.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALLPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRRELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKYSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"OM933712.1","fmin":"0","fmax":"882","strand":"-","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGCTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCCGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGTACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008248","ARO_id":"47040","ARO_name":"KPC-118","CARD_short_name":"KPC-118","ARO_description":"Carbapenem-hydrolyzing class A beta-lactamase KPC-118.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7667":{"model_id":"7667","model_name":"KPC-119","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10494":{"protein_sequence":{"accession":"UNN26049.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEHDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"OM933713.1","fmin":"0","fmax":"882","strand":"-","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACATGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008249","ARO_id":"47041","ARO_name":"KPC-119","CARD_short_name":"KPC-119","ARO_description":"Carbapenem-hydrolyzing class A beta-lactamase KPC-119.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7668":{"model_id":"7668","model_name":"KPC-120","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10495":{"protein_sequence":{"accession":"UNN26051.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVRWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARYTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"OM933715.1","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCGGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCTATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008250","ARO_id":"47042","ARO_name":"KPC-120","CARD_short_name":"KPC-120","ARO_description":"Carbapenem-hydrolyzing class A beta-lactamase KPC-120.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7669":{"model_id":"7669","model_name":"KPC-121","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10496":{"protein_sequence":{"accession":"UNN26053.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKYSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"OM933717.1","fmin":"0","fmax":"885","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGTACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3008251","ARO_id":"47043","ARO_name":"KPC-121","CARD_short_name":"KPC-121","ARO_description":"Carbapenem-hydrolyzing class A beta-lactamase KPC-121.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7670":{"model_id":"7670","model_name":"KPC-122","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10497":{"protein_sequence":{"accession":"UNN26056.1","sequence":"MSLYRRLILLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKYSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"OM933720.1","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAATTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGTACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3008252","ARO_id":"47044","ARO_name":"KPC-122","CARD_short_name":"KPC-122","ARO_description":"Carbapenem-hydrolyzing class A beta-lactamase KPC-122.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7671":{"model_id":"7671","model_name":"KPC-124","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10498":{"protein_sequence":{"accession":"UOX08352.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELNSAIPGDARYTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKYSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"ON221403.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCTATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGTACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008253","ARO_id":"47045","ARO_name":"KPC-124","CARD_short_name":"KPC-124","ARO_description":"Inhibitor-resistant carbapenem-hydrolyzing class A beta-lactamase KPC-124.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7672":{"model_id":"7672","model_name":"KPC-126","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10499":{"protein_sequence":{"accession":"UPY21302.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSVIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"OM830488.1","fmin":"0","fmax":"882","strand":"-","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGTCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008254","ARO_id":"47046","ARO_name":"KPC-126","CARD_short_name":"KPC-126","ARO_description":"Carbapenem-hydrolyzing class A beta-lactamase KPC-126.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7673":{"model_id":"7673","model_name":"KPC-127","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10500":{"protein_sequence":{"accession":"URC16702.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELELNSTIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"ON521725.1","fmin":"31","fmax":"919","strand":"-","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGGAGCTGAACTCCACCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008255","ARO_id":"47047","ARO_name":"KPC-127","CARD_short_name":"KPC-127","ARO_description":"Carbapenem-hydrolyzing class A beta-lactamase KPC-127.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7674":{"model_id":"7674","model_name":"KPC-128","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10501":{"protein_sequence":{"accession":"URC16704.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARYTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGMANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"ON521727.1","fmin":"5","fmax":"887","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCTATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCATGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008256","ARO_id":"47048","ARO_name":"KPC-128","CARD_short_name":"KPC-128","ARO_description":"Carbapenem-hydrolyzing class A beta-lactamase KPC-128.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7675":{"model_id":"7675","model_name":"KPC-129","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10502":{"protein_sequence":{"accession":"USG13864.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELHSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"ON751738.1","fmin":"0","fmax":"906","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGCACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008257","ARO_id":"47049","ARO_name":"KPC-129","CARD_short_name":"KPC-129","ARO_description":"Class A beta-lactamase KPC-129.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7676":{"model_id":"7676","model_name":"KPC-130","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10503":{"protein_sequence":{"accession":"USK12023.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARGTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKYSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"ON794466.1","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGGTACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGTACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008258","ARO_id":"47050","ARO_name":"KPC-130","CARD_short_name":"KPC-130","ARO_description":"Class A beta-lactamase KPC-130.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7677":{"model_id":"7677","model_name":"KPC-131","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10504":{"protein_sequence":{"accession":"USQ89943.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTAGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"ON823194.1","fmin":"1332","fmax":"2214","strand":"-","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGGCCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008259","ARO_id":"47051","ARO_name":"KPC-131","CARD_short_name":"KPC-131","ARO_description":"Carbapenem-hydrolyzing class A beta-lactamase KPC-131.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7678":{"model_id":"7678","model_name":"KPC-132","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10505":{"protein_sequence":{"accession":"UUF81222.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKSRAPNKDDKYSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"OP081092.1","fmin":"0","fmax":"909","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGTCCCGGGCGCCTAACAAGGATGACAAGTACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008260","ARO_id":"47052","ARO_name":"KPC-132","CARD_short_name":"KPC-132","ARO_description":"Inhibitor-resistant class A beta-lactamase KPC-132.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7679":{"model_id":"7679","model_name":"KPC-133","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10506":{"protein_sequence":{"accession":"UUG60968.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARGTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"OP081531.1","fmin":"0","fmax":"927","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGGTACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008261","ARO_id":"47053","ARO_name":"KPC-133","CARD_short_name":"KPC-133","ARO_description":"Carbapenem-hydrolyzing class A beta-lactamase KPC-133.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7680":{"model_id":"7680","model_name":"KPC-136","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10507":{"protein_sequence":{"accession":"WEG44273.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAILGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"OQ579152.1","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCTAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008262","ARO_id":"47054","ARO_name":"KPC-136","CARD_short_name":"KPC-136","ARO_description":"Carbapenem-hydrolyzing class A beta-lactamase KPC-136.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7681":{"model_id":"7681","model_name":"KPC-137","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10508":{"protein_sequence":{"accession":"WNR58488.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAILDDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"OR596987.1","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCTAGACGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008263","ARO_id":"47055","ARO_name":"KPC-137","CARD_short_name":"KPC-137","ARO_description":"Inhibitor-resistant class A beta-lactamase KPC-137.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7682":{"model_id":"7682","model_name":"KPC-138","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10509":{"protein_sequence":{"accession":"UXO98494.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELEPNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGAANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVNSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"OP432320.1","fmin":"0","fmax":"897","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCCGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCGCGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCAACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008264","ARO_id":"47056","ARO_name":"KPC-138","CARD_short_name":"KPC-138","ARO_description":"Inhibitor-resistant extended-spectrum class A beta-lactamase KPC-138.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7683":{"model_id":"7683","model_name":"KPC-139","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10510":{"protein_sequence":{"accession":"UXO99692.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARYTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"OP503887.1","fmin":"0","fmax":"900","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCTATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008265","ARO_id":"47057","ARO_name":"KPC-139","CARD_short_name":"KPC-139","ARO_description":"Inhibitor-resistant carbapenem-hydrolyzing class A beta-lactamase KPC-139.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7684":{"model_id":"7684","model_name":"KPC-140","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10511":{"protein_sequence":{"accession":"UXO99693.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARNTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"OP503888.1","fmin":"0","fmax":"927","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCAATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008266","ARO_id":"47058","ARO_name":"KPC-140","CARD_short_name":"KPC-140","ARO_description":"Inhibitor-resistant carbapenem-hydrolyzing class A beta-lactamase KPC-140.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7685":{"model_id":"7685","model_name":"KPC-141","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10512":{"protein_sequence":{"accession":"UXO99694.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARYTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"OP503889.1","fmin":"0","fmax":"885","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCTATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008267","ARO_id":"47059","ARO_name":"KPC-141","CARD_short_name":"KPC-141","ARO_description":"Inhibitor-resistant carbapenem-hydrolyzing class A beta-lactamase KPC-141.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7686":{"model_id":"7686","model_name":"KPC-142","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10513":{"protein_sequence":{"accession":"UXO99695.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"OP503890.1","fmin":"0","fmax":"903","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008268","ARO_id":"47060","ARO_name":"KPC-142","CARD_short_name":"KPC-142","ARO_description":"Inhibitor-resistant carbapenem-hydrolyzing class A beta-lactamase KPC-142.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7687":{"model_id":"7687","model_name":"KPC-143","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10514":{"protein_sequence":{"accession":"UXO99696.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARYTSSPRAVSESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"OP503891.1","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCTATACCTCATCGCCGCGCGCCGTGTCGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008269","ARO_id":"47061","ARO_name":"KPC-143","CARD_short_name":"KPC-143","ARO_description":"Inhibitor-resistant carbapenem-hydrolyzing class A beta-lactamase KPC-143.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7688":{"model_id":"7688","model_name":"KPC-144","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10515":{"protein_sequence":{"accession":"UXP87111.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSTIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"OP559533.1","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCACCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008270","ARO_id":"47062","ARO_name":"KPC-144","CARD_short_name":"KPC-144","ARO_description":"Inhibitor-resistant carbapenem-hydrolyzing class A beta-lactamase KPC-144.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7689":{"model_id":"7689","model_name":"KPC-145","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10516":{"protein_sequence":{"accession":"UYF23564.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARYTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYARAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"OP626310.1","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCTATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACGCCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008271","ARO_id":"47063","ARO_name":"KPC-145","CARD_short_name":"KPC-145","ARO_description":"Inhibitor-resistant extended-spectrum class A beta-lactamase KPC-145.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7690":{"model_id":"7690","model_name":"KPC-146","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10517":{"protein_sequence":{"accession":"UZC76861.1","sequence":"MSMYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"OP696903.1","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCAATGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3008272","ARO_id":"47064","ARO_name":"KPC-146","CARD_short_name":"KPC-146","ARO_description":"Carbapenem-hydrolyzing class A beta-lactamase KPC-146.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7691":{"model_id":"7691","model_name":"KPC-147","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10518":{"protein_sequence":{"accession":"UZC76862.1","sequence":"MSLYRRLVMLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"OP696904.1","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTATGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008273","ARO_id":"47065","ARO_name":"KPC-147","CARD_short_name":"KPC-147","ARO_description":"Carbapenem-hydrolyzing class A beta-lactamase KPC-147.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7692":{"model_id":"7692","model_name":"KPC-148","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10519":{"protein_sequence":{"accession":"MCW0253507.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKYSEAVYTRAPNKDDKYSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"JAOZYA010000028.1","fmin":"56455","fmax":"57382","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGTACAGCGAGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGTACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008274","ARO_id":"47066","ARO_name":"KPC-148","CARD_short_name":"KPC-148","ARO_description":"Class A beta-lactamase KPC-148.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7693":{"model_id":"7693","model_name":"KPC-149","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10520":{"protein_sequence":{"accession":"UZF98429.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGSTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKYSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"OP778041.1","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAGCACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGTACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008275","ARO_id":"47067","ARO_name":"KPC-149","CARD_short_name":"KPC-149","ARO_description":"Carbapenem-hydrolyzing class A beta-lactamase KPC-149.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7694":{"model_id":"7694","model_name":"KPC-150","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10521":{"protein_sequence":{"accession":"UZH56920.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWEHSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKYSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"OP787490.1","fmin":"0","fmax":"873","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGTACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008276","ARO_id":"47068","ARO_name":"KPC-150","CARD_short_name":"KPC-150","ARO_description":"Inhibitor-resistant class A beta-lactamase KPC-150.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7695":{"model_id":"7695","model_name":"KPC-151","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10522":{"protein_sequence":{"accession":"UZQ18806.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVSANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"OP823148.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTCGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008277","ARO_id":"47069","ARO_name":"KPC-151","CARD_short_name":"KPC-151","ARO_description":"Inhibitor-resistant extended-spectrum class A beta-lactamase KPC-151.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7696":{"model_id":"7696","model_name":"KPC-152","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10523":{"protein_sequence":{"accession":"UZT70951.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKYTRAPNKDDKYSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"OP856888.1","fmin":"0","fmax":"918","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGTACACCCGGGCGCCTAACAAGGATGACAAGTACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008278","ARO_id":"47070","ARO_name":"KPC-152","CARD_short_name":"KPC-152","ARO_description":"Inhibitor-resistant extended-spectrum class A beta-lactamase KPC-152.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7697":{"model_id":"7697","model_name":"KPC-153","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10524":{"protein_sequence":{"accession":"UZZ47414.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKYSDAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"OP884096.1","fmin":"0","fmax":"888","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGTACAGCGATGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008279","ARO_id":"47071","ARO_name":"KPC-153","CARD_short_name":"KPC-153","ARO_description":"Inhibitor-resistant extended-spectrum class A beta-lactamase KPC-153.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7698":{"model_id":"7698","model_name":"KPC-154","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10525":{"protein_sequence":{"accession":"WAY00162.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKYSRAPNKDDKYSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"OQ096263.1","fmin":"37210","fmax":"38122","strand":"-","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGTACAGCCGGGCGCCTAACAAGGATGACAAGTACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008280","ARO_id":"47072","ARO_name":"KPC-154","CARD_short_name":"KPC-154","ARO_description":"Inhibitor-resistant extended-spectrum class A beta-lactamase KPC-154.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7699":{"model_id":"7699","model_name":"KPC-155","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10526":{"protein_sequence":{"accession":"WBG96004.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELEPNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYAANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"OQ139542.1","fmin":"0","fmax":"879","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCCGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGCGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008281","ARO_id":"47073","ARO_name":"KPC-155","CARD_short_name":"KPC-155","ARO_description":"Inhibitor-resistant class A beta-lactamase KPC-155.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7700":{"model_id":"7700","model_name":"KPC-156","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10527":{"protein_sequence":{"accession":"WCS94746.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLDVNGQ"},"dna_sequence":{"accession":"OQ390084.1","fmin":"286","fmax":"1168","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGACGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008282","ARO_id":"47074","ARO_name":"KPC-156","CARD_short_name":"KPC-156","ARO_description":"Carbapenem-hydrolyzing class A beta-lactamase KPC-156.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7701":{"model_id":"7701","model_name":"KPC-157","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10528":{"protein_sequence":{"accession":"MDG1646356.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDSAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"JAPQEX020000004.1","fmin":"57056","fmax":"57938","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAGCGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43787","NCBI_taxonomy_name":"Klebsiella huaxiensis","NCBI_taxonomy_id":"2153354"}}}},"ARO_accession":"3008283","ARO_id":"47075","ARO_name":"KPC-157","CARD_short_name":"KPC-157","ARO_description":"Carbapenem-hydrolyzing class A beta-lactamase KPC-157.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7702":{"model_id":"7702","model_name":"KPC-158","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10529":{"protein_sequence":{"accession":"WDE35082.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTVNDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"OQ305823.1","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGTAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008284","ARO_id":"47076","ARO_name":"KPC-158","CARD_short_name":"KPC-158","ARO_description":"Inhibitor-resistant carbapenem-hydrolyzing class A beta-lactamase KPC-158.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7703":{"model_id":"7703","model_name":"KPC-159","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10530":{"protein_sequence":{"accession":"WDQ79090.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARETSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"OQ450354.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGAGACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008285","ARO_id":"47077","ARO_name":"KPC-159","CARD_short_name":"KPC-159","ARO_description":"Inhibitor-resistant extended-spectrum class A beta-lactamase KPC-159.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7704":{"model_id":"7704","model_name":"KPC-160","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10531":{"protein_sequence":{"accession":"WEG44274.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"OQ579136.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008286","ARO_id":"47078","ARO_name":"KPC-160","CARD_short_name":"KPC-160","ARO_description":"Carbapenem-hydrolyzing class A beta-lactamase KPC-160.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7705":{"model_id":"7705","model_name":"KPC-161","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10532":{"protein_sequence":{"accession":"WEG44275.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAADDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"OQ579137.1","fmin":"0","fmax":"915","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008287","ARO_id":"47079","ARO_name":"KPC-161","CARD_short_name":"KPC-161","ARO_description":"Carbapenem-hydrolyzing class A beta-lactamase KPC-161.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7706":{"model_id":"7706","model_name":"KPC-162","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10533":{"protein_sequence":{"accession":"WEG44276.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"OQ579138.1","fmin":"0","fmax":"903","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008288","ARO_id":"47080","ARO_name":"KPC-162","CARD_short_name":"KPC-162","ARO_description":"Carbapenem-hydrolyzing class A beta-lactamase KPC-162.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7707":{"model_id":"7707","model_name":"KPC-163","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10534":{"protein_sequence":{"accession":"WEG44277.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"OQ579139.1","fmin":"0","fmax":"900","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008289","ARO_id":"47081","ARO_name":"KPC-163","CARD_short_name":"KPC-163","ARO_description":"Carbapenem-hydrolyzing class A beta-lactamase KPC-163.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7708":{"model_id":"7708","model_name":"KPC-164","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10535":{"protein_sequence":{"accession":"WEG44278.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"OQ579140.1","fmin":"0","fmax":"891","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008290","ARO_id":"47082","ARO_name":"KPC-164","CARD_short_name":"KPC-164","ARO_description":"Carbapenem-hydrolyzing class A beta-lactamase KPC-164.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7709":{"model_id":"7709","model_name":"KPC-165","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10536":{"protein_sequence":{"accession":"WEG44279.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELDSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"OQ579141.1","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGGACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008291","ARO_id":"47083","ARO_name":"KPC-165","CARD_short_name":"KPC-165","ARO_description":"Carbapenem-hydrolyzing class A beta-lactamase KPC-165.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7710":{"model_id":"7710","model_name":"KPC-166","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10537":{"protein_sequence":{"accession":"WEM34776.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELEHSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"OQ592369.1","fmin":"82","fmax":"961","strand":"-","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008292","ARO_id":"47084","ARO_name":"KPC-166","CARD_short_name":"KPC-166","ARO_description":"Carbapenem-hydrolyzing class A beta-lactamase KPC-166.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7711":{"model_id":"7711","model_name":"KPC-167","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10538":{"protein_sequence":{"accession":"WEG44934.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARYTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKYSEDDKYSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"OQ592370.1","fmin":"0","fmax":"900","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCTATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGTACAGCGAGGATGACAAGTACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008293","ARO_id":"47085","ARO_name":"KPC-167","CARD_short_name":"KPC-167","ARO_description":"Class A beta-lactamase KPC-167.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7712":{"model_id":"7712","model_name":"KPC-168","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10539":{"protein_sequence":{"accession":"WNH41911.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGNARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"OR568564.1","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCAATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008294","ARO_id":"47086","ARO_name":"KPC-168","CARD_short_name":"KPC-168","ARO_description":"Inhibitor-resistant carbapenem-hydrolyzing class A beta-lactamase KPC-168.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7713":{"model_id":"7713","model_name":"KPC-169","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10540":{"protein_sequence":{"accession":"WGW19922.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"OQ856767.1","fmin":"0","fmax":"873","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008295","ARO_id":"47087","ARO_name":"KPC-169","CARD_short_name":"KPC-169","ARO_description":"Inhibitor-resistant extended-spectrum class A beta-lactamase KPC-169.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7714":{"model_id":"7714","model_name":"KPC-170","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10541":{"protein_sequence":{"accession":"WMP15087.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARNTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"OR449906.1","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCAATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008296","ARO_id":"47088","ARO_name":"KPC-170","CARD_short_name":"KPC-170","ARO_description":"Inhibitor-resistant extended-spectrum class A beta-lactamase KPC-170.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7715":{"model_id":"7715","model_name":"KPC-171","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10542":{"protein_sequence":{"accession":"WGW19924.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAADSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"OQ856769.1","fmin":"0","fmax":"906","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008297","ARO_id":"47089","ARO_name":"KPC-171","CARD_short_name":"KPC-171","ARO_description":"Inhibitor-resistant carbapenem-hydrolyzing class A beta-lactamase KPC-171.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7716":{"model_id":"7716","model_name":"KPC-172","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10543":{"protein_sequence":{"accession":"WGW19926.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARETSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"OQ856771.1","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGAAACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008298","ARO_id":"47090","ARO_name":"KPC-172","CARD_short_name":"KPC-172","ARO_description":"Inhibitor-resistant extended-spectrum class A beta-lactamase KPC-172.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7717":{"model_id":"7717","model_name":"KPC-173","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10544":{"protein_sequence":{"accession":"WGW19927.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELKLNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"OQ856772.1","fmin":"0","fmax":"888","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008299","ARO_id":"47091","ARO_name":"KPC-173","CARD_short_name":"KPC-173","ARO_description":"Inhibitor-resistant extended-spectrum class A beta-lactamase KPC-173.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7718":{"model_id":"7718","model_name":"KPC-174","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10545":{"protein_sequence":{"accession":"WGW19928.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"OQ856773.1","fmin":"0","fmax":"879","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008300","ARO_id":"47092","ARO_name":"KPC-174","CARD_short_name":"KPC-174","ARO_description":"Inhibitor-resistant carbapenem-hydrolyzing class A beta-lactamase KPC-174.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7719":{"model_id":"7719","model_name":"KPC-175","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10546":{"protein_sequence":{"accession":"WGW19929.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"OQ856774.1","fmin":"0","fmax":"885","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008301","ARO_id":"47093","ARO_name":"KPC-175","CARD_short_name":"KPC-175","ARO_description":"Inhibitor-resistant extended-spectrum class A beta-lactamase KPC-175.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7720":{"model_id":"7720","model_name":"KPC-176","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10547":{"protein_sequence":{"accession":"WOE87885.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNPAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"OR687591.1","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACCCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008302","ARO_id":"47094","ARO_name":"KPC-176","CARD_short_name":"KPC-176","ARO_description":"Inhibitor-resistant carbapenem-hydrolyzing class A beta-lactamase KPC-176.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7721":{"model_id":"7721","model_name":"KPC-177","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10548":{"protein_sequence":{"accession":"WGW19920.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQNTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"OQ856765.1","fmin":"0","fmax":"921","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008303","ARO_id":"47095","ARO_name":"KPC-177","CARD_short_name":"KPC-177","ARO_description":"Inhibitor-resistant carbapenem-hydrolyzing class A beta-lactamase KPC-177.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7722":{"model_id":"7722","model_name":"KPC-178","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10549":{"protein_sequence":{"accession":"WGW18280.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAILGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKYSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"OQ926587.1","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCTAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGTACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008304","ARO_id":"47096","ARO_name":"KPC-178","CARD_short_name":"KPC-178","ARO_description":"Inhibitor-resistant class A beta-lactamase KPC-178.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7723":{"model_id":"7723","model_name":"KPC-179","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10550":{"protein_sequence":{"accession":"WIU89430.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNTAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"OR115556.1","fmin":"0","fmax":"885","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACACCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008305","ARO_id":"47097","ARO_name":"KPC-179","CARD_short_name":"KPC-179","ARO_description":"Class A beta-lactamase KPC-179.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7724":{"model_id":"7724","model_name":"KPC-180","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10551":{"protein_sequence":{"accession":"WJR95055.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDHWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"OR206047.1","fmin":"1","fmax":"883","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCACTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008306","ARO_id":"47098","ARO_name":"KPC-180","CARD_short_name":"KPC-180","ARO_description":"Inhibitor-resistant carbapenem-hydrolyzing class A beta-lactamase KPC-180.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7725":{"model_id":"7725","model_name":"KPC-181","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10552":{"protein_sequence":{"accession":"WKT28610.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSDAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"OR282795.1","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGATGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008307","ARO_id":"47099","ARO_name":"KPC-181","CARD_short_name":"KPC-181","ARO_description":"Carbapenem-hydrolyzing class A beta-lactamase KPC-181.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7726":{"model_id":"7726","model_name":"KPC-182","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10553":{"protein_sequence":{"accession":"WKT28611.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLAIEGLGVNGQ"},"dna_sequence":{"accession":"OR282796.1","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGATCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008308","ARO_id":"47100","ARO_name":"KPC-182","CARD_short_name":"KPC-182","ARO_description":"Carbapenem-hydrolyzing class A beta-lactamase KPC-182.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7727":{"model_id":"7727","model_name":"KPC-183","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10554":{"protein_sequence":{"accession":"WKT28615.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKYSKDDKYSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"OR282800.1","fmin":"0","fmax":"900","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGTACAGCAAGGATGACAAGTACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008309","ARO_id":"47101","ARO_name":"KPC-183","CARD_short_name":"KPC-183","ARO_description":"Carbapenem-hydrolyzing class A beta-lactamase KPC-183.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7728":{"model_id":"7728","model_name":"KPC-184","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10555":{"protein_sequence":{"accession":"WKT28616.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKYSDAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"OR282801.1","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGTACAGCGATGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008310","ARO_id":"47102","ARO_name":"KPC-184","CARD_short_name":"KPC-184","ARO_description":"Carbapenem-hydrolyzing class A beta-lactamase KPC-184.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7729":{"model_id":"7729","model_name":"KPC-185","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10556":{"protein_sequence":{"accession":"WLF01972.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARGTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYAANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"OR359279.1","fmin":"0","fmax":"879","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGGTACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGCGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008311","ARO_id":"47103","ARO_name":"KPC-185","CARD_short_name":"KPC-185","ARO_description":"Inhibitor-resistant extended-spectrum class A beta-lactamase KPC-185.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7730":{"model_id":"7730","model_name":"KPC-186","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10557":{"protein_sequence":{"accession":"WMI40670.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDATSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"OR466746.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCTACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008312","ARO_id":"47104","ARO_name":"KPC-186","CARD_short_name":"KPC-186","ARO_description":"Inhibitor-resistant extended-spectrum class A beta-lactamase KPC-186.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7731":{"model_id":"7731","model_name":"KPC-187","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10558":{"protein_sequence":{"accession":"WMI45073.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDHWELELNSAIPGDARYTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"OR466751.1","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCACTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCTATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008313","ARO_id":"47105","ARO_name":"KPC-187","CARD_short_name":"KPC-187","ARO_description":"Inhibitor-resistant class A beta-lactamase KPC-187.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7732":{"model_id":"7732","model_name":"KPC-188","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10559":{"protein_sequence":{"accession":"WMP15088.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"OR483145.1","fmin":"0","fmax":"906","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008314","ARO_id":"47106","ARO_name":"KPC-188","CARD_short_name":"KPC-188","ARO_description":"Inhibitor-resistant class A beta-lactamase KPC-188.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7733":{"model_id":"7733","model_name":"KPC-189","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10560":{"protein_sequence":{"accession":"WMQ58826.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSTIPGDARYTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"OR501577.1","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCACCATCCCAGGCGATGCGCGCTATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008315","ARO_id":"47107","ARO_name":"KPC-189","CARD_short_name":"KPC-189","ARO_description":"Extended-spectrum class A beta-lactamase KPC-189.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7734":{"model_id":"7734","model_name":"KPC-190","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10561":{"protein_sequence":{"accession":"WMQ75103.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARYTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTVNDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"OR499110.1","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCTATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGTAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008316","ARO_id":"47108","ARO_name":"KPC-190","CARD_short_name":"KPC-190","ARO_description":"Inhibitor-resistant class A beta-lactamase KPC-190.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7735":{"model_id":"7735","model_name":"KPC-191","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10562":{"protein_sequence":{"accession":"WMQ75104.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDAPTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"OR499111.1","fmin":"0","fmax":"879","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCCTACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008317","ARO_id":"47109","ARO_name":"KPC-191","CARD_short_name":"KPC-191","ARO_description":"Inhibitor-resistant class A beta-lactamase KPC-191.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7736":{"model_id":"7736","model_name":"KPC-192","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10563":{"protein_sequence":{"accession":"WMZ17075.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"OR529436.1","fmin":"0","fmax":"912","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008318","ARO_id":"47110","ARO_name":"KPC-192","CARD_short_name":"KPC-192","ARO_description":"Inhibitor-resistant carbapenem-hydrolyzing class A beta-lactamase KPC-192.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7737":{"model_id":"7737","model_name":"KPC-193","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10564":{"protein_sequence":{"accession":"WNH41912.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKANKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"OR568565.1","fmin":"0","fmax":"891","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008319","ARO_id":"47111","ARO_name":"KPC-193","CARD_short_name":"KPC-193","ARO_description":"Class A beta-lactamase KPC-193.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7738":{"model_id":"7738","model_name":"KPC-194","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10565":{"protein_sequence":{"accession":"WNI39959.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARYTSSLRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"OR578928.1","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCTATACCTCATCGCTGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008320","ARO_id":"47112","ARO_name":"KPC-194","CARD_short_name":"KPC-194","ARO_description":"Inhibitor-resistant extended-spectrum class A beta-lactamase KPC-194.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7739":{"model_id":"7739","model_name":"KPC-195","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10566":{"protein_sequence":{"accession":"WNR58177.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALDGLGVNGQ"},"dna_sequence":{"accession":"OR590804.1","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGATGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008321","ARO_id":"47113","ARO_name":"KPC-195","CARD_short_name":"KPC-195","ARO_description":"Carbapenem-hydrolyzing class A beta-lactamase KPC-195.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7740":{"model_id":"7740","model_name":"KPC-196","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10567":{"protein_sequence":{"accession":"WNV60940.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELELNSAIPGDARYTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"OR612035.1","fmin":"0","fmax":"888","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCTATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008322","ARO_id":"47114","ARO_name":"KPC-196","CARD_short_name":"KPC-196","ARO_description":"Inhibitor-resistant carbapenem-hydrolyzing class A beta-lactamase KPC-196.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7741":{"model_id":"7741","model_name":"KPC-197","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10568":{"protein_sequence":{"accession":"WOE87882.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELNSAIPGDERDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKYSDSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"OR633287.1","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGAACTCCGCCATCCCAGGCGATGAGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGTACAGCGACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008323","ARO_id":"47115","ARO_name":"KPC-197","CARD_short_name":"KPC-197","ARO_description":"Inhibitor-resistant extended-spectrum class A beta-lactamase KPC-197.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7742":{"model_id":"7742","model_name":"KPC-201","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10569":{"protein_sequence":{"accession":"USV27793.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKYSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"ON297687.1","fmin":"9","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGTACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008324","ARO_id":"47116","ARO_name":"KPC-201","CARD_short_name":"KPC-201","ARO_description":"Inhibitor-resistant extended-spectrum class A beta-lactamase KPC-201.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7743":{"model_id":"7743","model_name":"KPC-202","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10570":{"protein_sequence":{"accession":"WPM47153.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAANSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"OR839185.1","fmin":"0","fmax":"912","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008325","ARO_id":"47117","ARO_name":"KPC-202","CARD_short_name":"KPC-202","ARO_description":"Inhibitor-resistant carbapenem-hydrolyzing class A beta-lactamase KPC-202.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7744":{"model_id":"7744","model_name":"KPC-203","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10571":{"protein_sequence":{"accession":"MDY6716274.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPMLAVYTRAPNKDDKYSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"JAXHPW010000039.1","fmin":"3946","fmax":"4849","strand":"-","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTATGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGTACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008326","ARO_id":"47118","ARO_name":"KPC-203","CARD_short_name":"KPC-203","ARO_description":"Inhibitor-resistant extended-spectrum class A beta-lactamase KPC-203.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7745":{"model_id":"7745","model_name":"KPC-204","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10572":{"protein_sequence":{"accession":"WQQ44875.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"OR979533.1","fmin":"0","fmax":"891","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008327","ARO_id":"47119","ARO_name":"KPC-204","CARD_short_name":"KPC-204","ARO_description":"Inhibitor-resistant carbapenem-hydrolyzing class A beta-lactamase KPC-204.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7746":{"model_id":"7746","model_name":"KPC-205","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10573":{"protein_sequence":{"accession":"MEA1860518.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNNRAPNKDDKYSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"JAYEEW010000028.1","fmin":"8800","fmax":"9697","strand":"-","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAACCGGGCGCCTAACAAGGATGACAAGTACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008328","ARO_id":"47120","ARO_name":"KPC-205","CARD_short_name":"KPC-205","ARO_description":"Inhibitor-resistant class A beta-lactamase KPC-205.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7747":{"model_id":"7747","model_name":"KPC-206","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10574":{"protein_sequence":{"accession":"WQY95155.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTYSSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"PP051499.1","fmin":"0","fmax":"888","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTATTCCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3008329","ARO_id":"47121","ARO_name":"KPC-206","CARD_short_name":"KPC-206","ARO_description":"Inhibitor-resistant extended-spectrum class A beta-lactamase KPC-206.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7748":{"model_id":"7748","model_name":"KPC-207","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10575":{"protein_sequence":{"accession":"WRW33974.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELEQNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"PP125175.1","fmin":"0","fmax":"885","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCAGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008330","ARO_id":"47122","ARO_name":"KPC-207","CARD_short_name":"KPC-207","ARO_description":"Inhibitor-resistant extended-spectrum class A beta-lactamase KPC-207.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7749":{"model_id":"7749","model_name":"KPC-208","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10576":{"protein_sequence":{"accession":"WRW33975.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELEQNSAIPGDARYTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"PP125176.1","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCAGAACTCCGCCATCCCAGGCGATGCGCGCTATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008331","ARO_id":"47123","ARO_name":"KPC-208","CARD_short_name":"KPC-208","ARO_description":"Inhibitor-resistant extended-spectrum class A beta-lactamase KPC-208.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7750":{"model_id":"7750","model_name":"KPC-209","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10577":{"protein_sequence":{"accession":"WVD92252.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRATSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"PP165529.1","fmin":"5","fmax":"905","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008332","ARO_id":"47124","ARO_name":"KPC-209","CARD_short_name":"KPC-209","ARO_description":"Inhibitor-resistant extended-spectrum class A beta-lactamase KPC-209.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7751":{"model_id":"7751","model_name":"KPC-211","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10578":{"protein_sequence":{"accession":"WVD92244.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"PP194258.1","fmin":"0","fmax":"870","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008333","ARO_id":"47125","ARO_name":"KPC-211","CARD_short_name":"KPC-211","ARO_description":"Carbapenem-hydrolyzing class A beta-lactamase KPC-211.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7752":{"model_id":"7752","model_name":"KPC-212","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10579":{"protein_sequence":{"accession":"WVD92245.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDLWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"PP194259.1","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCTCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008334","ARO_id":"47126","ARO_name":"KPC-212","CARD_short_name":"KPC-212","ARO_description":"Carbapenem-hydrolyzing class A beta-lactamase KPC-212.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7753":{"model_id":"7753","model_name":"KPC-213","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10580":{"protein_sequence":{"accession":"WVD92246.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLGRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"PP194260.1","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGGCCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008335","ARO_id":"47127","ARO_name":"KPC-213","CARD_short_name":"KPC-213","ARO_description":"Inhibitor-resistant carbapenem-hydrolyzing class A beta-lactamase KPC-213.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7754":{"model_id":"7754","model_name":"KPC-214","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10581":{"protein_sequence":{"accession":"WVD92247.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDAHDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"PP194261.1","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCACGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008336","ARO_id":"47128","ARO_name":"KPC-214","CARD_short_name":"KPC-214","ARO_description":"Inhibitor-resistant carbapenem-hydrolyzing class A beta-lactamase KPC-214.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7755":{"model_id":"7755","model_name":"KPC-215","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10582":{"protein_sequence":{"accession":"WVD92249.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSASPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"PP194263.1","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCAGCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008337","ARO_id":"47129","ARO_name":"KPC-215","CARD_short_name":"KPC-215","ARO_description":"Inhibitor-resistant carbapenem-hydrolyzing class A beta-lactamase KPC-215.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7756":{"model_id":"7756","model_name":"KPC-216","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10583":{"protein_sequence":{"accession":"WWO49380.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELKNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKYSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"PP379169.1","fmin":"0","fmax":"885","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAAGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGTACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008338","ARO_id":"47130","ARO_name":"KPC-216","CARD_short_name":"KPC-216","ARO_description":"Inhibitor-resistant carbapenem-hydrolyzing class A beta-lactamase KPC-216.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7757":{"model_id":"7757","model_name":"KPC-217","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10584":{"protein_sequence":{"accession":"WZW61255.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSDIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKYSDAVIAAAARLALEGLGVTGQ"},"dna_sequence":{"accession":"PP693362.1","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGACATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGTACAGCGATGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCACGGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3008339","ARO_id":"47131","ARO_name":"KPC-217","CARD_short_name":"KPC-217","ARO_description":"Inhibitor-resistant class A beta-lactamase KPC-217.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7758":{"model_id":"7758","model_name":"KPC-218","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10585":{"protein_sequence":{"accession":"WZW61256.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAILGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKYSDAVIAAAARLALEGLGVTGQ"},"dna_sequence":{"accession":"PP693363.1","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCTAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGTACAGCGATGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCACGGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008340","ARO_id":"47132","ARO_name":"KPC-218","CARD_short_name":"KPC-218","ARO_description":"Inhibitor-resistant class A beta-lactamase KPC-218.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7759":{"model_id":"7759","model_name":"KPC-223","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10586":{"protein_sequence":{"accession":"WZW71004.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVFWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"PP701811.1","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCTTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008341","ARO_id":"47133","ARO_name":"KPC-223","CARD_short_name":"KPC-223","ARO_description":"Carbapenem-hydrolyzing class A beta-lactamase KPC-223.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7760":{"model_id":"7760","model_name":"KPC-224","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10587":{"protein_sequence":{"accession":"XAM88516.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELEQNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"PP728767.1","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCAGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008342","ARO_id":"47134","ARO_name":"KPC-224","CARD_short_name":"KPC-224","ARO_description":"Inhibitor-resistant carbapenem-hydrolyzing class A beta-lactamase KPC-224.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7761":{"model_id":"7761","model_name":"KPC-225","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10588":{"protein_sequence":{"accession":"XAM74258.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIHTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKYSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"PP723735.1","fmin":"0","fmax":"867","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGTACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3008343","ARO_id":"47135","ARO_name":"KPC-225","CARD_short_name":"KPC-225","ARO_description":"Inhibitor-resistant carbapenem-hydrolyzing class A beta-lactamase KPC-225.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7762":{"model_id":"7762","model_name":"KPC-226","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10589":{"protein_sequence":{"accession":"XAR02267.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"PP770481.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008344","ARO_id":"47136","ARO_name":"KPC-226","CARD_short_name":"KPC-226","ARO_description":"Inhibitor-resistant extended-spectrum class A beta-lactamase KPC-226.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7763":{"model_id":"7763","model_name":"KPC-227","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10590":{"protein_sequence":{"accession":"XAR02237.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARYTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"PP770482.1","fmin":"0","fmax":"891","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCTATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008345","ARO_id":"47137","ARO_name":"KPC-227","CARD_short_name":"KPC-227","ARO_description":"Inhibitor-resistant carbapenem-hydrolyzing class A beta-lactamase KPC-227.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7764":{"model_id":"7764","model_name":"KPC-228","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10591":{"protein_sequence":{"accession":"XBP46894.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"PP860922.1","fmin":"0","fmax":"870","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008346","ARO_id":"47138","ARO_name":"KPC-228","CARD_short_name":"KPC-228","ARO_description":"Inhibitor-resistant extended-spectrum class A beta-lactamase KPC-228.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7765":{"model_id":"7765","model_name":"KPC-230","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10592":{"protein_sequence":{"accession":"XCN99469.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDSWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"PP988013.1","fmin":"0","fmax":"900","strand":"-","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACAGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008347","ARO_id":"47139","ARO_name":"KPC-230","CARD_short_name":"KPC-230","ARO_description":"Inhibitor-resistant extended-spectrum class A beta-lactamase KPC-230.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7766":{"model_id":"7766","model_name":"KPC-231","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10593":{"protein_sequence":{"accession":"XFH17878.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNYAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKYSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"PQ117760.1","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTACGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGTACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008348","ARO_id":"47140","ARO_name":"KPC-231","CARD_short_name":"KPC-231","ARO_description":"Carbapenem-hydrolyzing class A beta-lactamase KPC-231.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7767":{"model_id":"7767","model_name":"KPC-232","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10594":{"protein_sequence":{"accession":"XFH17880.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDKPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKYSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"PQ117762.1","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACAAACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGTACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008349","ARO_id":"47141","ARO_name":"KPC-232","CARD_short_name":"KPC-232","ARO_description":"Carbapenem-hydrolyzing class A beta-lactamase KPC-232.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7768":{"model_id":"7768","model_name":"KPC-233","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10595":{"protein_sequence":{"accession":"XGD00488.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPIYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"PQ287843.1","fmin":"0","fmax":"900","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTATCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008350","ARO_id":"47142","ARO_name":"KPC-233","CARD_short_name":"KPC-233","ARO_description":"Inhibitor-resistant carbapenem-hydrolyzing class A beta-lactamase KPC-233.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7769":{"model_id":"7769","model_name":"KPC-234","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10596":{"protein_sequence":{"accession":"XHE66866.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARGTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVDGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"PQ311675.1","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGGTACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGGATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008351","ARO_id":"47143","ARO_name":"KPC-234","CARD_short_name":"KPC-234","ARO_description":"Inhibitor-resistant carbapenem-hydrolyzing class A beta-lactamase KPC-234.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7770":{"model_id":"7770","model_name":"KPC-236","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10597":{"protein_sequence":{"accession":"XHO32892.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQRAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"PQ394549.1","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCGGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008352","ARO_id":"47144","ARO_name":"KPC-236","CARD_short_name":"KPC-236","ARO_description":"Carbapenem-hydrolyzing class A beta-lactamase KPC-236.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7771":{"model_id":"7771","model_name":"KPC-237","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10598":{"protein_sequence":{"accession":"XHO32893.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"PQ394550.1","fmin":"0","fmax":"879","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008353","ARO_id":"47145","ARO_name":"KPC-237","CARD_short_name":"KPC-237","ARO_description":"Carbapenem-hydrolyzing class A beta-lactamase KPC-237.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7772":{"model_id":"7772","model_name":"KPC-238","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10599":{"protein_sequence":{"accession":"XHO32894.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGEYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKYSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"PQ394551.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGAGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGTACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008354","ARO_id":"47146","ARO_name":"KPC-238","CARD_short_name":"KPC-238","ARO_description":"Carbapenem-hydrolyzing class A beta-lactamase KPC-238.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7773":{"model_id":"7773","model_name":"KPC-239","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10600":{"protein_sequence":{"accession":"XHO32895.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGDGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKYSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"PQ394552.1","fmin":"0","fmax":"879","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGTACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008355","ARO_id":"47147","ARO_name":"KPC-239","CARD_short_name":"KPC-239","ARO_description":"Carbapenem-hydrolyzing class A beta-lactamase KPC-239.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7774":{"model_id":"7774","model_name":"KPC-240","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10601":{"protein_sequence":{"accession":"XHO32896.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWESAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKYSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"PQ394553.1","fmin":"0","fmax":"870","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGTACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008356","ARO_id":"47148","ARO_name":"KPC-240","CARD_short_name":"KPC-240","ARO_description":"Carbapenem-hydrolyzing class A beta-lactamase KPC-240.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7775":{"model_id":"7775","model_name":"KPC-241","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10602":{"protein_sequence":{"accession":"XHO32897.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"PQ394554.1","fmin":"0","fmax":"873","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTCTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008357","ARO_id":"47149","ARO_name":"KPC-241","CARD_short_name":"KPC-241","ARO_description":"Carbapenem-hydrolyzing class A beta-lactamase KPC-241.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7776":{"model_id":"7776","model_name":"KPC-242","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10603":{"protein_sequence":{"accession":"XHO32898.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARYTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"PQ394555.1","fmin":"0","fmax":"909","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCTATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008358","ARO_id":"47150","ARO_name":"KPC-242","CARD_short_name":"KPC-242","ARO_description":"Carbapenem-hydrolyzing class A beta-lactamase KPC-242.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7777":{"model_id":"7777","model_name":"KPC-47","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10604":{"protein_sequence":{"accession":"QEO76001.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSTIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGAANDYAVVWPTGRAPIVLAVYTRAPNKDDKYSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"MN422012.1","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCACCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCGCGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGTACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008359","ARO_id":"47151","ARO_name":"KPC-47","CARD_short_name":"KPC-47","ARO_description":"Inhibitor-resistant extended-spectrum class A beta-lactamase KPC-47.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7778":{"model_id":"7778","model_name":"KPC-48","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10605":{"protein_sequence":{"accession":"QEO76002.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELEPNSTIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKYSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"MN422013.1","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCCGAACTCCACCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGTACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008360","ARO_id":"47152","ARO_name":"KPC-48","CARD_short_name":"KPC-48","ARO_description":"Inhibitor-resistant extended-spectrum class A beta-lactamase KPC-48.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7779":{"model_id":"7779","model_name":"KPC-53","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10606":{"protein_sequence":{"accession":"QOS10027.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKYSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"CP058327.1","fmin":"64885","fmax":"65773","strand":"-","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGTACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008361","ARO_id":"47153","ARO_name":"KPC-53","CARD_short_name":"KPC-53","ARO_description":"Inhibitor-resistant extended-spectrum class A beta-lactamase KPC-53.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7780":{"model_id":"7780","model_name":"KPC-67","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10607":{"protein_sequence":{"accession":"QMU31921.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKDDKDDKYSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"MT809697.1","fmin":"37205","fmax":"38105","strand":"-","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGGATGACAAGGATGACAAGTACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008362","ARO_id":"47154","ARO_name":"KPC-67","CARD_short_name":"KPC-67","ARO_description":"Inhibitor-resistant carbapenem-hydrolyzing class A beta-lactamase KPC-67.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7781":{"model_id":"7781","model_name":"KPC-68","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10608":{"protein_sequence":{"accession":"QMU31938.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKYSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"MT809698.1","fmin":"12172","fmax":"13060","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGTACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008363","ARO_id":"47155","ARO_name":"KPC-68","CARD_short_name":"KPC-68","ARO_description":"Inhibitor-resistant extended-spectrum class A beta-lactamase KPC-68.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7782":{"model_id":"7782","model_name":"KPC-69","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10609":{"protein_sequence":{"accession":"QMU32012.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWGLELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKYSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"MT809700.1","fmin":"37224","fmax":"38112","strand":"-","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGGGCTGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGTACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008364","ARO_id":"47156","ARO_name":"KPC-69","CARD_short_name":"KPC-69","ARO_description":"Inhibitor-resistant extended-spectrum class A beta-lactamase KPC-69.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7783":{"model_id":"7783","model_name":"KPC-70","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10610":{"protein_sequence":{"accession":"QMU32028.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARYTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYARAPNKDDKYSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"MT809701.1","fmin":"37208","fmax":"38090","strand":"-","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCTATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACGCCCGGGCGCCTAACAAGGATGACAAGTACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008365","ARO_id":"47157","ARO_name":"KPC-70","CARD_short_name":"KPC-70","ARO_description":"Inhibitor-resistant extended-spectrum class A beta-lactamase KPC-70.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7784":{"model_id":"7784","model_name":"KPC-84","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10611":{"protein_sequence":{"accession":"QSE38127.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGPANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"MW657985.1","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCCCGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008366","ARO_id":"47158","ARO_name":"KPC-84","CARD_short_name":"KPC-84","ARO_description":"Inhibitor-resistant carbapenem-hydrolyzing class A beta-lactamase KPC-84.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7785":{"model_id":"7785","model_name":"KPC-85","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10612":{"protein_sequence":{"accession":"QTV25836.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSVIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKYSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"MW896839.1","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGTCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGTACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008367","ARO_id":"47159","ARO_name":"KPC-85","CARD_short_name":"KPC-85","ARO_description":"Carbapenem-hydrolyzing class A beta-lactamase KPC-85.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7786":{"model_id":"7786","model_name":"KPC-88","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10613":{"protein_sequence":{"accession":"QUR41144.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGYARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"MZ067231.1","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCTATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGCACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008368","ARO_id":"47160","ARO_name":"KPC-88","CARD_short_name":"KPC-88","ARO_description":"Inhibitor-resistant extended-spectrum class A beta-lactamase KPC-88.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7787":{"model_id":"7787","model_name":"KPC-89","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10614":{"protein_sequence":{"accession":"QWW21252.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGMANDYAVVWPTGRAPIVLAVYTRAPNKDDKYSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"MZ401141.1","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCATGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGTACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008369","ARO_id":"47161","ARO_name":"KPC-89","CARD_short_name":"KPC-89","ARO_description":"Carbapenem-hydrolyzing class A beta-lactamase KPC-89.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7788":{"model_id":"7788","model_name":"KPC-91","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10615":{"protein_sequence":{"accession":"QWW21254.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALLPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELNSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKYSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"MZ404505.1","fmin":"0","fmax":"882","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGCTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGAGCTGAACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGTACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008370","ARO_id":"47162","ARO_name":"KPC-91","CARD_short_name":"KPC-91","ARO_description":"Carbapenem-hydrolyzing class A beta-lactamase KPC-91.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7789":{"model_id":"7789","model_name":"KPC-92","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10616":{"protein_sequence":{"accession":"QXG83132.1","sequence":"MSLYRRLVLLSCLSWPLAGFSATALTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGFLAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAAAVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELDSAIPGDARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAVPADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKYSEAVIAAAARLALEGLGVNGQ"},"dna_sequence":{"accession":"MZ461464.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGTCACTGTATCGCCGTCTAGTTCTGCTGTCTTGTCTCTCATGGCCGCTGGCTGGCTTTTCTGCCACCGCGCTGACCAACCTCGTCGCGGAACCATTCGCTAAACTCGAACAGGACTTTGGCGGCTCCATCGGTGTGTACGCGATGGATACCGGCTCAGGCGCAACTGTAAGTTACCGCGCTGAGGAGCGCTTCCCACTGTGCAGCTCATTCAAGGGCTTTCTTGCTGCCGCTGTGCTGGCTCGCAGCCAGCAGCAGGCCGGCTTGCTGGACACACCCATCCGTTACGGCAAAAATGCGCTGGTTCCGTGGTCACCCATCTCGGAAAAATATCTGACAACAGGCATGACGGTGGCGGAGCTGTCCGCGGCCGCCGTGCAATACAGTGATAACGCCGCCGCCAATTTGTTGCTGAAGGAGTTGGGCGGCCCGGCCGGGCTGACGGCCTTCATGCGCTCTATCGGCGATACCACGTTCCGTCTGGACCGCTGGGAGCTGGACTCCGCCATCCCAGGCGATGCGCGCGATACCTCATCGCCGCGCGCCGTGACGGAAAGCTTACAAAAACTGACACTGGGCTCTGCACTGGCTGCGCCGCAGCGGCAGCAGTTTGTTGATTGGCTAAAGGGAAACACGACCGGCAACCACCGCATCCGCGCGGCGGTGCCGGCAGACTGGGCAGTCGGAGACAAAACCGGAACCTGCGGAGTGTATGGCACGGCAAATGACTATGCCGTCGTCTGGCCCACTGGGCGCGCACCTATTGTGTTGGCCGTCTACACCCGGGCGCCTAACAAGGATGACAAGTACAGCGAGGCCGTCATCGCCGCTGCGGCTAGACTCGCGCTCGAGGGATTGGGCGTCAACGGGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008371","ARO_id":"47163","ARO_name":"KPC-92","CARD_short_name":"KPC-92","ARO_description":"Inhibitor-resistant extended-spectrum class A beta-lactamase KPC-92.","ARO_category":{"36198":{"category_aro_accession":"3000059","category_aro_cvterm_id":"36198","category_aro_name":"KPC beta-lactamase","category_aro_description":"Klebsiella pneumoniae carbapenem resistant (KPC) beta-lactamases are notorious for their ability to efficiently hydrolyze carbapenems, unlike other Ambler Class A beta-lactamases.  There are currently 9 variants reported worldwide.  These enzymes were first isolated from Klebsiella pneumoniae strains in 2001 in the United States.  Hospital outbreaks have since been reported in Greece and Israel and KPC carrying strains are now endemic to New York facilities.  KPC-1 and KPC-2 have been shown to be identical and are now referred to as KPC-2.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7790":{"model_id":"7790","model_name":"LHK-7","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10617":{"protein_sequence":{"accession":"AAT46346.1","sequence":"MKKRITPFSRFASKGLFACSAGMLLVTVAHAANTAAAPAGMDAMVQTVMQAHQIPGMAIAIIQPGKTTYHNYGVASRETGQPVRETTLFEIGSLSKPFTALVAQRAETEGRIDLSAPASRYVAALRGSAFDRITLRQLGTYSAGGLPLQFPDNVTTPADVLAYYQHWQPVHPAGTTRLYSNPSIGLMGLAASQATGESFAGLLGTTVLHPLGMNSTYLQVPPEARSRYAMGYTAAGKAVRVSPGPLDEETYGVKSTTADMAGFLLAHMDPARSKGALQSALQQTRVPVYCAGQTRQGLGWESYQDWKNLDVLLAGNSNQMVFEPQPVKACPAGTMNDPDVWVNKTGSTAGFGAYAVFLPARQTGIVILANRNFPIADRIRLAHGILTALH"},"dna_sequence":{"accession":"AY632076.1","fmin":"0","fmax":"1173","strand":"+","sequence":"ATGAAAAAACGGATTACCCCATTTTCCCGCTTTGCATCAAAAGGCCTTTTCGCCTGTAGCGCAGGCATGTTGCTGGTGACGGTGGCACATGCTGCCAATACGGCAGCAGCACCAGCCGGCATGGATGCCATGGTACAAACCGTGATGCAGGCACACCAGATTCCGGGCATGGCCATTGCCATCATCCAGCCAGGAAAGACCACTTATCACAATTATGGTGTCGCCTCCCGCGAAACCGGCCAGCCGGTCCGGGAAACCACCCTGTTTGAAATCGGGTCCCTTTCCAAACCGTTTACTGCACTGGTCGCCCAGCGGGCTGAAACCGAAGGCCGGATTGACCTGTCTGCACCGGCCAGCCGCTACGTTGCCGCCCTGCGAGGCAGTGCATTCGACCGGATCACCCTCAGGCAGCTCGGTACTTATAGCGCAGGCGGATTACCGCTCCAGTTTCCTGACAATGTCACCACCCCGGCAGACGTGCTGGCTTATTACCAGCATTGGCAACCTGTCCATCCGGCAGGTACCACCCGGCTGTATTCCAATCCGAGCATTGGCCTGATGGGGCTGGCTGCCAGTCAGGCAACCGGAGAGTCCTTTGCCGGCCTGCTCGGGACAACGGTGCTGCACCCCCTCGGCATGAACTCGACCTATCTGCAAGTGCCCCCGGAGGCCCGTTCACGTTATGCCATGGGATATACCGCCGCCGGAAAAGCGGTCAGGGTCAGCCCCGGTCCGCTGGATGAGGAAACCTACGGCGTCAAGTCCACAACCGCAGACATGGCCGGATTTTTATTGGCGCATATGGACCCTGCGCGCAGCAAAGGTGCATTGCAGTCGGCATTACAGCAAACACGTGTACCGGTTTATTGCGCCGGACAGACCCGGCAAGGACTGGGCTGGGAAAGTTATCAAGACTGGAAAAACCTAGACGTGCTGCTGGCGGGAAATTCAAATCAAATGGTGTTTGAGCCGCAGCCGGTAAAAGCCTGTCCTGCCGGCACCATGAATGATCCTGATGTGTGGGTCAACAAGACCGGTTCTACTGCGGGATTCGGCGCTTATGCCGTATTCCTGCCTGCCCGACAGACCGGCATTGTCATCCTGGCCAACCGTAATTTCCCGATTGCAGACCGTATCCGGCTCGCTCACGGGATTTTGACCGCATTGCACTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41458","NCBI_taxonomy_name":"Laribacter hongkongensis","NCBI_taxonomy_id":"168471"}}}},"ARO_accession":"3008372","ARO_id":"47164","ARO_name":"LHK-7","CARD_short_name":"LHK-7","ARO_description":"Class C beta-lactamase LHK-7.","ARO_category":{"43878":{"category_aro_accession":"3005418","category_aro_cvterm_id":"43878","category_aro_name":"LHK beta-lactamase","category_aro_description":"LHK beta-lactamases are class C beta-lactamases found in Laribacter hongkongensis.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7791":{"model_id":"7791","model_name":"MIR-24","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10618":{"protein_sequence":{"accession":"UVW30759.1","sequence":"MMTKSLSCALLLSVASSAFAAPMSEKQLAEVVERTVTPLMNAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEIALGDPVAKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDTASLLRFYQNWQPQWKPGTTRLYANASLGLFGALAVKPSGMSYEQAMTTRVFKPLKLDHTWINVPKAEEAHYAWGYREGKAVHVSPGMLDAEAYGVKTNVKDMASWLIANMKPDSLQAPSLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVGGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILDALQ"},"dna_sequence":{"accession":"OP297847.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGACAAAATCCCTAAGCTGTGCCCTGCTGCTCAGCGTCGCCAGCTCTGCATTCGCCGCACCGATGTCCGAAAAACAGCTGGCTGAGGTGGTGGAACGTACCGTTACGCCGCTGATGAACGCGCAGGCCATTCCGGGTATGGCGGTGGCGGTAATTTATCAGGGTCAGCCACACTACTTTACCTTCGGTAAAGCCGATGTTGCGGCGAACAAACCCGTCACCCCGCAAACCCTGTTTGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTACTGGGCGGCGATGCCATTGCCCGGGGTGAAATAGCGCTGGGCGATCCGGTAGCAAAATACTGGCCTGAGCTCACGGGCAAGCAGTGGCAGGGCATTCGCATGCTGGATCTGGCAACCTACACCGCAGGCGGTCTGCCGTTACAGGTGCCGGATGAGGTCACGGATACCGCCTCTCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCGGGTACCACGCGTCTTTACGCTAACGCCAGCCTCGGTCTTTTTGGTGCGCTGGCGGTTAAACCTTCCGGCATGAGCTATGAGCAGGCCATGACGACGCGGGTCTTTAAACCCCTCAAGCTGGACCATACCTGGATTAACGTCCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGATACCGTGAGGGTAAAGCGGTCCACGTTTCGCCAGGGATGCTGGACGCGGAAGCCTATGGCGTAAAAACTAACGTGAAGGATATGGCGAGCTGGCTGATAGCCAACATGAAGCCGGATTCTCTTCAGGCTCCCTCACTCAAGCAAGGCATTGCTCTGGCGCAGTCTCGCTACTGGCGCGTGGGGGCCATGTATCAGGGGTTGGGCTGGGAGATGCTCAACTGGCCGGTCGATGCCAAAACCGTCGTCGGAGGCAGTGATAACAAGGTGGCGCTGGCACCATTGCCCGTGGCAGAAGTGAATCCACCCGCGCCGCCGGTTAAGGCCTCCTGGGTCCATAAAACAGGCTCGACGGGTGGGTTTGGCAGCTACGTGGCATTTATTCCTGAAAAGCAGCTCGGCATTGTGATGCTGGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCGTATCCTCGACGCGCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43769","NCBI_taxonomy_name":"Enterobacter roggenkampii","NCBI_taxonomy_id":"1812935"}}}},"ARO_accession":"3008373","ARO_id":"47165","ARO_name":"MIR-24","CARD_short_name":"MIR-24","ARO_description":"Cephalosporin-hydrolyzing class C beta-lactamase MIR-24.","ARO_category":{"36197":{"category_aro_accession":"3000058","category_aro_cvterm_id":"36197","category_aro_name":"MIR beta-lactamase","category_aro_description":"MIR beta-lactamases are plasmid-mediated beta-lactamases that confer resistance to oxyimino- and alpha-methoxy beta-lactams.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7792":{"model_id":"7792","model_name":"MIR-25","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10619":{"protein_sequence":{"accession":"UXG78561.1","sequence":"MMTKSLSCALLLSVASAAFAAPMSEKQLAEVVERTVTPLMNAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEIALGDPVAKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDTASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMSYEQAMTTRVFKPLKLDHTWINVPKAEEAHYAWGYREGKAVHVSPGMLDAEAYGVKTNVKDMASWLIANMKPDSLQAPSLKQGIAVAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVGGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQLGIVILANKSYPNPARVEAAYRILDALQ"},"dna_sequence":{"accession":"OP346114.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGACAAAATCCCTAAGCTGTGCCCTGCTGCTCAGCGTCGCCAGCGCTGCATTCGCCGCACCGATGTCCGAAAAACAGCTGGCTGAGGTGGTGGAACGTACCGTTACGCCGCTGATGAACGCGCAGGCCATTCCGGGTATGGCGGTGGCGGTAATTTATCAGGGTCAGCCACACTACTTTACCTTCGGTAAAGCCGATGTTGCGGCGAACAAACCCGTCACCCCGCAAACCCTGTTTGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTACTGGGCGGCGATGCCATTGCCCGGGGTGAAATAGCGCTGGGCGATCCGGTAGCAAAATACTGGCCTGAGCTCACGGGCAAGCAGTGGCAGGGCATTCGCATGCTGGATCTGGCAACCTATACCGCAGGCGGTCTGCCGTTACAGGTGCCGGATGAGGTCACGGATACCGCCTCTCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCGGGTACCACGCGTCTTTACGCTAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTCAAACCTTCCGGCATGAGCTATGAGCAGGCCATGACGACGCGGGTCTTTAAACCCCTCAAGCTGGACCATACCTGGATTAACGTCCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGATACCGTGAGGGTAAAGCGGTCCACGTTTCGCCAGGGATGCTGGACGCGGAAGCCTATGGCGTAAAAACTAACGTGAAGGATATGGCGAGCTGGCTGATAGCCAACATGAAGCCGGATTCTCTTCAGGCTCCCTCACTCAAGCAAGGCATTGCTGTGGCGCAGTCTCGCTACTGGCGCGTGGGGGCCATGTATCAGGGGTTGGGCTGGGAGATGCTCAACTGGCCGGTCGATGCCAAAACCGTCGTCGGAGGCAGTGATAACAAGGTGGCGCTGGCACCATTGCCCGTGGCAGAAGTGAATCCACCCGCGCCGCCGGTTAAGGCCTCCTGGGTCCATAAAACAGGCTCGACGGGTGGGTTTGGCAGCTACGTGGCATTTATTCCTGAAAAGCAGCTCGGCATTGTGATACTGGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCGTATCCTCGACGCGCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43769","NCBI_taxonomy_name":"Enterobacter roggenkampii","NCBI_taxonomy_id":"1812935"}}}},"ARO_accession":"3008374","ARO_id":"47166","ARO_name":"MIR-25","CARD_short_name":"MIR-25","ARO_description":"Cephalosporin-hydrolyzing class C beta-lactamase MIR-25.","ARO_category":{"36197":{"category_aro_accession":"3000058","category_aro_cvterm_id":"36197","category_aro_name":"MIR beta-lactamase","category_aro_description":"MIR beta-lactamases are plasmid-mediated beta-lactamases that confer resistance to oxyimino- and alpha-methoxy beta-lactams.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7793":{"model_id":"7793","model_name":"MIR-27","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10620":{"protein_sequence":{"accession":"HDT5730486.1","sequence":"MMTKSLSCALLLSVTSSAFAATMSEKQLAEVVERTVTPLMNAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEIALGDPVAKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDTASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMSYEQAMTTRVFKPLKLDHTWINVPKAEEAHYAWGYREGKAVHVSPGMLDAEAYGVKTNVKDMASWLIANMKPDSLEAPSLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVGGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILDALQ"},"dna_sequence":{"accession":"DAPAES010000003.1","fmin":"17177","fmax":"18323","strand":"-","sequence":"ATGATGACAAAATCCCTAAGCTGTGCCCTGCTGCTCAGCGTCACCAGCTCTGCATTCGCCGCAACGATGTCCGAAAAACAGCTGGCTGAGGTGGTGGAACGTACCGTTACGCCGCTGATGAACGCGCAGGCCATTCCGGGTATGGCGGTGGCGGTAATTTATCAGGGTCAGCCACACTACTTTACCTTCGGTAAAGCCGATGTTGCGGCGAACAAACCCGTCACCCCGCAAACCCTGTTTGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTACTGGGCGGCGATGCCATTGCCCGGGGTGAAATAGCGCTGGGCGATCCGGTAGCAAAATACTGGCCTGAGCTCACGGGCAAGCAGTGGCAGGGCATTCGCATGCTGGATCTGGCAACCTATACCGCAGGCGGTCTGCCGTTACAGGTGCCGGATGAGGTCACGGATACCGCCTCTCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCGGGTACCACGCGTCTTTACGCTAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTCAAACCTTCCGGCATGAGCTATGAGCAGGCCATGACGACGCGGGTCTTTAAACCCCTCAAGCTGGACCATACCTGGATTAACGTCCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGATACCGTGAGGGTAAAGCGGTCCACGTTTCGCCAGGGATGCTGGACGCGGAAGCCTATGGCGTAAAAACTAACGTGAAGGATATGGCGAGCTGGCTGATAGCCAACATGAAGCCGGATTCTCTTGAGGCTCCCTCACTCAAGCAAGGCATTGCTCTGGCGCAGTCTCGCTACTGGCGCGTGGGGGCTATGTATCAGGGGCTGGGCTGGGAGATGCTCAACTGGCCGGTCGATGCCAAAACCGTCGTCGGAGGCAGTGATAACAAGGTGGCGCTGGCACCATTGCCCGTGGCAGAAGTGAATCCACCCGCGCCGCCAGTCAAAGCCTCCTGGGTCCATAAAACAGGCTCGACGGGCGGGTTTGGCAGCTACGTGGCATTTATTCCTGAAAAGCAGCTCGGCATTGTGATGCTCGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCGTATCCTCGACGCGCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43769","NCBI_taxonomy_name":"Enterobacter roggenkampii","NCBI_taxonomy_id":"1812935"}}}},"ARO_accession":"3008375","ARO_id":"47167","ARO_name":"MIR-27","CARD_short_name":"MIR-27","ARO_description":"Cephalosporin-hydrolyzing class C beta-lactamase MIR-27.","ARO_category":{"36197":{"category_aro_accession":"3000058","category_aro_cvterm_id":"36197","category_aro_name":"MIR beta-lactamase","category_aro_description":"MIR beta-lactamases are plasmid-mediated beta-lactamases that confer resistance to oxyimino- and alpha-methoxy beta-lactams.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7794":{"model_id":"7794","model_name":"MIR-28","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10621":{"protein_sequence":{"accession":"MCK7256087.1","sequence":"MMTKSLSCALLLSVASSAFAAPMSEKQLAEVVERTVTPLMNAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEIALGDPAAKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDTASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMSYEQAMTTRVFKPLKLDHTWINVPKAEEAHYAWGYREGKAVHVSPGMLDAEAYGVKTNVKDMASWLIANMKPDSLQAPSLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVGGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILDALQ"},"dna_sequence":{"accession":"JAKMJR010000004.1","fmin":"472886","fmax":"474032","strand":"+","sequence":"ATGATGACAAAATCCCTAAGCTGTGCCCTGCTGCTCAGCGTCGCCAGCTCTGCATTCGCCGCACCGATGTCCGAAAAACAGCTGGCTGAGGTGGTGGAACGTACCGTTACGCCGCTGATGAACGCGCAGGCCATTCCGGGTATGGCGGTGGCGGTAATTTATCAGGGTCAGCCACACTACTTTACCTTCGGTAAAGCCGATGTTGCGGCGAACAAACCCGTCACCCCGCAAACCCTGTTTGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTACTGGGCGGCGATGCCATTGCCCGGGGTGAAATAGCGCTGGGCGATCCGGCAGCAAAATACTGGCCTGAGCTCACGGGCAAGCAGTGGCAGGGCATTCGCATGCTGGATCTGGCAACCTACACCGCAGGCGGTCTGCCGTTACAGGTGCCGGATGAGGTCACGGATACCGCCTCTCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAACCGGGCACCACGCGTCTTTACGCTAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTTAAACCTTCCGGCATGAGCTATGAGCAGGCCATGACGACGCGGGTCTTTAAACCCCTCAAGCTGGACCATACCTGGATTAACGTCCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGATACCGTGAGGGTAAAGCGGTCCACGTTTCGCCAGGGATGCTGGACGCGGAAGCCTATGGCGTAAAAACTAACGTGAAGGATATGGCGAGCTGGCTGATAGCCAACATGAAGCCGGATTCTCTTCAGGCTCCCTCACTCAAGCAAGGCATTGCTCTGGCGCAGTCTCGCTACTGGCGCGTGGGGGCCATGTATCAGGGGTTGGGCTGGGAGATGCTCAACTGGCCGGTCGATGCCAAAACCGTCGTCGGAGGCAGTGATAACAAGGTGGCGCTGGCACCATTGCCCGTGGCAGAAGTGAATCCACCCGCGCCGCCGGTCAAGGCCTCCTGGGTCCATAAAACAGGCTCGACGGGCGGGTTTGGCAGCTACGTGGCATTTATTCCTGAAAAGCAGCTCGGCATTGTGATGCTGGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCGTATCCTCGACGCGCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43769","NCBI_taxonomy_name":"Enterobacter roggenkampii","NCBI_taxonomy_id":"1812935"}}}},"ARO_accession":"3008376","ARO_id":"47168","ARO_name":"MIR-28","CARD_short_name":"MIR-28","ARO_description":"Cephalosporin-hydrolyzing class C beta-lactamase MIR-28.","ARO_category":{"36197":{"category_aro_accession":"3000058","category_aro_cvterm_id":"36197","category_aro_name":"MIR beta-lactamase","category_aro_description":"MIR beta-lactamases are plasmid-mediated beta-lactamases that confer resistance to oxyimino- and alpha-methoxy beta-lactams.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7795":{"model_id":"7795","model_name":"MIR-30","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10622":{"protein_sequence":{"accession":"QLC81076.1","sequence":"MMTKSLSCALLLSVTSAAFAAPMSETQLAEVVERTVTPLMNAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEIALGDPVAKYWPELTGKQWQSIRMLDLATYTAGGLPLQVPDEVTDTASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMSYEQAMTTRVFKPLKLDHTWINVPKAEEAHYAWGYREGKAVHVSPGMLDAEAYGVKTNVKDMASWVIANMKPDSLQAPSLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVGGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILDALQ"},"dna_sequence":{"accession":"CP058253.1","fmin":"414921","fmax":"416067","strand":"-","sequence":"ATGATGACAAAATCCCTAAGCTGTGCCCTGCTGCTCAGCGTCACCAGCGCTGCATTCGCCGCACCGATGTCCGAAACACAGCTGGCTGAGGTGGTGGAACGTACCGTTACGCCGCTGATGAACGCGCAGGCCATTCCGGGTATGGCGGTGGCGGTAATTTATCAGGGTCAGCCACACTACTTTACCTTCGGTAAAGCCGATGTTGCGGCGAACAAACCCGTCACCCCGCAAACCCTGTTTGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTACTGGGCGGCGATGCCATTGCCCGGGGTGAAATAGCGCTGGGCGATCCGGTAGCAAAATACTGGCCTGAGCTCACGGGCAAGCAGTGGCAGAGCATTCGCATGCTGGATCTGGCAACCTATACCGCAGGCGGTCTGCCGTTACAGGTGCCGGATGAGGTCACGGATACCGCCTCTCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCGGGCACCACGCGTCTTTACGCTAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTTAAACCTTCCGGCATGAGCTATGAGCAGGCCATGACGACGCGGGTCTTTAAACCCCTCAAGCTGGACCATACCTGGATTAACGTCCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGATACCGTGAGGGTAAAGCGGTCCACGTTTCGCCAGGGATGCTGGACGCGGAAGCCTATGGCGTAAAAACTAACGTGAAGGATATGGCGAGCTGGGTGATAGCCAACATGAAGCCGGATTCTCTTCAGGCTCCCTCACTCAAGCAAGGCATTGCTCTGGCGCAGTCTCGCTACTGGCGCGTGGGGGCTATGTATCAGGGGTTAGGCTGGGAGATGCTCAACTGGCCGGTCGATGCCAAAACCGTCGTCGGAGGCAGTGATAACAAGGTGGCGCTGGCACCATTGCCCGTGGCAGAAGTGAATCCACCCGCGCCGCCGGTTAAGGCCTCCTGGGTCCATAAAACAGGCTCGACGGGCGGGTTTGGCAGCTACGTGGCATTTATTCCTGAAAAGCAGCTCGGCATTGTGATGCTGGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCGTATCCTCGACGCGCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43769","NCBI_taxonomy_name":"Enterobacter roggenkampii","NCBI_taxonomy_id":"1812935"}}}},"ARO_accession":"3008377","ARO_id":"47169","ARO_name":"MIR-30","CARD_short_name":"MIR-30","ARO_description":"Cephalosporin-hydrolyzing class C beta-lactamase MIR-30.","ARO_category":{"36197":{"category_aro_accession":"3000058","category_aro_cvterm_id":"36197","category_aro_name":"MIR beta-lactamase","category_aro_description":"MIR beta-lactamases are plasmid-mediated beta-lactamases that confer resistance to oxyimino- and alpha-methoxy beta-lactams.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7796":{"model_id":"7796","model_name":"MIR-31","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10623":{"protein_sequence":{"accession":"XAJ73569.1","sequence":"MMTKSLSCALLLSVASAAFAAPMSEKQLAEVVERTVTPLMNAQAIPGMAVALIYQGQPHYFTFGRADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEVALGDPVAKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDTASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMSYEQAMTTRVFKPLKLDHTWINVPKAEEAHYAWGYREGKAVHVSPGMLDAEAYGVKTNVKDMASWVIANMKPDSLQAPSLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVGGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILDALQ"},"dna_sequence":{"accession":"PP740503.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGACAAAATCCCTAAGCTGTGCCCTGCTGCTCAGCGTCGCCAGCGCTGCATTCGCCGCACCGATGTCCGAAAAACAGCTGGCTGAGGTGGTGGAACGTACCGTTACGCCGCTGATGAACGCGCAGGCCATTCCGGGTATGGCGGTGGCGTTAATTTATCAGGGTCAGCCACACTACTTTACCTTCGGTAGAGCAGATGTTGCGGCGAACAAACCCGTCACCCCGCAAACCCTGTTTGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTACTGGGCGGCGATGCCATTGCCCGGGGTGAAGTAGCGCTGGGCGATCCGGTAGCAAAATACTGGCCTGAGCTCACGGGCAAGCAGTGGCAGGGCATTCGCATGCTGGATCTGGCAACCTATACCGCAGGCGGTCTGCCGTTACAGGTGCCGGATGAGGTCACGGATACCGCCTCTCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCGGGTACCACGCGTCTTTACGCTAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTTAAACCTTCCGGCATGAGCTATGAGCAGGCCATGACGACGCGGGTCTTTAAACCCCTCAAGCTGGACCATACCTGGATTAACGTCCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGATACCGTGAGGGTAAAGCGGTCCACGTTTCGCCAGGGATGCTGGACGCGGAAGCCTATGGCGTAAAAACTAACGTGAAGGATATGGCGAGCTGGGTGATAGCCAACATGAAGCCGGATTCTCTTCAGGCTCCCTCACTCAAGCAAGGCATTGCTCTGGCGCAGTCTCGCTACTGGCGCGTGGGGGCTATGTATCAGGGGTTGGGCTGGGAGATGCTCAACTGGCCGGTCGATGCCAAAACCGTCGTCGGAGGCAGTGATAACAAGGTGGCGCTGGCACCATTGCCCGTGGCAGAAGTGAATCCACCCGCACCGCCGGTCAAAGCCTCCTGGGTCCATAAAACAGGCTCGACGGGCGGGTTTGGCAGCTACGTGGCATTTATTCCTGAAAAGCAGCTCGGCATTGTGATGCTGGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCGTATCCTCGACGCGCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43769","NCBI_taxonomy_name":"Enterobacter roggenkampii","NCBI_taxonomy_id":"1812935"}}}},"ARO_accession":"3008378","ARO_id":"47170","ARO_name":"MIR-31","CARD_short_name":"MIR-31","ARO_description":"Cephalosporin-hydrolyzing class C beta-lactamase MIR-31.","ARO_category":{"36197":{"category_aro_accession":"3000058","category_aro_cvterm_id":"36197","category_aro_name":"MIR beta-lactamase","category_aro_description":"MIR beta-lactamases are plasmid-mediated beta-lactamases that confer resistance to oxyimino- and alpha-methoxy beta-lactams.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7797":{"model_id":"7797","model_name":"MIR-32","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10624":{"protein_sequence":{"accession":"XAJ73570.1","sequence":"MMTKSLSCALLLSVASSAFAAPMSEKQLAEVVERTVTPLMNAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGEAIARGEVALGDPVAKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDGVTDTASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMSYEQAMTTRVFKPLKLDHTWINVPKAEEAHYAWGYREGKAVHVSPGMLDAEAYGVKTNVKDMASWVIANMKPDSLQAPSLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVGGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILDALQ"},"dna_sequence":{"accession":"PP740504.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGACAAAATCCCTAAGCTGTGCCCTGCTGCTCAGCGTCGCCAGCTCTGCATTCGCCGCACCGATGTCCGAAAAACAGCTGGCTGAGGTGGTGGAACGTACCGTTACGCCGCTGATGAACGCGCAGGCCATTCCGGGTATGGCGGTGGCGGTAATTTATCAGGGTCAGCCACACTACTTTACCTTCGGTAAAGCCGATGTTGCGGCGAACAAACCCGTCACCCCGCAAACCCTGTTTGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTACTGGGCGGCGAAGCCATTGCCCGGGGTGAAGTAGCGCTGGGCGATCCGGTAGCAAAATACTGGCCTGAGCTCACGGGCAAGCAGTGGCAGGGCATTCGCATGCTGGATCTGGCAACCTATACCGCAGGCGGTCTGCCGTTACAGGTGCCGGATGGGGTCACGGATACCGCTTCTCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAACCGGGCACCACGCGTCTTTACGCTAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTTAAACCTTCCGGCATGAGCTATGAGCAGGCCATGACGACGCGGGTCTTTAAACCCCTCAAGCTGGACCATACCTGGATTAACGTCCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGATACCGTGAGGGTAAAGCGGTCCACGTTTCGCCAGGGATGCTGGACGCGGAAGCCTATGGCGTAAAAACTAACGTGAAGGATATGGCGAGCTGGGTGATAGCCAACATGAAGCCGGATTCTCTTCAGGCTCCCTCACTCAAGCAAGGCATTGCTCTGGCGCAGTCTCGCTACTGGCGCGTGGGGGCTATGTATCAGGGGTTGGGCTGGGAGATGCTCAACTGGCCGGTCGATGCCAAAACCGTCGTCGGAGGCAGTGATAACAAGGTGGCGCTGGCACCATTGCCCGTGGCAGAAGTGAATCCACCCGCGCCGCCGGTCAAGGCCTCCTGGGTCCATAAAACAGGCTCGACGGGCGGGTTTGGCAGCTACGTGGCATTTATTCCTGAAAAGCAGCTCGGCATTGTGATGCTGGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCGTATCCTCGACGCGCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43769","NCBI_taxonomy_name":"Enterobacter roggenkampii","NCBI_taxonomy_id":"1812935"}}}},"ARO_accession":"3008379","ARO_id":"47171","ARO_name":"MIR-32","CARD_short_name":"MIR-32","ARO_description":"Cephalosporin-hydrolyzing class C beta-lactamase MIR-32.","ARO_category":{"36197":{"category_aro_accession":"3000058","category_aro_cvterm_id":"36197","category_aro_name":"MIR beta-lactamase","category_aro_description":"MIR beta-lactamases are plasmid-mediated beta-lactamases that confer resistance to oxyimino- and alpha-methoxy beta-lactams.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7798":{"model_id":"7798","model_name":"MIR-33","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10625":{"protein_sequence":{"accession":"XAJ73571.1","sequence":"MMTKSLSCALLLSVTSSAFAAPMSEKQLAEVVERTVTPLMNAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEIALGDPVAKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDTASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMSYEQAMTTRVFKPLKLDHTWINVPKAEEAHYAWGYREGKAVHVSPGMLDAEAYGVKTNVKDMASWLIANMKPDSLQAPSLKKGIALAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVGGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILDALQ"},"dna_sequence":{"accession":"PP740505.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGACAAAATCCCTAAGCTGTGCCCTGCTGCTCAGCGTCACCAGCTCTGCATTCGCCGCACCGATGTCCGAAAAACAGCTGGCTGAGGTGGTGGAACGTACCGTTACGCCGCTGATGAACGCGCAGGCCATTCCGGGTATGGCGGTGGCGGTAATTTATCAGGGTCAGCCACACTACTTTACCTTCGGTAAAGCCGATGTTGCGGCGAACAAACCCGTCACCCCGCAAACCCTGTTTGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTACTGGGCGGCGATGCCATTGCCCGGGGTGAAATAGCGCTGGGCGATCCGGTAGCAAAATACTGGCCTGAGCTCACGGGCAAGCAGTGGCAGGGCATTCGCATGCTGGATCTGGCAACCTATACCGCAGGCGGTCTGCCGTTACAGGTGCCGGATGAGGTCACGGATACCGCCTCTCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCGGGCACCACGCGTCTTTACGCTAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTCAAACCTTCCGGCATGAGCTATGAGCAGGCCATGACGACGCGGGTCTTTAAACCCCTCAAGCTGGACCATACCTGGATTAACGTCCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGATACCGTGAGGGTAAAGCGGTCCACGTTTCGCCAGGGATGCTGGACGCGGAAGCCTATGGCGTAAAAACTAACGTGAAGGATATGGCGAGCTGGCTGATAGCCAACATGAAGCCGGATTCTCTTCAGGCTCCCTCACTCAAGAAAGGCATTGCTCTGGCGCAGTCTCGCTACTGGCGCGTGGGGGCTATGTATCAGGGGTTGGGCTGGGAGATGCTCAACTGGCCGGTCGATGCCAAAACCGTCGTCGGAGGCAGTGATAACAAGGTGGCGCTGGCACCATTGCCCGTGGCAGAAGTGAATCCACCCGCGCCGCCGGTCAAGGCCTCCTGGGTCCATAAAACAGGCTCGACGGGCGGGTTTGGCAGCTACGTGGCATTTATTCCTGAAAAGCAGCTCGGCATTGTGATGCTGGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCGTATCCTCGACGCGCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43769","NCBI_taxonomy_name":"Enterobacter roggenkampii","NCBI_taxonomy_id":"1812935"}}}},"ARO_accession":"3008380","ARO_id":"47172","ARO_name":"MIR-33","CARD_short_name":"MIR-33","ARO_description":"Cephalosporin-hydrolyzing class C beta-lactamase MIR-33.","ARO_category":{"36197":{"category_aro_accession":"3000058","category_aro_cvterm_id":"36197","category_aro_name":"MIR beta-lactamase","category_aro_description":"MIR beta-lactamases are plasmid-mediated beta-lactamases that confer resistance to oxyimino- and alpha-methoxy beta-lactams.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7799":{"model_id":"7799","model_name":"MIR-34","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10626":{"protein_sequence":{"accession":"XAJ73572.1","sequence":"MMTKSLSCALLLSVASSAFAAPMSEKQLAEVVERTVTPLMNAQAIPGMAVAVIYQGQPHYFTFGKADVTANKPVTPQTLFELGSISKTFTGVLGGDAIARGEIALGDPVAKYWPELTGKQWQSIRMLDLATYTAGGLPLQVPDEVTDTASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMSYEQAMTTRVFKPLKLDHTWINVPKAEEAHYAWGYREGKAVHVSPGMLDAEAYGVKTNVKDMASWVIANMKPDSLQAPSLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVDAKTVAGGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILDALQ"},"dna_sequence":{"accession":"PP740506.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGACAAAATCCCTAAGCTGTGCCCTGCTGCTCAGCGTCGCCAGTTCTGCATTCGCCGCACCGATGTCCGAAAAACAGCTGGCTGAGGTGGTGGAACGTACCGTTACGCCGCTGATGAACGCGCAGGCCATTCCGGGTATGGCGGTGGCGGTAATTTATCAGGGTCAGCCACACTACTTTACCTTCGGTAAAGCCGATGTTACGGCGAACAAACCCGTCACCCCGCAAACCCTGTTTGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTACTGGGCGGCGATGCCATTGCCCGGGGTGAAATAGCGCTGGGCGATCCGGTAGCAAAATACTGGCCTGAGCTCACGGGCAAGCAGTGGCAGAGCATTCGCATGCTGGATCTGGCAACCTATACCGCAGGCGGTCTGCCGTTACAGGTGCCGGATGAGGTCACGGATACCGCCTCTCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCGGGCACCACGCGTCTTTACGCTAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTCAAACCTTCCGGCATGAGCTATGAGCAGGCCATGACGACGCGGGTCTTTAAACCCCTCAAGCTGGACCATACCTGGATTAACGTCCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGATACCGTGAGGGTAAAGCGGTCCACGTTTCGCCAGGGATGCTGGACGCGGAAGCCTATGGCGTAAAAACTAACGTGAAGGATATGGCGAGCTGGGTGATAGCCAACATGAAGCCGGATTCTCTTCAGGCTCCCTCACTCAAGCAAGGCATTGCTCTGGCGCAGTCTCGCTACTGGCGCGTGGGGGCTATGTATCAGGGGTTGGGCTGGGAGATGCTCAACTGGCCGGTCGATGCCAAAACCGTCGCCGGAGGCAGTGATAACAAGGTGGCGCTGGCACCATTGCCCGTGGCAGAAGTGAATCCACCCGCACCGCCGGTCAAAGCCTCCTGGGTCCATAAAACAGGCTCGACGGGCGGGTTTGGCAGCTACGTGGCATTTATTCCTGAAAAGCAGCTCGGCATTGTGATGCTGGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCGTATCCTTGACGCGCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43769","NCBI_taxonomy_name":"Enterobacter roggenkampii","NCBI_taxonomy_id":"1812935"}}}},"ARO_accession":"3008381","ARO_id":"47173","ARO_name":"MIR-34","CARD_short_name":"MIR-34","ARO_description":"Cephalosporin-hydrolyzing class C beta-lactamase MIR-34.","ARO_category":{"36197":{"category_aro_accession":"3000058","category_aro_cvterm_id":"36197","category_aro_name":"MIR beta-lactamase","category_aro_description":"MIR beta-lactamases are plasmid-mediated beta-lactamases that confer resistance to oxyimino- and alpha-methoxy beta-lactams.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7800":{"model_id":"7800","model_name":"MIR-35","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10627":{"protein_sequence":{"accession":"XAJ73573.1","sequence":"MMTKSLSCALLLSVASAAFAAPMSEKQLAEVVERTVTPLMNAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEIALGDPVAKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDTASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMSYEQAMTTRVFKPLKLDHTWINVPKAEEAHYAWGYREGKAVHVSPGMLDAEAYGVKTNVKDMASWLIANMKPDSLEAPSLKQGIALAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVGGSDNKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILDALQ"},"dna_sequence":{"accession":"PP740507.1","fmin":"0","fmax":"1146","strand":"+","sequence":"ATGATGACAAAATCCCTAAGCTGTGCCCTGCTGCTCAGCGTCGCCAGCGCTGCATTCGCCGCACCGATGTCCGAAAAACAGCTGGCTGAGGTGGTGGAACGTACCGTTACGCCACTGATGAACGCGCAGGCCATTCCGGGTATGGCGGTGGCGGTAATTTATCAGGGTCAGCCACACTACTTTACCTTCGGTAAAGCCGATGTTGCGGCGAACAAACCCGTCACCCCGCAAACCCTGTTTGAGCTGGGCTCTATAAGTAAAACCTTCACCGGCGTACTGGGCGGCGATGCCATTGCCCGGGGTGAAATAGCGCTGGGCGATCCGGTAGCAAAATACTGGCCTGAGCTCACGGGCAAGCAGTGGCAGGGCATTCGCATGCTGGATCTGGCAACCTATACCGCAGGCGGTCTGCCGTTACAGGTGCCGGATGAGGTCACGGATACCGCCTCTCTGCTGCGCTTTTATCAAAACTGGCAGCCGCAGTGGAAGCCGGGCACCACGCGTCTTTACGCTAACGCCAGCATCGGTCTTTTTGGTGCGCTGGCGGTCAAACCTTCCGGCATGAGCTATGAGCAGGCCATGACGACGCGGGTCTTTAAACCCCTCAAGCTGGACCATACCTGGATTAACGTCCCGAAAGCGGAAGAGGCGCATTACGCCTGGGGATACCGTGAGGGTAAAGCGGTCCACGTTTCGCCAGGGATGCTGGACGCGGAAGCCTATGGCGTAAAAACTAACGTGAAGGATATGGCGAGCTGGCTGATAGCCAACATGAAGCCGGATTCTCTTGAGGCTCCCTCACTCAAGCAAGGCATTGCTCTGGCGCAGTCTCGCTACTGGCGCGTGGGGGCTATGTATCAGGGGCTGGGCTGGGAGATGCTCAACTGGCCGGTCGATGCCAAAACCGTCGTCGGAGGCAGTGATAACAAGGTGGCGCTGGCACCATTGCCCGTGGCAGAAGTGAATCCACCCGCGCCGCCGGTCAAGGCCTCCTGGGTCCATAAAACAGGCTCGACGGGCGGGTTTGGCAGCTACGTGGCATTTATTCCTGAAAAGCAGCTCGGCATTGTGATGCTGGCGAATAAAAGCTATCCGAACCCGGCACGCGTTGAGGCGGCATACCGTATCCTCGACGCGCTGCAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43769","NCBI_taxonomy_name":"Enterobacter roggenkampii","NCBI_taxonomy_id":"1812935"}}}},"ARO_accession":"3008382","ARO_id":"47174","ARO_name":"MIR-35","CARD_short_name":"MIR-35","ARO_description":"Cephalosporin-hydrolyzing class C beta-lactamase MIR-35.","ARO_category":{"36197":{"category_aro_accession":"3000058","category_aro_cvterm_id":"36197","category_aro_name":"MIR beta-lactamase","category_aro_description":"MIR beta-lactamases are plasmid-mediated beta-lactamases that confer resistance to oxyimino- and alpha-methoxy beta-lactams.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7801":{"model_id":"7801","model_name":"MOX-15","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10628":{"protein_sequence":{"accession":"QUW44775.1","sequence":"MQQRQSILWGALATLMWAGLAHAGDKAATDPLRPVVDASIRPLLKEHRIPGMAVAVLKDGKAHYFNYGVADRERAVGVSEQTLFEIGSVSKTLTATLGAYAVVQGGFELDDKASLFAPWLKGSAFDNITMGELATYSAGGLPLQFPEEVDSLEKMQAYYRQWTPAYSPGSHRQYANPSIGLFGYLAASSMKQPFDRLMEQTILPGLGLYHTYLTVPEQAMGHYAYGYSKEDKPIRVTPGMLADEAYGIKTSSADLLRFVKANISGVDNAAMQQAIDLTHQGQYAVGEMTQGLGWERYAYPVSEQTLLAGNSPAMIYNANPAAPAPAATGHPVLFNKTGSTNGFGAYVAFVPAKGIGIVMLANRNYPNEARIKAAHAILTKLAR"},"dna_sequence":{"accession":"MZ133817.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCAACAACGACAATCCATCCTGTGGGGCGCTCTGGCCACCCTGATGTGGGCCGGTCTGGCTCATGCCGGTGACAAGGCGGCGACCGATCCCCTGCGCCCCGTGGTGGATGCCAGCATCCGGCCGCTGCTCAAGGAGCACAGGATCCCGGGCATGGCGGTGGCCGTGCTCAAGGATGGCAAGGCCCACTATTTCAACTACGGTGTGGCCGATCGGGAGCGCGCAGTCGGTGTCAGCGAGCAGACCCTGTTCGAGATAGGCTCCGTGAGCAAGACCCTGACCGCGACGCTGGGGGCCTACGCCGTGGTGCAGGGGGGCTTCGAGCTCGATGACAAGGCGAGTCTGTTCGCCCCCTGGCTCAAGGGATCCGCCTTTGACAACATCACCATGGGGGAGCTGGCTACCTACAGCGCGGGCGGCTTGCCGCTGCAATTCCCCGAGGAGGTGGATTCGCTCGAGAAGATGCAGGCCTACTACCGCCAGTGGACCCCAGCCTACTCGCCGGGTTCCCATCGCCAGTACGCCAACCCCAGCATCGGGCTCTTTGGCTATCTGGCGGCGAGCAGCATGAAGCAGCCGTTCGATCGCCTGATGGAGCAGACGATCCTGCCGGGGCTTGGCCTGTACCATACCTACCTCACTGTGCCCGAGCAGGCCATGGGGCACTACGCCTACGGCTACTCGAAGGAGGACAAGCCCATCCGCGTCACTCCCGGCATGCTGGCGGACGAGGCCTACGGCATCAAGACCAGCTCGGCGGATCTGCTGCGCTTTGTGAAGGCGAACATCAGCGGGGTGGATAATGCGGCCATGCAGCAGGCCATCGACCTGACTCACCAGGGCCAGTATGCGGTGGGGGAGATGACCCAGGGACTGGGCTGGGAGCGTTACGCCTATCCCGTCAGCGAGCAGACGCTGCTGGCGGGCAACTCCCCGGCGATGATTTACAATGCCAACCCGGCGGCGCCCGCGCCCGCTGCAACAGGGCACCCTGTGCTCTTCAACAAGACCGGCTCGACCAACGGCTTCGGGGCCTATGTGGCCTTCGTGCCGGCCAAAGGGATTGGCATCGTCATGCTGGCCAATCGCAACTACCCCAACGAGGCGCGCATCAAGGCGGCCCACGCCATCCTGACGAAACTGGCCAGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36936","NCBI_taxonomy_name":"Aeromonas caviae","NCBI_taxonomy_id":"648"}}}},"ARO_accession":"3008383","ARO_id":"47175","ARO_name":"MOX-15","CARD_short_name":"MOX-15","ARO_description":"CMY-1\/MOX family class C beta-lactamase MOX-15.","ARO_category":{"36222":{"category_aro_accession":"3000083","category_aro_cvterm_id":"36222","category_aro_name":"MOX beta-lactamase","category_aro_description":"MOX beta-lactamases are plasmid-mediated AmpC-type beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7802":{"model_id":"7802","model_name":"MOX-16","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10629":{"protein_sequence":{"accession":"BDC77865.1","sequence":"MQQRQSILWGAVATLMWAGLAHAGEASPVDPLRPVVDASIQPLLKEHRIPGMAVAVLKDGKAHYFNYGVANRESGASVSEQTLFEIGSVSKTLTATLGAYAVVKGAMQLDDKASRHAPWLKGSVFDSITMGELATYSAGGLPLQFPEEVDSSEKMRAYYRQWAPVYSPGSHRQYSNPSIGLFGHLAASSLKQPFAQLMEQTLLPGLGMHHTYVNVPKQAMASYAYGYSKEDKPIRVNPGMLADEAYGIKTSSADLLAFVKANIGGVDDKALQQAISLTHKGHYSVGGMTQGLGWESYAYPVTEQTLLAGNSAKEILEVNPTAAPRESGSQVLFNKTGSSNGFGAYVAFVPARGIGIVMLANRNYPIPARVKAAHAILAQLAG"},"dna_sequence":{"accession":"LC659430.1","fmin":"0","fmax":"1149","strand":"+","sequence":"ATGCAACAACGACAATCCATCCTGTGGGGGGCCGTGGCCACCCTGATGTGGGCCGGTCTGGCCCATGCAGGTGAGGCTTCACCGGTCGATCCCCTGCGCCCCGTGGTGGATGCCAGCATCCAGCCGCTGCTCAAGGAGCACAGGATCCCGGGCATGGCGGTGGCCGTGCTCAAGGATGGCAAGGCCCACTATTTCAATTACGGGGTGGCCAACCGGGAGAGCGGGGCCAGCGTCAGCGAGCAGACCCTGTTCGAGATAGGATCCGTGAGCAAGACCCTGACTGCGACCCTGGGGGCCTATGCGGTGGTCAAGGGAGCGATGCAGCTGGATGACAAGGCGAGCCGGCACGCGCCCTGGCTCAAGGGATCCGTCTTTGACAGCATCACCATGGGGGAGCTTGCCACCTACAGCGCCGGAGGCCTGCCACTGCAATTCCCCGAGGAGGTGGATTCATCCGAGAAGATGCGCGCCTACTACCGCCAGTGGGCCCCTGTCTATTCGCCGGGCTCCCATCGCCAGTACTCCAACCCCAGCATAGGGCTGTTCGGCCACCTGGCGGCGAGCAGCCTGAAGCAGCCATTTGCCCAGTTGATGGAGCAGACCCTGCTGCCCGGGCTCGGCATGCACCACACCTATGTCAATGTGCCGAAGCAGGCCATGGCGAGTTATGCCTATGGCTATTCGAAAGAGGACAAGCCCATCCGGGTCAACCCTGGCATGCTGGCGGACGAGGCCTACGGCATCAAGACCAGCTCGGCGGATCTGCTCGCCTTCGTGAAGGCCAACATCGGCGGGGTTGATGACAAGGCGTTGCAGCAGGCCATCTCCCTGACCCACAAAGGGCATTACTCGGTAGGCGGGATGACCCAGGGGCTGGGTTGGGAGAGTTACGCCTATCCCGTCACCGAGCAGACATTGCTGGCGGGCAATTCGGCCAAGGAGATCCTCGAAGTCAATCCGACGGCGGCTCCCCGGGAGTCGGGGAGCCAGGTGCTCTTCAACAAGACCGGCTCGTCCAATGGCTTTGGCGCCTATGTGGCCTTCGTGCCGGCCAGGGGGATCGGCATCGTCATGCTGGCCAATCGCAACTATCCCATCCCGGCCAGGGTGAAGGCGGCCCACGCCATCCTGGCGCAGTTGGCCGGTTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36936","NCBI_taxonomy_name":"Aeromonas caviae","NCBI_taxonomy_id":"648"}}}},"ARO_accession":"3008384","ARO_id":"47176","ARO_name":"MOX-16","CARD_short_name":"MOX-16","ARO_description":"CMY-1\/MOX family class C beta-lactamase MOX-16.","ARO_category":{"36222":{"category_aro_accession":"3000083","category_aro_cvterm_id":"36222","category_aro_name":"MOX beta-lactamase","category_aro_description":"MOX beta-lactamases are plasmid-mediated AmpC-type beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7803":{"model_id":"7803","model_name":"MOX-17","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10630":{"protein_sequence":{"accession":"UUT29086.1","sequence":"MQQRQSILWGALATLMWAGLAHAGDKAATDPLRPVVDASIRPLLKEHRIPGMAVAVLKDGKAHYFNYGVADRERAVGVSEQTLFEIGSVSKPLTATLGAYAVVKGAMQLDDKASRHAPWLKGSAFDSITMGELATYSAGGLPLQFPEEVDSLEKMQAYYRQWTPAYSPGSHRQYSNPSIGLFGHLAASSMKQPFAQLMEQTLLPGLGLHHTYVNVPKQAMASYAYGYSKEDKPIRVSPGMLADEAYGIKTSSADLLRFVKANISGVDDKALQQAISLTHKGHYSVGGMTQGLGWESYAYPVSEQTLLAGNSPAMMAAPAPAAAGHPVLFNKTGSTSGFGAYVAFVPAKGIGIVMLANRNYPIPARVKAAHAILTQLAR"},"dna_sequence":{"accession":"OP142444.1","fmin":"0","fmax":"1137","strand":"+","sequence":"ATGCAACAACGACAATCCATCCTGTGGGGCGCTTTGGCCACCCTGATGTGGGCCGGTCTGGCTCATGCCGGTGACAAGGCGGCGACCGATCCCCTGCGCCCCGTGGTGGATGCCAGCATCCGGCCGCTGCTCAAGGAGCACAGGATCCCGGGCATGGCGGTGGCCGTGCTCAAGGATGGCAAGGCCCACTATTTCAACTACGGTGTGGCCGATCGGGAGCGCGCGGTCGGTGTCAGCGAGCAGACCCTGTTCGAGATAGGCTCCGTGAGCAAGCCCCTGACCGCGACCCTAGGAGCCTATGCGGTGGTCAAGGGAGCGATGCAACTGGATGACAAGGCGAGCCGGCACGCCCCCTGGCTCAAGGGATCCGCCTTTGACAGCATCACCATGGGGGAGCTGGCTACCTACAGCGCGGGCGGCTTGCCGCTGCAATTCCCCGAGGAGGTGGATTCGCTCGAGAAGATGCAGGCCTACTACCGCCAGTGGACCCCAGCCTACTCGCCGGGTTCCCATCGCCAGTACTCTAACCCCAGCATAGGGCTGTTCGGCCACCTGGCGGCGAGCAGCATGAAGCAGCCGTTTGCCCAGTTGATGGAGCAGACGCTCCTGCCGGGGCTTGGCCTGCACCACACCTATGTCAATGTGCCGAAGCAGGCCATGGCGAGTTATGCCTATGGCTATTCGAAAGAGGACAAGCCCATCAGGGTCAGCCCCGGCATGCTGGCGGACGAGGCCTACGGCATCAAGACCAGCTCGGCGGATCTGCTGCGCTTTGTGAAGGCCAACATCAGCGGGGTTGATGACAAGGCGTTGCAGCAGGCCATCTCCCTGACCCACAAAGGGCACTACTCGGTAGGCGGGATGACCCAGGGACTGGGTTGGGAGAGTTACGCCTATCCCGTCAGCGAGCAGACATTGCTGGCGGGCAACTCCCCGGCGATGATGGCGGCGCCCGCGCCCGCTGCGGCAGGGCACCCTGTGCTCTTCAACAAGACCGGCTCGACCAGCGGCTTCGGCGCCTATGTGGCCTTCGTGCCGGCCAAAGGGATCGGCATCGTCATGCTGGCCAACCGCAACTATCCTATCCCGGCCAGGGTGAAAGCGGCCCACGCCATCCTGACGCAACTGGCCAGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36936","NCBI_taxonomy_name":"Aeromonas caviae","NCBI_taxonomy_id":"648"}}}},"ARO_accession":"3008385","ARO_id":"47177","ARO_name":"MOX-17","CARD_short_name":"MOX-17","ARO_description":"CMY-1\/MOX family class C beta-lactamase MOX-17.","ARO_category":{"36222":{"category_aro_accession":"3000083","category_aro_cvterm_id":"36222","category_aro_name":"MOX beta-lactamase","category_aro_description":"MOX beta-lactamases are plasmid-mediated AmpC-type beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7804":{"model_id":"7804","model_name":"MOX-18","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10631":{"protein_sequence":{"accession":"BDS51123.1","sequence":"MQQRQSILWGAVATLMWAGLAHAGETSPIDPLRPVVDASIRPLLKEHRIPGMAVAVLKDGKAHYFNYGVADRERAVGVSEQTLFEIGSVSKPLTATLGAYAVVKGAMQLDDKASRHAPWLKGSAFDSITMGELATYSAGGLPLQFPEEVDSLEKMQAYYRQWTPAYSPGSHRQYSNPSIGLFGHLAASSLKQPFAQLMEQTLLPGLGLHHTYVNVPKQAMASYAYGYSKEDKPIRVSPGMLADEAYGIKTSSADLLRFVKANISGVDDKALQQAISLTHKGHYSVGGMTQGLGWESYAYPVSEQTLLAGNSAKVILEANPTAAPRESGSQMLFNKTGSTSGFGAYVAFVPAKGIGIVMLANRNYPIPARVKAAHAILTQLAR"},"dna_sequence":{"accession":"LC732553.1","fmin":"0","fmax":"1149","strand":"+","sequence":"ATGCAACAACGACAATCCATCCTGTGGGGGGCCGTGGCCACCCTGATGTGGGCCGGTCTGGCCCATGCAGGTGAGACTTCACCGATCGATCCCCTGCGCCCCGTGGTGGATGCCAGCATCCGGCCGCTGCTCAAGGAGCACAGGATCCCGGGCATGGCGGTGGCCGTGCTCAAGGATGGCAAGGCCCACTATTTCAACTACGGTGTGGCCGATCGGGAGCGCGCAGTCGGTGTCAGCGAGCAGACCCTGTTCGAGATAGGCTCCGTGAGCAAGCCCCTGACCGCGACCCTAGGAGCCTATGCGGTGGTCAAGGGAGCGATGCAACTGGATGACAAGGCGAGCCGGCACGCCCCCTGGCTCAAGGGATCCGCCTTTGACAGCATCACCATGGGGGAGCTGGCTACCTACAGCGCGGGCGGCTTGCCGCTGCAATTCCCCGAGGAGGTGGATTCGCTCGAGAAGATGCAGGCCTACTACCGCCAGTGGACCCCAGCCTACTCGCCGGGTTCCCATCGCCAGTACTCTAACCCCAGCATAGGGCTGTTCGGCCACCTGGCGGCGAGCAGCCTGAAGCAGCCGTTTGCCCAGTTGATGGAGCAGACGCTCCTGCCGGGGCTTGGCCTGCACCACACCTATGTCAATGTGCCGAAGCAGGCCATGGCGAGTTATGCCTATGGCTATTCGAAAGAGGACAAGCCCATCAGGGTCAGCCCCGGCATGCTGGCGGACGAGGCCTACGGCATCAAGACCAGCTCGGCGGATCTGCTGCGCTTTGTGAAGGCCAACATCAGCGGGGTTGATGACAAGGCGTTGCAGCAGGCCATCTCCCTGACCCACAAAGGGCACTACTCGGTAGGCGGGATGACCCAGGGACTGGGTTGGGAGAGTTACGCCTATCCCGTCAGCGAGCAGACATTGCTGGCGGGCAATTCGGCCAAGGTGATCCTCGAAGCCAATCCGACGGCGGCGCCCCGGGAGTCGGGGAGCCAGATGCTCTTCAACAAGACCGGCTCGACCAGCGGCTTCGGCGCCTATGTGGCCTTCGTGCCGGCCAAAGGGATCGGCATCGTCATGCTGGCCAACCGCAACTATCCTATCCCGGCCAGGGTGAAAGCAGCCCACGCCATCCTGACGCAACTGGCCAGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36936","NCBI_taxonomy_name":"Aeromonas caviae","NCBI_taxonomy_id":"648"}}}},"ARO_accession":"3008386","ARO_id":"47178","ARO_name":"MOX-18","CARD_short_name":"MOX-18","ARO_description":"CMY-1\/MOX family class C beta-lactamase MOX-18.","ARO_category":{"36222":{"category_aro_accession":"3000083","category_aro_cvterm_id":"36222","category_aro_name":"MOX beta-lactamase","category_aro_description":"MOX beta-lactamases are plasmid-mediated AmpC-type beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7805":{"model_id":"7805","model_name":"MOX-19","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10632":{"protein_sequence":{"accession":"BDS51124.1","sequence":"MQQRQSILWGALATLMWAGLAHAGDKAATDPLRPVVDASIRPLLKEHRIPGMAVAVLKDGKAHYFNYGVADRERAVGVSEQTLFEIGSVSKTLTATLGAYAVVQGGFELDDKASLFAPWLKGSAFDNITMGELATYSAGGLPLQFPEEVDSLEKMQAYYRQWTPAYSPGSHRQYANPSIGLFGYLAASSMKQPFDRLMEQTILPGLGLYHTYLNVPEQAMGHYAYGYSKEDKPIRVTPGMLADEAYGIKTSSADLLRFVKANISGVDNAAMQQAIDLTHQGQYAVGEMTQGLGWERYAYPVSEQTLLAGNSPAMIYNANPAVPAPAAAGHPVLFNKTGSTNGFGAYVAFVPAKGIGIVMLANRNYPNEARIKAAHAILTKLAR"},"dna_sequence":{"accession":"LC732554.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCAACAACGACAATCCATCCTGTGGGGCGCTCTGGCCACCCTGATGTGGGCCGGTCTGGCTCATGCCGGTGACAAGGCGGCGACCGATCCCCTGCGCCCCGTGGTGGATGCCAGCATCCGGCCGCTGCTCAAGGAACACAGGATCCCGGGCATGGCGGTGGCCGTGCTCAAGGATGGCAAGGCCCACTATTTCAACTACGGTGTGGCCGATCGGGAGCGCGCGGTCGGTGTCAGCGAGCAGACCCTGTTCGAGATAGGCTCCGTGAGCAAGACCCTGACCGCGACCCTGGGGGCCTACGCCGTGGTGCAGGGGGGCTTCGAGCTCGATGACAAGGCGAGTCTGTTCGCCCCCTGGCTCAAGGGATCCGCCTTTGACAACATCACCATGGGGGAGCTGGCTACCTACAGCGCGGGCGGCTTGCCGCTGCAATTCCCCGAGGAGGTGGATTCGCTCGAGAAGATGCAGGCCTACTACCGCCAGTGGACCCCAGCCTACTCGCCGGGTTCCCATCGCCAGTACGCCAACCCCAGCATCGGGCTCTTTGGCTATCTGGCGGCGAGCAGCATGAAGCAGCCGTTCGATCGCCTGATGGAGCAGACGATCCTGCCGGGGCTTGGCCTGTACCATACCTACCTCAATGTGCCCGAGCAGGCCATGGGGCACTACGCCTACGGCTACTCGAAGGAGGACAAGCCGATCCGCGTCACTCCCGGCATGCTGGCGGACGAGGCCTACGGCATCAAGACCAGCTCGGCGGATCTGCTGCGCTTTGTGAAGGCGAACATCAGCGGGGTGGATAATGCGGCCATGCAGCAGGCCATCGACCTGACTCACCAGGGCCAGTATGCGGTGGGGGAGATGACCCAGGGACTGGGCTGGGAGCGTTACGCCTATCCCGTCAGCGAGCAGACGCTGCTGGCGGGCAACTCCCCGGCGATGATTTACAATGCCAACCCGGCGGTGCCCGCGCCCGCTGCGGCAGGGCACCCTGTGCTCTTCAACAAGACCGGCTCGACCAACGGCTTCGGGGCCTATGTGGCCTTCGTGCCGGCCAAAGGGATTGGCATCGTCATGCTGGCCAATCGCAACTACCCCAACGAGGCGCGCATCAAGGCGGCTCACGCCATCCTGACGAAACTGGCCAGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36936","NCBI_taxonomy_name":"Aeromonas caviae","NCBI_taxonomy_id":"648"}}}},"ARO_accession":"3008387","ARO_id":"47179","ARO_name":"MOX-19","CARD_short_name":"MOX-19","ARO_description":"CMY-1\/MOX family class C beta-lactamase MOX-19.","ARO_category":{"36222":{"category_aro_accession":"3000083","category_aro_cvterm_id":"36222","category_aro_name":"MOX beta-lactamase","category_aro_description":"MOX beta-lactamases are plasmid-mediated AmpC-type beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7806":{"model_id":"7806","model_name":"MOX-20","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10633":{"protein_sequence":{"accession":"BDS51125.1","sequence":"MQQRQSILWGAVATLMWAGLAHAGETSPVDPLRPVVDASIRPLLKEHRIPGMAVAVLKDGKAHYFNYGVADRERAVGVSEQTLFEIGSVSKPLTATLGAYAVVKGAMQLDDKASRHAPWLKGSAFDSITMGELATYSAGGLPLQFPEEVDSLEKMQAYYRQWTPAYSPGSHRQYSNPSIGLFGHLAASSLKQPFAQLMEQTLLPGLGLHHTYVNVPKQAMASYAYGYSKEDKPIRVSPGMLADEAYGIKTSSADLLRFVKANISGVDDKALQQAISLTHKGHYSVGGMTQGLGWESYAYPVSEQTLLAGNSAKVILEANPTAAPRESGSQMLFNKTGSTSGFGAYVAFVPAKGIGIVMLANRNYPIPARVKAAHAILTQLAR"},"dna_sequence":{"accession":"LC732555.1","fmin":"0","fmax":"1149","strand":"+","sequence":"ATGCAACAACGACAATCCATCCTGTGGGGGGCCGTGGCCACCCTGATGTGGGCCGGTCTGGCCCATGCAGGTGAGACTTCACCGGTCGATCCCCTGCGCCCCGTGGTGGATGCCAGCATCCGGCCGCTGCTCAAGGAGCACAGGATTCCGGGCATGGCGGTGGCCGTGCTCAAGGATGGCAAGGCCCACTATTTCAACTACGGTGTGGCCGATCGGGAGCGCGCAGTCGGTGTCAGCGAGCAGACCCTGTTCGAGATAGGCTCCGTGAGCAAGCCCCTGACCGCGACCCTAGGAGCCTATGCGGTGGTCAAGGGAGCGATGCAACTGGATGACAAGGCGAGCCGGCACGCCCCCTGGCTCAAGGGATCCGCCTTTGACAGCATCACCATGGGGGAGCTGGCTACCTACAGCGCGGGCGGCTTGCCGCTGCAATTCCCCGAGGAGGTGGATTCGCTCGAGAAGATGCAGGCCTACTACCGCCAGTGGACCCCAGCCTACTCGCCGGGTTCCCATCGCCAGTACTCTAACCCCAGCATAGGGCTGTTCGGCCACCTGGCGGCGAGCAGCCTGAAGCAGCCGTTTGCCCAGTTGATGGAGCAGACGCTCCTGCCGGGGCTTGGCCTGCACCACACCTATGTCAATGTGCCGAAGCAGGCCATGGCGAGTTATGCCTATGGCTATTCGAAAGAGGACAAGCCCATCAGGGTCAGCCCCGGCATGCTGGCGGACGAGGCCTACGGCATCAAGACCAGCTCGGCGGATCTGCTGCGCTTTGTGAAGGCCAACATCAGCGGGGTTGATGACAAGGCGTTGCAGCAGGCCATCTCCCTGACCCACAAAGGGCACTACTCGGTAGGCGGGATGACCCAGGGACTGGGTTGGGAGAGTTACGCCTATCCCGTCAGCGAGCAGACATTGCTGGCGGGCAATTCGGCCAAGGTGATCCTCGAAGCCAATCCGACGGCGGCGCCCCGGGAGTCGGGGAGCCAGATGCTCTTCAACAAGACCGGCTCGACCAGCGGCTTCGGCGCCTATGTGGCCTTCGTGCCGGCCAAAGGGATCGGCATCGTCATGCTGGCCAACCGCAACTATCCTATCCCGGCCAGGGTGAAAGCGGCCCACGCCATCCTGACGCAACTGGCCAGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36936","NCBI_taxonomy_name":"Aeromonas caviae","NCBI_taxonomy_id":"648"}}}},"ARO_accession":"3008388","ARO_id":"47180","ARO_name":"MOX-20","CARD_short_name":"MOX-20","ARO_description":"CMY-1\/MOX family class C beta-lactamase MOX-20.","ARO_category":{"36222":{"category_aro_accession":"3000083","category_aro_cvterm_id":"36222","category_aro_name":"MOX beta-lactamase","category_aro_description":"MOX beta-lactamases are plasmid-mediated AmpC-type beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7807":{"model_id":"7807","model_name":"MOX-21","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10634":{"protein_sequence":{"accession":"BDS51126.1","sequence":"MQQRQSILWGALATLMWAGLAHAGDKAATDPLRPVVDASIRPLLKEHRIPGMAVAVLKDGKAHYFNYGVADRERAVGVSEQTLFEIGSVSKTLTATLGAYAVVQGGFELDDKASLFAPWLKGSAFDSITMGELATYSAGGLPLQFPEEVDSLEKMQAYYRQWTPAYSPGSHRQYSNPSIGLFGHLAASSMKQPFAQLMEQTLLPGLGLHHTYVNVPKQAMASYAYGYSKEDKPIRVSPGMLADEAYGIKTSSADLLRFVKANISGVDDKALQQAISLTHKGHYSVGGMTQGLGWESYAYPVSEQTLLAGNSAKVILEANPTAAPRESGSQMLFNKTGSTSGFGAYVAFVPAKGIGIAMLANRNYPIPARVKAAHAILTQLAR"},"dna_sequence":{"accession":"LC732556.1","fmin":"0","fmax":"1149","strand":"+","sequence":"ATGCAACAACGACAATCCATCCTGTGGGGCGCTCTGGCCACCCTGATGTGGGCCGGTCTGGCTCATGCCGGTGACAAGGCGGCGACCGATCCCCTGCGCCCCGTGGTGGATGCCAGCATCCGGCCGCTGCTCAAGGAGCACAGGATCCCGGGCATGGCGGTGGCGGTGCTGAAAGATGGCAAGGCCCACTATTTCAACTACGGTGTGGCTGATCGGGAGCGCGCGGTCGGTGTGAGCGAGCAGACCCTGTTCGAGATAGGCTCCGTGAGCAAGACCCTGACCGCGACGCTGGGGGCCTACGCCGTGGTGCAGGGGGGCTTCGAGCTCGATGACAAGGCGAGTCTGTTCGCCCCCTGGCTCAAGGGATCCGCCTTTGACAGCATCACCATGGGGGAGCTGGCTACCTACAGCGCGGGCGGCTTGCCGCTGCAATTCCCCGAGGAGGTGGATTCGCTCGAGAAGATGCAGGCCTACTACCGCCAGTGGACCCCAGCCTACTCGCCGGGTTCCCATCGCCAGTACTCTAACCCCAGCATAGGGCTGTTCGGCCACCTGGCGGCGAGCAGCATGAAGCAGCCGTTTGCCCAGTTGATGGAGCAGACGCTCCTGCCGGGGCTTGGCCTGCACCACACCTATGTCAATGTGCCGAAGCAGGCCATGGCGAGTTATGCCTATGGCTATTCGAAAGAGGACAAGCCCATCAGGGTCAGCCCCGGCATGCTGGCGGACGAGGCCTACGGCATCAAGACCAGCTCGGCGGATCTGCTGCGCTTTGTGAAGGCCAACATCAGCGGGGTTGATGACAAGGCGTTGCAGCAGGCCATCTCCCTGACCCACAAAGGGCACTACTCGGTAGGCGGGATGACCCAGGGACTGGGTTGGGAGAGTTACGCCTATCCCGTCAGCGAGCAGACATTGCTGGCGGGCAATTCGGCCAAGGTGATCCTCGAAGCCAATCCGACGGCGGCGCCCCGGGAGTCGGGGAGCCAGATGCTCTTCAACAAGACCGGCTCGACCAGCGGCTTCGGCGCCTATGTGGCCTTCGTGCCGGCCAAAGGGATCGGCATCGCCATGCTGGCCAACCGCAACTATCCTATCCCGGCCAGGGTGAAAGCGGCCCACGCCATCCTGACGCAACTGGCCAGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36936","NCBI_taxonomy_name":"Aeromonas caviae","NCBI_taxonomy_id":"648"}}}},"ARO_accession":"3008389","ARO_id":"47181","ARO_name":"MOX-21","CARD_short_name":"MOX-21","ARO_description":"CMY-1\/MOX family class C beta-lactamase MOX-21.","ARO_category":{"36222":{"category_aro_accession":"3000083","category_aro_cvterm_id":"36222","category_aro_name":"MOX beta-lactamase","category_aro_description":"MOX beta-lactamases are plasmid-mediated AmpC-type beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7808":{"model_id":"7808","model_name":"MOX-22","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10635":{"protein_sequence":{"accession":"BDT38927.1","sequence":"MQQRQSILWGALATLMWAGLAHAGETSPVDPLRPVVDASIRPLLKEHRIPGMAVAVLKDGKAHYFNYGVADRERAVGVSEQTLFEIGSVSKPLTATLGAYAVVKGAMQLDDKASRHAPWLKGSAFDSITMGELATYSAGGLPLQFPEEVDSLEKMQAYYRQWTPAYSPGSHRQYSNPSIGLFGHLAASSMKQPFAQLMEQTLLPGLGLHHTYVNVPKQAMASYAYGYSKEDKPIRVSPGMLADEAYGIKTSSADLLRFVKANISGVDDKALQQAISLTHKGHYSVGGMTQGLGWESYAYPVSEQTLLAGNSAKVILEANPTAAPRESGSQMLFNKTGSTSGFGAYVAFVPAKGIGIVMLANRNYPIPARVKAAHAILTQLAR"},"dna_sequence":{"accession":"LC733692.1","fmin":"0","fmax":"1149","strand":"+","sequence":"ATGCAACAACGACAATCCATCCTGTGGGGCGCTCTGGCCACCCTGATGTGGGCCGGTCTGGCCCATGCAGGTGAGACTTCACCGGTCGATCCCCTGCGCCCCGTGGTGGATGCCAGCATCCGGCCGCTGCTCAAGGAGCACAGGATCCCGGGCATGGCGGTGGCCGTGCTCAAGGATGGCAAGGCCCACTATTTCAACTACGGTGTGGCCGATCGGGAGCGCGCAGTCGGTGTCAGCGAGCAGACCCTGTTCGAGATAGGCTCCGTGAGCAAGCCCCTGACCGCGACCCTAGGAGCCTATGCGGTGGTCAAGGGAGCGATGCAACTGGATGACAAGGCGAGCCGGCACGCCCCCTGGCTCAAGGGATCCGCCTTTGACAGCATCACCATGGGGGAGCTGGCTACCTACAGCGCGGGCGGCTTGCCGCTGCAATTCCCCGAGGAGGTGGATTCGCTCGAGAAGATGCAGGCCTACTACCGCCAGTGGACCCCAGCCTACTCGCCGGGTTCCCATCGCCAGTACTCTAACCCCAGCATAGGGCTGTTCGGCCACCTGGCGGCGAGCAGCATGAAGCAGCCGTTTGCCCAGTTGATGGAGCAGACGCTCCTGCCGGGGCTTGGCCTGCACCACACCTATGTCAATGTGCCGAAGCAGGCCATGGCGAGTTATGCCTATGGCTATTCGAAAGAGGACAAGCCCATCAGGGTCAGCCCCGGCATGCTGGCGGACGAGGCCTACGGCATCAAGACCAGCTCGGCGGATCTGCTGCGCTTTGTGAAGGCCAACATCAGCGGGGTTGATGACAAGGCGTTGCAGCAGGCCATCTCCCTGACCCACAAAGGGCACTACTCGGTAGGCGGGATGACCCAGGGACTGGGTTGGGAGAGTTACGCCTATCCCGTCAGCGAGCAGACATTGCTGGCGGGCAATTCGGCCAAGGTGATCCTCGAAGCCAATCCGACGGCGGCGCCCCGGGAGTCGGGGAGCCAGATGCTCTTCAACAAGACCGGCTCGACCAGCGGCTTCGGCGCCTATGTGGCCTTCGTGCCGGCCAAAGGGATCGGCATCGTCATGCTGGCCAACCGCAACTATCCTATCCCGGCCAGGGTGAAAGCGGCCCACGCCATCCTGACGCAACTGGCCAGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36936","NCBI_taxonomy_name":"Aeromonas caviae","NCBI_taxonomy_id":"648"}}}},"ARO_accession":"3008390","ARO_id":"47182","ARO_name":"MOX-22","CARD_short_name":"MOX-22","ARO_description":"CMY-1\/MOX family class C beta-lactamase MOX-22.","ARO_category":{"36222":{"category_aro_accession":"3000083","category_aro_cvterm_id":"36222","category_aro_name":"MOX beta-lactamase","category_aro_description":"MOX beta-lactamases are plasmid-mediated AmpC-type beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7809":{"model_id":"7809","model_name":"MOX-23","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10636":{"protein_sequence":{"accession":"BDT38928.1","sequence":"MQQRQSILWGAVATLMWAGLAHAGETSPVDPLRPVVDASIQPLLKEHRIPGMAVAVLKDGKAHYFNYGVADRERAVGVSEQTLFEIGSVSKPLTATLGAYAVVKGAMQLDDKASLFAPWLKGSAFDSITMGELATYSAGGLPLQFPEEVDSLEKMQAYYRQWTPAYSPGSHRQYSNPSIGLFGHLAASSMKQPFAQLMEQTLLPGLGLHHTYVNVPKQAMASYAYGYSKEDKPIRVSPGMLADEAYGIKTSSADLLRFVKANISGVDDKALQQAISLTHKGHYSVGGMTQGLGWERYAYPVSEQTLLAGNSAKVILEANPTAAPRESGSQMLFNKTGSTSGFGAYVAFVPAKGIGIVMLANRNYPIPARVKAAHAILTQLAR"},"dna_sequence":{"accession":"LC733693.1","fmin":"0","fmax":"1149","strand":"+","sequence":"ATGCAACAACGACAATCCATCCTGTGGGGGGCCGTGGCCACCCTGATGTGGGCCGGTCTGGCCCATGCAGGTGAGACTTCACCGGTCGATCCCCTGCGCCCCGTGGTGGATGCCAGCATCCAGCCGCTGCTCAAGGAGCACAGGATCCCGGGCATGGCGGTGGCCGTGCTGAAAGATGGCAAGGCCCACTATTTCAACTACGGTGTGGCTGATCGGGAGCGCGCGGTCGGTGTCAGCGAGCAGACCCTGTTCGAGATAGGCTCCGTGAGCAAGCCCCTGACCGCGACCCTAGGAGCCTATGCGGTGGTCAAGGGAGCGATGCAACTGGATGACAAGGCGAGTCTGTTCGCCCCCTGGCTCAAGGGATCCGCCTTTGACAGCATCACCATGGGGGAGCTGGCTACCTACAGCGCGGGCGGCTTGCCGCTGCAATTCCCCGAGGAGGTTGATTCGCTCGAGAAGATGCAGGCCTACTACCGCCAGTGGACCCCAGCCTACTCGCCGGGTTCCCATCGCCAGTACTCTAACCCCAGCATAGGGCTGTTCGGCCACCTGGCGGCGAGCAGCATGAAGCAGCCGTTTGCCCAGTTGATGGAGCAGACGCTCCTGCCGGGGCTTGGCCTGCACCACACCTATGTCAATGTGCCGAAGCAGGCCATGGCGAGTTATGCCTATGGCTATTCGAAAGAGGACAAGCCCATCAGGGTCAGCCCCGGCATGCTGGCGGACGAGGCCTACGGCATCAAGACCAGCTCGGCGGATCTGCTGCGCTTTGTGAAGGCCAACATCAGCGGGGTTGATGACAAGGCGTTGCAGCAGGCCATCTCCCTGACCCACAAAGGGCACTACTCGGTAGGCGGGATGACCCAGGGACTGGGTTGGGAGCGTTACGCCTATCCCGTCAGCGAGCAGACATTGCTGGCGGGCAATTCGGCCAAGGTGATCCTCGAAGCCAATCCGACGGCGGCGCCCCGGGAGTCGGGGAGCCAGATGCTCTTCAACAAGACCGGCTCGACCAGCGGCTTCGGCGCCTATGTGGCCTTCGTGCCGGCCAAAGGGATCGGCATCGTCATGCTGGCCAACCGCAACTATCCTATCCCGGCCAGGGTGAAAGCGGCCCACGCCATCCTGACGCAACTGGCCAGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36936","NCBI_taxonomy_name":"Aeromonas caviae","NCBI_taxonomy_id":"648"}}}},"ARO_accession":"3008391","ARO_id":"47183","ARO_name":"MOX-23","CARD_short_name":"MOX-23","ARO_description":"CMY-1\/MOX family class C beta-lactamase MOX-23.","ARO_category":{"36222":{"category_aro_accession":"3000083","category_aro_cvterm_id":"36222","category_aro_name":"MOX beta-lactamase","category_aro_description":"MOX beta-lactamases are plasmid-mediated AmpC-type beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7810":{"model_id":"7810","model_name":"MOX-24","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10637":{"protein_sequence":{"accession":"BDT38929.1","sequence":"MQQRQSILWGALATLMWAGLAHAGDKAATDPLRPVVDASIRPLLKEHRIPGMAVAVLKDGKAHYFNYGVADRERAVGVSEQTLFEIGSVSKTLTATLGAYAVVQGSFELDDKASQFAPWLKGSAFDNITMGELATYSAGGLPLQFPEEVDSLEKMQAYYRQWTPAYSPGSHRQYANPSIGLFGYLAASSMKQPFDRLMEQTILPGLGLYHTYLNVPEQAMGHYAYGYSKEDKPIRVTPGMLADEAYGIKTSSADLLRFVKANISGVDNAAMQQAIDLTHQGQYAVGEMTQGLGWERYAYPVSEQTLLAGNSPAMIYNANPAAPAPAATGHPVLFNKTGSTNGFGAYVAFVPAKGIGVVMLANRNYPNEARIKAAHAILTQLAR"},"dna_sequence":{"accession":"LC733694.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCAACAACGACAATCCATCCTGTGGGGCGCTCTGGCCACCCTGATGTGGGCCGGTCTGGCTCATGCCGGTGACAAGGCGGCGACCGATCCCCTGCGCCCCGTGGTGGATGCCAGCATCCGGCCGCTGCTCAAGGAGCACAGGATCCCGGGCATGGCGGTGGCCGTGCTCAAGGATGGCAAGGCCCACTATTTCAACTACGGTGTGGCCGATCGGGAGCGCGCAGTCGGTGTCAGCGAGCAGACCCTGTTCGAGATAGGCTCCGTGAGCAAGACCCTGACCGCGACGCTGGGGGCCTACGCCGTGGTGCAGGGGAGCTTCGAGCTCGATGACAAGGCGAGTCAGTTCGCCCCCTGGCTCAAGGGATCCGCCTTTGACAACATCACCATGGGGGAGCTGGCTACCTACAGCGCGGGCGGCTTGCCGCTGCAATTCCCCGAGGAGGTGGATTCGCTCGAGAAGATGCAGGCCTACTACCGCCAGTGGACCCCAGCCTACTCGCCGGGTTCCCATCGCCAGTACGCCAACCCCAGCATCGGGCTCTTTGGCTATCTGGCGGCGAGCAGCATGAAGCAGCCGTTCGATCGCCTGATGGAGCAGACGATCCTGCCGGGGCTTGGCCTGTACCATACCTACCTCAATGTGCCCGAGCAGGCCATGGGGCACTACGCCTACGGCTACTCGAAGGAGGACAAGCCCATCCGCGTCACTCCCGGCATGCTGGCGGACGAGGCCTACGGCATCAAGACCAGCTCGGCGGATCTGCTGCGCTTTGTGAAGGCCAACATCAGCGGGGTGGATAATGCGGCCATGCAGCAGGCCATCGATCTGACTCACCAGGGCCAGTATGCGGTGGGGGAGATGACCCAGGGACTGGGCTGGGAGCGTTACGCCTATCCCGTCAGCGAGCAGACGCTTCTGGCGGGCAACTCCCCGGCGATGATTTACAATGCCAACCCGGCGGCGCCCGCGCCCGCTGCAACAGGGCACCCTGTGCTCTTCAACAAGACCGGCTCGACCAACGGCTTCGGGGCCTATGTTGCCTTCGTGCCGGCCAAAGGGATCGGCGTCGTCATGCTGGCCAATCGCAACTACCCCAACGAGGCGCGCATCAAGGCGGCCCACGCCATCCTGACGCAACTGGCCAGATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36936","NCBI_taxonomy_name":"Aeromonas caviae","NCBI_taxonomy_id":"648"}}}},"ARO_accession":"3008392","ARO_id":"47184","ARO_name":"MOX-24","CARD_short_name":"MOX-24","ARO_description":"CMY-1\/MOX family class C beta-lactamase MOX-24.","ARO_category":{"36222":{"category_aro_accession":"3000083","category_aro_cvterm_id":"36222","category_aro_name":"MOX beta-lactamase","category_aro_description":"MOX beta-lactamases are plasmid-mediated AmpC-type beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7811":{"model_id":"7811","model_name":"MOX-25","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10638":{"protein_sequence":{"accession":"BDT38930.1","sequence":"MQQRQSILWGALATLMWAGLAHAGDKAATDPLRPVVDASIRPLLKEHRIPGMAVAVLKDGKAHYFNYGVADRERAVGVSEQTLFEIGSVSKTLTATLGAYAVVQGGFELDDKASLFAPWLKGSAFDNITMGELATYSAGGLPLQFPEEVDSLEKMQAYYRQWTPAYSPGSHRQYANPSIGLFGYLAASSMKQPFDRLMEQTILPGLGLYHTYLNVPEQAMGHYAYGYSKEDKPIRVTPGMLADEAYGIKTSSADLLRFVKANISGVDNAAMQQAIDLTHQGQYAVGEMTQGLGWERYAYPVSEQTLLAGNSPAMIYNANPAAPAPAATGHPVLFNKTGSTNGFGAYVAFVPAKGIGVVMLANRNYPNEARIKAAHAILTQLAR"},"dna_sequence":{"accession":"LC733695.1","fmin":"0","fmax":"1152","strand":"+","sequence":"ATGCAACAACGACAATCCATCCTGTGGGGCGCTCTGGCCACCCTGATGTGGGCCGGTCTGGCTCATGCCGGTGACAAGGCGGCGACCGATCCCCTGCGCCCCGTGGTGGATGCCAGCATCCGGCCGCTACTCAAGGAGCACAGGATCCCGGGCATGGCGGTGGCCGTGCTCAAGGATGGCAAGGCCCACTATTTCAACTACGGTGTGGCCGATCGGGAGCGCGCGGTCGGTGTCAGCGAGCAGACCCTGTTCGAGATAGGCTCCGTGAGCAAGACCCTGACCGCGACGCTGGGGGCCTACGCCGTGGTGCAGGGGGGCTTCGAGCTCGATGACAAGGCGAGTCTGTTCGCCCCCTGGCTCAAGGGATCCGCCTTTGACAACATCACCATGGGGGAGCTGGCTACCTACAGCGCGGGCGGCTTGCCGCTGCAATTCCCCGAGGAGGTGGATTCGCTCGAGAAGATGCAGGCCTACTACCGCCAGTGGACCCCAGCCTACTCGCCGGGTTCCCATCGCCAGTACGCCAACCCCAGCATCGGGCTCTTTGGCTATCTGGCGGCGAGCAGCATGAAGCAGCCGTTCGATCGCCTGATGGAGCAGACGATCCTGCCGGGGCTTGGCCTGTACCATACCTACCTCAATGTGCCCGAGCAGGCCATGGGGCACTACGCCTACGGCTACTCGAAGGAGGACAAGCCCATCCGCGTCACTCCCGGCATGCTGGCGGACGAGGCCTACGGCATCAAGACCAGCTCGGCGGATCTGCTGCGCTTTGTGAAGGCCAACATCAGCGGGGTGGATAATGCGGCCATGCAGCAGGCCATCGATCTGACTCACCAGGGCCAGTATGCGGTGGGGGAGATGACCCAGGGACTGGGCTGGGAGCGTTACGCCTATCCCGTCAGCGAGCAGACGCTGCTGGCGGGCAACTCCCCGGCGATGATTTACAATGCCAACCCGGCGGCGCCCGCGCCCGCTGCAACAGGGCACCCTGTGCTCTTCAACAAGACCGGCTCGACCAACGGCTTCGGGGCCTATGTGGCCTTCGTGCCGGCCAAAGGGATCGGCGTCGTCATGCTGGCCAATCGCAACTACCCCAACGAGGCGCGCATCAAGGCGGCCCACGCCATCCTGACGCAACTGGCCAGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36936","NCBI_taxonomy_name":"Aeromonas caviae","NCBI_taxonomy_id":"648"}}}},"ARO_accession":"3008393","ARO_id":"47185","ARO_name":"MOX-25","CARD_short_name":"MOX-25","ARO_description":"CMY-1\/MOX family class C beta-lactamase MOX-25.","ARO_category":{"36222":{"category_aro_accession":"3000083","category_aro_cvterm_id":"36222","category_aro_name":"MOX beta-lactamase","category_aro_description":"MOX beta-lactamases are plasmid-mediated AmpC-type beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7812":{"model_id":"7812","model_name":"MUN-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10639":{"protein_sequence":{"accession":"WVP99768.1","sequence":"MKQKVPLSKMNMTKTLLSVMLCCCCSIMAFGQNMTQEIEKIIKGKQASVGVAIIHNDDIIAIANEDKYPTMSVFKFHIAVTALKKMEAENIPLDKMVYIKQKEMLKNTYSPLRDKYPDQGIRISYRDIIKYTVSISDNNTCDWLIRFVGGIDKVDSYIKSLGIKDMNFTETEESMHTDIMLCYNNWSTPLAIAQLLKKLHTENILTKEHFAFLETAMLDCVSGKNKLIAGLPTDIKFGHKTGRSNRTADGIQISEGDAGVIYLPNGEKCYIVVLIKDSRESDDDNAKIMADISNIVYRHLNK"},"dna_sequence":{"accession":"PP229523.1","fmin":"0","fmax":"909","strand":"+","sequence":"ATGAAACAAAAAGTTCCACTATCAAAAATGAACATGACAAAAACGCTATTATCAGTTATGCTTTGTTGCTGTTGCAGCATTATGGCTTTCGGGCAGAACATGACCCAAGAAATTGAAAAGATTATCAAAGGGAAGCAAGCGTCTGTCGGGGTAGCAATTATCCATAATGACGATATAATTGCCATTGCCAACGAGGACAAATATCCCACTATGAGTGTATTCAAATTCCATATAGCAGTGACAGCTCTGAAAAAAATGGAAGCAGAGAATATTCCGCTGGACAAAATGGTGTATATCAAACAGAAAGAAATGCTGAAAAACACGTATAGCCCGTTAAGGGATAAATATCCCGACCAAGGGATTCGTATATCTTATAGGGATATAATCAAATACACAGTATCGATTAGCGACAACAACACATGCGATTGGTTAATAAGGTTTGTTGGTGGTATTGATAAAGTGGACTCCTACATAAAATCTCTTGGGATAAAGGATATGAATTTCACGGAGACAGAGGAAAGCATGCATACGGACATTATGTTATGCTACAACAATTGGAGCACACCATTAGCTATTGCGCAATTGCTCAAGAAACTTCATACAGAAAATATTTTGACAAAAGAGCATTTTGCGTTTTTAGAGACAGCCATGCTTGATTGTGTGTCTGGCAAGAACAAACTAATAGCGGGGTTGCCTACCGATATAAAATTTGGGCATAAAACGGGACGTTCTAACCGAACTGCTGATGGCATACAGATAAGCGAGGGAGATGCAGGAGTGATATATCTTCCCAACGGTGAGAAGTGCTACATTGTCGTTTTGATAAAGGATTCTCGTGAGTCTGATGATGATAACGCCAAAATAATGGCAGATATATCAAATATAGTTTATCGTCATTTGAATAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3008394","ARO_id":"47186","ARO_name":"MUN-1","CARD_short_name":"MUN-1","ARO_description":"MUN family extended-spectrum class A beta-lactamase MUN-1.","ARO_category":{"46662":{"category_aro_accession":"3007871","category_aro_cvterm_id":"46662","category_aro_name":"MUN beta-lactamase","category_aro_description":"MUN is a family of extended-spectrum class A beta-lactamases which enzymatic inactivate beta-lactam and cephalosporin antibiotics.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7813":{"model_id":"7813","model_name":"MUN-6","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10640":{"protein_sequence":{"accession":"UVR94859.1","sequence":"MKQKVPLSKMNMTKTLLSVMLCCCCSIMAFGQNMTQEIEKIIKGKQASVGVAIIHNDDIIAIANEDKYPTMSVFKFHIAVTALKKMEAENIPLDKMVYIKQKEMLKNTYSPLRDKYPDQGIRISYRDIIKYTVSISDNNTCDWLIRFVGGIDKVDSYIKSLGIKDMNFTETEESMLTDIMLCYNNWSTPLAIAQLLKKLHTENILTKEHFAFLETAMLDCVSGKNKLIAGLPTDIKFGHKTGRSNRTADGIQISEGDAGVIYLPNGEKCYIVVLIKDSRESDDDNAKIMADISNIVYRHLNK"},"dna_sequence":{"accession":"CP103256.1","fmin":"3726857","fmax":"3727766","strand":"-","sequence":"ATGAAACAAAAAGTTCCACTATCAAAAATGAACATGACAAAAACGCTATTATCAGTTATGCTTTGTTGCTGTTGCAGCATTATGGCTTTCGGGCAGAACATGACCCAAGAAATTGAAAAGATTATCAAAGGGAAGCAAGCGTCTGTCGGGGTAGCAATTATCCATAATGACGATATAATTGCCATTGCCAACGAGGACAAATATCCCACTATGAGTGTATTCAAATTCCATATAGCAGTGACAGCTCTGAAAAAAATGGAAGCAGAGAATATTCCGCTGGACAAAATGGTGTATATCAAACAGAAAGAAATGCTGAAAAACACGTATAGCCCGTTAAGGGATAAATATCCCGACCAAGGGATTCGTATATCTTATAGGGATATAATCAAATACACAGTATCGATTAGCGACAACAACACATGCGATTGGTTAATAAGGTTTGTTGGTGGTATTGATAAAGTGGACTCCTACATAAAATCTCTTGGGATAAAGGATATGAATTTCACGGAGACAGAGGAAAGCATGCTTACGGACATTATGTTATGCTACAACAATTGGAGCACACCATTAGCTATTGCGCAATTGCTCAAGAAACTTCATACAGAAAATATTTTGACAAAAGAGCATTTTGCGTTTTTAGAGACAGCCATGCTTGATTGTGTGTCTGGCAAGAACAAACTAATAGCGGGGTTGCCTACCGATATAAAATTTGGGCATAAAACGGGACGTTCTAACCGAACTGCTGATGGCATACAGATAAGCGAGGGAGATGCAGGAGTGATATATCTTCCCAACGGTGAGAAGTGCTACATTGTCGTTTTGATAAAGGATTCTCGTGAGTCTGATGATGATAACGCCAAAATAATGGCAGATATATCAAATATAGTTTATCGTCATTTGAATAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39660","NCBI_taxonomy_name":"Parabacteroides distasonis","NCBI_taxonomy_id":"823"}}}},"ARO_accession":"3008395","ARO_id":"47187","ARO_name":"MUN-6","CARD_short_name":"MUN-6","ARO_description":"MUN family extended-spectrum class A beta-lactamase MUN-6.","ARO_category":{"46662":{"category_aro_accession":"3007871","category_aro_cvterm_id":"46662","category_aro_name":"MUN beta-lactamase","category_aro_description":"MUN is a family of extended-spectrum class A beta-lactamases which enzymatic inactivate beta-lactam and cephalosporin antibiotics.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7814":{"model_id":"7814","model_name":"NDM-48","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10641":{"protein_sequence":{"accession":"UZC76860.1","sequence":"MELPNIMHPVAKLSTALAAALMLSGCMHGEIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLLVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGLVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR"},"dna_sequence":{"accession":"OP696902.1","fmin":"0","fmax":"813","strand":"+","sequence":"ATGGAATTGCCCAATATTATGCACCCGGTCGCGAAGCTGAGCACCGCATTAGCCGCTGCATTGATGCTGAGCGGGTGCATGCACGGTGAAATCCGCCCGACGATTGGCCAGCAAATGGAAACTGGCGACCAACGGTTTGGCGATCTGGTTTTCCGCCAGCTCGCACCGAATGTCTGGCAGCACACTTCCTATCTCGACATGCCGGGTTTCGGGGCAGTCGCTTCCAACGGTTTGATCGTCAGGGATGGCGGCCGCGTGCTGTTGGTCGATACCGCCTGGACCGATGACCAGACCGCCCAGATCCTCAACTGGATCAAGCAGGAGATCAACCTGCCGGTCGCGCTGGCGGTGGTGACTCACGCGCATCAGGACAAGATGGGCGGTATGGACGCGCTGCATGCGGCGGGGATTGCGACTTATGCCAATGCGTTGTCGAACCAGCTTGCCCCGCAAGAGGGGCTGGTTGCGGCGCAACACAGCCTGACTTTCGCCGCCAATGGCTGGGTCGAACCAGCAACCGCGCCCAACTTTGGCCCGCTCAAGGTATTTTACCCCGGCCCCGGCCACACCAGTGACAATATCACCGTTGGGATCGACGGCACCGACATCGCTTTTGGTGGCTGCCTGATCAAGGACAGCAAGGCCAAGTCGCTCGGCAATCTCGGTGATGCCGACACTGAGCACTACGCCGCGTCAGCGCGCGCGTTTGGTGCGGCGTTCCCCAAGGCCAGCATGATCGTGATGAGCCATTCCGCCCCCGATAGCCGCGCCGCAATCACTCATACGGCCCGCATGGCCGACAAGCTGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3008396","ARO_id":"47188","ARO_name":"NDM-48","CARD_short_name":"NDM-48","ARO_description":"Subclass B1 metallo-beta-lactamase NDM-48.","ARO_category":{"36196":{"category_aro_accession":"3000057","category_aro_cvterm_id":"36196","category_aro_name":"NDM beta-lactamase","category_aro_description":"NDM beta-lactamases or New Delhi metallo-beta-lactamases are class B beta-lactamases that confer resistance to a broad range of antibiotics including carbapenems, cephalosporins and penicillins.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7815":{"model_id":"7815","model_name":"NDM-49","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10642":{"protein_sequence":{"accession":"WAS27907.1","sequence":"MELPNIMHPVAKLSTALAAALMLSGCMPGEIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLLVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGLVAAQHSLTFAANGWVEPATAPNFGRLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR"},"dna_sequence":{"accession":"OP966824.1","fmin":"0","fmax":"813","strand":"+","sequence":"ATGGAATTGCCCAATATTATGCACCCGGTCGCGAAGCTGAGCACCGCATTAGCCGCTGCATTGATGCTGAGCGGGTGCATGCCCGGTGAAATCCGCCCGACGATTGGCCAGCAAATGGAAACTGGCGACCAACGGTTTGGCGATCTGGTTTTCCGCCAGCTCGCACCGAATGTCTGGCAGCACACTTCCTATCTCGACATGCCGGGTTTCGGGGCAGTCGCTTCCAACGGTTTGATCGTCAGGGATGGCGGCCGCGTGCTGTTGGTCGATACCGCCTGGACCGATGACCAGACCGCCCAGATCCTCAACTGGATCAAGCAGGAGATCAACCTGCCGGTCGCGCTGGCGGTGGTGACTCACGCGCATCAGGACAAGATGGGCGGTATGGACGCGCTGCATGCGGCGGGGATTGCGACTTATGCCAATGCGTTGTCGAACCAGCTTGCCCCGCAAGAGGGGCTGGTTGCGGCGCAACACAGCCTGACTTTCGCCGCCAATGGCTGGGTCGAACCAGCAACCGCGCCCAACTTTGGCCGGCTCAAGGTATTTTACCCCGGCCCCGGCCACACCAGTGACAATATCACCGTTGGGATCGACGGCACCGACATCGCTTTTGGTGGCTGCCTGATCAAGGACAGCAAGGCCAAGTCGCTCGGCAATCTCGGTGATGCCGACACTGAGCACTACGCCGCGTCAGCGCGCGCGTTTGGTGCGGCGTTCCCCAAGGCCAGCATGATCGTGATGAGCCATTCCGCCCCCGATAGCCGCGCCGCAATCACTCATACGGCCCGCATGGCCGACAAGCTGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3008397","ARO_id":"47189","ARO_name":"NDM-49","CARD_short_name":"NDM-49","ARO_description":"Subclass B1 metallo-beta-lactamase NDM-49.","ARO_category":{"36196":{"category_aro_accession":"3000057","category_aro_cvterm_id":"36196","category_aro_name":"NDM beta-lactamase","category_aro_description":"NDM beta-lactamases or New Delhi metallo-beta-lactamases are class B beta-lactamases that confer resistance to a broad range of antibiotics including carbapenems, cephalosporins and penicillins.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7816":{"model_id":"7816","model_name":"NDM-50","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10643":{"protein_sequence":{"accession":"EMM3083081.1","sequence":"MELPNIMHPVAKLSTALAAALILSGCMPGEIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMNALHAAGIATYANALSNQLAPQEGLVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR"},"dna_sequence":{"accession":"ABJWWM030000052.1","fmin":"6678","fmax":"7491","strand":"+","sequence":"ATGGAATTGCCCAATATTATGCACCCGGTCGCGAAGCTGAGCACCGCATTAGCCGCTGCATTGATACTGAGCGGGTGCATGCCCGGTGAAATCCGCCCGACGATTGGCCAGCAAATGGAAACTGGCGACCAACGGTTTGGCGATCTGGTTTTCCGCCAGCTCGCACCGAATGTCTGGCAGCACACTTCCTATCTCGACATGCCGGGTTTCGGGGCAGTCGCTTCCAACGGTTTGATCGTCAGGGATGGCGGCCGCGTGCTGGTGGTCGATACCGCCTGGACCGATGACCAGACCGCCCAGATCCTCAACTGGATCAAGCAGGAGATCAACCTGCCGGTCGCGCTGGCGGTGGTGACTCACGCGCATCAGGACAAGATGGGCGGTATGAACGCGCTGCATGCGGCGGGGATTGCGACTTATGCCAATGCGTTGTCGAACCAGCTTGCCCCGCAAGAGGGGCTGGTTGCGGCGCAACACAGCCTGACTTTCGCCGCCAATGGCTGGGTCGAACCAGCAACCGCGCCCAACTTTGGCCCGCTCAAGGTATTTTACCCCGGCCCCGGCCACACCAGTGACAATATCACCGTTGGGATCGACGGCACCGACATCGCTTTTGGTGGCTGCCTGATCAAGGACAGCAAGGCCAAGTCGCTCGGCAATCTCGGTGATGCCGACACTGAGCACTACGCCGCGTCAGCGCGCGCGTTTGGTGCGGCGTTCCCCAAGGCCAGCATGATCGTGATGAGCCATTCCGCCCCCGATAGCCGCGCCGCAATCACTCATACGGCCCGCATGGCCGACAAGCTGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008398","ARO_id":"47190","ARO_name":"NDM-50","CARD_short_name":"NDM-50","ARO_description":"Subclass B1 metallo-beta-lactamase NDM-50.","ARO_category":{"36196":{"category_aro_accession":"3000057","category_aro_cvterm_id":"36196","category_aro_name":"NDM beta-lactamase","category_aro_description":"NDM beta-lactamases or New Delhi metallo-beta-lactamases are class B beta-lactamases that confer resistance to a broad range of antibiotics including carbapenems, cephalosporins and penicillins.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7817":{"model_id":"7817","model_name":"NDM-51","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10644":{"protein_sequence":{"accession":"WEG43790.1","sequence":"MELPNIMHPVAKLSTALAAALMLSGCMPGEIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLLVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGLVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSDPDSRAAITHTARMADKLR"},"dna_sequence":{"accession":"OQ442836.1","fmin":"0","fmax":"813","strand":"+","sequence":"ATGGAATTGCCCAATATTATGCACCCGGTCGCGAAGCTGAGCACCGCATTAGCCGCTGCATTGATGCTGAGCGGGTGCATGCCCGGTGAAATCCGCCCGACGATTGGCCAGCAAATGGAAACTGGCGACCAACGGTTTGGCGATCTGGTTTTCCGCCAGCTCGCACCGAATGTCTGGCAGCACACTTCCTATCTCGACATGCCGGGTTTCGGGGCAGTCGCTTCCAACGGTTTGATCGTCAGGGATGGCGGCCGCGTGCTGTTGGTCGATACCGCCTGGACCGATGACCAGACCGCCCAGATCCTCAACTGGATCAAGCAGGAGATCAACCTGCCGGTCGCGCTGGCGGTGGTGACTCACGCGCATCAGGACAAGATGGGCGGTATGGACGCGCTGCATGCGGCGGGGATTGCGACTTATGCCAATGCGTTGTCGAACCAGCTTGCCCCGCAAGAGGGGCTGGTTGCGGCGCAACACAGCCTGACTTTCGCCGCCAATGGCTGGGTCGAACCAGCAACCGCGCCCAACTTTGGCCCGCTCAAGGTATTTTACCCCGGCCCCGGCCACACCAGTGACAATATCACCGTTGGGATCGACGGCACCGACATCGCTTTTGGTGGCTGCCTGATCAAGGACAGCAAGGCCAAGTCGCTCGGCAATCTCGGTGATGCCGACACTGAGCACTACGCCGCGTCAGCGCGCGCGTTTGGTGCGGCGTTCCCCAAGGCCAGCATGATCGTGATGAGCCATTCCGACCCCGATAGCCGCGCCGCAATCACTCATACGGCCCGCATGGCCGACAAGCTGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3008399","ARO_id":"47191","ARO_name":"NDM-51","CARD_short_name":"NDM-51","ARO_description":"Subclass B1 metallo-beta-lactamase NDM-51.","ARO_category":{"36196":{"category_aro_accession":"3000057","category_aro_cvterm_id":"36196","category_aro_name":"NDM beta-lactamase","category_aro_description":"NDM beta-lactamases or New Delhi metallo-beta-lactamases are class B beta-lactamases that confer resistance to a broad range of antibiotics including carbapenems, cephalosporins and penicillins.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7818":{"model_id":"7818","model_name":"NDM-52","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10645":{"protein_sequence":{"accession":"WEM34775.1","sequence":"MELPNIMHPVAKLSTALAAALMLSGCMPGEIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMAALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR"},"dna_sequence":{"accession":"OQ564973.1","fmin":"0","fmax":"813","strand":"+","sequence":"ATGGAATTGCCCAATATTATGCACCCGGTCGCGAAGCTGAGCACCGCATTAGCCGCTGCATTGATGCTGAGCGGGTGCATGCCCGGTGAAATCCGCCCGACGATTGGCCAGCAAATGGAAACTGGCGACCAACGGTTTGGCGATCTGGTTTTCCGCCAGCTCGCACCGAATGTCTGGCAGCACACTTCCTATCTCGACATGCCGGGTTTCGGGGCAGTCGCTTCCAACGGTTTGATCGTCAGGGATGGCGGCCGCGTGCTGGTGGTCGATACCGCCTGGACCGATGACCAGACCGCCCAGATCCTCAACTGGATCAAGCAGGAGATCAACCTGCCGGTCGCGCTGGCGGTGGTGACTCACGCGCATCAGGACAAGATGGGCGGTATGGCCGCGCTGCATGCGGCGGGGATTGCGACTTATGCCAATGCGTTGTCGAACCAGCTTGCCCCGCAAGAGGGGATGGTTGCGGCGCAACACAGCCTGACTTTCGCCGCCAATGGCTGGGTCGAACCAGCAACCGCGCCCAACTTTGGCCCGCTCAAGGTATTTTACCCCGGCCCCGGCCACACCAGTGACAATATCACCGTTGGGATCGACGGCACCGACATCGCTTTTGGTGGCTGCCTGATCAAGGACAGCAAGGCCAAGTCGCTCGGCAATCTCGGTGATGCCGACACTGAGCACTACGCCGCGTCAGCGCGCGCGTTTGGTGCGGCGTTCCCCAAGGCCAGCATGATCGTGATGAGCCATTCCGCCCCCGATAGCCGCGCCGCAATCACTCATACGGCCCGCATGGCCGACAAGCTGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008400","ARO_id":"47192","ARO_name":"NDM-52","CARD_short_name":"NDM-52","ARO_description":"Subclass B1 metallo-beta-lactamase NDM-52.","ARO_category":{"36196":{"category_aro_accession":"3000057","category_aro_cvterm_id":"36196","category_aro_name":"NDM beta-lactamase","category_aro_description":"NDM beta-lactamases or New Delhi metallo-beta-lactamases are class B beta-lactamases that confer resistance to a broad range of antibiotics including carbapenems, cephalosporins and penicillins.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7819":{"model_id":"7819","model_name":"NDM-53","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10646":{"protein_sequence":{"accession":"WEG44271.1","sequence":"MELPNIMHPVAKLSTALAAALMLSGCMPGEIHPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLLVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGLVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR"},"dna_sequence":{"accession":"OQ595422.1","fmin":"0","fmax":"813","strand":"+","sequence":"ATGGAATTGCCCAATATTATGCACCCGGTCGCGAAGCTGAGCACCGCATTAGCCGCTGCATTGATGCTGAGCGGGTGCATGCCCGGTGAAATCCACCCGACGATTGGCCAGCAAATGGAAACTGGCGACCAACGGTTTGGCGATCTGGTTTTCCGCCAGCTCGCACCGAATGTCTGGCAGCACACTTCCTATCTCGACATGCCGGGTTTCGGGGCAGTCGCTTCCAACGGTTTGATCGTCAGGGATGGCGGCCGCGTGCTGTTGGTCGATACCGCCTGGACCGATGACCAGACCGCCCAGATCCTCAACTGGATCAAGCAGGAGATCAACCTGCCGGTCGCGCTGGCGGTGGTGACTCACGCGCATCAGGACAAGATGGGCGGTATGGACGCGCTGCATGCGGCGGGGATTGCGACTTATGCCAATGCGTTGTCGAACCAGCTTGCCCCGCAAGAGGGGCTGGTTGCGGCGCAACACAGCCTGACTTTCGCCGCCAATGGCTGGGTCGAACCAGCAACCGCGCCCAACTTTGGCCCGCTCAAGGTATTTTACCCCGGCCCCGGCCACACCAGTGACAATATCACCGTTGGGATCGACGGCACCGACATCGCTTTTGGTGGCTGCCTGATCAAGGACAGCAAGGCCAAGTCGCTCGGCAATCTCGGTGATGCCGACACTGAGCACTACGCCGCGTCAGCGCGCGCGTTTGGTGCGGCGTTCCCCAAGGCCAGCATGATCGTGATGAGCCATTCCGCCCCCGATAGCCGCGCCGCAATCACTCATACGGCCCGCATGGCCGACAAGCTGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3008401","ARO_id":"47193","ARO_name":"NDM-53","CARD_short_name":"NDM-53","ARO_description":"Subclass B1 metallo-beta-lactamase NDM-53.","ARO_category":{"36196":{"category_aro_accession":"3000057","category_aro_cvterm_id":"36196","category_aro_name":"NDM beta-lactamase","category_aro_description":"NDM beta-lactamases or New Delhi metallo-beta-lactamases are class B beta-lactamases that confer resistance to a broad range of antibiotics including carbapenems, cephalosporins and penicillins.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7820":{"model_id":"7820","model_name":"NDM-54","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10647":{"protein_sequence":{"accession":"WEG44272.1","sequence":"MELPNIMHPVAKLSTALAAALMLSGCMPGEILPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR"},"dna_sequence":{"accession":"OQ595423.1","fmin":"0","fmax":"813","strand":"+","sequence":"ATGGAATTGCCCAATATTATGCACCCGGTCGCGAAGCTGAGCACCGCATTAGCCGCTGCATTGATGCTGAGCGGGTGCATGCCCGGTGAAATCCTCCCGACGATTGGCCAGCAAATGGAAACTGGCGACCAACGGTTTGGCGATCTGGTTTTCCGCCAGCTCGCACCGAATGTCTGGCAGCACACTTCCTATCTCGACATGCCGGGTTTCGGGGCAGTCGCTTCCAACGGTTTGATCGTCAGGGATGGCGGCCGCGTGCTGGTGGTCGATACCGCCTGGACCGATGACCAGACCGCCCAGATCCTCAACTGGATCAAGCAGGAGATCAACCTGCCGGTCGCGCTGGCGGTGGTGACTCACGCGCATCAGGACAAGATGGGCGGTATGGACGCGCTGCATGCGGCGGGGATTGCGACTTATGCCAATGCGTTGTCGAACCAGCTTGCCCCGCAAGAGGGGATGGTTGCGGCGCAACACAGCCTGACTTTCGCCGCCAATGGCTGGGTCGAACCAGCAACCGCGCCCAACTTTGGCCCGCTCAAGGTATTTTACCCCGGCCCCGGCCACACCAGTGACAATATCACCGTTGGGATCGACGGCACCGACATCGCTTTTGGTGGCTGCCTGATCAAGGACAGCAAGGCCAAGTCGCTCGGCAATCTCGGTGATGCCGACACTGAGCACTACGCCGCGTCAGCGCGCGCGTTTGGTGCGGCGTTCCCCAAGGCCAGCATGATCGTGATGAGCCATTCCGCCCCCGATAGCCGCGCCGCAATCACTCATACGGCCCGCATGGCCGACAAGCTGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008402","ARO_id":"47194","ARO_name":"NDM-54","CARD_short_name":"NDM-54","ARO_description":"Subclass B1 metallo-beta-lactamase NDM-54.","ARO_category":{"36196":{"category_aro_accession":"3000057","category_aro_cvterm_id":"36196","category_aro_name":"NDM beta-lactamase","category_aro_description":"NDM beta-lactamases or New Delhi metallo-beta-lactamases are class B beta-lactamases that confer resistance to a broad range of antibiotics including carbapenems, cephalosporins and penicillins.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7821":{"model_id":"7821","model_name":"NDM-55","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10648":{"protein_sequence":{"accession":"WEY36504.1","sequence":"MELPNIMHPVAKLSTALAAALMLSGCMPGEIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLLVDTAWTDDQTTQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGLVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR"},"dna_sequence":{"accession":"OQ708894.1","fmin":"0","fmax":"813","strand":"+","sequence":"ATGGAATTGCCCAATATTATGCACCCGGTCGCGAAGCTGAGCACCGCATTAGCCGCTGCATTGATGCTGAGCGGGTGCATGCCCGGTGAAATCCGCCCGACGATTGGCCAGCAAATGGAAACTGGCGACCAACGGTTTGGCGATCTGGTTTTCCGCCAGCTCGCACCGAATGTCTGGCAGCACACTTCCTATCTCGACATGCCGGGTTTCGGGGCAGTCGCTTCCAACGGTTTGATCGTCAGGGATGGCGGCCGCGTGCTGTTGGTCGATACCGCCTGGACCGATGACCAGACCACCCAGATCCTCAACTGGATCAAGCAGGAGATCAACCTGCCGGTCGCGCTGGCGGTGGTGACTCACGCGCATCAGGACAAGATGGGCGGTATGGACGCGCTGCATGCGGCGGGGATTGCGACTTATGCCAATGCGTTGTCGAACCAGCTTGCCCCGCAAGAGGGGCTGGTTGCGGCGCAACACAGCCTGACTTTCGCCGCCAATGGCTGGGTCGAACCAGCAACCGCGCCCAACTTTGGCCCGCTCAAGGTATTTTACCCCGGCCCCGGCCACACCAGTGACAATATCACCGTTGGGATCGACGGCACCGACATCGCTTTTGGTGGCTGCCTGATCAAGGACAGCAAGGCCAAGTCGCTCGGCAATCTCGGTGATGCCGACACTGAGCACTACGCCGCGTCAGCGCGCGCGTTTGGTGCGGCGTTCCCCAAGGCCAGCATGATCGTGATGAGCCATTCCGCCCCCGATAGCCGCGCCGCAATCACTCATACGGCCCGCATGGCCGACAAGCTGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3008403","ARO_id":"47195","ARO_name":"NDM-55","CARD_short_name":"NDM-55","ARO_description":"Subclass B1 metallo-beta-lactamase NDM-55.","ARO_category":{"36196":{"category_aro_accession":"3000057","category_aro_cvterm_id":"36196","category_aro_name":"NDM beta-lactamase","category_aro_description":"NDM beta-lactamases or New Delhi metallo-beta-lactamases are class B beta-lactamases that confer resistance to a broad range of antibiotics including carbapenems, cephalosporins and penicillins.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7822":{"model_id":"7822","model_name":"NDM-56","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10649":{"protein_sequence":{"accession":"WGO19549.1","sequence":"MELPNIMHPVAKLSTALAAALMLSGCMPGEIRPTIGQQMETGDQRFGDLVFRQLAPTVWQHTSYLDMPGFGAVASNGLIVRDGGRVRLVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGLVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPQASMIVMSHSAPESRAAITHTARMADTLR"},"dna_sequence":{"accession":"OQ870699.1","fmin":"0","fmax":"813","strand":"+","sequence":"ATGGAATTGCCCAATATTATGCACCCGGTCGCGAAGCTGAGCACCGCATTAGCCGCTGCATTGATGCTGAGCGGGTGCATGCCCGGTGAAATCCGCCCGACGATTGGCCAGCAAATGGAAACTGGCGACCAACGGTTTGGCGATCTGGTTTTCCGCCAGCTCGCACCGACTGTCTGGCAGCACACTTCCTATCTCGACATGCCGGGTTTCGGGGCAGTCGCTTCCAACGGTTTGATCGTCAGGGATGGCGGCCGCGTGCGGTTGGTCGATACCGCCTGGACCGATGACCAGACCGCCCAGATCCTCAACTGGATCAAGCAGGAGATCAACCTGCCGGTCGCGCTGGCGGTGGTGACTCACGCGCATCAGGACAAGATGGGCGGTATGGACGCGCTGCATGCGGCGGGGATTGCGACTTATGCCAATGCGTTGTCGAACCAGCTTGCCCCGCAAGAGGGGCTGGTTGCGGCGCAACACAGCCTGACTTTCGCCGCCAATGGCTGGGTCGAACCAGCAACCGCGCCCAACTTTGGCCCGCTCAAGGTATTTTACCCCGGCCCCGGCCACACCAGTGACAATATCACCGTTGGGATCGACGGCACCGACATCGCTTTTGGTGGCTGCCTGATCAAGGACAGCAAGGCCAAGTCGCTCGGCAATCTCGGTGATGCCGACACTGAGCACTACGCCGCGTCAGCGCGCGCGTTTGGTGCGGCGTTCCCCCAGGCCAGCATGATCGTGATGAGCCATTCCGCCCCCGAGAGCCGCGCCGCAATCACTCATACGGCCCGCATGGCCGACACGCTGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3008404","ARO_id":"47196","ARO_name":"NDM-56","CARD_short_name":"NDM-56","ARO_description":"Subclass B1 metallo-beta-lactamase NDM-56.","ARO_category":{"36196":{"category_aro_accession":"3000057","category_aro_cvterm_id":"36196","category_aro_name":"NDM beta-lactamase","category_aro_description":"NDM beta-lactamases or New Delhi metallo-beta-lactamases are class B beta-lactamases that confer resistance to a broad range of antibiotics including carbapenems, cephalosporins and penicillins.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7823":{"model_id":"7823","model_name":"NDM-57","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10650":{"protein_sequence":{"accession":"WGO19550.1","sequence":"MGLPNIMHPVAKLSTALAAALMLSGCMPGEIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLLVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGLVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR"},"dna_sequence":{"accession":"OQ870700.1","fmin":"0","fmax":"813","strand":"+","sequence":"ATGGGATTGCCCAATATTATGCACCCGGTCGCGAAGCTGAGCACCGCATTAGCCGCTGCATTGATGCTGAGCGGGTGCATGCCCGGTGAAATCCGCCCGACGATTGGCCAGCAAATGGAAACTGGCGACCAACGGTTTGGCGATCTGGTTTTCCGCCAGCTCGCACCGAATGTCTGGCAGCACACTTCCTATCTCGACATGCCGGGTTTCGGGGCAGTCGCTTCCAACGGTTTGATCGTCAGGGATGGCGGCCGCGTGCTGTTGGTCGATACCGCCTGGACCGATGACCAGACCGCCCAGATCCTCAACTGGATCAAGCAGGAGATCAACCTGCCGGTCGCGCTGGCGGTGGTGACTCACGCGCATCAGGACAAGATGGGCGGTATGGACGCGCTGCATGCGGCGGGGATTGCGACTTATGCCAATGCGTTGTCGAACCAGCTTGCCCCGCAAGAGGGGCTGGTTGCGGCGCAACACAGCCTGACTTTCGCCGCCAATGGCTGGGTCGAACCAGCAACCGCGCCCAACTTTGGCCCGCTCAAGGTATTTTACCCCGGCCCCGGCCACACCAGTGACAATATCACCGTTGGGATCGACGGCACCGACATCGCTTTTGGTGGCTGCCTGATCAAGGACAGCAAGGCCAAGTCGCTCGGCAATCTCGGTGATGCCGACACTGAGCACTACGCCGCGTCAGCGCGCGCGTTTGGTGCGGCGTTCCCCAAGGCCAGCATGATCGTGATGAGCCATTCCGCCCCCGATAGCCGCGCCGCAATCACTCATACGGCCCGCATGGCCGACAAGCTGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3008405","ARO_id":"47197","ARO_name":"NDM-57","CARD_short_name":"NDM-57","ARO_description":"Subclass B1 metallo-beta-lactamase NDM-57.","ARO_category":{"36196":{"category_aro_accession":"3000057","category_aro_cvterm_id":"36196","category_aro_name":"NDM beta-lactamase","category_aro_description":"NDM beta-lactamases or New Delhi metallo-beta-lactamases are class B beta-lactamases that confer resistance to a broad range of antibiotics including carbapenems, cephalosporins and penicillins.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7824":{"model_id":"7824","model_name":"NDM-58","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10651":{"protein_sequence":{"accession":"WIF29698.1","sequence":"MELPNIMHPVAKLSTALAAALMLSGCMPGEIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYSGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR"},"dna_sequence":{"accession":"OR081828.1","fmin":"0","fmax":"813","strand":"+","sequence":"ATGGAATTGCCCAATATTATGCACCCGGTCGCGAAGCTGAGCACCGCATTAGCCGCTGCATTGATGCTGAGCGGGTGCATGCCCGGTGAAATCCGCCCGACGATTGGCCAGCAAATGGAAACTGGCGACCAACGGTTTGGCGATCTGGTTTTCCGCCAGCTCGCACCGAATGTCTGGCAGCACACTTCCTATCTCGACATGCCGGGTTTCGGGGCAGTCGCTTCCAACGGTTTGATCGTCAGGGATGGCGGCCGCGTGCTGGTGGTCGATACCGCCTGGACCGATGACCAGACCGCCCAGATCCTCAACTGGATCAAGCAGGAGATCAACCTGCCGGTCGCGCTGGCGGTGGTGACTCACGCGCATCAGGACAAGATGGGCGGTATGGACGCGCTGCATGCGGCGGGGATTGCGACTTATGCCAATGCGTTGTCGAACCAGCTTGCCCCGCAAGAGGGGATGGTTGCGGCGCAACACAGCCTGACTTTCGCCGCCAATGGCTGGGTCGAACCAGCAACCGCGCCCAACTTTGGCCCGCTCAAGGTATTTTACTCCGGCCCCGGCCACACCAGTGACAATATCACCGTTGGGATCGACGGCACCGACATCGCTTTTGGTGGCTGCCTGATCAAGGACAGCAAGGCCAAGTCGCTCGGCAATCTCGGTGATGCCGACACTGAGCACTACGCCGCGTCAGCGCGCGCGTTTGGTGCGGCGTTCCCCAAGGCCAGCATGATCGTGATGAGCCATTCCGCCCCCGATAGCCGCGCCGCAATCACTCATACGGCCCGCATGGCCGACAAGCTGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008406","ARO_id":"47198","ARO_name":"NDM-58","CARD_short_name":"NDM-58","ARO_description":"Subclass B1 metallo-beta-lactamase NDM-58.","ARO_category":{"36196":{"category_aro_accession":"3000057","category_aro_cvterm_id":"36196","category_aro_name":"NDM beta-lactamase","category_aro_description":"NDM beta-lactamases or New Delhi metallo-beta-lactamases are class B beta-lactamases that confer resistance to a broad range of antibiotics including carbapenems, cephalosporins and penicillins.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7825":{"model_id":"7825","model_name":"NDM-60","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10652":{"protein_sequence":{"accession":"WJL30768.1","sequence":"MELPNIMHPVAKLSTALAAALMLSGCMPGEIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLLVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGLVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTNIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR"},"dna_sequence":{"accession":"OR139852.1","fmin":"0","fmax":"813","strand":"+","sequence":"ATGGAATTGCCCAATATTATGCACCCGGTCGCGAAGCTGAGCACCGCATTAGCCGCTGCATTGATGCTGAGCGGGTGCATGCCCGGTGAAATCCGCCCGACGATTGGCCAGCAAATGGAAACTGGCGACCAACGGTTTGGCGATCTGGTTTTCCGCCAGCTCGCACCGAATGTCTGGCAGCACACTTCCTATCTCGACATGCCGGGTTTCGGGGCAGTCGCTTCCAACGGTTTGATCGTCAGGGATGGCGGCCGCGTGCTGTTGGTCGATACCGCCTGGACCGATGACCAGACCGCCCAGATCCTCAACTGGATCAAGCAGGAGATCAACCTGCCGGTCGCGCTGGCGGTGGTGACTCACGCGCATCAGGACAAGATGGGCGGTATGGACGCGCTGCATGCGGCGGGGATTGCGACTTATGCCAATGCGTTGTCGAACCAGCTTGCCCCGCAAGAGGGGCTGGTTGCGGCGCAACACAGCCTGACTTTCGCCGCCAATGGCTGGGTCGAACCAGCAACCGCGCCCAACTTTGGCCCGCTCAAGGTATTTTACCCCGGCCCCGGCCACACCAGTGACAATATCACCGTTGGGATCGACGGCACCAACATCGCTTTTGGTGGCTGCCTGATCAAGGACAGCAAGGCCAAGTCGCTCGGCAATCTCGGTGATGCCGACACTGAGCACTACGCCGCGTCAGCGCGCGCGTTTGGTGCGGCGTTCCCCAAGGCCAGCATGATCGTGATGAGCCATTCCGCCCCCGATAGCCGCGCCGCAATCACTCATACGGCCCGCATGGCCGACAAGCTGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3008407","ARO_id":"47199","ARO_name":"NDM-60","CARD_short_name":"NDM-60","ARO_description":"Subclass B1 metallo-beta-lactamase NDM-60.","ARO_category":{"36196":{"category_aro_accession":"3000057","category_aro_cvterm_id":"36196","category_aro_name":"NDM beta-lactamase","category_aro_description":"NDM beta-lactamases or New Delhi metallo-beta-lactamases are class B beta-lactamases that confer resistance to a broad range of antibiotics including carbapenems, cephalosporins and penicillins.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7826":{"model_id":"7826","model_name":"NDM-61","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10653":{"protein_sequence":{"accession":"HDV0005713.1","sequence":"MELPNIMHPVAKLSTALAAALMLSGCMPGEIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMGALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASVRAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR"},"dna_sequence":{"accession":"DAPGEA010000082.1","fmin":"350","fmax":"1163","strand":"+","sequence":"ATGGAATTGCCCAATATTATGCACCCGGTCGCGAAGCTGAGCACCGCATTAGCCGCTGCATTGATGCTGAGCGGGTGCATGCCCGGTGAAATCCGCCCGACGATTGGCCAGCAAATGGAAACTGGCGACCAACGGTTTGGCGATCTGGTTTTCCGCCAGCTCGCACCGAATGTCTGGCAGCACACTTCCTATCTCGACATGCCGGGTTTCGGGGCAGTCGCTTCCAACGGTTTGATCGTCAGGGATGGCGGCCGCGTGCTGGTGGTCGATACCGCCTGGACCGATGACCAGACCGCCCAGATCCTCAACTGGATCAAGCAGGAGATCAACCTGCCGGTCGCGCTGGCGGTGGTGACTCACGCGCATCAGGACAAGATGGGCGGTATGGGCGCGCTGCATGCGGCGGGGATTGCGACTTATGCCAATGCGTTGTCGAACCAGCTTGCCCCGCAAGAGGGGATGGTTGCGGCGCAACACAGCCTGACTTTCGCCGCCAATGGCTGGGTCGAACCAGCAACCGCGCCCAACTTTGGCCCGCTCAAGGTATTTTACCCCGGCCCCGGCCACACCAGTGACAATATCACCGTTGGGATCGACGGCACCGACATCGCTTTTGGTGGCTGCCTGATCAAGGACAGCAAGGCCAAGTCGCTCGGCAATCTCGGTGATGCCGACACTGAGCACTACGCCGCGTCAGTGCGCGCGTTTGGTGCGGCGTTCCCCAAGGCCAGCATGATCGTGATGAGCCATTCCGCCCCCGATAGCCGCGCCGCAATCACTCATACGGCCCGCATGGCCGACAAGCTGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008408","ARO_id":"47200","ARO_name":"NDM-61","CARD_short_name":"NDM-61","ARO_description":"Subclass B1 metallo-beta-lactamase NDM-61.","ARO_category":{"36196":{"category_aro_accession":"3000057","category_aro_cvterm_id":"36196","category_aro_name":"NDM beta-lactamase","category_aro_description":"NDM beta-lactamases or New Delhi metallo-beta-lactamases are class B beta-lactamases that confer resistance to a broad range of antibiotics including carbapenems, cephalosporins and penicillins.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7827":{"model_id":"7827","model_name":"NDM-64","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10654":{"protein_sequence":{"accession":"WVS53334.1","sequence":"MELPNIMHPVAKLSTALAAVLMLSGCMPGEIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR"},"dna_sequence":{"accession":"PP238488.1","fmin":"0","fmax":"813","strand":"+","sequence":"ATGGAATTGCCCAATATTATGCACCCGGTCGCGAAGCTGAGCACCGCATTAGCCGCTGTATTGATGCTGAGCGGGTGCATGCCCGGTGAAATCCGCCCGACGATTGGCCAGCAAATGGAAACTGGCGACCAACGGTTTGGCGATCTGGTTTTCCGCCAGCTCGCACCGAATGTCTGGCAGCACACTTCCTATCTCGACATGCCGGGTTTCGGGGCAGTCGCTTCCAACGGTTTGATCGTCAGGGATGGCGGCCGCGTGCTGGTGGTCGATACCGCCTGGACCGATGACCAGACCGCCCAGATCCTCAACTGGATCAAGCAGGAGATCAACCTGCCGGTCGCGCTGGCGGTGGTGACTCACGCGCATCAGGACAAGATGGGCGGTATGGACGCGCTGCATGCGGCGGGGATTGCGACTTATGCCAATGCGTTGTCGAACCAGCTTGCCCCGCAAGAGGGGATGGTTGCGGCGCAACACAGCCTGACTTTCGCCGCCAATGGCTGGGTCGAACCAGCAACCGCGCCCAACTTTGGCCCGCTCAAGGTATTTTACCCCGGCCCCGGCCACACCAGTGACAATATCACCGTTGGGATCGACGGCACCGACATCGCTTTTGGTGGCTGCCTGATCAAGGACAGCAAGGCCAAGTCGCTCGGCAATCTCGGTGATGCCGACACTGAGCACTACGCCGCGTCAGCGCGCGCGTTTGGTGCGGCGTTCCCCAAGGCCAGCATGATCGTGATGAGCCATTCCGCCCCCGATAGCCGCGCCGCAATCACTCATACGGCCCGCATGGCCGACAAGCTGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008409","ARO_id":"47201","ARO_name":"NDM-64","CARD_short_name":"NDM-64","ARO_description":"Subclass B1 metallo-beta-lactamase NDM-64.","ARO_category":{"36196":{"category_aro_accession":"3000057","category_aro_cvterm_id":"36196","category_aro_name":"NDM beta-lactamase","category_aro_description":"NDM beta-lactamases or New Delhi metallo-beta-lactamases are class B beta-lactamases that confer resistance to a broad range of antibiotics including carbapenems, cephalosporins and penicillins.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7828":{"model_id":"7828","model_name":"NDM-65","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10655":{"protein_sequence":{"accession":"WVW91587.1","sequence":"MELPNIMHPVAKLSTALAAALMLSGCMPGEIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLSDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR"},"dna_sequence":{"accession":"PP296993.1","fmin":"0","fmax":"813","strand":"+","sequence":"ATGGAATTGCCCAATATTATGCACCCGGTCGCGAAGCTGAGCACCGCATTAGCCGCTGCATTGATGCTGAGCGGGTGCATGCCCGGTGAAATCCGCCCGACGATTGGCCAGCAAATGGAAACTGGCGACCAACGGTTTGGCGATCTGGTTTTCCGCCAGCTCGCACCGAATGTCTGGCAGCACACTTCCTATCTCGACATGCCGGGTTTCGGGGCAGTCGCTTCCAACGGTTTGATCGTCAGGGATGGCGGCCGCGTGCTGGTGGTCGATACCGCCTGGACCGATGACCAGACCGCCCAGATCCTCAACTGGATCAAGCAGGAGATCAACCTGCCGGTCGCGCTGGCGGTGGTGACTCACGCGCATCAGGACAAGATGGGCGGTATGGACGCGCTGCATGCGGCGGGGATTGCGACTTATGCCAATGCGTTGTCGAACCAGCTTGCCCCGCAAGAGGGGATGGTTGCGGCGCAACACAGCCTGACTTTCGCCGCCAATGGCTGGGTCGAACCAGCAACCGCGCCCAACTTTGGCCCGCTCAAGGTATTTTACCCCGGCCCCGGCCACACCAGTGACAATATCACCGTTGGGATCGACGGCACCGACATCGCTTTTGGTGGCTGCCTGATCAAGGACAGCAAGGCCAAGTCGCTCGGCAATCTCAGTGATGCCGACACTGAGCACTACGCCGCGTCAGCGCGCGCGTTTGGTGCGGCGTTCCCCAAGGCCAGCATGATCGTGATGAGCCATTCCGCCCCCGATAGCCGCGCCGCAATCACTCATACGGCCCGCATGGCCGACAAGCTGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3008410","ARO_id":"47202","ARO_name":"NDM-65","CARD_short_name":"NDM-65","ARO_description":"Subclass B1 metallo-beta-lactamase NDM-65.","ARO_category":{"36196":{"category_aro_accession":"3000057","category_aro_cvterm_id":"36196","category_aro_name":"NDM beta-lactamase","category_aro_description":"NDM beta-lactamases or New Delhi metallo-beta-lactamases are class B beta-lactamases that confer resistance to a broad range of antibiotics including carbapenems, cephalosporins and penicillins.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7829":{"model_id":"7829","model_name":"NDM-66","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10656":{"protein_sequence":{"accession":"WXB24425.1","sequence":"MELPNIMHPVAKLSTALAAALMLSGCMPGEIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLLVRDGGRVLLVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGLVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR"},"dna_sequence":{"accession":"PP479854.1","fmin":"123","fmax":"936","strand":"+","sequence":"ATGGAATTGCCCAATATTATGCACCCGGTCGCGAAGCTGAGCACCGCATTAGCCGCTGCATTGATGCTGAGCGGGTGCATGCCCGGTGAAATCCGCCCGACGATTGGCCAGCAAATGGAAACTGGCGACCAACGGTTTGGCGATCTGGTTTTCCGCCAGCTCGCACCGAATGTCTGGCAGCACACTTCCTATCTCGACATGCCGGGTTTCGGGGCAGTCGCTTCCAACGGTTTGCTCGTCAGGGATGGCGGCCGCGTGCTGTTGGTCGATACCGCCTGGACCGATGACCAGACCGCCCAGATCCTCAACTGGATCAAGCAGGAGATCAACCTGCCGGTCGCGCTGGCGGTGGTGACTCACGCGCATCAGGACAAGATGGGCGGTATGGACGCGCTGCATGCGGCGGGGATTGCGACTTATGCCAATGCGTTGTCGAACCAGCTTGCCCCGCAAGAGGGGCTGGTTGCGGCGCAACACAGCCTGACTTTCGCCGCCAATGGCTGGGTCGAACCAGCAACCGCGCCCAACTTTGGCCCGCTCAAGGTATTTTACCCCGGCCCCGGCCACACCAGTGACAATATCACCGTTGGGATCGACGGCACCGACATCGCTTTTGGTGGCTGCCTGATCAAGGACAGCAAGGCCAAGTCGCTCGGCAATCTCGGTGATGCCGACACTGAGCACTACGCCGCGTCAGCGCGCGCGTTTGGTGCGGCGTTCCCCAAGGCCAGCATGATCGTGATGAGCCATTCCGCCCCCGATAGCCGCGCCGCAATCACTCATACGGCCCGCATGGCCGACAAGCTGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3008411","ARO_id":"47203","ARO_name":"NDM-66","CARD_short_name":"NDM-66","ARO_description":"Subclass B1 metallo-beta-lactamase NDM-66.","ARO_category":{"36196":{"category_aro_accession":"3000057","category_aro_cvterm_id":"36196","category_aro_name":"NDM beta-lactamase","category_aro_description":"NDM beta-lactamases or New Delhi metallo-beta-lactamases are class B beta-lactamases that confer resistance to a broad range of antibiotics including carbapenems, cephalosporins and penicillins.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7830":{"model_id":"7830","model_name":"NDM-67","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10657":{"protein_sequence":{"accession":"WXH45424.1","sequence":"MELPNIMHPVAKLSTALAAALMLSGCMPGEIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGVVASNGLIVRDGGRVLLVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGLVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR"},"dna_sequence":{"accession":"PP503724.1","fmin":"119","fmax":"932","strand":"+","sequence":"ATGGAATTGCCCAATATTATGCACCCGGTCGCGAAGCTGAGCACCGCATTAGCCGCTGCATTGATGCTGAGCGGGTGCATGCCCGGTGAAATCCGCCCGACGATTGGCCAGCAAATGGAAACTGGCGACCAACGGTTTGGCGATCTGGTTTTCCGCCAGCTCGCACCGAATGTCTGGCAGCACACTTCCTATCTCGACATGCCGGGTTTCGGGGTAGTCGCTTCCAACGGTTTGATCGTCAGGGATGGCGGCCGCGTGCTGTTGGTCGATACCGCCTGGACCGATGACCAGACCGCCCAGATCCTCAACTGGATCAAGCAGGAGATCAACCTGCCGGTCGCGCTGGCGGTGGTGACTCACGCGCATCAGGACAAGATGGGCGGTATGGACGCGCTGCATGCGGCGGGGATTGCGACTTATGCCAATGCGTTGTCGAACCAGCTTGCCCCGCAAGAGGGGCTGGTTGCGGCGCAACACAGCCTGACTTTCGCCGCCAATGGCTGGGTCGAACCAGCAACCGCGCCCAACTTTGGCCCGCTCAAGGTATTTTACCCCGGCCCCGGCCACACCAGTGACAATATCACCGTTGGGATCGACGGCACCGACATCGCTTTTGGTGGCTGCCTGATCAAGGACAGCAAGGCCAAGTCGCTCGGCAATCTCGGTGATGCCGACACTGAGCACTACGCCGCGTCAGCGCGCGCGTTTGGTGCGGCGTTCCCCAAGGCCAGCATGATCGTGATGAGCCATTCCGCCCCCGATAGCCGCGCCGCAATCACTCATACGGCCCGCATGGCCGACAAGCTGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3008412","ARO_id":"47204","ARO_name":"NDM-67","CARD_short_name":"NDM-67","ARO_description":"Subclass B1 metallo-beta-lactamase NDM-67.","ARO_category":{"36196":{"category_aro_accession":"3000057","category_aro_cvterm_id":"36196","category_aro_name":"NDM beta-lactamase","category_aro_description":"NDM beta-lactamases or New Delhi metallo-beta-lactamases are class B beta-lactamases that confer resistance to a broad range of antibiotics including carbapenems, cephalosporins and penicillins.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7831":{"model_id":"7831","model_name":"NDM-68","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10658":{"protein_sequence":{"accession":"WXH45425.1","sequence":"MELPNIMHPVAKLSTALAAALMLSGCMPGEIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLLVDTAWTDDQTAQILNWIKQELNLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGLVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR"},"dna_sequence":{"accession":"PP503725.1","fmin":"119","fmax":"932","strand":"+","sequence":"ATGGAATTGCCCAATATTATGCACCCGGTCGCGAAGCTGAGCACCGCATTAGCCGCTGCATTGATGCTGAGCGGGTGCATGCCCGGTGAAATCCGCCCGACGATTGGCCAGCAAATGGAAACTGGCGACCAACGGTTTGGCGATCTGGTTTTCCGCCAGCTCGCACCGAATGTCTGGCAGCACACTTCCTATCTCGACATGCCGGGTTTCGGGGCAGTCGCTTCCAACGGTTTGATCGTCAGGGATGGCGGCCGCGTGCTGTTGGTCGATACCGCCTGGACCGATGACCAGACCGCCCAGATCCTCAACTGGATCAAGCAGGAGCTCAACCTGCCGGTCGCGCTGGCGGTGGTGACTCACGCGCATCAGGACAAGATGGGCGGTATGGACGCGCTGCATGCGGCGGGGATTGCGACTTATGCCAATGCGTTGTCGAACCAGCTTGCCCCGCAAGAGGGGCTGGTTGCGGCGCAACACAGCCTGACTTTCGCCGCCAATGGCTGGGTCGAACCAGCAACCGCGCCCAACTTTGGCCCGCTCAAGGTATTTTACCCCGGCCCCGGCCACACCAGTGACAATATCACCGTTGGGATCGACGGCACCGACATCGCTTTTGGTGGCTGCCTGATCAAGGACAGCAAGGCCAAGTCGCTCGGCAATCTCGGTGATGCCGACACTGAGCACTACGCCGCGTCAGCGCGCGCGTTTGGTGCGGCGTTCCCCAAGGCCAGCATGATCGTGATGAGCCATTCCGCCCCCGATAGCCGCGCCGCAATCACTCATACGGCCCGCATGGCCGACAAGCTGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3008413","ARO_id":"47205","ARO_name":"NDM-68","CARD_short_name":"NDM-68","ARO_description":"Subclass B1 metallo-beta-lactamase NDM-68.","ARO_category":{"36196":{"category_aro_accession":"3000057","category_aro_cvterm_id":"36196","category_aro_name":"NDM beta-lactamase","category_aro_description":"NDM beta-lactamases or New Delhi metallo-beta-lactamases are class B beta-lactamases that confer resistance to a broad range of antibiotics including carbapenems, cephalosporins and penicillins.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7832":{"model_id":"7832","model_name":"NDM-69","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10659":{"protein_sequence":{"accession":"BFJ38853.1","sequence":"MKLPNIMHPVAKLSTALAAALMLSGCMPGEIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR"},"dna_sequence":{"accession":"LC810945.1","fmin":"136","fmax":"949","strand":"+","sequence":"ATGAAATTGCCCAATATTATGCACCCGGTCGCGAAGCTGAGCACCGCATTAGCCGCTGCATTGATGCTGAGCGGGTGCATGCCCGGTGAAATCCGCCCGACGATTGGCCAGCAAATGGAAACTGGCGACCAACGGTTTGGCGATCTGGTTTTCCGCCAGCTCGCACCGAATGTCTGGCAGCACACTTCCTATCTCGACATGCCGGGTTTCGGGGCAGTCGCTTCCAACGGTTTGATCGTCAGGGATGGCGGCCGCGTGCTGGTGGTCGATACCGCCTGGACCGATGACCAGACCGCCCAGATCCTCAACTGGATCAAGCAGGAGATCAACCTGCCGGTCGCGCTGGCGGTGGTGACTCACGCGCATCAGGACAAGATGGGCGGTATGGACGCGCTGCATGCGGCGGGGATTGCGACTTATGCCAATGCGTTGTCGAACCAGCTTGCCCCGCAAGAGGGGATGGTTGCGGCGCAACACAGCCTGACTTTCGCCGCCAATGGCTGGGTCGAACCAGCAACCGCGCCCAACTTTGGCCCGCTCAAGGTATTTTACCCCGGCCCCGGCCACACCAGTGACAATATCACCGTTGGGATCGACGGCACCGACATCGCTTTTGGTGGCTGCCTGATCAAGGACAGCAAGGCCAAGTCGCTCGGCAATCTCGGTGATGCCGACACTGAGCACTACGCCGCGTCAGCGCGCGCGTTTGGTGCGGCGTTCCCCAAGGCCAGCATGATCGTGATGAGCCATTCCGCCCCCGATAGCCGCGCCGCAATCACTCATACGGCCCGCATGGCCGACAAGCTGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3008414","ARO_id":"47206","ARO_name":"NDM-69","CARD_short_name":"NDM-69","ARO_description":"Subclass B1 metallo-beta-lactamase NDM-69.","ARO_category":{"36196":{"category_aro_accession":"3000057","category_aro_cvterm_id":"36196","category_aro_name":"NDM beta-lactamase","category_aro_description":"NDM beta-lactamases or New Delhi metallo-beta-lactamases are class B beta-lactamases that confer resistance to a broad range of antibiotics including carbapenems, cephalosporins and penicillins.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7833":{"model_id":"7833","model_name":"NDM-70","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10660":{"protein_sequence":{"accession":"XBS36002.1","sequence":"MELPNIMHPVAKLSTALAAALMLSGCMPGEIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLLVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGLVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFAGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR"},"dna_sequence":{"accession":"PP895199.1","fmin":"0","fmax":"813","strand":"+","sequence":"ATGGAATTGCCCAATATTATGCACCCGGTCGCGAAGCTGAGCACCGCATTAGCCGCTGCATTGATGCTGAGCGGGTGCATGCCCGGTGAAATCCGCCCGACGATTGGCCAGCAAATGGAAACTGGCGACCAACGGTTTGGCGATCTGGTTTTCCGCCAGCTCGCACCGAATGTCTGGCAGCACACTTCCTATCTCGACATGCCGGGTTTCGGGGCAGTCGCTTCCAACGGTTTGATCGTCAGGGATGGCGGCCGCGTGCTGTTGGTCGATACCGCCTGGACCGATGACCAGACCGCCCAGATCCTCAACTGGATCAAGCAGGAGATCAACCTGCCGGTCGCGCTGGCGGTGGTGACTCACGCGCATCAGGACAAGATGGGCGGTATGGACGCGCTGCATGCGGCGGGGATTGCGACTTATGCCAATGCGTTGTCGAACCAGCTTGCCCCGCAAGAGGGGCTGGTTGCGGCGCAACACAGCCTGACTTTCGCCGCCAATGGCTGGGTCGAACCAGCAACCGCGCCCAACTTTGGCCCGCTCAAGGTATTTTACCCCGGCCCCGGCCACACCAGTGACAATATCACCGTTGGGATCGACGGCACCGACATCGCTTTTGCTGGCTGCCTGATCAAGGACAGCAAGGCCAAGTCGCTCGGCAATCTCGGTGATGCCGACACTGAGCACTACGCCGCGTCAGCGCGCGCGTTTGGTGCGGCGTTCCCCAAGGCCAGCATGATCGTGATGAGCCATTCCGCCCCCGATAGCCGCGCCGCAATCACTCATACGGCCCGCATGGCCGACAAGCTGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3008415","ARO_id":"47207","ARO_name":"NDM-70","CARD_short_name":"NDM-70","ARO_description":"Subclass B1 metallo-beta-lactamase NDM-70.","ARO_category":{"36196":{"category_aro_accession":"3000057","category_aro_cvterm_id":"36196","category_aro_name":"NDM beta-lactamase","category_aro_description":"NDM beta-lactamases or New Delhi metallo-beta-lactamases are class B beta-lactamases that confer resistance to a broad range of antibiotics including carbapenems, cephalosporins and penicillins.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7834":{"model_id":"7834","model_name":"NDM-71","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10661":{"protein_sequence":{"accession":"XFH17879.1","sequence":"MELPNIMHPVAKLSTALAAALMLSGCMPGEIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEIDLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR"},"dna_sequence":{"accession":"PQ117761.1","fmin":"0","fmax":"813","strand":"+","sequence":"ATGGAATTGCCCAATATTATGCACCCGGTCGCGAAGCTGAGCACCGCATTAGCCGCTGCATTGATGCTGAGCGGGTGCATGCCCGGTGAAATCCGCCCGACGATTGGCCAGCAAATGGAAACTGGCGACCAACGGTTTGGCGATCTGGTTTTCCGCCAGCTCGCACCGAATGTCTGGCAGCACACTTCCTATCTCGACATGCCGGGTTTCGGGGCAGTCGCTTCCAACGGTTTGATCGTCAGGGATGGCGGCCGCGTGCTGGTGGTCGATACCGCCTGGACCGATGACCAGACCGCCCAGATCCTCAACTGGATCAAGCAGGAGATCGACCTGCCGGTCGCGCTGGCGGTGGTGACTCACGCGCATCAGGACAAGATGGGCGGTATGGACGCGCTGCATGCGGCGGGGATTGCGACTTATGCCAATGCGTTGTCGAACCAGCTTGCCCCGCAAGAGGGGATGGTTGCGGCGCAACACAGCCTGACTTTCGCCGCCAATGGCTGGGTCGAACCAGCAACCGCGCCCAACTTTGGCCCGCTCAAGGTATTTTACCCCGGCCCCGGCCACACCAGTGACAATATCACCGTTGGGATCGACGGCACCGACATCGCTTTTGGTGGCTGCCTGATCAAGGACAGCAAGGCCAAGTCGCTCGGCAATCTCGGTGATGCCGACACTGAGCACTACGCCGCGTCAGCGCGCGCGTTTGGTGCGGCGTTCCCCAAGGCCAGCATGATCGTGATGAGCCATTCCGCCCCCGATAGCCGCGCCGCAATCACTCATACGGCCCGCATGGCCGACAAGCTGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008416","ARO_id":"47208","ARO_name":"NDM-71","CARD_short_name":"NDM-71","ARO_description":"Subclass B1 metallo-beta-lactamase NDM-71.","ARO_category":{"36196":{"category_aro_accession":"3000057","category_aro_cvterm_id":"36196","category_aro_name":"NDM beta-lactamase","category_aro_description":"NDM beta-lactamases or New Delhi metallo-beta-lactamases are class B beta-lactamases that confer resistance to a broad range of antibiotics including carbapenems, cephalosporins and penicillins.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7835":{"model_id":"7835","model_name":"NDM-72","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10662":{"protein_sequence":{"accession":"XFH17881.1","sequence":"MELPNIMHPVAKLSTALAAALMLNGCMPGEIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLLVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGLVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR"},"dna_sequence":{"accession":"PQ117763.1","fmin":"0","fmax":"813","strand":"+","sequence":"ATGGAATTGCCCAATATTATGCACCCGGTCGCGAAGCTGAGCACCGCATTAGCCGCTGCATTGATGCTGAACGGGTGCATGCCCGGTGAAATCCGCCCGACGATTGGCCAGCAAATGGAAACTGGCGACCAACGGTTTGGCGATCTGGTTTTCCGCCAGCTCGCACCGAATGTCTGGCAGCACACTTCCTATCTCGACATGCCGGGTTTCGGGGCAGTCGCTTCCAACGGTTTGATCGTCAGGGATGGCGGCCGCGTGCTGTTGGTCGATACCGCCTGGACCGATGACCAGACCGCCCAGATCCTCAACTGGATCAAGCAGGAGATCAACCTGCCGGTCGCGCTGGCGGTGGTGACTCACGCGCATCAGGACAAGATGGGCGGTATGGACGCGCTGCATGCGGCGGGGATTGCGACTTATGCCAATGCGTTGTCGAACCAGCTTGCCCCGCAAGAGGGGCTGGTTGCGGCGCAACACAGCCTGACTTTCGCCGCCAATGGCTGGGTCGAACCAGCAACCGCGCCCAACTTTGGCCCGCTCAAGGTATTTTACCCCGGCCCCGGCCACACCAGTGACAATATCACCGTTGGGATCGACGGCACCGACATCGCTTTTGGTGGCTGCCTGATCAAGGACAGCAAGGCCAAGTCGCTCGGCAATCTCGGTGATGCCGACACTGAGCACTACGCCGCGTCAGCGCGCGCGTTTGGTGCGGCGTTCCCCAAGGCCAGCATGATCGTGATGAGCCATTCCGCCCCCGATAGCCGCGCCGCAATCACTCATACGGCCCGCATGGCCGACAAGCTGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008417","ARO_id":"47209","ARO_name":"NDM-72","CARD_short_name":"NDM-72","ARO_description":"Subclass B1 metallo-beta-lactamase NDM-72.","ARO_category":{"36196":{"category_aro_accession":"3000057","category_aro_cvterm_id":"36196","category_aro_name":"NDM beta-lactamase","category_aro_description":"NDM beta-lactamases or New Delhi metallo-beta-lactamases are class B beta-lactamases that confer resistance to a broad range of antibiotics including carbapenems, cephalosporins and penicillins.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7836":{"model_id":"7836","model_name":"NDM-73","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10663":{"protein_sequence":{"accession":"XHO32899.1","sequence":"MELPNIMHPVAKLSSALAAALMLSGCMPGEIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR"},"dna_sequence":{"accession":"PQ394556.1","fmin":"0","fmax":"813","strand":"+","sequence":"ATGGAATTGCCCAATATTATGCACCCGGTCGCGAAGCTGAGCAGCGCATTAGCCGCTGCATTGATGCTGAGCGGGTGCATGCCCGGTGAAATCCGCCCGACGATTGGCCAGCAAATGGAAACTGGCGACCAACGGTTTGGCGATCTGGTTTTCCGCCAGCTCGCACCGAATGTCTGGCAGCACACTTCCTATCTCGACATGCCGGGTTTCGGGGCAGTCGCTTCCAACGGTTTGATCGTCAGGGATGGCGGCCGCGTGCTGGTGGTCGATACCGCCTGGACCGATGACCAGACCGCCCAGATCCTCAACTGGATCAAGCAGGAGATCAACCTGCCGGTCGCGCTGGCGGTGGTGACTCACGCGCATCAGGACAAGATGGGCGGTATGGACGCGCTGCATGCGGCGGGGATTGCGACTTATGCCAATGCGTTGTCGAACCAGCTTGCCCCGCAAGAGGGGATGGTTGCGGCGCAACACAGCCTGACTTTCGCCGCCAATGGCTGGGTCGAACCAGCAACCGCGCCCAACTTTGGCCCGCTCAAGGTATTTTACCCCGGCCCCGGCCACACCAGTGACAATATCACCGTTGGGATCGACGGCACCGACATCGCTTTTGGTGGCTGCCTGATCAAGGACAGCAAGGCCAAGTCGCTCGGCAATCTCGGTGATGCCGACACTGAGCACTACGCCGCGTCAGCGCGCGCGTTTGGTGCGGCGTTCCCCAAGGCCAGCATGATCGTGATGAGCCATTCCGCCCCCGATAGCCGCGCCGCAATCACTCATACGGCCCGCATGGCCGACAAGCTGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008418","ARO_id":"47210","ARO_name":"NDM-73","CARD_short_name":"NDM-73","ARO_description":"Subclass B1 metallo-beta-lactamase NDM-73.","ARO_category":{"36196":{"category_aro_accession":"3000057","category_aro_cvterm_id":"36196","category_aro_name":"NDM beta-lactamase","category_aro_description":"NDM beta-lactamases or New Delhi metallo-beta-lactamases are class B beta-lactamases that confer resistance to a broad range of antibiotics including carbapenems, cephalosporins and penicillins.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7837":{"model_id":"7837","model_name":"NDM-74","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10664":{"protein_sequence":{"accession":"XHO32900.1","sequence":"MELPNIMHPVAKLSTALAAALMLSGCMPGEIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMAALHAAGIATYANALSNQLAPQKGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR"},"dna_sequence":{"accession":"PQ394557.1","fmin":"0","fmax":"813","strand":"+","sequence":"ATGGAATTGCCCAATATTATGCACCCGGTCGCGAAGCTGAGCACCGCATTAGCCGCTGCATTGATGCTGAGCGGGTGCATGCCCGGTGAAATCCGCCCGACGATTGGCCAGCAAATGGAAACTGGCGACCAACGGTTTGGCGATCTGGTTTTCCGCCAGCTCGCACCGAATGTCTGGCAGCACACTTCCTATCTCGACATGCCGGGTTTCGGGGCAGTCGCTTCCAACGGTTTGATCGTCAGGGATGGCGGCCGCGTGCTGGTGGTCGATACCGCCTGGACCGATGACCAGACCGCCCAGATCCTCAACTGGATCAAGCAGGAGATCAACCTGCCGGTCGCGCTGGCGGTGGTGACTCACGCGCATCAGGACAAGATGGGCGGTATGGCCGCGCTGCATGCGGCGGGGATTGCGACTTATGCCAATGCGTTGTCGAACCAGCTTGCCCCGCAAAAGGGGATGGTTGCGGCGCAACACAGCCTGACTTTCGCCGCCAATGGCTGGGTCGAACCAGCAACCGCGCCCAACTTTGGCCCGCTCAAGGTATTTTACCCCGGCCCCGGCCACACCAGTGACAATATCACCGTTGGGATCGACGGCACCGACATCGCTTTTGGTGGCTGCCTGATCAAGGACAGCAAGGCCAAGTCGCTCGGCAATCTCGGTGATGCCGACACTGAGCACTACGCCGCGTCAGCGCGCGCGTTTGGTGCGGCGTTCCCCAAGGCCAGCATGATCGTGATGAGCCATTCCGCCCCCGATAGCCGCGCCGCAATCACTCATACGGCCCGCATGGCCGACAAGCTGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3008419","ARO_id":"47211","ARO_name":"NDM-74","CARD_short_name":"NDM-74","ARO_description":"Subclass B1 metallo-beta-lactamase NDM-74.","ARO_category":{"36196":{"category_aro_accession":"3000057","category_aro_cvterm_id":"36196","category_aro_name":"NDM beta-lactamase","category_aro_description":"NDM beta-lactamases or New Delhi metallo-beta-lactamases are class B beta-lactamases that confer resistance to a broad range of antibiotics including carbapenems, cephalosporins and penicillins.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7839":{"model_id":"7839","model_name":"OXA-1000","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10666":{"protein_sequence":{"accession":"QWA20199.1","sequence":"MTKKALFFAIGTIFLSACSFNTVEQHQIQSISTNKNSEKIKTLFDQAQTEGVLVIKREQTEEVYGNDLKRASTEYVPASTFKMVNALIGLEHHKATPTEVFKWDGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMSKEVKRIGFGNADIGSKVDDFWLVGPLKITPQQEVQFAYKLAHKTLPFSKNVQEQVQSMLFIEEKNGQKIYAKSGWGWDVDPQVGWFTGWVVQPQGEIIAFSLNLEMKKGIPSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"MZ265752.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGACTAAAAAAGCTCTTTTCTTTGCCATTGGTACGATATTTTTATCGGCGTGTTCTTTTAACACCGTAGAACAGCATCAAATACAGTCAATTTCTACCAATAAAAACTCAGAGAAAATTAAAACGTTGTTTGATCAAGCACAAACTGAAGGTGTTTTAGTTATAAAACGTGAGCAAACAGAGGAAGTCTATGGCAATGATCTTAAAAGAGCATCAACCGAATATGTTCCCGCCTCTACCTTTAAAATGGTAAATGCTTTGATTGGACTTGAGCATCATAAAGCAACGCCAACTGAAGTGTTTAAATGGGATGGGCAAAAGCGTTTATTTCCCGATTGGGAAAAAGACATGACATTAGGCGATGCTATGAAAGCTTCTGCTATTCCAGTTTATCAAGAACTAGCTCGACGAATTGGCCTTGATCTTATGTCTAAAGAGGTAAAGCGCATTGGTTTCGGTAATGCTGATATTGGTTCAAAAGTAGATGATTTTTGGCTTGTTGGCCCACTTAAAATTACACCTCAACAAGAAGTACAGTTTGCTTATAAATTAGCCCATAAAACTCTTCCCTTTAGCAAAAATGTACAAGAACAAGTTCAATCTATGCTGTTCATAGAAGAAAAAAATGGACAAAAAATTTATGCCAAAAGTGGTTGGGGATGGGATGTTGACCCACAAGTTGGTTGGTTTACAGGCTGGGTAGTTCAACCTCAGGGAGAAATTATAGCTTTCTCACTTAATCTAGAAATGAAAAAAGGCATACCTAGCTCTATTCGAAAAGAAATTGCTTATAAGGGATTAGAACAACTCGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3008421","ARO_id":"47213","ARO_name":"OXA-1000","CARD_short_name":"OXA-1000","ARO_description":"OXA-213 family carbapenem-hydrolyzing class D beta-lactamase OXA-1000.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46495":{"category_aro_accession":"3007706","category_aro_cvterm_id":"46495","category_aro_name":"OXA-213-like beta-lactamase","category_aro_description":"OXA-213-like enzymes have been identified to be intrinsic to A. calcoaceticus and have been subsequently detected in A. pittii. Phylogenetic analysis of OXA-213-like proteins identified two distinct subgroups within the OXA family. The first group was linked to A. pittii and the second group to A. calcoaceticus. The carbapenemase activity of these OXAs may be related to the species-dependent effect.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7840":{"model_id":"7840","model_name":"OXA-1001","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10667":{"protein_sequence":{"accession":"QWA20201.1","sequence":"MKFKMKGLFCVILSSLAFSGCVYDSKLQRPVISERETEIPLLFNQAQTQAVFVTYDGIHLKSYGNDLSRAKTEYIPASTFKMLNALIGLQNAKATNTEVFHWNGEKRAFSAWEKDMTLAEAMQASAVPVYQELARRIGLELMREEVKRVGFGNAEIGQQVDNFWLVGPLKISPEQEVQFAYQLAMKQLPFDRNVQQQVKDMLYIERRGDSKLYAKSGWGMDVEPQVGWYTGWVEQPNGKVTAFALNMKMQAGDDPAERKQLTLSILDKLGLFFYLR"},"dna_sequence":{"accession":"MZ265754.1","fmin":"0","fmax":"831","strand":"+","sequence":"ATGAAGTTTAAAATGAAAGGTTTATTTTGTGTCATCCTCAGTAGTTTGGCATTTTCAGGTTGTGTTTATGATTCAAAACTACAACGCCCAGTCATATCAGAGCGAGAAACTGAGATTCCTTTATTATTTAATCAAGCACAGACTCAAGCTGTGTTTGTTACTTATGATGGGATTCATCTAAAAAGTTATGGTAATGATCTAAGCCGAGCAAAGACTGAATATATTCCTGCATCTACATTTAAGATGTTGAATGCTTTAATTGGCTTGCAAAATGCAAAAGCAACCAATACTGAAGTATTTCATTGGAATGGTGAAAAGCGCGCTTTTTCAGCATGGGAAAAAGATATGACTTTGGCAGAAGCGATGCAGGCTTCAGCTGTTCCCGTATATCAGGAGCTTGCTCGACGTATTGGCTTGGAATTGATGCGTGAAGAAGTGAAGCGTGTAGGTTTTGGTAATGCGGAGATTGGTCAGCAAGTCGATAATTTTTGGTTGGTGGGTCCTTTAAAAATCTCCCCTGAACAAGAAGTTCAATTTGCCTATCAACTGGCGATGAAGCAATTACCTTTTGATCGAAATGTACAGCAACAAGTCAAAGATATGCTTTATATCGAGAGACGTGGTGACAGTAAACTGTATGCTAAAAGTGGTTGGGGAATGGATGTTGAACCTCAAGTGGGTTGGTATACGGGATGGGTTGAACAACCCAATGGCAAGGTGACTGCATTTGCGTTAAATATGAAAATGCAAGCAGGTGATGATCCAGCTGAACGTAAACAATTAACCTTAAGTATTTTGGACAAATTGGGTCTATTTTTTTATTTAAGATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39090","NCBI_taxonomy_name":"Acinetobacter bereziniae","NCBI_taxonomy_id":"106648"}}}},"ARO_accession":"3008422","ARO_id":"47214","ARO_name":"OXA-1001","CARD_short_name":"OXA-1001","ARO_description":"OXA-229 family carbapenem-hydrolyzing class D beta-lactamase OXA-1001.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46498":{"category_aro_accession":"3007709","category_aro_cvterm_id":"46498","category_aro_name":"OXA-229-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-229.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7841":{"model_id":"7841","model_name":"OXA-1002","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10668":{"protein_sequence":{"accession":"QWA20202.1","sequence":"MTKKALFFAIGTMFLSACSFNTVQQHQIQSISTNKNSEKIKSLFDQAQTTGVLVIKCGQTEEVYGNDLKRASTEYVPASTFKMLNALIGLEHHKATPTEVFKWDVQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMSKEVKRIGFGNADIGSKVDNFWLVGPLKITPQQEAQFAYKLAHKTLPFSKNVQEQVQSMLFIEEKNGRKIYAKSGWGWDVEPQVGWLTGWVVQPQGEIIAFSLNLEMKKGIPSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"MZ265755.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGACTAAAAAAGCTCTTTTCTTTGCCATTGGTACGATGTTTTTATCGGCATGTTCTTTTAATACCGTACAACAACATCAAATACAGTCAATTTCTACCAATAAAAACTCAGAGAAAATTAAATCGTTGTTTGATCAAGCACAAACTACAGGTGTTTTAGTTATAAAATGTGGGCAAACAGAGGAAGTCTATGGCAATGATCTTAAAAGAGCATCAACCGAATATGTTCCCGCCTCTACCTTTAAAATGTTAAATGCTTTGATTGGACTTGAGCATCATAAAGCAACACCAACTGAAGTGTTTAAATGGGATGTGCAAAAGCGTTTATTTCCCGATTGGGAAAAAGACATGACATTAGGCGATGCTATGAAAGCTTCTGCTATTCCAGTTTATCAGGAACTAGCTCGACGAATTGGCCTTGATCTTATGTCTAAAGAGGTAAAACGCATTGGTTTCGGTAATGCTGATATTGGTTCAAAAGTAGATAATTTTTGGCTTGTTGGCCCACTTAAAATTACACCTCAACAAGAAGCCCAGTTTGCTTATAAATTAGCCCACAAAACTCTTCCTTTTAGCAAAAATGTGCAAGAACAAGTTCAATCTATGCTGTTCATAGAAGAAAAAAATGGACGGAAAATTTATGCCAAAAGTGGTTGGGGATGGGATGTGGAGCCTCAAGTGGGCTGGTTAACAGGCTGGGTCGTTCAACCTCAAGGAGAAATTATAGCGTTCTCACTTAATTTAGAAATGAAAAAAGGCATACCTAGTTCTATTCGAAAAGAAATTGCTTATAAAGGATTAGAGCAGCTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3008423","ARO_id":"47215","ARO_name":"OXA-1002","CARD_short_name":"OXA-1002","ARO_description":"OXA-213 family carbapenem-hydrolyzing class D beta-lactamase OXA-1002.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46495":{"category_aro_accession":"3007706","category_aro_cvterm_id":"46495","category_aro_name":"OXA-213-like beta-lactamase","category_aro_description":"OXA-213-like enzymes have been identified to be intrinsic to A. calcoaceticus and have been subsequently detected in A. pittii. Phylogenetic analysis of OXA-213-like proteins identified two distinct subgroups within the OXA family. The first group was linked to A. pittii and the second group to A. calcoaceticus. The carbapenemase activity of these OXAs may be related to the species-dependent effect.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7842":{"model_id":"7842","model_name":"OXA-1003","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10669":{"protein_sequence":{"accession":"QWA20203.1","sequence":"MYKKVLVVATATLFLSACSSNTVKQHQIHAISANKNSEEIKSLFDQAYTTGVLVIKRGQTEEIYGNDLKRASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMAKEVKRIGFGNADIGSKVDNFWLVGPLKITPEQETQFAYELANKTLPFSKNVQEQVQSMMFIEEKNGRKIYAKSGWGWDVEPQVGWLTGWVVQPQGEIVAFSLNLEMKKGIPSSIRKEIAYKGLEQLGVL"},"dna_sequence":{"accession":"MZ265756.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGTATAAAAAAGTCCTTGTCGTTGCGACAGCTACTCTATTTTTATCTGCCTGCTCTTCTAACACGGTAAAACAACATCAAATACACGCTATTTCCGCCAATAAAAATTCAGAAGAAATTAAATCTCTGTTTGATCAGGCATACACCACGGGAGTTTTAGTGATTAAGCGTGGGCAGACCGAAGAAATTTATGGCAATGATCTTAAAAGAGCATCAACAGAATATGTTCCCGCCTCTACCTTTAAAATGCTAAATGCTTTAATTGGACTTGAACACCATAAAGCAACGACAACAGAAGTATTTAAATGGGACGGGCAAAAGCGTTTGTTTCCTGATTGGGAAAAGGACATGACTCTAGGCGATGCAATGAAAGCTTCTGCTATTCCAGTTTATCAAGAACTAGCGCGAAGAATTGGACTTGATCTTATGGCTAAAGAGGTAAAACGTATTGGTTTCGGTAATGCGGACATTGGTTCAAAAGTAGATAATTTTTGGCTTGTAGGTCCACTTAAAATTACACCTGAACAAGAAACCCAATTTGCTTATGAATTAGCTAATAAAACTCTTCCTTTTAGTAAAAATGTACAAGAACAAGTCCAATCAATGATGTTCATAGAAGAAAAAAATGGACGTAAAATTTATGCTAAAAGTGGTTGGGGATGGGATGTTGAACCACAGGTTGGCTGGTTAACCGGCTGGGTCGTTCAACCACAAGGAGAAATTGTAGCGTTCTCACTCAATTTAGAAATGAAAAAAGGAATTCCTAGTTCTATTCGAAAAGAAATTGCTTATAAAGGATTAGAACAACTCGGTGTTTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"47899","NCBI_taxonomy_name":"Acinetobacter oleivorans","NCBI_taxonomy_id":"1148157"}}}},"ARO_accession":"3008424","ARO_id":"47216","ARO_name":"OXA-1003","CARD_short_name":"OXA-1003","ARO_description":"OXA-213 family carbapenem-hydrolyzing class D beta-lactamase OXA-1003.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46495":{"category_aro_accession":"3007706","category_aro_cvterm_id":"46495","category_aro_name":"OXA-213-like beta-lactamase","category_aro_description":"OXA-213-like enzymes have been identified to be intrinsic to A. calcoaceticus and have been subsequently detected in A. pittii. Phylogenetic analysis of OXA-213-like proteins identified two distinct subgroups within the OXA family. The first group was linked to A. pittii and the second group to A. calcoaceticus. The carbapenemase activity of these OXAs may be related to the species-dependent effect.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7843":{"model_id":"7843","model_name":"OXA-1004","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10670":{"protein_sequence":{"accession":"QWA20204.1","sequence":"MPKKLKLLFLSVVVMPSITLLGCQNIQQHVQTLVAQKQTEDQIATAFENIQTSGVLVTYDGKAIQKYGNALNRANQRYIPASTFKMLNALIGIQHHKTSPNEVFKWNGQKRAFTSWEKDLTLAEAMQASAVPVYQELARRIGLELMASEVKRVGYGNQSIGTQVDNFWLVGPLEITPVEEVKFAYALAKKQLAFDSSTQQQVKDMLLIEDIQGTKIYAKSGWGMDVNPQVGWWTGWVEQPNGQVTAFSLNMEMKKAAHAEARKAIVYQALQQLGLIRQ"},"dna_sequence":{"accession":"MZ265757.1","fmin":"0","fmax":"837","strand":"+","sequence":"ATGCCGAAAAAATTAAAATTACTCTTTCTATCTGTAGTTGTGATGCCCTCAATAACACTGTTGGGCTGCCAAAATATTCAGCAACACGTTCAAACTTTAGTCGCGCAGAAACAGACTGAAGATCAGATCGCAACTGCATTTGAAAATATCCAGACTTCCGGTGTCCTGGTCACCTATGATGGCAAAGCTATTCAAAAATATGGCAATGCGCTTAACCGGGCCAATCAGCGCTATATTCCTGCTTCCACCTTTAAAATGTTGAATGCCTTGATTGGTATCCAGCATCATAAGACTTCACCGAATGAAGTATTTAAATGGAATGGACAAAAGCGGGCATTTACCAGCTGGGAAAAAGACTTGACCCTGGCAGAAGCCATGCAGGCTTCGGCTGTACCTGTGTATCAGGAACTGGCGCGCCGTATCGGTCTGGAATTAATGGCCAGTGAAGTAAAACGGGTCGGGTATGGCAATCAGTCGATTGGAACGCAAGTGGATAATTTCTGGTTAGTGGGACCTTTAGAAATTACCCCTGTGGAGGAAGTAAAATTTGCCTATGCCTTGGCGAAAAAACAACTTGCATTTGACTCATCAACCCAGCAACAAGTTAAAGATATGTTGCTGATTGAAGATATTCAGGGCACCAAAATCTATGCCAAAAGTGGATGGGGCATGGATGTAAACCCTCAGGTGGGATGGTGGACAGGTTGGGTAGAACAACCCAATGGTCAGGTCACTGCATTTTCACTGAATATGGAAATGAAAAAGGCAGCACATGCAGAAGCACGTAAAGCCATTGTTTATCAGGCCCTGCAACAGCTCGGTTTAATTAGGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41219","NCBI_taxonomy_name":"Acinetobacter courvalinii","NCBI_taxonomy_id":"280147"}}}},"ARO_accession":"3008425","ARO_id":"47217","ARO_name":"OXA-1004","CARD_short_name":"OXA-1004","ARO_description":"OXA-294 family class D beta-lactamase OXA-1004.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46504":{"category_aro_accession":"3007715","category_aro_cvterm_id":"46504","category_aro_name":"OXA-294-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-294.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7844":{"model_id":"7844","model_name":"OXA-1005","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10671":{"protein_sequence":{"accession":"QWA20205.1","sequence":"MKILILLLLVSCLGLTACSLPVSSSPSQSTSTQSTQAIAQLFDQAQSAGVLVIQRDQQIQVYGNDLSRADTEYVPASTFKMLNALIGLQHGKATTNEIFKWDGKKRSFSAWEKDMTLGQAMQASAVPVYQELARRIGLELMEQEVRRIQFGNQHIGQQVDNFWLVGPLKITPKQEVEFVSALAQEQLAFDPQVQQQVKAMLLLQEQQAYRLYAKSGWGMDVEPQVGWLTGWVETPQAEIVAFSLNMQMQNGMDPAIRLEILQQALAELGLYPKAEG"},"dna_sequence":{"accession":"MZ265758.1","fmin":"0","fmax":"831","strand":"+","sequence":"ATGAAAATTCTGATTTTACTGCTTTTAGTTAGTTGCTTGGGCCTGACGGCGTGTAGCCTGCCCGTTTCATCTTCCCCATCTCAAAGCACTTCAACTCAATCTACCCAAGCCATTGCCCAATTATTTGATCAGGCGCAAAGCGCAGGTGTTTTAGTGATTCAGCGTGATCAACAGATACAGGTCTATGGCAATGATTTAAGCCGTGCAGATACCGAATATGTTCCCGCCTCTACTTTTAAAATGCTCAATGCCCTGATTGGCCTGCAACATGGTAAAGCCACAACCAATGAAATTTTTAAATGGGATGGCAAGAAACGCAGTTTTTCAGCCTGGGAAAAAGACATGACTCTCGGCCAAGCCATGCAAGCTTCTGCTGTACCCGTCTATCAGGAACTGGCACGTCGCATTGGCCTTGAATTGATGGAACAGGAAGTGAGACGTATTCAATTCGGCAATCAACATATTGGGCAGCAGGTCGATAACTTCTGGTTGGTAGGCCCTTTGAAAATCACTCCAAAACAGGAAGTCGAATTTGTCTCTGCGCTTGCTCAAGAGCAGCTTGCCTTTGATCCTCAAGTCCAGCAACAAGTCAAAGCCATGTTACTTTTACAGGAACAGCAAGCTTATCGCCTATATGCCAAATCCGGTTGGGGCATGGATGTGGAACCGCAAGTCGGCTGGCTCACCGGCTGGGTTGAAACACCGCAGGCTGAAATCGTGGCATTTTCGCTGAATATGCAGATGCAAAATGGTATGGATCCGGCGATCCGCCTTGAGATTTTGCAGCAGGCTTTGGCCGAATTAGGGCTTTATCCAAAAGCTGAAGGATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39096","NCBI_taxonomy_name":"Acinetobacter schindleri","NCBI_taxonomy_id":"108981"}}}},"ARO_accession":"3008426","ARO_id":"47218","ARO_name":"OXA-1005","CARD_short_name":"OXA-1005","ARO_description":"OXA-134 family carbapenem-hydrolyzing class D beta-lactamase OXA-1005.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46489":{"category_aro_accession":"3007700","category_aro_cvterm_id":"46489","category_aro_name":"OXA-134-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-134.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7845":{"model_id":"7845","model_name":"OXA-1006","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10672":{"protein_sequence":{"accession":"QWA20206.1","sequence":"MKKFVLPLLSISILLSLTACSSVQTTFQNVSLVSNEKNKEAIKGYFDEAQTQGVIVIKDNEHVAMYGNSLTRAHTQYVPASTFKILNALIGLENNKVTTDEMFKWDGNKKAFSIWEKDMNLGEAMKLSAVPVYQELASRIGLDLMQKEVKRVNFGNANIGTQVDNFWLVGPLKISPIQEVKFADDLAHNKLPFKIETQETVKNMLLIKEINGSKIYAKSGWGMDVKPQVGWLTGWVEQPTGKIISFSLNLEMKKNMAGSIRNEITYKTLANLGII"},"dna_sequence":{"accession":"MZ265759.1","fmin":"0","fmax":"828","strand":"+","sequence":"ATGAAAAAATTTGTACTCCCTTTACTTAGTATTTCAATTTTATTGTCTTTGACTGCATGCTCATCAGTTCAAACTACATTTCAAAATGTTTCATTGGTTTCAAATGAAAAAAATAAAGAGGCTATCAAAGGTTACTTTGATGAGGCCCAAACTCAAGGTGTAATTGTTATTAAGGATAATGAACACGTTGCTATGTATGGAAATAGTTTAACACGAGCACATACACAATATGTTCCAGCATCAACATTTAAAATTTTGAATGCTTTAATTGGATTAGAGAATAATAAAGTAACCACAGATGAGATGTTTAAGTGGGATGGTAACAAAAAAGCTTTCTCAATTTGGGAAAAAGATATGAACCTAGGGGAGGCAATGAAATTATCTGCAGTTCCTGTATATCAAGAGCTTGCAAGTCGTATTGGTTTAGATTTAATGCAGAAAGAAGTAAAACGGGTTAATTTTGGTAATGCTAATATTGGAACTCAAGTCGATAATTTTTGGTTAGTTGGTCCTTTGAAGATTTCACCTATACAAGAGGTTAAATTTGCTGATGATCTTGCACATAACAAATTACCATTCAAAATAGAGACACAAGAAACAGTTAAAAATATGCTTCTAATTAAAGAAATTAATGGAAGTAAAATTTATGCCAAAAGTGGTTGGGGGATGGACGTTAAACCTCAAGTAGGTTGGTTAACTGGTTGGGTGGAACAGCCTACAGGGAAGATAATTTCATTTTCATTAAATTTAGAAATGAAAAAAAATATGGCAGGTTCTATCCGTAATGAAATTACTTATAAAACATTAGCGAATCTTGGGATCATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39092","NCBI_taxonomy_name":"Acinetobacter johnsonii","NCBI_taxonomy_id":"40214"}}}},"ARO_accession":"3008427","ARO_id":"47219","ARO_name":"OXA-1006","CARD_short_name":"OXA-1006","ARO_description":"Class D beta-lactamase OXA-1006.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7846":{"model_id":"7846","model_name":"OXA-1007","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10673":{"protein_sequence":{"accession":"QWA20207.1","sequence":"MYKKVLVVATATLFLSACSSNTVKQHQIHSISANKNSQEIKSLFDQAHTTGVLVIKRGQTEEIFGNDLKRASTEYVPASTFKMLNALIGLEHHKATTAEVFKWDRQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMAKEVKRIGFGNADIGSKVDNFWLVGPLKITPEQETQFAYELANKTLPFSKNVQEQVQSMVFIEEKNGRKIYAKSGWGWDVEPQVGWLTGWVVQPQGEIVAFSLNLEMKKGIPSSIRKEIAYKGLEQLGVL"},"dna_sequence":{"accession":"MZ265760.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGTATAAAAAAGTCCTTGTCGTTGCAACAGCTACTCTATTTTTATCTGCCTGCTCTTCTAATACGGTAAAACAACACCAAATACACTCTATTTCCGCCAATAAAAATTCACAAGAAATTAAATCTCTGTTTGATCAGGCACACACCACGGGAGTTTTAGTGATTAAGCGTGGGCAGACCGAAGAAATTTTTGGCAATGATCTTAAAAGAGCATCAACAGAATATGTTCCCGCCTCTACATTTAAAATGCTAAATGCTTTAATTGGACTTGAACATCATAAAGCAACGACAGCTGAAGTATTTAAATGGGACCGGCAAAAGCGTTTGTTTCCTGATTGGGAAAAGGACATGACTTTAGGCGATGCAATGAAAGCTTCTGCTATTCCAGTTTATCAAGAACTAGCCCGAAGAATTGGACTTGATCTTATGGCTAAAGAGGTAAAACGTATTGGTTTCGGTAATGCGGACATTGGTTCAAAAGTAGATAATTTTTGGCTTGTCGGCCCACTTAAAATTACACCTGAACAAGAAACCCAATTTGCTTATGAATTAGCTAATAAAACTCTTCCATTTAGTAAAAATGTACAAGAACAAGTCCAATCAATGGTGTTCATAGAAGAAAAAAATGGACGTAAAATTTATGCTAAAAGTGGTTGGGGATGGGATGTTGAACCACAAGTTGGCTGGTTAACAGGCTGGGTCGTTCAACCGCAAGGAGAAATTGTGGCATTCTCGCTCAATTTAGAAATGAAAAAAGGAATTCCTAGTTCTATTCGAAAAGAAATTGCTTATAAAGGATTAGAACAACTCGGTGTTTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"47899","NCBI_taxonomy_name":"Acinetobacter oleivorans","NCBI_taxonomy_id":"1148157"}}}},"ARO_accession":"3008428","ARO_id":"47220","ARO_name":"OXA-1007","CARD_short_name":"OXA-1007","ARO_description":"OXA-213 family carbapenem-hydrolyzing class D beta-lactamase OXA-1007.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46495":{"category_aro_accession":"3007706","category_aro_cvterm_id":"46495","category_aro_name":"OXA-213-like beta-lactamase","category_aro_description":"OXA-213-like enzymes have been identified to be intrinsic to A. calcoaceticus and have been subsequently detected in A. pittii. Phylogenetic analysis of OXA-213-like proteins identified two distinct subgroups within the OXA family. The first group was linked to A. pittii and the second group to A. calcoaceticus. The carbapenemase activity of these OXAs may be related to the species-dependent effect.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7847":{"model_id":"7847","model_name":"OXA-1008","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10674":{"protein_sequence":{"accession":"QWA20208.1","sequence":"MTKKALFFAISTIFLSACSFNTVQQHQIHAISTHKNSEEIKSLFDQAQTTGVLVIKRGNTEEIYGNDLKRASTEYVPASTFKMLNALVGLEHHKATTTEVFKWDGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMSKEVKRIGFGNADIGSKVDNFWLVGPLKITPQQEAQFAYELAYTTLPFSKNVQEQVQSMVFVEEKNGRKIYAKSGWGWDVEPQVGWLTGWVVQPQGEIVAFSLNLEMKKGTPSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"MZ265761.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGACTAAAAAAGCTCTTTTCTTTGCCATTAGTACCATATTTTTGTCAGCATGTTCTTTCAATACAGTACAACAGCACCAAATACACGCTATTTCTACACATAAAAATTCAGAAGAAATAAAATCACTGTTTGATCAAGCACAGACCACAGGTGTTTTGGTTATTAAGCGCGGAAATACAGAGGAAATTTATGGCAATGATCTTAAAAGAGCATCAACCGAATATGTCCCCGCATCTACTTTTAAAATGTTAAATGCTCTAGTTGGTCTTGAACATCATAAAGCAACAACAACTGAAGTGTTCAAATGGGATGGACAAAAGCGTTTATTTCCTGATTGGGAAAAGGATATGACTCTGGGTGATGCAATGAAAGCTTCTGCTATTCCCGTGTATCAAGAACTAGCTCGACGAATTGGCCTTGATCTTATGTCCAAAGAGGTCAAGCGTATTGGTTTCGGTAATGCTGATATTGGTTCAAAAGTAGATAATTTTTGGCTTGTCGGTCCACTCAAAATTACGCCTCAACAGGAAGCACAGTTTGCTTATGAATTAGCATATACAACTCTTCCCTTTAGCAAAAATGTACAAGAACAAGTTCAATCTATGGTGTTCGTAGAAGAAAAAAACGGACGTAAAATTTACGCTAAAAGCGGTTGGGGATGGGATGTGGAGCCTCAAGTGGGCTGGTTAACAGGCTGGGTCGTTCAACCACAAGGAGAAATTGTAGCGTTCTCTCTCAATTTAGAAATGAAAAAAGGAACACCCAGTTCTATTCGAAAAGAAATTGCTTATAAAGGATTAGAACAGCTAGGTATTTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42801","NCBI_taxonomy_name":"Acinetobacter lactucae","NCBI_taxonomy_id":"1785128"}}}},"ARO_accession":"3008429","ARO_id":"47221","ARO_name":"OXA-1008","CARD_short_name":"OXA-1008","ARO_description":"OXA-213 family carbapenem-hydrolyzing class D beta-lactamase OXA-1008.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46495":{"category_aro_accession":"3007706","category_aro_cvterm_id":"46495","category_aro_name":"OXA-213-like beta-lactamase","category_aro_description":"OXA-213-like enzymes have been identified to be intrinsic to A. calcoaceticus and have been subsequently detected in A. pittii. Phylogenetic analysis of OXA-213-like proteins identified two distinct subgroups within the OXA family. The first group was linked to A. pittii and the second group to A. calcoaceticus. The carbapenemase activity of these OXAs may be related to the species-dependent effect.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7848":{"model_id":"7848","model_name":"OXA-1009","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10675":{"protein_sequence":{"accession":"QWA20209.1","sequence":"MYKKALIAATSILFLSSCSSNTVKQHQIHSISANKNSEEIKSLFDQAQTTGVLVIKRGQTEEIYGNDLKRASTAYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMSKEVKRVGFGNANIGSKVDNFWLVGPLKITPQQETQFAYQLAHKTLPFSQDVQEQVQSMVFIEEKNGSKIYAKSGWGWDVEPQVGWLTGWVVQPQGEIVAFSLNLEMKKGTPSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"MZ265762.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGTATAAAAAAGCCCTTATCGCTGCAACAAGTATCCTATTTTTATCCTCCTGTTCTTCCAATACGGTAAAACAACATCAAATACACTCTATTTCTGCCAATAAAAATTCAGAAGAAATTAAATCACTGTTTGATCAGGCACAGACCACGGGTGTTTTGGTGATTAAGCGAGGACAAACAGAAGAAATTTATGGCAATGATCTTAAAAGAGCATCGACCGCCTATGTTCCCGCCTCTACCTTTAAAATGTTAAATGCTTTAATTGGACTTGAACATCATAAGGCAACTACAACTGAAGTGTTTAAATGGGATGGACAAAAACGCTTATTTCCTGATTGGGAAAAGGACATGACACTGGGCGATGCCATGAAAGCTTCTGCGATTCCAGTTTACCAAGAATTAGCCCGACGAATTGGTCTAGATCTTATGTCCAAAGAGGTGAAACGAGTTGGTTTTGGTAATGCTAACATTGGTTCAAAAGTAGATAATTTTTGGCTCGTTGGCCCTCTAAAAATTACACCTCAACAAGAAACCCAATTTGCTTATCAATTAGCCCATAAAACGCTTCCATTTAGCCAAGATGTACAAGAACAAGTTCAATCAATGGTGTTCATAGAGGAAAAAAATGGAAGTAAAATTTATGCCAAAAGTGGTTGGGGATGGGATGTTGAACCACAAGTTGGTTGGCTAACAGGCTGGGTCGTTCAACCACAAGGAGAAATTGTGGCATTTTCACTTAATTTAGAAATGAAAAAAGGAACTCCTAGTTCTATCCGAAAAGAAATTGCTTATAAAGGATTAGAACAACTCGGTATTTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39094","NCBI_taxonomy_name":"Acinetobacter calcoaceticus","NCBI_taxonomy_id":"471"}}}},"ARO_accession":"3008430","ARO_id":"47222","ARO_name":"OXA-1009","CARD_short_name":"OXA-1009","ARO_description":"OXA-213 family carbapenem-hydrolyzing class D beta-lactamase OXA-1009.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46495":{"category_aro_accession":"3007706","category_aro_cvterm_id":"46495","category_aro_name":"OXA-213-like beta-lactamase","category_aro_description":"OXA-213-like enzymes have been identified to be intrinsic to A. calcoaceticus and have been subsequently detected in A. pittii. Phylogenetic analysis of OXA-213-like proteins identified two distinct subgroups within the OXA family. The first group was linked to A. pittii and the second group to A. calcoaceticus. The carbapenemase activity of these OXAs may be related to the species-dependent effect.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7849":{"model_id":"7849","model_name":"OXA-1010","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10676":{"protein_sequence":{"accession":"QWA20210.1","sequence":"MTKKALFLAISTIFLSACSFNTVQQHQIHAISTDKNSEEIKSLFDQAQTTGVLVIKRGKTEEIYGNDLKRASTEYVPASTFKMLNALIGLEHHKATTIEVFKWDGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMSKEVKRIGFGNADIGSKVDNFWLVGPLKITPQQEAQFAYELAHKTLPFSKNVQEQVQSMVFVEEKNGRKLYAKSGWGWDVEPQVGWLTGWVVQPQGEIVAFSLNLEMKKGIPSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"MZ265763.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGACTAAAAAAGCTCTTTTCCTTGCTATTAGTACCATATTTTTGTCAGCATGTTCTTTCAATACAGTACAACAGCATCAAATACACGCTATTTCTACCGATAAAAATTCAGAAGAAATTAAATCACTGTTTGATCAAGCACAGACCACTGGTGTTTTGGTTATTAAGCGTGGAAAGACAGAGGAAATTTATGGCAATGATCTTAAAAGAGCATCAACCGAATATGTCCCTGCATCTACCTTTAAAATGTTAAATGCTCTAATTGGTCTTGAACATCATAAAGCAACAACAATTGAAGTGTTCAAATGGGACGGGCAAAAGCGTTTGTTTCCTGATTGGGAAAAAGATATGACCTTAGGCGATGCCATGAAAGCTTCTGCTATTCCTGTGTATCAAGAACTAGCTCGACGAATTGGCCTTGATCTTATGTCCAAAGAGGTCAAGCGTATTGGTTTCGGTAATGCTGATATTGGTTCAAAAGTAGATAATTTTTGGCTTGTCGGTCCACTCAAAATTACGCCTCAACAGGAAGCACAGTTTGCTTATGAATTAGCACATAAAACTCTTCCCTTTAGCAAAAATGTACAAGAACAAGTTCAATCTATGGTGTTCGTAGAAGAAAAAAACGGACGTAAACTTTACGCTAAAAGCGGCTGGGGATGGGATGTTGAGCCTCAAGTGGGATGGTTAACAGGCTGGGTCGTTCAACCTCAAGGAGAAATTGTAGCGTTCTCACTCAATTTAGAAATGAAAAAAGGAATACCTAGTTCTATTCGAAAAGAAATTGCTTATAAAGGATTAGAACAGCTAGGTATTTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42801","NCBI_taxonomy_name":"Acinetobacter lactucae","NCBI_taxonomy_id":"1785128"}}}},"ARO_accession":"3008431","ARO_id":"47223","ARO_name":"OXA-1010","CARD_short_name":"OXA-1010","ARO_description":"OXA-213 family carbapenem-hydrolyzing class D beta-lactamase OXA-1010.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46495":{"category_aro_accession":"3007706","category_aro_cvterm_id":"46495","category_aro_name":"OXA-213-like beta-lactamase","category_aro_description":"OXA-213-like enzymes have been identified to be intrinsic to A. calcoaceticus and have been subsequently detected in A. pittii. Phylogenetic analysis of OXA-213-like proteins identified two distinct subgroups within the OXA family. The first group was linked to A. pittii and the second group to A. calcoaceticus. The carbapenemase activity of these OXAs may be related to the species-dependent effect.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7851":{"model_id":"7851","model_name":"OXA-1012","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10678":{"protein_sequence":{"accession":"QWQ82939.1","sequence":"MRVLALSAVFLVASIIGMPAVAKEWQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGQTRDIATWNRDHNLITAMKYSVVPVYQEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISATEQISFLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYSTSKIGWWVGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP"},"dna_sequence":{"accession":"MZ368699.1","fmin":"0","fmax":"789","strand":"+","sequence":"ATGCGTGTATTAGCCTTATCGGCTGTGTTTTTGGTGGCATCGATTATCGGAATGCCTGCGGTAGCAAAGGAATGGCAAGAAAACAAAAGTTGGAATGCTCACTTTACTGAACATAAATCACAGGGCGTAGTTGTGCTCTGGAATGAGAATAAGCAGCAAGGATTTACCAATAATCTTAAACGGGCGAACCAAGCATTTTTACCCGCATCTACCTTTAAAATTCCCAATAGCTTGATCGCCCTCGATTTGGGCGTGGTTAAGGATGAACACCAAGTCTTTAAGTGGGATGGACAGACGCGCGATATCGCCACTTGGAATCGCGATCATAATCTAATCACCGCGATGAAATATTCAGTTGTGCCTGTTTATCAAGAATTTGCCCGCCAAATTGGCGAGGCACGTATGAGCAAGATGCTACATGCTTTCGATTATGGTAATGAGGACATTTCGGGCAATGTAGACAGTTTCTGGCTCGACGGTGGTATTCGAATTTCGGCCACGGAGCAAATCAGCTTTTTAAGAAAGCTGTATCACAATAAGTTACACGTATCGGAGCGCAGCCAGCGTATTGTCAAACAAGCCATGCTGACCGAAGCCAATGGTGACTATATTATTCGGGCTAAAACTGGATACTCGACTAGTAAGATTGGCTGGTGGGTCGGTTGGGTTGAACTTGATGATAATGTGTGGTTTTTTGCGATGAATATGGATATGCCCACATCGGATGGTTTAGGGCTGCGCCAAGCCATCACAAAAGAAGTGCTCAAACAGGAAAAAATTATTCCCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3008433","ARO_id":"47225","ARO_name":"OXA-1012","CARD_short_name":"OXA-1012","ARO_description":"OXA-48 family class D beta-lactamase OXA-1012.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46510":{"category_aro_accession":"3007721","category_aro_cvterm_id":"46510","category_aro_name":"OXA-48-like beta-lactamase","category_aro_description":"OXA-48-type beta-lactamases are now routinely encountered in bacterial infections caused by carbapenam-resistant Enterobacterales. OXA-48-like proteins confer resistance to penicillin (which is efficiently hydrolyzed) and carbapenam antibiotics (which is more slowly broken down). The spectrum of activity of these variants varies, with some hydrolyzing expanded-spectrum oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7852":{"model_id":"7852","model_name":"OXA-1013","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10679":{"protein_sequence":{"accession":"QWW93433.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDEKGEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIRLEHHKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"MZ424303.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGGAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCCGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008434","ARO_id":"47226","ARO_name":"OXA-1013","CARD_short_name":"OXA-1013","ARO_description":"OXA-51 family carbapenem-hydrolyzing class D beta-lactamase OXA-1013.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7853":{"model_id":"7853","model_name":"OXA-1014","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10680":{"protein_sequence":{"accession":"QWY90351.1","sequence":"MRPLLFSALLLLSGHAQASEWNDSQAVDKLFGAAGVKGTFVLYDVQRQRYVGHDRERAETRFVPASTYKVANSLIGLSTGAVKSADEVLPYGGKPQRFKAWEHDMSLREAIKASNVPVYQELARRIGLERMRADVSRLGYGNAEIGQVVDNFWLVGPLKISAMEQTRFLLRLAQGELPFPAPVQSTVRAMTLLESGPGWELHGKTGWCFDCTPELGWWVGWVKRNERLYGFALNIDMPGGEADIGKRVELGKASLKALGILP"},"dna_sequence":{"accession":"MZ449317.1","fmin":"0","fmax":"789","strand":"+","sequence":"ATGCGCCCTCTCCTCTTCAGCGCCCTTCTCCTGCTTTCCGGGCATGCCCAGGCCAGCGAATGGAACGACAGCCAGGCCGTGGACAAGCTATTCGGCGCGGCCGGGGTGAAAGGCACCTTCGTCCTCTACGATGTGCAGCGGCAGCGCTATGTCGGCCATGACCGGGAGCGCGCGGAAACTCGCTTCGTTCCTGCCTCCACCTACAAGGTGGCGAACAGCCTGATCGGCTTATCCACAGGGGCGGTTAAATCCGCCGACGAGGTTCTTCCCTATGGCGGCAAGCCCCAGCGCTTCAAGGCCTGGGAGCACGACATGAGCCTGCGCGAGGCGATCAAGGCATCGAACGTACCGGTCTACCAGGAACTGGCGCGACGCATCGGCCTGGAGCGGATGCGCGCCGATGTCTCGCGCCTGGGTTACGGCAACGCGGAAATCGGCCAGGTTGTGGATAACTTCTGGTTGGTGGGACCGCTGAAGATCAGCGCGATGGAACAGACCCGCTTTCTGCTCCGACTGGCGCAGGGAGAATTGCCATTCCCCGCCCCGGTGCAGTCCACCGTGCGCGCCATGACCCTGCTGGAAAGCGGCCCGGGCTGGGAGCTGCACGGCAAGACCGGCTGGTGCTTCGACTGCACGCCGGAGCTCGGCTGGTGGGTGGGCTGGGTGAAGCGCAACGAGCGGCTCTACGGCTTCGCCCTGAACATCGACATGCCCGGCGGCGAGGCCGACATCGGCAAGCGCGTCGAACTGGGCAAGGCCAGTCTCAAGGCTCTCGGGATACTGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008435","ARO_id":"47227","ARO_name":"OXA-1014","CARD_short_name":"OXA-1014","ARO_description":"OXA-50 family oxacillin-hydrolyzing class D beta-lactamase OXA-1014.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46513":{"category_aro_accession":"3007724","category_aro_cvterm_id":"46513","category_aro_name":"OXA-50-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-50.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7854":{"model_id":"7854","model_name":"OXA-1015","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10681":{"protein_sequence":{"accession":"QWY90352.1","sequence":"MKTFAAYVITACLSSTALASSITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNNLARASKEYLPASTFKIPDAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLSLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLFLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKGTEVYFFAFNMDIDNENKLPLRKSIPTKIMASEGIIGG"},"dna_sequence":{"accession":"MZ449318.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGAAAACATTTGCCGCATATGTAATTACTGCGTGTCTTTCAAGTACGGCATTAGCTAGTTCAATTACAGAAAATACGTCTTGGAACAAAGAGTTCTCTGCCGAAGCCGTCAATGGTGTTTTCGTGCTTTGTAAAAGTAGCAGTAAATCCTGCGCTACCAATAACTTAGCTCGTGCATCAAAGGAATATCTTCCAGCATCAACATTTAAGATCCCCGACGCAATTATCGGCCTAGAAACTGGTGTCATAAAGAATGAGCATCAGGTTTTCAAATGGGACGGAAAGCCAAGAGCCATGAAACAATGGGAAAGAGACTTGAGCTTAAGAGGGGCAATACAAGTTTCAGCGGTTCCCGTATTTCAACAAATCGCCAGAGAAGTTGGCGAAGTAAGAATGCAGAAATACCTTAAAAAATTTTCATATGGCAACCAGAATATCAGTGGTGGCATTGACAAATTCTGGTTGGAGGGTCAGCTAAGAATTTCCGCAGTTAATCAAGTGGAGTTTCTAGAGTCTCTATTTTTAAATAAATTGTCAGCATCAAAAGAAAATCAGCTAATAGTAAAAGAGGCTTTGGTAACGGAGGCTGCGCCTGAATATCTTGTGCATTCAAAAACTGGTTTTTCTGGTGTGGGAACTGAGTCAAATCCTGGTGTCGCATGGTGGGTTGGTTGGGTTGAGAAGGGAACAGAGGTTTACTTTTTCGCCTTTAACATGGATATAGACAACGAAAATAAGTTGCCGCTAAGAAAATCCATTCCCACCAAAATCATGGCAAGTGAGGGCATCATTGGTGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"47924","NCBI_taxonomy_name":"Pseudomonas indoloxydans","NCBI_taxonomy_id":"404407"}}}},"ARO_accession":"3008436","ARO_id":"47228","ARO_name":"OXA-1015","CARD_short_name":"OXA-1015","ARO_description":"OXA-10 family class D beta-lactamase OXA-1015.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46486":{"category_aro_accession":"3007697","category_aro_cvterm_id":"46486","category_aro_name":"OXA-10-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-10.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7850":{"model_id":"7850","model_name":"OXA-1011","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11361":{"protein_sequence":{"accession":"WP_211816370.1","sequence":"MTIRIFAIFFSTLIFATFAHAQEGTLERSDWKKFFDDYQAKGTIVVADERQADRILSVFDQARATKRYSPASTFKIPHTLFALDVGAVRDEFQVFRWDGIKRSFAGHNQDQNLRSAMRNSTLWVYELFAREIGEEKAKRYLKQIGYGNADPSTSKGDYWIDGTLEISAYEQISFLRKLYRNELPFRVEHQRLVKDLMITEAGRNWILRAKTGWEGRFGWWVGWVEWPTGAVFFALNIDTPNRMDDLFKREAIVRAILHSIDALPPN"},"dna_sequence":{"accession":"NG_076852.1","fmin":"100","fmax":"901","strand":"+","sequence":"ATGACAATCCGAATCTTTGCAATATTTTTCTCCACTCTTATTTTTGCCACTTTCGCGCATGCACAAGAAGGCACGCTAGAACGTTCTGACTGGAAGAAGTTCTTCGACGATTACCAAGCCAAAGGCACGATAGTTGTGGCAGACGAACGTCAAGCAGATCGCATCCTATCGGTTTTTGATCAAGCACGGGCGACAAAACGTTACTCGCCTGCATCAACATTCAAGATTCCACACACACTTTTTGCACTTGATGTAGGTGCTGTTCGTGATGAGTTCCAGGTTTTCCGATGGGACGGTATTAAACGAAGCTTTGCAGGACACAATCAAGACCAAAACTTGCGATCAGCTATGCGAAACTCTACGCTCTGGGTTTATGAGCTATTTGCAAGAGAGATCGGTGAGGAAAAAGCCAAACGCTATTTAAAGCAAATAGGTTATGGCAACGCCGACCCTTCGACAAGCAAAGGCGATTATTGGATAGATGGCACTCTAGAAATTTCTGCGTACGAACAGATTTCGTTTCTCAGAAAACTCTATCGAAATGAATTGCCATTTCGGGTAGAGCATCAGCGCTTGGTCAAAGATCTCATGATTACGGAAGCCGGGCGCAACTGGATTCTGCGCGCAAAGACTGGCTGGGAAGGTAGGTTTGGCTGGTGGGTGGGATGGGTTGAGTGGCCTACCGGCGCCGTATTCTTCGCATTGAATATCGATACGCCAAACAGAATGGATGATCTTTTCAAAAGAGAGGCAATCGTGCGGGCAATCCTCCACTCTATCGACGCGTTGCCGCCCAACTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43788","NCBI_taxonomy_name":"Klebsiella michiganensis","NCBI_taxonomy_id":"1134687"}}}},"ARO_accession":"3008432","ARO_id":"47224","ARO_name":"OXA-1011","CARD_short_name":"OXA-1011","ARO_description":"Class D beta-lactamase OXA-1011.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7855":{"model_id":"7855","model_name":"OXA-1016","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10682":{"protein_sequence":{"accession":"QWY90353.1","sequence":"MKHIFLVFLILCSNFALAEDKAISAIFSTEGVDGTIILKSLRGDKTITHNDARASRRFASASTFKIFNTLIAVQENVVSLSGTAFRWDGKTHDFPDWNRDQTLESAFKVSCVWCYQEIAKQVGEETYRRYLALARYGALSNVADSTTFWLDGSYTVSAVEQVALLKKIYLRELPFRDDAYDALKRVMLAEQTDSYKLYAKTGWAARMNPQIGWYVGYVETSDDVWFFAINLTLRSETDLGLRQQITKAVLRAERIIP"},"dna_sequence":{"accession":"MZ449319.1","fmin":"0","fmax":"774","strand":"+","sequence":"ATGAAGCATATTTTTTTGGTCTTTCTGATTCTTTGCTCAAATTTTGCTCTCGCTGAGGACAAAGCTATTTCGGCTATTTTTTCCACAGAAGGTGTTGATGGGACCATCATTTTGAAGTCGTTGCGAGGAGATAAGACAATCACGCACAATGATGCACGCGCTTCTCGCCGATTCGCGTCAGCCTCGACTTTCAAGATATTCAACACGCTGATTGCAGTTCAAGAAAACGTGGTGAGTTTGTCGGGTACTGCATTCCGATGGGATGGAAAAACGCATGACTTCCCCGACTGGAACCGTGACCAAACACTTGAAAGCGCATTCAAAGTTTCTTGTGTGTGGTGCTATCAGGAAATCGCCAAGCAAGTGGGGGAAGAAACTTATCGACGCTATCTTGCGCTTGCAAGGTATGGTGCTCTGAGCAACGTGGCAGACAGTACAACCTTTTGGCTTGATGGCAGCTATACGGTCAGCGCCGTCGAGCAAGTGGCTCTGTTGAAAAAAATCTATCTGCGAGAACTTCCGTTTCGCGATGACGCCTACGACGCTTTAAAGCGGGTGATGCTGGCAGAGCAGACTGACAGCTACAAGCTTTACGCAAAGACTGGCTGGGCAGCAAGAATGAACCCTCAAATTGGGTGGTACGTTGGATATGTTGAAACATCCGATGATGTATGGTTTTTTGCCATCAATTTGACCTTGAGGTCAGAAACTGACTTAGGTTTGCGCCAGCAAATAACAAAGGCTGTGCTTAGGGCTGAACGCATTATTCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"47924","NCBI_taxonomy_name":"Pseudomonas indoloxydans","NCBI_taxonomy_id":"404407"}}}},"ARO_accession":"3008437","ARO_id":"47229","ARO_name":"OXA-1016","CARD_short_name":"OXA-1016","ARO_description":"OXA-372 family carbapenem-hydrolyzing class D beta-lactamase OXA-1016.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46506":{"category_aro_accession":"3007717","category_aro_cvterm_id":"46506","category_aro_name":"OXA-372-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-372.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7856":{"model_id":"7856","model_name":"OXA-1017","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10683":{"protein_sequence":{"accession":"QXJ78545.1","sequence":"MAIRIFAILFSIFSLATFAHAQEGTLERSDWRKFFSEFQAKGTIVVADERQADRAMLVFDPVRSKKRYSPASTFKIPHTLFALDAGAVRDEFQIFRWDGVNRGFAGHNQDQDLRSAIRNSTVWVYELFAKEIGDDKARRYLKKIDYGNADPSTSNGDYWIEGSLAISAQEQIAFLRKLYRNELPFRVEHQRLVKDLMIVEAGRNWILRAKTGWKGRMGWWVGWVEWPTGSVFFALNIDTPNRMDDLFKREAIVRAILRSIEALPPNPAVNSDAAR"},"dna_sequence":{"accession":"MZ497412.1","fmin":"0","fmax":"828","strand":"+","sequence":"ATGGCAATCCGAATCTTCGCGATACTTTTCTCCATTTTTTCTCTTGCCACTTTCGCGCATGCGCAAGAAGGCACGCTAGAACGTTCTGACTGGAGGAAGTTTTTCAGCGAATTTCAAGCCAAAGGCACGATAGTTGTGGCAGACGAACGCCAAGCGGATCGTGCCATGTTGGTTTTTGATCCTGTGCGATCGAAGAAACGCTACTCGCCTGCATCGACATTCAAGATACCTCATACACTTTTTGCACTTGATGCAGGCGCTGTTCGTGATGAGTTCCAGATTTTTCGATGGGACGGCGTTAACAGGGGCTTTGCAGGCCACAATCAAGACCAAGATTTGCGATCAGCAATACGGAATTCTACTGTTTGGGTGTATGAGCTATTTGCAAAGGAAATTGGTGATGACAAAGCTCGGCGCTATTTGAAGAAAATCGACTATGGCAACGCCGATCCTTCGACAAGTAATGGCGATTACTGGATAGAAGGCAGCCTTGCAATCTCGGCGCAGGAGCAAATTGCATTTCTCAGGAAGCTCTATCGTAACGAGCTGCCCTTTCGGGTAGAACATCAGCGCTTGGTCAAGGATCTCATGATTGTGGAAGCCGGTCGCAACTGGATACTGCGTGCAAAGACGGGCTGGAAAGGCCGTATGGGTTGGTGGGTAGGATGGGTTGAGTGGCCGACTGGCTCCGTATTCTTCGCACTGAATATTGATACGCCAAACAGAATGGATGATCTTTTCAAGAGGGAGGCAATCGTGCGGGCAATCCTTCGCTCTATTGAAGCGTTACCGCCCAACCCGGCAGTCAACTCGGACGCTGCGCGATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3008438","ARO_id":"47230","ARO_name":"OXA-1017","CARD_short_name":"OXA-1017","ARO_description":"OXA-2 family class D beta-lactamase OXA-1017.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46493":{"category_aro_accession":"3007704","category_aro_cvterm_id":"46493","category_aro_name":"OXA-2-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-2.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7857":{"model_id":"7857","model_name":"OXA-1018","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10684":{"protein_sequence":{"accession":"QYH55590.1","sequence":"MRPLLFSALLLLFGHTQASEWNDSQAVDKLFGAAGVKGTFVLYDVQRQRYVGHDRERAETRFVPASTYKVANSLIGLSTGAVRSADEVLPYGGKPQRFKAWEHDMSLRDAIKASNVPVYQELARRIGLERMRANVSRLGYGNAEIGQVVDNFWLVGPLKISAMEQTRFLLRLAQGELPFPAPVQSTVRAMTLLESGPGWELHGKTGWCFDCTPELGWWVGWVKRNERLYGFALNIDMPGGEADIGKRVELGKASLKALGILP"},"dna_sequence":{"accession":"MZ672117.1","fmin":"0","fmax":"789","strand":"+","sequence":"ATGCGCCCTCTCCTCTTCAGTGCCCTTCTCCTGCTTTTCGGGCATACCCAGGCCAGCGAATGGAACGACAGCCAGGCCGTGGACAAGCTATTCGGCGCGGCCGGGGTGAAAGGCACCTTCGTCCTCTACGATGTGCAGCGGCAGCGCTATGTCGGCCATGACCGGGAGCGCGCGGAAACCCGCTTCGTTCCCGCTTCCACCTACAAGGTGGCGAACAGCCTGATCGGCTTATCCACAGGGGCGGTTAGATCCGCCGACGAGGTTCTTCCCTATGGCGGCAAGCCCCAGCGCTTCAAGGCCTGGGAGCACGACATGAGCCTGCGCGACGCGATCAAGGCATCGAACGTACCGGTCTACCAGGAACTGGCGCGGCGCATCGGCCTGGAGCGGATGCGCGCCAATGTCTCGCGCCTGGGTTACGGCAACGCGGAAATCGGCCAGGTTGTGGATAACTTCTGGTTGGTGGGACCGCTGAAGATCAGCGCGATGGAACAGACCCGCTTTCTGCTCCGACTGGCGCAGGGAGAATTGCCATTCCCCGCCCCGGTGCAGTCCACCGTGCGCGCCATGACCCTGCTGGAAAGCGGCCCGGGCTGGGAGCTGCACGGCAAGACCGGCTGGTGCTTCGACTGCACGCCGGAACTCGGCTGGTGGGTGGGCTGGGTGAAGCGCAACGAGCGGCTCTACGGCTTCGCCCTGAACATCGACATGCCCGGCGGCGAGGCCGACATCGGCAAGCGCGTCGAACTGGGCAAGGCCAGTCTCAAGGCTCTCGGGATACTGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008439","ARO_id":"47231","ARO_name":"OXA-1018","CARD_short_name":"OXA-1018","ARO_description":"OXA-50 family oxacillin-hydrolyzing class D beta-lactamase OXA-1018.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46513":{"category_aro_accession":"3007724","category_aro_cvterm_id":"46513","category_aro_name":"OXA-50-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-50.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7858":{"model_id":"7858","model_name":"OXA-1019","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10685":{"protein_sequence":{"accession":"QYH55591.1","sequence":"MRPLLFSALLLLSGHTQASEWNDSQAVDKLFGAAGVKGTFVLYDVQRQRYVGHDRERAETRFVPASTYKVANSLIGLSTGAVRSADEVLPYGGKPQRFKVWEHDMSLRDAIEASNVPVYQELARRIGLERMRANVSRLGYGNAEIGQVVDNFWLVGPLKISAMEQTRFLLRLAQGELPFPAPVQSTVRAMTLLESGPGWELHGKTGWCFDCTPELGWWVGWVKRNERLYGFALNIDMPGGEADTGKRVELGKASLKALGILP"},"dna_sequence":{"accession":"MZ672118.1","fmin":"0","fmax":"789","strand":"+","sequence":"ATGCGCCCTCTCCTCTTCAGCGCCCTTCTCCTGCTCTCCGGGCATACCCAGGCCAGCGAATGGAACGACAGCCAGGCCGTGGACAAGCTATTCGGCGCGGCCGGGGTGAAAGGCACCTTCGTCCTCTACGATGTGCAGCGGCAGCGCTATGTCGGCCATGACCGGGAGCGCGCGGAAACCCGCTTCGTTCCCGCTTCCACCTACAAGGTGGCGAACAGCCTGATCGGCTTATCCACAGGGGCGGTTAGATCCGCCGACGAGGTTCTTCCCTATGGCGGCAAGCCCCAGCGCTTCAAGGTCTGGGAGCACGACATGAGCCTGCGCGACGCGATCGAGGCATCGAACGTACCGGTCTACCAGGAACTGGCGCGGCGCATCGGCCTGGAGCGGATGCGCGCCAATGTCTCCCGCCTGGGTTACGGCAACGCGGAAATCGGCCAGGTTGTGGATAACTTCTGGTTGGTGGGACCGCTGAAGATCAGCGCGATGGAACAAACCCGCTTTCTGCTCCGACTGGCGCAGGGAGAGTTGCCATTCCCCGCCCCGGTGCAGTCCACCGTGCGCGCCATGACCCTGCTGGAAAGCGGCCCGGGCTGGGAGCTGCACGGCAAGACCGGCTGGTGCTTCGACTGCACGCCGGAACTCGGCTGGTGGGTGGGCTGGGTGAAGCGCAACGAGCGGCTCTACGGCTTCGCCCTGAACATCGACATGCCCGGCGGCGAGGCCGACACCGGAAAGCGTGTCGAACTGGGCAAGGCCAGTCTCAAGGCTCTCGGGATACTGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008440","ARO_id":"47232","ARO_name":"OXA-1019","CARD_short_name":"OXA-1019","ARO_description":"OXA-50 family oxacillin-hydrolyzing class D beta-lactamase OXA-1019.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46513":{"category_aro_accession":"3007724","category_aro_cvterm_id":"46513","category_aro_name":"OXA-50-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-50.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7859":{"model_id":"7859","model_name":"OXA-1020","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10686":{"protein_sequence":{"accession":"QYH55592.1","sequence":"MRPLLFSALLLLSGHTQASEWNDSQAVDKLFGAAGVKGTFVLYDVQRQCYVGHDRERAETRFVPASTYKVANSLIGLSTGAVRSADEVLPYGGKPQRFKAWEHDMSLREAIKASNVPVYQELARRIGLERMRANVSRLGYGNAEIGQVVDNFWLVGPLKISAMEQTRFLLRLAQGELPFPAPVQSTVRAMTLLESGPGWELHGKTGWCFDCTPELGWWVGWVKRNERLYGFALNIDMPGGEADIGKRVELGKASLKVLGILP"},"dna_sequence":{"accession":"MZ672119.1","fmin":"0","fmax":"789","strand":"+","sequence":"ATGCGCCCTCTCCTCTTCAGTGCCCTTCTCCTGCTTTCCGGGCATACCCAGGCCAGCGAATGGAACGACAGCCAGGCCGTGGACAAGCTATTCGGCGCGGCCGGGGTGAAAGGCACCTTCGTCCTCTACGATGTGCAGCGGCAGTGCTATGTCGGCCATGACCGGGAGCGCGCGGAAACCCGCTTCGTTCCCGCTTCCACCTACAAGGTGGCGAACAGCCTGATCGGCTTATCCACAGGGGCGGTTAGATCCGCCGACGAGGTTCTTCCCTATGGCGGCAAGCCCCAGCGCTTCAAGGCCTGGGAGCACGACATGAGCCTGCGCGAGGCGATCAAGGCATCGAACGTACCGGTCTACCAGGAACTGGCGCGGCGCATCGGCCTGGAGCGGATGCGCGCCAATGTCTCGCGCCTGGGTTACGGCAACGCGGAAATCGGCCAGGTTGTGGATAACTTCTGGTTGGTGGGACCGCTGAAGATCAGCGCGATGGAACAGACCCGCTTTCTGCTCCGACTGGCGCAGGGAGAATTGCCATTCCCCGCCCCGGTGCAGTCCACCGTGCGCGCCATGACCCTGCTGGAAAGCGGCCCGGGCTGGGAGCTGCACGGCAAGACCGGCTGGTGCTTCGACTGCACGCCGGAACTCGGCTGGTGGGTGGGCTGGGTGAAGCGCAACGAGCGGCTCTACGGCTTCGCCCTGAACATCGACATGCCCGGCGGCGAGGCCGACATCGGCAAGCGCGTCGAACTGGGCAAGGCCAGTCTCAAGGTTCTCGGGATACTGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008441","ARO_id":"47233","ARO_name":"OXA-1020","CARD_short_name":"OXA-1020","ARO_description":"OXA-50 family oxacillin-hydrolyzing class D beta-lactamase OXA-1020.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46513":{"category_aro_accession":"3007724","category_aro_cvterm_id":"46513","category_aro_name":"OXA-50-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-50.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7860":{"model_id":"7860","model_name":"OXA-1021","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10687":{"protein_sequence":{"accession":"QYH55593.1","sequence":"MRPLFFSALLLLFSGHAQASEWNDSQAVDKLFGAAGVKGTFVLYDVQRQRYVGHDRGRAETRFVPASTYKVANSLIGLSTGAVKSADEVLPYGGKPQRFKAWEHDMSLRDAIKASNVPVYQELARRIGLERMRANVSRLGYGNAEIGQVVDNFWLVGPLKISAMEQTRFLLRLAQGELPFPAPVQSTVRAMTLLESGPGWELHGKTGWCFDCTPELGWWVGWVKRNERLYGFALNIDMPGGEADIGKRVELGKASLTALGILP"},"dna_sequence":{"accession":"MZ672120.1","fmin":"0","fmax":"792","strand":"+","sequence":"ATGCGCCCTCTCTTCTTCAGCGCCCTTCTCCTACTCTTCTCCGGGCATGCCCAGGCCAGCGAATGGAACGACAGCCAGGCTGTGGACAAGCTCTTCGGCGCGGCCGGGGTGAAAGGCACCTTCGTCCTCTACGATGTGCAGCGGCAGCGCTATGTCGGCCATGACCGGGGACGCGCGGAAACCCGCTTCGTTCCCGCTTCCACCTACAAGGTGGCGAACAGCCTGATCGGCTTATCCACAGGGGCGGTTAAATCCGCCGACGAGGTTCTTCCCTATGGCGGCAAGCCCCAGCGGTTCAAGGCCTGGGAACACGACATGAGCCTGCGCGACGCGATCAAGGCATCGAACGTACCGGTCTACCAGGAGCTGGCGCGACGCATCGGCCTGGAACGGATGCGCGCCAATGTTTCCCGCCTGGGTTACGGCAATGCGGAAATCGGCCAGGTTGTGGATAACTTCTGGCTGGTGGGACCGCTGAAGATCAGCGCGATGGAGCAGACCCGCTTTCTGCTCCGACTGGCACAGGGAGAATTGCCATTCCCCGCCCCGGTGCAGTCCACCGTGCGCGCCATGACCCTGCTGGAAAGCGGCCCGGGCTGGGAGCTGCACGGCAAGACCGGCTGGTGCTTCGACTGCACGCCGGAACTCGGCTGGTGGGTAGGCTGGGTGAAGCGCAACGAGCGGCTCTATGGCTTCGCCTTGAACATCGACATGCCCGGCGGCGAGGCCGACATCGGCAAGCGCGTCGAACTGGGCAAGGCCAGTCTCACGGCCCTCGGGATACTGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008442","ARO_id":"47234","ARO_name":"OXA-1021","CARD_short_name":"OXA-1021","ARO_description":"OXA-50 family oxacillin-hydrolyzing class D beta-lactamase OXA-1021.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46513":{"category_aro_accession":"3007724","category_aro_cvterm_id":"46513","category_aro_name":"OXA-50-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-50.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7861":{"model_id":"7861","model_name":"OXA-1022","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10688":{"protein_sequence":{"accession":"QYH55594.1","sequence":"MRPLLFSALLLLSGHAQASEWNDSQAVDKLFGAAGVKGTFVLYDVQRQRYVGHDRERAETRFVPASTYKVANSLIGLSTGAVKSADEVLPYGGKPQRFKAWEHDMSLRDAIEASNVPVYQELARRIGLERMRANVSRLGYGNAEIGQVVDNFWLVGPLKISAMEQTRFLLRLAQGELPFPAPVQSTVRAMTLLESGQGWELHGKTGWCFDCTPELGWWVGWVKRNERLYGFALNIDMPGGEADIGKRVELGKASLKALGILP"},"dna_sequence":{"accession":"MZ672121.1","fmin":"0","fmax":"789","strand":"+","sequence":"ATGCGCCCTCTCCTCTTCAGCGCCCTTCTCCTGCTCTCCGGGCATGCCCAGGCCAGCGAATGGAACGACAGCCAGGCCGTGGACAAGCTATTCGGCGCGGCCGGGGTGAAAGGCACCTTCGTCCTCTACGATGTGCAGCGGCAGCGCTATGTCGGCCATGACCGGGAGCGCGCGGAAACTCGCTTCGTTCCTGCCTCCACCTACAAGGTGGCGAACAGCCTGATTGGCTTATCCACAGGGGCGGTTAAATCCGCCGACGAGGTTCTTCCCTATGGCGGCAAGCCCCAGCGCTTCAAGGCCTGGGAGCACGACATGAGCCTGCGCGATGCGATCGAGGCATCGAACGTACCGGTCTACCAGGAACTGGCGCGGCGCATCGGCCTGGAGCGGATGCGCGCCAATGTCTCGCGCCTGGGTTACGGCAACGCGGAAATCGGCCAGGTTGTGGATAACTTCTGGTTGGTGGGACCGCTGAAGATCAGCGCGATGGAGCAGACCCGCTTTCTGCTCCGACTGGCGCAGGGAGAATTGCCATTCCCCGCCCCGGTGCAGTCCACCGTGCGCGCCATGACCCTGCTGGAAAGCGGCCAGGGCTGGGAGCTGCACGGCAAGACCGGCTGGTGCTTCGACTGCACGCCGGAACTCGGCTGGTGGGTGGGCTGGGTGAAGCGCAACGAGCGGCTCTACGGCTTCGCCCTGAACATCGACATGCCCGGCGGCGAGGCCGACATCGGCAAGCGCGTCGAACTGGGCAAGGCCAGTCTCAAGGCTCTCGGGATACTGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008443","ARO_id":"47235","ARO_name":"OXA-1022","CARD_short_name":"OXA-1022","ARO_description":"OXA-50 family oxacillin-hydrolyzing class D beta-lactamase OXA-1022.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46513":{"category_aro_accession":"3007724","category_aro_cvterm_id":"46513","category_aro_name":"OXA-50-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-50.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. 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All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7862":{"model_id":"7862","model_name":"OXA-1023","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10689":{"protein_sequence":{"accession":"QYH55595.1","sequence":"MRPLLFSALLLLSGHAQASEWNDSQAVDKLFGAAGVKGTFVLYNVQRQRYVGHDRERAETRFVPASTYKVANSLIGLSTGAVKSADEVLPYGGKPQRFKAWEHDMSLRDAIKASNVPVYQELARRIGLERMHANVSRLGYGNAEIGQVVDNFWLVGPLKISAMEQTRFLLRLAQGELPFPVPVQSTVRAMTLLESGPGWELHGKTGWCFDCTPELGWWVGWVKRNERLYGFALNIDMPGGEADIGKRVELGKASLKALGILP"},"dna_sequence":{"accession":"MZ672122.1","fmin":"0","fmax":"789","strand":"+","sequence":"ATGCGCCCTCTCCTCTTCAGCGCCCTTCTCCTGCTCTCCGGGCATGCCCAGGCCAGCGAATGGAACGACAGCCAGGCCGTGGACAAGCTATTCGGCGCGGCCGGGGTGAAAGGCACCTTCGTCCTCTACAATGTGCAGCGGCAGCGCTATGTCGGCCACGACCGGGAGCGCGCGGAAACTCGCTTCGTTCCCGCTTCCACCTACAAGGTGGCGAACAGCCTGATTGGCTTATCCACAGGGGCGGTTAAATCCGCCGACGAGGTTCTTCCCTATGGCGGCAAGCCCCAGCGCTTCAAGGCCTGGGAGCACGACATGAGCCTGCGCGACGCGATCAAGGCATCGAACGTACCGGTCTACCAGGAACTGGCGCGGCGCATCGGCCTGGAGCGGATGCACGCCAATGTCTCGCGCCTGGGTTACGGCAACGCGGAAATAGGCCAGGTTGTGGATAACTTCTGGTTGGTGGGACCGCTGAAGATCAGCGCGATGGAACAGACCCGCTTTCTGCTCCGACTGGCGCAGGGAGAATTGCCATTCCCCGTCCCGGTGCAGTCCACCGTGCGCGCCATGACCCTGCTGGAAAGCGGCCCGGGCTGGGAGCTGCACGGCAAGACCGGCTGGTGCTTCGACTGCACGCCGGAACTCGGCTGGTGGGTGGGCTGGGTGAAGCGCAACGAGCGGCTCTACGGCTTCGCCCTGAACATCGACATGCCCGGCGGCGAGGCCGATATCGGCAAGCGCGTCGAACTGGGCAAGGCCAGTCTCAAGGCTCTCGGGATACTGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008444","ARO_id":"47236","ARO_name":"OXA-1023","CARD_short_name":"OXA-1023","ARO_description":"OXA-50 family oxacillin-hydrolyzing class D beta-lactamase OXA-1023.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. 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Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46513":{"category_aro_accession":"3007724","category_aro_cvterm_id":"46513","category_aro_name":"OXA-50-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-50.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7863":{"model_id":"7863","model_name":"OXA-1024","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10690":{"protein_sequence":{"accession":"QYH55596.1","sequence":"MRPLLFSALLLLSGHAQASEWNDSQAVDKLFGAAGVKGTFVLYDVQRQRYVGHDRERAETRFVPASTYKVANSLIGLSTGAVKSADEVLPYGGKPQRFKAWEHDMSLRDAIEASNVPVYQELARRIGLERMRANVSRLGYGNAEIGQVVDNFWLVGPLKISAMEQTRFLLRLAQGELPFPAPVQSTVRTMTLLESGPGWELHGKTGWCFDCTPELGWWVGWVKRNERLYGFALNIDMPGGEADIGKRVELGKASLKALGILP"},"dna_sequence":{"accession":"MZ672123.1","fmin":"0","fmax":"789","strand":"+","sequence":"ATGCGCCCTCTCCTCTTCAGCGCCCTTCTCCTGCTCTCCGGGCATGCCCAGGCCAGCGAATGGAACGACAGCCAGGCCGTGGACAAGCTATTCGGCGCGGCCGGGGTGAAAGGCACCTTCGTCCTCTACGATGTGCAGCGGCAGCGCTATGTCGGCCATGACCGGGAGCGCGCGGAAACTCGCTTCGTTCCTGCCTCCACCTACAAGGTGGCGAACAGCCTGATTGGCTTATCCACAGGGGCGGTTAAATCCGCCGACGAGGTTCTTCCCTATGGCGGCAAGCCCCAGCGCTTCAAGGCCTGGGAGCACGACATGAGCCTGCGCGATGCGATCGAGGCATCGAACGTACCGGTCTACCAGGAACTGGCGCGGCGCATCGGCCTGGAGCGGATGCGCGCCAATGTCTCGCGCCTGGGTTACGGCAACGCGGAAATCGGCCAGGTTGTGGATAACTTCTGGTTGGTGGGACCGCTGAAGATCAGCGCGATGGAACAGACCCGCTTTCTGCTCCGACTGGCGCAGGGAGAATTGCCATTCCCCGCCCCGGTGCAGTCCACCGTGCGCACCATGACCCTGCTGGAAAGCGGCCCGGGCTGGGAGCTGCACGGCAAGACCGGCTGGTGCTTCGACTGCACGCCGGAACTCGGCTGGTGGGTGGGCTGGGTGAAGCGCAACGAGCGGCTCTACGGCTTCGCCCTGAACATCGACATGCCCGGCGGCGAGGCCGACATCGGCAAGCGCGTCGAACTGGGCAAGGCCAGTCTCAAGGCTCTCGGGATACTGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008445","ARO_id":"47237","ARO_name":"OXA-1024","CARD_short_name":"OXA-1024","ARO_description":"OXA-50 family oxacillin-hydrolyzing class D beta-lactamase OXA-1024.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. 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Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46513":{"category_aro_accession":"3007724","category_aro_cvterm_id":"46513","category_aro_name":"OXA-50-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-50.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. 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All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7864":{"model_id":"7864","model_name":"OXA-1025","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10691":{"protein_sequence":{"accession":"QYH55597.1","sequence":"MRPLLFSALLLLSGHTQASEWNDSQAVDKLFGAAGVKGTFVLYDVQRQRYVGHDRERAETRFVPASTYKVANSLIGLSTGAVRSADEVLPYGGKPQRFKAWEHDMSLREAIKASNVPVYQELARRIGLERMRANVSRLGYGNAEIGQVVDNFWLVGPLKISAMEQTHFLLRLAQGELPFPAPVQSTVRAMTLLESSPGWELHGKTGWCFDCTPELGWWVGWVKRNERLYGFALNIDMPGGEADIGKRVELGKASLKALGILP"},"dna_sequence":{"accession":"MZ672124.1","fmin":"0","fmax":"789","strand":"+","sequence":"ATGCGCCCCCTCCTCTTCAGTGCCCTTCTCCTGCTTTCCGGGCATACCCAGGCCAGCGAATGGAACGACAGCCAGGCCGTGGACAAGCTATTCGGCGCGGCCGGGGTGAAAGGCACCTTCGTCCTCTACGATGTGCAGCGGCAGCGCTATGTCGGCCATGACCGGGAGCGCGCGGAAACCCGCTTCGTTCCCGCTTCCACCTACAAGGTGGCGAACAGCCTGATCGGCTTATCCACAGGGGCGGTTAGATCCGCCGACGAGGTTCTTCCCTATGGCGGCAAGCCCCAGCGCTTCAAGGCCTGGGAGCACGACATGAGCCTGCGCGAGGCGATCAAGGCATCGAACGTACCGGTCTACCAGGAACTGGCGCGGCGCATCGGCCTGGAGCGGATGCGCGCCAATGTCTCGCGCCTGGGTTACGGCAACGCGGAAATCGGCCAGGTTGTGGATAACTTCTGGTTGGTGGGACCGCTGAAGATCAGCGCGATGGAACAGACCCACTTTCTGCTCCGACTGGCGCAGGGAGAATTGCCATTCCCCGCCCCGGTGCAGTCCACCGTGCGCGCCATGACCCTGCTGGAAAGCAGCCCGGGCTGGGAACTGCACGGCAAGACCGGCTGGTGCTTCGACTGCACGCCGGAACTCGGCTGGTGGGTGGGCTGGGTGAAGCGCAACGAGCGGCTCTACGGCTTCGCCCTGAACATCGACATGCCCGGCGGCGAGGCCGACATCGGCAAGCGCGTCGAACTGGGCAAGGCCAGTCTCAAGGCTCTCGGGATACTGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008446","ARO_id":"47238","ARO_name":"OXA-1025","CARD_short_name":"OXA-1025","ARO_description":"OXA-50 family oxacillin-hydrolyzing class D beta-lactamase OXA-1025.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46513":{"category_aro_accession":"3007724","category_aro_cvterm_id":"46513","category_aro_name":"OXA-50-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-50.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7865":{"model_id":"7865","model_name":"OXA-1026","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10692":{"protein_sequence":{"accession":"QYH55598.1","sequence":"MRPLLFSALLLLSGHAQASEWNDSRAVDKLFGAAGVKGTFVLYDVQRQRYVGHDRERAETRFVPASTYKVANSLIGLSTGAVRSADEVLPYGGKPQRFKAWEHDMSLREAIKASNVPVYQELARRIGLERMRANVSRLGYGNAEIGQVVDNFWLVGPLNISAMEQTHFLLRLAQGELPFPAPVQSTVRAMTLLESGPGWELHGKTGWCFDCTPELGWWVGWVKRNERLYGFALNIDMPGGEADIGKRVELGKASLKALGILP"},"dna_sequence":{"accession":"MZ672125.1","fmin":"0","fmax":"789","strand":"+","sequence":"ATGCGCCCTCTCCTCTTCAGCGCCCTTCTCCTGCTCTCCGGGCATGCCCAGGCCAGCGAATGGAACGACAGCCGGGCCGTGGACAAGCTATTCGGAGCGGCCGGTGTGAAAGGCACCTTCGTCCTTTACGATGTGCAGCGGCAGCGCTATGTCGGCCATGACCGGGAGCGCGCGGAAACCCGCTTCGTTCCCGCTTCCACCTACAAGGTGGCGAACAGCCTGATCGGCTTATCCACAGGGGCGGTTAGATCCGCCGACGAGGTTCTTCCCTATGGCGGCAAGCCCCAGCGCTTCAAGGCCTGGGAGCACGACATGAGCCTGCGCGAGGCGATCAAGGCATCGAACGTACCGGTCTACCAGGAACTGGCGCGGCGCATCGGCCTGGAGCGGATGCGCGCCAATGTCTCGCGCCTGGGTTACGGCAACGCGGAAATCGGCCAGGTTGTGGATAACTTCTGGTTGGTGGGACCGCTGAATATCAGCGCGATGGAACAGACCCACTTTCTGCTCCGACTGGCGCAGGGAGAATTGCCATTCCCCGCCCCGGTGCAGTCCACCGTGCGCGCCATGACCCTGCTGGAAAGCGGCCCGGGCTGGGAGCTGCACGGCAAGACCGGCTGGTGCTTCGACTGCACGCCGGAACTCGGCTGGTGGGTGGGCTGGGTGAAGCGCAACGAGCGGCTCTACGGCTTCGCCCTGAACATCGACATGCCCGGCGGCGAGGCCGACATCGGCAAGCGCGTCGAACTGGGCAAGGCCAGTCTCAAGGCTCTCGGGATACTGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008447","ARO_id":"47239","ARO_name":"OXA-1026","CARD_short_name":"OXA-1026","ARO_description":"OXA-50 family oxacillin-hydrolyzing class D beta-lactamase OXA-1026.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46513":{"category_aro_accession":"3007724","category_aro_cvterm_id":"46513","category_aro_name":"OXA-50-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-50.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. 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All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7866":{"model_id":"7866","model_name":"OXA-1027","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10693":{"protein_sequence":{"accession":"QYH55599.1","sequence":"MRPLLFSALLLLSGHAQASEWNDSQAVDKLFGAAGVKGTFVLYDVQRQRYVGHDRERAETRFVPASTYKVANSLIGLSTGAVRSADEVLPYGGKPQRFKAWEHDMSLREAIKASNVPVYQELARRIGLERMRANVSRLGYGNAEIGQVVDNFWLVGPLKISAMEQTRFLLRLAQGELPFPAPVQSTVRAMTLLESGPGWELHGKTGWCFDCTPELGWWVGWVKRNERLYGFALNIDMPGGEADIGKRVELGKASLKALGILP"},"dna_sequence":{"accession":"MZ672126.1","fmin":"0","fmax":"789","strand":"+","sequence":"ATGCGCCCTCTCCTCTTCAGCGCCCTTCTCCTGCTCTCCGGGCATGCCCAGGCCAGCGAATGGAACGACAGCCAGGCCGTGGACAAGCTATTCGGCGCGGCCGGTGTGAAAGGCACCTTCGTCCTCTACGATGTGCAGCGGCAGCGCTATGTCGGCCATGACCGGGAGCGCGCGGAAACCCGCTTCGTTCCCGCTTCCACCTACAAGGTGGCGAACAGCCTGATCGGCTTATCCACAGGGGCGGTTAGATCCGCCGACGAGGTTCTTCCCTATGGCGGCAAACCCCAGCGCTTCAAGGCCTGGGAGCACGACATGAGCCTGCGCGAGGCGATCAAGGCATCGAACGTACCGGTCTACCAGGAACTGGCGCGGCGCATCGGCCTGGAGCGGATGCGCGCCAATGTCTCGCGCCTGGGTTACGGCAACGCGGAAATCGGCCAGGTTGTGGATAACTTCTGGTTGGTGGGACCGCTGAAGATCAGCGCGATGGAACAGACCCGCTTTCTGCTCCGACTGGCGCAGGGAGAATTGCCATTCCCCGCCCCGGTGCAGTCCACCGTGCGCGCCATGACCCTGCTGGAAAGCGGCCCGGGCTGGGAGCTGCACGGCAAGACCGGCTGGTGCTTCGACTGCACGCCGGAACTCGGCTGGTGGGTGGGCTGGGTGAAGCGCAACGAGCGGCTCTACGGCTTCGCCCTGAACATCGACATGCCCGGCGGCGAGGCCGACATCGGCAAGCGCGTCGAACTGGGCAAGGCCAGTCTCAAGGCTCTCGGGATACTGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008448","ARO_id":"47240","ARO_name":"OXA-1027","CARD_short_name":"OXA-1027","ARO_description":"OXA-50 family oxacillin-hydrolyzing class D beta-lactamase OXA-1027.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. 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Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46513":{"category_aro_accession":"3007724","category_aro_cvterm_id":"46513","category_aro_name":"OXA-50-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-50.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7867":{"model_id":"7867","model_name":"OXA-1028","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10694":{"protein_sequence":{"accession":"QYH55600.1","sequence":"MRPLLFSALLLLSGHTQASEWNDSQAVDKLFGAAGVKGTFVLYDVQRQCYVGHDRERAETRFVPASTYKVANSLIGLSTGAVRSADEVLPYGGKPQRFKAWEHDMSLREAIKASNVPVYQELARRIGLERMRANVSRLGYGNAEIGQVVDNFWLVGPLKISAMEQTRFLIRLAQGELPFPAPVQSTVRAMTLLESGPGWELHGKTGWCFDCTPELGWWVGWVKRNERLYGFALNIDMPGGEADIGKRVELGKASLKALGILP"},"dna_sequence":{"accession":"MZ672127.1","fmin":"0","fmax":"789","strand":"+","sequence":"ATGCGCCCTCTCCTCTTCAGTGCCCTTCTCCTGCTTTCCGGGCATACCCAGGCCAGCGAATGGAACGACAGCCAGGCCGTGGACAAGCTATTCGGCGCGGCCGGGGTGAAAGGCACCTTCGTCCTCTACGATGTGCAGCGGCAGTGCTATGTCGGCCATGACCGGGAGCGCGCGGAAACCCGCTTCGTTCCCGCTTCCACCTACAAGGTGGCGAACAGCCTGATCGGCTTATCCACAGGGGCGGTTAGATCCGCCGACGAGGTTCTTCCCTATGGCGGCAAGCCCCAGCGCTTCAAGGCCTGGGAGCACGACATGAGCCTGCGCGAGGCGATCAAGGCATCGAACGTACCGGTCTACCAGGAACTGGCGCGGCGCATCGGCCTGGAGCGGATGCGCGCCAATGTCTCGCGCCTGGGTTACGGCAACGCGGAAATCGGCCAGGTTGTGGATAACTTCTGGTTGGTGGGACCGCTGAAGATCAGCGCGATGGAACAGACCCGCTTTCTGATCCGACTGGCGCAGGGAGAATTGCCATTCCCCGCCCCGGTGCAGTCCACCGTGCGCGCCATGACCCTGCTGGAAAGCGGCCCGGGCTGGGAGCTGCACGGCAAGACCGGCTGGTGCTTCGACTGCACGCCGGAGCTCGGCTGGTGGGTGGGCTGGGTGAAGCGCAACGAGCGGCTCTACGGCTTCGCCCTGAACATCGACATGCCCGGCGGCGAGGCCGACATCGGCAAGCGCGTCGAACTGGGCAAGGCCAGTCTCAAGGCTCTCGGGATACTGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008449","ARO_id":"47241","ARO_name":"OXA-1028","CARD_short_name":"OXA-1028","ARO_description":"OXA-50 family oxacillin-hydrolyzing class D beta-lactamase OXA-1028.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46513":{"category_aro_accession":"3007724","category_aro_cvterm_id":"46513","category_aro_name":"OXA-50-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-50.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7868":{"model_id":"7868","model_name":"OXA-1029","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10695":{"protein_sequence":{"accession":"QYH55601.1","sequence":"MRPLLFSALLLLSGPTQASEWNDSQAVDKLFGAAGVKGTFVLYDVQRQRYVGHDRERAETRFVPASTYKVANSLIGLSTGAVRSADEVLPYGGKPQRFKAWEHDMSLRDAIEASNVPVYQELARRIGLERMRANVSRLGYGNAEIGQVVDNFWLVGPLKISAMEQTRFLLRLAQGELPFPAPVQSTVRAMTLLESGPGWELHGKTGWCFDCTPELGWWVGWVKRNERLYGFALNIDMPGGEADTGKRVELGKASLKALGILP"},"dna_sequence":{"accession":"MZ672128.1","fmin":"0","fmax":"789","strand":"+","sequence":"ATGCGCCCTCTCCTCTTCAGCGCCCTTCTCCTGCTCTCCGGGCCTACCCAGGCCAGCGAATGGAACGACAGCCAGGCCGTGGACAAGCTATTCGGCGCGGCCGGGGTGAAAGGCACCTTCGTCCTCTACGATGTGCAGCGGCAGCGCTATGTCGGCCATGACCGGGAGCGCGCGGAAACCCGCTTCGTTCCCGCTTCCACCTACAAGGTGGCGAACAGCCTGATCGGCTTATCCACAGGGGCGGTTAGATCCGCCGATGAGGTTCTTCCCTATGGCGGCAAGCCCCAGCGCTTCAAGGCCTGGGAGCACGACATGAGCCTGCGCGACGCGATCGAGGCATCGAACGTACCGGTCTACCAGGAACTGGCGCGGCGCATCGGCCTGGAGCGGATGCGCGCCAATGTCTCCCGCCTGGGTTACGGCAACGCGGAAATCGGCCAGGTTGTGGATAACTTCTGGTTGGTGGGACCGCTGAAGATCAGCGCGATGGAACAGACCCGCTTTCTGCTCCGACTGGCGCAGGGAGAATTGCCATTCCCCGCCCCGGTGCAGTCCACCGTGCGCGCCATGACCCTGCTGGAAAGCGGCCCGGGCTGGGAGCTGCACGGCAAGACCGGCTGGTGCTTCGACTGCACGCCGGAACTCGGCTGGTGGGTGGGCTGGGTGAAGCGCAACGAGCGGCTCTACGGCTTCGCCCTGAACATCGACATGCCCGGCGGCGAGGCCGACACCGGAAAGCGTGTCGAACTGGGCAAGGCCAGTCTCAAGGCTCTCGGGATACTGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008450","ARO_id":"47242","ARO_name":"OXA-1029","CARD_short_name":"OXA-1029","ARO_description":"OXA-50 family oxacillin-hydrolyzing class D beta-lactamase OXA-1029.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46513":{"category_aro_accession":"3007724","category_aro_cvterm_id":"46513","category_aro_name":"OXA-50-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-50.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7869":{"model_id":"7869","model_name":"OXA-1030","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10696":{"protein_sequence":{"accession":"QYH55602.1","sequence":"MRPLLFSALLLLSGHTQASEWNDSRAVDKLFGAAGVKGTFVLYDVQRQRYVGHDRERAETRFVPASTYKVANSLIGLSTGAVRSADEVLPYGGKPQRFKAWEHDMSLRDAIKASNVPVYQELARRIGLERMRANVSRLGYGNAEIGQVVDNFWLVGPLKISAMEQTRFLLRLAQGELPFPAPVQSTVRAMTLLESGPGWELHGKTGWCFDCTPELGWWVGWVKRNERLYGFALNIDMPGGEADIGKRVELGKASLKALGILP"},"dna_sequence":{"accession":"MZ672129.1","fmin":"0","fmax":"789","strand":"+","sequence":"ATGCGCCCTCTCCTCTTCAGTGCCCTTCTCCTGCTTTCCGGGCATACCCAGGCCAGCGAATGGAACGACAGCCGGGCCGTGGACAAGCTATTCGGCGCGGCCGGGGTGAAAGGCACCTTCGTCCTCTACGATGTGCAGCGGCAGCGCTATGTCGGCCATGACCGGGAGCGCGCGGAAACCCGCTTCGTTCCCGCTTCCACCTACAAGGTGGCGAACAGCCTGATCGGCTTATCCACAGGGGCGGTTAGATCCGCCGACGAGGTTCTTCCCTATGGCGGCAAGCCCCAGCGCTTCAAGGCCTGGGAGCACGACATGAGCCTGCGCGACGCGATCAAGGCATCGAACGTACCGGTCTACCAGGAACTGGCGCGGCGCATCGGCCTGGAGCGGATGCGCGCCAATGTCTCGCGCCTGGGTTACGGCAACGCGGAAATCGGCCAGGTTGTGGATAACTTCTGGTTGGTGGGACCGCTGAAGATCAGCGCGATGGAACAGACCCGCTTTCTGCTCCGACTGGCGCAGGGAGAATTGCCATTCCCCGCCCCGGTGCAGTCCACCGTGCGCGCCATGACCCTGCTGGAAAGCGGCCCGGGCTGGGAGCTGCACGGCAAGACCGGCTGGTGCTTCGACTGCACGCCGGAACTCGGCTGGTGGGTGGGCTGGGTGAAGCGCAACGAGCGGCTCTACGGCTTCGCCCTGAACATCGACATGCCCGGCGGCGAGGCCGACATCGGCAAGCGCGTCGAACTGGGCAAGGCCAGTCTCAAGGCTCTCGGGATACTGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008451","ARO_id":"47243","ARO_name":"OXA-1030","CARD_short_name":"OXA-1030","ARO_description":"OXA-50 family oxacillin-hydrolyzing class D beta-lactamase OXA-1030.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46513":{"category_aro_accession":"3007724","category_aro_cvterm_id":"46513","category_aro_name":"OXA-50-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-50.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7870":{"model_id":"7870","model_name":"OXA-1031","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10697":{"protein_sequence":{"accession":"QYH55603.1","sequence":"MRPLLFSALLLLSGHAQASEWNDSQAVDKLFGAAGVKGTFVLYDVQRQRYVGHDRERAETRFVPASTYKVANSLIGLSTGAVRSADEVLPYGGKPQRFKAWEHDMSLRDAIKASNVPVYQELARRIGLERMRANVSRLGYGNAEIGQVVDNFWLVGPLKISAMEQTRFLLRLAQGELPFPAPVQSTVRAMTLLESGPGWELHGKTGWCFDCTPELGWWVGWVKRNERLYGFALNIDMSGGEADIGKRVELGKASLKALGILP"},"dna_sequence":{"accession":"MZ672130.1","fmin":"0","fmax":"789","strand":"+","sequence":"ATGCGCCCTCTCCTCTTCAGCGCCCTTCTCCTGCTCTCCGGGCATGCCCAGGCCAGCGAATGGAACGACAGCCAGGCCGTGGACAAGCTATTCGGCGCGGCCGGTGTGAAAGGCACCTTCGTCCTCTACGATGTGCAGCGGCAGCGCTATGTCGGCCATGACCGGGAGCGCGCGGAAACCCGCTTCGTTCCCGCTTCCACCTACAAGGTGGCGAACAGCCTGATCGGCTTATCCACAGGGGCGGTTAGATCCGCCGACGAGGTTCTTCCCTATGGCGGCAAACCCCAGCGCTTCAAGGCCTGGGAGCACGACATGAGCCTGCGCGACGCGATCAAGGCATCGAACGTACCGGTCTACCAGGAACTGGCGCGGCGCATCGGCCTGGAGCGGATGCGCGCCAATGTCTCGCGCCTGGGTTACGGCAACGCGGAAATCGGCCAGGTTGTGGATAACTTCTGGTTGGTGGGACCGCTGAAGATCAGCGCGATGGAACAGACCCGCTTTCTGCTCCGACTGGCGCAGGGAGAATTGCCATTCCCCGCCCCGGTGCAGTCCACCGTGCGCGCCATGACCCTGCTGGAAAGCGGCCCGGGCTGGGAGCTGCACGGCAAGACCGGCTGGTGCTTCGACTGCACGCCGGAACTCGGCTGGTGGGTGGGCTGGGTGAAGCGCAACGAGCGGCTCTACGGCTTCGCCCTGAACATCGACATGTCCGGCGGCGAGGCCGACATCGGCAAGCGCGTCGAACTGGGCAAGGCCAGTCTCAAGGCTCTCGGGATACTGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008452","ARO_id":"47244","ARO_name":"OXA-1031","CARD_short_name":"OXA-1031","ARO_description":"OXA-50 family oxacillin-hydrolyzing class D beta-lactamase OXA-1031.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46513":{"category_aro_accession":"3007724","category_aro_cvterm_id":"46513","category_aro_name":"OXA-50-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-50.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7871":{"model_id":"7871","model_name":"OXA-1032","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10698":{"protein_sequence":{"accession":"QYH55604.1","sequence":"MRPLLFSALLLLSGHAQASEWNDSQAVDKLFGAAGVKGTFVLYDVQRQRYVGHDRERAETRFVPASTYKVANSLIGLSTGAVKSADEVLPYGGKPQRFKAWEHDMSLRDAIEASNVPVYQELARRIGLERMRANVSRLGYGNAEIGQVVDNFWLVGPLKISAMEQTRFLLRLAQGELPFPAPVQSTVRAMTLLESGPGWELHGKTGWCFDCTPELGWWVGWVKRNERLYGFALNIDMPGGEADIGKRVELGKASLKALGILP"},"dna_sequence":{"accession":"MZ672131.1","fmin":"0","fmax":"789","strand":"+","sequence":"ATGCGCCCTCTCCTCTTCAGCGCCCTTCTCCTGCTCTCCGGGCATGCCCAGGCCAGCGAATGGAACGACAGCCAGGCCGTGGACAAGCTATTCGGCGCGGCCGGGGTGAAAGGCACCTTCGTCCTCTACGATGTGCAGCGGCAGCGCTATGTCGGCCATGACCGGGAGCGCGCGGAAACTCGCTTCGTTCCTGCCTCCACCTACAAGGTGGCGAACAGCCTGATTGGCTTATCCACAGGGGCGGTTAAATCCGCCGACGAGGTTCTTCCCTATGGCGGCAAGCCCCAGCGCTTCAAGGCCTGGGAGCACGACATGAGCCTGCGCGATGCGATCGAGGCATCGAACGTACCGGTCTACCAGGAACTGGCGCGGCGCATCGGCCTGGAGCGGATGCGCGCCAATGTCTCGCGCCTGGGTTACGGCAACGCGGAAATCGGCCAGGTTGTGGATAACTTCTGGTTGGTGGGACCGCTGAAGATCAGCGCGATGGAACAGACCCGCTTTCTGCTCCGACTGGCCCAGGGAGAATTGCCATTCCCCGCCCCGGTGCAGTCCACCGTGCGCGCTATGACCCTGCTGGAAAGCGGCCCGGGCTGGGAGCTGCACGGCAAGACCGGCTGGTGCTTCGACTGCACGCCGGAACTCGGCTGGTGGGTGGGCTGGGTGAAGCGCAACGAGCGGCTCTACGGCTTCGCCCTGAACATCGACATGCCCGGCGGCGAGGCCGACATCGGCAAGCGCGTCGAACTGGGCAAGGCCAGTCTCAAGGCTCTCGGGATACTGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008453","ARO_id":"47245","ARO_name":"OXA-1032","CARD_short_name":"OXA-1032","ARO_description":"OXA-50 family oxacillin-hydrolyzing class D beta-lactamase OXA-1032.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46513":{"category_aro_accession":"3007724","category_aro_cvterm_id":"46513","category_aro_name":"OXA-50-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-50.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7872":{"model_id":"7872","model_name":"OXA-1033","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10699":{"protein_sequence":{"accession":"QYH55605.1","sequence":"MRPLLLSALLLLSGHTQASEWNDSQAVDKLFGAAGVKGTFVLYDVQRQRYVGHDRERAETRFVPASTYKVANSLIGLSTGAVRSADEVLPYGGKPQRFKAWEHDMSLRDAIEASNVPVYQELARRIGLERMRANVSRLGYGNAEIGQVVDNFWLVGPLKISAMEQTRFLIRLAQGELPFPAPVQSTVRAMTLLESGPGWELHGKTGWCFDCTPELGWWVGWVKRNERLYGFALNIDMPGGEADIGKRVELGKASLKALGILP"},"dna_sequence":{"accession":"MZ672132.1","fmin":"0","fmax":"789","strand":"+","sequence":"ATGCGCCCTCTCCTCTTGAGTGCCCTTCTCCTGCTTTCCGGGCATACCCAGGCCAGCGAATGGAACGACAGCCAGGCCGTGGACAAGCTATTCGGCGCGGCCGGGGTGAAAGGCACCTTCGTCCTCTACGATGTGCAGCGGCAGCGCTATGTCGGCCATGACCGGGAGCGCGCGGAAACCCGCTTCGTTCCCGCTTCCACCTACAAGGTGGCGAACAGCCTGATCGGCTTATCCACAGGGGCGGTTAGATCCGCCGACGAGGTTCTTCCCTATGGCGGCAAGCCCCAGCGCTTCAAGGCCTGGGAGCACGACATGAGCCTGCGCGATGCGATCGAGGCATCGAACGTACCGGTCTACCAGGAACTGGCGCGGCGCATCGGCCTGGAGCGGATGCGCGCCAATGTCTCGCGCCTGGGTTACGGCAACGCGGAAATCGGCCAGGTTGTGGATAACTTCTGGTTGGTGGGACCGCTGAAGATCAGCGCGATGGAACAGACCCGCTTTCTGATCCGACTGGCGCAGGGAGAATTGCCATTCCCCGCCCCGGTGCAGTCCACCGTGCGCGCCATGACCCTGCTGGAAAGCGGCCCGGGCTGGGAGCTGCACGGCAAGACCGGCTGGTGCTTCGACTGCACGCCGGAGCTCGGCTGGTGGGTGGGCTGGGTGAAGCGCAACGAGCGGCTCTACGGCTTCGCCCTGAACATCGACATGCCCGGCGGCGAGGCCGACATCGGCAAGCGCGTCGAACTGGGCAAGGCCAGTCTCAAGGCTCTCGGGATACTGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008454","ARO_id":"47246","ARO_name":"OXA-1033","CARD_short_name":"OXA-1033","ARO_description":"OXA-50 family oxacillin-hydrolyzing class D beta-lactamase OXA-1033.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46513":{"category_aro_accession":"3007724","category_aro_cvterm_id":"46513","category_aro_name":"OXA-50-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-50.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7873":{"model_id":"7873","model_name":"OXA-1034","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10700":{"protein_sequence":{"accession":"QYH55606.1","sequence":"MRPLLLSALLLLSGHTQASEWNDSQAVDKLFGAAGVKGTFVLYDVQRQRYVGHDRERAETRFVPASTYKVANSLIGLSTGAVRSADEVLPYGGKPQRFKAWEHDMSLRDAIKASNVPVYQELARRIGLERMRANVSRLGYGNAEIGQVVDNFWLVGPLKISAMEQTRFLLRLAQGELPFPAPVQSTVRAMTLLESGPGWELHGKTGWCFDCTPELGWWVGWVKRNERLYGFALNIDMPGGEADIGKRVELGKASLKALGILP"},"dna_sequence":{"accession":"MZ672133.1","fmin":"0","fmax":"789","strand":"+","sequence":"ATGCGCCCTCTCCTCTTGAGTGCCCTTCTCCTGCTTTCCGGGCATACCCAGGCCAGCGAATGGAACGACAGCCAGGCCGTGGACAAGCTATTCGGCGCGGCCGGGGTGAAAGGCACCTTCGTCCTCTACGATGTGCAGCGGCAGCGCTATGTTGGCCATGACCGGGAGCGCGCGGAAACCCGCTTCGTTCCCGCTTCCACCTACAAGGTGGCGAACAGCCTGATCGGCTTATCCACAGGGGCGGTTAGATCCGCCGACGAGGTTCTTCCCTATGGCGGCAAGCCCCAGCGCTTCAAGGCCTGGGAGCACGACATGAGCCTGCGCGACGCGATCAAGGCATCGAACGTACCGGTCTACCAGGAACTGGCGCGGCGCATCGGCCTGGAGCGGATGCGCGCCAATGTCTCGCGCCTGGGTTACGGCAACGCGGAAATCGGCCAGGTTGTGGATAACTTCTGGTTGGTGGGACCGCTGAAGATCAGCGCGATGGAACAGACCCGCTTTCTGCTCCGACTGGCGCAGGGAGAATTGCCATTCCCCGCCCCGGTGCAGTCCACCGTGCGCGCCATGACCCTGCTGGAAAGCGGCCCGGGCTGGGAGCTGCACGGCAAGACCGGCTGGTGCTTCGACTGCACGCCGGAACTCGGCTGGTGGGTGGGCTGGGTGAAGCGCAACGAGCGGCTCTACGGCTTCGCCCTGAACATCGACATGCCCGGCGGCGAGGCCGACATCGGCAAGCGCGTCGAACTGGGCAAGGCCAGTCTCAAGGCTCTCGGGATACTGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008455","ARO_id":"47247","ARO_name":"OXA-1034","CARD_short_name":"OXA-1034","ARO_description":"OXA-50 family oxacillin-hydrolyzing class D beta-lactamase OXA-1034.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46513":{"category_aro_accession":"3007724","category_aro_cvterm_id":"46513","category_aro_name":"OXA-50-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-50.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7874":{"model_id":"7874","model_name":"OXA-1035","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10701":{"protein_sequence":{"accession":"QYZ89869.1","sequence":"MRPLLFSTLLLLSGHAQASEWNDSQAVDKLFGAAGVKGTFVLYDVQRQRYVGHDRERAETRFVPASTYKVANSLIGLSTGAVRSADEVLPYGGKPQRFKAWEHDMSLRDAIEASNVPVYQELARRIGLERMRANVSRLGYGNAEIGQVVDNFWLVGPLKISAMEQTRFLLRLAQGELPFPAPVQSTVRAMTLLESGPGWELHGKTGWCFDCTPELGWWVGWVKRNERLYGFALNIDMPGGEADIGKRVELGKASLKALGILP"},"dna_sequence":{"accession":"MZ720789.1","fmin":"0","fmax":"789","strand":"+","sequence":"ATGCGCCCTCTCCTCTTCAGTACCCTTCTCCTGCTTTCCGGGCATGCCCAGGCCAGCGAATGGAACGACAGCCAGGCCGTGGACAAGCTATTCGGCGCGGCCGGGGTGAAAGGCACCTTCGTCCTCTACGATGTGCAGCGGCAGCGCTATGTCGGCCATGACCGGGAGCGCGCGGAAACCCGCTTCGTTCCCGCTTCCACCTACAAGGTGGCGAACAGCCTGATCGGCTTATCCACAGGGGCGGTTAGATCCGCCGACGAGGTTCTTCCCTATGGCGGCAAGCCCCAGCGCTTCAAGGCCTGGGAGCACGACATGAGCCTGCGCGACGCAATCGAGGCATCGAACGTACCGGTCTACCAGGAACTGGCGCGGCGCATCGGCCTGGAGCGGATGCGCGCCAATGTCTCGCGTCTGGGTTACGGCAACGCGGAAATCGGCCAGGTTGTGGATAACTTCTGGTTGGTGGGACCGCTGAAGATCAGCGCGATGGAACAGACCCGCTTTCTGCTCCGACTGGCGCAGGGAGAATTGCCATTCCCCGCCCCGGTGCAGTCCACCGTGCGCGCCATGACCCTGCTGGAAAGCGGCCCGGGCTGGGAGCTGCACGGCAAGACCGGCTGGTGCTTCGACTGCACGCCGGAACTCGGCTGGTGGGTGGGCTGGGTGAAGCGCAACGAGCGGCTCTACGGCTTCGCCCTGAACATCGACATGCCCGGCGGCGAGGCCGACATCGGCAAGCGCGTCGAACTGGGCAAGGCCAGTCTCAAGGCTCTCGGGATACTGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008456","ARO_id":"47248","ARO_name":"OXA-1035","CARD_short_name":"OXA-1035","ARO_description":"OXA-50 family oxacillin-hydrolyzing class D beta-lactamase OXA-1035.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46513":{"category_aro_accession":"3007724","category_aro_cvterm_id":"46513","category_aro_name":"OXA-50-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-50.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7875":{"model_id":"7875","model_name":"OXA-1036","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10702":{"protein_sequence":{"accession":"AUX87883.1","sequence":"MWMLKAISCSVLSWMLLSACSQQPLKDQMQQPLMMQQPRLAELNHMFQAVGSAVVFVTYDGEKLQRFGNDLQRAETAYIPASTFKMLNALIGLQQRKTTTTEVFLWDGKARAMKSWERDMTLAEAMQVSAVPIYQTLARRIGLPLMQKELHRVGYGNAQIGTQVDRFWLDGPLKITPQQEAEFAYRLATQTLPFDAHVQQEVKQMLYVERRGVAKLYAKSGWGADVKPQVGWYVGWVEQPNGKILAFALNMQIQNEQQLAMRKQLTLDALDKLSIFPYL"},"dna_sequence":{"accession":"CP026412.1","fmin":"1625490","fmax":"1626330","strand":"+","sequence":"ATGTGGATGCTAAAAGCGATATCTTGTTCAGTTTTAAGCTGGATGCTGTTAAGTGCATGCAGTCAGCAACCTCTTAAGGACCAAATGCAGCAGCCATTGATGATGCAACAACCACGGTTAGCTGAGTTGAATCATATGTTTCAAGCAGTGGGCAGTGCGGTAGTTTTTGTTACTTATGATGGGGAAAAATTGCAGCGTTTTGGCAATGATTTGCAAAGAGCTGAAACTGCCTATATACCTGCTTCAACTTTTAAAATGTTAAATGCTTTAATTGGTTTACAGCAGCGTAAAACCACGACCACTGAAGTATTTTTATGGGATGGAAAAGCACGCGCAATGAAAAGTTGGGAACGGGATATGACTTTGGCTGAGGCGATGCAAGTCTCAGCAGTTCCCATCTATCAAACCTTGGCTCGACGCATTGGTCTGCCGTTGATGCAAAAAGAGCTTCATCGAGTTGGTTATGGAAATGCTCAGATTGGTACACAGGTTGATCGCTTTTGGTTAGATGGACCCTTAAAAATTACACCGCAACAAGAAGCTGAATTTGCTTACAGACTTGCGACCCAGACCTTACCTTTTGATGCACATGTGCAACAAGAGGTGAAACAAATGCTTTATGTGGAGCGTCGTGGTGTTGCTAAGTTGTATGCTAAGTCAGGATGGGGAGCCGATGTAAAACCTCAGGTGGGTTGGTATGTGGGATGGGTGGAACAGCCCAATGGCAAAATTTTGGCCTTTGCTTTAAATATGCAGATACAGAATGAGCAGCAATTGGCAATGCGTAAACAGCTCACCCTAGATGCTTTAGATAAACTTAGTATCTTTCCTTATTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36837","NCBI_taxonomy_name":"Acinetobacter sp.","NCBI_taxonomy_id":"472"}}}},"ARO_accession":"3008457","ARO_id":"47249","ARO_name":"OXA-1036","CARD_short_name":"OXA-1036","ARO_description":"Carbapenem-hydrolyzing class D beta-lactamase OXA-1036.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7876":{"model_id":"7876","model_name":"OXA-1037","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10703":{"protein_sequence":{"accession":"BDB16607.1","sequence":"MPRMLLSGLLAAGLFCALPASAASGCMLFADGTGKPVSTQGDCAAQLTPASTFKIPLALMGYDSGFLVDEQLPALPFKAGDPDFLPEWKQTTTPSSWMQFSVIWYSQRLTEWLGEARFQHYVDSFDYGNRDLEGNPGKHDGLTQAWLSASLAISPQEQARFLGKMVSGKLPVSAKTLHHTANLMRQPDIDGWQIHGKTGMGYPKLLDGSLDREQQIGWFVGWASKQGKTLIFVHTVIQTPGKQFASLRAREEVFAALPARLKTL"},"dna_sequence":{"accession":"LC650580.1","fmin":"0","fmax":"795","strand":"+","sequence":"ATGCCCCGTATGCTGTTGTCCGGTCTGCTTGCCGCTGGCCTCTTCTGTGCACTGCCTGCCAGCGCCGCTTCTGGCTGCATGCTGTTTGCCGACGGCACCGGCAAACCCGTCAGCACCCAGGGGGACTGTGCCGCCCAGTTGACCCCGGCCTCCACCTTCAAGATCCCGCTGGCACTGATGGGCTATGACAGCGGCTTCCTGGTGGATGAACAACTGCCGGCCCTGCCGTTCAAGGCCGGTGATCCTGATTTCCTGCCGGAGTGGAAACAGACCACCACCCCGAGCAGCTGGATGCAATTCTCGGTCATCTGGTACTCGCAGCGCCTCACCGAGTGGCTGGGAGAGGCTCGCTTCCAGCACTACGTGGACAGCTTCGACTACGGCAACCGGGATCTCGAAGGCAACCCAGGCAAGCACGACGGTCTGACCCAGGCCTGGCTCAGCGCCAGCCTCGCCATCAGCCCCCAGGAGCAAGCCCGCTTCCTTGGCAAGATGGTGAGCGGCAAGCTGCCGGTCTCCGCCAAGACCCTGCACCATACCGCCAACCTGATGCGTCAGCCCGACATCGACGGTTGGCAGATCCACGGCAAGACCGGCATGGGTTACCCCAAGCTGCTGGATGGCAGCCTGGACAGGGAGCAGCAGATCGGCTGGTTCGTCGGCTGGGCCAGCAAACAGGGCAAGACGCTCATCTTCGTCCACACCGTAATCCAGACGCCGGGCAAGCAGTTCGCTTCCCTCAGGGCCAGGGAGGAGGTGTTCGCCGCCCTGCCGGCCCGGTTGAAGACACTCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36936","NCBI_taxonomy_name":"Aeromonas caviae","NCBI_taxonomy_id":"648"}}}},"ARO_accession":"3008458","ARO_id":"47250","ARO_name":"OXA-1037","CARD_short_name":"OXA-1037","ARO_description":"Class D beta-lactamase OXA-1037.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7877":{"model_id":"7877","model_name":"OXA-1040","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10704":{"protein_sequence":{"accession":"UBS26085.1","sequence":"MKKFILPIFSISILVSLSACSSIKTKSEDNFHISSQQHEKAIKSYFDEAQTQGVIIIKEGKNLSTYGNALARANKEYVPASTFKMLNALIGLENHKATTNEIFKWDGKKRTYPMWEKDMTLGEAMALSAVPVYQELARRTGLELMQKEVKRVNFGNTNIGTQVDNFWLVGPLKITPVQEVNFADDLAHNRLPFKLETQEEVKKMLLIKEVNGSKIYAKSGWRMGVTPQVGWLTGWVEQANGKKIPFSLNLEMKEGMSGSIRNEITYKSLENLGII"},"dna_sequence":{"accession":"OK271078.1","fmin":"0","fmax":"828","strand":"+","sequence":"ATGAAAAAATTTATACTTCCTATATTCAGCATTTCTATTCTAGTTTCTCTCAGTGCATGTTCATCTATTAAAACTAAATCTGAAGATAATTTTCATATTTCTTCTCAGCAACATGAAAAAGCTATTAAAAGCTATTTTGATGAAGCTCAAACACAGGGTGTAATTATTATTAAAGAGGGTAAAAATCTTAGCACCTATGGTAATGCTCTTGCACGAGCAAATAAAGAATATGTCCCTGCATCAACATTTAAGATGCTAAATGCTTTAATCGGGCTAGAAAATCATAAAGCAACAACAAATGAGATTTTCAAATGGGATGGTAAAAAAAGAACTTATCCTATGTGGGAGAAAGATATGACTTTAGGTGAGGCAATGGCATTGTCAGCAGTTCCAGTATATCAAGAGCTTGCAAGACGGACTGGCCTAGAGCTAATGCAGAAAGAAGTAAAGCGGGTTAATTTTGGAAATACAAATATTGGAACACAGGTCGATAATTTTTGGTTAGTTGGCCCCCTTAAAATTACACCAGTACAAGAAGTTAATTTTGCCGATGACCTTGCACATAACCGATTACCTTTTAAATTAGAAACTCAAGAAGAAGTTAAAAAAATGCTTCTAATTAAAGAAGTAAATGGTAGTAAGATTTATGCAAAAAGTGGATGGAGAATGGGTGTTACTCCACAGGTAGGTTGGTTGACTGGTTGGGTGGAGCAAGCTAATGGAAAAAAAATCCCCTTTTCGCTCAACTTAGAAATGAAAGAAGGAATGTCTGGTTCTATTCGTAATGAAATTACTTATAAGTCGCTAGAAAATCTTGGAATCATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008459","ARO_id":"47251","ARO_name":"OXA-1040","CARD_short_name":"OXA-1040","ARO_description":"OXA-24 family carbapenem-hydrolyzing class D beta-lactamase OXA-1040.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46500":{"category_aro_accession":"3007711","category_aro_cvterm_id":"46500","category_aro_name":"OXA-24-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-24.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7878":{"model_id":"7878","model_name":"OXA-1041","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10705":{"protein_sequence":{"accession":"UDL18775.1","sequence":"MSRILLSGLLAAGLFCALPASATTGCLLFADGSGKPLSAQGDCASQLTPASTFKIPLALMGYESGFLVDEQLPALPFKAGDPDFLPEWKQTTTPSNWMKFSVIWYSQRLTEWLGEARFQQYVDRFDYGNRELSGNPGKHDGLTQAWLSSSLAISPQEQARFLGKLVSGKLPVSAEAVRRTSTLLRQPDIDGWQIHGKTGMGYPKLLDGSLNRDQQIGWFVGWASKQDKKLIFVHTVVQKPGKQFASLRAKEEVFAALPTELKKL"},"dna_sequence":{"accession":"OK576522.1","fmin":"0","fmax":"795","strand":"+","sequence":"ATGTCCCGCATTCTGTTGTCCGGCCTGCTTGCCGCCGGCCTCTTCTGTGCCTTGCCCGCCAGCGCCACCACGGGTTGCCTGCTGTTTGCCGATGGCAGCGGCAAACCCCTCAGCGCCCAGGGTGACTGCGCCAGCCAGCTGACGCCTGCCTCCACCTTCAAGATCCCACTCGCGCTGATGGGCTATGAGAGCGGCTTCCTGGTGGATGAACAGTTGCCCGCCCTGCCATTCAAAGCCGGTGACCCTGACTTCCTGCCGGAGTGGAAGCAGACCACCACCCCGAGCAACTGGATGAAATTCTCGGTGATCTGGTATTCCCAACGCCTCACCGAATGGCTGGGAGAGGCGCGCTTCCAGCAGTACGTCGACCGCTTCGACTACGGCAACCGGGAGCTCTCGGGCAACCCGGGCAAGCACGACGGTCTGACCCAGGCCTGGCTCAGCTCCAGCCTCGCCATCAGCCCCCAGGAACAGGCCCGCTTCCTCGGCAAGCTGGTGAGCGGCAAGCTGCCGGTCTCCGCCGAGGCGGTGCGCCGCACCAGCACGCTGCTGCGTCAGCCCGACATCGATGGCTGGCAGATCCACGGCAAGACCGGCATGGGCTACCCCAAGCTGCTGGATGGCAGCCTCAACCGGGATCAGCAGATCGGCTGGTTCGTCGGCTGGGCCAGCAAGCAGGACAAGAAGCTCATCTTCGTGCACACAGTGGTGCAAAAACCCGGCAAGCAGTTCGCGTCCCTCAGGGCAAAGGAAGAGGTGTTTGCCGCCTTGCCAACAGAGCTGAAGAAACTCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3008460","ARO_id":"47252","ARO_name":"OXA-1041","CARD_short_name":"OXA-1041","ARO_description":"Carbapenem-hydrolyzing class D beta-lactamase OXA-1041.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7879":{"model_id":"7879","model_name":"OXA-1042","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10706":{"protein_sequence":{"accession":"BDB58062.1","sequence":"MKNTIHINFAIFLIIANIIYSSASASTDISTVASPLFEGTEGCFLLYDASTNAEIAQFNKAKCATQMAPDSTFKIALSLMAFDAEIIDQKTIFKWDKTPKRMEIWNSNHTPKTWMQFSVVWVSQEITQKIGLNKIKNYLKDFDYGNQDFSGDKERNNGLTEAWLESSLKISPEEQIQFLRKIINHNLPVKNSAIENTIENMYLQDLDNSTKLYGKTGAGFTANRTLQNGWFEGFIISKSGHKYVFVSALTGNLGSNLTSSIKAKKNAITILNTLNL"},"dna_sequence":{"accession":"LC651191.1","fmin":"0","fmax":"831","strand":"+","sequence":"ATGAAAAACACAATACATATCAACTTCGCTATTTTTTTAATAATTGCAAATATTATCTACAGCAGCGCCAGTGCATCAACAGATATCTCTACTGTTGCATCTCCATTATTTGAAGGAACTGAAGGTTGTTTTTTACTTTACGATGCATCCACAAACGCTGAAATTGCTCAATTCAATAAAGCAAAGTGTGCAACGCAAATGGCACCAGATTCAACTTTCAAGATCGCATTATCACTTATGGCATTTGATGCGGAAATAATAGATCAGAAAACCATATTCAAATGGGATAAAACCCCCAAAAGAATGGAGATCTGGAACAGCAATCATACACCAAAGACGTGGATGCAATTTTCTGTTGTTTGGGTTTCGCAAGAAATAACCCAAAAAATTGGATTAAATAAAATCAAGAATTATCTCAAAGATTTTGATTATGGAAATCAAGACTTCTCTGGAGATAAAGAAAGAAACAACGGATTAACAGAAGCATGGCTCGAAAGTAGCTTAAAAATTTCACCAGAAGAACAAATTCAATTCCTGCGTAAAATTATTAATCACAATCTCCCAGTTAAAAACTCAGCCATAGAAAACACCATAGAGAACATGTATCTACAAGATCTGGATAATAGTACAAAACTGTATGGGAAAACTGGTGCAGGATTCACAGCAAATAGAACCTTACAAAACGGATGGTTTGAAGGGTTTATTATAAGCAAATCAGGACATAAATATGTTTTTGTGTCCGCACTTACAGGAAACTTGGGGTCGAATTTAACATCAAGCATAAAAGCCAAGAAAAATGCGATCACCATTCTAAACACACTAAATTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39677","NCBI_taxonomy_name":"Aeromonas veronii","NCBI_taxonomy_id":"654"}}}},"ARO_accession":"3008461","ARO_id":"47253","ARO_name":"OXA-1042","CARD_short_name":"OXA-1042","ARO_description":"OXA-1 family class D beta-lactamase OXA-1042.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46485":{"category_aro_accession":"3007696","category_aro_cvterm_id":"46485","category_aro_name":"OXA-1-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-1.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7880":{"model_id":"7880","model_name":"OXA-1043","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10707":{"protein_sequence":{"accession":"QUN38553.1","sequence":"MKPWRHALFAFAGLLAAASSGAHPVCTVVADAATGKVLVQQGDCTTRVTPASTFKVAIGLMGFDAGVLKDAHTPTLDFHAGYPDWGGAPWREPTDPARWMKLSIFWYSQQVTQALGQARFQQYTSAFGYGNADVTSNEGERPGVMGAWVNASLRISPLEQVAFMRRIAQRTLPVSAHAYDMIARITLIDAQPGGWTVHGKTGTGSPGIQYDAAHAYGWFVGWATQGARTLVFANLIQDDARQTPNAGLRARDTFLAALPTLAEPARPQ"},"dna_sequence":{"accession":"CP073669.1","fmin":"2245541","fmax":"2246348","strand":"+","sequence":"TTGAAGCCCTGGCGCCATGCGCTGTTCGCCTTCGCCGGCCTCCTGGCCGCCGCGTCTTCCGGCGCCCATCCCGTCTGCACGGTCGTCGCCGACGCCGCCACCGGCAAGGTGCTCGTGCAGCAGGGCGATTGCACGACCCGCGTGACGCCGGCATCGACGTTCAAGGTCGCAATCGGCCTGATGGGCTTCGACGCCGGCGTGCTGAAGGACGCGCACACGCCCACGCTCGATTTCCATGCCGGCTACCCCGACTGGGGCGGGGCGCCGTGGCGCGAGCCGACCGACCCGGCACGCTGGATGAAGCTGTCGATCTTCTGGTATTCGCAGCAGGTCACGCAGGCGCTGGGGCAAGCGCGCTTCCAGCAGTACACGAGCGCGTTCGGCTACGGCAACGCCGACGTCACCAGCAACGAGGGCGAACGGCCCGGGGTGATGGGCGCGTGGGTCAATGCGTCGCTACGCATCTCGCCGCTCGAACAGGTCGCGTTCATGCGCAGGATCGCGCAACGGACGCTGCCCGTCAGCGCGCACGCGTACGACATGATCGCGCGCATCACGCTGATCGACGCGCAACCGGGCGGCTGGACGGTGCACGGCAAGACCGGCACCGGCTCGCCCGGTATCCAGTACGACGCCGCACACGCATACGGCTGGTTCGTCGGCTGGGCGACGCAGGGTGCGCGCACGCTGGTGTTCGCGAACCTGATCCAGGACGACGCGCGGCAGACGCCGAATGCCGGCCTGCGCGCGCGCGACACGTTCCTCGCGGCGCTGCCGACGCTCGCCGAACCGGCCCGGCCGCAATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41647","NCBI_taxonomy_name":"Burkholderia cenocepacia","NCBI_taxonomy_id":"95486"}}}},"ARO_accession":"3008462","ARO_id":"47254","ARO_name":"OXA-1043","CARD_short_name":"OXA-1043","ARO_description":"Class D beta-lactamase OXA-1043.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7881":{"model_id":"7881","model_name":"OXA-1044","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10708":{"protein_sequence":{"accession":"UGY75799.1","sequence":"MKTLQFGLIALITTFGSACTTISPSVETAKNQQQQSAQQQIQQAFDQLQTTGVIVIKDKHGLHSYGNDLSRAQTPYVPASTFKMLNALIGLEHGKATSTEVFKWDGQKRSFPAWEKDMTLGQAMQASAVPVYQELARRIGLDLMKKEVQRIGYGNQQIGTVVDNFWLVGPLQITPVQEILFVEKLANTQLAFKPDVQHAVQDMLLIEQKPNYKLYAKSGWGMDLEPQVGWWTGWVETATGEKVYFALNMHMKTGISASEREQLVKQSLTALGII"},"dna_sequence":{"accession":"OL809969.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAAAACTTTACAATTTGGACTCATCGCCCTCATTACAACCTTCGGTTCCGCATGTACCACAATAAGCCCCTCCGTAGAAACAGCTAAAAACCAACAGCAACAAAGTGCTCAGCAGCAGATCCAACAGGCCTTCGATCAACTCCAAACCACTGGGGTGATTGTCATTAAGGATAAACATGGCTTACACAGCTACGGCAATGACTTGAGCCGTGCTCAGACACCCTATGTACCCGCCTCTACCTTTAAAATGCTGAATGCATTAATCGGACTAGAACATGGTAAAGCAACCAGCACCGAGGTATTTAAATGGGATGGTCAAAAGCGCAGCTTCCCTGCTTGGGAAAAAGACATGACTTTAGGGCAAGCCATGCAAGCATCTGCCGTTCCCGTTTATCAGGAGCTAGCACGGCGCATTGGCCTAGACCTGATGAAAAAAGAAGTACAGCGCATTGGATATGGCAATCAACAGATTGGCACCGTTGTCGATAATTTTTGGTTAGTCGGTCCACTGCAAATTACGCCTGTTCAAGAAATCCTTTTTGTAGAGAAGCTGGCCAATACACAACTCGCTTTTAAACCCGATGTACAACATGCAGTACAAGACATGCTGCTGATTGAACAAAAACCGAATTATAAACTCTACGCCAAATCTGGTTGGGGCATGGACCTAGAACCGCAAGTGGGCTGGTGGACAGGCTGGGTCGAAACAGCAACAGGTGAAAAAGTGTATTTTGCTTTGAATATGCATATGAAAACAGGGATTTCAGCCAGCGAGCGTGAGCAACTGGTCAAACAAAGTCTGACAGCACTGGGAATAATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39092","NCBI_taxonomy_name":"Acinetobacter johnsonii","NCBI_taxonomy_id":"40214"}}}},"ARO_accession":"3008463","ARO_id":"47255","ARO_name":"OXA-1044","CARD_short_name":"OXA-1044","ARO_description":"OXA-211 family carbapenem-hydrolyzing class D beta-lactamase OXA-1044.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46494":{"category_aro_accession":"3007705","category_aro_cvterm_id":"46494","category_aro_name":"OXA-211-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-211.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7882":{"model_id":"7882","model_name":"OXA-1045","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10709":{"protein_sequence":{"accession":"UHC46317.1","sequence":"MTKKALFFAIGTMFLSACSFNTVEQHQIQSISTNKNSEKIKSLFDQAQTEGVLVIKRGQTEEVYGNDLKRASTEYVPASTFKMLNALIGLEHHKAMPTEVFKWDGQKRLFPDWEKDMTLGDAMKASTIPVYQELARRIGLDLMSKEVKRVGFGNADIGSKVDNFWLVGPLKITPQQEAQFAYELAHKTLPFSKNVQEQVQSMLFIEEKNGRKIYAKSGWGWDVDPQVGWFTGWVVQPQGEIVAFSLNLEMKKGIPSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"OL790815.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGACTAAAAAAGCTCTTTTCTTTGCCATTGGTACGATGTTTTTATCGGCATGTTCTTTTAATACGGTAGAACAGCATCAAATACAGTCAATTTCTACCAATAAAAACTCAGAGAAAATTAAATCGTTGTTTGATCAAGCACAAACTGAAGGTGTTTTAGTTATAAAACGTGGACAAACAGAGGAAGTCTATGGCAATGATCTTAAAAGAGCATCAACCGAATATGTTCCCGCCTCTACCTTTAAAATGTTAAATGCTTTGATTGGACTTGAGCATCATAAAGCAATGCCAACTGAAGTGTTTAAATGGGATGGGCAAAAACGTTTATTTCCTGATTGGGAAAAGGACATGACTCTAGGCGATGCTATGAAAGCTTCTACTATTCCAGTTTATCAGGAACTAGCTCGACGAATTGGCCTTGATCTTATGTCTAAAGAGGTAAAACGCGTTGGTTTCGGTAATGCTGATATTGGTTCAAAAGTAGATAATTTTTGGCTTGTTGGCCCACTTAAAATTACACCTCAGCAGGAAGCACAGTTTGCTTATGAATTAGCCCATAAAACTCTTCCCTTTAGCAAAAATGTACAAGAACAAGTTCAATCTATGCTGTTCATAGAAGAAAAAAATGGACGGAAAATTTATGCCAAAAGTGGTTGGGGATGGGATGTTGACCCACAAGTTGGTTGGTTTACAGGCTGGGTAGTTCAACCACAAGGAGAAATTGTAGCTTTCTCACTTAATTTAGAAATGAAAAAAGGCATACCTAGTTCTATTCGAAAAGAAATTGCTTATAAAGGATTAGAGCAGCTAGGTATTTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3008464","ARO_id":"47256","ARO_name":"OXA-1045","CARD_short_name":"OXA-1045","ARO_description":"OXA-213 family carbapenem-hydrolyzing class D beta-lactamase OXA-1045.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46495":{"category_aro_accession":"3007706","category_aro_cvterm_id":"46495","category_aro_name":"OXA-213-like beta-lactamase","category_aro_description":"OXA-213-like enzymes have been identified to be intrinsic to A. calcoaceticus and have been subsequently detected in A. pittii. Phylogenetic analysis of OXA-213-like proteins identified two distinct subgroups within the OXA family. The first group was linked to A. pittii and the second group to A. calcoaceticus. The carbapenemase activity of these OXAs may be related to the species-dependent effect.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7883":{"model_id":"7883","model_name":"OXA-1046","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10710":{"protein_sequence":{"accession":"UHO07581.1","sequence":"MKTFAAYVIIACLSSTALAGSITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNPNISGGIDKFGLEGQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGIIGG"},"dna_sequence":{"accession":"OL901270.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGAAAACATTTGCCGCATATGTAATTATCGCGTGTCTTTCGAGTACGGCATTAGCTGGTTCAATTACAGAAAATACGTCTTGGAACAAAGAGTTCTCTGCCGAAGCCGTCAATGGTGTCTTCGTGCTTTGTAAAAGTAGCAGTAAATCCTGCGCTACCAATGACTTAGCTCGTGCATCAAAGGAATATCTTCCAGCATCAACATTTAAGATCCCCAACGCAATTATCGGCCTAGAAACTGGTGTCATAAAGAATGAGCATCAGGTTTTCAAATGGGACGGAAAGCCAAGAGCCATGAAGCAATGGGAAAGAGACTTGACCTTAAGAGGGGCAATACAAGTTTCAGCTGTTCCCGTATTTCAACAAATCGCCAGAGAAGTTGGCGAAGTAAGAATGCAGAAATACCTTAAAAAATTTTCCTATGGCAACCCGAATATCAGTGGTGGCATTGACAAATTCGGGTTGGAAGGCCAGCTTAGAATTTCCGCAGTTAATCAAGTGGAGTTTCTAGAGTCTCTATATTTAAATAAATTGTCAGCATCTAAAGAAAACCAGCTAATAGTAAAAGAGGCTTTGGTAACGGAGGCGGCACCTGAATATCTAGTGCATTCAAAAACTGGTTTTTCTGGTGTGGGAACTGAGTCAAATCCTGGTGTCGCATGGTGGGTTGGGTGGGTTGAGAAGGAGACAGAGGTTTACTTTTTCGCCTTTAACATGGATATAGACAACGAAAGTAAGTTGCCGCTAAGAAAATCCATTCCCACCAAAATCATGGAAAGTGAGGGCATCATTGGTGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008465","ARO_id":"47257","ARO_name":"OXA-1046","CARD_short_name":"OXA-1046","ARO_description":"OXA-10 family class D beta-lactamase OXA-1046.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46486":{"category_aro_accession":"3007697","category_aro_cvterm_id":"46486","category_aro_name":"OXA-10-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-10.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7884":{"model_id":"7884","model_name":"OXA-1047","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10711":{"protein_sequence":{"accession":"UHO07585.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDVKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHTATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"OL901274.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGTAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATACGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAACAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008466","ARO_id":"47258","ARO_name":"OXA-1047","CARD_short_name":"OXA-1047","ARO_description":"OXA-51 family carbapenem-hydrolyzing class D beta-lactamase OXA-1047.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7885":{"model_id":"7885","model_name":"OXA-1048","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10712":{"protein_sequence":{"accession":"UHO07586.1","sequence":"MNIKALLLITSAIFISACSPYIVSANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLAGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"OL901275.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGTCTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACTACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGCGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008467","ARO_id":"47259","ARO_name":"OXA-1048","CARD_short_name":"OXA-1048","ARO_description":"OXA-51 family carbapenem-hydrolyzing class D beta-lactamase OXA-1048.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7886":{"model_id":"7886","model_name":"OXA-1049","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10713":{"protein_sequence":{"accession":"UHO07587.1","sequence":"MAIRIFAILFSIFSLATFAHAQEGTLERSDWRKFFSEFQAKGTIVVADERQADRAMLVFDPVRSKKRYSPASTFKIPHTLFALDAGAVRDEFQIFRWDGVNRGFAGHNQDQDLRSAMRNSTVWVYELFAKEIGDDKARRYLKKIDYGNAYPSTSNGDYWIEGSLAISAQEQIAFLRKLYRNELPFRVEHQRLVKDLMIVEAGRNWILRAKTGWEGRMGWWVGWVEWPTGSVFFALNIDTPNRMDDLFKREAIVRAILRSIEALPPNPAVNSDAAR"},"dna_sequence":{"accession":"OL901276.1","fmin":"0","fmax":"828","strand":"+","sequence":"ATGGCAATCCGAATCTTCGCGATACTTTTCTCCATTTTTTCTCTTGCCACTTTCGCGCATGCGCAAGAAGGCACGCTAGAACGTTCTGACTGGAGGAAGTTTTTCAGCGAATTTCAAGCCAAAGGCACGATAGTTGTGGCAGACGAACGCCAAGCGGATCGTGCCATGTTGGTTTTTGATCCTGTGCGATCGAAGAAACGCTACTCGCCTGCATCGACATTCAAGATACCTCATACACTTTTTGCACTTGATGCAGGCGCTGTTCGTGATGAGTTCCAGATTTTTCGATGGGACGGCGTTAACAGGGGCTTTGCAGGCCACAATCAAGACCAAGATTTGCGATCAGCAATGCGGAATTCTACTGTTTGGGTGTATGAGCTATTTGCAAAGGAAATTGGTGATGACAAAGCTCGGCGCTATTTGAAGAAAATCGACTATGGCAACGCCTATCCTTCGACAAGTAATGGCGATTACTGGATAGAAGGCAGCCTTGCAATCTCGGCGCAGGAGCAAATTGCATTTCTCAGGAAGCTCTATCGTAACGAGCTGCCCTTTCGGGTAGAACATCAGCGCTTGGTCAAGGATCTCATGATTGTGGAAGCCGGTCGCAACTGGATACTGCGTGCAAAGACGGGCTGGGAAGGCCGTATGGGTTGGTGGGTAGGATGGGTTGAGTGGCCGACTGGCTCCGTATTCTTCGCACTGAATATTGATACGCCAAACAGAATGGATGATCTTTTCAAGAGGGAGGCAATCGTGCGGGCAATCCTTCGCTCTATTGAAGCGTTACCGCCCAACCCGGCAGTCAACTCGGACGCTGCGCGATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008468","ARO_id":"47260","ARO_name":"OXA-1049","CARD_short_name":"OXA-1049","ARO_description":"OXA-2 family class D beta-lactamase OXA-1049.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46493":{"category_aro_accession":"3007704","category_aro_cvterm_id":"46493","category_aro_name":"OXA-2-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-2.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7887":{"model_id":"7887","model_name":"OXA-1050","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10714":{"protein_sequence":{"accession":"UHO07589.1","sequence":"MYKKVLIVATSILFLSACSSNTVEQHQIYSISANKNSEEIKSLFDQAQTTGVLVIKREQKEEIYGNDLKRASTEYVPASTFKMLNALIGLEHHKATATEVFKWDGQKRLFPDWEKDMTLGNAMKASAIPVYQELARRIGLDLMSKEVKRIGFGNANIGSKVDNFWLVGPLKITPQQEAQFAYQLAHKTLPFSKDVQEQVQSMVFIEEKNGRRIYAKSGWGWDVKPQVGWLTGWVVQPQGEIVAFSLNLEMKKGTPSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"OL901278.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGTATAAAAAAGTCCTTATCGTTGCAACAAGCATCCTATTTTTATCTGCCTGTTCTTCTAATACGGTGGAACAACATCAAATATATTCTATTTCTGCCAATAAAAATTCAGAAGAAATTAAATCACTGTTTGATCAAGCGCAGACCACAGGCGTTTTGGTTATTAAGCGAGAGCAAAAAGAAGAAATTTATGGCAATGACCTTAAAAGAGCATCAACTGAATATGTTCCAGCTTCTACCTTTAAAATGTTAAATGCTTTAATTGGACTTGAACACCATAAGGCAACTGCAACTGAAGTGTTTAAATGGGATGGGCAAAAACGTTTATTTCCTGACTGGGAAAAAGATATGACTCTGGGCAATGCCATGAAAGCTTCTGCTATTCCAGTTTATCAAGAATTAGCCCGACGAATTGGTCTAGACCTTATGTCTAAAGAGGTGAAACGAATTGGTTTCGGTAATGCCAATATTGGTTCAAAAGTAGATAATTTTTGGCTTGTTGGTCCACTAAAAATCACACCTCAACAAGAAGCCCAGTTTGCTTATCAATTGGCCCATAAAACACTTCCATTCAGCAAAGATGTACAAGAACAAGTTCAATCAATGGTGTTCATCGAGGAAAAGAATGGACGTAGAATTTATGCCAAAAGTGGTTGGGGATGGGATGTTAAACCACAAGTTGGTTGGTTAACAGGCTGGGTCGTTCAACCACAAGGAGAAATTGTGGCATTCTCACTTAATTTAGAAATGAAAAAAGGAACTCCTAGCTCTATTCGCAAAGAAATTGCTTATAAAGGCTTAGAACAATTAGGGATTCTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39094","NCBI_taxonomy_name":"Acinetobacter calcoaceticus","NCBI_taxonomy_id":"471"}}}},"ARO_accession":"3008469","ARO_id":"47261","ARO_name":"OXA-1050","CARD_short_name":"OXA-1050","ARO_description":"OXA-213 family carbapenem-hydrolyzing class D beta-lactamase OXA-1050.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46495":{"category_aro_accession":"3007706","category_aro_cvterm_id":"46495","category_aro_name":"OXA-213-like beta-lactamase","category_aro_description":"OXA-213-like enzymes have been identified to be intrinsic to A. calcoaceticus and have been subsequently detected in A. pittii. Phylogenetic analysis of OXA-213-like proteins identified two distinct subgroups within the OXA family. The first group was linked to A. pittii and the second group to A. calcoaceticus. The carbapenemase activity of these OXAs may be related to the species-dependent effect.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7888":{"model_id":"7888","model_name":"OXA-1051","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10715":{"protein_sequence":{"accession":"UHO07590.1","sequence":"MRTRLFPLLGISISIFLSACSSPFIGPKDILPISTTKLSQQTIGSYFNEAQTQGVIVIKDGQNIDTYGNDLTRANTQYVPASTFKMLNALIGLENNKATVDEVFKWDGKKRSYSIWEKDMNLGEAMKLSAVPVYQELAKRIGLDLMQKEVKRVDFGNSNIGTKVDEFWLVGPLKITPIQEVEFADKLAHEELPFKQQVQKQVQDMLLIKEVEGNKIYAKSGWGMNVTPQVGWLTGWVEQPNGKKIAFSLNIEMKPNMSGSVRNEIALKSLKQLGII"},"dna_sequence":{"accession":"OL901279.1","fmin":"0","fmax":"831","strand":"+","sequence":"GTGCGAACACGTTTATTTCCTTTATTAGGCATATCTATTTCAATTTTTTTAAGTGCATGCTCCTCTCCATTTATCGGACCTAAAGACATCTTACCCATTTCTACTACTAAGCTAAGTCAACAAACGATTGGCAGTTACTTTAATGAAGCTCAGACTCAGGGCGTTATTGTTATTAAGGATGGGCAAAATATTGATACTTATGGTAATGATTTAACCAGAGCCAATACACAATATGTACCTGCATCAACTTTTAAGATGTTAAATGCTTTAATTGGTTTGGAAAACAATAAAGCTACAGTCGATGAAGTTTTTAAATGGGATGGGAAAAAACGTTCATATTCTATATGGGAGAAAGATATGAATTTGGGTGAAGCCATGAAGTTATCAGCGGTTCCTGTATATCAAGAACTCGCAAAACGGATAGGCTTGGATCTGATGCAAAAAGAAGTTAAACGAGTCGATTTTGGTAATTCAAATATTGGGACAAAAGTTGATGAATTTTGGTTGGTAGGTCCATTAAAGATTACTCCTATTCAAGAAGTTGAGTTTGCTGACAAACTTGCCCATGAAGAGCTACCATTCAAACAGCAAGTCCAAAAACAAGTTCAAGATATGCTGTTAATAAAGGAAGTAGAGGGTAACAAGATTTATGCTAAGAGTGGTTGGGGAATGAATGTCACCCCTCAGGTAGGTTGGTTAACAGGTTGGGTGGAACAACCTAACGGGAAAAAAATAGCTTTTTCATTGAACATTGAGATGAAACCAAACATGTCTGGTTCAGTCCGTAATGAAATAGCACTTAAATCATTAAAACAATTAGGTATTATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39094","NCBI_taxonomy_name":"Acinetobacter calcoaceticus","NCBI_taxonomy_id":"471"}}}},"ARO_accession":"3008470","ARO_id":"47262","ARO_name":"OXA-1051","CARD_short_name":"OXA-1051","ARO_description":"OXA-679 family carbapenem-hydrolyzing class D beta-lactamase OXA-1051.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46522":{"category_aro_accession":"3007733","category_aro_cvterm_id":"46522","category_aro_name":"OXA-679-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-679.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7889":{"model_id":"7889","model_name":"OXA-1052","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10716":{"protein_sequence":{"accession":"UIC40481.1","sequence":"MKFKMKGLFCVILSSLAFSGCVYDSKLQRPVISERETEIPLLFNQAQTQAVFVTYDGIHLKSYGNDLSRAKTEYIPASTFKMLNALIGLQNAKATNTEVFHWNGEKRAFSAWEKDMTLAEAMQASAVPVYQELARRIGLELMREEVKRVGFGNAEIGQQVDNFWLVGPLKISPEQEVQFAYQLAMKQLPFDRNVQQQVKDMLYIERRGDSKLYAKSGWGMDVEPQVGWYTGWVEQPNGKVTAFALNMSMQAGDDPAERKQLTLSILDKLGLFFYLR"},"dna_sequence":{"accession":"OM105665.1","fmin":"0","fmax":"831","strand":"+","sequence":"ATGAAGTTTAAAATGAAAGGTTTATTTTGTGTCATCCTCAGTAGTTTGGCATTTTCAGGTTGTGTTTATGATTCAAAACTACAACGCCCAGTCATATCAGAGCGAGAAACTGAGATTCCTTTATTATTTAATCAAGCACAGACTCAAGCTGTGTTTGTTACTTATGATGGGATTCATCTAAAAAGTTATGGTAATGATCTAAGCCGAGCAAAGACTGAATATATTCCTGCATCTACATTTAAGATGTTGAATGCTTTAATTGGCTTGCAAAATGCAAAAGCAACCAATACTGAAGTATTTCATTGGAATGGTGAAAAGCGCGCTTTTTCAGCATGGGAAAAAGATATGACTTTGGCAGAAGCGATGCAGGCTTCAGCTGTTCCCGTATATCAGGAGCTTGCTCGACGTATTGGCTTGGAATTGATGCGTGAAGAAGTGAAGCGTGTAGGTTTTGGTAATGCGGAGATTGGTCAGCAAGTCGATAATTTTTGGTTGGTGGGTCCTTTAAAAATCTCCCCTGAACAAGAAGTTCAATTTGCCTATCAACTGGCAATGAAGCAATTACCTTTTGATCGAAATGTACAGCAACAAGTCAAAGATATGCTTTATATCGAGAGACGTGGTGACAGTAAACTGTATGCTAAAAGTGGTTGGGGAATGGATGTTGAACCTCAAGTGGGTTGGTATACGGGATGGGTTGAACAACCCAATGGCAAGGTGACTGCATTTGCGTTAAATATGAGCATGCAAGCAGGTGATGATCCAGCTGAACGTAAACAATTAACCTTAAGTATTTTGGACAAATTGGGTCTATTTTTTTATTTAAGATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39090","NCBI_taxonomy_name":"Acinetobacter bereziniae","NCBI_taxonomy_id":"106648"}}}},"ARO_accession":"3008471","ARO_id":"47263","ARO_name":"OXA-1052","CARD_short_name":"OXA-1052","ARO_description":"OXA-229 family carbapenem-hydrolyzing class D beta-lactamase OXA-1052.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46498":{"category_aro_accession":"3007709","category_aro_cvterm_id":"46498","category_aro_name":"OXA-229-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-229.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7890":{"model_id":"7890","model_name":"OXA-1053","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10717":{"protein_sequence":{"accession":"BDD79959.1","sequence":"MKTFAAYVITACLSSTALASSITENTFWNKEFSAEAVNGVFVLCKSSSKSCATNNLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLSLRGAIQVSAVPVFQKIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLFLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKGTEVYFFAFNMDIDNENKLPLRKSIPTKIMASEGIIGG"},"dna_sequence":{"accession":"LC664104.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGAAAACATTTGCCGCATATGTAATTACTGCGTGTCTTTCAAGTACGGCATTAGCTAGTTCAATTACAGAAAATACGTTTTGGAACAAAGAGTTCTCTGCCGAAGCCGTCAATGGTGTTTTCGTGCTTTGTAAAAGTAGCAGTAAATCCTGCGCTACCAATAACTTAGCTCGTGCATCAAAGGAATATCTTCCAGCATCAACATTTAAGATCCCCAACGCAATTATCGGCCTAGAAACTGGTGTCATAAAGAATGAGCATCAGGTTTTCAAATGGGACGGAAAGCCAAGAGCCATGAAACAATGGGAAAGAGACTTGAGCTTAAGAGGGGCAATACAAGTTTCAGCGGTTCCCGTATTTCAAAAAATCGCCAGAGAAGTTGGCGAAGTAAGAATGCAGAAATATCTTAAAAAATTTTCATATGGTAACCAGAATATCAGTGGTGGCATTGACAAATTCTGGTTGGAGGGTCAGCTTAGAATTTCCGCAGTTAATCAAGTGGAGTTTCTAGAGTCTCTATTTTTAAATAAATTGTCAGCATCAAAAGAAAATCAGCTAATAGTAAAAGAGGCTTTGGTAACGGAGGCTGCGCCTGAATATCTTGTGCATTCAAAAACTGGTTTTTCTGGTGTGGGAACTGAGTCAAATCCTGGTGTCGCATGGTGGGTTGGTTGGGTTGAGAAGGGAACAGAGGTTTACTTTTTCGCCTTTAACATGGATATAGACAACGAAAATAAGTTGCCGCTAAGAAAATCCATTCCCACCAAAATCATGGCAAGTGAGGGCATCATTGGTGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36810","NCBI_taxonomy_name":"Aeromonas hydrophila","NCBI_taxonomy_id":"644"}}}},"ARO_accession":"3008472","ARO_id":"47264","ARO_name":"OXA-1053","CARD_short_name":"OXA-1053","ARO_description":"OXA-10 family class D beta-lactamase OXA-1053.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46486":{"category_aro_accession":"3007697","category_aro_cvterm_id":"46486","category_aro_name":"OXA-10-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-10.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7891":{"model_id":"7891","model_name":"OXA-1055","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10718":{"protein_sequence":{"accession":"UKA98426.1","sequence":"MRVLALSAVFLVASIIGMPAVAKEWQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGQTRDIATWNRDHNLITAMKYSVVPVYQEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISATEQISFLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYSTRSKIGWWVGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP"},"dna_sequence":{"accession":"OM321042.1","fmin":"0","fmax":"792","strand":"+","sequence":"ATGCGTGTATTAGCCTTATCGGCTGTGTTTTTGGTGGCATCGATTATCGGAATGCCTGCGGTAGCAAAGGAATGGCAAGAAAACAAAAGTTGGAATGCTCACTTTACTGAACATAAATCACAGGGCGTAGTTGTGCTCTGGAATGAGAATAAGCAGCAAGGATTTACCAATAATCTTAAACGGGCGAACCAAGCATTTTTACCCGCATCTACCTTTAAAATTCCCAATAGCTTGATCGCCCTCGATTTGGGCGTGGTTAAGGATGAACACCAAGTCTTTAAGTGGGATGGACAGACGCGCGATATCGCCACTTGGAATCGCGATCATAATCTAATCACCGCGATGAAATATTCAGTTGTGCCTGTTTATCAAGAATTTGCCCGCCAAATTGGCGAGGCACGTATGAGCAAGATGCTACATGCTTTCGATTATGGTAATGAGGACATTTCGGGCAATGTAGACAGTTTCTGGCTCGACGGTGGTATTCGAATTTCGGCCACGGAGCAAATCAGCTTTTTAAGAAAGCTGTATCACAATAAGTTACACGTATCGGAGCGCAGCCAGCGTATTGTCAAACAAGCCATGCTGACCGAAGCCAATGGTGACTATATTATTCGGGCTAAAACTGGATACTCGACTAGATCTAAGATTGGCTGGTGGGTCGGTTGGGTTGAACTTGATGATAATGTGTGGTTTTTTGCGATGAATATGGATATGCCCACATCGGATGGTTTAGGGCTGCGCCAAGCCATCACAAAAGAAGTGCTCAAACAGGAAAAAATTATTCCCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008473","ARO_id":"47265","ARO_name":"OXA-1055","CARD_short_name":"OXA-1055","ARO_description":"OXA-48 family class D beta-lactamase OXA-1055.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46510":{"category_aro_accession":"3007721","category_aro_cvterm_id":"46510","category_aro_name":"OXA-48-like beta-lactamase","category_aro_description":"OXA-48-type beta-lactamases are now routinely encountered in bacterial infections caused by carbapenam-resistant Enterobacterales. OXA-48-like proteins confer resistance to penicillin (which is efficiently hydrolyzed) and carbapenam antibiotics (which is more slowly broken down). The spectrum of activity of these variants varies, with some hydrolyzing expanded-spectrum oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7892":{"model_id":"7892","model_name":"OXA-1056","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10719":{"protein_sequence":{"accession":"UKC75978.1","sequence":"MSKFFITFLVFLWSLSAVAEDQVLAGLFSQHGMKGTIVISSLHNEKTFIYNEPRANLKFSTASTFKILNTLISLEEKAISGKDDVLKWDGHIYDFPDWNHDQTLESAFKVSCVWCFQELARRVGAEKYRNYLRESAYGELREPFMETTFWLDGSLQISAIEQVDFLKKVYLRTLPFNATSYETLRQIMLVEKTPAYTMWAKTGWATRVKPQVGWYVGYVETPKDVWFFATNIEIRDEKDLPLRQKLTRAALQAKGVIE"},"dna_sequence":{"accession":"OM460738.1","fmin":"0","fmax":"777","strand":"+","sequence":"ATGAGTAAGTTCTTTATTACCTTCTTAGTTTTTCTATGGTCGTTGTCAGCAGTCGCTGAAGACCAAGTGCTTGCCGGACTCTTTTCGCAGCACGGCATGAAGGGAACGATAGTGATCTCGTCGCTACACAACGAGAAGACCTTCATCTACAACGAACCTCGCGCAAATCTGAAATTCTCGACTGCATCAACATTTAAAATACTGAATACGCTGATCTCGCTTGAGGAAAAGGCCATTTCCGGAAAAGACGACGTGCTGAAATGGGATGGGCATATTTACGACTTTCCAGATTGGAATCATGACCAGACATTGGAAAGTGCGTTCAAAGTTTCATGCGTCTGGTGTTTTCAGGAGCTTGCGCGTCGAGTCGGCGCGGAAAAATATCGAAATTATTTGCGCGAGTCGGCTTACGGAGAATTACGCGAACCCTTCATGGAAACAACATTCTGGCTTGATGGCTCCCTTCAAATTAGCGCAATTGAACAAGTGGATTTCCTCAAGAAAGTATATCTGCGTACACTCCCGTTTAACGCGACATCCTATGAAACGCTAAGACAAATCATGCTTGTTGAGAAAACGCCGGCATATACGATGTGGGCCAAGACAGGTTGGGCAACGAGAGTAAAACCACAAGTGGGCTGGTATGTGGGCTATGTCGAAACTCCAAAGGATGTTTGGTTCTTTGCCACGAATATTGAGATTCGTGACGAAAAGGACTTGCCACTACGCCAGAAGTTGACGCGAGCCGCACTTCAAGCAAAAGGAGTCATCGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008474","ARO_id":"47266","ARO_name":"OXA-1056","CARD_short_name":"OXA-1056","ARO_description":"OXA-198 family carbapenem-hydrolyzing class D beta-lactamase OXA-1056.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46492":{"category_aro_accession":"3007703","category_aro_cvterm_id":"46492","category_aro_name":"OXA-198-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-198.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7893":{"model_id":"7893","model_name":"OXA-1057","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10720":{"protein_sequence":{"accession":"UKC75979.1","sequence":"MSKFFITFLVFLWSLSAVAEDQVLAGLFSQHGMKGTIVISSLHNEKTFIYNEPRANLKFSTASTFKILNTLISLEEKAISGKDDVLKWDGHIYDFPDWNHDQTLESAFKVSCVWCFQELARRVGAEKYRNYLRESAYGELREPFVETTFWLDGSLQISAIEQVDFLKKVYLRTLPFNATSYETLRQIMLVEKTPAYTMWAKTGWAARVKPQVGWYVGYVETPKDVWFFATNIETRDEKDLPLRQKLTRAALQAKGVIE"},"dna_sequence":{"accession":"OM460739.1","fmin":"0","fmax":"777","strand":"+","sequence":"ATGAGTAAGTTCTTTATTACCTTCTTAGTTTTTCTATGGTCGTTGTCAGCAGTCGCTGAAGACCAAGTGCTTGCCGGACTCTTTTCGCAGCACGGCATGAAGGGAACGATAGTGATCTCGTCGCTACACAACGAGAAGACCTTCATCTACAACGAACCTCGCGCAAATCTGAAATTCTCGACTGCATCAACATTTAAAATACTGAATACGCTGATCTCGCTTGAGGAAAAAGCCATTTCCGGAAAAGACGACGTGCTGAAATGGGATGGGCATATTTACGACTTTCCAGATTGGAATCATGACCAGACATTGGAAAGTGCGTTCAAAGTTTCATGCGTCTGGTGTTTTCAGGAGCTTGCGCGTCGAGTCGGCGCGGAAAAATATCGAAATTATTTGCGCGAGTCGGCTTACGGAGAATTACGCGAACCCTTCGTGGAAACAACATTCTGGCTTGATGGCTCCCTTCAAATTAGCGCAATTGAACAAGTGGATTTCCTCAAGAAAGTATATCTGCGTACACTCCCGTTTAACGCGACATCCTATGAAACGCTAAGACAAATCATGCTTGTTGAGAAAACGCCGGCATATACGATGTGGGCCAAGACAGGTTGGGCAGCAAGAGTAAAACCACAAGTGGGCTGGTATGTGGGCTATGTCGAAACTCCAAAGGATGTTTGGTTCTTTGCCACGAATATTGAGACTCGTGACGAAAAGGACTTGCCACTACGCCAGAAGTTGACGCGAGCCGCACTTCAAGCAAAAGGAGTCATCGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"47926","NCBI_taxonomy_name":"Pseudomonas oleovorans","NCBI_taxonomy_id":"301"}}}},"ARO_accession":"3008475","ARO_id":"47267","ARO_name":"OXA-1057","CARD_short_name":"OXA-1057","ARO_description":"OXA-198 family carbapenem-hydrolyzing class D beta-lactamase OXA-1057.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46492":{"category_aro_accession":"3007703","category_aro_cvterm_id":"46492","category_aro_name":"OXA-198-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-198.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7894":{"model_id":"7894","model_name":"OXA-1058","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10721":{"protein_sequence":{"accession":"ULU82603.1","sequence":"MNSKALLLITSAIFISACSPYIVTANPNHSASKSDVKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"OM617740.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACAGCAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGTAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAACAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008476","ARO_id":"47268","ARO_name":"OXA-1058","CARD_short_name":"OXA-1058","ARO_description":"OXA-51 family carbapenem-hydrolyzing class D beta-lactamase OXA-1058.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7895":{"model_id":"7895","model_name":"OXA-1059","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10722":{"protein_sequence":{"accession":"ULU82604.1","sequence":"MNIQTLLLITSAIFISACSPYIVTANPNHSASKSDVKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"OM617741.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTCAAACACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGTAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAACAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008477","ARO_id":"47269","ARO_name":"OXA-1059","CARD_short_name":"OXA-1059","ARO_description":"OXA-51 family carbapenem-hydrolyzing class D beta-lactamase OXA-1059.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7896":{"model_id":"7896","model_name":"OXA-1060","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10723":{"protein_sequence":{"accession":"ULU82605.1","sequence":"MNIKTLLLITSAIFISACSPYIVSANPNHSASKSDVKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"OM617742.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAACACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGTCTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGTAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGTCAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAACAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008478","ARO_id":"47270","ARO_name":"OXA-1060","CARD_short_name":"OXA-1060","ARO_description":"OXA-51 family carbapenem-hydrolyzing class D beta-lactamase OXA-1060.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7897":{"model_id":"7897","model_name":"OXA-1061","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10724":{"protein_sequence":{"accession":"ULU82606.1","sequence":"MNIKTLLLITSAIFISACSPYIVTANPNHSASKSDVKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEKLGIL"},"dna_sequence":{"accession":"OM617743.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAACACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGTAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAACAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAAAAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008479","ARO_id":"47271","ARO_name":"OXA-1061","CARD_short_name":"OXA-1061","ARO_description":"OXA-51 family carbapenem-hydrolyzing class D beta-lactamase OXA-1061.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7898":{"model_id":"7898","model_name":"OXA-1062","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10725":{"protein_sequence":{"accession":"ULU82607.1","sequence":"MNIKSLLLITSAIFISACSPYIVTANPNHSASKSDVKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGRDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"OM617744.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAAGCCTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGTAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAACAAAATATACGCAAAAAGTGGTTGGGGAAGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008480","ARO_id":"47272","ARO_name":"OXA-1062","CARD_short_name":"OXA-1062","ARO_description":"OXA-51 family carbapenem-hydrolyzing class D beta-lactamase OXA-1062.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7899":{"model_id":"7899","model_name":"OXA-1063","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10726":{"protein_sequence":{"accession":"ULU82608.1","sequence":"MNIKTLLLITSAIFISACSPYIVTANPNHSASKSDVKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGRDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"OM617745.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAACACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGTAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAACAAAATATACGCAAAAAGTGGTTGGGGAAGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008481","ARO_id":"47273","ARO_name":"OXA-1063","CARD_short_name":"OXA-1063","ARO_description":"OXA-51 family carbapenem-hydrolyzing class D beta-lactamase OXA-1063.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7900":{"model_id":"7900","model_name":"OXA-1064","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10727":{"protein_sequence":{"accession":"ULU82609.1","sequence":"MNIKTLLLITSAIFISACSPYIVTANPNHSASKSDVKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAQSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"OM617746.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAACACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGTAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAACAAAATATACGCACAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008482","ARO_id":"47274","ARO_name":"OXA-1064","CARD_short_name":"OXA-1064","ARO_description":"OXA-51 family carbapenem-hydrolyzing class D beta-lactamase OXA-1064.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7901":{"model_id":"7901","model_name":"OXA-1065","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10728":{"protein_sequence":{"accession":"ULU82610.1","sequence":"MNIKTLLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"OM617747.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAACACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTAGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAACAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008483","ARO_id":"47275","ARO_name":"OXA-1065","CARD_short_name":"OXA-1065","ARO_description":"OXA-51 family carbapenem-hydrolyzing class D beta-lactamase OXA-1065.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7902":{"model_id":"7902","model_name":"OXA-1066","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10729":{"protein_sequence":{"accession":"ULU82612.1","sequence":"MNIKTLLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"OM617749.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAACACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGGTGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATAACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008484","ARO_id":"47276","ARO_name":"OXA-1066","CARD_short_name":"OXA-1066","ARO_description":"OXA-51 family carbapenem-hydrolyzing class D beta-lactamase OXA-1066.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7903":{"model_id":"7903","model_name":"OXA-1067","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10730":{"protein_sequence":{"accession":"ULU82615.1","sequence":"MNIKTLLLITSAIFISACSPYIVSANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQEVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"OM617752.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAACCCTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGTCTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACTACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTAGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAGAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008485","ARO_id":"47277","ARO_name":"OXA-1067","CARD_short_name":"OXA-1067","ARO_description":"OXA-51 family carbapenem-hydrolyzing class D beta-lactamase OXA-1067.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7904":{"model_id":"7904","model_name":"OXA-1068","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10731":{"protein_sequence":{"accession":"ULU82617.1","sequence":"MNIISILLITSAIFISACSPYIVSANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQEVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"OM617754.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATCATAAGCATCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGTCTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACTACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTAGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAGAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008486","ARO_id":"47278","ARO_name":"OXA-1068","CARD_short_name":"OXA-1068","ARO_description":"OXA-51 family carbapenem-hydrolyzing class D beta-lactamase OXA-1068.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7905":{"model_id":"7905","model_name":"OXA-1069","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10732":{"protein_sequence":{"accession":"ULU82618.1","sequence":"MNIKTLLLITSAIFISACSPYIVSANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWGGQKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"OM617755.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAACACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGTCTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACTACAGAAGTATTTAAGTGGGGCGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008487","ARO_id":"47279","ARO_name":"OXA-1069","CARD_short_name":"OXA-1069","ARO_description":"OXA-51 family carbapenem-hydrolyzing class D beta-lactamase OXA-1069.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7906":{"model_id":"7906","model_name":"OXA-1070","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10733":{"protein_sequence":{"accession":"ULU82619.1","sequence":"MNIKALLLITSAIFISACSPYIVSANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"OM617756.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGTCTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAACAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008488","ARO_id":"47280","ARO_name":"OXA-1070","CARD_short_name":"OXA-1070","ARO_description":"OXA-51 family carbapenem-hydrolyzing class D beta-lactamase OXA-1070.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7907":{"model_id":"7907","model_name":"OXA-1071","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10734":{"protein_sequence":{"accession":"ULU82620.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEVHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEILGIL"},"dna_sequence":{"accession":"OM617757.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGTACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAAATATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008489","ARO_id":"47281","ARO_name":"OXA-1071","CARD_short_name":"OXA-1071","ARO_description":"OXA-51 family carbapenem-hydrolyzing class D beta-lactamase OXA-1071.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7908":{"model_id":"7908","model_name":"OXA-1072","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10735":{"protein_sequence":{"accession":"ULU82621.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEVHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLDIL"},"dna_sequence":{"accession":"OM617758.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGTACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGATATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008490","ARO_id":"47282","ARO_name":"OXA-1072","CARD_short_name":"OXA-1072","ARO_description":"OXA-51 family carbapenem-hydrolyzing class D beta-lactamase OXA-1072.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7909":{"model_id":"7909","model_name":"OXA-1073","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10736":{"protein_sequence":{"accession":"ULU82622.1","sequence":"MNIKTLLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANNTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"OM617759.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAACACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAATACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008491","ARO_id":"47283","ARO_name":"OXA-1073","CARD_short_name":"OXA-1073","ARO_description":"OXA-51 family carbapenem-hydrolyzing class D beta-lactamase OXA-1073.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7910":{"model_id":"7910","model_name":"OXA-1074","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10737":{"protein_sequence":{"accession":"ULU82623.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDDKAEKIKNLFNEAHTTGVLVIHQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"OM617760.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGACAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCATCAAGGTCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008492","ARO_id":"47284","ARO_name":"OXA-1074","CARD_short_name":"OXA-1074","ARO_description":"OXA-51 family carbapenem-hydrolyzing class D beta-lactamase OXA-1074.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7911":{"model_id":"7911","model_name":"OXA-1075","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10738":{"protein_sequence":{"accession":"ULU82624.1","sequence":"MNIKTLLLITSAIFISACSPYIVSANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAESGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"OM617761.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAACACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGTCTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACTACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAGAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008493","ARO_id":"47285","ARO_name":"OXA-1075","CARD_short_name":"OXA-1075","ARO_description":"OXA-51 family carbapenem-hydrolyzing class D beta-lactamase OXA-1075.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7912":{"model_id":"7912","model_name":"OXA-1076","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10739":{"protein_sequence":{"accession":"ULU82625.1","sequence":"MNIKALLLITSAIFISACSPYIVTTNPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKTTTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"OM617762.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTACTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGACAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGACGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCATTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008494","ARO_id":"47286","ARO_name":"OXA-1076","CARD_short_name":"OXA-1076","ARO_description":"OXA-51 family carbapenem-hydrolyzing class D beta-lactamase OXA-1076.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7913":{"model_id":"7913","model_name":"OXA-1077","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10740":{"protein_sequence":{"accession":"ULU82626.1","sequence":"MNIKTLLLITSAIFISACSPYIVSANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"OM617763.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAACACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGTCTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACTACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTAGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008495","ARO_id":"47287","ARO_name":"OXA-1077","CARD_short_name":"OXA-1077","ARO_description":"OXA-51 family carbapenem-hydrolyzing class D beta-lactamase OXA-1077.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7914":{"model_id":"7914","model_name":"OXA-1078","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10741":{"protein_sequence":{"accession":"ULU82627.1","sequence":"MNIKTLLLITSTIFISACSPYIVTANPNHSTSKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEIFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"OM617764.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAACACTCTTACTTATAACAAGCACTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCACTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAATATTTAAGTGGGACGGGCAAAAAAGGCTGTTCCCAGAATGGGAAAAGGACATGACCCTAGGTGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACGCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008496","ARO_id":"47288","ARO_name":"OXA-1078","CARD_short_name":"OXA-1078","ARO_description":"OXA-51 family carbapenem-hydrolyzing class D beta-lactamase OXA-1078.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7915":{"model_id":"7915","model_name":"OXA-1079","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10742":{"protein_sequence":{"accession":"ULU82628.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDDKAEKIKNLFNEAHTTGVLVIHQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEIFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYSNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"OM617765.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGACAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCATCAAGGTCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAATATTTAAGTGGGACGGGCAAAAAAGGCTGTTCCCAGAATGGGAAAAGGACATGACCCTAGGTGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATAGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008497","ARO_id":"47289","ARO_name":"OXA-1079","CARD_short_name":"OXA-1079","ARO_description":"OXA-51 family carbapenem-hydrolyzing class D beta-lactamase OXA-1079.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7916":{"model_id":"7916","model_name":"OXA-1080","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10743":{"protein_sequence":{"accession":"ULU82629.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDVKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLDIL"},"dna_sequence":{"accession":"OM617766.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGTAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAACAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGATATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008498","ARO_id":"47290","ARO_name":"OXA-1080","CARD_short_name":"OXA-1080","ARO_description":"OXA-51 family carbapenem-hydrolyzing class D beta-lactamase OXA-1080.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7917":{"model_id":"7917","model_name":"OXA-1081","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10744":{"protein_sequence":{"accession":"ULU82656.1","sequence":"MKKFILPIFSISILVSLSACSSIKTKSEDNFHISSQQHEKAIKSYFDEAQTQGVIIIKEGKNLSTYGNALARANKEYVPASTFKMLIALIGLENHKATTNEIFKWDGKKRTYPMWEKDMTLGEAMALSAVPVYQELARRIGLELMQKEVKRVNFGNTNIGTQVDNFWLVGPLKITPVQEVNFADDLAHNRLPFKLETQEEVKKMLLIKEVNGSKIYAKSGWGMDVTAQVGWLTGWVEQANGKKIPFSLNLEMKEGMSGSIRNEITYKSLENLGII"},"dna_sequence":{"accession":"OM638107.1","fmin":"0","fmax":"828","strand":"-","sequence":"ATGAAAAAATTTATACTTCCTATATTCAGCATTTCTATTCTAGTTTCTCTCAGTGCATGTTCATCTATTAAAACTAAATCTGAAGATAATTTTCATATTTCTTCTCAGCAACATGAAAAAGCTATTAAAAGCTATTTTGATGAAGCTCAAACACAGGGTGTAATTATTATTAAAGAGGGTAAAAATCTTAGCACCTATGGTAATGCTCTTGCACGAGCAAATAAAGAATATGTCCCTGCATCAACATTTAAGATGCTAATTGCTTTAATCGGGCTAGAAAATCATAAAGCAACAACAAATGAGATTTTCAAATGGGATGGTAAAAAAAGAACTTATCCTATGTGGGAGAAAGATATGACTTTAGGTGAGGCAATGGCATTATCAGCAGTTCCAGTATATCAAGAGCTTGCAAGACGGATTGGCCTAGAGCTAATGCAGAAAGAAGTAAAGCGGGTTAATTTTGGAAATACAAATATTGGAACACAGGTCGATAATTTTTGGTTAGTTGGCCCCCTTAAAATTACACCAGTACAAGAAGTTAATTTTGCCGATGACCTTGCACATAACCGATTACCTTTTAAATTAGAAACTCAAGAAGAAGTTAAAAAAATGCTTCTAATTAAAGAAGTAAATGGTAGTAAGATTTATGCAAAAAGTGGATGGGGAATGGATGTTACTGCACAGGTAGGTTGGTTGACTGGTTGGGTGGAGCAAGCTAATGGAAAAAAAATCCCCTTTTCGCTCAACTTAGAAATGAAAGAAGGAATGTCTGGTTCTATTCGTAATGAAATTACTTATAAGTCGCTAGAAAATCTTGGAATCATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39090","NCBI_taxonomy_name":"Acinetobacter bereziniae","NCBI_taxonomy_id":"106648"}}}},"ARO_accession":"3008499","ARO_id":"47291","ARO_name":"OXA-1081","CARD_short_name":"OXA-1081","ARO_description":"OXA-24 family carbapenem-hydrolyzing class D beta-lactamase OXA-1081.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46500":{"category_aro_accession":"3007711","category_aro_cvterm_id":"46500","category_aro_name":"OXA-24-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-24.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7918":{"model_id":"7918","model_name":"OXA-1082","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10745":{"protein_sequence":{"accession":"ULU82657.1","sequence":"MAIRIFAILFSIFSLATFAHAQEGTLERSDWRKFFSEFQAKGTIVVADERQADRAMLVFDPVRSKKRYSPASTFKIPHTLFALDAGAVRDEFQIFRWDGVNRGFAGHNQDQDLRSAMRNSTVWVYELFAKEIGDDKARRYLKKIDYGNADPSTSNGDYWIECSLAISAQEQIAFLRKLYRNELPFRVEHQRLVKDLMIVEAGRNWILRAKTGWEGRMGWWVGWVEWPTGSVFFALNIDTPNRMDDLFKREAIVRAILRSIEALPPNPAVNSDAAR"},"dna_sequence":{"accession":"OM638108.1","fmin":"0","fmax":"828","strand":"-","sequence":"ATGGCAATCCGAATCTTCGCGATACTTTTCTCCATTTTTTCTCTTGCCACTTTCGCGCATGCGCAAGAAGGCACGCTAGAACGTTCTGACTGGAGGAAGTTTTTCAGCGAATTTCAAGCCAAAGGCACGATAGTTGTGGCAGACGAACGCCAAGCGGATCGTGCCATGTTGGTTTTTGATCCTGTGCGATCGAAGAAACGCTACTCGCCTGCATCGACATTCAAGATACCTCATACACTTTTTGCACTTGATGCAGGCGCTGTTCGTGATGAGTTCCAGATTTTTCGATGGGACGGCGTTAACAGGGGCTTTGCAGGCCACAATCAAGACCAAGATTTGCGATCAGCAATGCGGAATTCTACTGTTTGGGTGTATGAGCTATTTGCAAAGGAAATTGGTGATGACAAAGCTCGGCGCTATTTGAAGAAAATCGACTATGGCAACGCCGATCCTTCGACAAGTAATGGCGATTACTGGATAGAATGCAGCCTTGCAATCTCGGCGCAGGAGCAAATTGCATTTCTCAGGAAGCTCTATCGTAACGAGCTGCCCTTTCGGGTAGAACATCAGCGCTTGGTCAAGGATCTCATGATTGTGGAAGCCGGTCGCAACTGGATACTGCGTGCAAAGACGGGCTGGGAAGGCCGTATGGGTTGGTGGGTAGGATGGGTTGAGTGGCCGACTGGCTCCGTATTCTTCGCACTGAATATTGATACGCCAAACAGAATGGATGATCTTTTCAAGAGGGAGGCAATCGTGCGGGCAATCCTTCGCTCTATTGAAGCGTTACCGCCCAACCCGGCAGTCAACTCGGACGCTGCGCGATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008500","ARO_id":"47292","ARO_name":"OXA-1082","CARD_short_name":"OXA-1082","ARO_description":"OXA-2 family class D beta-lactamase OXA-1082.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46493":{"category_aro_accession":"3007704","category_aro_cvterm_id":"46493","category_aro_name":"OXA-2-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-2.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7919":{"model_id":"7919","model_name":"OXA-1083","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10746":{"protein_sequence":{"accession":"ULU82658.1","sequence":"MAIRIFAILFSIFSLATFAHAQEGTLERSDWRKFFSEFQAKGTIVVADERQADRAMLVFDPVRSKKRYSPASTFKIPHTLFALDAGAVRDEFQIFRWDGVNRGFAGHNQDQDLRSAIRNSTVWVYELFAKEIGDDKARRYLKKIDYGNADPSTSNGDYWIEGSLAISAQEQIAFLRKLYRNELPFRVEHQRLVKDLMIVEAGRNWILRAKTGWEGRMGWWVGWVEWPTGPVFFALNIDTPNRMDDLFKREAIVRAILRSIEALPPNPAVNSDAAR"},"dna_sequence":{"accession":"OM638109.1","fmin":"0","fmax":"828","strand":"-","sequence":"ATGGCAATCCGAATCTTCGCGATACTTTTCTCCATTTTTTCTCTTGCCACTTTCGCGCATGCGCAAGAAGGCACGCTAGAACGTTCTGACTGGAGGAAGTTTTTCAGCGAATTTCAAGCCAAAGGCACGATAGTTGTGGCAGACGAACGCCAAGCGGATCGTGCCATGTTGGTTTTTGATCCTGTGCGATCGAAGAAACGCTACTCGCCTGCATCGACATTCAAGATACCTCATACACTTTTTGCACTTGATGCAGGCGCTGTTCGTGATGAGTTCCAGATTTTTCGATGGGACGGCGTTAACAGGGGCTTTGCAGGCCACAATCAAGACCAAGATTTGCGATCAGCAATACGGAATTCTACTGTTTGGGTGTATGAGCTATTTGCAAAGGAAATTGGTGATGACAAAGCTCGGCGCTATTTGAAGAAAATCGACTATGGCAACGCCGATCCTTCGACAAGTAATGGCGATTACTGGATAGAAGGCAGCCTTGCAATCTCGGCGCAGGAGCAAATTGCATTTCTCAGGAAGCTCTATCGTAACGAGCTGCCCTTTCGGGTAGAACATCAGCGCTTGGTCAAGGATCTCATGATTGTGGAAGCCGGTCGCAACTGGATACTGCGTGCAAAGACGGGCTGGGAAGGCCGTATGGGTTGGTGGGTAGGATGGGTTGAGTGGCCGACTGGCCCCGTATTCTTCGCACTGAATATTGATACGCCAAACAGAATGGATGATCTTTTCAAGAGGGAGGCAATCGTGCGGGCAATCCTTCGCTCTATTGAAGCGTTACCGCCCAACCCGGCAGTCAACTCGGACGCTGCGCGATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008501","ARO_id":"47293","ARO_name":"OXA-1083","CARD_short_name":"OXA-1083","ARO_description":"OXA-2 family class D beta-lactamase OXA-1083.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46493":{"category_aro_accession":"3007704","category_aro_cvterm_id":"46493","category_aro_name":"OXA-2-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-2.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7920":{"model_id":"7920","model_name":"OXA-1084","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10747":{"protein_sequence":{"accession":"ULU82659.1","sequence":"MAIRIFAILFSIFSLATFAHAQEGTLERSDWRKFFSEFQAKGTIVVADERQADRAMLVFDPVRSKKRYSPASTFKIPHTLFALDAGAVRDEFQIFRWDGVNRGFAGHNQDQDLRSAMRNSTVWVYELFAKEIGDDKARRYLKKIDYGNADSLTSNGDYWIEGSLAISAQEQIAFLRKLYRNELPFRVEHQRLVKDLMIVEAGRNWILRAKTGWEGRMGWWVGWVEWPTGSVFFALNIDTPNRMDDLFKREAIVRAILRSIEALPPNPAVNSDAAR"},"dna_sequence":{"accession":"OM638110.1","fmin":"0","fmax":"828","strand":"+","sequence":"ATGGCAATCCGAATCTTCGCGATACTTTTCTCCATTTTTTCTCTTGCCACTTTCGCGCATGCGCAAGAAGGCACGCTAGAACGTTCTGACTGGAGGAAGTTTTTCAGCGAATTTCAAGCCAAAGGCACGATAGTTGTGGCAGACGAACGCCAAGCGGATCGTGCCATGTTGGTTTTTGATCCTGTGCGATCGAAGAAACGCTACTCGCCTGCATCGACATTCAAGATACCTCATACACTTTTTGCACTTGATGCAGGCGCTGTTCGTGATGAGTTCCAGATTTTTCGATGGGACGGCGTTAACAGGGGCTTTGCAGGCCACAATCAAGACCAAGATTTGCGATCAGCAATGCGGAATTCTACTGTTTGGGTGTATGAGCTATTTGCAAAGGAAATTGGTGATGACAAAGCTCGGCGCTATTTGAAGAAAATCGACTATGGCAACGCCGATTCTTTGACAAGTAATGGCGATTACTGGATAGAAGGCAGCCTTGCAATCTCGGCGCAGGAGCAAATTGCATTTCTCAGGAAGCTCTATCGTAACGAGCTGCCCTTTCGGGTAGAACATCAGCGCTTGGTCAAGGATCTCATGATTGTGGAAGCCGGTCGCAACTGGATACTGCGTGCAAAGACGGGCTGGGAAGGCCGTATGGGTTGGTGGGTAGGATGGGTTGAGTGGCCGACTGGCTCCGTATTCTTCGCACTGAATATTGATACGCCAAACAGAATGGATGATCTTTTCAAGAGGGAGGCAATCGTGCGGGCAATCCTTCGCTCTATTGAAGCGTTACCGCCCAACCCGGCAGTCAACTCGGACGCTGCGCGATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008502","ARO_id":"47294","ARO_name":"OXA-1084","CARD_short_name":"OXA-1084","ARO_description":"OXA-2 family class D beta-lactamase OXA-1084.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46493":{"category_aro_accession":"3007704","category_aro_cvterm_id":"46493","category_aro_name":"OXA-2-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-2.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7921":{"model_id":"7921","model_name":"OXA-1085","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10748":{"protein_sequence":{"accession":"ULU82660.1","sequence":"MAIRIFAILFSIFSLATFAHAQEGTLERSDWRKFFSEFQAKGTIVVADERQADRAMLVFDPVRSKKRYSPASTFKIPHTLFALDAGAVRDEFQIFRWDGVNRGFAGHNQDQDLRSAMRNSTVWVYELFAKEIGDDKARRYLKKIDYGNADPSTSNGDCSLAISAQEQIAFLRKLYRNELPFRVEHQRLVKDLMIVEAGRNWILRAKTGWEGRMGWWVGWVEWPTGSVFFALNIDTPNRMDDLFKREAIVRAILRSIEALPPNPAVNSDAAR"},"dna_sequence":{"accession":"OM638111.1","fmin":"0","fmax":"816","strand":"+","sequence":"ATGGCAATCCGAATCTTCGCGATACTTTTCTCCATTTTTTCTCTTGCCACTTTCGCGCATGCGCAAGAAGGCACGCTAGAACGTTCTGACTGGAGGAAGTTTTTCAGCGAATTTCAAGCCAAAGGCACGATAGTTGTGGCAGACGAACGCCAAGCGGATCGTGCCATGTTGGTTTTTGATCCTGTGCGATCGAAGAAACGCTACTCGCCTGCATCGACATTCAAGATACCTCATACACTTTTTGCACTTGATGCAGGCGCTGTTCGTGATGAGTTCCAGATTTTTCGATGGGACGGCGTTAACAGGGGCTTTGCAGGCCACAATCAAGACCAAGATTTGCGATCAGCAATGCGGAATTCTACTGTTTGGGTGTATGAGCTATTTGCAAAGGAAATTGGTGATGACAAAGCTCGGCGCTATTTGAAGAAAATCGACTATGGCAACGCCGATCCTTCGACAAGTAATGGCGATTGCAGCCTTGCAATCTCGGCGCAGGAGCAAATTGCATTTCTCAGGAAGCTCTATCGTAACGAGCTGCCCTTTCGGGTAGAACATCAGCGCTTGGTCAAGGATCTCATGATTGTGGAAGCCGGTCGCAACTGGATACTGCGTGCAAAGACGGGCTGGGAAGGCCGTATGGGTTGGTGGGTAGGATGGGTTGAGTGGCCGACTGGCTCCGTATTCTTCGCACTGAATATTGATACGCCAAACAGAATGGATGATCTTTTCAAGAGGGAGGCAATCGTGCGGGCAATCCTTCGCTCTATTGAAGCGTTACCGCCCAACCCGGCAGTCAACTCGGACGCTGCGCGATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008503","ARO_id":"47295","ARO_name":"OXA-1085","CARD_short_name":"OXA-1085","ARO_description":"OXA-2 family class D beta-lactamase OXA-1085.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46493":{"category_aro_accession":"3007704","category_aro_cvterm_id":"46493","category_aro_name":"OXA-2-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-2.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7922":{"model_id":"7922","model_name":"OXA-1086","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10749":{"protein_sequence":{"accession":"ULU82664.1","sequence":"MKTFAAYVIIACLSSTALAGSITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFKIPNAIIGLETSVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNPNISGGIDKFGLEGQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGIIGG"},"dna_sequence":{"accession":"OM643280.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGAAAACATTTGCCGCATATGTAATTATCGCGTGTCTTTCGAGTACGGCATTAGCTGGTTCAATTACAGAAAATACGTCTTGGAACAAAGAGTTCTCTGCCGAAGCCGTCAATGGTGTCTTCGTGCTTTGTAAAAGTAGCAGTAAATCCTGCGCTACCAATGACTTAGCTCGTGCATCAAAGGAATATCTTCCAGCATCAACATTTAAGATCCCCAACGCAATTATCGGCCTAGAAACTAGTGTCATAAAGAATGAGCATCAGGTTTTCAAATGGGACGGAAAGCCAAGAGCCATGAAGCAATGGGAAAGAGACTTGACCTTAAGAGGGGCAATACAAGTTTCAGCTGTTCCCGTATTTCAACAAATCGCCAGAGAAGTTGGCGAAGTAAGAATGCAGAAATACCTTAAAAAATTTTCCTATGGCAACCCGAATATCAGTGGTGGCATTGACAAATTCGGGTTGGAAGGCCAGCTTAGAATTTCCGCAGTTAATCAAGTGGAGTTTCTAGAGTCTCTATATTTAAATAAATTGTCAGCATCTAAAGAAAACCAGCTAATAGTAAAAGAGGCTTTGGTAACGGAGGCGGCACCTGAATATCTAGTGCATTCAAAAACTGGTTTTTCTGGTGTGGGAACTGAGTCAAATCCTGGTGTCGCATGGTGGGTTGGGTGGGTTGAGAAGGAGACAGAGGTTTACTTTTTCGCCTTTAACATGGATATAGACAACGAAAGTAAGTTGCCGCTAAGAAAATCCATTCCCACCAAAATCATGGAAAGTGAGGGCATCATTGGTGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008504","ARO_id":"47296","ARO_name":"OXA-1086","CARD_short_name":"OXA-1086","ARO_description":"OXA-10 family class D beta-lactamase OXA-1086.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46486":{"category_aro_accession":"3007697","category_aro_cvterm_id":"46486","category_aro_name":"OXA-10-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-10.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7923":{"model_id":"7923","model_name":"OXA-1087","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10750":{"protein_sequence":{"accession":"UTS94245.1","sequence":"MKTFAAYVITACLSSTALASSITENTFWNKEFSAEAVNGVFVLCKSSSKSCATNNLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLSLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEDQLRISAVNQVEFLESLFLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKGTEVYFFAFNMDIDNENKLPLRKSIPTKIMASEGIIGG"},"dna_sequence":{"accession":"ON651492.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGAAAACATTTGCCGCATATGTAATTACTGCGTGTCTTTCAAGTACGGCATTAGCTAGTTCAATTACAGAAAATACGTTTTGGAACAAAGAGTTCTCTGCCGAAGCCGTCAATGGTGTTTTCGTGCTTTGTAAAAGTAGCAGTAAATCCTGCGCTACCAATAACTTAGCTCGTGCATCAAAGGAATATCTTCCAGCATCAACATTTAAGATCCCCAACGCAATTATCGGCCTAGAAACTGGTGTCATAAAGAATGAGCATCAGGTTTTCAAATGGGACGGAAAGCCAAGAGCCATGAAACAATGGGAAAGAGACTTGAGCTTAAGAGGGGCAATACAAGTTTCAGCGGTTCCCGTATTTCAACAAATCGCCAGAGAAGTTGGCGAAGTAAGAATGCAGAAATATCTTAAAAAATTTTCATATGGTAACCAGAATATCAGTGGTGGCATTGACAAATTCTGGTTGGAGGATCAGCTTAGAATTTCCGCAGTTAATCAAGTGGAGTTTCTAGAGTCTCTATTTTTAAATAAATTGTCAGCATCAAAAGAAAATCAGCTAATAGTAAAAGAGGCTTTGGTAACGGAGGCTGCGCCTGAATATCTTGTGCATTCAAAAACTGGTTTTTCTGGTGTGGGAACTGAGTCAAATCCTGGTGTCGCATGGTGGGTTGGTTGGGTTGAGAAGGGAACAGAGGTTTACTTTTTCGCCTTTAACATGGATATAGACAACGAAAATAAGTTGCCGCTAAGAAAATCCATTCCCACCAAAATCATGGCAAGTGAGGGCATCATTGGTGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008505","ARO_id":"47297","ARO_name":"OXA-1087","CARD_short_name":"OXA-1087","ARO_description":"OXA-10 family class D beta-lactamase OXA-1087.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46486":{"category_aro_accession":"3007697","category_aro_cvterm_id":"46486","category_aro_name":"OXA-10-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-10.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7924":{"model_id":"7924","model_name":"OXA-1088","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10751":{"protein_sequence":{"accession":"ULU82667.1","sequence":"MKTFAAYVIIACLSSTALAGSITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGTDKFWLEDQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGIIGG"},"dna_sequence":{"accession":"OM681521.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGAAAACATTTGCCGCATATGTAATTATCGCGTGTCTTTCGAGTACGGCATTAGCTGGTTCAATTACAGAAAATACGTCTTGGAACAAAGAGTTCTCTGCCGAAGCCGTCAATGGTGTCTTCGTGCTTTGTAAAAGTAGCAGTAAATCCTGCGCTACCAATGACTTAGCTCGTGCATCAAAGGAATATCTTCCAGCATCAACATTTAAGATCCCCAACGCAATTATCGGCCTAGAAACTGGTGTCATAAAGAATGAGCATCAGGTTTTCAAATGGGACGGAAAGCCAAGAGCCATGAAGCAATGGGAAAGAGACTTGACCTTAAGAGGGGCAATACAAGTTTCAGCTGTTCCCGTATTTCAACAAATCGCCAGAGAAGTTGGCGAAGTAAGAATGCAGAAATACCTTAAAAAATTTTCCTATGGCAACCAGAATATCAGTGGTGGCACTGACAAATTCTGGTTGGAAGACCAGCTTAGAATTTCCGCAGTTAATCAAGTGGAGTTTCTAGAGTCTCTATATTTAAATAAATTGTCAGCATCTAAAGAAAACCAGCTAATAGTAAAAGAGGCTTTGGTAACGGAGGCGGCACCTGAATATCTAGTGCATTCAAAAACTGGTTTTTCTGGTGTGGGAACTGAGTCAAATCCTGGTGTCGCATGGTGGGTTGGGTGGGTTGAGAAGGAGACAGAGGTTTACTTTTTCGCCTTTAACATGGATATAGACAACGAAAGTAAGTTGCCGCTAAGAAAATCCATTCCCACCAAAATCATGGAAAGTGAGGGCATCATTGGTGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008506","ARO_id":"47298","ARO_name":"OXA-1088","CARD_short_name":"OXA-1088","ARO_description":"OXA-10 family class D beta-lactamase OXA-1088.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46486":{"category_aro_accession":"3007697","category_aro_cvterm_id":"46486","category_aro_name":"OXA-10-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-10.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7925":{"model_id":"7925","model_name":"OXA-1089","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10752":{"protein_sequence":{"accession":"GAP12525.1","sequence":"MRRTRVLVLSFTLLLALLAACNPLQTATSQPLPNTTVQTETDLPVSEEKPELENFFEGMKGAFVLYDLNGQKTIRFNTQRCAEPFLPASTFKILNALIGLETGVISDENYKIAWDGTNYEIASWNQDQTLATAFQNSVVWYYQELARRVGEERMRHYVELADYGNRDISGKIDTFWLEGGLRISADQQVDFLKRFYQNDLPFSTSSIDIVKKIMILESTDSYTFRGKTGSVQRVPIHTGWFVGYLERDGNVYFFATNIESTDPDGFASGAAAREITENILVEEGLLPPR"},"dna_sequence":{"accession":"DF967972.1","fmin":"292413","fmax":"293283","strand":"+","sequence":"ATGCGTAGAACCCGGGTCCTCGTGTTGAGTTTTACACTCCTCCTGGCTTTACTGGCAGCTTGCAACCCACTCCAGACCGCCACGTCCCAACCCTTGCCGAACACAACCGTTCAGACGGAAACCGACCTTCCGGTTTCCGAAGAAAAACCGGAACTGGAAAATTTCTTCGAGGGAATGAAGGGCGCCTTTGTGTTGTACGACTTGAATGGTCAGAAAACGATCCGTTTCAATACACAGCGCTGCGCCGAACCCTTCCTGCCGGCGTCCACCTTCAAAATTCTAAACGCCCTAATTGGTTTGGAGACCGGCGTTATCTCGGACGAAAATTACAAGATTGCGTGGGACGGCACGAACTACGAGATCGCCTCCTGGAATCAGGATCAGACCCTCGCGACGGCGTTCCAAAATTCGGTCGTCTGGTATTACCAGGAACTCGCCCGGCGCGTCGGGGAAGAGAGAATGCGGCATTATGTGGAATTGGCCGATTATGGCAACCGGGACATCTCTGGCAAGATCGATACATTCTGGCTGGAAGGCGGCCTTCGAATATCAGCCGACCAACAGGTGGATTTTCTGAAGCGGTTCTATCAAAATGATCTGCCGTTTTCCACCTCATCGATCGACATCGTGAAGAAGATCATGATTTTGGAGTCGACCGATTCCTATACCTTTCGCGGAAAAACCGGATCGGTTCAACGTGTTCCCATCCACACCGGCTGGTTCGTGGGTTACCTGGAACGGGATGGGAATGTGTATTTCTTCGCGACCAACATTGAAAGCACCGATCCGGATGGATTTGCAAGCGGTGCGGCCGCGAGGGAAATTACAGAGAATATCCTGGTCGAGGAGGGTCTGCTGCCGCCCCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"47918","NCBI_taxonomy_name":"Longilinea arvoryzae","NCBI_taxonomy_id":"360412"}}}},"ARO_accession":"3008507","ARO_id":"47299","ARO_name":"OXA-1089","CARD_short_name":"OXA-1089","ARO_description":"Carbapenem-hydrolyzing class D beta-lactamase OXA-1089.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7926":{"model_id":"7926","model_name":"OXA-1090","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10753":{"protein_sequence":{"accession":"KCZ55067.1","sequence":"MIRHVVGFALGLTALMSACQAMPERPETLDDVLVAQGLTPETAALVIYRLEDGDTWETSGDRPESRFVAASTSKIPHTLIALETGAVTGPDEWFEWDGETRFSPGWNESQSFATAFQRSTVWIYQAVTPRIGSAVLHDWLERFDYGNADVGSKSDIQTYWLKGPLAISAREQVAFLARLSAHTLPLSARTYELAIPMMQADQGEGWTLYAKTGWKHVEGETDIGWYVGWLEQTDGPAPGTYVFAMNMDMDAANPALEKRKTVVHEGLIAVGALE"},"dna_sequence":{"accession":"AWFF01000032.1","fmin":"200409","fmax":"201234","strand":"-","sequence":"ATGATCCGGCATGTCGTCGGCTTTGCATTGGGCCTGACAGCGCTAATGAGCGCCTGTCAGGCCATGCCTGAGCGCCCGGAGACGCTGGATGATGTATTGGTGGCACAGGGGCTGACACCTGAGACGGCAGCCCTTGTGATCTATCGTCTTGAAGATGGTGACACCTGGGAGACGAGCGGCGACCGGCCGGAGAGCCGGTTTGTCGCTGCCTCTACCTCAAAAATCCCTCACACATTGATCGCGCTTGAAACCGGCGCTGTGACTGGCCCGGACGAGTGGTTCGAATGGGATGGCGAGACACGGTTCTCGCCGGGCTGGAATGAAAGCCAGAGCTTTGCCACGGCATTCCAGCGCTCAACGGTATGGATCTACCAGGCCGTAACGCCGCGCATTGGCAGCGCAGTCCTGCATGACTGGCTCGAACGGTTCGATTATGGGAATGCCGATGTGGGAAGTAAGTCTGATATTCAGACTTACTGGCTGAAGGGGCCACTCGCGATCTCTGCGCGAGAGCAGGTGGCGTTCCTCGCTAGGCTGTCAGCGCATACGCTGCCGCTGTCTGCGCGCACGTATGAGCTTGCCATTCCCATGATGCAGGCAGACCAGGGAGAAGGTTGGACGCTCTACGCCAAGACGGGGTGGAAGCATGTGGAGGGCGAAACCGATATTGGCTGGTATGTCGGCTGGCTGGAGCAAACAGACGGCCCCGCACCGGGGACATATGTTTTCGCCATGAATATGGACATGGATGCAGCCAATCCCGCGCTCGAAAAGCGCAAGACCGTGGTGCATGAGGGGCTTATCGCAGTGGGCGCGCTGGAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"47912","NCBI_taxonomy_name":"Hyphomonas beringensis","NCBI_taxonomy_id":"1280946"}}}},"ARO_accession":"3008508","ARO_id":"47300","ARO_name":"OXA-1090","CARD_short_name":"OXA-1090","ARO_description":"Carbapenem-hydrolyzing class D beta-lactamase OXA-1090.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7927":{"model_id":"7927","model_name":"OXA-1091","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10754":{"protein_sequence":{"accession":"ABQ37031.1","sequence":"MPLISRRHALALMAGASLVPARASAHVAPPRNEIRAGLAQRFTDMGTQGTFFAYKVEEYLIIASDTERSGAAKLPASTFKIANALIALETGVVADPDTDMFKWDGVTRSIEAWNKDHTLRSAIAVSAVPVFQEIARRIGPERMQKYLEELDYGNHDIGGGIDQFWLTGALRIDPVEQVDFIDRLRRGALPVSKRSQDLTRDIIPVTKVGDAVIHAKSGLLGKEQGSLGWMVGWVEKGDQPTVFALNMDCPEPRHVKARMTLTQACLKDIGAL"},"dna_sequence":{"accession":"CP000494.1","fmin":"5256874","fmax":"5257693","strand":"-","sequence":"ATGCCCCTGATCAGCCGCCGCCATGCGCTCGCTTTGATGGCCGGCGCCAGCCTGGTGCCGGCGCGCGCATCCGCCCATGTCGCGCCGCCCCGCAACGAGATCCGCGCCGGGCTCGCTCAACGCTTCACCGACATGGGCACCCAGGGCACGTTCTTCGCTTATAAGGTCGAGGAGTATCTGATCATTGCCAGCGACACCGAGCGCTCGGGCGCGGCGAAGCTGCCGGCCTCGACCTTCAAGATCGCGAACGCGCTGATCGCGCTGGAGACCGGCGTCGTCGCCGATCCCGACACCGACATGTTCAAATGGGACGGCGTCACGCGATCGATCGAGGCCTGGAACAAGGATCATACGCTGCGCAGCGCGATCGCGGTGTCGGCGGTGCCGGTGTTTCAGGAGATCGCGCGGCGCATCGGCCCCGAGCGGATGCAGAAATATCTCGAGGAGCTCGATTACGGCAATCACGACATCGGCGGCGGCATCGATCAGTTCTGGCTGACCGGCGCGCTTCGCATCGATCCGGTGGAGCAGGTCGACTTCATCGACCGACTCAGGCGTGGTGCGCTGCCGGTCTCCAAGCGCAGCCAGGATCTGACGCGCGATATCATCCCCGTGACCAAGGTCGGTGATGCCGTCATCCACGCCAAGTCCGGCCTGCTCGGCAAGGAGCAGGGCTCGCTCGGTTGGATGGTCGGCTGGGTCGAGAAGGGTGACCAGCCGACCGTGTTTGCGCTCAACATGGATTGCCCCGAGCCACGCCATGTCAAAGCGCGGATGACGCTGACCCAGGCCTGCCTGAAGGATATCGGCGCATTGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43390","NCBI_taxonomy_name":"Bradyrhizobium sp.","NCBI_taxonomy_id":"376"}}}},"ARO_accession":"3008509","ARO_id":"47301","ARO_name":"OXA-1091","CARD_short_name":"OXA-1091","ARO_description":"Oxacillin-hydrolyzing class D beta-lactamase OXA-1091.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7928":{"model_id":"7928","model_name":"OXA-1092","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10755":{"protein_sequence":{"accession":"UMW71111.1","sequence":"MNIKTLLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEVHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLEIMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQHEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"OL944013.1","fmin":"15","fmax":"840","strand":"+","sequence":"ATGAACATTAAAACACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGTACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAAATCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAACATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008510","ARO_id":"47302","ARO_name":"OXA-1092","CARD_short_name":"OXA-1092","ARO_description":"OXA-51 family carbapenem-hydrolyzing class D beta-lactamase OXA-1092.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7929":{"model_id":"7929","model_name":"OXA-1093","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10756":{"protein_sequence":{"accession":"UMW71112.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDDKAEKIKNLFNEAHTTGVLVIHQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEIFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"OL944014.1","fmin":"9","fmax":"834","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGACAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCATCAAGGTCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAATATTTAAGTGGGACGGGCAAAAAAGGCTGTTCCCAGAATGGGAAAAGGACATGACCCTAGGTGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008511","ARO_id":"47303","ARO_name":"OXA-1093","CARD_short_name":"OXA-1093","ARO_description":"OXA-51 family carbapenem-hydrolyzing class D beta-lactamase OXA-1093.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7930":{"model_id":"7930","model_name":"OXA-1094","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10757":{"protein_sequence":{"accession":"UNN26046.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDDKAEKIKNLFNEAHTTGVLVIHQGQTQQSYGNDLARASTEYVPASTFKMLNALIGREHHKATTTEVFKWDGEKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"OM933710.1","fmin":"0","fmax":"825","strand":"-","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGACAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCATCAAGGTCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCGTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAATGGGATGGGGAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTCTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008512","ARO_id":"47304","ARO_name":"OXA-1094","CARD_short_name":"OXA-1094","ARO_description":"OXA-51 family carbapenem-hydrolyzing class D beta-lactamase OXA-1094.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7931":{"model_id":"7931","model_name":"OXA-1095","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10758":{"protein_sequence":{"accession":"UNN26050.1","sequence":"MNKYFTCYVVASLFLSGCTVQHNLINETPSQIVQGHNQVIHQYFDEKNTSGVLVIQTDKKITLYGNALSRANTEYVPASTFKMLNALIGLENQKTDINEIFKWKGEKRSFTAWEKDMTLGEAMKLSAVPVYQELARRIGLDLMQKEVKRIGFGNAEIGQQVDNFWLVGPLKVTPIQEVEFVSQLAHTQLPFSEKVQANVKNMLLLEESNGYKIFGKTGWAAMDIKPQVGWLTGWVEQPDGKIVAFALNMEMRSEMPASIRNELLMKSLKQLNII"},"dna_sequence":{"accession":"OM933714.1","fmin":"0","fmax":"825","strand":"-","sequence":"ATGAATAAATATTTTACTTGCTATGTGGTTGCTTCTCTTTTTCTTTCTGGTTGTACGGTTCAGCATAATTTAATAAATGAAACCCCGAGTCAGATTGTTCAAGGACATAATCAGGTGATTCATCAATACTTTGATGAAAAAAACACCTCAGGTGTGCTGGTTATTCAAACAGATAAAAAAATTACTCTATATGGTAATGCTCTAAGCCGCGCAAATACAGAATATGTGCCAGCCTCTACATTTAAAATGTTGAATGCCCTGATCGGATTGGAGAACCAGAAAACGGATATTAATGAAATATTTAAATGGAAGGGCGAGAAAAGGTCATTTACCGCTTGGGAAAAAGACATGACACTAGGAGAAGCCATGAAGCTTTCTGCAGTCCCAGTCTATCAGGAACTTGCGCGACGTATCGGTCTTGATCTCATGCAAAAAGAAGTAAAACGTATTGGTTTCGGTAATGCTGAAATTGGACAGCAGGTTGATAATTTCTGGTTGGTAGGACCATTAAAGGTTACGCCTATTCAAGAGGTAGAGTTTGTTTCCCAATTAGCACATACACAGCTTCCATTTAGTGAAAAAGTGCAGGCTAATGTAAAAAATATGCTTCTTTTAGAAGAGAGTAATGGCTACAAAATTTTTGGAAAGACTGGTTGGGCAGCAATGGATATAAAACCACAAGTGGGCTGGTTGACCGGCTGGGTTGAGCAGCCAGATGGAAAAATTGTCGCTTTTGCATTAAATATGGAAATGCGGTCAGAAATGCCGGCATCTATACGTAATGAATTATTGATGAAATCATTAAAACAGCTGAATATTATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008513","ARO_id":"47305","ARO_name":"OXA-1095","CARD_short_name":"OXA-1095","ARO_description":"OXA-23 family carbapenem-hydrolyzing class D beta-lactamase OXA-1095.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46499":{"category_aro_accession":"3007710","category_aro_cvterm_id":"46499","category_aro_name":"OXA-23-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases, specifically imipenem, derived from OXA-23, first identified in Acinetobacter baumannii.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7932":{"model_id":"7932","model_name":"OXA-1096","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10759":{"protein_sequence":{"accession":"UNN26055.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDDKAEKIKNLFNEAHTTGVLVIHQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGEKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFCQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"OM933719.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGACAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCATCAAGGTCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAATGGGATGGGGAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTCTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTTGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008514","ARO_id":"47306","ARO_name":"OXA-1096","CARD_short_name":"OXA-1096","ARO_description":"OXA-51 family carbapenem-hydrolyzing class D beta-lactamase OXA-1096.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7933":{"model_id":"7933","model_name":"OXA-1097","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10760":{"protein_sequence":{"accession":"UNN26057.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDVKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWFVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"OM933721.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGTAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAACAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGTTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008515","ARO_id":"47307","ARO_name":"OXA-1097","CARD_short_name":"OXA-1097","ARO_description":"OXA-51 family carbapenem-hydrolyzing class D beta-lactamase OXA-1097.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7934":{"model_id":"7934","model_name":"OXA-1098","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10761":{"protein_sequence":{"accession":"UNN26058.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDVKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKLDGKKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"OM933722.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGTAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTTGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAACAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008516","ARO_id":"47308","ARO_name":"OXA-1098","CARD_short_name":"OXA-1098","ARO_description":"OXA-51 family carbapenem-hydrolyzing class D beta-lactamase OXA-1098.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7935":{"model_id":"7935","model_name":"OXA-1099","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10762":{"protein_sequence":{"accession":"UNN26059.1","sequence":"MSKKNFILIFIFVILISCKNTEKISNETTLIDNIFTNSNAEGTLVIYNLNDDKYIIHNKERAEQRFYPASTFKIYNSLIGLNEKAVKDVDEVFYKYNGEKVFLESWAKDSNLRYAIKNSQVPAYKELARRIGLKKMKENIEKLDFGNKSIGDSVDTFWLEGLLEISAMEQVKLLTKLAQNELPYPIEIQKAISDITILEQTYNYTLHGKTGLADSKNMTTEPIGWFVGWLEENDNIYVFALNIDNINSDDLAKRINIVKESLKALNLLK"},"dna_sequence":{"accession":"OM977008.1","fmin":"0","fmax":"810","strand":"+","sequence":"ATGTCTAAAAAAAATTTTATATTAATATTTATTTTTGTTATTTTAATATCTTGTAAAAATACAGAAAAAATATCAAATGAAACTACATTAATAGATAATATATTTACTAATAGCAATGCTGAAGGAACATTAGTTATATATAATTTAAATGATGATAAATATATAATTCATAATAAAGAAAGAGCTGAACAAAGATTTTATCCAGCATCAACATTTAAAATATATAATAGTTTAATAGGCTTAAATGAAAAAGCAGTTAAAGATGTAGATGAAGTATTTTATAAATATAATGGCGAAAAAGTTTTTCTCGAATCTTGGGCTAAAGACTCTAATTTAAGATATGCAATTAAAAATTCGCAAGTACCGGCATATAAAGAATTAGCAAGAAGAATAGGTCTTAAAAAGATGAAAGAGAATATAGAAAAACTAGATTTTGGTAATAAAAGTATAGGTGATAGTGTAGATACTTTTTGGCTTGAAGGACTTTTGGAAATAAGTGCGATGGAGCAAGTTAAATTATTAACTAAATTAGCTCAAAATGAATTACCGTATCCTATAGAAATACAAAAAGCTATTTCTGATATTACTATACTAGAGCAAACTTACAATTATACGCTTCATGGAAAAACTGGATTAGCTGATTCTAAAAACATGACAACTGAGCCTATTGGTTGGTTCGTAGGCTGGCTTGAAGAAAATGATAATATATACGTCTTTGCTTTAAATATTGATAATATCAATTCAGATGACCTTGCAAAAAGGATAAATATAGTAAAAGAAAGTTTAAAAGCATTAAATTTATTAAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36935","NCBI_taxonomy_name":"Brachyspira pilosicoli","NCBI_taxonomy_id":"52584"}}}},"ARO_accession":"3008517","ARO_id":"47309","ARO_name":"OXA-1099","CARD_short_name":"OXA-1099","ARO_description":"OXA-63 family oxacillin-hydrolyzing class D beta-lactamase OXA-1099.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46521":{"category_aro_accession":"3007732","category_aro_cvterm_id":"46521","category_aro_name":"OXA-63-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-63.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7936":{"model_id":"7936","model_name":"OXA-1100","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10763":{"protein_sequence":{"accession":"UNN26060.1","sequence":"MSKKNFILIFIFVILISCKNTEKISNETTLIDNIFTNSNAEGTLVIYNLNDDKYVIHNKERAEQRFYPASTFKIYNSLIGLNEKAVKDVDEVFYKYNGEKVFLESWAKDSNLRYAIKNSQVPAYKELARRIGLKKMKENIEKLDFGNKSIGDSVDTFWLEGPLEISAMEQIKLLTKLAQNELPYPIEIQKAVSDITILEQTYNYTLHGKTGLADSKNMTTEPIGWFVGWLEENDNIYVFALNIDNINSDDLAKRINIVKESLKALNLLK"},"dna_sequence":{"accession":"OM977009.1","fmin":"0","fmax":"810","strand":"+","sequence":"ATGTCTAAAAAAAATTTTATATTAATATTTATTTTTGTTATTTTAATATCTTGTAAAAATACAGAAAAAATATCAAATGAAACTACATTAATAGATAATATATTTACTAATAGCAATGCTGAAGGAACATTAGTTATATATAATTTAAATGATGATAAATATGTAATTCATAATAAAGAAAGAGCTGAACAAAGATTTTATCCAGCATCAACATTTAAAATATATAATAGTTTAATAGGCTTAAATGAAAAAGCAGTTAAAGATGTAGATGAAGTATTTTATAAATATAATGGCGAAAAAGTTTTTCTTGAATCTTGGGCTAAGGACTCTAATTTAAGATATGCAATTAAAAATTCGCAAGTACCGGCATATAAAGAATTAGCAAGAAGAATAGGTCTTAAAAAGATGAAAGAGAATATAGAAAAACTAGATTTTGGTAATAAAAGTATAGGTGATAGTGTAGATACTTTTTGGCTTGAAGGACCTTTGGAAATAAGTGCGATGGAGCAAATTAAATTATTAACTAAATTAGCTCAAAATGAATTACCGTATCCTATAGAAATACAAAAAGCTGTTTCTGATATTACTATACTAGAGCAAACTTACAATTATACGCTTCATGGAAAAACTGGATTAGCTGATTCTAAAAACATGACAACTGAGCCTATTGGTTGGTTCGTAGGCTGGCTTGAAGAAAATGATAATATATACGTCTTTGCTTTAAATATTGATAATATCAATTCAGATGACCTTGCAAAAAGGATAAATATAGTAAAAGAAAGTTTAAAAGCATTAAATTTATTAAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36935","NCBI_taxonomy_name":"Brachyspira pilosicoli","NCBI_taxonomy_id":"52584"}}}},"ARO_accession":"3008518","ARO_id":"47310","ARO_name":"OXA-1100","CARD_short_name":"OXA-1100","ARO_description":"OXA-63 family oxacillin-hydrolyzing class D beta-lactamase OXA-1100.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46521":{"category_aro_accession":"3007732","category_aro_cvterm_id":"46521","category_aro_name":"OXA-63-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-63.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7937":{"model_id":"7937","model_name":"OXA-1101","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10764":{"protein_sequence":{"accession":"UNN26061.1","sequence":"MSKKNFILIFIFIILISCKNTEKISNETTLIDNIFTNSNAEGTLVIYNLNDDKYIIHNKERAEQRFYPASTFKIYNSLIGLNEKVVKDVDEVFYKYNGEKVFLESWAKDSNLRYAIKNSQVPAYKELARRIGLKKMKENIEKLDFGNKSIGDSVDTFWLEGPLEISAMEQVKLLTKLAQNELPYPIEIQKAVSDITILEQTYNYTLHGKTGLADSKNMTTEPIGWFVGWLEENDNIYVFALNIDNINSDDLAKRINIVKESLKALNLLK"},"dna_sequence":{"accession":"OM977010.1","fmin":"0","fmax":"810","strand":"+","sequence":"ATGTCTAAAAAAAATTTCATATTAATATTTATTTTTATTATTTTAATATCTTGTAAAAATACAGAAAAAATATCAAATGAAACTACATTAATAGATAATATATTTACTAATAGCAATGCTGAAGGAACATTAGTTATATATAATTTAAATGATGATAAATATATAATTCATAATAAAGAAAGAGCTGAACAAAGATTTTATCCAGCATCAACATTTAAAATATATAATAGTTTAATAGGCTTAAATGAAAAAGTAGTTAAAGATGTAGATGAAGTATTTTATAAATATAATGGCGAAAAAGTTTTTCTCGAATCTTGGGCTAAGGACTCTAATTTAAGATATGCAATTAAAAATTCGCAAGTACCGGCATATAAAGAATTAGCAAGAAGAATAGGTCTTAAAAAGATGAAAGAGAATATAGAAAAACTAGATTTTGGTAATAAAAGTATAGGTGATAGTGTAGATACTTTTTGGCTTGAAGGACCTTTGGAAATAAGTGCGATGGAGCAAGTTAAATTATTAACTAAATTAGCTCAAAATGAATTACCGTATCCTATAGAAATACAAAAAGCTGTTTCTGATATTACTATACTAGAGCAAACTTACAATTATACGCTTCATGGAAAAACTGGATTAGCTGATTCTAAAAACATGACAACTGAGCCTATTGGTTGGTTCGTAGGCTGGCTTGAAGAAAATGATAATATATACGTCTTTGCTTTAAATATTGATAATATCAATTCAGATGACCTTGCAAAAAGGATAAATATAGTAAAAGAAAGTTTAAAAGCATTAAATTTATTAAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36935","NCBI_taxonomy_name":"Brachyspira pilosicoli","NCBI_taxonomy_id":"52584"}}}},"ARO_accession":"3008519","ARO_id":"47311","ARO_name":"OXA-1101","CARD_short_name":"OXA-1101","ARO_description":"OXA-63 family oxacillin-hydrolyzing class D beta-lactamase OXA-1101.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46521":{"category_aro_accession":"3007732","category_aro_cvterm_id":"46521","category_aro_name":"OXA-63-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-63.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7938":{"model_id":"7938","model_name":"OXA-1102","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10765":{"protein_sequence":{"accession":"UNN26062.1","sequence":"MYKKISILILIFVILISCKNTEKTSDETTLIDNIFTNSNTEGTLVIYDLNENKYIIHNKERAEQRFYPASTFKIYNSLIGLYEKAVKDVDEVFYKYNGEKVFLESWAKDSNLRYAIKNSQVPAYKELARRIGLEKMKENIEKLDFGNKNIGDCVDTFWLEGPLEISAMEQVKLLTKLAQNELPYPIEIQEAVSDITILEQTDNYTFHGKTGLADSDNMTTNPIGWFVGWLEENNNIYVFALNIDNVNSDDLEKRISIVKESLKSLNLLK"},"dna_sequence":{"accession":"OM977011.1","fmin":"0","fmax":"810","strand":"+","sequence":"ATGTATAAAAAAATTTCTATATTAATATTAATTTTTGTTATTTTAATATCTTGTAAAAATACAGAAAAAACATCAGATGAAACTACATTGATAGATAACATATTCACTAACAGCAATACAGAAGGAACATTAGTTATATACGATTTAAATGAGAATAAATATATAATTCATAACAAAGAAAGAGCTGAACAAAGATTTTATCCTGCCTCAACATTTAAAATTTATAATAGTTTAATAGGCTTATATGAGAAAGCAGTTAAAGATGTAGACGAAGTATTTTATAAATATAATGGTGAAAAAGTTTTCCTTGAATCTTGGGCTAAGGACTCTAATTTAAGATATGCAATTAAAAATTCACAAGTACCAGCATATAAAGAATTAGCAAGAAGAATAGGCCTTGAAAAAATGAAAGAAAACATAGAAAAACTAGATTTTGGTAATAAAAATATAGGTGACTGTGTAGATACTTTTTGGCTTGAGGGCCCTTTGGAAATAAGTGCAATGGAACAAGTTAAATTATTAACTAAATTAGCTCAAAATGAATTGCCATATCCTATAGAAATACAAGAAGCTGTTTCTGATATTACTATACTAGAACAAACAGATAATTATACATTTCATGGAAAAACTGGATTAGCTGATTCCGACAACATGACAACTAACCCTATTGGCTGGTTTGTAGGCTGGCTTGAAGAAAATAATAATATATACGTCTTTGCTTTAAATATTGACAATGTCAATTCTGATGATCTTGAAAAAAGAATAAGCATAGTAAAGGAAAGTTTGAAATCACTAAATTTACTAAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"47903","NCBI_taxonomy_name":"Brachyspira pulli","NCBI_taxonomy_id":"310721"}}}},"ARO_accession":"3008520","ARO_id":"47312","ARO_name":"OXA-1102","CARD_short_name":"OXA-1102","ARO_description":"OXA-63 family oxacillin-hydrolyzing class D beta-lactamase OXA-1102.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46521":{"category_aro_accession":"3007732","category_aro_cvterm_id":"46521","category_aro_name":"OXA-63-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-63.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7939":{"model_id":"7939","model_name":"OXA-1103","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10766":{"protein_sequence":{"accession":"UNN26063.1","sequence":"MYKKISILILIFVILISCKNTEKTSDETTLIDNIFTNSNTEGTLVIYDLNENKYIIHNKERAEQRFYPASTFKIYNSLIGLYEKAVKDVDEVFYKYNGEKVFLESWVKDSNLRYAIKNSQVPAYKELARRIGLEKMKENIEKLDFGNKNIGDSVDTFWLEGPLEISAMEQVKLLTKLAQNELPYPIEIQEAVSDITILEQTDNYTFHGKTGLADSDNITTNPIGWFVGWLEENNNIYVFALNIDNVNSDDLEKRISIVKESLKSLNLLK"},"dna_sequence":{"accession":"OM977012.1","fmin":"0","fmax":"810","strand":"+","sequence":"ATGTATAAAAAAATTTCTATATTAATATTAATTTTTGTTATTTTAATATCTTGTAAAAATACAGAAAAAACATCAGATGAAACTACATTGATAGATAACATATTCACTAACAGCAATACAGAAGGAACATTAGTTATATACGATTTAAATGAGAATAAATATATAATTCATAACAAAGAAAGAGCTGAACAAAGATTTTATCCTGCATCAACATTTAAAATTTATAATAGTTTAATAGGCTTATATGAGAAAGCAGTTAAAGATGTAGACGAAGTATTTTATAAATATAATGGTGAAAAAGTTTTCCTTGAATCTTGGGTTAAGGACTCTAATTTAAGATATGCAATTAAAAATTCACAAGTACCAGCATATAAAGAATTAGCAAGAAGAATAGGTCTTGAAAAAATGAAAGAAAACATAGAAAAACTAGATTTTGGTAATAAAAATATAGGTGACAGTGTAGATACTTTTTGGCTTGAGGGCCCTTTGGAAATAAGTGCAATGGAACAAGTTAAATTATTAACTAAATTAGCTCAAAATGAATTGCCATATCCTATAGAAATACAAGAAGCTGTTTCTGATATTACTATACTAGAACAAACAGATAATTATACATTTCATGGAAAAACTGGATTAGCTGATTCCGACAACATTACAACTAACCCTATTGGCTGGTTTGTAGGCTGGCTTGAAGAAAATAATAATATATACGTCTTTGCTTTAAATATTGACAATGTCAATTCTGATGATCTTGAAAAAAGAATAAGCATAGTAAAGGAAAGTTTGAAATCACTAAATTTACTAAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"47903","NCBI_taxonomy_name":"Brachyspira pulli","NCBI_taxonomy_id":"310721"}}}},"ARO_accession":"3008521","ARO_id":"47313","ARO_name":"OXA-1103","CARD_short_name":"OXA-1103","ARO_description":"OXA-63 family oxacillin-hydrolyzing class D beta-lactamase OXA-1103.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46521":{"category_aro_accession":"3007732","category_aro_cvterm_id":"46521","category_aro_name":"OXA-63-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-63.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7940":{"model_id":"7940","model_name":"OXA-1104","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10767":{"protein_sequence":{"accession":"UNN26064.1","sequence":"MYKKISILILIFVILISCKNTEKTSDETTLIDNIFTNSNTEGTLVIYDLNENKYIIHNKERAEQRFYPASTFKIYNSLIGLYEKAVKDVDEVFYKYNGEKVFLESWVKDSNLRYAIKNSQVPAYKELARRIGLEKMKENIEKLDFGNKNIGDSVDTFWLEGPLEISAMEQVKLLTKLAQNELPYPIEIQEAVSDITILEQNDNYTLHGKTGLADSENMTTNPIGWFVGWLEENNNIYIFALNIDNVNSDDLEKRISIVKESLKSLNLLK"},"dna_sequence":{"accession":"OM977013.1","fmin":"0","fmax":"810","strand":"+","sequence":"ATGTATAAAAAAATTTCTATATTAATATTAATTTTTGTTATTTTAATATCTTGTAAAAATACAGAAAAAACATCAGATGAAACTACATTGATAGATAACATATTCACTAACAGCAATACAGAAGGAACATTAGTTATATACGATTTAAATGAGAATAAATATATAATTCATAACAAAGAAAGAGCTGAACAAAGATTTTATCCTGCATCAACATTTAAAATTTATAATAGTTTAATAGGCTTATATGAGAAAGCAGTTAAAGATGTAGACGAAGTATTTTATAAATATAATGGTGAAAAAGTTTTCCTTGAATCTTGGGTTAAGGACTCTAATTTAAGATATGCAATTAAAAATTCACAAGTACCAGCATATAAAGAATTAGCAAGAAGAATAGGTCTTGAAAAAATGAAAGAAAACATAGAAAAACTAGATTTTGGTAATAAAAATATAGGTGACAGTGTAGATACTTTTTGGCTTGAGGGCCCTTTGGAAATAAGTGCAATGGAACAAGTTAAATTATTAACTAAATTAGCTCAAAATGAATTGCCATATCCTATAGAAATACAAGAAGCTGTTTCTGATATTACTATACTAGAACAAAATGATAATTATACACTTCATGGGAAAACGGGATTAGCTGATTCCGAAAACATGACAACTAACCCTATTGGCTGGTTTGTAGGCTGGCTTGAAGAAAATAATAATATATACATCTTTGCTTTAAATATTGACAATGTCAATTCTGATGATCTTGAAAAAAGAATAAGCATAGTAAAGGAAAGTTTGAAATCACTAAATTTACTAAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"47903","NCBI_taxonomy_name":"Brachyspira pulli","NCBI_taxonomy_id":"310721"}}}},"ARO_accession":"3008522","ARO_id":"47314","ARO_name":"OXA-1104","CARD_short_name":"OXA-1104","ARO_description":"OXA-63 family oxacillin-hydrolyzing class D beta-lactamase OXA-1104.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46521":{"category_aro_accession":"3007732","category_aro_cvterm_id":"46521","category_aro_name":"OXA-63-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-63.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7941":{"model_id":"7941","model_name":"OXA-1105","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10768":{"protein_sequence":{"accession":"UNN26065.1","sequence":"MYKKISILILIFVILISCKNTEKTSDETTLIDNIFTNSNTEGTLVIYDLNENKYIIHNKERAEQRFYPASTFKIYNSLIGLYEKAVKDVDEVFYKYNGEKVFLESWAKDSNLRYAIKNSQVPAYKELARRIGLEKMKENIEKLDFGNKNIGDSVDTFWLEGPLEISAMEQVKLLTKLAQNELPYPIEIQEAVSDITILEQNDNYTLHGKTGLADSENMTTNPIGWFVGWLEENNNIYIFALNIDNVNSDDLEKRISIVKESLKSLNLLK"},"dna_sequence":{"accession":"OM977014.1","fmin":"0","fmax":"810","strand":"+","sequence":"ATGTATAAAAAAATTTCTATATTAATATTAATTTTTGTTATTTTAATATCTTGTAAAAATACAGAAAAAACATCAGATGAAACTACATTGATAGATAACATATTCACTAACAGCAATACAGAAGGAACATTAGTTATATACGATTTAAATGAGAATAAATATATAATTCATAACAAAGAAAGAGCTGAACAAAGATTTTATCCCGCATCAACATTTAAAATTTATAATAGTTTAATAGGCTTATATGAGAAAGCAGTTAAAGATGTAGACGAAGTATTTTATAAATATAATGGTGAAAAAGTTTTCCTTGAATCTTGGGCTAAGGACTCCAATTTAAGATATGCAATTAAAAATTCACAAGTACCAGCATATAAAGAATTAGCAAGAAGAATAGGCCTTGAAAAAATGAAAGAAAACATAGAAAAACTAGATTTTGGTAATAAAAATATAGGTGACAGTGTAGATACTTTTTGGCTTGAGGGCCCTTTGGAAATAAGTGCAATGGAACAAGTTAAATTATTAACTAAATTAGCTCAAAATGAATTGCCATATCCTATAGAAATACAAGAAGCTGTTTCTGATATTACTATACTAGAACAAAATGATAATTATACACTTCATGGGAAAACGGGATTAGCTGATTCCGAAAACATGACAACTAACCCTATTGGCTGGTTTGTAGGCTGGCTTGAAGAAAATAATAATATATACATCTTTGCTTTAAATATTGACAATGTCAATTCTGATGATCTTGAAAAAAGAATAAGCATAGTAAAGGAAAGTTTGAAATCACTAAATTTACTAAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"47903","NCBI_taxonomy_name":"Brachyspira pulli","NCBI_taxonomy_id":"310721"}}}},"ARO_accession":"3008523","ARO_id":"47315","ARO_name":"OXA-1105","CARD_short_name":"OXA-1105","ARO_description":"OXA-63 family oxacillin-hydrolyzing class D beta-lactamase OXA-1105.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46521":{"category_aro_accession":"3007732","category_aro_cvterm_id":"46521","category_aro_name":"OXA-63-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-63.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7942":{"model_id":"7942","model_name":"OXA-1106","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10769":{"protein_sequence":{"accession":"UNN26066.1","sequence":"MYKKISILILIFVILISCKNTEKTSDETTLIDNIFTNSNTEGTLVIYDLNENKYIIHNKERAEQIFYPASTFKIYNSLIGLYEKAVKDVDEVFYKYNGEKVFLESWVKDSNLRYAIKNSQVPAYKELARRIGLEKMKENIEKLDFGNKNIGDSVDTFWLEGPLEISAMEQVKLLTKLAQNELPYPIEIQEAVSDITILEQTDNYTFHGKTGLADSDNMTTNPIGWFVGWLEENNNIYVFALNIDNVNSDDLEKRISIVKESLKSLNLLK"},"dna_sequence":{"accession":"OM977015.1","fmin":"0","fmax":"810","strand":"+","sequence":"ATGTATAAAAAAATTTCTATATTAATATTAATTTTTGTTATTTTAATATCTTGTAAAAATACAGAAAAAACATCAGATGAAACTACATTGATAGATAACATATTCACTAACAGCAATACAGAAGGAACATTAGTTATATACGATTTAAATGAGAATAAATATATAATTCATAACAAAGAAAGAGCTGAACAAATATTTTATCCTGCATCAACATTTAAAATTTATAATAGTTTAATAGGCTTATATGAGAAAGCAGTTAAAGATGTAGACGAAGTATTTTATAAATATAATGGTGAAAAAGTTTTCCTTGAATCTTGGGTTAAGGACTCTAATTTAAGATATGCAATTAAAAATTCACAAGTACCAGCATATAAAGAATTAGCAAGAAGAATAGGTCTTGAAAAAATGAAAGAAAACATAGAAAAACTAGATTTTGGTAATAAAAATATAGGTGACAGTGTAGATACTTTTTGGCTTGAGGGCCCTTTGGAAATAAGTGCAATGGAACAAGTTAAATTATTAACTAAATTAGCTCAAAATGAATTGCCATATCCTATAGAAATACAAGAAGCTGTTTCTGATATTACTATACTAGAACAAACAGATAATTATACATTTCATGGAAAAACTGGATTAGCTGATTCCGACAACATGACAACTAACCCTATTGGCTGGTTTGTAGGCTGGCTTGAAGAAAATAATAATATATACGTCTTTGCTTTAAATATTGACAATGTCAATTCTGATGATCTTGAAAAAAGAATAAGCATAGTAAAGGAAAGTTTGAAATCACTAAATTTACTAAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"47903","NCBI_taxonomy_name":"Brachyspira pulli","NCBI_taxonomy_id":"310721"}}}},"ARO_accession":"3008524","ARO_id":"47316","ARO_name":"OXA-1106","CARD_short_name":"OXA-1106","ARO_description":"OXA-63 family oxacillin-hydrolyzing class D beta-lactamase OXA-1106.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46521":{"category_aro_accession":"3007732","category_aro_cvterm_id":"46521","category_aro_name":"OXA-63-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-63.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7943":{"model_id":"7943","model_name":"OXA-1107","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10770":{"protein_sequence":{"accession":"UNN26067.1","sequence":"MYKKISILILIFVILISCKNTEKTSDETTLIDNIFTNSNTEGTLVIYDLNENKYIIHNKERAEQRFYPASTFKIYNSLIGLYEKAVKDVDEVFYKYNGEKVFLESWAKDSNLRYAIKNSQVPAYKELARRIGLEKMKENIEKLDFGNKNIGDSVDTFWLEGPLEISAMEQVKLLTKLAQNELPYPIEIQEAVSDITILEQTDNYTFHGKTGLADSDNITTNPIGWFVGWLEENNNIYVFALNIDNVNSDDLEKRISIVKESLKSLNLLK"},"dna_sequence":{"accession":"OM977016.1","fmin":"0","fmax":"810","strand":"+","sequence":"ATGTATAAAAAAATTTCTATATTAATATTAATTTTTGTTATTTTAATATCTTGTAAAAATACAGAAAAAACATCAGATGAAACTACATTGATAGATAACATATTCACTAACAGCAATACAGAAGGAACATTAGTTATATACGATTTAAATGAGAATAAATATATAATTCATAACAAAGAAAGAGCTGAACAAAGATTTTATCCCGCATCAACATTTAAAATTTATAATAGTTTAATAGGCTTATATGAGAAAGCAGTTAAAGATGTAGACGAAGTATTTTATAAATATAATGGTGAAAAAGTTTTCCTTGAATCTTGGGCTAAGGACTCCAATTTAAGATATGCAATTAAAAATTCACAAGTACCAGCATATAAAGAATTAGCAAGAAGAATAGGCCTTGAAAAAATGAAAGAAAACATAGAAAAACTAGATTTTGGTAATAAAAATATAGGTGACAGTGTAGATACTTTTTGGCTTGAGGGCCCTTTGGAAATAAGTGCAATGGAACAAGTTAAATTATTAACTAAATTAGCTCAAAATGAATTGCCATATCCTATAGAAATACAAGAAGCTGTTTCTGATATTACTATACTAGAACAAACAGATAATTATACATTTCATGGAAAAACTGGATTAGCTGATTCCGACAACATTACAACTAACCCTATTGGCTGGTTTGTAGGCTGGCTTGAAGAAAATAATAATATATACGTCTTTGCTTTAAATATTGACAATGTCAATTCTGATGATCTTGAAAAAAGAATAAGCATAGTAAAGGAAAGTTTGAAATCACTAAATTTACTAAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"47903","NCBI_taxonomy_name":"Brachyspira pulli","NCBI_taxonomy_id":"310721"}}}},"ARO_accession":"3008525","ARO_id":"47317","ARO_name":"OXA-1107","CARD_short_name":"OXA-1107","ARO_description":"OXA-63 family oxacillin-hydrolyzing class D beta-lactamase OXA-1107.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46521":{"category_aro_accession":"3007732","category_aro_cvterm_id":"46521","category_aro_name":"OXA-63-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-63.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7944":{"model_id":"7944","model_name":"OXA-1108","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10771":{"protein_sequence":{"accession":"UOF88498.1","sequence":"MNKKIKLIFILIFSINLFANDVELENLFKKYQVEGTLVLESLNTKKVDIYNEKRANTAFSPASTFKIPNTLIALNEGVVNKDSIIVWDKKVREFDAWNKDQTLQSAFKSSCVWCYKEFASKIGVEKYKKYLKELNYGNKTIGKDVTDFWLDESLRITAFEEIRFLKQLQANNLAFKQEDINLLKELMIDEKSENYVVRAKTGWEGKYGWYVGYVETKNDVWFFALNIDTKTKEDLAKRKALTLEALKTKGIID"},"dna_sequence":{"accession":"OM617734.1","fmin":"0","fmax":"762","strand":"+","sequence":"ATGAATAAAAAAATAAAACTAATTTTTATTTTAATTTTTTCAATAAATTTATTCGCAAATGATGTGGAACTTGAAAATTTATTTAAAAAATACCAAGTTGAAGGAACTTTAGTATTAGAGTCTTTAAATACAAAAAAAGTAGATATTTATAATGAAAAGAGAGCAAATACAGCATTTTCTCCTGCTTCAACATTTAAAATACCAAATACTTTGATAGCTTTAAATGAAGGTGTTGTAAACAAAGATTCTATAATAGTTTGGGATAAAAAAGTAAGAGAATTTGATGCTTGGAATAAAGACCAAACTTTACAATCAGCTTTCAAAAGTTCATGTGTTTGGTGTTATAAAGAGTTCGCTTCAAAAATTGGAGTTGAAAAATATAAAAAGTATCTAAAAGAGCTTAATTATGGAAATAAAACAATAGGCAAAGATGTAACTGATTTTTGGTTGGATGAGAGTTTGAGAATTACAGCTTTTGAAGAGATAAGATTTTTAAAACAATTACAAGCAAACAATTTAGCTTTTAAACAAGAAGATATAAATCTTTTAAAAGAGTTGATGATTGATGAAAAAAGCGAAAATTATGTAGTTAGAGCAAAAACAGGTTGGGAAGGAAAATATGGTTGGTATGTTGGTTATGTTGAAACAAAAAATGATGTTTGGTTTTTTGCTTTAAATATCGACACAAAAACAAAAGAAGATTTAGCAAAAAGAAAAGCTTTAACTTTAGAAGCTTTAAAAACAAAAGGGATTATAGATTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42842","NCBI_taxonomy_name":"Aliarcobacter butzleri","NCBI_taxonomy_id":"28197"}}}},"ARO_accession":"3008526","ARO_id":"47318","ARO_name":"OXA-1108","CARD_short_name":"OXA-1108","ARO_description":"Class D beta-lactamase OXA-1108.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7945":{"model_id":"7945","model_name":"OXA-1109","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10772":{"protein_sequence":{"accession":"UOM32496.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDDKAEKIKNLFNEAHTTGVLVIHQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGEKRLFPEWEKNMTLGDAMKASAIQVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"ON101846.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGACAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCATCAAGGTCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAATGGGATGGGGAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCAGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTCTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008527","ARO_id":"47319","ARO_name":"OXA-1109","CARD_short_name":"OXA-1109","ARO_description":"OXA-51 family carbapenem-hydrolyzing class D beta-lactamase OXA-1109.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7946":{"model_id":"7946","model_name":"OXA-1110","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10773":{"protein_sequence":{"accession":"UOM32497.1","sequence":"MKILIFLPLLSCLSLTACSLPVSSSPSQITSTQSTQTIAQLFDQAQSSGVLGIQRGQQIQVYGNDLSRANTEYVPASTFKMLNALIGLQHGKATTNEIFKWDGKKRSFSAWEKDMTLGQAMQASAVPVYQELARRIGLELMQQEVQRIQFGNQQIGQQVDNFWLVGPLKVTPKQEVQFVSVLAREQLAFDPQVQQQVKAMLFLQERKAYRLYVKSGWGMDVEPQVGWLTGWVETPQAEIVAFSLNMQMQNGIDPAIRLEILQQALAELGLYPKAEG"},"dna_sequence":{"accession":"ON101847.1","fmin":"0","fmax":"831","strand":"+","sequence":"ATGAAAATTCTGATTTTTCTGCCTTTACTGAGTTGCTTGAGCCTGACAGCGTGTAGCCTGCCCGTTTCATCTTCCCCATCTCAGATCACTTCAACTCAATCTACCCAAACCATTGCCCAATTATTTGATCAGGCGCAAAGCTCTGGCGTTTTAGGGATTCAGCGTGGTCAACAGATACAGGTCTATGGTAATGATTTAAGTCGTGCAAATACCGAATATGTTCCTGCTTCTACTTTTAAAATGCTCAATGCCCTGATTGGCCTGCAACATGGCAAAGCTACAACCAATGAAATTTTTAAATGGGATGGCAAGAAACGCAGTTTTTCAGCTTGGGAAAAAGACATGACTCTCGGCCAAGCCATGCAAGCGTCTGCTGTACCCGTTTATCAGGAACTGGCACGTCGTATTGGCCTTGAACTGATGCAACAGGAAGTACAACGCATCCAATTTGGTAATCAGCAGATTGGTCAACAGGTCGATAACTTCTGGTTGGTAGGCCCTTTGAAAGTTACTCCAAAACAGGAAGTCCAATTTGTTTCTGTGTTGGCCCGAGAGCAACTGGCCTTTGATCCTCAAGTCCAGCAACAAGTCAAAGCCATGTTATTTTTACAGGAGCGGAAAGCTTATCGACTATATGTCAAATCCGGTTGGGGCATGGATGTGGAACCGCAAGTCGGCTGGCTCACCGGCTGGGTTGAAACACCGCAGGCTGAAATCGTGGCATTTTCACTCAATATGCAGATGCAAAATGGTATAGATCCGGCGATCCGCCTTGAAATTTTGCAGCAGGCTTTGGCCGAATTAGGGCTTTATCCAAAAGCTGAAGGATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36948","NCBI_taxonomy_name":"Acinetobacter lwoffii","NCBI_taxonomy_id":"28090"}}}},"ARO_accession":"3008528","ARO_id":"47320","ARO_name":"OXA-1110","CARD_short_name":"OXA-1110","ARO_description":"OXA-134 family carbapenem-hydrolyzing class D beta-lactamase OXA-1110.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46489":{"category_aro_accession":"3007700","category_aro_cvterm_id":"46489","category_aro_name":"OXA-134-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-134.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7947":{"model_id":"7947","model_name":"OXA-1111","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10774":{"protein_sequence":{"accession":"UOM32498.1","sequence":"MKILILLPLLSCLGLTACTSPVSSFPSQITSTQSTQAIAQLFDQAQSSGVLVIQRGQKVQVYGNDLSRAGTEYVPASTFKMLNALIGLQHGKATTNEIFKWDGKKRSFTAWEKDMTLGQAMQASAVPVYQELARRIGLELMQQEVQRIQFGNQQIGQQVDNFWLVGPLKVTPKQEVQFVSALAREQLAFDPQVQQQVKAMLFLQERKAYRLYVKSGWGMDVEPQVGWLTGWVETPQAEIVAFSLNMQMQNGIDPAIRLEILQQALAELGLYPKAEG"},"dna_sequence":{"accession":"ON101848.1","fmin":"0","fmax":"831","strand":"+","sequence":"ATGAAAATTCTGATTTTGCTACCTTTACTGAGTTGCTTGGGCCTGACAGCGTGTACCTCACCTGTTTCATCTTTCCCTTCTCAGATCACTTCAACTCAATCGACTCAAGCCATTGCCCAATTATTTGATCAGGCGCAAAGTTCTGGCGTTTTAGTGATTCAGCGTGGTCAAAAAGTACAGGTCTATGGCAATGATTTAAGCCGTGCAGGTACCGAATATGTTCCAGCCTCTACTTTCAAAATGCTCAATGCCCTGATTGGTCTACAACATGGTAAAGCCACAACCAATGAGATTTTTAAATGGGATGGCAAGAAACGCAGCTTTACCGCCTGGGAAAAAGACATGACGCTCGGCCAAGCCATGCAAGCTTCTGCGGTACCGGTCTATCAAGAGCTGGCGCGTCGTATTGGTCTGGAATTAATGCAACAGGAAGTACAACGCATCCAATTTGGTAATCAGCAGATTGGTCAACAGGTCGATAACTTCTGGTTGGTAGGCCCTTTGAAAGTTACTCCAAAACAGGAAGTCCAATTTGTTTCTGCGTTGGCCCGAGAGCAACTGGCCTTTGATCCTCAAGTCCAGCAACAAGTCAAAGCCATGTTATTTTTACAGGAGCGGAAAGCTTATCGACTATATGTCAAATCCGGTTGGGGCATGGATGTGGAACCGCAAGTCGGCTGGCTCACCGGCTGGGTTGAAACACCGCAGGCTGAAATCGTGGCATTTTCACTCAATATGCAGATGCAAAATGGTATAGATCCGGCGATCCGCCTTGAAATTTTGCAGCAGGCTTTGGCCGAATTAGGGCTTTATCCAAAAGCTGAAGGATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36948","NCBI_taxonomy_name":"Acinetobacter lwoffii","NCBI_taxonomy_id":"28090"}}}},"ARO_accession":"3008529","ARO_id":"47321","ARO_name":"OXA-1111","CARD_short_name":"OXA-1111","ARO_description":"OXA-134 family carbapenem-hydrolyzing class D beta-lactamase OXA-1111.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46489":{"category_aro_accession":"3007700","category_aro_cvterm_id":"46489","category_aro_name":"OXA-134-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-134.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7948":{"model_id":"7948","model_name":"OXA-1112","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10775":{"protein_sequence":{"accession":"UOM32499.1","sequence":"MKILILLPLFSCLGLTACSLPVSSSPSQITSIQSTQAIAQLFDQAQSAGVLVIQRVQQIQVYGNNLSRAGTEYVPASTFKMLNALIGLQHGKATTNEIFKWDGKKRSFAAWEKDMTLGEAMQASAVPVYQELARRIGLELMQQEVQRIQFGNQQIGQQVDNFWLVGPLKVTPKQEVQFVSALAREQLAFDPQVQQQVKAMLFLQERKAYRLYVKSGWGMDVEPQVGWLTGWVETPQAEIVAFSLNMQMQNGIDPAIRLEILQQALAELGLYPKAEG"},"dna_sequence":{"accession":"ON101849.1","fmin":"0","fmax":"831","strand":"+","sequence":"ATGAAAATTCTGATTTTGCTGCCTTTATTTAGTTGCTTGGGACTGACGGCGTGTAGTCTGCCCGTTTCATCCTCCCCCTCTCAGATCACTTCAATTCAATCGACTCAAGCCATTGCCCAATTATTTGATCAGGCGCAAAGCGCTGGCGTTTTAGTGATTCAGCGTGTTCAACAGATACAGGTCTATGGTAATAATTTAAGTCGTGCAGGTACCGAATATGTTCCCGCCTCTACTTTTAAAATGCTCAATGCCCTGATTGGCCTACAACATGGCAAAGCCACAACCAATGAAATTTTTAAATGGGATGGCAAGAAACGCAGTTTTGCAGCCTGGGAAAAAGACATGACTCTCGGCGAAGCCATGCAAGCTTCTGCTGTACCCGTGTATCAGGAACTGGCACGTCGCATTGGCCTTGAATTGATGCAACAGGAAGTACAACGCATCCAATTTGGTAATCAGCAGATTGGTCAACAGGTCGATAACTTCTGGTTGGTAGGCCCTTTGAAAGTTACTCCAAAACAGGAAGTCCAATTTGTTTCTGCGTTGGCCCGAGAGCAACTGGCCTTTGATCCTCAAGTCCAGCAACAAGTCAAAGCCATGTTATTTTTACAGGAGCGGAAAGCTTATCGACTATATGTCAAATCCGGTTGGGGCATGGATGTGGAACCGCAAGTCGGCTGGCTCACCGGCTGGGTTGAAACACCGCAGGCTGAAATCGTGGCATTTTCACTCAATATGCAGATGCAAAATGGTATAGATCCGGCAATCCGCCTTGAAATTTTGCAGCAGGCTTTGGCCGAATTAGGGCTTTATCCAAAAGCTGAAGGATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36948","NCBI_taxonomy_name":"Acinetobacter lwoffii","NCBI_taxonomy_id":"28090"}}}},"ARO_accession":"3008530","ARO_id":"47322","ARO_name":"OXA-1112","CARD_short_name":"OXA-1112","ARO_description":"OXA-134 family carbapenem-hydrolyzing class D beta-lactamase OXA-1112.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46489":{"category_aro_accession":"3007700","category_aro_cvterm_id":"46489","category_aro_name":"OXA-134-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-134.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7949":{"model_id":"7949","model_name":"OXA-1113","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10776":{"protein_sequence":{"accession":"UOM32500.1","sequence":"MTKKALFFAIGTIFLSACSFNTVEQHQIQSISTNKNSKKIKSLFDQAQTEGVLVIKRGQIEEVYGNDLKRASTEYVPASTFKMLNALIGLEHHKATPTEVFKWDGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMSKEVKRIGFGNADIGSKVDDFWLVGPLKITPQQEAQFAYELAHKTLPFSKNVQEQVQSMLFIEEKNGRKIYAKSGWGWDVEPQVGWLTGWVVQPQGKIVAFSLNLEMKKGIPSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"ON101850.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGACTAAAAAAGCTCTTTTCTTTGCCATTGGTACGATATTTTTATCGGCATGTTCTTTTAATACGGTAGAACAGCATCAAATACAGTCAATTTCTACCAATAAAAACTCAAAGAAAATTAAATCATTGTTTGATCAAGCACAAACTGAAGGTGTTTTAGTTATAAAACGTGGGCAAATAGAGGAAGTCTATGGCAATGATCTTAAAAGAGCATCAACCGAATATGTTCCCGCCTCTACCTTTAAGATGTTAAATGCTTTGATTGGACTTGAGCATCATAAAGCAACACCAACTGAAGTGTTTAAATGGGATGGGCAAAAGCGTTTATTTCCCGATTGGGAAAAAGACATGACATTAGGCGATGCGATGAAAGCTTCTGCTATTCCAGTTTATCAGGAACTAGCTCGACGAATTGGCCTTGATCTTATGTCTAAAGAGGTCAAACGCATTGGTTTCGGTAATGCTGATATTGGTTCAAAAGTAGATGATTTTTGGCTTGTTGGCCCACTTAAAATTACACCTCAACAAGAAGCCCAGTTTGCTTATGAACTAGCCCATAAAACTCTTCCTTTTAGCAAAAATGTGCAAGAACAAGTTCAATCTATGCTGTTCATAGAAGAAAAAAATGGACGGAAAATTTATGCCAAAAGTGGTTGGGGATGGGATGTGGAGCCTCAAGTGGGCTGGTTAACAGGCTGGGTCGTTCAACCTCAAGGAAAAATTGTAGCGTTCTCACTCAATTTAGAAATGAAAAAAGGCATACCTAGTTCTATTCGAAAAGAAATTGCTTATAAGGGATTAGAGCAGCTAGGTATTTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3008531","ARO_id":"47323","ARO_name":"OXA-1113","CARD_short_name":"OXA-1113","ARO_description":"OXA-213 family carbapenem-hydrolyzing class D beta-lactamase OXA-1113.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46495":{"category_aro_accession":"3007706","category_aro_cvterm_id":"46495","category_aro_name":"OXA-213-like beta-lactamase","category_aro_description":"OXA-213-like enzymes have been identified to be intrinsic to A. calcoaceticus and have been subsequently detected in A. pittii. Phylogenetic analysis of OXA-213-like proteins identified two distinct subgroups within the OXA family. The first group was linked to A. pittii and the second group to A. calcoaceticus. The carbapenemase activity of these OXAs may be related to the species-dependent effect.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7950":{"model_id":"7950","model_name":"OXA-1114","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10777":{"protein_sequence":{"accession":"UOM32501.1","sequence":"MTKKALFFAIGTIFLSACSFNTVEQHQIQSISTNKNSEKIKTLFDQAQTEGVLVIKREQTEEVYGNDLKRASTEYVPASTFKMVNALIGLEHHKATPTEVFKWDGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMSKEVKRIGFGNADIGSKVDNFWLVGPLKITPQQEVQFAYKLAHKTLPFSKNVQEQVQSMLFIEEKNGQKIYAKSGWGWDVDPQVGWFTGWVVQPQGEIIAFSLNLEMKKGISSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"ON101851.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGACTAAAAAAGCTCTTTTCTTTGCCATTGGTACGATATTTTTATCGGCGTGTTCTTTTAACACCGTAGAACAGCATCAAATACAGTCAATTTCTACCAATAAAAACTCAGAGAAAATTAAAACGTTGTTTGATCAAGCACAAACTGAAGGTGTTTTAGTTATAAAACGTGAGCAAACAGAGGAAGTCTATGGCAATGATCTTAAAAGAGCATCAACCGAATATGTTCCCGCCTCTACCTTTAAAATGGTAAATGCTTTGATTGGACTTGAGCATCATAAAGCAACGCCAACTGAAGTGTTTAAATGGGATGGGCAAAAGCGTTTATTTCCCGATTGGGAAAAAGACATGACTCTAGGCGATGCTATGAAAGCTTCTGCTATTCCAGTTTATCAGGAACTAGCTCGACGAATTGGCCTTGATCTTATGTCTAAAGAGGTAAAGCGCATTGGTTTCGGTAATGCTGATATTGGTTCAAAAGTAGATAATTTTTGGCTTGTTGGCCCACTTAAAATTACACCTCAACAAGAAGTACAGTTTGCTTATAAATTAGCCCATAAAACTCTTCCCTTTAGCAAAAATGTACAAGAACAAGTTCAATCTATGCTGTTCATAGAAGAAAAAAATGGACAAAAAATTTATGCCAAAAGTGGTTGGGGATGGGATGTTGACCCACAAGTTGGTTGGTTTACAGGCTGGGTAGTTCAACCTCAGGGAGAAATTATAGCTTTCTCACTTAATTTAGAAATGAAGAAAGGCATATCTAGTTCTATTCGAAAAGAAATTGCTTATAAAGGATTAGAACAACTCGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3008532","ARO_id":"47324","ARO_name":"OXA-1114","CARD_short_name":"OXA-1114","ARO_description":"OXA-213 family carbapenem-hydrolyzing class D beta-lactamase OXA-1114.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46495":{"category_aro_accession":"3007706","category_aro_cvterm_id":"46495","category_aro_name":"OXA-213-like beta-lactamase","category_aro_description":"OXA-213-like enzymes have been identified to be intrinsic to A. calcoaceticus and have been subsequently detected in A. pittii. Phylogenetic analysis of OXA-213-like proteins identified two distinct subgroups within the OXA family. The first group was linked to A. pittii and the second group to A. calcoaceticus. The carbapenemase activity of these OXAs may be related to the species-dependent effect.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7951":{"model_id":"7951","model_name":"OXA-1115","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10778":{"protein_sequence":{"accession":"UOM32502.1","sequence":"MTKKALFFAIGTMFLSACSFNTVEQHQIQSISTNKNSEKIKSLFDQAQTTGVLVIKRGQTEEVYGNDLKRASTEYVPASTFKMVNALIGLEHHKATPTEVFKWDGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMSKEVKRIGFGNADIGSKVDNFWLVGPLKITPQQEVQFAYKLAHKTLPFSKNVQEQVQSMLFIEEKNGRKIYAKSGWGWDVEPQVGWFTGWVVQPQGEIVAFSLNLEMKKGIPSTIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"ON101852.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGACTAAAAAAGCTCTTTTCTTTGCCATTGGTACGATGTTTTTGTCTGCATGTTCTTTTAATACGGTAGAACAACATCAAATACAGTCAATTTCTACCAATAAAAACTCAGAGAAAATTAAATCGTTGTTTGATCAAGCACAAACTACAGGTGTTTTAGTTATAAAACGTGGGCAAACAGAGGAAGTCTATGGCAATGATCTTAAAAGAGCATCAACCGAATATGTTCCCGCCTCTACCTTTAAAATGGTAAATGCTTTGATTGGACTTGAGCATCATAAAGCAACGCCAACTGAAGTGTTTAAATGGGATGGGCAAAAGCGTTTATTTCCCGATTGGGAAAAAGACATGACATTAGGCGATGCTATGAAAGCTTCTGCTATTCCAGTTTATCAGGAACTAGCTCGACGAATTGGCCTTGATCTTATGTCTAAAGAGGTAAAACGCATTGGTTTCGGTAATGCTGATATTGGTTCAAAAGTAGATAATTTTTGGCTTGTTGGCCCACTTAAAATTACACCTCAACAAGAAGTACAGTTTGCTTATAAATTAGCCCACAAAACTCTTCCCTTTAGCAAAAATGTACAAGAACAAGTTCAATCTATGCTGTTCATAGAAGAAAAAAATGGACGAAAAATTTATGCCAAAAGTGGTTGGGGATGGGATGTGGAGCCTCAAGTGGGCTGGTTTACAGGCTGGGTAGTTCAACCACAAGGAGAAATTGTAGCGTTCTCACTCAATTTAGAAATGAAGAAAGGCATACCTAGTACTATTCGAAAAGAAATTGCTTATAAGGGATTAGAGCAGCTAGGTATTTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3008533","ARO_id":"47325","ARO_name":"OXA-1115","CARD_short_name":"OXA-1115","ARO_description":"OXA-213 family carbapenem-hydrolyzing class D beta-lactamase OXA-1115.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46495":{"category_aro_accession":"3007706","category_aro_cvterm_id":"46495","category_aro_name":"OXA-213-like beta-lactamase","category_aro_description":"OXA-213-like enzymes have been identified to be intrinsic to A. calcoaceticus and have been subsequently detected in A. pittii. Phylogenetic analysis of OXA-213-like proteins identified two distinct subgroups within the OXA family. The first group was linked to A. pittii and the second group to A. calcoaceticus. The carbapenemase activity of these OXAs may be related to the species-dependent effect.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7952":{"model_id":"7952","model_name":"OXA-1116","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10779":{"protein_sequence":{"accession":"UOM32503.1","sequence":"MKILILWPLLSYLSLTACSFPVSNSPSQITSTQSIQAIAKLFDQAQSSGVLVIQRGPHLQVYGNDLSRAHTEYVPASTFKIFNALIGLQHGKATTNEIFKWDGKKRSFAAWEKDMTLGQAMQASAVPVYQELARRIGLELMEQEVRRIQFGNQHIGQQVDNFWLVGPLKITPKQEVEFASALAQEQLAFDPRFQQQVKTMLLLQERQAYRLYAKSGWGMDVEPQVGWLTGWIETPQDEIVAFSLNMQMQSNMDPAIRLKILQQALAELGLYPKAEG"},"dna_sequence":{"accession":"ON101853.1","fmin":"0","fmax":"831","strand":"+","sequence":"ATGAAAATTCTTATTTTGTGGCCTTTACTCAGTTACTTGAGCCTGACAGCCTGTAGCTTCCCTGTTTCAAATTCGCCCTCTCAAATCACTTCAACTCAATCTATTCAAGCTATTGCAAAGTTATTTGATCAGGCACAAAGCTCTGGCGTTTTAGTAATTCAACGGGGTCCACATCTACAGGTCTATGGCAATGATTTGAGTCGTGCACATACCGAATATGTTCCTGCTTCAACCTTTAAAATATTTAATGCTCTGATTGGCCTGCAACATGGTAAAGCCACGACCAATGAAATCTTTAAATGGGATGGCAAGAAGCGCAGTTTTGCAGCCTGGGAAAAAGACATGACTCTCGGCCAAGCCATGCAAGCTTCTGCTGTACCCGTCTATCAGGAACTAGCACGTCGCATTGGCCTTGAATTGATGGAACAGGAAGTGAGACGTATTCAATTCGGCAATCAACATATTGGGCAGCAGGTCGATAACTTCTGGTTGGTAGGCCCTTTGAAAATCACTCCAAAACAGGAAGTCGAATTTGCCTCTGCGCTTGCTCAAGAGCAACTTGCCTTTGATCCTCGGTTTCAGCAGCAAGTTAAAACCATGTTACTGTTACAGGAGCGACAAGCTTATCGACTATATGCCAAATCTGGTTGGGGTATGGATGTGGAGCCGCAAGTCGGCTGGCTCACCGGCTGGATCGAAACACCTCAGGACGAAATTGTGGCATTTTCACTGAATATGCAGATGCAAAGTAATATGGATCCGGCGATCCGCCTTAAAATTTTGCAGCAGGCCTTGGCCGAATTAGGGCTTTATCCCAAAGCTGAAGGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39096","NCBI_taxonomy_name":"Acinetobacter schindleri","NCBI_taxonomy_id":"108981"}}}},"ARO_accession":"3008534","ARO_id":"47326","ARO_name":"OXA-1116","CARD_short_name":"OXA-1116","ARO_description":"OXA-134 family carbapenem-hydrolyzing class D beta-lactamase OXA-1116.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46489":{"category_aro_accession":"3007700","category_aro_cvterm_id":"46489","category_aro_name":"OXA-134-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-134.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7953":{"model_id":"7953","model_name":"OXA-1117","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10780":{"protein_sequence":{"accession":"UOX08353.1","sequence":"MNIKALLLITSAIFISACSPYIVSANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLKMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"ON212676.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGTCTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACTACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAAAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008535","ARO_id":"47327","ARO_name":"OXA-1117","CARD_short_name":"OXA-1117","ARO_description":"OXA-51 family carbapenem-hydrolyzing class D beta-lactamase OXA-1117.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7954":{"model_id":"7954","model_name":"OXA-1118","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10781":{"protein_sequence":{"accession":"UOX08354.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLQMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"ON212677.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCCCTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTAGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAACAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTACAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008536","ARO_id":"47328","ARO_name":"OXA-1118","CARD_short_name":"OXA-1118","ARO_description":"OXA-51 family carbapenem-hydrolyzing class D beta-lactamase OXA-1118.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7955":{"model_id":"7955","model_name":"OXA-1119","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10782":{"protein_sequence":{"accession":"URF41644.1","sequence":"MRVLALSAVFLVASIIGMPAVAKEWQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGQTRDIAAWNRDHDLITAMKYSVVPVYQEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISATQQIAFLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYSIRIEPKIGWWVGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP"},"dna_sequence":{"accession":"ON586156.1","fmin":"0","fmax":"798","strand":"+","sequence":"ATGCGTGTATTAGCCTTATCGGCTGTGTTTTTGGTGGCATCGATTATCGGAATGCCAGCGGTAGCAAAGGAATGGCAAGAAAACAAAAGTTGGAATGCTCACTTTACTGAACATAAATCACAGGGCGTAGTTGTGCTCTGGAATGAGAATAAGCAGCAAGGATTTACCAATAATCTTAAACGGGCGAACCAAGCATTTTTACCCGCATCTACCTTTAAAATTCCCAATAGCTTGATCGCCCTCGATTTGGGCGTGGTTAAGGATGAACACCAAGTCTTTAAGTGGGATGGACAGACGCGTGATATCGCCGCTTGGAATCGTGACCATGACTTAATTACCGCGATGAAGTACTCAGTTGTGCCTGTTTATCAAGAATTTGCCCGCCAAATTGGTGAGGCACGTATGAGTAAAATGCTGCACGCCTTCGATTATGGCAATGAGGATATCTCGGGCAATGTAGACAGTTTTTGGCTCGATGGTGGTATTCGCATTTCGGCTACCCAGCAAATCGCTTTTTTACGCAAGCTGTATCACAACAAGCTGCACGTTTCTGAGCGTAGTCAGCGCATCGTGAAACAAGCCATGCTGACCGAAGCCAATGGCGACTATATTATTCGGGCTAAAACGGGATACTCGATTAGAATCGAACCTAAGATTGGCTGGTGGGTTGGTTGGGTTGAACTTGATGATAATGTGTGGTTTTTTGCGATGAATATGGATATGCCCACATCGGATGGTTTAGGGCTGCGCCAAGCCATCACAAAAGAAGTGCTCAAACAGGAGAAAATTATTCCCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3008537","ARO_id":"47329","ARO_name":"OXA-1119","CARD_short_name":"OXA-1119","ARO_description":"OXA-48 family class D beta-lactamase OXA-1119.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46510":{"category_aro_accession":"3007721","category_aro_cvterm_id":"46510","category_aro_name":"OXA-48-like beta-lactamase","category_aro_description":"OXA-48-type beta-lactamases are now routinely encountered in bacterial infections caused by carbapenam-resistant Enterobacterales. OXA-48-like proteins confer resistance to penicillin (which is efficiently hydrolyzed) and carbapenam antibiotics (which is more slowly broken down). The spectrum of activity of these variants varies, with some hydrolyzing expanded-spectrum oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7956":{"model_id":"7956","model_name":"OXA-1120","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10783":{"protein_sequence":{"accession":"USC31971.1","sequence":"MKTFAAYVITACLSSTALASSITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNNLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLSLRGAIQVSALPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLFLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKGTEVYFFAFNMDIDNENKLPLRKSIPTKIMASEGIIGG"},"dna_sequence":{"accession":"ON721379.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGAAAACATTTGCCGCATATGTAATTACTGCGTGTCTTTCAAGTACGGCATTAGCTAGTTCAATTACAGAAAATACGTCTTGGAACAAAGAGTTCTCTGCCGAAGCCGTCAATGGTGTTTTCGTGCTTTGTAAAAGTAGCAGTAAATCCTGCGCTACCAATAACTTAGCTCGTGCATCAAAGGAATATCTTCCAGCATCAACATTTAAGATCCCCAACGCAATTATCGGCCTAGAAACTGGTGTCATAAAGAATGAGCATCAGGTTTTCAAATGGGACGGAAAGCCAAGAGCCATGAAACAATGGGAAAGAGACTTGAGCTTAAGAGGGGCAATACAAGTTTCAGCGCTTCCCGTATTTCAACAAATCGCCAGAGAAGTTGGCGAAGTAAGAATGCAGAAATACCTTAAAAAATTTTCATATGGCAACCAGAATATCAGTGGTGGCATTGACAAATTCTGGTTGGAGGGTCAGCTAAGAATTTCCGCAGTTAATCAAGTGGAGTTTCTAGAGTCTCTATTTTTAAATAAATTGTCAGCATCAAAAGAAAATCAGCTAATAGTAAAAGAGGCTTTGGTAACGGAGGCTGCGCCTGAATATCTTGTGCATTCAAAAACTGGTTTTTCTGGTGTGGGAACTGAGTCAAATCCTGGTGTCGCATGGTGGGTTGGTTGGGTTGAGAAGGGAACAGAGGTTTACTTTTTCGCCTTTAACATGGATATAGACAACGAAAATAAGTTGCCGCTAAGAAAATCCATTCCCACCAAAATCATGGCAAGTGAGGGCATCATTGGTGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3008538","ARO_id":"47330","ARO_name":"OXA-1120","CARD_short_name":"OXA-1120","ARO_description":"OXA-10 family class D beta-lactamase OXA-1120.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46486":{"category_aro_accession":"3007697","category_aro_cvterm_id":"46486","category_aro_name":"OXA-10-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-10.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7957":{"model_id":"7957","model_name":"OXA-1121","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10784":{"protein_sequence":{"accession":"UTS94210.1","sequence":"MNIKTLLLITSAIFISACSPYIVTASPNHSASKSDEKAEKIKNLFNEVHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAISVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGSLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"ON651457.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAACACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAGTCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGTACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTTCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTTCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008539","ARO_id":"47331","ARO_name":"OXA-1121","CARD_short_name":"OXA-1121","ARO_description":"OXA-51 family carbapenem-hydrolyzing class D beta-lactamase OXA-1121.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7958":{"model_id":"7958","model_name":"OXA-1122","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10785":{"protein_sequence":{"accession":"UTS94211.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVREPVNYFV"},"dna_sequence":{"accession":"ON651458.1","fmin":"0","fmax":"804","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGGTGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAGAGCCTGTAAATTATTTTGTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008540","ARO_id":"47332","ARO_name":"OXA-1122","CARD_short_name":"OXA-1122","ARO_description":"OXA-51 family carbapenem-hydrolyzing class D beta-lactamase OXA-1122.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7959":{"model_id":"7959","model_name":"OXA-1123","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10786":{"protein_sequence":{"accession":"UTS94212.1","sequence":"MNIKTLLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEVHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWIVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"ON651459.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAACACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGTACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGATTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008541","ARO_id":"47333","ARO_name":"OXA-1123","CARD_short_name":"OXA-1123","ARO_description":"OXA-51 family carbapenem-hydrolyzing class D beta-lactamase OXA-1123.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7960":{"model_id":"7960","model_name":"OXA-1124","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10787":{"protein_sequence":{"accession":"UTS94227.1","sequence":"MRPLLFSALLLLSGHAQASEWNDSQAVDKLFGAAGVKGTFVLYDVQRQRYVGHDRERAETRFVPASTYKMANSLIGLSTGAVKSADEVLPYGGKPQRFKAWEHDMSLRDAIKASNVPVYQELARRIGLERMRANVSRLGYGNAEIGQVVDNFWLVGPLKISAMEQTRFLLRLAQGELPFPAPVQSTVRAMTLLESGPGWELHGKTGWCFDCTPELGWWVGWVKRNERLYGFALNIDMPGGEADIGKRVELGKASLKALGILP"},"dna_sequence":{"accession":"ON651474.1","fmin":"0","fmax":"789","strand":"+","sequence":"ATGCGCCCTCTCCTCTTCAGCGCCCTTCTCCTGCTCTCCGGGCATGCCCAGGCCAGCGAATGGAACGACAGCCAGGCCGTGGACAAGCTATTCGGCGCGGCCGGGGTGAAAGGCACCTTCGTCCTCTACGATGTGCAGCGGCAGCGCTATGTCGGCCATGACCGGGAGCGCGCGGAAACTCGCTTCGTTCCTGCCTCCACCTACAAGATGGCGAACAGCCTGATTGGCTTATCCACAGGGGCGGTTAAATCCGCCGACGAGGTTCTTCCCTATGGCGGCAAGCCCCAGCGCTTCAAGGCCTGGGAGCACGACATGAGCCTGCGCGACGCGATCAAGGCATCGAACGTACCGGTCTACCAGGAACTGGCGCGACGCATCGGCCTGGAGCGGATGCGCGCCAATGTCTCGCGCCTGGGTTACGGCAACGCGGAAATCGGCCAGGTTGTGGATAACTTCTGGTTGGTGGGACCGCTGAAGATCAGCGCGATGGAACAGACCCGCTTTCTGCTCCGACTGGCGCAGGGAGAATTGCCATTCCCCGCCCCGGTGCAGTCCACCGTGCGCGCCATGACCCTGCTGGAAAGCGGCCCGGGCTGGGAGCTGCACGGCAAGACCGGCTGGTGCTTCGACTGCACGCCGGAACTCGGCTGGTGGGTGGGCTGGGTGAAGCGCAACGAGCGGCTCTACGGCTTCGCCCTGAACATCGACATGCCCGGCGGCGAGGCCGACATCGGCAAGCGCGTCGAACTGGGCAAGGCCAGTCTCAAGGCTCTCGGGATACTGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008542","ARO_id":"47334","ARO_name":"OXA-1124","CARD_short_name":"OXA-1124","ARO_description":"OXA-50 family oxacillin-hydrolyzing class D beta-lactamase OXA-1124.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46513":{"category_aro_accession":"3007724","category_aro_cvterm_id":"46513","category_aro_name":"OXA-50-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-50.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7961":{"model_id":"7961","model_name":"OXA-1125","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10788":{"protein_sequence":{"accession":"UTS94228.1","sequence":"MRPLLFSALLLLSGHTQASEWNDSQAVDKLFGAAGVKGTFVLYDVQRQCYVGHDRERAETRFVPASTYKVANSLIGLSTGAVRSADEVLPYGGKPQRFKAWEHDMSLRDAIKASNVPVYQELARRIGLERMRANVSRLGYGNAEIGQVVDNFWLVGPLKISAMEQTRFLLRLAQGELPFPAPVQSTVRAMTLLESGPGWELHGKTGWCFDCTPELGWWVGWVKRNERLYGFALNIDMPGGEADIGKRVELGKASLKALGILP"},"dna_sequence":{"accession":"ON651475.1","fmin":"0","fmax":"789","strand":"+","sequence":"ATGCGCCCTCTCCTCTTCAGTGCCCTTCTCCTGCTTTCCGGGCATACCCAGGCCAGCGAATGGAACGACAGCCAGGCCGTGGACAAGCTATTCGGCGCGGCCGGGGTGAAAGGCACCTTCGTCCTCTACGATGTGCAGCGGCAGTGCTATGTCGGCCATGACCGGGAGCGCGCGGAAACCCGCTTCGTTCCCGCTTCCACCTACAAGGTGGCGAACAGCCTGATCGGCTTATCCACAGGGGCGGTTAGATCCGCCGACGAGGTTCTTCCCTATGGCGGCAAGCCCCAGCGCTTCAAGGCCTGGGAGCACGACATGAGCCTGCGCGACGCGATCAAGGCATCGAACGTACCGGTCTACCAGGAACTGGCGCGGCGCATCGGCCTGGAGCGGATGCGCGCCAATGTCTCGCGCCTGGGTTACGGCAACGCGGAAATCGGCCAGGTTGTGGATAACTTCTGGTTGGTGGGACCGCTGAAGATCAGCGCGATGGAACAGACCCGCTTTCTGCTCCGACTGGCGCAGGGAGAATTGCCATTCCCCGCCCCGGTGCAGTCCACCGTGCGCGCCATGACCCTGCTGGAAAGCGGCCCGGGCTGGGAGCTGCACGGCAAGACCGGCTGGTGCTTCGACTGCACGCCGGAACTCGGCTGGTGGGTGGGCTGGGTGAAGCGCAACGAGCGGCTCTACGGCTTCGCCCTGAACATCGACATGCCCGGCGGCGAGGCCGACATCGGCAAGCGCGTCGAACTGGGCAAGGCCAGTCTCAAGGCTCTCGGGATACTGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008543","ARO_id":"47335","ARO_name":"OXA-1125","CARD_short_name":"OXA-1125","ARO_description":"OXA-50 family oxacillin-hydrolyzing class D beta-lactamase OXA-1125.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46513":{"category_aro_accession":"3007724","category_aro_cvterm_id":"46513","category_aro_name":"OXA-50-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-50.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7962":{"model_id":"7962","model_name":"OXA-1126","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10789":{"protein_sequence":{"accession":"UTS94229.1","sequence":"MRPLLFSALLLLSGHTQASEWNDSQAVDKLFGAAGVKGTFVLYDVQRQRYVGHDRERAETRFVPASTYKVANSLIGLSTGAVRSADEGLPYGGKPQRFKAWEHDMSLREAIKASNVPVYQELARRIGLERMRANVSRLGYGNAEIGQVVDNFWLVGPLKISAMEQTHFLLRLAQGELPFPAPVQSTVRAMTLLESGPGWELHGKTGWCFDCTPELGWWVGWVKRNERLYGFALNIDMPGGEADIGKRVELGKASLKALGILP"},"dna_sequence":{"accession":"ON651476.1","fmin":"0","fmax":"789","strand":"+","sequence":"ATGCGCCCTCTCCTCTTCAGTGCCCTTCTCCTGCTTTCCGGGCATACCCAGGCCAGCGAATGGAACGACAGCCAGGCCGTGGACAAGCTATTCGGCGCGGCCGGGGTGAAAGGCACCTTCGTCCTCTACGATGTGCAGCGGCAGCGCTATGTCGGCCATGACCGGGAGCGCGCGGAAACCCGCTTCGTTCCCGCTTCCACCTACAAGGTGGCGAACAGCCTGATCGGCTTATCCACAGGGGCGGTTAGATCCGCCGACGAGGGTCTTCCCTATGGCGGCAAGCCCCAGCGCTTCAAGGCCTGGGAGCACGACATGAGCCTGCGCGAGGCGATCAAGGCATCGAACGTACCGGTCTACCAGGAACTGGCGCGGCGCATCGGCCTGGAGCGGATGCGCGCCAATGTCTCGCGCCTGGGTTACGGCAACGCGGAAATCGGCCAGGTTGTGGATAACTTCTGGTTGGTGGGACCGCTGAAGATCAGCGCGATGGAACAGACCCACTTTCTGCTCCGACTGGCGCAGGGAGAATTGCCATTCCCCGCCCCGGTGCAGTCCACCGTGCGCGCCATGACCCTGCTGGAAAGCGGCCCGGGCTGGGAGCTGCACGGCAAGACCGGCTGGTGCTTCGACTGCACGCCGGAACTCGGCTGGTGGGTGGGCTGGGTGAAGCGCAACGAGCGGCTCTACGGCTTCGCCCTGAACATCGACATGCCCGGCGGCGAGGCCGACATCGGCAAGCGCGTCGAACTGGGCAAGGCCAGTCTCAAGGCTCTCGGGATACTGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008544","ARO_id":"47336","ARO_name":"OXA-1126","CARD_short_name":"OXA-1126","ARO_description":"OXA-50 family oxacillin-hydrolyzing class D beta-lactamase OXA-1126.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46513":{"category_aro_accession":"3007724","category_aro_cvterm_id":"46513","category_aro_name":"OXA-50-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-50.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7963":{"model_id":"7963","model_name":"OXA-1127","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10790":{"protein_sequence":{"accession":"UTS94231.1","sequence":"MRPLLFSALLLLSGHAQASEWNDSQAVDKLFGAAGVKGTFVLYDVQRQLYVGHDRERAETRFVPASTYKVANSLIGLSTGAVRSADEVLPYGGKPQRFKAWEHDMSLRDAIKASNVPVYQELARRIGLERMRANVSRLGYGNAEIGQVVDNFWLVGPLKISAMEQTRFLLRLAQGELPFPAPVQSTVRAMTLLESGPGWELHGKTGWCFDCTPELGWWVGWVKRNERLYGFALNIDMPGGEADIGKRVELGKASLKALGILP"},"dna_sequence":{"accession":"ON651478.1","fmin":"0","fmax":"789","strand":"+","sequence":"ATGCGCCCTCTCCTCTTCAGCGCCCTTCTCCTGCTCTCCGGGCATGCCCAGGCCAGCGAATGGAACGACAGCCAGGCCGTGGACAAGCTATTCGGAGCGGCCGGTGTGAAAGGCACCTTCGTCCTCTACGATGTGCAGCGGCAGCTCTATGTCGGCCATGACCGGGAGCGCGCGGAAACCCGCTTCGTTCCCGCTTCCACCTACAAGGTGGCGAACAGCCTGATCGGCTTATCCACAGGGGCGGTTAGATCCGCCGACGAGGTTCTTCCCTATGGCGGCAAGCCCCAGCGCTTCAAGGCCTGGGAGCACGACATGAGCCTGCGCGACGCGATCAAGGCATCGAACGTACCGGTCTACCAGGAACTGGCGCGGCGCATCGGCCTGGAGCGGATGCGCGCCAATGTCTCGCGCCTGGGTTACGGCAACGCGGAAATCGGCCAGGTTGTGGATAACTTCTGGTTGGTGGGACCGCTGAAGATCAGCGCGATGGAACAGACCCGCTTTCTGCTCCGACTGGCGCAGGGAGAATTGCCATTCCCCGCCCCGGTGCAGTCCACCGTGCGCGCCATGACCCTGCTGGAAAGCGGCCCGGGCTGGGAGCTGCACGGCAAGACCGGCTGGTGCTTCGACTGCACGCCGGAACTCGGCTGGTGGGTGGGCTGGGTGAAGCGCAACGAGCGGCTCTACGGCTTCGCCCTGAACATCGACATGCCCGGCGGCGAGGCCGACATCGGCAAGCGCGTCGAACTGGGCAAGGCCAGTCTCAAGGCTCTCGGGATACTGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008545","ARO_id":"47337","ARO_name":"OXA-1127","CARD_short_name":"OXA-1127","ARO_description":"OXA-50 family oxacillin-hydrolyzing class D beta-lactamase OXA-1127.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46513":{"category_aro_accession":"3007724","category_aro_cvterm_id":"46513","category_aro_name":"OXA-50-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-50.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7964":{"model_id":"7964","model_name":"OXA-1128","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10791":{"protein_sequence":{"accession":"UTS94232.1","sequence":"MRPLLFSALLLLSGHTQASEWNDSQAVDKLFGAAGVKGTFVLYDVQRQRYAGHDRERAETRFVPASTYKVANSLIGLSTGAVRSADEVLPYGGKPQRFKAWEHDMSLRDAIKASNVPVYQELARRIGLERMRANVSRLGYGNAEIGQVVDNFWLVGPLKISAMEQTRFLLRLAQGELPFPAPVQSTVRAMTLLESGPGWELHGKTGWCFDCTPELGWWVGWVKRNERLYGFALNIDMPGGEADIGKRVELGKASLKALGILP"},"dna_sequence":{"accession":"ON651479.1","fmin":"0","fmax":"789","strand":"+","sequence":"ATGCGCCCTCTCCTCTTCAGTGCCCTTCTCCTGCTTTCCGGGCATACCCAGGCCAGCGAATGGAACGACAGCCAGGCCGTGGACAAGCTATTCGGCGCGGCCGGGGTGAAAGGCACCTTCGTCCTCTACGATGTGCAGCGGCAGCGCTATGCCGGCCATGACCGGGAGCGCGCGGAAACCCGCTTCGTTCCCGCTTCCACCTACAAGGTGGCGAACAGCCTGATCGGCTTATCCACAGGGGCGGTTAGATCCGCCGACGAGGTTCTTCCCTATGGCGGCAAGCCCCAGCGCTTCAAGGCCTGGGAGCACGACATGAGCCTGCGCGACGCGATCAAGGCATCGAACGTACCGGTCTACCAGGAACTGGCGCGGCGCATCGGCCTGGAGCGGATGCGCGCCAATGTCTCGCGCCTGGGTTACGGCAACGCGGAAATCGGCCAGGTTGTGGATAACTTCTGGTTGGTGGGACCGCTGAAGATCAGCGCGATGGAACAGACCCGCTTTCTGCTCCGACTGGCGCAGGGAGAATTGCCATTCCCCGCCCCGGTGCAGTCCACCGTGCGCGCCATGACCCTGCTGGAAAGCGGCCCGGGCTGGGAGCTGCACGGCAAGACCGGCTGGTGCTTCGACTGCACGCCGGAACTCGGCTGGTGGGTGGGCTGGGTGAAGCGCAACGAGCGGCTCTACGGCTTCGCCCTGAACATCGACATGCCCGGCGGCGAGGCCGACATCGGCAAGCGCGTCGAACTGGGCAAGGCCAGTCTCAAGGCTCTCGGGATACTGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008546","ARO_id":"47338","ARO_name":"OXA-1128","CARD_short_name":"OXA-1128","ARO_description":"OXA-50 family oxacillin-hydrolyzing class D beta-lactamase OXA-1128.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46513":{"category_aro_accession":"3007724","category_aro_cvterm_id":"46513","category_aro_name":"OXA-50-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-50.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7965":{"model_id":"7965","model_name":"OXA-1129","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10792":{"protein_sequence":{"accession":"UTS94233.1","sequence":"MRPLLFSALLLLSGHTQASEWNDSQAVDKLFGAAGVKGTFVLYDVQRQRYVGHDRERAETRFVPASTYKVANSLIGLSTGAVRSADEVLPYGGKPQRFKAWEHDMSLRDAIEASNVPVYQELARRIGLERMRANVSRLSYGNAEIGQVVDNFWLVGPLKISAMEQTRFLLRLAQGELPFPAPVQSTVRAMTLLESGPGWELHGKTGWCFDCTPELGWWVGWVKRYERLYGFALNIDMPGGEADTGKRVELGKASLKALGILP"},"dna_sequence":{"accession":"ON651480.1","fmin":"0","fmax":"789","strand":"+","sequence":"ATGCGCCCTCTCCTCTTCAGCGCCCTTCTCCTGCTCTCCGGGCATACCCAGGCCAGCGAATGGAACGACAGCCAGGCCGTGGACAAGCTATTCGGCGCGGCCGGGGTGAAAGGCACCTTCGTCCTCTACGATGTGCAGCGGCAGCGCTATGTCGGCCATGACCGGGAGCGCGCGGAAACCCGCTTCGTTCCCGCTTCCACCTACAAGGTGGCGAACAGCCTGATCGGCTTATCCACAGGGGCGGTTAGATCCGCCGATGAGGTTCTTCCCTATGGCGGCAAGCCCCAGCGCTTCAAGGCCTGGGAGCACGACATGAGCCTGCGCGACGCGATCGAGGCATCGAACGTACCGGTCTACCAAGAACTGGCGCGGCGCATCGGCCTGGAGCGGATGCGCGCCAATGTCTCCCGCCTGAGTTACGGCAACGCGGAAATCGGCCAGGTTGTGGATAACTTCTGGTTGGTGGGACCGCTGAAGATCAGCGCGATGGAACAGACCCGCTTTCTGCTCCGACTGGCGCAGGGAGAATTGCCATTCCCCGCCCCGGTGCAGTCCACCGTGCGCGCCATGACCCTGCTGGAAAGCGGCCCGGGCTGGGAGCTGCACGGCAAGACCGGCTGGTGCTTCGACTGCACGCCGGAACTCGGCTGGTGGGTGGGCTGGGTGAAGCGCTACGAGCGGCTCTACGGCTTCGCCCTGAACATCGACATGCCCGGCGGCGAGGCCGACACCGGAAAGCGTGTCGAACTGGGCAAGGCCAGTCTCAAGGCTCTCGGGATACTGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008547","ARO_id":"47339","ARO_name":"OXA-1129","CARD_short_name":"OXA-1129","ARO_description":"OXA-50 family oxacillin-hydrolyzing class D beta-lactamase OXA-1129.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46513":{"category_aro_accession":"3007724","category_aro_cvterm_id":"46513","category_aro_name":"OXA-50-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-50.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7966":{"model_id":"7966","model_name":"OXA-1130","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10793":{"protein_sequence":{"accession":"UTS94234.1","sequence":"MRPLLLSALLLLSGHTQASEWNDSQAVDKLFGAAGVKGTFVLYDVQRQRYVGHDRERAETRFVPASTYKVANSLIGLSTGAVRSADEVLPYGGKPQRFKAWEHDMSLREAIKASNVPVYQELARRIGLERMRANVSRLGYGNAEIGQVVDNFWLVGPLKISAMEQTRFLLRLAQGELPFPAPVQSTVRAMTLLESGPGWELHGKTGWCFDCTPELGWWVGWVKRNERLYGFALNIDMPGGEADIGKRVELGKASLKALGILP"},"dna_sequence":{"accession":"ON651481.1","fmin":"0","fmax":"789","strand":"+","sequence":"ATGCGCCCTCTCCTCTTGAGTGCCCTTCTCCTGCTTTCCGGGCATACCCAGGCCAGCGAATGGAACGACAGCCAGGCCGTGGACAAGCTATTCGGCGCGGCCGGGGTGAAAGGCACCTTCGTCCTCTACGATGTGCAGCGGCAGCGCTATGTCGGCCATGACCGGGAGCGCGCGGAAACCCGCTTCGTTCCCGCTTCCACCTACAAGGTGGCGAACAGCCTGATCGGCTTATCCACAGGGGCGGTTAGATCCGCCGACGAGGTTCTTCCCTATGGCGGCAAGCCCCAGCGCTTCAAGGCCTGGGAGCACGACATGAGCCTGCGCGAGGCGATCAAGGCATCGAACGTACCGGTCTACCAGGAACTGGCGCGGCGCATCGGCCTGGAGCGGATGCGCGCCAATGTCTCGCGCCTGGGTTACGGCAACGCGGAAATCGGCCAGGTTGTGGATAACTTCTGGTTGGTGGGACCGCTGAAGATCAGCGCGATGGAACAGACCCGCTTTCTGCTCCGACTGGCGCAGGGAGAATTGCCATTCCCCGCCCCGGTGCAGTCCACCGTGCGCGCCATGACCCTGCTGGAAAGCGGCCCGGGCTGGGAGCTGCACGGCAAGACCGGCTGGTGCTTCGACTGCACGCCGGAACTCGGCTGGTGGGTGGGCTGGGTGAAGCGCAACGAGCGGCTCTACGGCTTCGCCCTGAACATCGACATGCCCGGCGGCGAGGCCGACATCGGCAAGCGCGTCGAACTGGGCAAGGCCAGTCTCAAGGCTCTCGGGATACTGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008548","ARO_id":"47340","ARO_name":"OXA-1130","CARD_short_name":"OXA-1130","ARO_description":"OXA-50 family oxacillin-hydrolyzing class D beta-lactamase OXA-1130.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46513":{"category_aro_accession":"3007724","category_aro_cvterm_id":"46513","category_aro_name":"OXA-50-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-50.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7967":{"model_id":"7967","model_name":"OXA-1131","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10794":{"protein_sequence":{"accession":"UTS94235.1","sequence":"MRPLLFSALLLLSGHAQASEWNDSQAVDKLFGAAGVKGTFVLYDVQRQRYVGHDRERAETRFVPASTYKVANSLIGLSTGAVRSADEVLPYGGKPQRFKAWEHDMSLREAIKASNVPVYQELARRIGLERMRANVSRLGYGNAEIGQVVDNFWLVGPLKISAMEQTHFLLRLAQGELPFPAPVQSTVRAMTLLESGPGWELHGKTGWCFDCTPELGWWVGWVKRNERLYGFALNIDMPGGEADIGKRVELGKASLKALGILP"},"dna_sequence":{"accession":"ON651482.1","fmin":"0","fmax":"789","strand":"+","sequence":"ATGCGCCCTCTCCTCTTCAGCGCCCTTCTCCTGCTCTCCGGGCATGCCCAGGCCAGCGAATGGAACGACAGCCAGGCCGTGGACAAGCTATTCGGCGCGGCCGGGGTGAAAGGCACCTTCGTCCTCTACGATGTGCAGCGGCAGCGCTATGTCGGCCATGACCGGGAGCGCGCGGAAACCCGCTTCGTTCCCGCTTCCACCTACAAGGTGGCGAACAGCCTGATCGGCTTATCCACAGGGGCGGTTAGATCCGCCGACGAGGTTCTTCCCTATGGCGGCAAGCCCCAGCGCTTCAAGGCCTGGGAGCACGACATGAGCCTGCGCGAGGCGATCAAGGCATCGAACGTACCGGTCTACCAGGAACTGGCGCGGCGCATCGGCCTGGAGCGGATGCGCGCCAATGTCTCGCGCCTGGGTTACGGCAACGCGGAAATCGGCCAGGTTGTGGATAACTTCTGGTTGGTGGGACCGCTGAAGATCAGCGCGATGGAACAGACCCACTTTCTGCTCCGACTGGCGCAGGGAGAATTGCCATTCCCCGCCCCGGTGCAGTCCACCGTGCGCGCCATGACCCTGCTGGAAAGCGGCCCGGGCTGGGAGCTGCACGGCAAGACCGGCTGGTGCTTCGACTGCACGCCGGAACTCGGCTGGTGGGTGGGCTGGGTGAAGCGCAACGAGCGGCTCTACGGCTTCGCCCTGAACATCGACATGCCCGGCGGCGAGGCCGACATCGGCAAGCGCGTCGAACTGGGCAAGGCCAGTCTCAAGGCTCTCGGGATACTGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008549","ARO_id":"47341","ARO_name":"OXA-1131","CARD_short_name":"OXA-1131","ARO_description":"OXA-50 family oxacillin-hydrolyzing class D beta-lactamase OXA-1131.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46513":{"category_aro_accession":"3007724","category_aro_cvterm_id":"46513","category_aro_name":"OXA-50-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-50.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7968":{"model_id":"7968","model_name":"OXA-1132","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10795":{"protein_sequence":{"accession":"UTS94236.1","sequence":"MRPLLFSALLLLSGHTQASEWNDSQAVDKLFGAAGVKGTFVLYDVQRQRYVGHDRERAETRFVPASTYKVANSLIGLSTGAVRSADEVLPYGGKPQRFKAWEHDMSLRDAIEASNVPVYQELARRIGLERMRANVSRLGYGNTEIGQVVDNFWLVGPLKISAMEQTRFLLRLAQGELPFPAPVQSTVRAMTLLESGPGWELHGKTGWCFDCTPELGWWVGWVKRNERLYGFALNIDMPGGEADTGKRVELGKASLKALGILP"},"dna_sequence":{"accession":"ON651483.1","fmin":"0","fmax":"789","strand":"+","sequence":"ATGCGCCCTCTCCTCTTCAGCGCCCTTCTCCTGCTCTCCGGGCATACCCAGGCCAGCGAATGGAACGACAGCCAGGCCGTGGACAAGCTATTCGGCGCGGCCGGGGTGAAAGGCACCTTCGTCCTCTACGATGTGCAGCGGCAGCGCTATGTCGGCCATGACCGGGAGCGCGCGGAAACCCGCTTCGTTCCCGCTTCCACCTACAAGGTGGCGAACAGCCTGATCGGCTTATCCACAGGGGCGGTTAGATCCGCCGATGAGGTTCTTCCCTATGGCGGCAAGCCCCAGCGCTTCAAGGCCTGGGAGCACGACATGAGCCTGCGCGACGCGATCGAGGCATCGAACGTACCGGTCTACCAGGAACTGGCGCGGCGCATCGGCCTGGAGCGGATGCGCGCCAATGTCTCCCGCCTGGGTTACGGCAACACGGAAATCGGCCAGGTTGTGGATAACTTCTGGTTGGTGGGACCGCTGAAGATCAGCGCGATGGAACAGACCCGCTTTCTGCTCCGACTGGCGCAGGGAGAATTGCCATTCCCCGCCCCGGTGCAGTCCACCGTGCGCGCCATGACCCTGCTGGAAAGCGGCCCGGGCTGGGAGCTGCACGGCAAGACCGGCTGGTGCTTCGACTGCACGCCGGAACTCGGCTGGTGGGTGGGCTGGGTGAAGCGCAACGAGCGGCTCTACGGCTTCGCCCTGAACATCGACATGCCCGGCGGCGAGGCCGACACCGGAAAGCGTGTCGAACTGGGCAAGGCCAGTCTCAAGGCTCTCGGGATACTGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008550","ARO_id":"47342","ARO_name":"OXA-1132","CARD_short_name":"OXA-1132","ARO_description":"OXA-50 family oxacillin-hydrolyzing class D beta-lactamase OXA-1132.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46513":{"category_aro_accession":"3007724","category_aro_cvterm_id":"46513","category_aro_name":"OXA-50-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-50.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7969":{"model_id":"7969","model_name":"OXA-1133","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10796":{"protein_sequence":{"accession":"UTS94237.1","sequence":"MRPLLFSALLLLSGHTQASEWNDSQAVDKLFGAAGVKGTFVLYDVQRQRYVGHDRERAETRFVPASTYKVANSLIGLSTGAVRSADEVLPYGGKPQRFKAWEHDMSLRDAIEASNVPVYQELARRIGLERMRANVSRLSYGNAEIGQVVDNFWLVGPLKISAMEQTRFLLRLAQGELPFPAPVQSTVRAMTLLESGPGWELHGKTGWCFDCTPELGWWVGWVKRNERLYGFALNIDMPGGEADTGKRVELGKASLKALGILP"},"dna_sequence":{"accession":"ON651484.1","fmin":"0","fmax":"789","strand":"+","sequence":"ATGCGCCCTCTCCTCTTCAGCGCCCTTCTCCTGCTCTCCGGGCATACCCAGGCCAGCGAATGGAACGACAGCCAGGCCGTGGACAAGCTATTCGGCGCGGCCGGGGTGAAAGGCACCTTCGTCCTCTACGATGTGCAGCGGCAGCGCTATGTCGGCCATGACCGGGAGCGCGCGGAAACCCGCTTCGTTCCCGCTTCCACCTACAAGGTGGCGAACAGCCTGATCGGCTTATCCACAGGGGCGGTTAGATCCGCCGATGAGGTTCTTCCCTATGGCGGCAAGCCCCAGCGCTTCAAGGCCTGGGAGCACGACATGAGCCTGCGCGACGCGATCGAGGCATCGAACGTACCGGTCTACCAAGAACTGGCGCGGCGCATCGGCCTGGAGCGGATGCGCGCCAATGTCTCCCGCCTGAGTTACGGCAACGCGGAAATCGGCCAGGTTGTGGATAACTTCTGGTTGGTGGGACCGCTGAAGATCAGCGCGATGGAACAGACCCGCTTTCTGCTCCGACTGGCGCAGGGAGAATTGCCATTCCCCGCCCCGGTGCAGTCCACCGTGCGCGCCATGACCCTGCTGGAAAGCGGCCCGGGCTGGGAGCTGCACGGCAAGACCGGCTGGTGCTTCGACTGCACGCCGGAACTCGGCTGGTGGGTGGGCTGGGTGAAGCGCAACGAGCGGCTCTACGGCTTCGCCCTGAACATCGACATGCCCGGCGGCGAGGCCGACACCGGAAAGCGTGTCGAACTGGGCAAGGCCAGTCTCAAGGCTCTCGGGATACTGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008551","ARO_id":"47343","ARO_name":"OXA-1133","CARD_short_name":"OXA-1133","ARO_description":"OXA-50 family oxacillin-hydrolyzing class D beta-lactamase OXA-1133.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46513":{"category_aro_accession":"3007724","category_aro_cvterm_id":"46513","category_aro_name":"OXA-50-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-50.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7970":{"model_id":"7970","model_name":"OXA-1134","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10797":{"protein_sequence":{"accession":"UTS94238.1","sequence":"MRPLLFSALLLLSEHTQASEWNDSQAVDKLFGAAGVKGTFVLYDVQRQRYVGHDRERAETRFVPASTYKVANSLIGLSTGAVRSADEVLPYGGKPQRFKAWEHDMSLRDAIEASNVPVYQELARRIGLERMRANVSRLGYGNTEIGQVVDNFWLVGPLKISAMEQTRFLLRLAQGELPFPAPVQSTVRAMTLLESGPGWELHGKTGWCFDCTPELGWWVGWVKRNERLYGFALNIDMPGGEADTGKRVELGKASLKALGILP"},"dna_sequence":{"accession":"ON651485.1","fmin":"0","fmax":"789","strand":"+","sequence":"ATGCGCCCTCTCCTCTTCAGCGCCCTTCTCCTGCTCTCCGAGCATACCCAGGCCAGCGAATGGAACGACAGCCAGGCCGTGGACAAGCTATTCGGCGCGGCCGGGGTGAAAGGCACCTTCGTCCTCTACGATGTGCAGCGGCAGCGCTATGTCGGCCATGACCGGGAGCGCGCGGAAACCCGCTTCGTTCCCGCTTCCACCTACAAGGTGGCGAACAGCCTGATCGGCTTATCCACAGGGGCGGTTAGATCCGCCGATGAGGTTCTTCCCTATGGCGGCAAGCCCCAGCGCTTCAAGGCCTGGGAGCACGACATGAGCCTGCGCGACGCGATCGAGGCATCGAACGTACCGGTCTACCAGGAACTGGCGCGGCGCATCGGCCTGGAGCGGATGCGCGCCAATGTCTCCCGCCTGGGTTACGGCAACACGGAAATCGGCCAGGTTGTGGATAACTTCTGGTTGGTGGGACCGCTGAAGATCAGCGCGATGGAACAGACCCGCTTTCTGCTCCGACTGGCGCAGGGAGAATTGCCATTCCCCGCCCCGGTGCAGTCCACCGTGCGCGCCATGACCCTGCTGGAAAGCGGCCCGGGCTGGGAGCTGCACGGCAAGACCGGCTGGTGCTTCGACTGCACGCCGGAACTCGGCTGGTGGGTGGGCTGGGTGAAGCGCAACGAGCGGCTCTACGGCTTCGCCCTGAACATCGACATGCCCGGCGGCGAGGCCGACACCGGAAAGCGTGTCGAACTGGGCAAGGCCAGTCTCAAGGCTCTCGGGATACTGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008552","ARO_id":"47344","ARO_name":"OXA-1134","CARD_short_name":"OXA-1134","ARO_description":"OXA-50 family oxacillin-hydrolyzing class D beta-lactamase OXA-1134.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46513":{"category_aro_accession":"3007724","category_aro_cvterm_id":"46513","category_aro_name":"OXA-50-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-50.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7971":{"model_id":"7971","model_name":"OXA-1135","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10798":{"protein_sequence":{"accession":"UTS94239.1","sequence":"MRPLLFSALLLLSGHTQASEWNDSQAVDKLFGAAGVKGTFVLYDVQRQRYVGHDRERAETRFVPASTYKVANSLIGLSTGAVRSADEVLPYGGKPQRFKAWEHDMSLRDAIEASNVPVYQELARRIGLERMRANVSRLGYGNAEIGQVVDNFWLVGPLKISAMEQTRFLLRLAQGELPFPAPVQSTVRAMTLLESGPGWELHGKTGWCFDCTPELGWWVGWVKRNERLYGFALNIDMPGGEADTGKRVELGKASLKALGILP"},"dna_sequence":{"accession":"ON651486.1","fmin":"0","fmax":"789","strand":"+","sequence":"ATGCGCCCTCTCCTCTTCAGCGCCCTTCTCCTGCTCTCCGGGCATACCCAGGCCAGCGAATGGAACGACAGCCAGGCCGTGGACAAGCTATTCGGCGCGGCCGGGGTGAAAGGCACCTTCGTCCTCTACGATGTGCAGCGGCAGCGCTATGTCGGCCATGACCGGGAGCGCGCGGAAACCCGCTTCGTTCCCGCTTCCACCTACAAGGTGGCGAACAGCCTGATCGGCTTATCCACAGGGGCGGTTAGATCCGCCGATGAGGTTCTTCCCTATGGCGGCAAGCCCCAGCGCTTCAAGGCCTGGGAGCACGACATGAGCCTGCGCGACGCGATCGAGGCATCGAACGTACCGGTCTACCAGGAACTGGCGCGGCGCATCGGCCTGGAGCGGATGCGCGCCAATGTCTCCCGCCTGGGTTACGGCAACGCGGAAATCGGCCAGGTTGTGGATAACTTCTGGTTGGTGGGACCGCTGAAGATCAGCGCGATGGAACAGACCCGCTTTCTGCTCCGACTGGCGCAGGGAGAATTGCCATTCCCCGCCCCGGTGCAGTCCACCGTGCGCGCCATGACCCTGCTGGAAAGCGGCCCGGGCTGGGAGCTGCACGGCAAGACCGGCTGGTGCTTCGACTGCACGCCGGAACTCGGCTGGTGGGTGGGCTGGGTGAAGCGCAACGAGCGGCTCTACGGCTTCGCCCTGAACATCGACATGCCCGGCGGCGAGGCCGACACCGGAAAGCGTGTCGAACTGGGCAAGGCCAGTCTCAAGGCTCTCGGGATACTGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008553","ARO_id":"47345","ARO_name":"OXA-1135","CARD_short_name":"OXA-1135","ARO_description":"OXA-50 family oxacillin-hydrolyzing class D beta-lactamase OXA-1135.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46513":{"category_aro_accession":"3007724","category_aro_cvterm_id":"46513","category_aro_name":"OXA-50-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-50.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7972":{"model_id":"7972","model_name":"OXA-1136","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10799":{"protein_sequence":{"accession":"UTS94244.1","sequence":"MAIRIFAILFSTFVFGTFAHAQEGMRERSDWRKFFSEFQAKGTIVVADERQTDRVILVFDQVRSEKRYSPASTFKIPHTLFALDAGAARDEFQVFRWDGIKRSFAAHNQDQDLRSAMRNSTVWIYELFAKEIGEDKARRYLKQIDYGNAGPSTSNGDYWIDGNLAIAAQEQIAFLRKLYHNELPFRVEHQRLVKDLMIVEAGRNWILRAKTGWEGRMGWWVGWVEWPTGPVFFALNIDTPNRMDDLFKREAIVRAILRSIEALPPNPAVNSDAAR"},"dna_sequence":{"accession":"ON651491.1","fmin":"0","fmax":"828","strand":"+","sequence":"ATGGCAATCCGAATCTTCGCAATACTTTTCTCCACTTTTGTTTTTGGCACGTTCGCGCATGCACAAGAAGGCATGCGCGAACGTTCTGACTGGCGGAAGTTTTTCAGCGAATTTCAAGCCAAAGGCACGATAGTTGTGGCAGACGAACGCCAAACAGATCGTGTCATATTGGTTTTTGATCAGGTGCGGTCAGAGAAACGCTACTCGCCGGCCTCGACATTCAAGATTCCACATACACTTTTTGCACTTGACGCAGGCGCTGCACGTGATGAGTTTCAAGTTTTCCGATGGGACGGCATCAAAAGAAGCTTTGCAGCTCACAACCAAGACCAAGACTTGCGATCAGCAATGCGGAATTCTACTGTCTGGATTTATGAGCTATTTGCAAAAGAGATCGGTGAAGACAAGGCTCGACGCTATTTGAAGCAAATCGACTATGGCAACGCCGGTCCTTCGACAAGTAATGGCGATTACTGGATAGATGGCAATCTTGCTATCGCGGCACAAGAACAGATTGCATTTCTCAGGAAGCTCTATCATAACGAGTTGCCCTTTCGGGTAGAACATCAGCGCTTGGTCAAGGACCTCATGATTGTGGAAGCCGGTCGCAACTGGATACTGCGCGCAAAGACGGGCTGGGAAGGCCGCATGGGTTGGTGGGTAGGATGGGTTGAGTGGCCGACTGGCCCCGTATTCTTCGCACTGAATATTGATACGCCAAACAGGATGGATGACCTTTTCAAAAGGGAGGCAATAGTGCGGGCAATCCTTCGCTCTATCGAAGCGTTGCCGCCCAACCCGGCAGTCAACTCGGACGCAGCGCGATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008554","ARO_id":"47346","ARO_name":"OXA-1136","CARD_short_name":"OXA-1136","ARO_description":"OXA-2 family class D beta-lactamase OXA-1136.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46493":{"category_aro_accession":"3007704","category_aro_cvterm_id":"46493","category_aro_name":"OXA-2-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-2.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7973":{"model_id":"7973","model_name":"OXA-1137","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10800":{"protein_sequence":{"accession":"UTS94246.1","sequence":"MTKKAFFFAISTIFLSACSFNTVQHHQIHAISTHKNSEEIKSLFDQAQTTGVLVIKRGNTEEIYGNDLKRASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMSKEVKRIGFGNADIGSKVDNFWLVGPLKITPQQEAQFAYELAHKTLPFSKNVQEQVQSMVFVEEKNGRKIYAKSGWGWDVEPQVGWLTGWVVQPQGEIVAFSLNLEMKKGTPSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"ON651493.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGACTAAAAAAGCTTTTTTCTTTGCCATTAGTACCATATTTTTGTCAGCATGTTCTTTCAATACAGTACAACATCACCAAATACACGCTATTTCTACTCATAAAAATTCAGAAGAAATAAAATCACTGTTTGATCAAGCACAGACCACAGGTGTTTTGGTTATTAAGCGCGGAAATACAGAGGAAATTTATGGCAATGATCTAAAAAGGGCATCAACTGAATATGTCCCTGCATCTACCTTTAAAATGCTAAATGCTCTAATTGGTCTTGAACATCATAAAGCAACAACCACTGAAGTGTTCAAATGGGATGGACAAAAGCGTTTATTTCCTGATTGGGAAAAGGATATGACTCTAGGTGATGCCATGAAAGCTTCTGCTATTCCTGTGTATCAAGAACTAGCTCGACGAATTGGCCTTGATCTTATGTCCAAAGAGGTCAAGCGTATTGGTTTCGGTAATGCTGATATTGGTTCAAAAGTAGATAATTTTTGGCTTGTCGGTCCACTCAAAATTACGCCTCAACAGGAAGCACAGTTTGCTTATGAATTAGCACATAAAACTCTTCCCTTTAGCAAAAATGTACAAGAACAAGTTCAATCTATGGTGTTTGTAGAAGAAAAAAACGGACGTAAAATTTACGCTAAAAGCGGTTGGGGATGGGATGTGGAGCCTCAAGTGGGCTGGTTAACAGGCTGGGTCGTTCAACCACAAGGAGAAATTGTAGCGTTCTCTCTCAATTTAGAAATGAAAAAAGGAACACCCAGTTCTATTCGAAAAGAAATTGCTTATAAAGGATTAGAACAGCTAGGTATTTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42801","NCBI_taxonomy_name":"Acinetobacter lactucae","NCBI_taxonomy_id":"1785128"}}}},"ARO_accession":"3008555","ARO_id":"47347","ARO_name":"OXA-1137","CARD_short_name":"OXA-1137","ARO_description":"OXA-213 family carbapenem-hydrolyzing class D beta-lactamase OXA-1137.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46495":{"category_aro_accession":"3007706","category_aro_cvterm_id":"46495","category_aro_name":"OXA-213-like beta-lactamase","category_aro_description":"OXA-213-like enzymes have been identified to be intrinsic to A. calcoaceticus and have been subsequently detected in A. pittii. Phylogenetic analysis of OXA-213-like proteins identified two distinct subgroups within the OXA family. The first group was linked to A. pittii and the second group to A. calcoaceticus. The carbapenemase activity of these OXAs may be related to the species-dependent effect.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7974":{"model_id":"7974","model_name":"OXA-1138","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10801":{"protein_sequence":{"accession":"UTS94247.1","sequence":"MTKKALFFAIGTMFLSACSFNTVEQHQIQSISTNKNSEKIKSLFDQAQTTGVLVIKRGQTEEVYGNDLKRASTEYVPASTFKMLNALIGLEHHKATPTEVFKWDGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMSKEVKRIGFGNADIGSKVDDFWLVGPLKITPQQEAQFAYELAHKTLPFSKNMQEQVQSMLFIEEKNGRKIYAKSGWGWDVEPQVGWLTGWVVQPQGEIIAFSLNLEMKKGIPTSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"ON651494.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGACTAAAAAAGCTCTTTTCTTTGCCATTGGTACGATGTTTTTGTCTGCATGTTCTTTTAATACGGTAGAACAACATCAAATACAGTCAATTTCTACCAATAAAAACTCAGAGAAAATTAAATCGTTGTTTGATCAAGCACAAACTACAGGTGTTTTAGTTATAAAACGTGGGCAAACAGAGGAAGTCTATGGCAATGATCTTAAAAGAGCATCAACCGAATATGTTCCCGCCTCTACCTTTAAAATGTTAAATGCTTTGATTGGACTTGAGCATCATAAAGCAACACCAACTGAAGTGTTTAAATGGGATGGGCAAAAGCGTTTATTTCCCGATTGGGAAAAAGATATGACATTAGGCGATGCGATGAAAGCTTCTGCTATTCCAGTTTATCAGGAACTAGCTCGACGAATTGGCCTTGATCTTATGTCTAAAGAGGTAAAACGCATTGGTTTCGGTAATGCTGATATTGGTTCAAAAGTAGATGATTTTTGGCTTGTTGGTCCACTTAAAATTACACCTCAACAAGAAGCCCAGTTTGCTTATGAACTAGCCCATAAAACTCTTCCTTTTAGCAAAAATATGCAAGAACAAGTTCAATCTATGCTGTTCATAGAAGAAAAAAATGGACGGAAAATTTATGCCAAAAGTGGTTGGGGATGGGATGTGGAGCCTCAAGTGGGCTGGTTAACAGGCTGGGTCGTTCAACCACAAGGAGAAATTATAGCTTTCTCACTTAATTTAGAAATGAAAAAAGGCATACCTACCTCTATTCGAAAAGAAATTGCTTATAAGGGATTGGAACAACTCGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3008556","ARO_id":"47348","ARO_name":"OXA-1138","CARD_short_name":"OXA-1138","ARO_description":"OXA-213 family carbapenem-hydrolyzing class D beta-lactamase OXA-1138.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46495":{"category_aro_accession":"3007706","category_aro_cvterm_id":"46495","category_aro_name":"OXA-213-like beta-lactamase","category_aro_description":"OXA-213-like enzymes have been identified to be intrinsic to A. calcoaceticus and have been subsequently detected in A. pittii. Phylogenetic analysis of OXA-213-like proteins identified two distinct subgroups within the OXA family. The first group was linked to A. pittii and the second group to A. calcoaceticus. The carbapenemase activity of these OXAs may be related to the species-dependent effect.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7975":{"model_id":"7975","model_name":"OXA-1139","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10802":{"protein_sequence":{"accession":"UTS94248.1","sequence":"MKKFILPIFSISTLLSLSACSTIQNKFENTSDISDQQHEKAIKSYFDEAQTQGVIIIKEGKNIRIYGNNLVRAHTEYVPASTFKMLNALIGLENHKATTTEIFKWDGKKRSYPMWEKDMTLGDAMALSAVPVYQELARRTGLDLMQKEVKRVGFGNMNIGTQVNNFWLVGPLKITPIQEANFADDLANNRLPFKLETQEEVKKMLLIKEVNGSKIYAKSGWGMDVTPQVGWLTGWVEKSNGEKVPFSLNLEMKQGMSGSIRNEITYKSLENLGII"},"dna_sequence":{"accession":"ON651495.1","fmin":"0","fmax":"828","strand":"+","sequence":"ATGAAAAAATTTATACTTCCTATCTTCAGCATTTCTACTCTACTTTCTCTCAGTGCATGCTCAACTATTCAAAATAAATTTGAAAATACTTCTGATATTTCTGATCAGCAACATGAAAAAGCCATTAAAAGCTATTTTGATGAAGCTCAAACACAAGGTGTAATCATTATTAAAGAGGGAAAGAATATTAGAATCTATGGTAATAACCTGGTACGAGCACATACAGAATATGTCCCTGCGTCAACATTTAAGATGCTAAATGCCTTAATTGGATTAGAAAATCATAAAGCTACAACAACTGAGATTTTCAAATGGGATGGTAAAAAAAGATCTTATCCTATGTGGGAAAAAGATATGACTTTAGGTGATGCCATGGCACTTTCAGCAGTTCCTGTATATCAAGAACTTGCAAGACGGACTGGCTTAGATCTAATGCAAAAAGAAGTTAAACGGGTTGGTTTTGGTAATATGAACATCGGGACACAAGTTAATAACTTCTGGTTAGTTGGCCCCCTCAAGATTACACCAATACAAGAGGCTAATTTTGCCGATGATCTTGCGAATAATCGATTACCCTTTAAATTAGAAACTCAAGAAGAAGTAAAAAAAATGCTTCTGATTAAAGAAGTCAATGGTAGTAAAATTTATGCGAAAAGTGGATGGGGAATGGATGTGACCCCTCAAGTAGGTTGGTTAACAGGTTGGGTAGAAAAATCTAATGGCGAAAAAGTTCCCTTTTCTCTAAACCTAGAAATGAAGCAAGGAATGTCTGGTTCTATTCGTAATGAAATTACTTATAAATCATTAGAAAATTTAGGGATTATATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008557","ARO_id":"47349","ARO_name":"OXA-1139","CARD_short_name":"OXA-1139","ARO_description":"OXA-143 family carbapenem-hydrolyzing class D beta-lactamase OXA-1139.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46490":{"category_aro_accession":"3007701","category_aro_cvterm_id":"46490","category_aro_name":"OXA-143-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-143.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7976":{"model_id":"7976","model_name":"OXA-1140","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10803":{"protein_sequence":{"accession":"UUM03673.1","sequence":"MRPLLFSALLLLSGHTQASEWNDSQAVDKLFGAAGVKGTFVLYDVQRQCYVGHDRERAETRFVPASTYKVANSLIGLSTGAVRSADEVLPYGGKPQRFKAWEHDMSLREAIKASNVPVYQELARRIGLERMRANVSRLGYGNAEIGQVVDNFWLVGPMKISAMEQTRFLLRLAQGELPFPAPVQSTVRAMTLLESGPGWELHGKTGWCFDCTPELGWWVGWVKRNERLYGFALNIDMPGGEADIGKRVELGKASLKALGILP"},"dna_sequence":{"accession":"OP131857.1","fmin":"0","fmax":"789","strand":"+","sequence":"ATGCGCCCTCTCCTCTTCAGTGCCCTTCTCCTGCTTTCCGGGCATACCCAGGCCAGCGAATGGAACGACAGCCAGGCCGTGGACAAGCTCTTCGGCGCGGCCGGGGTGAAAGGCACCTTCGTCCTCTACGATGTGCAGCGGCAGTGCTATGTCGGCCATGACCGGGAGCGCGCGGAAACCCGCTTCGTTCCCGCTTCCACCTACAAGGTGGCGAACAGCCTGATCGGCTTATCCACAGGGGCGGTTAGATCCGCCGACGAGGTTCTTCCCTATGGCGGCAAGCCCCAGCGCTTCAAGGCCTGGGAGCACGACATGAGCCTGCGCGAGGCGATCAAGGCATCGAACGTACCGGTCTACCAGGAACTGGCGCGGCGCATCGGCCTGGAGCGGATGCGCGCCAATGTCTCGCGCCTGGGTTACGGCAACGCGGAAATCGGCCAGGTTGTGGATAACTTCTGGTTGGTGGGACCGATGAAGATCAGCGCGATGGAACAGACCCGCTTTCTGCTCCGACTGGCGCAGGGAGAATTGCCATTCCCCGCCCCGGTGCAGTCCACCGTGCGCGCCATGACCCTGCTGGAAAGCGGCCCGGGCTGGGAGCTGCACGGCAAGACCGGCTGGTGCTTCGACTGCACGCCGGAACTCGGCTGGTGGGTGGGCTGGGTGAAGCGCAACGAGCGGCTCTACGGCTTCGCCCTGAACATCGACATGCCCGGCGGCGAGGCCGACATCGGCAAGCGCGTCGAACTGGGCAAGGCCAGTCTCAAGGCTCTCGGGATACTGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008558","ARO_id":"47350","ARO_name":"OXA-1140","CARD_short_name":"OXA-1140","ARO_description":"OXA-50 family oxacillin-hydrolyzing class D beta-lactamase OXA-1140.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46513":{"category_aro_accession":"3007724","category_aro_cvterm_id":"46513","category_aro_name":"OXA-50-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-50.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7977":{"model_id":"7977","model_name":"OXA-1141","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10804":{"protein_sequence":{"accession":"UUM03674.1","sequence":"MKTFAAYVIIACLSSTALAGSITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIGKFWLEDQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGIIGG"},"dna_sequence":{"accession":"OP131858.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGAAAACATTTGCCGCATATGTAATTATCGCGTGTCTTTCGAGTACGGCATTAGCTGGTTCAATTACAGAAAATACGTCTTGGAACAAAGAGTTCTCTGCCGAAGCCGTCAATGGTGTCTTCGTGCTTTGTAAAAGTAGCAGTAAATCCTGCGCTACCAATGACTTAGCTCGTGCATCAAAGGAATATCTTCCAGCATCAACATTTAAGATCCCCAACGCAATTATCGGCCTAGAAACTGGTGTCATAAAGAATGAGCATCAGGTTTTCAAATGGGACGGAAAGCCAAGAGCCATGAAGCAATGGGAAAGAGACTTGACCTTAAGAGGGGCAATACAAGTTTCAGCTGTTCCCGTATTTCAACAAATCGCCAGAGAAGTTGGCGAAGTAAGAATGCAGAAATACCTTAAAAAATTTTCCTATGGCAACCAGAATATCAGTGGTGGCATTGGCAAATTCTGGTTGGAAGACCAGCTTAGAATTTCCGCAGTTAATCAAGTGGAGTTTCTAGAGTCTCTATATTTAAATAAATTGTCAGCATCTAAAGAAAACCAGCTAATAGTAAAAGAGGCTTTGGTAACGGAGGCGGCACCTGAATATCTAGTGCATTCAAAAACTGGTTTTTCTGGTGTGGGAACTGAGTCAAATCCTGGTGTCGCATGGTGGGTTGGGTGGGTTGAGAAGGAGACAGAGGTTTACTTTTTCGCCTTTAACATGGATATAGACAACGAAAGTAAGTTGCCGCTAAGAAAATCCATTCCCACCAAAATCATGGAAAGTGAGGGCATCATTGGTGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"47927","NCBI_taxonomy_name":"Pseudomonas parasichuanensis","NCBI_taxonomy_id":"2892329"}}}},"ARO_accession":"3008559","ARO_id":"47351","ARO_name":"OXA-1141","CARD_short_name":"OXA-1141","ARO_description":"OXA-10 family class D beta-lactamase OXA-1141.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46486":{"category_aro_accession":"3007697","category_aro_cvterm_id":"46486","category_aro_name":"OXA-10-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-10.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7978":{"model_id":"7978","model_name":"OXA-1142","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10805":{"protein_sequence":{"accession":"UUM03675.1","sequence":"MKPWRPALLAFAGLLAAASSGAHPVCTVVADAATGKVLVQQGDCTTRVTPASTFKVAIGLMGFDAGVLKDAHTPTLDFHAGYPDWGGAPWREPTDPARWMKLSIFWYSQQVTQALGQARFQQYTSAFGYGNADVTSNEGERPGVMGAWVNASLRISPLEQVAFMRRITQRTLPVSAHAYDMIARITLIDAQPGGWTVHGKTGTGSPGIQYDAAHAYGWFVGWATQGARTLVFANLIQDDARQTPNAGLRARDTFLAALPTLAEPARPQ"},"dna_sequence":{"accession":"OP131859.1","fmin":"0","fmax":"807","strand":"+","sequence":"TTGAAGCCCTGGCGCCCTGCGCTGCTCGCCTTCGCCGGCCTCCTGGCCGCCGCGTCTTCCGGCGCCCATCCCGTCTGCACGGTCGTCGCCGACGCCGCCACCGGCAAGGTGCTCGTGCAGCAGGGCGATTGCACGACCCGCGTGACGCCGGCATCGACGTTCAAGGTCGCAATCGGCCTGATGGGCTTCGACGCCGGCGTGCTGAAGGACGCGCACACGCCCACGCTCGATTTCCATGCCGGCTACCCCGACTGGGGCGGGGCGCCGTGGCGCGAGCCGACCGACCCGGCACGCTGGATGAAGCTGTCGATCTTCTGGTATTCGCAGCAGGTCACGCAGGCGCTGGGGCAAGCGCGCTTCCAGCAGTACACGAGCGCGTTCGGCTACGGCAACGCCGACGTCACCAGCAACGAGGGCGAACGGCCCGGCGTGATGGGCGCGTGGGTCAATGCGTCGCTACGCATCTCGCCGCTCGAACAGGTCGCGTTCATGCGCAGGATCACGCAACGGACGCTGCCCGTCAGCGCGCACGCGTACGACATGATCGCGCGCATCACGCTGATCGACGCGCAACCGGGCGGCTGGACGGTACACGGCAAGACCGGCACCGGCTCGCCCGGTATCCAGTACGACGCCGCACACGCATACGGCTGGTTCGTCGGCTGGGCGACGCAGGGTGCGCGCACGCTGGTGTTCGCGAACCTGATCCAGGACGACGCGCGGCAGACGCCGAATGCCGGCCTGCGCGCGCGCGACACGTTCCTCGCGGCGCTGCCGACGCTCGCCGAACCGGCCCGGCCGCAATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41647","NCBI_taxonomy_name":"Burkholderia cenocepacia","NCBI_taxonomy_id":"95486"}}}},"ARO_accession":"3008560","ARO_id":"47352","ARO_name":"OXA-1142","CARD_short_name":"OXA-1142","ARO_description":"Class D beta-lactamase OXA-1142.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7979":{"model_id":"7979","model_name":"OXA-1143","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10806":{"protein_sequence":{"accession":"UUM03676.1","sequence":"MPRMLLSGLLAAGLFCALPASAASGCMLFADGTGKPVSTQGDCAAQLTPASTFKIPLALMGYDSGFLVDEQLPALPFKAGDPDFLPEWKQTTTPSSWMQFSVIWYSQRLTEWLGEARFQHYVDSFDYGNRDLEGNPGKHDGLTQAWLSASLAISPQEQARFLGKMVSGKLPVSAKTLHHTANLMRQPDIDGWQIHGKTGMGYPKLLDGSLDREQQIGWFVGWASKQGKTLIFVHTVIQKPGKQFASLRAREEVFAALPARLKTL"},"dna_sequence":{"accession":"OP131860.1","fmin":"0","fmax":"795","strand":"+","sequence":"ATGCCCCGTATGCTGTTGTCCGGTCTGCTTGCCGCTGGCCTCTTCTGTGCACTGCCTGCCAGCGCCGCTTCTGGCTGCATGCTGTTTGCCGACGGCACCGGCAAACCCGTCAGCACCCAGGGGGACTGTGCCGCCCAGTTGACCCCGGCCTCCACCTTCAAGATCCCGCTGGCACTGATGGGCTATGACAGCGGCTTCCTGGTGGATGAACAACTGCCGGCCCTGCCGTTCAAGGCCGGTGATCCTGATTTCCTGCCGGAGTGGAAACAGACCACCACCCCGAGCAGCTGGATGCAATTCTCGGTCATCTGGTACTCGCAGCGCCTCACCGAGTGGCTGGGAGAGGCTCGCTTCCAGCACTACGTGGACAGCTTCGACTACGGCAACCGGGATCTCGAAGGCAACCCAGGCAAGCACGACGGTCTGACCCAGGCCTGGCTCAGCGCCAGCCTCGCCATCAGCCCCCAGGAGCAAGCCCGCTTCCTTGGCAAGATGGTGAGCGGCAAGCTGCCGGTCTCCGCCAAGACCCTGCACCATACCGCCAACCTGATGCGTCAGCCCGACATCGACGGTTGGCAGATCCACGGCAAGACCGGCATGGGTTACCCCAAGCTGCTGGATGGCAGCCTGGACAGGGAGCAGCAGATCGGCTGGTTCGTCGGCTGGGCCAGCAAACAGGGCAAGACGCTCATCTTCGTCCACACCGTAATCCAGAAGCCGGGCAAGCAGTTCGCTTCCCTCAGGGCCAGGGAGGAGGTGTTCGCCGCCCTGCCGGCCCGGTTGAAGACACTCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36936","NCBI_taxonomy_name":"Aeromonas caviae","NCBI_taxonomy_id":"648"}}}},"ARO_accession":"3008561","ARO_id":"47353","ARO_name":"OXA-1143","CARD_short_name":"OXA-1143","ARO_description":"Class D beta-lactamase OXA-1143.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7980":{"model_id":"7980","model_name":"OXA-1144","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10807":{"protein_sequence":{"accession":"UUM03677.1","sequence":"MKFKMKGLFCVILSSLAFSGCVYDSKLQRPVISERETEIPLLFNQAQTQAVFVTYDGIHLKSYGNDLSRAKTEYIPASTFKMLNALIGLQNAKATNTEVFHWNGEKRAFSAWEKDMTLAEAMQASAVPVYQELARRIGLELMREEVKRVGFGNAEIGQQVDNFWLVGPLKISPEQEVKFAYQLAMKQLPFDRNVQQQVKDMLYIERRGDSKLYAKSGWGMDVEPQVGWYTGWVEQPNGKVTAFALNMKMQAEDDPAERKQLTLSILDKLGLFFYLR"},"dna_sequence":{"accession":"OP131861.1","fmin":"0","fmax":"831","strand":"+","sequence":"ATGAAGTTTAAAATGAAAGGTTTATTTTGTGTTATCCTCAGTAGTTTGGCATTTTCAGGTTGTGTTTATGATTCAAAACTACAACGCCCAGTCATATCAGAGCGAGAAACTGAGATTCCTTTATTATTTAATCAAGCACAGACTCAAGCTGTGTTTGTTACTTATGATGGGATTCATCTAAAAAGTTATGGTAATGATCTAAGCCGAGCAAAGACTGAATATATTCCTGCATCTACATTTAAGATGTTGAATGCTTTAATTGGATTGCAAAATGCAAAAGCAACCAATACTGAAGTATTTCATTGGAATGGTGAAAAGCGCGCTTTTTCAGCATGGGAAAAAGATATGACTTTGGCAGAAGCGATGCAGGCTTCAGCTGTTCCCGTATATCAGGAGCTTGCTCGACGTATTGGCTTGGAGTTGATGCGTGAAGAAGTGAAGCGTGTAGGTTTTGGCAATGCGGAGATTGGTCAGCAAGTCGATAATTTTTGGTTGGTGGGTCCTTTAAAAATCTCCCCTGAACAAGAAGTTAAATTTGCCTATCAACTGGCGATGAAGCAATTACCTTTTGATCGAAATGTACAGCAACAAGTCAAAGATATGCTTTATATCGAGAGACGTGGTGACAGTAAACTGTATGCTAAAAGTGGTTGGGGAATGGATGTTGAACCTCAAGTGGGTTGGTATACGGGATGGGTTGAACAACCCAATGGCAAGGTGACTGCATTTGCGTTAAATATGAAAATGCAAGCAGAGGATGATCCAGCTGAACGTAAACAATTAACCTTAAGTATTTTGGACAAATTGGGTCTATTTTTTTATTTAAGATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39090","NCBI_taxonomy_name":"Acinetobacter bereziniae","NCBI_taxonomy_id":"106648"}}}},"ARO_accession":"3008562","ARO_id":"47354","ARO_name":"OXA-1144","CARD_short_name":"OXA-1144","ARO_description":"OXA-229 family carbapenem-hydrolyzing class D beta-lactamase OXA-1144.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46498":{"category_aro_accession":"3007709","category_aro_cvterm_id":"46498","category_aro_name":"OXA-229-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-229.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7981":{"model_id":"7981","model_name":"OXA-1145","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10808":{"protein_sequence":{"accession":"UUM03678.1","sequence":"MIMSKKLTCLALFTAIFFAIPMTACQNFSQQKQQLMTQKNEQQQISSLFQSAQTSGVLVIYDGKKIQSYGNDIHRADQRYIPASTFKMLNALIGIQHHKTTPDELFKWDGKKRAFSSWEKDLTLAEAMQASAVPVYQELARRIGLELMTREVKRVGYGNKNIGTQVDNFWLVGPLKITPVEEVRFAYALAKQKLPFDQPTQQQVKAMLLVDQIQGTKIYAKSGWGMDVSPQVGWWTGWIEQPNGKITAFSLNMQMSQPEHADARKAIVYQALQQLGLLAH"},"dna_sequence":{"accession":"OP131862.1","fmin":"0","fmax":"843","strand":"+","sequence":"ATGATCATGTCGAAAAAATTAACATGTCTGGCCCTGTTTACAGCCATCTTTTTTGCGATTCCCATGACGGCTTGTCAAAATTTTAGCCAACAAAAGCAACAGCTCATGACACAAAAAAATGAGCAGCAGCAGATCTCAAGTTTATTCCAGAGTGCCCAAACCAGTGGTGTTTTGGTGATTTATGATGGCAAGAAAATTCAAAGCTATGGCAATGATATACATCGCGCAGATCAGCGCTATATTCCTGCCTCAACCTTTAAAATGCTAAACGCCTTGATTGGTATACAACATCATAAGACCACACCAGATGAACTGTTTAAATGGGATGGCAAAAAGCGGGCATTCAGCAGTTGGGAAAAAGATTTAACCTTAGCTGAAGCGATGCAGGCATCGGCGGTACCTGTGTATCAAGAGTTGGCAAGACGTATTGGCTTGGAGTTAATGACCCGTGAAGTGAAGCGTGTGGGTTATGGCAATAAAAATATTGGGACACAAGTTGATAATTTCTGGTTAGTTGGCCCATTAAAAATCACCCCCGTAGAAGAAGTTCGCTTTGCCTATGCGTTGGCAAAACAGAAATTGCCATTTGACCAGCCAACACAGCAACAAGTCAAAGCGATGTTATTGGTGGATCAGATTCAGGGAACTAAAATCTATGCAAAAAGTGGTTGGGGCATGGATGTTAGCCCACAAGTGGGATGGTGGACAGGCTGGATTGAACAGCCAAATGGTAAGATCACAGCCTTCTCACTGAATATGCAAATGAGCCAGCCTGAGCATGCAGATGCACGTAAAGCGATTGTGTATCAAGCCTTGCAACAGTTGGGATTGTTAGCCCATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42970","NCBI_taxonomy_name":"Acinetobacter proteolyticus","NCBI_taxonomy_id":"1217713"}}}},"ARO_accession":"3008563","ARO_id":"47355","ARO_name":"OXA-1145","CARD_short_name":"OXA-1145","ARO_description":"OXA-286 family carbapenem-hydrolyzing class D beta-lactamase OXA-1145.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46503":{"category_aro_accession":"3007714","category_aro_cvterm_id":"46503","category_aro_name":"OXA-286-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-286.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7982":{"model_id":"7982","model_name":"OXA-1146","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10809":{"protein_sequence":{"accession":"UUT09020.1","sequence":"MRVLALSAVFLVASIIGMPAVAKEWQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGQTRDIATWNRDHNLITAMKYSVVPVYQEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISATEQISFLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYSTEPKIGWWVGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP"},"dna_sequence":{"accession":"OP158702.1","fmin":"0","fmax":"792","strand":"+","sequence":"ATGCGTGTATTAGCCTTATCGGCTGTGTTTTTGGTGGCATCGATTATCGGAATGCCTGCGGTAGCAAAGGAATGGCAAGAAAACAAAAGTTGGAATGCTCACTTTACTGAACATAAATCACAGGGCGTAGTTGTGCTCTGGAATGAGAATAAGCAGCAAGGATTTACCAATAATCTTAAACGGGCGAACCAAGCATTTTTACCCGCATCTACCTTTAAAATTCCCAATAGCTTGATCGCCCTCGATTTGGGCGTGGTTAAGGATGAACACCAAGTCTTTAAGTGGGATGGACAGACGCGCGATATCGCCACTTGGAATCGCGATCATAATCTAATCACCGCGATGAAATATTCAGTTGTGCCTGTTTATCAAGAATTTGCCCGCCAAATTGGCGAGGCACGTATGAGCAAGATGCTACATGCTTTCGATTATGGTAATGAGGACATTTCGGGCAATGTAGACAGTTTCTGGCTCGACGGTGGTATTCGAATTTCGGCCACGGAGCAAATCAGCTTTTTAAGAAAGCTGTATCACAATAAGTTACACGTATCGGAGCGCAGCCAGCGTATTGTCAAACAAGCCATGCTGACCGAAGCCAATGGTGACTATATTATTCGGGCTAAAACTGGATACTCGACTGAACCTAAGATTGGCTGGTGGGTCGGTTGGGTTGAACTTGATGATAATGTGTGGTTTTTTGCGATGAATATGGATATGCCCACATCGGATGGTTTAGGGCTGCGCCAAGCCATCACAAAAGAAGTGCTCAAACAGGAAAAAATTATTCCCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3008564","ARO_id":"47356","ARO_name":"OXA-1146","CARD_short_name":"OXA-1146","ARO_description":"OXA-48 family class D beta-lactamase OXA-1146.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46510":{"category_aro_accession":"3007721","category_aro_cvterm_id":"46510","category_aro_name":"OXA-48-like beta-lactamase","category_aro_description":"OXA-48-type beta-lactamases are now routinely encountered in bacterial infections caused by carbapenam-resistant Enterobacterales. OXA-48-like proteins confer resistance to penicillin (which is efficiently hydrolyzed) and carbapenam antibiotics (which is more slowly broken down). The spectrum of activity of these variants varies, with some hydrolyzing expanded-spectrum oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7983":{"model_id":"7983","model_name":"OXA-1147","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10810":{"protein_sequence":{"accession":"UUT09021.1","sequence":"MKTFAAYVITACLSSTALAGSITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFKIPSAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGTVFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGIIGG"},"dna_sequence":{"accession":"OP158703.1","fmin":"0","fmax":"807","strand":"+","sequence":"ATGAAAACATTTGCCGCATATGTAATTACCGCGTGTCTTTCGAGTACGGCATTAGCTGGTTCAATTACAGAAAATACGTCTTGGAACAAAGAGTTCTCTGCCGAAGCCGTCAATGGTGTCTTCGTGCTTTGTAAAAGTAGCAGTAAATCCTGCGCTACCAATGACTTAGCTCGTGCATCAAAGGAATATCTTCCAGCATCAACATTTAAGATCCCCAGCGCAATTATCGGCCTAGAAACTGGTGTCATAAAGAATGAGCATCAGGTTTTCAAATGGGACGGAAAGCCAAGAGCCATGAAGCAATGGGAAAGAGACTTGACCTTAAGAGGGGCAATACAAGTTTCAGCTGTTCCCGTATTTCAACAAATCGCCAGAGAAGTTGGCGAAGTAAGAATGCAGAAATACCTTAAAAAATTTTCCTATGGCAACCAGAATATCAGTGGTGGCATTGACAAATTCTGGTTGGAAGGCCAGCTTAGAATTTCCGCAGTTAATCAAGTGGAGTTTCTAGAGTCTCTATATTTAAATAAATTGTCAGCATCTAAAGAAAACCAGCTAATAGTAAAAGAGGCTTTGGTAACGGAGGCGGCACCTGAATATCTAGTGCATTCAAAAACTGGTACTGTTTTTTCTGGTGTGGGAACTGAGTCAAATCCTGGTGTCGCATGGTGGGTTGGGTGGGTTGAGAAGGAGACAGAGGTTTACTTTTTCGCCTTTAACATGGATATAGACAACGAAAGTAAGTTGCCGCTAAGAAAATCCATTCCCACCAAAATCATGGAAAGTGAGGGCATCATTGGTGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36944","NCBI_taxonomy_name":"Providencia rettgeri","NCBI_taxonomy_id":"587"}}}},"ARO_accession":"3008565","ARO_id":"47357","ARO_name":"OXA-1147","CARD_short_name":"OXA-1147","ARO_description":"OXA-10 family class D beta-lactamase OXA-1147.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46486":{"category_aro_accession":"3007697","category_aro_cvterm_id":"46486","category_aro_name":"OXA-10-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-10.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7984":{"model_id":"7984","model_name":"OXA-1148","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10811":{"protein_sequence":{"accession":"HCE3953098.1","sequence":"MKTFAAYVIIACLSSTALAGSITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFKIPTAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGIIGG"},"dna_sequence":{"accession":"DAHLVQ010000131.1","fmin":"363","fmax":"1164","strand":"+","sequence":"ATGAAAACATTTGCCGCATATGTAATTATCGCGTGTCTTTCGAGTACGGCATTAGCTGGTTCAATTACAGAAAATACGTCTTGGAACAAAGAGTTCTCTGCCGAAGCCGTCAATGGTGTCTTCGTGCTTTGTAAAAGTAGCAGTAAATCCTGCGCTACCAATGACTTAGCTCGTGCATCAAAGGAATATCTTCCAGCATCAACATTTAAGATCCCCACCGCAATTATCGGCCTAGAAACTGGTGTCATAAAGAATGAGCATCAGGTTTTCAAATGGGACGGAAAGCCAAGAGCCATGAAGCAATGGGAAAGAGACTTGACCTTAAGAGGGGCAATACAAGTTTCAGCTGTTCCCGTATTTCAACAAATCGCCAGAGAAGTTGGCGAAGTAAGAATGCAGAAATACCTTAAAAAATTTTCCTATGGCAACCAGAATATCAGTGGTGGCATTGACAAATTCTGGTTGGAAGGCCAGCTTAGAATTTCCGCAGTTAATCAAGTGGAGTTTCTAGAGTCTCTATATTTAAATAAATTGTCAGCATCTAAAGAAAACCAGCTAATAGTAAAAGAGGCTTTGGTAACGGAGGCGGCACCTGAATATCTAGTGCATTCAAAAACTGGTTTTTCTGGTGTGGGAACTGAGTCAAATCCTGGTGTCGCATGGTGGGTTGGGTGGGTTGAGAAGGAGACAGAGGTTTACTTTTTCGCCTTTAACATGGATATAGACAACGAAAGTAAGTTGCCGCTAAGAAAATCCATTCCCACCAAAATCATGGAAAGTGAGGGCATCATTGGTGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008566","ARO_id":"47358","ARO_name":"OXA-1148","CARD_short_name":"OXA-1148","ARO_description":"OXA-10 family class D beta-lactamase OXA-1148.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46486":{"category_aro_accession":"3007697","category_aro_cvterm_id":"46486","category_aro_name":"OXA-10-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-10.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7985":{"model_id":"7985","model_name":"OXA-1149","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10812":{"protein_sequence":{"accession":"UVA78447.1","sequence":"MKRILSRWRRVAVMLRLASSVVAYGVLPSPAHALELSRASAAGAPSVAAPVHLTERADWGKFFAAENVKGTVVVLDGKTQTYQAYDSARAERRMSPASTYKIFNSLLALESGALDNERETIPWDGKPRRMKAWNAELNLRDAFRVSCYPCYQVVSHKIPRAYAQAKLDAVGYGNRTIGRVNDTYWVDDSLQISAREQVDFLQRLARGTLPFSARSQDIVRQISIVEANMDYVLHGKTGWFVDKKPDIGWWVGWLERDGNLTMIALNIDMNGDADGPKRARIVREVLKNLKLI"},"dna_sequence":{"accession":"CP102780.1","fmin":"4595946","fmax":"4596825","strand":"-","sequence":"ATGAAACGAATTCTCTCTCGCTGGCGCCGCGTGGCCGTCATGCTGCGCCTGGCGTCGTCGGTCGTCGCGTATGGTGTGCTGCCTTCGCCAGCACACGCGCTGGAATTGTCGCGGGCGTCAGCAGCGGGAGCACCTTCCGTGGCAGCCCCCGTCCACCTGACCGAGCGCGCCGACTGGGGCAAGTTCTTCGCGGCGGAAAACGTGAAGGGCACGGTCGTTGTGCTCGACGGCAAGACACAGACGTATCAGGCATATGATTCGGCGCGCGCCGAGCGGCGTATGTCACCGGCGTCGACATACAAGATATTCAACAGTCTGCTGGCGCTGGAATCGGGCGCGCTGGACAACGAGCGCGAGACGATTCCGTGGGACGGCAAACCACGCCGGATGAAGGCGTGGAATGCGGAGTTGAATCTGCGCGACGCGTTTCGTGTGTCTTGCTACCCGTGCTACCAAGTCGTTTCGCACAAGATTCCGCGCGCGTATGCGCAGGCGAAGCTCGACGCCGTCGGGTACGGTAACCGGACCATCGGTCGCGTGAACGACACCTATTGGGTGGATGACAGTTTGCAGATCTCGGCGCGTGAGCAGGTCGATTTTCTGCAACGTCTGGCGCGTGGCACGTTGCCGTTCTCGGCCCGTTCGCAGGACATCGTCCGGCAGATTTCCATCGTCGAAGCGAACATGGACTATGTTCTGCACGGCAAGACGGGCTGGTTTGTCGACAAGAAGCCGGATATCGGCTGGTGGGTGGGCTGGCTCGAGCGTGACGGCAATCTGACGATGATTGCGCTGAACATCGATATGAACGGTGACGCCGACGGACCGAAGCGCGCGCGTATCGTGCGTGAGGTGCTGAAGAACCTGAAGTTGATCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"47920","NCBI_taxonomy_name":"Pandoraea commovens","NCBI_taxonomy_id":"2508289"}}}},"ARO_accession":"3008567","ARO_id":"47359","ARO_name":"OXA-1149","CARD_short_name":"OXA-1149","ARO_description":"OXA-62 family carbapenem-hydrolyzing class D beta-lactamase OXA-1149.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46520":{"category_aro_accession":"3007731","category_aro_cvterm_id":"46520","category_aro_name":"OXA-62-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-62.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7986":{"model_id":"7986","model_name":"OXA-1150","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10813":{"protein_sequence":{"accession":"UVU92354.1","sequence":"MTKKALFFAIGTMFLSACSFNTVQQHQIQSISTNKNSEKIKSLFDQAQTEGVLVIKRGQTEEIYGNDLKRSSTEYVPASTFKMLNALIGLEHHKATPTEVFKWDGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMSKEVKRIGFGNADIGSKVDDFWLVGPLKITPQQEAQFAYELAHKTLPFSKNLQEQVQSMVFIEEKNGRKIYAKSGWGWDVDPQVGWFTGWIVQPQGEIVAFSLNLEMKKGIPSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"OP297830.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGACTAAAAAAGCTCTTTTCTTTGCCATTGGTACGATGTTTTTGTCGGCATGTTCTTTTAATACCGTACAACAACATCAAATACAGTCAATTTCTACCAATAAAAACTCAGAGAAAATTAAATCATTGTTTGATCAAGCACAAACTGAAGGTGTTTTAGTTATAAAACGTGGGCAAACAGAGGAAATCTATGGCAATGATCTTAAAAGATCATCAACCGAATATGTTCCCGCCTCTACCTTTAAAATGTTAAATGCTTTGATTGGACTTGAGCATCATAAAGCAACACCAACTGAAGTGTTTAAATGGGATGGGCAAAAGCGTTTGTTTCCTGATTGGGAAAAGGACATGACTCTAGGCGATGCGATGAAAGCTTCTGCTATTCCAGTTTATCAGGAACTAGCTCGACGAATTGGCCTTGATCTTATGTCTAAAGAGGTAAAACGCATTGGTTTCGGTAATGCTGATATTGGTTCAAAAGTAGATGATTTTTGGCTTGTTGGTCCACTTAAAATTACACCTCAACAAGAAGCCCAGTTTGCTTATGAACTAGCCCATAAAACTCTTCCTTTTAGCAAAAATCTGCAAGAACAAGTTCAATCTATGGTGTTCATAGAAGAAAAAAATGGACGAAAAATTTATGCCAAAAGTGGTTGGGGATGGGATGTGGATCCTCAAGTGGGCTGGTTTACAGGCTGGATCGTTCAACCTCAAGGAGAAATTGTAGCGTTCTCACTCAATTTAGAAATGAAAAAAGGCATACCTAGTTCTATTCGAAAAGAAATTGCTTATAAGGGATTAGAGCAGCTAGGTATTTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3008568","ARO_id":"47360","ARO_name":"OXA-1150","CARD_short_name":"OXA-1150","ARO_description":"OXA-213 family carbapenem-hydrolyzing class D beta-lactamase OXA-1150.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46495":{"category_aro_accession":"3007706","category_aro_cvterm_id":"46495","category_aro_name":"OXA-213-like beta-lactamase","category_aro_description":"OXA-213-like enzymes have been identified to be intrinsic to A. calcoaceticus and have been subsequently detected in A. pittii. Phylogenetic analysis of OXA-213-like proteins identified two distinct subgroups within the OXA family. The first group was linked to A. pittii and the second group to A. calcoaceticus. The carbapenemase activity of these OXAs may be related to the species-dependent effect.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7987":{"model_id":"7987","model_name":"OXA-1151","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10814":{"protein_sequence":{"accession":"UVU92356.1","sequence":"MYKKVLIVATSILFLSACSSNTVKQHQIHSISANKNSEAIKSLFDQAQTTGVLVIKRGQTEEIYGNDLKRASTSYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMSKEVKRVGFGNANIGSKVDNFWLVGPLKITPQQETQFAYQLAHKTLPFSQDVQEQVQSMVFIEEKNGTKIYAKSGWGWDIEPQVGWLTGWVVQPQGEIVAFSLNLEMKKGTPSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"OP297832.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGTATAAAAAAGTCCTTATCGTTGCAACAAGTATTCTATTTTTATCCGCCTGTTCTTCCAATACGGTAAAACAACATCAAATACACTCTATTTCTGCCAATAAAAATTCAGAAGCAATTAAATCACTGTTTGATCAGGCACAGACCACGGGTGTTTTGGTGATTAAGCGAGGACAAACAGAAGAAATTTATGGCAATGATCTTAAAAGAGCATCAACCTCCTATGTTCCCGCCTCTACCTTTAAAATGTTAAATGCTTTAATTGGACTTGAACATCATAAGGCAACTACAACTGAAGTATTTAAATGGGATGGGCAAAAACGTTTATTTCCGGATTGGGAAAAAGACATGACACTGGGCGATGCCATGAAAGCTTCTGCGATTCCAGTTTACCAAGAATTAGCCCGACGAATTGGTCTGGATCTTATGTCCAAAGAGGTGAAACGAGTTGGTTTTGGTAATGCTAACATTGGTTCAAAAGTAGATAATTTTTGGCTCGTTGGCCCTCTAAAAATTACACCTCAACAAGAAACCCAATTTGCTTATCAATTAGCCCATAAAACGCTTCCATTTAGCCAAGATGTACAAGAACAAGTTCAATCAATGGTGTTCATAGAAGAAAAAAATGGAACTAAAATTTATGCCAAAAGTGGTTGGGGATGGGATATTGAACCACAAGTTGGTTGGTTAACAGGCTGGGTCGTTCAACCACAAGGAGAAATTGTGGCATTCTCACTTAATTTAGAAATGAAAAAAGGAACTCCTAGCTCTATTCGCAAAGAAATTGCTTATAAAGGCTTAGAACAACTGGGTATCTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39094","NCBI_taxonomy_name":"Acinetobacter calcoaceticus","NCBI_taxonomy_id":"471"}}}},"ARO_accession":"3008569","ARO_id":"47361","ARO_name":"OXA-1151","CARD_short_name":"OXA-1151","ARO_description":"OXA-213 family carbapenem-hydrolyzing class D beta-lactamase OXA-1151.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46495":{"category_aro_accession":"3007706","category_aro_cvterm_id":"46495","category_aro_name":"OXA-213-like beta-lactamase","category_aro_description":"OXA-213-like enzymes have been identified to be intrinsic to A. calcoaceticus and have been subsequently detected in A. pittii. Phylogenetic analysis of OXA-213-like proteins identified two distinct subgroups within the OXA family. The first group was linked to A. pittii and the second group to A. calcoaceticus. The carbapenemase activity of these OXAs may be related to the species-dependent effect.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7988":{"model_id":"7988","model_name":"OXA-1152","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10815":{"protein_sequence":{"accession":"UYF23589.1","sequence":"MKRILSRWRRAAVVLRLASAVVAHGLLPSPAHALELSRASAAAAPSVAAPVHVTERADWGKFFAAENVKGTVVVLDGKTQTYQAYDSARAERRMSPASTYKIFNSLLALESGALDNERETIPWDGKPRRIKAWNAELNLRDAFRVSCYPCYQVVSHKIPRAYAQAKLDAVGYGNRTIGRVNDTYWVDDSLQISAREQVDFLQRLARGTLPFSARSQDIVRQISIVEANADYVLHGKTGWFVDKKPDIGWWVGWLERDGNLTMIALNIDMNGDADGPKRARIVREVLKNLKLI"},"dna_sequence":{"accession":"OP626812.1","fmin":"0","fmax":"879","strand":"+","sequence":"ATGAAACGAATTCTCTCTCGCTGGCGTCGCGCGGCTGTCGTGCTGCGTCTGGCGTCGGCGGTCGTCGCGCATGGTCTGCTGCCCTCGCCAGCACACGCGCTGGAATTGTCGCGGGCGTCAGCCGCTGCGGCACCTTCCGTGGCAGCGCCCGTCCACGTGACCGAGCGTGCCGACTGGGGCAAGTTCTTTGCGGCGGAAAACGTGAAGGGCACGGTCGTCGTGCTCGACGGCAAGACACAGACGTATCAGGCGTACGACTCGGCGCGCGCCGAGCGGCGCATGTCCCCGGCGTCGACGTACAAGATATTCAACAGTCTGCTGGCGCTGGAATCGGGTGCGCTGGACAACGAGCGCGAGACGATTCCGTGGGACGGCAAACCGCGCCGGATTAAGGCGTGGAATGCAGAATTGAATCTGCGCGACGCGTTTCGCGTGTCTTGCTACCCGTGCTATCAGGTCGTTTCGCACAAGATTCCGCGTGCGTATGCGCAGGCGAAGCTCGACGCCGTCGGGTACGGTAACCGGACCATCGGTCGGGTGAACGACACCTATTGGGTGGACGACAGTTTGCAGATCTCAGCGCGCGAGCAAGTCGACTTCCTGCAGCGTCTGGCGCGTGGCACGTTGCCGTTCTCCGCGCGTTCGCAGGACATCGTCCGGCAGATTTCCATCGTCGAAGCGAACGCCGACTATGTGCTGCACGGCAAGACCGGCTGGTTCGTCGACAAGAAGCCGGATATCGGCTGGTGGGTGGGCTGGCTGGAGCGTGACGGCAATCTGACGATGATCGCGCTGAACATCGACATGAACGGCGACGCCGACGGCCCGAAGCGTGCGCGTATCGTGCGTGAGGTGCTGAAGAACCTGAAGTTGATCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42786","NCBI_taxonomy_name":"Pandoraea sputorum","NCBI_taxonomy_id":"93222"}}}},"ARO_accession":"3008570","ARO_id":"47362","ARO_name":"OXA-1152","CARD_short_name":"OXA-1152","ARO_description":"OXA-62 family carbapenem-hydrolyzing class D beta-lactamase OXA-1152.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46520":{"category_aro_accession":"3007731","category_aro_cvterm_id":"46520","category_aro_name":"OXA-62-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-62.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7989":{"model_id":"7989","model_name":"OXA-1153","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10816":{"protein_sequence":{"accession":"BDS51117.1","sequence":"MSRILLPGLFAAGLFCAFPASAASGCMLFADGTGKPLSAEGECAAQLTPASTFKIPLALMGYDSGFLVDEELPALPFKPGDADFLPEWRETATPSRWMTYSVIWYSQRLTEWLGEARFQHYVDRFDYGNRDLSGNPGKHDGLTQAWLSSSLTISPQEQARFLGRMVSGKLPVSAQTLQHTANILKVSEIDGWQIHGKTGMGYPKKLDGSLDRDQQIGWFVGWASKPGKQLIFVHTLVQRPGKQFASLKAKEEVLAALPAKLKTL"},"dna_sequence":{"accession":"LC732273.1","fmin":"0","fmax":"795","strand":"+","sequence":"ATGTCCCGTATTCTGTTGCCCGGCCTGTTTGCCGCCGGACTCTTCTGTGCCTTTCCCGCCAGCGCTGCCTCAGGCTGCATGCTGTTTGCCGATGGCACAGGCAAACCCCTCAGTGCCGAGGGAGAGTGTGCCGCCCAGCTGACCCCCGCCTCCACCTTCAAGATCCCGCTGGCCCTGATGGGTTATGACAGCGGCTTCCTGGTGGATGAAGAGCTGCCCGCCCTGCCGTTCAAACCCGGCGATGCCGACTTTCTGCCCGAATGGCGTGAGACCGCCACCCCGAGCCGCTGGATGACCTATTCGGTGATCTGGTATTCCCAGCGCCTTACCGAATGGCTGGGGGAGGCGCGCTTCCAGCACTACGTCGACCGCTTCGACTATGGCAACCGGGATCTCTCGGGCAACCCGGGCAAGCACGACGGTCTGACCCAGGCCTGGCTCAGTTCGAGCCTGACCATCAGCCCCCAGGAGCAGGCCCGCTTCCTCGGCAGGATGGTGAGCGGCAAGCTGCCGGTCTCCGCCCAAACCCTGCAGCACACCGCCAATATCCTCAAGGTGAGCGAGATCGACGGCTGGCAGATCCACGGCAAGACCGGCATGGGCTACCCGAAAAAACTGGATGGCAGCCTCGACCGGGATCAGCAAATAGGCTGGTTCGTCGGCTGGGCCAGCAAACCGGGCAAACAGCTCATCTTCGTCCACACCCTGGTGCAGAGACCCGGCAAGCAGTTCGCCTCCCTCAAGGCCAAGGAAGAGGTGCTGGCCGCCCTGCCGGCCAAACTGAAAACCCTGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"47902","NCBI_taxonomy_name":"Aeromonas taiwanensis","NCBI_taxonomy_id":"633417"}}}},"ARO_accession":"3008571","ARO_id":"47363","ARO_name":"OXA-1153","CARD_short_name":"OXA-1153","ARO_description":"Class D beta-lactamase OXA-1153.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7990":{"model_id":"7990","model_name":"OXA-1154","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10817":{"protein_sequence":{"accession":"BDS51118.1","sequence":"MPRMLLSGLLAAGLFCALPASAASGCMLFADGTGKPVSTQGDCAAQLTPASTFKIPLALMGYDSGFLVDEQLPALPFKAGDPDFLPEWKQTTTPSSWMQFSVIWYSQRLTEWLGEARFQHYVDSFDYGNRDLEGNPGKHDGLTQAWLSASLAISPQEQARFLGKMVSGKLPVSAQTLRHTANLLRQPDIDGWQIHGKTGMGYPKLLDGSLDREQQIGWFVGWASKQDKTLIFVHTVIQTPGKQFASLRAREEVFAALPARLKTL"},"dna_sequence":{"accession":"LC732548.1","fmin":"0","fmax":"795","strand":"+","sequence":"ATGCCCCGTATGCTGTTGTCCGGTCTGCTTGCCGCCGGCCTCTTCTGTGCACTGCCTGCCAGCGCCGCTTCTGGCTGCATGCTGTTTGCCGATGGCACCGGCAAACCCGTCAGCACCCAGGGGGACTGTGCCGCCCAGTTGACCCCGGCCTCCACCTTCAAGATCCCGCTGGCACTGATGGGCTATGACAGCGGCTTTCTGGTGGATGAACAACTGCCGGCCCTGCCGTTCAAGGCCGGTGATCCTGATTTCCTGCCGGAGTGGAAACAGACCACCACCCCGAGCAGCTGGATGCAATTCTCGGTCATCTGGTACTCGCAGCGCCTCACCGAGTGGCTGGGAGAAGCTCGCTTCCAGCACTACGTGGACAGCTTCGACTACGGCAACCGGGATCTCGAAGGCAACCCGGGCAAGCACGACGGTCTGACCCAGGCCTGGCTGAGCGCCAGCCTCGCCATCAGCCCCCAGGAGCAAGCCCGCTTCCTTGGCAAGATGGTGAGCGGCAAGCTGCCGGTCTCCGCCCAGACCCTGCGCCATACCGCCAACCTGCTGCGTCAGCCCGACATCGACGGTTGGCAGATCCACGGCAAGACCGGCATGGGTTACCCCAAGCTGCTGGATGGCAGCCTGGACAGGGAGCAGCAGATCGGCTGGTTCGTCGGCTGGGCCAGCAAACAGGACAAAACGCTCATCTTCGTCCACACCGTTATCCAGACGCCGGGCAAGCAGTTCGCTTCCCTCAGGGCCAGGGAGGAGGTGTTCGCCGCCCTGCCGGCCCGGTTGAAGACACTCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36936","NCBI_taxonomy_name":"Aeromonas caviae","NCBI_taxonomy_id":"648"}}}},"ARO_accession":"3008572","ARO_id":"47364","ARO_name":"OXA-1154","CARD_short_name":"OXA-1154","ARO_description":"Class D beta-lactamase OXA-1154.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7991":{"model_id":"7991","model_name":"OXA-1155","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10818":{"protein_sequence":{"accession":"BDS51119.1","sequence":"MPRMLLSGLLAAGLFCALPASAASGCMLFADGTGKPVSTQGDCAAQLTPASTFKIPLALMGYDSGFLVDEQLPALPFKAGDPDFLPEWKQTTTPSSWMQFSVIWYSQRLTEWLGEARFQHYVDSFDYGNRDLEGNPGKHDGLTQAWLSTSLAISPQEQARFLGKMVSGKLPVSAQTLRHTANLMRQPDIDGWQIHGKTGMGYPKLLDGSLDREQQIGWFVGWASKQDKTLIFVHTVIQKPGTQFASLRAREEVFAALPARLKTL"},"dna_sequence":{"accession":"LC732549.1","fmin":"0","fmax":"795","strand":"+","sequence":"ATGCCCCGTATGCTGTTGTCCGGTCTGCTTGCCGCCGGCCTCTTCTGTGCACTGCCTGCCAGCGCCGCTTCTGGCTGCATGCTGTTTGCCGATGGCACCGGCAAACCCGTCAGCACCCAGGGGGACTGTGCCGCCCAGTTGACCCCGGCCTCCACCTTCAAGATCCCGCTGGCACTGATGGGCTATGACAGCGGCTTTCTGGTGGATGAACAACTGCCGGCCCTGCCGTTCAAGGCCGGTGATCCTGATTTCCTGCCGGAGTGGAAACAGACCACCACCCCGAGCAGCTGGATGCAATTCTCGGTCATCTGGTACTCGCAGCGCCTCACCGAGTGGCTGGGAGAGGCTCGCTTCCAGCACTACGTGGACAGCTTCGACTACGGCAACCGGGATCTCGAAGGCAACCCGGGCAAGCACGACGGTCTGACCCAAGCCTGGCTCAGCACCAGCCTCGCCATCAGCCCCCAGGAGCAAGCCCGCTTCCTTGGCAAGATGGTGAGCGGCAAGCTACCGGTCTCCGCCCAGACCCTGCGCCATACCGCCAACCTGATGCGTCAGCCCGACATCGACGGTTGGCAGATCCACGGCAAGACCGGCATGGGCTACCCCAAGCTGCTGGATGGCAGCCTGGACAGGGAGCAGCAGATCGGCTGGTTCGTCGGCTGGGCCAGCAAACAGGACAAGACGCTCATCTTCGTCCACACCGTTATCCAGAAGCCGGGCACGCAGTTCGCTTCCCTCAGGGCCAGGGAGGAGGTGTTCGCCGCCCTGCCGGCCCGGTTGAAGACACTCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36936","NCBI_taxonomy_name":"Aeromonas caviae","NCBI_taxonomy_id":"648"}}}},"ARO_accession":"3008573","ARO_id":"47365","ARO_name":"OXA-1155","CARD_short_name":"OXA-1155","ARO_description":"Class D beta-lactamase OXA-1155.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7992":{"model_id":"7992","model_name":"OXA-1156","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10819":{"protein_sequence":{"accession":"BDS51120.1","sequence":"MPRMLLSGLLAAGLFCALPASAASGCMLFADGTGKPVSTQGDCAAQLTPASTFKIPLALMGYDSGFLVDEQLPALPFKAGDPDFLPEWKQTTTPSSWMKNSVIWYSQRLTEWLGEARFQHYVDSFDYGNRDLEGNPGKHDGLTQAWLSASLAISPQEQARFLGKMVSGKLPVSAQTLRHTANLMRQPDIDGWQIHGKTGMGYPKLLDGSLDREQQIGWFVGWASKQDKTLIFVHTVIQKPGKQFASIKAKEEVLAALPDQLKHL"},"dna_sequence":{"accession":"LC732550.1","fmin":"0","fmax":"795","strand":"+","sequence":"ATGCCCCGTATGCTGTTGTCCGGTCTGCTTGCCGCTGGCCTCTTCTGTGCACTGCCTGCCAGCGCCGCTTCTGGCTGCATGCTGTTTGCGGATGGCACCGGCAAACCCGTCAGCACCCAGGGGGACTGTGCCGCCCAGTTGACCCCGGCCTCCACCTTCAAGATCCCGCTGGCACTGATGGGCTATGACAGCGGCTTCCTGGTGGATGAACAACTGCCGGCCCTGCCGTTCAAGGCCGGTGATCCTGATTTCCTGCCGGAGTGGAAACAGACCACCACCCCGAGCAGTTGGATGAAGAACTCCGTCATCTGGTATTCCCAGCGCCTCACCGAGTGGCTGGGAGAGGCTCGCTTCCAGCACTACGTGGACAGCTTCGACTACGGCAACCGGGATCTCGAAGGCAACCCGGGCAAGCACGACGGTCTGACCCAGGCCTGGCTCAGCGCCAGCCTCGCCATCAGCCCCCAGGAGCAAGCCCGCTTCCTTGGCAAGATGGTGAGCGGCAAGCTGCCGGTCTCCGCCCAGACCCTGCGCCATACCGCCAACCTGATGCGTCAGCCCGACATCGACGGTTGGCAGATCCACGGCAAGACCGGCATGGGTTACCCCAAGCTGCTGGATGGCAGCCTGGACAGGGAGCAGCAGATCGGCTGGTTCGTCGGCTGGGCCAGCAAACAGGACAAAACGCTCATCTTCGTCCACACCGTTATCCAGAAGCCGGGCAAGCAGTTCGCCTCCATCAAGGCGAAAGAGGAGGTGCTGGCTGCCCTGCCTGATCAGCTCAAGCATCTCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36936","NCBI_taxonomy_name":"Aeromonas caviae","NCBI_taxonomy_id":"648"}}}},"ARO_accession":"3008574","ARO_id":"47366","ARO_name":"OXA-1156","CARD_short_name":"OXA-1156","ARO_description":"Class D beta-lactamase OXA-1156.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7993":{"model_id":"7993","model_name":"OXA-1157","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10820":{"protein_sequence":{"accession":"BDS51121.1","sequence":"MSRLLLSSLLAAGLLAALPASAASGCFLYADGNGQTLSSEGDCSSQLQPASTFKIPLALMGYDSGYLVDEEHPALPYKPSYDGWLPAWRETTTPRRWETYSVVWFSQQITEWLGMERFQQYVDRFDYGNRDLSGNPGKHDGLTQAWLSSSLAISPEEQARFLGKMLSGKLPVSAQTLQYTTNILKVNEIDGWQIHGKTGMGYPKKLDGSLNRDQQIGWFVGWASKPGKQLLFVHTVVQKPGKQFASLKAKEEVLAALPGKLKTL"},"dna_sequence":{"accession":"LC732551.1","fmin":"0","fmax":"795","strand":"+","sequence":"ATGTCCCGCCTGCTTCTCTCCAGCCTGCTGGCTGCCGGTTTGCTCGCAGCCCTGCCTGCCTCCGCCGCCAGCGGCTGCTTTCTCTATGCTGACGGCAACGGCCAGACCCTCTCCAGCGAAGGGGACTGCTCCAGCCAGCTGCAGCCCGCGTCCACCTTCAAGATCCCGCTGGCGCTGATGGGTTACGACAGTGGCTATCTGGTGGATGAAGAGCATCCGGCACTGCCTTACAAACCGAGCTATGACGGCTGGCTGCCCGCCTGGCGTGAAACCACCACCCCGCGCCGCTGGGAAACCTACTCGGTCGTCTGGTTCTCCCAGCAGATCACCGAATGGCTGGGGATGGAGCGCTTCCAGCAATATGTCGACCGCTTCGACTACGGCAACCGGGATCTCTCCGGCAATCCGGGCAAACATGACGGCCTGACCCAGGCCTGGCTCAGCTCCAGCCTCGCCATCAGTCCGGAGGAGCAGGCCCGCTTCCTCGGCAAGATGCTCAGCGGCAAGCTGCCGGTTTCGGCGCAGACCCTGCAGTACACCACCAATATCCTCAAGGTGAACGAGATCGACGGCTGGCAGATCCACGGCAAAACCGGCATGGGCTACCCGAAGAAGCTGGATGGCAGCCTCAACCGCGATCAGCAGATCGGCTGGTTCGTCGGCTGGGCCAGCAAACCGGGCAAACAGCTGCTCTTCGTCCATACCGTGGTGCAAAAGCCCGGCAAGCAGTTCGCCTCCCTCAAGGCGAAAGAAGAGGTGCTGGCCGCATTGCCCGGGAAGCTGAAGACCCTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39677","NCBI_taxonomy_name":"Aeromonas veronii","NCBI_taxonomy_id":"654"}}}},"ARO_accession":"3008575","ARO_id":"47367","ARO_name":"OXA-1157","CARD_short_name":"OXA-1157","ARO_description":"OXA-12 family class D beta-lactamase OXA-1157.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46488":{"category_aro_accession":"3007699","category_aro_cvterm_id":"46488","category_aro_name":"OXA-12-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-12.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7994":{"model_id":"7994","model_name":"OXA-1158","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10821":{"protein_sequence":{"accession":"BDS51122.1","sequence":"MPRMLLSGLLAAGLFCALPASAASGCMLFADGTGKPVSTQGDCAAQLTPASTFKIPLALMGYDSGFLVDEQLPALPFKAGDPDFLPEWKQTTTPSSWMQLSVIWYSQRLTEWLGEARFQHYVDSFDYGNRDLEGNPGKHDGLTQAWLSASLAISPQEQARFLGKMVSGKLPVSAKTLRHTANLMRQPDIDGWQIHGKTGMGYPKLLDGSLDREQQIGWFVGWASKQDKTLIFVHTVIQKPGKQFASLRAREEVFAALPARLKTL"},"dna_sequence":{"accession":"LC732552.1","fmin":"0","fmax":"795","strand":"+","sequence":"ATGCCCCGTATGCTGTTGTCCGGTCTGCTTGCCGCTGGCCTCTTCTGTGCACTGCCTGCCAGCGCCGCTTCTGGCTGCATGCTGTTTGCGGATGGAACCGGCAAACCCGTCAGCACCCAGGGGGACTGTGCCGCCCAGTTGACCCCGGCCTCCACCTTCAAGATCCCGCTGGCACTGATGGGCTATGACAGCGGCTTTCTGGTGGATGAACAGCTGCCGGCCCTGCCGTTCAAGGCCGGTGACCCTGATTTCCTGCCGGAATGGAAACAGACCACCACCCCGAGCAGCTGGATGCAATTATCGGTCATCTGGTACTCGCAGCGCCTCACCGAGTGGCTGGGAGAAGCTCGCTTCCAGCACTACGTGGACAGCTTCGACTACGGCAACCGGGATCTCGAAGGCAACCCGGGCAAGCACGACGGTCTGACCCAGGCCTGGCTCAGCGCCAGCCTCGCCATCAGCCCCCAGGAGCAAGCCCGCTTCCTTGGCAAGATGGTGAGCGGCAAGCTGCCGGTCTCCGCCAAGACCCTGCGCCATACCGCCAACCTGATGCGTCAGCCCGACATCGACGGTTGGCAGATCCACGGCAAGACCGGCATGGGTTACCCCAAGCTGCTGGATGGCAGCCTGGACAGGGAGCAGCAGATCGGCTGGTTCGTCGGCTGGGCCAGCAAACAGGACAAGACGCTCATCTTCGTCCACACCGTTATCCAGAAGCCGGGCAAGCAGTTCGCTTCCCTCAGGGCCAGGGAGGAGGTGTTCGCCGCCCTGCCGGCCCGGTTGAAGACACTCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36936","NCBI_taxonomy_name":"Aeromonas caviae","NCBI_taxonomy_id":"648"}}}},"ARO_accession":"3008576","ARO_id":"47368","ARO_name":"OXA-1158","CARD_short_name":"OXA-1158","ARO_description":"Class D beta-lactamase OXA-1158.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7995":{"model_id":"7995","model_name":"OXA-1159","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10822":{"protein_sequence":{"accession":"BDT38932.1","sequence":"MPRMLLSGLLAAGLFCALPASAASGCMLFADGTGKPVSTQGDCAAQLTPASTFKIPLALMGYDSGFLVDEQLPALPFKAGDPDFLPEWKQTTTPSSWMQFSVIWYSQRLTEWLGEARFQHYVDSFDYGNRDLEGNQGKHDGLTQAWLSASLAISPQEQARFLGKMVSGKLPVSAKTLRHTANLMRQPDIDGWQIHGKTGMGYPKLLDGSLDREQQIGWFVGWASKQDKTLIFVHTVIQKPGKQFASLRAREEVFAALPARLKTL"},"dna_sequence":{"accession":"LC733697.1","fmin":"0","fmax":"795","strand":"+","sequence":"ATGCCCCGTATGCTGTTGTCCGGTCTGCTTGCCGCCGGCCTCTTCTGTGCACTGCCTGCCAGCGCCGCTTCTGGCTGCATGCTGTTTGCCGATGGAACCGGCAAACCCGTCAGCACCCAGGGGGACTGTGCCGCCCAGTTGACCCCGGCCTCCACCTTCAAGATCCCGCTGGCACTGATGGGCTATGACAGCGGCTTCCTGGTGGATGAACAACTGCCGGCCCTGCCGTTCAAGGCCGGTGATCCTGATTTCCTGCCGGAGTGGAAACAGACCACCACCCCGAGCAGCTGGATGCAATTCTCGGTCATCTGGTACTCGCAGCGCCTCACCGAGTGGCTGGGAGAGGCTCGCTTCCAGCACTACGTGGACAGCTTCGACTACGGCAACCGGGATCTCGAAGGCAACCAGGGCAAGCACGACGGTCTGACCCAGGCCTGGCTCAGCGCCAGCCTCGCCATCAGCCCCCAGGAGCAAGCCCGCTTCCTTGGCAAGATGGTGAGCGGCAAGCTGCCGGTCTCCGCCAAGACCCTGCGCCATACCGCCAACCTGATGCGTCAGCCCGACATCGACGGTTGGCAGATCCACGGCAAGACCGGCATGGGTTACCCCAAGCTGCTGGATGGCAGCCTGGACAGGGAGCAGCAGATCGGCTGGTTCGTCGGCTGGGCCAGCAAACAGGACAAGACGCTCATCTTCGTCCACACCGTTATCCAGAAGCCGGGCAAGCAGTTCGCTTCCCTCAGGGCCAGGGAGGAGGTGTTCGCCGCCCTGCCGGCCCGGTTGAAGACACTCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36936","NCBI_taxonomy_name":"Aeromonas caviae","NCBI_taxonomy_id":"648"}}}},"ARO_accession":"3008577","ARO_id":"47369","ARO_name":"OXA-1159","CARD_short_name":"OXA-1159","ARO_description":"Class D beta-lactamase OXA-1159.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7996":{"model_id":"7996","model_name":"OXA-1160","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10823":{"protein_sequence":{"accession":"BDT38933.1","sequence":"MPRMLLSGLLAAGLFCALPASAASGCMLFADGTGKPVSTQGDCAAQLTPASTFKIPLALMGYDSGFLVDEQLPALPFKAGDPDFLPEWKQTTTPSSWMQFSVIWYSQRLTEWLGEARFQHYVDSFDYGNRDLEGNPGKHDGLTQAWLSTSLAISPQEQARFLGKMVSGKLPVSAQTLRHTANLMRQPDIDGWQIHGKTGMGYPKLLDGSLDREQQIGWFVGWASKQDKTLIFVHTVIQKPGKQFASLRAREEVFAALPARLKTL"},"dna_sequence":{"accession":"LC733698.1","fmin":"0","fmax":"795","strand":"+","sequence":"ATGCCCCGTATGCTGTTGTCCGGTCTGCTTGCCGCCGGCCTCTTCTGTGCACTGCCTGCCAGCGCCGCTTCTGGCTGCATGCTGTTTGCCGATGGCACCGGCAAACCCGTCAGCACCCAGGGGGACTGTGCCGCCCAGTTGACCCCGGCCTCCACCTTCAAGATCCCGCTGGCACTGATGGGCTATGACAGCGGCTTTCTGGTGGATGAACAACTGCCGGCCCTGCCGTTCAAGGCCGGTGATCCTGATTTCCTGCCGGAGTGGAAACAGACCACCACCCCGAGCAGCTGGATGCAATTCTCGGTCATCTGGTACTCGCAGCGCCTCACCGAGTGGCTGGGAGAGGCTCGCTTCCAGCACTACGTGGACAGCTTCGACTACGGCAACCGGGATCTCGAAGGCAACCCGGGCAAGCACGACGGTCTGACCCAGGCCTGGCTCAGCACCAGCCTCGCCATCAGCCCCCAGGAGCAAGCCCGCTTCCTTGGCAAGATGGTGAGCGGCAAGCTGCCGGTCTCCGCCCAGACCCTGCGCCATACCGCCAACCTGATGCGTCAGCCCGACATCGACGGTTGGCAGATCCACGGCAAGACCGGCATGGGCTACCCCAAGCTGCTGGATGGCAGCCTGGACAGGGAGCAGCAGATCGGCTGGTTCGTCGGCTGGGCCAGCAAACAGGACAAGACGCTCATCTTCGTCCACACCGTTATCCAGAAGCCGGGCAAGCAGTTCGCTTCCCTCAGGGCCAGGGAGGAGGTGTTCGCCGCCCTGCCGGCCCGGTTGAAGACACTCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36936","NCBI_taxonomy_name":"Aeromonas caviae","NCBI_taxonomy_id":"648"}}}},"ARO_accession":"3008578","ARO_id":"47370","ARO_name":"OXA-1160","CARD_short_name":"OXA-1160","ARO_description":"Class D beta-lactamase OXA-1160.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7997":{"model_id":"7997","model_name":"OXA-1161","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10824":{"protein_sequence":{"accession":"BDT38934.1","sequence":"MPRMLLSGLLAAGLFCALPASAASGCMLFADGTGKPVSTQGDCAAQLTPASTFKIPLALMGYDSGFLVDEQLPALPFKAGDPDFLPEWKQTTTPSSWMQFSVIWYSQRLTEWLGEARFQHYVDSFDYGNRDLEGNPGKHDGLTQAWLSASLAISPQEQARFLGKMVSGKLPVSAKTLRHTANLMRQPDIDGWQIHGKTGMGYPKLLDGSLDREQQIGWFVGWASKQDKTLIFVHTVIQKPGKQFASLRAREEVFAALPARLKTL"},"dna_sequence":{"accession":"LC733699.1","fmin":"0","fmax":"795","strand":"+","sequence":"ATGCCCCGTATGCTGTTGTCCGGTCTGCTTGCCGCTGGCCTCTTCTGTGCACTGCCTGCCAGCGCCGCTTCTGGCTGCATGCTGTTTGCGGATGGAACCGGCAAACCCGTCAGCACCCAGGGGGACTGTGCCGCCCAGTTGACCCCGGCCTCCACCTTCAAGATCCCGCTGGCACTGATGGGCTATGACAGCGGCTTTCTGGTGGATGAACAGCTGCCGGCCCTGCCGTTCAAGGCCGGTGACCCTGATTTCCTGCCGGAATGGAAACAGACCACCACCCCGAGCAGCTGGATGCAATTCTCGGTCATCTGGTACTCGCAGCGCCTCACCGAGTGGCTGGGAGAAGCTCGCTTCCAGCACTACGTGGACAGCTTCGACTACGGCAACCGGGATCTCGAAGGCAACCCGGGCAAGCACGACGGTCTGACCCAGGCCTGGCTCAGCGCCAGCCTCGCCATCAGCCCCCAGGAGCAAGCCCGCTTCCTTGGCAAGATGGTGAGCGGCAAGCTGCCGGTCTCCGCCAAGACCCTGCGCCATACCGCCAACCTGATGCGTCAGCCCGACATCGACGGTTGGCAGATCCACGGCAAGACCGGCATGGGTTACCCCAAGCTGCTGGATGGCAGCCTGGACAGGGAGCAGCAGATCGGCTGGTTCGTCGGCTGGGCCAGCAAACAGGACAAGACGCTCATCTTCGTCCACACCGTTATCCAGAAGCCGGGCAAGCAGTTCGCTTCCCTCAGGGCCAGGGAGGAGGTGTTCGCCGCCCTGCCGGCCCGGTTGAAGACACTCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36936","NCBI_taxonomy_name":"Aeromonas caviae","NCBI_taxonomy_id":"648"}}}},"ARO_accession":"3008579","ARO_id":"47371","ARO_name":"OXA-1161","CARD_short_name":"OXA-1161","ARO_description":"Class D beta-lactamase OXA-1161.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7998":{"model_id":"7998","model_name":"OXA-1162","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10825":{"protein_sequence":{"accession":"BDT38935.1","sequence":"MSRLLLSSLLAAGLLAALPASAASGCFLYADGNGQTLSSEGDCSSQLPPASTFKIPLALMGYDSGYLVDEEHPALPYKPSYDGWLPAWRETTTPRRWETYSVVWFSQQITEWLGMERFQQYVDRFDYGNRDLSGNPGKHDGLTQAWLSSSLAISPEEQARFLGKMLSGKLPVSAQTLQYTANILKVSEIDGWQIHGKTGMGYPKKLDGSLNRDQQIGWFVGWASKPGKQLIFVHTVVQKPGKQFASIKAKEEVLAALPAQLKKQ"},"dna_sequence":{"accession":"LC733700.1","fmin":"0","fmax":"795","strand":"+","sequence":"ATGTCCCGCCTGCTTCTCTCCAGCCTGCTGGCTGCCGGTCTGCTCGCAGCCCTGCCTGCCTCCGCCGCCAGCGGCTGCTTTCTCTATGCTGACGGCAACGGCCAGACCCTCTCCAGTGAAGGGGACTGCTCCAGCCAGCTGCCGCCCGCGTCCACCTTCAAGATCCCGCTGGCGCTGATGGGTTACGACAGCGGCTATCTGGTGGATGAAGAGCATCCGGCACTGCCTTACAAACCGAGCTATGACGGCTGGCTGCCCGCCTGGCGCGAAACCACTACCCCGCGCCGCTGGGAAACCTACTCGGTGGTCTGGTTCTCCCAGCAGATCACCGAATGGCTAGGGATGGAGCGCTTCCAACAATATGTCGACCGCTTCGACTACGGCAACCGGGATCTCTCCGGCAATCCGGGCAAACATGACGGCCTGACCCAGGCCTGGCTCAGCTCCAGCCTCGCCATCAGTCCGGAGGAGCAGGCCCGCTTCCTCGGCAAGATGCTGAGCGGCAAGCTGCCGGTCTCGGCGCAGACCCTGCAGTACACCGCCAATATCCTCAAGGTGAGCGAGATCGACGGCTGGCAGATCCACGGCAAAACCGGCATGGGCTACCCGAAGAAGCTGGATGGCAGCCTCAACCGCGATCAGCAGATCGGCTGGTTCGTCGGCTGGGCCAGCAAACCGGGCAAGCAGCTGATCTTCGTCCATACCGTGGTGCAAAAGCCAGGCAAGCAGTTCGCCTCTATCAAGGCTAAAGAAGAGGTGCTGGCCGCCCTGCCTGCACAACTTAAAAAGCAGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39677","NCBI_taxonomy_name":"Aeromonas veronii","NCBI_taxonomy_id":"654"}}}},"ARO_accession":"3008580","ARO_id":"47372","ARO_name":"OXA-1162","CARD_short_name":"OXA-1162","ARO_description":"OXA-12 family class D beta-lactamase OXA-1162.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46488":{"category_aro_accession":"3007699","category_aro_cvterm_id":"46488","category_aro_name":"OXA-12-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-12.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7999":{"model_id":"7999","model_name":"OXA-1163","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10826":{"protein_sequence":{"accession":"BDT38936.1","sequence":"MPRMLLSGLLAAGLFCALPASAASGCMLFADGTGKPVSTQGDCAAQLTPASTFKIPLALMGYDSGFLVDEQLPALPFKAGDPDFLPEWKQTTTPSSWMQFSVIWYSQRLTEWLGEARFQHYVDSFDYGNRDLEGNPGKHDGLTQAWLSASLAISPQEQARFLGKMVSGKLPVSAQTLRHTANLMRQPDIDGWQIHGKTGMGYPKLLDGSLDREQQIGWFVGWASKQDKTLIFVHTVIQKPGKQFASLRAREEVFAALPARLKTL"},"dna_sequence":{"accession":"LC733701.1","fmin":"0","fmax":"795","strand":"+","sequence":"ATGCCCCGTATGCTGTTGTCCGGTCTGCTTGCCGCCGGCCTCTTCTGTGCACTGCCTGCCAGCGCCGCTTCTGGCTGCATGCTGTTTGCCGATGGCACCGGCAAACCCGTCAGCACCCAGGGGGACTGTGCCGCCCAGTTGACCCCGGCCTCCACCTTCAAGATCCCGCTGGCACTGATGGGCTATGACAGCGGCTTTCTGGTGGATGAACAACTGCCGGCCCTGCCGTTCAAGGCCGGTGACCCTGATTTCCTGCCGGAGTGGAAACAGACCACCACCCCGAGCAGCTGGATGCAATTCTCGGTCATCTGGTACTCGCAGCGCCTCACCGAGTGGCTGGGAGAAGCTCGCTTCCAGCACTACGTGGACAGCTTCGACTACGGCAACCGGGATCTTGAAGGCAACCCGGGCAAGCACGACGGTCTGACCCAGGCCTGGCTCAGCGCCAGCCTTGCCATCAGCCCCCAGGAGCAAGCCCGCTTCCTCGGCAAGATGGTGAGCGGCAAGCTGCCGGTCTCCGCCCAGACCCTGCGCCATACCGCCAACCTGATGCGTCAGCCCGACATCGACGGTTGGCAGATCCACGGCAAGACCGGCATGGGTTACCCCAAGCTGCTGGATGGCAGCCTGGACAGGGAGCAGCAGATCGGCTGGTTCGTCGGCTGGGCCAGCAAACAGGACAAGACGCTCATCTTCGTCCACACCGTTATCCAGAAGCCGGGCAAGCAGTTCGCTTCCCTCAGGGCCAGGGAGGAGGTGTTCGCCGCCCTGCCGGCCCGGTTGAAGACACTCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36936","NCBI_taxonomy_name":"Aeromonas caviae","NCBI_taxonomy_id":"648"}}}},"ARO_accession":"3008581","ARO_id":"47373","ARO_name":"OXA-1163","CARD_short_name":"OXA-1163","ARO_description":"Class D beta-lactamase OXA-1163.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8000":{"model_id":"8000","model_name":"OXA-1164","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10827":{"protein_sequence":{"accession":"UZF98455.1","sequence":"MTKKALFFAIGTMFLSACSFNTVEQHQIQSISTNKNSKKIKSLFDQAQTEGVLVIKRGQIEEVYGNDLKRASTEYVPASTFKMLNALIGLEHHKATPTEVFKWDGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMSKEVKRIGFGNADIGSKVHDFWLVGPLKITPQQEAQFAYELAHKTLPFSKNVQEQVQSMLFIEEKNGRKIYAKSGWGWDVDPQVGWFTGWVVQSQGEIIAFSLNLEMKKGIPSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"OP745004.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGACTAAAAAAGCTCTTTTCTTTGCCATTGGTACGATGTTTTTATCGGCATGTTCTTTTAATACGGTAGAACAGCATCAAATACAGTCAATTTCTACCAATAAAAACTCAAAGAAAATTAAATCATTGTTTGATCAAGCACAAACTGAAGGTGTTTTAGTTATAAAACGTGGGCAAATAGAGGAAGTCTATGGCAATGATCTTAAAAGAGCATCAACCGAATATGTTCCCGCCTCTACCTTTAAGATGTTAAATGCTTTGATTGGACTTGAGCATCATAAAGCAACACCAACTGAAGTGTTTAAATGGGATGGGCAAAAGCGTTTATTTCCCGATTGGGAAAAAGACATGACATTAGGCGATGCGATGAAAGCTTCTGCTATTCCAGTTTATCAGGAACTAGCTCGACGAATTGGCCTTGATCTTATGTCTAAAGAGGTAAAACGCATTGGTTTCGGTAATGCTGATATTGGTTCAAAAGTACATGATTTTTGGCTTGTTGGTCCACTTAAAATTACACCTCAACAAGAAGCCCAGTTTGCTTATGAACTAGCCCATAAAACTCTTCCTTTTAGCAAAAATGTGCAAGAACAAGTTCAATCTATGCTGTTCATAGAAGAAAAAAATGGACGAAAAATTTATGCCAAAAGTGGTTGGGGATGGGATGTTGACCCACAAGTTGGTTGGTTTACAGGCTGGGTCGTTCAATCTCAGGGAGAAATTATAGCTTTCTCACTTAATTTAGAAATGAAGAAAGGCATACCTAGCTCTATTCGAAAAGAAATTGCTTATAAAGGATTGGAACAACTCGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3008582","ARO_id":"47374","ARO_name":"OXA-1164","CARD_short_name":"OXA-1164","ARO_description":"OXA-213 family carbapenem-hydrolyzing class D beta-lactamase OXA-1164.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46495":{"category_aro_accession":"3007706","category_aro_cvterm_id":"46495","category_aro_name":"OXA-213-like beta-lactamase","category_aro_description":"OXA-213-like enzymes have been identified to be intrinsic to A. calcoaceticus and have been subsequently detected in A. pittii. Phylogenetic analysis of OXA-213-like proteins identified two distinct subgroups within the OXA family. The first group was linked to A. pittii and the second group to A. calcoaceticus. The carbapenemase activity of these OXAs may be related to the species-dependent effect.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8001":{"model_id":"8001","model_name":"OXA-1165","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10828":{"protein_sequence":{"accession":"UZF98457.1","sequence":"MTKKALFFAIGTMFLSACSFNTVQQHQIQSISTNKNSEKIKSLFDQAQTEGVLVIKRGQTEEIYGNDLKRASTEYVPASTFKMLNALIGLEHHKTTPTEVFKWDGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMSKEVKRIGFGNADIGSKVDDFWLVGPLKITPQQEAQFAYELAHKTLPFSKNVQEQVQSMLFIEEKNGRKIYAKSGWGWDVEPQVGWLTGWVVQPQGKIVAFSLNLEMKKGIPSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"OP745006.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGACTAAAAAAGCTCTTTTCTTTGCCATTGGTACGATGTTTTTATCGGCATGTTCTTTTAATACCGTACAACAACATCAAATACAGTCAATTTCTACCAATAAAAACTCAGAGAAAATTAAATCATTGTTTGATCAAGCACAAACTGAAGGTGTTTTAGTTATAAAACGTGGGCAAACAGAGGAAATCTATGGCAATGATCTTAAAAGAGCATCAACCGAATATGTTCCCGCCTCTACCTTTAAGATGTTAAATGCTTTGATTGGACTTGAGCATCATAAAACAACACCAACTGAAGTGTTTAAATGGGATGGGCAAAAGCGTTTGTTTCCTGATTGGGAAAAGGACATGACTCTAGGCGATGCGATGAAAGCTTCTGCTATTCCAGTTTATCAGGAACTAGCTCGACGAATTGGCCTTGATCTTATGTCTAAAGAGGTAAAACGCATTGGTTTCGGTAATGCTGATATTGGTTCAAAAGTAGATGATTTTTGGCTTGTTGGCCCACTTAAAATTACACCTCAACAAGAAGCCCAGTTTGCTTATGAACTAGCCCATAAAACTCTTCCTTTTAGCAAAAATGTGCAAGAACAAGTTCAATCTATGCTGTTCATAGAAGAAAAAAATGGACGGAAAATTTATGCCAAAAGTGGTTGGGGATGGGATGTGGAGCCTCAAGTGGGCTGGTTAACAGGCTGGGTCGTTCAACCTCAAGGAAAAATTGTAGCGTTCTCACTCAATTTAGAAATGAAAAAAGGCATACCTAGTTCTATTCGAAAAGAAATTGCTTATAAGGGATTAGAGCAGCTAGGTATTTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3008583","ARO_id":"47375","ARO_name":"OXA-1165","CARD_short_name":"OXA-1165","ARO_description":"OXA-213 family carbapenem-hydrolyzing class D beta-lactamase OXA-1165.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46495":{"category_aro_accession":"3007706","category_aro_cvterm_id":"46495","category_aro_name":"OXA-213-like beta-lactamase","category_aro_description":"OXA-213-like enzymes have been identified to be intrinsic to A. calcoaceticus and have been subsequently detected in A. pittii. Phylogenetic analysis of OXA-213-like proteins identified two distinct subgroups within the OXA family. The first group was linked to A. pittii and the second group to A. calcoaceticus. The carbapenemase activity of these OXAs may be related to the species-dependent effect.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8002":{"model_id":"8002","model_name":"OXA-1166","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10829":{"protein_sequence":{"accession":"UZF98459.1","sequence":"MTKKALFFAIGTMFLSACSFNTVEQHQIQSISTNKNSEKIKSLFDQAQTEGVLVIKRGQIEEVYGNALKRASTEYVPASTFKMLNALIGLEHHKATPTEVFKWDGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMSKEVKRIGFGNADIGSKVDDFWLVGPLKITPQQEAQFAYELAHKTLPFSKNMQEQVQSMLFIEEKNGRKIYAKSGWGWDVEPQVGWLTGWVVQPQGEIIAFSLNLEMKKGIPSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"OP745008.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGACTAAAAAAGCTCTCTTCTTTGCCATTGGTACGATGTTTTTATCGGCATGTTCTTTTAATACGGTAGAACAGCATCAAATACAGTCAATTTCTACCAATAAAAACTCAGAGAAAATTAAATCATTGTTTGATCAAGCACAAACTGAAGGTGTTTTAGTTATAAAACGTGGGCAAATAGAGGAAGTCTATGGCAATGCTCTTAAAAGAGCATCAACCGAATATGTTCCCGCCTCTACCTTTAAAATGTTAAATGCTTTGATTGGACTTGAGCATCATAAAGCAACGCCAACTGAAGTGTTTAAATGGGATGGGCAAAAGCGTTTATTTCCCGATTGGGAAAAAGACATGACATTAGGCGATGCGATGAAAGCTTCTGCTATTCCAGTTTATCAGGAACTAGCTCGACGAATTGGTCTTGATCTTATGTCTAAAGAGGTAAAACGCATTGGTTTCGGTAATGCTGATATTGGTTCAAAAGTAGATGATTTTTGGCTTGTTGGTCCACTTAAAATTACACCTCAACAAGAAGCCCAGTTTGCTTATGAACTAGCCCATAAAACTCTTCCTTTTAGCAAAAATATGCAAGAACAAGTTCAATCTATGCTGTTCATAGAAGAAAAAAATGGACGGAAAATTTATGCCAAAAGTGGTTGGGGATGGGATGTGGAGCCTCAAGTGGGCTGGTTAACAGGCTGGGTCGTTCAACCTCAGGGAGAAATTATAGCTTTCTCACTTAATTTAGAAATGAAGAAAGGCATACCTAGTTCTATTCGAAAAGAAATTGCTTATAAAGGATTAGAGCAGCTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3008584","ARO_id":"47376","ARO_name":"OXA-1166","CARD_short_name":"OXA-1166","ARO_description":"OXA-213 family carbapenem-hydrolyzing class D beta-lactamase OXA-1166.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46495":{"category_aro_accession":"3007706","category_aro_cvterm_id":"46495","category_aro_name":"OXA-213-like beta-lactamase","category_aro_description":"OXA-213-like enzymes have been identified to be intrinsic to A. calcoaceticus and have been subsequently detected in A. pittii. Phylogenetic analysis of OXA-213-like proteins identified two distinct subgroups within the OXA family. The first group was linked to A. pittii and the second group to A. calcoaceticus. The carbapenemase activity of these OXAs may be related to the species-dependent effect.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8003":{"model_id":"8003","model_name":"OXA-1167","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10830":{"protein_sequence":{"accession":"UZH96289.1","sequence":"MRVLALSAVFLVASIIGMPAVAKEWQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGQTRDIATWNRDHNLITAMKYSVVPVYQEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISATEQISFLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYSTSIEPKIGWWVGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP"},"dna_sequence":{"accession":"OP802841.1","fmin":"0","fmax":"798","strand":"+","sequence":"ATGCGTGTATTAGCCTTATCGGCTGTGTTTTTGGTGGCATCGATTATCGGAATGCCTGCGGTAGCAAAGGAATGGCAAGAAAACAAAAGTTGGAATGCTCACTTTACTGAACATAAATCACAGGGCGTAGTTGTGCTCTGGAATGAGAATAAGCAGCAAGGATTTACCAATAATCTTAAACGGGCGAACCAAGCATTTTTACCCGCATCTACCTTTAAAATTCCCAATAGCTTGATCGCCCTCGATTTGGGCGTGGTTAAGGATGAACACCAAGTCTTTAAGTGGGATGGACAGACGCGCGATATCGCCACTTGGAATCGCGATCATAATCTAATCACCGCGATGAAATATTCAGTTGTGCCTGTTTATCAAGAATTTGCCCGCCAAATTGGCGAGGCACGTATGAGCAAGATGCTACATGCTTTCGATTATGGTAATGAGGACATTTCGGGCAATGTAGACAGTTTCTGGCTCGACGGTGGTATTCGAATTTCGGCCACGGAGCAAATCAGCTTTTTAAGAAAGCTGTATCACAATAAGTTACACGTATCGGAGCGCAGCCAGCGTATTGTCAAACAAGCCATGCTGACCGAAGCCAATGGTGACTATATTATTCGGGCTAAAACTGGATACTCGACTAGTATCGAACCTAAGATTGGCTGGTGGGTCGGTTGGGTTGAACTTGATGATAATGTGTGGTTTTTTGCGATGAATATGGATATGCCCACATCGGATGGTTTAGGGCTGCGCCAAGCCATCACAAAAGAAGTGCTCAAACAGGAAAAAATTATTCCCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008585","ARO_id":"47377","ARO_name":"OXA-1167","CARD_short_name":"OXA-1167","ARO_description":"OXA-48 family class D beta-lactamase OXA-1167.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46510":{"category_aro_accession":"3007721","category_aro_cvterm_id":"46510","category_aro_name":"OXA-48-like beta-lactamase","category_aro_description":"OXA-48-type beta-lactamases are now routinely encountered in bacterial infections caused by carbapenam-resistant Enterobacterales. OXA-48-like proteins confer resistance to penicillin (which is efficiently hydrolyzed) and carbapenam antibiotics (which is more slowly broken down). The spectrum of activity of these variants varies, with some hydrolyzing expanded-spectrum oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8004":{"model_id":"8004","model_name":"OXA-1168","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10831":{"protein_sequence":{"accession":"UZQ18795.1","sequence":"MKTFAAYVITACLSSTALASSITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNNLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLSLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGISGGIDKFWLEGQLRISAVNQVEFLESLFLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKGTEVYFFAFNMDIDNENKLPLRKSIPTKIMASEGIIGG"},"dna_sequence":{"accession":"OP806895.1","fmin":"0","fmax":"813","strand":"+","sequence":"ATGAAAACATTTGCCGCATATGTAATTACTGCGTGTCTTTCAAGTACGGCATTAGCTAGTTCAATTACAGAAAATACGTCTTGGAACAAAGAGTTCTCTGCCGAAGCCGTCAATGGTGTTTTCGTGCTTTGTAAAAGTAGCAGTAAATCCTGCGCTACCAATAACTTAGCTCGTGCATCAAAGGAATATCTTCCAGCATCAACATTTAAGATCCCCAACGCAATTATCGGCCTAGAAACTGGTGTCATAAAGAATGAGCATCAGGTTTTCAAATGGGACGGAAAGCCAAGAGCCATGAAACAATGGGAAAGAGACTTGAGCTTAAGAGGGGCAATACAAGTTTCAGCGGTTCCCGTATTTCAACAAATCGCCAGAGAAGTTGGCGAAGTAAGAATGCAGAAATACCTTAAAAAATTTTCATATGGCAACCAGAATATCAGTGGTGGTATCAGTGGTGGCATTGACAAATTCTGGTTGGAGGGTCAGCTAAGAATTTCCGCAGTTAATCAAGTGGAGTTTCTAGAGTCTCTATTTTTAAATAAATTGTCAGCATCAAAAGAAAATCAGCTAATAGTAAAAGAGGCTTTGGTAACGGAGGCTGCGCCTGAATATCTTGTGCATTCAAAAACTGGTTTTTCTGGTGTGGGAACTGAGTCAAATCCTGGTGTCGCATGGTGGGTTGGTTGGGTTGAGAAGGGAACAGAGGTTTACTTTTTCGCCTTTAACATGGATATAGACAACGAAAATAAGTTGCCGCTAAGAAAATCCATTCCCACCAAAATCATGGCAAGTGAGGGCATCATTGGTGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008586","ARO_id":"47378","ARO_name":"OXA-1168","CARD_short_name":"OXA-1168","ARO_description":"OXA-10 family class D beta-lactamase OXA-1168.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46486":{"category_aro_accession":"3007697","category_aro_cvterm_id":"46486","category_aro_name":"OXA-10-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-10.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8005":{"model_id":"8005","model_name":"OXA-1169","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10832":{"protein_sequence":{"accession":"UZQ18796.1","sequence":"MKTFAAYVITACLSSTALASSITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNNLARASKEYLPASTFKIPTAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLSLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLFLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKGTEVYFFAFNMDIDNENKLPLRKSIPTKIMASEGIIGG"},"dna_sequence":{"accession":"OP806896.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGAAAACATTTGCCGCATATGTAATTACTGCGTGTCTTTCAAGTACGGCATTAGCTAGTTCAATTACAGAAAATACGTCTTGGAACAAAGAGTTCTCTGCCGAAGCCGTCAATGGTGTTTTCGTGCTTTGTAAAAGTAGCAGTAAATCCTGCGCTACCAATAACTTAGCTCGTGCATCAAAGGAATATCTTCCAGCATCAACATTTAAGATCCCCACCGCAATTATCGGCCTAGAAACTGGTGTCATAAAGAATGAGCATCAGGTTTTCAAATGGGACGGAAAGCCAAGAGCCATGAAACAATGGGAAAGAGACTTGAGCTTAAGAGGGGCAATACAAGTTTCAGCGGTTCCCGTATTTCAACAAATCGCCAGAGAAGTTGGCGAAGTAAGAATGCAGAAATACCTTAAAAAATTTTCATATGGCAACCAGAATATCAGTGGTGGCATTGACAAATTCTGGTTGGAGGGTCAGCTAAGAATTTCCGCAGTTAATCAAGTGGAGTTTCTAGAGTCTCTATTTTTAAATAAATTGTCAGCATCAAAAGAAAATCAGCTAATAGTAAAAGAGGCTTTGGTAACGGAGGCTGCGCCTGAATATCTTGTGCATTCAAAAACTGGTTTTTCTGGTGTGGGAACTGAGTCAAATCCTGGTGTCGCATGGTGGGTTGGTTGGGTTGAGAAGGGAACAGAGGTTTACTTTTTCGCCTTTAACATGGATATAGACAACGAAAATAAGTTGCCGCTAAGAAAATCCATTCCCACCAAAATCATGGCAAGTGAGGGCATCATTGGTGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008587","ARO_id":"47379","ARO_name":"OXA-1169","CARD_short_name":"OXA-1169","ARO_description":"OXA-10 family class D beta-lactamase OXA-1169.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46486":{"category_aro_accession":"3007697","category_aro_cvterm_id":"46486","category_aro_name":"OXA-10-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-10.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8006":{"model_id":"8006","model_name":"OXA-1170","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10833":{"protein_sequence":{"accession":"UZQ18797.1","sequence":"MKTFAAYVITACLSSTALASSITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNNLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLSLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFRLEGQLRISAVNQVEFLESLFLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKGTEVYFFAFNMDIDNENKLPLRKSIPTKIMASEGIIGG"},"dna_sequence":{"accession":"OP806897.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGAAAACATTTGCCGCATATGTAATTACTGCGTGTCTTTCAAGTACGGCATTAGCTAGTTCAATTACAGAAAATACGTCTTGGAACAAAGAGTTCTCTGCCGAAGCCGTCAATGGTGTTTTCGTGCTTTGTAAAAGTAGCAGTAAATCCTGCGCTACCAATAACTTAGCTCGTGCATCAAAGGAATATCTTCCAGCATCAACATTTAAGATCCCCAACGCAATTATCGGCCTAGAAACTGGTGTCATAAAGAATGAGCATCAGGTTTTCAAATGGGACGGAAAGCCAAGAGCCATGAAACAATGGGAAAGAGACTTGAGCTTAAGAGGGGCAATACAAGTTTCAGCGGTTCCCGTATTTCAACAAATCGCCAGAGAAGTTGGCGAAGTAAGAATGCAGAAATACCTTAAAAAATTTTCATATGGCAACCAGAATATCAGTGGTGGCATTGACAAATTCAGGTTGGAGGGTCAGCTAAGAATTTCCGCAGTTAATCAAGTGGAGTTTCTAGAGTCTCTATTTTTAAATAAATTGTCAGCATCAAAAGAAAATCAGCTAATAGTAAAAGAGGCTTTGGTAACGGAGGCTGCGCCTGAATATCTTGTGCATTCAAAAACTGGTTTTTCTGGTGTGGGAACTGAGTCAAATCCTGGTGTCGCATGGTGGGTTGGTTGGGTTGAGAAGGGAACAGAGGTTTACTTTTTCGCCTTTAACATGGATATAGACAACGAAAATAAGTTGCCGCTAAGAAAATCCATTCCCACCAAAATCATGGCAAGTGAGGGCATCATTGGTGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008588","ARO_id":"47380","ARO_name":"OXA-1170","CARD_short_name":"OXA-1170","ARO_description":"OXA-10 family class D beta-lactamase OXA-1170.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46486":{"category_aro_accession":"3007697","category_aro_cvterm_id":"46486","category_aro_name":"OXA-10-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-10.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8007":{"model_id":"8007","model_name":"OXA-1171","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10834":{"protein_sequence":{"accession":"UZQ18798.1","sequence":"MKTFAAYVITACLSSTALASSITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNNLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLSLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGKQNISGGIDKFWLEGQLRISAVNQVEFLESLFLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKGTEVYFFAFNMDIDNENKLPLRKSIPTKIMASEGIIGG"},"dna_sequence":{"accession":"OP806898.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGAAAACATTTGCCGCATATGTAATTACTGCGTGTCTTTCAAGTACGGCATTAGCTAGTTCAATTACAGAAAATACGTCTTGGAACAAAGAGTTCTCTGCCGAAGCCGTCAATGGTGTTTTCGTGCTTTGTAAAAGTAGCAGTAAATCCTGCGCTACCAATAACTTAGCTCGTGCATCAAAGGAATATCTTCCAGCATCAACATTTAAGATCCCCAACGCAATTATCGGCCTAGAAACTGGTGTCATAAAGAATGAGCATCAGGTTTTCAAATGGGACGGAAAGCCAAGAGCCATGAAACAATGGGAAAGAGACTTGAGCTTAAGAGGGGCAATACAAGTTTCAGCGGTTCCCGTATTTCAACAAATCGCCAGAGAAGTTGGCGAAGTAAGAATGCAGAAATACCTTAAAAAATTTTCATATGGCAAGCAGAATATCAGTGGTGGCATTGACAAATTCTGGTTGGAGGGTCAGCTAAGAATTTCCGCAGTTAATCAAGTGGAGTTTCTAGAGTCTCTATTTTTAAATAAATTGTCAGCATCAAAAGAAAATCAGCTAATAGTAAAAGAGGCTTTGGTAACGGAGGCTGCGCCTGAATATCTTGTGCATTCAAAAACTGGTTTTTCTGGTGTGGGAACTGAGTCAAATCCTGGTGTCGCATGGTGGGTTGGTTGGGTTGAGAAGGGAACAGAGGTTTACTTTTTCGCCTTTAACATGGATATAGACAACGAAAATAAGTTGCCGCTAAGAAAATCCATTCCCACCAAAATCATGGCAAGTGAGGGCATCATTGGTGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008589","ARO_id":"47381","ARO_name":"OXA-1171","CARD_short_name":"OXA-1171","ARO_description":"OXA-10 family class D beta-lactamase OXA-1171.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46486":{"category_aro_accession":"3007697","category_aro_cvterm_id":"46486","category_aro_name":"OXA-10-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-10.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. 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The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8008":{"model_id":"8008","model_name":"OXA-1172","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10835":{"protein_sequence":{"accession":"UZQ18799.1","sequence":"MAIRIFAILFSIFSLATFAHAQEGTLERSDWRKFFSEFQAKGTIVVADERQADRAMLVFDPVRSKKRYSPASTFKIPHTLFALDAGAVRDEFQIFRWDGVNRGFAGHNQDQDLRSAMRNSTVWVYELFAKEIGDDKARRYLKKIDYGNADPSTSNGDYWIEGIAISAQEQIAFLRKLYRNELPFRVEHQRLVKDLMIVEAGRNWILRAKTGWEGRMGWWVGWVEWPTGSVFFALNIDTPNRMDDLFKREAIVRAILRSIEALPPNPAVNSDAAR"},"dna_sequence":{"accession":"OP806899.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGGCAATCCGAATCTTCGCGATACTTTTCTCCATTTTTTCTCTTGCCACTTTCGCGCATGCGCAAGAAGGCACGCTAGAACGTTCTGACTGGAGGAAGTTTTTCAGCGAATTTCAAGCCAAAGGCACGATAGTTGTGGCAGACGAACGCCAAGCGGATCGTGCCATGTTGGTTTTTGATCCTGTGCGATCGAAGAAACGCTACTCGCCTGCATCGACATTCAAGATACCTCATACACTTTTTGCACTTGATGCAGGCGCTGTTCGTGATGAGTTCCAGATTTTTCGATGGGACGGCGTTAACAGGGGCTTTGCAGGCCACAATCAAGACCAAGATTTGCGATCAGCAATGCGGAATTCTACTGTTTGGGTGTATGAGCTATTTGCAAAGGAAATTGGTGATGACAAAGCTCGGCGCTATTTGAAGAAAATCGACTATGGCAACGCCGATCCTTCGACAAGTAATGGCGATTACTGGATAGAAGGCATTGCAATCTCGGCGCAGGAGCAAATTGCATTTCTCAGGAAGCTCTATCGTAACGAGCTGCCCTTTCGGGTAGAACATCAGCGCTTGGTCAAGGATCTCATGATTGTGGAAGCCGGTCGCAACTGGATACTGCGTGCAAAGACGGGCTGGGAAGGCCGTATGGGTTGGTGGGTAGGATGGGTTGAGTGGCCGACTGGCTCCGTATTCTTCGCACTGAATATTGATACGCCAAACAGAATGGATGATCTTTTCAAGAGGGAGGCAATCGTGCGGGCAATCCTTCGCTCTATTGAAGCGTTACCGCCCAACCCGGCAGTCAACTCGGACGCTGCGCGATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008590","ARO_id":"47382","ARO_name":"OXA-1172","CARD_short_name":"OXA-1172","ARO_description":"OXA-2 family class D beta-lactamase OXA-1172.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46493":{"category_aro_accession":"3007704","category_aro_cvterm_id":"46493","category_aro_name":"OXA-2-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-2.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8009":{"model_id":"8009","model_name":"OXA-1173","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10836":{"protein_sequence":{"accession":"UZQ18800.1","sequence":"MAIRIFAILFSIFSLATFAHAQEGTLERSDWRKFFSEFQAKGTIVVADERQADRAMLVFDPVRSKKRYSPASTFKIPHTLFALDAGAVRDEFQIFRWDGVKRSFAGHNKDQDLRSAMRNSTVWVYELFAKEIGDGKARRYLKQIGYGNADPSTSHGDYWIEGSLAISAQEQIAFLRKLYQNDLPFRVEHQRLVKDLMIVEAGRNWILRAKTGWEGSMGWWVGWVEWPTGPVFFALNIDTPNRMDDLFKREAIARAILLSIEALPPNPAVHSDAAR"},"dna_sequence":{"accession":"OP806900.1","fmin":"0","fmax":"828","strand":"+","sequence":"ATGGCAATCCGAATCTTCGCGATACTTTTCTCCATTTTTTCTCTTGCCACTTTCGCGCATGCGCAAGAAGGCACGCTAGAACGTTCTGACTGGAGGAAGTTTTTCAGCGAATTTCAAGCCAAAGGCACGATAGTTGTGGCAGACGAACGCCAAGCGGATCGTGCCATGTTGGTTTTTGATCCTGTGCGATCGAAGAAACGCTACTCGCCTGCGTCGACATTCAAGATTCCACATACACTTTTTGCACTTGATGCAGGCGCCGTTCGCGATGAGTTTCAGATTTTCCGCTGGGACGGCGTCAAAAGGAGCTTTGCAGGTCACAATAAAGACCAAGATTTGCGATCAGCAATGCGAAATTCTACTGTCTGGGTTTATGAGCTATTTGCAAAGGAAATCGGTGATGGCAAGGCTCGACGCTATTTGAAGCAAATCGGCTATGGCAACGCCGATCCTTCGACAAGTCATGGCGATTACTGGATAGAAGGCAGCCTTGCAATCTCAGCACAGGAACAGATCGCGTTTCTCAGAAAGCTCTATCAAAACGATCTGCCCTTTAGGGTGGAACATCAGCGCTTGGTCAAGGATCTGATGATTGTGGAAGCGGGACGCAACTGGATTCTGCGCGCGAAGACGGGCTGGGAAGGCAGCATGGGTTGGTGGGTGGGGTGGGTTGAATGGCCAACCGGTCCCGTATTCTTTGCCTTGAATATCGATACGCCAAACAGAATGGACGATCTTTTCAAGAGGGAAGCAATAGCGCGAGCGATACTTCTCTCTATCGAAGCGTTGCCGCCCAACCCGGCAGTCCACTCGGACGCTGCGCGATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008591","ARO_id":"47383","ARO_name":"OXA-1173","CARD_short_name":"OXA-1173","ARO_description":"OXA-2 family class D beta-lactamase OXA-1173.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46493":{"category_aro_accession":"3007704","category_aro_cvterm_id":"46493","category_aro_name":"OXA-2-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-2.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8010":{"model_id":"8010","model_name":"OXA-1174","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10837":{"protein_sequence":{"accession":"UZQ18801.1","sequence":"MRPLLFSALLLLSGHAQASEWNDSQAVDKLFGAAGVKGTFVLYDVQRQRYVGHDRERAETRFVPASTYKVANSLIGLSTGAVRSADEVLPYGGKPQRFKAWEHDMSLRDAIEASNVPVYQELARRIGLERMRANVSRLGYGNAEIGQVVDNFWLVGPLKISAMEQTRFLLRLAQGELPFPAPVQSTVRTMTLLESGPGWELHGKTGWCFDCTPELGWWVGWVKRNERLYGFALNIDMPGGEADIGKRVELGKASLKALGILP"},"dna_sequence":{"accession":"OP806901.1","fmin":"0","fmax":"789","strand":"+","sequence":"ATGCGCCCTCTCCTCTTCAGCGCCCTTCTCCTGCTCTCCGGGCATGCCCAGGCCAGCGAATGGAACGACAGCCAGGCCGTGGACAAGCTATTCGGCGCGGCCGGGGTGAAAGGCACCTTCGTCCTCTACGATGTGCAGCGGCAGCGCTATGTCGGCCATGACCGGGAGCGCGCGGAAACTCGCTTCGTTCCTGCCTCCACCTACAAGGTGGCGAACAGCCTGATCGGCTTATCCACAGGGGCGGTTAGATCCGCCGACGAGGTTCTTCCCTATGGCGGCAAGCCCCAGCGCTTCAAGGCCTGGGAGCACGACATGAGCCTGCGCGATGCGATCGAGGCATCGAACGTACCGGTCTACCAGGAACTGGCGCGGCGCATCGGCCTGGAGCGGATGCGCGCCAATGTCTCGCGCCTGGGTTACGGCAACGCGGAAATCGGCCAGGTTGTGGATAACTTCTGGTTGGTGGGACCGCTGAAGATCAGCGCGATGGAACAGACCCGCTTTCTGCTCCGACTGGCGCAGGGAGAATTGCCATTCCCCGCCCCGGTGCAGTCCACCGTGCGCACCATGACCCTGCTGGAAAGCGGCCCGGGCTGGGAGCTGCACGGCAAGACCGGCTGGTGCTTCGACTGCACGCCGGAACTCGGCTGGTGGGTGGGCTGGGTGAAGCGCAACGAGCGGCTCTACGGCTTCGCCCTGAACATCGACATGCCCGGCGGCGAGGCCGACATCGGCAAGCGCGTCGAACTGGGCAAGGCCAGTCTCAAGGCTCTCGGGATACTGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008592","ARO_id":"47384","ARO_name":"OXA-1174","CARD_short_name":"OXA-1174","ARO_description":"OXA-50 family oxacillin-hydrolyzing class D beta-lactamase OXA-1174.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46513":{"category_aro_accession":"3007724","category_aro_cvterm_id":"46513","category_aro_name":"OXA-50-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-50.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8011":{"model_id":"8011","model_name":"OXA-1175","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10838":{"protein_sequence":{"accession":"UZQ18794.1","sequence":"MKTFAAYVITACLSSTALASSITENTFWNKEFSAEAVNGVFVLCKSSSKSCATNNLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDGKPRVFKWDGKPRAMKQWERDLSLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLFLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKGTEVYFFAFNMDIDNENKLPLRKSIPTKIMASEGIIGG"},"dna_sequence":{"accession":"OP806894.1","fmin":"0","fmax":"828","strand":"+","sequence":"ATGAAAACATTTGCCGCATATGTAATTACTGCGTGTCTTTCAAGTACGGCATTAGCTAGTTCAATTACAGAAAATACGTTTTGGAACAAAGAGTTCTCTGCCGAAGCCGTCAATGGTGTTTTCGTGCTTTGTAAAAGTAGCAGTAAATCCTGCGCTACCAATAACTTAGCTCGTGCATCAAAGGAATATCTTCCAGCATCAACATTTAAGATCCCCAACGCAATTATCGGCCTAGAAACTGGTGTCATAAAGAATGAGCATCAGGTTTTCAAATGGGACGGAAAGCCAAGGGTTTTCAAATGGGACGGAAAGCCAAGAGCCATGAAACAATGGGAAAGAGACTTGAGCTTAAGAGGGGCAATACAAGTTTCAGCGGTTCCCGTATTTCAACAAATCGCCAGAGAAGTTGGCGAAGTAAGAATGCAGAAATATCTTAAAAAATTTTCATATGGTAACCAGAATATCAGTGGTGGCATTGACAAATTCTGGTTGGAGGGTCAGCTTAGAATTTCCGCAGTTAATCAAGTGGAGTTTCTAGAGTCTCTATTTTTAAATAAATTGTCAGCATCAAAAGAAAATCAGCTAATAGTAAAAGAGGCTTTGGTAACGGAGGCTGCGCCTGAATATCTTGTGCATTCAAAAACTGGTTTTTCTGGTGTGGGAACTGAGTCAAATCCTGGTGTCGCATGGTGGGTTGGTTGGGTTGAGAAGGGAACAGAGGTTTACTTTTTCGCCTTTAACATGGATATAGACAACGAAAATAAGTTGCCGCTAAGAAAATCCATTCCCACCAAAATCATGGCAAGTGAGGGCATCATTGGTGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008593","ARO_id":"47385","ARO_name":"OXA-1175","CARD_short_name":"OXA-1175","ARO_description":"OXA-10 family class D beta-lactamase OXA-1175.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46486":{"category_aro_accession":"3007697","category_aro_cvterm_id":"46486","category_aro_name":"OXA-10-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-10.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8012":{"model_id":"8012","model_name":"OXA-1176","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10839":{"protein_sequence":{"accession":"BDT65866.1","sequence":"MFSRWSKPFVLAATVCAMAMSAATAHAELIVRNDLKRVFDEAGVSGTFVLMDISADRTYVVDPARAARRMHPASTFKIPNSLIAFDTGAVRDDHEVLPYGGKPQPYKQWEHDMALPEAIRLSAVPIYQEVARRVGLERMQAYVDAFDYGNRQLGSVIDQFWLRGPLEISAFEEARFTSRMALKQLPVKPRTWDMVHRMLLIEQQGDAALYAKTGVATEYRPEIGWWVGWVERAGRVYAFALNIDMPREGDMAKRIPLGKQLMQALEVWPAP"},"dna_sequence":{"accession":"LC739023.1","fmin":"0","fmax":"816","strand":"+","sequence":"ATGTTCTCTCGTTGGTCGAAACCTTTCGTGCTTGCCGCCACGGTGTGCGCCATGGCGATGAGCGCCGCCACTGCCCACGCCGAGCTCATCGTGCGCAACGATCTCAAGCGCGTGTTCGACGAGGCCGGCGTCTCCGGCACCTTCGTGCTGATGGATATCAGCGCCGACCGCACCTACGTCGTTGACCCGGCCCGCGCCGCGCGGCGCATGCATCCGGCCTCAACTTTCAAGATCCCGAACAGCCTCATCGCCTTCGACACGGGCGCAGTGCGTGACGATCATGAAGTGCTGCCATACGGCGGCAAGCCGCAGCCCTACAAGCAGTGGGAGCACGACATGGCGCTGCCCGAGGCGATCCGCCTGTCGGCCGTGCCGATCTACCAGGAAGTGGCGCGCCGCGTCGGCCTTGAGCGCATGCAGGCGTATGTCGATGCGTTCGACTATGGCAATCGCCAGCTTGGCAGCGTGATCGACCAGTTCTGGCTGCGCGGTCCGCTCGAAATCTCGGCGTTTGAAGAGGCGCGCTTCACCAGCCGCATGGCGCTCAAGCAGCTGCCGGTGAAGCCGCGCACGTGGGACATGGTCCATCGCATGCTGCTGATCGAGCAGCAAGGCGATGCCGCGCTGTACGCCAAGACCGGCGTCGCCACGGAATACCGGCCGGAGATCGGCTGGTGGGTCGGTTGGGTCGAGCGTGCCGGGCGCGTCTATGCCTTTGCGCTGAACATCGACATGCCGCGCGAGGGCGACATGGCCAAGCGCATTCCGCTCGGCAAGCAGTTGATGCAGGCGCTGGAGGTGTGGCCGGCACCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42837","NCBI_taxonomy_name":"Ralstonia mannitolilytica","NCBI_taxonomy_id":"105219"}}}},"ARO_accession":"3008594","ARO_id":"47386","ARO_name":"OXA-1176","CARD_short_name":"OXA-1176","ARO_description":"OXA-60 family carbapenem-hydrolyzing class D beta-lactamase OXA-1176.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46518":{"category_aro_accession":"3007729","category_aro_cvterm_id":"46518","category_aro_name":"OXA-60-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-60.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8013":{"model_id":"8013","model_name":"OXA-1177","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10840":{"protein_sequence":{"accession":"BDT65865.1","sequence":"MMKLRHAATGAFLAALATFAHAEHPICTLVADAATGKVVVQEGKCNERVTPASTFKLALAVMGYDAGFLKDPHTPVEHFRRGDPDWGGQPWRQPVDPTLWLKYSVVWYSQRITHAMGAQTFASYVRKLDYGNMDVSGDLGKNNGLDRSWITSSLKISPEEQVGFLRRLVTRQLPVSAQTYEMVDRIVQTWQVPGGWAVQGKTGTAGPAPGNTSADGTWDQAHAYGWFVGWAKKGGQTYVFANLIQDDKIEPTSGGIRSRDAMLARLAQVLAAAKP"},"dna_sequence":{"accession":"LC739022.1","fmin":"0","fmax":"828","strand":"+","sequence":"ATGATGAAACTCCGCCACGCCGCCACCGGCGCCTTCCTTGCCGCGCTGGCCACCTTCGCCCATGCCGAACACCCTATCTGCACGCTCGTTGCCGATGCAGCCACGGGCAAGGTCGTCGTGCAGGAGGGCAAGTGCAACGAGCGCGTGACGCCGGCGTCCACCTTCAAGCTGGCGCTGGCCGTCATGGGCTACGACGCCGGCTTCCTGAAAGATCCGCACACGCCGGTCGAACACTTCAGGCGCGGCGACCCCGACTGGGGCGGCCAGCCGTGGCGCCAGCCTGTCGACCCGACGCTGTGGCTCAAGTATTCGGTGGTCTGGTATTCCCAGCGCATCACCCACGCGATGGGCGCGCAGACGTTCGCCTCGTACGTGCGCAAGCTCGACTACGGCAACATGGATGTGAGCGGCGACCTGGGCAAGAACAACGGCCTGGACCGCTCGTGGATCACCTCGTCGCTGAAGATATCGCCCGAGGAGCAGGTCGGCTTTCTGCGCCGGCTCGTCACCCGGCAGTTGCCGGTGTCGGCGCAGACGTACGAGATGGTCGACCGCATCGTGCAGACGTGGCAGGTGCCGGGCGGCTGGGCCGTGCAGGGCAAGACGGGCACGGCGGGCCCGGCACCGGGCAATACCTCGGCCGACGGCACGTGGGATCAGGCGCACGCTTACGGCTGGTTTGTCGGCTGGGCGAAGAAAGGAGGCCAGACCTACGTGTTTGCGAACCTGATCCAGGACGACAAGATCGAGCCCACCTCGGGCGGCATCCGCTCGCGCGATGCGATGCTGGCGCGCCTGGCGCAGGTGCTGGCTGCCGCCAAGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42837","NCBI_taxonomy_name":"Ralstonia mannitolilytica","NCBI_taxonomy_id":"105219"}}}},"ARO_accession":"3008595","ARO_id":"47387","ARO_name":"OXA-1177","CARD_short_name":"OXA-1177","ARO_description":"OXA-22 family class D beta-lactamase OXA-1177.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46497":{"category_aro_accession":"3007708","category_aro_cvterm_id":"46497","category_aro_name":"OXA-22-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-22.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8014":{"model_id":"8014","model_name":"OXA-1178","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10841":{"protein_sequence":{"accession":"UZZ47413.1","sequence":"MKLLKILSLVCLSISIGACAEHSMSRAKTSTIPQVNNSIIDQNVQALFNEISADAVFVTYDGQNIKKYGTHLDRAKTAYIPASTFKIANALIGLENHKATSTEIFKWDGKPRFFKEWDKDFTLGEAMQASTVPVYQELARRIGPSLMQSELQRIGYGNMQIGTEVDQFWLKGPLTITPIQEVKFVYDLAQGQLPFKPEVQQQVKEMLYVERRGENRLYAKSGWGMAVDPQVGWYVGFVEKADGQVVAFALNMQMKAGDDSALRKQLSLDVLDKLGVFHYL"},"dna_sequence":{"accession":"OP895673.1","fmin":"0","fmax":"843","strand":"+","sequence":"ATGAAATTATTAAAAATATTGAGTTTAGTTTGCTTAAGCATAAGTATTGGGGCTTGTGCTGAGCATAGTATGAGTCGAGCAAAAACAAGTACAATTCCACAAGTGAATAACTCAATCATCGATCAGAATGTTCAAGCGCTTTTTAATGAAATCTCAGCTGATGCTGTGTTTGTCACATATGATGGTCAAAATATTAAAAAATATGGCACGCATTTAGACCGAGCAAAAACAGCTTATATTCCTGCATCTACATTTAAAATTGCCAATGCACTAATTGGTTTAGAAAATCATAAAGCAACATCTACAGAAATATTTAAGTGGGATGGAAAGCCACGTTTTTTTAAAGAATGGGACAAAGATTTTACTTTGGGCGAAGCCATGCAAGCATCTACAGTGCCTGTATATCAAGAATTGGCACGTCGTATTGGTCCAAGCTTAATGCAAAGTGAATTGCAACGTATTGGTTATGGCAATATGCAAATAGGCACGGAAGTTGATCAATTTTGGTTGAAAGGGCCTTTGACAATTACACCTATACAAGAAGTAAAGTTTGTGTATGATTTAGCCCAAGGGCAATTGCCTTTTAAACCTGAAGTTCAGCAACAAGTGAAAGAGATGTTGTATGTAGAGCGCAGAGGGGAGAATCGTCTATATGCTAAAAGTGGCTGGGGAATGGCTGTAGACCCGCAAGTGGGTTGGTATGTGGGTTTTGTTGAAAAGGCAGATGGGCAAGTGGTGGCATTTGCTTTAAATATGCAAATGAAAGCTGGTGATGATAGTGCTCTACGTAAACAATTGTCTTTAGATGTGCTAGATAAGTTGGGTGTTTTTCATTATTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008596","ARO_id":"47388","ARO_name":"OXA-1178","CARD_short_name":"OXA-1178","ARO_description":"OXA-58 family carbapenem-hydrolyzing class D beta-lactamase OXA-1178.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46517":{"category_aro_accession":"3007728","category_aro_cvterm_id":"46517","category_aro_name":"OXA-58-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-58.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8015":{"model_id":"8015","model_name":"OXA-1181","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10842":{"protein_sequence":{"accession":"WAS27905.1","sequence":"MRVLALSAVFLVASIIGMPAVAKEWQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGQTRDIAAWNRDHDLITAMKYSVVPVYQEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISATQQIAFLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYSTRIEPKIGWWVGWVELDDNVWFFAMNMDMPTWDGLGLRQAITKEVLKQEKIIP"},"dna_sequence":{"accession":"OP966822.1","fmin":"0","fmax":"798","strand":"+","sequence":"ATGCGTGTATTAGCCTTATCGGCTGTGTTTTTGGTGGCATCGATTATCGGAATGCCAGCGGTAGCAAAGGAATGGCAAGAAAACAAAAGTTGGAATGCTCACTTTACTGAACATAAATCACAGGGCGTAGTTGTGCTCTGGAATGAGAATAAGCAGCAAGGATTTACCAATAATCTTAAACGGGCGAACCAAGCATTTTTACCCGCATCTACCTTTAAAATTCCCAATAGCTTGATCGCCCTCGATTTGGGCGTGGTTAAGGATGAACACCAAGTCTTTAAGTGGGATGGACAGACGCGTGATATCGCCGCTTGGAATCGTGACCATGACTTAATTACCGCGATGAAGTACTCAGTTGTGCCTGTTTATCAAGAATTTGCCCGCCAAATTGGTGAGGCACGTATGAGTAAAATGCTGCACGCCTTCGATTATGGCAATGAGGATATCTCGGGCAATGTAGACAGTTTTTGGCTCGATGGTGGTATTCGCATTTCGGCTACCCAGCAAATCGCTTTTTTACGCAAGCTGTATCACAACAAGCTGCACGTTTCTGAGCGTAGTCAGCGCATCGTGAAACAAGCCATGCTGACCGAAGCCAATGGCGACTATATTATTCGGGCTAAAACGGGATACTCGACTAGAATCGAACCTAAGATTGGCTGGTGGGTTGGTTGGGTTGAACTTGATGATAATGTGTGGTTTTTTGCGATGAATATGGATATGCCCACATGGGATGGTTTAGGGCTGCGCCAAGCCATCACAAAAGAAGTGCTCAAACAGGAGAAAATTATTCCCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3008597","ARO_id":"47389","ARO_name":"OXA-1181","CARD_short_name":"OXA-1181","ARO_description":"OXA-48 family class D beta-lactamase OXA-1181.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46510":{"category_aro_accession":"3007721","category_aro_cvterm_id":"46510","category_aro_name":"OXA-48-like beta-lactamase","category_aro_description":"OXA-48-type beta-lactamases are now routinely encountered in bacterial infections caused by carbapenam-resistant Enterobacterales. OXA-48-like proteins confer resistance to penicillin (which is efficiently hydrolyzed) and carbapenam antibiotics (which is more slowly broken down). The spectrum of activity of these variants varies, with some hydrolyzing expanded-spectrum oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8016":{"model_id":"8016","model_name":"OXA-1182","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10843":{"protein_sequence":{"accession":"WAS27906.1","sequence":"MKKFILPIFSISTLLSLSACSSIQTKFEDTFHTSDQQHEKAIKSYFDEAQTQGVIIIKEGKNISIYGNNLARAHTEYVPASTFKMLNALIGLENHKATKTEIFKWDGKKRSYPMWEKDMTLGEAMALSAVPVYQELARRTGLDLMQKEVKRVGFGNMNIGIQVDNFWLVGPLKITPIQEVNFADDLANNRLPFKLETQEEVKKMLLIKEVNGSKIYAKSGWGMDVSPQVGWLTGWVEKSNGEKVPFSLNLEMKQGMSGSIRNEITYKSLENLGII"},"dna_sequence":{"accession":"OP966823.1","fmin":"0","fmax":"828","strand":"+","sequence":"ATGAAAAAATTTATACTTCCTATTTTCAGCATTTCTACTCTACTTTCTCTCAGTGCATGTTCATCTATTCAAACTAAATTTGAAGATACTTTTCATACTTCTGATCAGCAACATGAAAAAGCCATTAAAAGCTATTTTGATGAAGCTCAAACACAGGGTGTAATCATTATTAAAGAGGGAAAAAATATTAGTATCTATGGTAATAACTTGGCACGAGCACATACTGAATATGTCCCTGCATCAACATTTAAGATGCTAAATGCCTTAATTGGACTAGAAAATCATAAAGCTACAAAAACTGAGATTTTCAAATGGGATGGTAAAAAAAGATCTTATCCTATGTGGGAAAAAGATATGACTTTAGGCGAGGCCATGGCCCTTTCAGCAGTTCCTGTATATCAAGAGCTTGCAAGACGGACTGGTTTAGACCTAATGCAAAAAGAAGTTAAACGGGTTGGTTTTGGTAATATGAACATTGGAATACAAGTTGATAACTTCTGGTTGGTTGGCCCCCTTAAAATTACACCAATACAAGAAGTGAATTTTGCCGATGATCTTGCGAATAATCGATTACCCTTTAAATTAGAAACTCAAGAAGAAGTCAAAAAGATGCTTCTGATTAAAGAAGTCAATGGTAGTAAAATTTATGCTAAAAGTGGATGGGGAATGGATGTAAGCCCGCAAGTAGGTTGGTTAACAGGTTGGGTAGAAAAATCTAATGGCGAAAAAGTTCCCTTTTCTCTAAACCTAGAAATGAAGCAAGGAATGTCTGGTTCTATTCGTAATGAAATTACTTATAAATCATTAGAAAATTTAGGGATAATATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008598","ARO_id":"47390","ARO_name":"OXA-1182","CARD_short_name":"OXA-1182","ARO_description":"OXA-143 family carbapenem-hydrolyzing class D beta-lactamase OXA-1182.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46490":{"category_aro_accession":"3007701","category_aro_cvterm_id":"46490","category_aro_name":"OXA-143-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-143.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8017":{"model_id":"8017","model_name":"OXA-1183","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10844":{"protein_sequence":{"accession":"MCU9167541.1","sequence":"MAIRIFAILFSIFSLATFAHAQEGTLERSDWRKFFSEFQAKGTIVVADERQADRAMLVFDPVRSKKRYSPASTFKIPHTLFALDAGAVRDEFQIFRWDGVNRGFAGHNQDQDLRSAMRNSTVWVYELFAKEIGDDKARRYLKKIDYGNAVPSTSNGDYWIEGSLAISAQEQIAFLRKLYRNELPFRVEHQRLVKDLMIVEAGRNWILRAKTGWEGRMGWWVGWVEWPTGSVFFALNIDTPNRMDDLFKREAIVRAILRSIEALPPNPAVNSDAAR"},"dna_sequence":{"accession":"JAOVDG010000079.1","fmin":"609","fmax":"1437","strand":"+","sequence":"ATGGCAATCCGAATCTTCGCGATACTTTTCTCCATTTTTTCTCTTGCCACTTTCGCGCATGCGCAAGAAGGCACGCTAGAACGTTCTGACTGGAGGAAGTTTTTCAGCGAATTTCAAGCCAAAGGCACGATAGTTGTGGCAGACGAACGCCAAGCGGATCGTGCCATGTTGGTTTTTGATCCTGTGCGATCGAAGAAACGCTACTCGCCTGCATCGACATTCAAGATACCTCATACACTTTTTGCACTTGATGCAGGCGCTGTTCGTGATGAGTTCCAGATTTTTCGATGGGACGGCGTTAACAGGGGCTTTGCAGGCCACAATCAAGACCAAGATTTGCGATCAGCAATGCGGAATTCTACTGTTTGGGTGTATGAGCTATTTGCAAAGGAAATTGGTGATGACAAAGCTCGGCGCTATTTGAAGAAAATCGACTATGGCAACGCCGTTCCTTCGACAAGTAATGGCGATTACTGGATAGAAGGCAGCCTTGCAATCTCGGCGCAGGAGCAAATTGCATTTCTCAGGAAGCTCTATCGTAACGAGCTGCCCTTTCGGGTAGAACATCAGCGCTTGGTCAAGGATCTCATGATTGTGGAAGCCGGTCGCAACTGGATACTGCGTGCAAAGACGGGCTGGGAAGGCCGTATGGGTTGGTGGGTAGGATGGGTTGAGTGGCCGACTGGCTCCGTATTCTTCGCACTGAATATTGATACGCCAAACAGAATGGATGATCTTTTCAAGAGGGAGGCAATCGTGCGGGCAATCCTTCGCTCTATTGAAGCGTTACCGCCCAACCCGGCAGTCAACTCGGACGCTGCGCGATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008599","ARO_id":"47391","ARO_name":"OXA-1183","CARD_short_name":"OXA-1183","ARO_description":"OXA-2 family class D beta-lactamase OXA-1183.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46493":{"category_aro_accession":"3007704","category_aro_cvterm_id":"46493","category_aro_name":"OXA-2-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-2.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8018":{"model_id":"8018","model_name":"OXA-1184","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10845":{"protein_sequence":{"accession":"MCU9347355.1","sequence":"MKTFAAYVITACLSSTALASSITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNNLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLSLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFSLEGQLRISAVNQVEFLESLFLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKGTEVYFFAFNMDIDNENKLPLRKSIPTKIMASEGIIGG"},"dna_sequence":{"accession":"JAOVCE010000049.1","fmin":"11959","fmax":"12760","strand":"+","sequence":"ATGAAAACATTTGCCGCATATGTAATTACTGCGTGTCTTTCAAGTACGGCATTAGCTAGTTCAATTACAGAAAATACGTCTTGGAACAAAGAGTTCTCTGCCGAAGCCGTCAATGGTGTTTTCGTGCTTTGTAAAAGTAGCAGTAAATCCTGCGCTACCAATAACTTAGCTCGTGCATCAAAGGAATATCTTCCAGCATCAACATTTAAGATCCCCAACGCAATTATCGGCCTAGAAACTGGTGTCATAAAGAATGAGCATCAGGTTTTCAAATGGGACGGAAAGCCAAGAGCCATGAAACAATGGGAAAGAGACTTGAGCTTAAGAGGGGCAATACAAGTTTCAGCGGTTCCCGTATTTCAACAAATCGCCAGAGAAGTTGGCGAAGTAAGAATGCAGAAATACCTTAAAAAATTTTCATATGGCAACCAGAATATCAGTGGTGGCATTGACAAATTCTCGTTGGAGGGTCAGCTAAGAATTTCCGCAGTTAATCAAGTGGAGTTTCTAGAGTCTCTATTTTTAAATAAATTGTCAGCATCAAAAGAAAATCAGCTAATAGTAAAAGAGGCTTTGGTAACGGAGGCTGCGCCTGAATATCTTGTGCATTCAAAAACTGGTTTTTCTGGTGTGGGAACTGAGTCAAATCCTGGTGTCGCATGGTGGGTTGGTTGGGTTGAGAAGGGAACAGAGGTTTACTTTTTCGCCTTTAACATGGATATAGACAACGAAAATAAGTTGCCGCTAAGAAAATCCATTCCCACCAAAATCATGGCAAGTGAGGGCATCATTGGTGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008600","ARO_id":"47392","ARO_name":"OXA-1184","CARD_short_name":"OXA-1184","ARO_description":"OXA-10 family class D beta-lactamase OXA-1184.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46486":{"category_aro_accession":"3007697","category_aro_cvterm_id":"46486","category_aro_name":"OXA-10-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-10.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8019":{"model_id":"8019","model_name":"OXA-1185","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10846":{"protein_sequence":{"accession":"BDU78995.1","sequence":"MYKKALIVATSILFLSACSSNTVKQHQIHSISANKNSEEIRSLFDQAQTTGVLVIKRGQTEEIYGNDLKRASTAYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMSKEVKRIGFGNADIGSKVDNFWLVGPLKITPEQETQFAYKLANKTLPFSKNVQEQVQSMVFIEEKNGSKIYAKSGWGWDVEPQVGWLTGWVVQPQGEIVAFSLNLEMKKGTPSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"LC742738.1","fmin":"21","fmax":"843","strand":"+","sequence":"ATGTATAAAAAAGCCCTTATCGTTGCAACAAGTATCCTATTTTTATCCGCCTGTTCTTCCAATACGGTAAAACAACATCAAATACACTCTATTTCTGCCAATAAAAATTCAGAAGAAATTAGGTCACTGTTTGATCAGGCACAAACCACGGGTGTTTTGGTGATTAAGCGAGGACAAACAGAAGAAATTTATGGCAATGATCTTAAAAGAGCATCAACCGCCTATGTTCCCGCTTCTACCTTTAAAATGTTAAATGCTTTAATTGGACTTGAACATCATAAGGCAACTACAACTGAAGTATTTAAATGGGATGGGCAAAAACGTTTATTTCCGGATTGGGAAAAGGACATGACACTGGGCGATGCCATGAAAGCTTCTGCTATTCCAGTTTATCAAGAACTAGCTCGTCGTATTGGACTTGATCTTATGTCTAAAGAGGTAAAACGTATTGGTTTCGGTAATGCGGACATTGGTTCAAAAGTAGATAATTTTTGGCTTGTAGGTCCACTTAAAATTACACCTGAGCAAGAAACCCAATTTGCTTATAAATTAGCTAATAAAACTCTTCCATTTAGTAAAAATGTACAAGAACAAGTTCAATCAATGGTGTTCATAGAGGAAAAAAATGGAAGTAAAATTTATGCCAAAAGTGGTTGGGGATGGGATGTTGAACCGCAAGTTGGTTGGTTAACAGGCTGGGTCGTTCAACCACAAGGAGAAATTGTGGCATTTTCACTTAATTTAGAAATGAAAAAAGGAACTCCTAGCTCTATTCGCAAAGAAATTGCTTATAAAGGCTTAGAACAACTGGGTATCTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39094","NCBI_taxonomy_name":"Acinetobacter calcoaceticus","NCBI_taxonomy_id":"471"}}}},"ARO_accession":"3008601","ARO_id":"47393","ARO_name":"OXA-1185","CARD_short_name":"OXA-1185","ARO_description":"OXA-213 family carbapenem-hydrolyzing class D beta-lactamase OXA-1185.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46495":{"category_aro_accession":"3007706","category_aro_cvterm_id":"46495","category_aro_name":"OXA-213-like beta-lactamase","category_aro_description":"OXA-213-like enzymes have been identified to be intrinsic to A. calcoaceticus and have been subsequently detected in A. pittii. Phylogenetic analysis of OXA-213-like proteins identified two distinct subgroups within the OXA family. The first group was linked to A. pittii and the second group to A. calcoaceticus. The carbapenemase activity of these OXAs may be related to the species-dependent effect.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8020":{"model_id":"8020","model_name":"OXA-1186","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10847":{"protein_sequence":{"accession":"WEG43791.1","sequence":"MSKFFITFLVFLWPLSAVAEDQVLAGLFSQHGMKGTIVISSLHNEKTFIYNEPRANLKFSTASTFKILNTLISLEEKAISGKDDVLKWDGHIYDFPDWNHDQTLESAFKVSCVWCFQELARRVGAEKYRNYLRESAYGELREPFMETTFWLDGSLQISAIEQVDFLKKVYLRTLPFNATSYETLRQIMLVEKTPAYTMWAKTGWAARVKPQVGWYVGYVETPKDVWFFATNIETRDEKDLPLRQKLTRAALQAKGVIE"},"dna_sequence":{"accession":"OQ442837.1","fmin":"0","fmax":"777","strand":"+","sequence":"ATGAGTAAGTTCTTTATTACCTTCTTAGTTTTTCTATGGCCGTTGTCAGCAGTCGCTGAAGACCAAGTGCTTGCCGGACTCTTTTCGCAGCACGGCATGAAGGGAACGATAGTGATCTCGTCGCTACACAACGAGAAGACCTTCATCTACAACGAACCTCGCGCAAATCTGAAATTCTCGACTGCATCAACATTTAAAATACTGAATACGCTGATCTCGCTTGAGGAAAAGGCCATTTCCGGAAAAGACGACGTGCTGAAATGGGATGGGCATATTTACGACTTTCCAGATTGGAATCATGACCAGACATTGGAAAGTGCGTTCAAAGTTTCATGCGTCTGGTGTTTTCAGGAGCTTGCGCGTCGAGTCGGCGCGGAAAAATATCGAAATTATTTGCGCGAGTCGGCTTACGGAGAATTACGCGAACCCTTCATGGAAACAACATTCTGGCTTGATGGCTCCCTTCAAATTAGCGCAATTGAACAAGTGGATTTCCTCAAGAAAGTATATCTGCGTACACTCCCGTTTAACGCGACATCCTATGAAACGCTAAGACAAATCATGCTTGTTGAGAAAACGCCGGCATATACGATGTGGGCCAAGACAGGTTGGGCAGCGAGAGTAAAACCACAAGTGGGCTGGTATGTGGGCTATGTCGAAACTCCAAAGGATGTTTGGTTCTTTGCCACGAATATTGAGACTCGTGACGAAAAGGACTTGCCACTACGCCAGAAGTTGACGCGAGCCGCACTTCAAGCAAAAGGAGTCATCGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36915","NCBI_taxonomy_name":"Citrobacter freundii","NCBI_taxonomy_id":"546"}}}},"ARO_accession":"3008602","ARO_id":"47394","ARO_name":"OXA-1186","CARD_short_name":"OXA-1186","ARO_description":"OXA-198 family carbapenem-hydrolyzing class D beta-lactamase OXA-1186.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46492":{"category_aro_accession":"3007703","category_aro_cvterm_id":"46492","category_aro_name":"OXA-198-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-198.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8021":{"model_id":"8021","model_name":"OXA-1187","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10848":{"protein_sequence":{"accession":"WEG44936.1","sequence":"MAIRIFAILFSIFSLATFAHAQEGTLERSDWRKFFSEFQAKGTIVVADERQADRAMLVFDPVRSKKRYSPASTFKIPHTLFALDAGAVRDEFQIFRWDGVNRGFAGHNQDQDLRSAMRNSTVWVYELFAKEIGDDKARRYLKKIDYGNADPSTSNGDYLEGSLAISAQEQIAFLRKLYRNELPFRVEHQRLVKDLMIVEAGRNWILRAKTGWEGRMGWWVGWVEWPTGSVFFALNIDTPNRMDDLFKREAIVRAILRSIEALPPNPAVNSDAAR"},"dna_sequence":{"accession":"OQ592372.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGGCAATCCGAATCTTCGCGATACTTTTCTCCATTTTTTCTCTTGCCACTTTCGCGCATGCGCAAGAAGGCACGCTAGAACGTTCTGACTGGAGGAAGTTTTTCAGCGAATTTCAAGCCAAAGGCACGATAGTTGTGGCAGACGAACGCCAAGCGGATCGTGCCATGTTGGTTTTTGATCCTGTGCGATCGAAGAAACGCTACTCGCCTGCATCGACATTCAAGATACCTCATACACTTTTTGCACTTGATGCAGGCGCTGTTCGTGATGAGTTCCAGATTTTTCGATGGGACGGCGTTAACAGGGGCTTTGCAGGCCACAATCAAGACCAAGATTTGCGATCAGCAATGCGGAATTCTACTGTTTGGGTGTATGAGCTATTTGCAAAGGAAATTGGTGATGACAAAGCTCGGCGCTATTTGAAGAAAATCGACTATGGCAACGCCGATCCTTCGACAAGTAATGGCGATTACTTAGAAGGCAGCCTTGCAATCTCGGCGCAGGAGCAAATTGCATTTCTCAGGAAGCTCTATCGTAACGAGCTGCCCTTTCGGGTAGAACATCAGCGCTTGGTCAAGGATCTCATGATTGTGGAAGCCGGTCGCAACTGGATACTGCGTGCAAAGACGGGCTGGGAAGGCCGTATGGGTTGGTGGGTAGGATGGGTTGAGTGGCCGACTGGCTCCGTATTCTTCGCACTGAATATTGATACGCCAAACAGAATGGATGATCTTTTCAAGAGGGAGGCAATCGTGCGGGCAATCCTTCGCTCTATTGAAGCGTTACCGCCCAACCCGGCAGTCAACTCGGACGCTGCGCGATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008603","ARO_id":"47395","ARO_name":"OXA-1187","CARD_short_name":"OXA-1187","ARO_description":"OXA-2 family class D beta-lactamase OXA-1187.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46493":{"category_aro_accession":"3007704","category_aro_cvterm_id":"46493","category_aro_name":"OXA-2-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-2.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8022":{"model_id":"8022","model_name":"OXA-1188","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10849":{"protein_sequence":{"accession":"MBK3756226.1","sequence":"MRPLLFSALLLLSGHAQASEWNDSQAVDKLFGAAGVKGTFVLHDVQRQRYVGHDRERAETRFVPASTYKVANSLIGLSTGAVKSADEVLPYGGKPQRFKAWEHDMSLRDAIKASNVPVYQELARRIGLERMRANVSRLGYGNAEIGQVVDNFWLVGPLKISAMEQTRFLLRLAQGELPFPAPVQSTVRAMTLLESGPGWELHGKTGWCFDCTPELGWWVGWVKRNERLYGFALNIDMPGGEADIGKRVELGKASLKALGILP"},"dna_sequence":{"accession":"WIFR01000007.1","fmin":"162361","fmax":"163150","strand":"+","sequence":"ATGCGCCCTCTCCTCTTCAGCGCCCTTCTCCTGCTCTCCGGGCATGCCCAGGCCAGCGAATGGAACGACAGCCAGGCCGTGGACAAGCTATTCGGCGCGGCCGGGGTGAAAGGCACCTTCGTCCTCCACGATGTGCAGCGGCAGCGCTATGTCGGCCACGACCGGGAGCGCGCGGAAACTCGCTTCGTTCCTGCCTCCACCTACAAGGTGGCGAACAGCCTGATTGGCTTATCCACAGGGGCGGTTAAATCCGCCGACGAGGTTCTTCCCTATGGCGGCAAGCCCCAGCGCTTCAAGGCCTGGGAGCACGACATGAGCCTGCGCGACGCGATCAAGGCATCGAACGTACCGGTCTACCAGGAACTGGCGCGACGCATCGGCCTGGAGCGGATGCGCGCCAATGTCTCGCGCCTGGGTTACGGCAACGCGGAAATCGGCCAGGTTGTGGATAACTTCTGGTTGGTGGGACCGCTGAAGATCAGCGCGATGGAACAGACCCGCTTTCTGCTCCGACTGGCGCAGGGAGAATTGCCATTCCCCGCCCCGGTGCAGTCCACCGTGCGCGCCATGACCCTGCTGGAAAGCGGCCCGGGCTGGGAGCTGCACGGCAAGACCGGCTGGTGCTTCGACTGCACGCCGGAACTCGGCTGGTGGGTGGGCTGGGTGAAGCGCAACGAGCGGCTCTACGGCTTCGCCCTGAACATCGACATGCCCGGCGGCGAGGCCGACATCGGCAAGCGCGTCGAACTGGGCAAGGCCAGTCTCAAGGCTCTCGGGATACTGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008604","ARO_id":"47396","ARO_name":"OXA-1188","CARD_short_name":"OXA-1188","ARO_description":"OXA-50 family oxacillin-hydrolyzing class D beta-lactamase OXA-1188.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46513":{"category_aro_accession":"3007724","category_aro_cvterm_id":"46513","category_aro_name":"OXA-50-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-50.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8023":{"model_id":"8023","model_name":"OXA-1189","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10850":{"protein_sequence":{"accession":"EKU39511.1","sequence":"MYKKALFFAIGTVFLSACSSHTVEQPQTHFIPANKNSEEIKSLFDQAQTTGVLVIKREKAEEVYGNDLKRASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMSKEVKRIGFGNANIGSKVDNFWLVGPLKITPEQEAQFAYQLAHKTLPFSKNVQEQVQSMMFIEEKNGNKIYAKSGWGLDVEPQVGWLTGWVVQPQGEIVAFSLNLEMKKGTPSSIRKEIAYKSLEQLGIL"},"dna_sequence":{"accession":"AMSS01000032.1","fmin":"8646","fmax":"9468","strand":"+","sequence":"ATGTATAAAAAAGCGCTTTTCTTTGCAATTGGTACCGTATTTTTATCAGCCTGTTCTTCCCACACGGTAGAACAACCTCAAACACATTTTATTCCCGCCAATAAAAATTCAGAAGAAATTAAATCACTGTTTGATCAGGCACAGACCACGGGTGTTTTGGTGATTAAGCGAGAAAAAGCTGAAGAAGTGTATGGTAATGATCTTAAGAGAGCATCTACTGAATATGTTCCCGCTTCTACCTTTAAAATGTTAAATGCTTTAATTGGACTTGAGCATCATAAGGCAACTACAACTGAAGTGTTTAAATGGGATGGACAAAAACGCTTATTTCCTGATTGGGAAAAAGACATGACACTAGGCGATGCGATGAAAGCTTCGGCTATTCCAGTCTATCAAGAATTAGCGAGACGAATTGGTCTAGATCTTATGTCTAAAGAGGTGAAACGAATTGGTTTCGGTAATGCTAACATCGGTTCAAAAGTAGATAATTTTTGGCTTGTTGGCCCACTAAAAATCACACCTGAACAAGAAGCCCAGTTTGCTTATCAATTGGCTCATAAAACCCTGCCATTTAGCAAAAATGTACAAGAACAAGTTCAATCAATGATGTTTATAGAGGAAAAAAATGGAAATAAAATTTATGCAAAAAGTGGTTGGGGATTGGATGTTGAACCACAAGTTGGTTGGTTAACTGGCTGGGTTGTTCAACCTCAAGGAGAAATTGTGGCATTCTCACTTAATTTAGAAATGAAAAAAGGAACACCTAGCTCTATTCGCAAAGAGATTGCTTATAAAAGTTTAGAACAACTGGGTATCTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36837","NCBI_taxonomy_name":"Acinetobacter sp.","NCBI_taxonomy_id":"472"}}}},"ARO_accession":"3008605","ARO_id":"47397","ARO_name":"OXA-1189","CARD_short_name":"OXA-1189","ARO_description":"OXA-213 family carbapenem-hydrolyzing class D beta-lactamase OXA-1189.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46495":{"category_aro_accession":"3007706","category_aro_cvterm_id":"46495","category_aro_name":"OXA-213-like beta-lactamase","category_aro_description":"OXA-213-like enzymes have been identified to be intrinsic to A. calcoaceticus and have been subsequently detected in A. pittii. Phylogenetic analysis of OXA-213-like proteins identified two distinct subgroups within the OXA family. The first group was linked to A. pittii and the second group to A. calcoaceticus. The carbapenemase activity of these OXAs may be related to the species-dependent effect.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8024":{"model_id":"8024","model_name":"OXA-1190","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10851":{"protein_sequence":{"accession":"TNL63909.1","sequence":"MKFKMKGLFCVILSSLAFSGCVYDSKLQRPVISERETEIPLLFNQAQTQAVFVTYDGIHLKSYGNDLSRAKTEYIPASTFKMLNALIGLQNAKATNTEIFHWNGEKRAFSAWEKDMTLAEAMQASAVPVYQELARRIGLELMREEVKRVGFGNAEIGQQVDNFWLVGPLKISPEQEVKFAYQLAMKQLPFDRNVQQQVKDMLYIERRGDSKLYAKSGWGMDVEPQVGWYTGWVEQPDGKVTAFALNMNMQAGDDPAERKQLTLSILDKLGLFFYLR"},"dna_sequence":{"accession":"SIRG01000003.1","fmin":"15354","fmax":"16185","strand":"+","sequence":"ATGAAGTTTAAAATGAAAGGTTTATTTTGTGTCATCCTCAGTAGTTTGGCATTTTCAGGTTGTGTTTATGATTCAAAACTACAACGCCCAGTCATATCAGAGCGAGAAACTGAAATTCCTTTATTATTTAATCAAGCACAGACTCAAGCTGTGTTTGTTACTTATGATGGGATTCATCTAAAAAGTTATGGTAATGATCTAAGCCGAGCAAAGACTGAATATATTCCTGCATCTACATTTAAGATGTTGAATGCTTTAATTGGCTTGCAAAATGCAAAAGCAACCAATACTGAAATATTTCATTGGAATGGTGAAAAGCGCGCTTTTTCAGCATGGGAAAAAGATATGACTTTGGCAGAAGCGATGCAGGCTTCAGCTGTTCCCGTATATCAGGAGCTTGCTCGACGTATTGGCTTGGAATTGATGCGTGAAGAAGTGAAGCGTGTAGGTTTTGGCAATGCGGAGATTGGTCAGCAAGTCGATAATTTTTGGTTGGTGGGTCCTTTAAAAATCTCCCCTGAACAAGAAGTTAAATTTGCCTATCAACTGGCGATGAAGCAATTACCTTTTGATCGAAATGTACAGCAACAAGTCAAAGATATGCTTTATATCGAGAGACGTGGTGACAGTAAACTGTATGCTAAAAGTGGTTGGGGAATGGATGTTGAACCTCAAGTGGGTTGGTATACGGGATGGGTTGAACAACCCGATGGCAAGGTGACTGCATTTGCGTTAAATATGAACATGCAAGCAGGTGATGATCCAGCTGAACGTAAACAATTAACCTTAAGTATTTTGGACAAATTGGGTCTATTTTTTTATTTAAGATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39090","NCBI_taxonomy_name":"Acinetobacter bereziniae","NCBI_taxonomy_id":"106648"}}}},"ARO_accession":"3008606","ARO_id":"47398","ARO_name":"OXA-1190","CARD_short_name":"OXA-1190","ARO_description":"OXA-229 family carbapenem-hydrolyzing class D beta-lactamase OXA-1190.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46498":{"category_aro_accession":"3007709","category_aro_cvterm_id":"46498","category_aro_name":"OXA-229-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-229.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8025":{"model_id":"8025","model_name":"OXA-1191","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10852":{"protein_sequence":{"accession":"RSZ28318.1","sequence":"MKFKMKGLFYVILSSLAFSGCVYDSKLQRPVISGRETEIPLLFNQAQTQAVFVTYDGIHLKSYGNDLSRAKTEYIPASTFKMLNALIGLQNAKATNTEIFHWNGEKRAFSAWEKDMTLAEAMQASAVPVYQELARRIGFELMREEVKRVGFGNAEIGQQVDNFWLVGPLKISPEQEVQFAYQLAMKQLPFDRNVQQQVKDMLYIERRGDSKLYAKSGWGMDVEPQVGWYTGWVEQPNGKVTAFALNMKMQAGDDPAERKQLTLSILDKLGLFFYLR"},"dna_sequence":{"accession":"LKDJ02000001.1","fmin":"229992","fmax":"230823","strand":"+","sequence":"ATGAAGTTTAAAATGAAAGGTTTATTTTATGTCATCCTCAGTAGTTTGGCATTTTCAGGTTGTGTTTATGATTCAAAACTACAACGCCCAGTCATATCAGGGCGAGAAACTGAGATTCCTTTATTATTTAATCAAGCACAGACTCAAGCTGTGTTTGTTACTTATGATGGGATTCATCTAAAAAGTTATGGTAATGATCTAAGCCGAGCAAAGACTGAATATATTCCTGCATCTACATTTAAGATGTTGAATGCTTTAATTGGCTTGCAAAATGCAAAAGCAACCAATACTGAAATATTTCATTGGAATGGTGAAAAGCGCGCTTTTTCAGCATGGGAAAAAGATATGACTTTGGCAGAAGCGATGCAGGCTTCAGCTGTTCCCGTATATCAGGAGCTTGCTCGACGTATTGGCTTCGAATTGATGCGTGAAGAAGTGAAGCGTGTAGGTTTTGGCAATGCGGAGATTGGTCAGCAAGTCGATAATTTTTGGTTGGTGGGTCCTTTAAAAATCTCCCCTGAACAAGAAGTTCAATTTGCCTATCAACTGGCGATGAAGCAATTACCTTTTGATCGAAATGTACAGCAACAAGTCAAAGATATGCTTTATATCGAGAGACGTGGTGACAGTAAACTGTATGCTAAAAGTGGTTGGGGAATGGATGTTGAACCTCAAGTGGGTTGGTATACGGGATGGGTTGAACAACCCAATGGCAAGGTGACTGCATTTGCGTTAAATATGAAAATGCAAGCAGGGGATGATCCAGCTGAACGTAAACAATTAACCTTAAGTATTTTGGACAAATTGGGTCTATTTTTTTATTTAAGATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39090","NCBI_taxonomy_name":"Acinetobacter bereziniae","NCBI_taxonomy_id":"106648"}}}},"ARO_accession":"3008607","ARO_id":"47399","ARO_name":"OXA-1191","CARD_short_name":"OXA-1191","ARO_description":"OXA-229 family carbapenem-hydrolyzing class D beta-lactamase OXA-1191.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46498":{"category_aro_accession":"3007709","category_aro_cvterm_id":"46498","category_aro_name":"OXA-229-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-229.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8026":{"model_id":"8026","model_name":"OXA-1193","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10853":{"protein_sequence":{"accession":"MBJ8552058.1","sequence":"MKFKMKGLFCVILSSLAFSGCVYDSKLQRPVISERETEIPLLFNQAQTQAVFVTYDGIHLKSYGNDLSRAKTEYIPASTFKMLNALIGLQNAKATNTEVFHWNGEKRAFSAWEKDMTLAEAMQASAVPVYQELARRIGLELMREEVKRVGFGNAEIGQQVDNFWLVGPLKISPEQEVQFAYQLAMKQLPFDRNVQQQVKDMLYIESRGDSKLYAKSGWGMDVEPQVGWYTGWVEQPNGKVTAFALNMKMQAGDDPAERKQLTLSILDKLGLFFYLR"},"dna_sequence":{"accession":"JADWNY010000007.1","fmin":"15894","fmax":"16725","strand":"+","sequence":"ATGAAGTTTAAAATGAAAGGTTTATTTTGTGTCATCCTCAGTAGTTTGGCATTTTCAGGTTGTGTTTATGATTCAAAACTACAACGCCCAGTCATATCAGAGCGAGAAACTGAGATTCCTTTATTATTTAATCAAGCACAGACTCAAGCTGTGTTTGTTACTTATGATGGGATTCATCTAAAAAGTTATGGTAATGATCTAAGCCGAGCAAAGACTGAATATATTCCTGCATCTACATTTAAGATGTTGAATGCTTTAATTGGCTTGCAAAATGCAAAAGCAACCAATACTGAAGTATTTCATTGGAATGGTGAAAAGCGCGCTTTTTCAGCATGGGAAAAAGATATGACTTTGGCAGAAGCGATGCAGGCTTCAGCTGTTCCCGTATATCAGGAGCTTGCTCGACGTATTGGCTTGGAATTGATGCGTGAAGAAGTGAAGCGTGTAGGTTTTGGTAATGCGGAGATTGGTCAGCAAGTCGACAATTTTTGGTTGGTGGGTCCTTTAAAAATCTCCCCTGAACAAGAAGTTCAATTTGCCTATCAACTGGCGATGAAGCAATTACCTTTTGATCGAAATGTACAGCAACAAGTCAAAGATATGCTTTATATAGAAAGTCGTGGTGACAGCAAACTATATGCTAAAAGTGGTTGGGGAATGGATGTTGAACCTCAAGTGGGTTGGTATACGGGATGGGTTGAACAACCCAATGGCAAGGTGACTGCATTTGCGTTAAATATGAAAATGCAAGCAGGTGATGATCCAGCTGAACGTAAACAATTAACCTTAAGTATTTTGGACAAATTGGGTCTATTTTTTTATTTAAGATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39090","NCBI_taxonomy_name":"Acinetobacter bereziniae","NCBI_taxonomy_id":"106648"}}}},"ARO_accession":"3008608","ARO_id":"47400","ARO_name":"OXA-1193","CARD_short_name":"OXA-1193","ARO_description":"OXA-229 family carbapenem-hydrolyzing class D beta-lactamase OXA-1193.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46498":{"category_aro_accession":"3007709","category_aro_cvterm_id":"46498","category_aro_name":"OXA-229-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-229.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8027":{"model_id":"8027","model_name":"OXA-1194","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10854":{"protein_sequence":{"accession":"MBJ8450702.1","sequence":"MKFKMKGLFCVILSSLAFSGCVYDSKLQRPVISEREIEIPLLFNQAQTQAVFVTYDGIHLKSYGNDLSRAKTEYIPASTFKMLNALIGLQNAKATNTEVFHWNGEKRAFSAWEKDMTLAEAMQASAVPVYQELARRIGLELMREEVKRVGFGNAEIGQQVDNFWLVGPLKISPEQEVQFAYQLAMKQLPFDSNVQQQVKDMLYIERRGDSKLYAKSGWGMDVEPQVGWYTGWVEQPNGKVTAFALNMNMQAGNDPAERKQLTLSILDKLGLFFYLR"},"dna_sequence":{"accession":"JADWNU010000003.1","fmin":"16425","fmax":"17256","strand":"+","sequence":"ATGAAGTTTAAAATGAAAGGTTTATTTTGTGTCATCCTCAGTAGTTTGGCATTTTCAGGTTGTGTTTATGATTCAAAACTACAACGCCCAGTCATATCAGAGCGAGAAATTGAGATTCCTTTATTATTTAATCAAGCACAGACTCAAGCTGTGTTTGTTACTTATGATGGGATTCATCTAAAAAGTTATGGTAATGATCTAAGCCGAGCAAAGACTGAATATATTCCTGCATCTACATTTAAGATGTTGAATGCTTTAATTGGCTTGCAAAATGCAAAAGCAACCAATACTGAAGTATTTCATTGGAATGGTGAAAAGCGCGCTTTTTCAGCATGGGAAAAAGATATGACTTTGGCAGAAGCGATGCAGGCTTCAGCTGTTCCCGTATATCAGGAGCTTGCTCGACGTATTGGCTTGGAATTGATGCGTGAAGAAGTGAAGCGTGTAGGTTTTGGCAATGCGGAGATTGGTCAGCAAGTCGATAATTTTTGGTTGGTGGGTCCTTTAAAAATCTCCCCTGAACAAGAAGTTCAATTTGCCTATCAACTGGCAATGAAGCAATTGCCTTTTGATTCAAATGTACAGCAACAAGTCAAAGATATGCTTTATATCGAGAGACGTGGTGACAGTAAACTGTATGCTAAAAGTGGTTGGGGAATGGATGTTGAACCTCAAGTGGGTTGGTATACGGGATGGGTTGAACAACCCAATGGCAAGGTGACTGCATTTGCGTTAAATATGAACATGCAAGCAGGTAATGATCCAGCTGAACGTAAACAATTAACCTTAAGTATTTTGGACAAATTGGGTCTATTTTTTTATTTAAGATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39090","NCBI_taxonomy_name":"Acinetobacter bereziniae","NCBI_taxonomy_id":"106648"}}}},"ARO_accession":"3008609","ARO_id":"47401","ARO_name":"OXA-1194","CARD_short_name":"OXA-1194","ARO_description":"OXA-229 family carbapenem-hydrolyzing class D beta-lactamase OXA-1194.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46498":{"category_aro_accession":"3007709","category_aro_cvterm_id":"46498","category_aro_name":"OXA-229-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-229.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8028":{"model_id":"8028","model_name":"OXA-1198","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10855":{"protein_sequence":{"accession":"WEY36498.1","sequence":"MRPLLFSALLLLSGHAQASEWNDSQAVDKLFGAAGVKGTFVLYDVQRQRYVGHDRERAETRFVPASTYKVANSLIGLSTGAVRSADEVLPYGGKPQHFKAWEHDMSLRDAIKASNVPVYQELARRIGLERMRANVSRLGYGNAEIGQVVDNFWLVGPLKISAMEQTRFLLRLAQGELPFPAPVQSTVRAMTLLESGPGWELHGKTGWCFDCTPELGWWVGWVKRNERLYGFALNIDMPGGEADIGKRVELGKASLKALGILP"},"dna_sequence":{"accession":"OQ695552.1","fmin":"0","fmax":"789","strand":"+","sequence":"ATGCGCCCTCTCCTCTTCAGCGCCCTTCTCCTGCTCTCCGGGCATGCCCAGGCCAGCGAATGGAACGACAGCCAGGCCGTGGACAAGCTATTCGGCGCGGCCGGTGTGAAAGGCACCTTCGTCCTCTACGATGTGCAGCGGCAGCGCTATGTCGGCCATGACCGGGAGCGCGCGGAAACCCGCTTCGTTCCCGCTTCCACCTACAAGGTGGCGAACAGCCTGATCGGCTTATCCACAGGGGCGGTTAGATCCGCCGACGAGGTTCTTCCCTATGGCGGCAAACCCCAGCACTTCAAGGCCTGGGAGCACGACATGAGCCTGCGCGACGCGATCAAGGCATCGAACGTACCGGTCTACCAGGAACTGGCGCGGCGCATCGGCCTGGAGCGGATGCGCGCCAATGTCTCGCGCCTGGGTTACGGCAACGCGGAAATCGGCCAGGTTGTGGATAACTTCTGGTTGGTGGGACCGCTGAAGATCAGCGCGATGGAACAGACCCGCTTTCTGCTCCGACTGGCGCAGGGAGAATTGCCATTCCCCGCCCCGGTGCAGTCCACCGTGCGCGCCATGACCCTGCTGGAAAGCGGCCCGGGCTGGGAGCTGCACGGCAAGACCGGCTGGTGCTTCGACTGCACGCCGGAACTCGGCTGGTGGGTGGGCTGGGTGAAGCGCAACGAGCGGCTCTACGGCTTCGCCCTGAACATCGACATGCCCGGCGGCGAGGCCGACATCGGCAAGCGCGTCGAACTGGGCAAGGCCAGTCTCAAGGCTCTCGGGATACTGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008610","ARO_id":"47402","ARO_name":"OXA-1198","CARD_short_name":"OXA-1198","ARO_description":"OXA-50 family oxacillin-hydrolyzing class D beta-lactamase OXA-1198.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46513":{"category_aro_accession":"3007724","category_aro_cvterm_id":"46513","category_aro_name":"OXA-50-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-50.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8029":{"model_id":"8029","model_name":"OXA-1199","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10856":{"protein_sequence":{"accession":"WFP34012.1","sequence":"MRPLLLSALLLLSGHTQASEWNDSQAVDKLFGAAGVKGTFVLYDVQRQRYVGHDRERAETRFVPASTYKVANSLIGLSTGAVRSADEVLPYGGKPQRFKAWEHDMSLRDAIKASNVPVYQELARRIGLERMRANVSRLGYGNAEIGQVVDNFWLVGPLKISAMEQTRLLLRLAQGELPFPAPVQSTVRAMTLLESGPGWELHGKTGWCFDCTPELGWWVGWVKRNERLYGFALNIDMPGGEADIGKRVELGKASLKALGILP"},"dna_sequence":{"accession":"OQ709074.1","fmin":"0","fmax":"789","strand":"+","sequence":"ATGCGCCCTCTCCTCTTGAGTGCCCTTCTCCTGCTTTCCGGGCATACCCAGGCCAGCGAATGGAACGACAGCCAGGCCGTGGACAAGCTATTCGGCGCGGCCGGGGTGAAAGGCACCTTCGTCCTCTACGATGTGCAGCGGCAGCGCTATGTTGGCCATGACCGGGAGCGCGCGGAAACCCGCTTCGTTCCCGCTTCCACCTACAAGGTGGCGAACAGCCTGATCGGCTTATCCACAGGGGCGGTTAGATCCGCCGACGAGGTTCTTCCCTATGGCGGCAAGCCCCAGCGCTTCAAGGCCTGGGAGCACGACATGAGCCTGCGCGACGCGATCAAGGCATCGAACGTACCGGTCTACCAGGAACTGGCGCGGCGCATCGGCCTGGAGCGGATGCGCGCCAATGTCTCGCGCCTGGGTTACGGCAACGCGGAAATCGGCCAGGTTGTGGATAACTTCTGGTTGGTGGGACCGCTGAAGATCAGCGCGATGGAACAGACCCGCCTTCTGCTCCGACTGGCGCAGGGAGAATTGCCATTCCCCGCCCCGGTGCAGTCCACCGTGCGCGCCATGACCCTGCTGGAAAGCGGCCCGGGCTGGGAGCTGCACGGCAAGACCGGCTGGTGCTTCGACTGCACGCCGGAACTCGGCTGGTGGGTGGGCTGGGTGAAGCGCAACGAGCGGCTCTACGGCTTCGCCCTGAACATCGACATGCCCGGCGGCGAGGCCGACATCGGCAAGCGCGTCGAACTGGGCAAGGCCAGTCTCAAGGCTCTCGGGATACTGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008611","ARO_id":"47403","ARO_name":"OXA-1199","CARD_short_name":"OXA-1199","ARO_description":"OXA-50 family oxacillin-hydrolyzing class D beta-lactamase OXA-1199.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46513":{"category_aro_accession":"3007724","category_aro_cvterm_id":"46513","category_aro_name":"OXA-50-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-50.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8030":{"model_id":"8030","model_name":"OXA-1200","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10857":{"protein_sequence":{"accession":"WGG88838.1","sequence":"MRVLALSAVFLVASIIGMPAVAKEWQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGQTRDIATWNRDHNLITAMKYSVVPVYQEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISATEQISFLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYSTRIGWWVGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP"},"dna_sequence":{"accession":"OQ813782.1","fmin":"0","fmax":"786","strand":"+","sequence":"ATGCGTGTATTAGCCTTATCGGCTGTGTTTTTGGTGGCATCGATTATCGGAATGCCTGCGGTAGCAAAGGAATGGCAAGAAAACAAAAGTTGGAATGCTCACTTTACTGAACATAAATCACAGGGCGTAGTTGTGCTCTGGAATGAGAATAAGCAGCAAGGATTTACCAATAATCTTAAACGGGCGAACCAAGCATTTTTACCCGCATCTACCTTTAAAATTCCCAATAGCTTGATCGCCCTCGATTTGGGCGTGGTTAAGGATGAACACCAAGTCTTTAAGTGGGATGGACAGACGCGCGATATCGCCACTTGGAATCGCGATCATAATCTAATCACCGCGATGAAATATTCAGTTGTGCCTGTTTATCAAGAATTTGCCCGCCAAATTGGCGAGGCACGTATGAGCAAGATGCTACATGCTTTCGATTATGGTAATGAGGACATTTCGGGCAATGTAGACAGTTTCTGGCTCGACGGTGGTATTCGAATTTCGGCCACGGAGCAAATCAGCTTTTTAAGAAAGCTGTATCACAATAAGTTACACGTATCGGAGCGCAGCCAGCGTATTGTCAAACAAGCCATGCTGACCGAAGCCAATGGTGACTATATTATTCGGGCTAAAACTGGATACTCGACTAGGATTGGCTGGTGGGTCGGTTGGGTTGAACTTGATGATAATGTGTGGTTTTTTGCGATGAATATGGATATGCCCACATCGGATGGTTTAGGGCTGCGCCAAGCCATCACAAAAGAAGTGCTCAAACAGGAAAAAATTATTCCCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008612","ARO_id":"47404","ARO_name":"OXA-1200","CARD_short_name":"OXA-1200","ARO_description":"OXA-48 family class D beta-lactamase OXA-1200.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46510":{"category_aro_accession":"3007721","category_aro_cvterm_id":"46510","category_aro_name":"OXA-48-like beta-lactamase","category_aro_description":"OXA-48-type beta-lactamases are now routinely encountered in bacterial infections caused by carbapenam-resistant Enterobacterales. OXA-48-like proteins confer resistance to penicillin (which is efficiently hydrolyzed) and carbapenam antibiotics (which is more slowly broken down). The spectrum of activity of these variants varies, with some hydrolyzing expanded-spectrum oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8031":{"model_id":"8031","model_name":"OXA-1201","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10858":{"protein_sequence":{"accession":"WGJ78634.1","sequence":"MRVLALSAVFLVASIIGMPAVSKEWQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGQTRDIAAWNRDHDLITAMKYSVVPVYQEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISATQQIAFLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYSTSIEPKIGWWVGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP"},"dna_sequence":{"accession":"OQ858941.1","fmin":"0","fmax":"798","strand":"+","sequence":"ATGCGTGTATTAGCCTTATCGGCTGTGTTTTTGGTGGCATCGATTATCGGAATGCCAGCGGTATCAAAGGAATGGCAAGAAAACAAAAGTTGGAATGCTCACTTTACTGAACATAAATCACAGGGCGTAGTTGTGCTCTGGAATGAGAATAAGCAGCAAGGATTTACCAATAATCTTAAACGGGCGAACCAAGCATTTTTACCCGCATCTACCTTTAAAATTCCCAATAGCTTGATCGCCCTCGATTTGGGCGTGGTTAAGGATGAACACCAAGTCTTTAAGTGGGATGGACAGACGCGTGATATCGCCGCTTGGAATCGTGACCATGACTTAATTACCGCGATGAAGTACTCAGTTGTGCCTGTTTATCAAGAATTTGCCCGCCAAATTGGTGAGGCACGTATGAGTAAAATGCTGCACGCCTTCGATTATGGCAATGAGGATATCTCGGGCAATGTAGACAGTTTTTGGCTCGATGGTGGTATTCGCATTTCGGCTACCCAGCAAATCGCTTTTTTACGCAAGCTGTATCACAACAAGCTGCACGTTTCTGAGCGTAGTCAGCGCATCGTGAAACAAGCCATGCTGACCGAAGCCAATGGCGACTATATTATTCGGGCTAAAACGGGATACTCGACTAGTATCGAACCTAAGATTGGCTGGTGGGTTGGTTGGGTTGAACTTGATGATAATGTGTGGTTTTTTGCGATGAATATGGATATGCCCACATCGGATGGTTTAGGGCTGCGCCAAGCCATCACAAAAGAAGTGCTCAAACAGGAGAAAATTATTCCCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008613","ARO_id":"47405","ARO_name":"OXA-1201","CARD_short_name":"OXA-1201","ARO_description":"OXA-48 family class D beta-lactamase OXA-1201.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46510":{"category_aro_accession":"3007721","category_aro_cvterm_id":"46510","category_aro_name":"OXA-48-like beta-lactamase","category_aro_description":"OXA-48-type beta-lactamases are now routinely encountered in bacterial infections caused by carbapenam-resistant Enterobacterales. OXA-48-like proteins confer resistance to penicillin (which is efficiently hydrolyzed) and carbapenam antibiotics (which is more slowly broken down). The spectrum of activity of these variants varies, with some hydrolyzing expanded-spectrum oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8032":{"model_id":"8032","model_name":"OXA-1202","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10859":{"protein_sequence":{"accession":"WHL50409.1","sequence":"MKTFAAYVITACLSSTALASSITENTFWNKEFSAEAVNGVFVLCKSSSKSCATNNLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLSLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLFLNKLSASKENQLIAKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKGTEVYFFAFNMDIDNENKLPLRKSIPTKIMASEGIIGG"},"dna_sequence":{"accession":"OQ948126.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGAAAACATTTGCCGCATATGTAATTACTGCGTGTCTTTCAAGTACGGCATTAGCTAGTTCAATTACAGAAAATACGTTTTGGAACAAAGAGTTCTCTGCCGAAGCCGTCAATGGTGTTTTCGTGCTTTGTAAAAGTAGCAGTAAATCCTGCGCTACCAATAACTTAGCTCGTGCATCAAAGGAATATCTTCCAGCATCAACATTTAAGATCCCCAACGCAATTATCGGCCTAGAAACTGGTGTCATAAAGAATGAGCATCAGGTTTTCAAATGGGACGGAAAGCCAAGAGCCATGAAGCAATGGGAAAGAGACTTGAGCTTAAGAGGGGCAATACAAGTTTCAGCGGTTCCCGTATTTCAACAAATCGCCAGAGAAGTTGGCGAAGTAAGAATGCAGAAATATCTTAAAAAATTTTCATATGGTAACCAGAATATCAGTGGTGGCATTGACAAATTCTGGTTGGAGGGTCAGCTTAGAATTTCCGCAGTTAATCAAGTGGAGTTTCTAGAGTCTCTATTTTTAAATAAATTGTCAGCATCAAAAGAAAATCAGCTAATAGCAAAAGAGGCTTTGGTAACGGAGGCTGCGCCTGAATATCTTGTGCATTCAAAAACTGGTTTTTCTGGTGTGGGAACTGAGTCAAATCCTGGTGTCGCATGGTGGGTTGGTTGGGTTGAGAAGGGAACAGAGGTTTACTTTTTCGCCTTTAACATGGATATAGACAACGAAAATAAGTTGCCGCTAAGAAAATCCATTCCCACCAAAATCATGGCAAGTGAGGGCATCATTGGTGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008614","ARO_id":"47406","ARO_name":"OXA-1202","CARD_short_name":"OXA-1202","ARO_description":"OXA-10 family class D beta-lactamase OXA-1202.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46486":{"category_aro_accession":"3007697","category_aro_cvterm_id":"46486","category_aro_name":"OXA-10-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-10.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8033":{"model_id":"8033","model_name":"OXA-1203","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10860":{"protein_sequence":{"accession":"WMF72384.1","sequence":"MKTFAAYVITACLSSTALASSITENTFWNKEFSAEAVNGVFVLCKSSSKSCATNNLARASKEYLPVSTFKIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLSLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLFLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKGTEVYFFAFNMDIDNENKLPLRKSIPTKIMASEGIIGG"},"dna_sequence":{"accession":"CP121188.1","fmin":"19808","fmax":"20609","strand":"+","sequence":"ATGAAAACATTTGCCGCATATGTAATTACTGCGTGTCTTTCAAGTACGGCATTAGCTAGTTCAATTACAGAAAATACGTTTTGGAACAAAGAGTTCTCTGCCGAAGCCGTCAATGGTGTTTTCGTGCTTTGTAAAAGTAGCAGTAAATCCTGCGCTACCAATAACTTAGCTCGTGCATCAAAGGAATATCTTCCAGTATCAACATTTAAGATCCCCAACGCAATTATCGGCCTAGAAACTGGTGTCATAAAGAATGAGCATCAGGTTTTCAAATGGGACGGAAAGCCAAGAGCCATGAAACAATGGGAAAGAGACTTGAGCTTAAGAGGGGCAATACAAGTTTCAGCGGTTCCCGTATTTCAACAAATCGCCAGAGAAGTTGGCGAAGTAAGAATGCAGAAATATCTTAAAAAATTTTCATATGGTAACCAGAATATCAGTGGTGGCATTGACAAATTCTGGTTGGAGGGTCAGCTTAGAATTTCCGCAGTTAATCAAGTGGAGTTTCTAGAGTCTCTATTTTTAAATAAATTGTCAGCATCAAAAGAAAATCAGCTAATAGTAAAAGAGGCTTTGGTAACGGAGGCTGCGCCTGAATATCTTGTGCATTCAAAAACTGGTTTTTCTGGTGTGGGAACTGAGTCAAATCCTGGTGTCGCATGGTGGGTTGGTTGGGTTGAGAAGGGAACAGAGGTTTACTTTTTCGCCTTTAACATGGATATAGACAACGAAAATAAGTTGCCGCTAAGAAAATCCATTCCCACCAAAATCATGGCAAGTGAGGGCATCATTGGTGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008615","ARO_id":"47407","ARO_name":"OXA-1203","CARD_short_name":"OXA-1203","ARO_description":"OXA-10 family class D beta-lactamase OXA-1203.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46486":{"category_aro_accession":"3007697","category_aro_cvterm_id":"46486","category_aro_name":"OXA-10-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-10.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8034":{"model_id":"8034","model_name":"OXA-1204","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10861":{"protein_sequence":{"accession":"WHU50588.1","sequence":"MKTFAAYVITACLSSTALASSITENTFWNKEFSAEAVNGVFVLCKSSSKSCATNNLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLSLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFGLEGQLRISAVNQVEFLESLFLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKGTEVYFFAFNMDIDNENKLPLRKSIPTKIMASEGIIGG"},"dna_sequence":{"accession":"OR025344.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGAAAACATTTGCCGCATATGTAATTACTGCGTGTCTTTCAAGTACGGCATTAGCTAGTTCAATTACAGAAAATACGTTTTGGAACAAAGAGTTCTCTGCCGAAGCCGTCAATGGTGTTTTCGTGCTTTGTAAAAGTAGCAGTAAATCCTGCGCTACCAATAACTTAGCTCGTGCATCAAAGGAATATCTTCCAGCATCAACATTTAAGATCCCCAACGCAATTATCGGCCTAGAAACTGGTGTCATAAAGAATGAGCATCAGGTTTTCAAATGGGACGGAAAGCCAAGAGCCATGAAACAATGGGAAAGAGACTTGAGCTTAAGAGGGGCAATACAAGTTTCAGCGGTTCCCGTATTTCAACAAATCGCCAGAGAAGTTGGCGAAGTAAGAATGCAGAAATATCTTAAAAAATTTTCATATGGTAACCAGAATATCAGTGGTGGCATTGACAAATTCGGGTTGGAGGGTCAGCTTAGAATTTCCGCAGTTAATCAAGTGGAGTTTCTAGAGTCTCTATTTTTAAATAAATTGTCAGCATCAAAAGAAAATCAGCTAATAGTAAAAGAGGCTTTGGTAACGGAGGCTGCGCCTGAATATCTTGTGCATTCAAAAACTGGTTTTTCTGGTGTGGGAACTGAGTCAAATCCTGGTGTCGCATGGTGGGTTGGTTGGGTTGAGAAGGGAACAGAGGTTTACTTTTTCGCCTTTAACATGGATATAGACAACGAAAATAAGTTGCCGCTAAGAAAATCCATTCCCACCAAAATCATGGCAAGTGAGGGCATCATTGGTGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008616","ARO_id":"47408","ARO_name":"OXA-1204","CARD_short_name":"OXA-1204","ARO_description":"OXA-10 family class D beta-lactamase OXA-1204.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46486":{"category_aro_accession":"3007697","category_aro_cvterm_id":"46486","category_aro_name":"OXA-10-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-10.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8035":{"model_id":"8035","model_name":"OXA-1205","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10862":{"protein_sequence":{"accession":"WIF29729.1","sequence":"MRVLALSAVFLVASIIGMPAVAKEWQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGQTRDIAAWNRDHDLITAMKYSVVPVYQEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISATQQIAFLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYSTSIEPKIGWWVGWVELDDNVWFFAMNMDMPTWDGLGLRQAITKEVLKQEKIIP"},"dna_sequence":{"accession":"OR076750.1","fmin":"0","fmax":"798","strand":"+","sequence":"ATGCGTGTATTAGCCTTATCGGCTGTGTTTTTGGTGGCATCGATTATCGGAATGCCAGCGGTAGCAAAGGAATGGCAAGAAAACAAAAGTTGGAATGCTCACTTTACTGAACATAAATCACAGGGCGTAGTTGTGCTCTGGAATGAGAATAAGCAGCAAGGATTTACCAATAATCTTAAACGGGCGAACCAAGCATTTTTACCCGCATCTACCTTTAAAATTCCCAATAGCTTGATCGCCCTCGATTTGGGCGTGGTTAAGGATGAACACCAAGTCTTTAAGTGGGATGGACAGACGCGTGATATCGCCGCTTGGAATCGTGACCATGACTTAATTACCGCGATGAAGTACTCAGTTGTGCCTGTTTATCAAGAATTTGCCCGCCAAATTGGTGAGGCACGTATGAGTAAAATGCTGCACGCCTTCGATTATGGCAATGAGGATATCTCGGGCAATGTAGACAGTTTTTGGCTCGATGGTGGTATTCGCATTTCGGCTACCCAGCAAATCGCTTTTTTACGCAAGCTGTATCACAACAAGCTGCACGTTTCTGAGCGTAGTCAGCGCATCGTGAAACAAGCCATGCTGACCGAAGCCAATGGCGACTATATTATTCGGGCTAAAACGGGATACTCGACTAGCATCGAACCTAAGATTGGCTGGTGGGTTGGTTGGGTTGAACTTGATGATAATGTGTGGTTTTTTGCGATGAATATGGATATGCCCACATGGGATGGTTTAGGGCTGCGCCAAGCCATCACAAAAGAAGTGCTCAAACAGGAGAAAATTATTCCCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3008617","ARO_id":"47409","ARO_name":"OXA-1205","CARD_short_name":"OXA-1205","ARO_description":"OXA-48 family class D beta-lactamase OXA-1205.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46510":{"category_aro_accession":"3007721","category_aro_cvterm_id":"46510","category_aro_name":"OXA-48-like beta-lactamase","category_aro_description":"OXA-48-type beta-lactamases are now routinely encountered in bacterial infections caused by carbapenam-resistant Enterobacterales. OXA-48-like proteins confer resistance to penicillin (which is efficiently hydrolyzed) and carbapenam antibiotics (which is more slowly broken down). The spectrum of activity of these variants varies, with some hydrolyzing expanded-spectrum oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8036":{"model_id":"8036","model_name":"OXA-1206","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10863":{"protein_sequence":{"accession":"WMQ57530.1","sequence":"MNNRLARLLAPVAFGLGLLAAHVPALAAPQEIPLDAAALFRQAGTTGTMVIYDLRRDRMLTYNPSRAATPYSPASTFKIMNSMIGLETGAVADVDHDKLPWDGKVWLVGGKAVLPEACNADVPLRVALPNSCVPAYQALARRVGSAAYQRYLGASHYGNADSSGPVDRFWLNGKLQISAYQQIDFLKGLVQRTLPFSPATFNAVDDITVLERTAAYTLHGKTGWADSARPAVGWLVGWVERGDDGYLFALNLDLLRPEHARARMEIARAALRQAGALPE"},"dna_sequence":{"accession":"OR062596.1","fmin":"0","fmax":"840","strand":"+","sequence":"ATGAACAATCGTCTTGCCCGTCTGCTGGCGCCGGTGGCATTCGGCCTCGGCCTGCTTGCCGCTCACGTGCCCGCGCTGGCCGCACCCCAGGAAATTCCGCTCGATGCCGCGGCGCTGTTCCGCCAGGCCGGTACCACCGGCACCATGGTGATCTACGACCTGCGGCGCGACCGCATGCTGACCTACAACCCGTCGCGCGCCGCCACGCCCTACTCGCCGGCATCGACCTTCAAGATCATGAATTCCATGATCGGCCTCGAGACCGGCGCGGTGGCCGACGTCGACCATGACAAGCTGCCGTGGGACGGCAAGGTCTGGCTGGTCGGCGGCAAGGCCGTGCTACCCGAGGCCTGCAACGCCGACGTGCCGCTGCGCGTGGCCCTGCCCAACTCCTGCGTGCCGGCCTACCAGGCGCTGGCGCGCCGGGTCGGCAGCGCGGCCTACCAGCGCTACCTGGGCGCGTCGCACTATGGCAATGCCGACAGCTCCGGGCCGGTGGACCGCTTCTGGCTGAACGGCAAGCTGCAGATCAGCGCCTACCAGCAGATCGATTTCCTGAAGGGCCTGGTGCAGCGCACCCTGCCGTTCTCGCCCGCCACCTTCAACGCCGTGGACGACATCACGGTGCTGGAGCGCACCGCCGCCTACACCCTGCACGGCAAGACCGGCTGGGCCGACTCGGCCAGGCCGGCGGTGGGCTGGCTGGTGGGCTGGGTCGAGCGCGGCGACGACGGCTACCTGTTCGCGCTCAACCTGGACCTGCTGCGGCCGGAACATGCCAGGGCGCGGATGGAGATCGCGCGCGCGGCGCTGCGGCAGGCGGGGGCGTTGCCGGAATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"47905","NCBI_taxonomy_name":"Cupriavidus taiwanensis","NCBI_taxonomy_id":"164546"}}}},"ARO_accession":"3008618","ARO_id":"47410","ARO_name":"OXA-1206","CARD_short_name":"OXA-1206","ARO_description":"Class D beta-lactamase OXA-1206.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8037":{"model_id":"8037","model_name":"OXA-1207","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10864":{"protein_sequence":{"accession":"WJL30769.1","sequence":"MRVLALSAVFLVASIIGMPAVAKEWQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGQTRDIAAWNRDHDLITAMKYSVVPVYQEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISATQQIAFLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYSTGIEPKIGWWVGWVELDDNVWFFAMNMDMPTWDGLGLRQAITKEVLKQEKIIP"},"dna_sequence":{"accession":"OR139853.1","fmin":"0","fmax":"798","strand":"+","sequence":"ATGCGTGTATTAGCCTTATCGGCTGTGTTTTTGGTGGCATCGATTATCGGAATGCCAGCGGTAGCAAAGGAATGGCAAGAAAACAAAAGTTGGAATGCTCACTTTACTGAACATAAATCACAGGGCGTAGTTGTGCTCTGGAATGAGAATAAGCAGCAAGGATTTACCAATAATCTTAAACGGGCGAACCAAGCATTTTTACCCGCATCTACCTTTAAAATTCCCAATAGCTTGATCGCCCTCGATTTGGGCGTGGTTAAGGATGAACACCAAGTCTTTAAGTGGGATGGACAGACGCGTGATATCGCCGCTTGGAATCGTGACCATGACTTAATTACCGCGATGAAGTACTCAGTTGTGCCTGTTTATCAAGAATTTGCCCGCCAAATTGGTGAGGCACGTATGAGTAAAATGCTGCACGCCTTCGATTATGGCAATGAGGATATCTCGGGCAATGTAGACAGTTTTTGGCTCGATGGTGGTATTCGCATTTCGGCTACCCAGCAAATCGCTTTTTTACGCAAGCTGTATCACAACAAGCTGCACGTTTCTGAGCGTAGTCAGCGCATCGTGAAACAAGCCATGCTGACCGAAGCCAATGGCGACTATATTATTCGGGCTAAAACGGGATACTCGACTGGAATCGAACCTAAGATTGGCTGGTGGGTTGGTTGGGTTGAACTTGATGATAATGTGTGGTTTTTTGCGATGAATATGGATATGCCCACATGGGATGGTTTAGGGCTGCGCCAAGCCATCACAAAAGAAGTGCTCAAACAGGAGAAAATTATTCCCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3008619","ARO_id":"47411","ARO_name":"OXA-1207","CARD_short_name":"OXA-1207","ARO_description":"OXA-48 family class D beta-lactamase OXA-1207.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46510":{"category_aro_accession":"3007721","category_aro_cvterm_id":"46510","category_aro_name":"OXA-48-like beta-lactamase","category_aro_description":"OXA-48-type beta-lactamases are now routinely encountered in bacterial infections caused by carbapenam-resistant Enterobacterales. OXA-48-like proteins confer resistance to penicillin (which is efficiently hydrolyzed) and carbapenam antibiotics (which is more slowly broken down). The spectrum of activity of these variants varies, with some hydrolyzing expanded-spectrum oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8038":{"model_id":"8038","model_name":"OXA-1208","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10865":{"protein_sequence":{"accession":"BEK62627.1","sequence":"MKTLQLGLIVLITTFGSACTTINPSVEAAKNQQQQGTQRQIQQAFDQLQTTGVIVIKDQHGLHSYGNDLSRAQTPYVPASTFKMLNALIGLEHDKATINEVFKWDGQKRSFPAWEKDMTLGQAMQASAVPVYQELARRIGLDLMQKEVQRIEYGNQQIGTVVDNFWLVGPLQITPVQEVLFVEKLANKKLAFKPEVQRAVQDMLLIEQKPNYKLYAKSGWGMDIEPQVGWWTGWVEYPDREKVYFSLNMHIKTGIPASVREQLVKQSLTTLGLI"},"dna_sequence":{"accession":"LC771429.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAAAACTTTACAGTTGGGACTCATCGTCCTCATTACAACCTTCGGTTCTGCTTGTACCACAATAAACCCCTCCGTAGAAGCAGCTAAAAACCAGCAACAGCAAGGTACGCAACGGCAGATCCAACAAGCCTTCGATCAACTCCAAACCACGGGGGTGATTGTCATTAAGGATCAGCATGGCTTACACAGCTACGGCAATGACCTAAGCCGCGCTCAGACACCGTATGTGCCCGCTTCTACCTTTAAAATGCTGAATGCCTTAATCGGACTAGAGCATGACAAGGCAACCATTAACGAAGTATTTAAATGGGATGGTCAAAAGCGTAGCTTTCCTGCATGGGAAAAAGACATGACTTTAGGGCAAGCCATGCAGGCATCTGCCGTTCCCGTTTATCAGGAGCTAGCACGGCGCATTGGTCTAGACCTGATGCAAAAAGAAGTGCAACGCATTGAATATGGCAATCAACAGATTGGCACCGTTGTCGATAATTTTTGGTTAGTCGGCCCACTGCAAATTACGCCTGTCCAAGAAGTCCTTTTTGTCGAAAAGCTGGCAAATAAAAAGCTTGCATTTAAACCAGAAGTGCAACGGGCGGTACAAGACATGCTACTGATTGAACAGAAACCGAATTATAAACTTTATGCAAAATCAGGTTGGGGCATGGACATAGAACCGCAAGTTGGTTGGTGGACAGGCTGGGTAGAATATCCCGATCGTGAAAAGGTCTATTTCTCTTTAAATATGCACATTAAAACGGGAATTCCAGCCAGCGTACGTGAGCAACTGGTTAAACAAAGCTTGACTACATTGGGTCTAATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36837","NCBI_taxonomy_name":"Acinetobacter sp.","NCBI_taxonomy_id":"472"}}}},"ARO_accession":"3008620","ARO_id":"47412","ARO_name":"OXA-1208","CARD_short_name":"OXA-1208","ARO_description":"OXA-211 family carbapenem-hydrolyzing class D beta-lactamase OXA-1208.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46494":{"category_aro_accession":"3007705","category_aro_cvterm_id":"46494","category_aro_name":"OXA-211-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-211.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8039":{"model_id":"8039","model_name":"OXA-1211","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10866":{"protein_sequence":{"accession":"WKT28618.1","sequence":"MRVLALSAVFLVASIIGMPAVAKEWQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGQTRDIAAWNRDHDLITAMKYSVVPVYQEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISATQQIAFLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYLTRIEPKIGWWVGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP"},"dna_sequence":{"accession":"OR282803.1","fmin":"0","fmax":"798","strand":"+","sequence":"ATGCGTGTATTAGCCTTATCGGCTGTGTTTTTGGTGGCATCGATTATCGGAATGCCAGCGGTAGCAAAGGAATGGCAAGAAAACAAAAGTTGGAATGCTCACTTTACTGAACATAAATCACAGGGCGTAGTTGTGCTCTGGAATGAGAATAAGCAGCAAGGATTTACCAATAATCTTAAACGGGCGAACCAAGCATTTTTACCCGCATCTACCTTTAAAATTCCCAATAGCTTGATCGCCCTCGATTTGGGCGTGGTTAAGGATGAACACCAAGTCTTTAAGTGGGATGGACAGACGCGTGATATCGCCGCTTGGAATCGTGACCATGACTTAATTACCGCGATGAAGTACTCAGTTGTGCCTGTTTATCAAGAATTTGCCCGCCAAATTGGTGAGGCACGTATGAGTAAAATGCTGCACGCCTTCGATTATGGCAATGAGGATATCTCGGGCAATGTAGACAGTTTTTGGCTCGATGGTGGTATTCGCATTTCGGCTACCCAGCAAATCGCTTTTTTACGCAAGCTGTATCACAACAAGCTGCACGTTTCTGAGCGTAGTCAGCGCATCGTGAAACAAGCCATGCTGACCGAAGCCAATGGCGACTATATTATTCGGGCTAAAACGGGATACTTGACTAGAATCGAACCTAAGATTGGCTGGTGGGTTGGTTGGGTTGAACTTGATGATAATGTGTGGTTTTTTGCGATGAATATGGATATGCCCACATCGGATGGTTTAGGGCTGCGCCAAGCCATCACAAAAGAAGTGCTCAAACAGGAGAAAATTATTCCCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008621","ARO_id":"47413","ARO_name":"OXA-1211","CARD_short_name":"OXA-1211","ARO_description":"OXA-48 family class D beta-lactamase OXA-1211.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46510":{"category_aro_accession":"3007721","category_aro_cvterm_id":"46510","category_aro_name":"OXA-48-like beta-lactamase","category_aro_description":"OXA-48-type beta-lactamases are now routinely encountered in bacterial infections caused by carbapenam-resistant Enterobacterales. OXA-48-like proteins confer resistance to penicillin (which is efficiently hydrolyzed) and carbapenam antibiotics (which is more slowly broken down). The spectrum of activity of these variants varies, with some hydrolyzing expanded-spectrum oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8040":{"model_id":"8040","model_name":"OXA-1212","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10867":{"protein_sequence":{"accession":"WKT28619.1","sequence":"MRVLALSAVFLVASIIGMPAVAKEWQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGQTRDIATWNRDHNLITAMKYSVVPVYQEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISATEQISFLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYSTRIEPNIGWWVGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP"},"dna_sequence":{"accession":"OR282804.1","fmin":"0","fmax":"798","strand":"+","sequence":"ATGCGTGTATTAGCCTTATCGGCTGTGTTTTTGGTGGCATCGATTATCGGAATGCCTGCGGTAGCAAAGGAATGGCAAGAAAACAAAAGTTGGAATGCTCACTTTACTGAACATAAATCACAGGGCGTAGTTGTGCTCTGGAATGAGAATAAGCAGCAAGGATTTACCAATAATCTTAAACGGGCGAACCAAGCATTTTTACCCGCATCTACCTTTAAAATTCCCAATAGCTTGATCGCCCTCGATTTGGGCGTGGTTAAGGATGAACACCAAGTCTTTAAGTGGGATGGACAGACGCGCGATATCGCCACTTGGAATCGCGATCATAATCTAATCACCGCGATGAAATATTCAGTTGTGCCTGTTTATCAAGAATTTGCCCGCCAAATTGGCGAGGCACGTATGAGCAAGATGCTACATGCTTTCGATTATGGTAATGAGGACATTTCGGGCAATGTAGACAGTTTCTGGCTCGACGGTGGTATTCGAATTTCGGCCACGGAGCAAATCAGCTTTTTAAGAAAGCTGTATCACAATAAGTTACACGTATCGGAGCGCAGCCAGCGTATTGTCAAACAAGCCATGCTGACCGAAGCCAATGGTGACTATATTATTCGGGCTAAAACTGGATACTCGACTAGAATCGAACCTAATATTGGCTGGTGGGTCGGTTGGGTTGAACTTGATGATAATGTGTGGTTTTTTGCGATGAATATGGATATGCCCACATCGGATGGTTTAGGGCTGCGCCAAGCCATCACAAAAGAAGTGCTCAAACAGGAAAAAATTATTCCCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008622","ARO_id":"47414","ARO_name":"OXA-1212","CARD_short_name":"OXA-1212","ARO_description":"OXA-48 family class D beta-lactamase OXA-1212.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46510":{"category_aro_accession":"3007721","category_aro_cvterm_id":"46510","category_aro_name":"OXA-48-like beta-lactamase","category_aro_description":"OXA-48-type beta-lactamases are now routinely encountered in bacterial infections caused by carbapenam-resistant Enterobacterales. OXA-48-like proteins confer resistance to penicillin (which is efficiently hydrolyzed) and carbapenam antibiotics (which is more slowly broken down). The spectrum of activity of these variants varies, with some hydrolyzing expanded-spectrum oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8041":{"model_id":"8041","model_name":"OXA-1213","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10868":{"protein_sequence":{"accession":"WKT28620.1","sequence":"MRVLALSAVFLVASIIEMPAVAKEWQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGQTRDIATWNRDHNLITAMKYSVVPVYQEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISATEQISFLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYSTGIEPKIGWWVGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP"},"dna_sequence":{"accession":"OR282805.1","fmin":"0","fmax":"798","strand":"+","sequence":"ATGCGTGTATTAGCCTTATCGGCTGTGTTTTTGGTGGCATCGATTATCGAAATGCCTGCGGTAGCAAAGGAATGGCAAGAAAACAAAAGTTGGAATGCTCACTTTACTGAACATAAATCACAGGGCGTAGTTGTGCTCTGGAATGAGAATAAGCAGCAAGGATTTACCAATAATCTTAAACGGGCGAACCAAGCATTTTTACCCGCATCTACCTTTAAAATTCCCAATAGCTTGATCGCCCTCGATTTGGGCGTGGTTAAGGATGAACACCAAGTCTTTAAGTGGGATGGACAGACGCGCGATATCGCCACTTGGAATCGCGATCATAATCTAATCACCGCGATGAAATATTCAGTTGTGCCTGTTTATCAAGAATTTGCCCGCCAAATTGGCGAGGCACGTATGAGCAAGATGCTACATGCTTTCGATTATGGTAATGAGGACATTTCGGGCAATGTAGACAGTTTCTGGCTCGACGGTGGTATTCGAATTTCGGCCACGGAGCAAATCAGCTTTTTAAGAAAGCTGTATCACAATAAGTTACACGTATCGGAGCGCAGCCAGCGTATTGTCAAACAAGCCATGCTGACCGAAGCCAATGGTGACTATATTATTCGGGCTAAAACTGGATACTCGACTGGAATCGAACCTAAGATTGGCTGGTGGGTCGGTTGGGTTGAACTTGATGATAATGTGTGGTTTTTTGCGATGAATATGGATATGCCCACATCGGATGGTTTAGGGCTGCGCCAAGCCATCACAAAAGAAGTGCTCAAACAGGAAAAAATTATTCCCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3008623","ARO_id":"47415","ARO_name":"OXA-1213","CARD_short_name":"OXA-1213","ARO_description":"OXA-48 family class D beta-lactamase OXA-1213.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46510":{"category_aro_accession":"3007721","category_aro_cvterm_id":"46510","category_aro_name":"OXA-48-like beta-lactamase","category_aro_description":"OXA-48-type beta-lactamases are now routinely encountered in bacterial infections caused by carbapenam-resistant Enterobacterales. OXA-48-like proteins confer resistance to penicillin (which is efficiently hydrolyzed) and carbapenam antibiotics (which is more slowly broken down). The spectrum of activity of these variants varies, with some hydrolyzing expanded-spectrum oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8042":{"model_id":"8042","model_name":"OXA-1214","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10869":{"protein_sequence":{"accession":"WLF01973.1","sequence":"MNIKALLLITSAIFISACSPYIVSANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQIYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"OR367330.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGTCTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAATCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACTACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008624","ARO_id":"47416","ARO_name":"OXA-1214","CARD_short_name":"OXA-1214","ARO_description":"OXA-51 family carbapenem-hydrolyzing class D beta-lactamase OXA-1214.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8043":{"model_id":"8043","model_name":"OXA-1215","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10870":{"protein_sequence":{"accession":"WLF01980.1","sequence":"MIMSKKLTCLALFTAIFFAIPMAACQSFSQQKQQLSTQKNEQQQISSLFQSAQTRGVLMIYDGKKIQSYGNDLDRAEQRYIPASTFKMLNALIGIQHHKTTPDEVFKWDGKKRAFSSWEKDLTLAEAMQASAVPVYQELARRIGLELMTREVKRVGYGNKNIGTQVDNFWLVGPLKITPVEEVRFAYALAKQKLPFDQPTQQQVKAMLLVDQIQGTKIYAKSGWGMDVSPQVGWWTGWIAQPNGKITAFSLNMQMSQPEHADARKAIVYQALQQLGLLAH"},"dna_sequence":{"accession":"OR367337.1","fmin":"0","fmax":"843","strand":"+","sequence":"ATGATCATGTCGAAAAAATTAACATGTCTGGCCCTGTTTACAGCCATCTTTTTTGCGATTCCCATGGCCGCTTGTCAAAGTTTTAGTCAACAAAAGCAACAGCTTTCGACACAGAAAAATGAACAGCAACAGATTTCAAGCTTATTTCAGAGTGCCCAAACCCGTGGTGTTTTGATGATTTATGATGGCAAGAAAATTCAAAGCTATGGCAATGATCTTGATCGTGCAGAACAGCGCTATATTCCTGCCTCAACCTTTAAAATGCTAAATGCCTTGATTGGTATACAACATCATAAGACCACACCAGATGAAGTGTTTAAATGGGATGGCAAAAAGCGGGCATTCAGCAGTTGGGAAAAAGATTTAACCTTAGCTGAAGCGATGCAGGCATCGGCGGTACCTGTGTATCAGGAACTAGCAAGACGTATTGGCTTGGAGTTAATGACCCGTGAAGTGAAGCGTGTGGGTTATGGCAATAAAAATATTGGGACACAAGTTGATAATTTCTGGTTAGTTGGCCCATTAAAAATCACCCCCGTAGAAGAAGTTCGCTTTGCCTATGCGTTGGCAAAACAGAAATTGCCATTTGACCAGCCAACACAGCAACAAGTCAAAGCGATGTTATTGGTGGATCAGATTCAGGGAACTAAAATCTATGCAAAAAGTGGTTGGGGCATGGATGTTAGCCCGCAAGTGGGATGGTGGACAGGCTGGATTGCACAGCCAAATGGTAAGATCACAGCCTTCTCACTGAATATGCAAATGAGCCAGCCTGAGCATGCAGATGCACGTAAAGCGATTGTGTATCAAGCCTTGCAACAGTTGGGATTGTTAGCCCATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42970","NCBI_taxonomy_name":"Acinetobacter proteolyticus","NCBI_taxonomy_id":"1217713"}}}},"ARO_accession":"3008625","ARO_id":"47417","ARO_name":"OXA-1215","CARD_short_name":"OXA-1215","ARO_description":"OXA-286 family carbapenem-hydrolyzing class D beta-lactamase OXA-1215.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46503":{"category_aro_accession":"3007714","category_aro_cvterm_id":"46503","category_aro_name":"OXA-286-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-286.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8044":{"model_id":"8044","model_name":"OXA-1216","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10871":{"protein_sequence":{"accession":"WLF01981.1","sequence":"MNKYFTCYVVASLFLSGCTVQHNLINETPSKIVQVHNQVINQYFDEKNTSGVLVIQTDKKINLYGNALSRANTEYVPASTFKMLNALIGLENQKTDINEIFKWKGEKRSFTAWEKDMTLGEAMKLSAVPVYQELARRIGLDLMQKEVKRIGFGNAEIGQQVDNFWLVGPLKVTPIQEVEFVSQLAHTQLPFSEKVQANVKNMLLLEESNGYKIFGKTGWAMDIKPQVGWLTGWVEQPDGKIVAFALNMEMRSEMPASIRNELLMKSLKQLNII"},"dna_sequence":{"accession":"OR367338.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGAATAAATATTTTACTTGCTATGTGGTTGCTTCTCTTTTTCTTTCTGGTTGTACGGTTCAGCATAATTTAATAAATGAAACCCCGAGTAAGATTGTTCAAGTACATAATCAGGTGATTAATCAATACTTTGATGAAAAAAACACCTCAGGTGTGCTGGTTATTCAAACAGATAAAAAAATTAATCTATATGGTAATGCTCTAAGCCGCGCAAATACAGAATATGTGCCAGCCTCTACATTTAAAATGTTGAATGCCCTGATCGGATTGGAGAACCAGAAAACGGATATTAATGAAATATTTAAATGGAAGGGCGAGAAAAGGTCATTTACCGCTTGGGAAAAAGACATGACACTAGGAGAAGCCATGAAGCTTTCTGCAGTCCCAGTCTATCAGGAACTTGCGCGACGTATCGGTCTTGATCTCATGCAAAAAGAAGTAAAACGTATTGGTTTCGGTAATGCTGAAATTGGACAGCAGGTTGATAATTTCTGGTTGGTAGGACCATTAAAGGTTACGCCTATTCAAGAGGTAGAGTTTGTTTCCCAATTAGCACATACACAGCTTCCATTTAGTGAAAAAGTGCAGGCTAATGTAAAAAATATGCTTCTTTTAGAAGAGAGTAATGGCTACAAAATTTTTGGAAAGACTGGTTGGGCAATGGATATAAAACCACAAGTGGGCTGGTTGACCGGCTGGGTTGAGCAGCCAGATGGAAAAATTGTCGCTTTTGCATTAAATATGGAAATGCGGTCAGAAATGCCGGCATCTATACGTAATGAATTATTGATGAAATCATTAAAACAGCTGAATATTATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008626","ARO_id":"47418","ARO_name":"OXA-1216","CARD_short_name":"OXA-1216","ARO_description":"OXA-23 family carbapenem-hydrolyzing class D beta-lactamase OXA-1216.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46499":{"category_aro_accession":"3007710","category_aro_cvterm_id":"46499","category_aro_name":"OXA-23-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases, specifically imipenem, derived from OXA-23, first identified in Acinetobacter baumannii.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8045":{"model_id":"8045","model_name":"OXA-1217","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10872":{"protein_sequence":{"accession":"WLY62585.1","sequence":"MNIKALLLITSAIFISACSPYIVSANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"OR449067.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGTCTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTAGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008627","ARO_id":"47419","ARO_name":"OXA-1217","CARD_short_name":"OXA-1217","ARO_description":"OXA-51 family carbapenem-hydrolyzing class D beta-lactamase OXA-1217.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8046":{"model_id":"8046","model_name":"OXA-1218","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10873":{"protein_sequence":{"accession":"WLY62588.1","sequence":"MNIKALLLITSAIFISACSPYIVSANPNHSASKSDVKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"OR449070.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGTCTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGTAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAACAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008628","ARO_id":"47420","ARO_name":"OXA-1218","CARD_short_name":"OXA-1218","ARO_description":"OXA-51 family carbapenem-hydrolyzing class D beta-lactamase OXA-1218.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8047":{"model_id":"8047","model_name":"OXA-1219","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10874":{"protein_sequence":{"accession":"WLY62589.1","sequence":"MNIKALLLITSAIFISACSPYIVSANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQEVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"OR449071.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGTCTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGTTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTAGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAGAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008629","ARO_id":"47421","ARO_name":"OXA-1219","CARD_short_name":"OXA-1219","ARO_description":"OXA-51 family carbapenem-hydrolyzing class D beta-lactamase OXA-1219.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8048":{"model_id":"8048","model_name":"OXA-1220","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10875":{"protein_sequence":{"accession":"WLY62590.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASVIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"OR449072.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGTTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAACAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008630","ARO_id":"47422","ARO_name":"OXA-1220","CARD_short_name":"OXA-1220","ARO_description":"OXA-51 family carbapenem-hydrolyzing class D beta-lactamase OXA-1220.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8049":{"model_id":"8049","model_name":"OXA-1221","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10876":{"protein_sequence":{"accession":"WLY62597.1","sequence":"MNKYFTCYVVASLFLSGCTVQHNLINETQSQIVQGHNQVIHQYFDEKNTSGVLVIQTDKKINLYGNALSRANTEYVPASTFKMLNALIGLENQKTDINEIFKWKGEKRSFTAWEKDMTLGEAMKLSAVPVYQELARRIGLDLMQKEVKRISFGNAEIGQQVDNFWLVGPLKVTPIQEVEFVSQLAHTQLPFSEKVQANVKNMLLLEESNGYKIFGKTGWAMDIKPQVGWLTGWVEQPDGKIIAFALNMEMRSEMPASIRNELLMKSLKQLNII"},"dna_sequence":{"accession":"OR438755.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGAATAAATATTTTACTTGCTATGTGGTTGCTTCTCTTTTTCTTTCTGGTTGTACGGTTCAGCATAATTTAATAAATGAAACCCAGAGTCAGATTGTTCAAGGACATAATCAGGTGATTCATCAATACTTTGATGAAAAAAACACCTCAGGTGTGCTGGTTATTCAAACAGATAAAAAAATTAATTTGTATGGTAATGCTCTAAGCCGCGCAAATACAGAATATGTGCCAGCCTCTACATTTAAAATGTTGAATGCCCTGATCGGACTGGAGAACCAGAAAACGGATATTAATGAAATATTTAAATGGAAGGGCGAGAAAAGGTCATTTACCGCTTGGGAAAAAGACATGACACTAGGAGAAGCCATGAAGCTTTCTGCAGTCCCAGTCTATCAGGAACTTGCGCGACGTATCGGTCTTGATCTCATGCAAAAAGAAGTAAAACGTATTAGTTTCGGTAATGCTGAAATTGGACAGCAGGTTGATAATTTCTGGTTGGTAGGGCCATTAAAGGTTACGCCTATTCAAGAGGTAGAGTTTGTTTCTCAATTGGCGCATACACAGCTTCCATTTAGTGAAAAAGTGCAGGCTAATGTAAAAAATATGCTTCTTTTAGAAGAGAGTAATGGCTACAAAATTTTTGGAAAGACTGGTTGGGCAATGGATATAAAACCACAAGTGGGCTGGTTGACCGGCTGGGTTGAGCAGCCAGATGGGAAAATTATCGCTTTTGCATTAAATATGGAAATGCGGTCAGAAATGCCTGCATCTATACGTAATGAATTATTGATGAAATCATTAAAACAGCTGAATATTATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39672","NCBI_taxonomy_name":"Acinetobacter radioresistens","NCBI_taxonomy_id":"40216"}}}},"ARO_accession":"3008631","ARO_id":"47423","ARO_name":"OXA-1221","CARD_short_name":"OXA-1221","ARO_description":"OXA-23 family carbapenem-hydrolyzing class D beta-lactamase OXA-1221.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46499":{"category_aro_accession":"3007710","category_aro_cvterm_id":"46499","category_aro_name":"OXA-23-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases, specifically imipenem, derived from OXA-23, first identified in Acinetobacter baumannii.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8050":{"model_id":"8050","model_name":"OXA-1222","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10877":{"protein_sequence":{"accession":"BER91150.1","sequence":"MTKKALFFAIGTMFLSACSFNTVQQHQIQSISTNKNSEKIKSLFEQAQTEGVLVIKRGQTEEIYGNDLKRSSTEYVPASTFKMLNALIGLEHHKATPTEVFKWYGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMSKEVKRIGFGNADIGSKVDDFWLVGPLKITPQQEVRFAYKLANKTLPFSNNVQEQVQSMLFIEEKNGRKIYAKSGWGWDVDPQVGWFTGWIVQPQGEIIAFSLNLEMKKGIPSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"LC777321.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGACTAAAAAAGCTCTTTTCTTTGCCATTGGTACGATGTTTTTGTCGGCATGTTCTTTTAATACCGTACAACAACATCAAATACAGTCAATTTCTACCAATAAAAACTCAGAGAAAATTAAATCATTGTTTGAACAAGCACAAACTGAAGGTGTTTTAGTTATAAAACGTGGGCAAACAGAGGAAATCTATGGCAATGATCTTAAAAGATCATCAACCGAATATGTTCCCGCCTCTACCTTTAAAATGTTAAATGCTTTGATAGGACTTGAGCATCATAAAGCAACACCAACTGAAGTGTTTAAATGGTATGGGCAAAAGCGTTTATTTCCCGATTGGGAAAAAGACATGACCTTAGGTGATGCTATGAAAGCTTCTGCTATTCCAGTTTATCAGGAACTAGCTCGACGAATTGGCCTTGATCTTATGTCTAAAGAGGTAAAACGCATTGGTTTCGGTAATGCTGATATTGGTTCAAAAGTAGATGATTTTTGGCTTGTTGGTCCACTTAAAATTACACCTCAACAAGAAGTACGGTTTGCTTATAAATTAGCCAACAAAACTCTTCCCTTTAGCAATAATGTACAAGAACAAGTTCAATCTATGCTGTTCATTGAAGAAAAAAATGGACGAAAAATTTATGCCAAAAGTGGTTGGGGATGGGATGTGGATCCTCAAGTGGGTTGGTTTACAGGCTGGATCGTTCAACCTCAGGGAGAAATTATAGCTTTCTCACTTAATTTAGAAATGAAGAAAGGCATACCTAGTTCTATTCGAAAAGAAATTGCTTATAAAGGATTAGAGCAGCTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3008632","ARO_id":"47424","ARO_name":"OXA-1222","CARD_short_name":"OXA-1222","ARO_description":"OXA-213 family carbapenem-hydrolyzing class D beta-lactamase OXA-1222.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46495":{"category_aro_accession":"3007706","category_aro_cvterm_id":"46495","category_aro_name":"OXA-213-like beta-lactamase","category_aro_description":"OXA-213-like enzymes have been identified to be intrinsic to A. calcoaceticus and have been subsequently detected in A. pittii. Phylogenetic analysis of OXA-213-like proteins identified two distinct subgroups within the OXA family. The first group was linked to A. pittii and the second group to A. calcoaceticus. The carbapenemase activity of these OXAs may be related to the species-dependent effect.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8051":{"model_id":"8051","model_name":"OXA-1223","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10878":{"protein_sequence":{"accession":"WOL30562.1","sequence":"MNKFFTCYVVASLFLSGCTVQHNLINETPSQIVQGHNQVIHQYFDEKNTSGVLVIQTDKKINLYGNALSRANTEYVPASTFKMLNALIGLENQKTDINEIFKWKGEKRSFTAWEKDMTLGEAMKLSAVPVYQELARRIGLDLMQKEVKRIGFGNAEIGQQVDNFWLVGPLKVTPIQEVEFVSQLAHTQLPFSEKVQANVKNMLLLEESNGYKIFGKTGWAMDIKPQVGWLTGWVEQPDGKIVAFALNMEMRSEMPASIRNELLMKSLKQLNII"},"dna_sequence":{"accession":"OR695062.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGAATAAATTTTTTACTTGCTATGTGGTTGCTTCTCTTTTTCTTTCTGGTTGTACGGTTCAGCATAATTTAATAAATGAAACCCCGAGTCAGATTGTTCAAGGACATAATCAGGTGATTCATCAATACTTTGATGAAAAAAACACCTCAGGTGTGCTGGTTATTCAAACAGATAAAAAAATTAATCTATATGGTAATGCTCTAAGCCGCGCAAATACAGAATATGTGCCAGCCTCTACATTTAAAATGTTGAATGCCCTGATCGGATTGGAGAACCAGAAAACGGATATTAATGAAATATTTAAATGGAAGGGCGAGAAAAGGTCATTTACCGCTTGGGAAAAAGACATGACACTAGGAGAAGCCATGAAGCTTTCTGCAGTCCCAGTCTATCAGGAACTTGCGCGACGTATCGGTCTTGATCTCATGCAAAAAGAAGTAAAACGTATTGGTTTCGGTAATGCTGAAATTGGACAGCAGGTTGATAATTTCTGGTTGGTAGGACCATTAAAGGTTACGCCTATTCAAGAGGTAGAGTTTGTTTCCCAATTAGCACATACACAGCTTCCATTTAGTGAAAAAGTGCAGGCTAATGTAAAAAATATGCTTCTTTTAGAAGAGAGTAATGGCTACAAAATTTTTGGAAAGACTGGTTGGGCAATGGATATAAAACCACAAGTGGGCTGGTTGACCGGCTGGGTTGAGCAGCCAGATGGAAAAATTGTCGCTTTTGCATTAAATATGGAAATGCGGTCAGAAATGCCGGCATCTATACGTAATGAATTATTGATGAAATCATTAAAACAGCTGAATATTATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008633","ARO_id":"47425","ARO_name":"OXA-1223","CARD_short_name":"OXA-1223","ARO_description":"OXA-23 family carbapenem-hydrolyzing class D beta-lactamase OXA-1223.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46499":{"category_aro_accession":"3007710","category_aro_cvterm_id":"46499","category_aro_name":"OXA-23-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases, specifically imipenem, derived from OXA-23, first identified in Acinetobacter baumannii.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8052":{"model_id":"8052","model_name":"OXA-1224","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10879":{"protein_sequence":{"accession":"WPK95947.1","sequence":"MTKKALFFAIGTMFLSACSFNTVQQHQIQSISTNKNSEKIKSLFDQAQTPGVLVIKRGQTEEVYGNDLKTASTEYVPASTFKMLNALIGLEHHKATPTEVFKWDGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMSKEVKRIGFGNADIGSKVDDFWLVGPLKITPQQEAQFAYELAHKTLPFSKNVQEQVQSMLFIEEKNGRKIYAKSGWGWDVEPQVGWLTGWVVQPQGEIVAFSLNLEMKKGIPSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"OR815355.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGACTAAAAAAGCTCTTTTCTTTGCCATTGGTACGATGTTTTTGTCGGCATGTTCTTTTAATACCGTACAACAACATCAAATACAGTCAATTTCTACCAATAAAAACTCAGAGAAAATTAAATCGTTGTTTGATCAAGCACAAACTCCAGGTGTTTTAGTTATAAAACGTGGGCAAACAGAGGAAGTCTATGGCAATGATCTTAAAACAGCATCAACCGAATATGTTCCCGCCTCTACCTTTAAAATGTTAAATGCTTTGATTGGACTTGAGCATCATAAAGCAACACCAACTGAAGTGTTTAAATGGGATGGGCAAAAGCGTTTATTTCCCGATTGGGAAAAAGACATGACATTAGGCGATGCGATGAAAGCTTCTGCTATTCCAGTCTATCAGGAACTAGCTCGACGAATTGGCCTTGATCTTATGTCTAAAGAGGTAAAACGCATTGGTTTCGGTAATGCTGATATTGGTTCAAAAGTAGATGATTTTTGGCTTGTTGGTCCACTTAAAATTACACCTCAACAAGAAGCCCAGTTTGCTTATGAACTAGCCCATAAAACTCTTCCTTTTAGCAAGAATGTGCAAGAACAAGTTCAATCTATGCTGTTCATAGAAGAAAAAAATGGACGGAAAATTTATGCCAAAAGTGGTTGGGGATGGGATGTGGAGCCTCAAGTGGGCTGGTTAACAGGCTGGGTCGTTCAACCTCAAGGAGAAATTGTAGCGTTCTCACTCAATTTAGAAATGAAAAAAGGCATACCTAGTTCTATTCGAAAAGAAATTGCTTATAAGGGATTAGAGCAGCTAGGTATTTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3008634","ARO_id":"47426","ARO_name":"OXA-1224","CARD_short_name":"OXA-1224","ARO_description":"OXA-213 family carbapenem-hydrolyzing class D beta-lactamase OXA-1224.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46495":{"category_aro_accession":"3007706","category_aro_cvterm_id":"46495","category_aro_name":"OXA-213-like beta-lactamase","category_aro_description":"OXA-213-like enzymes have been identified to be intrinsic to A. calcoaceticus and have been subsequently detected in A. pittii. Phylogenetic analysis of OXA-213-like proteins identified two distinct subgroups within the OXA family. The first group was linked to A. pittii and the second group to A. calcoaceticus. The carbapenemase activity of these OXAs may be related to the species-dependent effect.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8053":{"model_id":"8053","model_name":"OXA-1225","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10880":{"protein_sequence":{"accession":"WRW33976.1","sequence":"MKKFILPIFSISILVSLSACSSIKTKSEDNFHISSQQHEKAIKSYFDEAQTQGVIIIKEGKNLSTYGNALARANKEYVPASTFKMLNALIGLENHKATTNEIFKWDGKKRTYPMWEKDMTLGEAMALSAVPVYQELARRIGLELMQKEVKRVNFGNTNIGTQVDNFWLVGPLKITPVQEVNFADDLAHNRLPFKLETQEEVKKMLLIKEVNGSKIYAKSGWGMDVTLQVGWLTGWVEQANGKKIPFSLNLEMKEGMSGSIRNEITYKSLENLGII"},"dna_sequence":{"accession":"PP125276.1","fmin":"0","fmax":"828","strand":"+","sequence":"ATGAAAAAATTTATACTTCCTATATTCAGCATTTCTATTCTAGTTTCTCTCAGTGCATGTTCATCTATTAAAACTAAATCTGAAGATAATTTTCATATTTCTTCTCAGCAACATGAAAAAGCTATTAAAAGCTATTTTGATGAAGCTCAAACACAGGGTGTAATTATTATTAAAGAGGGTAAAAATCTTAGCACCTATGGTAATGCTCTTGCACGAGCAAATAAAGAATATGTCCCTGCATCAACATTTAAGATGCTAAATGCTTTAATCGGGCTAGAAAATCATAAAGCAACAACAAATGAGATTTTCAAATGGGATGGTAAAAAAAGAACTTATCCTATGTGGGAGAAAGATATGACTTTAGGTGAGGCAATGGCATTGTCAGCAGTTCCAGTATATCAAGAGCTTGCAAGACGGATTGGCCTAGAGCTAATGCAGAAAGAAGTAAAGCGGGTTAATTTTGGAAATACAAATATTGGAACACAGGTCGATAATTTTTGGTTAGTTGGCCCCCTTAAAATTACACCAGTACAAGAAGTTAATTTTGCCGATGACCTTGCACATAACCGATTACCTTTTAAATTAGAAACTCAAGAAGAAGTTAAAAAAATGCTTCTAATTAAAGAAGTAAATGGTAGTAAGATTTATGCAAAAAGTGGATGGGGAATGGATGTTACTCTACAGGTAGGTTGGTTGACTGGTTGGGTGGAGCAAGCTAATGGAAAAAAAATCCCCTTTTCGCTCAACTTAGAAATGAAAGAAGGAATGTCTGGTTCTATTCGTAATGAAATTACTTATAAGTCGCTAGAAAATCTTGGAATCATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39090","NCBI_taxonomy_name":"Acinetobacter bereziniae","NCBI_taxonomy_id":"106648"}}}},"ARO_accession":"3008635","ARO_id":"47427","ARO_name":"OXA-1225","CARD_short_name":"OXA-1225","ARO_description":"OXA-24 family carbapenem-hydrolyzing class D beta-lactamase OXA-1225.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46500":{"category_aro_accession":"3007711","category_aro_cvterm_id":"46500","category_aro_name":"OXA-24-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-24.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8054":{"model_id":"8054","model_name":"OXA-1226","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10881":{"protein_sequence":{"accession":"WVW91586.1","sequence":"MRVLALSAVFLVASIIGMPAVAKEWQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGQTRDIAAWNRDHDLITAMKYSVVPVYQEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISAIQQIAFLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYSTRIEPKIGWWVGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP"},"dna_sequence":{"accession":"PP296992.1","fmin":"0","fmax":"798","strand":"+","sequence":"ATGCGTGTATTAGCCTTATCGGCTGTGTTTTTGGTGGCATCGATTATCGGAATGCCAGCGGTAGCAAAGGAATGGCAAGAAAACAAAAGTTGGAATGCTCACTTTACTGAACATAAATCACAGGGCGTAGTTGTGCTCTGGAATGAGAATAAGCAGCAAGGATTTACCAATAATCTTAAACGGGCGAACCAAGCATTTTTACCCGCATCTACCTTTAAAATTCCCAATAGCTTGATCGCCCTCGATTTGGGCGTGGTTAAGGATGAACACCAAGTCTTTAAGTGGGATGGACAGACGCGTGATATCGCCGCTTGGAATCGTGACCATGACTTAATTACCGCGATGAAGTACTCAGTTGTGCCTGTTTATCAAGAATTTGCCCGCCAAATTGGTGAGGCACGTATGAGTAAAATGCTGCACGCCTTCGATTATGGCAATGAGGATATCTCGGGCAATGTAGACAGTTTTTGGCTCGATGGTGGTATTCGCATTTCGGCTATCCAGCAAATCGCTTTTTTACGCAAGCTGTATCACAACAAGCTGCACGTTTCTGAGCGTAGTCAGCGCATCGTGAAACAAGCCATGCTGACCGAAGCCAATGGCGACTATATTATTCGGGCTAAAACGGGATACTCGACTAGAATCGAACCTAAGATTGGCTGGTGGGTTGGTTGGGTTGAACTTGATGATAATGTGTGGTTTTTTGCGATGAATATGGATATGCCCACATCGGATGGTTTAGGGCTGCGCCAAGCCATCACAAAAGAAGTGCTCAAACAGGAGAAAATTATTCCCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3008636","ARO_id":"47428","ARO_name":"OXA-1226","CARD_short_name":"OXA-1226","ARO_description":"OXA-48 family class D beta-lactamase OXA-1226.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46510":{"category_aro_accession":"3007721","category_aro_cvterm_id":"46510","category_aro_name":"OXA-48-like beta-lactamase","category_aro_description":"OXA-48-type beta-lactamases are now routinely encountered in bacterial infections caused by carbapenam-resistant Enterobacterales. OXA-48-like proteins confer resistance to penicillin (which is efficiently hydrolyzed) and carbapenam antibiotics (which is more slowly broken down). The spectrum of activity of these variants varies, with some hydrolyzing expanded-spectrum oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8055":{"model_id":"8055","model_name":"OXA-1227","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10882":{"protein_sequence":{"accession":"BFF41851.1","sequence":"MKRILSRWRRAAVVLRLASAVVAHGLLPSPAHALELSRASAAAAPSVAAPVHVTERADWGKFFAAENVKGTVVVLDGKTQTYQAYDSARAERRMSPASTYKIFNSLLALESGALGNERETIPWDGKPRRIKAWNAELNLRDAFRVSCYPCYQVVSHKIPRAYAQAKLDAVGYGNRTIGRVNDTYWVDDSLQISAREQVDFLQRLARGTLPFSARSQDIVRQISIVEANADYVLHGKTGWFVDKKPDIGWWVGWLERDGNLTMIALNIDMNGDADGPKRARIVREVLKNLKLI"},"dna_sequence":{"accession":"LC797989.1","fmin":"0","fmax":"879","strand":"+","sequence":"ATGAAACGAATTCTCTCTCGCTGGCGTCGCGCGGCTGTCGTGCTGCGTCTGGCGTCGGCGGTCGTCGCGCATGGTCTGCTGCCCTCGCCAGCACACGCGCTGGAATTGTCGCGGGCGTCAGCCGCGGCAGCACCTTCCGTGGCAGCGCCCGTCCACGTGACCGAGCGTGCCGACTGGGGCAAGTTCTTTGCGGCGGAAAACGTGAAGGGCACGGTCGTCGTGCTCGACGGCAAGACACAGACGTATCAGGCGTACGACTCGGCGCGCGCCGAGCGGCGCATGTCCCCGGCGTCGACGTACAAGATATTCAACAGTCTGCTGGCGCTGGAATCGGGTGCGCTGGGCAACGAGCGCGAGACGATTCCGTGGGACGGCAAACCGCGCCGGATTAAGGCGTGGAATGCAGAATTGAATCTGCGTGACGCGTTTCGTGTGTCTTGCTACCCGTGCTATCAGGTCGTTTCGCACAAGATTCCGCGTGCGTATGCGCAGGCGAAGCTCGACGCCGTCGGGTACGGTAACCGGACCATCGGTCGGGTGAACGACACCTATTGGGTGGACGACAGTTTGCAGATCTCAGCGCGCGAGCAAGTCGACTTCCTGCAGCGTCTGGCGCGTGGCACGTTGCCGTTCTCCGCGCGTTCGCAGGACATCGTCCGGCAGATTTCCATCGTCGAAGCGAACGCCGACTATGTGCTGCACGGCAAGACCGGCTGGTTCGTCGACAAGAAGCCGGATATCGGCTGGTGGGTGGGCTGGCTGGAGCGTGACGGTAATCTGACGATGATCGCGCTGAACATCGACATGAACGGCGACGCCGACGGCCCGAAGCGTGCGCGTATCGTGCGTGAGGTGCTGAAGAACCTGAAGTTGATCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42786","NCBI_taxonomy_name":"Pandoraea sputorum","NCBI_taxonomy_id":"93222"}}}},"ARO_accession":"3008637","ARO_id":"47429","ARO_name":"OXA-1227","CARD_short_name":"OXA-1227","ARO_description":"OXA-62 family carbapenem-hydrolyzing class D beta-lactamase OXA-1227.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46520":{"category_aro_accession":"3007731","category_aro_cvterm_id":"46520","category_aro_name":"OXA-62-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-62.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8056":{"model_id":"8056","model_name":"OXA-1228","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10883":{"protein_sequence":{"accession":"BFF41852.1","sequence":"MKRILSRWRRAAVVLRLTSAVVAHGLLPSPAHALELSRASAAAAPSVAAPVRVTERADWGKFFAAENVKGTVVVLDGKTQTYQAYDSARAERRMSPASTYKIFNSLLALESGALDNERETIPWDGKPRRIKAWNAELNLRDAFRVSCYPCYQVVSHKIPRAYAQAKLDAVGYGNRTIGRVNDTYWVDDSLQISAREQVDFLQRLARGTLPFSARSQDIVRQISIVEANADYVLHGKTGWFVDKKPDIGWWVGWLERDGNLTMIALNIDMNGDADGPKRARIVREVLKNLKLI"},"dna_sequence":{"accession":"LC797990.1","fmin":"0","fmax":"879","strand":"+","sequence":"ATGAAACGAATTCTCTCTCGCTGGCGTCGCGCGGCTGTCGTGCTGCGTCTGACGTCGGCGGTCGTCGCGCATGGTCTGCTGCCCTCGCCAGCACACGCGCTGGAATTGTCGCGGGCGTCAGCCGCGGCAGCACCTTCCGTGGCAGCGCCCGTCCGCGTGACCGAGCGTGCCGACTGGGGCAAGTTCTTTGCGGCGGAAAACGTGAAGGGCACGGTCGTCGTGCTCGACGGCAAGACACAGACGTATCAGGCGTACGACTCGGCGCGCGCCGAGCGGCGCATGTCCCCGGCGTCCACGTACAAGATTTTCAACAGTCTGCTGGCGCTGGAATCGGGTGCGCTGGACAACGAGCGCGAGACGATTCCGTGGGACGGCAAACCGCGCCGGATTAAGGCGTGGAATGCAGAATTGAATCTGCGCGACGCGTTTCGCGTGTCTTGCTACCCGTGCTATCAGGTCGTTTCGCACAAGATTCCGCGTGCGTATGCGCAGGCGAAGCTCGACGCCGTCGGGTACGGTAACCGAACCATCGGTCGGGTGAACGACACCTATTGGGTGGACGACAGTTTGCAGATCTCGGCGCGCGAGCAAGTCGACTTCCTGCAGCGTCTGGCGCGTGGCACGTTGCCGTTCTCCGCGCGTTCGCAGGACATCGTCCGGCAGATTTCCATCGTCGAAGCGAACGCCGACTATGTGCTGCACGGCAAGACCGGCTGGTTCGTCGACAAGAAGCCGGATATCGGCTGGTGGGTGGGCTGGCTGGAGCGTGACGGCAATCTGACGATGATCGCGCTGAACATCGACATGAACGGCGACGCCGACGGCCCGAAGCGTGCGCGTATCGTGCGTGAGGTGCTGAAGAACCTGAAGTTGATCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42786","NCBI_taxonomy_name":"Pandoraea sputorum","NCBI_taxonomy_id":"93222"}}}},"ARO_accession":"3008638","ARO_id":"47430","ARO_name":"OXA-1228","CARD_short_name":"OXA-1228","ARO_description":"OXA-62 family carbapenem-hydrolyzing class D beta-lactamase OXA-1228.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46520":{"category_aro_accession":"3007731","category_aro_cvterm_id":"46520","category_aro_name":"OXA-62-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-62.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8057":{"model_id":"8057","model_name":"OXA-1229","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10884":{"protein_sequence":{"accession":"WVW91693.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDDKAEKIKNLFNEAHTTGVLVIHQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGEKRLFPEWEKNLTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"PP328940.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGACAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCATCAAGGTCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAATGGGATGGGGAAAAAAGGCTATTCCCAGAATGGGAAAAGAACTTGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTCTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008639","ARO_id":"47431","ARO_name":"OXA-1229","CARD_short_name":"OXA-1229","ARO_description":"OXA-51 family carbapenem-hydrolyzing class D beta-lactamase OXA-1229.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8058":{"model_id":"8058","model_name":"OXA-1230","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10885":{"protein_sequence":{"accession":"WVW91694.1","sequence":"MNIKTLLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEVHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSFNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"PP328941.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAACACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGTACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTGGGTTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCTTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008640","ARO_id":"47432","ARO_name":"OXA-1230","CARD_short_name":"OXA-1230","ARO_description":"OXA-51 family carbapenem-hydrolyzing class D beta-lactamase OXA-1230.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8059":{"model_id":"8059","model_name":"OXA-1231","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10886":{"protein_sequence":{"accession":"WVW91695.1","sequence":"MKTFAAYVITACLSSTALASSITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNNLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLSLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFCLEGQLRISAVNQVEFLESLFLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKGTEVYFFAFNMDIDNENKLPLRKSIPTKIMASEGIIGG"},"dna_sequence":{"accession":"PP328942.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGAAAACATTTGCCGCATATGTAATTACTGCGTGTCTTTCAAGTACGGCATTAGCTAGTTCAATTACAGAAAATACGTCTTGGAACAAAGAGTTCTCTGCCGAAGCCGTCAATGGTGTTTTCGTGCTTTGTAAAAGTAGCAGTAAATCCTGCGCTACCAATAACTTAGCTCGTGCATCAAAGGAATATCTTCCAGCATCAACATTTAAGATCCCCAACGCAATTATCGGCCTAGAAACTGGTGTCATAAAGAATGAGCATCAGGTTTTCAAATGGGACGGAAAGCCAAGAGCCATGAAACAATGGGAAAGAGACTTGAGCTTAAGAGGGGCAATACAAGTTTCAGCGGTTCCCGTATTTCAACAAATCGCCAGAGAAGTTGGCGAAGTAAGAATGCAGAAATACCTTAAAAAATTTTCATATGGCAACCAGAATATCAGTGGTGGCATTGACAAATTCTGCTTGGAGGGTCAGCTAAGAATTTCCGCAGTTAATCAAGTGGAGTTTCTAGAGTCTCTATTTTTAAATAAATTGTCAGCATCAAAAGAAAATCAGCTAATAGTAAAAGAGGCTTTGGTAACGGAGGCTGCGCCTGAATATCTTGTGCATTCAAAAACTGGTTTTTCTGGTGTGGGAACTGAGTCAAATCCTGGTGTCGCATGGTGGGTTGGTTGGGTTGAGAAGGGAACAGAGGTTTACTTTTTCGCCTTTAACATGGATATAGACAACGAAAATAAGTTGCCGCTAAGAAAATCCATTCCCACCAAAATCATGGCAAGTGAGGGCATCATTGGTGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008641","ARO_id":"47433","ARO_name":"OXA-1231","CARD_short_name":"OXA-1231","ARO_description":"OXA-10 family class D beta-lactamase OXA-1231.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46486":{"category_aro_accession":"3007697","category_aro_cvterm_id":"46486","category_aro_name":"OXA-10-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-10.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8060":{"model_id":"8060","model_name":"OXA-1232","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10887":{"protein_sequence":{"accession":"WVW91696.1","sequence":"MKTFAAYVITACLSSTALASSITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNNLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLSLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDIFWLEDQLRISAVNQVEFLESLFLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKGTEVYFFAFNMDIDNENKLPLRKSIPTKIMASEGIIGG"},"dna_sequence":{"accession":"PP328943.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGAAAACATTTGCCGCATATGTAATTACTGCGTGTCTTTCAAGTACGGCATTAGCTAGTTCAATTACAGAAAATACGTCTTGGAACAAAGAGTTCTCTGCCGAAGCCGTCAATGGTGTTTTCGTGCTTTGTAAAAGTAGCAGTAAATCCTGCGCTACCAATAACTTAGCTCGTGCATCAAAGGAATATCTTCCAGCATCAACATTTAAGATCCCCAACGCAATTATCGGCCTAGAAACTGGTGTCATAAAGAATGAGCATCAGGTTTTCAAATGGGACGGAAAGCCAAGAGCCATGAAACAATGGGAAAGAGACTTGAGCTTAAGAGGGGCAATACAAGTTTCAGCGGTTCCCGTATTTCAACAAATCGCCAGAGAAGTTGGCGAAGTAAGAATGCAGAAATACCTTAAAAAATTTTCATATGGCAACCAGAATATCAGTGGTGGCATTGACATATTCTGGTTGGAGGATCAGCTAAGAATTTCCGCAGTTAATCAAGTGGAGTTTCTAGAGTCTCTATTTTTAAATAAATTGTCAGCATCAAAAGAAAATCAGCTAATAGTAAAAGAGGCTTTGGTAACGGAGGCTGCGCCTGAATATCTTGTGCATTCAAAAACTGGTTTTTCTGGTGTGGGAACTGAGTCAAATCCTGGTGTCGCATGGTGGGTTGGTTGGGTTGAGAAGGGAACAGAGGTTTACTTTTTCGCCTTTAACATGGATATAGACAACGAAAATAAGTTGCCGCTAAGAAAATCCATTCCCACCAAAATCATGGCAAGTGAGGGCATCATTGGTGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008642","ARO_id":"47434","ARO_name":"OXA-1232","CARD_short_name":"OXA-1232","ARO_description":"OXA-10 family class D beta-lactamase OXA-1232.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46486":{"category_aro_accession":"3007697","category_aro_cvterm_id":"46486","category_aro_name":"OXA-10-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-10.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8061":{"model_id":"8061","model_name":"OXA-1233","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10888":{"protein_sequence":{"accession":"WVW91697.1","sequence":"MKTFAAYVITACLSSTALASSITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNNLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLSLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLEALFLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKGTEVYFFAFNMDIDNENKLPLRKSIPTKIMASEGIIGG"},"dna_sequence":{"accession":"PP328944.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGAAAACATTTGCCGCATATGTAATTACTGCGTGTCTTTCAAGTACGGCATTAGCTAGTTCAATTACAGAAAATACGTCTTGGAACAAAGAGTTCTCTGCCGAAGCCGTCAATGGTGTTTTCGTGCTTTGTAAAAGTAGCAGTAAATCCTGCGCTACCAATAACTTAGCTCGTGCATCAAAGGAATATCTTCCAGCATCAACATTTAAGATCCCCAACGCAATTATCGGCCTAGAAACTGGTGTCATAAAGAATGAGCATCAGGTTTTCAAATGGGACGGAAAGCCAAGAGCCATGAAACAATGGGAAAGAGACTTGAGCTTAAGAGGGGCAATACAAGTTTCAGCGGTTCCCGTATTTCAACAAATCGCCAGAGAAGTTGGCGAAGTAAGAATGCAGAAATACCTTAAAAAATTTTCATATGGCAACCAGAATATCAGTGGTGGCATTGACAAATTCTGGTTGGAGGGTCAGCTAAGAATTTCCGCAGTTAATCAAGTGGAGTTTCTAGAGGCTCTATTTTTAAATAAATTGTCAGCATCAAAAGAAAATCAGCTAATAGTAAAAGAGGCTTTGGTAACGGAGGCTGCGCCTGAATATCTTGTGCATTCAAAAACTGGTTTTTCTGGTGTGGGAACTGAGTCAAATCCTGGTGTCGCATGGTGGGTTGGTTGGGTTGAGAAGGGAACAGAGGTTTACTTTTTCGCCTTTAACATGGATATAGACAACGAAAATAAGTTGCCGCTAAGAAAATCCATTCCCACCAAAATCATGGCAAGTGAGGGCATCATTGGTGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"47926","NCBI_taxonomy_name":"Pseudomonas oleovorans","NCBI_taxonomy_id":"301"}}}},"ARO_accession":"3008643","ARO_id":"47435","ARO_name":"OXA-1233","CARD_short_name":"OXA-1233","ARO_description":"OXA-10 family class D beta-lactamase OXA-1233.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46486":{"category_aro_accession":"3007697","category_aro_cvterm_id":"46486","category_aro_name":"OXA-10-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-10.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8062":{"model_id":"8062","model_name":"OXA-1234","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10889":{"protein_sequence":{"accession":"WVW91705.1","sequence":"MTKKALFFAISTIFLSACSFNTVQQHQIHAISTHKNSEEIKSLFDQAQTTGVLVIKRGNTEEIYGNDLKRASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMSKEVKRIGFGNTDIGSKVDNFWLVGPLKITPQQEAQFAYELAHKTLPFSKNVQEQVQSMVFVEEKNGRKIYAKSGWGWDVEPQVGWLTGWVVQPQGEIVAFSLNLEMKKGTPSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"PP328952.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGACTAAAAAAGCTCTTTTCTTTGCCATTAGTACCATATTTTTGTCAGCATGTTCTTTCAATACAGTACAACAGCACCAAATACACGCTATTTCTACCCATAAAAATTCAGAAGAAATAAAATCACTGTTTGATCAAGCACAGACCACAGGTGTTTTGGTTATTAAGCGCGGAAATACAGAGGAAATTTATGGCAATGATCTAAAAAGGGCATCAACTGAATATGTCCCTGCATCTACCTTTAAAATGTTAAATGCTCTAATTGGTCTTGAACATCATAAAGCAACAACAACTGAAGTGTTCAAATGGGATGGACAAAAGCGTTTATTTCCTGATTGGGAAAAGGATATGACTCTAGGTGATGCCATGAAAGCTTCTGCTATTCCTGTGTATCAAGAACTAGCTCGACGAATTGGCCTTGATCTTATGTCCAAAGAGGTCAAGCGTATTGGTTTCGGTAATACTGATATTGGTTCAAAAGTAGATAATTTTTGGCTTGTCGGTCCACTCAAAATTACGCCTCAACAGGAAGCACAGTTTGCTTATGAATTAGCACATAAAACTCTTCCCTTTAGCAAAAATGTACAAGAACAAGTTCAATCTATGGTGTTCGTAGAAGAAAAAAACGGACGTAAAATTTACGCTAAAAGCGGTTGGGGATGGGATGTGGAGCCTCAAGTGGGCTGGTTAACAGGCTGGGTCGTTCAACCACAAGGAGAAATTGTAGCGTTCTCACTCAATTTAGAAATGAAAAAAGGAACACCTAGTTCTATTCGAAAAGAAATTGCTTATAAAGGATTAGAACAGCTAGGTATTTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36837","NCBI_taxonomy_name":"Acinetobacter sp.","NCBI_taxonomy_id":"472"}}}},"ARO_accession":"3008644","ARO_id":"47436","ARO_name":"OXA-1234","CARD_short_name":"OXA-1234","ARO_description":"OXA-213 family carbapenem-hydrolyzing class D beta-lactamase OXA-1234.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46495":{"category_aro_accession":"3007706","category_aro_cvterm_id":"46495","category_aro_name":"OXA-213-like beta-lactamase","category_aro_description":"OXA-213-like enzymes have been identified to be intrinsic to A. calcoaceticus and have been subsequently detected in A. pittii. Phylogenetic analysis of OXA-213-like proteins identified two distinct subgroups within the OXA family. The first group was linked to A. pittii and the second group to A. calcoaceticus. The carbapenemase activity of these OXAs may be related to the species-dependent effect.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8063":{"model_id":"8063","model_name":"OXA-1235","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10890":{"protein_sequence":{"accession":"WVW91706.1","sequence":"MTKKALFFAIGTIFLSACSFNTVEQHQIQSISTNKNSEKIKTLFDQAQIEGVLVIKREQTEEVYGNDLKRVSTEYVPASTFKMLNALIGLEHHKATPTEVFKWDGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMSKEVKRIGFGNADIGSKVDDFWLVGPLKITPQQEVQFAYKLANKTLPFSKNVQEQVQSMVFIEEKNGRKIYAKSGWGWDVEPQVGWLTGWVVQPQGEIIAFSLNLEMKKGIPSSIRKEITYKGLEQLGIL"},"dna_sequence":{"accession":"PP328953.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGACTAAAAAAGCTCTTTTCTTTGCCATTGGTACGATATTTTTATCGGCGTGTTCTTTTAATACCGTAGAACAGCATCAAATACAGTCAATTTCTACCAATAAAAACTCAGAGAAAATTAAAACGTTGTTTGATCAAGCACAAATTGAAGGTGTTTTAGTTATAAAACGTGAGCAAACAGAGGAAGTCTATGGCAATGATCTTAAAAGAGTATCAACCGAATATGTTCCCGCCTCTACCTTTAAAATGTTAAATGCTTTGATAGGACTTGAGCATCATAAAGCAACACCAACTGAAGTGTTTAAATGGGATGGGCAAAAGCGTTTATTTCCCGATTGGGAAAAAGACATGACCTTAGGTGATGCTATGAAAGCTTCTGCTATTCCAGTTTATCAGGAACTAGCTCGACGAATTGGCCTTGATCTTATGTCTAAAGAGGTAAAACGCATTGGTTTCGGTAATGCTGATATTGGTTCAAAAGTAGATGATTTTTGGCTTGTTGGTCCACTTAAAATTACACCTCAACAAGAAGTACAGTTTGCTTATAAATTAGCCAACAAAACTCTTCCCTTTAGCAAAAATGTACAAGAACAAGTTCAATCTATGGTGTTCATTGAAGAAAAAAATGGACGAAAAATTTATGCCAAAAGTGGTTGGGGATGGGATGTGGAGCCTCAAGTGGGCTGGTTAACAGGCTGGGTAGTTCAACCTCAGGGAGAAATTATAGCTTTCTCACTTAATTTAGAAATGAAAAAAGGCATACCTAGCTCTATTCGAAAAGAAATTACTTATAAGGGATTGGAACAACTCGGTATTTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3008645","ARO_id":"47437","ARO_name":"OXA-1235","CARD_short_name":"OXA-1235","ARO_description":"OXA-213 family carbapenem-hydrolyzing class D beta-lactamase OXA-1235.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46495":{"category_aro_accession":"3007706","category_aro_cvterm_id":"46495","category_aro_name":"OXA-213-like beta-lactamase","category_aro_description":"OXA-213-like enzymes have been identified to be intrinsic to A. calcoaceticus and have been subsequently detected in A. pittii. Phylogenetic analysis of OXA-213-like proteins identified two distinct subgroups within the OXA family. The first group was linked to A. pittii and the second group to A. calcoaceticus. The carbapenemase activity of these OXAs may be related to the species-dependent effect.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8064":{"model_id":"8064","model_name":"OXA-1236","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10891":{"protein_sequence":{"accession":"WVW91707.1","sequence":"MNKYFTCYVVASLFLSGCTVQHNLINETPSQIVQGHNQVIHQYFDEKNTSGVLVIQTDKKINLYGNALSRANTEYVPASTFKMLNALIGLENQKTDINEIFKWKGEKRSFTAWEKDMTLGEAMKLSAVPVYQELARRIGLDLMQKEVKRIGFGNAEIGQQVDNFWLVGPLKVTPIQEVEFVSQLAHTQLPFSEKVQANVKNMLLLEESNGYKIFGKTGWAMDINSQVGWLTGWVEQPDGKIVAFALNMEMRSEMPASIRNELLMKSLKQLNII"},"dna_sequence":{"accession":"PP328954.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGAATAAATATTTTACTTGCTATGTGGTTGCTTCTCTTTTTCTTTCTGGTTGTACGGTTCAGCATAATTTAATAAATGAAACCCCGAGTCAGATTGTTCAAGGACATAATCAGGTGATTCATCAATACTTTGATGAAAAAAACACCTCAGGTGTGCTGGTTATTCAAACAGATAAAAAAATTAATCTATATGGTAATGCTCTAAGCCGCGCAAATACAGAATATGTGCCAGCCTCTACATTTAAAATGTTGAATGCCCTGATCGGATTGGAGAACCAGAAAACGGATATTAATGAAATATTTAAATGGAAGGGCGAGAAAAGGTCATTTACCGCTTGGGAAAAAGACATGACACTAGGAGAAGCCATGAAGCTTTCTGCAGTCCCAGTCTATCAGGAACTTGCGCGACGTATCGGTCTTGATCTCATGCAAAAAGAAGTAAAACGTATTGGTTTCGGTAATGCTGAAATTGGACAGCAGGTTGATAATTTCTGGTTGGTAGGACCATTAAAGGTTACGCCTATTCAAGAGGTAGAGTTTGTTTCCCAATTAGCACATACACAGCTTCCATTTAGTGAAAAAGTGCAGGCTAATGTAAAAAATATGCTTCTTTTAGAAGAGAGTAATGGCTACAAAATTTTTGGAAAGACTGGTTGGGCAATGGATATAAACTCACAAGTGGGCTGGTTGACCGGCTGGGTTGAGCAGCCAGATGGAAAAATTGTCGCTTTTGCATTAAATATGGAAATGCGGTCAGAAATGCCGGCATCTATACGTAATGAATTATTGATGAAATCATTAAAACAGCTGAATATTATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39513","NCBI_taxonomy_name":"Acinetobacter variabilis","NCBI_taxonomy_id":"70346"}}}},"ARO_accession":"3008646","ARO_id":"47438","ARO_name":"OXA-1236","CARD_short_name":"OXA-1236","ARO_description":"OXA-23 family carbapenem-hydrolyzing class D beta-lactamase OXA-1236.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46499":{"category_aro_accession":"3007710","category_aro_cvterm_id":"46499","category_aro_name":"OXA-23-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases, specifically imipenem, derived from OXA-23, first identified in Acinetobacter baumannii.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8065":{"model_id":"8065","model_name":"OXA-1237","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10892":{"protein_sequence":{"accession":"MEH1710178.1","sequence":"MTKKALFFAIGTMFLSACSFNTVEQHQTQSISTNKNSEKIKSLFDQAQTEGVLVIKRGQTEEVYGNDLKRASTEYVPASTFKMLNALIGLEHHKATPTEVFKWDGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLNLMSKEVKRISFGNADIGSKVDNFWLVGPLKITPQQEVQFAYKLAHKTLPFSKNVQEQVQSMLFIEEKNGRKIYAKSGWGWDVEPQVGWFTGWIVQPQGEIIAFSLNLEMKKGIPSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"JBALBL010000003.1","fmin":"271820","fmax":"272642","strand":"+","sequence":"ATGACTAAAAAAGCTCTTTTCTTTGCCATTGGTACGATGTTTTTATCGGCATGTTCTTTTAATACGGTAGAACAGCATCAAACACAGTCAATTTCTACCAATAAAAACTCAGAGAAAATTAAATCATTGTTTGATCAAGCACAAACTGAAGGTGTTTTAGTTATAAAACGTGGGCAAACAGAGGAAGTCTATGGCAATGATCTTAAAAGAGCATCAACCGAATATGTTCCCGCCTCTACCTTTAAAATGTTAAATGCTTTGATAGGACTTGAGCATCATAAAGCAACACCAACTGAAGTGTTTAAATGGGATGGGCAAAAGCGTTTATTTCCCGATTGGGAAAAAGACATGACATTAGGCGATGCTATGAAAGCTTCTGCTATTCCAGTTTATCAGGAACTAGCTCGACGAATTGGCCTTAATCTTATGTCTAAAGAGGTAAAACGCATTAGTTTCGGTAATGCTGATATTGGTTCAAAAGTAGATAATTTTTGGCTTGTTGGCCCACTTAAAATTACACCTCAACAAGAAGTACAGTTTGCTTATAAATTAGCCCACAAAACTCTTCCCTTTAGCAAAAATGTACAAGAACAAGTTCAATCTATGCTGTTCATAGAAGAAAAAAATGGACGGAAAATTTATGCAAAAAGTGGTTGGGGATGGGATGTGGAGCCTCAAGTGGGCTGGTTTACAGGTTGGATCGTTCAACCTCAGGGAGAAATTATAGCTTTCTCACTTAATTTAGAAATGAAGAAAGGCATACCTAGTTCTATTCGAAAAGAAATTGCTTATAAGGGATTAGAGCAGCTAGGTATTTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3008647","ARO_id":"47439","ARO_name":"OXA-1237","CARD_short_name":"OXA-1237","ARO_description":"OXA-213 family carbapenem-hydrolyzing class D beta-lactamase OXA-1237.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46495":{"category_aro_accession":"3007706","category_aro_cvterm_id":"46495","category_aro_name":"OXA-213-like beta-lactamase","category_aro_description":"OXA-213-like enzymes have been identified to be intrinsic to A. calcoaceticus and have been subsequently detected in A. pittii. Phylogenetic analysis of OXA-213-like proteins identified two distinct subgroups within the OXA family. The first group was linked to A. pittii and the second group to A. calcoaceticus. The carbapenemase activity of these OXAs may be related to the species-dependent effect.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8066":{"model_id":"8066","model_name":"OXA-1238","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10893":{"protein_sequence":{"accession":"WWV75918.1","sequence":"MPTRSPLRALAAALSLSALCLPAQARMLCTVVADVADGRIVFQDGTQDACAARYTPASTFKLAIALMGYDAGILQDAHAPVWDYQPSYPDWGGDDWCKPVDPTHWIKYSVFWYSQQIGEKLGLARLQQYTTAFGYGNQDVSGHPGKNNGTRGAWHVSSLRISPLEQLDFLRRLARRQLPVKPQAYDMAEILFDAGVDADGWKIHGKTGTGSPGSFGDYDREHAYGWYVGWARKNGRELVFARLIQDEKAARPNAGMRAREQLLAGLPGWLGAAGQR"},"dna_sequence":{"accession":"PP446293.1","fmin":"0","fmax":"831","strand":"+","sequence":"ATGCCTACACGCAGCCCCTTGCGCGCGCTCGCCGCCGCGCTGTCTCTTTCCGCCCTTTGCCTGCCCGCGCAGGCCCGCATGCTCTGCACCGTCGTGGCCGACGTCGCGGACGGACGCATCGTGTTCCAGGACGGCACGCAGGACGCCTGCGCGGCCCGCTATACGCCGGCGTCGACCTTCAAGCTCGCCATCGCCCTGATGGGCTACGACGCCGGCATTCTGCAGGACGCGCATGCGCCGGTCTGGGATTACCAGCCGAGCTACCCGGACTGGGGCGGCGACGACTGGTGCAAGCCTGTCGATCCGACGCACTGGATCAAGTACTCCGTTTTCTGGTATTCGCAGCAGATCGGCGAGAAGCTGGGCCTGGCGCGCCTGCAGCAATACACGACCGCGTTTGGCTACGGCAACCAGGATGTGTCGGGCCACCCGGGAAAGAACAATGGCACGCGGGGCGCCTGGCACGTATCGTCGCTGCGGATCTCGCCGCTGGAACAGCTCGATTTCCTGCGCAGGCTGGCCAGGCGGCAGCTGCCGGTCAAGCCGCAGGCCTATGACATGGCGGAGATCCTGTTCGACGCAGGGGTCGATGCGGATGGCTGGAAGATCCATGGCAAGACGGGCACGGGATCGCCGGGCAGCTTCGGTGATTACGACCGCGAACACGCCTATGGTTGGTATGTGGGCTGGGCCCGCAAGAACGGTCGCGAGCTGGTCTTCGCCCGGCTGATCCAGGACGAGAAGGCGGCGAGGCCGAACGCCGGCATGCGCGCGCGCGAGCAACTGCTGGCCGGGTTGCCGGGCTGGCTGGGCGCGGCCGGACAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"47897","NCBI_taxonomy_name":"Achromobacter sp.","NCBI_taxonomy_id":"134375"}}}},"ARO_accession":"3008648","ARO_id":"47440","ARO_name":"OXA-1238","CARD_short_name":"OXA-1238","ARO_description":"Class D beta-lactamase OXA-1238.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8067":{"model_id":"8067","model_name":"OXA-1239","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10894":{"protein_sequence":{"accession":"EJN1410585.1","sequence":"MSGKSHFILAVSFVLSTACLAIPPAAAAQKLTCTLIVDETSGDVLHRDGTCDKAFAPMSTFKLPLAIMGYDADILLDATTPRWDYKPEFNGYKTQQKPTDPTIWLKDSIVWYSQELTRRLGDKRFSDYIKRFDYGNKDVSGDPGKHNGLTHAWLASSLKISPEEQVGFLRRFLRGELPVSEDALEMTKAIMPHFEAGDWDVQGKTGTGALSDAKGGKAPIGWFVGWATRDDRRVIFARLTVGAKKGEQPAGPAARDDFLKMLPNLSENF"},"dna_sequence":{"accession":"ABHGGG010000117.1","fmin":"3369","fmax":"4179","strand":"+","sequence":"ATGAGCGGAAAAAGTCATTTCATCCTTGCGGTATCATTCGTTCTTTCAACGGCTTGCCTGGCAATTCCGCCAGCGGCGGCCGCGCAAAAACTGACCTGCACGCTGATTGTTGATGAGACAAGCGGCGACGTCCTGCATCGGGATGGCACCTGCGACAAGGCGTTTGCGCCGATGTCGACATTCAAACTGCCTTTGGCCATCATGGGCTACGATGCAGATATCCTGCTCGATGCGACCACGCCGCGCTGGGATTACAAGCCGGAATTCAACGGCTACAAAACACAGCAGAAGCCGACCGATCCGACCATCTGGCTCAAGGATTCCATCGTCTGGTACTCACAGGAACTGACGCGCCGCCTCGGCGACAAACGCTTTTCCGATTACATCAAGCGTTTTGATTACGGCAACAAGGATGTTTCCGGCGATCCCGGCAAGCATAACGGCTTGACCCACGCGTGGCTCGCCTCGTCGCTAAAGATTTCGCCGGAGGAGCAGGTGGGCTTCCTGCGCCGTTTCCTGCGCGGAGAATTGCCGGTCTCGGAGGATGCGCTGGAAATGACGAAAGCCATCATGCCGCATTTCGAGGCCGGCGATTGGGACGTGCAGGGCAAGACTGGCACCGGCGCGCTTTCCGATGCCAAGGGCGGCAAGGCGCCGATCGGCTGGTTCGTCGGCTGGGCGACGCGCGACGATCGCCGCGTCATCTTCGCCCGCCTGACGGTCGGGGCGAAGAAGGGCGAGCAGCCGGCCGGCCCCGCCGCCCGCGATGATTTCCTCAAGATGCTTCCGAACCTGTCGGAAAACTTCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008649","ARO_id":"47441","ARO_name":"OXA-1239","CARD_short_name":"OXA-1239","ARO_description":"Carbapenem-hydrolyzing class D beta-lactamase OXA-1239.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8068":{"model_id":"8068","model_name":"OXA-1240","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10895":{"protein_sequence":{"accession":"WYF30524.1","sequence":"MRVLALSAVFLVASIIGMPAVAKEWQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGQTRDIATWNRDHNLITAMKYSVVPVYQEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISATEQISFLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYGTKIGWWVGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP"},"dna_sequence":{"accession":"PP551583.1","fmin":"0","fmax":"786","strand":"+","sequence":"ATGCGTGTATTAGCCTTATCGGCTGTGTTTTTGGTGGCATCGATTATCGGAATGCCTGCGGTAGCAAAGGAATGGCAAGAAAACAAAAGTTGGAATGCTCACTTTACTGAACATAAATCACAGGGCGTAGTTGTGCTCTGGAATGAGAATAAGCAGCAAGGATTTACCAATAATCTTAAACGGGCGAACCAAGCATTTTTACCCGCATCTACCTTTAAAATTCCCAATAGCTTGATCGCCCTCGATTTGGGCGTGGTTAAGGATGAACACCAAGTCTTTAAGTGGGATGGACAGACGCGCGATATCGCCACTTGGAATCGCGATCATAATCTAATCACCGCGATGAAATATTCAGTTGTGCCTGTTTATCAAGAATTTGCCCGCCAAATTGGCGAGGCACGTATGAGCAAGATGCTACATGCTTTCGATTATGGTAATGAGGACATTTCGGGCAATGTAGACAGTTTCTGGCTCGACGGTGGTATTCGAATTTCGGCCACGGAGCAAATCAGCTTTTTAAGAAAGCTGTATCACAATAAGTTACACGTATCGGAGCGCAGCCAGCGTATTGTCAAACAAGCCATGCTGACCGAAGCCAATGGCGACTATATTATTCGGGCTAAAACTGGATACGGTACTAAGATTGGCTGGTGGGTCGGTTGGGTTGAACTTGATGATAATGTGTGGTTTTTTGCGATGAATATGGATATGCCCACATCGGATGGTTTAGGGCTGCGCCAAGCCATCACAAAAGAAGTGCTCAAACAGGAAAAAATTATTCCCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36946","NCBI_taxonomy_name":"Providencia stuartii","NCBI_taxonomy_id":"588"}}}},"ARO_accession":"3008650","ARO_id":"47442","ARO_name":"OXA-1240","CARD_short_name":"OXA-1240","ARO_description":"OXA-48 family class D beta-lactamase OXA-1240.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46510":{"category_aro_accession":"3007721","category_aro_cvterm_id":"46510","category_aro_name":"OXA-48-like beta-lactamase","category_aro_description":"OXA-48-type beta-lactamases are now routinely encountered in bacterial infections caused by carbapenam-resistant Enterobacterales. OXA-48-like proteins confer resistance to penicillin (which is efficiently hydrolyzed) and carbapenam antibiotics (which is more slowly broken down). The spectrum of activity of these variants varies, with some hydrolyzing expanded-spectrum oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8069":{"model_id":"8069","model_name":"OXA-1241","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10896":{"protein_sequence":{"accession":"EMS7317483.1","sequence":"MNKYFTCYVVASLFLSGCTVQHNLINETPSQIVQGHNQVIHQYFDEKNTSGVLVIQTDKKINLYGNALSRANTEYVPASTFKMLNALIGLENQKTDINEIFKWKGEKRSFTAWEKDMTLGEAMKLSAVPVYQELARRIGLDLMQKEVKRIGFGNAEIGQQVDNFWLVGPLKVTPIQEVEFVSQLAHTQLPFSEKVQANVKNMLLLEESNGYKIFGKTGWAMDIKRQVGWLTGWVEQPDGKIVAFALNMEMRSEMPASIRNELLMKSLKQLNII"},"dna_sequence":{"accession":"ABRAKC010000017.1","fmin":"250","fmax":"1072","strand":"+","sequence":"ATGAATAAATATTTTACTTGCTATGTGGTTGCTTCTCTTTTTCTTTCTGGTTGTACGGTTCAGCATAATTTAATAAATGAAACCCCGAGTCAGATTGTTCAAGGACATAATCAGGTGATTCATCAATACTTTGATGAAAAAAACACCTCAGGTGTGCTGGTTATTCAAACAGATAAAAAAATTAATCTATATGGTAATGCTCTAAGCCGCGCAAATACAGAATATGTGCCAGCCTCTACATTTAAAATGTTGAATGCCCTGATCGGATTGGAGAACCAGAAAACGGATATTAATGAAATATTTAAATGGAAGGGCGAGAAAAGGTCATTTACCGCTTGGGAAAAAGACATGACACTAGGAGAAGCCATGAAGCTTTCTGCAGTCCCAGTCTATCAGGAACTTGCGCGACGTATCGGTCTTGATCTCATGCAAAAAGAAGTAAAACGTATTGGTTTCGGTAATGCTGAAATTGGACAGCAGGTTGATAATTTCTGGTTGGTAGGACCATTAAAGGTTACGCCTATTCAAGAGGTAGAGTTTGTTTCCCAATTAGCACATACACAGCTTCCATTTAGTGAAAAAGTGCAGGCTAATGTAAAAAATATGCTTCTTTTAGAAGAGAGTAATGGCTACAAAATTTTTGGAAAGACTGGTTGGGCAATGGATATAAAACGACAAGTGGGCTGGTTGACCGGCTGGGTTGAGCAGCCAGATGGAAAAATTGTCGCTTTTGCATTAAATATGGAAATGCGGTCAGAAATGCCGGCATCTATACGTAATGAATTATTGATGAAATCATTAAAACAGCTGAATATTATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008651","ARO_id":"47443","ARO_name":"OXA-1241","CARD_short_name":"OXA-1241","ARO_description":"OXA-23 family carbapenem-hydrolyzing class D beta-lactamase OXA-1241.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46499":{"category_aro_accession":"3007710","category_aro_cvterm_id":"46499","category_aro_name":"OXA-23-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases, specifically imipenem, derived from OXA-23, first identified in Acinetobacter baumannii.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8070":{"model_id":"8070","model_name":"OXA-1242","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10897":{"protein_sequence":{"accession":"URT56864.1","sequence":"MRVLALSAVFLVASIIGMPAVAKEWQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGQTRDIATWNRDHNLITAMKYSVVPVYQEFSRQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISATEQISFLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYSTRIEPKIGWWVGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP"},"dna_sequence":{"accession":"ON651448.1","fmin":"0","fmax":"798","strand":"+","sequence":"ATGCGTGTATTAGCCTTATCGGCTGTGTTTTTGGTGGCATCGATTATCGGAATGCCTGCGGTAGCAAAGGAATGGCAAGAAAACAAAAGTTGGAATGCTCACTTTACTGAACATAAATCACAGGGCGTAGTTGTGCTCTGGAATGAGAATAAGCAGCAAGGATTTACCAATAATCTTAAACGGGCGAACCAAGCATTTTTACCCGCATCTACCTTTAAAATTCCCAATAGCTTGATCGCCCTCGATTTGGGCGTGGTTAAGGATGAACACCAAGTCTTTAAGTGGGATGGACAGACGCGCGATATCGCCACTTGGAATCGCGATCATAATCTAATCACCGCGATGAAATATTCAGTTGTGCCTGTTTATCAAGAATTTTCCCGCCAAATTGGCGAGGCACGTATGAGCAAGATGCTACATGCTTTCGATTATGGTAATGAGGACATTTCGGGCAATGTAGACAGTTTCTGGCTCGACGGTGGTATTCGAATTTCGGCCACGGAGCAAATCAGCTTTTTAAGAAAGCTGTATCACAATAAGTTACACGTATCGGAGCGCAGCCAGCGTATTGTCAAACAAGCCATGCTGACCGAAGCCAATGGTGACTATATTATTCGGGCTAAAACTGGATACTCGACTAGAATCGAACCTAAGATTGGCTGGTGGGTCGGTTGGGTTGAACTTGATGATAATGTGTGGTTTTTTGCGATGAATATGGATATGCCCACATCGGATGGTTTAGGGCTGCGCCAAGCCATCACAAAAGAAGTGCTCAAACAGGAAAAAATTATTCCCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008652","ARO_id":"47444","ARO_name":"OXA-1242","CARD_short_name":"OXA-1242","ARO_description":"OXA-48 family class D beta-lactamase OXA-1242.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46510":{"category_aro_accession":"3007721","category_aro_cvterm_id":"46510","category_aro_name":"OXA-48-like beta-lactamase","category_aro_description":"OXA-48-type beta-lactamases are now routinely encountered in bacterial infections caused by carbapenam-resistant Enterobacterales. OXA-48-like proteins confer resistance to penicillin (which is efficiently hydrolyzed) and carbapenam antibiotics (which is more slowly broken down). The spectrum of activity of these variants varies, with some hydrolyzing expanded-spectrum oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8071":{"model_id":"8071","model_name":"OXA-1243","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10898":{"protein_sequence":{"accession":"WZN32242.1","sequence":"MAIRIFAILFSIFSLATFAHAQEGTLERSDWRKFFSEFQAKGTIVVADERQADRAMLVFDPVRSKKRYSPASTFKIPHTLFALDAGAVRDEFQIFRWDGVNRGFAGHNQDQDLRSAMRNSTVWVYELFAKEIGDDKARRYLKKIDYGNADPSTSNGDYWIEGSLAKTAQEQIAKLRKLYRNELPFRVEHQRLVKDLMIVEAGRNWILRAKTGWEGRMGWWVGWVEWPTGSVFFALNIDTPNRMDDLFKREAIVRAILRSIEALPPNPAVNSDAAR"},"dna_sequence":{"accession":"PP682640.1","fmin":"1085","fmax":"1913","strand":"+","sequence":"ATGGCAATCCGAATCTTCGCGATACTTTTCTCCATTTTTTCTCTTGCCACTTTCGCGCATGCGCAAGAAGGCACGCTAGAACGTTCTGACTGGAGGAAGTTTTTCAGCGAATTTCAAGCCAAAGGCACGATAGTTGTGGCAGACGAACGCCAAGCGGATCGTGCCATGTTGGTTTTTGATCCTGTGCGATCGAAGAAACGCTACTCGCCTGCATCGACATTCAAGATACCTCATACACTTTTTGCACTTGATGCAGGCGCTGTTCGTGATGAGTTCCAGATTTTTCGATGGGACGGCGTTAACAGGGGCTTTGCAGGCCACAATCAAGACCAAGATTTGCGATCAGCAATGCGGAATTCTACTGTTTGGGTGTATGAGCTATTTGCAAAGGAAATTGGTGATGACAAAGCTCGGCGCTATTTGAAGAAAATCGACTATGGCAACGCCGATCCTTCGACAAGTAATGGCGATTACTGGATAGAAGGCAGCCTTGCAAAGACGGCGCAGGAGCAAATTGCAAAACTCAGGAAGCTCTATCGTAACGAGCTGCCCTTTCGGGTAGAACATCAGCGCTTGGTCAAGGATCTCATGATTGTGGAAGCCGGTCGCAACTGGATACTGCGTGCAAAGACGGGCTGGGAAGGCCGTATGGGTTGGTGGGTAGGATGGGTTGAGTGGCCGACTGGCTCCGTATTCTTCGCACTGAATATTGATACGCCAAACAGAATGGATGATCTTTTCAAGAGGGAGGCAATCGTGCGGGCAATCCTTCGCTCTATTGAAGCGTTACCGCCCAACCCGGCAGTCAACTCGGACGCTGCGCGATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42713","NCBI_taxonomy_name":"Klebsiella sp.","NCBI_taxonomy_id":"576"}}}},"ARO_accession":"3008653","ARO_id":"47445","ARO_name":"OXA-1243","CARD_short_name":"OXA-1243","ARO_description":"OXA-2 family class D beta-lactamase OXA-1243.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46493":{"category_aro_accession":"3007704","category_aro_cvterm_id":"46493","category_aro_name":"OXA-2-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-2.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8072":{"model_id":"8072","model_name":"OXA-1244","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10899":{"protein_sequence":{"accession":"XAP03053.1","sequence":"MRPLLFSALLLLSGHTQASEWNDSQAVDKLFGAAGVKGTFVLYDVQRQRYVGHDRERAETRFVPASTYKVANSLIGLSTGAVRSADEVLPYGGKPQRFKAWEHDMSLRDAIKASNVPVYQELARRIGLERMRANVSRLGYGNAEIGQVVDNFWLVGPLKISAMEQTRFLLRLAQGELPFPAPVQSTVRAMTLLESGPGWELHGKTGWCFDCTPELGWWVGWVKRNERLYGLALNIDMPGGEADIGKRVELGKASLKALGILP"},"dna_sequence":{"accession":"PP766712.1","fmin":"0","fmax":"789","strand":"+","sequence":"ATGCGCCCCCTCCTCTTCAGTGCCCTTCTCCTGCTTTCCGGGCATACCCAGGCCAGCGAATGGAACGACAGCCAGGCCGTGGACAAGCTATTCGGCGCGGCCGGGGTGAAAGGCACCTTCGTCCTCTACGATGTGCAGCGGCAGCGCTATGTCGGCCATGACCGGGAGCGCGCGGAAACCCGCTTCGTTCCCGCTTCCACCTACAAGGTGGCGAACAGCCTGATCGGCTTATCCACAGGGGCGGTTAGATCCGCCGACGAGGTTCTTCCCTATGGCGGCAAGCCCCAGCGCTTCAAGGCCTGGGAGCACGACATGAGCCTGCGCGACGCGATCAAGGCATCGAACGTACCGGTCTACCAGGAACTGGCGCGGCGCATCGGCCTGGAGCGGATGCGCGCCAATGTCTCGCGCCTGGGTTACGGCAACGCGGAAATCGGCCAGGTTGTGGATAACTTCTGGTTGGTGGGACCGCTGAAGATCAGCGCGATGGAACAGACCCGCTTTCTGCTCCGACTGGCGCAGGGAGAATTGCCATTCCCCGCCCCGGTGCAGTCCACCGTGCGCGCCATGACCCTGCTGGAAAGCGGCCCGGGCTGGGAGCTGCACGGCAAGACCGGCTGGTGCTTCGACTGCACGCCGGAACTCGGCTGGTGGGTGGGCTGGGTGAAGCGCAACGAGCGGCTCTACGGATTAGCCCTGAACATCGACATGCCCGGCGGCGAGGCCGACATCGGCAAGCGCGTCGAACTGGGCAAGGCCAGTCTCAAGGCTCTCGGGATACTGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008654","ARO_id":"47446","ARO_name":"OXA-1244","CARD_short_name":"OXA-1244","ARO_description":"OXA-50 family oxacillin-hydrolyzing class D beta-lactamase OXA-1244.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46513":{"category_aro_accession":"3007724","category_aro_cvterm_id":"46513","category_aro_name":"OXA-50-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-50.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8073":{"model_id":"8073","model_name":"OXA-1245","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10900":{"protein_sequence":{"accession":"XAP03054.1","sequence":"MRPLLFSALLLLSGHAQASEWNDSQAVDKLFGAAGVKGTFVLYDVQRQRYVGHDRERAETRFVPASTYKVANSLIGLSTGAVKSADEVLPYGGKPQRFKAWEHDMSLRDAIKASNVQVYQELARRIGLERMRANVSRLGYGNAEIGQVVDNFWLVGPLKISAMEQTRFLLRLAQGELPFPAPVQSTVRAMTLLESGPGWELHGKTGWCFDCTPELGWWVGWVKRNERLYGFALNIDMPGGEADIGKRVELGKASLKALGILP"},"dna_sequence":{"accession":"PP766713.1","fmin":"0","fmax":"789","strand":"+","sequence":"ATGCGCCCTCTCCTCTTCAGCGCCCTTCTCCTGCTCTCCGGGCATGCCCAGGCCAGCGAATGGAACGACAGCCAGGCCGTGGACAAGCTATTCGGCGCGGCCGGGGTGAAAGGCACCTTCGTCCTCTACGATGTGCAGCGGCAGCGCTATGTCGGCCATGACCGGGAGCGCGCGGAAACTCGCTTCGTTCCTGCCTCCACCTACAAGGTGGCGAACAGCCTGATTGGCTTATCCACAGGGGCGGTTAAATCCGCCGACGAGGTTCTTCCCTATGGCGGCAAGCCCCAGCGCTTCAAGGCCTGGGAGCACGACATGAGCCTGCGCGACGCGATCAAGGCATCGAACGTACAGGTCTACCAGGAACTGGCGCGACGCATCGGCCTGGAGCGGATGCGCGCCAATGTCTCGCGCCTGGGTTACGGCAACGCGGAAATCGGCCAGGTTGTGGATAACTTCTGGTTGGTGGGACCGCTGAAGATCAGCGCGATGGAACAGACCCGCTTTCTGCTCCGACTGGCGCAGGGAGAATTGCCATTCCCCGCCCCGGTGCAGTCCACCGTGCGCGCCATGACCCTGCTGGAAAGCGGCCCGGGCTGGGAGCTGCACGGCAAGACCGGCTGGTGCTTCGACTGCACGCCGGAACTCGGCTGGTGGGTGGGCTGGGTGAAGCGCAACGAGCGGCTCTACGGCTTCGCCCTGAACATCGACATGCCCGGCGGCGAGGCCGACATCGGCAAGCGCGTCGAACTGGGCAAGGCCAGTCTCAAGGCTCTCGGGATACTGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008655","ARO_id":"47447","ARO_name":"OXA-1245","CARD_short_name":"OXA-1245","ARO_description":"OXA-50 family oxacillin-hydrolyzing class D beta-lactamase OXA-1245.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46513":{"category_aro_accession":"3007724","category_aro_cvterm_id":"46513","category_aro_name":"OXA-50-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-50.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8074":{"model_id":"8074","model_name":"OXA-1246","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10901":{"protein_sequence":{"accession":"XAP03055.1","sequence":"MRPLLFSALLLLSGHAQASEWNDSQAVDKLFGAAGVKGTFVLYDVQRQRYVGHDRERAETRFVPASTYKVANSLIGLSTGAVRSADEVLPYGGKPQRFKAWEHDMSLRDAIEASNVPVYQELARRIGLERMRANVSRLGYGNAEIGQAVDNFWLVGPLKISAMEQTRFLLRLAQGELPFPAPVQSTVRAMTLLESGPGWELHGKTGWCFDCTPELGWWVGWVKRNERLYGFALNIDMPGGEADIGKRVELGKASLKALGILP"},"dna_sequence":{"accession":"PP766714.1","fmin":"0","fmax":"789","strand":"+","sequence":"ATGCGCCCTCTCCTCTTCAGCGCCCTTCTCCTGCTCTCCGGGCATGCCCAGGCCAGCGAATGGAACGACAGCCAGGCCGTGGACAAGCTATTCGGCGCGGCCGGGGTGAAAGGCACCTTCGTCCTCTACGATGTGCAGCGGCAGCGCTATGTCGGCCACGACCGGGAGCGCGCGGAAACTCGCTTCGTTCCTGCCTCCACCTACAAGGTGGCGAACAGCCTGATTGGCTTATCCACAGGGGCGGTTAGATCCGCCGACGAGGTTCTTCCCTATGGCGGCAAGCCCCAGCGCTTCAAGGCCTGGGAGCACGACATGAGCCTGCGCGATGCGATCGAGGCATCGAACGTACCGGTCTACCAGGAACTGGCGCGGCGCATCGGCCTGGAGCGGATGCGCGCCAATGTCTCGCGCCTGGGTTACGGCAACGCGGAAATCGGCCAGGCTGTGGATAACTTCTGGTTGGTGGGACCGCTGAAGATCAGCGCGATGGAACAGACCCGCTTTCTGCTCCGACTGGCCCAGGGAGAATTGCCATTCCCCGCCCCGGTGCAGTCCACCGTGCGCGCCATGACCCTGCTGGAAAGCGGCCCGGGCTGGGAGCTGCACGGCAAGACCGGCTGGTGCTTCGACTGCACGCCGGAACTCGGCTGGTGGGTGGGCTGGGTGAAGCGCAACGAGCGGCTCTACGGCTTCGCCCTGAACATCGACATGCCCGGCGGCGAGGCCGACATCGGCAAGCGCGTCGAACTGGGCAAGGCCAGTCTCAAGGCTCTCGGGATACTGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008656","ARO_id":"47448","ARO_name":"OXA-1246","CARD_short_name":"OXA-1246","ARO_description":"OXA-50 family oxacillin-hydrolyzing class D beta-lactamase OXA-1246.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46513":{"category_aro_accession":"3007724","category_aro_cvterm_id":"46513","category_aro_name":"OXA-50-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-50.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8075":{"model_id":"8075","model_name":"OXA-1247","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10902":{"protein_sequence":{"accession":"XAP03056.1","sequence":"MKTFAAYVITACLSSTALASSITENTFWNKEFSAEAVNGVFVLCKSSSKSCATNNLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLSLRGAIQVSALPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLFLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKGTEVYFFAFNMDIDNENKLPLRKSIPTKIMASEGIIGG"},"dna_sequence":{"accession":"PP766715.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGAAAACATTTGCCGCATATGTAATTACTGCGTGTCTTTCAAGTACGGCATTAGCTAGTTCAATTACAGAAAATACGTTTTGGAACAAAGAGTTCTCTGCCGAAGCCGTCAATGGTGTTTTCGTGCTTTGTAAAAGTAGCAGTAAATCCTGCGCTACCAATAACTTAGCTCGTGCATCAAAGGAATATCTTCCAGCATCAACATTTAAGATCCCCAACGCAATTATCGGCCTAGAAACTGGTGTCATAAAGAATGAGCATCAGGTTTTCAAATGGGACGGAAAGCCAAGAGCCATGAAACAATGGGAAAGAGACTTGAGCTTAAGAGGGGCAATACAAGTTTCAGCGCTTCCCGTATTTCAACAAATCGCCAGAGAAGTTGGCGAAGTAAGAATGCAGAAATATCTTAAAAAATTTTCATATGGTAACCAGAATATCAGTGGTGGCATTGACAAATTCTGGTTGGAGGGTCAGCTTAGAATTTCCGCAGTTAATCAAGTGGAGTTTCTAGAGTCTCTATTTTTAAATAAATTGTCAGCATCAAAAGAAAATCAGCTAATAGTAAAAGAGGCTTTGGTAACGGAGGCTGCGCCTGAATATCTTGTGCATTCAAAAACTGGTTTTTCTGGTGTGGGAACTGAGTCAAATCCTGGTGTCGCATGGTGGGTTGGTTGGGTTGAGAAGGGAACAGAGGTTTACTTTTTCGCCTTTAACATGGATATAGACAACGAAAATAAGTTGCCGCTAAGAAAATCCATTCCCACCAAAATCATGGCAAGTGAGGGCATCATTGGTGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008657","ARO_id":"47449","ARO_name":"OXA-1247","CARD_short_name":"OXA-1247","ARO_description":"OXA-10 family class D beta-lactamase OXA-1247.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46486":{"category_aro_accession":"3007697","category_aro_cvterm_id":"46486","category_aro_name":"OXA-10-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-10.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8076":{"model_id":"8076","model_name":"OXA-1248","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10903":{"protein_sequence":{"accession":"XAP03057.1","sequence":"MKTFAAYVIIACLSSTALAGSITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAFPVFQQIAREVGEVRMQKYLKNFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGIIGG"},"dna_sequence":{"accession":"PP766716.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGAAAACATTTGCCGCATATGTAATTATCGCGTGTCTTTCGAGTACGGCATTAGCTGGTTCAATTACAGAAAATACGTCTTGGAACAAAGAGTTCTCTGCCGAAGCCGTCAATGGTGTCTTCGTGCTTTGTAAAAGTAGCAGTAAATCCTGCGCTACCAATGACTTAGCTCGTGCATCAAAGGAATATCTTCCAGCATCAACATTTAAGATCCCCAACGCAATTATCGGCCTAGAAACTGGTGTCATAAAGAATGAGCATCAGGTTTTCAAATGGGACGGAAAGCCAAGAGCCATGAAGCAATGGGAAAGAGACTTGACCTTAAGAGGGGCAATACAAGTTTCAGCTTTTCCCGTATTTCAACAAATCGCCAGAGAAGTTGGCGAAGTAAGAATGCAGAAATACCTTAAAAACTTTTCCTATGGCAACCAGAATATCAGTGGTGGCATTGACAAATTCTGGTTGGAAGGCCAGCTTAGAATTTCCGCAGTTAATCAAGTGGAGTTTCTAGAGTCTCTATATTTAAATAAATTGTCAGCATCTAAAGAAAACCAGCTAATAGTAAAAGAGGCTTTGGTAACGGAGGCGGCACCTGAATATCTAGTGCATTCAAAAACTGGTTTTTCTGGTGTGGGAACTGAGTCAAATCCTGGTGTCGCATGGTGGGTTGGGTGGGTTGAGAAGGAGACAGAGGTTTACTTTTTCGCCTTTAACATGGATATAGACAACGAAAGTAAGTTGCCGCTAAGAAAATCCATTCCCACCAAAATCATGGAAAGTGAGGGCATCATTGGTGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008658","ARO_id":"47450","ARO_name":"OXA-1248","CARD_short_name":"OXA-1248","ARO_description":"OXA-10 family class D beta-lactamase OXA-1248.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46486":{"category_aro_accession":"3007697","category_aro_cvterm_id":"46486","category_aro_name":"OXA-10-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-10.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8077":{"model_id":"8077","model_name":"OXA-1249","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10904":{"protein_sequence":{"accession":"XBP46893.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKTTTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMPKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"PP858917.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCCCTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTCTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGACAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGACGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGCCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCATTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008659","ARO_id":"47451","ARO_name":"OXA-1249","CARD_short_name":"OXA-1249","ARO_description":"OXA-51 family carbapenem-hydrolyzing class D beta-lactamase OXA-1249.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8078":{"model_id":"8078","model_name":"OXA-1250","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10905":{"protein_sequence":{"accession":"XBP46885.1","sequence":"MRPLLFSALLLLSGHTQASEWNDSQAVDKLFGAAGVKGTFVLYDVQRQRYVGHDRERAETRFVPASTYKVANSLIGLSTGAVRSADEVLPYGGKPQRFKAWEHVMSLREAIKASNVPVYQELARRIGLERMRANVSRLGYGNAEIGQVVDNFWLVGPLKISAMEQTHFLLRLAQGELPFPAPVQSTVRAMTLLESGPGWELHGKTGWCFDCTPELGWWVGWVKRNERLYGFALNIDMPGGEADIGKRVELGKASLKALGILP"},"dna_sequence":{"accession":"PP850000.1","fmin":"0","fmax":"789","strand":"+","sequence":"ATGCGCCCCCTCCTCTTCAGTGCCCTTCTCCTGCTTTCCGGGCATACCCAGGCCAGCGAATGGAACGACAGCCAGGCCGTGGACAAGCTATTCGGCGCGGCCGGGGTGAAAGGCACCTTCGTCCTCTACGATGTGCAGCGGCAGCGCTATGTCGGCCATGACCGGGAGCGCGCGGAAACCCGCTTCGTTCCCGCTTCCACCTACAAGGTGGCGAACAGCCTGATCGGCTTATCCACAGGGGCGGTTAGATCCGCCGACGAGGTTCTTCCCTATGGCGGCAAGCCCCAGCGCTTCAAGGCCTGGGAGCACGTCATGAGCCTGCGCGAGGCGATCAAGGCATCGAACGTACCGGTCTACCAGGAACTGGCGCGGCGCATCGGCCTGGAGCGGATGCGCGCCAATGTCTCGCGCCTGGGTTACGGCAACGCGGAAATCGGCCAGGTTGTGGATAACTTCTGGTTGGTGGGACCGCTGAAGATCAGCGCGATGGAACAGACCCACTTTCTGCTCCGACTGGCGCAGGGAGAATTGCCATTCCCCGCCCCGGTGCAGTCCACCGTGCGCGCCATGACCCTGCTGGAAAGCGGCCCGGGCTGGGAGCTGCACGGCAAGACCGGCTGGTGCTTCGACTGCACGCCGGAACTCGGCTGGTGGGTGGGCTGGGTGAAGCGCAACGAGCGGCTCTACGGCTTCGCCCTGAACATCGACATGCCCGGCGGCGAGGCCGACATCGGCAAGCGCGTCGAACTGGGCAAGGCCAGTCTCAAGGCTCTCGGGATACTGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008660","ARO_id":"47452","ARO_name":"OXA-1250","CARD_short_name":"OXA-1250","ARO_description":"OXA-50 family oxacillin-hydrolyzing class D beta-lactamase OXA-1250.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46513":{"category_aro_accession":"3007724","category_aro_cvterm_id":"46513","category_aro_name":"OXA-50-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-50.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8079":{"model_id":"8079","model_name":"OXA-1251","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11359":{"protein_sequence":{"accession":"XBP46887.1","sequence":"MTVRLVSRALGAALFASALTLPARADVLCTLVADAADGRILFQQGTRQDCTQRYTPASTFKLPIALMGADAGILQGPHQPVWNYQPAYPDWGGEAWRQPTDPARWIKYSVVWYSQLTARALGQERFQRYTSAFGYGNADVSGEPGKHNGTDGAWIISSLRISPFEQVDFLRKFVNRQLPVKAAAYDLAENLFEVGEADGWRLYGKTGTGSPGSHGVYTPANAYGWFVGWARKDDRQLVFARLLQDEGATQPNAGLRARDGLMRDWAAMVTAPRK"},"dna_sequence":{"accession":"PP850002.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGACAGTTCGACTCGTTTCGCGCGCCCTGGGCGCAGCCCTCTTTGCGTCCGCCCTGACCCTGCCCGCCCGGGCGGACGTCCTGTGCACCCTGGTGGCCGACGCCGCCGACGGCCGCATCCTGTTCCAGCAGGGCACGCGGCAGGACTGCACGCAGCGCTACACCCCCGCCTCGACCTTCAAGCTGCCCATCGCCCTGATGGGCGCGGATGCCGGCATCCTGCAGGGCCCGCACCAGCCCGTCTGGAACTACCAGCCCGCTTATCCCGACTGGGGCGGCGAGGCCTGGCGCCAGCCCACCGATCCGGCTCGCTGGATCAAGTATTCGGTGGTCTGGTACTCGCAGTTGACCGCCAGGGCGCTGGGGCAGGAGCGCTTCCAGCGCTACACCTCCGCGTTCGGTTATGGCAACGCGGACGTCTCGGGTGAACCCGGCAAGCACAACGGCACCGATGGCGCGTGGATCATCTCCTCGCTGCGCATTTCGCCGTTTGAGCAGGTGGACTTCCTGCGCAAGTTCGTCAACCGGCAACTGCCCGTCAAGGCGGCTGCCTATGACCTGGCCGAGAACCTGTTCGAGGTCGGCGAAGCCGACGGCTGGCGCCTGTACGGCAAGACCGGAACCGGCTCGCCCGGCAGCCACGGTGTCTACACGCCGGCCAACGCCTATGGCTGGTTCGTCGGCTGGGCGCGCAAGGACGACCGCCAACTGGTGTTTGCCCGCCTGCTGCAGGACGAGGGGGCGACCCAGCCCAATGCCGGCCTGCGCGCCCGCGACGGCCTGATGCGCGACTGGGCCGCCATGGTCACGGCGCCCCGCAAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39091","NCBI_taxonomy_name":"Achromobacter ruhlandii","NCBI_taxonomy_id":"72557"}}}},"ARO_accession":"3008661","ARO_id":"47453","ARO_name":"OXA-1251","CARD_short_name":"OXA-1251","ARO_description":"OXA-258 family class D beta-lactamase OXA-1251.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8080":{"model_id":"8080","model_name":"OXA-1252","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10907":{"protein_sequence":{"accession":"XBP46888.1","sequence":"MRPLLFSALLLLSGHTQASEWNDSQAVDKLFGAAGVKGTFVLYDVQRQRYVGHDRERAETRFVPASTYKVANSLIGLSTGAVRSAYEVLPYGGKPQRFKAWEHDMSLRDAIKASNVPVYQELARRIGLERMRANVSRLGYGNAEIGQVVDNFWLVGPLKISAMEQTRFLLRLAQGELPFPAPVQSTVRAMTLLESGPGWELHGKTGWCFDCTPELGWWVGWVKRNERLYGFALNIDMPGGEADIGKRVELGKASLKALGILP"},"dna_sequence":{"accession":"PP850003.1","fmin":"0","fmax":"789","strand":"+","sequence":"ATGCGCCCCCTCCTCTTCAGTGCCCTTCTCCTGCTTTCCGGGCATACCCAGGCCAGCGAATGGAACGACAGCCAGGCCGTGGACAAGCTATTCGGCGCGGCCGGGGTGAAAGGCACCTTCGTCCTCTACGATGTGCAGCGGCAGCGCTATGTCGGCCATGACCGGGAGCGCGCGGAAACCCGCTTCGTTCCCGCTTCCACCTACAAGGTGGCGAACAGCCTGATCGGCTTATCCACAGGGGCGGTTAGATCCGCCTACGAGGTTCTTCCCTATGGCGGCAAGCCCCAGCGCTTCAAGGCCTGGGAGCACGACATGAGCCTGCGCGACGCGATCAAGGCATCGAACGTACCGGTCTACCAGGAACTGGCGCGGCGCATCGGCCTGGAGCGGATGCGCGCCAATGTCTCGCGCCTGGGTTACGGCAACGCGGAAATCGGCCAGGTTGTGGATAACTTCTGGTTGGTGGGACCGCTGAAGATCAGCGCGATGGAACAGACCCGCTTTCTGCTCCGACTGGCGCAGGGAGAATTGCCATTCCCCGCCCCGGTGCAGTCCACCGTGCGCGCCATGACCCTGCTGGAAAGCGGCCCGGGCTGGGAGCTGCACGGCAAGACCGGCTGGTGCTTCGACTGCACGCCGGAACTCGGCTGGTGGGTGGGCTGGGTGAAGCGCAACGAGCGGCTCTACGGATTCGCCCTGAACATCGACATGCCCGGCGGCGAGGCCGACATCGGCAAGCGCGTCGAACTGGGCAAGGCCAGTCTCAAGGCTCTCGGGATACTGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008662","ARO_id":"47454","ARO_name":"OXA-1252","CARD_short_name":"OXA-1252","ARO_description":"OXA-50 family oxacillin-hydrolyzing class D beta-lactamase OXA-1252.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46513":{"category_aro_accession":"3007724","category_aro_cvterm_id":"46513","category_aro_name":"OXA-50-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-50.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8081":{"model_id":"8081","model_name":"OXA-1253","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10908":{"protein_sequence":{"accession":"XBP46889.1","sequence":"MRPLLFSALLLLSGHTQASEWNDSQAVDKLFGAAGVKGTFVLYDVQRQCYVGHDRERAETRFVPASTYKVANSLIGLSTGAVRSADEVLPYGGKPQRFKAWEHDMSLREAIKASNVPVYQELARRIGLERMRANVSRLGYGNAEIGQVGDNFWLVGPLKISAMEQTRFLIRLAQGELPFPAPVQSTVRAMTLLESGPGWELHGKTGWCFDCTPELGWWVGWVKRNERLYGFALNIDMPGGEADIGKRVELGKASLKALGILP"},"dna_sequence":{"accession":"PP850004.1","fmin":"0","fmax":"789","strand":"+","sequence":"ATGCGCCCTCTCCTCTTCAGTGCCCTTCTCCTGCTTTCCGGGCATACCCAGGCCAGCGAATGGAACGACAGCCAGGCCGTGGACAAGCTATTCGGCGCGGCCGGGGTGAAAGGCACCTTCGTCCTCTACGATGTGCAGCGGCAGTGCTATGTCGGCCATGACCGGGAGCGCGCGGAAACCCGCTTCGTTCCCGCTTCCACCTACAAGGTGGCGAACAGCCTGATCGGCTTATCCACAGGGGCGGTTAGATCCGCCGACGAGGTTCTTCCCTATGGCGGCAAGCCCCAGCGCTTCAAGGCCTGGGAGCACGACATGAGCCTGCGCGAGGCGATCAAGGCATCGAACGTACCGGTCTACCAGGAACTGGCGCGGCGCATCGGCCTGGAGCGGATGCGCGCCAATGTCTCGCGCCTGGGTTACGGCAACGCGGAAATCGGCCAGGTTGGGGATAACTTCTGGTTGGTGGGACCGCTGAAGATCAGCGCGATGGAACAGACCCGCTTTCTGATCCGACTGGCGCAGGGAGAATTGCCATTCCCCGCCCCGGTGCAGTCCACCGTGCGCGCCATGACCCTGCTGGAAAGCGGCCCGGGCTGGGAGCTGCACGGCAAGACCGGCTGGTGCTTCGACTGCACGCCGGAACTCGGCTGGTGGGTGGGCTGGGTGAAGCGCAACGAGCGGCTCTACGGCTTCGCCCTGAACATCGACATGCCCGGCGGCGAGGCCGACATCGGCAAGCGCGTCGAACTGGGCAAGGCCAGTCTCAAGGCTCTCGGGATACTGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008663","ARO_id":"47455","ARO_name":"OXA-1253","CARD_short_name":"OXA-1253","ARO_description":"OXA-50 family oxacillin-hydrolyzing class D beta-lactamase OXA-1253.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46513":{"category_aro_accession":"3007724","category_aro_cvterm_id":"46513","category_aro_name":"OXA-50-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-50.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8082":{"model_id":"8082","model_name":"OXA-1254","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10909":{"protein_sequence":{"accession":"XBP46890.1","sequence":"MRPLLFSALLLLSGHTQASEWNDSQAVDKLFGAAGVKGTFVLYDVQRQRYVGHDRERAETRFVPASTYKVANSLIGLSTGAVRSADEVLPYGGKPQRFKAWEHDMSLREAIKASNVPVYQELARRIGLERMRGNVSRLGYGNAEIGQVVDNFWLVGPLKISAMEQTHFLLRLAQGELPFPAPVQSTVRAMTLLESGPGWELHGKTGWCFDCTPELGWWVGWVKRNERLYGFALNIDMPGGEADIGKRVELGKASLKALGILP"},"dna_sequence":{"accession":"PP850005.1","fmin":"0","fmax":"789","strand":"+","sequence":"ATGCGCCCCCTCCTCTTCAGTGCCCTTCTCCTGCTTTCCGGGCATACCCAGGCCAGCGAATGGAACGACAGCCAGGCCGTGGACAAGCTATTCGGCGCGGCCGGGGTGAAAGGCACCTTCGTCCTCTACGATGTGCAGCGGCAGCGCTATGTCGGCCATGACCGGGAGCGCGCGGAAACCCGCTTCGTTCCCGCTTCCACCTACAAGGTGGCGAACAGCCTGATCGGCTTATCCACAGGGGCGGTTAGATCCGCCGACGAGGTTCTTCCCTATGGCGGCAAGCCCCAGCGCTTCAAGGCCTGGGAGCACGACATGAGCCTGCGCGAGGCGATCAAGGCATCGAACGTACCGGTCTACCAGGAACTGGCGCGGCGCATCGGCCTGGAGCGGATGCGCGGCAATGTCTCGCGCCTGGGTTACGGCAACGCGGAAATCGGCCAGGTTGTGGATAACTTCTGGTTGGTGGGACCGCTGAAGATCAGCGCGATGGAACAGACCCACTTTCTGCTCCGACTGGCGCAGGGAGAATTGCCATTCCCCGCCCCGGTGCAGTCCACCGTGCGCGCCATGACCCTGCTGGAAAGCGGCCCGGGCTGGGAGCTGCACGGCAAGACCGGCTGGTGCTTCGACTGCACGCCGGAACTCGGCTGGTGGGTGGGCTGGGTGAAGCGCAACGAGCGGCTCTACGGCTTCGCCCTGAACATCGACATGCCCGGCGGCGAGGCCGACATCGGCAAGCGCGTCGAACTGGGCAAGGCCAGTCTCAAGGCTCTCGGGATACTGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008664","ARO_id":"47456","ARO_name":"OXA-1254","CARD_short_name":"OXA-1254","ARO_description":"OXA-50 family oxacillin-hydrolyzing class D beta-lactamase OXA-1254.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46513":{"category_aro_accession":"3007724","category_aro_cvterm_id":"46513","category_aro_name":"OXA-50-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-50.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8083":{"model_id":"8083","model_name":"OXA-1255","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10910":{"protein_sequence":{"accession":"XBP46891.1","sequence":"MRPLLFSALLLLSGHTQASEWNDSQAVDKLFGAAGVKGTFVLYDVQRQRYVGHDRERAETRFVPASTYKVANSLIGLSTGAVRSADEVLPYGGKPQRFKAWEHDMSLREAIKASNVPVYQELARRIGLERMRANVSRLGYGNAEIGQVVDNFWLVGPLKISAVEQTHFLLRLAQGELPFPAPVQSTVRAMTLLESGPGWELHGKTGWCFDCTPELGWWVGWVKRNERLYGFALNIDMPGGEADIGKRVELGKASLKALGILP"},"dna_sequence":{"accession":"PP850006.1","fmin":"0","fmax":"789","strand":"+","sequence":"ATGCGCCCTCTCCTCTTCAGTGCCCTTCTCCTGCTTTCCGGGCATACCCAGGCCAGCGAATGGAACGACAGCCAGGCCGTGGACAAGCTATTCGGCGCGGCCGGGGTGAAAGGCACCTTCGTCCTCTACGATGTGCAGCGGCAGCGCTATGTCGGCCATGACCGGGAGCGCGCGGAAACCCGCTTCGTTCCCGCTTCCACCTACAAGGTGGCGAACAGCCTGATCGGCTTATCCACAGGGGCGGTTAGATCCGCCGACGAGGTTCTTCCCTATGGCGGCAAGCCCCAGCGCTTCAAGGCCTGGGAGCACGACATGAGCCTGCGCGAGGCGATCAAGGCATCGAACGTACCGGTCTACCAGGAACTGGCGCGGCGCATCGGCCTGGAGCGGATGCGCGCCAATGTCTCGCGCCTGGGTTACGGCAACGCGGAAATCGGCCAGGTTGTGGATAACTTCTGGTTGGTGGGACCGCTGAAGATCAGCGCGGTGGAACAGACCCACTTTCTGCTCCGACTGGCGCAGGGAGAATTGCCATTCCCCGCCCCGGTGCAGTCCACCGTGCGCGCCATGACCCTGCTGGAAAGCGGCCCGGGCTGGGAGCTGCACGGCAAGACCGGCTGGTGCTTCGACTGCACGCCGGAACTCGGCTGGTGGGTGGGCTGGGTGAAGCGCAACGAGCGGCTCTACGGCTTCGCCCTGAACATCGACATGCCCGGCGGCGAGGCCGACATCGGCAAGCGCGTCGAACTGGGCAAGGCCAGTCTCAAGGCTCTCGGGATACTGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008665","ARO_id":"47457","ARO_name":"OXA-1255","CARD_short_name":"OXA-1255","ARO_description":"OXA-50 family oxacillin-hydrolyzing class D beta-lactamase OXA-1255.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46513":{"category_aro_accession":"3007724","category_aro_cvterm_id":"46513","category_aro_name":"OXA-50-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-50.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8084":{"model_id":"8084","model_name":"OXA-1256","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10911":{"protein_sequence":{"accession":"XBP46892.1","sequence":"MRPLLFSALLLLSGHTQASEWNDSQAVDKLFGAAGVKGTFVLYDVQRQRYVGHDRERAETRFVPASTYKVANSLIGLSTGAVRSADEVLPYGGKPQRFKAWEHDMSLRDAIEASNVPVYQELARRIGLERMRANVSRLGYGNAEIGQVVDSFWLVGPLKISAMEQTRFLLRLAQGELPFPAPVQSTVRAMTLLESGPGWELHGKTGWCFDCTPELGWWVGWVKRNERLYGFALNIDMPGGEADTGKRVELGKASLKALGILP"},"dna_sequence":{"accession":"PP850007.1","fmin":"0","fmax":"789","strand":"+","sequence":"ATGCGCCCTCTCCTCTTCAGCGCCCTTCTCCTGCTCTCCGGGCATACCCAGGCCAGCGAATGGAACGACAGCCAGGCCGTGGACAAGCTATTCGGCGCGGCCGGGGTGAAAGGCACCTTCGTCCTCTACGATGTGCAGCGGCAGCGCTATGTCGGCCATGACCGGGAGCGCGCGGAAACCCGCTTCGTTCCCGCTTCCACCTACAAGGTGGCGAACAGCCTGATCGGCTTATCCACAGGGGCGGTTAGATCCGCCGACGAGGTTCTTCCCTATGGCGGCAAGCCCCAGCGCTTCAAGGCCTGGGAGCACGACATGAGCCTGCGCGACGCGATCGAGGCATCGAACGTACCGGTCTACCAGGAACTGGCGCGGCGCATCGGCCTGGAGCGGATGCGCGCCAATGTCTCCCGCCTGGGTTACGGCAACGCGGAAATCGGCCAGGTTGTGGATAGCTTCTGGTTGGTGGGACCGCTGAAGATCAGCGCGATGGAACAGACCCGCTTTCTGCTCCGACTGGCGCAGGGAGAGTTGCCATTCCCCGCCCCGGTGCAGTCCACCGTGCGCGCCATGACCCTGCTGGAAAGCGGCCCGGGCTGGGAGCTGCACGGCAAGACCGGCTGGTGCTTCGACTGCACGCCGGAACTCGGCTGGTGGGTGGGCTGGGTGAAGCGCAACGAGCGGCTCTACGGCTTCGCCCTGAACATCGACATGCCCGGCGGCGAGGCCGACACCGGAAAGCGTGTCGAACTGGGCAAGGCCAGTCTCAAGGCTCTCGGGATACTGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008666","ARO_id":"47458","ARO_name":"OXA-1256","CARD_short_name":"OXA-1256","ARO_description":"OXA-50 family oxacillin-hydrolyzing class D beta-lactamase OXA-1256.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46513":{"category_aro_accession":"3007724","category_aro_cvterm_id":"46513","category_aro_name":"OXA-50-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-50.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8085":{"model_id":"8085","model_name":"OXA-1257","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10912":{"protein_sequence":{"accession":"XBS36001.1","sequence":"MKTFAAYVIIACLSSTALAGSITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMRKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGIIGG"},"dna_sequence":{"accession":"PP895198.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGAAAACATTTGCCGCATATGTAATTATCGCGTGTCTTTCGAGTACGGCATTAGCTGGTTCAATTACAGAAAATACGTCTTGGAACAAAGAGTTCTCTGCCGAAGCCGTCAATGGTGTCTTCGTGCTTTGTAAAAGTAGCAGTAAATCCTGCGCTACCAATGACTTAGCTCGTGCATCAAAGGAATATCTTCCAGCATCAACATTTAAGATCCCCAACGCAATTATCGGCCTAGAAACTGGTGTCATAAAGAATGAGCATCAGGTTTTCAAATGGGACGGAAAGCCAAGAGCCATGAAGCAATGGGAAAGAGACTTGACCTTAAGAGGGGCAATACAAGTTTCAGCTGTTCCCGTATTTCAACAAATCGCCAGAGAAGTTGGCGAAGTAAGAATGCGGAAATACCTTAAAAAATTTTCCTATGGCAACCAGAATATCAGTGGTGGCATTGACAAATTCTGGTTGGAAGGCCAGCTTAGAATTTCCGCAGTTAATCAAGTGGAGTTTCTAGAGTCTCTATATTTAAATAAATTGTCAGCATCTAAAGAAAACCAGCTAATAGTAAAAGAGGCTTTGGTAACGGAGGCGGCACCTGAATATCTAGTGCATTCAAAAACTGGTTTTTCTGGTGTGGGAACTGAGTCAAATCCTGGTGTCGCATGGTGGGTTGGGTGGGTTGAGAAGGAGACAGAGGTTTACTTTTTCGCCTTTAACATGGATATAGACAACGAAAGTAAGTTGCCGCTAAGAAAATCCATTCCCACCAAAATCATGGAAAGTGAGGGCATCATTGGTGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008667","ARO_id":"47459","ARO_name":"OXA-1257","CARD_short_name":"OXA-1257","ARO_description":"OXA-10 family class D beta-lactamase OXA-1257.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46486":{"category_aro_accession":"3007697","category_aro_cvterm_id":"46486","category_aro_name":"OXA-10-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-10.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8086":{"model_id":"8086","model_name":"OXA-1258","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10913":{"protein_sequence":{"accession":"WFP96649.1","sequence":"MKLFQYCAVMLFSMGLMACAPSQIQNHQPVTSHFNAVNPALNIKTLFKEVHADVVFVTFDGKSLNEYGTNLNRADTAYIPASTFKIVNALIGLQHEKANTQEVFKWDGKPKFIKSWERDMTLAEAMQASAVPVYQTLARRTGLPLMQKELERIGYGNMQVGAQVDQFWLKGPLTITLDEQVNFLYQHGKGQLAFKPEVQQKVKEMLYVERRGESRLYAKSGWGMDVDPQVGWYVGFVEKADGQVVSFALNMQIKDGDDVNLRKQLTLDALDKLGVFHYL"},"dna_sequence":{"accession":"CP121303.1","fmin":"2452347","fmax":"2453187","strand":"-","sequence":"ATGAAATTATTTCAATATTGTGCTGTGATGCTTTTCAGCATGGGGCTTATGGCATGTGCGCCATCTCAAATTCAAAACCATCAACCTGTCACATCTCATTTCAATGCTGTAAATCCTGCATTAAATATTAAGACTTTGTTTAAAGAAGTTCATGCAGATGTTGTTTTTGTGACGTTTGATGGAAAATCATTAAATGAATATGGAACAAATTTAAACCGTGCCGATACTGCTTATATTCCTGCATCAACGTTTAAAATCGTAAATGCGCTTATTGGTTTGCAACATGAAAAAGCTAATACTCAAGAAGTATTTAAATGGGATGGAAAGCCTAAATTTATTAAGTCTTGGGAACGTGACATGACTTTGGCAGAGGCAATGCAAGCATCTGCTGTGCCAGTTTATCAAACTTTGGCGCGTCGAACGGGTTTGCCTTTAATGCAAAAGGAGTTGGAGCGAATTGGTTATGGCAATATGCAAGTGGGTGCACAGGTCGATCAGTTTTGGTTGAAAGGTCCATTAACTATTACCCTAGATGAACAAGTGAATTTTTTATATCAACATGGTAAAGGGCAGTTGGCGTTTAAACCTGAAGTTCAGCAAAAAGTGAAAGAAATGTTGTATGTGGAGCGCAGAGGGGAGAGTCGTTTATATGCGAAAAGTGGTTGGGGAATGGATGTTGATCCCCAAGTGGGGTGGTATGTGGGTTTTGTTGAAAAGGCAGATGGTCAGGTTGTAAGTTTTGCTTTGAATATGCAAATAAAAGATGGTGATGATGTAAATTTAAGGAAGCAACTTACTTTAGATGCGTTAGATAAGTTGGGTGTTTTTCATTATTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36837","NCBI_taxonomy_name":"Acinetobacter sp.","NCBI_taxonomy_id":"472"}}}},"ARO_accession":"3008668","ARO_id":"47460","ARO_name":"OXA-1258","CARD_short_name":"OXA-1258","ARO_description":"Class D beta-lactamase OXA-1258.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8087":{"model_id":"8087","model_name":"OXA-1259","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10914":{"protein_sequence":{"accession":"MDY6529736.1","sequence":"MKLFQYCAVMLFSIGLMACAPSQINNHQPVTSHFNAVNPTLNIKTLFKEVHADAVFVTFDGKSLNEYGTNLNRADTAYIPASTFKIVNALIGLQHEKANTQEVFKWDGKPKFIKSWERDMTLAEAMQASAVPVYQTLARRTGLPLMQKELERIGYGNMQVCAQVDQFWLKGPLTITPNEQVKFLYQLGKGQLAFKPEVQQKVKEMLYVESRGESRLYAKSGWGMDVDPQVGWYVGFVEKANGQVVSFALNMQIKDGDDVNLRKQLTLDALDKLGVFHYL"},"dna_sequence":{"accession":"JAXHPQ010000007.1","fmin":"10478","fmax":"11318","strand":"-","sequence":"ATGAAATTATTTCAATATTGTGCTGTGATGCTTTTCAGCATAGGGCTTATGGCATGTGCGCCATCTCAAATTAATAACCATCAACCTGTCACATCTCATTTCAATGCTGTAAATCCGACATTAAATATTAAGACTTTGTTTAAAGAAGTTCATGCAGATGCTGTTTTTGTGACGTTTGATGGAAAATCATTAAATGAATATGGAACAAATTTAAACCGTGCCGATACTGCTTATATTCCTGCATCAACGTTTAAAATCGTAAATGCGCTTATTGGTTTGCAACATGAAAAAGCTAATACTCAAGAAGTATTTAAATGGGATGGAAAGCCTAAATTTATTAAGTCTTGGGAACGTGACATGACTTTGGCAGAGGCAATGCAAGCATCTGCTGTGCCAGTTTATCAAACTTTGGCGCGTCGAACGGGTTTGCCTTTAATGCAAAAGGAGTTGGAGCGAATTGGTTATGGCAATATGCAAGTGTGTGCACAGGTCGATCAGTTTTGGTTGAAAGGTCCATTAACTATTACCCCAAATGAACAAGTGAAATTTTTATATCAACTTGGTAAAGGGCAGTTGGCATTTAAACCTGAAGTTCAGCAAAAAGTGAAAGAAATGTTGTATGTAGAGAGCAGAGGGGAGAGTCGTTTATATGCGAAAAGTGGTTGGGGAATGGATGTTGATCCCCAAGTGGGGTGGTATGTGGGTTTTGTTGAAAAGGCAAATGGTCAGGTTGTAAGTTTTGCTTTGAATATGCAAATAAAAGATGGTGATGATGTAAATTTAAGGAAGCAACTTACTTTAGATGCGTTAGATAAGTTGGGTGTTTTTCATTATTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"47898","NCBI_taxonomy_name":"Acinetobacter faecalis","NCBI_taxonomy_id":"2665161"}}}},"ARO_accession":"3008669","ARO_id":"47461","ARO_name":"OXA-1259","CARD_short_name":"OXA-1259","ARO_description":"OXA-1258 family class D beta-lactamase OXA-1259.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8088":{"model_id":"8088","model_name":"OXA-1260","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10915":{"protein_sequence":{"accession":"MDY6551534.1","sequence":"MKLFQYCAVMLFSIGLMACAPSQINNHQPVTSHFNAVNPTLNIKTLFKEVHADAVFVTFDGKSLNEYGTNLNRADTAYIPASTFKIVNALIGLQHEKANTQEVFKWDGKPKFIKSWERDMTLAEAMQASAVPVYQTLARRTGLPLMQKELERIGYGNMQVCAQVDQFWLKGPLTITPNEQVKFLYQLGKGQLAFKPEVQQKVKEMLYVESRGESRLYAKSGWGMDVDPQVGWYVGFVEKANVQVVSFALNMQIKDGDDVNLRKQLTLDALDKLGVFHYL"},"dna_sequence":{"accession":"JAXHPO010000090.1","fmin":"809","fmax":"1649","strand":"-","sequence":"ATGAAATTATTTCAATATTGTGCTGTGATGCTTTTCAGCATAGGGCTTATGGCATGTGCGCCATCTCAAATTAATAACCATCAACCTGTCACATCTCATTTCAATGCTGTAAATCCGACATTAAATATTAAGACTTTGTTTAAAGAAGTTCATGCAGATGCTGTTTTTGTGACGTTTGATGGAAAATCATTAAATGAATATGGAACAAATTTAAACCGTGCCGATACTGCTTATATTCCTGCATCAACGTTTAAAATCGTAAATGCGCTTATTGGTTTGCAACATGAAAAAGCTAATACTCAAGAAGTATTTAAATGGGATGGAAAGCCTAAATTTATTAAGTCTTGGGAACGTGACATGACTTTGGCAGAGGCAATGCAAGCATCTGCTGTGCCAGTTTATCAAACTTTGGCGCGTCGAACGGGTTTGCCTTTAATGCAAAAGGAGTTGGAGCGAATTGGTTATGGCAATATGCAAGTGTGTGCACAGGTCGATCAGTTTTGGTTGAAAGGTCCATTAACTATTACCCCAAATGAACAAGTGAAATTTTTATATCAACTTGGTAAAGGGCAGTTGGCGTTTAAACCTGAAGTTCAGCAAAAAGTGAAAGAAATGTTGTATGTAGAGAGCAGAGGGGAGAGTCGTTTATATGCGAAAAGTGGTTGGGGAATGGATGTTGATCCCCAAGTGGGGTGGTATGTGGGTTTTGTTGAAAAGGCAAATGTTCAGGTTGTAAGTTTTGCTTTGAATATGCAAATAAAAGATGGTGATGATGTAAATTTAAGGAAGCAACTTACTTTAGATGCGTTAGATAAGTTGGGTGTTTTTCATTATTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"47898","NCBI_taxonomy_name":"Acinetobacter faecalis","NCBI_taxonomy_id":"2665161"}}}},"ARO_accession":"3008670","ARO_id":"47462","ARO_name":"OXA-1260","CARD_short_name":"OXA-1260","ARO_description":"OXA-1258 family class D beta-lactamase OXA-1260.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8089":{"model_id":"8089","model_name":"OXA-1261","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10916":{"protein_sequence":{"accession":"MDY6449478.1","sequence":"MKLFQYCAVMLFSMGLMACAPSQIQNHQPVTSHFNAVNPALNIKTLFKEVHADVVFVTFDGKSLNEYGTNLNRADTAYIPASTFKIVNALIGLQHEKANTQEVFKWDGKPKFIKSWERDMTLAEAMQASAVPVYQTLARRTGLPLMQKELERIGYGNMQVGAQVDQFWLKGPLTITPNEQVQFLYQLGKGQLAFKPEVQQKVKEMLYVERRGENRLYAKSGWGMDVDPQVGWYVGFVEKADGQVVSFALNMQMKDGDDVNLRKQLTLDALDKLGVFHYL"},"dna_sequence":{"accession":"JAXHPG010000001.1","fmin":"261669","fmax":"262509","strand":"-","sequence":"ATGAAATTATTTCAATATTGTGCTGTGATGCTTTTCAGCATGGGGCTTATGGCATGTGCGCCATCTCAAATTCAAAACCATCAACCTGTCACATCTCATTTCAATGCTGTAAATCCTGCATTAAATATTAAGACTTTGTTTAAAGAAGTTCATGCAGATGTTGTTTTTGTGACGTTTGATGGAAAATCATTAAATGAATATGGAACAAATTTAAACCGTGCCGATACTGCTTATATTCCTGCATCAACGTTTAAAATCGTAAATGCGCTTATTGGTTTGCAACATGAAAAAGCTAATACTCAAGAAGTATTTAAATGGGATGGAAAGCCTAAATTTATTAAGTCTTGGGAACGTGACATGACTTTGGCAGAGGCAATGCAAGCATCTGCTGTGCCAGTTTATCAAACTTTGGCGCGTCGAACGGGTTTGCCTTTAATGCAAAAGGAGTTGGAGCGAATTGGTTATGGCAATATGCAAGTGGGTGCACAGGTCGATCAGTTTTGGTTGAAAGGTCCATTAACCATTACCCCAAATGAACAAGTGCAATTTTTATATCAACTTGGTAAAGGGCAGTTGGCGTTTAAACCTGAAGTTCAGCAAAAAGTGAAAGAAATGTTGTATGTGGAGCGCAGAGGGGAGAATCGTTTATATGCGAAAAGTGGTTGGGGAATGGATGTTGATCCCCAAGTGGGTTGGTATGTAGGTTTTGTTGAAAAGGCAGATGGTCAGGTTGTAAGTTTTGCTTTGAATATGCAAATGAAAGATGGTGATGATGTAAATTTACGGAAGCAACTGACTTTAGATGCGTTAGATAAGTTGGGTGTTTTTCATTATTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"47898","NCBI_taxonomy_name":"Acinetobacter faecalis","NCBI_taxonomy_id":"2665161"}}}},"ARO_accession":"3008671","ARO_id":"47463","ARO_name":"OXA-1261","CARD_short_name":"OXA-1261","ARO_description":"OXA-1258 family class D beta-lactamase OXA-1261.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8090":{"model_id":"8090","model_name":"OXA-1262","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10917":{"protein_sequence":{"accession":"MDY6481403.1","sequence":"MKLFQYCAVMLFSMGLMACVPSQIQNHQPVTSHLSVVNPALKIQVLFKEVHADAVFVTFDGTKLNAYGTHLNRADTAYIPASTFKIVNALIGLQHGKANTQEVFKWDGKPKFIKSWERDMTLAEAMQASAVPVYQTLARRTGLPLMQKELERIGYGNMQVGAQVDQFWLKGPLTITPNEQVQFLYQLGKGQLAFKPEVQQKVKEMLYVERRGENRLYAKSGWGMDVDPQVGWYVGFVEKADGQVVSFALNMQMKDGDDVNLRKQLTLDALDKLGVFHYL"},"dna_sequence":{"accession":"JAXHPF010000002.1","fmin":"217780","fmax":"218620","strand":"-","sequence":"ATGAAATTATTTCAATATTGTGCTGTGATGCTTTTCAGCATGGGGCTTATGGCATGTGTGCCATCTCAAATTCAAAACCATCAACCTGTCACATCTCATTTAAGTGTTGTGAATCCTGCTTTAAAAATTCAGGTTTTATTTAAAGAGGTACATGCAGATGCTGTTTTTGTGACTTTCGATGGGACAAAACTCAATGCATATGGCACACATTTGAACCGTGCCGATACTGCTTATATTCCTGCATCAACGTTTAAAATCGTAAATGCGCTTATTGGTTTGCAACATGGAAAAGCCAATACTCAAGAAGTTTTTAAATGGGATGGAAAGCCTAAATTTATTAAGTCTTGGGAACGTGACATGACTTTGGCAGAGGCAATGCAAGCATCTGCTGTGCCAGTTTATCAAACTTTGGCGCGTCGAACGGGTTTGCCTTTAATGCAAAAGGAGTTGGAGCGAATTGGTTATGGCAATATGCAAGTGGGTGCACAGGTCGATCAGTTTTGGTTGAAAGGTCCATTAACCATTACCCCAAATGAACAAGTGCAATTTTTATATCAACTTGGTAAAGGGCAGTTGGCGTTTAAACCTGAAGTTCAGCAAAAAGTGAAAGAAATGTTGTATGTGGAGCGCAGAGGGGAGAATCGTTTATATGCGAAAAGTGGTTGGGGAATGGATGTTGATCCCCAAGTGGGTTGGTATGTAGGTTTTGTTGAAAAGGCAGATGGTCAGGTTGTAAGTTTTGCTTTGAATATGCAAATGAAAGATGGTGATGATGTAAATTTACGGAAGCAACTGACTTTAGATGCGTTAGATAAGTTGGGTGTTTTTCATTATTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"47898","NCBI_taxonomy_name":"Acinetobacter faecalis","NCBI_taxonomy_id":"2665161"}}}},"ARO_accession":"3008672","ARO_id":"47464","ARO_name":"OXA-1262","CARD_short_name":"OXA-1262","ARO_description":"OXA-1258 family class D beta-lactamase OXA-1262.","ARO_category":{"36029":{"category_aro_accession":"3000020","category_aro_cvterm_id":"36029","category_aro_name":"IMP beta-lactamase","category_aro_description":"Plasmid mediated IMP-type carbapenemases, of which at least 26 varieties are currently known, became established in Japan in the 1990s in enteric gram-negative organisms, Pseudomonas and Acinetobacter species. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8091":{"model_id":"8091","model_name":"OXA-1263","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10918":{"protein_sequence":{"accession":"MDY6468282.1","sequence":"MKLFQYSAVMILSMGLMACAPSQIQNHQPVTSHLSAVNPALNIQALFKEVHADAVFVTFDGTKLNAYGTHLNRADTAYIPASTFKIVNVLIGLQHGKANTQEVFKWDGKPKFIKSWERDMTLAEAMQASAVPVYQTLAHRTGLPLMQKELERIGYGNMQVGSQVDQFRLKGPLTITPNEQVKFLYQLGKGQLAFKPEVQQQVKEMLYVERRGKSRLYAKSGWGMDVDPQVGWYVGFVEKADGQVVSFALNMQMKEGDDVNLRKQLTLDALDKLGVFHYL"},"dna_sequence":{"accession":"JAXHPD010000006.1","fmin":"108551","fmax":"109391","strand":"+","sequence":"ATGAAATTATTTCAATATTCTGCTGTGATGATTCTCAGCATGGGGCTTATGGCATGTGCGCCATCTCAAATTCAAAATCATCAACCTGTCACATCTCATTTAAGTGCTGTAAACCCCGCTTTAAACATTCAGGCTTTATTTAAAGAAGTACATGCAGATGCTGTTTTTGTGACTTTCGATGGTACAAAACTCAATGCGTATGGCACACATTTGAACCGTGCCGATACGGCTTATATTCCTGCATCAACGTTTAAAATCGTAAATGTGCTTATTGGTTTGCAACATGGAAAAGCAAATACTCAAGAAGTATTTAAATGGGATGGAAAGCCTAAATTTATTAAGTCTTGGGAACGTGACATGACTTTAGCAGAGGCAATGCAAGCGTCTGCTGTGCCTGTTTATCAAACTTTGGCGCATCGAACGGGTTTGCCTTTAATGCAAAAGGAGTTGGAGCGAATTGGTTATGGCAATATGCAAGTGGGTTCACAGGTCGATCAGTTTCGGTTGAAAGGTCCATTAACTATTACCCCAAATGAACAAGTGAAATTTTTATATCAACTCGGCAAAGGGCAGTTGGCGTTTAAACCTGAAGTTCAGCAACAAGTGAAAGAGATGTTGTATGTGGAGCGTAGAGGAAAGAGTCGTTTATATGCCAAGAGTGGTTGGGGTATGGATGTTGACCCGCAAGTGGGTTGGTATGTGGGTTTTGTTGAGAAGGCAGATGGTCAGGTTGTGAGTTTTGCTTTGAATATGCAAATGAAAGAGGGTGATGATGTGAATTTGCGGAAGCAACTGACTTTAGATGCGTTAGATAAGTTGGGTGTTTTTCATTATTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"47898","NCBI_taxonomy_name":"Acinetobacter faecalis","NCBI_taxonomy_id":"2665161"}}}},"ARO_accession":"3008673","ARO_id":"47465","ARO_name":"OXA-1263","CARD_short_name":"OXA-1263","ARO_description":"OXA-1258 family class D beta-lactamase OXA-1263.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8092":{"model_id":"8092","model_name":"OXA-1264","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10919":{"protein_sequence":{"accession":"XGJ10589.1","sequence":"MKKIISRWRRGVFGLRVALAVVSPMVFAVPAHATEAAGGSAGTKAAAVHMKERADWGKFFDAEGVKGTIVVLDGRTQTYQAFDTARAERRMSPASTYKIFNSLLALESGALDNEREIIPWDGKPRRGKYWNAAMDLRTAFRVSCLPCYQVVSHKIARQFAQSKLNEAGYGNHTIGRAADAYWVDDSLQISAREQVDFLQRLARGTLPFSARSQDIVRQISIVEANPDYVLHGKTGWFVDKKPDIGWWVGWIERDGNITSVALNIDLKDDADAPKRARIVRAVLSSLQLI"},"dna_sequence":{"accession":"PQ196143.1","fmin":"0","fmax":"870","strand":"+","sequence":"ATGAAAAAGATAATTTCTCGCTGGCGGCGTGGTGTCTTCGGGCTGCGGGTTGCGCTCGCGGTCGTGTCTCCCATGGTGTTCGCCGTTCCGGCGCATGCGACGGAAGCGGCGGGCGGGTCCGCGGGGACTAAGGCCGCTGCGGTGCACATGAAGGAGCGTGCCGATTGGGGCAAGTTCTTCGATGCGGAAGGTGTTAAGGGAACGATCGTGGTGCTCGACGGACGCACGCAAACGTATCAGGCGTTCGACACGGCGCGCGCCGAGCGGCGGATGTCGCCTGCATCGACGTACAAGATCTTCAACAGCCTGCTGGCGCTCGAGTCGGGCGCCCTCGATAACGAACGCGAGATCATTCCCTGGGACGGCAAGCCGCGACGCGGGAAGTACTGGAACGCGGCGATGGATCTGCGCACGGCGTTTCGCGTGTCGTGTTTGCCGTGCTATCAGGTGGTCTCGCACAAGATTGCGCGTCAGTTTGCACAGAGCAAACTCAATGAGGCCGGGTATGGGAACCACACTATCGGTCGTGCCGCAGACGCCTACTGGGTCGACGACAGCTTGCAGATCTCGGCACGCGAGCAGGTCGATTTCCTGCAACGTCTCGCGCGAGGGACGTTACCGTTCTCTGCACGCTCGCAAGACATCGTGCGTCAGATTTCGATTGTCGAGGCCAATCCTGATTACGTGTTGCATGGCAAGACGGGCTGGTTCGTCGACAAGAAGCCGGACATCGGCTGGTGGGTGGGCTGGATTGAGCGCGACGGCAACATCACGAGCGTAGCGTTGAACATCGATCTGAAGGACGATGCCGATGCGCCCAAGCGCGCCCGTATCGTTCGTGCCGTGCTCAGTAGTTTGCAGTTGATCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42785","NCBI_taxonomy_name":"Pandoraea apista","NCBI_taxonomy_id":"93218"}}}},"ARO_accession":"3008674","ARO_id":"47466","ARO_name":"OXA-1264","CARD_short_name":"OXA-1264","ARO_description":"OXA-62 family carbapenem-hydrolyzing class D beta-lactamase OXA-1264.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46520":{"category_aro_accession":"3007731","category_aro_cvterm_id":"46520","category_aro_name":"OXA-62-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-62.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8093":{"model_id":"8093","model_name":"OXA-1265","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10920":{"protein_sequence":{"accession":"XGJ10591.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDKKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"PQ196145.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATAAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTGTTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008675","ARO_id":"47467","ARO_name":"OXA-1265","CARD_short_name":"OXA-1265","ARO_description":"OXA-51 family carbapenem-hydrolyzing class D beta-lactamase OXA-1265.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8094":{"model_id":"8094","model_name":"OXA-1266","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10921":{"protein_sequence":{"accession":"XGJ10592.1","sequence":"MTKKALFFAIGTMFLSACSFNTVEQHQIQSISTNKNSKKIKSLFDQAQTEGVLVIKRGQIEEIYGNDLKRASTEYVPASTFKMLNALIGLEHHKATPTEVFKWDGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMSKEVKRIGFGNADIGSKVHDFWLVGPLKITPQQEAQFAYELAHKTLPFSKNVQEQVQSMLFIEEKNGRKIYAKSGWGWDVDPQVGWFTGWVVQSQGEIIAFSLNLEMKKGIPSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"PQ196146.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGACTAAAAAAGCTCTTTTCTTTGCCATTGGTACGATGTTTTTATCGGCATGTTCTTTTAATACGGTAGAACAGCATCAAATACAGTCAATTTCTACCAATAAAAACTCAAAGAAAATTAAATCATTGTTTGATCAAGCACAAACTGAAGGTGTTTTAGTTATAAAACGTGGGCAAATAGAGGAAATCTATGGCAATGATCTTAAAAGAGCATCAACCGAATATGTTCCCGCCTCTACCTTTAAGATGTTAAATGCTTTGATTGGACTTGAGCATCATAAAGCAACACCAACTGAAGTGTTTAAATGGGATGGGCAAAAGCGTTTATTTCCCGATTGGGAAAAAGACATGACATTAGGCGATGCGATGAAAGCTTCTGCTATTCCAGTTTATCAGGAACTAGCTCGACGAATTGGCCTTGATCTTATGTCTAAAGAGGTAAAACGCATTGGTTTCGGTAATGCTGATATTGGTTCAAAAGTACATGATTTTTGGCTTGTTGGTCCACTTAAAATTACACCTCAACAAGAAGCCCAGTTTGCTTATGAACTAGCCCATAAAACTCTTCCTTTTAGCAAAAATGTGCAAGAACAAGTTCAATCTATGCTGTTCATAGAAGAAAAAAATGGACGAAAAATTTATGCCAAAAGTGGTTGGGGATGGGATGTTGACCCACAAGTTGGTTGGTTTACAGGCTGGGTCGTTCAATCTCAGGGAGAAATTATAGCTTTCTCACTTAATTTAGAAATGAAGAAAGGCATACCTAGCTCTATTCGAAAAGAAATTGCTTATAAAGGATTGGAACAACTCGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3008676","ARO_id":"47468","ARO_name":"OXA-1266","CARD_short_name":"OXA-1266","ARO_description":"OXA-213 family carbapenem-hydrolyzing class D beta-lactamase OXA-1266.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46495":{"category_aro_accession":"3007706","category_aro_cvterm_id":"46495","category_aro_name":"OXA-213-like beta-lactamase","category_aro_description":"OXA-213-like enzymes have been identified to be intrinsic to A. calcoaceticus and have been subsequently detected in A. pittii. Phylogenetic analysis of OXA-213-like proteins identified two distinct subgroups within the OXA family. The first group was linked to A. pittii and the second group to A. calcoaceticus. The carbapenemase activity of these OXAs may be related to the species-dependent effect.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8095":{"model_id":"8095","model_name":"OXA-1267","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10922":{"protein_sequence":{"accession":"XGB73484.1","sequence":"MHPLLFSALLLLSGHTQASEWNDSQAVDKLFGAAGVKGTFVLYDVQRQCYVGHDRERAETRFVPASTYKVANSLIGLSTGAVRSADEVLPYGGKPQRFKAWEHDMSLREAIKASNVPVYQELARRIGLERMRANVSRLGYGNAEIGQVVDNFWLVGPLKISAMEQTRFLLRLAQGELPFPAPVQSTVRAMTLLESGPGWELHGKTGWCFDCTPELGWWVGWVKRNERLYGFALNIDMPGGEADIGKRVELGKASLKALGILP"},"dna_sequence":{"accession":"PQ203856.1","fmin":"0","fmax":"789","strand":"+","sequence":"ATGCACCCTCTCCTCTTCAGTGCCCTTCTCCTGCTTTCCGGGCATACCCAGGCCAGCGAATGGAACGACAGCCAGGCCGTGGACAAGCTATTCGGCGCGGCCGGGGTGAAAGGCACCTTCGTCCTCTACGATGTGCAGCGGCAGTGCTATGTCGGCCATGACCGGGAGCGCGCGGAAACCCGCTTCGTTCCCGCTTCCACCTACAAGGTGGCGAACAGCCTGATCGGCTTATCCACAGGGGCGGTTAGATCCGCCGACGAGGTTCTTCCCTATGGCGGCAAGCCCCAGCGCTTCAAGGCCTGGGAGCACGACATGAGCCTGCGCGAGGCGATCAAGGCATCGAACGTACCGGTCTACCAGGAACTGGCGCGGCGCATCGGCCTGGAGCGGATGCGCGCCAATGTCTCGCGCCTGGGTTACGGCAACGCGGAAATCGGCCAGGTTGTGGATAACTTCTGGTTGGTGGGACCGCTGAAGATCAGCGCGATGGAACAGACCCGCTTTCTGCTCCGACTGGCGCAGGGAGAATTGCCATTCCCCGCCCCGGTGCAGTCCACCGTGCGCGCCATGACCCTGCTGGAAAGCGGCCCGGGCTGGGAGCTGCACGGCAAGACCGGCTGGTGCTTCGACTGCACGCCGGAACTCGGCTGGTGGGTGGGCTGGGTGAAGCGCAACGAGCGGCTCTACGGCTTCGCCCTGAACATCGACATGCCCGGCGGCGAGGCCGACATCGGCAAGCGCGTCGAACTGGGCAAGGCCAGTCTCAAGGCTCTCGGGATACTGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008677","ARO_id":"47469","ARO_name":"OXA-1267","CARD_short_name":"OXA-1267","ARO_description":"OXA-50 family oxacillin-hydrolyzing class D beta-lactamase OXA-1267.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46513":{"category_aro_accession":"3007724","category_aro_cvterm_id":"46513","category_aro_name":"OXA-50-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-50.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8096":{"model_id":"8096","model_name":"OXA-1268","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10923":{"protein_sequence":{"accession":"XGB73485.1","sequence":"MRPLLFSALLLLSGHAQASEWNDSQAVDKLFGAAGVKGTFVLYDVQRQRYVGHDRERAETRFVPASTYKVANSLIGLSTGAVRSADEVLPYGGKPQRFKAWEHDMSLRDAIEASNVPVYQELARRIGLERMRANVSRLGYGNAEIGQVVDNFWLVGPLKISAMEQTRFLLRLAQGELPFPAPVQSTVRAMTLLESGQGWELHGKTGWCFDCTPELGWWVGWVKRNERLYGFALNIDMPGGEADIGKRVELGKASLKALGILP"},"dna_sequence":{"accession":"PQ203857.1","fmin":"0","fmax":"789","strand":"+","sequence":"ATGCGCCCTCTCCTCTTCAGCGCCCTTCTCCTGCTCTCCGGGCATGCCCAGGCCAGCGAATGGAACGACAGCCAGGCCGTGGACAAGCTATTCGGCGCGGCCGGGGTGAAAGGCACCTTCGTCCTCTACGATGTGCAGCGGCAGCGCTATGTCGGCCATGACCGGGAGCGCGCGGAAACTCGCTTCGTTCCTGCCTCCACCTACAAGGTGGCGAACAGCCTGATTGGCTTATCCACAGGGGCGGTTAGATCCGCCGACGAGGTTCTTCCCTATGGCGGCAAGCCCCAGCGCTTCAAGGCCTGGGAGCACGACATGAGCCTGCGCGATGCGATCGAGGCATCGAACGTACCGGTCTACCAGGAACTGGCGCGGCGCATCGGCCTGGAGCGGATGCGCGCCAATGTCTCGCGCCTGGGTTACGGCAACGCGGAAATCGGCCAGGTTGTGGATAACTTCTGGTTGGTGGGACCGCTGAAGATCAGCGCGATGGAACAGACCCGCTTTCTGCTCCGACTGGCGCAGGGAGAATTGCCATTCCCCGCCCCGGTGCAGTCCACCGTGCGCGCCATGACCCTGCTGGAAAGCGGCCAGGGCTGGGAGCTGCACGGCAAGACCGGCTGGTGCTTCGACTGCACGCCGGAACTCGGCTGGTGGGTGGGCTGGGTGAAGCGCAACGAGCGGCTCTACGGCTTCGCCCTGAACATCGACATGCCCGGCGGCGAGGCCGACATCGGCAAGCGCGTCGAACTGGGCAAGGCCAGTCTCAAGGCTCTCGGGATACTGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008678","ARO_id":"47470","ARO_name":"OXA-1268","CARD_short_name":"OXA-1268","ARO_description":"OXA-50 family oxacillin-hydrolyzing class D beta-lactamase OXA-1268.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46513":{"category_aro_accession":"3007724","category_aro_cvterm_id":"46513","category_aro_name":"OXA-50-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-50.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8097":{"model_id":"8097","model_name":"OXA-1269","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10924":{"protein_sequence":{"accession":"XGB73486.1","sequence":"MRPLLFCALLLLSGHTQASEWNDSQAVDKLFGAAGVKGTFVLYDVQRQCYVGHDRERAETRFVPASTYKVANSLIGLSTGAVRSADEVLPYGGKPQRFKAWEHDMSLREAIKASNVPVYQELARRIGLERMRANVSRLGYGNAEIGQVVDNFWLVGPLKISAMEQTRFLIRLAQGELPFPAPVQSTVRAMTLLESGPGWELHGKTGWCFDCTPELGWWVGWVKRNERLYGFALNIDMPGGEADIGKRVELGKASLKALGILP"},"dna_sequence":{"accession":"PQ203858.1","fmin":"0","fmax":"789","strand":"+","sequence":"ATGCGCCCTCTCCTCTTCTGTGCCCTTCTCCTGCTTTCCGGGCATACCCAGGCCAGCGAATGGAACGACAGCCAGGCCGTGGACAAGCTATTCGGCGCGGCCGGGGTGAAAGGCACCTTCGTCCTCTACGATGTGCAGCGGCAGTGCTATGTCGGCCATGACCGGGAGCGCGCGGAAACCCGCTTCGTTCCCGCTTCCACCTACAAGGTGGCGAACAGCCTGATCGGCTTATCCACAGGGGCGGTTAGATCCGCCGACGAGGTTCTTCCCTATGGCGGCAAGCCCCAGCGCTTCAAGGCCTGGGAGCACGACATGAGCCTGCGCGAGGCGATCAAGGCATCGAACGTACCGGTCTACCAGGAACTGGCGCGGCGCATCGGCCTGGAGCGGATGCGCGCCAATGTCTCGCGCCTGGGTTACGGCAACGCGGAAATCGGCCAGGTTGTGGATAACTTCTGGTTGGTGGGACCGCTGAAGATCAGCGCGATGGAACAGACCCGCTTTCTGATCCGACTGGCGCAGGGAGAATTGCCATTCCCCGCCCCGGTGCAGTCCACCGTGCGCGCCATGACCCTGCTGGAAAGCGGCCCGGGCTGGGAGCTGCACGGCAAGACCGGCTGGTGCTTCGACTGCACGCCGGAGCTCGGCTGGTGGGTGGGCTGGGTGAAGCGCAACGAGCGGCTCTACGGCTTCGCCCTGAACATCGACATGCCCGGCGGCGAGGCCGACATCGGCAAGCGCGTCGAACTGGGCAAGGCCAGTCTCAAGGCTCTCGGGATACTGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008679","ARO_id":"47471","ARO_name":"OXA-1269","CARD_short_name":"OXA-1269","ARO_description":"OXA-50 family oxacillin-hydrolyzing class D beta-lactamase OXA-1269.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46513":{"category_aro_accession":"3007724","category_aro_cvterm_id":"46513","category_aro_name":"OXA-50-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-50.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8098":{"model_id":"8098","model_name":"OXA-1270","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10925":{"protein_sequence":{"accession":"XGB73487.1","sequence":"MRPLLFSALLLLSGHAQASEWNDTQAVNKLFGAAGVKGTFVLYDVQRQRYVGHDRERAETRFVPASTYKVANSLIGLSTGAVKSADEVLPYGGKPQRFKAWEHDMSLRDAIKASNVPVYQELARRIGLERMRANVSRLGYGNAEIGQVVDNFWLVGPLKISAMEQTRFLLRLAQGELPFPAPVQSTVRAMTLLESGPGWELHGKTGWCFDCTPELGWWVGWVKRNERLYGFALNIDMPGGEADIGKRVELGKASLKALGILP"},"dna_sequence":{"accession":"PQ203859.1","fmin":"0","fmax":"789","strand":"+","sequence":"ATGCGCCCTCTCCTCTTCAGCGCCCTTCTCCTGCTCTCCGGGCATGCCCAGGCCAGCGAATGGAACGACACCCAGGCCGTGAACAAGCTATTCGGCGCGGCCGGGGTGAAAGGCACCTTCGTCCTCTACGATGTGCAGCGGCAGCGCTATGTCGGCCATGACCGGGAGCGCGCGGAAACTCGCTTCGTTCCTGCCTCCACCTACAAGGTGGCGAACAGCCTGATTGGCTTATCCACAGGGGCGGTTAAATCCGCCGACGAGGTTCTTCCCTATGGCGGCAAGCCCCAGCGCTTCAAGGCCTGGGAGCACGACATGAGCCTGCGCGACGCGATCAAGGCATCGAACGTACCGGTCTACCAGGAACTGGCGCGACGCATCGGCCTGGAGCGGATGCGCGCCAATGTCTCGCGCCTGGGTTACGGCAACGCGGAAATCGGCCAGGTTGTGGATAACTTCTGGTTGGTGGGACCGCTGAAGATCAGCGCGATGGAACAGACCCGCTTTCTGCTCCGACTGGCGCAGGGAGAATTGCCATTCCCCGCCCCGGTGCAGTCCACCGTGCGCGCCATGACCCTGCTGGAAAGCGGCCCGGGCTGGGAGCTGCACGGCAAGACCGGCTGGTGCTTCGACTGCACGCCGGAACTCGGCTGGTGGGTGGGCTGGGTGAAGCGCAACGAGCGGCTCTACGGCTTCGCCCTGAACATCGACATGCCCGGCGGCGAGGCCGACATCGGCAAGCGCGTCGAACTGGGCAAGGCCAGTCTCAAGGCTCTCGGGATACTGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008680","ARO_id":"47472","ARO_name":"OXA-1270","CARD_short_name":"OXA-1270","ARO_description":"OXA-50 family oxacillin-hydrolyzing class D beta-lactamase OXA-1270.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46513":{"category_aro_accession":"3007724","category_aro_cvterm_id":"46513","category_aro_name":"OXA-50-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-50.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8099":{"model_id":"8099","model_name":"OXA-1271","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10926":{"protein_sequence":{"accession":"XGB73488.1","sequence":"MRPLLFSALLLLSGHTQASEWNDSQAVDKLFGAAGVKGTFVLYDVQRQRYVGHDRERAETRFVPASTYKVANSLIGLSTGAVRSADEVLPYGGKPQRFKAWEHDMSLRDAIKASNVPVYQELARRIGLERMRANVSRLGYGNAEIGQVVDNFWLVGPLKISAMEQTRFLIRLAQGELPFPAPVQSTVSAMTLLESGPGWELHGKTGWCFDCTPELGWWVGWVKRNERLYGFALNIDMPGGEADIGKRVELGKASLKALGILP"},"dna_sequence":{"accession":"PQ203860.1","fmin":"0","fmax":"789","strand":"+","sequence":"ATGCGCCCCCTCCTCTTCAGTGCCCTTCTCCTGCTTTCCGGGCATACCCAGGCCAGCGAATGGAACGACAGCCAGGCCGTGGACAAGCTATTCGGCGCGGCCGGGGTGAAAGGCACCTTCGTCCTCTACGATGTGCAGCGGCAGCGCTATGTCGGCCATGACCGGGAGCGCGCGGAAACCCGCTTCGTTCCCGCTTCCACCTACAAGGTGGCGAACAGCCTGATCGGCTTATCCACAGGGGCGGTTAGATCCGCCGACGAGGTTCTTCCCTATGGCGGCAAGCCCCAGCGCTTCAAGGCCTGGGAGCACGACATGAGCCTGCGCGACGCGATTAAGGCATCGAACGTACCGGTCTACCAGGAACTGGCGCGGCGCATCGGCCTGGAGCGGATGCGCGCCAATGTCTCGCGCCTGGGTTACGGCAACGCGGAAATCGGCCAGGTTGTGGATAACTTCTGGTTGGTGGGACCGCTGAAGATCAGCGCGATGGAACAGACCCGCTTTCTGATCCGACTGGCGCAGGGAGAATTGCCATTCCCCGCCCCGGTGCAGTCCACCGTGAGCGCCATGACCCTGCTGGAAAGCGGCCCGGGCTGGGAGCTGCACGGCAAGACCGGCTGGTGCTTCGACTGCACGCCGGAGCTCGGCTGGTGGGTGGGCTGGGTGAAGCGCAACGAGCGGCTCTACGGCTTCGCCCTGAACATCGACATGCCCGGCGGCGAGGCCGACATCGGCAAGCGCGTCGAACTGGGCAAGGCCAGTCTCAAGGCTCTCGGGATACTGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008681","ARO_id":"47473","ARO_name":"OXA-1271","CARD_short_name":"OXA-1271","ARO_description":"OXA-50 family oxacillin-hydrolyzing class D beta-lactamase OXA-1271.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46513":{"category_aro_accession":"3007724","category_aro_cvterm_id":"46513","category_aro_name":"OXA-50-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-50.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8100":{"model_id":"8100","model_name":"OXA-1272","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10927":{"protein_sequence":{"accession":"XGB73489.1","sequence":"MRPLLFSALLLLSGHAQASEWNDSQAVDKLFGAAGVKGTFVLYDVQRQRYVGHDRERAETRFVPASTYKVANSLIGLSTGAVKSADEVLPYGGKPQRFKAWEHDMSLRDAIEASNVPVYQELARRIGLERMRANVSRLGYGNAEIGQAVGNFWLVGPLKISAMEQTRFLLRLAQGELPFPAPVQSTVRAMTLLESGPGWELHGKTGWCFDCTPELGWWVGWVKRNERLYGFALNIDMPGGEADIGKRVELGKASLKALGILP"},"dna_sequence":{"accession":"PQ203861.1","fmin":"0","fmax":"789","strand":"+","sequence":"ATGCGCCCTCTCCTCTTCAGCGCCCTTCTCCTGCTCTCCGGGCATGCCCAGGCCAGCGAATGGAACGACAGCCAGGCCGTGGACAAGCTATTCGGCGCGGCCGGGGTGAAAGGCACCTTCGTCCTCTACGATGTGCAGCGGCAGCGCTATGTCGGCCACGACCGGGAGCGCGCGGAAACTCGCTTCGTTCCTGCCTCCACCTACAAGGTGGCGAACAGCCTGATTGGCTTATCCACAGGGGCGGTTAAATCCGCCGACGAGGTTCTTCCCTATGGCGGCAAGCCCCAGCGCTTCAAGGCCTGGGAGCACGACATGAGCCTGCGCGATGCGATCGAGGCATCGAACGTACCGGTCTACCAGGAACTGGCGCGGCGCATCGGCCTGGAGCGGATGCGCGCCAATGTCTCGCGCCTGGGTTACGGCAACGCGGAAATCGGCCAGGCTGTGGGTAACTTCTGGTTGGTGGGACCGCTGAAGATCAGCGCGATGGAACAGACCCGCTTTCTGCTCCGACTGGCCCAGGGAGAATTGCCATTCCCCGCCCCGGTGCAGTCCACCGTGCGCGCCATGACCCTGCTGGAAAGCGGCCCGGGCTGGGAGCTGCACGGCAAGACCGGCTGGTGCTTCGACTGCACGCCGGAACTCGGCTGGTGGGTGGGCTGGGTGAAGCGCAACGAGCGGCTCTACGGCTTCGCCCTGAACATCGACATGCCCGGCGGCGAGGCCGACATCGGCAAGCGCGTCGAACTGGGCAAGGCCAGTCTCAAGGCTCTCGGGATACTGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008682","ARO_id":"47474","ARO_name":"OXA-1272","CARD_short_name":"OXA-1272","ARO_description":"OXA-50 family oxacillin-hydrolyzing class D beta-lactamase OXA-1272.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46513":{"category_aro_accession":"3007724","category_aro_cvterm_id":"46513","category_aro_name":"OXA-50-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-50.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8101":{"model_id":"8101","model_name":"OXA-1273","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10928":{"protein_sequence":{"accession":"XGB73490.1","sequence":"MRPLLFSALLLLSGHAQASEWNDSQAVDKLFGAAGVKGTFVLYDVQRQRYVGHDRQRAETRFVPASTYKVANSLIGLSTGAVKSADEVLPYGGKPQRFKAWEHDMSLRDAIEASNVPVYQELARRIGLERMRANVSRLGYGNAEIGQVVDNFWLVGPLKISAMEQTRFLLRLAQGELPFPAPVQSTVRTMTLLESGPGWELHGKTGWCFDCTPELGWWVGWVKRNERLYGFALNIDMPGGEADIGKRVELGKASLKALGILP"},"dna_sequence":{"accession":"PQ203862.1","fmin":"0","fmax":"789","strand":"+","sequence":"ATGCGCCCTCTCCTCTTCAGCGCCCTTCTCCTGCTCTCCGGGCATGCTCAGGCCAGCGAATGGAACGACAGCCAGGCCGTGGACAAGCTATTCGGCGCGGCCGGGGTGAAAGGCACCTTCGTCCTTTACGATGTGCAGCGGCAGCGCTATGTCGGCCATGACCGGCAGCGCGCGGAAACCCGCTTCGTTCCCGCTTCCACCTACAAGGTGGCGAACAGCCTGATCGGCTTATCCACAGGGGCGGTTAAATCCGCCGACGAGGTTCTTCCCTATGGCGGCAAGCCCCAGCGCTTCAAGGCCTGGGAGCACGACATGAGCCTGCGCGACGCGATCGAGGCATCGAACGTACCGGTCTACCAGGAACTGGCGCGGCGCATCGGCCTGGAGCGGATGCGCGCCAATGTCTCGCGCCTGGGTTACGGCAACGCGGAAATCGGCCAGGTTGTGGATAACTTCTGGTTGGTGGGACCGCTGAAGATCAGCGCGATGGAACAGACCCGCTTTCTGCTCCGACTGGCGCAGGGAGAATTGCCATTCCCCGCCCCGGTGCAGTCCACCGTGCGCACCATGACCCTGCTGGAAAGCGGCCCGGGCTGGGAGCTGCACGGCAAGACCGGCTGGTGCTTCGACTGCACACCGGAACTCGGCTGGTGGGTGGGCTGGGTGAAGCGCAACGAGCGGCTCTACGGCTTCGCCCTGAACATCGACATGCCCGGCGGCGAGGCCGACATCGGCAAGCGCGTCGAACTGGGCAAGGCCAGTCTCAAGGCTCTCGGGATACTGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008683","ARO_id":"47475","ARO_name":"OXA-1273","CARD_short_name":"OXA-1273","ARO_description":"OXA-50 family oxacillin-hydrolyzing class D beta-lactamase OXA-1273.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46513":{"category_aro_accession":"3007724","category_aro_cvterm_id":"46513","category_aro_name":"OXA-50-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-50.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8102":{"model_id":"8102","model_name":"OXA-1274","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10929":{"protein_sequence":{"accession":"XGB73491.1","sequence":"MRPLLFSALLLLSGHAQASEWNDSQAVDKLFGAAGVKGTFVLYDVQRQRYVGHDRERAETRFVPASTYKVANSLIGLSTGAVRSADEVLPYGGKPQRFKAWEHDMSLRDAIKASNVPVYQELARRIGLERMRANVSHLGYGNAEIGQVVDNFWLVGPLKISAMEQTRFLLRLAQGELPFPAPVQSTVRAMTLLESGQGWELHGKTGWCFDCTPELGWWVGWVKRNERLYGFALNIDMPGGEADIGKRVELGKASLKALGILP"},"dna_sequence":{"accession":"PQ203863.1","fmin":"0","fmax":"789","strand":"+","sequence":"ATGCGCCCTCTCCTCTTCAGCGCCCTTCTCCTGCTCTCCGGGCATGCCCAGGCCAGCGAATGGAACGACAGCCAGGCCGTGGACAAGCTATTCGGCGCGGCCGGTGTGAAAGGCACCTTCGTCCTTTACGATGTGCAGCGGCAGCGCTATGTCGGCCATGACCGGGAGCGCGCGGAAACCCGCTTCGTTCCCGCTTCCACCTACAAGGTGGCGAACAGCCTGATCGGCTTATCCACAGGGGCGGTTAGATCCGCCGACGAGGTTCTTCCCTATGGCGGCAAGCCCCAGCGCTTCAAGGCCTGGGAGCACGACATGAGCCTGCGCGACGCGATCAAGGCATCGAACGTACCGGTCTACCAGGAACTGGCGCGGCGCATCGGCCTGGAGCGGATGCGCGCCAATGTCTCGCACCTGGGTTATGGCAACGCGGAAATCGGCCAGGTTGTGGATAACTTCTGGTTGGTGGGACCGCTGAAGATCAGCGCGATGGAACAGACCCGCTTTCTGCTCCGACTGGCGCAGGGAGAATTGCCATTCCCCGCCCCGGTGCAGTCCACCGTGCGCGCCATGACCCTGCTGGAAAGCGGCCAGGGCTGGGAGCTGCACGGCAAGACCGGCTGGTGCTTCGACTGCACGCCGGAACTCGGCTGGTGGGTGGGCTGGGTGAAGCGCAACGAGCGGCTCTACGGCTTCGCCCTGAACATCGACATGCCCGGCGGCGAGGCCGACATCGGCAAGCGCGTCGAACTGGGCAAGGCCAGTCTCAAGGCTCTCGGGATACTGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008684","ARO_id":"47476","ARO_name":"OXA-1274","CARD_short_name":"OXA-1274","ARO_description":"OXA-50 family oxacillin-hydrolyzing class D beta-lactamase OXA-1274.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46513":{"category_aro_accession":"3007724","category_aro_cvterm_id":"46513","category_aro_name":"OXA-50-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-50.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8103":{"model_id":"8103","model_name":"OXA-1275","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10930":{"protein_sequence":{"accession":"XGB73492.1","sequence":"MRLLFFSALLLLFGQAQASEWNDSQAVDKLFEAAGMKGTFVLYDVQRQGYVGHDRARAQTRFVPASTYKVAHSLIGLSTGAVKSADEVLPYGGKPQRFKAWEHDMSLREAIRASNVPVYQELARRIGLQRMRANLARMDYGNGEVGQVVDNFWLVGPLEISALEQTRFLARLAQGELPFPEPVQATVRDMTLMEHGPDWELHGKTGWCFDCTPELGWWVGWVKRDERLYTFALNIDMPGGEADIGKRVELGKAALKALGVLP"},"dna_sequence":{"accession":"PQ203864.1","fmin":"0","fmax":"789","strand":"+","sequence":"ATGCGCCTTCTCTTCTTCAGCGCCCTTCTCCTGCTCTTCGGACAGGCCCAGGCCAGCGAATGGAACGACAGCCAGGCTGTGGACAAGCTATTCGAAGCCGCCGGGATGAAAGGCACCTTCGTTCTCTACGACGTGCAGCGGCAGGGTTATGTCGGCCACGACCGAGCACGCGCGCAGACCCGCTTCGTCCCTGCCTCCACCTATAAGGTGGCGCACAGCCTGATCGGTTTATCCACAGGCGCGGTGAAGTCCGCCGACGAGGTCCTGCCCTATGGCGGCAAGCCCCAGCGCTTCAAGGCCTGGGAGCATGACATGAGCCTGCGCGAGGCGATCCGTGCATCCAACGTGCCGGTCTACCAGGAACTGGCGCGGCGCATCGGCCTGCAGCGTATGCGCGCCAACCTCGCCCGCATGGACTATGGAAATGGCGAGGTCGGGCAGGTTGTGGACAACTTCTGGCTGGTGGGGCCACTGGAGATCAGCGCGCTGGAGCAGACCCGTTTCCTCGCCCGGCTGGCACAGGGAGAACTGCCGTTTCCCGAGCCGGTGCAGGCCACCGTGCGCGACATGACCCTGATGGAACACGGCCCGGACTGGGAGCTGCACGGCAAGACCGGCTGGTGTTTCGATTGCACGCCGGAACTCGGCTGGTGGGTCGGCTGGGTGAAGCGCGACGAGCGCCTCTACACCTTCGCCCTGAACATCGACATGCCCGGCGGCGAGGCCGACATCGGCAAGCGCGTCGAACTGGGCAAGGCCGCTCTCAAGGCCCTGGGCGTGCTGCCCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008685","ARO_id":"47477","ARO_name":"OXA-1275","CARD_short_name":"OXA-1275","ARO_description":"OXA-50-var family class D beta-lactamase OXA-1275.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46513":{"category_aro_accession":"3007724","category_aro_cvterm_id":"46513","category_aro_name":"OXA-50-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-50.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8104":{"model_id":"8104","model_name":"OXA-1276","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10931":{"protein_sequence":{"accession":"XGB73493.1","sequence":"MRPLLFSALLLLSGHTQASEWNDSQAVDKLFGAAGVKGTFVLYDVQRQRYVGHDRERAETRFVPASTYKVANSLIGLSTGAVKSADEVLPYGGKPQRFKAWEHDMSLRDAIKASNVPVYQELARRIGLERMRANVSRLGYGNAEIGQVVDNFWLVGPLKISAMEQTRFLLRLAQGELPFPAPVQSTVRAMTLLESGPGWELHGKTGWCFDCTPELGWWVGWVKRNERLYGFALNIDMPGGEADIGKRVELGKASLKALGILP"},"dna_sequence":{"accession":"PQ203865.1","fmin":"0","fmax":"789","strand":"+","sequence":"ATGCGCCCCCTCCTCTTCAGTGCCCTTCTCCTGCTTTCCGGGCATACCCAGGCCAGCGAATGGAACGACAGCCAGGCCGTGGACAAGCTATTCGGCGCGGCCGGGGTGAAAGGCACCTTCGTCCTCTACGATGTGCAGCGGCAGCGCTATGTCGGCCATGACCGGGAGCGCGCGGAAACTCGCTTCGTTCCTGCCTCCACCTACAAGGTGGCGAACAGCCTGATCGGCTTATCCACAGGGGCGGTTAAATCCGCCGACGAGGTTCTTCCCTATGGCGGCAAGCCCCAGCGCTTCAAGGCCTGGGAGCACGACATGAGCCTGCGCGACGCGATCAAGGCATCGAACGTACCGGTCTACCAGGAACTGGCGCGACGCATCGGCCTGGAGCGGATGCGCGCCAATGTCTCGCGCCTGGGTTACGGCAACGCGGAAATCGGCCAGGTTGTGGATAACTTCTGGTTGGTGGGACCGCTGAAGATCAGCGCGATGGAACAGACCCGCTTTCTGCTCCGACTGGCGCAGGGAGAATTGCCATTCCCCGCCCCGGTGCAGTCCACCGTGCGCGCCATGACCCTGCTGGAAAGCGGCCCGGGCTGGGAGCTGCACGGCAAGACCGGCTGGTGCTTCGACTGCACGCCGGAACTCGGCTGGTGGGTGGGCTGGGTGAAGCGCAACGAGCGGCTCTACGGCTTCGCCCTGAACATCGACATGCCCGGCGGCGAGGCCGACATCGGCAAGCGCGTCGAACTGGGCAAGGCCAGTCTCAAGGCTCTCGGGATACTGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008686","ARO_id":"47478","ARO_name":"OXA-1276","CARD_short_name":"OXA-1276","ARO_description":"OXA-50 family oxacillin-hydrolyzing class D beta-lactamase OXA-1276.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46513":{"category_aro_accession":"3007724","category_aro_cvterm_id":"46513","category_aro_name":"OXA-50-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-50.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8105":{"model_id":"8105","model_name":"OXA-1277","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10932":{"protein_sequence":{"accession":"XGB73494.1","sequence":"MRPLLFSALLLLSGHAQASEWNDSRAVDKLFGAAGVKGTFVLYDVQRQRYVGHDRERAETRFVPASTYKVANSLIGLSTGAVRSADEVLPYGGKPQRFKAWEHDMSLRDAIKASNVPVYQELARRIGLERMRANVSRLGYGNAEIGQVVDNFWLVGPLKISAMEQTRFLLRLAQGELPFPAPVQSTVRAMTLLESGPGWELHGKTGWCFDCTPELGWWVGWVKRNERLYGFALNIDMPGGEADIGKRVELGKASLKALRILP"},"dna_sequence":{"accession":"PQ203866.1","fmin":"0","fmax":"789","strand":"+","sequence":"ATGCGCCCTCTCCTCTTCAGCGCCCTTCTCCTGCTCTCCGGGCATGCCCAGGCCAGCGAATGGAACGACAGCCGGGCCGTGGACAAGCTATTCGGAGCGGCCGGTGTGAAAGGCACCTTCGTCCTTTACGATGTGCAGCGGCAGCGCTATGTCGGCCATGACCGGGAGCGCGCGGAAACCCGCTTCGTTCCCGCTTCCACCTACAAGGTGGCGAACAGCCTTATCGGCTTATCCACAGGGGCGGTTAGATCCGCCGACGAGGTTCTTCCCTATGGCGGCAAACCCCAGCGCTTCAAGGCCTGGGAGCACGACATGAGCCTGCGCGACGCGATCAAGGCATCGAACGTACCGGTCTACCAGGAACTGGCGCGGCGCATCGGCCTGGAGCGGATGCGCGCCAATGTCTCGCGCCTGGGTTACGGCAACGCGGAAATCGGCCAGGTTGTGGATAACTTCTGGTTGGTGGGACCGCTGAAGATCAGCGCGATGGAGCAGACCCGCTTTCTGCTCCGACTGGCGCAGGGAGAATTGCCATTCCCCGCCCCGGTGCAGTCCACCGTGCGCGCCATGACCCTGCTGGAAAGCGGCCCGGGCTGGGAGCTGCACGGCAAGACCGGCTGGTGCTTCGACTGCACGCCGGAACTCGGCTGGTGGGTGGGCTGGGTGAAGCGCAACGAGCGGCTCTACGGCTTCGCCCTGAACATCGACATGCCCGGCGGCGAGGCCGACATCGGCAAGCGCGTCGAACTGGGCAAGGCCAGTCTCAAGGCTCTCAGGATACTGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008687","ARO_id":"47479","ARO_name":"OXA-1277","CARD_short_name":"OXA-1277","ARO_description":"OXA-50 family oxacillin-hydrolyzing class D beta-lactamase OXA-1277.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46513":{"category_aro_accession":"3007724","category_aro_cvterm_id":"46513","category_aro_name":"OXA-50-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-50.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8106":{"model_id":"8106","model_name":"OXA-1278","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10933":{"protein_sequence":{"accession":"XGB73495.1","sequence":"MRPLLFSALLLLSGHAQASEWNDSQAVDKLFGAAGVKGTFVLYDVQRQRYVGHDRERAETRFVPASTYKVANSLIGLSTGAVRSADEVLPYGGKPQRFKAWEHDMSLREAIKASNVPVYQELARRIGLERMRANVSRLGYGNAETGQVVDNFWLVGPLKISAMEQTRFLLRLAQGELPFPAPVQSTVRAMTLLESGPGWELHGKTGWCFDCTPELGWWVGWVKRNERLYGFALNIDMPGGEADIGKRVELGKASLKALGILP"},"dna_sequence":{"accession":"PQ203867.1","fmin":"0","fmax":"789","strand":"+","sequence":"ATGCGCCCTCTCCTCTTCAGCGCCCTTCTCCTGCTCTCCGGGCATGCCCAGGCCAGCGAATGGAACGACAGCCAGGCTGTGGACAAGCTATTCGGCGCGGCCGGGGTGAAAGGCACCTTCGTCCTCTACGATGTGCAGCGGCAGCGCTATGTCGGCCATGACCGGGAGCGCGCGGAAACTCGCTTCGTTCCCGCTTCCACCTACAAGGTGGCGAACAGCCTGATCGGCTTATCCACAGGGGCGGTTAGATCCGCCGACGAGGTTCTTCCCTATGGCGGCAAGCCCCAGCGCTTCAAGGCCTGGGAGCACGACATGAGCCTGCGCGAGGCGATCAAGGCATCGAACGTACCGGTCTACCAGGAACTGGCGCGGCGCATCGGCCTGGAGCGGATGCGCGCCAATGTCTCGCGCCTGGGTTACGGCAACGCGGAAACCGGCCAGGTTGTGGATAACTTCTGGTTGGTGGGACCGCTGAAGATCAGCGCGATGGAACAGACCCGCTTTCTGCTCCGACTGGCCCAGGGAGAATTGCCATTCCCCGCCCCGGTGCAGTCCACCGTGCGCGCCATGACCCTGCTGGAAAGCGGCCCGGGCTGGGAGCTGCACGGCAAGACCGGCTGGTGCTTCGACTGCACGCCGGAACTCGGCTGGTGGGTGGGCTGGGTGAAGCGCAACGAGCGGCTCTACGGCTTCGCCCTGAACATCGACATGCCCGGCGGCGAGGCCGACATCGGCAAGCGCGTCGAACTGGGCAAGGCCAGTCTCAAGGCTCTCGGGATACTGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008688","ARO_id":"47480","ARO_name":"OXA-1278","CARD_short_name":"OXA-1278","ARO_description":"OXA-50 family oxacillin-hydrolyzing class D beta-lactamase OXA-1278.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46513":{"category_aro_accession":"3007724","category_aro_cvterm_id":"46513","category_aro_name":"OXA-50-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-50.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8107":{"model_id":"8107","model_name":"OXA-1279","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10934":{"protein_sequence":{"accession":"XGB73496.1","sequence":"MRPLLFSALLLLSGHTQASEWNDSQAVDKLFGAAGVKGTFVLYDVQRQRYVGHDRERAETRFVPASTYKVANSLIGLSSGAVKSADEVLPYGGKPQRFKAWEHDMSLRDAIKASNVPVYQELARRIGLERMRANVSRLGYGNAEIGQVVDNFWLVGPLKISAMEQTRFLLRLAQGELPFPAPVQSTVRAMTLLESGPGWELHGKTGWCFDCTPELGWWVGWVKRNERLYGFALNIDMPGGEADIGKRVELGKASLKALGILP"},"dna_sequence":{"accession":"PQ203868.1","fmin":"0","fmax":"789","strand":"+","sequence":"ATGCGCCCTCTCCTCTTCAGTGCCCTTCTCCTGCTTTCCGGGCATACCCAGGCCAGCGAATGGAACGACAGCCAGGCCGTGGACAAGCTATTCGGCGCGGCCGGGGTGAAAGGCACCTTCGTCCTCTACGATGTGCAGCGGCAGCGCTATGTCGGCCATGACCGGGAGCGCGCGGAAACCCGCTTCGTTCCTGCCTCCACCTACAAGGTGGCGAACAGCCTGATCGGCTTATCCTCAGGGGCGGTTAAATCCGCCGACGAGGTTCTTCCCTATGGCGGCAAGCCCCAGCGCTTCAAGGCCTGGGAGCACGACATGAGCCTGCGCGACGCGATCAAGGCATCGAACGTACCGGTCTACCAGGAACTGGCGCGACGCATCGGCCTGGAGCGGATGCGCGCCAATGTCTCGCGCCTGGGTTACGGCAACGCGGAAATCGGCCAGGTTGTGGATAACTTCTGGTTGGTGGGACCGCTGAAGATCAGCGCGATGGAACAGACCCGCTTTCTGCTCCGACTGGCGCAGGGAGAATTGCCATTCCCCGCCCCGGTGCAGTCCACCGTGCGCGCCATGACCCTGCTGGAAAGCGGCCCGGGCTGGGAGCTGCACGGCAAGACCGGCTGGTGCTTCGACTGCACGCCGGAACTCGGCTGGTGGGTGGGCTGGGTGAAGCGCAACGAGCGGCTCTACGGCTTCGCCCTGAACATCGACATGCCCGGCGGCGAGGCCGACATCGGCAAGCGCGTCGAACTGGGCAAGGCCAGTCTCAAGGCTCTCGGGATACTGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008689","ARO_id":"47481","ARO_name":"OXA-1279","CARD_short_name":"OXA-1279","ARO_description":"OXA-50 family oxacillin-hydrolyzing class D beta-lactamase OXA-1279.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46513":{"category_aro_accession":"3007724","category_aro_cvterm_id":"46513","category_aro_name":"OXA-50-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-50.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8108":{"model_id":"8108","model_name":"OXA-1280","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10935":{"protein_sequence":{"accession":"XGB73497.1","sequence":"MRPLLFSALLLLSGHAQASEWNDSQAVDKLFGAAGVKGTFVLYDVQRQHYVGHDRERAETRFVPASTYKVANSLIGLSTGAVRSADEVLPYGGKPQRFKAWEHDMSLREAIKASNVPVYQELARRIGLERMRANVSRLGYGNAEIGQVVDNFWLVGPLKISAMEQTHFLLRLAQGELPFPAPVQSTVRAMTLLESGPGWELHGKTGWCFDCTPELGWWVGWVKRNERLYGFALNIDMPGGEADIGKRVELGKASLKALGILP"},"dna_sequence":{"accession":"PQ203869.1","fmin":"0","fmax":"789","strand":"+","sequence":"ATGCGCCCTCTCCTCTTCAGCGCCCTTCTCCTGCTCTCCGGGCATGCCCAGGCCAGCGAATGGAACGACAGCCAGGCCGTGGACAAGCTATTCGGCGCGGCCGGGGTGAAAGGCACCTTCGTCCTCTACGATGTGCAGCGGCAGCACTATGTCGGCCATGACCGGGAGCGCGCGGAAACTCGCTTCGTTCCTGCCTCCACCTACAAGGTGGCGAACAGCCTGATCGGCTTATCCACAGGGGCGGTTAGATCCGCCGACGAGGTTCTTCCCTATGGCGGCAAGCCCCAGCGCTTCAAGGCCTGGGAGCACGACATGAGCCTGCGCGAGGCGATCAAGGCATCGAACGTACCGGTCTACCAGGAACTGGCGCGGCGCATCGGCCTGGAGCGGATGCGCGCCAATGTCTCGCGCCTGGGTTACGGCAACGCGGAAATCGGCCAGGTTGTGGATAACTTCTGGTTGGTGGGACCGCTGAAGATCAGCGCGATGGAACAGACCCACTTTCTGCTCCGACTGGCGCAGGGAGAATTGCCATTCCCCGCCCCGGTGCAGTCCACCGTGCGCGCCATGACCCTGCTGGAAAGCGGCCCGGGCTGGGAGCTGCACGGCAAGACCGGCTGGTGCTTCGACTGCACGCCGGAACTCGGCTGGTGGGTGGGCTGGGTGAAGCGCAACGAGCGGCTCTACGGCTTCGCCCTGAACATCGACATGCCCGGCGGCGAGGCCGACATCGGCAAGCGCGTCGAACTGGGCAAGGCCAGTCTCAAGGCTCTCGGGATACTGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008690","ARO_id":"47482","ARO_name":"OXA-1280","CARD_short_name":"OXA-1280","ARO_description":"OXA-50 family oxacillin-hydrolyzing class D beta-lactamase OXA-1280.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46513":{"category_aro_accession":"3007724","category_aro_cvterm_id":"46513","category_aro_name":"OXA-50-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-50.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8109":{"model_id":"8109","model_name":"OXA-1281","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10936":{"protein_sequence":{"accession":"XGB73498.1","sequence":"MRPLLFSALLLLSGHTQASEWNDSQAVDKLFGAAGVKGTFVLYDVQRQRYVGHDRERAETRFVPASTYKVANSLIGLSTGAVRSADEVLPYGGKPQRFKAWEHDMSLREAIKASNVPVYQELARRIGLERMRANVSRLGYGNAEIGQVVDNFWLVGPLKISAMEQTRFLLRLAQGELPFPVPVQSTVRAMTLLESGPGWELHGKTGWCFDCTPELGWWVGWVKRNERLYGFALNIDMPGGEADIGKRVELGKASLKTLGILP"},"dna_sequence":{"accession":"PQ203870.1","fmin":"0","fmax":"789","strand":"+","sequence":"ATGCGCCCCCTCCTCTTCAGTGCCCTTCTCCTGCTTTCCGGGCATACCCAGGCCAGCGAATGGAACGACAGCCAGGCCGTGGACAAGCTATTCGGCGCGGCCGGGGTGAAAGGCACCTTCGTCCTCTACGATGTGCAGCGGCAGCGCTATGTCGGCCATGACCGGGAGCGCGCGGAAACCCGCTTCGTTCCCGCTTCCACCTACAAGGTGGCGAACAGCCTGATCGGCTTATCCACAGGGGCGGTTAGATCCGCCGACGAGGTTCTTCCCTATGGCGGCAAGCCCCAGCGCTTCAAGGCCTGGGAGCACGACATGAGCCTGCGCGAGGCGATCAAGGCATCGAACGTACCGGTCTACCAGGAACTGGCGCGGCGCATCGGCCTGGAGCGGATGCGCGCCAATGTCTCGCGCCTGGGTTACGGCAACGCGGAAATAGGCCAGGTTGTGGATAACTTCTGGTTGGTGGGACCGCTGAAGATCAGCGCGATGGAACAGACCCGCTTTCTGCTCCGACTGGCGCAGGGAGAATTGCCATTCCCCGTCCCGGTGCAGTCCACCGTGCGCGCCATGACCCTGCTGGAAAGCGGCCCGGGCTGGGAGCTGCACGGCAAGACCGGCTGGTGCTTCGACTGCACGCCGGAACTCGGCTGGTGGGTGGGCTGGGTGAAGCGCAACGAGCGGCTCTACGGCTTCGCCCTGAACATCGACATGCCCGGCGGCGAGGCCGATATCGGCAAGCGCGTCGAACTGGGCAAGGCCAGTCTCAAGACTCTCGGGATACTGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008691","ARO_id":"47483","ARO_name":"OXA-1281","CARD_short_name":"OXA-1281","ARO_description":"OXA-50 family oxacillin-hydrolyzing class D beta-lactamase OXA-1281.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46513":{"category_aro_accession":"3007724","category_aro_cvterm_id":"46513","category_aro_name":"OXA-50-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-50.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8110":{"model_id":"8110","model_name":"OXA-1282","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10937":{"protein_sequence":{"accession":"XGB73499.1","sequence":"MRPLLFSALLLLSGHTQASEWNDSQAVDKLFGAAGVKGTFVLYDVQRQRYVGHDRERAETRFVPASTYKVANSLIGLSTGAVRSADEVLPYGGKPQRFKAWEHDMSLRDAIKASNVPVYQELARRIGLERMRANVSRLGYGNAEIGQVVDNFWLVGPLKISAMEQTRFLLRLAQGELPLPAPVQSTVRAVTLLESGPGWELHGKTGWCFDCTPELGWWVGWVKRNERLYGFALNIDMPGGEADIGKRVELGKASLKALGILP"},"dna_sequence":{"accession":"PQ203871.1","fmin":"0","fmax":"789","strand":"+","sequence":"ATGCGCCCTCTCCTCTTCAGCGCCCTGCTCCTGCTCTCCGGGCATACCCAGGCCAGCGAATGGAACGACAGCCAGGCCGTGGACAAGCTATTCGGCGCGGCCGGGGTGAAAGGCACCTTCGTCCTCTACGATGTGCAGCGGCAGCGCTATGTCGGTCATGACCGGGAGCGCGCGGAAACCCGCTTCGTTCCCGCTTCCACCTACAAGGTGGCGAACAGCCTGATCGGCTTATCCACAGGGGCGGTTAGATCCGCCGACGAGGTTCTTCCCTATGGCGGCAAGCCCCAGCGCTTCAAGGCCTGGGAGCACGACATGAGCCTGCGCGACGCGATCAAGGCATCGAACGTACCGGTCTACCAGGAACTGGCGCGGCGCATCGGCCTGGAGCGGATGCGCGCCAATGTCTCCCGCCTGGGTTACGGCAACGCGGAAATCGGCCAGGTTGTGGATAACTTCTGGTTGGTGGGACCGCTGAAGATCAGCGCGATGGAACAGACCCGCTTTCTGCTCCGACTGGCGCAGGGAGAATTGCCATTGCCCGCCCCGGTGCAGTCCACCGTGCGCGCCGTGACCCTGCTGGAAAGCGGCCCGGGCTGGGAGCTGCACGGCAAGACCGGCTGGTGCTTCGACTGCACGCCGGAACTCGGCTGGTGGGTGGGCTGGGTGAAGCGCAACGAGCGGCTCTACGGCTTCGCCCTGAACATCGACATGCCCGGCGGCGAGGCCGACATCGGCAAACGCGTCGAACTGGGCAAGGCCAGTCTCAAGGCTCTCGGGATACTGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008692","ARO_id":"47484","ARO_name":"OXA-1282","CARD_short_name":"OXA-1282","ARO_description":"OXA-50 family oxacillin-hydrolyzing class D beta-lactamase OXA-1282.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46513":{"category_aro_accession":"3007724","category_aro_cvterm_id":"46513","category_aro_name":"OXA-50-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-50.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8111":{"model_id":"8111","model_name":"OXA-1283","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10938":{"protein_sequence":{"accession":"XGB73500.1","sequence":"MRPLLFSALLLLSGHTQASEWNDSQAVDKLFGAAGVKGTFVLYDVQRQCYVGHDRERAETRFVPASTYKVANSLIGLSTGAVRSADEVLPYGGKPQRFKAWEHDMSLREAIKASNVPVYEELARRIGLERMRANVSRLGYGNAEIGQVVDNFWLVGPLKISAMEQTRFLLRLAQGELPFPAPVQSTVRAMTLLESGPGWELHGKTGWCFDCTPELGWWVGWVKRNERLYGFALNIDMPGGEADIGKRVELGKASLKALGILP"},"dna_sequence":{"accession":"PQ203872.1","fmin":"0","fmax":"789","strand":"+","sequence":"ATGCGCCCTCTCCTCTTCAGTGCCCTTCTCCTGCTTTCCGGGCATACCCAGGCCAGCGAATGGAACGACAGCCAGGCCGTGGACAAGCTATTCGGCGCGGCCGGGGTGAAAGGCACCTTCGTCCTCTACGATGTGCAGCGGCAGTGCTATGTCGGCCATGACCGGGAGCGCGCGGAAACCCGCTTCGTTCCCGCTTCCACCTACAAGGTGGCGAACAGCCTGATCGGCTTATCCACAGGGGCGGTTAGATCCGCCGACGAGGTTCTTCCCTATGGCGGCAAGCCCCAGCGCTTCAAGGCCTGGGAGCACGACATGAGCCTGCGCGAGGCGATCAAGGCATCGAACGTACCGGTCTACGAGGAACTGGCGCGGCGCATCGGCCTGGAGCGGATGCGCGCCAATGTCTCGCGCCTGGGTTACGGCAACGCGGAAATCGGCCAGGTTGTGGATAACTTCTGGTTGGTGGGACCGCTGAAGATCAGCGCGATGGAACAGACCCGCTTTCTGCTCCGACTGGCGCAGGGAGAATTGCCATTCCCCGCCCCGGTGCAGTCCACCGTGCGCGCCATGACCCTGCTGGAAAGCGGCCCGGGCTGGGAGCTGCACGGCAAGACAGGCTGGTGCTTCGACTGCACGCCGGAACTCGGCTGGTGGGTGGGCTGGGTGAAGCGCAACGAGCGGCTCTACGGCTTCGCCCTGAACATCGACATGCCCGGCGGCGAGGCCGACATCGGCAAGCGCGTCGAACTGGGCAAGGCCAGTCTCAAGGCTCTCGGGATACTGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008693","ARO_id":"47485","ARO_name":"OXA-1283","CARD_short_name":"OXA-1283","ARO_description":"OXA-50 family oxacillin-hydrolyzing class D beta-lactamase OXA-1283.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46513":{"category_aro_accession":"3007724","category_aro_cvterm_id":"46513","category_aro_name":"OXA-50-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-50.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8112":{"model_id":"8112","model_name":"OXA-1284","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10939":{"protein_sequence":{"accession":"XGB73501.1","sequence":"MRLLFFSALLLLFGQAQASEWNDSQAVDKLFEAAGMKGTFVLYDVQRQGYVGHDRARAQTRFVPASTYKVAHSLIGLSTGAVKSADEVLPYGGKPQRFKAWEHDMSLREAIRASNVPVYQELARRIGLQRMRANLARMDYGNGEVGQVVDNFWLVGPLEISALEQTRFLARLAQGELPFPEQVQATVRDMTLMEHGPDWELHGKTGWCFDCTPELGWWVGWVKRDERLYTFALNIDMPGGEADIGKRVELGKAALKALGVLP"},"dna_sequence":{"accession":"PQ203873.1","fmin":"0","fmax":"789","strand":"+","sequence":"ATGCGCCTTCTCTTCTTCAGCGCCCTTCTCCTGCTCTTCGGACAGGCCCAGGCCAGCGAATGGAACGACAGCCAGGCTGTGGACAAGCTATTCGAAGCCGCCGGGATGAAAGGCACCTTCGTTCTCTACGACGTGCAGCGGCAGGGTTATGTCGGCCACGACCGAGCACGCGCGCAGACCCGCTTCGTCCCTGCCTCCACCTATAAGGTGGCGCACAGCCTGATCGGTTTATCCACAGGCGCGGTGAAGTCTGCCGACGAGGTCCTGCCCTATGGCGGCAAGCCCCAGCGCTTCAAGGCCTGGGAGCATGACATGAGCCTGCGCGAGGCGATCCGTGCATCCAACGTGCCGGTCTACCAGGAACTGGCGCGGCGCATCGGCCTGCAGCGTATGCGCGCCAACCTCGCCCGCATGGACTATGGAAATGGCGAGGTCGGGCAGGTTGTGGACAACTTCTGGCTGGTGGGGCCACTGGAGATCAGCGCGCTGGAGCAGACCCGTTTCCTCGCCCGGCTGGCACAGGGAGAACTGCCGTTTCCCGAGCAGGTGCAGGCCACCGTGCGCGACATGACCCTGATGGAACACGGCCCGGACTGGGAGCTGCACGGCAAGACCGGCTGGTGTTTCGATTGCACGCCGGAACTCGGCTGGTGGGTCGGCTGGGTGAAGCGCGACGAGCGCCTCTACACCTTCGCCCTGAACATCGACATGCCCGGCGGCGAGGCCGACATCGGCAAGCGCGTCGAACTGGGCAAGGCCGCTCTCAAGGCCCTGGGCGTGCTGCCCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008694","ARO_id":"47486","ARO_name":"OXA-1284","CARD_short_name":"OXA-1284","ARO_description":"OXA-50-var family class D beta-lactamase OXA-1284.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46513":{"category_aro_accession":"3007724","category_aro_cvterm_id":"46513","category_aro_name":"OXA-50-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-50.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8113":{"model_id":"8113","model_name":"OXA-1285","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10940":{"protein_sequence":{"accession":"XGB73502.1","sequence":"MRPLLFSALLLLSGHAQASEWNDSQAVDKLFGAAGVKGTFVLYDVQRQRYVGHDRERAETRFVPASTYKVANSLIGLSTGAVRSADEVLPYGGKPQRFKAWEHDMSLRDAIKASNVPVYQELARRIGLERMRANVSRLGYGNAEIGQVVDNFWLVGPLKISAMEQTRFLLRLAQGELPFPAPVQSTVRAMTLLESGPGWELHGKTGWCFDCTPELGWWVGWVKRNERLYGFALNIDMPGREADIGKRVELGKASLKALGILP"},"dna_sequence":{"accession":"PQ203874.1","fmin":"0","fmax":"789","strand":"+","sequence":"ATGCGCCCTCTCCTCTTCAGCGCCCTTCTCCTGCTCTCCGGGCATGCCCAGGCCAGCGAATGGAACGACAGCCAGGCCGTGGACAAGCTATTCGGCGCGGCCGGGGTGAAAGGCACCTTCGTCCTCTACGATGTGCAGCGGCAGCGCTATGTCGGCCATGACCGGGAGCGCGCGGAAACCCGCTTCGTTCCCGCTTCCACCTACAAGGTGGCGAACAGCCTGATCGGCTTATCCACAGGGGCGGTTAGATCCGCCGACGAGGTTCTTCCCTATGGCGGCAAGCCCCAGCGCTTCAAGGCCTGGGAGCACGACATGAGCCTGCGCGACGCGATCAAGGCATCGAACGTACCGGTCTACCAGGAACTGGCGCGGCGCATCGGCCTGGAGCGGATGCGCGCCAATGTCTCGCGCCTGGGTTACGGCAACGCGGAAATCGGCCAGGTTGTGGATAACTTCTGGTTGGTGGGACCGCTGAAGATCAGCGCGATGGAACAGACCCGCTTTCTGCTCCGACTGGCGCAGGGAGAATTGCCATTCCCCGCCCCGGTGCAGTCCACCGTGCGCGCCATGACCCTGCTGGAAAGCGGCCCGGGCTGGGAGCTGCACGGCAAGACCGGCTGGTGCTTCGACTGCACGCCGGAACTCGGCTGGTGGGTGGGCTGGGTGAAGCGCAACGAGCGGCTCTACGGCTTCGCCCTGAACATCGACATGCCCGGCCGCGAGGCCGACATCGGCAAGCGCGTCGAACTGGGCAAGGCCAGTCTCAAGGCTCTCGGGATACTGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008695","ARO_id":"47487","ARO_name":"OXA-1285","CARD_short_name":"OXA-1285","ARO_description":"OXA-50 family oxacillin-hydrolyzing class D beta-lactamase OXA-1285.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46513":{"category_aro_accession":"3007724","category_aro_cvterm_id":"46513","category_aro_name":"OXA-50-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-50.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8114":{"model_id":"8114","model_name":"OXA-1286","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10941":{"protein_sequence":{"accession":"XGB73503.1","sequence":"MRPLLFSALLLLSGHTQASEWNDSQAVDKLFGAAGVKGTFVLYDVQRQRYVGHDRERAETRFVPASTYKVANSLIGLSTGAVRSADEVLPYGGKPQRFKAWEHDMSLRDAIEASNVPVYQELARRIGLERMRANVSRLGYGNAEIGQVVDNFWLVGPLKISAMEQTRFLIRLAQGELPFPAPVQSTVRAMTLLESGPGWELHGKTGWCFDCTPELGWWVGWVKCNERLYGFALNIDMPGGEADIGKRVELGKASLKALGILP"},"dna_sequence":{"accession":"PQ203875.1","fmin":"0","fmax":"789","strand":"+","sequence":"ATGCGCCCTCTCCTCTTCAGTGCCCTTCTCCTGCTTTCCGGGCATACCCAGGCCAGCGAATGGAACGACAGCCAGGCCGTGGACAAGCTATTCGGCGCGGCCGGGGTGAAAGGCACCTTCGTCCTCTACGATGTGCAGCGGCAGCGCTATGTCGGCCATGACCGGGAGCGCGCGGAAACCCGCTTCGTTCCCGCTTCCACCTACAAGGTGGCGAACAGCCTGATCGGCTTATCCACAGGGGCGGTTAGATCCGCCGACGAGGTTCTTCCCTATGGCGGCAAGCCCCAGCGCTTCAAGGCCTGGGAGCACGACATGAGCCTGCGCGATGCGATCGAGGCATCGAACGTACCGGTCTACCAGGAACTGGCGCGGCGCATCGGCCTGGAGCGGATGCGCGCCAATGTCTCGCGCCTGGGTTACGGCAACGCGGAAATCGGCCAGGTTGTGGATAACTTCTGGTTGGTGGGACCGCTGAAGATCAGCGCGATGGAACAGACCCGCTTTCTGATCCGACTGGCGCAGGGAGAATTGCCATTCCCCGCCCCGGTGCAGTCCACCGTGCGCGCCATGACCCTGCTGGAAAGCGGCCCGGGCTGGGAGCTGCACGGCAAGACCGGCTGGTGCTTCGACTGCACGCCGGAACTCGGCTGGTGGGTGGGCTGGGTGAAGTGCAACGAGCGGCTCTACGGCTTCGCCCTGAACATCGACATGCCCGGCGGCGAGGCCGACATCGGCAAGCGCGTCGAACTGGGCAAGGCCAGTCTCAAGGCTCTCGGGATACTGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008696","ARO_id":"47488","ARO_name":"OXA-1286","CARD_short_name":"OXA-1286","ARO_description":"OXA-50 family oxacillin-hydrolyzing class D beta-lactamase OXA-1286.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46513":{"category_aro_accession":"3007724","category_aro_cvterm_id":"46513","category_aro_name":"OXA-50-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-50.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8115":{"model_id":"8115","model_name":"OXA-1287","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10942":{"protein_sequence":{"accession":"XGB73504.1","sequence":"MRPLLFSALLLLSGHTQASEWNDSQAVDKLFGAAGVKGTFVLYDVQRQRYVGHDRERAETRFVPASTYKVANSLIGLSTGAVRSADEVLSYGGKPQRFKAWEHDMSLRDAIKASNVPVYQELARRIGLERMRANVSRLGYGNAEIGQVVDNFWLVGPLKISAMEQTRFLLRLAQGELPFPAPVQSTVRAMTLLESSPGWELHGKTGWCFDCTPELGWWVGWVKRNERLYGFALNIDMPGGEADIGKRVELGKASLKALGILP"},"dna_sequence":{"accession":"PQ203876.1","fmin":"0","fmax":"789","strand":"+","sequence":"ATGCGCCCTCTCCTCTTCAGTGCCCTTCTCCTGCTTTCCGGGCATACCCAGGCCAGCGAATGGAACGACAGCCAGGCCGTGGACAAGCTATTCGGCGCGGCCGGGGTGAAAGGCACCTTCGTCCTCTACGATGTGCAGCGGCAGCGCTATGTCGGCCATGACCGGGAGCGCGCGGAAACCCGCTTCGTTCCCGCTTCCACCTACAAGGTGGCGAACAGCCTGATCGGCTTATCCACAGGGGCGGTTAGATCCGCCGACGAGGTTCTTTCCTATGGCGGCAAGCCCCAGCGCTTCAAGGCCTGGGAGCACGACATGAGCCTGCGCGACGCGATCAAGGCATCGAACGTACCGGTCTACCAGGAACTGGCGCGGCGCATCGGCCTGGAGCGGATGCGCGCCAATGTCTCGCGCCTGGGTTACGGCAACGCGGAAATCGGCCAGGTTGTGGATAACTTCTGGTTGGTGGGACCGCTGAAGATCAGCGCGATGGAACAGACCCGCTTTCTGCTCCGACTGGCGCAGGGAGAATTGCCATTCCCCGCCCCGGTGCAGTCCACCGTGCGCGCCATGACCCTGCTGGAAAGCAGCCCGGGCTGGGAGCTGCACGGCAAGACCGGCTGGTGCTTCGACTGCACGCCGGAACTCGGCTGGTGGGTGGGCTGGGTGAAGCGCAACGAGCGGCTCTACGGCTTCGCCCTGAACATCGACATGCCCGGCGGCGAGGCCGACATCGGCAAGCGCGTCGAACTGGGCAAGGCCAGTCTCAAGGCTCTCGGGATACTGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008697","ARO_id":"47489","ARO_name":"OXA-1287","CARD_short_name":"OXA-1287","ARO_description":"OXA-50 family oxacillin-hydrolyzing class D beta-lactamase OXA-1287.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46513":{"category_aro_accession":"3007724","category_aro_cvterm_id":"46513","category_aro_name":"OXA-50-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-50.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8116":{"model_id":"8116","model_name":"OXA-1288","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10943":{"protein_sequence":{"accession":"XGB73505.1","sequence":"MRPLLFSALLLLSGHTQASEWNDSQAVDKLFGAAGVKGTFVLYDVQRQRYVGHDRERAETRFVPASTYKVANSLIGLSTGAVRSADEVLPYGGKPQRFKAWEHDMSLRDAIKASNVPVYQELARRIGLERMRANVSRLGYGNAEIGQVVDNFWLVGPLKISAMEQTRFLLRLAQGELPFPAPVQSTVRAMTLLESSPGWELHGKTGWCFDCTPELGWWVGWVKRNERLYGFALNIDMPGGEADIGKRVELGKASLKALGILP"},"dna_sequence":{"accession":"PQ203877.1","fmin":"0","fmax":"789","strand":"+","sequence":"ATGCGCCCTCTCCTCTTCAGTGCCCTTCTCCTGCTTTCCGGGCATACCCAGGCCAGCGAATGGAACGACAGCCAGGCCGTGGACAAGCTATTCGGCGCGGCCGGGGTGAAAGGCACCTTCGTCCTCTACGATGTGCAGCGGCAGCGCTATGTTGGCCATGACCGGGAGCGCGCGGAAACCCGCTTCGTTCCCGCTTCCACCTACAAGGTGGCGAACAGCCTGATCGGCTTATCCACAGGGGCGGTTAGATCCGCCGACGAGGTTCTTCCCTATGGCGGCAAGCCCCAGCGCTTCAAGGCCTGGGAGCACGACATGAGCCTGCGCGACGCGATCAAGGCATCGAACGTACCGGTCTACCAGGAACTGGCGCGGCGCATCGGCCTGGAGCGGATGCGCGCCAATGTCTCGCGCCTGGGTTACGGCAACGCGGAAATCGGCCAGGTTGTGGATAACTTCTGGTTGGTGGGACCGCTGAAGATCAGCGCGATGGAACAGACCCGCTTTCTGCTCCGACTGGCGCAGGGAGAATTGCCATTCCCCGCCCCGGTGCAGTCCACCGTGCGCGCCATGACCCTGCTGGAAAGCAGCCCGGGCTGGGAGCTGCACGGCAAGACCGGCTGGTGCTTCGACTGCACGCCGGAACTCGGCTGGTGGGTGGGCTGGGTGAAGCGCAACGAGCGGCTCTACGGCTTCGCCCTGAACATCGACATGCCCGGCGGCGAGGCCGACATCGGCAAGCGCGTCGAACTGGGCAAGGCCAGTCTCAAGGCTCTCGGGATACTGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008698","ARO_id":"47490","ARO_name":"OXA-1288","CARD_short_name":"OXA-1288","ARO_description":"OXA-50 family oxacillin-hydrolyzing class D beta-lactamase OXA-1288.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46513":{"category_aro_accession":"3007724","category_aro_cvterm_id":"46513","category_aro_name":"OXA-50-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-50.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8117":{"model_id":"8117","model_name":"OXA-1289","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10944":{"protein_sequence":{"accession":"XGB73506.1","sequence":"MRPLLFSALLLLSGHAQASEWNDSQAVDKLFGAAGVKGTFVLYDVQRQRYVGHDRERAETRFVPASTYKVANSLIGLSTGAVKSADEVLPYGGKPQRFKAWEHDMSLRDAIEASNVPVYQELARRIGLERMRANVSRLGYGNAEIGQAVDNFWLVGPLKISAMEQTRFLLRLAQGELPFPAPVQSTVRAMTLLESGPGWELHGKTGWCFDCTPELGWWVGWVKRNERLYGFALNIDMPGGEADIGKRVELGKASLKALGILP"},"dna_sequence":{"accession":"PQ203878.1","fmin":"0","fmax":"789","strand":"+","sequence":"ATGCGCCCTCTCCTCTTCAGCGCCCTTCTCCTGCTCTCCGGGCATGCCCAGGCCAGCGAATGGAACGACAGCCAGGCCGTGGACAAGCTATTCGGCGCGGCCGGGGTGAAAGGCACCTTCGTCCTCTACGATGTGCAGCGGCAGCGCTATGTCGGCCACGACCGGGAGCGCGCGGAAACTCGCTTCGTTCCTGCCTCCACCTACAAGGTGGCGAACAGCCTGATTGGCTTATCCACAGGGGCGGTTAAATCCGCCGACGAGGTTCTTCCCTATGGCGGCAAGCCCCAGCGCTTCAAGGCCTGGGAGCACGACATGAGCCTGCGCGATGCGATCGAGGCATCGAACGTACCGGTCTACCAGGAACTGGCGCGGCGCATCGGCCTGGAGCGGATGCGCGCCAATGTCTCGCGCCTGGGTTACGGCAACGCGGAAATCGGCCAGGCTGTGGATAACTTCTGGTTGGTGGGACCGCTGAAGATCAGCGCGATGGAACAGACCCGCTTTCTGCTCCGACTGGCGCAGGGAGAATTGCCATTCCCCGCCCCGGTGCAGTCCACCGTGCGCGCCATGACCCTGCTGGAAAGCGGCCCGGGCTGGGAGCTGCACGGCAAGACCGGCTGGTGCTTCGACTGCACGCCGGAACTCGGCTGGTGGGTGGGCTGGGTGAAGCGCAACGAGCGGCTCTACGGCTTCGCCCTGAACATCGACATGCCCGGCGGCGAGGCCGACATCGGCAAGCGCGTCGAACTGGGCAAGGCCAGTCTCAAGGCTCTCGGGATACTGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008699","ARO_id":"47491","ARO_name":"OXA-1289","CARD_short_name":"OXA-1289","ARO_description":"OXA-50 family oxacillin-hydrolyzing class D beta-lactamase OXA-1289.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46513":{"category_aro_accession":"3007724","category_aro_cvterm_id":"46513","category_aro_name":"OXA-50-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-50.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8118":{"model_id":"8118","model_name":"OXA-1290","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10945":{"protein_sequence":{"accession":"XGB73507.1","sequence":"MRLLFFSALLLLFGQAQASEWNDSQAVDKLFEAAGMKGTFVLYDVQRQGYVGHDRARAQTRFVPASTYKVAHSLIGLSTGAVKSADEVLPYGGKPQRFKAWEHDMSLREAIRASNVPVYQELARRIGLQRMRANLARMDYGNGEVGQVVDNFWLVGPLEISALEQTRFLARLAQGELPFPEQVQATVRDMTLMEHGPDWELHGKTGWCFDCTPELGWWVGWVKRDESLYTFALNIDMPGGEADIGKRVELGKAALKALGVLP"},"dna_sequence":{"accession":"PQ203879.1","fmin":"0","fmax":"789","strand":"+","sequence":"ATGCGCCTTCTCTTCTTCAGCGCCCTTCTCCTGCTCTTCGGACAGGCCCAGGCCAGCGAATGGAACGACAGCCAGGCTGTGGACAAGCTATTCGAAGCCGCCGGGATGAAAGGCACCTTCGTTCTCTACGACGTGCAGCGGCAGGGTTATGTCGGCCACGACCGAGCACGCGCGCAGACCCGCTTCGTCCCTGCCTCCACCTATAAGGTGGCGCACAGCCTGATCGGTTTATCCACAGGCGCGGTGAAGTCCGCCGACGAGGTCCTGCCCTATGGCGGCAAGCCCCAGCGCTTCAAGGCCTGGGAGCATGACATGAGCCTGCGCGAGGCGATCCGTGCATCCAACGTGCCGGTCTACCAGGAACTGGCGCGGCGCATCGGCCTGCAGCGTATGCGCGCCAACCTCGCCCGCATGGACTATGGAAATGGCGAGGTCGGGCAGGTTGTGGACAACTTCTGGCTGGTGGGGCCACTGGAGATCAGCGCGCTGGAGCAGACCCGTTTCCTCGCCCGGCTGGCACAGGGAGAACTGCCGTTTCCCGAGCAGGTGCAGGCCACCGTGCGCGACATGACCCTGATGGAACACGGCCCGGACTGGGAGCTGCACGGCAAAACCGGCTGGTGTTTCGATTGCACGCCGGAACTCGGCTGGTGGGTCGGCTGGGTGAAGCGCGACGAGAGCCTCTACACCTTCGCCCTGAACATCGACATGCCCGGCGGCGAGGCCGACATCGGCAAGCGCGTCGAACTGGGCAAGGCCGCTCTCAAGGCCCTGGGCGTGCTGCCCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008700","ARO_id":"47492","ARO_name":"OXA-1290","CARD_short_name":"OXA-1290","ARO_description":"OXA-50-var family class D beta-lactamase OXA-1290.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46513":{"category_aro_accession":"3007724","category_aro_cvterm_id":"46513","category_aro_name":"OXA-50-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-50.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8119":{"model_id":"8119","model_name":"OXA-1291","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10946":{"protein_sequence":{"accession":"XGB73508.1","sequence":"MRPLLFSALLLLSGHTQASEWNDSQAVGKLFGAAGVKGTFVLYDVQRQCYVGHDRERAETRFVPASTYKVANSLIGLSTGAVRSADEVLPYGGKPQRFKAWEHDMSLREAIKASNVPVYQELARRIGLERMRANVSRLGYGNAEIGQVVDNFWLVGPLKISAMEQTRFLLRLAQGELPFPAPVQSTVRAMTLLESGPGWELHGKTGWCFDCTPELGWWVGWVKRNERLYGFALNIDMPGGEADIGKRVELGKASLKALGILP"},"dna_sequence":{"accession":"PQ203880.1","fmin":"0","fmax":"789","strand":"+","sequence":"ATGCGCCCTCTCCTCTTCAGTGCCCTTCTCCTGCTTTCCGGGCATACCCAGGCCAGCGAATGGAACGACAGCCAGGCCGTGGGCAAGCTATTCGGCGCGGCCGGGGTGAAAGGCACCTTCGTCCTCTACGATGTGCAGCGGCAGTGCTATGTCGGCCATGACCGGGAGCGCGCGGAAACCCGCTTCGTTCCCGCTTCCACCTACAAGGTGGCGAACAGCCTGATCGGCTTATCCACAGGGGCGGTTAGATCCGCCGACGAGGTTCTTCCCTATGGCGGCAAGCCCCAGCGCTTCAAGGCCTGGGAGCACGACATGAGCCTGCGCGAGGCGATCAAGGCATCGAACGTACCGGTCTACCAGGAACTGGCGCGGCGCATCGGCCTGGAGCGGATGCGCGCCAATGTCTCGCGCCTGGGTTACGGCAACGCGGAAATCGGCCAGGTTGTGGATAACTTCTGGTTGGTGGGACCGCTGAAGATCAGCGCGATGGAGCAGACCCGCTTTCTGCTCCGACTGGCGCAGGGAGAATTGCCATTCCCCGCCCCGGTGCAGTCCACCGTGCGCGCCATGACCCTGCTGGAAAGCGGCCCGGGCTGGGAGCTGCACGGCAAGACCGGCTGGTGCTTCGACTGCACGCCGGAACTCGGCTGGTGGGTGGGCTGGGTGAAGCGCAACGAGCGGCTCTACGGCTTCGCCCTGAACATCGACATGCCCGGCGGCGAGGCCGACATCGGCAAGCGCGTCGAACTGGGCAAGGCCAGTCTCAAGGCTCTCGGGATACTGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008701","ARO_id":"47493","ARO_name":"OXA-1291","CARD_short_name":"OXA-1291","ARO_description":"OXA-50 family oxacillin-hydrolyzing class D beta-lactamase OXA-1291.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46513":{"category_aro_accession":"3007724","category_aro_cvterm_id":"46513","category_aro_name":"OXA-50-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-50.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8120":{"model_id":"8120","model_name":"OXA-1292","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10947":{"protein_sequence":{"accession":"XGB73509.1","sequence":"MRPLLFSALLLLSGHTQASEWNDSQAVDKLFGAAGVKGTFVLYDVQRQRYVGHDRERAETRFVPASTYKVANSLIGLSTGAVRSADEVLPYGGKPQRFKAWEHDMSLRDAIKASNVPVYQELARRIGLERMRANVSRLGYGNAEIGQVVDNFWLVGPLKISAMEQTRFLLRLAQGELPFPAPVQSTVRAMTLLESGPGWELHGKTGWCFDCTPELGWWVGWVKRNERLYGFALNIDMPGGEADIGKRVELSKASLKALGILP"},"dna_sequence":{"accession":"PQ203881.1","fmin":"0","fmax":"789","strand":"+","sequence":"ATGCGCCCCCTCCTCTTCAGTGCCCTTCTCCTGCTTTCCGGGCATACCCAGGCCAGCGAATGGAACGACAGCCAGGCCGTGGACAAGCTATTCGGCGCGGCCGGGGTGAAAGGCACCTTCGTCCTCTACGATGTGCAGCGGCAGCGCTATGTCGGCCATGACCGGGAGCGCGCGGAAACCCGCTTCGTTCCCGCTTCCACCTACAAGGTGGCGAACAGCCTGATCGGCTTATCCACAGGGGCGGTTAGATCCGCCGACGAGGTTCTTCCCTATGGCGGCAAGCCCCAGCGCTTCAAGGCCTGGGAGCACGACATGAGCCTGCGCGACGCGATCAAGGCATCGAACGTACCGGTCTACCAGGAACTGGCGCGGCGCATCGGCCTGGAGCGGATGCGCGCCAATGTCTCGCGCCTGGGTTACGGCAACGCGGAAATCGGCCAGGTTGTGGATAACTTCTGGTTGGTGGGACCGCTGAAGATCAGCGCGATGGAACAGACCCGCTTTCTGCTCCGACTGGCGCAGGGAGAATTGCCATTCCCCGCCCCGGTGCAGTCCACCGTGCGCGCCATGACCCTGCTGGAAAGCGGCCCGGGCTGGGAGCTGCACGGCAAGACCGGCTGGTGCTTCGACTGCACGCCGGAACTCGGCTGGTGGGTGGGCTGGGTGAAGCGCAACGAGCGGCTCTACGGCTTCGCCCTGAACATCGACATGCCCGGCGGCGAGGCCGACATCGGCAAGCGCGTCGAACTGAGCAAGGCCAGTCTCAAGGCTCTCGGGATACTGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008702","ARO_id":"47494","ARO_name":"OXA-1292","CARD_short_name":"OXA-1292","ARO_description":"OXA-50 family oxacillin-hydrolyzing class D beta-lactamase OXA-1292.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46513":{"category_aro_accession":"3007724","category_aro_cvterm_id":"46513","category_aro_name":"OXA-50-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-50.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8121":{"model_id":"8121","model_name":"OXA-1293","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10948":{"protein_sequence":{"accession":"XGB73510.1","sequence":"MRPLLFSALLLLSGHTQASEWNDSQAVDKLFGAAGVKGTFVLYDVQRQCYVGHDRERAETRFVPASTYKVANSLIGLSTGAVRSADEVLPYGGKPQRFKAWEHDMSLRDAIEASNVPVYQELARRIGLERMRANVSRLGYGNAEIGQVVDNFWLVGPLKISAMEQTRFLLRLAQGELPFPAPVQSTVRAMTLLESGPGWELHGKTGWCFDCTPELGWWVGWVKRNERLYGFALNIDMPGGEADIGKRVELGKASLKALGILP"},"dna_sequence":{"accession":"PQ203882.1","fmin":"0","fmax":"789","strand":"+","sequence":"ATGCGCCCTCTCCTCTTCAGTGCCCTTCTCCTGCTTTCCGGGCATACCCAGGCCAGCGAATGGAACGACAGCCAGGCCGTGGACAAGCTATTCGGCGCGGCCGGGGTGAAAGGCACCTTCGTCCTCTACGATGTGCAGCGGCAGTGCTATGTCGGCCATGACCGGGAGCGCGCGGAAACCCGCTTCGTTCCCGCTTCCACCTACAAGGTGGCGAACAGCCTGATCGGCTTATCCACAGGGGCGGTTAGATCCGCCGACGAGGTTCTTCCCTATGGCGGCAAGCCCCAGCGCTTCAAGGCCTGGGAGCACGACATGAGCCTGCGCGATGCGATCGAGGCATCGAACGTACCGGTCTACCAGGAACTGGCGCGGCGCATCGGCCTGGAGCGGATGCGCGCCAATGTCTCGCGCCTGGGTTACGGCAACGCGGAAATCGGCCAGGTTGTGGATAACTTCTGGTTGGTGGGACCGCTGAAGATCAGCGCGATGGAACAGACCCGCTTTCTGCTCCGACTGGCGCAGGGAGAATTGCCATTCCCCGCCCCGGTGCAGTCCACCGTGCGCGCCATGACCCTGCTGGAAAGCGGCCCGGGCTGGGAGCTGCACGGCAAGACCGGCTGGTGCTTCGACTGCACGCCGGAACTCGGCTGGTGGGTGGGCTGGGTGAAGCGCAACGAGCGGCTCTACGGCTTCGCCCTGAACATCGACATGCCCGGCGGCGAGGCCGACATCGGCAAGCGCGTCGAACTGGGCAAGGCCAGTCTCAAGGCTCTCGGGATACTGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008703","ARO_id":"47495","ARO_name":"OXA-1293","CARD_short_name":"OXA-1293","ARO_description":"OXA-50 family oxacillin-hydrolyzing class D beta-lactamase OXA-1293.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46513":{"category_aro_accession":"3007724","category_aro_cvterm_id":"46513","category_aro_name":"OXA-50-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-50.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8122":{"model_id":"8122","model_name":"OXA-1294","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10949":{"protein_sequence":{"accession":"XGB73511.1","sequence":"MRLLFFSALLLLFGQAQASEWNDSQAVDKLFEAAGMKGTFVLYDVQRQGYVGHDRARAQTRFVPASTYKVAHSLIGLSTGAVKSADEVLPYGGKPQRFKAWEHDMSLREAIRASNVPVYQELARRIGLQRMRANLARMDYGNGEVGQVVDNFWLVGPLEISALEQTRFLARLAQGELPFPEQVQATVRDMTLMEHGPDWELHGKTGWCFDCTPELGWWVGWVKRDERLYTFALNIDMPGGEADIGKRLELGKAALKALGVLP"},"dna_sequence":{"accession":"PQ203883.1","fmin":"0","fmax":"789","strand":"+","sequence":"ATGCGCCTTCTCTTCTTCAGCGCCCTTCTCCTGCTCTTCGGACAGGCCCAGGCCAGCGAATGGAACGACAGCCAGGCTGTGGACAAGCTATTCGAAGCCGCCGGGATGAAAGGCACCTTCGTTCTCTACGACGTGCAGCGGCAGGGTTATGTCGGCCACGACCGAGCACGCGCGCAGACCCGCTTCGTCCCTGCCTCCACCTATAAGGTGGCGCACAGCCTGATCGGTTTATCCACAGGCGCGGTGAAGTCTGCCGACGAGGTCCTGCCCTATGGCGGCAAGCCCCAGCGCTTCAAGGCCTGGGAGCATGACATGAGCCTGCGCGAGGCGATCCGTGCATCCAACGTGCCGGTCTACCAGGAACTGGCGCGGCGCATCGGCCTGCAGCGTATGCGCGCCAACCTCGCCCGCATGGACTATGGAAATGGCGAGGTCGGGCAGGTTGTGGACAACTTCTGGCTGGTGGGGCCACTGGAGATCAGCGCGCTGGAGCAGACCCGTTTCCTCGCCCGGCTGGCACAGGGAGAACTGCCGTTTCCCGAGCAGGTGCAGGCCACCGTGCGCGACATGACCCTGATGGAACACGGCCCGGACTGGGAGCTGCACGGCAAGACCGGCTGGTGTTTCGATTGCACGCCGGAACTCGGCTGGTGGGTCGGCTGGGTGAAGCGCGACGAGCGCCTCTACACCTTCGCCCTGAACATCGACATGCCCGGCGGCGAGGCCGACATCGGCAAGCGCCTCGAACTGGGCAAGGCCGCTCTCAAGGCCCTGGGCGTGCTGCCCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008704","ARO_id":"47496","ARO_name":"OXA-1294","CARD_short_name":"OXA-1294","ARO_description":"OXA-50-var family class D beta-lactamase OXA-1294.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46513":{"category_aro_accession":"3007724","category_aro_cvterm_id":"46513","category_aro_name":"OXA-50-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-50.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8123":{"model_id":"8123","model_name":"OXA-1295","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10950":{"protein_sequence":{"accession":"XGB73513.1","sequence":"MRPLLFSALLLLSGHAQASEWNDSQAVDKLFGAAGVKGTFVLYDVQRQRYVGHDRQRAETRFVPASTYKVANSLIGLSTGAVRSADEVLPYGGKPQRFKAWEHDMSLRDAIEASNVPVYQELARRIGLERMRANVSRLGYGNAEIGQVVDNFWLVGPLKISAMEQTRFLLRLAQGELPFPAPVQSTVRTMTLLESGPGWELHGKTGWCFDCTPELGWWVGWVKRNERLYGFALNIDMPGGEADIGKRVELGKASLKALGILP"},"dna_sequence":{"accession":"PQ203885.1","fmin":"0","fmax":"789","strand":"+","sequence":"ATGCGCCCTCTCCTCTTCAGCGCCCTTCTCCTGCTCTCCGGGCATGCTCAGGCCAGCGAATGGAACGACAGCCAGGCCGTGGACAAGCTATTCGGCGCGGCCGGGGTGAAAGGCACCTTCGTCCTTTACGATGTGCAGCGGCAGCGCTATGTCGGCCATGACCGGCAGCGCGCGGAAACCCGCTTCGTTCCCGCTTCCACCTACAAGGTGGCGAACAGCCTGATCGGCTTATCCACAGGGGCGGTTAGATCCGCCGACGAGGTTCTTCCCTATGGCGGCAAGCCCCAGCGCTTCAAGGCCTGGGAGCACGACATGAGCCTGCGCGACGCGATCGAGGCATCGAACGTACCGGTCTACCAGGAACTGGCGCGGCGCATCGGCCTGGAGCGGATGCGCGCCAATGTCTCGCGCCTGGGTTACGGCAACGCGGAAATCGGCCAGGTTGTGGATAACTTCTGGTTGGTGGGACCGCTGAAGATCAGCGCGATGGAACAGACCCGCTTTCTGCTCCGACTGGCGCAGGGAGAATTGCCATTCCCCGCCCCGGTGCAGTCCACCGTGCGCACCATGACCCTGCTGGAAAGCGGCCCGGGCTGGGAGCTGCACGGCAAGACCGGCTGGTGCTTCGACTGCACACCGGAACTCGGCTGGTGGGTGGGCTGGGTGAAGCGCAACGAGCGGCTCTACGGCTTCGCCCTGAACATCGACATGCCCGGCGGCGAGGCCGACATCGGCAAGCGCGTCGAACTGGGCAAGGCCAGTCTCAAGGCTCTCGGGATACTGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008705","ARO_id":"47497","ARO_name":"OXA-1295","CARD_short_name":"OXA-1295","ARO_description":"OXA-50 family oxacillin-hydrolyzing class D beta-lactamase OXA-1295.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46513":{"category_aro_accession":"3007724","category_aro_cvterm_id":"46513","category_aro_name":"OXA-50-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-50.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8124":{"model_id":"8124","model_name":"OXA-1296","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10951":{"protein_sequence":{"accession":"XGB73514.1","sequence":"MRPLLFSALLLLSGPTQASEWNDSQAVDKLFGAAGVKGTFVLYDVQRQRYIGHDRERAETRFVPASTYKVANSLIGLSTGAVRSADEVLPYGGKPQRFKAWEHDMSLRDAIEASNVPVYQELARRIGLERMRANVSRLGYGNAEIGQVVDNFWLVGPLKISAMEQTRFLLRLAQGELPFPAPVQSTVRAMTLLESGPGWELHGKTGWCFDCTPELGWWVGWVKRNERLYGFALNIDMPGGEADTGKRVELGKASLKALGILP"},"dna_sequence":{"accession":"PQ203886.1","fmin":"0","fmax":"789","strand":"+","sequence":"ATGCGCCCTCTCCTCTTCAGCGCCCTTCTCCTACTCTCCGGGCCTACCCAGGCCAGCGAATGGAACGACAGCCAGGCCGTGGACAAGCTATTCGGCGCGGCCGGGGTGAAAGGCACCTTCGTCCTCTACGATGTGCAGCGGCAGCGCTATATCGGCCATGACCGGGAGCGCGCGGAAACCCGCTTCGTTCCCGCTTCCACCTACAAGGTGGCGAACAGCCTGATCGGCTTATCCACAGGGGCGGTTAGATCCGCCGACGAGGTTCTTCCCTATGGCGGCAAGCCCCAGCGCTTCAAGGCCTGGGAGCACGACATGAGCCTGCGCGACGCGATCGAGGCATCGAACGTACCGGTCTACCAGGAACTGGCGCGGCGCATCGGCCTGGAGCGGATGCGCGCCAATGTCTCCCGCCTGGGTTACGGCAACGCGGAAATCGGCCAGGTTGTGGATAACTTCTGGTTGGTGGGACCGCTGAAGATCAGCGCGATGGAACAGACCCGCTTTCTGCTCCGACTGGCGCAGGGAGAATTGCCATTCCCCGCCCCGGTGCAGTCCACCGTGCGCGCCATGACCCTGCTGGAAAGCGGCCCGGGCTGGGAGCTGCACGGCAAGACCGGCTGGTGCTTCGACTGCACGCCGGAACTCGGCTGGTGGGTGGGCTGGGTGAAGCGCAACGAGCGGCTCTACGGCTTCGCCCTGAACATCGACATGCCCGGCGGCGAGGCCGACACCGGAAAGCGTGTCGAACTGGGCAAGGCCAGTCTCAAGGCTCTCGGGATACTGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008706","ARO_id":"47498","ARO_name":"OXA-1296","CARD_short_name":"OXA-1296","ARO_description":"OXA-50 family oxacillin-hydrolyzing class D beta-lactamase OXA-1296.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46513":{"category_aro_accession":"3007724","category_aro_cvterm_id":"46513","category_aro_name":"OXA-50-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-50.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8125":{"model_id":"8125","model_name":"OXA-1297","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10952":{"protein_sequence":{"accession":"XGB73515.1","sequence":"MRPLLFSALLLLSGHTQASEWNDSQAVDKLFGAAGVKGTFVLYDVQRQCYVGHDRERAETRFVPASTYKVANSLIGLSTGAVRSADEVLPYGGKPQRFKAWEHDMSLRDAIEASNVPVYQELARRIGLERMRANVSRLGYGNAEIGQVVDNFWLVGPLKISAMEQTRFLIRLAQGELPFPAPVQSTVRAMTLLESGPGWELHGKTGWCFDCTPELGWWVGWVKRNERLYGFALNIDMPGGEADIGKRVELGKASLKALGILP"},"dna_sequence":{"accession":"PQ203887.1","fmin":"0","fmax":"789","strand":"+","sequence":"ATGCGCCCTCTCCTCTTCAGTGCCCTTCTCCTGCTTTCCGGGCATACCCAGGCCAGCGAATGGAACGACAGCCAGGCCGTGGACAAGCTATTCGGCGCGGCCGGGGTGAAAGGCACCTTCGTCCTCTACGATGTGCAGCGGCAGTGCTATGTCGGCCATGACCGGGAGCGCGCGGAAACCCGCTTCGTTCCCGCTTCCACCTACAAGGTGGCGAACAGCCTGATCGGCTTATCCACAGGGGCGGTTAGATCCGCCGACGAGGTTCTTCCCTATGGCGGCAAGCCCCAGCGCTTCAAGGCCTGGGAGCACGACATGAGCCTGCGCGATGCGATCGAGGCATCGAACGTACCGGTCTACCAGGAACTGGCGCGGCGCATCGGCCTGGAGCGGATGCGCGCCAATGTCTCGCGCCTGGGTTACGGCAACGCGGAAATCGGCCAGGTTGTGGATAACTTCTGGTTGGTGGGACCGCTGAAGATCAGCGCGATGGAACAGACCCGCTTTCTGATCCGACTGGCGCAGGGAGAATTGCCATTCCCCGCCCCGGTGCAGTCCACCGTGCGCGCCATGACCCTGCTGGAAAGCGGCCCGGGCTGGGAGCTGCACGGCAAGACCGGCTGGTGCTTCGACTGCACGCCGGAGCTCGGCTGGTGGGTGGGCTGGGTGAAGCGCAACGAGCGGCTCTACGGCTTCGCCCTGAACATCGACATGCCCGGCGGCGAGGCCGACATCGGCAAGCGCGTCGAACTGGGCAAGGCCAGTCTCAAGGCTCTCGGGATACTGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008707","ARO_id":"47499","ARO_name":"OXA-1297","CARD_short_name":"OXA-1297","ARO_description":"OXA-50 family oxacillin-hydrolyzing class D beta-lactamase OXA-1297.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46513":{"category_aro_accession":"3007724","category_aro_cvterm_id":"46513","category_aro_name":"OXA-50-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-50.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8126":{"model_id":"8126","model_name":"OXA-1298","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10953":{"protein_sequence":{"accession":"XGB73516.1","sequence":"MRPLLFSALLLLSGHAQASEWNDSQAVDKLFGAAGVKGTFVLYDVQRQRYVGHDRERAETRFVPASTYKVANSLIGLSTGAVRSADEVLPYGGKPQRFKAWEHDMSLRDAIEASNVPVYQELARRIGLERMRANVSRLGYGNAEIGQVVDNFWLVGPLKISAMEQTRFLLRLAQGELPFPAPVQSTVRAMTLLESGPGWELHGKTGWCFDCTPELGWWVGWVKRNERLYGFALNIDMPGGEADTGKRVELGKASLKALGILP"},"dna_sequence":{"accession":"PQ203888.1","fmin":"0","fmax":"789","strand":"+","sequence":"ATGCGCCCTCTCCTCTTCAGCGCCCTTCTCCTGCTCTCCGGGCATGCCCAGGCCAGCGAATGGAACGACAGCCAGGCCGTGGACAAGCTATTCGGCGCGGCCGGGGTGAAAGGCACCTTCGTCCTCTACGATGTGCAGCGGCAGCGCTATGTCGGCCACGACCGGGAGCGCGCGGAAACTCGCTTCGTTCCTGCCTCCACCTACAAGGTGGCGAACAGCCTGATTGGCTTATCCACAGGGGCGGTTAGATCCGCCGACGAGGTTCTTCCCTATGGCGGCAAGCCCCAGCGCTTCAAGGCCTGGGAGCACGACATGAGCCTGCGCGATGCGATCGAGGCATCGAACGTACCGGTCTACCAGGAACTGGCGCGGCGCATCGGCCTGGAGCGGATGCGCGCCAATGTCTCGCGCCTGGGTTACGGCAACGCGGAAATCGGCCAGGTTGTGGATAACTTCTGGTTGGTGGGACCGCTGAAGATCAGCGCGATGGAACAGACCCGCTTTCTGCTCCGACTGGCCCAGGGAGAATTGCCATTCCCCGCCCCGGTGCAGTCCACCGTGCGCGCCATGACCCTGCTGGAAAGCGGCCCGGGCTGGGAGCTGCACGGCAAGACCGGCTGGTGCTTCGACTGCACGCCGGAACTCGGCTGGTGGGTGGGCTGGGTGAAGCGCAACGAGCGGCTCTACGGCTTCGCCCTGAACATCGACATGCCCGGCGGCGAGGCCGACACCGGCAAGCGCGTCGAACTGGGCAAGGCCAGTCTCAAGGCTCTCGGGATACTGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008708","ARO_id":"47500","ARO_name":"OXA-1298","CARD_short_name":"OXA-1298","ARO_description":"OXA-50 family oxacillin-hydrolyzing class D beta-lactamase OXA-1298.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46513":{"category_aro_accession":"3007724","category_aro_cvterm_id":"46513","category_aro_name":"OXA-50-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-50.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8127":{"model_id":"8127","model_name":"OXA-1299","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10954":{"protein_sequence":{"accession":"XGB73517.1","sequence":"MRPLLFSALLLLSGHTQASEWNDSQAVDKLFGAAGVKGTFVLYDVQRQRYVGHDRERAETRFVPASTYKVANSLIGLSTGAVRSADEVLPYGGKPQRFKAWEHDMSLRDAIKAPNVPVYQELARRIGLERMRANVSRLGYGNAEIGQVVDNFWLVGPLKISAMEQTRFLLRLAQGELPFPAPVQSTVRAMTLLESGPGWELHGKTGWCFDCTPELGWWVGWVKRNERLYGFALNIDMPGGEADIGKRVELGKASLKALGILP"},"dna_sequence":{"accession":"PQ203889.1","fmin":"0","fmax":"789","strand":"+","sequence":"ATGCGCCCCCTCCTCTTCAGTGCCCTTCTCCTGCTTTCCGGGCATACCCAGGCCAGCGAATGGAACGACAGCCAGGCCGTGGACAAGCTATTCGGCGCGGCCGGGGTGAAAGGCACCTTCGTCCTCTACGATGTGCAGCGGCAGCGCTATGTCGGCCATGACCGGGAGCGCGCGGAAACCCGCTTCGTTCCCGCTTCCACCTACAAGGTGGCGAACAGCCTGATCGGCTTATCCACAGGGGCGGTTAGATCCGCCGACGAGGTTCTTCCCTATGGCGGCAAGCCCCAGCGCTTCAAGGCCTGGGAGCACGACATGAGCCTGCGCGACGCGATTAAGGCACCGAACGTACCGGTCTACCAGGAACTGGCGCGGCGCATCGGCCTGGAGCGGATGCGCGCCAATGTCTCGCGCCTGGGTTACGGCAACGCGGAAATCGGCCAGGTTGTGGATAACTTCTGGTTGGTGGGACCGCTGAAGATCAGCGCGATGGAACAGACCCGCTTTCTGCTCCGACTGGCGCAGGGAGAATTGCCATTCCCCGCCCCGGTGCAGTCCACCGTGCGCGCCATGACCCTGCTGGAAAGCGGCCCGGGCTGGGAGCTGCACGGCAAGACCGGCTGGTGCTTCGACTGCACGCCGGAACTCGGCTGGTGGGTGGGCTGGGTGAAGCGCAACGAGCGGCTCTACGGCTTCGCCCTGAACATCGACATGCCCGGCGGCGAGGCCGACATCGGCAAGCGCGTCGAACTGGGCAAGGCCAGTCTCAAGGCTCTCGGGATACTGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008709","ARO_id":"47501","ARO_name":"OXA-1299","CARD_short_name":"OXA-1299","ARO_description":"OXA-50 family oxacillin-hydrolyzing class D beta-lactamase OXA-1299.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46513":{"category_aro_accession":"3007724","category_aro_cvterm_id":"46513","category_aro_name":"OXA-50-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-50.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8128":{"model_id":"8128","model_name":"OXA-1300","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10955":{"protein_sequence":{"accession":"XGB73518.1","sequence":"MRPLLFSALLLLSGHAQVSEWNDSQAVDKLFGAAGVKGTFVLYDVQRQRYVGHDRERAETRFVPASTYKVANSLIGLSTGAVRSADEVLPYGGKPQRFKAWEHDMSLRDAIKASNVPVYQELARRIGLERMRANVSRLGYGNAEIGQVVDNFWLVGPLKISAMEQTRFLLRLAQGELPFPAPVQSTVRAMTLLESGPGWELHGKTGWCFDCTPELGWWVGWVKRNERLYGFALNIDMPGGEADIGKRVELGKASLKALGILP"},"dna_sequence":{"accession":"PQ203890.1","fmin":"0","fmax":"789","strand":"+","sequence":"ATGCGCCCTCTCCTCTTCAGCGCCCTTCTCCTGCTCTCCGGGCATGCCCAGGTCAGCGAATGGAACGACAGCCAGGCCGTGGACAAGCTATTCGGCGCGGCCGGTGTGAAAGGCACCTTCGTCCTCTACGATGTGCAGCGGCAGCGCTATGTCGGCCATGACCGGGAGCGCGCGGAAACCCGCTTCGTTCCCGCTTCCACCTACAAGGTGGCGAACAGCCTGATCGGCTTATCCACAGGGGCGGTTAGATCCGCCGACGAGGTTCTTCCCTATGGCGGCAAACCCCAGCGCTTCAAGGCCTGGGAGCACGACATGAGCCTGCGCGACGCGATCAAGGCATCGAACGTACCGGTCTACCAGGAACTGGCGCGGCGCATCGGCCTGGAGCGGATGCGCGCCAATGTCTCGCGCCTGGGTTACGGCAACGCGGAAATCGGCCAGGTTGTGGATAACTTCTGGTTGGTGGGACCGCTGAAGATCAGCGCGATGGAACAGACCCGCTTTCTGCTCCGACTGGCGCAGGGAGAATTGCCATTCCCCGCCCCGGTGCAGTCCACCGTGCGCGCCATGACCCTGCTGGAAAGCGGCCCGGGCTGGGAGCTGCACGGCAAGACCGGCTGGTGCTTCGACTGCACGCCGGAACTCGGCTGGTGGGTGGGCTGGGTGAAGCGCAACGAGCGGCTCTACGGCTTCGCCCTGAACATCGACATGCCCGGCGGCGAGGCCGACATCGGCAAGCGCGTCGAACTGGGCAAGGCCAGTCTCAAGGCTCTCGGGATACTGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008710","ARO_id":"47502","ARO_name":"OXA-1300","CARD_short_name":"OXA-1300","ARO_description":"OXA-50 family oxacillin-hydrolyzing class D beta-lactamase OXA-1300.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46513":{"category_aro_accession":"3007724","category_aro_cvterm_id":"46513","category_aro_name":"OXA-50-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-50.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8129":{"model_id":"8129","model_name":"OXA-1301","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10956":{"protein_sequence":{"accession":"XGB73519.1","sequence":"MRPLLFSALLLLSGHTQASEWNDSQAVDKLFGAAGVKGTFVLYDVQRQRYVGHDRERAETRFVPASTYKVANSLIGLSTGAVRSADEVLPYGGKPQRFKAWEHDMSLRDAIKASNVPVYQELARRIGLERMRANVSRLGYGNAEIGQVVDNFWLVGPLKISAMEQTRFLLRLAQGELPFPAPVQSTVRAMTLLESGPGWELHGKTGWCFDCTPELGWWAGWVKRNERLYGFALNIDMPGGEADIGKRVELGKASLKALGILP"},"dna_sequence":{"accession":"PQ203891.1","fmin":"0","fmax":"789","strand":"+","sequence":"ATGCGCCCTCTCCTCTTCAGTGCCCTTCTCCTGCTTTCCGGGCATACCCAGGCCAGCGAATGGAACGACAGCCAGGCCGTGGACAAGCTATTCGGCGCGGCCGGGGTGAAAGGCACCTTCGTCCTCTACGATGTGCAGCGGCAGCGCTATGTTGGCCATGACCGGGAGCGCGCGGAAACCCGCTTCGTTCCCGCTTCCACCTACAAGGTGGCGAACAGCCTGATCGGCTTATCCACAGGGGCGGTTAGATCCGCCGACGAGGTTCTTCCCTATGGCGGCAAGCCCCAGCGCTTCAAGGCCTGGGAGCACGACATGAGCCTGCGCGACGCGATCAAGGCATCGAACGTACCGGTCTACCAGGAACTGGCGCGGCGCATCGGCCTGGAGCGGATGCGCGCCAATGTCTCGCGCCTGGGTTACGGCAACGCGGAAATCGGCCAGGTTGTGGATAACTTCTGGTTGGTGGGACCGCTGAAGATCAGCGCGATGGAACAGACCCGCTTTCTGCTCCGACTGGCGCAGGGAGAATTGCCATTCCCCGCCCCGGTGCAGTCCACCGTGCGCGCCATGACCCTGCTGGAAAGCGGCCCGGGCTGGGAGCTGCACGGCAAGACCGGCTGGTGCTTCGACTGCACGCCGGAACTCGGCTGGTGGGCGGGCTGGGTGAAGCGCAACGAGCGGCTCTACGGCTTCGCCCTGAACATCGACATGCCCGGCGGCGAGGCCGACATCGGCAAGCGCGTCGAACTGGGCAAGGCCAGTCTCAAGGCTCTCGGGATACTGCCCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008711","ARO_id":"47503","ARO_name":"OXA-1301","CARD_short_name":"OXA-1301","ARO_description":"OXA-50 family oxacillin-hydrolyzing class D beta-lactamase OXA-1301.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46513":{"category_aro_accession":"3007724","category_aro_cvterm_id":"46513","category_aro_name":"OXA-50-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-50.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8130":{"model_id":"8130","model_name":"OXA-1302","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10957":{"protein_sequence":{"accession":"XGD01540.1","sequence":"MKTFAAYVIIACLSSTALAGSITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPVSTFKIPTAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGIIGG"},"dna_sequence":{"accession":"PQ218334.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGAAAACATTTGCCGCATATGTAATTATCGCGTGTCTTTCGAGTACGGCATTAGCTGGTTCAATTACAGAAAATACGTCTTGGAACAAAGAGTTCTCTGCCGAAGCCGTCAATGGTGTCTTCGTGCTTTGTAAAAGTAGCAGTAAATCCTGCGCTACCAATGACTTAGCTCGTGCATCAAAGGAATATCTTCCAGTATCAACATTTAAGATCCCCACCGCAATTATCGGCCTAGAAACTGGTGTCATAAAGAATGAGCATCAGGTTTTCAAATGGGACGGAAAGCCAAGAGCCATGAAGCAATGGGAAAGAGACTTGACCTTAAGAGGGGCAATACAAGTTTCAGCTGTTCCCGTATTTCAACAAATCGCCAGAGAAGTTGGCGAAGTAAGAATGCAGAAATACCTTAAAAAATTTTCCTATGGCAACCAGAATATCAGTGGTGGCATTGACAAATTCTGGTTGGAAGGCCAGCTTAGAATTTCCGCAGTTAATCAAGTGGAGTTTCTAGAGTCTCTATATTTAAATAAATTGTCAGCATCTAAAGAAAACCAGCTAATAGTAAAAGAGGCTTTGGTAACGGAGGCGGCACCTGAATATCTAGTGCATTCAAAAACTGGTTTTTCTGGTGTGGGAACTGAGTCAAATCCTGGTGTCGCATGGTGGGTTGGGTGGGTTGAGAAGGAGACAGAGGTTTACTTTTTCGCCTTTAACATGGATATAGACAACGAAAGTAAGTTGCCGCTAAGAAAATCCATTCCCACCAAAATCATGGAAAGTGAGGGCATCATTGGTGGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"47928","NCBI_taxonomy_name":"Pseudomonas soli","NCBI_taxonomy_id":"1306993"}}}},"ARO_accession":"3008712","ARO_id":"47504","ARO_name":"OXA-1302","CARD_short_name":"OXA-1302","ARO_description":"OXA-10 family class D beta-lactamase OXA-1302.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46486":{"category_aro_accession":"3007697","category_aro_cvterm_id":"46486","category_aro_name":"OXA-10-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-10.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8131":{"model_id":"8131","model_name":"OXA-1303","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10958":{"protein_sequence":{"accession":"EMI2597407.1","sequence":"MKKFILPIFSISILVSLSACSSIETKSEDNFHISSQQHEKAIKSYFDEAQTQGVIIIKEGKNLSTYGNALARANKEYVPASTFKMLNALIGLENHKATTNEIFKWDGKKRTYPMWEKDMTLGEAMALSAVPVYQELARRTGLELMQKEVKRVNFGNTNIGTQVDNFWLVGPLKITPVQEVNFADDLAHNRLPFKLETQEEVKKMLLIKEVNGSKIYAKSGWGMGVTPQVGWLTGWVEQANGKKIPFSLNLEMKEGMSGSIRNEITYKSLENLGII"},"dna_sequence":{"accession":"ABNMOX020000018.1","fmin":"1730","fmax":"2558","strand":"-","sequence":"ATGAAAAAATTTATACTTCCTATATTCAGCATTTCTATTCTAGTTTCTCTCAGTGCATGTTCATCTATTGAAACTAAATCTGAAGATAATTTTCATATTTCTTCTCAGCAACATGAAAAAGCTATTAAAAGCTATTTTGATGAAGCTCAAACACAGGGTGTAATTATTATTAAAGAGGGTAAAAATCTTAGCACCTATGGTAATGCTCTTGCACGAGCAAATAAAGAATATGTCCCTGCATCAACATTTAAGATGCTAAATGCTTTAATCGGGCTAGAAAATCATAAAGCAACAACAAATGAGATTTTCAAATGGGATGGTAAAAAAAGAACTTATCCTATGTGGGAGAAAGATATGACTTTAGGTGAGGCAATGGCATTGTCAGCAGTTCCAGTATATCAAGAGCTTGCAAGACGGACTGGCCTAGAGCTAATGCAGAAAGAAGTAAAGCGGGTTAATTTTGGAAATACAAATATTGGAACACAGGTCGATAATTTTTGGTTAGTTGGCCCCCTTAAAATTACACCAGTACAAGAAGTTAATTTTGCCGATGACCTTGCACATAACCGATTACCTTTTAAATTAGAAACTCAAGAAGAAGTTAAAAAAATGCTTCTAATTAAAGAAGTAAATGGTAGTAAGATTTATGCAAAAAGTGGATGGGGAATGGGTGTTACTCCACAGGTAGGTTGGTTGACTGGTTGGGTGGAGCAAGCTAATGGAAAAAAAATCCCCTTTTCGCTCAACTTAGAAATGAAAGAAGGAATGTCTGGTTCTATTCGTAATGAAATTACTTATAAGTCGCTAGAAAATCTTGGAATCATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008713","ARO_id":"47505","ARO_name":"OXA-1303","CARD_short_name":"OXA-1303","ARO_description":"OXA-24 family carbapenem-hydrolyzing class D beta-lactamase OXA-1303.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46500":{"category_aro_accession":"3007711","category_aro_cvterm_id":"46500","category_aro_name":"OXA-24-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-24.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8132":{"model_id":"8132","model_name":"OXA-1304","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10959":{"protein_sequence":{"accession":"XHO32915.1","sequence":"MRVLALSAVFLVASIIGMPAVAKEWQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGQTRDIATWNRDHNLITAMKYSVVAVYQEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISATEQISFLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYSTGIEPKIGWWVGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP"},"dna_sequence":{"accession":"PQ399801.1","fmin":"0","fmax":"798","strand":"+","sequence":"ATGCGTGTATTAGCCTTATCGGCTGTGTTTTTGGTGGCATCGATTATCGGAATGCCTGCGGTAGCAAAGGAATGGCAAGAAAACAAAAGTTGGAATGCTCACTTTACTGAACATAAATCACAGGGCGTAGTTGTGCTCTGGAATGAGAATAAGCAGCAAGGATTTACCAATAATCTTAAACGGGCGAACCAAGCATTTTTACCCGCATCTACCTTTAAAATTCCCAATAGCTTGATCGCCCTCGATTTGGGCGTGGTTAAGGATGAACACCAAGTCTTTAAGTGGGATGGACAGACGCGCGATATCGCCACTTGGAATCGCGATCATAATCTAATCACCGCGATGAAATATTCAGTTGTGGCTGTTTATCAAGAATTTGCCCGCCAAATTGGCGAGGCACGTATGAGCAAGATGCTACATGCTTTCGATTATGGTAATGAGGACATTTCGGGCAATGTAGACAGTTTCTGGCTCGACGGTGGTATTCGAATTTCGGCCACGGAGCAAATCAGCTTTTTAAGAAAGCTGTATCACAATAAGTTACACGTATCGGAGCGCAGCCAGCGTATTGTCAAACAAGCCATGCTGACCGAAGCCAATGGTGACTATATTATTCGGGCTAAAACTGGATACTCGACTGGAATCGAACCTAAGATTGGCTGGTGGGTCGGTTGGGTTGAACTTGATGATAATGTGTGGTTTTTTGCGATGAATATGGATATGCCCACATCGGATGGTTTAGGGCTGCGCCAAGCCATCACAAAAGAAGTGCTCAAACAGGAAAAAATTATTCCCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3008714","ARO_id":"47506","ARO_name":"OXA-1304","CARD_short_name":"OXA-1304","ARO_description":"OXA-48 family class D beta-lactamase OXA-1304.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46510":{"category_aro_accession":"3007721","category_aro_cvterm_id":"46510","category_aro_name":"OXA-48-like beta-lactamase","category_aro_description":"OXA-48-type beta-lactamases are now routinely encountered in bacterial infections caused by carbapenam-resistant Enterobacterales. OXA-48-like proteins confer resistance to penicillin (which is efficiently hydrolyzed) and carbapenam antibiotics (which is more slowly broken down). The spectrum of activity of these variants varies, with some hydrolyzing expanded-spectrum oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8133":{"model_id":"8133","model_name":"OXA-1305","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10960":{"protein_sequence":{"accession":"XHO32901.1","sequence":"MRVLALSAVFLVASIIGMPAVAKEWQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGQTRDIAAWNRDHDLITAMKYSVVPVYQEFARQIGEARISKMLHAFDYGNEDISGNVDSFWLDGGIRISATQQIAFLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYSTRIEPKIGWWVGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP"},"dna_sequence":{"accession":"PQ394558.1","fmin":"0","fmax":"798","strand":"+","sequence":"ATGCGTGTATTAGCCTTATCGGCTGTGTTTTTGGTGGCATCGATTATCGGAATGCCAGCGGTAGCAAAGGAATGGCAAGAAAACAAAAGTTGGAATGCTCACTTTACTGAACATAAATCACAGGGCGTAGTTGTGCTCTGGAATGAGAATAAGCAGCAAGGATTTACCAATAATCTTAAACGGGCGAACCAAGCATTTTTACCCGCATCTACCTTTAAAATTCCCAATAGCTTGATCGCCCTCGATTTGGGCGTGGTTAAGGATGAACACCAAGTCTTTAAGTGGGATGGACAGACGCGTGATATCGCCGCTTGGAATCGTGACCATGACTTAATTACCGCGATGAAGTACTCAGTTGTGCCTGTTTATCAAGAATTTGCCCGCCAAATTGGTGAGGCACGTATAAGTAAAATGCTGCACGCCTTCGATTATGGCAATGAGGATATCTCGGGCAATGTAGACAGTTTTTGGCTCGATGGTGGTATTCGCATTTCGGCTACCCAGCAAATCGCTTTTTTACGCAAGCTGTATCACAACAAGCTGCACGTTTCTGAGCGTAGTCAGCGCATCGTGAAACAAGCCATGCTGACCGAAGCCAATGGCGACTATATTATTCGGGCTAAAACGGGATACTCGACTAGAATCGAACCTAAGATTGGCTGGTGGGTTGGTTGGGTTGAACTTGATGATAATGTGTGGTTTTTTGCGATGAATATGGATATGCCCACATCGGATGGTTTAGGGCTGCGCCAAGCCATCACAAAAGAAGTGCTCAAACAGGAGAAAATTATTCCCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008715","ARO_id":"47507","ARO_name":"OXA-1305","CARD_short_name":"OXA-1305","ARO_description":"OXA-48 family class D beta-lactamase OXA-1305.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46510":{"category_aro_accession":"3007721","category_aro_cvterm_id":"46510","category_aro_name":"OXA-48-like beta-lactamase","category_aro_description":"OXA-48-type beta-lactamases are now routinely encountered in bacterial infections caused by carbapenam-resistant Enterobacterales. OXA-48-like proteins confer resistance to penicillin (which is efficiently hydrolyzed) and carbapenam antibiotics (which is more slowly broken down). The spectrum of activity of these variants varies, with some hydrolyzing expanded-spectrum oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8134":{"model_id":"8134","model_name":"OXA-1306","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10961":{"protein_sequence":{"accession":"XHO32902.1","sequence":"MRVLTLSAVFLVASIIGMPAVAKEWQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGQTRDIATWNRDHNLITAMKYSVVPVYQEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISATEQISFLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYSTRIEPKIGWWVGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP"},"dna_sequence":{"accession":"PQ394559.1","fmin":"0","fmax":"798","strand":"+","sequence":"ATGCGTGTATTAACCTTATCGGCTGTGTTTTTGGTGGCATCGATTATCGGAATGCCTGCGGTAGCAAAGGAATGGCAAGAAAACAAAAGTTGGAATGCTCACTTTACTGAACATAAATCACAGGGCGTAGTTGTGCTCTGGAATGAGAATAAGCAGCAAGGATTTACCAATAATCTTAAACGGGCGAACCAAGCATTTTTACCCGCATCTACCTTTAAAATTCCCAATAGCTTGATCGCCCTCGATTTGGGCGTGGTTAAGGATGAACACCAAGTCTTTAAGTGGGATGGACAGACGCGCGATATCGCCACTTGGAATCGCGATCATAATCTAATCACCGCGATGAAATATTCAGTTGTGCCTGTTTATCAAGAATTTGCCCGCCAAATTGGCGAGGCACGTATGAGCAAGATGCTACATGCTTTCGATTATGGTAATGAGGACATTTCGGGCAATGTAGACAGTTTCTGGCTCGACGGTGGTATTCGAATTTCGGCCACGGAGCAAATCAGCTTTTTAAGAAAGCTGTATCACAATAAGTTACACGTATCGGAGCGCAGCCAGCGTATTGTCAAACAAGCCATGCTGACCGAAGCCAATGGTGACTATATTATTCGGGCTAAAACTGGATACTCGACTAGAATCGAACCTAAGATTGGCTGGTGGGTCGGTTGGGTTGAACTTGATGATAATGTGTGGTTTTTTGCGATGAATATGGATATGCCCACATCGGATGGTTTAGGGCTGCGCCAAGCCATCACAAAAGAAGTGCTCAAACAGGAAAAAATTATTCCCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008716","ARO_id":"47508","ARO_name":"OXA-1306","CARD_short_name":"OXA-1306","ARO_description":"OXA-48 family class D beta-lactamase OXA-1306.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46510":{"category_aro_accession":"3007721","category_aro_cvterm_id":"46510","category_aro_name":"OXA-48-like beta-lactamase","category_aro_description":"OXA-48-type beta-lactamases are now routinely encountered in bacterial infections caused by carbapenam-resistant Enterobacterales. OXA-48-like proteins confer resistance to penicillin (which is efficiently hydrolyzed) and carbapenam antibiotics (which is more slowly broken down). The spectrum of activity of these variants varies, with some hydrolyzing expanded-spectrum oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8135":{"model_id":"8135","model_name":"OXA-1307","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10962":{"protein_sequence":{"accession":"XHO32903.1","sequence":"MRVLALSAVFLVASIIGMPAVAKEWQENKSWNSHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGQTRDIAAWNRDHDLITAMKYSVVPVYQEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISATQQIAFLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYSTSIEPKIGWWVGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP"},"dna_sequence":{"accession":"PQ394560.1","fmin":"0","fmax":"798","strand":"+","sequence":"ATGCGTGTATTAGCCTTATCGGCTGTGTTTTTGGTGGCATCGATTATCGGAATGCCAGCGGTAGCAAAGGAATGGCAAGAAAACAAAAGTTGGAATTCTCACTTTACTGAACATAAATCACAGGGCGTAGTTGTGCTCTGGAATGAGAATAAGCAGCAAGGATTTACCAATAATCTTAAACGGGCGAACCAAGCATTTTTACCCGCATCTACCTTTAAAATTCCCAATAGCTTGATCGCCCTCGATTTGGGCGTGGTTAAGGATGAACACCAAGTCTTTAAGTGGGATGGACAGACGCGTGATATCGCCGCTTGGAATCGTGACCATGACTTAATTACCGCGATGAAGTACTCAGTTGTGCCTGTTTATCAAGAATTTGCCCGCCAAATTGGTGAGGCACGTATGAGTAAAATGCTGCACGCCTTCGATTATGGCAATGAGGATATCTCGGGCAATGTAGACAGTTTTTGGCTCGATGGTGGTATTCGCATTTCGGCTACCCAGCAAATCGCTTTTTTACGCAAGCTGTATCACAACAAGCTGCACGTTTCTGAGCGTAGTCAGCGCATCGTGAAACAAGCCATGCTGACCGAAGCCAATGGCGACTATATTATTCGGGCTAAAACGGGATACTCGACTAGTATCGAACCTAAGATTGGCTGGTGGGTTGGTTGGGTTGAACTTGATGATAATGTGTGGTTTTTTGCGATGAATATGGATATGCCCACATCGGATGGTTTAGGGCTGCGCCAAGCCATCACAAAAGAAGTGCTCAAACAGGAGAAAATTATTCCCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008717","ARO_id":"47509","ARO_name":"OXA-1307","CARD_short_name":"OXA-1307","ARO_description":"OXA-48 family class D beta-lactamase OXA-1307.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46510":{"category_aro_accession":"3007721","category_aro_cvterm_id":"46510","category_aro_name":"OXA-48-like beta-lactamase","category_aro_description":"OXA-48-type beta-lactamases are now routinely encountered in bacterial infections caused by carbapenam-resistant Enterobacterales. OXA-48-like proteins confer resistance to penicillin (which is efficiently hydrolyzed) and carbapenam antibiotics (which is more slowly broken down). The spectrum of activity of these variants varies, with some hydrolyzing expanded-spectrum oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8136":{"model_id":"8136","model_name":"OXA-1308","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10963":{"protein_sequence":{"accession":"XHO32904.1","sequence":"MRVLALSAVFLVASIIGMPAVAKEWQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQVFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGQTRDIAAWNRDHDLITAMKYSVVPVYQEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISATQQIAFLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYSTRIEPKIGWWVGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP"},"dna_sequence":{"accession":"PQ394561.1","fmin":"0","fmax":"798","strand":"+","sequence":"ATGCGTGTATTAGCCTTATCGGCTGTGTTTTTGGTGGCATCGATTATCGGAATGCCAGCGGTAGCAAAGGAATGGCAAGAAAACAAAAGTTGGAATGCTCACTTTACTGAACATAAATCACAGGGCGTAGTTGTGCTCTGGAATGAGAATAAGCAGCAAGGATTTACCAATAATCTTAAACGGGCGAACCAAGTATTTTTACCCGCATCTACCTTTAAAATTCCCAATAGCTTGATCGCCCTCGATTTGGGCGTGGTTAAGGATGAACACCAAGTCTTTAAGTGGGATGGACAGACGCGTGATATCGCCGCTTGGAATCGTGACCATGACTTAATTACCGCGATGAAGTACTCAGTTGTGCCTGTTTATCAAGAATTTGCCCGCCAAATTGGTGAGGCACGTATGAGTAAAATGCTGCACGCCTTCGATTATGGCAATGAGGATATCTCGGGCAATGTAGACAGTTTTTGGCTCGATGGTGGTATTCGCATTTCGGCTACCCAGCAAATCGCTTTTTTACGCAAGCTGTATCACAACAAGCTGCACGTTTCTGAGCGTAGTCAGCGCATCGTGAAACAAGCCATGCTGACCGAAGCCAATGGCGACTATATTATTCGGGCTAAAACGGGATACTCGACTAGAATCGAACCTAAGATTGGCTGGTGGGTTGGTTGGGTTGAACTTGATGATAATGTGTGGTTTTTTGCGATGAATATGGATATGCCCACATCGGATGGTTTAGGGCTGCGCCAAGCCATCACAAAAGAAGTGCTCAAACAGGAGAAAATTATTCCCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008718","ARO_id":"47510","ARO_name":"OXA-1308","CARD_short_name":"OXA-1308","ARO_description":"OXA-48 family class D beta-lactamase OXA-1308.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46510":{"category_aro_accession":"3007721","category_aro_cvterm_id":"46510","category_aro_name":"OXA-48-like beta-lactamase","category_aro_description":"OXA-48-type beta-lactamases are now routinely encountered in bacterial infections caused by carbapenam-resistant Enterobacterales. OXA-48-like proteins confer resistance to penicillin (which is efficiently hydrolyzed) and carbapenam antibiotics (which is more slowly broken down). The spectrum of activity of these variants varies, with some hydrolyzing expanded-spectrum oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8137":{"model_id":"8137","model_name":"OXA-1309","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10964":{"protein_sequence":{"accession":"XHO32905.1","sequence":"MRVLALSAVFLVASIIGMPAVAKEWQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNIKRANQAFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGQTRDIAAWNRDHDLITAMKYSVVPVYQEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISATQQIAFLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYSTSIEPKIGWWVGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP"},"dna_sequence":{"accession":"PQ394562.1","fmin":"0","fmax":"798","strand":"+","sequence":"ATGCGTGTATTAGCCTTATCGGCTGTGTTTTTGGTGGCATCGATTATCGGAATGCCAGCGGTAGCAAAGGAATGGCAAGAAAACAAAAGTTGGAATGCTCACTTTACTGAACATAAATCACAGGGCGTAGTTGTGCTCTGGAATGAGAATAAGCAGCAAGGATTTACCAATAATATTAAACGGGCGAACCAAGCATTTTTACCCGCATCTACCTTTAAAATTCCCAATAGCTTGATCGCCCTCGATTTGGGCGTGGTTAAGGATGAACACCAAGTCTTTAAGTGGGATGGACAGACGCGTGATATCGCCGCTTGGAATCGTGACCATGACTTAATTACCGCGATGAAGTACTCAGTTGTGCCTGTTTATCAAGAATTTGCCCGCCAAATTGGTGAGGCACGTATGAGTAAAATGCTGCACGCCTTCGATTATGGCAATGAGGATATCTCGGGCAATGTAGACAGTTTTTGGCTCGATGGTGGTATTCGCATTTCGGCTACCCAGCAAATCGCTTTTTTACGCAAGCTGTATCACAACAAGCTGCACGTTTCTGAGCGTAGTCAGCGCATCGTGAAACAAGCCATGCTGACCGAAGCCAATGGCGACTATATTATTCGGGCTAAAACGGGATACTCGACTAGTATCGAACCTAAGATTGGCTGGTGGGTTGGTTGGGTTGAACTTGATGATAATGTGTGGTTTTTTGCGATGAATATGGATATGCCCACATCGGATGGTTTAGGGCTGCGCCAAGCCATCACAAAAGAAGTGCTCAAACAGGAGAAAATTATTCCCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008719","ARO_id":"47511","ARO_name":"OXA-1309","CARD_short_name":"OXA-1309","ARO_description":"OXA-48 family class D beta-lactamase OXA-1309.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46510":{"category_aro_accession":"3007721","category_aro_cvterm_id":"46510","category_aro_name":"OXA-48-like beta-lactamase","category_aro_description":"OXA-48-type beta-lactamases are now routinely encountered in bacterial infections caused by carbapenam-resistant Enterobacterales. OXA-48-like proteins confer resistance to penicillin (which is efficiently hydrolyzed) and carbapenam antibiotics (which is more slowly broken down). The spectrum of activity of these variants varies, with some hydrolyzing expanded-spectrum oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8138":{"model_id":"8138","model_name":"OXA-725","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10965":{"protein_sequence":{"accession":"CAA56560.1","sequence":"MSRLLLSSLLATGLLAALPASAASGCFLYADGNGQTLSSEGDCSSQLPPASTFKIPLALMGYDSGFLVDEEHPALPFKPGYDDWLPAWRETTTPRRWETYSVVWFSQQITEWLGMERFQQYVDRFDYGNRDLSGNPGKHDGLTQAWLSSSLAISPEEQARFLGKMVSGKLPVSAQTLQYTANILKVSEIDGWQIHGKTGMGYPKKLDGSLNRDQQIGWFVGWASKPGKQLIFVHTVVQKPGKQFASLKAKEEVLAALPAKLKTL"},"dna_sequence":{"accession":"X80276.1","fmin":"0","fmax":"795","strand":"+","sequence":"ATGTCCCGCCTGCTTCTCTCCAGCCTGCTGGCCACCGGTCTGCTCGCAGCCCTGCCTGCCTCCGCCGCCAGCGGCTGCTTTCTCTATGCTGACGGCAACGGCCAGACTCTCTCCAGCGAAGGGGACTGCTCCAGCCAGCTACCGCCCGCCTCCACCTTCAAGATCCCGCTGGCGCTGATGGGCTATGACAGCGGCTTTCTGGTAGATGAAGAGCATCCGGCACTGCCCTTCAAACCGGGTTACGACGACTGGCTGCCCGCCTGGCGCGAAACCACTACCCCGCGCCGCTGGGAAACCTACTCGGTGGTCTGGTTCTCCCAGCAGATCACCGAATGGCTGGGGATGGAGCGTTTCCAGCAGTATGTCGACCGCTTCGACTACGGCAACCGGGATCTCTCCGGCAATCCGGGCAAGCATGACGGTCTGACTCAGGCCTGGCTCAGCTCCAGCCTCGCCATCAGCCCGGAGGAGCAGGCCCGCTTCCTCGGCAAAATGGTGAGCGGCAAGCTGCCTGTTTCGGCGCAGACCCTGCAGTACACTGCCAATATCCTCAAGGTGAGCGAGATCGACGGCTGGCAGATCCACGGCAAGACCGGCATGGGCTACCCGAAGAAGCTGGATGGCAGCCTCAACCGCGATCAGCAGATCGGCTGGTTCGTCGGCTGGGCCAGCAAACCGGGCAAGCAGCTGATCTTCGTCCATACCGTGGTGCAAAAGCCCGGCAAGCAGTTCGCCTCCCTCAAAGCGAAAGAAGAGGTGCTGGCCGCCCTGCCGGCCAAACTGAAAACCCTGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36957","NCBI_taxonomy_name":"Aeromonas sobria","NCBI_taxonomy_id":"646"}}}},"ARO_accession":"3008720","ARO_id":"47512","ARO_name":"OXA-725","CARD_short_name":"OXA-725","ARO_description":"OXA-12 family class D beta-lactamase AmpS\/OXA-725.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46488":{"category_aro_accession":"3007699","category_aro_cvterm_id":"46488","category_aro_name":"OXA-12-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-12.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8139":{"model_id":"8139","model_name":"OXA-790","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10966":{"protein_sequence":{"accession":"QBC36167.1","sequence":"MTVRRLSCALGAALSLCALGGGPVQAAVLCTVVADAADGRILFQQGTQQACAERYTPASTFKLAIALMGADAGILQGPHEPVWNYQPAYPDWGGDAWRQPTDPARWIKYSVVWYSQLTAKALGQDRFQRYTSAFGYGNADVSGEPGKHNGTDGAWIISSLRISPLEQLAFLRKLVNRQLPVKAAAYELAENLFEVGQADGWRLYGRTGTGSPGSNGVYTAANAYGWFVGWARKDGRQLVYARLLQDERATRPNAGLRARDELVRDWPAMAGAWRP"},"dna_sequence":{"accession":"MK388911.1","fmin":"0","fmax":"828","strand":"+","sequence":"ATGACCGTTCGACGCCTTTCGTGCGCCCTTGGCGCAGCCCTTTCCCTGTGCGCGCTGGGCGGCGGCCCCGTCCAGGCCGCCGTCCTGTGCACCGTGGTGGCCGACGCCGCCGACGGCCGCATCCTGTTCCAGCAAGGCACGCAGCAGGCCTGCGCCGAGCGCTACACGCCGGCCTCGACCTTCAAGCTGGCCATCGCCCTGATGGGCGCCGACGCCGGCATCCTGCAAGGCCCGCACGAGCCGGTCTGGAACTACCAGCCCGCCTATCCCGACTGGGGCGGCGACGCCTGGCGCCAGCCCACCGATCCGGCGCGCTGGATCAAGTATTCGGTGGTCTGGTATTCACAGCTGACGGCCAAGGCGCTGGGACAGGACCGCTTCCAGCGCTACACCAGCGCGTTCGGCTACGGCAATGCGGACGTCTCGGGCGAGCCCGGCAAGCACAACGGCACCGACGGCGCGTGGATCATCTCGTCGCTGCGCATTTCGCCGCTGGAACAACTGGCTTTCCTGCGCAAGCTGGTGAATCGGCAATTGCCGGTCAAGGCCGCCGCCTATGAGCTGGCCGAAAACCTCTTCGAGGTGGGCCAGGCCGATGGCTGGCGCCTGTATGGCAGAACCGGCACCGGGTCGCCCGGCAGCAACGGCGTCTACACGGCGGCCAATGCCTACGGCTGGTTCGTCGGCTGGGCGCGCAAGGATGGCCGCCAGCTGGTGTACGCCCGCCTGCTGCAGGATGAGCGCGCCACCCGGCCCAACGCCGGCCTGCGCGCCCGCGACGAGCTGGTGCGCGACTGGCCGGCCATGGCCGGCGCGTGGCGCCCGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36941","NCBI_taxonomy_name":"Achromobacter xylosoxidans","NCBI_taxonomy_id":"85698"}}}},"ARO_accession":"3008721","ARO_id":"47513","ARO_name":"OXA-790","CARD_short_name":"OXA-790","ARO_description":"OXA-114 family class D beta-lactamase OXA-790.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46487":{"category_aro_accession":"3007698","category_aro_cvterm_id":"46487","category_aro_name":"OXA-114-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-114.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8140":{"model_id":"8140","model_name":"OXA-791","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10967":{"protein_sequence":{"accession":"QBC36168.1","sequence":"MTVRRLSCALGAALSLSALGGGPVQAAVLCTVVADAADGRILFQQGTQQACAERYTPASTFKLAIALMGADAGILQGPHEPVWNYQPAYPDWGGDAWRQPTDPARWIKYSVVWYSQLTAKALGQDRFQRYTSAFGYGNADVSGEPGKHNGTDGAWIISSLRISPLEQLAFLRKVVNRQLPVKAAAYELADNLFEVGQADGWRLYGRTGTGSPGSNGVYTAANAYGWFVGWARKDGRQLVYARLLQDERATQPNAGLRARDELVRDWPAMAGAWRP"},"dna_sequence":{"accession":"MK388912.1","fmin":"0","fmax":"828","strand":"+","sequence":"ATGACCGTTCGACGCCTTTCGTGCGCCCTTGGCGCAGCCCTTTCCCTGTCCGCGCTGGGCGGCGGCCCCGTCCAGGCCGCCGTCCTGTGCACCGTGGTGGCCGACGCCGCCGACGGCCGCATCCTGTTTCAGCAAGGCACGCAGCAGGCCTGCGCCGAGCGCTACACGCCGGCCTCGACCTTCAAGCTGGCCATCGCCCTGATGGGCGCCGACGCCGGCATCCTGCAAGGCCCGCACGAGCCGGTCTGGAACTACCAGCCCGCCTATCCCGACTGGGGCGGCGACGCCTGGCGCCAGCCCACCGATCCGGCGCGCTGGATCAAGTATTCGGTGGTCTGGTATTCACAGCTGACGGCCAAGGCGCTGGGACAGGACCGCTTCCAGCGCTACACCAGCGCGTTCGGCTACGGCAATGCGGACGTCTCCGGCGAGCCCGGCAAGCACAACGGCACCGACGGCGCGTGGATCATTTCGTCGCTGCGCATTTCGCCGCTGGAACAACTGGCTTTCCTGCGCAAGGTGGTGAACCGGCAATTGCCGGTCAAGGCCGCCGCCTATGAGCTGGCGGACAACCTCTTCGAGGTGGGCCAGGCCGATGGCTGGCGCCTGTATGGCAGGACCGGCACCGGGTCGCCCGGCAGCAACGGCGTCTACACGGCGGCCAATGCCTACGGCTGGTTCGTCGGCTGGGCGCGCAAGGATGGCCGCCAACTGGTGTACGCCCGCCTGCTGCAGGACGAGCGCGCCACCCAGCCCAACGCCGGCCTGCGCGCCCGCGACGAGCTGGTGCGCGACTGGCCGGCCATGGCCGGCGCGTGGCGCCCGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36941","NCBI_taxonomy_name":"Achromobacter xylosoxidans","NCBI_taxonomy_id":"85698"}}}},"ARO_accession":"3008722","ARO_id":"47514","ARO_name":"OXA-791","CARD_short_name":"OXA-791","ARO_description":"OXA-114 family class D beta-lactamase OXA-791.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46487":{"category_aro_accession":"3007698","category_aro_cvterm_id":"46487","category_aro_name":"OXA-114-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-114.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8141":{"model_id":"8141","model_name":"OXA-933","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10968":{"protein_sequence":{"accession":"QOI60719.1","sequence":"MRVLALSAVFLVASIIGMPAVAKEWQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGQTRDIATWNRDHNLITAMKYSVVPVYQEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLNGGIRISATEQISFLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYSTRIEPKIGWWVGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP"},"dna_sequence":{"accession":"MW073108.1","fmin":"0","fmax":"798","strand":"+","sequence":"ATGCGTGTATTAGCCTTATCGGCTGTGTTTTTGGTGGCATCGATTATCGGAATGCCTGCGGTAGCAAAGGAATGGCAAGAAAACAAAAGTTGGAATGCTCACTTTACTGAACATAAATCACAGGGCGTAGTTGTGCTCTGGAATGAGAATAAGCAGCAAGGATTTACCAATAATCTTAAACGGGCGAACCAAGCATTTTTACCCGCATCTACCTTTAAAATTCCCAATAGCTTGATCGCCCTCGATTTGGGCGTGGTTAAGGATGAACACCAAGTCTTTAAGTGGGATGGACAGACGCGCGATATCGCCACTTGGAATCGCGATCATAATCTAATCACCGCGATGAAATATTCAGTTGTGCCTGTTTATCAAGAATTTGCCCGCCAAATTGGCGAGGCACGTATGAGCAAGATGCTACATGCTTTCGATTATGGTAATGAGGACATTTCGGGCAATGTAGACAGTTTCTGGCTCAACGGTGGTATTCGAATTTCGGCCACGGAGCAAATCAGCTTTTTAAGAAAGCTGTATCACAATAAGTTACACGTATCGGAGCGCAGCCAGCGTATTGTCAAACAAGCCATGCTGACCGAAGCCAATGGTGACTATATTATTCGGGCTAAAACTGGATACTCGACTAGAATCGAACCTAAGATTGGCTGGTGGGTCGGTTGGGTTGAACTTGATGATAATGTGTGGTTTTTTGCGATGAATATGGATATGCCCACATCGGATGGTTTAGGGCTGCGCCAAGCCATCACAAAAGAAGTGCTCAAACAGGAAAAAATTATTCCCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3008723","ARO_id":"47515","ARO_name":"OXA-933","CARD_short_name":"OXA-933","ARO_description":"OXA-48 family class D beta-lactamase OXA-933.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46510":{"category_aro_accession":"3007721","category_aro_cvterm_id":"46510","category_aro_name":"OXA-48-like beta-lactamase","category_aro_description":"OXA-48-type beta-lactamases are now routinely encountered in bacterial infections caused by carbapenam-resistant Enterobacterales. OXA-48-like proteins confer resistance to penicillin (which is efficiently hydrolyzed) and carbapenam antibiotics (which is more slowly broken down). The spectrum of activity of these variants varies, with some hydrolyzing expanded-spectrum oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8142":{"model_id":"8142","model_name":"OXA-934","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10969":{"protein_sequence":{"accession":"QOI60720.1","sequence":"MRVLALSAVFLVASIIGMPAVAKEWQENKSWNAYFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGQTRDIATWNRDHNLITAMKYSVVPVYQEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISATEQISFLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYSTRIEPKIGWWVGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP"},"dna_sequence":{"accession":"MW073109.1","fmin":"0","fmax":"798","strand":"+","sequence":"ATGCGTGTATTAGCCTTATCGGCTGTGTTTTTGGTGGCATCGATTATCGGAATGCCTGCGGTAGCAAAGGAATGGCAAGAAAACAAAAGTTGGAATGCTTACTTTACTGAACATAAATCACAGGGCGTAGTTGTGCTCTGGAATGAGAATAAGCAGCAAGGATTTACCAATAATCTTAAACGGGCGAACCAAGCATTTTTACCCGCATCTACCTTTAAAATTCCCAATAGCTTGATCGCCCTCGATTTGGGCGTGGTTAAGGATGAACACCAAGTCTTTAAGTGGGATGGACAGACGCGCGATATCGCCACTTGGAATCGCGATCATAATCTAATCACCGCGATGAAATATTCAGTTGTGCCTGTTTATCAAGAATTTGCCCGCCAAATTGGCGAGGCACGTATGAGCAAGATGCTACATGCTTTCGATTATGGTAATGAGGACATTTCGGGCAATGTAGACAGTTTCTGGCTCGACGGTGGTATTCGAATTTCGGCCACGGAGCAAATCAGCTTTTTAAGAAAGCTGTATCACAATAAGTTACACGTATCGGAGCGCAGCCAGCGTATTGTCAAACAAGCCATGCTGACCGAAGCCAATGGTGACTATATTATTCGGGCTAAAACTGGATACTCGACTAGAATCGAACCTAAGATTGGCTGGTGGGTCGGTTGGGTTGAACTTGATGATAATGTGTGGTTTTTTGCGATGAATATGGATATGCCCACATCGGATGGTTTAGGGCTGCGCCAAGCCATCACAAAAGAAGTGCTCAAACAGGAAAAAATTATTCCCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36770","NCBI_taxonomy_name":"Klebsiella aerogenes","NCBI_taxonomy_id":"548"}}}},"ARO_accession":"3008724","ARO_id":"47516","ARO_name":"OXA-934","CARD_short_name":"OXA-934","ARO_description":"OXA-48 family class D beta-lactamase OXA-934.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46510":{"category_aro_accession":"3007721","category_aro_cvterm_id":"46510","category_aro_name":"OXA-48-like beta-lactamase","category_aro_description":"OXA-48-type beta-lactamases are now routinely encountered in bacterial infections caused by carbapenam-resistant Enterobacterales. OXA-48-like proteins confer resistance to penicillin (which is efficiently hydrolyzed) and carbapenam antibiotics (which is more slowly broken down). The spectrum of activity of these variants varies, with some hydrolyzing expanded-spectrum oxyimino-cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8143":{"model_id":"8143","model_name":"OXA-936","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10970":{"protein_sequence":{"accession":"NAR97865.1","sequence":"MKLSKLYTLTVLIGFGLSGVACQHIHTPVLFNQIENDQTKQIASLFENVQTTGVLITFDGQAYKAYGNDLNRAKTAYIPASTFKILNALIGIEHDKTSPNEVFKWDGQKRAFESWEKDLTLAEAMQASAVPVYQALAQRIGLDLMAKEVKRIGFGNTRIGTQVDNFWLIGPLKITPIEEAQFAYRLAKQELPFTPKTQQQVIDMLLVDEIRGTKVYAKSGWGMDITPQVGWWTGWIEDPNGKVIAFSLNMEMNQPAHAAARKEIVYQALTQLKLL"},"dna_sequence":{"accession":"WTTR01000009.1","fmin":"43413","fmax":"44241","strand":"-","sequence":"ATGAAGCTATCAAAATTATACACCCTCACTGTGCTCATAGGATTTGGATTAAGCGGTGTCGCCTGCCAGCATATCCATACTCCAGTCTTATTCAATCAAATTGAAAACGATCAAACAAAGCAGATCGCTTCCTTGTTTGAGAATGTTCAAACAACAGGTGTTCTAATTACCTTTGATGGACAGGCGTATAAAGCATACGGTAATGATCTGAATCGTGCCAAAACTGCGTATATCCCAGCATCTACTTTCAAAATATTAAATGCTTTGATTGGCATTGAACATGATAAAACTTCACCAAATGAAGTATTTAAGTGGGATGGTCAGAAGCGTGCTTTTGAAAGTTGGGAAAAAGATCTGACTTTAGCTGAAGCCATGCAAGCTTCTGCTGTACCTGTTTATCAAGCGCTTGCCCAGAGAATCGGATTGGATTTGATGGCAAAGGAAGTCAAAAGAATCGGCTTCGGTAATACACGCATCGGAACACAAGTTGATAACTTCTGGCTCATTGGACCTTTAAAAATCACGCCAATCGAAGAAGCTCAATTTGCTTACAGGCTTGCGAAACAGGAGTTACCGTTTACCCCAAAAACACAACAGCAAGTGATTGATATGCTGCTGGTGGATGAAATACGGGGAACTAAAGTTTACGCCAAAAGTGGTTGGGGAATGGATATTACTCCGCAAGTAGGATGGTGGACTGGATGGATTGAAGATCCGAACGGAAAAGTGATCGCTTTTTCTCTCAATATGGAAATGAATCAACCTGCGCATGCAGCTGCACGTAAAGAAATTGTTTATCAGGCACTTACGCAATTGAAATTGTTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36938","NCBI_taxonomy_name":"Acinetobacter haemolyticus","NCBI_taxonomy_id":"29430"}}}},"ARO_accession":"3008725","ARO_id":"47517","ARO_name":"OXA-936","CARD_short_name":"OXA-936","ARO_description":"OXA-214 family carbapenem-hydrolyzing class D beta-lactamase OXA-936.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46496":{"category_aro_accession":"3007707","category_aro_cvterm_id":"46496","category_aro_name":"OXA-214-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-214.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8144":{"model_id":"8144","model_name":"OXA-944","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10971":{"protein_sequence":{"accession":"QQP64032.1","sequence":"MSNNRFKFKIKSSVLIILSSLAFSGCVSKLNLHDPASSQRTSEIPLLFNYAQTQAVFVTYDGTQFKRYGNDLNRAKTAYIPASTFKMLNALIGLQHAKATNTEVFKWNGEKRSFPAWEKDMTLAEAMQASAVPVYQELARRIGLDLMSKEVKRVGFGNTQIGQQVDNFWLVGPLKITPEQEAKFAYQLAKKTLPFDDAVQQQVKDMLYIERRGDSKLYAKSGWGMDVEPQVGWYTGWIEQPNGQITAFALNMHMQTGDDPAERKQLTLSILDKLGLFFYLR"},"dna_sequence":{"accession":"MW474777.1","fmin":"0","fmax":"846","strand":"-","sequence":"ATGAGTAATAACCGATTTAAATTTAAAATAAAAAGCAGTGTATTGATCATCCTGAGTAGTTTGGCTTTTTCAGGTTGTGTTTCGAAGCTTAATTTGCATGATCCAGCTTCATCACAAAGAACAAGTGAAATCCCATTGCTGTTTAATTATGCGCAAACTCAAGCCGTCTTTGTGACTTATGATGGAACTCAATTTAAACGTTATGGGAATGATTTAAATAGAGCCAAGACTGCGTATATTCCAGCCTCTACTTTTAAAATGTTGAATGCCTTAATTGGTTTGCAACATGCGAAAGCGACGAATACAGAAGTATTTAAGTGGAATGGTGAAAAAAGATCTTTTCCTGCATGGGAAAAAGATATGACCTTGGCAGAAGCAATGCAGGCTTCAGCCGTACCTGTATATCAGGAGCTAGCACGGCGTATTGGCTTGGATTTGATGAGTAAAGAAGTCAAGCGTGTTGGTTTTGGCAATACACAAATTGGTCAACAGGTGGATAATTTCTGGTTGGTTGGTCCATTGAAAATCACCCCAGAGCAAGAAGCTAAATTTGCTTATCAATTGGCAAAGAAAACATTGCCTTTTGATGATGCTGTACAGCAACAAGTTAAAGATATGCTCTATATCGAAAGACGGGGTGATTCCAAGCTTTATGCCAAAAGTGGTTGGGGAATGGATGTGGAGCCACAAGTGGGTTGGTATACAGGATGGATAGAACAGCCGAATGGTCAGATCACCGCTTTTGCTTTAAATATGCACATGCAGACAGGAGATGATCCTGCCGAACGTAAGCAACTGACATTAAGTATCTTAGATAAATTAGGCTTATTCTTTTATTTGAGATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42558","NCBI_taxonomy_name":"Acinetobacter guillouiae","NCBI_taxonomy_id":"106649"}}}},"ARO_accession":"3008726","ARO_id":"47518","ARO_name":"OXA-944","CARD_short_name":"OXA-944","ARO_description":"OXA-274 family carbapenem-hydrolyzing class D beta-lactamase OXA-944.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46502":{"category_aro_accession":"3007713","category_aro_cvterm_id":"46502","category_aro_name":"OXA-274-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-274.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8145":{"model_id":"8145","model_name":"OXA-950","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10972":{"protein_sequence":{"accession":"BCT36858.1","sequence":"MSRLLLSGLLGAGLLFSLPASAATGCFLYADGNGQTLSSEGDCSSQLPPASTFKIPLALMGYDSGFLVDEEHPALPFKPGYDDWLPAWRETTTPRRWETYSVVWFSQQITEWLGMERFQQYVDRFDYGNRDLSGNPGKHDGLTQAWLSASLAISPQEQARFLGKMVSGKLPVSAQTLQYTANILKVSEIDGWQIHGKTGMGYPKKLDGSLNREQQIGWFVGWASKPGKQLIFVHTVVQKPGKQFASLKAKEEVLAALPAKLKTL"},"dna_sequence":{"accession":"LC610783.1","fmin":"0","fmax":"795","strand":"+","sequence":"ATGTCCCGCCTTCTGTTATCCGGCCTGCTCGGCGCAGGCCTGCTGTTCTCACTGCCGGCCAGCGCCGCCACCGGCTGCTTTCTCTATGCCGACGGCAACGGCCAGACCCTCTCCAGCGAAGGGGATTGCTCAAGCCAGCTACCACCCGCGTCCACCTTCAAGATCCCGCTGGCGCTGATGGGCTACGACAGCGGCTTTCTGGTGGACGAAGAGCACCCGGCACTGCCTTTCAAGCCGGGTTACGACGACTGGCTGCCCGCCTGGCGGGAAACAACCACCCCGCGCCGCTGGGAAACCTACTCGGTGGTCTGGTTCTCCCAGCAGATCACCGAATGGCTGGGGATGGAGCGCTTCCAGCAGTACGTCGACCGTTTTGACTACGGCAACCGGGATCTCTCCGGCAATCCAGGCAAGCACGACGGCCTGACCCAGGCCTGGCTCAGTGCCAGCCTCGCCATCAGCCCACAGGAGCAGGCCCGCTTCCTCGGCAAGATGGTGAGCGGCAAGCTGCCGGTGTCGGCGCAGACCCTGCAGTACACCGCCAACATCCTCAAGGTGAGCGAGATCGACGGCTGGCAGATCCACGGCAAGACCGGCATGGGCTACCCGAAGAAGCTGGATGGCAGCCTCAACCGGGAGCAGCAGATCGGCTGGTTCGTCGGCTGGGCCAGCAAGCCGGGCAAGCAGCTCATCTTCGTCCATACCGTGGTGCAGAAACCCGGCAAACAGTTCGCCTCGCTCAAGGCCAAGGAAGAGGTGCTGGCCGCCCTGCCGGCCAAACTGAAAACCCTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36810","NCBI_taxonomy_name":"Aeromonas hydrophila","NCBI_taxonomy_id":"644"}}}},"ARO_accession":"3008727","ARO_id":"47519","ARO_name":"OXA-950","CARD_short_name":"OXA-950","ARO_description":"OXA-12 family class D beta-lactamase OXA-950.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46488":{"category_aro_accession":"3007699","category_aro_cvterm_id":"46488","category_aro_name":"OXA-12-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-12.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8146":{"model_id":"8146","model_name":"OXA-951","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10973":{"protein_sequence":{"accession":"BCT36861.1","sequence":"MSRLLLSGLLGAGLLFSLPASAATGCFLYADGNGQTLSSEGDCSSQLPPASTFKIPLALMGYDSGFLVDEEHPALPFKPGYDDWLPAWRETTTPRRWETYSVVWFSQQITEWLGMDRFQQYVDRFDYGNRDLSGNPGKHDGLTQAWLSSSLAISPQEQARFLGKMVSGKLPVSAQTLQYTANILKVSEIDGWQIHGKTGMGYPKKLDGSLNRDQQIGWFVGWASKPGKQLIFVHTVVQKPGKQFASLKAKEEVLAALPAKLKTL"},"dna_sequence":{"accession":"LC610789.1","fmin":"0","fmax":"795","strand":"+","sequence":"ATGTCCCGCCTTCTGTTATCCGGCCTGCTCGGCGCAGGCCTGCTCTTTTCGCTGCCGGCCAGCGCCGCCACCGGCTGCTTTCTCTATGCCGACGGCAACGGCCAGACCCTCTCCAGCGAAGGGGATTGTTCAAGCCAGCTGCCACCCGCGTCCACCTTCAAAATCCCGCTGGCGCTGATGGGTTATGACAGCGGCTTTCTGGTAGACGAAGAGCACCCGGCACTGCCCTTCAAGCCGGGTTACGACGACTGGCTGCCCGCCTGGCGGGAGACCACCACCCCGCGCCGCTGGGAAACCTACTCGGTGGTCTGGTTCTCCCAGCAGATCACCGAATGGCTGGGGATGGATCGCTTCCAGCAGTACGTCGATCGTTTCGACTACGGCAACCGGGATCTTTCCGGCAACCCCGGCAAACACGACGGTCTGACCCAGGCCTGGCTCAGTTCCAGCCTCGCCATCAGTCCACAGGAGCAGGCCCGCTTCCTCGGCAAGATGGTGAGCGGCAAGCTGCCGGTGTCGGCGCAGACCCTGCAGTACACCGCCAACATCCTCAAGGTGAGCGAGATCGACGGCTGGCAAATCCACGGCAAGACCGGCATGGGTTACCCGAAGAAGCTGGATGGCAGCCTCAACCGGGATCAGCAGATCGGCTGGTTCGTCGGCTGGGCCAGCAAACCGGGCAAGCAGCTCATCTTCGTCCATACCGTGGTGCAAAAACCCGGCAAGCAGTTCGCCTCCCTCAAGGCCAAGGAAGAGGTGCTGGCCGCCCTGCCGGCCAAACTGAAAACCCTGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39651","NCBI_taxonomy_name":"Aeromonas dhakensis","NCBI_taxonomy_id":"196024"}}}},"ARO_accession":"3008728","ARO_id":"47520","ARO_name":"OXA-951","CARD_short_name":"OXA-951","ARO_description":"OXA-12 family class D beta-lactamase OXA-951.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46488":{"category_aro_accession":"3007699","category_aro_cvterm_id":"46488","category_aro_name":"OXA-12-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-12.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8147":{"model_id":"8147","model_name":"OXA-952","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10974":{"protein_sequence":{"accession":"QTG68655.1","sequence":"MKFKMKGLFCVILSSLAFSGCVYDSKLQRPVISERETEIPLLFNQAQTQAVFVTYDGIHLKSYGNDLSRAKTEYIPASTFKMLNALIGLQNAKATNTEVFHWNGEKRAFSAWEKDMTLAEAMQASAVPVYQELARRIGLELMREEVKRVGFGNAEIGQQVDNFWLVGPLKISPEQEVKFAYQLAMKQLPFDRNVQQQVKDMLYIERRGDSKLYAKSGWGMDVEPQVGWYTGWVEQPNGKVTAFALNMKMQAGDDPAERKQLTLSILDKLGLFFYLR"},"dna_sequence":{"accession":"MW805229.1","fmin":"0","fmax":"831","strand":"+","sequence":"ATGAAGTTTAAAATGAAAGGTTTATTTTGTGTCATCCTCAGTAGTTTGGCATTTTCAGGTTGTGTTTATGATTCAAAACTACAACGCCCAGTCATATCAGAGCGAGAAACTGAGATTCCTTTATTATTTAATCAAGCACAGACTCAAGCTGTGTTTGTTACTTATGATGGGATTCATCTAAAAAGTTATGGTAATGATCTAAGCCGAGCAAAGACTGAATATATTCCTGCATCTACATTTAAGATGTTGAATGCTTTAATTGGCTTGCAAAATGCAAAAGCAACCAATACTGAAGTATTTCATTGGAATGGTGAAAAGCGCGCTTTTTCAGCATGGGAAAAAGATATGACTTTGGCAGAAGCGATGCAGGCTTCAGCTGTTCCCGTATATCAGGAGCTTGCTCGACGTATTGGCTTGGAGTTGATGCGTGAAGAAGTGAAGCGTGTAGGTTTTGGCAATGCGGAGATTGGTCAGCAAGTCGATAATTTTTGGTTGGTGGGTCCTTTAAAAATCTCCCCTGAACAAGAAGTTAAATTTGCCTATCAACTGGCGATGAAGCAATTACCTTTTGATCGAAATGTACAGCAACAAGTCAAAGATATGCTTTATATCGAGAGACGTGGTGACAGTAAACTGTATGCTAAAAGTGGTTGGGGAATGGATGTTGAACCTCAAGTGGGTTGGTATACGGGATGGGTTGAACAACCCAATGGCAAGGTGACTGCATTTGCGTTAAATATGAAAATGCAAGCAGGGGATGATCCAGCTGAACGTAAACAATTAACCTTAAGTATTTTGGACAAATTGGGTCTATTTTTTTATTTAAGATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39090","NCBI_taxonomy_name":"Acinetobacter bereziniae","NCBI_taxonomy_id":"106648"}}}},"ARO_accession":"3008729","ARO_id":"47521","ARO_name":"OXA-952","CARD_short_name":"OXA-952","ARO_description":"OXA-229 family carbapenem-hydrolyzing class D beta-lactamase OXA-952.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46498":{"category_aro_accession":"3007709","category_aro_cvterm_id":"46498","category_aro_name":"OXA-229-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-229.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8148":{"model_id":"8148","model_name":"OXA-953","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10975":{"protein_sequence":{"accession":"QTG68656.1","sequence":"MKFKMKGLFCVILSSLAFSGCVYDSKLQRPVISERETEIPLLFNQAQTQAVFVTYDGIHLKSYGNDLSRAKTQYIPASTFKMLNALIGLQNAKATNTEVFHWNGEKRAFSAWEKDMTLAEAMQASAVPVYQELARRIGLELMREEVKRVGFGNAEIGQQVDNFWLVGPLKISPEQEVQFAYQLAMKQLPFDRNVQQQVKDMLYIERRGDSKLYAKSGWGMDVEPQVGWYTGWVEQPNGKVTAFALNMNMQAGDDPAERKQLTLSILDKLGLFFYLR"},"dna_sequence":{"accession":"MW805235.1","fmin":"0","fmax":"831","strand":"+","sequence":"ATGAAGTTTAAAATGAAAGGTTTATTTTGTGTCATCCTCAGTAGTTTGGCATTTTCAGGTTGTGTTTATGATTCAAAACTACAACGCCCAGTCATATCAGAGCGAGAAACTGAGATTCCTTTATTATTTAATCAAGCACAGACTCAAGCTGTGTTTGTTACTTATGATGGGATTCATCTAAAAAGTTATGGTAATGATCTAAGCCGAGCAAAGACTCAATATATTCCTGCATCTACATTTAAGATGTTGAATGCTTTAATTGGCTTGCAAAATGCAAAAGCAACCAATACTGAAGTATTTCATTGGAATGGTGAAAAGCGCGCTTTTTCAGCATGGGAAAAAGATATGACTTTGGCAGAAGCGATGCAGGCTTCAGCTGTTCCCGTATATCAGGAGCTTGCTCGACGTATTGGCTTGGAATTGATGCGTGAAGAAGTGAAGCGTGTAGGTTTTGGTAATGCAGAGATTGGTCAGCAAGTCGATAATTTTTGGTTGGTGGGTCCTTTAAAAATCTCCCCTGAACAAGAAGTTCAATTTGCCTATCAACTGGCGATGAAGCAATTACCTTTTGATCGAAATGTACAGCAACAAGTCAAAGATATGCTTTATATCGAGAGACGTGGTGACAGTAAACTGTATGCTAAAAGTGGTTGGGGAATGGATGTTGAACCTCAAGTGGGTTGGTATACGGGATGGGTTGAACAACCCAATGGCAAGGTGACTGCATTTGCGTTAAATATGAACATGCAAGCAGGTGATGATCCAGCTGAACGTAAACAATTAACCTTAAGTATTTTGGACAAATTGGGTCTATTTTTTTATTTAAGATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39090","NCBI_taxonomy_name":"Acinetobacter bereziniae","NCBI_taxonomy_id":"106648"}}}},"ARO_accession":"3008730","ARO_id":"47522","ARO_name":"OXA-953","CARD_short_name":"OXA-953","ARO_description":"OXA-229 family carbapenem-hydrolyzing class D beta-lactamase OXA-953.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46498":{"category_aro_accession":"3007709","category_aro_cvterm_id":"46498","category_aro_name":"OXA-229-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-229.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8149":{"model_id":"8149","model_name":"OXA-954","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10976":{"protein_sequence":{"accession":"QTG68657.1","sequence":"MNIKTLLLITSAIFISACSPYIVSANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"MW805236.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAACACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGTCTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACTACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008731","ARO_id":"47523","ARO_name":"OXA-954","CARD_short_name":"OXA-954","ARO_description":"OXA-51 family carbapenem-hydrolyzing class D beta-lactamase OXA-954.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8150":{"model_id":"8150","model_name":"OXA-955","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10977":{"protein_sequence":{"accession":"EMM9379972.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDVKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASALPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGGDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"AAYMEH030000029.1","fmin":"4","fmax":"829","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGTAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTCTTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAACAAAATATACGCAAAAAGTGGTTGGGGAGGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008732","ARO_id":"47524","ARO_name":"OXA-955","CARD_short_name":"OXA-955","ARO_description":"OXA-51 family carbapenem-hydrolyzing class D beta-lactamase OXA-955.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8151":{"model_id":"8151","model_name":"OXA-956","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10978":{"protein_sequence":{"accession":"MBS2780954.1","sequence":"MSRILLPGLLAAGLIFSLPASAASGCMLFADGTGKPISSQGDCSSQLPPASTFKIPLALMGYDSGFLVDENLPALPFKPGDDDWLPAWRETTTPSRWLTYSVVWYSQRLTEWLGMERFQQYVDRFDYGNRDLAGNPGKHDGLTQAWLSSSLAISPQEQARFLGKMVSGKLPVSAQTLQHTANILRQPDIDGWQIHGKTGMGYPKLLDGTLNRDQQIGWFVGWASKPGKQLIFVHTVVQKPGKQFASLKAKEEVFAALPDQLKKL"},"dna_sequence":{"accession":"JAGUQQ010000007.1","fmin":"11387","fmax":"12182","strand":"+","sequence":"ATGTCCCGGATCCTGTTACCCGGCCTGCTCGCAGCAGGCCTGATATTCTCACTGCCCGCCAGCGCGGCCTCCGGCTGCATGCTGTTTGCCGATGGCACAGGCAAGCCCATCAGCAGCCAGGGGGATTGCTCCAGCCAGTTGCCACCCGCCTCCACCTTCAAGATACCGCTGGCGCTGATGGGTTATGACAGCGGCTTCCTGGTGGATGAAAATCTGCCCGCCCTGCCATTCAAACCCGGCGACGATGACTGGTTGCCCGCCTGGCGCGAGACCACTACCCCGAGCCGCTGGCTCACCTACTCTGTGGTCTGGTACTCCCAGCGTCTCACCGAGTGGCTGGGGATGGAGCGCTTCCAGCAGTATGTCGACCGCTTCGACTACGGCAACCGTGATCTTGCGGGCAATCCCGGCAAGCACGATGGTCTGACCCAGGCCTGGCTCAGTTCGAGCCTCGCCATCAGCCCTCAGGAGCAGGCCCGCTTCCTCGGCAAGATGGTGAGCGGCAAGTTGCCGGTCTCCGCACAGACACTGCAGCACACGGCCAATATCCTGCGCCAGCCCGACATCGATGGCTGGCAGATCCACGGCAAGACCGGCATGGGCTACCCCAAGCTGCTGGATGGCACCCTCAATCGGGATCAGCAGATCGGCTGGTTCGTCGGCTGGGCCAGCAAACCGGGCAAGCAGCTCATCTTTGTCCACACTGTCGTGCAAAAGCCCGGCAAGCAATTCGCCTCGCTCAAGGCGAAGGAAGAGGTGTTTGCCGCCCTGCCTGACCAGCTGAAGAAGCTGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36795","NCBI_taxonomy_name":"Aeromonas salmonicida","NCBI_taxonomy_id":"645"}}}},"ARO_accession":"3008733","ARO_id":"47525","ARO_name":"OXA-956","CARD_short_name":"OXA-956","ARO_description":"Class D beta-lactamase OXA-956.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8152":{"model_id":"8152","model_name":"OXA-957","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10979":{"protein_sequence":{"accession":"QWJ89343.1","sequence":"MKLFFCFALLILISVKAFGQIDLQRPFQDCALEGSITVFDYKNKKWTFSDRSDARRETLPASTFKVINSLIALETGAVEDEKEVFKWDGRRREVDAWNADTDMENAFRNSTVWFYEELAKRAGKEKYREILKKSRYGNGKIDGGEGVNFWVTGEFGVTPENQIKFLKAFYEERLPFSRRSFEIVKRIMLEEKADKYTLRAKTGWTRFGGKDTGWWIGYVERSDNTYFFATRVTKPRETQNPRFGECRKLITRDVLRQMKIIE"},"dna_sequence":{"accession":"MZ126685.1","fmin":"0","fmax":"789","strand":"+","sequence":"ATGAAACTTTTTTTTTGTTTCGCGCTTTTGATTTTAATCTCCGTAAAGGCTTTTGGACAGATCGATCTCCAGAGGCCTTTTCAAGATTGCGCGTTAGAGGGAAGCATCACCGTCTTTGATTACAAAAACAAAAAATGGACGTTCAGCGACCGGAGCGACGCGCGGCGCGAGACGCTGCCGGCTTCGACCTTTAAGGTCATCAATTCGCTGATCGCGCTCGAAACAGGCGCGGTCGAAGACGAAAAAGAGGTTTTCAAATGGGACGGCCGGCGGCGCGAGGTCGATGCGTGGAACGCCGACACCGATATGGAAAACGCTTTTCGAAATTCGACCGTCTGGTTTTATGAAGAATTGGCGAAACGCGCCGGCAAGGAAAAATACCGCGAGATTCTCAAAAAAAGCCGTTACGGAAACGGGAAAATCGACGGCGGCGAGGGCGTTAATTTCTGGGTTACCGGAGAGTTCGGCGTCACGCCGGAAAATCAGATAAAATTTTTGAAGGCGTTCTACGAAGAACGGCTTCCCTTTTCGCGCCGGAGTTTCGAGATCGTCAAACGCATCATGCTCGAAGAAAAAGCGGATAAATACACATTGCGCGCGAAAACCGGCTGGACGCGTTTCGGCGGAAAGGATACGGGCTGGTGGATCGGCTACGTCGAACGCAGCGACAATACATACTTTTTCGCCACGCGCGTAACGAAACCGCGCGAGACGCAAAACCCGCGCTTCGGCGAATGCCGCAAACTGATTACGCGCGACGTTTTGCGGCAAATGAAAATCATCGAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36791","NCBI_taxonomy_name":"uncultured bacterium","NCBI_taxonomy_id":"77133"}}}},"ARO_accession":"3008734","ARO_id":"47526","ARO_name":"OXA-957","CARD_short_name":"OXA-957","ARO_description":"Class D beta-lactamase OXA-957.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8153":{"model_id":"8153","model_name":"OXA-958","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10980":{"protein_sequence":{"accession":"QVO43823.1","sequence":"MSRLLLSSLLAAGLLTALPASAASGCFLYADGNGQTLSSEGDCSSQLPPASTFKIPLALMGYDSGFLVDEEHPALPFKPGYDDWLPAWRETTTPRRWETYSVVWFSQQITEWLGMERFQQYVDRFDYGNRDLSGNPGKHDGLTQAWLSSSLAISPEEQARFLGKMVSGKLPVSAQTLQYTANILKVSEIDGWQIHGKTGMGYPKKLDGSLNRDQQIGWFVGWASKLGKQLIFVHTVVQKPGKQFASLKAKEEVLAALPAQLKKL"},"dna_sequence":{"accession":"MZ092816.1","fmin":"0","fmax":"795","strand":"+","sequence":"ATGTCCCGCCTGCTTCTCTCCAGCCTGCTGGCTGCCGGTCTGCTAACCGCTCTGCCTGCCTCCGCCGCCAGCGGCTGTTTTCTCTATGCTGACGGCAACGGCCAGACCCTCTCCAGCGAAGGGGACTGCTCCAGCCAGCTGCCGCCAGCGTCTACCTTCAAGATCCCGCTGGCGCTGATGGGTTACGACAGCGGTTTTCTGGTGGATGAAGAGCATCCAGCACTGCCCTTCAAACCGGGTTACGACGACTGGCTGCCCGCCTGGCGCGAAACCACCACCCCGCGCCGCTGGGAAACCTACTCGGTGGTCTGGTTCTCCCAGCAGATCACCGAATGGCTGGGGATGGAGCGCTTCCAGCAGTACGTCGACCGCTTCGACTACGGCAACCGGGATCTCTCCGGCAATCCGGGCAAGCATGACGGCCTGACCCAGGCCTGGCTAAGCTCCAGCCTTGCCATCAGCCCGGAGGAGCAGGCCCGCTTCCTCGGCAAGATGGTGAGCGGCAAGCTGCCGGTCTCGGCGCAGACCCTGCAGTACACCGCCAACATCCTCAAGGTGAGCGAGATCGATGGCTGGCAAATCCACGGCAAGACCGGCATGGGCTACCCGAAGAAGCTGGATGGCAGCCTCAACCGCGATCAGCAGATCGGCTGGTTCGTCGGCTGGGCCAGCAAACTGGGCAAGCAGCTGATCTTCGTCCATACCGTAGTGCAAAAGCCCGGCAAGCAGTTCGCCTCCCTCAAGGCGAAAGAAGAGGTGCTGGCCGCCCTGCCCGCACAACTCAAAAAGCTCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36947","NCBI_taxonomy_name":"Aeromonas allosaccharophila","NCBI_taxonomy_id":"656"}}}},"ARO_accession":"3008735","ARO_id":"47527","ARO_name":"OXA-958","CARD_short_name":"OXA-958","ARO_description":"OXA-12 family class D beta-lactamase OXA-958.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46488":{"category_aro_accession":"3007699","category_aro_cvterm_id":"46488","category_aro_name":"OXA-12-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-12.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8154":{"model_id":"8154","model_name":"OXA-959","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10981":{"protein_sequence":{"accession":"QVO43824.1","sequence":"MSRLLLSSLLAAGLLAALPASAASGCFLYADGNGQTLSSEGDCSSQLPPASTFKIPLALMGYDSGFLVDEEHPALPFKPGYDDWLPAWRETTTPRRWETYSVVWFSQQITEWLGMERFQQYVDRFDYGNRDLSGNPGKHDGLTQAWLSSSLAISPEEQARFLGKMVSGKLPVSAQTLQYTANILKVSEIDGWQIHGKTGMGYPKKLDGSLNRDQQIGWFVGWASKPGKQLIFVHTVVQKPGKQFASLKAKEEVLAALPGKLKTL"},"dna_sequence":{"accession":"MZ092817.1","fmin":"0","fmax":"795","strand":"+","sequence":"ATGTCCCGCCTGCTTCTCTCCAGCCTGCTGGCTGCCGGTCTGCTCGCCGCTCTGCCTGCCTCCGCCGCCAGCGGCTGTTTTCTCTATGCTGACGGCAACGGCCAGACCCTCTCCAGCGAAGGGGACTGCTCCAGCCAGCTGCCGCCCGCATCCACCTTCAAGATCCCGCTGGCACTGATGGGCTATGACAGCGGCTTTCTGGTGGATGAAGAGCATCCAGCACTGCCCTTCAAACCGGGTTACGACGACTGGCTGCCCGCCTGGCGCGAAACCACTACCCCGCGCCGCTGGGAAACCTACTCGGTGGTCTGGTTCTCCCAGCAGATCACCGAATGGCTGGGGATGGAGCGCTTCCAGCAATACGTCGACCGCTTCGACTACGGCAACCGGGATCTCTCCGGCAATCCGGGCAAGCATGACGGCCTGACCCAGGCCTGGCTAAGCTCCAGCCTCGCCATAAGCCCGGAGGAGCAGGCCCGCTTCCTCGGCAAGATGGTGAGCGGCAAGCTGCCGGTCTCGGCGCAGACCCTGCAGTACACCGCCAATATCCTCAAGGTGAGCGAGATCGATGGCTGGCAAATCCACGGCAAGACCGGCATGGGCTACCCGAAGAAGCTGGATGGCAGCCTCAACCGCGATCAGCAGATCGGCTGGTTCGTCGGCTGGGCCAGCAAACCGGGCAAGCAGCTGATCTTCGTCCATACCGTGGTGCAAAAGCCCGGCAAGCAGTTCGCCTCCCTCAAGGCGAAAGAAGAGGTGCTGGCCGCCCTGCCCGGGAAGCTGAAGACCCTGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36947","NCBI_taxonomy_name":"Aeromonas allosaccharophila","NCBI_taxonomy_id":"656"}}}},"ARO_accession":"3008736","ARO_id":"47528","ARO_name":"OXA-959","CARD_short_name":"OXA-959","ARO_description":"OXA-12 family class D beta-lactamase OXA-959.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46488":{"category_aro_accession":"3007699","category_aro_cvterm_id":"46488","category_aro_name":"OXA-12-like beta-lactamase","category_aro_description":"A subfamily of oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-12.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8155":{"model_id":"8155","model_name":"OXA-960","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10982":{"protein_sequence":{"accession":"QVO43834.1","sequence":"MNKGLHRKRLSKRLLLPMLLCLLAQQTQAVAAAQTKVSEVGSEVTVEGWQEVRRWDKLFESAGVKGCLLLLDQKRSLGLSNNLSRAAEGFIPASTFKIPSSLIALQTGAVRDETSRFSWDGKVREIAAWNRDQSFRTAMKYSVVPVYQQLAREIGPKVMAAMVRQLEYGNQNIGGQADSFWLDGQLRITAFQQVDFLQQLHDNKLPVSERSQRIVKQMMLTEASTDYIIRAKTGYGVQQTPAIGWWVGWLELDDNTVYFAINLELTSASQLPLRQQLVKQVLKQELLLP"},"dna_sequence":{"accession":"MZ092827.1","fmin":"0","fmax":"870","strand":"+","sequence":"ATGAATAAAGGTTTGCACAGAAAGCGCCTGAGTAAGCGTTTGCTGCTGCCCATGTTGTTGTGTTTATTGGCTCAGCAAACGCAGGCAGTGGCAGCGGCGCAGACCAAGGTCAGTGAAGTCGGCTCTGAGGTCACGGTCGAGGGTTGGCAAGAGGTACGCCGCTGGGACAAGTTGTTTGAATCTGCAGGTGTTAAAGGCTGTTTGCTGCTTTTGGATCAAAAGCGTTCTTTGGGGCTATCTAACAATCTAAGTCGCGCCGCCGAAGGCTTTATTCCTGCTTCTACCTTCAAGATCCCCTCTAGCCTGATTGCGTTGCAAACCGGGGCGGTGCGCGATGAAACCAGTCGTTTTAGCTGGGACGGAAAAGTTCGGGAAATTGCTGCCTGGAACCGGGATCAGAGTTTTCGCACCGCAATGAAGTACTCCGTGGTGCCTGTGTATCAGCAGCTGGCCAGGGAGATAGGCCCCAAAGTGATGGCAGCTATGGTGCGGCAACTGGAATATGGTAATCAGAATATCGGTGGCCAAGCGGACAGCTTCTGGCTCGACGGTCAACTTAGGATAACGGCGTTCCAACAAGTGGATTTTCTGCAGCAACTGCATGACAACAAGTTGCCTGTGTCTGAGCGCAGCCAGCGAATTGTCAAACAGATGATGCTGACCGAAGCGAGTACTGACTATATCATTCGCGCCAAGACAGGCTATGGTGTACAGCAAACGCCGGCCATAGGTTGGTGGGTCGGTTGGTTGGAGTTGGACGACAATACTGTCTATTTCGCCATTAATCTGGAGCTGACCTCCGCAAGCCAGTTACCGTTGCGCCAACAACTGGTGAAACAGGTGCTCAAGCAGGAACTGCTACTGCCTTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"47931","NCBI_taxonomy_name":"Shewanella chilikensis","NCBI_taxonomy_id":"558541"}}}},"ARO_accession":"3008737","ARO_id":"47529","ARO_name":"OXA-960","CARD_short_name":"OXA-960","ARO_description":"OXA-55 family carbapenem-hydrolyzing class D beta-lactamase OXA-960.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46516":{"category_aro_accession":"3007727","category_aro_cvterm_id":"46516","category_aro_name":"OXA-55-like beta-lactamase","category_aro_description":"A subfamily of carbapanem-hydrolyzing class D OXA beta-lactamases derived from OXA-55.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8156":{"model_id":"8156","model_name":"OXA-961","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10983":{"protein_sequence":{"accession":"QVO43835.1","sequence":"MNKGLHRKRLSKRLLLPMLLCLLAQQTQAVAAAQTKVSDVGSEVMAEGWQEVRRWDKLFESAGVKGSLLLWDQKRSLGLSNNLSRAAEGFIPASTFKIPSSLIALQTGAVRDETSRFSWDGKVREIAAWNRDQSFRTAMKYSVVPVYQQLAREIGPTVMAAMVRQLEYGNQDVGGQADSFWLDGQLRITAFQQVDFLQQLHDNKLPVSERSQRIVKQMMLTEASTDYIIRAKTGYGVQQTPAIGWWVGWLELDDNTVYFAINLDLTSASQLPLRQQLVKQVLKQEQLLP"},"dna_sequence":{"accession":"MZ092828.1","fmin":"0","fmax":"870","strand":"+","sequence":"ATGAATAAAGGTTTGCACCGAAAGCGACTGAGTAAGCGTTTGCTGCTGCCCATGTTGCTGTGTTTATTGGCTCAGCAAACGCAGGCAGTGGCAGCGGCGCAGACCAAGGTCAGTGACGTCGGCTCTGAGGTCATGGCCGAGGGTTGGCAAGAGGTACGTCGCTGGGACAAGCTGTTCGAATCCGCAGGTGTTAAAGGCAGTTTGCTGCTTTGGGATCAAAAGCGTTCTTTGGGGCTATCCAACAATCTAAGTCGCGCCGCCGAAGGCTTTATTCCGGCTTCTACCTTTAAGATCCCCTCCAGCCTTATTGCGTTGCAAACCGGGGCGGTGCGCGATGAAACCAGTCGTTTTAGCTGGGACGGAAAAGTTCGGGAAATTGCTGCCTGGAACCGGGATCAGAGTTTTCGCACCGCAATGAAGTACTCCGTGGTGCCTGTGTATCAGCAGTTGGCAAGGGAGATAGGCCCCACGGTGATGGCGGCTATGGTGCGGCAGCTGGAATATGGCAATCAGGATGTCGGCGGCCAAGCGGACAGCTTTTGGCTCGACGGCCAACTGAGAATTACAGCATTTCAACAAGTGGATTTTCTGCAGCAACTGCATGACAACAAGTTGCCTGTGTCTGAGCGCAGCCAGCGAATTGTCAAACAGATGATGCTGACCGAAGCGAGTACTGACTATATTATTCGCGCCAAGACAGGCTATGGTGTACAGCAAACGCCGGCCATAGGTTGGTGGGTCGGTTGGTTGGAGTTGGACGACAATACTGTCTATTTCGCCATTAACCTGGATCTGACCTCCGCCAGCCAGTTACCGTTGCGCCAACAACTGGTGAAACAGGTGCTCAAGCAGGAACAGCTACTGCCTTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"47931","NCBI_taxonomy_name":"Shewanella chilikensis","NCBI_taxonomy_id":"558541"}}}},"ARO_accession":"3008738","ARO_id":"47530","ARO_name":"OXA-961","CARD_short_name":"OXA-961","ARO_description":"OXA-55 family carbapenem-hydrolyzing class D beta-lactamase OXA-961.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46516":{"category_aro_accession":"3007727","category_aro_cvterm_id":"46516","category_aro_name":"OXA-55-like beta-lactamase","category_aro_description":"A subfamily of carbapanem-hydrolyzing class D OXA beta-lactamases derived from OXA-55.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8157":{"model_id":"8157","model_name":"OXA-962","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10984":{"protein_sequence":{"accession":"QVO43836.1","sequence":"MNKGLHRKRLSKRLLLPMLLCLLAQQTQVVAAAQTKVSDVGSEVTAEGWQEVRRWDKLFESAGVKGCLLLWDQKRSLGLSNNLSRAAEGFIPASTFKIPSSLIALQTGAVRDETSRFSWDGKVREIAAWNRDQSFRTAMKYSVVPVYQQLAREIGPKVMAAMVRQLQYGNQDIGGQADSFWLDGQLRITAFQQLDFLQQLHDNKLPVSERSQRIVKQMMLTEASTDYIIRAKTGYGVRHTPAIGWWVGWLELDDNTVYFAINLDLASAGQLPLRQQLVKQVLKQEQLLP"},"dna_sequence":{"accession":"MZ092829.1","fmin":"0","fmax":"870","strand":"+","sequence":"ATGAATAAAGGTTTGCACAGAAAACGCCTGAGTAAGCGTTTGCTGCTGCCCATGTTGCTGTGTTTATTGGCTCAACAAACGCAGGTTGTGGCAGCGGCGCAGACCAAGGTCAGTGACGTCGGCTCTGAGGTCACGGCCGAGGGGTGGCAAGAGGTACGCCGCTGGGACAAACTGTTCGAATCCGCAGGTGTTAAAGGCTGTTTGCTGCTTTGGGATCAAAAGCGTTCTTTGGGGCTCTCCAACAATCTAAGTCGCGCCGCCGAAGGTTTTATTCCGGCTTCTACCTTTAAGATCCCCTCCAGCCTTATTGCGTTGCAAACCGGGGCAGTGCGCGATGAAACCAGTCGTTTTAGCTGGGACGGAAAGGTTCGTGAAATTGCTGCCTGGAACCGGGACCAGAGTTTTCGCACCGCAATGAAGTATTCTGTGGTGCCTGTGTATCAGCAGTTGGCAAGGGAGATAGGCCCCAAAGTGATGGCAGCTATGGTGCGGCAGCTGCAATATGGCAATCAGGATATCGGCGGTCAAGCGGACAGTTTCTGGCTCGACGGCCAACTTAGGATAACGGCGTTTCAACAGCTGGATTTTCTGCAGCAACTGCATGACAACAAGTTGCCTGTGTCCGAGCGCAGCCAGCGAATAGTCAAACAGATGATGCTGACCGAAGCGAGTACTGACTATATCATTCGTGCCAAGACAGGCTATGGTGTGCGGCATACGCCGGCCATAGGTTGGTGGGTCGGTTGGTTGGAGTTGGACGACAACACTGTCTATTTCGCCATTAACCTGGATCTGGCCTCGGCCGGCCAGTTACCGTTGCGCCAACAACTGGTGAAACAGGTGCTCAAGCAGGAACAGCTACTGCCTTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"47932","NCBI_taxonomy_name":"Shewanella indica","NCBI_taxonomy_id":"768528"}}}},"ARO_accession":"3008739","ARO_id":"47531","ARO_name":"OXA-962","CARD_short_name":"OXA-962","ARO_description":"OXA-55 family carbapenem-hydrolyzing class D beta-lactamase OXA-962.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46516":{"category_aro_accession":"3007727","category_aro_cvterm_id":"46516","category_aro_name":"OXA-55-like beta-lactamase","category_aro_description":"A subfamily of carbapanem-hydrolyzing class D OXA beta-lactamases derived from OXA-55.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8158":{"model_id":"8158","model_name":"OXA-963","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10985":{"protein_sequence":{"accession":"QVO43837.1","sequence":"MNKGLHRKRLSKRLLLPMLLCLLAQQTQAVAAEQTKVSDVSSEVTAEGWQEVRRWDKLFESAGVKGSLLLWDQKRSLGLSNNLSRAAEGFIPASTFKIPSSLIALETGAVRDETSRFSWDGKVREIAAWNRDQSFRTAMKYSVVPVYQQLAREIGPKVMAAMVRQLQYGNQDIGGQADSFWLDGQLRITAFQQVVFLRQLHDNKLPVSERSQRIVKQMMLTEASTDYIIRAKTGYGVRRTPAIGWWVGWLELDDNTVYFAVNLDLASASQLPLRQQLVKQVLKQEQLLP"},"dna_sequence":{"accession":"MZ092830.1","fmin":"0","fmax":"870","strand":"+","sequence":"ATGAATAAAGGTTTGCACAGAAAGCGCCTGAGTAAGCGTTTGCTGCTGCCCATGTTGCTGTGTTTATTGGCTCAACAAACGCAGGCTGTGGCAGCTGAGCAGACCAAGGTCAGTGACGTCAGCTCTGAGGTCACGGCCGAGGGTTGGCAAGAGGTACGTCGCTGGGACAAGCTGTTCGAATCCGCAGGTGTTAAAGGCAGTTTACTGCTTTGGGATCAAAAGCGTTCTTTGGGGCTCTCCAACAATCTAAGTCGCGCCGCCGAAGGCTTTATTCCGGCTTCCACCTTCAAGATCCCCTCCAGCCTTATTGCGTTGGAAACCGGGGCGGTGCGCGATGAAACCAGTCGTTTTAGCTGGGACGGAAAGGTTCGTGAAATTGCCGCCTGGAACAGAGACCAGAGTTTTCGCACCGCAATGAAGTACTCTGTGGTGCCTGTATATCAGCAGTTGGCCAGGGAGATAGGCCCCAAAGTGATGGCAGCTATGGTGCGGCAGCTGCAATATGGCAATCAGGATATCGGTGGCCAAGCGGACAGCTTCTGGCTCGACGGCCAACTGAGAATTACAGCATTTCAACAAGTGGTTTTTCTAAGGCAACTGCATGACAACAAGTTGCCTGTGTCCGAGCGCAGCCAGCGAATTGTCAAACAGATGATGCTGACCGAAGCGAGTACTGACTATATTATTCGCGCCAAGACAGGCTATGGTGTGCGGCGTACGCCGGCCATAGGTTGGTGGGTCGGTTGGTTGGAGTTGGACGACAACACTGTCTATTTCGCCGTTAACCTGGATCTGGCCTCGGCCAGCCAGTTACCGTTGCGCCAACAACTGGTGAAACAGGTGCTCAAGCAGGAACAGCTGCTGCCTTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36891","NCBI_taxonomy_name":"Shewanella algae","NCBI_taxonomy_id":"38313"}}}},"ARO_accession":"3008740","ARO_id":"47532","ARO_name":"OXA-963","CARD_short_name":"OXA-963","ARO_description":"OXA-55 family carbapenem-hydrolyzing class D beta-lactamase OXA-963.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46516":{"category_aro_accession":"3007727","category_aro_cvterm_id":"46516","category_aro_name":"OXA-55-like beta-lactamase","category_aro_description":"A subfamily of carbapanem-hydrolyzing class D OXA beta-lactamases derived from OXA-55.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8159":{"model_id":"8159","model_name":"OXA-964","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10986":{"protein_sequence":{"accession":"QVO43838.1","sequence":"MNKGLHRKRLSKRLLLPMLLCLLAQQTQAVAAEQTKVSDVGSEVTAEGWQEVRRWDKLFESAGVKGSLLLWDQKRSLGLSNNLSRAAEGFIPASTFKIPSSLIALETGAVRDETSRFSWDGKVREIAAWNRDQSFRTAMKYSVVPVYQQLAREIGPKVMAAMVRQLDYGNQDIGGQADSFWLDGQLRITAFQQVDFLRQLHDNKLPVSERSQRIVKQMMLTEASTDYIIRAKTGYGVRRTPAIGWWVGWLELDDNTVYFAVNLDLASASQLPLRQQLVKQVLKQEQLLP"},"dna_sequence":{"accession":"MZ092831.1","fmin":"0","fmax":"870","strand":"+","sequence":"ATGAATAAAGGTTTGCACAGAAAGCGCCTGAGTAAGCGTTTGCTGCTGCCCATGTTGCTGTGTTTATTGGCTCAACAAACGCAGGCTGTGGCAGCTGAGCAGACCAAGGTCAGTGACGTCGGCTCTGAGGTCACGGCCGAGGGTTGGCAAGAGGTACGCCGCTGGGACAAGCTGTTCGAATCCGCAGGTGTTAAAGGCAGTTTACTGCTTTGGGATCAAAAGCGTTCTTTGGGGCTCTCCAACAATCTAAGTCGCGCCGCCGAAGGCTTTATTCCGGCTTCCACCTTCAAGATCCCCTCCAGCCTTATTGCGTTGGAAACCGGGGCGGTGCGCGATGAAACCAGTCGTTTTAGCTGGGACGGAAAGGTTCGTGAAATTGCCGCCTGGAACAGGGACCAGAGTTTTCGCACCGCAATGAAGTACTCTGTGGTGCCTGTGTATCAGCAGTTGGCCAGGGAGATAGGCCCCAAAGTGATGGCAGCTATGGTGCGGCAGCTGGATTATGGCAATCAGGATATCGGTGGCCAAGCGGACAGCTTCTGGCTCGACGGCCAACTGAGAATTACAGCATTTCAACAAGTGGATTTTCTAAGGCAACTGCATGACAACAAGTTGCCTGTGTCCGAGCGCAGCCAGCGAATTGTCAAACAGATGATGCTGACCGAAGCGAGTACTGACTATATTATTCGCGCCAAGACAGGCTATGGTGTGCGGCGTACGCCGGCCATAGGTTGGTGGGTCGGTTGGTTGGAGTTGGACGACAACACTGTCTATTTCGCCGTTAACCTGGATCTGGCCTCGGCCAGCCAGTTACCGTTGCGCCAACAACTGGTGAAACAGGTGCTCAAGCAGGAACAGCTGCTGCCTTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36891","NCBI_taxonomy_name":"Shewanella algae","NCBI_taxonomy_id":"38313"}}}},"ARO_accession":"3008741","ARO_id":"47533","ARO_name":"OXA-964","CARD_short_name":"OXA-964","ARO_description":"OXA-55 family carbapenem-hydrolyzing class D beta-lactamase OXA-964.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46516":{"category_aro_accession":"3007727","category_aro_cvterm_id":"46516","category_aro_name":"OXA-55-like beta-lactamase","category_aro_description":"A subfamily of carbapanem-hydrolyzing class D OXA beta-lactamases derived from OXA-55.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8160":{"model_id":"8160","model_name":"OXA-965","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10987":{"protein_sequence":{"accession":"QVO43839.1","sequence":"MNKGLHRKRLSKRLLLPMLLCLLAQQTQAVAAEQTKVSDVSSGVTAEGWQEVRRWDKLFESAGVKGSLLLWDQKRSLGLSNNLSRAAEGFIPASTFKIPSSLIALETGAVRDETSRFSWDGKVREIAAWNRDQSFRTAMKYSVVPVYQQLAREIGPKVMAAMVRQLEYGNQDISGQADSFWLDGQLKITAFQQVDFLRQLHDNKLPVSELSQRIVKQMMLTEASTDYIIRAKTGYGVRRTPAIGWWVGWLELDDNTVYFAINLDLASASQLPLRQQLVKQVLKQEQLLP"},"dna_sequence":{"accession":"MZ092832.1","fmin":"0","fmax":"870","strand":"+","sequence":"ATGAATAAAGGTTTGCACAGAAAGCGCCTGAGTAAGCGTTTGCTGCTGCCCATGTTGCTGTGTTTATTGGCTCAACAAACGCAGGCTGTGGCAGCTGAGCAGACCAAGGTCAGTGACGTCAGCTCTGGGGTCACGGCCGAGGGTTGGCAAGAGGTACGCCGCTGGGACAAGCTGTTCGAATCCGCAGGAGTTAAAGGCAGTTTGCTGCTTTGGGATCAAAAGCGTTCTTTGGGGCTCTCCAACAATCTAAGTCGCGCCGCCGAAGGCTTTATTCCGGCTTCCACCTTCAAGATCCCATCCAGCCTTATTGCGTTGGAAACCGGGGCGGTGCGCGATGAAACCAGTCGTTTTAGCTGGGACGGAAAGGTTCGTGAAATTGCCGCCTGGAACAGGGACCAGAGTTTTCGCACCGCAATGAAGTACTCTGTGGTGCCTGTATATCAGCAGTTGGCCAGGGAGATAGGCCCCAAAGTGATGGCAGCTATGGTGCGGCAGCTGGAATATGGCAATCAGGATATCAGTGGCCAAGCGGACAGCTTCTGGCTCGACGGCCAACTTAAGATAACGGCGTTCCAACAAGTGGATTTTCTAAGGCAACTGCATGACAACAAGTTACCTGTGTCCGAGCTCAGCCAGCGAATTGTCAAACAGATGATGCTGACCGAAGCGAGTACTGACTATATTATTCGCGCCAAGACAGGCTATGGTGTGCGGCGCACGCCGGCCATAGGTTGGTGGGTCGGTTGGTTGGAGTTGGACGACAACACTGTCTATTTCGCCATTAACCTGGATCTGGCCTCGGCCAGCCAGTTACCGTTGCGCCAACAACTGGTGAAGCAGGTGCTCAAGCAGGAACAGCTGCTGCCTTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36891","NCBI_taxonomy_name":"Shewanella algae","NCBI_taxonomy_id":"38313"}}}},"ARO_accession":"3008742","ARO_id":"47534","ARO_name":"OXA-965","CARD_short_name":"OXA-965","ARO_description":"OXA-55 family carbapenem-hydrolyzing class D beta-lactamase OXA-965.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46516":{"category_aro_accession":"3007727","category_aro_cvterm_id":"46516","category_aro_name":"OXA-55-like beta-lactamase","category_aro_description":"A subfamily of carbapanem-hydrolyzing class D OXA beta-lactamases derived from OXA-55.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8161":{"model_id":"8161","model_name":"OXA-966","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10988":{"protein_sequence":{"accession":"QWA20165.1","sequence":"MNKYFTCYVVASLFLSGCTVQHNLINETQSQIVQGHNQVIHQYFDEKNTSGVLVIQTDKKINLYGNALSRANTEYVPASTFKMLNALIGLENQKTDINEIFKWKGEKRSFTAWEKDMTLGEAMKLSAVPVYQELARRIGLDLMQKEVERIDFGNTEIGQQVDNFWLVGPLKVTPIQEVEFVSQLAHTQLPFSEKVQANVKNMLLLEESNGYKIFGKTGWAMDIKPQVGWLTGWVEQPDGKIVAFALNMEMRSEMPASIRNELLMKSLKQLNII"},"dna_sequence":{"accession":"MZ265718.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGAATAAATATTTTACTTGCTATGTGGTTGCTTCTCTTTTTCTTTCTGGTTGTACGGTTCAGCATAATTTAATAAATGAAACCCAGAGTCAGATTGTTCAAGGACATAATCAGGTGATTCATCAATACTTTGATGAAAAAAACACCTCAGGTGTGCTGGTTATTCAAACAGATAAAAAAATTAATCTGTATGGTAATGCTCTAAGCCGCGCAAATACAGAATATGTGCCAGCCTCTACATTTAAAATGTTGAATGCCCTGATCGGATTGGAGAACCAGAAAACGGATATTAATGAAATATTTAAATGGAAGGGCGAGAAAAGGTCATTTACCGCTTGGGAAAAAGACATGACACTAGGAGAAGCCATGAAGCTTTCCGCAGTCCCAGTCTATCAGGAACTTGCAAGACGTATTGGTCTTGATCTCATGCAAAAAGAAGTAGAACGTATTGATTTCGGTAATACTGAAATTGGACAGCAGGTTGATAATTTCTGGTTGGTAGGGCCATTAAAGGTTACGCCTATTCAAGAGGTAGAGTTTGTTTCTCAATTGGCGCATACACAGCTTCCATTTAGTGAAAAAGTACAGGCTAATGTAAAAAATATGCTTCTTTTAGAAGAGAGTAATGGCTACAAAATTTTTGGAAAGACTGGTTGGGCAATGGATATAAAACCACAAGTGGGCTGGTTGACCGGCTGGGTTGAGCAGCCAGATGGAAAAATTGTCGCTTTTGCATTAAATATGGAAATGCGGTCAGAAATGCCGGCATCTATACGTAATGAATTATTGATGAAATCATTAAAACAGCTGAATATTATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39672","NCBI_taxonomy_name":"Acinetobacter radioresistens","NCBI_taxonomy_id":"40216"}}}},"ARO_accession":"3008743","ARO_id":"47535","ARO_name":"OXA-966","CARD_short_name":"OXA-966","ARO_description":"OXA-23 family carbapenem-hydrolyzing class D beta-lactamase OXA-966.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46499":{"category_aro_accession":"3007710","category_aro_cvterm_id":"46499","category_aro_name":"OXA-23-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases, specifically imipenem, derived from OXA-23, first identified in Acinetobacter baumannii.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8162":{"model_id":"8162","model_name":"OXA-967","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10989":{"protein_sequence":{"accession":"QWA20166.1","sequence":"MNKYFTCYVVASLFLSGCTVQHNLINETQSQIVQGHNQVIHQYFDEKNTSGVLVIQTDKKINLYGNALSRANTEYVPASTFKMLNALIGLENQKTDINEIFKWKGEKRSFTAWEKDMTLGEAMKLSAVPVYQELARRIGLDLMQKEVERIDFGNAEIGQQVDNFWLIGPLKVTPIQEVEFVSQLAHTQLPFSEKVQANVKNMLLLEESNGYKIFGKTGWAMDIKPQVGWLTGWVEQPDGKIVAFALNMEMRSEMPASIRNELLMKSLKQLNII"},"dna_sequence":{"accession":"MZ265719.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGAATAAATATTTTACTTGCTATGTGGTTGCTTCTCTTTTTCTTTCTGGTTGTACGGTTCAGCATAATTTAATAAATGAAACCCAGAGTCAGATTGTTCAAGGACATAATCAGGTGATTCATCAATACTTTGATGAAAAAAACACCTCAGGTGTGCTGGTTATTCAAACAGATAAAAAAATTAATTTGTATGGTAATGCTCTAAGCCGCGCAAATACAGAATATGTGCCAGCCTCTACATTTAAAATGTTGAATGCCCTGATCGGACTGGAGAACCAGAAAACGGATATTAATGAAATATTTAAATGGAAGGGCGAGAAAAGGTCATTTACCGCTTGGGAAAAAGACATGACACTAGGAGAAGCCATGAAGCTTTCTGCAGTCCCAGTCTATCAGGAACTTGCAAGACGTATCGGTCTTGATCTCATGCAAAAAGAAGTAGAACGTATTGATTTCGGTAATGCTGAAATTGGACAGCAGGTTGACAATTTCTGGTTGATAGGCCCATTAAAGGTCACGCCTATTCAAGAGGTAGAGTTTGTTTCTCAATTGGCACATACACAGCTTCCATTTAGTGAAAAAGTGCAGGCTAATGTAAAAAATATGCTACTTCTAGAAGAGAGTAATGGCTACAAGATTTTTGGAAAGACTGGTTGGGCAATGGATATAAAACCACAAGTGGGCTGGTTGACCGGCTGGGTTGAGCAGCCAGATGGAAAAATTGTCGCTTTTGCATTAAATATGGAAATGCGGTCAGAAATGCCGGCATCTATACGTAATGAATTATTGATGAAATCATTAAAACAGCTGAATATTATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39672","NCBI_taxonomy_name":"Acinetobacter radioresistens","NCBI_taxonomy_id":"40216"}}}},"ARO_accession":"3008744","ARO_id":"47536","ARO_name":"OXA-967","CARD_short_name":"OXA-967","ARO_description":"OXA-23 family carbapenem-hydrolyzing class D beta-lactamase OXA-967.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46499":{"category_aro_accession":"3007710","category_aro_cvterm_id":"46499","category_aro_name":"OXA-23-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases, specifically imipenem, derived from OXA-23, first identified in Acinetobacter baumannii.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8163":{"model_id":"8163","model_name":"OXA-968","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10990":{"protein_sequence":{"accession":"QWA20167.1","sequence":"MNKYFTCYVFASLFLSGCTVQHNLINETPSQIVQGHNQVIHQYFDEKSTSGVLVIQTDKKINLYGNALSRANTEYVPASTFKMLNALIGLENQKTDINEIFKWKGEKRSFTAWEKDMILGEAMKLSAVPVYQELARRIGLDLMQKEVERIDFGNAEIGQQVDNFWLIGPLKVTPIQEVEFVSQLAHTQLPFSEKVQANVKNMLLLEESNGYKIFGKTGWAMDIKPQVGWLTGWVEQPDGKIVAFALNMEMQSGMPASIRNELLMKSLKQLNII"},"dna_sequence":{"accession":"MZ265720.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGAATAAATATTTTACTTGCTATGTGTTTGCTTCTCTTTTTCTTTCTGGTTGTACGGTTCAGCATAATTTAATAAATGAAACCCCGAGTCAGATTGTTCAAGGACATAATCAGGTGATTCATCAATACTTTGATGAAAAAAGCACCTCAGGTGTGCTGGTTATTCAAACAGATAAAAAAATTAATCTGTATGGTAATGCTCTAAGCCGCGCAAATACAGAATATGTGCCAGCCTCTACATTTAAAATGTTGAATGCCCTGATCGGATTGGAGAACCAGAAAACGGATATTAATGAAATATTTAAATGGAAGGGCGAGAAAAGGTCATTTACCGCTTGGGAAAAAGACATGATACTAGGAGAAGCCATGAAGCTTTCTGCAGTCCCAGTCTATCAGGAACTTGCGCGACGTATCGGTCTTGATCTCATGCAAAAAGAAGTAGAACGTATTGATTTCGGTAATGCTGAAATTGGACAGCAGGTCGATAATTTCTGGTTGATAGGCCCATTAAAGGTCACGCCTATTCAAGAGGTAGAGTTTGTTTCTCAATTGGCACATACACAGCTTCCATTTAGTGAAAAAGTGCAGGCTAATGTAAAAAATATGCTACTTCTAGAAGAGAGTAATGGCTACAAGATTTTTGGAAAGACTGGTTGGGCAATGGATATAAAACCACAAGTGGGCTGGTTGACCGGCTGGGTTGAGCAGCCAGATGGAAAAATTGTCGCTTTTGCACTAAATATGGAAATGCAGTCAGGAATGCCGGCATCTATACGTAATGAATTATTGATGAAATCATTAAAACAGCTAAATATTATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39672","NCBI_taxonomy_name":"Acinetobacter radioresistens","NCBI_taxonomy_id":"40216"}}}},"ARO_accession":"3008745","ARO_id":"47537","ARO_name":"OXA-968","CARD_short_name":"OXA-968","ARO_description":"OXA-23 family carbapenem-hydrolyzing class D beta-lactamase OXA-968.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46499":{"category_aro_accession":"3007710","category_aro_cvterm_id":"46499","category_aro_name":"OXA-23-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases, specifically imipenem, derived from OXA-23, first identified in Acinetobacter baumannii.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8164":{"model_id":"8164","model_name":"OXA-969","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10991":{"protein_sequence":{"accession":"QWA20168.1","sequence":"MNKYFTCYVVASLFLSGCTVQHNLINETQSQIVQGHNQVIHQYFDEKNTSGVLVIQTDKKINLYGNALSRANTEYVPASTFKILNALIGLEKQKTDINEIFKWKGEKRSFTTWEKDMTLGEAIKLSAVPVYQELARRIGLDLMQKEVERIDFGNAEIGQQVDNFWLIGPLKVTPIQEVEFVSQLAHTQLPFSEKVQANVKNMLLLEESNGYKIFGKTGWVMDIKPQVGWLTGWVEQPDGKVVAFALNMEMQSEMPASIRNELLMKSLKQLNII"},"dna_sequence":{"accession":"MZ265721.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGAATAAATATTTTACTTGCTATGTGGTTGCTTCTCTTTTTCTTTCTGGTTGTACGGTTCAGCATAATTTAATAAATGAAACCCAGAGTCAGATTGTTCAAGGACATAATCAGGTGATTCATCAATACTTTGATGAAAAAAACACCTCAGGTGTGCTGGTTATTCAAACAGATAAAAAAATTAATTTGTATGGTAATGCTCTAAGCCGAGCAAATACAGAATATGTGCCAGCTTCTACATTTAAAATTTTGAATGCCCTGATCGGACTGGAGAAACAGAAAACGGATATTAATGAAATATTTAAATGGAAGGGCGAGAAAAGGTCATTTACCACTTGGGAAAAAGACATGACACTAGGAGAAGCCATAAAGCTTTCTGCAGTCCCAGTCTATCAGGAACTTGCAAGACGTATCGGTCTTGATCTCATGCAAAAAGAAGTAGAACGTATCGATTTCGGTAATGCTGAAATTGGACAGCAGGTTGACAATTTCTGGTTGATAGGCCCATTAAAGGTCACGCCTATTCAAGAGGTAGAGTTTGTTTCTCAATTGGCACATACACAGCTTCCCTTTAGTGAAAAAGTGCAGGCTAATGTAAAAAATATGCTACTTCTAGAAGAGAGTAATGGCTACAAGATTTTTGGAAAGACTGGTTGGGTAATGGATATAAAACCACAAGTGGGCTGGTTGACCGGCTGGGTTGAGCAGCCAGATGGAAAAGTTGTCGCTTTTGCATTAAATATGGAAATGCAGTCAGAAATGCCTGCATCTATACGTAATGAATTATTGATGAAATCATTAAAACAGCTGAATATTATTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39672","NCBI_taxonomy_name":"Acinetobacter radioresistens","NCBI_taxonomy_id":"40216"}}}},"ARO_accession":"3008746","ARO_id":"47538","ARO_name":"OXA-969","CARD_short_name":"OXA-969","ARO_description":"OXA-23 family carbapenem-hydrolyzing class D beta-lactamase OXA-969.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46499":{"category_aro_accession":"3007710","category_aro_cvterm_id":"46499","category_aro_name":"OXA-23-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases, specifically imipenem, derived from OXA-23, first identified in Acinetobacter baumannii.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8165":{"model_id":"8165","model_name":"OXA-970","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10992":{"protein_sequence":{"accession":"QWA20169.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGILSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"MZ265722.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCAACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGTTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCCGCTATTCCAGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAGCTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGGTGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACTTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008747","ARO_id":"47539","ARO_name":"OXA-970","CARD_short_name":"OXA-970","ARO_description":"OXA-51 family carbapenem-hydrolyzing class D beta-lactamase OXA-970.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8166":{"model_id":"8166","model_name":"OXA-971","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10993":{"protein_sequence":{"accession":"QWA20170.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGKKRLFPEWEKNMTLGDAMKASAIPVYQDLARRNGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"MZ265723.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGTTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGATGGTAAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTAATGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAGTTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCATTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008748","ARO_id":"47540","ARO_name":"OXA-971","CARD_short_name":"OXA-971","ARO_description":"OXA-51 family carbapenem-hydrolyzing class D beta-lactamase OXA-971.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8167":{"model_id":"8167","model_name":"OXA-972","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10994":{"protein_sequence":{"accession":"QWA20171.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDKKAEKIKNLFNEAHTTGVLIIQQDQTQQSYGNDLARASTKYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLELLGIL"},"dna_sequence":{"accession":"MZ265724.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAATATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATAAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAATTATCCAACAAGACCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCAAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGACGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACGCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGCATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACTATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008749","ARO_id":"47541","ARO_name":"OXA-972","CARD_short_name":"OXA-972","ARO_description":"OXA-51 family carbapenem-hydrolyzing class D beta-lactamase OXA-972.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8168":{"model_id":"8168","model_name":"OXA-973","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10995":{"protein_sequence":{"accession":"QWA20172.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDKKAEKIKNLFNEAHATGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWNGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQHEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"MZ265725.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATAAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACGCTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACCACAGAAGTATTTAAGTGGAACGGGCAAAAAAGGCTGTTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAACATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008750","ARO_id":"47542","ARO_name":"OXA-973","CARD_short_name":"OXA-973","ARO_description":"OXA-51 family carbapenem-hydrolyzing class D beta-lactamase OXA-973.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8169":{"model_id":"8169","model_name":"OXA-974","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10996":{"protein_sequence":{"accession":"QWA20173.1","sequence":"MNIKALLLITSAIFISACSPYIVTANPNHSASKSDKKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKSTTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"MZ265726.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATAAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCATCATAAGTCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCATTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008751","ARO_id":"47543","ARO_name":"OXA-974","CARD_short_name":"OXA-974","ARO_description":"OXA-51 family carbapenem-hydrolyzing class D beta-lactamase OXA-974.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8170":{"model_id":"8170","model_name":"OXA-975","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10997":{"protein_sequence":{"accession":"QWA20174.1","sequence":"MNFQALLLITSAIFISACSPYIVTANPNYSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRIGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTGWVVQPQGNIVAFSLNLEMKKGISSSVRKEITYRSLEQLSIL"},"dna_sequence":{"accession":"MZ265727.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACTTTCAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGACTGCTAATCCAAATTACAGTGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATAGGCCTTGAGCACCATAAGGCAACCACTACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTATTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAACAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATATCTAGCTCTGTTCGAAAAGAGATTACTTATAGAAGTTTAGAACAATTAAGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008752","ARO_id":"47544","ARO_name":"OXA-975","CARD_short_name":"OXA-975","ARO_description":"OXA-51 family carbapenem-hydrolyzing class D beta-lactamase OXA-975.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8171":{"model_id":"8171","model_name":"OXA-976","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10998":{"protein_sequence":{"accession":"QWA20175.1","sequence":"MNIKTLLLITSAIFISACSPYIVTANPNHSASKSDEKAEKIKNLFNEVHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHYKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSPKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"MZ265728.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAACACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGTTCACCTTATATAGTGACTGCTAATCCAAATCACAGCGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGTACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACTATAAGGCAACCACCACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCCAAAAGTCCAAGATGAAGTGCAATCCATGTTATTTATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGTTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008753","ARO_id":"47545","ARO_name":"OXA-976","CARD_short_name":"OXA-976","ARO_description":"OXA-51 family carbapenem-hydrolyzing class D beta-lactamase OXA-976.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8172":{"model_id":"8172","model_name":"OXA-977","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"10999":{"protein_sequence":{"accession":"QWA20176.1","sequence":"MNIKALLLITSAIFISACSPYIVSANPNHSASKSDDKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKDMTLGDAMKASAIPVYQDLARRIGLELMSKEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVDPQVGWLTGWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"},"dna_sequence":{"accession":"MZ265729.1","fmin":"0","fmax":"825","strand":"+","sequence":"ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGTCTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGACAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACTACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGGACATGACCCTAGGCGATGCCATGAAAGCTTCTGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAAGGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTGGTGGGTCCTTTAAAAATTACGCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCCTTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGTTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAGACCCACAAGTAGGCTGGTTAACTGGATGGGTTGTTCAGCCTCAAGGAAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35507","NCBI_taxonomy_name":"Acinetobacter baumannii","NCBI_taxonomy_id":"470"}}}},"ARO_accession":"3008754","ARO_id":"47546","ARO_name":"OXA-977","CARD_short_name":"OXA-977","ARO_description":"OXA-51 family carbapenem-hydrolyzing class D beta-lactamase OXA-977.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46514":{"category_aro_accession":"3007725","category_aro_cvterm_id":"46514","category_aro_name":"OXA-51-like beta-lactamase","category_aro_description":"The maximum number of blaOXA belonged to the OXA-51-like subfamily. An earlier study had reported that OXA-51-like enzymes were present exclusively in A. baumannii. Similar to most of the other OXA-type carbapenemases, the OXA-51-like enzymes show weak carbapenemase activity; however, the presence of the insertion sequence ISAba1 upstream of the blaOXA-51-like gene may provide a promoter that allows the overproduction of carbapenemase, and this results in carbapenem resistance.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8173":{"model_id":"8173","model_name":"OXA-978","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11000":{"protein_sequence":{"accession":"QWA20177.1","sequence":"MTKKALFFAIGTMFLSACSFNTVQQHQIQSISTNKNSEKIKSLFDQAQTEGVLVIKRGQTEEIYGNDIKRSSTEYVPASTFKMLNALIGLEHHKATPTEVFKWDGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGFDLMSKEVKRIGFGNADIGSKADDFWLVGPLKITPQQEAQFAYELAHKTLPFSKNVQEQVQSMLFIEEKNGRKIYAKSGWGWDVEPQVGWLTGWVVQPQGEIIAFSLNLEMKKGIPSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"MZ265730.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGACTAAAAAAGCTCTTTTCTTTGCCATTGGTACGATGTTTTTGTCGGCATGTTCTTTTAATACCGTACAACAACATCAAATACAGTCAATTTCTACCAATAAAAACTCAGAGAAAATTAAATCATTGTTTGATCAAGCACAAACTGAAGGTGTTTTAGTTATAAAACGTGGGCAAACAGAGGAAATCTATGGCAATGATATTAAAAGATCATCAACCGAATATGTTCCCGCCTCTACCTTTAAAATGTTAAATGCTTTGATTGGACTTGAGCATCATAAAGCAACACCAACTGAAGTGTTTAAATGGGATGGGCAAAAGCGTTTGTTTCCTGATTGGGAAAAGGACATGACTCTAGGCGATGCGATGAAAGCTTCTGCTATTCCAGTTTATCAGGAACTAGCTCGACGAATTGGCTTTGATCTTATGTCTAAAGAGGTAAAACGCATTGGTTTCGGTAATGCTGATATTGGTTCAAAAGCAGATGATTTTTGGCTCGTTGGTCCACTTAAAATTACACCTCAACAAGAAGCCCAGTTTGCTTATGAACTAGCCCATAAAACTCTTCCTTTTAGCAAAAATGTGCAAGAACAAGTTCAATCTATGCTGTTCATAGAAGAAAAAAATGGACGGAAAATTTATGCCAAAAGTGGTTGGGGATGGGATGTAGAGCCTCAAGTGGGCTGGTTAACAGGCTGGGTAGTTCAACCTCAAGGAGAAATTATAGCGTTCTCACTTAATTTAGAAATGAAAAAAGGCATACCTAGTTCTATTCGAAAAGAAATTGCTTATAAGGGATTAGAGCAGCTAGGTATTTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3008755","ARO_id":"47547","ARO_name":"OXA-978","CARD_short_name":"OXA-978","ARO_description":"OXA-213 family carbapenem-hydrolyzing class D beta-lactamase OXA-978.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46495":{"category_aro_accession":"3007706","category_aro_cvterm_id":"46495","category_aro_name":"OXA-213-like beta-lactamase","category_aro_description":"OXA-213-like enzymes have been identified to be intrinsic to A. calcoaceticus and have been subsequently detected in A. pittii. Phylogenetic analysis of OXA-213-like proteins identified two distinct subgroups within the OXA family. The first group was linked to A. pittii and the second group to A. calcoaceticus. The carbapenemase activity of these OXAs may be related to the species-dependent effect.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8174":{"model_id":"8174","model_name":"OXA-979","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11001":{"protein_sequence":{"accession":"QWA20178.1","sequence":"MIKQALFFAISTIFLSACSFNTVQQQQIHAISTHKNSEEIKSLFDQAQTTGVLVIKRGNTEEIYGNDLKRASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMSKEVKRIGFGNADIGSKVDNFWLVGPLKITPQQEAQFADELAHKTLPFSKNVQEQVQSMVFVEEKNGRKIYAKSGWGWDVEPQVGWLTGWVVQPQGEIVAFSLNLEMKKGTPSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"MZ265731.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGATTAAACAAGCTCTTTTCTTTGCCATTAGTACCATATTTTTGTCAGCATGTTCTTTCAATACAGTACAACAGCAGCAAATACACGCTATTTCTACTCATAAAAATTCAGAAGAAATAAAATCGCTGTTTGATCAAGCACAGACCACAGGTGTTTTGGTTATTAAGCGTGGAAATACAGAGGAAATTTATGGCAATGATCTAAAAAGGGCATCAACCGAATATGTCCCTGCATCTACCTTTAAAATGCTAAATGCTTTAATTGGTCTTGAACATCATAAAGCAACAACAACTGAAGTGTTTAAATGGGATGGACAAAAGCGTTTATTTCCTGATTGGGAAAAGGATATGACTCTAGGTGATGCCATGAAAGCTTCTGCTATTCCAGTTTATCAAGAACTAGCTCGACGAATTGGCCTTGATCTTATGTCCAAAGAGGTCAAGCGTATTGGTTTCGGTAATGCTGATATTGGTTCAAAAGTAGATAATTTTTGGCTTGTCGGTCCACTCAAAATTACGCCTCAACAGGAAGCACAGTTTGCTGATGAATTAGCACATAAAACTCTTCCTTTTAGCAAAAATGTACAAGAACAAGTTCAATCTATGGTGTTCGTAGAAGAAAAAAACGGACGTAAAATTTACGCTAAAAGCGGTTGGGGATGGGATGTGGAGCCTCAAGTGGGCTGGTTAACAGGCTGGGTCGTTCAACCACAAGGAGAAATTGTAGCGTTCTCACTCAATTTAGAAATGAAAAAAGGAACACCTAGTTCTATTCGAAAAGAAATTGCTTATAAAGGATTAGAACAGCTAGGTATTTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42801","NCBI_taxonomy_name":"Acinetobacter lactucae","NCBI_taxonomy_id":"1785128"}}}},"ARO_accession":"3008756","ARO_id":"47548","ARO_name":"OXA-979","CARD_short_name":"OXA-979","ARO_description":"OXA-213 family carbapenem-hydrolyzing class D beta-lactamase OXA-979.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46495":{"category_aro_accession":"3007706","category_aro_cvterm_id":"46495","category_aro_name":"OXA-213-like beta-lactamase","category_aro_description":"OXA-213-like enzymes have been identified to be intrinsic to A. calcoaceticus and have been subsequently detected in A. pittii. Phylogenetic analysis of OXA-213-like proteins identified two distinct subgroups within the OXA family. The first group was linked to A. pittii and the second group to A. calcoaceticus. The carbapenemase activity of these OXAs may be related to the species-dependent effect.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8175":{"model_id":"8175","model_name":"OXA-980","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11002":{"protein_sequence":{"accession":"QWA20179.1","sequence":"MTKKALFFAIGTMFLSACSFNTVEQHQIQLISTNKNSEKIKSLFDQAQTEGVLVIKRGQIEEVYGNDLKRASTEYFPASTFKMLNALIGLEHHKATPTEVFKWDGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMSKEVKRIGFGNADIGSKVDNFWLVGPLKITPQQEVQFAYKLAHKTLPFSKNVQEQVQSMLFIEEKNGRKIYAKSGWGWDVEPQVGWFTGWIVQPQGEIIAFSLNLEMKKGIPSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"MZ265732.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGACTAAAAAAGCTCTTTTCTTTGCCATTGGTACGATGTTTTTATCGGCATGTTCTTTTAATACGGTAGAACAGCATCAAATACAGTTAATTTCTACCAATAAAAACTCAGAGAAAATTAAATCATTGTTTGATCAAGCACAAACTGAAGGTGTTTTAGTTATAAAACGTGGGCAAATAGAGGAAGTCTATGGCAATGATCTTAAAAGAGCATCAACCGAATATTTTCCCGCCTCTACCTTTAAAATGTTAAATGCTTTGATTGGACTTGAGCATCATAAAGCAACGCCAACTGAAGTGTTTAAATGGGATGGGCAAAAGCGTTTATTTCCCGATTGGGAAAAAGACATGACATTAGGCGATGCTATGAAAGCTTCTGCTATTCCAGTTTATCAGGAACTAGCTCGACGAATTGGCCTTGATCTTATGTCTAAAGAGGTAAAGCGCATTGGTTTCGGTAATGCTGATATTGGTTCAAAAGTAGATAATTTTTGGCTTGTTGGCCCACTTAAAATTACACCTCAACAAGAAGTACAGTTTGCTTATAAATTAGCCCACAAAACTCTTCCCTTTAGCAAAAATGTACAAGAACAAGTTCAATCTATGCTGTTCATAGAAGAAAAAAATGGACGAAAAATTTATGCCAAAAGTGGTTGGGGATGGGATGTGGAGCCTCAAGTGGGCTGGTTTACAGGCTGGATCGTTCAACCTCAGGGAGAAATTATAGCTTTCTCACTTAATTTAGAAATGAAGAAAGGCATACCTAGTTCTATTCGAAAAGAAATTGCTTATAAGGGATTAGAGCAGCTAGGTATTTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42801","NCBI_taxonomy_name":"Acinetobacter lactucae","NCBI_taxonomy_id":"1785128"}}}},"ARO_accession":"3008757","ARO_id":"47549","ARO_name":"OXA-980","CARD_short_name":"OXA-980","ARO_description":"OXA-213 family carbapenem-hydrolyzing class D beta-lactamase OXA-980.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46495":{"category_aro_accession":"3007706","category_aro_cvterm_id":"46495","category_aro_name":"OXA-213-like beta-lactamase","category_aro_description":"OXA-213-like enzymes have been identified to be intrinsic to A. calcoaceticus and have been subsequently detected in A. pittii. Phylogenetic analysis of OXA-213-like proteins identified two distinct subgroups within the OXA family. The first group was linked to A. pittii and the second group to A. calcoaceticus. The carbapenemase activity of these OXAs may be related to the species-dependent effect.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8176":{"model_id":"8176","model_name":"OXA-981","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11003":{"protein_sequence":{"accession":"QWA20180.1","sequence":"MNKKLNLALLCFLSILCAACQSNQQLSANSHTENHNTRAAEIPLLFDEMHTQAVFVTYDGQHFQSYGNALQRADTAYVPASTFKMLNALIGLQNHKATNTEVFKWDGQKRAMSIWEKDMTLSDAMKVSAVPVYQELARRIGLDLMQKEVTRVGYGNTDIGTVVDRFWLDGPLKITPKQEAQFAYQLATQQLPFDQNVQSQVKDMLYVESRGQSKLFAKSGLSMKNGQPDIGWYTGWVEQADGKIVAFSINMQMVQGLDVNSRQQATLDILDKLGIFFYL"},"dna_sequence":{"accession":"MZ265733.1","fmin":"0","fmax":"840","strand":"+","sequence":"ATGAATAAAAAATTGAATTTGGCACTTTTGTGTTTTTTGAGTATTTTGTGTGCAGCTTGTCAGTCTAATCAACAACTGTCGGCTAATTCACATACTGAAAACCACAATACCCGCGCAGCAGAAATCCCGCTTCTTTTCGATGAGATGCATACTCAAGCAGTATTTGTGACCTATGACGGTCAGCATTTTCAGAGCTACGGTAATGCTTTACAAAGAGCAGATACTGCCTACGTTCCTGCTTCGACATTTAAAATGTTAAATGCATTGATTGGACTGCAAAATCATAAAGCAACCAACACCGAAGTCTTTAAATGGGATGGTCAAAAAAGGGCAATGTCGATCTGGGAAAAAGACATGACCTTATCCGATGCCATGAAAGTTTCAGCTGTACCGGTTTATCAAGAATTGGCGCGTCGTATTGGCTTGGATTTGATGCAAAAGGAAGTAACGCGGGTTGGATATGGCAATACGGATATTGGCACTGTTGTTGATCGTTTTTGGCTAGATGGACCACTGAAGATTACACCTAAACAAGAAGCCCAATTTGCATATCAATTGGCAACACAACAATTGCCATTTGATCAAAATGTGCAAAGCCAAGTTAAAGATATGCTGTATGTGGAAAGTCGAGGGCAATCCAAGCTTTTTGCCAAGTCTGGTTTGAGCATGAAAAATGGGCAACCTGACATCGGTTGGTATACGGGTTGGGTTGAACAAGCCGATGGCAAAATTGTGGCTTTTTCCATCAATATGCAAATGGTACAGGGGCTAGATGTCAATAGCCGTCAGCAGGCAACACTGGATATCTTGGATAAATTGGGCATATTTTTTTATTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42557","NCBI_taxonomy_name":"Acinetobacter gerneri","NCBI_taxonomy_id":"202952"}}}},"ARO_accession":"3008758","ARO_id":"47550","ARO_name":"OXA-981","CARD_short_name":"OXA-981","ARO_description":"Class D beta-lactamase OXA-981.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8177":{"model_id":"8177","model_name":"OXA-982","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11004":{"protein_sequence":{"accession":"QWA20181.1","sequence":"MSKKLKLLALCAAVISAATLVGCQNIQSQAQPLVLKKQTQDQIATAFENIQTTGVLVTYDGKNFQKYGNDLSRADQRYIPASTFKMLNALIGIQHHKTSPNEVFKWDGQKRAFRSWEKDLTLAEAMQASAVPVYQELARRIGLELMASEVKRVGYGNQNIGTQVDNFWLVGPLEITPVEEVKFAYALAKQQLPFDPSTQQQVRDMLLIENVQGTRIYAKSGWGMDVNPQVGWWTGWIEQPNGQVTAFSLNMEMKKAEHADARKAIIYQALQQLGLLPQ"},"dna_sequence":{"accession":"MZ265734.1","fmin":"0","fmax":"837","strand":"+","sequence":"ATGTCTAAAAAATTAAAATTACTCGCGCTTTGTGCAGCTGTGATCTCAGCTGCAACACTGGTTGGTTGTCAAAATATTCAGTCCCAAGCTCAACCTCTAGTCTTAAAGAAACAGACGCAGGATCAGATCGCAACTGCATTCGAAAATATCCAGACAACCGGTGTATTGGTCACCTATGATGGCAAAAATTTTCAAAAATATGGCAATGATCTCAGCCGTGCAGATCAGCGTTACATTCCTGCCTCAACTTTTAAAATGCTCAATGCCTTGATTGGTATACAGCACCATAAAACCTCACCTAATGAAGTGTTTAAATGGGATGGACAGAAACGGGCTTTTCGTAGCTGGGAGAAGGACTTAACGCTTGCTGAGGCGATGCAAGCTTCAGCTGTACCTGTCTATCAGGAGCTGGCGCGCCGTATCGGTCTAGAATTAATGGCAAGTGAAGTAAAGCGGGTTGGTTATGGTAATCAAAATATAGGGACGCAAGTTGATAATTTTTGGTTAGTGGGGCCTTTAGAAATTACGCCAGTTGAGGAAGTAAAATTTGCCTATGCCTTAGCCAAACAGCAACTTCCATTTGATCCCTCAACACAGCAGCAAGTCAGAGATATGTTGTTGATCGAAAATGTTCAGGGAACCAGAATCTATGCCAAGAGTGGTTGGGGAATGGATGTAAATCCTCAAGTTGGATGGTGGACGGGTTGGATTGAACAACCAAATGGTCAAGTCACAGCATTTTCGCTGAATATGGAAATGAAAAAAGCAGAACATGCGGATGCGCGTAAAGCGATTATTTATCAAGCTTTACAACAGTTAGGTTTATTACCTCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"47901","NCBI_taxonomy_name":"Acinetobacter vivianii","NCBI_taxonomy_id":"1776742"}}}},"ARO_accession":"3008759","ARO_id":"47551","ARO_name":"OXA-982","CARD_short_name":"OXA-982","ARO_description":"OXA-294 family class D beta-lactamase OXA-982.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46504":{"category_aro_accession":"3007715","category_aro_cvterm_id":"46504","category_aro_name":"OXA-294-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-294.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8178":{"model_id":"8178","model_name":"OXA-983","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11005":{"protein_sequence":{"accession":"QWA20182.1","sequence":"MKFKMKGLFCVILSSLAFSGCVYDSKLQRPVISERETEIPLLFNQAQTQAVFVTYDGIHLKSYGNDLSRAKTEYIPASTFKMLNALIGLQNAKATNTEVFHWNGEKRAFSAWEKDMTLAEAMQASAVPVYQELARRIGLELMREEVKRVGFGNAEIGQQVDNFWLVGPLKISPEQEVQFAYQLAMKQLPFDRNVQQQVKDMLYIERRGDSKLYAKSGWGMDVEPQVGWYTGWVEQPDGKVTAFALNMNMQAGDDPAERKQLTLSILDKLGLFFYLR"},"dna_sequence":{"accession":"MZ265735.1","fmin":"0","fmax":"831","strand":"+","sequence":"ATGAAGTTTAAAATGAAAGGTTTATTTTGTGTCATCCTCAGTAGTTTGGCATTTTCAGGTTGTGTTTATGATTCAAAACTACAACGCCCAGTCATATCAGAGCGAGAAACTGAGATTCCTTTATTATTTAATCAAGCACAGACTCAAGCTGTGTTTGTTACTTATGATGGGATTCATCTAAAAAGTTATGGTAATGATCTAAGCCGAGCAAAGACTGAATATATTCCTGCATCTACATTTAAGATGTTGAATGCTTTAATTGGCTTGCAAAATGCAAAAGCAACCAATACTGAAGTATTTCATTGGAATGGTGAAAAGCGCGCTTTTTCAGCATGGGAAAAAGATATGACTTTGGCAGAAGCGATGCAGGCTTCAGCTGTTCCCGTATATCAGGAGCTTGCTCGACGTATTGGCTTGGAATTGATGCGTGAAGAAGTGAAGCGTGTAGGTTTTGGCAATGCGGAGATTGGTCAGCAAGTCGATAATTTTTGGTTGGTGGGTCCTTTAAAAATCTCCCCTGAACAAGAAGTTCAATTTGCCTATCAACTGGCAATGAAGCAATTACCTTTTGATCGAAATGTACAGCAACAAGTCAAAGATATGCTTTATATCGAGAGACGTGGTGACAGTAAACTGTATGCTAAAAGTGGTTGGGGAATGGATGTTGAACCTCAAGTGGGTTGGTATACGGGATGGGTTGAACAACCCGATGGCAAGGTGACTGCATTTGCGTTAAATATGAACATGCAAGCAGGTGATGATCCAGCTGAACGTAAACAATTAACCTTAAGTATTTTGGACAAATTGGGTCTATTTTTTTATTTAAGATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39090","NCBI_taxonomy_name":"Acinetobacter bereziniae","NCBI_taxonomy_id":"106648"}}}},"ARO_accession":"3008760","ARO_id":"47552","ARO_name":"OXA-983","CARD_short_name":"OXA-983","ARO_description":"OXA-229 family carbapenem-hydrolyzing class D beta-lactamase OXA-983.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46498":{"category_aro_accession":"3007709","category_aro_cvterm_id":"46498","category_aro_name":"OXA-229-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-229.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8179":{"model_id":"8179","model_name":"OXA-984","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11006":{"protein_sequence":{"accession":"QWA20183.1","sequence":"MPKKLKLLVLSVVVMPSIILLGCQNIQPHVQALVTQKQTEDQIATAFENIQTSGVLVTYDGKTIQTYGNALNRADQRYIPASTFKMLNALIGIQHHKTSPNEVFKWDGQKRAFTSWEKDLTLAEAMQASAVPVYQELARRIGLELMASEVKRVGYGNQSIGTQVDNFWLVGPLEITPVEEVKFAYALAKKQLAFDSSTQQQVKDMLLIEDIQGTKIYAKSGWGMDVNPQVGWWTGWVEQPNGQVTAFSLNMEMKKAAHAEARKAIVYQALQQLGLIGQ"},"dna_sequence":{"accession":"MZ265736.1","fmin":"0","fmax":"837","strand":"+","sequence":"ATGCCGAAAAAATTAAAATTACTCGTTCTATCTGTAGTTGTGATGCCCTCAATAATATTATTGGGCTGCCAAAATATTCAGCCACACGTTCAAGCTTTAGTCACACAGAAACAGACTGAAGATCAGATCGCAACTGCATTTGAAAATATCCAGACCTCCGGTGTACTGGTCACTTATGATGGCAAAACTATTCAAACATATGGCAATGCGCTTAACCGGGCCGATCAGCGCTATATTCCGGCTTCTACTTTTAAAATGCTGAATGCTTTGATTGGTATCCAGCATCATAAGACTTCACCGAATGAAGTATTTAAATGGGATGGACAGAAGCGGGCTTTTACCAGCTGGGAAAAAGACTTAACCCTGGCAGAAGCCATGCAGGCTTCGGCTGTACCTGTGTATCAGGAACTGGCGCGCCGTATCGGTCTGGAATTAATGGCCAGTGAAGTAAAACGGGTCGGGTATGGCAATCAGTCGATTGGAACGCAAGTGGATAATTTCTGGTTAGTGGGACCTTTAGAAATTACCCCTGTTGAGGAAGTAAAATTTGCCTATGCCTTGGCGAAAAAACAACTTGCATTTGACTCATCAACCCAGCAACAAGTTAAAGATATGTTGCTGATTGAAGATATTCAGGGCACCAAAATCTATGCCAAAAGCGGATGGGGCATGGATGTAAATCCTCAGGTGGGATGGTGGACAGGTTGGGTAGAACAACCCAATGGACAGGTCACTGCATTTTCACTGAATATGGAAATGAAAAAGGCAGCACATGCAGAAGCACGTAAAGCCATTGTTTATCAGGCCCTGCAACAGCTCGGTTTAATTGGGCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41219","NCBI_taxonomy_name":"Acinetobacter courvalinii","NCBI_taxonomy_id":"280147"}}}},"ARO_accession":"3008761","ARO_id":"47553","ARO_name":"OXA-984","CARD_short_name":"OXA-984","ARO_description":"OXA-294 family class D beta-lactamase OXA-984.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46504":{"category_aro_accession":"3007715","category_aro_cvterm_id":"46504","category_aro_name":"OXA-294-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-294.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8180":{"model_id":"8180","model_name":"OXA-985","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11007":{"protein_sequence":{"accession":"QWA20184.1","sequence":"MSKKALFFAISTIFLSACSFNTVQQHQIHAISTHKNSEEIKSLFDRAQTTGVLVIKRGQTEEIYGNDLKRASTEYVPASTFKMLNALIGLEHHKATPTEVFKWDGQKRLFPDWEKDMTLGEAMKASAIPVYQELARRIGLDLMSKEVKRIGFGNADIGSKVDNFWLVGPLKITPQQEAQFAYELAHKTLPFSKNVQEQVQSMVFVEEKNGRKIYAKSGWGWDVDPQVGWLTGWVIQPQGEIVAFSLNLEMKKGTPSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"MZ265737.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGTCTAAAAAAGCTCTTTTCTTTGCCATTAGTACTATATTTTTGTCAGCATGTTCTTTCAATACAGTACAACAGCACCAAATACATGCTATTTCTACTCATAAAAATTCAGAAGAAATTAAATCACTGTTTGATCGGGCACAGACCACGGGAGTTTTAGTGATTAAGCGTGGGCAAACCGAAGAAATTTATGGCAATGATCTTAAAAGAGCATCAACCGAATATGTTCCCGCCTCTACATTTAAAATGCTAAATGCTTTGATTGGACTTGAACATCATAAAGCAACACCAACTGAAGTGTTTAAATGGGACGGGCAAAAGCGTTTATTTCCTGATTGGGAAAAGGATATGACTCTGGGTGAGGCCATGAAAGCTTCTGCTATTCCTGTCTATCAAGAACTAGCGCGAAGAATTGGCCTTGATCTTATGTCCAAAGAGGTCAAGCGTATTGGTTTCGGTAATGCTGATATTGGTTCAAAAGTAGATAATTTTTGGCTTGTCGGTCCACTCAAAATTACACCTCAACAGGAAGCACAGTTTGCTTATGAATTAGCACATAAAACTCTTCCCTTTAGCAAAAATGTACAAGAACAAGTTCAATCTATGGTGTTCGTAGAAGAAAAAAACGGACGTAAAATTTACGCTAAAAGCGGTTGGGGATGGGATGTGGATCCTCAAGTGGGCTGGTTAACAGGCTGGGTCATTCAACCACAAGGTGAAATTGTGGCATTCTCGCTCAATTTAGAAATGAAAAAAGGAACACCTAGTTCTATTCGAAAAGAAATTGCTTATAAAGGATTAGAGCAGCTAGGTATTTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42801","NCBI_taxonomy_name":"Acinetobacter lactucae","NCBI_taxonomy_id":"1785128"}}}},"ARO_accession":"3008762","ARO_id":"47554","ARO_name":"OXA-985","CARD_short_name":"OXA-985","ARO_description":"OXA-213 family carbapenem-hydrolyzing class D beta-lactamase OXA-985.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46495":{"category_aro_accession":"3007706","category_aro_cvterm_id":"46495","category_aro_name":"OXA-213-like beta-lactamase","category_aro_description":"OXA-213-like enzymes have been identified to be intrinsic to A. calcoaceticus and have been subsequently detected in A. pittii. Phylogenetic analysis of OXA-213-like proteins identified two distinct subgroups within the OXA family. The first group was linked to A. pittii and the second group to A. calcoaceticus. The carbapenemase activity of these OXAs may be related to the species-dependent effect.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8181":{"model_id":"8181","model_name":"OXA-986","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11008":{"protein_sequence":{"accession":"QWA20185.1","sequence":"MTKKALFFAIGTMFLSACSFNTVQQHQIQSISTNKNSEKIKSLFDQAQTEGVLVIKRGQTEEIYGNDLKRSSTEYVPASTFKMLNALIGLEHHKATPTEVFKWDGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMSKEVKRIGFSNADIGSKVDNFWLVGPLKITPQQEAQFAYELAHKTLPFSKNVQEQVQSMLFIEEKNGRKIYAKSGWGWDVEPQVGWFTGWVVQPQGEIVAFSLNLEMKKGIPSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"MZ265738.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGACTAAAAAAGCTCTTTTCTTTGCCATTGGTACGATGTTTTTGTCGGCATGTTCTTTTAATACCGTACAACAACATCAAATACAGTCAATTTCTACCAATAAAAACTCAGAGAAAATTAAATCATTGTTTGATCAAGCACAAACTGAAGGTGTTTTAGTTATAAAACGTGGGCAAACAGAGGAAATCTATGGCAATGATCTTAAAAGATCATCAACCGAATATGTTCCCGCCTCTACCTTTAAAATGTTAAATGCTTTGATTGGACTTGAGCATCATAAAGCAACACCAACTGAAGTGTTTAAATGGGATGGGCAAAAGCGTTTGTTTCCTGATTGGGAAAAGGACATGACTCTAGGCGATGCGATGAAAGCTTCTGCTATTCCAGTTTATCAGGAACTAGCTCGACGAATTGGCCTTGATCTTATGTCTAAAGAGGTAAAACGCATTGGTTTCAGTAATGCTGATATTGGTTCAAAAGTAGATAATTTTTGGCTTGTCGGTCCACTCAAAATTACGCCTCAACAGGAAGCACAGTTTGCGTATGAATTAGCACATAAAACTCTTCCCTTTAGCAAAAATGTACAAGAACAAGTTCAATCTATGCTGTTCATAGAAGAAAAAAATGGACGAAAAATTTATGCCAAAAGTGGTTGGGGATGGGATGTGGAGCCTCAAGTGGGCTGGTTTACAGGCTGGGTCGTTCAACCTCAAGGAGAAATTGTAGCGTTCTCACTCAATTTAGAAATGAAGAAAGGCATACCTAGTTCTATTCGAAAAGAAATTGCTTATAAGGGATTAGAGCAGCTAGGTATTTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3008763","ARO_id":"47555","ARO_name":"OXA-986","CARD_short_name":"OXA-986","ARO_description":"OXA-213 family carbapenem-hydrolyzing class D beta-lactamase OXA-986.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46495":{"category_aro_accession":"3007706","category_aro_cvterm_id":"46495","category_aro_name":"OXA-213-like beta-lactamase","category_aro_description":"OXA-213-like enzymes have been identified to be intrinsic to A. calcoaceticus and have been subsequently detected in A. pittii. Phylogenetic analysis of OXA-213-like proteins identified two distinct subgroups within the OXA family. The first group was linked to A. pittii and the second group to A. calcoaceticus. The carbapenemase activity of these OXAs may be related to the species-dependent effect.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8182":{"model_id":"8182","model_name":"OXA-987","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11009":{"protein_sequence":{"accession":"QWA20186.1","sequence":"MYKKVLVVATATLFLSACSSNTVKQHQIHSISANKNSEEIKYLFDQAQTTGVLVIKRGQTEEIYGNDLKRASTAYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMSKEVKRIGFGNANIGSKVDNFWLVGPLKITPQQETQFAYQLALKTLPFSQDVQEQVQSMVFIEEKNGSKIYAKSGWGWDVEPQVGWLTGWVIQPQGEIVAFSLNLEMKKGIPSSIRKEIAYKGLEQLGVL"},"dna_sequence":{"accession":"MZ265739.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGTATAAAAAAGTCCTTGTCGTTGCGACAGCTACTCTATTTTTATCTGCCTGCTCCTCTAACACGGTAAAACAACATCAAATACATTCTATTTCCGCCAATAAAAATTCAGAAGAAATTAAATATCTGTTTGATCAGGCACAGACCACAGGAGTTTTAGTGATTAAGCGTGGGCAAACCGAAGAAATTTATGGCAATGATCTTAAAAGAGCATCAACCGCTTATGTTCCCGCCTCTACCTTTAAAATGTTAAATGCTTTAATTGGACTTGAACATCATAAGGCAACTACAACTGAAGTATTTAAATGGGATGGGCAAAAACGTTTATTTCCTGATTGGGAAAAGGACATGACACTGGGCGATGCCATGAAAGCTTCTGCGATTCCAGTTTACCAAGAATTAGCCCGACGAATTGGTCTAGATCTTATGTCTAAAGAGGTGAAACGAATTGGTTTTGGTAATGCTAACATTGGTTCAAAAGTAGATAATTTTTGGCTCGTTGGCCCTCTAAAAATTACACCTCAACAAGAAACCCAATTTGCTTATCAATTAGCCCTTAAAACGCTTCCATTTAGCCAAGATGTACAAGAACAAGTTCAATCAATGGTGTTCATAGAGGAAAAAAATGGAAGTAAAATTTATGCCAAAAGTGGTTGGGGGTGGGATGTTGAACCACAAGTTGGCTGGTTAACCGGTTGGGTCATTCAACCACAAGGAGAAATTGTGGCATTCTCGCTCAATTTAGAAATGAAAAAAGGAATTCCTAGTTCTATTCGAAAAGAAATTGCTTATAAAGGATTAGAACAACTCGGTGTTTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"47899","NCBI_taxonomy_name":"Acinetobacter oleivorans","NCBI_taxonomy_id":"1148157"}}}},"ARO_accession":"3008764","ARO_id":"47556","ARO_name":"OXA-987","CARD_short_name":"OXA-987","ARO_description":"OXA-213 family carbapenem-hydrolyzing class D beta-lactamase OXA-987.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46495":{"category_aro_accession":"3007706","category_aro_cvterm_id":"46495","category_aro_name":"OXA-213-like beta-lactamase","category_aro_description":"OXA-213-like enzymes have been identified to be intrinsic to A. calcoaceticus and have been subsequently detected in A. pittii. Phylogenetic analysis of OXA-213-like proteins identified two distinct subgroups within the OXA family. The first group was linked to A. pittii and the second group to A. calcoaceticus. The carbapenemase activity of these OXAs may be related to the species-dependent effect.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8183":{"model_id":"8183","model_name":"OXA-988","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11010":{"protein_sequence":{"accession":"QWA20187.1","sequence":"MTKKALFFAIGTMFLSACSFNTVQQHQIQSISTNKNSEKIKSLFEQAQTEGVLVIKRGQTEEIYGNDLKRSSTEYVPASTFKMLNALIGLEHHKATPTEVFKWYGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMSKEVKRIGFGNADIGSKVDDFWLVGPLKITPQQEVRFAYKLANKTLPFSKNVQEQVQSMLFIEEKNGRKIYAKSGWGWDVDPQVGWFTGWIVQPQGEIIAFSLNLEMKKGIPSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"MZ265740.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGACTAAAAAAGCTCTTTTCTTTGCCATTGGTACGATGTTTTTGTCGGCATGTTCTTTTAATACCGTACAACAACATCAAATACAGTCAATTTCTACCAATAAAAACTCAGAGAAAATTAAATCATTGTTTGAACAAGCACAAACTGAAGGTGTTTTAGTTATAAAACGTGGGCAAACAGAGGAAATCTATGGCAATGATCTTAAAAGATCATCAACCGAATATGTTCCCGCCTCTACCTTTAAAATGTTAAATGCTTTGATAGGACTTGAGCATCATAAAGCAACACCAACTGAAGTGTTTAAATGGTATGGGCAAAAGCGTTTATTTCCCGATTGGGAAAAAGACATGACTCTAGGCGATGCGATGAAAGCTTCTGCTATTCCAGTTTATCAGGAACTAGCTCGACGAATTGGCCTTGATCTTATGTCTAAAGAGGTAAAACGCATTGGTTTCGGTAATGCTGATATTGGTTCAAAAGTAGATGATTTTTGGCTTGTTGGTCCACTTAAAATTACACCTCAACAAGAAGTACGGTTTGCTTATAAATTAGCCAACAAAACTCTTCCCTTTAGCAAAAATGTACAAGAACAAGTTCAATCTATGCTGTTCATTGAAGAAAAAAATGGACGAAAAATTTATGCCAAAAGTGGTTGGGGATGGGATGTGGATCCTCAAGTGGGTTGGTTTACAGGCTGGATCGTTCAACCTCAGGGAGAAATTATAGCTTTCTCACTTAATTTAGAAATGAAGAAAGGCATACCTAGTTCTATTCGAAAAGAAATTGCTTATAAAGGATTAGAGCAGCTAGGTATTTTATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3008765","ARO_id":"47557","ARO_name":"OXA-988","CARD_short_name":"OXA-988","ARO_description":"OXA-213 family carbapenem-hydrolyzing class D beta-lactamase OXA-988.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46495":{"category_aro_accession":"3007706","category_aro_cvterm_id":"46495","category_aro_name":"OXA-213-like beta-lactamase","category_aro_description":"OXA-213-like enzymes have been identified to be intrinsic to A. calcoaceticus and have been subsequently detected in A. pittii. Phylogenetic analysis of OXA-213-like proteins identified two distinct subgroups within the OXA family. The first group was linked to A. pittii and the second group to A. calcoaceticus. The carbapenemase activity of these OXAs may be related to the species-dependent effect.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8184":{"model_id":"8184","model_name":"OXA-989","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11011":{"protein_sequence":{"accession":"QWA20188.1","sequence":"MIKQALFFAISTIFLSACSFNTVQQQQIHAISTHKNSEEIKSLFDQAQTTGVLVIKRGNTEEIYGNDLKRASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMSKEVKRIGFGNADIGSKVDDFWLVGPLKITPQQETQFADELAHKTLPFSKNVQEQVQSMVFVEEKNGRKIYAKSGWGWDVEPQVGWLTGWVVQPQGEIVAFSLNLEMKKGTPSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"MZ265741.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGATTAAACAAGCTCTTTTCTTTGCCATTAGTACCATATTTTTGTCAGCATGTTCTTTCAATACAGTACAACAGCAGCAAATACACGCTATTTCTACTCATAAAAATTCAGAAGAAATAAAATCTCTGTTTGATCAAGCACAGACCACAGGTGTTTTGGTTATTAAGCGCGGAAATACAGAGGAAATTTATGGCAATGATCTAAAAAGGGCATCAACCGAATATGTCCCTGCATCTACCTTTAAAATGCTAAATGCTTTAATTGGTCTTGAACATCATAAAGCAACAACAACTGAAGTGTTTAAATGGGATGGACAAAAGCGTTTATTTCCTGATTGGGAAAAGGATATGACTCTAGGTGATGCCATGAAAGCTTCTGCTATTCCTGTGTATCAAGAACTAGCTCGACGAATTGGCCTTGATCTTATGTCCAAAGAGGTCAAGCGTATTGGCTTCGGTAATGCTGATATTGGTTCAAAAGTAGATGATTTTTGGCTTGTAGGTCCACTCAAAATTACGCCTCAACAGGAAACACAGTTTGCTGATGAATTAGCACATAAAACTCTTCCCTTTAGCAAAAATGTACAAGAACAAGTCCAATCTATGGTGTTCGTAGAAGAAAAAAACGGACGTAAAATTTACGCTAAAAGCGGTTGGGGATGGGATGTGGAGCCTCAAGTGGGCTGGTTAACAGGCTGGGTCGTTCAACCACAAGGAGAAATTGTAGCGTTCTCACTCAATTTAGAAATGAAAAAAGGAACACCTAGTTCTATTCGAAAAGAAATTGCTTATAAAGGATTAGAACAGCTAGGTATTTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42801","NCBI_taxonomy_name":"Acinetobacter lactucae","NCBI_taxonomy_id":"1785128"}}}},"ARO_accession":"3008766","ARO_id":"47558","ARO_name":"OXA-989","CARD_short_name":"OXA-989","ARO_description":"OXA-213 family carbapenem-hydrolyzing class D beta-lactamase OXA-989.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46495":{"category_aro_accession":"3007706","category_aro_cvterm_id":"46495","category_aro_name":"OXA-213-like beta-lactamase","category_aro_description":"OXA-213-like enzymes have been identified to be intrinsic to A. calcoaceticus and have been subsequently detected in A. pittii. Phylogenetic analysis of OXA-213-like proteins identified two distinct subgroups within the OXA family. The first group was linked to A. pittii and the second group to A. calcoaceticus. The carbapenemase activity of these OXAs may be related to the species-dependent effect.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8185":{"model_id":"8185","model_name":"OXA-990","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11012":{"protein_sequence":{"accession":"QWA20189.1","sequence":"MYKKALIAATSILFLSSCSSNTVKQHQIHSISANKNSEEIKSLFDQAQTMGVLVIKREQTEEIYGNDLKRASTAYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPDWEKDMTLGDAMKASAIPVYQELARRIGLDLMSKEVKRVGFGNASIGSKVDNFWLVGPLKITPQQETQFAYQLALKTLPFSKNVQEQVQSMVFIEEKNGSKIYAKSGWGWDVEPQVGWLTGWVVQPQGEIVAFSLNLEMKKGTASSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"MZ265742.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGTATAAAAAAGCCCTTATCGCAGCAACAAGTATCCTATTTTTATCCTCCTGTTCTTCCAATACGGTAAAACAACATCAAATACACTCTATTTCTGCCAATAAAAATTCAGAAGAAATTAAATCACTGTTTGATCAGGCACAGACCATGGGTGTTTTGGTGATTAAGCGAGAGCAAACAGAAGAAATTTATGGCAATGATCTTAAAAGAGCATCAACCGCCTATGTTCCCGCCTCTACCTTTAAAATGTTAAATGCTTTAATTGGACTTGAACATCATAAGGCAACTACAACTGAAGTATTTAAATGGGATGGGCAAAAACGTTTATTTCCTGATTGGGAAAAGGACATGACACTGGGTGATGCCATGAAAGCTTCTGCGATTCCAGTTTACCAAGAATTAGCCCGACGAATTGGTCTAGATCTTATGTCTAAAGAGGTGAAACGAGTTGGTTTTGGTAATGCTAGCATTGGTTCAAAAGTAGATAATTTTTGGCTTGTTGGCCCTCTAAAAATTACACCTCAACAAGAAACCCAATTTGCTTATCAATTAGCCCTTAAAACTCTTCCATTCAGCAAAAATGTACAAGAACAAGTTCAATCAATGGTGTTCATAGAGGAAAAAAATGGAAGTAAAATTTATGCCAAAAGTGGTTGGGGATGGGATGTTGAACCACAAGTTGGTTGGTTAACAGGCTGGGTCGTTCAACCACAAGGAGAAATTGTCGCATTCTCACTTAATTTAGAAATGAAAAAAGGAACTGCTAGCTCTATTCGCAAAGAAATTGCTTATAAAGGCTTAGAACAACTGGGCATTTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39094","NCBI_taxonomy_name":"Acinetobacter calcoaceticus","NCBI_taxonomy_id":"471"}}}},"ARO_accession":"3008767","ARO_id":"47559","ARO_name":"OXA-990","CARD_short_name":"OXA-990","ARO_description":"OXA-213 family carbapenem-hydrolyzing class D beta-lactamase OXA-990.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46495":{"category_aro_accession":"3007706","category_aro_cvterm_id":"46495","category_aro_name":"OXA-213-like beta-lactamase","category_aro_description":"OXA-213-like enzymes have been identified to be intrinsic to A. calcoaceticus and have been subsequently detected in A. pittii. Phylogenetic analysis of OXA-213-like proteins identified two distinct subgroups within the OXA family. The first group was linked to A. pittii and the second group to A. calcoaceticus. The carbapenemase activity of these OXAs may be related to the species-dependent effect.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8186":{"model_id":"8186","model_name":"OXA-991","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11013":{"protein_sequence":{"accession":"QWA20190.1","sequence":"MKTLILLPLLSCLSLTACSLPVSNSSSQITSTQSIQTIAKLFDQAQSSGVLVIQRGPHLQVYGNDLSRAHTEYIPASTFKMLNALIGLQHGKATTNEIFKWDGKKRSFAAWEKDMTLGQAMQASAVPVYQELARRIGLELMQQEVQRIRFGNQQIGQHIDNFWLVGPLKVTPKQEVKFASALAQEQLAFDPQVQQQVKAMLLLQERQAYRLYAKSGWGMDVEPQVGWLTGWIETPQDEIVAFSLNMQMQSNMDPAIRLKILQQALAELGLYPKAEG"},"dna_sequence":{"accession":"MZ265743.1","fmin":"0","fmax":"831","strand":"+","sequence":"ATGAAAACTCTTATTTTGTTGCCTTTACTTAGTTGCTTGAGCCTGACAGCCTGTAGCTTGCCTGTTTCAAATTCGTCCTCTCAAATCACTTCAACTCAATCTATTCAAACCATTGCCAAATTATTTGATCAGGCACAAAGCTCTGGCGTTTTAGTAATTCAACGGGGCCCACATCTACAGGTCTATGGCAATGATTTGAGTCGTGCACATACCGAATATATTCCTGCTTCAACCTTTAAAATGCTCAATGCCCTGATTGGCCTGCAACATGGTAAAGCCACGACCAATGAAATCTTTAAATGGGATGGCAAGAAGCGCAGTTTTGCAGCCTGGGAAAAAGACATGACTCTCGGCCAAGCCATGCAAGCTTCTGCTGTACCCGTCTATCAGGAACTGGCACGTCGCATTGGTCTGGAACTAATGCAACAGGAAGTGCAACGCATTCGATTTGGTAATCAGCAGATTGGTCAGCATATCGACAACTTCTGGTTAGTCGGACCTTTGAAAGTTACTCCAAAACAGGAAGTCAAATTTGCCTCTGCGCTTGCTCAAGAGCAACTTGCCTTTGATCCTCAAGTCCAGCAACAAGTCAAAGCCATGTTACTGTTACAGGAGCGACAAGCTTATCGACTATATGCCAAATCTGGTTGGGGTATGGATGTGGAGCCGCAAGTCGGCTGGCTCACCGGCTGGATCGAAACACCTCAGGACGAAATCGTGGCATTTTCACTGAATATGCAGATGCAAAGTAATATGGATCCGGCGATCCGTCTTAAAATTTTGCAGCAGGCCTTGGCCGAATTAGGGCTTTATCCGAAAGCTGAAGGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39096","NCBI_taxonomy_name":"Acinetobacter schindleri","NCBI_taxonomy_id":"108981"}}}},"ARO_accession":"3008768","ARO_id":"47560","ARO_name":"OXA-991","CARD_short_name":"OXA-991","ARO_description":"OXA-134 family carbapenem-hydrolyzing class D beta-lactamase OXA-991.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46489":{"category_aro_accession":"3007700","category_aro_cvterm_id":"46489","category_aro_name":"OXA-134-like beta-lactamase","category_aro_description":"A subfamily of carbapenem-hydrolyzing class D OXA beta-lactamases derived from OXA-134.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8187":{"model_id":"8187","model_name":"OXA-992","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11014":{"protein_sequence":{"accession":"QWA20191.1","sequence":"MTKKALFFAIATMFLSACSFDTVEQHQIQSISTNKNSEKIQSLFDQAQTTGVLIIKRGQTEEVYGNDLKRASTEYVPASTFKMLNALIGLEHHKATPTEVFKWDGQKRLFPDWEKDMTLDDAMKASAIPVYQELARRIGLDLMSKEVKRIGFGNADIGSKIDNFWLVGPLKITPQQEAQFAYELAHKTLPFSKNVQEQVQSMLFIEEKNGRKIYAKSGWGWDVEPQVGWFTGWVVQPQGEIVAFALNLEMKKGIPSSIRKEIAYKGLEQLGIL"},"dna_sequence":{"accession":"MZ265744.1","fmin":"0","fmax":"822","strand":"+","sequence":"ATGACTAAAAAAGCTCTTTTCTTTGCCATTGCTACGATGTTTTTATCGGCGTGTTCTTTTGATACCGTAGAACAACATCAAATACAGTCAATTTCTACCAATAAAAACTCAGAGAAAATTCAATCATTGTTTGATCAAGCACAAACTACAGGTGTTTTAATTATAAAACGTGGCCAAACAGAGGAAGTCTATGGCAATGATCTTAAAAGAGCATCAACCGAATATGTTCCCGCCTCTACCTTTAAAATGTTAAATGCTTTGATCGGACTTGAGCATCATAAAGCAACACCAACTGAAGTGTTTAAATGGGATGGGCAAAAGCGTTTATTTCCCGATTGGGAAAAAGACATGACCCTAGATGATGCAATGAAAGCTTCTGCTATTCCAGTTTATCAGGAACTAGCTCGACGAATTGGTCTTGATCTTATGTCTAAAGAGGTGAAGCGTATTGGTTTCGGTAATGCTGATATTGGTTCAAAAATAGATAATTTTTGGCTTGTTGGTCCACTTAAAATTACACCTCAACAAGAAGCCCAGTTTGCTTATGAACTAGCCCATAAAACTCTTCCTTTTAGCAAAAATGTGCAAGAACAAGTTCAATCTATGTTGTTCATAGAAGAAAAAAATGGACGAAAAATTTATGCTAAAAGTGGTTGGGGATGGGATGTTGAACCACAAGTTGGTTGGTTTACAGGCTGGGTGGTTCAACCACAAGGAGAAATTGTAGCGTTCGCACTTAATTTAGAAATGAAAAAAGGAATACCTAGTTCTATTCGAAAAGAAATTGCTTATAAAGGATTAGAACAATTAGGTATTTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36787","NCBI_taxonomy_name":"Acinetobacter pittii","NCBI_taxonomy_id":"48296"}}}},"ARO_accession":"3008769","ARO_id":"47561","ARO_name":"OXA-992","CARD_short_name":"OXA-992","ARO_description":"OXA-213 family carbapenem-hydrolyzing class D beta-lactamase OXA-992.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46495":{"category_aro_accession":"3007706","category_aro_cvterm_id":"46495","category_aro_name":"OXA-213-like beta-lactamase","category_aro_description":"OXA-213-like enzymes have been identified to be intrinsic to A. calcoaceticus and have been subsequently detected in A. pittii. Phylogenetic analysis of OXA-213-like proteins identified two distinct subgroups within the OXA family. The first group was linked to A. pittii and the second group to A. calcoaceticus. The carbapenemase activity of these OXAs may be related to the species-dependent effect.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8188":{"model_id":"8188","model_name":"OXA-993","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11015":{"protein_sequence":{"accession":"QWA20192.1","sequence":"MSKKLKLLALCATVISAATLVGCQNIQSQAQPLVLKKQTQDQIATAFENIQTTGVLVTYDGKKFQKYGNDLSRADQRYIPASTFKMLNALIGIQHHKTSPNEVFKWDGQKRAFRSWEKDLTLAEAMQASAVPVYQELARRIGLELMASEVKRVGYGNQNIGTQVDNFWLVGPLEITPVEEVKFAYALAKQQLPFDPSTQQQVRDMLLIENVQGTRIYAKSGWGMDVNPQVGRWTGWVEQPNGQVTAFSLNMEMKKAEHADARKAIVYQALQQLGLLPQ"},"dna_sequence":{"accession":"MZ265745.1","fmin":"0","fmax":"837","strand":"+","sequence":"ATGTCTAAAAAATTAAAATTACTCGCGCTATGTGCAACTGTAATCTCAGCTGCAACACTGGTCGGTTGTCAAAATATTCAGTCCCAAGCTCAACCTCTAGTCTTAAAGAAACAGACGCAGGATCAGATCGCAACTGCATTCGAAAATATCCAGACAACTGGTGTATTGGTCACCTATGATGGCAAAAAATTTCAAAAATATGGCAATGATCTCAGCCGTGCAGATCAGCGTTACATTCCTGCCTCAACTTTTAAAATGCTCAATGCCTTGATTGGTATACAGCACCATAAAACCTCACCTAATGAAGTGTTTAAATGGGATGGACAGAAGCGGGCTTTTCGTAGCTGGGAGAAGGACTTAACGCTTGCTGAGGCAATGCAGGCTTCGGCTGTACCTGTCTATCAGGAGTTGGCGCGCCGTATCGGTCTAGAATTAATGGCAAGTGAAGTAAAGCGGGTTGGCTACGGTAATCAAAATATAGGGACGCAAGTTGATAATTTTTGGTTGGTGGGGCCTTTGGAGATTACGCCAGTTGAGGAAGTGAAATTTGCTTATGCCTTAGCCAAACAGCAACTTCCATTTGATCCCTCAACACAGCAGCAAGTCAGAGATATGTTGTTGATCGAAAATGTTCAGGGAACCAGAATCTATGCCAAAAGCGGTTGGGGAATGGATGTAAATCCTCAAGTCGGACGGTGGACAGGTTGGGTCGAACAACCAAATGGTCAAGTCACTGCATTTTCGCTGAATATGGAAATGAAAAAAGCAGAACATGCGGATGCGCGTAAAGCGATTGTTTATCAAGCTTTACAACAGTTAGGTTTATTACCTCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"47901","NCBI_taxonomy_name":"Acinetobacter vivianii","NCBI_taxonomy_id":"1776742"}}}},"ARO_accession":"3008770","ARO_id":"47562","ARO_name":"OXA-993","CARD_short_name":"OXA-993","ARO_description":"OXA-294 family class D beta-lactamase OXA-993.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46504":{"category_aro_accession":"3007715","category_aro_cvterm_id":"46504","category_aro_name":"OXA-294-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-294.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8189":{"model_id":"8189","model_name":"OXA-994","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11016":{"protein_sequence":{"accession":"QWA20193.1","sequence":"MSKKLKLLALCATVISAATLVGCQNIQSQAQPLVLKKQTQDQIATAFENIQTTGVLVTYDGKNFQKYGNDLSRADQRYIPASTFKMLNALIGIQHHKTSPNEVFKWDGQKRAFRSWEKDLTLAEGMQASAVPVYQELARRIGLELMASEVKRVGYGNQNIGAQVDNFWLVGPLEITPVEEVKFAYALAKQQLPFDPSTQQQVRDMLLIENVQGTRIYAKSGWGIDVNPQVGWWTGWIEQPNGQITAFSLNMEMKKAEHADARKAIVYQALQQLGLLPQ"},"dna_sequence":{"accession":"MZ265746.1","fmin":"0","fmax":"837","strand":"+","sequence":"ATGTCTAAAAAATTAAAATTACTCGCGCTATGTGCAACTGTAATCTCAGCTGCAACACTGGTCGGTTGTCAAAATATTCAGTCCCAAGCTCAACCTCTAGTCTTAAAGAAACAGACGCAGGATCAGATCGCAACTGCATTCGAAAATATCCAGACAACTGGTGTATTAGTCACCTATGATGGTAAAAATTTTCAAAAATATGGCAATGATCTCAGCCGTGCAGATCAGCGTTACATTCCGGCCTCAACTTTTAAAATGCTCAATGCCTTGATTGGTATACAGCACCATAAAACCTCACCTAATGAAGTGTTTAAATGGGATGGACAGAAACGGGCTTTCCGTAGCTGGGAGAAGGACTTAACGCTTGCTGAGGGAATGCAGGCTTCGGCTGTACCTGTCTATCAGGAGCTGGCGCGCCGTATCGGTCTAGAATTAATGGCAAGTGAAGTAAAGCGGGTTGGCTACGGTAATCAAAATATAGGGGCGCAAGTTGATAATTTTTGGTTAGTGGGGCCTTTGGAGATTACGCCAGTTGAGGAAGTAAAATTTGCTTATGCCTTAGCCAAACAGCAACTTCCATTTGATCCCTCAACACAGCAGCAAGTCAGAGATATGTTGTTGATCGAAAATGTTCAGGGAACCAGAATCTATGCCAAGAGTGGTTGGGGAATAGATGTAAATCCTCAAGTTGGATGGTGGACGGGTTGGATTGAACAACCAAATGGTCAAATCACAGCATTTTCGCTGAATATGGAAATGAAAAAAGCAGAACATGCGGATGCGCGTAAAGCGATTGTTTATCAAGCTTTACAACAGTTAGGTTTATTACCTCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"47901","NCBI_taxonomy_name":"Acinetobacter vivianii","NCBI_taxonomy_id":"1776742"}}}},"ARO_accession":"3008771","ARO_id":"47563","ARO_name":"OXA-994","CARD_short_name":"OXA-994","ARO_description":"OXA-294 family class D beta-lactamase OXA-994.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46504":{"category_aro_accession":"3007715","category_aro_cvterm_id":"46504","category_aro_name":"OXA-294-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-294.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8190":{"model_id":"8190","model_name":"OXA-995","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11017":{"protein_sequence":{"accession":"QWA20194.1","sequence":"MPKKLKLLFLCIAAMPSITLLGCQNIQPHVQTLAAQKQTEDQIATAFENIQTSGVLVTYDGKAIQTYGNALNRANQRYIPASTFKMLNALIGIQHHKTSPNEVFKWDGQKRAFTSWEKDLTLAEAMQASAVPVYQELARRIGLELMTSEVKRVGYGNQSIGTQVDNFWLVGPLEITPVEEVKFAYALAKEQLAFDSSTQQQVKDMLLIEDIQGTKIYAKSGWGMDVNPQVGWWTGWVEQPNGQVTAFSLNMEMKKAAHAEARKAIVYQALQQLGLIRQ"},"dna_sequence":{"accession":"MZ265747.1","fmin":"0","fmax":"837","strand":"+","sequence":"ATGCCGAAAAAATTAAAATTACTCTTTCTATGTATAGCTGCGATGCCCTCGATAACACTGTTGGGCTGCCAAAATATTCAGCCACACGTTCAAACTTTAGCCGCGCAGAAACAGACTGAAGATCAGATCGCAACTGCATTTGAAAATATCCAGACCTCCGGTGTACTGGTCACCTATGATGGCAAAGCTATTCAAACATATGGCAATGCGCTTAACCGGGCCAATCAGCGTTATATTCCGGCTTCCACCTTTAAAATGCTGAATGCCTTGATTGGTATCCAGCATCACAAGACTTCACCGAATGAAGTATTTAAATGGGATGGACAGAAGCGGGCATTTACCAGCTGGGAAAAAGACTTAACCCTGGCAGAAGCCATGCAGGCTTCGGCTGTACCTGTATATCAGGAACTGGCACGCCGTATCGGTCTGGAATTAATGACCAGTGAAGTAAAACGGGTCGGGTATGGCAATCAGTCAATTGGAACGCAAGTGGATAATTTCTGGTTAGTGGGGCCTTTAGAAATTACCCCTGTGGAGGAAGTAAAATTTGCCTATGCCTTGGCGAAAGAACAACTTGCATTTGACTCATCAACCCAGCAACAAGTTAAAGATATGTTGCTGATTGAAGATATTCAGGGCACCAAAATCTATGCCAAAAGTGGTTGGGGCATGGATGTAAATCCTCAGGTGGGATGGTGGACAGGTTGGGTAGAACAACCCAATGGACAGGTCACTGCATTTTCACTGAATATGGAAATGAAAAAGGCAGCACATGCAGAAGCACGTAAAGCCATTGTTTATCAGGCCCTGCAACAGCTCGGTTTAATTAGACAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41219","NCBI_taxonomy_name":"Acinetobacter courvalinii","NCBI_taxonomy_id":"280147"}}}},"ARO_accession":"3008772","ARO_id":"47564","ARO_name":"OXA-995","CARD_short_name":"OXA-995","ARO_description":"OXA-294 family class D beta-lactamase OXA-995.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46504":{"category_aro_accession":"3007715","category_aro_cvterm_id":"46504","category_aro_name":"OXA-294-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-294.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8191":{"model_id":"8191","model_name":"OXA-996","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11018":{"protein_sequence":{"accession":"QWA20195.1","sequence":"MPKKLKLLALSVVVMPSIILLGCQNIQPHVQTLVAQKQTEDQIATAFENIQTSGVLVTYDGKAIQKYGNALNRADQRYIPASTFKMLNALIGIQHHKTSPNEVFKWDGQKRAFTSWEKDLTLAEAMQASAVPVYQELARRIGLELMASEVKRVGYGNQSIGTQVDNFWLVGPLEITPVEEVKFAYALAKKQLAFDSSTQQQVKDMLLIEDIQGTKIYAKSGWGMDVNPQVGWWTGWVEQPNGQVTAFSLNMEMKKAAHAEARKAIVYQALQQLGLLPQ"},"dna_sequence":{"accession":"MZ265748.1","fmin":"0","fmax":"837","strand":"+","sequence":"ATGCCGAAAAAATTAAAATTACTCGCTCTATCTGTAGTTGTGATGCCCTCAATAATATTATTGGGCTGCCAAAATATTCAGCCACACGTTCAAACTTTAGTCGCGCAGAAACAGACTGAAGATCAGATCGCAACTGCATTTGAAAATATCCAGACCTCCGGTGTACTGGTTACCTATGATGGCAAAGCTATTCAAAAATATGGCAATGCGCTTAATCGGGCCGATCAGCGCTATATTCCTGCTTCCACCTTTAAAATGTTGAATGCCTTGATTGGTATCCAGCATCATAAGACTTCACCGAATGAAGTATTTAAATGGGATGGACAGAAGCGGGCATTTACCAGCTGGGAAAAAGACTTAACCCTGGCAGAAGCCATGCAGGCTTCGGCTGTACCTGTGTATCAGGAACTGGCGCGCCGTATCGGTCTGGAATTAATGGCCAGTGAAGTAAAACGGGTCGGGTATGGCAATCAGTCGATTGGAACGCAAGTGGATAATTTCTGGTTAGTGGGACCTTTAGAAATTACCCCTGTGGAGGAAGTAAAATTTGCCTATGCCTTGGCGAAAAAACAACTTGCATTTGACTCATCAACCCAGCAACAAGTTAAAGATATGTTGCTGATTGAAGATATTCAGGGCACCAAAATCTATGCCAAAAGTGGATGGGGCATGGATGTAAATCCTCAGGTGGGATGGTGGACAGGTTGGGTAGAACAACCCAATGGTCAGGTCACTGCATTTTCACTGAATATGGAAATGAAAAAGGCAGCACATGCAGAAGCACGTAAAGCTATTGTGTATCAGGCTTTACAACAACTGGGTCTATTGCCCCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41219","NCBI_taxonomy_name":"Acinetobacter courvalinii","NCBI_taxonomy_id":"280147"}}}},"ARO_accession":"3008773","ARO_id":"47565","ARO_name":"OXA-996","CARD_short_name":"OXA-996","ARO_description":"OXA-294 family class D beta-lactamase OXA-996.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46504":{"category_aro_accession":"3007715","category_aro_cvterm_id":"46504","category_aro_name":"OXA-294-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-294.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8192":{"model_id":"8192","model_name":"OXA-997","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11019":{"protein_sequence":{"accession":"QWA20196.1","sequence":"MSKKLKLLALCATVISAATLVGCQNIQSQAQPLALKKQAQDQIATAFENIQTTGVLVTYDGKNFQKYGNDLSRADQRYIPASTFKMLNALIGIQHHKTSPNEVFKWDGQKRAFRSWEKDLTLAEGMQASAVPVYQELARRIGLELMASEVKRVGYGNQNIGPQVDNFWLVGPLEITPVEEVKFAYALAKQQLPFDPSTQQQVRDMLLIENVQGTRIYAKSGWGMDVNPQVGWWTGWVEQPNGQITAFSLNMEMKKAEHADARKAIVYQALQQLGLLPQ"},"dna_sequence":{"accession":"MZ265749.1","fmin":"0","fmax":"837","strand":"+","sequence":"ATGTCTAAAAAATTAAAATTACTCGCGCTATGCGCAACTGTGATCTCAGCTGCAACACTGGTCGGTTGTCAAAATATTCAGTCCCAAGCCCAACCTTTAGCCCTAAAGAAACAGGCTCAGGATCAGATCGCAACTGCATTCGAAAATATCCAGACAACTGGTGTATTGGTCACCTATGATGGCAAAAATTTTCAAAAATATGGCAATGATCTCAGCCGTGCAGATCAGCGTTACATTCCTGCCTCAACTTTTAAAATGCTCAATGCCTTGATTGGTATACAGCATCATAAAACCTCACCCAATGAAGTGTTTAAATGGGATGGACAGAAGCGGGCTTTTCGTAGCTGGGAGAAGGACTTAACGCTTGCTGAGGGAATGCAGGCTTCGGCTGTACCTGTCTATCAGGAGCTGGCGCGCCGTATCGGTCTAGAATTAATGGCAAGTGAAGTAAAGCGGGTTGGCTACGGTAATCAAAATATAGGGCCGCAAGTTGATAATTTTTGGTTAGTGGGGCCTTTGGAGATTACGCCAGTTGAGGAAGTAAAATTTGCTTATGCCTTAGCCAAACAGCAACTTCCATTTGATCCCTCAACACAGCAGCAAGTCAGAGATATGTTGTTGATCGAAAATGTTCAGGGAACTAGAATCTATGCCAAAAGTGGTTGGGGAATGGATGTAAATCCTCAAGTCGGATGGTGGACAGGTTGGGTCGAACAACCAAATGGTCAAATCACTGCATTTTCGCTGAATATGGAAATGAAAAAAGCAGAACATGCAGATGCGCGTAAAGCGATTGTTTATCAAGCTTTACAACAGTTAGGTTTATTACCCCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"47901","NCBI_taxonomy_name":"Acinetobacter vivianii","NCBI_taxonomy_id":"1776742"}}}},"ARO_accession":"3008774","ARO_id":"47566","ARO_name":"OXA-997","CARD_short_name":"OXA-997","ARO_description":"OXA-294 family class D beta-lactamase OXA-997.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46504":{"category_aro_accession":"3007715","category_aro_cvterm_id":"46504","category_aro_name":"OXA-294-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-294.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8193":{"model_id":"8193","model_name":"OXA-998","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11020":{"protein_sequence":{"accession":"QWA20197.1","sequence":"MPKKLKLLVLSVVVMPSIILLGCQNIQPHVQTLVTQKQTEDQIATAFENIQTSGVLVTYDGKAIQKYGNALNRANQRYIPASTFKMLNALIGIQHHKTSPNEVFKWDGQKRAFTSWEKDLTLAEAMQASAVPVYQELARRIGLELIASEVKRVGYGNQSIGTQVDNFWLVGPLEITPVEEVKFAYALAKKQLAFDSSTQQQVKDMLLIEDIQGTKLYAKSGWGMDVNPQVGWWTGWVEQPNGQVTAFSLNMEMKKAAHAEARKAIVYQALQQLGLLPQ"},"dna_sequence":{"accession":"MZ265750.1","fmin":"0","fmax":"837","strand":"+","sequence":"ATGCCGAAAAAATTAAAATTACTCGTTCTATCTGTAGTTGTGATGCCCTCAATAATATTGTTGGGCTGCCAAAATATTCAGCCACACGTTCAAACTTTAGTCACGCAGAAACAGACTGAAGATCAGATCGCAACTGCATTTGAAAATATCCAGACCTCCGGTGTACTGGTCACCTATGATGGCAAAGCTATTCAAAAATATGGCAATGCGCTTAACCGGGCCAATCAGCGCTATATTCCGGCTTCCACCTTTAAAATGCTGAATGCCTTGATTGGTATCCAGCATCATAAGACTTCACCGAATGAAGTATTTAAATGGGATGGACAGAAGCGGGCATTTACCAGCTGGGAAAAAGACTTAACCCTGGCAGAAGCCATGCAGGCTTCGGCTGTACCTGTGTATCAGGAACTGGCGCGCCGTATCGGTCTGGAATTAATAGCCAGTGAAGTAAAACGGGTCGGGTATGGCAATCAGTCGATTGGAACGCAAGTGGATAATTTCTGGTTAGTGGGGCCTTTAGAAATTACCCCTGTGGAGGAAGTAAAATTTGCCTATGCCTTGGCGAAAAAACAACTTGCATTTGACTCATCAACCCAGCAACAAGTTAAAGATATGTTGCTGATTGAAGATATTCAGGGCACCAAACTCTATGCCAAAAGTGGATGGGGCATGGATGTAAATCCTCAGGTGGGATGGTGGACAGGTTGGGTAGAACAACCCAATGGTCAGGTCACTGCATTTTCACTGAATATGGAAATGAAAAAGGCAGCACATGCAGAAGCACGTAAAGCTATTGTGTATCAGGCTTTACAACAACTGGGTCTATTGCCCCAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41219","NCBI_taxonomy_name":"Acinetobacter courvalinii","NCBI_taxonomy_id":"280147"}}}},"ARO_accession":"3008775","ARO_id":"47567","ARO_name":"OXA-998","CARD_short_name":"OXA-998","ARO_description":"OXA-294 family class D beta-lactamase OXA-998.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"46504":{"category_aro_accession":"3007715","category_aro_cvterm_id":"46504","category_aro_name":"OXA-294-like beta-lactamase","category_aro_description":"A subfamily of extended-spectrum oxacillin-hydrolyzing class D OXA beta-lactamases derived from OXA-294.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8194":{"model_id":"8194","model_name":"OXA-999","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11021":{"protein_sequence":{"accession":"QWA20198.1","sequence":"MNKKLNLALLCFLSILCAACQSNQQLSAHSHTENHNTRAAEIPLLFDEMHTQAVFVTYDGQHFQSYGNALQRADTAYVPASTFKMLNALIGLQNHKATNTEVFKWDGQKRAMSIWEKDMTLSDAMKVSAVPVYQELARRIGLDLMQKEVTRVGYGNANIGTVVDRFWLDGPLKITPKQEAQFAYQLATQQLPFDQKVQSQVKDMLYVESRGQSKLFAKSGLSMKNGQPDIGWYTGWVEQADGKIVAFSINMQMVQGLDVNSRQQATLDILDKLGIFFYL"},"dna_sequence":{"accession":"MZ265751.1","fmin":"0","fmax":"840","strand":"+","sequence":"ATGAATAAAAAATTGAATTTGGCACTTTTGTGCTTTTTGAGTATTTTGTGTGCAGCTTGTCAGTCTAATCAACAACTGTCGGCTCATTCACATACTGAAAATCACAACACCCGTGCAGCAGAAATCCCGCTTCTTTTCGATGAGATGCATACTCAAGCAGTATTTGTGACCTATGACGGTCAGCATTTTCAGAGCTACGGTAATGCTTTACAAAGAGCAGATACTGCCTACGTTCCTGCTTCGACATTTAAAATGTTAAATGCATTGATTGGACTGCAAAATCATAAAGCAACCAACACCGAAGTCTTTAAATGGGATGGTCAAAAAAGGGCAATGTCGATCTGGGAAAAAGACATGACCTTATCCGATGCCATGAAAGTTTCGGCTGTGCCTGTTTATCAAGAATTGGCGCGTCGTATTGGCTTAGATTTGATGCAAAAGGAAGTAACGCGGGTTGGATATGGCAATGCCAATATCGGCACTGTTGTAGATCGTTTTTGGCTAGATGGACCACTAAAGATAACTCCTAAACAAGAAGCCCAATTTGCATATCAATTGGCAACGCAACAATTGCCATTTGACCAAAAAGTACAAAGCCAAGTTAAAGATATGTTGTATGTGGAAAGTCGTGGGCAATCCAAACTTTTTGCCAAGTCTGGTTTGAGCATGAAAAATGGACAGCCTGATATCGGTTGGTATACGGGTTGGGTTGAACAAGCTGATGGTAAAATTGTGGCCTTTTCTATCAATATGCAAATGGTGCAGGGCTTAGATGTCAATAGCCGTCAGCAGGCAACGCTGGATATCTTGGATAAATTGGGCATATTTTTTTATTTATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42557","NCBI_taxonomy_name":"Acinetobacter gerneri","NCBI_taxonomy_id":"202952"}}}},"ARO_accession":"3008776","ARO_id":"47568","ARO_name":"OXA-999","CARD_short_name":"OXA-999","ARO_description":"Class D beta-lactamase OXA-999.","ARO_category":{"36026":{"category_aro_accession":"3000017","category_aro_cvterm_id":"36026","category_aro_name":"OXA beta-lactamase","category_aro_description":"OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d. The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.","category_aro_class_name":"AMR Gene Family"},"35973":{"category_aro_accession":"0000056","category_aro_cvterm_id":"35973","category_aro_name":"oxacillin","category_aro_description":"Oxacillin is a penicillinase-resistant beta-lactam. It is similar to methicillin, and has replaced methicillin in clinical use. Oxacillin, especially in combination with other antibiotics, is effective against many penicillinase-producing strains of Staphylococcus aureus and Staphylococcus epidermidis.","category_aro_class_name":"Antibiotic"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8195":{"model_id":"8195","model_name":"OXY-1-11","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11022":{"protein_sequence":{"accession":"QLX89879.1","sequence":"MLKSSWRKTALMAAAAVPLLLASGSLWASADAIQQKLADLEKRSGGRLGVALINTADDSQTLYRGDERFAMCSTGKVMAAAAVLKQSESNPEVVNKRLEIKKSDLVVWSPITEKHLQSGMTLAELSAAALQYSDNTAMNKMISYLGGPEKVTAFAQSIGDVTFRLDRTEPALNSAIPGDKRDTTTPLAMAESLRKLTLGNALGEQQRAQLVTWLKGNTTGGQSIRAGLPASWAVGDKTGGGDYGTTNDIAVIWPENHAPLVLVTYFTQPQQDAKSRKEVLAAAAKIVTERL"},"dna_sequence":{"accession":"CP056453.1","fmin":"4671971","fmax":"4672847","strand":"+","sequence":"ATGTTGAAAAGTTCGTGGCGTAAAACCGCCCTGATGGCCGCCGCCGCCGTTCCGCTGCTGCTGGCGAGCGGTTCATTATGGGCCAGTGCCGATGCTATCCAGCAAAAGCTGGCTGATTTAGAAAAACGTTCCGGCGGTCGGCTGGGCGTAGCGCTGATTAACACGGCAGATGATTCGCAAACCCTCTATCGCGGCGATGAACGTTTTGCCATGTGCAGCACCGGTAAAGTGATGGCCGCCGCCGCGGTGTTAAAACAGAGCGAAAGCAATCCAGAGGTGGTGAATAAAAGGCTGGAGATTAAAAAATCGGATTTAGTGGTCTGGAGCCCGATCACCGAAAAACATCTGCAAAGCGGAATGACCCTGGCGGAACTCAGCGCGGCGGCGCTGCAGTACAGCGACAATACCGCGATGAATAAGATGATTAGCTACCTTGGCGGACCGGAAAAGGTGACCGCATTCGCCCAGAGTATCGGGGATGTCACTTTTCGTCTCGATCGTACGGAGCCGGCGCTGAACAGCGCGATTCCCGGCGATAAGCGCGATACCACCACCCCGTTGGCGATGGCCGAAAGCCTGCGCAAGCTGACGCTGGGCAATGCGCTGGGCGAACAGCAGCGCGCCCAGTTAGTGACGTGGCTAAAAGGCAATACCACCGGCGGGCAAAGCATTCGCGCAGGCCTGCCCGCAAGCTGGGCGGTCGGGGATAAAACCGGCGGCGGAGATTACGGCACCACCAACGATATCGCGGTGATCTGGCCGGAAAATCATGCCCCGCTGGTGCTGGTGACCTATTTTACCCAGCCGCAGCAGGATGCGAAAAGCCGCAAAGAGGTGTTAGCCGCGGCGGCAAAAATCGTCACCGAAAGGCTTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3008777","ARO_id":"47569","ARO_name":"OXY-1-11","CARD_short_name":"OXY-1-11","ARO_description":"Extended-spectrum class A beta-lactamase OXY-1-11.","ARO_category":{"38788":{"category_aro_accession":"3002388","category_aro_cvterm_id":"38788","category_aro_name":"OXY beta-lactamase","category_aro_description":"OXY beta-lactamases are chromosomal class A beta-lactamases that are found in Klebsiella oxytoca. At constitutive low levels, OXY beta-lactamases confer resistance to aminopenicillins and carboxypenicillins. At high induced levels,  OXY beta-lactamases confer resistance to penicillins, cephalosporins and aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8196":{"model_id":"8196","model_name":"OXY-1-12","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11023":{"protein_sequence":{"accession":"OEG79869.1","sequence":"MLKSSWHKTALMAAAVPLLLASGSLWASADAIQQKLADLEKRSGGRLGVALINTADDSQTLYRGDERFAMCSTGKVMAAAAVLKQSESNPEVVNKRLEIKKSDLVVWSPITEKHLQSGMTLAELSAAALQYSDNTAMNKMISYLGGPEKVTAFAQSIGDVTFRLDRTEPALNSAIPGDKRDTTTPLAMAESLRKLTLGNALGEQQRAQLVTWLKGNTTGGQSIRAGLPASWAVGDKTGAGDYGTTNDIAVIWPENHAPLVLVTYFTQPQQDAKSRKEVLAAAAKIVTEGL"},"dna_sequence":{"accession":"LJFC02000166.1","fmin":"129022","fmax":"129895","strand":"+","sequence":"ATGTTGAAAAGTTCGTGGCATAAAACCGCCCTGATGGCCGCCGCCGTTCCGCTGCTGCTGGCGAGCGGTTCATTATGGGCCAGTGCCGATGCTATCCAGCAAAAGCTGGCTGATTTAGAAAAACGTTCCGGCGGTCGGCTGGGCGTAGCGCTGATTAACACGGCAGATGATTCGCAAACCCTCTATCGCGGCGATGAACGTTTTGCCATGTGCAGCACCGGTAAAGTGATGGCCGCCGCCGCGGTGTTAAAACAGAGCGAAAGCAATCCAGAGGTGGTGAATAAAAGGCTGGAGATTAAAAAATCGGATTTAGTGGTCTGGAGCCCGATCACCGAAAAACATCTGCAAAGCGGAATGACCCTGGCGGAACTCAGCGCGGCGGCGCTGCAGTACAGCGACAATACCGCGATGAATAAGATGATTAGCTACCTTGGCGGACCGGAAAAGGTGACCGCATTCGCCCAGAGTATCGGGGATGTCACTTTTCGTCTCGATCGTACGGAGCCGGCGCTGAACAGCGCGATTCCCGGCGATAAGCGCGATACCACCACCCCGTTGGCGATGGCCGAAAGCCTGCGCAAGCTGACGCTGGGCAATGCGCTGGGCGAACAGCAGCGCGCCCAGTTAGTGACGTGGCTAAAAGGCAATACTACCGGCGGGCAAAGCATTCGCGCAGGCCTGCCCGCAAGCTGGGCGGTCGGGGATAAAACCGGCGCCGGAGATTACGGCACCACCAACGATATCGCGGTGATCTGGCCGGAAAATCATGCCCCGCTGGTGCTGGTGACCTATTTTACCCAGCCGCAGCAGGATGCGAAAAGCCGCAAAGAGGTGTTAGCCGCGGCGGCAAAAATCGTCACCGAAGGGCTTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43788","NCBI_taxonomy_name":"Klebsiella michiganensis","NCBI_taxonomy_id":"1134687"}}}},"ARO_accession":"3008778","ARO_id":"47570","ARO_name":"OXY-1-12","CARD_short_name":"OXY-1-12","ARO_description":"Extended-spectrum class A beta-lactamase OXY-1-12.","ARO_category":{"38788":{"category_aro_accession":"3002388","category_aro_cvterm_id":"38788","category_aro_name":"OXY beta-lactamase","category_aro_description":"OXY beta-lactamases are chromosomal class A beta-lactamases that are found in Klebsiella oxytoca. At constitutive low levels, OXY beta-lactamases confer resistance to aminopenicillins and carboxypenicillins. At high induced levels,  OXY beta-lactamases confer resistance to penicillins, cephalosporins and aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8197":{"model_id":"8197","model_name":"OXY-1-13","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11024":{"protein_sequence":{"accession":"QUG45386.1","sequence":"MLKSSWRKTALMAAAVPLLLASGSLWASADAIQQKLADLEKRSGGRLGVALINTADDSQTLYRGDERFAMCSTGKVMAAAAVLKQSESNPEVVNKRLEIKKSDLVVWSPITEKHLQSGMTLAELSAAALQYSDNTAMNKMISYLGGPEKVTAFAQSIGDVTFRLDRTEPALNSAIPGDKRDTTTPLAMAESLRKLTLGNALGEQQRAQLVTWLKGNTTGGQSIRAGLPASWVVGDKTGAGDYGTTNDIAVIWPENHAPLVLVTYFTQPQQDAKSRKEVLAAAAKIVTKGL"},"dna_sequence":{"accession":"CP073305.1","fmin":"4910875","fmax":"4911748","strand":"+","sequence":"ATGTTGAAAAGTTCGTGGCGTAAAACCGCCCTGATGGCCGCCGCCGTTCCGCTGCTGCTGGCGAGCGGTTCATTATGGGCCAGTGCCGATGCTATCCAGCAAAAGCTGGCTGATTTAGAAAAACGTTCCGGCGGTCGGCTGGGCGTAGCGCTGATTAACACGGCAGATGATTCGCAAACCCTCTATCGCGGCGATGAACGTTTTGCCATGTGCAGCACCGGTAAAGTGATGGCCGCCGCCGCGGTGTTAAAACAGAGCGAAAGCAATCCAGAGGTGGTGAATAAAAGGCTGGAGATTAAAAAATCGGATTTAGTGGTCTGGAGCCCGATCACCGAAAAACATCTGCAAAGCGGAATGACCCTGGCGGAACTCAGCGCGGCGGCGCTGCAGTACAGCGACAATACCGCGATGAATAAGATGATTAGCTACCTTGGCGGACCGGAAAAGGTGACAGCATTCGCCCAGAGTATCGGGGATGTCACTTTTCGTCTCGATCGTACGGAGCCGGCGCTGAACAGCGCGATTCCCGGCGATAAGCGCGATACCACCACCCCGTTGGCGATGGCCGAAAGCCTGCGCAAGCTGACGCTGGGCAATGCGCTGGGCGAACAGCAGCGCGCCCAGTTAGTGACGTGGCTAAAAGGCAATACCACCGGCGGGCAAAGCATTCGCGCAGGCCTGCCCGCAAGCTGGGTGGTCGGGGATAAAACCGGCGCCGGAGATTACGGCACCACCAACGATATCGCGGTGATCTGGCCGGAAAATCATGCCCCGCTGGTGCTGGTGACCTATTTTACCCAGCCGCAGCAGGATGCGAAAAGCCGCAAAGAGGTGTTAGCCGCGGCGGCAAAAATCGTCACCAAAGGGCTTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43788","NCBI_taxonomy_name":"Klebsiella michiganensis","NCBI_taxonomy_id":"1134687"}}}},"ARO_accession":"3008779","ARO_id":"47571","ARO_name":"OXY-1-13","CARD_short_name":"OXY-1-13","ARO_description":"Extended-spectrum class A beta-lactamase OXY-1-13.","ARO_category":{"38788":{"category_aro_accession":"3002388","category_aro_cvterm_id":"38788","category_aro_name":"OXY beta-lactamase","category_aro_description":"OXY beta-lactamases are chromosomal class A beta-lactamases that are found in Klebsiella oxytoca. At constitutive low levels, OXY beta-lactamases confer resistance to aminopenicillins and carboxypenicillins. At high induced levels,  OXY beta-lactamases confer resistance to penicillins, cephalosporins and aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8198":{"model_id":"8198","model_name":"OXY-1-16","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11025":{"protein_sequence":{"accession":"MXJ81313.1","sequence":"MLKSSWRKTALMAAVAVPLLLASGSLWASADAIQQKLADLEKRSGGRLGVALINTADNSHTLYRGDERFAMCSTGKVMAAAAVLKQSESNPEVVNKRLEIKKSDLVVWSPIAEKHLQSGMTLAELSAAALQYSDNTAMNKMISYLGGPEKVTAFAQSIGDVTFRLDRTEPALNSAIPGDKRDTTTPLAMAESLRKLTLGNALGEQQRAQLVTWLKGNTTGGQSIRAGLPASWAVGDKTGAGDYGTTNDIAVIWPENHAPLVLVTYFTQPQQDAKSRKEVLAAAAKIVTEGL"},"dna_sequence":{"accession":"WUMF01000005.1","fmin":"80389","fmax":"81265","strand":"+","sequence":"ATGTTGAAAAGTTCGTGGCGTAAAACCGCCCTGATGGCCGCCGTCGCCGTTCCGCTGCTGCTGGCGAGCGGTTCATTATGGGCCAGTGCCGATGCTATCCAGCAAAAGCTGGCTGATTTAGAAAAACGTTCCGGCGGTCGGCTGGGCGTAGCGCTGATTAACACGGCAGATAATTCGCACACCCTCTATCGCGGCGATGAACGTTTTGCCATGTGCAGCACCGGTAAAGTGATGGCCGCCGCCGCGGTGTTAAAACAGAGCGAAAGCAATCCAGAGGTGGTGAATAAAAGGCTGGAGATTAAAAAATCGGATTTAGTGGTCTGGAGCCCGATCGCCGAAAAACATCTGCAAAGCGGAATGACCCTGGCGGAACTCAGCGCGGCGGCGCTGCAGTACAGCGACAATACCGCGATGAATAAGATGATTAGCTACCTTGGCGGACCGGAAAAGGTGACCGCATTCGCCCAGAGTATCGGGGATGTCACTTTTCGTCTCGATCGTACGGAGCCGGCGCTGAACAGCGCGATTCCCGGCGATAAGCGCGATACCACCACCCCGTTGGCGATGGCCGAAAGCCTGCGCAAGCTGACGCTGGGCAATGCGCTGGGCGAACAGCAGCGCGCCCAGTTAGTGACGTGGCTAAAAGGCAATACCACCGGCGGGCAAAGCATTCGCGCAGGCCTGCCCGCAAGCTGGGCGGTCGGGGATAAAACCGGCGCCGGAGATTACGGCACCACCAACGATATCGCGGTGATCTGGCCGGAAAATCATGCCCCGCTGGTGCTGGTGACCTATTTTACCCAGCCGCAGCAGGATGCGAAAAGCCGCAAAGAGGTGTTAGCCGCGGCGGCAAAAATCGTTACCGAAGGGCTTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43788","NCBI_taxonomy_name":"Klebsiella michiganensis","NCBI_taxonomy_id":"1134687"}}}},"ARO_accession":"3008780","ARO_id":"47572","ARO_name":"OXY-1-16","CARD_short_name":"OXY-1-16","ARO_description":"Extended-spectrum class A beta-lactamase OXY-1-16.","ARO_category":{"38788":{"category_aro_accession":"3002388","category_aro_cvterm_id":"38788","category_aro_name":"OXY beta-lactamase","category_aro_description":"OXY beta-lactamases are chromosomal class A beta-lactamases that are found in Klebsiella oxytoca. At constitutive low levels, OXY beta-lactamases confer resistance to aminopenicillins and carboxypenicillins. At high induced levels,  OXY beta-lactamases confer resistance to penicillins, cephalosporins and aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8199":{"model_id":"8199","model_name":"OXY-1-17","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11026":{"protein_sequence":{"accession":"QHS46647.1","sequence":"MLKSSWRKTALMAAAAVPLLLASGSLWASADAIQQKLADLEKRSGGRLGVALINTADNSHTLYRGDERFAMCSTGKVMAAAAVLKQSESNPEVVNKRLEIKKSDLVVWSPIAEKHLQSGMTLAELSAAALQYSDNTAMNKMISYLGGPEKVTAFAQSIGDVTFRLDRTEPALNSAIPGDKRDTTTPLAMAESLRKLTLGNALGEQQRAQLVTWLKGNTTGGQSIRAGLPASWAVGDKTGAGDYGTTNDIAVIWPENHAPLVLVTYFTQPQQDAKSRKEVLAAAAKIVTEGL"},"dna_sequence":{"accession":"CP048108.1","fmin":"2989578","fmax":"2990454","strand":"+","sequence":"ATGTTGAAAAGTTCGTGGCGTAAAACCGCCCTGATGGCCGCCGCCGCCGTTCCGCTGCTGCTGGCGAGCGGTTCATTATGGGCCAGTGCCGATGCTATCCAGCAAAAGCTGGCTGATTTAGAAAAACGTTCCGGCGGTCGGCTGGGCGTAGCGCTGATTAACACGGCAGATAATTCGCACACCCTCTATCGCGGCGATGAACGTTTTGCCATGTGCAGCACCGGTAAAGTGATGGCCGCCGCCGCGGTGTTAAAACAGAGCGAAAGCAATCCAGAGGTGGTGAATAAAAGGCTGGAGATTAAAAAATCGGATTTAGTGGTCTGGAGCCCGATCGCCGAAAAACATCTGCAAAGCGGAATGACCCTGGCGGAACTCAGCGCGGCGGCGCTGCAGTACAGCGACAATACCGCGATGAATAAGATGATTAGCTACCTTGGCGGACCGGAAAAGGTGACCGCATTCGCCCAGAGTATCGGGGATGTCACTTTTCGTCTCGATCGTACGGAGCCGGCGCTGAACAGCGCGATTCCCGGCGATAAGCGCGATACCACCACCCCGTTGGCGATGGCCGAAAGCCTGCGCAAGCTGACGCTGGGCAATGCGCTGGGCGAACAGCAGCGCGCCCAGTTAGTGACGTGGCTAAAAGGCAATACCACCGGCGGGCAAAGCATTCGCGCAGGCCTGCCCGCAAGCTGGGCGGTCGGGGATAAAACCGGCGCCGGAGATTACGGCACCACCAACGATATCGCGGTGATCTGGCCGGAAAATCATGCCCCGCTGGTGCTGGTGACCTATTTTACCCAGCCGCAGCAGGATGCGAAAAGCCGCAAAGAGGTGTTAGCCGCGGCGGCAAAAATCGTTACCGAAGGGCTTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43788","NCBI_taxonomy_name":"Klebsiella michiganensis","NCBI_taxonomy_id":"1134687"}}}},"ARO_accession":"3008781","ARO_id":"47573","ARO_name":"OXY-1-17","CARD_short_name":"OXY-1-17","ARO_description":"Extended-spectrum class A beta-lactamase OXY-1-17.","ARO_category":{"38788":{"category_aro_accession":"3002388","category_aro_cvterm_id":"38788","category_aro_name":"OXY beta-lactamase","category_aro_description":"OXY beta-lactamases are chromosomal class A beta-lactamases that are found in Klebsiella oxytoca. At constitutive low levels, OXY beta-lactamases confer resistance to aminopenicillins and carboxypenicillins. At high induced levels,  OXY beta-lactamases confer resistance to penicillins, cephalosporins and aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8200":{"model_id":"8200","model_name":"OXY-1-18","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11027":{"protein_sequence":{"accession":"QNE50014.1","sequence":"MLKSSWRKTALMAAAAVPLLLASGSLWASADAIQQKLADLEKRSGGRLGVALINTADDSQTLYRGDERFAMCSTGKVMAAAAVLKRSESNPEVVNKRLEIKKSDLVVWSPITEKHLQSGMTLAELSAAALQYSDNTAMNKMISYLGGPEKVTAFAQSIGDVTFRLDRTEPALNSAIPGDKRDTTTPLAMAESLRKLTLGNALGEQQRAQLVTWLKGNTTGGQSIRAGLPASWVVGDKTGAGDYGTTNDIAVIWPENHAPLVLVTYFTQPQQDAKSRKEVLAAAAKIVTEGL"},"dna_sequence":{"accession":"CP060111.1","fmin":"4576168","fmax":"4577044","strand":"+","sequence":"ATGTTGAAAAGTTCGTGGCGTAAAACCGCCCTGATGGCCGCCGCCGCCGTTCCGCTGCTGCTGGCGAGCGGTTCATTATGGGCCAGTGCCGATGCTATCCAGCAAAAGCTGGCTGATTTAGAAAAACGTTCCGGCGGTCGGCTGGGCGTAGCGCTGATTAACACGGCAGATGATTCGCAAACCCTCTATCGCGGCGATGAACGTTTTGCCATGTGCAGCACCGGTAAAGTGATGGCCGCCGCCGCGGTGTTAAAACGGAGCGAAAGCAATCCAGAGGTGGTGAATAAAAGGCTGGAGATTAAAAAATCGGATTTAGTGGTCTGGAGCCCGATCACCGAAAAACATCTGCAAAGCGGAATGACCCTGGCGGAACTCAGCGCGGCGGCGCTGCAGTACAGCGACAATACCGCGATGAATAAGATGATTAGCTACCTTGGCGGACCGGAAAAGGTGACCGCATTCGCCCAGAGTATCGGGGATGTCACTTTTCGTCTCGATCGTACGGAGCCGGCGCTGAACAGCGCGATTCCCGGCGATAAGCGCGATACCACCACCCCGTTGGCGATGGCCGAAAGCCTGCGCAAGCTGACGCTGGGCAATGCGCTGGGCGAACAGCAGCGCGCCCAGTTAGTGACGTGGCTAAAAGGCAATACCACCGGCGGGCAAAGCATTCGCGCAGGCCTGCCCGCAAGCTGGGTGGTCGGGGATAAAACCGGCGCCGGAGATTACGGCACCACCAACGATATCGCGGTGATCTGGCCGGAAAATCATGCCCCGCTGGTGCTGGTGACCTATTTTACCCAGCCGCAGCAGGATGCGAAAAGCCGCAAAGAGGTGTTAGCCGCGGCGGCAAAAATCGTCACCGAAGGGCTTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43788","NCBI_taxonomy_name":"Klebsiella michiganensis","NCBI_taxonomy_id":"1134687"}}}},"ARO_accession":"3008782","ARO_id":"47574","ARO_name":"OXY-1-18","CARD_short_name":"OXY-1-18","ARO_description":"Extended-spectrum class A beta-lactamase OXY-1-18.","ARO_category":{"38788":{"category_aro_accession":"3002388","category_aro_cvterm_id":"38788","category_aro_name":"OXY beta-lactamase","category_aro_description":"OXY beta-lactamases are chromosomal class A beta-lactamases that are found in Klebsiella oxytoca. At constitutive low levels, OXY beta-lactamases confer resistance to aminopenicillins and carboxypenicillins. At high induced levels,  OXY beta-lactamases confer resistance to penicillins, cephalosporins and aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8201":{"model_id":"8201","model_name":"OXY-1-19","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11028":{"protein_sequence":{"accession":"MBG2697728.1","sequence":"MLKSSWRKTALMAAAAVPLLLASGSLWASADAIQQKLADLEKRSGGRLGVALINTADDSQTLYRGDERFAMCSTGKVMAAAAVLKQSESNPEVVNKRLEIKKSDLVVWSPITEKHLQSGMTLAELSAAALQYSDNTAMNKMISYLGGPEKVTAFAQSIGDVTFRLDRTEPAMNSAIPGDKRDTTTPLAMAESLRKLTLGNALGEQQRAQLVTWLKGNTTGGQSIRAGLPASWAVGDKTGAGDYGTTNDIAVIWPENHAPLVLVTYFTQPQQDAKSRKEVLAAAAKIVTEGL"},"dna_sequence":{"accession":"JADRUQ010000001.1","fmin":"79609","fmax":"80485","strand":"+","sequence":"ATGTTGAAAAGTTCGTGGCGTAAAACCGCCCTGATGGCCGCCGCCGCCGTTCCGCTGCTGCTGGCGAGCGGTTCATTATGGGCCAGTGCCGATGCTATCCAGCAAAAGCTGGCTGATTTAGAAAAACGTTCCGGCGGTCGGCTGGGCGTAGCGCTGATTAACACGGCAGATGATTCGCAAACCCTCTATCGCGGCGATGAACGTTTTGCCATGTGCAGCACCGGTAAAGTGATGGCCGCCGCCGCGGTGTTAAAACAGAGCGAAAGCAATCCAGAGGTGGTGAATAAAAGGCTGGAGATTAAAAAATCGGATTTAGTGGTCTGGAGCCCGATCACCGAAAAACATCTGCAAAGCGGAATGACCCTGGCGGAACTCAGCGCGGCGGCGCTGCAGTACAGCGACAATACCGCGATGAATAAGATGATTAGCTACCTTGGCGGACCGGAAAAGGTGACCGCATTCGCCCAGAGTATCGGGGATGTCACTTTTCGTCTCGATCGTACGGAGCCGGCGATGAACAGCGCGATTCCCGGCGATAAGCGCGATACCACCACCCCGTTGGCGATGGCCGAAAGCCTGCGCAAGCTGACGCTGGGCAATGCGCTGGGCGAACAGCAGCGCGCCCAGTTAGTGACGTGGCTAAAAGGCAATACCACCGGCGGGCAAAGCATTCGCGCAGGCCTGCCCGCAAGCTGGGCGGTCGGGGATAAAACCGGCGCCGGAGATTACGGCACCACCAACGATATTGCGGTGATCTGGCCGGAAAATCATGCCCCGCTGGTGCTGGTGACCTATTTTACCCAGCCGCAGCAGGATGCGAAAAGCCGCAAAGAGGTGTTAGCCGCGGCGGCAAAAATCGTCACCGAAGGGCTTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43788","NCBI_taxonomy_name":"Klebsiella michiganensis","NCBI_taxonomy_id":"1134687"}}}},"ARO_accession":"3008783","ARO_id":"47575","ARO_name":"OXY-1-19","CARD_short_name":"OXY-1-19","ARO_description":"Extended-spectrum class A beta-lactamase OXY-1-19.","ARO_category":{"38788":{"category_aro_accession":"3002388","category_aro_cvterm_id":"38788","category_aro_name":"OXY beta-lactamase","category_aro_description":"OXY beta-lactamases are chromosomal class A beta-lactamases that are found in Klebsiella oxytoca. At constitutive low levels, OXY beta-lactamases confer resistance to aminopenicillins and carboxypenicillins. At high induced levels,  OXY beta-lactamases confer resistance to penicillins, cephalosporins and aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8202":{"model_id":"8202","model_name":"OXY-10-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11029":{"protein_sequence":{"accession":"PXW47003.1","sequence":"MIKCSWRKTALIAAAFPLLLCSSSLWANDDAIQQKLADLEKSTGGRLGVALIDTSDNSQVLYRGDERFAMCSTGKVMAAAAVLKQSEADNQVLNKRLEIKKSDLVIWSPVTEKHLQSGMTLAELSAATLQYSDNTAMNKMIGYLGGPDKVTAFARSIGDVTFRLDRTEPALNTAIPGDERDTTTPLAMAESLHKLTLGSALGEQQRAQLVTWLKGNTTGGQSIRAGLPANWVVGDKTGAGDYGTTNDIAVIWPENHAPLVLVTYFTQPQQDAKSRKEVLAAAAKIVTEGL"},"dna_sequence":{"accession":"QJJG01000004.1","fmin":"70930","fmax":"71803","strand":"-","sequence":"ATGATTAAATGTTCGTGGCGTAAAACCGCCCTGATTGCCGCCGCCTTTCCTTTATTGCTCTGTAGCAGTTCATTATGGGCCAATGACGATGCTATTCAGCAGAAGCTCGCTGATTTAGAAAAAAGTACCGGCGGTCGACTGGGCGTCGCGCTGATTGACACCTCAGATAATTCTCAAGTTCTATATCGTGGTGACGAGCGTTTTGCCATGTGCAGCACCGGTAAAGTGATGGCCGCCGCCGCGGTGTTAAAGCAAAGCGAAGCCGATAATCAAGTATTGAATAAAAGGCTGGAGATTAAGAAATCGGATCTGGTGATCTGGAGCCCGGTGACCGAAAAACATCTGCAGAGCGGAATGACGCTGGCGGAATTAAGCGCCGCAACCCTGCAATATAGCGATAACACCGCGATGAATAAGATGATTGGTTATCTTGGCGGACCAGACAAAGTGACCGCATTCGCCCGCAGCATTGGCGATGTCACTTTTCGTCTTGATCGTACGGAGCCTGCACTAAACACCGCGATCCCGGGTGATGAACGCGATACCACCACGCCGCTGGCGATGGCCGAAAGCCTGCACAAGCTGACGCTGGGTAGTGCTCTGGGTGAACAGCAGCGCGCCCAGTTAGTGACATGGTTGAAAGGCAACACCACCGGCGGGCAGAGCATTCGTGCGGGACTGCCTGCGAACTGGGTCGTGGGAGATAAAACCGGAGCCGGTGATTACGGCACGACCAATGATATCGCCGTTATCTGGCCGGAAAATCATGCTCCGCTGGTGTTAGTCACTTATTTCACCCAACCACAGCAGGATGCGAAAAGCCGCAAAGAGGTATTAGCCGCAGCGGCAAAAATTGTGACCGAAGGGCTGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3008784","ARO_id":"47576","ARO_name":"OXY-10-1","CARD_short_name":"OXY-10-1","ARO_description":"Extended-spectrum class A beta-lactamase OXY-10-1.","ARO_category":{"38788":{"category_aro_accession":"3002388","category_aro_cvterm_id":"38788","category_aro_name":"OXY beta-lactamase","category_aro_description":"OXY beta-lactamases are chromosomal class A beta-lactamases that are found in Klebsiella oxytoca. At constitutive low levels, OXY beta-lactamases confer resistance to aminopenicillins and carboxypenicillins. At high induced levels,  OXY beta-lactamases confer resistance to penicillins, cephalosporins and aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8203":{"model_id":"8203","model_name":"OXY-11-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11030":{"protein_sequence":{"accession":"QGN37045.1","sequence":"MIKSLWHKAALTAVATVPLLLASGSLWATTDTIQQKLAELEKSSGGRLGVALINTADNSQTLYRGNERFAMCSTGKVMAAAAVLKESENNKDVVNKRLEIKESDLVVWSPISEKHLKNGMTLAELSAATLQYSDNTAMNKIIGYLGGPDNVTAFARSIGDTTFRLDRTEPTLNTAIPGDERDTTTPQAMAESLQKLTLGNALGEQQRARLVTWLKGNTTGGQSIRAGLPESWVVGDKTGAGDYGTTNDIAVIWPENQAPLVLVTYFTQPQQDAKNRKDVLAAAAKIVTEGL"},"dna_sequence":{"accession":"CP046115.1","fmin":"1479410","fmax":"1480286","strand":"-","sequence":"ATGATTAAAAGTTTGTGGCATAAAGCCGCCCTGACGGCCGTCGCCACCGTTCCACTACTGCTCGCAAGCGGTTCGTTATGGGCAACTACCGATACAATCCAGCAGAAGCTGGCTGAATTAGAAAAGAGTTCCGGCGGCAGGCTAGGCGTGGCGCTGATTAACACCGCAGATAATTCTCAAACCTTATATCGCGGCAATGAACGTTTTGCGATGTGCAGCACCGGGAAAGTGATGGCTGCCGCCGCGGTGTTAAAAGAGAGTGAGAACAATAAAGATGTGGTGAATAAACGGCTGGAGATTAAAGAATCCGATCTGGTGGTGTGGAGCCCGATTAGCGAAAAACATCTCAAGAACGGAATGACGCTGGCCGAACTGAGCGCGGCGACGCTGCAATACAGCGACAATACCGCGATGAATAAGATTATTGGCTACCTCGGCGGCCCGGACAACGTGACCGCCTTCGCCCGCAGTATCGGCGATACCACCTTTCGTCTCGATCGTACGGAGCCGACGCTAAATACCGCCATTCCGGGCGATGAGCGCGATACTACCACGCCGCAGGCGATGGCCGAGAGCCTGCAGAAGTTAACGCTGGGCAATGCTCTGGGCGAACAGCAGCGCGCCCGGTTGGTGACCTGGCTGAAAGGCAACACCACCGGCGGGCAAAGCATTCGCGCAGGCCTGCCTGAAAGCTGGGTTGTTGGAGATAAAACCGGCGCCGGGGATTATGGCACCACCAACGATATCGCCGTCATCTGGCCGGAAAATCAGGCTCCGCTGGTACTGGTGACTTACTTTACCCAGCCGCAGCAGGATGCGAAAAACCGCAAAGATGTCTTAGCCGCGGCGGCAAAAATCGTCACCGAAGGGCTGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3008785","ARO_id":"47577","ARO_name":"OXY-11-1","CARD_short_name":"OXY-11-1","ARO_description":"Extended-spectrum class A beta-lactamase OXY-11-1.","ARO_category":{"38788":{"category_aro_accession":"3002388","category_aro_cvterm_id":"38788","category_aro_name":"OXY beta-lactamase","category_aro_description":"OXY beta-lactamases are chromosomal class A beta-lactamases that are found in Klebsiella oxytoca. At constitutive low levels, OXY beta-lactamases confer resistance to aminopenicillins and carboxypenicillins. At high induced levels,  OXY beta-lactamases confer resistance to penicillins, cephalosporins and aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8204":{"model_id":"8204","model_name":"OXY-12-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11031":{"protein_sequence":{"accession":"QLT77668.1","sequence":"MIKCSWRKTALIAAALPLLLCSSSLWANADAIQQKLTDLEKSSGGRLGVALINTTDNSQILYRGDERFAMCSTGKVMAAAAVLKQSEADNQVLNKRLEIKKSDLVVWSPVTEKHLQSGMTLAELSAATLQYSDNTAMNKMIGYLGGPDKVTAFARSIGDVTFRLDRTEPALNTAIPGDERDTTTPLAMAESLHKLTLGNALGEQQRAQLVTWLKGNTTGGQSIRAGLPASWVVGDKTGAGDYGTTNDIAVIWPENHAPLVLVTYFTQPQQDAKSRKEVLAAAAKIVTEGL"},"dna_sequence":{"accession":"CP056483.1","fmin":"4480742","fmax":"4481615","strand":"+","sequence":"ATGATTAAATGTTCGTGGCGTAAAACCGCCCTGATTGCCGCCGCCTTGCCTTTATTGCTCTGTAGCAGTTCATTATGGGCCAATGCCGATGCTATTCAGCAGAAGCTGACTGATTTAGAAAAAAGCTCCGGCGGCAGGTTGGGCGTGGCGCTGATTAATACTACAGATAATTCTCAAATCTTATATCGCGGAGATGAACGTTTTGCCATGTGCAGCACCGGTAAAGTGATGGCCGCCGCCGCGGTGTTAAAGCAAAGCGAAGCCGATAATCAAGTATTGAATAAAAGGCTGGAGATTAAGAAATCAGATTTGGTGGTCTGGAGTCCGGTGACCGAAAAACATCTGCAGAGTGGAATGACGCTGGCGGAATTAAGCGCCGCAACCTTGCAATATAGCGACAACACCGCGATGAATAAGATGATTGGTTATCTTGGCGGACCAGACAAAGTGACCGCATTCGCCCGCAGCATTGGCGATGTCACTTTTCGTCTTGATCGTACGGAGCCTGCACTAAACACCGCGATTCCGGGTGATGAACGCGATACCACCACGCCGCTGGCGATGGCCGAAAGTCTGCACAAGCTGACGCTGGGTAATGCTCTGGGTGAACAGCAGCGCGCACAGTTAGTGACATGGTTGAAAGGCAACACCACTGGCGGGCAGAGCATTCGTGCGGGGCTGCCTGCAAGCTGGGTCGTGGGAGATAAAACCGGTGCTGGTGATTACGGCACGACCAATGATATCGCCGTTATCTGGCCGGAAAATCATGCCCCGCTGGTGTTAGTCACTTATTTCACCCAACCACAGCAGGATGCGAAAAGCCGCAAAGAGGTATTAGCCGCAGCGGCAAAAATTGTGACCGAAGGGCTGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42713","NCBI_taxonomy_name":"Klebsiella sp.","NCBI_taxonomy_id":"576"}}}},"ARO_accession":"3008786","ARO_id":"47578","ARO_name":"OXY-12-1","CARD_short_name":"OXY-12-1","ARO_description":"Extended-spectrum class A beta-lactamase OXY-12-1.","ARO_category":{"38788":{"category_aro_accession":"3002388","category_aro_cvterm_id":"38788","category_aro_name":"OXY beta-lactamase","category_aro_description":"OXY beta-lactamases are chromosomal class A beta-lactamases that are found in Klebsiella oxytoca. At constitutive low levels, OXY beta-lactamases confer resistance to aminopenicillins and carboxypenicillins. At high induced levels,  OXY beta-lactamases confer resistance to penicillins, cephalosporins and aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8205":{"model_id":"8205","model_name":"OXY-12-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11032":{"protein_sequence":{"accession":"MBA7932644.1","sequence":"MIKTSWRKSALITAALPLLLCSSSLWANVDAIQQKLTDLEKSSGGRLGVALINTRDNSQILYRGDERFAMCSTGKVMAAAAVLKQSEADNQVLNKRLEIKKSDLVVWSPVTEKHLQSGMTLAELSAATLQYSDNTAMNKMIGYLGGPDKVTAFARSIGDVTFRLDRTEPALNTAIPGDERDTTTPLAMAESLHKLTLGNALGEQQRAQLVTWLKGNTTGGQSIRAGLPASWVVGDKTGAGDYGTTNDIAVIWPENHAPLVLVTYFTQPQQDAKSRKEVLAAAAKIVTEGL"},"dna_sequence":{"accession":"JABXQS010000001.1","fmin":"3280378","fmax":"3281251","strand":"+","sequence":"ATGATTAAAACTTCGTGGCGTAAAAGCGCCCTGATTACCGCCGCCCTGCCTTTATTGCTCTGTAGCAGTTCATTATGGGCCAATGTCGATGCTATTCAGCAGAAGCTGACTGATTTAGAAAAAAGCTCCGGCGGCAGGTTGGGCGTGGCGCTGATTAATACTAGAGATAATTCTCAAATCTTATATCGCGGAGATGAACGTTTTGCCATGTGCAGCACCGGTAAAGTGATGGCCGCCGCCGCGGTGTTAAAGCAAAGCGAAGCCGATAATCAAGTATTGAATAAAAGGCTGGAGATTAAGAAATCAGATTTGGTGGTCTGGAGTCCGGTGACCGAAAAACATCTGCAGAGCGGAATGACGCTGGCGGAATTAAGCGCCGCAACCCTGCAATATAGCGACAATACCGCGATGAATAAGATGATTGGTTATCTTGGCGGACCAGACAAAGTGACCGCATTCGCCCGCAGCATTGGTGATGTCACTTTTCGTCTTGATCGTACGGAGCCTGCGCTAAACACCGCGATTCCGGGTGATGAACGCGATACCACCACGCCGCTGGCGATGGCCGAAAGCCTGCACAAGCTGACGCTGGGTAATGCGCTGGGTGAACAACAGCGCGCACAGTTAGTGACATGGTTGAAAGGCAACACCACCGGCGGGCAGAGCATTCGTGCGGGCCTGCCTGCAAGCTGGGTCGTGGGAGATAAAACCGGAGCCGGTGATTACGGCACGACCAATGATATCGCCGTTATCTGGCCGGAAAATCATGCCCCGCTGGTGTTAGTGACTTATTTCACCCAACCACAGCAGGATGCGAAAAGCCGCAAAGAGGTATTAGCCGCAGCGGCAAAAATTGTGACCGAAGGGCTGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42713","NCBI_taxonomy_name":"Klebsiella sp.","NCBI_taxonomy_id":"576"}}}},"ARO_accession":"3008787","ARO_id":"47579","ARO_name":"OXY-12-2","CARD_short_name":"OXY-12-2","ARO_description":"Extended-spectrum class A beta-lactamase OXY-12-2.","ARO_category":{"38788":{"category_aro_accession":"3002388","category_aro_cvterm_id":"38788","category_aro_name":"OXY beta-lactamase","category_aro_description":"OXY beta-lactamases are chromosomal class A beta-lactamases that are found in Klebsiella oxytoca. At constitutive low levels, OXY beta-lactamases confer resistance to aminopenicillins and carboxypenicillins. At high induced levels,  OXY beta-lactamases confer resistance to penicillins, cephalosporins and aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8206":{"model_id":"8206","model_name":"OXY-2-17","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11033":{"protein_sequence":{"accession":"ALC79260.1","sequence":"MIKSSWRKIAMLAAAVPLLLASGALWASTDAIHQKLTDLEKRSGGRLGVALINTADNSQILYRGDERFAMCSTSKVMAAAAVLKQSESNKEVVNKRLDINAADLVVWSPITEKHLQSGMTLAELSAATLQYSDNTAMNLIIGYLGGPEKVTAFARSIGDATFRLDRTEPTLNTAIPGDERDTSTPLAMAESLRKLTLGDALGEQQRAQLVTWLKGNTTGGQSIRAGLPESWVVGDKTGAGDYGTTNDIAVIWPENHAPLVLVTYFTQPQQDAKNRKEVLAAATKIVTEGL"},"dna_sequence":{"accession":"KT001249.1","fmin":"0","fmax":"873","strand":"+","sequence":"ATGATAAAAAGTTCGTGGCGTAAAATTGCAATGCTAGCCGCCGCCGTTCCGCTGCTGCTGGCGAGCGGCGCACTGTGGGCCAGTACCGATGCTATCCATCAGAAGCTGACAGATCTCGAGAAGCGTTCAGGCGGCAGGTTGGGCGTGGCGCTAATCAACACGGCAGATAATTCTCAAATCTTATATCGCGGCGACGAGCGTTTTGCCATGTGCAGCACCAGTAAAGTGATGGCCGCCGCCGCGGTATTAAAACAGAGCGAAAGCAATAAAGAGGTGGTAAATAAAAGGCTGGATATTAACGCAGCCGATTTGGTGGTCTGGAGTCCGATTACCGAAAAACATCTCCAGAGCGGAATGACGCTGGCTGAGCTAAGCGCGGCGACGCTGCAATATAGCGACAATACGGCGATGAATCTGATCATCGGCTACCTTGGCGGGCCGGAAAAAGTCACCGCCTTCGCCCGCAGTATCGGCGATGCCACCTTTCGTCTCGATCGTACGGAGCCCACGCTGAATACCGCCATCCCGGGCGATGAGCGTGATACCAGCACGCCGCTGGCGATGGCTGAAAGCCTGCGCAAGCTGACGCTTGGCGATGCGCTGGGCGAACAGCAACGCGCCCAGTTAGTTACCTGGCTGAAAGGCAATACCACCGGCGGGCAAAGCATTCGCGCGGGCCTGCCTGAAAGTTGGGTGGTCGGCGATAAAACCGGCGCCGGAGATTACGGCACCACCAATGATATTGCGGTTATCTGGCCGGAAAATCACGCTCCGCTGGTATTAGTCACCTACTTTACCCAGCCGCAGCAGGATGCGAAAAACCGCAAAGAGGTGTTAGCCGCAGCGACAAAAATCGTGACCGAAGGGCTTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3008788","ARO_id":"47580","ARO_name":"OXY-2-17","CARD_short_name":"OXY-2-17","ARO_description":"Extended-spectrum class A beta-lactamase OXY-2-17.","ARO_category":{"38788":{"category_aro_accession":"3002388","category_aro_cvterm_id":"38788","category_aro_name":"OXY beta-lactamase","category_aro_description":"OXY beta-lactamases are chromosomal class A beta-lactamases that are found in Klebsiella oxytoca. At constitutive low levels, OXY beta-lactamases confer resistance to aminopenicillins and carboxypenicillins. At high induced levels,  OXY beta-lactamases confer resistance to penicillins, cephalosporins and aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8207":{"model_id":"8207","model_name":"OXY-2-18","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11034":{"protein_sequence":{"accession":"CAA0290077.1","sequence":"MIKSSWRKIAMLAAAVPLLLASGALWASTDAIHQKLTDLEKRSGGRLGVALINTADNSQILYRGDERFAMCSTSKVMAAAAVLKQSESNKEVVNKRLEINAADLVVWSPITEKHLQSGMTLAELSAATLQYSDNTAMNLIIGYLGGPEKVTAFARSIGDATFRLDRTEPTLNTAIPGDERDTSTPLAMAESLRKLTLGNALGEQQRAQLVTWLKGNTTGGQSIRAGLPESWVVGDKTGAGDYGTTNDIAVIWPENHAPLVLVTYFTQPQQDAKNRKEVLAAAAKIVTEGL"},"dna_sequence":{"accession":"CACSHZ010000084.1","fmin":"200746","fmax":"201619","strand":"-","sequence":"ATGATAAAAAGTTCGTGGCGTAAAATTGCAATGCTAGCCGCCGCCGTTCCGCTGCTGCTGGCGAGCGGCGCACTGTGGGCCAGTACCGATGCTATCCATCAGAAGCTGACAGATCTCGAGAAGCGTTCAGGCGGCAGGTTGGGCGTGGCGCTAATCAACACGGCAGATAATTCTCAAATCTTATATCGCGGCGACGAGCGTTTTGCCATGTGCAGCACCAGTAAAGTGATGGCCGCCGCCGCGGTATTAAAACAGAGCGAAAGCAATAAAGAGGTGGTAAATAAAAGGCTGGAGATTAACGCAGCCGATTTGGTGGTCTGGAGTCCGATTACCGAAAAACATCTCCAGAGCGGAATGACGCTGGCTGAGCTAAGCGCGGCGACGCTGCAATATAGCGACAATACGGCGATGAATCTGATCATCGGCTACCTTGGCGGGCCGGAAAAAGTCACCGCCTTCGCCCGCAGTATCGGCGATGCCACCTTTCGTCTCGATCGTACGGAGCCCACGCTGAATACCGCCATCCCGGGCGATGAGCGTGATACCAGCACGCCGCTGGCGATGGCTGAAAGCCTGCGCAAGCTGACGCTTGGCAATGCGCTGGGCGAACAGCAACGCGCCCAGTTAGTCACCTGGCTGAAAGGCAATACCACCGGCGGGCAAAGCATTCGCGCGGGCCTGCCTGAAAGCTGGGTGGTCGGCGATAAAACCGGCGCCGGAGATTACGGCACCACCAATGATATTGCGGTTATCTGGCCGGAAAATCACGCTCCGCTGGTATTAGTCACCTACTTTACCCAGCCGCAGCAGGATGCGAAAAACCGCAAAGAGGTGTTAGCCGCAGCGGCAAAAATCGTGACCGAAGGGCTTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3008789","ARO_id":"47581","ARO_name":"OXY-2-18","CARD_short_name":"OXY-2-18","ARO_description":"Extended-spectrum class A beta-lactamase OXY-2-18.","ARO_category":{"38788":{"category_aro_accession":"3002388","category_aro_cvterm_id":"38788","category_aro_name":"OXY beta-lactamase","category_aro_description":"OXY beta-lactamases are chromosomal class A beta-lactamases that are found in Klebsiella oxytoca. At constitutive low levels, OXY beta-lactamases confer resistance to aminopenicillins and carboxypenicillins. At high induced levels,  OXY beta-lactamases confer resistance to penicillins, cephalosporins and aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8208":{"model_id":"8208","model_name":"OXY-2-19","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11035":{"protein_sequence":{"accession":"ALC79262.1","sequence":"MIKSSWRKIAMLAAAVPLLLASGALWASTDAIHQKLTDLEKRSGGRLGVALINTADNSQILYRGDERFAMCSTSKVMAAAAVLKQSESNKEVVNKRLEINAADLVVWSPITEKHLQSGMTLAELSAATLQYSDNTAMNLIIGYLGGPEKVTAFARSIGDATFRLDRTEPTLNTAIPGDERDTSTPLAMAESLRKLTLGDALGEQQRAQLVTWLKGNTTGGQSIRAGLPESWVVGDKTGGGDYGTTNDIAVIWPEDHAPLVLVTYFTQPQQDAKNRKEVLAAAAKIVTEGL"},"dna_sequence":{"accession":"KT001251.1","fmin":"0","fmax":"873","strand":"+","sequence":"ATGATAAAAAGTTCGTGGCGTAAAATTGCAATGCTAGCCGCCGCCGTTCCGCTGCTGCTGGCGAGCGGCGCACTGTGGGCCAGTACCGATGCTATCCATCAGAAGCTGACAGATCTCGAGAAGCGTTCAGGCGGCAGGTTGGGCGTGGCGCTAATCAACACGGCAGATAATTCTCAAATCTTATATCGCGGCGACGAGCGTTTTGCCATGTGCAGCACCAGTAAAGTGATGGCCGCCGCCGCGGTATTAAAACAGAGCGAAAGCAATAAAGAGGTGGTAAATAAAAGGCTGGAGATTAACGCAGCCGATTTGGTGGTCTGGAGCCCGATTACCGAAAAACATCTCCAGAGCGGAATGACGCTGGCTGAGCTAAGCGCGGCGACGCTGCAATATAGCGACAATACGGCGATGAATCTGATCATCGGCTACCTTGGCGGGCCGGAAAAAGTCACCGCCTTCGCCCGCAGTATCGGCGATGCCACCTTTCGTCTCGATCGTACGGAGCCCACGCTGAATACCGCCATCCCGGGCGATGAGCGTGATACCAGCACGCCGCTGGCGATGGCTGAAAGCCTGCGCAAGCTGACGCTTGGCGATGCGCTGGGCGAACAGCAACGCGCCCAGTTAGTCACCTGGCTGAAAGGCAATACCACCGGCGGGCAAAGCATTCGCGCGGGCCTGCCTGAAAGCTGGGTGGTCGGCGATAAAACCGGCGGCGGAGATTACGGCACCACCAATGATATTGCGGTTATCTGGCCGGAAGATCACGCTCCGCTGGTATTAGTCACCTACTTTACCCAGCCGCAGCAGGATGCGAAAAACCGCAAAGAGGTGTTAGCCGCAGCGGCAAAAATCGTGACCGAAGGGCTTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3008790","ARO_id":"47582","ARO_name":"OXY-2-19","CARD_short_name":"OXY-2-19","ARO_description":"Extended-spectrum class A beta-lactamase OXY-2-19.","ARO_category":{"38788":{"category_aro_accession":"3002388","category_aro_cvterm_id":"38788","category_aro_name":"OXY beta-lactamase","category_aro_description":"OXY beta-lactamases are chromosomal class A beta-lactamases that are found in Klebsiella oxytoca. At constitutive low levels, OXY beta-lactamases confer resistance to aminopenicillins and carboxypenicillins. At high induced levels,  OXY beta-lactamases confer resistance to penicillins, cephalosporins and aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8209":{"model_id":"8209","model_name":"OXY-2-20","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11036":{"protein_sequence":{"accession":"MBZ7692543.1","sequence":"MIKSSWRKIAMLAAAVPLLLASSALWASTDAIHQKLTDLEKRSGGRLGVALINTADNSQILYRGDERFAMCSTSKVMAAAAVLKQSESNKEVVNKRLEINAADLVVWSPITEKHLQSGMTLAELSAATLQYSDNTAMNLIIGYLGGPEKVTAFARSIGDATFRLDRTEPTLNTAIPGDERDTSTPLAMAESLRKLTLGNALGEQQRAQLVTWLKGNTTGGQSIRAGLPESWVVGDKTGAGDYGTTNDIAVIWPENHAPLVLVTYFTQPQQDAKNRKEVLAAATKIVTEGL"},"dna_sequence":{"accession":"VNUM01000003.1","fmin":"39807","fmax":"40680","strand":"-","sequence":"ATGATAAAAAGTTCGTGGCGTAAAATTGCAATGCTAGCCGCCGCCGTTCCGCTGCTGCTGGCGAGCAGCGCACTGTGGGCCAGTACCGATGCTATCCATCAGAAGCTGACAGATCTCGAGAAGCGTTCAGGCGGCAGGTTGGGCGTGGCGCTAATCAACACGGCAGATAATTCTCAAATCTTATATCGCGGCGACGAGCGTTTTGCCATGTGCAGCACCAGTAAAGTGATGGCCGCCGCCGCGGTATTAAAACAGAGCGAAAGCAATAAAGAGGTGGTAAATAAAAGGCTGGAGATTAACGCAGCCGATTTGGTGGTCTGGAGTCCGATTACCGAAAAACATCTCCAGAGCGGAATGACGCTGGCTGAGCTAAGCGCGGCGACGCTGCAATATAGCGACAATACGGCGATGAATCTGATCATCGGCTACCTTGGCGGGCCGGAAAAAGTCACCGCCTTCGCCCGCAGTATCGGCGATGCCACCTTTCGTCTCGATCGTACGGAGCCCACGCTGAATACCGCCATCCCGGGCGATGAGCGTGATACCAGCACGCCGCTGGCGATGGCTGAAAGCCTGCGCAAGCTGACGCTTGGCAATGCGCTGGGCGAACAGCAACGCGCCCAGTTAGTCACCTGGCTGAAAGGCAATACCACCGGCGGGCAAAGCATTCGCGCGGGCCTGCCTGAAAGCTGGGTGGTCGGCGATAAAACCGGCGCCGGAGATTACGGCACCACCAATGATATTGCGGTTATCTGGCCGGAAAATCACGCTCCGCTGGTATTAGTCACCTACTTTACCCAGCCGCAGCAGGATGCGAAAAACCGCAAAGAGGTGTTAGCCGCAGCGACAAAAATCGTGACCGAAGGGCTTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3008791","ARO_id":"47583","ARO_name":"OXY-2-20","CARD_short_name":"OXY-2-20","ARO_description":"Extended-spectrum class A beta-lactamase OXY-2-20.","ARO_category":{"38788":{"category_aro_accession":"3002388","category_aro_cvterm_id":"38788","category_aro_name":"OXY beta-lactamase","category_aro_description":"OXY beta-lactamases are chromosomal class A beta-lactamases that are found in Klebsiella oxytoca. At constitutive low levels, OXY beta-lactamases confer resistance to aminopenicillins and carboxypenicillins. At high induced levels,  OXY beta-lactamases confer resistance to penicillins, cephalosporins and aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8210":{"model_id":"8210","model_name":"OXY-2-21","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11037":{"protein_sequence":{"accession":"SBL39456.1","sequence":"MIKSSWRKIAILAAAVPLLLASGALWASTDAIHQKLTDLEKRSGGRLGVALINTADNSQILYRGDERFAMCSTSKVMAAAAVLKQSESNKEVVNKRLEINAADLVVWSPITEKHLQSGMTLAELSAATLQYSDNTAMNLIIGYLGGPEKVTAFARSIGDATFRLDRTEPTLNTAIPGDERDTSTPLAMAESLRKLTLGNALGEQQRAQLVTWLKGNTTGGQSIRAGLPESWVVGDKTGAGDYGTTNDIAVIWPEDHAPLVLVTYFTQPQQDAKNRKEVLAAAAKIVTEGL"},"dna_sequence":{"accession":"FLAI01000001.1","fmin":"590655","fmax":"591528","strand":"+","sequence":"ATGATAAAAAGTTCGTGGCGTAAAATTGCAATTCTAGCCGCCGCCGTTCCGCTGCTGCTGGCGAGCGGCGCACTGTGGGCCAGTACCGATGCTATCCATCAGAAGCTGACAGATCTCGAGAAGCGTTCAGGCGGCAGGTTGGGCGTGGCGCTAATCAACACGGCAGATAATTCTCAAATCTTATATCGCGGCGACGAGCGTTTTGCCATGTGCAGCACCAGTAAAGTGATGGCCGCCGCCGCGGTATTAAAACAGAGCGAAAGCAATAAAGAGGTGGTAAATAAAAGGCTGGAGATTAACGCAGCCGATTTGGTGGTCTGGAGTCCGATTACCGAAAAACATCTCCAGAGCGGAATGACGCTGGCTGAGCTAAGCGCGGCGACGCTGCAATATAGCGACAATACGGCGATGAATCTGATCATCGGCTACCTTGGCGGGCCGGAAAAAGTCACCGCCTTCGCCCGCAGTATCGGCGATGCCACCTTTCGTCTCGATCGTACGGAGCCCACGCTGAATACCGCCATCCCGGGCGATGAGCGTGATACCAGCACGCCGCTGGCGATGGCTGAAAGCCTGCGCAAGCTGACGCTTGGCAATGCGCTGGGCGAACAGCAACGCGCCCAGTTAGTCACCTGGCTGAAAGGCAATACCACCGGCGGGCAAAGCATTCGCGCGGGCCTGCCTGAAAGCTGGGTGGTCGGCGATAAAACCGGCGCCGGAGATTACGGCACCACCAATGATATTGCGGTTATCTGGCCGGAAGATCACGCTCCGCTGGTATTAGTCACCTACTTTACCCAGCCGCAGCAGGATGCGAAAAACCGCAAAGAGGTGTTAGCCGCAGCGGCAAAAATCGTGACCGAAGGGCTTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3008792","ARO_id":"47584","ARO_name":"OXY-2-21","CARD_short_name":"OXY-2-21","ARO_description":"Extended-spectrum class A beta-lactamase OXY-2-21.","ARO_category":{"38788":{"category_aro_accession":"3002388","category_aro_cvterm_id":"38788","category_aro_name":"OXY beta-lactamase","category_aro_description":"OXY beta-lactamases are chromosomal class A beta-lactamases that are found in Klebsiella oxytoca. At constitutive low levels, OXY beta-lactamases confer resistance to aminopenicillins and carboxypenicillins. At high induced levels,  OXY beta-lactamases confer resistance to penicillins, cephalosporins and aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8211":{"model_id":"8211","model_name":"OXY-2-22","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11038":{"protein_sequence":{"accession":"QMF99399.1","sequence":"MIKSSWRKIAMLAAAVPLLLASGALWASTDAIHQKLTDLEKRSGGRLGVALINTADNSQILYRGDERFAMCSTSKVMAAAAVLKQSESNKEVVNKRLEINAADLVVWSPITEKHLQSGMTLAELSAATLQYSDNTAMNLIIGYLGGPEKVTAFARSIGDETFRLDRTEPTLNTAIPGDERDTSTPLAMAESLRKLTLGDALGEQQRAQLVTWLKGNTTGGQSIRAGLPESWVVGDKTGAGDYGTTNDIAVIWPENHAPLVLVTYFTQPQQDAKNRKEVLAAAAKIVTEGL"},"dna_sequence":{"accession":"CP057330.1","fmin":"4406764","fmax":"4407637","strand":"+","sequence":"ATGATAAAAAGTTCGTGGCGTAAAATTGCAATGCTAGCCGCCGCCGTTCCACTGCTGTTGGCGAGCGGCGCACTGTGGGCCAGTACCGATGCTATCCATCAGAAGCTGACAGATCTCGAGAAGCGTTCAGGCGGCAGGTTGGGCGTGGCGCTAATCAACACGGCAGATAATTCTCAAATCTTATATCGCGGCGACGAGCGTTTTGCCATGTGCAGCACCAGTAAAGTGATGGCCGCCGCCGCGGTATTAAAACAGAGCGAAAGCAATAAAGAGGTGGTAAATAAAAGGCTGGAGATTAACGCAGCCGATTTGGTGGTCTGGAGTCCGATTACCGAAAAACATCTCCAGAGCGGAATGACGCTGGCTGAGCTAAGCGCGGCGACGCTGCAATATAGCGACAATACGGCGATGAATCTGATCATCGGCTACCTTGGCGGGCCGGAAAAAGTCACCGCCTTCGCCCGCAGTATCGGCGATGAGACCTTTCGTCTCGATCGTACGGAGCCCACGCTGAATACCGCCATCCCGGGCGATGAGCGTGATACCAGCACGCCGCTGGCGATGGCTGAAAGCCTGCGCAAGCTGACGCTTGGCGATGCGCTGGGCGAACAGCAACGCGCCCAGTTAGTCACCTGGCTGAAAGGCAATACCACCGGCGGGCAAAGCATTCGCGCGGGCCTGCCTGAAAGCTGGGTGGTCGGCGATAAAACCGGCGCCGGAGATTACGGCACCACCAATGATATTGCGGTTATCTGGCCGGAAAATCACGCTCCGCTGGTATTAGTCACCTACTTTACCCAGCCGCAGCAGGATGCGAAAAACCGCAAAGAGGTGTTAGCCGCAGCGGCAAAAATCGTGACCGAAGGGCTTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3008793","ARO_id":"47585","ARO_name":"OXY-2-22","CARD_short_name":"OXY-2-22","ARO_description":"Extended-spectrum class A beta-lactamase OXY-2-22.","ARO_category":{"38788":{"category_aro_accession":"3002388","category_aro_cvterm_id":"38788","category_aro_name":"OXY beta-lactamase","category_aro_description":"OXY beta-lactamases are chromosomal class A beta-lactamases that are found in Klebsiella oxytoca. At constitutive low levels, OXY beta-lactamases confer resistance to aminopenicillins and carboxypenicillins. At high induced levels,  OXY beta-lactamases confer resistance to penicillins, cephalosporins and aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8212":{"model_id":"8212","model_name":"OXY-2-23","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11039":{"protein_sequence":{"accession":"SBL53835.1","sequence":"MIKSSWRKIAMLAAAVPLLLASGALWASTDAIHQKLTALEKRSGGRLGVALINTADNSQILYRGDERFAMCSTSKVMAAAAVLKQSESNKEVVNKRLEINAADLVVWSPITEKHLQSGMTLAELSAATLQYSDNTAMNLIIGYLGGPEKVTAFARSIGDATFRLDRTEPNTAIPGDERDTSTPLAMAESLRKLTLGNALGEQQRAQLVTWLKGNTTGGQSIRAGLPESWVVGDKTGAGDYGTTNDIAVIWPENHAPLVLVTYFTQPQQDAKNRKEVLAAAAKIVTEGL"},"dna_sequence":{"accession":"FKZK01000002.1","fmin":"314693","fmax":"315560","strand":"+","sequence":"ATGATAAAAAGTTCGTGGCGTAAAATTGCAATGCTAGCCGCCGCCGTTCCGCTGCTGCTGGCGAGCGGCGCACTGTGGGCCAGTACCGATGCTATCCATCAGAAGCTGACAGCTCTCGAGAAGCGTTCAGGCGGCAGGTTGGGCGTGGCGCTAATCAACACGGCAGATAATTCTCAAATCTTATATCGCGGCGACGAGCGTTTTGCCATGTGCAGCACCAGTAAAGTGATGGCCGCCGCCGCGGTATTAAAACAGAGCGAAAGCAATAAAGAGGTGGTAAATAAAAGGCTGGAGATTAACGCAGCCGATTTGGTGGTCTGGAGTCCGATTACCGAAAAACATCTCCAGAGCGGAATGACGCTGGCTGAGCTAAGCGCGGCGACGCTGCAATATAGCGACAATACGGCGATGAATCTGATCATCGGCTACCTTGGCGGGCCGGAAAAAGTCACCGCCTTCGCCCGCAGTATCGGCGATGCCACCTTTCGTCTCGATCGTACGGAGCCCAATACCGCCATCCCGGGCGATGAGCGTGATACCAGCACGCCGCTGGCGATGGCTGAAAGCCTGCGCAAGCTGACGCTTGGCAATGCGCTGGGCGAACAGCAACGCGCCCAGTTAGTCACCTGGCTGAAAGGCAATACCACCGGCGGGCAAAGCATTCGCGCGGGCCTGCCTGAAAGCTGGGTGGTCGGCGATAAAACCGGCGCCGGAGATTACGGCACCACCAATGATATTGCGGTTATCTGGCCGGAAAATCACGCTCCGCTGGTATTAGTCACCTACTTTACCCAGCCGCAGCAGGATGCGAAAAACCGCAAAGAGGTGTTAGCCGCAGCGGCAAAAATCGTGACCGAAGGGCTTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3008794","ARO_id":"47586","ARO_name":"OXY-2-23","CARD_short_name":"OXY-2-23","ARO_description":"Extended-spectrum class A beta-lactamase OXY-2-23.","ARO_category":{"38788":{"category_aro_accession":"3002388","category_aro_cvterm_id":"38788","category_aro_name":"OXY beta-lactamase","category_aro_description":"OXY beta-lactamases are chromosomal class A beta-lactamases that are found in Klebsiella oxytoca. At constitutive low levels, OXY beta-lactamases confer resistance to aminopenicillins and carboxypenicillins. At high induced levels,  OXY beta-lactamases confer resistance to penicillins, cephalosporins and aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8213":{"model_id":"8213","model_name":"OXY-2-24","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11040":{"protein_sequence":{"accession":"SAP44621.1","sequence":"MIKSSWRKIAMLAAAVPLLLASGALWASTDAIHQKLTALEKRSGGRLGVALINTADNSQILYRGDERFAMCSTSKVMAAAAVLKQSESNKEVVNKRLEINAADLVVWSPITEKHLQSGMTLAELSAATLQYSDNTAMNLIIGYLGGPEKVTAFARSIGDATFRLDRTEPNTAIPGDERDTSTPLAMAESLRKLTLGNALGEQQRAQLVTWLKGNTTGGQSIRAGLPESWVVGDKTGTGDYGTTNDIAVIWPENHAPLVLVTYFTQPQQDAKNRKEVLAAAAKIVTEGL"},"dna_sequence":{"accession":"FKYZ01000006.1","fmin":"146836","fmax":"147703","strand":"+","sequence":"ATGATAAAAAGTTCGTGGCGTAAAATTGCAATGCTAGCCGCCGCCGTTCCGCTGCTGCTGGCGAGCGGCGCACTGTGGGCCAGTACCGATGCTATCCATCAGAAGCTGACAGCTCTCGAGAAGCGTTCAGGCGGCAGGTTGGGCGTGGCGCTAATCAACACGGCAGATAATTCTCAAATCTTATATCGCGGCGACGAGCGTTTTGCCATGTGCAGCACCAGTAAAGTGATGGCCGCCGCCGCGGTATTAAAACAGAGCGAAAGCAATAAAGAGGTGGTAAATAAAAGGCTGGAGATTAACGCAGCCGATTTGGTGGTCTGGAGTCCGATTACCGAAAAACATCTCCAGAGCGGAATGACGCTGGCTGAGCTAAGCGCGGCGACGCTGCAATATAGCGACAATACGGCGATGAATCTGATCATCGGCTACCTTGGCGGGCCGGAAAAAGTCACCGCCTTCGCCCGCAGTATCGGCGATGCCACCTTTCGTCTCGATCGTACGGAGCCCAATACCGCCATCCCGGGCGATGAGCGTGATACCAGCACGCCGCTGGCGATGGCTGAAAGCCTGCGCAAGCTGACGCTTGGCAATGCGCTGGGCGAACAGCAACGCGCCCAGTTAGTCACCTGGCTGAAAGGCAATACCACCGGCGGGCAAAGCATTCGCGCGGGCCTGCCTGAAAGCTGGGTGGTCGGCGATAAAACCGGCACCGGAGATTACGGCACCACCAATGATATTGCGGTTATCTGGCCGGAAAATCACGCTCCGCTGGTATTAGTCACCTACTTTACCCAGCCGCAGCAGGATGCGAAAAACCGCAAAGAGGTGTTAGCCGCAGCGGCAAAAATCGTGACCGAAGGGCTTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3008795","ARO_id":"47587","ARO_name":"OXY-2-24","CARD_short_name":"OXY-2-24","ARO_description":"Extended-spectrum class A beta-lactamase OXY-2-24.","ARO_category":{"38788":{"category_aro_accession":"3002388","category_aro_cvterm_id":"38788","category_aro_name":"OXY beta-lactamase","category_aro_description":"OXY beta-lactamases are chromosomal class A beta-lactamases that are found in Klebsiella oxytoca. At constitutive low levels, OXY beta-lactamases confer resistance to aminopenicillins and carboxypenicillins. At high induced levels,  OXY beta-lactamases confer resistance to penicillins, cephalosporins and aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8214":{"model_id":"8214","model_name":"OXY-2-25","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11041":{"protein_sequence":{"accession":"PDO72816.1","sequence":"MIKSSWRKIAMLAAAVPLLLASGALWASTDAIHQKLTALEKRSGGRLGVALINTADNSQILYRGDERFAMCSTSKVMAAAAVLKQSESNKEVVNKRLEINAADLVVWSPITEKHLQSGMTLAELSAATLQYSDTTAMNLIIGYLGGPEKVTAFARSIGDATFRLDRTEPTLNTAIPGDERDTSTPLAMAESLRKLTLGNALGEQQRAQLVTWLKGNTTGGQSIRAGLPESWVVGDKTGTGDYGTTNDIAVIWPENHAPLVLVTYFTQPQQDAKNRKEVLAAAAKIVTEGL"},"dna_sequence":{"accession":"PCMV01000012.1","fmin":"164084","fmax":"164957","strand":"+","sequence":"ATGATAAAAAGTTCGTGGCGTAAAATTGCAATGCTAGCCGCCGCCGTTCCGCTGCTGCTGGCGAGCGGCGCACTGTGGGCCAGTACCGATGCTATCCATCAGAAGCTGACAGCTCTCGAGAAGCGTTCAGGCGGCAGGTTGGGCGTGGCGCTAATCAACACGGCAGATAATTCTCAAATCTTATATCGCGGCGACGAGCGTTTTGCCATGTGCAGCACCAGTAAAGTGATGGCCGCCGCCGCGGTATTAAAACAGAGCGAAAGCAATAAAGAGGTGGTAAATAAAAGGCTGGAGATTAACGCAGCCGATTTGGTGGTCTGGAGTCCGATTACCGAAAAACATCTCCAGAGCGGAATGACGCTGGCTGAGCTAAGCGCGGCGACGCTGCAATATAGCGACACTACGGCGATGAATCTGATCATCGGCTACCTTGGCGGGCCGGAAAAAGTCACCGCCTTCGCCCGCAGTATCGGCGATGCCACCTTTCGTCTCGATCGTACGGAGCCCACGCTGAATACCGCCATCCCGGGCGATGAGCGTGATACCAGCACGCCGCTGGCGATGGCTGAAAGCCTGCGCAAGCTGACGCTTGGCAATGCGCTGGGCGAACAGCAACGCGCCCAGTTAGTCACCTGGCTGAAAGGCAATACCACCGGCGGGCAAAGCATTCGCGCGGGCCTGCCTGAAAGCTGGGTGGTCGGCGATAAAACCGGCACCGGAGATTACGGCACCACCAATGATATTGCGGTTATCTGGCCGGAAAATCACGCTCCGCTGGTATTAGTCACCTACTTTACCCAGCCGCAGCAGGATGCGAAAAACCGCAAAGAGGTGTTAGCCGCAGCGGCAAAAATCGTGACCGAAGGGCTTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3008796","ARO_id":"47588","ARO_name":"OXY-2-25","CARD_short_name":"OXY-2-25","ARO_description":"Extended-spectrum class A beta-lactamase OXY-2-25.","ARO_category":{"38788":{"category_aro_accession":"3002388","category_aro_cvterm_id":"38788","category_aro_name":"OXY beta-lactamase","category_aro_description":"OXY beta-lactamases are chromosomal class A beta-lactamases that are found in Klebsiella oxytoca. At constitutive low levels, OXY beta-lactamases confer resistance to aminopenicillins and carboxypenicillins. At high induced levels,  OXY beta-lactamases confer resistance to penicillins, cephalosporins and aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8215":{"model_id":"8215","model_name":"OXY-2-26","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11042":{"protein_sequence":{"accession":"CAF2893366.1","sequence":"MIKSSWRKIAMLAAAVPLLLASGALWASTDAIHQKLTDLEKRSGGRLGVALINTADNSQILYRGDERFAMCSTSKVMAAAAILKQSESNKEVVNKRLDINAADLVVWSPITEKHLQSGMTLAELSAATLQYSDNTAMNLIIGYLGGPEKVTAFARSIGDATFRLDRTEPTLNTAIPGDERDTSTPLAMAESLRKLTLGNALGEQQRAQLVTWLKGNTTGGQSIRAGLPESWVVGDKTGAGDYGTTNDIAVIWPENHAPLVLVTYFTQPQQDAKNRKEVLAAATKIVTEGL"},"dna_sequence":{"accession":"CAJNWH010000001.1","fmin":"4302632","fmax":"4303505","strand":"+","sequence":"ATGATAAAAAGTTCGTGGCGTAAAATTGCAATGCTAGCCGCCGCCGTTCCGCTGCTGCTGGCGAGCGGCGCACTGTGGGCCAGTACCGATGCTATCCATCAGAAGCTGACAGATCTCGAGAAGCGTTCAGGCGGCAGGTTGGGCGTGGCGCTAATCAACACGGCAGATAATTCTCAAATCTTATATCGCGGCGACGAGCGTTTTGCCATGTGCAGCACCAGTAAAGTGATGGCCGCCGCCGCGATATTAAAACAGAGCGAAAGCAATAAAGAGGTGGTAAATAAAAGGCTGGATATTAACGCAGCCGATTTGGTGGTCTGGAGTCCGATTACCGAAAAACATCTCCAGAGCGGAATGACGCTGGCTGAGCTAAGCGCAGCGACGCTGCAATATAGCGACAATACGGCGATGAATCTGATCATCGGCTACCTTGGCGGGCCGGAAAAAGTCACCGCCTTCGCCCGCAGTATCGGCGATGCCACCTTTCGTCTCGATCGTACGGAGCCCACGCTGAATACCGCCATCCCGGGCGATGAGCGTGATACCAGCACGCCGCTGGCGATGGCTGAAAGCCTGCGCAAGCTGACGCTTGGCAATGCGCTGGGCGAACAGCAACGCGCCCAGTTAGTCACCTGGCTGAAAGGCAATACCACCGGCGGGCAAAGCATTCGCGCGGGCCTGCCTGAAAGCTGGGTGGTCGGCGATAAAACCGGCGCCGGAGATTACGGCACCACCAATGATATTGCGGTTATCTGGCCGGAAAATCACGCTCCGCTGGTATTAGTCACCTACTTTACCCAGCCGCAGCAGGATGCGAAAAACCGCAAAGAGGTGTTAGCCGCAGCGACAAAAATCGTGACCGAAGGGCTTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3008797","ARO_id":"47589","ARO_name":"OXY-2-26","CARD_short_name":"OXY-2-26","ARO_description":"Extended-spectrum class A beta-lactamase OXY-2-26.","ARO_category":{"38788":{"category_aro_accession":"3002388","category_aro_cvterm_id":"38788","category_aro_name":"OXY beta-lactamase","category_aro_description":"OXY beta-lactamases are chromosomal class A beta-lactamases that are found in Klebsiella oxytoca. At constitutive low levels, OXY beta-lactamases confer resistance to aminopenicillins and carboxypenicillins. At high induced levels,  OXY beta-lactamases confer resistance to penicillins, cephalosporins and aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8216":{"model_id":"8216","model_name":"OXY-2-27","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11043":{"protein_sequence":{"accession":"MBZ7699249.1","sequence":"MIKSSWRKIAMLAAAVPLLLASGALWASTDAIHQKLTDLEKRSGGRLGVALINTADNSHILYRGDERFAMCSTSKVMAAAAVLKQSESNKEVVNKRLEINAADLVVWSPITEKHLQSGMTLAELSAATLQYSDNTAMNLIIGYLGGPEKVTAFARSIGDATFRLDRTEPTLNTAIPGDERDTSTPLAMAESLRKLTLGDALGEQQRAQLVTWLKGNTTGGQSIRAGLPESWVVGDKTGAGDYGTTNDIAVIWPEDHAPLVLVTYFTQPQQDAKNRKEVLAAAAKIVTEGL"},"dna_sequence":{"accession":"VNUT01000008.1","fmin":"17437","fmax":"18310","strand":"-","sequence":"ATGATAAAAAGTTCGTGGCGTAAAATTGCAATGCTAGCCGCCGCCGTTCCGCTGCTGCTGGCGAGCGGCGCACTGTGGGCCAGTACCGATGCTATCCATCAGAAGCTGACAGATCTCGAGAAGCGTTCAGGCGGCAGGTTGGGCGTGGCGCTAATCAACACGGCAGATAATTCTCATATCTTATATCGCGGCGACGAGCGTTTTGCCATGTGCAGCACCAGTAAAGTGATGGCCGCCGCCGCGGTATTAAAACAGAGCGAAAGCAATAAAGAGGTGGTAAATAAAAGGCTGGAGATTAACGCAGCCGATTTGGTGGTCTGGAGTCCGATTACCGAAAAACATCTCCAGAGCGGAATGACGCTGGCTGAGCTAAGCGCGGCGACGCTGCAATATAGCGACAATACGGCGATGAATCTGATCATCGGCTACCTTGGCGGGCCGGAAAAAGTCACCGCCTTCGCCCGCAGTATCGGCGATGCCACCTTTCGTCTCGATCGTACGGAGCCCACGCTGAATACCGCCATCCCGGGCGATGAGCGTGATACCAGCACGCCGCTGGCGATGGCTGAAAGCCTGCGCAAGCTGACGCTTGGCGATGCGCTGGGCGAACAGCAACGCGCCCAGTTAGTCACCTGGCTGAAAGGCAATACCACCGGCGGGCAAAGCATTCGCGCGGGCCTGCCTGAAAGCTGGGTGGTCGGAGATAAAACCGGCGCCGGAGATTACGGCACCACCAATGATATTGCGGTTATCTGGCCGGAAGATCACGCTCCGCTGGTATTAGTCACCTACTTTACCCAGCCGCAGCAGGATGCGAAAAACCGCAAAGAGGTGTTAGCCGCAGCGGCAAAAATCGTGACCGAAGGGCTTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3008798","ARO_id":"47590","ARO_name":"OXY-2-27","CARD_short_name":"OXY-2-27","ARO_description":"Extended-spectrum class A beta-lactamase OXY-2-27.","ARO_category":{"38788":{"category_aro_accession":"3002388","category_aro_cvterm_id":"38788","category_aro_name":"OXY beta-lactamase","category_aro_description":"OXY beta-lactamases are chromosomal class A beta-lactamases that are found in Klebsiella oxytoca. At constitutive low levels, OXY beta-lactamases confer resistance to aminopenicillins and carboxypenicillins. At high induced levels,  OXY beta-lactamases confer resistance to penicillins, cephalosporins and aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8217":{"model_id":"8217","model_name":"OXY-2-28","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11044":{"protein_sequence":{"accession":"HAT2769319.1","sequence":"MIKSSWRKIAMLAAVPLLLASGALWASTDAIHQKLTDLEKRSGGRLGVALINTADNSQILYRGDERFAMCSTSKVMAAAAVLKQSESNKEVVNKRLEINAADLVVWSPITEKHLQSGMTLAELSAATLQYSDNTAMNLIIGYLGGPEKVTAFARSIGDATFRLDRTEPTLNTAIPGDERDTSTPLAMAESLRKLTLGDALGEQQRAQLVTWLKGNTTGGQSIRAGLPESWVVGDKTGAGDYGTTNDIAVICPEDHAPLVLVTYFTQPQQDAKNRKEVLAAAAKIVTEGL"},"dna_sequence":{"accession":"DACSOX010000001.1","fmin":"173022","fmax":"173892","strand":"-","sequence":"ATGATAAAAAGTTCGTGGCGTAAAATTGCAATGCTAGCCGCCGTTCCGCTGCTGCTGGCGAGCGGCGCACTGTGGGCCAGTACCGATGCTATCCATCAGAAGCTGACAGATCTCGAGAAGCGTTCAGGCGGCAGGTTGGGCGTGGCGCTAATCAACACGGCAGATAATTCTCAAATCTTATATCGCGGCGACGAGCGTTTTGCCATGTGCAGCACCAGTAAAGTGATGGCCGCCGCCGCGGTATTAAAACAGAGCGAAAGCAATAAAGAGGTGGTAAATAAAAGGCTGGAGATTAACGCAGCCGATTTGGTGGTCTGGAGTCCGATTACCGAAAAACATCTCCAGAGCGGAATGACGCTGGCTGAGCTAAGCGCGGCGACGCTGCAATATAGCGACAATACGGCGATGAATCTGATCATCGGCTACCTTGGCGGGCCGGAAAAAGTCACCGCCTTCGCCCGCAGTATCGGCGATGCCACCTTTCGTCTCGATCGTACGGAGCCCACGCTGAATACCGCCATCCCGGGCGATGAGCGTGATACCAGCACGCCGCTGGCGATGGCTGAAAGCCTACGCAAGCTGACGCTTGGCGATGCGCTGGGCGAACAGCAACGCGCCCAGTTAGTCACCTGGCTGAAAGGCAATACCACCGGCGGGCAAAGCATTCGCGCGGGCCTGCCTGAAAGCTGGGTGGTCGGCGATAAAACCGGCGCCGGAGATTACGGCACCACCAATGATATTGCGGTTATCTGTCCGGAAGATCACGCTCCGCTGGTATTAGTCACCTACTTTACCCAGCCGCAGCAGGATGCGAAAAACCGCAAAGAGGTGTTAGCCGCAGCGGCAAAAATCGTGACCGAAGGGCTTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3008799","ARO_id":"47591","ARO_name":"OXY-2-28","CARD_short_name":"OXY-2-28","ARO_description":"Extended-spectrum class A beta-lactamase OXY-2-28.","ARO_category":{"38788":{"category_aro_accession":"3002388","category_aro_cvterm_id":"38788","category_aro_name":"OXY beta-lactamase","category_aro_description":"OXY beta-lactamases are chromosomal class A beta-lactamases that are found in Klebsiella oxytoca. At constitutive low levels, OXY beta-lactamases confer resistance to aminopenicillins and carboxypenicillins. At high induced levels,  OXY beta-lactamases confer resistance to penicillins, cephalosporins and aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8218":{"model_id":"8218","model_name":"OXY-2-30","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11045":{"protein_sequence":{"accession":"UNI52884.1","sequence":"MIKSSWRKIAMLAAVPLLLASGALWASTDAIHQKLTDLEKRSGGRLGVALINTADNSQILYRGDERFAMCSTSKVMAAAAVLKQSESNKEVVNKRLEINAADLVVWSPITEKHLQSGMTLAELSAATLQYSDNTAMNLIIGYLGGPEKVTAFARSIGDATFRLDRTEPTLNTAIPGDERDTSTPLAMAESLRKLTLGDALGEQQRAQLVTWLKGNTTGGQSIRAGLPESWVVGDKTGSGDYGTTNDIAVIWPEDHAPLVLVTYFTQPQQDAKNRKEVLAAAAKIVTEGL"},"dna_sequence":{"accession":"CP093271.1","fmin":"4297978","fmax":"4298848","strand":"+","sequence":"ATGATAAAAAGTTCGTGGCGTAAAATTGCAATGCTAGCCGCCGTTCCGCTGCTGCTGGCGAGCGGCGCACTGTGGGCCAGTACCGATGCTATCCATCAGAAGCTGACAGATCTCGAGAAGCGTTCAGGCGGCAGGTTGGGCGTGGCGCTAATCAACACGGCAGATAATTCTCAAATCTTATATCGCGGCGACGAGCGTTTTGCCATGTGCAGCACCAGTAAAGTGATGGCCGCCGCCGCGGTATTAAAACAGAGCGAAAGCAATAAAGAGGTGGTAAATAAAAGGCTGGAGATTAACGCAGCCGATTTGGTGGTCTGGAGTCCGATTACCGAAAAACATCTCCAGAGCGGAATGACGCTGGCTGAGCTAAGCGCGGCGACGCTGCAATATAGCGACAATACGGCGATGAATCTGATCATCGGCTACCTTGGCGGGCCGGAAAAAGTCACCGCCTTCGCCCGCAGTATCGGCGATGCCACCTTTCGTCTCGATCGTACGGAGCCCACGCTGAATACCGCCATCCCGGGCGATGAGCGTGATACCAGCACGCCGCTGGCGATGGCTGAAAGCCTACGCAAGCTGACGCTTGGCGATGCGCTGGGCGAACAGCAACGCGCCCAGTTAGTCACCTGGCTGAAAGGCAATACCACCGGCGGGCAAAGCATTCGCGCGGGCCTGCCTGAAAGCTGGGTGGTCGGCGATAAAACCGGCTCCGGAGATTACGGCACCACCAATGATATTGCGGTTATCTGGCCGGAAGATCACGCTCCGCTGGTATTAGTCACCTACTTTACCCAGCCGCAGCAGGATGCGAAAAACCGCAAAGAGGTGTTAGCCGCAGCGGCAAAAATCGTGACCGAAGGGCTTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3008800","ARO_id":"47592","ARO_name":"OXY-2-30","CARD_short_name":"OXY-2-30","ARO_description":"Extended-spectrum class A beta-lactamase OXY-2-30.","ARO_category":{"38788":{"category_aro_accession":"3002388","category_aro_cvterm_id":"38788","category_aro_name":"OXY beta-lactamase","category_aro_description":"OXY beta-lactamases are chromosomal class A beta-lactamases that are found in Klebsiella oxytoca. At constitutive low levels, OXY beta-lactamases confer resistance to aminopenicillins and carboxypenicillins. At high induced levels,  OXY beta-lactamases confer resistance to penicillins, cephalosporins and aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8219":{"model_id":"8219","model_name":"OXY-3-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11046":{"protein_sequence":{"accession":"VUT06406.1","sequence":"MMKTSWRKSALIAAALPLLLCSSSLWANAIQQKLADLEKSTGGRLGVALIDTTDNSQILYRGDERFAMCSTGKVMAAAAVLKQSESNKDVVNKMLEIKASDLVVWSPVTEKHLQSGMTLAELSAAALQYSDNTAMNKMIGYLGGPEKVTAFARSIGDVTFRLDRTEPALNTAIPGDERDTTTPLAMAESLHKLTLGNALGEQQRAQLVTWLKGNTTGGQSIRAGLPASWVVGDKTGAGDYGTTNDIAVIWPENHAPLVLVTYFTQPLQDAKSRKDVLAAAAKIVTEGL"},"dna_sequence":{"accession":"CABGHF010000056.1","fmin":"139522","fmax":"140389","strand":"-","sequence":"ATGATGAAAACTTCGTGGCGTAAAAGCGCCCTGATTGCCGCCGCTCTGCCTTTATTGCTCTGTAGCAGTTCATTATGGGCCAATGCTATTCAGCAGAAGCTGGCCGATTTGGAAAAAAGTACCGGCGGTCGACTGGGCGTCGCGCTGATTGACACCACAGATAATTCTCAAATTCTATATCGCGGTGACGAGCGTTTTGCTATGTGCAGTACCGGTAAAGTGATGGCTGCCGCCGCGGTGTTAAAACAGAGTGAAAGCAATAAAGATGTGGTGAATAAAATGCTGGAGATTAAAGCATCAGATCTGGTGGTCTGGAGCCCGGTGACTGAAAAACATCTGCAGAGCGGAATGACGTTGGCGGAATTAAGCGCCGCCGCGCTGCAATATAGCGACAATACCGCGATGAATAAGATGATTGGTTATCTTGGCGGACCGGAAAAAGTGACCGCCTTCGCCCGCAGTATCGGCGATGTCACTTTTCGTCTCGATCGTACGGAGCCTGCACTAAACACCGCGATCCCGGGTGACGAACGCGATACCACCACGCCGCTGGCGATGGCCGAAAGCCTGCACAAGCTGACGCTGGGTAATGCGCTGGGTGAACAACAGCGCGCACAGTTAGTGACATGGTTGAAAGGCAACACCACCGGCGGGCAGAGTATTCGTGCGGGGCTGCCTGCAAGCTGGGTCGTGGGAGATAAAACCGGAGCTGGTGATTACGGCACCACCAATGATATCGCCGTTATCTGGCCGGAAAATCATGCTCCGCTGGTATTAGTCACTTATTTCACCCAACCGCTGCAGGATGCGAAAAGCCGCAAAGATGTGCTAGCCGCAGCGGCAAAAATTGTGACCGAAGGGCTTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"47915","NCBI_taxonomy_name":"Klebsiella spallanzanii","NCBI_taxonomy_id":"2587528"}}}},"ARO_accession":"3008801","ARO_id":"47593","ARO_name":"OXY-3-2","CARD_short_name":"OXY-3-2","ARO_description":"Extended-spectrum class A beta-lactamase OXY-3-2.","ARO_category":{"38788":{"category_aro_accession":"3002388","category_aro_cvterm_id":"38788","category_aro_name":"OXY beta-lactamase","category_aro_description":"OXY beta-lactamases are chromosomal class A beta-lactamases that are found in Klebsiella oxytoca. At constitutive low levels, OXY beta-lactamases confer resistance to aminopenicillins and carboxypenicillins. At high induced levels,  OXY beta-lactamases confer resistance to penicillins, cephalosporins and aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8220":{"model_id":"8220","model_name":"OXY-3-3","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11047":{"protein_sequence":{"accession":"VUS24148.1","sequence":"MMKTSWRKSALIAAALPLLLCSSSLWANAIQQKLADLEKSTGGRLGVALIDTTDNSQILYRGDERFAMCSTGKVMAAAAVLKQSESNKDVVNKRLEIKASDLVVWSPVTEKHLQSGMTLAELSAAALQYSDNTAMNKMIGYLGGPEKVTAFARSIGDVTFRLDRTEPALNTAIPGDERDTTTPLAMAESLHKLTLGNALGEQQRAQLVTWLKGNTTGGQSIRAGLPASWVVGDKTGAGDYGTTNDIAVIWPENHAPLVLVTYFTQPLQDAKSRKDVLAAAAKIVTEGL"},"dna_sequence":{"accession":"CABGGS010000001.1","fmin":"686748","fmax":"687615","strand":"+","sequence":"ATGATGAAAACTTCGTGGCGTAAAAGCGCCCTGATTGCCGCCGCCCTGCCTTTATTGCTCTGTAGCAGTTCATTATGGGCCAATGCTATTCAGCAGAAGCTGGCCGATTTGGAAAAAAGTACCGGCGGGCGACTGGGCGTCGCGCTGATTGACACCACAGATAATTCTCAAATTCTATATCGCGGTGACGAGCGTTTTGCTATGTGCAGTACCGGTAAAGTGATGGCTGCCGCCGCGGTGTTAAAACAGAGCGAAAGCAATAAAGATGTGGTGAATAAAAGGCTGGAGATTAAAGCATCGGATCTGGTGGTCTGGAGCCCGGTGACTGAAAAACATCTGCAGAGCGGAATGACGTTGGCGGAATTAAGCGCCGCCGCGCTGCAATATAGCGACAATACCGCGATGAATAAGATGATTGGTTATCTTGGCGGACCGGAAAAAGTGACCGCCTTCGCCCGCAGTATCGGCGATGTCACTTTTCGTCTCGATCGTACGGAGCCTGCACTAAACACCGCGATCCCGGGTGACGAACGCGATACCACCACGCCGCTGGCGATGGCCGAAAGCCTGCACAAGCTGACGCTGGGTAATGCGCTGGGTGAACAACAGCGCGCACAGTTAGTGACATGGTTGAAAGGCAACACCACCGGCGGGCAGAGTATTCGTGCGGGGCTGCCTGCAAGCTGGGTCGTGGGAGATAAAACCGGAGCTGGTGATTACGGCACCACCAATGATATCGCCGTTATCTGGCCGGAAAATCATGCTCCGCTGGTATTAGTCACTTATTTCACCCAACCGCTGCAGGATGCGAAAAGCCGCAAAGATGTGCTAGCCGCAGCGGCAAAAATCGTGACCGAAGGGCTGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"47915","NCBI_taxonomy_name":"Klebsiella spallanzanii","NCBI_taxonomy_id":"2587528"}}}},"ARO_accession":"3008802","ARO_id":"47594","ARO_name":"OXY-3-3","CARD_short_name":"OXY-3-3","ARO_description":"Extended-spectrum class A beta-lactamase OXY-3-3.","ARO_category":{"38788":{"category_aro_accession":"3002388","category_aro_cvterm_id":"38788","category_aro_name":"OXY beta-lactamase","category_aro_description":"OXY beta-lactamases are chromosomal class A beta-lactamases that are found in Klebsiella oxytoca. At constitutive low levels, OXY beta-lactamases confer resistance to aminopenicillins and carboxypenicillins. At high induced levels,  OXY beta-lactamases confer resistance to penicillins, cephalosporins and aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8221":{"model_id":"8221","model_name":"OXY-4-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11048":{"protein_sequence":{"accession":"VUS33624.1","sequence":"MLKSSWRKSALMAAAVPLLLASGSLWASADTLQQKLADLEKRSGGRLGVALINTADDSQTLYRGDERFAMCSTGKVMAAAAVFKQSESHPDVVNKRLEIKKSDLVVWSPITEKHLQSGMTLAELSAAALQYSDNTAMNKIIGYLGGPEKVTAFAQSIGDVTFRLDRMEPALNSAIPGDKRDTTTPLAMAESLRKLTLGNALGEQQRAQLVTWLKGNTTGGQSIRAGLPASWAVGDKTGGGDYGTTNDIAVIWPENHAPLVLVTYFTQPQQDAKSRKEVLAAAAKIVTEGL"},"dna_sequence":{"accession":"CABGHC010000001.1","fmin":"1048283","fmax":"1049156","strand":"+","sequence":"ATGTTGAAAAGTTCGTGGCGTAAAAGCGCCCTGATGGCCGCCGCCGTTCCGCTACTGCTGGCGAGCGGTTCATTATGGGCCAGTGCCGATACTCTCCAGCAGAAGCTGGCTGATTTAGAAAAACGTTCCGGCGGTCGGCTGGGCGTGGCGCTGATTAACACGGCAGATGATTCGCAGACCCTCTATCGCGGCGACGAACGTTTTGCCATGTGCAGCACCGGTAAAGTGATGGCCGCCGCCGCGGTGTTCAAACAGAGCGAAAGCCATCCCGATGTGGTGAATAAAAGGCTGGAGATTAAAAAATCGGATTTAGTGGTCTGGAGCCCGATTACCGAAAAACATCTGCAAAGCGGAATGACCCTGGCGGAACTCAGCGCTGCGGCGCTGCAGTATAGCGACAATACCGCGATGAATAAGATTATCGGTTACCTTGGCGGGCCGGAAAAAGTCACCGCATTCGCCCAGAGCATCGGTGACGTTACTTTTCGTCTCGATCGGATGGAGCCGGCGCTGAACAGCGCGATTCCCGGTGATAAGCGCGATACCACCACCCCATTGGCGATGGCCGAAAGTCTGCGTAAGCTGACGCTGGGCAATGCGCTGGGCGAACAGCAGCGCGCCCAGTTAGTGACATGGCTGAAAGGCAATACCACCGGCGGGCAAAGCATTCGTGCAGGCCTGCCCGCAAGCTGGGCGGTCGGGGATAAAACCGGCGGCGGAGATTACGGCACCACCAACGATATCGCGGTGATCTGGCCGGAAAATCATGCTCCGCTGGTGCTAGTGACCTATTTTACCCAACCGCAGCAGGATGCGAAAAGCCGCAAAGAGGTGCTAGCCGCGGCGGCGAAAATCGTGACCGAAGGGCTGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"47914","NCBI_taxonomy_name":"Klebsiella pasteurii","NCBI_taxonomy_id":"2587529"}}}},"ARO_accession":"3008803","ARO_id":"47595","ARO_name":"OXY-4-2","CARD_short_name":"OXY-4-2","ARO_description":"Extended-spectrum class A beta-lactamase OXY-4-2.","ARO_category":{"38788":{"category_aro_accession":"3002388","category_aro_cvterm_id":"38788","category_aro_name":"OXY beta-lactamase","category_aro_description":"OXY beta-lactamases are chromosomal class A beta-lactamases that are found in Klebsiella oxytoca. At constitutive low levels, OXY beta-lactamases confer resistance to aminopenicillins and carboxypenicillins. At high induced levels,  OXY beta-lactamases confer resistance to penicillins, cephalosporins and aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8222":{"model_id":"8222","model_name":"OXY-4-3","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11049":{"protein_sequence":{"accession":"QUE96219.1","sequence":"MLKSSWRKSALMAAVVPLLLASGSLWASADTLQQKLADLEKRSGGRLGVALINTADDSQTLYRGDERFAMCSTGKVMAAAAVLKQSESHPDVVNKRLEIKKSDLVVWSPITEKHLQSGMTLAELSAAALQYSDNTAMNKIIGYLGGPEKVTAFAQSIGDVTFRLDRMEPALNSAIPGDKRDTTTPLAMAESLRKLTLGNALGEQQRAQLVTWLKGNTTGGQSIRAGLPASWAVGDKTGGGDYGTTNDIAVIWPENHAPLVLVTYFTQPQQDAKSRKEVLAAAAKIVTEGL"},"dna_sequence":{"accession":"CP073236.1","fmin":"5453997","fmax":"5454870","strand":"-","sequence":"ATGTTGAAAAGTTCGTGGCGTAAAAGCGCCCTGATGGCCGCCGTCGTTCCGCTACTGCTGGCGAGCGGTTCATTATGGGCCAGTGCCGATACTCTCCAGCAGAAGCTGGCTGATTTAGAAAAACGTTCCGGCGGTCGGCTGGGCGTGGCGCTGATTAACACGGCAGATGATTCGCAGACCCTCTATCGCGGCGACGAACGTTTTGCCATGTGCAGCACCGGTAAAGTGATGGCCGCCGCCGCGGTGTTAAAACAGAGCGAAAGCCATCCCGATGTGGTGAATAAAAGGCTGGAGATTAAAAAATCGGATTTAGTGGTCTGGAGCCCGATTACCGAAAAACATCTGCAAAGCGGAATGACCCTGGCGGAACTCAGCGCTGCGGCGCTGCAGTATAGCGACAATACCGCGATGAATAAGATTATCGGTTACCTTGGCGGGCCGGAAAAAGTCACCGCATTCGCCCAGAGCATCGGTGACGTTACTTTTCGTCTCGATCGGATGGAGCCGGCGCTGAACAGCGCGATTCCCGGTGATAAGCGCGATACCACCACCCCATTGGCGATGGCCGAAAGTCTGCGTAAGCTGACGCTGGGCAATGCGCTGGGCGAACAGCAGCGCGCCCAGTTAGTGACATGGCTGAAAGGCAATACCACCGGCGGGCAAAGCATTCGTGCAGGCCTGCCCGCAAGCTGGGCGGTCGGGGATAAAACCGGCGGCGGAGATTACGGCACCACCAACGATATCGCGGTGATCTGGCCGGAAAATCATGCTCCGCTGGTGCTAGTGACCTATTTTACCCAACCGCAGCAGGATGCGAAAAGCCGCAAAGAGGTGCTAGCCGCGGCGGCGAAAATCGTGACCGAAGGGCTGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"47914","NCBI_taxonomy_name":"Klebsiella pasteurii","NCBI_taxonomy_id":"2587529"}}}},"ARO_accession":"3008804","ARO_id":"47596","ARO_name":"OXY-4-3","CARD_short_name":"OXY-4-3","ARO_description":"Extended-spectrum class A beta-lactamase OXY-4-3.","ARO_category":{"38788":{"category_aro_accession":"3002388","category_aro_cvterm_id":"38788","category_aro_name":"OXY beta-lactamase","category_aro_description":"OXY beta-lactamases are chromosomal class A beta-lactamases that are found in Klebsiella oxytoca. At constitutive low levels, OXY beta-lactamases confer resistance to aminopenicillins and carboxypenicillins. At high induced levels,  OXY beta-lactamases confer resistance to penicillins, cephalosporins and aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8223":{"model_id":"8223","model_name":"OXY-4-4","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11050":{"protein_sequence":{"accession":"VUS34372.1","sequence":"MLKSSWRKSALMAAAVPLLLASGSLWASADTLQQKLADLEKRSGGRLGVALINTADDSQTLYRGDERFAMCSTGKVMAAAAVLKQSESHPDVVNKRLEIKKSDLVVWSPITEKHLQSGMTLAELSAAALQYSDNTAMNKIIGYLGGPEKVTAFAQNIGDVTFRLDRMEPALNSAIPGDKRDTTTPLAMAESLRKLTLGNALGEQQRAQLVTWLKGNTTGGQSIRAGLPASWAVGDKTGGGDYGTTNDIAVIWPENHAPLVLVTYFTQPQQDAKSRKEVLAAAAKIVTEGL"},"dna_sequence":{"accession":"CABGHE010000001.1","fmin":"1127453","fmax":"1128326","strand":"+","sequence":"ATGTTGAAAAGTTCGTGGCGTAAAAGCGCCCTGATGGCCGCCGCCGTTCCGCTACTGCTGGCGAGCGGTTCATTATGGGCCAGTGCCGATACTCTCCAGCAGAAGCTGGCTGATTTAGAAAAACGTTCCGGCGGTCGGCTGGGCGTGGCGCTGATTAACACGGCAGATGATTCGCAGACCCTCTATCGCGGCGACGAACGTTTTGCCATGTGCAGCACCGGTAAAGTGATGGCCGCCGCCGCGGTGTTAAAACAGAGCGAAAGCCATCCCGATGTGGTGAATAAAAGGCTGGAGATTAAAAAATCGGATTTAGTGGTCTGGAGCCCGATTACCGAAAAACATCTGCAAAGCGGAATGACCCTGGCGGAACTCAGCGCTGCGGCGCTGCAGTATAGCGACAATACCGCGATGAATAAGATTATCGGTTACCTTGGCGGGCCGGAAAAAGTCACCGCATTCGCCCAGAACATCGGTGACGTTACTTTTCGTCTCGATCGGATGGAGCCGGCGCTGAACAGCGCGATTCCCGGTGATAAGCGCGATACCACCACCCCATTGGCGATGGCCGAAAGTCTGCGTAAGCTGACGCTGGGCAATGCGCTGGGCGAACAGCAGCGCGCCCAGTTAGTGACATGGCTGAAAGGCAATACCACCGGCGGGCAAAGCATTCGTGCAGGCCTGCCCGCAAGCTGGGCGGTCGGGGATAAAACCGGCGGCGGAGATTACGGCACCACCAACGATATCGCGGTGATCTGGCCGGAAAATCATGCTCCGCTGGTGCTAGTGACCTATTTTACCCAACCGCAGCAGGATGCGAAAAGCCGCAAAGAGGTGCTAGCCGCGGCGGCGAAAATCGTGACCGAAGGGCTGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"47914","NCBI_taxonomy_name":"Klebsiella pasteurii","NCBI_taxonomy_id":"2587529"}}}},"ARO_accession":"3008805","ARO_id":"47597","ARO_name":"OXY-4-4","CARD_short_name":"OXY-4-4","ARO_description":"Extended-spectrum class A beta-lactamase OXY-4-4.","ARO_category":{"38788":{"category_aro_accession":"3002388","category_aro_cvterm_id":"38788","category_aro_name":"OXY beta-lactamase","category_aro_description":"OXY beta-lactamases are chromosomal class A beta-lactamases that are found in Klebsiella oxytoca. At constitutive low levels, OXY beta-lactamases confer resistance to aminopenicillins and carboxypenicillins. At high induced levels,  OXY beta-lactamases confer resistance to penicillins, cephalosporins and aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8224":{"model_id":"8224","model_name":"OXY-4-5","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11051":{"protein_sequence":{"accession":"VUS34048.1","sequence":"MLKSSWRKSALMAAAVPLLLASGSLWASADTLQQKLADLEKRSGGRLGVALINTADDSQTLYRGDERFAMCSTGKVMAAAAVLKQSESHPDVVNKRLEIKKSDLVVWSPITEKHLQSGMTLAELSAAALQYSDNTAMNKIIGYLGGPEKVTAFAQSIGDVTFRLDRMEPALNSAIPGDKRDTTTPLAMAESLRKLTLGNALGEQQRAQLVTWLKGNTTGGQSIRAGLPASWAVGDKTGGGDYGTTNDIAVIWPENHAPLVLVTYFTQLQQDAKSRKEVLAAAAKIVTEGL"},"dna_sequence":{"accession":"CABGHB010000001.1","fmin":"1091466","fmax":"1092339","strand":"+","sequence":"ATGTTGAAAAGTTCGTGGCGTAAAAGCGCCCTGATGGCCGCCGCCGTTCCGCTACTGCTGGCGAGCGGTTCATTATGGGCCAGTGCCGATACTCTCCAGCAGAAGCTGGCTGATTTAGAAAAACGTTCCGGCGGTCGGCTGGGCGTGGCGCTGATTAACACGGCAGATGATTCGCAGACCCTCTATCGCGGCGACGAACGTTTTGCCATGTGCAGCACCGGTAAAGTGATGGCCGCCGCCGCGGTGTTAAAACAGAGCGAAAGCCATCCCGATGTGGTGAATAAAAGGCTGGAGATTAAAAAATCGGATTTAGTGGTCTGGAGCCCGATTACCGAAAAACATCTGCAAAGCGGAATGACCCTGGCGGAACTCAGCGCTGCGGCGCTGCAGTATAGCGACAATACCGCGATGAATAAGATTATCGGTTACCTTGGCGGGCCGGAAAAAGTCACCGCATTCGCCCAGAGCATCGGTGACGTTACTTTTCGTCTCGATCGGATGGAGCCGGCGCTGAACAGCGCGATTCCCGGTGATAAGCGCGATACCACCACCCCATTGGCGATGGCCGAAAGTCTGCGTAAGCTGACGCTGGGCAATGCGCTGGGCGAACAGCAGCGCGCCCAGTTAGTGACATGGCTGAAAGGCAATACCACCGGCGGGCAAAGCATTCGTGCAGGCCTGCCCGCAAGCTGGGCGGTCGGGGATAAAACCGGCGGCGGAGATTACGGCACCACCAACGATATCGCGGTGATCTGGCCGGAAAATCATGCTCCGCTGGTGCTAGTGACCTATTTTACCCAACTGCAGCAGGATGCGAAAAGCCGCAAAGAGGTGCTAGCCGCGGCGGCGAAAATCGTGACCGAAGGGCTGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"47914","NCBI_taxonomy_name":"Klebsiella pasteurii","NCBI_taxonomy_id":"2587529"}}}},"ARO_accession":"3008806","ARO_id":"47598","ARO_name":"OXY-4-5","CARD_short_name":"OXY-4-5","ARO_description":"Extended-spectrum class A beta-lactamase OXY-4-5.","ARO_category":{"38788":{"category_aro_accession":"3002388","category_aro_cvterm_id":"38788","category_aro_name":"OXY beta-lactamase","category_aro_description":"OXY beta-lactamases are chromosomal class A beta-lactamases that are found in Klebsiella oxytoca. At constitutive low levels, OXY beta-lactamases confer resistance to aminopenicillins and carboxypenicillins. At high induced levels,  OXY beta-lactamases confer resistance to penicillins, cephalosporins and aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8225":{"model_id":"8225","model_name":"OXY-5-10","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11052":{"protein_sequence":{"accession":"MBC3630379.1","sequence":"MLKSSWRKTALMAAAVPLLLASGSLWASADAIQQKLADLEKRSGGRLGVALINTADDSQTLYRGDERFAMCSTGKVMVAAAVLKQSESNPEVVNKRLEIKKADLVVWSPITEKHLQSGMTLAELSAAALQYSDNTAMNKIIGYLGGPEKVTAFAQSIGDVTFRLDRMEPALNSAIPGDKRDTTTPLAMAESLRKLTLGNALGEQQRTQLVTWLKGNTTGGQSIRAGLPASWAVGDKTGAGDYGTTNDIAVIWPENHAPLVLVTYFTQPQQDAKSRKEVLAAAAKIVTEGL"},"dna_sequence":{"accession":"JACOEB010000001.1","fmin":"150967","fmax":"151840","strand":"+","sequence":"ATGTTGAAAAGTTCGTGGCGTAAAACCGCCCTGATGGCCGCCGCCGTTCCGCTGCTGCTGGCGAGCGGTTCATTATGGGCCAGTGCCGATGCTATCCAGCAAAAGCTGGCTGATTTAGAAAAACGTTCCGGCGGTCGGCTGGGCGTAGCGCTGATTAATACGGCAGATGATTCGCAAACCCTCTATCGCGGCGATGAACGGTTTGCCATGTGCAGCACCGGTAAAGTGATGGTCGCCGCCGCGGTGTTAAAACAGAGCGAAAGCAATCCAGAGGTAGTGAATAAAAGGCTGGAGATTAAAAAAGCGGATTTAGTAGTCTGGAGCCCGATTACCGAAAAACATCTGCAAAGCGGAATGACCCTGGCGGAACTCAGCGCGGCGGCTCTGCAGTACAGCGACAACACCGCGATGAATAAGATTATCGGTTACCTTGGCGGGCCGGAAAAAGTCACCGCATTCGCCCAGAGTATCGGTGACGTTACTTTTCGTCTCGATCGCATGGAGCCGGCGCTGAACAGCGCGATTCCCGGCGATAAGCGCGATACCACCACCCCGTTGGCGATGGCCGAAAGCCTGCGCAAGCTGACGCTGGGCAATGCGCTGGGCGAACAGCAGCGCACCCAGTTAGTGACGTGGCTAAAAGGCAATACCACCGGCGGGCAAAGCATTCGCGCAGGCCTGCCCGCAAGCTGGGCGGTCGGGGATAAAACCGGCGCCGGAGATTACGGCACCACCAACGATATCGCGGTGATCTGGCCGGAAAATCATGCCCCGCTGGTGCTGGTGACCTATTTTACCCAGCCGCAGCAGGATGCGAAAAGCCGCAAAGAGGTGTTAGCCGCGGCGGCAAAAATCGTCACCGAAGGGCTTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43788","NCBI_taxonomy_name":"Klebsiella michiganensis","NCBI_taxonomy_id":"1134687"}}}},"ARO_accession":"3008807","ARO_id":"47599","ARO_name":"OXY-5-10","CARD_short_name":"OXY-5-10","ARO_description":"Extended-spectrum class A beta-lactamase OXY-5-10.","ARO_category":{"38788":{"category_aro_accession":"3002388","category_aro_cvterm_id":"38788","category_aro_name":"OXY beta-lactamase","category_aro_description":"OXY beta-lactamases are chromosomal class A beta-lactamases that are found in Klebsiella oxytoca. At constitutive low levels, OXY beta-lactamases confer resistance to aminopenicillins and carboxypenicillins. At high induced levels,  OXY beta-lactamases confer resistance to penicillins, cephalosporins and aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8226":{"model_id":"8226","model_name":"OXY-5-11","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11053":{"protein_sequence":{"accession":"UPI86066.1","sequence":"MLKSSWRKTALMAAAVPLLLASGSLWASADAIQQKLADLEKRSGGRLGVALINTADNSQTLYRGDERFAMCSTGKVMAAAAVLKQSESNPEVVNKRLEIKKADLVVWSPITEKHLQSGMTLAELSAAALQYSDNTAMNKIIGYLGGPEKVTAFAQSIGDVTFRLDRMEPALNSAIPGDKRDTTTPLAMAESLRKLTLGNALGEQQRAQLVTWLKGNTTGGQSIRAGLPASWAVGDKTGAGDYGTTNDIAVIWPENHAPLVLVTYFTQPQQDAKSRKEVLAAAAKIVTEGL"},"dna_sequence":{"accession":"CP095761.1","fmin":"4380895","fmax":"4381768","strand":"+","sequence":"ATGTTGAAAAGTTCGTGGCGTAAAACCGCCCTGATGGCCGCCGCCGTTCCGCTGCTGCTGGCGAGCGGTTCATTATGGGCCAGTGCCGATGCTATCCAGCAAAAGCTGGCTGATTTAGAAAAACGTTCCGGCGGTCGGCTGGGCGTAGCGCTGATTAATACGGCAGATAATTCGCAAACCCTCTATCGCGGCGATGAACGGTTTGCCATGTGCAGCACCGGTAAAGTGATGGCCGCCGCCGCGGTGTTAAAACAGAGCGAAAGCAATCCAGAGGTAGTGAATAAAAGGCTGGAGATTAAAAAAGCGGATTTAGTAGTCTGGAGCCCGATTACCGAAAAACATCTGCAAAGCGGAATGACCCTGGCGGAACTCAGCGCGGCGGCGCTGCAGTACAGCGACAACACCGCGATGAATAAGATTATCGGTTACCTTGGCGGGCCGGAAAAAGTCACCGCATTCGCCCAGAGTATCGGTGACGTTACTTTTCGTCTCGATCGCATGGAGCCGGCGCTGAACAGCGCGATTCCCGGCGATAAGCGCGATACCACCACCCCGTTGGCGATGGCCGAAAGCCTGCGCAAGCTGACGCTGGGCAATGCGCTGGGCGAACAGCAGCGCGCCCAGTTAGTGACGTGGCTAAAAGGCAATACCACCGGCGGGCAAAGCATTCGCGCAGGCCTGCCCGCAAGCTGGGCGGTCGGGGATAAAACCGGCGCCGGAGATTACGGCACCACCAACGATATCGCGGTGATCTGGCCGGAAAATCATGCCCCGCTGGTGCTGGTGACCTATTTTACCCAGCCGCAGCAGGATGCGAAAAGCCGCAAAGAGGTGTTAGCCGCGGCGGCAAAAATCGTCACCGAAGGGCTTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43788","NCBI_taxonomy_name":"Klebsiella michiganensis","NCBI_taxonomy_id":"1134687"}}}},"ARO_accession":"3008808","ARO_id":"47600","ARO_name":"OXY-5-11","CARD_short_name":"OXY-5-11","ARO_description":"Extended-spectrum class A beta-lactamase OXY-5-11.","ARO_category":{"38788":{"category_aro_accession":"3002388","category_aro_cvterm_id":"38788","category_aro_name":"OXY beta-lactamase","category_aro_description":"OXY beta-lactamases are chromosomal class A beta-lactamases that are found in Klebsiella oxytoca. At constitutive low levels, OXY beta-lactamases confer resistance to aminopenicillins and carboxypenicillins. At high induced levels,  OXY beta-lactamases confer resistance to penicillins, cephalosporins and aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8227":{"model_id":"8227","model_name":"OXY-5-6","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11054":{"protein_sequence":{"accession":"QLO26335.1","sequence":"MLKSSWRKTALMAAAVPLLLASGSLWASADAIQQKLADLEKRSGGRLGVALINTADDSQTLYRGDERFAMCSTGKVMAAAAVLKQSESNPEVVNKRLEIKKADLVVWSPITEKHLQSGMTLAELSAAALQYSDNTAMNKIIGYLGGPEKVTAFAQSIGDVTFRLDRMEPALNSAIPGDERDTTTPLAMAESLRKLTLGNALGEQQRAQLVTWLKGNTTGGQSIRAGLPASWAVGDKTGAGDYGTTNDIAVIWPENHAPLVLVTYFTQPQQDAKSRKEVLAAAAKIVTEGL"},"dna_sequence":{"accession":"CP055325.1","fmin":"4352948","fmax":"4353821","strand":"+","sequence":"ATGTTGAAAAGTTCGTGGCGTAAAACCGCCCTGATGGCCGCCGCCGTTCCGCTGCTGCTGGCGAGCGGTTCATTATGGGCCAGTGCCGATGCTATCCAGCAAAAGCTGGCTGATTTAGAAAAACGTTCCGGCGGTCGGCTGGGCGTAGCGCTGATTAATACGGCAGATGATTCGCAAACCCTCTATCGCGGCGATGAACGGTTTGCCATGTGCAGCACCGGTAAAGTGATGGCCGCCGCCGCGGTGTTAAAACAGAGCGAAAGCAATCCAGAGGTAGTGAATAAAAGGCTGGAGATTAAAAAAGCGGATTTAGTAGTCTGGAGCCCGATTACCGAAAAACATCTGCAAAGCGGAATGACCCTGGCGGAACTCAGCGCGGCGGCGCTGCAGTACAGCGACAATACCGCGATGAATAAGATTATCGGTTACCTTGGCGGGCCGGAAAAAGTCACCGCATTCGCCCAGAGTATCGGTGACGTTACTTTTCGTCTCGATCGCATGGAGCCGGCGCTGAACAGCGCGATTCCCGGCGATGAGCGCGATACCACCACCCCGTTGGCGATGGCCGAAAGCCTGCGCAAGCTGACGCTGGGCAATGCGCTGGGCGAACAGCAGCGCGCCCAGTTAGTGACGTGGCTAAAAGGCAATACCACCGGCGGGCAAAGCATTCGCGCAGGCCTGCCCGCAAGCTGGGCGGTCGGGGATAAAACCGGCGCCGGAGATTACGGCACCACCAACGATATCGCGGTGATCTGGCCGGAAAATCATGCCCCGCTGGTGCTGGTGACCTATTTTACCCAGCCGCAGCAGGATGCGAAAAGCCGCAAAGAGGTGTTAGCCGCGGCGGCAAAAATCGTCACCGAAGGGCTTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43788","NCBI_taxonomy_name":"Klebsiella michiganensis","NCBI_taxonomy_id":"1134687"}}}},"ARO_accession":"3008809","ARO_id":"47601","ARO_name":"OXY-5-6","CARD_short_name":"OXY-5-6","ARO_description":"Extended-spectrum class A beta-lactamase OXY-5-6.","ARO_category":{"38788":{"category_aro_accession":"3002388","category_aro_cvterm_id":"38788","category_aro_name":"OXY beta-lactamase","category_aro_description":"OXY beta-lactamases are chromosomal class A beta-lactamases that are found in Klebsiella oxytoca. At constitutive low levels, OXY beta-lactamases confer resistance to aminopenicillins and carboxypenicillins. At high induced levels,  OXY beta-lactamases confer resistance to penicillins, cephalosporins and aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8228":{"model_id":"8228","model_name":"OXY-5-7","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11055":{"protein_sequence":{"accession":"QLP37798.1","sequence":"MLKSSWRKTALMAAAVPLLLASGSLWASADAIQQKLADLEKRSGGRLGVALINTADDSQTLYRGDERFAMCSTGKVMAAAAVLKQSESNPEVVNKRLEIKKSDLVVWSPITEKHLQSGMTLAELSAAALQYSDNTAMNKIIGYLGGPEKVTAFAQSIGDVTFRLDRMEPALNSAIPGDKRDTTTPLAMAESLRKLTLGNALGEQQRAQLVTWLKGNTTGGQSIRAGLPASWVVGDKTGAGDYGTTNDIAVIWPENHAPLVLVTYFTQPQQDAKSRKEVLAAAAKIVTEGL"},"dna_sequence":{"accession":"CP058212.1","fmin":"4461815","fmax":"4462688","strand":"+","sequence":"ATGTTGAAAAGTTCGTGGCGTAAAACCGCCCTGATGGCCGCCGCCGTTCCGCTGCTGCTGGCGAGCGGTTCATTATGGGCCAGTGCCGATGCTATCCAGCAAAAGCTGGCTGATTTAGAAAAACGTTCCGGCGGTCGGCTGGGCGTAGCGCTGATTAACACGGCAGATGATTCGCAAACCCTCTATCGCGGCGATGAACGTTTTGCCATGTGCAGCACCGGTAAAGTGATGGCCGCCGCCGCGGTGTTAAAACAGAGCGAAAGCAATCCAGAGGTGGTGAATAAAAGGCTGGAGATTAAAAAATCGGATTTAGTGGTCTGGAGCCCGATTACCGAAAAACATCTGCAAAGCGGAATGACCCTGGCGGAACTCAGCGCTGCGGCGCTGCAGTATAGCGACAATACCGCGATGAATAAGATTATCGGTTACCTTGGCGGGCCGGAAAAAGTCACCGCATTCGCCCAGAGCATCGGTGACGTTACTTTTCGTCTCGATCGGATGGAGCCGGCGCTGAACAGCGCGATTCCCGGTGATAAGCGCGATACCACCACCCCATTGGCGATGGCCGAAAGCCTGCGCAAGCTGACGCTGGGCAATGCGCTGGGCGAACAGCAGCGCGCCCAGTTAGTGACGTGGCTAAAAGGCAATACCACCGGCGGGCAAAGCATTCGCGCAGGCCTGCCCGCAAGCTGGGTGGTCGGGGATAAAACCGGCGCCGGAGATTACGGCACCACCAACGATATCGCGGTGATCTGGCCGGAAAATCATGCCCCGCTGGTGCTGGTGACCTATTTTACCCAGCCGCAGCAGGATGCGAAAAGCCGCAAAGAGGTGTTAGCCGCGGCGGCAAAAATCGTCACCGAAGGGCTTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43788","NCBI_taxonomy_name":"Klebsiella michiganensis","NCBI_taxonomy_id":"1134687"}}}},"ARO_accession":"3008810","ARO_id":"47602","ARO_name":"OXY-5-7","CARD_short_name":"OXY-5-7","ARO_description":"Extended-spectrum class A beta-lactamase OXY-5-7.","ARO_category":{"38788":{"category_aro_accession":"3002388","category_aro_cvterm_id":"38788","category_aro_name":"OXY beta-lactamase","category_aro_description":"OXY beta-lactamases are chromosomal class A beta-lactamases that are found in Klebsiella oxytoca. At constitutive low levels, OXY beta-lactamases confer resistance to aminopenicillins and carboxypenicillins. At high induced levels,  OXY beta-lactamases confer resistance to penicillins, cephalosporins and aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8229":{"model_id":"8229","model_name":"OXY-5-8","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11056":{"protein_sequence":{"accession":"QMR57622.1","sequence":"MLKSSWRKTALMAAAVPLLLASGSLWASADAIQQKLADLEKRSGGRLGVALINTADDSQTLYRGDERFAMCSTGKVMAAAAVLKQSESNPEVVNKRLEIKKADLVVWSPITEKHLQSGMTLAELSAAALQYSDNTAMNKIIGYLGGPEKVTAFALSIGDVTFRLDRMEPALNSAIPGDKRDTTTPLAMAESLRKLTLGNALGEQQRTQLVTWLKGNTTGGQSIRAGLPASWAVGDKTGAGDYGTTNDIAVIWPENHAPLVLVTYFTQPQQDAKSRKEVLAAAAKIVTEGL"},"dna_sequence":{"accession":"CP055985.1","fmin":"4819368","fmax":"4820241","strand":"-","sequence":"ATGTTGAAAAGTTCGTGGCGTAAAACCGCCCTGATGGCCGCCGCCGTTCCGCTGCTGCTGGCGAGCGGTTCATTATGGGCCAGTGCCGATGCTATCCAGCAAAAGCTGGCTGATTTAGAAAAACGTTCCGGCGGTCGGCTGGGCGTAGCGCTGATTAACACGGCAGATGATTCGCAAACCCTCTATCGCGGCGATGAACGGTTTGCCATGTGCAGCACCGGTAAAGTGATGGCCGCCGCCGCGGTGTTAAAACAGAGCGAAAGCAATCCAGAGGTAGTGAATAAAAGGCTGGAGATTAAAAAAGCGGATTTAGTAGTCTGGAGCCCGATTACCGAAAAACATCTGCAAAGCGGAATGACCCTGGCGGAACTCAGCGCGGCGGCGCTGCAGTACAGCGACAATACCGCGATGAATAAGATTATCGGTTACCTTGGCGGGCCGGAAAAAGTCACCGCATTCGCCCTGAGTATCGGTGACGTTACTTTTCGTCTCGATCGCATGGAGCCGGCGCTGAACAGCGCGATTCCCGGCGATAAGCGCGATACCACCACCCCGTTGGCGATGGCCGAAAGCCTGCGCAAGCTGACGCTGGGCAATGCGCTGGGCGAACAGCAGCGCACCCAGTTAGTGACGTGGCTAAAAGGCAACACCACCGGCGGGCAAAGCATTCGCGCAGGCCTGCCCGCAAGCTGGGCGGTCGGGGATAAAACCGGCGCCGGAGATTACGGCACCACCAACGATATCGCGGTGATCTGGCCGGAAAATCATGCCCCGCTGGTGCTGGTGACTTATTTTACCCAGCCGCAGCAGGATGCGAAAAGCCGCAAAGAGGTGTTAGCCGCGGCGGCAAAAATCGTCACCGAAGGGCTTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43788","NCBI_taxonomy_name":"Klebsiella michiganensis","NCBI_taxonomy_id":"1134687"}}}},"ARO_accession":"3008811","ARO_id":"47603","ARO_name":"OXY-5-8","CARD_short_name":"OXY-5-8","ARO_description":"Extended-spectrum class A beta-lactamase OXY-5-8.","ARO_category":{"38788":{"category_aro_accession":"3002388","category_aro_cvterm_id":"38788","category_aro_name":"OXY beta-lactamase","category_aro_description":"OXY beta-lactamases are chromosomal class A beta-lactamases that are found in Klebsiella oxytoca. At constitutive low levels, OXY beta-lactamases confer resistance to aminopenicillins and carboxypenicillins. At high induced levels,  OXY beta-lactamases confer resistance to penicillins, cephalosporins and aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8230":{"model_id":"8230","model_name":"OXY-6-10","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11057":{"protein_sequence":{"accession":"QLO53791.1","sequence":"MLKSSWRKSALMAAAAVPLLLASGSLWASADAIQQKLANLEKRSGGRLGVALINTADDSQTLYRGDERFAMCSTGKVMAAAAVLKQSESHPDVVNKRLEIKKSDLVVWSPITEKHLQSGMTLAELSAAALQYSDNTAMNKMISYLGGPEKVTAFAQSIGDVTFRLDRTEPALNSAIPGDKRDTTTPLAMAESLRKLTLVNALGEQQRAQLVTWLKGNTTGGQSIRAGLPASWAVGDKTGAGDYGTTNDIAVIWPENHAPLVLVTYFTQPQQDAKSRKEVLAAAAKIVTEGL"},"dna_sequence":{"accession":"CP055315.1","fmin":"4323852","fmax":"4324728","strand":"+","sequence":"ATGTTGAAAAGTTCGTGGCGTAAAAGCGCCCTGATGGCCGCCGCCGCCGTTCCGCTGCTGCTGGCGAGCGGTTCATTATGGGCCAGTGCCGATGCTATCCAGCAAAAGCTGGCTAATTTAGAAAAACGGTCCGGTGGCCGGCTGGGCGTGGCGCTGATTAACACGGCGGATGATTCGCAAACCCTTTATCGCGGCGACGAACGTTTTGCCATGTGCAGCACCGGTAAAGTGATGGCCGCCGCCGCGGTGTTAAAGCAGAGCGAAAGCCATCCCGATGTGGTGAATAAAAGGCTGGAGATTAAAAAATCGGATTTAGTGGTCTGGAGCCCGATTACCGAAAAACATCTGCAAAGCGGAATGACCCTGGCGGAACTCAGCGCGGCGGCGCTGCAGTACAGCGACAATACCGCGATGAATAAGATGATTAGCTACCTTGGCGGACCGGAAAAGGTGACCGCATTCGCCCAGAGCATCGGGGACGTTACTTTTCGTCTCGATCGTACGGAGCCGGCGCTGAACAGCGCGATACCCGGCGATAAGCGCGATACCACCACCCCGTTGGCGATGGCCGAAAGCCTGCGCAAGCTGACGCTGGTCAATGCGCTGGGCGAACAGCAGCGCGCCCAGTTAGTGACGTGGCTAAAAGGCAATACCACCGGCGGGCAAAGCATTCGCGCAGGCCTGCCCGCAAGCTGGGCGGTCGGGGATAAAACCGGCGCCGGAGATTACGGCACCACCAACGATATCGCGGTGATCTGGCCGGAAAATCATGCCCCGCTGGTGTTAGTGACCTATTTTACCCAGCCGCAGCAGGATGCGAAAAGCCGCAAAGAGGTGTTAGCCGCGGCGGCGAAAATCGTGACCGAAGGGCTGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"47913","NCBI_taxonomy_name":"Klebsiella grimontii","NCBI_taxonomy_id":"2058152"}}}},"ARO_accession":"3008812","ARO_id":"47604","ARO_name":"OXY-6-10","CARD_short_name":"OXY-6-10","ARO_description":"Extended-spectrum class A beta-lactamase OXY-6-10.","ARO_category":{"38788":{"category_aro_accession":"3002388","category_aro_cvterm_id":"38788","category_aro_name":"OXY beta-lactamase","category_aro_description":"OXY beta-lactamases are chromosomal class A beta-lactamases that are found in Klebsiella oxytoca. At constitutive low levels, OXY beta-lactamases confer resistance to aminopenicillins and carboxypenicillins. At high induced levels,  OXY beta-lactamases confer resistance to penicillins, cephalosporins and aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8231":{"model_id":"8231","model_name":"OXY-6-11","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11058":{"protein_sequence":{"accession":"QQQ22795.1","sequence":"MLKSSWRKSALMAAAAVPLLLASGSLWASADAIQQKLADLEKRSGGRLGVALINTADDSQTLYRGDERFAMCSTGKVMAAAAVLKQSESHPDVVNKRLEIKKSDLVVWSPITEKHLQSGMTLAELSAAALQYSDNTAMNKMISYLGGPEKVTAFAQSIGDVTFRLDRTEPALNSAIPGDKRDTTTPLAMAESLRKLTLGNALGEQQRAQLMTWLKGNTTGGQSIRAGLPASWAVGDKTGAGDYGTTNDIAVIWPENHAPLVLVTYFTQPQQDAKSRKEVLAAAAKIVTEGL"},"dna_sequence":{"accession":"CP067433.1","fmin":"31310","fmax":"32186","strand":"-","sequence":"ATGTTGAAAAGTTCGTGGCGTAAAAGCGCCCTGATGGCCGCCGCCGCCGTTCCGCTGCTGCTGGCGAGCGGTTCATTATGGGCCAGTGCCGATGCTATCCAGCAAAAGCTGGCTGATTTAGAAAAACGGTCCGGTGGCCGGCTGGGCGTGGCGCTGATTAACACGGCGGATGATTCGCAAACCCTTTATCGCGGCGACGAACGTTTTGCCATGTGCAGCACCGGTAAAGTGATGGCCGCCGCCGCGGTGTTAAAGCAGAGCGAAAGCCATCCCGATGTGGTGAATAAAAGGCTGGAGATTAAAAAATCGGATTTAGTGGTCTGGAGCCCGATTACCGAAAAACATCTGCAAAGCGGAATGACCCTGGCGGAACTCAGCGCGGCGGCGCTGCAGTACAGCGACAATACCGCGATGAATAAGATGATTAGCTACCTTGGCGGACCGGAAAAGGTGACCGCATTCGCCCAGAGCATCGGGGACGTTACTTTTCGTCTCGATCGTACGGAGCCGGCGCTGAACAGCGCGATACCCGGCGATAAGCGCGATACCACCACCCCGTTGGCGATGGCCGAAAGCCTGCGCAAGCTGACGCTGGGCAATGCGCTGGGCGAACAGCAGCGCGCCCAGTTAATGACGTGGCTAAAAGGCAATACCACCGGCGGGCAAAGCATTCGCGCAGGCCTGCCCGCAAGCTGGGCGGTCGGGGATAAAACCGGCGCCGGAGATTACGGCACCACCAACGATATCGCGGTGATCTGGCCGGAAAATCATGCCCCGCTGGTGTTAGTGACCTATTTTACCCAGCCGCAGCAGGATGCGAAAAGCCGCAAAGAGGTGTTAGCCGCGGCGGCGAAAATCGTGACCGAAGGGCTGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"47913","NCBI_taxonomy_name":"Klebsiella grimontii","NCBI_taxonomy_id":"2058152"}}}},"ARO_accession":"3008813","ARO_id":"47605","ARO_name":"OXY-6-11","CARD_short_name":"OXY-6-11","ARO_description":"Extended-spectrum class A beta-lactamase OXY-6-11.","ARO_category":{"38788":{"category_aro_accession":"3002388","category_aro_cvterm_id":"38788","category_aro_name":"OXY beta-lactamase","category_aro_description":"OXY beta-lactamases are chromosomal class A beta-lactamases that are found in Klebsiella oxytoca. At constitutive low levels, OXY beta-lactamases confer resistance to aminopenicillins and carboxypenicillins. At high induced levels,  OXY beta-lactamases confer resistance to penicillins, cephalosporins and aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8232":{"model_id":"8232","model_name":"OXY-6-5","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11059":{"protein_sequence":{"accession":"QLT10828.1","sequence":"MLKSSWRKSALMAAAVPLLLASGSLWASADAIQQKLADLEKRSGGRLGVALINTADDSQTLYRGDERFAMCSTGKVMAAAAVLKQSESHPDVVNKRLEIKKSDLVVWSPITEKHLQSGMTLAELSAAALQYSDNTAMNKMISYLGGPEKVTAFAQSIGDVTFRLDRTEPALNSAIPGDKRDTTTPLAMAESLRKLTLGNALGEQQRAQLVTWLKGNTTGGQSIRAGLPANWAVGDKTGAGDYGTTNDIAVIWPENHAPLVLVTYFTQPQQDAKSRKEVLAAAAKIVTEGL"},"dna_sequence":{"accession":"CP056150.1","fmin":"4518796","fmax":"4519669","strand":"+","sequence":"ATGTTGAAAAGTTCGTGGCGTAAAAGCGCCCTGATGGCCGCCGCCGTTCCGCTGCTGCTGGCGAGCGGTTCATTATGGGCCAGTGCCGATGCTATCCAGCAAAAGCTGGCTGATTTAGAAAAACGGTCCGGTGGCCGGCTGGGCGTGGCGCTGATTAACACGGCGGATGATTCGCAAACCCTTTATCGCGGCGACGAACGTTTTGCCATGTGCAGCACCGGTAAAGTGATGGCCGCCGCCGCGGTGTTAAAGCAGAGCGAAAGCCATCCCGATGTGGTGAATAAAAGGCTGGAGATTAAAAAATCGGATTTAGTGGTCTGGAGCCCGATTACCGAAAAACATCTGCAAAGCGGAATGACCCTGGCGGAACTCAGCGCGGCGGCGCTGCAGTACAGCGACAATACCGCGATGAATAAGATGATTAGCTACCTTGGCGGACCGGAAAAGGTGACCGCATTCGCCCAGAGCATCGGGGACGTTACTTTTCGTCTCGATCGTACGGAGCCGGCGCTGAACAGCGCGATACCCGGCGATAAGCGCGATACCACCACCCCGTTGGCGATGGCCGAAAGCCTGCGCAAGCTGACGCTGGGCAATGCGCTGGGCGAACAGCAGCGCGCCCAGTTAGTGACGTGGCTAAAAGGCAATACCACCGGCGGGCAAAGCATTCGCGCAGGCCTGCCCGCAAACTGGGCGGTCGGGGATAAAACCGGCGCCGGAGATTACGGCACCACCAACGATATCGCGGTGATCTGGCCGGAAAATCATGCCCCGCTGGTGTTAGTGACCTATTTTACCCAGCCGCAGCAGGATGCGAAAAGCCGCAAAGAGGTGTTAGCCGCGGCGGCGAAAATCGTGACCGAAGGGCTGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"47913","NCBI_taxonomy_name":"Klebsiella grimontii","NCBI_taxonomy_id":"2058152"}}}},"ARO_accession":"3008814","ARO_id":"47606","ARO_name":"OXY-6-5","CARD_short_name":"OXY-6-5","ARO_description":"Extended-spectrum class A beta-lactamase OXY-6-5.","ARO_category":{"38788":{"category_aro_accession":"3002388","category_aro_cvterm_id":"38788","category_aro_name":"OXY beta-lactamase","category_aro_description":"OXY beta-lactamases are chromosomal class A beta-lactamases that are found in Klebsiella oxytoca. At constitutive low levels, OXY beta-lactamases confer resistance to aminopenicillins and carboxypenicillins. At high induced levels,  OXY beta-lactamases confer resistance to penicillins, cephalosporins and aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8233":{"model_id":"8233","model_name":"OXY-6-7","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11060":{"protein_sequence":{"accession":"UNF11602.1","sequence":"MLKSSWRKSALMAAAAVPLLLASGSLWASADAIQQKLANLEKRSGGRLGVALINTADDSQTLYRGDERFAMCSTGKVMAAAAVLKQSESHPDVLNKRLEIKKSDLVVWSPITEKHLQSGMTLAELSAAALQYSDNTAMNKMISYLGGPEKVTAFAQSIGDVTFRLDRTEPALNSAIPGDKRDTTTPLAMAESLRKLTLGNALGEQQRAQLVTWLKGNTTGGQSIRAGLPASWAVGDKTGAGDYGTTNDIAVIWPENHAPLVLVTYFTQPQQDAKSRKEVLAAAAKIVTEGL"},"dna_sequence":{"accession":"CP091752.1","fmin":"4194727","fmax":"4195603","strand":"+","sequence":"ATGTTGAAAAGTTCGTGGCGTAAAAGCGCCCTGATGGCCGCCGCCGCCGTTCCGCTGCTGCTGGCGAGCGGTTCATTATGGGCCAGTGCCGATGCTATCCAGCAAAAGCTGGCTAATTTAGAAAAACGGTCCGGTGGCCGGCTGGGCGTGGCGCTGATTAACACGGCGGATGATTCGCAAACCCTTTATCGCGGCGACGAACGTTTTGCCATGTGCAGCACCGGTAAAGTGATGGCCGCCGCCGCGGTGTTAAAGCAGAGCGAAAGCCATCCCGATGTGTTGAATAAAAGGCTGGAGATTAAAAAATCGGATTTAGTGGTCTGGAGCCCGATTACCGAAAAACATCTGCAAAGCGGAATGACCCTGGCGGAACTCAGCGCGGCGGCGCTGCAGTACAGCGACAATACCGCGATGAATAAGATGATTAGCTACCTTGGCGGACCGGAAAAGGTGACCGCATTCGCCCAGAGCATCGGGGACGTTACTTTTCGTCTCGATCGTACGGAGCCGGCGCTGAACAGCGCGATACCCGGCGATAAGCGCGATACCACCACCCCGTTGGCGATGGCCGAAAGCCTGCGCAAGCTGACGCTGGGCAATGCGCTGGGCGAACAGCAGCGCGCCCAGTTAGTGACGTGGCTAAAAGGCAATACCACCGGCGGGCAAAGCATTCGCGCAGGCCTGCCCGCAAGCTGGGCGGTCGGGGATAAAACCGGCGCCGGAGATTACGGCACCACCAACGATATCGCGGTGATCTGGCCGGAAAATCATGCCCCGCTGGTGTTAGTGACCTATTTTACCCAGCCGCAGCAGGATGCGAAAAGCCGCAAAGAGGTGTTAGCCGCGGCGGCGAAAATCGTGACCGAAGGGCTGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"47913","NCBI_taxonomy_name":"Klebsiella grimontii","NCBI_taxonomy_id":"2058152"}}}},"ARO_accession":"3008815","ARO_id":"47607","ARO_name":"OXY-6-7","CARD_short_name":"OXY-6-7","ARO_description":"Extended-spectrum class A beta-lactamase OXY-6-7.","ARO_category":{"38788":{"category_aro_accession":"3002388","category_aro_cvterm_id":"38788","category_aro_name":"OXY beta-lactamase","category_aro_description":"OXY beta-lactamases are chromosomal class A beta-lactamases that are found in Klebsiella oxytoca. At constitutive low levels, OXY beta-lactamases confer resistance to aminopenicillins and carboxypenicillins. At high induced levels,  OXY beta-lactamases confer resistance to penicillins, cephalosporins and aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8234":{"model_id":"8234","model_name":"OXY-7-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11061":{"protein_sequence":{"accession":"ALC79265.1","sequence":"MLKNSWRKSALMAAAVPLLLASGSLWASADTIQQKLADLEKSSGGRLGVALINTADDSQTLYRGDERFAMCSTGKVMAAAAVLKQSESHPDVVNKRLEIKKSDLVVWSPITEKHLQSGMTLAELSAAALQYSDNTAMNKMISYLGGPEKVTAFAQSIGDVTFRLDRTEPALNSAIPGDKRDTTTPLAMAESLRKLTLGNALGEQQRAQLVTWLKGNTTGGQSIRAGLPESWAVGDKTGAGDYGTTNDIAVIWPENHAPLVLVTYFTQPQQDAKSRKEVLAAAAKIVTEGL"},"dna_sequence":{"accession":"KT001254.1","fmin":"0","fmax":"873","strand":"+","sequence":"ATGTTGAAAAATTCGTGGCGTAAAAGCGCCCTGATGGCCGCCGCAGTTCCGCTACTGCTGGCGAGCGGTTCATTATGGGCCAGTGCCGATACTATCCAGCAGAAGCTGGCTGATTTAGAAAAAAGTTCCGGCGGCCGGCTGGGCGTGGCGCTGATTAACACGGCGGATGATTCGCAGACCCTCTATCGCGGCGATGAACGTTTTGCCATGTGCAGCACCGGTAAAGTGATGGCCGCCGCCGCGGTGTTAAAGCAGAGCGAAAGCCATCCCGATGTGGTGAATAAAAGGCTGGAGATTAAAAAATCGGATTTAGTGGTCTGGAGCCCGATTACCGAAAAACATCTGCAAAGCGGAATGACCCTGGCGGAACTCAGCGCTGCGGCTCTGCAGTACAGCGACAATACCGCGATGAATAAGATGATTAGCTACCTTGGCGGACCGGAAAAGGTGACCGCATTCGCCCAGAGCATCGGGGACGTTACTTTTCGTCTCGATCGTACGGAGCCGGCGCTGAACAGCGCGATACCCGGCGATAAGCGCGATACCACCACCCCGTTGGCAATGGCCGAAAGCCTGCGCAAGCTGACGTTAGGCAATGCGCTGGGCGAACAGCAGCGCGCCCAGTTAGTGACATGGCTAAAAGGCAATACCACCGGCGGGCAAAGCATTCGCGCAGGCCTGCCCGAAAGCTGGGCGGTCGGGGATAAAACCGGCGCCGGAGATTACGGCACCACCAACGATATCGCGGTGATCTGGCCGGAAAATCATGCCCCGCTGGTGCTAGTGACCTATTTTACCCAACCGCAGCAGGATGCGAAAAGCCGCAAAGAGGTGTTAGCCGCGGCGGCGAAAATCGTGACCGAAGGGCTGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3008816","ARO_id":"47608","ARO_name":"OXY-7-1","CARD_short_name":"OXY-7-1","ARO_description":"Extended-spectrum class A beta-lactamase OXY-7-1.","ARO_category":{"38788":{"category_aro_accession":"3002388","category_aro_cvterm_id":"38788","category_aro_name":"OXY beta-lactamase","category_aro_description":"OXY beta-lactamases are chromosomal class A beta-lactamases that are found in Klebsiella oxytoca. At constitutive low levels, OXY beta-lactamases confer resistance to aminopenicillins and carboxypenicillins. At high induced levels,  OXY beta-lactamases confer resistance to penicillins, cephalosporins and aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8235":{"model_id":"8235","model_name":"OXY-8-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11062":{"protein_sequence":{"accession":"QBG09484.1","sequence":"MIKTSWRKIALIAATLPLLLCSSSLWANADAIQRKLTDLEKSSGGRLGVALINTTDNSQILYRGDERFAMCSTGKVMAAAAVLKQSEVDNQVLNKRLEIKKSDLVVWSPVTEKHLQSGMTLAELSAATLQYSDNTAMNKMIGYLGGPDKVTAFARSIGDVTFRLDRTEPALNTAIPGDERDTTTPLAMAEILHKLTLGNALGEQQRAQLVTWLKGNTTGGQSIRAGLPAGWVVGDKTGAGDYGTTNDIAVIWPENHAPLVLVTYFTQPQQDAKSRKEVLAAAAKIVTEGL"},"dna_sequence":{"accession":"CP036175.1","fmin":"4399698","fmax":"4400571","strand":"+","sequence":"ATGATTAAAACTTCGTGGCGTAAAATCGCCCTGATTGCCGCCACCCTGCCTTTATTGCTCTGTAGCAGTTCATTATGGGCCAATGCCGATGCTATTCAGCGGAAGCTGACTGATTTAGAAAAAAGCTCCGGCGGCAGGTTGGGCGTGGCGCTGATTAACACTACAGATAATTCTCAAATTTTATATCGCGGAGATGAACGTTTTGCCATGTGCAGCACCGGTAAAGTGATGGCCGCTGCCGCGGTGTTAAAGCAAAGCGAAGTCGATAATCAAGTATTGAATAAAAGACTGGAGATTAAGAAATCAGATTTGGTGGTCTGGAGTCCGGTGACCGAAAAACATCTGCAGAGCGGAATGACGCTGGCGGAATTAAGCGCCGCAACCCTGCAATATAGCGATAACACCGCGATGAATAAGATGATTGGTTATCTTGGCGGACCAGACAAAGTGACCGCATTCGCCCGCAGCATTGGCGATGTCACTTTTCGTCTTGATCGTACGGAGCCTGCGCTGAACACCGCGATCCCGGGTGATGAACGCGATACCACCACGCCGCTGGCGATGGCCGAAATCCTGCACAAGCTGACGCTGGGTAATGCTCTGGGTGAACAGCAGCGCGCCCAGTTAGTGACATGGTTGAAAGGCAACACCACCGGCGGGCAGAGTATTCGTGCGGGCCTGCCTGCAGGCTGGGTCGTGGGAGATAAAACCGGCGCCGGTGATTACGGCACGACCAATGATATCGCCGTTATCTGGCCGGAAAATCATGCCCCGCTGGTGTTAGTCACTTATTTCACCCAACCACAGCAGGATGCGAAAAGCCGCAAAGAGGTATTAGCCGCAGCGGCAAAAATCGTGACCGAAGGGCTGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43787","NCBI_taxonomy_name":"Klebsiella huaxiensis","NCBI_taxonomy_id":"2153354"}}}},"ARO_accession":"3008817","ARO_id":"47609","ARO_name":"OXY-8-1","CARD_short_name":"OXY-8-1","ARO_description":"Extended-spectrum class A beta-lactamase OXY-8-1.","ARO_category":{"38788":{"category_aro_accession":"3002388","category_aro_cvterm_id":"38788","category_aro_name":"OXY beta-lactamase","category_aro_description":"OXY beta-lactamases are chromosomal class A beta-lactamases that are found in Klebsiella oxytoca. At constitutive low levels, OXY beta-lactamases confer resistance to aminopenicillins and carboxypenicillins. At high induced levels,  OXY beta-lactamases confer resistance to penicillins, cephalosporins and aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8236":{"model_id":"8236","model_name":"OXY-8-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11063":{"protein_sequence":{"accession":"VUT22948.1","sequence":"MIKCSWRKTALIAATLPLLLCSSSLWANADAIQRKLTDLEKSSGGRLGVALINTTDNSQILYRGDERFAMCSTGKVMAAAAVLKQSEVDNQVLNKRLEIKKSDLVVWSPVTEKHLQSGMTLAELSAATLQYSDNTAMNKMIGYLGGPDKVTAFARSIGDVTFRLDRTEPALNTAIPGDERDTTTPLAMAESLHKLTLGNALGEQQRAQLVTWLKGNTTGGQSISAGLPAGWVVGDKTGAGDYGTTNDIAVIWPENHAPLVLVTYFTQPQQDAKSRKEVLAAAAKIVTEGL"},"dna_sequence":{"accession":"CABGGQ010000064.1","fmin":"86928","fmax":"87801","strand":"-","sequence":"ATGATTAAATGTTCGTGGCGTAAAACCGCCCTGATTGCCGCCACCCTGCCTTTATTGCTCTGTAGCAGTTCATTATGGGCCAATGCCGATGCTATTCAGCGGAAGCTGACTGATTTAGAAAAAAGCTCCGGCGGCAGGTTGGGCGTGGCGCTGATTAACACTACAGATAATTCTCAAATCTTATATCGCGGAGATGAACGTTTTGCCATGTGCAGCACCGGTAAAGTGATGGCCGCTGCCGCGGTGTTAAAGCAAAGCGAAGTCGATAATCAAGTATTGAATAAAAGACTGGAGATTAAGAAATCAGATTTGGTGGTCTGGAGTCCGGTGACCGAAAAACATCTGCAGAGCGGAATGACGCTGGCGGAATTAAGCGCCGCAACCCTGCAATATAGCGACAACACCGCGATGAATAAGATGATTGGTTATCTTGGCGGACCAGACAAAGTGACCGCATTCGCCCGCAGCATTGGCGATGTCACTTTTCGTCTTGATCGTACGGAGCCTGCACTAAACACCGCGATCCCGGGTGATGAACGCGATACCACCACGCCGCTGGCGATGGCCGAAAGCCTGCACAAGCTGACGCTGGGTAATGCGCTGGGTGAACAGCAGCGCGCACAGTTAGTGACATGGTTGAAAGGCAATACCACCGGTGGGCAGAGCATTAGCGCGGGGCTGCCTGCAGGCTGGGTCGTGGGAGATAAAACCGGCGCCGGTGATTACGGCACGACCAATGATATCGCCGTTATCTGGCCGGAAAATCATGCCCCGCTGGTGTTAGTCACTTATTTCACCCAACCACAGCAGGATGCGAAAAGCCGCAAAGAGGTATTAGCCGCAGCGGCAAAAATCGTGACCGAAGGGCTGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43787","NCBI_taxonomy_name":"Klebsiella huaxiensis","NCBI_taxonomy_id":"2153354"}}}},"ARO_accession":"3008818","ARO_id":"47610","ARO_name":"OXY-8-2","CARD_short_name":"OXY-8-2","ARO_description":"Extended-spectrum class A beta-lactamase OXY-8-2.","ARO_category":{"38788":{"category_aro_accession":"3002388","category_aro_cvterm_id":"38788","category_aro_name":"OXY beta-lactamase","category_aro_description":"OXY beta-lactamases are chromosomal class A beta-lactamases that are found in Klebsiella oxytoca. At constitutive low levels, OXY beta-lactamases confer resistance to aminopenicillins and carboxypenicillins. At high induced levels,  OXY beta-lactamases confer resistance to penicillins, cephalosporins and aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8237":{"model_id":"8237","model_name":"OXY-8-3","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11064":{"protein_sequence":{"accession":"VUS23187.1","sequence":"MIKTSWRKIALIAATLPLLLCSSSLWANADAIQRKLTDLEKSSGGRLGVALINTTDNSQILYRGDERFAMCSTGKVMAAAAVLKQSEADNQVLNKRLEIKKSDLVVWSPVTEKHLQSGMTLAELSAATLQYSDNTAMNKMIGYLGGPDKVTAFARSIDDVTFRLDRTEPALNTAIPGDERDTTTPLAMAESLHKLTLGNALGEQQRAQLVTWLKGNTTGGQSISAGLPAGWVVGDKTGAGDYGTTNDIAVIWPENHAPLVLVTYFTQPQQDAKSRKEVLAAAAKIVTEGL"},"dna_sequence":{"accession":"CABGGW010000001.1","fmin":"393713","fmax":"394586","strand":"+","sequence":"ATGATTAAAACTTCGTGGCGTAAAATCGCCCTGATTGCCGCCACCCTGCCTTTATTGCTCTGTAGCAGTTCATTATGGGCCAATGCCGATGCTATTCAGCGGAAGCTGACTGATTTAGAAAAAAGCTCCGGCGGCAGGTTGGGCGTGGCGCTGATTAACACTACAGATAATTCTCAAATCTTATATCGCGGAGATGAACGTTTTGCCATGTGCAGCACCGGTAAAGTGATGGCCGCTGCCGCGGTGTTAAAGCAAAGCGAAGCCGATAATCAAGTATTGAATAAAAGGCTGGAGATTAAGAAATCAGATTTGGTGGTCTGGAGTCCGGTGACCGAGAAACATCTGCAGAGCGGAATGACGCTGGCGGAATTAAGTGCCGCAACCCTGCAATATAGCGACAACACCGCGATGAATAAGATGATTGGTTATCTTGGCGGACCAGACAAAGTGACCGCATTCGCCCGCAGCATTGACGATGTCACTTTTCGTCTTGATCGTACGGAGCCTGCACTAAACACCGCGATCCCGGGTGATGAACGCGATACCACCACGCCGCTGGCGATGGCCGAAAGCCTGCACAAGCTGACGCTGGGTAATGCTCTGGGTGAACAGCAGCGCGCCCAGTTAGTGACATGGTTGAAAGGCAACACCACCGGCGGGCAGAGCATTAGCGCGGGGCTGCCTGCAGGCTGGGTCGTGGGAGATAAAACCGGCGCCGGTGATTACGGCACGACCAATGATATCGCCGTTATCTGGCCGGAAAATCATGCCCCGCTGGTGTTAGTCACTTATTTCACCCAACCACAGCAGGATGCGAAAAGCCGCAAAGAGGTATTAGCCGCAGCGGCAAAAATCGTGACCGAAGGGCTGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43787","NCBI_taxonomy_name":"Klebsiella huaxiensis","NCBI_taxonomy_id":"2153354"}}}},"ARO_accession":"3008819","ARO_id":"47611","ARO_name":"OXY-8-3","CARD_short_name":"OXY-8-3","ARO_description":"Extended-spectrum class A beta-lactamase OXY-8-3.","ARO_category":{"38788":{"category_aro_accession":"3002388","category_aro_cvterm_id":"38788","category_aro_name":"OXY beta-lactamase","category_aro_description":"OXY beta-lactamases are chromosomal class A beta-lactamases that are found in Klebsiella oxytoca. At constitutive low levels, OXY beta-lactamases confer resistance to aminopenicillins and carboxypenicillins. At high induced levels,  OXY beta-lactamases confer resistance to penicillins, cephalosporins and aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8238":{"model_id":"8238","model_name":"OXY-9-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11065":{"protein_sequence":{"accession":"VUS47486.1","sequence":"MMKTSWRKSALIAAALPLLLCSSSLWANAIQQKLADLEKNTGGRLGVALIDTTDNSQVLYRGDEHFAMCSTGKVMAAAAVLKQSEADNQVLNKRLEIKKSDLVVWSPVTEKHLQSGMTLAELSAAALQYSDNTAMNKMIGYLGGPEKVTAFAHSIGDVTFRLDRTEPTLNTAIPGDERDTTTPLAMAESLHKLTLGYALGEQQRAQLVTWLKGNTTGGQSISAGLPAGWVVGDKTGAGEYGTTNDIAVIWPENHAPLVLVTYFTQPQQDAKSRKDVLAAAAKIVTEGLQHK"},"dna_sequence":{"accession":"CABGGU010000083.1","fmin":"240","fmax":"1116","strand":"-","sequence":"ATGATGAAAACTTCGTGGCGTAAAAGCGCCCTGATTGCCGCCGCCCTGCCTTTATTGCTCTGTAGCAGTTCATTATGGGCCAATGCTATTCAGCAGAAGCTGGCTGATTTGGAAAAAAATACCGGCGGTCGACTGGGCGTCGCGCTGATTGACACCACAGATAATTCTCAAGTTCTATATCGCGGTGACGAGCATTTTGCTATGTGCAGCACCGGTAAAGTGATGGCCGCTGCCGCGGTGTTAAAGCAAAGCGAAGCCGATAATCAAGTACTGAATAAAAGGCTGGAGATTAAAAAATCGGATCTGGTGGTCTGGAGCCCGGTGACGGAAAAACATCTGCAGAGCGGAATGACGTTGGCGGAATTAAGCGCCGCCGCGCTGCAATATAGCGACAATACCGCGATGAATAAGATGATTGGTTATCTTGGCGGACCAGAAAAAGTGACCGCCTTCGCCCACAGTATCGGCGATGTCACTTTTCGTCTCGATCGTACGGAGCCAACGCTAAACACCGCGATTCCGGGTGATGAACGCGATACCACCACGCCGCTGGCGATGGCTGAAAGTCTGCACAAGCTGACGCTGGGTTATGCGCTGGGTGAACAACAGCGCGCACAGTTAGTGACATGGTTGAAAGGTAACACCACCGGTGGGCAGAGCATTAGCGCAGGCCTGCCTGCAGGCTGGGTCGTGGGAGATAAAACCGGAGCCGGAGAGTACGGCACCACCAATGATATCGCCGTTATCTGGCCGGAAAATCATGCCCCGCTGGTGTTAGTCACTTATTTCACCCAACCGCAGCAGGATGCGAAAAGCCGCAAAGATGTGCTAGCCGCAGCGGCAAAAATCGTGACCGAAGGCCTGCAGCATAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"47915","NCBI_taxonomy_name":"Klebsiella spallanzanii","NCBI_taxonomy_id":"2587528"}}}},"ARO_accession":"3008820","ARO_id":"47612","ARO_name":"OXY-9-1","CARD_short_name":"OXY-9-1","ARO_description":"Extended-spectrum class A beta-lactamase OXY-9-1.","ARO_category":{"38788":{"category_aro_accession":"3002388","category_aro_cvterm_id":"38788","category_aro_name":"OXY beta-lactamase","category_aro_description":"OXY beta-lactamases are chromosomal class A beta-lactamases that are found in Klebsiella oxytoca. At constitutive low levels, OXY beta-lactamases confer resistance to aminopenicillins and carboxypenicillins. At high induced levels,  OXY beta-lactamases confer resistance to penicillins, cephalosporins and aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8239":{"model_id":"8239","model_name":"PAD-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11066":{"protein_sequence":{"accession":"KXF74838.1","sequence":"MTISLSRRQALAGSLLAVPALASLTSAARAQSGGKLENELAKLEDRHGGRIGVAILNLATGDKIGHRADERFLLCSTFKALTAGYILARVDRGEEELDRRIVHAKKDLVTWSPITEKHVGGAGMSVAELCLATVTLSDNTAANLLLNSFGGPAGLTAFLRSIGDETTRLDRFETELNVHEKPGDLRDTTTPAAMLETLRKLLFGDVLSRSSRAQLAAWMVMNKTGDEKLRAGFPADWMIGDKTGGNGDKYGNSNDVAVAWSPDRGAVIVSAYCEIPSVSEKERAAILAEIGRIASRV"},"dna_sequence":{"accession":"LNTU01000040.1","fmin":"32461","fmax":"33355","strand":"+","sequence":"ATGACGATATCCCTTTCCCGCCGGCAGGCACTTGCCGGAAGTCTGCTCGCCGTTCCGGCATTGGCCTCGCTGACAAGCGCCGCACGGGCGCAGAGCGGCGGCAAGCTGGAGAACGAACTCGCAAAGCTTGAAGACAGGCATGGCGGCCGTATCGGCGTCGCGATCCTCAATCTCGCCACCGGCGACAAGATCGGACATCGTGCCGACGAACGCTTCCTGCTGTGCAGTACCTTCAAGGCCCTGACGGCAGGCTATATCCTCGCCCGCGTCGACAGAGGCGAGGAAGAGCTCGACCGGCGGATCGTCCATGCGAAGAAGGATCTGGTCACCTGGTCGCCGATCACGGAAAAGCACGTCGGCGGCGCCGGCATGTCCGTGGCCGAGCTCTGCCTGGCGACCGTGACCCTGAGCGACAACACCGCCGCCAATCTGCTGCTCAATAGCTTCGGCGGGCCGGCGGGGCTGACGGCATTTTTGCGCTCCATCGGTGACGAGACCACGCGGCTCGACCGTTTCGAAACCGAGCTGAATGTGCATGAAAAGCCGGGTGACCTGCGCGACACCACGACGCCCGCGGCCATGCTGGAGACGCTGCGCAAGCTTCTCTTCGGTGACGTGCTTTCCCGCTCCTCGCGCGCCCAGCTTGCCGCCTGGATGGTCATGAACAAAACGGGCGACGAAAAATTGCGGGCGGGCTTTCCCGCTGACTGGATGATCGGCGACAAGACCGGAGGCAATGGCGACAAATACGGCAACAGTAACGACGTCGCGGTCGCCTGGTCACCGGACCGGGGCGCCGTCATCGTGTCAGCCTATTGCGAGATACCGTCGGTCTCCGAAAAGGAGCGCGCCGCCATTCTGGCCGAAATCGGGCGGATCGCTTCGCGGGTCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"47921","NCBI_taxonomy_name":"Paramesorhizobium deserti","NCBI_taxonomy_id":"1494590"}}}},"ARO_accession":"3008821","ARO_id":"47613","ARO_name":"PAD-1","CARD_short_name":"PAD-1","ARO_description":"Carbapenem-hydrolyzing class A beta-lactamase PAD-1.","ARO_category":{"46663":{"category_aro_accession":"3007872","category_aro_cvterm_id":"46663","category_aro_name":"PAD beta-lactamase","category_aro_description":"PAD is a family of carbapenem-hydrolyzing class A beta-lactamases which enzymatically inactivate beta-lactam and carbapenem antibiotics.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8240":{"model_id":"8240","model_name":"PAM-5","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11067":{"protein_sequence":{"accession":"WVW91709.1","sequence":"MRFLASLALPLFAANLALAAPKPLPQLEAYEGLQAWLVPVEPLRISDHVWQIGTASISALLVKTDAGAVLIDGGMPQVADHLLANMKKLGVQPQDLRLILHSHAHIDHVGPLAAIKRATGAVLVSNAESAVLLQRGGADDIHFGSGMLFAPLTPERLVQDGETVTLGDTTFTVHFTPGHTPGSMSWTWTDTQDGKPLRIAYADSLSAPGYQLRDNARYPHLVDAFRASFAAVRALPCDLLLTPHAEGSGWDYTNAEKPHPAPVSCKAYADKAEQKLDQMLAEQAKSR"},"dna_sequence":{"accession":"PP331844.1","fmin":"0","fmax":"864","strand":"+","sequence":"ATGCGTTTCCTCGCCAGCCTCGCGCTGCCCCTGTTCGCCGCCAACCTGGCGCTCGCCGCCCCCAAGCCCCTGCCGCAGCTGGAGGCCTATGAAGGGCTGCAAGCCTGGCTGGTGCCGGTGGAACCGCTGCGCATCAGCGACCACGTCTGGCAGATCGGCACCGCCAGCATCAGTGCCCTGCTGGTGAAGACCGACGCCGGCGCGGTGCTCATCGACGGCGGCATGCCCCAGGTGGCCGACCACCTGCTGGCCAATATGAAGAAGCTCGGCGTGCAGCCCCAGGACCTGCGCCTGATCCTCCACAGCCATGCCCACATCGACCACGTCGGCCCACTGGCGGCGATCAAGCGCGCCACCGGTGCCGTGCTGGTGAGCAACGCCGAATCCGCCGTGCTGCTGCAACGTGGCGGCGCCGACGACATCCACTTCGGCAGCGGCATGCTCTTCGCCCCGCTGACGCCCGAGCGCCTGGTGCAGGACGGCGAGACGGTGACCCTGGGCGACACCACCTTCACCGTGCATTTCACCCCGGGCCACACCCCGGGCAGCATGAGCTGGACCTGGACCGACACCCAGGACGGCAAGCCCCTGCGCATCGCCTACGCCGACAGCCTCAGCGCGCCGGGCTACCAACTGCGCGACAACGCCCGCTACCCCCACCTGGTCGACGCCTTCCGTGCCAGCTTCGCCGCCGTCCGCGCCCTGCCCTGCGACCTGCTGCTGACACCCCACGCCGAAGGCAGCGGCTGGGACTACACCAACGCCGAAAAGCCGCACCCGGCCCCGGTGAGCTGCAAGGCCTATGCGGACAAAGCCGAGCAGAAGCTCGACCAGATGCTCGCCGAGCAGGCAAAGTCGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"45944","NCBI_taxonomy_name":"Pseudomonas tohonis","NCBI_taxonomy_id":"2725477"}}}},"ARO_accession":"3008822","ARO_id":"47614","ARO_name":"PAM-5","CARD_short_name":"PAM-5","ARO_description":"Subclass B3 metallo-beta-lactamase PAM-5.","ARO_category":{"45940":{"category_aro_accession":"3007198","category_aro_cvterm_id":"45940","category_aro_name":"PAM beta-lactamase","category_aro_description":"A family of subclass B3 metallo-beta-lactamases discovered in Pseudomonas alcaligenes and found in other members of the Pseudomonas genus. PAM beta-lactamases hydrolyze cephalosporins and carbenems.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8241":{"model_id":"8241","model_name":"PC1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11068":{"protein_sequence":{"accession":"CAA27733.1","sequence":"MKKLIFLIVIALVLSACNSNSSHAKELNDLEKKYNAHIGVYALDTKSGKEVKFNSDKRFAYASTSKAINSAILLEQVPYNKLNKKVHINKDDIVAYSPILEKYVGKDITLKALIEASMTYSDNTANNKIIKEIGGIKKVKQRLKELGDKVTNPVRYEIELNYYSPKSKKDTSTPAAFGKTLNKLIANGKLSKENKKFLLDLMLNNKSGDTLIKDGVPKDYKVADKSGQAITYASRNDVAFVYPKGQSEPIVLVIFTNKDNKSDKPNDKLISETAKSVMKEF"},"dna_sequence":{"accession":"X04121.1","fmin":"139","fmax":"985","strand":"+","sequence":"TTGAAAAAGTTAATATTTTTAATTGTAATTGCTTTAGTTTTAAGTGCATGTAATTCAAACAGTTCACATGCCAAAGAGTTAAATGATTTAGAAAAAAAATATAATGCTCATATTGGTGTTTATGCTTTAGATACTAAAAGTGGTAAGGAAGTAAAATTTAATTCAGATAAGAGATTTGCCTATGCTTCAACTTCAAAAGCGATAAATAGTGCTATTTTGTTAGAACAAGTACCTTATAATAAGTTAAATAAAAAAGTACATATTAACAAAGATGATATAGTTGCTTATTCTCCTATTTTAGAAAAATATGTAGGAAAAGATATCACTTTAAAAGCACTTATTGAGGCTTCAATGACATATAGTGATAATACAGCAAACAATAAAATTATAAAAGAAATCGGTGGAATCAAAAAAGTTAAACAACGTCTAAAAGAACTAGGAGATAAAGTAACAAATCCAGTTAGATATGAGATAGAATTAAATTACTATTCACCAAAGAGCAAAAAAGATACTTCAACACCTGCTGCCTTCGGTAAGACCCTTAATAAACTTATCGCCAATGGAAAATTAAGCAAAGAAAACAAAAAATTCTTACTTGATTTAATGTTAAATAATAAAAGCGGAGATACTTTAATTAAAGACGGTGTTCCAAAAGACTATAAGGTTGCTGATAAAAGTGGTCAAGCAATAACATATGCTTCTAGAAATGATGTTGCTTTTGTTTATCCTAAGGGCCAATCTGAACCTATTGTTTTAGTCATTTTTACGAATAAAGACAATAAAAGTGATAAGCCAAATGATAAGTTGATAAGTGAAACCGCCAAGAGTGTAATGAAGGAATTTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35508","NCBI_taxonomy_name":"Staphylococcus aureus","NCBI_taxonomy_id":"1280"}}}},"ARO_accession":"3008823","ARO_id":"47615","ARO_name":"PC1","CARD_short_name":"PC1","ARO_description":"BlaZ family penicillin-hydrolyzing class A beta-lactamase PC1.","ARO_category":{"41361":{"category_aro_accession":"3004197","category_aro_cvterm_id":"41361","category_aro_name":"BlaZ beta-lactamase","category_aro_description":"BlaZ beta-lactamases are Class A beta-lactamases. These beta-lactamases are responsible for penicillin resistance in Staphylococcus aureus.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8242":{"model_id":"8242","model_name":"PDC-477","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11069":{"protein_sequence":{"accession":"QSG71713.1","sequence":"MRDTRFSCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYTQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"MW672263.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCTCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACACCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCCGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACTCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATTCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008824","ARO_id":"47616","ARO_name":"PDC-477","CARD_short_name":"PDC-477","ARO_description":"Inhibitor-resistant class C beta-lactamase PDC-477.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8243":{"model_id":"8243","model_name":"PDC-478","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11070":{"protein_sequence":{"accession":"QSG71714.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQLPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAESYGVKTSAADLLRFVDANLHPERLNRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"MW672264.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGTCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGCTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAAGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGAACAGGCCATGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008825","ARO_id":"47617","ARO_name":"PDC-478","CARD_short_name":"PDC-478","ARO_description":"Inhibitor-resistant class C beta-lactamase PDC-478.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8244":{"model_id":"8244","model_name":"PDC-479","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11071":{"protein_sequence":{"accession":"QTG68650.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQLPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAKGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"MW805184.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGCTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCAAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008826","ARO_id":"47618","ARO_name":"PDC-479","CARD_short_name":"PDC-479","ARO_description":"Inhibitor-resistant extended-spectrum class C beta-lactamase PDC-479.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8245":{"model_id":"8245","model_name":"PDC-480","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11072":{"protein_sequence":{"accession":"QTG68652.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFIATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNLSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAKGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"MW805186.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCATCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCTGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCAAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008827","ARO_id":"47619","ARO_name":"PDC-480","CARD_short_name":"PDC-480","ARO_description":"Inhibitor-resistant extended-spectrum class C beta-lactamase PDC-480.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8246":{"model_id":"8246","model_name":"PDC-481","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11073":{"protein_sequence":{"accession":"QTG68653.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFTATLAGYALAQNKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVPGPLDAKGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"MW805187.1","fmin":"0","fmax":"1191","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGAACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCCCCGGCCCGCTGGATGCCAAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008828","ARO_id":"47620","ARO_name":"PDC-481","CARD_short_name":"PDC-481","ARO_description":"Inhibitor-resistant extended-spectrum class C beta-lactamase PDC-481.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8247":{"model_id":"8247","model_name":"PDC-482","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11074":{"protein_sequence":{"accession":"QUR41145.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEASADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALTQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPRPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGREQQGKVPLKR"},"dna_sequence":{"accession":"MZ067233.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCTCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGACCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTTCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCCGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCGGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008829","ARO_id":"47621","ARO_name":"PDC-482","CARD_short_name":"PDC-482","ARO_description":"Inhibitor-resistant extended-spectrum class C beta-lactamase PDC-482.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8248":{"model_id":"8248","model_name":"PDC-483","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11075":{"protein_sequence":{"accession":"QUR41146.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNLSIGLFGYLAARSLGQPFERIMEQRLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRQWAQALDATHRGYYKVGDMTQGLGWEAYDWPIALKRLQAGNSTPMALQPHRVARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLTR"},"dna_sequence":{"accession":"MZ067234.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTGGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGTTATGGGCTGGCGTCGAAAGAGGACGGTCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAAGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTACACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCTGAGCATCGGTCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAGCGGATCATGGAGCAGCGCCTGTTCCCGGCCCTGGGCCTCGAACAGACTCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTCCGGGTCGGCCCCGGCCCACTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGACTGGACCGGCAGTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCGCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGGTCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGACGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008830","ARO_id":"47622","ARO_name":"PDC-483","CARD_short_name":"PDC-483","ARO_description":"Inhibitor-resistant class C beta-lactamase PDC-483.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8249":{"model_id":"8249","model_name":"PDC-484","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11076":{"protein_sequence":{"accession":"QWW93428.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQLPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNLSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"MZ424298.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGTCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGCTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCTGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCATGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008831","ARO_id":"47623","ARO_name":"PDC-484","CARD_short_name":"PDC-484","ARO_description":"Class C beta-lactamase PDC-484.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8250":{"model_id":"8250","model_name":"PDC-485","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11077":{"protein_sequence":{"accession":"QWW93429.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTYLDVPEAALAQYAQGYGKDDRPLQAGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"MZ424299.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGTCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCTACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCCCTACAGGCCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008832","ARO_id":"47624","ARO_name":"PDC-485","CARD_short_name":"PDC-485","ARO_description":"Class C beta-lactamase PDC-485.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8251":{"model_id":"8251","model_name":"PDC-486","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11078":{"protein_sequence":{"accession":"QWW93430.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQSYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAHAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"MZ424300.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGTCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGAGCTACGGCAAGGACGACCGCCCCCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGATTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCCACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008833","ARO_id":"47625","ARO_name":"PDC-486","CARD_short_name":"PDC-486","ARO_description":"Class C beta-lactamase PDC-486.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8252":{"model_id":"8252","model_name":"PDC-487","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11079":{"protein_sequence":{"accession":"QWW93431.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLTSKEDGRRVTPETLFEIGSVSKTFTATLAGYALTQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAGGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"MZ424301.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGACCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGACCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGGAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCACTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008834","ARO_id":"47626","ARO_name":"PDC-487","CARD_short_name":"PDC-487","ARO_description":"Inhibitor-resistant extended-spectrum class C beta-lactamase PDC-487.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8253":{"model_id":"8253","model_name":"PDC-488","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11080":{"protein_sequence":{"accession":"QWW93432.1","sequence":"MRDTRFPCLCGIAASTLLFAATPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLRFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNLSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"MZ424302.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCGCCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCATTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCGGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCTGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCTAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTATGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008835","ARO_id":"47627","ARO_name":"PDC-488","CARD_short_name":"PDC-488","ARO_description":"Class C beta-lactamase PDC-488.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8254":{"model_id":"8254","model_name":"PDC-489","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11081":{"protein_sequence":{"accession":"QYZ75852.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPDPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"MZ701696.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCTTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGACCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATTCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008836","ARO_id":"47628","ARO_name":"PDC-489","CARD_short_name":"PDC-489","ARO_description":"Class C beta-lactamase PDC-489.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8255":{"model_id":"8255","model_name":"PDC-490","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11082":{"protein_sequence":{"accession":"QYZ75853.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYTQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"MZ701697.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAACTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACACCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008837","ARO_id":"47629","ARO_name":"PDC-490","CARD_short_name":"PDC-490","ARO_description":"Class C beta-lactamase PDC-490.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8256":{"model_id":"8256","model_name":"PDC-491","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11083":{"protein_sequence":{"accession":"QYZ75854.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMAPQPHRIARLPAPQALKGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"MZ701698.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCCGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGAAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008838","ARO_id":"47630","ARO_name":"PDC-491","CARD_short_name":"PDC-491","ARO_description":"Class C beta-lactamase PDC-491.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8257":{"model_id":"8257","model_name":"PDC-492","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11084":{"protein_sequence":{"accession":"QYZ75855.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPLERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"MZ701699.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTAGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGCTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCACTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008839","ARO_id":"47631","ARO_name":"PDC-492","CARD_short_name":"PDC-492","ARO_description":"Class C beta-lactamase PDC-492.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8258":{"model_id":"8258","model_name":"PDC-493","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11085":{"protein_sequence":{"accession":"QYZ75856.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGLLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"MZ701700.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTAGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCTGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCACTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008840","ARO_id":"47632","ARO_name":"PDC-493","CARD_short_name":"PDC-493","ARO_description":"Class C beta-lactamase PDC-493.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8259":{"model_id":"8259","model_name":"PDC-494","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11086":{"protein_sequence":{"accession":"QYZ75857.1","sequence":"MRDTRFPCLCGIAASTLLFADTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"MZ701701.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCGACACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCATTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCTAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTATGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008841","ARO_id":"47633","ARO_name":"PDC-494","CARD_short_name":"PDC-494","ARO_description":"Class C beta-lactamase PDC-494.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8260":{"model_id":"8260","model_name":"PDC-495","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11087":{"protein_sequence":{"accession":"QYZ75858.1","sequence":"MRDTRFPCLCGIAASTLLFAATSAIAGEAPADRLKTLVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASLHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYTPGSQRLYSNPSIGLFGYLAARSLGQPFERIMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDKPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQAPEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"MZ701702.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCCTCCACACTGCTGTTCGCCGCCACCTCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGACACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGATATTCCGGGCCTGGCCGTGGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCTTCGAAAGAGGACGGTCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGTGCCAGCCTGCACTGGCCGGCGCTGCAAGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAAGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACACGCCGGGCAGCCAGCGCCTCTACTCCAACCCGAGCATCGGTCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGATCATGGAGCAGCAACTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTATGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAAGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCGGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGACTGCCCGCGCCACAGGCGCCGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATCCCAGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAATTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008842","ARO_id":"47634","ARO_name":"PDC-495","CARD_short_name":"PDC-495","ARO_description":"Class C beta-lactamase PDC-495.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8261":{"model_id":"8261","model_name":"PDC-496","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11088":{"protein_sequence":{"accession":"QYZ75859.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLYPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"MZ701703.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTAGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGTATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008843","ARO_id":"47635","ARO_name":"PDC-496","CARD_short_name":"PDC-496","ARO_description":"Class C beta-lactamase PDC-496.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8262":{"model_id":"8262","model_name":"PDC-497","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11089":{"protein_sequence":{"accession":"UAX43329.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAKGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"MZ895127.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAACTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCAAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008844","ARO_id":"47636","ARO_name":"PDC-497","CARD_short_name":"PDC-497","ARO_description":"Inhibitor-resistant extended-spectrum class C beta-lactamase PDC-497.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8263":{"model_id":"8263","model_name":"PDC-498","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11090":{"protein_sequence":{"accession":"UGN25765.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTVTLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIVRLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"OL516038.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGTCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAACTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGTCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008845","ARO_id":"47637","ARO_name":"PDC-498","CARD_short_name":"PDC-498","ARO_description":"Class C beta-lactamase PDC-498.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8264":{"model_id":"8264","model_name":"PDC-499","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11091":{"protein_sequence":{"accession":"UGN25766.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRAGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTSGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"OL516039.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGATGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGCCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACTCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAGCGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008846","ARO_id":"47638","ARO_name":"PDC-499","CARD_short_name":"PDC-499","ARO_description":"Class C beta-lactamase PDC-499.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8265":{"model_id":"8265","model_name":"PDC-500","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11092":{"protein_sequence":{"accession":"UGN25767.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIDLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQPKVPLKR"},"dna_sequence":{"accession":"OL516040.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGACCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGCCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008847","ARO_id":"47639","ARO_name":"PDC-500","CARD_short_name":"PDC-500","ARO_description":"Inhibitor-resistant class C beta-lactamase PDC-500.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8266":{"model_id":"8266","model_name":"PDC-501","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11093":{"protein_sequence":{"accession":"UGW32402.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPSPLDAESYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTSGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"OL774881.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCAGCCCGCTGGATGCCGAAAGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAGCGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008848","ARO_id":"47640","ARO_name":"PDC-501","CARD_short_name":"PDC-501","ARO_description":"Class C beta-lactamase PDC-501.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8267":{"model_id":"8267","model_name":"PDC-502","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11094":{"protein_sequence":{"accession":"UGW32403.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRRYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRAGPGPLDAEAYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"OL774882.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGTCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCGCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGCCGGTCCCGGCCCGCTGGATGCCGAAGCCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008849","ARO_id":"47641","ARO_name":"PDC-502","CARD_short_name":"PDC-502","ARO_description":"Class C beta-lactamase PDC-502.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8268":{"model_id":"8268","model_name":"PDC-503","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11095":{"protein_sequence":{"accession":"UGW32404.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDDISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPPRAGPGPLGAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"OL774883.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGACATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCCACGGGCCGGTCCCGGCCCGCTGGGTGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008850","ARO_id":"47642","ARO_name":"PDC-503","CARD_short_name":"PDC-503","ARO_description":"Class C beta-lactamase PDC-503.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8269":{"model_id":"8269","model_name":"PDC-504","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11096":{"protein_sequence":{"accession":"UGW32405.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDDISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPPRVGPGPLGAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"OL774884.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGACATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCCACGGGTCGGTCCCGGCCCGCTGGGTGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008851","ARO_id":"47643","ARO_name":"PDC-504","CARD_short_name":"PDC-504","ARO_description":"Class C beta-lactamase PDC-504.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8270":{"model_id":"8270","model_name":"PDC-505","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11097":{"protein_sequence":{"accession":"UGW32406.1","sequence":"MRDTRFPCLCGIAASTLLFAATPAIAGEAPADRLKALVDAAVQPAMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLRFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRAGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"OL774885.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCGCCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCATTGGTCGACGCCGCCGTACAACCGGCGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCGGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGCCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCTAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTATGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008852","ARO_id":"47644","ARO_name":"PDC-505","CARD_short_name":"PDC-505","ARO_description":"Class C beta-lactamase PDC-505.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8271":{"model_id":"8271","model_name":"PDC-506","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11098":{"protein_sequence":{"accession":"UGW32407.1","sequence":"MRDTRFPCLCGIAASTLLFAATPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERIMEQRLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRAGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRQWAQALDATHRGYYKVGDMTQGLGWEAYDWPIALKRLQAGNSTPMALQPHRVARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLAR"},"dna_sequence":{"accession":"OL774886.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCGCCACCCCGGCCATTGCCGGCGAGGCCCCTGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTGGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGTTATGGGCTGGCGTCGAAAGAGGACGGTCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAAGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTACACCGCCGGCGGCTTGCCGCTTCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGTCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAGCGGATCATGGAGCAGCGCCTGTTCCCGGCCCTGGGCCTCGAACAGACTCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTCCGGGCCGGCCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGACTGGACCGGCAGTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCGCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGGTCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGGCGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008853","ARO_id":"47645","ARO_name":"PDC-506","CARD_short_name":"PDC-506","ARO_description":"Class C beta-lactamase PDC-506.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8272":{"model_id":"8272","model_name":"PDC-507","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11099":{"protein_sequence":{"accession":"UHO07588.1","sequence":"MRDTRFPCLCGIAASTLLFAATPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQPKVPLKR"},"dna_sequence":{"accession":"OL901277.1","fmin":"0","fmax":"1173","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCGCCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGCCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008854","ARO_id":"47646","ARO_name":"PDC-507","CARD_short_name":"PDC-507","ARO_description":"Class C beta-lactamase PDC-507.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8273":{"model_id":"8273","model_name":"PDC-508","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11100":{"protein_sequence":{"accession":"UHO07593.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRVSQHWPALQGSRFDGISLLDLATYTAGGLPLKFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLKQTHLDVPEAALAQYAQGYGKDDRPLRAGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTSGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"OL989851.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTAGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGTCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGAAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCAAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCCCTACGGGCCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAGCGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008855","ARO_id":"47647","ARO_name":"PDC-508","CARD_short_name":"PDC-508","ARO_description":"Class C beta-lactamase PDC-508.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8274":{"model_id":"8274","model_name":"PDC-509","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11101":{"protein_sequence":{"accession":"UHO07595.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRAGPSPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"OL989853.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTAGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCCCTACGGGCCGGTCCCAGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATCCCGGGCCGCGACCTGGGGCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008856","ARO_id":"47648","ARO_name":"PDC-509","CARD_short_name":"PDC-509","ARO_description":"Class C beta-lactamase PDC-509.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8275":{"model_id":"8275","model_name":"PDC-510","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11102":{"protein_sequence":{"accession":"UKA98423.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIDLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPIAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"OM368331.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGACCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCATTGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008857","ARO_id":"47649","ARO_name":"PDC-510","CARD_short_name":"PDC-510","ARO_description":"Inhibitor-resistant class C beta-lactamase PDC-510.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8276":{"model_id":"8276","model_name":"PDC-511","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11103":{"protein_sequence":{"accession":"UKA98424.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMAPQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"OM368332.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGATGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACTCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCCGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008858","ARO_id":"47650","ARO_name":"PDC-511","CARD_short_name":"PDC-511","ARO_description":"Class C beta-lactamase PDC-511.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8277":{"model_id":"8277","model_name":"PDC-512","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11104":{"protein_sequence":{"accession":"ULU82598.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFTATLAGYALAQGKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRAGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"OM572560.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGGCAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGATGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGCCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACTCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008859","ARO_id":"47651","ARO_name":"PDC-512","CARD_short_name":"PDC-512","ARO_description":"Class C beta-lactamase PDC-512.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8278":{"model_id":"8278","model_name":"PDC-513","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11105":{"protein_sequence":{"accession":"ULU82665.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALTQDKMRLDDRASQHWPALQGSHFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRRYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"OM681519.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGACCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCACTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCGCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008860","ARO_id":"47652","ARO_name":"PDC-513","CARD_short_name":"PDC-513","ARO_description":"Class C beta-lactamase PDC-513.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8279":{"model_id":"8279","model_name":"PDC-514","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11106":{"protein_sequence":{"accession":"UMO60339.1","sequence":"MRDTRFPCLCGIAASTLLFAATPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGSLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"OM813005.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCGCCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCATTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCTCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCTAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTATGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008861","ARO_id":"47653","ARO_name":"PDC-514","CARD_short_name":"PDC-514","ARO_description":"Class C beta-lactamase PDC-514.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8280":{"model_id":"8280","model_name":"PDC-515","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11107":{"protein_sequence":{"accession":"UMO60340.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAKGYGVKTSAADLLRFVDANLHPERLDRLWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"OM813006.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTTCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCAAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCTCTGGGCGCAGGCGCTTGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008862","ARO_id":"47654","ARO_name":"PDC-515","CARD_short_name":"PDC-515","ARO_description":"Inhibitor-resistant extended-spectrum class C beta-lactamase PDC-515.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8281":{"model_id":"8281","model_name":"PDC-516","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11108":{"protein_sequence":{"accession":"UMO60341.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLNAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"OM813007.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCTTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGAATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATTCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008863","ARO_id":"47655","ARO_name":"PDC-516","CARD_short_name":"PDC-516","ARO_description":"Class C beta-lactamase PDC-516.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8282":{"model_id":"8282","model_name":"PDC-517","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11109":{"protein_sequence":{"accession":"UNZ81761.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQDYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPITLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"ON053203.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTTATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGACTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCCGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCACCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008864","ARO_id":"47656","ARO_name":"PDC-517","CARD_short_name":"PDC-517","ARO_description":"Class C beta-lactamase PDC-517.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8283":{"model_id":"8283","model_name":"PDC-518","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11110":{"protein_sequence":{"accession":"UOU25743.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGQGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"ON191577.1","fmin":"0","fmax":"1182","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTAGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008865","ARO_id":"47657","ARO_name":"PDC-518","CARD_short_name":"PDC-518","ARO_description":"Class C beta-lactamase PDC-518.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8284":{"model_id":"8284","model_name":"PDC-519","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11111":{"protein_sequence":{"accession":"URY98700.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALTQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"ON713451.1","fmin":"0","fmax":"1197","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGACCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTATGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008866","ARO_id":"47658","ARO_name":"PDC-519","CARD_short_name":"PDC-519","ARO_description":"Inhibitor-resistant cephalosporin-hydrolyzing class C beta-lactamase PDC-519.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8285":{"model_id":"8285","model_name":"PDC-520","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11112":{"protein_sequence":{"accession":"UTQ48800.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDRAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRAGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"ON960903.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCGGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGCCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008867","ARO_id":"47659","ARO_name":"PDC-520","CARD_short_name":"PDC-520","ARO_description":"Class C beta-lactamase PDC-520.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8286":{"model_id":"8286","model_name":"PDC-521","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11113":{"protein_sequence":{"accession":"UTS94203.1","sequence":"MRDTGFPCLCGIAASTLLFAATSAIAGEAPADRLKTLVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASLHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYTPGSQRLYSNPSIGLFGYLAARSLGQPFERIMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDKPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSSLEQQGKVPLKR"},"dna_sequence":{"accession":"ON651450.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCGGATTCCCCTGCCTGTGCGGCATCGCCGCCTCCACACTGCTGTTCGCCGCCACCTCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGACACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGATATTCCGGGCCTGGCCGTGGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCTTCGAAAGAGGACGGTCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCTGCACTGGCCGGCGCTGCAAGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAAGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACACGCCGGGCAGCCAGCGCCTCTACTCCAACCCGAGCATCGGTCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGATCATGGAGCAGCAACTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCTCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAAGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCGGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGACTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGTCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCTGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCAGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008868","ARO_id":"47660","ARO_name":"PDC-521","CARD_short_name":"PDC-521","ARO_description":"Class C beta-lactamase PDC-521.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8287":{"model_id":"8287","model_name":"PDC-522","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11114":{"protein_sequence":{"accession":"UTS94204.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDERASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"ON651451.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGAGCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008869","ARO_id":"47661","ARO_name":"PDC-522","CARD_short_name":"PDC-522","ARO_description":"Class C beta-lactamase PDC-522.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8288":{"model_id":"8288","model_name":"PDC-523","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11115":{"protein_sequence":{"accession":"UTS94205.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"ON651452.1","fmin":"0","fmax":"1137","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGTCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008870","ARO_id":"47662","ARO_name":"PDC-523","CARD_short_name":"PDC-523","ARO_description":"Class C beta-lactamase PDC-523.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8289":{"model_id":"8289","model_name":"PDC-524","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11116":{"protein_sequence":{"accession":"UTS94206.1","sequence":"MRDTRFPCLCGIAASTLLFTATPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERIMEQRLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRQWAQALDATHRGYYKVGDMTQGLGWEAYDWPIALKRLQAGNSTPMALQPHRVARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPSRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLAR"},"dna_sequence":{"accession":"ON651453.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCACCGCCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTGGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGTTATGGGCTGGCGTCGAAAGAGGACGGTCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAAGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTACACCGCCGGCGGCTTGCCGCTTCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGTCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAGCGGATCATGGAGCAGCGCCTGTTCCCGGCCCTGGGCCTCGAACAGACTCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTCCGGGTCGGCCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGACTGGACCGGCAGTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCGCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGGTCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATCCCGAGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGGCGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008871","ARO_id":"47663","ARO_name":"PDC-524","CARD_short_name":"PDC-524","ARO_description":"Class C beta-lactamase PDC-524.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8290":{"model_id":"8290","model_name":"PDC-525","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11117":{"protein_sequence":{"accession":"UTS94207.1","sequence":"MRDTGFPCLCGIAASTLLFAATSAIAGEAPADRLKTLVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASLHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYTPGSQRLYSNPSIGLFGYLAARSLDQPFERIMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDKPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"ON651454.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCGGATTCCCCTGCCTGTGCGGCATCGCCGCCTCCACACTGCTGTTCGCCGCCACCTCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGACACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGATATTCCGGGCCTGGCCGTGGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCTTCGAAAGAGGACGGTCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCTGCACTGGCCGGCGCTGCAAGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAAGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACACGCCGGGCAGCCAGCGCCTCTACTCCAACCCGAGCATCGGTCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGACCAGCCGTTCGAACGGATCATGGAGCAGCAACTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCTCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAAGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCGGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGACTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGTCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATCCCAGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAATTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008872","ARO_id":"47664","ARO_name":"PDC-525","CARD_short_name":"PDC-525","ARO_description":"Class C beta-lactamase PDC-525.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8291":{"model_id":"8291","model_name":"PDC-526","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11118":{"protein_sequence":{"accession":"UTS94208.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERIMEQRLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRQWAQALDATHRGYYKVGDMTQGLGWEAYDWPIALKRLQAGNSTPMALQPHRVARLPAPQALEGQRLLNKPGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLAR"},"dna_sequence":{"accession":"ON651455.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAAGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTACACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGTCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAGCGGATCATGGAGCAGCGCCTGTTCCCGGCCCTGGGCCTCGAACAGACTCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTCCGGGTCGGCCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGACTGGACCGGCAGTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCGCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGGTCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGCCCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGGCGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008873","ARO_id":"47665","ARO_name":"PDC-526","CARD_short_name":"PDC-526","ARO_description":"Class C beta-lactamase PDC-526.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8292":{"model_id":"8292","model_name":"PDC-527","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11119":{"protein_sequence":{"accession":"UTS94209.1","sequence":"MRDTRFPCLCGIAASTLLFTATPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERIMEQRLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRQWAQALDATHRGYYKVGDMTQGLGWEAYDWPIALKRLQAGNSTPMALQPHRVARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAIFSGLEQQAKVPLAR"},"dna_sequence":{"accession":"ON651456.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCACCGCCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTGGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGTTATGGGCTGGCGTCGAAAGAGGACGGTCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAAGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTACACCGCCGGCGGCTTGCCGCTTCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGTCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAGCGGATCATGGAGCAGCGCCTGTTCCCGGCCCTGGGCCTCGAACAGACTCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTCCGGGTCGGCCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGACTGGACCGGCAGTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCGCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGGTCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCTTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGGCGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008874","ARO_id":"47666","ARO_name":"PDC-527","CARD_short_name":"PDC-527","ARO_description":"Class C beta-lactamase PDC-527.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8293":{"model_id":"8293","model_name":"PDC-528","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11120":{"protein_sequence":{"accession":"UUM03669.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTVTLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"OP131853.1","fmin":"0","fmax":"1137","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGTCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAACTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008875","ARO_id":"47667","ARO_name":"PDC-528","CARD_short_name":"PDC-528","ARO_description":"Class C beta-lactamase PDC-528.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8294":{"model_id":"8294","model_name":"PDC-529","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11121":{"protein_sequence":{"accession":"UUM03670.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERIMEQRLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRQWAQALDATHRGYYKVGDMTQGLGWEAYDWPIALKRLQAGNSTPMALQPHRVARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLAR"},"dna_sequence":{"accession":"OP131854.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAAGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGTCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAGCGGATCATGGAGCAGCGCCTGTTCCCGGCCCTGGGCCTCGAACAGACTCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTCCGGGTCGGCCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGACTGGACCGGCAGTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCGCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGGTCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGGCGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008876","ARO_id":"47668","ARO_name":"PDC-529","CARD_short_name":"PDC-529","ARO_description":"Class C beta-lactamase PDC-529.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8295":{"model_id":"8295","model_name":"PDC-530","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11122":{"protein_sequence":{"accession":"UUM03671.1","sequence":"MRDTGFPCLCGIAASTLLFAATSAIAGEAPADRLKTLVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLAAKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASLHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRRWQPTYTPGSQRLYSNPSIGLFGYLAARSLGQPFERIMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDKPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"OP131855.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCGGATTCCCCTGCCTGTGCGGCATCGCCGCCTCCACACTGCTGTTCGCCGCCACCTCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGACACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGATATTCCGGGCCTGGCCGTGGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCTGCGAAAGAGGACGGTCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCTGCACTGGCCGGCGCTGCAAGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAAGACCAGGCACAGATCCGCGACTACTACCGCCGGTGGCAGCCGACCTACACGCCGGGCAGCCAGCGCCTCTACTCCAACCCGAGCATCGGTCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGATCATGGAGCAGCAACTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGTTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAAGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCGGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGACTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGTCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATCCCAGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAATTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008877","ARO_id":"47669","ARO_name":"PDC-530","CARD_short_name":"PDC-530","ARO_description":"Class C beta-lactamase PDC-530.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8296":{"model_id":"8296","model_name":"PDC-531","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11123":{"protein_sequence":{"accession":"UVB72393.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIDLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRLWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"OP219677.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTTCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGACCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCTCTGGGCGCAGGCGCTTGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008878","ARO_id":"47670","ARO_name":"PDC-531","CARD_short_name":"PDC-531","ARO_description":"Inhibitor-resistant class C beta-lactamase PDC-531.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8297":{"model_id":"8297","model_name":"PDC-532","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11124":{"protein_sequence":{"accession":"UWQ12886.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKGQAQIRDYYRQWQPTYAPGSQRRYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"OP381061.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGTCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGGCCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCGCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008879","ARO_id":"47671","ARO_name":"PDC-532","CARD_short_name":"PDC-532","ARO_description":"Class C beta-lactamase PDC-532.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8298":{"model_id":"8298","model_name":"PDC-533","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11125":{"protein_sequence":{"accession":"UWQ12887.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALTQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPIAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"OP381062.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGACCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTTCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCATTGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008880","ARO_id":"47672","ARO_name":"PDC-533","CARD_short_name":"PDC-533","ARO_description":"Class C beta-lactamase PDC-533.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8299":{"model_id":"8299","model_name":"PDC-534","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11126":{"protein_sequence":{"accession":"UZQ18791.1","sequence":"MRDTRFPCLCGIAASTLLFAATPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPCPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQPKVPLKR"},"dna_sequence":{"accession":"OP806891.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCGCCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCTGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGCCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008881","ARO_id":"47673","ARO_name":"PDC-534","CARD_short_name":"PDC-534","ARO_description":"Class C beta-lactamase PDC-534.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8300":{"model_id":"8300","model_name":"PDC-535","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11127":{"protein_sequence":{"accession":"UZQ18792.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNLSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"OP806892.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCTGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008882","ARO_id":"47674","ARO_name":"PDC-535","CARD_short_name":"PDC-535","ARO_description":"Class C beta-lactamase PDC-535.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8301":{"model_id":"8301","model_name":"PDC-536","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11128":{"protein_sequence":{"accession":"UZQ18793.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTVTLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPIAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"OP806893.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGTCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAACTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCATTGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008883","ARO_id":"47675","ARO_name":"PDC-536","CARD_short_name":"PDC-536","ARO_description":"Class C beta-lactamase PDC-536.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8302":{"model_id":"8302","model_name":"PDC-537","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11129":{"protein_sequence":{"accession":"MCU9339802.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNLSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAKGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"JAOVCH010000012.1","fmin":"118584","fmax":"119778","strand":"-","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCTGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCAAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008884","ARO_id":"47676","ARO_name":"PDC-537","CARD_short_name":"PDC-537","ARO_description":"Inhibitor-resistant extended-spectrum class C beta-lactamase PDC-537.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8303":{"model_id":"8303","model_name":"PDC-538","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11130":{"protein_sequence":{"accession":"WAW84756.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALTQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPSPLDAEGYGVKTSAADLLRFVDANLHPERLDKPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"OQ060500.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGACCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAATGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCAGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAAGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCACTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATCCCGGGCCGCGACTTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008885","ARO_id":"47677","ARO_name":"PDC-538","CARD_short_name":"PDC-538","ARO_description":"Class C beta-lactamase PDC-538.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8304":{"model_id":"8304","model_name":"PDC-539","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11131":{"protein_sequence":{"accession":"WAW84757.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGTLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"OQ060501.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCATCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCACGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008886","ARO_id":"47678","ARO_name":"PDC-539","CARD_short_name":"PDC-539","ARO_description":"Class C beta-lactamase PDC-539.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8305":{"model_id":"8305","model_name":"PDC-540","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11132":{"protein_sequence":{"accession":"WDE35084.1","sequence":"MRDTRFPCLCGIAASTLLFAATPAIAGEAPADRLKALVDAAVQPAMKANDIPGMAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRAGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"OQ408540.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCGCCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCATTGGTCGACGCCGCCGTACAACCGGCGATGAAGGCCAATGACATTCCGGGCATGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGCCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCTAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTATGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008887","ARO_id":"47679","ARO_name":"PDC-540","CARD_short_name":"PDC-540","ARO_description":"Class C beta-lactamase PDC-540.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8306":{"model_id":"8306","model_name":"PDC-541","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11133":{"protein_sequence":{"accession":"WDE35085.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASNGRQVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"OQ408541.1","fmin":"0","fmax":"1188","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008888","ARO_id":"47680","ARO_name":"PDC-541","CARD_short_name":"PDC-541","ARO_description":"Class C beta-lactamase PDC-541.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8307":{"model_id":"8307","model_name":"PDC-542","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11134":{"protein_sequence":{"accession":"WDE35086.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDRAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTYLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPITLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"OQ408542.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCGGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCTACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCCGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCACCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008889","ARO_id":"47681","ARO_name":"PDC-542","CARD_short_name":"PDC-542","ARO_description":"Class C beta-lactamase PDC-542.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8308":{"model_id":"8308","model_name":"PDC-543","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11135":{"protein_sequence":{"accession":"WEG44941.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALTQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLNRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"OQ592377.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGACCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGAACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008890","ARO_id":"47682","ARO_name":"PDC-543","CARD_short_name":"PDC-543","ARO_description":"Class C beta-lactamase PDC-543.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8309":{"model_id":"8309","model_name":"PDC-544","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11136":{"protein_sequence":{"accession":"WEG44942.1","sequence":"MRDTRFPCLCGIAASTLLFATTPTIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALTQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDGRPLRAGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"OQ592378.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGACCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGACCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGTTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGGCCGCCCGCTACGGGCCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008891","ARO_id":"47683","ARO_name":"PDC-544","CARD_short_name":"PDC-544","ARO_description":"Class C beta-lactamase PDC-544.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8310":{"model_id":"8310","model_name":"PDC-545","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11137":{"protein_sequence":{"accession":"WEG44943.1","sequence":"MRDTRFPCLCGIAASTLLFAATPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRAGLGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"OQ592379.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCGCCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCATTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCAGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGCCGGTCTCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCTAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTATGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008892","ARO_id":"47684","ARO_name":"PDC-545","CARD_short_name":"PDC-545","ARO_description":"Class C beta-lactamase PDC-545.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8311":{"model_id":"8311","model_name":"PDC-546","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11138":{"protein_sequence":{"accession":"MDF1649292.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLEALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"JARGMM010000012.1","fmin":"118637","fmax":"119831","strand":"-","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGGAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGTCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCCCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008893","ARO_id":"47685","ARO_name":"PDC-546","CARD_short_name":"PDC-546","ARO_description":"Class C beta-lactamase PDC-546.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8312":{"model_id":"8312","model_name":"PDC-547","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11139":{"protein_sequence":{"accession":"MDF2239218.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNDFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"JARHLA010000011.1","fmin":"85708","fmax":"86902","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGTTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGACTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008894","ARO_id":"47686","ARO_name":"PDC-547","CARD_short_name":"PDC-547","ARO_description":"Class C beta-lactamase PDC-547.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8313":{"model_id":"8313","model_name":"PDC-548","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11140":{"protein_sequence":{"accession":"WFG63533.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGQLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"OQ726057.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGTCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCAGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCAATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAGCCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008895","ARO_id":"47687","ARO_name":"PDC-548","CARD_short_name":"PDC-548","ARO_description":"Class C beta-lactamase PDC-548.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8314":{"model_id":"8314","model_name":"PDC-549","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11141":{"protein_sequence":{"accession":"WFG63534.1","sequence":"MRDTRFPCLCGIAASTLLFAATPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQLPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQPKVPLKR"},"dna_sequence":{"accession":"OQ726058.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCGCCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGCTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGCCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008896","ARO_id":"47688","ARO_name":"PDC-549","CARD_short_name":"PDC-549","ARO_description":"Class C beta-lactamase PDC-549.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8315":{"model_id":"8315","model_name":"PDC-550","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11142":{"protein_sequence":{"accession":"WFG63535.1","sequence":"MRDTRFPCLCGIAASTLLFAATPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIDLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQPKVPLKR"},"dna_sequence":{"accession":"OQ726059.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCGCCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGACCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGCCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008897","ARO_id":"47689","ARO_name":"PDC-550","CARD_short_name":"PDC-550","ARO_description":"Class C beta-lactamase PDC-550.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8316":{"model_id":"8316","model_name":"PDC-551","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11143":{"protein_sequence":{"accession":"WFG63536.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQLPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRLWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"OQ726060.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTTCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGCTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCTCTGGGCGCAGGCGCTTGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008898","ARO_id":"47690","ARO_name":"PDC-551","CARD_short_name":"PDC-551","ARO_description":"Class C beta-lactamase PDC-551.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8317":{"model_id":"8317","model_name":"PDC-552","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11144":{"protein_sequence":{"accession":"WFG63537.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFIATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"OQ726061.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCATCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGTCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCAATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAGCCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008899","ARO_id":"47691","ARO_name":"PDC-552","CARD_short_name":"PDC-552","ARO_description":"Class C beta-lactamase PDC-552.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8318":{"model_id":"8318","model_name":"PDC-553","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11145":{"protein_sequence":{"accession":"WJR95504.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"OR206050.1","fmin":"0","fmax":"1188","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCTTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATTCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008900","ARO_id":"47692","ARO_name":"PDC-553","CARD_short_name":"PDC-553","ARO_description":"Class C beta-lactamase PDC-553.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8319":{"model_id":"8319","model_name":"PDC-554","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11146":{"protein_sequence":{"accession":"WKB14826.1","sequence":"MRDTRFPCLCGIAASTLLFAATPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAKGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"OR232964.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCGCCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCATTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCAAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCTAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTATGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008901","ARO_id":"47693","ARO_name":"PDC-554","CARD_short_name":"PDC-554","ARO_description":"Class C beta-lactamase PDC-554.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8320":{"model_id":"8320","model_name":"PDC-555","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11147":{"protein_sequence":{"accession":"WKB14827.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"OR232965.1","fmin":"0","fmax":"1182","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCTTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATTCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008902","ARO_id":"47694","ARO_name":"PDC-555","CARD_short_name":"PDC-555","ARO_description":"Class C beta-lactamase PDC-555.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8321":{"model_id":"8321","model_name":"PDC-556","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11148":{"protein_sequence":{"accession":"WKB14828.1","sequence":"MRDTRFSCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAKGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"OR232966.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCTCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCAAAGGCTACGGGGTGAAGACCAGCGCCGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACTCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATTCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008903","ARO_id":"47695","ARO_name":"PDC-556","CARD_short_name":"PDC-556","ARO_description":"Class C beta-lactamase PDC-556.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8322":{"model_id":"8322","model_name":"PDC-557","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11149":{"protein_sequence":{"accession":"WKB14829.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGSLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPQRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"OR232967.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCATTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTGGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGTTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCATCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCTCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACTCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACAGAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATTCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008904","ARO_id":"47696","ARO_name":"PDC-557","CARD_short_name":"PDC-557","ARO_description":"Class C beta-lactamase PDC-557.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8323":{"model_id":"8323","model_name":"PDC-558","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11150":{"protein_sequence":{"accession":"WKB14830.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQLPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAKGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"OR232968.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTAGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGCTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCAAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008905","ARO_id":"47697","ARO_name":"PDC-558","CARD_short_name":"PDC-558","ARO_description":"Class C beta-lactamase PDC-558.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8324":{"model_id":"8324","model_name":"PDC-559","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11151":{"protein_sequence":{"accession":"WKB14831.1","sequence":"MRDTRFPCLCGIAASTLLFAATPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFIATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAKGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"OR232969.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCGCCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCATTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCATCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCAAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCTAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTATGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008906","ARO_id":"47698","ARO_name":"PDC-559","CARD_short_name":"PDC-559","ARO_description":"Class C beta-lactamase PDC-559.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8325":{"model_id":"8325","model_name":"PDC-560","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11152":{"protein_sequence":{"accession":"WKB14832.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRAGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTSGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"OR232970.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCACGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGCCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAGCGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008907","ARO_id":"47699","ARO_name":"PDC-560","CARD_short_name":"PDC-560","ARO_description":"Class C beta-lactamase PDC-560.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8326":{"model_id":"8326","model_name":"PDC-561","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11153":{"protein_sequence":{"accession":"WKB14833.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFDIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQLPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"OR232971.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATTGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGACGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTGGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGATATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGCTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAACTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATTCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008908","ARO_id":"47700","ARO_name":"PDC-561","CARD_short_name":"PDC-561","ARO_description":"Class C beta-lactamase PDC-561.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8327":{"model_id":"8327","model_name":"PDC-562","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11154":{"protein_sequence":{"accession":"WKB14834.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMAHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"OR232972.1","fmin":"0","fmax":"1185","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGTTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008909","ARO_id":"47701","ARO_name":"PDC-562","CARD_short_name":"PDC-562","ARO_description":"Class C beta-lactamase PDC-562.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8328":{"model_id":"8328","model_name":"PDC-563","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11155":{"protein_sequence":{"accession":"WKB14835.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDADGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"OR232973.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTAGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGACGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008910","ARO_id":"47702","ARO_name":"PDC-563","CARD_short_name":"PDC-563","ARO_description":"Class C beta-lactamase PDC-563.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8329":{"model_id":"8329","model_name":"PDC-564","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11156":{"protein_sequence":{"accession":"WLF01983.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPLERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"OR387360.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGTCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGCTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCAATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAGCCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008911","ARO_id":"47703","ARO_name":"PDC-564","CARD_short_name":"PDC-564","ARO_description":"Class C beta-lactamase PDC-564.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8330":{"model_id":"8330","model_name":"PDC-565","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11157":{"protein_sequence":{"accession":"WLF01984.1","sequence":"MRDTRLPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"OR387361.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGACTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCACGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008912","ARO_id":"47704","ARO_name":"PDC-565","CARD_short_name":"PDC-565","ARO_description":"Class C beta-lactamase PDC-565.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8331":{"model_id":"8331","model_name":"PDC-566","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11158":{"protein_sequence":{"accession":"WLF01985.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGSLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"OR387362.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCATTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTGGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGTTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCATCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCTCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACTCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATTCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008913","ARO_id":"47705","ARO_name":"PDC-566","CARD_short_name":"PDC-566","ARO_description":"Class C beta-lactamase PDC-566.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8332":{"model_id":"8332","model_name":"PDC-567","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11159":{"protein_sequence":{"accession":"WLF01986.1","sequence":"MRDTRFPCLCGIAASILLFATTPAIADEASADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNLSIGLFGYLAARSLGQPFERFMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"OR387363.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCATACTGCTGTTCGCCACCACCCCGGCCATTGCCGACGAGGCCTCGGCAGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTAGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCTGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGTCAGCCGTTCGAACGGTTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAAGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATTCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008914","ARO_id":"47706","ARO_name":"PDC-567","CARD_short_name":"PDC-567","ARO_description":"Class C beta-lactamase PDC-567.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8333":{"model_id":"8333","model_name":"PDC-568","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11160":{"protein_sequence":{"accession":"WLF01987.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALTQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDMPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"OR387364.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGACCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTTCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACATGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008915","ARO_id":"47707","ARO_name":"PDC-568","CARD_short_name":"PDC-568","ARO_description":"Class C beta-lactamase PDC-568.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8334":{"model_id":"8334","model_name":"PDC-569","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11161":{"protein_sequence":{"accession":"WLF01988.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSINGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"OR387365.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCTTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCATCAACGGCTTCGGCGCCTACGTGGCGTTCATTCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008916","ARO_id":"47708","ARO_name":"PDC-569","CARD_short_name":"PDC-569","ARO_description":"Class C beta-lactamase PDC-569.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8335":{"model_id":"8335","model_name":"PDC-570","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11162":{"protein_sequence":{"accession":"WLF01989.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRRYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPSPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"OR387366.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGTCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCGCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCAGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008917","ARO_id":"47709","ARO_name":"PDC-570","CARD_short_name":"PDC-570","ARO_description":"Class C beta-lactamase PDC-570.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8336":{"model_id":"8336","model_name":"PDC-571","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11163":{"protein_sequence":{"accession":"WLF01990.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALTQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRAGPGPLDAEGYGVKSSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"OR387367.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGACCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTTCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGCCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGAGCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008918","ARO_id":"47710","ARO_name":"PDC-571","CARD_short_name":"PDC-571","ARO_description":"Class C beta-lactamase PDC-571.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8337":{"model_id":"8337","model_name":"PDC-572","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11164":{"protein_sequence":{"accession":"WLF01991.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPLERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"OR387368.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCTTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGCTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATTCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008919","ARO_id":"47711","ARO_name":"PDC-572","CARD_short_name":"PDC-572","ARO_description":"Class C beta-lactamase PDC-572.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8338":{"model_id":"8338","model_name":"PDC-573","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11165":{"protein_sequence":{"accession":"WLF01992.1","sequence":"MRDTRFSCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQTQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAKGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"OR387369.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCTCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGACACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCAAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATTCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008920","ARO_id":"47712","ARO_name":"PDC-573","CARD_short_name":"PDC-573","ARO_description":"Class C beta-lactamase PDC-573.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8339":{"model_id":"8339","model_name":"PDC-574","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11166":{"protein_sequence":{"accession":"WLF01993.1","sequence":"MRDTRFPCLCGIAASTLLLATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"OR387370.1","fmin":"0","fmax":"1185","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGCTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAACTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008921","ARO_id":"47713","ARO_name":"PDC-574","CARD_short_name":"PDC-574","ARO_description":"Class C beta-lactamase PDC-574.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8340":{"model_id":"8340","model_name":"PDC-575","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11167":{"protein_sequence":{"accession":"WMI45072.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"OR466748.1","fmin":"0","fmax":"1173","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008922","ARO_id":"47714","ARO_name":"PDC-575","CARD_short_name":"PDC-575","ARO_description":"Class C beta-lactamase PDC-575.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8341":{"model_id":"8341","model_name":"PDC-576","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11168":{"protein_sequence":{"accession":"WMP15086.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQLPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"OR474398.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGCTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGTCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCAATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAGCCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008923","ARO_id":"47715","ARO_name":"PDC-576","CARD_short_name":"PDC-576","ARO_description":"Class C beta-lactamase PDC-576.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8342":{"model_id":"8342","model_name":"PDC-577","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11169":{"protein_sequence":{"accession":"WPB15230.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"OR609871.1","fmin":"0","fmax":"1170","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAACTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGATCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATTCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008924","ARO_id":"47716","ARO_name":"PDC-577","CARD_short_name":"PDC-577","ARO_description":"Inhibitor-resistant extended-spectrum class C beta-lactamase PDC-577.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8343":{"model_id":"8343","model_name":"PDC-578","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11170":{"protein_sequence":{"accession":"WPG58515.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSAQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"OR807246.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGCGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008925","ARO_id":"47717","ARO_name":"PDC-578","CARD_short_name":"PDC-578","ARO_description":"Class C beta-lactamase PDC-578.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8344":{"model_id":"8344","model_name":"PDC-579","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11171":{"protein_sequence":{"accession":"WPG58516.1","sequence":"MRDTRFSCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"OR807247.1","fmin":"0","fmax":"1188","strand":"+","sequence":"ATGCGCGATACCAGATTCTCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGTTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCATCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAAGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008926","ARO_id":"47718","ARO_name":"PDC-579","CARD_short_name":"PDC-579","ARO_description":"Class C beta-lactamase PDC-579.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8345":{"model_id":"8345","model_name":"PDC-580","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11172":{"protein_sequence":{"accession":"WPG58517.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLRFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSINGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"OR807248.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCTTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCGGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCATCAACGGCTTCGGCGCCTACGTGGCGTTCATTCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008927","ARO_id":"47719","ARO_name":"PDC-580","CARD_short_name":"PDC-580","ARO_description":"Class C beta-lactamase PDC-580.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8346":{"model_id":"8346","model_name":"PDC-581","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11173":{"protein_sequence":{"accession":"WPG58519.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTKGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"OR807250.1","fmin":"0","fmax":"1173","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGTCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCAATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAGCCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAAGGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008928","ARO_id":"47720","ARO_name":"PDC-581","CARD_short_name":"PDC-581","ARO_description":"Class C beta-lactamase PDC-581.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8347":{"model_id":"8347","model_name":"PDC-582","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11174":{"protein_sequence":{"accession":"WVW91588.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQGKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKGQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRAGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"PP310000.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGGCAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGGCCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGCCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008929","ARO_id":"47721","ARO_name":"PDC-582","CARD_short_name":"PDC-582","ARO_description":"Class C beta-lactamase PDC-582.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8348":{"model_id":"8348","model_name":"PDC-583","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11175":{"protein_sequence":{"accession":"WVW91589.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKGQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRAGPGPLGAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"PP310001.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGGCCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGCCGGTCCCGGCCCGCTGGGTGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008930","ARO_id":"47722","ARO_name":"PDC-583","CARD_short_name":"PDC-583","ARO_description":"Class C beta-lactamase PDC-583.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8349":{"model_id":"8349","model_name":"PDC-584","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11176":{"protein_sequence":{"accession":"WVW91590.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKGQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTYLDVPEAALAQYAQGYGKDDRPLRAGPGPLGAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"PP310002.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGGCCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCTACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGCCGGTCCCGGCCCGCTGGGTGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008931","ARO_id":"47723","ARO_name":"PDC-584","CARD_short_name":"PDC-584","ARO_description":"Class C beta-lactamase PDC-584.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8350":{"model_id":"8350","model_name":"PDC-585","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11177":{"protein_sequence":{"accession":"WVW91591.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKGQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRAGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"PP310003.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGGCCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGCCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008932","ARO_id":"47724","ARO_name":"PDC-585","CARD_short_name":"PDC-585","ARO_description":"Class C beta-lactamase PDC-585.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8351":{"model_id":"8351","model_name":"PDC-586","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11178":{"protein_sequence":{"accession":"WVW91686.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGSLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"PP328933.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGTCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCTCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCAATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAGCCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008933","ARO_id":"47725","ARO_name":"PDC-586","CARD_short_name":"PDC-586","ARO_description":"Class C beta-lactamase PDC-586.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8352":{"model_id":"8352","model_name":"PDC-587","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11179":{"protein_sequence":{"accession":"WVW91687.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGLLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"PP328934.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCTGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008934","ARO_id":"47726","ARO_name":"PDC-587","CARD_short_name":"PDC-587","ARO_description":"Class C beta-lactamase PDC-587.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8353":{"model_id":"8353","model_name":"PDC-588","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11180":{"protein_sequence":{"accession":"WVW91688.1","sequence":"MRDTRFPCLCGIAASTLLFAATPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"PP328935.1","fmin":"0","fmax":"1179","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCGCCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAACTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008935","ARO_id":"47727","ARO_name":"PDC-588","CARD_short_name":"PDC-588","ARO_description":"Class C beta-lactamase PDC-588.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8354":{"model_id":"8354","model_name":"PDC-589","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11181":{"protein_sequence":{"accession":"WVW91689.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSICLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"PP328936.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCTGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCCCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCATGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008936","ARO_id":"47728","ARO_name":"PDC-589","CARD_short_name":"PDC-589","ARO_description":"Class C beta-lactamase PDC-589.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8355":{"model_id":"8355","model_name":"PDC-590","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11182":{"protein_sequence":{"accession":"WVW91690.1","sequence":"MRDTRFSCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"PP328937.1","fmin":"0","fmax":"1173","strand":"+","sequence":"ATGCGCGATACCAGATTCTCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008937","ARO_id":"47729","ARO_name":"PDC-590","CARD_short_name":"PDC-590","ARO_description":"Class C beta-lactamase PDC-590.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8356":{"model_id":"8356","model_name":"PDC-591","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11183":{"protein_sequence":{"accession":"WVW91691.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLEAEGYGVKTNAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"PP328938.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGAAGCCGAAGGCTACGGGGTGAAGACCAACGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008938","ARO_id":"47730","ARO_name":"PDC-591","CARD_short_name":"PDC-591","ARO_description":"Class C beta-lactamase PDC-591.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8357":{"model_id":"8357","model_name":"PDC-592","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11184":{"protein_sequence":{"accession":"WVW91692.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"PP328939.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACTCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAGCCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008939","ARO_id":"47731","ARO_name":"PDC-592","CARD_short_name":"PDC-592","ARO_description":"Class C beta-lactamase PDC-592.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8358":{"model_id":"8358","model_name":"PDC-593","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11185":{"protein_sequence":{"accession":"WYJ56550.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRRYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLNAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"PP558379.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCGCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGAATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008940","ARO_id":"47732","ARO_name":"PDC-593","CARD_short_name":"PDC-593","ARO_description":"Class C beta-lactamase PDC-593.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8359":{"model_id":"8359","model_name":"PDC-594","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11186":{"protein_sequence":{"accession":"WYJ56551.1","sequence":"MRDTRFPCLCGIAASTLLFAATPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAKGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"PP558380.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCGCCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAACTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCAAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008941","ARO_id":"47733","ARO_name":"PDC-594","CARD_short_name":"PDC-594","ARO_description":"Class C beta-lactamase PDC-594.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8360":{"model_id":"8360","model_name":"PDC-595","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11187":{"protein_sequence":{"accession":"WYJ56552.1","sequence":"MRDTRFPCLCGIAASTLLFAATPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"PP558381.1","fmin":"0","fmax":"1137","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCGCCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCATTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTATGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008942","ARO_id":"47734","ARO_name":"PDC-595","CARD_short_name":"PDC-595","ARO_description":"Class C beta-lactamase PDC-595.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8361":{"model_id":"8361","model_name":"PDC-596","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11188":{"protein_sequence":{"accession":"WYJ56553.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALTQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDMPEAALAQYAQGYGKDDRPLRAGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"PP558382.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGACCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTTCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACATGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGCCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008943","ARO_id":"47735","ARO_name":"PDC-596","CARD_short_name":"PDC-596","ARO_description":"Class C beta-lactamase PDC-596.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8362":{"model_id":"8362","model_name":"PDC-597","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11189":{"protein_sequence":{"accession":"WYJ56554.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGSLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"PP558383.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCTCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008944","ARO_id":"47736","ARO_name":"PDC-597","CARD_short_name":"PDC-597","ARO_description":"Class C beta-lactamase PDC-597.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8363":{"model_id":"8363","model_name":"PDC-598","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11190":{"protein_sequence":{"accession":"WYJ56555.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGLGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"PP558384.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAACTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCTCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008945","ARO_id":"47737","ARO_name":"PDC-598","CARD_short_name":"PDC-598","ARO_description":"Class C beta-lactamase PDC-598.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8364":{"model_id":"8364","model_name":"PDC-599","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11191":{"protein_sequence":{"accession":"WYJ56556.1","sequence":"MRDTRFPCLCGIAASTLLFATTPGIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALTQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRAGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"PP558385.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGGCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGACCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGCCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008946","ARO_id":"47738","ARO_name":"PDC-599","CARD_short_name":"PDC-599","ARO_description":"Class C beta-lactamase PDC-599.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8365":{"model_id":"8365","model_name":"PDC-600","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11192":{"protein_sequence":{"accession":"WYJ56557.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"PP558386.1","fmin":"0","fmax":"1188","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGTTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008947","ARO_id":"47739","ARO_name":"PDC-600","CARD_short_name":"PDC-600","ARO_description":"Class C beta-lactamase PDC-600.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8366":{"model_id":"8366","model_name":"PDC-601","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11193":{"protein_sequence":{"accession":"WZE64859.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAKGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"PP625997.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATTGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAACTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCAAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATTCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTACCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008948","ARO_id":"47740","ARO_name":"PDC-601","CARD_short_name":"PDC-601","ARO_description":"Class C beta-lactamase PDC-601.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8367":{"model_id":"8367","model_name":"PDC-602","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11194":{"protein_sequence":{"accession":"XCV17526.1","sequence":"MRDTRFPCLCGIAASTLLFAATPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERIMEQRLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRQWAQALDATHRGYYKVGDMTQGLGWEAYDWPIALKRLQAGNSTPMALQPHRVARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAIFSGLEQQAKVPLAR"},"dna_sequence":{"accession":"PQ002814.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCGCCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTGGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGTTATGGGCTGGCGTCGAAAGAGGACGGTCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAAGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGTCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAGCGGATCATGGAGCAGCGCCTGTTCCCGGCCCTGGGCCTCGAACAGACTCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTCCGGGTCGGCCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGACTGGACCGGCAGTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCGCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGGTCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCTTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGGCGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008949","ARO_id":"47741","ARO_name":"PDC-602","CARD_short_name":"PDC-602","ARO_description":"Class C beta-lactamase PDC-602.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8368":{"model_id":"8368","model_name":"PDC-603","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11195":{"protein_sequence":{"accession":"XCV17527.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGINLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"PQ002815.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAACCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAACTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008950","ARO_id":"47742","ARO_name":"PDC-603","CARD_short_name":"PDC-603","ARO_description":"Class C beta-lactamase PDC-603.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8369":{"model_id":"8369","model_name":"PDC-604","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11196":{"protein_sequence":{"accession":"XCV17528.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMHLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"PQ002816.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCACCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008951","ARO_id":"47743","ARO_name":"PDC-604","CARD_short_name":"PDC-604","ARO_description":"Class C beta-lactamase PDC-604.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8370":{"model_id":"8370","model_name":"PDC-605","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11197":{"protein_sequence":{"accession":"XCV17529.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMAPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"PQ002817.1","fmin":"0","fmax":"1188","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAACTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008952","ARO_id":"47744","ARO_name":"PDC-605","CARD_short_name":"PDC-605","ARO_description":"Class C beta-lactamase PDC-605.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8371":{"model_id":"8371","model_name":"PDC-606","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11198":{"protein_sequence":{"accession":"XCV17530.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWSALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"PQ002818.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGTCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008953","ARO_id":"47745","ARO_name":"PDC-606","CARD_short_name":"PDC-606","ARO_description":"Class C beta-lactamase PDC-606.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8372":{"model_id":"8372","model_name":"PDC-607","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11199":{"protein_sequence":{"accession":"XCV17531.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPPDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"PQ002819.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCCGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008954","ARO_id":"47746","ARO_name":"PDC-607","CARD_short_name":"PDC-607","ARO_description":"Class C beta-lactamase PDC-607.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8373":{"model_id":"8373","model_name":"PDC-608","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11200":{"protein_sequence":{"accession":"XGB73452.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRCYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"PQ203824.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGTCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCTGCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008955","ARO_id":"47747","ARO_name":"PDC-608","CARD_short_name":"PDC-608","ARO_description":"Class C beta-lactamase PDC-608.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8374":{"model_id":"8374","model_name":"PDC-609","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11201":{"protein_sequence":{"accession":"XGB73453.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRGGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"PQ203825.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGGCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008956","ARO_id":"47748","ARO_name":"PDC-609","CARD_short_name":"PDC-609","ARO_description":"Class C beta-lactamase PDC-609.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8375":{"model_id":"8375","model_name":"PDC-610","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11202":{"protein_sequence":{"accession":"XGB73454.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKDDGRRVTPETLFEIGSVSKTFIATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"PQ203826.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGATGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCATCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGTCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCCCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCATGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008957","ARO_id":"47749","ARO_name":"PDC-610","CARD_short_name":"PDC-610","ARO_description":"Class C beta-lactamase PDC-610.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8376":{"model_id":"8376","model_name":"PDC-611","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11203":{"protein_sequence":{"accession":"XGB73455.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFIATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPIAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"PQ203827.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCTGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCATCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCATTGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008958","ARO_id":"47750","ARO_name":"PDC-611","CARD_short_name":"PDC-611","ARO_description":"Class C beta-lactamase PDC-611.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8377":{"model_id":"8377","model_name":"PDC-612","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11204":{"protein_sequence":{"accession":"XGB73456.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFIATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRRYSNLSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"PQ203828.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCATCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGTCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCGCTATTCCAACCTGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008959","ARO_id":"47751","ARO_name":"PDC-612","CARD_short_name":"PDC-612","ARO_description":"Class C beta-lactamase PDC-612.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8378":{"model_id":"8378","model_name":"PDC-613","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11205":{"protein_sequence":{"accession":"XGB73457.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRRYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGCGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"PQ203829.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGTCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCGCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTGCGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008960","ARO_id":"47752","ARO_name":"PDC-613","CARD_short_name":"PDC-613","ARO_description":"Class C beta-lactamase PDC-613.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8379":{"model_id":"8379","model_name":"PDC-614","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11206":{"protein_sequence":{"accession":"XGB73458.1","sequence":"MRDTRFPCLCGIAASTLLFAATPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPSPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"PQ203830.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCGCCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCATTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTGGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCAGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008961","ARO_id":"47753","ARO_name":"PDC-614","CARD_short_name":"PDC-614","ARO_description":"Class C beta-lactamase PDC-614.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8380":{"model_id":"8380","model_name":"PDC-615","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11207":{"protein_sequence":{"accession":"XGB73459.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIDLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"PQ203831.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTAGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGACCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008962","ARO_id":"47754","ARO_name":"PDC-615","CARD_short_name":"PDC-615","ARO_description":"Class C beta-lactamase PDC-615.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8381":{"model_id":"8381","model_name":"PDC-616","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11208":{"protein_sequence":{"accession":"XGB73460.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFIATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRLWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"PQ203832.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTTCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCATCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCTCTGGGCGCAGGCGCTTGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008963","ARO_id":"47755","ARO_name":"PDC-616","CARD_short_name":"PDC-616","ARO_description":"Class C beta-lactamase PDC-616.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8382":{"model_id":"8382","model_name":"PDC-617","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11209":{"protein_sequence":{"accession":"XGB73461.1","sequence":"MRDTRFSCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"PQ203833.1","fmin":"0","fmax":"1197","strand":"+","sequence":"ATGCGCGATACCAGATTCTCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008964","ARO_id":"47756","ARO_name":"PDC-617","CARD_short_name":"PDC-617","ARO_description":"Class C beta-lactamase PDC-617.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8383":{"model_id":"8383","model_name":"PDC-618","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11210":{"protein_sequence":{"accession":"XGB73462.1","sequence":"MRDTRFSCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRAGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMAPQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"PQ203834.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCTCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGCCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCCGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACTCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCCGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATTCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008965","ARO_id":"47757","ARO_name":"PDC-618","CARD_short_name":"PDC-618","ARO_description":"Class C beta-lactamase PDC-618.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8384":{"model_id":"8384","model_name":"PDC-619","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11211":{"protein_sequence":{"accession":"XGB73463.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKAGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"PQ203835.1","fmin":"0","fmax":"1170","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGATGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGTTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGTCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008966","ARO_id":"47758","ARO_name":"PDC-619","CARD_short_name":"PDC-619","ARO_description":"Class C beta-lactamase PDC-619.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8385":{"model_id":"8385","model_name":"PDC-620","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11212":{"protein_sequence":{"accession":"XGB73464.1","sequence":"MRDTGFPCLCGIAASTLLFAATSAIAGEAPADRLKTLVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASLHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYTPGSQRLYSNPSIGLFGYLAARSLGQPFERIMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDKPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"PQ203836.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCGGATTCCCCTGCCTGTGCGGCATCGCCGCCTCCACACTGCTGTTCGCCGCCACCTCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGACACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGATATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCTGCACTGGCCGGCGCTGCAAGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAAGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACACGCCGGGCAGCCAGCGCCTCTACTCCAACCCGAGCATCGGTCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGATCATGGAGCAGCAACTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTATGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAAGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCGGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATCCCAGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAATTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008967","ARO_id":"47759","ARO_name":"PDC-620","CARD_short_name":"PDC-620","ARO_description":"Class C beta-lactamase PDC-620.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8386":{"model_id":"8386","model_name":"PDC-621","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11213":{"protein_sequence":{"accession":"XGB73465.1","sequence":"MRDTRFPCLCGIAASTLLFATTLAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALTQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"PQ203837.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCTGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGACCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGTTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008968","ARO_id":"47760","ARO_name":"PDC-621","CARD_short_name":"PDC-621","ARO_description":"Class C beta-lactamase PDC-621.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8387":{"model_id":"8387","model_name":"PDC-622","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11214":{"protein_sequence":{"accession":"XGB73466.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDHPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"PQ203838.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGACGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAACTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCACCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACTAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008969","ARO_id":"47761","ARO_name":"PDC-622","CARD_short_name":"PDC-622","ARO_description":"Class C beta-lactamase PDC-622.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8388":{"model_id":"8388","model_name":"PDC-623","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11215":{"protein_sequence":{"accession":"XGB73467.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERFMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"PQ203839.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGACGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGTTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAAGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008970","ARO_id":"47762","ARO_name":"PDC-623","CARD_short_name":"PDC-623","ARO_description":"Class C beta-lactamase PDC-623.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8389":{"model_id":"8389","model_name":"PDC-624","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11216":{"protein_sequence":{"accession":"XGB73468.1","sequence":"MRDTGFPCLCGIAASTLLFAATSAIAGEAPADRLKTLVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLAAKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASLHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYTPGSQRLYSNPSIGLFGYLAARSLGQPFERIMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDKPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"PQ203840.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCGGATTCCCCTGCCTGTGCGGCATCGCCGCCTCCACACTGCTGTTCGCCGCCACCTCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGACACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGATATTCCGGGCCTGGCCGTGGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCTGCGAAAGAGGACGGTCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCTGCACTGGCCGGCGCTGCAAGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAAGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACACGCCGGGCAGCCAGCGCCTCTACTCCAACCCGAGCATCGGTCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGATCATGGAGCAGCAACTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCTCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAAGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCGGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGACTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATCCCAGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAATTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAACGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008971","ARO_id":"47763","ARO_name":"PDC-624","CARD_short_name":"PDC-624","ARO_description":"Class C beta-lactamase PDC-624.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8390":{"model_id":"8390","model_name":"PDC-625","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11217":{"protein_sequence":{"accession":"XGB73469.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLYKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"PQ203841.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTAGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGTACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008972","ARO_id":"47764","ARO_name":"PDC-625","CARD_short_name":"PDC-625","ARO_description":"Class C beta-lactamase PDC-625.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8391":{"model_id":"8391","model_name":"PDC-626","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11218":{"protein_sequence":{"accession":"XGB73470.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"PQ203842.1","fmin":"0","fmax":"1185","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTAGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008973","ARO_id":"47765","ARO_name":"PDC-626","CARD_short_name":"PDC-626","ARO_description":"Class C beta-lactamase PDC-626.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8392":{"model_id":"8392","model_name":"PDC-627","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11219":{"protein_sequence":{"accession":"XGB73471.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPESLFEIGSVSKTFTATLAGYALTQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRRYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPHALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"PQ203843.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGTCCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGACCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCGCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACATGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008974","ARO_id":"47766","ARO_name":"PDC-627","CARD_short_name":"PDC-627","ARO_description":"Class C beta-lactamase PDC-627.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8393":{"model_id":"8393","model_name":"PDC-628","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11220":{"protein_sequence":{"accession":"XGB73472.1","sequence":"MRDTRFPCLCGIAASTLLFAATPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERIMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPIPLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"PQ203844.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATTGCCGCTTCCACACTGCTGTTCGCCGCCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGATATTCCGGGCCTGGCCGTGGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCTTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAAGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGATCATGGAGCAGCAACTGTTCCCGGCGCTGGGCCTCGAACAGACCCACCTCGACGTCCCCGAGGCGGCGCTGGCGCAGTATGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGTGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCCCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGTTTCGGCGCCTATGTGGCGTTCATCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTACCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008975","ARO_id":"47767","ARO_name":"PDC-628","CARD_short_name":"PDC-628","ARO_description":"Class C beta-lactamase PDC-628.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8394":{"model_id":"8394","model_name":"PDC-629","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11221":{"protein_sequence":{"accession":"XGB73473.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDSISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"PQ203845.1","fmin":"0","fmax":"1185","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGTCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACAGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTTATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCCCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008976","ARO_id":"47768","ARO_name":"PDC-629","CARD_short_name":"PDC-629","ARO_description":"Class C beta-lactamase PDC-629.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8395":{"model_id":"8395","model_name":"PDC-630","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11222":{"protein_sequence":{"accession":"XGB73474.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRQVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"PQ203846.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCAGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGATCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATTCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008977","ARO_id":"47769","ARO_name":"PDC-630","CARD_short_name":"PDC-630","ARO_description":"Class C beta-lactamase PDC-630.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8396":{"model_id":"8396","model_name":"PDC-631","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11223":{"protein_sequence":{"accession":"XGB73475.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRRYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPQRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"PQ203847.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGTCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCGCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCAGAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008978","ARO_id":"47770","ARO_name":"PDC-631","CARD_short_name":"PDC-631","ARO_description":"Class C beta-lactamase PDC-631.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8397":{"model_id":"8397","model_name":"PDC-632","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11224":{"protein_sequence":{"accession":"XGB73476.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIHDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"PQ203848.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTAGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCACGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCCCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008979","ARO_id":"47771","ARO_name":"PDC-632","CARD_short_name":"PDC-632","ARO_description":"Class C beta-lactamase PDC-632.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8398":{"model_id":"8398","model_name":"PDC-633","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11225":{"protein_sequence":{"accession":"XGB73477.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKNDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"PQ203849.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCACGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGAACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008980","ARO_id":"47772","ARO_name":"PDC-633","CARD_short_name":"PDC-633","ARO_description":"Class C beta-lactamase PDC-633.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8399":{"model_id":"8399","model_name":"PDC-634","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11226":{"protein_sequence":{"accession":"XGB73478.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQHLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"PQ203850.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCTGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCACACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCACCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008981","ARO_id":"47773","ARO_name":"PDC-634","CARD_short_name":"PDC-634","ARO_description":"Class C beta-lactamase PDC-634.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8400":{"model_id":"8400","model_name":"PDC-635","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11227":{"protein_sequence":{"accession":"XGB73479.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNSFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"PQ203851.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAGCCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACAGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008982","ARO_id":"47774","ARO_name":"PDC-635","CARD_short_name":"PDC-635","ARO_description":"Class C beta-lactamase PDC-635.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8401":{"model_id":"8401","model_name":"PDC-636","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11228":{"protein_sequence":{"accession":"XGB73480.1","sequence":"MRDTRFPCLCGIAASILLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFSDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERFMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"PQ203852.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCATACTGCTGTTCGCCACCACCCCGGCCATTGCCGACGAGGCCCCGGCAGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCTCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGTTCATGGAGCAGCAATTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAAGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTACCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008983","ARO_id":"47775","ARO_name":"PDC-636","CARD_short_name":"PDC-636","ARO_description":"Class C beta-lactamase PDC-636.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8402":{"model_id":"8402","model_name":"PDC-637","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11229":{"protein_sequence":{"accession":"XGB73481.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIADEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQLFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDKPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQAKVPLKR"},"dna_sequence":{"accession":"PQ203853.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGACGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGTGCCAGCCAGCACTGGCCGGCGCTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAACTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGTTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAAGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCACTGAAGCGCCTACAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGATCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATTCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGCCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008984","ARO_id":"47776","ARO_name":"PDC-637","CARD_short_name":"PDC-637","ARO_description":"Class C beta-lactamase PDC-637.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8403":{"model_id":"8403","model_name":"PDC-638","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11230":{"protein_sequence":{"accession":"XGB73482.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"PQ203854.1","fmin":"0","fmax":"1191","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTATGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008985","ARO_id":"47777","ARO_name":"PDC-638","CARD_short_name":"PDC-638","ARO_description":"Class C beta-lactamase PDC-638.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8404":{"model_id":"8404","model_name":"PDC-639","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11231":{"protein_sequence":{"accession":"XGB73483.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRRYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWEQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFIPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"PQ203855.1","fmin":"0","fmax":"1194","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTCGCCGGCTATGCCCTGGCCCAGGACAAGATGCGTCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCGCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGGCTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGCCCGCTGGATGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGAGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGCTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCATCCCGGGCCGCGACCTGGGCCTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008986","ARO_id":"47778","ARO_name":"PDC-639","CARD_short_name":"PDC-639","ARO_description":"Class C beta-lactamase PDC-639.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8405":{"model_id":"8405","model_name":"PDC-640","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11232":{"protein_sequence":{"accession":"XHE66940.1","sequence":"MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRVTPETLFEIGSVSKTFTATLAGYALAQDKMRLDDRASQHWPALQGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRDYYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRVGPGAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMALQPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR"},"dna_sequence":{"accession":"PQ323406.1","fmin":"0","fmax":"1185","strand":"+","sequence":"ATGCGCGATACCAGATTCCCCTGCCTGTGCGGCATCGCCGCTTCCACACTGCTGTTCGCCACCACCCCGGCCATTGCCGGCGAGGCCCCGGCGGATCGCCTGAAGGCACTGGTCGACGCCGCCGTACAACCGGTGATGAAGGCCAATGACATTCCGGGCCTGGCCGTAGCCATCAGCCTGAAAGGAGAACCGCATTACTTCAGCTATGGGCTGGCCTCGAAAGAGGACGGCCGCCGGGTGACGCCGGAGACCCTGTTCGAGATCGGCTCGGTGAGCAAGACCTTCACCGCCACCCTAGCCGGCTATGCCCTGGCCCAGGACAAGATGCGCCTCGACGACCGCGCCAGCCAGCACTGGCCGGCACTGCAGGGCAGCCGCTTCGACGGCATCAGCCTGCTCGACCTCGCGACCTATACCGCCGGCGGCTTGCCGCTGCAGTTCCCCGACTCGGTGCAGAAGGACCAGGCACAGATCCGCGACTACTACCGCCAGTGGCAGCCGACCTACGCGCCGGGCAGCCAGCGCCTCTATTCCAACCCGAGCATCGGCCTGTTCGGCTATCTCGCCGCGCGCAGCCTGGGCCAGCCGTTCGAACGACTCATGGAGCAGCAAGTGTTCCCGGCACTGGGCCTCGAACAGACCCACCTCGACGTGCCCGAGGCGGCGCTGGCGCAGTACGCCCAGGGCTACGGCAAGGACGACCGCCCGCTACGGGTCGGTCCCGGTGCCGAAGGCTACGGGGTGAAGACCAGCGCGGCCGACCTGCTGCGCTTCGTCGATGCCAACCTGCATCCGGAGCGCCTGGACAGGCCCTGGGCGCAGGCGCTCGATGCCACCCATCGCGGTTACTACAAGGTCGGCGACATGACCCAGGGCCTGGGCTGGGAAGCCTACGACTGGCCGATCTCCCTGAAGCGCCTGCAGGCCGGCAACTCGACGCCGATGGCGCTGCAACCGCACAGGATCGCCAGGCTGCCCGCGCCACAGGCGCTGGAGGGCCAGCGCCTGCTGAACAAGACCGGTTCCACCAACGGCTTCGGCGCCTACGTGGCGTTCGTCCCGGGCCGCGACCTGGGACTGGTGATCCTGGCCAACCGCAACTATCCCAATGCCGAGCGGGTGAAGATCGCCTACGCCATCCTCAGCGGCCTGGAGCAGCAGGGCAAGGTGCCGCTGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3008987","ARO_id":"47779","ARO_name":"PDC-640","CARD_short_name":"PDC-640","ARO_description":"Class C beta-lactamase PDC-640.","ARO_category":{"36237":{"category_aro_accession":"3000098","category_aro_cvterm_id":"36237","category_aro_name":"PDC beta-lactamase","category_aro_description":"PDC beta-lactamases are class C beta-lactamases that are found in Pseudomonas aeruginosa.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8406":{"model_id":"8406","model_name":"PEN-A10","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11233":{"protein_sequence":{"accession":"PRF31748.1","sequence":"MTHSSQRRILLLAAATAPLALSLGACAARDATVSDAASPVGAVPASFAALERAAGGRLGVCAIDTATGRRALHRADERFPFCSTFKAMLGAAVLAQSVAHPGLLQQRVTYGRSDLVNYSPVTERHVDTGMTVAELCAATIQYSDNTAANELMKRIGGPAAVTAYARSIGDDTFRLDRWETELNTALPGDLRDTTTPAAMAASLRMLVLGDALPPAQRAQLIEWLRGNKVGDKRIRAGVPTGWRVGDKTGTGDYGTTNDAGVLWPPSRAPIVLAVYYTQARADAKAKDDVIAAATRIAISTLG"},"dna_sequence":{"accession":"PVGE01000083.1","fmin":"166904","fmax":"167813","strand":"-","sequence":"ATGACTCATTCATCTCAACGTCGAATCCTGTTGCTGGCTGCCGCGACGGCGCCGCTCGCGTTGTCCCTCGGCGCGTGCGCGGCGCGCGATGCGACGGTGTCCGACGCAGCGTCGCCTGTCGGCGCGGTGCCGGCATCGTTCGCCGCGCTCGAACGCGCAGCCGGCGGCCGGCTCGGCGTCTGCGCGATCGATACCGCGACCGGCCGGCGCGCGCTGCATCGCGCCGACGAGCGCTTCCCGTTCTGCAGCACCTTCAAGGCGATGCTCGGCGCGGCGGTGCTCGCGCAGAGCGTCGCGCATCCCGGCCTGCTGCAGCAGCGCGTGACGTACGGCCGGTCCGATCTCGTCAACTACTCGCCGGTGACCGAGCGACACGTCGACACTGGCATGACGGTCGCTGAGCTTTGCGCGGCGACGATCCAGTACAGCGACAACACGGCCGCGAACGAGCTGATGAAGCGGATCGGCGGCCCGGCAGCGGTCACGGCCTATGCGCGCTCGATCGGCGACGACACGTTCCGCCTCGATCGCTGGGAGACCGAACTGAATACCGCGCTGCCGGGCGATCTTCGCGACACGACGACGCCGGCGGCGATGGCCGCGAGCCTGCGCATGCTCGTGCTCGGCGACGCGTTGCCGCCCGCGCAGCGCGCGCAGCTGATCGAATGGCTGCGCGGCAACAAGGTCGGCGACAAACGCATCCGCGCGGGCGTGCCGACCGGCTGGCGCGTCGGCGACAAGACGGGCACCGGCGACTACGGGACGACGAACGATGCCGGCGTGCTGTGGCCGCCGTCGCGCGCGCCGATCGTGCTTGCCGTCTACTACACGCAGGCGCGTGCCGATGCGAAGGCGAAAGACGACGTGATCGCGGCCGCGACGCGGATCGCGATCTCGACGCTCGGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43748","NCBI_taxonomy_name":"Burkholderia multivorans","NCBI_taxonomy_id":"87883"}}}},"ARO_accession":"3008988","ARO_id":"47780","ARO_name":"PEN-A10","CARD_short_name":"PEN-A10","ARO_description":"Class A beta-lactamase PEN-A10.","ARO_category":{"46664":{"category_aro_accession":"3007873","category_aro_cvterm_id":"46664","category_aro_name":"PEN-A beta-lactamase","category_aro_description":"PEN-A is a family of class A beta-lactamases which enzymatically inactivate beta-lactam antibiotics.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8407":{"model_id":"8407","model_name":"PEN-A11","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11234":{"protein_sequence":{"accession":"PRE46797.1","sequence":"MTHSSQRRILLLAAATAPLALSLGACAARDAAVSDAASPVGAAPASLAALERAAGGRLGVCAIDTATGRRALHRADERFPFCSTFKAMLGAAVLAQSVAHPGLLQQRVTYGRSDLVNYSPVTERHVDTGMTVAELCAATIQYSDNTAANELMKRIGGPAAVTAYARSIGDDTFRLDRWETELNTALPGDLRDTTTPAAMAASLRVLVLGDALPPAQRTQLIEWLRGNKVGDKRIRAGVPTGWRVGDKTGTGDYGTTNDAGVLWPPSRAPIVLAVYYTQARADAKAKDDVIAAATRIAIATLG"},"dna_sequence":{"accession":"PVFR01000052.1","fmin":"11143","fmax":"12052","strand":"+","sequence":"ATGACTCATTCATCTCAACGTCGAATCCTGTTGCTGGCTGCCGCGACGGCGCCGCTCGCGTTGTCCCTCGGCGCGTGCGCGGCGCGCGATGCGGCGGTGTCCGACGCAGCGTCGCCTGTCGGCGCGGCGCCGGCATCGTTGGCCGCGCTCGAACGTGCAGCCGGCGGCCGGCTCGGCGTCTGCGCGATCGATACCGCGACCGGCCGGCGCGCGCTGCATCGCGCGGACGAGCGCTTCCCGTTCTGCAGCACCTTCAAGGCGATGCTCGGGGCGGCGGTGCTCGCGCAGAGCGTCGCGCATCCCGGCCTGCTGCAGCAGCGCGTGACGTACGGTCGGTCCGATCTTGTCAACTACTCGCCGGTGACCGAGCGACACGTCGACACCGGCATGACGGTCGCCGAGCTTTGCGCGGCGACGATCCAGTACAGCGACAACACGGCCGCGAACGAGCTGATGAAGCGGATCGGCGGCCCGGCGGCGGTCACGGCCTATGCGCGCTCGATCGGCGACGACACGTTCCGCCTCGATCGCTGGGAGACCGAACTGAATACCGCGCTGCCGGGCGATCTTCGCGACACGACGACGCCGGCGGCGATGGCCGCGAGCCTGCGCGTGCTCGTGCTCGGCGATGCGTTGCCGCCCGCGCAGCGCACGCAGCTGATCGAATGGCTGCGCGGCAACAAGGTCGGCGACAAGCGCATCCGCGCGGGCGTGCCGACCGGCTGGCGCGTCGGCGACAAGACGGGCACCGGCGACTACGGGACGACGAACGATGCCGGCGTGCTGTGGCCGCCGTCGCGCGCGCCGATCGTGCTTGCCGTCTACTACACGCAGGCGCGTGCCGATGCGAAGGCGAAGGACGACGTGATCGCGGCCGCGACGCGGATCGCGATCGCGACGCTCGGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43748","NCBI_taxonomy_name":"Burkholderia multivorans","NCBI_taxonomy_id":"87883"}}}},"ARO_accession":"3008989","ARO_id":"47781","ARO_name":"PEN-A11","CARD_short_name":"PEN-A11","ARO_description":"Class A beta-lactamase PEN-A11.","ARO_category":{"46664":{"category_aro_accession":"3007873","category_aro_cvterm_id":"46664","category_aro_name":"PEN-A beta-lactamase","category_aro_description":"PEN-A is a family of class A beta-lactamases which enzymatically inactivate beta-lactam antibiotics.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8408":{"model_id":"8408","model_name":"PEN-A12","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11235":{"protein_sequence":{"accession":"MBR8242798.1","sequence":"MTHSSQRRILLLAAATAPLALSLGACAARDAAVSDAALPVGAAPASFAALERAAGGRLGVCAIDAATGRRALHRADERFPFCSTFKAMLGAAVLAQSVAHPGLLQQRVTYGRSDLVNYSPVTERHVDTGMTVAELCAATIQYSDNTAANELMKRIGGPAAVTAYARSIGDDTFRLDRWETELNTALPGDLRDTTTPAAMAASLRVLVLGDALPPAQRAQLIEWLRGNKVGDKRIRAGVPTGWRVGDKTGTGDYGTTNDAGVLWPPSRAPIVLAVYYTQARADAKAKDDVIAAATRIAIATLG"},"dna_sequence":{"accession":"JAGSUL010000009.1","fmin":"229377","fmax":"230286","strand":"-","sequence":"ATGACTCATTCATCTCAACGTCGAATCCTGTTGCTCGCTGCCGCAACGGCGCCGCTCGCGTTGTCCCTCGGCGCGTGCGCGGCGCGCGATGCAGCGGTGTCCGACGCAGCGTTGCCTGTCGGCGCGGCGCCGGCATCGTTCGCCGCGCTCGAACGCGCAGCCGGCGGCCGGCTCGGCGTCTGCGCGATCGATGCCGCGACCGGCCGGCGCGCGCTGCATCGCGCCGACGAGCGCTTCCCGTTCTGCAGCACCTTCAAGGCGATGCTCGGTGCGGCGGTGCTCGCGCAGAGCGTCGCGCATCCCGGCCTGCTGCAGCAGCGCGTGACGTACGGTCGGTCCGATCTCGTCAACTACTCGCCGGTGACCGAGCGACACGTCGACACCGGCATGACGGTCGCCGAGCTTTGCGCGGCGACGATCCAGTACAGCGACAACACGGCCGCGAACGAGCTGATGAAGCGGATCGGCGGCCCGGCGGCGGTCACGGCCTATGCGCGCTCGATCGGCGACGACACGTTCCGCCTCGATCGCTGGGAGACCGAACTGAATACCGCGCTGCCGGGCGATCTTCGCGACACGACGACGCCCGCGGCGATGGCTGCGAGCCTGCGCGTGCTCGTGCTCGGCGATGCGTTGCCGCCCGCGCAGCGCGCGCAGCTGATCGAATGGCTGCGCGGCAACAAGGTCGGCGACAAGCGCATCCGCGCGGGCGTGCCGACCGGCTGGCGCGTCGGCGACAAGACGGGCACCGGCGACTACGGGACGACGAACGATGCCGGCGTGCTGTGGCCGCCGTCGCGCGCGCCGATCGTGCTTGCCGTCTACTACACGCAGGCGCGTGCCGATGCGAAGGCGAAAGACGACGTGATCGCGGCCGCGACGCGGATCGCGATCGCGACGCTCGGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43748","NCBI_taxonomy_name":"Burkholderia multivorans","NCBI_taxonomy_id":"87883"}}}},"ARO_accession":"3008990","ARO_id":"47782","ARO_name":"PEN-A12","CARD_short_name":"PEN-A12","ARO_description":"Class A beta-lactamase PEN-A12.","ARO_category":{"46664":{"category_aro_accession":"3007873","category_aro_cvterm_id":"46664","category_aro_name":"PEN-A beta-lactamase","category_aro_description":"PEN-A is a family of class A beta-lactamases which enzymatically inactivate beta-lactam antibiotics.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8409":{"model_id":"8409","model_name":"PEN-A13","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11236":{"protein_sequence":{"accession":"PRG25577.1","sequence":"MTHSPQRRILLLAAATAPLALSLGACAARDAAVSDAASPVGAAPASFAALERAAGGRLGVCAIDTATGRRALHRADERFRFCSTFKAMLAAAVLAQSVAHPGLLQQRVTYGRSDLVNYSPVTERHVDTGMTVAELCAATIQYSDNTAANELMKRIGGPAAVTAYARSIGDDTFRLDRWETELNTALPGDLRDTTTPAAMAASLRVLVLGDALPPAQRAQLIEWLRGNKVGDKRIRAGVPTGWRVGDKTGTGDYGTTNDAGVLWPPSRAPIVLAVYYTQARADAKAKDDVIAAATRIAIATLA"},"dna_sequence":{"accession":"PVGS01000019.1","fmin":"181036","fmax":"181945","strand":"-","sequence":"ATGACTCATTCACCTCAACGTCGAATCCTGTTGCTGGCTGCCGCGACGGCGCCGCTCGCGTTGTCCCTCGGCGCGTGCGCGGCGCGCGATGCGGCGGTGTCCGACGCAGCGTCGCCTGTCGGCGCGGCGCCGGCATCGTTCGCCGCGCTCGAACGCGCAGCCGGCGGCCGGCTCGGCGTCTGCGCGATCGATACCGCGACGGGCCGGCGCGCGCTGCATCGCGCCGACGAGCGCTTTCGGTTCTGCAGCACCTTCAAGGCGATGCTCGCTGCGGCGGTGCTCGCGCAGAGCGTCGCGCATCCTGGCCTGCTGCAGCAGCGCGTGACGTACGGCCGGTCCGATCTCGTCAACTACTCGCCGGTGACCGAGCGACACGTCGACACCGGCATGACGGTCGCCGAGCTTTGCGCGGCGACGATCCAGTACAGCGACAACACGGCCGCGAACGAGCTGATGAAGCGGATCGGCGGCCCGGCAGCGGTCACGGCCTATGCGCGCTCGATCGGCGACGATACGTTCCGCCTCGATCGCTGGGAGACCGAACTGAACACCGCGCTGCCGGGCGATCTTCGCGACACGACGACGCCCGCGGCGATGGCCGCGAGCCTGCGCGTGCTCGTGCTCGGCGACGCGTTGCCGCCCGCGCAGCGCGCGCAGCTGATCGAATGGCTGCGCGGCAACAAGGTCGGCGACAAGCGCATCCGGGCGGGCGTGCCGACCGGCTGGCGCGTCGGCGACAAGACGGGCACCGGCGACTACGGGACGACGAACGATGCCGGCGTGCTGTGGCCGCCGTCGCGCGCGCCGATCGTGCTTGCCGTCTACTACACGCAGGCGCGTGCCGATGCGAAGGCGAAAGACGACGTGATCGCGGCCGCGACGCGGATCGCGATCGCGACGCTCGCGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43748","NCBI_taxonomy_name":"Burkholderia multivorans","NCBI_taxonomy_id":"87883"}}}},"ARO_accession":"3008991","ARO_id":"47783","ARO_name":"PEN-A13","CARD_short_name":"PEN-A13","ARO_description":"Class A beta-lactamase PEN-A13.","ARO_category":{"46664":{"category_aro_accession":"3007873","category_aro_cvterm_id":"46664","category_aro_name":"PEN-A beta-lactamase","category_aro_description":"PEN-A is a family of class A beta-lactamases which enzymatically inactivate beta-lactam antibiotics.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8410":{"model_id":"8410","model_name":"PEN-A15","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11237":{"protein_sequence":{"accession":"PTO45445.1","sequence":"MTHSPQRRILLLAAATAPLALSLGACAARDATVSDAASRVGAAPASFAALERAAGGRLGVCAIDTATGRRALHRADERFPFCSTFKAMLGAAVLAQSVAHPGLLQQRVTYGRSDLVNYSPVTERHVDTGMTVAELCAATIQYSDNTAANELMKRIGGPAAVTAYARSIGDDTFRLDRWETELNTALPGDLRDTTTPAAMAASLRVLVLGDALPPAQRAQLIEWLRGNKVGDKRIRAGVPTGWRVGDKTGTGAYGTTNDAGVLWPPSRAPIVLAVYYTQARADAKAKDDVIAAATRIAIATLG"},"dna_sequence":{"accession":"PZZC01000063.1","fmin":"17479","fmax":"18388","strand":"+","sequence":"ATGACTCATTCACCTCAACGTCGAATCCTGTTGCTGGCTGCCGCGACAGCGCCGCTCGCGTTGTCCCTCGGCGCGTGCGCGGCGCGCGATGCGACGGTGTCCGACGCAGCGTCGCGTGTCGGCGCGGCGCCGGCATCGTTCGCCGCGCTCGAGCGGGCCGCCGGCGGCCGGCTCGGCGTCTGCGCGATCGATACCGCGACCGGCCGGCGCGCGCTGCATCGCGCCGACGAGCGCTTCCCGTTCTGCAGCACCTTCAAGGCGATGCTCGGCGCGGCGGTGCTCGCGCAGAGCGTCGCGCATCCCGGCCTGCTGCAGCAGCGCGTGACGTACGGCCGGTCCGATCTCGTCAACTACTCGCCGGTGACCGAGCGACACGTCGACACCGGCATGACGGTCGCCGAGCTTTGCGCGGCGACGATCCAGTACAGCGACAACACGGCCGCGAACGAGCTGATGAAGCGGATCGGCGGCCCGGCAGCGGTCACGGCCTATGCGCGCTCGATCGGCGACGACACGTTCCGCCTCGATCGCTGGGAGACCGAACTGAATACCGCGCTGCCGGGCGATCTTCGCGACACGACGACGCCGGCGGCGATGGCCGCGAGCCTGCGCGTGCTCGTGCTCGGCGACGCGTTGCCGCCCGCGCAGCGCGCGCAGCTGATCGAATGGCTGCGCGGCAACAAGGTCGGCGACAAACGCATCCGCGCGGGCGTGCCGACCGGCTGGCGCGTCGGCGACAAGACGGGCACCGGCGCCTACGGGACGACGAACGATGCCGGCGTGCTGTGGCCGCCGTCGCGCGCGCCGATCGTGCTTGCCGTCTACTACACGCAGGCGCGTGCCGATGCGAAGGCGAAGGACGACGTGATCGCGGCCGCGACGCGGATCGCGATCGCGACGCTCGGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43748","NCBI_taxonomy_name":"Burkholderia multivorans","NCBI_taxonomy_id":"87883"}}}},"ARO_accession":"3008992","ARO_id":"47784","ARO_name":"PEN-A15","CARD_short_name":"PEN-A15","ARO_description":"Class A beta-lactamase PEN-A15.","ARO_category":{"46664":{"category_aro_accession":"3007873","category_aro_cvterm_id":"46664","category_aro_name":"PEN-A beta-lactamase","category_aro_description":"PEN-A is a family of class A beta-lactamases which enzymatically inactivate beta-lactam antibiotics.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8411":{"model_id":"8411","model_name":"PEN-A16","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11238":{"protein_sequence":{"accession":"MBU9400921.1","sequence":"MTHSSQRRILLLAAATAPLALSLGACAARDAAVSDAASPVGAAPASFAALERAAGGRLGVCAIDTATGRRALYRADERFPFCSTFKAMLAAAVLAQSVAHPGLLQQRVTYGRSDLVNYSPVTERHVDTGMTVAELCAATIQYSDNTAANELMKRIGGPAAVTAYARSIGDDTFRLDRWETELNTALPGDLRDTTTPAAMAASLRVLVLGDALPLAQRAQLIEWLRGNKVGDKRIRAGVPTGWRVGDKTGTGDYGTTNDAGVLWPPSRAPIVLAVYYTQARADAKAKDDVIAAATRIAIATLG"},"dna_sequence":{"accession":"JAHPNG010000011.1","fmin":"112447","fmax":"113356","strand":"-","sequence":"ATGACTCATTCATCTCAACGTCGAATCCTGTTGCTGGCTGCCGCGACGGCGCCGCTCGCGTTGTCCCTCGGCGCGTGCGCGGCGCGCGATGCGGCGGTGTCCGACGCAGCGTCGCCTGTCGGCGCGGCGCCGGCATCGTTCGCCGCGCTCGAACGTGCAGCCGGCGGCCGGCTCGGCGTCTGCGCGATCGATACCGCGACCGGCCGGCGCGCGCTGTATCGCGCCGACGAGCGCTTTCCGTTCTGCAGCACCTTCAAGGCGATGCTCGCCGCGGCGGTGCTCGCGCAGAGCGTCGCGCATCCTGGCCTGCTGCAGCAGCGCGTGACGTACGGCCGGTCCGATCTCGTCAACTACTCGCCGGTGACCGAGCGACACGTCGACACTGGCATGACGGTCGCCGAGCTTTGCGCGGCGACGATCCAGTACAGCGACAACACGGCCGCGAACGAGCTGATGAAGCGGATCGGCGGCCCGGCGGCGGTCACGGCCTATGCGCGCTCGATCGGCGACGACACGTTCCGCCTCGATCGCTGGGAGACCGAACTGAATACCGCGCTGCCGGGCGATCTTCGCGACACGACGACGCCCGCGGCGATGGCCGCGAGCCTGCGTGTGCTCGTGCTCGGCGACGCGTTGCCGCTCGCGCAGCGCGCGCAGCTGATCGAATGGCTGCGCGGCAACAAGGTCGGCGACAAACGCATCCGCGCGGGCGTGCCGACCGGCTGGCGCGTCGGCGACAAGACGGGCACCGGCGACTACGGGACGACGAACGATGCCGGCGTGCTGTGGCCGCCGTCGCGCGCGCCGATCGTGCTTGCCGTCTACTACACGCAGGCGCGTGCCGATGCGAAGGCGAAAGACGACGTGATCGCGGCCGCGACGCGGATCGCGATCGCGACGCTCGGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43748","NCBI_taxonomy_name":"Burkholderia multivorans","NCBI_taxonomy_id":"87883"}}}},"ARO_accession":"3008993","ARO_id":"47785","ARO_name":"PEN-A16","CARD_short_name":"PEN-A16","ARO_description":"Class A beta-lactamase PEN-A16.","ARO_category":{"46664":{"category_aro_accession":"3007873","category_aro_cvterm_id":"46664","category_aro_name":"PEN-A beta-lactamase","category_aro_description":"PEN-A is a family of class A beta-lactamases which enzymatically inactivate beta-lactam antibiotics.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8412":{"model_id":"8412","model_name":"PEN-A17","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11239":{"protein_sequence":{"accession":"PRH49453.1","sequence":"MTHSSQRRILLLAAATAPLALSLGACAARDATVSDAPSPVGASPASFAALERAAGGRLGVCAIDTATGRRALHRADERFPFCSTFKAMLGAAVLAQSVAHPGLLQQRVTYGRSDLVNYSPVTERHVDTGMTVAELCAATIQYSDNTAANELMKRIGGPAAVTAYARSIGDDTFRLDRWETELNTALPGDLRDTTTPAAMAASLRVLVLGDALPHAQRAQLIEWLRGNKVGDKRIRAGVPTAWRVGDKTGTGDYGTTNDAGVLWPPSRAPIVLAVYYTQARADAKAKDDVIAAATRIAIATLG"},"dna_sequence":{"accession":"PVHL01000015.1","fmin":"148900","fmax":"149809","strand":"+","sequence":"ATGACTCATTCATCTCAACGTCGAATCCTGTTGCTGGCTGCCGCGACGGCGCCGCTCGCGTTGTCCCTCGGCGCGTGCGCGGCGCGCGATGCGACGGTGTCCGACGCGCCGTCGCCTGTCGGCGCGTCGCCGGCATCGTTCGCCGCGCTCGAACGCGCAGCCGGCGGCCGGCTCGGCGTCTGCGCGATCGATACCGCGACCGGGCGGCGCGCGCTGCATCGCGCGGACGAGCGCTTCCCATTCTGCAGCACCTTCAAGGCGATGCTCGGCGCGGCGGTGCTCGCGCAGAGCGTCGCGCATCCCGGCCTGCTGCAGCAGCGCGTGACGTACGGCCGGTCCGATCTCGTCAACTACTCGCCGGTGACCGAGCGGCACGTCGACACCGGCATGACGGTCGCCGAGCTCTGCGCGGCGACGATCCAGTACAGCGACAACACGGCCGCGAACGAGCTGATGAAGCGGATCGGCGGCCCGGCGGCGGTCACGGCCTATGCGCGCTCGATCGGCGACGACACGTTCCGCCTCGATCGCTGGGAGACCGAACTGAATACCGCGCTGCCGGGCGATCTTCGCGACACGACGACGCCCGCGGCGATGGCCGCGAGCCTGCGCGTGCTCGTGCTCGGCGATGCGTTGCCGCACGCGCAGCGCGCGCAGCTGATCGAATGGCTGCGCGGCAACAAGGTCGGCGACAAGCGCATCCGCGCGGGCGTGCCGACCGCCTGGCGCGTCGGCGACAAGACGGGCACCGGCGACTACGGGACGACGAACGATGCCGGCGTGCTGTGGCCGCCGTCGCGCGCGCCGATCGTGCTTGCCGTCTACTACACGCAGGCGCGTGCCGATGCGAAGGCGAAGGACGACGTGATCGCGGCCGCGACGCGGATCGCGATCGCGACGCTCGGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43748","NCBI_taxonomy_name":"Burkholderia multivorans","NCBI_taxonomy_id":"87883"}}}},"ARO_accession":"3008994","ARO_id":"47786","ARO_name":"PEN-A17","CARD_short_name":"PEN-A17","ARO_description":"Class A beta-lactamase PEN-A17.","ARO_category":{"46664":{"category_aro_accession":"3007873","category_aro_cvterm_id":"46664","category_aro_name":"PEN-A beta-lactamase","category_aro_description":"PEN-A is a family of class A beta-lactamases which enzymatically inactivate beta-lactam antibiotics.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8413":{"model_id":"8413","model_name":"PEN-A18","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11240":{"protein_sequence":{"accession":"UQO71494.1","sequence":"MTHSPQRRILLLAAATAPLALSLGACATRDAAVSDAASPVGAAPASFAALERAAGGRLGVCAIDTATGRRALHRADERFPFCSTFKAMLGAAVLAQSVAHPGLLQQRVTYGRSDLVNYSPVTERHVDTGMTVAELCAATIQYSDNTAANELMKRIGGPAAVTAYARSIGDDTFRLDRWETELNTALPGDLRDTTTPAAMAASLRVLVLGDALPLAQRAQLIEWLRGNKVGDKRIRAGVPTGWRVGDKTGTGDYGTTNDAGVLWPPSRAPIVLAVYYTQARADAKAKDDVIAAATRIAIATLG"},"dna_sequence":{"accession":"CP090717.1","fmin":"650728","fmax":"651637","strand":"+","sequence":"ATGACTCATTCACCTCAACGTCGAATCCTGTTGCTGGCTGCCGCGACGGCGCCGCTCGCGTTGTCCCTCGGCGCGTGCGCGACGCGCGATGCGGCGGTGTCCGACGCAGCGTCGCCTGTCGGCGCGGCGCCGGCATCGTTCGCCGCGCTCGAACGCGCAGCCGGCGGCCGGCTCGGCGTCTGCGCGATCGATACCGCGACCGGCCGGCGCGCGCTGCATCGCGCCGACGAGCGCTTCCCGTTCTGCAGCACCTTCAAGGCGATGCTCGGCGCGGCGGTGCTCGCGCAGAGCGTCGCGCATCCCGGCCTGCTGCAGCAGCGCGTGACGTACGGCCGGTCCGATCTCGTCAACTACTCGCCGGTGACCGAGCGACACGTCGACACCGGCATGACGGTTGCCGAGCTTTGCGCGGCGACGATCCAGTACAGCGACAACACGGCCGCGAACGAGTTGATGAAGCGGATCGGCGGCCCGGCGGCGGTCACGGCCTATGCGCGCTCGATCGGCGACGACACGTTCCGCCTCGATCGCTGGGAGACCGAACTGAATACCGCGCTGCCAGGCGATCTTCGCGACACGACGACGCCCGCGGCGATGGCCGCGAGCCTGCGCGTGCTCGTGCTCGGCGATGCGTTGCCGCTCGCGCAGCGCGCGCAGCTGATCGAATGGCTGCGCGGCAACAAGGTCGGCGACAAGCGCATCCGCGCGGGCGTGCCGACCGGCTGGCGCGTCGGCGACAAGACGGGCACCGGCGACTACGGGACGACGAACGATGCCGGCGTGCTGTGGCCGCCGTCGCGCGCGCCGATCGTGCTTGCCGTCTACTACACGCAGGCGCGTGCCGATGCGAAGGCGAAGGACGACGTGATCGCGGCCGCGACGCGGATCGCGATCGCGACGCTCGGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43748","NCBI_taxonomy_name":"Burkholderia multivorans","NCBI_taxonomy_id":"87883"}}}},"ARO_accession":"3008995","ARO_id":"47787","ARO_name":"PEN-A18","CARD_short_name":"PEN-A18","ARO_description":"Class A beta-lactamase PEN-A18.","ARO_category":{"46664":{"category_aro_accession":"3007873","category_aro_cvterm_id":"46664","category_aro_name":"PEN-A beta-lactamase","category_aro_description":"PEN-A is a family of class A beta-lactamases which enzymatically inactivate beta-lactam antibiotics.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8414":{"model_id":"8414","model_name":"PEN-A19","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11241":{"protein_sequence":{"accession":"PRE60969.1","sequence":"MTHSSQRRILLLAAATAPLALSLGACAARDAAVSDAASPVGASPASFAALERAAGGRLGVCAIDTATGRRALYRADERFPFCSTFKAMLAAAVLAQSVAHPGLLQQRVTYGRSDLVNYSPVTERHVDTGMTVAELCAATIQYSDNTAANELMKRIGGPAAVTAYARSIGDDTFRLDRWETELNTALPGDLRDTTTPAAMAASLRVLVLGDALPPAQRAQLIEWLRGNKVGDKRIRAGVPTGWRVGDKTGTGDYGTTNDAGVLWPPSRAPIVLAVYYTQARADAKAKDDVIAAATRIAIATLP"},"dna_sequence":{"accession":"PVFO01000062.1","fmin":"43938","fmax":"44847","strand":"+","sequence":"ATGACTCATTCATCTCAACGTCGAATCCTGTTGCTGGCTGCCGCGACGGCGCCGCTCGCGTTGTCCCTCGGCGCGTGCGCGGCGCGCGATGCGGCGGTGTCCGACGCAGCGTCGCCTGTCGGCGCGTCGCCGGCATCGTTCGCCGCACTCGAACGCGCAGCCGGCGGCCGGCTCGGCGTCTGCGCGATCGATACCGCGACCGGCCGGCGCGCGCTGTATCGCGCCGACGAGCGCTTCCCGTTCTGCAGCACCTTCAAGGCGATGCTCGCTGCGGCGGTGCTCGCGCAGAGCGTCGCGCATCCTGGCCTGCTGCAGCAGCGCGTGACGTACGGCCGGTCCGATCTCGTCAACTATTCGCCCGTGACCGAGCGACACGTCGACACCGGCATGACGGTCGCCGAGCTCTGCGCGGCGACGATCCAGTACAGCGACAACACGGCCGCGAACGAGCTGATGAAGCGGATCGGCGGCCCGGCGGCGGTCACGGCCTATGCGCGCTCGATCGGCGACGACACGTTCCGCCTCGATCGCTGGGAGACCGAACTGAACACCGCGCTGCCGGGCGATCTTCGCGACACGACGACGCCCGCTGCGATGGCCGCGAGCCTGCGCGTGCTCGTGCTCGGCGATGCGTTGCCGCCCGCGCAGCGGGCGCAGCTGATCGAATGGCTGCGCGGCAACAAGGTCGGCGACAAGCGCATCCGCGCGGGCGTGCCGACCGGTTGGCGCGTCGGCGACAAGACGGGCACCGGCGACTACGGGACGACGAACGATGCCGGCGTGCTGTGGCCGCCGTCGCGCGCGCCGATCGTGCTTGCCGTCTACTACACGCAGGCGCGTGCCGATGCGAAGGCGAAGGACGACGTGATCGCGGCCGCGACGCGGATCGCGATCGCGACGCTCCCGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43748","NCBI_taxonomy_name":"Burkholderia multivorans","NCBI_taxonomy_id":"87883"}}}},"ARO_accession":"3008996","ARO_id":"47788","ARO_name":"PEN-A19","CARD_short_name":"PEN-A19","ARO_description":"Class A beta-lactamase PEN-A19.","ARO_category":{"46664":{"category_aro_accession":"3007873","category_aro_cvterm_id":"46664","category_aro_name":"PEN-A beta-lactamase","category_aro_description":"PEN-A is a family of class A beta-lactamases which enzymatically inactivate beta-lactam antibiotics.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8415":{"model_id":"8415","model_name":"PEN-A1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11242":{"protein_sequence":{"accession":"BAG46675.1","sequence":"MTHSSQRRILLLAAATAPLALSLGACAARDATVSDAASPVGAAPASFAALERAAGGRLGVCAIDTATGRRALHRADERFPFCSTFKAMLGAAVLAQSVAHPGLLQQRVTYGRSDLVNYSPVTERHVDTGMTVAELCAATIQYSDNTAANELMKRIGGPAAVTAYARSIGDDTFRLDRWETELNTALPGDLRDTTTPAAMAANLRVLVLGDALPPAQRAQLIEWLRGNKVGDKRIRAGVPTGWRVGDKTGTGDYGTTNDVGVLWPPSRAPIVLAVYYTQTRADAKAKDDVIAAATRIASATLA"},"dna_sequence":{"accession":"AP009386.1","fmin":"1834932","fmax":"1835841","strand":"-","sequence":"ATGACTCATTCATCTCAACGTCGAATCCTGTTGCTGGCTGCCGCGACGGCGCCGCTCGCGTTGTCCCTCGGCGCGTGCGCGGCGCGCGATGCGACGGTGTCCGACGCAGCGTCGCCTGTCGGCGCGGCGCCGGCATCGTTCGCCGCGCTCGAACGCGCAGCCGGCGGCCGGCTCGGCGTCTGCGCGATCGATACCGCGACCGGGCGGCGCGCGCTGCATCGCGCGGACGAGCGCTTCCCGTTCTGCAGCACCTTCAAGGCGATGCTCGGCGCGGCGGTGCTCGCGCAGAGCGTCGCGCATCCGGGCCTGCTGCAGCAGCGCGTGACGTACGGCCGGTCCGATCTCGTCAACTATTCGCCCGTGACCGAGCGGCACGTCGACACCGGCATGACGGTCGCCGAGCTCTGCGCGGCGACGATCCAGTACAGCGACAACACGGCCGCGAACGAGCTGATGAAGCGGATCGGCGGCCCGGCAGCGGTCACGGCCTATGCGCGCTCGATCGGCGACGACACGTTCCGCCTCGATCGCTGGGAGACCGAACTGAACACCGCGCTGCCGGGCGATCTTCGCGACACGACGACACCCGCTGCGATGGCCGCGAACCTGCGCGTGCTCGTGCTCGGCGACGCGTTGCCGCCCGCGCAGCGCGCGCAGCTGATCGAGTGGCTGCGCGGTAACAAGGTCGGCGACAAGCGCATCCGCGCGGGCGTGCCGACCGGCTGGCGCGTCGGCGACAAGACGGGCACCGGCGACTACGGGACGACGAACGATGTCGGCGTGCTGTGGCCGCCGTCGCGCGCGCCGATCGTGCTTGCCGTCTACTACACGCAGACGCGTGCCGATGCGAAGGCGAAGGACGACGTGATCGCTGCCGCGACGCGGATCGCGAGCGCGACGCTCGCGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43748","NCBI_taxonomy_name":"Burkholderia multivorans","NCBI_taxonomy_id":"87883"}}}},"ARO_accession":"3008997","ARO_id":"47789","ARO_name":"PEN-A1","CARD_short_name":"PEN-A1","ARO_description":"Class A beta-lactamase PEN-A1.","ARO_category":{"46664":{"category_aro_accession":"3007873","category_aro_cvterm_id":"46664","category_aro_name":"PEN-A beta-lactamase","category_aro_description":"PEN-A is a family of class A beta-lactamases which enzymatically inactivate beta-lactam antibiotics.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8416":{"model_id":"8416","model_name":"PEN-A20","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11243":{"protein_sequence":{"accession":"SAJ99033.1","sequence":"MTHSSQRRILLLAAATAPLALSLGACAARDAAVSDAALPVGAAPASFAALERAAGGRLGVCAIDAATGRRALHRADERFPFCSTFKAMLAAAVLAQSVAHPGLLQQRVTYGRSDLVNYSPVTERHVDTGMTVAELCAATIQYSDNTAANELMKRIGGPAAVTAYARSIGDDTFRLDRWETELNTALPGDLRDTTTPAAMAASLRVLVLGDALPPAQRAQLIEWLRGNKVGDKRIRAGVPTGWRVGDKTGTGDYGTTNDAGVLWPPSRAPIVLAVYYTQARADAKAKDDVIAAATRIAIATLG"},"dna_sequence":{"accession":"FKJW01000005.1","fmin":"692507","fmax":"693416","strand":"+","sequence":"ATGACTCATTCATCTCAACGTCGAATCCTGTTGCTCGCTGCCGCAACGGCGCCGCTCGCATTGTCCCTCGGCGCGTGCGCGGCGCGCGATGCAGCGGTGTCCGACGCAGCGTTGCCTGTCGGCGCGGCGCCGGCATCGTTCGCCGCGCTCGAACGCGCAGCCGGCGGCCGGCTCGGCGTCTGCGCGATCGATGCCGCGACCGGCCGGCGCGCGCTGCATCGCGCCGACGAGCGCTTCCCGTTCTGCAGCACCTTCAAGGCGATGCTCGCCGCGGCGGTGCTCGCGCAGAGCGTCGCGCATCCCGGCCTGCTGCAGCAGCGCGTGACGTACGGTCGGTCCGATCTCGTCAACTACTCGCCGGTGACCGAGCGACACGTCGACACCGGCATGACGGTCGCCGAGCTTTGCGCGGCGACGATCCAGTACAGCGACAACACGGCCGCGAACGAGCTGATGAAGCGGATCGGCGGCCCGGCGGCGGTCACGGCCTATGCGCGCTCGATCGGCGACGACACGTTCCGCCTCGATCGCTGGGAGACCGAACTGAATACCGCGCTGCCGGGCGATCTTCGCGACACGACGACGCCCGCGGCGATGGCCGCGAGCCTGCGCGTGCTCGTGCTCGGCGATGCGTTGCCGCCCGCGCAGCGCGCGCAGCTGATCGAATGGCTGCGCGGCAACAAGGTCGGCGACAAGCGCATCCGCGCGGGCGTGCCGACCGGCTGGCGCGTCGGCGACAAGACGGGCACCGGCGACTACGGGACGACGAACGATGCCGGCGTGCTGTGGCCGCCGTCGCGCGCGCCGATCGTGCTTGCCGTCTACTACACGCAGGCGCGTGCCGATGCGAAGGCGAAGGACGACGTGATCGCGGCCGCGACGCGGATCGCGATCGCGACGCTCGGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43748","NCBI_taxonomy_name":"Burkholderia multivorans","NCBI_taxonomy_id":"87883"}}}},"ARO_accession":"3008998","ARO_id":"47790","ARO_name":"PEN-A20","CARD_short_name":"PEN-A20","ARO_description":"Class A beta-lactamase PEN-A20.","ARO_category":{"46664":{"category_aro_accession":"3007873","category_aro_cvterm_id":"46664","category_aro_name":"PEN-A beta-lactamase","category_aro_description":"PEN-A is a family of class A beta-lactamases which enzymatically inactivate beta-lactam antibiotics.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8417":{"model_id":"8417","model_name":"PEN-A21","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11244":{"protein_sequence":{"accession":"PRF76784.1","sequence":"MTHSPQRRILLLAAATAPLALSLGACAARDATVSDTASPVGAAPASFAALERAAGGRLGVCAIDTATGRRALHRADERFPFCSTFKAMLGAAVLAQSVAHPGLLQQRVTYGRSDLVNYSPVTERHVDTGMTVAELCAATIQYSDNTAANELMKRIGGPAAVTAYARSIGDDTFRLDRWETELNTALPGDLRDTTTPAAMAASLRVLVLGDALPAAQRAQLSEWLRGNKVGDKRIRAGVPTAWRVGDKTGTGDYGTTNDAGVLWPPSRAPIVLAVYYTQARADAKAKDDVIAAATRIAIATLG"},"dna_sequence":{"accession":"PVGJ01000044.1","fmin":"45644","fmax":"46553","strand":"-","sequence":"ATGACTCATTCACCTCAACGTCGAATCCTGTTGCTGGCTGCCGCGACGGCGCCGCTCGCGTTGTCCCTCGGCGCGTGCGCGGCGCGCGATGCGACGGTGTCCGACACAGCGTCGCCTGTCGGCGCGGCGCCGGCATCGTTCGCTGCGCTCGAGCGCGCCGCCGGCGGCCGGCTCGGCGTCTGCGCGATCGATACCGCGACGGGCCGGCGCGCGCTGCATCGCGCCGACGAGCGCTTCCCGTTCTGCAGCACCTTCAAGGCGATGCTCGGCGCGGCGGTGCTCGCGCAGAGCGTCGCGCATCCCGGCCTGCTGCAGCAGCGCGTGACGTACGGCCGGTCCGATCTCGTCAACTACTCGCCGGTGACCGAGCGACACGTCGACACCGGCATGACGGTTGCCGAGCTTTGCGCGGCGACGATCCAGTACAGCGACAACACGGCCGCGAACGAGCTGATGAAGCGGATCGGCGGCCCGGCGGCGGTCACGGCCTATGCGCGCTCGATCGGCGACGACACGTTCCGCCTCGATCGCTGGGAGACCGAACTGAATACCGCGCTGCCGGGCGACCTTCGCGACACGACGACGCCCGCTGCGATGGCCGCGAGCCTGCGCGTGCTCGTGCTCGGCGACGCGTTGCCGGCCGCGCAGCGCGCGCAGCTGAGCGAATGGCTGCGCGGCAACAAGGTCGGCGACAAACGCATCCGCGCGGGCGTGCCGACCGCCTGGCGCGTCGGCGACAAGACGGGCACCGGCGACTACGGGACGACGAACGATGCCGGCGTGCTGTGGCCGCCGTCGCGCGCGCCGATCGTGCTTGCCGTCTACTACACGCAGGCGCGTGCCGATGCGAAGGCGAAGGACGACGTGATCGCGGCCGCGACGCGGATCGCGATCGCGACGCTCGGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43748","NCBI_taxonomy_name":"Burkholderia multivorans","NCBI_taxonomy_id":"87883"}}}},"ARO_accession":"3008999","ARO_id":"47791","ARO_name":"PEN-A21","CARD_short_name":"PEN-A21","ARO_description":"Class A beta-lactamase PEN-A21.","ARO_category":{"46664":{"category_aro_accession":"3007873","category_aro_cvterm_id":"46664","category_aro_name":"PEN-A beta-lactamase","category_aro_description":"PEN-A is a family of class A beta-lactamases which enzymatically inactivate beta-lactam antibiotics.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8418":{"model_id":"8418","model_name":"PEN-A22","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11245":{"protein_sequence":{"accession":"PRH12942.1","sequence":"MTHSPQRRILLLAAATAPLALSLGACAARDATVSDAASPVGLPASFAALERAAGGRLGVCAIDTATGRRALHRADERFPFCSTFKAMLGAAVLAQSVAHPGLLQQRVTYGRSDLVNYSPVTERHVDTGMTVAELCAATIQYSDNTAANELMKRIGGPAAVTAYARSIGDDTFRLDRWETELNTALPGDLRDTTTPAAMAASLRVLVLGDALPAAQRAQLIEWLRGNKVGDKRIRAGVPTAWRVGDKTGTGDYGTTNDAGVLWPPSRAPIVLAVYYTQARADAKAKDDVIAAATRIAIATLG"},"dna_sequence":{"accession":"PVHD01000001.1","fmin":"172720","fmax":"173626","strand":"-","sequence":"ATGACTCATTCACCTCAACGTCGAATCCTGTTGCTGGCTGCCGCGACGGCGCCGCTCGCGTTGTCCCTCGGCGCGTGCGCGGCGCGCGATGCGACGGTGTCCGACGCAGCGTCGCCTGTCGGCTTGCCGGCATCGTTCGCCGCGCTCGAACGCGCAGCCGGCGGCCGGCTCGGCGTCTGCGCGATCGATACCGCGACCGGCCGGCGCGCGCTGCATCGCGCGGACGAGCGCTTCCCGTTCTGCAGCACCTTCAAGGCGATGCTCGGGGCGGCGGTGCTCGCGCAGAGCGTCGCGCATCCCGGCCTGCTGCAGCAGCGCGTGACGTACGGTCGGTCCGATCTCGTCAACTACTCGCCGGTGACCGAGCGACACGTCGACACCGGCATGACGGTCGCCGAGCTTTGCGCGGCGACGATCCAGTACAGCGACAACACGGCCGCGAACGAGCTGATGAAGCGGATCGGCGGCCCGGCGGCGGTCACGGCCTATGCGCGCTCGATCGGCGACGACACGTTCCGCCTCGATCGCTGGGAGACCGAACTGAATACCGCGCTGCCGGGCGATCTTCGCGACACGACGACGCCCGCGGCGATGGCCGCGAGCCTGCGCGTGCTCGTGCTCGGCGATGCGTTGCCGGCCGCGCAGCGCGCGCAGCTGATCGAATGGCTGCGCGGTAACAAGGTCGGCGACAAGCGCATCCGCGCGGGCGTGCCGACCGCCTGGCGCGTCGGCGACAAGACGGGCACCGGCGACTACGGGACGACGAACGATGCCGGCGTGCTGTGGCCGCCGTCGCGCGCGCCGATCGTGCTTGCCGTCTACTACACGCAGGCGCGTGCTGATGCGAAGGCGAAGGACGACGTGATCGCGGCCGCGACGCGGATCGCGATCGCGACGCTCGGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43748","NCBI_taxonomy_name":"Burkholderia multivorans","NCBI_taxonomy_id":"87883"}}}},"ARO_accession":"3009000","ARO_id":"47792","ARO_name":"PEN-A22","CARD_short_name":"PEN-A22","ARO_description":"Class A beta-lactamase PEN-A22.","ARO_category":{"46664":{"category_aro_accession":"3007873","category_aro_cvterm_id":"46664","category_aro_name":"PEN-A beta-lactamase","category_aro_description":"PEN-A is a family of class A beta-lactamases which enzymatically inactivate beta-lactam antibiotics.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8419":{"model_id":"8419","model_name":"PEN-A23","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11246":{"protein_sequence":{"accession":"PRF03901.1","sequence":"MTHSSQRRILLLAAATAPLALSLGACAARDAAVSDAASPVGASPASFAALERAAGGRLGVCAIDTATGRRALHRADERFPFCSTFKAMLGAAVLAQSVAHPGLLRQRVTYGRSDLVNYSPVTERHVDTGMTVAELCAATIQYSDNTAANELMKRIGGPAAVTAYARSIGDDTFRLDRWETELNTALPGDLRDTTTPAAMAASLRVLVLGDALPPAQRARLIEWLRGNKVGDKRIRAGVPTAWRVGDKTGTGDYGTTNDAGVLWPPSRAPIVLAVYYTQARADAKAKDDVIAAATRIAIATLA"},"dna_sequence":{"accession":"PVGA01000003.1","fmin":"1101","fmax":"2010","strand":"+","sequence":"ATGACTCATTCATCTCAACGTCGAATCCTGTTGCTGGCTGCCGCGACGGCGCCGCTCGCGTTGTCCCTCGGCGCGTGCGCGGCGCGCGATGCGGCGGTGTCCGACGCAGCGTCGCCTGTCGGCGCGTCGCCGGCATCGTTCGCCGCGCTCGAACGCGCAGCCGGCGGCCGGCTCGGCGTCTGCGCGATCGATACCGCGACCGGGCGGCGCGCGCTGCATCGCGCGGACGAGCGCTTCCCGTTCTGCAGCACCTTCAAGGCGATGCTCGGCGCGGCGGTGCTCGCGCAGAGCGTCGCGCATCCCGGCCTGCTGCGGCAGCGCGTGACGTACGGCCGGTCCGATCTCGTCAACTACTCGCCGGTGACCGAGCGGCACGTCGACACCGGCATGACGGTCGCCGAGCTCTGCGCGGCGACGATCCAGTACAGCGACAACACGGCCGCGAACGAGCTGATGAAGCGGATCGGCGGCCCGGCAGCGGTCACGGCCTATGCGCGCTCGATCGGCGACGACACGTTCCGCCTCGATCGCTGGGAGACCGAACTGAATACCGCGCTGCCGGGCGATCTTCGCGACACGACGACGCCCGCGGCGATGGCCGCGAGCCTGCGTGTGCTCGTGCTCGGCGACGCGTTGCCGCCCGCGCAGCGCGCGCGGCTGATCGAATGGCTGCGCGGCAACAAGGTCGGCGACAAGCGCATCCGCGCGGGCGTGCCGACCGCCTGGCGCGTCGGCGACAAGACGGGCACCGGCGACTACGGGACGACGAACGATGCCGGCGTGCTGTGGCCGCCGTCGCGCGCGCCGATCGTGCTTGCCGTCTACTACACGCAGGCGCGTGCCGATGCGAAGGCGAAGGACGACGTGATCGCGGCCGCGACGCGGATCGCGATCGCGACGCTCGCGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43748","NCBI_taxonomy_name":"Burkholderia multivorans","NCBI_taxonomy_id":"87883"}}}},"ARO_accession":"3009001","ARO_id":"47793","ARO_name":"PEN-A23","CARD_short_name":"PEN-A23","ARO_description":"Class A beta-lactamase PEN-A23.","ARO_category":{"46664":{"category_aro_accession":"3007873","category_aro_cvterm_id":"46664","category_aro_name":"PEN-A beta-lactamase","category_aro_description":"PEN-A is a family of class A beta-lactamases which enzymatically inactivate beta-lactam antibiotics.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8420":{"model_id":"8420","model_name":"PEN-A24","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11247":{"protein_sequence":{"accession":"PRG23231.1","sequence":"MPHSPQRRILLLAAATAPLALSLGACAARDAAVSDAASPVGASPASFAALERAAGGRLGVCAIDTATGRRALYRADERFPFCSTFKAMLAAAVLAQSVAHPGLLQQRVTYGRSDLVNYSPVTERHVDTGMTVAELCAATIQYSDNTAANELMKRIGGPAAVTAYARSIGDDTFRLDRWETELNTALPGDLRDTTTPAAMAASLRVLVLGDALPPAQRAQLIEWLRGNKVGDKRIRAGVPTGWRVGDKTGTGDYGTTNDAGVLWPPSRAPIVLAVYYTQARADAKAKDDVIAAATRIAIATLA"},"dna_sequence":{"accession":"PVGQ01000030.1","fmin":"158752","fmax":"159661","strand":"+","sequence":"ATGCCTCATTCACCTCAACGTCGAATCCTGTTGCTGGCTGCCGCGACGGCGCCGCTCGCGTTGTCCCTCGGCGCGTGCGCGGCGCGCGATGCGGCGGTGTCCGACGCAGCGTCGCCTGTCGGCGCGTCGCCGGCATCGTTCGCCGCACTCGAACGCGCGGCCGGCGGCCGGCTCGGCGTCTGCGCGATCGATACCGCGACGGGCCGGCGCGCGCTGTATCGCGCCGACGAGCGCTTCCCGTTCTGCAGCACCTTCAAGGCGATGCTCGCTGCGGCGGTGCTCGCGCAGAGCGTCGCGCATCCTGGCCTGCTGCAGCAGCGCGTGACGTACGGCCGGTCCGATCTCGTCAACTACTCGCCGGTGACCGAGCGACACGTCGACACCGGCATGACGGTCGCCGAGCTTTGCGCGGCGACGATCCAGTACAGCGACAACACGGCCGCGAACGAGCTGATGAAGCGGATCGGCGGCCCGGCAGCGGTCACGGCCTATGCGCGCTCGATCGGCGACGATACGTTCCGCCTCGATCGCTGGGAGACCGAACTGAACACCGCGCTGCCGGGCGATCTTCGCGACACGACGACGCCCGCGGCGATGGCCGCGAGCCTGCGCGTGCTCGTGCTCGGCGACGCGTTGCCGCCCGCGCAGCGCGCGCAGTTGATCGAATGGCTGCGCGGCAACAAGGTCGGCGACAAGCGCATCCGGGCGGGCGTGCCGACCGGCTGGCGCGTCGGCGACAAGACGGGCACCGGCGACTACGGGACGACGAACGATGCCGGCGTGCTGTGGCCGCCGTCGCGCGCGCCGATCGTGCTTGCCGTCTACTACACGCAGGCGCGTGCCGATGCGAAGGCGAAGGACGACGTGATCGCGGCCGCGACGCGGATCGCGATCGCGACGCTCGCGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43748","NCBI_taxonomy_name":"Burkholderia multivorans","NCBI_taxonomy_id":"87883"}}}},"ARO_accession":"3009002","ARO_id":"47794","ARO_name":"PEN-A24","CARD_short_name":"PEN-A24","ARO_description":"Class A beta-lactamase PEN-A24.","ARO_category":{"46664":{"category_aro_accession":"3007873","category_aro_cvterm_id":"46664","category_aro_name":"PEN-A beta-lactamase","category_aro_description":"PEN-A is a family of class A beta-lactamases which enzymatically inactivate beta-lactam antibiotics.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8421":{"model_id":"8421","model_name":"PEN-A25","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11248":{"protein_sequence":{"accession":"PRF70551.1","sequence":"MTHSSQRRILLLAAATAPLALSLGACAARDAAVSDAASPVGASPASFAALERAAGGRLGVCAIDAATGRRALYRADERFPFCSTIKAMLAAAVLAQSVAHPGLLQQRVTYGRSDLVNYSPVTERHVDTGMTVAELCAATIQYSDNTAANELMKRIGGPAAVTAYARSIGDDTFRLDRWETELNTALPGDLRDTTTPAAMAASLRVLVLGDALPPAQRAQLIEWLRGNKVGDKRIRAGVPTGWRVGDKTGTGDYGTTNDAGVLWPPSRAPIVLAVYYTQARADAKAKDEVIAAATRIAIATLA"},"dna_sequence":{"accession":"PVGL01000065.1","fmin":"30109","fmax":"31018","strand":"+","sequence":"ATGACTCATTCATCTCAACGTCGAATCCTGTTGCTGGCTGCCGCGACGGCGCCGCTCGCGTTGTCCCTCGGCGCGTGCGCGGCGCGCGATGCGGCGGTGTCCGACGCAGCGTCGCCTGTCGGCGCGTCGCCGGCATCGTTCGCCGCGCTCGAACGCGCAGCCGGCGGCCGGCTCGGCGTCTGCGCGATCGATGCCGCGACCGGCCGGCGCGCGCTGTATCGCGCCGACGAGCGCTTTCCGTTCTGCAGCACCATCAAGGCGATGCTCGCCGCGGCGGTGCTCGCGCAGAGCGTCGCGCATCCCGGCCTGCTGCAGCAACGCGTGACGTACGGCCGGTCCGATCTCGTCAACTATTCGCCCGTGACCGAGCGGCACGTCGACACCGGCATGACGGTCGCCGAGCTCTGCGCGGCGACGATCCAGTACAGCGACAACACGGCCGCGAACGAGCTGATGAAGCGGATCGGCGGCCCGGCGGCCGTCACGGCCTATGCGCGCTCGATCGGCGACGACACGTTCCGCCTCGATCGCTGGGAGACCGAACTGAACACCGCGCTGCCGGGCGATCTTCGCGACACGACGACGCCCGCTGCGATGGCCGCGAGCCTGCGCGTGCTCGTGCTCGGCGACGCGTTGCCGCCCGCGCAGCGCGCGCAGCTGATCGAATGGCTGCGCGGCAACAAGGTCGGCGACAAGCGCATCCGCGCGGGCGTGCCGACCGGCTGGCGCGTCGGCGACAAGACGGGCACCGGCGACTACGGGACGACGAACGATGCCGGCGTGCTGTGGCCGCCGTCGCGCGCGCCGATCGTGCTTGCCGTCTACTACACGCAGGCGCGTGCCGATGCGAAGGCGAAGGACGAGGTGATCGCGGCCGCGACGCGGATCGCGATCGCGACGCTCGCGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43748","NCBI_taxonomy_name":"Burkholderia multivorans","NCBI_taxonomy_id":"87883"}}}},"ARO_accession":"3009003","ARO_id":"47795","ARO_name":"PEN-A25","CARD_short_name":"PEN-A25","ARO_description":"Class A beta-lactamase PEN-A25.","ARO_category":{"46664":{"category_aro_accession":"3007873","category_aro_cvterm_id":"46664","category_aro_name":"PEN-A beta-lactamase","category_aro_description":"PEN-A is a family of class A beta-lactamases which enzymatically inactivate beta-lactam antibiotics.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8422":{"model_id":"8422","model_name":"PEN-A26","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11249":{"protein_sequence":{"accession":"PRE61420.1","sequence":"MTHSPQRRILLLAAATAPLALSLGACAARDAAVSDTASPVGAAPASFAALERAAGGRLGVCAIDTATGRRALYRAGERFPFCSTFKAMLAAAVLAQSVAHPGLLQQRVTYGRSDLVNYSPVTERHVDTGMTVAELCAATIQYSDNTAANELMKRIGGPAAVTAYARSIGDDTFRLDRWETEPNTALPGDLRDTTTPEAMAASLRVLVLGDALPPAQRAQLIEWLRGNKVGDKRIRAGVPTGWRVGDKTGTGDYGTTNDAGVLWPPSRAPIVLAVYYTQARADAKAKDDVIAAATRIAIATLA"},"dna_sequence":{"accession":"PVFS01000052.1","fmin":"25745","fmax":"26654","strand":"-","sequence":"ATGACTCATTCACCTCAACGTCGAATCCTGTTGCTGGCTGCCGCGACGGCGCCGCTCGCGTTGTCCCTCGGCGCGTGCGCGGCGCGCGATGCGGCGGTGTCCGACACAGCGTCGCCTGTCGGCGCGGCGCCGGCATCGTTCGCCGCACTCGAACGCGCAGCCGGCGGCCGGCTCGGCGTCTGCGCGATCGATACCGCGACGGGCCGGCGCGCGCTGTATCGCGCCGGCGAGCGCTTCCCGTTCTGCAGCACCTTCAAGGCGATGCTCGCTGCGGCGGTGCTCGCGCAGAGCGTCGCACATCCTGGCCTGCTGCAGCAGCGCGTGACGTACGGCCGGTCCGATCTCGTCAACTATTCGCCCGTGACCGAGCGGCACGTCGACACCGGCATGACGGTCGCCGAGCTCTGCGCGGCGACGATCCAGTACAGCGACAACACGGCCGCGAACGAGCTGATGAAGCGGATCGGCGGCCCGGCAGCGGTCACGGCCTATGCGCGCTCGATCGGCGACGATACGTTTCGCCTCGATCGCTGGGAGACCGAACCGAACACCGCGCTGCCGGGCGATCTTCGCGACACGACGACGCCCGAGGCGATGGCCGCGAGCCTGCGCGTGCTCGTGCTCGGCGACGCGTTGCCGCCCGCGCAGCGGGCGCAGCTGATCGAATGGCTGCGCGGCAACAAGGTCGGCGACAAGCGCATCCGCGCGGGCGTGCCGACCGGCTGGCGCGTCGGCGACAAGACGGGCACCGGCGACTACGGGACGACGAACGATGCCGGCGTGCTGTGGCCGCCGTCGCGCGCGCCGATCGTGCTTGCCGTCTACTACACGCAGGCGCGTGCCGATGCGAAGGCGAAGGACGACGTGATCGCGGCCGCGACGCGGATCGCGATCGCGACGCTCGCGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43748","NCBI_taxonomy_name":"Burkholderia multivorans","NCBI_taxonomy_id":"87883"}}}},"ARO_accession":"3009004","ARO_id":"47796","ARO_name":"PEN-A26","CARD_short_name":"PEN-A26","ARO_description":"Class A beta-lactamase PEN-A26.","ARO_category":{"46664":{"category_aro_accession":"3007873","category_aro_cvterm_id":"46664","category_aro_name":"PEN-A beta-lactamase","category_aro_description":"PEN-A is a family of class A beta-lactamases which enzymatically inactivate beta-lactam antibiotics.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8423":{"model_id":"8423","model_name":"PEN-A27","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11250":{"protein_sequence":{"accession":"PRF07752.1","sequence":"MTHSPQRRILLLAAATAPLALSLGACAARDAAVSDTASPVGAAPASFAALERAAGGRLGVCAIDTATGRRALYRAGERFPFCSTFKAMLAAAVLAQSVAHPGLLQQRVTYGRSDLVNYSPVTERHVDTGMTVAELCAATIQYSDSTAANELMKRIGGPAAVTAYARSIGDDTFRLDRWETELNTALPGDLRDTTTPEAMAASLRVLVLGDALPPAQRAQLIEWLRGNKVGDKRIRAGVPTGWRVGDKTGTGDYGTTNDAGVLWPPSRAPIVLAVYYTQARADAKAKDDVIAAATRIAIATLA"},"dna_sequence":{"accession":"PVFV01000050.1","fmin":"230201","fmax":"231110","strand":"+","sequence":"ATGACTCATTCACCTCAACGTCGAATCCTGTTGCTGGCTGCCGCGACGGCGCCGCTCGCGTTGTCCCTCGGCGCGTGCGCGGCGCGCGATGCGGCGGTGTCCGACACAGCGTCGCCTGTCGGCGCGGCGCCGGCATCGTTCGCCGCACTCGAACGCGCAGCCGGCGGCCGGCTCGGCGTCTGCGCGATCGATACCGCGACGGGCCGGCGCGCGCTGTATCGCGCCGGCGAGCGCTTCCCGTTCTGCAGCACCTTCAAGGCGATGCTCGCTGCGGCGGTGCTCGCGCAGAGCGTCGCACATCCTGGCCTGCTGCAGCAGCGCGTGACGTACGGCCGGTCCGATCTCGTCAACTATTCGCCCGTGACCGAGCGGCACGTCGACACCGGCATGACGGTCGCCGAGCTCTGCGCGGCGACGATCCAGTACAGCGACAGCACGGCCGCGAACGAGCTGATGAAGCGGATCGGCGGCCCGGCAGCGGTCACGGCCTATGCGCGCTCGATCGGCGACGATACGTTTCGCCTCGATCGCTGGGAGACCGAACTGAACACCGCGCTGCCGGGCGATCTTCGCGACACGACGACGCCCGAGGCGATGGCCGCGAGCCTGCGCGTGCTCGTGCTCGGCGACGCGTTGCCGCCCGCGCAGCGGGCGCAGCTGATCGAATGGCTGCGCGGCAACAAGGTCGGCGACAAGCGCATCCGCGCGGGCGTGCCGACCGGCTGGCGCGTCGGCGACAAGACGGGCACCGGCGACTACGGGACGACGAACGATGCCGGCGTGCTGTGGCCGCCGTCGCGCGCGCCGATCGTGCTTGCCGTCTACTACACGCAGGCGCGTGCCGATGCGAAGGCGAAGGACGACGTGATCGCGGCCGCGACGCGGATCGCGATCGCGACGCTCGCGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43748","NCBI_taxonomy_name":"Burkholderia multivorans","NCBI_taxonomy_id":"87883"}}}},"ARO_accession":"3009005","ARO_id":"47797","ARO_name":"PEN-A27","CARD_short_name":"PEN-A27","ARO_description":"Class A beta-lactamase PEN-A27.","ARO_category":{"46664":{"category_aro_accession":"3007873","category_aro_cvterm_id":"46664","category_aro_name":"PEN-A beta-lactamase","category_aro_description":"PEN-A is a family of class A beta-lactamases which enzymatically inactivate beta-lactam antibiotics.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8424":{"model_id":"8424","model_name":"PEN-A28","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11251":{"protein_sequence":{"accession":"SAJ87944.1","sequence":"MTHSSQRRILLLAAAAAPLALSVGACAARDAAVSDAASPVGAAPASFAALERAAGGRLGVCAIDTATGRRTLHRADERFPFCSTFKAMLGAAVLAQSVAHPGLLQQRVTYGRSDLVSYSPVTERHVDTGMTVAELCAATIQYSDNTAANELMKLIGGPAAVTAYARSIGDDTFRLDRWETELNTALPGDLRDTTTPAAMAASLRVLVLGDALPAAQRAQLIEWLRGNKVGDKRIRAGVPTGWRVGDKTGTGDYGTTNDAGVLWPPSRAPIVLAVYYTQTRADAKAKDDVIATATRIAIATLG"},"dna_sequence":{"accession":"FKJT01000002.1","fmin":"616394","fmax":"617303","strand":"+","sequence":"ATGACTCATTCATCTCAACGTCGAATCCTGTTGCTGGCTGCCGCGGCGGCGCCGCTCGCGTTGTCCGTCGGCGCATGCGCGGCGCGCGATGCGGCGGTGTCCGACGCAGCGTCGCCTGTCGGCGCGGCGCCGGCATCGTTCGCCGCGCTCGAACGCGCGGCCGGCGGCCGGCTCGGCGTCTGCGCGATCGATACCGCGACCGGGCGGCGCACGTTGCATCGCGCGGACGAGCGCTTCCCTTTCTGCAGCACCTTCAAGGCGATGCTCGGCGCGGCGGTGCTCGCGCAAAGCGTCGCGCATCCCGGCCTGCTGCAGCAGCGCGTGACGTACGGCCGGTCCGATCTCGTCAGCTACTCGCCGGTGACCGAGCGACACGTCGACACCGGCATGACGGTCGCCGAGCTCTGCGCGGCGACGATCCAGTACAGCGACAACACGGCCGCGAACGAGCTGATGAAGCTGATCGGCGGCCCGGCGGCGGTCACGGCCTATGCGCGCTCGATCGGCGACGACACGTTCCGGCTCGATCGCTGGGAGACCGAGCTGAATACCGCGCTGCCGGGCGATCTTCGCGACACGACGACGCCCGCGGCGATGGCCGCGAGCCTGCGCGTGCTCGTGCTCGGCGATGCGTTGCCGGCCGCGCAGCGCGCGCAGCTGATCGAATGGCTGCGCGGCAACAAGGTCGGCGACAAGCGTATCCGCGCGGGCGTGCCGACCGGCTGGCGCGTCGGCGACAAGACGGGCACCGGCGACTACGGGACGACGAACGATGCCGGCGTGCTGTGGCCGCCGTCGCGCGCGCCGATCGTGCTTGCCGTCTACTACACGCAGACGCGTGCCGATGCGAAGGCGAAGGACGACGTGATCGCGACCGCGACGCGGATCGCGATCGCGACGCTCGGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43748","NCBI_taxonomy_name":"Burkholderia multivorans","NCBI_taxonomy_id":"87883"}}}},"ARO_accession":"3009006","ARO_id":"47798","ARO_name":"PEN-A28","CARD_short_name":"PEN-A28","ARO_description":"Class A beta-lactamase PEN-A28.","ARO_category":{"46664":{"category_aro_accession":"3007873","category_aro_cvterm_id":"46664","category_aro_name":"PEN-A beta-lactamase","category_aro_description":"PEN-A is a family of class A beta-lactamases which enzymatically inactivate beta-lactam antibiotics.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8425":{"model_id":"8425","model_name":"PEN-A29","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11252":{"protein_sequence":{"accession":"PRF24721.1","sequence":"MTHSSQRRILLLAAAAAPLALSVGACAARDAAVSDAASPVGAAPASFAALERAAGGRLGVCAIDTATGRRALHRADERFPFCSTFKAMLGAAVLAQSVAHPGLLQQRVTYGQSDLVSYSPVTERHVDTGMTVAELCAATIQYSDNTAANELMKLIGGPAAVTAYARSIGDDTFRLDRWETELNTALPGDLRDTTTPAAMAASLRVLVLGDALPAAQRAQLIEWLRGNKVGDKRIRAGVPAGWRVGDKTGTGDYGTTNDVGVLWPPSRAPIVLAVYYTQTRADAKAKDDVIATATRIAIATLG"},"dna_sequence":{"accession":"PVFY01000023.1","fmin":"180338","fmax":"181247","strand":"-","sequence":"ATGACTCATTCATCTCAACGTCGAATCCTGTTGCTGGCTGCCGCGGCGGCGCCGCTCGCGTTGTCCGTCGGCGCATGCGCGGCGCGCGATGCGGCGGTGTCCGACGCAGCGTCGCCTGTCGGCGCGGCGCCGGCATCGTTCGCCGCGCTCGAACGCGCGGCCGGCGGCCGGCTCGGCGTCTGCGCGATCGATACCGCGACCGGGCGGCGCGCGTTGCATCGCGCGGACGAGCGCTTCCCGTTTTGCAGCACCTTCAAGGCGATGCTCGGCGCGGCGGTGCTCGCGCAAAGCGTCGCGCATCCCGGCCTGCTGCAGCAGCGCGTGACGTACGGCCAGTCCGATCTCGTCAGCTACTCGCCGGTGACCGAGCGACACGTCGACACCGGCATGACGGTCGCCGAGCTCTGCGCGGCGACGATCCAGTACAGCGACAACACAGCCGCGAACGAGCTGATGAAGCTGATCGGCGGCCCGGCGGCGGTCACGGCCTATGCGCGCTCGATCGGCGACGACACGTTCCGGCTCGATCGCTGGGAGACCGAGCTGAATACCGCGCTGCCGGGCGATCTTCGCGACACGACGACGCCCGCGGCGATGGCCGCGAGCCTGCGCGTGCTCGTGCTCGGCGATGCGTTGCCGGCCGCACAGCGCGCGCAGCTGATCGAATGGCTGCGCGGCAACAAGGTCGGCGACAAGCGTATCCGCGCGGGCGTGCCGGCCGGCTGGCGCGTCGGCGACAAGACGGGCACCGGCGACTACGGGACGACGAACGATGTCGGCGTGCTGTGGCCGCCGTCGCGCGCGCCGATCGTGCTTGCCGTCTACTACACGCAGACGCGTGCCGATGCGAAGGCGAAGGACGACGTGATCGCGACCGCGACGCGGATCGCGATCGCGACGCTCGGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43748","NCBI_taxonomy_name":"Burkholderia multivorans","NCBI_taxonomy_id":"87883"}}}},"ARO_accession":"3009007","ARO_id":"47799","ARO_name":"PEN-A29","CARD_short_name":"PEN-A29","ARO_description":"Class A beta-lactamase PEN-A29.","ARO_category":{"46664":{"category_aro_accession":"3007873","category_aro_cvterm_id":"46664","category_aro_name":"PEN-A beta-lactamase","category_aro_description":"PEN-A is a family of class A beta-lactamases which enzymatically inactivate beta-lactam antibiotics.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8426":{"model_id":"8426","model_name":"PEN-A2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11253":{"protein_sequence":{"accession":"MBU9633967.1","sequence":"MTHSPQRRILLLAAATAPLALSLGACAARDATVSDAASPVGAAPASFAALERAAGGRLGVCAIDTATGRRALHRADERFPFCSTFKAMLGAAVLAQSVAHPGLLQQRVTYGRSDLVNYSPVTERHVDTGMTVAELCAATIQYSDNTAANELMKRIGGPAAVTAYARSIGDDTFRLDRWETELNTALPGDLRDTTTPAAMAASLRVLVLGDALPPAQRAQLIEWLRGNKVGDKRIRAGVPTGWRVGDKTGTGDYGTTNDAGVLWPPSRAPIVLAVYYTQARADAKAKDDVIAAATRIAIATLARAATRE"},"dna_sequence":{"accession":"JAHPOU010000001.1","fmin":"179001","fmax":"179928","strand":"-","sequence":"ATGACTCATTCACCTCAACGTCGAATCCTGTTGCTGGCTGCCGCGACGGCGCCGCTCGCGTTGTCCCTCGGCGCGTGCGCGGCGCGCGATGCGACGGTGTCCGACGCAGCGTCGCCTGTCGGCGCGGCGCCGGCATCGTTCGCCGCACTCGAACGCGCGGCCGGCGGCCGGCTCGGCGTCTGCGCGATCGATACCGCGACGGGCCGGCGCGCGCTGCATCGCGCCGACGAGCGCTTTCCGTTCTGCAGCACCTTCAAGGCGATGCTCGGCGCGGCGGTGCTCGCGCAGAGCGTCGCGCATCCGGGCCTGCTGCAGCAGCGCGTGACGTACGGCCGGTCCGATCTCGTCAACTATTCGCCCGTGACCGAGCGGCACGTCGACACCGGCATGACGGTCGCCGAGCTCTGCGCGGCGACGATCCAGTACAGCGACAACACGGCTGCGAACGAGCTGATGAAGCGGATCGGCGGCCCGGCAGCGGTCACGGCCTATGCGCGCTCGATCGGCGACGACACGTTCCGCCTCGATCGCTGGGAGACCGAACTGAACACCGCGCTGCCGGGCGATCTTCGCGACACGACGACACCCGCTGCGATGGCCGCGAGCCTGCGCGTGCTCGTGCTCGGCGATGCGTTGCCGCCCGCGCAGCGCGCGCAGCTGATCGAATGGCTGCGCGGCAACAAGGTCGGCGACAAGCGCATCCGCGCGGGCGTGCCGACCGGCTGGCGCGTCGGCGACAAGACGGGCACCGGCGACTACGGGACGACGAACGATGCCGGCGTGCTGTGGCCGCCGTCGCGCGCGCCGATCGTACTTGCCGTCTACTACACGCAGGCGCGTGCCGATGCGAAGGCGAAGGACGACGTGATCGCGGCCGCGACGCGGATCGCGATCGCGACGCTCGCGCGAGCGGCCACGCGTGAATGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43748","NCBI_taxonomy_name":"Burkholderia multivorans","NCBI_taxonomy_id":"87883"}}}},"ARO_accession":"3009008","ARO_id":"47800","ARO_name":"PEN-A2","CARD_short_name":"PEN-A2","ARO_description":"Class A beta-lactamase PEN-A2.","ARO_category":{"46664":{"category_aro_accession":"3007873","category_aro_cvterm_id":"46664","category_aro_name":"PEN-A beta-lactamase","category_aro_description":"PEN-A is a family of class A beta-lactamases which enzymatically inactivate beta-lactam antibiotics.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8427":{"model_id":"8427","model_name":"PEN-A30","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11254":{"protein_sequence":{"accession":"PRF30389.1","sequence":"MTHSSQRRILLLAAAAAPLALSVGACAARDAAVSDAASAVGAAPASFAALERAAGGRLGVCAIDTATGRRTLHRADERFPFCSTFKAMLGAAVLAQSVAHPGLLQQRVTYGRSDLVSYSPVTERHVDTGMTVAELCAATIQYSDNTAANELMKLIGGPAAVTAYARSIGDDTFRLDRWETELNTALPGDLRDTTTPAAMAASLRVLVLGDALPAAQRAQLIEWLRGNKVGDRRIRAGVPTGWRVGDKTGTGDYGTTNDVGVLWPPSRAPIVLAVYYTQTRADAKAKDDVIATATRIAIATLG"},"dna_sequence":{"accession":"PVGF01000057.1","fmin":"204570","fmax":"205479","strand":"+","sequence":"ATGACTCATTCATCTCAACGTCGAATCCTGTTGCTGGCTGCCGCGGCGGCGCCGCTCGCGTTGTCCGTCGGCGCATGCGCGGCGCGCGATGCGGCGGTGTCCGACGCAGCGTCGGCTGTCGGCGCGGCGCCGGCATCGTTCGCCGCGCTCGAACGCGCGGCCGGCGGCCGGCTCGGCGTCTGCGCGATCGATACCGCGACCGGGCGGCGCACGTTGCATCGCGCGGACGAGCGCTTCCCTTTCTGCAGCACCTTCAAGGCGATGCTCGGCGCGGCGGTGCTCGCGCAAAGCGTCGCGCATCCCGGCCTGCTGCAGCAGCGCGTGACGTACGGCCGGTCCGATCTCGTCAGCTACTCGCCGGTGACCGAGCGACACGTCGACACCGGCATGACGGTCGCCGAGCTCTGCGCGGCGACGATCCAGTACAGCGACAACACGGCCGCGAACGAGCTGATGAAGCTGATCGGCGGCCCGGCGGCGGTCACGGCCTATGCGCGCTCGATCGGCGACGACACGTTCCGGCTCGATCGCTGGGAGACCGAGCTGAATACCGCGCTGCCGGGCGATCTTCGCGACACGACGACGCCCGCGGCGATGGCCGCGAGCCTGCGCGTGCTCGTGCTCGGCGATGCGTTGCCGGCCGCGCAGCGCGCGCAGCTGATCGAATGGCTGCGCGGCAACAAGGTCGGCGACAGGCGTATCCGCGCGGGCGTGCCGACCGGCTGGCGCGTCGGCGACAAGACGGGCACCGGCGACTACGGGACGACGAACGATGTCGGCGTGCTGTGGCCGCCGTCGCGCGCGCCGATCGTGCTTGCCGTCTACTACACGCAGACGCGTGCCGATGCGAAGGCGAAGGACGACGTGATCGCGACCGCGACGCGGATCGCGATCGCGACGCTCGGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43748","NCBI_taxonomy_name":"Burkholderia multivorans","NCBI_taxonomy_id":"87883"}}}},"ARO_accession":"3009009","ARO_id":"47801","ARO_name":"PEN-A30","CARD_short_name":"PEN-A30","ARO_description":"Class A beta-lactamase PEN-A30.","ARO_category":{"46664":{"category_aro_accession":"3007873","category_aro_cvterm_id":"46664","category_aro_name":"PEN-A beta-lactamase","category_aro_description":"PEN-A is a family of class A beta-lactamases which enzymatically inactivate beta-lactam antibiotics.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8428":{"model_id":"8428","model_name":"PEN-A31","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11255":{"protein_sequence":{"accession":"KHS16526.1","sequence":"MTHSSQRRILLLAAATAPLALSLGACAARDAAVSDAALPVGAAPASFAALERAAGGRLGVCAIDAATGRRALHRADERFPFCSTFKAMLAAAVLAQSVAHPGLLQQRVTYGRSDLVNYSPVTERYVDTGMAVAELCAATIQYSDNTAANELMKRIGGPAAVTAYARSIGDDTFRLDRWETELNTALPGDLRDTTTPAAMAASLRVLVLGDALPPAQRAQLIEWLRGNKVGDKRIRAGVPTGWRVGDKTGTGDYGTTNDAGVLWPPSRAPIVLAVYYTQARADAKAKDDVIAAATQIAIATLG"},"dna_sequence":{"accession":"JFHP01000003.1","fmin":"850218","fmax":"851127","strand":"-","sequence":"ATGACTCATTCATCTCAACGTCGAATCCTGTTGCTCGCTGCCGCAACGGCGCCGCTCGCGTTGTCCCTCGGCGCGTGCGCGGCGCGCGATGCAGCGGTGTCCGACGCAGCGTTGCCTGTCGGCGCGGCGCCGGCATCGTTCGCCGCGCTCGAACGCGCAGCCGGCGGCCGGCTCGGCGTCTGCGCGATCGATGCCGCGACCGGCCGGCGCGCGCTGCATCGCGCCGACGAGCGCTTTCCGTTCTGCAGCACCTTCAAGGCGATGCTCGCCGCGGCGGTGCTCGCGCAGAGCGTCGCGCATCCCGGCCTGCTGCAGCAGCGCGTGACGTATGGCCGGTCCGATCTGGTCAACTATTCGCCGGTGACCGAGCGATACGTCGACACCGGCATGGCGGTCGCCGAGCTCTGCGCGGCGACGATCCAGTACAGCGACAACACGGCCGCGAACGAGCTGATGAAGCGGATCGGCGGCCCGGCGGCGGTCACGGCCTATGCGCGCTCGATCGGCGACGACACGTTCCGCCTCGATCGCTGGGAGACCGAACTGAATACCGCGCTGCCGGGCGATCTTCGCGACACGACGACGCCCGCGGCGATGGCCGCGAGCCTGCGCGTGCTCGTGCTCGGCGATGCGTTGCCGCCCGCGCAGCGCGCGCAGCTGATCGAATGGCTGCGCGGCAACAAGGTCGGCGACAAGCGCATCCGCGCGGGCGTGCCGACCGGCTGGCGCGTCGGCGACAAGACGGGCACCGGCGACTACGGTACGACGAACGATGCCGGCGTGCTGTGGCCGCCGTCGCGCGCGCCGATCGTGCTTGCCGTCTACTACACGCAGGCGCGTGCCGATGCGAAGGCGAAGGACGACGTGATCGCGGCCGCGACGCAGATCGCGATCGCGACGCTCGGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43748","NCBI_taxonomy_name":"Burkholderia multivorans","NCBI_taxonomy_id":"87883"}}}},"ARO_accession":"3009010","ARO_id":"47802","ARO_name":"PEN-A31","CARD_short_name":"PEN-A31","ARO_description":"Class A beta-lactamase PEN-A31.","ARO_category":{"46664":{"category_aro_accession":"3007873","category_aro_cvterm_id":"46664","category_aro_name":"PEN-A beta-lactamase","category_aro_description":"PEN-A is a family of class A beta-lactamases which enzymatically inactivate beta-lactam antibiotics.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8429":{"model_id":"8429","model_name":"PEN-A32","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11256":{"protein_sequence":{"accession":"MCO1416124.1","sequence":"MTHSSQRRILLLAAAAAPLALSVGACAARDAAVSDAASPVGAAPASFAALERAAGGRLGVCAIDTATGRRTLHRADERFPFCSTFKAMLGAAVLAQSVAHPGLLQQRVTYGRSDLVSYSPVTERHVDTGMTVAELCAATIQYSDNTAANELMKLIGGPAAVTAYARSIGDDTFRLDRWETELNTALPGDLRDTTTPAAMAASLRVLVLGDALPAAQRAQLIEWLRGNKVGDKRIRAGVPAGWRVGDKTGTGDYGTTNDAGVLWPPSRAPIVLAVYYTQTRADAKAKDDVIATATRIAIATLG"},"dna_sequence":{"accession":"JAKFAI010000002.1","fmin":"1840161","fmax":"1841070","strand":"-","sequence":"ATGACTCATTCATCTCAACGTCGAATCCTGTTGCTGGCTGCCGCGGCGGCGCCGCTCGCGTTGTCCGTCGGCGCATGCGCGGCGCGCGATGCGGCGGTGTCCGACGCAGCGTCGCCTGTCGGCGCGGCGCCGGCATCGTTCGCCGCGCTCGAACGCGCGGCCGGCGGCCGGCTCGGCGTCTGCGCGATCGATACCGCGACCGGGCGGCGCACGTTGCATCGCGCGGACGAGCGCTTCCCTTTCTGCAGCACCTTCAAGGCGATGCTCGGCGCGGCGGTGCTCGCGCAAAGCGTCGCGCATCCCGGCCTGCTGCAGCAGCGCGTGACGTACGGCCGGTCCGATCTCGTCAGCTACTCGCCGGTGACCGAGCGACACGTCGACACCGGCATGACGGTCGCCGAGCTCTGCGCGGCGACGATCCAGTACAGCGACAACACGGCCGCGAACGAGCTGATGAAGCTGATCGGCGGCCCGGCGGCGGTCACGGCCTATGCGCGCTCGATCGGCGACGACACGTTCCGGCTCGATCGCTGGGAGACCGAGCTGAATACCGCGCTGCCGGGCGATCTTCGCGACACGACGACGCCCGCGGCGATGGCCGCGAGCCTGCGCGTGCTCGTGCTCGGCGATGCGTTGCCGGCCGCACAGCGCGCGCAGCTGATCGAATGGCTGCGCGGCAACAAGGTCGGCGACAAGCGTATCCGCGCGGGCGTGCCGGCCGGCTGGCGCGTCGGCGACAAGACGGGCACCGGCGACTACGGGACGACGAACGATGCCGGCGTGCTGTGGCCGCCGTCGCGCGCGCCGATCGTGCTTGCCGTCTACTACACGCAGACGCGTGCCGATGCGAAGGCGAAGGACGACGTGATCGCGACCGCGACGCGGATCGCGATCGCGACGCTCGGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43748","NCBI_taxonomy_name":"Burkholderia multivorans","NCBI_taxonomy_id":"87883"}}}},"ARO_accession":"3009011","ARO_id":"47803","ARO_name":"PEN-A32","CARD_short_name":"PEN-A32","ARO_description":"Class A beta-lactamase PEN-A32.","ARO_category":{"46664":{"category_aro_accession":"3007873","category_aro_cvterm_id":"46664","category_aro_name":"PEN-A beta-lactamase","category_aro_description":"PEN-A is a family of class A beta-lactamases which enzymatically inactivate beta-lactam antibiotics.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8430":{"model_id":"8430","model_name":"PEN-A33","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11257":{"protein_sequence":{"accession":"AOJ95146.1","sequence":"MTHSSQRRILLLAAAAAPLALSVGACAARDAAVSDAASPVGAAPASFAALERAAGGRLGVCAIDTATGRRALHRADERFPFCSTFKAMLGAAVLAQSVAHPGLLQQRVTYGRSDLVSYSPVTERHVDTGMTVAELCAATIQYSDNTAANELMKLIGGPAAVTAYARSIGDDTFRLDRWETELNTALPGDLRDTTTPAAMAASLRVLVLGDALPAAQRAQLIEWLRGNKVGDKRIRAGVPAGWRVGDKTGTGDYGTTNDAGVMWPPSRAPIVLAVYYTQTRADAKAKDDVIATATRIAIATLG"},"dna_sequence":{"accession":"CP013431.1","fmin":"754574","fmax":"755483","strand":"+","sequence":"ATGACTCATTCATCTCAACGTCGAATCCTGTTGCTGGCTGCCGCGGCGGCGCCGCTCGCGTTGTCCGTCGGCGCATGCGCGGCGCGCGATGCGGCGGTGTCCGACGCAGCGTCGCCTGTCGGCGCGGCGCCGGCATCGTTCGCCGCGCTCGAACGCGCGGCCGGCGGCCGGCTCGGCGTCTGCGCGATCGATACCGCGACCGGGCGGCGCGCGTTGCATCGCGCGGACGAGCGCTTCCCTTTCTGCAGCACCTTCAAGGCGATGCTCGGCGCGGCGGTGCTCGCGCAAAGCGTCGCGCATCCCGGCCTGCTGCAGCAGCGCGTGACGTACGGCCGGTCCGATCTCGTCAGCTACTCGCCGGTGACCGAGCGACACGTCGACACCGGCATGACGGTCGCCGAGCTCTGCGCGGCGACGATCCAGTACAGCGACAACACGGCCGCGAACGAGCTGATGAAGCTGATCGGCGGCCCGGCGGCGGTCACGGCCTATGCGCGCTCGATCGGCGACGACACGTTCCGGCTCGATCGCTGGGAGACCGAGCTGAATACCGCGCTGCCGGGCGATCTTCGCGACACGACGACGCCCGCGGCGATGGCCGCGAGCCTGCGCGTGCTCGTGCTCGGCGATGCGTTGCCGGCCGCACAGCGCGCGCAGCTGATCGAATGGCTGCGCGGCAACAAGGTCGGCGACAAGCGTATCCGCGCGGGCGTGCCGGCCGGCTGGCGCGTCGGCGACAAGACGGGCACCGGCGACTACGGGACGACGAACGATGCCGGCGTGATGTGGCCGCCGTCGCGCGCGCCGATCGTGCTTGCCGTCTACTACACGCAGACGCGTGCCGATGCGAAGGCGAAGGACGACGTGATCGCGACCGCGACGCGGATCGCGATCGCGACGCTCGGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43748","NCBI_taxonomy_name":"Burkholderia multivorans","NCBI_taxonomy_id":"87883"}}}},"ARO_accession":"3009012","ARO_id":"47804","ARO_name":"PEN-A33","CARD_short_name":"PEN-A33","ARO_description":"Class A beta-lactamase PEN-A33.","ARO_category":{"46664":{"category_aro_accession":"3007873","category_aro_cvterm_id":"46664","category_aro_name":"PEN-A beta-lactamase","category_aro_description":"PEN-A is a family of class A beta-lactamases which enzymatically inactivate beta-lactam antibiotics.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8431":{"model_id":"8431","model_name":"PEN-A34","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11258":{"protein_sequence":{"accession":"UQO45168.1","sequence":"MTHSSQRRILLLAAAAAPLALSVGACAARDAAVSDAASPVGAAPASFAALERAAGGRLGVCAIDTATGRRALHRADERFPFCSTFKAMLGAAVLAQSVAHPGLLQQRVTYGRSDLVSYSPVTERHVDTGMTVAELCAATIQYSDNTAANELMKLIGGPAAVTAYARSIGDDTFRLDRWETELNTALPGDLRDTTTPAAMAASLRVLVLVLGDALPAAQRAQLIEWLRGNKVGDKRIRAGVPAGWRVGDKTGTGDYGTTNDAGVMWPPSRAPIVLAVYYTQTRADAKAKDDVIATATRIAIATLG"},"dna_sequence":{"accession":"CP090735.1","fmin":"578537","fmax":"579452","strand":"+","sequence":"ATGACTCATTCATCTCAACGTCGAATCCTGTTGCTGGCTGCCGCGGCGGCGCCGCTCGCGTTGTCCGTCGGCGCATGCGCGGCGCGCGATGCGGCGGTGTCCGACGCAGCGTCGCCTGTCGGCGCGGCGCCGGCATCGTTCGCCGCGCTCGAACGCGCGGCCGGCGGCCGGCTCGGCGTCTGCGCGATCGATACCGCGACCGGGCGGCGCGCGTTGCATCGCGCGGACGAGCGCTTCCCTTTCTGCAGCACCTTCAAGGCGATGCTCGGCGCGGCGGTGCTCGCGCAAAGCGTCGCGCATCCCGGCCTGCTGCAGCAGCGCGTGACGTACGGCCGGTCCGATCTCGTCAGCTACTCGCCGGTGACCGAGCGACACGTCGACACCGGCATGACGGTCGCCGAGCTCTGCGCGGCGACGATCCAGTACAGCGACAACACGGCCGCGAACGAGCTGATGAAGCTGATCGGCGGCCCGGCGGCGGTCACGGCCTATGCGCGCTCGATCGGCGACGACACGTTCCGGCTCGATCGCTGGGAGACCGAGCTGAATACCGCGCTGCCGGGCGATCTTCGCGACACGACGACGCCCGCGGCGATGGCCGCGAGCCTGCGCGTGCTCGTGCTCGTGCTCGGCGATGCGTTGCCGGCCGCACAGCGCGCGCAGCTGATCGAATGGCTGCGCGGCAACAAGGTCGGCGACAAGCGTATCCGCGCGGGCGTGCCGGCCGGCTGGCGCGTCGGCGACAAGACGGGCACCGGCGACTACGGGACGACGAACGATGCCGGCGTGATGTGGCCGCCGTCGCGCGCGCCGATCGTGCTTGCCGTCTACTACACGCAGACGCGTGCCGATGCGAAGGCGAAGGACGACGTGATCGCGACCGCGACGCGGATCGCGATCGCGACGCTCGGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43748","NCBI_taxonomy_name":"Burkholderia multivorans","NCBI_taxonomy_id":"87883"}}}},"ARO_accession":"3009013","ARO_id":"47805","ARO_name":"PEN-A34","CARD_short_name":"PEN-A34","ARO_description":"Class A beta-lactamase PEN-A34.","ARO_category":{"46664":{"category_aro_accession":"3007873","category_aro_cvterm_id":"46664","category_aro_name":"PEN-A beta-lactamase","category_aro_description":"PEN-A is a family of class A beta-lactamases which enzymatically inactivate beta-lactam antibiotics.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8432":{"model_id":"8432","model_name":"PEN-A35","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11259":{"protein_sequence":{"accession":"PRG97828.1","sequence":"MTHSSQRRILLLAAAAAPLALSVGACAARDAPTDNAASPGGAAPASFAALERAAGGRLGVCAIDTATGRRALHRADERFPFCSTFKAMLGAAVLAQSVAHPGLLQQRVTYGRSDLVSYSPVTERHVDTGMTVAELCAATIQYSDNTAANELMKLIGGPAAVTAYARSIGDDTFRLDRWETELNTALPGDLRDTTTPAAMAASLRVLVLGDALPAAQRAQLIEWLRGNKVGDKRIRAGVPAGWRVGDKTGTGDYGTTNDAGVLWPPSRAPIVLAVYYTQTRADAKAKDDVIATATRIAIATLG"},"dna_sequence":{"accession":"PVHF01000072.1","fmin":"208216","fmax":"209125","strand":"+","sequence":"ATGACTCATTCATCTCAACGTCGAATCCTGTTGCTGGCTGCCGCGGCGGCGCCGCTCGCGTTGTCCGTCGGCGCATGCGCGGCGCGCGATGCGCCGACGGACAACGCAGCGTCGCCTGGCGGCGCGGCACCGGCATCGTTCGCCGCGCTCGAACGCGCGGCCGGCGGCCGGCTCGGCGTCTGCGCGATCGATACCGCGACCGGGCGGCGCGCGTTGCATCGCGCGGACGAGCGCTTCCCTTTCTGCAGCACCTTCAAGGCGATGCTCGGCGCGGCGGTGCTCGCGCAAAGCGTCGCGCATCCCGGCCTGCTGCAGCAGCGCGTGACGTACGGCCGGTCCGATCTCGTCAGCTACTCGCCGGTGACCGAGCGACACGTCGACACCGGCATGACGGTCGCCGAGCTCTGCGCGGCGACGATCCAGTACAGCGACAACACGGCCGCGAACGAACTGATGAAGCTGATCGGCGGCCCGGCGGCGGTCACGGCCTATGCGCGCTCGATCGGCGACGACACGTTCCGGCTCGATCGCTGGGAGACCGAGCTGAATACCGCGCTGCCGGGCGATCTTCGCGACACGACGACGCCCGCGGCGATGGCCGCGAGCCTGCGCGTGCTCGTGCTCGGCGATGCGTTGCCGGCCGCACAGCGCGCGCAGCTGATCGAATGGCTGCGCGGCAACAAGGTCGGCGACAAGCGTATCCGCGCGGGCGTGCCGGCCGGCTGGCGCGTCGGCGACAAGACGGGCACCGGCGACTACGGGACGACGAACGATGCCGGCGTGCTGTGGCCGCCGTCGCGCGCGCCGATCGTGCTTGCCGTCTACTACACGCAGACGCGTGCCGATGCGAAGGCGAAGGACGACGTGATCGCGACCGCGACGCGGATCGCGATCGCGACGCTCGGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43748","NCBI_taxonomy_name":"Burkholderia multivorans","NCBI_taxonomy_id":"87883"}}}},"ARO_accession":"3009014","ARO_id":"47806","ARO_name":"PEN-A35","CARD_short_name":"PEN-A35","ARO_description":"Class A beta-lactamase PEN-A35.","ARO_category":{"46664":{"category_aro_accession":"3007873","category_aro_cvterm_id":"46664","category_aro_name":"PEN-A beta-lactamase","category_aro_description":"PEN-A is a family of class A beta-lactamases which enzymatically inactivate beta-lactam antibiotics.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8433":{"model_id":"8433","model_name":"PEN-A37","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11260":{"protein_sequence":{"accession":"UQN71920.1","sequence":"MTHSSQRRILLLAAAAAPLALSVGACAARDAPTDNAASPGGAAPASFAALERAAGGRLGVCAIDTATGRRTLHRADERFPFCSTFKAMLGAAVLAQSVAHPGLLQQRVTYGRSDLVSYSPVTERHVDTGMTVAELCAATIQYSDNTAANELMKLIGGPAAVTAYARSIGDDTFRLDRWETELNTALPGDLRDTTTPAAMAASLRVLVLGDALPAAQRAQLIEWLRGNKVGDKRIRAGVPAGWRVGDKTGTGDYGTTNDVGVMWPPSRAPIVLAVYYTQTRADAKAKDDVIATATRIAIATLG"},"dna_sequence":{"accession":"CP090776.1","fmin":"1705594","fmax":"1706503","strand":"-","sequence":"ATGACTCATTCATCTCAACGTCGAATCCTGTTGCTGGCTGCCGCGGCGGCGCCGCTCGCGTTGTCCGTCGGCGCATGCGCGGCGCGCGATGCGCCGACGGACAACGCAGCGTCGCCTGGCGGCGCGGCACCGGCATCGTTCGCCGCGCTCGAACGCGCGGCCGGCGGCCGGCTCGGCGTCTGCGCGATCGATACCGCGACCGGGCGGCGCACGTTGCATCGCGCGGACGAGCGCTTCCCTTTCTGCAGCACCTTCAAGGCGATGCTCGGCGCGGCGGTGCTCGCGCAAAGCGTCGCGCATCCCGGCCTGCTGCAGCAGCGCGTGACGTACGGCCGGTCCGATCTCGTCAGCTACTCGCCGGTGACCGAGCGACACGTCGACACCGGCATGACGGTCGCCGAGCTCTGCGCGGCGACGATCCAGTACAGCGACAACACGGCCGCGAACGAGCTGATGAAGCTGATCGGCGGCCCGGCGGCGGTCACGGCCTATGCGCGCTCGATCGGCGACGACACGTTCCGGCTCGATCGCTGGGAGACCGAGCTGAATACCGCGCTGCCGGGCGATCTTCGCGACACGACGACGCCCGCGGCGATGGCCGCGAGCCTGCGCGTGCTCGTGCTCGGCGATGCGTTGCCGGCCGCACAGCGCGCGCAGCTGATCGAATGGCTGCGCGGCAACAAGGTCGGCGACAAGCGTATCCGCGCGGGCGTGCCGGCCGGCTGGCGCGTCGGCGACAAGACGGGCACCGGCGACTACGGGACGACGAACGATGTCGGCGTGATGTGGCCGCCGTCGCGCGCGCCGATCGTGCTTGCCGTCTACTACACGCAGACGCGTGCCGATGCGAAGGCGAAGGACGACGTGATCGCGACCGCGACGCGGATCGCGATCGCGACGCTCGGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43748","NCBI_taxonomy_name":"Burkholderia multivorans","NCBI_taxonomy_id":"87883"}}}},"ARO_accession":"3009015","ARO_id":"47807","ARO_name":"PEN-A37","CARD_short_name":"PEN-A37","ARO_description":"Class A beta-lactamase PEN-A37.","ARO_category":{"46664":{"category_aro_accession":"3007873","category_aro_cvterm_id":"46664","category_aro_name":"PEN-A beta-lactamase","category_aro_description":"PEN-A is a family of class A beta-lactamases which enzymatically inactivate beta-lactam antibiotics.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8434":{"model_id":"8434","model_name":"PEN-A38","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11261":{"protein_sequence":{"accession":"PRG97326.1","sequence":"MTHSSQRRILLLAAAAAPLALSVCACAARDASTDNAASPGGAAPASFAALERAAGGRLGVCAIDTATGRRALHRADERFPFCSTFKAMLGAAVLAQSVAHPGLLQQRVTYGRSDLVSYSPVTERHVDTGMTVAELCAATIQYSDNTAANELMKLIGGPAAVTAYARSIGDDTFRLDRWETELNTALPGDLRDTTTPAAMAASLRVLVLGDALPAAQRAQLIEWLRGNKVGDKRIRAGVPAGWRVGDKTGTGDYGTTNDAGVLWPPSRAPIVLAVYYTQTRADAKAKDDVIAAATRIAIATLG"},"dna_sequence":{"accession":"PVGW01000007.1","fmin":"181991","fmax":"182900","strand":"-","sequence":"ATGACTCATTCATCCCAACGTCGAATCCTGCTGCTGGCTGCCGCGGCGGCGCCGCTCGCGTTGTCCGTTTGCGCATGCGCGGCGCGCGATGCGTCGACGGACAACGCAGCGTCGCCTGGCGGCGCGGCACCGGCATCGTTCGCCGCGCTCGAACGCGCGGCCGGCGGCCGGCTCGGCGTCTGCGCGATCGATACCGCGACCGGGCGGCGCGCGTTGCATCGCGCGGACGAGCGCTTCCCTTTCTGCAGCACCTTCAAGGCGATGCTCGGCGCGGCGGTGCTCGCGCAAAGCGTCGCGCATCCCGGCCTGCTGCAGCAGCGCGTGACGTACGGCCGGTCCGATCTCGTCAGCTACTCGCCGGTGACCGAGCGACACGTCGACACCGGCATGACGGTCGCCGAGCTCTGCGCGGCGACGATCCAGTACAGCGACAACACGGCCGCGAACGAACTGATGAAGCTGATCGGCGGACCGGCGGCGGTCACGGCCTATGCGCGCTCGATCGGCGACGACACGTTCCGGCTCGATCGCTGGGAGACCGAGCTGAATACCGCGCTGCCGGGCGATCTTCGCGACACGACGACGCCCGCGGCGATGGCCGCGAGCCTGCGCGTGCTCGTGCTCGGCGATGCGTTGCCGGCCGCGCAGCGCGCGCAGCTGATCGAATGGCTGCGCGGCAACAAGGTCGGCGACAAGCGTATCCGCGCGGGCGTGCCGGCCGGCTGGCGCGTCGGCGACAAGACGGGCACCGGCGACTACGGGACGACGAACGATGCCGGCGTGCTGTGGCCGCCGTCGCGCGCGCCGATCGTGCTTGCCGTCTACTACACGCAGACGCGTGCCGATGCGAAGGCGAAGGACGACGTGATCGCGGCCGCGACGCGGATCGCGATCGCGACGCTCGGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43748","NCBI_taxonomy_name":"Burkholderia multivorans","NCBI_taxonomy_id":"87883"}}}},"ARO_accession":"3009016","ARO_id":"47808","ARO_name":"PEN-A38","CARD_short_name":"PEN-A38","ARO_description":"Class A beta-lactamase PEN-A38.","ARO_category":{"46664":{"category_aro_accession":"3007873","category_aro_cvterm_id":"46664","category_aro_name":"PEN-A beta-lactamase","category_aro_description":"PEN-A is a family of class A beta-lactamases which enzymatically inactivate beta-lactam antibiotics.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8435":{"model_id":"8435","model_name":"PEN-A3","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11262":{"protein_sequence":{"accession":"PRE15547.1","sequence":"MTHSSQRRILLLAAATAPLALSLGACAARDAAVSDAASPVGAAPASFAALERAAGGRLGVCAIDTATGRRALHRADERFPFCSTFKAMLGAAVLAQSVAHPGLLQQRVTYGRSDLVNYSPVTERHVDTGMTVAELCAATIQYSDNTAANELMKRIGGPAAVTAYARSIGDDTFRLDRWETELNTALPGDLRDTTTPAAMAASLRVLVLGDALPPAQRAQLIEWLRGNKVGDKRIRAGVPTGWRVGDKTGTGDYGTTNDAGVLWPPSRAPIVLAVYYTQARADAKAKDDVIAAATRIAIATLA"},"dna_sequence":{"accession":"PVFL01000048.1","fmin":"237093","fmax":"238002","strand":"+","sequence":"ATGACTCATTCATCTCAACGTCGAATCCTGTTGCTGGCTGCCGCGACGGCGCCGCTCGCGTTGTCCCTCGGCGCGTGCGCGGCGCGCGATGCGGCGGTGTCCGACGCAGCGTCGCCTGTCGGCGCGGCGCCGGCATCGTTCGCCGCACTCGAACGCGCAGCCGGCGGCCGGCTCGGCGTCTGCGCGATCGATACCGCGACGGGCCGGCGCGCGCTGCATCGCGCCGACGAGCGCTTCCCGTTCTGCAGCACCTTCAAGGCGATGCTCGGCGCGGCGGTGCTCGCGCAGAGCGTCGCGCATCCGGGCCTGCTGCAGCAGCGCGTGACGTACGGCCGGTCCGATCTCGTCAACTATTCGCCCGTGACCGAGCGGCACGTCGACACCGGCATGACGGTTGCCGAGCTCTGCGCGGCGACGATCCAGTACAGCGACAACACGGCCGCGAACGAGCTGATGAAGCGGATCGGCGGCCCGGCAGCGGTCACGGCCTATGCGCGCTCGATCGGCGACGACACGTTCCGCCTCGATCGCTGGGAGACCGAACTGAATACCGCGCTGCCGGGCGATCTTCGCGACACGACGACGCCCGCGGCGATGGCCGCGAGCCTGCGCGTGCTCGTGCTCGGCGACGCGTTGCCGCCCGCGCAGCGCGCGCAGCTGATCGAATGGCTGCGCGGCAACAAGGTCGGCGACAAGCGCATCCGCGCGGGCGTGCCGACCGGCTGGCGCGTCGGCGACAAGACGGGCACCGGCGACTACGGGACGACGAACGATGCCGGCGTGCTGTGGCCGCCGTCGCGCGCGCCGATCGTGCTTGCCGTCTACTACACGCAGGCGCGTGCCGATGCGAAGGCGAAGGACGACGTGATCGCGGCCGCGACGCGGATCGCGATCGCGACGCTCGCGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43748","NCBI_taxonomy_name":"Burkholderia multivorans","NCBI_taxonomy_id":"87883"}}}},"ARO_accession":"3009017","ARO_id":"47809","ARO_name":"PEN-A3","CARD_short_name":"PEN-A3","ARO_description":"Class A beta-lactamase PEN-A3.","ARO_category":{"46664":{"category_aro_accession":"3007873","category_aro_cvterm_id":"46664","category_aro_name":"PEN-A beta-lactamase","category_aro_description":"PEN-A is a family of class A beta-lactamases which enzymatically inactivate beta-lactam antibiotics.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8436":{"model_id":"8436","model_name":"PEN-A5","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11263":{"protein_sequence":{"accession":"PRE07490.1","sequence":"MTHSPQRRILLLAAATAPLALSLGACAARDAAVSDAASPVGAAPASFAALERAAGGRLGVCAIDTATGRRALHRADERFPFCSTFKAMLGAAVLAQSVAHPGLLQQRVTYGRSDLVNYSPVTERHVDTGMTVAELCAATIQYSDNTAANELMKRIGGPAAVTAYARSIGDDTFRLDRWETELKTALPGDLRDTTTPAAMAASLRVLVLGDALPPAQRAQLIEWLRGNKVGDKRIRAGVPTGWRVGDKTGTGDYGTTNDAGVLWPPSRAPIVLAVYYTQARADAKAKDDVIAAATRIAIATLA"},"dna_sequence":{"accession":"PVFH01000008.1","fmin":"141626","fmax":"142535","strand":"-","sequence":"ATGACTCATTCACCTCAACGTCGAATCCTGTTGCTGGCTGCCGCGACGGCGCCGCTCGCGTTGTCCCTCGGCGCGTGCGCGGCGCGCGATGCGGCGGTGTCCGACGCAGCGTCGCCTGTCGGCGCGGCGCCGGCATCGTTCGCCGCACTCGAACGCGCGGCCGGCGGCCGGCTCGGCGTCTGCGCGATCGATACCGCGACGGGCCGGCGCGCGCTGCATCGCGCCGACGAGCGCTTCCCGTTCTGCAGCACCTTCAAGGCGATGCTCGGCGCGGCGGTGCTCGCGCAGAGCGTCGCGCATCCCGGCCTGCTGCAGCAGCGCGTGACGTACGGCCGGTCCGATCTCGTCAACTACTCGCCCGTGACCGAGCGGCACGTCGACACCGGCATGACGGTCGCCGAGCTCTGCGCGGCGACGATCCAGTACAGCGACAACACGGCCGCGAACGAGCTGATGAAGCGGATCGGCGGCCCGGCGGCCGTCACGGCCTATGCGCGCTCGATCGGCGACGACACGTTCCGCCTCGATCGCTGGGAGACCGAACTGAAAACCGCGCTGCCGGGCGATCTTCGCGACACGACGACGCCCGCTGCGATGGCCGCGAGCCTGCGCGTGCTCGTGCTCGGCGACGCGTTGCCGCCCGCGCAGCGCGCGCAGCTGATCGAATGGCTGCGCGGCAACAAGGTCGGCGACAAGCGCATCCGCGCGGGCGTGCCGACCGGCTGGCGCGTCGGCGACAAGACGGGCACCGGCGACTACGGGACGACGAACGATGCCGGCGTGCTGTGGCCGCCGTCGCGCGCGCCGATCGTGCTTGCCGTCTACTACACGCAGGCGCGTGCCGATGCGAAGGCGAAGGACGACGTGATCGCGGCCGCGACGCGGATCGCGATCGCGACGCTCGCGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43748","NCBI_taxonomy_name":"Burkholderia multivorans","NCBI_taxonomy_id":"87883"}}}},"ARO_accession":"3009018","ARO_id":"47810","ARO_name":"PEN-A5","CARD_short_name":"PEN-A5","ARO_description":"Class A beta-lactamase PEN-A5.","ARO_category":{"46664":{"category_aro_accession":"3007873","category_aro_cvterm_id":"46664","category_aro_name":"PEN-A beta-lactamase","category_aro_description":"PEN-A is a family of class A beta-lactamases which enzymatically inactivate beta-lactam antibiotics.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8437":{"model_id":"8437","model_name":"PEN-A6","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11264":{"protein_sequence":{"accession":"PRF35301.1","sequence":"MTHSPQRRILLLAAATAPLALSLGACAARDATVSDAASPVGAAPASFAALERAAGGRLGVCAIDTATGRRALHRADERFPFCSTFKAMLGAAVLAQSVAHPGLLQQRVTYGRSDLVNYSPVTERHVDTGMTVAELCAATIQYSDNTAANELMKRIGGPAAVTAYARSIGDDTFRLDRWETELNTALPGDLRDTTTPAAMAASLRVLVLGDALPPAQRTQLIEWLRGNKVGDKRIRAGVPTAWRVGDKTGTGDYGTTNDAGVLWPPSRAPIVLAVYYTQARADAKAKDDVIAAATRIAIATLA"},"dna_sequence":{"accession":"PVGD01000114.1","fmin":"276438","fmax":"277347","strand":"+","sequence":"ATGACTCATTCACCTCAACGTCGAATCCTGTTGCTGGCTGCCGCGACGGCGCCGCTCGCGTTGTCCCTCGGCGCGTGCGCGGCGCGCGATGCGACGGTGTCCGACGCAGCGTCGCCTGTCGGCGCGGCGCCGGCATCGTTCGCCGCGCTCGAACGCGCAGCCGGCGGCCGGCTCGGCGTCTGCGCGATCGATACCGCGACGGGCCGGCGCGCGCTGCATCGCGCCGACGAGCGCTTTCCGTTCTGCAGCACCTTCAAGGCGATGCTCGGCGCGGCGGTGCTCGCGCAGAGCGTCGCGCATCCCGGCCTGCTGCAGCAACGCGTGACGTACGGCCGGTCCGATCTCGTCAACTATTCGCCCGTGACCGAGCGGCACGTCGACACCGGCATGACGGTCGCCGAGCTTTGCGCGGCGACGATCCAGTACAGCGACAACACGGCCGCGAACGAGCTGATGAAGCGGATCGGCGGCCCGGCGGCGGTCACGGCCTATGCGCGCTCGATCGGCGACGACACGTTCCGCCTCGATCGCTGGGAGACCGAACTGAATACCGCGCTGCCGGGCGATCTTCGCGACACGACGACGCCCGCTGCGATGGCCGCGAGCCTGCGCGTGCTCGTGCTCGGCGATGCGTTGCCGCCCGCGCAGCGCACGCAGCTGATCGAATGGCTGCGCGGTAACAAGGTCGGCGACAAGCGCATCCGCGCGGGCGTGCCGACCGCCTGGCGCGTCGGCGACAAGACGGGCACCGGCGACTACGGGACGACGAACGATGCCGGCGTGCTGTGGCCGCCGTCGCGCGCGCCGATCGTGCTTGCCGTCTACTACACGCAGGCGCGTGCCGATGCGAAGGCGAAGGACGACGTGATCGCGGCCGCGACGCGGATCGCGATCGCGACGCTCGCGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43748","NCBI_taxonomy_name":"Burkholderia multivorans","NCBI_taxonomy_id":"87883"}}}},"ARO_accession":"3009019","ARO_id":"47811","ARO_name":"PEN-A6","CARD_short_name":"PEN-A6","ARO_description":"Class A beta-lactamase PEN-A6.","ARO_category":{"46664":{"category_aro_accession":"3007873","category_aro_cvterm_id":"46664","category_aro_name":"PEN-A beta-lactamase","category_aro_description":"PEN-A is a family of class A beta-lactamases which enzymatically inactivate beta-lactam antibiotics.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8438":{"model_id":"8438","model_name":"PEN-A7","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11265":{"protein_sequence":{"accession":"MBU9498712.1","sequence":"MTHSPQRRILLLAAATAPLALSLGACAARDATVSDAASPVGAAPASFAALERAAGGRLGVCAIDTATGRRALHRADERFPFCSTFKAMLGAAVLAQSVAHPGLLQQRVTYGRSDLVNYSPVTERHVDTGMTVAELCAATIQYSDNTAANELMKRIGGPAAVTAYARSIGDDTFRLDRWETELNTALPGDLRDTTTPAAMAASLRVLVLGDALPPAQRTQLIEWLRGNKVGDKRIRAGVPTGWRVGDKTGTGDYGTTNDAGVLWPPSRAPIVLAVYYTQARADAKAKDDVIAAATRIAIATLG"},"dna_sequence":{"accession":"JAHPNU010000001.1","fmin":"191029","fmax":"191938","strand":"+","sequence":"ATGACTCATTCACCTCAACGTCGAATCCTGTTGCTGGCTGCCGCGACGGCGCCGCTCGCGTTGTCCCTCGGCGCGTGCGCGGCGCGCGATGCGACGGTGTCCGACGCAGCGTCGCCTGTCGGCGCGGCGCCGGCATCGTTCGCCGCGCTCGAGCGTGCCGCCGGCGGCCGGCTCGGCGTCTGCGCGATCGATACCGCGACCGGCCGGCGCGCGCTGCATCGCGCCGACGAGCGCTTCCCGTTCTGCAGCACCTTCAAGGCGATGCTCGGCGCGGCGGTGCTCGCGCAGAGCGTCGCGCATCCCGGCCTGCTGCAGCAGCGCGTGACGTACGGTCGGTCCGATCTCGTCAACTACTCGCCGGTGACCGAGCGACACGTCGACACCGGCATGACGGTCGCCGAGCTCTGCGCGGCGACGATCCAGTACAGCGACAACACGGCCGCGAACGAGCTGATGAAGCGGATCGGCGGCCCGGCAGCGGTCACGGCCTATGCGCGCTCGATCGGCGACGACACGTTCCGCCTCGATCGCTGGGAGACCGAACTGAACACCGCGCTGCCGGGCGATCTTCGCGACACGACGACGCCCGCGGCGATGGCCGCGAGCCTGCGCGTGCTCGTGCTCGGCGATGCGTTGCCGCCCGCGCAGCGCACGCAGCTGATCGAATGGCTGCGCGGCAACAAGGTCGGCGACAAACGCATCCGCGCGGGCGTGCCGACCGGCTGGCGCGTCGGCGACAAGACGGGCACCGGCGACTACGGGACGACGAACGATGCCGGTGTGCTGTGGCCGCCGTCGCGCGCGCCGATCGTGCTTGCCGTCTACTACACGCAGGCGCGTGCCGATGCGAAGGCGAAGGACGACGTGATCGCGGCCGCGACGCGGATCGCGATCGCGACGCTCGGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43748","NCBI_taxonomy_name":"Burkholderia multivorans","NCBI_taxonomy_id":"87883"}}}},"ARO_accession":"3009020","ARO_id":"47812","ARO_name":"PEN-A7","CARD_short_name":"PEN-A7","ARO_description":"Class A beta-lactamase PEN-A7.","ARO_category":{"46664":{"category_aro_accession":"3007873","category_aro_cvterm_id":"46664","category_aro_name":"PEN-A beta-lactamase","category_aro_description":"PEN-A is a family of class A beta-lactamases which enzymatically inactivate beta-lactam antibiotics.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8439":{"model_id":"8439","model_name":"PEN-A8","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11266":{"protein_sequence":{"accession":"AIO74009.1","sequence":"MTHSPQRRILLLAAATAPLALSLGACAARDAAVSDAASPVGAAPASFAALERAAGGRLGVCAIDTATGRRALHRADERFPFCSTFKAMLAAAVLAQSVAHPGLLQQRVTYGRSDLVNYSPVTERHVDTGMTVAELCAATIQYSDNTAANELMKRIGGPAAVTAYARSIGDDTFRLDRWETELNTALPGDLRDTTTPAAMAASLRVLVLGDALPPAQRAQLIEWLRGNKVGDKRIRAGVPTGWRVGDKTGTGDYGTTNDAGVLWPPSRAPIVLAVYYTQARADAKAKDDVIAAATRIAIATLA"},"dna_sequence":{"accession":"CP008729.1","fmin":"1975072","fmax":"1975981","strand":"+","sequence":"ATGACTCATTCACCTCAACGTCGAATCCTGTTGCTGGCTGCCGCGACGGCGCCGCTCGCGTTGTCCCTCGGCGCGTGCGCGGCGCGCGATGCGGCGGTGTCCGACGCAGCGTCGCCCGTCGGCGCGGCGCCGGCATCGTTCGCCGCGCTCGAACGCGCAGCCGGCGGCCGGCTCGGCGTCTGCGCGATCGATACCGCGACGGGCCGGCGCGCGCTGCATCGCGCCGACGAGCGCTTTCCGTTCTGCAGCACCTTCAAGGCGATGCTCGCTGCGGCGGTGCTCGCGCAGAGCGTCGCGCATCCTGGCCTGCTGCAGCAGCGCGTGACGTACGGCCGGTCCGATCTCGTCAACTACTCGCCGGTGACCGAGCGACACGTCGACACCGGCATGACGGTCGCCGAGCTTTGCGCGGCGACGATCCAGTACAGCGACAACACGGCCGCGAACGAGCTGATGAAGCGGATCGGCGGCCCGGCAGCGGTCACGGCCTATGCGCGCTCGATCGGCGACGATACGTTCCGCCTCGATCGCTGGGAGACCGAACTGAACACCGCGCTGCCGGGCGATCTTCGCGACACGACGACGCCCGCGGCGATGGCCGCGAGCCTGCGCGTGCTCGTGCTCGGCGACGCGTTGCCGCCCGCGCAGCGCGCGCAGCTGATCGAATGGCTGCGCGGCAACAAGGTCGGCGACAAGCGCATCCGGGCGGGCGTGCCGACCGGCTGGCGCGTCGGCGACAAGACGGGCACCGGCGACTACGGGACGACGAACGATGCCGGCGTGCTGTGGCCGCCGTCGCGCGCGCCGATCGTGCTTGCCGTCTACTACACGCAGGCGCGTGCCGATGCGAAGGCGAAAGACGACGTGATCGCGGCCGCGACGCGGATCGCGATCGCGACGCTCGCGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43748","NCBI_taxonomy_name":"Burkholderia multivorans","NCBI_taxonomy_id":"87883"}}}},"ARO_accession":"3009021","ARO_id":"47813","ARO_name":"PEN-A8","CARD_short_name":"PEN-A8","ARO_description":"Class A beta-lactamase PEN-A8.","ARO_category":{"46664":{"category_aro_accession":"3007873","category_aro_cvterm_id":"46664","category_aro_name":"PEN-A beta-lactamase","category_aro_description":"PEN-A is a family of class A beta-lactamases which enzymatically inactivate beta-lactam antibiotics.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8440":{"model_id":"8440","model_name":"PEN-A9","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11267":{"protein_sequence":{"accession":"AYZ01688.1","sequence":"MTHSSQRRILLLAAATAPLALSLGACAARDAAVSDAASPVGAAPASFAALERAAGGRLGVCAIDTATGRRALHRADERFPFCSTFKAMLAAAVLAQSVEHPGLLQQRVTYGRSDLVNYSPVTERHVDTGMTVAELCAATIQYSDNTAANELMKRIGGPAAVTAYARSIGDDTFRLDRWETELNTALPGDLRDTTTPAAMAASLRVLVLGDALPAAQRAQLIEWLRGNKVGDKRIRAGVPTGWRVGDKTGTGDYGTTNDAGVLWPPSRAPIVLAVYYTQARADAKAKDDVIAAATRIAIATLA"},"dna_sequence":{"accession":"CP033747.1","fmin":"2254588","fmax":"2255497","strand":"-","sequence":"ATGACTCATTCATCTCAACGTCGAATCCTGTTGCTGGCTGCCGCGACGGCGCCGCTCGCGTTGTCCCTCGGCGCGTGCGCGGCGCGCGATGCGGCGGTGTCCGACGCAGCGTCGCCTGTCGGCGCGGCGCCGGCATCGTTCGCCGCGCTCGAACGCGCAGCCGGCGGCCGGCTCGGCGTCTGCGCGATCGATACCGCGACCGGCCGGCGCGCGCTGCATCGCGCGGACGAGCGCTTCCCGTTCTGCAGCACCTTCAAGGCGATGCTCGCCGCGGCGGTGCTCGCGCAGAGCGTCGAGCATCCCGGCCTGCTGCAGCAGCGCGTGACGTATGGCCGGTCCGATCTCGTCAACTATTCGCCGGTGACCGAGCGACACGTCGACACCGGCATGACGGTCGCCGAGCTCTGCGCGGCGACGATCCAGTACAGCGACAACACGGCCGCGAACGAGCTGATGAAGCGGATCGGCGGCCCGGCGGCGGTCACGGCCTATGCGCGCTCGATCGGCGACGATACGTTCCGCCTCGATCGCTGGGAGACCGAACTGAACACCGCGCTGCCGGGCGACCTTCGCGACACGACGACGCCCGCGGCGATGGCCGCGAGCCTGCGCGTGCTCGTGCTCGGCGACGCGTTGCCGGCCGCGCAGCGCGCGCAGCTGATCGAATGGCTGCGCGGCAACAAGGTCGGCGACAAACGCATCCGCGCGGGCGTGCCGACCGGCTGGCGCGTCGGCGACAAGACGGGCACCGGCGACTACGGGACGACGAACGATGCCGGCGTGCTGTGGCCGCCGTCGCGCGCGCCGATCGTGCTTGCCGTCTACTACACGCAGGCGCGTGCCGATGCGAAGGCGAAGGACGACGTGATCGCGGCCGCGACGCGGATCGCGATCGCGACGCTCGCGTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"43748","NCBI_taxonomy_name":"Burkholderia multivorans","NCBI_taxonomy_id":"87883"}}}},"ARO_accession":"3009022","ARO_id":"47814","ARO_name":"PEN-A9","CARD_short_name":"PEN-A9","ARO_description":"Class A beta-lactamase PEN-A9.","ARO_category":{"46664":{"category_aro_accession":"3007873","category_aro_cvterm_id":"46664","category_aro_name":"PEN-A beta-lactamase","category_aro_description":"PEN-A is a family of class A beta-lactamases which enzymatically inactivate beta-lactam antibiotics.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8441":{"model_id":"8441","model_name":"PEN-B1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11268":{"protein_sequence":{"accession":"ACJ63454.1","sequence":"MTYSSKRRTLLLAAATAPLVLTATACASRQAAAPDPATAAAAAAADAMAPAAAAATLADLERDAGGRLGVCAIDTASGRVIEHRAGERFPFCSTFKAMLSAAVLAQSVERPGLLQQRVKYTKADLVNYSPVSEKHVGAGMTVAALCEATIQYSDNSAANLLMKLIGGPSAVTAYARSIGDDAFRLDRWETELNTALPGDPRDTTTPAAMAASIRVLTLGDALPAAQRAQLVAWLRGNKVGDKRIRAGVPAGWTVGDKTGTGDYGTTNDAGVIWPTSRAPIVLAVYYTQTRADARAKDDVIASVARIVAQTFG"},"dna_sequence":{"accession":"EU872211.1","fmin":"0","fmax":"939","strand":"+","sequence":"ATGACCTACTCATCGAAACGTCGAACCCTGTTGCTGGCCGCCGCGACGGCGCCGCTCGTTCTCACCGCCACCGCGTGCGCGTCGCGGCAGGCCGCTGCGCCGGACCCGGCCACGGCGGCGGCAGCGGCTGCCGCGGACGCCATGGCGCCCGCCGCGGCAGCAGCGACGCTCGCCGATCTCGAACGCGACGCGGGCGGCCGTCTCGGCGTATGCGCGATCGACACGGCGAGCGGCCGGGTCATCGAGCATCGCGCGGGCGAGCGCTTCCCGTTCTGCAGTACGTTCAAGGCGATGCTGAGTGCGGCGGTGCTCGCGCAGAGCGTCGAGCGGCCGGGCTTGCTGCAACAGCGCGTGAAGTATACGAAGGCCGACCTCGTCAACTATTCGCCGGTGTCGGAGAAGCATGTCGGCGCGGGCATGACGGTGGCCGCGCTGTGCGAGGCGACGATCCAGTACAGCGACAATTCGGCCGCGAACCTGCTGATGAAGCTGATCGGCGGCCCGTCGGCGGTCACCGCCTACGCGCGCTCGATCGGCGACGACGCGTTCCGGCTCGATCGATGGGAGACCGAACTGAATACCGCGTTGCCGGGCGACCCGCGCGACACGACGACGCCCGCCGCGATGGCCGCCAGCATACGCGTGCTGACGCTCGGCGACGCACTGCCGGCCGCGCAGCGTGCGCAGCTCGTCGCGTGGCTGCGCGGCAACAAGGTCGGCGACAAGCGGATTCGTGCGGGCGTGCCGGCCGGATGGACCGTCGGCGACAAGACCGGTACTGGCGACTACGGGACGACGAACGACGCGGGCGTCATCTGGCCGACGTCGCGCGCGCCGATCGTGCTGGCCGTGTACTACACGCAGACGCGAGCCGATGCGCGGGCGAAGGATGACGTGATCGCGTCGGTCGCGCGCATCGTCGCGCAGACGTTCGGTTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41647","NCBI_taxonomy_name":"Burkholderia cenocepacia","NCBI_taxonomy_id":"95486"}}}},"ARO_accession":"3009023","ARO_id":"47815","ARO_name":"PEN-B1","CARD_short_name":"PEN-B1","ARO_description":"Class A beta-lactamase PEN-B1.","ARO_category":{"46665":{"category_aro_accession":"3007874","category_aro_cvterm_id":"46665","category_aro_name":"PEN-B beta-lactamase","category_aro_description":"PEN-B is a family of class A beta-lactamase enzymes which inactivate beta-lactam antibiotics.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8442":{"model_id":"8442","model_name":"PEN-B2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11269":{"protein_sequence":{"accession":"ACO36249.1","sequence":"MTYSSKRRTLLLAAATAPLVLTATACASRQAAAPDPATAAAAAAADAMAPAAAAATLADLERDAGGRLGVCAIDTASGRIIEHRAGERFPFCSTFKAMLSAAVLAQSVERPGLLQQRVTYTKADLVNYSPVSEKHVGSGMTVAALCEAAIQYSDNSAANLLMKLIGGPSAVTVYARSIGDDTFRLDRWETELNTALPGDPRDTTTPAAMAASLRVLTLGDALPAAQRAQLVAWLRGNKVGDKRIRAGVPAGWTVGDKTGTGDYGTTNDAGVIWPTSRAPIVLAVYYTQTRADARAKDDVIASVARIVAQTFG"},"dna_sequence":{"accession":"FJ386399.1","fmin":"0","fmax":"939","strand":"+","sequence":"ATGACCTACTCATCGAAACGTCGAACCCTGTTGCTGGCCGCCGCGACGGCGCCGCTCGTTCTCACCGCCACCGCGTGCGCGTCGCGGCAGGCCGCTGCGCCGGACCCGGCCACGGCGGCGGCAGCGGCTGCCGCGGACGCCATGGCGCCCGCCGCGGCAGCAGCGACGCTCGCCGATCTCGAACGCGACGCGGGCGGCCGTCTCGGCGTATGCGCGATCGACACGGCGAGCGGCCGGATCATCGAGCATCGCGCGGGCGAGCGCTTCCCGTTCTGCAGTACGTTCAAGGCGATGCTGAGTGCGGCGGTGCTCGCGCAGAGCGTCGAGCGGCCGGGCTTGCTGCAACAGCGCGTGACGTATACGAAGGCCGACCTCGTCAACTATTCGCCGGTGTCGGAGAAGCATGTCGGCTCGGGCATGACGGTGGCCGCGCTGTGCGAGGCGGCGATCCAGTACAGCGACAATTCGGCCGCGAACCTGCTGATGAAGCTGATCGGCGGCCCGTCGGCGGTCACCGTCTACGCGCGCTCGATCGGCGACGACACGTTCCGGCTCGATCGATGGGAGACCGAACTGAATACCGCGTTGCCGGGCGACCCGCGCGACACGACGACGCCCGCCGCGATGGCCGCCAGCCTACGCGTGCTGACGCTCGGCGACGCACTGCCGGCCGCGCAGCGTGCGCAGCTCGTCGCGTGGCTGCGCGGCAACAAGGTCGGCGACAAGCGGATTCGTGCGGGCGTGCCGGCCGGATGGACCGTCGGCGACAAGACCGGTACTGGCGACTACGGGACGACGAACGACGCGGGCGTCATCTGGCCGACGTCGCGCGCGCCGATCGTGCTGGCCGTGTACTACACGCAGACGCGAGCCGATGCGCGGGCGAAGGATGACGTGATCGCGTCGGTCGCGCGCATCGTCGCGCAGACGTTCGGTTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41647","NCBI_taxonomy_name":"Burkholderia cenocepacia","NCBI_taxonomy_id":"95486"}}}},"ARO_accession":"3009024","ARO_id":"47816","ARO_name":"PEN-B2","CARD_short_name":"PEN-B2","ARO_description":"Class A beta-lactamase PEN-B2.","ARO_category":{"46665":{"category_aro_accession":"3007874","category_aro_cvterm_id":"46665","category_aro_name":"PEN-B beta-lactamase","category_aro_description":"PEN-B is a family of class A beta-lactamase enzymes which inactivate beta-lactam antibiotics.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8443":{"model_id":"8443","model_name":"PEN-B3","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11270":{"protein_sequence":{"accession":"ACO36251.1","sequence":"MTYSSKRRTLLLAAATAPLVLTATACASRQAAAPDPATAAAAAAADAMAPAAAAATLADLERDAGGRLGVCAIDTASGRVIEHRAGERFPFCSTFKAMLSAAVLAQSVERPGLLQQRVTYTKADLVNYSPVSEKHVGAGMTVAALCEATIQYSDNSAANLLMKLIGGPSAVTVYARSIGDDAFRLDRWETELNTALPGDPRDTTTPAAMAASIRVLTLGDALPAAQRAQLVAWLRGNKVGDKRIRAGVPAGWTVGDKTGTGDYGTTNDAGVIWPTSRAPIVLAVYYTQTRADARAKDDVIASVARIVAQTFG"},"dna_sequence":{"accession":"FJ386401.1","fmin":"0","fmax":"939","strand":"+","sequence":"ATGACCTACTCATCGAAACGTCGAACCCTGTTGCTGGCCGCCGCGACGGCGCCGCTCGTTCTCACCGCCACCGCGTGCGCGTCGCGGCAGGCCGCTGCGCCGGACCCGGCCACGGCGGCGGCAGCGGCTGCCGCGGACGCCATGGCGCCCGCCGCGGCAGCAGCGACGCTCGCCGATCTCGAACGCGACGCGGGCGGCCGTCTCGGCGTATGCGCGATCGACACGGCGAGCGGCCGGGTCATCGAGCATCGCGCGGGCGAGCGCTTCCCGTTCTGCAGTACGTTCAAGGCGATGCTGAGTGCGGCGGTGCTCGCGCAGAGCGTCGAGCGGCCGGGCTTGCTGCAACAGCGCGTGACGTATACGAAGGCCGACCTCGTCAACTATTCGCCGGTGTCGGAGAAGCATGTCGGCGCGGGCATGACGGTGGCCGCGCTGTGCGAGGCGACGATCCAGTACAGCGACAATTCGGCCGCGAACCTGCTGATGAAGCTGATCGGCGGCCCGTCGGCGGTCACCGTCTACGCGCGCTCGATCGGCGACGACGCGTTCCGGCTCGATCGATGGGAGACCGAACTGAATACCGCGTTGCCGGGCGACCCGCGCGACACGACGACGCCCGCCGCGATGGCCGCCAGCATACGCGTGCTGACGCTCGGCGACGCACTGCCGGCCGCGCAGCGTGCGCAGCTCGTCGCGTGGCTGCGCGGCAACAAGGTCGGCGACAAGCGGATTCGTGCGGGCGTGCCGGCCGGATGGACCGTCGGCGACAAGACCGGTACTGGCGACTACGGGACGACGAACGACGCGGGCGTCATCTGGCCGACGTCGCGCGCGCCGATCGTGCTGGCCGTGTACTACACGCAGACGCGAGCCGATGCGCGGGCGAAGGATGACGTGATCGCGTCGGTCGCGCGCATCGTCGCGCAGACGTTCGGTTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41647","NCBI_taxonomy_name":"Burkholderia cenocepacia","NCBI_taxonomy_id":"95486"}}}},"ARO_accession":"3009025","ARO_id":"47817","ARO_name":"PEN-B3","CARD_short_name":"PEN-B3","ARO_description":"Class A beta-lactamase PEN-B3.","ARO_category":{"46665":{"category_aro_accession":"3007874","category_aro_cvterm_id":"46665","category_aro_name":"PEN-B beta-lactamase","category_aro_description":"PEN-B is a family of class A beta-lactamase enzymes which inactivate beta-lactam antibiotics.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8444":{"model_id":"8444","model_name":"PEN-B4","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11271":{"protein_sequence":{"accession":"ACO36252.1","sequence":"MTYSSKRRTLLLAAATAPLVLTATACASRQAAAPDPATAAAAAAADAMAPAAAAATLADLERDAGGRLGVCAIDTASGRVIEHRAGERFPFCSTFKAMLSAAVLAQSVERPGLLQQRVTYTKADLVNYSPVSEKHVGAGMTVAALCEATIQYSDNSAANLLMKLIGGPSAVTAYARSIGDDAFRLDRWETELNTALPGDPRDTTTPAAMAASIRVLTLGDALPAAQRAQLVAWLRGNKVGDKRIRAGVPAGWTVGDKTGTGDYGTTNDAGVIWPTSRAPIVLAVYYTQTRADARAKDDVIASVARIVAQTFG"},"dna_sequence":{"accession":"FJ386402.1","fmin":"0","fmax":"939","strand":"+","sequence":"ATGACCTACTCATCGAAACGTCGAACCCTGTTGCTGGCCGCCGCGACGGCGCCGCTCGTTCTCACCGCCACCGCGTGCGCGTCGCGGCAGGCCGCTGCGCCGGACCCGGCCACGGCGGCGGCAGCGGCTGCCGCGGACGCCATGGCGCCCGCCGCGGCAGCAGCGACGCTCGCCGATCTCGAACGCGACGCGGGCGGCCGTCTCGGCGTATGCGCGATCGACACGGCGAGCGGCCGGGTCATCGAGCATCGCGCGGGCGAGCGCTTCCCGTTCTGCAGTACGTTCAAGGCGATGCTGAGTGCGGCGGTGCTCGCGCAGAGCGTCGAGCGGCCGGGCTTGCTGCAACAGCGCGTGACGTATACGAAGGCCGACCTCGTCAACTATTCGCCGGTGTCGGAGAAGCATGTCGGCGCGGGCATGACGGTGGCCGCGCTGTGCGAGGCGACGATCCAGTACAGCGACAATTCGGCCGCGAACCTGCTGATGAAGCTGATCGGCGGCCCGTCGGCGGTCACCGCCTACGCGCGCTCGATCGGCGACGACGCGTTCCGGCTCGATCGATGGGAGACCGAACTGAATACCGCGTTGCCGGGCGACCCGCGCGACACGACGACGCCCGCCGCGATGGCCGCCAGCATACGCGTGCTGACGCTCGGCGACGCACTGCCGGCCGCGCAGCGTGCGCAGCTCGTCGCGTGGCTGCGCGGCAACAAGGTCGGCGACAAGCGGATTCGTGCGGGCGTGCCGGCCGGATGGACCGTCGGCGACAAGACCGGTACTGGCGACTACGGGACGACGAACGACGCGGGCGTCATCTGGCCGACGTCGCGCGCGCCGATCGTGCTGGCCGTGTACTACACGCAGACGCGAGCCGATGCGCGGGCGAAGGATGACGTGATCGCGTCGGTCGCGCGCATCGTCGCGCAGACGTTCGGTTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41647","NCBI_taxonomy_name":"Burkholderia cenocepacia","NCBI_taxonomy_id":"95486"}}}},"ARO_accession":"3009026","ARO_id":"47818","ARO_name":"PEN-B4","CARD_short_name":"PEN-B4","ARO_description":"Class A beta-lactamase PEN-B4.","ARO_category":{"46665":{"category_aro_accession":"3007874","category_aro_cvterm_id":"46665","category_aro_name":"PEN-B beta-lactamase","category_aro_description":"PEN-B is a family of class A beta-lactamase enzymes which inactivate beta-lactam antibiotics.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8445":{"model_id":"8445","model_name":"PER-17","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11272":{"protein_sequence":{"accession":"XDO57252.1","sequence":"MNVIIKAVVTASTLLMVSFSSFETSAQSPLLKEQIESIVIGKKATVGVAVWGPDDLEPLLINPFEKFPMQSVFKLHLAMLVLHQVDQGKLDLNQTVIVNRAKVLQNTWAPIMKAYQGDEFSVPVQQLLQYSVSLTDNVACDLLFELVGGPAALHDYIQSMGIKETAVVANEAQMHADDQVQYQNWTSMKGAAEILKKFEQKTQLSETSQALLWKWMVETTTGPERLKGLLPAGTVVAHKTGTSGIKAGKTAATNDLGIILLPDGRPLLVAVFVKDSAESSRTNEAIIAQVAQTAYQFELKKLSALSPN"},"dna_sequence":{"accession":"PQ119971.1","fmin":"0","fmax":"927","strand":"+","sequence":"ATGAATGTCATTATAAAAGCTGTAGTTACTGCCTCGACGCTACTGATGGTATCTTTTAGTTCATTCGAAACCTCAGCGCAATCCCCACTGTTAAAAGAGCAAATTGAATCCATAGTCATTGGAAAAAAAGCCACTGTAGGCGTTGCAGTGTGGGGGCCTGACGATCTGGAACCTTTACTGATTAATCCTTTTGAAAAATTCCCAATGCAAAGTGTATTTAAATTGCATTTAGCTATGTTGGTACTGCATCAGGTTGATCAGGGAAAGTTGGATTTAAATCAGACCGTTATCGTAAACAGGGCTAAGGTTTTACAGAATACCTGGGCTCCGATAATGAAAGCGTATCAGGGAGACGAGTTTAGTGTTCCAGTGCAGCAACTGCTGCAATACTCGGTCTCGCTCACCGATAACGTGGCCTGTGATTTGTTATTTGAACTGGTTGGTGGACCAGCTGCTTTGCATGACTATATCCAGTCTATGGGTATAAAGGAGACCGCTGTGGTCGCAAATGAAGCGCAGATGCACGCCGATGATCAGGTGCAGTATCAAAACTGGACCTCGATGAAAGGTGCTGCAGAGATCCTGAAAAAGTTTGAGCAAAAAACACAGCTGTCTGAAACCTCGCAGGCTTTGTTATGGAAGTGGATGGTCGAAACCACCACAGGACCAGAGCGGTTAAAAGGTTTGTTACCAGCTGGTACTGTGGTCGCACATAAAACTGGTACTTCGGGTATCAAAGCCGGAAAAACTGCGGCCACTAATGATTTAGGTATCATTCTGTTGCCTGATGGACGGCCCTTGCTGGTTGCTGTTTTTGTGAAAGACTCAGCCGAGTCAAGCCGAACCAATGAAGCTATCATTGCGCAGGTTGCTCAGACTGCGTATCAATTTGAATTGAAAAAGCTTTCTGCCCTAAGCCCAAATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3009027","ARO_id":"47819","ARO_name":"PER-17","CARD_short_name":"PER-17","ARO_description":"Extended-spectrum class A beta-lactamase PER-17.","ARO_category":{"36195":{"category_aro_accession":"3000056","category_aro_cvterm_id":"36195","category_aro_name":"PER beta-lactamase","category_aro_description":"PER beta-lactamases are plasmid-mediated extended spectrum beta-lactamases found in the Enterobacteriaceae family.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8446":{"model_id":"8446","model_name":"PER-18","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11273":{"protein_sequence":{"accession":"XHO32906.1","sequence":"MNVIIKAVVTASTLLMVSFSSFETSAQSPLLKEQIESIVIGKKATVGVAVWGPDDLEPLLINPFEKFPMQSVFKLHLAMLVLHQVDQGKLDLNQTVIVNRAKVLQNTWSPMMEEHPGDEFTVAVQQLLQYSVSHSDNVACDLLFELVGGPAALDAYIRSIGVKETAVVANEAQMHADGQVQYQNWTSMKGAAEILRKFEQKTQLSETSQALLWKWMVETTTGPERLKGLLPAGTVVAHKTGTSGVRAGKTAATNDLGIILLPDGRPLLVAVFVKDSAESSRTNEAIIAQVAQAAYQFELKKLSALSPN"},"dna_sequence":{"accession":"PQ394563.1","fmin":"0","fmax":"927","strand":"+","sequence":"ATGAATGTCATTATAAAAGCTGTAGTTACTGCCTCGACGCTACTGATGGTATCTTTTAGTTCATTCGAAACCTCTGCACAATCTCCGCTGTTAAAAGAGCAAATTGAATCCATAGTCATTGGAAAAAAAGCCACTGTAGGCGTTGCAGTGTGGGGGCCTGACGATCTGGAACCTTTACTGATTAATCCTTTTGAAAAATTCCCAATGCAAAGTGTATTTAAATTGCATTTAGCTATGTTGGTACTGCATCAGGTTGATCAGGGAAAGTTGGATTTAAATCAGACCGTTATCGTTAACAGGGCTAAGGTTTTACAGAATACCTGGTCGCCCATGATGGAAGAGCATCCGGGCGATGAATTTACTGTTGCTGTGCAGCAGTTGTTGCAATATTCGGTGTCGCATAGTGACAACGTGGCTTGTGATTTGTTATTCGAACTGGTTGGAGGGCCTGCAGCCTTAGATGCCTACATCCGTTCTATAGGAGTGAAAGAGACGGCTGTGGTCGCAAATGAAGCGCAGATGCACGCCGATGGTCAGGTGCAGTATCAAAACTGGACCTCGATGAAGGGGGCCGCAGAGATCCTGAGAAAGTTTGAGCAAAAAACACAGCTGTCTGAAACCTCGCAGGCTTTGTTATGGAAGTGGATGGTCGAAACCACCACAGGACCAGAGCGGTTAAAAGGTTTGTTACCAGCTGGTACTGTGGTCGCACATAAAACTGGTACTTCGGGTGTCAGAGCCGGGAAAACTGCGGCCACTAATGATTTAGGTATCATTCTGTTGCCTGATGGACGGCCCTTGCTGGTTGCTGTTTTTGTGAAAGACTCAGCCGAGTCAAGCCGAACTAATGAAGCTATCATTGCGCAGGTTGCTCAGGCTGCGTATCAATTTGAATTGAAAAAGCTTTCTGCCCTAAGCCCAAATTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3009028","ARO_id":"47820","ARO_name":"PER-18","CARD_short_name":"PER-18","ARO_description":"Extended-spectrum class A beta-lactamase PER-18.","ARO_category":{"36195":{"category_aro_accession":"3000056","category_aro_cvterm_id":"36195","category_aro_name":"PER beta-lactamase","category_aro_description":"PER beta-lactamases are plasmid-mediated extended spectrum beta-lactamases found in the Enterobacteriaceae family.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8447":{"model_id":"8447","model_name":"PJM-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11274":{"protein_sequence":{"accession":"KAF1723741.1","sequence":"MTLRSTLLSALVALVLPSAALASDATTAKACADDAGWNDPAMPLKVYGNTWYVGTCGISALLVTSDEGHILVDAATPQAGPQILANIRALGFKPEDVRAIVFSHEHFDHAGSLAELQQATGAPVYARSPAVATLKRGASDRSDPQHEVLDPFAPVQQVVVLDDDGVVRVGPLALQVVPTPGHTPGGTSWTWRSCEGDDCRQMVYADSLTAISDDVYRYSDDAAHPGYVAAFRETLARVAALECDILVTPHPSASQLWSRIGPRADRPLVDTSACRTYARTATQRLDKRLADEASKPPVPAP"},"dna_sequence":{"accession":"PDWW01000024.1","fmin":"35568","fmax":"36474","strand":"+","sequence":"ATGACGCTCCGCTCCACCCTGCTTTCCGCTCTGGTCGCGCTCGTGCTTCCCTCCGCCGCGCTCGCTTCCGACGCGACCACGGCCAAAGCCTGCGCCGACGATGCCGGCTGGAACGATCCCGCCATGCCGCTGAAGGTCTACGGCAACACCTGGTACGTCGGCACGTGCGGCATCAGCGCCTTGCTGGTGACCTCCGATGAAGGCCACATCCTGGTCGACGCCGCCACGCCGCAGGCCGGCCCGCAGATCCTCGCCAATATCCGCGCCCTCGGCTTCAAGCCGGAGGACGTGCGTGCCATCGTGTTCTCGCACGAGCACTTCGACCATGCCGGCAGCCTGGCCGAGTTGCAGCAGGCCACGGGCGCGCCGGTGTATGCGCGTTCCCCTGCCGTTGCCACGCTCAAGCGCGGCGCCAGCGATCGCAGCGATCCGCAGCATGAGGTACTCGATCCGTTCGCGCCGGTCCAGCAGGTGGTCGTACTCGACGACGACGGCGTGGTGCGTGTCGGTCCGCTCGCCCTGCAGGTCGTTCCCACGCCGGGACACACGCCCGGCGGCACCAGCTGGACTTGGCGCTCGTGCGAGGGCGACGACTGCCGGCAGATGGTCTATGCCGACAGCCTGACCGCGATCTCCGACGATGTGTACCGCTACAGTGACGATGCGGCGCATCCCGGTTACGTGGCGGCATTCCGCGAGACGCTGGCCCGGGTCGCGGCACTCGAGTGCGACATCCTGGTGACGCCACATCCGTCGGCCAGCCAACTCTGGTCCCGCATCGGTCCCCGCGCCGACCGCCCGCTGGTCGACACCAGCGCCTGCCGCACCTATGCACGGACCGCGACGCAGCGGCTGGACAAGCGGCTCGCGGACGAAGCGTCGAAGCCCCCCGTGCCTGCGCCTTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"46123","NCBI_taxonomy_name":"Pseudoxanthomonas japonensis","NCBI_taxonomy_id":"69284"}}}},"ARO_accession":"3009029","ARO_id":"47821","ARO_name":"PJM-2","CARD_short_name":"PJM-2","ARO_description":"Subclass B3 metallo-beta-lactamase PJM-2.","ARO_category":{"46121":{"category_aro_accession":"3007373","category_aro_cvterm_id":"46121","category_aro_name":"PJM beta-lactamase","category_aro_description":"A family of subclass B3 metallo-beta-lactamases with activity against a range of beta-lactam antibiotics.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8448":{"model_id":"8448","model_name":"PLA-4","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11275":{"protein_sequence":{"accession":"AAS87023.1","sequence":"MRQYRFALLPLLAALALPGWAHQATVTTVKQAESQLQGRVGYAELDLASGQLLAGYRSDERFPMMSTFKVLLCGAVLSRVDAGEEQLDRRIHYRQQDLVEYSPVTEKHLTDGLTVGELCAAAITLSDNTAANLLLTTLGGPQGLTSFLRHSGDQTSRLDRWETELNEARPGDVRDTTTPQAMARTLRNLLTGRVLSSASQQQLQRWMVEDKVAGPLLRSVLPAGWFIADKTGAGNRGSRGIIAALGPDGKAARIVVIYLTGTPAAMDERNKQIAAIGATLVTHWSADENRP"},"dna_sequence":{"accession":"AY507664.1","fmin":"161","fmax":"1037","strand":"+","sequence":"ATGCGTCAATATCGATTCGCCCTTCTCCCATTGTTAGCCGCCCTGGCGCTCCCCGGTTGGGCGCATCAAGCTACGGTGACGACGGTTAAACAAGCCGAAAGCCAGCTTCAGGGTCGGGTCGGCTACGCCGAACTGGATTTAGCTTCCGGGCAACTGCTGGCCGGCTATCGTTCTGACGAACGGTTCCCGATGATGAGCACTTTTAAAGTTCTGCTCTGCGGCGCAGTCTTGTCGCGTGTCGATGCCGGTGAAGAACAGCTCGATCGCCGTATCCATTACCGGCAGCAGGATCTGGTGGAATATTCGCCGGTGACGGAAAAGCATCTTACCGATGGGCTCACCGTGGGCGAACTGTGCGCTGCCGCCATTACCCTGAGCGATAATACGGCGGCAAACCTGCTGTTGACCACTCTCGGCGGCCCGCAGGGGCTGACCAGCTTCCTGCGCCACAGCGGCGACCAGACTTCGCGGCTTGACCGTTGGGAAACGGAACTCAATGAAGCGCGGCCGGGCGACGTGCGAGATACCACGACTCCGCAAGCGATGGCCAGGACACTGCGAAATCTGTTGACCGGTCGCGTGCTTTCCAGCGCCTCGCAGCAGCAGTTGCAACGCTGGATGGTAGAGGACAAAGTTGCGGGGCCGCTGTTGCGATCGGTGCTCCCGGCGGGCTGGTTTATTGCCGATAAGACCGGAGCCGGCAATCGCGGTTCGCGCGGGATCATCGCTGCTCTCGGTCCGGACGGTAAAGCTGCGCGCATCGTGGTGATTTATTTGACCGGGACCCCCGCCGCAATGGATGAACGCAATAAACAGATTGCGGCCATCGGCGCAACGCTGGTCACGCACTGGTCCGCAGACGAGAACAGACCCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41225","NCBI_taxonomy_name":"Raoultella planticola","NCBI_taxonomy_id":"575"}}}},"ARO_accession":"3009030","ARO_id":"47822","ARO_name":"PLA-4","CARD_short_name":"PLA-4","ARO_description":"Class A beta-lactamase PLA-4.","ARO_category":{"43893":{"category_aro_accession":"3005433","category_aro_cvterm_id":"43893","category_aro_name":"PLA beta-lactamase","category_aro_description":"PLA beta-lactamases are class A beta-lactamase found in Raoultella planticola.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8449":{"model_id":"8449","model_name":"PLA-5","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11276":{"protein_sequence":{"accession":"ABB72997.1","sequence":"MRQYRFALLPLLAALALPGWAHQATVTTVKQAESQLQGRVGYAELDLASGQLLAGYRSDERFPMMSTFKVLLCGAVLSRVDAGEEQLDRRIHYRQQDLVEYSPVTEKHLTDGLTVGELCAAAITLSDNTAANLLLTTLGGPQGLTSFLRHSGDQTSRLDRWETELNEARPGDVRDTTTPQAMARTLRNLLTGRVLSSASQQQLQRWMVEDKVAGPLLRSVLPAGWFIADKTGAGNRGSRGIIAALGPDGKAARIVVIYLTGTPATMDERNKQIAAIGATLITHWSADENRP"},"dna_sequence":{"accession":"DQ249871.1","fmin":"187","fmax":"1063","strand":"+","sequence":"ATGCGTCAATATCGATTCGCCCTTCTCCCATTGTTAGCCGCCCTGGCGCTCCCCGGTTGGGCGCATCAAGCTACGGTGACGACGGTTAAACAAGCCGAAAGCCAGCTTCAGGGTCGGGTCGGCTACGCCGAACTGGATTTAGCTTCCGGGCAACTGCTGGCCGGCTATCGTTCTGACGAACGGTTCCCGATGATGAGCACTTTTAAAGTTCTGCTCTGCGGCGCAGTCTTGTCGCGTGTCGATGCTGGTGAAGAACAGCTCGATCGCCGTATCCATTACCGGCAGCAGGATCTGGTGGAATATTCGCCGGTGACGGAAAAGCATCTTACCGATGGGCTCACCGTGGGCGAACTGTGTGCTGCCGCCATTACCCTGAGCGATAATACGGCGGCAAACCTGCTGTTGACCACTCTCGGCGGCCCGCAGGGGCTGACCAGCTTCCTGCGCCACAGCGGCGACCAGACTTCGCGGCTTGACCGTTGGGAAACGGAACTCAATGAAGCGCGGCCGGGCGACGTGCGAGATACCACGACTCCGCAAGCGATGGCCAGGACACTGCGAAATCTGCTGACCGGTCGCGTGCTTTCCAGCGCCTCGCAGCAGCAGTTGCAACGCTGGATGGTAGAGGACAAAGTTGCGGGGCCGCTGTTGCGATCGGTGCTGCCGGCGGGCTGGTTTATTGCCGATAAGACCGGAGCCGGCAATCGCGGCTCGCGCGGGATCATCGCGGCTCTCGGTCCGGACGGTAAAGCTGCGCGCATCGTGGTGATTTATTTGACCGGGACCCCCGCCACAATGGATGAACGCAATAAACAGATTGCGGCCATCGGCGCAACGCTGATCACGCACTGGTCCGCAGACGAGAACAGACCCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"41225","NCBI_taxonomy_name":"Raoultella planticola","NCBI_taxonomy_id":"575"}}}},"ARO_accession":"3009031","ARO_id":"47823","ARO_name":"PLA-5","CARD_short_name":"PLA-5","ARO_description":"Class A beta-lactamase PLA-5.","ARO_category":{"43893":{"category_aro_accession":"3005433","category_aro_cvterm_id":"43893","category_aro_name":"PLA beta-lactamase","category_aro_description":"PLA beta-lactamases are class A beta-lactamase found in Raoultella planticola.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8450":{"model_id":"8450","model_name":"PNC-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11277":{"protein_sequence":{"accession":"BFD45354.1","sequence":"MTKPQITLFAALAATAAISWMAFSARSYAAEAGAQVQTNPRQDEIKSLVDKTIAPLMARQDIPGMAVGIVFDGQSYVFDYGVADKATNKPVTDDTLFEIGSVSKTFTATLATYAQAAGALSLTDKVSRRAPEFAGTPFGDVKLLNLGTHTTGGMPQQVPDNVTNIDEMTQYLKAWKPAKPTGTARTYSNISIGALGWITARAMHDDFATLMSDHVFKPLDLKHTFIKVPEDQQANYAWGYKNGKPIRVSPGVFEQEAYGVKTTASDLLRFVNANLGEAVHDRRLRHAIYATRTSYFFDAPMTQDLAWEQYPYPVTVETLIEGNSTRMSMESTPARELTPPMAPAPVSWVNKTGSTSGFGTYVAFVPSKQMAIVLLANKNYPMEERLRAAHRILTTLDGSRPAPTAPAK"},"dna_sequence":{"accession":"LC795949.1","fmin":"0","fmax":"1227","strand":"+","sequence":"ATGACCAAACCCCAAATCACCCTGTTTGCCGCCCTCGCGGCGACCGCCGCAATTAGCTGGATGGCGTTCAGTGCGCGCAGTTATGCCGCCGAGGCCGGCGCGCAAGTTCAGACGAATCCCCGGCAAGACGAGATCAAATCGCTCGTCGATAAGACCATCGCGCCGCTGATGGCGCGTCAGGACATTCCCGGCATGGCCGTCGGCATCGTTTTCGACGGCCAGTCCTATGTCTTCGATTACGGTGTTGCCGACAAGGCCACCAACAAGCCCGTCACCGACGACACCCTGTTCGAGATCGGCTCCGTCAGCAAGACGTTCACAGCCACGCTCGCCACCTACGCGCAAGCCGCTGGCGCACTCTCCCTAACCGACAAGGTCAGTCGTCGCGCCCCCGAATTCGCGGGCACACCGTTCGGCGACGTCAAACTGCTGAATCTCGGCACGCACACCACCGGCGGCATGCCGCAACAGGTGCCGGACAACGTCACCAACATCGACGAGATGACGCAGTACCTCAAAGCGTGGAAGCCCGCCAAGCCGACCGGCACCGCGCGCACGTACTCGAACATCAGCATCGGCGCGCTCGGCTGGATTACCGCTCGCGCCATGCACGACGATTTCGCCACGCTCATGTCGGATCACGTCTTCAAGCCACTCGATCTGAAGCACACCTTCATCAAGGTGCCGGAAGATCAGCAGGCAAATTACGCGTGGGGATATAAGAACGGCAAACCGATTCGCGTCTCGCCCGGTGTGTTCGAGCAGGAAGCGTACGGCGTGAAGACGACCGCCTCCGACTTGTTGCGCTTCGTCAACGCCAACCTCGGCGAGGCAGTTCATGACCGGCGTCTGCGTCACGCGATCTACGCGACGCGCACCAGCTACTTCTTCGATGCGCCGATGACGCAAGACCTCGCGTGGGAACAGTATCCGTATCCCGTCACGGTTGAAACGCTGATCGAGGGCAACTCCACGCGGATGTCGATGGAATCGACCCCTGCGCGAGAACTCACGCCGCCGATGGCACCGGCGCCGGTATCGTGGGTCAACAAAACGGGATCGACGAGCGGGTTCGGCACATATGTGGCCTTCGTCCCGTCTAAGCAGATGGCGATCGTACTACTCGCCAACAAGAATTACCCGATGGAAGAACGGCTGCGCGCCGCGCATCGGATTCTGACGACGCTCGACGGCAGCCGTCCGGCACCGACAGCACCTGCGAAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42786","NCBI_taxonomy_name":"Pandoraea sputorum","NCBI_taxonomy_id":"93222"}}}},"ARO_accession":"3009032","ARO_id":"47824","ARO_name":"PNC-1","CARD_short_name":"PNC-1","ARO_description":"Class C beta-lactamase PNC-1.","ARO_category":{"46666":{"category_aro_accession":"3007875","category_aro_cvterm_id":"46666","category_aro_name":"PNC beta-lactamase","category_aro_description":"PNC is a family of extended-spectrum class C beta-lactamases which enzymatically inactivate cephalosporin antibiotics.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8451":{"model_id":"8451","model_name":"PNC-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11278":{"protein_sequence":{"accession":"BFF41853.1","sequence":"MTKPQITLFAALAATAAISWMAFSARSYAAEAGAQVQTNPRQDEIKSLVDKTIAPLMARQDIPGMAVGIVFDGQSYVFDYGVADKATNKPVTDDTLFEIGSVSKTFTATLATYAQAAGALSLTDKVSRRAPEFAGTPFGDVKLLNLGTHTTGGMPQQVPDNVTNIDEMTQYLKAWKPAKPTGTARTYSNISIGALGWITARAMHDDFATLMSDHVFKPLDLKHTFIKVPEDQQANYAWGYKNGKPIRVSPGVFEQEAYGVKTTASDLLRFVNANLGEAVHDRRLRHAIYATRTSYFFDAPMTQDLAWEQYPYPVTVEALIEGNSTRMSMESTPARELTPPMAPAPVSWVNKTGSTSGFGTYVAFVPSKQMAIVLLANKNYPMEERLRAAHRILTTLDGSRPAPTAPAK"},"dna_sequence":{"accession":"LC797991.1","fmin":"0","fmax":"1227","strand":"+","sequence":"ATGACCAAACCCCAAATCACCCTGTTTGCCGCCCTCGCGGCGACCGCCGCAATTAGCTGGATGGCGTTCAGTGCGCGCAGTTATGCCGCCGAGGCCGGAGCGCAAGTTCAGACGAATCCCCGGCAAGACGAGATCAAATCGCTCGTCGATAAGACCATCGCGCCGCTGATGGCGCGTCAGGACATTCCCGGCATGGCCGTCGGCATCGTTTTCGACGGCCAGTCCTATGTCTTCGATTACGGTGTTGCCGACAAGGCCACCAACAAGCCCGTCACCGACGACACCCTGTTCGAGATCGGCTCCGTCAGCAAGACGTTCACAGCCACGCTCGCCACGTACGCGCAAGCCGCTGGCGCACTCTCCCTAACCGACAAGGTCAGTCGTCGCGCCCCCGAATTCGCGGGCACACCGTTCGGCGACGTCAAACTGCTGAATCTCGGCACGCACACCACCGGCGGCATGCCGCAACAGGTGCCGGACAACGTCACCAACATCGACGAGATGACGCAGTACCTCAAAGCGTGGAAGCCCGCCAAGCCGACCGGCACCGCGCGCACGTACTCGAACATCAGCATCGGCGCGCTCGGCTGGATTACCGCTCGCGCCATGCACGACGATTTCGCCACGCTCATGTCGGATCACGTCTTCAAGCCACTCGATCTGAAGCACACCTTCATCAAGGTGCCGGAAGATCAGCAGGCAAATTACGCGTGGGGATATAAGAACGGCAAACCGATTCGCGTCTCGCCCGGTGTGTTCGAGCAGGAAGCGTACGGCGTGAAGACGACCGCCTCCGACTTGTTGCGCTTCGTCAACGCCAACCTCGGCGAGGCAGTTCATGACCGGCGTCTGCGTCACGCGATCTACGCGACGCGCACCAGCTACTTCTTCGATGCGCCGATGACGCAAGACCTCGCGTGGGAACAGTATCCGTATCCCGTCACGGTCGAAGCGCTGATCGAGGGCAACTCCACGCGGATGTCGATGGAATCGACCCCCGCGCGCGAACTCACGCCGCCGATGGCACCGGCCCCGGTATCGTGGGTCAACAAAACGGGATCGACGAGCGGGTTCGGTACATATGTGGCCTTCGTCCCGTCTAAGCAGATGGCGATCGTACTACTCGCCAACAAGAATTACCCGATGGAAGAACGGCTGCGCGCCGCGCATCGGATTCTGACGACGCTCGACGGCAGCCGTCCGGCACCGACAGCACCTGCGAAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42786","NCBI_taxonomy_name":"Pandoraea sputorum","NCBI_taxonomy_id":"93222"}}}},"ARO_accession":"3009033","ARO_id":"47825","ARO_name":"PNC-2","CARD_short_name":"PNC-2","ARO_description":"Extended-spectrum class C beta-lactamase PNC-2.","ARO_category":{"46666":{"category_aro_accession":"3007875","category_aro_cvterm_id":"46666","category_aro_name":"PNC beta-lactamase","category_aro_description":"PNC is a family of extended-spectrum class C beta-lactamases which enzymatically inactivate cephalosporin antibiotics.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8452":{"model_id":"8452","model_name":"PNC-3","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11279":{"protein_sequence":{"accession":"BFF41854.1","sequence":"MTKPQITLFAALAATAAISWMAFSARSYAAEAGAQVQTNPRQDEIKSLVDKTIAPLMARQDIPGMAVGIVFDGQSYVFDYGVADKAANKPVTDDTLFEIGSVSKTFTATLATYAQAAGALSLTDKVSRRAPEFAGTPFGDVKLLNLGTHTTGGMPQQVPDNVTNIDEMTQYLKAWKPAKPTGTARTYSNISIGALGWITARAMHDDFATLMSDHVFKPLDLKHTFIKVPEDQQANYAWGYKNGKPIRVSPGVFEQEAYGVKTTASDLLRFVNANLGEAVHDRRLRHAIYATRTSYFFDAPMTQDLAWEQYPYPVTVETLIEGNSTRMSMESTPARELTPPMAPAPVSWVNKTGSTSGFGTYVAFVPSKQMAIVLLANKNYPMEERLRAAHRILTTLDGSRPAPTAPAK"},"dna_sequence":{"accession":"LC797992.1","fmin":"0","fmax":"1227","strand":"+","sequence":"ATGACCAAACCCCAAATCACCCTGTTTGCCGCCCTCGCGGCGACCGCCGCAATTAGCTGGATGGCGTTCAGTGCGCGCAGTTATGCCGCCGAGGCCGGAGCGCAAGTTCAGACGAATCCCCGGCAAGACGAGATCAAATCGCTCGTCGATAAGACCATCGCGCCGCTGATGGCGCGTCAGGACATTCCCGGCATGGCCGTCGGCATCGTTTTCGACGGCCAGTCCTATGTCTTCGATTACGGTGTCGCCGACAAGGCCGCCAACAAGCCCGTCACCGACGACACCCTGTTCGAGATCGGCTCCGTCAGCAAGACGTTCACAGCCACGCTCGCCACGTACGCGCAAGCCGCTGGCGCACTCTCCCTAACCGACAAGGTCAGTCGTCGCGCCCCCGAATTCGCGGGCACACCGTTCGGCGACGTCAAACTGCTGAATCTCGGCACGCACACCACCGGCGGCATGCCGCAACAGGTGCCGGACAACGTCACCAACATCGACGAGATGACGCAGTACCTCAAAGCGTGGAAGCCCGCCAAGCCGACCGGCACCGCGCGCACGTACTCGAACATCAGCATCGGCGCGCTCGGCTGGATTACCGCTCGCGCCATGCACGACGATTTCGCCACGCTCATGTCGGATCACGTCTTCAAGCCACTCGATCTGAAGCACACCTTCATCAAGGTGCCGGAAGATCAGCAGGCAAATTACGCGTGGGGATATAAGAACGGCAAGCCGATTCGCGTCTCGCCCGGTGTGTTCGAGCAGGAAGCGTACGGCGTGAAGACGACTGCCTCCGACTTGTTGCGCTTTGTCAACGCCAACCTCGGCGAGGCGGTCCATGACCGGCGTCTGCGTCATGCGATCTACGCGACGCGCACCAGCTACTTCTTCGATGCGCCGATGACGCAAGACCTCGCGTGGGAACAGTATCCGTACCCCGTCACGGTCGAAACGCTGATCGAGGGCAACTCCACCCGGATGTCGATGGAATCGACCCCTGCGCGCGAACTCACGCCGCCGATGGCACCGGCGCCGGTATCGTGGGTCAACAAAACGGGATCAACGAGCGGGTTCGGCACATATGTGGCCTTCGTCCCGTCTAAGCAGATGGCGATCGTACTACTCGCCAACAAGAATTACCCGATGGAAGAACGGCTGCGCGCCGCGCATCGGATTCTGACGACGCTCGACGGCAGCCGTCCGGCACCGACAGCACCTGCGAAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42786","NCBI_taxonomy_name":"Pandoraea sputorum","NCBI_taxonomy_id":"93222"}}}},"ARO_accession":"3009034","ARO_id":"47826","ARO_name":"PNC-3","CARD_short_name":"PNC-3","ARO_description":"Extended-spectrum class C beta-lactamase PNC-3.","ARO_category":{"46666":{"category_aro_accession":"3007875","category_aro_cvterm_id":"46666","category_aro_name":"PNC beta-lactamase","category_aro_description":"PNC is a family of extended-spectrum class C beta-lactamases which enzymatically inactivate cephalosporin antibiotics.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8453":{"model_id":"8453","model_name":"RAA-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11280":{"protein_sequence":{"accession":"QWY17602.1","sequence":"MKSIKLLLILFSGFIFAQQSVLDKKINSIIKDKKATVGISVLGFENNFQYHKNGKKKLPMLSVFKFHIAATVLDWVDKGKLSLEQKIFIKKEDLLKDTWSPIRDQYPDGNIEMSLDEIIRYTVAWSDNNGCDILLKLIGGTETIQKFINSKGIKNFQIKNNEEQMHKASKYVYENYTTTQSLALLYKQFFQGKIISEKSTHYLYNIMLNTETGKNKLKEQLPPKTVAHKTGSSGKYEGLTIAENDSGIVTLPNGKHYSIVVFVNNSTEPEAVNCKMISDISKTVWDYFNK"},"dna_sequence":{"accession":"MZ424297.1","fmin":"0","fmax":"873","strand":"+","sequence":"ATGAAAAGCATCAAATTACTTTTAATCCTGTTTTCGGGCTTTATATTTGCCCAACAATCGGTTTTAGACAAAAAAATAAATTCTATTATTAAAGATAAAAAAGCAACGGTCGGAATTTCTGTTTTAGGATTTGAAAATAATTTTCAATATCATAAAAATGGTAAAAAAAAGCTTCCAATGCTCAGTGTTTTTAAATTTCATATTGCTGCAACAGTTTTGGATTGGGTAGATAAGGGAAAACTTTCTTTGGAGCAGAAAATTTTCATAAAAAAGGAAGATCTTCTTAAAGATACCTGGTCGCCTATTCGTGATCAATATCCCGATGGAAATATTGAAATGAGTCTTGACGAAATCATCCGTTACACCGTTGCATGGAGTGATAATAATGGTTGCGACATTCTTCTGAAATTGATTGGAGGCACAGAAACAATACAAAAATTTATAAATTCTAAAGGAATTAAAAATTTTCAAATTAAGAATAATGAAGAGCAGATGCACAAAGCCTCAAAATATGTTTACGAAAATTATACAACCACCCAATCTTTAGCATTGCTTTATAAACAGTTTTTTCAGGGAAAAATTATTTCAGAAAAATCTACACATTATTTATATAATATCATGCTGAACACGGAAACCGGCAAAAATAAGCTTAAAGAACAACTTCCTCCGAAAACTGTTGCACACAAAACTGGCTCTTCTGGAAAATATGAAGGCTTAACAATTGCTGAAAATGACAGCGGAATTGTTACTTTGCCCAACGGTAAGCACTACTCTATTGTCGTTTTTGTGAATAATTCTACCGAACCGGAAGCAGTAAACTGTAAGATGATTTCAGATATTTCAAAAACAGTTTGGGATTATTTTAATAAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36951","NCBI_taxonomy_name":"Riemerella anatipestifer","NCBI_taxonomy_id":"34085"}}}},"ARO_accession":"3009035","ARO_id":"47827","ARO_name":"RAA-1","CARD_short_name":"RAA-1","ARO_description":"Extended-spectrum beta-lactamase RAA-1.","ARO_category":{"46667":{"category_aro_accession":"3007876","category_aro_cvterm_id":"46667","category_aro_name":"RAA beta-lactamase","category_aro_description":"RAA is a family of class A extended-spectrum beta-lactamases which enzymatically inactivate cephalosporin antibiotics.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8454":{"model_id":"8454","model_name":"RAHN-3","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11281":{"protein_sequence":{"accession":"USK11983.1","sequence":"MMKNTLRKTVLMAAAVVPMLAFSAVSWAQTATKMTSVQQQLAALEKDSGGRLGVMLINTEDNSQIAYRADERFAMCSTSKFMAASAILKQSETQTELLNRRVSLKKSDLVNYNPITEKHLDTGMTVGELAAAALQYSDNTAMNKLIEQLGGPQKVTEYARTLGDKTFRLDRTEPTLNTAIPGDDRDTTSPRAMALSLQHVTLGSALAEPQRAQLVEWMKGNTTGAMSIRAGLPATWVVGDKTGSGDYGTTNDIAVIWPDNKAPLILITYFTQPQKDAKSRRDVLASAAKIVTQGY"},"dna_sequence":{"accession":"ON698182.1","fmin":"0","fmax":"888","strand":"+","sequence":"ATGATGAAAAATACCCTGCGTAAAACTGTGCTGATGGCGGCGGCTGTAGTGCCAATGCTCGCATTCAGTGCGGTGTCATGGGCGCAAACGGCGACAAAAATGACGTCTGTGCAGCAGCAACTTGCGGCGCTGGAAAAAGACAGCGGCGGTCGTCTTGGTGTGATGCTGATTAATACTGAAGACAATTCCCAGATTGCTTACCGCGCTGATGAACGTTTTGCCATGTGCAGCACCAGCAAGTTCATGGCCGCGTCAGCCATTCTTAAACAGAGCGAAACGCAAACGGAGTTGCTGAACCGCCGCGTCAGCCTCAAAAAATCTGATCTGGTAAATTATAACCCGATCACCGAAAAGCATCTCGATACCGGCATGACGGTAGGCGAACTGGCTGCCGCCGCCTTGCAGTACAGCGATAATACCGCCATGAATAAACTGATTGAGCAGCTTGGTGGCCCGCAGAAAGTCACGGAATACGCCCGTACGCTCGGCGATAAAACGTTCCGTCTGGACCGCACTGAACCAACGCTGAACACCGCCATTCCGGGGGATGACCGCGACACCACTTCACCGCGTGCGATGGCTCTGAGTCTGCAACACGTCACGCTGGGCAGCGCGCTGGCTGAACCGCAACGCGCGCAACTGGTGGAATGGATGAAAGGCAACACGACCGGCGCGATGAGTATCCGTGCGGGGCTGCCTGCGACCTGGGTGGTCGGCGATAAAACCGGCAGCGGCGATTACGGCACAACCAATGATATTGCGGTGATCTGGCCGGATAATAAGGCACCACTGATCCTGATTACCTATTTCACCCAGCCGCAGAAAGACGCTAAATCCCGCCGCGATGTGCTGGCTTCTGCCGCGAAGATTGTGACGCAGGGTTATTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"47929","NCBI_taxonomy_name":"Rahnella aquatilis","NCBI_taxonomy_id":"34038"}}}},"ARO_accession":"3009036","ARO_id":"47828","ARO_name":"RAHN-3","CARD_short_name":"RAHN-3","ARO_description":"Extended-spectrum class A beta-lactamase RAHN-3.","ARO_category":{"43899":{"category_aro_accession":"3005439","category_aro_cvterm_id":"43899","category_aro_name":"RAHN beta-lactamase","category_aro_description":"RAHN beta-lactamases are class A beta-lactamases found in Rahnella aquatilis.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8455":{"model_id":"8455","model_name":"RAHN-4","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11282":{"protein_sequence":{"accession":"USK11984.1","sequence":"MMKNTLRKTVLMAAAVVPMLAFSAPSWAQTATKMTSVQQQLTALEKESGGRLGVMLIDTADNSQIAYRADERFAMCSTSKFMAASAILKESEVKKNLLTQHVGLKKSDLVNYNPITEKHLNEGMTIGELAAAALQYSDNTAMNKLIEHLGGPHKVTDYARTLGDNTFRLDRTEPTLNTAIPGDERDTTSPRAMALSLQHATLGSALAEPQRAQLVEWMKGNTTGAMSIRAGLPATWIVGDKTGSGDYGTTNDIAVIWPENKAPLVLVTYFTQPEKDAKSRRDVLASAAKIVTQGY"},"dna_sequence":{"accession":"ON698183.1","fmin":"0","fmax":"888","strand":"+","sequence":"ATGATGAAAAATACCCTGCGTAAAACCGTGCTGATGGCAGCGGCTGTGGTGCCAATGCTCGCATTCAGCGCGCCGTCATGGGCGCAAACTGCGACGAAAATGACGTCAGTTCAGCAACAGCTGACGGCGCTGGAAAAAGAAAGCGGCGGACGTCTTGGCGTGATGCTGATTGATACTGCGGACAACTCGCAAATTGCTTATCGTGCGGATGAACGTTTTGCGATGTGCAGCACCAGTAAGTTCATGGCGGCTTCGGCGATCCTGAAAGAGAGCGAAGTGAAGAAAAATCTCCTTACTCAGCATGTCGGGCTGAAAAAATCGGATCTGGTGAATTACAACCCGATTACCGAAAAGCATCTCAACGAGGGTATGACGATTGGCGAACTGGCAGCAGCGGCCTTGCAATACAGTGATAACACCGCCATGAATAAGCTTATCGAACATCTCGGCGGGCCACACAAAGTCACCGATTATGCACGTACGCTGGGCGACAACACTTTCCGTCTGGATCGCACCGAACCGACGCTGAACACCGCCATTCCGGGCGATGAGCGCGACACCACGTCACCGCGTGCGATGGCGCTGAGCCTGCAACACGCGACGCTGGGCTCCGCGCTGGCGGAACCGCAGCGCGCACAACTGGTGGAATGGATGAAAGGGAATACCACCGGCGCGATGAGCATCCGCGCAGGATTACCGGCGACCTGGATTGTCGGCGATAAAACCGGCAGCGGTGATTACGGCACGACCAATGATATCGCAGTGATCTGGCCTGAAAACAAAGCGCCGCTGGTGCTGGTGACGTATTTCACCCAACCCGAAAAAGATGCAAAATCCCGTCGTGATGTGCTGGCAAGTGCGGCGAAGATTGTGACGCAGGGTTATTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"47929","NCBI_taxonomy_name":"Rahnella aquatilis","NCBI_taxonomy_id":"34038"}}}},"ARO_accession":"3009037","ARO_id":"47829","ARO_name":"RAHN-4","CARD_short_name":"RAHN-4","ARO_description":"Extended-spectrum class A beta-lactamase RAHN-4.","ARO_category":{"43899":{"category_aro_accession":"3005439","category_aro_cvterm_id":"43899","category_aro_name":"RAHN beta-lactamase","category_aro_description":"RAHN beta-lactamases are class A beta-lactamases found in Rahnella aquatilis.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8456":{"model_id":"8456","model_name":"RAHN-5","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11283":{"protein_sequence":{"accession":"USK11985.1","sequence":"MMKNTLRKTVLMAAAVVPMLAFSAPSWAQTATKMTSVQQQLTALEKESGGRLGVMLIDTADNSQIAYRADERFAMCSTSKFMAASAILKESEVKKNLLTQHVGLKKSDLVNYNPITEKHLNEGMTIGELAAAALQYSDNTAMNKLIEHLGGPNKVTDYARTLGDNTFRLDRTEPTLNTAIPGDERDTTSPRAMALSLQHATLGSALAEPQRAQLVEWMKGNTTGAMSIRAGLPATWIVGDKTGSGDYGTTNDIAVIWPENKAPLVLVTYFTQPEKDAKSRRDVLASAAKIVTQGY"},"dna_sequence":{"accession":"ON698184.1","fmin":"0","fmax":"888","strand":"+","sequence":"ATGATGAAAAATACCCTGCGTAAAACCGTGCTGATGGCAGCGGCTGTGGTGCCAATGCTCGCATTCAGCGCGCCGTCATGGGCGCAAACTGCGACGAAAATGACGTCAGTTCAGCAACAGCTGACGGCGCTGGAAAAAGAAAGCGGCGGACGTCTTGGCGTGATGCTGATTGATACGGCGGACAACTCGCAAATTGCTTATCGTGCGGATGAACGTTTTGCGATGTGCAGCACCAGCAAATTCATGGCGGCTTCGGCGATCCTGAAAGAGAGCGAAGTGAAGAAAAATCTCCTTACCCAACATGTCGGGCTGAAAAAATCGGATCTGGTGAATTACAACCCGATTACCGAAAAGCATCTCAACGAGGGTATGACGATTGGCGAACTGGCGGCAGCGGCCTTGCAATACAGTGATAACACCGCCATGAATAAGCTTATCGAACATCTCGGCGGGCCAAATAAAGTCACCGATTATGCACGTACGCTGGGCGACAACACTTTCCGTCTGGATCGCACCGAACCGACGCTGAATACCGCCATTCCGGGCGATGAGCGCGACACCACGTCACCGCGTGCGATGGCGCTGAGCCTGCAACACGCGACGCTGGGCTCCGCGCTGGCGGAACCGCAGCGCGCACAACTGGTGGAATGGATGAAAGGGAATACCACCGGCGCGATGAGCATCCGCGCAGGATTACCGGCGACCTGGATTGTCGGCGACAAAACCGGCAGCGGCGATTACGGCACGACCAATGATATCGCAGTGATCTGGCCTGAAAACAAAGCGCCGCTGGTGCTGGTGACGTATTTCACCCAACCCGAAAAAGATGCAAAATCCCGTCGTGATGTGCTCGCCAGTGCGGCCAAGATTGTGACGCAGGGTTATTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"47929","NCBI_taxonomy_name":"Rahnella aquatilis","NCBI_taxonomy_id":"34038"}}}},"ARO_accession":"3009038","ARO_id":"47830","ARO_name":"RAHN-5","CARD_short_name":"RAHN-5","ARO_description":"Extended-spectrum class A beta-lactamase RAHN-5.","ARO_category":{"43899":{"category_aro_accession":"3005439","category_aro_cvterm_id":"43899","category_aro_name":"RAHN beta-lactamase","category_aro_description":"RAHN beta-lactamases are class A beta-lactamases found in Rahnella aquatilis.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8457":{"model_id":"8457","model_name":"RAHN-6","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11284":{"protein_sequence":{"accession":"USK11986.1","sequence":"MMKNTLRKTVLMAAAVVPMLAFSAPSWAQTATKMTSVQQQLTALEKESGGRLGVMLIDTADNSQIAYRADERFAMCSTSKFMAASAILKESEVKKNLLTQHVALKKSDLVNYNPITEKHLNEGMTIGELAAAALQYSDNTAMNKLIEHLGGPNKVTDYARTLGDNTFRLDRTEPTLNTAIPGDERDTTSPRAMALSLQHATLGSALAEPQRAQLVEWMKGNTTGAMSIRAGLPATWIVGDKTGSGDYGTTNDIAVIWPENKAPLVLVTYFTQPEKDAKSRRDVLASAAKIVTQGY"},"dna_sequence":{"accession":"ON698185.1","fmin":"0","fmax":"888","strand":"+","sequence":"ATGATGAAAAATACCCTGCGTAAAACCGTGCTGATGGCAGCGGCTGTGGTGCCAATGCTCGCATTCAGCGCGCCGTCATGGGCGCAAACTGCGACGAAAATGACGTCAGTTCAGCAACAGCTGACGGCGCTGGAAAAAGAAAGCGGCGGACGTCTTGGCGTGATGCTGATTGATACGGCGGACAACTCTCAAATTGCTTATCGTGCGGATGAACGTTTTGCGATGTGCAGCACCAGTAAGTTCATGGCGGCTTCGGCGATCCTGAAAGAGAGCGAAGTGAAGAAAAATCTCCTTACTCAGCATGTCGCGTTGAAAAAATCGGATCTGGTGAATTACAACCCGATTACCGAAAAGCATCTCAACGAGGGTATGACGATTGGCGAACTGGCGGCAGCGGCCTTGCAATACAGTGATAACACCGCCATGAATAAGCTTATCGAACATCTCGGCGGGCCAAATAAAGTCACCGATTATGCACGTACGCTGGGCGACAACACTTTCCGTCTGGATCGCACTGAACCGACGCTGAATACCGCCATTCCGGGCGATGAGCGCGACACCACGTCACCGCGTGCGATGGCGCTGAGCCTGCAACACGCGACGCTGGGCTCCGCGCTGGCGGAACCGCAGCGCGCACAACTGGTGGAATGGATGAAAGGGAATACTACCGGCGCGATGAGCATCCGCGCAGGTTTACCGGCGACCTGGATTGTCGGCGATAAAACCGGCAGCGGTGATTACGGCACGACCAATGATATCGCAGTGATCTGGCCTGAAAACAAAGCGCCGCTGGTGCTGGTGACGTATTTCACCCAACCCGAAAAAGATGCAAAATCCCGTCGTGATGTGCTCGCCAGTGCGGCCAAGATAGTGACGCAGGGTTATTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"47929","NCBI_taxonomy_name":"Rahnella aquatilis","NCBI_taxonomy_id":"34038"}}}},"ARO_accession":"3009039","ARO_id":"47831","ARO_name":"RAHN-6","CARD_short_name":"RAHN-6","ARO_description":"Extended-spectrum class A beta-lactamase RAHN-6.","ARO_category":{"43899":{"category_aro_accession":"3005439","category_aro_cvterm_id":"43899","category_aro_name":"RAHN beta-lactamase","category_aro_description":"RAHN beta-lactamases are class A beta-lactamases found in Rahnella aquatilis.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8458":{"model_id":"8458","model_name":"RASA-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11285":{"protein_sequence":{"accession":"AKP72088.1","sequence":"MKMNTLKLIIISFTFLIINSCATVHDNNLKYQIEKIISSKKGDFGISIIDENNNIIEINGNKSYPLLSTFKFPIALTILHKVENGELLMQQQIFIKKEELLENTWSPFKEKYPNGNISISLEEALHWMIVYSDNNMTDILLRLIGGTNAVEKFIDDENFVIKNNEDEMHKDWNSQFINKSTPNSFTKLLKNFSEGKMLNSENTKWLYESMVNSKTGVKRLKGKLPNVKIAQRAGTSFTNDDGITGAINNVGIMQLPNNQKIYITVFIHNTSEEFNKGEEIIADIAKTTYEFYTKE"},"dna_sequence":{"accession":"CP007504.1","fmin":"2031238","fmax":"2032126","strand":"+","sequence":"ATGAAAATGAATACATTAAAACTGATAATAATTTCATTTACGTTTCTAATAATCAATTCATGTGCTACGGTACATGATAATAACCTAAAGTATCAAATAGAAAAAATCATCTCATCCAAAAAAGGTGATTTTGGCATCTCAATTATTGACGAAAATAACAACATCATCGAAATTAATGGAAATAAATCTTACCCTTTACTGAGCACTTTTAAATTTCCAATTGCTTTGACAATACTACACAAAGTTGAAAATGGTGAACTATTAATGCAACAACAAATCTTCATAAAAAAAGAAGAATTGCTGGAAAATACTTGGAGTCCATTTAAAGAAAAATACCCAAACGGAAACATTTCAATTTCATTAGAAGAAGCACTTCATTGGATGATTGTTTACAGCGACAACAATATGACTGATATTCTACTCCGTTTAATAGGTGGAACTAACGCCGTAGAAAAATTTATTGATGATGAAAACTTTGTCATTAAGAACAATGAAGATGAAATGCACAAAGACTGGAATTCTCAATTTATTAACAAATCAACACCAAATTCATTCACGAAACTTTTAAAGAACTTTTCCGAAGGAAAAATGTTAAACTCTGAAAATACGAAATGGCTATATGAATCTATGGTTAATAGCAAAACAGGTGTGAAACGATTAAAAGGCAAACTACCTAATGTTAAAATTGCACAGAGAGCTGGCACTTCTTTCACAAATGATGATGGAATCACAGGCGCAATAAACAATGTAGGCATAATGCAACTTCCTAATAATCAAAAAATTTATATAACTGTATTCATACACAATACTTCGGAAGAATTCAACAAGGGTGAGGAAATAATTGCTGATATTGCTAAAACGACTTATGAATTTTATACAAAAGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36951","NCBI_taxonomy_name":"Riemerella anatipestifer","NCBI_taxonomy_id":"34085"}}}},"ARO_accession":"3009040","ARO_id":"47832","ARO_name":"RASA-1","CARD_short_name":"RASA-1","ARO_description":"Extended-spectrum class A beta-lactamase RASA-1.","ARO_category":{"46668":{"category_aro_accession":"3007877","category_aro_cvterm_id":"46668","category_aro_name":"RASA beta-lactamase","category_aro_description":"RASA is a family of extended-spectrum class A beta-lactamases which enzymatically inactivate cephalosporin antibiotics.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8459":{"model_id":"8459","model_name":"RSC1-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11286":{"protein_sequence":{"accession":"AUW34363.1","sequence":"MYGKTITRVGGVAITALFLGAGSCVAGDDVEKRVRAVVDAAIRPAMQAHAIPGIAVAVSLNGEQYYFNYGVASKESGQMVTEDTIFEIGSVSKTFTTTLASYAQESGALSLSDHASQYLPSLRGSSFDSISLLDLATYTPGGLPLQFPDAVDSHEKMIGYYYNWKPTYAAGTHRLYSNPSIGLLGFLTAESMGEPFEDLLEKKLFPKLGLRQSYIRVPQEQMSHYAYGYSREDKPIRVGPGVLDAEAYGVKSSSADMIHFVEANMQAADLDEPLQHAIAATHRGYYKVGDMTQGLGWEFYPYPIELDRLLAGNSAKMILEANEITRLNPPLIPKGDVLINKTGSTSGFGAYVAFVPTKGIGIVMLANKNYPIPARVKAAHQVLTALDARTGSNAHH"},"dna_sequence":{"accession":"MG739508.1","fmin":"0","fmax":"1191","strand":"+","sequence":"ATGTACGGAAAAACCATAACCAGAGTGGGGGGCGTTGCCATTACCGCGCTGTTCCTCGGTGCCGGCAGCTGCGTCGCCGGGGATGATGTAGAAAAAAGGGTCAGGGCTGTCGTGGACGCAGCCATTCGGCCGGCTATGCAGGCGCATGCCATCCCTGGCATCGCGGTGGCGGTATCACTCAATGGGGAGCAGTATTACTTTAACTACGGCGTCGCCTCCAAAGAGAGTGGGCAGATGGTCACCGAGGATACGATTTTCGAGATCGGCTCGGTCAGTAAAACCTTCACGACGACCCTCGCATCCTACGCGCAGGAAAGTGGAGCGCTCTCCCTATCCGACCACGCAAGCCAATACCTGCCTTCGCTACGTGGCAGCAGTTTCGACAGCATCAGCCTGCTCGATCTTGCGACCTACACGCCCGGCGGTCTGCCGCTGCAGTTTCCGGACGCTGTGGACAGTCACGAAAAGATGATCGGTTATTACTACAACTGGAAACCGACCTATGCCGCCGGAACACACAGGCTCTACTCGAACCCGAGCATCGGCCTGCTCGGCTTTCTAACCGCTGAAAGCATGGGTGAGCCTTTCGAAGATCTACTGGAAAAGAAGCTGTTCCCGAAGCTCGGCCTAAGGCAGAGCTACATCAGGGTTCCACAAGAGCAGATGAGCCACTACGCGTACGGTTATAGCCGAGAGGACAAACCGATCAGGGTGGGCCCAGGCGTTCTGGATGCCGAGGCTTATGGCGTGAAATCCAGCTCGGCCGACATGATTCATTTCGTCGAGGCAAACATGCAGGCGGCTGATCTGGATGAGCCGCTGCAACATGCGATTGCCGCAACGCATAGGGGCTACTACAAGGTCGGCGACATGACTCAGGGGCTGGGATGGGAGTTTTACCCCTACCCGATAGAACTCGACCGTTTGCTTGCGGGCAACTCGGCCAAAATGATCCTTGAAGCGAATGAAATTACTCGACTCAACCCTCCGCTGATTCCGAAGGGCGACGTGCTCATTAACAAGACAGGCTCGACGAGCGGTTTTGGTGCATACGTGGCCTTTGTTCCAACCAAGGGTATCGGCATCGTGATGCTGGCGAACAAGAACTACCCCATCCCTGCAAGGGTGAAAGCCGCCCACCAAGTATTGACGGCCCTGGATGCTCGGACTGGATCTAATGCACACCATTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36791","NCBI_taxonomy_name":"uncultured bacterium","NCBI_taxonomy_id":"77133"}}}},"ARO_accession":"3009041","ARO_id":"47833","ARO_name":"RSC1-1","CARD_short_name":"RSC1-1","ARO_description":"Class C beta-lactamase RSC1-1.","ARO_category":{"46669":{"category_aro_accession":"3007878","category_aro_cvterm_id":"46669","category_aro_name":"RSC1 beta-lactamase","category_aro_description":"RSC1 is a family of class C beta-lactamases which inactivate cephalosporin antibiotics.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8460":{"model_id":"8460","model_name":"RSD1-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11287":{"protein_sequence":{"accession":"AUW34360.1","sequence":"MKSYVDKKWMIIFLIVCVSCTSKAIKKEAFPGFKPFFDEYGVQGCFILYDLKNDNYEIYNSQRCEQGFLPASSFKILNAMIGLETGVVTSKDMVIPWDGVTREVESWNRDHTLASAIQNSVVPYFQEMARRIGPERMKKYVNEADYGQMDVTAQTIDHFWLRGNSRITPWEQMNFLLNFYQNKLPISETNIDIVKQLIILEENERWIFRGKTGWAKQDGQNIGWLIGYYENDKNTWLYVCNVEASDNNIENFKASRRGITEKVFKSMGLME"},"dna_sequence":{"accession":"MG739505.1","fmin":"0","fmax":"816","strand":"+","sequence":"ATGAAAAGTTACGTAGACAAGAAATGGATGATAATCTTTCTTATAGTGTGTGTATCCTGTACTTCAAAGGCGATAAAAAAAGAAGCATTTCCTGGTTTTAAACCTTTCTTTGATGAATACGGCGTGCAGGGTTGTTTTATTCTCTACGACCTGAAGAATGATAATTACGAGATATATAACTCTCAACGATGTGAGCAGGGCTTTCTGCCCGCTTCTTCGTTTAAGATCCTTAACGCCATGATTGGACTGGAAACCGGTGTTGTGACCAGTAAAGACATGGTTATCCCCTGGGATGGGGTTACAAGGGAGGTGGAAAGCTGGAACAGGGACCATACACTGGCCTCAGCCATCCAGAATTCGGTGGTTCCTTATTTCCAGGAAATGGCCCGCCGCATAGGTCCTGAAAGGATGAAAAAGTATGTCAATGAAGCCGATTACGGGCAAATGGATGTAACGGCCCAGACTATTGATCATTTCTGGCTAAGGGGGAATTCCCGCATCACTCCCTGGGAACAGATGAACTTTCTGCTGAACTTCTACCAGAATAAGCTGCCCATTTCTGAAACCAACATTGATATTGTCAAGCAACTGATCATCCTTGAAGAAAATGAACGTTGGATCTTTAGGGGCAAGACAGGCTGGGCCAAACAGGATGGTCAGAACATTGGCTGGCTGATCGGTTATTATGAAAATGATAAAAATACCTGGCTTTATGTCTGCAACGTTGAGGCTTCAGATAACAATATCGAGAACTTCAAAGCCAGCAGACGCGGCATTACTGAAAAAGTGTTTAAATCAATGGGTTTGATGGAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36791","NCBI_taxonomy_name":"uncultured bacterium","NCBI_taxonomy_id":"77133"}}}},"ARO_accession":"3009042","ARO_id":"47834","ARO_name":"RSD1-1","CARD_short_name":"RSD1-1","ARO_description":"Class D beta-lactamase RSD1-1.","ARO_category":{"46670":{"category_aro_accession":"3007879","category_aro_cvterm_id":"46670","category_aro_name":"RSD1","category_aro_description":"RSD1 is a family of class D beta-lactamases which confer resistance to beta-lactam antibiotics.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8462":{"model_id":"8462","model_name":"SED-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11289":{"protein_sequence":{"accession":"WWB25208.1","sequence":"MFKKRGHQTVLIAAALAFFTASSPLLARTLGDPAQVQQKLAALEKQSGGRLGVALINTGDRSQILYRGDERFAMCSTSKAMVAAAVLKQSETQHDILQQKMVIKKADLTNWNPVTEKYVDKEMTLAELSAAALQYSDNTAMNKLLEHLGGTRSVTAFARSIGDTTFRLDRKEPELNTAIPGDERDTTSPLAMAKSLHKLTLGDALAGAQRAQLVEWLKGNTTGGQSIRAGLPKSWVVGDKTGGGDYGTTNDIAVIWPEDRAPLILVTYFTQPQQDAKGRKDILAAAAKIVTEGL"},"dna_sequence":{"accession":"PP336699.1","fmin":"0","fmax":"885","strand":"+","sequence":"ATGTTTAAAAAACGAGGTCATCAGACGGTACTTATTGCCGCCGCGCTCGCTTTCTTTACTGCCAGTTCACCGCTTTTGGCTCGCACGCTCGGAGATCCCGCACAGGTCCAACAAAAGCTGGCAGCATTAGAAAAACAATCAGGTGGCCGACTGGGCGTTGCGCTGATTAATACCGGCGATCGTTCGCAAATCCTTTATCGCGGTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAGGCGATGGTCGCTGCTGCGGTATTAAAACAGAGTGAAACTCAACACGATATTTTGCAGCAGAAAATGGTCATCAAAAAAGCCGATCTGACGAACTGGAATCCGGTAACGGAAAAATATGTCGATAAAGAGATGACATTAGCGGAGCTAAGCGCTGCCGCTCTGCAATACAGCGATAATACGGCAATGAATAAATTACTTGAGCATCTGGGCGGTACCCGTAGCGTCACGGCCTTTGCCCGCTCAATTGGCGACACCACGTTTCGTCTGGACCGGAAAGAACCCGAACTGAACACCGCCATCCCTGGCGATGAGCGCGACACCACGTCGCCGCTGGCGATGGCGAAAAGCCTGCACAAACTGACGCTGGGCGATGCGCTGGCTGGCGCACAGCGTGCACAGCTTGTCGAATGGTTGAAAGGCAATACGACCGGCGGCCAGAGCATTCGTGCCGGACTCCCGAAAAGCTGGGTGGTTGGCGATAAAACCGGAGGCGGTGATTATGGCACAACCAATGATATCGCGGTGATCTGGCCCGAAGATCGTGCGCCGCTGATCCTCGTCACCTACTTTACACAGCCACAGCAGGATGCCAAAGGGCGTAAAGATATTCTGGCCGCCGCAGCAAAAATTGTGACGGAAGGACTTTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36919","NCBI_taxonomy_name":"Citrobacter amalonaticus","NCBI_taxonomy_id":"35703"}}}},"ARO_accession":"3009044","ARO_id":"47836","ARO_name":"SED-2","CARD_short_name":"SED-2","ARO_description":"Class A beta-lactamase SED-2.","ARO_category":{"46671":{"category_aro_accession":"3007880","category_aro_cvterm_id":"46671","category_aro_name":"SED beta-lactamase","category_aro_description":"SED is a family of broad-spectrum class A beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8463":{"model_id":"8463","model_name":"SFC-2","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11290":{"protein_sequence":{"accession":"UAN48719.1","sequence":"MSRTGRLSVFFSAIFPLLTLTNMAEAASQPPQVTVDKLKRLENDFGGRIGVYAIDTGSNKTFGYRANERFPLCSSFKGFLAAAVLSKSQQQEGLLNQRIRYDNRVMEPHSPVTEKQITTGMTVAELSAATLQYSDNGAANLLLEKLIGGPEGMTSFMRSIGDNVFRLDRWELELNSAIPGDDRDTSTPKAVAESMQKLAFGNVLGLMERHQLMDWFKGNTTGGARIRASVPANWVVGDKTGTCGVYGTANDYAVIWPVGHAPIVLAVYTSKPDKESKHSDAVIADASRIVLESFNIDALRMATGKSIGF"},"dna_sequence":{"accession":"CP074147.1","fmin":"4981568","fmax":"4982498","strand":"-","sequence":"ATGTCACGCACCGGTCGACTGTCTGTATTTTTCTCTGCCATATTTCCCCTGTTGACTCTGACTAATATGGCGGAGGCTGCGTCCCAACCCCCACAAGTAACAGTGGATAAATTGAAAAGGTTGGAAAATGATTTTGGAGGGCGAATTGGGGTTTATGCTATTGATACTGGCTCAAATAAAACTTTTGGTTATAGAGCTAACGAGCGTTTTCCTCTCTGTAGTTCATTTAAAGGCTTCCTTGCTGCGGCAGTATTATCGAAAAGCCAGCAGCAAGAGGGCTTACTGAACCAGCGAATTCGCTATGACAATCGAGTTATGGAGCCTCATTCTCCTGTGACTGAAAAACAGATTACGACCGGCATGACAGTTGCCGAGTTGTCTGCTGCCACTCTGCAGTACAGTGATAATGGAGCCGCCAACCTGTTGCTCGAAAAGCTTATTGGTGGCCCTGAAGGAATGACGTCGTTTATGCGTTCTATTGGCGACAATGTATTTCGTCTGGACCGATGGGAACTGGAGTTGAATTCCGCCATTCCTGGTGATGATAGAGATACATCAACACCCAAAGCTGTTGCAGAAAGTATGCAAAAGCTGGCATTTGGAAATGTGCTTGGATTAATGGAGCGCCACCAACTGATGGATTGGTTTAAAGGGAATACAACAGGAGGAGCAAGAATACGTGCAAGCGTACCTGCAAACTGGGTGGTTGGAGACAAAACGGGTACTTGTGGTGTCTATGGTACAGCCAACGATTATGCAGTGATCTGGCCTGTAGGGCATGCGCCAATTGTTCTGGCTGTCTATACATCAAAACCAGACAAAGAATCCAAACACAGCGATGCTGTTATAGCAGATGCATCGCGCATTGTTCTTGAAAGCTTTAATATTGACGCATTACGTATGGCTACAGGAAAGTCTATCGGCTTCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39520","NCBI_taxonomy_name":"Serratia sp.","NCBI_taxonomy_id":"616"}}}},"ARO_accession":"3009045","ARO_id":"47837","ARO_name":"SFC-2","CARD_short_name":"SFC-2","ARO_description":"Carbapenem-hydrolyzing class A beta-lactamase SFC-2.","ARO_category":{"43903":{"category_aro_accession":"3005443","category_aro_cvterm_id":"43903","category_aro_name":"SFC beta-lactamase","category_aro_description":"SFC beta-lactamases are class A beta-lactamases found in Serratia fonticola.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8464":{"model_id":"8464","model_name":"SFDC-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11291":{"protein_sequence":{"accession":"QUF57747.1","sequence":"MLKKSLSCVLLLATSSSVFAAPQTEKQIADIVNRTVAPLMQEQGIPGMAVAVIYQGQPYYFTWGLADVAGKQPVTQQTLFELGSVSKTFTGVLGGDAIARGEINLSDPASKYWPALSGKQWQGITLLHLATYTAGGLPLQIPENVTDEASLQNYYQTWQPQWAPGTKRLYSNASIGLFGALMVKPSGMSFEQAMTQRVFQPLKLSQTWINVPQQEDKHYAWGYRDGKAVRVSPGMFDAEAYGVKSSIEDMASWVQANMAPAKVKDASLQKGITLAQSRYWHAGDMYQGLGWEMLNWPVKEKTVVEGSDNKNALAALSVTKITPPAPLSSASWVHKTGSTGGFGSYVAFIPQQDLGIVMLANKNYPNPVRVEAAYRILEALQK"},"dna_sequence":{"accession":"MW896115.1","fmin":"0","fmax":"1149","strand":"+","sequence":"ATGCTGAAGAAATCCCTATCCTGTGTGCTGTTGCTCGCCACCTCAAGTTCAGTGTTTGCCGCACCGCAAACGGAAAAACAGATAGCCGACATTGTTAATCGCACCGTTGCGCCATTGATGCAAGAGCAGGGCATTCCCGGCATGGCCGTGGCGGTGATTTATCAGGGGCAGCCTTACTACTTCACCTGGGGATTGGCAGACGTTGCCGGCAAGCAACCCGTCACGCAGCAGACCTTATTCGAGCTGGGTTCGGTCAGTAAAACGTTCACAGGAGTGCTGGGCGGTGATGCCATTGCTCGCGGTGAAATCAACCTAAGCGATCCGGCGAGCAAGTACTGGCCAGCACTGTCTGGCAAGCAATGGCAGGGGATCACCTTGCTGCACCTGGCAACCTATACCGCCGGTGGCTTACCGCTGCAGATACCGGAAAATGTTACCGATGAAGCATCGCTGCAGAATTATTATCAAACCTGGCAACCGCAGTGGGCTCCGGGCACCAAGCGCCTATACTCGAACGCCAGTATTGGCCTGTTTGGCGCACTGATGGTCAAACCGTCAGGCATGAGTTTTGAACAGGCGATGACCCAACGCGTGTTCCAACCGTTGAAGCTATCGCAAACCTGGATAAACGTGCCGCAGCAGGAAGATAAGCACTACGCCTGGGGCTATCGCGATGGGAAAGCGGTTCGCGTTTCTCCGGGCATGTTTGATGCCGAAGCCTACGGCGTTAAGTCGTCGATAGAGGATATGGCAAGCTGGGTTCAGGCTAACATGGCGCCTGCTAAAGTGAAGGATGCCTCGCTGCAGAAGGGGATTACGCTTGCCCAGTCGCGCTACTGGCATGCCGGTGATATGTATCAAGGTCTGGGTTGGGAAATGCTGAACTGGCCGGTTAAAGAGAAAACTGTGGTCGAGGGTAGCGATAATAAAAACGCACTGGCAGCGCTGAGCGTCACAAAAATCACTCCGCCAGCGCCACTATCAAGCGCCTCTTGGGTACATAAAACTGGCTCAACCGGTGGATTTGGCAGCTATGTAGCCTTCATTCCTCAACAGGATCTCGGCATCGTGATGCTGGCTAACAAAAATTATCCTAATCCTGTGCGGGTTGAGGCGGCTTATCGCATTCTTGAAGCGTTACAGAAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39675","NCBI_taxonomy_name":"Serratia fonticola","NCBI_taxonomy_id":"47917"}}}},"ARO_accession":"3009046","ARO_id":"47838","ARO_name":"SFDC-1","CARD_short_name":"SFDC-1","ARO_description":"Extended-spectrum class C beta-lactamase SFDC-1.","ARO_category":{"46672":{"category_aro_accession":"3007881","category_aro_cvterm_id":"46672","category_aro_name":"SFDC beta-lactamase","category_aro_description":"SFDC is a family of extended-spectrum class C beta-lactamases which confer resistance to cephalosporin antibiotics.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8466":{"model_id":"8466","model_name":"SHV-229","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11293":{"protein_sequence":{"accession":"QYZ89891.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLKRKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"MZ748304.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGAAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACATCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAACACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3009048","ARO_id":"47840","ARO_name":"SHV-229","CARD_short_name":"SHV-229","ARO_description":"Broad-spectrum class A beta-lactamase SHV-229.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8467":{"model_id":"8467","model_name":"SHV-230","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11294":{"protein_sequence":{"accession":"UZV42324.1","sequence":"MRYIRLCIISLLATLPLPVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGASKRGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"OP762696.1","fmin":"0","fmax":"861","strand":"-","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGCCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTAGCAAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3009049","ARO_id":"47841","ARO_name":"SHV-230","CARD_short_name":"SHV-230","ARO_description":"Extended-spectrum class A beta-lactamase SHV-230.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8468":{"model_id":"8468","model_name":"SHV-231","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11295":{"protein_sequence":{"accession":"WAK12382.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADRTGGSKRGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"OP951208.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTACTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAGGACCGGAGGTAGCAAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3009050","ARO_id":"47842","ARO_name":"SHV-231","CARD_short_name":"SHV-231","ARO_description":"Inhibitor-resistant extended-spectrum class A beta-lactamase SHV-231.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8469":{"model_id":"8469","model_name":"SHV-232","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11296":{"protein_sequence":{"accession":"WKB12817.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLASVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"OR224963.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGTGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCTCCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGCATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATATATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3009051","ARO_id":"47843","ARO_name":"SHV-232","CARD_short_name":"SHV-232","ARO_description":"Class A beta-lactamase SHV-232.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8470":{"model_id":"8470","model_name":"SHV-233","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11297":{"protein_sequence":{"accession":"WPL92335.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMGDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGASERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"OR826346.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGGGCGATAACAGCGCCGCCAATCTGCTACTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTAGCGAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3009052","ARO_id":"47844","ARO_name":"SHV-233","CARD_short_name":"SHV-233","ARO_description":"Inhibitor-resistant class A beta-lactamase SHV-233.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8471":{"model_id":"8471","model_name":"SHV-234","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11298":{"protein_sequence":{"accession":"WPM90266.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMLSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIDDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"OR863406.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGTTGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACATCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGACGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3009053","ARO_id":"47845","ARO_name":"SHV-234","CARD_short_name":"SHV-234","ARO_description":"Inhibitor-resistant class A beta-lactamase SHV-234.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8472":{"model_id":"8472","model_name":"SHV-235","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11299":{"protein_sequence":{"accession":"WPM90267.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPADARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"OR863407.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACATCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGCCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATCGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3009054","ARO_id":"47846","ARO_name":"SHV-235","CARD_short_name":"SHV-235","ARO_description":"Class A beta-lactamase SHV-235.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8473":{"model_id":"8473","model_name":"SHV-236","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11300":{"protein_sequence":{"accession":"WPM90268.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDAHDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"OR863408.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCACGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGCATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3009055","ARO_id":"47847","ARO_name":"SHV-236","CARD_short_name":"SHV-236","ARO_description":"Class A beta-lactamase SHV-236.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8474":{"model_id":"8474","model_name":"SHV-237","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11301":{"protein_sequence":{"accession":"WPM90269.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPVGLTAFLRQIGDNVTRLDRWETELNEALPGEARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"OR863410.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGTAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGAGGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAACACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3009056","ARO_id":"47848","ARO_name":"SHV-237","CARD_short_name":"SHV-237","ARO_description":"Class A beta-lactamase SHV-237.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8475":{"model_id":"8475","model_name":"SHV-238","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11302":{"protein_sequence":{"accession":"WPO27054.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADRTGASKRGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"OR880707.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAGGACCGGAGCTAGCAAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3009057","ARO_id":"47849","ARO_name":"SHV-238","CARD_short_name":"SHV-238","ARO_description":"Inhibitor-resistant extended-spectrum class A beta-lactamase SHV-238.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8476":{"model_id":"8476","model_name":"SHV-239","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11303":{"protein_sequence":{"accession":"WPR17817.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMISTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIDDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"OR876331.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATTAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACATCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGACGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACCCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3009058","ARO_id":"47850","ARO_name":"SHV-239","CARD_short_name":"SHV-239","ARO_description":"Inhibitor-resistant class A beta-lactamase SHV-239.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8477":{"model_id":"8477","model_name":"SHV-240","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11304":{"protein_sequence":{"accession":"WPR17818.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMISTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"OR876332.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATAAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATCGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3009059","ARO_id":"47851","ARO_name":"SHV-240","CARD_short_name":"SHV-240","ARO_description":"Inhibitor-resistant class A beta-lactamase SHV-240.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8478":{"model_id":"8478","model_name":"SHV-241","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11305":{"protein_sequence":{"accession":"WPR17819.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMISTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGEQGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"OR876333.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACCCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATAAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGAGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACAGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATCGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3009060","ARO_id":"47852","ARO_name":"SHV-241","CARD_short_name":"SHV-241","ARO_description":"Inhibitor-resistant class A beta-lactamase SHV-241.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8479":{"model_id":"8479","model_name":"SHV-242","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11306":{"protein_sequence":{"accession":"WPR17820.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMRDNSAANLLLATVGGPAGLTAFLRQIDDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"OR876334.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACATCTTGCCGACGGCATGACGGTCGGCGAACTCTGTGCCGCCGCCATTACCATGAGAGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCGGGATTGACTGCCTTTTTGCGCCAGATCGACGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3009061","ARO_id":"47853","ARO_name":"SHV-242","CARD_short_name":"SHV-242","ARO_description":"Inhibitor-resistant class A beta-lactamase SHV-242.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8480":{"model_id":"8480","model_name":"SHV-243","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11307":{"protein_sequence":{"accession":"WPR17821.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRRETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLMQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"OR876335.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACTAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACATCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCAACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCCGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTTCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGATGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTGGCGAACGGGGTGCGCGCGGCATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3009062","ARO_id":"47854","ARO_name":"SHV-243","CARD_short_name":"SHV-243","ARO_description":"Class A beta-lactamase SHV-243.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8481":{"model_id":"8481","model_name":"SHV-244","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11308":{"protein_sequence":{"accession":"WXU52833.1","sequence":"MRFIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGASKRGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"PP532823.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTTTATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTAGCAAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3009063","ARO_id":"47855","ARO_name":"SHV-244","CARD_short_name":"SHV-244","ARO_description":"Class A beta-lactamase SHV-244.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8482":{"model_id":"8482","model_name":"SHV-245","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11309":{"protein_sequence":{"accession":"XBP46884.1","sequence":"MRYIRLCIISLLATLPLAVHASPQPLEQIKQSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADRTGASKRGARGIVALLGPNNKAERIVVIYLRDTPASMAELDQQIAGIGAALIEHWQR"},"dna_sequence":{"accession":"PP847210.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCTGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAGGACCGGAGCTAGCAAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCTCGATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3009064","ARO_id":"47856","ARO_name":"SHV-245","CARD_short_name":"SHV-245","ARO_description":"Class A beta-lactamase SHV-245.","ARO_category":{"36024":{"category_aro_accession":"3000015","category_aro_cvterm_id":"36024","category_aro_name":"SHV beta-lactamase","category_aro_description":"SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8483":{"model_id":"8483","model_name":"SRT-4","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11310":{"protein_sequence":{"accession":"UBX54502.1","sequence":"MTKMNRLAAALIAALILPTAHAAQQQDIDAVIQPLMKKYGVPGMAIAVSVDGKQQIYPYGVASKQTGKPITEQTLFEVGSLSKTFTATLAVYAQQQGKLSFKDPASRYLPELRGSAFDGVSLLNLATHTSGLPLFVPDDVTNNAQLMAYYRAWQPKHPAGSYRVYSNLGIGMLGMIAAKSLDQPFIQAMEQGMLPALGMSHTYVQVPAAQMANYAQGYSKDDKPVRVNPGPLDAESYGIKSNARDLIRYLDANLQQVKVAQPWRDALAATHIGYYKAGAFTQDLMWENYPYPVKLSRLIEGNNAGMIMNGTPATAITPPQPELRAGWYNKTGSTGGFSTYAVFIPAKNIAVVMLANKWFPNDDRVEAAYHIIQALEKR"},"dna_sequence":{"accession":"OK340848.1","fmin":"4","fmax":"1141","strand":"-","sequence":"ATGACGAAAATGAACCGCCTGGCGGCCGCGCTGATCGCCGCACTGATCCTGCCGACCGCGCACGCCGCGCAGCAGCAGGATATCGACGCCGTTATTCAGCCGCTGATGAAAAAATATGGCGTGCCGGGCATGGCGATCGCCGTGTCGGTCGACGGCAAACAGCAGATTTACCCGTATGGCGTCGCCTCGAAGCAGACCGGCAAACCGATCACCGAGCAGACGCTGTTTGAAGTGGGCTCGCTGAGCAAAACCTTCACCGCGACGCTGGCGGTCTATGCGCAGCAGCAGGGCAAGCTGTCGTTTAAAGACCCGGCCAGCCGCTATCTGCCCGAGCTGCGCGGCAGCGCCTTCGACGGCGTCAGCCTGCTGAATCTGGCGACCCACACCTCCGGCCTGCCGCTGTTCGTGCCGGACGACGTGACCAACAACGCCCAGCTGATGGCCTACTACCGGGCCTGGCAGCCGAAACACCCGGCGGGTAGCTACCGCGTCTATTCCAACCTCGGCATCGGCATGTTGGGCATGATCGCCGCCAAGAGCCTCGACCAGCCGTTTATCCAGGCGATGGAACAGGGGATGCTGCCGGCGTTGGGCATGAGCCACACCTACGTGCAGGTGCCGGCGGCGCAGATGGCCAACTATGCGCAGGGTTACAGCAAGGACGATAAACCGGTGCGGGTCAACCCCGGCCCGCTGGACGCCGAGTCTTACGGCATCAAGTCCAACGCCCGCGATCTGATTCGCTATCTGGACGCCAACCTGCAGCAGGTGAAGGTGGCGCAGCCATGGCGCGACGCGCTGGCCGCGACGCACATCGGTTATTACAAGGCGGGTGCGTTCACGCAGGATCTGATGTGGGAGAACTACCCGTATCCGGTGAAACTGTCGCGTTTGATTGAAGGCAACAACGCGGGGATGATCATGAACGGCACGCCGGCCACCGCCATCACGCCGCCGCAGCCGGAATTGCGCGCCGGTTGGTATAACAAAACCGGTTCCACCGGCGGTTTCTCCACCTATGCGGTATTTATCCCGGCGAAAAATATCGCCGTGGTGATGCTGGCCAACAAGTGGTTCCCGAACGACGATCGCGTCGAGGCGGCTTACCACATCATCCAGGCGCTGGAGAAGCGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36783","NCBI_taxonomy_name":"Serratia marcescens","NCBI_taxonomy_id":"615"}}}},"ARO_accession":"3009065","ARO_id":"47857","ARO_name":"SRT-4","CARD_short_name":"SRT-4","ARO_description":"Class C beta-lactamase SRT-4.","ARO_category":{"36234":{"category_aro_accession":"3000095","category_aro_cvterm_id":"36234","category_aro_name":"SRT beta-lactamase","category_aro_description":"SRT beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8484":{"model_id":"8484","model_name":"TEM-239","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11311":{"protein_sequence":{"accession":"QBC36181.1","sequence":"MSIQQYFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"MK497256.1","fmin":"0","fmax":"864","strand":"+","sequence":"ATGAGTATTCAACAATATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36806","NCBI_taxonomy_name":"Neisseria gonorrhoeae","NCBI_taxonomy_id":"485"}}}},"ARO_accession":"3009066","ARO_id":"47858","ARO_name":"TEM-239","CARD_short_name":"TEM-239","ARO_description":"Class A beta-lactamase TEM-239.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8485":{"model_id":"8485","model_name":"TEM-248","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11312":{"protein_sequence":{"accession":"UUT29265.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETVVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"OP142511.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGGTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3009067","ARO_id":"47859","ARO_name":"TEM-248","CARD_short_name":"TEM-248","ARO_description":"Class A beta-lactamase TEM-248.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8486":{"model_id":"8486","model_name":"TEM-249","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11313":{"protein_sequence":{"accession":"UUT29266.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKDW"},"dna_sequence":{"accession":"OP142512.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGNGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGGATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3009068","ARO_id":"47860","ARO_name":"TEM-249","CARD_short_name":"TEM-249","ARO_description":"Class A beta-lactamase TEM-249.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8487":{"model_id":"8487","model_name":"TEM-250","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11314":{"protein_sequence":{"accession":"WEG44935.1","sequence":"MSIQHFRVALIPFFAAFCFPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDHWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGKRGSRGIIAALGPDGKPSRIVVIYMTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"OQ592371.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCTTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATCATTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTAAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACATGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3009069","ARO_id":"47861","ARO_name":"TEM-250","CARD_short_name":"TEM-250","ARO_description":"Class A beta-lactamase TEM-250.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8488":{"model_id":"8488","model_name":"TEM-251","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11315":{"protein_sequence":{"accession":"WGO19551.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMISTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRLEPELNEAIPNDERDTTTPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"OQ870701.1","fmin":"0","fmax":"861","strand":"-","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATAAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTTGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGACGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3009070","ARO_id":"47862","ARO_name":"TEM-251","CARD_short_name":"TEM-251","ARO_description":"Class A beta-lactamase TEM-251.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8489":{"model_id":"8489","model_name":"TEM-252","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11316":{"protein_sequence":{"accession":"XCA96001.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDSWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGKRGSRGIIAALGPDGKPSRIVVIYTTGGQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"PP933208.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATAGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTAAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGGGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3009071","ARO_id":"47863","ARO_name":"TEM-252","CARD_short_name":"TEM-252","ARO_description":"Class A beta-lactamase TEM-252.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8490":{"model_id":"8490","model_name":"TEM-253","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11317":{"protein_sequence":{"accession":"XDB68957.1","sequence":"MSIQHFRVALIPFSAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQTAEIGASLIKHW"},"dna_sequence":{"accession":"PQ037599.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTCTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGACCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3009072","ARO_id":"47864","ARO_name":"TEM-253","CARD_short_name":"TEM-253","ARO_description":"Class A beta-lactamase TEM-253.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8491":{"model_id":"8491","model_name":"TEM-254","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11318":{"protein_sequence":{"accession":"XDB68958.1","sequence":"MSIQHFRVALIPFSAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMLSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRGEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"PQ037600.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTCTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGCTGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTGGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3009073","ARO_id":"47865","ARO_name":"TEM-254","CARD_short_name":"TEM-254","ARO_description":"Class A beta-lactamase TEM-254.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8492":{"model_id":"8492","model_name":"TEM-255","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11319":{"protein_sequence":{"accession":"XGD00489.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTIASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"PQ284151.1","fmin":"549","fmax":"1410","strand":"-","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTATAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3009074","ARO_id":"47866","ARO_name":"TEM-255","CARD_short_name":"TEM-255","ARO_description":"Class A beta-lactamase TEM-255.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8493":{"model_id":"8493","model_name":"TEM-256","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11320":{"protein_sequence":{"accession":"XGD00490.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVTGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"PQ284152.1","fmin":"700","fmax":"1561","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTACAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3009075","ARO_id":"47867","ARO_name":"TEM-256","CARD_short_name":"TEM-256","ARO_description":"Class A beta-lactamase TEM-256.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8494":{"model_id":"8494","model_name":"TEM-257","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11321":{"protein_sequence":{"accession":"XGD00491.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTVPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"PQ284153.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGGTGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3009076","ARO_id":"47868","ARO_name":"TEM-257","CARD_short_name":"TEM-257","ARO_description":"Class A beta-lactamase TEM-257.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8495":{"model_id":"8495","model_name":"TEM-258","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11322":{"protein_sequence":{"accession":"XHJ89682.1","sequence":"MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDKLGARVGYIELDLNSGKILESFRPEERFPMLSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW"},"dna_sequence":{"accession":"PQ362078.1","fmin":"0","fmax":"861","strand":"+","sequence":"ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATAAGTTGGGTGCACGAGTGGGTTACATCGAGCTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGCTGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACCCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3009077","ARO_id":"47869","ARO_name":"TEM-258","CARD_short_name":"TEM-258","ARO_description":"Class A beta-lactamase TEM-258.","ARO_category":{"36023":{"category_aro_accession":"3000014","category_aro_cvterm_id":"36023","category_aro_name":"TEM beta-lactamase","category_aro_description":"TEM-1 is the most commonly-encountered beta-lactamase in gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1. Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid.  Although the inhibitor-resistant beta-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM beta-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM beta-lactamases. Inhibitor-resistant TEM beta-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam-lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin\/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin\/tazobactam, although resistance has been described.","category_aro_class_name":"AMR Gene Family"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8497":{"model_id":"8497","model_name":"VEB-18","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11324":{"protein_sequence":{"accession":"ANU78819.1","sequence":"MKIVKRILLVLLSLFFTIAYSNAQTDNLTLKIENVLKAKNARIGVAIFNSNEKDTLKINNDFHFPMQSVMKFPIALAVLSEIDKGNLSFEQKIEITPQDLLPKMWSPIKEEFPNGTTLTIEQILNYTVSESDNIGCDILLKLIGGTDSVQKFLNANHFTDISIKANEEQMHKDWNTQYQNWATPTAMNKLLIDTYNNKNQLLSKKSYDFIWKIMRETTTGSNRLKGQLPKNTIVAHKTGTSGINNGIAAATNDVGVITLPNGQLIFISVFVAESKETSEINEKIISDIAKITWDYYLNK"},"dna_sequence":{"accession":"KX539265.1","fmin":"2975","fmax":"3875","strand":"+","sequence":"ATGAAAATCGTAAAAAGGATATTATTAGTATTGTTAAGTTTATTTTTTACAATTGCGTATTCAAATGCTCAAACTGACAACTTAACTTTGAAAATTGAGAATGTTTTAAAGGCAAAAAATGCCAGAATAGGAGTAGCAATATTCAACAGCAATGAGAAGGATACTTTGAAGATTAATAACGACTTCCATTTCCCGATGCAAAGCGTTATGAAATTTCCGATTGCTTTAGCCGTTTTGTCTGAGATAGATAAAGGGAATCTTTCTTTTGAACAAAAAATAGAGATTACCCCTCAAGACCTTTTGCCTAAAATGTGGAGTCCGATTAAAGAGGAATTCCCTAATGGAACAACTTTGACGATTGAACAAATACTAAATTATACAGTATCAGAGAGCGACAATATTGGTTGTGATATTTTGCTAAAATTAATCGGAGGAACTGATTCTGTTCAAAAATTCTTGAATGCTAATCATTTCACTGATATTTCAATCAAAGCAAACGAAGAACAAATGCACAAGGATTGGAATACCCAATATCAAAATTGGGCAACCCCAACAGCGATGAACAAACTGTTAATAGATACTTATAATAATAAGAACCAATTACTTTCTAAAAAAAGTTATGATTTTATTTGGAAAATTATGAGAGAAACAACAACAGGAAGTAACCGATTAAAAGGACAATTACCAAAGAATACAATTGTTGCTCATAAAACAGGGACTTCCGGAATAAATAATGGAATTGCAGCAGCCACTAATGATGTTGGGGTAATTACTTTACCGAATGGACAATTAATTTTTATAAGCGTATTTGTTGCAGAGTCCAAAGAAACTTCGGAAATTAATGAAAAGATTATTTCAGACATTGCAAAAATAACGTGGGATTACTATTTGAATAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39615","NCBI_taxonomy_name":"Vibrio parahaemolyticus","NCBI_taxonomy_id":"670"}}}},"ARO_accession":"3009079","ARO_id":"47871","ARO_name":"VEB-18","CARD_short_name":"VEB-18","ARO_description":"Extended-spectrum class A beta-lactamase VEB-18.","ARO_category":{"36182":{"category_aro_accession":"3000043","category_aro_cvterm_id":"36182","category_aro_name":"VEB beta-lactamase","category_aro_description":"VEB beta-lactamases or Vietnamese extended-spectrum beta-lactamases are class A beta-lactamases that confer high-level resistance to oxyimino cephalosporins and to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8498":{"model_id":"8498","model_name":"VEB-28","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11325":{"protein_sequence":{"accession":"QRV13259.1","sequence":"MKIVKRILLVLLSLFFTVVYSNAQTDNLTLKIESVLKAKNARIGVAIFNSNEKDTLKINNDFHFPMQSVMKFPIALAVLSEIDKGNLSFEQKIEITPQDLLPKTWSPIKEEFPNGTTLTIEQILNYTVSESDNIGCDILLKLIGGTDSVQKFLNANHFTDISIKANEEQMHKDWNTQYQNWATPTAMNKLLIDTYNNKNQLLSKKSYDFIWKIMRETTTGSNRLKGQLPKNTIVAHKTGTSGINNGIAAATNDVGVITLPNGQLIFISVFVAESKETSEINEKIISDIAKITWNYYLNK"},"dna_sequence":{"accession":"MW598511.1","fmin":"0","fmax":"900","strand":"+","sequence":"ATGAAAATCGTAAAAAGGATATTATTAGTATTGTTAAGTTTATTTTTTACAGTTGTGTATTCAAATGCTCAAACTGACAACTTAACTTTGAAAATTGAGAGTGTTTTAAAGGCAAAAAATGCCAGAATAGGAGTAGCAATATTCAACAGCAATGAGAAGGATACTTTGAAGATTAATAACGACTTCCATTTCCCGATGCAAAGCGTTATGAAATTTCCGATTGCTTTAGCCGTTTTGTCTGAGATAGATAAAGGGAATCTTTCTTTTGAACAAAAAATAGAGATTACCCCTCAAGACCTTTTGCCTAAAACGTGGAGTCCGATTAAAGAGGAATTCCCTAATGGAACAACTTTGACGATTGAACAAATACTAAATTATACAGTATCAGAGAGCGACAATATTGGTTGTGATATTTTGCTAAAATTAATCGGAGGAACTGATTCTGTTCAAAAATTCTTGAATGCTAATCATTTCACTGATATTTCAATCAAAGCAAACGAAGAACAAATGCACAAGGATTGGAATACCCAATATCAAAATTGGGCAACCCCAACAGCGATGAACAAACTGTTAATAGATACTTATAATAATAAGAACCAATTACTTTCTAAAAAAAGTTATGATTTTATTTGGAAAATTATGAGAGAAACAACAACAGGAAGTAACCGATTAAAAGGACAATTACCAAAGAATACAATTGTTGCTCATAAAACAGGGACTTCCGGAATAAATAATGGAATTGCAGCAGCCACTAATGATGTTGGGGTAATTACTTTACCGAATGGACAATTAATTTTTATAAGCGTATTTGTTGCAGAGTCCAAAGAAACTTCGGAAATTAATGAAAAGATTATTTCAGACATTGCAAAAATAACGTGGAATTACTATTTGAATAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39677","NCBI_taxonomy_name":"Aeromonas veronii","NCBI_taxonomy_id":"654"}}}},"ARO_accession":"3009080","ARO_id":"47872","ARO_name":"VEB-28","CARD_short_name":"VEB-28","ARO_description":"Extended-spectrum class A beta-lactamase VEB-28.","ARO_category":{"36182":{"category_aro_accession":"3000043","category_aro_cvterm_id":"36182","category_aro_name":"VEB beta-lactamase","category_aro_description":"VEB beta-lactamases or Vietnamese extended-spectrum beta-lactamases are class A beta-lactamases that confer high-level resistance to oxyimino cephalosporins and to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8499":{"model_id":"8499","model_name":"VEB-29","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11326":{"protein_sequence":{"accession":"QWO25673.1","sequence":"MKIVKRILLVLLSLFFTVEYSNAQTDNLTLKIENVLKAKNARIGVAIFNSNEKDTLKINNDFHYPMQSVMKFPIALAVLSEIDKGNLSFEQKIEITPQDLLPKMWSPIKEEFPNGTTLTIEQILNYTVSETDNIGCDILLKLIGGTDSVQKFLNANHFTDISIKANEEQMHKDWNTQYQNWATPTAMNKLLIDTYNNKNQLLSKKSYDFIWKIMRETTTGSNRLKGQLPKNTIVAHKTGTSGINNGITAATNDVGVITLPNGQLIFISVFVAESKETSEINEKIISDIAKITWDYYLNK"},"dna_sequence":{"accession":"MZ359765.1","fmin":"0","fmax":"900","strand":"+","sequence":"ATGAAAATCGTAAAAAGGATATTATTAGTATTGTTAAGTTTATTTTTTACAGTTGAGTATTCAAATGCTCAAACTGACAACTTAACTTTGAAAATTGAGAATGTTTTAAAGGCAAAAAATGCCAGAATAGGAGTAGCAATATTCAACAGCAATGAGAAGGATACTTTGAAGATTAATAACGACTTCCATTACCCGATGCAAAGCGTTATGAAATTTCCGATTGCTTTAGCCGTTTTGTCTGAGATAGATAAAGGGAATCTTTCTTTTGAACAAAAAATAGAGATTACCCCTCAAGACCTTTTGCCTAAAATGTGGAGTCCGATTAAAGAGGAATTCCCTAATGGAACAACTTTGACGATTGAACAAATACTAAATTATACAGTATCAGAGACCGACAATATTGGTTGTGATATTTTGCTAAAATTAATCGGAGGAACTGATTCTGTTCAAAAATTCTTGAATGCTAATCATTTCACTGATATTTCAATCAAAGCAAACGAAGAACAAATGCACAAGGATTGGAATACCCAATATCAAAATTGGGCAACCCCAACAGCGATGAACAAACTGTTAATAGATACTTATAATAATAAGAACCAATTACTTTCTAAAAAAAGTTATGATTTTATTTGGAAAATTATGAGAGAAACAACAACAGGAAGTAACCGATTAAAAGGACAATTACCAAAGAATACAATTGTTGCTCATAAAACAGGGACTTCCGGAATAAATAATGGAATTACAGCAGCCACTAATGATGTTGGGGTAATTACTTTACCGAATGGACAATTAATTTTTATAAGCGTATTTGTTGCAGAGTCCAAAGAAACTTCGGAAATTAATGAAAAGATTATTTCAGACATTGCAAAAATAACGTGGGATTACTATTTGAATAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3009081","ARO_id":"47873","ARO_name":"VEB-29","CARD_short_name":"VEB-29","ARO_description":"Extended-spectrum class A beta-lactamase VEB-29.","ARO_category":{"36182":{"category_aro_accession":"3000043","category_aro_cvterm_id":"36182","category_aro_name":"VEB beta-lactamase","category_aro_description":"VEB beta-lactamases or Vietnamese extended-spectrum beta-lactamases are class A beta-lactamases that confer high-level resistance to oxyimino cephalosporins and to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8500":{"model_id":"8500","model_name":"VEB-30","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11327":{"protein_sequence":{"accession":"QWT89343.1","sequence":"MKIVKRILLVLLSLFFTVVYSNAQADNLTLKIENVLKAKNARIGVAIFNSNEKDTLKINNDFHFPMQSVMKFPIALAVLSEIDKGNLSFEQKIEITPQDLLPKMWSPIKEEFPNGTTLTIEQILNYTVSETDNIGCDILLKLIGGTDSVQKFLNANHFTDISIKANEEQMHKDWNTQYQNWATPTAMNKLLIDTYNNKNQLLSKKSYDFIWKIMRETTTGSNRLKGQLPKNTIVAHKTGTSGINNGITAATNDVGVITLPNGQLIFISVFVAESKETSEINEKIISDIAKITWDYYLNK"},"dna_sequence":{"accession":"MZ394841.1","fmin":"0","fmax":"900","strand":"+","sequence":"ATGAAAATCGTAAAAAGGATATTATTAGTATTGTTAAGTTTATTTTTTACAGTTGTGTATTCAAATGCTCAAGCTGACAACTTAACTTTGAAAATTGAGAATGTTTTAAAGGCAAAAAATGCCAGAATAGGAGTAGCAATATTCAACAGCAATGAGAAGGATACTTTGAAGATTAATAACGACTTCCATTTCCCGATGCAAAGCGTTATGAAATTTCCGATTGCTTTAGCCGTTTTGTCTGAGATAGATAAAGGGAATCTTTCTTTTGAACAAAAAATAGAGATTACCCCTCAAGACCTTTTGCCTAAAATGTGGAGTCCGATTAAAGAGGAATTCCCTAATGGAACAACTTTGACGATTGAACAAATACTAAATTATACAGTATCAGAGACCGACAATATTGGTTGTGATATTTTGCTAAAATTAATCGGAGGAACTGATTCTGTTCAAAAATTCTTGAATGCTAATCATTTCACTGATATTTCAATCAAAGCAAACGAAGAACAAATGCACAAGGATTGGAATACCCAATATCAAAATTGGGCAACCCCAACAGCGATGAACAAACTGTTAATAGATACTTATAATAATAAGAACCAATTACTTTCTAAAAAAAGTTATGATTTTATTTGGAAAATTATGAGAGAAACAACAACAGGAAGTAACCGATTAAAAGGACAATTACCAAAGAATACAATTGTTGCTCATAAAACAGGGACTTCCGGAATAAATAATGGAATTACAGCAGCCACTAATGATGTTGGGGTAATTACTTTACCGAATGGACAATTAATTTTTATAAGCGTATTTGTTGCAGAGTCCAAAGAAACTTCGGAAATTAATGAAAAGATTATTTCAGACATTGCAAAAATAACGTGGGATTACTATTTGAATAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3009082","ARO_id":"47874","ARO_name":"VEB-30","CARD_short_name":"VEB-30","ARO_description":"Extended-spectrum class A beta-lactamase VEB-30.","ARO_category":{"36182":{"category_aro_accession":"3000043","category_aro_cvterm_id":"36182","category_aro_name":"VEB beta-lactamase","category_aro_description":"VEB beta-lactamases or Vietnamese extended-spectrum beta-lactamases are class A beta-lactamases that confer high-level resistance to oxyimino cephalosporins and to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8501":{"model_id":"8501","model_name":"VEB-31","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11328":{"protein_sequence":{"accession":"UUU46289.1","sequence":"MKIVKRILLVLLSLFFTIVYSNAQTDNLTLKIENVLKAKNARIGVAIFNSNEKDTLKINNDFHFPMQSVMKFLIALAVLSEIDKGNLSFEQKIEITPQDLLPKTWSPIKEEFPNGTTLTIEQILNYTVSESDNIGCDILLKLIGGTDSVQKFLNANHFTDISIKANEEQMHKDWNTQYQNWATPTAMNKLLIDTYNNKNQLLSKKSYDFIWKIMRETTTGSNRLKGQLPKNTIVAHKTGTSGINNGIAAATNDVGVITLPNGQLIFISVFVAESKETSEINEKIISDIAKITWNYYLNK"},"dna_sequence":{"accession":"OP171927.1","fmin":"0","fmax":"900","strand":"+","sequence":"ATGAAAATCGTAAAAAGGATATTATTAGTATTGTTAAGTTTATTTTTTACAATTGTGTATTCAAATGCTCAAACTGACAACTTAACTTTGAAAATTGAGAATGTTTTAAAGGCAAAAAATGCCAGAATAGGAGTAGCAATATTCAACAGCAATGAGAAGGATACTTTGAAGATTAATAACGACTTCCATTTCCCGATGCAAAGCGTTATGAAATTTCTGATTGCTTTAGCCGTTTTGTCTGAGATAGATAAAGGGAATCTTTCTTTTGAACAAAAAATAGAGATTACCCCTCAAGACCTTTTGCCTAAAACGTGGAGTCCGATTAAAGAGGAATTCCCTAATGGAACAACTTTGACGATTGAACAAATACTAAATTATACAGTATCAGAGAGCGACAATATTGGTTGTGATATTTTGCTAAAATTAATCGGAGGAACTGATTCTGTTCAAAAATTCTTGAATGCTAATCATTTCACTGATATTTCAATCAAAGCAAACGAAGAACAAATGCACAAGGATTGGAATACCCAATATCAAAATTGGGCAACCCCAACAGCGATGAACAAACTGTTAATAGATACTTATAATAATAAGAACCAATTACTTTCTAAAAAAAGTTATGATTTTATTTGGAAAATTATGAGAGAAACAACAACAGGAAGTAACCGATTAAAAGGACAATTACCAAAGAATACAATTGTTGCTCATAAAACAGGGACTTCCGGAATAAATAATGGAATTGCAGCAGCCACTAATGATGTTGGGGTAATTACTTTACCGAATGGACAATTAATTTTTATAAGCGTATTTGTTGCAGAGTCCAAAGAAACTTCGGAAATTAATGAAAAGATTATTTCAGACATTGCAAAAATAACGTGGAATTACTATTTGAATAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35915","NCBI_taxonomy_name":"Klebsiella pneumoniae","NCBI_taxonomy_id":"573"}}}},"ARO_accession":"3009083","ARO_id":"47875","ARO_name":"VEB-31","CARD_short_name":"VEB-31","ARO_description":"Extended-spectrum class A beta-lactamase VEB-31.","ARO_category":{"36182":{"category_aro_accession":"3000043","category_aro_cvterm_id":"36182","category_aro_name":"VEB beta-lactamase","category_aro_description":"VEB beta-lactamases or Vietnamese extended-spectrum beta-lactamases are class A beta-lactamases that confer high-level resistance to oxyimino cephalosporins and to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8502":{"model_id":"8502","model_name":"VEB-32","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11329":{"protein_sequence":{"accession":"BEV74467.1","sequence":"MKIVKRILLVLLSLFFTVVYSNAQTDNLTLKIENVLKEKNARIGVAIFNSNEKDTFKINNDFHFPMQSVMKFPIALAVLSEIDKGNLSFEQKIEITPQDLLPKTWSPIKEEFPNGTTLTIEQILNYTVSESDNIGCDILLKLIGGTDSVQKFLNANHFTDISIKANEEQMHKDWNTQYQNWATPTAMNKLLIDTYNNKNQLLSKKSYDFIWKIMRETTTGSNRLKGQLPKNTIVAHKTGTSGINNGIAAATNDVGVITLPNGQLIFISVFVAESKETSEINEKIISDIAKITWNYYLNK"},"dna_sequence":{"accession":"LC794539.1","fmin":"0","fmax":"900","strand":"+","sequence":"ATGAAAATCGTAAAAAGGATATTATTAGTATTGTTAAGTTTATTTTTTACAGTTGTGTATTCAAATGCTCAAACTGACAACTTAACTTTGAAAATTGAGAATGTTTTAAAGGAAAAAAATGCCAGAATAGGAGTAGCAATATTCAACAGCAATGAGAAGGATACTTTTAAGATTAATAACGACTTCCATTTCCCGATGCAAAGCGTTATGAAATTTCCGATTGCTTTAGCCGTTTTGTCTGAGATAGATAAAGGGAATCTTTCTTTTGAACAAAAAATAGAGATTACCCCTCAAGACCTTTTGCCTAAAACGTGGAGTCCGATTAAAGAGGAATTCCCTAATGGAACAACTTTGACGATTGAACAAATACTAAATTATACAGTATCAGAGAGCGACAATATTGGTTGTGATATTTTGCTAAAATTAATCGGAGGAACTGATTCTGTTCAAAAATTCTTGAATGCTAATCATTTCACTGATATTTCAATCAAAGCAAACGAAGAACAAATGCACAAGGATTGGAATACCCAATATCAAAATTGGGCAACCCCAACAGCGATGAACAAACTGTTAATAGATACTTATAATAATAAGAACCAATTACTTTCTAAAAAAAGTTATGATTTTATTTGGAAAATTATGAGAGAAACAACAACAGGAAGTAACCGATTAAAAGGACAATTACCAAAGAATACAATTGTTGCTCATAAAACAGGGACTTCCGGAATAAATAATGGAATTGCAGCAGCCACTAATGATGTTGGGGTAATTACTTTACCGAATGGACAATTAATTTTTATAAGCGTATTTGTTGCAGAGTCCAAAGAAACTTCGGAAATTAATGAAAAGATTATTTCAGACATTGCAAAAATAACGTGGAATTACTATTTGAATAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39677","NCBI_taxonomy_name":"Aeromonas veronii","NCBI_taxonomy_id":"654"}}}},"ARO_accession":"3009084","ARO_id":"47876","ARO_name":"VEB-32","CARD_short_name":"VEB-32","ARO_description":"Extended-spectrum class A beta-lactamase VEB-32.","ARO_category":{"36182":{"category_aro_accession":"3000043","category_aro_cvterm_id":"36182","category_aro_name":"VEB beta-lactamase","category_aro_description":"VEB beta-lactamases or Vietnamese extended-spectrum beta-lactamases are class A beta-lactamases that confer high-level resistance to oxyimino cephalosporins and to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8503":{"model_id":"8503","model_name":"VEB-33","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11330":{"protein_sequence":{"accession":"BEV74468.1","sequence":"MKIVKRILLVLLSLFFTVVYSNAQTDNLTLKIENVLKAKNARIGVAIFNSNEKDTFKINNDFHFPMQSVMKFPIALAVLSEIDKGNLSFEQKIEITPQDLLPKTWSPIKDEFPNGTTLTIEQILNYTVSESDNIGCDILLKLIGGTDSVQKFLNANHFTDISIKANEEQMHKDWNTQYQNWATPTAMNKLLIDTYNNKNQLLSKKSYDFIWKIMRETTTGSNRLKGQLPKNTIVAHKTGTSGINNGIAAATNDVGVITLPNGQLIFISVFVAESKETSEINEKIISDIAKITWNYYLNK"},"dna_sequence":{"accession":"LC794540.1","fmin":"0","fmax":"900","strand":"+","sequence":"ATGAAAATCGTAAAAAGGATATTATTAGTATTGTTAAGTTTATTTTTTACAGTTGTGTATTCAAATGCTCAAACTGACAACTTAACTTTGAAAATTGAGAATGTTTTAAAGGCAAAAAATGCCAGAATAGGAGTAGCAATATTCAACAGCAATGAGAAGGATACTTTTAAGATTAATAACGACTTCCATTTCCCGATGCAAAGCGTTATGAAATTTCCGATTGCTTTAGCCGTTTTGTCTGAGATAGATAAAGGGAATCTTTCTTTTGAACAAAAAATAGAGATTACCCCTCAAGACCTTTTGCCTAAAACGTGGAGTCCGATTAAAGATGAATTCCCTAATGGAACAACTTTGACGATTGAACAAATACTAAATTATACAGTATCAGAGAGCGACAATATTGGTTGTGATATTTTGCTAAAATTAATCGGAGGAACTGATTCTGTTCAAAAATTCTTGAATGCTAATCATTTCACTGATATTTCAATCAAAGCAAACGAAGAACAAATGCACAAGGATTGGAATACCCAATATCAAAATTGGGCAACCCCAACAGCGATGAACAAACTGTTAATAGATACTTATAATAATAAGAACCAATTACTTTCTAAAAAAAGTTATGATTTTATTTGGAAAATTATGAGAGAAACAACAACAGGAAGTAACCGATTAAAAGGACAATTACCAAAGAATACAATTGTTGCTCATAAAACAGGGACTTCCGGAATAAATAATGGAATTGCAGCAGCCACTAATGATGTTGGGGTAATTACTTTACCGAATGGACAATTAATTTTTATAAGCGTATTTGTTGCAGAGTCCAAAGAAACTTCGGAAATTAATGAAAAGATTATTTCAGACATTGCAAAAATAACGTGGAATTACTATTTGAATAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39677","NCBI_taxonomy_name":"Aeromonas veronii","NCBI_taxonomy_id":"654"}}}},"ARO_accession":"3009085","ARO_id":"47877","ARO_name":"VEB-33","CARD_short_name":"VEB-33","ARO_description":"Extended-spectrum class A beta-lactamase VEB-33.","ARO_category":{"36182":{"category_aro_accession":"3000043","category_aro_cvterm_id":"36182","category_aro_name":"VEB beta-lactamase","category_aro_description":"VEB beta-lactamases or Vietnamese extended-spectrum beta-lactamases are class A beta-lactamases that confer high-level resistance to oxyimino cephalosporins and to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8504":{"model_id":"8504","model_name":"VEB-34","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11331":{"protein_sequence":{"accession":"WVW91708.1","sequence":"MKIVKRILLVLLSLFFTVEYSNAQTDNLTLKIENVLKAKNARIGVAIFNSNEKDTLKINNDFHYPMQSVMKFPIALAVLSEIDKGNLSFEQKIEITPQDLLPKTWSPIKEEFPNGTTLTIEQILNYTVSESDNIGCDILLKLIGGTDSVQKFLNANHFTDISIKANEEQMHKDWNTQYQNWATPTAMNKLLIDTYNNKNQLLSKKSYDFIWKIMRETTTGSNRLKGQLPKNTIVAHKTGTSGINNGIAAATNDVGVITLPNGQLIFISVFVAESKETSEINEKIISDIAKITWNYYLNK"},"dna_sequence":{"accession":"PP328955.1","fmin":"0","fmax":"900","strand":"+","sequence":"ATGAAAATCGTAAAAAGGATATTATTAGTATTGTTAAGTTTATTTTTTACAGTTGAGTATTCAAATGCTCAAACTGACAACTTAACTTTGAAAATTGAGAATGTTTTAAAGGCAAAAAATGCCAGAATAGGAGTAGCAATATTCAACAGCAATGAGAAGGATACTTTGAAGATTAATAACGACTTCCATTACCCGATGCAAAGCGTTATGAAATTTCCGATTGCTTTAGCCGTTTTGTCTGAGATAGATAAAGGGAATCTTTCTTTTGAACAAAAAATAGAGATTACCCCTCAAGACCTTTTGCCTAAAACGTGGAGTCCGATTAAAGAGGAATTCCCTAATGGAACAACTTTGACGATTGAACAAATACTAAATTATACAGTATCAGAGAGCGACAATATTGGTTGTGATATTTTGCTAAAATTAATCGGAGGAACTGATTCTGTTCAAAAATTCTTGAATGCTAATCATTTCACTGATATTTCAATCAAAGCAAACGAAGAACAAATGCACAAGGATTGGAATACCCAATATCAAAATTGGGCAACCCCAACAGCGATGAACAAACTGTTAATAGATACTTATAATAATAAGAACCAATTACTTTCTAAAAAAAGTTATGATTTTATTTGGAAAATTATGAGAGAAACAACAACAGGAAGTAACCGATTAAAAGGACAATTACCAAAGAATACAATTGTTGCTCATAAAACAGGGACTTCCGGAATAAATAATGGAATTGCAGCAGCCACTAATGATGTTGGGGTAATTACTTTACCGAATGGACAATTAATTTTTATAAGCGTATTTGTTGCAGAGTCCAAAGAAACTTCGGAAATTAATGAAAAGATTATTTCAGACATTGCAAAAATAACGTGGAATTACTATTTGAATAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39513","NCBI_taxonomy_name":"Acinetobacter variabilis","NCBI_taxonomy_id":"70346"}}}},"ARO_accession":"3009086","ARO_id":"47878","ARO_name":"VEB-34","CARD_short_name":"VEB-34","ARO_description":"Extended-spectrum class A beta-lactamase VEB-34.","ARO_category":{"36182":{"category_aro_accession":"3000043","category_aro_cvterm_id":"36182","category_aro_name":"VEB beta-lactamase","category_aro_description":"VEB beta-lactamases or Vietnamese extended-spectrum beta-lactamases are class A beta-lactamases that confer high-level resistance to oxyimino cephalosporins and to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8505":{"model_id":"8505","model_name":"VEB-35","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11332":{"protein_sequence":{"accession":"XHO32907.1","sequence":"MKIVKRILLVLLSLFFTVVYSNAQTDNLTLKIENVLKAKNARIGVAIFNSNEKDTLKINNDFHFPMQSVMKFPIALAVLSEIDKGNLSFEQKIEITPQDLLPKTWSPIKEEFPNGTTLTIEQILNYTVSESDNIGCDILLKLIGGTDSVQKFLNANHFTDISIKANEEQMHKDWNTQYQNWATPTAMNKLLIDTYNNKNQLLSKKSYDFIWKIMRETTTGSNRLKGQLPKNTIVAHKIGTSGINNGIAAATNDVGVITLPNGQLIFISVFVAESKETSEINEKIISDIAKITWNYYLNK"},"dna_sequence":{"accession":"PQ394564.1","fmin":"0","fmax":"900","strand":"+","sequence":"ATGAAAATCGTAAAAAGGATATTATTAGTATTGTTAAGTTTATTTTTTACAGTTGTGTATTCAAATGCTCAAACTGACAACTTAACTTTGAAAATTGAGAATGTTTTAAAGGCAAAAAATGCCAGAATAGGAGTAGCAATATTCAACAGCAATGAGAAGGATACTTTGAAGATTAATAACGACTTCCATTTCCCGATGCAAAGCGTTATGAAATTTCCGATTGCTTTAGCCGTTTTGTCTGAGATAGATAAAGGGAATCTTTCTTTTGAACAAAAAATAGAGATTACCCCTCAAGACCTTTTGCCTAAAACGTGGAGTCCGATTAAAGAGGAATTCCCTAATGGAACAACTTTGACGATTGAACAAATACTAAATTATACAGTATCAGAGAGCGACAATATTGGTTGTGATATTTTGCTAAAATTAATCGGAGGAACTGATTCTGTTCAAAAATTCTTGAATGCTAATCATTTCACTGATATTTCAATCAAAGCAAACGAAGAACAAATGCACAAGGATTGGAATACCCAATATCAAAATTGGGCAACCCCAACAGCGATGAACAAACTGTTAATAGATACTTATAATAATAAGAACCAATTACTTTCTAAAAAAAGTTATGATTTTATTTGGAAAATTATGAGAGAAACAACAACAGGAAGTAACCGATTAAAAGGACAATTACCAAAGAATACAATTGTTGCTCATAAAATAGGGACTTCCGGAATAAATAATGGAATTGCAGCAGCCACTAATGATGTTGGGGTAATTACTTTACCGAATGGACAATTAATTTTTATAAGCGTATTTGTTGCAGAGTCCAAAGAAACTTCGGAAATTAATGAAAAGATTATTTCAGACATTGCAAAAATAACGTGGAATTACTATTTGAATAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36944","NCBI_taxonomy_name":"Providencia rettgeri","NCBI_taxonomy_id":"587"}}}},"ARO_accession":"3009087","ARO_id":"47879","ARO_name":"VEB-35","CARD_short_name":"VEB-35","ARO_description":"Extended-spectrum class A beta-lactamase VEB-35.","ARO_category":{"36182":{"category_aro_accession":"3000043","category_aro_cvterm_id":"36182","category_aro_name":"VEB beta-lactamase","category_aro_description":"VEB beta-lactamases or Vietnamese extended-spectrum beta-lactamases are class A beta-lactamases that confer high-level resistance to oxyimino cephalosporins and to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8506":{"model_id":"8506","model_name":"VEB-36","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11333":{"protein_sequence":{"accession":"XHO32908.1","sequence":"MKIVKRILLVLLSLFFTVVYSNAQADNLTLKIENVLKAKNARIGVAIFNSNEKDTLKINNDFHFPMQSVMKFPIALAVLSEIDKGNLSFEQKIEITPQDLLPKMWSPIKEEFPNGTTLTIEQILNYTVSETDNIGCDILLKLIGGTDSVQKFLNANHFTDISIKANEEQMHKDWNTQYQNWATPTAMNKLLIDTYNNKNQLLSKKSYDFIWKIMRETTTGSNRLKGQLPKNTIVAHKTGTSGINNGIAAATNDVGVITLPNGQLIFISVFVAESKETSEINEKIISDIAKITWNYYLNK"},"dna_sequence":{"accession":"PQ394565.1","fmin":"0","fmax":"900","strand":"+","sequence":"ATGAAAATCGTAAAAAGGATATTATTAGTATTGTTAAGTTTATTTTTTACAGTTGTGTATTCAAATGCTCAAGCTGACAACTTAACTTTGAAAATTGAGAATGTTTTAAAGGCAAAAAATGCCAGAATAGGAGTAGCAATATTCAACAGCAATGAGAAGGATACTTTGAAGATTAATAACGACTTCCATTTCCCGATGCAAAGCGTTATGAAATTTCCGATTGCTTTAGCCGTTTTGTCTGAGATAGATAAAGGGAATCTTTCTTTTGAACAAAAAATAGAGATTACCCCTCAAGACCTTTTGCCTAAAATGTGGAGTCCGATTAAAGAGGAATTCCCTAATGGAACAACTTTGACGATTGAACAAATACTAAATTATACAGTATCAGAGACCGACAATATTGGTTGTGATATTTTGCTAAAATTAATCGGAGGAACTGATTCTGTTCAAAAATTCTTGAATGCTAATCATTTCACTGATATTTCAATCAAAGCAAACGAAGAACAAATGCACAAGGATTGGAATACCCAATATCAAAATTGGGCAACCCCAACAGCGATGAACAAACTGTTAATAGATACTTATAATAATAAGAACCAATTACTTTCTAAAAAAAGTTATGATTTTATTTGGAAAATTATGAGAGAAACAACAACAGGAAGTAACCGATTAAAAGGACAATTACCAAAGAATACAATTGTTGCTCATAAAACAGGGACTTCCGGAATAAATAATGGAATTGCAGCAGCCACTAATGATGTTGGGGTAATTACTTTACCGAATGGACAATTAATTTTTATAAGCGTATTTGTTGCAGAGTCCAAAGAAACTTCGGAAATTAATGAAAAGATTATTTCAGACATTGCAAAAATAACGTGGAATTACTATTTGAATAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35914","NCBI_taxonomy_name":"Escherichia coli","NCBI_taxonomy_id":"562"}}}},"ARO_accession":"3009088","ARO_id":"47880","ARO_name":"VEB-36","CARD_short_name":"VEB-36","ARO_description":"Extended-spectrum class A beta-lactamase VEB-36.","ARO_category":{"36182":{"category_aro_accession":"3000043","category_aro_cvterm_id":"36182","category_aro_name":"VEB beta-lactamase","category_aro_description":"VEB beta-lactamases or Vietnamese extended-spectrum beta-lactamases are class A beta-lactamases that confer high-level resistance to oxyimino cephalosporins and to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8507":{"model_id":"8507","model_name":"VEB-37","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11334":{"protein_sequence":{"accession":"XHO32909.1","sequence":"MKIVKRILLVLLSLFFTVVYSNAQADNLTLKIENVLKAKNARIGVAIFNSNEKDTLKINNDFHFPMQSVMKFPIALAVLSEIDKGNLSFEQKIEITPQDLLPKMWSPIKEEFPNGTTLTIEQILNYTVSESDNIGCDILLKLIGGTDSVQKFLNANHFTDISIKANEEQMHKDWNTQYQNWATPTAMNKLLIDTYNNKNQLLSKKSYDFIWKIMRERTTGSNRLKGQLPKNTIVAHKTGTSGINNGIAAATNDVGVITLPNGQLIFISVFVAESKETSEINEKIISDIAKITWDYYLNK"},"dna_sequence":{"accession":"PQ394566.1","fmin":"0","fmax":"900","strand":"+","sequence":"ATGAAAATCGTAAAAAGGATATTATTAGTATTGTTAAGTTTATTTTTTACAGTTGTGTATTCAAATGCTCAAGCTGACAACTTAACTTTGAAAATTGAGAATGTTTTAAAGGCAAAAAATGCCAGAATAGGAGTAGCAATATTCAACAGCAATGAGAAGGATACTTTGAAGATTAATAACGACTTCCATTTCCCGATGCAAAGCGTTATGAAATTTCCGATTGCTTTAGCCGTTTTGTCTGAGATAGATAAAGGGAATCTTTCTTTTGAACAAAAAATAGAGATTACCCCTCAAGACCTTTTGCCTAAAATGTGGAGTCCGATTAAAGAGGAATTCCCTAATGGAACAACTTTGACGATTGAACAAATACTAAATTATACAGTATCAGAGAGCGACAATATTGGTTGTGATATTTTGCTAAAATTAATCGGAGGAACTGATTCTGTTCAAAAATTCTTGAATGCTAATCATTTCACTGATATTTCAATCAAAGCAAACGAAGAACAAATGCACAAGGATTGGAATACCCAATATCAAAATTGGGCAACCCCAACAGCGATGAACAAACTGTTAATAGATACTTATAATAATAAGAACCAATTACTTTCTAAAAAAAGTTATGATTTTATTTGGAAAATTATGAGAGAAAGAACAACAGGAAGTAACCGATTAAAAGGACAATTACCAAAGAATACAATTGTTGCTCATAAAACAGGGACTTCCGGAATAAATAATGGAATTGCAGCAGCCACTAATGATGTTGGGGTAATTACTTTACCGAATGGACAATTAATTTTTATAAGCGTATTTGTTGCAGAGTCCAAAGAAACTTCGGAAATTAATGAAAAGATTATTTCAGACATTGCAAAAATAACGTGGGATTACTATTTGAATAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3009089","ARO_id":"47881","ARO_name":"VEB-37","CARD_short_name":"VEB-37","ARO_description":"Extended-spectrum class A beta-lactamase VEB-37.","ARO_category":{"36182":{"category_aro_accession":"3000043","category_aro_cvterm_id":"36182","category_aro_name":"VEB beta-lactamase","category_aro_description":"VEB beta-lactamases or Vietnamese extended-spectrum beta-lactamases are class A beta-lactamases that confer high-level resistance to oxyimino cephalosporins and to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8508":{"model_id":"8508","model_name":"VEB-38","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11335":{"protein_sequence":{"accession":"XHO32910.1","sequence":"MKIVKRILLVLLSLFFTVVYSNAQTDNLTLKIENVLKAKNARIGVAIFNSNEKDTLKINNDFHFPMQSVMKFPIALAVLSEIDKGNLSFEQKIEITPQDLLPKMWSPIKEEFPNGTTLTIEQILNYTVSESDNIGCDILLKLIGGTDSVQKFLNANHFTDISIKANEEQMHKDWNTQYQNWATPTAMNKLLIDTYNNKNQLLSKKSYDFIWKIMRETTTGSNRLKGQLPKNTIVAHKTGTSGINNGIAAATNDVGVITLPNGQLIFISVFVAESKETSEINEKIISDIAKITWNYYLNK"},"dna_sequence":{"accession":"PQ394567.1","fmin":"0","fmax":"900","strand":"+","sequence":"ATGAAAATCGTAAAAAGGATATTATTAGTATTGTTAAGTTTATTTTTTACAGTTGTGTATTCAAATGCTCAAACTGACAACTTAACTTTGAAAATTGAGAATGTTTTAAAGGCAAAAAATGCCAGAATAGGAGTAGCAATATTCAACAGCAATGAGAAGGATACTTTGAAGATTAATAACGACTTCCATTTCCCGATGCAAAGCGTTATGAAATTTCCGATTGCTTTAGCCGTTTTGTCTGAGATAGATAAAGGGAATCTTTCTTTTGAACAAAAAATAGAGATTACCCCTCAAGACCTTTTGCCTAAAATGTGGAGTCCGATTAAAGAGGAATTCCCTAATGGAACAACTTTGACGATTGAACAAATACTAAATTATACAGTATCAGAGAGCGACAATATTGGTTGTGATATTTTGCTAAAATTAATCGGAGGAACTGATTCTGTTCAAAAATTCTTGAATGCTAATCATTTCACTGATATTTCAATCAAAGCAAACGAAGAACAAATGCACAAGGATTGGAATACCCAATATCAAAATTGGGCAACCCCAACAGCGATGAACAAACTGTTAATAGATACTTATAATAATAAGAACCAATTACTTTCTAAAAAAAGTTATGATTTTATTTGGAAAATTATGAGAGAAACAACAACAGGAAGTAACCGATTAAAAGGACAATTACCAAAGAATACAATTGTTGCTCATAAAACAGGGACTTCCGGAATAAATAATGGAATTGCAGCAGCCACTAATGATGTTGGGGTAATTACTTTACCGAATGGACAATTAATTTTTATAAGCGTATTTGTTGCAGAGTCCAAAGAAACTTCGGAAATTAATGAAAAGATTATTTCAGACATTGCAAAAATAACGTGGAATTACTATTTGAATAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36771","NCBI_taxonomy_name":"Proteus mirabilis","NCBI_taxonomy_id":"584"}}}},"ARO_accession":"3009090","ARO_id":"47882","ARO_name":"VEB-38","CARD_short_name":"VEB-38","ARO_description":"Extended-spectrum class A beta-lactamase VEB-38.","ARO_category":{"36182":{"category_aro_accession":"3000043","category_aro_cvterm_id":"36182","category_aro_name":"VEB beta-lactamase","category_aro_description":"VEB beta-lactamases or Vietnamese extended-spectrum beta-lactamases are class A beta-lactamases that confer high-level resistance to oxyimino cephalosporins and to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8509":{"model_id":"8509","model_name":"VEB-39","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11336":{"protein_sequence":{"accession":"XHO32911.1","sequence":"MKIVKRILLVLLSLFFTVVYSNAQTDNLTLKIENVLKAKNARIGVAIFNSNEKDTLKINNDFHFPMQSVMKFPIALAVLSEIDKGNLSFEQKIEITPQDLLPKTWSPIKEEFPNGTTLTIEQILHYTVSESDNIGCDILLKLIGGTDSVQKFLNANHFTDISIKANEEQMHKDWNTQYQNWATPTAMNKLLIDTYNNKNQLLSKKSYDFIWKIMRETTTGSNRLKGQLPKNTIVAHKTGTSGINNGIAAATNDVGVITLPNGQLIFISVFVAESKETSEINEKIISDIAKITWNYYLNK"},"dna_sequence":{"accession":"PQ394568.1","fmin":"0","fmax":"900","strand":"+","sequence":"ATGAAAATCGTAAAAAGGATATTATTAGTATTGTTAAGTTTATTTTTTACAGTTGTGTATTCAAATGCTCAAACTGACAACTTAACTTTGAAAATTGAGAATGTTTTAAAGGCAAAAAATGCCAGAATAGGAGTAGCAATATTCAACAGCAATGAGAAGGATACTTTGAAGATTAATAACGACTTCCATTTCCCGATGCAAAGCGTTATGAAATTTCCGATTGCTTTAGCCGTTTTGTCTGAGATAGATAAAGGGAATCTTTCTTTTGAACAAAAAATAGAGATTACCCCTCAAGACCTTTTGCCTAAAACGTGGAGTCCGATTAAAGAGGAATTCCCTAATGGAACAACTTTGACGATTGAACAAATACTACATTATACAGTATCAGAGAGCGACAATATTGGTTGTGATATTTTGCTAAAATTAATCGGAGGAACTGATTCTGTTCAAAAATTCTTGAATGCTAATCATTTCACTGATATTTCAATCAAAGCAAACGAAGAACAAATGCACAAGGATTGGAATACCCAATATCAAAATTGGGCAACCCCAACAGCGATGAACAAACTGTTAATAGATACTTATAATAATAAGAACCAATTACTTTCTAAAAAAAGTTATGATTTTATTTGGAAAATTATGAGAGAAACAACAACAGGAAGTAACCGATTAAAAGGACAATTACCAAAGAATACAATTGTTGCTCATAAAACAGGGACTTCCGGAATAAATAATGGAATTGCAGCAGCCACTAATGATGTTGGGGTAATTACTTTACCGAATGGACAATTAATTTTTATAAGCGTATTTGTTGCAGAGTCCAAAGAAACTTCGGAAATTAATGAAAAGATTATTTCAGACATTGCAAAAATAACGTGGAATTACTATTTGAATAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3009091","ARO_id":"47883","ARO_name":"VEB-39","CARD_short_name":"VEB-39","ARO_description":"Extended-spectrum class A beta-lactamase VEB-39.","ARO_category":{"36182":{"category_aro_accession":"3000043","category_aro_cvterm_id":"36182","category_aro_name":"VEB beta-lactamase","category_aro_description":"VEB beta-lactamases or Vietnamese extended-spectrum beta-lactamases are class A beta-lactamases that confer high-level resistance to oxyimino cephalosporins and to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8510":{"model_id":"8510","model_name":"VIM-88","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11337":{"protein_sequence":{"accession":"XHO32912.1","sequence":"MLKVISSLLVYMTASVMAVASPLAHSGEPSGEYPTVYEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEAEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSANVLYGGCAVHELSSTSAGNVADADLAEWPTSVERIQKHYPEAEVVIPGHGLPGGLDLLQHTANVVKAHKNRSVAE"},"dna_sequence":{"accession":"PQ394569.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGTTAAAAGTTATTAGTAGTTTATTGGTCTACATGACCGCGTCTGTCATGGCTGTCGCAAGTCCGTTAGCCCATTCCGGGGAGCCGAGTGGTGAGTATCCGACAGTCTACGAAATTCCGGTCGGAGAGGTCCGACTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCGGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAAAAGCAAATTGGACTTCCCGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGCAGAGGGGAACGAGATTCCCACGCATTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAGCTCTTCTATCCTGGTGCTGCGCATTCGACCGACAATCTGGTTGTATACGTCCCGTCAGCGAACGTGCTATACGGTGGTTGTGCCGTTCATGAGTTGTCAAGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCGTTGAGCGGATTCAAAAACACTACCCGGAAGCAGAGGTCGTCATTCCCGGGCACGGTCTACCGGGCGGTCTAGACTTGCTCCAGCACACAGCGAACGTTGTCAAAGCACACAAAAATCGCTCAGTCGCCGAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3009092","ARO_id":"47884","ARO_name":"VIM-88","CARD_short_name":"VIM-88","ARO_description":"Subclass B1 metallo-beta-lactamase VIM-88.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8511":{"model_id":"8511","model_name":"VIM-89","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11338":{"protein_sequence":{"accession":"XHO32913.1","sequence":"MFKLLSKLLVYLTASIMAIASPLAFSVDSSGEYPTVSEIPVGGVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEVEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSASVLYGGCAIYELSRTSAGNVADADLAEWPTSIERIQQHYPEAQFVIPGHGLPGGLDLLKHTTNVVKAHTNRSVVE"},"dna_sequence":{"accession":"PQ394570.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGTTCAAACTTTTGAGTAAGTTATTGGTCTATTTGACCGCGTCTATCATGGCTATTGCGAGTCCGCTCGCTTTTTCCGTAGATTCTAGCGGTGAGTATCCGACAGTCAGCGAAATTCCGGTCGGGGGGGTCCGGCTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCAGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAGAAGCAAATTGGACTTCCTGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGTAGAGGGGAACGAGATTCCCACGCACTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAACTCTTCTATCCTGGTGCTGCGCATTCGACCGACAACTTAGTTGTGTACGTCCCGTCTGCGAGTGTGCTCTATGGTGGTTGTGCGATTTATGAGTTGTCACGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCATTGAGCGGATTCAACAACACTACCCGGAAGCACAGTTCGTCATTCCGGGGCACGGCCTGCCGGGCGGTCTAGACTTGCTCAAGCACACAACGAATGTTGTAAAAGCGCACACAAATCGCTCAGTCGTTGAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3009093","ARO_id":"47885","ARO_name":"VIM-89","CARD_short_name":"VIM-89","ARO_description":"Subclass B1 metallo-beta-lactamase VIM-89.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8512":{"model_id":"8512","model_name":"VIM-90","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11339":{"protein_sequence":{"accession":"XHO32914.1","sequence":"MFKLLSKLLVYLTASIMAIASPLAFSVDSSGEYPTVSEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEVEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSASVLYGGCAIYELSRTSAGNVPDADLAEWPTSIERIQQHYPEAQFVIPGHGLPGGLDLLKHTTNVVKAHTNRSVVE"},"dna_sequence":{"accession":"PQ394571.1","fmin":"0","fmax":"801","strand":"+","sequence":"ATGTTCAAACTTTTGAGTAAGTTATTGGTCTATTTGACCGCGTCTATCATGGCTATTGCGAGTCCGCTCGCTTTTTCCGTAGATTCTAGCGGTGAGTATCCGACAGTCAGCGAAATTCCGGTCGGGGAGGTCCGGCTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCAGTCTACCCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAGAAGCAAATTGGACTTCCTGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGTAGAGGGGAACGAGATTCCCACGCACTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAACTCTTCTATCCTGGTGCTGCGCATTCGACCGACAACTTAGTTGTGTACGTCCCGTCTGCGAGTGTGCTCTATGGTGGTTGTGCGATTTATGAGTTGTCACGCACGTCTGCGGGGAACGTGCCCGATGCCGATCTGGCTGAATGGCCCACCTCCATTGAGCGGATTCAACAACACTACCCGGAAGCACAGTTCGTCATTCCGGGGCACGGCCTGCCGGGCGGTCTAGACTTGCTCAAGCACACAACGAATGTTGTAAAAGCGCACACAAATCGCTCAGTCGTTGAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3009094","ARO_id":"47886","ARO_name":"VIM-90","CARD_short_name":"VIM-90","ARO_description":"Subclass B1 metallo-beta-lactamase VIM-90.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8513":{"model_id":"8513","model_name":"VIM-91","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11340":{"protein_sequence":{"accession":"MFC1252596.1","sequence":"MFKLLSKLLVYLTASIMAIASPLAFSVDSSGEYPTVSEIPVGEVRLYQIADGVWSHIATQSFDGAVYSSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEVEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSASVLYGGCAIYELSRTSAGNVADADLAEWPTSIERIQQHYPEAQFVIPGHGLPGGLDLLKHTTNVVKAHTNRSVVE"},"dna_sequence":{"accession":"JBHOJN010000016.1","fmin":"88223","fmax":"89024","strand":"+","sequence":"ATGTTCAAACTTTTGAGTAAGTTATTGGTCTATTTGACCGCGTCTATCATGGCTATTGCGAGTCCGCTCGCTTTTTCCGTAGATTCTAGCGGTGAGTATCCGACAGTCAGCGAAATTCCGGTCGGGGAGGTCCGGCTTTACCAGATTGCCGATGGTGTTTGGTCGCATATCGCAACGCAGTCGTTTGATGGCGCAGTCTACTCGTCCAATGGTCTCATTGTCCGTGATGGTGATGAGTTGCTTTTGATTGATACAGCGTGGGGTGCGAAAAACACAGCGGCACTTCTCGCGGAGATTGAGAAGCAAATTGGACTTCCTGTAACGCGTGCAGTCTCCACGCACTTTCATGACGACCGCGTCGGCGGCGTTGATGTCCTTCGGGCGGCTGGGGTGGCAACGTACGCATCACCGTCGACACGCCGGCTAGCCGAGGTAGAGGGGAACGAGATTCCCACGCACTCTCTAGAAGGACTCTCATCGAGCGGGGACGCAGTGCGCTTCGGTCCAGTAGAACTCTTCTATCCTGGTGCTGCGCATTCGACCGACAACTTAGTTGTGTACGTCCCGTCTGCGAGTGTGCTCTATGGTGGTTGTGCGATTTATGAGTTGTCACGCACGTCTGCGGGGAACGTGGCCGATGCCGATCTGGCTGAATGGCCCACCTCCATTGAGCGGATTCAACAACACTACCCGGAAGCACAGTTCGTCATTCCGGGGCACGGCCTGCCGGGCGGTCTAGACTTGCTCAAGCACACAACGAATGTTGTAAAAGCGCACACAAATCGCTCAGTCGTTGAGTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3009095","ARO_id":"47887","ARO_name":"VIM-91","CARD_short_name":"VIM-91","ARO_description":"Subclass B1 metallo-beta-lactamase VIM-91.","ARO_category":{"36030":{"category_aro_accession":"3000021","category_aro_cvterm_id":"36030","category_aro_name":"VIM beta-lactamase","category_aro_description":"The Verone integron-encoded metallo-beta-lactamase (VIM) family was reported from Italy in 1999. There are, to date, 23 reported variants.  VIM enzymes mostly occur in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae. Integron-associated, sometimes within plasmids. Hydrolyses all beta-lactams except monobactams, and evades all beta-lactam inhibitors.  There is a strong incidence of these in East Asia.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8514":{"model_id":"8514","model_name":"YOC-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11341":{"protein_sequence":{"accession":"QIU91361.1","sequence":"MQKMLNGVLALAALSFSTAGIAAPKTLTAEQIAQAVNRTIVPLLKEQAIPGMAVAVIYQGQPYYYTWGKADVQNNRPVTTQTLFELGSVSKTFTGVLGGDAVARGEIKLSDKANQYWPELNARQWQGITMLDLATYTAGGLPLQVPDNVTDNASLLEFYQQWQPKWAPGTTRLYANSSIGLFGALAVKPSGLGFEEAMNQRVLQPLNLKHTWITVPASEEKNYAWGYRDGQPVHVSPGMLDAESYGVKSSVTDMAAWLQANMAPQHASSPTLKKGLEMAQARYWRIGSMYQGLGWEMLNWPVNGAAMAKDGDGAVALAPHPAAAVEPPVPAVAASWVHKTGSTGGFGAYVAFIPEQQLGIVMLANKSYPNPARIQAGYTILKALQ"},"dna_sequence":{"accession":"CP050811.1","fmin":"4073465","fmax":"4074623","strand":"-","sequence":"ATGCAAAAAATGTTGAATGGCGTACTGGCGCTGGCCGCACTTTCGTTCTCTACGGCGGGCATTGCTGCGCCGAAAACGCTTACCGCGGAGCAGATAGCTCAGGCGGTGAATCGTACTATCGTGCCTCTGCTTAAAGAGCAGGCGATCCCGGGAATGGCGGTAGCGGTGATTTATCAGGGCCAGCCGTATTACTATACCTGGGGTAAAGCGGATGTGCAGAACAACCGTCCGGTCACCACGCAGACGCTGTTCGAACTCGGCTCCGTTAGCAAAACTTTCACCGGCGTACTGGGTGGTGATGCCGTTGCCCGTGGTGAAATCAAGCTCAGCGATAAAGCAAACCAGTACTGGCCAGAGCTTAACGCCAGGCAGTGGCAAGGGATTACCATGCTGGACCTGGCGACCTATACCGCGGGCGGCCTGCCGCTGCAGGTGCCGGATAACGTCACGGACAACGCTTCGCTGCTTGAGTTCTATCAGCAGTGGCAGCCGAAATGGGCGCCGGGCACCACCCGGTTGTATGCCAACAGCAGCATTGGCCTTTTCGGCGCGCTGGCGGTAAAACCTTCCGGGCTTGGCTTTGAAGAGGCCATGAACCAGCGTGTACTGCAGCCGCTGAATCTGAAACACACGTGGATAACCGTTCCGGCATCAGAAGAGAAAAACTACGCCTGGGGCTATCGCGACGGCCAGCCGGTCCACGTTTCACCCGGCATGCTGGATGCCGAATCCTACGGCGTGAAATCCTCGGTCACGGATATGGCCGCCTGGCTGCAGGCGAACATGGCTCCGCAGCATGCCAGCAGCCCGACGTTGAAGAAAGGGCTGGAGATGGCACAGGCGCGCTACTGGCGCATTGGCAGCATGTATCAGGGGCTGGGTTGGGAGATGCTCAACTGGCCGGTTAATGGCGCAGCAATGGCGAAAGACGGTGATGGCGCTGTGGCGCTGGCACCGCACCCGGCAGCCGCAGTAGAACCACCGGTTCCTGCCGTTGCCGCCTCCTGGGTGCATAAAACCGGCTCCACCGGCGGCTTTGGGGCTTACGTCGCATTTATCCCGGAGCAGCAGCTTGGTATCGTGATGCTGGCAAACAAAAGCTACCCGAATCCGGCACGCATCCAGGCCGGATACACCATCCTGAAAGCGTTACAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"47934","NCBI_taxonomy_name":"Yokenella regensburgei","NCBI_taxonomy_id":"158877"}}}},"ARO_accession":"3009096","ARO_id":"47888","ARO_name":"YOC-1","CARD_short_name":"YOC-1","ARO_description":"Class C beta-lactamase YOC-1.","ARO_category":{"46673":{"category_aro_accession":"3007882","category_aro_cvterm_id":"46673","category_aro_name":"YOC beta-lactamase","category_aro_description":"YOC is a family of class C beta-lactamases which inactivate cephalosporin antibiotics.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"2222":{"model_id":"2222","model_name":"VEB-16","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"3416":{"protein_sequence":{"accession":"AAK14294.1","sequence":"MKIVKRILLVLLSLFFTVEYSNAQTDNLTLKIENVLKAKNARIGVAIFNSNEKDTLKINNDFHFPMQSVMKFPIALAVLSEIDKGNLSFEQKIEITPQDLLPKTWSPIKEEFPNGTTLTIEQILNYTVSESDNIGCDILLKLIGGTDSVQKFLNANHFTDISIKANEEQMHKDWNTQYQNWATPTAMNKLLIDTYNNKNQLLSKKSYDFIWKIMRETTTGSNRLKGQLPKNTIVAHKTGTSGINNGIAAATNDVGVITLPNGQLIFISVFVAESKETSEINEKIISDIAKITWNYYLNK"},"dna_sequence":{"accession":"AF324834.1","fmin":"0","fmax":"900","strand":"+","sequence":"ATGAAAATCGTAAAAAGGATATTATTAGTATTGTTAAGTTTATTTTTTACAGTTGAGTATTCAAATGCTCAAACTGACAACTTAACTTTGAAAATTGAGAATGTTTTAAAGGCAAAAAATGCCAGAATAGGAGTAGCAATATTCAACAGCAATGAGAAGGATACTTTGAAGATTAATAACGACTTCCATTTCCCGATGCAAAGCGTTATGAAATTTCCGATTGCTTTAGCCGTTTTGTCTGAGATAGATAAAGGGAATCTTTCTTTTGAACAAAAAATAGAGATTACCCCTCAAGACCTTTTGCCTAAAACGTGGAGTCCGATTAAAGAGGAATTCCCTAATGGAACAACTTTGACGATTGAACAAATACTAAATTATACAGTATCAGAGAGCGACAATATTGGTTGTGATATTTTGCTAAAATTAATCGGAGGAACTGATTCTGTTCAAAAATTCTTGAATGCTAATCATTTCACTGATATTTCAATCAAAGCAAACGAAGAACAAATGCACAAGGATTGGAATACCCAATATCAAAATTGGGCAACCCCAACAGCGATGAACAAACTGTTAATAGATACTTATAATAATAAGAACCAATTACTTTCTAAAAAAAGTTATGATTTTATTTGGAAAATTATGAGAGAAACAACAACAGGAAGTAACCGATTAAAAGGACAATTACCAAAGAATACAATTGTTGCTCATAAAACAGGGACTTCCGGAATAAATAATGGAATTGCAGCAGCCACTAATGATGTTGGGGTAATTACTTTACCGAATGGACAATTAATTTTTATAAGCGTATTTGTTGCAGAGTCCAAAGAAACTTCGGAAATTAATGAAAAGATTATTTCAGACATTGCAAAAATAACGTGGAATTACTATTTGAATAAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3003712","ARO_id":"40366","ARO_name":"VEB-16","CARD_short_name":"VEB-16","ARO_description":"VEB-16 (VEB-1b) is a beta-lactamase that is found in Pseudomonas aeruginosa.","ARO_category":{"36182":{"category_aro_accession":"3000043","category_aro_cvterm_id":"36182","category_aro_name":"VEB beta-lactamase","category_aro_description":"VEB beta-lactamases or Vietnamese extended-spectrum beta-lactamases are class A beta-lactamases that confer high-level resistance to oxyimino cephalosporins and to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"3779":{"model_id":"3779","model_name":"YRC-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"750"}},"model_sequences":{"sequence":{"6072":{"protein_sequence":{"accession":"ABA70720.1","sequence":"MMHKTLSCALLLVASGSTFATPQTEKKLSGIVDNVVIPLMKEQAIPGMAVAVIYQGQPYYFTWGMADVAGKQPVTQQTLFELGSVSKTFTGVLGGDAIARGEIKLSDPVSKYWPALSGKQWEGISLLNLATYTAGGLPLQVPDNITDETSLQNYYETWQPQWAPGTKRFYSNASIGMFGKLAVKPSGMSFEQAMNKRVFQPLNLTHTWIHVPEREEKHYAWGYRDGKAVHVSPGMLDAEAYGVKSSIKDMASWVRANMTPSEVKDASLQKGILLAQSRYLQVGDMYQGLGWEMLNWPMKATIAVGGSDNKVALAPLSAVEINPPAPALNSSWVHKTGSTGGFGSYVAFIPEKNLGIVMLANKSYPNPARVEAAYRILEALSVE"},"dna_sequence":{"accession":"DQ185144.1","fmin":"380","fmax":"1532","strand":"+","sequence":"ATGATGCATAAAACCCTTTCCTGTGCGCTGCTGCTCGTCGCGTCAGGTTCCACGTTTGCCACGCCTCAAACGGAAAAAAAACTCAGTGGAATTGTTGATAACGTTGTTATTCCTTTGATGAAAGAACAGGCCATTCCCGGCATGGCGGTGGCGGTGATCTATCAGGGCCAACCTTACTACTTTACCTGGGGAATGGCTGATGTCGCAGGCAAACAGCCTGTTACGCAGCAGACGTTATTCGAGCTCGGCTCCGTGAGTAAAACCTTCACCGGCGTGCTGGGTGGCGATGCCATTGCTCGTGGGGAAATTAAACTTAGTGATCCAGTGAGTAAATACTGGCCAGCGCTTTCCGGGAAACAATGGGAAGGGATTAGTTTGCTGAATTTGGCAACCTATACCGCTGGTGGCTTGCCGCTCCAGGTACCGGATAACATTACTGATGAGACGTCATTGCAGAATTACTATGAAACCTGGCAGCCACAGTGGGCTCCGGGCACCAAGCGTTTTTATTCAAACGCCAGTATTGGGATGTTTGGCAAACTGGCGGTTAAACCTTCAGGCATGAGCTTTGAGCAGGCGATGAACAAACGCGTGTTCCAGCCATTGAATCTCACGCATACTTGGATACATGTTCCTGAACGTGAAGAAAAACACTATGCGTGGGGCTATCGCGATGGGAAAGCCGTTCATGTTTCTCCGGGGATGCTGGACGCTGAAGCCTACGGCGTGAAATCCTCAATAAAGGATATGGCAAGCTGGGTGCGGGCTAACATGACGCCTTCTGAAGTAAAAGATGCCTCGCTGCAAAAGGGGATTTTGCTTGCCCAGTCGCGGTACTTGCAAGTGGGTGACATGTATCAGGGGTTGGGCTGGGAAATGCTGAACTGGCCGATGAAAGCAACAATCGCGGTCGGCGGTAGCGATAATAAAGTCGCACTCGCGCCGCTAAGTGCGGTAGAAATTAACCCGCCAGCGCCAGCATTAAATAGCTCGTGGGTACATAAAACTGGCTCAACCGGCGGATTTGGAAGCTACGTGGCTTTCATTCCCGAGAAGAATCTCGGCATCGTGATGCTGGCGAACAAAAGTTATCCTAACCCTGCGCGTGTCGAAGCAGCTTACCGCATCCTTGAAGCTTTGTCCGTGGAATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"42660","NCBI_taxonomy_name":"Yersinia ruckeri","NCBI_taxonomy_id":"29486"}}}},"ARO_accession":"3005035","ARO_id":"43233","ARO_name":"YRC-1","CARD_short_name":"YRC-1","ARO_description":"YRC-1 is a ampC-like beta-lactamase that confers resistance to penams and cephalosporins. It is an ambler class C beta-lactamase.","ARO_category":{"43232":{"category_aro_accession":"3005034","category_aro_cvterm_id":"43232","category_aro_name":"YRC beta-lactamase","category_aro_description":"YRC is a ambler class C beta-lactamase from Yersinia ruckeri. It confers resistance penams and cephalosporins.","category_aro_class_name":"AMR Gene Family"},"35927":{"category_aro_accession":"0000008","category_aro_cvterm_id":"35927","category_aro_name":"cefoxitin","category_aro_description":"Cefoxitin is a cephamycin antibiotic often grouped with the second generation cephalosporins. Cefoxitin is bactericidal and acts by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. Cefoxitin's 7-alpha-methoxy group and 3' leaving group make it a poor substrate for most beta-lactamases.","category_aro_class_name":"Antibiotic"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"35980":{"category_aro_accession":"0000063","category_aro_cvterm_id":"35980","category_aro_name":"cefuroxime","category_aro_description":"Cefuroxime is a second-generation cephalosporin antibiotic with increased stability with beta-lactamases than first-generation cephalosporins. Cefuroxime is active against Gram-positive organisms but less active against methicillin-resistant strains.","category_aro_class_name":"Antibiotic"},"35981":{"category_aro_accession":"0000064","category_aro_cvterm_id":"35981","category_aro_name":"amoxicillin","category_aro_description":"Amoxicillin is a moderate-spectrum, bacteriolytic, beta-lactam antibiotic used to treat bacterial infections caused by susceptible microorganisms. A derivative of penicillin, it has a wider range of treatment but remains relatively ineffective against Gram-negative bacteria. It is commonly taken with clavulanic acid, a beta-lactamase inhibitor. Like other beta-lactams, amoxicillin interferes with the synthesis of peptidoglycan.","category_aro_class_name":"Antibiotic"},"37084":{"category_aro_accession":"3000704","category_aro_cvterm_id":"37084","category_aro_name":"cefalotin","category_aro_description":"Cefalotin is a semisynthetic cephalosporin antibiotic activate against staphylococci. It is resistant to staphylococci beta-lactamases but hydrolyzed by enterobacterial beta-lactamases.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1294":{"model_id":"1294","model_name":"SED-1","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"550"}},"model_sequences":{"sequence":{"3310":{"protein_sequence":{"accession":"AAK63223.1","sequence":"MLKERFRQTVFIAAAVMPFIFSSTSLHAQATSDVQQVQKKLAALEKQSGGRLGVALINTADNSQVLYRADERFAMCSTSKVMTAAAVLKQSETHDGILQQKMTIKKADLTNWNPVTEKYVGNTMTLAELSAATLQYSDNTAMNKLLAHLGGPGNVTAFARSIGDTTFRLDRKEPELNTAIPGDERDTTSPLAMAKSLRKLTLGDALAGPQRAQLVDWLKGNTTGGQSIRAGLPAHWVVGDKTGAGDYGTTNDIAVIWPEDRAPLVLVTYFTQPQQDAKWRKDVLAAAAKIVTEGK"},"dna_sequence":{"accession":"AF321608.1","fmin":"0","fmax":"888","strand":"+","sequence":"ATGCTTAAGGAACGGTTTCGCCAGACGGTATTTATCGCTGCCGCTGTTATGCCCTTCATTTTTAGTAGCACTTCACTGCATGCGCAGGCGACGTCAGACGTGCAGCAGGTTCAGAAAAAGCTGGCGGCGCTGGAAAAGCAATCTGGCGGACGCCTGGGCGTGGCGCTGATTAATACCGCGGATAATTCGCAGGTGCTGTACCGCGCAGACGAGCGTTTTGCGATGTGCAGCACCAGTAAGGTCATGACCGCCGCCGCGGTATTAAAACAGAGTGAAACCCATGACGGTATTTTGCAGCAAAAAATGACCATTAAAAAAGCCGATCTGACCAACTGGAATCCCGTAACAGAGAAATATGTGGGTAATACGATGACATTAGCTGAGCTAAGCGCAGCGACGTTACAGTACAGCGATAATACCGCCATGAATAAACTGCTGGCGCATCTTGGCGGCCCCGGCAACGTCACGGCGTTTGCACGTTCCATTGGCGACACGACGTTTCGTCTCGATCGCAAAGAGCCGGAATTAAACACCGCCATTCCCGGCGATGAGCGCGACACAACATCGCCGCTGGCCATGGCCAAAAGTCTGCGTAAACTCACGCTGGGCGACGCGCTGGCAGGGCCCCAGCGCGCGCAGCTTGTCGACTGGCTGAAAGGCAACACCACCGGAGGCCAGAGCATTCGTGCCGGCCTTCCTGCACACTGGGTGGTGGGCGATAAAACCGGGGCGGGTGATTACGGCACCACGAATGACATCGCAGTGATCTGGCCGGAAGACCGCGCCCCGCTGGTGCTGGTAACCTATTTCACACAGCCACAGCAGGATGCGAAATGGCGTAAAGATGTCCTGGCCGCGGCGGCGAAAATTGTGACGGAAGGAAAGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"40168","NCBI_taxonomy_name":"Citrobacter sedlakii","NCBI_taxonomy_id":"67826"}}}},"ARO_accession":"3003561","ARO_id":"40167","ARO_name":"SED-1","CARD_short_name":"SED-1","ARO_description":"SED-1 is a chromosomal-encoded class A beta-lactamase identified in Citrobacter sedlakii.","ARO_category":{"46671":{"category_aro_accession":"3007880","category_aro_cvterm_id":"46671","category_aro_name":"SED beta-lactamase","category_aro_description":"SED is a family of broad-spectrum class A beta-lactamases.","category_aro_class_name":"AMR Gene Family"},"35980":{"category_aro_accession":"0000063","category_aro_cvterm_id":"35980","category_aro_name":"cefuroxime","category_aro_description":"Cefuroxime is a second-generation cephalosporin antibiotic with increased stability with beta-lactamases than first-generation cephalosporins. Cefuroxime is active against Gram-positive organisms but less active against methicillin-resistant strains.","category_aro_class_name":"Antibiotic"},"35981":{"category_aro_accession":"0000064","category_aro_cvterm_id":"35981","category_aro_name":"amoxicillin","category_aro_description":"Amoxicillin is a moderate-spectrum, bacteriolytic, beta-lactam antibiotic used to treat bacterial infections caused by susceptible microorganisms. A derivative of penicillin, it has a wider range of treatment but remains relatively ineffective against Gram-negative bacteria. It is commonly taken with clavulanic acid, a beta-lactamase inhibitor. Like other beta-lactams, amoxicillin interferes with the synthesis of peptidoglycan.","category_aro_class_name":"Antibiotic"},"35995":{"category_aro_accession":"0000078","category_aro_cvterm_id":"35995","category_aro_name":"piperacillin","category_aro_description":"Piperacillin is an acetylureidopenicillin and has an extended spectrum of targets relative to other beta-lactam antibiotics. It inhibits cell wall synthesis in bacteria, and is usually taken with the beta-lactamase inhibitor tazobactam to overcome penicillin-resistant bacteria.","category_aro_class_name":"Antibiotic"},"37084":{"category_aro_accession":"3000704","category_aro_cvterm_id":"37084","category_aro_name":"cefalotin","category_aro_description":"Cefalotin is a semisynthetic cephalosporin antibiotic activate against staphylococci. It is resistant to staphylococci beta-lactamases but hydrolyzed by enterobacterial beta-lactamases.","category_aro_class_name":"Antibiotic"},"40523":{"category_aro_accession":"3003832","category_aro_cvterm_id":"40523","category_aro_name":"ticarcillin","category_aro_description":"Ticarcillin is a carboxypenicillin used for the treatment of Gram-negative bacteria, particularly P. aeruginosa. Ticarcillin's antibiotic properties arise from its ability to prevent cross-linking of peptidoglycan during cell wall synthesis, when the bacteria try to divide, causing cell death.","category_aro_class_name":"Antibiotic"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"1237":{"model_id":"1237","model_name":"Mycobacterium tuberculosis rpoB with mutations conferring resistance to rifampicin","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"13304":"D435G","13305":"D435V","13306":"D435Y","13353":"H445D","13354":"H445L","13355":"H445R","13356":"H445Y","13384":"L430P","13385":"L452P","13395":"M434I","13410":"Q432P","13420":"S450L","13421":"S450W","13887":"G981D","13915":"T676P","13920":"V170F","13922":"V359A","16044":"T444Var","16045":"H445Var","16046":"K446Var","16047":"R447Var","16048":"R448Var","16049":"L449Var","14117":"D435A","14118":"D435F","14119":"D435N","14123":"D545E","14135":"H445C","14136":"H445F","14137":"H445G","14138":"H445N","14139":"H445P","14141":"I491F","14155":"Q432K","14156":"Q432L","14162":"S431T","14163":"S441L","14164":"S441Q","14165":"S450F","14166":"S450Q","14167":"S450Y","14198":"L440Var","14200":"G442Var","14201":"L443Var","14208":"S450Var","14209":"A451Var","14210":"L452Var","14184":"G426Var","14185":"T427Var","14186":"S428Var","14187":"Q429Var","14188":"L430Var","14189":"S431Var","14190":"Q432Var","14191":"F433Var","14192":"M434Var","14193":"D435Var","14194":"Q436Var","14195":"N437Var","14196":"N438Var","14197":"P439Var","16041":"S441Var","14333":"G426S","14334":"T427P","14335":"T427S","14336":"T427A","14337":"T427G","14338":"T427N","14339":"T427I","14340":"S428G","14341":"S428R","14342":"S428T","14343":"S428I","14344":"Q429L","14345":"Q429P","14346":"Q429H","14347":"L430R","14349":"S431G","14351":"S431R","14352":"S431N","14354":"Q432E","14355":"Q432N","14358":"Q432H","14359":"M434L","14360":"M434R","14361":"M434V","14362":"M434T","14366":"Q436N","14367":"N437Y","14371":"D435H","14372":"D435L","14374":"D435E","14375":"Q436R","14376":"Q436P","14377":"N437H","14378":"N437D","14379":"N437S","14380":"N437I","14381":"N438H","14382":"P439S","14383":"P439L","14384":"P439A","14385":"S441A","14387":"S441V","14389":"S441M","14390":"S441K","14391":"G442E","14392":"S441W","14393":"L443S","14394":"T444P","14395":"L443W","14396":"L443F","14397":"T444S","14398":"T444I","14400":"H445S","14401":"K446Q","14409":"H445T","14411":"H445Q","14412":"K446R","14413":"K446E","14414":"K446T","14415":"R448L","14416":"R448K","14417":"R448Q","14418":"L449M","14420":"S450A","14422":"S450G","14424":"A451G","14425":"S450V","14426":"S450M","14427":"S450C","14430":"A451V","14431":"L452V","14432":"L452M","9788":"P45L","9790":"I480V","9791":"F503S","9792":"L731P","9793":"R827H","9794":"H835R","9795":"G836S","9796":"Q975H","3254":"L457R","3253":"L452R","3263":"D435T","3994":"A286V","4001":"E423A","3995":"L440P","4000":"Q409H","4033":"R447H","4106":"L457P","4032":"K446N","4078":"L430M","4107":"L464M","4044":"T427H","4109":"L490V","4049":"N438K","4038":"F505L","4015":"R447P","4080":"D435K","4110":"R552C","4111":"E592D","4041":"G426D","4051":"G442A","4025":"H445E","4028":"L430V","4036":"L440M","4012":"S428Q","4030":"N437T","4046":"Q432D","4073":"Q432R","4076":"Q436H","4013":"Q436L","4039":"S493L","8237":"P439T","14183":"F425Var","9786":"P45S","9797":"I1106T","4021":"S431I"},"CRyPTIC-R":{"13304":"D435G","13305":"D435V","13306":"D435Y","13353":"H445D","13354":"H445L","13355":"H445R","13356":"H445Y","13384":"L430P","13385":"L452P","13395":"M434I","13410":"Q432P","13420":"S450L","13421":"S450W","13887":"G981D","13915":"T676P","13920":"V170F","13922":"V359A","14117":"D435A","14118":"D435F","14119":"D435N","14123":"D545E","14135":"H445C","14136":"H445F","14137":"H445G","14138":"H445N","14139":"H445P","14141":"I491F","14155":"Q432K","14156":"Q432L","14162":"S431T","14163":"S441L","14164":"S441Q","14165":"S450F","14166":"S450Q","14167":"S450Y","14198":"L440Var","14200":"G442Var","14201":"L443Var","14202":"T444Var","14203":"H445Var","14204":"K446Var","14205":"R447Var","14206":"R448Var","14207":"L449Var","14208":"S450Var","14209":"A451Var","14210":"L452Var","14184":"G426Var","14185":"T427Var","14186":"S428Var","14187":"Q429Var","14188":"L430Var","14189":"S431Var","14190":"Q432Var","14191":"F433Var","14192":"M434Var","14193":"D435Var","14194":"Q436Var","14195":"N437Var","14196":"N438Var","14197":"P439Var","14199":"S441Var","14183":"F425Var"},"clinical":{"13304":"D435G","13305":"D435V","13306":"D435Y","13353":"H445D","13354":"H445L","13355":"H445R","13356":"H445Y","13384":"L430P","13385":"L452P","13395":"M434I","13410":"Q432P","13420":"S450L","13421":"S450W","13887":"G981D","13915":"T676P","13920":"V170F","13922":"V359A","16044":"T444Var","16045":"H445Var","16046":"K446Var","16047":"R447Var","16048":"R448Var","16049":"L449Var","14117":"D435A","14118":"D435F","14119":"D435N","14123":"D545E","14135":"H445C","14136":"H445F","14137":"H445G","14138":"H445N","14139":"H445P","14141":"I491F","14155":"Q432K","14156":"Q432L","14162":"S431T","14163":"S441L","14164":"S441Q","14165":"S450F","14166":"S450Q","14167":"S450Y","14198":"L440Var","14200":"G442Var","14201":"L443Var","14202":"T444Var","14203":"H445Var","14204":"K446Var","14205":"R447Var","14206":"R448Var","14207":"L449Var","14208":"S450Var","14209":"A451Var","14210":"L452Var","14184":"G426Var","14185":"T427Var","14186":"S428Var","14187":"Q429Var","14188":"L430Var","14189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mutation","param_description":"A sequence change where, compared to a reference sequence, one codon is replaced by a termination codon through a nucleotide substitution. These are described as a substitution of the wildtype codon to a termination codon. Format is given as [wild type AA][position][Ter], for example Q42Ter where Q42 is a wildtype amino acid replaced by a premature termination codon.","param_type_id":"40394","param_value":{"4074":"S441Ter","18573":"Q432Ter"}},"40330":{"param_type":"multiple resistance variants","param_description":"A set of nucleotide or amino acid substitutions that are all required to confer resistance to an antibiotic drug or drug class, encoded as: [wild-type 1][position 1][mutation 1],[wild-type 2][position 2][mutation 2], etc. For example, D63Y,T142K.","param_type_id":"40330","param_value":{"4061":"D435Y,L430R","4105":"H445P,K446Q","4058":"H445S,M434V","4059":"H445S,P454H","4108":"E481G,P483L","4067":"L430R,D435V","4065":"S450L,F433V","4066":"S450L,H445C","4060":"H445Y,E460G","4057":"S450L,S540A","4068":"L430P,M434I","13237":"H445D,S450L","4062":"D435E,S441L"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"2300"},"41342":{"param_type":"deletion mutation from peptide sequence","param_description":"A peptide sequence change between the translation initiation (start) and termination (stop) codon where, compared to a reference sequence, one or more amino acids are deleted and therefore are not present. These represent in-frame deletions which do not result in frameshift variants and may include multiple amino acids. Format is given by [wildtype AA][position]del for a single peptide deletion or [wildtype AA][position]_[wildtype AA][position]del for a deleted peptide range, e.g. K527del or Q517_N518del.","param_type_id":"41342","param_value":{"18574":"Q432del","18575":"F433del","18576":"M434del","18577":"D435del","18578":"N437del","18579":"H445del","18581":"P439del","18582":"Q436del"}}},"model_sequences":{"sequence":{"8799":{"protein_sequence":{"accession":"NP_215181.1","sequence":"MADSRQSKTAASPSPSRPQSSSNNSVPGAPNRVSFAKLREPLEVPGLLDVQTDSFEWLIGSPRWRESAAERGDVNPVGGLEEVLYELSPIEDFSGSMSLSFSDPRFDDVKAPVDECKDKDMTYAAPLFVTAEFINNNTGEIKSQTVFMGDFPMMTEKGTFIINGTERVVVSQLVRSPGVYFDETIDKSTDKTLHSVKVIPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTSEQIVERFGFSEIMRSTLEKDNTVGTDEALLDIYRKLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYKVNKKLGLHVGEPITSSTLTEEDVVATIEYLVRLHEGQTTMTVPGGVEVPVETDDIDHFGNRRLRTVGELIQNQIRVGMSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIKEFFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGLEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSVYARVNPFGFIETPYRKVVDGVVSDEIVYLTADEEDRHVVAQANSPIDADGRFVEPRVLVRRKAGEVEYVPSSEVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAPLVGTGMELRAAIDAGDVVVAEESGVIEEVSADYITVMHDNGTRRTYRMRKFARSNHGTCANQCPIVDAGDRVEAGQVIADGPCTDDGEMALGKNLLVAIMPWEGHNYEDAIILSNRLVEEDVLTSIHIEEHEIDARDTKLGAEEITRDIPNISDEVLADLDERGIVRIGAEVRDGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDEDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLADGTPVDIILNTHGVPRRMNIGQILETHLGWCAHSGWKVDAAKGVPDWAARLPDELLEAQPNAIVSTPVFDGAQEAELQGLLSCTLPNRDGDVLVDADGKAMLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMECWAMQAYGAAYTLQELLTIKSDDTVGRVKVYEAIVKGENIPEPGIPESFKVLLKELQSLCLNVEVLSSDGAAIELREGEDEDLERAAANLGINLSRNESASVEDLA"},"dna_sequence":{"accession":"NC_000962.3","fmin":"759806","fmax":"763325","strand":"+","sequence":"TTGGCAGATTCCCGCCAGAGCAAAACAGCCGCTAGTCCTAGTCCGAGTCGCCCGCAAAGTTCCTCGAATAACTCCGTACCCGGAGCGCCAAACCGGGTCTCCTTCGCTAAGCTGCGCGAACCACTTGAGGTTCCGGGACTCCTTGACGTCCAGACCGATTCGTTCGAGTGGCTGATCGGTTCGCCGCGCTGGCGCGAATCCGCCGCCGAGCGGGGTGATGTCAACCCAGTGGGTGGCCTGGAAGAGGTGCTCTACGAGCTGTCTCCGATCGAGGACTTCTCCGGGTCGATGTCGTTGTCGTTCTCTGACCCTCGTTTCGACGATGTCAAGGCACCCGTCGACGAGTGCAAAGACAAGGACATGACGTACGCGGCTCCACTGTTCGTCACCGCCGAGTTCATCAACAACAACACCGGTGAGATCAAGAGTCAGACGGTGTTCATGGGTGACTTCCCGATGATGACCGAGAAGGGCACGTTCATCATCAACGGGACCGAGCGTGTGGTGGTCAGCCAGCTGGTGCGGTCGCCCGGGGTGTACTTCGACGAGACCATTGACAAGTCCACCGACAAGACGCTGCACAGCGTCAAGGTGATCCCGAGCCGCGGCGCGTGGCTCGAGTTTGACGTCGACAAGCGCGACACCGTCGGCGTGCGCATCGACCGCAAACGCCGGCAACCGGTCACCGTGCTGCTCAAGGCGCTGGGCTGGACCAGCGAGCAGATTGTCGAGCGGTTCGGGTTCTCCGAGATCATGCGATCGACGCTGGAGAAGGACAACACCGTCGGCACCGACGAGGCGCTGTTGGACATCTACCGCAAGCTGCGTCCGGGCGAGCCCCCGACCAAAGAGTCAGCGCAGACGCTGTTGGAAAACTTGTTCTTCAAGGAGAAGCGCTACGACCTGGCCCGCGTCGGTCGCTATAAGGTCAACAAGAAGCTCGGGCTGCATGTCGGCGAGCCCATCACGTCGTCGACGCTGACCGAAGAAGACGTCGTGGCCACCATCGAATATCTGGTCCGCTTGCACGAGGGTCAGACCACGATGACCGTTCCGGGCGGCGTCGAGGTGCCGGTGGAAACCGACGACATCGACCACTTCGGCAACCGCCGCCTGCGTACGGTCGGCGAGCTGATCCAAAACCAGATCCGGGTCGGCATGTCGCGGATGGAGCGGGTGGTCCGGGAGCGGATGACCACCCAGGACGTGGAGGCGATCACACCGCAGACGTTGATCAACATCCGGCCGGTGGTCGCCGCGATCAAGGAGTTCTTCGGCACCAGCCAGCTGAGCCAATTCATGGACCAGAACAACCCGCTGTCGGGGTTGACCCACAAGCGCCGACTGTCGGCGCTGGGGCCCGGCGGTCTGTCACGTGAGCGTGCCGGGCTGGAGGTCCGCGACGTGCACCCGTCGCACTACGGCCGGATGTGCCCGATCGAAACCCCTGAGGGGCCCAACATCGGTCTGATCGGCTCGCTGTCGGTGTACGCGCGGGTCAACCCGTTCGGGTTCATCGAAACGCCGTACCGCAAGGTGGTCGACGGCGTGGTTAGCGACGAGATCGTGTACCTGACCGCCGACGAGGAGGACCGCCACGTGGTGGCACAGGCCAATTCGCCGATCGATGCGGACGGTCGCTTCGTCGAGCCGCGCGTGCTGGTCCGCCGCAAGGCGGGCGAGGTGGAGTACGTGCCCTCGTCTGAGGTGGACTACATGGACGTCTCGCCCCGCCAGATGGTGTCGGTGGCCACCGCGATGATTCCCTTCCTGGAGCACGACGACGCCAACCGTGCCCTCATGGGGGCAAACATGCAGCGCCAGGCGGTGCCGCTGGTCCGTAGCGAGGCCCCGCTGGTGGGCACCGGGATGGAGCTGCGCGCGGCGATCGACGCCGGCGACGTCGTCGTCGCCGAAGAAAGCGGCGTCATCGAGGAGGTGTCGGCCGACTACATCACTGTGATGCACGACAACGGCACCCGGCGTACCTACCGGATGCGCAAGTTTGCCCGGTCCAACCACGGCACTTGCGCCAACCAGTGCCCCATCGTGGACGCGGGCGACCGAGTCGAGGCCGGTCAGGTGATCGCCGACGGTCCCTGTACTGACGACGGCGAGATGGCGCTGGGCAAGAACCTGCTGGTGGCCATCATGCCGTGGGAGGGCCACAACTACGAGGACGCGATCATCCTGTCCAACCGCCTGGTCGAAGAGGACGTGCTCACCTCGATCCACATCGAGGAGCATGAGATCGATGCTCGCGACACCAAGCTGGGTGCGGAGGAGATCACCCGCGACATCCCGAACATCTCCGACGAGGTGCTCGCCGACCTGGATGAGCGGGGCATCGTGCGCATCGGTGCCGAGGTTCGCGACGGGGACATCCTGGTCGGCAAGGTCACCCCGAAGGGTGAGACCGAGCTGACGCCGGAGGAGCGGCTGCTGCGTGCCATCTTCGGTGAGAAGGCCCGCGAGGTGCGCGACACTTCGCTGAAGGTGCCGCACGGCGAATCCGGCAAGGTGATCGGCATTCGGGTGTTTTCCCGCGAGGACGAGGACGAGTTGCCGGCCGGTGTCAACGAGCTGGTGCGTGTGTATGTGGCTCAGAAACGCAAGATCTCCGACGGTGACAAGCTGGCCGGCCGGCACGGCAACAAGGGCGTGATCGGCAAGATCCTGCCGGTTGAGGACATGCCGTTCCTTGCCGACGGCACCCCGGTGGACATTATTTTGAACACCCACGGCGTGCCGCGACGGATGAACATCGGCCAGATTTTGGAGACCCACCTGGGTTGGTGTGCCCACAGCGGCTGGAAGGTCGACGCCGCCAAGGGGGTTCCGGACTGGGCCGCCAGGCTGCCCGACGAACTGCTCGAGGCGCAGCCGAACGCCATTGTGTCGACGCCGGTGTTCGACGGCGCCCAGGAGGCCGAGCTGCAGGGCCTGTTGTCGTGCACGCTGCCCAACCGCGACGGTGACGTGCTGGTCGACGCCGACGGCAAGGCCATGCTCTTCGACGGGCGCAGCGGCGAGCCGTTCCCGTACCCGGTCACGGTTGGCTACATGTACATCATGAAGCTGCACCACCTGGTGGACGACAAGATCCACGCCCGCTCCACCGGGCCGTACTCGATGATCACCCAGCAGCCGCTGGGCGGTAAGGCGCAGTTCGGTGGCCAGCGGTTCGGGGAGATGGAGTGCTGGGCCATGCAGGCCTACGGTGCTGCCTACACCCTGCAGGAGCTGTTGACCATCAAGTCCGATGACACCGTCGGCCGCGTCAAGGTGTACGAGGCGATCGTCAAGGGTGAGAACATCCCGGAGCCGGGCATCCCCGAGTCGTTCAAGGTGCTGCTCAAAGAACTGCAGTCGCTGTGCCTCAACGTCGAGGTGCTATCGAGTGACGGTGCGGCGATCGAACTGCGCGAAGGTGAGGACGAGGACCTGGAGCGGGCCGCGGCCAACCTGGGAATCAATCTGTCCCGCAACGAATCCGCAAGTGTCGAGGATCTTGCGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3003283","ARO_id":"39867","ARO_name":"Mycobacterium tuberculosis rpoB with mutations conferring resistance to rifampicin","CARD_short_name":"Mtub_rpoB_RIF","ARO_description":"Point mutations that occurs in Mycobacterium tuberculosis rpoB resulting in resistance to rifampicin.","ARO_category":{"36349":{"category_aro_accession":"3000210","category_aro_cvterm_id":"36349","category_aro_name":"rifamycin-resistant beta-subunit of RNA polymerase (rpoB)","category_aro_description":"Rifampin resistant RNA polymerases include amino acids substitutions which disrupt the affinity of rifampin for its binding site. These mutations are frequently concentrated in the rif I region of the beta-subunit and most often involve amino acids which make direct interactions with rifampin. However, mutations which also confer resistance can occur outside this region and may involve amino acids which do not directly make contact with rifampin.","category_aro_class_name":"AMR Gene Family"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36656":{"category_aro_accession":"3000517","category_aro_cvterm_id":"36656","category_aro_name":"rifaximin","category_aro_description":"Rifaximin is a semi-synthetic rifamycin used to treat traveller's diarrhea. Rifaximin inhibits RNA synthesis by binding to the beta subunit of bacterial RNA polymerase.","category_aro_class_name":"Antibiotic"},"36669":{"category_aro_accession":"3000530","category_aro_cvterm_id":"36669","category_aro_name":"rifabutin","category_aro_description":"Rifabutin is a semisynthetic rifamycin used in tuberculosis therapy. It inhibits DNA-dependent RNA synthesis.","category_aro_class_name":"Antibiotic"},"36673":{"category_aro_accession":"3000534","category_aro_cvterm_id":"36673","category_aro_name":"rifapentine","category_aro_description":"Rifapentine is a semisynthetic rifamycin that inhibits DNA-dependent RNA synthesis. It is often used in the treatment of tuberculosis and leprosy.","category_aro_class_name":"Antibiotic"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"},"35998":{"category_aro_accession":"0001002","category_aro_cvterm_id":"35998","category_aro_name":"antibiotic target replacement","category_aro_description":"Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"6069":{"model_id":"6069","model_name":"Mycobacterium tuberculosis fgd1 with mutation conferring resistance to delamanid","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"14322":"V1Var"},"WHO-R":{"14322":"V1Var"},"clinical":{"14322":"V1Var"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"8892":{"protein_sequence":{"accession":"NP_214921.1","sequence":"MAELKLGYKASAEQFAPRELVELAVAAEAHGMDSATVSDHFQPWRHQGGHAPFSLSWMTAVGERTNRLLLGTSVLTPTFRYNPAVIAQAFATMGCLYPNRVFLGVGTGEALNEIATGYEGAWPEFKERFARLRESVGLMRQLWSGDRVDFDGDYYRLKGASIYDVPDGGVPVYIAAGGPAVAKYAGRAGDGFICTSGKGEELYTEKLMPAVREGAAAADRSVDGIDKMIEIKISYDPDPELALNNTRFWAPLSLTAEQKHSIDDPIEMEKAADALPIEQIAKRWIVASDPDEAVEKVGQYVTWGLNHLVFHAPGHDQRRFLELFQSDLAPRLRRLG"},"dna_sequence":{"accession":"NC_000962.3","fmin":"490782","fmax":"491793","strand":"+","sequence":"GTGGCTGAACTGAAGCTAGGTTACAAAGCATCGGCCGAACAATTCGCACCGCGCGAGCTCGTCGAACTAGCCGTCGCCGCCGAAGCCCACGGCATGGACAGCGCGACCGTCAGCGACCATTTTCAGCCTTGGCGCCACCAGGGCGGCCATGCCCCGTTCTCGCTGTCCTGGATGACCGCTGTCGGCGAACGTACCAACCGGCTGCTGCTGGGCACTTCGGTGCTGACCCCCACCTTCCGCTACAACCCCGCCGTCATCGCTCAGGCTTTCGCCACCATGGGATGCCTGTACCCGAACCGTGTTTTCCTTGGCGTGGGCACCGGTGAGGCGCTGAACGAAATCGCCACCGGATACGAGGGCGCCTGGCCGGAGTTCAAGGAGCGGTTCGCCCGGCTGCGTGAATCGGTGGGGCTAATGCGGCAGCTGTGGAGCGGTGACCGCGTCGACTTTGACGGCGACTATTACCGGCTCAAGGGTGCCTCGATCTACGACGTGCCCGACGGGGGCGTGCCCGTCTACATCGCCGCCGGCGGCCCGGCGGTGGCCAAGTACGCCGGCCGCGCCGGTGACGGCTTCATCTGTACGTCCGGCAAGGGCGAGGAGCTCTACACCGAGAAGCTGATGCCGGCGGTACGAGAAGGCGCCGCTGCCGCTGACCGATCCGTCGACGGCATCGACAAGATGATCGAAATCAAGATCTCCTACGACCCCGACCCGGAGCTGGCATTGAACAACACCCGGTTTTGGGCGCCGCTGTCGTTGACAGCTGAGCAGAAGCACAGCATCGACGACCCGATCGAGATGGAGAAGGCCGCCGATGCGCTGCCAATCGAACAGATCGCCAAGCGCTGGATCGTGGCGTCGGACCCCGACGAAGCCGTCGAAAAGGTAGGTCAATACGTGACATGGGGCCTGAACCACCTGGTATTTCACGCACCAGGACATGACCAGCGCCGGTTTCTGGAGCTCTTCCAGTCGGACCTGGCACCCAGGTTGCGGCGACTTGGCTGA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"39507","NCBI_taxonomy_name":"Mycobacterium tuberculosis H37Rv","NCBI_taxonomy_id":"83332"}}}},"ARO_accession":"3007849","ARO_id":"46639","ARO_name":"Mycobacterium tuberculosis fgd1 with mutation conferring resistance to delamanid","CARD_short_name":"Mtub_fgd1_DLM","ARO_description":"Mutations in the F420-dependent glucose-6-phosphate dehydrogenase fgd1 which confer resistance to the nitroimidazole antibiotic delamanid.","ARO_category":{"46641":{"category_aro_accession":"3007851","category_aro_cvterm_id":"46641","category_aro_name":"delamanid-resistant fgd1","category_aro_description":"Genetic variants of F420-dependent glucose-6-phosphate dehydrogenase Fgd1 with mutations associated with resistance to the nitroimidazole antibiotic delamanid.","category_aro_class_name":"AMR Gene Family"},"41931":{"category_aro_accession":"3004490","category_aro_cvterm_id":"41931","category_aro_name":"delamanid","category_aro_description":"A novel nitroimidazole antibiotic for treating Mycobacterium tuberculosis infection. Delamanid inhibits bacterial cell wall growth by mycolic acid synthesis disruption and is particularly effective in combination therapies against multidrug-resistant tuberculosis.","category_aro_class_name":"Antibiotic"},"41239":{"category_aro_accession":"3004115","category_aro_cvterm_id":"41239","category_aro_name":"nitroimidazole antibiotic","category_aro_description":"Nitroimidazoles are a group of drugs that have both antiprotozoal and antibacterial activity, classified with respect to the location of the nitro functional group.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8516":{"model_id":"8516","model_name":"CfiA28","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11343":{"protein_sequence":{"accession":"MBE7399711.1","sequence":"MKTVFILISMLFPVAVMAQKSVKISDDISITQLSDKVYTYVSLAEIEGWGMVPSNGMIVINNHQAALLDTPINDAQTEMLVNWVTDSLHAKVTTFIPNHWHGDCIGGLGYLQRKGVQSYANQMTIDLAKEKGLPVPEHGFTDSLTVSLDGMPLQCYYLGGGHATDNIVVWLPTENILFGGCMLKDNQATSIGNISDADVTAWPKTLDKVKAKFPSARYVVPGHGNYGGTELIEHTKQIVNQYIESTSKP"},"dna_sequence":{"accession":"JADDIJ010000014.1","fmin":"17","fmax":"767","strand":"+","sequence":"ATGAAAACAGTATTTATCCTTATCTCCATGCTTTTCCCTGTCGCAGTTATGGCACAGAAAAGCGTAAAAATATCCGATGATATCAGTATCACCCAACTCTCAGACAAAGTGTACACTTATGTATCCCTCGCCGAAATCGAAGGATGGGGTATGGTACCTTCCAACGGGATGATTGTTATCAACAACCACCAGGCAGCGTTGCTGGACACACCGATCAATGACGCACAAACGGAAATGCTGGTCAACTGGGTGACAGACTCTTTGCATGCCAAAGTCACCACGTTTATCCCGAACCACTGGCACGGCGATTGTATTGGCGGACTGGGTTACCTGCAAAGGAAAGGTGTCCAATCATACGCGAACCAGATGACGATAGACCTCGCCAAGGAAAAAGGGTTGCCCGTACCGGAACATGGATTCACCGATTCACTGACCGTCAGCTTGGACGGCATGCCTCTCCAATGCTATTATTTAGGAGGCGGGCATGCGACCGACAATATCGTGGTTTGGCTGCCGACAGAGAATATCCTTTTTGGCGGATGTATGCTTAAAGACAACCAGGCGACAAGCATCGGCAATATCTCGGACGCGGACGTGACGGCATGGCCGAAAACTCTCGATAAGGTAAAAGCCAAGTTCCCCTCGGCCCGCTACGTCGTGCCCGGACATGGTAACTATGGCGGAACCGAACTGATAGAGCATACCAAGCAGATCGTGAACCAATATATAGAAAGCACTTCAAAACCATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35916","NCBI_taxonomy_name":"Bacteroides fragilis","NCBI_taxonomy_id":"817"}}}},"ARO_accession":"3009098","ARO_id":"47890","ARO_name":"CfiA28","CARD_short_name":"CfiA28","ARO_description":"Subclass B1 metallo-beta-lactamase CfiA28.","ARO_category":{"41364":{"category_aro_accession":"3004200","category_aro_cvterm_id":"41364","category_aro_name":"CfiA beta-lactamase","category_aro_description":"CfiA beta-lactamases are chromosomal-encoded carbapenemase commonly found in Bacteroides fragilis isolates.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8517":{"model_id":"8517","model_name":"CfiA29","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11344":{"protein_sequence":{"accession":"URY98714.1","sequence":"MKTVFILISMLFPVAVMAQKSVKISDDISITQLSDKVYTYVSLAEIEGWGMVPSNGMIVINNHQAALLDTPINDAQTETLVNWVTDSLHAKVTTFIPNHWHGDCIGGLGYLQKKGVQSYANQMTIDLAKEKGLPVPEHGFTDSLTVSLDGMPLQCYYLGGGHATDNIVVWLPTENILFGGCMLKDNQTTSIGNISDADVTAWPKTLDKVKAKFPSARYVVPGHGDYGGTELIEHTKQIVNQYIESTSKP"},"dna_sequence":{"accession":"OL739393.1","fmin":"0","fmax":"750","strand":"+","sequence":"ATGAAAACAGTATTTATCCTTATCTCCATGCTTTTCCCTGTCGCAGTTATGGCACAGAAAAGCGTAAAAATATCCGATGATATCAGTATCACCCAACTCTCGGACAAAGTGTACACTTATGTATCCCTCGCCGAAATCGAAGGATGGGGCATGGTACCTTCCAACGGGATGATTGTTATCAACAACCACCAGGCAGCGTTGCTGGACACACCGATCAATGACGCACAAACGGAAACGCTGGTCAACTGGGTGACAGACTCTTTGCATGCCAAAGTCACCACGTTTATCCCGAACCACTGGCACGGCGATTGTATTGGCGGACTGGGGTACCTGCAAAAGAAAGGTGTCCAATCATACGCGAACCAGATGACGATAGACCTCGCCAAGGAAAAAGGGTTGCCCGTACCGGAACATGGATTCACCGATTCACTGACCGTCAGTCTGGACGGCATGCCTCTCCAATGTTATTATTTAGGAGGCGGACATGCGACCGACAATATCGTGGTTTGGCTGCCGACAGAGAATATCCTTTTTGGCGGATGTATGCTTAAAGACAACCAAACGACAAGCATCGGCAACATCTCGGACGCGGACGTGACGGCATGGCCGAAAACTCTCGATAAGGTAAAAGCCAAGTTCCCCTCGGCCCGCTACGTCGTGCCCGGACATGGCGACTATGGCGGAACCGAACTGATAGAGCATACCAAGCAGATCGTGAACCAATATATAGAAAGCACCTCAAAGCCATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35916","NCBI_taxonomy_name":"Bacteroides fragilis","NCBI_taxonomy_id":"817"}}}},"ARO_accession":"3009099","ARO_id":"47891","ARO_name":"CfiA29","CARD_short_name":"CfiA29","ARO_description":"Subclass B1 metallo-beta-lactamase CfiA29.","ARO_category":{"41364":{"category_aro_accession":"3004200","category_aro_cvterm_id":"41364","category_aro_name":"CfiA beta-lactamase","category_aro_description":"CfiA beta-lactamases are chromosomal-encoded carbapenemase commonly found in Bacteroides fragilis isolates.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8518":{"model_id":"8518","model_name":"CfiA30","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11345":{"protein_sequence":{"accession":"WCS94747.1","sequence":"MKTVFILISMLFPVAVMAQKSVKISDDISITQLSDKVYTYVSLAEIEGWGMVPSNGMIVINNHQAALLDTPINDAQTEMLVNWVTDSLHAKVTTFIPNHWHGDCIGGLGYLQKKGVQSYANQMTIDLAKEKGLPVPEHGFTDSLTVSLDGMPLQCYYLGGGHATDNIVVWLPTENILFGGCMLKDNQATSIGNISDADVTAWPKTLDKVKAKFPSARYVVPGHGDYGGTELIEHTKQIVNQYIESTSKP"},"dna_sequence":{"accession":"OQ379238.1","fmin":"0","fmax":"750","strand":"+","sequence":"ATGAAAACAGTATTTATCCTTATCTCCATGCTTTTCCCTGTCGCAGTTATGGCACAGAAAAGCGTAAAAATATCCGATGACATCAGTATCACCCAACTCTCGGACAAAGTGTACACTTATGTATCCCTCGCCGAAATCGAAGGATGGGGTATGGTACCTTCCAACGGGATGATTGTTATCAACAACCACCAGGCAGCGTTGCTGGACACACCGATCAATGACGCACAAACGGAAATGCTGGTCAACTGGGTGACAGACTCTTTGCATGCCAAAGTCACCACGTTTATCCCGAACCACTGGCACGGCGATTGTATTGGCGGACTGGGTTACCTGCAAAAGAAAGGTGTCCAATCATACGCGAACCAGATGACGATAGACCTCGCCAAGGAAAAAGGGTTGCCCGTACCGGAACATGGATTCACCGATTCACTGACCGTCAGCTTGGACGGCATGCCTCTCCAATGTTATTATTTAGGAGGCGGACATGCGACCGACAATATCGTGGTTTGGCTGCCGACAGAGAATATCCTTTTTGGCGGATGTATGCTTAAAGACAACCAGGCGACAAGCATCGGCAACATCTCGGACGCGGACGTGACGGCATGGCCGAAAACTCTCGATAAGGTAAAAGCCAAGTTCCCCTCGGCCCGCTACGTCGTGCCCGGACATGGCGACTATGGCGGAACCGAACTGATAGAGCATACCAAGCAGATCGTGAACCAATATATAGAAAGCACTTCAAAGCCATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35916","NCBI_taxonomy_name":"Bacteroides fragilis","NCBI_taxonomy_id":"817"}}}},"ARO_accession":"3009100","ARO_id":"47892","ARO_name":"CfiA30","CARD_short_name":"CfiA30","ARO_description":"Subclass B1 metallo-beta-lactamase CfiA30.","ARO_category":{"41364":{"category_aro_accession":"3004200","category_aro_cvterm_id":"41364","category_aro_name":"CfiA beta-lactamase","category_aro_description":"CfiA beta-lactamases are chromosomal-encoded carbapenemase commonly found in Bacteroides fragilis isolates.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8519":{"model_id":"8519","model_name":"CfiA31","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11346":{"protein_sequence":{"accession":"WCS94748.1","sequence":"MKTVFILISMLFPVAVMAQKSVKISDDISITQLSDKVYTYVSLAEIEGWGMVPSNGMIVINNHQAALLDTPINDAQTETLVNWVTDSLHAKVTTFIPNHWHGDCIGGLGYLQRKGVQSYANQMTIDLAKEKGLPVPEHGFTDSLTVSLDGMPLQCYYLGGGHATDNIVVWLPTENILFGGCMLKDNQATSIGNISDADVTAWPKTLDKVKAKFPSARYVVPGHGDYGGTELIEHTKQIVNQYIESTSKP"},"dna_sequence":{"accession":"OQ379239.1","fmin":"0","fmax":"750","strand":"+","sequence":"ATGAAAACAGTATTTATCCTTATCTCCATGCTTTTCCCTGTCGCAGTTATGGCACAGAAAAGCGTAAAAATATCCGATGACATCAGTATCACCCAACTCTCGGACAAAGTGTACACTTATGTATCCCTCGCCGAAATCGAAGGATGGGGTATGGTACCTTCCAACGGGATGATTGTTATCAACAACCACCAGGCAGCGTTGCTGGACACACCGATCAATGACGCACAAACGGAAACGCTGGTCAACTGGGTGACAGACTCTTTGCATGCCAAAGTCACCACGTTTATCCCGAACCACTGGCACGGCGATTGTATTGGCGGACTGGGTTACCTGCAAAGGAAAGGTGTCCAATCATACGCGAACCAGATGACGATAGACCTCGCCAAGGAAAAAGGGTTGCCCGTACCGGAACATGGATTCACCGATTCACTGACCGTCAGCTTGGACGGCATGCCTCTCCAATGCTATTATTTAGGAGGCGGGCATGCGACCGACAATATCGTGGTTTGGCTGCCGACAGAGAATATCCTTTTTGGCGGATGTATGCTTAAAGACAACCAGGCGACAAGCATCGGCAACATCTCGGACGCAGACGTGACGGCATGGCCGAAAACTCTCGATAAGGTAAAAGCCAAGTTCCCCTCGGCCCGCTACGTCGTGCCCGGACATGGCGACTATGGCGGAACCGAACTGATAGAGCATACCAAGCAGATCGTGAACCAATATATAGAAAGCACCTCAAAGCCATAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"35916","NCBI_taxonomy_name":"Bacteroides fragilis","NCBI_taxonomy_id":"817"}}}},"ARO_accession":"3009101","ARO_id":"47893","ARO_name":"CfiA31","CARD_short_name":"CfiA31","ARO_description":"Subclass B1 metallo-beta-lactamase CfiA31.","ARO_category":{"41364":{"category_aro_accession":"3004200","category_aro_cvterm_id":"41364","category_aro_name":"CfiA beta-lactamase","category_aro_description":"CfiA beta-lactamases are chromosomal-encoded carbapenemase commonly found in Bacteroides fragilis isolates.","category_aro_class_name":"AMR Gene Family"},"35939":{"category_aro_accession":"0000020","category_aro_cvterm_id":"35939","category_aro_name":"carbapenem","category_aro_description":"Carbapenems are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Carbapenem antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5956":{"model_id":"5956","model_name":"Mycobacterium avium gyrA with mutation conferring resistance to fluoroquinolone","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"12925":"D95G","12926":"D95Y"},"Curated-R":{"12925":"D95G","12926":"D95Y"},"clinical":{"12925":"D95G","12926":"D95Y"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1150"}},"model_sequences":{"sequence":{"8678":{"protein_sequence":{"accession":"ABK64957.1","sequence":"MTDTTLPPGGDAADRVEPVDIQQEMQRSYIDYAMSVIVGRALPEVRDGLKPVHRRVLYAMYDSGFRPDRSHAKSARSVAETMGNYHPHGDASIYDTLVRMAQPWSLRYPLVDGQGNFGSPGNDPPAAMRYTEARLTPLAMEMLREIDEETVDFIPNYDGRVQEPTVLPSRFPNLLANGSGGIAVGMATNIPPHNLGELAEAVFWALDNYEADEEATLAAVMERVKGPDFPTSGLIVGTQGIADAYKTGRGSIRMRGVVEVEEDSRGRTSLVITELPYQVNHDNFITSIAEQVRDGKLAGISNIEDQSSDRVGLRIVIELKRDAVAKVVLNNLYKHTQLQTSFGANMLAIVDGVPRTLRLDQLIRHYVDHQLDVIVRRTTYRLRKANERAHILRGLVKALDALDEVIALIRASETVDIARQGLIELLDIDEIQAQAILDMQLRRLAALERQRIIDDLAKIEAEIADLEDILAKPERQRGIVRDELAEIVEKHGDARRTRIVAADGDVSDEDLIAREDVVVTITETGYAKRTKTDLYRSQKRGGKGVQGAGLKQDDIVRHFFVCSTHDWILFFTTQGRVYRAKAYELPEASRTARGQHVANLLAFQPEERIAQVIQIRSYEDAPYLVLATRNGLVKKTKLTDFDSNRSGGIVAINLRDNDELVGAVLCSAEDDLLLVSANGQSIRFSATDEALRPMGRATSGVQGMRFNADDYLLSLNVVREGTYLLVATSGGYAKRTAIEEYPVQGRGGKGVLTVMYDRRRGRLVGALIVDEDSELYAITSGGGVIRTAAGQVRKAGRQTKGVRLMNLGEGDTLLAIARNAEEAADEAVEESDGAAGSDG"},"dna_sequence":{"accession":"CP000479.1","fmin":"7301","fmax":"9821","strand":"+","sequence":"ATGACTGACACCACGCTGCCACCCGGCGGTGACGCCGCCGACCGCGTCGAACCGGTCGACATCCAGCAGGAGATGCAGCGCAGCTACATCGATTACGCGATGAGCGTGATCGTCGGCCGCGCGCTGCCCGAGGTGCGCGACGGCCTCAAGCCGGTGCACCGCCGGGTGCTCTACGCCATGTACGACTCGGGTTTCCGCCCGGACCGCAGCCACGCCAAATCGGCGCGGTCGGTCGCCGAAACGATGGGCAACTACCACCCGCACGGCGACGCCTCGATCTACGACACCCTGGTGCGGATGGCCCAGCCGTGGTCGCTGCGCTATCCGTTGGTCGACGGGCAGGGCAATTTTGGTTCGCCGGGCAACGACCCGCCGGCCGCGATGCGGTACACCGAGGCGCGGCTGACCCCGCTGGCCATGGAGATGCTGCGCGAAATCGACGAGGAGACAGTCGATTTCATTCCCAACTACGACGGCCGGGTGCAAGAGCCGACGGTGCTGCCCAGCCGGTTCCCCAACCTGCTGGCCAACGGGTCGGGGGGCATCGCGGTCGGCATGGCCACCAACATCCCGCCGCACAACCTCGGCGAGCTCGCCGAGGCGGTGTTCTGGGCGCTGGACAATTACGAGGCCGACGAAGAGGCCACCCTGGCCGCCGTGATGGAACGGGTGAAAGGACCCGACTTCCCGACTTCGGGCCTGATCGTCGGCACGCAGGGCATCGCCGACGCCTACAAGACCGGCCGCGGCTCCATCCGGATGCGCGGAGTCGTTGAGGTGGAAGAGGATTCGCGCGGTCGCACCTCGCTGGTCATCACCGAGTTGCCGTATCAGGTCAACCACGACAACTTCATCACCTCGATCGCCGAGCAGGTGCGCGACGGCAAGCTGGCCGGCATCTCCAACATCGAGGACCAGTCCAGCGACCGGGTCGGGCTGCGCATCGTCATCGAGCTCAAGCGCGACGCCGTCGCCAAGGTGGTGCTGAACAACCTCTACAAGCACACCCAGCTGCAGACCAGCTTCGGCGCCAACATGCTGGCCATCGTCGATGGGGTGCCGCGCACCCTGCGGCTCGACCAGCTGATCCGCCACTACGTCGACCACCAACTCGACGTCATCGTCCGGCGCACCACCTACCGGTTGCGCAAGGCCAACGAGCGGGCCCACATCCTGCGCGGTCTGGTCAAGGCGCTCGATGCGCTCGACGAGGTCATCGCCCTGATCCGGGCGTCGGAAACCGTCGACATCGCGCGGCAGGGCTTGATCGAGCTGCTCGACATCGACGAGATCCAGGCCCAGGCGATCCTGGACATGCAGCTGCGCCGGCTGGCCGCCCTGGAGCGGCAGCGCATCATCGACGACCTGGCCAAGATCGAGGCCGAGATCGCCGACCTGGAGGACATCCTGGCCAAGCCGGAACGGCAACGCGGCATTGTGCGCGACGAGCTCGCCGAGATCGTCGAAAAGCACGGCGACGCGCGGCGCACCCGGATCGTGGCCGCCGACGGCGACGTCAGCGACGAGGATCTGATCGCCCGCGAGGACGTCGTCGTCACCATCACCGAGACCGGCTACGCCAAGCGCACCAAGACCGACCTGTACCGCAGCCAGAAGCGGGGCGGCAAGGGCGTGCAGGGCGCCGGCCTCAAACAGGACGACATCGTGCGGCACTTCTTCGTGTGCTCGACGCACGACTGGATCCTGTTCTTCACCACCCAGGGCCGGGTCTACCGCGCCAAGGCCTACGAACTGCCCGAGGCGTCTCGCACCGCCCGCGGTCAGCACGTGGCCAACCTGCTGGCGTTCCAGCCCGAGGAGCGGATCGCCCAGGTGATCCAGATCCGCAGCTATGAGGACGCCCCCTACCTGGTGCTGGCCACCCGCAACGGCCTGGTGAAGAAGACCAAGCTGACCGACTTCGACTCGAACCGTTCGGGCGGCATCGTGGCGATCAACCTGCGCGACAACGACGAACTCGTGGGCGCGGTGTTGTGCTCGGCCGAGGACGATCTGCTGCTGGTGTCGGCCAACGGCCAGTCCATCCGGTTCTCGGCGACCGACGAGGCGCTGCGCCCGATGGGCCGCGCCACCTCCGGTGTGCAGGGCATGCGCTTCAACGCCGACGACTACCTGCTGTCGCTCAACGTGGTCCGCGAGGGCACCTACCTGCTGGTGGCGACGTCCGGCGGGTACGCCAAGCGCACCGCGATCGAGGAGTATCCGGTGCAGGGCCGCGGCGGCAAGGGCGTGCTGACCGTGATGTATGACCGCCGCCGTGGCAGGCTGGTGGGTGCGCTGATTGTGGACGAGGACAGCGAGCTGTACGCGATCACCTCCGGCGGCGGTGTCATCCGCACCGCGGCGGGCCAGGTCCGTAAGGCGGGACGGCAGACCAAGGGCGTCCGGCTGATGAATCTGGGTGAGGGCGACACGCTGCTGGCCATCGCCCGCAACGCCGAGGAAGCCGCGGACGAGGCCGTCGAGGAGAGCGACGGTGCCGCGGGGTCGGACGGCTAG","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"46240","NCBI_taxonomy_name":"Mycobacterium avium 104","NCBI_taxonomy_id":"243243"}}}},"ARO_accession":"3007473","ARO_id":"46239","ARO_name":"Mycobacterium avium gyrA with mutation conferring resistance to fluoroquinolone","CARD_short_name":"Mavi_gyrA_FLO","ARO_description":"Amino acid substitution mutations in Mycobacterium avium gyrA observed to confer resistance to fluoroquinolone antibiotics.","ARO_category":{"39876":{"category_aro_accession":"3003292","category_aro_cvterm_id":"39876","category_aro_name":"fluoroquinolone resistant gyrA","category_aro_description":"DNA gyrase is responsible for DNA supercoiling and consists of two alpha and two beta subunits. GyrA point mutations confer resistance by preventing fluoroquinolone antibiotics from binding the alpha-subunit.","category_aro_class_name":"AMR Gene Family"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35988":{"category_aro_accession":"0000071","category_aro_cvterm_id":"35988","category_aro_name":"levofloxacin","category_aro_description":"Levofloxacin is a synthetic chemotherapeutic antibiotic of the fluoroquinolone drug class. Its main target is topoisomerase IV, inhibiting its function and disrupting DNA replication.","category_aro_class_name":"Antibiotic"},"35991":{"category_aro_accession":"0000074","category_aro_cvterm_id":"35991","category_aro_name":"moxifloxacin","category_aro_description":"Moxifloxacin is a fourth generation synthetic fluoroquinolone chemotherapeutic agent, and has been shown to be significantly more active than levofloxacin (4 to 8 times more) against Streptococcus pneumoniae. It acts by inhibiting bacterial DNA topoisomerases.","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7517":{"model_id":"7517","model_name":"CMH-26","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11352":{"protein_sequence":{"accession":"XAJ73532.1","sequence":"MMKKSLSCALLLSVACSAFAAPMSEKQLADVVERTVTPLMKAQAIPGMAVAVIYQGQPHYFTFGKADVAANKPVTPQTLFELGSVSKTFTGVLGGDAIARKEISLADPVTKYWPELTGKQWQGIRLIDLATYTAGGLPLQVPDDVTDNASLLRFYQSWQPKWAPGTTRLYANTSIGLFGSLAVKPSGMRFEQAMAERVFKPLKLNHTWINVPHAEEPHYAWGYREGKAVHVSPGMLDAEAYGVKSNVKDMASWVMANMAPETLPPSTLQQGIALAQSRYWRVGAMYQGLGWEMLNWQVDAKTVVDGSDNKVALAPLLVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANKSYPNPVRVETAYRILDALQ"},"dna_sequence":{"accession":"PP740466.1","fmin":"0","fmax":"1143","strand":"+","sequence":"ATGATGAAAAAATCCCTAAGCTGCGCCCTGCTGCTCAGCGTTGCCTGCTCTGCTTTTGCCGCGCCGATGTCAGAAAAACAGCTGGCTGACGTCGTGGAACGTACCGTTACGCCCCTGATGAAGGCGCAGGCCATACCCGGAATGGCCGTGGCCGTCATTTATCAGGGCCAGCCACACTATTTTACTTTCGGTAAAGCAGACGTCGCGGCGAATAAGCCCGTCACGCCGCAAACCTTATTTGAACTGGGCTCCGTCAGTAAAACCTTCACTGGCGTGCTGGGTGGCGATGCCATTGCCCGCAAAGAGATTTCGCTGGCCGACCCGGTCACGAAATATTGGCCTGAATTGACGGGCAAGCAGTGGCAAGGCATTCGCCTGATCGACCTGGCAACCTATACCGCAGGCGGATTGCCGTTGCAGGTACCGGATGATGTCACCGATAACGCCTCTCTGCTGCGTTTCTACCAGTCCTGGCAGCCAAAGTGGGCCCCGGGTACCACGCGTCTGTACGCCAACACCAGCATCGGTTTGTTTGGCTCACTGGCCGTTAAACCGTCCGGCATGCGCTTCGAGCAGGCCATGGCGGAGCGGGTCTTTAAGCCCCTGAAACTCAACCATACGTGGATAAACGTTCCACACGCTGAAGAGCCGCACTACGCATGGGGTTATCGTGAGGGAAAAGCGGTCCACGTTTCGCCTGGTATGCTGGATGCAGAAGCCTATGGCGTGAAATCTAACGTCAAAGATATGGCGAGCTGGGTGATGGCCAATATGGCACCTGAGACACTCCCGCCGTCCACTCTGCAGCAGGGTATTGCGCTGGCGCAGTCTCGCTACTGGCGCGTGGGTGCCATGTATCAAGGGTTAGGCTGGGAGATGCTCAACTGGCAGGTCGACGCCAAAACCGTGGTGGATGGCAGCGACAATAAGGTCGCACTGGCGCCGTTGCTGGTCGCAGAAGTGAATCCTCCGGCTCCGCCAGTAAAAGCCTCCTGGGTGCATAAAACGGGCTCTACGGGTGGGTTTGGCAGCTACGTGGCGTTTATTCCTGAAAAGCAGATCGGTATTGTGATGCTCGCAAATAAAAGCTATCCGAACCCGGTACGGGTGGAAACGGCTTACCGTATCCTCGACGCGCTACAG","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36884","NCBI_taxonomy_name":"Enterobacter cloacae","NCBI_taxonomy_id":"550"}}}},"ARO_accession":"3008099","ARO_id":"46891","ARO_name":"CMH-26","CARD_short_name":"CMH-26","ARO_description":"Class C beta-lactamase CMH-26.","ARO_category":{"42891":{"category_aro_accession":"3004776","category_aro_cvterm_id":"42891","category_aro_name":"CMH beta-lactamase","category_aro_description":"CMH is a class C beta-lactamase gene family belonging to Enterobacter cloacae.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"7567":{"model_id":"7567","model_name":"CTX-M-260","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11355":{"protein_sequence":{"accession":"WFP45935.1","sequence":"MVKKSLRQFTLMATATVTLLLGSVPLYAQTADVQQKLAELERQSGGRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKKSESEPKLLNQRVEIKKSDLVNYNPIAEKHVNGTMSLAELSAAALQYSDNVAMNKLIAHVGGPASVTAFARQLGDETFRLDRTEPTLNTAIPGDPRYTTSPRAMAQTLRNLTLGKALGDSQRAQLVTWMKGNTTGAASIQAGLPASWVVGDKTGSGDYGTTNDIAVIWPKDRAPLILVTYFTQPQPKAESRRDVLASAAKIVTDGL"},"dna_sequence":{"accession":"OQ726107.1","fmin":"0","fmax":"873","strand":"+","sequence":"ATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACTGTCACGCTGTTATTGGGAAGTGTGCCGCTGTATGCGCAGACGGCGGACGTACAGCAAAAACTTGCCGAATTAGAGCGGCAGTCCGGAGGCAGACTGGGTGTGGCATTGATTAATACGGCAGATAATTCGCAAATACTGTATCGTGCTGATGAGCGCTTCGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAGAGCGAACCGAAGCTGTTAAACCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAGAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCTGCCGCGCTACAGTACAGCGATAACGTCGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCTCGACAGCTGGGAGACGAGACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCTGGCGATCCGCGTTACACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAGGCATTGGGCGACAGCCAACGGGCGCAGCTCGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGTATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCGGCAGCGGTGACTATGGCACCACCAACGATATTGCGGTGATCTGGCCAAAAGATCGTGCGCCGCTGATTCTGGTAACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGTCGTCGCGATGTATTAGCGTCGGCGGCTAAGATCGTCACCGACGGTTTG","partial":"1"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36810","NCBI_taxonomy_name":"Aeromonas hydrophila","NCBI_taxonomy_id":"644"}}}},"ARO_accession":"3008149","ARO_id":"46941","ARO_name":"CTX-M-260","CARD_short_name":"CTX-M-260","ARO_description":"Extended-spectrum class A beta-lactamase CTX-M-260.","ARO_category":{"36025":{"category_aro_accession":"3000016","category_aro_cvterm_id":"36025","category_aro_name":"CTX-M beta-lactamase","category_aro_description":"These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (eg, ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. Despite their name, a few are more active on ceftazidime than cefotaxime.  CTX-M-15 was recently found in bacterial strains expressing NDM-1 and were responsible for resistance to aztreonam.","category_aro_class_name":"AMR Gene Family"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"5925":{"model_id":"5925","model_name":"Escherichia coli PBP3 mutants conferring resistance to beta-lactam antibiotics","model_type":"protein variant model","model_type_id":"40293","model_description":"Protein Variant Models (PVM) perform a similar search as Protein Homolog Models (PHM), i.e. detect protein sequences based on their similarity to a curated reference sequence, but secondarily screen query sequences for curated sets of mutations to differentiate them from antibiotic susceptible wild-type alleles. PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, e.g. a mutated gyrase resistant to aminocoumarin antibiotics. PVMs include a protein reference sequence (often from antibiotic susceptible wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value and contains at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off but still contains at least one curated mutation from amongst the mapped resistance variants.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"1100"},"41344":{"param_type":"insertion mutation from peptide sequence","param_description":"A peptide sequence change between the translation initiation (start) and termination (stop) codon where, compared to the reference sequence, one or more amino acids are inserted. These represent in-frame insertions which do not result in frameshift variants and where the insertion is not a duplication of a sequence immediately N-terminal (5'), and are denoted with wildtype flanking residues. Format is given by [wildtype AA position]_[wildtype AA position]ins[AA sequence], e.g. K464_D465insE or P46_A47insYS.","param_type_id":"41344","param_value":{"18568":"N330_R335insTIPY"}},"snp":{"Curated-R":{"18568":"D95Y"}}},"model_sequences":{"sequence":{"8644":{"protein_sequence":{"accession":"CAA38861.1","sequence":"MKAAAKTQKPKRQEEHANFISWRFALLCGCILLALAFLLGRVAWLQVISPDMLVKEGDMRSLRVQQVSTSRGMITDRSGRPLAVSVPVKAIWADPKEVHDAGGISVGDRWKALANALNIPLDQLSARINANPKGRFIYLARQVNPDMADYIKKLKLPGIHLREESRRYYPSGEVTAHLIGFTNVDSQGIEGVEKSFDKWLTGQPGERIVRKDRYGRVIEDISSTDSQAAHNLALSIDERLQALVYRELNNAVAFNKAESGSAVLVDVNTGEVLAMANSPSYNPNNLSGTPKEAMRNRTITDVFEPGSTVKPMVVMTALQRGVVRENSVLNTIPYRINGHEIKDVARYSELTLTGVLQKSSNVGVSKLALAMPSSALVDTYSRFGLGKATNLGLVGERSGLYPQKQRWSDIERATFSFGYGLMVTPLQLARVYATIGSYGIYRPLSITKVDPPVPGERVFPESIVRTVVHMMESVALPGGGGVKAAIKGYRIAIKTGTAKKVGPDGRYINKYIAYTAGVAPASQPRFALVVVINDPQAGKYYGGAVSAPVFGAIMGGVLRTMNIEPDALTTGDKNEFVINQGEGTGGRS"},"dna_sequence":{"accession":"X55034.1","fmin":"7942","fmax":"9709","strand":"+","sequence":"ATGAAAGCAGCGGCGAAAACGCAGAAACCAAAACGTCAGGAAGAACATGCCAACTTTATCAGTTGGCGTTTTGCGTTGTTATGCGGCTGTATTCTCCTGGCGCTGGCTTTTCTGCTCGGACGCGTAGCGTGGTTACAAGTTATCTCCCCGGATATGCTGGTGAAAGAGGGCGACATGCGTTCTCTTCGCGTTCAGCAAGTTTCCACCTCCCGCGGCATGATTACTGACCGTTCTGGTCGCCCGTTAGCGGTGAGCGTGCCGGTAAAAGCGATTTGGGCTGACCCGAAAGAAGTGCATGACGCTGGCGGTATCAGCGTCGGTGACCGCTGGAAGGCGCTGGCTAACGCGCTCAATATTCCGCTGGATCAGCTTTCAGCCCGCATTAACGCCAACCCGAAAGGGCGCTTTATTTATCTGGCGCGTCAGGTGAACCCTGACATGGCGGACTACATCAAAAAACTGAAACTGCCGGGGATTCATCTGCGTGAAGAGTCTCGCCGTTACTATCCGTCCGGCGAAGTGACTGCTCACCTCATCGGCTTTACTAACGTCGATAGTCAAGGGATTGAGGGCGTTGAGAAGAGTTTCGATAAATGGCTTACCGGGCAGCCGGGTGAGCGCATTGTGCGTAAAGACCGCTATGGTCGCGTAATTGAAGATATTTCTTCTACTGACAGCCAGGCAGCGCACAACCTGGCGCTGAGTATTGATGAACGCCTGCAGGCGCTGGTTTATCGCGAACTGAACAACGCGGTGGCCTTTAACAAGGCTGAATCTGGTAGCGCCGTGCTGGTGGATGTCAACACCGGTGAAGTGCTGGCGATGGCTAACAGCCCGTCATACAACCCTAACAATCTGAGCGGCACGCCGAAAGAGGCGATGCGTAACCGTACCATCACCGACGTGTTTGAACCGGGCTCAACGGTTAAACCGATGGTGGTAATGACCGCGTTGCAACGTGGCGTGGTGCGGGAAAACTCGGTACTCAATACCATTCCTTATCGAATTAACGGCCACGAAATCAAAGACGTGGCACGCTACAGCGAATTAACCCTGACCGGGGTATTACAGAAGTCGAGTAACGTCGGTGTTTCCAAGCTGGCGTTAGCGATGCCGTCCTCAGCGTTAGTAGATACTTACTCACGTTTTGGACTGGGAAAAGCGACCAATTTGGGGTTGGTCGGAGAACGCAGTGGCTTATATCCTCAAAAACAACGGTGGTCTGACATAGAGAGGGCCACCTTCTCTTTCGGCTACGGGCTAATGGTAACACCATTACAGTTAGCGCGAGTCTACGCAACTATCGGCAGCTACGGCATTTATCGCCCACTGTCGATTACCAAAGTTGACCCCCCGGTTCCCGGTGAACGTGTCTTCCCGGAATCCATTGTCCGCACTGTGGTGCATATGATGGAAAGCGTGGCGCTACCAGGCGGCGGCGGCGTGAAGGCGGCGATTAAAGGCTATCGTATCGCCATTAAAACCGGTACCGCGAAAAAGGTCGGGCCGGACGGTCGCTACATCAATAAATATATTGCTTATACCGCAGGCGTTGCGCCTGCGAGTCAGCCGCGCTTCGCGCTGGTTGTTGTTATCAACGATCCGCAGGCGGGTAAATACTACGGCGGCGCCGTTTCCGCGCCGGTCTTTGGTGCCATCATGGGCGGCGTATTGCGTACCATGAACATCGAGCCGGATGCGCTGACAACGGGCGATAAAAATGAATTTGTGATTAATCAAGGCGAGGGGACAGGTGGCAGATCGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36839","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. W3110","NCBI_taxonomy_id":"316407"}}}},"ARO_accession":"3007423","ARO_id":"46179","ARO_name":"Escherichia coli PBP3 mutants conferring resistance to beta-lactam antibiotics","CARD_short_name":"Ecol_PBP3_BLA","ARO_description":"Mutant PBP3 in E. coli conferring resistance to beta-lactams, including beta-lactam\/beta-lactamase inhibitor combinations.","ARO_category":{"40661":{"category_aro_accession":"3003938","category_aro_cvterm_id":"40661","category_aro_name":"Penicillin-binding protein mutations conferring resistance to beta-lactam antibiotics","category_aro_description":"Mutations in PBP transpeptidases that change the affinity for penicillin thereby conferring resistance to penicillin antibiotics.","category_aro_class_name":"AMR Gene Family"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36689":{"category_aro_accession":"3000550","category_aro_cvterm_id":"36689","category_aro_name":"aztreonam","category_aro_description":"Aztreonam was the first monobactam discovered, and is greatly effective against Gram-negative bacteria while inactive against Gram-positive bacteria. Artreonam is a poor substrate for beta-lactamases, and may even act as an inhibitor. In Gram-negative bacteria, Aztreonam interferes with filamentation, inhibiting cell division and leading to cell death.","category_aro_class_name":"Antibiotic"},"36995":{"category_aro_accession":"3000651","category_aro_cvterm_id":"36995","category_aro_name":"ceftaroline","category_aro_description":"Ceftaroline is a novel cephalosporin active against methicillin resistant Staphylococcus aureus. Like other cephalosporins it binds penicillin-binding proteins to inhibit cell wall synthesis. It strongly binds with PBP2a, associated with methicillin resistance. It is taken orally as the prodrug ceftaroline fosamil.","category_aro_class_name":"Antibiotic"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"}}},"8524":{"model_id":"8524","model_name":"OXY-1-7","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"500"}},"model_sequences":{"sequence":{"11360":{"protein_sequence":{"accession":"AWG41961.1","sequence":"MLKSSWRKTALMAAAAVPLLLASGSLWASADAIQQKLADLEKRSGGRLGVALINTADDSQTLYRGDERFAMCSTGKVMAAAAVLKQSESNPEVVNKRLEIKKSDLVVWSPITEKHLQSGMTLAELSAAALQYSDNTAMNKMISYLGGPEKVTAFAQSIGDVTFRLDRTEPALNSAIPGDKRDTTTPLAMAESLRKLTLGNALGEQQRAQLVTWLKGNTTGGQSIRAGLPASWVVGDKTGAGDYGTTNDIAVIWPENHAPLVLVTYFTQPQQDAKSRKEVLAAAAKIVTEGL"},"dna_sequence":{"accession":"MG028661.1","fmin":"0","fmax":"876","strand":"+","sequence":"ATGTTGAAAAGTTCGTGGCGTAAAACCGCCCTGATGGCCGCCGCCGCCGTTCCGCTGCTGCTGGCGAGCGGTTCATTATGGGCCAGTGCCGATGCTATCCAGCAAAAGCTGGCTGATTTAGAAAAACGTTCCGGCGGTCGGCTGGGCGTAGCGCTGATTAACACGGCAGATGATTCGCAAACCCTCTATCGCGGCGATGAACGTTTTGCCATGTGCAGCACCGGTAAAGTGATGGCCGCCGCCGCGGTGTTAAAACAGAGCGAAAGCAATCCAGAGGTGGTGAATAAAAGGCTGGAGATTAAAAAATCGGATTTAGTGGTCTGGAGCCCGATCACCGAAAAACATCTGCAAAGCGGAATGACCCTGGCGGAACTCAGCGCGGCGGCGCTGCAGTACAGCGACAATACCGCGATGAATAAGATGATTAGCTACCTTGGCGGACCGGAAAAGGTGACCGCATTCGCCCAGAGTATCGGGGATGTCACTTTTCGTCTCGATCGTACGGAGCCGGCGCTGAACAGCGCGATTCCCGGCGATAAGCGCGATACCACCACCCCGTTGGCGATGGCCGAAAGCCTGCGCAAGCTGACGCTGGGCAATGCGCTGGGCGAACAGCAGCGCGCCCAGTTAGTAACGTGGCTAAAAGGCAATACCACCGGCGGGCAAAGCATTCGCGCAGGCCTGCCCGCAAGCTGGGTGGTCGGGGATAAAACCGGCGCCGGAGATTACGGCACCACCAACGATATCGCGGTGATCTGGCCGGAAAATCATGCCCCGCTGGTGCTGGTGACCTATTTTACCCAGCCGCAGCAGGATGCGAAAAGCCGCAAAGAGGTGTTAGCCGCGGCGGCAAAAATCGTCACCGAAGGGCTTTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36788","NCBI_taxonomy_name":"Klebsiella oxytoca","NCBI_taxonomy_id":"571"}}}},"ARO_accession":"3009192","ARO_id":"48038","ARO_name":"OXY-1-7","CARD_short_name":"OXY-1-7","ARO_description":"OXY-1-7 is a OXY family class A extended-spectrum beta-lactamase identified from Klebsiella oxytoca.","ARO_category":{"38788":{"category_aro_accession":"3002388","category_aro_cvterm_id":"38788","category_aro_name":"OXY beta-lactamase","category_aro_description":"OXY beta-lactamases are chromosomal class A beta-lactamases that are found in Klebsiella oxytoca. At constitutive low levels, OXY beta-lactamases confer resistance to aminopenicillins and carboxypenicillins. At high induced levels,  OXY beta-lactamases confer resistance to penicillins, cephalosporins and aztreonam.","category_aro_class_name":"AMR Gene Family"},"35923":{"category_aro_accession":"0000004","category_aro_cvterm_id":"35923","category_aro_name":"monobactam","category_aro_description":"Monobactams are a class of beta-lactam antibiotics with a broad spectrum of antibacterial activity, and have a structure which renders them highly resistant to beta-lactamases. Unlike penams and cephems, monobactams do not have any ring fused to its four-member lactam structure. Monobactam antibiotics are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"209":{"model_id":"209","model_name":"AAC(3)-Ib\/AAC(6')-Ib3 bifunctional protein","model_type":"protein homolog model","model_type_id":"40292","model_description":"Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.","model_param":{"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"600"}},"model_sequences":{"sequence":{"271":{"protein_sequence":{"accession":"AAL82588.1","sequence":"MSIIATVKIGPDEISAMRAVLDLFGKEFEDIPTYSDRQPTNEYLANLLHSETFIALAAFDRGTAIGGLAAYVLPKFEQARSEIYIYDLAVASSHRRLGVATALISHLKRVAVELGAYVIYVQADYGDDPAVALYTKLGVREDVMHFDIDPLTNSNDSVTLRLMTEHDLAMLYEWVNRSHIVEWWGGEEARPTLADVQEQYLPSVLAQESVTPYIAMLNGEPIGYAQSYVALGGGDGWWEEETDPGVRGIDQSLANASQLGKGLGTKLVRALVELLFNDPEVTKIQTDPSPSNLRAIRCYEKAGFERQGTVTTPDGPAVYMVQTRQAFERTRSDA"},"dna_sequence":{"accession":"AF355189.1","fmin":"1434","fmax":"2439","strand":"+","sequence":"ATGAGCATCATTGCAACCGTCAAGATCGGCCCTGACGAAATTTCAGCCATGAGGGCTGTGCTCGATCTCTTCGGCAAAGAGTTTGAGGACATTCCAACCTACTCTGATCGCCAGCCGACCAATGAGTATCTTGCCAATCTTCTGCACAGCGAGACGTTCATCGCGCTCGCTGCTTTTGACCGCGGAACAGCAATAGGTGGGCTCGCAGCCTACGTTCTACCCAAGTTCGAGCAAGCGCGAAGCGAGATCTACATTTATGACTTGGCAGTCGCTTCCAGCCATCGAAGGCTAGGAGTCGCAACTGCCCTGATTAGCCACCTGAAGCGTGTGGCGGTTGAACTTGGCGCGTATGTAATCTATGTGCAAGCAGACTACGGTGACGATCCGGCAGTCGCTCTCTACACAAAGCTTGGAGTTCGGGAAGACGTCATGCACTTCGACATTGATCCATTGACCAACAGCAACGATTCCGTCACACTGCGCCTCATGACTGAGCATGACCTTGCGATGCTCTATGAGTGGGTAAATCGATCTCATATCGTCGAGTGGTGGGGCGGAGAAGAAGCACGCCCGACACTTGCTGACGTACAGGAACAGTACTTGCCAAGCGTTTTAGCGCAAGAGTCCGTCACTCCATACATTGCAATGCTGAATGGAGAGCCGATTGGGTATGCCCAGTCGTACGTTGCTCTTGGAGGCGGGGACGGATGGTGGGAAGAAGAAACCGATCCAGGAGTACGCGGAATAGACCAGTCACTGGCGAATGCATCACAACTGGGCAAAGGCTTGGGAACCAAGCTGGTTCGAGCTCTGGTTGAGTTGCTGTTCAATGATCCCGAGGTCACCAAGATCCAAACGGACCCGTCGCCGAGCAACTTGCGAGCGATCCGATGCTACGAGAAAGCGGGGTTTGAGAGGCAAGGTACCGTAACCACCCCAGATGGTCCAGCCGTGTACATGGTTCAAACACGCCAGGCATTCGAGCGAACACGCAGTGATGCCTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36752","NCBI_taxonomy_name":"Pseudomonas aeruginosa","NCBI_taxonomy_id":"287"}}}},"ARO_accession":"3002600","ARO_id":"39000","ARO_name":"AAC(3)-Ib\/AAC(6')-Ib3 bifunctional protein","CARD_short_name":"AAC_3Ib_AAC_6Ib","ARO_description":"AAC(3)-Ib\/AAC(6')-Ib3 is an integron-encoded aminoglycoside acetyltransferase in P. aeruginosa.","ARO_category":{"46171":{"category_aro_accession":"3007419","category_aro_cvterm_id":"46171","category_aro_name":"aminoglycoside bifunctional resistance protein","category_aro_description":"Bifunctional aminoglycoside-inactivating enzymes composed of two separate functional domains. These proteins possess activity from both enzyme components, thereby conferring resistance to the combination of antibiotics from both domains, and may include acetylation, phosphorylation or nucleotidylation activity.","category_aro_class_name":"AMR Gene Family"},"35922":{"category_aro_accession":"0000003","category_aro_cvterm_id":"35922","category_aro_name":"astromicin","category_aro_description":"Astromicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Astromicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35932":{"category_aro_accession":"0000013","category_aro_cvterm_id":"35932","category_aro_name":"amikacin","category_aro_description":"Amikacin is an aminoglycoside antibiotic that works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35953":{"category_aro_accession":"0000035","category_aro_cvterm_id":"35953","category_aro_name":"sisomicin","category_aro_description":"Sisomicin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Sisomicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35966":{"category_aro_accession":"0000049","category_aro_cvterm_id":"35966","category_aro_name":"kanamycin A","category_aro_description":"Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"35969":{"category_aro_accession":"0000052","category_aro_cvterm_id":"35969","category_aro_name":"tobramycin","category_aro_description":"Tobramycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Tobramycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Antibiotic"},"46133":{"category_aro_accession":"3007382","category_aro_cvterm_id":"46133","category_aro_name":"gentamicin","category_aro_description":"Gentamicin is a commonly used aminoglycoside antibiotic derived from members of the Micromonospora genus of bacteria. It acts by binding the 30S ribosomal subunit, thus inhibiting protein synthesis. Gentamicin is typically used to treat Gram-negative infections of the repiratory and urinary tract, as well as infections of the bone and soft tissue. It also exhibits considerable nephrotoxicity and ototoxicity. Gentamicin is administered as a mixture of gentamicin type C (which makes about around 80% of the complex) and types A, B, and X (distributed in the remaining 20% of the complex).","category_aro_class_name":"Antibiotic"},"35935":{"category_aro_accession":"0000016","category_aro_cvterm_id":"35935","category_aro_name":"aminoglycoside antibiotic","category_aro_description":"Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth.","category_aro_class_name":"Drug Class"},"36000":{"category_aro_accession":"0001004","category_aro_cvterm_id":"36000","category_aro_name":"antibiotic inactivation","category_aro_description":"Enzymatic inactivation of antibiotic to confer drug resistance.","category_aro_class_name":"Resistance Mechanism"}}},"431":{"model_id":"431","model_name":"Escherichia coli AcrAB-TolC with MarR mutations conferring resistance to ciprofloxacin and tetracycline","model_type":"protein overexpression model","model_type_id":"41091","model_description":"Protein Overexpression Models (POM) are similar to Protein Variant Models (PVM) in that they include a protein reference sequence, a curated BLASTP bitscore cut-off, and mapped resistance variants. Whereas PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, reporting only those with curated mutations conferring AMR, POMs are restricted to regulatory proteins and report both wild-type sequences and\/or sequences with mutations leading to overexpression of efflux complexes. The former lead to efflux of antibiotics at basal levels, while the latter can confer clinical resistance. POMs include a protein reference sequence (often from wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Perfect RGI match is 100% identical to the wild-type reference protein sequence along its entire length, a Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value may or may not contain at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off may or may not contain at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"2102":"Y137H","2103":"R94S","2104":"L78M","2105":"V45E","2106":"R73C","2107":"R73S","2108":"R77C","2109":"G103S","2130":"I49S","2131":"A70T","2132":"R77L","2852":"R94H","7640":"S3N","8206":"R58L","2133":"V96E"},"Curated-R":{"2102":"Y137H","2103":"R94S","2104":"L78M","2105":"V45E","2106":"R73C","2107":"R73S","2108":"R77C","2109":"G103S","2130":"I49S","2131":"A70T","2132":"R77L","2852":"R94H","7640":"S3N","8206":"R58L","3898":"R58L","2133":"V96E"},"clinical":{"2102":"Y137H","2103":"R94S","2104":"L78M","2105":"V45E","2106":"R73C","2107":"R73S","2108":"R77C","2109":"G103S","2130":"I49S","2131":"A70T","2132":"R77L","2852":"R94H","7640":"S3N","8206":"R58L","2133":"V96E"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"210"},"40394":{"param_type":"nonsense mutation","param_description":"A sequence change where, compared to a reference sequence, one codon is replaced by a termination codon through a nucleotide substitution. These are described as a substitution of the wildtype codon to a termination codon. Format is given as [wild type AA][position][Ter], for example Q42Ter where Q42 is a wildtype amino acid replaced by a premature termination codon.","param_type_id":"40394","param_value":{"3898":"E31Ter"}}},"model_sequences":{"sequence":{"2097":{"protein_sequence":{"accession":"AAC74603.2","sequence":"MKSTSDLFNEIIPLGRLIHMVNQKKDRLLNEYLSPLDITAAQFKVLCSIRCAACITPVELKKVLSVDLGALTRMLDRLVCKGWVERLPNPNDKRGVLVKLTTGGAAICEQCHQLVGQDLHQELTKNLTADEVATLEYLLKKVLP"},"dna_sequence":{"accession":"U00096.1","fmin":"1619119","fmax":"1619554","strand":"+","sequence":"GTGAAAAGTACCAGCGATCTGTTCAATGAAATTATTCCATTGGGTCGCTTAATCCATATGGTTAATCAGAAGAAAGATCGCCTGCTTAACGAGTATCTGTCTCCGCTGGATATTACCGCGGCACAGTTTAAGGTGCTCTGCTCTATCCGCTGCGCGGCGTGTATTACTCCGGTTGAACTGAAAAAGGTATTGTCGGTCGACCTGGGAGCACTGACCCGTATGCTGGATCGCCTGGTCTGTAAAGGCTGGGTGGAAAGGTTGCCGAACCCGAATGACAAGCGCGGCGTACTGGTAAAACTTACCACCGGCGGCGCGGCAATATGTGAACAATGCCATCAATTAGTTGGCCAGGACCTGCACCAAGAATTAACAAAAAACCTGACGGCGGACGAAGTGGCAACACTTGAGTATTTGCTTAAGAAAGTCCTGCCGTAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36849","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. MG1655","NCBI_taxonomy_id":"511145"}}}},"ARO_accession":"3003378","ARO_id":"39962","ARO_name":"Escherichia coli AcrAB-TolC with MarR mutations conferring resistance to ciprofloxacin and tetracycline","CARD_short_name":"Ecol_MarR_MULT","ARO_description":"MarR is a repressor of the mar operon marRAB, thus regulating the expression of marA, the activator of multidrug efflux pump AcrAB.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"37084":{"category_aro_accession":"3000704","category_aro_cvterm_id":"37084","category_aro_name":"cefalotin","category_aro_description":"Cefalotin is a semisynthetic cephalosporin antibiotic activate against staphylococci. It is resistant to staphylococci beta-lactamases but hydrolyzed by enterobacterial beta-lactamases.","category_aro_class_name":"Antibiotic"},"37250":{"category_aro_accession":"3000870","category_aro_cvterm_id":"37250","category_aro_name":"triclosan","category_aro_description":"Triclosan is a common antibacterial agent added to many consumer products as a biocide.  It is an inhibitor of fatty acid biosynthesis by blocking enoyl-carrier protein reductase (FabI).","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"43746":{"category_aro_accession":"3005386","category_aro_cvterm_id":"43746","category_aro_name":"disinfecting agents and antiseptics","category_aro_description":"Disinfectants that can also interact with antimicrobial resistance mechanisms, e.g. molecule efflux, and thus are the targets of disinfectant resistance.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"2306":{"model_id":"2306","model_name":"Escherichia coli AcrAB-TolC with AcrR mutation conferring resistance to ciprofloxacin, tetracycline, and ceftazidime","model_type":"protein overexpression model","model_type_id":"41091","model_description":"Protein Overexpression Models (POM) are similar to Protein Variant Models (PVM) in that they include a protein reference sequence, a curated BLASTP bitscore cut-off, and mapped resistance variants. Whereas PVMs are designed to detect AMR acquired via mutation of house-keeping genes or antibiotic targets, reporting only those with curated mutations conferring AMR, POMs are restricted to regulatory proteins and report both wild-type sequences and\/or sequences with mutations leading to overexpression of efflux complexes. The former lead to efflux of antibiotics at basal levels, while the latter can confer clinical resistance. POMs include a protein reference sequence (often from wild-type alleles), a curated bit-score cut-off, and mapped resistance variants. Mapped resistance variants may include any or all of single point mutations, insertions, or deletions curated from the scientific literature. A Perfect RGI match is 100% identical to the wild-type reference protein sequence along its entire length, a Strict RGI match has a BLASTP bit-score above the curated BLASTP cutoff value may or may not contain at least one curated mutation from amongst the mapped resistance variants, while a Loose RGI match has a bit-score less than the curated BLASTP bit-score cut-off may or may not contain at least one curated mutation from amongst the mapped resistance variants.","model_param":{"snp":{"param_type":"single resistance variant","param_description":"A sequence change where, compared to a reference sequence, one amino acid is replaced by one other amino acid that is associated with elevated resistance to antibiotic(s) relative to wild type. Format is given as [wild-type][position][mutation], e.g. R184Q or R447Var where Var represents any possible substitution.","param_type_id":"36301","param_value":{"3903":"R45C"},"Curated-R":{"3903":"R45C"},"clinical":{"3903":"R45C"}},"blastp_bit_score":{"param_type":"BLASTP bit-score","param_description":"The BLASTP bit-score is a numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)\/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. This parameter is used by AMR detection models that use a protein reference sequence, e.g. the protein homolog model. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of RGI Strict match (above bit-score cut-off) or Loose match (below bit-score cut-off).","param_type_id":"40725","param_value":"375"}},"model_sequences":{"sequence":{"5225":{"protein_sequence":{"accession":"AAC73566.1","sequence":"MARKTKQEAQETRQHILDVALRLFSQQGVSSTSLGEIAKAAGVTRGAIYWHFKDKSDLFSEIWELSESNIGELELEYQAKFPGDPLSVLREILIHVLESTVTEERRRLLMEIIFHKCEFVGEMAVVQQAQRNLCLESYDRIEQTLKHCIEAKMLPADLMTRRAAIIMRGYISGLMENWLFAPQSFDLKKEARDYVAILLEMYLLCPTLRNPATNE"},"dna_sequence":{"accession":"U00096.3","fmin":"485760","fmax":"486408","strand":"+","sequence":"ATGGCACGAAAAACCAAACAAGAAGCGCAAGAAACGCGCCAACACATCCTCGATGTGGCTCTACGTCTTTTCTCACAGCAGGGGGTATCATCCACCTCGCTGGGCGAGATTGCAAAAGCAGCTGGCGTTACGCGCGGTGCAATCTACTGGCATTTTAAAGACAAGTCGGATTTGTTCAGTGAGATCTGGGAACTGTCAGAATCCAATATTGGTGAACTAGAGCTTGAGTATCAGGCAAAATTCCCTGGCGATCCACTCTCAGTATTAAGAGAGATATTAATTCATGTTCTTGAATCCACGGTGACAGAAGAACGGCGTCGATTATTGATGGAGATTATATTCCACAAATGCGAATTTGTCGGAGAAATGGCTGTTGTGCAACAGGCACAACGTAATCTCTGTCTGGAAAGTTATGACCGTATAGAACAAACGTTAAAACATTGTATTGAAGCGAAAATGTTGCCTGCGGATTTAATGACGCGTCGCGCAGCAATTATTATGCGCGGCTATATTTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCTTTTGATCTTAAAAAAGAAGCCCGCGATTACGTTGCCATCTTACTGGAGATGTATCTCCTGTGCCCCACGCTTCGTAATCCTGCCACTAACGAATAA","partial":"0"},"NCBI_taxonomy":{"NCBI_taxonomy_cvterm_id":"36849","NCBI_taxonomy_name":"Escherichia coli str. K-12 substr. MG1655","NCBI_taxonomy_id":"511145"}}}},"ARO_accession":"3003807","ARO_id":"40492","ARO_name":"Escherichia coli AcrAB-TolC with AcrR mutation conferring resistance to ciprofloxacin, tetracycline, and ceftazidime","CARD_short_name":"Ecol_AcrR_MULT","ARO_description":"AcrR is a repressor of the AcrAB-TolC multidrug efflux complex. AcrR mutations result in high level antibiotic resistance. The mutations associated with this model are specific to E. coli.","ARO_category":{"36005":{"category_aro_accession":"0010004","category_aro_cvterm_id":"36005","category_aro_name":"resistance-nodulation-cell division (RND) antibiotic efflux pump","category_aro_description":"Directed pumping of antibiotic out of a cell to confer resistance. Resistance-nodulation-division (RND) proteins are found in both prokaryotic and eukaryotic cells and have diverse substrate specificities and physiological roles. However, there are relatively few RND transporters and they are secondary transporters, energized not by ATP binding\/hydrolysis but by proton movement down the transmembrane electrochemical gradient.","category_aro_class_name":"AMR Gene Family"},"35949":{"category_aro_accession":"0000030","category_aro_cvterm_id":"35949","category_aro_name":"tigecycline","category_aro_description":"Tigecycline is an glycylcycline antibiotic. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35954":{"category_aro_accession":"0000036","category_aro_cvterm_id":"35954","category_aro_name":"ciprofloxacin","category_aro_description":"Ciprofloxacin is a bacteriocidal fluoroquinolone. It blocks bacterial DNA replication by binding to the toposiomerase II or IV-DNA complex (or cleavable complex), thereby causing double-stranded breaks in the bacterial chromosome.","category_aro_class_name":"Antibiotic"},"35968":{"category_aro_accession":"0000051","category_aro_cvterm_id":"35968","category_aro_name":"tetracycline","category_aro_description":"Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome.","category_aro_class_name":"Antibiotic"},"35977":{"category_aro_accession":"0000060","category_aro_cvterm_id":"35977","category_aro_name":"ceftazidime","category_aro_description":"Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections.","category_aro_class_name":"Antibiotic"},"36308":{"category_aro_accession":"3000169","category_aro_cvterm_id":"36308","category_aro_name":"rifampin","category_aro_description":"Rifampin is a semi-synthetic rifamycin, and inhibits RNA synthesis by binding to RNA polymerase. Rifampin is the mainstay agent for the treatment of tuberculosis, leprosy and complicated Gram-positive infections.","category_aro_class_name":"Antibiotic"},"36524":{"category_aro_accession":"3000385","category_aro_cvterm_id":"36524","category_aro_name":"chloramphenicol","category_aro_description":"Chloramphenicol is a bacteriostatic antimicrobial originally derived from the bacterium Streptomyces venezuelae. It was the first antibiotic to be manufactured synthetically on a large scale. It functions by inhibiting peptidyl transferase activity of the bacterial ribosome, binding to A2451 and A2452 residues in the 23S rRNA of the 50S ribosomal subunit and preventing peptide bond formation.","category_aro_class_name":"Antibiotic"},"36981":{"category_aro_accession":"3000637","category_aro_cvterm_id":"36981","category_aro_name":"ampicillin","category_aro_description":"Ampicillin is a penicillin derivative that is highly acid stable, with its activity similar to benzylpenicillin.","category_aro_class_name":"Antibiotic"},"37084":{"category_aro_accession":"3000704","category_aro_cvterm_id":"37084","category_aro_name":"cefalotin","category_aro_description":"Cefalotin is a semisynthetic cephalosporin antibiotic activate against staphylococci. It is resistant to staphylococci beta-lactamases but hydrolyzed by enterobacterial beta-lactamases.","category_aro_class_name":"Antibiotic"},"37250":{"category_aro_accession":"3000870","category_aro_cvterm_id":"37250","category_aro_name":"triclosan","category_aro_description":"Triclosan is a common antibacterial agent added to many consumer products as a biocide.  It is an inhibitor of fatty acid biosynthesis by blocking enoyl-carrier protein reductase (FabI).","category_aro_class_name":"Antibiotic"},"35920":{"category_aro_accession":"0000001","category_aro_cvterm_id":"35920","category_aro_name":"fluoroquinolone antibiotic","category_aro_description":"The fluoroquinolones are a family of synthetic broad-spectrum antibiotics that are 4-quinolone-3-carboxylates. These compounds interact with topoisomerase II (DNA gyrase) to disrupt bacterial DNA replication, damage DNA, and cause cell death.","category_aro_class_name":"Drug Class"},"35951":{"category_aro_accession":"0000032","category_aro_cvterm_id":"35951","category_aro_name":"cephalosporin","category_aro_description":"Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms.","category_aro_class_name":"Drug Class"},"35960":{"category_aro_accession":"0000042","category_aro_cvterm_id":"35960","category_aro_name":"glycylcycline","category_aro_description":"Glycylcyclines are a new class of antibiotics derived from tetracycline. These tetracycline analogues are specifically designed to overcome two common mechanisms of tetracycline resistance. Presently, there is only one glycylcycline antibiotic for clinical use: tigecycline. It works by inhibiting action of the prokaryotic 30S ribosome, preventing the binding of aminoacyl-tRNA.","category_aro_class_name":"Drug Class"},"36017":{"category_aro_accession":"3000008","category_aro_cvterm_id":"36017","category_aro_name":"penicillin beta-lactam","category_aro_description":"Penicilins (Penams) are a group of antibiotics derived from Penicillium fungi that share a skeleton beta-lactam moiety fused with a thiazolidine ring. Penicillin-like antibiotics are historically significant because they are the first drugs that were effective against many previously serious diseases such as syphilis and Staphylococcus infections. Penicillins are still widely used today, though many types of bacteria are now resistant. All penicillins are beta-lactam antibiotics in the penam sub-group, and are used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms.","category_aro_class_name":"Drug Class"},"36189":{"category_aro_accession":"3000050","category_aro_cvterm_id":"36189","category_aro_name":"tetracycline antibiotic","category_aro_description":"These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes.","category_aro_class_name":"Drug Class"},"36296":{"category_aro_accession":"3000157","category_aro_cvterm_id":"36296","category_aro_name":"rifamycin antibiotic","category_aro_description":"Rifamycin antibiotics are a group of broad-spectrum ansamycin antibiotics that inhibit bacterial RNA polymerase by binding to a highly conserved region, blocking the oligonucleotide exit tunnel, and preventing the extension of nascent mRNAs.","category_aro_class_name":"Drug Class"},"36526":{"category_aro_accession":"3000387","category_aro_cvterm_id":"36526","category_aro_name":"phenicol antibiotic","category_aro_description":"Phenicols are broad spectrum bacteriostatic antibiotics acting on bacterial protein synthesis. More specifically, the phenicols block peptide elongation by binding to the peptidyltansferase centre of the 70S ribosome.","category_aro_class_name":"Drug Class"},"43746":{"category_aro_accession":"3005386","category_aro_cvterm_id":"43746","category_aro_name":"disinfecting agents and antiseptics","category_aro_description":"Disinfectants that can also interact with antimicrobial resistance mechanisms, e.g. molecule efflux, and thus are the targets of disinfectant resistance.","category_aro_class_name":"Drug Class"},"36298":{"category_aro_accession":"3000159","category_aro_cvterm_id":"36298","category_aro_name":"efflux pump complex or subunit conferring antibiotic resistance","category_aro_description":"Efflux proteins that pump antibiotic out of a cell to confer resistance.","category_aro_class_name":"Efflux Component"},"36590":{"category_aro_accession":"3000451","category_aro_cvterm_id":"36590","category_aro_name":"protein(s) and two-component regulatory system modulating antibiotic efflux","category_aro_description":"Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux.","category_aro_class_name":"Efflux Regulator"},"35997":{"category_aro_accession":"0001001","category_aro_cvterm_id":"35997","category_aro_name":"antibiotic target alteration","category_aro_description":"Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance.","category_aro_class_name":"Resistance Mechanism"},"36001":{"category_aro_accession":"0010000","category_aro_cvterm_id":"36001","category_aro_name":"antibiotic efflux","category_aro_description":"Antibiotic resistance via the transport of antibiotics out of the cell.","category_aro_class_name":"Resistance Mechanism"}}},"_version":"4.0.1","_comment":{"description":"This file contains the complete data for all of CARD's AMR detection models, including reference sequences, SNP mapping data, model parameters, and ARO classification.","access":"public"},"_timestamp":"2025-05-29T14:18:07+00:00"}